@article {pmid40638214, year = {2025}, author = {Paintsil, EK and Adu-Asiamah, CK and Boahen, KG and Akenten, CW and Kwarteng, A and Berg, S and Obiri-Danso, K and May, J and Dekker, D and Ofori, LA}, title = {Genomic insights into the diversity, antimicrobial resistance and zoonotic potential of Campylobacter fetus across diverse hosts and geographies.}, journal = {Microbial genomics}, volume = {11}, number = {7}, pages = {}, doi = {10.1099/mgen.0.001446}, pmid = {40638214}, issn = {2057-5858}, mesh = {Animals ; *Campylobacter fetus/genetics/drug effects/classification/isolation & purification/pathogenicity ; Humans ; Cattle ; *Campylobacter Infections/microbiology/veterinary ; Sheep ; Genome, Bacterial ; Genetic Variation ; *Zoonoses/microbiology ; Phylogeny ; Genomics ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Reptiles/microbiology ; }, abstract = {Introduction. Campylobacter fetus causes reproductive diseases in livestock and can lead to zoonotic infections such as bacteraemia, particularly in immunocompromised individuals. Despite its significance, its genomic characteristics remain poorly understood. This study analysed 114 publicly available C. fetus genomes to provide global insights into genetic diversity, antimicrobial resistance (AMR) and zoonotic risk.Results. A total of 32 distinct sequence types (STs) were identified across 111 of the 114 C. fetus genomes, spanning 6 continents and diverse hosts (cattle, humans, sheep and reptiles). The majority of strains from cattle (75.6%, n/N=34/45) were assigned to ST-4, which was the most prevalent overall (n=45), while human-associated genomes exhibited the highest diversity with 16 STs. C. fetus subsp. venerealis (Cfv) and its biovar intermedius (Cfvi) genomes clustered closely, forming distinct branches at the biovar level; however, six Cfv genomes were located within Cfvi clades, suggesting a shared ancestry. C. fetus subsp. testudinum (Cft), primarily isolated from humans (60.0%, n/N=18/30), exhibited a more diverse genetic profile, with 20 STs. Cfv from North America and Cfvi from South America formed distinct geographic clusters, while C. fetus subsp. fetus genomes showed no clear geographic patterns, indicating global spread. Pangenomic analysis revealed substantial variation in gene presence/absence in Cft. Five AMR genes were detected, with tet(O) (n=3) being the most common. A total of 220 plasmid contigs were identified across 47 genomes, predominantly in Cfvi (66.8%, n/N=147/220) and Cfv (29.1%, n/N=64/220). Horizontal gene transfer analysis identified 140 genomic islands across 41 genomes, and virulence factor analysis revealed cheY as the sole conserved virulence gene across 35 genomes.Conclusion. These findings provide critical insights into the genomic diversity, zoonotic potential and global distribution of C. fetus, emphasizing the need for integrated genomic and epidemiological strategies to assess its impact on human and animal health.}, }
@article {pmid40637797, year = {2025}, author = {Giani, NM and Lim, SJ and Anderson, LC and Paterson, AT and Engel, AS and Campbell, BJ}, title = {Variation in accessory and horizontal gene transfer-associated genes drives lucinid endosymbiont diversity.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf074}, pmid = {40637797}, issn = {1574-6941}, abstract = {Lucinid bivalves harbor environmentally acquired endosymbionts within the class Gammaproteobacteria and genus Candidatus Thiodiazotropha. Despite recent studies focused on lucinid endosymbiont genomic and functional diversity, processes influencing species diversity have been understudied. From the analysis of 333 metagenome-assembled genomes (MAGs) from 40 host species across eight waterbodies and 77 distinct locations, 272 were high quality MAGs of Ca. Thiodiazotropha endosymbionts that represented 11 genomospecies. Of those, two new genomospecies from lucinids collected from The Bahamas and Florida (USA) were identified, Ca. Thiodiazotropha fisheri and Ca. Thiodiazotropha grosi. Metabolic specialization was evident, such as potential adaptations to diverse carbon sources based on detection of C1 metabolic genes in eight genomospecies. Genes associated with defense, symbiosis/pathogenesis, and horizontal gene transfer (HGT) were also distinct across genomospecies. For instance, Ca. T. taylori exhibited lower abundances of HGT-associated genes compared to other genomospecies, particularly Ca. T. endolucinida, Ca. T. lotti, and Ca. T. weberae. HGT-associated genes were linked to previously unreported retron-type reverse transcriptases, dsDNA phages, and phage resistance. Collectively, the pangenome highlights how lucinid endosymbiont diversity has been shaped by geographic and host-specific interactions linked to gene loss and HGT through time.}, }
@article {pmid40633655, year = {2025}, author = {Parab, AS and Ghose, M and Manohar, CS}, title = {Antibiotic-resistant bacteria in marine productive zones of the eastern Arabian Sea: Implications for human and environmental health.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {383}, number = {}, pages = {126793}, doi = {10.1016/j.envpol.2025.126793}, pmid = {40633655}, issn = {1873-6424}, abstract = {The increasing threat of antibiotic resistance is a major global concern affecting human and environmental health. Marine environments, though underexplored, are emerging as significant reservoirs for antibiotic resistance genes (ARGs). This study provides genome-resolved shotgun metagenomic insights into the seasonal and spatial dynamics of ARGs in the chlorophyll maximum zones of the eastern Arabian Sea, focusing on bacterial communities from coastal (30 m) and offshore (600 m) depths. Using a shotgun metagenomic approach, 31 potential ARGs were identified across both non-monsoon and monsoon seasons, with higher abundance observed in offshore stations during the non-monsoon season. Multidrug resistance genes such as blaEFM-1, catB2 and mexK, conferring resistance to carbapenems, chloramphenicol and multiple antibiotics, were prevalent in taxa like Staphylococcus sp., Qipengyuania sp. and Alcanivorax sp. Clinically relevant taxa, including Pseudomonas sp. and Staphylococcus sp., harbored ARGs, which may raise concerns regarding potential seafood-mediated ARG transmission. The significant enrichment and co-localization of mobile genetic elements (MGEs) with ARGs suggest enhanced horizontal gene transfer among native marine bacteria in the offshore environments. However, the limited distribution of ARGs and the absence of associated MGEs during the monsoon season may result from dilution caused by freshwater influx. Comparative functional analysis revealed stress-related functional enrichment in ARG-carrying metagenomic assembled genomes, suggesting environmental stress may enhance the spread of ARGs within offshore microbial communities. These findings challenge the coastal-centric view of marine antibiotic resistance by identifying offshore waters as underrecognized ARG reservoirs. Establishing a genomic baseline for One Health ARG surveillance, this study underscores the urgent need to integrate offshore regions into global monitoring frameworks to protect marine ecosystems and safeguard public health.}, }
@article {pmid40628208, year = {2025}, author = {Wu, Y and Tan, D and Wang, D and Ogendi, GM and Balcazar, JL and Zhu, D and Sun, M and Hu, F}, title = {Bacteriophage facilitated transmission of multidrug efflux pump regulatory genes in Pseudomonas aeruginosa.}, journal = {Journal of hazardous materials}, volume = {495}, number = {}, pages = {139151}, doi = {10.1016/j.jhazmat.2025.139151}, pmid = {40628208}, issn = {1873-3336}, abstract = {The emergence of multidrug-resistant Pseudomonas aeruginosa strains, primarily driven by efflux pumps that expel antibiotics, poses a serious global health threat. Phages, particularly members of the class Caudoviricetes (94.7 %), play a significant role in the horizontal transfer of genetic material among bacterial hosts, potentially contributing to the acquisition and spread of antibiotic resistance genes. In this study, analysis of 6712 P. aeruginosa genomes from the JGI-IMG/VR virus database revealed that all P. aeruginosa RefSeq genome assemblies (GCF accessions) contained efflux pump genes (MexAB-oprM, MexCD-oprJ, and MexEF-oprN) as well as their associated regulatory genes (mexT, mexR, and nfxB). Notably, these genes can be transmitted through phage-mediated horizontal gene transfer, as evidenced by their detection in viral sequences. Among phages harboring these genes, 43.9 % were identified as lysogenic. These phages were predominantly associated with aquatic (33.2 %), human (19.0 %), and terrestrial (16.4 %) environments worldwide, highlighting the potential risks of environmental contamination. Experimental validation using PA1 and PAO1 strains confirmed the role of phages in facilitating horizontal gene transfer. These findings highlight the urgent need to implement surveillance and mitigation measures targeting phage-associated antibiotic resistance dissemination, with direct implications for both public health and environmental safety.}, }
@article {pmid40626882, year = {2025}, author = {Bello-López, E and Kawabata, A and Cantero, J and Mendoza, S and Pertile, E and Perez-Osegura, A and Cevallos, MA and Peralta, H and Aguilar-Vera, A and Castillo-Ramirez, S}, title = {Genomic epidemiology reveals antibiotic resistance transfer and polyclonal dissemination of Acinetobacter baumannii in a Paraguayan hospital.}, journal = {Antimicrobial agents and chemotherapy}, volume = {}, number = {}, pages = {e0007725}, doi = {10.1128/aac.00077-25}, pmid = {40626882}, issn = {1098-6596}, abstract = {Acinetobacter baumannii is a major nosocomial pathogen worldwide and, specifically, in Latin America. Genomic epidemiology has been instrumental in determining the transmission dynamics of A. baumannii in many countries of the world, yet some Latin American countries have conducted no genomic epidemiology studies. Here, we conduct the first genomic epidemiology study about this pathogen in Paraguay. We sequenced 43 isolates from a big tertiary hospital in Paraguay collected from different wards in 2021 and 2022. Our genomic epidemiology analyses, including almost 200 genomes and considering the main international clones (ICs), show that IC1, IC2, IC4, IC5, and IC7 were found in the hospital. We found novel genetic variation (three novel sequence types as per the Oxford MLST scheme and one as per the Pasteur scheme) within IC7. Antibiotic susceptibility tests show that all but one of the Paraguayan isolates were resistant to carbapenems. Notably, 98% were classified as multidrug-resistant. We detected plasmids in almost all the Paraguayan isolates. Furthermore, we detected cases of recent horizontal transfer of important antibiotic resistance genes between different ICs. On a general note, our findings highlight polyclonal spreading across different hospital wards and horizontal transfer of clinically relevant antibiotic resistance genes among the different clones. On a more local note, this is the first genomic epidemiology study of A. baumannii in Paraguay and will be a reference point for future studies in the country and the region.}, }
@article {pmid40623962, year = {2025}, author = {Monte, DFM and de Lima Rocha, AD and Lemos, MLP and de Lima, LA and Cabrera, JM and da Silva, NJ and Huang, X and Chen, Z and Brown, EW and Allard, MW and Bell, RL and Toro, M and Meng, J and de Oliveira, CJB}, title = {High Prevalence of Plasmid-Mediated Quinolone Resistance in Salmonella enterica Serovars Isolated From Surface Water.}, journal = {Environmental microbiology}, volume = {27}, number = {7}, pages = {e70140}, doi = {10.1111/1462-2920.70140}, pmid = {40623962}, issn = {1462-2920}, support = {U01FDU001418//U.S. Department of Health and Human Services/ ; Finance Code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)/ ; 420755/2023-3//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; 3136678/2020-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; 88887.898770/2023-00//Fundação de Apoio à Pesquisa do Estado da Paraíba (FAPESQ)/ ; //Financiadora de Estudo e Projetos (FINEP)/ ; }, mesh = {*Quinolones/pharmacology ; *Salmonella enterica/genetics/drug effects/isolation & purification/classification ; *Plasmids/genetics ; *Anti-Bacterial Agents/pharmacology ; Phylogeny ; Brazil ; *Drug Resistance, Bacterial/genetics ; Serogroup ; Multilocus Sequence Typing ; Microbial Sensitivity Tests ; Whole Genome Sequencing ; *Fresh Water/microbiology ; Prevalence ; }, abstract = {Considering the increasing reports of Salmonella enterica strains resistant to quinolones, antimicrobials frequently employed as therapeutic agents globally, our goal was to investigate the occurrence of plasmid-mediated quinolone resistance (PMQR) determinants in S. enterica recovered from natural surface waters in Paraíba state, Brazil. Water samples (n = 230) were collected monthly in triplicate using modified Moore swabs from 29 sampling sites belonging to 10 large dams. After conventional microbial isolation, representative isolates (n = 938) were submitted to whole genome sequencing, assembly and annotation. Antimicrobial resistance genes (ARGs) were identified, and core genome multilocus sequence typing (cgMLST) was used to infer phylogenetic relationships. Among recovered S. enterica, 130 (13.9%) isolates harboured PMQR determinants; 124 (95.4%) harboured qnrB19, while 6 (4.6%) harboured qnrS1. Multiple other ARGs associated with resistance to aminoglycosides, β-lactams, sulphonamides, tetracyclines and fosfomycin were identified. The diversity of ARGs and plasmids suggests a highly complex resistance landscape. Phylogenetic analysis revealed clustering by serovar and sequence type but not by resistance profile or geographic origin. The absence of association between phylogeny and ARGs highlights the potential role of horizontal gene transfer in disseminating resistance genes in water. Our findings reinforce the importance of antimicrobial resistance surveillance in surface waters.}, }
@article {pmid40623055, year = {2025}, author = {Frazão, N and Seixas, E and Mischler, M and Moura-de-Sousa, J and Barreto, HC and Gordo, I}, title = {Clonal interference and genomic repair during strain coexistence in the gut.}, journal = {PLoS genetics}, volume = {21}, number = {7}, pages = {e1011777}, doi = {10.1371/journal.pgen.1011777}, pmid = {40623055}, issn = {1553-7404}, abstract = {Humans and other mammals are colonized by multiple strains of Escherichia coli, but the tempo and mode of evolution of different coexisting strains, between whom horizontal gene transfer (HGT) can occur, is poorly understood. Here, we follow in real time the evolution of two phylogenetic distinct strains of E. coli that co-colonize the mouse gut with different population sizes. We find qualitative differences in evolutionary dynamics between strains within the same host. In the strain with larger population size intense clonal interference occurs and polymorphism at a neutral marker locus is maintained, while in the strain with lower population size complete selective sweeps and loss of neutral marker polymorphism occurs. Strain coexistence is also accompanied by rich dynamics of HGT from one strain to the other. Strikingly, a rare HGT event could restore a previously lost genomic region in the recipient strain. Furthermore, we detect for the first time a case of phage piracy in the gut, where a putative phage satellite, lacking essential genes for their own replication, was likely mobilized by a helper phage to transfer between bacterial hosts. Our results show that HGT is a key mechanism underlying genetic exchanges and adaptive genomic repair in the mammalian gut.}, }
@article {pmid40622509, year = {2025}, author = {Can, A and Baysal, Ö}, title = {A Chitinase Gene Belonging to Serratia marcescens GBS19 Reveals Horizontal Gene Transfer within Bacterial Strains Besides its Biocontrol Potential Against Myzus persicae.}, journal = {Biochemical genetics}, volume = {}, number = {}, pages = {}, pmid = {40622509}, issn = {1573-4927}, abstract = {Microorganisms produce diverse enzymes with applications in biological control and pest management. Chitinase enzymes degrade chitin, a structural component of insect exoskeletons and fungal cell walls, offering sustainable and environmentally friendly solutions for agricultural pest and pathogen management. This study focused on the chiA gene from our original strain belonging to Serratia marcescens identified using multi locus sequencing and ribosomal DNA analysis, amplified via PCR, cloned into expression vectors, and expressed as a recombinant protein. The chiA enzyme was purified using His-tag affinity chromatography and showed optimal activity at 40 °C and pH 5. The purified chiA enzyme exhibited strong insecticidal activity against Myzus persicae, with an lethal dose50 of 15.8 ppm. The comparative genomic analysis using MUMMER4 and MAUVE, identified horizontal gene transfer (HGT) events and genomic rearrangements within reference strain and our strain GBS19. The recombinant chiA enzyme exhibited 98.4% similarity with reference chiA sequences, highlighting its evolutionary conservation. Molecular docking studies confirmed a binding affinity of - 5.74 kcal/mol between the enzyme and chitin monomers, supported by interaction studies with modeled chitin layer. In addition, we have also predicted the most variable mutations required for enzyme stability and enzymatic activity enhancement in cloned amino acid sequence using protein AI tool, which will also guide us further studies linked to site-directed mutagenesis. This study demonstrates the potential of S. marcescens chitinase as an effective biocontrol agent against Myzus persicae. It underscores the importance of recombinant DNA technology in sustainable agriculture and sheds light on the evolutionary adaptation of chitinase genes through HGT and mutational events.}, }
@article {pmid40621911, year = {2025}, author = {Yu, J and Gao, J-W and Cao, K and He, D-Y and Xu, L and Fu, G-Y and Sun, C}, title = {Characterization of two novel species of the genus Flagellimonas reveals the key role of vertical inheritance in the evolution of alginate utilization loci.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0091725}, doi = {10.1128/spectrum.00917-25}, pmid = {40621911}, issn = {2165-0497}, abstract = {Flavobacteriaceae is the major participant in the degradation of algal polysaccharides. With diverse polysaccharide utilization loci (PULs) and specific carbohydrate-active enzymes (CAZymes), Flavobacteriaceae strains appear to have different abilities in algal polysaccharide degradation and therefore change their roles in the bacterial community. Here, we identified two novel isolates as two novel species of genus Flagellimonas with the names Flagellimonas alginolytica sp. nov. and Flagellimonas cixiensis sp. nov. Furthermore, the comprehensive genomic comparison of 41 Flagellimonas genomes revealed that Flagellimonas strains were diverse in the CAZymes and PUL profiles and exhibited a preference for polysaccharides derived from brown algae. The evolutionary analysis of alginate utilization loci (AUL) in this genus illuminated that the function genes in AULs, that is, PL7 and PL17, were more reliant on the stable inheritance from ancestors associated with gene duplication and loss rather than horizontal gene transfer (HGT) from outside, and the AUL structures exhibited a trend of simplification which resulted in the incidental decrease in alginate degradation ability. This study highlights the important role of vertical inheritance in the evolution of AULs and proves that the discrepancy in AUL structure can arouse phenotypic differences, providing a new perspective on the evolution of AUL and the niche adaptation mechanism of Flavobacteriaceae strains.IMPORTANCEFlavobacteriaceae play an important role in the marine carbon cycle with their noteworthy ability in algal polysaccharides degradation, which is primarily reliant on diverse polysaccharide utilization loci (PULs). Our study highlights the crucial role of vertical inheritance in the evolution of alginate utilization loci (AUL) in Flagellimonas strains and reveals the AUL structural simplification found in Flagellimonas strains that will lead to the reduction of alginate degradation ability. These insights advance understanding of niche adaptation strategy and related evolutionary mechanisms of Flavobacteriaceae strains.}, }
@article {pmid40619778, year = {2025}, author = {Bhide, AJ}, title = {Redefining the nitroplast: Recent insights into the endosymbiontto- organelle transition.}, journal = {Journal of biosciences}, volume = {50}, number = {}, pages = {}, pmid = {40619778}, issn = {0973-7138}, mesh = {*Symbiosis/genetics ; Gene Transfer, Horizontal ; Photosynthesis/genetics ; *Plastids/genetics ; Cyanobacteria/genetics ; Rhodophyta/genetics ; Mitochondria/genetics ; Chlorophyta/genetics ; Alphaproteobacteria/genetics ; Biological Evolution ; Evolution, Molecular ; Dinoflagellida/genetics ; }, abstract = {One of the most remarkable events in cellular evolution is the endosymbiosis of α-proteobacteria with a single archaean host cell, a rare evolutionary process, which eventually led to the transformation of symbionts into fully functional mitochondrial organelles in eukaryotes. Evolutionary events related to plants occurred almost 1.6 billion years ago, when eukaryotic heterotrophs acquired a β-cyanobacterium (containing 1B RUBISCO) in what is termed as primary endosymbiosis. Further, this composite cell lineage evolved into three photosynthetic lineages: green algae (plants), red algae and the glaucophytes. Thereafter, a secondary, and tertiary endosymbiosis event occurred giving rise to distinct kinds of green and red-derived photosynthetic plastids, which can be observed in a few haptophytes and dinoflagellates respectively. Eventually, these endosymbionts acquired characteristic cellular properties such as two/multiple envelope membranes and reduction of their genomes through either loss or concerted endosymbiotic gene transfer (EGT) into the nucleus, which ultimately led to the decline of more than three quarters of coding capacity and complete loss of several metabolic pathways. This loss, however, is partly compensated by import of nuclearencoded proteins as well as proteins acquired by horizontal gene transfer (HGT). For most proteins, specific transport mechanisms from nucleus/cytoplasm to organelle exist. The proteins are typically translated as a preprotein with specific signal sequences targeted to the organelle membrane. These membranes harbour receptors, in some cases soluble receptors, for recognition of these signal sequences. Proteins are then internalised using a set of translocation machineries (Gould et al. 2006).}, }
@article {pmid40614847, year = {2025}, author = {Wang, R and Chen, H and Liu, Y}, title = {Metagenomic insights into the characteristics and co-migration of antibiotic resistome and metal(loid) resistance genes in urban landfill soil and groundwater.}, journal = {Environmental research}, volume = {285}, number = {Pt 1}, pages = {122285}, doi = {10.1016/j.envres.2025.122285}, pmid = {40614847}, issn = {1096-0953}, abstract = {The heavy metals and antibiotic resistance genes (ARGs) in landfills showed a significant correlation; however, the relationship between metal(loid) resistance genes (MRGs) and ARGs in contaminated environments, as well as whether they co-migrate with human pathogenic bacteria (HPB), remains unclear. This study is the first to report the characteristics and co-migration of ARGs and MRGs in the soil and groundwater of aged urban landfill sites. Our findings indicated that quinolone, efflux, and macrolide-lincosamide-streptogramin represented the most abundant ARGs identified. Notably, ARG abundance was higher in groundwater compared to soil, with subtype diversity reflecting a similar trend; however, microbial diversity in soil was greater. Metagenome-assembled genomes data indicated a higher risk of antibiotic-resistant HPB in groundwater. It is imperative to focus on HPB that co-carry ARGs and MRGs alongside mobile genetic elements (MGEs), such as Ralstonia pickettii and Pseudomonas stutzeri. Genes conferring resistance to copper and mercury, as well as MGEs such as qacEdelta and intI1, played a critical role in promoting horizontal gene transfer of antibiotic resistance. MRG may promote ARG migration by affecting the permeability of the cell membrane. Procrustes analysis revealed a strong similarity (87 %) between heavy metals and MRG structures. Variance partitioning analyses demonstrated that both heavy metals and biological factors jointly governed landfill ARGs (96.2 %), exerting a more substantial influence in groundwater than in soil. This study serves as a reference for managing landfill, while emphasizing the importance of addressing the co-migration of MRGs and ARGs in pathogens when controlling the spread of risks.}, }
@article {pmid40612915, year = {2025}, author = {Vasta, GR and Bianchet, MA}, title = {F-type lectins: Structural and functional aspects, and potential biomedical applications.}, journal = {BBA advances}, volume = {8}, number = {}, pages = {100166}, pmid = {40612915}, issn = {2667-1603}, abstract = {Among the multiple animal lectin families recognized to date, F-type lectins (FTLs), fucose-binding lectins characterized by an FTL domain (FTLD), constitute the most recent lectin family to be identified and structurally characterized. The structure of the FTL from the European eel Anguilla anguilla revealed a novel jellyroll lectin fold (the "F-type" fold) with unique fucose- and calcium-binding sequence motifs. The FTL lectin family comprises proteins that may exhibit single or multiple FTLD, in combination with structurally and functionally distinct domains, and can form oligomeric associations that display high-avidity multivalent binding. Differences in fine carbohydrate specificity among tandemly arrayed FTLDs present in any FTL polypeptide subunit, together with the expression of multiple FTL isoforms in a single individual supports a broad diversity in ligand recognition. Widely distributed in invertebrates, protochordates, ectothermic vertebrates, birds, and monotreme and marsupial mammals, the FTLD is also present in some bacterial proteins and viruses but absent in placental mammals. The taxonomically broad, and discontinuous distribution of the FTLD, suggests an extensive structural and functional diversification of this lectin family, including horizontal gene transfer in viruses and prokaryotic organisms, together with possible gene loss and/or cooption along the lineages leading to the mammals. FTLs' biological roles range from pathogen recognition in innate immunity to fertilization, cell adhesion and cell aggregation, and as bacterial virulence factors, among others. The specificity of FTLs for fucosylated moieties should provide ample opportunities for novel applications in glycan and cell separation, and innovative diagnostic, preventive, and therapeutic approaches in cancer and infectious disease.}, }
@article {pmid40479505, year = {2025}, author = {Pianezza, R and Scarpa, A and Haider, A and Signor, S and Kofler, R}, title = {Spatiotemporal Tracking of Three Novel Transposable Element Invasions in Drosophila melanogaster over the Last 30 Years.}, journal = {Molecular biology and evolution}, volume = {42}, number = {7}, pages = {}, doi = {10.1093/molbev/msaf143}, pmid = {40479505}, issn = {1537-1719}, support = {NSF-EPSCoR-1826834 and NSF-EPSCoR-2032756//National Science Foundation/ ; P35093 and P34965//Austrian Science Fund (FWF)/ ; }, mesh = {Animals ; *DNA Transposable Elements ; *Drosophila melanogaster/genetics ; Gene Transfer, Horizontal ; Evolution, Molecular ; Genome, Insect ; }, abstract = {Transposable elements (TEs) are repetitive sequences capable of mobilizing within genomes, exerting a significant influence on evolution throughout the tree of life. Using a novel approach that does not require prior knowledge of the sequence of repeats, we identified three novel TE invasions in Drosophila melanogaster: McLE spread between 1990-2000, Souslik between 2009-2012, and Transib1 between 2013-2016. We recapitulate previous findings, revealing that a total of 11 TEs invaded D. melanogaster over the past two centuries. These 11 invasions increased the fly genome by ∼1 Mbp. Using data from over 1,400 arthropod genomes, we provide evidence that these TE invasions were triggered by horizontal transfers, with Drosophila simulans and species of the Drosophila willistoni group acting as putative donors. Through the analysis of ∼600 short-read datasets spanning diverse geographic regions, we reveal the rapidity of TE invasions: Transib1 swiftly multiplied from three isolated epicenters in 2014 to all investigated populations in just 2 years. Our findings suggest that anthropogenic activities, which facilitate the range and population expansions of D. melanogaster, could have accelerated the rate of horizontal transposon transfer as well as the spread of the TEs into the worldwide population. Given the significant impact of TEs on evolution and the potential involvement of humans in their dispersal, our research has crucial implications for both evolution and ecology.}, }
@article {pmid40612392, year = {2025}, author = {Ma, Y and Lei, Z and Zhang, Y and Liu, Q and Zhang, F and Zu, H and Yang, X and Li, Z and Lu, B}, title = {Tracing the evolutionary trajectory of the IncP-2 plasmid co-harboring bla IMP-45 and bla VIM-1: an outbreak of Pseudomonas aeruginosa co-producing IMP-45 and VIM-1 carbapenemases in China.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1623241}, pmid = {40612392}, issn = {2235-2988}, mesh = {*beta-Lactamases/genetics/metabolism ; *Pseudomonas aeruginosa/genetics/drug effects/enzymology/isolation &amp; purification ; *Plasmids/genetics ; Humans ; China/epidemiology ; *Pseudomonas Infections/epidemiology/microbiology ; *Bacterial Proteins/genetics/metabolism ; *Disease Outbreaks ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; Microbial Sensitivity Tests ; Molecular Docking Simulation ; Evolution, Molecular ; Drug Resistance, Multiple, Bacterial/genetics ; }, abstract = {BACKGROUND: Carbapenem-resistant Pseudomonas aeruginosa (CRPA) poses a significant global health risk, particularly for immunocompromised individuals. This study documents an outbreak of CRPA strains co-harboring bla VIM-1 and bla IMP-45 on IncP-2 plasmids in a Chinese tertiary hospital, resulting in poor outcomes for transplant patients.<br><br>METHODS: 17 ST313 VIM-1-IMP-45 CRPA strains were collected from transplant patients, and antibiotic susceptibility was tested via microbroth dilution. Whole genome sequencing (WGS) identified drug resistance and virulence mechanisms, analyzed ST313 P. aeruginosa phylogeny, and traced bla VIM-1 and bla IMP-45 origins. Conjugation experiments were conducted to assess the conjugative potential of the IncP-2 plasmid co-harboring bla VIM-1 and bla IMP-45. Structural and molecular docking studies explored the PBP3 (P527S) mutation's role in aztreonam resistance.<br><br>RESULTS: From February 2022 to July 2024, 17 ST313 VIM-1-IMP-45 CRPA strains from 10 transplant patients were identified. All strains were extensively drug-resistant but sensitive to colistin and cefiderocol. WGS showed bla IMP-45 and bla VIM-1 on an IncP-2 megaplasmid. Phylogenetic analysis indicated high homology with plasmids carrying bla IMP-45. Further analysis of the genetic environment showed that the IncP-2 plasmid co-harboring bla VIM-1 and bla IMP-45 was formed by the insertion of a Tn3-family transposon carrying bla VIM-1 into the IncP-2 plasmid carrying bla IMP-45. In addition aztreonam-resistant strains (14/15) had a PBP3 (P527S) mutation, with molecular docking studies suggesting reduced aztreonam binding.<br><br>CONCLUSIONS: This study reports a clonal outbreak of ST313 P. aeruginosa strains co-producing IMP-45 and VIM-1 carbapenemases in a tertiary hospital. The evolutionary path of the IncP-2 plasmid co-harboring bla IMP-45 and bla VIM-1 was elucidated.}, }
@article {pmid40609725, year = {2025}, author = {Chen, M and Song, L and Ye, C and Grossart, HP and Yang, Y and Li, S and Liao, H and Gong, Y and Che, R and Zhang, Q}, title = {Dynamic relationships of antibiotic resistomes and greenhouse gas-functioning microbes across diverse habitats.}, journal = {Environmental research}, volume = {284}, number = {}, pages = {122272}, doi = {10.1016/j.envres.2025.122272}, pmid = {40609725}, issn = {1096-0953}, abstract = {Reservoir ecosystems with diverse habitats form critical interfaces where antibiotic resistance genes (ARGs) and greenhouse gas (GHG) emissions converge. Despite their distribution and ecological implications of ARGs across diverse habitats remain greatly unknown. There is a critical gap in dissecting the interlinkages between antibiotic resistomes and GHG-functioning microbes. Thus, we aimed to investigate the relationship between antibiotic resistomes and GHG-functioning microbes in various habitats of the Three Gorges reservoir, encompassing water, sediment, and riparian top- and sub-soil. We provide a comprehensive assessment of ARG abundance and diversity across four habitats. Significant differences in ARG, with riparian zones exhibiting more than twice the ARG abundance of water. Horizontal gene transfer of ARGs was more frequent in water, suggesting a pivotal role in aquatic ARG dissemination. The GHG-functioning microbes displayed habitat-specific composition and diversity, with key genera like Neisseria and Azoarcus in riparian subsoil, contrasting with Streptomyces in other habitats. The dynamic relationship of antibiotic resistomes and GHG-functioning microbes ranges from synergistic to competitive in varied habitats, reflecting antibiotic resistomes can influence ecological function stability. This study emphasizes the importance of considering resistomes in the context of global change, advancing our understanding of environmental management and conservation strategies in these critical ecosystems.}, }
@article {pmid40607640, year = {2025}, author = {Jia, X and Zhang, X and Chen, X and Fernie, AR and Wen, W}, title = {The horizontally transferred gene, CsMTAN, rewired purine traffic to build caffeine factories in tea leaves.}, journal = {Journal of integrative plant biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jipb.13957}, pmid = {40607640}, issn = {1744-7909}, support = {32161133017//National Natural Science Foundation of China/ ; 32494781//National Natural Science Foundation of China/ ; }, abstract = {Purine-related metabolites are central to primary metabolic pathways in plants and serve as precursors for purine alkaloid biosynthesis in caffeinated species such as tea plants (Camellia sinensis). In this study, metabolite profiling of two tissues (young and mature leaves) was performed across 183 genetically diverse tea accessions, identifying and quantifying 10 purine alkaloid-related metabolites. Metabolite genome-wide association studies revealed 17 significant loci associated with these metabolites, including both known loci such as caffeine synthase and 16 novel loci (P < 1.05 × 10[-5]). Through functional annotation and in vitro enzymatic assay, we characterized 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (CsMTAN) as the causal gene underlying natural variation in adenosine and adenine content. CsMTAN can catalyze the degradation of both 5'-methylthioadenosine and S-adenosylhomocysteine to release adenine. The T → A nucleotide substitution at SNP55151898, which leads to a phenylalanine → tyrosine substitution at residue 179 (F179Y), resulted in a significant alteration of enzyme activity in vitro, as evidenced by an approximately 50% reduction in adenine abundance (P < 0.05). Transient overexpression of CsMTAN-A and CsMTAN-T in Nicotiana benthamiana both significantly increased adenine content and dramatically decreased adenosine content, providing direct evidence for the functional involvement of CsMTAN in plant purine metabolism. CsMTAN-T overexpression resulted in significantly lower adenosine level than CsMTAN-A (P < 0.05). Phylogenetic analysis across 115 species and protein structural modeling revealed a distinct evolutionary divergence between plant MTAN evolution and species phylogeny, strongly suggesting the occurrence of horizontal gene transfer events in the evolutionary history of plant MTANs. This study thus furthered our understanding of the genetics and molecular mechanisms regulating purine metabolism and purine alkaloid biosynthesis in tea plants and provided novel targets for molecular breeding and synthetic biology applications.}, }
@article {pmid40607638, year = {2025}, author = {Hou, J and Liu, M and Yang, K and Liu, B and Liu, H and Liu, J}, title = {Genetic variation for adaptive evolution in response to changed environments in plants.}, journal = {Journal of integrative plant biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jipb.13961}, pmid = {40607638}, issn = {1744-7909}, support = {No. 32030006//National Natural Science Foundation of China/ ; No. 32270302//National Natural Science Foundation of China/ ; 2024NSFSC0340//Natural Science Foundation of Sichuan Province/ ; }, abstract = {Plants adapt to their local environments through natural or artificial selection of optimal phenotypes. Recent advances in genomics and computational biology, which integrate phenotypic and multi-omics data, have facilitated the rapid identification of key genes and allelic variations that underlie these adaptive evolutionary processes. Understanding the underlying molecular mechanisms has significantly enhanced our knowledge of how plants respond to changed habitats, including various biotic and abiotic stresses. In this review, we highlight recent progress in elucidating the genetic basis of phenotypic variation in morphological traits and stress responses, as well as the emergence of new ecotypes, subspecies, and species during adaptive evolution across varied environments. This occurs through allelic divergences in both coding and non-coding regions in both model and non-model plants. Furthermore, the terrestrialization and early diversification of land plants involved the acquisition of additional genes, primarily through horizontal gene transfer and whole-genome duplication, which facilitated the development of complex molecular pathways to adapt to increasingly diverse environments. Finally, we discuss emerging trends and prospects for exploring and utilizing beneficial alleles for environmental adaptation, to guide crop breeding efforts in response to global climate change.}, }
@article {pmid40606176, year = {2025}, author = {Du, H and Lu, C and Latif, MZ and Du, J and Liu, Y and Li, H and Ding, X}, title = {Thermophilic microbial agents promote the fermentation progression of spent mushroom compost and pig manure.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1575397}, pmid = {40606176}, issn = {1664-302X}, abstract = {Livestock and poultry manure, as a significant organic resource, had an enormous annual production but a utilization rate of less than 50%. Improperly managed manure had become the primary source of agricultural non-point pollution, posing severe challenges to the ecological environment. Achieving efficient resource utilization of livestock manure was a critical step in promoting green agricultural development. Existing research indicated that microbial activity significantly influences the transfer and dissemination of antibiotic resistance genes (ARGs) and the community dynamics of human pathogenic bacteria (HPB) during pig manure composting. However, the specific mechanisms remain unclear. This study innovatively introduced two thermophilic microbial agents (TMS1 and CTMS2) into a pig manure-spent mushroom compost (SMC) aerobic composting system to systematically investigate their regulatory effects on pollutant reduction. The results showed that persistent ARGs (ErmF, ErmQ, ErmX, blaR1, QnrA1, QnrA6, bla-F, QnrA2, QnrA5, Qnra4 and bla-VIM) primarily rely on vertical gene transfer (VGT) for dissemination, whereas easily removable ARGs (tetX, tetW, tetG, tetC, suI1 and suI2) were regulated by both horizontal gene transfer (HGT) and VGT. Notably, the co-addition of thermophilic microbial agents and SMC reduced persistent ARGs by lg0.45-3.73, significantly decreased the abundances of HPB such as Bacteroides and Treponema, and reduced the enrichment of related metabolic pathways, greatly improving compost quality. In stark contrast, the control group (with only SMC and no thermophilic microbial agents) exhibited ARG proliferation. Overall, the application of thermophilic microbial agents not only extended the high temperature phase of composting by over 30% and shortened the composting cycle by 50%, but more importantly, it achieved comprehensive improvement in compost quality by selectively enriching functional microbial communities such as Pseudomonas. This study provides a theoretical foundation and data support for the industrial application of CTMS2 in the safe production of organic fertilizers and the synergistic control of environmental risks.}, }
@article {pmid40606165, year = {2025}, author = {Jers, C and Mišetić, H and Ravikumar, V and Garg, A and Franjević, D and Domazet-Lošo, T and Mijakovic, I}, title = {Gene age and genome organization in Escherichia coli and Bacillus subtilis.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1512923}, pmid = {40606165}, issn = {1664-302X}, abstract = {Using genomic phylostratigraphy, we examined the organization of Escherichia coli and Bacillus subtilis genomes from the perspective of evolutionary age of their genes. Phylostratigraphy analysis classifies individual genes into age-related bins, called phylostrata. Based on this analysis, several common features emerged in the genomes of the two model bacteria. More recent genes tend to be shorter and are expressed less frequently, or only in specific conditions. In terms of genomic location, new genes are enriched in areas containing prophages, suggesting a link with horizontal gene transfer. Interestingly, while most bacterial transcription regulators belong to the oldest phylostrata, they regulate expression of both older and more recent genes alike. A large fraction of bacterial operons contains genes from different phylostrata. This suggests that newer genes are integrated in the existing framework for regulating gene expression, and that the establishment of new regulatory circuits typically do not accompany acquisition of new genes. One striking difference between E. coli and B. subtilis genomes was observed. About 87.0% of all E. coli genes belong to the evolutionary oldest physlostratum. In B. subtilis, this number is only 71.8%, indicating a more eventful evolutionary past in terms of acquisition of new genes, either by gene emergence or by horizontal transfer.}, }
@article {pmid40604389, year = {2025}, author = {Yang, J and Wang, L and Liang, Q and Wang, Y and Yang, X and Wu, X and Pei, X}, title = {Microbiome, resistome, and potential transfer of antibiotic resistance genes in Chinese wet market under One Health sectors.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {406}, pmid = {40604389}, issn = {1471-2180}, support = {TB2024045//Special Funding for Postdoctoral Research Projects in Sichuan Province/ ; 2022ZDZX0017//Department of Science and Technology of Sichuan Province (Major Science and Technology Projects)/ ; 2022ZDZX0017//Department of Science and Technology of Sichuan Province (Major Science and Technology Projects)/ ; 2022ZDZX0017//Department of Science and Technology of Sichuan Province (Major Science and Technology Projects)/ ; }, }
@article {pmid40602897, year = {2025}, author = {Liang, S and Zhang, W and Semaha, P and Rocher, D and Liu, L and Gao, Y}, title = {Microelectrolysis facilitated the plasmid-mediated horizontal transfer of antibiotic resistance genes at the microbial community level.}, journal = {Journal of environmental sciences (China)}, volume = {157}, number = {}, pages = {470-477}, doi = {10.1016/j.jes.2025.01.029}, pmid = {40602897}, issn = {1001-0742}, mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents ; Wastewater/microbiology ; }, abstract = {The escalating global dissemination of plasmid-mediated antibiotic resistance poses a formidable threat to global health. Conjugation stands as a pivotal mechanism for horizontal gene transfer among bacterial populations, facilitating the spread of antibiotic resistance genes (ARGs). Microelectrolysis has garnered attention as an efficacious strategy for mitigating antibiotic concentrations in wastewater, yet its potential impact on ARG horizontal transfer remain largely unexplored. This comprehensive investigation unveils that microelectrolysis not only influences but significantly accelerates the conjugative transfer of ARG-harboring plasmids. Remarkably, this phenomenon is corroborated at the microbial community scale, underscoring its ecological relevance. Alarmingly, the study highlights the vulnerability of intestinal microorganisms to acquire antibiotic resistance under electrolytic stimulation, posing heightened risks to both animal and human health. Delving deeper, the study elucidates the underlying mechanisms responsible for this enhanced conjugative transfer. It reveals that microelectrolysis augments the abundance of mating-competent cells, triggers the generation of reactive oxygen species, inflicts modest membrane damage, and upregulates the expression of genes critical for conjugation. These findings collectively contribute to a more profound comprehension of the environmental dissemination dynamics and associated public health implications of ARGs in the context of wastewater treatment employing microelectrolytic technologies.}, }
@article {pmid40602895, year = {2025}, author = {Li, S and Xi, Y and Wang, K and Wan, N and Liu, H and Ho, SH}, title = {Responses of antibiotic resistance genes and microbial community in the microalgae-bacteria system under sulfadiazine: Mechanisms and implications.}, journal = {Journal of environmental sciences (China)}, volume = {157}, number = {}, pages = {443-456}, doi = {10.1016/j.jes.2024.12.003}, pmid = {40602895}, issn = {1001-0742}, mesh = {*Microalgae/physiology ; *Sulfadiazine/toxicity ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/drug effects ; *Water Pollutants, Chemical/toxicity ; Waste Disposal, Fluid/methods ; *Microbiota/drug effects ; Anti-Bacterial Agents ; Genes, Bacterial ; Sewage/microbiology ; }, abstract = {Microalgae-bacteria system is an emerging alternative for sustainable wastewater treatment. Exploring the structure and diversity of microbial community in microalgae-bacteria system under sulfadiazine stress can contribute to the understanding of the sulfadiazine behavior in environments. Furthermore, as important carriers of antibiotic resistance genes (ARGs), microalgae can influence the profiles of ARGs either directly or indirectly through the secretion of metabolites. However, the effects of sulfadiazine on ARGs dissemination of microalgae-bacteria systems remain underreported. Herein, the impacts of sulfadiazine (1 mg/L) on the structural diversity and metabolic activity of microorganisms were examined in microalgae-bacteria systems. Results showed that microalgae-bacteria system could remove NH4[+]-N better (about 72.3 %) than activated sludge system, and hydrolysis was the first step in sulfadiazine degradation. A high level of intI1 (5.7 × 10[4] copies/mL) was detected in the initial media of the microalgae-bacteria system. Microalgae could hamper the rate of horizontal gene transfer activation. Compared with activated sludge system, the abundance of sul genes (sul1, sul2, sul3, and sulA) was significantly lowered after treating with microalgae-bacteria system. Additionally, the number of proteins and the sum of polysaccharides in the extracellular polymeric substances of the activated sludge system were lower than those of the microalgae-bacteria system. Microalgae can alter microbial communities. The genus Rozellomycota predominated all samples. Fungi with relatively high abundance increased in the microalgae-bacteria system, including Dipodascaceae, Rhodotorula, and Geotrichum. These results offer valuable insights into the application processes involving microalgae-bacteria system.}, }
@article {pmid40601807, year = {2025}, author = {Wang, Y and Feng, Z and Wu, W and Zhan, Z and Huang, J and Guo, C and He, J}, title = {Emergence of highly virulent Aeromonas dhakensis in channel catfish aquaculture: Genomic insights into pathogenicity and antimicrobial resistance.}, journal = {Virulence}, volume = {16}, number = {1}, pages = {2525933}, doi = {10.1080/21505594.2025.2525933}, pmid = {40601807}, issn = {2150-5608}, mesh = {Animals ; *Fish Diseases/microbiology/pathology ; *Ictaluridae/microbiology ; *Gram-Negative Bacterial Infections/microbiology/veterinary/pathology ; Virulence ; *Aeromonas/pathogenicity/genetics/drug effects/isolation &amp; purification ; Aquaculture ; Virulence Factors/genetics ; Genome, Bacterial ; Whole Genome Sequencing ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Genomics ; *Drug Resistance, Bacterial ; }, abstract = {Aeromonas dhakensis has emerged as a significant pathogen in aquaculture, causing severe disease outbreaks and resulting in substantial economic losses. However, its pathogenic mechanism and virulence factors remain largely unexplored. In this study, we isolated a highly virulent strain of A. dhakensis, CWH5, from a severe disease outbreak in farmed channel catfish (Ictalurus punctatus). Through comprehensive whole-genome analysis, we elucidated its pathogenicity and the genetic basis for its high virulence and multi-antimicrobial resistance in channel catfish. Experimental infections showed that CWH5 exhibited exceptional virulence, with an LD50 of (5.37 ± 0.31) ×10[5] CFU/fish and causing 100% mortality within 24 h at a concentration of 10[7] CFU/fish. Histopathological examinations revealed severe multi-organ damage, including extensive hepatocellular necrosis, gill epithelial destruction, and fin tissue deterioration. Whole-genome sequencing revealed a 4.92 Mb circular chromosome encoding sophisticated virulence mechanisms, such as complete Type III, IV, and VI secretion systems, and a vast arsenal of 60 antibiotic resistance genes across 15 drug classes. Comparative genomic analysis positioned CWH5 within the A. dhakensis clade, sharing the highest sequence similarity with A. dhakensis CIP 107,500[T]. The co-localization of virulence and resistance determinants within mobile genetic elements suggests the potential for horizontal gene transfer. Our work underscored the importance of A. dhakensis CWH5 as an emerging pathogen in channel catfish aquaculture, providing crucial insights into the molecular mechanisms of its exceptional virulence and implying significant implications for disease management and antimicrobial resistance surveillance in aquaculture settings.}, }
@article {pmid40600175, year = {2025}, author = {Etesami, H}, title = {The dual nature of plant growth-promoting bacteria: Benefits, risks, and pathways to sustainable deployment.}, journal = {Current research in microbial sciences}, volume = {9}, number = {}, pages = {100421}, pmid = {40600175}, issn = {2666-5174}, abstract = {Plant growth-promoting bacteria (PGPB) are pivotal in sustainable agriculture, enhancing crop productivity and reducing reliance on chemical inputs. However, their dual role as beneficial agents and potential stressors remains underexplored. This review examines the paradoxical adverse effects of PGPB, challenging the predominantly optimistic narrative surrounding their use. At the plant level, unintended consequences include hormonal imbalances (e.g., auxin-induced root inhibition), phytotoxic metabolite production (e.g., hydrogen cyanide), and trade-offs between growth and defense mechanisms. At the soil level, risks encompass disrupted microbial diversity, altered nutrient cycling, and horizontal gene transfer that may foster pathogenicity. These outcomes are driven by environmental factors (soil pH and moisture), host-specific interactions, and application practices. Mitigation strategies emphasize rigorous strain selection, optimized dosing, and integrated soil management to balance efficacy with ecological safety. Advances in multi-omics technologies and synthetic consortia design offer predictive insights into strain behavior, while long-term ecological assessments are critical to address legacy impacts. The review underscores the necessity of a nuanced, evidence-based approach to PGPB deployment, harmonizing agricultural benefits with environmental stewardship. By addressing knowledge gaps in microbial ecology and risk assessment, this work supports strategies prioritizing both agricultural resilience and soil biodiversity to ensure PGPB contribute sustainably to global food security.}, }
@article {pmid40600145, year = {2025}, author = {Piispa, M and Vainio, A and Halkilahti, J and Lyytikäinen, O and Räisänen, K}, title = {Detecting plasmid-mediated dissemination of bla KPC-3 and bla OXA-48-like genes in Enterobacterales across Finnish healthcare organizations using hybrid genome assembly.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1567913}, pmid = {40600145}, issn = {1664-302X}, abstract = {The spread of carbapenemase-producing Enterobacterales (CPE) is a global concern. While the majority of the CPE outbreaks are due to clonal spread, recent findings highlight the transmission of carbapenemase gene-carrying plasmids across various bacterial species, exacerbated by extensive antibiotic use in hospitals. This study aimed to identify plasmid-mediated horizontal transfer of carbapenemase genes among Enterobacterales isolated from patient samples and hospital environment samples in three healthcare organizations in Finland. Using a hybrid assembly of short and long reads, we could complete the genome assembly and compare the plasmids harboring the bla KPC-3 and bla OXA-48-like genes. Our findings reveal indications of interspecies and intraspecies plasmid-mediated gene transfer of bla KPC-3 and bla OXA-48-like, emphasizing the role of horizontal gene transfer (HGT) in outbreaks. The study underscores the need for comprehensive infection control and surveillance beyond specific species to prevent the spread of antimicrobial resistance genes. These results suggest that expanding outbreak investigations to an interspecies level could be beneficial.}, }
@article {pmid40600140, year = {2025}, author = {Shahed, K and Islam, SI and Sangsawad, P and Jung, WK and Permpoonpattana, P and Linh, NV}, title = {Benchmarking pangenome dynamics and horizontal gene transfer in Mycobacterium marinum evolution.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1537826}, pmid = {40600140}, issn = {1664-302X}, abstract = {Horizontal gene transfer (HGT) is a key driver of microbial evolution, promoting genetic diversity and contributing to the emergence of antibiotic resistance. This study explores the pangenome dynamics and HGT in Mycobacterium marinum (M. marinum), a close relative of Mycobacterium tuberculosis. Multiple pangenome datasets were analyzed to quantify gene gain, loss, and pangenome openness, utilizing Panstripe and a Generalized Linear Model (GLM) framework to assess gene presence/absence across strains. Additionally, a comparative benchmarking analysis of gene ontology (GO) annotations were conducted using eggNOG and InterProScan to evaluate their functional annotation accuracy. Our findings demonstrated significant differences in gene gain and loss rates, suggesting variations in annotation accuracy and the presence of mobile genetic elements (MGE). Single nucleotide polymorphisms (SNPs) were also identified, highlighting the genetic variability that may impact strain-specific traits such as pathogenicity and antibiotic resistance. Pangenome of M. marinum was characterized as highly open, with substantial variability in gene content, reflecting ongoing genetic exchange and adaptability. Functional annotation benchmarking demonstrated that eggNOG and InterProScan provided complementary insights, with each tool excelling in distinct strengths of gene function identification. Overall, these findings highlight the complex interplay between HGT, pangenome evolution, and antibiotic resistance in M. marinum, and the analytical framework presented here provides a robust approach for future studies aiming to inform therapeutic interventions and vaccine development.}, }
@article {pmid40600027, year = {2025}, author = {Lewicka, AJ and Lyczakowski, JJ and Pardyak, L and Dubniewicz, K and Latowski, D and Arent, Z}, title = {Beyond serology: saccharide profiling enables identification of antigenically similar Leptospira and prompts re-evaluation of bacterial lipopolysaccharide evolution.}, journal = {Frontiers in molecular biosciences}, volume = {12}, number = {}, pages = {1581587}, pmid = {40600027}, issn = {2296-889X}, abstract = {Leptospirosis is a zoonotic infectious disease of growing importance in both human and veterinary medicine. Gram-negative spirochetes of Leptospira are traditionally classified into serovars based on their antigenic identity, which must be ascertained to design effective treatment procedures for humans and appropriate vaccination strategies in pets and livestock. Unfortunately, identifying Leptospira serovars is challenging and currently requires access to a wide panel of reference strains, animal-derived antisera, or monoclonal antibodies. Here, we describe a new method for the identification of Leptospira serovars that is based on monosaccharide composition analysis of the polysaccharide part of bacterial lipopolysaccharide (LPS) structures. Our approach requires no animal sacrifice and can be implemented in any laboratory equipped for chromatographic analysis. An LPS sugar fingerprint that is specific to each bacterial isolate that we studied can be generated. Importantly, sugar profiling of LPS enables distinguishing Leptospira serovars that are antigenically very similar. Using our new approach, we discover that the LPS structures of two cattle pathogens belonging to two different species: Leptospira interrogans and Leptospira borgpetersenii, and to one serovar: Hardjo, can be distinguished despite sharing major similarities. Through extensive phylogenetic analysis, we reveal which specific glycosyltransferases of the LPS biosynthesis rfb locus likely drove the emergence of these similarities and identify a single glycosyltransferase that might have contributed to the formation of saccharide differences in the LPS structure. Our findings have implications for future work on the evolution of bacterial polysaccharide synthesis and highlight the importance of preventing horizontal gene transfer between pathogenic bacteria.}, }
@article {pmid40597104, year = {2025}, author = {Blais, C and Colp, MJ and Sarre, LA and de Mendoza, A and Archibald, JM}, title = {Epigenetic silencing and genome dynamics determine the fate of giant virus endogenizations in Acanthamoeba.}, journal = {BMC biology}, volume = {23}, number = {1}, pages = {171}, pmid = {40597104}, issn = {1741-7007}, support = {GBMF5782//Gordon and Betty Moore Foundation/ ; GBMF5782//Gordon and Betty Moore Foundation/ ; GBMF5782//Gordon and Betty Moore Foundation/ ; RGPIN-2019-05058//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2019-05058//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2019-05058//Natural Sciences and Engineering Research Council of Canada/ ; ERC-StG 950230/ERC_/European Research Council/International ; ERC-StG 950230/ERC_/European Research Council/International ; }, mesh = {*Acanthamoeba/virology/genetics ; *Giant Viruses/genetics/physiology ; *Epigenesis, Genetic ; *Gene Silencing ; *Virus Integration/genetics ; *Genome, Protozoan ; *Genome, Viral ; Gene Transfer, Horizontal ; }, abstract = {BACKGROUND: Endogenized giant viruses are emerging as major contributors to the genome evolution of microbial eukaryotes, with both degraded and fully functional latent viruses being found integrated in diverse lineages. The mechanisms that determine the fate of viral integrants are poorly understood, however. Acanthamoeba is a unicellular eukaryote known for undergoing lateral gene transfer (LGT) with viruses. Here we have leveraged chromosome-scale assemblies of two strains of Acanthamoeba, Neff and C3, to investigate the genomic mechanisms that mediate the fate of viral integrations in eukaryotic genomes.<br><br>RESULTS: Viral integrations in the C3 and Neff genomes are largely non-overlapping and disproportionately found in sub-telomeric regions. Multiple partial copies of these insertions are found throughout the Neff genome, but they are not expressed, do not obviously encode functions associated with their own mobility, and are colonized by host mobile elements. Viral regions are hypermethylated and highly condensed, suggesting that the expression of recently acquired viral DNA is suppressed in heterochromatic regions.<br><br>CONCLUSIONS: We propose a model for the trajectory of viral sequences in Acanthamoeba: (i) integration of DNA from giant viruses, (ii) epigenetic suppression of the viral DNAs, allowing them to persist in the genome, and (iii) deterioration of viral genomes by point mutation, mobile element colonization, and intra- and inter-chromosomal recombination. Viral integrations in Acanthamoeba spp. are transient and may not have long-lasting effects on the fitness of the amoeba. Our work highlights the importance of host genome dynamics and epigenetic silencing for understanding the evolution of endogenized viral elements.}, }
@article {pmid40596330, year = {2025}, author = {Puangseree, J and Hein, ST and Prathan, R and Srisanga, S and Chuanchuen, R}, title = {Genomic insights into multidrug - resistant Salmonella enterica isolates from pet dogs and cats.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {22104}, pmid = {40596330}, issn = {2045-2322}, support = {N42A660897//National Research Council of Thailand/ ; HEAF67310045//Thailand Science Research and Innovation Fund Chulalongkorn University (Fundamental Fund) Fiscal year 2567/ ; }, mesh = {Animals ; Dogs ; Cats ; *Salmonella enterica/genetics/drug effects/isolation &amp; purification ; *Drug Resistance, Multiple, Bacterial/genetics ; *Pets/microbiology ; Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; Plasmids/genetics ; *Salmonella Infections, Animal/microbiology ; *Dog Diseases/microbiology ; Microbial Sensitivity Tests ; *Cat Diseases/microbiology ; Genomics ; Genome, Bacterial ; }, abstract = {Companion animals are recognized as potential reservoirs and transmitters of antimicrobial resistance (AMR) within the One Health framework. However, in-depth knowledge on AMR in pet animals remains limited. This study aimed to characterize Salmonella from companion dogs and cats using Whole Genome Sequencing (WGS). A total of 25 Salmonella obtained from clinically healthy household dogs and cats were serotyped and had their antimicrobial susceptibility tested. A discrepancy between the serovars identified by traditional slide agglutination tests and those determined by WGS analysis was observed. The isolates exhibited multidrug resistance (MDR) (n = 18) and harbored several resistance genes either chromosomally encoded or plasmid associated. Tn3 and IS26 were commonly found flanking AMR genes and class 1 integrons, while an unusual qacL-IS256-sul3 arrangement was also frequently observed. Similar AMR genes and insertion sequences were found among dogs and cats from different provinces, suggesting clonal spread and horizontal gene transfer of AMR. The similarity between plasmids (i.e., IncX1 and IncI1 plasmid) carrying AMR genes (e.g., aadA1, qacL, sul3, blaTEM-1B, qnrS1, dfrA, tetA) in Salmonella from pets in this study and those from other sources (e.g., humans, food producing animals and environment) in different countries was revealed, suggesting that pet dogs and cats may play a significant role in the global spread of AMR. The finding underscores the role of household pets as silent reservoirs of MDR Salmonella and the need for a One Health approach to tackle the issue. Public health campaigns promoting hygiene practices among pet owners should be encouraged. Pet animals should be incorporated into AMR monitoring and surveillance programs as a component of One Health framework.}, }
@article {pmid40595289, year = {2025}, author = {Kador, SM and Islam, KT and Rubaiyat, RN and Bhuiyan, MIU and Chakrovarty, T and Rahman, MS and Islam, OK and Islam, MT}, title = {Abundance and transmission of antibiotic resistance and virulence genes through mobile genetic elements in integrated chicken and fish farming system.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {20953}, pmid = {40595289}, issn = {2045-2322}, support = {22-FoBST 05//Research Cell, Jashore University of Science and Technology/ ; SRG-221252//Special Research Grant, Ministry of Science and Technology, Bangladesh/ ; }, mesh = {Animals ; *Chickens/microbiology ; *Interspersed Repetitive Sequences/genetics ; Aquaculture ; Fishes ; *Virulence Factors/genetics ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/pathogenicity/drug effects ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Virulence/genetics ; Bangladesh ; }, abstract = {Integrated chicken and fish farming systems, common in Bangladesh, present significant public health risks due to the spread of antimicrobial resistance genes (ARGs) and virulence factors (VFGs) through mobile genetic elements (MGEs). This study employs metagenomic sequencing to explore the diversity and abundance of ARGs, VFGs, and MGEs in various environmental samples from these farming systems. A total of 384 ARGs were detected, with tetracycline resistance genes such as tetM and tetX being the most abundant, alongside macrolide-lincosamide-streptogramin and aminoglycoside resistance genes. Droppings harbored the highest proportion of ARGs (62.2%), whereas sediment served as a reservoir for multi-metal resistance genes. Virulence factors associated with immune modulation, such as pvdL and tssH, and biofilm formation genes like algC were particularly prevalent in sediment and droppings. Among MGEs, plasmids and transposons like Tn6072 and Tn4001 were the most abundant, playing a critical role in horizontal gene transfer. Bacterial genera including Bacteroides, Clostridium, and Escherichia were strongly associated with MGEs, indicating their role in the dissemination of resistance and virulence traits. Statistical analyses revealed significant differences in the abundance of ARGs, VFGs, and MGEs across sample types, with sediment and droppings identified as hotspots for gene exchange. These findings underscore the urgent need for improved antibiotic stewardship and waste management practices to limit the spread of antimicrobial resistance and pathogenic bacteria within integrated farming environments.}, }
@article {pmid40595025, year = {2025}, author = {Wedell, N}, title = {Harnessing lateral gene transfer and endosymbiosis for adaptation.}, journal = {Nature reviews. Genetics}, volume = {}, number = {}, pages = {}, pmid = {40595025}, issn = {1471-0064}, }
@article {pmid40594904, year = {2025}, author = {Sayem, M and Rafi, MA and Mishu, ID and Mahmud, Z}, title = {Comprehensive genomic analysis reveals virulence and antibiotic resistance genes in a multidrug-resistant Bacillus cereus isolated from hospital wastewater in Bangladesh.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {22915}, pmid = {40594904}, issn = {2045-2322}, mesh = {*Bacillus cereus/genetics/pathogenicity/isolation &amp; purification/drug effects ; *Wastewater/microbiology ; Bangladesh ; *Drug Resistance, Multiple, Bacterial/genetics ; Phylogeny ; Hospitals ; Virulence/genetics ; Genome, Bacterial ; Whole Genome Sequencing ; Genomics/methods ; Anti-Bacterial Agents/pharmacology ; Virulence Factors/genetics ; Humans ; }, abstract = {Hospital wastewater represents a significant reservoir for antimicrobial-resistant bacteria, including multidrug-resistant (MDR) Bacillus cereus, a pathogen of growing concern due to its potential impact on public health and environmental safety. This study characterizes the genomic features, antimicrobial resistance (AMR) mechanisms, and virulence potential of Bacillus cereus MBC, isolated from hospital wastewater in Dhaka, Bangladesh. Using whole-genome sequencing (WGS) and advanced bioinformatics, we analyzed the isolate's taxonomy, phylogenetics, functional annotation, and biosynthetic potential. The genome, spanning 5.6 Mb with a GC content of 34.84%, contained 5,881 protein-coding sequences, including 1,424 hypothetical proteins, and 28 genes associated with AMR. Phylogenetic analysis revealed a close genetic relationship with Bacillus cereus ATCC 14579, sharing virulence factors such as hemolysin BL (HBL), non-hemolytic enterotoxin (NHE), and cytotoxin K (CytK), all contributing to its pathogenicity. The ability to form biofilms further enhances the strain's persistence and resistance in hospital environments. AMR profiling identified genes conferring resistance to beta-lactams (e.g., BcI, BcII, BcIII), tetracyclines (tetB(P)), glycopeptides (vanY), and fosfomycin, highlighting the bacterium's capacity to resist a wide array of antibiotics. Functional annotation revealed metabolic pathways involved in iron acquisition and the biosynthesis of siderophores such as petrobactin and bacillibactin, reinforcing the bacterium's adaptability in nutrient-limited environments. Mobile genetic elements, including prophages, CRISPR-Cas systems, and transposable elements, suggest significant horizontal gene transfer (HGT), enhancing genetic plasticity and resistance spread. Pangenomic analysis, involving 125 B. cereus strains, revealed a high degree of genetic diversity and close relationships with strains from clinical, food, and agricultural environments, emphasizing the overlap between clinical and environmental reservoirs of resistance. The strain's isolation from hospital wastewater underscores the complex interplay between environmental contaminants and bacterial evolution, which fosters MDR traits. Our findings underscore the urgent need for enhanced genomic surveillance and wastewater management strategies to mitigate the spread of MDR B. cereus and AMR genes in hospital environments.}, }
@article {pmid40592271, year = {2025}, author = {Fan, Q and Bai, J and Jiao, T and Zhao, Z and Hou, F}, title = {Circular transmission network and reverse contribution pattern of antibiotic resistance genes in the Qinghai-Tibet Plateau ecosystem.}, journal = {Journal of hazardous materials}, volume = {495}, number = {}, pages = {139054}, doi = {10.1016/j.jhazmat.2025.139054}, pmid = {40592271}, issn = {1873-3336}, abstract = {The dissemination of antibiotic resistance genes (ARGs) poses a major global public health challenge, yet transmission mechanisms within extreme ecosystems are poorly understood. Using metagenomics and metagenome-assembled genome (MAG) analysis, we investigated ARG composition, risk, and pathways across a complete Qinghai-Tibet Plateau food chain (soil, earthworm, herbage, yak, pika, snowfinch, herdsman). Contrary to conventional theory, ARG assemblages correlated negatively with microbial diversity. Our MAG-centric approach provided direct evidence that Horizontal Gene Transfer (HGT), including striking bacteria-archaea cross-domain transfer of 18 ARGs, predominates ARG dissemination, with specialized 'ARG reservoir' host phyla (e.g., Pseudomonadota) decoupling ARG functional diversity from overall microbial community structure. Earthworms function as 'ARG bioamplifiers', enriching 79.81 % of soil ARGs and contributing 49.43 % to herbage. Crucially, apex consumers (snowfinches, herdsmen) are not merely recipients; their feces drive a significant 'reverse contribution' of high-risk ARGs back into the ecosystem, establishing a complete circular ARG feedback network. Herdsman feces contained all Rank I-IV high-risk ARGs, while snowfinch feces held Rank II/IV, highlighting human activities' impact on escalating ARG risks in this extreme setting. These findings, particularly the novel HGT mechanisms and host specialization insights, challenge the traditional unidirectional transmission model, presenting a new paradigm for managing antibiotic resistance risks in extreme ecosystems within the One Health framework.}, }
@article {pmid40592212, year = {2025}, author = {Byczkowska-Rostkowska, Z and Gajewska, J and Chajęcka-Wierzchowska, W}, title = {Whole genome analysis and antimicrobial resistance assessment of Staphylococcus epidermidis isolated from food sources.}, journal = {The Science of the total environment}, volume = {993}, number = {}, pages = {179999}, doi = {10.1016/j.scitotenv.2025.179999}, pmid = {40592212}, issn = {1879-1026}, abstract = {Coagulase-negative staphylococci (CoNS), including Staphylococcus epidermidis, are commonly occurrence in a variety of food products. Historically considered non-pathogenic, these microorganisms were excluded from routine food safety monitoring protocols. However, their increasing involvement in nosocomial infections underscores their pathogenic potential. Emerging evidence suggests that the food chain may serve as a reservoir and transmission route for antibiotic-resistant bacteria. In this study, 26 S. epidermidis isolates obtained from ready-to-eat food were subjected to whole-genome sequencing and comprehensive bioinformatics analyses. The antimicrobial susceptibility of the isolates was also evaluated against a broad spectrum of agents including aminoglycosides, β-lactams, fluoroquinolones, glycopeptides, lincosamides, macrolides, nitrofurantoins, oxalidinones, phenicols, steroids, sulphonamides and tetracyclines. Sequence typing revealed the presence of 17 distinct sequence types (STs), with ST329 being the most frequently identified (8/26, 30.77 %), followed by ST88 and ST152 (each 2/26; 7.69 %). Notably, one isolate harbored a novel multi-locus sequence type. Phenotypically resistance to erythromycin was most prevalent (21/26, 80.77 %), followed by resistance to clindamycin (19/26, 73.08 %). Genomic analysis confirmed the presence of multiple antimicrobial resistance genes including norA/C, vanT, mecA, dfrC and multidrug resistance genes. The carrying of mobile genetic elements was demonstrated by 25/26 (96.15 %) strains. These findings indicate that S. epidermidis strains isolated from ready-to-eat foods not only exhibit multidrug resistance but also carry a diverse array of antimicrobial resistance genes. The potential for horizontal gene transfer to commensal or pathogenic bacteria highlights the need for increased surveillance and risk assessment concerning CoNS in the food supply.}, }
@article {pmid40407375, year = {2025}, author = {Lyra de Holanda Fonseca, D and Scheunemann, GS and Fortes, BN and Ishida, K and Galhardo, RS}, title = {Interaction of the SXT/R391 element ICEPmiJpn1 with its natural host Proteus mirabilis.}, journal = {Microbiology spectrum}, volume = {13}, number = {7}, pages = {e0033925}, pmid = {40407375}, issn = {2165-0497}, support = {2019/19435-3//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2020/00535-5//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2021/15170-5//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2021/10577-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2022/03986-3//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; finance code 01//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; }, mesh = {*Proteus mirabilis/genetics/pathogenicity/drug effects/physiology ; Conjugation, Genetic ; Gene Transfer, Horizontal ; Biofilms/growth &amp; development ; Escherichia coli/genetics ; *DNA Transposable Elements/genetics ; Proteus Infections/microbiology ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; *Interspersed Repetitive Sequences ; Bacterial Proteins/genetics ; }, abstract = {Integrative and conjugative elements (ICEs) of the SXT/R391 family are mobile genetic elements that integrate into the bacterial host chromosome and can be transferred horizontally, spreading antimicrobial resistance genes. Our study aimed to evaluate aspects of the relationship between ICEPmiJpn1, one of the most widespread SXT/R391 variants, with its natural host Proteus mirabilis. For this investigation, we used isogenic strains (containing or not the ICEPmiJpn1) that enabled us to evaluate the influence of this element on several physiological aspects of P. mirabilis as well as the effect of different P. mirabilis genetic backgrounds on the conjugative transmission of the element. ICEPmiJpn1 did not impact the fitness, self-recognition, swarming, pathogenicity, and persistence abilities of this bacterium but increased biofilm formation in one strain. Additionally, conjugative transfer of the element to Escherichia coli is widely variable when different P. mirabilis strains are used as donors in mating assays. Our results indicate that ICEPmiJpn1 has no adverse effects on the physiology or pathogenicity of P. mirabilis, reflecting a stable association between this element and its host. Furthermore, the findings support the notion that ICE transfer between bacteria is influenced not only by element-specific regulators but also by strain-specific factors.IMPORTANCEMobile genetic elements play a key role in the spread of antimicrobial resistance, raising concerns about multidrug-resistant bacteria, yet their interactions with bacterial hosts are not well characterized. This study explores the relationship between ICEPmiJpn1, a globally distributed SXT/R391 integrative and conjugative element (ICE), and its natural host Proteus mirabilis, revealing minimal effects on bacterial fitness and pathogenicity. Nevertheless, strain-specific factors significantly influence conjugative transfer. These findings highlight the need for further research on host-dependent regulatory mechanisms that drive the spread of these elements. Understanding these dynamics is essential for developing strategies to mitigate the dissemination of antibiotic resistance in clinically relevant bacterial populations.}, }
@article {pmid40590551, year = {2025}, author = {Renno, AJ and Shields, RC and McLellan, LK}, title = {Bacterial evolution in the oral microbiome: the role of conjugative elements and horizontal gene transfer.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {e0006625}, doi = {10.1128/jb.00066-25}, pmid = {40590551}, issn = {1098-5530}, abstract = {As one of the most diverse bacterial populations within the human body, the oral microbiome encodes a wealth of genetic information. Horizontal gene transfer, driven by mobile genetic elements, takes advantage of this information to influence bacterial evolution and the spread of phenotypes (antibiotic resistances, virulence attributes, and metabolic capabilities) among oral microbes. Although widespread within microbial communities, fundamental aspects of the mobile elements that drive horizontal gene transfer within the oral cavity remain poorly understood. In this review, we explore what is known about the role of horizontal gene transfer in bacterial evolution within the oral microbiome and the elements that facilitate this transfer, with a specific focus on conjugative DNA transfer. Conjugative elements are found in virtually all bacterial phylogenetic clades, and some can mediate genetic exchange between distantly related organisms. This is of particular interest in the diverse microcosm of the oral cavity, specifically how it drives the evolution and virulence of dental pathogens. Finally, we highlight advances in our understanding of the unique biology within dental plaque and how these might influence our understanding of bacterial gene transfer, and thus human health and disease.}, }
@article {pmid40589066, year = {2025}, author = {Collins, N and Levy, Y and Kolomeisky, AB}, title = {Theoretical Understanding of Target Search Dynamics in Horizontal Gene Transfer in Bacteria.}, journal = {The journal of physical chemistry. B}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jpcb.5c02436}, pmid = {40589066}, issn = {1520-5207}, abstract = {Horizontal gene transfer (HGT) is a fundamental process of increasing genetic diversity in microbial species. It allows bacterial cells to acquire new beneficial traits quickly by incorporating new genetic material into existing genomes. Despite the critical importance of HGT phenomena, the underlying molecular mechanisms are still poorly understood. Recent experiments investigated the dynamics of conjugation HGT processes in which DNA is transmitted directly from the donor to the recipient bacterial cell. It is accomplished by special mobile genetic particles known as integrative and conjugative elements (ICE). However, the molecular picture of how ICE can efficiently find the unique integration sites in a new genome is not yet clear. We present a novel theoretical model to explain the dynamic processes in HGT after ICE reaches the recipient cell. It is shown that the target search for integration sites can be viewed as a set of stochastic transitions between discrete states, allowing us to obtain an explicit description of the dynamic properties using analytical calculations supported by Monte Carlo computer simulations. Search times are found to depend on the location of integration sites, the size of the genome, the effective diffusion rate of mobile genetic elements, and the binding/unbinding transitions between ICE and DNA. Theoretical estimates for search times agree well with experimental observations for integration in Bacillus subtilis bacterial species. Physical-chemical arguments are presented to explain the dynamics of the ICE target search. This study clarifies some important mechanistic aspects of HGT phenomena.}, }
@article {pmid40588591, year = {2025}, author = {Mancuso, CP and Baker, JS and Qu, EB and Tripp, AD and Balogun, IO and Lieberman, TD}, title = {Intraspecies warfare restricts strain coexistence in human skin microbiomes.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {40588591}, issn = {2058-5276}, support = {1DP2GM140922//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, abstract = {Determining why only a fraction of encountered or applied strains engraft in a given person's microbiome is crucial for understanding and engineering these communities. Previous work has established that metabolic competition between bacteria can restrict colonization success in vivo, but other mechanisms may also prevent successful engraftment. Here we combine genomic analysis and high-throughput agar competition assays to demonstrate that intraspecies warfare presents a significant barrier to strain coexistence in the human skin microbiome by profiling 14,884 pairwise interactions between Staphylococcus epidermidis isolates cultured from 18 people from 6 families. We find that intraspecies antagonisms are abundant, mechanistically diverse, independent of strain relatedness and consistent with rapid evolution via horizontal gene transfer. Critically, these antagonisms are significantly depleted among strains residing on the same person relative to random assemblages, indicating a significant in vivo role. Wide variation in antimicrobial production and resistance suggests trade-offs between these factors and other fitness determinants. Together, our results emphasize that accounting for intraspecies warfare may be essential to the design of long-lasting probiotic therapeutics.}, }
@article {pmid40587929, year = {2025}, author = {Chen, J and Guo, Y and Lin, Y and Zhang, Y and Qian, Q and Zhang, X and Lin, P and Chen, C and Xie, S}, title = {Fate, mobility and pathogenicity of antibiotic resistome in a full-scale drinking water treatment plant: Highlighting the chlorination risks.}, journal = {Journal of environmental management}, volume = {390}, number = {}, pages = {126425}, doi = {10.1016/j.jenvman.2025.126425}, pmid = {40587929}, issn = {1095-8630}, abstract = {Drinking water treatment plants (DWTPs) serve as the last barrier in preventing the spread of antibiotic resistance genes (ARGs) into tap water, yet the distribution and dissemination mechanisms of ARGs in DWTPs remain unclear. In this study, the antibiotic resistome of a full-scale DWTP using Nansi Lake (an important node of the South-to-North Water Diversion Project's eastern route, China) as water source was investigated based on metagenomic analysis. The results showed that coagulation and chlorination were the two crucial processes increasing the relative abundance of ARGs in the DWTP, and the former predominantly enhanced that of sulfonamide RGs, while the latter increased that of bacitracin, aminoglycoside and multidrug RGs. ARG hosts and mobile genetic elements (MGEs) both played significant roles in ARG compositions. The persistence of Sphingorhabdus during the conventional treatment stages and the dissemination potential of plasmids accounted for the relative abundance of sulfonamide RGs, while the chlorine and multidrug resistance of Acinetobacter, Acidovorax, and Pseudomonas, along with the coexistence of various MGEs, suggested the persistence and transmission risk of ARGs after chlorination. Ozonation and activated carbon filtration could eliminate some human-pathogenic bacteria (HPB), but the chlorination process significantly increased the relative abundance of HPB. The multidrug-resistant HPB such as Acinetobacter calcoaceticus and Acinetobacter haemolyticus were the key targets for risk control in the DWTP. Our findings provide new insights into the fate, mobility, and pathogenicity of ARGs in a typical DWTP, offering beneficial guidance for decision-making in the risk control of ARGs in DWTPs.}, }
@article {pmid40585299, year = {2025}, author = {Chai, Z and Guo, Z and Chen, X and Yang, Z and Wang, X and Zhang, F and Kang, F and Liu, W and Liang, S and Ren, H and Yue, J and Jin, Y}, title = {Comprehensive profiling of integrative conjugative elements (ICEs) in Mollicutes: distinct catalysts of gene flow and genome shaping.}, journal = {NAR genomics and bioinformatics}, volume = {7}, number = {2}, pages = {lqaf083}, pmid = {40585299}, issn = {2631-9268}, mesh = {*Genome, Bacterial ; Gene Transfer, Horizontal ; *Conjugation, Genetic ; *Gene Flow ; *Tenericutes/genetics ; Evolution, Molecular ; Phylogeny ; }, abstract = {Mollicutes, known as the simplest bacteria with streamlined genomes, were traditionally thought to evolve mainly through gene loss. Recent studies have highlighted their rapid evolutionary capabilities and genetic exchange within individual genomes; however, their evolutionary trajectory remains elusive. By comprehensive screening 1433 available Mollicutes genomes, we revealed widespread horizontal gene transfer (HGT) in 83.9% of investigated species. These genes involve type IV secretion systems and DNA integration, inferring the unique role of integrative conjugative elements (ICEs) or integrative and mobilizable elements (IMEs) as self-transmissible genetic elements. We systematically identified 263 ICEs/IMEs across most Mollicutes genera, being intact or fragmented, showing a strong correlation with HGT frequency (cor 0.573, P = .002). Their transfer tendency was highlighted across species sharing ecological niches, notably in livestock-associated mycoplasmas and insect-vectored spiroplasmas. ICEs/IMEs not only act as gene shuttles ferrying various phenotypic genes, but also promote increased large-scale chromosomal transfer events, shaping the host genomes profoundly. Additionally, we provided novel evidence that Ureaplasma ICE facilitates genetic exchange and the spread of antibiotic resistance gene tet(M) among other pathogens. These findings suggest that, despite the gene-loss pressure associated with the compact genomes of Mollicutes, ICEs/IMEs play a crucial role by introducing substantial genetic resources, providing essential opportunities for evolutionary adaptation.}, }
@article {pmid40584034, year = {2025}, author = {Alhejaili, AY and Zhou, G and Halawa, H and Huang, J and Fallatah, O and Hirayban, R and Iftikhar, S and AlAsmari, A and Milner, M and Banzhaf, M and Alzaidi, AA and Rajeh, AA and Al-Otaiby, MA and Alabbad, SS and Bukhari, D and Aljurayyan, AN and Aljasham, AT and Alzeyadi, ZA and Alajel, SM and Alanazi, RH and Alghoribi, M and Almutairi, MM and Pain, A and Senok, A and Moradigaravand, D and Al Salem, W}, title = {Methicillin-resistant Staphylococcus aureus in Saudi Arabia: genomic evidence of recent clonal expansion and plasmid-driven resistance dissemination.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1602985}, pmid = {40584034}, issn = {1664-302X}, abstract = {OBJECTIVES: Staphylococcus aureus is a leading cause of hospital-acquired infections worldwide. Over recent decades, methicillin-resistant Staphylococcus aureus (MRSA), which is resistant to multiple antimicrobials, has emerged as a significant pathogenic strain in both hospital and community settings. The rapid emergence and dissemination of MRSA clones are driven by a dynamic and evolving population, spreading swiftly across regions on epidemiological time scales. Despite the vast geographical expanse and diverse demographics of the Kingdom of Saudi Arabia and the broader West Asia region, the population diversity of MRSA in hospitals in these areas remains underexplored.<br><br>METHODS: We conducted a large-scale genomic analysis of a systematic Staphylococcus aureus collection obtained from 34 hospitals across all provinces of KSA, from diverse body sites between 2022 and 2024. The dataset comprised 581 MRSA and 31 methicillin-susceptible Staphylococcus aureus (MSSA) isolates, all subjected to whole-genome sequencing. A combination of phylogenetic and population genomics approaches was utilized to analyze the genomic data. Hybrid sequencing approach was employed to retrieve the complete plasmid content.<br><br>RESULTS: The population displayed remarkable diversity, comprising 48 distinct sequence types (STs), with the majority harboring community-associated SCCmec loci (types IVa, V/VII, and VI). Virulence factors associated with community-acquired MRSA (CA-MRSA), including Panton-Valentine Leukocidin (PVL) genes, were identified in 12 distinct STs. Dominant clones, including ST8-t008 (USA300), ST88-t690, ST672-t3841, ST6-t304, and ST5-t311, were associated with infections at various body sites and were widely disseminated across the country. Linezolid and vancomycin resistance were mediated by cfr-carrying plasmids and mutations in the vraR gene (involved in cell-wall stress response) and the murF gene (involved in peptidoglycan biosynthesis) in five isolates, respectively. Phylodynamic analysis revealed rapid expansion of the dominant clones, with their emergence estimated to have occurred 10-20 years ago. Plasmidome analysis uncovered a diverse repertoire of blaZ-containing plasmids and the sharing of erm(C)-encoding plasmids among major clades. The acquisition of plasmids coincided with clonal expansion.<br><br>CONCLUSIONS: Our results highlight the recent concurrent expansion and geographical dissemination of CA-MRSA clones across hospitals. These findings also underscore the interplay between clonal spread and horizontal gene transfer in shaping the resistance landscape of MRSA.}, }
@article {pmid40582582, year = {2025}, author = {Munshi, ID and Mathuria, A and Sharma, H and Acharya, M and Chaudhary, A and Jain, K and Ragini,  and Dahiya, S and Arora, R and Singh, V and Saini, A and Mani, I}, title = {Emerging concept of genomic islands in bacterial adaptation and pathogenicity.}, journal = {Research in microbiology}, volume = {}, number = {}, pages = {104303}, doi = {10.1016/j.resmic.2025.104303}, pmid = {40582582}, issn = {1769-7123}, abstract = {Genomic Islands (GEIs) are distinct DNA segments acquired through horizontal gene transfer (HGT), driving bacterial evolution and adaptation. These include Pathogenicity Islands (PAIs), Symbiosis Islands, Antibiotic Resistance Islands, Xenobiotic-Degradation Islands, and Nitrogen Fixation Islands. GEIs contribute to genetic diversity, enhancing bacterial pathogenicity, symbiosis, antibiotic resistance, and xenobiotic degradation. Characterized by variations in GC content, codon bias, and integration sites, they distinguish themselves from the core genome. Advances in genome sequencing and bioinformatics have deepened our understanding of GEIs in bacteria like Salmonella, Vibrio, E. coli, and many more, offering insights into microbial evolution, pathogenicity, and antibiotic resistance mechanisms.}, }
@article {pmid40581000, year = {2025}, author = {Fraikin, N and Samuel, B and Burstein, D and Lesterlin, C}, title = {Strategies for zygotic gene expression during plasmid establishment.}, journal = {Plasmid}, volume = {}, number = {}, pages = {102754}, doi = {10.1016/j.plasmid.2025.102754}, pmid = {40581000}, issn = {1095-9890}, abstract = {Conjugative plasmids are key drivers of horizontal gene transfer and the spread of antimicrobial resistance. Their successful establishment in new hosts requires overcoming diverse bacterial defence mechanisms, such as restriction-modification systems, CRISPR-Cas systems, and the SOS response. Plasmids achieve this through a leading region-encoded zygotic program of anti-defence genes expressed early in conjugation. This program employs diverse strategies, including single-stranded promoters, repressed double-stranded promoters, and protein translocation. This review explores the diversity of these zygotic programs, the mechanisms underlying their timely regulation, and the array of anti-defence functions they encode. Further investigation of leading region genes is crucial for discovering novel counter-defence strategies and understanding their tailored regulation across diverse plasmid and bacterial species, ultimately enabling us to better understand and potentially manipulate plasmid transfer.}, }
@article {pmid40580037, year = {2025}, author = {}, title = {Correction to 'GutMetaNet: an integrated database for exploring horizontal gene transfer and functional redundancy in the human gut microbiome'.}, journal = {Nucleic acids research}, volume = {53}, number = {12}, pages = {}, doi = {10.1093/nar/gkaf654}, pmid = {40580037}, issn = {1362-4962}, }
@article {pmid40579721, year = {2025}, author = {O'Donnell, S and Rezende, G and Vernadet, JP and Snirc, A and Ropars, J}, title = {Harbouring Starships: The accumulation of large Horizontal Gene Transfers in Domesticated and Pathogenic Fungi.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evaf125}, pmid = {40579721}, issn = {1759-6653}, abstract = {Human-related environments, including food and clinical settings, present microorganisms with atypical and challenging conditions that necessitate adaptation. Several cases of novel horizontally acquired genetic material associated with adaptive traits have been recently described, contained within giant transposons named Starships. While a handful of Starships have been identified in domesticated species, their abundance has not yet been systematically explored in human-associated fungi. Here, we investigated whether Starships have shaped the genomes of two major genera of fungi occurring in food and clinical environments, Aspergillus and Penicillium, providing a unique opportunity to study several independent events of adaptation to similar niches. We found in all cases that the domesticated strains or species exhibited significantly greater Starship content compared with close relatives from non-human-related environments, containing an enrichment in genes involved in adaptation to food. We found a similar pattern in clinical contexts. Our findings have clear implications for agriculture, human health and the food industry as we implicate Starships as a widely recurrent mechanism of gene transfer aiding the rapid adaptation of fungi to novel environments.}, }
@article {pmid40578739, year = {2025}, author = {Yang, Y and Tang, X and Zhang, P and Mo, C and Huang, F and Wen, Z}, title = {Effect of microplastics on antibiotic resistome risk in composting.}, journal = {Environmental research}, volume = {284}, number = {}, pages = {122241}, doi = {10.1016/j.envres.2025.122241}, pmid = {40578739}, issn = {1096-0953}, abstract = {Microplastics are a growing concern worldwide because of their impact on the environment and human health. Composting is an effective method for managing antibiotic resistome risk in organic waste, yet the effects of microplastics on antibiotic resistome risk in composting are not well understood. In this study of laying hen manure, the microplastic polypropylene increased the temperature of the compost but did not significantly affect the total composition, abundance and risk score of antibiotic resistance genes (ARGs) during composting. The dominant phyla on microplastics and manure were Actinobacteria, Firmicutes and Proteobacteria. Escherichia (bin.70), Oceanobacillus (bin.85) and Mycobacterium (bin.79) were the main ARG hosts. Among them, the abundance of the ARG host Mycobacterium (bin.79) was significantly higher in microplastics than in manure. Furthermore, ARG transfer occurred between the ARG host Mycobacterium (bin.79) and other microorganisms on microplastics and manure. These findings indicate that while microplastics may not strongly affect the overall antibiotic resistome risk during composting, they increase the likelihood of horizontal gene transfer in specific ARG hosts. This underscores the critical need to control both microplastic and resistance contamination.}, }
@article {pmid40434128, year = {2025}, author = {Zhao, R and Nawrocki, A and Møller-Jensen, J and Liu, G and Olsen, JE and Thomsen, LE}, title = {Mechanistic divergence between SOS response activation and antibiotic-induced plasmid conjugation in Escherichia coli.}, journal = {Microbiology spectrum}, volume = {13}, number = {7}, pages = {e0009025}, doi = {10.1128/spectrum.00090-25}, pmid = {40434128}, issn = {2165-0497}, support = {//China Scholarship Council/ ; }, mesh = {*SOS Response, Genetics/drug effects ; *Escherichia coli/genetics/drug effects/metabolism ; *Anti-Bacterial Agents/pharmacology ; *Plasmids/genetics/metabolism ; *Conjugation, Genetic/drug effects ; Escherichia coli Proteins/genetics/metabolism ; Cefotaxime/pharmacology ; Ciprofloxacin/pharmacology ; Gene Expression Regulation, Bacterial/drug effects ; Mitomycin/pharmacology ; Gene Transfer, Horizontal ; }, abstract = {The SOS response is a critical DNA damage repair mechanism in bacteria, designed to counteract genotoxic stress and ensure survival. This system can be activated by different classes of antimicrobial agents, each inducing the SOS response through different mechanisms. Moreover, it has been observed that certain antibiotics can enhance conjugative plasmid transfer frequencies. However, while previous studies have suggested that the SOS response contributes to horizontal transfer of certain genes, its role in plasmid conjugation remains unclear. In this study, we investigated the relationship between the SOS response and conjugation of IncI1 and IncFII plasmids harboring various blaCTX-M resistance genes. Results showed that cefotaxime and mitomycin C induced both the SOS response and conjugation, while ciprofloxacin induced the SOS response without affecting conjugation frequencies. Further analysis of SOS mutants, ranging from constitutively inactive to hyper-induced states, revealed no correlation between SOS levels and conjugation frequencies, despite upregulation of tra gene expression in a SOS hyper-induced strain. Proteomic analysis revealed that cefotaxime-induced conjugation was associated with increased transfer and pilus protein expression. In contrast, the SOS hyper-induced strain displayed limited upregulation of plasmid-encoded proteins, suggesting post-transcriptional regulation. Additionally, putative LexA binding sites on the IncI1 plasmid revealed potential SOS-mediated regulation of plasmid genes, highlighting the interaction between the SOS response and plasmid, although it did not significantly affect conjugation.IMPORTANCEPlasmids play a critical role in the dissemination of antibiotic resistance through conjugation. Recent research suggests that the use of antibiotics not only selects for already resistant variants but further increases the rate of plasmid-encoded conjugative transmission by increasing expression of the conjugative system. At the same time, these antibiotics are known to induce the stress-related SOS response in bacteria. To be able to counteract an antibiotic-induced increase in conjugative transfer of resistance plasmid, there is a need for a fundamental understanding of the regulation of transmission, including whether this happens through activation of the SOS response. In this research, we show that antibiotic-induced conjugation and induction of the SOS response happen through different mechanisms, and thus that future strategies to control the spread of antibiotics cannot interfere with the SOS response as its target.}, }
@article {pmid40408992, year = {2025}, author = {Zhang, S and Li, J and Lai, J and Zhang, Q and Zhao, Z and Li, B}, title = {Transfer dynamics of intracellular and extracellular last-resort antibiotic resistome in hospital wastewater.}, journal = {Water research}, volume = {283}, number = {}, pages = {123833}, doi = {10.1016/j.watres.2025.123833}, pmid = {40408992}, issn = {1879-2448}, mesh = {*Wastewater/microbiology ; Hospitals ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; }, abstract = {The increasing prevalence of last-resort antibiotic resistance genes (LARGs) has posed severe public health hazards. Previous studies focused primarily on the profiles of intracellular LARGs (iLARGs) in hospital wastewater (HWW), while largely neglecting the expression patterns of iLARGs and the presence of extracellular LARGs (eLARGs). Currently, wastewater resistomes and transfer dynamics of LARGs are still poorly characterized. This study integrates Nanopore-metagenomic and metatranscriptomic sequencing to conduct the comprehensive longitudinal analysis of both iLARGs and eLARGs in HWW. Our study firstly revealed the distinct seasonal patterns of iLARGs and eLARGs. Specifically, iLARGs showed higher abundance during colder seasons, whereas eLARGs showed higher abundance in warm seasons. Both clinical pathogens and functional bacteria of wastewater treatments were identified as important hosts of LARGs, while clinical pathogens played predominant roles in the high expression levels of LARGs. Acinetobacter spp. was identified as major host of blaNDM-1 in HWW, which is unrestricted by plasmid host range compatibility. However, HWW treatments could not remove LARGs effectively and instead facilitated their transmission by enhancing the expression and horizontal transfer of mobile genetic element (MGE)-derived LARGs. Our study provides comprehensive insights for the atlas and transfer dynamics of LARGs in HWW for the development of control strategies under worldwide spread of antibiotic resistance.}, }
@article {pmid40578617, year = {2025}, author = {Villarroel, CA and Gonzalez-Gonzalez, A and Chamorro, M and Villarreal, P and Cubillos, FA and Ramírez, CC}, title = {Discovery of the first aphid-infecting nudiviruses reveal bidirectional host-virus gene transfer.}, journal = {Journal of invertebrate pathology}, volume = {}, number = {}, pages = {108393}, doi = {10.1016/j.jip.2025.108393}, pmid = {40578617}, issn = {1096-0805}, abstract = {Nudiviruses are double-stranded DNA viruses that infect invertebrate species, ranging from aquatic arthropods to insects from diverse orders. Remnants of nudiviral infections have been found as introgressions in the genome of several insect hosts, such as aphids pest species (Hemiptera: Aphididae). However, a nudivirus infecting aphids has yet to be reported. Here, we describe the complete genome sequences of two nudiviruses found in the aphid Neuquenaphis staryi, a species that branched out early in the Aphididae family and is endemic to southern beech forests in South America. These nudiviruses (NsNV-1 and NsNV-2) share 98% of nucleotide identity between them and belong to the Alphanudivirus genus. Notably, we found that the prevalence of NsNV-1 was 16 times higher than NsNV-2 in natural N. staryi populations, and co-infections were not observed. Furthermore, we show that horizontal gene transfer between aphids and nudiviruses has been bidirectional, providing evidence of their dynamic co-evolutionary relationship. This study provides the first documentation of nudivirus infections in aphids and expands our understanding of the evolutionary interactions between nudiviruses and their insect hosts.}, }
@article {pmid40578104, year = {2025}, author = {Li, X and Wang, H and Abdelrahman, HA and Kelly, AM and Roy, LA and Soto, E and Wang, L}, title = {Resistome and microbiome shifts in catfish rearing water: the influence of temperature and antibiotic treatments.}, journal = {Water research}, volume = {285}, number = {}, pages = {124074}, doi = {10.1016/j.watres.2025.124074}, pmid = {40578104}, issn = {1879-2448}, abstract = {The increasing reliance on aquaculture for sustainable protein production highlights the need for responsible antibiotic use to manage bacterial infections, particularly in intensive farming systems. This study investigated the effects of three FDA-approved antibiotics (Aquaflor®, Romet®, Terramycin®) at common fish bacterial disease outbreak temperatures (20 °C, 25 °C, and 30 °C) on the microbiome and resistome of aquaculture water using a catfish model system. Metagenomic analyses evaluated the abundance, diversity, and mobility of antimicrobial resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). The impact of temperature on Aquaflor- and Romet-induced changes in ARG abundance, richness, and resistome composition followed a U-shaped trend, with the least effect observed at 25 °C. Of the three antibiotics tested, Terramycin exerted the most significant influence on the water microbiome and resistome, enriching tetracycline resistance genes and co-selecting for floR, sul, and dfrA genes. Temperature also induced notable shifts in the ARB population, with Mantel tests revealing strong correlations between ARG profiles and changes in the overall bacterial community and ARB populations. While certain ARG classes consistently remained associated with specific host phyla, others shifted, highlighting the potential for horizontal gene transfer (HGT) as a critical mechanism for disseminating resistance genes like tet(C), particularly after antibiotic treatment. This is further supported by the observed reduction in plasmid numbers following treatment, which coincided with increased HGT events. Our findings highlight the pivotal role of temperature in influencing resistome dynamics, emphasizing the importance of accounting for environmental factors when applying antibiotics to effectively mitigate antimicrobial resistance in aquaculture systems.}, }
@article {pmid40576355, year = {2025}, author = {López, L and Jumbo, M and Mosquera, P and Donoso, G and Graham, J and Trueba, G}, title = {Oral and parenteral treatment with a third-generation cephalosporin promotes the proliferation of diverse ESBL-producing Escherichia coli in the chicken intestinal tract.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0022725}, doi = {10.1128/msphere.00227-25}, pmid = {40576355}, issn = {2379-5042}, abstract = {The global rise of antimicrobial resistance is a major public health threat, with Escherichia coli facilitating the spread of extended-spectrum beta-lactamase (ESBL) genes like blaCTX-M, which confer resistance to third-generation cephalosporins (3GCs). This study examines the impact of 3GC treatment on resistant E. coli clones and horizontal gene transfer (HGT) of ESBL genes in broiler chickens in Quito, Ecuador. Fifteen-day-old Ross broilers were divided into three groups: oral ceftriaxone (100 mg/kg), parenteral ceftriaxone (100 mg/kg intramuscular), and control (no treatment). The study included three phases: baseline, antimicrobial administration (5 days), and recovery (15 days). Fecal cultures on McConkey agar, with and without ceftriaxone (2 µg/mL), measured the ratio of 3GC-resistant lactose fermenters. Regardless of the administration route, ceftriaxone significantly increased resistant coliforms (>80%). Five E. coli colonies per animal and time point were analyzed using single-gene typing, with clonal candidates subjected to whole-genome sequencing. Clonal analysis revealed high genetic diversity, averaging three distinct clones per animal. A unique lineage (H34) emerged exclusively during treatment, and new clones appeared post-treatment. The blaCTX-M-55 variant was the most abundant ESBL gene, persisting despite fluctuations in other blaCTX-M variants. Comparative plasmid analysis suggested blaCTX-M-55 HGT, as plasmids were identified in two genetically distinct E. coli isolates from the same host. Most plasmids belonged to IncFII, with IncX1 and IncN also present. These findings highlight how 3GC treatments rapidly impact ESBL-producing E. coli diversity in the intestine.IMPORTANCEThe global rise of antimicrobial resistance (AMR) poses a critical public health challenge, with Escherichia coli playing a central role in the spread of extended-spectrum beta-lactamase (ESBL) genes like blaCTX-M, which confer resistance to third-generation cephalosporins (3GCs). This study highlights the significant impact of 3GC treatment on the frequency and diversity of 3GC-resistant E. coli clones and horizontal gene transfer of ESBL genes in the intestinal microbiota of broiler chickens. Understanding how antimicrobial treatments drive resistance dynamics in animal populations is crucial for developing strategies to mitigate AMR in both human and veterinary settings.}, }
@article {pmid40573425, year = {2025}, author = {Lewandowska, N and Bloch, S and Łukasiak, A and Wesołowski, W and Węgrzyn, G and Nejman-Faleńczyk, B}, title = {The Role of Bacteriophage-Derived Small RNA Molecules in Bacterial and Phage Interactions.}, journal = {Viruses}, volume = {17}, number = {6}, pages = {}, doi = {10.3390/v17060834}, pmid = {40573425}, issn = {1999-4915}, support = {2018/29/B/NZ1/00549//National Science Center/ ; 2018/30/E/NZ1/00400//National Science Center/ ; }, mesh = {*Bacteriophages/genetics/physiology ; *Bacteria/virology/genetics ; *RNA, Small Untranslated/genetics/metabolism ; *RNA, Viral/genetics/metabolism ; Gene Expression Regulation, Bacterial ; *Host Microbial Interactions ; RNA, Bacterial/genetics ; Host-Pathogen Interactions ; Gene Transfer, Horizontal ; }, abstract = {Small regulatory RNAs (sRNAs) play a critical role in bacterial gene expression, modulating various cellular processes, including stress responses, metabolism, virulence, and many others. While well-characterized in bacterial systems, an emerging class of phage-derived sRNAs has been identified, suggesting an underexplored regulatory network at phage-host interactions. These sRNAs, encoded within phage genomes, influence both bacterial and viral life cycles by modulating transcriptional and post-transcriptional gene expression processes. The interplay between phage-derived sRNAs and the host genome reveals a complex network of gene regulation, with an impact on bacterial fitness, pathogenesis, and horizontal gene transfer. This review explores the diverse functions of phage-encoded sRNAs, highlighting recent discoveries and their impact on bacterial physiology and phage-host interactions.}, }
@article {pmid40572258, year = {2025}, author = {Gonzalez Moreno, PJ and Nishiguchi, MK}, title = {The Competitive Edge: T6SS-Mediated Interference Competition by Vibrionaceae Across Marine Ecological Niches.}, journal = {Microorganisms}, volume = {13}, number = {6}, pages = {}, pmid = {40572258}, issn = {2076-2607}, support = {NSF DBI-2214028//U.S. National Science Foundation/ ; EXO 80NSSC18K1053/NASA/NASA/United States ; School of Natural Sciences//University of California, Merced/ ; }, abstract = {Interference competition, wherein bacteria actively antagonize and damage their microbial neighbors, is a key ecological strategy governing microbial community structure and composition. To gain a competitive edge, bacteria can deploy a diverse array of antimicrobial weapons-ranging from diffusible toxins to contact-mediated systems in order to eliminate their bacterial rivals. Among Gram-negative bacteria, the type VI secretion system (T6SS) has emerged as a potent and sophisticated contact-dependent mechanism that enables the delivery of toxic cargo into neighboring cells, thereby promoting the colonization and dominance of a bacterial taxon within an ecological niche. In this review, we examine the ecological significance of T6SS-mediated interference competition by members of the Vibrionaceae family across a range of marine habitats that include free-living microbial communities and host-associated niches such as coral and squid symbioses. Additionally, we explore the ecological impact of T6SS-mediated competition in modulating biofilm community structure and promoting horizontal gene transfer within those complex microbial populations. Together, these insights underscore the ecological versatility of the T6SS and emphasize its role in driving antagonistic bacterial interactions and shaping microbial community dynamics within marine ecosystems.}, }
@article {pmid40572209, year = {2025}, author = {Antequera-Zambrano, L and Parra-Sánchez, &#xc1; and González-Paz, L and Fernandez, E and Martinez-Navarrete, G}, title = {Distribution of Genetic Determinants Associated with CRISPR-Cas Systems and Resistance to Antibiotics in the Genomes of Archaea and Bacteria.}, journal = {Microorganisms}, volume = {13}, number = {6}, pages = {}, pmid = {40572209}, issn = {2076-2607}, abstract = {The CRISPR-Cas system represents an adaptive immune mechanism found across diverse Archaea and Bacteria, allowing them to defend against invading genetic elements such as viruses and plasmids. Despite its broad distribution, the prevalence and complexity of CRISPR-Cas systems differ significantly between these domains. This study aimed to characterize and compare the genomic distribution, structural features, and functional implications of CRISPR-Cas systems and associated antibiotic resistance genes in 30 archaeal and 30 bacterial genomes. Through bioinformatic analyses of CRISPR arrays, cas gene architectures, direct repeats (DRs), and thermodynamic properties, we observed that Archaea exhibit a higher number and greater complexity of CRISPR loci, with more diverse cas gene subtypes exclusively of Class 1. Bacteria, in contrast, showed fewer CRISPR loci, comprising a mix of Class 1 and Class 2 systems, with Class 1 representing the majority (~75%) of the detected systems. Notably, Bacteria lacking CRISPR-Cas systems displayed a higher prevalence of antibiotic resistance genes, suggesting a possible inverse correlation between the presence of these immune systems and the acquisition of such genes. Phylogenetic and thermodynamic analyses further highlighted domain-specific adaptations and conservation patterns. These findings support the hypothesis that CRISPR-Cas systems play a dual role: first, as a defense mechanism preventing the integration of foreign genetic material-reflected in the higher complexity and diversity of CRISPR loci in Archaea-and second, as a regulator of horizontal gene transfer, evidenced by the lower frequency of antibiotic resistance genes in organisms with active CRISPR-Cas systems. Together, these results underscore the evolutionary and functional diversification of CRISPR-Cas systems in response to environmental and selective pressures.}, }
@article {pmid40572139, year = {2025}, author = {Balata, D and Rosado, T and Pina-Martins, F and Manageiro, V and Menezes, C and Ferreira, E and Paulo, OS and Caniça, M and Dias, E}, title = {Prediction of Antibiotic Resistance Genes in Cyanobacterial Strains by Whole Genome Sequencing.}, journal = {Microorganisms}, volume = {13}, number = {6}, pages = {}, pmid = {40572139}, issn = {2076-2607}, support = {PTDC/BIA-BMA/31451/2017; UIDB/00211/2020//Portuguese Foundation for Science and Technology/ ; }, abstract = {Cyanobacteria are ubiquitous in freshwater environments, but their role in aquatic resistome remains unclear. In this work, we performed whole genome sequencing on 43 cyanobacterial strains isolated from Portuguese fresh/wastewaters. From 43 available non-axenic unicyanoabacterial cultures (containing only one cyanobacterial strain and their co-occurring bacteria), it was possible to recover 41 cyanobacterial genomes from the genomic assemblies using a genome binning software, 26 of which were classified as high-quality based on completeness, contamination, N50 and contig number thresholds. By using the comprehensive antibiotic resistance database (CARD) on the assembled samples, we detected four antibiotic resistance gene (ARG) variants, conferring resistance in pathogenic bacteria to tetracyclines, fluoroquinolones (adeF-type) and macrolides (ermF-type, mefC-type and mphG-type). Among these, adeF-type was the most prevalent gene, found across 11 cyanobacterial genomes from the Nostocales order. Planktothrix presented the highest variety of close ARG matches, with hits for the macrolide resistance genes ermF-type, mefC-type and mphG-type. An analysis of the genomic assemblies also revealed an additional 12 ARGs in bacteria from the phyla Firmicutes, Proteobacteria and Bacteroidetes, present in the cyanobacterial cultures, foreseeing the horizontal gene transfer of ARGs with cyanobacteria. Additionally, more than 200 partial ARGs were detected on each recovered cyanobacterial genome, allowing for future studies of antibiotic resistance genotype/phenotype in cyanobacteria. These findings highlight the importance of further efforts to understand the role of cyanobacteria on the aquatic resistome from a One Health perspective.}, }
@article {pmid40572111, year = {2025}, author = {Lucero, J and Nishiguchi, MK}, title = {Host-Associated Biofilms: Vibrio fischeri and Other Symbiotic Bacteria Within the Vibrionaceae.}, journal = {Microorganisms}, volume = {13}, number = {6}, pages = {}, pmid = {40572111}, issn = {2076-2607}, support = {1T32GM141862-24S3/NH/NIH HHS/United States ; DBI 2214038//National Science Foundation/ ; }, abstract = {Biofilm formation is important for microbial survival, adaptation, and persistence within mutualistic and pathogenic systems in the Vibironaceae. Biofilms offer protection against environmental stressors, immune responses, and antimicrobial treatments by increasing host colonization and resilience. This review examines the mechanisms of biofilm formation in Vibrio species, focusing on quorum sensing, cyclic-di-GMP signaling, and host-specific adaptations that influence biofilm structure and function. We discuss how biofilms differ between mutualistic and pathogenic species based on environmental and host signals. Recent advances in omics technologies such as transcriptomics and metabolomics have enhanced research in biofilm regulation under different conditions. Horizontal gene transfer and phase variation promote the greater fitness of bacterial biofilms due to the diversity of environmental isolates that utilize biofilms to colonize host species. Despite progress, questions remain regarding the long-term effects of biofilm formation and persistence on host physiology and biofilm community dynamics. Research integrating multidisciplinary approaches will help advance our understanding of biofilms and their implications for influencing microbial adaptation, symbiosis, and disease. These findings have applications in biotechnology and medicine, where the genetic manipulation of biofilm regulation can enhance or disrupt microbiome stability and pathogen resistance, eventually leading to targeted therapeutic strategies.}, }
@article {pmid40571945, year = {2025}, author = {Elmahdy, MH and Azmy, AF and Dishisha, T and El-Gendy, AO and Sebak, M}, title = {Fundamental changes in the antimicrobial resistance profile of Klebsiella quasipneumoniae ATCC 700603 in response to meropenem stress.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {369}, pmid = {40571945}, issn = {1471-2180}, mesh = {*Meropenem/pharmacology ; *Klebsiella/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; Bacterial Proteins/genetics/metabolism ; beta-Lactamases/genetics/metabolism ; *Drug Resistance, Bacterial/genetics ; Stress, Physiological ; Gene Transfer, Horizontal ; Gene Expression Regulation, Bacterial/drug effects ; }, abstract = {BACKGROUND: Klebsiella is one of the most challenging superbugs having a high tendency to acquire rapid resistance to many antibiotics, even the ones recognized as the last resort. In several hospitals and environmental niches, Klebsiella is continuously exposed to residual amounts of antibiotics at sub-inhibitory concentrations forming an environmental stress motivating them to adapt and evolve antimicrobial resistance. In the present study, meropenem (MEM) resistance was induced experimentally in a MEM-sensitive strain of K. quasipneumoniae ATCC 700603 through sequential sub-culturing in presence of sub-inhibitory concentrations of MEM over a period of 20 days. To uncover the possible mechanisms standing behind the evolution of antimicrobial resistance upon successive exposure to stress of MEM rather than horizontal gene transfer (HGT) of antibiotic resistance genes.<br><br>RESULTS: Fully adapted cells of the 20th generation (G20) showed MEM-resistance with elevated minimum inhibitory concentration (MIC) by 256-fold compared to the parent cells (G0). The main mechanism of resistance was the production of carbapenemases, which was assured by different tests including nitrocefin, modified-Hodge test (MHT), and modified carbapenem inactivation method (mCIM). The degradation of MEM reached 65.93% by the produced carbapenemases of G20 as determined by the HPLC analysis. Transcriptomics analysis of the class D carbapenemase encoding gene, blaOXA-2, revealed that it was significantly over-expressed by a 3.12-fold (p&#x2009;<&#x2009;0.05) in G20 compared to G0.<br><br>CONCLUSION: The evolved MEM resistance aroused mainly from MEM degradation by carbapenemases, neither increased efflux nor decreased influx of MEM. The rational use of antibiotics is essential to reduce bacterial exposure to the environmental basal levels of antibiotics and decreasing the evolution of antimicrobial resistance.}, }
@article {pmid40570498, year = {2025}, author = {Zhang, X and Jiao, P and Li, B and Zhang, XX and Ma, L}, title = {Phage lysis-mediated reduction of antibiotic-resistant bacteria alleviates micro/nanoplastic-driven antimicrobial resistance dissemination in anaerobic digestion.}, journal = {Water research}, volume = {285}, number = {}, pages = {124046}, doi = {10.1016/j.watres.2025.124046}, pmid = {40570498}, issn = {1879-2448}, abstract = {Micro/nanoplastics (MPs/NPs) prevalent in anaerobic digestion (AD) have posed escalating threats to antimicrobial resistance (AMR) dissemination, yet mechanistic insights remain insufficient. Here we investigated polypropylene (PP)-MPs (200 μm) and PP-NPs (100 nm) at environmentally relevant concentrations (10, 50, and 100 mg/g TS) on antibiotic resistance gene (ARG) dynamics and transfer mechanisms using metagenomics and bioinformatic modeling. PP-MPs/NPs significantly elevated (6.4-17.8 %, p < 0.05) ARG abundance through selective enrichment of aminoglycoside, mupirocin, multidrug, polymyxin, sulfonamide, tetracycline, and novobiocin ARGs. Metagenomic assembly revealed the particle-induced ecological niche specialization of antibiotic-resistant bacteria (ARB), notably the multi-resistant ESKAPE pathogen Enterobacter hormaechei (53.4-69.4 % enrichment, p < 0.05), which harbored mobile aadA, qacEdelta1, and sul1 via conjugative plasmids. Mechanistically, MPs/NPs facilitated horizontal gene transfer (HGT) through synergism of plasmids and phages. The enhanced abundance of conjugation elements, enriched plasmid-borne ARGs, and extensive HGT events promoted plasmid-conjugative transfer, while the strongly correlated ARG-carrying lysogenic phage-host pairs highlighted phage-mediated transfer under MPs/NPs. The significant increase of phage-to-host-ratio (1.0-1.2 folds) revealed the underestimated role of phages lysing ARB under MPs/NPs stress, thereby contributing to ARG load reduction. A novel risk assessment framework prioritizing prevalence, enrichment, mobility, and host pathogenicity identified dfrA3, mefB, OXA-347, and tet44 as high-risk biomarkers and quantified 1.5-9.9 % increased health risks in digestate-exposed scenarios. These findings reveal the neglected role of phage lysis driving ARG reduction, providing actionable targets for mitigating plastic-driven resistance in AD.}, }
@article {pmid40452436, year = {2025}, author = {Tannier, E and Tricou, T and Benali, S and de Vienne, DM}, title = {HGTs are not SPRs: In the Presence of Ghost Lineages, Series of Horizontal Gene Transfers do not Result in Series of Subtree Pruning and Regrafting.}, journal = {Molecular biology and evolution}, volume = {42}, number = {6}, pages = {}, doi = {10.1093/molbev/msaf128}, pmid = {40452436}, issn = {1537-1719}, support = {ANR-19-CE45-0010//Agence Nationale de la Recherche/ ; }, mesh = {*Gene Transfer, Horizontal ; *Phylogeny ; *Models, Genetic ; Evolution, Molecular ; Computer Simulation ; }, abstract = {When a gene is horizontally transferred (HGT), under the "replacement" model where the transferred gene replaces its homolog in the recipient genome, the corresponding gene phylogeny departs from the species phylogeny by a Subtree Prune and Regraft (SPR) operation: the "recipient branch" is moved from its initial position to attach to the "donor branch". Based on this observation, various methods have used SPRs to infer HGTs. We examine this apparent equivalence in the light of ghost lineages, i.e. related species absent from the phylogeny because they are extinct, unknown, or have not been sampled. In this case, an SPR is not directly interpretable by an HGT from the donor branch, because HGTs can have ghost lineages as donors. A possible and frequent interpretation-that we call "induced HGT"-is that the transferred gene leaves the sampled phylogeny for a ghost lineage at the donor branch and is transferred back from a ghost lineage at the recipient branch. We show by simulations that this interpretation is misleading in a significant number of cases. For instance, if the studied phylogeny represents 1% of all the species susceptible to exchange genetic material with the 100 sampled species, and 11 transfers occurred, then SPRs do not correspond to induced HGTs in around 50% of the cases. This leaves the question of a coherent interpretation of SPR in the presence of ghosts open and applies to a certain extent to other phylogenetic simulation or inference methods of HGT, like reconciliation, or phylogenetic networks.}, }
@article {pmid40568145, year = {2025}, author = {Brezner, S and Garushyants, SK and Wolf, YI and Koonin, EV and Snir, S}, title = {Evolution of gene order in prokaryotes is driven primarily by gene gain and loss.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.04.03.647019}, pmid = {40568145}, issn = {2692-8205}, abstract = {UNLABELLED: Evolution of bacterial and archaeal genomes is highly dynamic including extensive gene gain via horizontal gene transfer and gene loss as well as different types of genome rearrangements, such as inversions and translocations, so that gene order is not highly conserved even among closely related organisms. We sought to quantify the contributions of different genome dynamics processes to the evolution of the gene order relying on the recently developed "jump" model of gene translocation. The jump model has been completely solved analytically and provides the exact distribution of syntenic gene block lengths (SBL) in compared genomes based on gene translocations alone. Comparing the SBL distribution predicted by the jump model with the distributions empirically observed for multiple groups of closely related bacterial and archaeal genomes, we obtained robust estimates of the genome rearrangement to gene flux (gain and loss) ratio. In most groups of bacteria and archaea, this ratio was found to be on the order of 0.1 indicating that the loss of synteny in the evolution of bacteria and archaea is driven primarily by gene gain and loss rather than by gene translocation.<br><br>SIGNIFICANCE: Evolution of bacterial and archaeal genomes is a highly dynamic process that includes extensive gene gain via horizontal gene transfer and gene loss as well as different types of genome rearrangements, so that gene order is not highly conserved even among closely related organisms. We developed a theoretical framework to quantify the contributions of different genome dynamics processes to the evolution of the gene order and found that in most groups of bacteria and archaea, the genome rearrangement to gene flux (combined gain and loss) is on the order of 0.1. Thus, the loss of genomic synteny in the evolution of bacteria and archaea appears to be driven primarily by gene gain and loss rather than by gene translocation.}, }
@article {pmid40565594, year = {2025}, author = {Saccone, S and Brancato, D and Bruno, F and Coniglio, E and Sturiale, V and Federico, C}, title = {Origin and Evolution of Genes in Eukaryotes: Mechanisms, Dynamics, and Functional Implications.}, journal = {Genes}, volume = {16}, number = {6}, pages = {}, doi = {10.3390/genes16060702}, pmid = {40565594}, issn = {2073-4425}, mesh = {Humans ; *Evolution, Molecular ; Animals ; *Eukaryota/genetics ; Gene Duplication ; Gene Transfer, Horizontal ; Selection, Genetic ; }, abstract = {The origin and evolution of genes are central themes in evolutionary biology and genomics, shedding light on how molecular innovations shape biological complexity and adaptation. This review explores the principal mechanisms underlying gene emergence in eukaryotes, including gene duplication, de novo gene birth, horizontal gene transfer, viral gene domestication, and exon shuffling. We examine the population dynamics that govern the fixation of new genes, their functional integration, and the selective forces acting upon them-from purifying selection to adaptive innovation. Examples such as NOTCH2NL and SRGAP2C, which originated through recent segmental duplications followed by neofunctionalization, illustrate how duplicate-derived de novo genes can play a key role in human brain development. In addition, we highlight the emerging relevance of nuclear architecture in determining the evolutionary fate of new genes, offering a spatial dimension to gene innovation. We also discuss methodological approaches for detecting new genes and inferring selection, and finally, we highlight the emerging role of the human pangenome in revealing hidden gene diversity and its implications for evolutionary and biomedical research. Understanding gene innovation not only enhances our grasp of evolutionary processes but also informs clinical studies on disease susceptibility and human uniqueness.}, }
@article {pmid40565227, year = {2025}, author = {Fu, W and Wang, Y and Ge, Y and Gao, H and Sun, X and Deng, Z and Wang, L and Chen, S and He, X and Wu, G}, title = {Molecular Insight into the Recognition of DNA by the DndCDE Complex in DNA Phosphorothioation.}, journal = {International journal of molecular sciences}, volume = {26}, number = {12}, pages = {}, doi = {10.3390/ijms26125765}, pmid = {40565227}, issn = {1422-0067}, support = {32170030//National Natural Science Foundation of China/ ; 2020YFA0907300//National Key R&amp;D Program of China/ ; 2022YFA0912200//National Key R&amp;D Program of China/ ; }, mesh = {Escherichia coli/metabolism/genetics ; *Escherichia coli Proteins/metabolism/chemistry/genetics ; Protein Binding ; *DNA, Bacterial/metabolism/chemistry ; *DNA/metabolism/chemistry ; Streptomyces lividans/metabolism/genetics ; *Bacterial Proteins/metabolism/chemistry ; Models, Molecular ; }, abstract = {In a vast variety of prokaryotes such as Escherichia coli and Streptomyces lividans, the DNA degradation (Dnd) CDE protein complex (consisting of DndC, DndD, and DndE), together with the DndA/IscS protein and the DndFGH complex, function as a defense barrier to prevent the invasion of non-self-DNA. The DndCDE complex introduces phosphorothioation (PT) modifications into DNA, and the DndFGH complex specifically cleaves non-PT DNA and, thus, restricts horizontal gene transfer and phage invasion. Despite the central importance of the DndCDE complex in DNA PT modification, which catalyzes the oxygen-sulfur swap on DNA, our understanding of this key complex remains poor. Here, we employed protein structure prediction to provide a reasonably reliable prediction of the structure of the DndCDE complex and a 23 bp DNA-DndCDE complex. We found that among the three proteins in the DndCDE complex, DndC, especially its "specificity loop", plays a key role in recognizing the consensus PT modification sequence. In addition, the DndD protein is found to possess a highly conserved structural surface on its globular domain, presumably mediating the dimerization of DndD as well as the DndCDE complex. Furthermore, our normal mode analysis showed that there exists a dynamic transition between a closed and an open state for the DndCDE complex, facilitating its association and release of DNA. Our conclusions were corroborated by biochemical assays using purified proteins. On the whole, we provide molecular insights into the assembly and DNA-recognition mechanism of a central protein complex involved in DNA phosphorothioation.}, }
@article {pmid40560800, year = {2025}, author = {Ruf, A and Blumenkamp, P and Ludwig, C and Lippegaus, A and Brachmann, A and Klingl, A and Goesmann, A and Brinkrolf, K and Papenfort, K and Robatzek, S}, title = {Extracellular Vesicles From Xylella fastidiosa Carry sRNAs and Genomic Islands, Suggesting Roles in Recipient Cells.}, journal = {Journal of extracellular vesicles}, volume = {14}, number = {6}, pages = {e70102}, pmid = {40560800}, issn = {2001-3078}, support = {EXC 2051 - Project-ID 390713860//Deutsche Forschungsgemeinschaft/ ; INST 95/1435-1 FUGG//Deutsche Forschungsgemeinschaft/ ; RO 3550/16-1//Deutsche Forschungsgemeinschaft/ ; RO 3550/17-1//Deutsche Forschungsgemeinschaft/ ; RO 3550/18-1//Deutsche Forschungsgemeinschaft/ ; SPP2389 - Project-ID 503931087//Deutsche Forschungsgemeinschaft/ ; ERC Adv Grant 884235//H2020 European Research Council/ ; }, mesh = {*Extracellular Vesicles/metabolism/genetics ; *Genomic Islands/genetics ; *Xylella/genetics/pathogenicity/metabolism ; *RNA, Small Untranslated/genetics/metabolism ; Plant Diseases/microbiology ; Gene Transfer, Horizontal ; RNA, Bacterial/genetics/metabolism ; Bacterial Proteins/metabolism/genetics ; Virulence ; RNA-Binding Proteins/metabolism ; }, abstract = {Xylella fastidiosa (Xf) is a Gram-negative bacterial plant pathogen responsible for severe diseases in a variety of economically important crops. A critical aspect of its virulence is the production of extracellular vesicles (EVs). In this study, we discovered that DNA-binding proteins and nonribosomal RNA-binding proteins are abundant in the corona of Xf-EVs. DNA-seq revealed enrichment of three genomic islands (GIs) in EVs, which carry molecular signatures indicative of horizontal gene transfer (HGT). The most abundant GI encodes five homologous small RNAs designated sXFs. RNA sequencing revealed a distinct pattern of noncoding RNAs enriched in EVs, including four island-encoded sXFs. One of the sXF's stem-loops contains motifs for binding the RNA chaperone Hfq, which is also abundant in EVs. Predicted target analysis suggests that sXFs play a role in regulation of natural competence in bacteria. Additionally, sXF plant target prediction identifies a coiled-coil nucleotide-binding domain leucine-rich repeat receptor (CNL) immune gene that is downregulated following Xf infection and Xf-EV treatment. We propose a model where Xf releases nucleic acid carrying EVs with two functions: one to deliver RNA-related cargo that regulates gene expression in both bacterial and plant cells, and another to deliver DNA-related cargo for the genetic transfer of genomic islands. We highlight island-encoded sXFs as potential virulence factors and vesiduction as a mechanism of HGT of sXFs in Xf. Taken together, our data on Xf-EV cargoes provide a molecular framework for understanding the virulence of Xf.}, }
@article {pmid40559614, year = {2025}, author = {Martz, K and Alomar, D and Karim, M and Knezevic, S and D'Costa, VM}, title = {Characterization of the Diversity in Host Range of an Extensively Drug-Resistant (XDR) Type IV Secretion System-Encoding Plasmid in Acinetobacter.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {6}, pages = {}, pmid = {40559614}, issn = {2076-0817}, support = {PJ4-175369/CAPMC/CIHR/Canada ; PJT-178191/CAPMC/CIHR/Canada ; }, mesh = {*Plasmids/genetics ; *Acinetobacter baumannii/genetics/drug effects/pathogenicity ; *Drug Resistance, Multiple, Bacterial/genetics ; Humans ; *Type IV Secretion Systems/genetics ; Acinetobacter Infections/microbiology ; *Host Specificity ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The World Health Organization (WHO) cites antimicrobial resistance as among the greatest threats to human health. The multidrug-resistant pathogen Acinetobacter baumannii, recognized as a priority pathogen for healthcare and research, is responsible for a diverse array of infections including respiratory tract, soft tissue and wound, and bloodstream infections. Despite this importance, the mechanisms of its pathogenesis remain poorly understood. Conjugation represents a central mechanism for bacterial adaptation and evolution and is responsible for the spread of genes that promote pathogen survival, antibiotic resistance, virulence, and biofilm formation. Our laboratory recently characterized a large group of almost 120 Type IV Secretion System (T4SS)-encoding plasmids in Acinetobacter, distributed globally across 20 countries spanning four continents, and demonstrated that an XDR A. baumannii plasmid from this family was transmissible to another A. baumannii strain. This research investigated the potential diversity of host strains for this representative member plasmid. Using the GC1 lineage strain A. baumannii AB5075-UW harbouring the XDR plasmid p1AB5075 and a series of previously characterized clinical and environmental Acinetobacter strains, conjugative analyses demonstrated transfer of the XDR plasmid to both A. baumannii strains of more genetically divergent sequence types and to non-baumannii Acinetobacter species both inside and outside the Acinetobacter calcoaceticus-baumannii (ACB) complex. Successful recipients included diverse strains of both clinical and environmental origin within the Acinetobacter genus. Collectively, this research could provide insights into an important genetic element for future surveillance.}, }
@article {pmid40559557, year = {2025}, author = {Enciso-Martínez, Y and Barrios-Villa, E and Ballesteros-Monrreal, MG and Navarro-Ocaña, A and Valencia, D and González-Aguilar, GA and Martínez-Téllez, MA and Palomares-Navarro, JJ and Ayala-Zavala, F}, title = {Virulence and Antibiotic Resistance of aEPEC/STEC Escherichia coli Pathotypes with Serotype Links to Shigella boydii 16 Isolated from Irrigation Water.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/pathogens14060549}, pmid = {40559557}, issn = {2076-0817}, mesh = {Humans ; Virulence ; Serogroup ; *Shigella boydii/genetics/isolation &amp; purification/drug effects/pathogenicity/classification ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; *Water Microbiology ; *Drug Resistance, Bacterial ; HeLa Cells ; *Shiga-Toxigenic Escherichia coli/genetics/drug effects/isolation &amp; purification/pathogenicity/classification ; Agricultural Irrigation ; Virulence Factors/genetics ; Microbial Sensitivity Tests ; }, abstract = {Irrigation water can serve as a reservoir and transmission route for pathogenic Escherichia coli, posing a threat to food safety and public health. This study builds upon a previous survey conducted in Hermosillo, Sonora (Mexico), where 445 samples were collected from a local Honeydew melon farm and associated packing facilities. Among the 32 E. coli strains recovered, two strains, A34 and A51, were isolated from irrigation water and selected for further molecular characterization by PCR, due to their high pathogenic potential. Both strains were identified as hybrid aEPEC/STEC pathotypes carrying bfpA and stx1 virulence genes. Adhesion assays in HeLa cells revealed aggregative and diffuse patterns, suggesting enhanced colonization capacity. Phylogenetic analysis classified A34 within group B2 as associated with extraintestinal pathogenicity and antimicrobial resistance, while A51 was unassigned to any known phylogroup. Serotyping revealed somatic antigens shared with Shigella boydii 16, suggesting possible horizontal gene transfer or antigenic convergence. Antibiotic susceptibility testing showed resistance to multiple β-lactam antibiotics, including cephalosporins, linked to the presence of blaCTX-M-151 and blaCTX-M-9. Although no plasmid-mediated quinolone resistance genes were detected, resistance may involve efflux pumps or mutations in gyrA and parC. These findings are consistent with previous reports of E. coli adaptability in agricultural environments, suggesting potential genetic adaptability. While our data support the presence of virulence and resistance markers, further studies would be required to demonstrate mechanisms such as horizontal gene transfer or adaptive evolution.}, }
@article {pmid40558211, year = {2025}, author = {Enshaie, E and Nigam, S and Patel, S and Rai, V}, title = {Livestock Antibiotics Use and Antimicrobial Resistance.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/antibiotics14060621}, pmid = {40558211}, issn = {2079-6382}, abstract = {Background/Objectives: Antibiotic resistance or antimicrobial resistance (AMR) in livestock is a growing global concern that threatens both human and animal health. The overuse and misuse of antibiotics in livestock production have led to an increased propensity for the development of AMR bacterial strains in animals, which can be spread to humans through the consumption of contaminated animal products, direct contact, or environmental exposure. This review aims to summarize the development and transmission of AMR in livestock, explore its underlying mechanisms and impact on human and animal health, and discuss current practices and potential strategies for mitigation and prevention. Methods: For this narrative review, we searched articles on PubMed and Google Scholar using the terms antibiotic resistance, livestock, and environment, alone or in combination. Results: The history of antibiotic use in livestock and its link to increased AMR, along with the involved mechanisms, including the enzymatic breakdown of antibiotics, alterations in bacterial targets, horizontal gene transfer, and efflux pumps, are important. Antibiotics in livestock are used for growth promotion, disease prevention and control, and metaphylactic use. The role of livestock and the environment as reservoirs for resistant pathogens, their impact on human health, chronic infections, allergic reactions, toxicity, and the development of untreatable diseases is important to understand AMR. Conclusions: Given the widespread use of antibiotics and the potential consequences of AMR, collaborative global efforts, increased public awareness, coordinated regulations, and advancements in biological technology are required to mitigate the threat AMR poses to human and animal health. Regulatory solutions and the development of new therapeutic alternatives like antimicrobial peptides and bacteriophage therapy, and preventive measures such as DNA and mRNA vaccines, are future perspectives.}, }
@article {pmid40558188, year = {2025}, author = {Mohammed, EAH and Kovács, B and Kuunya, R and Mustafa, EOA and Abbo, ASH and Pál, K}, title = {Antibiotic Resistance in Aquaculture: Challenges, Trends Analysis, and Alternative Approaches.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/antibiotics14060598}, pmid = {40558188}, issn = {2079-6382}, support = {TKP2021-NKTA-32//National Research, Development, and Innovation Fund of Hungary/ ; }, abstract = {Antibiotic resistance in aquaculture has emerged as a global crisis, representing a serious threat to the health of aquatic animals, environment, and human. The extensive use of antibiotics in aquaculture has led to rapid development of resistant bacterial strains, resulting in environmental contamination and the dissemination of resistant genes. Understanding of the research trends, key contributors, and thematic evolution of this field is essential for guiding future studies and policy interventions. The study aimed to conduct a bibliometric analysis of research on antibiotic resistance development in aquaculture, identifying key areas of research, leading contributors, emerging challenges, and alternative solutions. Data were extracted from the Web of Science (WoS) database covering the period from 2000 to 2025. A systematic search strategy was employed, utilizing terms including "antibiotic resistance" AND "bacteria," AND "aquaculture". Relevant publications were extracted from the WoS using these keywords. R-tool was then used to analyze the obtained metadata including keywords, citation patterns, and co-authored country. The analysis revealed a remarkable increase in publications over the past 25 years, with key contributions from China, India, and the USA. The most significant articles focused on the presence of multidrug resistant bacteria in the aquatic environments and, antibiotic-resistant genes, and horizontal gene transfer. Probiotics are the alternative solution to overcome the antibiotic resistance and enhance aquaculture sustainability. Future research should focus on the interdisciplinary collaboration, novel antimicrobial alternatives, and global monitoring approaches.}, }
@article {pmid40558133, year = {2025}, author = {Ye, Z and Li, M and Jing, Y and Liu, K and Wu, Y and Peng, Z}, title = {What Are the Drivers Triggering Antimicrobial Resistance Emergence and Spread? Outlook from a One Health Perspective.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/antibiotics14060543}, pmid = {40558133}, issn = {2079-6382}, support = {2022YFF1103100//National Key Research and Development Program of China/ ; 32172314//National Natural Science Foundation of China/ ; 22193064//National Natural Science Foundation of China/ ; }, abstract = {Antimicrobial resistance (AMR) has emerged as a critical global public health threat, exacerbating healthcare burdens and imposing substantial economic costs. Currently, AMR contributes to nearly five million deaths annually worldwide, surpassing mortality rates of any single infectious disease. The economic burden associated with AMR-related disease management is estimated at approximately $730 billion per year. This review synthesizes current research on the mechanisms and multifaceted drivers of AMR development and dissemination through the lens of the One Health framework, which integrates human, animal, and environmental health perspectives. Intrinsic factors, including antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs), enable bacteria to evolve adaptive resistance mechanisms such as enzymatic inactivation, efflux pumps, and biofilm formation. Extrinsic drivers span environmental stressors (e.g., antimicrobials, heavy metals, disinfectants), socioeconomic practices, healthcare policies, and climate change, collectively accelerating AMR proliferation. Horizontal gene transfer and ecological pressures further facilitate the spread of antimicrobial-resistant bacteria across ecosystems. The cascading impacts of AMR threaten human health and agricultural productivity, elevate foodborne infection risks, and impose substantial economic burdens, particularly in low- and middle-income countries. To address this complex issue, the review advocates for interdisciplinary collaboration, robust policy implementation (e.g., antimicrobial stewardship), and innovative technologies (e.g., genomic surveillance, predictive modeling) under the One Health paradigm. Such integrated strategies are essential to mitigate AMR transmission, safeguard global health, and ensure sustainable development.}, }
@article {pmid40558095, year = {2025}, author = {Milhomem Pilati Rodrigues, B and Janssen, L and da Silva, LA and Acacio, SSVG and Magalhães, MT and Ribeiro, BM}, title = {Experimental and evolutionary evidence for horizontal transfer of an envelope fusion protein gene between thogotoviruses and baculoviruses.}, journal = {Journal of virology}, volume = {}, number = {}, pages = {e0214824}, doi = {10.1128/jvi.02148-24}, pmid = {40558095}, issn = {1098-5514}, abstract = {Baculoviruses are insect-specific viruses with large, double-stranded DNA genomes classified into four genera. Alphabaculoviruses, which infect lepidoptera, are further divided into group I (G1-α) and group II (G2-α). The GP64 protein, essential for cell attachment and viral entry in G1-α baculoviruses, is thought to have originated through horizontal gene transfer (HGT) from thogotoviruses (family Orthomyxoviridae). This study investigates the functional substitution of GP64 by thogotovirus fusion proteins. Through RNA-seq data mining, we identified a novel thogotovirus, Melitaea didyma thogotovirus 1 (MediTHOV-1), in lepidopteran hosts. Phylodynamic analysis of G1-α baculovirus and thogotovirus glycoproteins suggests that the HGT event occurred during the Mesozoic era. To test functional substitution, we constructed recombinant Autographa californica multiple nucleopolyhedrovirus (AcMNPV) carrying either the envelope fusion protein (EFP) genes from MediTHOV-1 or Apis thogotovirus 1 (ATHOV-1), while deleted for its native gp64 gene. Our results show that, while the MediTHOV-1 glycoprotein failed to rescue AcMNPV infectivity, the ATHOV-1 fusion protein (EFP) partially restored infectivity, albeit with reduced efficiency. Cryo-electron microscopy revealed lower incorporation of ATHOV-1 EFP into viral envelopes compared to GP64. The recombinant AcMNPV carrying ATHOV-1 EFP (Ac-ATHOVGPgp64Δ) displayed delayed replication kinetics and lower viral titers. Interestingly, ATHOV-1 EFP significantly enhanced baculovirus entry and gene transduction in mosquito cells. These findings provide experimental support for the HGT hypothesis, demonstrating the functional incorporation of a thogotovirus glycoprotein into a baculovirus. This study sheds light on the evolutionary relationship between baculovirus GP64 and glycoproteins, offering insights into viral evolution and potential biotechnological applications in gene delivery and protein expression.IMPORTANCEBaculoviruses are widely utilized for the biological control of insect pests and as versatile biotechnological tools, with their effectiveness largely dependent on the activity of their envelope fusion proteins (EFPs). Thogotoviruses, in contrast, are emerging vector-borne pathogens of significant concern. In this study, we present the first successful functional substitution of the baculovirus GP64 protein with a thogotovirus EFP, alongside the identification of what appears to be a lepidopteran-associated thogotovirus, Melitaea didyma thogothovirus 1. Our work provides functional and phylogenetic insights into the evolutionary relationship between these distantly related viral groups, particularly the hypothesized horizontal gene transfer event that gave rise to baculoviral gp64 gene. These findings offer a deeper understanding of the determinants underlying the adaptation of baculoviral glycoproteins to novel hosts. Furthermore, the discovery of novel viral genes highlights promising opportunities for biotechnological advancements, including the development of enhanced baculovirus-based gene delivery systems and tools for protein expression.}, }
@article {pmid40556893, year = {2025}, author = {Di Marcantonio, L and Chiatamone Ranieri, S and Toro, M and Marchegiano, A and Cito, F and Sulli, N and Del Matto, I and Di Lollo, V and Alessiani, A and Foschi, G and Platone, I and Paoletti, M and D'Alterio, N and Garofolo, G and Janowicz, A}, title = {Comprehensive regional study of ESBL Escherichia coli: genomic insights into antimicrobial resistance and inter-source dissemination of ESBL genes.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1595652}, pmid = {40556893}, issn = {1664-302X}, abstract = {INTRODUCTION: The global dissemination of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (E. coli) poses a significant public health challenge, particularly in regions with high antimicrobial resistance (AMR) occurrence. This study investigated the occurrence, genomic characteristics, and dissemination dynamics of ESBL-producing E. coli in Abruzzo, Italy, by analyzing 956 isolates from humans, livestock, wildlife, and food products.<br><br>METHODS: Phenotypic and genomic analyses were performed on the isolates to assess ESBL-E. coli occurrence and characteristics. Multilocus sequence typing (MLST) was used to identify sequence types (STs), and plasmid profiling alongside synteny analysis was conducted to investigate horizontal gene transfer and resistance gene integration. Spatial analysis was also carried out to identify hotspots of ESBL-positive isolates.<br><br>RESULTS: An overall ESBL-E. coli occurrence of 14.1% (135/956 samples) was found, with significant variation across hosts: companion animals exhibited the highest occurrence (16.2%), followed by livestock and food matrices (14.6%), and wildlife (7.0%). Spatial analysis identified a hotspot in northeastern Abruzzo, where ESBL-positive isolates were 5.34 times more likely to occur (p&#x202f;<&#x202f;0.001). MLST identified 58 sequence types (STs), with ST131 dominating human isolates (12/19). In cattle, predominant sequence types were ST16565 (5 isolates) and ST540 (4 isolates); in poultry, ST43 (5 isolates), ST10 (4 isolates), and ST6215 (3 isolates) were most common; ST206 (8 isolates) was predominant in swine; and in dogs, ST10 (4 isolates) and ST3580 (3 isolates) were most prevalent. Genomic analysis revealed host-specific distributions of ESBL genes: bla CTX-M-15 predominated in humans and dogs, while bla CTX-M-1 was most common in pigs. Plasmid profiling revealed IncF and IncI plasmids as key vectors for horizontal gene transfer. Synteny analysis showed identical flanking regions of bla CTX-M-1 and bla CTX-M-15 across phylogenetically distant strains, suggesting chromosomal integration and stable maintenance of resistance genes.<br><br>DISCUSSION: These findings underscore the interconnectedness of human, animal, and environmental reservoirs in AMR dissemination. The high genetic diversity observed within farms and the detection of shared clusters across hosts emphasize the need for integrated One Health interventions, including reduced antibiotic use in livestock and enhanced surveillance of high-risk environments. This study provides critical insights into local AMR dynamics, offering a model for regional mitigation strategies.}, }
@article {pmid40556891, year = {2025}, author = {Chekole, WS and Potgieter, L and Adamu, H and Sternberg-Lewerin, S and Tessema, TS and Magnusson, U}, title = {Genomic insights into antimicrobial resistance and virulence of E. coli in central Ethiopia: a one health approach.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1597580}, pmid = {40556891}, issn = {1664-302X}, abstract = {Antimicrobial resistance is a global threat causing millions of deaths annually. The study aimed to identify antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and virulence genes (VGs) and track their dissemination among E. coli isolates. Seventy-seven isolates from calves, environments, and human sources were studied. The study involved WGS sequencing, bacterial strains characterized; pan genome, multi-locus sequence typing, and serotyping using O-, and H-typing. The ARGs, VGs, and MGEs were identified using ABRicate against selected respective databases. A maximum likelihood SNP (single nucleotide polymorphism) tree was constructed and visualized with an interactive tree of life (IToL). Descriptive statistics were used to analyze the data. Seventy-seven of the isolates were identified as E. coli, later grouped into 5 clades and four known phylogroups. ST10 and O16:H48 were most prevalent in 12 and 42 isolates, respectively. There were about 106 unique ARGs detected between 1.3% and 91.9%, with 57 detected in 40% of isolates. In terms of ARGs, the most common were bla-ampH (90.9%), bla-AmpC1 (89.6%), tet(A) (84.4%), mdf(A) (81.8%), aph(3")-Ib (79%), sul2 (79%), aph(6)-Id (75%), and bla-PBP (70%). It was found that 95 percent (96/106) of ARGs came from at least two sources. The majority of detected ARGs exhibited high concordance between phenotypic resistance and ARGs profiles (JSI ≥ 0.5). In eight isolates, mutations in the gyrA (3) and par-C/E (5) genes led to ciprofloxacin and nalidixic acid resistance. The most common co-occurrences of ARG and MGE were Tn3 with bla-TEM-105 (34), Int1 with sul1 (13), and dhfr7 (11). Meanwhile, the most frequently detected VGs (n ≥ 71 isolates) included elfA-G, fimB-I, hcpA-C, espL, ibeC, entA, fepA-C, ompA, ecpA-E, fepD, fes, and ibeB. Nearly, 88.3% (128/1450) VGs were shared in isolates from at least two sources. ETEC (53.2%), EAEC (22.1%), and STEC (14.3%) were the three most frequently predicted pathotypes. Despite significant ST diversity, ARGs and VGs showed an extensive distribution among the study groups. These findings suggest limited clonal transmission of isolates. In comparison, the wide distribution of ARGs and VGs may be attributed to horizontal gene transfer driven by similar antibiotic selection pressures in the study area.}, }
@article {pmid40556499, year = {2025}, author = {Yang, Y and Jin, X and Zhao, Z}, title = {Distribution and Evolutionary Trajectories of β-Lactamases in Vibrio: Genomic Insights from CARB-Type Enzymes in the Harveyi and Cholerae Clades.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evaf128}, pmid = {40556499}, issn = {1759-6653}, abstract = {Antibiotic resistance mediated by β-lactamases (BLs), encoded by bla genes, is a significant global health threat, necessitating systematic studies of their diversity and evolution, particularly among pathogenic bacteria lineages. Leveraging over 6,000 quality-filtered Vibrio genomes alongside six newly sequenced marine symbiotic strains representing 128 nominal and 57 unclassified Vibrio species, our study extends taxonomic breadth and resolution for investigating BL diversity. We identified 4,431 BLs across 41 species, encompassing all four Ambler Classes (A∼D). Among these, CARBenicillin-hydrolyzing Class A BLs (CARBs encoded by blaCARB family) were the most prevalent (60.7%) and exhibited a clade-centric distribution particularly in Harveyi clade and V. cholerae, underscoring influence of specific ecological and evolutionary pressures. We refined CARB classification into two subfamilies: CARB-17-like (blaCARB-17-like) confined to Harveyi clade, and CARB-1-like (blaCARB-1-like) found exclusively outside Harveyi clade, based on phylogenetic placement, sequence similarity, and inheritance patterns, providing a clearer framework for delineating their functional and phylogenetic nuances. Notably, blaCARB-17-like genes in non-pathogenic Harveyi Subclade II showed significantly relaxed selection, accompanied by unusual mutations within key conserved motifs especially catalytic serine residues, suggesting evolutionary drift that may compromise canonical enzymatic activity. Furthermore, blaCARB-17-like genes, present as a single copy, emerged as a core gene in Harveyi clade, showing promise as a diagnostic marker for clinically significant Harveyi clade species, despite limited yet significant interspecies genetic exchanges mediated by recombination or mobile genetic elements. Our study advances the understanding of BL evolution and genomic distribution in Vibrio, with broad implications for diagnostic applications and resistance management strategies.}, }
@article {pmid40556036, year = {2025}, author = {Li, Y and Liu, X and Yang, J and Li, R and Wang, M and Kuang, S}, title = {Characteristics of intracellular/extracellular antibiotic resistance genes and microbial community in sludge compost under sulfadiazine stress.}, journal = {Environmental technology}, volume = {}, number = {}, pages = {1-11}, doi = {10.1080/09593330.2025.2522480}, pmid = {40556036}, issn = {1479-487X}, abstract = {The accumulation of emerging antibiotics in sewage sludge, which serves as a repository for antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), is raising growing concern. To accurately assess the environmental risks, it is essential to separately investigate intracellular and extracellular ARGs (iARGs and eARGs) due to their distinct roles in resistance persistence and horizontal gene transfer. However, the impact of sulfadiazine (SDZ) on iARGs and eARGs, and the mechanisms involved in the composting process remain under further investigation. In this study, composts with SDZ concentrations of 5 and 50 mg/kg were constructed, and ARGs, microbial community composition and functional pathways were analyzed. The results showed that the abundance of iARGs varied significantly under SDZ selective pressure, while eARGs showed no significant differences. Specifically, i-erm decreased in the 50SDZ group, likely due to competition for ecological niches. The abundance of ermA, ermB and ermF decreased by approximately 97%, 85%, and 84%, respectively. i-sul increased by 127% to 156% in SDZ-added groups but not dose-dependently. Bacillus, Paracoccus, Pseudomonas, and Caproiciproducens were predominant in the SDZ-added groups. The abundance of potential ARG hosts, such as Bacillus and Paracoccus, increased significantly, with Paracoccus showing 2.3-fold and 1.8-fold higher abundance in the 50SDZ and 5SDZ treatments, respectively, compared to the CK. Functional genes related to the ABC-2 type transport system, signal transduction, and genome maintenance decreased with SDZ application. These findings suggested that the dynamics of ARGs should be continuously monitored during sludge composting and land application of compost products to reduce their environmental risks.}, }
@article {pmid40555322, year = {2025}, author = {Ying, S and Zhang, Z and Xiang, R}, title = {Metagenomic and Whole-Genome Characterization of Carbapenem-Resistant Acinetobacter baumannii Carrying blaOXA-23 Gene within the Tn2006 Transposon Among ICU Patients.}, journal = {Journal of global antimicrobial resistance}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgar.2025.06.009}, pmid = {40555322}, issn = {2213-7173}, abstract = {PURPOSE: To characterize carbapenem-resistant Acinetobacter baumannii carrying blaOXA-23 genes within the Tn2006 transposon using metagenomic and whole-genome sequencing, focusing on their genetic features, antimicrobial resistance, and potential for clonal spread and horizontal gene transfer among ICU patients.<br><br>METHODS: Bronchoalveolar lavage fluid samples from 28 ICU patients were analyzed using mNGS to detect pathogens and resistance genes. A. baumannii isolates underwent whole-genome sequencing for genetic diversity assessment. Antimicrobial susceptibility testing and comparative genomic analysis were performed.<br><br>RESULTS: mNGS revealed mixed infections in 71.4% of patients, identifying multiple bacteria, viruses, fungi, and mycoplasma species. A. baumannii was detected in 25 samples, often alongside other pathogens. All isolates harbored blaOXA-23 within Tn2006 on the chromosome and belonged to sequence type ST2, indicating clonal dissemination despite significant genetic diversity (up to 2,969 SNP differences). The isolates were highly resistant to multiple antibiotics but remained susceptible to tigecycline and colistin. Comparative genomic analysis with 238 global CRAB genomes confirmed the prevalence of the Tn2006 transposon carrying blaOXA-23 in ST2 strains, emphasizing the potential for rapid spread of this resistance mechanism.<br><br>CONCLUSION: The widespread presence of multidrug-resistant A. baumannii carrying blaOXA-23 within Tn2006 among ICU patients poses a significant public health concern. The high rate of mixed infections and the potential for horizontal gene transfer complicate infection management in critically ill patients. Enhanced infection control measures, continuous surveillance, and targeted interventions are urgently needed to prevent further dissemination of these resistant strains in hospital settings.}, }
@article {pmid40459279, year = {2025}, author = {Parras-Moltó, M and Lund, D and Ebmeyer, S and Larsson, DGJ and Johnning, A and Kristiansson, E}, title = {The transfer of antibiotic resistance genes between evolutionarily distant bacteria.}, journal = {mSphere}, volume = {10}, number = {6}, pages = {e0011425}, doi = {10.1128/msphere.00114-25}, pmid = {40459279}, issn = {2379-5042}, mesh = {*Gene Transfer, Horizontal ; *Bacteria/genetics/drug effects/classification ; Phylogeny ; *Drug Resistance, Bacterial/genetics ; Genome, Bacterial ; Anti-Bacterial Agents/pharmacology ; Evolution, Molecular ; *Genes, Bacterial ; Humans ; }, abstract = {UNLABELLED: Infections from antibiotic-resistant bacteria threaten human health globally. Resistance is often caused by mobile antibiotic resistance genes (ARGs) shared horizontally between bacterial genomes. Many ARGs originate from environmental and commensal bacteria and are transferred between divergent bacterial hosts before they reach pathogens. This process remains, however, poorly understood, which complicates the development of countermeasures that reduce the spread of ARGs. In this study, we aimed to systematically analyze the ARGs transferred between the most evolutionarily distant bacteria, defined here based on their phylum. We implemented an algorithm that identified inter-phylum transfers (IPTs) by combining ARG-specific phylogenetic trees with the taxonomy of the bacterial hosts. From the analysis of almost 1 million ARGs identified in >400,000 bacterial genomes, we identified 661 IPTs, which included transfers between all major bacterial phyla. The frequency of IPTs varies substantially between ARG classes and was highest for the aminoglycoside resistance gene AAC(3), while the levels for beta-lactamases were generally lower. ARGs involved in IPTs also differed between phyla, where, for example, tetracycline ARGs were commonly transferred between Firmicutes and Proteobacteria, but rarely between Actinobacteria and Proteobacteria. The results, furthermore, show that conjugative systems are seldom shared between bacterial phyla, suggesting that other mechanisms drive the dissemination of ARGs between divergent hosts. We also show that bacterial genomes involved in IPTs of ARGs are either over- or underrepresented in specific environments. These IPTs were also found to be more recent compared to transfers associated with bacteria isolated from water, soil, and sediment. While macrolide and tetracycline ARGs involved in IPTs almost always were >95% identical between phyla, corresponding β-lactamases showed a median identity of <60%. We conclude that inter-phylum transfer is recurrent, and our results offer new insights into how ARGs are disseminated between evolutionarily distant bacteria.<br><br>IMPORTANCE: Antibiotic-resistant infections pose a growing threat to global health. This study reveals how genes conferring antibiotic resistance can move between bacteria that belong to different phyla lineages previously thought to be too evolutionarily distant for frequent gene exchange. By analyzing nearly 1 million resistance genes from over 400,000 bacterial genomes, the researchers uncovered hundreds of inter-phylum transfer events, exposing surprising patterns in how different classes of resistance genes spread. The findings highlight that conjugative systems are less common than expected in cross-phyla transfers and suggest that alternative mechanisms may play key roles. This new understanding of how resistance genes leap between vastly different bacterial groups can inform strategies to slow the emergence of drug-resistant infections, aiding in the development of more effective public health interventions.}, }
@article {pmid40298963, year = {2025}, author = {Karki, S and Barth, ZK and Aylward, FO}, title = {Ancient Host-Virus Gene Transfer Hints at a Diverse Pre-LECA Virosphere.}, journal = {Journal of molecular evolution}, volume = {93}, number = {3}, pages = {295-305}, pmid = {40298963}, issn = {1432-1432}, support = {2141862//National Science Foundation/ ; }, mesh = {Phylogeny ; *DNA Viruses/genetics ; Evolution, Molecular ; *Eukaryota/genetics/virology ; *Gene Transfer, Horizontal ; DNA-Directed DNA Polymerase/genetics ; DNA-Directed RNA Polymerases/genetics ; }, abstract = {The details surrounding the early evolution of eukaryotes and their viruses are largely unknown. Several key enzymes involved in DNA synthesis and transcription are shared between eukaryotes and large DNA viruses in the phylum Nucleocytoviricota, but the evolutionary relationships between these genes remain unclear. In particular, previous studies of eukaryotic DNA and RNA polymerases often show deep-branching clades of eukaryotes and viruses indicative of ancient gene exchange. Here, we performed updated phylogenetic analysis of eukaryotic and viral family B DNA polymerases, multimeric RNA polymerases, and mRNA-capping enzymes to explore their evolutionary relationships. Our results show that viral enzymes form clades that are typically adjacent to eukaryotes, suggesting that they originate prior to the emergence of the Last Eukaryotic Common Ancestor (LECA). The machinery for viral DNA replication, transcription, and mRNA capping are all key processes needed for the maintenance of virus factories, which are complex structures formed by many nucleocytoviruses during infection, indicating that viruses capable of making these structures are ancient. These findings hint at a diverse and complex pre-LECA virosphere and indicate that large DNA viruses may encode proteins that are relics of extinct proto-eukaryotic lineages.}, }
@article {pmid40197024, year = {2025}, author = {Gillett, DL and Selinidis, M and Seamons, T and George, D and Igwe, AN and Del Valle, I and Egbert, RG and Hofmockel, KS and Johnson, AL and Matthews, KRW and Masiello, CA and Stadler, LB and Chappell, J and Silberg, JJ}, title = {A roadmap to understanding and anticipating microbial gene transfer in soil communities.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {89}, number = {2}, pages = {e0022524}, doi = {10.1128/mmbr.00225-24}, pmid = {40197024}, issn = {1098-5557}, mesh = {*Soil Microbiology ; *Microbiota/genetics ; *Gene Transfer, Horizontal ; Soil/chemistry ; Bacteria/genetics ; Synthetic Biology ; Biotechnology ; }, abstract = {SUMMARYEngineered microbes are being programmed using synthetic DNA for applications in soil to overcome global challenges related to climate change, energy, food security, and pollution. However, we cannot yet predict gene transfer processes in soil to assess the frequency of unintentional transfer of engineered DNA to environmental microbes when applying synthetic biology technologies at scale. This challenge exists because of the complex and heterogeneous characteristics of soils, which contribute to the fitness and transport of cells and the exchange of genetic material within communities. Here, we describe knowledge gaps about gene transfer across soil microbiomes. We propose strategies to improve our understanding of gene transfer across soil communities, highlight the need to benchmark the performance of biocontainment measures in situ, and discuss responsibly engaging community stakeholders. We highlight opportunities to address knowledge gaps, such as creating a set of soil standards for studying gene transfer across diverse soil types and measuring gene transfer host range across microbiomes using emerging technologies. By comparing gene transfer rates, host range, and persistence of engineered microbes across different soils, we posit that community-scale, environment-specific models can be built that anticipate biotechnology risks. Such studies will enable the design of safer biotechnologies that allow us to realize the benefits of synthetic biology and mitigate risks associated with the release of such technologies.}, }
@article {pmid40553200, year = {2025}, author = {Xie, X and Ren, Z and Wang, R and Tian, K and Huang, X and Lyu, Y and Cao, G and Fu, J}, title = {Mobile Genomic Island GEI-FN1A in Aeromonas salmonicida FN1 Contributes to the Spread of Antibiotic-Resistance Genes.}, journal = {Current microbiology}, volume = {82}, number = {8}, pages = {345}, pmid = {40553200}, issn = {1432-0991}, support = {ZR2022MH107//Shandong Provincial Natural Science Foundation/ ; M-2023040//TCM science and technology project of Shandong Province/ ; }, mesh = {*Genomic Islands ; Anti-Bacterial Agents/pharmacology ; Animals ; Gene Transfer, Horizontal ; *Aeromonas salmonicida/genetics/drug effects/isolation &amp; purification ; *Drug Resistance, Multiple, Bacterial/genetics ; Chickens ; Whole Genome Sequencing ; Genome, Bacterial ; Feces/microbiology ; Soil Microbiology ; Genes, Bacterial ; Bacterial Proteins/genetics ; Microbial Sensitivity Tests ; }, abstract = {Antibiotics are used to treat severe bacterial infections. However, owing to excessive antibiotic use, bacteria under high selective pressure for antibiotics develop resistance through spontaneous mutation or by acquiring antibiotic-resistance genes (ARGs) through horizontal gene transfer (HGT). Horizontal transfer of ARGs among bacteria in the environment can lead to the emergence of multidrug-resistant (MDR) bacteria that infect animals and humans, thus causing disease outbreaks. In this study, MDR strain FN1 was isolated from a feces-contaminated soil sample from a chicken farm under pressure from the antibiotic florfenicol (16 mg/L) and identified as Aeromonas salmonicida. Whole-genome sequencing and analysis revealed the 86.8-kb antibiotic-resistant genomic island, GEI-FN1A, in the FN1 genome. Genome annotation revealed that GEI-FN1A carried several ARGs, including two tetracycline-resistance genes [tetR and tet(A)], three aminoglycoside-resistance genes [aph(6), aph(3"), and aac(3)], one trimethoprim-resistance gene (dfrB4), two chloramphenicol/florfenicol-resistance genes (catB3 and floR), three macrolide-resistance genes [mphR(A), mrx(A), and mph(A)] and two sul1 genes. GEI-FN1A also contained genes encoding integrase, transposase, and recombinase, which mediate the horizontal transfer of MDR genes. These findings suggest that GEI-FN1A in A. salmonicida FN1 can potentially spread ARGs among environmental bacteria.}, }
@article {pmid40553195, year = {2025}, author = {Sonkar, V and Devtalla, H and Kumar, S}, title = {Pesticide-driven antimicrobial resistance in water bodies: insights on environmental concerns, health implications and mitigation strategies.}, journal = {Environmental geochemistry and health}, volume = {47}, number = {7}, pages = {282}, pmid = {40553195}, issn = {1573-2983}, mesh = {*Pesticides/toxicity/analysis ; *Water Pollutants, Chemical/toxicity/analysis ; *Drug Resistance, Microbial/drug effects ; Humans ; India ; Agriculture ; Water Microbiology ; }, abstract = {Pesticide contamination in water bodies is an emerging driver of antimicrobial resistance (AMR), posing severe environmental and public health risks. Due to excessive agricultural use, pesticides routinely end up in water bodies due to leaching, improper disposal, and agricultural runoff. Pesticides act as selective pressures, promoting resistant microbial strains by providing evolutionary pressure for the strains to thrive. Pesticides facilitate the dissemination of resistance genes through several mechanisms; horizontal gene transfer, bio-film formation, and co-selection with heavy metals. Pathogens carrying antibiotic resistance genes, are emerging as a threat to global populations exposed to contaminated water, as they are increasingly more challenging to treat with traditional antibiotics. Moreover, these issues escalate due to the overlap in disposal of agricultural runoffs and untreated hospital waste into water bodies leading to co-selection pressure facilitating multi drug resistance. Current review examines the critical role of pesticides contamination in driving AMR in Indian aquatic ecosystems, a novel intersection threatening global health and deteriorating aquatic life. However, existing policies are insufficient, necessitating stricter regulations to control the problem. There also needs to be stronger laws in place to limit and monitor pollution in the water bodies. The increasing incidences of health issues linked to resistant strains in Indian population, need to be tackled more comprehensively. Mitigation requires stringent agricultural regulations, improved waste management, and interdisciplinary strategies to curb this growing threat.}, }
@article {pmid40552317, year = {2025}, author = {Jafari, E and Azizian, R and Tabasi, M and Banakar, M and Bagheri Lankarani, K}, title = {Human Gut Bacteriophageome: Insights Into Drug Resistance Mechanisms in Tuberculosis.}, journal = {Interdisciplinary perspectives on infectious diseases}, volume = {2025}, number = {}, pages = {8811027}, pmid = {40552317}, issn = {1687-708X}, abstract = {Tuberculosis (TB), caused by Mycobacterium tuberculosis, remains a major global health burden. The emergence of drug-resistant strains presents a critical challenge in TB management. The recent research has explored the interaction between TB and the human gut bacteriophage community (phageome). The gut phageome plays a crucial role in regulating microbial diversity and functionality, and its composition and function have been linked to various health conditions. Examining the gut phageome through metagenomic analysis provides insights into its composition, role in health, and interactions with the host immune system. Exploring the interaction between the gut phageome and M. tuberculosis may reveal how phages affect the bacterium's pathogenicity, survival, and mechanisms of drug resistance. Understanding the gut phageome's impact on TB drug resistance could inform novel therapeutic strategies, such as phage therapy, and highlight the importance of microbiome-based interventions in combating drug-resistant TB strains. This review explores the role of the gut phageome in influencing drug resistance in TB, focusing on interaction mechanisms and potential therapeutic implications, synthesizing current research findings, and identifying knowledge gaps in this emerging field. This review also synthesizes the current evidence on the gut phageome's role in TB drug resistance, focusing on phage-mediated horizontal gene transfer (e.g., rpoB, katG), immune modulation, and preclinical efficacy of mycobacteriophage therapies. Key findings highlight phage cocktails (e.g., DS6A, D29 LysB) as promising adjuncts to antibiotics, reducing M. tuberculosis burden in murine models. These insights advocate for phage therapy as a complementary strategy against drug-resistant TB, urging clinical validation to bridge the existing knowledge gaps.}, }
@article {pmid40551445, year = {2025}, author = {Deshamukhya, C and Das, BJ and Dhar, D and Bhattacharjee, A}, title = {Influence of AHL and Imipenem on blaNDM Conjugation and sRNA Rydb Expression in Escherichia coli.}, journal = {Journal of basic microbiology}, volume = {}, number = {}, pages = {e70074}, doi = {10.1002/jobm.70074}, pmid = {40551445}, issn = {1521-4028}, abstract = {The rise of carbapenem resistance in Escherichia coli is mainly due to the rapid spread of carbapenemase-encoding genes through horizontal gene transfer, particularly via bacterial conjugation. Recent research has highlighted the role of a small RNA molecule known as RydB in bacterial conjugation, specifically through its interaction with the protein SdiA. This study investigated the effects of sub-inhibitory concentrations of imipenem and N-acyl homoserine lactones (AHLs) on the expression of rydB in E. coli strains that overexpress sdiA. Additionally, we examined how AHLs influence the bacterial conjugation of plasmids that contain carbapenem resistance genes. We selected a carbapenem-resistant isolate of E. coli harbouring the blaNDM gene and its corresponding plasmid-cured derivative, based on the overexpression of the sdiA gene in response to AHLs. Conjugation experiments were conducted, both without AHL treatment and with AHL treatments, to assess the transferability of the blaNDM plasmid. The transcriptional response of rydB gene was evaluated in the plasmid-cured derivative, the native type, the transconjugant, and E. coli J53. Our findings indicated that AHLs and imipenem inhibit the expression of the rydB gene. Interestingly, while RydB does not seem to impact bacterial conjugation when suppressed by these agents, the combination of AHLs enhances the conjugation of plasmid that carry the blaNDM gene. This study enhances our understanding of the regulatory roles that quorum sensing signal molecules, including C4 AHL and C12AHL, as well as imipenem, play in bacterial conjugation and sRNA expression.}, }
@article {pmid40548977, year = {2025}, author = {Bhadra, S and Das, C and Bawali, S and Bhattacharya, A}, title = {Evolutionary analysis of the Leishmania major orthologues for the newly identified cyclic AMP response proteins.}, journal = {Archives of microbiology}, volume = {207}, number = {8}, pages = {184}, pmid = {40548977}, issn = {1432-072X}, mesh = {*Leishmania major/genetics/metabolism ; Phylogeny ; *Evolution, Molecular ; *Protozoan Proteins/genetics/metabolism/chemistry ; *Cyclic AMP/metabolism ; Gene Transfer, Horizontal ; }, abstract = {Cyclic AMP (cAMP) signalling is largely noncanonical in kinetoplastids. With virtual absence of canonical cAMP effectors including cyclic nucleotide sensitive protein kinase A regulatory subunits. Through a number of RNAi screens, a group of novel cAMP-responsive effectors were identified from Trypanosoma with 11 members, assigned as cAMP Response Proteins (CARPs, CARP1 to 11). Four of the CARPs were reported earlier, recently the remaining seven were identified. Except for CARP3 and CARP11, the orthologues for other CARPs can be identified from Leishmania. An intricate evolutionary analysis performed earlier indicated CARP1 and CARP4 from Leishmania major comprise features of horizontally transferred genes. Aiming for comprehensive understanding of the evolution of CARPs, the study further extends the evolutionary analysis to newly annotated CARP orthologues from L. major. The study reveals the phylogenetic relation among kinetoplastid CARP orthologues and functional divergence. A systemic codon adaptation profiling suggested horizontal transfer for some of the CARPs. Alongside, structural analysis highlighted heterogeneity among the T. brucei and L. major orthologues.}, }
@article {pmid40548945, year = {2025}, author = {}, title = {Correction to 'Enhancing insights into diseases through horizontal gene transfer event detection from gut microbiome'.}, journal = {Nucleic acids research}, volume = {53}, number = {12}, pages = {}, doi = {10.1093/nar/gkaf631}, pmid = {40548945}, issn = {1362-4962}, }
@article {pmid40548717, year = {2025}, author = {Xu, C and Li, X and Zhang, Y and Li, Y and Li, Y and Zhang, R and Dong, N}, title = {Interorder horizontal gene transfer of tet(X3) between Acinetobacter spp. and Enterobacteriaceae.}, journal = {Antimicrobial agents and chemotherapy}, volume = {}, number = {}, pages = {e0194524}, doi = {10.1128/aac.01945-24}, pmid = {40548717}, issn = {1098-6596}, }
@article {pmid40544776, year = {2025}, author = {Huang, W and Wang, F and Su, Y and Huang, H and Luo, J}, title = {Underestimated roles of phages in biological wastewater treatment systems: Recent advances and challenges.}, journal = {Journal of hazardous materials}, volume = {495}, number = {}, pages = {139007}, doi = {10.1016/j.jhazmat.2025.139007}, pmid = {40544776}, issn = {1873-3336}, abstract = {Bacteriophages (phages) are vital components in biological wastewater ecosystems, whose concentrations are far exceeding those bacteria. Despite their importance, they are often overlooked and regarded as the "dark matter" in biological treatment processes. Phages play a pivotal role in shaping the dynamic evolution of host microbial communities within wastewater treatment plants (WWTPs), driving their functional evolution through interactions with host microorganisms. Phages are crucial in driving microbial ecological dynamics and regulating metabolic functions. At the macroscopic scale, the organic matters released through viral shunting demonstrate enhanced bioavailability and facilitated organic element cycling based on viral shuttle-mediated bio-pump. Additionally, at the micro-scale, gene transfer mediated by phages can assist functional microorganisms in enhancing metabolic efficiency and adapting to environmental stress. However, this process also introduces environmental risks, particularly the dissemination of antibiotic resistance genes through horizontal gene transfer and plasmids. Phages offer distinct advantages over conventional chemical and physical methods, including superior efficiency and environmental sustainability. Nonetheless, the development of phage-based biocontrol strategies is constrained by phage specificity and the complexity of biological treatment systems. Recent advances in artificial intelligence and genetic technologies provide promising avenues for optimizing phage applications. Further research into phage ecology is essential to lay a theoretical foundation for enhancing operational stability, treatment efficiency, and targeted biocontrol strategies.}, }
@article {pmid40544537, year = {2025}, author = {Sinha, S and Upadhyay, LSB}, title = {Understanding antimicrobial resistance (AMR) mechanisms and advancements in AMR diagnostics.}, journal = {Diagnostic microbiology and infectious disease}, volume = {113}, number = {2}, pages = {116949}, doi = {10.1016/j.diagmicrobio.2025.116949}, pmid = {40544537}, issn = {1879-0070}, abstract = {The overuse and abuse of antibiotics, which results in the evolution of resistant microorganisms, is the primary cause of the global health catastrophe known as antimicrobial resistance (AMR). The enzymatic breakdown of antibiotics, target site modification, efflux pump overexpression, and the formation of biofilm are some of the mechanisms responsible for acquiring antimicrobial resistance (AMR). These mechanisms enable bacteria to evade or neutralize the effects of antimicrobial agents, complicating treatment options and increasing mortality rates. The rapid dissemination of resistance genes via horizontal gene transfer further exacerbates the problem, necessitating urgent intervention. Advanced AMR diagnostics are transforming the fight against antimicrobial resistance. Biosensors enable rapid, point-of-care detection; Cluster regularly interspaced short palindromic repeat (CRISPR) technologies offer precise identification of resistance genes; and mass spectrometry provides fast, accurate profiling. Automated systems streamline workflows and boost throughput, while flow cytometry delivers real-time, single-cell analysis of phenotypic resistance. Together, these innovations accelerate detection and support targeted antimicrobial stewardship, essential for combating the global AMR threat. This review covers the mechanisms underlying antimicrobial resistance (AMR) and recent advancements in AMR diagnostic technologies.}, }
@article {pmid40542629, year = {2025}, author = {Aristova, EO and Volkhin, IA and Denisova, AA and Nikitin, PA and Petrukhin, ER}, title = {[De Novo Gene Birth].}, journal = {Molekuliarnaia biologiia}, volume = {59}, number = {1}, pages = {22-31}, pmid = {40542629}, issn = {0026-8984}, mesh = {*Evolution, Molecular ; Humans ; *Gene Duplication ; *Gene Transfer, Horizontal ; Animals ; }, abstract = {According to classic ideas, new genes emerge from old genes by duplication or horizontal transfer. Analyses of a large number of genomes in recent decades have shown that some genes have no visible homologs and have presumably emerged de novo from previously noncoding sequences. The review considers possible mechanisms of de novo gene formation, the properties of protein sequences encoded by such genes, and features of their expression and selection. The problem of identification of de novo arising gene is discussed separately.}, }
@article {pmid40540566, year = {2025}, author = {Woods, PH and Speth, DR and Laso-Pérez, R and Utter, DR and Ruff, SE and Orphan, VJ}, title = {Identification of key steps in the evolution of anaerobic methanotrophy in Candidatus Methanovorans (ANME-3) archaea.}, journal = {Science advances}, volume = {11}, number = {25}, pages = {eadq5232}, pmid = {40540566}, issn = {2375-2548}, mesh = {*Methane/metabolism ; Anaerobiosis ; Phylogeny ; *Evolution, Molecular ; Genome, Archaeal ; *Archaea/genetics/metabolism ; Metagenomics ; Gene Transfer, Horizontal ; }, abstract = {Despite their large environmental impact and multiple independent emergences, the processes leading to the evolution of anaerobic methanotrophic archaea (ANME) remain unclear. This work uses comparative metagenomics of a recently evolved but understudied ANME group, "Candidatus Methanovorans" (ANME-3), to identify evolutionary processes and innovations at work in ANME, which may be obscured in earlier evolved lineages. We identified horizontal transfer of hdrA homologs and convergent evolution in carbon and energy metabolic genes as potential early steps in Methanovorans evolution. We also identified the erosion of genes required for methylotrophic methanogenesis along with horizontal acquisition of multiheme cytochromes and other loci uniquely associated with ANME. The assembly and comparative analysis of multiple Methanovorans genomes offers important functional context for understanding the niche-defining metabolic differences between methane-oxidizing ANME and their methanogen relatives. Furthermore, this work illustrates the multiple evolutionary modes at play in the transition to a globally important metabolic niche.}, }
@article {pmid40379877, year = {2025}, author = {Gonzalez-Duran, E and Kroop, X and Schadach, A and Bock, R}, title = {Suppression of plastid-to-nucleus gene transfer by DNA double-strand break repair.}, journal = {Nature plants}, volume = {11}, number = {6}, pages = {1154-1164}, pmid = {40379877}, issn = {2055-0278}, mesh = {*DNA Breaks, Double-Stranded ; *Plastids/genetics ; *DNA Repair ; *Nicotiana/genetics ; *Cell Nucleus/genetics ; *Gene Transfer, Horizontal ; Symbiosis/genetics ; }, abstract = {Plant nuclear genomes contain thousands of genes of mitochondrial and plastid origin as the result of endosymbiotic gene transfer (EGT). EGT is a still-ongoing process, but the molecular mechanisms determining its frequency remain largely unknown. Here we demonstrate that nuclear double-strand break (DSB) repair is a strong suppressor of EGT. Through large-scale genetic screens in tobacco plants, we found that EGT from plastids to the nucleus occurs more frequently in somatic cells when individual DSB repair pathways are inactive. This effect is explained by the expected increase in the number and residence time of DSBs available as integration sites for organellar DNA. We also show that impaired DSB repair causes EGT to increase 5- to 20-fold in the male gametophyte. Together, our data (1) uncover DSB levels as a key determinant of EGT frequency, (2) reveal the strong mutagenic potential of organellar DNA and (3) suggest that changes in DNA repair capacity can impact EGT across evolutionary timescales.}, }
@article {pmid40544427, year = {2025}, author = {Lamberte, LE and Darby, EM and Kiu, R and Moran, RA and Acuna-Gonzalez, A and Sim, K and Shaw, AG and Kroll, JS and Belteki, G and Clarke, P and Felgate, H and Webber, MA and Rowe, W and Hall, LJ and Van Schaik, W}, title = {Staphylococcus haemolyticus is a reservoir of antibiotic resistance genes in the preterm infant gut.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2519700}, doi = {10.1080/19490976.2025.2519700}, pmid = {40544427}, issn = {1949-0984}, abstract = {Staphylococcus haemolyticus is an important cause of sepsis in preterm infants, with gut colonization being recognized as a risk factor for infection. To better understand the diversity of S. haemolyticus among preterm infants, we generated genome sequences of S. haemolyticus strains (n = 140) from 44 stool samples of 22 preterm infants from four hospitals in England. Core genome phylogenetic analyses, incorporating 126 publicly available S. haemolyticus genome sequences, showed that 85/140 (60.1%) of the isolates, from three different hospitals, formed a clonal group with 78/85 (91.7%) strains having Multi-Locus Sequence Type (ST) 49. Antibiotic resistance genes were prevalent in the genomes. There was a strong association between the presence of mecA and phenotypic resistance to oxacillin, and the aacA-aphD gene and phenotypic resistance to gentamicin. While mecA was near-ubiquitous, none of the strains from the preterm infant cohort had a complete Staphylococcal Cassette Chromosome mec (SCCmec) element. The aacA-aphD gene was associated with the transposon Tn4001 in multiple chromosomal and plasmid contexts. Our data suggest the existence of a distinct sub-population of S. haemolyticus that has adapted to colonize the gut of preterm infants, and widespread horizontal gene transfer and recombination among this frequent colonizer of the preterm infant gut.}, }
@article {pmid40544087, year = {2025}, author = {Bhattacharya, D and Van Etten, J and Panayotakis, G and McDermott, T and Stephens, TG}, title = {Gene transfer drives community cooperation in geothermal habitats.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2025.06.004}, pmid = {40544087}, issn = {1878-4380}, abstract = {Cyanidiophyceae red algae dominate many geothermal habitats and provide important tools for investigating the evolution of extremophilic eukaryotes and associated microbial communities. We propose that resource sharing drove genome reduction in Cyanidiophyceae and enabled the neofunctionalization of genes in multi-enzyme pathways. Utilizing arsenic detoxification as a model, we discuss how the sharing of gene functions by other members of the microbial assemblage weakened selection on homologs in the Cyanidiophyceae, allowing long-term gene persistence via the putative gain of novel functions. This hypothesis, referred to as the Integrated Horizontal Gene Transfer (HGT) Model (IHM), attempts more generally to explain how extremophilic eukaryotes may have transitioned from 'hot start' milieus by functional innovations driven by the duplication and divergence of HGT-derived genes.}, }
@article {pmid40543345, year = {2025}, author = {Li, S and Jiang, Y and Wang, J and Bartlam, M and Wang, Y}, title = {Chiral naproxen enhances horizontal transfer of antibiotic resistance genes in biofilms: Molecular docking reveals stereoselective mechanisms.}, journal = {Journal of hazardous materials}, volume = {495}, number = {}, pages = {138980}, doi = {10.1016/j.jhazmat.2025.138980}, pmid = {40543345}, issn = {1873-3336}, abstract = {The dissemination of antibiotic resistance genes (ARGs) is a growing global health concern. This study investigates how the chiral enantiomers of the non-antibiotic drug naproxen (NAP) influence ARG dissemination in biofilms. Metagenomic sequencing and binning analyses revealed that NAP enantiomers selectively enriched ARGs and their bacterial hosts, enhancing resistance to specific antibiotics. Notably, the stereoselective effects of NAP enantiomers not only shaped microbial community composition but also affected the potential for ARG spread. Mechanistically, exposure to R-NAP, in comparison to S-NAP, resulted in a 1.53-fold increase in reactive oxygen species (ROS) production, an 18.20 % enhancement in cell membrane permeability, and a 1.93-fold rise in the abundance of genes associated with the type IV secretion system (T4SS). These physiological and genetic changes promoted microbial aggregation and DNA conjugation, particularly enhancing the transfer of the sul1 gene within the Aquabacter genus through the coordinated action of T4SS, two-component systems (TCS), and quorum sensing (QS). Molecular docking and qRT-PCR analyses further revealed that the stereoselectivity of NAP enantiomers stemmed from their distinct binding interactions with proteins involved in horizontal gene transfer, shedding light on the molecular mechanisms underlying ARG dissemination under chiral NAP exposure.}, }
@article {pmid40541684, year = {2025}, author = {Sies, AN and Nowlan, JP and Schnell, LJ and Lumsden, JS and Russell, S and Cameron, ADS}, title = {Discovery and assembly of plasmids in the fish pathogen Tenacibaculum.}, journal = {Plasmid}, volume = {}, number = {}, pages = {102753}, doi = {10.1016/j.plasmid.2025.102753}, pmid = {40541684}, issn = {1095-9890}, abstract = {Members of the marine bacterial genus Tenacibaculum cause disease in finfish and outbreaks result in significant animal harm and losses in aquaculture around the globe. Plasmids have not been previously identified in Tenacibaculum, but long-read DNA sequencing of genomes from disease-associated Tenacibaculum isolates collected between 2017 and 2020 in British Columbia, Canada, revealed circular putative plasmids in three Tenacibaculum species. In addition to high-quality circular assembly, the putative plasmids contained genes encoding plasmid replication, mobility, and partitioning proteins. Genes for type B conjugation machinery and type 6iii secretion system components were also identified on each of the two largest plasmid sequences. Several protocols were tested to visualize and enrich Tenacibaculum plasmid DNA. Rolling-circle replication with Phi29 DNA polymerase amplified putative plasmids smaller than 100 kb. Alkaline lysis extraction provided weak enrichment of putative plasmid DNA, and plasmids could not be confidently resolved by Eckhardt extraction and electrophoresis in agarose gels. The newly assembled plasmids matched previously sequenced Tenacibaculum contigs, highlighting that publicly available Tenacibaculum genomes contain unrecognized plasmids. The discovery of putative plasmids in Tenacibaculum is significant because plasmids often confer important functions to host cells and serve as vehicles for horizontal gene transfer within and beyond the host species.}, }
@article {pmid40539803, year = {2025}, author = {Mapiki, P and Laiser, E and Mufungwe, J and Shawa, M and Siamujompa, M and Johnson, T and Namukonde, N and Mwaanga, P and Hang'ombe, BM}, title = {Bacteriological quality of fresh and processed black soldier fly Hermetia illucens larvae reared on chicken manure in Kitwe, Zambia.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0057024}, doi = {10.1128/spectrum.00570-24}, pmid = {40539803}, issn = {2165-0497}, abstract = {UNLABELLED: Black soldier fly larvae (BSFL) have high nutrient content and are rapidly becoming an alternative protein source for animal feed. However, microbial contamination is a potential risk due to the environment in which they are reared. This study assessed the bacteriological quality of fresh and processed BSFL by comparing the processed BSFL using two traditional methods (oven-dried and sun-dried), on their effectiveness at reducing the bacterial load and further elucidated bacterial composition. PCR was used to identify extended-spectrum β-lactamase (ESBL) and mecA genes in Escherichia coli and Staphylococcus spp., respectively. A total of 51 fresh BSFL samples were collected from a commercial poultry farm in Kitwe, Zambia. The results showed various bacterial genera, with a higher diversity among gram-positive isolates. The comparison of the effectiveness of two traditional processing methods for BSFL, sun-drying and oven-drying, showed that both methods significantly reduced the bacterial load, with oven-drying causing a larger reduction. While various genera were identified, we focused on E. coli and Staphylococcus spp. This is because some E. coli harbor ESBLs that hydrolyze β-lactam antibiotics like cephalosporins and penicillin, leading to resistance. Similarly, the genus Staphylococcus was selected since some strains are potentially pathogenic and contain the mecA gene that encodes resistance to β-lactam antibiotics. Molecular characterization of the isolated strains revealed blaCTX-M and blaTEM genes among E. coli, but the mecA gene was not detected among Staphylococcus. This study revealed that BSFL harbor bacteria of zoonotic significance, emphasizing the need for good processing methods to eliminate potential risks.<br><br>IMPORTANCE: Isolation and identification of Escherichia coli and Staphylococcus spp. in processed black soldier fly larvae (BSFL) samples meant for animal feed indicate insufficient processing methods and pose a public health risk. For instance, some E. coli harbor extended-spectrum &#x3b2;-lactamases (ESBLs) that hydrolyze &#x3b2;-lactam antibiotics like cephalosporins and penicillin, leading to resistance. In addition, some E. coli commensals can transfer antimicrobial resistance genes to pathogenic bacteria through horizontal gene transfer using various mobile genetic elements, leading to resistance. Similarly, for Staphylococcus spp., some strains of the genus Staphylococcus are potentially pathogenic and contain the mecA gene that encodes resistance to &#x3b2;-lactam antibiotics. In this study, we used PCR to screen E. coli isolates for the two commonly reported ESBL genes in Zambia, blaCTX-M and blaTEM, and Sanger sequencing was used to reveal blaCTX-M gene alleles. Our results highlight the importance of using adequate processing methods for BSFL to eliminate potential health risks to animal feed.}, }
@article {pmid40535478, year = {2025}, author = {Zhang, Y and Su, Z and Qiu, X and Liu, H and Wen, D and Chen, L}, title = {Distinct ARG profiles associated with class 1 integrons in municipal and industrial wastewater treatment plants.}, journal = {Environmental science and ecotechnology}, volume = {26}, number = {}, pages = {100586}, pmid = {40535478}, issn = {2666-4984}, abstract = {Class 1 integrons facilitate horizontal gene transfer, significantly influencing antibiotic resistance gene (ARG) dissemination within microbial communities. Wastewater treatment plants (WWTPs) are critical reservoirs of ARGs and integrons, yet the integron-mediated dynamics of ARG transfer across different WWTP types remain poorly understood. Here we show distinct ARG profiles associated with class 1 integrons in municipal and industrial WWTPs using a novel approach combining nested-like high-throughput qPCR and PacBio sequencing. Although industrial WWTPs contained higher absolute integron abundances, their relative ARG content was lower (1.27 × 10[7]-9.59 × 10[7] copies/ng integron) compared to municipal WWTPs (3.72 × 10[7]-1.98 × 10[8] copies/ng integron). Of the 132,084 coding sequences detected from integrons, 56.8 % encoded antibiotic resistance, with industrial plants showing lower ARG proportions, reduced ARG array diversity, and greater incorporation of non-ARG sequences. These findings suggest industrial WWTP integrons integrate a broader array of exogenous genes, reflecting adaptation to complex wastewater compositions. This work enhances our understanding of integron-driven ARG dynamics in wastewater and offers a robust strategy for environmental integron analysis.}, }
@article {pmid40533044, year = {2025}, author = {Tian, Y and Li, J and Meng, J and Li, J}, title = {Deciphering antibiotic resistance gene transfer in activated sludge systems for piggery wastewater: behaviors, hosts and drivers.}, journal = {Environmental research}, volume = {}, number = {}, pages = {122166}, doi = {10.1016/j.envres.2025.122166}, pmid = {40533044}, issn = {1096-0953}, abstract = {Understanding the transfer and driving mechanisms of antibiotic resistance genes (ARGs) in activated sludge is essential for mitigating environmental risks, particularly during real wastewater treatment where these processes remain poorly characterized. This study investigated the prevalence of ARGs in a sequencing batch reactor (SBR) - up-flow microaerobic sludge reactor (UMSR) system treating high-risk piggery wastewater and revealed critical pathways for resistance propagation. Ten prevalent ARG subtypes, categorized into three types, were selected as target genes, exhibiting a total relative abundance of 0.52 copies per 16S rRNA in raw wastewater. The SBR-UMSR system reduced total ARGs by 0.04 log in wastewater, with half of subtypes decreasing 0.14-1.30 log, despite 0.23-0.58 log enrichment in sludge. By integrating correlation analysis with partial least-squares path modeling, this study identified Burkholderiaceae as the primary potential host of ARGs and pinpointed other high-risk hosts. It further revealed two crucial mechanisms: (1) conjugation-mediated horizontal gene transfer dominated ARG propagation, and (2) bacterial community succession served as the main driving force for ARG transfer. This study advances mechanistic understanding of ARG transmission in real wastewater systems, providing critical insights for optimizing sludge management to mitigate antibiotic resistance risks.}, }
@article {pmid40530826, year = {2025}, author = {Carolak, E and Czajkowska, J and Stypułkowska, A and Waszczuk, W and Dutkiewicz, A and Grzymajlo, K}, title = {Being a better version of yourself: genetically engineered probiotic bacteria as host defense enhancers in the control of intestinal pathogens.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2519696}, doi = {10.1080/19490976.2025.2519696}, pmid = {40530826}, issn = {1949-0984}, mesh = {*Probiotics ; Humans ; *Gastrointestinal Microbiome ; Genetic Engineering ; Animals ; *Microorganisms, Genetically-Modified/genetics ; *Bacteria/genetics ; }, abstract = {Intestinal pathogens pose a significant global health burden, and traditional antibiotic treatments often disrupt the beneficial gut microbiota that plays a crucial role in maintaining host health through pathogen prevention and immune regulation. Although probiotics have emerged as promising therapeutic agents, their efficacy is limited by strain-dependent variations, survival challenges in the gastrointestinal tract, and inconsistent immune responses. Recent advances in genetic engineering, particularly CRISPR-Cas systems and their combinations with complementary technologies, such as Cre-lox and RecE/T, have enabled the precise modification of probiotic strains to enhance their therapeutic potential. These enhanced probiotics demonstrate improved functionality through multiple mechanisms, including increased adhesion via the expression of specific proteins (InlA, FnBPA, and LAP), targeted antimicrobial activity through engineered sensing systems (Lactococcus lactis detecting Vibrio cholerae CAI-1), and enhanced immunomodulation through cytokine production. Results have demonstrated the potential of genetically modified probiotics in preventing and treating gastrointestinal infections through mechanisms that include competitive exclusion, bacteriocin production, intestinal barrier reinforcement, and immune modulation. However, challenges remain in ensuring genetic stability and preventing horizontal gene transfer. Future research should focus on optimizing probiotic strains for targeted applications while addressing biosafety concerns. By understanding the complex interplay between probiotics, pathogens, and host immunity, innovative strategies can be developed to harness the full therapeutic potential of probiotic interventions in maintaining gut health.}, }
@article {pmid40529306, year = {2025}, author = {Xu, J and Zhang, M and Yan, Y and Li, Z and Lu, X}, title = {Intestinal flora metabolites indole-3-butyric acid and disodium succinate promote IncI2 mcr-1-carrying plasmid transfer.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1564810}, pmid = {40529306}, issn = {2235-2988}, mesh = {*Plasmids/genetics ; Reactive Oxygen Species/metabolism ; *Indoles/metabolism/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Escherichia coli/genetics/drug effects ; *Gene Transfer, Horizontal/drug effects ; Conjugation, Genetic/drug effects ; *Succinic Acid/metabolism ; Cell Membrane Permeability/drug effects ; Drug Resistance, Bacterial/genetics ; }, abstract = {INTRODUCTION: Plasmid-driven horizontal transfer of resistance genes in bacterial communities is a major factor in the spread of resistance worldwide. The gut microbiome, teeming with billions of microorganisms, serves as a reservoir for resistance genes. The metabolites of gut microorganisms strongly influence the physiology of their microbial community, but the role of the metabolites in the transfer of resistance genes remains unclear.<br><br>METHODS: A dual-fluorescence conjugation model was established. We assessed the effects of different concentrations of indole-3-butyric acid (IBA) and disodium succinate (DS) on plasmid transfer using conjugation assays. The growth of bacteria (donors, recipients, and transconjugants), the reactive oxygen species (ROS) levels and membrane permeability were measured under IBA and DS exposure. The plasmid copy number, and transcriptional levels of conjugation-related genes (including the related genes of the regulation of ROS production, the SOS response, cell membrane permeability, pilus generation, ATP synthesis, and the type IV secretion system (T4SS)) were evaluated by qPCR.<br><br>RESULTS: In this study, we demonstrated that IBA and DS at low concentrations, which can also be ingested through diet, enhance the interspecies transfer ratio of IncI2 mcr-1-carrying plasmid in Escherichia coli. At 20 mg/L, the transfer ratios in the presence of IBA or DS increased by 2.5- and 2.7-fold compared to that of the control, respectively. Exposure to this concentration of IBA or DS increased the production of reactive oxygen species (ROS), the SOS response, cell membrane permeability, and plasmid copy number. The transcription of genes of the related pathways and of pilus, ATP, and the T4SS was upregulated.<br><br>DISCUSSION: Our findings revealed that low-dose gut microbiota metabolites-particularly those with dietary origins-promote plasmid-mediated resistance gene dissemination through multifaceted mechanisms involving oxidative stress, SOS activation, and conjugation machinery enhancement. This highlights potential public health risks associated with microbiota metabolites, especially those utilized in food production.}, }
@article {pmid40528005, year = {2025}, author = {Baker, BA and McCarthy, CGP and López-García, P and Leroy, RB and Susko, E and Roger, AJ and Eme, L and Moreira, D}, title = {Phylogenomic analyses indicate the archaeal superphylum DPANN originated from free-living euryarchaeal-like ancestors.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {40528005}, issn = {2058-5276}, support = {787904//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 101141745//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 803151//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 101141745//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 803151//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 812811//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 812811//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; }, abstract = {The episymbiotic DPANN archaea are thought to be one of the four major archaeal clades. However, the monophyly and placement of DPANN within the archaeal tree remain debated, and their fast-evolving reduced genomes render phylogenetic reconstructions challenging. Here we used 126 highly conserved protein markers, extensive taxon sampling representing the 11 known DPANN phyla and in-depth phylogenomic analyses to reassess DPANN monophyly and their relationships to other archaea. Our analyses robustly support the monophyly and placement within Euryarchaeota, and we identify the probably free-living Altiarchaeota as the earliest diverging DPANN branch. Our phylogenies suggest DPANN probably acquired several hallmark proteins through ancient horizontal gene transfer events from different bacterial donors, notably Patescibacteria and Omnitrophota, two bacterial phyla that also exhibit episymbiotic lifestyles. Overall, the monophyletic DPANN archaea probably evolved from a free-living, euryarchaeal-like ancestor, with proteins of bacterial origin playing a role in the emergence of their episymbiotic lifestyle.}, }
@article {pmid40527192, year = {2025}, author = {Yin, Y and Xiao, K and Wang, YF and Cao, JM and Dong, JP and Zhu, D and Zhu, YG}, title = {Nanoplastics released from textile washing enrich antibiotic resistance and virulence genes in sewage sludge microbiomes.}, journal = {Environment international}, volume = {202}, number = {}, pages = {109611}, doi = {10.1016/j.envint.2025.109611}, pmid = {40527192}, issn = {1873-6750}, abstract = {The washing of synthetic textiles is a major source of microplastic pollution, contributing to the widespread presence of nanoplastics (NPs) in wastewater treatment plants (WWTPs). However, the role of laundry-released NPs in shaping microbial communities and facilitating the spread of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in sludge remains unclear. Here, we quantified the concentration and size distribution of NPs released during the washing of polyamide (PA), polypropylene (PP), and polyethylene terephthalate (PET) textiles using nanoparticle tracking analysis. Substantial NP release was observed, with concentrations ranging from 3.4 × 10[7] to 1.7 × 10[8] particles mL[-1], and sizes between 130 and 240 nm. We then evaluated their impact on ARG and VFG profiles, as well as bacterial communities in anaerobic sludge through metagenomic and 16S rRNA gene sequencing. Laundry-released NPs significantly increased the abundance of ARGs, VFGs, and mobile genetic elements (MGEs) in sludge, with D8A-2 and Halomonas identified as potential ARG and VFG hosts. Notably, the mechanisms driving ARG enrichment varied by NP type. PA-released NPs elevated reactive oxygen species levels in bacterial communities, facilitating horizontal gene transfer via MGEs, while PP- and PET-released NPs enhanced ARG enrichment through both horizontal gene transfer and shifts in bacterial community composition. These findings highlight the risks posed by laundry-released NPs accumulating in WWTPs, emphasizing the urgent need for improved wastewater management strategies to mitigate their environmental and public health impacts.}, }
@article {pmid40520376, year = {2025}, author = {Cao, H and Shen, Y and Ma, K and Zheng, D and Xu, Y and Qiao, X}, title = {Molecular characterization of clinical non-typhoidal Salmonella isolates shows high antimicrobial resistance burden in Jiangsu, China.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1587421}, pmid = {40520376}, issn = {1664-302X}, abstract = {Non-typhoidal Salmonella (NTS) poses a significant global health burden due to its association with gastroenteritis and rising antimicrobial resistance (AMR). This study conducted a genomic analysis of 62 Salmonella isolates from outpatient cases in Jiangsu, China, to monitor the epidemiological characteristics of NTS, including genetic diversity, AMR profiles, and resistance transmission mechanisms 18 serovars and 21 sequence types (STs) were identified by whole genome sequencing, with S. enteritidis (27.42%) and S. typhimurium (19.35%) predominating. 61 resistance genes from ten different antimicrobial categories were found by genotypic AMR screening. 90.32% of isolates had β-lactam resistance genes, indicating a high frequency of extended-spectrum β-lactamases (ESBL). Serovar-dependent resistance patterns were highlighted by the most varied AMR profile (40/61 genes) found in S. typhimurium. The co-occurrence of genes for aminoglycoside resistance, sul2, and blaTEM indicated clustering driven by mobile genetic elements. A plasmid in a S. Stanley isolate harbored 12 AMR genes, which showed structural changes suggestive of horizontal gene transfer and active recombination. These findings underscore the role of plasmids in disseminating MDR and the urgent need for enhanced antimicrobial stewardship, food safety protocols, and One Health interventions to mitigate the spread of resistant Salmonella clones.}, }
@article {pmid40517254, year = {2025}, author = {Gozashti, L and Corbett-Detig, R}, title = {Double-stranded DNA viruses may serve as vectors for horizontal transfer of intron-generating transposons.}, journal = {Mobile DNA}, volume = {16}, number = {1}, pages = {25}, pmid = {40517254}, issn = {1759-8753}, support = {R35GM128932/GM/NIGMS NIH HHS/United States ; }, abstract = {Specialized transposable elements capable of generating introns, termed introners, are one of the major drivers of intron gain in eukaryotes. Horizontal transfer of transposable elements (HTT) is thought to play an important role in shaping introner distributions. Viruses could function as vehicles of introner HTT since they often integrate into host genomes and have been implicated in widespread HTT in eukaryotes. We annotated integrated viral elements in diverse dinoflagellate genomes with active introners and queried viral elements for introner sequences. We find that 25% of viral elements contain introners. The vast majority of viral elements represent maverick-polinton-like double-stranded DNA (dsDNA) viruses in the family eupolintoviridae as well as giant dsDNA viruses. By querying a previously annotated set of eupolintoviral proviruses, we show that introners populate full-length elements with machinery required for transposition as well as viral infection. Introners in the vast majority of viral elements are younger than or similar in age to others in their host genome, suggesting that most viral elements acquired introners after integration. However, a subset of viral elements shows the opposite pattern wherein viral introners are significantly older than other introners, possibly consistent with virus-to-host horizontal transfer. Together, our results suggest that dsDNA viruses may serve as vectors for HTT of introners between individuals and species, resulting in the introduction of intron-generating transposons to new lineages.}, }
@article {pmid40069292, year = {2025}, author = {Lang, AS and Buchan, A and Burrus, V}, title = {Interactions and evolutionary relationships among bacterial mobile genetic elements.}, journal = {Nature reviews. Microbiology}, volume = {23}, number = {7}, pages = {423-438}, pmid = {40069292}, issn = {1740-1534}, mesh = {*Interspersed Repetitive Sequences/genetics ; *Bacteria/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial ; }, abstract = {Mobile genetic elements (MGEs) have profound influence on the ecology and evolution of organisms, including bacteria. During the past two decades, a great number of new types of MGEs have been discovered that now seem to be prevalent in diverse bacterial lineages. With the rapid discovery of new categories of MGEs comes an array of new acronyms that present a challenge to grasp. Moreover, it is now clear that there are complex evolutionary connections and molecular interactions among MGEs, and that these entities are not discrete, independent genetic elements acting in isolation. Different types of MGEs share and exchange genes, and coresident MGEs interact with each other within cells, in both cooperative and antagonistic ways. This all greatly affects the end results that are felt by the host organism. In this Review, we strive to clarify emerging bacterial MGE terms and elements while also presenting a comprehensive overview of the current knowledge landscape regarding MGEs in bacteria, their evolutionary relationships and interactions with their host and with one another.}, }
@article {pmid40516885, year = {2025}, author = {Cunha da Silva, G and Rossi, CC}, title = {Defense systems and mobile elements in Staphylococcus haemolyticus: a genomic view of resistance dissemination.}, journal = {Microbial pathogenesis}, volume = {206}, number = {}, pages = {107808}, doi = {10.1016/j.micpath.2025.107808}, pmid = {40516885}, issn = {1096-1208}, abstract = {Staphylococcus haemolyticus is a multidrug-resistant opportunistic pathogen and a major reservoir of antimicrobial resistance (AMR) genes within the Staphylococcaceae family. Its high genomic plasticity, frequent association with mobile genetic elements (MGEs), and prevalence in clinical settings underscore its relevance as both a threat and a conduit for resistance dissemination. In this study, we performed a comprehensive pan-genomic analysis of the S. haemolyticus defensome - including restriction-modification (RM), abortive infection (Abi), and CRISPR-Cas systems - across 692 high-quality genomes. Our results reveal a highly diverse and modular repertoire of immune systems, often organized in physical clusters and frequently associated with MGEs. We identified evidence of antagonistic interactions, with both defense and anti-defense elements encoded on plasmids and prophages. CRISPR spacer analysis showed a predominant targeting of phages, and genomes encoding CRISPR-Cas systems exhibited a lower abundance of MGEs and AMR genes, suggesting a trade-off between defense and gene acquisition. RNA-seq data from one reference strain indicate that only a fraction of the defensome is actively transcribed under standard conditions, hinting at environment-responsive regulation. Together, these findings provide new insights into the genomic strategies sustaining the persistence and adaptability of S. haemolyticus in clinical environments. The interplay between its immune systems and mobilome likely contributes not only to its evolutionary trajectory, but also to its role in the horizontal transfer of resistance determinants among pathogenic staphylococci. A deeper understanding of this immune-mobilome interface may help inform future strategies to limit the spread of resistance.}, }
@article {pmid40516407, year = {2025}, author = {Fang, C and Liu, H and Chen, X and Lu, H and Ren, C and Hu, Z and Wang, Y and Zhang, J}, title = {Thioredoxin-mediated sulfur cycling and biogenic sulfur encapsulation synergistically enhance co-removal of nitrogen, sulfamethoxazole, and resistance genes in constructed wetlands.}, journal = {Water research}, volume = {284}, number = {}, pages = {123939}, doi = {10.1016/j.watres.2025.123939}, pmid = {40516407}, issn = {1879-2448}, abstract = {The interplay between sulfur-driven denitrification and antibiotic resistance genes (ARGs) proliferation remains unresolved in constructed wetlands (CWs), where sulfide accumulation and reactive oxygen species generation paradoxically enhance nitrogen removal while compromising microbial integrity. To resolve this conflict, this study engineered a FeS2@S° composite filler that synergized thioredoxin (Trx)-mediated sulfur cycling and biogenic sulfur (bio-S[0]) encapsulation. Upregulation of trxA/B genes (2.3-fold increase) enabled Trx to convert toxic sulfide into adhesive bio-S[0], exhibiting higher microbial adhesion that shielded functional denitrifiers like Thiomonas (84.03 % viability under SMX stress). Concurrently, sulfur vacancies (SVs) at FeS2 {210} crystal facets generated hydroxyl radicals (•OH) and singlet oxygen ([1]O2) via vacancy-activated pathways, selectively degrading about 73.00 % of extracellular polymeric substance (EPS)-bound ARGs while suppressing horizontal gene transfer (tolC downregulation). The 6:4 FeS2@S[0] system achieved 68.66 % total nitrogen removal and 50.17 % sulfamethoxazole degradation, outperforming conventional substrates by 28.00-39.00 %, alongside a 61.24-67.31 % reduction in ARG abundance. A self-sustaining sulfur cycle recycled about 89.00 % of sulfides into bio-S[0] or FeS2, minimizing H2S emissions (0.045 mg·m[-2]·h[-1]) and maintaining electron flux. By bridging Trx-driven redox homeostasis and bio-S[0]'s physical protection, this work redefines CWs as robust systems capable of simultaneous nitrogen retention, antibiotic degradation, and ARGs suppression, establishing a transformative paradigm for sustainable wastewater treatment.}, }
@article {pmid40513520, year = {2025}, author = {Wu, K and Yang, J and Zhang, T and Zuo, J and Lin, H and Wang, J and Zhang, A and Lei, C and Wang, H}, title = {Emergence and traceability of Salmonella enterica serotype Mbandaka harboring blaOXA-10 from chickens in China.}, journal = {Veterinary microbiology}, volume = {307}, number = {}, pages = {110593}, doi = {10.1016/j.vetmic.2025.110593}, pmid = {40513520}, issn = {1873-2542}, abstract = {Salmonella enterica serotype Mbandaka (S. Mbandaka), a multi-host adapted non-typhoidal Salmonella, has emerged as a significant public health concern in recent years. In this study, we isolated S. Mbandaka strains carrying a multidrug-resistant IncHI2A/IncHI2 plasmid from deceased chickens in China and performed whole-genome sequencing and comparative genomic analyses to investigate their global dissemination and evolutionary adaptation. The multidrug-resistant IncHI2A/IncHI2 plasmid in isolate YK35 harbored multiple antibiotic resistance genes (ARGs) including blaOXA-10, which was firstly observed in S. Mbandaka in China. It exhibited high sequence identity with IncHI2A/IncHI2 plasmids identified in other bacterial species, including S. Typhimurium, Klebsiella aerogenes, and E. coli, which suggested the cross-species dissemination of IncHI2A/IncHI2 plasmids and ARGs. Global genomic epidemiology classified S. Mbandaka strains into seven distinct clades, with the majority originating from the USA and the UK. The pan-genomic analysis indicated an open pan-genome structure, with continuous expansion of accessory genes, particularly those associated with replication, recombination, repair, and defense mechanisms, underscoring the evolutionary adaptation of S. Mbandaka to external environments. Evolutionary analysis further traced the international transmission routes of S. Mbandaka, revealing potential cross-regional spread, particularly from the USA and the UK to other countries, including China. The findings emphasize the global spread and evolutionary adaptation of S. Mbandaka, likely driven by international trade and horizontal gene transfer, including the acquisition of ARGs, which have contributed to its increasing public health risks. This study underscores the urgent need for enhanced surveillance and control measures to mitigate the spread of S. Mbandaka and its antibiotic resistance, particularly in the context of global food supply chains and international trade.}, }
@article {pmid40506592, year = {2025}, author = {Singh, H and Pandya, S and Jasani, S and Patel, M and Kaur, T and Rustagi, S and Shreaz, S and Yadav, AN}, title = {Integrons: the hidden architects of bacterial adaptation, evolution, and the challenges of antimicrobial resistance.}, journal = {Antonie van Leeuwenhoek}, volume = {118}, number = {7}, pages = {90}, pmid = {40506592}, issn = {1572-9699}, mesh = {*Integrons/genetics ; *Bacteria/genetics/drug effects ; *Evolution, Molecular ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; *Adaptation, Physiological ; }, abstract = {Integrons, a diverse group of genetic elements, have emerged as key players in bacterial adaptation and evolution. These elements, commonly found in both environmental as well as clinical settings, facilitate the acquisition, exchange, and expression of integron cassettes, allowing bacteria to rapidly adapt to changing environments and acquire antibiotic resistance. This review provides an in-depth exploration of the various classes of clinical integrons, including class 1, 2, and 3, highlighting their origins, distribution, and associated mobile elements. We delve into the astonishing success of "class 1 integrons", emphasizing their ability to recognize diverse attachment sites known as "attC sites" and getting integrated within many different integron cassettes from diverse sources. Class 1 integrons are able to propagate widely among bacterial hosts due to their lack of host specificity, interaction with transposons, and broad host range plasmids. Moreover, we discuss the substantial impact of class 1 integrons in antimicrobial resistance, as they accumulate an array of resistance genes through strong positive selection. Additionally, we address the challenging issue regarding the evolution and function of integrons and integron cassettes, including the role of promoters, origins of integron cassettes, and the abundance of unknown proteins encoded within them. The future prospects of integron research are also explored, highlighting the need to understand cassette expression patterns, assess the contribution of chromosomal/superintegron arrays to host fitness, unravel the mechanisms of cassette generation, and investigate the connection between the SOS induction and horizontal gene transfer. Overall, this review underlines the significance of integrons as hidden architects driving bacterial adaptation and evolution, providing valuable insights into their ecological and evolutionary dynamics, and shaping the future direction of research in this field.}, }
@article {pmid40505955, year = {2025}, author = {Kaneko, S and Fukushima, H and Nakahama, M and Tsuge, K and Ishii, J and Aizawa, Y and Itaya, M and Kondo, A}, title = {Versatile Methodology for Efficient Large-sized DNA Delivery between Microorganisms without in vitro purification.}, journal = {Journal of molecular biology}, volume = {}, number = {}, pages = {169289}, doi = {10.1016/j.jmb.2025.169289}, pmid = {40505955}, issn = {1089-8638}, abstract = {Purified DNA plasmids traditionally used for microbial transformation have been supplanted by extracellular plasmids released via host bacterial lysis, offering an alternative approach for DNA-plasmid delivery. Specifically, shuttle vector plasmids liberated from host Bacillus subtilis were directly employed for the transformation of chemically competent cells Escherichia coli, eliminating the need for biochemical purification. This unconventional DNA delivery technique, referred to as 'Cell Lysis Technology to provide Transformable Extra-cellular DNA; CELyTED', has been successfully adapted for the transformation of microorganism Saccharomyces cerevisiae as well. The protocol includes optimized conditions for efficient cell lysis of the donor host cells. Notably, ' CELyTED ' enables the introduction of large-sized DNA plasmids exceeding 50 kb into target microorganisms mitigating the potential adverse effects of physical shearing during the purification process. This simplicity in the delivery protocol makes it versatile for both prokaryotic and eukaryotic microorganisms, establishing a fundamental platform in the synthetic genome field. Our study demonstrates the feasibility of introducing large DNA plasmids into cells E. coli and S. cerevisiae using the lysate of donor host cells, showcasing the potential of 'CELyTED ' as a streamlined approach in genetic transformation methodologies.}, }
@article {pmid40505265, year = {2025}, author = {Chen, M and Wang, G and Ma, B and Musat, N and Shen, P and Wei, Z and Wei, Y and Richnow, HH and Zhang, J}, title = {Deciphering the transfer of antimicrobial resistance genes in the urban water cycle from water source to reuse: a review.}, journal = {Environment international}, volume = {201}, number = {}, pages = {109584}, doi = {10.1016/j.envint.2025.109584}, pmid = {40505265}, issn = {1873-6750}, abstract = {Antimicrobial resistance genes (ARGs) threaten ecosystems and human health, impacting United Nations Sustainable Development Goal 3 (Good Health and Well-being). This review examines ARG occurrence and transfer within the urban water cycle (UWC) from drinking water source to wastewater reuse, highlighting molecular mechanisms and research gaps. Quantitative and metagenomic data reveal that UWC amplifies ARG spread, with plasmid-mediated ARGs rising from ∼ 2.23 % to ∼ 49.51 % and high-risk ARGs increasing from ∼ 0.25 % to ∼ 5.07 %, enhancing horizontal gene transfer in receiving waters. The primary sources of ARGs in UWC are wastewater treatment plants and combined sewage overflows. Multidrug-resistant Pseudomonas aeruginosa in drinking water treatment plant and multidrug-resistant fecal coliforms in wastewater treatment plants should be emphasized. These pose significant risks to both the environment and human health and underscore the urgent need for targeted monitoring and mitigation strategies within the UWC to safeguard public health and aquatic ecosystems. Future research should: (1) map ARG dynamics across the entire UWC, (2) identify hosts of high-risk ARGs and key pathogens, (3) elucidate HGT mechanisms and risk transmission, and (4) develop targeted control technologies for high-risk ARGs at critical UWC points. These insights will inform strategies to ensure water security and curb ARG proliferation in aquatic environments.}, }
@article {pmid40503823, year = {2025}, author = {Karlsson, PA and Zhang, T and Järhult, JD and Joffré, E and Wang, H}, title = {Heterogeneity and metabolic diversity among Enterococcus species during long-term colonization.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0316024}, doi = {10.1128/spectrum.03160-24}, pmid = {40503823}, issn = {2165-0497}, abstract = {Urinary tract infections (UTIs), traditionally dominated by Gram-negative pathogens, are increasingly complicated by antimicrobial-resistant Enterococcus spp. in hospital settings, particularly during the use of indwelling catheters. This study screened urine samples from 210 catheterized intensive care unit patients at Uppsala University Hospital (June 2020-September 2021), identifying 39 unique PhenePlate™-RF types across E. faecium, E. faecalis, and E. durans. E. faecium isolates showed considerable diversity, primarily within clonal complex 17 (CC17), known for its virulence and antibiotic resistance. We identified multiple lineages and sequence types (STs), such as in patient HWP143, who had isolates from both ST80 and ST22 (an ancestral CC17 lineage). Notably, metabolic adaptations, such as increased L-arabinose metabolism, and shifts in antibiotic resistance were observed. Variations and similarities in plasmid content between individual lineages suggest horizontal gene transfer. E. faecalis isolates exhibited less diversity, but still significant metabolic variability across patients and mixed infections, as seen in patient HWP051, colonized by both ST16 (CC58) and ST287. E. durans, though less common, shared important metabolic traits with E. faecium and displayed polyclonal characteristics, highlighting its potential role in UTIs and the complexity of enterococcal infections. E. durans was sometimes misidentified, underlining the need for accurate identification methods. This research underscores the importance of understanding genetic and metabolic diversity, plasmid variations, and horizontal gene transfer (HGT) in Enterococcus spp., which influence antibiotic resistance, virulence, and ultimately, treatment outcomes.IMPORTANCEOur study, performed in Uppsala University Hospital, Sweden, uncovers novel insights into the genetic and metabolic diversity of Enterococcus species, focusing on E. faecium, E. faecalis, and E. durans. Unlike prior studies, which often have focused on single lineages, we reveal multiple clones and lineages within individual catheterized intensive care unit patients, including clones from clonal complex 17 and the emerging sequence type (ST) 192, highlighting notable metabolic adaptations and shifts in antibiotic resistance. The detection of mixed colonization with varied ST types and E. durans misidentification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry further emphasizes the challenges in Enterococcus species identification. Our findings have significant implications for understanding the complexity of Enterococcus infections, stressing the need to consider genetic and metabolic diversity to improve disease management and treatment outcomes.}, }
@article {pmid40501780, year = {2025}, author = {Dubinkina, V and Smith, B and Zhao, C and Pino, C and Pollard, KS}, title = {Linkage of nucleotide and functional diversity varies across gut bacteria.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.06.06.658399}, pmid = {40501780}, issn = {2692-8205}, abstract = {Understanding the forces shaping genomic diversity within bacterial species is essential for interpreting microbiome evolution, ecology, and host associations. Here, we analyze over one hundred prevalent gut bacterial species using the Unified Human Gut Genome (UHGG) collection to characterize patterns of intra-specific genomic variability. Gene content divergence scales predictably with divergence in core genome single nucleotide polymorphisms (SNPs), though there is substantial variability in evolutionary dynamics across species. Overall, accessory genes exhibit consistently faster linkage decay compared to core SNPs, highlighting the fluidity of functional repertoires within species boundaries. This signal is strongest for mobile genetic elements, which show minimal linkage to core genome SNPs. Together, our findings reveal species-specific recombination regimes in the gut microbiome, underscoring the importance of accounting for horizontal gene transfer and genome plasticity in microbiome-wide association studies and evolutionary models.}, }
@article {pmid40501577, year = {2025}, author = {Babajanyan, SG and Garushyants, SK and Wolf, YI and Koonin, EV}, title = {Evolution of antivirus defense in prokaryotes depending on the environmental virus prevalence and virome dynamics.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.05.27.656525}, pmid = {40501577}, issn = {2692-8205}, abstract = {UNLABELLED: Prokaryotes can acquire antivirus immunity via two fundamentally distinct types of processes: direct interaction with the virus as in CRISPR-Cas adaptive immunity systems and horizontal gene transfer (HGT) which is the main route of transmission of innate immunity systems. These routes of defense evolution are not mutually exclusive and can operate simultaneously, but empirical observations suggest that at least in some bacterial and archaeal species, one or the other route dominates the defense landscape. We hypothesized that the observed dichotomy stems from different life-history tradeoffs characteristic of these organisms. To test this hypothesis, we analyzed a mathematical model of a well-mixed prokaryote population under a stochastically changing viral prevalence. Optimization of the long-term population growth rate reveals two contrasting modes of defense evolution. In stable, predictable and fluctuating, unpredictable environments with a moderate viral prevalence, direct interaction with the virus and horizontal transfer of defense genes become the optimal routes of immunity acquisition, respectively. In the HGT-dominant mode, we observed a universal distribution of the fraction of microbes with different immune repertoires. Under very low virus prevalence, the cost of immunity exceeds the benefits such that the optimal state of a prokaryote is complete defense systems. By contrast, under very high virus prevalence, horizontal spread of defense systems dominates regardless of the stability of the virome. These findings might explain consistent but enigmatic patterns in the spread of antivirus defense systems among prokaryotes such as the ubiquity of adaptive immunity in hyperthermophiles contrasting their patchy distribution among mesophiles.<br><br>IMPORTANCE: The virus-host arms race is a major component of the evolutionary process in all organisms that drove the evolution of a broad variety of immune mechanisms. In the last few years, over 200 distinct antivirus defense systems have been discovered in prokaryotes. There are two major modes of immunity acquisition: innate immune systems spread through microbial populations via horizontal gene transfer (HGT) whereas adaptive-type immune systems acquire immunity via direct interaction with the virus. We developed a mathematical model to explore the short term evolution of prokaryotic immunity and show that in stable environments with predictable viral repertoires, adaptive-type immunity is the optimal defense strategy whereas in fluctuating environments with unpredictable virus composition, HGT dominates the immune landscape.}, }
@article {pmid40500700, year = {2025}, author = {Salem, S and Osama, D and Abdelsalam, NA and Shata, AH and Mouftah, SF and Elhadidy, M}, title = {Comparative genomics of Acinetobacter baumannii from Egyptian healthcare settings reveals high-risk clones and resistance gene mobilization.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {803}, pmid = {40500700}, issn = {1471-2334}, mesh = {*Acinetobacter baumannii/genetics/drug effects/isolation &amp; purification/classification ; Egypt/epidemiology ; Humans ; *Acinetobacter Infections/microbiology/epidemiology ; Anti-Bacterial Agents/pharmacology ; Pilot Projects ; Microbial Sensitivity Tests ; *Drug Resistance, Multiple, Bacterial/genetics ; Genomics ; Whole Genome Sequencing ; Virulence Factors/genetics ; Genome, Bacterial ; Gene Transfer, Horizontal ; Multilocus Sequence Typing ; beta-Lactamases/genetics ; Health Facilities ; Bacterial Proteins/genetics ; }, abstract = {BACKGROUND: Acinetobacter baumannii (A. baumannii) has emerged as a major public health threat in low- and middle-income countries (LMICs), particularly in Egypt, due to its remarkable ability to acquire and transfer resistance genes, as highlighted in the WHO bacterial Priority Pathogens List 2024 classification. This pilot study aimed to characterize 18 A. baumannii isolates from Egyptian healthcare settings, focusing on clonal lineages, antibiotic resistance determinants, horizontal gene transfer potential, and the presence of virulence factors and chromosomal mutations.<br><br>METHODS: Antimicrobial susceptibility testing was performed to determine resistance profiles using minimum inhibitory concentrations. Whole-genome sequencing was used to identify &#x3b2;-lactamase, carbapenemase, and other antibiotic resistance genes (ARGs), as well as mobile genetic elements (MGEs). Clonal relationships among isolates were assessed via core genome multilocus sequence typing (cgMLST).<br><br>RESULTS: Phenotypic analysis revealed that 72% of the isolates were extensively drug-resistant (XDR), exhibiting resistance to all tested antibiotics except colistin. Clonal diversity analysis identified 11 Oxford sequence types (STs), including two novel STs (ST3309[OXF] and ST3321[OXF]), and six international clonal (IC) groups, with IC2 being the most prevalent. Additionally, eight Pasteur STs were detected, with ST570[PAS] being the most frequent. The cgMLST analysis showed that two Egyptian ST570[PAS] isolates clustered with a strain from Saudi Arabia, suggesting potential regional transmission. Genomic analysis revealed the widespread dissemination of ARGs via MGEs, particularly rep plasmids and insertion sequence elements, which contributed significantly to genomic diversity and antibiotic resistance.<br><br>CONCLUSIONS: This pilot study highlights the clonal diversity of A. baumannii in Egypt and underscores the critical role of MGEs in the spread of resistance genes. Targeted genomic surveillance and infection control are essential to curb the spread of high-risk resistant A. baumannii clones in Egyptian clinical settings.}, }
@article {pmid40500303, year = {2025}, author = {Shang, KM and Ma, H and Elsheikha, HM and Wei, YJ and Zhao, JX and Qin, Y and Li, JM and Zhao, ZY and Zhang, XX}, title = {Comprehensive genome catalog analysis of the resistome, virulome and mobilome in the wild rodent gut microbiota.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {101}, pmid = {40500303}, issn = {2055-5008}, support = {No.32170538//the National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Genome, Bacterial ; Virulence Factors/genetics ; *Rodentia/microbiology ; *Bacteria/genetics/drug effects/classification/pathogenicity/isolation &amp; purification ; Interspersed Repetitive Sequences ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Animals, Wild/microbiology ; }, abstract = {Wild rodent's gut microbiota serves as a crucial reservoir of antibiotic resistance genes (ARGs), where antimicrobial-resistant bacteria interact with mobile genetic elements (MGEs) to facilitate horizontal gene transfer. This study analyzed 12,255 gut-derived bacterial genomes from wild rodents to characterize the distribution of ARGs and virulence factor genes (VFGs), and to identify their bacterial hosts. A total of 8119 ARGs and 7626 VFGs were identified. The most prevalent ARGs conferred resistance to elfamycin, followed by those associated with multi-class antibiotic resistance. Enterobacteriaceae, particularly Escherichia coli, harbored the highest numbers of ARGs and VFGs. A strong correlation between the presence of MGEs, ARGs, and VFGs was observed, highlighting the potential for co-selection and mobilization of resistance and virulence traits. These findings underscore the importance of expanded surveillance to monitor and mitigate the risk of transmission of resistant and potentially pathogenic bacteria from wild rodents to human and animal populations.}, }
@article {pmid40499773, year = {2025}, author = {Ma, Y and Dong, X and Sun, Y and Li, B and Ma, H and Li, H and Zhao, X and Ran, S and Zhang, J and Ye, Y and Li, J}, title = {Diversity and Functional Roles of Viral Communities in Gene Transfer and Antibiotic Resistance in Aquaculture Waters and Microplastic Biofilms.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126636}, doi = {10.1016/j.envpol.2025.126636}, pmid = {40499773}, issn = {1873-6424}, abstract = {This study presents a comprehensive metagenomic analysis of viral communities in seawater and microplastic biofilms, uncovering their diversity, functional roles, and ecological significance. We identified 4,999 DNA and 22 RNA viral operational taxonomic units. Seawater samples exhibited greater viral diversity, while microplastic biofilms harbored specialized viral assemblages with enriched metabolic functions, particularly in carbohydrate and amino acid metabolism. Auxiliary metabolic genes were detected, suggesting viral involvement in microbial metabolism and nutrient cycling. The dominance of lytic viruses (98 and 100%) indicates a significant role in microbial regulation. Moreover, antibiotic resistance genes and virulence factors were found, highlighting microplastic biofilms as potential re2servoirs for gene transfer, raising concerns about antibiotic resistance dissemination. The detection of Klebsiella pneumoniae OmpK37 in viruses further underscores the risk of horizontal gene transfer. These findings emphasize the ecological implications of virus-host interactions in marine environments and the urgent need for continued monitoring of viral dynamics in anthropogenically influenced ecosystems.}, }
@article {pmid40498454, year = {2025}, author = {Brezner, S and Garushyants, SK and Wolf, YI and Koonin, EV and Snir, S}, title = {Evolution of gene order in prokaryotes is driven primarily by gene gain and loss.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {24}, pages = {e2502752122}, doi = {10.1073/pnas.2502752122}, pmid = {40498454}, issn = {1091-6490}, support = {Intramural Research Program//HHS | NIH (NIH)/ ; 2021139.//US-Israel Binational Science Foundation/ ; }, mesh = {*Evolution, Molecular ; *Archaea/genetics ; *Gene Order ; Genome, Archaeal ; Genome, Bacterial ; Models, Genetic ; *Bacteria/genetics ; *Prokaryotic Cells/metabolism ; Gene Transfer, Horizontal ; *Gene Deletion ; }, abstract = {Evolution of bacterial and archaeal genomes is highly dynamic, including extensive gene gain via horizontal gene transfer (HGT) and gene loss as well as different types of genome rearrangements, such as inversions and translocations, so that gene order is not highly conserved even among closely related organisms. We sought to quantify the contributions of different genome dynamics processes to the evolution of the gene order in prokaryote genomes, relying on the recently developed, simple, stochastic model of genome rearrangement through single gene translocations ("jump" model). The jump model was completely solved analytically in our previous work and provides the exact distribution of syntenic gene block lengths (SBL) in compared genomes based on gene translocations alone. Comparing the SBL distribution predicted by the jump model with the distributions empirically observed for multiple groups of closely related bacterial and archaeal genomes, we obtained robust estimates of the genome rearrangement to gene flux (gain and loss) ratio. In most groups of bacteria and archaea, this ratio was found to be on the order of 0.1 indicating that the loss of synteny in the evolution of bacteria and archaea is driven primarily by gene gain and loss rather than by gene translocation.}, }
@article {pmid40497057, year = {2025}, author = {Mediouni, M and Diallo, AB and Makarenkov, V}, title = {Quantifying antimicrobial resistance in food-producing animals in North America.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1542472}, pmid = {40497057}, issn = {1664-302X}, abstract = {The global misuse of antimicrobial medication has further exacerbated the problem of antimicrobial resistance (AMR), enriching the pool of genetic mechanisms previously adopted by bacteria to evade antimicrobial drugs. AMR can be either intrinsic or acquired. It can be acquired either by selective genetic modification or by horizontal gene transfer that allows microorganisms to incorporate novel genes from other organisms or environments into their genomes. To avoid an eventual antimicrobial mistreatment, the use of antimicrobials in farm animal has been recently reconsidered in many countries. We present a systematic review of the literature discussing the cases of AMR and the related restrictions applied in North American countries (including Canada, Mexico, and the USA). The Google Scholar, PubMed, Embase, Web of Science, and Cochrane databases were searched to find plausible information on antimicrobial use and resistance in food-producing animals, covering the time period from 2015 to 2024. A total of 580 articles addressing the issue of antibiotic resistance in food-producing animals in North America met our inclusion criteria. Different AMR rates, depending on the bacterium being observed, the antibiotic class being used, and the farm animal being considered, have been identified. We determined that the highest average AMR rates have been observed for pigs (60.63% on average), the medium for cattle (48.94% on average), and the lowest for poultry (28.43% on average). We also found that Cephalosporines, Penicillins, and Tetracyclines are the antibiotic classes with the highest average AMR rates (65.86%, 61.32%, and 58.82%, respectively), whereas the use of Sulfonamides and Quinolones leads to the lowest average AMR (21.59% and 28.07%, respectively). Moreover, our analysis of antibiotic-resistant bacteria shows that Streptococcus suis (S. suis) and S. auerus provide the highest average AMR rates (71.81% and 69.48%, respectively), whereas Campylobacter spp. provides the lowest one (29.75%). The highest average AMR percentage, 57.46%, was observed in Mexico, followed by Canada at 45.22%, and the USA at 42.25%, which is most probably due to the presence of various AMR control strategies, such as stewardship programs and AMR surveillance bodies, existing in Canada and the USA. Our review highlights the need for better strategies and regulations to control the spread of AMR in North America.}, }
@article {pmid40495475, year = {2025}, author = {Wang, JY and Dunon, V and Ardevol, VN and Béguet, J and Jechalke, S and Pauwelyn, E and Lavigne, R and Smalla, K and Martin-Laurent, F and Springael, D}, title = {Dynamics of IS1071 and Its Accessory Gene Functions During Start-Up of an On-Farm Biopurification System.}, journal = {Environmental microbiology}, volume = {27}, number = {6}, pages = {e70120}, doi = {10.1111/1462-2920.70120}, pmid = {40495475}, issn = {1462-2920}, support = {222625//European Union's 7th Framework Programme (FP7) for Research and Technological Development/ ; RUN/19/001//KU Leuven/ ; C14/20/063//KU Leuven/ ; G0E8122N//the Research Foundation - Flanders (FWO) and the National Natural Science Foundation of China (NSFC)/ ; 202107650033//China Scholarship Council Fellowship/ ; }, mesh = {*DNA Transposable Elements/genetics ; *Microbiota/genetics ; *Pesticides/metabolism ; *Bacteria/genetics/metabolism/classification ; Wastewater/microbiology ; Farms ; Biodegradation, Environmental ; Betaproteobacteria/genetics/metabolism ; }, abstract = {Insertion sequences (IS) are drivers of bacterial diversification by facilitating recruitment and horizontal transfer of adaptive genes involving composite transposon structures, but their evolutionary role at the community level is rarely addressed. This study explores the dynamics of IS1071 and the cargo of IS1071-associated putative composite transposons in the establishment of a pesticide-degrading microbiome in an on-farm biopurification system (BPS)-which treats pesticide-contaminated wastewater and is considered a hotspot of microbial evolution-during the crucial start-up phase. Pesticide mineralisation assays and quantitative PCR targeting pesticide catabolic genes showed that the microbial community, upon feeding on the pesticide-contaminated wastewater, rapidly evolved into a pesticide-degrading microbiome. Concomitantly, an increase in the relative abundances of several mobile genetic elements, including IS1071, was observed, as well as a striking enrichment of xenobiotic catabolic genes in the cargo of putative IS1071-flanked composite transposons. The IS1071 cargo catabolic genes diversified over time and were mainly of Betaproteobacterial origin. Clear changes in community composition were observed both in the total bacterial community and the Betaproteobacterial community. We conclude that IS1071 supports the rapid establishment of pesticide catabolism in the BPS microbiome, highlighting the contribution of IS elements to microbial community adaptation to environmental changes.}, }
@article {pmid40494306, year = {2025}, author = {Slot, J and Hoffmeister, D}, title = {Psychedelic fungi.}, journal = {Current biology : CB}, volume = {35}, number = {11}, pages = {R513-R518}, doi = {10.1016/j.cub.2025.02.026}, pmid = {40494306}, issn = {1879-0445}, mesh = {*Hallucinogens/metabolism ; *Fungi/metabolism/genetics ; Humans ; Psilocybin/metabolism ; Animals ; }, abstract = {Several species of fungi, collectively known as 'psychedelic fungi', produce a range of psychoactive substances, such as psilocybin, ibotenic acid, muscimol and lysergic acid amides. These substances interact with neurotransmitter receptors in the human brain to induce profound psychological effects. These substances are found across multiple fungal phyla, in the mushroom-forming genera Psilocybe, Amanita, and others, and also the ergot-producing Claviceps and insect-pathogenic Massospora. The ecological roles of these psychedelics may include deterring predators or facilitating spore dispersal. Enzymes for psychedelic compound biosynthesis are encoded in metabolic gene clusters that are sometimes dispersed by horizontal gene transfer, resulting in a patchy distribution of psychedelics among species. The (re-)emerging science of these strange substances creates new opportunities and challenges for science and humanity at large.}, }
@article {pmid40493666, year = {2025}, author = {Gumustop, I and Genel, I and Kurt, IC and Ortakci, F}, title = {Comparative genomics of Lentilactobacillus buchneri reveals strain-level hyperdiversity and broad-spectrum CRISPR immunity against human and livestock gut phages.}, journal = {PloS one}, volume = {20}, number = {6}, pages = {e0325832}, pmid = {40493666}, issn = {1932-6203}, mesh = {Animals ; Humans ; *Bacteriophages/genetics/immunology ; *Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Genomics ; Livestock/microbiology/virology ; Cattle ; Genome, Bacterial ; Plasmids/genetics ; Prophages/genetics ; }, abstract = {This study conducted a comparative genomic investigation of 40 strains of Lentilactobacillus buchneri isolated from various environments-including fermented foods, silage, cattle rumen, and the nasopharynx-to identify species-level diversity and assess their CRISPR immunity. An average genome size of 2.55 ± 0.07 Mb, a GC content of 44.18 ± 0.15%, and 2444 ± 83 coding sequences were identified. Prophages were found in all strains except for two, while 17 strains contained plasmids. No genes associated with bacteriocins were identified. CRISPR analysis revealed the presence of 42 Type II-A and 45 Type I-E systems, with each strain having at least one Type II-A system (~ 2 systems per strain). Among the 33 tested strains, 29 encoded complete LbCas9 proteins, consisting of 1371 amino acids. In-silico analysis of PAM in Type II-A systems revealed a 5'-DNAWDHV-3' motif, with a noted preference for 5'-AAAA-3' at positions 3-6. The spacers found in CRISPR arrays targeted proteins involved in plasmid mobilization as well as components of phage tails, indicating their roles in inhibiting horizontal gene transfer and providing defense against phages. Remarkably, 27 spacers from 24 strains were found to match phages associated with human gut microbiomes, with several showing the ability to cross-target phages from livestock, kefir, and wastewater. This research expands the genomic understanding of L. buchneri from 10 to 40 genomes, uncovering the dynamics of CRISPR-phage co-evolution. The defined PAM preferences of the identified CRISPR systems, together with the broad predicted target range of their spacers, highlight their potential for biotechnological applications-most notably targeted CRISPRization of L. buchneri strains and in-silico-guided phage control during fermentation. These findings deepen our understanding of the ecological adaptability of L. buchneri and provide a foundation for future industrial exploitation of its native CRISPR immunity.}, }
@article {pmid40353659, year = {2025}, author = {Sobkowiak, A and Schwierzeck, V and van Almsick, V and Scherff, N and Schuler, F and Bessonov, K and Robertson, J and Harmsen, D and Mellmann, A}, title = {The dark matter of bacterial genomic surveillance-antimicrobial resistance plasmid transmissions in the hospital setting.}, journal = {Journal of clinical microbiology}, volume = {63}, number = {6}, pages = {e0012125}, doi = {10.1128/jcm.00121-25}, pmid = {40353659}, issn = {1098-660X}, support = {SEED 019/23//Interdisciplinary Center of Clinical Research, University Muenster/ ; NUM 2.0 Grant No. 01KX2121 Project: Collateral Effects of Pandemics - CollPan//German Federal Ministry of Education and Research (BMBF) Network of University Medicine 2.0/ ; }, mesh = {*Plasmids/genetics ; Humans ; Multilocus Sequence Typing ; *Drug Resistance, Multiple, Bacterial/genetics ; Whole Genome Sequencing ; Tertiary Care Centers ; Anti-Bacterial Agents/pharmacology ; *Cross Infection/microbiology/epidemiology/transmission ; *Gram-Negative Bacteria/genetics/drug effects/isolation &amp; purification ; Genome, Bacterial ; *Gram-Negative Bacterial Infections/microbiology/epidemiology/transmission ; Gene Transfer, Horizontal ; Hospitals ; Molecular Epidemiology ; Microbial Sensitivity Tests ; }, abstract = {UNLABELLED: Dissemination of antimicrobial resistance (AMR) is a growing global public health burden. The aim of this study was to characterize AMR plasmid transmissions within a tertiary care hospital and identify relevant AMR plasmid transmission pathways. During an 18-month observation period, 540 clinical gram-negative multidrug-resistant bacterial (MDRB) isolates were collected during routine hospital surveillance and subjected to Pacific Biosciences long-read whole genome sequencing. Potential clonal transmissions were determined based on core genome multilocus sequence typing (cgMLST), and plasmid transmissions were detected using a novel real-time applicable tool for plasmid transmission detection. Potential transmissions were validated using epidemiological data. Among the 471 eligible MDRB isolates, we detected 1,539 plasmids; 84.41% of these were circularized. We identified 38 potential clonal transmissions in 24 clusters based on cgMLST and 121 potential plasmid transmissions in 24 clusters containing genetically related AMR plasmids. Among the latter clusters, 10 contained different multilocus sequence types (involving 2-38 isolates, median: 3 isolates), and nine contained multiple species (2-18 isolates, median: 4). Epidemiological data confirmed 19 clonal transmissions (in seven clusters) and an additional 12 plasmid transmissions (within eight plasmid clusters). Among these, we identified seven cases of intra-host and five patient-to-patient plasmid transmissions. We demonstrate that intra-host and patient-to-patient transmissions of AMR plasmids can be identified by combining long-read sequencing with real-time applicable tools during routine molecular surveillance. In addition, our study highlights that more than a decade of bacterial genomic surveillance missed at least one-third of all AMR transmission events due to plasmids.<br><br>IMPORTANCE: Antimicrobial resistance (AMR) poses a significant threat to human health. Most AMR determinants are encoded extra-chromosomally on plasmids. Although current infection control strategies primarily focus on clonal transmission of multidrug-resistant bacteria, until today, AMR plasmid transmission routes are neither understood nor analyzed in the hospital setting. In our study, we simultaneously determined both clonal, that is, based on chromosomes, and AMR plasmid transmissions during routine molecular surveillance by combining long-read sequencing with a novel real-time applicable software tool and validated all potential transmission events with epidemiological data. Our analysis determined not only the yet unknown plasmid transmissions within healthcare facilities or within the community but also resulted, in addition to the clonal transmissions, in at least a third more transmissions due to AMR plasmids.}, }
@article {pmid40315481, year = {2025}, author = {Ottenbrite, M and Yilmaz, G and Chan, M and Devenish, J and Kang, M and Dan, H and Lau, C and Capitani, S and Carrillo, C and Bessonov, K and Nash, J and Topp, E and Guan, J}, title = {Food-borne microbes influence conjugative transfer of antimicrobial resistance plasmids in pre-disturbed gut microbiome.}, journal = {Canadian journal of microbiology}, volume = {71}, number = {}, pages = {1-11}, doi = {10.1139/cjm-2024-0168}, pmid = {40315481}, issn = {1480-3275}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/genetics ; Mice ; *Conjugation, Genetic ; *Plasmids/genetics ; Anti-Bacterial Agents/pharmacology ; Salmonella typhimurium/genetics/drug effects ; *Gene Transfer, Horizontal ; Feces/microbiology ; Bacteria/genetics/drug effects ; Female ; Food Microbiology ; Streptomycin/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Drug Resistance, Bacterial ; }, abstract = {Ingestion of antibiotic-resistant bacteria following antibiotic treatments may lead to the transfer of antimicrobial resistance genes (ARGs) within a disturbed gut microbiota. However, it remains unclear whether and how microbes present in food matrices influence ARG transfer. Thus, a previously established mouse model, which demonstrated the conjugative transfer of a multi-drug resistance plasmid (pIncA/C) from Salmonella Heidelberg (donor) to Salmonella Typhimurium (recipient), was used to assess the effects of food-borne microbes derived from fresh carrots on pIncA/C transfer. Mice were pre-treated with ampicillin, streptomycin, sulfamethazine, or left untreated as a control to facilitate bacterial colonization. Contrary to previous findings where high-density colonization of the donor and recipient bacteria occurred in the absence of food-borne microbes, the presence of these microbes resulted in a low abundance of S. Typhimurium and no detection of S. Typhimurium transconjugants in the fecal samples from any of the mice. However, in mice pre-treated with streptomycin, a significant reduction in microbial species richness allowed for the significant enrichment of Enterobacteriaceae and pIncA/C transfer to bacteria from the genera Escherichia, Enterobacter, Citrobacter, and Proteus. These findings suggest that food-borne microbes may enhance ARG dissemination by influencing the population dynamics of bacterial hosts within a pre-disturbed gut microbiome.}, }
@article {pmid40492734, year = {2025}, author = {Samadi, ZF and Hodroj, ZR and Jabbour, ZC and Hussein, HM and Kurdi, A and Shoukair, D and Bitar, RF and Chebaro, HH and Al Semaani, JMJ and Al Hajjar, MT and Zeaiter, HH and Hamadeh, L and Mahfouz, R and Noueihed, LH and Hachem, JH and Khalil, MI and El Hajj, R and Matar, GM and Abou Fayad, AG}, title = {Nationwide surveillance of carbapenem-resistant Gram-negative pathogens in the Lebanese environment.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0193224}, doi = {10.1128/aem.01932-24}, pmid = {40492734}, issn = {1098-5336}, abstract = {UNLABELLED: Gram-negative ESKAPE pathogens with carbapenem resistance pose a significant health threat. Despite extensive research on the spread of these pathogens within Lebanese hospital settings, their emergence in environmental settings remains understudied. This study aimed to explore the environmental spread of carbapenem resistance among Gram-negative bacteria isolated from environmental samples in nine districts across Lebanon. A total of 250 samples were collected from wild animals, sewage, water, and soil between June 2022 and September 2023. Samples were streaked on MacConkey agar plates supplemented with 2 mg/L meropenem. Bacterial species were identified primarily using API20E. Antimicrobial susceptibility profiles were determined by the disk diffusion method and the Vitek 2 compact system. Meropenem-resistant Gram-negative bacteria were further characterized by whole-genome sequencing, and each of the bacterial species, sequence types, resistance genes, and plasmids was detected by sequence data analysis. We successfully isolated 130 carbapenem-resistant isolates from various samples, 67 of which belonged to the ESKAPE pathogens list and showed a multidrug-resistant (MDR) profile. The distribution of the latter was as follows: Escherichia coli (65.67%), Acinetobacter baumannii (16.42%), Pseudomonas aeruginosa (11.94%), and Klebsiella pneumoniae (5.97%). Several carbapenem resistance genes were detected, with a prevalence of blaNDM-5 in Escherichia coli and Klebsiella pneumoniae, blaIMP-1 and mexAB-OprM efflux pumps in Pseudomonas aeruginosa, and blaOXA-23 in Acinetobacter baumannii. Our findings revealed a widespread distribution of carbapenem-resistant ESKAPE bacteria in Lebanon, underscoring the significant public health risk posed by these pathogens. This highlights the urgent need to address the dissemination of antibiotic resistance in Lebanese environmental settings.<br><br>IMPORTANCE: The emergence of antimicrobial resistance (AMR) extremely burdens public health and increases morbid and mortal threats in Lebanon. While the majority of the studies in our country target antimicrobial resistance in clinical settings, fewer studies focus on antimicrobial resistance dissemination in the environment. The significance of our research is that it sheds light on the environment as a less explored yet equally crucial sector in the spread of AMR. Here, we isolated carbapenemase-producing bacteria (Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii) that were categorized as multidrug resistant (MDR) from diverse environmental sources in multiple provinces across Lebanon. The finding of carbapenem-resistant bacteria carrying plasmids represents a potential risk due to the possible spread of resistance genes via horizontal gene transfer across the environment and hospital settings. This highly recommends the implementation of regular surveillance to monitor the spread of antimicrobial resistance among environmental bacteria, which consequently leads to its spread within communities and thus poses a great threat to human health.}, }
@article {pmid40492084, year = {2025}, author = {Vezina, B and Morampalli, BR and Nguyen, HA and Gomez-Simmonds, A and Peleg, AY and Macesic, N}, title = {The rise and global spread of IMP carbapenemases (1996-2023): a genomic epidemiology study.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.05.25.25328332}, pmid = {40492084}, abstract = {BACKGROUND: IMP carbapenemases confer extensive drug resistance and are increasingly noted worldwide. Despite this, little is known regarding the global epidemiology of IMP carbapenemases.<br><br>METHODS: We comprehensively identified bla IMP genes in all publicly available bacterial genomes, then systematically analysed the distribution of variants across species, lineages, plasmids and mobile elements, examining patterns over time, across geographic regions and by source. Structural analysis of IMP variants was performed.<br><br>FINDINGS: 4,556 bla IMP -containing genomes were identified from 1996-2023, including 52 bla IMP variants across 93 bacterial species. Key variants (bla IMP-1 , bla IMP-4 , bla IMP-7 , bla IMP-8 and bla IMP-13) achieved global endemicity, while bla IMP-26 and bla IMP-27 were regionally endemic in Southeast Asia and North America, respectively. bla IMP dissemination was driven by horizontal gene transfer, facilitating inter-species spread. Proliferation of multidrug-resistant Enterobacter hormaechei , Pseudomonas aeruginosa and Klebsiella pneumoniae lineages led to local outbreaks. Dereplication removed 3,175/4,556 (69.9%) genomes, indicating that most bla IMP -containing genomes were highly related. bla IMP variants were associated with mobile genetic element combinations including class 1 integrons and insertion sequences (99.7%), aiding mobilisation into &#x2265;52 plasmid clusters, predominantly IncHI2A, IncN, IncL/M and IncC. Genomes of environmental and animal origin accounted for 10.0% and 1.1% of the dataset, respectively. Evidence of cross-source transmission was limited, with most spillover occurring between genomes of human and environmental origin. Structural analysis revealed a conserved carbapenemase structure (mean lDDT 0.977), with convergent missense mutations at seven catalytically relevant sites.<br><br>INTERPRETATION: Global analysis enabled us to historically reconstruct the emergence and variant-specific epidemiologies of bla IMP carbapenemase genes. Intersecting mobile elements enabled bla IMP genes to spread across multiple plasmids and bacterial genera, facilitating global and multi-source spread within a One Health framework. Additionally, convergent evolutionary patterns indicate that IMP variants may continue evolving, potentially evading novel beta-lactam antimicrobial agents.<br><br>FUNDING: NHMRC EL1 (APP1176324) to N.M.; NHMRC PF (APP1117940) to A.Y.P.; NIH/NIAID R01AI175414 to A.G-S.<br><br>RESEARCH IN CONTEXT PANEL: Evidence before this study: Despite being a major cause of carbapenem resistance in Gram negative infections, little is known about the global epidemiology of IMP carbapenemases. IMP carbapenemases are metallo-beta-lactamases that were first identified in 1991 and have evolved into 96 different IMP variants. On May 21 2025, we searched all published reports available in PubMed using the terms "'IMP' and 'carbapenemase' genomics NOT (Review[Publication Type]) NOT (Case Reports[Publication Type]) NOT PCR" with no language restrictions and no publication date restrictions. We identified 223 articles, 62 and 121 of which reported single species or a single study centre/country, respectively. Only 6 articles employed genomics to examine multi-species and multi-geographical isolates, though this was in the context of carbapenem resistance more broadly rather than IMP carbapenemases specifically. The most relevant study included 38 globally distributed genomes across four species and tracked seven blaIMP variants across mobile genetic elements.Added value of this study: To our knowledge, this global characterisation provides the most comprehensive account of bla IMP carbapenemase gene epidemiology. To analyse the global distribution and diversity of bla IMP genes, we compiled all available public genome data resulting in a dataset of 4,646 genomes. This has allowed us to identify local, regional and international spread of bla IMP variants and determine the contributions of clonal expansion, plasmid proliferation and co-localised mobile genetic elements. We demonstrated that key bla IMP variants display global (IMP-1, IMP-4, IMP-7, IMP-8 and IMP-13) and regional (IMP-26 within Southeast Asia and IMP-27 within North America) endemicity and that these patterns have been previously unacknowledged, reframing the previous understanding that IMP carbapenemases were largely confined to the Asia-Pacific region. Our observation of convergent evolutionary patterns raise concern that IMP variants may continue to evolve, potentially evading new &#x3b2;-lactam antimicrobials. This analysis has revealed the under-recognised contribution IMP carbapenemases make to global carbapenem resistance. Implications of all the available evidence: These findings provide the first comprehensive atlas of bla IMP carbapenemase gene dissemination and underscore the silent global spread of IMP carbapenemases. We note the critical need for enhanced surveillance systems, particularly in low- and middle-income countries, that can detect complex plasmid-mediated and mobile genetic element-associated spread, as we noted with bla IMP carbapenemase genes. Moreover, our analyses show that systematic sampling across human, animal, and environmental reservoirs is crucial to address the One Health dimensions of emerging antimicrobial resistance threats. The study provides a framework for future interventions aimed at tracking and stopping the spread of IMP carbapenemases and calls for co-ordinated, real-time public health responses to this growing challenge.}, }
@article {pmid40490413, year = {2025}, author = {Gang, D and Li, Z and Yu, H and Hu, C and Qu, J}, title = {PFAS Stress on Functional Expression of Periphyton Communities and Trade-off Strategies for Horizontal/Vertical Transfer of Resistance Genes.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c02692}, pmid = {40490413}, issn = {1520-5851}, abstract = {The dissemination of antibiotic resistance genes (ARGs) induced by perfluoroalkyl and polyfluoroalkyl substances (PFAS) and their ecological impacts have gained significant attention. Periphyton communities on sediments play crucial hydroecological roles and serve as bioindicators of PFAS contamination. However, research on their microbial structure and ARG dissemination in response to PFAS remains limited. This study explored how PFAS stress influences periphyton communities' ecological functions and ARGs dynamics. PFAS varying exposure inhibited communities' formation by decreasing biomass (3.0-26.2%) and significantly reducing protein and polysaccharides (p < 0.05) of periphyton communities. Methanogenic archaea abundance increased by 4.79-159290 times, while Variovorax and Nitrospira decreased by 1266.1-2303.5 and 36.1-140.4 times, respectively. Notably, PFAS enhanced ARGs families (multidrug, aminoglycoside, and glycopeptide) and subtypes (macB, evgS, tetA58, and bcrA), strengthening correlations between the mobile genetic elements (MGEs) and antibiotic efflux (R[2] = 0.941) or target alteration (R[2] = 0.961). Horizontal gene transfer (HGT) mediated by MGEs played a dominant role in ARGs dissemination compared to vertical gene transfer in periphyton communities. Mechanistic insights revealed that PFAS-induced reactive oxygen species elevation, increased membrane permeability, enhanced energy provision, and overexpression of adherent molecular genes collectively facilitated HGT-driven ARGs spread. This study provides new insights into the complex interactions between PFAS and ARGs and its potential risks in microbial habitats.}, }
@article {pmid40488491, year = {2025}, author = {Franco, MEE and Nickerson, MN and Bowen, BP and Louie, K and Northen, TR and U'Ren, JM}, title = {Hyperdiverse, bioactive, and interaction-specific metabolites produced only in co-culture suggest diverse competitors may fuel secondary metabolism of xylarialean fungi.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0046825}, doi = {10.1128/msystems.00468-25}, pmid = {40488491}, issn = {2379-5077}, abstract = {Xylariales is one of the largest and most ecologically diverse fungal orders that is well-known for its chemical diversity. Enhanced secondary metabolism of Xylariales taxa is associated with increased gene duplication and horizontal gene transfer (HGT) of biosynthetic gene clusters (BGCs), especially in generalist taxa with both greater saprotrophic abilities and broader host ranges as foliar endophytic symbionts. Thus, one hypothesis for BGC diversification among more generalist fungi is that diverse competitive interactions-in both their free-living and symbiotic life stages with many hosts-may exert selective pressure for HGT and a diverse metabolic repertoire. Here, we used untargeted metabolomics to examine how competition (pairwise co-cultures) between seven xylarialean fungi influenced their metabolite production. Of the >9,000 total features detected, 6,115 and 2,071 were over-represented in co-cultures vs monocultures, respectively. For each strain, each additional co-culture interaction resulted in an 11- to 14-fold increase in metabolite richness compared to monocultures, reflecting the limited amount of metabolite overlap among different co-culture combinations. Phylogenetic relatedness and BGC content did not impact the diversity of metabolites produced in co-culture; however, co-cultures between more ecologically distinct fungi elicited the strongest metabolic response. Overall, the diversity, specificity, and putative bioactivity of metabolites over-represented in co-culture support the role of widespread and diverse competitive fungal interactions to drive xylarialean metabolic diversification. Additionally, as fungal-produced plant hormones were only detected in co-culture, our results reveal the potential for in planta interactions among fungal endophytes to influence the host plant.IMPORTANCESaprotrophic and endophytic xylarialean fungi are among the most prolific producers of bioactive secondary metabolites, with numerous industrial uses as antibiotics, pharmaceuticals, and insecticidal toxins. Fungal secondary metabolites are typically encoded in biosynthetic gene clusters (sets of physically clustered genes), but the products of most clusters are unknown as the genes are not active in typical culture conditions. Co-cultures can help to "turn on" fungal secondary metabolite production, yet factors that can influence co-culture outcomes are largely unknown. Here, we used untargeted metabolomics to assess how differences in genomic content, ecology, and phylogenetic relatedness among seven diverse xylarialean fungal strains impact metabolic production in co-culture. As expected, co-culturing significantly increased metabolite diversity, as well as the abundance of putatively bioactive metabolites. Each new pairwise combination produced different metabolites, indicative of strain-specific responses to competitors. This new information will enable further characterization of the immense biotechnological potential of xylarialean fungi.}, }
@article {pmid40485081, year = {2025}, author = {Tran, V and Langschied, F and Muelbaier, H and Dosch, J and Arthen, F and Balint, M and Ebersberger, I}, title = {Feature architecture-aware ortholog search with fDOG reveals the distribution of plant cell wall-degrading enzymes across life.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msaf120}, pmid = {40485081}, issn = {1537-1719}, abstract = {The decomposition of plant material is a key driver of the global carbon cycle, traditionally attributed to fungi and bacteria. However, some invertebrates also possess orthologs to bacterial or fungal cellulolytic enzymes, likely acquired via horizontal gene transfer. This reticulated mode of evolution necessitates ortholog searches in large taxon sets to comprehensively map the repertoire of plant cell wall degrading enzymes (PCDs) across the tree of life, a task surpassing capacities of current software. Here, we use fDOG, a novel profile-based ortholog search tool to trace 235 potential PCDs across more than 18,000 taxa. fDOG allows to start the ortholog search from a single protein sequence as a seed, it performs on par with state-of-the-art software that require the comparison of entire proteomes, and it is unique in routinely scoring protein feature architecture differences between the seed protein and its orthologs. Visualizing the presence-absence patterns of PCD orthologs using a UMAP highlights taxa where recent changes in the enzyme repertoire indicate a change in lifestyle. Three invertebrates have a particularly rich set of PCD orthologs encoded in their genome. Only few of the orthologs show differing protein feature architectures relative to the seed that suggest functional modifications. Thus, the corresponding species represent lineages within the invertebrates that may contribute to the global carbon cycle. This study shows how fDOG can be used to create a multi-scale view on the taxonomic distribution of a metabolic capacity that ranges from tree of life-wide surveys to individual feature architecture changes within a species.}, }
@article {pmid40473141, year = {2025}, author = {Luo, Y and Liao, H and Wu, L and Wu, M and Luo, Y and Yao, Y and Ji, W and Gao, L and Xia, X}, title = {Temperature adaptability drives functional diversity and horizontal gene transfer within microbial communities in Daqu solid-state fermentation.}, journal = {Bioresource technology}, volume = {433}, number = {}, pages = {132770}, doi = {10.1016/j.biortech.2025.132770}, pmid = {40473141}, issn = {1873-2976}, abstract = {The spontaneous solid-state fermentation of high-temperature Daqu (HTD) is a temperature-dependent stacking bioprocessing for enriching microbiota and enzymes to guarantee efficient substrate utilization and fermentation. However, there is a lack of clarity regarding how temperature adaptability affects HTD microbial assembly, domestication direction, and metabolic profile. Here, the flavor substances, microbial assembly, metabolic network, and horizontal gene transfer (HGT) events of three HTDs from Renshu (RS), Jiushang (JS), and Maoyuan (MY) were analyzed. 125 volatile compounds were identified, tetramethylpyrazine, 3-methyl-butanoic acid, phenylethyl alcohol, and trimethylpyrazine were clarified as the typical flavor substances. Bacillus and Kroppenstedtia were the shared dominant bacterial genera. Paecilomyces, Aspergillus, Rasamsonia, and Lichtheimia were dominant fungal genera. Differences in flavor metabolism, microbial structure, and key enzyme metabolism are strongly correlated with sample distance. As proximity decreases, the microbial structural and functional metabolic traits tend to exhibit greater similarity. The frequency of HGT events was analyzed using MetaCHIP, 49, 9 and 69 groups of HGT events occurred in RS, JS, and MY, respectively. HGT events occurred most abundantly in Bacillaceae, and the microbial taxa with a closer phylogenetic relationship possessed the highest incidence of HGT. Specifically, the occurrence of HGT was mainly associated with high-temperature adaptability. It was also linked to characteristic flavor metabolism. Our results revealed the effects of temperature stress on microbial regulation of HTD and adaptive transfer of relevant genes in stacked fermented HTDs. This work provides important insights into HTD quality classification and regulation of solid-state fermentation quality and efficiency through microbial domestication.}, }
@article {pmid40473138, year = {2025}, author = {Wang, F and Li, Y and Zhang, L and Su, Y and Zhang, Y and Hong, S and Zhan, M and Xie, B}, title = {Biochar alleviates adverse effects of polystyrene microplastics on anaerobic digestion performance of food waste and antibiotic resistance gene propagation.}, journal = {Bioresource technology}, volume = {434}, number = {}, pages = {132771}, doi = {10.1016/j.biortech.2025.132771}, pmid = {40473138}, issn = {1873-2976}, abstract = {This study systematically evaluated the efficacy of feedstock-derived biochars (maize straw, rice husk, bamboo) in mitigating polystyrene microplastic (PSMP)-induced inhibition of food waste anaerobic digestion performance and antibiotic resistance gene (ARG) dissemination. Biochar addition increased cumulative methane production by 4.3%-8.3% and reduced total ARG absolute abundance by 35.5%-72.1%. Maize straw-derived biochar demonstrated superior mitigation capacity, attributed to its elevated specific surface area, functional group density, and electrical conductivity compared to other biochar. Mechanistically, biochar alleviated PSMP-induced inhibition of organic conversion and acid accumulation through metabolic pathway enhancement. Biochar enhanced methanogenesis by facilitating direct interspecies electron transfer and enriching diverse methanogenic archaea, thereby promoting metabolic pathway diversification. Additionally, biochar reduced ARG abundance through direct adsorption, reactive oxygen species suppression, selective inhibition of potential host bacteria, and horizontal gene transfer interference. This study confirmed that biochar addition simultaneously mitigates PSMP-induced suppression of methanogenesis and ARG propagation while elucidating the underlying mechanisms.}, }
@article {pmid40472788, year = {2025}, author = {Lunde, TM and Tansirichaiya, S and Xue, Y and Al-Haroni, M}, title = {Evolutionary dynamics of Tn916 in Streptococcus oralis: Fitness cost and persistent metabolic shifts post-acquisition.}, journal = {Archives of oral biology}, volume = {177}, number = {}, pages = {106317}, doi = {10.1016/j.archoralbio.2025.106317}, pmid = {40472788}, issn = {1879-1506}, abstract = {OBJECTIVES: The acquisition and transfer of mobile genetic elements (MGEs) are major drivers of antibiotic resistance in bacterial populations. Despite the fitness cost associated with the acquisition of MGEs, the mechanisms underlying their persistence remain poorly understood. This study investigates the evolutionary dynamics of the integrative conjugative element (ICE) Tn916 in a naïve Streptococcus oralis host, focusing on growth rates and metabolic activity.<br><br>METHODS: We tracked the evolutionary trajectory of Tn916 in S. oralis by monitoring changes in growth rates and maximum metabolic activities over 1000 generations. Comparative analyses were conducted between Tn916-free and Tn916-carrying populations to assess fitness cost and evolutionary adaptations.<br><br>RESULTS: Following Tn916 integration, the S. oralis host exhibited a significant initial fitness cost, characterized by reduced growth rates and maximum metabolic activity. However, within 500 generations, the fitness cost was mitigated, and by 1000 generations, evolved Tn916- transconjugant populations outcompeted their unevolved counterparts. Despite the restoration of growth rates, a persistent reduction in maximum metabolic rate was observed, suggesting resource reallocation favoring growth and ICE maintenance.<br><br>CONCLUSION: The acquisition of Tn916 imposes initial fitness cost on S. oralis, but the cost is rapidly mitigated through evolution, leading to competitive advantages in the long term. However, the persistence of lower maximum metabolic rate indicates that Tn916 acquisition affects cellular functions beyond growth, underscoring the need to monitor metabolic activity to fully understand the impact of horizontal gene transfer, MGEs, and ICEs on bacterial populations.}, }
@article {pmid40471191, year = {2025}, author = {Ramirez, P and Martinez Montoya, H and Aramayo, R and Mateos, M}, title = {Diverse toxin repertoire but limited metabolic capacities inferred from the draft genome assemblies of three Spiroplasma (Citri clade) strains associated with Drosophila.}, journal = {Microbial genomics}, volume = {11}, number = {6}, pages = {}, doi = {10.1099/mgen.0.001408}, pmid = {40471191}, issn = {2057-5858}, mesh = {Animals ; *Drosophila/microbiology ; Phylogeny ; *Spiroplasma/genetics/metabolism/classification ; *Genome, Bacterial ; *Bacterial Toxins/genetics/metabolism ; Symbiosis ; }, abstract = {Spiroplasma (class Mollicutes) is a diverse wall-less bacterial genus whose members are strictly dependent on eukaryotic hosts (mostly arthropods and plants), with which they engage in pathogenic to mutualistic interactions. Spiroplasma are generally fastidious to culture in vitro, especially those that are vertically transmitted by their hosts, which include flies in the genus Drosophila. Drosophila has been invaded by at least three independent clades of Spiroplasma: Poulsonii (the best studied, contains reproductive manipulators and defensive mutualists associated with two major clades of Drosophila and has amongst the highest substitution rates within bacteria), Citri (restricted to the repleta group of Drosophila) and Ixodetis. We report the first genome drafts of Drosophila-associated Citri clade Spiroplasma: strain sMoj from Drosophila mojavensis, strain sAld-Tx from Drosophila aldrichi from Texas (newly discovered; also associated with Drosophila mulleri) and strain sHy2 from Drosophila hydei (the only Drosophila species known to naturally also harbour a Poulsonii clade strain, thereby providing an arena for horizontal gene transfer). Compared to their Poulsonii clade counterparts, we infer that the three Citri clade strains have the following: (1) equal or worse DNA repair abilities; (b) more limited metabolic capacities, which may underlie their comparatively lower titres and transmission efficiency; and (c) similar content of toxin domains, including at least one ribosome-inactivating protein, which is implicated in the Poulsonii-conferred defence against natural enemies. As a byproduct of our phylogenomic analyses and exhaustive search for certain toxin domains in public databases, we document the toxin repertoire in close relatives of Drosophila-associated Spiroplasma, and in a very divergent newly discovered lineage (i.e. 'clade X'). Phylogenies of toxin-encoding genes or domains imply substantial exchanges between closely and distantly related strains. Surprisingly, despite encoding several toxin genes and achieving relatively high prevalences in certain natural populations (sAld-Tx in this study; sMoj in prior work), fitness assays of sMoj (this study) and sAld-Tx (prior work) in the context of wasp parasitism fail to detect a beneficial effect to their hosts. Thus, how Citri clade strains persist in their Drosophila host populations remains elusive.}, }
@article {pmid40471045, year = {2025}, author = {Hayward, C and Whiley, H and Ashbolt, NJ}, title = {The plumbing problem: rising antimicrobial resistance in building water systems.}, journal = {Current opinion in infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1097/QCO.0000000000001119}, pmid = {40471045}, issn = {1473-6527}, abstract = {PURPOSE OF REVIEW: This review examines the interplay between biological and anthropogenic factors in the development and persistence of antimicrobial resistance (AMR) within building plumbing systems, which is of particular concern in high risk setting such as healthcare facilities. The review highlights the role of biofilms and amoeba as reservoirs for AMR and explores how engineering and design decisions, governance structures, and cleaning protocols influence microbial resistance dynamics.<br><br>RECENT FINDINGS: Biofilms provide a protective environment that facilitates horizontal gene transfer and enhances bacterial resistance to disinfection. Amoeba-hosted bacteria can evade standard cleaning practices, further promoting AMR persistence. Emerging technologies, such as digital twin modelling, offer new opportunities to optimize risk mitigation strategies. However, more consideration is needed to be given to design or management decision that may have unintended consequences, such as unintended design outcomes, such as increased biofilm growth from tap mixers and low-flow fixtures, and ineffective cleaning protocols, which can inadvertently worsen AMR.<br><br>SUMMARY: Effectively managing AMR in plumbing systems requires a multidisciplinary approach that integrates microbiology, engineering, and policy. Data driven risk assessments can identify high-risk areas that may require design changes but also can enable targeted cleaning strategies, reducing reliance on widespread disinfection that may drive resistance. Future policies must consider system-wide implications to prevent unintended consequences. By addressing both biological and anthropogenic drivers, we can develop sustainable solutions to mitigate AMR risks in healthcare and beyond.}, }
@article {pmid40468151, year = {2025}, author = {Pourrostami Niavol, K and Bordoloi, A and McKelvey, S and Suri, RPS}, title = {How does food waste to municipal sludge ratio affect anaerobic digestion: performance evaluation and fate of antibiotic resistance genes.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {40468151}, issn = {1614-7499}, abstract = {Anaerobic co-digestion of food waste (FW) and sewage sludge (SS) has shown superior performance over anaerobic mono-digestion. However, the fate of antibiotic resistance genes (ARGs) under various co-digestion ratios has been rarely reported to date. Thus, this study investigates the effects of FW:SS ratios on the digester's performance and the fate of ARGs at different FW:SS ratios. The results demonstrated that at a 50:50 FW:SS ratio, 738 mL.g[-1] VS of biogas and 393 mL.g[-1] VS of methane were produced in the system on day 18. Response surface methodology (RSM) was also used for optimization, showing 42.5% FW is the optimal FW content for maximum biogas and minimum H2S production. The distribution of select ARGs (qnrS, tetA, emrB, blaTEM, ampR) was tracked in the liquid and solid fraction of the digestate. Results illustrated a decrease (83-99% reduction) in the overall abundance of the ARGs in the solid fraction after AD. A similar trend was observed for the ARGs in the liquid fractions (65-99% reduction), except for ermB which became 1.74-10.6-fold higher in the final digestate. Also, at 50% FW, the abundance of intl1 increased in the liquid and solid fraction of digestate, indicating increased potential of ARG dissemination via horizontal gene transfer.}, }
@article {pmid40467884, year = {2025}, author = {Jung, G and Zin, H and Son, B and Shin, H and Kim, J}, title = {Characterization of a plasmid dependent DNA phage targeting Escherichia coli harboring a conjugative plasmid and its impact on gut microbiota.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {19701}, pmid = {40467884}, issn = {2045-2322}, support = {2022R1A6A1A03055869//National Research Foundation of Korea/ ; R2024057//National Institute of Fisheries Science/ ; }, mesh = {*Escherichia coli/virology/genetics ; *Plasmids/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; Phylogeny ; *Bacteriophages/genetics ; Conjugation, Genetic ; Feces/microbiology ; Gene Transfer, Horizontal ; }, abstract = {The emergence and spread of antimicrobial resistance in bacteria pose a significant global threat to public health. One of the main drivers of this spread is the horizontal transfer of antimicrobial resistance genes via conjugative plasmids. In this study, we isolated a novel phage, PDP46, which specifically targets Escherichia coli strains carrying a conjugative plasmid that encodes antibiotic resistance genes. PDP46 requires a conjugative IncF plasmid for infection, enabling it to selectively target bacterial strains capable of plasmid-mediated gene transfer. Phylogenetic analysis based on the major capsid protein revealed that PDP46 clusters with several phages that use O-antigen as a receptor. However, the tail fiber of PDP46 differs from those of the clustered phages, suggesting that the tail fiber structure of PDP46 may play a key role in its plasmid-dependent infectivity. Furthermore, to explore its therapeutic potential, we evaluated PDP46's effects on the gut microbiota using an in vitro human fecal incubation model. Our findings suggest that phage PDP46 could inhibit the growth of target bacteria harboring conjugative plasmids without disrupting overall microbial diversity. By inhibiting the growth of donor cells carrying antibiotic resistance-associated plasmids, PDP46 may serve as a targeted gut microbiota modulator.}, }
@article {pmid40467487, year = {2025}, author = {Nakayama, T and Harada, R and Yabuki, A and Nomura, M and Shiba, K and Inaba, K and Inagaki, Y}, title = {Marked Genome Reduction Driven by a Parasitic Lifestyle: Two Complete Genomes of Endosymbiotic Bacteria Possibly Hosted by a Dinoflagellate.}, journal = {Microbes and environments}, volume = {40}, number = {2}, pages = {}, doi = {10.1264/jsme2.ME25005}, pmid = {40467487}, issn = {1347-4405}, mesh = {*Symbiosis ; Phylogeny ; *Genome, Bacterial ; *Dinoflagellida/microbiology/physiology ; *Gammaproteobacteria/genetics/classification/isolation &amp; purification/physiology ; Base Composition ; Gene Transfer, Horizontal ; Genome Size ; }, abstract = {Bacteria with endosymbiotic lifestyles often show marked genome reduction. While the shrinkage of genomes in intracellular symbionts of animals, including parasitic bacteria, has been extensively exami-ned, less is known about symbiotic bacteria associated with single-celled eukaryotes. We herein report the genomes of two novel gammaproteobacterial lineages, RS3 and XS4, identified as putative parasitic endosymbionts of the dinoflagellate Citharistes regius. Phylogenetic ana-lyses suggest that RS3 and XS4 belong to the family Fastidiosibacteraceae within the order Beggiatoales, forming independent lineages therein. The genomes of RS3 and XS4 are 529 and 436‍ ‍kbp in size, respectively, revealing marked reductions from related bacterial genomes. XS4, which has a very reduced genome with a low GC content, uses a different genetic code, in which UGA assigned tryptophan. The small genomes of RS3 and XS4 encode a limited number of proteins, retaining only approximately 20% of the predicted ancestral proteome. Metabolic reconstruction suggests that RS3 and XS4 are parasitic symbionts that are heavily dependent on their host for essential metabolites. Furthermore, we found that the ancestor of both genomes likely acquired an ADP:ATP antiporter gene via horizontal gene transfer, an event that may have enabled their evolution as energy parasites by facilitating the acquisition of ATP from their host. These results on novel bacteria with highly reduced genomes expand our understanding of the phylogenetic and genomic diversities of endosymbiotic bacteria in protists.}, }
@article {pmid40158282, year = {2025}, author = {Feng, Y and Li, T and Zhao, S and Li, X and Zhai, Y and Yuan, L and Liu, J and Hu, G and He, D and Pan, Y}, title = {Genetic characterization and transmission of the multidrug resistance gene cfr in fecal and environmental pathways on a chicken farm in China.}, journal = {Poultry science}, volume = {104}, number = {6}, pages = {105079}, pmid = {40158282}, issn = {1525-3171}, mesh = {Animals ; China ; *Chickens ; *Drug Resistance, Multiple, Bacterial/genetics ; *Escherichia coli/genetics/drug effects ; Feces/microbiology ; Plasmids ; *Klebsiella pneumoniae/genetics/drug effects ; *Poultry Diseases/microbiology/transmission/epidemiology ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; *Bacterial Proteins/genetics/metabolism ; Gene Transfer, Horizontal ; }, abstract = {The emergence and spread of the multidrug-resistant gene cfr have raised significant public health concerns worldwide. To investigate its prevalence and dissemination dynamics, 18 cfr-positive strains were isolated in 2021 from fecal and environmental samples. Antimicrobial susceptibility testing showed that all strains were 100 % multidrug-resistant. Conjugation experiments demonstrated that a cfr- carrying IncFII(K)-IncR-IncFIB multi-replicon plasmid could transfer to E. coli J53. S1-nuclease digestion and Southern blotting identified cfr on plasmids of varying sizes, while whole-genome sequencing confirmed its presence on multiple plasmid types: IncX4, IncN, IncFII(K)-IncR-IncFIB, IncFIB-IncFII-IncR-IncHI2-IncHI2A multi-replicon plasmids, and two plasmids of unknown types. Genetic environment analysis revealed that cfr is categorized into five distinct structures (Types I-V). Reverse PCR results showed that Types I, II, and IV can form three circular intermediates of varying lengths (cfr-IS26). Network analysis further indicated strong association between cfr, tet(M), and dfrA14 mediated by IS26. Phylogenetic analysis revealed that the four ST1140 E. coli strains and all nine K. pneumoniae strains showed minimal genetic divergence. These findings suggest both clonal and horizontal transmission of cfr within the poultry farm. Continuous monitoring of cfr in animal-related environments is essential to mitigate its potential transfer to humans.}, }
@article {pmid40466317, year = {2025}, author = {Li, W and Zeng, J and Zheng, N and Ge, C and Li, Y and An, X and Yao, H}, title = {Astragalus polysaccharide slows the dissemination of antibiotic resistance genes and reduces the prevalence of opportunistic pathogens in the fish gut.}, journal = {Journal of environmental management}, volume = {389}, number = {}, pages = {126058}, doi = {10.1016/j.jenvman.2025.126058}, pmid = {40466317}, issn = {1095-8630}, abstract = {There is irrefutable evidence that the overuse of antibiotics in aquaculture contributes to the propagation and dissemination of antibiotic resistance genes (ARGs). In recent years, traditional Chinese medicines such as astragalus polysaccharide (APS) have been widely used as feed additives in aquaculture because of their ability to promote growth and enhance immunity and disease resistance. However, few studies have assessed whether APS exacerbates the ecological and health risk of ARG transmission. In this study, microcosm experiments were conducted with different concentrations of APS to assess the effects on the gut resistome and microbial community of a fish (Cyprinus carpio) using amplicon sequencing technology and high-throughput quantitative PCR. The results indicated that APS significantly reduced the total abundance of ARGs and mobile genetic elements (MGEs) in the gut (26.67 %-38.24 %). APS exposure led to a decrease in the abundance of Chlamydiae and opportunistic pathogens of the genus Aeromonas (41.54 %-87.86 %) in the gut. Network analysis revealed that Aeromonas is a potential host for most ARGs and MGEs, which exhibited similar trends in abundance changes. Functional analysis via PICRUSt2 indicated that APS markedly downregulated pathway activity related to drug resistance: antimicrobial, infectious diseases: bacterial and biofilm formation. The structural equation model based on partial least-squares path model indicated that the bacterial community, MGEs, and functional modules collectively determined the composition and distribution of gut ARGs under APS exposure. In summary, our study evaluated the health risks of the use of APS as a feed supplement, ensuring its appropriate use and sustainable aquaculture practices.}, }
@article {pmid40465274, year = {2025}, author = {Hassen, B and Hammami, S}, title = {Environmental Phages: Ecosystem Dynamics, Biotechnological Applications and their limits, and Future Directions.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxaf136}, pmid = {40465274}, issn = {1365-2672}, abstract = {Phages, the most abundant biological entities on Earth, play a crucial role in various microbial ecosystems, significantly impacting biogeochemical cycles and bacterial evolution. They inhabit diverse environments, including soil, water, and extreme conditions, where they contribute to the contribute to regulating microbial populations, facilitate genetic exchange and aid in nutrient cycling. Recent research has highlighted their potential in addressing antibiotic resistance, enhancing wastewater treatment, promoting agricultural sustainability, and tackling environmental issues. However, their ability to disseminate antibiotic resistance genes through horizontal gene transfer raises important concerns, warranting a thorough assessment of their ecological and biotechnological applications. This review synthesizes current knowledge on the diversity, ecological roles, and practical uses of environmental phages, emphasizing both their benefits and limitations. By analyzing recent findings and real-world applications, it provides insights into the challenges encountered and future directions for leveraging phages in environmental management, biotechnology, and healthcare.}, }
@article {pmid40462285, year = {2025}, author = {Ding, P and Lu, J and Lei, T and Guo, Y and Zhu, B and Zhao, Y and Wang, Y and Engelstädter, J and Schembri, MA and Guo, J}, title = {Antidepressant drugs promote the spread of broad-host-range plasmid in mouse and human gut microbiota.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2514138}, doi = {10.1080/19490976.2025.2514138}, pmid = {40462285}, issn = {1949-0984}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/genetics ; Humans ; Mice ; *Plasmids/genetics ; *Antidepressive Agents/pharmacology ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; *Gene Transfer, Horizontal/drug effects ; RNA, Ribosomal, 16S/genetics ; Duloxetine Hydrochloride/pharmacology ; Drug Resistance, Bacterial/genetics ; Male ; Mice, Inbred C57BL ; }, abstract = {Antibiotic resistance is a global public health challenge. The gut microbiota serves as a reservoir for antibiotic resistance genes (ARGs), facilitating their transfer between bacteria. With the rising incidence of major depressive disorders (MDD), antidepressant prescriptions have surged. Previous pure-culture studies suggest that antidepressants exhibit antibiotic-like side effects, but their impact on gene transfer in microbial communities remains unclear. Here, we report that clinically relevant doses of antidepressants duloxetine and sertraline enhance the transfer of a broad-host range conjugative plasmid across bacterial phyla from mice gut microbiota. Tests in human gut simulators confirmed that duloxetine facilitates plasmid transfer in human gut microbiota. Mechanistic analyses revealed that antidepressants increase reactive oxygen species levels and alter bacterial cell membrane permeability. Using fluorescence-activated cell sorting and 16S rRNA gene sequencing, we discovered that antidepressants alter plasmid transfer patterns at both phylum and genus levels, driving ARG exchange among opportunistic pathogens. Our findings suggest that antidepressant use may promote the spread of antibiotic resistance between commensal and pathogenic bacteria, raising important public health concerns.}, }
@article {pmid40458482, year = {2025}, author = {Islam, MS and Polash, MA and Haque, MH}, title = {First Molecular Characterization and Antibiogram of Bacteria Isolated From Dairy Farm Wastewater in Bangladesh.}, journal = {Veterinary medicine international}, volume = {2025}, number = {}, pages = {7253393}, pmid = {40458482}, issn = {2090-8113}, abstract = {This pioneering study in Bangladesh combines phenotypic and genotypic approaches to characterize antibiotic-resistant bacteria in dairy farm wastewater, addressing a critical gap in regional antimicrobial resistance (AMR) research. Dairy farming is integral to global food production, yet the wastewater generated by these operations is a significant source of environmental and public health concerns, particularly in the context of antibiotic resistance. This study aimed to isolate and identify antibiotic-resistant bacteria from dairy farm wastewater and evaluate their antibiogram profiles to inform effective management strategies. A total of 60 wastewater samples were collected and subjected to conventional bacterial characterization, followed by molecular detection via PCR and 16S rRNA gene sequencing. The study identified Pseudomonas aeruginosa (35%), Escherichia coli (30%), Bacillus subtilis (16.67%), and Acinetobacter junii (8.33%) as the predominant bacterial species. Sequencing results demonstrated high compatibility with reference sequences, confirming the identities of the isolates. Antibiogram analysis revealed significant resistance patterns: P. aeruginosa exhibited the highest resistance to penicillin (85.71%) and amoxicillin (76.19%), while demonstrating greater sensitivity to ciprofloxacin and cotrimoxazole. E. coli showed notable resistance to penicillin (88.89%), amoxicillin, and ceftriaxone, while B. subtilis and A. junii also demonstrated high levels of resistance to multiple antibiotics. Notably, a substantial proportion of the isolates exhibited multidrug resistance (MDR), with MAR indices ranging from 0.37 to 0.75. Moreover, several antibiotic resistance genes (ARGs) including penA, bla TEM , bla CTX-M , tetA, tetB, tetC, and ermB were detected across the bacterial species, with high prevalence rates in P. aeruginosa and A. junii, suggesting the potential for horizontal gene transfer and further spread of resistance. These findings underscore the critical need for a One Health approach to mitigate the risks posed by antibiotic-resistant bacteria in dairy farm wastewater, emphasizing the critical importance of responsible antibiotic use and sustainable farming practices to protect public health and environmental integrity.}, }
@article {pmid40457174, year = {2025}, author = {Okuno, M and Yamamoto, T and Ogura, Y}, title = {Blastn2dotplots: multiple dot-plot visualizer for genome comparisons.}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {146}, pmid = {40457174}, issn = {1471-2105}, support = {24K10210//Japan Society for the Promotion of Science/ ; }, mesh = {*Software ; *Genomics/methods ; *Sequence Alignment/methods ; *Genome ; Computer Graphics ; }, abstract = {BACKGROUND: Dot-plots, along with linear comparisons, are fundamental visualization methods in genome comparisons, widely used for analyzing structural variations, repeat regions, and sequence similarities. However, existing tools often have limitations in visualization flexibility, particularly requiring the concatenation of multiple sequences into a single continuous axis. This constraint can make it difficult to apply highlights or user-defined grid lines effectively, reducing interpretability in comparative genomic analyses.<br><br>RESULTS: We developed blastn2dotplots, a Python 3-based tool that utilizes the Matplotlib library to generate customizable dot-plots from local blastn results. Unlike traditional approaches, blastn2dotplots treats each alignment as a separate subplot, allowing for independent axis labeling, adjustable spacing between plots, and enhanced visualization flexibility. Users can highlight specific regions of interest, apply custom grid lines, and tailor the display to suit different genomic analyses. This tool is particularly useful for chromosomal structure analyses, detection of horizontal gene transfer events, and visualization of repetitive elements, offering an intuitive and adaptable framework for sequence comparison.<br><br>CONCLUSIONS: By addressing key limitations of existing dot-plot visualization tools, blastn2dotplots enhances the clarity and flexibility of comparative genomic analyses. Its ability to handle multiple alignments separately while preserving independent axis control and customization options makes it a valuable resource for a wide range of genomic studies. This tool provides a novel and effective solution for researchers needing precise and adaptable visualization of sequence alignments, thereby maximizing the potential of dot-plots in bioinformatics.}, }
@article {pmid40455052, year = {2025}, author = {Zhang, YQ and Cheng, LC and Zhao, FJ and Chen, MM and Wang, P}, title = {Chiral Pesticides Selectively Influence the Dissemination of Antibiotic Resistance Genes: An Overlooked Environmental Risk.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c13010}, pmid = {40455052}, issn = {1520-5851}, abstract = {The global spread of antibiotic resistance genes (ARGs) poses a critical threat to public health and environmental safety. Among environmental factors, the widespread use of chiral pesticides has raised ecological concerns, yet their enantioselective impacts on ARG propagation remain largely unexplored. Here, we investigate how chiral pesticides influence microbial ARG dissemination at the enantiomeric level. Using flurtamone as a model, we successfully separated and quantitatively analyzed its enantiomers (R-flurtamone and S-flurtamone) and evaluated their effects at environmentally relevant concentrations (0-80 μg/L). Remarkably, R-flurtamone significantly enhanced the horizontal transfer of ARGs, surpassing the effects of Rac-flurtamone, whereas S-flurtamone exerted a negligible influence. Mechanistic insights revealed that R-flurtamone is more easily recognized by bacterial cells and induces more cellular stress responses. Additionally, R-flurtamone induced an increase in cell membrane permeability, excessive reactive oxygen species (ROS) production, SOS responses, and boosted ATP levels, further accelerating ARG propagation. By integrating experimental findings with molecular simulations, we elucidated the enantioselective mechanisms underpinning ARG transfer. This study highlights the overlooked risks associated with racemic chiral pesticides at the enantiomeric level and provides a foundation for mitigating ARG dissemination in agricultural and environmental systems.}, }
@article {pmid40453648, year = {2025}, author = {}, title = {Correction to 'Current state and future prospects of Horizontal Gene Transfer detection'.}, journal = {NAR genomics and bioinformatics}, volume = {7}, number = {2}, pages = {lqaf078}, doi = {10.1093/nargab/lqaf078}, pmid = {40453648}, issn = {2631-9268}, mesh = {*Gene Transfer, Horizontal ; Humans ; }, abstract = {[This corrects the article DOI: 10.1093/nar/lqaf005.].}, }
@article {pmid40451789, year = {2025}, author = {Yue, X and Yang, J and Qi, J and Gao, S and Huo, Q and Guo, X and Guo, H and Luo, J and Wang, Y and Zhao, Y and Liu, R and Wang, H and Yi, S and Fu, Y and Ji, X and Wei, Y and He, W and Guo, B}, title = {Loss of Pathogenicity and Evidence of Horizontal Gene Transfer in Colletotrichum gloeosporioides From a Medicinal Plant.}, journal = {Molecular plant pathology}, volume = {26}, number = {6}, pages = {e70098}, doi = {10.1111/mpp.70098}, pmid = {40451789}, issn = {1364-3703}, support = {GX2346//Xi'an Beilin District Science and Technology Plan Project/ ; 2018ZDXM-SF-016//Key Research and Development Plan Project of Shaanxi Province/ ; 23JHQ056//Shaanxi Institute of Basic Sciences Project/ ; 2023-JC-YB-165//Natural Science Basis Research Plan in Shaanxi Province of China/ ; }, mesh = {*Colletotrichum/pathogenicity/genetics ; *Gene Transfer, Horizontal/genetics ; *Plants, Medicinal/microbiology ; Phylogeny ; *Huperzia/microbiology ; Virulence/genetics ; }, abstract = {Colletotrichum gloeosporioides is a major agricultural pathogen of crops that has also been identified as an endophyte of the medicinal plant Huperzia serrata. Both H. serrata and C. gloeosporioides produce huperzine A, a potential treatment for Alzheimer's disease. In this study, a nonpathogenic C. gloeosporioides strain (NWUHS001) was isolated and its genome sequenced. Gene structure prediction identified 15,413 protein-coding genes and 879 noncoding RNAs. Through PHI-base database prediction, we found that NWUHS001 lacks two key pathogenicity genes CgDN3 and cap20, which may be the cause of its nonpathogenicity. Comparative genomic analysis showed that the number of genes encoding pectin lyase B (pelB), pectin lyase (pnl) and polygalacturonase (pg) in NWUHS001 was significantly lower than that in pathogenic strains during the expansion of mycelium into host tissues. This caused slow growth and incapability to penetrate host cells. In contrast, in NWUHS001, genes involved in carbon acquisition such as ribose and amino sugar metabolic pathways were enriched, indicating active metabolite exchange with the host. In addition, by comparing the genome of NWUHS001 with that of the host H. serrata, we found that polyketosynthetase (pksIII), a key gene in the host huperzine A biosynthetic pathway, may possibly have been acquired from the fungus by horizontal gene transfer (HGT). This study explained the possible genetic evolution mechanism of C. gloeosporioides from pathogenicity to nonpathogenicity, which is of value for studying the interaction between microorganisms and plants. It also provided clues to the genetic evolution of the biosynthetic pathway of huperzine A.}, }
@article {pmid40451201, year = {2025}, author = {Spirin, S and Grishin, A and Rusinov, I and Alexeevski, A and Karyagina, A}, title = {Restriction-Modification Systems Specific toward GGATC, GATGC, and GATGG. Part 2. Functionality and Structure.}, journal = {Biochemistry. Biokhimiia}, volume = {90}, number = {4}, pages = {513-521}, doi = {10.1134/S0006297925600152}, pmid = {40451201}, issn = {1608-3040}, mesh = {*DNA Restriction-Modification Enzymes/metabolism/chemistry ; DNA Modification Methylases/metabolism/chemistry ; Substrate Specificity ; }, abstract = {The structural and functional basics of protein functionality of restriction-modification systems recognizing GGATC/GATCC, GATGC/GCATC, and GATGG/CCATC sites have been studied using bioinformatics methods. Such systems include a single restriction endonuclease and either two separate DNA methyltransferases or a single fusion DNA methyltransferase with two catalytic domains. It is known that some of these systems methylate both adenines in the recognition sites to 6-methyladenine, but the role of each of the two DNA methyltransferases remained unknown. In this work, we proved the functionality of most known systems. Based on the analysis of structures of related DNA methyltransferases, we hypothesized which of the adenines within the recognition site is modified by each of the DNA methyltransferases and suggested a possible molecular mechanism of changes in the DNA methyltransferase specificity from GATGG to GATGC during horizontal transfer of its gene.}, }
@article {pmid40451200, year = {2025}, author = {Spirin, S and Rusinov, I and Makarikova, O and Alexeevski, A and Karyagina, A}, title = {Restriction-Modification Systems Specific toward GGATC, GATGC, and GATGG. Part 1. Evolution and Ecology.}, journal = {Biochemistry. Biokhimiia}, volume = {90}, number = {4}, pages = {502-512}, doi = {10.1134/S0006297925600115}, pmid = {40451200}, issn = {1608-3040}, mesh = {*Evolution, Molecular ; *DNA Restriction-Modification Enzymes/metabolism/genetics/chemistry ; *DNA Restriction Enzymes/metabolism/genetics/chemistry ; Phylogeny ; }, abstract = {The article presents the results of studies on the evolution of proteins from restriction-modification systems consisting of restriction endonucleases with the REase_AlwI family domain and either two DNA methyltransferases, each with the MethyltransfD12 family domain, or a single DNA methyltransferase with two domains of this family. It was found that all such systems recognized one of the three DNA sequences, namely GGATC, GATGC or GATGG. Based on the sequence similarity, restriction endonucleases of these systems could be attributed to three clades that unambiguously corresponded to the RM system specificity. The DNA methyltransferase domains of these systems were classified into two groups based on sequence similarity, with the two domains of each system belonging to different groups. Within each group, the domains were attributed to three clades according to their specificity. An evidence of multiple interspecific horizontal transfer of entire restriction-modification systems has been found, as well as the transfer of individual genes between the systems (including the transfer of one of DNA methyltransferases accompanied by changes in its specificity). Evolutionary relationships of DNA methyltransferases from the studied systems with other DNA methyltransferases, including orphan DNA methyltransferases, have been revealed.}, }
@article {pmid40445756, year = {2025}, author = {Holt, JD and Peng, Y and Dalia, TN and Dalia, AB and Nadell, CD}, title = {Environmental DNA adsorption to chitin can promote horizontal gene transfer by natural transformation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {22}, pages = {e2420708122}, doi = {10.1073/pnas.2420708122}, pmid = {40445756}, issn = {1091-6490}, support = {826672//Simons Foundation (SF)/ ; R35GM151158//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R35GM128674//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, mesh = {*Chitin/metabolism/chemistry ; *Gene Transfer, Horizontal ; *Vibrio cholerae/genetics/metabolism ; *DNA, Environmental/genetics/chemistry ; Adsorption ; Fimbriae, Bacterial/metabolism/genetics ; *Transformation, Bacterial ; }, abstract = {Horizontal gene transfer by natural transformation (NT) is induced in Vibrio cholerae upon attachment to chitin surfaces in the aquatic environment. Here, we show that free environmental DNA adsorbs to chitin surfaces under physiologically realistic conditions. Using live-cell imaging and a fluorescent NT reporter, we demonstrate with cellular resolution microscopy that V. cholerae utilizes chitin-bound DNA as a reservoir for genetic exchange. Additionally, we demonstrate that uptake of DNA from this chitin-bound reservoir requires the forceful retraction of competence type IV pili. These findings uncover a role for retraction force in driving pilus-dependent NT and suggest that chitin particle surfaces can act as hotspots for horizontal gene transfer.}, }
@article {pmid40444634, year = {2025}, author = {Ellison, TJ and Ellison, CK}, title = {Improved DNA binding to a type IV minor pilin increases natural transformation.}, journal = {Nucleic acids research}, volume = {53}, number = {10}, pages = {}, pmid = {40444634}, issn = {1362-4962}, support = {R35GM150916/NH/NIH HHS/United States ; DFS6023/DRCRF/Damon Runyon Cancer Research Foundation/United States ; }, mesh = {*Acinetobacter/genetics/metabolism ; *Fimbriae Proteins/metabolism/genetics/chemistry ; Gene Transfer, Horizontal ; *Transformation, Bacterial ; *DNA, Bacterial/metabolism ; Protein Binding ; Fimbriae, Bacterial/metabolism/genetics ; DNA-Binding Proteins/metabolism ; }, abstract = {Bacteria take up environmental DNA using dynamic appendages called type IV pili (T4P) to elicit horizontal gene transfer in a process called natural transformation. Natural transformation is widespread amongst bacteria yet the parameters that enhance or limit this process across species are poorly understood. We show that the most naturally transformable species known, Acinetobacter baylyi, owes this property to uniquely high levels of DNA binding by its orphan minor pilin, FimT. Expression of A. baylyi FimT in a closely related Acinetobacter pathogen substantially improves its capacity for natural transformation, showing that the acquisition of a single gene is sufficient to increase rates of horizontal gene transfer. We show that, compared with its homologs, A. baylyi FimT contains multiple regions of positively charged residues that additively promote DNA binding efficiency. These results demonstrate the importance of T4P-DNA binding in establishing natural transformation rates and provide a basis for improving or limiting this mechanism of horizontal gene transfer in different species.}, }
@article {pmid40443099, year = {2025}, author = {Chen, H and Qin, X and Chen, Y and Zhang, H and Feng, Y and Tan, J and Chen, X and Hu, L and Xie, J and Xie, J and Yang, Z}, title = {Chromosome-level genome assembly of Pinus massoniana provides insights into conifer adaptive evolution.}, journal = {GigaScience}, volume = {14}, number = {}, pages = {}, doi = {10.1093/gigascience/giaf056}, pmid = {40443099}, issn = {2047-217X}, support = {Guike AD19254004//Guangxi Science and Technology Base and Talent/ ; 2024YFD2201301-1//National Key R&amp;D Program of China/ ; No.2022YFD2201600//National Key R&amp;D Program of China/ ; 2022YFD2200602//National Key R&amp;D Program of China/ ; 2019A26//Bagui Scholar/ ; 2019AQ17//Bagui Young Scholar/ ; 32371906//National Natural Science Foundation of China/ ; 32022057//National Natural Science Foundation of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent/ ; QNTD202305//Fundamental Research Funds for the Central Universities/ ; BFUKF202413//Fundamental Research Funds for the Central Universities/ ; }, mesh = {*Pinus/genetics/metabolism ; *Genome, Plant ; *Evolution, Molecular ; *Chromosomes, Plant/genetics ; *Adaptation, Physiological/genetics ; Genomics/methods ; Phylogeny ; }, abstract = {Pinus massoniana, a conifer of significant economic and ecological value in China, is renowned for its wide adaptability and oleoresin production. We sequenced and assembled the chromosomal-level P. massoniana genome, revealing 80,366 protein-coding genes and significant gene family expansions associated with stress response and plant-pathogen interactions. Long-intron genes, which are predominantly presented in low-copy gene families, are strongly linked to the recent long terminal repeat burst in the Pinus genome. By reanalyzing population transcriptomic data, we identified genetic markers linked to oleoresin synthesis, including those within the CYP450 and TPS gene families. The results suggest that the genes of the resin terpene biosynthesis pathway can be activated in several cell types, and the oleoresin yield may depend on the rate-limiting enzymes. Using a multiomics algorithm, we identified several regulatory factors, including PmMYB4 and PmbZIP2, that interact with TPS and CYP450 genes, potentially playing a role in oleoresin production. This was further validated through molecular genetics analyses. We observed signatures of adaptive evolution in dispersed duplicates and horizontal gene transfer events that have contributed to the species adaptation. This study provides insights for further research into the evolutionary biology of conifers and lays the groundwork for genomic-assisted breeding and sustainable management of Masson pine.}, }
@article {pmid40440992, year = {2025}, author = {Zhao, H and Zhao, HM and Wu, F and Liu, BL and Li, H and Li, YW and Cai, QY and Xiang, L and Mo, CH and Li, QX}, title = {Perfluorooctane sulfonate (PFOS) promotes transformational transfer of antibiotic resistance genes and cross-resistance between antibiotics and PFOS.}, journal = {Water research}, volume = {284}, number = {}, pages = {123868}, doi = {10.1016/j.watres.2025.123868}, pmid = {40440992}, issn = {1879-2448}, abstract = {Both per- and polyfluoroalkyl substances (PFASs) pollution and antibiotic resistance genes (ARGs) dissemination pose significant threats to global public health. PFASs and ARGs coexist in the environment, but little research was done on associations between PFASs and ARGs dissemination. This study demonstrated that perfluorooctane sulfonate (PFOS) increased ARGs transformation by 1.5-1.7-fold in Escherichia coli DH5α carrying pBR322 plasmid as a model. Moreover, pre-exposure of DH5α to PFOS increased ARGs transformation up to 7-fold. PFOS triggered up-regulation of the gene of outer membrane protein A (OmpA), enhancing cell membrane permeability and thus increasing ARGs transformation. Interestingly, the presence of ARGs decreased ompA gene expression and consequently lowered the accumulation and toxicity response of transformants to PFOS, which established cross-resistance between antibiotics and PFOS. This cross-resistance is attributed to the multifunctional role of the OmpA that acted as a major channel for ARGs entry into cells and facilitated cellular accumulation of PFOS. The OmpA-mediated cellular accumulation was also observed in structurally analogous PFASs (perfluorohexylsulfonic acid and pentadecafluorooctanoic acid), indicating a potential universality in the cross-resistance between antibiotics and PFASs. The United States, Canada and China are likely being confronted with high risks of PFOS-induced ARGs dissemination based on the global risk assessments. These findings demonstrate the overlooked eco-environmental risks associated with the interactions among PFASs, ARGs, and microorganisms, highlighting adaptability of organisms to chemical stress.}, }
@article {pmid40440354, year = {2025}, author = {Marcarian, HQ and Sivakoses, A and Arias, AM and Ihedioha, OC and Lee, BR and Bishop, MC and Bothwell, ALM}, title = {Renal cancer cells acquire immune surface protein through trogocytosis and horizontal gene transfer.}, journal = {PloS one}, volume = {20}, number = {5}, pages = {e0325043}, pmid = {40440354}, issn = {1932-6203}, mesh = {Humans ; *Kidney Neoplasms/genetics/immunology/pathology/metabolism ; *Carcinoma, Renal Cell/genetics/immunology/pathology/metabolism ; *Gene Transfer, Horizontal ; Gene Expression Regulation, Neoplastic ; Carbonic Anhydrase IX ; Tumor Microenvironment/immunology ; Leukocyte Common Antigens/metabolism/genetics ; Cell Line, Tumor ; *Membrane Proteins/metabolism/genetics ; Biomarkers, Tumor/metabolism ; }, abstract = {Trogocytosis is an underappreciated phenomenon that shapes the immune microenvironment surrounding many types of solid tumors. The consequences of membrane-bound proteins being deposited from a donor immune cell to a recipient cancer cell via trogocytosis are still unclear. Here, we report that human clear cell renal carcinoma tumors stably express the lymphoid markers CD45, CD56, CD14, and CD16. Flow cytometry performed on fresh kidney tumors revealed consistent CD45 expression on tumor cells, as well as varying levels of the other markers mentioned previously. These results were consistent with our immunofluorescent analysis, which also revealed colocalization of lymphoid markers with carbonic anhydrase 9, a standard kidney tumor marker. RNA analysis showed a significant upregulation of genes typically associated with immune cells by tumor cells. Finally, we show evidence of chromosomal DNA being transferred from immune cells to tumor cells through physical contact. This horizontal gene transfer has transcriptional consequences in the recipient tumor cell, resulting in a fusion phenotype that expresses both immune and cancer specific proteins. This work demonstrates a novel mechanism by which tumor cell protein expression is altered through the acquisition of surface membrane fragments and genomic DNA from infiltrating lymphocytes. These results alter the way in which we understand tumor-immune cell interactions and may reveal new insights into the mechanisms by which tumors develop. Additionally, further studies into trogocytosis and other mechanisms of contact-mediated cellular transfer will help push the field towards the next generation of immunotherapies and biomarkers for treating renal cell carcinoma and other cancers.}, }
@article {pmid40438350, year = {2025}, author = {Peng, H and Fu, J}, title = {Unveiling horizontal gene transfer in the gut microbiome: bioinformatic strategies and challenges in metagenomics analysis.}, journal = {National science review}, volume = {12}, number = {6}, pages = {nwaf128}, pmid = {40438350}, issn = {2053-714X}, }
@article {pmid40436596, year = {2025}, author = {Tan, G and Lin, K and Hu, M and Wang, Y and Li, X and Li, X and Chen, S and Zhang, Q and Zheng, Z}, title = {Uncovering the resistome and mobilome across different types of ready-to-eat fermented foods.}, journal = {Food research international (Ottawa, Ont.)}, volume = {213}, number = {}, pages = {116577}, doi = {10.1016/j.foodres.2025.116577}, pmid = {40436596}, issn = {1873-7145}, mesh = {*Fermented Foods/microbiology ; *Food Microbiology ; *Fast Foods/microbiology ; Interspersed Repetitive Sequences ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; Metagenomics ; Dairy Products/microbiology ; Vegetables/microbiology ; }, abstract = {Antimicrobial resistance in food poses a significant threat to public health, and the persistence of antibiotic resistance genes (ARGs) in ready-to-eat fermented foods (RTE-FFs) is a growing concern. However, information on the diversity, origins, and transferability of ARGs in RTE-FFs is limited. This study investigated the distribution of ARGs and mobile genetic elements (MGEs) in four types of RTE-FFs: soybean, dairy, meat, and vegetable products. Using whole metagenomic sequencing, we identified significant variations in the bacterial diversity, ARG profiles, and MGE profiles among these food types. Bean-based RTE-FFs exhibited the highest diversity of ARGs and MGEs, while dairy products showed the lowest diversity (p < 0.05). Eight types of ARGs were significantly more prevalent in bean-based foods than in the other food categories (p < 0.05). Several ARGs were highly abundant in the RTE-FFs, including aphA2, blaTEM-116, PBP1a, PBP1b, OqxA, OqxBgb, lsa(A), tet(34), and tet(58). Plasmids carried the highest number of ARGs among all MGEs, particularly those associated with beta-lactam, macrolide-lincosamide-streptogramin, tetracycline, and aminoglycoside resistance, suggesting a higher risk with plasmid-mediated transfer, especially in bean-based RTE-FFs. Metagenomic binning analysis recovered 76 high-quality metagenome-assembled genomes (MAGs), including four novel species. A total of 13 types of ARGs, encompassing 95 subtypes, were identified across the MAGs; Bacillus paranthracis, Enterococcus casseliflavus, and Enterococcus gallinarum had the most ARGs (16, 12, and 14, respectively). Dairy RTE-FFs (yogurt and cheese) contained a high abundance of Streptococcus thermophilus resistant to beta-lactams (PBP1b) and tetracycline (tetB(60)), raising concerns about ARG transfer in these food products. Bean RTE-FFs (sufu) harbored two pathogenic Acinetobacter species carrying carbapenem resistance genes (blaOXA-180, blaOXA-211, and blaOXA-230). No ARGs were found in the MGEs (prophages, insertion sequences, or transposons) within the MAGs. Overall, our results provide valuable insights into the antibiotic resistome and mobilome of various RTE-FFs to inform food production and management practices.}, }
@article {pmid40436163, year = {2025}, author = {Gagneja, S and Capalash, N and Sharma, P}, title = {Whole genome sequence analysis of an environmental isolate Bacillus subtilis K3C: Genome plasticity and acquisition of hyaluronic acid capsule traits through horizontal multigene transfer.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {144696}, doi = {10.1016/j.ijbiomac.2025.144696}, pmid = {40436163}, issn = {1879-0003}, abstract = {B. subtilis K3C was isolated from an environmental sample. Genomic analysis revealed that the GRAS strain harbors a circular chromosome of 4,120,051 bp composed of 4361 protein coding sequences with a GC content of 43.4 %, 80 tRNA, and 3 rRNA genes. Two regions containing complete assembly of prophages encoded by 83 prophage genes were present suggesting the role of bacteriophage infection in evolutionary accumulation of strain-specific genes contributing towards strain diversification. Strong recombination, repair, transfer and competence systems were identified, suggesting their role in strain fitness and evolutionary process. Pan-genomic analysis revealed 3824 protein homologs as the bacterial core genome shared among different strains and 390 singletons in the pan-genome orthologous groups. The hyaluronic acid capsule trait in the isolate seems to be acquired through selective pressure to adapt in environmentally stressed niches. Phyloproteomic analysis showed that the acquired genes responsible for HA production were phylogenetically closer to Streptococcal clade, evidencing the role of horizontal gene transfer. The bacterial genome showed the presence of multiple HA genes translating HasB and HasC proteins suggesting gene dosage in the strain. However, no gene rearrangement events seem to have taken course as the HA genes were integrated in different contigs of the genome.}, }
@article {pmid40433443, year = {2025}, author = {Dahal, U and Bansal, A}, title = {Unravelling Prokaryotic Codon Usage: Insights from Phylogeny, Influencing Factors and Pathogenicity.}, journal = {Current genomics}, volume = {26}, number = {2}, pages = {81-94}, pmid = {40433443}, issn = {1389-2029}, abstract = {Analyzing prokaryotic codon usage trends has become a crucial topic of study with significant ramifications for comprehending microbial genetics, classification, evolution, and the control of gene expression. This review study explores the numerous facets of prokaryotic codon usage patterns, looking at different parameters like habitat and lifestyle across broad groups of prokaryotes by emphasizing the role of codon reprogramming in adaptive strategies and its integration into systems biology. We also explored the numerous variables driving codon usage bias, including natural selection, mutation, horizontal gene transfer, codon-anticodon interaction, and genomic composition in prokaryotes through a thorough study of current literature. Furthermore, a special session on codon usage on pathogenic prokaryotes and the role of codon usage in the phylogeny of prokaryotes has been discussed. We also looked at the various software and indices that have been recently applied to prokaryotic genomes. The promising directions that lay ahead to map the future of codon usage research on prokaryotes have been emphasized. Codon usage variations across prokaryotic communities could be better understood by combining environmental, metagenomic, and system biology approaches.}, }
@article {pmid40431712, year = {2025}, author = {Nikulina, AN and Nikulin, NA and Suzina, NE and Zimin, AA}, title = {Treatment of E. coli Infections with T4-Related Bacteriophages Belonging to Class Caudoviricetes: Selecting Phage on the Basis of Their Generalized Transduction Capability.}, journal = {Viruses}, volume = {17}, number = {5}, pages = {}, doi = {10.3390/v17050701}, pmid = {40431712}, issn = {1999-4915}, support = {&#x2116;24-64-00017//Russian Science Foundation/ ; }, mesh = {*Phage Therapy/methods ; *Escherichia coli/virology ; *Escherichia coli Infections/therapy ; *Bacteriophage T4/genetics/physiology ; *Transduction, Genetic ; Humans ; Gene Transfer, Horizontal ; *Coliphages/genetics/physiology ; Animals ; }, abstract = {The problem of the multidrug resistance of pathogenic bacteria is a serious concern, one which only becomes more pressing with every year that passes, motivating scientists to look for new therapeutic agents. In this situation, phage therapy, i.e., the use of phages to combat bacterial infections, is back in the spotlight of research interest. Bacterial viruses are highly strain-specific towards their hosts, which makes them particularly valuable for targeting pathogenic variants amidst non-pathogenic microflora, represented by such commensals of animals and humans as E. coli, S. aureus, etc. However, selecting phages for the treatment of bacterial infections is a complex task. The prospective candidates should meet a number of criteria; in particular, the selected phage must not contain potentially dangerous genes (e.g., antibiotic resistance genes, genes of toxins and virulence factors etc.)-or be capable of transferring them from their hosts. This work introduces a new approach to selecting T4-related coliphages; it allows one to identify strains which may be safer in terms of involvement in the horizontal gene transfer. The approach is based on the search for genes that reduce the frequency of genetic transduction.}, }
@article {pmid40431550, year = {2025}, author = {Elbir, H}, title = {No Genomic Signatures Were Found in Escherichia coli Isolates from Camels With or Without Clinical Endometritis.}, journal = {Veterinary sciences}, volume = {12}, number = {5}, pages = {}, doi = {10.3390/vetsci12050457}, pmid = {40431550}, issn = {2306-7381}, abstract = {Clinical endometritis is a leading cause of infertility in she-camels. We commonly isolate E. coli from camel uteri with and without endometritis during our routine diagnosis of conception failure. From an epidemiological standpoint, it is critical to know if certain E. coli genotypes and virulence factors are specifically associated with endometritis. Thus, we aimed to compare the abundance of virulence elements and genotypes in uterine E. coli from camels with and without endometritis and understand their evolution. For this investigation, we retrieved data from the genomes of 28 E. coli isolates from humans, cats, dogs, horses, cows, and birds and 14 sequenced genomes of camel uterine E. coli isolates. We found no specific E. coli genotype or virulence factor associated with endometritis. Instead, multiple genotypes and high genomic diversity were observed. Moreover, horizontal gene transfer driven by genomic islands and plasmids contributed to the genetic diversity of the isolates, resulting in the acquisition of virulence genes, metabolic characteristics, and antibiotic resistance determinants to trimethoprim, sulfonamide, streptomycin, and tetracycline. Additionally, the phylogenetic position of the E. coli isolates from camel uteri suggests that they originated from intestinal strains. In conclusion, there was no evidence of E. coli specialization, and E. coli alone may not be able to develop endometritis, as other factors are required. Also, we elucidated the mechanism behind the diversity of the gene repertoire of E. coli isolated from camel uteri. These findings provide insight into the evolutionary origins of E. coli isolates from camel uteri.}, }
@article {pmid40431301, year = {2025}, author = {Wang, K and Zhang, C and Munang'andu, HM and Xu, C and Cai, W and Yan, X and Tao, Z}, title = {Comparative Genomic Analysis of Two Vibrio harveyi Strains from Larimichthys crocea with Divergent Virulence Profiles.}, journal = {Microorganisms}, volume = {13}, number = {5}, pages = {}, doi = {10.3390/microorganisms13051129}, pmid = {40431301}, issn = {2076-2607}, support = {42376108//National Natural Science Foundation of China/ ; }, abstract = {Vibrio harveyi is a significant pathogen in marine aquaculture, causing vibriosis in various marine species. This study presents a comparative genomic analysis of two V. harveyi strains, N8T11 and 45T2, which exhibit differing virulence profiles. Virulence assays revealed that N8T11 caused 92% mortality in infected fish, while 45T2 resulted in 0% mortality. Whole-genome sequencing revealed that strain N8T11 harbors five plasmids (pN8T11a, pN8T11b, pN8T11c, pN8T11d and pN8T11e) absent in 45T2, encoding genes potentially linked to virulence, such as siderophore-mediated iron acquisition and stress response mechanisms. Pan-genome analysis highlighted substantial genomic plasticity within V. harveyi, with mobile genetic elements, including plasmids and prophages, contributing to horizontal gene transfer. Conjugation experiments demonstrated that all five N8T11 plasmids can transfer to 45T2 with efficiencies up to 87%, with pN8T11b remaining stable across multiple subcultures, enabling the dissemination of virulence-associated genes. These findings suggest that plasmid-mediated gene transfer plays a role in the virulence variability observed between V. harveyi strains. This study contributes to understanding the genomic factors underlying pathogenicity in V. harveyi and provides insights for future research aimed at controlling vibriosis in aquaculture.}, }
@article {pmid40431267, year = {2025}, author = {Duarte, MLO and Rodrigues, DLN and de Lima, GBV and Ariute, JC and Gouveia, GV and de Simoni Gouveia, JJ and Azevedo, V and Brenig, B and Guédon, E and Tavares, GC and da Costa, MM and Pereira, UP and Aburjaile, FF}, title = {In Silico Characterization of Resistance and Virulence Genes in Aeromonas jandaei Strains Isolated from Oreochromis niloticus in Brazil.}, journal = {Microorganisms}, volume = {13}, number = {5}, pages = {}, doi = {10.3390/microorganisms13051094}, pmid = {40431267}, issn = {2076-2607}, support = {408898/2022-4//CNPq/MCTI/CT-Sa&#xfa;de n&#xba; 52/2022/ ; }, abstract = {Understanding the genetic characteristics of Aeromonas jandaei in Brazilian aquaculture is crucial for developing effective control strategies against this fish pathogen. The present study conducted a genomic analysis of Brazilian A. jandaei strains with the objective of investigating their virulence potential and resistance profiles. Four Brazilian isolates were subjected to sequencing, and comparative genomic analyses were conducted in conjunction with 48 publicly available A. jandaei genomes. The methods employed included quality assessment, de novo assembly, annotation, and analyses of antimicrobial resistance and virulence factors. The results demonstrated the presence of fluoroquinolone resistance genes within the core genome. Notably, these antibiotics are not authorized for use in aquaculture in Brazil, suggesting that their resistance determinants may originate from other selective pressures or horizontal gene transfer unrelated to aquaculture practices. The analysis identified significant virulence mechanisms, including T2SS, T3SS, and notably T6SS (vgrG3 gene), which was more prevalent in Brazilian isolates. Additionally, genes associated with motility, adhesion, and heavy metal resistance were identified. These findings highlight the enhanced adaptability of Brazilian A. jandaei strains and raise concerns about antimicrobial resistance in aquaculture, emphasizing the need for improved regulatory oversight and control strategies.}, }
@article {pmid40428151, year = {2025}, author = {Müller, GA}, title = {The Transformation Experiment of Frederick Griffith II: Inclusion of Cellular Heredity for the Creation of Novel Microorganisms.}, journal = {Bioengineering (Basel, Switzerland)}, volume = {12}, number = {5}, pages = {}, doi = {10.3390/bioengineering12050532}, pmid = {40428151}, issn = {2306-5354}, abstract = {So far, synthetic biology approaches for the construction of artificial microorganisms have fostered the transformation of acceptor cells with genomes from donor cells. However, this strategy seems to be limited to closely related bacterial species only, due to the need for a "fit" between donor and acceptor proteomes and structures. "Fitting" of cellular regulation of metabolite fluxes and turnover between donor and acceptor cells, i.e. cybernetic heredity, may be even more difficult to achieve. The bacterial transformation experiment design 1.0, as introduced by Frederick Griffith almost one century ago, may support integration of DNA, macromolecular, topological, cybernetic and cellular heredity: (i) attenuation of donor Pneumococci of (S) serotype fosters release of DNA, and hypothetically of non-DNA structures compatible with subsequent transfer to and transformation of acceptor Pneumococci from (R) to (S) serotype; (ii) use of intact donor cells rather than of subcellular or purified fractions may guarantee maximal diversity of the structural and cybernetic matter and information transferred; (iii) "Blending" or mixing and fusion of donor and acceptor Pneumococci may occur under accompanying transfer of metabolites and regulatory circuits. A Griffith transformation experiment design 2.0 is suggested, which may enable efficient exchange of DNA as well as non-DNA structural and cybernetic matter and information, leading to unicellular hybrid microorganisms with large morphological/metabolic phenotypic differences and major features compared to predeceding cells. The prerequisites of horizontal gene and somatic cell nuclear transfer, the molecular mechanism of transformation, the machineries for the biogenesis of bacterial cytoskeleton, micelle-like complexes and membrane landscapes are briefly reviewed on the basis of underlying conceptions, ranging from Darwin's "gemmules" to "stirps", cytoplasmic and "plasmon" inheritance, "rhizene agency", "communicology", "transdisciplinary membranology" to up to Kirschner's "facilitated variation".}, }
@article {pmid40426537, year = {2025}, author = {Touaitia, R and Mairi, A and Ibrahim, NA and Basher, NS and Idres, T and Touati, A}, title = {Staphylococcus aureus: A Review of the Pathogenesis and Virulence Mechanisms.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/antibiotics14050470}, pmid = {40426537}, issn = {2079-6382}, support = {grant number IMSIU-DDRSP2501//Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University (IMSIU)/ ; }, abstract = {Staphylococcus aureus is a formidable human pathogen responsible for infections ranging from superficial skin lesions to life-threatening systemic diseases. This review synthesizes current knowledge on its pathogenesis, emphasizing colonization dynamics, virulence mechanisms, biofilm formation, and antibiotic resistance. By analyzing studies from PubMed, Scopus, and Web of Science, we highlight the pathogen's adaptability, driven by surface adhesins (e.g., ClfB, SasG), secreted toxins (e.g., PVL, TSST-1), and metabolic flexibility in iron acquisition and amino acid utilization. Nasal, skin, and oropharyngeal colonization are reservoirs for invasive infections, with biofilm persistence and horizontal gene transfer exacerbating antimicrobial resistance, particularly in methicillin-resistant S. aureus (MRSA). The review underscores the clinical challenges of multidrug-resistant strains, including vancomycin resistance and decolonization strategies' failure to target single anatomical sites. Key discussions address host-microbiome interactions, immune evasion tactics, and the limitations of current therapies. Future directions advocate for novel anti-virulence therapies, multi-epitope vaccines, and AI-driven diagnostics to combat evolving resistance. Strengthening global surveillance and interdisciplinary collaboration is critical to mitigating the public health burden of S. aureus.}, }
@article {pmid40426515, year = {2025}, author = {Olanrewaju, TO and Dooley, JSG and Coleman, HM and McGonigle, C and Arnscheidt, J}, title = {Bacterivorous Ciliate Tetrahymena pyriformis Facilitates vanA Antibiotic Resistance Gene Transfer in Enterococcus faecalis.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/antibiotics14050448}, pmid = {40426515}, issn = {2079-6382}, abstract = {Background: Wastewater treatment plants (WWTPs) are hotspots for the emergence and spread of antibiotic resistance genes (ARGs). In activated sludge treatment systems, bacterivorous protozoa play a crucial role in biological processes, yet their impact on the horizontal gene transfer in Gram-positive enteric bacteria remains largely unexplored. This study investigated whether the ciliate Tetrahymena pyriformis facilitates the transfer of antibiotic resistance genes between Enterococcus faecalis strains. Methods: Conjugation assays were conducted under laboratory conditions using a vanA-carrying donor and a rifampicin-resistant recipient at an initial bacterial concentration of 10[9] CFU/mL and ciliate density of 10[5] N/mL. Results: Transconjugant numbers peaked at 2 h when experiments started with recipient bacteria harvested in the exponential growth phase, and at 24 h when bacteria were in the stationary phase. In both cases, vanA gene transfer frequency was highest at 24 h (10[-4]-10[-5] CFU/mL), and the presence of energy sources increased gene transfer frequency by one order of magnitude. Conclusions: These findings suggest that ciliate grazing may contribute to vanA gene transfer in WWTP effluents, potentially facilitating its dissemination among permissive bacteria. Given the ecological and public health risks associated with vanA gene persistence in wastewater systems, understanding protozoan-mediated gene transfer is crucial for mitigating the spread of antibiotic resistance in aquatic environments.}, }
@article {pmid40425158, year = {2025}, author = {Chrismas, N and Bird, K and Laundon, D and Lieng, C and Hesketh-Best, P and Cunliffe, M}, title = {Adaptive traits for chitin utilization in the saprotrophic aquatic chytrid fungus Rhizoclosmatium globosum.}, journal = {Proceedings. Biological sciences}, volume = {292}, number = {2047}, pages = {20250337}, doi = {10.1098/rspb.2025.0337}, pmid = {40425158}, issn = {1471-2954}, support = {//HORIZON EUROPE European Research Council/ ; //Natural Environment Research Council/ ; }, mesh = {*Chitin/metabolism ; Chitinases/metabolism/genetics ; *Chytridiomycota/genetics/physiology/metabolism/enzymology ; Genome, Fungal ; Phylogeny ; Fungal Proteins/metabolism/genetics ; }, abstract = {The Chytridiomycota (chytrids) are early diverging fungi, many of which function in ecosystems as saprotrophs; however, associated adaptive traits are poorly understood. We focused on chitin degradation, a common ecosystem function of aquatic chytrids, using the model chitinophilic Rhizoclosmatium globosum and comparison of other chytrid genomes. Zoospores are chemotactic to the chitin monomer N-acetylglucosamine and accelerate development when grown with chitin. The R. globosum secretome is dominated by different glycoside hydrolase (GH) family GH18 chitinases, with abundance matching reciprocal transcriptome mRNA sequences. Models of the secreted chitinases indicate a range of sizes and domain configurations. Along with R. globosum, the genomes of other chitinophilic chytrids also have expanded inventories of GH-encoding genes responsible for chitin processing. Several R. globosum GH18 chitinases have bacteria-like chitin-binding module domains, also present in the genomes of other chitinophilic chytrids yet absent in non-chitinophilic chytrids. Chemotaxis, increased abundance and diversity of secreted chitinases, complemented with the acquisition of novel chitin-binding capability, are probably adaptive traits that facilitate chitin saprotrophy. Our study reveals the underpinning mechanisms that have supported the niche expansion of some chytrids to utilize lucrative chitin-rich particles in aquatic ecosystems and is a demonstration of the adaptive ability of this successful fungal group.}, }
@article {pmid40422289, year = {2025}, author = {Derriche, M and Nouvel, LX and Gaudino, M and Sagné, E and Simon, E and Robert, H and Pot, G and Meyer, G and de la Fe, C and Arfi, Y and Maillard, R and Citti, C and Baranowski, E}, title = {Bacterial conjugation in the ruminant pathogen Mycoplasma agalactiae is influenced by eukaryotic host factors.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0086825}, doi = {10.1128/aem.00868-25}, pmid = {40422289}, issn = {1098-5336}, abstract = {Horizontal gene transfer (HGT) plays a pivotal role in the evolution and adaptation of genome-reduced mycoplasmas. The conjugative properties of these organisms are key in this phenomenon but are largely understudied, particularly in vivo. In the present study, the ruminant pathogen Mycoplasma agalactiae was used as a model organism to document mycoplasma conjugation in environments of increasing complexity, from axenic to cell and organotypic culture conditions. Compared to axenic mating conditions, mycoplasma co-cultivation with goat epithelial cells or bovine precision-cut lung slices resulted in enhanced mating frequencies with high rates of M. agalactiae integrative and conjugative element (ICEA) self-dissemination. These results were conditioned by the presence of eukaryotic cells in the culture and influenced by competition between mating partners but were not limited to M. agalactiae, as similar results were observed with Mycoplasma bovis. Mycoplasma conjugation ex vivo was further characterized by analyzing mycoplasma chromosomal transfer (MCT), a newly discovered mechanism of horizontal exchange of chromosomal DNA that generates mosaic genomes. Compared to ICEA transfer, MCT was detected at lower rates under cell and organotypic culture conditions, suggesting a negative impact of these cellular environments on MCT or its progeny. Finally, mating experiments under nutrient-deprived conditions identified nucleotide stress as a potential factor influencing the modulation of mycoplasma conjugation by eukaryotic host cells. In conclusion, these results suggest that HGT in vivo is likely underestimated and provide valuable models to further study mycoplasma conjugation ex vivo.IMPORTANCEConjugation is an evolutionary shortcut that bacteria use to exchange genetic information with their neighbors. Despite the fast evolution rate of the genome-reduced mycoplasmas, their conjugative properties remain largely understudied, particularly in vivo. Here we used the ruminant pathogen Mycoplasma agalactiae to study how mycoplasmas conjugate in co-culture with host-derived cells and tissues. Interestingly, conjugation was stimulated when mycoplasmas were co-cultured with eukaryotic cells. This was documented by monitoring the self-propagation of a mobile genetic element known as integrative and conjugative element (ICE) and the exchange of chromosomal DNA leading to the formation of mosaic genomes. While ICE transfer was observed at high frequency, only a few mosaic genomes were detected in the presence of eukaryotic cells. Further data point toward nucleotide stress as a possible factor modulating mycoplasma conjugation in cellular environments. These results suggest that mycoplasma-host interactions may stimulate conjugation in vivo.}, }
@article {pmid40419976, year = {2025}, author = {Vidal-Quist, JC and Ortego, F and Lambrecht, BN and Rombauts, S and Hernández-Crespo, P}, title = {Stage-specific transcriptomic analysis reveals insights into the development, reproduction and biological function of allergens in the European house dust mite Dermatophagoides pteronyssinus.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {527}, pmid = {40419976}, issn = {1471-2164}, support = {01M01521//Fonds Wetenschappelijk Onderzoek/ ; }, mesh = {Animals ; Female ; Male ; *Allergens/genetics/metabolism ; *Gene Expression Profiling ; *Dermatophagoides pteronyssinus/genetics/growth &amp; development/physiology ; Reproduction/genetics ; *Transcriptome ; Gene Expression Regulation, Developmental ; }, abstract = {BACKGROUND: House dust mites (HDMs) such as Dermatophagoides pteronyssinus are major allergy elicitors worldwide, yet their gene expression across developmental stages remains underexplored. Herein, we report a comprehensive RNAseq analysis of larvae, nymphs, and adult males and females, mapped to a recently published high-quality genome with extended functional annotations.<br><br>RESULTS: Analysis of differentially expressed genes (DEG) revealed that female-biased expression was the most prevalent profile (16% of genes), while males exhibited the highest fold-change differences. DEG data, combined with network clustering and functional enrichment analysis, highlighted distinct genes and biological processes for each stage and sex: females showed upregulation of genes related to cell division and oogenesis, with vitellogenins among the most abundant transcripts; males exhibited increased expression of genes encoding putative seminal fluid proteins (e.g. endopeptidases, serpins, antimicrobial peptides), and those involved in reproductive regulation (e.g. testis-specific serine kinases); while juveniles displayed enhanced expression of genes related to energy metabolism and growth. Further analysis of endocrine pathways revealed non-canonic mechanisms compared to insect models, particularly in ecdysteroid and sesquiterpenoid biosynthesis and regulation. Expression patterns in genes involved in cuticle formation were also identified, reflecting their role in developmental transitions and sexual differentiation. Allergen and allergen-related gene expression showed an overall increase in feeding juveniles, as well as sex-biased expression, with Der p 27 upregulated in females. These findings provide insight into the physiological roles of allergens in digestion, immunity, and muscle formation, among other functions. Additionally, seven new horizontally transferred genes, including a DNA-repair photolyase linked to females, and novel multigene families (e.g. 119 male-specific beta-propeller proteins, 70 hypothetical cuticular proteins, 23 tetraspanin-like proteins, 5 female-associated putative odorant-binding proteins) were identified.<br><br>CONCLUSIONS: This study provides the first genome-wide transcriptomic analysis of a HDM across life stages and sexes, expanding our understanding of the molecular mechanisms underlying mite development, sexual reproduction, and allergen expression. The generated data, fully available via supplementary spreadsheet and the ORCAE online platform, provide a valuable foundation for future allergy research and the development of new mite control strategies.}, }
@article {pmid40305681, year = {2025}, author = {Bennett, BD and Meier, DAO and Lanclos, VC and Asrari, H and Coates, JD and Thrash, JC}, title = {Polyhydroxybutyrate production by freshwater SAR11 (LD12).}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, doi = {10.1093/ismejo/wraf087}, pmid = {40305681}, issn = {1751-7370}, mesh = {Phylogeny ; *Fresh Water/microbiology ; *Hydroxybutyrates/metabolism ; *Polyhydroxyalkanoates/metabolism/biosynthesis ; Escherichia coli/genetics/metabolism ; *Alphaproteobacteria/metabolism/genetics/classification ; Bacterial Proteins/genetics/metabolism ; Gene Transfer, Horizontal ; Polyhydroxybutyrates ; }, abstract = {SAR11 bacteria (order Pelagibacterales) are oligotrophs and often the most abundant bacterioplankton in aquatic environments. A subset of sequenced SAR11 genomes, predominantly in the brackish and freshwater SAR11 subclades, contain homologs of pha genes, which in other organisms confer the ability to store carbon and energy via polyhydroxyalkanoate (PHA) polymers. Here, we investigated the relevance of PHA production to SAR11 biology. Phylogenetics showed that Pha proteins occurred on a long branch and provided evidence for origin at the common ancestor of the brackish IIIa and freshwater LD12 subclades, followed by horizontal transfer within SAR11. Using the LD12 representative "Candidatus Fonsibacter ubiquis" strain LSUCC0530, we found that many LSUCC0530 cells contained a single Nile red-staining granule, confirmed that the cells produced polyhydroxybutyrate, a common form of PHA, and estimated the total polyhydroxybutyrate content in the cells. We heterologously expressed the LSUCC0530 phaCAB locus in Escherichia coli, finding it to be functional and the likely origin of the polyhydroxybutyrate. We also determined that, irrespective of changes to carbon, nitrogen, and phosphorus concentrations, a similar fraction of LSUCC0530 cells generated polyhydroxybutyrate granules and expression of the phaCAB locus remained constant. We suggest that polyhydroxybutyrate synthesis in LSUCC0530 may be constitutively active due to the slow growth dynamics and minimal regulation that characterize SAR11 bacteria. This work characterizes polymer storage in SAR11, providing new insights into the likely fitness advantage for cells harboring this metabolism.}, }
@article {pmid40417658, year = {2025}, author = {Bhuvaragavan, S and Sruthi, K and Nivetha, R and Keerthana, CB and Marieshwari, BN and Janarthanan, S}, title = {PacBio-based de novo transcriptomics of the coconut rhinoceros beetle Oryctes rhinoceros identifies physiologically important full-length genes and sheds insights into the molecular relationship (chitin synthase) between Scarabaeidae (Coleoptera) and Hymenoptera.}, journal = {3 Biotech}, volume = {15}, number = {6}, pages = {182}, pmid = {40417658}, issn = {2190-572X}, abstract = {UNLABELLED: The sparser molecular data in non-model insects such as Oryctes rhinoceros prompted us to investigate and identify its physiologically important genes using the novel PacBio Iso-Seq Sequel II platform with single-molecule real-time (SMRT) technology. SMRT library was prepared from various tissues and sequenced. In total, 16,916,297 subreads clustered into 17,547 contigs which collapsed to form 8708 full-length sequences out of which 4352 functionally annotated transcripts were identified. Genes involved in innate immunity, growth and development, hormonal regulation, cellular process, peritrophic membrane, melanogenesis, integument, circulation, cuticle formation, glycan metabolism, etc., were identified. The transcripts' orthologues were identified predominantly in Coleoptera and Hymenoptera in which chitin synthase (CHS), toll, haemocytin, serine protease/limulus clotting factor c, vitellogenin and trehalose transporter exhibited significant molecular relationships between these two insect orders. Chitin synthase 8 (CHS-8) found in ant has been identified for the first time in the order Coleoptera. (O. rhinoceros) at the translational level and projected a potential to explore evolution (horizontal gene transfer) of CHS in insects. The findings will bridge the molecular data between the genome and transcriptome of O. rhinoceros, thus helping develop molecular targets for its control and management.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04348-9.}, }
@article {pmid40409398, year = {2025}, author = {Zhang, Y and Zou, D and Ji, Y and Liu, S and Jiang, Y and Fan, F and Zou, C}, title = {The combined effect of microplastics and tetracycline on soil microbial communities and ARGs.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126482}, doi = {10.1016/j.envpol.2025.126482}, pmid = {40409398}, issn = {1873-6424}, abstract = {Microplastics (MPs), due to their difficult degradation and adsorption characteristics, are highly prone to form compound contamination with antibiotic residues in the soil environment, thereby disrupting the soil ecosystem. To address this issue of compound contamination, this study investigated the effects of compound contamination composed of three common MPs-polyethylene (PE), polyamide (PA), and polyvinyl chloride (PVC)-combined with tetracycline(TC), on the structure of soil microbial communities and resistance genes. The results showed that the effects of composite pollution on soil physicochemical properties, enzyme activities, bacterial communities, and antibiotic resistance genes (ARGs) were more significant compared to single-contaminant pollution. Among the composite contaminants, TC combined with PVC and PE significantly increased the absolute abundance of the tetC gene, while the composite contamination of TC with PA had the greatest effect on bacterial diversity. This also increased the relative abundance of the phylum Actinobacteria and significantly affected the relative abundance of the phylum Ascomycetes. In addition, significant correlations were found between soil physicochemical properties, enzyme activities, microbial communities, and ARGs. A positive correlation between the intl1 integrator gene and all target genes suggests that horizontal gene transfer contributes to the enrichment of ARGs. Furthermore, the bacterial genera correlated with ARGs-Ascomycetes, Acidobacteria, Actinobacteria, and Anaplasma-are the major bacterial hosts for ARGs in soil samples. This study provides data to support the investigation of combined microplastic and antibiotic contamination in soil.}, }
@article {pmid40408144, year = {2025}, author = {Quiñonero-Coronel, MDM and Cabello-Yeves, PJ and Haro-Moreno, JM and Rodriguez-Valera, F and Garcillán-Barcia, MP}, title = {The type IV secretion system of Patescibacteria is homologous to the bacterial monoderm conjugation machinery.}, journal = {Microbial genomics}, volume = {11}, number = {5}, pages = {}, doi = {10.1099/mgen.0.001409}, pmid = {40408144}, issn = {2057-5858}, mesh = {Phylogeny ; *Type IV Secretion Systems/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; *Conjugation, Genetic ; Computational Biology ; }, abstract = {The Candidate Phyla Radiation, also known as Patescibacteria, represents a vast and diverse division of bacteria that has come to light via culture-independent 'omics' technologies. Their limited biosynthetic capacity, along with evidence of their growth as obligate epibionts on other bacteria, suggests a broad reliance on host organisms for their survival. Nevertheless, our understanding of the molecular mechanisms governing their metabolism and lifestyle remains limited. The type IV secretion system (T4SS) represents a superfamily of translocation systems with a wide range of functional roles. T4SS genes have been identified in the Patescibacteria class Saccharimonadia as essential for their epibiotic growth. In this study, we used a comprehensive bioinformatics approach to investigate the diversity and distribution of T4SS within Patescibacteria. The phylogenetic analysis of the T4SS signature protein VirB4 suggests that most of these proteins cluster into a distinct monophyletic group with a shared ancestry to the MPFFATA class of T4SS. This class is found in the conjugative elements of Firmicutes, Actinobacteria, Tenericutes and Archaea, indicating a possible horizontal gene transfer from these monoderm micro-organisms to Patescibacteria. We identified additional T4SS components near virB4, particularly those associated with the MPFFATA class, as well as homologues of other T4SS classes, such as VirB2-like pilins, and observed their varied arrangements across different Patescibacteria classes. The absence of a relaxase in most of these T4SS clusters suggests that the system has been co-opted for other functions in Patescibacteria. The proximity of T4SS components to the origin of replication (gene dnaA) in some Patescibacteria suggests a potential mechanism for increased expression. The broad ubiquity of a phylogenetically distinct T4SS, combined with its chromosomal location, underscores the significance of T4SS in the biology of Patescibacteria.}, }
@article {pmid40407872, year = {2025}, author = {Suhajda, &#xc1; and Al-Nussairawi, M and Amara, I and Sörös, C and Tömösközi-Farkas, R and Kriszt, B and Farkas, M and Cserháti, M}, title = {Co-Occurrence of Beauvericin and Fumonisin Producing Ability of Fusarium Strains Isolated from Crop Plants in Hungary.}, journal = {Current microbiology}, volume = {82}, number = {7}, pages = {302}, pmid = {40407872}, issn = {1432-0991}, support = {TKP2021-NVA-22//"The feasibility of the circular economy during national defense activities" of 2021 Thematic Excellence Programme of the National Research Development and Innovation Office/ ; TKP2021-NVA-22//"The feasibility of the circular economy during national defense activities" of 2021 Thematic Excellence Programme of the National Research Development and Innovation Office/ ; TKP2021-NVA-22//"The feasibility of the circular economy during national defense activities" of 2021 Thematic Excellence Programme of the National Research Development and Innovation Office/ ; TKP2021-NVA-22//"The feasibility of the circular economy during national defense activities" of 2021 Thematic Excellence Programme of the National Research Development and Innovation Office/ ; TKP2021-NVA-22//"The feasibility of the circular economy during national defense activities" of 2021 Thematic Excellence Programme of the National Research Development and Innovation Office/ ; }, mesh = {*Depsipeptides/metabolism ; *Fusarium/metabolism/isolation &amp; purification/genetics/classification ; *Fumonisins/metabolism/analysis ; *Zea mays/microbiology ; Hungary ; Mycotoxins/metabolism ; Fungal Proteins/genetics/metabolism ; *Crops, Agricultural/microbiology ; Peptide Synthases/genetics ; }, abstract = {Beauvericin (BEA) is an emerging mycotoxin with wide-ranging bioactivity (antimicrobial and insecticide), making it a potential target for drug and pesticide development. BEA primarily produced by Beauveria, Isaria, and Fusarium species. The BEA-producing abilities of a collection of 100 Fusarium strains isolated from maize were tested using a gene-specific primer (Beas_1, Beas_2) by PCR. Among all, 23 were found to have the beauvericin synthetase (BEAS) gene sequence, which is responsible for the production of BEA. Fusarium proliferatum (6) and F. verticillioides (14) strains were producing the highest BEA concentrations. The toxin-producing ability of the strains was investigated in small bioreactors. Parallel with BEA, the most frequent Fusarium toxins such as deoxynivalenol (DON), T2, HT-2, zearalenone (ZEA), fumonisin B1 (FB1), and fumonisin B2 (FB2) were also measured. Only FB1 and FB2 were observed above the detection limit, the coexistence of the FBs and BEA was measured in high concentration. In all BEA-producing strains, the FBs production could be detected. The highest BEA concentration was 3131 mg/kg, and the highest FB1 and FB2 concentrations were 4393 mg/kg and 1390 mg/kg, respectively. In the present study, the gene sequences responsible for the production of BEA in F. verticilloides isolates have not only been detected but also demonstrated with UHPLC-ESI-MS/MS to be capable of biosynthesis. From the phylogenic analysis of the BEAS gene sequences, the assumption could be made that the ability to produce BEA was conferred via horizontal gene transfer.}, }
@article {pmid40407325, year = {2025}, author = {Mom, J and Valette, O and Pieulle, L and Pelicic, V}, title = {Unraveling the molecular mechanisms of DNA capture by the Com pilus in naturally transformable monoderm bacteria.}, journal = {mBio}, volume = {}, number = {}, pages = {e0085125}, doi = {10.1128/mbio.00851-25}, pmid = {40407325}, issn = {2150-7511}, abstract = {UNLABELLED: Transformation is a mechanism of horizontal gene transfer widespread in bacteria. The first step in transformation-capture of exogenous DNA-is mediated by surface-exposed filaments belonging to the type 4 filament (T4F) superfamily. How these protein polymers, composed of major and minor pilin subunits, interact with DNA remains poorly understood. Here, we address this question for the Com pilus, a widespread T4F mediating DNA capture in competent monoderm species. Our functional analysis, performed in Streptococcus sanguinis, was guided by a complete structural model of the Com pilus. We show that the major pilin ComGC does not bind DNA. In contrast, a systematic mutational analysis of electropositive residues exposed at the filament surface in the four minor pilins (ComGD, ComGE, ComGF, and ComGG) reveals that the interface between ComGD and ComGF is important for DNA capture. Sequential mutations in these two interacting subunits lead to complete abolition of transformation, without affecting piliation. We further demonstrate the physical interaction between ComGD and ComGF using disulfide crosslinking, upon mutagenesis of two strategically positioned residues into cysteines. A structural model of the Com pilus tip interacting with DNA recapitulates all these findings and highlights a novel mode of DNA-binding, conserved in hundreds of monoderm species.<br><br>IMPORTANCE: Bacteria are capable of evolving and diversifying very rapidly by acquiring new genetic material via horizontal gene transfer (HGT). Transformation is a widespread mechanism of HGT, which results from the capture of extracellular DNA by surface-exposed pili belonging to the type 4 filament (T4F) superfamily. How T4F-composed of major and minor pilins-interact with DNA remains poorly understood, especially in monoderm species that use a unique T4F for DNA capture, known as Com pilus or T4dP. The significance of this work is in characterizing a novel mode of DNA-binding by showing that the interface between two minor pilins, part of a tip-located complex of four pilins-found in different T4F-has been functionalized in monoderms to capture DNA. This is an evolutionary mechanism promoting the exceptional functional versatility of T4F.}, }
@article {pmid40403929, year = {2025}, author = {Shin, JI and Park, SH and Park, C and Jung, SH and Lee, DG}, title = {Genomic investigation of NDM-1 producing Enterobacterales transmission in a South Korean hospital.}, journal = {Journal of global antimicrobial resistance}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgar.2025.05.010}, pmid = {40403929}, issn = {2213-7173}, abstract = {OBJECTIVES: Prolonged detection of multispecies New Delhi metallo-β-lactamase (NDM)-1-producing Enterobacterales was observed previously in clinical and environmental samples collected from a South Korean hospital. This study aimed to investigate the transmission mechanisms of blaNDM-1 and assess the role of environmental reservoirs in its persistence.<br><br>METHODS: Epidemiological data were collected, and antibiotic susceptibility testing, carbapenemases detection, and whole-genome sequencing were performed on 42 clinical and 13 environmental isolates collected between November 2018 and February 2021, during the pre-outbreak, outbreak (July-September 2019), and post-outbreak periods. Long-read complete-genome sequencing was performed on four clinical and four environmental isolates to characterize plasmids carrying blaNDM-1 and associated mobile genetic elements (MGEs). Phylogenetic analyses were also performed.<br><br>RESULTS: blaNDM-1 was detected in 15 different species across clinical and environmental isolates. During the 2019 outbreak, clonal spread of Klebsiella pneumoniae and Klebsiella quasipneumoniae in the hospital was the primary mechanism of dissemination. During the post-outbreak period, horizontal gene transfer (HGT), mediated by the IncX3 plasmid carrying blaNDM-1, was the dominant transmission mechanism. This plasmid, detected in both clinical and environmental isolates, showed high genetic conservation with IncX3 plasmids reported worldwide. These plasmids contained conserved MGEs, including the IS26-dsbD-trpF-ble-blaNDM-1 structure.<br><br>CONCLUSION: This study highlights the dual roles of clonal spread and plasmid-mediated HGT in the dissemination of blaNDM-1 in hospital settings. The persistence of highly conserved IncX3 plasmids in environmental isolates underscores the complexity of carbapenem resistance control. Comprehensive infection control strategies targeting patient-to-patient transmission and environmental reservoirs are crucial for mitigating the spread of NDM-producing Enterobacterales.}, }
@article {pmid40402828, year = {2025}, author = {Bremer, N and Martin, WF and Steel, M}, title = {Surprising effects of differential loss in genome evolution: the last-one-out.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnaf051}, pmid = {40402828}, issn = {1574-6968}, abstract = {Gene loss is an important process in genome evolution, though its power is often underestimated. If a gene is present at the root of a phylogenetic tree and can be lost in one lineage across the tree, it can potentially be lost in all, leading to gene extinction. Just before gene extinction, there will be one lineage that still retains the gene, generating a 'last-one-out' distribution. Such an isolated gene presence will emulate the result of recent lateral gene acquisition, even though its distribution was generated by loss. How probable is it to observe 'last-one-out' distributions in real data? Here we mathematically derive this probability and find that it is surprisingly high, depending upon the tree and the gene loss rate. Examples from real data show that loss can readily account for observed frequencies of last-one-out gene distributions that might otherwise be attributed to lateral gene transfer.}, }
@article {pmid40402243, year = {2025}, author = {Gozashti, L and Nakamoto, A and Russell, S and Corbett-Detig, R}, title = {Horizontal transmission of functionally diverse transposons is a major source of new introns.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {21}, pages = {e2414761122}, doi = {10.1073/pnas.2414761122}, pmid = {40402243}, issn = {1091-6490}, support = {R35GM128932//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R00GM135583//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; GRFP//NSF | NSF Graduate Research Fellowship Program (GRFP)/ ; }, mesh = {*Introns/genetics ; *DNA Transposable Elements/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Phylogeny ; Genome ; Retroelements/genetics ; Eukaryota/genetics ; Animals ; Humans ; }, abstract = {Since the discovery of spliceosomal introns in eukaryotic genomes, the proximate molecular and evolutionary processes that generate new introns have remained a critical mystery. Specialized transposable elements (TEs), introners, are thought to be one of the major drivers of intron gain in diverse eukaryotes. However, the molecular mechanism(s) and evolutionary processes driving introner propagation within and between lineages remain elusive. Here, we analyze 8,716 genomes, revealing 1,093 introner families in 201 species spanning 1.7 billion years of evolution. Introners are derived from functionally diverse TEs including families of terminal-inverted-repeat DNA TEs, retrotransposons, cryptons, and helitrons as well as mobile elements with unknown molecular mechanisms. We identify eight cases where introners recently transferred between divergent host species and show that giant viruses that integrate into genomes may facilitate introner transfer across lineages. We propose that ongoing intron gain is primarily a consequence of TE activity in eukaryotes, thereby resolving a key mystery of genome structure evolution.}, }
@article {pmid40401976, year = {2025}, author = {Qamar, MU and Sierra, R and Jabeen, K and Rizwan, M and Rashid, A and Dar, YF and Andrey, DO}, title = {Genomic characterization of plasmids harboring blaNDM-1, blaNDM-5, and blaNDM-7 carbapenemase alleles in clinical Klebsiella pneumoniae in Pakistan.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0235924}, doi = {10.1128/spectrum.02359-24}, pmid = {40401976}, issn = {2165-0497}, abstract = {UNLABELLED: Klebsiella pneumoniae is notorious for causing healthcare-associated infections, which become more complicated by the acquisition of blaNDM genes via mobile genetic elements. Although Pakistan is a well-established hot spot of blaNDM-positive K. pneumoniae, detailed molecular descriptions of blaNDM-carrying plasmids are scarce. Seven K. pneumoniae isolates harboring blaNDM were recovered from clinical sample sources during a 6 month period and tested for antimicrobial susceptibility. A long-read approach was used for whole-genome sequencing to obtain circularized plasmids and chromosomes for typing, annotation, and comparative analysis. The isolates were susceptible to colistin and tigecycline only among the tested antibiotics. We identified five sequence types (STs): ST11, ST16, ST716, ST464, and ST2856. Notably, three strains possessed the hypervirulent capsule KL2, while five were classified as O locus type O2a. Evidence of genetic diversity was further highlighted by the presence of four IncC plasmids harboring blaNDM-1, two IncX3 plasmids harboring blaNDM-5, and a single hybrid IncFIB/IncHI1B plasmid harboring blaNDM-7. These plasmids also carried additional antimicrobial resistance (AMR) genes conferring resistance to aminoglycosides, cephalosporins, and fluoroquinolones. We identified the plasmidome of the K. pneumoniae isolates and characterized the New Delhi metallo-beta-lactamase (NDM)-carrying plasmids. Genetic analysis confirmed the presence of blaNDM-1 and blaNDM-5 on broad host range plasmids and blaNDM-7 in a previously unreported hybrid plasmid backbone. We emphasized the critical role of plasmids in spreading blaNDM in the clinical setting in Pakistan. Hence, we stressed the urgent need for enhanced surveillance, not least in low-middle income countries, infection control measures, and adherence to the "Access," "Watch," and "Reserve" guidelines in antibiotics use.<br><br>IMPORTANCE: Infections caused by NDM-producing Klebsiella pneumoniae are a significant challenge to treat and represent a crucial health burden in low- and middle-income countries (LMICs). Most of the blaNDM are located on plasmids that promote horizontal gene transfer. However, there is a lack of comprehensive information on the genetic context of the NDM-carrying plasmids in Pakistan. This study presents a detailed analysis of seven NDM-plasmids in clinical K. pneumoniae isolates, shedding light on their high-risk sequence types and multiple resistance determinants. We also describe the plasmid-bearing NDM alleles (blaNDM-1, blaNDM-5, and blaNDM-7). Notably, we are the first to report blaNDM-7 on the hybrid IncFIB/IncHI1B backbone in Pakistan, a plasmid that has rarely been reported previously globally. Understanding the plasmid genomic landscape is paramount to comprehensively understanding the AMR scenario in this LMIC.}, }
@article {pmid40400687, year = {2025}, author = {Guerrero-Flores, S and Contreras-Peruyero, H and Ibarra-Rodríguez, JM and Lovaco-Flores, JA and Nieto-de la Rosa, FS and Fontove-Herrera, F and Sélem-Mojica, N}, title = {Topological data analysis captures horizontal gene transfer in antimicrobial resistance gene families among clinically relevant bacteria.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1461293}, pmid = {40400687}, issn = {1664-302X}, abstract = {Antibiotic resistance, projected to cause 10 million deaths annually by 2050, remains a critical health threat. Hospitals drive multidrug resistance via horizontal gene transfer. The 2023 Critical Assessment of Massive Data Analysis challenge presents resistance markers from 146 Johns Hopkins bacterial isolates, aiming to analyze resistomes without metadata or genomic sequences. Persistent homology, a topological data analysis method, effectively captures processes beyond vertical inheritance. A 1-hole is a topological feature representing a loop or gap in the data, where relationships form a circular structure rather than a linear one. Unlike vertical inheritance, which lacks topological 1-holes, horizontal gene transfer generates distinct patterns. Since antimicrobial resistance genes often spread via horizontal gene transfer, we simulated vertical and horizontal inheritance in bacterial resistomes. The number of 1-holes from simulations and a documented horizontal gene transfer case was analyzed using persistence barcodes. In a simulated population of binary sequences, we observed that, on average, two 1-holes form for every three genomes undergoing horizontal gene transfer. Using a presence-absence gene table, we confirmed the existence of 1-holes in a documented case of horizontal gene transfer between two bacterial genera in a Pittsburgh hospital. Notably, the Critical Assessment of Massive Data Analysis resistomes of Klebsiella and Escherichia exhibit 1-holes, while Enterobacter shows none. Lastly, we provide a mathematical example of a non-tree-like space that contains no 1-holes. Persistent homology provides a framework for uncovering complex clinical patterns, offering an alternative to understanding resistance mobility using presence-absence data, which could be obtained through methods beyond genomic sequencing.}, }
@article {pmid40400517, year = {2025}, author = {Ohata, Y and Sugimoto, TN and Wybouw, N and Tagami, Y}, title = {Suppression of cytoplasmic incompatibility in the leaf-mining fly Liriomyza sativae with a nuclear Wolbachia insert.}, journal = {Royal Society open science}, volume = {12}, number = {5}, pages = {242137}, pmid = {40400517}, issn = {2054-5703}, abstract = {Cytoplasmic incompatibility (CI) drives maternally transmitted endosymbionts such as Wolbachia through insect populations by inducing embryonic mortality when infected males fertilize uninfected females. CI is controlled by Wolbachia cif operons that are categorized into multiple phylogenetic types. CI strength is further shaped by poorly understood host factors, including development and genetic background. To study the strength of CI across different host species, we genotyped a Japanese field population of Liriomyza sativae. By uncovering paternal transmission of Wolbachia genic elements, we collected strong evidence of horizontal genome transfer, including Type I and Type V cif operons, from Wolbachia into the nuclear genome of L. sativae. We established a transinfection of wLtri in L. sativae, a Wolbachia variant that induces strong CI in Liriomyza trifolii. No CI was observed in both intraspecific and interspecific reciprocal crosses with L. trifolii, suggesting that both uninfected females and infected males of L. sativae completely suppress wLtri-mediated CI. Our results raise the appealing hypothesis that host suppression of Wolbachia-induced CI might evolve owing to horizontal transfer of cif operons into the host nuclear genome.}, }
@article {pmid40398027, year = {2025}, author = {Zhang, J and Li, B and Shen, Z and Zhang, Z and Feng, J and Wong, JWC}, title = {Antibiotic resistance patterns and cross-family ARG transfer in families Burkholderiaceae and Sphingomonadaceae: A large-scale genome-wide analysis of over 10 K genomes.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138642}, doi = {10.1016/j.jhazmat.2025.138642}, pmid = {40398027}, issn = {1873-3336}, abstract = {Members of Burkholderiaceae and Sphingomonadaceae play an active role in pollutant degradation, yet their antibiotic resistance risks are frequently overlooked. This study analyzed 9406 Burkholderiaceae and 2343 Sphingomonadaceae genomes to investigate the distribution, horizontal gene transfer (HGT), and co-occurrence patterns of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs). ARGs were prevalent in Burkholderiaceae (93.2 % of genomes), dominated by bacitracin (89.0 %), multidrug (88.1 %), and beta-lactam (40.5 %) resistance, while Sphingomonadaceae exhibited lower ARG prevalence (11.6 %). Notably, Burkholderia and Caballeronia displayed high multidrug resistance (10.1 ARGs per genome) and frequent ARG-MRG co-occurrence (84.4 %). Strong ARG-MRG-MGE correlations were observed in Burkholderiaceae, suggesting MGEs play a key role in resistance dissemination. Additionally, ARGs correlated with metabolic genes, linking metabolic versatility to resistance. Genes like capO (chloramphenicol oxidase) and blaTEM-116 (beta-lactamase) were shared among distantly related genera, while mcr-5.1 (MCR phosphoethanolamine transferase) co-occurred with MRGs across Cupriavidus species, highlighting HGT and co-selection risks. ARG transfer between Burkholderiaceae, Sphingomonadaceae and clinical pathogens was frequent (114-1306 events/10,000 genome pairs), with sulfonamide resistance dominating (51.3 % of HGT). These findings highlight Burkholderiaceae and Sphingomonadaceae as critical reservoirs of resistance genes and emphasize the need for enhanced surveillance and mitigation strategies to curb the spread of multidrug resistance.}, }
@article {pmid40298401, year = {2025}, author = {Pan, T and Li, Q}, title = {Mobile genetic elements in Klebsiella pneumoniae.}, journal = {Journal of bacteriology}, volume = {207}, number = {5}, pages = {e0001225}, doi = {10.1128/jb.00012-25}, pmid = {40298401}, issn = {1098-5530}, mesh = {*Klebsiella pneumoniae/genetics/pathogenicity/drug effects ; *Interspersed Repetitive Sequences ; Humans ; Virulence/genetics ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; Plasmids/genetics ; Klebsiella Infections/microbiology ; Genome, Bacterial ; DNA Transposable Elements ; Drug Resistance, Multiple, Bacterial ; }, abstract = {Klebsiella pneumoniae is a clinically important pathogenic bacteria that poses a serious threat to human health. In particular, the emergence of hypervirulent and multidrug-resistant K. pneumoniae has posed great challenges in clinical anti-infective therapy. In the K. pneumoniae genome, mobile genetic elements (MGEs), such as plasmids, prophages, transposons, and insertion sequences, enhance bacterial viability and adaptation by mediating the horizontal transfer of virulence genes, antibiotic resistance genes, and other adaptive genes. This paper reviews the types and characteristics of the main MGEs in K. pneumoniae, focusing on their effects on bacterial virulence and antibiotic resistance, with the aim of providing clues for developing infection control measures and new antibacterial drugs.}, }
@article {pmid40397871, year = {2025}, author = {Granato, ET and Palmer, JD and Kirk, C and Sharp, C and Shillcock, G and Foster, KR}, title = {Horizontal gene transfer of molecular weapons can reshape bacterial competition.}, journal = {PLoS biology}, volume = {23}, number = {5}, pages = {e3003095}, doi = {10.1371/journal.pbio.3003095}, pmid = {40397871}, issn = {1545-7885}, mesh = {*Gene Transfer, Horizontal ; *Escherichia coli/genetics ; Plasmids/genetics ; Colicins/genetics ; *Bacteria/genetics ; }, abstract = {Bacteria commonly use molecular weaponry to kill or inhibit competitors. Genes encoding many weapons and their associated immunity mechanisms can be transmitted horizontally. These transfer events are striking because they appear to undermine bacterial weapons when given to competing strains. Here, we develop an ecological model of bacterial warfare to understand the impacts of horizontal gene transfer. Our model predicts that weapon gene transfer from an attacker to a target strain is possible, but will typically occur at a low rate such that transfer has a negligible impact on competition outcomes. We tested the model empirically using a transmissible plasmid encoding colicin E2, a potent antibacterial toxin produced by Escherichia coli. As predicted by the model, we find that toxin plasmid transfer is feasible during warfare, but the resulting transconjugants remain rare. However, exploring the model further reveals realistic conditions where transfer is predicted to have major impacts. Specifically, the model predicts that whenever competing strains have access to unique nutrients, transconjugants can proliferate and reach high abundances. In support of these predictions, short- and long-term experiments show that transconjugants can thrive when nutrient competition is relaxed. Our work shows how horizontal gene transfer can reshape bacterial warfare in a way that benefits a weapon gene and strains that receive it. Interestingly, we also find that there is little cost to a strain that transfers a weapon gene, which is expected to further enable the horizontal gene transfer of molecular weapons.}, }
@article {pmid40396743, year = {2025}, author = {Zhang, T and Han, Y and Peng, Y and Deng, Z and Shi, W and Xu, X and Wu, Y and Dong, X}, title = {The risk of pathogenicity and antibiotic resistance in deep-sea cold seep microorganisms.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0157124}, doi = {10.1128/msystems.01571-24}, pmid = {40396743}, issn = {2379-5077}, abstract = {UNLABELLED: Deep-sea cold seeps host high microbial biomass and biodiversity that thrive on hydrocarbon and inorganic compound seepage, exhibiting diverse ecological functions and unique genetic resources. However, potential health risks from pathogenic or antibiotic-resistant microorganisms in these environments remain largely overlooked, especially during resource exploitation and laboratory research. Here, we analyzed 165 metagenomes and 33 metatranscriptomes from 16 global cold seep sites to investigate the diversity and distribution of virulence factors (VFs), antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs). A total of 2,353 VFs are retrieved in 689 metagenome-assembled genomes (MAGs), primarily associated with indirect pathogenesis like adherence. In addition, cold seeps harbor nearly 100,000 ARGs, as important reservoirs, with high-risk ARGs (11.22%) presenting at low abundance. Compared to other environments, microorganisms in cold seeps exhibit substantial differences in VF and ARG counts, with potential horizontal gene transfer facilitating their spread. These virulome and resistome profiles provide valuable insights into the evolutionary and ecological implications of pathogenicity and antibiotic resistance in extreme deep-sea ecosystems. Collectively, these results indicate that cold seep sediments pose minimal public health risks, shedding light on environmental safety in deep-sea resource exploitation and research.<br><br>IMPORTANCE: In the "One Health" era, understanding pathogenicity and antibiotic resistance in vast and largely unexplored regions like deep-sea cold seeps is critical for assessing public health risks. These environments serve as critical reservoirs where resistant and virulent bacteria can persist, adapt, and undergo genetic evolution. The increasing scope of human activities, such as deep-sea mining, is disrupting these previously isolated ecosystems, heightening the potential for microbial exchange between deep-sea communities and human or animal populations. This interaction poses a significant risk for the dissemination of resistance and virulence genes, with potential consequences for global public health and ecosystem stability. This study offers the first comprehensive analysis of virulome, resistome, and mobilome profiles in cold seep microbial communities. While cold seeps act as reservoirs for diverse ARGs, high-risk ARGs are rare, and most VFs were low risk that contribute to ecological functions. These results provide a reference for monitoring the spread of pathogenicity and resistance in extreme ecosystems, informing environmental safety assessments during deep-sea resource exploitation.}, }
@article {pmid40390443, year = {2025}, author = {Xu, M and Gao, P and Chen, HQ and Gao, Y and Xiong, SJ and Wang, XH}, title = {[Effects of Typical Microplastics on Methanogenesis and Antibiotic Resistance Genes in Anaerobic Digestion of Sludge].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {46}, number = {5}, pages = {3189-3199}, doi = {10.13227/j.hjkx.202405273}, pmid = {40390443}, issn = {0250-3301}, mesh = {*Sewage/microbiology/chemistry ; *Methane/metabolism/biosynthesis ; *Drug Resistance, Microbial/genetics ; Anaerobiosis ; *Microplastics ; *Waste Disposal, Fluid/methods ; Bioreactors/microbiology ; Bacteria/genetics ; }, abstract = {Waste sludge is an important carrier of antibiotic resistance genes （ARGs） and an important place for the enrichment of microplastics （MPs）. To explore the impacts of typical MPs on sludge recycling and harmless disposal, the effects of polyamide （PA）, polyethylene （PE）, and polypropylene （PP） MPs on the methanogenesis efficiency of anaerobic digestion were investigated. Meanwhile, based on metagenomic sequencing, the effects of MPs on ARGs, mobile genetic elements （MGEs）, microbial community structure, and host bacteria during anaerobic digestion were analyzed. The results showed that PA-MPs, PE-MPs, and PP-MPs increased the distribution of methane production by 2.2%, 22.3%, and 28.8%, respectively. MPs promoted methanation by improving the dissolution and hydrolysis efficiency of organic matter, and the enrichment of hydrogenotrophic methanogens by PP-MPs further improved the methanogenic efficiency. PA-MPs contributed to the removal of ARGs, while PE-MPs and PP-MPs had adverse effects on the reduction of ARGs. Horizontal gene transfer mediated by integron and insertion sequences was an important factor in the spread of ARGs. Proteobacteria was the key host leading to the diffusion of ARGs. The removal of pathogens from Bacteroidetes by anaerobic digestion contributed to the reduction of ARGs. The selective enrichment or inhibition of Arenimonas, Acinetobacter, Actinobacillus, Nitrospira, and other important host bacteria by MPs was the major cause for the difference in the removal effect of ARGs.}, }
@article {pmid40382874, year = {2025}, author = {Miao, S and Zhang, Y and Wu, L and Wang, Y and Zuo, J}, title = {Resistance induction potency assessment of antibiotic production wastewater and associated resistome shaping mechanisms.}, journal = {Water research}, volume = {283}, number = {}, pages = {123811}, doi = {10.1016/j.watres.2025.123811}, pmid = {40382874}, issn = {1879-2448}, abstract = {Antibiotic production wastewater (APW) contains multiple substances known to select for and facilitate horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs); however, whether these substances can induce the evolution of antibiotic resistance in real wastewater environments and the fate of such resistance induction potency during the treatment process are poorly understood, nor are its relationship with wastewater quality parameters and function in shaping the antibiotic resistome. In this study, the impacts of filter-sterilized APW and municipal wastewater on the resistance selection of Escherichia coli and the transfer dynamics of conjugative RP4 plasmid-borne ARGs across indigenous sludge communities were evaluated. The resistance development and transfer processes were accelerated in APW owing to enhanced growth inhibition, oxidative stress, and membrane permeability, with antibiotic concentrations much lower than their minimum inhibition concentrations. The effects were reduced simultaneously with the removal of COD and NH3N, but APW effluents still exhibited significant resistance induction potency with wastewater quality parameters meeting discharge standards. In contrast, municipal wastewater did not result in any detectable changes. Based on the metagenomic assembly and binning, stronger resistance induction potency in the antibiotic production wastewater treatment plant endowed indigenous sludge and effluent with greater accumulation, genetic mobility, and pathogenic accessibility of ARGs than in the municipal wastewater treatment plant. Antibiotic resistome assembly was determined primarily by deterministic processes, driven jointly by resistance induction potency, mobilome variance, and microbiome shifts. These results provide novel insights into the application of bioassays to comprehensively evaluate the antibiotic resistance induction effects of APW and their relationships with the resistome to manage risks during the treatment process.}, }
@article {pmid39988053, year = {2025}, author = {Monesi, N and Fernandes, GM and Valer, FB and Uliana, JVC and Trinca, V and Azzolini, AECS and Gorab, E and Alberici, LC}, title = {Identification and characterization of a laterally transferred alternative oxidase (AOX) in a terrestrial insect, the dipteran Pseudolycoriella hygida.}, journal = {Biochimie}, volume = {233}, number = {}, pages = {60-74}, doi = {10.1016/j.biochi.2025.02.007}, pmid = {39988053}, issn = {1638-6183}, mesh = {Animals ; *Mitochondrial Proteins/genetics/metabolism/antagonists &amp; inhibitors ; *Oxidoreductases/genetics/metabolism/antagonists &amp; inhibitors ; *Plant Proteins/genetics/metabolism ; *Diptera/enzymology/genetics ; Mitochondria/enzymology/metabolism ; *Gene Transfer, Horizontal ; *Insect Proteins/genetics/metabolism ; Phylogeny ; Salicylamides ; }, abstract = {Alternative oxidase (AOX) (EC 1.10.3.11) is a terminal oxidase in the mitochondrial inner membrane that branches the canonical electron transport system (ETS). AOX is ubiquitous in plants, frequently found in fungi and protists and presents a more sporadic distribution in metazoans. More recently, AOX has gained attention due to its potential application in gene therapy for treatment of mitochondrial diseases. Here we characterized the AOX in the basal Dipteran, Pseudolycoriella hygida using a combination of genomic analyses, molecular, functional and in vivo survival assays. AOX is a single copy gene that encodes three developmental stage specific protein isoforms. AOX localizes to the mitochondria in adult thoracic muscles, which present cyanide-resistant respiration that is sensitive to the AOX inhibitor salicylhydroxamic acid (SHAM). Both the cyanide-resistant respiration and AOX levels gradually increase during aging, but are not influenced by thermal stress. Thoracic mitochondria respire using substrates derived from several metabolic routes, such as pyruvate, proline, acylcarnitine, NADH and glycerol-3P, and present values of oxidative phosphorylation capacity ((P-L)/E = 0.70) and coupling (P/L = 4.35; L/E = 0.21). Adult flies exhibit a high survival resistance for SHAM-sensitive complex III inhibition. Together, our results demonstrate the presence of a functional AOX in a terrestrial arthropod and provide insights regarding AOX function in animals and evolution of respiratory systems in metazoans. Psl. hygida emerges as a natural and valuable model for comprehensive AOX research at the whole-organism level which complements models expressing the heterologous enzyme.}, }
@article {pmid40381794, year = {2025}, author = {Yaikhan, T and Singkhamanan, K and Dechathai, T and Chukamnerd, A and Chusri, S and Pomwised, R and Wonglapsuwan, M and Surachat, K}, title = {Genome-based alert on a clinical Plesiomonas shigelloides PSU59 from Thailand: Resistance and virulence features.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {}, number = {}, pages = {105764}, doi = {10.1016/j.meegid.2025.105764}, pmid = {40381794}, issn = {1567-7257}, abstract = {Plesiomonas shigelloides, an aquatic Gram-negative bacterium, is increasingly recognized as an emerging pathogen with antimicrobial resistance (AMR) potential. This study provides a genome-based alert on P. shigelloides PSU59, isolated from a patient in Thailand. Whole-genome sequencing (WGS) revealed a 3.6 Mb draft genome (38 contigs, 51.9 % GC) encoding 3265 coding sequences and 129 RNA genes. Thirteen AMR genes were identified, including efflux pumps (adeF, tet(A)), target modifiers (dfrA1, sul2), and aminoglycoside-inactivating enzymes. Mobile genetic elements (MGEs) flanking resistance genes suggest horizontal gene transfer (HGT). Virulence analysis revealed 48 factors, notably flagellar genes (fliM, fliN, flhA) linked to motility. Phylogenetic comparison placed PSU59 in Clade 3, closely related to a food-derived strain. These results highlight the pathogenic and drug-resistant potential of P. shigelloides PSU59 and underscore the importance of genomic surveillance in tracking emerging threats among under-recognized pathogens.}, }
@article {pmid40381353, year = {2025}, author = {Xin, Y and Zhang, J and Tang, Q and Wei, M and Zhu, L and Zhao, Y and Cui, Y and Sun, T and Wei, Y and Richnow, HH}, title = {Virus-host interactions driving the transfer of antibiotic resistance genes in a river-reservoir system under heavy rainfall.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138605}, doi = {10.1016/j.jhazmat.2025.138605}, pmid = {40381353}, issn = {1873-3336}, abstract = {Global river systems are grappling with severe pollution from antibiotic resistance genes (ARGs), with river-reservoir (R-R) systems being a common feature in urban waterways. The intensified extreme rainfall events triggered by global climate change exacerbate the spread of ARGs posed by non-point source pollution and combined sewage overflows. This study employs a metagenomics approach to decipher the profile of ARGs and virus-host interactions driving their transfer under heavy rainfall in North Canal, Beijing, with extensive R-R systems. Results indicated that R-R systems contributed to ARGs reduction despite continuous discharge of treated wastewater into the North Canal. The ARGs assembly is predominantly governed by stochastic process, and heavy rainfall enhances the dispersal capability. Nonetheless, the deterministic process determined the assembly of both microbial and viral community. Heavy rainfall not only significantly increased the abundance and diversity of ARGs within the rivers with minimal change in the reservoir, but also promotes the horizontal gene transfer of ARGs with higher conjugative mobility. Although the species accumulation curves approached saturation, no viruses carrying ARGs were detected among the 23,835 non-redundant viral operational taxonomic units (vOTUs), and lytic phage-ARB interactions drove the ARGs reduction with higher VHRs, highlighting its contribution to the reduction of ARGs in R-R system after heavy rainfall.}, }
@article {pmid40379875, year = {2025}, author = {Guédon, G and Charron-Bourgoin, F and Lacroix, T and Hamadouche, T and Soler, N and Douzi, B and Chiapello, H and Leblond-Bourget, N}, title = {Massive acquisition of conjugative and mobilizable integrated elements fuels Faecalibacterium plasticity and hints at their adaptation to the gut.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {17013}, pmid = {40379875}, issn = {2045-2322}, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; Genome, Bacterial ; *Faecalibacterium/genetics/physiology ; *Conjugation, Genetic ; *Adaptation, Physiological/genetics ; Feces/microbiology ; Phylogeny ; }, abstract = {Faecalibacterium is one of the most abundant bacteria of the human gut microbiota of healthy adults and is recognized to have positive effects on health. Here, we precisely and comprehensively analyzed the conjugative mobilome of four complete Faecalibacterium genomes. Despite lacking any plasmid, these bacteria harbor a vast arsenal of 130 elements, including 17 integrative and conjugative elements (ICEs) and 83 integrative and mobilizable elements (IMEs), collectively comprising 14-23% of the genome. Genome comparison of two strains isolated from the same fecal sample (Faecalibacterium and Roseburia strains) revealed almost identical elements indicating that transfer of ICEs and IMEs shape gut microbiome. ICEs and IMEs from Faecalibacterium encode many and diverse predicted functions such as defense and stress response (phages, multidrug, antibiotics, oxidative stress, biliar salts, antimicrobial peptides), nutrient import and metabolisms (Fe[3+], carbohydrates) and riboflavin synthesis. This hints at their important role in the survival and adaptation of Faecalibacterium strains to the gut ecosystem. A rapid survey of 29 additional Faecalibacterium genomes uncovered many putative ICEs and IMEs, reinforcing their role in the rapid and massive evolution of Faecalibacterium genomes.}, }
@article {pmid40378740, year = {2025}, author = {Ding, Y and Dong, S and Ding, D and Chen, X and Xu, F and Niu, H and Xu, J and Fan, Y and Chen, R and Xia, Y and Qiu, X and Feng, H}, title = {Overlooked risk of dissemination and mobility of antibiotic resistance genes in freshwater aquaculture of the Micropterus salmoides in Zhejiang, China.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138604}, doi = {10.1016/j.jhazmat.2025.138604}, pmid = {40378740}, issn = {1873-3336}, abstract = {Residual antibiotics in aquaculture ecosystems can exert selective pressures on bacterial communities, driving bacteria to acquire antibiotic resistance genes (ARGs) through gene mutations or horizontal gene transfer (HGT). This study investigated the antibiotic resistance risk in freshwater aquaculture ecosystems of Micropterus salmoides in Zhejiang Province. The results revealed that oxytetracycline, ciprofloxacin and florfenicol were up to 300 ng/L, and the proportion of multidrug-resistant genes varied from 32.20 % to 50.70 % in the surveyed aquaculture water. Additionally, approximately 9.80 % of all annotated ARGs were identified as possessing plasmid-mediated horizontal transfer risks. The ARGs host prediction revealed that Actinobacteria carried the highest abundance of ARGs, up to 159.38 (coverage, ×/Gb). Furthermore, the abundance of Paer_emrE, ksgA, ompR and golS were positively correlated with Chlorophyll a concentration (p < 0.05), suggesting that algal blooms might facilitate the evolution and transfer of ARGs. Correlations between ARG abundances and total phosphorus, total nitrogen, pH, electrical conductivity indicated that modulating water quality parameters may serve as a viable strategy to mitigate the eco-environmental risk of ARGs in aquaculture water. This study identified antibiotic resistance characteristics in freshwater aquaculture ecosystems of Micropterus salmoides in Zhejiang Province, establishing a foundation on managing antibiotic resistance risks in such aquaculture environments.}, }
@article {pmid40378350, year = {2025}, author = {Bean, EL and Smith, JL and Grossman, AD}, title = {Identification of insertion sites for the integrative and conjugative element Tn916 in the Bacillus subtilis chromosome.}, journal = {PloS one}, volume = {20}, number = {5}, pages = {e0318964}, pmid = {40378350}, issn = {1932-6203}, mesh = {*Bacillus subtilis/genetics ; *Chromosomes, Bacterial/genetics ; *DNA Transposable Elements/genetics ; *Conjugation, Genetic ; Base Sequence ; Bacterial Proteins/metabolism/genetics ; Gene Transfer, Horizontal ; }, abstract = {Integrative and conjugative elements (ICEs) are found in many bacterial species and are mediators of horizontal gene transfer. Tn916 is an ICE found in several Gram-positive genera, including Enterococcus, Staphylococcus, Streptococcus, and Clostridioides (previously Clostridium). In contrast to the many ICEs that preferentially integrate into a single site, Tn916 can integrate into many sites in the host chromosome. The consensus integration motif for Tn916, based on analyses of approximately 200 independent insertions, is an approximately 16 bp AT-rich sequence. Here, we describe the identification and mapping of approximately 105 independent Tn916 insertions in the Bacillus subtilis chromosome. The insertions were distributed between 1,554 chromosomal sites, and approximately 99% of the insertions were in 303 sites and 65% were in only ten sites. One region, between ykuC and ykyB (kre), was a 'hotspot' for integration with ~22% of the insertions in that single location. In almost all of the top 99% of sites, Tn916 was found with similar frequencies in both orientations relative to the chromosome and relative to the direction of transcription, with a few notable exceptions. Using the sequences of all insertion regions, we determined a consensus motif which is similar to that previously identified for C. difficile. The insertion sites are largely AT-rich, and some sites overlap with regions bound by the nucleoid-associated protein Rok, a functional analog of H-NS of Gram-negative bacteria. Rok functions as a negative regulator of at least some horizontally acquired genes. We found that the presence or absence of Rok had little or no effect on insertion site specificity of Tn916.}, }
@article {pmid40378191, year = {2025}, author = {Policarpo, M and Salzburger, W and Maumus, F and Gilbert, C}, title = {Multiple horizontal transfers of immune genes between distantly related teleost fishes.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msaf107}, pmid = {40378191}, issn = {1537-1719}, abstract = {Horizontal gene transfer (HGT) is less frequent in eukaryotes than in prokaryotes, yet can have strong functional implications and was proposed as causal factor for major adaptations in several eukaryotic lineages. Most cases of eukaryote HGT reported to date are inter-domain transfers and few studies have investigated eukaryote-to-eukaryote HGTs. Here, we performed a large-scale survey of HGT among 242 species of ray-finned fishes. We found multiple lines of evidence supporting 19 teleost-to-teleost HGT events that involve 17 different genes in 11 teleost fish orders. The genes involved in these transfers show lower synonymous divergence than expected under vertical transmission, their phylogeny is inconsistent with that of teleost fishes, and they occur at non syntenic positions in donor and recipient lineages. The distribution of HGT events in the teleost tree is heterogenous, with eight of the 19 transfers occurring between the same two orders (Osmeriformes and Clupeiformes). Though we favor a scenario involving multiple HGT events, future work should evaluate whether hybridization between species belonging to different teleost orders may generate HGT-like patterns. Besides the previously reported transfer of an antifreeze protein, most transferred genes play roles in immunity or are pore forming proteins, suggesting that such genes may be more likely than others to confer strong selective advantage to the recipient species. Overall, our work shows that teleost-to-teleost HGT has occurred on multiple occasions, and it will be worth further quantifying these transfers and evaluating their impact on teleost evolution as more genomes are sequenced.}, }
@article {pmid40374465, year = {2025}, author = {Toribio-Celestino, L and San Millan, A}, title = {Plasmid-bacteria associations in the clinical context.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2025.04.011}, pmid = {40374465}, issn = {1878-4380}, abstract = {Antimicrobial resistance (AMR) is one of the most pressing global health problems, with plasmids playing a central role in its evolution and dissemination. Over the past decades, many studies have investigated the ecoevolutionary dynamics between plasmids and their bacterial hosts. However, what drives the epidemiological success of certain plasmid-bacterium associations remains unclear. In this opinion article, we review which factors influence these associations and underline that studying plasmid-host interactions of clinical relevance is critical for understanding the evolution and spread of AMR. We also highlight the increasing importance of integrating experimental research with bioinformatics and machine learning tools to study plasmid-bacteria dynamics. This combined approach will assist researchers to dissect the molecular mechanisms underlying successful plasmid-host associations and to design strategies to prevent and predict future high-risk associations.}, }
@article {pmid40373943, year = {2025}, author = {Bhuiya, S and Kaushik, S and Logheeswaran, J and Karthika, P and Prathiviraj, R and Selvin, J and Kiran, GS}, title = {Emergence of Recurrent Urinary Tract Infection: Dissecting the mechanism of Antimicrobial Resistance, Host-Pathogen Interaction, and Hormonal Imbalance.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {107698}, doi = {10.1016/j.micpath.2025.107698}, pmid = {40373943}, issn = {1096-1208}, abstract = {Urinary tract infection is one of the most common infections worldwide, causing numerous deaths every year. The gut-bladder axis has been recently found to be a key factor in initiating UTI pathogenesis, along with the imbalance in the gut microbiome, which is associated with advanced susceptibility to rUTI. The patients who suffer from UTIs are, more often than not, the ones who have the lowest levels of butyrate-producing gut bacteria. Antibiotics cause dysbiosis in the gut and increase the growth of uropathogenic strains. Moreover, the gut-vagina and vagina-bladder axes are involved in UTIs by transferring microbial species, modulating the immune response, and developing intracellular bacterial reservoirs in the bladder. The rising usage of antibiotics has raised antimicrobial resistance (AMR) worldwide and recently worsened the treatment of UTIs. Resistance mechanisms include enzymatic hydrolysis of antibiotics, efflux systems, biofilm formation, horizontal gene transfer, and a weakened host's immune system, allowing bacteria to escape from the treatments. Besides, in pregnant women and adolescents, the alterations in sex hormone levels increase the risk of rUTIs. Knowledge of microbiota that harbor in the gut-vagina and vagina-bladder axes might lead to the invention of nonantibiotic preventive and therapeutic techniques in the future. In conclusion, this review emphasizes the need for a study to understand the host-microbe interactions, gut health, and AMR to effectively deal with and prevent recurrent UTIs. Also, the review explores a comprehensive analysis of the epigenetic network between host UTIs and marker genes in E. coli.}, }
@article {pmid40373395, year = {2025}, author = {He, Y and Liu, C and Zhang, J and Wang, G and Liu, H and Peng, C and Liu, X and Wang, J}, title = {Invisible threat: Marine suspended particles mediate delayed decay of antibiotic resistome in coastal effluents.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138610}, doi = {10.1016/j.jhazmat.2025.138610}, pmid = {40373395}, issn = {1873-3336}, abstract = {Suspended particles are recognized as hotspots of antibiotic resistance genes (ARGs) in coastal waters. However, the dynamics of ARGs associated with suspended particles during sewage discharge into coastal environments remain poorly understood. This study simulated sewage influx into coastal waters using microcosms to investigate the decay dynamics of particle-associated (PA) and free-living (FL) ARGs. Results showed that four ARGs, including two sulfonamide resistance genes (sul1 and sul2) and two tetracycline resistance genes (tetB and tetG), exhibited significantly lower decay rates in the PA fraction than in the FL fraction. Specifically, bacterial decay (k = 0.96 day[-1]) and horizontal gene transfer decay (k = 0.62 day[-1]) were both slower in the PA fraction compared to the FL fraction (1.56 day[-1] and 1.98 day[-1], respectively). These results indicated that suspended particles slow down the decay of ARGs. Microbial community analysis revealed approximately 80 % similarity between sewage and seawater at day 0, but a marked increase in unique bacterial genera and unknown-source taxa was observed at day 15. These results suggest that sewage discharge rapidly alters the composition of native seawater communities. Furthermore, suspended particles harbored higher abundances of unknown-source bacteria and displayed stronger bacterial community interactions than the surrounding water. These findings advance our understanding of ARG persistence and microbial community dynamics, offering critical insights for understanding ARGs dissemination from wastewater discharge.}, }
@article {pmid40372033, year = {2025}, author = {Kiiru, S and Kasiano, P and Maina, J and Mwaniki, JN and Songoro, E and Kariuki, S}, title = {Molecular characterization of multidrug-resistant E. coli recovered from diarrheagenic children under 5 years from Mukuru Informal Settlement, Nairobi, Kenya, based on whole-genome sequencing analysis.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0142024}, doi = {10.1128/spectrum.01420-24}, pmid = {40372033}, issn = {2165-0497}, abstract = {UNLABELLED: High genomic plasticity within Escherichia coli enables it to acquire and accumulate genetic material through horizontal gene transfer. In this study, we sought to investigate the virulence genes, phylogroups, antibiotic resistance genes, plasmid replicons, multilocus sequence types (MLST), and core genome MLST of multidrug-resistant E. coli recovered from diarrheagenic children under 5 years from Mukuru Informal Settlement in Nairobi, Kenya. A total of 39 multidrug-resistant (MDR) strains had their DNA extracted, and whole-genome sequencing was done using the Illumina HiSeq 2000 platform. Twenty-six E. coli assemblies were analyzed using web-based bioinformatics tools available at the Centre for Genomic Epidemiology and EnteroBase. The isolates were categorized into four main phylogroups, where 10/26 (38.5%) belonged to the B2 phylogroup, 4/26 (15.4%) belonged to D, 3/26 (11.5%) belonged to A, 1/26 (3.8%) belonged to B1, while 8/26 (30.8%) were not determined. FimH30 was predominantly found in the most frequent phylogroup B2 and sequence type (ST) 131. The most common beta-lactam resistance genes were bla TEM-1B and blaCTXM 15, followed by three fluoroquinolone resistance genes [qnrS1 6/26 (23.1%), qnrB4 2/26 (7.7%), and aac(6')-Ib-cr, 8/26 (30.8%)]. Of 26 isolates, 15 had at least one amino acid substitution in the housekeeping genes gyrA (p.S83L), gyrA (p.D87N), parC (p.S80I), parC (p.E84V), parC (p.S57T), and parE (p.I529L), associated with resistance to fluoroquinolones. A total of 40 diverse virulence genes were detected among the isolates. Thirteen different STs were isolated from the E. coli genomes, which included ST 131, ST 3036, ST 38, ST 10, ST 12569, ST 15271, ST 2076, ST 311, ST 3572, ST 394, ST 453, ST 46, and ST 1722. Only two isolates (2/26, 7.7%) from the Municipal City Council clinic were genetically related. Additionally, the most abundant plasmid replicon identified belonged to the IncF family, IncFII(pRSB107), in particular, followed by the Col family. The study highlighted the first E. coli ST46 to harbor the bla NDM5 gene encoded in Col(BS512), IncFII(pRSB107), and IncFIB(AP001918) plasmid replicons in Kenya. We further demonstrated the diversity of MDR E. coli associated with diarrhea in an endemic setting in Kenya.<br><br>IMPORTANCE: This study investigated the molecular characterization of multidrug-resistant Escherichia coli isolated from diarrheagenic children under 5 years of age in Mukuru Informal Settlement in Nairobi, Kenya. This is an important addition to the genomic analysis data of multi-drug resistant diarrheal Escherichia coli in Kenya. The use of whole-genome sequencing to identify and characterize these isolates is valuable and provides valuable insights into the molecular epidemiology of E. coli in the region.}, }
@article {pmid40370256, year = {2025}, author = {Wachino, JI}, title = {Horizontal Gene Transfer Systems for Spread of Antibiotic Resistance in Gram-Negative Bacteria.}, journal = {Microbiology and immunology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1348-0421.13222}, pmid = {40370256}, issn = {1348-0421}, abstract = {Antibiotic-resistant bacteria have become a significant global threat to public health due to the increasing difficulty in treatment. These bacteria acquire resistance by incorporating various antibiotic resistance genes (ARGs) through specialized gene transfer mechanisms, allowing them to evade antibiotic attacks. Conjugation, transformation, and transduction are well-established mechanisms that drive the acquisition and dissemination of ARGs in Gram-negative bacteria. In particular, the horizontal transfer of plasmids carrying multiple ARGs is highly problematic, as it can instantly convert susceptible bacteria into multidrug-resistant ones. Transduction, mediated by bacteriophages that package ARG-containing chromosomal DNA from host cells, also plays a crucial role in ARG spread without requiring direct cell-to-cell contact. Recently, a novel horizontal gene transfer (HGT) mechanism involving outer membrane vesicles (OMVs) has been identified as a key player in ARG dissemination. OMVs-nanoscale, spherical structures produced by bacteria during growth-have been found to carry small plasmids and chromosomal DNA fragments containing ARGs from their host bacteria. This newly discovered transfer process, termed "vesiduction," enables intercellular DNA exchange and further contributes to the spread of antibiotic resistance. Additionally, mobile genetic elements such as transposons, insertion sequences, and site-specific recombination systems like integrons facilitate rearrangement of ARGs, including their translocation between chromosomes and plasmids. This review explores the molecular mechanisms underlying the HGT of ARGs, with a particular focus on clinically isolated antibiotic-resistant Gram-negative bacteria.}, }
@article {pmid40368010, year = {2025}, author = {Liu, H and Wang, L and Dong, Z and Wen, S and Liu, C and Wang, J and Wang, J and Zhu, L and Kim, YM and Wang, J}, title = {Insights into the drivers of antibiotic resistance gene migration in soil-lettuce system with manure application from different sources.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126444}, doi = {10.1016/j.envpol.2025.126444}, pmid = {40368010}, issn = {1873-6424}, abstract = {The application of livestock manure serves as a significant source of ARGs in soils. To study the impact of manure application on the migration of ARGs in the soil-plant system, we set different application ratios (1%, 3%, 8%) of chicken and cow manure for treatment. The study's results demonstrated that the application of organic fertilizers increased the quantity of resistance genes in soil, root, and leaf zones. This change was influenced by the type and proportion of the organic fertilizers used. ARGs and MGEs exhibited the highest absolute enrichment levels in leaf tissues (2.53 and 2.01 times, respectively) with the 3% cow manure treatment. In contrast, chicken manure exhibited the highest enrichment levels after the 1% addition (2.51 and 1.81 times, respectively). The applied manure exhibited a high degree of similarity in bacterial community composition with the soil-lettuce system, indicating that ARGs may spread through microorganisms in this system. This study demonstrated that the evolution of bacterial community structure plays a pivotal role in mediating and driving the migration of ARGs within manure-amended soil-plant ecosystems, providing a theoretical basis for understanding the transmission of ARGs in soils and plants due to agricultural production activities.}, }
@article {pmid40366029, year = {2025}, author = {Rojas-Villalobos, C and Ossandon, FJ and Castillo-Vilcahuaman, C and Sepúlveda-Rebolledo, P and Castro-Salinas, D and Zapata-Araya, A and Arisan, D and Perez-Acle, T and Issotta, F and Quatrini, R and Moya-Beltrán, A}, title = {MOBHunter: a data integration platform for identification and classification of mobile genetic elements in microbial genomes.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkaf396}, pmid = {40366029}, issn = {1362-4962}, support = {1221035//ANID/ ; ANID/BASAL/FB210008//ANID/ ; 32300527//PROYECTO FONDECYT POSTDOCTORADO/ ; 3140005//PROYECTO FONDECYT POSTDOCTORADO/ ; 21241467//ANID/BECAS/DOCTORADO NACIONAL/ ; USS-FIN-24-CNGD-26//Fondo VRID apoyo a congresos/ ; //VRID-Universidad San Sebasti&#xe1;n PROYECTO/USS-FIN-23-PDOC-03USS/ ; //Vicerrector&#xed;a de Investigaci&#xf3;n y Postgrado - Escuela de Postgrado - Universidad Tecnol&#xf3;gica Metropolitana/ ; USS-FIN-25-APCS-20//Vicerrector&#xed;a de Investigaci&#xf3;n y Doctorados de la Universidad San Sebasti&#xe1;n - Fondo/ ; }, abstract = {Horizontal gene transfer plays a critical role in microbial genome evolution and adaptation. Integrated foreign DNA fragments encompass various types of mobile genetic elements (MGEs), ranging from small transposons to conspicuous integrative and conjugative elements. These regions often confer advantageous traits, including antibiotic resistance or novel metabolic capabilities, and contain foreign sequence signatures and hallmark genes such as transposases, integrases, etc. While bioinformatic tools target specific MGE subsets using alignments, compositional signatures, or diagnostic gene mapping, no single platform offers a unified framework for comprehensive, evidence-based, MGE identification and classification. To address this challenge, we developed MOBHunter, an advanced bioinformatic pipeline that consolidates standalone tools and in-house algorithms. Unlike basic tool concatenation, MOBHunter yields consensus identifications, score-supported classifications, and enhanced web visualizations. The platform reduces end user analysis time by integrating data collection, processing, and interpretation into a unified workflow. It delivers robust classifications of MGEs into distinct families and provides a comprehensive overview of the flexible regions of any given input genome. URL: https://informatica.utem.cl/mobhunter/.}, }
@article {pmid40362661, year = {2025}, author = {Rybak, B and Werbowy, O and Debowski, K and Plotka, M and Kocot, AM}, title = {Coagulase-Negative Staphylococci Determined as Blood Culture Contamination Have High Virulence Characteristic Including Transfer of Antibiotic Resistance Determinants to Staphylococcus aureus and Escherichia coli.}, journal = {International journal of molecular sciences}, volume = {26}, number = {9}, pages = {}, doi = {10.3390/ijms26094424}, pmid = {40362661}, issn = {1422-0067}, mesh = {Biofilms/drug effects/growth &amp; development ; Humans ; *Escherichia coli/genetics/drug effects/pathogenicity ; *Staphylococcus aureus/drug effects/pathogenicity/genetics/isolation &amp; purification ; Coagulase/metabolism ; Anti-Bacterial Agents/pharmacology ; *Blood Culture ; *Drug Resistance, Bacterial/genetics ; Virulence/genetics ; Microbial Sensitivity Tests ; *Staphylococcus/drug effects/pathogenicity/genetics/isolation &amp; purification ; Staphylococcal Infections/microbiology ; Gene Transfer, Horizontal ; }, abstract = {This study aimed to evaluate the virulence of 36 clinical isolates estimated as blood culture contaminants (BCCs). MALDI-TOF MS classified all isolates as coagulase-negative staphylococci (CoNS) with the highest percentage of S. epidermidis (77.78%). All tested strains formed biofilms with greater ability at room temperature than 37 °C. CoNS were sensitive to vancomycin (0% resistance) and had relatively low resistance to linezolid and rifampicin (8.33 and 22.22% resistance). The highest resistance was observed for penicillin (94.44%). Moreover, we observed the transfer of antibiotic resistance genes from the tested CoNS to S. aureus and even to E. coli, although with lower efficiency. CoNS in planktonic form were completely combated by antiseptics after 10 and 60 s exposition, and activity against biofilms was time-dependent. The complete elimination of biofilms was observed after a 180 s exposure to Kodan and CITROclorex, and this exposure to Rivanol and Octenidyne showed still viable cells (>0.9 log CFU/mL). Our findings showed that a careful selection of antiseptics and extending the exposure time before blood collection can reduce the occurrence of blood culture contamination. However, our most important finding is the indication that CoNS naturally occurring on human skin and mucous membranes exhibit antibiotic resistance, and what is more, determinants of antibiotic resistance are transferred to both closely related Gram-positive bacteria and phylogenetically distant Gram-negative bacteria. Thus, our findings shed new light on CoNS-they indicate the necessity of their control due to the effective transfer of mobile genetic elements harboring antibiotic resistance genes, which may contribute to the spread of resistance genes and deepening the antibiotic crisis.}, }
@article {pmid40359552, year = {2025}, author = {Otten, L and Liu, H and Meeprom, N and Linan, A and Puglisi, C and Chen, K}, title = {Accumulation of numerous cellular T-DNA sequences in the genus Diospyros by multiple rounds of natural transformation.}, journal = {The Plant journal : for cell and molecular biology}, volume = {122}, number = {3}, pages = {e70202}, doi = {10.1111/tpj.70202}, pmid = {40359552}, issn = {1365-313X}, support = {32370382//National Natural Science Foundation of China/ ; (G242406 to KC)//Shanghai landscaping and city appearance administrative bureau/ ; }, mesh = {*Diospyros/genetics ; *DNA, Bacterial/genetics ; *Gene Transfer, Horizontal/genetics ; *Transformation, Genetic ; Genome, Plant/genetics ; Phylogeny ; Agrobacterium/genetics ; }, abstract = {Horizontal gene transfer (HGT) is an important phenomenon in the evolutionary history of plants. Natural transformation by Agrobacterium is a special case of HGT and leads to the insertion of cellular T-DNA (cT-DNA) sequences, for example, in Diospyros lotus. The genus Diospyros contains about 795 species with economically important members, like different types of persimmon (D. kaki, D. lotus, and D. virginiana) and ebony (e.g., D. ebenum). Whole genome sequences (WGS) from D. kaki, D. oleifera, D. lotus, and D. virginiana were investigated for cT-DNAs. These four species belong to one clade and contain 15 different cT-DNAs (DiTA to DiTO). The hexaploid species D. kaki cv. "Xiaoguo-tianshi" contains seven types of cT-DNA (DiTA to DiTG) on 27 of 42 homeologs, adding up to 628 kb of cT-DNA. Five of these seven cT-DNAs are non-fixed, as shown by empty chromosomal insertion sites. The evolutionary history of the Diospyros cT-DNAs was reconstructed using the divergence of their inverted repeats. Insert age varied from 3 to 12 million years. Partial cT-DNA sequences were detected in 35 additional species from five Diospyros clades. Our data highlight the unexpectedly large scale of natural Agrobacterium transformation in Diospyros and demonstrate the necessity of whole genome approaches for studies on the origin and evolution of cT-DNAs.}, }
@article {pmid40359213, year = {2025}, author = {Zhai, K and Yin, K and Lin, Y and Chen, S and Bi, Y and Xing, R and Ren, C and Chen, Z and Yu, Z and Chen, Z and Zhou, S}, title = {Free Radicals on Aging Microplastics Regulated the Prevalence of Antibiotic Resistance Genes in the Aquatic Environment: New Insight into the Effect of Microplastics on the Spreading of Biofilm Resistomes.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c12699}, pmid = {40359213}, issn = {1520-5851}, abstract = {The spread of antibiotic resistance genes (ARGs) by microplastics has received a great concern in coexisting "hotspots". Despite most microplastics suffering from natural aging, little is known about the effect of aging microplastics (A-MPs) on ARGs dissemination. Here, we demonstrated significant suppression of A-MPs on ARGs dissemination in natural rivers. Although ARGs and mobile genetic elements (MGEs) were effectively enriched on A-MPs, the relative abundance of ARGs and MGEs on A-MPs as well as in receiving water decreased by approximately 21.4% to 42.3% during a period of 30 days of dissemination. Further investigation revealed that [•]OH was consistently generated on A-MPs with a maximum value of 0.2 μmol/g. Importantly, scavenging of [•]OH significantly increased the relative abundance of ARGs and MGEs both on A-MPs and in receiving water 1.4-29.1 times, indicating the vital role of [•]OH in suppressing ARGs dissemination. Microbial analysis revealed that [•]OH inhibited the potential antibiotic-resistant bacteria in surface biofilms, such as Pseudomonas and Acinetobacter (with a decrease of 68.8% and 89.3%). These results demonstrated that [•]OH was extensively produced on A-MPs, which greatly reduced both the vertical and horizontal gene transfer of ARGs. This study provided new insights into the dissemination of ARGs through microplastics in natural systems.}, }
@article {pmid40358144, year = {2025}, author = {Mukherjee, SD and Suryavanshi, M and Knight, J and Lange, D and Miller, AW}, title = {Metagenomic and phylogenetic analyses reveal gene-level selection constrained by bacterial phylogeny, surrounding oxalate metabolism in the gut microbiota.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0091324}, doi = {10.1128/msphere.00913-24}, pmid = {40358144}, issn = {2379-5042}, abstract = {The gut microbiota is critical for neutralizing dietary toxins. Oxalate is a toxin commonly produced by plants to deter herbivory and is widely consumed in the human diet. Excess levels of systemic or urinary oxalate increase risk of multiple urologic and cardiometabolic diseases. The current study employed multiple amplicon-based and shotgun metagenomic methodologies, alongside comparative phylogenetic analyses, to interrogate evolutionary radiation surrounding microbial oxalate degradation within the human gut microbiome. In conservative genome-based estimates, over 30% of gut microbial species harbored at least one oxalate-handling gene, with the specific pathways used dependent on bacterial phylum. Co-occurrence analyses revealed interactions between specialist genes that can metabolize oxalate or its by-products, but not multi-functional genes that can act in more than one oxalate-related pathway. Specialization was rare at the genome level. Amplicon-based metagenomic sequencing of the oxalate-degrading gene, formyl-CoA transferase (frc), coupled with molecular clock phylogenetic analyses are indicative of rapid evolutionary divergence, constrained by phylum. This was corroborated by paired analyses of non-synonymous to synonymous substitutions (dN/dS ratios), which pointed toward neutral to positive selection. Sequence similarity network analyses of frc sequences suggest extensive horizontal gene transferring has occurred with the frc gene, which may have facilitated rapid divergence. The frc gene was primarily allocated to the Pseudomonodota phylum, particularly the Bradyrhizobium genus, which is a species capable of utilizing oxalate as a sole carbon and energy source. Collectively evidence provides strong support that, for oxalate metabolism, evolutionary selection occurs at the gene level, through horizontal gene transfer, rather than at the species level.IMPORTANCEA critical function of the gut microbiota is to neutralize dietary toxins, such as oxalate, which is highly prevalent in plant-based foods and is not degraded by host enzymes. However, little is known about the co-evolutionary patterns of plant toxins and the mammalian gut microbiota, which are expected to exhibit features of an evolutionary arms race. In the current work, we present molecular evidence that microbial genes for oxalate degradation are highly prevalent in humans, potentially driven by extensive horizontal gene transfer events. Phylogenetic analyses reveal that oxalate-degrading genes are under a positive selection pressure and have historically undergone rapid diversification events, which has led to diverse ecological strategies for handling oxalate by gut bacteria. Collectively, data shed light on potential evolutionary relationships between the diet and the gut microbiota that occur relatively independently of the mammalian host.}, }
@article {pmid40118050, year = {2025}, author = {Berridge, MV and Zobalova, R and Boukalova, S and Caicedo, A and Rushworth, SA and Neuzil, J}, title = {Horizontal mitochondrial transfer in cancer biology: Potential clinical relevance.}, journal = {Cancer cell}, volume = {43}, number = {5}, pages = {803-807}, doi = {10.1016/j.ccell.2025.03.002}, pmid = {40118050}, issn = {1878-3686}, mesh = {Humans ; *Neoplasms/genetics/pathology/metabolism ; *Mitochondria/genetics/metabolism ; *Gene Transfer, Horizontal ; Animals ; DNA, Mitochondrial/genetics ; Clinical Relevance ; }, abstract = {Recent research highlights horizontal mitochondrial transfer as a key biological phenomenon linked to cancer onset and progression. The transfer of mitochondria and their genomes between cancer and non-cancer cells shifts our understanding of intercellular gene trafficking, increasing the metabolic fitness of cancer cells and modulating antitumor immune responses. This process not only facilitates tumor progression but also presents potential therapeutic opportunities.}, }
@article {pmid40356790, year = {2025}, author = {,  and Casacuberta, J and Barro, F and Braeuning, A and de Maagd, R and Epstein, MM and Frenzel, T and Gallois, JL and Koning, F and Messéan, A and Moreno, FJ and Nogué, F and Savoini, G and Schulman, AH and Tebbe, C and Veromann, E and Ardizzone, M and De Sanctis, G and Dumont, AF and Ferrari, A and Gennaro, A and Gómez Ruiz, J&#xc1; and Goumperis, T and Kagkli, DM and Lewandowska, A and Camargo, AM and Franco, MN and Piffanelli, P and Raffaello, T and Rodrigues, M and Sánchez-Brunete, E}, title = {Assessment of genetically modified sugar beet KWS20-1 (application GMFF-2023-14732).}, journal = {EFSA journal. European Food Safety Authority}, volume = {23}, number = {5}, pages = {e9381}, doi = {10.2903/j.efsa.2025.9381}, pmid = {40356790}, issn = {1831-4732}, abstract = {Genetically modified sugar beet KWS20-1 was developed to confer tolerance to glyphosate-, dicamba- and glufosinate-ammonium-based herbicides. These properties were achieved by introducing the cp4 epsps, dmo and pat expression cassettes. The molecular characterisation data and bioinformatic analyses do not identify issues requiring further safety assessment. None of the identified differences in the agronomic/phenotypic and compositional characteristics tested between sugar beet KWS20-1 and its conventional counterpart need further assessment, except for pectin in roots, which underwent additional evaluation and was found not to raise any safety or nutritional concerns. The GMO Panel does not identify safety concerns regarding the potential toxicity and allergenicity of the CP4 EPSPS, DMO and PAT proteins as expressed in sugar beet KWS20-1, and finds no evidence that the genetic modification would change the overall safety of sugar beet KWS20-1 as food and feed. In the context of this application, the consumption of food and feed from sugar beet KWS20-1 does not represent a nutritional concern in humans and animals. The GMO Panel concludes that sugar beet KWS20-1 is as safe as the conventional counterpart and non-GM sugar beet reference varieties tested, and no post-market monitoring of food/feed is considered necessary. The scope of the application does not include cultivation and import of viable materials in the EU and the products would be expected to only contain residual amounts of DNA and protein. The environmental risk assessment was limited to the possible plant-to-bacteria horizontal gene transfer and the evaluation of potential interactions of KWS20-1 sugar beet products with biogeochemical cycles, and neither of them indicates a safety concern. The GMO Panel concludes that the sugar beet KWS20-1 is as safe as its conventional counterpart and the tested non-GM reference sugar beet varieties with respect to potential effects on human and animal health and the environment.}, }
@article {pmid40356278, year = {2025}, author = {Watanabe, Y and Kunishi, K and Matsui, H and Sakata, N and Noutoshi, Y and Toyoda, K and Ichinose, Y}, title = {Genomic Islands of Pseudomonas syringae pv. tabaci 6605: Identification of PtaGI-1 as a Pathogenicity Island With Effector Genes and a Tabtoxin Cluster.}, journal = {Molecular plant pathology}, volume = {26}, number = {5}, pages = {e70087}, doi = {10.1111/mpp.70087}, pmid = {40356278}, issn = {1364-3703}, support = {22H0234814//Japan Society for the Promotion of Science/ ; }, mesh = {*Genomic Islands/genetics ; *Pseudomonas syringae/genetics/pathogenicity ; *Multigene Family/genetics ; Virulence/genetics ; Nicotiana/microbiology ; *Bacterial Toxins/genetics ; Plant Diseases/microbiology ; Genes, Bacterial ; Mutation/genetics ; }, abstract = {Genomic islands (GIs) are 20-500 kb DNA regions that are thought to be acquired by horizontal gene transfer. GIs that confer pathogenicity and environmental adaptation have been reported in Pseudomonas species; however, GIs that enhance bacterial virulence have not. Here, we identified 110 kb and 103 kb GIs in P. syringae pv. tabaci 6605 (Pta6605), the causative agent of tobacco wildfire disease, which has the ability to produce tabtoxin as a phytotoxin. These GIs are partially homologous to known genomic islands in Pseudomonas aeruginosa and P. syringae pv. phaseolicola and were designated PtaGI-1 and PtaGI-2. Both PtaGIs conserve core genes, whereas each GI possesses different accessory genes. PtaGI-1 contains a tabtoxin biosynthetic gene cluster and three type III effector genes among its accessory genes, whereas PtaGI-2 also contains homologous genes to hsvABC, pathogenicity-related genes in Erwinia amylovora. Inoculation revealed that the PtaGI-1 mutant, but not the PtaGI-2 mutant, lost the ability to biosynthesise tabtoxin and to cause disease. Therefore, PtaGI-1 is thought to be a pathogenicity island. Both PtaGI-1 and PtaGI-2 have a pseudogene of tRNA[Lys] on the left border and an intact tRNA[Lys] gene on the right border. In a colony of Pta6605, both GIs can be excised at tRNA[Lys], and PtaGI-1 and PtaGI-2 exist in a circular form. These results indicate that tabtoxin biosynthesis genes in PtaGI-1 are required for disease development, and PtaGI-1 is necessary for Pta6605 virulence.}, }
@article {pmid40351943, year = {2025}, author = {Kumar, A and Sharma, A and Mehrishi, P and Solanki, S and Faujdar, SS and Khatun, A}, title = {Detection of the blaNDM-1 Gene in Carbapenem-Resistant Enterobacterales Causing Urinary Tract Infections in Patients at a Rural Teaching Hospital.}, journal = {Cureus}, volume = {17}, number = {4}, pages = {e81811}, pmid = {40351943}, issn = {2168-8184}, abstract = {BACKGROUND: Carbapenem-resistant Enterobacterales (CRE) pose a significant public health threat due to their resistance to last-line antibiotics. Urinary tract infections (UTIs) caused by multidrug-resistant organisms have become a major challenge in clinical settings. The spread of CRE is largely attributed to the acquisition of carbapenemase-encoding genes, horizontal gene transfer, and overuse of broad-spectrum antibiotics.<br><br>METHODOLOGY: A total of 9235 urine samples were analyzed, and more than 10[5] CFU/mL bacterial count was considered positive for UTI. These bacteria were identified and further screened for CRE and blaNDM-1 genes.<br><br>RESULTS: A total of 9235 urine samples were analyzed, out of which 555 were identified as Enterobacterales. Among these, 47 were confirmed as CRE, accounting for 8.5% of the Enterobacterales isolates. Out of 47 CRE, 28 were positive for the&#xa0;blaNDM-1 gene.<br><br>CONCLUSIONS: The study highlights the increasing burden of CRE and the urgent need for stringent antimicrobial stewardship, effective infection control measures, and the development of new therapeutic strategies to combat MDR infections. Additionally, risk factors associated with CRE infections, their implications on public health, and potential future therapeutic approaches are discussed.}, }
@article {pmid40350664, year = {2025}, author = {Sarink, MJ and Grassi, L and Tielens, AGM and Verbon, A and Vos, MC and Goessens, W and Strepis, N and Klaassen, CHW and van Hellemond, JJ}, title = {Acanthamoeba castellanii Can Facilitate Plasmid Transfer Between Environmental Pseudomonas spp.}, journal = {Journal of basic microbiology}, volume = {}, number = {}, pages = {e70051}, doi = {10.1002/jobm.70051}, pmid = {40350664}, issn = {1521-4028}, support = {//This work was funded by the Erasmus MC and the Netherlands Centre for One Health./ ; }, abstract = {The conditions in which antimicrobial resistance (AMR) genes are transferred in natural environments are poorly understood. Acanthamoeba castellanii (a cosmopolitan environmental amoeba) feeds on bacteria by phagocytosis, which places the consumed bacteria closely together in a food vacuole (phagosome) of the amoeba. This way, amoebae can facilitate genetic exchanges between intra-amoebal bacteria. We studied this phenomenon in the clinically relevant bacteria Pseudomonas oleovorans and Pseudomonas aeruginosa (strain 957). The internalization of both the plasmid donor and recipient bacteria was shown by confocal microscopy. In seven independent experiments, an on average 12-fold increase in transfer of the blaVIM-2 gene between these two Pseudomonas strains was observed in the presence of A. castellanii compared to its absence. Negligible or no plasmid transfer was observed from P. oleovorans to 18 other investigated strains of P. aeruginosa. AMR gene transfer via plasmids between Pseudomonas species is highly strain-dependent and A. castellanii can substantially enhance plasmid transfer. This process of plasmid transfer might also occur between other bacteria and predatory protozoa, such as amoebae that reside in the gut of humans and animals.}, }
@article {pmid40346915, year = {2025}, author = {Chen, SY and Huang, K and He, ZH and Zhao, FJ}, title = {Ampicillin Exposure and Glutathione Deficiency Synergistically Promote Conjugative Transfer of Plasmid-Borne Antibiotic Resistance Genes.}, journal = {Environmental microbiology}, volume = {27}, number = {5}, pages = {e70106}, doi = {10.1111/1462-2920.70106}, pmid = {40346915}, issn = {1462-2920}, support = {42090062//National Natural Science Foundation of China/ ; 336168//Research Council of Norway/ ; }, mesh = {*Glutathione/deficiency/metabolism ; *Ampicillin/pharmacology ; *Plasmids/genetics ; *Anti-Bacterial Agents/pharmacology ; *Conjugation, Genetic/drug effects ; Escherichia coli/genetics/drug effects ; Enterobacter/genetics/drug effects ; Oxidative Stress ; *Drug Resistance, Bacterial/genetics ; *Gene Transfer, Horizontal ; Soil Microbiology ; *Drug Resistance, Microbial/genetics ; }, abstract = {Plasmid-mediated conjugation is an important pathway for the spread of antibiotic resistance genes (ARGs), posing a significant risk to global public health. It has been reported that the conjugative transfer of ARGs could be enhanced by oxidative stress. Whether endogenous glutathione (GSH), a major non-protein thiol compound involved in cellular redox homeostasis, influences conjugative transfer is unknown. In this study, we show that the deletion of the GSH biosynthesis gene gshA and ampicillin exposure synergistically promoted the conjugative transfer of plasmid RP4 bearing multiple ARGs from the soil bacterium Enterobacter sp. CZ-1 to Escherichia coli S17-1λπ in co-culture experiments and to diverse soil bacteria belonging to eight phyla, including some potential human pathogens, in a soil incubation experiment. The deletion of gshA increased ROS generation and cell membrane permeability, and upregulated the expression of the genes involved in intracellular oxidative stress regulation, membrane permeability, plasmid replication, and the SOS response process, especially under ampicillin exposure. These results suggest that endogenous GSH is an important factor affecting the spread of plasmid-borne ARGs. Exposure to antibiotics and environmental stresses that cause a depletion of endogenous GSH in vivo are likely to increase the risk of ARG dissemination in the environment.}, }
@article {pmid40036506, year = {2025}, author = {Lin, J and Ni, S and Li, B and Guo, Y and Gao, X and Liu, Y and Yi, L and Wang, P and Chen, R and Yao, J and Wood, TK and Wang, X}, title = {A noncanonical intrinsic terminator in the HicAB toxin-antitoxin operon promotes the transmission of conjugative antibiotic resistance plasmids.}, journal = {Nucleic acids research}, volume = {53}, number = {5}, pages = {}, pmid = {40036506}, issn = {1362-4962}, support = {42188102//National Science Foundation of China/ ; 2022FY100600//Science &amp; Technology Fundamental Resources Investigation Program/ ; 2022RC1169//Science and Technology Innovation Program of Hunan Province/ ; 2019BT02Y262//Local Innovative and Research Teams Project of Guangdong Pearl River Talents Program/ ; SCSIO2023QY03//South China Sea Institute of Oceanology, Chinese Academy of Sciences/ ; //Ocean Negative Carbon Emissions Program/ ; }, mesh = {*Toxin-Antitoxin Systems/genetics ; *Operon ; *Plasmids/genetics ; *Conjugation, Genetic ; *Escherichia coli Proteins/genetics ; *Terminator Regions, Genetic ; Escherichia coli/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; Promoter Regions, Genetic ; *Bacterial Toxins/genetics ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; }, abstract = {Conjugative plasmids, major vehicles for the spread of antibiotic resistance genes, often contain multiple toxin-antitoxin (TA) systems. However, the physiological functions of TA systems remain obscure. By studying two TA families commonly found on colistin-resistant IncI2 mcr-1-bearing plasmids, we discovered that the HicAB TA, rather than the StbDE TA, acts as a crucial addiction module to increase horizontal plasmid-plasmid competition. In contrast to the canonical type II TA systems in which the TA genes are cotranscribed and/or the antitoxin gene has an additional promoter to allow for an increased antitoxin/toxin ratio, the HicAB TA system with the toxin gene preceding the antitoxin gene employs internal transcription termination to allow for a higher toxin production. This intrinsic terminator, featuring a G/C-rich hairpin with a UUU tract, lies upstream of the antitoxin gene, introducing a unique mechanism for the enhancing toxin/antitoxin ratio. Critically, the hicAB TA significantly contributes to plasmid competition and plasmid persistence in the absence of antibiotic selection, and deleting this intrinsic terminator alone diminishes this function. These findings align with the observed high occurrence of hicAB in IncI2 plasmids and the persistence of these plasmids after banning colistin as a feed additive. This study reveals how reprogramming the regulatory circuits of TA operons impacts plasmid occupancy in the microbial community and provides critical targets for combating antibiotic resistance.}, }
@article {pmid40345346, year = {2025}, author = {Zhang, Q and Yan, D and Chen, L}, title = {virK and mig-14 Constitute a PhoP-dependent Operon and Contribute to the Intracellular Survival and Polymyxin B Resistance of Salmonella Typhi.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {107668}, doi = {10.1016/j.micpath.2025.107668}, pmid = {40345346}, issn = {1096-1208}, abstract = {In bacteria, adjacent and functionally similar genes are typically transcribed as operons. The virulence genes virK and mig-14 are acquired through horizontal gene transfer in Salmonella. Previous studies have reported that these two genes have similar functions in terms of bacterial survival within macrophages and resistance to antimicrobial peptides. Nevertheless, the specific expression characteristics of the two genes remain unclear. This study revealed that virK and mig-14 were transcribed as a single operon in Salmonella Typhi. The virK-mig-14 operon was found to be activated under conditions of early hyperosmotic stress and polymyxin B stimulation, and its activation was dependent on the presence of the regulator PhoP. The luminescence assay demonstrated that the activity of the virK promoter was markedly elevated in an environment conducive to operon activation, whereas the mig-14 promoter exhibited no discernible change. This suggests that mig-14 is predominantly transcribed as a component of the operon. In the PhoP activation environment, which has a mildly acidic pH, low Mg[2+] levels, and intracellular macrophages, the virK-mig-14 operon exhibited significant activation. The absence of virK or mig-14 resulted in the impaired survival of Salmonella Typhi within macrophages and decreased its tolerance to polymyxin B. Collectively, this study shows that virK and mig-14 constitute an operon whose activation depends on PhoP and that it promotes S. Typhi's survival in macrophages and resistance to polymyxin B.}, }
@article {pmid39988070, year = {2025}, author = {Zhang, Y and Yang, C and Yao, J and Zhou, L and Zhang, X and Wang, H and Liu, L and Tu, Y and Li, X}, title = {Spread of the Fosfomycin resistance fosA3 gene via the IS26 mobile element between plasmids and the chromosome of carbapenem-resistant Escherichia coli in China.}, journal = {Journal of global antimicrobial resistance}, volume = {42}, number = {}, pages = {80-87}, doi = {10.1016/j.jgar.2025.02.011}, pmid = {39988070}, issn = {2213-7173}, mesh = {*Fosfomycin/pharmacology ; *Plasmids/genetics ; China ; *Escherichia coli/genetics/drug effects ; *Escherichia coli Proteins/genetics ; *Anti-Bacterial Agents/pharmacology ; Phylogeny ; Humans ; Whole Genome Sequencing ; Escherichia coli Infections/microbiology ; *Carbapenem-Resistant Enterobacteriaceae/genetics/drug effects ; Microbial Sensitivity Tests ; *Chromosomes, Bacterial/genetics ; *Interspersed Repetitive Sequences ; Carbapenems/pharmacology ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; }, abstract = {OBJECTIVE: This study investigated fosA3-positive strains selected from carbapenem-resistant Escherichia coli (CREC) and further characterized them through genomic and phenotypic analyses.<br><br>METHODS: fosA3-positive CREC strains were subjected to agar dilution. Whole-genome sequencing (WGS) was used to identify molecular mechanisms of fosfomycin resistance and to investigate plasmid structure characteristics through comparative analysis. Conjugative transfer experiments were used to evaluate plasmid transfer ability, followed by plasmid stability assessment. Growth rate analysis evaluated the fitness costs of transconjugants. Phylogenetic analysis was performed on fosA3-positive CREC strains. Furthermore, analysis of fos genes carrying E. coli sequence types (STs) from the NCBI database explored the evolution and spread of fosfomycin resistance.<br><br>RESULTS: Between 2016 and 2023, a total of 11.23% CREC strains (10/89) carrying fosA3 were collected from a hospital for further analysis. These ten fosA3-positive strains were also resistant to fluoroquinolones and ceftazidime-avibactam. The fosA3 gene was located within a similar genetic background (IS26-fosA3-1811bp-IS26) on plasmids or chromosomes. The fosA3-carrying IncFII(pHN7A8)-IncX3 cointegrate plasmid pEC00-2-145k was transferable, with fitness cost of 20% to host. Furthermore, three of ten fosA3-positive CREC strains belonged to ST156. Analysis of fos genes carrying E. coli strains from China in the NCBI database identified ST156 (5.39%, 147/2,725) and ST167 (5.21%, 142/2,725) as predominant STs.<br><br>CONCLUSIONS: This study revealed fosA3 in CREC strains was associated with IS26 and spreads fosfomycin resistance through horizontal transfer, occurring both on chromosomes and plasmids. The first fosA3-carrying cointegrate plasmid pHN7A8-IncX3-type in E. coli isolates was reported, highlighting a new route of fosfomycin resistance spread. Additionally, notable diversity of ST among fosA3-carrying E. coli strains highlights complexity of fosfomycin resistance dissemination and the importance of surveillance and control measures.}, }
@article {pmid39909367, year = {2025}, author = {Zhang, G and Li, C and Li, X and Li, Y and Li, Y and Zeng, X and Xu, C and Wu, S and Dong, N}, title = {Ibuprofen prevents the conjugative transfer of plasmid-mediated antimicrobial resistance genes.}, journal = {Journal of global antimicrobial resistance}, volume = {42}, number = {}, pages = {10-14}, doi = {10.1016/j.jgar.2025.01.012}, pmid = {39909367}, issn = {2213-7173}, mesh = {*Plasmids/genetics ; *Conjugation, Genetic/drug effects ; *Ibuprofen/pharmacology ; *Drug Resistance, Multiple, Bacterial/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology ; Humans ; Microbial Sensitivity Tests ; Escherichia coli/genetics/drug effects ; *Gene Transfer, Horizontal/drug effects ; }, abstract = {Refractory infections caused by multidrug-resistant bacteria pose a significant threat to public health. Here we report that ibuprofen inhibits conjugation of the RP4 plasmid and plasmids from clinical strains carrying different resistance genes including mcr-1, blaNDM, blaKPC, tet(X4), and tmexCD1-toprJ1. Mechanistic studies suggest that ibuprofen reduces ATP production and inhibits conjugation-related genes. The inhibitory effect of ibuprofen on conjugation has significant clinical implications for preventing the spread of multidrug resistance, opening new therapeutic avenues to combat multidrug-resistant bacteria.}, }
@article {pmid40343121, year = {2025}, author = {Liang, H and Qi, H and Wang, C and Wang, Y and Liu, M and Chen, J and Sun, X and Xia, T and Feng, S and Chen, C and Zheng, D}, title = {Analysis of the complete mitogenomes of three high economic value tea plants (Tea-oil Camellia) provide insights into evolution and phylogeny relationship.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1549185}, doi = {10.3389/fpls.2025.1549185}, pmid = {40343121}, issn = {1664-462X}, abstract = {INTRODUCTION: Tea-oil Camellia species play a crucial economic and ecological role worldwide, yet their mitochondrial genomes remain largely unexplored.<br><br>METHODS: In this study, we assembled and analyzed the complete mitochondrial genomes of Camellia oleifera and C. meiocarpa, revealing multi-branch structures that deviate from the typical circular mitochondrial genome observed in most plants. The assembled mitogenomes span 953,690 bp (C. oleifera) and 923,117 bp (C. meiocarpa), containing 74 and 76 annotated mitochondrial genes, respectively.<br><br>RESULTS: Comparative genomic analyses indicated that C. oleifera and C. meiocarpa share a closer genetic relationship, whereas C. drupifera is more distantly related. Codon usage analysis revealed that natural selection plays a dominant role in shaping codon bias in these mitochondrial genomes. Additionally, extensive gene transfer events were detected among the three species, highlighting the dynamic nature of mitochondrial genome evolution in Tea-oil Camellia. Phylogenetic reconstruction based on mitochondrial genes exhibited incongruence with chloroplast phylogenies, suggesting potential discordance due to hybridization events, incomplete lineage sorting (ILS), or horizontal gene transfer (HGT). Furthermore, we identified species-specific mitochondrial markers, which provide valuable molecular tools for distinguishing Tea-oil Camellia species.<br><br>DISCUSSION: Our findings enhance the understanding of mitochondrial genome evolution and genetic diversity in Tea-oil Camellia, offering essential genomic resources for phylogenetics, species identification, and evolutionary research in woody plants.}, }
@article {pmid40343117, year = {2025}, author = {Meng, D and Lu, T and He, M and Ren, Y and Fu, M and Zhang, Y and Yang, P and Lin, X and Yang, Y and Zhang, Y and Yang, Y and Jin, X}, title = {Organelle genomes of two Scaevola species, S. taccada and S. hainanensis, provide new insights into evolutionary divergence between Scaevola and its related species.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1587750}, doi = {10.3389/fpls.2025.1587750}, pmid = {40343117}, issn = {1664-462X}, abstract = {Chloroplast and mitochondrial genomes harbor crucial information that can be utilized for elucidating plant evolution and environmental adaptation. The organellar genomic characteristics of Goodeniaceae, a sister family to Asteraceae, remain unexplored. Here, using a combination of short-read and long-read sequencing technologies, we successfully assembled the complete organellar genomes of two Goodeniaceae species native to China, Scaevola taccada and S. hainanensis. Chloroplast genome collinearity analysis revealed that Scaevola expanded its genome length through inverted repeat expansion and large single copy fragment duplication, resulting in 181,022 bp (S. taccada) and 182,726 bp (S. hainanensis), ~30 kb increase compared to its related species. Mitochondrial genomes of two Scaevola species exhibit multi-ring topology, forming dual mitochondrial chromosomes of 314,251 bp (S. taccada) and 276,175 bp (S. hainanensis). Sequence variation analysis demonstrated substantial chloroplast sequence divergence (Pi = 0.45) and an increase in gene copy number within the genus. Relative synonymous codon usage (RSCU) analysis revealed that Scaevola chloroplast has a higher bias for A/U-ending codons than mitochondria, with chloroplasts RSCU values ranging from 0.32 to 1.94, whereas mitochondrial RSCU values ranging from 0.38 to 1.62. Phylogenetic analyses support the monophyly of the Asteraceae-Goodeniaceae sister group, whereas the extended evolutionary branches of Scaevola, coupled with mitochondrial collinearity analysis, indicate rapid organellar genome evolution of Scaevola. Organellar-nuclear horizontal gene transfer analysis identified specific increased in the copy numbers of photosynthesis-related genes and chloroplast-nuclear transfer events in S. taccada. Our study not only provides insights for understanding environmental adaptation mechanisms of coastal plants, but also contributes to elucidating organellar genome evolution in Scaevola and Goodeniaceae.}, }
@article {pmid40341387, year = {2025}, author = {Marin, MG and Quinones-Olvera, N and Wippel, C and Behruznia, M and Jeffrey, BM and Harris, M and Mann, BC and Rosenthal, A and Jacobson, KR and Warren, RM and Li, H and Meehan, CJ and Farhat, MR}, title = {Pitfalls of bacterial pan-genome analysis approaches: a case study of M. tuberculosis and two less clonal bacterial species.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btaf219}, pmid = {40341387}, issn = {1367-4811}, abstract = {UNLABELLED: Pan-genome analysis is a fundamental tool for studying bacterial genome evolution; however, the variety of methods used to define and measure the pan-genome poses challenges to the interpretation and reliability of results. Using Mycobacterium tuberculosis (Mtb)-characterized by clonal evolution, absence of horizontal gene transfer, and a small accessory genome-as a model system, we systematically evaluated sources of variability in pan-genome estimates. Our analysis revealed that differences in assembly type (short-read vs. hybrid), annotation pipeline, and pan-genome software, significantly impact predictions of core and accessory genome size. Extending our analysis to two additional bacterial species, Escherichia coli and Staphylococcus aureus, we observed consistent tool-dependent biases but species-specific patterns in pan-genome variability. Our findings highlight the need for robust quality control and careful methodological selection to accurately capture genome diversity and evolution. This work underscores the importance of integrating nucleotide- and protein-level analyses to improve the reliability and reproducibility of pan-genome studies across diverse bacterial populations.<br><br>AVAILABILITY: Panqc is freely available under an MIT license at https://github.com/maxgmarin/panqc.<br><br>CONTACT: maha_farhat@hms.harvard.edu.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid40339917, year = {2025}, author = {Schuster, HJ and van Mansfeld, R and van der Reijden, WA and van Houdt, R and Matamoros, S}, title = {VanB transposon analysis detects horizontal gene transfer in vancomycin resistant Enterococcus faecium: description of two outbreaks.}, journal = {The Journal of hospital infection}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jhin.2025.04.021}, pmid = {40339917}, issn = {1532-2939}, abstract = {BACKGROUND: Outbreaks with vancomycin resistant Enterococcus faecium (VRE) are common in hospitals worldwide. Whole genome MLST (wgMLST) is often used to identify outbreak strains, but VRE typing can still be challenging due to their limited genomic variation.<br><br>AIM: Developing a method for sequence analysis of vancomycin resistance genes in parallel to wgMLST and application of this new method for real-time investigation of two parallel VRE outbreaks.<br><br>METHODS: We developed a bioinformatics pipeline to compare the sequences of transposons containing vanB resistance genes. We used this pipeline in addition to wgMLST to investigate two separate ongoing VRE outbreaks. We also sequenced five separate colonies from 15 different samples and 10 vancomycin sensitive isolates.<br><br>FINDINGS: Of 46 strains collected during two outbreaks, we identified 26 and 9 strains to be part of the two outbreaks based on wgMLST clustering. In 6 strains we identified an identical vanB transposon but a different wgMLST cluster, indicating horizontal gene transfer. This potential outbreak spread would have been missed without transposon analysis. We found no variability in vanB transposon sequence or wgMLST profiles within different colonies from the same sample. We identified 1 vancomycin sensitive E. faecium in blood culture with a similar wgST as one of the outbreak strains.<br><br>CONCLUSIONS: Real-time analysis of transposons containing vancomycin resistance genes provides additional information for analysis of vanB-VRE outbreaks. It detects possible horizontal gene transfer which would not be detected using conventional methods. Transposon analysis is a valuable addition to whole genome sequence analysis during vanB-VRE outbreaks.}, }
@article {pmid40337914, year = {2025}, author = {Robertson, HM and Walker, JF and Moyroud, E}, title = {CAnDI: a new tool to investigate conflict in homologous gene trees and explain convergent trait evolution.}, journal = {Systematic biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/sysbio/syaf028}, pmid = {40337914}, issn = {1076-836X}, abstract = {Phenotypic convergence is found across the tree of life, and morphological similarities in distantly related species are often presumed to have evolved independently. However, clarifying the origins of traits has recently highlighted the complex nature of evolution, as apparent convergent features often share similar genetic foundations. Hence, the tree topology of genes that underlie such traits frequently conflicts with the overall history of species relationships. This conflict, which usually results from incomplete lineage sorting, introgression or horizontal gene transfer, creates both a challenge for systematists and an exciting opportunity to investigate the rich, complex network of information that connects molecular trajectories with trait evolution. Here we present a novel conflict identification program named CAnDI (Conflict And Duplication Identifier), which enables the analysis of conflict in homologous gene trees rather than inferred orthologs. We demonstrate that the analysis of conflicts in homologous trees using CAnDI yields more comparisons than in ortholog trees in six datasets from across the eukaryotic tree of life. Using the carnivorous trap of Caryophyllales, a charismatic group of flowering plants, as a case study we demonstrate that analysing conflict on entire homolog trees can aid in inferring the contribution of standing genetic variation to trait evolution: by dissecting all gene relationships within homolog trees, we find genomic evidence that the molecular basis of the pleisiomorphic mucilaginous sticky trap was likely present in the ancestor of all carnivorous Caryophyllales. We also show that many genes whose evolutionary trajectories group species with similar trap devices code for proteins contributing to plant carnivory and identify a LATERAL ORGAN BOUNDARY DOMAIN transcription factor as a possible candidate for regulating sticky trap development.}, }
@article {pmid40332509, year = {2025}, author = {Ye, T and Li, H and Hai, D and Zhaxi, Z and Duan, J and Lin, Y and Xie, J and Cheng, J and Li, B and Chen, T and Yu, X and Lyu, X and Xiao, X and Fu, Y and Jiang, D}, title = {A Hypovirulence-Associated Partitivirus and Re-Examination of Horizontal Gene Transfer Between Partitiviruses and Cellular Organisms.}, journal = {International journal of molecular sciences}, volume = {26}, number = {8}, pages = {}, doi = {10.3390/ijms26083853}, pmid = {40332509}, issn = {1422-0067}, support = {31861143043//ISF-NSFC/ ; AML2023A02//the funds of the National Key Laboratory of Agricultural Microbiology/ ; }, mesh = {*Gene Transfer, Horizontal ; *Ascomycota/virology/genetics ; Phylogeny ; *Fungal Viruses/genetics/pathogenicity ; *RNA Viruses/genetics ; RNA-Dependent RNA Polymerase/genetics ; Capsid Proteins/genetics ; Genome, Viral ; Virulence/genetics ; Animals ; }, abstract = {Previous research has unearthed the integration of the coat protein (CP) gene from alphapartitivirus into plant genomes. Nevertheless, the prevalence of this horizontal gene transfer (HGT) between partitiviruses and cellular organisms remains an enigma. In our investigation, we discovered a novel partitivirus, designated Sclerotinia sclerotiorum alphapartitivirus 1 (SsAPV1), from a hypovirulent strain of Sclerotinia sclerotiorum. Intriguingly, we traced homologs of the SsAPV1 CP to plant genomes, including Helianthus annuus. To delve deeper, we employed the CP and RNA-dependent RNA polymerase (RdRP) sequences of partitiviruses as "bait" to search the NCBI database for similar sequences. Our search unveiled a widespread occurrence of HGT between viruses from all five genera within the family Partitiviridae and other cellular organisms. Notably, numerous CP-like and RdRP-like genes were identified in the genomes of plants, protozoa, animals, fungi, and even, for the first time, in an archaeon. The majority of CP and RdRP genes were integrated into plant and insect genomes, respectively. Furthermore, we detected DNA fragments originating from the SsAPV1 RNA genome in some subcultures of virus-infected strains. It suggested that SsAPV1 RdRP may possesses reverse transcriptase activity, facilitating the integration of viral genes into cellular organism genomes, and this function requires further confirmation. Our study not only offers a hypovirulence-associated partitivirus with implications for fungal disease control but also sheds light on the extensive integration events between partitiviruses and cellular organisms and enhances our comprehension of the origins, evolution, and ecology of partitiviruses, as well as the genome evolution of cellular organisms.}, }
@article {pmid40328220, year = {2025}, author = {Doremus, MR and Hunter, MS}, title = {Symbiosis: An escalating arms race between a butterfly and bacterium.}, journal = {Current biology : CB}, volume = {35}, number = {9}, pages = {R339-R341}, doi = {10.1016/j.cub.2025.03.061}, pmid = {40328220}, issn = {1879-0445}, abstract = {Symbiotic bacteria such as Wolbachia can dramatically affect the reproduction of their arthropod hosts, in some instances causing male progeny to die as embryos. A recent paper describes an escalating arms race over Wolbachia-mediated male-killing in a tropical butterfly, with butterfly suppression of male-killing being overcome by acquisition of an additional male-killing gene via phage-mediated horizontal gene transfer.}, }
@article {pmid40328153, year = {2025}, author = {Chu, Y and Dong, X and Fang, S and Gan, L and Lee, X and Zhou, L}, title = {Viruses in human-impacted estuarine ecotones: Distribution, metabolic potential, and environmental risks.}, journal = {Water research}, volume = {282}, number = {}, pages = {123750}, doi = {10.1016/j.watres.2025.123750}, pmid = {40328153}, issn = {1879-2448}, abstract = {Estuaries, as dynamic ecological interfaces between marine and terrestrial systems, are characterized by high productivity and intricate microbial communities. Viruses exert critical regulatory effects on microbial processes, influencing ecological functions and contributing to environmental dynamics in estuarine ecosystems. Despite their significance, the diversity and ecological roles of estuarine viruses remain insufficiently understood. This study explored the viral biogeographic patterns, metabolic potential, and influencing factors in 30 subtropical estuaries in China. Few estuarine viruses (< 22 %) exhibited homology with known viruses, and the low overlap of virus clusters with other environments highlights their novelty and habitat specificity. Mantel tests and random forest analysis identified salinity, temperature, nutrients, and pollutants as key factors influencing viral composition and functional profiles. In addition, correlation analysis between virus and host confirmed significant virus-host interactions, while functional analyses highlighted the role of environmental conditions and horizontal gene transfer in shaping auxiliary metabolic genes linked to elemental biogeochemical cycles, particularly phosphorus, sulfur, and nitrogen. The detection of antibiotic resistance genes (ARGs) and virulence factors (VFs) within viral genomes underscores the role of viruses as reservoirs of ARGs and VFs in these ecosystems. These results demonstrate the profound influence of abiotic and host factors on viral community structures in subtropical estuarine ecotones and underscore the ecological significance of metabolic genes in biogeochemical cycling. By clarifying these interactions, this study advances the understanding of viral contributions to ecosystem functioning and biogeochemical dynamics in estuarine environments.}, }
@article {pmid40326718, year = {2025}, author = {Naseef Pathoor, N and Valsa, V and Ganesh, PS and Gopal, RK}, title = {From resistance to treatment: the ongoing struggle with Acinetobacter baumannii.}, journal = {Critical reviews in microbiology}, volume = {}, number = {}, pages = {1-22}, doi = {10.1080/1040841X.2025.2497791}, pmid = {40326718}, issn = {1549-7828}, abstract = {Acinetobacter baumannii (A. baumannii) has become a major hospital-acquired pathogen, well-known for its rapid development of resistance to multiple antibiotics. The rising incidence of antibiotic-resistant A. baumannii presents a significant global public health challenge. Gaining a deep understanding of the mechanisms behind this resistance is essential for creating effective treatment options. This comprehensive review explores the understanding of various antibiotic resistance mechanisms in A. baumannii. It covers intrinsic resistance, acquired resistance genes, efflux pumps, changes in outer membrane permeability, alterations in drug targets, biofilm formation, and horizontal gene transfer. Additionally, the review investigates the role of mobile genetic elements and the clinical implications of antibiotic resistance in A. baumannii infections. The insights provided may inform the development of new antimicrobial agents and the design of effective infection control strategies to curb the spread of multidrug-resistant (MDR) A. baumannii strains in healthcare environments. Unlike previous reviews, this study offers a more integrative perspective by also addressing the pathogen's environmental resilience, with particular emphasis on its resistance to desiccation and the formation of robust biofilms. It further evaluates both established and emerging therapeutic strategies, thereby expanding the current understanding of A. baumannii persistence and treatment.}, }
@article {pmid40325439, year = {2025}, author = {Urban, JM and Gerbi, SA and Spradling, AC}, title = {Chromosome-scale scaffolds of the fungus gnat genome reveal multi-Mb-scale chromosome-folding interactions, centromeric enrichments of retrotransposons, and candidate telomere sequences.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {443}, pmid = {40325439}, issn = {1471-2164}, support = {NIH/GM121455/NH/NIH HHS/United States ; }, abstract = {BACKGROUND: The lower Dipteran fungus gnat, Bradysia (aka Sciara) coprophila, has compelling chromosome biology. Paternal chromosomes are eliminated during male meiosis I and both maternal X sister chromatids are retained in male meiosis II. Embryos start with three copies of the X chromosome, but 1-2 copies are eliminated from somatic cells as part of sex determination, and one is eliminated in the germline to restore diploidy. In addition, there is gene amplification in larval polytene chromosomes, and the X polytene chromosome folds back on itself mediated by extremely long-range interactions between three loci. These developmentally normal events present opportunities to study chromosome behaviors that are unusual in other systems. Moreover, little is known about the centromeric and telomeric sequences of lower Dipterans in general, and there are recent claims of horizontally-transferred genes in fungus gnats. Overall, there is a pressing need to learn more about the fungus gnat chromosome sequences.<br><br>RESULTS: We produced the first chromosome-scale models of the X and autosomal chromosomes where each somatic chromosome is represented by a single scaffold. Extensive analysis supports the chromosome identity and structural accuracy of the scaffolds, demonstrating they are co-linear with historical polytene maps, consistent with evolutionary expectations, and have accurate centromere positions, chromosome lengths, and copy numbers. The positions of alleged horizontally-transferred genes in the nuclear chromosomes were broadly confirmed by genomic analyses of the chromosome scaffolds using Hi-C and single-molecule long-read datasets. The chromosomal context of repeats shows family-specific biases, such as retrotransposons correlated with the centromeres. Moreover, scaffold termini were enriched with arrays of retrotransposon-related sequence as well as nucleosome-length (~ 175 bp) satellite repeats. Finally, the Hi-C data captured Mb-scale physical interactions on the X chromosome that are seen in polytene spreads, and we characterize these interesting "fold-back regions" at the sequence level for the first time.<br><br>CONCLUSIONS: The chromosome scaffolds were shown to be of exceptional quality, including loci harboring horizontally-transferred genes. Repeat analyses demonstrate family-specific biases and telomere repeat candidates. Hi-C analyses revealed the sequences of ultra-long-range interactions on the X chromosome. The chromosome-scale scaffolds pave the way for further studies of the unusual chromosome movements in Bradysia coprophila.}, }
@article {pmid40127991, year = {2025}, author = {Barretto, LAF and Fowler, CC}, title = {Multifaceted Evolution of the PhoPQ Two-Component System in Salmonella enterica Enhanced the Expression of Horizontally Acquired Virulence Genes.}, journal = {Molecular microbiology}, volume = {123}, number = {5}, pages = {464-478}, doi = {10.1111/mmi.15355}, pmid = {40127991}, issn = {1365-2958}, support = {RGPIN-2020-03964//Natural Sciences and Engineering Research Council of Canada/ ; //NSREC CGS-M Scholarship/ ; //University of Alberta Faculty of Science/ ; }, mesh = {*Bacterial Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Virulence/genetics ; *Salmonella enterica/genetics/pathogenicity/metabolism ; Escherichia coli/genetics/metabolism ; Escherichia coli Proteins/genetics/metabolism ; Evolution, Molecular ; *Virulence Factors/genetics ; Gene Transfer, Horizontal ; }, abstract = {For a bacterium to adapt to a new environmental niche, its regulatory networks must evolve to effectively sense and respond to cues within that niche. For bacterial pathogens, which encounter harsh and dynamic host niches that require efficient coordination between detecting host cues and regulating virulence genes, this process is a key aspect of how virulence properties evolve. Here, we investigate how a widely conserved two-component regulatory system (TCS), PhoP/PhoQ (PhoPQ), evolved in Salmonella enterica to adopt a new role as a master regulator of gene expression within its species-specific intracellular niche: the Salmonella-containing vacuole (SCV). By comparing Salmonella PhoPQ with the closely related Escherichia coli PhoPQ ortholog, we demonstrate that optimizing virulence gene expression in Salmonella required a multifaceted evolution of several PhoPQ functional domains and establish that distinct genetic differences and mechanisms enhance virulence gene expression for different inducing cues. Interestingly, we find that the increased activity of the Salmonella PhoPQ system has a much more profound impact on the expression of H-NS-repressed, horizontally acquired virulence genes than on the ancestral members of the PhoP regulon. We observe that the PhoPQ systems of other related bacteria exhibit activity levels similar to the E. coli system, suggesting that the differences we observe are the result of Salmonella-specific adaptations that produced a more active PhoPQ system when encountering SCV conditions. Collectively, this study offers a window into the evolutionary adaptations of a TCS that enable it to assume an expanded regulatory role in a unique environment.}, }
@article {pmid40319560, year = {2025}, author = {Gross, N and Brodard, I and Overesch, G and Kittl, S}, title = {Genetic basis of β-lactam resistance in Corynebacterium auriscanis and association with otitis externa in dogs and cats.}, journal = {Veterinary microbiology}, volume = {305}, number = {}, pages = {110526}, doi = {10.1016/j.vetmic.2025.110526}, pmid = {40319560}, issn = {1873-2542}, abstract = {Corynebacterium (C.) auriscanis is an opportunistic pathogen regularly isolated from canine otitis externa, an important condition often hard to treat. We found a surprisingly high prevalence of β-lactam resistant isolates of C. auriscanis (47 %), even though β-lactams are not routinely used for otitis externa treatment in Switzerland. To determine the genetic base of this phenotype, a selection of isolates of C. auriscanis with high and low minimal inhibitory concentration values were subjected to whole genome sequencing. Comparative analysis revealed a gene cassette containing three genes (hdfR encoding a LysR-family transcriptional regulator, blaB encoding a β-lactamase related protein and pbp2c encoding a D,D-transpeptidase) as the likely resistance-encoding determinant in the isolates from otitis externa. This locus had previously been described in C. jeikeium as well as C. diphtheriae and was associated with mobile genetic elements. In our six C. auriscanis isolates the pbp2c locus was always associated with the same IS3 family transposase, an association also found on C. diphtheriae plasmid CP091096, indicating horizontal gene transfer between species. To elucidate the function of the three genes in the pbp2c locus, we constructed plasmids with different combinations of these genes, transformed β-lactam sensitive isolates with the plasmids and tested resistance in the mutants phenotypically. By doing so we confirmed Pbp2c to be the primary factor conferring β-lactam resistance and HdfR and BlaB being important for expression and regulation. Interestingly, resistance to all β-lactams including carbapenems was constitutive in one C. auriscanis transformant while an induction effect was visible for the other transformed C. auriscanis strain, C. glutamicum and C. rouxii as previously described for C. jeikeium. Therefore, testing of β-lactam resistance should be done in combination including induction in Corynebacterium spp.}, }
@article {pmid40318462, year = {2025}, author = {Zhang, T and Fan, L and Zhang, YN}, title = {Antibiotic resistance genes in aquatic systems: Sources, transmission, and risks.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {284}, number = {}, pages = {107392}, doi = {10.1016/j.aquatox.2025.107392}, pmid = {40318462}, issn = {1879-1514}, abstract = {The widespread use of antibiotics has significantly contributed to the spread of antibiotic resistance genes (ARGs), which have become a major challenge to global ecological and public health. Antibiotic resistance not only proliferates in clinical settings but also persists in aquatic systems, where its residues and cross-domain spread pose a dual threat to both ecosystems and human health. ARGs spread rapidly within microbial communities through horizontal gene transfer (HGT) and vertical gene transfer (VGT). Aquatic systems are the key transmission medium. This review summarizes recent studies on the Source-Transport-Sink dynamics of ARGs in aquatic environments, along with their environmental and health risk assessments, with a particular focus on the potential ecotoxicity of ARGs transmission. It also examines the distribution characteristics of ARGs across different regions and the ecological risk assessment methods employed, highlighting the limitations of existing models when addressing the complex behaviors of ARGs. By analyzing the potential hazards of ARGs to aquatic ecosystems and public health, this article aims to provide a scientific foundation for future research and the development of public policies.}, }
@article {pmid40314822, year = {2025}, author = {Bell I, PJ and Muniyan, R}, title = {Synergistic pathogenesis: exploring biofilms, efflux pumps and secretion systems in Acinetobacter baumannii and Staphylococcus aureus.}, journal = {Archives of microbiology}, volume = {207}, number = {6}, pages = {134}, pmid = {40314822}, issn = {1432-072X}, mesh = {*Biofilms/growth &amp; development ; *Acinetobacter baumannii/pathogenicity/drug effects/physiology/genetics ; Humans ; *Staphylococcus aureus/pathogenicity/drug effects/physiology/genetics/metabolism ; Anti-Bacterial Agents/pharmacology ; Virulence Factors/metabolism/genetics ; Staphylococcal Infections/microbiology/drug therapy ; Drug Resistance, Multiple, Bacterial ; Cross Infection/microbiology ; *Membrane Transport Proteins/metabolism/genetics ; Bacterial Proteins/metabolism/genetics ; Acinetobacter Infections/microbiology ; }, abstract = {Antimicrobial resistance (AMR) is a growing global health crisis, particularly among ESKAPE pathogens: Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species. Among them, A. baumannii and S. aureus are major contributors to nosocomial infections, with high prevalence in intensive care units and immunocompromised patients. Their ability to resist multiple antibiotic classes complicates treatment strategies, leading to increased morbidity and mortality. Key resistance mechanisms, including biofilm formation, efflux pump activity, and horizontal gene transfer, enhance their survival and persistence. Furthermore, interactions during polymicrobial infections intensify disease severity through synergistic effects that promote both virulence and resistance. The epidemiological burden of these pathogens highlights the urgent need for novel antimicrobial strategies and targeted interventions. This review explores their virulence factors, resistance mechanisms, pathogenic interactions, and clinical implications, emphasizing the necessity of innovative therapeutic approaches to combat their growing threat.}, }
@article {pmid40311358, year = {2025}, author = {Gómez-Brandón, M and Aira, M and Probst, M and Liu, N and Zhang, Z and Zhu, YG and Domínguez, J}, title = {Earthworms attenuate antibiotic resistance genes and mobile genetic elements during vermicomposting of sewage sludge.}, journal = {Journal of environmental management}, volume = {384}, number = {}, pages = {125562}, doi = {10.1016/j.jenvman.2025.125562}, pmid = {40311358}, issn = {1095-8630}, abstract = {Sewage sludge is among the richest reservoirs of antibiotic resistance genes (ARGs) that may spread to urban environment. Further investigation is warranted for removal of sludge-borne ARGs in large-scale vermicomposting systems. Under this scenario, there is the necessity to unveil the role of the widely-used earthworm species Eisenia andrei, since the current body of literature mostly focuses on E. fetida. The present study sought to evaluate the changes in sludge-borne ARGs and mobile genetic elements in a pilot-scale vermireactor in the presence of E. andrei in response to both gut- and cast-associated processes (GAPs and CAPs, respectively), by coupling high-throughput quantitative PCR and Illumina sequencing. After gut transit, large decreases in the relative abundances and number of the genes conferring resistance to major antibiotic classes, including some specific genes classified as of potentially high risk to human health, were recorded in the fresh casts. Likewise, genes encoding resistance to heavy metals were about nine-times lower in the egested materials than in the initial sludge. Genes coding for integrases or insertional sequences also exhibited reduced abundance as a result of GAP and CAP processes, suggesting that vermicompost appears to be less prone to horizontal gene transfer than untreated sludge. These findings provide evidence about the capacity of the earthworm E. andrei to diminish the risk of ARG spread during vermicomposting, reinforcing its potential for bioremediation purposes by transforming large quantities of waste into an improved fertiliser. This is crucial to propel vermicomposting technology forward and achieve transition toward net zero-waste process.}, }
@article {pmid40310292, year = {2025}, author = {Alejandre-Sixtos, JE and Aguirre-Martínez, K and Cruz-López, J and Mares-Rivera, A and Álvarez-Martínez, SM and Zamorano-Sánchez, D}, title = {Insights on the regulation and function of the CRISPR/Cas transposition system located in the pathogenicity island VpaI-7 from Vibrio parahaemolyticus RIMD2210633.}, journal = {Infection and immunity}, volume = {}, number = {}, pages = {e0016925}, doi = {10.1128/iai.00169-25}, pmid = {40310292}, issn = {1098-5522}, abstract = {CRISPR/Cas-mediated transposition is a recently recognized strategy for horizontal gene transfer in a variety of bacterial species. However, our understanding of the factors that control their function in their natural hosts is still limited. In this work, we report our initial genetic characterization of the elements associated with the CRISPR/Cas-transposition machinery (CASTm) from Vibrio parahaemolyticus (VpaCASTm), which are encoded within the pathogenicity island VpaI-7. Our results revealed that the components of the VpaCASTm and their associated CRISPR arrays (VpaCAST system) are transcriptionally active in their native genetic context. Furthermore, we were able to detect the presence of polycistrons and several internal promoters within the loci that compose the VpaCAST system. Our results also suggest that the activity of the promoter of the atypical CRISPR array is not repressed by the baseline activity of its known regulator VPA1391 in V. parahaemolyticus. In addition, we found that the activity of the promoter of tniQ was modulated by a regulatory cascade involving ToxR, LeuO, and H-NS. Since it was previously reported that the activity of the VpaCAST system was less efficient than that of the VchCAST system at promoting transposition of a miniaturized CRISPR-associated transposon (mini-CAST) in Escherichia coli, we analyzed if the transposition efficiency mediated by the VpaCAST system could be enhanced inside its natural host V. parahaemolyticus. We provide evidence that this might be the case, suggesting that there could be host induction factors in V. parahaemolyticus that could enable more efficient transposition of CASTs.IMPORTANCEMobile genetic elements such as transposons play important roles in the evolutionary trajectories of bacterial genomes. The success of transposon dissemination depends on their ability to carry selectable markers that improve the fitness of the host cell or loci with addictive traits such as the toxin-antitoxin systems. Here we aimed to characterize a transposon from Vibrio parahaemolyticus that carries and could disseminate multiple virulence factors. This transposon belongs to a recently discovered family of transposons whose transposition is guided by crRNA. We showed that the transposition machinery of this transposon is transcribed in V. parahaemolyticus and that there are likely host-associated factors that favor transposition in the natural host V. parahaemolyticus over transposition in Escherichia coli.}, }
@article {pmid40307209, year = {2025}, author = {Song, X and Wang, Y and Wang, Y and Zhao, K and Tong, D and Gao, R and Lv, X and Kong, D and Ruan, Y and Wang, M and Tang, X and Li, F and Luo, Y and Zhu, Y and Xu, J and Ma, B}, title = {Rhizosphere-triggered viral lysogeny mediates microbial metabolic reprogramming to enhance arsenic oxidation.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {4048}, pmid = {40307209}, issn = {2041-1723}, support = {42277283//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42090060//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41991334//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Rhizosphere ; *Arsenic/metabolism ; Oxidation-Reduction ; *Oryza/microbiology/virology/metabolism ; Soil Microbiology ; *Lysogeny/genetics ; Microbiota/genetics ; Gene Transfer, Horizontal ; Metagenome ; Plant Roots/microbiology/virology ; Oxidoreductases/genetics/metabolism ; Metabolic Reprogramming ; }, abstract = {The rhizosphere is a critical hotspot for metabolic activities involving arsenic (As). While recent studies indicate many functions for soil viruses, much remains overlooked regarding their quantitative impact on rhizosphere processes. Here, we analyze time-series metagenomes of rice (Oryza sativa L.)rhizosphere and bulk soil to explore how viruses mediate rhizosphere As biogeochemistry. We observe the rhizosphere favors lysogeny in viruses associated with As-oxidizing microbes, with a positive correlation between As oxidation and the prevalence of these microbial hosts. Moreover, results demonstrate these lysogenic viruses enrich both As oxidation and phosphorus co-metabolism genes and mediated horizontal gene transfers (HGTs) of As oxidases. In silico simulation with genome-scale metabolic models (GEMs) and in vitro validation with experiments estimate that rhizosphere lysogenic viruses contribute up to 25% of microbial As oxidation. These findings enhance our comprehension of the plant-microbiome-virome interplay and highlight the potential of rhizosphere viruses for improving soil health in sustainable agriculture.}, }
@article {pmid40306591, year = {2025}, author = {Sam-On, MFS and Mustafa, S and Mohd Hashim, A and Abdul Malek, AZ}, title = {Probiogenomic insights into Bacillus velezensis MFSS1 for controlling aquaculture pathogens.}, journal = {Microbial pathogenesis}, volume = {205}, number = {}, pages = {107645}, doi = {10.1016/j.micpath.2025.107645}, pmid = {40306591}, issn = {1096-1208}, abstract = {Bacillus velezensis MFSS1 (previously known as B. subtilis FS6) was reported to have good probiotic criteria and antibacterial activity against Vibrio spp. and Aeromonas spp., through phenotypic analysis. However, whole genome sequencing is required for commercialising a new probiotic, especially due to reports on probiotics that can cause horizontal gene transfer towards the host microbiome. Therefore, this study aims to investigate the comprehensive genomic characteristics of B. velezensis MFSS1, focusing on its antimicrobial genes against aquaculture pathogens, its probiotic traits, and safety assessment. The bacterial genome was sequenced using Oxford Nanopore sequencing, resulting in 7 contigs with a total length of 3,914,361 base pairs and an average G + C content of 46.58 %. The analysis using ContEst16S and average nucleotide identity revealed that the bacterium previously reported as B. subtilis is actually B. velezensis. Additionally, secondary metabolites against pathogens were predicted using the antiSMASH website, which identified eight secondary metabolites: Bacillibactin, Bacilysin, Surfactin, Difficidin, Fengycin, Bacillaene, Macrolactin H, and Plantazolicin. Furthermore, several probiotic markers were detected, functioning in acid tolerance, bile salt tolerance, adhesion, osmotic stress, and intestinal persistence during the delivery of the bacteria to the host. Interestingly, the in silico safety assessment of the bacterium revealed a lack of 96 antibiotic resistance genes and confirmed it as non-pathogenic to humans, compared with genomic bacteria from ATCC. The study indicates that B. velezensis MFSS1 is a good probiotic through genomic analysis and can be commercialised to control aquaculture pathogens and reduce reliance on antibiotics.}, }
@article {pmid40306109, year = {2025}, author = {Huang, X and Hou, Y and Zhao, M and Chen, J and Zhu, Z and Liu, H and Wang, M and Hua, L and Chen, H and Wu, B and Peng, Z}, title = {Identification of a broad-spectrum lytic Bordetella phage and assessments of its potential for combating Bordetella infections.}, journal = {Virology}, volume = {608}, number = {}, pages = {110545}, doi = {10.1016/j.virol.2025.110545}, pmid = {40306109}, issn = {1096-0341}, abstract = {Bordetella bronchiseptica (Bb) is a zoonotic respiratory pathogen that frequently causes infections in farming and companion animals, posing threats to agricultural economics and public health. However, Bb strains are intrinsically resistant to several antibiotics commonly used to treat respiratory infections. Phage therapy has been recognized as a promising strategy to combat bacterial infections. In this study, a novel Bordetella phage, designated PY223, was isolated using Bb strains as indicators. Genome network analysis with different phages showed PY223 was related to 15 viral clusters but was not included in any of these clusters. PY223 did not carry any known genes involved in lysogeny and/or horizontal gene transfer. Host range analysis showed that PY223 exhibited the capacity to lyse 70 Bb strains isolated from pigs and/or cats. Measurement of the one-step growth curve showed that PY223 had an incubation period of 10 min and a rapid growth period of 80 min. The burst size was estimated to be approximately 10[9] PFU/cell. In addition, PY223 displayed the capacity to inhibit the growth of Bb for up to 17 h. PY223 was stable under environmental temperatures ranging from 4 °C to 60 °C and/or pH values between 5.0 and 9.0. It remained stable even when exposed to UV light for 30 min. Notably, PY223 effectively eliminated Bb biofilms, inhibited the growth of prophage-harboring Bb strains, and cleared Bb from the environment. In vivo testing in mouse models highlighted its excellent potential for treating respiratory Bordetella infections.}, }
@article {pmid40304893, year = {2025}, author = {Domingues, S and Lima, T and Escobar, C and Plantade, J and Charpentier, X and da Silva, GJ}, title = {Large DNA fragment ISEc9-mediated transposition during natural transformation allows interspecies dissemination of antimicrobial resistance genes.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, pmid = {40304893}, issn = {1435-4373}, abstract = {PURPOSE: Antimicrobial resistance poses a significant global health challenge, contributing to a lack of effective therapeutic agents, especially against Gram-negative bacteria. Resistance dissemination is accelerated by horizontal gene transfer (HGT) mechanisms. The extended-spectrum beta lactamases CTX-M confer resistance to several beta-lactams, are usually embedded into plasmids and thought to be mainly disseminated by conjugation. However, an increasing number of isolates carry these enzyme-encoding genes in the chromosome, suggesting that they can spread by other means of HGT. In this study, we aimed to test the involvement of natural transformation in the chromosomal acquisition of a blaCTX-M gene.<br><br>METHODS: Natural transformation assays were performed during motility on wet surfaces. Acquisition of foreign DNA by transformants was screened by antimicrobial susceptibility testing, polymerase-chain reaction (PCR) and whole genome sequencing (WGS).<br><br>RESULTS: Acinetobacter baumannii A118, a naturally competent clinical strain, was transformed with naked DNA from Salmonella enterica serovar Typhimurium Sal25, which was isolated from swine meat. The transformation occurred at low frequency (2.7&#x2009;&#xd7;&#x2009;10[-&#x2009;8] &#xb1; 2.04&#x2009;&#xd7;&#x2009;10[-&#x2009;8] transformants per recipient) and blaCTX-M was acquired in one transformant, which was named ACI. WGS of the transformant revealed the acquisition of the blaCTX-M-32 as part of a ca. 36 Kb DNA fragment through an ISEc9-mediated transposition event; various mobile genetic elements and other resistance genes were co-transferred. The blaCTX-M-32 gene was subsequently transferred within A. baumannii at a higher frequency (1.8&#x2009;&#xd7;&#x2009;10[-&#x2009;6] &#xb1; 2.49&#x2009;&#xd7;&#x2009;10[-&#x2009;6] transformants per recipient).<br><br>CONCLUSION: Our results highlight the importance of natural transformation events in the dissemination of antimicrobial resistance genes and mobile genetic elements between and within species.}, }
@article {pmid40304813, year = {2025}, author = {Qin, S and Wang, H and Wang, M and Shao, B and Ma, C and Yang, B and Jin, X}, title = {Mitochondrial genome evolution in the orchid subfamily Cypripedioideae (Orchidaceae).}, journal = {Functional &amp; integrative genomics}, volume = {25}, number = {1}, pages = {96}, pmid = {40304813}, issn = {1438-7948}, support = {2022YFF1301704)//National Key Research and Development Program of China/ ; }, mesh = {*Orchidaceae/genetics/classification ; *Evolution, Molecular ; *Genome, Mitochondrial ; Phylogeny ; }, abstract = {In this study, the mitogenomes of nine species in the subfamily Cypripedioideae were newly sequenced and assembled using both short and long reads for evolutionary analyses. Complete multi-chromosomal mitogenomes were obtained for Cypripedium subtropicum, C. henryi, Phragmipedium humboldtii, Phr. kovachii, and Paphiopedilum micranthum, and draft assemblies were obtained for four additional Paphiopedilum species. Thirty-nine protein-coding genes were annotated and shared in nine sampled species. sdh4 was discovered in all species of Cypripedioideae, and rpl10 was detected in four species of Paphiopedilum. These two genes might have been horizontally transferred from non-orchid plants at different times. Approximately 101 to 998 repeat sequences were identified with total lengths of 417,136 to 785,960 bp in the mitogenomes of Cypripedioideae. There were 634 and 662 RNA editing sites in C. subtropicum and Pa. gratrixianum, respectively, and C-to-U editing was dominant. The nad and ccm genes exhibited high frequencies of RNA editing. Our study revealed the complexity of orchid mitogenomes, including evidence for the horizontal transfer of rpl10 and sdh4.}, }
@article {pmid40303475, year = {2025}, author = {Lu, J and Zhang, R and Yu, Y and Lou, H and Li, D and Bao, Q and Feng, C}, title = {Identification of a novel chromosome-encoded fosfomycin resistance gene fosC3 in Aeromonas caviae.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1577167}, pmid = {40303475}, issn = {1664-302X}, abstract = {BACKGROUND: Owing to the rapid emerging of multidrug-, even pandrug-resistant pathogens, and lack of new antibiotics, the older antibiotic, fosfomycin, has been reused in recent years in the clinical practice, especially for treatment of uropathogen infections. With the increased use of fosfomycin, bacterial resistance to it has also increased drastically. Elucidating the resistance mechanism to the antimicrobial has become an urgent task.<br><br>METHODS: The putative fosfomycin resistance gene fosC3 was cloned, and minimal inhibitory concentrations were determined by the agar dilution method. Enzyme kinetic parameters were measured by high-performance liquid chromatography. Bioinformatics analysis was applied to understand the evolutionary characteristics of FosC3.<br><br>RESULTS: The A. caviae strain DW0021 exhibited high level resistance to several antimicrobials including kanamycin, streptomycin, chloramphenicol, florfenicol, tetracycline, and especially higher to fosfomycin (> 1,024&#x202f;&#x3bc;g/mL), while genome annotation indicated that no function-characterized resistance gene was associated with fosfomycin resistance. A novel functional gene designated fosC3 responsible for fosfomycin resistance was identified in the chromosome of A. caviae DW0021. Among the function-characterized proteins, FosC3 shared the highest amino acid similarity of 58.65% with FosC2. No mobile genetic element (MGE) was found surrounding the fosC3 gene. The recombinant pMD19-fosC3/DH5&#x3b1; displayed a MIC value of 32&#x202f;&#x3bc;g/mL to fosfomycin, which revealed a 128-fold increase of MIC value to fosfomycin compared to the control pMD19/E. coli DH5&#x3b1; (0.25&#x202f;&#x3bc;g/mL). FosC3 was phylogenetically close to FosC2 and exhibited a k cat and K m of 82,442&#x202f;&#xb1;&#x202f;1,475&#x202f;s[-1], 70.99&#x202f;&#xb1;&#x202f;4.31&#x202f;&#x3bc;M, respectively, and a catalytic efficiency of (1.2&#x202f;&#xb1;&#x202f;0.3)&#x202f;&#xd7;&#x202f;10[3]&#x202f;&#x3bc;M[-1]&#xb7;s[-1].<br><br>CONCLUSION: In this work, a novel functional fosfomycin thiol transferase, FosC3, which shared the highest protein sequence similarity with FosC2, was identified in A. caviae. The fosfomycin inactivation enzyme FosC3 could effectively inactivate fosfomycin by chemical modification. It is implied that such mechanism facilitates A. caviae to respond to fosfomycin exposure, thereby enhancing survival. However, fosC3 was not related with any MGE, which differs from many other fosfomycin thiol transferase genes. As a result, fosC3 is not expected to be transmitted to other species through horizontal gene transfer mechanism. Our findings will contribute to the resistance mechanism of the common pathogenic A. caviae.}, }
@article {pmid40303018, year = {2024}, author = {Jia, Y and Zheng, Z and Yang, B and Zhang, H and Wang, Z and Liu, Y}, title = {A Broad-Spectrum Horizontal Transfer Inhibitor Prevents Transmission of Plasmids Carrying Multiple Antibiotic Resistance Genes.}, journal = {Transboundary and emerging diseases}, volume = {2024}, number = {}, pages = {7063673}, pmid = {40303018}, issn = {1865-1682}, mesh = {*Gene Transfer, Horizontal/drug effects ; *Plasmids/genetics/drug effects ; *Zidovudine/pharmacology ; *Anti-Bacterial Agents/pharmacology ; Animals ; *Bacteria/drug effects/genetics ; *Drug Resistance, Bacterial/genetics ; }, abstract = {The dissemination of antimicrobial resistance (AMR) severely degrades the performance of antibiotics and constantly paralyzes the global health system. In particular, plasmid-mediated transfer of antibiotic resistance genes (ARGs) across bacteria is recognized as the primary driver. Therefore, antiplasmid transfer approaches are urgently warranted to resolve this intractable problem. Herein, we demonstrated the potential of azidothymidine (AZT), an FDA-approved anti-HIV drug, as a broad-spectrum horizontal transfer inhibitor to effectively prevent the transmission of multiple ARGs, including mcr-1, bla NDM-5, and tet(X4), both in vitro and in vivo. It was also noteworthy that the inhibitory effect of AZT was proved to be valid within and across bacterial genera under different mating conditions. Mechanistic studies revealed that AZT dissipated bacterial proton motive force, which was indispensable for ATP synthesis and flagellar motility. In addition, AZT downregulated bacterial secretion systems involving general and type IV secretion systems (T4SS). Furthermore, the thymidine kinase, which is associated with DNA synthesis, turned out to be the potential target of AZT. Collectively, our work demonstrates the broad inhibitory effect of AZT in preventing ARGs transmission, opening new horizons for controlling AMR.}, }
@article {pmid40302206, year = {2025}, author = {Drebes Dörr, NC and Lemopoulos, A and Blokesch, M}, title = {Exploring Mobile Genetic Elements in Vibrio cholerae.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evaf079}, pmid = {40302206}, issn = {1759-6653}, abstract = {Members of the bacterial species Vibrio cholerae are known both as prominent constituents of marine environments and as the causative agents of cholera, a severe diarrheal disease. While strains responsible for cholera have been extensively studied over the past century, less is known about their environmental counterparts, despite their contributions to the species' pangenome. This study analyzed the genome compositions of 46 V. cholerae strains, including pandemic and non-pandemic, toxigenic, and environmental variants, to investigate the diversity of mobile genetic elements (MGEs), embedded bacterial defense systems, and phage-associated signatures. Our findings include both conserved and novel MGEs across strains, pointing to shared evolutionary pathways and ecological niches. The defensome analysis revealed a wide array of antiphage/anti-plasmid mechanisms, extending well beyond the traditional CRISPR-Cas and restriction-modification systems. This underscores the dynamic arms race between V. cholerae and MGEs and suggests that non-pandemic strains may act as reservoirs for emerging defense strategies. Moreover, the study showed that MGEs are integrated into genomic hotspots, which may serve as critical platforms for the exchange of defense systems, thereby enhancing V. cholerae's adaptive capabilities against phage attacks and other invading MGEs. Overall, this research offers new insights into V. cholerae's genetic complexity and potential adaptive strategies, offering a better understanding of the differences between environmental strains and their pandemic counterparts, as well as the possible evolutionary pathways that led to the emergence of pandemic strains.}, }
@article {pmid40301684, year = {2025}, author = {Wagner, TM and Torres-Puig, S and Yimthin, T and Irobalieva, RN and Heller, M and Kaessmeyer, S and Démoulins, T and Jores, J}, title = {Extracellular vesicles of minimalistic Mollicutes as mediators of immune modulation and horizontal gene transfer.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {674}, pmid = {40301684}, issn = {2399-3642}, mesh = {*Extracellular Vesicles/immunology/metabolism ; *Gene Transfer, Horizontal ; Animals ; Cattle ; Plasmids/genetics ; *Tenericutes/genetics/immunology ; Mycoplasma/genetics/immunology ; Proteomics ; Mycoplasma mycoides/genetics/immunology ; *Immunomodulation ; }, abstract = {Extracellular vesicles (EVs) are central components of bacterial secretomes, including the small, cell wall-less Mollicutes. Although EV release in Mollicutes has been reported, EV proteomic composition and function have not been explored yet. We developed a protocol for isolating EVs of the pathogens Mycoplasma mycoides subsp. capri (Mmc) and Mycoplasma (Mycoplasmopsis) bovis and examined their functionality. Proteomic analysis demonstrated that EVs mirror the proteome of the EV-producing bacteria. EVs exhibited nuclease activity, effectively digesting both circular and linear DNA. Notably, M. bovis EVs elicited immune responses in bovine primary blood cells, like those induced by live M. bovis. Our findings reveal that EVs can carry plasmids and enable their horizontal transfer, known as vesiduction. Specifically, the natural plasmid pKMK1, with an unknown transmission route, was detected in EVs of Mmc 152/93 and the tetM-containing pIVB08 plasmid was associated with EVs released by an Mmc GM12 strain carrying this plasmid. pIVB08 could be transferred via homo- and heterologous vesiduction to Mmc, M. capricolum subsp. capricolum and M. leachii. Vesiduction was impeded by membrane disruption but resisted DNase and Proteinase K treatment, suggesting that EVs protect their cargo. These findings enhance our understanding of Mollicutes EVs, particularly in host interactions and horizontal gene transfer.}, }
@article {pmid40301564, year = {2025}, author = {Xue, W and Hong, J and Zhao, R and Yao, H and Zhang, Y and Dai, Z and Wang, T}, title = {Spatial entropy drives the maintenance and dissemination of transferable plasmids.}, journal = {Molecular systems biology}, volume = {}, number = {}, pages = {}, pmid = {40301564}, issn = {1744-4292}, support = {2024YFA0920200//MOST | National Key Research and Development Program of China (NKPs)/ ; 32470701//MOST | National Natural Science Foundation of China (NSFC)/ ; HSE499011086//Shenzhen Institute of Synthetic Biology (iSynBio)/ ; }, abstract = {The dissemination of transferable plasmids, a major type of mobile genetic elements (MGEs), is one main driver of antibiotic resistance outbreaks. While the plasmid persistence condition in well-mixed environments has been extensively studied, most microbiota in nature are spatially heterogeneous. However, our knowledge regarding how spatial landscape shapes plasmid maintenance and dissemination remains limited. Here we establish a theoretical framework describing plasmid spread over a metacommunity of multiple patches. By analyzing the gene flow dynamics on randomly generated landscapes, we show that plasmid survival and dispersal are dictated by a simple feature of the landscape, spatial entropy. Reducing entropy speeds up plasmid range expansion and allows the global maintenance of many plasmids that are predicted to be lost by classic theories. The entropy's effects are experimentally validated in E. coli metacommunities transferring a conjugative plasmid. We further examine a vast collection of prokaryotic genomes and show that prokaryotes from low-entropy environments indeed carry more abundant MGEs and antibiotic resistance genes. Our work provides critical insights into the management and control of antimicrobial resistance.}, }
@article {pmid40301151, year = {2025}, author = {Kaufmann, H and Salvador, C and Salazar, VW and Cruz, N and Dias, GM and Tschoeke, D and Campos, L and Sawabe, T and Miyazaki, M and Maruyama, F and Thompson, F and Thompson, C}, title = {Genomic Repertoire of Twenty-Two Novel Vibrionaceae Species Isolated from Marine Sediments.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {36}, pmid = {40301151}, issn = {1432-184X}, mesh = {*Geologic Sediments/microbiology ; *Vibrionaceae/genetics/classification/isolation &amp; purification ; *Genome, Bacterial ; Phylogeny ; Japan ; *Seawater/microbiology ; Genetic Variation ; }, abstract = {The genomic repertoire of vibrios has been extensively studied, particularly regarding their metabolic plasticity, symbiotic interactions, and resistance mechanisms to environmental stressors. However, little is known about the genomic diversity and adaptations of vibrios inhabiting deep-sea marine sediments. In this study, we investigated the genomic diversity of vibrios isolated from deep-sea core sediments collected using a manned submersible off Japan. A total of 50 vibrio isolates were obtained and characterized phenotypically, and by genome sequencing. From this total, we disclosed 22 novel species examining genome-to-genome distance, average amino acid identity, and phenotypes (Alivibrio: 1; Enterovibrio: 1; Photobacterium: 8; Vibrio: 12). The novel species have fallen within known clades (e.g., Fisheri, Enterovibrio, Profundum, and Splendidus) and novel clades (JAMM0721, JAMM0388, JAMM0395). The 28 remainder isolates were identified as known species: Aliivibrio sifiae (2), A. salmonicida (1), Enterovibrio baiacu (1), E. norvegicus (1), Photobacterium profundum (3), P. angustum (1), P. chitiniliticum (1), P. frigidiphilum (1), Photobacterium indicum (1), P. sanguinicancri (1). P. swingsii (2), Vibrio alginolyticus (3), V. anguillarum (1), V. campbellii (1), V. fluvialis (1), V. gigantis (1), V. lentus (1), V. splendidus (4), and V. tasmaniensis (1). Genomic analyses revealed that all 50 vibrios harbored genes associated with high-pressure adaptation, including sensor kinases, chaperones, autoinducer-2 (AI-2) signaling, oxidative damage repair, polyunsaturated fatty acid biosynthesis, and stress response mechanisms related to periplasmic and outer membrane protein misfolding under heat shock and osmotic stress. Additionally, alternative sigma factors, trimethylamine oxide (TMAO) respiration, and osmoprotectant acquisition pathways were identified, further supporting their ability to thrive in deep-sea environments. Notably, the genomes exhibited a high prevalence of antibiotic resistance genes, with antibiotic efflux pumps being the most abundant group. The ugd gene expanded in number in some novel species (Photobacterium satsumensis sp. nov. JAMM1754: 4 copies; Vibrio makurazakiensis sp. nov. JAMM1826: 3 copies). This gene may confer antibiotic (polymyxin) resistance to these vibrios.}, }
@article {pmid40300599, year = {2025}, author = {Ba, F and Zhang, Y and Wang, L and Ji, X and Liu, WQ and Ling, S and Li, J}, title = {Integrase enables synthetic intercellular logic via bacterial conjugation.}, journal = {Cell systems}, volume = {}, number = {}, pages = {101268}, doi = {10.1016/j.cels.2025.101268}, pmid = {40300599}, issn = {2405-4720}, abstract = {Integrases have been widely used in synthetic biology for genome engineering and genetic circuit design. They mediate DNA recombination to alter the genotypes of single cell lines in vivo, with these changes being permanently recorded and inherited via vertical gene transfer. However, integrase-based intercellular DNA messaging and its regulation via horizontal gene transfer remain underexplored. Here, we introduce a versatile strategy to design, build, and test integrase-based intercellular DNA messaging through bacterial conjugation. First, we screened conjugative plasmids and recipient cells for efficient conjugation. Then, we established a layered framework to describe the interactions among hierarchical E. coli strains and implemented dual-layer Boolean logic gates to demonstrate intercellular DNA messaging and management. Finally, we expanded the design to include four-layer single-processing pathways and dual-layer multi-processing systems. This strategy advances intercellular DNA messaging, hierarchical signal processing, and the application of integrase in systems and synthetic biology.}, }
@article {pmid40298586, year = {2025}, author = {Niño-Vega, GA and Ortiz-Ramírez, JA and López-Romero, E}, title = {Novel Antibacterial Approaches and Therapeutic Strategies.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {4}, pages = {}, pmid = {40298586}, issn = {2079-6382}, abstract = {The increase in multidrug-resistant organisms worldwide is a major public health threat driven by antibiotic overuse, horizontal gene transfer (HGT), environmental drivers, and deficient infection control in hospitals. In this article, we discuss these factors and summarize the new drugs and treatment strategies suggested to combat the increasing challenges of multidrug-resistant (MDR) bacteria. New treatments recently developed involve targeting key processes involved in bacterial growth, such as riboswitches and proteolysis, and combination therapies to improve efficacy and minimize adverse effects. It also tackles the challenges of the Gram-negative bacterial outer membrane, stressing that novel strategies are needed to evade permeability barriers, efflux pumps, and resistance mechanisms. Other approaches, including phage therapy, AMPs, and AI in drug discovery, are also discussed as potential alternatives. Finally, this review points out the urgency for continued research and development (R&amp;D), industry-academic partnerships, and financial engines to ensure that MDR microbes do not exceed the value of antibacterial therapies.}, }
@article {pmid40298491, year = {2025}, author = {Karampatakis, T and Tsergouli, K and Behzadi, P}, title = {Carbapenem-Resistant Pseudomonas aeruginosa's Resistome: Pan-Genomic Plasticity, the Impact of Transposable Elements and Jumping Genes.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {4}, pages = {}, pmid = {40298491}, issn = {2079-6382}, abstract = {Pseudomonas aeruginosa, a Gram-negative, motile bacterium, may cause significant infections in both community and hospital settings, leading to substantial morbidity and mortality. This opportunistic pathogen can thrive in various environments, making it a public health concern worldwide. P. aeruginosa's genomic pool is highly dynamic and diverse, with a pan-genome size ranging from 5.5 to 7.76 Mbp. This versatility arises from its ability to acquire genes through horizontal gene transfer (HGT) via different genetic elements (GEs), such as mobile genetic elements (MGEs). These MGEs, collectively known as the mobilome, facilitate the spread of genes encoding resistance to antimicrobials (ARGs), resistance to heavy metals (HMRGs), virulence (VGs), and metabolic functions (MGs). Of particular concern are the acquired carbapenemase genes (ACGs) and other β-lactamase genes, such as classes A, B [metallo-β-lactamases (MBLs)], and D carbapenemases, which can lead to increased antimicrobial resistance. This review emphasizes the importance of the mobilome in understanding antimicrobial resistance in P. aeruginosa.}, }
@article {pmid40298490, year = {2025}, author = {Garcia-Torné, M and Falcó, I and Borrell, X and Bautista, A and Mazigh, R and Aznar, R and Sánchez, G and Farré, M and Llorca, M}, title = {Comprehensive Study of Antibiotics and Antibiotic Resistance Genes in Wastewater and Impacted Mediterranean Water Environments.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {4}, pages = {}, pmid = {40298490}, issn = {2079-6382}, support = {869178-Aquatic Pollutants//Water JPI/ ; ON-HEALTH 2021 SGR 01150//Government of Catalonia/ ; CEX2021-001189-S//Spanish Ministry of Science and Innovation/ ; PRE2021-099409//Spanish Ministry of Science and Innovation/ ; MS21-006//Ministry of Universities of the Government of Spain, financed by the European Union (NextGeneration EU)/ ; }, abstract = {Background: The spread of antimicrobial resistance is a central public health problem. Wastewater treatment plants and impacted environments are well-known hotspots for antibiotic resistance. However, there is still limited knowledge regarding where antibiotic resistance genes (ARGs) acquire mobility. Method: In this study, we aimed to gather evidence on the seasonal patterns of ARG spread in two Mediterranean areas from NE and E of Spain (Ebro River and Ebro Delta, and Xúquer River and Albufera de València), correlating ARG presence, with special focus on the faecal bacteria Escherichia coli, with antibiotic residues and environmental conditions. The analytical methodology employed was based on a suspect screening approach, while a novel prioritisation approach for antibiotics was proposed to identify those areas more susceptible to the spread of ARG. Results: Our findings demonstrate that ARG levels in wastewater were similar across different seasons, although a greater diversity of ARGs was recorded in summer. We hypothesise that horizontal gene transfer among aquatic bacterial populations during the northeastern Mediterranean summer, when temperatures reach approximately 35~40 °C, could be a key driver of ARG dissemination. By contrast, the highest concentrations of antibiotics in winter samples, with temperatures around 5~10 °C, may promote the spread of microbial resistance. Conclusions: Our key findings highlight that water temperature and sunlight irradiation are crucial factors influencing antibiotic levels and microbial abundance, requiring further investigation in future studies.}, }
@article {pmid40294085, year = {2025}, author = {Bellotti, G and Cortimiglia, C and Antinori, ME and Cocconcelli, PS and Puglisi, E}, title = {Comprehensive genome-wide analysis for the safety assessment of microbial biostimulants in agricultural applications.}, journal = {Microbial genomics}, volume = {11}, number = {4}, pages = {}, pmid = {40294085}, issn = {2057-5858}, mesh = {*Agriculture/methods ; Whole Genome Sequencing ; *Genome, Bacterial ; *Bacteria/genetics/drug effects ; Virulence Factors/genetics ; *Fertilizers/microbiology ; Interspersed Repetitive Sequences ; }, abstract = {Microbial biostimulants (MBs) offer a sustainable approach to agriculture by helping to reduce reliance on synthetic fertilizers. However, as MBs are intentionally released into the environment, their safety should be rigorously assessed. While taxa with qualified presumption of safety (QPS) benefit from established safety indications, non-QPS taxa lack such guidance. To address this gap, we propose a pipeline combining whole genome sequencing (WGS) and extensive literature search (ELS) data to evaluate microbial safety. We analysed public genomes of three QPS species (Rhodopseudomonas palustris, Bacillus velezensis, Priestia megaterium) and four non-QPS genera (Arthrobacter, Azotobacter, Azospirillum, Herbaspirillum), screening them for virulence factors (VFs), antimicrobial resistance (AMR) genes and mobile genetic elements (MGEs). Results confirmed the safety of QPS taxa, revealing no VFs and only a few intrinsic and non-clinically relevant AMRs. Among non-QPS taxa, VF hits were more prevalent in Azotobacter and Azospirillum spp., though they were mostly related to beneficial plant interactions rather than pathogenicity. AMR genes in non-QPS taxa were primarily associated with efflux pumps or were sporadically distributed. Notably, the only genus-wide pattern observed was that most Azospirillum and Herbaspirillum genomes harboured chromosomally encoded β-lactamases sharing similar genetic structures; however, the detected β-lactamase (bla) genes were distantly related to clinically relevant bla variants, and the absence of MGEs suggests a low risk of horizontal gene transfer, indicating the overall safety of these genera. In general, this WGS-ELS framework provides a robust tool for assessing the safety of non-QPS MBs, supporting regulatory decision-making and ensuring their safe use in sustainable agriculture while safeguarding public health.}, }
@article {pmid40289079, year = {2025}, author = {Tsiklauri, R and Kobakhidze, S and Tsereteli, M and Jimsherishvili, L and Kakabadze, N and Koulouris, S and Kotetishvili, M}, title = {Genome data cross-contamination versus interdomain recombination: Equus caballus and Mus musculus genetic loci in the insertion sequence-rich genomes of two clonally related methicillin-resistant Staphylococcus aureus strains from China.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {251}, pmid = {40289079}, issn = {1471-2180}, mesh = {*Methicillin-Resistant Staphylococcus aureus/genetics/classification/isolation &amp; purification ; China ; *Genome, Bacterial ; Animals ; *Recombination, Genetic ; Staphylococcal Infections/microbiology/veterinary ; Horses/microbiology ; *DNA Transposable Elements ; DNA, Bacterial/genetics ; }, abstract = {BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) represents a significant global health threat, responsible for infections in both humans and animals. Determining genetic patterns associated with the genome plasticity of MRSA is critical for predicting the evolutionary trajectories of its emerging pathogenic clones.<br><br>RESULTS: The specific genetic loci of the MRSA strains WH3018 and WH9628 from Wuhan, China, ranging in size from 399 to 3,622 base pairs, were determined to be highly homologous (DNA identity: 90.95-100%) to corresponding chromosomal regions from Equus caballus and Mus musculus in the GenBank database. These eukaryotic-associated loci included the microsatellite DNAs or Y chromosome-specific regions from E. caballus, or 45&#xa0;S-28&#xa0;S ribosomal RNA/H19 loci from M. musculus, all exhibiting recurrent patterns across the genomes of both MRSA strains. The SplitsTree and RDP4 analyses did not reveal significant recombination signals for the eukaryotic-associated loci that had mimicked interdomain recombination events in the MRSA strains WH3018 and WH9628. The G&#x2009;+&#x2009;C content of these loci (47.6-65.0%) was notably higher than that of the S. aureus reference genome (32.5%). Furthermore, the MRSA genomes showed a significantly larger number and greater diversity of insertion sequences (ISs) (38 ISs per genome) compared to the S. aureus reference genome (16 ISs). Additionally, these genomes also exhibited an extensive decay of prophages and the accumulation of pseudo-transposases.<br><br>CONCLUSIONS: The recurring patterns of the eukaryotic-associated loci strongly suggested genome data contamination across the genomes of the MRSA strains WH3018 and WH9628. These MRSA genomes likely underwent extensive prophage decay and an increased proliferation of pseudo-transposases.}, }
@article {pmid40288735, year = {2025}, author = {Wang, M and Masoudi, A and Wang, C and Feng, J and Yu, Z and Liu, J}, title = {Urban afforestation converges soil resistome and mitigates the abundance of human pathogenic bacteria.}, journal = {Environmental research}, volume = {278}, number = {}, pages = {121693}, doi = {10.1016/j.envres.2025.121693}, pmid = {40288735}, issn = {1096-0953}, abstract = {Afforestation has emerged as a nature-based strategy for climate mitigation and urban sustainability, yet its effects on antibiotic resistance genes (ARGs) in soils remain underexplored. This study investigates how the conversion of croplands into plantation forests affects the soil resistome, bacterial communities, and physicochemical properties in an urban environment. Using high-throughput metagenomic and 16S rRNA amplicon sequencing, we analyzed soil samples from croplands and afforested plots with Chinese pine (Pinus tabulaeformis) and Chinese scholar (Sophora japonica) trees, across two-time points post-afforestation. Our results show that afforestation promotes the convergence of both bacterial and ARG communities over time, accompanied by a significant reduction in the relative abundance of human pathogenic bacteria. Afforested soils exhibited a lower prevalence of high-risk ARGs (e.g., qnrA, qnrB from the quinolone class) and reduced co-occurrence between ARGs and mobile genetic elements (MGEs), particularly transposases and recombinases, suggesting diminished horizontal gene transfer. Additionally, afforestation-induced changes in soil pH and nutrient dynamics emerged as key ecological factors shaping ARG profiles. Differences between afforestation types were also observed, with Pinus plantations presenting lower ARG-derived risks than Sophora forests. This study supports afforestation as a nature-based solution for enhancing urban sustainability, reducing public health risks, and achieving resilient ecosystems under anthropogenic influence.}, }
@article {pmid40288673, year = {2025}, author = {Kabeya, N and Ramos-Llorens, M and Nakano, Y and Gomes-Dos-Santos, A and Teixeira, A and Fujibayashi, M and Haro, JG and Navarro, JC and Castro, LFC and Haga, Y and Monroig, &#xd3;}, title = {Methyl-end desaturases determine the capability for de novo biosynthesis of polyunsaturated fatty acids in bivalves.}, journal = {Biochimica et biophysica acta. Molecular and cell biology of lipids}, volume = {1870}, number = {5}, pages = {159617}, doi = {10.1016/j.bbalip.2025.159617}, pmid = {40288673}, issn = {1879-2618}, abstract = {Recent studies have shown that many invertebrate species possess methyl-end desaturases (herein referred to as 'ωx'), enabling biosynthesis of polyunsaturated fatty acids (PUFA). However, the phylogenetic distribution of these enzymes across the animal kingdom remains puzzling, possibly due to horizontal gene transfer (HGT) and/or independent large-scale gene loss in certain invertebrate lineages. In molluscs, ωx genes have been identified in various cephalopods and gastropods but remain barely explored in bivalves. The increasing availability of genomic and transcriptomic resources enables a comprehensive exploration of the ωx gene repertoire in bivalves. To elucidate the distribution of ωx in bivalves, we conducted a broad homology search across existing genome and transcriptome assemblies, followed by functional characterisation of ωx in lineage representative species. Our results revealed no ωx-like sequences in any of the 65 Pteriomorphia species, suggesting gene loss in this clade. However, ωx-like sequences were found in Protobranchia, Palaeoheterodonta and Imparidentia. We analysed ωx from Solemya pusilla (Protobranchia), Lanceolaria oxyrhyncha and Margaritifera margaritifera (Palaeoheterodonta), and Ruditapes philippinarum and Tridacna crocea (Imparidentia). Except for M. margaritifera, which had two ωx genes, each species had a single ωx gene. Functional analysis showed Δ15Δ17Δ19 desaturase activity in the R. philippinarum and T. crocea ωx, while the L. oxyrhyncha ωx exhibited Δ15Δ17 activity but not Δ19. Both ωx from M. margaritifera showed no detectable activity in yeast. Interestingly, the S. pusilla ωx exhibited Δ12 desaturase activity. These findings highlight the diversity of ωx desaturation capabilities in bivalves, with significant gene loss in Pteriomorphia.}, }
@article {pmid40284824, year = {2025}, author = {Silva, V and Caniça, M and de la Rivière, R and Barros, P and Cabral, JA and Poeta, P and Igrejas, G}, title = {Bats as Hosts of Antimicrobial-Resistant Mammaliicoccus lentus and Staphylococcus epidermidis with Zoonotic Relevance.}, journal = {Veterinary sciences}, volume = {12}, number = {4}, pages = {}, pmid = {40284824}, issn = {2306-7381}, abstract = {Bats are increasingly recognized as reservoirs for antimicrobial-resistant bacteria, playing a potential role in the dissemination of resistance genes across species and regions. In this study, 105 bats from 19 species in Portugal were sampled to investigate the presence, antimicrobial resistance, and genetic characteristics of Mammaliicoccus and Staphylococcus isolates. Thirteen Mammaliicoccus lentus and Staphylococcus epidermidis were recovered. Antimicrobial susceptibility testing revealed multidrug resistance in three isolates, with S. epidermidis carrying mph(C), msr(A), and dfrC genes, and M. lentus harboring salB, tet(K), and str. Notably, qacA was detected in S. epidermidis, highlighting its plasmid-associated potential for horizontal gene transfer to more pathogenic bacteria. Heavy metal resistance genes (arsB and cadD) were also identified, suggesting the role of environmental factors in co-selecting antimicrobial resistance. Molecular typing revealed the S. epidermidis strain as ST297, a clone associated with both healthy humans and invasive infections. These findings emphasize the need for monitoring bats as reservoirs of resistance determinants, particularly in the context of zoonotic and environmental health. The presence of mobile genetic elements and plasmids further underscores the potential for the dissemination of resistance. This study reinforces the importance of adopting a One Health approach to mitigate the risks associated with antimicrobial resistance.}, }
@article {pmid40284646, year = {2025}, author = {Alglave, L and Faure, K and Mullié, C}, title = {Plasmid Dissemination in Multispecies Carbapenemase-Producing Enterobacterales Outbreaks Involving Clinical and Environmental Strains: A Narrative Review.}, journal = {Microorganisms}, volume = {13}, number = {4}, pages = {}, pmid = {40284646}, issn = {2076-2607}, abstract = {Outbreaks involving carbapenemase-producing enterobacteria (CPE) have become a common occurrence in healthcare settings. While clonal dissemination is firmly established as a cause for these outbreaks, horizontal gene transfers (HGTs) between different species of Enterobacterales found in clinical and environmental isolates are less so. To gather evidence backing up this hypothesis, a review covering the 2013-2024 period was performed. HGTs between different species of clinical and environmental Enterobacterales were identified in thirteen papers, half of those published within the last three years. A combination of short- and long-read whole genome sequencing (WGS) was predominantly used to identify mobile genetic elements and plasmids. The more frequently reported carbapenemases were KPCs, followed by NDMs and IMPs. Predictably, broad-host-range plasmids were responsible for over 50% of HGTs, with the IncA/C group being in the lead. Klebsiella pneumoniae and Enterobacter cloacae complexes were the most frequent species identified in clinical samples, while Citrobacter freundii dominated environmental ones. Drains and pipework frequently constituted CPE reservoirs in protracted outbreaks, alternating epidemic outbursts with silent phases. Including WGS in a systematic environmental surveillance would help in swiftly identifying those CPE reservoirs and possibly help better control plasmid outbursts by allowing the implementation of adequate infection prevention and control measures.}, }
@article {pmid40284645, year = {2025}, author = {González-Sánchez, A and Lozano-Aguirre, L and Jiménez-Flores, G and López-Sámano, M and García-de Los Santos, A and Cevallos, MA and Le Borgne, S}, title = {Physiology, Heavy Metal Resistance, and Genome Analysis of Two Cupriavidus gilardii Strains Isolated from the Naica Mine (Mexico).}, journal = {Microorganisms}, volume = {13}, number = {4}, pages = {}, pmid = {40284645}, issn = {2076-2607}, abstract = {Here, we report the characterization of two Cupriavidus strains, NOV2-1 and OV2-1, isolated from an iron-oxide deposit in an underground tunnel of the Naica mine in Mexico. This unique biotope, characterized by its high temperature (≈50 °C) and the presence of heavy metals, is no longer available for sampling at this time. The genomes of NOV2-1 and OV2-1 comprised two replicons: a chromosome of 3.58 and 3.53 Mb, respectively, and a chromid of 2.1 Mb in both strains. No plasmids were found. The average nucleotide identity and the core genome phylogeny showed that NOV2-1 and OV2-1 belonged to the Cupriavidus gilardii species. NOV2-1 and OV2-1 grew up to 48 °C, with an optimal temperature of 42 °C. Discrete differences were observed between C. gilardii CCUG38401[T], NOV2-1, and OV2-1 in the biochemical tests. NOV2-1 and OV2-1 presented resistance to zinc, lead, copper, cadmium, nickel, and cobalt. Several complete and incomplete gene clusters related to the resistance to these heavy metals (ars, czc, cop 1, sil-cop 2, cup, mmf, and mer) were detected in the genome of these strains. Although further studies are needed to determine the origin and role of the detected gene clusters, it is suggested that the czc system may have been mobilized by horizontal gene transfer. This study expands the extreme biotopes where Cupriavidus strains can be retrieved.}, }
@article {pmid40283102, year = {2025}, author = {Zhao, Y and Wang, Y and Lu, J and Zhu, B and Li, AD}, title = {Exploring the Ecological Impacts of Herbicides on Antibiotic Resistance Genes and Microbial Communities.}, journal = {Life (Basel, Switzerland)}, volume = {15}, number = {4}, pages = {}, pmid = {40283102}, issn = {2075-1729}, support = {BK20230742//the Natural Science Foundation of Jiangsu Province/ ; GWJJ2024100202//2024 Annual Project of the National Health Commission (NHC) Capacity Building and Continuing Education Center/ ; M2022083//Scientific Research Project of Jiangsu Health Committee/ ; ZDXK202249//Jiangsu Provincial Medical Key Discipline/ ; 2024ZB315//Jiangsu Funding Program for Excellent Postdoctor/ ; }, abstract = {The widespread application of herbicides has profound ecological consequences, particularly regarding the distribution of antibiotic resistance genes (ARGs) and microbial communities. In this study, we analyzed herbicide-related metagenomic data to assess the impact of herbicide exposure on ARGs and microbial populations. Our results demonstrate that herbicide application significantly increased the abundance of ARGs, particularly those associated with multidrug resistance, sulfonamides, and bacitracin, with notable increases in subtypes such as bacA and sul1. Microbial community analyses revealed a dominance of Pseudomonadota and Actinomycetota, along with a significant down-regulation of genera like Fibrisoma, Gilsonvirus, Limnobacter, and Wilnyevirus in the experimental group. Additionally, herbicide exposure led to a marked reduction in biodiversity. When threshold values were relaxed, correlation analyses revealed a co-occurrence pattern between multiple genes and sul1, suggesting that horizontal gene transfer plays a pivotal role in the spread of antibiotic resistance in herbicide-contaminated soils. Moreover, environmental factors were found to significantly influence both microbial community composition and ARG distribution. These findings highlight the complex ecological effects of herbicides on microbial diversity and the dissemination of resistance genes, emphasizing the need for further research into the long-term environmental and public health implications of herbicide use.}, }
@article {pmid40280885, year = {2025}, author = {Kaur, A and Sunny, A and Jones, JB and Goss, EM}, title = {Investigating Plasmids Diversity in X. euvesicatoria pv. perforans Population.}, journal = {Phytopathology}, volume = {}, number = {}, pages = {}, doi = {10.1094/PHYTO-02-25-0042-FI}, pmid = {40280885}, issn = {0031-949X}, abstract = {Plasmids are key drivers of horizontal gene transfer. These genetic elements promote diversification and rapid adaptation of bacterial populations to changing environments by transferring beneficial traits within and between bacterial species. Xanthomonas euvesicatoria pv. perforans is a devastating plant pathogen that causes bacterial spot disease in tomato and pepper. The pathogen population in Florida contains several distinct genetic lineages that differ in relative frequency. The objective of this study was to characterize plasmid diversity and gene content, and plasmid distribution in relation to chromosomal phylogeny. Our in silico-based plasmid prediction revealed the presence of diverse plasmids ranging from ~16 kb to ~235 kb. A network approach based on shared k-mer content uncovered ten distinct plasmid groups with high genetic similarity (cliques). Interestingly, these plasmid cliques were confined to specific phylogenetic clusters suggesting potential incompatibility or restricted plasmid movement between clusters. Some of the predicted plasmids carry virulence genes coding for type III secretion effectors (T3SEs), including transcriptional activator-like effectors (TALEs) and genes related to biocide resistance, such as copper. We also identified gene reshuffling between the plasmids, likely carried out by transposons present within them. Overall, these results provide foundational insights into plasmid diversity in Xanthomonas euvesicatoria pv. perforans with implications for the role of these mobile genetic elements in genome dynamics and pathogen adaptation.}, }
@article {pmid40279390, year = {2025}, author = {Djermoun, S and Rode, DKH and Jiménez-Siebert, E and Netter, N and Lesterlin, C and Drescher, K and Bigot, S}, title = {Biofilm architecture determines the dissemination of conjugative plasmids.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {17}, pages = {e2417452122}, doi = {10.1073/pnas.2417452122}, pmid = {40279390}, issn = {1091-6490}, support = {ANR-19-ARMB-0006-01//Agence Nationale de la Recherche (ANR)/ ; 16GW0245//Bundesministerium f&#xfc;r Bildung und Forschung (BMBF)/ ; RF20200502684//Association Vaincre la Mucoviscidose (French CF Association)/ ; 955910//EC | H2020 | PRIORITY 'Excellent science' | H2020 Marie Sk&#x142;odowska-Curie Actions (MSCA)/ ; TMCG-3 _ 213801/SNSF_/Swiss National Science Foundation/Switzerland ; DR 982/6-1 part of SPP 2389//Deutsche Forschungsgemeinschaft (DFG)/ ; 57552336//Deutscher Akademischer Austauschdienst France (DAAD France)/ ; 47902YJ//Germaine de Stael swiss Academy of Engineering Sciences/ ; }, mesh = {*Biofilms/growth &amp; development ; *Plasmids/genetics ; *Escherichia coli/genetics/physiology ; *Conjugation, Genetic ; Gene Transfer, Horizontal ; Microscopy, Fluorescence ; }, abstract = {Plasmid conjugation is a contact-dependent horizontal gene transfer mechanism that significantly contributes to the dissemination of antibiotic resistance among bacteria. While the molecular mechanisms of conjugation have been extensively studied, our understanding of plasmid transfer dynamics within spatially structured bacterial communities and the influence of community architecture on plasmid dissemination remains limited. In this study, we use live-cell fluorescence microscopy to investigate the propagation of the broad host range RP4 conjugative plasmid in Escherichia coli populations exhibiting varying levels of spatial organization. In high-density, two-dimensional cell monolayers, direct and tight contact between donors and recipients is not only necessary but also sufficient to trigger RP4 plasmid transfer, ensuring optimal plasmid propagation. In three-dimensional mature biofilms, the emergent community architecture limits the ability of donor cells to enter regions with high cell density, which hinders the establishment of direct contacts with recipients and impedes plasmid transfer in biofilms. In contrast, microcolonies, early-stage biofilms, and biofilms with a lower surface coverage leave open access points for donor cells in regions that later emerge as high-cell-density regions in mature biofilms, which facilitates plasmid transfer. These findings reveal the crucial role of bacterial community architecture in determining the efficiency of plasmid dissemination.}, }
@article {pmid40278619, year = {2025}, author = {Pei, Y and Hamar, P and Pei, DS}, title = {Deciphering Multidrug-Resistant Pseudomonas aeruginosa: Mechanistic Insights and Environmental Risks.}, journal = {Toxics}, volume = {13}, number = {4}, pages = {}, pmid = {40278619}, issn = {2305-6304}, support = {CSTB2024TIAD-CYKJCXX0017//Sichuan-Chongqing Special Key Project/ ; }, abstract = {The rise of multidrug-resistant (MDR) Pseudomonas aeruginosa (P. aeruginosa) presents a significant challenge to clinical treatment and environmental risks. This review delves into the complex mechanisms underlying MDR development in P. aeruginosa, such as genetic mutations, horizontal gene transfer (HGT), and the interaction between virulence factors and resistance genes. It evaluates current detection methods, from traditional bacteriology to advanced molecular techniques, emphasizing the need for rapid and accurate diagnostics. This review also examines therapeutic strategies, including broad-spectrum antibiotics, novel drug candidates, combination therapies, and innovative approaches like RNA interference, CRISPR-Cas9 gene editing, and bridge RNA-guided gene editing. Importantly, this review highlights the distribution, migration, and environmental risks of MDR P. aeruginosa, underscoring its adaptability to diverse environments. It concludes by stressing the necessity for continued research and development in antimicrobial resistance, advocating for an integrated approach that combines genomics, clinical practice, and environmental considerations to devise innovative solutions and preserve antibiotic efficacy.}, }
@article {pmid40278556, year = {2025}, author = {Zeng, Y and Feng, R and Huang, C and Liu, J and Yang, F}, title = {Antibiotic Resistance Genes in Agricultural Soils: A Comprehensive Review of the Hidden Crisis and Exploring Control Strategies.}, journal = {Toxics}, volume = {13}, number = {4}, pages = {}, pmid = {40278556}, issn = {2305-6304}, support = {42277033//the National Natural Science Foundation of China/ ; 202401AT070304//Basic Research Foundation of Yunnan Province of China/ ; Y2024QC28//Central Public-interest Scientific Institution Basal Research Fund/ ; 23JCYBJC00250//Tianjin Municipal Natural Science Foundation/ ; }, abstract = {This paper aims to review the sources, occurrence patterns, and potential risks of antibiotic resistance genes (ARGs) in agricultural soils and discuss strategies for their reduction. The pervasive utilization of antibiotics has led to the accumulation of ARGs in the soil. ARGs can be transferred among microorganisms via horizontal gene transfer, thereby increasing the likelihood of resistance dissemination and heightening the threat to public health. In this study, we propose that physical, chemical, and bioremediation approaches, namely electrokinetic remediation, advanced oxidation, and biochar application, can effectively decrease the abundance of ARGs in the soil. This study also highlights the significance of various control measures, such as establishing a strict regulatory mechanism for veterinary drugs, setting standards for the control of ARGs in organic fertilizers, and conducting technical guidance and on-farm soil monitoring to reduce the environmental spread of ARGs and protect public health.}, }
@article {pmid40275408, year = {2025}, author = {Pérez-Carrascal, OM and Pratama, AA and Sullivan, MB and Küsel, K}, title = {Unveiling plasmid diversity and functionality in pristine groundwater.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {42}, pmid = {40275408}, issn = {2524-6372}, abstract = {BACKGROUND: Plasmids are key in creating a dynamic reservoir of genetic diversity, yet their impact on Earth's continental subsurface-an important microbial reservoir-remains unresolved. We analyzed 32 metagenomic samples from six groundwater wells within a hillslope aquifer system to assess the genetic and functional diversity of plasmids and to evaluate the role of these plasmids in horizontal gene transfer (HGT).<br><br>RESULTS: Our results revealed 4,609 non-redundant mobile genetic elements (MGEs), with 14% (664) confidently classified as plasmids. These plasmids displayed well-specific populations, with fewer than 15% shared across wells. Plasmids were linked to diverse microbial phyla, including Pseudomonadota (42.17%), Nitrospirota (3.31%), Candidate Phyla Radiation (CPR) bacteria (2.56%), and Omnitrophota (2.11%). The presence of plasmids in the dominant CPR bacteria is significant, as this group remains underexplored in this context. Plasmid composition strongly correlated with well-specific microbial communities, suggesting local selection pressures. Functional analyses highlighted that conjugative plasmids carry genes crucial for metabolic processes, such as cobalamin biosynthesis and hydrocarbon degradation. Importantly, we found no evidence of high confidence emerging antibiotic resistance genes, contrasting with findings from sewage and polluted groundwater.<br><br>CONCLUSIONS: Overall, our study emphasizes the diversity, composition, and eco-evolutionary role of plasmids in the groundwater microbiome. The absence of known antibiotic resistance genes highlights the need to preserve groundwater in its pristine state to safeguard its unique genetic and functional landscape.}, }
@article {pmid40275130, year = {2025}, author = {Medina-Chávez, NO and Rodriguez-Cruz, UE and Souza, V and De la Torre-Zavala, S and Travisano, M}, title = {Salty secrets of Halobacterium salinarum AD88: a new archaeal ecotype isolated from Cuatro Cienegas Basin.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {399}, pmid = {40275130}, issn = {1471-2164}, support = {IG200319,IN204822//PAPIIT-DGAPA, UNAM/ ; NASA IDEAS16002//NASA IDEAS/ ; }, mesh = {*Halobacterium salinarum/genetics/isolation &amp; purification/classification/metabolism ; Phylogeny ; Genome, Archaeal ; Mexico ; Genomics ; }, abstract = {The Cuatro Cienegas Basin (CCB) in Mexico, represents a unique ecological habitat, characterized by extreme and fluctuating conditions, providing a window into ancient evolutionary processes. This basin, characterized by hypersalinity and phosphorus scarcity, harbors diverse microbial communities that exhibit remarkable adaptations to oligotrophic conditions. Among these, Halobacterium salinarum, a halophilic archaeon known for its polyploid genome and metabolic versatility, has been extensively studied as a model for extremophile survival. However, only a limited number of H. salinarum strains have been successfully cultured and characterized to date. Here, we report the isolation and genomic analysis of a novel Halobacterium salinarum strain, AD88, from microbial mats at the Archaean Domes site in the CCB. This strain displays unique genomic features, including smaller plasmid sizes and distinctive metabolic pathways for phosphorus and sulfur utilization. Comparative analyses with other Halobacterium strains revealed genetic innovations, such as genes involved in sulfolipid biosynthesis, enabling membrane stability in phosphorus-depleted environments, and adaptations for horizontal gene transfer, which facilitate genomic flexibility in response to environmental pressures. This study reveals that H. salinarum AD88 is the first recorded diploid strain of Halobacterium, a feature previously undocumented in this genus. Phylogenomic reconstruction positioned AD88 tightly within the Halobacterium clade, reflecting its evolutionary history within the genus. Pangenome analysis further highlighted the open nature of the Halobacterium genus, with AD88 contributing novel accessory genes linked to ecological specialization. These findings emphasize the evolutionary significance of the CCB as a natural laboratory for studying microbial adaptation and expand our understanding of archaeal genomic diversity and functional innovation under extreme conditions.}, }
@article {pmid40274494, year = {2025}, author = {Good, BH and Bhatt, AS and McDonald, MJ}, title = {Unraveling the tempo and mode of horizontal gene transfer in bacteria.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2025.03.009}, pmid = {40274494}, issn = {1878-4380}, abstract = {Research on horizontal gene transfer (HGT) has surged over the past two decades, revealing its critical role in accelerating evolutionary rates, facilitating adaptive innovations, and shaping pangenomes. Recent experimental and theoretical results have shown how HGT shapes the flow of genetic information within and between populations, expanding the range of possibilities for microbial evolution. These advances set the stage for a new wave of research seeking to predict how HGT shapes microbial evolution within natural communities, especially during rapid ecological shifts. In this article, we highlight these developments and outline promising research directions, emphasizing the necessity of quantifying the rates of HGT within diverse ecological contexts.}, }
@article {pmid40273693, year = {2025}, author = {Yan, X and Xin, Y and Zhu, L and Tang, Q and Chen, M and Wei, Y and Zhang, J and Richnow, HH}, title = {Neglected role of virus-host interactions driving antibiotic resistance genes reduction in an urban river receiving treated wastewater.}, journal = {Water research}, volume = {282}, number = {}, pages = {123627}, doi = {10.1016/j.watres.2025.123627}, pmid = {40273693}, issn = {1879-2448}, abstract = {Treated wastewater from wastewater treatment plants (WWTPs) is a major contributor to the transfer of antibiotic resistance genes (ARGs) into urban rivers. However, the role of viral communities in this process remains poorly understood. This study focused on North Canal in Beijing, China, which receives over 80 % of its water from treated wastewater, to investigate the impact of viral communities on ARGs transfer. Results showed significant seasonal variation in the abundance and composition of ARGs, with 30 high-risk ARGs detected, accounting for 1.50 % ± 1.28 % of total ARGs. The assembly of ARGs in North Canal followed a stochastic process of homogenizing dispersal, with conjugative mobility playing a key role in horizontal gene transfer with Pseudomonas as primary host for HGT. The potential conjugative mobility of ARGs is significantly higher in wet season (69.4 % ± 17.3 %) compared to dry season (42.9 % ± 17.1 %), with conjugation frequencies ranging from 1.18 × 10[-6] to 2.26 × 10[-4]. Viral species accumulation curves approaching saturation indicated the well captured viral diversity, and no phages carrying ARGs were found among 27,523 non-redundant viral operational taxonomic units. Most of the phages (89.2 % ± 3.8 %) were lytic in North Canal, which were observed to contribute to ARGs reduction by lysing their host bacteria, reflected by higher virus-host ratio and demonstrated by the phage lysis assays in treated wastewater and receiving river. We provided compelling evidence that phage-host interactions can reduce ARGs through host lysis, highlighting their potential role in mitigating ARG transmission in urban rivers receiving treated wastewater.}, }
@article {pmid40273218, year = {2025}, author = {Urriza, M and Dimaria, G and de Oliveira, LO and Catara, V and Murillo, J}, title = {Comparative genomics of native plasmids from plant pathogenic Gammaproteobacteria.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {}, number = {}, pages = {}, doi = {10.1093/dnares/dsaf009}, pmid = {40273218}, issn = {1756-1663}, abstract = {Plasmids are key in the evolution and adaptation of plant pathogenic Gammaproteobacteria (PPG), yet their diversity and functional contributions remain underexplored. Here, comparative genomics revealed extensive variation in plasmid size, replicon types, mobility, and genetic content across PPG. Most plasmids are small (<200 kb), except in Pantoea, exhibiting high coding densities (76-78%). Five ancestral replicon types were identified across multiple orders, indicating vertical descent yet efficient horizontal transfer across taxa, although with limited genetic conservation. Virulence plasmids are widespread (56-68%) but differ in virulence gene content across orders: type III effector (T3E) genes are common in Pseudomonas and Xanthomonas, but rare in Enterobacterales and Xylella, aligning with their smaller effector repertoires. Plasmids frequently carry regulatory genes, highlighting their role in bacterial phenotype modulation. Distinct patterns were observed among orders: Enterobacterales plasmids often harbor thiamine biosynthesis operons and transcriptional regulators but lack post-transcriptional regulators, while Pseudomonas and Xanthomonas plasmids are highly mobile, enriched in T3E genes, and exhibit high insertion sequence densities, fostering DNA mobility. Resistance to ultraviolet light is common, but not to antimicrobial compounds. These findings highlight the dynamic role of plasmids in spreading adaptive traits, shaping virulence, and driving the evolution of plant pathogenic bacteria.}, }
@article {pmid40269132, year = {2025}, author = {Kumar, T and Rekhi, A and Lee, Y and Tran, J and Nagtalon, AGD and Rohatgi, S and Cyphert, EL}, title = {Leveraging the microbiome to combat antibiotic resistant gynecological infections.}, journal = {npj antimicrobials and resistance}, volume = {3}, number = {1}, pages = {32}, pmid = {40269132}, issn = {2731-8745}, abstract = {The vaginal resistome can be considered a collection of the resistant determinants in the vaginal microbiome. Here we review the vaginal resistome including the microbes and resistant genes harbored in common gynecological infections, vaginal microbes that participate in horizontal gene transfer, host factors that contribute to the resistome, and common therapies. Finally, we provide perspective on technologies that can be leveraged to study the vaginal resistome and remaining challenges.}, }
@article {pmid40268300, year = {2025}, author = {Goyal, A and Chure, G}, title = {Paradox of the Sub-Plankton: Plausible Mechanisms and Open Problems Underlying Strain-Level Diversity in Microbial Communities.}, journal = {Environmental microbiology}, volume = {27}, number = {4}, pages = {e70094}, pmid = {40268300}, issn = {1462-2920}, mesh = {*Biodiversity ; *Microbiota ; *Bacteria/genetics/classification ; Gene Transfer, Horizontal ; Genetic Variation ; Ecosystem ; Biological Evolution ; }, abstract = {Microbial communities are often complex and highly diverse, typically with dozens of species sharing spatially-restricted environments. Within these species, genetic and ecological variation often exists at a much finer scale, with closely related strains coexisting and competing. While the coexistence of strains in communities has been heavily explored over the past two decades, we have no self-consistent theory of how this diversity is maintained. This question challenges our conventional understanding of ecological coexistence, typically framed around species with clear phenotypic and ecological differences. In this review, we synthesise plausible mechanisms underlying strain-level diversity (termed microdiversity), focusing on niche-based mechanisms such as nutrient competition, neutral mechanisms such as migration, and evolutionary mechanisms such as horizontal gene transfer. We critically assess the strengths and caveats of these mechanisms, acknowledging key gaps that persist in linking genetic similarity to ecological divergence. Finally, we highlight how the origin and maintenance of microdiversity could pose a major challenge to conventional ecological thinking. We articulate a call-to-arms for a dialogue between well-designed experiments and new theoretical frameworks to address this grand conceptual challenge in understanding microbial biodiversity.}, }
@article {pmid40267282, year = {2025}, author = {Yang, Z and Chen, H and Zhong, GH and Liu, J}, title = {cAMP-Mediated Biofilm eDNA Transfer Facilitates the Resilience of Soil Microbiome to Agrochemical Stress.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c00961}, pmid = {40267282}, issn = {1520-5118}, abstract = {Soil microorganisms utilize extracellular DNA (eDNA)-based biofilms as a defense against xenobiotics. However, the specific effects and transfer pathways of eDNA under persistent agrochemical exposure remain unclear. This study examined the transfer dynamics of carbofuran-hydrolase gene pchA from Pseudomonas stutzeri PS21. During biofilm formation, pchA was released from eDNA, leading to an enrichment of beneficial microorganisms such as Acidobacteria and Elusimicrobia, which enhanced organic compound metabolism and improved soil microbiome resilience. An increase in the pchA-associated mobile genetic elements and the colocalization of pchA with other bacterial species indicated the potential horizontal gene transfer (HGT) under carbofuran exposure. Additionally, carbofuran triggered a cAMP-dependent apoptotic pathway, leading to a 59.6% increase in pchA copy number, which suggested that cAMP played a role in initiating HGT. In conclusion, the cAMP-mediated interspecific transfer of pchA could enhance microbial coadaptation to carbofuran contamination, thereby strengthening the collective defense of soil microbiome against agrochemical stress.}, }
@article {pmid40262895, year = {2025}, author = {Lind, AL and McDonald, NA and Gerrick, ER and Bhatt, AS and Pollard, K}, title = {Contiguous and complete assemblies of Blastocystis gut microbiome-associated protists reveal evolutionary diversification to host ecology.}, journal = {Genome research}, volume = {}, number = {}, pages = {}, doi = {10.1101/gr.279080.124}, pmid = {40262895}, issn = {1549-5469}, abstract = {Blastocystis, an obligate host-associated protist, is the most common microbial eukaryote in the human gut and is widely distributed across vertebrate hosts. The evolutionary transition of Blastocystis from its free-living stramenopile ancestors to a radiation of host-associated organisms is poorly understood. To explore this, we cultured and sequenced eight strains representing the significant phylogenetic diversity of the genus using long-read, short-read, and Hi-C DNA sequencing, alongside gene annotation and RNA sequencing. Comparative genomic analyses revealed significant variation in gene content and genome structure across Blastocystis Notably, three strains from herbivorous tortoises, phylogenetically distant from human subtypes, have markedly larger genomes with longer introns and intergenic regions, and retain canonical stop codons absent in the human-associated strains. Despite these genetic differences, all eight isolates exhibit gene losses linked to the reduced cellular complexity of Blastocystis, including losses of cilia and flagella genes, microtubule motor genes, and signal transduction genes. Isolates from herbivorous tortoises contained higher numbers of plant carbohydrate-metabolizing enzymes, suggesting that like gut bacteria, these protists ferment plant material in the host gut. We find evidence that some of these carbohydrate-metabolizing enzymes were horizontally acquired from bacteria, indicating that horizontal gene transfer is an ongoing process in Blastocystis that has contributed to host-related adaptation. Together, these results highlight substantial genetic and metabolic diversity within the Blastocystis genus, indicating different lineages of Blastocystis have varied ecological roles in the host gut.}, }
@article {pmid40262702, year = {2025}, author = {Zhang, S and Sun, C}, title = {Ecological divergence of marine bacteria Alteromonas mediterranea.}, journal = {Molecular phylogenetics and evolution}, volume = {208}, number = {}, pages = {108359}, doi = {10.1016/j.ympev.2025.108359}, pmid = {40262702}, issn = {1095-9513}, abstract = {Alteromonas mediterranea, originally designated as A. macleodii, is a deep-sea ecotype that plays an important ecological role in the ocean. However, a comprehensive understanding of their biogeographic distribution and evolutionary histories remains limited. In this study, our analysis indicated that A. mediterranea members could adapt contrasting marine ecosystems and flourish in nutrient-rich habitats such as feces and coral reefs. No significant correlations between the relative abundance of A. mediterranea members and the environmental variables were identified. Phylogenetic analysis and geographic patterns of A. mediterranea strains suggested that they could be clustered into two clades (clade Ⅰ and clade Ⅱ). In contrast, many distinct genomic traits exist between these clades, such as the complete genes encoding cytochrome o ubiquinol oxidase only involved in clade Ⅱ. Genes were more likely to be lost in the evolutionary history of A. mediterranea relatives. Gene loss might be a major force in all phylogenetic groups driving the distinct clades. Adaptation to different biotopes resulted in the functional differentiation of A. mediterranea members, with the loss of genes encoding carbohydrate-active enzymes. Genes acquired horizontally from unclassified bacteria, and Proteobacteria represented by Gammaproteobacteria played key roles in the functional diversification of A. mediterranea in marine habitats. Given these data, these results are useful for information supplementation of A. mediterranea strains, particularly for making significant advances in understanding marine microbial ecology within different clonal frames using genome-wide recruitments.}, }
@article {pmid40261943, year = {2025}, author = {Gori, K and Baez-Ortega, A and Strakova, A and Stammnitz, MR and Wang, J and Chan, J and Hughes, K and Belkhir, S and Hammel, M and Moralli, D and Bancroft, J and Drydale, E and Allum, KM and Brignone, MV and Corrigan, AM and de Castro, KF and Donelan, EM and Faramade, IA and Hayes, A and Ignatenko, N and Karmacharya, R and Koenig, D and Lanza-Perea, M and Lopez Quintana, AM and Meyer, M and Neunzig, W and Pedraza-Ordoñez, F and Phuentshok, Y and Phuntsho, K and Ramirez-Ante, JC and Reece, JF and Schmeling, SK and Singh, S and Tapia Martinez, LJ and Taulescu, M and Thapa, S and Thapa, S and van der Wel, MG and Wehrle-Martinez, AS and Stratton, MR and Murchison, EP}, title = {Horizontal transfer of nuclear DNA in transmissible cancer.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {18}, pages = {e2424634122}, doi = {10.1073/pnas.2424634122}, pmid = {40261943}, issn = {1091-6490}, support = {102942/Z/13/A 222551/Z/21/Z//Wellcome Trust (WT)/ ; BB/Y514299/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, mesh = {Animals ; *Gene Transfer, Horizontal ; Dogs ; *Dog Diseases/genetics ; *Venereal Tumors, Veterinary/genetics ; *Cell Nucleus/genetics ; Marsupialia/genetics ; *DNA/genetics ; }, abstract = {Horizontal transfer of nuclear DNA between cells of host and cancer is a potential source of adaptive variation in cancer cells. An understanding of the frequency and significance of this process in naturally occurring tumors is, however, lacking. We screened for this phenomenon in the transmissible cancers of dogs and Tasmanian devils and found an instance in the canine transmissible venereal tumor (CTVT). This involved introduction of a 15-megabase dicentric genetic element, composed of 11 fragments of six chromosomes, to a CTVT sublineage occurring in Asia around 2,000 y ago. The element forms the short arm of a small submetacentric chromosome and derives from a dog with ancestry associated with the ancient Middle East. The introduced DNA fragment is transcriptionally active and has adopted the expression profile of CTVT. Its features suggest that it may derive from an engulfed apoptotic body. Our findings indicate that nuclear horizontal gene transfer, although likely a rare event in tumor evolution, provides a viable mechanism for the acquisition of genetic material in naturally occurring cancer genomes.}, }
@article {pmid40261018, year = {2025}, author = {Chi, W and Zhang, H and Li, X and Zhou, Y and Meng, Q and He, L and Yang, Y and Liu, S and Shi, K}, title = {Comparative genomic analysis of 255 Oenococcus oeni isolates from China: unveiling strain diversity and genotype-phenotype associations of acid resistance.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0326524}, doi = {10.1128/spectrum.03265-24}, pmid = {40261018}, issn = {2165-0497}, abstract = {Oenococcus oeni, the only species of lactic acid bacteria capable of fully completing malolactic fermentation under challenging wine conditions, continues to intrigue researchers owing to its remarkable adaptability, particularly in combating acid stress. However, the mechanism underlying its superior adaptation to wine stresses still remains elusive due to the lack of viable genetic manipulation tools for this species. In this study, we conducted genomic sequencing and acid resistance phenotype analysis of 255 O. oeni isolates derived from diverse wine regions across China, aiming to elucidate their strain diversity and genotype-phenotype associations of acid resistance through comparative genomics. A significant correlation between phenotypes and evolutionary relationships was observed. Notably, phylogroup B predominantly consisted of acid-resistant isolates, primarily originating from Shandong and Shaanxi wine regions. Furthermore, we uncovered a noteworthy linkage between prophage genomic islands and acid resistance phenotype. Using genome-wide association studies, we identified key genes correlated with acid resistance, primarily involved in carbohydrates and amino acid metabolism processes. This study offers profound insights into the genetic diversity and genetic basis underlying adaptation mechanisms to acid stress in O. oeni.IMPORTANCEThis study provides valuable insights into the genetic basis of acid resistance in Oenococcus oeni, a key lactic acid bacterium in winemaking. By analyzing 255 isolates from diverse wine regions in China, we identified significant correlations between strain diversity, genomic islands, and acid resistance phenotypes. Our findings reveal that certain prophage-related genomic islands and specific genes are closely linked to acid resistance, offering a deeper understanding of how O. oeni adapts to acidic environments. These discoveries not only advance our knowledge of microbial stress responses but also pave the way for selecting and engineering acid-resistant strains, enhancing malolactic fermentation efficiency and wine quality. This research underscores the importance of genomics in improving winemaking practices and addressing challenges posed by high-acidity wines.}, }
@article {pmid40259521, year = {2025}, author = {Gatica-Soria, LM and Roulet, ME and Tulle, WD and Sato, HA and Barrandeguy, ME and Sanchez-Puerta, MV}, title = {Highly variable mitochondrial chromosome content in a holoparasitic plant due to recurrent gains of foreign circular DNA.}, journal = {Physiologia plantarum}, volume = {177}, number = {2}, pages = {e70231}, doi = {10.1111/ppl.70231}, pmid = {40259521}, issn = {1399-3054}, support = {06/A092-T1//Secretar&#xed;a de Investigaci&#xf3;n, Internacionales y Posgrado, Universidad Nacional de Cuyo/ ; PICT2020-01018//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; PICT2021 -GTR_TI-00435//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; }, mesh = {Gene Transfer, Horizontal/genetics ; DNA, Mitochondrial/genetics ; *Chromosomes, Plant/genetics ; *DNA, Circular/genetics ; *Genome, Mitochondrial/genetics ; Evolution, Molecular ; Phylogeny ; }, abstract = {Multichromosomal mitochondrial genomes (mtDNAs) in eukaryotes exhibit remarkable structural diversity, yet intraspecific variability and the origin of the individual chromosomes remain poorly understood. We focus on a holoparasitic angiosperm with an mtDNA consisting of 65 chromosomes largely composed of foreign DNA acquired by horizontal gene transfer (HGT) from its mimosoid hosts. The frequency, timing and population dynamics of these HGT events have not been examined. Here, we sampled different individuals of the holoparasite Lophophytum mirabile, along with their host plants, to assess mtDNA intraspecific variability and capture recent events that may bring insights into the HGT process. We also gathered mitochondrial data from 43 mimosoids to identify older and recent HGT events and assess precisely the proportion of foreign DNA. Through comparative genomic and evolutionary analyses, we uncovered great intraspecific variability in chromosome content and defined the mitochondrial pangenome of L. mirabile with 105 distinct chromosomes. The estimated foreign content reaches 93.5% of the mtDNA, including 73 fully foreign chromosomes that support the circle-mediated HGT model as a key mechanism for their acquisition. We inferred recurrent DNA transfers from the host plants, leading to new mitochondrial chromosomes that replicate autonomously. Our results emphasize the importance of adopting a pangenomic approach to fully capture the genetic diversity and evolution of multichromosomal mitochondrial genomes. This study shows that HGT can strongly influence the mtDNA content and generate enormous intraspecific variability even in geographically close individuals.}, }
@article {pmid40258067, year = {2025}, author = {Christman, ND and Dalia, AB}, title = {The molecular basis for DNA-binding by competence T4P is distinct in a representative Gram-positive and Gram-negative species.}, journal = {PLoS pathogens}, volume = {21}, number = {4}, pages = {e1013128}, pmid = {40258067}, issn = {1553-7374}, support = {R35 GM128674/GM/NIGMS NIH HHS/United States ; }, mesh = {*Streptococcus pneumoniae/genetics/metabolism ; *Fimbriae, Bacterial/metabolism/genetics ; *DNA, Bacterial/metabolism/genetics ; *Fimbriae Proteins/metabolism/genetics ; *DNA-Binding Proteins/metabolism/genetics ; *Gram-Negative Bacteria/metabolism/genetics ; *DNA Transformation Competence ; Bacterial Proteins/metabolism/genetics ; *Gram-Positive Bacteria/metabolism/genetics ; Protein Binding ; }, abstract = {Competence type IV pili (T4P) are bacterial surface appendages that facilitate DNA uptake during horizontal gene transfer by natural transformation. These dynamic structures actively extend from the cell surface, bind to DNA in the environment, and then retract to import bound DNA into the cell. Competence T4P are found in diverse Gram-negative (diderm) and Gram-positive (monoderm) bacterial species. While the mechanism of DNA-binding by diderm competence T4P has been the recent focus of intensive study, relatively little is known about DNA-binding by monoderm competence T4P. Here, we use Streptococcus pneumoniae as a model system to address this question. Competence T4P likely bind to DNA via a tip-associated complex of proteins called minor pilins, and recent work highlights a high degree of structural conservation between the minor pilin tip complexes of monoderm and diderm competence T4P. In diderms, positively charged residues in one minor pilin, FimT, are critical for DNA-binding. We show that while these residues are conserved in ComGD, the FimT homolog of monoderms, they only play a minor role in DNA uptake for natural transformation. Instead, we find that two-positively charged residues in the neighboring minor pilin, ComGF (the PilW homolog of monoderms), play the dominant role in DNA uptake for natural transformation. Furthermore, we find that these residues are conserved in other monoderms, but not diderms. Together, these results suggest that the molecular basis for DNA-binding has either diverged or evolved independently in monoderm and diderm competence T4P.}, }
@article {pmid40253436, year = {2025}, author = {Huang, J and Zheng, X and Yu, T and Ali, M and Wiese, J and Hu, S and Huang, L and Huang, Y}, title = {Diverse lifestyles and adaptive evolution of uncultured UBA5794 actinobacteria, a sister order of "Candidatus actinomarinales".}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {39}, pmid = {40253436}, issn = {2524-6372}, support = {92351301, 32470005, 42376238, and 32393970//National Natural Science Foundation of China/ ; 91751000//Major Research Plan of the National Natural Science Foundation of China/ ; GML20240002//the PI Project of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; }, abstract = {Uncultured UBA5794 actinobacteria are frequently found in marine and inland water environments by using metagenomic approaches. However, knowledge about these actinobacteria is limited, hindering their isolation and cultivation, and they are always confused with "Candidatus Actinomarinales" based on 16S rRNA gene classification. Here, to conduct genomic characterization of them, we obtained three high-quality UBA5794 metagenome-assembled genomes (MAGs) from a hydrothermal sediment on the Carlsberg Ridge (CR) and retrieved 131 high-quality UBA5794 genomes from public datasets. Phylogenomic analysis confirms UBA5794 as an independent order within the class Acidimicrobiia. Genome-based metabolic predictions reveal that flexible metabolism and diversified energy acquisition, as well as heavy metal(loid) detoxification capacity, are crucial for the ability of UBA5794 to thrive in diverse environments. Moreover, there is separation between sponge-associated and free-living UBA5794 groups in phylogeny and functional potential, which can be attributed to the symbiotic nature of the sponge-associated group and the extensive horizontal gene transfer (HGT) events observed in these bacteria. Ancestral state reconstruction suggests that the UBA5794 clade may have originated from a free-living environment and then some members gradually migrated to the sponge host. Overall, our study sheds light on the ecological adaptation and evolutionary history of the ubiquitous but poorly understood UBA5794 actinobacteria.}, }
@article {pmid40251489, year = {2025}, author = {Bini, F and Soffritti, I and D'Accolti, M and Mazziga, E and Caballero, JD and David, S and Argimon, S and Aanensen, DM and Volta, A and Bisi, M and Mazzacane, S and Caselli, E}, title = {Profiling the resistome and virulome of Bacillus strains used for probiotic-based sanitation: a multicenter WGS analysis.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {382}, pmid = {40251489}, issn = {1471-2164}, support = {INV-004891/GATES/Gates Foundation/United States ; }, mesh = {*Bacillus/genetics/isolation &amp; purification/drug effects/classification/pathogenicity ; *Probiotics ; *Whole Genome Sequencing ; *Genome, Bacterial ; Polymorphism, Single Nucleotide ; *Sanitation ; Humans ; *Drug Resistance, Bacterial/genetics ; }, abstract = {BACKGROUND: Healthcare-associated infections (HAIs) caused by microbes that acquire antimicrobial resistance (AMR) represent an increasing threat to human health worldwide. The high use of chemical disinfectants aimed at reducing the presence of pathogens in the hospital environment can simultaneously favor the selection of resistant strains, potentially worsening AMR concerns. In the search for sustainable ways to control bioburden without affecting this aspect, probiotic-based sanitation (PBS) using Bacillus spp. was proposed to achieve stable reduction of pathogens, AMR, and associated HAIs. Although Bacillus probiotics are classified as nonpathogenic, comprehensive data about the potential genetic alterations of these probiotics following prolonged contact with surrounding pathogens are not yet available. This study aimed to assess in depth the genetic content of PBS-Bacillus isolates to evaluate any eventual variations that occurred during their usage.<br><br>RESULTS: WGS analysis was used for the precise identification of PBS-Bacillus species and detailed profiling of their SNPs, resistome, virulome, and mobilome. Analyses were conducted on both the original PBS detergent and 172 environmental isolates from eight hospitals sanitized with PBS over a 30-month period. The two species B. subtilis and B. velezensis were identified in both the original product and the hospital environment, and SNP analysis revealed the presence of two clusters in each species. No virulence/resistance genes or mobile conjugative plasmids were detected in either the original PBS-Bacillus strain or any of the analyzed environmental isolates, confirming their high genetic stability and their low/no tendency to be involved in horizontal gene transfer events.<br><br>CONCLUSIONS: The data obtained by metagenomic analysis revealed the absence of genetic sequences associated with PBS-Bacillus and the lack of alterations in all the environmental isolates analyzed, despite their continuous contact with surrounding pathogens. These results support the safety of the Bacillus species analyzed. Further metagenomic studies aimed at profiling the whole genomes of these and other species of Bacillus, possibly during longer periods and under stress conditions, would be of interest since they may provide further confirmation of their stability and safety.}, }
@article {pmid40250499, year = {2025}, author = {Yang, Y and Sun, Y and Zhou, Z and Song, Y and Zhu, Y and Zhou, W and Yue, M and Zhao, G and Jiang, H and Tang, B}, title = {Surveillance of Escherichia coli antimicrobial resistance in pig farms in Zhejiang province, China: high prevalence of multidrug resistance and risk-associated genes.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {107598}, doi = {10.1016/j.micpath.2025.107598}, pmid = {40250499}, issn = {1096-1208}, abstract = {OBJECTIVES: The global rise in antimicrobial resistance (AMR) poses a critical threat to public health, with the overuse of antibiotics in livestock being a key driver of this escalating problem. However, research on livestock-associated AMR remains limited, with few systematic monitoring efforts. This study addresses this gap by presenting findings from our surveillance of Escherichia coli resistance in pig farms in Zhejiang Province, China.<br><br>METHODS: The minimum inhibitory concentrations were determined via broth microdilution-based antimicrobial susceptibility testing. The complete genome sequence was acquired using both Illumina NovaSeq 6000 platforms. In the plasmid conjugation experiment, sodium azide-resistant E. coli strain J53 served as the recipient. The E. coli genomes were analyzed for AMR genes, multi-locus sequence typing (MLST) types, plasmid types, and virulence genes using the ABRicate.<br><br>RESULTS: A total of 51 E. coli strains from 90 fecal samples collected across six farms. Resistance rates for amoxicillin/clavulanic acid and sulfamethoxazole exceeded 90%, while resistance to ampicillin, florfenicol, tetracycline, and trimethoprim/sulfamethoxazole was above 80%. The prevalence of multidrug-resistant strains was 89.24%. Whole-genome sequencing revealed 58 acquired AMR genes and 17 virulence-associated genes, notably including the astA gene. Two strains exhibited meropenem resistance and carried blaNDM-5, located on IncI1-I plasmids. These strains shared an identical genetic context, characterized by an "IS26-IS30-blaNDM-5-bleMBL-dsdD-IS91" structure, which may promote horizontal gene transfer of blaNDM-5. Additionally, six strains harbored the tet(X4) gene.<br><br>CONCLUSIONS: Despite ongoing antibiotic reduction efforts, the high prevalence of resistant E. coli in pigs underscores the urgent need for sustained surveillance of AMR in animal populations to mitigate the threat of resistance.}, }
@article {pmid40250277, year = {2025}, author = {Han, Q and Yang, ML and Liu, ZS and Zhao, YH and Liu, XH and Ai, GM and Qin, WH and Liu, XY and Li, DF}, title = {Simultaneous high molecular weight PAHs degradation and chromate and arsenite detoxification by Altererythrobacter sp. H2.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138314}, doi = {10.1016/j.jhazmat.2025.138314}, pmid = {40250277}, issn = {1873-3336}, abstract = {The cooccurrence of high molecular weight PAHs and heavy metals Cr and As is frequently observed in soil and water and challenges public health and environmental management. Yet the limited microbial resources were reported to simultaneously detoxify PAHs, Cr(VI) and As(III), which restricts the bioremediation of co-contaminated soil by PAHs, Cr and As. Here, we isolated Altererythrobacter sp. H2 and found it could degrade various PAHs, including phenanthrene, fluoranthene, pyrene, benzo[a]anthracene, and benzo[a]pyrene, and tolerate and detoxify high concentrations of Cr(VI) and As(III). Genomic, transcriptomic, and biochemical assays reveal strain H2 degrades PAHs, reduces Cr(VI), and oxidize As(III) via a horizontally transferred RHO gene cluster, a chromate reductase ChrR, and a arsenite resistance gene cluster arsRBC. The horizontally transferred PAHs-degrading gene cluster encodes the Rieske dioxygenase three-component system and other enzymes required for PAHs degradation, which suggested those heavy metal-detoxifying bacteria could be excellent PAHs-degrading and heavy metal-detoxifying agents after accommodating a PAHs degradation gene cluster like strain H2 did. To our knowledge, strain H2 is the only reported Altererythrobacter member that uses a classical Rieske dioxygenase three-component system to initial PAHs degradation and the only one could simultaneously detoxify PAHs, Cr(VI), and As(III). Our study provides insights into the PAHs degradation mechanism of Altererythrobacter members and demonstrates the excellent potential of H2 in the bioremediation of both PAHs and heavy metal pollutants.}, }
@article {pmid40249581, year = {2025}, author = {Deslauriers, N and Boulianne, M}, title = {Genetic Comparison of Enterococcus Species Isolated from Osteomyelitis Lesions and the Barn Environment of Successive Broiler Chicken Flocks.}, journal = {Avian diseases}, volume = {68}, number = {S1}, pages = {421-426}, doi = {10.1637/aviandiseases-D-24-00081}, pmid = {40249581}, issn = {1938-4351}, mesh = {Animals ; *Chickens ; *Osteomyelitis/veterinary/microbiology/epidemiology ; *Poultry Diseases/microbiology/epidemiology ; *Enterococcus/genetics/isolation &amp; purification/classification ; *Gram-Positive Bacterial Infections/veterinary/microbiology/epidemiology ; Quebec/epidemiology ; *Housing, Animal ; Virulence ; }, abstract = {Osteomyelitis caused by Enterococcus cecorum is an emerging disease in broiler chickens in Canada. Other Enterococcus species have been reported as causative agents in certain outbreaks. The epidemiology of this disease is unknown, but contaminated barns are affected by recurring episodes. A broiler chicken flock located in Quebec, Canada, exhibited osteomyelitis lesions positive for E. cecorum and Enterococcus faecalis. Surprisingly, the following lot, in the same barn, revealed the presence of E. faecalis- and Enterococcus raffinosus-positive lesions but no E. cecorum. To better understand the epidemiology of these two outbreaks, verify the persistence of pathogenic isolates in the barn, and identify the possible transfer of genetic material between the Enterococcus species isolated from both events, 16 isolates (1 E. cecorum, 13 E. faecalis, and 2 E. raffinosus isolates) were sequenced, and their genomes were compared. Interestingly, more than one Enterococcus species could be isolated from the same lesion, while other lesions also revealed several nonclonal isolates from the same species. This might suggest the opportunistic nature of Enterococcus spp. as there was no predominant isolate in the lesions. The number of virulence genes varied from 1 to 34 across three Enterococcus species with no common virulence gene. The number and nature of antimicrobial resistance genes among those isolates were worrisome because they indicate the presence of multidrug resistance on the farm. Both plasmids and phages were shared by different Enterococcus species, which suggests potential horizontal gene transfer of mobile genetic elements within this enterococci population.}, }
@article {pmid40249005, year = {2025}, author = {Kerek, &#xc1; and Román, I and Szabó, &#xc1; and Kovács, D and Kardos, G and Kovács, L and Jerzsele, &#xc1;}, title = {Antibiotic resistance genes in Escherichia coli - literature review.}, journal = {Critical reviews in microbiology}, volume = {}, number = {}, pages = {1-35}, doi = {10.1080/1040841X.2025.2492156}, pmid = {40249005}, issn = {1549-7828}, abstract = {Antimicrobial resistance threatens humans and animals worldwide and is recognized as one of the leading global public health issues. Escherichia coli (E. coli) has an unquestionable role in carrying and transmitting antibiotic resistance genes (ARGs), which in many cases are encoded on plasmids or phage, thus creating the potential for horizontal gene transfer. In this literature review, the authors summarize the major antibiotic resistance genes occurring in E. coli bacteria, through the major antibiotic classes. The aim was not only listing the resistance genes against the clinically relevant antibiotics, used in the treatment of E. coli infections, but also to cover the entire resistance gene carriage in E. coli, providing a more complete picture. We started with the long-standing antibiotic groups (beta-lactams, aminoglycosides, tetracyclines, sulfonamides and diaminopyrimidines), then moved toward the newer groups (phenicols, peptides, fluoroquinolones, nitrofurans and nitroimidazoles), and in every group we summarized the resistance genes grouped by the mechanism of their action (enzymatic inactivation, antibiotic efflux, reduced permeability, etc.). We observed that the frequency of antibiotic resistance mechanisms changes in the different groups.}, }
@article {pmid40248430, year = {2025}, author = {Chen, S and Liao, L and Wang, M}, title = {Editorial: Opportunistic pathogens: pathogenesis and multi-drug resistance mechanisms.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1597769}, doi = {10.3389/fmicb.2025.1597769}, pmid = {40248430}, issn = {1664-302X}, }
@article {pmid40246490, year = {2025}, author = {Huang, L and Yang, Y and Xue, Y and Hu, S and Liang, T and Ye, J and Xue, X}, title = {A gene island from plasmid pkk5 of Burkholderia sp. KK1 confers arsenic resistance to Caballeronia jiangsuensis.}, journal = {Journal of environmental sciences (China)}, volume = {155}, number = {}, pages = {562-572}, doi = {10.1016/j.jes.2024.09.011}, pmid = {40246490}, issn = {1001-0742}, mesh = {*Arsenic/toxicity/metabolism ; *Burkholderia/genetics/metabolism ; *Plasmids/genetics ; Biodegradation, Environmental ; *Hypocreales/metabolism ; }, abstract = {Microorganisms play a critical role in the biotransformation of arsenic and the form which it exists in the environment. In this study, a methyl parathion-degrading bacterium Caballeronia jiangsuensis, isolated from an abandoned pesticide manufacturing plant, was used to analyze arsenic accumulation and transformation. The accumulation of trivalent organoarsenic compounds in C. jiangsuensis occurred to a greater extent than that of their pentavalent counterparts. The chromosome of C. jiangsuensis contains an arsenic gene island whose GC content is significantly lower than that of the genome, suggesting that the island was acquired via horizontal gene transfer. There was approximately 90 %-99 % similarity between the proteins encoded by the gene island and the corresponding sequence of the plasmid pkk5 from Burkholderia sp. KK1. The biotransformation of different arsenic species by C. jiangsuensis was subsequently analyzed. The results revealed that monomethylarsenic acid (MAs(V)) was rapidly demethylated to arsenate with very small amounts of intermediate monomethylarsonous acid (MAs(III)), whereas MAs(III) was largely oxidized to MAs(V) despite the occurrence of the gene arsI probably responsible for aerobic demethylation of MAs(III) in C. jiangsuensis. In addition, dimethylarsenic acid was partly demethylated to arsenate. Horizontal gene transfer of ars operon from a plasmid to other bacteria represents an adaptation to a specific environment. This study provides a new perspective for understanding arsenic biogeochemical cycling.}, }
@article {pmid40245502, year = {2025}, author = {Zhong, Y and Teo, JQ and Guo, S and Schlundt, J and Kwa, AL and Ong, RT}, title = {Characterization of mobile resistance elements in extended-spectrum β-lactamase producing gram-negative bacteria from aquatic environment.}, journal = {The Science of the total environment}, volume = {978}, number = {}, pages = {179353}, doi = {10.1016/j.scitotenv.2025.179353}, pmid = {40245502}, issn = {1879-1026}, mesh = {*beta-Lactamases/genetics ; *Gram-Negative Bacteria/genetics ; *Interspersed Repetitive Sequences ; *Water Microbiology ; *Drug Resistance, Bacterial/genetics ; Singapore ; }, abstract = {Extended-spectrum β-lactamase producing (ESBL) bacteria from aquatic environments can pose potential threats to public health due to their capability of spreading antimicrobial resistance (AMR) genes through mobile genetic elements (MGEs), such as plasmids, insertion sequences (ISs), transposons, and integrons. Currently, there is no policy for routine monitoring of AMR genes in aquatic environments and their roles in transmission are therefore unknown. Previous metagenomic and PCR-based culture-independent approaches are limited in recovering AMR resistant aquatic bacteria isolates and the data resolution generated are not able to provide detailed genetic comparison with known human pathogens particularly for determining genetic islands harbouring AMR genes. To address these gaps, we thus investigated the genetic profiles of ESBL-producing gram-negative aquatic bacteria found from water body sites within Singapore, examining the AMR genes carried and their associated MGEs. In total, 16 ESBL-producing gram-negative bacteria were identified, of which 8 were Escherichia coli, 3 Klebsiella pneumoniae, and 5 Aeromonas spp. Whole genome sequencing (WGS) analysis revealed the presence of 12 distinct classes of AMR genes, including 16 distinct variants of β-lactamase, of which blaCTX-M was the dominant beta-lactamase genotype in all 11 Enterobacterales. The AMR genetic islands in the aquatic bacteria were also found to share similar genetic structures similar to those of circulating ESBL bacteria causing human infections. These findings underscore the potential role of aquatic ESBL bacteria as AMR reservoirs for human pathogens, suggesting that aquatic bacteria may facilitate the hidden transmission of AMR mediated by MGEs through horizontal gene transfer across different sources and species, highlighting the importance of integrating environmental AMR monitoring into local surveillance strategies.}, }
@article {pmid40243369, year = {2025}, author = {Li, J and Chang, J and Ma, J and Zhou, W and Yang, Y and Wu, J and Guan, C and Yuan, X and Xu, L and Yu, B and Su, F and Ye, S and Chen, Y and Zhao, G and Tang, B}, title = {Genome-based assessment of antimicrobial resistance of Escherichia coli recovered from diseased swine in eastern China for a 12-year period.}, journal = {mBio}, volume = {}, number = {}, pages = {e0065125}, doi = {10.1128/mbio.00651-25}, pmid = {40243369}, issn = {2150-7511}, abstract = {The global rise of antimicrobial resistance (AMR), driven by antibiotic use in healthcare and agriculture, poses a major public health threat. While AMR in clinical settings is well studied, there is a gap in understanding the resistance profiles of Escherichia coli from diseased livestock, particularly regarding zoonotic transmission. This study analyzes 114 E. coli isolates from diseased swine over 12 years, revealing that 99.12% were multidrug-resistant. Resistance was highest for ampicillin and amoxicillin/clavulanic acid (100%), followed by ciprofloxacin (96.49%) and tetracycline (94.74%). Furthermore, 21.05% of isolates were resistant to colistin, and 1.75% to tigecycline. A total of 76 antimicrobial resistance genes (ARGs) were identified, with mcr-1 found in 18.42%, mcr-3 in 4.39%, and tet(X4) in 1.75%. Significant co-occurrence of ARGs and plasmids suggests potential for co-selective dissemination. This study is the first to report enterotoxigenic E. coli (ETEC) strains carrying both mcr-1 and mcr-3 genes. After the 2017 colistin ban in China, mcr-1 detection rates significantly decreased, while florfenicol resistance rates increased in 2018-2021 (94.29%) compared to 2010-2017 (79.55%). This work provides valuable insights into the AMR profiles of E. coli from diseased swine and highlights trends that can inform strategies for monitoring and controlling public health risks associated with zoonotic E. coli transmission.IMPORTANCEThis study highlights the critical role of diseased and deceased swine in the spread of antimicrobial resistance (AMR), providing new insights into the transmission of resistance genes in zoonotic contexts. By analyzing E. coli from diseased swine, we identify key resistance genes such as mcr-1, mcr-3, and tet(X4), which pose significant public health risks, especially regarding last-resort antibiotics like colistin. Moreover, the study identifies novel transmission patterns of mcr genes, including ETEC strains carrying the mcr-3 gene and strains harboring both mcr-1 and mcr-3 genes. The role of plasmids in horizontal gene transfer is also revealed, facilitating rapid AMR spread across species. The long-term persistence of resistant strains highlights the challenges in controlling AMR in livestock. These findings underscore the need for enhanced surveillance and a One Health approach to mitigate AMR risks across animal, human, and environmental health.}, }
@article {pmid40240954, year = {2025}, author = {Feng, Y and Liu, Y and Han, J and Huang, Y and Lee, J and Kokubugata, G and Qi, Z and Yan, X}, title = {Decoding the mitogenome of rosemary (Salvia rosmarinus): insights into genome evolution, structural dynamics and prospects for mitochondrial engineering.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {488}, pmid = {40240954}, issn = {1471-2229}, support = {G242412, G252409//Special Fund for Scientific Research of Shanghai Landscaping &amp; City Appearance Administrative Bureau/ ; G242412, G252409//Special Fund for Scientific Research of Shanghai Landscaping &amp; City Appearance Administrative Bureau/ ; G242412, G252409//Special Fund for Scientific Research of Shanghai Landscaping &amp; City Appearance Administrative Bureau/ ; LY21C030008//Natural Science Foundation of Zhejiang Province/ ; LY21C030008//Natural Science Foundation of Zhejiang Province/ ; LY21C030008//Natural Science Foundation of Zhejiang Province/ ; }, mesh = {*Genome, Mitochondrial/genetics ; *Evolution, Molecular ; Phylogeny ; *Salvia/genetics ; RNA Editing ; *Genome, Plant ; Genetic Engineering ; }, abstract = {BACKGROUND: Rosemary (Salvia rosmarinus), an aromatic evergreen shrub of the Salvia (Lamiaceae), is native to the Mediterranean region, thriving in rocky or arid soils. Widely used in food, pharmaceuticals, and cosmetics, its clonal reproduction poses significant challenges for breeding and germplasm innovation. While mitogenome engineering holds promise for introducing heritable mutations, incomplete mitogenome information for rosemary has hindered such efforts. This study addresses this gap by assembling and analyzing the complete mitogenome of S. rosmarinus, focusing on its structure, repetitive sequences, RNA editing events, intracellular gene transfer (IGT), and phylogenetic relationships.<br><br>RESULTS: The S. rosmarinus mitogenome spans 384,113&#xa0;bp with a GC content of 44.8%, containing 34 unique protein-coding genes and 114 simple sequence repeats. Comparative analysis revealed 28 homologous segments shared between the mitogenome and plastome, totaling 18,675&#xa0;bp in length. Furthermore, homologous fragments between nuclear and organellar genomes were identified, including 1,069,255&#xa0;bp of organelle-derived sequences in the nuclear genome, with 194,689&#xa0;bp from nuclear plastid DNA transfers (NUPTs) and 15,192&#xa0;bp from nuclear mitochondrial DNA transfers (NUMTs). NUPTs were more abundant and contributed more significantly to the total length. Synteny analysis of eight Lamiales species revealed extensive mitogenomic recombination and structural rearrangements. These findings highlight the dynamic nature of mitogenomes, offering insights into genome evolution and supporting future breeding programs to enhance the genetic diversity and adaptability of S. rosmarinus.<br><br>CONCLUSIONS: This study provides the first complete mitogenome of S. rosmarinus, revealing dispersed repeats, RNA editing, and horizontal gene transfer between the nuclear and organelle genomes. The mitogenome exhibits a typical circular structure with evidence of frequent recombination, providing valuable insights into Salvia mitochondrial genetics, genome evolution, and molecular biology.}, }
@article {pmid40238219, year = {2025}, author = {Cadamuro, RD and Elois, MA and Pilati, GVT and Savi, BP and Pessi, L and Jempierre, YFSH and Rodríguez-Lázaro, D and Fongaro, G}, title = {Role of Lysogenic Phages in the Dissemination of Antibiotic Resistance Genes Applied in the Food Chain.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {7}, pages = {}, pmid = {40238219}, issn = {2304-8158}, abstract = {Bacteriophages, first discovered in 1915, have re-emerged as critical players in microbial ecosystems, particularly in food production. Their ability to lysogenize bacterial hosts raises concerns about their role in the horizontal transfer of antibiotic resistance genes (ARGs) and virulence factors, contributing to the global challenge of antimicrobial resistance. Key studies reveal that ARG-carrying phages are prevalent across various stages of the food chain, including soil, vegetables, meat, dairy, and wastewater associated with food production. These findings demonstrate the potential for lysogenic phages to act as vectors for resistance gene dissemination, posing risks to public health. The review also explores emerging genetic elements, such as phage-inducible chromosomal islands and gene transfer agents, that further enhance the mobility of resistance and virulence genes. Advancements in metagenomic tools have improved our understanding of phage-mediated gene transfer, but significant knowledge gaps remain. Future research should aim to quantify these processes in real-world settings and develop strategies to mitigate the risks associated with lysogenic phages in food systems.}, }
@article {pmid40236771, year = {2025}, author = {Liu, W and Lau, HCH and Ding, X and Yin, X and Wu, WKK and Wong, SH and Sung, JJY and Zhang, T and Yu, J}, title = {Transmission of antimicrobial resistance genes from the environment to human gut is more pronounced in colorectal cancer patients than in healthy subjects.}, journal = {iMeta}, volume = {4}, number = {2}, pages = {e70008}, pmid = {40236771}, issn = {2770-596X}, abstract = {Antimicrobial resistance is a major global health concern. However, the source of gut resistome remains unsolved. We aimed to analyze the contribution of environmental antimicrobial resistance genes (ARGs) to colorectal cancer (CRC) patients. Here, we collected metagenomic data from 1,605 human stool samples (CRC = 748; healthy = 857) and 1,035 city-matched environmental samples, in which 110 CRC, 112 healthy, and 56 environmental samples were newly collected. Compared to healthy subjects, CRC patients had significantly higher ARG burden (p < 0.01) with increased levels of multidrug-resistant ARGs. Gut ARGs in CRC also had a closer similarity to environmental ARGs (p < 0.001). By comparing environmental and gut ARGs, 28 environmental ARGs were identified as CRC-specific ARGs, including SUL2 and MEXE, which were not identified in healthy subjects. Meanwhile, more mobile ARGs (mARGs) from the environment were observed in CRC patients compared to healthy subjects (p < 0.05). The hosts of mARGs were mainly pathogenic bacteria (e.g., Escherichia coli (E. coli) and Clostridium symbiosum (C. symbiosum)). Compared to healthy subjects, CRC patients showed elevated horizontal gene transfer efficiency from the environment to gut. Consistently, the abundance of pathobionts carrying specific mARGs (e.g., E. coli-SUL2 and C. symbiosum-SUL2) were significantly increased in CRC patients compared to healthy subjects (p < 0.05). We thus reveal a route of ARG dissemination from the environment into the gut of CRC patients.}, }
@article {pmid40234663, year = {2025}, author = {Luk-In, S and Phopin, K and Bangmuangngam, S and Chatsuwan, T and Wannigama, DL and Shein, AMS and Plongla, R and Lawung, R and Yainoy, S and Eiamphungporn, W and Chatupheeraphat, C and Tantimongcolwat, T}, title = {Inhibitory effects of benzyl isothiocyanate on widespread mcr-1-harbouring IncX4 plasmid transfer.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {12892}, pmid = {40234663}, issn = {2045-2322}, mesh = {*Plasmids/genetics ; *Klebsiella pneumoniae/genetics/drug effects ; *Escherichia coli/genetics/drug effects ; Colistin/pharmacology ; *Isothiocyanates/pharmacology ; *Escherichia coli Proteins/genetics ; Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; *Drug Resistance, Multiple, Bacterial/genetics/drug effects ; Humans ; Gene Transfer, Horizontal/drug effects ; Thailand ; }, abstract = {The global dissemination of mobile colistin resistance (mcr) genes represents a significant public health threat due to colistin's critical role in treating multidrug-resistant (MDR) bacterial infections. We identified high rates of carbapenem resistance in Escherichia coli (27.82%) and Klebsiella pneumoniae (57.98%) and colistin resistance in E. coli (7.52%) and K. pneumoniae (19.68%) among MDR clinical isolates in Thailand. We reported sequences of self-transferable IncX4 plasmids (~ 34 kb) that facilitated the spread of the mcr-1.1 gene among six diverse MDR strains, often co-transferring blaCTX-M-55. Additionally, E. coli ST101 was found to co-transfer mcr-1.1, mcr-3.5, blaCTX-M-55, and tet(X4) via three plasmids (~ 34-kb IncX4, ~ 84-kb IncFII, ~ 278-kb IncHI2), resulting in increases in MICs for colistin, ceftriaxone, and tigecycline. Core SNP analysis revealed that closely related IncX4 plasmids harbouring mcr-1 (< 35 SNP differences) were reported from at least 12 countries. We first demonstrated the inhibitory effects of benzyl isothiocyanate (BITC) on the conjugation of mcr-1-bearing IncX4 plasmids to 1.57 ± 1.00% to 48.86 ± 12.31% relative to control (100%), targeting VirB4 and VirB11 proteins, reducing ATPase activity by over 30%. This study highlights the widespread mcr-1-harbouring IncX4 plasmids and proposes BITC as a potential inhibitor to control the dissemination of colistin resistance.}, }
@article {pmid40230384, year = {2025}, author = {Sousa, M and Machado, I and Simões, LC and Simões, M}, title = {Biocides as drivers of antibiotic resistance: A critical review of environmental implications and public health risks.}, journal = {Environmental science and ecotechnology}, volume = {25}, number = {}, pages = {100557}, pmid = {40230384}, issn = {2666-4984}, abstract = {The widespread and indiscriminate use of biocides poses significant threats to global health, socioeconomic development, and environmental sustainability by accelerating antibiotic resistance. Bacterial resistance development is highly complex and influenced significantly by environmental factors. Increased biocide usage in households, agriculture, livestock farming, industrial settings, and hospitals produces persistent chemical residues that pollute soil and aquatic environments. Such contaminants contribute to the selection and proliferation of resistant bacteria and antimicrobial resistance genes (ARGs), facilitating their dissemination among humans, animals, and ecosystems. In this review, we conduct a critical assessment of four significant issues pertaining to this topic. Specifically, (i) the role of biocides in exerting selective pressure within the environmental resistome, thereby promoting the proliferation of resistant microbial populations and contributing to the global spread of antimicrobial resistance genes (ARGs); (ii) the role of biocides in triggering transient phenotypic adaptations in bacteria, including efflux pump overexpression, membrane alterations, and reduced porin expression, which often result in cross-resistance to multiple antibiotics; (iii) the capacity of biocides to disrupt bacteria and make the genetic content accessible, releasing DNA into the environment that remains intact under certain conditions, facilitating horizontal gene transfer and the spread of resistance determinants; (iv) the capacity of biocides to disrupt bacterial cells, releasing intact DNA into the environment and enhancing horizontal gene transfer of resistance determinants; and (iv) the selective interactions between biocides and bacterial biofilms in the environment, strengthening biofilm cohesion, inducing resistance mechanisms, and creating reservoirs for resistant microorganisms and ARG dissemination. Collectively, this review highlights the critical environmental and public health implications of biocide use, emphasizing an urgent need for strategic interventions to mitigate their role in antibiotic resistance proliferation.}, }
@article {pmid40228732, year = {2025}, author = {Zhang, R and Gong, C and Gao, Y and Chen, Y and Zhou, L and Lou, Q and Zhao, Y and Zhuang, H and Zhang, J and Shan, S and Wang, X and Qian, X and Lei, L and Wong, MH}, title = {Reducing antibiotic resistance genes in soil: The role of organic materials in reductive soil disinfestation.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {374}, number = {}, pages = {126245}, doi = {10.1016/j.envpol.2025.126245}, pmid = {40228732}, issn = {1873-6424}, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Genes, Bacterial ; }, abstract = {Increasing attention has been given to the role of reductive soil disinfestation (RSD) on antibiotic resistance genes (ARGs) in soil. The selection of organic materials in RSD is crucial to the effectiveness of the RSD method. However, the effects of distinct organic materials on ARGs remains unclear. In this study, we selected straw and rapeseed meal as the organic materials in RSD and explored their effects on ARGs. The results showed that using straw significantly reduced the abundance of ARGs, high-risk ARGs, and mobile genetic elements (MGEs) by 31.5 %-65.8 %, while using rapeseed meal led to ARGs enrichment. Structural equation modeling (SEM) analysis identified MGEs and microbial communities as the primary drivers of ARGS changes under different organic materials. The abundance of MGEs was effectively controlled in straw treatments, reducing the potential for horizontal gene transfer of ARGs. Bacterial diversity was significantly lower in the straw treatments compared to the rapeseed meal treatments, potentially leading to a reduced abundance of ARGs host bacteria. Network co-occurrence analysis further revealed that Symbiobacteraceae and Bacillus were potential bacterial hosts of ARGs. In straw treatments, these genera' abundance decreased by 12 %-100 % compared to the control (CK) and rapeseed meal groups, further inhibiting the spread of ARGs. These findings demonstrate that RSD with straw as the organic material is more effective in mitigating ARGs compared to rapeseed meal, providing insights into controlling soil antibiotic resistance risks and utilizing agricultural waste resources.}, }
@article {pmid40226105, year = {2025}, author = {Wen, Y and Wu, J and You, L and Wei, X and Wang, J and Li, S}, title = {Genomic analyses reveal presence of extensively drug-resistant Salmonella enterica serovars isolated from clinical samples in Guizhou province, China, 2019-2023.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1532036}, pmid = {40226105}, issn = {1664-302X}, abstract = {BACKGROUND: The emergence of extensively drug-resistant (XDR) Salmonella in humans poses a significant public health and therapeutic challenge. However, limited data are available on XDR Salmonella isolates from Guizhou province, China. This study aimed to investigate the molecular epidemiology and resistance patterns of XDR Salmonella isolates from clinical samples in this region.<br><br>METHODS: A total of 931 Salmonella isolates were screened for XDR isolates through antimicrobial susceptibility testing. These XDR isolates were subjected to whole-genome sequencing (WGS) and bioinformatic analysis to further systematically investigating the molecular epidemiology and resistance patterns of XDR Salmonella isolates.<br><br>RESULTS: Between 2019 and 2023, 931 Salmonella isolates were collected from clinical samples in Guizhou. Of these isolates, 51 (5.5%) were identified as XDR and classified into 16 serovars. Among the serovars, 15 corresponded to a specific sequence type, except for S. Typhimurium serovars. The predominant serovars, S. 1,4,[5],12:i:-, S. Enteritidis, and S. Kentucky, were divided into ST34, ST11, and ST198, respectively. Genomic analysis showed that all XDR isolates harbored at least eight antimicrobial resistance genes (ARGs) and multidrug efflux pumps. Highly prevalent point mutations in gyrA (D87 and S83) and parC (S80I) were detected, along with eight plasmid-mediated quinolone resistance (PMQR) genes. The qnrS1 gene was the most common (43.1%), followed by oqxA, aac-(6')-lb-cr variant, qnrB4, qnrS2, qnrA1, qepA2, and oqxB. The predominant &#x3b2;-lactamase gene was blaTEM-1 (54.9%), and blaCTX-M-55 (35.3%) was the most prevalent extended-spectrum &#x3b2;-lactamase subtype. Notably, blaNDM-1 gene was identified for the first time in Salmonella from Guizhou, and one S. 1,4,[5],12:i:- isolate contained the mcr-1.1 gene. ARGs profiles varied by serovars, with S. 1,4,[5],12:i:- isolates carrying the highest number. Ten plasmid types were identified, predominantly IncHI2/IncHI2A (47.5%). Key resistance genes such as tetA, PMQR, blaCTX-M , mcr-1.1, and blaNDM-1 were located on IncHI2/IncHI2A plasmids. Notably, 75.0% of the conjugative plasmids belonged to IncHI2/IncHI2A, indicating that horizontal gene transfer through conjugation facilitates ARGs dissemination. Core genome multilocus sequence typing (cgMLST) analysis revealed significant genetic diversity, with 39 core genome sequence types (cgSTs) identified and no evidence of outbreaks.<br><br>CONCLUSION: The rising prevalence of XDR Salmonella in Guizhou province is concerning. Initial whole-genome sequencing (WGS) data provide critical insights for understanding and controlling XDR Salmonella infections, aiding public health officials in identifying emerging threats and trends.}, }
@article {pmid40223056, year = {2025}, author = {Colp, MJ and Blais, C and Curtis, BA and Archibald, JM}, title = {The fate of artificial transgenes in Acanthamoeba castellanii.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {368}, pmid = {40223056}, issn = {1471-2164}, support = {GBMF5782//Gordon and Betty Moore Foundation/ ; }, mesh = {*Acanthamoeba castellanii/genetics ; *Transgenes/genetics ; Plasmids/genetics ; Transformation, Genetic ; }, abstract = {BACKGROUND: The soil amoeba Acanthamoeba castellanii is an emerging model organism with which to study a wide range of biomedical, microbiological, and evolutionary phenomena. While transformation systems were established for this organism more than two decades ago, the fate of artificial transgenes has not been well characterized. In this study, artificial transformation experiments were performed to investigate how the A. castellanii genome responds to foreign DNA presented in both circular and linear plasmid form.<br><br>RESULTS: Nanopore sequencing was used as a high throughput method to screen for transgene DNA in the resulting transformant cultures, and candidate transgene integrations were identified. Molecular biology experiments were performed to validate the sequence data and provide additional context on the fate of transgenes. A method was devised to estimate the rate of read chimerism in nanopore sequencing runs and accurately account for the effects of read chimerism in identifying putative transgene integrations. Based on the experimental data in hand, a potential mechanism for transgene maintenance in A. castellanii is proposed, one in which incoming foreign DNA is tandemly duplicated and telomeres are added to the ends.<br><br>CONCLUSIONS: Our results suggest that transformation of A. castellanii with foreign DNA leads to linear molecules that are maintained as telomere-containing, transgene-bearing minichromosomes, which may facilitate chromosomal integration. This process may allow lateral gene transfer by expanding the window of opportunity for exogenous DNA to be taken up and integrated into the A. castellanii genome. Similar mechanisms exist in other eukaryote groups, suggesting this may be a widespread feature of eukaryote genome biology.}, }
@article {pmid40220390, year = {2025}, author = {Xiao, B and Pu, Q and Ding, G and Wang, Z and Li, Y and Hou, J}, title = {Synergistic effect of horizontal transfer of antibiotic resistance genes between bacteria exposed to microplastics and per/polyfluoroalkyl substances: An explanation from theoretical methods.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138208}, doi = {10.1016/j.jhazmat.2025.138208}, pmid = {40220390}, issn = {1873-3336}, abstract = {Microplastics (MPs) and per/polyfluoroalkyl substances (PFASs), as emerging pollutants widely present in aquatic environments, pose a significant threat to human health through the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). Molecular dynamics simulations and machine learning can accurately capture the complex interactions between molecules. This study utilized them to identify the HGT risk between bacteria under MPs and PFASs stress. This study found that MPs and PFASs significantly increase the HGT risk between bacteria, up to 1.57 and 1.59 times, respectively. Notably, long-chain PFASs and perfluoroalkyl carboxylic acids increased the HGT risk by 1.38 and 1.40 times, respectively. Additionally, MPs primarily increase the HGT risk by enhancing hydrogen bonding interaction between key proteins in the HGT pathway and "active codons". The electronegativity and polarizability of PFASs critically influence the HGT risk, acting inversely and directly proportional, respectively. The HGT risk between bacteria under the combined stress from PP-MPs and PFASs exhibits a significant synergistic effect (synergistic effect value of 27.6), which markedly increases the HGT risk. Further analysis revealed that a smaller minimum distance and sharper RDF curve peaks between key proteins and "active codons" indicate higher HGT risk. This indicates that stronger interactions lead to higher HGT risk. This study identifies the characteristics of HGT risks between bacteria in aquatic environments under the individual and combined stresses from MPs and PFASs at the molecular level. It provides a theoretical basis for mitigating ARG transfer and comprehensively assessing the health risks posed by these emerging pollutants.}, }
@article {pmid40217451, year = {2025}, author = {Hotor, P and Kotey, FCN and Donkor, ES}, title = {Antibiotic resistance in hospital wastewater in West Africa: a systematic review and meta-analysis.}, journal = {BMC public health}, volume = {25}, number = {1}, pages = {1364}, pmid = {40217451}, issn = {1471-2458}, support = {D43TW012487/TW/FIC NIH HHS/United States ; D43TW012487/TW/FIC NIH HHS/United States ; D43TW012487/TW/FIC NIH HHS/United States ; }, mesh = {Africa, Western ; *Wastewater/microbiology ; *Hospitals ; Humans ; *Drug Resistance, Microbial ; *Drug Resistance, Bacterial ; Anti-Bacterial Agents ; }, abstract = {BACKGROUND: The occurrence of antibiotic-resistant bacteria (ARB) has become a global menace and therefore increases morbidity, mortality and healthcare costs. Globally, hospital wastewater (HWW) has been identified as a significant source of antibiotic-resistant elements.<br><br>OBJECTIVES: This review aims to systematically review and to perform meta-analyses from evidence on antibiotic resistance studies in HWW in West Africa.<br><br>METHODS: The review was conducted in compliance with PRISMA and included studies published between 1990 and 2024 in West Africa from the Scopus, PubMed, and Web of Science databases. Eligible studies that characterized resistant bacteria, genes, or antibiotic residues in HWW were included. Meta-analyses for resistant bacteria and genes as well risk of bias using the Newcastle-Ottawa scale were conducted.<br><br>RESULTS: Out of 23 studies reviewed, resistant bacteria were reported in 39% (E. coli), 26% (K. pneumoniae), and 17% (P. aeruginosa), while 17 studies reported ARGs, with blaTEM (29%), blaOXA- 48 (18%), blaSHV (18%), and mecA (18%) being the most common. Only 4% and 9% of studies focused on toxin genes and antibiotic residues, respectively. Meta-analysis showed pooled prevalence rates for resistant bacteria: E. coli 42.6% (95% CI: 26.7%-60.3%) and K. pneumoniae 32.1% (95% Cl: 28.8%- 36.5%), and ARGs: blaTEM 76.0% (95% CI =&#x2009;64.6%-84.6%) and blaSHV 59.3% (95% CI =&#x2009;19.5%-89.8%).<br><br>CONCLUSION: This systematic review highlights significant findings of high levels of ARGs and ARBs of public health concern in HWW in West Africa. This highlights the need to improve upon the monitoring of antibiotic resistance and treatment of HWW in West Africa.}, }
@article {pmid40216901, year = {2025}, author = {Robinson, LR and McDevitt, CJ and Regan, MR and Quail, SL and Swartz, M and Wadsworth, CB}, title = {Revisiting the potential impact of doxycycline post-exposure prophylaxis on the selection of doxycycline resistance in Neisseria commensals.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {12400}, pmid = {40216901}, issn = {2045-2322}, support = {R15 AI174182/AI/NIAID NIH HHS/United States ; R15AI174182/NH/NIH HHS/United States ; }, mesh = {*Doxycycline/pharmacology/therapeutic use ; Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Drug Resistance, Bacterial/genetics/drug effects ; *Post-Exposure Prophylaxis/methods ; *Neisseria/drug effects/genetics ; Gonorrhea/prevention &amp; control/microbiology ; Bacterial Proteins/genetics ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Female ; Male ; }, abstract = {Doxycycline post-exposure prophylaxis (doxy-PEP) is a strategy to reduce bacterial sexually transmitted infections. However, the impact of doxy-PEP on resistance emergence is as of yet unclear. Commensal Neisseria are known reservoirs of resistance for gonococci through horizontal gene transfer (HGT), and are more likely to experience bystander selection from doxy-PEP as they are universally carried. The consequences of doxycycline selection on commensal Neisseria will be critical to investigate to understand possible resistance mechanisms that may be transferred to an important human pathogen. Here, collection of commensals from human hosts demonstrated 46% of isolates carry doxycycline resistance; and doxycycline resistance was significantly greater in participants self-reporting doxycycline use in the past 6 months. High-level doxycycline resistance (> 8 µg/mL) was always associated with the ribosomal protection protein (tetM) and pConj. In vitro selection of Neisseria commensals (N. cinerea, N. canis, N. elongata, and N. subflava) resulted in 12 of 16 lineages evolving doxycycline resistance (> 1 µg/mL). An A46T substitution in the repressor of the Mtr efflux pump (MtrR) and a V57M substitution in the 30 ribosomal protein S10 were associated with elevated MICs. Mutations in ribosomal components also emerged (i.e., 16 S rRNA G1057C, RplX A14T). We find the MtrR 46T, RpsJ 57M, and RplX 14T in natural commensal populations. In vitro co-evolution of N. gonorrhoeae with Neisseria commensals demonstrated rapid transfer of the pConj plasmid to N. subflava and N. cinerea, and pbla to N. cinerea. This work underscores the importance of commensal Neisseria as reservoirs of doxycycline resistance, and demonstrates a link between doxycycline use and the emergence of resistance. Though novel chromosomal resistance mutations are nominated herein, resistance emergence in natural commensal populations appears to be mainly associated with acquisition of the tetM gene. A secondary danger to pConj acquisition, is spread of pbla and β-lactam resistance, which we demonstrate here in vitro. Ultimately, characterizing the contemporary prevalence of doxycycline resistance, and underlying resistance mechanisms, in commensal communities may help us to predict the long-term impact of doxy-PEP on Neisseria, and the likelihood of transferring resistance across species' boundaries.}, }
@article {pmid40216324, year = {2025}, author = {Muteeb, G and Kazi, RNA and Aatif, M and Azhar, A and Oirdi, ME and Farhan, M}, title = {Antimicrobial resistance: Linking molecular mechanisms to public health impact.}, journal = {SLAS discovery : advancing life sciences R &amp; D}, volume = {33}, number = {}, pages = {100232}, doi = {10.1016/j.slasd.2025.100232}, pmid = {40216324}, issn = {2472-5560}, abstract = {BACKGROUND: Antimicrobial resistance (AMR) develops into a worldwide health emergency through genetic and biochemical adaptations which enable microorganisms to resist antimicrobial treatment. β-lactamases (blaNDM, blaKPC) and efflux pumps (MexAB-OprM) working with mobile genetic elements facilitate fast proliferation of multidrug-resistant (MDR) and exttreme drug-resistant (XDR) phenotypes thus creating major concerns for healthcare systems and community health as well as the agricultural sector.<br><br>OBJECTIVES: The review dissimilarly unifies molecular resistance pathways with public health implications through the study of epidemiological data and monitoring approaches and innovative therapeutic solutions. Previous studies separating their attention between molecular genetics and clinical outcomes have been combined into our approach which delivers an all-encompassing analysis of AMR.<br><br>KEY INSIGHTS: The report investigates the resistance mechanisms which feature enzymatic degradation and efflux pump overexpression together with target modification and horizontal gene transfer because these factors represent important contributors to present-day AMR developments. This review investigates AMR effects on hospital and community environments where it affects pathogens including MRSA, carbapenem-resistant Klebsiella pneumoniae, and drug-resistant Pseudomonas aeruginosa. This document explores modern AMR management methods that comprise WHO GLASS molecular surveillance systems and three innovative strategies such as CRISPR-modified genome editing and bacteriophage treatments along with antimicrobial peptides and artificial intelligence diagnostic tools.<br><br>CONCLUSION: The resolution of AMR needs complete scientific and global operational methods alongside state-of-the-art therapeutic approaches. Worldwide management of drug-resistant infection burden requires both enhanced infection prevention procedures with next-generation antimicrobial strategies to reduce cases effectively.}, }
@article {pmid40215939, year = {2025}, author = {Chen, Y and Yan, Z and Su, P and Liu, S and Chen, X and Jiang, R and Lu, G and Yuan, S}, title = {Remediation strategy of biochar with different addition approaches on antibiotic resistance genes in riparian zones under dry wet alternation.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138207}, doi = {10.1016/j.jhazmat.2025.138207}, pmid = {40215939}, issn = {1873-3336}, abstract = {The global prevalence of antibiotic resistance genes (ARGs) has aroused increasing concern due to its threat to ecological security and human health. Although biochar has been widely used for pollution remediation including ARGs, little is known its regulation on antibiotics and ARGs propagation under riparian zones, where undergo frequent occurrence of dry and wet alternations (DWA) caused by water-level fluctuation. Therefore, this study investigated the regulative effects of biochar through different addition approaches on ARGs spread in riparian zone sediments. Under DWA, the presence of biochar (2 % w/w) inhibited microbial diversity and function expression, especially for tiled biochar. In addition, compared with DWA, the tiled biochar decreased ARGs abundance by 45.36 %, while the well-mixed increased that by 269.02 %. The ARGs abundance in sediments was positively correlated with mobile genetic element abundance (R[2]=0.996, p < 0.05), indicative of high horizontal gene transfer potential of ARGs. Metabolomics revealed that both DWA and biochar significantly altered microbial metabolism pathways in sediments, involving sulfur metabolism and histidine metabolism. Furthermore, ARGs propagation in riparian zones may be dominantly driven by MGEs, especially by transposases and integrase. These findings highlight the tiled biochar remediation effects on ARGs in riparian zones under DWA caused by global warming.}, }
@article {pmid40215278, year = {2025}, author = {Dalia, TN and Machouri, M and Lacrouts, C and Fauconnet, Y and Guerois, R and Andreani, J and Radicella, JP and Dalia, AB}, title = {DprA recruits ComM to facilitate recombination during natural transformation in Gram-negative bacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {15}, pages = {e2421764122}, pmid = {40215278}, issn = {1091-6490}, support = {R35 GM128674/GM/NIGMS NIH HHS/United States ; ANR-22-CE44-0044//Agence Nationale de la Recherche (ANR)/ ; R35GM128674//HHS | National Institutes of Health (NIH)/ ; }, mesh = {*Bacterial Proteins/metabolism/genetics/chemistry ; *Vibrio cholerae/genetics/metabolism ; *Helicobacter pylori/genetics/metabolism ; *Recombination, Genetic ; *Transformation, Bacterial ; *DNA Helicases/metabolism/genetics/chemistry ; Gene Transfer, Horizontal ; *Gram-Negative Bacteria/genetics/metabolism ; Membrane Proteins ; }, abstract = {Natural transformation (NT) represents one of the major modes of horizontal gene transfer in bacterial species. During NT, cells can take up free DNA from the environment and integrate it into their genome by homologous recombination. While NT has been studied for >90 y, the molecular details underlying this recombination remain poorly understood. Recent work has demonstrated that ComM is an NT-specific hexameric helicase that promotes recombinational branch migration in Gram-negative bacteria. How ComM is loaded onto the postsynaptic recombination intermediate during NT, however, remains unclear. Another NT-specific recombination mediator protein that is ubiquitously conserved in both Gram-positive and Gram-negative bacteria is DprA. Here, we uncover that DprA homologs in Gram-negative species contain a C-terminal winged helix domain that is predicted to interact with ComM by AlphaFold. Using Helicobacter pylori and Vibrio cholerae as model systems, we demonstrate that ComM directly interacts with the DprA winged-helix domain, and that this interaction is critical for DprA to recruit ComM to the recombination site to promote branch migration during NT. These results advance our molecular understanding of recombination during this conserved mode of horizontal gene transfer. Furthermore, they demonstrate how structural modeling can help uncover unexpected interactions between well-studied proteins to provide deep mechanistic insight into the molecular coordination required for their activity.}, }
@article {pmid40215220, year = {2025}, author = {Zhong, W and Zhou, Y and Che, M and Wang, L and Tian, X and Wang, C and Cheng, Y and Liu, H and Zhou, Z and Peng, G and Zhang, K and Luo, Y and Shi, K and Zhong, Z}, title = {Extended-spectrum β-lactamase-producing Escherichia coli isolated from captive primates: characteristics and horizontal gene transfer ability analysis.}, journal = {PloS one}, volume = {20}, number = {4}, pages = {e0321514}, pmid = {40215220}, issn = {1932-6203}, mesh = {Animals ; *beta-Lactamases/genetics/metabolism ; *Gene Transfer, Horizontal ; *Escherichia coli/genetics/isolation &amp; purification/enzymology/drug effects ; *Escherichia coli Infections/microbiology/veterinary ; China ; Phylogeny ; *Primates/microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Animals, Zoo/microbiology ; Microbial Sensitivity Tests ; }, abstract = {The rapid spread of extended-spectrum β-lactamases (ESBLs)-producing Escherichia coli (ESBL-EC) around the world has become a significant challenge for humans and animals. In this study, we aimed to examine the characteristics and horizontal gene transfer (HGT) capacity of ESBL-EC derived from captive primates. We screened for ESBL-EC among a total of 444 multidrug-resistant (MDR) E. coli strains isolated from 13 zoos in China using double-disk test. ESBL genes, mobile genetic elements (MGEs), and virulence-associated genes (VAGs) in ESBL-EC were detected through polymerase chain reaction (PCR). Furthermore, conjugation experiments were conducted to examine the HGT capacity of ESBL-EC, and the population structure (phylogenetic groups and MLST) was determined. Our results showed that a total of 69 (15.54%, 69/444) ESBL-EC strains were identified, and 5 variants of blaCTX and 3 variants of blaTEM were detected. The highest detection rate was blaCTX-M-55 (49.28%, 34/69), followed by blaCTX-M-15 (39.13%, 27/69). Ten MGEs were detected and the most prevalent was IS26 (78.26%, 54/69), followed by ISEcp1 (60.87%, 42/69). Eighteen combinations of MGEs were detected, in which ISEcp1 + IS26 was predominant (18.84%, n = 13). A total of 15 VAGs were detected and the most prevalent was fimC (84.06%, 58/69), followed by sitA (78.26%, 54/69). Furthermore, HGT ability analysis results showed that 40.58% (28/69) of ESBL-EC strains exhibited the ability to engage in conjugative transfer. Plasmid typing revealed that IncFIB (78.57%, 22/28) had the highest detection rates. Furthermore, antibiotic resistance genes (ARGs) of blaTEM-135, tetA and qnrS; MGEs of IS26, trbC and ISCR3/14 showed high rates of conjugative transfer. The population structure analysis showed that the phylogroup B1 and ST2161 were the most prevalent. ESBL-EC poses a potential threat to captive primates and may spread to other animals, humans, and the environment. It is imperative to implement measures to prevent the transmission of ESBL-EC among captive primates.}, }
@article {pmid40214801, year = {2025}, author = {Sun, J and Wang, X and He, Y and Han, M and Li, M and Wang, S and Chen, J and Zhang, Q and Yang, B}, title = {Environmental fate of antibiotic resistance genes in livestock farming.}, journal = {Archives of microbiology}, volume = {207}, number = {5}, pages = {120}, pmid = {40214801}, issn = {1432-072X}, support = {32272444//National Natural Science Foundation of China/ ; }, mesh = {*Livestock/microbiology ; Animals ; Humans ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects ; Animal Husbandry ; Farms ; Manure/microbiology ; Genes, Bacterial ; }, abstract = {As emerging environmental pollutants, antibiotic resistance genes (ARGs) are prevalent in livestock farms and their surrounding environments. Although existing studies have focused on ARGs in specific environmental media, comprehensive research on ARGs within farming environments and their adjacent areas remains scarce. This review explores the sources, pollution status, and transmission pathways of ARGs from farms to the surrounding environment. Drawing on the "One Health" concept, it also discusses the potential risks of ARGs transmission from animals to human pathogens and the resulting impact on human health. Our findings suggest that the emergence of ARGs in livestock farming environments primarily results from intrinsic resistance and genetic mutations, while their spread is largely driven by horizontal gene transfer. The distribution of ARGs varies according to the type of resistance genes, seasonal changes, and the medium in which they are present. ARGs are disseminated into the surrounding environment via pathways such as manure application, wastewater discharge, and aerosol diffusion. They may be absorbed by humans, accumulating in the intestinal microbiota and subsequently affecting human health. The spread of ARGs is influenced by the interplay of microbial communities, antibiotics, heavy metals, emerging pollutants, and environmental factors. Additionally, we have outlined three control strategies: reducing the emergence of ARGs at the source, controlling their spread, and minimizing human exposure. This article provides a theoretical framework and scientific guidance for understanding the cross-media migration of microbial resistance in livestock farming environments.}, }
@article {pmid40210157, year = {2025}, author = {Li, C and Zhu, YX and Shen, XX and Gao, Y and Xu, M and Chen, MK and An, MY}, title = {Exploring the distribution and transmission mechanism of ARGs in crab aquaculture ponds and ditches using metagenomics.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {374}, number = {}, pages = {126209}, doi = {10.1016/j.envpol.2025.126209}, pmid = {40210157}, issn = {1873-6424}, mesh = {*Aquaculture ; Ponds/microbiology ; Animals ; Metagenomics ; *Brachyura ; *Drug Resistance, Microbial/genetics ; China ; Bacteria/genetics ; Environmental Monitoring ; }, abstract = {Aquaculture provides notable economic benefits; however, the excessive use of antibiotics has resulted in the production and spread of antibiotic resistance genes (ARGs). The intricate pollution dynamics in aquaculture areas complicate the comprehension of the distribution and transmission of ARGs in aquaculture systems. Using metagenomic sequencing technology, this study used eight ponds and four ditches in a large crab aquaculture area in Taizhou City, where Proteobacteria (61.58 %) and Acidobacteria (6.04 %) were identified as the dominant phyla and Thiobacillus (1.84 %) and Lysobacter (0.99 %) were the dominant genera. Network and linear discriminant analysis effect size (LEfse) analyses showed that Proteobacteria and Lysobacter were the main host phyla of ARGs, and Lysobacter, which are key host bacteria in ponds, played an important role in determining the abundance of ARGs in ponds. Co-occurrence network analysis (spearman r > 0.7, p < 0.01) revealed that prophages can dominate the spread of ARGs by carrying several ARG subtypes (rsmA, OXA-21, THIN-B and lnuF). Analysis of variance demonstrated that functions related to the horizontal gene transfer (HGT) of ARGs, such as EPS synthesis (lptF), oxidative stress (gor and ompR), ATP synthesis (lapB and vcaM), and cell membrane permeability (yajC and gspJ), were significantly expressed in the pond (p < 0.05), confirming that ARGs had stronger transmission potential in the pond. The Mantel test and partial least squares path modeling (PLS-PM) analysis showed that ARGs exist in bacteria and spread among them through mobile genetic elements and HGT. This study revealed the distribution and transmission mechanism of ARGs in the ponds and ditches of a crab aquaculture system and provided a theoretical basis for controlling the spread of ARGs in crab aquaculture in this area.}, }
@article {pmid40209969, year = {2025}, author = {Dündar, T and Köksal Çakırlar, F}, title = {Antimicrobial resistance in coagulase negative staphylococci: Genome analysis and role of horizontal gene transfer.}, journal = {Research in microbiology}, volume = {}, number = {}, pages = {104298}, doi = {10.1016/j.resmic.2025.104298}, pmid = {40209969}, issn = {1769-7123}, abstract = {Coagulase-negative staphylococci (CNS) are emerging as significant contributors to antimicrobial resistance, yet their genomic characteristics remain incompletely understood. This study presents a whole-genome analysis of 12 multidrug-resistant CNS strains (Staphylococcus epidermidis, Staphylococcus haemolyticus, Staphylococcus hominis) isolated from blood cultures, focusing on antimicrobial resistance genes, mobile genetic elements (MGEs), and horizontal gene transfer (HGT) mechanisms. We identified 22 resistance genes conferring resistance to 11 antimicrobial classes, many of which were plasmid-associated. Notably, we report the first detection of the ISSha1 insertion sequence in S. hominis, along with novel resistance plasmids, including pGO1 and VRSAp in S. haemolyticus and pAMα1 in S. hominis. The identification of bacteriophage-derived sequences in S. haemolyticus and S. hominis suggests a role for phages in genetic exchange. CRISPR sequences and a Cas gene were detected in S. hominis, suggesting a potential but unconfirmed role in restricting gene transfer. Additionally, pGO1 was identified as a conjugative plasmid, while pAMα1 and VRSAp were determined to be mobilizable, reinforcing the role of CNS in resistance dissemination. These results highlight CNS as reservoirs of antimicrobial resistance genes and emphasize the importance of species-specific genomic surveillance. Proactive monitoring of CNS is crucial for controlling antimicrobial resistance in clinical settings.}, }
@article {pmid40209228, year = {2025}, author = {Den Uyl, PA and Kiledal, EA and Errera, RM and Chaganti, SR and Godwin, CM and Raymond, HA and Dick, GJ}, title = {Genomic Identification and Characterization of Saxitoxin Producing Cyanobacteria in Western Lake Erie Harmful Algal Blooms.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {15}, pages = {7600-7612}, doi = {10.1021/acs.est.4c10888}, pmid = {40209228}, issn = {1520-5851}, mesh = {*Lakes/microbiology ; *Saxitoxin ; *Cyanobacteria/genetics ; *Harmful Algal Bloom ; }, abstract = {Saxitoxins (STXs), a group of closely related neurotoxins, are among the most potent natural toxins known. While genes encoding STX biosynthesis have been observed in Lake Erie, the organism(s) responsible for producing STXs in the Laurentian Great Lakes have not been identified. We identified a full suite of STX biosynthesis genes in a Dolichospermum metagenome-assembled genome (MAG). The content of sxt genes suggest that this organism can produce STX, decarbamoyl and deoxy-decarbamoyl saxitoxins, and other congeners. The absence of sxtX indicates this organism is unable to produce neosaxitoxin, a potent congener. However, a distinct, lower abundance sxt operon from an unidentified organism did contain sxtX, indicating neosaxitoxin biosynthesis potential. Metatranscriptomic data confirmed STX biosynthesis gene expression. We also recovered highly similar Dolichospermum MAGs lacking sxt genes, implying gene loss or horizontal gene transfer. sxtA was detected by quantitative polymerase chain reaction during 47 of 76 sampling dates between 2015 and 2019, demonstrating higher sensitivity than metagenomic approaches. sxtA gene abundance was positively correlated with temperature and particulate nitrogen:phosphorus ratio and negatively correlated with ammonium concentration. All Dolichospermum MAGs had genes required for nitrogen fixation. Collectively, this study provides a foundation for understanding potential new threats to Lake Erie water quality.}, }
@article {pmid40207493, year = {2025}, author = {Swain, PP and Sahoo, RK}, title = {Blocking horizontal transfer of antibiotic resistance genes: an effective strategy in combating antibiotic resistance.}, journal = {Critical reviews in microbiology}, volume = {}, number = {}, pages = {1-20}, doi = {10.1080/1040841X.2025.2489463}, pmid = {40207493}, issn = {1549-7828}, abstract = {Antimicrobial resistance (AMR) poses a significant public health threat, with emerging and novel forms of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) potentially crossing international borders and challenging the global health systems. The rate of development of antibiotic resistance surpasses the development of new antibiotics. Consequently, there is a growing threat of bacteria acquiring resistance even to newer antibiotics further complicating the treatment of bacterial infections. Horizontal gene transfer (HGT) is the key mechanism for the spread of antibiotic resistance in bacteria through the processes of conjugation, transformation, and transduction. Several compounds, other than antibiotics, have also been shown to promote HGT of ARGs. Given the crucial role of HGT in the dissemination of ARGs, inhibition of HGT is a key strategy to mitigate AMR. Therefore, this review explores the contribution of HGT in bacterial evolution, identifies specific hotspots andhighlights the role of HGT inhibitors in impeding the spread of ARGs. By specifically focusing on the HGT mechanism and its inhibition, these inhibitors offer a highly promising approach to combating AMR.}, }
@article {pmid40207084, year = {2025}, author = {Katonge, JH and Ally, ZK}, title = {Evolutionary relationships and genetic diversity in the BlaTEM gene among selected gram-negative bacteria.}, journal = {Biochemistry and biophysics reports}, volume = {42}, number = {}, pages = {101985}, pmid = {40207084}, issn = {2405-5808}, abstract = {This study investigates the genetic diversity and evolutionary relationships of the blaTEM gene, a major determinant of beta-lactam antibiotic resistance. We analyzed nucleotide sequences of 32 β-lactamase-producing strains from Klebsiella pneumoniae, Escherichia coli, Pseudomonas aeruginosa, Proteus mirabilis, and Acinetobacter baumannii obtained from public databases. Sequence analysis revealed 32 distinct sequences with 298 segregating sites and 303 mutations, indicating substantial genetic variability. A high level of haplotype diversity was observed, with 24 distinct haplotypes, reflecting evolutionary pressures and horizontal gene transfer. Phylogenetic analysis showed clear clades, suggesting the evolutionary relationships among blaTEM variants and interspecies gene transfer. The resistance profiles correlated with the genetic findings, particularly mutations. This analysis draws attention to the ongoing adaptive evolution of antibiotic resistance mechanisms, as well as the need for continued monitoring and novel therapeutic strategies. Further research with larger sample sizes and functional validation is needed to fully understand the implications of these variants in antibiotic resistance.}, }
@article {pmid40204742, year = {2025}, author = {Napit, R and Gurung, A and Poudel, A and Chaudhary, A and Manandhar, P and Sharma, AN and Raut, S and Pradhan, SM and Joshi, J and Poyet, M and Groussin, M and Rajbhandari, RM and Karmacharya, DB}, title = {Metagenomic analysis of human, animal, and environmental samples identifies potential emerging pathogens, profiles antibiotic resistance genes, and reveals horizontal gene transfer dynamics.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {12156}, pmid = {40204742}, issn = {2045-2322}, mesh = {*Gene Transfer, Horizontal ; Animals ; Humans ; *Metagenomics/methods ; Feces/microbiology ; *Bacteria/genetics/drug effects ; Nepal ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; Virulence Factors/genetics ; Birds/microbiology ; Metagenome ; }, abstract = {Antimicrobial resistance (AMR) poses a significant threat to global health. The indiscriminate use of antibiotics has accelerated the emergence and spread of drug-resistant bacteria, compromising our ability to treat infectious diseases. A One Health approach is essential to address this urgent issue, recognizing the interconnectedness of human, animal, and environmental health. This study investigated the prevalence and transmission of AMR in a temporary settlement in Kathmandu, Nepal. By employing shotgun metagenomics, we analyzed a diverse range of samples, including human fecal samples, avian fecal samples, and environmental samples. Our analysis revealed a complex interplay of pathogenic bacteria, virulence factors (VF), and antimicrobial resistance genes (ARGs) across these different domains. We identified a diverse range of bacterial species, including potential pathogens, in both human and animal samples. Notably, Prevotella spp. was the dominant gut bacterium in human samples. Additionally, we detected a wide range of phages and viruses, including Stx-2 converting phages, which can contribute to the virulence of Shiga toxin-producing E. coli (STEC) strains. Our analysis revealed the presence of 72 virulence factor genes and 53 ARG subtypes across the studied samples. Poultry samples exhibited the highest number of ARG subtypes, suggesting that the intensive use of antibiotics in poultry production may contribute to the dissemination of AMR. Furthermore, we observed frequent horizontal gene transfer (HGT) events, with gut microbiomes serving as key reservoirs for ARGs. This study underscores the critical role of a One Health approach in addressing AMR. By integrating human, animal, and environmental health perspectives, we can better understand the complex dynamics of AMR and develop effective strategies for prevention and control. Our findings highlight the urgent need for robust surveillance systems, judicious antibiotic use, and improved hygiene practices to mitigate the impact of AMR on public health.}, }
@article {pmid40204671, year = {2025}, author = {Luo, G and Fan, L and Liang, B and Guo, J and Gao, SH}, title = {Determining Antimicrobial Resistance in the Plastisphere: Lower Risks of Nonbiodegradable vs Higher Risks of Biodegradable Microplastics.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {15}, pages = {7722-7735}, doi = {10.1021/acs.est.5c00246}, pmid = {40204671}, issn = {1520-5851}, mesh = {*Microplastics ; Biodegradation, Environmental ; Biodegradable Plastics ; *Drug Resistance, Microbial/genetics ; }, abstract = {The plastisphere is a potential contributor to global antimicrobial resistance (AMR), posing potential threats to public and environmental health. However, comprehensively quantifying the contribution of microplastics with different biodegradability to AMR is lacking. In this study, we systematically quantified AMR risk mediated by biodegradable and nonbiodegradable microplastics using abundance-based methods and a custom AMR risk ranking framework that includes antimicrobial resistance genes (ARGs) abundance, mobility, and host pathogenicity. Our results demonstrated that biodegradable microplastics exhibited higher AMR risk compared to that of nonbiodegradable plastics. Key resistance genes, including those for multidrug, bacitracin, and aminoglycoside resistance, were predominant. Machine learning analysis identified cell motility as the most significant signature associated with AMR risk, highlighting its potential role in promoting ARGs dissemination. In addition, biodegradable microplastics promoted oxidative stress and SOS responses, which likely enhanced horizontal gene transfer (HGT) and AMR. Metagenome-assembled genomes (MAGs) analysis uncovered the colocalization of microplastic degradation genes, ARGs, and virulence factors (VFs), further supporting the elevated risk in biodegradable plastisphere. The proximity of ARGs to mobile genetic elements (MGEs) suggests that microplastic degradation processes might favor ARGs mobility. These findings would contribute critical insights into AMR dissemination in the plastisphere, emphasizing the need for integrated environmental and public health strategies under the context of One Health.}, }
@article {pmid40202301, year = {2025}, author = {Mahillon, M and Debonneville, C and Groux, R and Roquis, D and Brodard, J and Faoro, F and Foissac, X and Schumpp, O and Dittmer, J}, title = {From insect endosymbiont to phloem colonizer: comparative genomics unveils the lifestyle transition of phytopathogenic Arsenophonus strains.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0149624}, doi = {10.1128/msystems.01496-24}, pmid = {40202301}, issn = {2379-5077}, abstract = {UNLABELLED: Bacteria infecting the plant phloem represent a growing threat worldwide. While these organisms often resist in vitro culture, they multiply both in plant sieve elements and hemipteran vectors. Such cross-kingdom parasitic lifestyle has emerged in diverse taxa via distinct ecological routes. In the genus Arsenophonus, the phloem pathogens "Candidatus Arsenophonus phytopathogenicus" (Ap) and "Ca. Phlomobacter fragariae" (Pf) have evolved from insect endosymbionts, but the genetic mechanisms underlying this transition have not been explored. To fill this gap, we obtained the genomes of both strains from insect host metagenomes. The resulting assemblies are highly similar in size and functional repertoire, rich in viral sequences, and closely resemble the genomes of several facultative endosymbiotic Arsenophonus strains of sap-sucking hemipterans. However, a phylogenomic analysis demonstrated distinct origins, as Ap belongs to the "Triatominarum" clade, whereas Pf represents a distant species. We identified a set of orthologs encoded only by Ap and Pf in the genus, including hydrolytic enzymes likely targeting plant substrates. In particular, both bacteria encode putative plant cell wall-degrading enzymes and cysteine peptidases related to xylellain, a papain-like peptidase from Xylella fastidiosa, for which close homologs are found in diverse Pseudomonadota infecting the plant vasculature. In silico predictions and gene expression analyses further support a role during phloem colonization for several of the shared orthologs. We conclude that the double emergence of phytopathogenicity in Arsenophonus may have been mediated by a few horizontal gene transfer events, involving genes acquired from other Pseudomonadota, including phytopathogens.<br><br>IMPORTANCE: We investigate the genetic mechanisms of a transition in bacterial lifestyle. We focus on two phloem pathogens belonging to the genus Arsenophonus: "Candidatus Arsenophonus phytopathogenicus" and "Ca. Phlomobacter fragariae." Both bacteria cause economically significant pathologies, and they have likely emerged among facultative insect endosymbionts. Our genomic analyses show that both strains are highly similar to other strains of the genus associated with sap-sucking hemipterans, suggesting a recent lifestyle shift. Importantly, although the phytopathogenic Arsenophonus strains belong to distant clades, they share a small set of orthologs unique in the genus pangenome. We provide evidence that several of these genes produce hydrolytic enzymes that are secreted and may target plant substrates. The acquisition and exchange of these genes may thus have played a pivotal role in the lifestyle transition of the phytopathogenic Arsenophonus strains.}, }
@article {pmid40199202, year = {2025}, author = {Ferheen, I and Cimarelli, L and Marcheggiani, S and Klümper, U and Spurio, R}, title = {Plastic-mediated transformation: A new route to navigate plasmid-borne antibiotic resistance genes.}, journal = {The Science of the total environment}, volume = {976}, number = {}, pages = {179125}, doi = {10.1016/j.scitotenv.2025.179125}, pmid = {40199202}, issn = {1879-1026}, mesh = {*Plasmids/genetics ; *Plastics ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; *Drug Resistance, Microbial/genetics ; *Transformation, Bacterial ; }, abstract = {Among the anthropogenic sources of pollution, accumulation of plastic polymers in aquatic ecosystems is scaling at unprecedented rates and emerging as a new niche for bacterial colonization and horizontal gene transfer (HGT). The current study focuses on determining the ability of bacteria to acquire plasmid DNA from the extracellular environment under exposure to different treatments (soil, CaCl2 salt solution, soil plus CaCl2, Escherichia coli cell-free extract, and plastic debris) that simulate possible conditions experienced by microorganisms in natural environments. The transformation frequency of two plasmids (pACYC:Hyg and pBAV-1k) was tested following two experimental approaches: single species microcosm of E. coli cells (SSM) and bacterial consortium microcosm (BCM) of strains isolated from freshwater ecosystems. Plastic fragments (with consistent results obtained using polypropylene) proved to be remarkably efficient in increasing the bacterial competence towards plasmid DNA uptake as compared to the other conditions. Moreover, the effects of different plastic polymers and four incubation conditions on bacterial DNA transformation were analyzed to gain deeper insight into the exchange of genetic material. Our findings from both experimental approaches demonstrate that simultaneous incubation of microorganisms, plasmids, and plastic fragments enhances the bacterial ability to uptake plasmids and to express genes required for survival under stress conditions. The two microcosm models prove to be promising tools to mimic natural transformation events leading to the dissemination of antibiotic-resistant genes via HGT in the environment.}, }
@article {pmid40199074, year = {2025}, author = {Li, ZY and Cui, YW and Liang, HK and Yan, HJ and Yang, RC}, title = {Tetracycline degradation by a mixed culture of halotolerant fungi-bacteria under static magnetic field: Mechanism and antibiotic resistance genes transfer.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138181}, doi = {10.1016/j.jhazmat.2025.138181}, pmid = {40199074}, issn = {1873-3336}, abstract = {Efficient antibiotics removal lowers the transmission risk of antibiotic resistance genes (ARGs). However, low efficiency limits the application of biological methods for antibiotics removal. Herein, a mixed culture of halotolerant fungi-bacteria was used for treatment of saline wastewater containing tetracycline (TC). Furthermore, static magnetic field (SMF) was used to increase TC removal. The study examined the effectiveness of SMF in removing antibiotics from saline wastewater and the associated risk of ARGs transmission. The results demonstrated that the application of a 40 mT SMF significantly improved the TC removal efficiency by 37.09 %, compared to the control (SMF=0) The TC was mainly removed through biodegradation and adsorption. In biodegradation, SMF enhanced electron transport system activity, and activities of lignin-degrading enzymes which led to higher TC biodegradation. The activity of lactate dehydrogenase and malondialdehyde decreased, lowering the damage of microbial cell membranes by TC. During the adsorption process, higher generation of extracellular polymeric substances was observed under SMF, which caused an increase in TC removal via adsorption. Microbial community analysis revealed that SMF facilitated the enrichment of TC-degrading microorganisms. Under SMF, vertical gene transfer of ARGs increased, while horizontal gene transfer risk decreased due to a reduction in mobile genetic elements (intl1) abundance. This study demonstrates that SMF is a promising strategy for enhancing TC removal efficiency, providing a basis for improved antibiotic wastewater management.}, }
@article {pmid40195311, year = {2025}, author = {Rao, BD and Gomez-Gil, E and Peter, M and Balogh, G and Nunes, V and MacRae, JI and Chen, Q and Rosenthal, PB and Oliferenko, S}, title = {Horizontal acquisition of prokaryotic hopanoid biosynthesis reorganizes membrane physiology driving lifestyle innovation in a eukaryote.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {3291}, pmid = {40195311}, issn = {2041-1723}, support = {ALTF 712-2022//European Molecular Biology Organization (EMBO)/ ; CC0102/ARC_/Arthritis Research UK/United Kingdom ; 103741/Z/14/Z//Wellcome Trust (Wellcome)/ ; 220790/Z/20/Z//Wellcome Trust (Wellcome)/ ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Schizosaccharomyces/genetics/metabolism/physiology ; *Gene Transfer, Horizontal ; Sterols/metabolism/biosynthesis ; *Intramolecular Transferases/genetics/metabolism ; *Cell Membrane/metabolism ; *Triterpenes/metabolism ; }, abstract = {Horizontal gene transfer is a source of metabolic innovation and adaptation to new environments. How new metabolic functionalities are integrated into host cell biology is largely unknown. Here, we probe this fundamental question using the fission yeast Schizosaccharomyces japonicus, which has acquired a squalene-hopene cyclase Shc1 through horizontal gene transfer. We show that Shc1-dependent production of hopanoids, mimics of eukaryotic sterols, allows S. japonicus to thrive in anoxia, where sterol biosynthesis is not possible. We demonstrate that glycerophospholipid fatty acyl asymmetry, prevalent in S. japonicus, is crucial for accommodating both sterols and hopanoids in membranes and explain how Shc1 functions alongside the sterol biosynthetic pathway to support membrane properties. Reengineering experiments in the sister species S. pombe show that hopanoids entail new traits in a naïve organism, but the acquisition of a new enzyme may trigger profound reorganization of the host metabolism and physiology.}, }
@article {pmid40190753, year = {2025}, author = {Nahum, Y and Muhvich, J and Morones-Ramirez, JR and Casillas-Vega, NG and Zaman, MH}, title = {Biofilms as potential reservoirs of antimicrobial resistance in vulnerable settings.}, journal = {Frontiers in public health}, volume = {13}, number = {}, pages = {1568463}, pmid = {40190753}, issn = {2296-2565}, mesh = {*Biofilms/drug effects/growth &amp; development ; Humans ; *Wastewater/microbiology ; *Drug Resistance, Bacterial ; *Vulnerable Populations ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial ; }, abstract = {Antimicrobial resistance is a major global health threat, characterized by the ability of microorganisms to withstand the effects of antimicrobial agents. Biofilms, as unique microbial communities, significantly contribute to this threat. They provide a protective environment for pathogens, facilitate horizontal gene transfer, and create an ideal setting for the persistence and evolution of resistant bacteria. This issue can be particularly important in low-income settings and vulnerable communities, such as formal and informal refugee and migrant camps. These settings usually have limited access to healthcare resources and appropriate treatments, contributing to the selective pressure that promotes the survival and proliferation of resistant bacteria. Thus, biofilms formed in wastewater in these areas can play a critical role in spreading antimicrobial resistance or acting as hidden reservoirs for future outbreaks. While emerging efforts focus on detecting antibiotic resistance genes and planktonic bacteria in wastewater, biofilms may be a source of under-appreciated antimicrobial resistance, creating a significant gap in our understanding of resistance dynamics in wastewater systems. Incorporating biofilm surveillance into wastewater monitoring strategies in vulnerable settings can help develop a more comprehensive understanding of resistance transmission and more effective intervention measures in these settings.}, }
@article {pmid40189939, year = {2025}, author = {Wang, H and Wang, D and Shao, B and Li, J and Li, Z and Chase, MW and Li, J and Feng, Y and Wen, Y and Qin, S and Chen, B and Wu, Z and Jin, X}, title = {Unequally Abundant Chromosomes and Unusual Collections of Transferred Sequences Characterize Mitochondrial Genomes of Gastrodia (Orchidaceae), One of the Largest Mycoheterotrophic Plant Genera.}, journal = {Molecular biology and evolution}, volume = {42}, number = {4}, pages = {}, pmid = {40189939}, issn = {1537-1719}, support = {2022YFF1301704//National Key Research and Development Program of China/ ; 2023-QYCX-02//Linzhi Science and Technology Program/ ; 31870195//National Natural Science Foundation of China/ ; }, mesh = {*Genome, Mitochondrial ; *Chromosomes, Plant/genetics ; *Gastrodia/genetics ; Evolution, Molecular ; Phylogeny ; Genome, Plant ; DNA Copy Number Variations ; *Orchidaceae/genetics ; Heterotrophic Processes ; }, abstract = {The mystery of genomic alternations in heterotrophic plants is among the most intriguing in evolutionary biology. Compared to plastid genomes (plastomes) with parallel size reduction and gene loss, mitochondrial genome (mitogenome) variation in heterotrophic plants remains underexplored in many aspects. To further unravel the evolutionary outcomes of heterotrophy, we present a comparative mitogenomic study with 13 de novo assemblies of Gastrodia (Orchidaceae), one of the largest fully mycoheterotrophic plant genera, and its relatives. Analyzed Gastrodia mitogenomes range from 0.56 to 2.1 Mb, each consisting of numerous, unequally abundant chromosomes or contigs. Size variation might have evolved through chromosome rearrangements followed by stochastic loss of "dispensable" chromosomes, with deletion-biased mutations. The discovery of a hyper-abundant (∼15 times intragenomic average) chromosome in two assemblies represents the hitherto most extreme copy number variation in any mitogenomes, with similar architectures discovered in two metazoan lineages. Transferred sequence contents highlight asymmetric evolutionary consequences of heterotrophy: despite drastically reduced intracellular plastome transfers convergent across heterotrophic plants, their rarity of horizontally acquired sequences sharply contrasts parasitic plants, where massive transfers from their hosts prevail. Rates of sequence evolution are markedly elevated but not explained by copy number variation, extending prior findings of accelerated molecular evolution from parasitic to heterotrophic plants. Putative evolutionary scenarios for these mitogenomic convergence and divergence fit well with the common (e.g. plastome contraction) and specific (e.g. host identity) aspects of the two heterotrophic types. These idiosyncratic mycoheterotrophs expand known architectural variability of plant mitogenomes and provide mechanistic insights into their content and size variation.}, }
@article {pmid40188791, year = {2025}, author = {Huang, X and Tan, Z and Wei, J and Bai, X}, title = {Super-robust synthetic microorganism can get chlorine resistance in advance and transfer their inserted DNA sequence in genome to indigenous bacteria in water.}, journal = {Water research}, volume = {281}, number = {}, pages = {123594}, doi = {10.1016/j.watres.2025.123594}, pmid = {40188791}, issn = {1879-2448}, abstract = {CRISPR-Cas gene editing tools have brought us to an era of synthetic biology that will change the world. Synthetic microorganisms (SMs) have brought enormous economic benefits and will contribute more in the future. Among them, super-robust SMs can overcome the stresses in bioproduction and further increase yield. However, when they are released into the environments, little is known about their fates and risks to human health. In this study, it was found that the gene editing super-robust SM could transfer its inserted DNA sequence in genome to the indigenous bacteria in surface water and showed stronger resistance to chlorine compared with wild-type bacteria. Chlorine disinfection did slight damage on cell membrane of super-robust SM, which decreased ATP leakage and DNA damage, and thereby promoted bacterial survival. Chlorine-injured super-robust SM retained high respiratory activity, and could resuscitate and regenerate. Less damage on super-robust SM cell membrane could prevent chlorine from entering the cells and resulted in lower ROS generation. Its DNA repair system and antioxidant system could still function under high concentrations of chlorine exposure. These findings provided new insights into the fates and environmental risks of SMs as an emerging biological pollutant in water supply system.}, }
@article {pmid40188040, year = {2025}, author = {Yang, Y and Liu, W and Zhao, Z and Guo, K and Wang, X and Lou, Z and Yang, X and Gong, L and Wang, K and Liu, X and Xu, H and Liu, Q and Zheng, B and Jiang, X}, title = {Genomic insights and epidemiology of mcr-1-Carrying Escherichia albertii isolated from agricultural soil in China.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {344}, pmid = {40188040}, issn = {1471-2164}, mesh = {China/epidemiology ; *Soil Microbiology ; Phylogeny ; *Escherichia/genetics/isolation &amp; purification/drug effects/classification ; *Genomics ; Humans ; Genome, Bacterial ; Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; *Escherichia coli Proteins/genetics ; Drug Resistance, Bacterial/genetics ; Agriculture ; }, abstract = {BACKGROUND: Polymyxins are critical in treating multidrug-resistant Gram-negative bacteria infections, yet their overuse has spurred the emergence of polymyxin-resistant pathogens globally. This study aims to analyze the genomic characteristics of the Escherichia albertii strain 6S-65-1 carrying the mcr-1 gene and to investigate the global epidemiology of mcr-1-carrying E. albertii strains.<br><br>RESULTS: In this study, we identified and analyzed a polymyxin-resistant Escherichia albertii strain (6S-65-1) carrying the mcr-1 gene, isolated from agricultural soil in China. Whole-genome sequencing and comparative genomic analyses revealed two chromosomal integrations of the mcr-1 gene within Tn6330 transposon structures, indicating its capacity for horizontal gene transfer. Strain 6S-65-1 also harbors other antimicrobial resistance genes, including tet(A), sul3, and aph (3')-Ia, enhancing its resistance profile. Comparative genomic analysis of E. albertii genomes in the NCBI database revealed that mcr-1-carrying E. albertii strains are geographically restricted to China and Japan, and have been isolated from both animals and humans. Phylogenetic analysis revealed that strain 6S-65-1 was most closely related to a human-derived strain from Japan (SAMD00164101), with both strains carried virulence genes (cdt, paa, and eae) that enable them to form attaching and effacing (A/E) lesions. Among all publicly available ST4619 E. albertii genomes, strain 6S-65-1 is the first to carry the mcr-1 gene.<br><br>CONCLUSION: Our findings offer new insights into the epidemiology and genomic features of mcr-1-carrying E. albertii, underscoring the need for targeted management strategies to curb its spread. These findings underscore the importance of "One Health" approaches to antimicrobial resistance, which require coordinated efforts across human, animal and the environmental health sectors.}, }
@article {pmid40186988, year = {2025}, author = {Liu, L and Zhang, QH and Li, MZ and Li, RT and He, Z and Dechesne, A and Smets, BF and Sheng, GP}, title = {Single-cell analysis reveals antibiotic affects conjugative transfer by modulating bacterial growth rather than conjugation efficiency.}, journal = {Environment international}, volume = {198}, number = {}, pages = {109385}, doi = {10.1016/j.envint.2025.109385}, pmid = {40186988}, issn = {1873-6750}, mesh = {*Anti-Bacterial Agents/pharmacology ; Single-Cell Analysis ; *Conjugation, Genetic/drug effects ; *Escherichia coli/drug effects/genetics/growth &amp; development ; *Gene Transfer, Horizontal/drug effects ; Drug Resistance, Bacterial/genetics ; Plasmids ; }, abstract = {Antibiotic resistance genes (ARGs) pose a significant threat to human health and the environment. Quantifying the efficiency of horizontal gene transfer (HGT) is challenging due to diverse biological and environmental influences. Single-cell level approaches are well-suited for investigating conjugative transfer, given its reliance on cell-to-cell contact nature and its capacity to offer insights into population-level responses. This study introduces a self-developed system for automated time-lapse image acquisition and analysis. Using a custom dual-chamber microfluidic chip and Python-based image analysis pipeline, we dynamically quantify the ARGs conjugation efficiency at single-cell level. By combining experiments with individual-based modelling, we isolate the effects of subinhibitory antibiotic concentrations on conjugation efficiency from those related to bacterial growth dynamics. No significant variation in Escherichia coli conjugation efficiency was observed across kanamycin concentrations (0 to 50 mg l[-1]). Moreover, recipient cells with higher growth rates show a greater propensity for plasmid acquisition, suggesting the physiological state of cells pre-conjugation influences their susceptibility to gene transfer. Our methodology eliminates population growth bias, revealing the intrinsic nature of conjugation efficiency. This approach advances our understanding of the factors influencing HGT efficiency and holds promise for studying other microbial interactions. SYNOPSIS: This study employs single-cell analysis to reveal that subinhibitory concentrations of antibiotics affect the conjugative transfer of antibiotic resistance genes by modulating bacterial growth rate rather than conjugation efficiency.}, }
@article {pmid40183128, year = {2025}, author = {Bolzoni, L and Scaltriti, E and Bracchi, C and Angelone, S and Menozzi, I and Taddei, R and Alba, P and Carfora, V and Diaconu, EL and Morganti, M and Dodi, A and Berni, M and Manni, L and Vinci, M and Tambassi, M and Mazzera, L and Venturelli, I and Ambretti, S and Battisti, A and Pongolini, S}, title = {Emergence of Salmonella enterica carrying bla OXA-181 carbapenemase gene, Italy, 2021 to 2024.}, journal = {Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin}, volume = {30}, number = {13}, pages = {}, pmid = {40183128}, issn = {1560-7917}, mesh = {*beta-Lactamases/genetics ; *Salmonella enterica/genetics/isolation &amp; purification/enzymology ; Humans ; Animals ; *Bacterial Proteins/genetics ; Italy/epidemiology ; Swine/microbiology ; Phylogeny ; Plasmids/genetics ; Microbial Sensitivity Tests ; *Salmonella Infections/microbiology/epidemiology ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; }, abstract = {Between 2021 and 2024, we detected carbapenemase gene blaOXA-181 in 16 of 11,398 Salmonella enterica (SE) isolates: 10 SE 1,4,[5],12:i:-, three Bovismorbificans, two London and one Rissen from pigs, humans, pork meat and wild roe deer. The gene was first detected in pig isolates, later in humans, suggesting zoonotic transmission. Phylogenetic analysis indicated that horizontal transfer, mainly through plasmids, contributed to the spread. These findings highlight a possible emerging public health threat and the importance of One Health surveillance.}, }
@article {pmid40173243, year = {2025}, author = {Tsoi, R and Son, HI and Hamrick, GS and Tang, K and Bethke, JH and Lu, J and Maddamsetti, R and You, L}, title = {A predatory gene drive for targeted control of self-transmissible plasmids.}, journal = {Science advances}, volume = {11}, number = {14}, pages = {eads4735}, pmid = {40173243}, issn = {2375-2548}, mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; Conjugation, Genetic ; *Gene Drive Technology/methods ; }, abstract = {Suppressing plasmid transfer in microbial communities has profound implications due to the role of horizontal gene transfer (HGT) in spreading and maintaining diverse functional traits such as metabolic functions, virulence factors, and antibiotic resistance. However, existing tools for inhibiting HGT are limited in their modes of delivery, efficacy, and scalability. Here, we present a versatile denial-of-spread (DoS) strategy to target and eliminate specific conjugative plasmids. Our strategy exploits retrotransfer, whereby an engineered DoS plasmid is introduced into host cells containing a target plasmid. Acting as a predatory gene drive, DoS propagates itself at the expense of the target plasmid, through competition or active elimination. Once the target plasmid is eradicated, DoS is removed via induced plasmid suicide, resulting in a community containing neither plasmid. The strategy is tunable and scalable for various conjugative plasmids, different mechanisms of plasmid inheritance interruption, and diverse environmental contexts. DoS represents a new tool for precise control of gene persistence in microbial communities.}, }
@article {pmid40173202, year = {2025}, author = {Loyo, CL and Grossman, AD}, title = {A phage-encoded counter-defense inhibits an NAD-degrading anti-phage defense system.}, journal = {PLoS genetics}, volume = {21}, number = {4}, pages = {e1011551}, pmid = {40173202}, issn = {1553-7404}, support = {R35 GM122538/GM/NIGMS NIH HHS/United States ; R35 GM148343/GM/NIGMS NIH HHS/United States ; T32 GM007287/GM/NIGMS NIH HHS/United States ; }, mesh = {*Bacillus subtilis/virology/genetics ; *NAD/metabolism ; *Bacteriophages/genetics ; *Bacterial Proteins/genetics/metabolism ; *Bacillus Phages/genetics/pathogenicity ; Gene Transfer, Horizontal ; }, abstract = {Bacteria contain a diverse array of genes that provide defense against predation by phages. Anti-phage defense genes are frequently located on mobile genetic elements and spread through horizontal gene transfer. Despite the many anti-phage defense systems that have been identified, less is known about how phages overcome the defenses employed by bacteria. The integrative and conjugative element ICEBs1 in Bacillus subtilis contains a gene, spbK, that confers defense against the temperate phage SPβ through an abortive infection mechanism. Using genetic and biochemical analyses, we found that SpbK is an NADase that is activated by binding to the SPβ phage portal protein YonE. The presence of YonE stimulates NADase activity of the TIR domain of SpbK and causes cell death. We also found that the SPβ-like phage Φ3T has a counter-defense gene that prevents SpbK-mediated abortive infection and enables the phage to produce viable progeny, even in cells expressing spbK. We made SPβ-Φ3T hybrid phages that were resistant to SpbK-mediated defense and identified a single gene in Φ3T (phi3T_120, now called nip for NADase inhibitor from phage) that was both necessary and sufficient to block SpbK-mediated anti-phage defense. We found that Nip binds to the TIR (NADase) domain of SpbK and inhibits NADase activity. Our results provide insight into how phages overcome bacterial immunity by inhibiting enzymatic activity of an anti-phage defense protein.}, }
@article {pmid40173128, year = {2025}, author = {Sichert, A}, title = {A single enzyme becomes a Swiss Army knife.}, journal = {PLoS biology}, volume = {23}, number = {4}, pages = {e3003072}, pmid = {40173128}, issn = {1545-7885}, mesh = {Gene Transfer, Horizontal ; *Diatoms/genetics/enzymology ; Photosynthesis/genetics ; Phaeophyceae/genetics/enzymology/metabolism ; Alginates/metabolism ; }, abstract = {An alga that abandoned photosynthesis? This Primer explores a PLOS Biology study showing that a single horizontal gene transfer event allowed the diatom Nitzschia sing1 to evolve a complete enzymatic machinery to break down alginate from brown algae, unlocking a new ecological niche.}, }
@article {pmid40168690, year = {2025}, author = {Jaafar, T and Carvalhais, E and Shrestha, A and Cochrane, R and Meaney, J and Brumwell, S and Hamadache, S and Nasrollahi, V and Karas, BJ}, title = {Engineering conjugative plasmids for inducible horizontal DNA transfer.}, journal = {Canadian journal of microbiology}, volume = {71}, number = {}, pages = {1-9}, doi = {10.1139/cjm-2024-0241}, pmid = {40168690}, issn = {1480-3275}, mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; *Conjugation, Genetic ; Promoter Regions, Genetic ; *Escherichia coli/genetics ; *Genetic Engineering/methods ; Arabinose/metabolism ; }, abstract = {Rapidly developing microbial resistance to existing antimicrobials poses a growing threat to public health and global food security. Current chemical-based treatments target cells by inhibiting growth or metabolic function, but their effectiveness is diminishing. To address the growing antimicrobial resistance crisis, there is an urgent need for innovative therapies. Conjugative plasmids, a natural mechanism of horizontal gene transfer in bacteria, have been repurposed to deliver toxic genetic cargo to recipient cells, showing promise as next-generation antimicrobial agents. However, the ecological risks posed by unintended gene transfer require robust biocontainment strategies. In this study, we developed inducible conjugative plasmids to solve these challenges. Utilizing an arabinose-inducible promoter, we evaluated 13 plasmids with single essential gene deletions, identifying trbC and trbF as strong candidates for stringent regulation. These plasmids demonstrated inducibility in both cis and trans configurations, with induction resulting in up to a 5-log increase in conjugation efficiency compared to uninduced conditions. Although challenges such as reduced conjugation efficiency and promoter leakiness persist, this work establishes a foundation for the controlled transfer of plasmids, paving the way for safer and more effective antimicrobial technologies.}, }
@article {pmid40168346, year = {2025}, author = {Lim, ZH and Zheng, P and Quek, C and Nowrousian, M and Aachmann, FL and Jedd, G}, title = {Diatom heterotrophy on brown algal polysaccharides emerged through horizontal gene transfer, gene duplication, and neofunctionalization.}, journal = {PLoS biology}, volume = {23}, number = {4}, pages = {e3003038}, pmid = {40168346}, issn = {1545-7885}, mesh = {*Gene Transfer, Horizontal ; *Gene Duplication ; *Diatoms/genetics/metabolism ; *Polysaccharides/metabolism ; Phylogeny ; Heterotrophic Processes ; Alginates/metabolism ; Phaeophyceae/genetics ; Polysaccharide-Lyases/genetics/metabolism ; Evolution, Molecular ; }, abstract = {A major goal of evolutionary biology is to identify the genetic basis for the emergence of complex adaptive traits. Diatoms are ancestrally photosynthetic microalgae. However, in the genus Nitzschia, loss of photosynthesis led to a group of free-living secondary heterotrophs whose manner of acquiring chemical energy is unclear. Here, we sequence the genome of the non-photosynthetic diatom Nitzschia sing1 and identify the genetic basis for its catabolism of the brown algal cell wall polysaccharide alginate. N. sing1 obtained an endolytic alginate lyase enzyme by horizontal gene transfer (HGT) from a marine bacterium. Subsequent gene duplication through unequal crossing over and transposition led to 91 genes in three distinct gene families. One family retains the ancestral endolytic enzyme function. By contrast, the two others underwent domain duplication, gain, loss, rearrangement, and mutation to encode novel functions that can account for oligosaccharide import through the endomembrane system and the exolytic production of alginate monosaccharides. Together, our results show how a single HGT event followed by substantial gene duplication and neofunctionalization led to alginate catabolism and access to a new ecological niche.}, }
@article {pmid40166311, year = {2025}, author = {Inglis, LK and Grigson, SR and Roach, MJ and Edwards, RA}, title = {Prophages as a source of antimicrobial resistance genes in the human microbiome.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40166311}, issn = {2692-8205}, support = {RC2 DK116713/DK/NIDDK NIH HHS/United States ; }, abstract = {Prophages-viruses that integrate into bacterial genomes-are ubiquitous in the microbial realm. Prophages contribute significantly to horizontal gene transfer, including the potential spread of antimicrobial resistance (AMR) genes, because they can collect host genes. Understanding their role in the human microbiome is essential for fully understanding AMR dynamics and possible clinical implications. We analysed almost 15,000 bacterial genomes for prophages and AMR genes. The bacteria were isolated from diverse human body sites and geographical regions, and their genomes were retrieved from GenBank. AMR genes were detected in 6.6% of bacterial genomes, with a higher prevalence in people with symptomatic diseases. We found a wide variety of AMR genes combating multiple drug classes. We discovered AMR genes previously associated with plasmids, such as blaOXA-23 in Acinetobacter baumannii prophages or genes found in prophages in species they had not been previously described in, such as mefA-msrD in Gardnerella prophages, suggesting prophage-mediated gene transfer of AMR genes. Prophages encoding AMR genes were found at varying frequencies across body sites and geographical regions, with Asia showing the highest diversity of AMR genes.}, }
@article {pmid40166188, year = {2025}, author = {Gonçalves, C and Steenwyk, JL and Rinker, DC and Opulente, DA and LaBella, AL and Harrison, MC and Wolters, JF and Zhou, X and Shen, XX and Covo, S and Groenewald, M and Hittinger, CT and Rokas, A}, title = {Stable hypermutators revealed by the genomic landscape of DNA repair genes among yeast species.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40166188}, issn = {2692-8205}, support = {R01 AI153356/AI/NIAID NIH HHS/United States ; T32 HG002760/HG/NHGRI NIH HHS/United States ; }, abstract = {Mutator phenotypes are short-lived due to the rapid accumulation of deleterious mutations. Yet, recent observations reveal that certain fungi can undergo prolonged accelerated evolution after losing DNA repair genes. Here, we surveyed 1,154 yeast genomes representing nearly all known yeast species of the subphylum Saccharomycotina to examine the relationship between reduced DNA repair repertoires and elevated evolutionary rates. We identified three distantly related lineages-encompassing 12% of species-with substantially reduced sets of DNA repair genes and the highest evolutionary rates in the entire subphylum. Two of these "faster-evolving lineages" (FELs)-a subclade within the order Pichiales and the Wickerhamiella/Starmerella (W/S) clade (order Dipodascales)-are described here for the first time, while the third corresponds to a previously documented Hanseniaspora FEL. Examination of DNA repair gene repertoires revealed a set of genes predominantly absent in these three FELs, suggesting a potential role in the observed acceleration of evolutionary rates. Genomic signatures in the W/S clade are consistent with a substantial mutational burden, including pronounced A|T bias and signatures of endogenous DNA damage. The W/S clade appears to mitigate UV-induced damage through horizontal acquisition of a bacterial photolyase gene, underscoring how gene loss may be offset by nonvertical evolution. These findings highlight how the loss of DNA repair genes gave rise to hypermutators that persist across macroevolutionary timescales, with horizontal gene transfer as an avenue for partial functional compensation.}, }
@article {pmid40166157, year = {2025}, author = {Gozashti, L and Corbett-Detig, R}, title = {Double-stranded DNA viruses may serve as vectors for horizontal transfer of intron-generating transposons.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40166157}, issn = {2692-8205}, support = {R35 GM128932/GM/NIGMS NIH HHS/United States ; }, abstract = {Specialized transposable elements capable of generating introns, termed introners, are one of the major drivers of intron gain in eukaryotes. Horizontal gene transfer (HGT) is thought to play an important role in shaping introner distributions. Viruses could function as vehicles of introner HGT since they often integrate into host genomes and have been implicated in widespread HGT in eukaryotes. We annotated integrated viral elements in diverse dinoflagellate genomes with active introners and queried viral elements for introner sequences. We find that 25% of viral elements contain introners. The vast majority of viral elements represent maverick-polinton-like double-stranded DNA (dsDNA) viruses as well as giant dsDNA viruses. By querying a previously annotated set of maverick-polinton-like proviruses, we show that introners populate full-length elements with machinery required for transposition as well as viral infection. Introners in the vast majority of viral elements are younger than or similar in age to others in their host genome, suggesting that most viral elements acquired introners after integration. However, a subset of viral elements show the opposite pattern wherein viral introners are significantly older than other introners, possibly consistent with virus-to-host horizontal transfer. Together, our results suggest that dsDNA viruses may serve as vectors for HGT of introners between individuals and species, resulting in the introduction of intron-generating transposons to new lineages.}, }
@article {pmid40165783, year = {2025}, author = {Herbert, A and Hancock, CN and Cox, B and Schnabel, G and Moreno, D and Carvalho, R and Jones, J and Paret, M and Geng, X and Wang, H}, title = {Corrigendum: Oxytetracycline and streptomycin resistance genes in Xanthomonas arboricola pv. pruni, the causal agent of bacterial spot in peach.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1580418}, doi = {10.3389/fmicb.2025.1580418}, pmid = {40165783}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2022.821808.].}, }
@article {pmid40165089, year = {2025}, author = {Ma, Y and López-Pujol, J and Yan, D and Deng, Z and Zhou, Z and Niu, J}, title = {Complete mitochondrial genomes of the hemiparasitic genus Cymbaria (Orobanchaceae): insights into repeat-mediated recombination, phylogenetic relationships, and horizontal gene transfer.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {314}, pmid = {40165089}, issn = {1471-2164}, support = {31860106//National Natural Science Foundation of China/ ; 2019ZD008//Major Science and Technology Projects of Inner Mongolia Autonomous Region/ ; }, mesh = {*Genome, Mitochondrial ; *Phylogeny ; *Gene Transfer, Horizontal ; *Orobanchaceae/genetics/classification ; Recombination, Genetic ; RNA, Transfer/genetics ; Repetitive Sequences, Nucleic Acid ; Evolution, Molecular ; }, abstract = {BACKGROUND: The Orobanchaceae family is widely recognized as an exemplary model system for examining the evolutionary dynamics of parasitic plants. However, reports on the mitochondrial genome (mitogenome) of the hemiparasitic tribe Cymbarieae are currently lacking. Here, we sequenced, assembled and characterized the complete mitogenome of the genus Cymbaria L. sensu stricto (C. mongolica and C. daurica).<br><br>RESULTS: A total of 51 unique mitochondrial genes, including 33 protein-coding genes, three rRNA genes, and 15 tRNA genes, are shared by the mitogenomes of the two hemiparasitic plants, exhibiting the gene content characteristic of autotrophic plants. The mitogenomes of C. mongolica and C. daurica are characterized by a pentacyclic chromosome structure (their major conformation), with lengths of 1,576,465&#xa0;bp and 1,539,836&#xa0;bp, respectively. Moreover, we identified and validated the presence of four minor conformations mediated by four pairs of large repeats (>&#x2009;1000&#xa0;bp in size) in C. mongolica and eight minor conformations mediated by six large repeats in C. daurica. We further explored codon usage, RNA editing sites, selective pressure, and nucleotide diversity in two Cymbaria mitogenomes. Phylogenetic analyses of 26 species of Lamiales revealed that the two Cymbaria species form a sister clade to the other lineages of Orobanchaceae. Extensive mitogenomic rearrangements are also observed between Cymbaria and five closely related species. Although we identified mitochondrial plastid sequences in the Cymbaria mitogenomes, The mitochondrial plastid sequences (MTPTs) in their mitogenomes represent only 2.37% and 1.74%, respectively. Additionally, there is minimal evidence of intracellular and horizontal gene transfer, with only a few genes (rpl22, rps3, and ycf2) showing low bootstrap support (BS&#x2009;&#x2264;&#x2009;70%) for the relationships with the potential host plants Allium mongolicum, Leymus chinensis, and Saposhnikovia divaricata, respectively.<br><br>CONCLUSIONS: We reported the mitochondrial genome in hemiparasitic Cymbaria species for the first time, which are characterized by multiple repeat-mediated recombination and little to no intracellular and horizontal gene transfer. Our findings provide valuable genetic insights for further studies on the mitogenome evolution of hemiparasitic plants.}, }
@article {pmid40164788, year = {2025}, author = {}, title = {Horizontal gene transfer of cold shock protein genes boosted wheat adaptation and expansion.}, journal = {Nature plants}, volume = {11}, number = {4}, pages = {676-677}, pmid = {40164788}, issn = {2055-0278}, }
@article {pmid40162837, year = {2025}, author = {Major, SR and Polinski, JM and Penn, K and Rodrigue, M and Harke, MJ}, title = {Novel and diverse features identified in the genomes of bacteria isolated from a hydrothermal vent plume.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {4}, pages = {e0259324}, pmid = {40162837}, issn = {1098-5336}, support = {22-08846//Dalio Foundation/ ; }, mesh = {*Hydrothermal Vents/microbiology ; *Genome, Bacterial ; *Bacteria/genetics/isolation &amp; purification/classification ; Phylogeny ; Multigene Family ; Seawater/microbiology ; Gene Transfer, Horizontal ; }, abstract = {Hydrothermal vent plumes (HVPs), formed by high-temperature vent emissions, are rich in compounds that support chemosynthesis and serve as reservoirs of microbial diversity and genetic innovation. Through turbulence, mixing, and interaction with subsea currents, vent communities are thought to disperse across ocean basins. In this study, we focused on the plume of the Moytirra hydrothermal vent field, a relatively unexplored site, to investigate its microbial inhabitants. We cultured bacteria from the Moytirra HVP using 11 different media types and performed complete genome sequencing on 12 isolates. Our analyses revealed four putatively novel species from the Thalassobaculum, Sulfitobacter, Idiomarina, and Christiangramia genera. Comparative genomics identified unique genomic islands containing biosynthetic gene clusters, including a novel Non-Ribosomal Peptide Synthetase/Polyketide Synthase cluster, toxin-antitoxin systems, and evidence of horizontal gene transfer facilitated by prophages. These findings underscore the potential of HVPs as a source of novel microbial species and biotechnologically relevant genes, contributing to our understanding of the biodiversity and genetic complexity of these extreme environments.IMPORTANCEHydrothermal vents are dynamic environments that offer unique nutrients for chemosynthetic organisms to drive biology in the deep-sea. The dynamics of these ecosystems are thought to drive genomic innovation in resident populations. Hydrothermal vent plumes (HVPs) mix with surrounding water, carrying local microbiota with them and dispersing for hundreds of kilometers. This study isolated bacteria from a HVP to capture a genomic snapshot of the microbial community, revealing four putatively novel species of bacteria within three taxonomic classes. The addition of these genomes to public databases provides valuable insights into the genomic function, architecture, and novel biosynthetic gene clusters of bacteria found in these extreme environments.}, }
@article {pmid40161755, year = {2025}, author = {Ratna, TA and Sharon, BM and Velin, CAB and Buttaro, BA and Palmer, KL}, title = {Factors affecting CRISPR-Cas defense against antibiotic resistance plasmids harbored by Enterococcus faecalis laboratory model strains and clinical isolates.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40161755}, issn = {2692-8205}, support = {R01 AI116610/AI/NIAID NIH HHS/United States ; }, abstract = {Enterococcus faecalis is a Gram-positive bacterium and opportunistic pathogen that acquires resistance to a wide range of antibiotics by horizontal gene transfer (HGT). The rapid increase of multidrug-resistant (MDR) bacteria including MDR E. faecalis necessitates the development of alternative therapies and a deeper understanding of the factors that impact HGT. CRISPR-Cas systems provide sequence-specific defense against HGT. From previous studies, we know that E. faecalis CRISPR-Cas provides sequence-specific anti-plasmid defense during agar plate biofilm mating and in the murine intestine. Those studies were mainly conducted using laboratory model strains with a single, CRISPR-targeted plasmid in the donor. MDR E. faecalis typically possess multiple plasmids that are diverse in sequence and may interact with each other to impact plasmid transfer and CRISPR-Cas efficacy. Here, we altered multiple parameters of our standard in vitro conjugation assays to assess CRISPR-Cas efficacy, including the number and genotype of plasmids in the donor; laboratory model strains as donor versus recent human isolates as donor; and the biofilm substrate utilized during conjugation. We found that the plasmids pTEF2 and pCF10, which are not targeted by CRISPR-Cas in our recipient, enhance the conjugative transfer of the CRISPR-targeted plasmid pTEF1 into both wild-type and CRISPR-Cas-deficient (via deletion of cas9) recipient cells. However, the effect of pTEF2 on pTEF1 transfer is much more pronounced, with a striking 6-log increase in pTEF1 conjugation frequency when pTEF2 is also present in the donor and recipients are deficient for CRISPR-Cas (compared to 4-log for pCF10). We also identified that E. faecalis Δcas9 has altered biofilm structure and thickness relative to the wild-type strain when cultured on a plastic substrate, but equivalent growth in the agar plate biofilms widely used for conjugation studies. Overall, this study provides insight about the interplay between plasmids and CRISPR-Cas defense, opening avenues for developing novel therapeutic strategies to curb HGT among bacterial pathogens, and highlighting pTEF2 as a plasmid for additional mechanistic study.}, }
@article {pmid40158280, year = {2025}, author = {Zhang, L and Ye, M and Dong, Y and Yuan, L and Xiang, J and Yu, X and Liao, Q and Ai, Q and Qiu, S and Zhang, D}, title = {Strict relationship between phenotypic and plasmid-associated genotypic of multidrug-resistant Escherichia coli isolated from Taihe Black-Boned Silky Fowl farms.}, journal = {Poultry science}, volume = {104}, number = {6}, pages = {105082}, pmid = {40158280}, issn = {1525-3171}, abstract = {Taihe Black-Boned Silky Fowl (TBSF) is a unique breed in China, characterized by a high concentration of melanin deposited throughout its body. Compared to broiler chickens, many antibiotics exhibit significantly longer withdrawal periods in TBSF. Given that antibiotic exposure is widely recognized as the primary selective pressure driving the persistence and dissemination of antibiotic resistance genes (ARGs) across diverse environments, it is crucial to investigate the occurrence and prevalence of ARGs within TBSF farming systems. In this study, 34 Escherichia coli strains isolated from 22 TBSF farms were subjected to phenotypic and genotypic analyses. The isolates were tested for susceptibility to 28 antimicrobial drugs representing nine antibiotic classes to determine their antimicrobial resistance phenotypes. Draft genome sequences of these E. coli strains were obtained, and the ARGs carried by mobile genetic elements, particularly plasmids, were analyzed for their association with susceptibility phenotype. The genetic context of key ARGs in these E. coli isolates was further characterized. Network analysis was employed to investigate the correlations between ARGs, phenotypes, and drug residues. The results demonstrated that high rates of antimicrobial resistance were observed, with 100 % and 29.4 % of isolates exhibiting resistance to four or more and eight or more antibiotic classes, respectively. According to whole-genome sequencing, a total of 143 ARGs were identified. The antimicrobial resistance phenotypes were consistently correlated with the presence of corresponding ARGs in the 34 E. coli genomes. 100 % of the β-lactams antibiotics resistant mechanism could be attributed to the presence of the resistance gene blaTEM and/or blaOXA-10. Similarly, resistance to tetracyclines, chloramphenicols, aminoglycosides, and fluoroquinolones was fully explained by the presence of tetR and/or tetA, floR and/or cmlA, ant(3'')-IIa, aph(3'')-Ib, aph(6)-Id, aac(3)-IId, and aadA, and qnrS and/or mutant gyrA/parC/mdtH. The majority of these key ARGs were found to be plasmid-associated. This study verified and highlighted the prevalent horizontal gene transfer of ARGs in TBSF farms. Factors such as hygiene status, biosecurity measures, and other environmental conditions might play a more significant role than antimicrobial usage in facilitating the horizontal gene transfer of ARGs in TBSF farms. Appropriate measures should be taken to control the transmission and dissemination of these mobile genetic elements associated ARGs and prevent their entry into the human clinical environment from TBSF breeding environment.}, }
@article {pmid40155375, year = {2025}, author = {von Rosen, T and Zdanowicz, R and El Hadeg, Y and Afanasyev, P and Boehringer, D and Leitner, A and Glockshuber, R and Weber-Ban, E}, title = {Substrates bind to residues lining the ring of asymmetrically engaged bacterial proteasome activator Bpa.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {3042}, pmid = {40155375}, issn = {2041-1723}, support = {310030_215606//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; ETH-17 17-2//Eidgen&#xf6;ssische Technische Hochschule Z&#xfc;rich (Federal Institute of Technology Zurich)/ ; }, mesh = {*Proteasome Endopeptidase Complex/metabolism ; *Bacterial Proteins/metabolism/genetics/chemistry ; *Cryoelectron Microscopy ; Protein Binding ; Mycobacterium tuberculosis/metabolism/genetics ; Models, Molecular ; Mutagenesis, Site-Directed ; Binding Sites ; Proteolysis ; Substrate Specificity ; }, abstract = {Mycobacteria harbor a proteasome that was acquired by Actinobacteria through horizontal gene transfer and that supports the persistence of the human pathogen Mycobacterium tuberculosis within host macrophages. The core particle of the proteasome (20S CP) associates with ring-shaped activator complexes to degrade protein substrates. One of these is the bacterial proteasome activator Bpa that stimulates the ATP-independent proteasomal degradation of the heat shock repressor HspR. In this study, we determine the cryogenic electron microscopy 3D reconstruction of the complex between Bpa and its natural substrate HspR at 4.1 Å global resolution. The resulting maps allow us to identify regions of Bpa that interact with HspR. Using structure-guided site-directed mutagenesis and in vitro biochemical assays, we confirm the importance of the identified residues for Bpa-mediated substrate recruitment and subsequent proteasomal degradation. Additionally, we show that the dodecameric Bpa ring associates asymmetrically with the heptameric α-rings of the 20S CP, adopting a conformation resembling a hinged lid, while still engaging all seven docking sites on the proteasome.}, }
@article {pmid40154852, year = {2025}, author = {He, L and Wang, W and Chen, H and Ma, L and Yu, L and Yang, Y and Qu, Y and Dai, P and Wang, D and Ma, X}, title = {Gene expressions of clinical Pseudomonas aeruginosa harboring RND efflux pumps on chromosome and involving a novel integron on a plasmid.}, journal = {Microbial pathogenesis}, volume = {203}, number = {}, pages = {107512}, doi = {10.1016/j.micpath.2025.107512}, pmid = {40154852}, issn = {1096-1208}, mesh = {*Pseudomonas aeruginosa/genetics/drug effects/isolation &amp; purification ; *Plasmids/genetics ; *Integrons/genetics ; Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; *Membrane Transport Proteins/genetics ; Humans ; Drug Resistance, Multiple, Bacterial/genetics ; Pseudomonas Infections/microbiology ; *Chromosomes, Bacterial/genetics ; Gene Expression Regulation, Bacterial ; Bacterial Proteins/genetics ; DNA Transposable Elements ; }, abstract = {The clinical strain of Pseudomonas aeruginosa XM8 harbored multiple RND-type antibiotic efflux pump genes and a novel integron In4881 on its plasmid pXM8-2, rendering it resistant to nearly all conventional antibiotics except colistin. The resistance was primarily attributed to the inactivation of the oprD gene and overexpression of several efflux pump genes, including mexAB-oprM, mexCD-oprJ, oprN-mexFE, and mexXY. In this study, the XM8 strain was comprehensively characterized using various methods. Antimicrobial susceptibility testing was performed using the BioMerieux VITEK2 system and manual double dilution methods. Gene expression levels of efflux pump-related genes were analyzed via quantitative real-time PCR. The bacterial chromosome and plasmid were sequenced using both Illumina and Nanopore platforms, and bioinformatics tools were employed to analyze mobile genetic elements associated with antibiotic resistance. The pXM8-2 plasmid containsed multiple mobile genetic elements, including integrons (In4881, In334, In413) and transposons (Tn3, TnAs1, TnAs3). Notably, In4881 was reported for the first time in this study. The presence of these elements highlights the potential for horizontal gene transfer and further spread of antibiotic resistance. Given the strong resistance profile of the XM8 strain, effective measures should be implemented to prevent the dissemination and prevalence of such multidrug-resistant bacteria.}, }
@article {pmid40154224, year = {2025}, author = {Hao, X and Sang, W and Li, F and Shen, L and Zhu, L and Rong, L and Jiang, D and Bai, L}, title = {Regulation of antibiotic resistance gene rebound by degrees of microecological niche occupation by microbiota carried in additives during the later phases of swine manure composting.}, journal = {Ecotoxicology and environmental safety}, volume = {294}, number = {}, pages = {118112}, doi = {10.1016/j.ecoenv.2025.118112}, pmid = {40154224}, issn = {1090-2414}, mesh = {*Composting/methods ; *Manure/microbiology ; Animals ; *Drug Resistance, Microbial/genetics ; *Soil Microbiology ; Swine ; *Microbiota ; Bacteria/genetics ; Genes, Bacterial ; Soil/chemistry ; Gene Transfer, Horizontal ; }, abstract = {The occupation of microecological niches (MNs) by bacteria carrying lower antibiotic resistance genes (ARGs) has been demonstrated an effective strategy for reducing ARGs in compost, thereby mitigating the associated land use risks. In this study, humus soil (HS), matured compost (MC), and their respective isolated microbial agents (HSM and MCM), which exhibit varying abundances of ARGs, were introduced as additives after the thermophilic phase to investigate their influence on ARG removal and the mechanisms underlying effective MN occupation. The addition of HS resulted in the most favorable outcomes, including the highest carbon degradation, minimized nitrogen loss, and an 83.16 % reduction in ARG abundance during the later composting stages. In comparison, ARG rebound levels were 61.77 %-285.33 % across other treatments and 729.23 % in the control. Distinct dominant bacterial genera and potential ARG-host bacterial communities were observed, which varied with different additives and contributed to MN occupation dynamics. The addition of the HS additive intensified competition among non-host bacteria, and diversified the interactions both between genes and between bacteria. These changes suppressed horizontal gene transfer (HGT) mediated by mobile genetic elements (MGEs) and altered the abundance and composition of both dominant and non-dominant potential host species. Furthermore, it shifted the relative importance of key physicochemical parameters, collectively enhancing ARG removal during composting. These findings elucidate the mechanisms by which MN adjustments contribute to ARG reduction, providing actionable insights for designing composting strategies that mitigate environmental ARG dissemination risks more effectively.}, }
@article {pmid40151755, year = {2025}, author = {Hota, S and Patil, SR and Mane, PM}, title = {Enterococcus: Understanding Their Resistance Mechanisms, Therapeutic Challenges, and Emerging Threats.}, journal = {Cureus}, volume = {17}, number = {2}, pages = {e79628}, pmid = {40151755}, issn = {2168-8184}, abstract = {The Enterococcus species originates as non-harmful bacteria indigenous to human intestines but has transformed into severe hospital-acquired pathogens due to antimicrobial resistance (AMR). The clinical species Enterococcus faecalis and Enterococcus faecium create the most relevant infections because they appear in urinary tract infections, bloodstream infections, endocarditis, and wound infections. Enterococcus species demonstrate multiple antibiotic class resistance and resistance determinant acquisition properties that make treatment difficult for medical professionals. Vancomycin-resistant enterococci (VRE) together with high-level aminoglycoside-resistant strains and resistance to both linezolid and daptomycin have exhausted available treatment options. The review investigates the development process of Enterococcus infections by examining virulence characteristics, which involve biofilm production and defense mechanisms against the immune response and transmission of resistance genes. A thorough investigation of medical publications used Google Scholar along with PubMed and ScienceDirect and Medical Subject Headings (MeSH) as appropriate search terms. The traditional classification of Enterococcus species from historical context to modern epidemiology and pathogenesis and available treatment and test approaches are explained in this review. This section examines two categories of resistance together with their mechanisms of action with a specific focus on vancomycin resistance produced by van gene clusters as well as its prevalence trends. An examination of how horizontal gene transfer functions in transferring resistance throughout healthcare facilities is included. The paper investigates the different symptoms of enterococcal infections together with diagnostic obstacles and treatment modalities. Drug-resistant Enterococcus infections continue to increase internationally, so healthcare professionals need new therapeutic methods, better antimicrobial policies, and stronger infection prevention measures. The examination surveys Enterococcus infections through an extensive evaluation of developing resistance patterns combined with emerging intervention requirements.}, }
@article {pmid40151212, year = {2025}, author = {van Almsick, VF and Sobkowiak, A and Scherff, N and Schuler, F and Oehm, JB and Böing, C and Mellmann, A and Schwierzeck, V}, title = {In-depth characterization of Klebsiella pneumoniae carbapenemase (KPC)-encoding plasmids points at transposon-related transmission of resistance genes.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1542828}, pmid = {40151212}, issn = {2235-2988}, mesh = {*Klebsiella pneumoniae/genetics/drug effects/enzymology ; *beta-Lactamases/genetics ; Humans ; *Plasmids/genetics ; *Klebsiella Infections/transmission/microbiology ; *DNA Transposable Elements/genetics ; *Bacterial Proteins/genetics/metabolism ; *Whole Genome Sequencing ; Germany ; Multilocus Sequence Typing ; Male ; Female ; Aged ; Middle Aged ; Anti-Bacterial Agents/pharmacology ; Tertiary Care Centers ; Cross Infection/microbiology/transmission ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; Genome, Bacterial/genetics ; }, abstract = {Antimicrobial resistance (AMR) is a growing threat in healthcare systems, particularly in the management of infections in critically ill patients. This study highlights how to identify clusters and putative sharing of mobile genetic elements, such as transposons, in the hospital setting using long-read whole genome sequencing (lrWGS). The approach described here can be employed to investigate the transmission dynamics of KPC-3-positive Klebsiella pneumoniae at multiple levels, from the entire isolate down to individual plasmids and transposons. Here, a bla KPC-3 harboring transposon cluster was identified by using a Mash-based distance calculation for plasmids. This approach was used to investigate a local accumulation of KPC-3-positive Klebsiella pneumoniae on surgical and infectious disease wards of a tertiary care center in Germany over a time of six months. In total, seven patients were affected. Core genome multi-locus sequence typing analysis (cgMLST) identified two distinct genetic clusters: a sequence type (ST) 307 cluster (n = 5) and a ST101 cluster (n = 2). All isolates carried a bla KPC-3 carbapenemase. Further Mash distance-based plasmid analysis was not consistent with plasmid transfer due to genetic heterogeneity, but identified a transposon cluster across all isolates. Infection control evaluation of patient movements within their hospital admission supports a possible clonal transmission. Subsequent infection control measures, including point prevalence screening and enhanced contact precautions, successfully contained further transmissions. The study illustrates the value of in-depth plasmid analysis in understanding the transmission dynamics and epidemiology of AMR, particularly in hospital environments.}, }
@article {pmid40150788, year = {2025}, author = {Müller, GA}, title = {The Transformation Experiment of Frederick Griffith I: Its Narrowing and Potential for the Creation of Novel Microorganisms.}, journal = {Bioengineering (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, pmid = {40150788}, issn = {2306-5354}, abstract = {The construction of artificial microorganisms often relies on the transfer of genomes from donor to acceptor cells. This synthetic biology approach has been considerably fostered by the J. Craig Venter Institute but apparently depends on the use of microorganisms, which are very closely related. One reason for this limitation of the "creative potential" of "classical" transformation is the requirement for adequate "fitting" of newly synthesized polypeptide components, directed by the donor genome, to interacting counterparts encoded by the pre-existing acceptor genome. Transformation was introduced in 1928 by Frederick Griffith in the course of the demonstration of the instability of pneumococci and their conversion from rough, non-pathogenic into smooth, virulent variants. Subsequently, this method turned out to be critical for the identification of DNA as the sole matter of inheritance. Importantly, the initial experimental design (1.0) also considered the inheritance of both structural (e.g., plasma membranes) and cybernetic information (e.g., metabolite fluxes), which, in cooperation, determine topological and cellular heredity, as well as fusion and blending of bacterial cells. In contrast, subsequent experimental designs (1.X) were focused on the use of whole-cell homogenates and, thereafter, of soluble and water-clear fractions deprived of all information and macromolecules other than those directing protein synthesis, including outer-membrane vesicles, bacterial prions, lipopolysaccharides, lipoproteins, cytoskeletal elements, and complexes thereof. Identification of the reasons for this narrowing may be helpful in understanding the potential of transformation for the creation of novel microorganisms.}, }
@article {pmid40149106, year = {2025}, author = {Olsen, NS and Riber, L}, title = {Metagenomics as a Transformative Tool for Antibiotic Resistance Surveillance: Highlighting the Impact of Mobile Genetic Elements with a Focus on the Complex Role of Phages.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {3}, pages = {}, pmid = {40149106}, issn = {2079-6382}, support = {NNF23OC0086264//Novo Nordisk Foundation/ ; }, abstract = {Extensive use of antibiotics in human healthcare as well as in agricultural and environmental settings has led to the emergence and spread of antibiotic-resistant bacteria, rendering many infections increasingly difficult to treat. Coupled with the limited development of new antibiotics, the rise of antimicrobial resistance (AMR) has caused a major health crisis worldwide, which calls for immediate action. Strengthening AMR surveillance systems is, therefore, crucial to global and national efforts in combating this escalating threat. This review explores the potential of metagenomics, a sequenced-based approach to analyze entire microbial communities without the need for cultivation, as a transformative and rapid tool for improving AMR surveillance strategies as compared to traditional cultivation-based methods. We emphasize the importance of monitoring mobile genetic elements (MGEs), such as integrons, transposons, plasmids, and bacteriophages (phages), in relation to their critical role in facilitating the dissemination of genetic resistance determinants via horizontal gene transfer (HGT) across diverse environments and clinical settings. In this context, the strengths and limitations of current bioinformatic tools designed to detect AMR-associated MGEs in metagenomic datasets, including the emerging potential of predictive machine learning models, are evaluated. Moreover, the controversial role of phages in AMR transmission is discussed alongside the potential of phage therapy as a promising alternative to conventional antibiotic treatment.}, }
@article {pmid40149092, year = {2025}, author = {Hernández, M and Falcó-Prieto, &#xc1; and Ugarte-Ruiz, M and Miguela-Villoldo, P and Ocampo-Sosa, A and Abad, D and Pérez-Sancho, M and Álvarez, J and Cadamuro, RD and Elois, MA and Fongaro, G and Quesada, A and González-Zorn, B and Domínguez, L and Eiros, JM and Rodríguez-Lázaro, D}, title = {Genome Analysis of 6222 Bacterial Isolates from Livestock and Food Environments in Spain to Decipher the Antibiotic Resistome.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {3}, pages = {}, pmid = {40149092}, issn = {2079-6382}, support = {AGL2016-74882-C3//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; }, abstract = {Background/Objectives: Antimicrobial resistance (AMR) poses a significant threat to global health and the economy, with projected costs ranging from $300 billion to $1 trillion annually and an estimated 10 million deaths per year by 2050. The food chain, from primary production to retail, represents a critical entry point for antimicrobial resistant bacteria into communities. This underscores the need for a coordinated "One Health" approach, integrating efforts in animal production, environmental health, and human healthcare to address this global concern. This study aimed to characterize the global resistome in Spanish primary production by sequencing 6222 bacterial genomes from animal origin. Methods and Results: Whole genome sequencing was performed on bacterial isolates collected from various farms and analyzed using a validated bioinformatic pipeline. The analysis revealed a diverse range of bacterial species, with Enterobacteriaceae being the most prevalent family. Escherichia coli was the most common species, followed by Salmonella enterica and Pseudomonas aeruginosa. This study identified 1072 antimicrobial resistance genes coding for 43 different classes of resistance, potentially conferring resistance to 81 antimicrobials. Additionally, 79 different plasmid types were detected, highlighting the potential for horizontal gene transfer. Conclusions: The resistome analysis revealed genes conferring resistance to various antibiotic classes, as well as antiseptics, disinfectants, and efflux pump-mediated resistance. This comprehensive characterization of AMR genes circulating in bacteria from primary production provides crucial insights into the ecology of AMR in Spanish livestock.}, }
@article {pmid40149046, year = {2025}, author = {Mitsuwan, W and Boripun, R and Saengsawang, P and Intongead, S and Boonplu, S and Chanpakdee, R and Morita, Y and Boonmar, S and Rojanakun, N and Suksriroj, N and Ruekaewma, C and Tenitsara, T}, title = {Multidrug Resistance, Biofilm-Forming Ability, and Molecular Characterization of Vibrio Species Isolated from Foods in Thailand.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {3}, pages = {}, pmid = {40149046}, issn = {2079-6382}, support = {SEAOHUN/2023-SC248//United States Agency for International Development (USAID) through the SEAOHUN 2023 One Health Research and Training (OHRT) Awards/ ; WU-CIA-03404/2024//Walailak University under the international research collaboration scheme/ ; }, abstract = {BACKGROUND: Vibrio species are common foodborne pathogens that cause gastrointestinal tract inflammation. Multidrug resistance (MDR) in Vibrio spp. is a global health concern, especially in aquaculture systems and food chain systems. This study aimed to detect Vibrio contamination in food collected from 14 markets in Nakhon Si Thammarat, Thailand, and determine their antibiotic susceptibility.<br><br>METHODS: One hundred and thirty-six food samples were investigated for Vibrio contamination. All isolates were tested for antibiogram and biofilm-forming ability. Moreover, the ceftazidime or cefotaxime resistance isolates were additionally investigated for extended-spectrum &#x3b2;-lactamase (ESBL) producers. The isolates were additionally examined for the presence of antibiotic resistance genes. The ESBL-suspected isolates with moderate-to-high biofilm-forming ability were further analyzed for their whole genome.<br><br>RESULTS: The prevalence of Vibrio contamination in food samples was 42.65%, with V. parahaemolyticus demonstrating the highest prevalence. Most isolates were resistant to &#x3b2;-lactam antibiotics, followed by aminoglycosides. The overall MDR of isolated Vibrio was 18.29%, with an average multiple antibiotic resistance (MAR) index of 16.41%. Most isolates were found to have &#x3b2;-lactam resistance-related genes (blaTEM) for 41.46%, followed by aminoglycoside resistance genes (aac(6')-Ib) for 18.29%. Most Vibrio showed moderate to strong biofilm-forming ability, particularly in MDR isolates (92.86%). Two ESBL-suspected isolates, one V. parahaemolyticus isolate and one V. navarrensis, were sequenced. Interestingly, V. parahaemolyticus was an ESBL producer that harbored the blaCTX-M-55 gene located in the mobile genetic element region. While V. navarrensis was not ESBL producer, this isolate carried the blaAmpC gene in the region of horizontal gene transfer event. Remarkably, the Inoviridae sp. DNA integration event was present in two Vibrio genomes.<br><br>CONCLUSIONS: These findings impact the understanding of antibiotic-resistant Vibrio spp. in food samples, which could be applied for implementing control measures in aquaculture farming and food safety plans.}, }
@article {pmid40148599, year = {2025}, author = {Patra, M and Pandey, AK and Dubey, SK}, title = {Sludge amended soil induced multidrug and heavy metal resistance in endophytic Exiguobacterium sp. E21L: genomics evidences.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {41}, number = {4}, pages = {114}, pmid = {40148599}, issn = {1573-0972}, support = {R/Dev./Sch./UGC Non-NET Fellowship/2023-24/72267//University Grants Commission/ ; 6031//IOE/ ; }, mesh = {*Metals, Heavy/pharmacology ; *Sewage/microbiology ; *Drug Resistance, Multiple, Bacterial/genetics ; *Soil Microbiology ; *Genome, Bacterial ; *Anti-Bacterial Agents/pharmacology ; *Genomics ; *Whole Genome Sequencing ; Phylogeny ; Microbial Sensitivity Tests ; Endophytes/genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; }, abstract = {The emergence of multidrug-resistant bacteria in agro-environments poses serious risks to public health and ecological balance. In this study, Exiguobacterium sp. E21L, an endophytic strain, was isolated from carrot leaves cultivated in soil amended with sewage treatment plant-derived sludge. The strain exhibited resistance to clinically relevant antibiotics, including beta-lactams, fluoroquinolones, aminoglycosides, and macrolides, with a high Multi-Antibiotic Resistance Index of 0.88. Whole-genome sequencing revealed a genome of 3.06 Mb, encoding 3894 protein-coding genes, including antimicrobial resistance genes (ARGs) such as blaNDM, ermF, tetW, and sul1, along with heavy metal resistance genes (HMRGs) like czcD, copB, and nikA. Genomic islands carrying ARGs and stress-related genes suggested potential horizontal gene transfer. The strain demonstrated robust biofilm formation, high cell hydrophobicity (> 80%), and significant auto-aggregation (90% at 48 h), correlating with genes associated with motility, quorum sensing, and stress adaptation. Notably, phenotypic assays confirmed survival under simulated gastrointestinal conditions, emphasizing its resilience in host-associated environments. Comparative genomics positioned Exiguobacterium sp. E21L near Exiguobacterium chiriqhucha RW-2, with a core genome of 2716 conserved genes. Functional annotations revealed genes involved in xenobiotic degradation, multidrug efflux pumps, and ABC-type transporters, indicating versatile resistance mechanisms and metabolic capabilities. The presence of ARGs, HMRGs, and MGEs (mobile genetic elements) highlights the potential role of Exiguobacterium sp. E21L as a reservoir for resistance determinants in agricultural ecosystems. These findings emphasized the need for stringent regulations on sludge-based fertilizers and advanced sludge treatment strategies to mitigate AMR risks in agro-environments.}, }
@article {pmid40148598, year = {2025}, author = {Wang, K and Guo, G and Bai, S and Ma, J and Zhang, Z and Xing, Z and Wang, W and Li, H and Liang, H and Li, Z and Si, X and Wang, J and Liu, Q and Xu, W and Yang, C and Song, RF and Li, J and He, T and Li, J and Zeng, X and Liang, J and Zhang, F and Qiu, X and Li, Y and Bu, T and Liu, WC and Zhao, Y and Huang, J and Zhou, Y and Song, CP}, title = {Horizontally acquired CSP genes contribute to wheat adaptation and improvement.}, journal = {Nature plants}, volume = {11}, number = {4}, pages = {761-774}, pmid = {40148598}, issn = {2055-0278}, support = {32230079//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Triticum/genetics/physiology ; *Gene Transfer, Horizontal ; *Plant Proteins/genetics/metabolism ; *Adaptation, Physiological/genetics ; Droughts ; Aegilops/genetics/physiology ; Photosynthesis ; Plants, Genetically Modified ; }, abstract = {Although horizontal gene transfer (HGT) often facilitates environmental adaptation of recipient organisms, whether and how they might affect crop evolution and domestication is unclear. Here we show that three genes encoding cold-shock proteins (CSPs) were transferred from bacteria to Triticeae, a tribe of the grass family that includes several major staple crops such as wheat, barley and rye. The acquired CSP genes in wheat (TaCSPs) are functionally conserved in their bacterial homologues by encoding a nucleic acid-binding protein. Experimental evidence indicates that TaCSP genes positively regulate drought response and improve photosynthetic efficiency under water-deficient conditions by directly targeting a type 1 metallothionein gene to increase reactive oxygen species scavenging, which in turn contributed to the geographic expansion of wheat. We identified an elite CSP haplotype in Aegilops tauschii, introduction of which to wheat significantly increased drought tolerance, photosynthetic efficiency and grain yields. These findings not only provide major insights into the role of HGT in crop adaptation and domestication, but also demonstrate that novel microbial genes introduced through HGT offer a stable and naturally optimized resource for transgenic crop breeding and improvement.}, }
@article {pmid40146211, year = {2025}, author = {Hornok, S and Keve, G and Tuska-Szalay, B}, title = {Transmission route-dependent genetic diversity of selected protozoan parasites as reflected by the phylogenetic analysis of the 18S rRNA gene.}, journal = {Acta veterinaria Hungarica}, volume = {73}, number = {1}, pages = {64-72}, doi = {10.1556/004.2025.01128}, pmid = {40146211}, issn = {0236-6290}, mesh = {*RNA, Ribosomal, 18S/genetics ; *Genetic Variation ; *Phylogeny ; Animals ; *Protozoan Infections, Animal/parasitology/transmission/epidemiology ; *Eukaryota/genetics/classification ; }, abstract = {In this pilot study, the genetic diversity of protozoan parasites was analysed according to their different transmission routes (life cycle strategies), focusing on those species which were recently discovered or molecularly analysed for the first time in Hungary or its geographical region. The results showed that among four apicomplexan parasites (Babesia gibsoni, Cytauxzoon europaeus, Sarcocystis morae and Hepatozoon felis) the latter had the highest genetic diversity as reflected by its 18S rRNA gene sequences showing high (1.75%) maximum intraspecific pairwise distance, and also, based on its phylogenetic clustering. This is probably related to the long evolutionary history of H. felis, the absence of its intravascular division and other life cycle characteristics precluding direct transmission between hosts. On the other hand, among non-apicomplexan protozoa (Trichomonas gallinae, Pentatrichomonas hominis, Tritrichomonas foetus and Acanthamoeba castellanii), the latter proved to have the highest genetic diversity (7.73%), most likely due to its long evolutionary history, lateral gene transfer, homologous recombination and the absence of direct host-to-host dispersal. Transmission mode had a significant impact on the genetic diversity among protozoan parasites, depending on life cycle strategies and consequent frequency/chance of sexual reproduction vs binary fission. In particular, the absence of direct transmission between hosts is a common trait of H. felis and A. castellanii, contributing to their high genetic diversity.}, }
@article {pmid40142381, year = {2025}, author = {Moriguchi, K and Nakamura, K and Takahashi, Y and Higo-Moriguchi, K and Kiyokawa, K and Suzuki, K}, title = {Genome-Wide Survey of Donor Chromosomal Genes Involved in Trans-Kingdom Conjugation via the RP4-T4SS Machinery.}, journal = {Microorganisms}, volume = {13}, number = {3}, pages = {}, pmid = {40142381}, issn = {2076-2607}, support = {JP16K07200//Japan Society for the Promotion of Science/ ; No grant number (donation)//Consortium for the Exploration of Microbial Functions Ohsumi Frontier Science Foundation/ ; }, abstract = {Trans-kingdom conjugation (TKC)/inter-domain conjugation is a horizontal gene transfer phenomenon that transfers DNA from eubacteria to eukaryotes and archaebacteria via a type IV secretion system encoded in IncP1-type broad-host-range plasmids. Although TKC is considered a potential gene introduction tool, donor chromosomal genes that influence TKC efficiency have rarely been analyzed, hindering targeted donor breeding. To identify potential TKC-related genes on a donor chromosome, a genome-wide screening of TKC-deficient mutants was performed using a comprehensive collection of Escherichia coli gene knockout mutants (Keio collection) as donors and a Saccharomyces cerevisiae strain as a recipient. Out of 3884 mutants, two mutants (∆aceE, ∆priA) showed a severe decrease in TKC efficiency by more than two orders of magnitude but not in bacterial conjugation. The effect on TKC efficiency by the two mutants was partly recovered by a preculture with a fresh culture medium before the TKC reaction, regardless of the presence of antibiotics. These results suggest that no single chromosomal target gene is solely responsible for universally blocking IncP1-type conjugation by impeding its function. The results also suggest the existence of an unidentified recognition or transfer mechanism distinct from bacterial conjugation, highlighting the novel roles of aceE and priA.}, }
@article {pmid40142377, year = {2025}, author = {Pazos, C and Gualoto, M and Oña, T and Velarde, E and Portilla, K and Cabrera-García, S and Banchón, C and Dávila, G and Hernández-Alomia, F and Bastidas-Caldes, C}, title = {Molecular Detection of blaTEM and blaSHV Genes in ESBL-Producing Acinetobacter baumannii Isolated from Antarctic Soil.}, journal = {Microorganisms}, volume = {13}, number = {3}, pages = {}, pmid = {40142377}, issn = {2076-2607}, abstract = {The phenomenon of antimicrobial resistance (AMR) in cold environments, exemplified by the Antarctic, calls into question the assumption that pristine ecosystems lack clinically significant resistance genes. This study examines the molecular basis of AMR in Acinetobacter spp. Isolated from Antarctic soil, focusing on the blaTEM and blaSHV genes associated with extended-spectrum beta-lactamase (ESBL) production; Soil samples were collected and processed to isolate Antarctic soil bacteria. Molecular detection was then conducted using polymerase chain reaction (PCR) to identify the bacteria species by 16S rRNA/rpoB and 10 different beta-lactamase-producing genes. PCR amplicons were sequenced to confirm gene identity and analyze genetic variability. Acinetobacter baumannii were identified by both microbiological and molecular tests. Notably, both the blaTEM and blaSHV genes encoding the enzymes responsible for resistance to penicillins and cephalosporins were identified, indicating the presence of resistance determinants in bacteria from extreme cold ecosystems. The nucleotide sequence analysis indicated the presence of conserved ARGs, which suggest stability and the potential for horizontal gene transfer within microbial communities. These findings emphasize that AMR is not confined to human-impacted environments but can emerge and persist in remote, cold habitats, potentially facilitated by natural reservoirs and global microbial dispersal. Understanding the presence and role of AMR in extreme environments provides insights into its global dissemination and supports the development of strategies to mitigate the spread of resistance genes in both environmental and clinical contexts.}, }
@article {pmid40141150, year = {2025}, author = {Rendueles, C and Garay-Novillo, JN and Rau, MH and Gaspar, P and Ruiz-Masó, J&#xc1; and Mahony, J and Rodríguez, A and Barra, JL and Del Solar, G and Martínez, B}, title = {A Plasmid-Encoded Surface Polysaccharide Partly Blocks Ceduovirus Infection in Lactococci.}, journal = {International journal of molecular sciences}, volume = {26}, number = {6}, pages = {}, pmid = {40141150}, issn = {1422-0067}, support = {PID2020-119697RB-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; }, mesh = {*Lactococcus/genetics ; *Plasmids/genetics ; *Lactococcus lactis/genetics/virology ; Bacteriophages/genetics ; Polysaccharides, Bacterial/metabolism ; CRISPR-Cas Systems ; }, abstract = {Bacteriophages (or phages) remain the leading cause of failure in dairy fermentations. Thereby, phage-resistant Lactococcus lactis and Lactococcus cremoris dairy starters are in continuous demand. In this work, our goal was to identify phage defense mechanisms against ceduoviruses encoded by two wild isolates of dairy origin named L. lactis IPLA517 and IPLA1064. These strains were previously subjected to experimental evolution to select derivatives that are resistant to the bacteriocin Lcn972. It was observed that the Lcn972[R] derivatives became sensitive to phage infection; however, the underlying mechanism was not defined. The long-read sequencing technologies applied in this work reveal that all of the Lcn972[R] derivatives shared the loss of a 41 kb endogenous plasmid (p41) that harbors a putative exopolysaccharide (EPS) gene cluster with significant homology to one described in Lactococcus garvieae. Using a CRISPR-Cas9-based approach, p41 was selectively cured from L. lactis IPLA1064. Phage infection assays with three ceduoviruses demonstrated that curing p41 restored phage sensitivity at levels comparable to the Lcn972[R]-IPLA1064 derivatives. Phage adsorption to Δp41 cells was also increased, consistent with the hypothesis of EPS production hindering access to the phage receptor protein Pip. Our results reinforce the role of EPSs in protecting Lactococcus against phage infection, a phenomenon that is rarely reported for ceduoviruses. Moreover, the results also exemplify the likely horizontal gene transfer that can occur between L. lactis and L. garvieae in a dairy environment.}, }
@article {pmid40135944, year = {2025}, author = {Zheng, Y and Zhu, X and Ding, C and Chu, W and Pang, X and Zhang, R and Ma, J and Xu, G}, title = {Multidrug-resistant hypervirulent Klebsiella pneumoniae: an evolving superbug.}, journal = {Future microbiology}, volume = {20}, number = {6}, pages = {499-511}, pmid = {40135944}, issn = {1746-0921}, mesh = {*Klebsiella pneumoniae/pathogenicity/drug effects/genetics ; Humans ; *Klebsiella Infections/microbiology/epidemiology ; *Drug Resistance, Multiple, Bacterial/genetics ; Virulence Factors/genetics ; Anti-Bacterial Agents/pharmacology ; Virulence ; China/epidemiology ; Asia/epidemiology ; Bacterial Proteins/genetics/metabolism ; }, abstract = {Multidrug-resistant hypervirulent Klebsiella pneumoniae (MDR-hvKP) combines high pathogenicity with multidrug resistance to become a new superbug. MDR-hvKP reports continue to emerge, shattering the perception that hypervirulent K. pneumoniae (hvKP) strains are antibiotic sensitive. Patients infected with MDR-hvKP strains have been reported in Asia, particularly China. Although hvKP can acquire drug resistance genes, MDR-hvKP seems to be more easily transformed from classical K. pneumoniae (cKP), which has a strong gene uptake ability. To better understand the biology of MDR-hvKP, this review discusses the virulence factors, resistance mechanisms, formation pathways, and identification of MDR-hvKP. Given their destructive and transmissible potential, continued surveillance of these organisms and enhanced control measures should be prioritized.}, }
@article {pmid40133813, year = {2025}, author = {Huang, X and Yu, C and Lu, L}, title = {Isolation and characterization of a roseophage representing a novel genus in the N4-like Rhodovirinae subfamily distributed in estuarine waters.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {295}, pmid = {40133813}, issn = {1471-2164}, mesh = {*Phylogeny ; *Bacteriophages/genetics/isolation &amp; purification/classification ; *Estuaries ; *Genome, Viral ; Rhodobacteraceae/genetics/virology/classification/isolation &amp; purification ; }, abstract = {BACKGROUND: Roseobacteraceae, often referred to as the marine roseobacter clade (MRC), are pivotal constituents of bacterial communities in coastal and pelagic marine environments. During the past two decades, 75 roseophages that infect various Roseobacteraceae lineages have been isolated. The N4-like roseophage clade, which encompasses 15 members, represents the largest clade among these roseophages. N4-like phages form a monophyletic group, classified as family Schitoviridae. And all N4-like roseophages form a unique clade within Schitoviridae and has been classified as the Rhodovirinae subfamily.<br><br>RESULTS: In this study, we isolated a novel roseophage, vB_DshP-R7L, that infects Dinoroseobacter shibae DFL12 from Xiamen Bay in the East China Sea. Conserved genes of Schitoviridae have been identified in the genome of vB_DshP-R7L, and following phylogenetic analysis suggests that the newly isolated phage is a member of the Rhodovirinae subfamily and represents the sole member of a novel genus, Gonggongvirus. The genome of vB_DshP-R7L harbors six auxiliary metabolic genes (AMGs), most of which potentially enhance DNA de novo synthesis. Additionally, a gene encoding ribosomal protein was identified. Comparative genomic analysis of AMG content among Rhodovirinae indicates a distinct evolutionary history characterized by independent ancient horizontal gene transfer events. Read-mapping analysis reveals the prevalence of vB_DshP-R7L and other Rhodovirinae roseophages in estuarine waters.<br><br>CONCLUSIONS: Our work illustrates the genomic features of a novel roseophage clade among the subfamily Rhodovirinae. The AMG content of vB_DshP-R7L is under severe purification selection, which reveals their possible ecological importance. We also demonstrated that vB_DshP-R7L and other Rhodovirinae roseophages are only detected in estuaries. Our isolation and characterization of this novel phage expands the understanding of the phylogeny, gene transfer history, and biogeography of Rhodovirinae infecting marine Roseobacteraceae.}, }
@article {pmid40131635, year = {2025}, author = {Silva, UCM and da Silva, DRC and Cuadros-Orellana, S and Moreira, LM and Leite, LR and Medeiros, JD and Felestrino, EB and Caneschi, WL and Almeida, NF and Silva, RS and Oliveira-Paiva, CA and Dos Santos, VL}, title = {Genomic and phenotypic insights into Serratia interaction with plants from an ecological perspective.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, pmid = {40131635}, issn = {1678-4405}, support = {N&#xb0; 477349/2013-7//CNPq/ ; N&#xb0; APQ-01819-13//Fapemig/ ; }, abstract = {We investigated the plant growth-promoting potential of two endophytic strains of Serratia marcescens, namely SmCNPMS2112 and SmUFMG85, which were isolated from the roots of the same maize (Zea mays) plant. The strains were evaluated in vitro for their ability to produce siderophores and indoleacetic acid, form biofilm, solubilize iron phosphate (Fe-P) and Araxá rock phosphate (RP), mineralize phytate, and for their ability to adhere and colonize host roots. Additionally, their plant growth-promoting potential was tested in vivo under greenhouse conditions using millet grown in soil under two fertilization schemes (triple superphosphate, TSP, or commercial rock phosphate, cRP). Both strains improved at least five physiological traits of millet or P content in soil. In order to elucidate the genetic basis of the plant growth-promoting ability of these strains, their genomes were compared. While both genomes exhibited a similar overall functional profile, each strain had unique features. SmCNPMS2112 contained genes related to arsenic and aromatic hydrocarbons degradation, whereas SmUFMG85 harbored genes related to rhamnolipid biosynthesis and chromium bioremediation. Also, we observe a unique repertoire of genes related to plant growth-promotion (PGP) in the SmUFMG85 genome, including oxalate decarboxylase (OxdC), associated with the catabolism of oxalic acid, and aerobactin siderophore (lucD) in the genome of SmCNPMS2112. The alkaline phosphatase was observed on two strains, but acid phosphatase was exclusive to SmUFMG85. Eighteen secondary metabolic gene clusters, such as those involved in the biosynthesis of macrolides and bacillomycin, among others, occur in both strains. Moreover, both genomes contained prophages, suggesting that viral-mediated horizontal gene transfer may be a key mechanism driving genomic variability in the endophytic environment. Indeed, the most genes unique and accessory of SmUFMG85 and SmCNPMS2112 were localized in genomic islands, highlighting genome plasticity and its underlying drivers. To investigate the ecological distribution of plant-interaction traits in the genus Serratia, the genomes of SmUFMG85 and SmCNPMS2112 strains were compared with those of other 19 Serratia strains of different species, which were isolated from different environments. We observe that many features for PGP are present in all genomes, regardless of niche, for instance: formation of flagella, fimbriae and pili, chemotaxis, biosynthesis of siderophores, indole-3-acetic acid (IAA) and volatile organic (VOC) and inorganic (VIC) compounds, such as acetoin and HCN. Also, all the analyzed genomes show an antimicrobial resistance repertoire of genes that confer resistance to several antibiotics belonging to the groups of aminoglycosides and quinolones, for instance. Also, from a niche partitioning perspective, secretion system preference and the ability to produce exopolysaccharides involved in biofilm formation are among the features that vary the most among strains, and most likely influence niche adaptation in Serratia spp., even though only the latter seems to be a feature specifically associated with virulence in the analyzed strains. Our results show that populations of bacteria sharing the same niche can present significant physiological and genomic differences, and reveal the intraspecific metabolic plasticity that underlie plant-bacteria interactions. Also, this study reveals the potential of two Serratia marcescens strains as bioinoculants in agriculture. Considering that Serratia spp. are regarded as low risk biological agents, despite the fact that they can be associated with human disease, we suggest that strain biosafety be evaluated using a combination of genome and phenotypic analyses, as presented herein.}, }
@article {pmid40121546, year = {2025}, author = {Wang, Q and Liu, C and Sun, Y and Li, X and Gu, W and Wang, N and Sun, S and Luo, Y}, title = {Dietary intake of enrofloxacin promotes the spread of antibiotic resistance from food to simulated human gut.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf045}, pmid = {40121546}, issn = {1751-7370}, abstract = {Antibiotic residues are commonly found in food. The effect of dietary exposure to veterinary antibiotics on the transmission of antibiotic resistant bacteria and antibiotic resistance genes from food to humans is unknown. We found that dietary exposure to enrofloxacin reduced microbial diversity, interactions and the immune responses, weakened the colonization resistance of the resident microbiota, and promoted the colonization of exogenous Escherichia coli K-12 MG1655 in the simulated human intestine both in vitro and in vivo experiments in mice. In addition to the growth advantages for potential most likely bacterial hosts of ARGs under enrofloxacin exposure, the dietary exposure to enrofloxacin promoted horizontal transfer of resistance plasmids and altered the simulated human gut antibiotic resistome in a time-dependent manner. Collectively, these findings demonstrated that dietary intake of enrofloxacin promoted the colonization of E. coli K-12 MG1655 in the simulated human intestine and the horizontal transfer of antibiotic resistance genes, highlighting the risk of antibiotic resistance transmission from food to humans mediated by dietary exposure to veterinary antibiotics.}, }
@article {pmid40120959, year = {2025}, author = {Wu, Z and Famous, M and Stoikidou, T and Bowden, FES and Dominic, G and Huws, SA and Godoy-Santos, F and Oyama, LB}, title = {Unravelling AMR dynamics in the rumenofaecobiome: Insights, challenges and implications for One Health.}, journal = {International journal of antimicrobial agents}, volume = {66}, number = {1}, pages = {107494}, doi = {10.1016/j.ijantimicag.2025.107494}, pmid = {40120959}, issn = {1872-7913}, abstract = {Antimicrobial resistance (AMR) is a critical global threat to human, animal and environmental health, exacerbated by horizontal gene transfer (HGT) via mobile genetic elements. This poses significant challenges that have a negative impact on the sustainability of the One Health approach, hindering its long-term viability and effectiveness in addressing the interconnectedness of global health. Recent studies on livestock animals, specifically ruminants, indicate that culturable ruminal bacteria harbour AMR genes with the potential for HGT. However, these studies have focused predominantly on using the faecobiome as a proxy to the rumen microbiome or using easily isolated and culturable bacteria, overlooking the unculturable population. These unculturable microbial groups could have a profound influence on the rumen resistome and AMR dynamics within livestock ecosystems, potentially holding critical insights for advanced understanding of AMR in One Health. In order to address this gap, this review of current research on the burden of AMR in livestock was undertaken, and it is proposed that combined study of the rumen microbiome and faecobiome, termed the 'rumenofaecobiome', should be performed to enhance understanding of the risks of AMR in ruminant livestock. This review discusses the complexities of the rumen microbiome and the risks of AMR transmission in this microbiome in a One Health context. AMR transmission dynamics and methodologies for assessing the risks of AMR in livestock are summarized, and future considerations for researching the impact of AMR in the rumen microbiome and the implications within the One Health framework are discussed.}, }
@article {pmid40120581, year = {2025}, author = {Scarampi, A and Lawrence, JM and Bombelli, P and Kosmützky, D and Zhang, JZ and Howe, CJ}, title = {Polyploid cyanobacterial genomes provide a reservoir of mutations, allowing rapid evolution of herbicide resistance.}, journal = {Current biology : CB}, volume = {35}, number = {7}, pages = {1549-1561.e3}, doi = {10.1016/j.cub.2025.02.044}, pmid = {40120581}, issn = {1879-0445}, mesh = {*Polyploidy ; *Mutation ; *Genome, Bacterial ; *Herbicide Resistance/genetics ; *Synechocystis/genetics/drug effects/physiology ; *Herbicides/pharmacology ; Evolution, Molecular ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Adaptive mechanisms in bacteria, which are widely assumed to be haploid or partially diploid, are thought to rely on the emergence of spontaneous mutations or lateral gene transfer from a reservoir of pre-existing variants within the surrounding environment. These variants then become fixed in the population upon exposure to selective pressures. Here, we show that multiple distinct wild-type (WT) substrains of the highly polyploid cyanobacterium Synechocystis sp. PCC 6803 can adapt rapidly to the potent herbicide methyl viologen (MV). Genome sequencing revealed that the mutations responsible for adaptation to MV were already present prior to selection in the genomes of the unadapted parental strains at low allelic frequencies. This indicates that chromosomal polyploidy in bacteria can provide cells with a reservoir of conditionally beneficial mutations that can become rapidly enriched and fixed upon selection. MV-resistant strains performed oxygenic photosynthesis less efficiently than WTs when MV was absent, suggesting trade-offs in cellular fitness associated with the evolution of MV resistance and a possible role for balancing selection in the maintenance of these alleles under ecologically relevant growth conditions. Resistance was associated with reduced intracellular accumulation of MV. Our results indicate that genome polyploidy plays a role in the rapid adaptation of some bacteria to stressful conditions, which may include xenobiotics, nutrient limitation, environmental stresses, and seasonal changes.}, }
@article {pmid40118394, year = {2025}, author = {Cuecas, A and Delgado, JA and Gonzalez, JM}, title = {Inferring inter-phylum gene transfer events from unique genes detected in Parageobacillus thermoglucosidasius.}, journal = {Molecular phylogenetics and evolution}, volume = {207}, number = {}, pages = {108329}, doi = {10.1016/j.ympev.2025.108329}, pmid = {40118394}, issn = {1095-9513}, mesh = {*Gene Transfer, Horizontal ; *Phylogeny ; Genome, Bacterial ; Evolution, Molecular ; Genes, Bacterial ; }, abstract = {A pan-genome includes the complete pool of genes of a species including those recently acquired. The new additions of genetic material to a genome are frequently linked to horizontal gene transfer (HGT) processes and can confer adaptive advantages improving the recipient functional response and growth. Previous studies have reported that Parageobacillus have frequent DNA exchange mainly with other members of the phylum Bacillota sharing similar environments. Nevertheless, the occurrence of transfer events between phylogenetically distant microorganisms is scarcely known. In this work, based on the pan-genome of Parageobacillus thermoglucosidasius, we detected a number of unique genes within the species which were used to carry out BLAST searches to find out similar genes in distant bacteria taxa. We aimed to infer potential inter-phylum HGT events. Results suggested genetic exchanges among different phyla. Among them Actinomycetota, Pseudomonadota and the Bacteroidota/Chlorobiota group were the dominant observed phyla. Those HGT events frequently involved ATP binding cassette transporters, enzymes of the C metabolism and transcriptional regulators. Based on the frequency of these genes within specific phyla, directional HGT events could be proposed. A dominant origin of the suggested HGT events could be within the Bacillota. This exploratory analysis indicates that Bacillota are frequent exporters of DNA both within the phylum and to phylogenetically distant groups. Long-distance HGT can assist to better understand microbial evolution, the relevance of HGT processes within the prokaryotes and the genomic plasticity of microorganisms.}, }
@article {pmid40113085, year = {2025}, author = {Ding, J and Zhang, M and Chang, J and Hu, Z and He, P and Wang, J and Feng, L}, title = {Characterization of a multidrug-resistant hypovirulent ST1859-KL35 klebsiella quasipneumoniae subsp. similipneumoniae strain co-harboring tmexCD2-toprJ2 and blaKPC-2.}, journal = {Journal of global antimicrobial resistance}, volume = {42}, number = {}, pages = {253-261}, doi = {10.1016/j.jgar.2025.03.009}, pmid = {40113085}, issn = {2213-7173}, abstract = {OBJECTIVES: The rise of multidrug-resistant (MDR) Klebsiella pneumoniae is a significant public health threat. Klebsiella quasipneumoniae is often misidentified as K. pneumoniae, and its genetic and virulence traits remain underexplored. This study characterizes the genomic and phenotypic features of a K. quasipneumoniae subsp. similipneumoniae strain (KP24).<br><br>METHODS: Antibiotic susceptibility was tested using microbroth dilution assay. Virulence was evaluated through serum killing assay and Galleria mellonella infection model. Whole genome sequencing (WGS) and bioinformatics analysis determined sequence typing, resistance profiles, and plasmid types. Conjugation assays assessed plasmid transferability, while phylogenetic analysis explored genetic relationships.<br><br>RESULTS: KP24 exhibited an MDR phenotype, including resistance to carbapenems, ceftazidime/avibactam, and tigecycline. KP24 showed significantly higher serum survival and G. mellonella lethality than ATCC700603, though it was less virulent than the hypervirulent strain NUTH-K2044. WGS identified KP24 as ST1859 and KL35, harboring the aerobactin virulence gene cluster (iucABCDiutA) and multiple resistance genes, including tmexCD2-toprJ2, blaKPC-2, blaOXA-10, blaIMP-4, and qnrS1. Notably, the tmexCD2-toprJ2 and blaKPC-2 genes were located on the same plasmid (pKP24-1), an uncommon co-existence. Conjugation assays confirmed the independent transferability of pKP24-1 to Escherichia coli J53. Phylogenetic analysis revealed that ST1859 forms a distinct monoclade with low genetic diversity, closely related to ST334, suggesting regional expansion and potential global dissemination.<br><br>CONCLUSIONS: KP24 represents a hypovirulent yet multidrug-resistant strain of K. quasipneumoniae subsp. similipneumoniae, with a concerning combination of virulence and resistance determinants. The co-location of tmexCD2-toprJ2 and blaKPC-2 on a transferable plasmid highlights the potential for horizontal gene transfer of critical resistance mechanisms.}, }
@article {pmid40111106, year = {2025}, author = {Kogay, R and Wolf, YI and Koonin, EV}, title = {Horizontal Transfer of Bacterial Operons into Eukaryote Genomes.}, journal = {Genome biology and evolution}, volume = {17}, number = {4}, pages = {}, pmid = {40111106}, issn = {1759-6653}, mesh = {*Gene Transfer, Horizontal ; *Operon/genetics ; Phylogeny ; *Bacteria/genetics ; Evolution, Molecular ; *Eukaryota/genetics ; *Genome, Bacterial ; *Genome ; }, abstract = {In prokaryotes, functionally linked genes are typically clustered into operons, which are transcribed into a single mRNA, providing for the coregulation of the production of the respective proteins, whereas eukaryotes generally lack operons. We explored the possibility that some prokaryotic operons persist in eukaryotic genomes after horizontal gene transfer (HGT) from bacteria. Extensive comparative analysis of prokaryote and eukaryote genomes revealed 33 gene pairs originating from bacterial operons, mostly encoding enzymes of the same metabolic pathways, and represented in distinct clades of fungi or amoebozoa. This amount of HGT is about an order of magnitude less than that observed for the respective individual genes. These operon fragments appear to be relatively recent acquisitions as indicated by their narrow phylogenetic spread and low intron density. In 20 of the 33 horizontally acquired operonic gene pairs, the genes are fused in the respective group of eukaryotes so that the encoded proteins become domains of a multifunctional protein ensuring coregulation and correct stoichiometry. We hypothesize that bacterial operons acquired via HGT initially persist in eukaryotic genomes under a neutral evolution regime and subsequently are either disrupted by genome rearrangement or undergo gene fusion which is then maintained by selection.}, }
@article {pmid40111082, year = {2025}, author = {Maeda, K and Sumita, T and Nishi, O and Sushida, H and Higashi, Y and Nakagawa, H and Suzuki, T and Iwao, E and Fanani, MZ and Nishiya, Y and Iida, Y}, title = {Adaptive evolution of sesquiterpene deoxyphomenone in mycoparasitism by Hansfordia pulvinata associated with horizontal gene transfer from Aspergillus species.}, journal = {mBio}, volume = {16}, number = {4}, pages = {e0400724}, pmid = {40111082}, issn = {2150-7511}, support = {17H05022, 20H02993, 24K08919//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; //G-7 Scholarship Foundation/ ; }, mesh = {*Gene Transfer, Horizontal ; *Aspergillus/genetics/metabolism ; Solanum lycopersicum/microbiology ; Multigene Family ; *Sesquiterpenes/metabolism ; Plant Diseases/microbiology ; Cladosporium/drug effects ; *Evolution, Molecular ; Antifungal Agents/metabolism/pharmacology ; Phylogeny ; }, abstract = {UNLABELLED: Leaf mold caused by the ascomycete fungus Cladosporium fulvum is a devastating disease of tomato plants. The mycoparasitic fungus Hansfordia pulvinata is an effective biocontrol agent that parasitizes C. fulvum hyphae on leaves and secretes 13-deoxyphomenone, an eremophilane-type sesquiterpene, which was also identified as a sporulation-inducing factor in Aspergillus oryzae. Here, we identified deoxyphomenone biosynthesis (DPH) gene clusters conserved in both H. pulvinata and Aspergillus section Flavi, including A. oryzae and A. flavus. Functional disruption of DPH1 orthologous genes encoding sesquiterpene cyclase in H. pulvinata, A. oryzae, and its close relative A. flavus revealed that deoxyphomenone in H. pulvinata had exogenic antifungal activity against C. fulvum and controlled endogenic sporulation in Aspergillus species. Complete DPH clusters, highly similar to those in H. pulvinata, were exclusive to Aspergillus section Flavi, while species in other Aspergillus sections contained fragmented DPH clusters. A comparative genomics analysis revealed that these DPH gene clusters share a common origin and are horizontally transferred from an ancestor of Aspergillus to H. pulvinata. Our results suggest that after horizontal transfer, H. pulvinata maintained the DPH cluster as the inhibitory effect of deoxyphomenone on spore germination and mycelial growth contributed to its mycoparasitism on the host fungus C. fulvum.<br><br>IMPORTANCE: Tomato leaf mold disease caused by C. fulvum poses a significant economic threat to tomato production globally. Breeders have developed tomato cultivars with Cf resistance genes. C. fulvum frequently evolves new races that overcome these genetic defenses, complicating control efforts. Additionally, the pathogen has developed resistance to chemical fungicides, prompting the need for sustainable alternatives like biocontrol agents. The mycoparasitic fungus H. pulvinata is crucial as an effective agent against C. fulvum. Clarifying the mechanism of mycoparasitism is significant, as it enhances its application as a biocontrol agent against plant pathogens. This study revealed how H. pulvinata produces deoxyphomenone, an antifungal compound, through horizontal gene transfer from Aspergillus species. It is hypothesized that mycoparasitism could be one of the mechanisms that facilitated horizontal gene transfer between fungi. These insights facilitate the development of eco-friendly, sustainable agricultural practices by reducing dependence on chemical fungicides and promoting natural pathogen control methods.}, }
@article {pmid40110960, year = {2025}, author = {Xu, P and Liu, X and Ke, L and Li, K and Wang, W and Jiao, Y}, title = {The genomic insights of intertidal adaptation in Bryopsis corticulans.}, journal = {The New phytologist}, volume = {246}, number = {4}, pages = {1691-1709}, doi = {10.1111/nph.70083}, pmid = {40110960}, issn = {1469-8137}, support = {2021YFA0909600//the National Key R&amp;D Program of China/ ; 2021YFA1300403//the National Key R&amp;D Program of China/ ; JCTD-2022-06//CAS Youth Interdisciplinary Team/ ; 32221001//the National Natural Science Foundation of China/ ; 32222007//the National Natural Science Foundation of China/ ; YSBR-093//CAS project for Young Scientists in Basic Research/ ; }, mesh = {*Adaptation, Physiological/genetics ; *Genomics ; Phylogeny ; *Genome, Plant ; Gene Transfer, Horizontal/genetics ; }, abstract = {Many marine green algae thrive in intertidal zones, adapting to complex light environments that fluctuate between low underwater light and intense sunlight. Exploring their genomic bases could help to comprehend the diversity of adaptation strategies in response to environmental pressures. Here, we developed a novel and practical strategy to assemble high-confidence algal genomes and sequenced a high-quality genome of Bryopsis corticulans, an intertidal zone macroalga in the Bryopsidales order of Chlorophyta that originated 678 million years ago. Comparative genomic analyses revealed a previously overlooked whole genome duplication event in a closely related species, Caulerpa lentillifera. A total of 100 genes were acquired through horizontal gene transfer, including a homolog of the cryptochrome photoreceptor CRY gene. We also found that all four species studied in Bryopsidales lack key photoprotective genes (LHCSR, PsbS, CYP97A3, and VDE) involved in the xanthophyll cycle and energy-dependent quenching processes. We elucidated that the expansion of light-harvesting antenna genes and the biosynthesis pathways for siphonein and siphonaxanthin in B. corticulans likely contribute to its adaptation to intertidal light conditions. Our study unraveled the underlying special genetic basis of Bryopsis' adaptation to intertidal environments, advancing our understanding of plant adaptive evolution.}, }
@article {pmid40108678, year = {2025}, author = {Debroas, D}, title = {Global analysis of the metaplasmidome: ecological drivers and spread of antibiotic resistance genes across ecosystems.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {77}, pmid = {40108678}, issn = {2049-2618}, mesh = {*Plasmids/genetics ; *Ecosystem ; *Bacteria/genetics/drug effects/classification ; Humans ; *Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Interspersed Repetitive Sequences/genetics ; Genes, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Microbiota/genetics/drug effects ; }, abstract = {BACKGROUND: Plasmids act as vehicles for the rapid spread of antibiotic resistance genes (ARGs). However, few studies of the resistome at the community level distinguish between ARGs carried by mobile genetic elements and those carried by chromosomes, and these studies have been limited to a few ecosystems. This is the first study to focus on ARGs carried by the metaplasmidome on a global scale.<br><br>RESULTS: This study shows that only a small fraction of the plasmids reconstructed from 27 ecosystems representing 9 biomes are catalogued in public databases. The abundance of ARGs harboured by the metaplasmidome was significantly explained by bacterial richness. Few plasmids with or without ARGs were shared between ecosystems or biomes, suggesting that plasmid distribution on a global scale is mainly driven by ecology rather than geography. The network linking plasmids to their hosts shows that these mobile elements have thus been shared between bacteria across geographically distant environmental niches. However, certain plasmids carrying ARGs involved in human health were identified as being shared between multiple ecosystems and hosted by a wide variety of hosts. Some of these mobile elements, identified as keystone plasmids, were characterised by an enrichment in antibiotic resistance genes (ARGs) and CAS-CRISPR components which may explain their ecological success. The ARGs accounted for 9.2% of the recent horizontal transfers between bacteria and plasmids.<br><br>CONCLUSIONS: By comprehensively analysing the plasmidome content of ecosystems, some key habitats have emerged as particularly important for monitoring the spread of ARGs in relation to human health. Of particular note is the potential for air to act as a vector for long-distance transport of ARGs and accessory genes across ecosystems and continents. Video Abstract.}, }
@article {pmid40104036, year = {2025}, author = {Yang, SM and Gruber, A and Jiroutová, K and Richtová, J and Vancová, M and Tesařová, M and Masařová, P and Dorrell, RG and Oborník, M}, title = {Localization of heme biosynthesis in the diatom Phaeodactylum tricornutum and differential expression of multi-copy enzymes.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1537037}, pmid = {40104036}, issn = {1664-462X}, abstract = {Heme is essential for all organisms. The composition and location of the pathway for heme biosynthesis, have been influenced by past endosymbiotic events and organelle evolution in eukaryotes. Endosymbioses led to temporary redundancy of the enzymes and the genes involved. Genes were transferred to the nucleus from different endosymbiotic partners, and their multiple copies were either lost or retained, resulting in a mosaic pathway. This mosaic is particularly complex in organisms with eukaryote-derived plastids, such as diatoms. The plastids of diatoms are clearly derived from red algae. However, it is not entirely clear whether they were acquired directly from a red algal ancestor or indirectly in higher-order endosymbioses. In the diatom Phaeodactylum tricornutum, most enzymes of the pathway are present in a single copy, but three, glutamyl-tRNA synthetase (GluRS), uroporphyrinogen decarboxylase (UROD) and coproporphyrinogen oxidase (CPOX), are encoded in multiple copies. These are not direct paralogs resulting from gene duplication within the lineage but were acquired horizontally during the plastid endosymbioses. While some iso-enzymes originate from the host cell, others originate either from the genome of the cyanobacterial ancestor of all plastids or from the nuclear genome of the eukaryotic ancestor of the diatom complex plastid, a rhodophyte or an alga containing rhodophyte-derived plastids, a situation known as pseudoparalogy. Using green fluorescent protein-tagged expression and immunogold labeling, we experimentally localized all enzymes of the pathway in P. tricornutum, and confirmed their localization in the plastid, with a few possible exceptions. Our meta-analyses of transcription data showed that the pseudoparalogs are differentially expressed in response to nitrate starvation, blue light, high light, high CO2, and the cell cycle. Taken together, our findings emphasize that the evolution of complex plastids via endosymbiosis has a direct impact not only on the genetics but also on the physiology of resulting organisms.}, }
@article {pmid40102781, year = {2025}, author = {Yang, H and Gan, Y and Jiang, S and Zhu, X and Xia, Y and Gong, D and Xie, X and Gong, Y and Zhang, Y and Lei, Q and Wang, M and Li, J}, title = {Genomic alterations in Bacteroides fragilis favor adaptation in colorectal cancer microenvironment.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {269}, pmid = {40102781}, issn = {1471-2164}, support = {Guizhou Education Technology [2024] No. 335//Natural Science Research Project of Guizhou Education Department in 2024/ ; (Zunyi City, Kehe HZ character (2024) No. 303)//Zunyi city Science and Technology Program project/ ; Guizhou Science and Technology Platform Talents [2021]1350-038//Zunyi Medical University 2021 Special Project for Academic New Seedling Cultivation and Innovative Exploration/ ; No. gzwjkj2019-1-123//Science and Technology Fund Project of Guizhou Health Care Commission/ ; No. [2011]57//Governor's Special Fund for Outstanding Scientific and Technological Education Talents in Guizhou Province/ ; QJJ [2023] 019//Scientific Research Program of Guizhou Provincial Department of Education/ ; }, mesh = {*Bacteroides fragilis/genetics/pathogenicity/isolation &amp; purification ; Humans ; *Colorectal Neoplasms/microbiology/genetics/pathology ; *Tumor Microenvironment ; Genome, Bacterial ; Adaptation, Physiological/genetics ; Phylogeny ; Genomics ; Whole Genome Sequencing ; Virulence/genetics ; Enterotoxins/genetics/metabolism ; }, abstract = {BACKGROUND: The occurrence and development of colorectal cancer (CRC) is an incredibly long process that involves continuous changes in the tumor microenvironment. These constant changes may ultimately result in genetic alterations and changes in the metabolic processes of some symbiotic bacteria as a way to adapt to the changing environment. Patients with CRC exhibit an altered abundance of Bacteroides fragilis (B. fragilis) as indicated by several studies. To better understand the genomic characteristics and virulence spectrum of B. fragilis strains in tumor tissues, B. fragilis strains were isolated from tumor and paracancerous tissues of CRC patients.<br><br>METHODS: The isolates were identified using 16&#xa0;S rRNA sequencing, morphological analysis, physiological and biochemical characterization and PCR, and they were then subjected to whole genome sequencing (WGS) analysis.<br><br>RESULTS: A strain of B. fragilis enterotoxin (BFT) bft1-producing ZY0302 and a non-enterotoxin-producing B. fragilis ZY0804 were isolated from cancerous and paraneoplastic tissues, respectively. Analysis based on the core and nonessential genes showed that the genomic profiles of the isolates, ZY0302 and ZY0804, differed from those of B. fragilis from other tissue sources. This core and the co-evolution of non-essential genes may be the result of their adaptation to fluctuations in the tumor microenvironment and enhancing their survival. In addition, the ZY0302 and ZY0804 genomes underwent extensive horizontal gene transfer and varying degrees of genomic rearrangements, inversions, insertions, and deletion events, which may favor the enhancement of bacteria's ability to adapt to environmental changes. For instance, the virulence factors, such as the capsular biosynthesis gene clusters and components of the type IV secretion system, acquired through horizontal gene transfer, may facilitated B. fragilis in evading immune responses and managing oxidative stress. Moreover, our analysis revealed that multiple virulence factors identified in the isolates were mainly involved in bacterial adhesion and colonization, oxidative stress, iron acquisition, and immune evasion. This observation is worth noting given that enzymes such as neuraminidase, lipase, hemolysin, protease, and phosphatase, along with genes responsible for LPS biosynthesis, which are recognized for their association with the virulence of B. fragilis, were prevalent among the isolates.<br><br>CONCLUSIONS: In summary, it is our assertion that the alterations observed in both core and nonessential genes of B. fragilis, which have been isolated from tissues of colorectal cancer patients, along with significant instances of horizontal gene transfer to the genome, are likely intended to enhance adaptation to the evolving conditions of the tumor microenvironment. This study may provide new insights into the interaction between B. fragilis and the CRC microenvironment.}, }
@article {pmid40100768, year = {2025}, author = {Chen, YW and Su, YC and Chen, WY and Wu, JH and Chen, JW and Su, SL and Chen, CS and Tsai, PF and Ko, WC and Chen, PL}, title = {Comprehensive Genomic Analysis of Antimicrobial Resistance in Aeromonas dhakensis.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {31}, number = {4}, pages = {97-106}, doi = {10.1089/mdr.2024.0212}, pmid = {40100768}, issn = {1931-8448}, mesh = {*Aeromonas/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology ; beta-Lactamases/genetics ; Microbial Sensitivity Tests/methods ; Humans ; Phylogeny ; Multilocus Sequence Typing ; Genome, Bacterial/genetics ; *Drug Resistance, Multiple, Bacterial/genetics ; Taiwan ; Gram-Negative Bacterial Infections/microbiology/drug therapy ; Genomics/methods ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Aeromonas dhakensis is prevalent in aquatic environments in Taiwan and known for its notable antimicrobial resistance. However, comprehensive pan-genomic studies for this species in Taiwan are limited. This study analyzed 28 clinical A. dhakensis isolates using single-molecule real-time sequencing technology, coupled with diverse databases, to elucidate the whole genomes. The focus was on phylogenetic relatedness, antimicrobial resistance genes, and mobile genetic elements. Genomic analysis and multilocus sequence typing were utilized to identify A. dhakensis strains of heterogeneous origins. The detection of various β-lactamase genes (blacphA, blaimiH, blaAQU, blaOXA, blaTEM-1, blaTRU-1, and blaVEB) in clinical A. dhakensis isolates raises concern, especially considering the use of carbapenems and third-generation cephalosporins in patients with severe infections. Notably, most A. dhakensis strains carry chromosome-encoded β-lactamases, including AmpC, metallo-β-lactamase, and oxacillinase, and were susceptible to cefepime in drug susceptibility tests. A. dhakensis strains were also susceptible to aminoglycosides, fluoroquinolones, tigecycline, and trimethoprim/sulfamethoxazole. Three of the 28 A. dhakensis isolates carried plasmids containing an array of drug resistance genes, suggesting this species is likely a recipient or donor of drug resistance genes through horizontal gene transfer. Our findings provide valuable insights into the antimicrobial resistance of A. dhakensis, highlighting the medical implications of its β-lactamase diversity and its potential role in the horizontal gene transfer of drug resistance genes.}, }
@article {pmid40098486, year = {2025}, author = {Coluzzi, C and Rocha, EPC}, title = {The Spread of Antibiotic Resistance Is Driven by Plasmids Among the Fastest Evolving and of Broadest Host Range.}, journal = {Molecular biology and evolution}, volume = {42}, number = {3}, pages = {}, pmid = {40098486}, issn = {1537-1719}, mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; *Host Specificity ; Drug Resistance, Bacterial/genetics ; Bacteria/genetics/drug effects ; Evolution, Molecular ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; }, abstract = {Microorganisms endure novel challenges for which other microorganisms in other biomes may have already evolved solutions. This is the case of nosocomial bacteria under antibiotic therapy because antibiotics are of ancient natural origin and resistances to them have previously emerged in environmental bacteria. In such cases, the rate of adaptation crucially depends on the acquisition of genes by horizontal transfer of plasmids from distantly related bacteria in different biomes. We hypothesized that such processes should be driven by plasmids among the most mobile and evolvable. We confirmed these predictions by showing that plasmid species encoding antibiotic resistance are very mobile, have broad host ranges, while showing higher rates of homologous recombination and faster turnover of gene repertoires than the other plasmids. These characteristics remain outstanding when we remove resistance plasmids from our dataset, suggesting that antibiotic resistance genes are preferentially acquired and carried by plasmid species that are intrinsically very mobile and plastic. Evolvability and mobility facilitate the transfer of antibiotic resistance, and presumably of other phenotypes, across distant taxonomic groups and biomes. Hence, plasmid species, and possibly those of other mobile genetic elements, have differentiated and predictable roles in the spread of novel traits.}, }
@article {pmid40094923, year = {2025}, author = {Cinthi, M and Coccitto, SN and Simoni, S and Gherardi, G and Palamara, AT and Di Lodovico, S and Di Giulio, M and Du, XD and Vignaroli, C and Brenciani, A and Giovanetti, E}, title = {The optrA, cfr(D) and vanA genes are co-located on linear plasmids in linezolid- and vancomycin-resistant enterococcal clinical isolates in Italy.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {80}, number = {5}, pages = {1362-1370}, doi = {10.1093/jac/dkaf082}, pmid = {40094923}, issn = {1460-2091}, mesh = {*Plasmids/genetics ; *Linezolid/pharmacology ; Humans ; *Enterococcus faecium/genetics/drug effects/isolation &amp; purification ; *Enterococcus faecalis/genetics/drug effects/isolation &amp; purification ; *Gram-Positive Bacterial Infections/microbiology ; Anti-Bacterial Agents/pharmacology ; *Vancomycin-Resistant Enterococci/genetics/drug effects/isolation &amp; purification ; Microbial Sensitivity Tests ; *Drug Resistance, Multiple, Bacterial/genetics ; Italy ; *Bacterial Proteins/genetics ; *Carbon-Oxygen Ligases/genetics ; Genes, Bacterial ; Gene Transfer, Horizontal ; }, abstract = {OBJECTIVES: To characterize the optrA-, cfr(D)- and vanA-carrying linear plasmids detected in three MDR enterococcal clinical isolates.<br><br>METHODS: Enterococcus faecium (868), E. faecium (1001) and Enterococcus faecalis (2048), which were linezolid- and vancomycin-resistant due to the presence of optrA, cfr(D) and vanA genes, were tested for their susceptibility to several antibiotics. Characterization of the genetic elements carrying antibiotic resistance genes and ST determination were achieved using WGS data. The plasmid topology was evaluated by S1-PFGE. Resistance gene transferability was assessed by filter-mating experiments.<br><br>RESULTS: The linezolid- and vancomycin-resistant enterococci also showed resistance to tedizolid, chloramphenicol, tetracycline, erythromycin, ampicillin and levofloxacin. Both E. faecium 868 and E. faecium 1001 belonged to ST80 (included in clade A1), whereas E. faecalis 2048 was associated with ST6. WGS analysis revealed a plasmid co-localization of the optrA, cfr(D) and vanA genes. optrA was carried by Tn6674-like or Tn7695-like transposons; cfr(D) was associated with a truncated guaA gene, both flanked by IS1216 with opposite polarity; vanA was found on a Tn1546-like transposon containing IS1542 and IS1251 transposases. PFGE of S1 nuclease-treated and untreated DNAs displayed the linear topology of optrA-, cfr(D)- and vanA-harbouring plasmids. Only E. faecium 868 was able to transfer linezolid and vancomycin genes to an enterococcal recipient.<br><br>CONCLUSIONS: To the best of our knowledge this is the first report on the occurrence of a linear plasmid in E. faecalis. Linear plasmids can play a key role in the spread of oxazolidinone and glycopeptide resistance with serious consequences for public health.}, }
@article {pmid40093628, year = {2025}, author = {Oh, H and Choi, Y and Lee, J}, title = {Antibiotic-Resistant Salmonella in Animal Products Jeopardize Human Health.}, journal = {Food science of animal resources}, volume = {45}, number = {2}, pages = {409-428}, pmid = {40093628}, issn = {2636-0780}, abstract = {Despite the significance of antibiotics in treating bacterial infections, antibiotic resistance is continuously increasing, thus posing a significant threat. In addition to strains resistant to individual drugs, multidrug-resistant (MDR) and pandrug-resistant strains, are emerging. Salmonella, a primary cause of global foodborne illness, is often transmitted through animal products. Antibiotic treatment is crucial for immunocompromised individuals, such as older adults and patients with weakened immune systems, due to their increased susceptibility to severe effects. MDR Salmonella, which can arise following antibiotic use in food animals, may transfer to humans, leading to significant health challenges. The emergence of Salmonella strains resistant to carbapenems, often considered a last-resort antibiotic class, is particularly concerning. Salmonella neutralizes antibiotics through mechanisms, such as horizontal gene transfer via plasmids, efflux/influx system regulation, and enzyme production that deactivate or alter antibiotics. The rise of megaplasmids in Salmonella is particularly alarming, as it may enable resistance to a broader range of antibiotics. This review summarizes the current state of the growing threat of MDR Salmonella and underscores the urgent need for a coordinated response.}, }
@article {pmid40092036, year = {2025}, author = {Balta, I and Lemon, J and Gadaj, A and Cretescu, I and Stef, D and Pet, I and Stef, L and McCleery, D and Douglas, A and Corcionivoschi, N}, title = {The interplay between antimicrobial resistance, heavy metal pollution, and the role of microplastics.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1550587}, pmid = {40092036}, issn = {1664-302X}, abstract = {Environmental pollution with heavy metals (HMs) and microplastics (MPs) could enhance the global health challenge antimicrobial resistance (AMR). Herein, we explore the complicated mechanics of how HMs, MPs, and AMR are interlinked within microbial ecosystems, as well as the co-selection and cross-resistance mechanisms. Unlike antibiotics, HMs have influenced microbial evolution for billions of years, promoting resistance mechanisms that predate antibiotic resistance genes (ARGs). At the same time, this conundrum is further complicated by the pervasive spread of MPs in the aquatic and terrestrial environments, acting as substrates for bacterial pathogenic biofilms and accelerates the horizontal gene transfer (HGT) of ARGs and heavy metal resistance genes (MRGs). This review highlights that HMs such as lead (Pb), mercury (Hg), arsenic (As), chromium (Cr), cadmium (Cd), and nickel (Ni) have persistently selected for resistance traits through efflux systems and genetic co-regulation. Together, these interactions are amplified by MPs that create genetic exchange hotspots due to biofilm formation. These dynamics are modulated by organic matter, which serves both as a nutrient source and a mediator of HM bioavailability, directly influencing ARG abundance. Soil and water ecosystems, including riverine systems and landfill leachate, are reservoirs for ARGs and ARG-MRG combinations, with notable contributions originating from anthropogenic activities. This review also emphasizes the urgent need for integrated environmental and public health strategies to mitigate pollutant-driven AMR. This work seeks to approach HMs and MPs as synergistic drivers of AMR such that both HMs and MPs are upstream (causes) levers, a foundation from which future research on sustainable environmental management practices and health policy (One Health Approach), aimed at curbing the spread of resistance determinants can proceed.}, }
@article {pmid40090954, year = {2025}, author = {Lund, D and Parras-Moltó, M and Inda-Díaz, JS and Ebmeyer, S and Larsson, DGJ and Johnning, A and Kristiansson, E}, title = {Genetic compatibility and ecological connectivity drive the dissemination of antibiotic resistance genes.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2595}, pmid = {40090954}, issn = {2041-1723}, support = {2018-02835//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2018-05771//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2019-03482//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2022-00945//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; }, mesh = {*Gene Transfer, Horizontal ; *Bacteria/genetics/drug effects ; Humans ; *Phylogeny ; Wastewater/microbiology ; Genome, Bacterial ; Animals ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Microbiota/genetics/drug effects ; Genes, Bacterial ; Metagenome ; Drug Resistance, Bacterial/genetics ; }, abstract = {The dissemination of mobile antibiotic resistance genes (ARGs) via horizontal gene transfer is a significant threat to public health globally. The flow of ARGs into and between pathogens, however, remains poorly understood, limiting our ability to develop strategies for managing the antibiotic resistance crisis. Therefore, we aim to identify genetic and ecological factors that are fundamental for successful horizontal ARG transfer. We used a phylogenetic method to identify instances of horizontal ARG transfer in ~1 million bacterial genomes. This data was then integrated with >20,000 metagenomes representing animal, human, soil, water, and wastewater microbiomes to develop random forest models that can reliably predict horizontal ARG transfer between bacteria. Our results suggest that genetic incompatibility, measured as nucleotide composition dissimilarity, negatively influences the likelihood of transfer of ARGs between evolutionarily divergent bacteria. Conversely, environmental co-occurrence increases the likelihood, especially in humans and wastewater, in which several environment-specific dissemination patterns are observed. This study provides data-driven ways to predict the spread of ARGs and provides insights into the mechanisms governing this evolutionary process.}, }
@article {pmid40090302, year = {2025}, author = {Wang, J and Hu, Y and An, L and Wang, J and Wu, F and Gu, J and Wang, X and Tiedje, JM}, title = {An efficient strategy for bdd electrode drive electro-catalysis triggering active species on lincomycin and antibiotic resistance genes removal: Electron transfer based on calculation modeling.}, journal = {Journal of hazardous materials}, volume = {491}, number = {}, pages = {137915}, doi = {10.1016/j.jhazmat.2025.137915}, pmid = {40090302}, issn = {1873-3336}, abstract = {Identifying the degradation pathway and the final by-products is essential, as their ecological risks are pertinent to the advancement of this technology and its potential application in practical environmental pollution treatment. Elucidating the reaction mechanisms of the degradation system represents the most effective strategy for controlling this process. This study thoroughly revealed that indirect oxidation predominates throughout the electrochemical system, while direct oxidation serves a significant auxiliary role under the synergistic influence. It elucidates the critical importance of electron transfer behavior at the electrode surface for pollutant degradation and unveil potential mechanisms underlying primary degradation reactions via integrating charge density differences and Bader atomic charge analysis. In situ electrochemical infrared spectroscopy (In situ EC-FTIR) and density functional calculation (DFT) were used to analyze the final by-product generation path. It further elucidated the correlation between antibiotic resistance gene (ARGs) and binding strength among base pairs. The oxidative stress process of antibiotic resistance bacteria (ARB) was explained in detail. To comprehensively assess the impact of electrochemical treatment on environmental microbial communities, combined horizontal gene transfer (HGT) experiments were conducted to confirm that electrolytically treated wastewater does not induce ecological stress effects on microorganisms. Finally, a small cyclic electrochemical system was employed to evaluate both ecological impacts and economic benefits associated with wastewater treatment, thereby providing a novel theoretical framework for this domain.}, }
@article {pmid40086311, year = {2025}, author = {Pereira, AP and Almeida-Santos, AC and Duarte, B and Antunes, P and Peixe, L and Freitas, AR and Novais, C}, title = {Insights towards the impact of subinhibitory chlorhexidine on antimicrobial susceptibility and horizontal gene transfer in Enterococcus faecium.}, journal = {The Science of the total environment}, volume = {972}, number = {}, pages = {179064}, doi = {10.1016/j.scitotenv.2025.179064}, pmid = {40086311}, issn = {1879-1026}, mesh = {*Enterococcus faecium/genetics/drug effects ; *Gene Transfer, Horizontal ; *Chlorhexidine/pharmacology ; Microbial Sensitivity Tests ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; }, abstract = {Enterococcus faecium, a human and animal commensal broadly distributed in the environment, is currently one of the most challenging multidrug-resistant (MDR) healthcare-associated pathogens worldwide. It is often exposed to chlorhexidine (CHX), a broad-spectrum antiseptic, extensively used in healthcare, domestic, and food production settings, and a diffused polluter. However, the impact of gradients of CHX concentrations, including at subinhibitory levels, on E. faecium adaptation to various antimicrobials remains unclear. Our study aimed to explore the effects of subinhibitory CHX concentrations on biocides and antibiotics susceptibility as well as in the transfer of clinically relevant antibiotic resistance genes among E. faecium (n = 11) from diverse sources and clonal backgrounds. Serial exposure to increasing CHX concentrations resulted in strain-specific MICCHX and MBCCHX changes among six E. faecium studied. These strains presented different CHX genotypes, namely the P102H mutation in DNA-binding response regulator ChtR in two strains showing twofold increased MICCHX and/or MBCCHX, and an absent EfrEF transporter in a strain exhibiting increased CHX susceptibility after exposure. Whole-genome comparison between parental and CHX-adapted strains found no alterations in genes with a recognized role in CHX reduced susceptibility. Additionally, in a different assay, subinhibitory CHX exposure enhanced the transfer (up to 12.5-fold) of vancomycin or linezolid resistance genes among most E. faecium strains tested, except one lacking a functional EfrEF transporter. Our data suggest that subinhibitory CHX concentrations could have a role in Enterococcus adaptation to CHX and in the spread of antibiotic resistance through horizontal transfer events. Further investigation is warranted to elucidate the underlying mechanisms driving these phenomena in E. faecium, ensuring the continued effectiveness of both CHX and antibiotics, and safeguarding Public Health.}, }
@article {pmid40083414, year = {2025}, author = {Shi, G and Dai, Y and Zhou, D and Chen, M and Zhang, J and Bi, Y and Liu, S and Wu, Q}, title = {An alignment- and reference-free strategy using k-mer present pattern for population genomic analyses.}, journal = {Mycology}, volume = {16}, number = {1}, pages = {309-323}, pmid = {40083414}, issn = {2150-1203}, abstract = {Pangenomes are replacing single reference genomes to capture all variants within a species or clade, but their analysis predominantly leverages graph-based methods that require multiple high-quality genomes and computationally intensive multiple-genome alignments. K-mer decomposition is an alternative to graph-based pangenomes. However, how to directly use k-mers for the population genetic analyses is unknown. Here, we developed a novel strategy that uses the variants of k-mer count in the genome for population analyses. To test the effectivity of this method, we compared it directly to the SNP-based method on the analysis of population structure and genetic diversity of 267 Saccharomyces cerevisiae strains within two simulated datasets and a real sequence dataset. The population structure identified with k-mers recapitulates that obtained using SNPs, indicating the effectiveness of k-mer-based approach, and higher genetic diversity within real dataset supported k-mers contained more genetic variants. Based on k-mer frequency, we found not only SNP but also some insertion/deletion and horizontal gene transfer (HGT) fragments related to the adaptive evolution of S. cerevisiae. Our study creates a framework for the alignment- and reference-free (ARF) method in population genetic analyses, which will be more pronounced in the species with no complete genome or highly diverged species.}, }
@article {pmid40081886, year = {2025}, author = {Muleshkova, T and Bazukyan, I and Papadimitriou, K and Gotcheva, V and Angelov, A and Dimov, SG}, title = {Exploring the Multifaceted Genus Acinetobacter: the Facts, the Concerns and the Oppoptunities the Dualistic Geuns Acinetobacter.}, journal = {Journal of microbiology and biotechnology}, volume = {35}, number = {}, pages = {e2411043}, pmid = {40081886}, issn = {1738-8872}, mesh = {*Acinetobacter/genetics/classification/isolation &amp; purification ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Genetic Variation ; Phylogeny ; Humans ; Biodegradation, Environmental ; Acinetobacter Infections/microbiology ; }, abstract = {In recent years, the research community has been interested in members of the Acinetobacter genus mainly because of their role as causative agents of nosocomial infections. However, this rich-in-species genus has been proven to play a significant role in several biotechnological processes, such as bioremediation and fermented foods production. To partially fill the lack of information on Acinetobacter's dualistic nature, in this review, based on literature data, we attempt to summarize the available information on the different roles the members of the genus play by considering their genetic constitution and metabolic properties. We analyzed reports of genetic divergence between the pathogenic and non-pathogenic species and isolates, which can be explained by their high adaptability to the different ecological niches. In turn, this adaptability could result from intrinsic genetic variability due to mechanisms of horizontal genetic transfer, as well as high mutability determined by the expression of error-prone DNA polymerases. Yet, we concluded that further studies are needed, especially whole-genome sequencing of non-pathogenic isolates, which for the moment are relatively scarce.}, }
@article {pmid40081035, year = {2025}, author = {Qv, M and Dai, D and Wu, Q and Wang, W and Li, L and Zhu, L}, title = {Metagenomic insight into the horizontal transfer mechanism of fluoroquinolone antibiotic resistance genes mediated by mobile genetic element in microalgae-bacteria consortia.}, journal = {Journal of environmental management}, volume = {380}, number = {}, pages = {124946}, doi = {10.1016/j.jenvman.2025.124946}, pmid = {40081035}, issn = {1095-8630}, mesh = {*Microalgae/genetics ; *Gene Transfer, Horizontal ; *Fluoroquinolones ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; *Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; }, abstract = {Antibiotics could accumulate in the environment with the discharge of wastewater from families, hospitals and livestock farms, which intensifies the spread of resistance genes around the world. Although microalgae-bacteria consortia (MBC) can efficiently remove antibiotics, the horizontal transfer mechanism of antibiotics resistance genes in MBC is still rarely reported. In this study, the removal efficiency of ofloxacin, norfloxacin and enrofloxacin by MBC under different antibiotic concentrations was investigated, while resistance genes in the MBC were identified and the mechanism of horizontal transfer was disclosed. The results showed that norfloxacin removal efficiency (up to 56.35 %) surpassed that of ofloxacin and enrofloxacin. The abundance of the fluoroquinolone resistance gene QnrS8 was the highest at 1331. The horizontal transfer of resistance gene QnrS8 and QnrS11 were mainly mediated by transposons. Fluoroquinolones increased the abundance of Brevundimonas (<0.10 % up to 9.63 %) and Bosea (0.96 % up to 17.67 %) involved in antibiotic removal. Arthrobacter and Acidovorax might be potential hosts which carried fluoroquinolone resistance genes. Structural equation model indicated that the key factor influencing the fluoroquinolone resistance genes abundance in MBC was transposons. These findings drew an insightful understanding of MBC application for fluoroquinolone antibiotics removal and the horizontal transfer mechanism of fluoroquinolone resistance genes.}, }
@article {pmid40079731, year = {2025}, author = {Elmarghani, ED and Pettersson, JH and Atterby, C and Hickman, RA and Seng, S and San, S and Osbjer, K and Magnusson, U and Mourkas, E and Järhult, JD}, title = {Genomic insights into extended-spectrum β-lactamase- and plasmid-borne AmpC-producing Escherichia coli transmission between humans and livestock in rural Cambodia.}, journal = {Journal of medical microbiology}, volume = {74}, number = {3}, pages = {}, pmid = {40079731}, issn = {1473-5644}, mesh = {Humans ; Cambodia/epidemiology ; *beta-Lactamases/genetics ; Animals ; *Escherichia coli/genetics/isolation &amp; purification/drug effects/classification/enzymology ; *Escherichia coli Infections/transmission/epidemiology/microbiology/veterinary ; *Plasmids/genetics ; *Livestock/microbiology ; *Phylogeny ; *Bacterial Proteins/genetics ; *Rural Population ; Male ; Female ; Adult ; Middle Aged ; Whole Genome Sequencing ; Feces/microbiology ; Multilocus Sequence Typing ; Young Adult ; Anti-Bacterial Agents/pharmacology ; Child ; Adolescent ; }, abstract = {Introduction. The global spread of extended-spectrum cephalosporinase-producing Escherichia coli (producing extended-spectrum β-lactamase or plasmid-borne AmpC, hereafter ESC-Ec) is a major public health concern. Whilst extensively studied in high-income countries, the transmission pathways between humans and animals in low- and middle-income countries (LMICs) remain unclear. In rural Cambodia, the asymptomatic carriage and transmission dynamics of ESC-Ec between humans and animals living in close proximity are poorly understood, highlighting the need for targeted research in this area.Gap statement. An enhanced understanding of the genetic epidemiology of ESC-Ec can enable mitigation strategies to reduce the burden of disease and drug-resistant infections in LMIC settings.Aim. This study aimed to investigate the genetic relatedness and genotypic antibiotic resistance profiles of ESC-Ec strains from humans and livestock in rural Cambodia and to identify patterns of antimicrobial resistance (AMR) gene transmission between hosts and across households and villages.Methodology. Faecal samples were collected from 307 humans and 285 livestock in 100 households in or near Kampong Cham Province in rural Cambodia. From these samples, 108 ESC-Ec strains were subjected to whole-genome sequencing. Core genome MLST (cgMLST) and phylogenetic analysis determined genetic relationships between strains. All strains were screened for the presence of antibiotic resistance genes and plasmids.Results. Human and livestock isolates were assigned to six phylogroups, with phylogroup A being the most common (56.5%). MLST identified 50 sequence types (STs), 17 of which were shared between humans and animals, with ST155 being the most prevalent. cgMLST revealed 97 distinct cgMLST sequence types (cgST), indicating strain sharing between humans and animals. Additionally, AMR gene analysis showed widespread resistance, with genes from the bla CTX-M group detected in 84.2% of isolates. Notably, AMR genes such as aph(3'')-Ib-sul2 co-occurred in 50% of isolates. Finally, plasmid analysis identified IncF plasmids in 75.9% of isolates, likely facilitating AMR gene transmission across hosts.Conclusions. Our findings demonstrate that ESC-Ec strains and their AMR genes are transmitted between humans and livestock in rural Cambodia, likely driven by both clonal spread and plasmid-mediated horizontal gene transfer. These results highlight the urgent need for antimicrobial stewardship and infection control strategies to mitigate the spread of multidrug-resistant pathogens in both human and animal populations.}, }
@article {pmid40078948, year = {2024}, author = {Zhou, Z and Chen, H}, title = {Evaluating human exposure to antibiotic resistance genes.}, journal = {Biosafety and health}, volume = {6}, number = {2}, pages = {98-100}, pmid = {40078948}, issn = {2590-0536}, abstract = {Antibiotic resistance is an escalating global concern, leading to millions of annual fatalities. Antibiotic resistance genes (ARGs) present in bacteria equip them to withstand the effects of antibiotics. Intra- and interspecific ARGs transmission through horizontal gene transfer further exacerbates resistance dissemination. The presence of ARGs in the environment heightens the probability of human exposure via direct inhalation, ingestion, or contact with polluted air, food, or water, posing substantial biosafety and health hazards. Consequently, ARGs represent a critical focal point in public health and environmental safety and are classified as emerging contaminants. This perspective underscores the necessity to assess ARG exposure within the One Health framework and to accord greater attention to the mitigation strategies and tactics associated with ARGs.}, }
@article {pmid40078945, year = {2024}, author = {Zhai, W and Wang, Y and Sun, H and Fu, B and Zhang, Q and Wu, C and Shen, J and Liu, D and Wang, Y}, title = {Epidemiology and genetic characterization of tet(X4)-positive Klebsiella pneumoniae and Klebsiella quasipneumoniae isolated from raw meat in Chengdu City, China.}, journal = {Biosafety and health}, volume = {6}, number = {2}, pages = {116-124}, pmid = {40078945}, issn = {2590-0536}, abstract = {The rapid spread of mobile tigecycline resistance presents a significant public health threat, particularly with the increasing prevalence of tet(X4)-positive Enterobacterales across various species. This study aimed to investigate the epidemic features and transmission dynamics of tet(X4)-positive Klebsiella pneumoniae (K. pneumoniae) through the analysis of 206 raw meats, including pork (n = 182), beef (n = 16), duck (n = 5), and chicken (n = 3). These samples were collected from schools, markets, and restaurants in Chengdu City, China. A total of 25 isolates were obtained from 13 administrative regions. All isolates exhibited resistance to tetracycline, tigecycline, ampicillin, chloramphenicol, and florfenicol. Over half of the isolates also demonstrated resistance to streptomycin (80 %), sulfamethoxazole/trimethoprim (72 %), ciprofloxacin (64 %), and ampicillin/sulbactam (56 %). Among these strains, 14 distinct sequence types (STs) were identified, revealing evidence of inter-regional clonal spread, notably among 9 K. pneumoniae ST3393. Phylogenetic analysis revealed the presence of two K. pneumoniae ST5 closely resembling hypervirulent K. pneumoniae from Jiangsu. Importantly, 12 isolates were capable of transferring tigecycline resistance to Escherichia coli J53. Further plasmid analysis showed that the tet(X4)-harboring plasmids in K. pneumoniae could be classified into four types, primarily belonging to the IncFIA(HI1)/HI1A/HI1B hybrid plasmid (n = 16) and IncFII plasmid (n = 7), which significantly contributed to the cross-species dissemination of tet(X4). In summary, this study highlights the prevalence of MDR tet(X4)-positive K. pneumoniae in Chengdu, driven predominantly by clonal expansion and plasmid-mediated horizontal gene transfer. These findings emphasize the importance of continuous surveillance of tet(X4)-positive K. pneumoniae in raw meat and the implementation of effective measures to control their spread.}, }
@article {pmid40076423, year = {2025}, author = {Aguirre-Carvajal, K and Cárdenas, S and Munteanu, CR and Armijos-Jaramillo, V}, title = {Rampant Interkingdom Horizontal Gene Transfer in Pezizomycotina? An Updated Inspection of Anomalous Phylogenies.}, journal = {International journal of molecular sciences}, volume = {26}, number = {5}, pages = {}, pmid = {40076423}, issn = {1422-0067}, support = {PRG.BIO.23.14.01//Universidad de Las Am&#xe9;ricas/ ; }, mesh = {*Gene Transfer, Horizontal ; *Phylogeny ; *Ascomycota/genetics ; Evolution, Molecular ; Proteome/genetics ; }, abstract = {Horizontal gene transfer (HGT) is a significant source of diversity in prokaryotes and a key factor in their genome evolution. Although similar processes have been postulated for eukaryotes, the validity of HGT's impact remains contested, particularly between long-distance-related organisms like those from different kingdoms. Among eukaryotes, the fungal subphylum Pezizomycotina has been frequently cited in the literature for experiencing HGT events, with over 600 publications on the subject. The proteomes of 421 Pezizomycotina species were meticulously examined to identify potential instances of interkingdom HGT. Furthermore, the phylogenies of over 275 HGT candidates previously reported were revisited. Manual scrutiny of 521 anomalous phylogenies revealed that only 1.5% display patterns indicative of interkingdom HGT. Moreover, novel interkingdom HGT searches within Pezizomycotina yielded few new contenders, casting doubt on the prevalence of such events within this subphylum. Although the detailed examination of phylogenies suggested interkingdom HGT, the evidence for lateral gene transfer is not conclusive. The findings suggest that expanding the number of homologous sequences could uncover vertical inheritance patterns that have been misclassified as HGT. Consequently, this research supports the notion that interkingdom HGT may be an extraordinary occurrence rather than a significant evolutionary driver in eukaryotic genomes.}, }
@article {pmid40075357, year = {2025}, author = {Donkor, ES and Odoom, A and Osman, AH and Darkwah, S and Kotey, FCN}, title = {A systematic review and meta-analysis on antibiotic resistance genes in Ghana.}, journal = {BMC medical genomics}, volume = {18}, number = {1}, pages = {47}, pmid = {40075357}, issn = {1755-8794}, support = {D43 TW012487/TW/FIC NIH HHS/United States ; D43TW012487//the Fogarty International Center of the National Institutes of Health through the Research and Capacity Building in Antimicrobial Resistance in West Africa (RECABAW) Training Programme/ ; }, mesh = {Ghana ; Humans ; Animals ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects ; Genes, Bacterial ; }, abstract = {BACKGROUND: Addressing antimicrobial resistance (AMR) poses a complex challenge, primarily because of the limited understanding of bacterial antibiotic resistance genes (ARGs) and the spread of these genes across different domains. To bridge this knowledge gap in Ghana, we undertook a comprehensive systematic review and meta-analysis to quantify and estimate the prevalence of circulating ARGs in bacteria isolated from human, animal, and environmental sources.<br><br>METHODS: A thorough literature search was conducted across three major databases-Web of Science, PubMed, and Scopus-to retrieve all relevant articles related to ARGs in Ghana from the inception of the databases to February 25, 2024. A risk-of-bias evaluation was performed using the Newcastle-Ottawa Scale (NOS), and the data analysis involved descriptive statistics and proportional meta-analysis.<br><br>RESULTS: Of the 371 articles initially obtained, 38 met the inclusion criteria. These studies adequately covered Ghana geographically. The most prevalent ESBL gene identified was blaCTX-M, with a prevalence of 31.6% (95% CI: 17.6-45.7), followed by blaTEM (19.5% [95% CI: 9.7-29.3]), and blaSHV (3.5% [95% CI: 0.3-6.6]). The pooled prevalence of carbapenemase genes ranged from 17.2% (95% CI: 6.9-27.6) for blaNDM to 10.3% (95% CI: 1.9-18.7) for blaOXA. Additionally, other ARGs, including sul1, qnrS, gyrA, erm(B), and mecA, were detected, with prevalence ranging from 3.9% (95% CI: 0.0-8.5) to 16.4% (95% CI: 3.1-29.8). Several ARGs were shared across human, animal, and environmental sources.<br><br>CONCLUSION: This review revealed that bacteria obtained from human, animal, and environmental samples in Ghana shared genes associated with AMR. This finding provides evidence on the interconnection of AMR across these three domains. Horizontal gene transfer, which enables the dissemination of ARGs between genetically diverse bacteria, can occur, necessitating a multidisciplinary approach to addressing antimicrobial resistance in Ghana.}, }
@article {pmid40073489, year = {2025}, author = {Han, NN and Wang, XP and Jin, JA and Li, WH and Yang, WY and Fan, NS and Jin, RC}, title = {Underrated risk of antibiotic resistance genes dissemination mediated by bioaerosols released from anaerobic biological wastewater treatment system.}, journal = {Water research}, volume = {279}, number = {}, pages = {123463}, doi = {10.1016/j.watres.2025.123463}, pmid = {40073489}, issn = {1879-2448}, mesh = {*Wastewater/microbiology ; Aerosols ; *Drug Resistance, Microbial/genetics ; Anaerobiosis ; Anti-Bacterial Agents/pharmacology ; Waste Disposal, Fluid ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Antibiotic resistance has been recognized as one of the most prevalent public health problems. The bioaerosol-mediated spread of antibiotic resistance genes (ARGs) is an important but underrated pathway. Therefore, this work investigated the comprehensive resistome and pathogen-induced risk in bioaerosols released from anaerobic ammonium oxidation (anammox) process under antibiotic stress. The results showed that the bioaerosol oxidation potential increased by 2.7 times after the addition of sulfamethoxazole (SMX) into the anammox system. Based on the metagenomic analyses, abundant ARGs were enriched in bioaerosols, especially novA, olec, msbA and patA. There were many antibiotic resistance contigs carrying at least two mobile genetic elements (MGEs) in bioaerosols. Compared to the control, SMX caused the significant increase in ARGs proportion in plasmids from 11.4 % to 19.4 %. Similarly, the abundance of the type IV secretion system protein encoding genes (mtrA and mtrB) increased by 30.2 % and 31.5 %, respectively, which was conducive to gene transfer between bacteria. In addition, SMX stress induced the reactive oxygen species (ROS) production and the upregulation of genes related to membrane protein and DNA replication, further facilitating ARGs transfer. The co-occurrence networks showed that Aquamicrobium and Microbacterium probably were the hosts of most ARGs. Notably, four abundant human pathogens were detected in bioaerosols from the anammox system, which raised concerns on the health risk of resistant bioaerosol diffusion. These findings reveal the potential of horizontal gene transfer through bioaerosols and provide a guidance for systematically assessing the risk of environmental antibiotic resistance and relevant pathogens.}, }
@article {pmid40072588, year = {2025}, author = {Zeng, Q and Liu, Q and Pu, Y and Gong, P and Li, Y and Sun, Y and Hao, Y and Yang, Q and Wu, Y and Yang, B and Shi, S and Gong, Z}, title = {Impacts of Naphthenic Acids (NAs) Exposure on Soil Bacterial Community and Antibiotic Resistance Genes (ARGs) Dissemination.}, journal = {Current microbiology}, volume = {82}, number = {5}, pages = {188}, pmid = {40072588}, issn = {1432-0991}, support = {2022-MS-311//Natural Science Foundation of Liaoning Province/ ; JYTMS20231059//Basic Scientific Research Project of Education Department of Liaoning Province/ ; H2022011//Horizontal Scientific Research Project (Microbial-enhanced treatment of petroleum hydrocarbon pollutants: Technical and engineering demonstration)/ ; }, mesh = {*Soil Microbiology ; *Bacteria/genetics/drug effects/classification/metabolism ; *Carboxylic Acids/metabolism/pharmacology ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Denitrification ; Reactive Oxygen Species/metabolism ; Microbiota/drug effects/genetics ; Nitrification/drug effects ; }, abstract = {Naphthenic acids (NAs) are indigenous and complex components in petroleum. In the context of increasing global energy demand, the increasing extraction of fossil resources leads to increased environmental release of NAs, resulting in various environmental risks. However, the impact of NAs exposure on soil microorganisms remains still unclear. This study constructed a microcosm system to explore bacterial community structure and function, biological risk generation, and the mechanism of antibiotic resistance genes (ARGs) dissemination under NAs exposure. After 28 days of NAs stimulation, the denitrifying bacteria were enriched and the abundance of genes related to nitrogen cycle was up-regulated, enhancing nitrification and denitrification. Meanwhile, NAs stimulated the production of extracellular polymeric substances (EPS) and the accumulation of reactive oxygen species (ROS), as well as activated the glutathione antioxidant system. Furthermore, the cell metabolic, repair, and transfer regulatory pathways were enhanced under NAs exposure. The networks of ARGs with genera and mobile genetic elements (MGEs) indicated that NAs exposure promoted the enrichment of ARGs in hosts, the selective accumulation of MGEs, and the induction of horizontal gene transfer (HGT) of ARGs. This study will provide valuable perspectives of interactions between NAs and its microecological environment, as well as ARGs transfer mechanisms.}, }
@article {pmid40071515, year = {2025}, author = {Medina, JS and Zhang, S and Narayanasamy, S and Wang, C and Al-Gashgari, B and Hong, PY}, title = {Metagenomic Insights in Antimicrobial Resistance Threats in Sludge from Aerobic and Anaerobic Membrane Bioreactors.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {11}, pages = {5636-5646}, pmid = {40071515}, issn = {1520-5851}, mesh = {*Sewage/microbiology ; *Bioreactors ; Anaerobiosis ; Metagenomics ; Aerobiosis ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; }, abstract = {Sludge is a biohazardous solid waste that is produced during wastewater treatment. It contains antibiotic resistance genes (ARGs) that pose significant antimicrobial resistance (AMR) threats. Herein, aerobic and anaerobic membrane bioreactors (AeMBRs and AnMBRs, respectively) were compared in terms of the volume of waste sludge generated by them, the presence of ARGs in the sludge, and the potential for horizontal gene transfer (HGT) events using metagenomics to determine which treatment process can better address AMR concerns associated with the generation of waste sludge. The estimated abundance of ARGs in the suspended sludge generated by the AnMBR per treated volume is, on average, 5-55 times lower than that of sludge generated by the AeMBR. Additionally, the ratio of potential HGT in the two independent runs was lower in the anaerobic sludge (0.6 and 0.9) compared with that in the aerobic sludge (2.4 and 1.6). The AnMBR sludge exhibited reduced HGT of ARGs involving potential opportunistic pathogens (0.09) compared with the AeMBR sludge (0.27). Conversely, the AeMBR sludge displayed higher diversity and more transfer events, encompassing genes that confer resistance to quinolones, rifamycin, multidrug, aminoglycosides, and tetracycline. A significant portion of these ARGs were transferred to Burkholderia sp. By contrast, the AnMBR showed a lower abundance of mobile genetic elements associated with conjugation and exhibited less favorable conditions for natural transformation. Our findings suggest that the risk of potential HGT to opportunistic pathogens is greater in the AeMBR sludge than in AnMBR sludge.}, }
@article {pmid40069391, year = {2025}, author = {Huang, YX and Rao, HY and Su, BS and Lv, JM and Lin, JJ and Wang, X and Xu, LN and Kong, XD and Sun, Y}, title = {The pan-genome of Spodoptera frugiperda provides new insights into genome evolution and horizontal gene transfer.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {407}, pmid = {40069391}, issn = {2399-3642}, support = {32100355, 32100352, 31871964//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Spodoptera/genetics ; Animals ; *Gene Transfer, Horizontal ; *Evolution, Molecular ; *Genome, Insect ; Genetic Variation ; }, abstract = {Spodoptera frugiperda is a common and severely damaging agricultural pest. In-depth analysis of its population genomics and transcriptomics is crucial for providing references for pest control efforts. This study, focused on the extensive variation in the genome size of S. frugiperda, constructed its pan-genome and identified 1.37 Gb of non-reference sequences, highlighting significant genetic variation within the population. Analysis of Long Terminal Repeat (LTR) Presence/Absence Variation (PAV) suggests that LTR alterations may be one of the driving factors for genome size variation. Additionally, population gene PAV analysis revealed that variable genes are enriched in functions like acetyltransferase activity, which might be associated with detoxification, implying diverse selection pressures related to detoxification in different S. frugiperda populations. Moreover, 19 horizontal gene transfer (HGT) acquired genes were identified in the reference genome used in this study, which responded to 16 different treatments. Notably, three HGT-acquired genes (SFR02618, SFR05248, and SFR05249) co-expressed with heat shock protein family and responded under treatments with Avermectin and Cypermethrin. This may indicate their involvement in a detoxification mechanism coordinated with heat shock proteins. These results offering new insights into its genomic evolution and the potential functions of HGT-acquired genes.}, }
@article {pmid40069285, year = {2025}, author = {Masuyer, G and Taverner, A and MacKay, J and Lima Marques, AR and Wang, Y and Hunter, T and Liu, K and Mrsny, RJ}, title = {Discovery of mono-ADP ribosylating toxins with high structural homology to Pseudomonas exotoxin A.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {413}, pmid = {40069285}, issn = {2399-3642}, mesh = {*Exotoxins/chemistry/metabolism/genetics ; *Bacterial Toxins/chemistry/metabolism/genetics ; *Pseudomonas aeruginosa Exotoxin A ; *ADP Ribose Transferases/chemistry/metabolism/genetics ; Crystallography, X-Ray ; Virulence Factors/chemistry/metabolism/genetics ; Amino Acid Sequence ; Humans ; Models, Molecular ; Phylogeny ; Bacterial Proteins/chemistry/metabolism/genetics ; }, abstract = {Mono-ADP-ribosyl transferase (mART) proteins are secreted virulence factors produced by several human pathogens, the founding member being diphtheria toxin (DT). Pseudomonas aeruginosa can also secrete a mART toxin, known as exotoxin A (PE), but with an organization of its three functional domains (receptor, translocation, and enzymatic elements) that is opposite to DT. Two additional PE-like toxins (PLTs) have been identified from Vibrio cholerae and Aeromonas hydrophila, suggesting more PLT family members may exist. Database mining discovered six additional putative homologues, considerably extending this group of PLTs across a wide range of bacterial species. Here, we examine sequence and structural information for these new family members with respect to previously identified PLTs. The X-ray crystal structures of four new homologues show the conservation of critical features responsible for structure and function. This study shows the potential of these newly described toxins for the development of novel drug delivery platforms. Additionally, genomic analysis suggests horizontal gene transfer to account for the wide distribution of PLTs across a range of eubacteria species, highlighting the need to monitor emerging pathogens and their virulence factors.}, }
@article {pmid40066988, year = {2025}, author = {Mašlaňová, I and Kovařovic, V and Botka, T and Švec, P and Sedláček, I and Šedo, O and Finstrlová, A and Neumann-Schaal, M and Kirstein, S and Schwendener, S and Staňková, E and Rovňáková, K and Petráš, P and Doškař, J and Perreten, V and Pantůček, R}, title = {Evidence of in vitro mecB-mediated β-lactam antibiotic resistance transfer to Staphylococcus aureus from Macrococcus psychrotolerans sp. nov., a psychrophilic bacterium from food-producing animals and human clinical specimens.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {4}, pages = {e0165224}, pmid = {40066988}, issn = {1098-5336}, support = {LX22NPO5103, LM2023042, LM2023067, 90254//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy/ ; NIPH 75010330//Ministerstvo Zdravotnictv&#xed; Cesk&#xe9; Republiky/ ; MUNI/A/1603/2024//Masarykova Univerzita/ ; }, mesh = {Humans ; Animals ; *Staphylococcus aureus/genetics/drug effects ; Phylogeny ; *beta-Lactam Resistance/genetics ; *Anti-Bacterial Agents/pharmacology ; *Bacterial Proteins/genetics/metabolism ; Livestock/microbiology ; Whole Genome Sequencing ; Gene Transfer, Horizontal ; Genome, Bacterial ; *Enterococcaceae/genetics/isolation &amp; purification/drug effects ; Plasmids ; Staphylococcal Infections/microbiology ; }, abstract = {Macrococci are usually found as commensals on the skin and mucosa of animals and have been isolated from mammal-derived fermented foods; however, they can also act as opportunistic pathogens. Here, we used whole-genome sequencing, comparative genomics, extensive biotyping, MALDI-TOF mass spectrometry, and chemotaxonomy to characterize Macrococcus sp. strains isolated from livestock and human-related specimens. Based on the results of polyphasic taxonomy, we propose the species Macrococcus psychrotolerans sp. nov. (type strain NRL/St 95/376[T] = CCM 8659[T] = DSM 111350[T]) belonging to the Macrococcus caseolyticus phylogenetic clade. It grows at 4°C, and the core genome of the isolates contains suspected genes contributing to low-temperature tolerance. Variable genetic elements include prophages, chromosomal islands, a composite staphylococcal cassette chromosome island, and many plasmids that affect the overall genome expansion and adaptation to specific ecological settings of the studied isolates. Large plasmids carrying the methicillin resistance gene mecB were identified in M. psychrotolerans sp. nov. strains and confirmed as self-transmissible to Staphylococcus aureus in vitro. In addition to plasmids with circular topology, a 150-kb-long linear plasmid with 14.1-kb-long inverted terminal repeats, harboring many IS elements and putative genes for a type IV secretion system was revealed. The described strains were isolated from human clinical material, food-producing animals, meat, and a wooden cheese board and have the potential to proliferate at refrigerator temperatures. Their presence in the food chain and human infections indicates that attention needs to be paid to this potential novel opportunistic pathogen.IMPORTANCEThe study offers insights into the phenotypic and genomic features of a novel species of the genus Macrococcus that occurs in livestock, food, and humans. The large number of diverse mobile genetic elements contributes to the adaptation of macrococci to various environments. The ability of the described microorganisms to grow at refrigerator temperatures, enabled by genes that are predicted to contribute to low-temperature tolerance, raises food safety concerns. Confirmed in vitro conjugative transfer of plasmid-borne mecB gene to S. aureus poses a significant risk of spread of broad β-lactam resistance. In addition, the intergeneric plasmid transfer to S. aureus is indicative of horizontal gene transfer events that may be more frequent than generally accepted. Determining a complete sequence and gene content of linear megaplasmid with exceptional topology for the Staphylococcaceae family suggests its possible role in shuttling adaptive traits through an exchange of genetic information.}, }
@article {pmid40066273, year = {2025}, author = {Han, B and Feng, C and Jiang, Y and Ye, C and Wei, Y and Liu, J and Zeng, Z}, title = {Mobile genetic elements encoding antibiotic resistance genes and virulence genes in Klebsiella pneumoniae: important pathways for the acquisition of virulence and resistance.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1529157}, pmid = {40066273}, issn = {1664-302X}, abstract = {Klebsiella pneumoniae is an opportunistic pathogen primarily associated with nosocomial infections, characterized by a propensity for multi-drug resistance and the potential evolution into hypervirulent strains. Based on its phenotypic and genotypic characteristics, K. pneumoniae can be classified into two types: classical K. pneumoniae (cKP) and hypervirulent K. pneumoniae (hvKP). The spread of mobile genetic elements (MGEs) in K. pneumoniae has led to the emergence of carbapenem-resistant K. pneumoniae (CRKP) and carbapenem-resistant hypervirulent K. pneumoniae (CR-hvKP). The emergence of CR-hvKP is particularly concerning due to its multidrug resistance, high pathogenicity, and increased transmissibility. This review summarizes the types of MGEs present in K. pneumoniae, the mechanisms of horizontal gene transfer (HGT) mediated by these mobile elements, their roles in the dissemination of antibiotic resistance genes (ARGs) and virulence genes, and the relationships among MGEs that resemble Russian dolls or exhibit hybrid characteristics. Additionally, the clinical treatment and epidemiological characteristics of CR-hvKP are discussed. Given the high variability and transmissibility of MGEs, continuous monitoring and control of the variation and transmission of such genetic material in K. pneumoniae should be prioritized.}, }
@article {pmid40064777, year = {2025}, author = {Crespo-Bellido, A and Martin, DP and Duffy, S}, title = {Recombination Analysis of Geminiviruses Using Recombination Detection Program (RDP).}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2912}, number = {}, pages = {125-143}, pmid = {40064777}, issn = {1940-6029}, mesh = {*Geminiviridae/genetics ; *Recombination, Genetic ; Software ; Algorithms ; Sequence Alignment ; Genome, Viral ; Evolution, Molecular ; Computational Biology/methods ; Phylogeny ; }, abstract = {Geminiviruses are recombination-prone, and characterizing this evolutionary process within their genomes is a frequent goal of researchers. RDP is a stand-alone Windows program combining many algorithms that detect and characterize recombination. It has been widely used by the geminivirus community (and beyond). Here we describe the use of RDP4 and RDP5 for analysis of geminiviral nucleotide sequences including: (i) obtaining a reasonable dataset for analysis, (ii) making a credible multiple sequence alignment and (iii) analyzing an alignment with RDP on that alignment. RDP to both characterize recombination events and to produce statistically recombination-free datasets for other molecular evolution analyses.}, }
@article {pmid40063617, year = {2025}, author = {Gaona, M and Corral, J and Sánchez Osuna, M and Campoy, S and Barbé, J and Pérez-Varela, M and Aranda, J}, title = {Reciprocal regulation between Acinetobacter baumannii and Enterobacter cloacae AdeR homologs: implications for antimicrobial resistance and pathogenesis.}, journal = {PloS one}, volume = {20}, number = {3}, pages = {e0315428}, pmid = {40063617}, issn = {1932-6203}, mesh = {*Enterobacter cloacae/genetics/drug effects/pathogenicity ; *Acinetobacter baumannii/genetics/drug effects/pathogenicity ; *Bacterial Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Anti-Bacterial Agents/pharmacology ; Animals ; Drug Resistance, Bacterial/genetics ; Promoter Regions, Genetic ; Microbial Sensitivity Tests ; Virulence/genetics ; Mice ; Membrane Transport Proteins ; }, abstract = {Acinetobacter baumannii and Enterobacter cloacae are phylogenetically distant Gram-negative bacterial pathogens that represent significant challenges in healthcare settings due to their remarkable ability to acquire antimicrobial resistance. This study investigates one of the most important efflux pump systems in A. baumannii, AdeABC-AdeRS, and identifies homologous components in E. cloacae. By constructing isogenic knockout mutants, we show that the AdeB pump component and the AdeR regulator are significant for antimicrobial resistance and pathogenicity in A. baumannii. Through in silico predictions, we identify homologs of AdeB and AdeR (ECL_01758 and ECL_01761, respectively) in E. cloacae. Notably, we demonstrate that while the inactivation of the E. cloacae gene encoding the AdeB protein does not impact on pathogenesis and only alters colistin susceptibility, a knockout mutant of the gene encoding the AdeR regulator significantly affects susceptibility to various antimicrobial classes, motility, and virulence. Additionally, we demonstrate that the AdeR regulators of A. baumannii and E. cloacae can functionally substitute for each other both in vitro and in vivo conditions. Electrophoretic mobility shift assays reveal that these regulators are capable of binding to the promoter regions of each other's species, where similar DNA motifs are present. Furthermore, cross-complementation tests show that the affected phenotypes in each species can be restored interchangeably. Moreover, phylogenomic analysis of previously published E.cloacae genomes and reconstructrion of ancestral states through the phylogenetic trees of the adeB and adeR genes suggest that these homologs are more likely derived from a common ancestor rather than through recent horizontal gene transfer. The findings of this work highlight that conserved regulatory functions concerning efflux pump expression can be maintained across species despite evolutionary divergence and open new perspectives for the control of bacterial infections.}, }
@article {pmid40061860, year = {2025}, author = {Zhang, S and Yang, J and Abbas, M and Yang, Q and Li, Q and Liu, M and Zhu, D and Wang, M and Tian, B and Cheng, A}, title = {Threats across boundaries: the spread of ESBL-positive Enterobacteriaceae bacteria and its challenge to the "one health" concept.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1496716}, pmid = {40061860}, issn = {1664-302X}, abstract = {β-lactam antibiotics are essential medications for treating human diseases. The spread of extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-PE) exists globally in multiple reservoirs and the natural environment and poses an immense threat to public health. Plasmid incompatibility groups, such as IncFIA, IncI1, IncY, IncFIB, IncN, IncFIC, IncX4, IncB/O/K/Z, IncHI1/2, and IncA/C, which exist in humans, animals, and the environment, carrying bla CTX-M, bla TEM, and bla SHV genes. The ISEcp1 upstream and orf477 downstream of bla CTX-M genes, as well as other mobile genetic elements (MGEs) such as IS903 and IS26, are involved in capturing and mobilizing antibiotic-resistant genes (ARGs). The bla CTX-M-15 gene is the most common among all discussed reservoirs. The environmental reservoir and propagation mode of ESBL-PE are increasing and difficult to control. The reasons include but are not limited to bacterial adaptability and horizontal gene transfer (HGT) mediated by MGEs and plasmids. Conjugation is a pathway of HGT that is almost uncontrollable. MGEs and plasmids such as Tn3, IS1380 families, IncI1, IncK, and IncN are facilitating HGT of bla CTX-M genes. This review highlights the need to monitor trends in antimicrobial resistance (AMR) in the natural environment. Therefore, policies such as antibiotic management plans, training for healthcare providers and/or patients, cautious use of antibiotics, the need for epidemiological networks, pre-travel consultations, World Health Organization (WHO) infection control and biosafety guidelines, and other intervention measures are considered desirable.}, }
@article {pmid40058530, year = {2025}, author = {Smykal, V and Tobita, H and Dolezel, D}, title = {Evolution of circadian clock and light-input pathway genes in Hemiptera.}, journal = {Insect biochemistry and molecular biology}, volume = {180}, number = {}, pages = {104298}, doi = {10.1016/j.ibmb.2025.104298}, pmid = {40058530}, issn = {1879-0240}, abstract = {Circadian clocks are timekeeping mechanisms that help organisms anticipate periodic alterations of day and night. These clocks are widespread, and in the case of animals, they rely on genetically related components. At the molecular level, the animal circadian clock consists of several interconnected transcription-translation feedback loops. Although the clock setup is generally conserved, some important differences exist even among various insect groups. Therefore, we decided to identify in silico all major clock components and closely related genes in Hemiptera. Our analyses indicate several lineage-specific alterations of the clock setup in Hemiptera, derived from gene losses observed in the complete gene set identified in the outgroup, Thysanoptera, which thus presents the insect lineage with a complete clock setup. Nilaparvata and Fulgoroidea, in general, lost the (6-4)-photolyase, while all Hemiptera lost FBXL3, and several lineage-specific losses of dCRY and jetlag were identified. Importantly, we identified non-canonical splicing variants of period and m-cry genes, which might provide another regulatory mechanism for clock functioning. Lastly, we performed a detailed reconstruction of Hemiptera's light input pathway genetic repertoire and explored the horizontal gene transfer of cryptochrome-DASH from plant to Bemisia. Altogether, this inventory reveals important trends in clock gene evolution and provides a reference for clock research in Hemiptera, including several lineages of important pest species.}, }
@article {pmid40057108, year = {2025}, author = {Wang, Y and Song, Y and Zhang, D and Xing, C and Liang, J and Wang, C and Yang, X and Liu, Z and Zhao, Z}, title = {Effects of nitrogen-driven eutrophication on the horizontal transfer of extracellular antibiotic resistance genes in water-sediment environments.}, journal = {Environmental research}, volume = {274}, number = {}, pages = {121317}, doi = {10.1016/j.envres.2025.121317}, pmid = {40057108}, issn = {1096-0953}, mesh = {*Eutrophication ; *Nitrogen ; *Geologic Sediments/microbiology ; *Gene Transfer, Horizontal ; *Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Bacteria/genetics ; *Drug Resistance, Bacterial/genetics ; Water Pollutants, Chemical ; }, abstract = {Excessive nitrogen and other nutrients can trigger the eutrophication of freshwater bodies. Antibiotic resistance genes (ARGs) are now recognized as environmental pollutants, with extracellular ARGs (eARGs) being the dominant form in sediments. However, research on the propagation characteristics of eARGs remains limited. This study investigated the transfer characteristics of kanamycin resistance (KR) genes in the pEASY-T1 plasmid to intracellular DNA (iDNA) and extracellular DNA (eDNA) in water and sediment microenvironments under increasing nitrogen concentrations, as well as the community structure of free-living (FL) and particle-attached (PA) bacteria. The results revealed KR genes relative abundance in free extracellular DNA (f-eDNA) and adsorbed extracellular DNA (a-eDNA) of the water initially decreased and then increased with rising nitrogen concentrations. Its abundance in iDNA of the sediments decreased significantly with increasing nitrogen content, with relative abundance ranging from 5.09 × 10[-4] to 1.14 × 10[-3] copies/16SrRNA. The transfer from eDNA to iDNA in the water showed a rising and then falling trend as nitrogen concentration rose. The transfer of iDNA from the water to iDNA in sediments exhibited the opposite pattern. Additionally, copper (Cu) and zinc (Zn) were identified as key factors influencing the abundance of KR genes in the water, but total phosphorus (TP) was the primary determinant of KR gene distribution in sediments according to random forest analysis. These findings reveal novel mechanisms of eARG propagation in eutrophic environments, providing a theoretical foundation for managing antibiotic resistance in aquatic ecosystems.}, }
@article {pmid40056814, year = {2025}, author = {Yasemi, M and Jalali, A and Asadzadeh, M and Komijani, M}, title = {Organophosphate pesticides and their potential in the change of microbial population and frequency of antibiotic resistance genes in aquatic environments.}, journal = {Chemosphere}, volume = {376}, number = {}, pages = {144296}, doi = {10.1016/j.chemosphere.2025.144296}, pmid = {40056814}, issn = {1879-1298}, mesh = {*Pesticides/toxicity ; *Drug Resistance, Microbial/genetics ; *Water Pollutants, Chemical/toxicity/analysis ; Lakes/microbiology ; Bacteria/drug effects/genetics ; Wetlands ; Organophosphates/toxicity ; Microbiota/drug effects/genetics ; Metals, Heavy/toxicity ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology/toxicity ; beta-Lactamases/genetics/metabolism ; Metagenomics ; }, abstract = {Heavy metals (HMs) and pesticides disrupt aquatic biodiversity and microbial communities, contributing to antibiotic resistance via cross-resistance and co-selection mechanisms. This study investigates the relationship between organophosphorus pesticides (OPs), HMs, microbial diversity, and antibiotic resistance genes (ARGs) in eight lakes and wetlands. Microbial communities were analyzed via metagenomics methods, and data were processed using CLC Genomics Workbench 22. ARGs, including tetA, tetB, qnrA, qnrS, CIT, Fox, KPC, CTX-M1, DHA, GES, OXA, IMP, VEB, NDM1, SHV, TEM, CTX-M, PER, and MOX, were identified through polymerase chain reaction (PCR). Element concentrations and pesticide were quantified using inductively coupled plasma mass spectrometry and gas chromatography-mass spectrometry, respectively. The results indicate that environmental elements and pesticides significantly influence microbial diversity. Proteobacteria (Gamma, Beta, Alpha) dominate over other bacteria in all locations. β-Lactamase resistance genes have a significant positive correlations with the concentrations of boron, iron, lithium, magnesium, sodium, and phosphorus (P-value<0.05). Positive correlations between phosphorus, iron, and beta-lactamase genes suggest that higher concentrations of these elements may increase resistance likelihood by promoting resistant bacterial growth or facilitating gene transfer. Additionally, tetA and tetB exhibited a significant positive correlation with parathion concentration. The results showed that OPs and HMs increase antibiotic resistance by causing gene mutations, altering gene expression, and promoting horizontal gene transfer, resulting in multidrug-resistant strains. This highlights the need for monitoring these pollutants as they affect microbial diversity and accelerate antibiotic resistance. Targeted measures, such as bioremediation and pollution control, are essential to mitigate risks to the environment and public health.}, }
@article {pmid40056564, year = {2025}, author = {Singh, H and Bagra, K and Dixit, S and Singh, AK and Singh, G}, title = {Association of infrastructure and operations with antibiotic resistance potential in the dairy environment in India.}, journal = {Preventive veterinary medicine}, volume = {239}, number = {}, pages = {106497}, doi = {10.1016/j.prevetmed.2025.106497}, pmid = {40056564}, issn = {1873-1716}, mesh = {*Dairying/methods ; India ; Animals ; Cattle ; *Anti-Bacterial Agents/pharmacology ; Manure/microbiology ; *Drug Resistance, Microbial ; Wastewater/microbiology ; *Drug Resistance, Bacterial ; Soil Microbiology ; }, abstract = {The dairy industry in developing countries is often associated with inappropriate use of antibiotics and the subsequent contamination of the environment with co-selectors of antibiotic resistance. However, the specific factors in dairy farm environments that influence antibiotic resistance levels and the subsequent exposure risks to farm workers are unknown. We examined the link between the infrastructure and operations of the dairy farm and the antibiotic resistance potential in India, which is the highest producer and consumer of dairy products globally. We sampled sixteen dairy farms in the Dehradun district, India, that varied in their herd size, infrastructure, and operational features during winter, summer, and monsoon. We collected samples of dung, manure, wastewater, manure-amended, and control soil from these farms. We quantified six antibiotic resistance genes (ARGs) (sul1, sul2, parC, mcr5, ermF, and tetW), an integron integrase gene cassette (intI1), and 16S rRNA gene copies as an indicator for total bacterial count. We observed that the infrastructure and the operations of the dairy farms were significantly associated with antibiotic resistance potential in the dairy environment. For example, with increased ventilation and exposure to external weather, the levels of sul2 (x͂=10[-1.63]) and parC (x͂=10[-4.24]) in manure increased. When farmers administered antibiotics without veterinary consultation, the relative levels of intI1 (x͂=10[-2.36]), sul2 (x͂=10[-1.58]), and tetW (x͂=10[-3.04]) in manure were lower than the cases where professional advice was sought. Small-scale farms had lower relative ARG levels than medium- and large-scale farms, except for mcr5 (x͂=10[-3.98]) in wastewater. In different sample types, the relative ARG levels trended as manure-amended soil (x͂=10[-2.34]) > wastewater (x͂=10[-2.90])> manure (x͂=10[-3.39])> dung (x͂=10[-2.54]). ARGs correlated with the marker for horizontal gene transfer, intI1, which exacerbates overall antibiotic resistance levels. Exposure assessment showed that the agriculture farm workers working in manure-amended agriculture farms are exposed to higher antibiotic resistance potential than dairy farm workers, who manually handle dung. Our study showed that the link between the dairy infrastructure (ventilation and floor type) and operations (scale of operation and veterinary consultation) and the antibiotic resistance potential in the dairy farm environment was statistically significant. This knowledge paves the way for designing interventions that can minimize the antibiotic resistance potential on dairy farms and in affected environments and thus reduce the public health burden of antibiotic-resistant infections in the dairy industry and dairy workers in India.}, }
@article {pmid40056523, year = {2025}, author = {Zhang, Q and Fan, Y and Qian, X and Zhang, Y}, title = {Unraveling the role of microplastics in antibiotic resistance: Insights from long-read metagenomics on ARG mobility and host dynamics.}, journal = {Journal of hazardous materials}, volume = {490}, number = {}, pages = {137804}, doi = {10.1016/j.jhazmat.2025.137804}, pmid = {40056523}, issn = {1873-3336}, mesh = {*Microplastics/toxicity ; Biofilms ; Metagenomics ; *Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; *Water Pollutants, Chemical/toxicity ; Plasmids/genetics ; Bacteria/genetics/drug effects ; Genes, Bacterial ; *Drug Resistance, Bacterial/genetics ; }, abstract = {As two emerging pollutants, microplastics (MPs) potentially serve as vectors for antibiotic resistance genes (ARGs) in aquatic environments, but the mechanisms driving ARG enrichment remain unclear. This study used long-read metagenomics to investigate ARG mobility and hosts dynamics within the biofilms of MPs and rocks in different water environments. We identified distinct enrichment patterns for microbial communities and ARGs, highlighting the significant role of horizontal gene transfer in ARG enrichment. Specifically, plasmid-encoded ARGs varied significantly among MP biofilms, rock biofilms, and water samples, while chromosome-encoded ARGs remained consistent across these environments, emphasizing the impact of plasmids on ARG enrichment. Despite this, 55.1 % of ARGs were on chromosomes, indicating that host organisms also play a crucial role. The related mechanisms driving ARG enrichment included enhanced cell adhesion, increased transmembrane transporter activity, and responses to environmental stressors, which led to an increased presence of plasmid-encoded ARGs on MP biofilms, facilitating more frequent horizontal gene transfer. Additionally, the diversity of hosts on MPs was notably lower compared to the water column, with specific bacteria, including Herbaspirillu, Limnohabitans, Polaromonas, Variovorax, Rubrivivax, and Thauera significantly driving ARG enrichment. This study highlights key mechanisms and bacterial taxa involved in ARG dynamics on MPs.}, }
@article {pmid40056518, year = {2025}, author = {Zhu, Y and Li, R and Yan, S and Li, Y and Xie, S}, title = {Copper contamination determined the impact of phages on microbially-driven nitrogen cycling in coastal wetland sediments.}, journal = {Journal of hazardous materials}, volume = {490}, number = {}, pages = {137870}, doi = {10.1016/j.jhazmat.2025.137870}, pmid = {40056518}, issn = {1873-3336}, mesh = {*Wetlands ; *Copper/toxicity/analysis ; *Geologic Sediments/microbiology/chemistry ; *Bacteriophages/physiology ; *Nitrogen Cycle/drug effects ; *Water Pollutants, Chemical/toxicity/analysis ; Nitrogen/metabolism ; Bacteria/metabolism/genetics ; Denitrification ; }, abstract = {Phages have garnered increasing attention due to their potential roles in biogeochemical cycling. However, their impacts on nitrogen cycling have primarily been inferred from the presence of putative auxiliary metabolic genes (AMGs) and the virus-host linkage, despite of very limited direct experimental evidence. In this study, a series of microcosms were established with the inoculation of either native or non-native phages to simulate coastal wetlands with different phage sources and different levels of copper (Cu) contamination. Metagenomics and metatranscriptomics were combined to reveal phages' regulation on microbially-driven nitrogen cycling and to explore how the effects were mediated by Cu stress. Phages significantly impacted denitrification-related genes, with their effects depending on Cu level. Phages inhibited nirK-type denitrification under Cu stress but led to up-regulation of nirS gene in the treatments without Cu addition. Non-native phages also promoted the transcription of genes related to nitrogen assimilation and organic nitrogen transformation. Detection of viral AMGs involved in glutamate synthesis suggested that horizontal gene transfer may be a crucial pathway for phages to facilitate microbial nitrogen uptake. Overall, these findings enhance the understanding of phages' impact on biogeochemical metabolism in coastal wetland, offering novel insights into the links of phages' regulation on microbial nitrogen cycling with Cu stress.}, }
@article {pmid40052062, year = {2025}, author = {Liu, Y and Liu, L and Wang, X and Shao, M and Wei, Z and Wang, L and Li, B and Li, C and Luo, X and Li, F and Zheng, H}, title = {Microplastics enhance the prevalence of antibiotic resistance genes in mariculture sediments by enriching host bacteria and promoting horizontal gene transfer.}, journal = {Eco-Environment &amp; Health}, volume = {4}, number = {1}, pages = {100136}, pmid = {40052062}, issn = {2772-9850}, abstract = {Microplastics (MPs) and antibiotic resistance genes (ARGs) pose significant challenges to the One Health framework due to their intricate and multifaceted ecological and environmental impacts. However, the understanding of how MP properties influence ARG prevalence in mariculture sediments remains limited. Herein, the polystyrene (PS) and polyvinyl chloride (PVC) MPs with different sizes (20-120 μm and 0.5-2.0 mm) were selected to evaluate their impacts and underlying mechanisms driving ARGs dissemination. The results showed that PS and PVC MPs increased the relative abundance of ARGs by 1.41-2.50-fold and 2.01-2.84-fold, respectively, compared with control, particularly high-risk genes. The polymer type effect was identified as more influential than the size effect in driving the sediment resistome evolution. PVC shifted the microbial community assembly from stochastic to deterministic processes, thus enriching ARG host pathogens. Furthermore, the highly hydrophobic PS not only recruited the host bacteria colonization but also facilitated ARG exchange within the plastisphere. The exogenous additives released by PVC (e.g., heavy metals, bisphenol A, and tridecyl ester) and the particles synergistically promoted ARG conjugative transfer by inducing oxidative stress and enhancing cell membrane permeability. These findings revealed how MPs characteristics facilitated the spread of ARGs in marine benthic ecosystems, underscoring the importance of mitigating MPs pollution to maintain mariculture ecosystem health, prevent zoonotic diseases, and balance global mariculture with ecological health.}, }
@article {pmid40051841, year = {2025}, author = {Vivekanandan, KE and Kumar, PV and Jaysree, RC and Rajeshwari, T}, title = {Exploring molecular mechanisms of drug resistance in bacteria and progressions in CRISPR/Cas9-based genome expurgation solutions.}, journal = {Global medical genetics}, volume = {12}, number = {2}, pages = {100042}, pmid = {40051841}, issn = {2699-9404}, abstract = {Antibiotic resistance in bacteria is a critical global health challenge, driven by molecular mechanisms such as genetic mutations, efflux pumps, enzymatic degradation of antibiotics, target site modifications, and biofilm formation. Horizontal gene transfer (HGT) further accelerates the spread of resistance genes across bacterial populations. These mechanisms contribute to the emergence of multidrug-resistant (MDR) strains, rendering conventional antibiotics ineffective. Recent advancements in CRISPR/Cas9-based genome editing offer innovative solutions to combat drug resistance. CRISPR/Cas9 enables precise targeting of resistance genes, facilitating their deletion or inactivation, and provides a potential method to eliminate resistance-carrying plasmids. Furthermore, phage-delivered CRISPR systems show promise in selectively killing resistant bacteria while leaving susceptible strains unaffected. Despite challenges such as efficient delivery, off-target effects, and potential bacterial resistance to CRISPR itself, ongoing research and technological innovations hold promise for using CRISPR-based antimicrobials to reverse bacterial drug resistance and develop more effective therapies. These abstract highlights the molecular mechanisms underlying bacterial drug resistance and explores how CRISPR/Cas9 technology could revolutionize treatment strategies against resistant pathogens.}, }
@article {pmid40051073, year = {2025}, author = {Saranya, SV and Prathiviraj, R and Chellapandi, P}, title = {Mobilome-Mediated Speciation: Genomic Insights Into Horizontal Gene Transfer in Methanosarcina.}, journal = {Journal of basic microbiology}, volume = {}, number = {}, pages = {e70013}, doi = {10.1002/jobm.70013}, pmid = {40051073}, issn = {1521-4028}, support = {//The authors express their gratitude to the Science and Engineering Research Board, Ministry of Science and Technology, Government of India (EEQ/2020/000095), and RUSA 2.0: Biological Science, Government of India (12/BDU/RUSA/TRP/BS) for their financial support. Funded by Department of Science and Technology, Ministry of Science and Technology, India, Science and Engineering Research Board, Grant/Award Number EEQ/2020/000095. Ministry of Education, India, Rashtriya Uchchatar Shiksha Abhiyan, RUSA 2.0: Biological Science, Government of India (12/BDU/RUSA/TRP/BS)./ ; }, abstract = {Speciation in prokaryotes is often driven by complex genetic exchanges such as horizontal gene transfer (HGT), which facilitates genomic divergence and adaptation. In this study, we inferred the evolutionary transitions of the mobilome (plasmids, transposons, and phages) between Methanosarcina and bacteria in driving speciation within the Methanosarcina genus. By conducting evolutionary and phylogenetic analyses of Methanosarcina acetivorans, M. barkeri, M. mazei, and M. siciliae, we identified key mobilome elements acquired through HGT from distantly related bacterial species. These mobile genetic elements have shaped genomic plasticity, enabling Methanosarcina to adapt to diverse environmental niches and potentially facilitating lineage divergence. The acquisition of mobilome-associated genes involved in antibiotic resistance, DNA repair, and stress responses suggests their significant role in the ecological speciation of Methanosarcina. Overall, we hypothesized that their mobile genetic element might have been acquired from distantly related bacteria by HGT and subsequently established as new functional homologs in the present lineage. This study provides insight into how mobilome-mediated gene flow contributes to genomic divergence and speciation within microbial populations, highlighting the broader significance of mobilome in microbial evolution and speciation processes.}, }
@article {pmid40051064, year = {2025}, author = {Saranya, SV and Chellapandi, P}, title = {Convergent Evolution of Coenzyme Metabolism in Methanosarcina mazei: Insights Into Primitive Life and Metabolic Adaptations.}, journal = {Journal of basic microbiology}, volume = {}, number = {}, pages = {e70015}, doi = {10.1002/jobm.70015}, pmid = {40051064}, issn = {1521-4028}, support = {//This paper was supported by Science and Engineering Research Board, Ministry of Science and Technology, Government of India and RUSA 2.0: Biological Science, Government of India./ ; }, abstract = {The convergent evolution of coenzyme metabolism in methanogens provides critical insights into primitive life and metabolic adaptations. This study investigated the molecular evolution and functional dynamics of eight coenzymes and cofactors in Methanosarcina mazei, a model methanogen essential for methane production and energy conservation in anaerobic environments. Phylogenetic and genetic diversity analyses of the 706 protein sequences revealed conserved evolutionary trajectories interspersed with lineage-specific adaptations driven by gene duplication, horizontal gene transfer, and selective pressures. Key findings included the purifying selection of methanofuran (Tajima's D = -2.9589) and coenzyme A (Tajima's D = -2.8555), indicating the conservation of critical metabolic functions. The coenzyme B biosynthesis pathway showed balanced selection (Tajima's D = 2.38602), reflecting its evolutionary plasticity. Phylogenetic analyses linked coenzyme F420 biosynthetic enzymes closely to Methanosarcina horonobensis, while coenzyme F430 enzymes highlighted prokaryotic specialization distinct from their eukaryotes. Coenzyme M biosynthetic genes have demonstrated unique evolutionary connections with species across domains, such as Methanothermobacter thermautotrophicus and Gekko japonicus, emphasizing their broad adaptive significance. These evolutionary trajectories reveal how M. mazei optimized its metabolic pathways to thrive in extreme anaerobic environments, bridging ancient metabolic systems from the Last Universal Common Ancestor with contemporary ecological adaptations.}, }
@article {pmid40050512, year = {2025}, author = {Chacón, RD and Ramírez, M and Suárez-Agüero, D and Pineda, APA and Astolfi-Ferreira, CS and Ferreira, AJP}, title = {Genomic Differences in Antimicrobial Resistance and Virulence Among Key Salmonella Strains of Serogroups B and D1 in Brazilian Poultry.}, journal = {Current microbiology}, volume = {82}, number = {4}, pages = {173}, pmid = {40050512}, issn = {1432-0991}, support = {Finance Code 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; fellowship 1D//Conselho Nacional de Pesquisa e Desenvolvimento Tecnol&#xf3;gico/ ; }, mesh = {Animals ; Brazil ; *Salmonella/genetics/drug effects/classification/pathogenicity ; *Poultry/microbiology ; *Salmonella Infections, Animal/microbiology ; Virulence/genetics ; *Anti-Bacterial Agents/pharmacology ; *Serogroup ; *Poultry Diseases/microbiology ; *Genome, Bacterial ; *Virulence Factors/genetics ; *Drug Resistance, Bacterial/genetics ; Phylogeny ; Whole Genome Sequencing ; Microbial Sensitivity Tests ; Genomics ; }, abstract = {Salmonella is a significant threat to Brazilian poultry, causing economic losses and public health risks. This study analyzed 15 Salmonella isolates along with 45 retrieved complete genomes, including serovars Gallinarum, Pullorum, Enteritidis, Typhimurium, and Heidelberg. Biochemical characterization, antimicrobial susceptibility testing, whole-genome sequencing, and comparative genomics were performed. The studied strains exhibited high levels of antimicrobial resistance, particularly to tilmicosin, penicillin/novobiocin, nalidixic acid, and streptomycin. Genomic analysis revealed diverse virulence factors and antibiotic resistance genes (ARGs), with zoonotic strains showing higher virulence compared to avian-adapted strains. Multiple plasmid types carrying ARGs were identified, highlighting the potential for horizontal gene transfer. Pangenomic and phylogenomic analyses differentiated Salmonella strains from serogroup D1 from those from serogroup B. These findings emphasize the need for comprehensive surveillance and control measures to mitigate the impact of Salmonella on both animal and human health in Brazil.}, }
@article {pmid40048953, year = {2025}, author = {Tamai, S and Okuno, M and Ogura, Y and Suzuki, Y}, title = {Genetic diversity of dissolved free extracellular DNA compared to intracellular DNA in wastewater treatment plants.}, journal = {The Science of the total environment}, volume = {970}, number = {}, pages = {178989}, doi = {10.1016/j.scitotenv.2025.178989}, pmid = {40048953}, issn = {1879-1026}, mesh = {*Wastewater ; *Waste Disposal, Fluid/methods ; *Genetic Variation ; DNA ; Environmental Monitoring ; Drug Resistance, Microbial/genetics ; Halogenation ; }, abstract = {Dissolved free extracellular DNA (free-exDNA) coexists with intracellular DNA (inDNA) in aquatic environments. Free-exDNA can be taken up by bacteria through transformation, and wastewater treatment plants (WWTPs) are positioned as potential hot spots for genetic contamination. However, studies comparing the composition of free-exDNA and inDNA is limited. This study employed colloidal adsorption and foam concentration method to recover free-exDNA from different WWTP stages and compared its diversity with inDNA via metagenomic analysis. Free-exDNA concentrations were observed to increase after chlorination. Genetic analysis revealed a higher abundance of specific genes following chlorination, suggesting that free-exDNA in effluent originated from bacterial death in secondary treated water. This result indicates that free-exDNA, which increases due to chlorination, is subsequently released into the catchment. Additionally, several high-risk antibiotic-resistance genes (ARGs) were detected that colocalized with mobile genetic elements. These ARGs were expected to have a high potential for gene transfer via transformation, and the risk was highlighted. Overall, these findings deepen our understanding of horizontal gene transfer risks in WWTPs.}, }
@article {pmid40045656, year = {2025}, author = {Zhang, M and Zhao, X and Ren, X}, title = {Research Progress on the Mechanisms of Algal-Microorganism Symbiosis in Enhancing Large-Scale Lipid Production.}, journal = {Journal of agricultural and food chemistry}, volume = {73}, number = {11}, pages = {6345-6360}, doi = {10.1021/acs.jafc.4c11580}, pmid = {40045656}, issn = {1520-5118}, mesh = {*Microalgae/metabolism/genetics ; *Symbiosis ; Biofuels ; Bacteria/metabolism/genetics ; Lipids/biosynthesis ; Lipid Metabolism ; }, abstract = {Microalgae, characterized by their exceptional lipid content, rapid growth, and robust adaptability, represent a promising biological resource. In natural and engineered ecosystems, microalgae engage in intricate symbiotic relationships with diverse microorganisms, a dynamic interplay essential for ecological resilience and metabolic optimization. This review examines the role of symbiotic microorganisms in microalgal growth and lipid accumulation, with particular emphasis on the biological regulatory mechanisms that govern these processes. These include nutrient exchange, phytohormone-mediated growth stimulation, cofactors, and quorum-sensing-driven community coordination. The review highlights how these microbial interactions facilitate optimal lipid production by enhancing metabolic pathways, thereby improving the efficiency of lipid accumulation in microalgae. Furthermore, the review investigates horizontal gene transfer as an evolutionary driver that fortifies algal-microbial consortia against environmental stressors, enabling robust performance in fluctuating conditions. The integration of these biological insights holds transformative potential for advancing next-generation bioenergy platforms, where algal-microbial systems could play a pivotal role in enhancing biofuel production, wastewater treatment, and sustainable agriculture.}, }
@article {pmid40043931, year = {2025}, author = {Li, HQ and Wang, WL and Shen, YJ and Su, JQ}, title = {Mangrove plastisphere as a hotspot for high-risk antibiotic resistance genes and pathogens.}, journal = {Environmental research}, volume = {274}, number = {}, pages = {121282}, doi = {10.1016/j.envres.2025.121282}, pmid = {40043931}, issn = {1096-0953}, mesh = {*Wetlands ; *Bacteria/genetics ; *Microplastics ; Geologic Sediments/microbiology ; *Genes, Bacterial ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; *Water Pollutants, Chemical ; }, abstract = {Microplastics (MPs) are critical vectors for the dissemination of antibiotic resistance genes (ARGs); however, the prevalence and ecological risks of high-risk ARGs in mangrove ecosystems-globally vital yet understudied coastal habitats-remain poorly understood. To address this gap, this study investigated polyethylene, polystyrene, and polyvinyl chloride incubated in mangrove sediments for one month, focusing on high-risk ARGs, virulence gene (VGs), and pathogenic antibiotic-resistant bacteria within the mangrove plastisphere. High-throughput PCR and metagenomic analyses revealed that high-risk ARGs, VGs, and mobile genetic elements (MGEs) were significantly enriched on MPs compared to surrounding sediments. Pathogenic bacteria and MGEs were also more abundant in the plastisphere, highlighting its role as a hotspot for ARG dispersal. Metagenome-assembled genome analysis identified Pseudomonas and Bacillus as key hosts for ARGs, MGEs, and VGs, particularly multidrug resistance genes, integrase genes, and adherence factors. Notably, polystyrene harbored the highest abundance of pathogenic bacteria carrying ARGs, MGEs, and VGs, and mangrove root exudates were found to amplify horizontal gene transfer on MPs, uncovering a previously overlooked mechanism driving antibiotic resistance in coastal ecosystems. These findings not only elucidate how MPs accelerate the spread of ARGs, but also underscore the urgent need for targeted mitigation strategies to address the adverse impacts microplastic pollution on human, animal, and environmental health.}, }
@article {pmid40038805, year = {2025}, author = {Diricks, M and Maurer, FP and Dreyer, V and Barilar, I and Utpatel, C and Merker, M and Wetzstein, N and Niemann, S}, title = {Genomic insights into the plasmidome of non-tuberculous mycobacteria.}, journal = {Genome medicine}, volume = {17}, number = {1}, pages = {19}, pmid = {40038805}, issn = {1756-994X}, support = {2004//German Cystic Fibrosis Association Mukoviszidose e.V/ ; EXC 2167//The Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germanys Excellence Strategy Precision Medicine in Inflammation/ ; }, mesh = {*Plasmids/genetics ; *Nontuberculous Mycobacteria/genetics ; *Genome, Bacterial ; *Genomics/methods ; Humans ; Phylogeny ; Mycobacterium Infections, Nontuberculous/microbiology ; }, abstract = {BACKGROUND: Non-tuberculous mycobacteria (NTM) are a diverse group of environmental bacteria that are increasingly associated with human infections and difficult to treat. Plasmids, which might carry resistance and virulence factors, remain largely unexplored in NTM.<br><br>METHODS: We used publicly available complete genome sequence data of 328 NTM isolates belonging to 125 species to study gene content, genomic diversity, and clusters of 196 annotated NTM plasmids. Furthermore, we analyzed 3755 draft genome assemblies from over 200 NTM species and 5415 short-read sequence datasets from six clinically relevant NTM species or complexes including M. abscessus, M. avium complex, M. ulcerans complex and M. kansasii complex, for the presence of these plasmids.<br><br>RESULTS: Between one and five plasmids were present in approximately one-third of the complete NTM genomes. The annotated plasmids varied widely in length (most between 10 and 400 kbp) and gene content, with many genes having an unknown function. Predicted gene functions primarily involved plasmid replication, segregation, maintenance, and mobility. Only a few plasmids contained predicted genes that are known to confer resistance to antibiotics commonly used to treat NTM infections. Out of 196 annotated plasmid sequences, 116 could be grouped into 31 clusters of closely related sequences, and about one-third were found across multiple NTM species. Among clinically relevant NTM, the presence of NTM plasmids showed significant variation between species, within (sub)species, and even among strains within (sub)lineages, such as dominant circulating clones of Mycobacterium abscessus.<br><br>CONCLUSIONS: Our analysis demonstrates that plasmids are a diverse and heterogeneously distributed feature in NTM bacteria. The frequent occurrence of closely related putative plasmid sequences across different NTM species suggests they may play a significant role in NTM evolution through horizontal gene transfer at least in some groups of NTM. However, further in vitro investigations and access to more complete genomes are necessary to validate our findings, elucidate gene functions, identify novel plasmids, and comprehensively assess the role of plasmids in NTM.}, }
@article {pmid40036335, year = {2025}, author = {Bergman, S and Birk, C and Holmqvist, E}, title = {ProQ prevents mRNA degradation through inhibition of poly(A) polymerase.}, journal = {Nucleic acids research}, volume = {53}, number = {5}, pages = {}, doi = {10.1093/nar/gkaf103}, pmid = {40036335}, issn = {1362-4962}, support = {2016-03656//Swedish Research Council/ ; ICA16-0021//Swedish Foundation for Strategic Research/ ; }, mesh = {*Salmonella typhimurium/genetics/pathogenicity ; *Bacterial Proteins/metabolism/genetics ; *Polynucleotide Adenylyltransferase/metabolism/genetics ; *Sigma Factor/metabolism/genetics ; *RNA Stability ; *RNA, Messenger/metabolism/genetics ; *Biofilms/growth &amp; development ; *Gene Expression Regulation, Bacterial ; RNA-Binding Proteins/metabolism/genetics ; 3' Untranslated Regions/genetics ; Polyadenylation ; }, abstract = {The RNA-binding protein ProQ interacts with many transcripts in the bacterial cell. ProQ binding is associated with increased messenger RNA (mRNA) levels, but a mechanistic explanation for this effect has been lacking. In Salmonella Typhimurium, ProQ affects key traits associated with infection, including motility and intracellular survival. However, the direct links between ProQ activity and these phenotypes are not well understood. Here, we demonstrate that ProQ promotes biofilm formation, another virulence-associated phenotype. This effect is strictly dependent on sigma factor RpoS. ProQ increases both RpoS protein and rpoS mRNA levels, but neither affects rpoS transcription nor translation. The rpoS mRNA is a ProQ target, and expression of the rpoS 3'UTR alone is strongly dependent on ProQ. RpoS expression becomes independent of ProQ in strains lacking poly(A) polymerase I (PAPI), indicating that ProQ protects against 3' end-dependent decay. Indeed, purified ProQ inhibits PAPI-mediated polyadenylation at RNA 3' ends. Finally, PAPI is required for ProQ's effect on expression of genes involved in biofilm, motility, osmotic stress, and virulence, indicating that inhibition of polyadenylation is a general function of ProQ.}, }
@article {pmid40035762, year = {2025}, author = {Raymond, JA}, title = {A horizontally transferred bacterial gene aids the freezing tolerance of Antarctic bdelloid rotifers.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {10}, pages = {e2421910122}, pmid = {40035762}, issn = {1091-6490}, support = {OPP-9814294//National Science Foundation (NSF)/ ; OPP-088000//National Science Foundation (NSF)/ ; }, mesh = {Antarctic Regions ; *Gene Transfer, Horizontal ; *Freezing ; Animals ; *Rotifera/genetics ; Genes, Bacterial ; Antifreeze Proteins/genetics/metabolism ; }, abstract = {Bdelloid rotifers are well known for their abilities to survive long periods of freezing as well as acquire foreign genes. Recently sequenced genomes of some bdelloid rotifers in England were found to encode several proteins similar to ice-binding proteins (IBPs) that are usually associated with freeze-thaw tolerance. Here, I describe bdelloid rotifers inhabiting an algal patch in Antarctica that have multiple homologs of these genes. Structures of the proteins predicted by AlphaFold show that they are well designed for ice-binding and a recombinant protein made for one of them showed strong ice-binding activity. The existence of multiple copies of these proteins is another characteristic of IBPs. Furthermore, multiple bdelloid rotifers in the algal patch were revived in less than an hour after storage at -25 °C for 24 y, an apparent record for laboratory-controlled studies. Several characteristics of these genes point to bacteria as their source: sequence homology, absence of introns, and a structural peculiarity so far found only in bacteria. The remarkable freezing tolerance of bdelloid rotifers can thus be at least partially attributed to horizontally acquired bacterial genes encoding IBPs.}, }
@article {pmid40035521, year = {2025}, author = {Kanakapura Sundararaj, B and Goyal, M and Samuelson, J}, title = {Targets for the diagnosis of Acanthamoeba eye infections include four cyst wall proteins and the mannose-binding domain of the trophozoite mannose-binding protein.}, journal = {mSphere}, volume = {10}, number = {3}, pages = {e0094824}, pmid = {40035521}, issn = {2379-5042}, support = {R01 GM129324/GM/NIGMS NIH HHS/United States ; Emerging Pathogens Initiative (EPI)//Howard Hughes Medical Institute (HHMI)/ ; }, mesh = {*Acanthamoeba/genetics/metabolism ; *Microscopy, Confocal ; *Trophozoites/metabolism ; *Protozoan Proteins/genetics/metabolism ; Animals ; Rabbits ; Humans ; Mannose-Binding Lectin/genetics/metabolism ; Amebiasis/diagnosis/parasitology ; Antibodies, Protozoan/immunology ; Cell Wall/metabolism/chemistry ; Acanthamoeba Keratitis/diagnosis/parasitology ; }, abstract = {Acanthamoebae, which are free-living amoebae, cause corneal inflammation (keratitis) and blindness, if not quickly diagnosed and effectively treated. The walls of Acanthamoeba cysts contain cellulose and have two layers connected by conical ostioles. Cysts are identified by in vivo confocal microscopy of the eye or calcofluor-white- or Giemsa-labeling of corneal scrapings, both of which demand great expertise. Trophozoites, which use a mannose-binding protein to adhere to keratinocytes, are identified in eye cultures that delay diagnosis and treatment. We recently used structural and experimental methods to characterize cellulose-binding domains of Luke and Leo lectins, which are abundant in the inner layer and ostioles. However, no antibodies have been made to these lectins or to a Jonah lectin and a laccase, which are abundant in the outer layer. Here, confocal microscopy of rabbit antibodies (rAbs) to recombinant Luke, Leo, Jonah, and laccase supported localizations of GFP-tagged proteins in walls of transfected Acanthamoebae. rAbs efficiently detected calcofluor white-labeled cysts of 10 of the 11 Acanthamoeba isolates tested, including six T4 genotypes that cause most cases of keratitis. Further, laccase shed into the medium during encystation was detected by an enzyme-linked immunoassay. Structural and experimental methods identified the mannose-binding domain (ManBD) of the Acanthamoeba mannose-binding protein, while rAbs to the ManBD efficiently detected DAPI-labeled trophozoites from all 11 Acanthamoeba isolates tested. We conclude that antibodies to four cyst wall proteins and the ManBD efficiently identify Acanthamoeba cysts and trophozoites, respectively.IMPORTANCEFree-living amoeba in the soil or water cause Acanthamoeba keratitis, which is diagnosed by identification of unlabeled cysts by in vivo confocal microscopy of the eye or calcofluor-white (CFW) labeled cysts by fluorescence microscopy of corneal scrapings. Alternatively, Acanthamoeba infections are diagnosed by the identification of trophozoites in eye cultures. Here, we showed that rabbit antibodies (rAbs) to four abundant cyst wall proteins (Jonah, Luke, Leo, and laccase) each efficiently identify CFW-labeled cysts of 10 of the 11 Acanthamoeba isolates tested. Further, laccase released into the medium by encysting Acanthamoebae was detected by an enzyme-linked immunoassay. We also showed that rAbs to the mannose-binding domain (ManBD) of the Acanthamoeba mannose-binding protein, which mediates adherence of trophozoites to keratinocytes, efficiently identify DAPI-labeled trophozoites of all 11 Acanthamoeba isolates tested. In summary, four wall proteins and the ManBD appear to be excellent targets for the diagnosis of Acanthamoeba cysts and trophozoites, respectively.}, }
@article {pmid40032822, year = {2025}, author = {Biller, SJ and Ryan, MG and Li, J and Burger, A and Eppley, JM and Hackl, T and DeLong, EF}, title = {Distinct horizontal gene transfer potential of extracellular vesicles versus viral-like particles in marine habitats.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2126}, pmid = {40032822}, issn = {2041-1723}, support = {OCE-2049004//National Science Foundation (NSF)/ ; OCE-2304066//National Science Foundation (NSF)/ ; 917971//Simons Foundation/ ; }, mesh = {*Gene Transfer, Horizontal ; *Extracellular Vesicles/metabolism ; *Ecosystem ; Seawater/microbiology/virology ; Interspersed Repetitive Sequences ; Viruses/genetics/metabolism ; }, abstract = {Horizontal gene transfer (HGT) is enabled in part through the movement of DNA within two broad groups of small (<0.2 µm), diffusible nanoparticles: extracellular vesicles (EVs) and virus-like particles (VLPs; including viruses, gene transfer agents, and phage satellites). The information enclosed within these structures represents a substantial portion of the HGT potential available in planktonic ecosystems, but whether some genes might be preferentially transported through one type of nanoparticle versus another is unknown. Here we use long-read sequencing to compare the genetic content of EVs and VLPs from the oligotrophic North Pacific. Fractionated EV-enriched and VLP-enriched subpopulations contain diverse DNA from the surrounding microbial community, but differ in their capacity and encoded functions. The sequences carried by both particle types are enriched in mobile genetic elements (MGEs) as compared with other cellular chromosomal regions, and we highlight how this property enables novel MGE discovery. Examining the Pelagibacter mobilome reveals >7200 distinct chromosomal fragments and MGEs, many differentially partitioned between EVs and VLPs. Together these results suggest that distinctions in nanoparticle contents contribute to the mode and trajectory of microbial HGT networks and evolutionary dynamics in natural habitats.}, }
@article {pmid40032228, year = {2025}, author = {Jiang, Z and Zeng, J and Wang, X and Yu, H and Yue, L and Wang, C and Chen, F and Wang, Z}, title = {Biodegradable microplastics and dissemination of antibiotic resistance genes: An undeniable risk associated with plastic additives.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {372}, number = {}, pages = {125952}, doi = {10.1016/j.envpol.2025.125952}, pmid = {40032228}, issn = {1873-6424}, mesh = {*Microplastics/toxicity ; *Escherichia coli/genetics/drug effects ; *Gene Transfer, Horizontal ; *Polyesters ; *Drug Resistance, Microbial/genetics ; *Biodegradable Plastics ; Dibutyl Phthalate/toxicity ; Plasticizers/toxicity ; Biodegradation, Environmental ; }, abstract = {Biodegradable plastics (BDPs) represent a promising alternative to conventional plastics; however, the release of microplastics (MPs) during degradation necessitates an urgent investigation into their biological effects. The potential risks associated with MPs and additives released from BDPs, particularly in facilitating the dissemination of antibiotic resistance genes (ARGs), remain largely unknown. This study aims to investigate the effects of polylactic acid (PLA) MPs and their common plasticizer, dibutyl phthalate (DBP), on the horizontal gene transfer (HGT) of ARGs using conjugative transfer and transformation model systems. The viability of Escherichia coli (E. coli) cells after exposure to PLA MPs (0.01, 0.1, 1, and 10 mg L[-1]), DBP (0.01, 0.1, 1, and 10 μg L[-1]) alone, or in combination (1 mg L[-1] PLA MPs + 1 μg L[-1]DBP) remained unaffected. Exposure to PLA MPs at environmentally relevant concentrations did not promote the HGT of ARGs. However, the addition of DBP significantly enhanced the transfer frequency by 1.5-1.8 folds compared to exposure to PLA MPs alone. The accelerated dissemination of ARGs was primarily attributed to the elevated levels of reactive oxygen species (by 26.2%), increased membrane permeability (by 19.4%), and the up-regulation of genes involved in mating pair formation (by 1.6-3.8 folds) and DNA translocation (by 1.5-3.4 folds). These findings underscore the critical role of additives and highlight the potential accumulative effects associated with prolonged exposure to high concentrations of PLA MPs, which should be considered for a comprehensive risk assessment of BDPs.}, }
@article {pmid40029705, year = {2025}, author = {Hong, J and Xue, W and Wang, T}, title = {Emergence of alternative stable states in microbial communities undergoing horizontal gene transfer.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {40029705}, issn = {2050-084X}, support = {12401660//National Natural Science Foundation of China/ ; HSE499011086//Shenzhen Institue of Synthetic Biology Scientific Research Program/ ; }, mesh = {*Gene Transfer, Horizontal ; *Microbiota/genetics ; Bacteria/genetics ; Models, Theoretical ; Microbial Interactions/genetics ; Interspersed Repetitive Sequences/genetics ; Ecosystem ; }, abstract = {Microbial communities living in the same environment often display alternative stable states, each characterized by a unique composition of species. Understanding the origin and determinants of microbiome multistability has broad implications in environments, human health, and microbiome engineering. However, despite its conceptual importance, how multistability emerges in complex communities remains largely unknown. Here, we focused on the role of horizontal gene transfer (HGT), one important aspect mostly overlooked in previous studies, on the stability landscape of microbial populations. Combining mathematical modeling and numerical simulations, we demonstrate that, when mobile genetic elements (MGEs) only affect bacterial growth rates, increasing HGT rate in general promotes multistability of complex microbiota. We further extend our analysis to scenarios where HGT changes interspecies interactions, microbial communities are subjected to strong environmental selections and microbes live in metacommunities consisting of multiple local habitats. We also discuss the role of different mechanisms, including interspecies interaction strength, the growth rate effects of MGEs, MGE epistasis and microbial death rates in shaping the multistability of microbial communities undergoing HGT. These results reveal how different dynamic processes collectively shape community multistability and diversity. Our results provide key insights for the predictive control and engineering of complex microbiota.}, }
@article {pmid40027803, year = {2025}, author = {Christman, ND and Dalia, AB}, title = {The molecular basis for DNA-binding by competence T4P is distinct in Gram-positive and Gram-negative species.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.17.638644}, pmid = {40027803}, issn = {2692-8205}, abstract = {UNLABELLED: Competence type IV pili (T4P) are bacterial surface appendages that facilitate DNA uptake during horizontal gene transfer by natural transformation. These dynamic structures actively extend from the cell surface, bind to DNA in the environment, and then retract to import bound DNA into the cell. Competence T4P are found in diverse Gram-negative (diderm) and Gram-positive (monoderm) bacterial species. While the mechanism of DNA-binding by diderm competence T4P has been the recent focus of intensive study, relatively little is known about DNA-binding by monoderm competence T4P. Here, we use Streptococcus pneumoniae as a model system to address this question. Competence T4P likely bind to DNA via a tip-associated complex of proteins called minor pilins, and recent work highlights a high degree of structural conservation between the minor pilin tip complexes of monoderm and diderm competence T4P. In diderms, positively charged residues in one minor pilin, FimT, are critical for DNA-binding. We show that while these residues are conserved in ComGD, the FimT homolog of monoderms, they only play a minor role in DNA uptake for natural transformation. Instead, we find that two-positively charged residues in the neighboring minor pilin, ComGF (the PilW homolog of monoderms), play the dominant role in DNA uptake for natural transformation. Furthermore, we find that these residues are conserved in other monoderms, but not diderms. Together, these results suggest that the molecular basis for DNA-binding has either diverged or evolved independently in monoderm and diderm competence T4P.<br><br>AUTHOR SUMMARY: Diverse bacteria use extracellular structures called competence type IV pili (T4P) to take up DNA from their environment. The uptake of DNA by T4P is the first step of natural transformation, a mode of horizontal gene transfer that contributes to the spread of antibiotic resistance and virulence traits in diverse clinically relevant Gram-negative (diderm) and Gram-positive (monoderm) bacterial species. While the mechanism of DNA binding by competence T4P in diderms has been an area of recent study, relatively little is known about how monoderm competence T4P bind DNA. Here, we explore how monoderm competence T4P bind DNA using Streptococcus pneumoniae as a model system. Our results indicate that while monoderm T4P and diderm T4P likely have conserved structural features, the DNA-binding mechanism of each system is distinct.}, }
@article {pmid40027742, year = {2025}, author = {Tabatabaee, Y and Zhang, C and Arasti, S and Mirarab, S}, title = {Species tree branch length estimation despite incomplete lineage sorting, duplication, and loss.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.20.639320}, pmid = {40027742}, issn = {2692-8205}, abstract = {UNLABELLED: Phylogenetic branch lengths are essential for many analyses, such as estimating divergence times, analyzing rate changes, and studying adaptation. However, true gene tree heterogeneity due to incomplete lineage sorting (ILS), gene duplication and loss (GDL), and horizontal gene transfer (HGT) can complicate the estimation of species tree branch lengths. While several tools exist for estimating the topology of a species tree addressing various causes of gene tree discordance, much less attention has been paid to branch length estimation on multi-locus datasets. For single-copy gene trees, some methods are available that summarize gene tree branch lengths onto a species tree, including coalescent-based methods that account for heterogeneity due to ILS. However, no such branch length estimation method exists for multi-copy gene family trees that have evolved with gene duplication and loss. To address this gap, we introduce the CASTLES-Pro algorithm for estimating species tree branch lengths while accounting for both GDL and ILS. CASTLES-Pro improves on the existing coalescent-based branch length estimation method CASTLES by increasing its accuracy for single-copy gene trees and extends it to handle multi-copy ones. Our simulation studies show that CASTLES-Pro is generally more accurate than alternatives, eliminating the systematic bias toward overestimating terminal branch lengths often observed when using concatenation. Moreover, while not theoretically designed for HGT, we show that CASTLES-Pro maintains relatively high accuracy under high rates of random HGT.<br><br>CODE AVAILABILITY: CASTLES-Pro is implemented inside the software package ASTER, available at https://github.com/chaoszhang/ASTER .<br><br>DATA AVAILABILITY: The datasets and scripts used in this study are available at https://github.com/ytabatabaee/CASTLES-Pro-paper .}, }
@article {pmid40027631, year = {2025}, author = {Schmidt, H and Raphael, BJ}, title = {The tree labeling polytope: a unified approach to ancestral reconstruction problems.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40027631}, issn = {2692-8205}, support = {U24 CA248453/CA/NCI NIH HHS/United States ; U24 CA264027/CA/NCI NIH HHS/United States ; }, abstract = {MOTIVATION: Reconstructing unobserved ancestral states of a phylogenetic tree provides insight into the history of evolving systems and is one of the fundamental problems in phylogenetics. For a fixed phylogenetic tree, the most parsimonious ancestral reconstruction - a solution to the small parsimony problem - can be efficiently found using the dynamic programming algorithms of Fitch-Hartigan and Sankoff. Ancestral reconstruction is important in many applications including inferring the routes of metastases in cancer, deriving the transmission history of viruses, determining the direction of cellular differentiation in organismal development, and detecting recombination and horizontal gene transfer in phylogenetic networks. However, most of these applications impose additional global constraints on the reconstructed ancestral states, which break the local structure required in the recurrences of Fitch-Hartigan and Sankoff.<br><br>RESULTS: We introduce an alternative, polyhedral approach to ancestral reconstruction problems using the tree labeling polytope, a geometric object whose vertices represent the feasible ancestral labelings of a tree. This framework yields a polynomial-time linear programming algorithm for the small parsimony problem. More importantly, the tree labeling polytope facilitates the incorporation of additional constraints that arise in modern ancestral reconstruction problems. We demonstrate the utility of our approach by deriving mixed-integer programming algorithms with a small number of integer variables and strong linear relaxations for three such problems: the parsimonious migration history problem, the softwired small parsimony problem on phylogenetic networks, and the convex recoloring problem on trees. Our algorithms outperform existing state-of-the-art methods on both simulated and real datasets. For instance, our algorithm scales to trace routes of cancer metastases in trees with thousands of leaves, enabling the analysis of large trees generated by recent single-cell sequencing technologies. On a mouse model of metastatic lung adenocarcinoma, the tree labeling polytope allows us to infer simpler migration histories compared to previous results.<br><br>AVAILABILITY: Python implementations of the algorithms provided in this work are available at: github.com/raphael-group/tree-labeling-polytope.}, }
@article {pmid40024690, year = {2025}, author = {Wajima, T and Tanaka, E and Uchiya, KI}, title = {Unique and Ingenious Mechanisms Underlying Antimicrobial Resistance and Spread of Haemophilus influenzae.}, journal = {Biological &amp; pharmaceutical bulletin}, volume = {48}, number = {3}, pages = {205-212}, doi = {10.1248/bpb.b23-00640}, pmid = {40024690}, issn = {1347-5215}, mesh = {*Haemophilus influenzae/drug effects ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Haemophilus Infections/drug therapy/microbiology ; *Drug Resistance, Bacterial/genetics ; Animals ; }, abstract = {Antimicrobial resistance (AMR) is a serious global concern. AMR pathogens are found in hospitals and communities. Haemophilus influenzae is a common pathogen associated with community-acquired infections. H. influenzae infections are usually treated with β-lactams, macrolides, and quinolones. However, the drug-resistant strains have emerged. The resistance mechanisms of H. influenzae are complex but are roughly characterized by the acquisition of a mutation in antimicrobial-targeting genes and exogenous resistant genes. Generally, the former cannot be transferred horizontally to a susceptible strain. However, several studies have demonstrated that, in the case of H. influenzae, both the former and the latter can be transferred horizontally. In this review, we provide an overview of the bacterial features and antimicrobial resistance of H. influenzae. We also summarize the unique and ingenious antimicrobial resistance mechanisms used by this pathogen based on the findings of recent studies. These are expected to facilitate the understanding of AMR pathogens in the community and develop strategies to combat infections.}, }
@article {pmid40023817, year = {2025}, author = {Shao, Y and Chen, M and Cai, J and Doi, Y and Chen, M and Wang, M and Zeng, M and Guo, Q}, title = {Cefotaxime-Resistant Neisseria meningitidis Sequence Type 4821 Causing Fulminant Meningitis.}, journal = {Emerging infectious diseases}, volume = {31}, number = {3}, pages = {591-595}, pmid = {40023817}, issn = {1080-6059}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Cefotaxime/therapeutic use/pharmacology ; *Neisseria meningitidis/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Child, Preschool ; *Meningitis, Meningococcal/microbiology/drug therapy ; Microbial Sensitivity Tests ; China ; Male ; Drug Resistance, Bacterial ; }, abstract = {We explored the role of commensal Neisseria in the emergence of third-generation cephalosporin-resistant N. meningitidis. Cefotaxime resistance-conferring penA795 was prevalent among commensal Neisseria isolates in Shanghai, China, and was acquired by a serogroup C quinolone-resistant sequence type 4821 N. meningitidis, Nm507, causing fulminant meningitis in an unvaccinated 2-year-old child.}, }
@article {pmid40019366, year = {2025}, author = {Hu, Y and Gong, C and Yang, Z and Han, H and Tian, T and Yang, X and Xie, W and Wang, S and Wu, Q and Zhou, X and Turlings, TCJ and Guo, Z and Zhang, Y}, title = {Functional Divergence of Plant-Derived Thaumatin-Like Protein Genes in Two Closely Related Whitefly Species.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {12}, number = {16}, pages = {e2502193}, pmid = {40019366}, issn = {2198-3844}, support = {2021YFD1400600//National Key R &amp; D Program of China/ ; GZB20240839//Postdoctoral Fellowship Program of CPSF/ ; Y2023XK15//Central Public-interest Scientific Institution Basal Research Fund/ ; Y2024XK01//Central Public-interest Scientific Institution Basal Research Fund/ ; //Beijing Key Laboratory for Pest Control and Sustainable Cultivation of Vegetables/ ; //Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences/ ; 788949//European Research Council Advanced/ ; CARS-23//Earmarked Fund for China Agriculture Research System/ ; 2024M753572//China Postdoctoral Science Foundation/ ; 32221004//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Hemiptera/genetics ; *Gene Transfer, Horizontal/genetics ; *Plant Proteins/genetics ; Phylogeny ; Insect Proteins/genetics ; Evolution, Molecular ; }, abstract = {The recent discovery that various insects have acquired functional genes through horizontal gene transfer (HGT) has prompted numerous studies into this puzzling and fascinating phenomenon. So far, horizontally transferred genes are found to be functionally conserved and largely retained their ancestral functions. It evidently has not yet been considered that horizontally transferred genes may evolve and can contribute to divergence between species. Here, it is first showed that the genomes of the two widespread and agriculturally important whiteflies Trialeurodes vaporariorum and Bemisia tabaci both contain a plant-derived thaumatin-like protein (TLP) gene, but with highly distinct functions in these closely related pests. In T. vaporariorum, TLP has maintained a function similar to that of the plant donor, acting as an antimicrobial protein to resist fungal infection; but in sharp contrast, in B. tabaci, TLP has evolved into an effector that suppresses plant defense responses. These findings reveal an as-yet undescribed scenario of cross-species functional differentiation of horizontally transferred genes and suggest that the HGT-mediated evolutionary novelty can contribute to ecotypic divergence and even speciation.}, }
@article {pmid40013789, year = {2025}, author = {Jin, M and Rouxel, O and Quintin, N and Geslin, C}, title = {Molecular piracy in deep-sea hydrothermal vent: phage-plasmid interactions revealed by phage-FISH in Marinitoga piezophila.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {3}, pages = {e0230624}, pmid = {40013789}, issn = {1098-5336}, mesh = {*Hydrothermal Vents/microbiology/virology ; *Plasmids/genetics ; *Bacteriophages/genetics/isolation &amp; purification ; *In Situ Hybridization, Fluorescence ; Gene Transfer, Horizontal ; Seawater/virology/microbiology ; DNA, Viral/genetics ; }, abstract = {UNLABELLED: Prokaryotes and mobile genetic elements (MGEs, such as viruses and plasmids) interact extensively, leading to horizontal gene transfer (HGT) and consequent microbial evolution and diversity. However, our knowledge of the interactions between MGEs in deep-sea hydrothermal ecosystems is limited. In this study, we adapted a phage-fluorescence in situ hybridization (phage-FISH) approach to visualize and quantify the dynamics of phage-plasmid interactions in an anaerobic, thermophilic deep-sea bacterium, Marinitoga piezophila. Notably, our results revealed that plasmid signals were detected in viral particles released from lysed cells, indicating that mitomycin C not only induced plasmid replication but also its packaging into phage particles. Further analysis of the DNA content in purified virions showed that the phage capsids incorporated plasmid DNA even without induction, and the majority of capsids (up to 70%) preferentially packaged plasmid DNA rather than viral DNA after induction. Therefore, this study provided direct evidence of molecular piracy in the deep-sea hydrothermal ecosystem, highlighting the important roles of selfish MGEs in virus-host interactions and HGT in extreme marine environments.<br><br>IMPORTANCE: Deep-sea hydrothermal vents are hotspots for microbes. Several studies revealed that virus-mediated horizontal gene transfer (HGT) in deep-sea hydrothermal vent ecosystems may be crucial to the survival and stability of prokaryotes in these extreme environments. However, little is known about the interaction between viruses and other mobile genetic elements (MGEs, such as plasmids), and how their interactions influence virus-mediated HGT in these ecosystems. In this study, we adapted a phage-fluorescence in situ hybridization approach to directly monitor the dynamics of phage-plasmid-host interactions at the single-cell level in the Marinitoga piezophila model. Interestingly, our results indicate that plasmid DNA could not only be induced by mitomycin C to a great extent but also hijacked viral assembly machinery to facilitate its propagation and spread. Therefore, the data presented here imply that the interaction between the viruses and other MGEs could play profound roles in virus-host interaction and virus-mediated HGT in the deep-sea hydrothermal ecosystem.}, }
@article {pmid40012781, year = {2025}, author = {Zhao, B and Zhang, R and Jin, B and Yu, Z and Wen, W and Zhao, T and Quan, Y and Zhou, J}, title = {Sludge water: a potential pathway for the spread of antibiotic resistance and pathogenic bacteria from hospitals to the environment.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1492128}, pmid = {40012781}, issn = {1664-302X}, abstract = {Hospitals play an important role in the spread of antibiotic resistance genes (ARGs) and antimicrobial resistance (AMR). The ARGs present in hospital wastewater tend to accumulate in activated sludge, with different ARGs exhibiting varying migration rates. As a result, sludge water produced during the activated sludge treatment process may be a significant source of ARGs entering the environment. Despite this, research into the behavior of ARGs during sludge concentration and dewatering remains limited. This study hypothesizes that ARGs might exhibit new behaviors in sludge water during sludge concentration. Using metagenomic analysis, we explored the distribution and migration risks of ARGs and human pathogenic bacteria (HPB) in sludge water, comparing them with those in hospital wastewater. The findings reveal a strong correlation between ARGs in sludge water and hospital wastewater, with subtypes such as arlR, efpA, and tetR showing higher abundance in sludge water. Although the horizontal gene transfer potential of ARGs is greater in hospital wastewater than in sludge water, the resistance mechanisms and migration pathways are similar even when their HPB host associations differ. ARGs in both environments are primarily transmitted through coexisting mobile genetic elements (MGEs). This suggests that sludge water serves as a critical route for the release of hospital-derived ARGs into the environment, posing potential threats to public health and ecological safety.}, }
@article {pmid40010677, year = {2025}, author = {Lapadula, WJ and Cañadas, MG and Ayub, MJ}, title = {Characterization of Ribosome inactivating protein genes and their transcripts in Trialeurodes vaporariorum.}, journal = {Gene}, volume = {948}, number = {}, pages = {149356}, doi = {10.1016/j.gene.2025.149356}, pmid = {40010677}, issn = {1879-0038}, mesh = {Animals ; *Ribosome Inactivating Proteins/genetics/metabolism ; *Hemiptera/genetics ; Insect Proteins/genetics/metabolism ; Female ; Transcriptome ; Phylogeny ; }, abstract = {Ribosome-inactivating proteins (RIPs) are rRNA N-glycosylases (EC 3.2.2.22) that depurinate an adenine residue from the conserved alpha-sarcin/ricin loop in rRNA, blocking protein synthesis. In previous research, we demonstrated that whiteflies from the Aleyrodidae family (e.g., Bemisia tabaci), mosquitoes from the Culicinae subfamily (e.g., Aedes aegypti), and flies of Sciaroidea superfamily (e.g., Contarinia nasturtii) acquired these genes via three independent horizontal gene transfer events. The temporal expression profiles analyzed in mosquitoes and flies are consistent with the expected for immune effector molecules of insects. Notably, in A. aegypti, we found that these genes contribute to immunity. In whiteflies, codon analysis suggests that RIP genes have evolved under the influence of natural selection. Public transcriptomic experiments have shown that these genes are expressed in the adult stage of B. tabaci. Despite computational findings supporting RIP genes functionality in whiteflies, no experimental studies have been conducted. Furthermore, there is currently no publicly available RNA-seq data evaluating gene expression throughout ontogeny in the Aleyrodidae family. In this work, we experimentally demonstrated the presence of these foreign genes in the genome of Trialeurodes vaporariorum. We quantified their expression across the life cycle stages of this species and analyzed their untranslated regions. The results obtained contribute to a deeper understanding of the biological roles that these ribotoxin encoding genes may play in whiteflies and other insects.}, }
@article {pmid40010597, year = {2025}, author = {Wang, X and Lin, Y and Li, S and Wang, J and Li, X and Zhang, D and Duan, D and Shao, Z}, title = {Metagenomic analysis reveals the composition and sources of antibiotic resistance genes in coastal water ecosystems of the Yellow Sea and Yangtze River Delta.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {371}, number = {}, pages = {125923}, doi = {10.1016/j.envpol.2025.125923}, pmid = {40010597}, issn = {1873-6424}, mesh = {China ; *Metagenomics ; *Seawater/microbiology ; *Drug Resistance, Microbial/genetics ; *Rivers/chemistry/microbiology ; Ecosystem ; Bacteria/genetics/drug effects ; Environmental Monitoring ; Genes, Bacterial ; }, abstract = {The rapid development of coastal areas has raised concerns about marine environmental pollution. In this study, metagenomics was employed to investigate antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and bacterial communities in the Yellow Sea and Yangtze River Delta in China. Multidrug resistance genes were the most abundant ARGs in these regions. Transposons and insertion_element_IS91 were the dominant MGEs, closely related to the horizontal gene transfer of ARGs. Temperature, dissolved oxygen, pH, and depth were identified as important environmental factors influencing the distribution of ARGs in seawater. Oil, agriculture, animal husbandry, and wastewater treatment plants are likely the primary sources of ARGs. From the perspective of ARG control, bacterial communities contributed the most to the development of the resistome and may carry ARGs, spreading from the Yangtze River Delta to the Yellow Sea along ocean currents. A comparison with Tara Oceans datasets revealed that the dominant ARG types and bacterial genera in coastal waters were consistent with global characteristics, with variations in ARG subtypes. This study expands knowledge on the distribution patterns of ARGs at an offshore scale and provides a reference for the prevention and control of resistant gene pollution in the Yellow Sea and Yangtze River Delta.}, }
@article {pmid40008406, year = {2025}, author = {Heida, A and Hamilton, MT and Gambino, J and Sanderson, K and Schoen, ME and Jahne, MA and Garland, J and Ramirez, L and Quon, H and Lopatkin, AJ and Hamilton, KA}, title = {Population Ecology-Quantitative Microbial Risk Assessment (QMRA) Model for Antibiotic-Resistant and Susceptible E. coli in Recreational Water.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {9}, pages = {4266-4281}, doi = {10.1021/acs.est.4c07248}, pmid = {40008406}, issn = {1520-5851}, mesh = {*Escherichia coli/drug effects ; Risk Assessment ; Water Microbiology ; Humans ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; Urinary Tract Infections/microbiology ; beta-Lactamases ; }, abstract = {Understanding and predicting the role of waterborne environments in transmitting antimicrobial-resistant (AMR) infections are critical for public health. A population ecology-quantitative microbial risk assessment (QMRA) model is proposed to evaluate urinary tract infection (UTI) development due to recreational waterborne exposures to Escherichia coli (E. coli) and antibiotic-resistant extended-spectrum β-lactamase-producing (ESBL) E. coli. The horizontal gene transfer (HGT) mechanism of conjugation and other evolutionary factors were modeled separately in the environment and the gut. Persistence/dilution dominated HGT in the environment; however, HGT highly impacted predicted ESBL populations in the body. Predicted disability life year (DALY) risks from exposure to ESBL E. coli at concentrations consistent with US recreational water criteria were less than the 10[-6] pppy benchmark value but greater than the susceptible E. coli DALY risks associated with a UTI health outcome. However, the prevailing susceptible dose-response relationship may underestimate ESBL risk if HGT rates in vivo approach those reported in vitro. A sensitivity analysis demonstrated that DALY values, E. coli/ESBL concentrations, and exposure parameters were influential on predicted risks. The model is a preliminary tool to begin the expansion of the QMRA paradigm to explore the impacts of evolutionary changes in AMR risk assessment.}, }
@article {pmid40007369, year = {2025}, author = {Li, S and Liu, Y and Zhang, Y and Huang, P and Bartlam, M and Wang, Y}, title = {Stereoselective behavior of naproxen chiral enantiomers in promoting horizontal transfer of antibiotic resistance genes.}, journal = {Journal of hazardous materials}, volume = {489}, number = {}, pages = {137692}, doi = {10.1016/j.jhazmat.2025.137692}, pmid = {40007369}, issn = {1873-3336}, mesh = {*Gene Transfer, Horizontal/drug effects ; *Naproxen/chemistry/pharmacology ; Stereoisomerism ; *Drug Resistance, Microbial/genetics ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; *Genes, Bacterial ; Rivers/microbiology ; *Water Pollutants, Chemical/chemistry ; Bacteria/genetics/drug effects ; }, abstract = {Antibiotic resistance poses a global threat to public health, with recent studies highlighting the role of non-antibiotic pharmaceuticals in the transmission of antibiotic resistance genes (ARGs). This study provides insights into the comprehensive profile, horizontal gene transfer potential, hosts, and public health risks associated with antibiotic resistomes in river ecosystems exposed to chiral naproxen (NAP). Our findings demonstrate that NAP stress selectively enriches ARGs and mobile genetic elements (MGEs), thereby bolstering bacterial resistance to specific antibiotics. Importantly, the spatial variation of NAP chiral enantiomers influences the enantioselective response of bacterial communities to antibiotics. While (S)-NAP and (R)-NAP exhibit differing degrees of horizontal transfer potential, (S/R)-NAP notably facilitates microbial aggregation and DNA transport via type IV secretion system (T4SS)-related functional genes, promoting the conjugation of sul1. Moreover, (S/R)-NAP promotes the horizontal transfer of ARGs by stimulating ROS production and altering cell membrane permeability. Chiral NAP exposure induces pathogens to acquire ARGs and accelerates the proliferation of Burkholderia. ARG-Rank analysis indicates that the health risk posed by (R)-NAP exposure surpasses that of (S)-NAP, with the highest risk observed when both enantiomers are present. This study elucidates the horizontal transfer and transmission mechanisms of ARGs under chiral NAP stress, underscoring the potential health hazards associated with NAP chiral enantiomers.}, }
@article {pmid40007158, year = {2025}, author = {Ma, S and Li, S and Lu, X and Zhang, Q and Dong, M and Wu, Y and Lv, D and Luo, L and Jin, W and Liu, X and Yang, W and Djalovic, I and Wang, T and Zhou, X and Chen, R}, title = {A transposon-based cargo system mediates gene trafficking and creates ultra-clean transgenic plants after stable transformation.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.70017}, pmid = {40007158}, issn = {1469-8137}, support = {2023ZD0403005//Biological Breeding-Major Projects/ ; 32171453//National Natural Science Foundation of China/ ; 20220101//CAAS-Syngenta Innovation Expansion Project/ ; 2021YFD1200700//National Key Research and Development Program of China/ ; //Innovation Program of Chinese Academy of Agricultural Sciences/ ; }, abstract = {Genetically modified crops have profound impacts on cost savings and environmental friendliness conferred by new traits, such as resistance to insects and herbicides. Selectable marker genes are essential for screening transformed cells, but they are undesirable in the final product due to the risks of horizontal gene transfer and extensive safety assessment requirements. Generating marker- and backbone-free lines can enhance the public acceptance of transgenic crops. Here, we established a transposon-mediated ultra-clean selectable transformant (TRUST) system for generating marker- and backbone-free transformants in a visibly controllable manner, facilitated by the integration of transposon elements, fluorescence proteins, and the anthocyanin biosynthesis gene. This system creates ultra-clean transgenic events that retain only the expression cassette of the gene of interest with an average probability of 15.5%. Additionally, long-read whole-genome sequencing confirmed the integrity of the expression cassette boundaries. The TRUST system is not only a powerful method for producing backbone-free transgenic plants but also increases the number of transgenic events originating from one starting event, thereby potentially leading to advances in the genetic engineering of recalcitrant crop varieties.}, }
@article {pmid40005743, year = {2025}, author = {Liu, F and Cheewangkoon, R and Zhao, RL}, title = {Discovery of a New Starship Transposon Driving the Horizontal Transfer of the ToxA Virulence Gene in Alternaria ventricosa.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, pmid = {40005743}, issn = {2076-2607}, support = {(Project ID: 31961143010,31970010,32300012)//National Natural Science Foundation of China/ ; }, abstract = {The virulence gene ToxA has been proposed to be horizontally transferred between three fungal wheat pathogens (Parastagonospora nodorum, Pyrenophora tritici-repentis, and Bipolaris sorokiniana) as part of a conserved ~14 kb ToxhAT transposon. Here, our analysis of 2137 fungal species-representative assemblies revealed that the ToxA gene is an isolate of Alternaria ventricosa and shows a remarkable 99.5% similarity to those found in B. sorokiniana and P. tritici-repentis. Analysis of the regions flanking ToxA within A. ventricosa revealed that it was embedded within a 14 kb genomic element nearly identical to the corresponding ToxhAT regions in B. sorokiniana, P. nodorum, and P. tritici-repentis. Comparative analysis further showed that ToxhAT in A. ventricosa resides within a larger mobile genetic element, which we identified as a member of the Starship transposon superfamily, named Frontier. Our analysis demonstrated that ToxhAT has been independently captured by three distinct Starships-Frontier, Sanctuary, and Horizon-which, despite having minimal sequence similarity outside of ToxhAT, facilitate its mobilization. These findings place Frontier, Sanctuary, and Horizon within a growing class of Starships implicated in the horizontal transfer of adaptive genes among fungal species. Moreover, we identified three distinct HGT events involving ToxA across these four fungal species, reinforcing the hypothesis of a single evolutionary origin for the ToxhAT transposon. These findings underscore the pivotal role of transposon-mediated HGT in the adaptive evolution of eukaryotic pathogens, offering new insights into how transposons facilitate genetic exchange and shape host-pathogen interactions in fungi.}, }
@article {pmid40001581, year = {2025}, author = {Liu, Z and Fan, X and Wu, Y and Zhang, W and Zhang, X and Xu, D and Wang, Y and Sun, K and Wang, W and Ye, N}, title = {Comparative Genomics of Bryopsis hypnoides: Structural Conservation and Gene Transfer Between Chloroplast and Mitochondrial Genomes.}, journal = {Biomolecules}, volume = {15}, number = {2}, pages = {}, pmid = {40001581}, issn = {2218-273X}, mesh = {*Genome, Mitochondrial/genetics ; *Genome, Chloroplast/genetics ; *Phylogeny ; *Genomics/methods ; Codon Usage ; Evolution, Molecular ; Gene Transfer, Horizontal ; RNA, Transfer/genetics ; }, abstract = {Bryopsis hypnoides, a unicellular multinucleate green alga in the genus Bryopsis, plays vital ecological roles and represents a key evolutionary link between unicellular and multicellular algae. However, its weak genetic baseline data have constrained the progress of evolutionary research. In this study, we successfully assembled and annotated the complete circular chloroplast and mitochondrial genomes of B. hypnoides. The chloroplast genome has a total length of 139,745 bp and contains 59 protein-coding genes, 2 rRNA genes, and 11 tRNA genes, with 31 genes associated with photosynthesis. The mitochondrial genome has a total length of 408,555 bp and contains 41 protein-coding genes, 3 rRNA genes, and 18 tRNA genes, with 18 genes involved in oxidative phosphorylation. Based on the data, we conducted a genetic comparison involving repeat sequences, phylogenetic relationships, codon usage preferences, and gene transfer between the two organellar genomes. The major results highlighted that (1) the chloroplast genome favors A/T repeats, whereas the mitochondrial genome prefers C/G repeats; (2) codon usage preference analysis indicated that both organellar genomes prefer codons ending in A/T, with a stronger bias observed in the chloroplast genome; and (3) sixteen fragments with high sequence identity were identified between the two organellar genomes, indicating potential gene transfer. These findings provide critical insights into the organellar genome characteristics and evolution of B. hypnoides.}, }
@article {pmid40001396, year = {2025}, author = {Sher, AA and Whitehead-Tillery, CE and Peer, AM and Bell, JA and Vocelle, DB and Dippel, JT and Zhang, L and Mansfield, LS}, title = {Dynamic Spread of Antibiotic Resistance Determinants by Conjugation to a Human-Derived Gut Microbiota in a Transplanted Mouse Model.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {2}, pages = {}, pmid = {40001396}, issn = {2079-6382}, support = {RN031097-DEHN//Albert C. and Lois E. Dehn Chair Endowment/ ; NC1202//United States Department of Agriculture/ ; GS100019//University Distinguished Professor Endowment, Michigan State University/ ; U19AI090872//National Institutes of Health, Enterics Research Investigational Network, Cooperative Research Center/ ; Stipend to Azam A. Sher//College of Veterinary Medicine/ ; }, abstract = {BACKGROUND: Antibiotic-resistant (AR) bacteria pose an increasing threat to public health, but the dynamics of antibiotic resistance gene (ARG) spread in complex microbial communities are poorly understood. Conjugation is a predominant direct cell-to-cell mechanism for the horizontal gene transfer (HGT) of ARGs. We hypothesized that commensal Escherichia coli donor strains would mediate the conjugative transfer of ARGs to phylogenetically distinct bacteria without antibiotic selection pressure in gastrointestinal tracts of mice carrying a human-derived microbiota with undetectable levels of E. coli. Our objective was to identify a mouse model to study the factors regulating AR transfer by conjugation in the gut.<br><br>METHODS: Two donor E. coli strains were engineered to carry chromosomally encoded red fluorescent protein, and an ARG- and green fluorescent protein (GFP)-encoding broad host range RP4 conjugative plasmid. Mice were orally gavaged with two donor strains (1) E. coli MG1655 or (2) human-derived mouse-adapted E. coli LM715-1 and their colonization assessed by culture over time. Fluorescence-activated cell sorting (FACS) and 16S rDNA sequencing were performed to trace plasmid spread to the microbiota.<br><br>RESULTS: E. coli LM715-1 colonized mice for ten days, while E. coli MG1655 was not recovered after 72 h. Bacterial cells from fecal samples on days 1 and 3 post inoculation were sorted by FACS. Samples from mice given donor E. coli LM715-1 showed an increase in cells expressing green but not red fluorescence compared to pre-inoculation samples. 16S rRNA gene sequencing analysis of FACS GFP positive cells showed that bacterial families Lachnospiraceae, Clostridiaceae, Pseudomonadaceae, Rhodanobacteraceae, Erysipelotrichaceae, Oscillospiraceae, and Butyricicoccaceae were the primary recipients of the RP4 plasmid.<br><br>CONCLUSIONS: Results show this ARG-bearing conjugative RP4 plasmid spread to diverse human gut bacterial taxa within a live animal where they persisted. These fluorescent marker strategies and human-derived microbiota transplanted mice provided a tractable model for investigating the dynamic spread of ARGs within gut microbiota and could be applied rigorously to varied microbiotas to understand conditions facilitating their spread.}, }
@article {pmid40001389, year = {2025}, author = {Pandova, M and Kizheva, Y and Hristova, P}, title = {Relationship Between CRISPR-Cas Systems and Acquisition of Tetracycline Resistance in Non-Clinical Enterococcus Populations in Bulgaria.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {2}, pages = {}, pmid = {40001389}, issn = {2079-6382}, support = {project No BG-RRP-2.004-0008//European Union-NextGenerationEU, National Recovery and Resilience Plan of the Republic of Bulgaria, SUMMIT 3.2.4./ ; }, abstract = {Non-clinical enterococci are relatively poorly studied by means of acquired antibiotic resistance to tetracycline and by the distribution, functionality and role of their CRISPR systems. Background: In our study, 72 enterococcal strains, isolated from various non-clinical origins, were investigated for their phenotypic and genotypic (tet(M), tet(O), tet(S), tet(L), tet(K), tet(T) and tet(W)) tetracycline resistance. Methods: The genetic determinants for HGT (MGEs (Int-Tn and prgW), inducible pheromones (cpd, cop and cff), aggregation substances (agg, asa1, prgB and asa373) and CRISPR-Cas systems were characterized by PCR and whole-genome sequencing. Results: Four tet genes (tetM, tetO, tetS and tetT) were detected in 39% (n = 28) of our enterococcal population, with tetM (31%) being dominant. The gene location was linked to the Tn6009 transposon. All strains that contained tet genes also had genes for HGT. No tet genes were found in E. casseliflavus and E. gilvus. In our study, 79% of all tet-positive strains correlated with non-functional CRISPR systems. The strain E. faecalis BM15 was the only one containing a combination of a functional CRISPR system (cas1, cas2, csn2 and csn1/cas9) and tet genes. The CRISPR subtype repeats II-A, III-B, IV-A2 and VI-B1 were identified among E. faecalis strains (CM4-II-A, III-B and VI-B1; BM5-IV-A2, II-A and III-B; BM12 and BM15-II-A). The subtype II-A was the most present. These repeats enclosed a great number of spacers (1-10 spacers) with lengths of 31 to 36 bp. One CRISPR locus was identified in plasmid (p.Firmicutes1 in strain E. faecalis BM5). We described the presence of CRISPR loci in the species E. pseudoavium, E. pallens and E. devriesei and their lack in E. gilvus, E. malodoratus and E. mundtii. Conclusions: Our findings generally describe the acquisition of foreign DNA as a consequence of CRISPR inactivation, and self-targeting spacers as the main cause.}, }
@article {pmid40001375, year = {2025}, author = {La Rosa, MC and Maugeri, A and Favara, G and La Mastra, C and Magnano San Lio, R and Barchitta, M and Agodi, A}, title = {The Impact of Wastewater on Antimicrobial Resistance: A Scoping Review of Transmission Pathways and Contributing Factors.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {2}, pages = {}, pmid = {40001375}, issn = {2079-6382}, abstract = {BACKGROUND/OBJECTIVES: Antimicrobial resistance (AMR) is a global issue driven by the overuse of antibiotics in healthcare, agriculture, and veterinary settings. Wastewater and treatment plants (WWTPs) act as reservoirs for antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs). The One Health approach emphasizes the interconnectedness of human, animal, and environmental health in addressing AMR. This scoping review analyzes wastewater's role in the AMR spread, identifies influencing factors, and highlights research gaps to guide interventions.<br><br>METHODS: This scoping review followed the PRISMA-ScR guidelines. A comprehensive literature search was conducted across the PubMed and Web of Science databases for articles published up to June 2024, supplemented by manual reference checks. The review focused on wastewater as a source of AMR, including hospital effluents, industrial and urban sewage, and agricultural runoff. Screening and selection were independently performed by two reviewers, with conflicts resolved by a third.<br><br>RESULTS: Of 3367 studies identified, 70 met the inclusion criteria. The findings indicated that antibiotic residues, heavy metals, and microbial interactions in wastewater are key drivers of AMR development. Although WWTPs aim to reduce contaminants, they often create conditions conducive to horizontal gene transfer, amplifying resistance. Promising interventions, such as advanced treatment methods and regulatory measures, exist but require further research and implementation.<br><br>CONCLUSIONS: Wastewater plays a pivotal role in AMR dissemination. Targeted interventions in wastewater management are essential to mitigate AMR risks. Future studies should prioritize understanding AMR dynamics in wastewater ecosystems and evaluating scalable mitigation strategies to support global health efforts.}, }
@article {pmid40000989, year = {2025}, author = {Zhao, M and Zhang, Y and Liu, S and Wang, F and Zhang, P}, title = {Eradication of Helicobacter pylori reshapes gut microbiota and facilitates the evolution of antimicrobial resistance through gene transfer and genomic mutations in the gut.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {90}, pmid = {40000989}, issn = {1471-2180}, support = {32201393//National Natural Science Foundation of China/ ; }, mesh = {*Gastrointestinal Microbiome/drug effects/genetics ; Humans ; *Helicobacter pylori/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; *Helicobacter Infections/microbiology/drug therapy ; *Gene Transfer, Horizontal ; *Feces/microbiology ; Mutation ; Metagenomics ; Klebsiella/genetics/drug effects ; Female ; Male ; Genome, Bacterial/genetics ; Adult ; Escherichia/genetics/drug effects ; Middle Aged ; Genes, Bacterial/genetics ; }, abstract = {Treating Helicobacter pylori (H. pylori) infection requires large quantities of antibiotics, thus dramatically promoting the enrichment and dissemination of antimicrobial resistance (AMR) in feces. However, the influence of H. pylori eradication on the AMR mobility and the gut microbiota evolution has yet to be thoroughly investigated. Here, a study involving 12 H. pylori-positive participants was conducted, and the pre- and post- eradication fecal samples were sequenced. Metagenomic analysis revealed that the eradication treatment drastically altered the gut microbiome, with the Escherichia and Klebsiella genera emerging as the predominant bacteria. Interestingly, the eradication treatment significantly increased the relative abundance and diversity of resistome and mobilome in gut microbiota. Eradication of H. pylori also enriched AMR genes (ARGs) conferring resistance to antibiotics not administered because of the co-location with other ARGs or mobile genetic elements (MGEs). Additionally, the Escherichia and Klebsiella genera were identified as the primary bacterial hosts of these highly transferable ARGs. Furthermore, the genomic variations associated with ARGs in Escherichia coli (E. coli) caused by the eradication treatment were profiled, including the parC, parE, and gyrA genes. These findings revealed that H. pylori eradication promoted the enrichment of ARGs and MGEs in the Escherichia and Klebsiella genera, and further facilitated bacterial evolution through the horizontal transfer of ARGs and genomic variations.}, }
@article {pmid39998220, year = {2025}, author = {Kwak, Y and Argandona, JA and Miao, S and Son, TJ and Hansen, AK}, title = {A dual insect symbiont and plant pathogen improves insect host fitness under arginine limitation.}, journal = {mBio}, volume = {16}, number = {4}, pages = {e0358824}, pmid = {39998220}, issn = {2150-7511}, support = {S10 OD010786/OD/NIH HHS/United States ; 2019-70016-29066//U.S. Department of Agriculture (USDA)/ ; }, mesh = {Animals ; *Symbiosis ; *Hemiptera/microbiology/physiology ; *Arginine/metabolism/deficiency ; Gene Transfer, Horizontal ; Host-Pathogen Interactions ; *Liberibacter/physiology/genetics ; Plant Diseases/microbiology ; }, abstract = {Some facultative bacterial symbionts are known to benefit insects, but nutritional advantages are rare among these non-obligate symbionts. Here, we demonstrate that the facultative symbiont Candidatus Liberibacter psyllaurous enhances the fitness of its psyllid insect host, Bactericera cockerelli, by providing nutritional benefits. L. psyllaurous, an unculturable pathogen of solanaceous crops, also establishes a close relationship with its insect vector, B. cockerelli, increasing in titer during insect development, vertically transmitting through eggs, and colonizing various tissues, including the bacteriome, which houses the obligate nutritional symbiont, Carsonella. Carsonella supplies essential amino acids to its insect host but has gaps in some of its essential amino acid pathways that the psyllid complements with its own genes, many of which have been acquired through horizontal gene transfer (HGT) from bacteria. Our findings reveal that L. psyllaurous increases psyllid fitness on plants by reducing developmental time and increasing adult weight. In addition, through metagenomic sequencing, we reveal that L. psyllaurous maintains complete pathways for synthesizing the essential amino acids arginine, lysine, and threonine, unlike the psyllid's other resident microbiota, Carsonella, and two co-occurring Wolbachia strains. RNA sequencing reveals the downregulation of a HGT collaborative psyllid gene (ASL), which indicates a reduced demand for arginine supplied by Carsonella when the psyllid is infected with L. psyllaurous. Notably, artificial diet assays show that L. psyllaurous enhances psyllid fitness on an arginine-deplete diet. These results corroborate the role of L. psyllaurous as a beneficial insect symbiont, contributing to the nutrition of its insect host.IMPORTANCEUnlike obligate symbionts that are permanently associated with their hosts, facultative symbionts rarely show direct nutritional contributions, especially under nutrient-limited conditions. This study demonstrates, for the first time, that Candidatus Liberibacter psyllaurous, a facultative symbiont and a plant pathogen, enhances the fitness of its Bactericera cockerelli host by supplying an essential nutrient arginine that is lacking in the plant sap diet. Our findings reveal how facultative symbionts can play a vital role in helping their insect hosts adapt to nutrient-limited environments. This work provides new insights into the dynamic interactions between insect hosts, their symbiotic microbes, and their shared ecological niches, broadening our understanding of symbiosis and its role in shaping adaptation and survival.}, }
@article {pmid39993662, year = {2025}, author = {Chen, M and Yan, X and Tang, Q and Liu, M and Yang, M and Chai, Y and Wei, Y and Shen, P and Zhang, J}, title = {Particle size transfer of antibiotic resistance genes in typical processes of municipal wastewater treatment plant.}, journal = {Bioresource technology}, volume = {424}, number = {}, pages = {132288}, doi = {10.1016/j.biortech.2025.132288}, pmid = {39993662}, issn = {1873-2976}, mesh = {*Particle Size ; *Sewage/microbiology ; *Wastewater ; *Water Purification/methods ; *Drug Resistance, Microbial/genetics ; Bioreactors ; Genes, Bacterial ; Gene Transfer, Horizontal ; Waste Disposal, Fluid/methods ; Cities ; }, abstract = {Occurrence and transfer of antibiotic resistance genes (ARGs) was investigated concerning sludge particle size in a typical wastewater treatment plant, and the roles of vertical (VGT) and horizontal gene transfer (HGT) in the spread of ARGs were explored. Results showed that although membrane bioreactor (MBR) effectively reduced the relative abundance of ARGs in the water phase, it concurrently enriched ARGs in MBR sludge, particularly for the largest-size particles (>150 μm). A decreasing trend in the relative abundance of ARGs was observed along with the decrease of sludge particle size, and larger-size particle sludge (>106 μm) formed a relatively stable composition of ARGs, while ARGs on smaller-size particle sludge (6.5-106 μm) fluctuate rapidly. Particle size does not affect the abundance distribution patterns or assembly mechanisms of ARGs as deterministic processes. The smallest-size particles were the primary attachment site for bacterial pathogens with highest diversity. Larger-size particle sludge (>106 μm) showed higher frequency of HGT, with Proteobacteria as the dominant hosts for this process.}, }
@article {pmid39990427, year = {2025}, author = {Cai, L and Havird, JC and Jansen, RK}, title = {Recombination and retroprocessing in broomrapes reveal a universal roadmap for mitochondrial evolution in heterotrophic plants.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39990427}, issn = {2692-8205}, support = {R35 GM142836/GM/NIGMS NIH HHS/United States ; }, abstract = {The altered life history strategies of heterotrophic organisms often leave a profound genetic footprint on energy metabolism related functions. In parasitic plants, the reliance on host-derived nutrients and loss of photosynthesis in holoparasites have led to highly degraded to absent plastid genomes, but its impact on mitochondrial genome (mitogenome) evolution has remained controversial. By examining mitogenomes from 45 Orobanchaceae species including three independent transitions to holoparasitism and key evolutionary intermediates, we identified measurable and predictable genetic alterations in genomic shuffling, RNA editing, and intracellular (IGT) and horizontal gene transfer (HGT) en route to a nonphotosynthetic lifestyle. In-depth comparative analyses revealed DNA recombination and repair processes, especially RNA-mediated retroprocessing, as significant drivers for genome structure evolution. In particular, we identified a novel RNA-mediated IGT and HGT mechanism, which has not been demonstrated in cross-species and inter-organelle transfers. Based on this, we propose a generalized dosage effect mechanism to explain the biased transferability of plastid DNA to mitochondria across green plants, especially in heterotrophic lineages like parasites and mycoheterotrophs. Evolutionary rates scaled with these genomic changes, but the direction and strength of selection varied substantially among genes and clades, resulting in high contingency in mitochondrial genome evolution. Finally, we describe a universal roadmap for mitochondrial evolution in heterotrophic plants where increased recombination and repair activities, rather than relaxed selection alone, lead to differentiated genome structure compared to free-living species.}, }
@article {pmid39988254, year = {2025}, author = {Hou, W and Yu, J and Shi, H and Xu, J and Chen, SS and Shaban, SS and Kim, Y and Bai, J}, title = {As a reservoir of antibiotic resistance genes and pathogens, the hydrodynamic characteristics drive their distribution patterns in Lake Victoria.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {370}, number = {}, pages = {125903}, doi = {10.1016/j.envpol.2025.125903}, pmid = {39988254}, issn = {1873-6424}, mesh = {*Lakes/microbiology/chemistry ; *Hydrodynamics ; *Bacteria/genetics ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Environmental Monitoring ; Drug Resistance, Bacterial/genetics ; }, abstract = {Antibiotic resistance genes (ARGs) and pathogenic bacteria pose significant challenges to human health, and hydrodynamic processes complicate their transmission mechanisms in lake ecosystems, particularly in tropical regions. Lake Victoria supports abundant water resources and provides livelihoods for millions of people, yet the environmental behavior of ARGs and pathogenic bacteria remains unclear. Herein, the novel insights into the co-occurrence patterns and transmission mechanisms of ARGs and pathogenic bacteria in Lake Victoria was investigated via molecular techniques and a hydrodynamic model. The results showed that as a large reservoir of ARGs and pathogenic bacteria, a total of 172 ARG subtypes and 93 pathogenic bacteria were identified in Lake Victoria. ARGs were spread through mobile genetic elements (tnpA4 and int2), enhancing the antibiotic resistance and virulence factors (secretion systems, regulatory factors, and toxins) of various pathogenic bacteria. The hydrodynamic model indicated that surface wind-driven currents and bottom compensatory flows shaped the outward dispersion of ARGs and pathogenic bacteria from the gulf. The NCM model suggested that water exchange accelerated the diffusion of antibiotics and pathogens, likely enhancing the deterministic assembly process of ARGs and the stochastic assembly process of pathogens. The PLS-PM model revealed that hydrodynamics directly influenced the accumulation of ARGs and pathogenic bacteria, and subsequently affected the diffusion and distribution patterns of ARGs and pathogens by facilitating the propagation of MGEs. Our study overcomes the limitations associated with lake and microenvironmental scale, providing insights and understanding into the transmission mechanisms of ARGs and pathogenic bacteria.}, }
@article {pmid39988071, year = {2025}, author = {Le, NT and Hoang, PH and Nguyen, Q and Truong, MNH and Van Dang, C and Ho, TH and Hoang, PL and Truong, DQ and Nguyen, HTT and Van Le, C and Phan, TTP}, title = {Emergence of mcr-8.2-mediated colistin resistance in Klebsiella pneumoniae isolated from pediatric diarrhea cases in southern Vietnam.}, journal = {Journal of global antimicrobial resistance}, volume = {42}, number = {}, pages = {120-126}, doi = {10.1016/j.jgar.2025.02.007}, pmid = {39988071}, issn = {2213-7173}, abstract = {BACKGROUND: Colistin resistance poses a growing global challenge, particularly in low- and middle-income countries where antibiotic misuse is prevalent. This study investigates the prevalence of colistin resistance in Klebsiella spp. and characterizes the genetic features of resistant isolates, focusing on the mcr-8.2 gene identified in a Klebsiella pneumoniae isolate from pediatric diarrheal cases in southern Vietnam.<br><br>METHODS: Stool samples were collected from 500 pediatric patients (aged 0-5 years) hospitalized with diarrhea in two tertiary hospitals in Ho Chi Minh City between March and September 2022. Samples were cultured on Violet Red Bile Glucose Agar, then presumptive Klebsiella spp. colonies were selected, purified on nutrient agar, and identified using MALDI-TOF MS. Colistin resistance was determined via minimum inhibitory concentration testing, and the presence of mcr genes was confirmed through polymerase chain reaction. Whole-genome sequencing was performed on the Klebsiella pneumoniae strain harboring mcr-8.2 to elucidate resistance mechanisms. Strain characterization was performed using multi-locus sequence typing, while conjugation experiments assessed horizontal gene transfer potential.<br><br>RESULTS: Among 121 Klebsiella spp. isolates, 49 (40.5%) were resistant to colistin. The mcr-1 gene was detected in 31 isolates (25.6%), whereas the mcr-8 was identified in a single isolate (0.8%), with a colistin MIC of 16 &#xb5;g/mL. Genomic analysis revealed 34 antibiotic resistance genes, including mcr-8.2 and multiple &#x3b2;-lactamase genes, alongside plasmid types IncFIB and IncFII. Chromosomal mutations in phoP, phoQ, and lpxM were also implicated in colistin resistance.<br><br>CONCLUSIONS: This study documents the emergence of mcr-8.2-mediated colistin resistance in K. pneumoniae from pediatric diarrhea in Vietnam and highlights a high prevalence of multidrug resistance in Klebsiella spp.. Continuous surveillance of mcr genes and novel therapeutic strategies are urgently needed.}, }
@article {pmid39987875, year = {2025}, author = {Pourrostami Niavol, K and Andaluri, G and Achary, MP and Suri, RPS}, title = {How does carbon to nitrogen ratio and carrier type affect moving bed biofilm reactor (MBBR): Performance evaluation and the fate of antibiotic resistance genes.}, journal = {Journal of environmental management}, volume = {377}, number = {}, pages = {124619}, doi = {10.1016/j.jenvman.2025.124619}, pmid = {39987875}, issn = {1095-8630}, mesh = {*Biofilms ; *Bioreactors ; *Nitrogen/metabolism ; *Carbon ; *Drug Resistance, Microbial/genetics ; Wastewater/microbiology ; Waste Disposal, Fluid/methods ; Denitrification ; Anti-Bacterial Agents/pharmacology ; }, abstract = {With the spread of antibiotic resistance genes (ARGs) in the environment, monitoring and controlling ARGs have become an emerging issue of concern in biological processes. Moving bed biofilm reactors (MBBR) have been gaining attention for application in wastewater treatment. Since the performance of MBBR depends on operational parameters and biocarriers, selection of suitable biocarriers and start-up conditions are vital for efficiency of MBBRs. This study investigates the effects of different carbon-to-nitrogen (C/N) ratios and carrier types on the fate of selected ARGs and microbial communities in four MBBR systems using two conventional (K3 and sponge biocarrier (SB)) and two modified carriers (Fe-Ca@SB and Ze-AC@SB). Results showed that the modified biocarriers achieved higher NH4-N removal and better simultaneous nitrification and denitrification (SND) performance (90%) at C/N of 20. However, as the C/N ratio decreased to 10 and 7, the performance of all bioreactors was approximately similar. Moreover, COD removal of 90% was achieved in all reactors regardless of C/N ratio and carrier type. Further studies on the fate of selected ARGs (tetA, blaTEM, ampR) showed that the C/N ratio could affect the abundance of target ARGs, especially for K3 biocarrier, with tetA being the most abundant gene. Also, as the C/N ratio decreased, intl1 was enriched using K3 and SB. However, for Ze-AC@SB, the increase in the abundance of ARGs and intl1 was the lowest making it a reliable carrier not only in MBBR performance but in the control of ARGs. Metagenomic studies showed that the C/N ratio and carrier type could alter the diversity and structure of the bacterial communities in different MBBR systems, with Proteobacteria being the most abundant phylum in all four systems.}, }
@article {pmid39987738, year = {2025}, author = {Su, H and Xu, W and Hu, X and Xu, Y and Wen, G and Cao, Y}, title = {The impact of microplastics on antibiotic resistance genes, metal resistance genes, and bacterial community in aquaculture environment.}, journal = {Journal of hazardous materials}, volume = {489}, number = {}, pages = {137704}, doi = {10.1016/j.jhazmat.2025.137704}, pmid = {39987738}, issn = {1873-3336}, mesh = {*Microplastics/toxicity ; Aquaculture ; *Water Pollutants, Chemical/toxicity ; *Bacteria/genetics/drug effects ; *Genes, Bacterial/drug effects ; *Drug Resistance, Microbial/genetics ; *Metals/pharmacology ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Microplastics are emerging contaminants. However, their effects on antibiotic resistance genes (ARGs), metal resistance genes (MRGs), and the structure and abundance of bacterial communities, particularly pathogens, in aquaculture environments remains poorly understood. Therefore, this study investigated the effect of microplastics of different sizes on the abundance and distribution of ARGs, MRGs, and bacterial communities in aquaculture environments. The results revealed that, compared with pond water, large microplastics harbored significantly higher ARG abundances, particularly for multidrug-resistant genes; notably, level-I- and -II-risk ARGs were more prevalent on microplastics, highlighting the potential for horizontal gene transfer. Microplastics also exhibited a propensity to aggregate pathogenic bacteria such as Brucella and Pseudomonas, which could pose direct risks to aquatic product safety and public health. Network and differential network analyses revealed significant correlations between bacterial genera and ARG/MRG abundance, particularly on microplastics. Therefore, our findings suggest that microplastics act as vectors for the spread of ARGs, MRGs, and pathogens in aquaculture, potentially leading to the formation of complexes of these materials that threaten ecosystem health and human well-being. This study provides critical insights into the need for targeted management strategies to mitigate microplastic pollution in aquaculture settings.}, }
@article {pmid39981300, year = {2025}, author = {Proença, M and Tanoeiro, L and Fox, JG and Vale, FF}, title = {Prophage dynamics in gastric and enterohepatic environments: unraveling ecological barriers and adaptive transitions.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf017}, pmid = {39981300}, issn = {2730-6151}, abstract = {Phage predation plays a critical role in shaping bacterial genetic diversity, with prophages playing a comparable role. However, the prevalence and genetic variability of prophages within the Helicobacter genus remain inadequately studied. Helicobacter species are clinically significant and occupy distinct digestive system regions, with gastric species (e.g. Helicobacter pylori) residing in the gastric mucosa and enterohepatic species colonizing the liver and intestines of various vertebrates. Here, we address this knowledge gap by analyzing prophage presence and diversity across 343 non-pylori Helicobacter genomes, mapping their distribution, comparing genomic features between gastric and enterohepatic prophages, and exploring their evolutionary relationships with hosts. We identified and analyzed a catalog of 119 new complete and 78 incomplete prophages. Our analysis reveals significant differences between gastric and enterohepatic species. Gastric prophages exhibit high synteny, and cluster in a few groups, indicating a more conserved genetic structure. In contrast, enterohepatic prophages show greater diversity in gene order and content, reflecting their adaptation to varied host environments. Helicobacter cinaedi stands out, harboring a large number of prophages among the enterohepatic species, forming a distinct cohesive group. Phylogenetic analyses reveal a co-evolutionary relationship between several prophages and their bacterial hosts-though exceptions, such as the enterohepatic prophages from H. canis, H. equorum, H. jaachi, and the gastric prophage from H. himalayensis-suggesting more complex co-evolutionary dynamics like host jumps, recombination, and horizontal gene transfer. The insights gained from this study enhance our understanding of prophage dynamics in Helicobacter, emphasizing their role in bacterial adaptation, virulence, and host specificity.}, }
@article {pmid39980242, year = {2025}, author = {Yonemitsu, MA and Sevigny, JK and Vandepas, LE and Dimond, JL and Giersch, RM and Gurney-Smith, HJ and Abbott, CL and Supernault, J and Withler, R and Smith, PD and Weinandt, SA and Garrett, FES and Child, ZJ and Sigo, RLW and Unsell, E and Crim, RN and Metzger, MJ}, title = {Multiple Lineages of Transmissible Neoplasia in the Basket Cockle (C. nuttallii) With Repeated Horizontal Transfer of Mitochondrial DNA.}, journal = {Molecular ecology}, volume = {34}, number = {6}, pages = {e17682}, doi = {10.1111/mec.17682}, pmid = {39980242}, issn = {1365-294X}, support = {//National Research Council/ ; 2208081//Division of Ocean Sciences/ ; A19AP00215//Bureau of Indian Affairs/ ; }, mesh = {Animals ; *DNA, Mitochondrial/genetics ; *Cardiidae/genetics ; *Phylogeny ; *Gene Transfer, Horizontal ; Neoplasms/genetics ; Washington ; }, abstract = {Transmissible cancers are clonal lineages of neoplastic cells able to infect multiple hosts, spreading through populations in the environment as an infectious disease. Transmissible cancers have been identified in Tasmanian devils, dogs, and bivalves. Several lineages of bivalve transmissible neoplasias (BTN) have been identified in multiple bivalve species. In 2019 in Puget Sound, Washington, USA, disseminated neoplasia was observed in basket cockles (Clinocardium nuttallii), a species that is important to the culture and diet of the Suquamish Tribe as well as other tribes with traditional access to the species. To test whether disseminated neoplasia in cockles is a previously unknown lineage of BTN, a nuclear locus was amplified from cockles from Agate Pass, Washington, and sequences revealed evidence of transmissible cancer in several individuals. We used a combination of cytology and quantitative PCR to screen collections of cockles from 11 locations in Puget Sound and along the Washington coastline to identify the extent of contagious cancer spread in this species. Two BTN lineages were identified in these cockles, with one of those lineages (CnuBTN1) being the most prevalent and geographically widespread. Within the CnuBTN1 lineage, multiple nuclear loci support the conclusion that all cancer samples form a single clonal lineage. However, the mitochondrial alleles in each cockle with CnuBTN1 are different from each other, suggesting mitochondrial genomes of this cancer have been replaced multiple times during its evolution, through horizontal transmission. The identification and analysis of these BTNs are critical for broodstock selection, management practices, and repopulation of declining cockle populations, which will enable continued cultural connection and dietary use of the cockles by Coast Salish Tribes.}, }
@article {pmid39979200, year = {2025}, author = {Huisman, JS and Bernhard, A and Igler, C}, title = {Should I stay or should I go: transmission trade-offs in phages and plasmids.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2025.01.007}, pmid = {39979200}, issn = {1878-4380}, abstract = {Mobile genetic elements (MGEs), like temperate bacteriophages and conjugative plasmids, are major vectors of virulence and antibiotic resistance in bacterial populations. For reproductive success, MGEs must balance horizontal and vertical transmission. Yet, the cost of horizontal transmission (metabolic burden or host death) puts these transmission modes at odds. Using virulence-transmission trade-off (VTT) theory, we identify three groups of environmental variables affecting the balance between horizontal and vertical transmission: host density, host physiology, and competitors. We find that general theoretical predictions of the optimal response to environmental cues align with experimental evidence on the regulation of transmission by phages and plasmids. We further highlight gaps between theory and experiments, differences between phages and plasmids, and suggest areas for future research.}, }
@article {pmid39976625, year = {2025}, author = {Lin, YJ and Chen, CH and Chang, IY and Chiang, RL and Wang, HY and Chiu, CH and Chen, YM}, title = {Genomic and transcriptomic insights into the virulence and adaptation of shock syndrome-causing Streptococcus anginosus.}, journal = {Microbiology (Reading, England)}, volume = {171}, number = {2}, pages = {}, doi = {10.1099/mic.0.001535}, pmid = {39976625}, issn = {1465-2080}, mesh = {*Streptococcus anginosus/genetics/pathogenicity ; *Genome, Bacterial ; Humans ; Virulence/genetics ; *Genomic Islands/genetics ; *Streptococcal Infections/microbiology ; Virulence Factors/genetics/metabolism ; Transcriptome ; Shock, Septic/microbiology ; Genomics ; Prophages/genetics ; Adolescent ; Gene Transfer, Horizontal ; Clustered Regularly Interspaced Short Palindromic Repeats ; Bacterial Proteins/genetics/metabolism ; Quorum Sensing/genetics ; }, abstract = {Streptococcus anginosus is a common isolate of the oral cavity and an opportunistic pathogen for systemic infections. Although the pyogenic infections caused by S. anginosus are similar to those caused by Streptococcus pyogenes, S. anginosus lacks most of the well-characterized virulence factors of S. pyogenes. To investigate the pathogenicity of S. anginosus, we analysed the genome of a newly identified S. anginosus strain, KH1, which was associated with toxic shock-like syndrome in an immunocompetent adolescent. The genome of KH1 contains nine genomic islands, two Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated systems and many phage-related proteins, indicating that the genome is influenced by prophages and horizontal gene transfer. Comparative genome analysis of 355 S. anginosus strains revealed a significant difference between the sizes of the pan genome and core genome, reflecting notable strain variations. We further analysed the transcriptomes of KH1 under conditions mimicking either the oral cavity or the bloodstream. We found that in an artificial saliva medium, the expression of a putative quorum quenching system and pyruvate oxidase for H2O2 production was upregulated, which could optimize the competitiveness of S. anginosus in the oral ecosystem. Conversely, in a modified serum medium, purine and glucan biosynthesis, competence and bacteriocin production were significantly upregulated, likely facilitating the survival of KH1 in the bloodstream. These findings indicate that S. anginosus can utilize diverse mechanisms to adapt to different environmental niches and establish infection, despite its lack of toxin production.}, }
@article {pmid39976429, year = {2025}, author = {Smith, EP and Valdivia, RH}, title = {Chlamydia trachomatis: a model for intracellular bacterial parasitism.}, journal = {Journal of bacteriology}, volume = {207}, number = {3}, pages = {e0036124}, pmid = {39976429}, issn = {1098-5530}, support = {R21 AI173599/AI/NIAID NIH HHS/United States ; R21 AI173599-02//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; }, mesh = {*Chlamydia trachomatis/genetics/physiology/pathogenicity ; Humans ; Animals ; *Chlamydia Infections/microbiology ; Virulence ; }, abstract = {Chlamydia comprises a diverse group of obligate intracellular bacteria that cause infections in animals, including humans. These organisms share fascinating biology, including distinct developmental stages, non-canonical cell surface structures, and adaptations to intracellular parasitism. Chlamydia trachomatis is of particular interest due to its significant clinical importance, causing both ocular and sexually transmitted infections. The strain L2/434/Bu, responsible for lymphogranuloma venereum, is the most common strain used to study chlamydial molecular and cell biology because it grows readily in cell culture and is amenable to genetic manipulation. Indeed, this strain has enabled researchers to tackle fundamental questions about the molecular mechanisms underlying Chlamydia's developmental transitions and biphasic lifecycle and cellular adaptations to obligate intracellular parasitism, including characterizing numerous conserved virulence genes and defining immune responses. However, L2/434/Bu is not representative of C. trachomatis strains that cause urogenital infections in humans, limiting its utility in addressing questions of host tropism and immune evasion in reproductive organs. Recent research efforts are shifting toward understanding the unique attributes of more clinically relevant C. trachomatis genovars.}, }
@article {pmid39975115, year = {2025}, author = {Bean, EL and Smith, JL and Grossman, AD}, title = {Identification of insertion sites for the integrative and conjugative element Tn916 in the Bacillus subtilis chromosome.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39975115}, issn = {2692-8205}, support = {R01 GM050895/GM/NIGMS NIH HHS/United States ; R35 GM122538/GM/NIGMS NIH HHS/United States ; R35 GM148343/GM/NIGMS NIH HHS/United States ; }, abstract = {Integrative and conjugative elements (ICEs) are found in many bacterial species and are mediators of horizontal gene transfer. Tn916 is an ICE found in several Gram-positive genera, including Enterococcus, Staphylococcus, Streptococcus, and Clostridum. In contrast to the many ICEs that preferentially integrate into a single site, Tn916 can integrate into many sites in the host chromosome. The consensus integration motif for Tn916, based on analyses of approximately 200 independent insertions, is an approximately 16 bp AT-rich sequence. Here, we describe the identification and mapping of approximately 10[5] independent Tn916 insertions in the Bacillus subtilis chromosome. The insertions were distributed between 1,554 chromosomal sites, and approximately 99% of the insertions were in 303 sites and 65% were in only ten sites. One region, between ykuC and ykyB (kre), was a 'hotspot' for integration with ~22% of the insertions in that single location. In almost all of the top 99% of sites, Tn916 was found with similar frequencies in both orientations relative to the chromosome and relative to the direction of transcription, with a few notable exceptions. Using the sequences of all insertion regions, we determined a consensus motif which is similar to that previously identified for Clostridium difficile. The insertion sites are largely AT-rich, and some sites overlap with regions bound by the nucleoid-associated protein Rok, a functional analog of H-NS of Gram-negative bacteria. Rok functions as a negative regulator of at least some horizontally acquired genes. We found that the presence or absence of Rok had little or no effect on insertion site specificity of Tn916.}, }
@article {pmid39974991, year = {2025}, author = {Hullinger, AC and Green, VE and Klancher, CA and Dalia, TN and Dalia, AB}, title = {Two transmembrane transcriptional regulators coordinate to activate chitin-induced natural transformation in Vibrio cholerae.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.09.30.615920}, pmid = {39974991}, issn = {2692-8205}, abstract = {UNLABELLED: Transcriptional regulators are a broad class of proteins that alter gene expression in response to environmental stimuli. Transmembrane transcriptional regulators (TTRs) are a subset of transcriptional regulators in bacteria that can directly regulate gene expression while remaining anchored in the membrane. Whether this constraint impacts the ability of TTRs to bind their DNA targets remains unclear. Vibrio cholerae uses two TTRs, ChiS and TfoS, to activate horizontal gene transfer by natural transformation in response to chitin by inducing the tfoR promoter (P tfoR). While TfoS was previously shown to bind and regulate P tfoR directly, the role of ChiS in P tfoR activation remains unclear. Here, we show that ChiS directly binds P tfoR upstream of TfoS, and that ChiS directly interacts with TfoS. By independently disrupting ChiS-P tfoR and ChiS-TfoS interactions, we show that ChiS-P tfoR interactions play the dominant role in P tfoR activation. Correspondingly, we show that in the absence of ChiS, recruitment of the P tfoR locus to the membrane is sufficient for P tfoR activation when TfoS is expressed at native levels. Finally, we show that the overexpression of TfoS can bypass the need for ChiS for P tfoR activation. All together, these data suggest a model whereby ChiS both (1) recruits the P tfoR DNA locus to the membrane for TfoS and (2) directly interacts with TfoS, thereby recruiting it to the membrane-proximal promoter. This work furthers our understanding of the molecular mechanisms that drive chitin-induced responses in V. cholerae and more broadly highlights how the membrane-embedded localization of TTRs can impact their activity.<br><br>AUTHOR SUMMARY: Living organisms inhabit diverse environments where they encounter a wide range of stressors. To survive, they must rapidly sense and respond to their surroundings. One universally conserved mechanism to respond to stimuli is via the action of DNA-binding transcriptional regulators. In bacterial species, these regulators are canonically cytoplasmic proteins that freely diffuse within the cytoplasm. In contrast, an emerging class of transmembrane transcriptional regulators (TTRs) directly regulate gene expression from the cell membrane. Prior work shows that two TTRs, TfoS and ChiS, cooperate to activate horizontal gene transfer by natural transformation in response to chitin in the facultative pathogen Vibrio cholerae . However, how these TTRs coordinate to activate this response has remained unclear. Here, we show that ChiS likely promotes TfoS-dependent activation of natural transformation by (1) relocalizing its target promoter to the membrane and (2) recruiting TfoS to the membrane proximal promoter through a direct interaction. Together, these results inform our understanding of both the V. cholerae chitin response and how TTR function can be impacted by their membrane localization.}, }
@article {pmid39970645, year = {2025}, author = {Wang, W and Tao, J and Pang, R and Zhang, L and Zhang, Y and Su, Y and Li, W and Hong, S and Kim, H and Zhan, M and Xie, B}, title = {Effect of alkaline-thermal pretreatment on biodegradable plastics degradation and dissemination of antibiotic resistance genes in co-compost system.}, journal = {Journal of hazardous materials}, volume = {489}, number = {}, pages = {137644}, doi = {10.1016/j.jhazmat.2025.137644}, pmid = {39970645}, issn = {1873-3336}, mesh = {Biodegradation, Environmental ; *Drug Resistance, Microbial/genetics ; *Composting ; *Biodegradable Plastics/chemistry/metabolism ; *Sodium Hydroxide/chemistry ; Genes, Bacterial ; Soil Microbiology ; Bacteria/genetics ; }, abstract = {Biodegradable plastics (BDPs) are an eco-friendly alternative to traditional plastics in organic waste, but their microbial degradation and impact on antibiotic resistance genes (ARGs) transmission during co-composting remain poorly understood. This study examines how alkaline-thermal pretreatment enhances BDPs degradation and influences the fate of ARGs and mobile genetic elements (MGEs) in co-composting. Pretreatment with 0.1 mol/L NaOH at 100℃ for 40 minutes increased the surface roughness and hydrophilicity of BDPs while reducing their molecular weight and thermal stability. Incorporating pretreated BDPs film (8 g/kg-TS) into the compost reduced the molecular weight of the BDPs by 59.70 % during the maturation stage, facilitating compost heating and prolonging the thermophilic stage. However, incomplete degradation of BDPs releases numerous smaller-sized microplastics, which can act as carriers for microorganisms, facilitating the dissemination of ARGs across environments and posing significant ecological and public health risks. Metagenomic analysis revealed that pretreatment enriched plastic-degrading bacteria, such as Thermobifida fusca, on BDPs surfaces and accelerated microbial plastic degradation during the thermophilic stage, but also increased ARGs abundance. Although pretreatment significantly reduced MGEs abundance (tnpA, IS19), the risk of ARGs dissemination remained. Three plastic-degrading bacteria (Pigmentiphaga sp002188465, Bacillus clausii, and Bacillus altitudinis) were identified as ARGs hosts, underscoring the need to address the risk of horizontal gene transfer of ARGs associated with pretreatment in organic waste management.}, }
@article {pmid39970091, year = {2024}, author = {Sazykin, IS and Sazykina, MA and Litsevich, AR}, title = {[Distribution of Antibiotic Resistance Genes in Microbial Communities: The Impact of Anthropogenic Pollution].}, journal = {Molekuliarnaia biologiia}, volume = {58}, number = {6}, pages = {937-952}, pmid = {39970091}, issn = {0026-8984}, mesh = {*Bacteria/genetics/drug effects/classification/metabolism ; *Oxidative Stress/drug effects/genetics ; Drug Resistance, Bacterial/genetics/drug effects ; Gene Transfer, Horizontal ; Humans ; Anti-Bacterial Agents/pharmacology ; Environmental Pollution ; Microbiota/drug effects/genetics ; Drug Resistance, Microbial/genetics ; Animals ; Genes, Bacterial ; Wastewater/microbiology ; Evolution, Molecular ; }, abstract = {Issues related to the spread of antibiotic resistance genes in environmental microbial communities are considered. "Hotspots" of adaptive evolution, accumulation, and spread of antibiotic-resistant bacteria and genetic material of antibiotic resistance are highlighted. Such "hotspots" include anthropogenic ecosystems, such as municipal wastewater treatment plants, municipal solid waste landfills, livestock enterprises, and agrocenoses. The influence of various types of pollutants and biotic factors on enhancement of mutagenesis and horizontal transfer of antibiotic resistance genes is considered. The role of mobile genetic elements in mobilization and accelerated spread of resistance determinants is shown. Special attention is paid to the role of oxidative stress and stress regulons, which are activated for realization and control of molecular genetic mechanisms of adaptive evolution of bacteria and the horizontal distribution of genetic material in bacterial populations. Oxidative stress is identified as one of the main activators of genome destabilization and adaptive evolution of bacteria.}, }
@article {pmid39970089, year = {2024}, author = {Shaskolskiy, BL and Kandinov, ID and Gryadunov, DA and Kravtsov, DV}, title = {[Unveiling Neisseria gonorrhoeae Survival: Genetic Variability, Pathogenesis, and Antimicrobial Drug Resistance].}, journal = {Molekuliarnaia biologiia}, volume = {58}, number = {6}, pages = {887-926}, pmid = {39970089}, issn = {0026-8984}, mesh = {*Neisseria gonorrhoeae/genetics/pathogenicity/drug effects/immunology ; Humans ; *Gonorrhea/drug therapy/microbiology/genetics/immunology ; *Drug Resistance, Bacterial/genetics ; Genetic Variation ; Female ; Gene Transfer, Horizontal ; Male ; Anti-Bacterial Agents/therapeutic use/pharmacology ; Immune Evasion/genetics ; Type IV Secretion Systems/genetics ; }, abstract = {Despite nearly a century of therapy for gonococcal infection with a variety of antimicrobials, more than 80 million cases of the disease are reported annually worldwide. The gonorrhea pathogen, Neisseria gonorrhoeae, exhibits an exceptional capability of developing antimicrobial resistance due to its high genetic flexibility. As an obligate pathogen, the gonococcus has evolved mechanisms to evade host defenses by engaging with the innate and adaptive immune responses in both men and women. N. gonorrhoeae can establish residence within epithelial cells, macrophages, and neutrophils. Strains resistant to each of the drugs used in gonorrhea therapy have emerged via genetic variation and horizontal gene transfer. The type IV secretion system plays a critical role in horizontal gene transfer (HGT), driving the evolvement of antimicrobial resistance. The review explores the pathogenesis and immune evasion mechanisms, antimicrobial resistance, genetic variability, laboratory analysis methods for the pathogen, and emerging trends in diagnosis and treatment of gonococcal infections.}, }
@article {pmid39966712, year = {2025}, author = {Hoile, AE and Holland, PWH and Mulhair, PO}, title = {Gene novelty and gene family expansion in the early evolution of Lepidoptera.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {161}, pmid = {39966712}, issn = {1471-2164}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Lepidoptera/genetics ; *Evolution, Molecular ; *Phylogeny ; *Gene Duplication ; *Multigene Family ; Gene Transfer, Horizontal ; Insect Proteins/genetics ; }, abstract = {BACKGROUND: Almost 10% of all known animal species belong to Lepidoptera: moths and butterflies. To understand how this incredible diversity evolved we assess the role of gene gain in driving early lepidopteran evolution. Here, we compared the complete genomes of 115 insect species, including 99 Lepidoptera, to search for novel genes coincident with the emergence of Lepidoptera.<br><br>RESULTS: We find 217 orthogroups or gene families which emerged on the branch leading to Lepidoptera; of these 177 likely arose by gene duplication followed by extensive sequence divergence, 2 are candidates for origin by horizontal gene transfer, and 38 have no known homology outside of Lepidoptera and possibly arose via de novo gene genesis. We focus on two new gene families that are conserved across all lepidopteran species and underwent extensive duplication, suggesting important roles in lepidopteran biology. One encodes a family of sugar and ion transporter molecules, potentially involved in the evolution of diverse feeding behaviours in early Lepidoptera. The second encodes a family of unusual propeller-shaped proteins that likely originated by horizontal gene transfer from Spiroplasma bacteria; we name these the Lepidoptera propellin genes.<br><br>CONCLUSION: We provide the first insights into the role of genetic novelty in the early evolution of Lepidoptera. This gives new insight into the rate of gene gain during the evolution of the order as well as providing context on the likely mechanisms of origin. We describe examples of new genes which were retained and duplicated further in all lepidopteran species, suggesting their importance in Lepidoptera evolution.}, }
@article {pmid39966674, year = {2025}, author = {Mondol, SM and Hossain, MA and Haque, FKM}, title = {Comprehensive genomic insights into a highly pathogenic clone ST656 of mcr8.1 containing multidrug-resistant Klebsiella pneumoniae from Bangladesh.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {5909}, pmid = {39966674}, issn = {2045-2322}, mesh = {*Klebsiella pneumoniae/genetics/drug effects/pathogenicity ; Bangladesh ; *Drug Resistance, Multiple, Bacterial/genetics ; *Genome, Bacterial ; *Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; Humans ; Genomics/methods ; Klebsiella Infections/microbiology ; Virulence Factors/genetics ; Microbial Sensitivity Tests ; Plasmids/genetics ; Colistin/pharmacology ; }, abstract = {Antimicrobial resistance (AMR) is a pressing global health issue, intensified by the spread of resistant pathogens like Klebsiella pneumoniae (K. pneumoniae), which frequently causes hospital-acquired infections. This study focuses on a multidrug-resistant K. pneumoniae sequence type (ST) 656 strain, isolated from canal water in Bangladesh. Whole-genome sequencing and comparative genomic analysis revealed extensive resistance mechanisms and genetic elements underlying its adaptability. The strain exhibited resistance to colistin and multiple β-lactam antibiotics, containing key resistance genes such as mcr8.1, blaLAP-2, blaTEM-1, blaSHV-11 and blaOXA-1, alongside genes for copper, zinc, and silver resistance, indicating survival capability in metal-rich environments. Virulence factor analysis identified genes supporting adhesion, biofilm formation, and immune evasion, amplifying its pathogenic potential. Plasmid and phage analyses revealed mobile genetic elements, highlighting the role of horizontal gene transfer in AMR dissemination. The study included a pangenome analysis using a dataset of 32 publicly available K. pneumoniae sequence type (ST) 656 genomes, demonstrating evidence of an expanding pangenome for K. pneumoniae ST656. This study emphasized the role of environmental sources in AMR spread and the importance of continued surveillance, particularly in settings with intensive antibiotic usage, to mitigate the spread of high-risk, multidrug-resistant clones like K. pneumoniae ST656.}, }
@article {pmid39965334, year = {2025}, author = {Zhang, J and Lei, H and Huang, J and Wong, JWC and Li, B}, title = {Co-occurrence and co-expression of antibiotic, biocide, and metal resistance genes with mobile genetic elements in microbial communities subjected to long-term antibiotic pressure: Novel insights from metagenomics and metatranscriptomics.}, journal = {Journal of hazardous materials}, volume = {489}, number = {}, pages = {137559}, doi = {10.1016/j.jhazmat.2025.137559}, pmid = {39965334}, issn = {1873-3336}, mesh = {*Anti-Bacterial Agents/pharmacology ; Chloramphenicol/pharmacology ; Metagenomics ; *Genes, Bacterial ; *Disinfectants/pharmacology ; *Bacteria/genetics/drug effects ; *Interspersed Repetitive Sequences ; Drug Resistance, Microbial/genetics ; Lincomycin/pharmacology ; Gene Transfer, Horizontal ; Transcriptome ; Metals/pharmacology ; *Drug Resistance, Bacterial/genetics ; }, abstract = {The burgeoning of antibiotic resistance has emerged as a pressing global challenge. To gain a deeper understanding of the interactions between antibiotic resistance genes (ARGs), biocide and metal resistance genes (BRGs&amp;MRGs), and mobile genetic elements (MGEs), this study utilized metagenomics and metatranscriptomics to investigate their co-occurrence and co-expression in two consortia subjected to long-term exposure to chloramphenicol and lincomycin. Long-term exposure to these antibiotics resulted in significant disparities in resistance profiles: ConsortiumCAP harbored 130 ARGs and 150 BRGs&amp;MRGs, while ConsortiumLIN contained 57 ARGs and 32 BRGs&amp;MRGs. Horizontal gene transfer (HGT) events were predicted at 125 and 300 instances in ConsortiumCAP and ConsortiumLIN, respectively, facilitating the emergence of multidrug-resistant bacteria, such as Caballeronia (10 ARGs, 2 BRGs&amp;MRGs), Cupriavidus (2 ARGs, 10 BRGs&amp;MRGs), and Bacillus (14 ARGs, 21 BRGs&amp;MRGs). Chloramphenicol exposure significantly enriched genes linked to phenicol resistance (floR, capO) and co-expressed ARGs and BRGs&amp;MRGs, while lincomycin exerted narrower effects on resistance genes. Additionally, both antibiotics modulated the expression of degradation genes and virulence factors, highlighting their role in altering bacterial substrate utilization and pathogenic traits. This study provides quantitative insights into the impact of antibiotics on microbial resistance profiles and functions at both DNA and RNA levels, highlighting the importance of reducing antibiotic pollution and limiting the spread of resistance genes in the environment.}, }
@article {pmid39965000, year = {2025}, author = {Hullinger, AC and Green, VE and Klancher, CA and Dalia, TN and Dalia, AB}, title = {Two transmembrane transcriptional regulators coordinate to activate chitin-induced natural transformation in Vibrio cholerae.}, journal = {PLoS genetics}, volume = {21}, number = {2}, pages = {e1011606}, pmid = {39965000}, issn = {1553-7404}, support = {R35 GM128674/GM/NIGMS NIH HHS/United States ; }, mesh = {*Vibrio cholerae/genetics/metabolism ; *Chitin/metabolism/genetics ; *Gene Expression Regulation, Bacterial ; *Promoter Regions, Genetic/genetics ; *Bacterial Proteins/genetics/metabolism ; *Transcription Factors/genetics/metabolism ; Gene Transfer, Horizontal ; }, abstract = {Transcriptional regulators are a broad class of proteins that alter gene expression in response to environmental stimuli. Transmembrane transcriptional regulators (TTRs) are a subset of transcriptional regulators in bacteria that can directly regulate gene expression while remaining anchored in the membrane. Whether this constraint impacts the ability of TTRs to bind their DNA targets remains unclear. Vibrio cholerae uses two TTRs, ChiS and TfoS, to activate horizontal gene transfer by natural transformation in response to chitin by inducing the tfoR promoter (PtfoR). While TfoS was previously shown to bind and regulate PtfoR directly, the role of ChiS in PtfoR activation remains unclear. Here, we show that ChiS directly binds PtfoR upstream of TfoS, and that ChiS directly interacts with TfoS. By independently disrupting ChiS-PtfoR and ChiS-TfoS interactions, we show that ChiS-PtfoR interactions play the dominant role in PtfoR activation. Correspondingly, we show that in the absence of ChiS, recruitment of the PtfoR locus to the membrane is sufficient for PtfoR activation when TfoS is expressed at native levels. Finally, we show that the overexpression of TfoS can bypass the need for ChiS for PtfoR activation. All together, these data suggest a model whereby ChiS both (1) recruits the PtfoR DNA locus to the membrane for TfoS and (2) directly interacts with TfoS, thereby recruiting it to the membrane-proximal promoter. This work furthers our understanding of the molecular mechanisms that drive chitin-induced responses in V. cholerae and more broadly highlights how the membrane-embedded localization of TTRs can impact their activity.}, }
@article {pmid39964597, year = {2025}, author = {Palanikumar, P and Nathan, B and Muthusamy, K and M, S and Natesan, S and Sampathrajan, V}, title = {Unravelling the Antibiotic Resistance: Molecular Insights and Combating Therapies.}, journal = {Applied biochemistry and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {39964597}, issn = {1559-0291}, abstract = {Antibiotics, the full-stop of invasive bacteria, have been used in clinical setups from unthreatening fever to massive challenging therapies. Constant dependency on medication upsurges the evasion of microbes from antibiotics contemporarily along with ecological footprint. Thus, the infested pathogen became resilient to antibiotics, disguised as multidrug-resistant bacteria (MDR), pandrug-resistant bacteria (PDR), and extensively drug-resistant bacteria (XDR). The etymology of genetic modifications and horizontal gene transfer played an external influence on the arising resurgence. Also, intrinsic parameters, such as antibiotic efflux pumps and the formation of biofilms, encouraged intense resistance to antibiotic drugs. This aggravated resistance in microbes builds up resistome in the environment due to selective pressure; thereby drastic devastation of people suffering from disastrous diseases is mournful. Since novelite approaches for broad-spectrum antibiotics against drug resistance microbes are grueling challenges in these crucial times. This scientific study has come up with neoteric methodologies to elude immediate consequences and health hazards. Inculcating ancestral treatment towards pharmacognosy as adjuvants to the prevailing hi-fi nanotechnology, phage and algal therapy, genome mining, and bioinformatics databases are the optimizing inventions for actual and prospective living.}, }
@article {pmid39960880, year = {2025}, author = {Zou, W and Ji, Y and Guan, J and Sun, Y}, title = {MOSTPLAS: a self-correction multi-label learning model for plasmid host range prediction.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {3}, pages = {}, pmid = {39960880}, issn = {1367-4811}, support = {11214924//Research Grants Council/ ; //City University of Hong Kong/ ; }, mesh = {*Plasmids/genetics ; *Algorithms ; Host Specificity ; Machine Learning ; Bacteria/genetics ; Computational Biology/methods ; Gene Transfer, Horizontal ; }, abstract = {MOTIVATION: Plasmids play an essential role in horizontal gene transfer, aiding their host bacteria in acquiring beneficial traits like antibiotic and metal resistance. There exist some plasmids that can transfer, replicate, or persist in multiple organisms. Identifying the relatively complete host range of these plasmids provides insights into how plasmids promote bacterial evolution. To achieve this, we can apply multi-label learning models for plasmid host range prediction. However, there are no databases providing the detailed and complete host labels of these broad-host-range plasmids. Without adequate well-annotated training samples, learning models can fail to extract discriminative feature representations for plasmid host prediction.<br><br>RESULTS: To address this problem, we propose a self-correction multi-label learning model called MOSTPLAS. We design a pseudo label learning algorithm and a self-correction asymmetric loss to facilitate the training of multi-label learning model with samples containing some unknown missing labels. We conducted a series of experiments on the NCBI RefSeq plasmid database, the PLSDB 2025 database, plasmids with experimentally determined host labels, the Hi-C dataset, and the DoriC dataset. The benchmark results against other plasmid host range prediction tools demonstrated that MOSTPLAS recognized more host labels while keeping a high precision.<br><br>MOSTPLAS is implemented with Python, which can be downloaded at https://github.com/wzou96/MOSTPLAS. All relevant data we used in the experiments can be found at https://zenodo.org/doi/10.5281/zenodo.14708999.}, }
@article {pmid39960859, year = {2025}, author = {Chess, MM and Foley, S and Ettensohn, CA}, title = {Horizontal Transfer of msp130 Genes and the Evolution of Metazoan Biocalcification.}, journal = {Genome biology and evolution}, volume = {17}, number = {2}, pages = {}, pmid = {39960859}, issn = {1759-6653}, support = {P41 HD095831/HD/NICHD NIH HHS/United States ; IOS2004952//National Science Foundation/ ; P41HD095831/NH/NIH HHS/United States ; }, mesh = {*Gene Transfer, Horizontal ; Animals ; *Phylogeny ; *Evolution, Molecular ; Calcification, Physiologic/genetics ; Gene Duplication ; Bacteria/genetics ; }, abstract = {The formation of calcified skeletons is crucial for the development, physiology, and ecology of many marine metazoans. The evolutionary origins of the genetic toolkit required for biocalcification are widely debated. MSP130 proteins, originally identified through their expression specifically by sea urchin skeletal cells, have been hypothesized to have been acquired by metazoans from bacteria through horizontal gene transfer. Here, we provide support for a horizontal gene transfer-based origin of metazoan MSP130 proteins by conducting phylogenetic and in silico protein analyses utilizing high-quality genomes. We show that msp130 genes underwent duplications within almost all biocalcifying bilaterian phyla and identify highly conserved intron-exon junctions specific to bilaterian msp130 genes. The absence of MSP130 proteins in calcifying, nonbilaterian metazoans and other basal eukaryotes suggests that an ancestral msp130 gene underwent a horizontal gene transfer event that predates bilaterians, but not metazoans. We report striking structural similarities between bilaterian and bacterial MSP130 proteins, with each containing a seven-bladed, barrel-like motif that encompasses a choice-of-anchor domain, and identify highly conserved, predicted Ca2+-binding sites associated with the barrels. These findings point to a conserved, ancient function for MSP130 proteins in biocalcification and support the view that lateral transfer of bacterial genes supported the appearance of calcified animal skeletons.}, }
@article {pmid39955358, year = {2025}, author = {Mahamud, SMI and Oishy, SH and Roy, S and Pal, K and Rubaiyat, RN and Ansary, MM}, title = {Comparative Genomic Analysis of 66 Bacteriophages Infecting Morganella morganii Strains.}, journal = {Current microbiology}, volume = {82}, number = {4}, pages = {137}, pmid = {39955358}, issn = {1432-0991}, mesh = {*Morganella morganii/virology/genetics ; *Bacteriophages/genetics/classification/isolation &amp; purification ; *Genome, Viral ; *Phylogeny ; *Genomics ; Host Specificity ; Base Composition ; Humans ; }, abstract = {Bacteriophages are viruses that specifically target bacteria and play a crucial role in influencing bacterial evolution and the transmission of antibiotic resistance. In this study, we explored the genomic profiles of 66 bacteriophages that infect Morganella morganii, an opportunistic pathogen associated with difficult-to-treat nosocomial and urinary tract infections. Our findings highlight the extraordinary diversity within this phage population, reflected in their genomic features, evolutionary relationships, and potential contributions to bacterial pathogenicity. The 66 phage genomes exhibited diversity in size, spanning from 6 to 115 kilobase pairs, reflecting a heterogeneous genetic material and coding potential. Their guanine-cytosine (G+C) content varied widely, from 43.3% to 64.6%, suggesting diverse evolutionary origins and adaptive strategies. Phylogenetic analysis identified ten distinct evolutionary clusters, some classified as singletons, highlighting unique evolutionary pathways. Several clusters included phages capable of infecting multiple M. morganii strains, indicating a broader host range and the potential for horizontal gene transfer. Genomic analysis also determined a substantial number of hypothetical proteins, underscoring the need for further investigation to clarify their functions. Importantly, we identified a wide array of antibiotic resistance and virulence-associated genes within these phage genomes, illuminating their potential to impact the treatment of M. morganii infections and develop new, more virulent strains. These findings highlight the critical role of phage-mediated gene transfer in shaping bacterial evolution and facilitating the transmission of antibiotic resistance.}, }
@article {pmid39954947, year = {2025}, author = {Souza, HCA and Panzenhagen, P and Dos Santos, AMP and Portes, AB and Fidelis, J and Conte-Junior, CA}, title = {Unravelling the advances of CRISPR-Cas9 as a precise antimicrobial therapy: A systematic review.}, journal = {Journal of global antimicrobial resistance}, volume = {42}, number = {}, pages = {51-60}, doi = {10.1016/j.jgar.2025.02.002}, pmid = {39954947}, issn = {2213-7173}, abstract = {UNLABELLED: Antimicrobial resistance is a critical public health threat, compromising treatment effectiveness. The spread of resistant pathogens, facilitated by genetic variability and horizontal gene transfer, primarily through plasmids, poses significant challenges to health systems.<br><br>OBJECTIVE: This review explores the potential of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technology and Cas9 nucleases in combating antimicrobial resistance.<br><br>METHODS: The literature review followed the PRISMA guidelines using PubMed, Embase, and Scopus databases until July 2023.<br><br>RESULTS: The Enterobacterales family, particularly Escherichia coli, was the main focus. The resistance genes targeted were mainly associated with &#x3b2;-lactam antibiotics, specifically bla genes, and colistin resistance linked to the mcr-1 gene. Plasmid vectors have been the primary delivery method for the CRISPR-Cas9 system, with conjugative plasmids resensitizing bacterial strains to various antimicrobials. Other delivery methods included electroporation, phage-mediated delivery, and nanoparticles. The efficacy of the CRISPR-Cas9 system in resensitizing bacterial strains ranged from 4.7% to 100%.<br><br>CONCLUSIONS: Despite challenges in delivery strategies and clinical application, studies integrating nanotechnology present promising approaches to overcome these limitations. This review highlights new perspectives for the clinical use of CRISPR-Cas9 as a specific and efficient antimicrobial agent, potentially replacing traditional broad-spectrum antimicrobials in the future.}, }
@article {pmid39954386, year = {2025}, author = {Vilar, LC and Rego, ACS and Miguel, MAL and Paranhos, RPDR and Laport, MS and Rossi, CC and Giambiagi-deMarval, M}, title = {Staphylococcus spp. and methicillin-resistance gene mecA dispersion in seawater: A case study of Guanabara Bay's recreational and touristic waters.}, journal = {Comparative immunology, microbiology and infectious diseases}, volume = {118}, number = {}, pages = {102326}, doi = {10.1016/j.cimid.2025.102326}, pmid = {39954386}, issn = {1878-1667}, mesh = {*Staphylococcus/genetics/drug effects/isolation &amp; purification ; *Seawater/microbiology ; *Methicillin Resistance/genetics ; *Bacterial Proteins/genetics ; *Anti-Bacterial Agents/pharmacology ; Humans ; Brazil ; Microbial Sensitivity Tests ; CRISPR-Cas Systems ; Bays/microbiology ; Staphylococcal Infections/microbiology ; Penicillin-Binding Proteins/genetics ; Genetic Variation ; }, abstract = {Environmental Staphylococci, particularly coagulase-negative Staphylococci (CoNS), are known reservoirs of antimicrobial resistance genes and human-animal opportunistic pathogens, yet their role within the One Health framework remains underexplored. In this study, we isolated 12 species of CoNS from two sites 10 km apart in Guanabara Bay, Rio de Janeiro, with the most frequent species being the opportunistic Staphylococcus saprophyticus (30.3 %), Staphylococcus warneri (25.7 %), and Staphylococcus epidermidis (16.7 %). GTG5-PCR fingerprinting revealed significant genetic diversity, yet identical profiles persisted across both sites throughout the year, indicating strain dispersion and persistence. Among the 66 strains analyzed, 42 exhibited resistance to clinically significant antimicrobials, including methicillin-resistant strains harboring the mecA gene. Remarkably, 22.7 % of the strains carried CRISPR-Cas systems, a frequency unusually high for Staphylococcus spp., suggesting that bacteriophage pressure in the seawater environment may drive this increase. The presence of antimicrobial-resistant CoNS in Guanabara Bay, a popular recreational area, represents a potential public health risk.}, }
@article {pmid39952999, year = {2025}, author = {Koper, P and Wysokiński, J and Żebracki, K and Decewicz, P and Dziewit, &#x141; and Kalita, M and Palusińska-Szysz, M and Mazur, A}, title = {Comparative analysis of Legionella lytica genome identifies specific metabolic traits and virulence factors.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {5554}, pmid = {39952999}, issn = {2045-2322}, support = {2019/03/X/NZ2/00976//Narodowe Centrum Nauki/ ; 2019/03/X/NZ2/00976//Narodowe Centrum Nauki/ ; 2019/03/X/NZ2/00976//Narodowe Centrum Nauki/ ; 2019/03/X/NZ2/00976//Narodowe Centrum Nauki/ ; 2019/03/X/NZ2/00976//Narodowe Centrum Nauki/ ; 2019/03/X/NZ2/00976//Narodowe Centrum Nauki/ ; }, mesh = {*Virulence Factors/genetics ; *Legionella/genetics/pathogenicity ; *Genome, Bacterial ; Plasmids/genetics ; Phylogeny ; Bacterial Proteins/genetics/metabolism ; Virulence/genetics ; Molecular Sequence Annotation ; }, abstract = {The complete genome of Legionella lytica PCM 2298 was sequenced and analyzed to provide insights into its genomic structure, virulence potential, and evolutionary position within the Legionella genus. The genome comprised a 3.2 Mbp chromosome and two plasmids, pLlyPCM2298_1 and pLlyPCM2298_2, contributing to a total genome size of 3.7 Mbp. Functional annotation identified 3,165 coding sequences, including genes associated with known virulence factors such as the major outer membrane protein (MOMP), the macrophage infectivity potentiator (Mip), and a comprehensive set of secretion systems (type II, type IVA, and type IVB Dot/Icm type IV secretion system). Notably, L. lytica contributed 383 unique genes to the Legionella pangenome, with 232 identified effector proteins, of which 35 were plasmid-encoded. The identification of unique genes, particularly those on plasmids, suggests an evolutionary strategy favoring horizontal gene transfer and niche adaptation. The effector repertoire included proteins with domains characteristic of host interaction strategies, such as ankyrin repeats and protein kinases. Comparative analyses showed that while L. lytica shares core virulence traits with other Legionella species, it has distinct features that may contribute to its adaptability and pathogenic potential. These findings underscore the genomic diversity within the genus and contribute to a deeper understanding of Legionella's ecological and clinical significance. A custom web application was developed using the R Shiny library, enabling users to interactively explore the expanded Legionella pangenome through UpSet plots.}, }
@article {pmid39952513, year = {2025}, author = {Ke, F and Liu, AK and Zhang, QY}, title = {Extra peptidase of a cyanophage confers its stronger lytic effect on bloom-forming Microcystis aeruginosa.}, journal = {International journal of biological macromolecules}, volume = {304}, number = {Pt 2}, pages = {140979}, doi = {10.1016/j.ijbiomac.2025.140979}, pmid = {39952513}, issn = {1879-0003}, mesh = {*Microcystis/virology ; *Bacteriophages/genetics ; *Peptide Hydrolases/metabolism/genetics ; Harmful Algal Bloom ; Viral Proteins/genetics/metabolism ; }, abstract = {Microcystis covers important cyanobacteria species that causes harmful algal blooms. Cyanophages are viruses that infect and lyse cyanobacteria and have been considered as potential cyanobacteria control strategy. Present study isolated two cyanophage strains, MaMV-CH01 (CH01) and MaMV-CH02 (CH02), infecting M. aeruginosa. Growth curves showed that CH01 has a stronger proliferation ability and host cell lysis capability than CH02. Combined with genomic, gene structure and function analysis, as well as biologic testing including infectivity, we confirmed that there is widespread horizontal gene transfer between the cyanophages and cyanobacteria, enabling the cyanophages to carry a series of auxiliary metabolic genes (AMG) related to host's metabolism. Moreover, compared with CH02, the cyanophage CH01 carrying extra AMG, a peptidase encoding gene (82R), exhibited stronger lytic activity against its host. Expression of CH01 82R in vitro showed strong bacteriostatic activity. Further, testing the cyanophage's ability to form plaques showed that the CH01(AMG[+]), which encodes the aforementioned peptidase, can form larger plaques, with an area of about threefold than that formed by CH02(AMG[-]). Above results indicated that the cyanophages with specific peptidase possessed stronger algicidal efficiency, which provided a direction for finding efficient cyanophages to regulate the population of bloom-forming cyanobacteria.}, }
@article {pmid39952130, year = {2025}, author = {Ding, L and Zhang, CM and Jiang, HY}, title = {Lipid-lowering drug clofibric acid promotes conjugative transfer of RP4 plasmid carrying antibiotic resistance genes by multiple mechanisms.}, journal = {Journal of hazardous materials}, volume = {489}, number = {}, pages = {137560}, doi = {10.1016/j.jhazmat.2025.137560}, pmid = {39952130}, issn = {1873-3336}, mesh = {*Plasmids/genetics ; *Clofibric Acid/pharmacology ; *Drug Resistance, Bacterial/genetics ; Escherichia coli/genetics/drug effects ; Reactive Oxygen Species/metabolism ; *Drug Resistance, Microbial/genetics ; *Gene Transfer, Horizontal/drug effects ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; *Conjugation, Genetic/drug effects ; }, abstract = {Antibiotic resistance represents a growing global health crisis, predominantly driven by the selective pressure imposed by antibiotics, which facilitates horizontal gene transfer. However, the potential role of non-antibiotic pharmaceuticals in promoting or enabling the spread of antibiotic resistance genes (ARGs) remains poorly understood. This study provided novel insights into the capacity of clofibric acid, a lipid-lowering drug, to enhance the conjugative transfer of ARGs, and deeply explored the underlying multiple mechanisms. The findings revealed that clofibric acid, at concentrations ranging from 0.01 to 1000 μg/L, significantly promoted the transfer efficiency of the RP4 plasmid carrying multiple ARGs. This enhancement was accompanied by a cascade of stress responses in bacterial cells, including elevated production of reactive oxygen species, increased secretion of extracellular polymeric substances, reduced bacterial surface zeta potential, and heightened cell membrane permeability. The physiological alterations were closely linked to significant changes in the expression of genes associated with these processes. Our results highlighted the potential of non-antibiotic pharmaceuticals to contribute to the dissemination of antibiotic resistance, offering a critical foundation for further research into the environmental and public health implications of such compounds.}, }
@article {pmid39952116, year = {2025}, author = {Hirayama, A and Akase, H and Hayase, Y and Maeda, S}, title = {Subminimal inhibitory concentrations of antibiotics and anaerobic conditions promote Escherichia coli cell-to-cell plasmid transformation in biofilms.}, journal = {Biochemical and biophysical research communications}, volume = {752}, number = {}, pages = {151464}, doi = {10.1016/j.bbrc.2025.151464}, pmid = {39952116}, issn = {1090-2104}, mesh = {*Biofilms/drug effects/growth &amp; development ; *Escherichia coli/genetics/drug effects/metabolism ; *Plasmids/genetics/metabolism ; *Anti-Bacterial Agents/pharmacology ; Anaerobiosis ; Microbial Sensitivity Tests ; Transformation, Bacterial ; }, abstract = {In recent years, subminimal inhibitory concentrations (sub-MIC) of antibiotics have been found to exert unexpected physiological effects on bacterial cells, beyond their common growth-inhibition properties. Our previous research demonstrated that sub-MIC ampicillin, combined with mild mechanical stimulation using glass balls, significantly promotes intercellular plasmid transformation (cell-to-cell plasmid transformation) in Escherichia coli within air-solid biofilms. In this study, we investigated whether other antibiotics with diverse mechanisms of action similarly enhance plasmid transformation. Our findings revealed that various antibiotics indeed promote cell-to-cell plasmid transformation, and this effect was observed under both aerobic and anaerobic conditions. Interestingly, anaerobic conditions resulted in higher frequencies of plasmid transformation compared to aerobic conditions. Supporting these results, we found that several single-gene knockouts of aerobic respiratory chain components under aerobic conditions also enhanced plasmid transformation. This suggests that the unavailability of aerobic respiration may favor the process of intercellular plasmid transfer. Collectively, our results indicate that a wide range of sub-MIC antibiotics can stimulate horizontal plasmid transfer and that anaerobic conditions are particularly conducive to this process. Based on these findings, we hypothesize that the anaerobic gut environment of antibiotic-treated animals or humans, characterized by biofilm-like high cell densities of antibiotic-exposed bacteria and regular peristaltic and segmental movements, could serve as a favorable niche for horizontal gene transfer via intercellular plasmid transformation.}, }
@article {pmid39950610, year = {2025}, author = {Jang, YJ and Oh, SD and Hong, JK and Park, JC and Lee, SK and Chang, A and Yun, DW and Lee, B}, title = {Impact of genetically modified herbicide-resistant maize on rhizosphere bacterial communities.}, journal = {GM crops &amp; food}, volume = {16}, number = {1}, pages = {186-198}, pmid = {39950610}, issn = {2164-5701}, mesh = {*Zea mays/genetics/microbiology/growth &amp; development/drug effects ; *Rhizosphere ; *Plants, Genetically Modified/genetics ; *Soil Microbiology ; *Bacteria/genetics/drug effects ; *Herbicides/pharmacology ; *RNA, Ribosomal, 16S/genetics ; Herbicide Resistance/genetics ; Acetyltransferases/genetics ; }, abstract = {Rhizosphere bacterial community studies offer valuable insights into the environmental implications of genetically modified (GM) crops. This study compared the effects of a non-GM maize cultivar, namely Hi-IIA, with those of a herbicide-resistant maize cultivar containing the phosphinothricin N-acetyltransferase gene on the rhizosphere bacterial community across growth stages. 16s rRNA amplicon sequencing and data analysis tools revealed no significant differences in bacterial community composition or diversity between the cultivars. Principal component analysis revealed that differences in community structure were driven by plant growth stages rather than plant type. Polymerase chain reaction analysis was conducted to examine the potential horizontal transfer of the introduced gene from the GM maize to rhizosphere microorganisms; however, the introduced gene was not detected in the soil genomic DNA. Overall, the environmental impact of GM maize, particularly on soil microorganisms, is negligible, and the cultivation of GM maize does not alter significantly the rhizosphere bacterial community.}, }
@article {pmid39947201, year = {2025}, author = {Yang, SNN and Kertesz, MA and Coleman, NV}, title = {Phylogenetic and Functional Diversity of Soluble Di-Iron Monooxygenases.}, journal = {Environmental microbiology}, volume = {27}, number = {2}, pages = {e70050}, pmid = {39947201}, issn = {1462-2920}, support = {//University of Sydney/ ; }, mesh = {*Phylogeny ; *Mixed Function Oxygenases/genetics/metabolism/chemistry ; *Bacteria/enzymology/genetics/classification ; Biodegradation, Environmental ; Gene Transfer, Horizontal ; Substrate Specificity ; Oxidation-Reduction ; Oxygenases/genetics/metabolism ; Bacterial Proteins/genetics/metabolism/chemistry ; Iron/metabolism ; }, abstract = {Monooxygenase (MO) enzymes are responsible for the oxidation of hydrocarbons and other compounds in the carbon and nitrogen cycles, are important for the biodegradation of pollutants and can act as biocatalysts for chemical manufacture. The soluble di-iron monooxygenases (SDIMOs) are of interest due to their broad substrate range, high enantioselectivity and ability to oxidise inert substrates such as methane. Here, we re-examine the phylogeny and functions of these enzymes, using recent advances in the field and expansions in sequence diversity in databases to highlight relationships between SDIMOs and revisit their classification. We discuss the impact of horizontal gene transfer on SDIMO phylogeny, the potential of SDIMOs for the biodegradation of pollutants and the importance of heterologous expression as a tool for understanding SDIMO functions and enabling their use as biocatalysts. Our analysis highlights current knowledge gaps, most notably, the unknown substrate ranges and physiological roles of enzymes that have so far only been detected via genome or metagenome sequencing. Enhanced understanding of the diversity and functions of the SDIMO enzymes will enable better prediction and management of biogeochemical processes and also enable new applications of these enzymes for biocatalysis and bioremediation.}, }
@article {pmid39947132, year = {2025}, author = {Wittmers, F and Poirier, C and Bachy, C and Eckmann, C and Matantseva, O and Carlson, CA and Giovannoni, SJ and Goodenough, U and Worden, AZ}, title = {Symbionts of predatory protists are widespread in the oceans and related to animal pathogens.}, journal = {Cell host &amp; microbe}, volume = {33}, number = {2}, pages = {182-199.e7}, doi = {10.1016/j.chom.2025.01.009}, pmid = {39947132}, issn = {1934-6069}, mesh = {*Symbiosis ; Animals ; *Choanoflagellata/physiology ; *Oceans and Seas ; *Phylogeny ; Humans ; Bacteria/genetics/classification ; Gene Transfer, Horizontal ; Genome, Bacterial ; Fishes/microbiology ; Eukaryota/physiology/genetics ; Microbiota ; }, abstract = {Protists are major predators of ocean microbial life, with an ancient history of entanglements with prokaryotes, but their delicate cell structures and recalcitrance to culturing hinder exploration of marine symbioses. We report that tiny oceanic protistan predators, specifically choanoflagellates-the closest living unicellular relatives of animals-and uncultivated MAST-3 form symbioses with four bacterial lineages related to animal symbionts. By targeting living phagotrophs on ship expeditions, we recovered genomes from physically associated uncultivated Legionellales and Rickettsiales. The evolutionary trajectories of Marinicoxiellaceae, Cosmosymbacterales, Simplirickettsiaceae, and previously named Gamibacteraceae vary, including host-engagement mechanisms unknown in marine bacteria, horizontally transferred genes that mediate pathogen-microbiome interactions, and nutritional pathways. These symbionts and hosts occur throughout subtropical and tropical oceans. Related bacteria were detected in public data from freshwater, fish, and human samples. Symbiont associations with animal-related protists, alongside relationships to animal pathogens, suggest an unexpectedly long history of shifting associations and possibilities for host expansion as environments change.}, }
@article {pmid39946809, year = {2025}, author = {Zeng, Q and Pu, Y and Liu, Q and Li, Y and Sun, Y and Hao, Y and Yang, Q and Yang, B and Wu, Y and Shi, S and Gong, Z}, title = {Effects of decabromodiphenyl ethane (DBDPE) exposure on soil microbial community: Nitrogen cycle, microbial defense and repair and antibiotic resistance genes transfer.}, journal = {Journal of environmental management}, volume = {376}, number = {}, pages = {124503}, doi = {10.1016/j.jenvman.2025.124503}, pmid = {39946809}, issn = {1095-8630}, mesh = {*Soil Microbiology ; *Nitrogen Cycle ; *Drug Resistance, Microbial/genetics ; Soil Pollutants/toxicity ; Bromobenzenes/toxicity ; Flame Retardants/toxicity ; Soil/chemistry ; Microbiota/drug effects ; }, abstract = {DBDPE, a widely used brominated flame retardant, is frequently detected in soil. However, the toxic effects of DBDPE on soil microbial communities remain unclear. This study investigated the effects of DBDPE on the microbial community shifts, the nitrogen cycle, microbial defense and repair, and antibiotic resistance genes (ARGs) transfer. After 28 days of DBDPE exposure, the soil microbial community was altered. Denitrifier were enriched by 4.07-78.22% under DBDPE exposure concentrations of 100-1000 ng/g. Additionally, the abundances of genes encoding enzymes involved in nitrification and denitrification processes were up-regulated at 100 ng/g DBDPE exposure, and further promoted at 1000 ng/g DBDPE exposure. Meanwhile, DBDPE exposure at concentrations of 100-1000 ng/g stimulated the production of extracellular polymers substances (EPS) (2155-2347 mg/kg), increased the accumulation of reactive oxygen species (ROS) (by 97.95-108.38%), and activated the antioxidant defense system of soil microorganisms, which correspondingly down-regulated catalase (CAT) genes (by 4.65-4.91%), while up-regulated superoxide dismutase (SOD) (by 0.52-2.63%) and glutathione (GSH) genes (by 19.03%-44.61%). Genes related to the tricarboxylic acid (TCA) cycle, glycerophospholipid metabolism, and peptidoglycan biosynthesis were up-regulated, enhancing cell membrane repair in response to DBDPE exposure. Moreover, the increase in DBDPE concentration selectively enriched and promoted the transmission of ARGs. The co-occurrence network of ARGs and mobile genetic elements (MGEs) revealed that DBDPE facilitated the horizontal gene transfer (HGT)-mediated transmission of transposase, ist, and insertion sequence-associated ARGs.}, }
@article {pmid39946805, year = {2025}, author = {Xu, Z and Li, C and Xiong, J and Hu, S and Ma, Y and Li, S and Ren, X and Huang, B and Pan, X}, title = {The ecological security risks of phthalates: A focus on antibiotic resistance gene dissemination in aquatic environments.}, journal = {Journal of environmental management}, volume = {376}, number = {}, pages = {124488}, doi = {10.1016/j.jenvman.2025.124488}, pmid = {39946805}, issn = {1095-8630}, mesh = {*Phthalic Acids/toxicity ; *Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Dibutyl Phthalate/toxicity ; Water Pollutants, Chemical/toxicity ; Anti-Bacterial Agents/toxicity ; }, abstract = {Antibiotic resistance genes (ARGs) have become a major focus in environmental safety and human health, with concerns about non-antibiotic substances like microplastics facilitating their horizontal gene transfer. Phthalate esters (PAEs), as ubiquitous plastic additives, are prevalent in aquatic environments, yet there remains a dearth of studies examining their impacts on ARG dissemination. This study focuses on dibutyl phthalate (DBP), a prototypical PAE, to assess its potential influence on the conjugative transfer of ARGs along with the related molecular mechanisms. The results revealed that DBP exposure at environmentally relevant concentrations significantly promoted the conjugative transfer of RP4 plasmid-mediated ARGs by up to 2.7-fold compared to that of the control group, whereas it severely suppressed the conjugation at a high concentration (100 μg/L). The promotion of conjugation transfer by low-concentration DBP (0.01-10 μg/L) was mainly attributed to the stimulation of ROS, enhanced membrane permeability, increased energy synthesis, increased polymeric substances secretion, and upregulation of conjugation-related genes. Conversely, high DBP exposure induced oxidative damage and reduced ATP synthesis, resulting in the suppression of ARG conjugation. Notably, donor and recipient bacteria responded differently to DBP-induced oxidative stress. This study explores the environmental behavior of DBP in the water environment from the perspective of ARG propagation and provides essential data and theoretical insights to raise public awareness about the ecological security risks of PAEs.}, }
@article {pmid39945525, year = {2025}, author = {Chang, TH and Pourtois, JD and Haddock, NL and Furukawa, D and Kelly, KE and Amanatullah, DF and Burgener, E and Milla, C and Banaei, N and Bollyky, PL}, title = {Prophages are infrequently associated with antibiotic resistance in Pseudomonas aeruginosa clinical isolates.}, journal = {mSphere}, volume = {10}, number = {3}, pages = {e0090424}, pmid = {39945525}, issn = {2379-5042}, support = {//Cystic Fibrosis Foundation (CFF)/ ; R01 HL148184-01, R01 AI12492093, R01 DC019965//HHS | National Institutes of Health (NIH)/ ; BURGEN23G0, BURGEN24A0-KB//Cystic Fibrosis Foundation (CFF)/ ; R01 DC019965/DC/NIDCD NIH HHS/United States ; //SU | Stanford Bio-X/ ; 1K23HL169902-01//HHS | National Institutes of Health (NIH)/ ; R01 HL148184/HL/NHLBI NIH HHS/United States ; K23 HL169902/HL/NHLBI NIH HHS/United States ; }, mesh = {*Prophages/genetics ; *Pseudomonas aeruginosa/virology/drug effects/genetics ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Pseudomonas Infections/microbiology ; *Cystic Fibrosis/microbiology ; *Microbial Sensitivity Tests ; *Drug Resistance, Bacterial ; Lysogeny ; }, abstract = {Lysogenic bacteriophages can integrate their genome into the bacterial chromosome in the form of a prophage and can promote genetic transfer between bacterial strains in vitro. However, the contribution of lysogenic bacteriophages to the incidence of antimicrobial resistance (AMR) in clinical settings is poorly understood. Here, in a set of 186 clinical isolates of Pseudomonas aeruginosa collected from respiratory cultures from 82 patients with cystic fibrosis, we evaluate the links between prophage counts and both genomic and phenotypic resistance to six anti-pseudomonal antibiotics: tobramycin, colistin, ciprofloxacin, meropenem, aztreonam, and piperacillin-tazobactam. We identified 239 different prophages in total. We find that P. aeruginosa isolates contain on average 3.06 ± 1.84 (SD) predicted prophages. We find no significant association between the number of prophages per isolate and the minimum inhibitory concentration for any of these antibiotics. We then investigate the relationship between particular prophages and AMR. We identify a single lysogenic phage associated with phenotypic resistance to the antibiotic tobramycin and, consistent with this association, we observe that AMR genes associated with resistance to tobramycin are more likely to be found when this prophage is present. However, we find that they are not encoded directly on prophage sequences. Additionally, we identify a single prophage statistically associated with ciprofloxacin resistance but do not identify any genes associated with ciprofloxacin phenotypic resistance. These findings suggest that prophages are only infrequently associated with the AMR genes in clinical isolates of P. aeruginosa.IMPORTANCEAntibiotic-resistant infections of Pseudomonas aeruginosa (Pa), a leading pathogen in patients with cystic fibrosis (CF), are a global health threat. While lysogenic bacteriophages are known to facilitate horizontal gene transfer, their role in promoting antibiotic resistance in clinical settings remains poorly understood. In our analysis of 186 clinical isolates of P. aeruginosa from CF patients, we find that prophage abundance does not predict phenotypic resistance to key antibiotics but that specific prophages are infrequently associated with tobramycin resistance genes. In addition, we do not find antimicrobial resistance (AMR) genes encoded directly on prophages. These results highlight that while phages can be associated with AMR, phage-mediated AMR transfer may be rare in clinical isolates and difficult to identify. This work is important for future efforts on mitigating AMR in CFCF and other vulnerable populations affected by Pa infections and advances our understanding of bacterial-phage dynamics in clinical infections.}, }
@article {pmid39940717, year = {2025}, author = {Subramanian, P and Kim, D and Ko, HR and Sim, JS and Mani, V and Lee, CM and Lee, SK and Park, S and Kim, DG and Yu, Y and Hahn, BS}, title = {Genomic and Transcriptomic Analysis of the Polyploidy Cyst Nematode, Heterodera trifolii, and Heterodera schachtii.}, journal = {International journal of molecular sciences}, volume = {26}, number = {3}, pages = {}, pmid = {39940717}, issn = {1422-0067}, support = {PJ01333201//Rural Development Administration/ ; }, mesh = {Animals ; *Polyploidy ; *Tylenchoidea/genetics ; Transcriptome/genetics ; Genome, Helminth ; Gene Expression Profiling/methods ; Genomics/methods ; Phylogeny ; Female ; Gene Transfer, Horizontal ; }, abstract = {Cyst nematodes remain a major threat to global agricultural production, causing huge losses. To understand the parasitism of the cyst nematodes Heterodera trifolii (HT) and Heterodera schachtii (HS), we constructed whole-genome assemblies using short- and long-read sequencing technologies. The nematode genomes were 379 Mb and 183 Mb in size, with the integrated gene models predicting 40,186 and 18,227 genes in HT and HS, respectively. We found more than half of the genes predicted in HT (64.7%) and HS (53.2%) were collinear to their nearest neighbor H. glycines (HG). Large-scale duplication patterns in HT and segmental duplications of more than half of the orthologous genes indicate that the genome of HT is polyploid in nature. Functional analysis of the genes indicated that 65.6% of the HG genes existed within the HT genome. Most abundant genes in HT and HS were involved in gene regulation, DNA integration, and chemotaxis. Differentially expressed genes showed upregulation of cuticle structural constituent genes during egg and female stages and cytoskeletal motor activity-related genes in juvenile stage 2 (J2). Horizontal gene transfer analyses identified four new vitamin biosynthesis genes, pdxK, pdxH, pdxS, and fabG, of bacterial origin, to be first reported in HT and HS. Mitogenomes of HT, HS, and HG showed similar structure, composition, and codon usage. However, rates of substitution of bases in the gene nad4l were significantly different between HT and HS. The described genomes, transcriptomes, and mitogenomes of plant-parasitic nematodes HT and HS are potential bio-resources used to identify several strategies of control of the nematode.}, }
@article {pmid39939755, year = {2025}, author = {Subramanian, S and Kerns, HR and Braverman, SG and Doore, SM}, title = {The structure of Shigella virus Sf14 reveals the presence of two decoration proteins and two long tail fibers.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {222}, pmid = {39939755}, issn = {2399-3642}, support = {R01 AI170608/AI/NIAID NIH HHS/United States ; U24 GM116789/GM/NIGMS NIH HHS/United States ; AI170608//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; U24GM116789-03//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, mesh = {*Capsid Proteins/chemistry/metabolism/genetics ; *Bacteriophages/genetics/metabolism/chemistry ; Shigella flexneri/virology/genetics/metabolism ; Models, Molecular ; Phylogeny ; Capsid/metabolism/chemistry ; Protein Conformation ; }, abstract = {Bacteriophage Sf14 infects the human pathogen Shigella flexneri. A previous low-resolution structure suggested the presence of a decoration protein on its T = 9 icosahedral capsid. Here, we determined high-resolution structures of the Sf14 capsid and neck, along with a moderate-resolution structure of the whole Sf14 tail and baseplate. These structures indicate the capsid has not one, but two different types of decoration proteins: a trimeric β-tulip lattice that covers the entire capsid and a set of Hoc-like proteins that bind preferentially to hexamers at the quasi-3-fold axes of symmetry. The neck also contains two sets of whiskers oriented in opposite directions, and the tail has two types of long tail fibers which may bind different receptors. Based on homology and phylogenetic analysis, Sf14 may be the product of multiple horizontal gene transfer events. The structures presented here can be used to investigate further hypotheses of phage structure-function relationships and structural diversity.}, }
@article {pmid39939538, year = {2025}, author = {Li, ZZ and Wang, Y and He, XY and Li, WG}, title = {The Taihangia mitogenome provides new insights into its adaptation and organelle genome evolution in Rosaceae.}, journal = {Planta}, volume = {261}, number = {3}, pages = {59}, pmid = {39939538}, issn = {1432-2048}, support = {31370434//National Natural Science Foundation of China/ ; }, mesh = {*Genome, Mitochondrial/genetics ; *Phylogeny ; *Rosaceae/genetics ; *Evolution, Molecular ; Genome, Plant/genetics ; Adaptation, Physiological/genetics ; Plastids/genetics ; Gene Transfer, Horizontal ; }, abstract = {We present the first Taihangia mitogenome, uncovering frequent rearrangements and significant length variation in Rosaceae, likely driven by hybridization and repeat content, alongside widespread mito-chloroplast phylogenetic conflicts. Taihangia, an ancient and endangered monotypic genus within the subfamily Rosoideae of the family Rosaceae, is endemic to cliffs and serves as an ideal material for studying the adaptations of cliff-dwelling plants and the evolutionary processes of the Rosaceae family. In this study, the mitogenome and plastome of T. rupestris var. ciliata were assembled, with lengths of 265,633 bp and 155,467 bp, both exhibiting typical circular structures. Positive selection was detected in the nad4L and sdh4 genes, likely playing a role in adaptation to harsh environments. Comparative genomic analysis indicated that repetitive sequences are likely the main contributors to genome size variation in Rosaceae and also influence horizontal gene transfer between organelle genomes. In T. rupestris var. ciliata, 20 mitochondrial plastid DNA sequences were identified, including 16 complete plastid genes. Moreover, frequent rearrangements were observed in the non-coding regions of mitogenome within the subfamily Rosoideae, potentially linked to the complex evolutionary history and the presence of repetitive sequences. In contrast, coding regions remained highly conserved (over 83% similarity) to maintain essential mitochondrial functions. Phylogenomic analysis of the two organelle genomes revealed conflicts in the phylogenetic relationships within Rosaceae, potentially due to the inconsistent mutation rates and frequent hybridization events in the evolutionary history of the family. In conclusion, the organelle genome analysis of Taihangia provides crucial genomic resources for understanding the evolution and adaptation of Rosaceae species.}, }
@article {pmid39937386, year = {2025}, author = {Lindeberg, A and Hellmuth, M}, title = {Simplifying and Characterizing DAGs and Phylogenetic Networks via Least Common Ancestor Constraints.}, journal = {Bulletin of mathematical biology}, volume = {87}, number = {3}, pages = {44}, pmid = {39937386}, issn = {1522-9602}, mesh = {*Phylogeny ; *Mathematical Concepts ; *Models, Genetic ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Algorithms ; Animals ; }, abstract = {Rooted phylogenetic networks, or more generally, directed acyclic graphs (DAGs), are widely used to model species or gene relationships that traditional rooted trees cannot fully capture, especially in the presence of reticulate processes or horizontal gene transfers. Such networks or DAGs are typically inferred from observable data (e.g., genomic sequences of extant species), providing only an estimate of the true evolutionary history. However, these inferred DAGs are often complex and difficult to interpret. In particular, many contain vertices that do not serve as least common ancestors (LCAs) for any subset of the underlying genes or species, thus may lack direct support from the observable data. In contrast, LCA vertices are witnessed by historical traces justifying their existence and thus represent ancestral states substantiated by the data. To reduce unnecessary complexity and eliminate unsupported vertices, we aim to simplify a DAG to retain only LCA vertices while preserving essential evolutionary information. In this paper, we characterize LCA -relevant and lca -relevant DAGs, defined as those in which every vertex serves as an LCA (or unique LCA) for some subset of taxa. We introduce methods to identify LCAs in DAGs and efficiently transform any DAG into an LCA -relevant or lca -relevant one while preserving key structural properties of the original DAG or network. This transformation is achieved using a simple operator " ⊖ " that mimics vertex suppression.}, }
@article {pmid39936903, year = {2025}, author = {Elena, AX and Orel, N and Fang, P and Herndl, GJ and Berendonk, TU and Tinta, T and Klümper, U}, title = {Jellyfish blooms-an overlooked hotspot and potential vector for the transmission of antimicrobial resistance in marine environments.}, journal = {mSystems}, volume = {10}, number = {3}, pages = {e0101224}, pmid = {39936903}, issn = {2379-5077}, support = {01DO2200, 01KI2404A//Bundesministerium f&#xfc;r Bildung und Forschung (BMBF)/ ; 16GW0355//Bundesministerium f&#xfc;r Bildung und Forschung (BMBF)/ ; 202004910327//China Scholarship Council (CSC)/ ; 793778//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; I04978//Austrian Science Fund (FWF)/ ; ARRS J7-2599, P1-0237//Javna Agencija za Raziskovalno Dejavnost RS (ARRS)/ ; Project ID: 57747282//DAAD/ ; Project ID: B|-DE/25-27-001//Public Agency for Scientific Research and Innovation of the Republic of Slovenia (ARIS)/ ; }, mesh = {Animals ; *Scyphozoa/microbiology/genetics ; RNA, Ribosomal, 16S/genetics ; Microbiota/drug effects/genetics ; Drug Resistance, Bacterial/genetics ; Metagenome ; Bacteria/drug effects/genetics ; Zooplankton/drug effects/genetics ; Interspersed Repetitive Sequences/genetics ; }, abstract = {Gelatinous zooplankton (GZ) represents an important component of marine food webs, capable of generating massive blooms with severe environmental impact. When these blooms collapse, considerable amounts of organic matter (GZ-OM) either sink to the seafloor or can be introduced into the ocean's interior, promoting bacterial growth and providing a colonizable surface for microbial interactions. We hypothesized that GZ-OM is an overlooked marine hotspot for transmitting antimicrobial resistance genes (ARGs). To test this, we first re-analyzed metagenomes from two previous studies that experimentally evolved marine microbial communities in the presence and absence of OM from Aurelia aurita and Mnemiopsis leidyi recovered from bloom events and thereafter performed additional time-resolved GZ-OM degradation experiments to improve sample size and statistical power of our analysis. We analyzed these communities for composition, ARG, and mobile genetic element (MGE) content. Communities exposed to GZ-OM displayed up to fourfold increased relative ARG and up to 10-fold increased MGE abundance per 16S rRNA gene copy compared to the controls. This pattern was consistent across ARG and MGE classes and independent of the GZ species, indicating that nutrient influx and colonizable surfaces drive these changes. Potential ARG carriers included genera containing potential pathogens raising concerns of ARG transfer to pathogenic strains. Vibrio was pinpointed as a key player associated with elevated ARGs and MGEs. Whole-genome sequencing of a Vibrio isolate revealed the genetic capability for ARG mobilization and transfer. This study establishes the first link between two emerging issues of marine coastal zones, jellyfish blooms and ARG spread, both likely increasing with future ocean change. Hence, jellyfish blooms are a quintessential "One Health" issue where decreasing environmental health directly impacts human health.IMPORTANCEJellyfish blooms are, in the context of human health, often seen as mainly problematic for oceanic bathing. Here we demonstrate that they may also play a critical role as marine environmental hotspots for the transmission of antimicrobial resistance (AMR). This study employed (re-)analyses of microcosm experiments to investigate how particulate organic matter introduced to the ocean from collapsed jellyfish blooms, specifically Aurelia aurita and Mnemiopsis leidyi, can significantly increase the presence of antimicrobial resistance genes and mobile genetic elements in marine microbial communities by up to one order of magnitude. By providing abundant nutrients and surfaces for bacterial colonization, organic matter from these blooms enhances ARG proliferation, including transfer to and mobility in potentially pathogenic bacteria like Vibrio. Understanding this connection highlights the importance of monitoring jellyfish blooms as part of marine health assessments and developing strategies to mitigate the spread of AMR in coastal ecosystems.}, }
@article {pmid39935761, year = {2025}, author = {Wijaya, AJ and Anžel, A and Richard, H and Hattab, G}, title = {Current state and future prospects of Horizontal Gene Transfer detection.}, journal = {NAR genomics and bioinformatics}, volume = {7}, number = {1}, pages = {lqaf005}, pmid = {39935761}, issn = {2631-9268}, mesh = {*Gene Transfer, Horizontal ; *Artificial Intelligence ; Computational Biology/methods ; }, abstract = {Artificial intelligence (AI) has been shown to be beneficial in a wide range of bioinformatics applications. Horizontal Gene Transfer (HGT) is a driving force of evolutionary changes in prokaryotes. It is widely recognized that it contributes to the emergence of antimicrobial resistance (AMR), which poses a particularly serious threat to public health. Many computational approaches have been developed to study and detect HGT. However, the application of AI in this field has not been investigated. In this work, we conducted a review to provide information on the current trend of existing computational approaches for detecting HGT and to decipher the use of AI in this field. Here, we show a growing interest in HGT detection, characterized by a surge in the number of computational approaches, including AI-based approaches, in recent years. We organize existing computational approaches into a hierarchical structure of computational groups based on their computational methods and show how each computational group evolved. We make recommendations and discuss the challenges of HGT detection in general and the adoption of AI in particular. Moreover, we provide future directions for the field of HGT detection.}, }
@article {pmid39933461, year = {2025}, author = {Mortezaei, Y and Gaballah, MS and Demirer, GN and Lammers, RW and Williams, MR}, title = {From wastewater to sludge: The role of microplastics in shaping anaerobic digestion performance and antibiotic resistance gene dynamics.}, journal = {Journal of hazardous materials}, volume = {489}, number = {}, pages = {137413}, doi = {10.1016/j.jhazmat.2025.137413}, pmid = {39933461}, issn = {1873-3336}, mesh = {*Microplastics/analysis ; *Sewage/microbiology ; *Wastewater ; Anaerobiosis ; *Drug Resistance, Microbial/genetics ; *Water Pollutants, Chemical/analysis ; Waste Disposal, Fluid ; Bioreactors ; }, abstract = {The presence of microplastics (MPs) in wastewater treatment plants (WWTPs) disrupt processes and threaten the effectiveness of anaerobic digestion (AD), raising critical environmental and operational concerns. This review assesses MP occurrence in WWTPs and its effects on biogas production and the fate of antibiotic resistance genes (ARGs) during AD to understand their impact on process efficiency and environmental health. Polypropylene (PP) and polyethylene (PE) are the most prevalent types of MPs which are found in WWTP influent at an average concentration of 801.5 particles per liter (P/L), decrease to 38.3 P/L in effluent, and accumulate in sludge at 70.5 P/L. The effect of MPs on AD performance is influenced by MP type, concentration, size, and AD conditions (i.e., feed substrate, reactor configuration, temperature, and incubation time). For example, certain MPs (polyamide 7 (PA7) and PP) increase methane production by 39.5 %, while aged MPs decrease it by 47.2 %. The review also explores how AD drives MP degradation mechanisms like oxidation, hydrolysis, mechanical stress, and biodegradation. Additionally, MPs significantly impact ARGs, with abundance increasing by 0.4-514.4 %, especially with aged MPs. Mechanistic effects of MPs on ARGs dissemination were also discussed, including horizontal gene transfer (reactive oxygen species production, cell membrane permeability, extracellular polymeric substances secretion, and ATP dynamics), vertical gene transfer, microbial community, and adsorbing pollutants. This analysis provides insights into the complex interactions between MPs, microbial processes, and ARGs, highlighting their implications for wastewater treatment and biogas production systems.}, }
@article {pmid39932282, year = {2025}, author = {Karki, S and Aylward, FO}, title = {Evolution of ubiquitin, cytoskeleton, and vesicular trafficking machinery in giant viruses.}, journal = {Journal of virology}, volume = {99}, number = {3}, pages = {e0171524}, pmid = {39932282}, issn = {1098-5514}, support = {2141862//National Science Foundation (NSF)/ ; }, mesh = {*Evolution, Molecular ; *Cytoskeleton/metabolism/virology ; *Ubiquitin/metabolism/genetics ; *Giant Viruses/genetics/metabolism ; Viral Proteins/metabolism/genetics ; Phylogeny ; Genome, Viral ; Gene Transfer, Horizontal ; DNA Viruses/genetics/metabolism ; }, abstract = {Members of the phylum Nucleocytoviricota, which include "giant viruses" known for their large physical dimensions and genome lengths, are a diverse group of dsDNA viruses that infect a wide range of eukaryotic hosts. The genomes of nucleocytoviruses frequently encode eukaryotic signature proteins (ESPs) such as RNA- and DNA-processing proteins, vesicular trafficking factors, cytoskeletal components, and proteins involved in ubiquitin signaling. Despite the prevalence of these genes in many nucleocytoviruses, the timing and number of gene acquisitions remains unclear. While the presence of DNA- and RNA-processing proteins in nucleocytoviruses likely reflects ancient gene transfers, the origins and evolutionary history of other proteins are largely unknown. In this study, we examined the distribution and evolutionary history of a subset of viral-encoded ESPs (vESPs) that are widespread in nucleocytoviruses. Our results demonstrate that most vESPs involved in vesicular trafficking were acquired multiple times independently by nucleocytoviruses at different time points after the emergence of the eukaryotic supergroups, while viral proteins associated with cytoskeletal and ubiquitin system proteins exhibited a more complex evolutionary pattern exhibited by both shallow and deep branching viral clades. This pattern reveals a dynamic interplay between the co-evoluton of eukaryotes and their viruses, suggesting that the viral acquisition of many genes involved in cellular processes has occurred both through ancient and more recent horizontal gene transfers. The timing and frequency of these gene acquisitions may provide insight into their role and functional significance during viral infection.IMPORTANCEThis research is pertinent for understanding the evolution of nucleocytoviruses and their interactions with eukaryotic hosts. By investigating the distribution and evolutionary history of viral-encoded eukaryotic signature proteins, the study reveals gene transfer patterns, highlighting how viruses acquire genes that allow them to manipulate host cellular processes. Identifying the timing and frequency of gene acquisitions related to essential cellular functions provides insights into their roles during viral infections. This work expands our understanding of viral diversity and adaptability, contributing valuable knowledge to virology and evolutionary biology, while offering new perspectives on the relationship between viruses and their hosts.}, }
@article {pmid39931631, year = {2024}, author = {Zhou, X and Wagh, K and Lv, G and Sharma, D and Lei, W}, title = {Genome drafting of nosocomial infection CRE Klebsiella pneumoniae confirming resistance to colistin and eravacycline, carrying bla NDM-1, mcr-1, and bla KPC-2, in neonatology from November to December 2023.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1528017}, pmid = {39931631}, issn = {2235-2988}, mesh = {Humans ; *Klebsiella pneumoniae/genetics/drug effects/isolation &amp; purification ; *Klebsiella Infections/microbiology/epidemiology ; *Cross Infection/microbiology ; Infant, Newborn ; *Colistin/pharmacology ; *beta-Lactamases/genetics ; *Anti-Bacterial Agents/pharmacology ; *Whole Genome Sequencing ; *Intensive Care Units, Neonatal ; *Disease Outbreaks ; *Genome, Bacterial/genetics ; *Microbial Sensitivity Tests ; Drug Resistance, Multiple, Bacterial/genetics ; Plasmids/genetics ; Neonatology ; Bacterial Proteins/genetics ; Carbapenem-Resistant Enterobacteriaceae/genetics/isolation &amp; purification/drug effects ; Male ; }, abstract = {BACKGROUND: Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a critical pathogen in healthcare settings, associated with high mortality due to its extensive antibiotic resistance. In this study, we report an outbreak of CRKP in a neonatal intensive care unit (NICU) within a 200-bed tertiary hospital. The main goal of this study was to characterize the phenotypic and genomic profiles of the CRKP isolates involved in the outbreak and to gain insights into their resistance mechanisms and transmission dynamics within the NICU.<br><br>METHODS: The study was conducted between November and December 2023 in a 5-bed NICU. Monthly surveillance cultures were performed to monitor colonization and infection with multidrug-resistant organisms. CRKP isolates were obtained from blood and nasal swabs of affected neonates. Identification and antimicrobial susceptibility testing were initially conducted using the Vitek[&#xae;]2 system with an N-395 card and further confirmed by 16S rRNA sequencing. Whole-genome sequencing (WGS) and antimicrobial resistance (AMR) profiling were performed to identify resistance genes and virulence factors. For genetic analysis, both Illumina short-read and Nanopore long-read sequencing were used, followed by hybrid assembly for enhanced genome resolution. Plasmid and resistance gene profiles were determined using AMRFinder and PlasmidFinder databases.<br><br>RESULTS: A total of three CRKP isolates (designated Kp1, Kp2, and Kp3) were identified. Kp1 and Kp2 belonged to sequence type (ST) ST23 and were genetically near-identical, differing by a single allele, while Kp3 was of a distinct sequence type, ST2096, with 245 allelic differences from Kp1 and Kp2. All isolates were resistant to colistin and carried resistance genes, including mcr-1 and bla NDM-1, bla KPC2 confirming carbapenem resistance. Efflux pump genes and aminoglycoside resistance genes were also detected, providing a multifaceted defence against antibiotics. Plasmid analysis identified several incompatibility groups (IncFI, IncHI, IncFIB, IncX), indicating the potential for horizontal gene transfer of resistance determinants.<br><br>CONCLUSION: This study highlights the complexity of CRKP outbreaks in neonatal care, with isolates exhibiting resistance mechanisms that complicate treatment. The plasmid profiles suggest these strains are reservoirs for multidrug-resistant genes, emphasizing the need for strict infection control and ongoing genomic surveillance. For neonatal care, these resistance challenges increase the risk of treatment failures and mortality, underscoring the importance of enhanced infection prevention and novel therapeutic strategies.}, }
@article {pmid39929813, year = {2025}, author = {Liang, H and Xu, Y and Sahu, SK and Wang, H and Li, L and Chen, X and Zeng, Y and Lorenz, M and Friedl, T and Melkonian, B and Wong, GK and Melkonian, M and Liu, H and Wang, S}, title = {Chromosome-level genomes of two Bracteacoccaceae highlight adaptations to biocrusts.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1492}, pmid = {39929813}, issn = {2041-1723}, mesh = {*Gene Transfer, Horizontal ; Adaptation, Physiological/genetics ; Phylogeny ; Stress, Physiological/genetics ; Chromosomes/genetics ; }, abstract = {Biological soil crusts (biocrusts) cover the majority of the world's dryland ground and are a significant component of the vegetation-free surface of the planet. They consist of an intimate association of microbial organisms, lichens, bryophytes and fungi. Biocrusts are severely endangered by anthropogenic disturbances despite their importance. The genus Bracteacoccus (Sphaeropleales, Chlorophyta) is a ubiquitous component of biocrusts from extreme environments. Here, we present the chromosome-level genome sequences of two Bracteacoccus species, B. bullatus and B. minor. Genome comparisons with other Archaeplastida identify genomic features that highlight the adaptation of these algae to abiotic stresses prevailing in such environments. These features include horizontal gene transfer events mainly from bacteria or fungi, gains and expansions of stress-related gene families, neofunctionalization of genes following gene duplications and genome structural variations. We also summarize transcriptional and metabolic responses of the lipid pathway of B. minor, based on multi-omics analyses, which is important for balancing the flexible conversion of polar membrane lipids and non-polar storage lipids to cope with various abiotic stresses. Under dehydration and high-temperature stress conditions B. minor differs considerably from other eukaryotic algae. Overall, these findings provide insights into the genetic basis of adaptation to abiotic stress in biocrust algae.}, }
@article {pmid39927357, year = {2024}, author = {Al-Bukhalifa, MA and Al-Tameemi, HM}, title = {First whole genome sequencing of Staphylococcus aureus isolates from Iraq: Insights into zoonotic relations and biofilm-related genes.}, journal = {Open veterinary journal}, volume = {14}, number = {12}, pages = {3269-3288}, pmid = {39927357}, issn = {2218-6050}, mesh = {*Biofilms ; Animals ; *Staphylococcus aureus/genetics/isolation &amp; purification/physiology ; Humans ; *Staphylococcal Infections/veterinary/microbiology ; *Whole Genome Sequencing ; Cats ; Iraq ; *Genome, Bacterial ; Dogs ; Cattle ; Sheep ; Zoonoses/microbiology ; }, abstract = {BACKGROUND: Staphylococcus aureus is a significant zoonotic pathogen capable of causing infections in both humans and animals. The bacterium's capacity to develop biofilms and resistance to many different antibiotics has raised significant concerns for public health. Furthermore, studies have demonstrated that horizontal gene transfer enables the transfer of deleterious features between strains found in humans and animals, consequently rendering treatment and control efforts more challenging.<br><br>AIM: This study aimed to investigate the relationships between human and animal isolates and biofilm-associated genes in local S. aureus strains using whole genome sequencing technique.<br><br>METHODS: We examined 111 suspected cases of S. aureus infection in humans and in animals and screened all S. aureus -positive isolates (11 isolates) for biofilm formation and antimicrobial profiles. Additionally, we sequenced and studied five S. aureus genomes isolated from humans, cows, sheep, cats, and dogs for significant biofilm-related genes and predicted their loci following annotation and deposition in the NCBI database.<br><br>RESULTS: The study showed that the isolates have genome sizes between 2.7 and 2.8 megabases, a GC content of 32.8%-33.1%, and a coding sequence count between 2,718 and 2,838. The cow isolate (MHB) and cat isolate (MHF) exhibited substantial genomic similarities with human isolates of S. aureus (N315) and the type strain of S. aureus (DSM 20231). The genomes of the human isolate (MHH) and the dog isolate (MHC) were comparable to S. aureus (N315). The sheep isolate (MHO) showed lesser genomic similarity and was closely related to S. aureus subsp. anaerobius. The genomes were submitted to the NCBI database with the following accession numbers: MHB (GCA_040196135.1), MHH (GCA_040196155.1), MHO (GCA_040195495.1), MHF (GCA_040195555.1), and MHC (GCA_040195445.1). The isolates were categorized by PubMLST typing into MHC (ST-1156), MHB (ST-6), MHF (ST-6), and MHO (a unique ST). We identified the accession numbers, locations, and lengths of biofilm-associated genes and regulators within the studied genomes.<br><br>CONCLUSION: The study is the first to conduct complete genome sequencing of Staphylococcus aureus in Iraq, allowing analysis of biofilm-associated genes in local isolates. It provides the first large-scale genomic investigation of genetic relationships among animal and human isolates in Iraq.}, }
@article {pmid39922005, year = {2025}, author = {Iqbal, S and Begum, F and Manishimwe, C and Rabaan, AA and Sabour, AA and Alshiekheid, MA and Shaw, P}, title = {Allelochemicals degradation and multifarious plant growth promoting potential of two Bacillus spp.: Insights into genomic potential and abiotic stress alleviation.}, journal = {Chemosphere}, volume = {373}, number = {}, pages = {144191}, doi = {10.1016/j.chemosphere.2025.144191}, pmid = {39922005}, issn = {1879-1298}, mesh = {*Bacillus/metabolism/physiology/genetics ; *Pheromones ; *Stress, Physiological ; *Soil Microbiology ; Biodegradation, Environmental ; Volatile Organic Compounds/metabolism ; Triticum/growth &amp; development/metabolism ; Plant Development/drug effects ; Soil Pollutants/metabolism/toxicity ; Germination/drug effects ; Plant Roots/growth &amp; development/metabolism/microbiology ; Bacillus subtilis ; Benzoic Acid/metabolism ; }, abstract = {The deposition of allelochemicals poses a challenge to continuous cropping. Microbial degradation is an efficient approach to degrade these hazardous compounds. The current study employed an integrated approach to explore the allelochemical degradation potential of Bacillus subtilis RS10 and Bacillus pumilus SF-4 and concurrently validate their capabilities to enhance plant growth and alleviate abiotic stress in pot experiments. During initial in vitro screening, both strains utilized more than 45% of benzoic acid within 60 h of incubation and showed maximum growth after 72 h. Meanwhile, the wheat seed germination rate was increased by 34.33% and 30% when treated with strain RS10 and SF-4, respectively. In addition, both strains demonstrated the capacity to promote wheat growth in terms of root length, shoot length, and plant weight in soil contaminated with p-hydroxybenzoic acid. To determine the associated mechanism of plant growth-promoting and allelochemical degradation, the culture extract of RS10 and SF-4 were analyzed using gas chromatography-mass spectrometry, which showed several plant growth-promoting volatile organic compounds, including propanediol and butanone. Genome-wide analysis unveiled several genetic loci associated with plant growth-promoting traits such as siderophore synthesis, phosphate solubilization, and biosynthesis of biocontrol compounds. Moreover, the in-depth comparative genome analysis, horizontal gene transfer, and strain-specific genes unveiled intriguing insight into the evolutionary dynamics of these strains and constraints driven by natural selection. In conclusion, the current study revealed the multifarious plant growth-promoting traits of strains RS10 and SF-4 and suggested an application of these strains as plant growth stimulators in soil contaminated with allelochemicals.}, }
@article {pmid39921128, year = {2025}, author = {Lavergne, JP and Page, A and Polard, P and Campo, N and Grangeasse, C}, title = {Quantitative phosphoproteomic reveals that the induction of competence modulates protein phosphorylation in Streptococcus pneumonaie.}, journal = {Journal of proteomics}, volume = {315}, number = {}, pages = {105399}, doi = {10.1016/j.jprot.2025.105399}, pmid = {39921128}, issn = {1876-7737}, mesh = {*Streptococcus pneumoniae/metabolism ; *Bacterial Proteins/metabolism/genetics ; Phosphorylation ; *Proteomics/methods ; *Phosphoproteins/metabolism ; Proteome/metabolism ; Protein Processing, Post-Translational ; }, abstract = {Competence in the pathogenic bacterium Streptococcus pneumoniae (S. pneumoniae) is a developmental genetic program that is key for natural genetic transformation and consequently bacterial horizontal gene transfer. Phosphoproteomic studies have revealed that protein phosphorylation on serine, threonine and tyrosine residues is a widespread regulatory post-translational modification in bacteria. In this study, we performed quantitative proteomic and phosphoproteomic analyses on S. pneumoniae as a function of competence induction. To calculate peptide abundance ratios between non-competent and competent samples we used dimethyl-tag labeling. Titanium dioxide (TiO2) beads were used for phosphopeptide enrichment and samples were analysed by LC-MS/MS. Our proteome analysis covers approximatively 63 % of the total bacterial protein content, identifying 82 proteins with significantly different abundance ratios, including some not previously linked to competence. 248 phosphopeptides were identified including 47 having different abundance ratios. Notably, the proteins with a change in phosphorylation in competent cells are different from the proteins with a change in expression, highlighting different pathways induced by competence and regulated by phosphorylation. This is the first report that phosphorylation of some proteins is regulated during competence in Streptococcus pneumoniae, a key pathway for the bacteria to evade vaccines or acquire antibiotic resistance. SIGNIFICANCE: S. pneumoniae is a prominent model for the study of competence that governs the development of natural genetic transformation. The latter largely accounts for the spread of antibiotic resistance and vaccine evasion in pneumococcal isolates. Many proteins specifically expressed during competence have been identified and extensively studied. However, the potential contribution of post-translational modifications, and notably phosphorylation, during the development of competence has never been investigated. In this study, we used a quantitative phosphoproteomic approach to determine both the protein expression and the protein phosphorylation patterns. Comparison of these patterns allows to highlight a series of proteins that are differentially phosphorylated in the two conditions. This result opens new avenues to decipher new regulatory pathways induced by competence and that are potentially key for natural genetic transformation. Interfering with theses regulatory pathways could represent a promising strategy to combat antibiotic resistance in the future.}, }
@article {pmid39921114, year = {2025}, author = {Farooq, S and Talat, A and Dhariwal, A and Petersen, FC and Khan, AU}, title = {Transgenerational gut dysbiosis: Unveiling the dynamics of antibiotic resistance through mobile genetic elements from mothers to infants.}, journal = {International journal of antimicrobial agents}, volume = {65}, number = {5}, pages = {107458}, doi = {10.1016/j.ijantimicag.2025.107458}, pmid = {39921114}, issn = {1872-7913}, mesh = {Humans ; Female ; Infant ; *Gastrointestinal Microbiome/genetics ; Infant, Newborn ; *Dysbiosis/microbiology ; Feces/microbiology ; Anti-Bacterial Agents/pharmacology ; Adult ; *Drug Resistance, Bacterial/genetics ; Mothers ; *Interspersed Repetitive Sequences ; Male ; *Bacteria/genetics/drug effects/isolation &amp; purification ; }, abstract = {OBJECTIVES: The initial microbial colonization of the gut is seeded by microbes transmitted from the mother's gut, skin, and vaginal tract. As the gut microbiome evolves, a few transmitted microbes persist throughout life. Understanding the impact of mother-to-neonate gut microbiome and antibiotic resistance genes (ARGs) transmission is crucial for establishing its role in infants' immunity against pathogens.<br><br>METHODS: This study primarily explores mother-neonate ARG transmission through 125 publicly available fecal metagenomes, isolated from eighteen mother-neonate pairs.<br><br>RESULTS: The core ARGs, detected in both mothers and their respective infants at all stages (birth, 1st, 2nd, 3rd, 4th, 8th and 12th months) included aminoglycosidases APH(3')-IIIa, Bifidobacterium adolescentis rpoB mutants conferring resistance to rifampicin, &#x3b2;-lactamases CblA-1, CfxA2, multidrug resistance gene CRP, diaminopyrimidine resistance gene dfrF, fluoroquinolone-resistance gene emrR, macrolide; lincosamide; streptogramin resistance gene ErmB, ErmG, macrolide resistance gene Mef(En2), nucleosidase SAT-4, and tetracycline-resistance genes tet(O), tet(Q), and tet(W). Most of these infants and mothers were not administered any antibiotics. In infants, ARGs were predominantly carried by Bacillota, Pseudomonadota, and Actinomycetota, similar to the mothers. The dominant ARG-carrying opportunistic pathogens were Escherichia coli, Klebsiella, and Streptococcus, found across all infant cohorts. All the core ARGs were associated with mobile genetic elements, signifying the role of horizontal gene transfer(HGT). We detected 132 virulence determinants, mostly E. coli-specific, including pilus chaperones, general secretion pathway proteins, type III secretion system effectors, and heme-binding proteins.<br><br>CONCLUSIONS: Maternal-neonate transmission of ARGs along with possible nosocomial infections, mode of delivery, breastfeeding versus formula feeding, and gestation period, must be considered for mother-neonate health.}, }
@article {pmid39919124, year = {2025}, author = {Rodriguez-Grande, J and Ortiz, Y and Garcia-Lopez, D and Garcillán-Barcia, MP and de la Cruz, F and Fernandez-Lopez, R}, title = {Encounter rates and engagement times limit the transmission of conjugative plasmids.}, journal = {PLoS genetics}, volume = {21}, number = {2}, pages = {e1011560}, pmid = {39919124}, issn = {1553-7404}, mesh = {*Plasmids/genetics ; *Conjugation, Genetic ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Escherichia coli/genetics ; Bacteria/genetics ; }, abstract = {Plasmid conjugation is a major route for the dissemination of antibiotic resistances and adaptive genes among bacterial populations. Obtaining precise conjugation rates is thus key to understanding how antibiotic resistances spread. Plasmid conjugation is typically modeled as a density-dependent process, where the formation of new transconjugants depends on the rate of encounters between donor and receptor cells. By analyzing conjugation dynamics at different cell concentrations, here we show that this assumption only holds at very low bacterial densities. At higher cell concentrations, conjugation becomes limited by the engagement time, the interval required between two successful matings. Plasmid conjugation therefore follows a Holling´s Type II functional response, characterized by the encounter rate and the engagement time, which represent, respectively, the density and frequency-dependent limits of plasmid transmission. Our results demonstrate that these parameters are characteristic of the transfer machinery, rather than the entire plasmid genome, and that they are robust to environmental and transcriptional perturbation. Precise parameterization of plasmid conjugation will contribute to better understanding the propagation dynamics of antimicrobial resistances.}, }
@article {pmid39918226, year = {2025}, author = {Prieto Farfan, AB and Llimpe Mitma de Barrón, Y and Mayorca Yarihuamán, MM and Príncipe Laines, FM and Paredes Pérez, MB and Calla Choque, JS and Barrón Pastor, HJ}, title = {Phylogenetic Analysis of Escherichia coli according to Phenotypic Resistance in Urinary Tract Infections in Children, Lima, Peru.}, journal = {Infection &amp; chemotherapy}, volume = {57}, number = {1}, pages = {93-101}, pmid = {39918226}, issn = {2093-2340}, support = {A18010321/UNMSM/Universidad Nacional Mayor de San Marcos/Peru ; }, abstract = {BACKGROUND: Phylogenetic studies are essential for understanding the virulence and resistance factors of bacteria, especially in evaluating their distribution within specific populations for effective infection control. Urinary tract infections (UTIs) caused by Escherichia coli are highly prevalent and pose significant health challenges from childhood to adulthood. The rising incidence of multidrug-resistant (MDR) strains highlights the urgent need for research aimed at developing preventive measures and epidemiological control strategies. This study aimed to analyze phylogenetically uropathogenic E. coli strains and their resistance phenotypes in children.<br><br>MATERIALS AND METHODS: A retrospective analysis was conducted on 111 urine culture samples collected from June 2023 to February 2024 at the Pediatric Emergency Hospital (PEH) in Lima, Peru. The phylogroups of E. coli were identified using Clermont's protocol based on polymerase chain reaction.<br><br>RESULTS: UTIs were predominantly observed in females (85.6%) and infants under two years old (42.3%). The most frequent uropathogenic E. coli phylogroups were B2 (30.6%), D (29.7%), and A (25.2%). These phylogroups showed significant correlation with MDR and the production of extended spectrum beta-lactamases (ESBL).<br><br>CONCLUSION: At PEH, UTIs in children are primarily caused by uropathogenic E. coli from the B2 and D phylogroups, which demonstrate high virulence and resistance factors. The correlation between these phylogroups, MDR, and ESBL production, along with the increasing infection rates associated with phylogroup A, suggests a potential for horizontal gene transfer. This underscores the urgent need for vigilant control measures.}, }
@article {pmid39913343, year = {2025}, author = {Davidovich, C and Erokhina, K and Gupta, CL and Zhu, YG and Su, JQ and Djordjevic, SP and Wyrsch, ER and Blum, SE and Cytryn, E}, title = {Occurrence of "under-the-radar" antibiotic resistance in anthropogenically affected produce.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {39913343}, issn = {1751-7370}, mesh = {*Lactuca/microbiology ; *Wastewater/microbiology ; *Escherichia coli/genetics/drug effects/isolation &amp; purification ; *Manure/microbiology ; *Agricultural Irrigation ; Anti-Bacterial Agents/pharmacology ; Soil Microbiology ; Animals ; Plasmids/genetics ; Gene Transfer, Horizontal ; Poultry/microbiology ; Drug Resistance, Bacterial ; }, abstract = {With global climate change, treated-wastewater irrigation and manure amendment are becoming increasingly important in sustainable agriculture in water- and nutrient-stressed regions. Yet, these practices can potentially disseminate pathogens and antimicrobial resistance determinants to crops, resulting in serious health risks to humans through the food chain. Previous studies demonstrated that pathogen and antimicrobial resistance indicators from wastewater and manure survive poorly in the environment, suggesting that ecological barriers prevent their dissemination. However, we recently found that these elements can persist below detection levels in low quality treated wastewater-irrigated soil, and potentially proliferate under favorable conditions. This "under-the-radar" phenomenon was further investigated here, in treated wastewater-irrigated and poultry litter-amended lettuce plants, using an enrichment platform that resembles gut conditions, and an analytical approach that combined molecular and cultivation-based techniques. Enrichment uncovered clinically relevant multidrug-resistant pathogen indicators and a myriad of antibiotic resistance genes in the litter amended and treated wastewater-irrigated lettuce that were not detected by direct analyses, or in the enriched freshwater irrigated samples. Selected resistant E. coli isolates were capable of horizontally transferring plasmids carrying multiple resistance genes to a susceptible strain. Overall, our study underlines the hidden risks of under-the-radar pathogen and antimicrobial resistance determinants in anthropogenically affected agroenvironments, providing a platform to improve quantitative microbial risk assessment models in the future.}, }
@article {pmid39908756, year = {2025}, author = {Xu, J and Ding, D and Fan, Y and Chen, R and Xia, Y and Liang, Y and Ding, Y and Feng, H}, title = {The overlooked risk of horizontal transfer of plasmid-borne antibiotic resistance genes induced by synthetic phenolic antioxidants.}, journal = {Journal of hazardous materials}, volume = {488}, number = {}, pages = {137459}, doi = {10.1016/j.jhazmat.2025.137459}, pmid = {39908756}, issn = {1873-3336}, mesh = {*Gene Transfer, Horizontal ; *Plasmids/genetics ; *Antioxidants/pharmacology ; *Phenols/toxicity ; Wastewater ; Butylated Hydroxyanisole/pharmacology ; Drug Resistance, Bacterial/genetics/drug effects ; Drug Resistance, Microbial/genetics ; Microbiota/drug effects ; Conjugation, Genetic/drug effects ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Plasmid-borne conjugation transfer of antibiotic resistance genes (ARGs) triggered by non-antibiotic stresses has attracted widespread attention, known to motivate conjugation through well-recognized reactive oxygen species and SOS response. However, a notable knowledge gap remains on the potential risks of reductive compounds, such as synthetic phenolic antioxidants (SPAs), in facilitating horizontal gene transfer by the other mechanisms beyond intracellular ROS. Therefore, intragenus and wastewater indigenous microbiota conjugation models were established to examine conjugative transfer frequency of RP4 plasmid under exposure of four extensively detected SPAs. The mechanisms were elucidated utilizing fluorescence detection, RT-qPCR, and transcriptomic analysis with 3-tert-butyl-4-hydroxyanisole (BHA) serving as a representative SPA. Results demonstrated that conjugation transfer frequencies of both models were significantly promoted without triggering SOS responses under exposure to high doses of BHA. Furthermore, BHA exposure benefited conjugation progress through improving membrane permeability of donors and ameliorating cellular energy supply. In addition, BHA exposure activated the RP4-encoded transfer apparatus by regulating the expression of associated genes. This study highlighted and provided a stark reminder about the potential horizontal gene transfer risks posed by SPAs exposure, which were regarded as a neglected driver in the dissemination of ARGs.}, }
@article {pmid39908303, year = {2025}, author = {Poncin, K and McKeand, SA and Lavender, H and Kurzyp, K and Harrison, OB and Roberti, A and Melia, C and Johnson, E and Maiden, MCJ and Greaves, DR and Exley, R and Tang, CM}, title = {Bacteriocin-like peptides encoded by a horizontally acquired island mediate Neisseria gonorrhoeae autolysis.}, journal = {PLoS biology}, volume = {23}, number = {2}, pages = {e3003001}, pmid = {39908303}, issn = {1545-7885}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Neisseria gonorrhoeae/metabolism/genetics/pathogenicity/physiology ; *Bacteriocins/metabolism/genetics ; Humans ; *Gene Transfer, Horizontal ; Bacteriolysis ; Genomic Islands ; Gonorrhea/microbiology ; }, abstract = {Neisseria gonorrhoeae is a human-specific pathogen that causes the important sexually transmitted infection, gonorrhoea, an inflammatory condition of the genitourinary tract. The bacterium is closely related to the meningococcus, a leading cause of bacterial meningitis. Both these invasive bacterial species undergo autolysis when in the stationary phase of growth. Autolysis is a form of programmed cell death (PCD) which is part of the life cycle of remarkably few bacteria and poses an evolutionary conundrum as altruistic death provides no obvious benefit for single-celled organisms. Here, we searched for genes present in these 2 invasive species but not in other members of the Neisseria genus. We identified a ~3.4 kb horizontally acquired region, we termed the nap island, which is largely restricted to the gonococcus and meningococcus. The nap island in the gonococcus encodes 3 cationic, bacteriocin-like peptides which have no detectable antimicrobial activity. Instead, the gonococcal Neisseria autolysis peptides (Naps) promote autolytic cell death when bacteria enter the stationary phase of growth. Furthermore, strains lacking the Naps exhibit reduced autolysis in assays of PCD. Expression of Naps is likely to be phase variable, explaining how PCD could have arisen in these important human pathogens. NapC also induces lysis of human cells, so the peptides are likely to have multiple roles during colonisation and disease. The acquisition of the nap island contributed to the emergence of PCD in the gonococcus and meningococcus and potentially to the appearance of invasive disease in Neisseria spp.}, }
@article {pmid39907470, year = {2025}, author = {Wang, X and Koster, Ad and Koenders, BB and Jonker, M and Brul, S and Ter Kuile, BH}, title = {De novo acquisition of antibiotic resistance in six species of bacteria.}, journal = {Microbiology spectrum}, volume = {13}, number = {3}, pages = {e0178524}, pmid = {39907470}, issn = {2165-0497}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Mutation ; *Gene Transfer, Horizontal ; *Microbial Sensitivity Tests ; Whole Genome Sequencing ; Bacteria/drug effects/genetics/classification ; Drug Resistance, Bacterial/genetics ; Fluoroquinolones/pharmacology ; Animals ; Drug Resistance, Multiple, Bacterial/genetics ; DNA Gyrase/genetics ; Bacterial Proteins/genetics/metabolism ; }, abstract = {Bacteria can become resistant to antibiotics in two ways: by acquiring resistance genes through horizontal gene transfer and by de novo development of resistance upon exposure to non-lethal concentrations. The importance of the second process, de novo build-up, has not been investigated systematically over a range of species and may be underestimated as a result. To investigate the DNA mutation patterns accompanying the de novo antibiotic resistance acquisition process, six bacterial species encountered in the food chain were exposed to step-wise increasing sublethal concentrations of six antibiotics to develop high levels of resistance. Phenotypic and mutational landscapes were constructed based on whole-genome sequencing at two time points of the evolutionary trajectory. In this study, we found that (1) all of the six strains can develop high levels of resistance against most antibiotics; (2) increased resistance is accompanied by different mutations for each bacterium-antibiotic combination; (3) the number of mutations varies widely, with Y. enterocolitica having by far the most; (4) in the case of fluoroquinolone resistance, a mutational pattern of gyrA combined with parC is conserved in five of six species; and (5) mutations in genes coding for efflux pumps are widely encountered in gram-negative species. The overall conclusion is that very similar phenotypic outcomes are instigated by very different genetic changes. The outcome of this study may assist policymakers when formulating practical strategies to prevent development of antimicrobial resistance in human and veterinary health care.IMPORTANCEMost studies on de novo development of antimicrobial resistance have been performed on Escherichia coli. To examine whether the conclusions of this research can be applied to more bacterial species, six species of veterinary importance were made resistant to six antibiotics, each of a different class. The rapid build-up of resistance observed in all six species upon exposure to non-lethal concentrations of antimicrobials indicates a similar ability to adjust to the presence of antibiotics. The large differences in the number of DNA mutations accompanying de novo resistance suggest that the mechanisms and pathways involved may differ. Hence, very similar phenotypes can be the result of various genotypes. The implications of the outcome are to be considered by policymakers in the area of veterinary and human healthcare.}, }
@article {pmid39904308, year = {2025}, author = {Whiteman, NK}, title = {Insect herbivory: An inordinate fondness for plant cell wall degrading enzymes.}, journal = {Current biology : CB}, volume = {35}, number = {3}, pages = {R107-R109}, doi = {10.1016/j.cub.2024.12.045}, pmid = {39904308}, issn = {1879-0445}, mesh = {Animals ; *Herbivory/physiology ; *Cell Wall/metabolism/enzymology ; *Coleoptera/physiology/enzymology/genetics ; Symbiosis ; Gene Transfer, Horizontal ; }, abstract = {Tens of thousands of species of leaf beetles rely on plant cell wall degrading enzymes in order to make the most of nutritionally depauperate plant tissues. Many of the genes encoding these enzymes were acquired from microbial donors, either through horizontal gene transfer or by hosting microbial endosymbionts. A new study explores how these insects have leveraged this metabolic potential to diversify and expand into new niches.}, }
@article {pmid39902196, year = {2024}, author = {Chen, R and Rao, R and Wang, C and Zhu, D and Yuan, F and Yue, L}, title = {Features and evolutionary adaptations of the mitochondrial genome of Garuga forrestii W. W. Sm.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1509669}, pmid = {39902196}, issn = {1664-462X}, abstract = {INTRODUCTION: Garuga forrestii W. W. Sm. is a tree species of the Burseraceae family, endemic to China, found in hot/warm-dry valleys. This species plays a crucial role in maintaining biodiversity in these ecosystems.<br><br>METHODS: We performed de novo assembly of the Garuga forrestii mitochondrial genome using PMAT (v.1.5.4), resulting in a typical circular molecule of 606,853 bp. The genome consists of 31 tRNA genes, 3 rRNA genes, 35 protein-coding genes, and 1 pseudogene. The study also investigates RNA editing sites and evolutionary patterns.<br><br>RESULTS: The mitochondrial genome exhibits a low proportion of repetitive sequences (3.30%), suggesting a highly conserved structure. A high copy number of the trnM-CAT gene (4 copies) is noted, which may contribute to genomic rearrangement and adaptive evolution. Among the 476 RNA editing sites, hydrophilic-hydrophobic and hydrophobic-hydrophobic editing events are most common, accounting for 77.10%. Negative selection predominates among most genes (Ka/Ks < 1), while a few genes (e.g., matR, nad3, rps1, rps12, and rps4) show signs of positive selection (Ka/Ks > 1), potentially conferring evolutionary advantages. Additionally, a significant A/T bias is observed at the third codon position. Phylogenomic analysis supports the APG IV classification, with no evidence of horizontal gene transfer.<br><br>DISCUSSION: This mitochondrial genome offers valuable insights into the adaptive mechanisms and evolutionary processes of Garuga forrestii. It enhances our understanding of the species' biogeography in tropical Southeast Asia and Southwest China, providing key information on the evolutionary history of this genus.}, }
@article {pmid39902180, year = {2024}, author = {Li, X and Zhu, Y and Lu, Y and Wu, K and Che, Y and Wang, X and Wang, W and Gao, J and Gao, J and Liu, Z and Zhou, Z}, title = {Population genetic analysis of clinical Mycobacterium abscessus complex strains in China.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1496896}, pmid = {39902180}, issn = {2235-2988}, mesh = {China/epidemiology ; Humans ; *Mycobacterium abscessus/genetics/classification/isolation &amp; purification/drug effects ; *Mycobacterium Infections, Nontuberculous/microbiology/epidemiology ; Multilocus Sequence Typing ; Genome, Bacterial ; Virulence Factors/genetics ; Genetic Variation ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; Genetics, Population ; Interspersed Repetitive Sequences ; Genomic Islands ; Genotype ; Phylogeny ; }, abstract = {BACKGROUND: To explore the genetic characteristics of the Mycobacterium abscessus complex (MABC) population in China, given its rising clinical importance among nontuberculous mycobacteria.<br><br>METHODS: We conducted population genetic analyses on 360 MABC genomes from China, focusing on core genome multilocus sequence typing (cgMLST), pan-genome characterization, population genetics, and antimicrobial resistance gene profiling.<br><br>RESULTS: Our analysis identified 273 M. abscessus subsp. abscessus (MabA) and 87 M. abscessus subsp. massiliense (MabM) isolates, uncovering 68 sequence types (STs), with ST5 being the most common. cgMLST classified 33.3% of isolates into six dominant circulating clones (DCCs) and 49.4% into 59 genomic clusters at a threshold of 25 different alleles, including 18 international clusters linking Chinese isolates with seven other countries. The MABC pan-genome is open, with MabA exhibiting greater accessory gene diversity and higher gene turnover compared to MabM. Mobile genetic elements (MGEs), such as prophages and genomic islands, were prevalent across all genomes. 139 to 151 virulence factors (VFs) were identified per genome, with distinct accessory VFs in MabA and MabM affecting immune modulation and metabolism. Resistance gene profiling revealed ubiquitous mtrA, RbpA, and bla MAB, with MabA-specific erm(41) conferring resistance to macrolides and &#x3b2;-lactams. Common rrs and rrl gene mutations indicated widespread resistance to aminoglycosides and macrolides, while gyrA mutations suggested emerging fluoroquinolone resistance. An acquired erm(46) gene, likely obtained via phage-mediated horizontal gene transfer, was detected in one MabA strain.<br><br>CONCLUSION: This study provides key genetic insights into the dynamics of MABC in China. The widespread distribution of DCCs, high genomic clustering rates, open pan-genome, and distinct resistance patterns between MabA and MabM, along with MGEs, highlight the need for targeted surveillance and tailored therapies to address emerging challenges in MABC infections.}, }
@article {pmid39901063, year = {2025}, author = {Wiśniewska, MM and Kyslík, J and Alama-Bermejo, G and Lövy, A and Kolísko, M and Holzer, AS and Kosakyan, A}, title = {Comparative transcriptomics reveal stage-dependent parasitic adaptations in the myxozoan Sphaerospora molnari.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {103}, pmid = {39901063}, issn = {1471-2164}, support = {19-25536Y//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 19-28399X//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 20-30321Y//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; CZ.02.1.01/0.0/0.0/16_019/0000759//ERD fund Centre for Research of Pathogenicity and Virulence Parasites/ ; }, mesh = {*Myxozoa/genetics/physiology/growth &amp; development ; Animals ; *Gene Expression Profiling ; *Transcriptome ; Carps/parasitology ; Host-Parasite Interactions/genetics ; Gills/parasitology ; *Adaptation, Physiological/genetics ; }, abstract = {BACKGROUND: Parasitism as a life strategy has independently evolved multiple times within the eukaryotic tree of life. Each lineage has developed mechanisms to invade hosts, exploit resources, and ensure replication, but our knowledge of survival mechanisms in many parasitic taxa remain extremely limited. One such group is the Myxozoa, which are obligate, dixenous cnidarians. Evidence suggests that myxozoans evolved from free-living ancestors to endoparasites around 600 million years ago and are likely one of the first metazoan parasites on Earth. Some myxozoans pose significant threats to farmed and wild fish populations, negatively impacting aquaculture and fish stocks; one such example is Sphaerospora molnari, which forms spores in the gills of common carp (Cyprinus carpio), disrupting gill epithelia and causing somatic and respiratory failure. Sphaerospora molnari undergoes sequential development in different organs of its host, with large numbers of morphologically distinct stages occurring in the blood, liver, and gills of carp. We hypothesize that these parasite life-stages differ in regards to their host exploitation, pathogenicity, and host immune evasion strategies and mechanisms. We performed stage-specific transcriptomic profiling to identify differentially expressed key functional gene groups that relate to these functions and provide a fundamental understanding of the mechanisms S. molnari uses to optimize its parasitic lifestyle. We aimed to identify genes that are likely related to parasite pathogenicity and host cell exploitation mechanisms, and we hypothesize that genes unique to S. molnari might be indicative of evolutionary innovations and specific adaptations to host environments.<br><br>RESULTS: We used parasite isolation protocols and comparative transcriptomics to study early proliferative and spore-forming stages of S. molnari, unveiling variation in gene expression between each stage. We discovered several apparent innovations in the S. molnari transcriptome, including proteins that are likely to function in the uptake of previously unknown key nutrients, immune evasion factors that may contribute to long-term survival in hosts, and proteins that likely improve adhesion to host cells that may have arisen from horizontal gene transfer. Notably, we identified genes that are similar to known virulence factors in other parasitic organisms, particularly blood and intestinal parasites like Plasmodium, Trypanosoma, and Giardia. Many of these genes are absent in published cnidarian and myxozoan datasets and appear to be specific to S. molnari; they may therefore represent potential innovations enabling Sphaerospora to exploit the host's blood system.<br><br>CONCLUSIONS: In order to address the threat posed by myxozoans to both cultured fish species and wild stocks, it is imperative to deepen our understanding of their genetics. Sphaerospora molnari offers an appealing model for stage-specific transcriptomic profiling and for identifying differentially expressed key functional gene groups related to parasite development. We identified genes that are thus far unique to S. molnari, which reveal their evolutionary novelty and likely role as adaptations to specific host niches. In addition, we describe the pathogenicity-associated genetic toolbox of S. molnari and discuss the implications of our discoveries for disease control by shedding light on specific targets for potential intervention strategies.}, }
@article {pmid39900484, year = {2025}, author = {Van Etten, J and Stephens, TG and Bhattacharya, D}, title = {Genetic Transfer in Action: Uncovering DNA Flow in an Extremophilic Microbial Community.}, journal = {Environmental microbiology}, volume = {27}, number = {2}, pages = {e70048}, pmid = {39900484}, issn = {1462-2920}, support = {//U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231/ ; 10.46936/10.25585/60000481//Joint Genome Institute/ ; NJ01180//National Institute of Food and Agriculture/ ; 80NSSC19K1542/NASA/NASA/United States ; NASA (80NSSC19K0462)/NASA/NASA/United States ; }, mesh = {*Gene Transfer, Horizontal ; *Bacteria/genetics ; *Extremophiles/genetics ; *DNA, Bacterial/genetics ; Genome, Bacterial ; *Microbiota ; }, abstract = {Horizontal genetic transfer (HGT) is a significant driver of genomic novelty in all domains of life. HGT has been investigated in many studies however, the focus has been on conspicuous protein-coding DNA transfers that often prove to be adaptive in recipient organisms and are therefore fixed longer-term in lineages. These results comprise a subclass of HGTs and do not represent exhaustive (coding and non-coding) DNA transfer and its impact on ecology. Uncovering exhaustive HGT can provide key insights into the connectivity of genomes in communities and how these transfers may occur. In this study, we use the term frequency-inverse document frequency (TF-IDF) technique, that has been used successfully to mine DNA transfers within real and simulated high-quality prokaryote genomes, to search for exhaustive HGTs within an extremophilic microbial community. We establish a pipeline for validating transfers identified using this approach. We find that most DNA transfers are within-domain and involve non-coding DNA. A relatively high proportion of the predicted protein-coding HGTs appear to encode transposase activity, restriction-modification system components, and biofilm formation functions. Our study demonstrates the utility of the TF-IDF approach for HGT detection and provides insights into the mechanisms of recent DNA transfer.}, }
@article {pmid39898629, year = {2025}, author = {Huang, S and Wei, DD and Hong, H and Chen, S and Fan, L-P and Huang, Q-S and Du, F-L and Xiang, T-X and Li, P and Zhang, W and Wan, L-G and Liu, Y}, title = {Capture of mobile genetic elements following intercellular conjugation promotes the production of ST11-KL64 CR-hvKP.}, journal = {Microbiology spectrum}, volume = {13}, number = {3}, pages = {e0134724}, pmid = {39898629}, issn = {2165-0497}, support = {82102411, 32370195, 82260403//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {*Klebsiella pneumoniae/genetics/pathogenicity/metabolism ; *Klebsiella Infections/microbiology ; *Conjugation, Genetic ; *Plasmids/genetics ; Humans ; *Interspersed Repetitive Sequences ; Virulence/genetics ; Gene Transfer, Horizontal ; Animals ; Whole Genome Sequencing ; Mice ; Anti-Bacterial Agents/pharmacology ; Carbapenems/pharmacology ; Carbapenem-Resistant Enterobacteriaceae/genetics/isolation &amp; purification ; }, abstract = {UNLABELLED: Sequence type (ST)11 carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) can cause life-threatening infections and is therefore of global concern. Despite its importance, the evolutionary history and mechanism for the emergence of ST11 CR-hvKP are unclear. In recent years, the detection rate of ST11 CR-hvKP has increased in a teaching hospital. Based on its clonal transmission, a conjugation experiment was performed between a hvKP strain AP8555 and a ST11 CRKP strain, resulting in two ST11 CR-hvKP strains. Research had confirmed that the virulence plasmid pAP855 was horizontally transferred to the CRKP strain to form the conjugant S270-Tc, which was recombined by mobile genetic elements to evolve into the conjugant S270-Tc-R. The S270-Tc-R had high virulence, high plasmid stability, and greater adaptability. Interestingly, it had high homology to clinically prevalent ST11 CR-hvKP strains using pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing (WGS). This is the first demonstration that plasmid recombination in vitro has led to the formation of ST11 CR-hvKP strains. The clinical setting is a multi-factorial and multi-selection pressure environment that may stimulate the evolution of conjugant strains in the transition period to local strains in the stable period, and surveillance is urgently needed for infection control.<br><br>IMPORTANCE: The emergence of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) heralded the onset of a new and rapidly worsening public health disaster on a global scale. More attention has been paid to its evolutionary history and mechanism, which currently remains unclear. In this study, a conjugation experiment was performed between a hvKP strain AP8555 and a ST11 CRKP strain, resulting in two ST11 CR-hvKP strains. We had confirmed that the virulence plasmid pAP855 was horizontally transferred to the CRKP strain to form the conjugant S270-Tc, which was recombined by mobile genetic elements to evolve into the conjugant S270-Tc-R. The S270-Tc-R had high virulence, high plasmid stability, and greater adaptability. Interestingly, it had high homology to clinically prevalent ST11 CR-hvKP strains using pulsed-field gel electrophoresis and whole-genome sequencing.}, }
@article {pmid39897699, year = {2025}, author = {Theobald, S and Vesth, T and Nybo, JL and Frisvad, JC and Kjærbølling, I and Mondo, S and LaButti, K and Haridas, S and Riley, R and Kuo, AA and Salamov, AA and Pangilinan, J and Lipzen, A and Koriabine, M and Yan, M and Barry, K and Clum, A and Lyhne, EK and Drula, E and Wiebenga, A and Müller, A and Lubbers, RJM and Kun, RS and Dos Santos Gomes, AC and Mäkelä, MR and Henrissat, B and Simmons, BA and Magnuson, JK and Hoof, JB and Mortensen, UH and Dyer, PS and Momany, M and Larsen, TO and Grigoriev, IV and Baker, SE and de Vries, RP and Andersen, MR}, title = {Comparative genomics of Aspergillus nidulans and section Nidulantes.}, journal = {Current research in microbial sciences}, volume = {8}, number = {}, pages = {100342}, pmid = {39897699}, issn = {2666-5174}, abstract = {Aspergillus nidulans is an important model organism for eukaryotic biology and the reference for the section Nidulantes in comparative studies. In this study, we de novo sequenced the genomes of 25 species of this section. Whole-genome phylogeny of 34 Aspergillus species and Penicillium chrysogenum clarifies the position of clades inside section Nidulantes. Comparative genomics reveals a high genetic diversity between species with 684 up to 2433 unique protein families. Furthermore, we categorized 2118 secondary metabolite gene clusters (SMGC) into 603 families across Aspergilli, with at least 40 % of the families shared between Nidulantes species. Genetic dereplication of SMGC and subsequent synteny analysis provides evidence for horizontal gene transfer of a SMGC. Proteins that have been investigated in A. nidulans as well as its SMGC families are generally present in the section Nidulantes, supporting its role as model organism. The set of genes encoding plant biomass-related CAZymes is highly conserved in section Nidulantes, while there is remarkable diversity of organization of MAT-loci both within and between the different clades. This study provides a deeper understanding of the genomic conservation and diversity of this section and supports the position of A. nidulans as a reference species for cell biology.}, }
@article {pmid39894155, year = {2025}, author = {Ren, B and Shi, X and Guo, J and Jin, P}, title = {Interaction of sulfate-reducing bacteria and methanogenic archaea in urban sewers, leads to increased risk of proliferation of antibiotic resistance genes.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {368}, number = {}, pages = {125777}, doi = {10.1016/j.envpol.2025.125777}, pmid = {39894155}, issn = {1873-6424}, mesh = {*Sewage/microbiology ; *Drug Resistance, Microbial/genetics ; *Archaea/genetics ; Bacteria/genetics/metabolism ; Anti-Bacterial Agents ; Biofilms ; Sulfates/metabolism ; Sulfamethoxazole ; Biodegradation, Environmental ; Waste Disposal, Fluid ; Tetracycline ; Cities ; Genes, Bacterial ; }, abstract = {Sewers are considered a potential reservoir of antibiotic resistance. However, the generation of antibiotic resistance genes (ARGs) in microbial communities in pipeline biofilms under antibiotic stress remains unexplored. In this study, the biodegradation efficiency of tetracycline (TCY) and sulfamethoxazole (SMX) was evaluated in a pilot reactor of the sewers. The results showed that under TCY and SMX stress, the degradation efficiency of sewage water was inhibited. The most abundant ARGs detected in the biofilm samples were TCY-related genes (e.g., tetW/N/W, tetC, and tetM), accounting for 34.1%. The microbial community composition varied, and the correlation analysis showed that antibiotic stress had a certain impact on the biological metabolic activity and function of the urban sewers. The community structure and diversity of biofilms enabled the evaluation of the bioconversion of antibiotics. Notably, Anaerocella and Paludibacter directly influenced the methanogenesis and sulfate reduction processes, playing a key role in the interaction between sulfate-reducing bacteria and methanogenic archaea. These microorganisms facilitated the proliferation of ARGs (tet and sul) in the biofilms through horizontal gene transfer. This study provides insight into the front-end control of ARGs, further improving sewage treatment plant processes and reducing the environmental and health risks caused by antibiotic abuse.}, }
@article {pmid39883727, year = {2025}, author = {Wielert, I and Kraus-Römer, S and Volkmann, TE and Craig, L and Higgins, PG and Maier, B}, title = {Pilin antigenic variants impact gonococcal lifestyle and antibiotic tolerance by modulating interbacterial forces.}, journal = {PLoS biology}, volume = {23}, number = {1}, pages = {e3003022}, pmid = {39883727}, issn = {1545-7885}, mesh = {*Neisseria gonorrhoeae/drug effects/genetics/physiology/immunology ; *Antigenic Variation ; *Fimbriae Proteins/genetics/immunology/metabolism/chemistry ; Anti-Bacterial Agents/pharmacology ; Humans ; Drug Resistance, Bacterial ; Fimbriae, Bacterial ; Bacterial Adhesion/drug effects ; Biofilms/growth &amp; development/drug effects ; Ciprofloxacin/pharmacology ; Antigens, Bacterial/genetics/immunology ; Gonorrhea/microbiology ; }, abstract = {Type 4 pili (T4P) are multifunctional filaments involved in adhesion, surface motility, biofilm formation, and horizontal gene transfer. These extracellular polymers are surface-exposed and, therefore, act as antigens. The human pathogen Neisseria gonorrhoeae uses pilin antigenic variation to escape immune surveillance, yet it is unclear how antigenic variation impacts most other functions of T4P. Here, we addressed this question by replacing the major pilin of a laboratory strain with pilins from clinical isolates. We reveal that the resulting strains vary substantially in their attractive forces. Strongly interacting bacteria form microcolonies while weakly interacting bacteria retain a planktonic lifestyle. In mixed microcolonies, different variant strains segregate in agreement with the differential strength of adhesion hypothesis. By combining structural predictions and laser tweezers experiments, we show that the C-terminal region of the pilin is crucial for attraction. Lifestyle affects growth kinetics and antibiotic tolerance. In the presence of ceftriaxone or ciprofloxacin, the killing kinetics indicate strongly increased tolerance of aggregating strains. We propose that pilin antigenic variation produces a mixed population containing variants optimized for growth, colonization, or survivability under external stress. Different environments select different variants, ensuring the survival and reproduction of the population as a whole.}, }
@article {pmid39882964, year = {2025}, author = {Warren, JM and Ceriotti, LF and Sanchez-Puerta, MV and Sloan, DB}, title = {Fungal-Derived tRNAs Are Expressed and Aminoacylated in Orchid Mitochondria.}, journal = {Molecular biology and evolution}, volume = {42}, number = {2}, pages = {}, pmid = {39882964}, issn = {1537-1719}, mesh = {*RNA, Transfer/genetics/metabolism ; *Orchidaceae/genetics/metabolism ; Genome, Mitochondrial ; Gene Transfer, Horizontal ; Mitochondria/genetics/metabolism ; }, abstract = {Plant mitochondrial genomes (mitogenomes) experience remarkable levels of horizontal gene transfer, including the recent discovery that orchids anciently acquired DNA from fungal mitogenomes. Thus far, however, there is no evidence that any of the genes from this interkingdom horizontal gene transfer are functional in orchid mitogenomes. Here, we applied a specialized sequencing approach to the orchid Corallorhiza maculata and found that some fungal-derived tRNA genes in the transferred region are transcribed, post-transcriptionally modified, and aminoacylated. In contrast, all the transferred protein-coding sequences appear to be pseudogenes. These findings show that fungal horizontal gene transfer has altered the composition of the orchid mitochondrial tRNA pool and suggest that these foreign tRNAs function in translation. The exceptional capacity of tRNAs for horizontal gene transfer and functional replacement is further illustrated by the diversity of tRNA genes in the C. maculata mitogenome, which also include genes of plastid and bacterial origin in addition to their native mitochondrial counterparts.}, }
@article {pmid39881475, year = {2025}, author = {Wang, P and Wang, H and Qi, S and Wang, W and Lu, H}, title = {Synergistic effects of quaternary ammonium compounds and antibiotics on the evolution of antibiotic resistance.}, journal = {Water research}, volume = {275}, number = {}, pages = {123206}, doi = {10.1016/j.watres.2025.123206}, pmid = {39881475}, issn = {1879-2448}, mesh = {*Quaternary Ammonium Compounds/pharmacology ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/drug effects ; Drug Synergism ; Wastewater/microbiology ; Escherichia coli/drug effects/genetics ; }, abstract = {The usage of quaternary ammonium compounds (QACs) as disinfectants has surged dramatically during the COVID-19 pandemic and thereafter. QACs can promote antimicrobial resistance, but the combined effects of QACs and antibiotics in driving resistance evolution were yet revealed. This study aimed to evaluate antibiotic resistance of wastewater microorganisms under coexposure to typical antibiotics and the most widely used QAC, dodecyl dimethyl benzyl ammonium chloride (DDBAC). DDBAC exhibited synergistic effects with multiple antibiotics (ampicillin, azithromycin, ciprofloxacin, kanamycin, polymyxin B) in enhancing activated sludge resistance by 1.53-6.67 folds, compared with antibiotics exposure alone. DDBAC-ampicillin coexposure enriched multidrug and aminoglycoside ARGs with relatively high horizontal gene transfer potential. The synergistic mechanism was further explored using sludge-isolated pathogenic E. coli. DDBAC at 1-10 mg/L alone did not induce notable resistance, but synergized with ampicillin on enhancing resistance by 6.56-22.90 folds. Based on mutation analysis and transcriptomics, DDBAC-enhanced resistance evolution was attributable to efflux pump upregulation, target modification, and inhibition of ATP synthesis (a less reported mechanism). Five DDBAC-induced, resistance-conferring mutant genes were highly enriched in globally collected E. coli strains from wastewater outflow (n = 537) than soil/sediments (n = 714, p < 0.05). Considering the strong adsorption and persistence of QACs, their coexistence with antibiotics poses elevated antimicrobial resistance risks, particularly in wastewater treatment systems with long solid retention time and sewage sludge applied farmland.}, }
@article {pmid39880121, year = {2025}, author = {Almeida-Santos, AC and Novais, C and Peixe, L and Freitas, AR}, title = {Vancomycin-resistant Enterococcus faecium: A current perspective on resilience, adaptation, and the urgent need for novel strategies.}, journal = {Journal of global antimicrobial resistance}, volume = {41}, number = {}, pages = {233-252}, doi = {10.1016/j.jgar.2025.01.016}, pmid = {39880121}, issn = {2213-7173}, mesh = {Humans ; *Enterococcus faecium/drug effects/genetics/physiology/pathogenicity ; *Vancomycin-Resistant Enterococci/genetics/drug effects/physiology ; *Gram-Positive Bacterial Infections/microbiology/epidemiology/drug therapy ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; *Adaptation, Physiological ; Virulence Factors/genetics ; Plasmids/genetics ; Animals ; Bacteriocins/genetics ; }, abstract = {Vancomycin-resistant Enterococcus faecium (VREfm) has become a critical opportunistic pathogen, urgently requiring new antimicrobial strategies due to its rising prevalence and significant impact on patient safety and healthcare costs. VREfm continues to evolve through mutations and the acquisition of new genes via horizontal gene transfer, contributing to resistance against several last-resort antibiotics. Although primarily hospital-associated, VREfm are also detected in the community, food chain, livestock, and environmental sources like wastewater, indicating diverse transmission pathways and the need for a One Health approach. Advances in genomics have shed light on VREfm's persistence in hospital settings, particularly its adaptation to the gastrointestinal tract of hospitalized patients, recent clonal shifts, and the dominance of specific clonal lineages. Despite extensive research, significant gaps remain in understanding the molecular mechanisms behind VREfm's unique adaptation to clinical environments. In this review, we aim to present an overview of VREfm current prevalence, mechanisms of resistance, and unveil the adaptive traits that have facilitated VREfm's rise and global success. A particular focus is given to key plasmids, namely linear plasmids, virulence factors, and bacteriocins as potential drivers in the global emergence of the ST78 clonal lineage. We also address diagnostic challenges and the limited treatment options available for VREfm, as well as emerging antibiotic alternatives aimed at restoring gut microbiota balance and curbing VREfm proliferation. A multifaceted approach combining research, clinical practices, and public health policies is crucial to mitigate the impact of this superbug and preserve antimicrobial effectiveness for future generations.}, }
@article {pmid39879767, year = {2025}, author = {Li, S and Bai, Y and Li, Z and Wang, A and Ren, NQ and Ho, SH}, title = {Overlooked role of extracellular polymeric substances in antibiotic-resistance gene transfer within microalgae-bacteria system.}, journal = {Journal of hazardous materials}, volume = {488}, number = {}, pages = {137206}, doi = {10.1016/j.jhazmat.2025.137206}, pmid = {39879767}, issn = {1873-3336}, mesh = {*Microalgae/genetics/metabolism ; *Extracellular Polymeric Substance Matrix/metabolism ; *Drug Resistance, Microbial/genetics ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects ; Genes, Bacterial ; *Gene Transfer, Horizontal ; *Drug Resistance, Bacterial/genetics ; Wastewater/microbiology ; }, abstract = {Controlling the spread of antibiotic-resistance genes (ARGs) under antibiotic stress has become an increasingly urgent issue. Microalgae possess the capability to remove antibiotics while concurrently inhibiting ARGs. Microalgae-bacteria systems can produce significant quantities of extracellular polymeric substances (EPS). However, the roles of EPS in the spread of ARGs have not been sufficiently explored, resulting in an insufficient understanding of the contribution of each EPS component and a lack of analysis on the complex interactions between EPS and ARGs. This study systematically explored the overlooked role of EPS in the transmission of ARGs within microalgae-bacteria systems. The current results showed that the potential of the microalgae-bacteria system for treating antibiotic wastewater. The tightly bound-EPS (TB-EPS) can acquire the higher absolute abundances of ARGs compared with the loosely bound-EPS (LB-EPS). The correlation coefficient between polysaccharides and TB-EPS ARGs was higher than that between polysaccharides and LB-EPS ARGs. The gene patterns of LB-EPS closely clustered with those of TB-EPS, while intracellular ARG gene patterns differed from both TB-EPS and LB-EPS. Metagenomic analyses indicated that the relative abundances of sul1 and sul2 were considerably higher at the beginning stage compared to the end stage. The abundance of Achromobacter, increased by the end stage, aligning with its potential to produce exopolysaccharide. Additionally, the absolute abundance of genes encoding exopolysaccharides (nagB and galE) and conjugative transfer transcription regulator (traF), increased over time. These findings enhanced our comprehension of the significance of EPS on the fate of ARGs in microalgae-bacteria systems during the treatment of antibiotic-contaminated wastewater.}, }
@article {pmid39878503, year = {2025}, author = {Ndovie, W and Havránek, J and Leconte, J and Koszucki, J and Chindelevitch, L and Adriaenssens, EM and Mostowy, RJ}, title = {Exploration of the genetic landscape of bacterial dsDNA viruses reveals an ANI gap amid extensive mosaicism.}, journal = {mSystems}, volume = {10}, number = {2}, pages = {e0166124}, pmid = {39878503}, issn = {2379-5077}, support = {2020/37/B/NZ8/03492//Narodowe Centrum Nauki (NCN)/ ; PPN/PPO/2018/1/00021//Narodowa Agencja Wymiany Akademickiej (NAWA)/ ; 2020/38/E/NZ8/00432//Narodowe Centrum Nauki (NCN)/ ; MR/X020258/1//UKRI | Medical Research Council (MRC)/ ; BB/X011011/1, BBS/E/F/000PR13634, BBS/E/F/000PR13635, BB/X011054/1, BBS/E/F/000PR13631//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; Installation Grant to Rafal Mostowy//European Molecular Biology Organization (EMBO)/ ; //International Visegrad Fund (IVF)/ ; }, mesh = {*Genome, Viral ; *DNA Viruses/genetics/classification ; *Mosaicism ; *Bacteria/virology ; Phylogeny ; Computational Biology/methods ; }, abstract = {Average nucleotide identity (ANI) is a widely used metric to estimate genetic relatedness, especially in microbial species delineation. While ANI calculation has been well optimized for bacteria and closely related viral genomes, accurate estimation of ANI below 80%, particularly in large reference data sets, has been challenging due to a lack of accurate and scalable methods. To bridge this gap, we introduce MANIAC, an efficient computational pipeline optimized for estimating ANI and alignment fraction (AF) in viral genomes with divergence around ANI of 70%. Using a rigorous simulation framework, we demonstrate MANIAC's accuracy and scalability compared to existing approaches, even to data sets of hundreds of thousands of viral genomes. Applying MANIAC to a curated data set of complete bacterial dsDNA viruses revealed a multimodal ANI distribution, with a distinct gap around 80%, akin to the bacterial ANI gap (~90%) but shifted, likely due to viral-specific evolutionary processes such as recombination dynamics and mosaicism. We then evaluated ANI and AF as predictors of genus-level taxonomy using a logistic regression model. We found that this model has strong predictive power (PR-AUC = 0.981), but that it works much better for virulent (PR-AUC = 0.997) than temperate (PR-AUC = 0.847) bacterial viruses. This highlights the complexity of taxonomic classification in temperate phages, known for their extensive mosaicism, and cautions against over-reliance on ANI in such cases. MANIAC can be accessed at https://github.com/bioinf-mcb/MANIAC.IMPORTANCEWe introduce a novel computational pipeline called MANIAC, designed to accurately assess average nucleotide identity (ANI) and alignment fraction (AF) between diverse viral genomes, scalable to data sets of over 100k genomes. Using computer simulations and real data analyses, we show that MANIAC could accurately estimate genetic relatedness between pairs of viral genomes of around 60%-70% ANI. We applied MANIAC to investigate the question of ANI discontinuity in bacterial dsDNA viruses, finding evidence for an ANI gap, akin to the one seen in bacteria but around ANI of 80%. We then assessed the ability of ANI and AF to predict taxonomic genus boundaries, finding its strong predictive power in virulent, but not in temperate phages. Our results suggest that bacterial dsDNA viruses may exhibit an ANI threshold (on average around 80%) above which recombination helps maintain population cohesiveness, as previously argued in bacteria.}, }
@article {pmid39874786, year = {2025}, author = {Chen, Y and Liu, Y and Zhao, C and Ma, J and Guo, J}, title = {Antibiotic resistance gene pollution in poultry farming environments and approaches for mitigation: A system review.}, journal = {Poultry science}, volume = {104}, number = {3}, pages = {104858}, pmid = {39874786}, issn = {1525-3171}, mesh = {Animals ; *Animal Husbandry/methods ; *Poultry ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Antibiotic resistance genes (ARG) pollution in poultry farming environments has become increasingly critical, primarily driven by the widespread use of antibiotics in animal husbandry. Prolonged antibiotic use has led to the emergence of ARGs and antibiotic-resistant bacteria, spreading via horizontal and vertical gene transfer. The complexity of ARG pollution in poultry farming arises from the unique farming practices, physiological characteristics of poultry, and manure management methods, with manure, wastewater, and air serving as significant vectors for ARG dissemination. Current research indicates that the spread of ARGs poses a significant threat to ecosystems and public health. In response to this growing concern, this review outlines the sources, distribution characteristics, and transmission mechanisms of ARGs in poultry farming environments. It also evaluates the efficacy of existing waste treatment technologies in mitigating ARG contamination. The review proposes several strategies to control ARG dissemination effectively, including reducing antibiotic usage, improving farming practices, optimizing waste management, and strengthening regulatory oversight. It also highlights the need for further research to address existing knowledge gaps and explore more efficient pollution control technologies and management measures. This review aims to provide theoretical support for protecting the environment and public health in the context of poultry farming.}, }
@article {pmid39874626, year = {2025}, author = {Li, J and Sun, D and Wu, J and Liu, F and Xu, Y and Wang, Y and Shui, X and Li, Q and Zhao, B}, title = {Lithium enhanced plasmid-mediated conjugative transfer of antimicrobial resistance genes in Escherichia coli: Different concentrations and mechanisms.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {279}, number = {}, pages = {107263}, doi = {10.1016/j.aquatox.2025.107263}, pmid = {39874626}, issn = {1879-1514}, mesh = {*Escherichia coli/drug effects/genetics ; *Plasmids/genetics ; *Drug Resistance, Bacterial/genetics ; *Conjugation, Genetic/drug effects ; *Water Pollutants, Chemical/toxicity ; Gene Expression Regulation, Bacterial/drug effects ; *Lithium/toxicity ; *Gene Transfer, Horizontal/drug effects ; *Lithium Chloride/toxicity ; }, abstract = {Conjugative transfer, a pivotal mechanism in the transmission of antimicrobial resistance genes, is susceptible to various environmental pollutants. As an emerging contaminant, lithium (Li) has garnered much attention due to its extensive applications. This research investigated the effects of Li on conjugative transfer process, examining biochemical and omics perspectives. Results revealed that Li could increase the conjugative transfer frequency of both donor and recipient via different mechanisms at varying concentrations. At 0.1 mg/L LiCl, a notable increase in conjugative transfer frequency occurred without ROS elevation. However, the surge of ROS was identified as a crucial regulator at 100 mg/L LiCl, as eliminating ROS would significantly decrease the conjugative transfer frequency. Besides, comparative transcriptome analysis revealed consistent variations in "SOS response", "quorum sensing" and "oxidative phosphorylation" pathways at both 0.1 mg/L and 100 mg/L LiCl concentrations, suggesting their pivotal roles as targets for Li regulation and is independent of Li concentration. While genes related to "conjugative transfer", "pili", "outer membrane protein" and "antioxidant enzyme" were only significantly regulated by 100 mg/L LiCl, possible to be the specific reasons for High (100 mg/L) LiCl increased conjugative transfer frequency. This study reveals the distinct effects and mechanisms of different concentration of Li on conjugative transfer in E. coli, providing a theoretical basis for the understanding of the environmental effects of Li.}, }
@article {pmid39874387, year = {2025}, author = {Li, Y and Pulford, CV and Díaz, P and Perez-Sepulveda, BM and Duarte, C and Predeus, AV and Wiesner, M and Heavens, D and Low, R and Schudoma, C and Montaño, A and Hall, N and Moreno, J and Hinton, JCD}, title = {Potential links between human bloodstream infection by Salmonella enterica serovar Typhimurium and international transmission to Colombia.}, journal = {PLoS neglected tropical diseases}, volume = {19}, number = {1}, pages = {e0012801}, pmid = {39874387}, issn = {1935-2735}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; Colombia/epidemiology ; *Salmonella typhimurium/genetics/isolation &amp; purification/drug effects/classification ; *Salmonella Infections/transmission/microbiology/epidemiology ; Phylogeny ; *Bacteremia/microbiology/epidemiology/transmission ; Drug Resistance, Multiple, Bacterial ; Whole Genome Sequencing ; Male ; Female ; Plasmids/genetics ; Anti-Bacterial Agents/pharmacology ; Adult ; Middle Aged ; Child, Preschool ; Adolescent ; Young Adult ; Child ; Infant ; Aged ; Genome, Bacterial ; }, abstract = {Salmonella enterica serovar Typhimurium is a prevalent food-borne pathogen that is usually associated with gastroenteritis infection. S. Typhimurium is also a major cause of bloodstream infections in sub-Saharan Africa, and is responsible for invasive non-typhoidal Salmonella (iNTS) disease. The pathogen also causes bloodstream infection in Colombia, but there has been a lack of information about the S. Typhimurium isolates that were responsible. Here, we investigated the genomic characteristics of 270 S. Typhimurium isolates from bloodstream infection patients in Colombia, collected between 1997 and 2017. We used whole-genome sequencing to analyse multidrug-resistant (MDR) profiles, plasmid distribution, and to define phylogenetic relationships. The study identified the distinct sequence types and phylogenetic clusters of S. Typhimurium prevalent in Colombia. The majority of isolates (90.8%) were ST19, which is distinct from the iNTS-associated S. Typhimurium in sub-Saharan Africa (ST313). The two prominent clusters of MDR S. Typhimurium were either DT104 or closely related to the LT2 reference strain. We used a phylogenetic approach to associate the Colombian clusters with global S. Typhimurium isolates from public databases. By putting the Colombian S. Typhimurium isolates in the context of the global spread of DT104, ST313 and LT2-related variants, we found that the Colombian clusters were introduced to the country via multiple independent events that were consistent with international transmission. We suggest that the acquisition of quinolone and chloramphenicol resistance by the Colombian S. Typhimurium isolates was driven by horizontal gene transfer. Three ST313 isolates that caused bloodstream infection in Colombia were identified. These ST313 isolates were related to the Malawian ST313 lineage 3 &amp; UK ST313, and shared a similarly high invasiveness index. To our knowledge, this is the first report of ST313 in Colombia.}, }
@article {pmid39873499, year = {2025}, author = {Liu, CC and Hsiao, WWL}, title = {Machine learning reveals the dynamic importance of accessory sequences for Salmonella outbreak clustering.}, journal = {mBio}, volume = {16}, number = {3}, pages = {e0265024}, pmid = {39873499}, issn = {2150-7511}, support = {286GET//Genome British Columbia (Genome BC)/ ; 286GET//Genome Canada (GC)/ ; R831778//Mitacs (Mitacs Canada)/ ; }, mesh = {*Disease Outbreaks ; *Machine Learning ; *Salmonella Infections/epidemiology/microbiology ; Genome, Bacterial ; *Salmonella enterica/genetics/classification/isolation &amp; purification ; Humans ; Animals ; Cluster Analysis ; Interspersed Repetitive Sequences ; Whole Genome Sequencing ; Molecular Epidemiology/methods ; }, abstract = {UNLABELLED: Bacterial typing at whole-genome scales is now feasible owing to decreasing costs in high-throughput sequencing and the recent advances in computation. The unprecedented resolution of whole-genome typing is achieved by genotyping the variable segments of bacterial genomes that can fluctuate significantly in gene content. However, due to the transient and hypervariable nature of many accessory elements, the value of the added resolution in outbreak investigations remains disputed. To assess the analytical value of bacterial accessory genomes in clustering epidemiologically related cases, we trained classifiers on a set of genomes collected from 24 Salmonella enterica outbreaks of food, animal, or environmental origin. The models demonstrated high precision and recall on unseen test data with near-perfect accuracy in classifying clonal and short-term outbreaks. Annotating the genomic features important for cluster classification revealed functional enrichment of molecular fingerprints in genes involved in membrane transportation, trafficking, and carbohydrate metabolism. Importantly, we discovered polymorphisms in mobile genetic elements (MGEs) and gain/loss of MGEs to be informative in defining outbreak clusters. To quantify the ability of MGE variations to cluster outbreak clones, we devised a reference-free tree-building algorithm inspired by colored de Bruijn graphs, which enabled topological comparisons between MGE and standard typing methods. Systematic evaluation of clustering MGEs on an unseen dataset of 34 Salmonella outbreaks yielded mixed results that exemplified the power of accessory sequence variations when core genomes of unrelated cases are insufficiently discriminatory, as well as the distortion of outbreak signals by microevolution events or the incomplete assembly of MGEs.<br><br>IMPORTANCE: Gene-by-gene typing is widely used to detect clusters of foodborne illnesses that share a common origin. It remains actively debated whether the inclusion of accessory sequences in bacterial typing schema is informative or deleterious for cluster definitions in outbreak investigations due to the potential confounding effects of horizontal gene transfer. By training machine learning models on a curated set of historical Salmonella outbreaks, we revealed an enriched presence of outbreak distinguishing features in a wide range of mobile genetic elements. Systematic comparison of the efficacy of clustering different accessory elements against standard sequence typing methods led to our cataloging of scenarios where accessory sequence variations were beneficial and uninformative to resolving outbreak clusters. The presented work underscores the complexity of the molecular trends in enteric outbreaks and seeks to inspire novel computational ways to exploit whole-genome sequencing data in enteric disease surveillance and management.}, }
@article {pmid39871141, year = {2025}, author = {Nichio, BTL and Chaves, RBR and Pedrosa, FO and Raittz, RT}, title = {Exploring diazotrophic diversity: unveiling Nif core distribution and evolutionary patterns in nitrogen-fixing organisms.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {81}, pmid = {39871141}, issn = {1471-2164}, mesh = {*Nitrogen Fixation/genetics ; *Evolution, Molecular ; Phylogeny ; Nitrogenase/genetics/metabolism ; *Bacterial Proteins/genetics ; Gene Transfer, Horizontal ; }, abstract = {BACKGROUND: Diazotrophs carry out biological nitrogen fixation (BNF) using the nitrogenase enzyme complex (NEC), which relies on nitrogenase encoded by nif genes. Horizontal gene transfer (HGT) and gene duplications have created significant diversity among these genes, making it challenging to identify potential diazotrophs. Previous studies have established a minimal set of Nif proteins, known as the Nif core, which includes NifH, NifD, NifK, NifE, NifN, and NifB. This study aimed to identify potential diazotroph groups based on the Nif core and to analyze the inheritance patterns of accessory Nif proteins related to Mo-nitrogenase, along with their impact on N2 fixation maintenance.<br><br>RESULTS: In a systematic study, 118 diazotrophs were identified, resulting in a database of 2,156 Nif protein sequences obtained with RAFTS&#xb3;G. Using this Nif database and a data mining strategy, we extended our analysis to 711 species and found that 544 contain the Nif core. A partial Nif core set was observed in eight species in this study. Finally, we cataloged 662 species with Nif core, of which 52 were novel. Our analysis generated 10,076 Nif proteins from these species and revealed some Nif core duplications. Additionally, we determined the optimal cluster value (k&#x2009;=&#x2009;10) for analyzing diazotrophic diversity. Combining synteny and phylogenetic analyses revealed distinct syntenies in the nif gene composition across ten groups.<br><br>CONCLUSIONS: This study advances our understanding of the distribution of nif genes, aiding in the prediction and classification of N&#x2082;-fixing organisms. Furthermore, we present a comprehensive overview of the diversity, distribution, and evolutionary relationships among diazotrophic organisms associated with the Nif core. The analysis revealed the phylogenetic and functional organization of different groups, identifying synteny patterns and new nif gene arrangements across various bacterial and archaeal species.The identified groups serve as a valuable framework for further exploration of the molecular mechanisms underlying biological nitrogen fixation and its evolutionary significance across different bacterial lineages.}, }
@article {pmid39870251, year = {2025}, author = {Oubohssaine, M and Rabeh, K and Hnini, M}, title = {Symbiosis vs pathogenesis in plants: Reflections and perspectives.}, journal = {Microbial pathogenesis}, volume = {200}, number = {}, pages = {107333}, doi = {10.1016/j.micpath.2025.107333}, pmid = {39870251}, issn = {1096-1208}, mesh = {*Symbiosis/physiology ; *Plants/microbiology ; *Plant Diseases/microbiology ; Quorum Sensing ; *Host-Pathogen Interactions ; Plant Growth Regulators/metabolism ; Volatile Organic Compounds/metabolism ; Ecosystem ; }, abstract = {Plant-microbe partnerships constitute a complex and intricately woven network of connections that have evolved over countless centuries, involving both cooperation and antagonism. In various contexts, plants and microorganisms engage in mutually beneficial partnerships that enhance crop health and maintain balance in ecosystems. However, these associations also render plants susceptible to a range of pathogens. Understanding the fundamental molecular mechanisms governing these associations is crucial, given the notable susceptibility of plants to external environmental influences. Based on quorum sensing signals, phytohormone, and volatile organic carbon (VOC) production and others molecules, microorganisms influence plant growth, health, and defense responses. This review explores the multifaceted relationships between plants and their associated microorganisms, encompassing mutualism, commensalism, and antagonism. The molecular mechanisms of symbiotic and pathogenic interactions share similarities but lead to different outcomes. While symbiosis benefits both parties, pathogenesis harms the host. Genetic adaptations optimize these interactions, involving coevolution driving process. Environmental factors influence outcomes, emphasizing the need for understanding and manipulation of microbial communities for beneficial results. Research directions include employing multi-omics techniques, functional studies, investigating environmental factors, understanding evolutionary trajectories, and harnessing knowledge to engineer synthetic microbial consortia for sustainable agriculture and disease management.}, }
@article {pmid39869787, year = {2025}, author = {Lin, C and Li, LJ and Yang, K and Xu, JY and Fan, XT and Chen, QL and Zhu, YG}, title = {Protozoa-enhanced conjugation frequency alters the dissemination of soil antibiotic resistance.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {39869787}, issn = {1751-7370}, support = {2021-DST-004//Ningbo S&amp;T project/ ; 2022S117//Ningbo Public Welfare project/ ; 42090063//National Natural Science Foundation of China/ ; }, mesh = {*Soil Microbiology ; *Conjugation, Genetic ; Plasmids/genetics ; Gene Transfer, Horizontal ; *Drug Resistance, Microbial/genetics ; *Acanthamoeba castellanii/physiology/genetics ; Animals ; Soil/parasitology ; Bacteria/genetics/drug effects ; Metagenomics ; }, abstract = {Protozoa, as primary predators of soil bacteria, represent an overlooked natural driver in the dissemination of antibiotic resistance genes (ARGs). However, the effects of protozoan predation on ARGs dissemination at the community level, along with the underlying mechanisms, remain unclear. Here we used fluorescence-activated cell sorting, qPCR, combined with metagenomics and reverse transcription quantitative PCR, to unveil how protozoa (Colpoda steinii and Acanthamoeba castellanii) influence the plasmid-mediated transfer of ARGs to soil microbial communities. Protozoan predation reduced the absolute abundance of plasmids but promoted the expression of conjugation-associated genes, leading to a 5-fold and 4.5-fold increase in conjugation frequency in the presence of C. steinii and A. castellanii, respectively. Excessive oxidative stress, increased membrane permeability, and the provoked SOS response closely associated with the increased conjugative transfer. Protozoan predation also altered the plasmid host range and selected for specific transconjugant taxa along with ARGs and virulence factors carried by transconjugant communities. This study underscores the role of protozoa in the plasmid-mediated conjugative transfer of ARGs, providing new insights into microbial mechanisms that drive the dissemination of environmental antibiotic resistance.}, }
@article {pmid39867821, year = {2025}, author = {Yan, Z and Wang, H and Zhu, Y and Wang, X and Wu, Y and Wang, Y and Zhang, R}, title = {Molecular Epidemiology of Type F Clostridium perfringens Among Diarrheal Patients and Virulence-Resistance Dynamics - 11 Provinces, China, 2024.}, journal = {China CDC weekly}, volume = {7}, number = {3}, pages = {69-76}, pmid = {39867821}, issn = {2096-7071}, abstract = {INTRODUCTION: Type F Clostridium perfringens (C. perfringens) represents a significant pathogen in human gastrointestinal diseases, primarily through its cpe gene encoding C. perfringens enterotoxin (CPE). This investigation examined the prevalence, antimicrobial resistance patterns, and genetic characteristics of Type F C. perfringens within the Chinese population.<br><br>METHODS: The study analyzed 2,068 stool samples collected from 11 provincial hospitals in 2024. Antimicrobial susceptibility testing was conducted following Clinical &amp; Laboratory Standards Institute (CLSI) guidelines, while whole-genome sequencing provided detailed genetic profiles. Evolutionary relationships and clonal transmission patterns were investigated through phylogenetic and genetic environment analyses.<br><br>RESULTS: The prevalence of Type F C. perfringens was 2.38%, with isolates predominantly identified in human clinical samples and higher detection rates in gastroenterology departments. Notably, 47.1% of isolates demonstrated high resistance to metronidazole, while all exhibited intermediate resistance to erythromycin. Phylogenetic analysis revealed high similarity among isolates from patients within the same province (single-nucleotide polymorphism (SNPs)<100), and genetic environment analysis indicated potential horizontal gene transfer between animal and human strains.<br><br>CONCLUSIONS: This investigation predominantly identified Type F C. perfringens in human clinical cases, with sporadic detection in pets and food products. These findings highlight the emergence of Type F C. perfringens outbreaks among diarrheal patients, emphasizing the necessity for targeted interventions as virulence factors increase.}, }
@article {pmid39865504, year = {2025}, author = {Sharp, PM and Bibollet-Ruche, F and Hahn, BH}, title = {Plasmodium falciparum CyRPA Glycan Binding Does Not Explain Adaptation to Humans.}, journal = {Genome biology and evolution}, volume = {17}, number = {2}, pages = {}, pmid = {39865504}, issn = {1759-6653}, support = {P30 AI045008/AI/NIAID NIH HHS/United States ; R01 AI120810/NH/NIH HHS/United States ; }, mesh = {*Plasmodium falciparum/genetics/metabolism/pathogenicity ; Humans ; *Polysaccharides/metabolism ; Animals ; *Protozoan Proteins/metabolism/genetics/chemistry ; Binding Sites ; Erythrocytes/parasitology ; Protein Binding ; Gorilla gorilla/parasitology ; Malaria, Falciparum/parasitology ; Adaptation, Physiological ; }, abstract = {The human malaria parasite Plasmodium falciparum evolved from a parasite that infects gorillas, termed Plasmodium praefalciparum. The sialic acids on glycans on the surface of erythrocytes differ between humans and other apes. It has recently been shown that the P. falciparum cysteine-rich protective antigen (PfCyRPA) binds human sialoglycans as an essential step in the erythrocyte invasion pathway, while that of the chimpanzee parasite, Plasmodium reichenowi has affinities matching ape glycans. Two amino acid changes, at sites 154 and 209, were shown to be sufficient to switch glycan binding preferences and inferred to reflect adaptation of P. falciparum to humans. However, we show that sites 154 and 209 are identical in P. falciparum and P. praefalciparum, with no other differences located in or near the CyRPA glycan binding sites. Thus, the gorilla precursor appears to have already been preadapted to bind human sialoglycans.}, }
@article {pmid39862584, year = {2025}, author = {Zheng, Z and Ji, W and Wang, X and Wang, X and Dai, S and Zhang, Z and Zhang, Y and Wang, X and Cao, S and Chen, M and Xie, B and Feng, J and Wu, D}, title = {Household waste-specific ambient air shows greater inhalable antimicrobial resistance risks in densely populated communities.}, journal = {Waste management (New York, N.Y.)}, volume = {194}, number = {}, pages = {309-317}, doi = {10.1016/j.wasman.2025.01.030}, pmid = {39862584}, issn = {1879-2456}, mesh = {China ; Humans ; *Air Microbiology ; *Particulate Matter/analysis ; *Air Pollutants/analysis ; *Drug Resistance, Microbial/genetics ; Environmental Monitoring ; Bacteria/genetics ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Household waste is a hotspot of antibiotic resistance, which can be readily emitted to the ambient airborne inhalable particulate matters (PM10) during the day-long storage in communities. Nevertheless, whether these waste-specific inhalable antibiotic resistance genes (ARGs) are associated with pathogenic bacteria or pose hazards to local residents have yet to be explored. By high-throughput metagenomic sequencing and culture-based antibiotic resistance validation, we analyzed 108 airborne PM10 and nearby environmental samples collected across different types of residential communities in Shanghai, the most populous city in China. Compared to the cold-dry period, the warm-humid season had significantly larger PM10-associated antibiotic resistomes in all types of residential communities (T-test, P < 0.001), most of airborne ARGs in which were estimatedly originated from disposed household waste (∼ 30 %). In addition, the airborne bacteria were assembled in a deterministic approach (iCAMP, P < 0.01), where the waste-specific bacteria taxa including Acinetobacter, Pseudomonas, Rhodococcus, and Kocuria had the predominant niches in the airborne microbial assemblages. Notably, these waste-sourced bacteria were also identified as the primary airborne hosts of ARGs encoding the aminoglycoside resistances. Among them, some antibiotic resistant human pathogens, such as Pseudomonas aeruginosa and Acinetobacter baumannii, not only exhibited higher ARG horizontal gene transfer (HGT) potential across the microbial assemblages, but also imposed direct infection risks on the local residents by 2 min inhalation exposure per day. When the daily exposure duration increased to 11 min, the infection-induced illness burden became unignorably high, especially in densely populated urban communities, being twofold greater than rural areas.}, }
@article {pmid39862048, year = {2025}, author = {Colinet, D and Haon, M and Drula, E and Boyer, M and Grisel, S and Belliardo, C and Koutsovoulos, GD and Berrin, JG and Danchin, EGJ}, title = {Functional Carbohydrate-Active Enzymes Acquired by Horizontal Gene Transfer from Plants in the Whitefly Bemisia tabaci.}, journal = {Genome biology and evolution}, volume = {17}, number = {2}, pages = {}, pmid = {39862048}, issn = {1759-6653}, mesh = {Animals ; *Gene Transfer, Horizontal ; *Hemiptera/genetics/enzymology ; Phylogeny ; *Glycoside Hydrolases/genetics/metabolism ; *Plants/genetics ; }, abstract = {Carbohydrate-active enzymes involved in the degradation of plant cell walls and/or the assimilation of plant carbohydrates for energy uptake are widely distributed in microorganisms. In contrast, they are less frequent in animals, although there are exceptions, including examples of carbohydrate-active enzymes acquired by horizontal gene transfer from bacteria or fungi in several of phytophagous arthropods and plant-parasitic nematodes. Although the whitefly Bemisia tabaci is a major agricultural pest, knowledge of horizontal gene transfer-acquired carbohydrate-active enzymes in this phloem-feeding insect of the Hemiptera order (subfamily Aleyrodinae) is still lacking. We performed a comprehensive and accurate detection of horizontal gene transfer candidates in B. tabaci and identified 136 horizontal gene transfer events, 14 of which corresponding to carbohydrate-active enzymes. The B. tabaci horizontal gene transfer-acquired carbohydrate-active enzymes were not only of bacterial or fungal origin, but some were also acquired from plants. Biochemical analysis revealed that members of the glycoside hydrolase families 17 and 152 acquired from plants are functional beta-glucanases with different substrate specificities, suggesting distinct roles. These two carbohydrate-active enzymes are the first characterized glycoside hydrolase families 17 and 152 glucanases in an animal. We identified a lower number of horizontal gene transfer events in the related Aleyrodinae Trialeurodes vaporariorum, with only three horizontal gene transfer-acquired carbohydrate-active enzymes, including a glycoside hydrolase family 152 glucanase, with phylogenetic analysis suggesting a unique horizontal gene transfer event in the ancestor of the Aleyrodinae. Another glycoside hydrolase family 152 carbohydrate-active enzyme, most likely independently acquired from plants, was also identified in two plant cell-feeding insects of the Thysanoptera order, highlighting the importance of plant-acquired carbohydrate-active enzymes in the biology of piercing-sucking insects.}, }
@article {pmid39861970, year = {2025}, author = {Saati-Santamaría, Z and Navarro-Gómez, P and Martínez-Mancebo, JA and Juárez-Mugarza, M and Flores, A and Canosa, I}, title = {Genetic and species rearrangements in microbial consortia impact biodegradation potential.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {39861970}, issn = {1751-7370}, support = {//University of Seville from the Ministry of Universities/ ; CLU-2018-04//Regional Government of Castilla y Le&#xf3;n/ ; //European NextGenerationEU program/ ; //University of Salamanca/ ; 101090267//EU Horizon Europe program/ ; ProyExcel_00358//Programa de Excelencia de la Junta de Andaluc&#xed;a/ ; //V Plan Propio de investigaci&#xf3;n of the University Pablo de Olavide/ ; }, mesh = {*Microbial Consortia/genetics ; Biodegradation, Environmental ; Plasmids/genetics ; *Ibuprofen/metabolism ; *Bacteria/genetics/metabolism/classification ; Gene Transfer, Horizontal ; Wastewater/microbiology ; Phylogeny ; }, abstract = {Genomic reorganisation between species and horizontal gene transfer have been considered the most important mechanism of biological adaptation under selective pressure. Still, the impact of mobile genes in microbial ecology is far from being completely understood. Here we present the collection and characterisation of microbial consortia enriched from environments contaminated with emerging pollutants, such as non-steroidal anti-inflammatory drugs. We have obtained and further enriched two ibuprofen-degrading microbial consortia from two unrelated wastewater treatment plants. We have also studied their ability to degrade the drug and the dynamics of the re-organisations of the genetic information responsible for its biodegradation among the species within the consortium. Our results show that genomic reorganisation within microorganisms and species rearrangements occur rapidly and efficiently during the selection process, which may be facilitated by plasmids and/or transposable elements located within the sequences. We show the evolution of at least two different plasmid backbones on samples from different locations, showing rearrangements of genomic information, including genes encoding activities for IBU degradation. As a result, we found variations in the expression pattern of the consortia after evolution under selective pressure, as an adaptation process to the new conditions. This work provides evidence for changes in the metagenomes of microbial communities that allow adaptation under a selective constraint -ibuprofen as a sole carbon source- and represents a step forward in knowledge that can inspire future biotechnological developments for drug bioremediation.}, }
@article {pmid39861872, year = {2025}, author = {Yakubovskij, VI and Morozova, VV and Kozlova, YN and Tikunov, AY and Fedorets, VA and Zhirakovskaya, EV and Babkin, IV and Bardasheva, AV and Tikunova, NV}, title = {Phage vB_KlebPS_265 Active Against Resistant/MDR and Hypermucoid K2 Strains of Klebsiella pneumoniae.}, journal = {Viruses}, volume = {17}, number = {1}, pages = {}, pmid = {39861872}, issn = {1999-4915}, support = {grant No 122110700002-2//Ministry of Science and Higher Education of the Russian Federation/ ; }, mesh = {*Klebsiella pneumoniae/virology/drug effects ; Genome, Viral ; Phylogeny ; *Bacteriophages/genetics/classification/isolation &amp; purification/physiology ; Klebsiella Infections/microbiology/therapy ; Humans ; Drug Resistance, Multiple, Bacterial ; Gene Transfer, Horizontal ; Siphoviridae/genetics/classification/isolation &amp; purification/physiology ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Klebsiella pneumoniae is an important opportunistic pathogen often resistant to antibiotics. Specific phages can be useful in eliminating infection caused by K. pneumoniae. Klebsiella phage vB_KlebPS_265 (KlebP_265) and its host strain were isolated from the sputum of a patient with Klebsiella infection. KlebP_265 was specific mainly to K. pneumoniae-type K2 strains including hypermucoid strains. Most of the hypermucoid KlebP_265-susceptible strains were antibiotic-resistant. This siphophage demonstrated good lytic activity and stability. The KlebP_265 genome was 46,962 bp and contained 88 putative genes; functions were predicted for 37 of them. No genes encoding integrases, toxins, or antibiotic resistance were found in the genome. So, KlebP_265 could potentially be a therapeutic phage. Comparative analysis indicated that KlebP_265 with the most relative Klebsiella phage DP01 formed the putative Dipiunovirus genus. Genome analysis revealed a large monophyletic group of phages related to KlebP_265 and DP01. This group is divided into two monophyletic clusters of phages forming new putative subfamilies Skatevirinae and Roufvirinae. Phylogenetic analysis showed extensive gene exchange between phages from the putative subfamilies. Horizontal transfer even involved conservative genes and led to clear genomic mosaicism, indicating multiple recombination events in the ancestral phages during evolution.}, }
@article {pmid39859430, year = {2025}, author = {Yuan, Z and Zhang, J and Duan, D}, title = {Vanadium-Dependent Haloperoxidase Gene Evolution in Brown Algae: Evidence for Horizontal Gene Transfer.}, journal = {International journal of molecular sciences}, volume = {26}, number = {2}, pages = {}, pmid = {39859430}, issn = {1422-0067}, support = {2022HWYQ-087//Shandong Province/ ; 41806202//National Natural Science Foundation of China/ ; 133137KYSB20210034//Chinese Academy of Sciences/ ; }, mesh = {*Gene Transfer, Horizontal ; *Phaeophyceae/genetics/enzymology ; Phylogeny ; *Evolution, Molecular ; *Peroxidases/genetics/metabolism ; *Vanadium/metabolism ; Multigene Family ; }, abstract = {Compared with green plants, brown algae are characterized by their ability to accumulate iodine, contributing to their ecological adaptability in high-iodide coastal environments. Vanadium-dependent haloperoxidase (V-HPO) is the key enzyme for iodine synthesis. Despite its significance, the evolutionary origin of V-HPO genes remains underexplored. This study investigates the genomic and evolutionary dynamics of V-HPOs in brown algae, focusing on Laminariales species, particularly Saccharina japonica. Genomic analyses revealed the extensive expansion of the V-HPO gene family in brown algae, with 88 V-HPOs identified in S. japonica, surpassing the number in red algae. Phylogenetic analysis demonstrated distinct evolutionary divergence between brown and red algal V-HPOs, with the brown algal clade closely related to bacterial V-HPOs. These findings suggest horizontal gene transfer (HGT) played a key role in acquiring V-HPO genes, particularly from Acidobacteriota, a bacterial phylum known for genomic plasticity. Additionally, enriched active transposable elements were identified around V-HPO genomic clusters, highlighting their role in tandem gene duplications and rapid HGT processes. Expression profiling further revealed dynamic regulation of V-HPOs in response to environmental conditions. This study provides new insights into how HGT has driven kelp genomic adaptations and enhances understanding of marine ecological success and evolutionary processes.}, }
@article {pmid39859334, year = {2025}, author = {Wang, C and Zhao, R and Yang, W and Jiang, W and Tang, H and Du, S and Chen, X}, title = {Cell-to-Cell Natural Transformation Mediated Efficient Plasmid Transfer Between Bacillus Species.}, journal = {International journal of molecular sciences}, volume = {26}, number = {2}, pages = {}, pmid = {39859334}, issn = {1422-0067}, support = {31970030//National Natural Science Foundation of China/ ; J1103513//National Fund for Fostering Talents of Basic Sciences/ ; None//Research (Innovative) Fund of the Laboratory of Wuhan University./ ; }, mesh = {*Plasmids/genetics ; *Transformation, Bacterial ; *Gene Transfer, Horizontal ; *Bacillus subtilis/genetics ; *Bacillus/genetics ; }, abstract = {Horizontal gene transfer (HGT) plays a pivotal role in bacterial evolution, shaping the genetic diversity of bacterial populations. It can occur through mechanisms such as conjugation, transduction, and natural transformation. Bacillus subtilis, a model Gram-positive bacterium, serves not only as a robust system for studying HGT but also as a versatile organism with established industrial applications, such as producing industrial enzymes, antibiotics, and essential metabolites. In this study, we characterize a novel method of plasmid transfer, termed Cell-to-Cell Natural Transformation for Plasmid Transfer (CTCNT-P), which efficiently facilitates plasmid transfer between naturally competent B. subtilis strains. This method involves co-culturing donor and recipient cells under antibiotic stress and achieves significantly higher efficiency compared to traditional methods such as Spizizen medium or electroporation-mediated transformation. Importantly, we demonstrate that CTCNT-P is applicable for plasmid transformation in wild B. subtilis isolates from natural environments and other Bacillus species, including Bacillus amyloliquefaciens, Bacillus licheniformis, and Bacillus thuringiensis. The simplicity and efficiency of CTCNT-P highlight its strong potential for industrial applications, including genetic modification of wild Bacillus strains for synthetic biology and the development of biocontrol agents.}, }
@article {pmid39859326, year = {2025}, author = {Kusada, H and Tamaki, H}, title = {Evidence for the Worldwide Distribution of a Bile Salt Hydrolase Gene in Enterococcus faecium Through Horizontal Gene Transfer.}, journal = {International journal of molecular sciences}, volume = {26}, number = {2}, pages = {}, pmid = {39859326}, issn = {1422-0067}, support = {JPMJGX23B2//Japan Science and Technology Agency/ ; 21ae0121047h0001//Japan Agency for Medical Research and Development/ ; }, mesh = {*Enterococcus faecium/genetics/enzymology ; *Gene Transfer, Horizontal ; Phylogeny ; *Amidohydrolases/genetics/metabolism ; Humans ; Plasmids/genetics ; *Bacterial Proteins/genetics/metabolism ; Bile Acids and Salts/metabolism ; }, abstract = {Bile salt hydrolase (BSH), a probiotic-related enzyme with cholesterol-assimilating and anti-hypercholesterolemic abilities, has been isolated from intestinal bacteria; however, BSH activity of bacteria in bile-salt-free (non-intestinal) environments is largely unknown. Here, we aimed to identify BSH from non-intestinal Enterococcus faecium and characterize its enzymatic function. We successfully isolated a plasmid-encoded bsh (efpBSH) from E. faecium, and the recombinant EfpBSH showed BSH activity that preferentially hydrolyzed taurine-conjugated bile salts, unlike the activity of known BSHs. EfpBSH functioned optimally at pH 4.0 and 50 °C. EfpBSH exhibited very low amino acid sequence similarity (48.46%) to EfBSH from E. faecalis T2 isolated from human urine, although 241 sequences with 100% identity to EfpBSH were found in both plasmids and chromosomes of E. faecium strains inhabiting intestinal and non-intestinal environments. Phylogenetically, EfpBSH was not affiliated with any known BSH phylogroup and was clearly distinguished from previously identified BSHs from intestinal lactic acid bacteria. Our genome database analysis demonstrated that horizontal gene transfer causes global efpBSH distribution among E. faecium strains in various environments (soil, water, and intestinal samples) and geographical regions (Asia, Africa, Europe, North America, South America, and Australia/Oceania). Overall, our findings are the first to indicate that BSH is not an intestine-specific enzyme and that hitherto-overlooked probiotic candidates with BSH activity can exist in diverse environments.}, }
@article {pmid39859280, year = {2025}, author = {Liu, X and Luo, H and Liu, ZJ and Yang, BY}, title = {Mitochondrial Genome Characteristics Reveal Evolution of Danxiaorchis yangii and Phylogenetic Relationships.}, journal = {International journal of molecular sciences}, volume = {26}, number = {2}, pages = {}, pmid = {39859280}, issn = {1422-0067}, mesh = {*Genome, Mitochondrial ; *Phylogeny ; *Evolution, Molecular ; *Orchidaceae/genetics/classification ; RNA, Transfer/genetics ; Codon Usage ; Base Composition ; Gene Transfer, Horizontal ; }, abstract = {Danxiaorchis yangii is a fully mycoheterotrophic orchid that lacks both leaves and roots, belonging to the genus Danxiaorchis in the subtribe Calypsoinae. In this study, we assembled and annotated its mitochondrial genome (397,867 bp, GC content: 42.70%), identifying 55 genes, including 37 protein-coding genes (PCGs), 16 tRNAs, and 2 rRNAs, and conducted analyses of relative synonymous codon usage (RSCU), repeat sequences, horizontal gene transfers (HGTs), and gene selective pressure (dN/dS). Additionally, we sequenced and assembled its plastome, which has a reduced size of 110,364 bp (GC content: 36.60%), comprising 48 PCGs, 26 tRNAs, and 4 rRNAs. We identified 64 potential chloroplast DNA fragments transferred to the mitogenome. Phylogenomic analysis focusing on 33 mitogenomes, with Vitis vinifera as the outgroup, indicated that D. yangii is grouped as follows: D. yangii + ((Dendrobium wilsonii + Dendrobium wilsonii henanense) + Phalaenopsis aphrodite). Phylogenetic analysis based on 83 plastid PCGs from these species showed that D. yangii is grouped as follows: (D. yangii + Pha. aphrodite) + (Den. wilsonii + Den. henanense). Gene selective pressure analysis revealed that most mitochondrial and plastid genes in D. yangii are under purifying selection, ensuring functional stability, and certain genes may have undergone positive selection or adaptive evolution, reflecting the species' adaptation to specific ecological environments. Our study provides valuable data on the plastomes and mitogenomes of D. yangii and lays the groundwork for future research on genetic variation, evolutionary relationships, and the breeding of orchids.}, }
@article {pmid39858976, year = {2025}, author = {He, Y and Dykes, GE and Kanrar, S and Liu, Y and Gunther, NW and Counihan, KL and Lee, J and Capobianco, JA}, title = {Comparative Genomic Analysis of Campylobacter Plasmids Identified in Food Isolates.}, journal = {Microorganisms}, volume = {13}, number = {1}, pages = {}, pmid = {39858976}, issn = {2076-2607}, support = {Current Research Information System number 8072-42000-093//U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), National Program 108/ ; }, abstract = {Campylobacter is one of the leading bacterial causes of gastroenteritis worldwide. It frequently contaminates poultry and other raw meat products, which are the primary sources of Campylobacter infections in humans. Plasmids, known as important mobile genetic elements, often carry genes for antibiotic resistance, virulence, and self-mobilization. They serve as the main vectors for transferring genetic material and spreading resistance and virulence among bacteria. In this study, we identified 34 new plasmids from 43 C. jejuni and C. coli strains isolated from retail meat using long-read and short-read genome sequencing. Pangenomic analysis of the plasmid assemblies and reference plasmids from GenBank revealed five distinct groups, namely, pTet, pVir, mega plasmids (>80 kb), mid plasmids (~30 kb), and small plasmids (<6 kb). Pangenomic analysis identified the core and accessory genes in each group, indicating a high degree of genetic similarity within groups and substantial diversity between the groups. The pTet plasmids were linked to tetracycline resistance phenotypes in host strains. The mega plasmids carry multiple genes (e.g., aph(3')-III, type IV and VI secretion systems, and type II toxin-antitoxin systems) important for plasmid mobilization, virulence, antibiotic resistance, and the persistence of Campylobacter. Together, the identification and comprehensive genetic characterization of new plasmids from Campylobacter food isolates contributes to understanding the mechanisms of gene transfer, particularly the spread of genetic determinants of virulence and antibiotic resistance in this important pathogen.}, }
@article {pmid39858487, year = {2025}, author = {Tahmasebi, H and Arjmand, N and Monemi, M and Babaeizad, A and Alibabaei, F and Alibabaei, N and Bahar, A and Oksenych, V and Eslami, M}, title = {From Cure to Crisis: Understanding the Evolution of Antibiotic-Resistant Bacteria in Human Microbiota.}, journal = {Biomolecules}, volume = {15}, number = {1}, pages = {}, pmid = {39858487}, issn = {2218-273X}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Microbiota/drug effects/genetics ; Methicillin-Resistant Staphylococcus aureus/drug effects/genetics ; *Bacteria/drug effects/genetics ; *Drug Resistance, Multiple, Bacterial/genetics ; *Drug Resistance, Bacterial/genetics ; }, abstract = {The growing prevalence of antibiotic-resistant bacteria within the human microbiome has become a pressing global health crisis. While antibiotics have revolutionized medicine by significantly reducing mortality and enabling advanced medical interventions, their misuse and overuse have led to the emergence of resistant bacterial strains. Key resistance mechanisms include genetic mutations, horizontal gene transfer, and biofilm formation, with the human microbiota acting as a reservoir for antibiotic resistance genes (ARGs). Industrialization and environmental factors have exacerbated this issue, contributing to a rise in infections with multidrug-resistant (MDR) bacteria, such as methicillin-resistant Staphylococcus aureus (MRSA) and carbapenem-resistant Enterobacteriaceae. These resistant pathogens compromise the effectiveness of essential treatments like surgical prophylaxis and chemotherapy, increase healthcare costs, and prolong hospital stays. This crisis highlights the need for a global One-Health approach, particularly in regions with weak regulatory frameworks. Innovative strategies, including next-generation sequencing (NGS) technologies, offer promising avenues for mitigating resistance. Addressing this challenge requires coordinated efforts, encompassing research, policymaking, public education, and antibiotic stewardship, to safeguard current antibiotics and foster the development of new therapeutic solutions. An integrated, multidimensional strategy is essential to tackle this escalating problem and ensure the sustainability of effective antimicrobial treatments.}, }
@article {pmid39858396, year = {2024}, author = {Dobrescu, M&#x218; and Țoc, DA and Pană, AG and Costache, C and Butiuc-Keul, A}, title = {The Difference a Year Can Make: How Antibiotic Resistance Mechanisms in Pseudomonas aeruginosa Have Changed in Northwestern Transylvania.}, journal = {Biomolecules}, volume = {15}, number = {1}, pages = {}, pmid = {39858396}, issn = {2218-273X}, support = {13517/15446/03.10.2022//Babe&#x219;-Bolyai University/ ; }, mesh = {*Pseudomonas aeruginosa/drug effects/genetics/isolation &amp; purification ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; Romania/epidemiology ; *Drug Resistance, Multiple, Bacterial/genetics ; Humans ; Integrons ; *Pseudomonas Infections/microbiology/drug therapy/epidemiology ; *Drug Resistance, Bacterial/genetics ; Bacterial Proteins/genetics ; }, abstract = {This study examines the prevalence and the mechanisms of antibiotic resistance in Pseudomonas aeruginosa isolates collected from healthcare units in Northwestern Transylvania, Romania, between 2022 and 2023. Given the alarming rise in antibiotic resistance, the study screened 34 isolates for resistance to 10 antibiotics, 46 ARGs, and integrase genes using PCR analysis. The results reveal a concerning increase in multidrug-resistant (MDR) and extensively drug-resistant (XDR) isolates over the two-year period. Notably, the prevalence of ARGs encoding resistance to sulfonamides and beta-lactams, particularly sul1 and blaOXA-50, has shown a significant rise. Furthermore, the study detected the emergence of new resistance mechanisms in the same time interval. These include target protection and even more specific mechanisms, such as metallo-beta-lactamases or enzymes involved in the methylation of 23S rRNA. Statistical analysis further confirmed the correlation between Class I integrons and several ARGs, underscoring the role of horizontal gene transfer in the dissemination of resistance. These findings emphasize the urgent need for updated treatment strategies and monitoring programs to effectively combat the spread of ARGs in clinical settings.}, }
@article {pmid39858353, year = {2025}, author = {Kløve, DC and Strube, ML and Heegaard, PMH and Astrup, LB}, title = {Mapping Antimicrobial Resistance in Staphylococcus epidermidis Isolates from Subclinical Mastitis in Danish Dairy Cows.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {1}, pages = {}, pmid = {39858353}, issn = {2079-6382}, abstract = {Background/Objectives: Although Staphylococcus epidermidis is a key cause of subclinical mastitis in Danish dairy cows, its sensitivity to antimicrobials remains unexplored. Here, we analyzed sixty S. epidermidis isolates derived from 42 dairy cows across six conventional dairy herds in Denmark. Methods: Phenotypic resistance was measured by antimicrobial susceptibility testing and minimum inhibitory concentration (MIC) analysis, and genotypic resistance was examined through whole-genome sequencing and identification of antimicrobial resistance genes (ARGs). Correspondence between phenotypic and genotypic resistance was then evaluated by Cohen's kappa statistics. Furthermore, the presence of plasmid replicon genes and the strain diversity among the S. epidermidis isolates was investigated to associate these findings with the observed AMR patterns. Results: Results showed that 30/60 isolates (50.0%) were resistant to penicillin phenotypically, while 35/60 (58.3%) were positive for a corresponding blaZ gene (κ = 0.83, p < 0.01). A fosB gene, encoding fosfomycin resistance, was detected in all 60/60 isolates (100.0%), but fosfomycin resistance was not analyzed phenotypically. Based on MIC analysis, 3/60 isolates (5.0%) were multi-drug resistant, showing resistance towards penicillin, erythromycin, and tetracycline. However, in 11/60 genomes (18.3%), ARGs encoding resistance towards ≥3 antimicrobial classes (e.g., beta-lactams, phosphonic acid, tetracyclines, aminoglycosides, macrolides, lincosamides, and fusidane) were detected. Eleven different ARGs were detected among the 60 isolates in total. No methicillin-resistant Staphylococcus epidermidis (MRSE) were recorded. Results further showed that each herd had one primary sequence type (ST) and resistance profile associated with it, and plasmid-mediated horizontal gene transfer of ARGs was indicated This study underscores the importance of routine resistance surveillance and species-specific diagnoses to improve treatment outcomes and ensure prudent use of antimicrobials.}, }
@article {pmid39856955, year = {2025}, author = {Zhang, Z and Zhao, H and Shi, C}, title = {Clonal Spread and Genetic Mechanisms Underpinning Ciprofloxacin Resistance in Salmonella enteritidis.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {2}, pages = {}, pmid = {39856955}, issn = {2304-8158}, support = {2024YFE0199000//National Key R&amp;D Program of China/ ; 32202193//National Natural Science Foundation of China/ ; 32472458//National Natural Science Foundation of China/ ; }, abstract = {Salmonella enteritidis is a major cause of foodborne illness worldwide, and the emergence of ciprofloxacin-resistant strains poses a significant threat to food safety and public health. This study aimed to investigate the prevalence, spread, and mechanisms of ciprofloxacin resistance in S. enteritidis isolates from food and patient samples in Shanghai, China. A total of 1625 S. enteritidis isolates were screened, and 34 (2.1%) exhibited resistance to ciprofloxacin. Pulsed-field gel electrophoresis (PFGE) results suggested that clonal spread might have persisted among these 34 isolates in the local area for several years. Multiple plasmid-mediated quinolone resistance (PMQR) genes, GyrA mutations in the quinolone resistance-determining region (QRDR), and overexpression of RND efflux pumps were identified as potential contributors to ciprofloxacin resistance. PMQR genes oqxAB, qnrA, qnrB, and aac(6')-Ib-cr as well as GyrA mutations S83Y, S83R, D87Y, D87G, D87N, and S83Y-D87Y were identified. The co-transfer of the PMQR gene oqxAB with the ESBL gene blaCTX-M-14/55 on an IncHI2 plasmid with a size of ~245 kbp was observed through conjugation, highlighting the role of horizontal gene transfer in the dissemination of antibiotic resistance. Sequencing of the oqxAB-bearing plasmid p12519A revealed a 248,746 bp sequence with a typical IncHI2 backbone. A 53,104 bp multidrug resistance region (MRR) was identified, containing two key antibiotic resistance determinants: IS26-oqxR-oqxAB-IS26 and IS26-ΔISEcp1-blaCTX-M-14-IS903B. The findings of this study indicate that ciprofloxacin-resistant S. Enteritidis poses a significant threat to food safety and public health. The persistence of clonal spread and the horizontal transfer of resistance genes highlight the need for enhanced surveillance and control measures to prevent the further spread of antibiotic resistance.}, }
@article {pmid39855970, year = {2025}, author = {Wang, D and Zhou, X and Fu, Q and Li, Y and Ni, BJ and Liu, X}, title = {Understanding bacterial ecology to combat antibiotic resistance dissemination.}, journal = {Trends in biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tibtech.2024.12.011}, pmid = {39855970}, issn = {1879-3096}, abstract = {The dissemination of antibiotic resistance from environmental sources is a growing concern. Despite the widespread occurrence of antibiotic resistance transmission events, there are actually multiple obstacles in the ecosystem that restrict the flow of bacteria and genes, in particular nonnegligible biological barriers. How these ecological factors help combat the dissemination of antibiotic resistance and relevant antibiotic resistance-diminishing organisms (ARDOs) deserves further exploration. This review summarizes the factors that influence the growth, metabolism, and environmental adaptation of antibiotic-resistant bacteria (ARB) and restrict the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). Additionally, this review discusses the achievements in the application of ARDOs to improve biotechnology for wastewater and solid waste remediation while highlighting current challenges limiting their broader implementation.}, }
@article {pmid39854814, year = {2025}, author = {Xu, Z and Li, S and Ma, Y and Li, C and Lu, H and Xiong, J and He, G and Li, R and Ren, X and Huang, B and Pan, X}, title = {Role of organophosphorus pesticides in facilitating plasmid-mediated conjugative transfer: Efficiency and mechanisms.}, journal = {Journal of hazardous materials}, volume = {487}, number = {}, pages = {137318}, doi = {10.1016/j.jhazmat.2025.137318}, pmid = {39854814}, issn = {1873-3336}, mesh = {*Plasmids/genetics ; *Pesticides/toxicity ; *Gene Transfer, Horizontal/drug effects ; Reactive Oxygen Species/metabolism ; *Malathion/toxicity ; *Dimethoate/toxicity ; *Organophosphorus Compounds/toxicity ; Cell Membrane Permeability/drug effects ; Escherichia coli/genetics/drug effects/metabolism ; *Conjugation, Genetic/drug effects ; Drug Resistance, Microbial/genetics ; }, abstract = {Non-antibiotic conditions, including organophosphorus pesticides (OPPs), have been implicated in the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) to varying degrees. While most studies focus on the toxicity of OPPs to humans and animals, their roles in ARG dissemination remain largely unexplored. In this study, we investigate the effects and involved molecular mechanisms of environmentally relevant concentrations of malathion and dimethoate, two representative OPPs, on plasmid-mediated conjugal transfer. By detecting reactive oxygen species (ROS) production and cell membrane permeability, we gained insights into the underlying processes. Furthermore, we substantiated the role of ROS and cell membrane permeability in plasmid-mediated conjugative transfer through the analysis of relevant antioxidant enzyme activities, cell membrane-related indices, and RNA sequences. Additionally, our examination of proton motive force and adenosine triphosphate content provided evidence that OPPs create conditions conducive to plasmid-mediated conjugative transfer from an energetic perspective. The findings of the present study highlight the potential risk of OPPs in promoting ARG spread, which could ultimately provide new theoretical support and direction for future research on the impacts of pesticides on ARG propagation.}, }
@article {pmid39852676, year = {2025}, author = {Bukari, Z and Emmanuel, T and Woodward, J and Ferguson, R and Ezughara, M and Darga, N and Lopes, BS}, title = {The Global Challenge of Campylobacter: Antimicrobial Resistance and Emerging Intervention Strategies.}, journal = {Tropical medicine and infectious disease}, volume = {10}, number = {1}, pages = {}, pmid = {39852676}, issn = {2414-6366}, abstract = {Antimicrobial resistance (AMR) in Campylobacter species, particularly C. jejuni and C. coli, poses a significant public health threat. These bacteria, which are commonly found in livestock, poultry, companion animals, and wildlife, are the leading causes of foodborne illnesses, often transmitted through contaminated poultry. Extensive exposure to antibiotics in human and veterinary medicine creates selection pressure, driving resistance through mechanisms such as point mutations, horizontal gene transfer, and efflux pumps. Resistance to fluoroquinolones, macrolides, and tetracyclines complicates treatment and increases the risk of severe infections. Drug-resistant Campylobacter is transmitted to humans via contaminated food, water, and direct contact with animals, highlighting its zoonotic potential. Addressing this challenge requires effective interventions. Pre-harvest strategies like biosecurity and immune-based methods reduce bacterial loads on farms, while post-harvest measures, including carcass decontamination and freezing, limit contamination. Emerging approaches, such as bacteriocins and natural antimicrobials, offer chemical-free alternatives. Integrated, multidisciplinary interventions across the food chain are essential to mitigate AMR transmission and enhance food safety. Sustainable agricultural practices, antimicrobial stewardship, and innovative solutions are critical to curbing Campylobacter resistance and protecting global public health. Our review examines the dynamics of antimicrobial resistance in Campylobacter and presents current strategies to mitigate Campylobacter-related AMR, offering valuable insights for antimicrobial control in the poultry industry.}, }
@article {pmid39847570, year = {2025}, author = {Al Sium, SM and Goswami, B and Chowdhury, SF and Naser, SR and Sarkar, MK and Faruq, MJ and Habib, MA and Akter, S and Banu, TA and Sarkar, MMH and Khan, MS}, title = {An insight into the genome-wide analysis of bacterial defense mechanisms in a uropathogenic Morganella morganii isolate from Bangladesh.}, journal = {PloS one}, volume = {20}, number = {1}, pages = {e0313141}, pmid = {39847570}, issn = {1932-6203}, mesh = {Bangladesh ; *Morganella morganii/genetics/isolation &amp; purification/pathogenicity ; Humans ; *Genome, Bacterial ; Phylogeny ; *Urinary Tract Infections/microbiology ; Genomic Islands ; Whole Genome Sequencing ; Virulence Factors/genetics ; }, abstract = {The gram-negative, facultative anaerobic bacterium Morganella morganii is linked to a number of illnesses, including nosocomial infections and urinary tract infections (UTIs). A clinical isolate from a UTI patient in Bangladesh was subjected to high-throughput whole genome sequencing and extensive bioinformatics analysis in order to gather knowledge about the genomic basis of bacterial defenses and pathogenicity in M. morganii. With an average nucleotide identity (ANI) of more than 97% similarity to a reference genome and phylogenetic analysis verified the isolate as M. morganii. Genome annotation identified 3,718 protein-coding sequences, including genes for metabolism, protein processing, stress response, energy, and membrane transport. The presence of biosynthetic gene clusters points to the isolate's ability to create bioactive compounds, including antibiotics. Genomic islands contained genes for metal transporters, stress proteins, toxin proteins, and genes related to horizontal gene transfer. The beta-lactam resistance gene blaDHA was found using antimicrobial resistance (AMR) gene analysis across three databases. The virulence genes kdsA and cheY, which may be involved in chemotaxis and lipopolysaccharide production, were also available in the isolate, suggesting its high pathogenicity. The genome contained mobile genetic components and defense mechanisms, such as restriction modification and CRISPR-Cas systems, indicating the bacterium's ability to defend itself against viral attacks. This thorough investigation sheds important light on M. morganii's pathogenicity and adaptive tactics by revealing its genetic characteristics, AMR, virulence components, and defense mechanisms. For the development of targeted treatments and preventing the onset of resistance in clinical care, it is essential to comprehend these genetic fingerprints.}, }
@article {pmid39846752, year = {2025}, author = {McKeithen-Mead, S and Anderson, ME and García-Heredia, A and Grossman, AD}, title = {Activation and modulation of the host response to DNA damage by an integrative and conjugative element.}, journal = {Journal of bacteriology}, volume = {207}, number = {2}, pages = {e0046224}, pmid = {39846752}, issn = {1098-5530}, support = {T32 GM007287/GM/NIGMS NIH HHS/United States ; R35 GM122538/GM/NIGMS NIH HHS/United States ; R35 GM148343/GM/NIGMS NIH HHS/United States ; R01 GM050895/GM/NIGMS NIH HHS/United States ; MathWorks Science Fellowship//MathWorks (The MathWorks, Inc.)/ ; }, mesh = {*Bacillus subtilis/genetics/virology/metabolism ; *DNA Damage ; *SOS Response, Genetics ; Bacterial Proteins/genetics/metabolism ; *Interspersed Repetitive Sequences ; Gene Expression Regulation, Bacterial ; Conjugation, Genetic ; Prophages/genetics ; Rec A Recombinases/metabolism/genetics ; }, abstract = {Mobile genetic elements help drive horizontal gene transfer and bacterial evolution. Conjugative elements and temperate bacteriophages can be stably maintained in host cells. They can alter host physiology and regulatory responses and typically carry genes that are beneficial to their hosts. We found that ICEBs1, an integrative and conjugative element (ICE) of Bacillus subtilis, inhibits the host response to DNA damage (the SOS response). Activation of ICEBs1 before DNA damage reduced host cell lysis that was caused by SOS-mediated activation of two resident prophages. Further, activation of ICEBs1 itself activated the SOS response in a subpopulation of cells, and this activation was attenuated by the functions of the ICEBs1 genes ydcT and yddA (now ramT and ramA; ram for RecA modulator). Double-mutant analyses indicated that RamA functions to inhibit and RamT functions to both inhibit and activate the SOS response. Both RamT and RamA caused a reduction in RecA filaments, one of the early steps in activation of the SOS response. We suspect that there are several different mechanisms by which mobile genetic elements that generate single-stranded DNA (ssDNA) during their life cycle inhibit the host SOS response and RecA function, as RamT and RamA differ from the known SOS inhibitors encoded by conjugative elements.IMPORTANCEBacterial genomes typically contain mobile genetic elements, including bacteriophages (viruses) and integrative and conjugative elements, that affect host physiology. ICEs can excise from the chromosome and undergo rolling-circle replication, producing ssDNA, a signal that indicates DNA damage and activates the host SOS response. We found that following excision and replication, ICEBs1 of B. subtilis stimulates the host SOS response and that ICEBs1 encodes two proteins that limit the extent of this response. These proteins also reduce the amount of cell killing caused by resident prophages following their activation by DNA damage. These proteins are different from those previously characterized that inhibit the host SOS response and represent a new way in which ICEs can affect their host cells.}, }
@article {pmid39843582, year = {2024}, author = {Silva, KPT and Khare, A}, title = {Antibiotic resistance mediated by gene amplifications.}, journal = {npj antimicrobials and resistance}, volume = {2}, number = {1}, pages = {35}, pmid = {39843582}, issn = {2731-8745}, support = {Intramural Research Program//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; Intramural Research Program//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; }, abstract = {Apart from horizontal gene transfer and sequence-altering mutational events, antibiotic resistance can emerge due to the formation of tandem repeats of genomic regions. This phenomenon, also known as gene amplification, has been implicated in antibiotic resistance in both laboratory and clinical scenarios, where the evolution of resistance via amplifications can affect treatment efficacy. Antibiotic resistance mediated by gene amplifications is unstable and consequently can be difficult to detect, due to amplification loss in the absence of the selective pressure of the antibiotic. Further, due to variable copy numbers in a population, amplifications result in heteroresistance, where only a subpopulation is resistant to an antibiotic. While gene amplifications typically lead to resistance by increasing the expression of resistance determinants due to the higher copy number, the underlying mechanisms of resistance are diverse. In this review article, we describe the various pathways by which gene amplifications cause antibiotic resistance, from efflux and modification of the antibiotic, to target modification and bypass. We also discuss how gene amplifications can engender resistance by alternate mutational outcomes such as altered regulation and protein structure, in addition to just an increase in copy number and expression. Understanding how amplifications contribute to bacterial survival following antibiotic exposure is critical to counter their role in the rise of antimicrobial resistance.}, }
@article {pmid39843314, year = {2025}, author = {Yang, QE and Gao, JT and Zhou, SG and Walsh, TR}, title = {Cutting-edge tools for unveiling the dynamics of plasmid-host interactions.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2024.12.013}, pmid = {39843314}, issn = {1878-4380}, abstract = {The plasmid-mediated transfer of antibiotic resistance genes (ARGs) in complex microbiomes presents a significant global health challenge. This review examines recent technological advancements that have enabled us to move beyond the limitations of culture-dependent detection of conjugation and have enhanced our ability to track and understand the movement of ARGs in real-world scenarios. We critically assess the applications of single-cell sequencing, fluorescence-based techniques and advanced high-throughput chromatin conformation capture (Hi-C) approaches in elucidating plasmid-host interactions at unprecedented resolution. We also evaluate emerging techniques such as CRISPR-based phage engineering and discuss their potential for developing targeted strategies to curb ARG dissemination. Emerging data derived from these technologies have challenged our previous paradigms on plasmid-host compatibility and an awareness of an emerging uncharted realm for ARGs.}, }
@article {pmid39840972, year = {2025}, author = {Zavan, L and Hor, L and Johnston, EL and Paxman, J and Heras, B and Kaparakis-Liaskos, M}, title = {Antigen 43 associated with Escherichia coli membrane vesicles contributes to bacterial cell association and biofilm formation.}, journal = {Microbiology spectrum}, volume = {13}, number = {3}, pages = {e0189024}, pmid = {39840972}, issn = {2165-0497}, support = {DP190101655//Department of Education and Training | Australian Research Council (ARC)/ ; DP180102987, DP190101613, DP210100673//Department of Education and Training | Australian Research Council (ARC)/ ; GNT1143638//DHAC | National Health and Medical Research Council (NHMRC)/ ; Inspiring Women Fellowship//Veski/ ; }, mesh = {*Biofilms/growth &amp; development ; *Escherichia coli Proteins/metabolism/genetics ; *Uropathogenic Escherichia coli/physiology/genetics/metabolism ; *Escherichia coli/physiology/metabolism ; *Adhesins, Escherichia coli/metabolism/genetics ; Humans ; *Antigens, Bacterial/metabolism/genetics ; Cell Membrane/metabolism ; Bacterial Adhesion ; *Extracellular Vesicles/metabolism ; }, abstract = {Bacterial membrane vesicles (MVs) are produced by all bacteria and contribute to numerous bacterial functions due to their ability to package and transfer bacterial cargo. In doing so, MVs have been shown to facilitate horizontal gene transfer, mediate antimicrobial activity, and promote biofilm formation. Uropathogenic Escherichia coli is a pathogenic Gram-negative organism that persists in the urinary tract of its host due to its ability to form persistent, antibiotic-resistant biofilms. The formation of these biofilms is dependent upon proteins such as Antigen 43 (Ag43), which belongs to the widespread Autotransporter group of bacterial surface proteins. In E. coli, the autotransporter Ag43 has been shown to contribute to bacterial cell aggregation and biofilm formation via self-association of Ag43 between neighboring Ag43-expressing bacteria. As MVs package bacterial proteins, we investigated whether MVs produced by E. coli contained Ag43, and the ability of Ag43-expressing MVs to facilitate cell aggregation and biofilm formation. We showed that Ag43 expressing E. coli produced MVs that contained Ag43 on their surface and had an enhanced ability to bind to E. coli bacteria. Furthermore, we demonstrated that the addition of Ag43-containing MVs to Ag43-expressing E. coli significantly enhanced biofilm formation. These findings reveal the contribution of MVs harboring autotransporters in promoting bacterial aggregation and enhancing biofilm formation, highlighting the impact of MVs and their specific composition to bacterial adaptation and pathogenesis.IMPORTANCEAutotransporter proteins are the largest family of outer membrane and secreted proteins in Gram-negative bacteria which contribute to pathogenesis by promoting aggregation, biofilm formation, persistence, and cytotoxicity. Although the roles of bacterial autotransporters are well known, the ability of bacterial membrane vesicles (MVs) naturally released from the surface of bacteria to contain autotransporters and their role in promoting virulence remains less investigated. Our findings reveal that MVs produced by E. coli contain the autotransporter protein Ag43. Furthermore, we show that Ag43-containing MVs function to enhance bacterial cell interactions and biofilm formation. By demonstrating the ability of MVs to carry functional autotransporter adhesins, this work highlights the importance of MVs in disseminating autotransporters beyond the bacterial cell membrane to ultimately promote cellular interactions and enhance biofilm development. Overall, these findings have significant implications in furthering our understanding of the numerous ways in which MVs can facilitate bacterial persistence and pathogenesis.}, }
@article {pmid39837262, year = {2025}, author = {Wang, Y and Liu, T and Sida, Y and Zhu, Y}, title = {Diversity and Evolution of the Mobilome Associated with Antibiotic Resistance Genes in Streptococcus anginosus.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {31}, number = {2}, pages = {52-63}, doi = {10.1089/mdr.2024.0229}, pmid = {39837262}, issn = {1931-8448}, mesh = {*Streptococcus anginosus/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology ; Humans ; *Drug Resistance, Bacterial/genetics ; *Interspersed Repetitive Sequences/genetics ; Genes, Bacterial/genetics ; Gene Transfer, Horizontal/genetics ; DNA Transposable Elements/genetics ; Microbial Sensitivity Tests ; }, abstract = {Streptococcus anginosus is an important cause of pyogenic infections, bacteremia, and chronic maxillary sinusitis. Mobile genetic elements (MGEs) play a key role in lateral gene transfer, resulting in broad transfer of antibiotic resistance genes (ARGs). However, studies on ARG-associated MGEs in S. anginosus are still rare. To fill this gap, we used sequencing data from 11 clinical S. anginosus to characterize their mobilome diversity through comparative analysis. We found 47 well-characterized MGEs, including 23 putative integrative and conjugative elements (ICEs), 16 prophages/integrative mobilizable elements, and 8 composites. They were inserted into 16 positions, 4 of which were hot spots. A comprehensive analysis revealed that ARG-associated ICEs belong to four groups as follows: single serine integrases (ICESan49.2), tyrosine integrases (ICESan26.2), triple serine integrase ICEs (ICESan195.1), and a putative transposon integrase (ICESan49.1), all of which were similar to ICEs/transposons widely distributed among other streptococci. The eight composites were composed of multiple ICEs or transposons through successive accretion events (tandem or/and internal integration). In conclusion, we found that S. anginosus accumulates a variety of ARG-associated ICE/composites that may enable S. anginosus to serve as an ARG-associated MGE repository for other streptococci. The analysis of composites here provides a paradigm to further study mobilome evolution.}, }
@article {pmid39837038, year = {2025}, author = {Zhao, M and Huang, K and Wen, F and Xia, H and Song, B}, title = {Biochar reduces plasmid-mediated antibiotic resistance gene transfer in earthworm ecological filters for rural sewage treatment.}, journal = {Journal of hazardous materials}, volume = {487}, number = {}, pages = {137230}, doi = {10.1016/j.jhazmat.2025.137230}, pmid = {39837038}, issn = {1873-3336}, mesh = {Animals ; *Charcoal/chemistry ; *Plasmids/genetics ; *Sewage/microbiology ; *Oligochaeta/genetics ; *Drug Resistance, Microbial/genetics ; *Gene Transfer, Horizontal ; Filtration ; Waste Disposal, Fluid/methods ; }, abstract = {The spread of antibiotic resistance genes (ARGs) in rural wastewater threatens both ecological environment and human health. Earthworm ecological filters (EEFs) represent a green technology for rural sewage treatment. However, their effectiveness in removing ARGs remains a significant challenge. This study aims to investigate the role and underlying mechanisms of biochar addition in enhancing ARGs removal in rural sewage using EEFs. To achieve this, the fate of chromosome- and plasmid-carried ARGs was quantified in constructed EEFs, both with and without biochar addition. The results showed that the biochar could effectively remove ARGs from rural sewage, with a better removal efficiency for plasmid-carried ARGs. The absolute abundance of plasmid-carried ARGs in the effluent was reduced by 0.4-11 times compared to chromosomal ones, showing removal stability improved by 13.11-74.51 %. Additionally, the functional microbial community attached on the high porosity of biochar surface promoted ARGs retention, increasing diffusion limitation in microbial assembly mechanisms by 4.61-29.44 %, which played a key role in plasmid-mediated horizontal gene transfer (HGT). Partial least squares structural equation modeling (PLS-SEM) revealed that biochar-mediated environmental changes and the HGT of mobile genetic elements (MGEs) were critical factors in reducing plasmid-carried ARGs in EEFs.}, }
@article {pmid39836086, year = {2025}, author = {Xia, R and Yin, X and Balcazar, JL and Huang, D and Liao, J and Wang, D and Alvarez, PJJ and Yu, P}, title = {Bacterium-Phage Symbiosis Facilitates the Enrichment of Bacterial Pathogens and Antibiotic-Resistant Bacteria in the Plastisphere.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {6}, pages = {2948-2960}, doi = {10.1021/acs.est.4c08265}, pmid = {39836086}, issn = {1520-5851}, mesh = {*Bacteriophages ; *Symbiosis ; *Bacteria ; Plastics ; Anti-Bacterial Agents ; }, abstract = {The plastisphere, defined as the ecological niche for microbial colonization of plastic debris, has been recognized as a hotspot of pathogenic and antibiotic-resistant bacteria. However, the interactions between bacteria and phages facilitated by the plastisphere, as well as their impact on microbial risks to public health, remain unclear. Here, we analyzed public metagenomic data from 180 plastisphere and environmental samples, stemming from four different habitats and two plastic types (biodegradable and nonbiodegradable plastics) and obtained 611 nonredundant metagenome-assembled genomes (MAGs) and 4061 nonredundant phage contigs. The plastisphere phage community exhibited decreased diversity and virulent proportion compared to those found in environments. Indexes of phage-host interaction networks indicated significant associations of phages with pathogenic and antibiotic-resistant bacteria (ARB), particularly for biodegradable plastics. Known phage-encoded auxiliary metabolic genes (AMGs) were involved in nutrient metabolism, antibiotic production, quorum sensing, and biofilm formation in the plastisphere, which contributed to enhanced competition and survival of pathogens and ARB hosts. Phages also carried transcriptionally active virulence factor genes (VFGs) and antibiotic resistance genes (ARGs), and could mediate their horizontal transfer in microbial communities. Overall, these discoveries suggest that plastisphere phages form symbiotic relationships with their hosts, and that phages encoding AMGs and mediating horizontal gene transfer (HGT) could increase the source of pathogens and antibiotic resistance from the plastisphere.}, }
@article {pmid39833926, year = {2025}, author = {Li, Z and Zhao, C and Mao, Z and Zhang, F and Dong, L and Song, C and Chen, Y and Fu, X and Ao, Z and Xiong, Y and Hui, Q and Song, W and Penttinen, P and Zhang, S}, title = {Structure and metabolic function of spatiotemporal pit mud microbiome.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {10}, pmid = {39833926}, issn = {2524-6372}, support = {2022HX04//Youth Fund of Postdoctor/ ; 2021JDJQ0038//Youth Fund of Sichuan Province/ ; }, abstract = {BACKGROUND: Pit mud (PM) hosts diverse microbial communities, which serve as a medium to impart flavor and quality to Baijiu and exhibit long-term tolerance to ethanol and acids, resulting in a unique ecosystem. However, the ecology and metabolic functions of PM remain poorly understood, as many taxa in PM represent largely novel lineages. In this study, we used a combination of metagenomic analysis and chemical derivatization LC-MS analysis to provide a comprehensive overview of microbial community structure, metabolic function, phylogeny, horizontal gene transfer, and the relationship with carboxyl compounds in spatiotemporal PM samples.<br><br>RESULTS: Our findings revealed three distinct stages in the spatiotemporal changes of prokaryotic communities in PM: an initial phase dominated by Lactobacillus, a transitional phase, and a final state of equilibrium. Significant variations in &#x3b1;- and &#x3b2;-diversity were observed across different spatial and temporal PM samples. We identified 178 medium- and high-quality non-redundant metagenome-assembled genomes (MAGs), and constructed their phylogenetic tree, depicting their roles in the carbon, nitrogen, and sulfur cycles. The Wood-Ljungdahl pathway and reverse TCA cycle were identified as the main carbon fixation mechanisms, with both hydrogenotrophic and aceticlastic methanogens playing a major role in methane production, and methylotrophic pathway observed in older PM. Furthermore, we identified relationships between prokaryotes and 29 carboxyl metabolites, including medium- and long-chain fatty acids. Horizontal gene transfer (HGT) was widespread in PM, particularly among clostridia, Bacteroidota, Bacilli, and Euryarchaeota, and was shown to play critical roles in fermentation dynamics, carbon fixation, methane production, and nitrogen and sulfur metabolism.<br><br>CONCLUSION: Our study provides new insights into the evolution and function of spatiotemporal PM, as well as its interactions with carboxyl metabolites. Lactobacillus dominated in new PM, while methanogens and clostridia were predominant in older or deeper PM layers. The three distinct stages of prokaryotic community development in PM and HGT played critical roles in metabolic function of spatiotemporal PM. Furthermore, this study highlights the importance of &#x3b1;-diversity, &#x3b2;-diversity, methanogens, and Clostridium as useful indicators for assessing PM quality in the production of high-quality Baijiu.}, }
@article {pmid39829789, year = {2025}, author = {Robinson, LR and McDevitt, CJ and Regan, MR and Quail, SL and Swartz, M and Wadsworth, CB}, title = {Re-visiting the potential impact of doxycycline post-exposure prophylaxis (doxy-PEP) on the selection of doxycycline resistance in Neisseria commensals.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39829789}, issn = {2692-8205}, support = {R15 AI174182/AI/NIAID NIH HHS/United States ; }, abstract = {Doxycycline post-exposure prophylaxis (doxy-PEP) is a preventative strategy demonstrated to reduce bacterial sexually transmitted infections in high-risk populations. However, the impact of doxy-PEP on antibiotic resistance acquisition in key members of our microbiomes, is as of yet unclear. For example, commensal Neisseria are known reservoirs of resistance for gonococci through horizontal gene transfer (HGT), and are more likely to experience bystander selection due to doxy-PEP as they are universally carried. Thus, the consequences of doxycycline selection on commensal Neisseria will be critical to investigate to understand possible resistance mechanisms that may be transferred to an important human pathogen. Here, we use in vitro antibiotic gradients to evolve four Neisseria commensals (N. cinerea, N. canis, N. elongata, and N. subflava, n=4 per species) across a 20-day time course; and use whole genome sequencing to nominate derived mutations. After selection, 12 of 16 replicates evolved doxycycline resistance (> 1 μg/mL). Across resistant lineages: An A46T substitution in the repressor of the Mtr efflux pump (MtrR) and a V57M substitution in the 30 ribosomal protein S10 were clearly associated with elevated MICs. Additional mutations in ribosomal components also emerged in strains with high MICs (i.e., 16S rRNA G1057C, RplX A14T). We find the MtrR 46T, RpsJ 57M, and RplX 14T circulating in natural commensal populations. Furthermore, in vitro co-evolution of N. gonorrhoeae with Neisseria commensals demonstrated rapid transfer of the pConj plasmid to N. subflava and N. cinerea, and pbla to N. cinerea. Finally, collection of novel commensals from human hosts reveals 46% of isolates carrying doxycycline resistance; and doxycycline resistance was significantly greater in participants self-reporting doxycycline use in the past 6 months. High-level doxycycline resistance (> 8 μg/mL) was always associated with carriage of the ribosomal protection protein (tetM) and pConj. Ultimately, characterizing the contemporary prevalence of doxycycline resistance, and underlying resistance mechanisms, in commensal communities may help us to predict the long-term impact of doxy-PEP on Neisseria, and the likelihood of transferring particular genotypes across species' boundaries.}, }
@article {pmid39827804, year = {2025}, author = {Ye, T and Li, Y and Zhou, X and Ye, Y and Liu, X and Xiong, W}, title = {Hormesis-like effects of black phosphorus nanosheets on the spread of multiple antibiotic resistance genes.}, journal = {Journal of hazardous materials}, volume = {487}, number = {}, pages = {137207}, doi = {10.1016/j.jhazmat.2025.137207}, pmid = {39827804}, issn = {1873-3336}, mesh = {*Phosphorus/toxicity/chemistry ; Hormesis ; *Nanostructures/toxicity/chemistry ; Plasmids/genetics ; Reactive Oxygen Species/metabolism ; *Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Gene Transfer, Horizontal/drug effects ; Escherichia coli/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic/drug effects ; }, abstract = {The production scalability and increasing demand for black phosphorus nanosheets (BPNSs) inevitably lead to environmental leakage. Although BPNSs' ecotoxicological effects have been demonstrated, their indirect health risks, such as inducing increased resistance in pathogenic bacteria, are often overlooked. This study explores the influence of BPNSs on the horizontal gene transfer of antibiotic resistance genes (ARGs) facilitated by the RP4 plasmid, which carries multiple resistance genes. The results indicated that BPNSs exhibited concentration-dependent hormesis-like effects on bacterial conjugation gene transfer. Specifically, at sub-inhibitory concentrations (0.0001-1 mg/L), BPNSs promoted both intra- and intergeneric conjugative transfer, demonstrating an initial increase followed by a decline, with transfer rates rising by 1.5-3.1-fold and 1.5-3.3-fold, respectively. BPNSs were found to induce reactive oxygen species (ROS) production, increase malondialdehyde levels, and trigger the SOS response, enhancing plasmid uptake. Additionally, BPNSs increased membrane permeability by forming pores and upregulating outer membrane porins (OMPs) genes. At higher BPNSs concentrations (0.1-1 mg/L), conjugative frequency was inhibited due to the disruption of the cellular antioxidant system and changes in the adsorption process. These findings underscore the influence of BPNSs on the conjugative transfer of ARGs, complementing current knowledge of the biotoxicity and potential ecological risks associated with BPNSs.}, }
@article {pmid39826759, year = {2025}, author = {Wang, C and Yin, X and Xu, X and Wang, D and Wang, Y and Zhang, T}, title = {Antibiotic resistance genes in anaerobic digestion: Unresolved challenges and potential solutions.}, journal = {Bioresource technology}, volume = {419}, number = {}, pages = {132075}, doi = {10.1016/j.biortech.2025.132075}, pmid = {39826759}, issn = {1873-2976}, mesh = {Anaerobiosis ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial/genetics ; *Drug Resistance, Bacterial/genetics ; Bacteria/genetics/drug effects ; }, abstract = {Antimicrobial resistance (AMR) threatens public health, necessitating urgent efforts to mitigate the global impact of antibiotic resistance genes (ARGs). Anaerobic digestion (AD), known for volatile solid reduction and energy generation, also presents a feasible approach for the removal of ARGs. This review encapsulates the existing understanding of ARGs and antibiotic-resistant bacteria (ARB) during the AD process, highlighting unresolved challenges pertaining to their detection and quantification. The questions raised and discussed include: Do current ARGs detection methods meet qualitative and quantitative requirements? How can we conduct risk assessments of ARGs? What happens to ARGs when they come into co-exposure with other emerging pollutants? How can the application of internal standards bolster the reliability of the AD resistome study? What are the potential future research directions that could enhance ARG elimination? Investigating these subjects will assist in shaping more efficient management strategies that employ AD for effective ARG control.}, }
@article {pmid39826720, year = {2025}, author = {Akhoon, BA and Qiao, Q and Stewart, A and Chen, J and Rodriguez Lopez, CM and Corbin, KR}, title = {Pangenomic analysis of the bacterial cellulose-producing genera Komagataeibacter and Novacetimonas.}, journal = {International journal of biological macromolecules}, volume = {298}, number = {}, pages = {139980}, doi = {10.1016/j.ijbiomac.2025.139980}, pmid = {39826720}, issn = {1879-0003}, mesh = {*Cellulose/biosynthesis ; Phylogeny ; *Genome, Bacterial ; *Genomics/methods ; *Acetobacteraceae/genetics/metabolism ; Multigene Family ; Genetic Variation ; }, abstract = {Bacterial cellulose holds significant commercial potential due to its unique structural and chemical properties, making it suitable for applications in electronics, medicine, and pharmaceuticals. However, large-scale BC production remains limited by challenges related to bacterial performance. In this study, we compared 79 microbial genomes from three genera-Komagataeibacter, Novacetimonas, and Gluconacetobacter-to investigate their pangenomes, genetic diversity, and evolutionary relationships. Through comparative genomic and phylogenetic analyses, we identified distinct genome compositions and evolutionary patterns that differ from previous reports. The role of horizontal gene transfer in shaping the genetic diversity and adaptability of these bacteria was also explored. Key determinants in BC production, such as variations in the bacterial cellulose biosynthesis (bcs) operon, carbohydrate uptake genes, and carbohydrate-active enzymes, were examined. Additionally, several biosynthetic gene clusters, including Linocin M18 and sactipeptides, which encode for antimicrobial peptides known as bacteriocins, were identified. These findings reveal new aspects of the genetic diversity in cellulose-producing bacteria and present a comprehensive genomic toolkit that will support future efforts to optimize BC production and improve microbial performance for commercial applications.}, }
@article {pmid39826686, year = {2025}, author = {Fu, Y and Morris, FC and Pereira, SC and Kostoulias, X and Jiang, Y and Vidor, C and Williams, G and Srikhanta, Y and Macesic, N and Yu, Y and Lyras, D and Peleg, AY}, title = {Mechanisms of blaIMP-4 dissemination across diverse carbapenem-resistant clinical isolates.}, journal = {Journal of global antimicrobial resistance}, volume = {41}, number = {}, pages = {189-194}, doi = {10.1016/j.jgar.2025.01.003}, pmid = {39826686}, issn = {2213-7173}, mesh = {Humans ; Plasmids/genetics ; *beta-Lactamases/genetics ; Microbial Sensitivity Tests ; *Carbapenems/pharmacology ; Australia ; *Bacterial Proteins/genetics ; Anti-Bacterial Agents/pharmacology ; Acinetobacter/genetics/drug effects ; *Carbapenem-Resistant Enterobacteriaceae/genetics/isolation &amp; purification/drug effects ; Gene Transfer, Horizontal ; Conjugation, Genetic ; Klebsiella pneumoniae/genetics ; Enterobacter/genetics/drug effects ; Klebsiella/genetics/drug effects ; }, abstract = {OBJECTIVE: The IMP-4 carbapenemase is an endemic cause of carbapenem resistance in the Asia-Pacific region. Our aim was to determine the dissemination mechanism of the blaIMP-4 gene.<br><br>METHODS: Twelve representative Australian IMP-4 clinical isolates from The Alfred Hospital (Victoria, Australia) were characterised using antimicrobial susceptibility testing, with their genome and plasmid assemblies analysed. The conjugation efficiencies of different plasmids were investigated using filter mating with four recipient strains across two species.<br><br>RESULTS: Selected IMP-4 isolates included six species and four genera (Enterobacter, Klebsiella, Serratia, and Acinetobacter), whereby isolates of the same species belonged to the same sequence type and were closely related. Four IMP-4 plasmid types were noted: IncHI2A types 1 and 2 (Klebsiella spp. and Enterobacter hormaechei, respectively), IncC (Serratia marcescens and Klebsiella pneumoniae), and a novel type in Acinetobacter pittii. Sequence homology was observed across all plasmids at the blaIMP-4 location, termed Region I, with IS26 on IncHI2A, and IS5075 and Tn3 resistance gene cassettes present on IncC plasmids. Genomic rearrangements mediated by IS26 or Tn3 and IS5075 were identified in Region I of plasmids from the same Inc type. The plasmids of each Inc type were capable of conjugative transfer with varying efficiency. IncH12A plasmids and K. pneumoniae IncC displayed higher transfer efficiencies than other plasmids examined in this study when using the recipient E. coli strain J53 (with conjugation efficiencies of 1.17&#xd7;10[-2] to 5.02&#xd7;10[-5], P < 0.001).<br><br>CONCLUSIONS: Clonal spread, Inc type, homologous region, and insertion sequences are important mobility factors in the dissemination and evolution of blaIMP-4 plasmids.}, }
@article {pmid39826554, year = {2025}, author = {Kirsch, R and Okamura, Y and García-Lozano, M and Weiss, B and Keller, J and Vogel, H and Fukumori, K and Fukatsu, T and Konstantinov, AS and Montagna, M and Moseyko, AG and Riley, EG and Slipinski, A and Vencl, FV and Windsor, DM and Salem, H and Kaltenpoth, M and Pauchet, Y}, title = {Symbiosis and horizontal gene transfer promote herbivory in the megadiverse leaf beetles.}, journal = {Current biology : CB}, volume = {35}, number = {3}, pages = {640-654.e7}, doi = {10.1016/j.cub.2024.12.028}, pmid = {39826554}, issn = {1879-0445}, mesh = {Animals ; *Coleoptera/genetics/physiology/microbiology ; *Gene Transfer, Horizontal ; *Symbiosis/genetics ; *Herbivory ; Biological Evolution ; Phylogeny ; }, abstract = {Beetles that feed on the nutritionally depauperate and recalcitrant tissues provided by the leaves, stems, and roots of living plants comprise one-quarter of herbivorous insect species. Among the key adaptations for herbivory are plant cell wall-degrading enzymes (PCWDEs) that break down the fastidious polymers in the cell wall and grant access to the nutritious cell content. While largely absent from the non-herbivorous ancestors of beetles, such PCWDEs were occasionally acquired via horizontal gene transfer (HGT) or by the uptake of digestive symbionts. However, the macroevolutionary dynamics of PCWDEs and their impact on evolutionary transitions in herbivorous insects remained poorly understood. Through genomic and transcriptomic analyses of 74 leaf beetle species and 50 symbionts, we show that multiple independent events of microbe-to-beetle HGT and specialized symbioses drove convergent evolutionary innovations in approximately 21,000 and 13,500 leaf beetle species, respectively. Enzymatic assays indicate that these events significantly expanded the beetles' digestive repertoires and thereby contributed to their adaptation and diversification. Our results exemplify how recurring HGT and symbiont acquisition catalyzed digestive and nutritional adaptations to herbivory and thereby contributed to the evolutionary success of a megadiverse insect taxon.}, }
@article {pmid39824780, year = {2025}, author = {Wu, X and Peng, J and Malik, AA and Peng, Z and Luo, Y and Fan, F and Lu, Y and Wei, G and Delgado-Baquerizo, M and Liesack, W and Jiao, S}, title = {A Global Relationship Between Genome Size and Encoded Carbon Metabolic Strategies of Soil Bacteria.}, journal = {Ecology letters}, volume = {28}, number = {1}, pages = {e70064}, doi = {10.1111/ele.70064}, pmid = {39824780}, issn = {1461-0248}, support = {42122050//National Science Foundation for Excellent Young Scholars of China/ ; 42277307 &amp; 41977038//National Natural Science Foundation of China/ ; 2021YFD1900500//National Key Research and Development Program of China/ ; }, mesh = {*Soil Microbiology ; *Carbon/metabolism ; *Genome Size ; *Bacteria/genetics/metabolism ; *Genome, Bacterial ; Gene Transfer, Horizontal ; Microbiota ; Biomass ; }, abstract = {Microbial traits are critical for carbon sequestration and degradation in terrestrial ecosystems. Yet, our understanding of the relationship between carbon metabolic strategies and genomic traits like genome size remains limited. To address this knowledge gap, we conducted a global-scale meta-analysis of 2650 genomes, integrated whole-genome sequencing data, and performed a continental-scale metagenomic field study. We found that genome size was tightly associated with an increase in the ratio between genes encoding for polysaccharide decomposition and biomass synthesis that we defined as the carbon acquisition-to-biomass yield ratio (A/Y). We also show that horizontal gene transfer played a major evolutionary role in the expanded bacterial capacities in carbon acquisition. Our continental-scale field study further revealed a significantly negative relationship between the A/Y ratio and soil organic carbon stocks. Our work demonstrates a global relationship between genome size and the encoded carbon metabolic strategies of soil bacteria across terrestrial microbiomes.}, }
@article {pmid39824112, year = {2025}, author = {Farooq, A and Rafique, A and Han, E and Park, SM}, title = {Global dissemination of the beta-lactam resistance gene blaTEM-1 among pathogenic bacteria.}, journal = {The Science of the total environment}, volume = {963}, number = {}, pages = {178521}, doi = {10.1016/j.scitotenv.2025.178521}, pmid = {39824112}, issn = {1879-1026}, mesh = {*Bacteria/genetics ; *beta-Lactam Resistance/genetics ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Phylogeny ; Genome, Bacterial ; Gene Transfer, Horizontal ; beta-Lactams ; }, abstract = {Antibiotic resistance presents a burgeoning global health crisis, with over 70 % of pathogenic bacteria now exhibiting resistance to at least one antibiotic. This study leverages a vast dataset of 618,853 pathogenic bacterial genomes from the NCBI pathogen detection database, offering comprehensive insights into antibiotic resistance patterns, species-specific profiles, and transmission dynamics of resistant pathogens. We centered our investigation on the beta-lactam resistance gene blaTEM-1, found in 43,339 genomes, revealing its extensive distribution across diverse species and isolation sources. The study unveiled the prevalence of 15 prominent antibiotic resistance genes (ARGs), including those conferring resistance to beta-lactam, aminoglycoside, and tetracycline antibiotics. Distinct resistance patterns were observed between Gram-positive and Gram-negative bacteria, indicating the influence of phylogeny on resistance dissemination. Notably, the blaTEM-1 gene demonstrated substantial prevalence across a wide array of bacterial species (8) and a high number of isolation sources (11). Genetic context analysis revealed associations between blaTEM-1 and mobile genetic elements (MGEs) like transposons and insertion sequences. Additionally, we observed recent horizontal transfer events involving clusters of blaTEM-1 genes and MGEs underscore the potential of MGEs in facilitating the mobilization of ARGs. Our findings underscore the importance of adopting a One Health approach to global genomic pathogen surveillance, aiming to uncover the transmission routes of ARGs and formulate strategies to address the escalating antibiotic resistance crisis.}, }
@article {pmid39824023, year = {2025}, author = {Guo, X and Yu, P and Guo, J and Zhao, HP and Lai, CY}, title = {Viral auxiliary roles in hydrolytic and biosynthetic metabolism regulate prokaryotic microbial interactions in anaerobic digestion.}, journal = {Water research}, volume = {274}, number = {}, pages = {123140}, doi = {10.1016/j.watres.2025.123140}, pmid = {39824023}, issn = {1879-2448}, mesh = {Anaerobiosis ; Hydrolysis ; *Microbial Interactions ; }, abstract = {Anaerobic digestion (AD) viruses have gained recognition as significant regulators of microbial interactions within AD communities, yet their ecological roles remain largely unexplored. In this study, we investigated the ecological roles of AD viruses in regulating microbial interactions among syntrophic hosts. We recovered 3921 diverse viral sequences from four full-scale anaerobic digesters and confirmed their widespread presence across 127 global metagenomic sampling sites (with >95 % sequence similarity), underscoring the ubiquity of prokaryotic viruses in AD-related systems. Through the construction of virus-prokaryote interactions (66.8 % validated at the transcriptional level) and analysis of viral-host transcriptional abundances, we identified significant associations between AD viruses and key processes, including hydrolysis, acidogenesis, and methanogenesis. Notably, polyvalent viruses were found to interact with both hydrolytic and fermentative communities. We further characterized viral auxiliary metabolism, hydrolytic substrate spectra, and microbial auxotrophy, showing that viruses not only could enhance the breakdown of complex substrates (e.g., cellulose, chitin, peptidoglycan) but also potentially supported the biosynthesis of essential nutrients (e.g., cysteine, methionine, heme, and cobalamin). These activities were proposed to regulate resource fluxes through alternating lysogenic and lytic cycles. Phylogenetic analysis of viral gene and horizontal gene transfer (HGT) identification suggest that AD viruses employ promiscuous infection on syntrophic hosts, potentially as an adaptive evolutionary strategy in the AD ecosystem. This study provides new insights into the ecological roles of AD viruses, highlighting their potential impact on the stability and functionality of AD systems.}, }
@article {pmid39823837, year = {2025}, author = {Zhang, S and Ye, Q and Wang, M and Zhu, D and Jia, R and Chen, S and Liu, M and Yang, Q and Zhao, X and Wu, Y and Huang, J and Ou, X and Sun, D and Tian, B and He, Y and Wu, Z and Cheng, A}, title = {Isolation and characterization of a broad-spectrum bacteriophage against multi-drug resistant Escherichia coli from waterfowl field.}, journal = {Poultry science}, volume = {104}, number = {2}, pages = {104787}, pmid = {39823837}, issn = {1525-3171}, mesh = {Animals ; *Escherichia coli/virology/drug effects/physiology ; *Drug Resistance, Multiple, Bacterial ; *Poultry Diseases/microbiology/prevention &amp; control ; *Escherichia coli Infections/veterinary/microbiology/prevention &amp; control ; *Ducks ; *Coliphages/physiology/isolation &amp; purification ; China ; Microbial Sensitivity Tests/veterinary ; *Myoviridae/isolation &amp; purification/physiology ; Feces/microbiology/virology ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Escherichia coli (E. coli) is a significant pathogen responsible for intestinal infections and foodborne diseases. The rise of antibiotic resistance poses a significant challenge to global public health. Traditional antibiotic therapy is becoming increasingly ineffective, highlighting the urgent need for innovative control strategies. This study explores the potential of bacteriophages as a sustainable alternative to traditional antibiotics. From 2021 to 2022, a total of 183 non-repetitive duck source fecal samples were collected from Mianyang City, Sichuan Province, and 126 strains of E. coli were isolated. The minimum inhibitory concentration (MIC) test showed that these strains exhibited high resistance to piperacillin (96.8%), tetracycline (88.9%), and chloramphenicol (86.5%). It is concerning that 93.7% of the isolates are classified as multidrug-resistant (MDR), posing a significant threat to existing treatment options. 20 bacteriophages were isolated from fecal and soil samples, among which 5 bacteriophages were selected for further analysis. Bacteriophage YP6 showed excellent lytic effects on MDR strains, especially strain MY104, as well as representative serotypes O1 (E. coli MY51) and O18 (E. coli MY106). The identification of YP6 as a member of the Myoviridae family was conducted using transmission electron microscopy, and it was found to have an optimal infection factor of 0.1. Bacteriophages exhibit significant thermal and pH stability, maintaining survival at temperatures up to 60 °C and pH ranges of 4 to 10. Whole genome sequencing confirmed that YP6 has a double stranded DNA genome of 139,323 base pairs (bp), and no antibiotic resistance or virulence genes were found, indicating a low possibility of horizontal gene transfer. In addition, YP6 effectively inhibits the formation of E. coli biofilm, which is a key factor in chronic infections. The in vivo experiments using Galleria mellonella (G. mellonella) larvae have shown that it has a significant protective effect against MDR E. coli infection. In summary, bacteriophage YP6 is expected to become a therapeutic agent against MDR E. coli infection due to its broad host range, environmental stability, and biofilm inhibition properties. Future research should optimize bacteriophage preparations, evaluate the safety and efficacy of animal models, and establish clinical application plans in the field of food safety.}, }
@article {pmid39818750, year = {2025}, author = {Shao, D and Ju, X and Wu, Y and Zhang, Y and Yan, Z and Li, Y and Wang, L and Parkhill, J and Walsh, TR and Wu, C and Shen, J and Wang, Y and Zhang, R and Shen, Y}, title = {Quaternary Ammonium Compounds: A New Driver and Hidden Threat for mcr-1 Prevalence in Hospital Wastewater and Human Feces.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {3}, pages = {1565-1576}, doi = {10.1021/acs.est.4c11368}, pmid = {39818750}, issn = {1520-5851}, mesh = {*Wastewater/microbiology ; Humans ; Feces/microbiology ; *Quaternary Ammonium Compounds ; Hospitals ; Escherichia coli/genetics ; Plasmids ; Escherichia coli Proteins/genetics ; Colistin ; Drug Resistance, Bacterial/genetics ; }, abstract = {The emergence of mobile colistin resistance gene mcr-1 has attracted global attention. The prevalence of mcr-1-positive Escherichia coli (MCRPEC) in humans largely decreased following the ban of colistin as an animal growth promoter in China. However, the prevalence of MCRPEC in the hospital environment and the relationship between disinfectants and mcr-1 remain unclear. We found that MCRPEC prevalence was low in the feces of healthy humans attending physical examinations in six hospitals (4.6%, 71/1532) but high in hospital wastewater (50.0%, 27/54). mcr-1 was mainly located on IncI2 (63.0% in wastewater and 62.0% in feces) and IncHI2 plasmids (18.5% in wastewater and 21.1% in feces). High similarity of the mcr-1 context and its carrying plasmids was observed in human and wastewater MCRPEC, with several isolates clustering together. The coexistence of the ESBL gene blaCTX-M with mcr-1 occurred in 19.7% of IncI2 plasmids. Notably, 60.0% of IncHI2 plasmids exhibited co-occurrence of mcr-1 with the disinfectant resistance gene (DRG) qacEΔ1, conferring resistance to quaternary ammonium compounds (QACs). We revealed that QACs, rather than the other two types of disinfectants─ortho-phthalaldehyde (OPA) and povidone-iodine (PVP-I)─select for plasmids carrying both qacEΔ1 and mcr-1 and elevate their conjugative transfer frequency. Monitoring of DRGs in MCRPEC and managing disinfectant use are urgently needed in healthcare settings to mitigate the spread of colistin resistance from hospital environments to inpatients.}, }
@article {pmid39817515, year = {2025}, author = {Djordjevic, M and Zivkovic, L and Ou, HY and Djordjevic, M}, title = {Nonlinear regulatory dynamics of bacterial restriction-modification systems modulates horizontal gene transfer susceptibility.}, journal = {Nucleic acids research}, volume = {53}, number = {2}, pages = {}, pmid = {39817515}, issn = {1362-4962}, support = {7750294//Science Fund of the Republic of Serbia/ ; //Ministry of Science and Technological Development of the Republic of Serbia/ ; 32370186//National Natural Science Foundation of China/ ; }, mesh = {*Gene Transfer, Horizontal ; *DNA Restriction-Modification Enzymes/metabolism/genetics ; Gene Expression Regulation, Bacterial ; *Bacteria/genetics ; Nonlinear Dynamics ; Bacterial Proteins/metabolism/genetics ; Plasmids/genetics ; Models, Genetic ; }, abstract = {Type II restriction-modification (R-M) systems play a pivotal role in bacterial defense against invading DNA, influencing the spread of pathogenic traits. These systems often involve coordinated expression of a regulatory protein (C) with restriction (R) enzymes, employing complex feedback loops for regulation. Recent studies highlight the crucial balance between R and M enzymes in controlling horizontal gene transfer (HGT). This manuscript introduces a mathematical model reflecting R-M system dynamics, informed by biophysical evidence, to minimize reliance on arbitrary parameters. Our analysis clarifies the observed variations in M-to-R ratios, emphasizing the regulatory role of the C protein. We analytically derived a stability diagram for C-regulated R-M systems, offering a more straightforward analysis method over traditional numerical approaches. Our findings reveal conditions leading to both monostability and bistability, linking changes in the M-to-R ratio to factors like cell division timing and plasmid replication rates. These variations may link adjusting defense against phage infection, or the acquisition of new genes such as antibiotic resistance determinants, to changing physiological conditions. We also performed stochastic simulations to show that system regulation may significantly increase M-to-R ratio variability, providing an additional mechanism to generate heterogeneity in bacterial population.}, }
@article {pmid39813956, year = {2025}, author = {Yang, QE and Lin, Z and Gan, D and Li, M and Liu, X and Zhou, S and Walsh, TR}, title = {Microplastics mediates the spread of antimicrobial resistance plasmids via modulating conjugal gene expression.}, journal = {Environment international}, volume = {195}, number = {}, pages = {109261}, doi = {10.1016/j.envint.2025.109261}, pmid = {39813956}, issn = {1873-6750}, mesh = {*Plasmids/genetics ; *Microplastics/toxicity ; *Conjugation, Genetic/drug effects ; *Drug Resistance, Bacterial/genetics ; Bacteria/genetics/drug effects ; }, abstract = {Antimicrobial resistance (AMR) and environmental degradation are existential global public health threats. Linking microplastics (MPs) and AMR is particularly concerning as MPs pollution would have significant ramifications on controlling of AMR; however, the effects of MPs on the spread and genetic mechanisms of AMR bacteria remain unclear. Herein, we performed Simonsen end-point conjugation to investigate the impact of four commonly used MPs on transfer of clinically relevant plasmids. The transfer breadth of a representative pA/C_MCR-8 plasmid across bacterial communities was confirmed by the cell sorting and 16S rRNA gene amplicon sequencing. Our study shows that exposure to four commonly found MPs promotes the conjugation rates of four clinically relevant AMR plasmids by up to 200-fold, when compared to the non-exposed group and that the transfer rates are MP concentrations demonstrate a positive correlation with higher transfer rates. Furthermore, we show that MPs induce the expression of plasmid-borne conjugal genes and SOS-linked genes such as recA, lexA, dinB and dinD. High-throughput sequencing of the broad transmission of plasmid pA/C_MCR-8, shows distribution over two main phyla, Pseudomonadota (50.0 %-95.0 %) and Bacillota (0.4 %-2.0 %). These findings definitively link two global health emergencies - AMR and environmental degradation via MPs, and to tackle global AMR, we must also now consider plastic utilisation and waste management.}, }
@article {pmid39812022, year = {2025}, author = {Gamblin, J and Lambert, A and Blanquart, F}, title = {Persistent, Private, and Mobile Genes: A Model for Gene Dynamics in Evolving Pangenomes.}, journal = {Molecular biology and evolution}, volume = {42}, number = {1}, pages = {}, pmid = {39812022}, issn = {1537-1719}, support = {FDT202304016561//Fondation pour la Recherche M&#xe9;dicale/ ; }, mesh = {*Evolution, Molecular ; *Models, Genetic ; *Genome, Bacterial ; Phylogeny ; Gene Transfer, Horizontal ; Salmonella enterica/genetics ; Algorithms ; Genes, Bacterial ; }, abstract = {The pangenome of a species is the set of all genes carried by at least one member of the species. In bacteria, pangenomes can be much larger than the set of genes carried by a single organism. Many questions remain unanswered regarding the evolutionary forces shaping the patterns of the presence/absence of genes in pangenomes of a given species. We introduce a new model for bacterial pangenome evolution along a species phylogeny that explicitly describes the timing of appearance of each gene in the species and accounts for three generic types of gene evolutionary dynamics: persistent genes that are present in the ancestral genome, private genes that are specific to a given clade, and mobile genes that are imported once into the gene pool and then undergo frequent horizontal gene transfers. We call this model the Persistent-Private-Mobile (PPM) model. We develop an algorithm fitting the PPM model and apply it to a dataset of 902 Salmonella enterica genomes. We show that the best fitting model is able to reproduce the global pattern of some multivariate statistics like the gene frequency spectrum and the parsimony vs. frequency plot. Moreover, the gene classification induced by the PPM model allows us to study the position of accessory genes on the chromosome depending on their category, as well as the gene functions that are most present in each category. This work paves the way for a mechanistic understanding of pangenome evolution, and the PPM model developed here could be used for dynamics-aware gene classification.}, }
@article {pmid39809568, year = {2025}, author = {Simões de Oliveira, G and Lentz, SAM and Müller, CZ and Guerra, RR and Dalmolin, TV and Volpato, FCZ and de Lima-Morales, D and Lamb Wink, P and Barth, AL and Rabinowitz, P and Martins, AF}, title = {Resistome and plasmidome genomic features of mcr-1.1-harboring Escherichia coli: a One Health approach.}, journal = {Journal of applied microbiology}, volume = {136}, number = {1}, pages = {}, doi = {10.1093/jambio/lxaf019}, pmid = {39809568}, issn = {1365-2672}, support = {//INPRA/ ; 465718/2014-0//CNPq/ ; 17/2551-0000514-7//FAPERGS/ ; 2022-0283//FIPE/ ; //HCPA/ ; }, mesh = {*Escherichia coli/genetics/drug effects/isolation &amp; purification ; *Plasmids/genetics ; Swine/microbiology ; Animals ; Brazil ; *Escherichia coli Proteins/genetics ; Chickens/microbiology ; Humans ; Anti-Bacterial Agents/pharmacology ; *Escherichia coli Infections/microbiology/veterinary ; Colistin/pharmacology ; Microbial Sensitivity Tests ; Drug Resistance, Multiple, Bacterial/genetics ; One Health ; Whole Genome Sequencing ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Genome, Bacterial ; }, abstract = {AIMS: This study evaluated the phenotypic and genotypic traits of mcr-1.1-harboring Escherichia coli isolates from chickens, pigs, humans, and farm environments. The resistome and the mobile genetic elements associated with the spread of mcr-1.1 in Southern Brazil were also characterized.<br><br>METHODS AND RESULTS: The 22 mcr-1.1-harboring E. coli isolates from different origins were selected for antimicrobial susceptibility testing and whole genome sequencing for characterization of the resistome, plasmids, and sequence types. All isolates presented several resistance genes and harbored the mcr-1.1 gene in a highly similar IncX4 plasmid. Furthermore, the mcr-1.1 gene co-occurred with the mcr-3.12 gene in a multidrug-resistant isolate from the farm environment.<br><br>CONCLUSIONS: These findings demonstrate that the mcr-1.1 gene in E. coli isolates from Brazil is spreading mainly by horizontal transfer of the IncX4 plasmid. The co-occurrence of mcr-1.1 and mcr-3.12 highlights pig farming as an important reservoir of colistin resistance.}, }
@article {pmid39807864, year = {2025}, author = {Nakatsu, G and Ko, D and Michaud, M and Franzosa, EA and Morgan, XC and Huttenhower, C and Garrett, WS}, title = {Virulence factor discovery identifies associations between the Fic gene family and Fap2[+] fusobacteria in colorectal cancer microbiomes.}, journal = {mBio}, volume = {16}, number = {2}, pages = {e0373224}, pmid = {39807864}, issn = {2150-7511}, support = {R01 CA154426/CA/NCI NIH HHS/United States ; //Cancer Research UK (CRUK)/ ; R01CA154426//HHS | NIH | National Cancer Institute (NCI)/ ; }, mesh = {Humans ; *Virulence Factors/genetics ; *Colorectal Neoplasms/microbiology ; *Fusobacterium/genetics/pathogenicity/isolation &amp; purification ; *Gastrointestinal Microbiome ; *Lectins/genetics/metabolism ; Genome, Bacterial ; Multigene Family ; *Fusobacteria/genetics/pathogenicity ; Feces/microbiology ; *Bacterial Proteins/genetics/metabolism ; }, abstract = {Fusobacterium is a bacterium associated with colorectal cancer (CRC) tumorigenesis, progression, and metastasis. Fap2 is a fusobacteria-specific outer membrane galactose-binding lectin that mediates Fusobacterium adherence to and invasion of CRC tumors. Advances in omics analyses provide an opportunity to profile and identify microbial genomic features that correlate with the cancer-associated bacterial virulence factor Fap2. Here, we analyze genomes of Fusobacterium colon tumor isolates and find that a family of post-translational modification enzymes containing Fic domains is associated with Fap2 positivity in these strains. We demonstrate that Fic family genes expand with the presence of Fap2 in the fusobacterial pangenome. Through comparative genomic analysis, we find that Fap2[+] Fusobacteriota are highly enriched with Fic gene families compared to other cancer-associated and human gut microbiome bacterial taxa. Using a global data set of CRC shotgun metagenomes, we show that fusobacterial Fic and Fap2 genes frequently co-occur in the fecal microbiomes of individuals with late-stage CRC. We further characterize specific Fic gene families harbored by Fap2[+] Fusobacterium animalis genomes and detect recombination events and elements of horizontal gene transfer via synteny analysis of Fic gene loci. Exposure of a F. animalis strain to a colon adenocarcinoma cell line increases gene expression of fusobacterial Fic and virulence-associated adhesins. Finally, we demonstrate that Fic proteins are synthesized by F. animalis as Fic peptides are detectable in F. animalis monoculture supernatants. Taken together, our study uncovers Fic genes as potential virulence factors in Fap2[+] fusobacterial genomes.IMPORTANCEAccumulating data support that bacterial members of the intra-tumoral microbiota critically influence colorectal cancer progression. Yet, relatively little is known about non-adhesin fusobacterial virulence factors that may influence carcinogenesis. Our genomic analysis and expression assays in fusobacteria identify Fic domain-containing genes, well-studied virulence factors in pathogenic bacteria, as potential fusobacterial virulence features. The Fic family proteins that we find are encoded by fusobacteria and expressed by Fusobacterium animalis merit future investigation to assess their roles in colorectal cancer development and progression.}, }
@article {pmid39805347, year = {2025}, author = {Sasikumar, J and Shaikh, HA and Naik, B and Laha, S and Das, SP}, title = {Emergence of fungal hybrids - Potential threat to humans.}, journal = {Microbial pathogenesis}, volume = {200}, number = {}, pages = {107278}, doi = {10.1016/j.micpath.2025.107278}, pmid = {39805347}, issn = {1096-1208}, mesh = {Humans ; *Fungi/genetics/pathogenicity ; *Hybridization, Genetic ; Genome, Fungal ; *Mycoses/microbiology ; Genetic Variation ; Virulence ; Epigenesis, Genetic ; Aspergillus/genetics/pathogenicity ; Gene Transfer, Horizontal ; Candida/genetics/pathogenicity ; }, abstract = {Fungal hybrids arise through the interbreeding of distinct species. This hybridization process fosters increased genetic diversity and the emergence of new traits. Mechanisms driving hybridization include the loss of heterozygosity, copy number variations, and horizontal gene transfer. Genetic mating barriers, changes in ploidy, chromosomal instability, and genomic diversity influence hybridization. These factors directly impact the fitness and adaptation of hybrid offspring. Epigenetic factors, including DNA methylation, histone modifications, non-coding RNAs, and chromatin remodelling, play a role in post-mating isolation in hybrids. In addition to all these mechanisms, successful hybridization in fungi is ensured by cellular mechanisms like mitochondrial inheritance, transposable elements, and other genome conversion mechanisms. These mechanisms support hybrid life and enhance the virulence and pathogenicity of fungal hybrids, which provoke diseases in host organisms. Recent advancements in sequencing have uncovered fungal hybrids in pathogens like Aspergillus, Candida, and Cryptococcus. Examples of these hybrids, such as Aspergillus latus, Candida metapsilosis, and Cryptococcus neoformans, induce severe human infections. Identifying fungal hybrids is challenging due to their altered genome traits. ITS sequencing has emerged as a promising method for diagnosing these hybrids. To prevent the emergence of novel hybrid fungal pathogens, it is crucial to develop effective diagnostic techniques and closely monitor pathogenic fungal populations for signs of hybridization. This comprehensive review delves into various facts about fungal hybridization, including its causes, genetic outcomes, barriers, diagnostic strategies, and examples of emerging fungal hybrids. The review emphasises the potential threat that fungal hybrids pose to human health and highlights their clinical significance.}, }
@article {pmid39803089, year = {2024}, author = {Yadav, KS and Pawar, S and Datkhile, K and Patil, SR}, title = {Study on the Mobile Colistin Resistance (mcr-1) Gene in Gram-Negative Bacilli in a Rural Tertiary Care Hospital in Western Maharashtra.}, journal = {Cureus}, volume = {16}, number = {12}, pages = {e75569}, pmid = {39803089}, issn = {2168-8184}, abstract = {BACKGROUND: Colistin, a last-resort antibiotic for treating multidrug-resistant Gram-negative bacterial infections, has increased resistance as a result of the emergence of the mcr-1 gene. The mcr-1gene, which confers colistin resistance, is often carried on plasmids, facilitating its spread by horizontal gene transfer among bacterial populations. The rising prevalence of mcr-1-mediated resistance poses significant challenges for infection control and treatment efficacy. This study aimed to detect and investigate the prevalence of the mcr-1 gene among Gram-negative bacilli isolated from clinical specimens in a rural tertiary care hospital and to analyze the plasmid-mediated mechanisms of colistin resistance.<br><br>MATERIALS AND METHODS: A cross-sectional study was conducted over two years at Krishna Institute of Medical Sciences, Karad. Gram-negative bacilli were isolated from clinical specimens and identified using standard methodology. Antimicrobial susceptibility testing was performed by using the Vitek-2 Compact (bioMerieux, Marcy-l'&#xc9;toile, France) method and the colistin-resistance broth microdilution method (BMD). Polymerase chain reaction (PCR) was done for the presence of mcr-1 gene in colistin-resistant isolates.<br><br>RESULTS: Out of 359 Gram-negative bacilli isolates, 93 (25.90%) demonstrated resistance to colistin. Among these resistant strains, the mcr-1 gene was identified in 13 (13.97%) of the isolates. The gene was predominantly found in Pseudomonas aeruginosa (8, 61.53%), followed by Klebsiella pneumoniae (3, 23.07%), Acinetobacter baumannii (2, 15.38%) among the 13 isolates. Out of the various specimens received, mcr-1 gene was found in endotracheal tube (4, 30.76%), urine (4, 30.76%), pus (3, 23.07%), sputum (1, 7.69%), and blood (1, 7.69%). Colistin minimum inhibitory concentration (MIC) value for these resistant isolates ranged from 4 to 16 &#xb5;g/ml.<br><br>CONCLUSION: The study highlights a significant prevalence of mcr-1 plasmid-mediated colistin resistance gene among Gram-negative bacilli in the hospital. This possibly highlights the frequent misuse of colistin in animal husbandry from this rural area. The findings underscore the importance of monitoring resistance patterns and implementing stringent infection control measures.}, }
@article {pmid39801834, year = {2025}, author = {Bustamante, M and Mei, S and Daras, IM and van Doorn, GS and Falcao Salles, J and de Vos, MGJ}, title = {An eco-evolutionary perspective on antimicrobial resistance in the context of One Health.}, journal = {iScience}, volume = {28}, number = {1}, pages = {111534}, pmid = {39801834}, issn = {2589-0042}, abstract = {The One Health approach musters growing concerns about antimicrobial resistance due to the increased use of antibiotics in healthcare and agriculture, with all of its consequences for human, livestock, and environmental health. In this perspective, we explore the current knowledge on how interactions at different levels of biological organization, from genetic to ecological interactions, affect the evolution of antimicrobial resistance. We discuss their role in different contexts, from natural systems with weak selection, to human-influenced environments that impose a strong pressure toward antimicrobial resistance evolution. We emphasize the need for an eco-evolutionary approach within the One Health framework and highlight the importance of horizontal gene transfer and microbiome interactions for increased understanding of the emergence and spread of antimicrobial resistance.}, }
@article {pmid39801293, year = {2025}, author = {Marquiegui-Alvaro, A and Kottara, A and Chacón, M and Cliffe, L and Brockhurst, M and Dixon, N}, title = {Genetic Bioaugmentation-Mediated Bioremediation of Terephthalate in Soil Microcosms Using an Engineered Environmental Plasmid.}, journal = {Microbial biotechnology}, volume = {18}, number = {1}, pages = {e70071}, pmid = {39801293}, issn = {1751-7915}, support = {BB/P01738X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T005742/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/W012723/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; EP/S022856/1//Engineering and Physical Sciences Research Council/ ; }, mesh = {*Plasmids/genetics ; *Soil Microbiology ; Biodegradation, Environmental ; *Pseudomonas putida/genetics/metabolism ; *Soil Pollutants/metabolism ; *Phthalic Acids/metabolism ; Gene Transfer, Horizontal ; Metabolic Engineering ; }, abstract = {Harnessing in situ microbial communities to clean-up polluted natural environments is a potentially efficient means of bioremediation, but often the necessary genes to breakdown pollutants are missing. Genetic bioaugmentation, whereby the required genes are delivered to resident bacteria via horizontal gene transfer, offers a promising solution to this problem. Here, we engineered a conjugative plasmid previously isolated from soil, pQBR57, to carry a synthetic set of genes allowing bacteria to consume terephthalate, a chemical component of plastics commonly released during their manufacture and breakdown. Our engineered plasmid caused a low fitness cost and was stably maintained in terephthalate-contaminated soil by the bacterium P. putida. Plasmid carriers efficiently bioremediated contaminated soil in model soil microcosms, achieving complete breakdown of 3.2 mg/g of terephthalate within 8 days. The engineered plasmid horizontally transferred the synthetic operon to P. fluorescens in situ, and the resulting transconjugants degraded 10 mM terephthalate during a 180-h incubation. Our findings show that environmental plasmids carrying synthetic catabolic operons can be useful tools for in situ engineering of microbial communities to perform clean-up even of complex environments like soil.}, }
@article {pmid39799916, year = {2025}, author = {Li, Y and Liu, X and Guo, S and Wang, L and Tang, J}, title = {The combination of polystyrene microplastics and di (2-ethylhexyl) phthalate promotes the conjugative transfer of antibiotic resistance genes between bacteria.}, journal = {Ecotoxicology and environmental safety}, volume = {289}, number = {}, pages = {117681}, doi = {10.1016/j.ecoenv.2025.117681}, pmid = {39799916}, issn = {1090-2414}, mesh = {*Diethylhexyl Phthalate/toxicity ; *Polystyrenes/toxicity ; *Microplastics/toxicity ; *Plasticizers/toxicity ; *Drug Resistance, Bacterial/genetics ; *Bacteria/drug effects/genetics ; *Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Gene Transfer, Horizontal/drug effects ; *Water Pollutants, Chemical/toxicity ; }, abstract = {Plastic pollution has become a common phenomenon. The process of plastic degradation is accompanied by the release of microplastics and plasticizers. However, the coexistence of microplastics and plasticizers on the transfer of antibiotic resistance genes (ARGs) has not been reported until now. Here, polystyrene (PS) microplastics and plasticizer di (2-ethylhexyl) phthalate (DEHP) were used for combined treatment experiment and their effects and mechanisms on the transfer of ARGs between bacteria were explored. By increasing cell membrane permeability and the expression of correlated genes, the combined treatment group showed promoting effects on the transfer of ARGs than that of control, with the highest promoting effects observed at 1 mg/L PS and 0.1 mg/L DEHP, which was 3.0 times higher in ARGs transfer rate than that of control. It was found that PS and DEHP treatment alone also led to a higher conjugative transfer frequency, and the frequency of the combined treatment was lower than that of the corresponding single treatment group. This indicated that the effects of DEHP and microplastics on ARGs transfer might be antagonistic. Transcriptome analysis indicated that the transfer of ARGs affects bacterial ion binding, oxidative stress, and energy metabolism processes, while the expression of genes related to cell membrane permeability, DNA repair, bacterial drug resistance, and quorum sensing also increase. This study may provide new insights for explaining the combined effects of various pollutants in the environment on the spread of ARGs.}, }
@article {pmid39799674, year = {2025}, author = {Li, Y and Qin, W and Xin, X and Tang, C and Huang, Y and He, X and Chen, L and Yu, G and Yu, F}, title = {Dynamic impact of polyethylene terephthalate nanoplastics on antibiotic resistance and microplastics degradation genes in the rhizosphere of Oryza sativa L.}, journal = {Journal of hazardous materials}, volume = {487}, number = {}, pages = {137173}, doi = {10.1016/j.jhazmat.2025.137173}, pmid = {39799674}, issn = {1873-3336}, mesh = {*Polyethylene Terephthalates/toxicity ; *Oryza/microbiology/drug effects/genetics/metabolism ; *Rhizosphere ; *Microplastics/toxicity/metabolism ; *Soil Pollutants/toxicity/metabolism ; Soil Microbiology ; *Drug Resistance, Microbial/genetics/drug effects ; Biodegradation, Environmental ; Genes, Bacterial ; }, abstract = {This study examined the effects of polyethylene terephthalate (PET) nanoplastics on the rhizosphere of Oryza sativa L., focusing on dynamic changes and interactions among microbial communities, antibiotic resistance genes (ARGs) and microplastic degradation genes (MDGs). PET exposure altered the structure and function of soil microbial, enabling specific microbial groups to thrive in polluted environments. High-dose PET treatments markedly increased the abundance and dissemination of ARGs, primarily via resistance mechanisms such as antibiotic efflux and target alteration. By providing additional carbon sources and surfaces for microbial attachment, PET stimulated the growth of microorganisms harboring MDGs, resulting in an increase in MDGs abundance. The elevated expression of MDGs facilitated the propagation of ARGs, with overlapping host microorganisms suggesting that certain microbial groups exhibit dual metabolic capabilities, enabling them to endure both antibiotic and microplastic pressures. Toxic byproducts of microplastic degradation, such as mono-ethylhexyl phthalate, further promoted ARGs dissemination by increasing horizontal gene transfer frequency. Structural equation modeling revealed that PET indirectly influenced ARGs and MDGs expression by altering soil C/N ratio, available phosphorus, and enzyme activities. Thus, nanoscale PET exacerbates ecological risks to soil microbial communities by driving co-propagation of ARGs and MDGs, highlighting the persistent threat of composite pollution to agroecosystems.}, }
@article {pmid39798650, year = {2025}, author = {Zhang, X and Guo, W and Zhang, Z and Gao, P and Tang, P and Liu, T and Yao, X and Li, J}, title = {Insights into the mobility and bacterial hosts of antibiotic resistance genes under dinotefuran selection pressure in aerobic granular sludge based on metagenomic binning and functional modules.}, journal = {Environmental research}, volume = {268}, number = {}, pages = {120807}, doi = {10.1016/j.envres.2025.120807}, pmid = {39798650}, issn = {1096-0953}, mesh = {*Sewage/microbiology ; *Guanidines/toxicity ; *Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; Metagenomics ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects ; Anti-Bacterial Agents ; Selection, Genetic ; Aerobiosis ; }, abstract = {Dinotefuran (DIN) is toxic to non-target organisms and accelerates the evolution of antibiotic resistance, which poses a problem for the stable operation of the activated sludge process in wastewater treatment plants (WWTPs). However, the emergence and the transfer mechanism of antibiotic resistance genes (ARGs) in activated sludge systems under DIN stress remains unclear. Thus, in the study, the potential impact of DIN on ARGs and virulence factor genes (VFGs) in aerobic granular sludge (AGS) was investigated in depth using metagenomic binning and functional modules. It was found that DIN stress increased the total abundance of ARGs, mobile genetic elements (MGEs), and VFGs in the AGS system, with the highest abundance of fabG (4.6%), tnpA (55.6%) and LPS (39.0%), respectively. The proliferation of the enteric pathogens Salmonella enterica and Escherichia coli in the system indicates that DIN induces exposure of harmless bacteria to the infected environment. The genera Nitrospira (1169 ARG subtypes) and Dechloromonas (663 ARG subtypes) were identified as the potentially antibiotic-resistant bacteria carrying the most ARGs and MGEs in the metagenome-assembled genomes. Co-localization patterns of some ARGs, MGEs, and the SOS response-related gene lexA were observed on metagenome-assembled contigs under high levels of DIN exposure, suggesting DIN stimulated ROS production (101.8% increase over control), altered cell membrane permeability, and increased the potential for horizontal gene transfer (HGT). Furthermore, the DNA damage caused by DIN in AGS led to the activation of the antioxidant system and the SOS repair response, which in turn promoted the expression of the type IV secretion system and HGT through the flagellar channel. This study extends the previously unappreciated DIN understanding of the spread and associated risks of ARGs and VFGs in the AGS system of WWTPs. It elucidates how DIN facilitates HGT, offering a scientific basis for controlling emerging contaminant-induced resistance.}, }
@article {pmid39797530, year = {2025}, author = {Liu, Y and Gong, C and Hu, Y and Han, H and Tian, T and Luo, Y and Yang, X and Xie, W and Wu, Q and Wang, S and Guo, Z and Zhang, Y}, title = {Silencing of the plant-derived horizontally transferred gene BtSC5DL effectively controls Bemisia tabaci MED.}, journal = {Pest management science}, volume = {}, number = {}, pages = {}, doi = {10.1002/ps.8638}, pmid = {39797530}, issn = {1526-4998}, support = {2021YFD1400600//National Key R&amp;D Program of China/ ; 32221004//National Natural Science Foundation of China/ ; CARS-23//Earmarked Fund for CARS/ ; Y2023XK15//Central Public-Interest Scientific Institution Basal Research Fund of the Chinese Academy of Agricultural Sciences./ ; Y2024XK01//Central Public-Interest Scientific Institution Basal Research Fund of the Chinese Academy of Agricultural Sciences./ ; //Beijing Key Laboratory for Pest Control and Sustainable Cultivation of Vegetables/ ; CAAS-ASTIP-IVFCAAS//Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences/ ; }, abstract = {BACKGROUND: The whitefly Bemisia tabaci is a notorious agricultural pest known for its ability to cause significant crop damage through direct feeding and virus transmission. Its remarkable adaptability and reproductive capacity are linked to its ability to acquire and integrate horizontally transferred genes (HTGs) into its genome. These HTGs increase the physiological and metabolic capacities of this pest, including cholesterol synthesis, which is critical for its survival and reproductive success. Among these genes, we identified a plant-derived B. tabaci Δ7-sterol C5-desaturase-like gene (BtSC5DL), which plays a pivotal role in B. tabaci cholesterol metabolism and reproductive biology.<br><br>RESULTS: In this study, we cloned and identified the BtSC5DL gene from B. tabaci Mediterranean (MED). Bioinformatics and molecular analyses revealed that BtSC5DL was transferred from plants to B. tabaci millions of years ago and is now stably expressed in this species. Silencing BtSC5DL through dsRNA feeding resulted in significant reductions in egg production and cholesterol content in B. tabaci MED. Furthermore, virus-induced gene silencing (VIGS) experiments confirmed that long-term suppression of BtSC5DL had a notable ability to control whitefly populations.<br><br>CONCLUSION: Our results demonstrate the crucial role of BtSC5DL in cholesterol biosynthesis in B. tabaci MED and suggest that the acquisition of this gene significantly enhances the reproductive capacity of this species. These findings provide a theoretical basis for the development of RNA interference (RNAi)-based pest control strategies targeting BtSC5DL, offering a potential new approach for the effective management of whitefly populations in agricultural settings. &#xa9; 2025 Society of Chemical Industry.}, }
@article {pmid39794121, year = {2025}, author = {Liu, Y and Botelho, J and Iranzo, J}, title = {Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer.}, journal = {Genome research}, volume = {35}, number = {2}, pages = {268-278}, pmid = {39794121}, issn = {1549-5469}, mesh = {*Gene Transfer, Horizontal ; Evolution, Molecular ; Phylogeny ; *Genetic Linkage ; *Archaea/genetics ; *Bacteria/genetics ; *Interspersed Repetitive Sequences/genetics ; Genome, Bacterial ; Genomics ; }, abstract = {Prokaryotes have evolved a wide repertoire of defense systems to prevent invasion by mobile genetic elements (MGEs). However, because MGEs are vehicles for the exchange of beneficial accessory genes, defense systems could consequently impede rapid adaptation in microbial populations. Here, we study how defense systems impact horizontal gene transfer (HGT) in the short term and long term. By combining comparative genomics and phylogeny-aware statistical methods, we quantify the association between the presence of seven widespread defense systems and the abundance of MGEs in the genomes of 196 bacterial and one archaeal species. We also calculate the differences in the rates of gene gain and loss between lineages that possess and lack each defense system. Our results show that the impact of defense systems on HGT is highly taxon and system dependent and, in most cases, not statistically significant. Timescale analysis reveals that defense systems must persist in a lineage for a relatively long time to exert an appreciable negative impact on HGT. In contrast, for shorter evolutionary timescales, frequent coacquisition of MGEs and defense systems results in a net positive association of the latter with HGT. Given the high turnover rates experienced by defense systems, we propose that the inhibitory effect of most defense systems on HGT is masked by their strong linkage with MGEs. These findings help explain the contradictory conclusions of previous research by pointing at mobility and within-host retention times as key factors that determine the impact of defense systems on genome plasticity.}, }
@article {pmid39793087, year = {2025}, author = {Zhang, Y and Tu, C and Bai, J and Li, X and Sun, Z and Xu, L}, title = {Metabolic enhancement contributed by horizontal gene transfer is essential for dietary specialization in leaf beetles.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {1}, pages = {e2415717122}, pmid = {39793087}, issn = {1091-6490}, support = {32370523//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Animals ; *Coleoptera/genetics/metabolism ; *Gene Transfer, Horizontal ; *Plant Leaves/parasitology/metabolism/genetics ; *Larva/metabolism/genetics/growth &amp; development ; *Cellulose/metabolism ; Diet ; }, abstract = {Horizontal gene transfer (HGT) from bacteria to insects is widely reported and often associated with the adaptation and diversification of insects. However, compelling evidence demonstrating how HGT-conferred metabolic adjustments enable species to adapt to surrounding environment remains scarce. Dietary specialization is an important ecological strategy adopted by animals to reduce inter- and intraspecific competition for limited resources. Adults of the leaf beetle Plagiodera versicolora (Coleoptera) preferentially consume new leaves; nevertheless, we found that they selectively oviposit on mature leaves, thereby establishing a distinct dietary niche separation between adults and larvae. Based on the de novo assembled chromosome-level genome, we identified two horizontally transferred genes with cellulose degradation potential, belonging to the glycosyl hydrolase 48 family (GH48-1 and GH48-2). Prokaryotic expression of the HGTs confirmed the cellulose degradation capability of the two genes. Knockdown of GH48 significantly hampered the growth and survival rate of larvae feeding on mature leaves compared to wild-type larvae, with no similar effect observed in adults. Replenishing the GH48-expressing bacteria compensated for the knockdown of these two genes and recurred larval adaptability to mature leaves. Taken together, our results highlight the advantage and metabolic enhancement conferred by the two cellulose-degrading HGTs in P. versicolora larvae, enabling their development on cellulose-enriched mature leaves and underscoring the indispensable role of HGTs in facilitating the adaptation of leaf beetles to plants.}, }
@article {pmid39791879, year = {2025}, author = {Kohlmeier, MG and O'Hara, GW and Ramsay, JP and Terpolilli, JJ}, title = {Closed genomes of commercial inoculant rhizobia provide a blueprint for management of legume inoculation.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {2}, pages = {e0221324}, pmid = {39791879}, issn = {1098-5336}, support = {UMU1810-001RTX, UMU1901-002RTX//Grains Research and Development Corporation (GRDC)/ ; FT170100235//Australian Research Council Future Fellowship/ ; }, mesh = {*Genome, Bacterial ; *Fabaceae/microbiology ; Australia ; Symbiosis ; Phylogeny ; *Agricultural Inoculants/genetics ; *Rhizobium/genetics ; *Rhizobiaceae/genetics ; Soil Microbiology ; Root Nodules, Plant/microbiology ; }, abstract = {UNLABELLED: Rhizobia are soil bacteria capable of establishing symbiosis within legume root nodules, where they reduce atmospheric N2 into ammonia and supply it to the plant for growth. Australian soils often lack rhizobia compatible with introduced agricultural legumes, so inoculation with exotic strains has become a common practice for over 50 years. While extensive research has assessed the N2-fixing capabilities of these inoculants, their genomics, taxonomy, and core and accessory gene phylogeny are poorly characterized. Furthermore, in some cases, inoculant strains have been developed from isolations made in Australia. It is unknown whether these strains represent naturalized exotic organisms, native rhizobia with a capacity to nodulate introduced legumes, or recombinant strains arising from horizontal transfer between introduced and native bacteria. Here, we describe the complete, closed genome sequences of 42 Australian commercial rhizobia. These strains span the genera, Bradyrhizobium, Mesorhizobium, Methylobacterium, Rhizobium, and Sinorhizobium, and only 23 strains were identified to species level. Within inoculant strain genomes, replicon structure and location of symbiosis genes were consistent with those of model strains for each genus, except for Rhizobium sp. SRDI969, where the symbiosis genes are chromosomally encoded. Genomic analysis of the strains isolated from Australia showed they were related to exotic strains, suggesting that they may have colonized Australian soils following undocumented introductions. These genome sequences provide the basis for accurate strain identification to manage inoculation and identify the prevalence and impact of horizontal gene transfer (HGT) on legume productivity.<br><br>IMPORTANCE: Inoculation of cultivated legumes with exotic rhizobia is integral to Australian agriculture in soils lacking compatible rhizobia. The Australian inoculant program supplies phenotypically characterized high-performing strains for farmers but in most cases, little is known about the genomes of these rhizobia. Horizontal gene transfer (HGT) of symbiosis genes from inoculant strains to native non-symbiotic rhizobia frequently occurs in Australian soils and can impact the long-term stability and efficacy of legume inoculation. Here, we present the analysis of reference-quality genomes for 42 Australian commercial rhizobial inoculants. We verify and classify the genetics, genome architecture, and taxonomy of these organisms. Importantly, these genome sequences will facilitate the accurate strain identification and monitoring of inoculants in soils and plant nodules, as well as enable detection of horizontal gene transfer to native rhizobia, thus ensuring the efficacy and integrity of Australia's legume inoculation program.}, }
@article {pmid39789078, year = {2025}, author = {Lee, D and Muir, P and Lundberg, S and Lundholm, A and Sandegren, L and Koskiniemi, S}, title = {A CRISPR-Cas9 system protecting E. coli against acquisition of antibiotic resistance genes.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {1545}, pmid = {39789078}, issn = {2045-2322}, mesh = {*CRISPR-Cas Systems ; *Escherichia coli/genetics/drug effects ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Plasmids/genetics ; Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; }, abstract = {Antimicrobial resistance (AMR) is an increasing problem worldwide, and new treatment options for bacterial infections are direly needed. Engineered probiotics show strong potential in treating or preventing bacterial infections. However, one concern with the use of live bacteria is the risk of the bacteria acquiring genes encoding for AMR or virulence factors through horizontal gene transfer (HGT), and the transformation of the probiotic into a superbug. Therefore, we developed an engineered CRISPR-Cas9 system that protects bacteria from horizontal gene transfer. We synthesized a CRISPR locus targeting eight AMR genes and cloned this with the Cas9 and transacting tracrRNA on a medium copy plasmid. We next evaluated the efficiency of the system to block HGT through transformation, transduction, and conjugation. Our results show that expression of the CRISPR-Cas9 system successfully protects E. coli MG1655 from acquiring the targeted resistance genes by transformation or transduction with 2-3 logs of protection depending on the system for transfer and the target gene. Furthermore, we show that the system blocks conjugation of a set of clinical plasmids, and that the system is also able to protect the probiotic bacterium E. coli Nissle 1917 from acquiring AMR genes.}, }
@article {pmid39788974, year = {2025}, author = {Scarpa, A and Pianezza, R and Gellert, HR and Haider, A and Kim, BY and Lai, EC and Kofler, R and Signor, S}, title = {Double trouble: two retrotransposons triggered a cascade of invasions in Drosophila species within the last 50 years.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {516}, pmid = {39788974}, issn = {2041-1723}, support = {P35093//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; P30 CA008748/CA/NCI NIH HHS/United States ; P34965//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; R01 HD108914/HD/NICHD NIH HHS/United States ; NSF-EPSCoR-2032756//National Science Foundation (NSF)/ ; R01 GM083300/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Retroelements/genetics ; *Gene Transfer, Horizontal ; *Phylogeny ; *Evolution, Molecular ; Drosophila/genetics ; Genome, Insect ; Drosophila melanogaster/genetics ; Introduced Species ; }, abstract = {Horizontal transfer of genetic material in eukaryotes has rarely been documented over short evolutionary timescales. Here, we show that two retrotransposons, Shellder and Spoink, invaded the genomes of multiple species of the melanogaster subgroup within the last 50 years. Through horizontal transfer, Spoink spread in D. melanogaster during the 1980s, while both Shellder and Spoink invaded D. simulans in the 1990s. Possibly following hybridization, D. simulans infected the island endemic species D. mauritiana (Mauritius) and D. sechellia (Seychelles) with both TEs after 1995. In the same approximate time-frame, Shellder also invaded D. teissieri, a species confined to sub-Saharan Africa. We find that the donors of Shellder and Spoink are likely American Drosophila species from the willistoni, cardini, and repleta groups. Thus, the described cascade of TE invasions could only become feasible after D. melanogaster and D. simulans extended their distributions into the Americas 200 years ago, likely aided by human activity. Our work reveals that cascades of TE invasions, likely initiated by human-mediated range expansions, could have an impact on the genomic and phenotypic evolution of geographically dispersed species. Within a few decades, TEs could invade many species, including island endemics, with distributions very distant from the donor of the TE.}, }
@article {pmid39788725, year = {2025}, author = {Robinson, LR and McDevitt, CJ and Regan, MR and Quail, SL and Wadsworth, CB}, title = {In vitro evolution of ciprofloxacin resistance in Neisseria commensals and derived mutation population dynamics in natural Neisseria populations.}, journal = {FEMS microbiology letters}, volume = {372}, number = {}, pages = {}, pmid = {39788725}, issn = {1574-6968}, support = {R15 AI174182/AI/NIAID NIH HHS/United States ; /GM/NIGMS NIH HHS/United States ; R15AI174182/NH/NIH HHS/United States ; SAMN41424178//SRA/ ; }, mesh = {*Ciprofloxacin/pharmacology ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; *Mutation ; *Neisseria/genetics/drug effects ; Humans ; Microbial Sensitivity Tests ; DNA Gyrase/genetics ; Evolution, Molecular ; DNA Topoisomerase IV/genetics ; Bacterial Proteins/genetics ; }, abstract = {Commensal Neisseria are members of a healthy human oropharyngeal microbiome; however, they also serve as a reservoir of antimicrobial resistance for their pathogenic relatives. Despite their known importance as sources of novel genetic variation for pathogens, we still do not understand the full suite of resistance mutations commensal species can harbor. Here, we use in vitro selection to assess the mutations that emerge in response to ciprofloxacin selection in commensal Neisseria by passaging four replicates of four different species in the presence of a selective antibiotic gradient for 20 days; then categorized derived mutations with whole genome sequencing. Ten out of sixteen selected cells lines across the four species evolved ciprofloxacin resistance (≥1 ug/ml); with resistance-contributing mutations primarily emerging in DNA gyrase subunit A and B (gyrA and gyrB), topoisomerase IV subunits C and E (parC and parE), and the multiple transferable efflux pump repressor (mtrR). Of note, these derived mutations appeared in the same loci responsible for ciprofloxacin-reduced susceptibility in the pathogenic Neisseria, suggesting conserved mechanisms of resistance across the genus. Additionally, we tested for zoliflodacin cross-resistance in evolved strain lines and found 6 lineages with elevated zoliflodacin minimum inhibitory concentrations. Finally, to interrogate the likelihood of experimentally derived mutations emerging and contributing to resistance in natural Neisseria, we used a population-based approach and identified GyrA 91I as a substitution circulating within commensal Neisseria populations and ParC 85C in a single gonococcal isolate. A small cluster of gonococcal isolates shared commensal alleles at parE, suggesting recent cross-species recombination events.}, }
@article {pmid39787839, year = {2025}, author = {Zhao, W and Hou, Y and Wei, L and Wei, W and Zhang, K and Duan, H and Ni, BJ}, title = {Chlorination-induced spread of antibiotic resistance genes in drinking water systems.}, journal = {Water research}, volume = {274}, number = {}, pages = {123092}, doi = {10.1016/j.watres.2025.123092}, pmid = {39787839}, issn = {1879-2448}, mesh = {*Drinking Water/microbiology ; *Halogenation ; *Drug Resistance, Microbial/genetics ; Water Purification ; Disinfection ; Chlorine ; }, abstract = {Chlorine, the most widely utilized disinfectant for drinking water globally, has recently been implicated in facilitating the spread of antibiotic resistance genes (ARGs), raising concerns about its underestimated environmental and ecological risks. However, given the current fragmented research focus and results, a comprehensive understanding of the potential mechanisms and influencing factors behind chlorination-promoted ARGs transmission in drinking water systems is crucial. This work is the first to systematically review the variations in abundance, transmission mechanisms, influencing factors, and mitigation strategies related to ARGs during the chlorination process. The results indicated that chlorination could induce genetic mutations and promote horizontal gene transfer through multiple pathways, including increased reactive oxygen species, enhanced membrane permeability, stimulation of the SOS response, and activation of efflux pumps. In addition, this work delves into significant discoveries regarding the factors affecting ARG transmission in drinking water, such as chlorine concentration, reaction time, disinfection byproducts, pipe materials, biofilms, and the water matrix. A series of effective strategies from water source to point-of-use were proposed aimed at mitigating ARGs transmission risks in the drinking water system. Finally, we address existing challenges and outline future research directions to overcome these bottlenecks. Overall, this review aims to advance our understanding of the role of chlorination in the dissemination of ARGs and to inspire innovative research ideas for optimizing disinfection techniques, minimizing the risks of antibiotic resistance transmission, and enhancing the safety of drinking water.}, }
@article {pmid39786570, year = {2025}, author = {Chen, J and Garfinkel, DJ and Bergman, CM}, title = {Horizontal Transfer and Recombination Fuel Ty4 Retrotransposon Evolution in Saccharomyces.}, journal = {Genome biology and evolution}, volume = {17}, number = {1}, pages = {}, pmid = {39786570}, issn = {1759-6653}, support = {R01 GM124216/GM/NIGMS NIH HHS/United States ; R01GM124216/NH/NIH HHS/United States ; //University of Georgia Research Foundation/ ; }, mesh = {*Retroelements ; *Gene Transfer, Horizontal ; *Saccharomyces/genetics ; *Evolution, Molecular ; *Recombination, Genetic ; Phylogeny ; Genome, Fungal ; Saccharomyces cerevisiae/genetics ; }, abstract = {Horizontal transposon transfer (HTT) plays an important role in the evolution of eukaryotic genomes; however, the detailed evolutionary history and impact of most HTT events remain to be elucidated. To better understand the process of HTT in closely related microbial eukaryotes, we studied Ty4 retrotransposon subfamily content and sequence evolution across the genus Saccharomyces using short- and long-read whole genome sequence data, including new PacBio genome assemblies for two Saccharomyces mikatae strains. We find evidence for multiple independent HTT events introducing the Tsu4 subfamily into specific lineages of Saccharomyces paradoxus, Saccharomyces cerevisiae, Saccharomyces eubayanus, Saccharomyces kudriavzevii and the ancestor of the S. mikatae/Saccharomyces jurei species pair. In both S. mikatae and S. kudriavzevii, we identified novel Ty4 clades that were independently generated through recombination between resident and horizontally transferred subfamilies. Our results reveal that recurrent HTT and lineage-specific extinction events lead to a complex pattern of Ty4 subfamily content across the genus Saccharomyces. Moreover, our results demonstrate how HTT can lead to coexistence of related retrotransposon subfamilies in the same genome that can fuel evolution of new retrotransposon clades via recombination.}, }
@article {pmid39780077, year = {2025}, author = {Lv, C and Abdullah, M and Su, CL and Chen, W and Zhou, N and Cheng, Z and Chen, Y and Li, M and Simpson, KW and Elsaadi, A and Zhu, Y and Lipkin, SM and Chang, YF}, title = {Genomic characterization of Escherichia coli with a polyketide synthase (pks) island isolated from ulcerative colitis patients.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {19}, pmid = {39780077}, issn = {1471-2164}, mesh = {Humans ; *Polyketide Synthases/genetics ; *Colitis, Ulcerative/microbiology/genetics ; *Escherichia coli/genetics/isolation &amp; purification ; *Phylogeny ; *Genomic Islands ; Genome, Bacterial ; Genomics ; Gene Transfer, Horizontal ; Virulence Factors/genetics ; Escherichia coli Infections/microbiology ; Peptides ; Polyketides ; }, abstract = {The E. coli strains harboring the polyketide synthase (pks) island encode the genotoxin colibactin, a secondary metabolite reported to have severe implications for human health and for the progression of colorectal cancer. The present study involves whole-genome-wide comparison and phylogenetic analysis of pks harboring E. coli isolates to gain insight into the distribution and evolution of these organisms. Fifteen E. coli strains isolated from patients with ulcerative colitis (UC) were sequenced, 13 of which harbored pks islands. In addition, 2,654 genomes from the public database were also screened for pks harboring E. coli genomes, 158 of which were pks-positive (pks[+]) isolates. Whole-genome-wide comparison and phylogenetic analysis revealed that 171 (158 + 13) pks[+] isolates belonged to phylogroup B2, and most of the isolates belong to sequence types ST73 and ST95. One isolate from a UC patient was of the sequence type ST8303. The maximum likelihood tree based on the core genome of pks[+] isolates revealed horizontal gene transfer across sequence types and serotypes. Virulome and resistome analyses revealed the0020preponderance of virulence genes and a reduced number of antimicrobial genes in pks[+] isolates. This study significantly contributes to understanding the evolution of pks islands in E. coli.}, }
@article {pmid39778056, year = {2025}, author = {Silva, JK and Hervé, V and Mies, US and Platt, K and Brune, A}, title = {A Novel Lineage of Endosymbiotic Actinomycetales: Genome Reduction and Acquisition of New Functions in Bifidobacteriaceae Associated With Termite Gut Flagellates.}, journal = {Environmental microbiology}, volume = {27}, number = {1}, pages = {e70010}, pmid = {39778056}, issn = {1462-2920}, support = {//Max-Planck-Gesellschaft/ ; }, mesh = {*Symbiosis ; Animals ; *Isoptera/microbiology ; *Genome, Bacterial ; *RNA, Ribosomal, 16S/genetics ; *Phylogeny ; *Actinomycetales/genetics/metabolism ; Gene Transfer, Horizontal ; Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology/parasitology ; Metagenome ; }, abstract = {Cellulolytic flagellates are essential for the symbiotic digestion of lignocellulose in the gut of lower termites. Most species are associated with host-specific consortia of bacterial symbionts from various phyla. 16S rRNA-based diversity studies and taxon-specific fluorescence in situ hybridization revealed a termite-specific clade of Actinomycetales that colonise the cytoplasm of Trichonympha spp. and other gut flagellates, representing the only known case of intracellular Actinomycetota in protists. Comparative analysis of eleven metagenome-assembled genomes from lower termites allowed us to describe them as new genera of Bifidobacteriaceae. Like the previously investigated Candidatus Ancillula trichonymphae, they ferment sugars via the bifidobacterium shunt but, unlike their free-living relatives, experienced significant genome erosion. Additionally, they acquired new functions by horizontal gene transfer from other gut bacteria, including the capacity to produce hydrogen. Members of the genus Ancillula (average genome size 1.56 ± 0.2 Mbp) retained most pathways for the synthesis of amino acids, including a threonine/serine exporter, providing concrete evidence for the basis of the mutualistic relationship with their host. By contrast, Opitulatrix species (1.23 ± 0.1 Mbp) lost most of their biosynthetic capacities, indicating that an originally mutualistic symbiosis is on the decline.}, }
@article {pmid39777960, year = {2025}, author = {Perez, MF and Angelov, A and Übelacker, M and Torres Tejerizo, GA and Farias, ME and Liebl, W and Dib, JR}, title = {Linear Plasmids in Micrococcus: Insights Into a Common Ancestor and Transfer by Conjugation.}, journal = {Environmental microbiology}, volume = {27}, number = {1}, pages = {e70020}, pmid = {39777960}, issn = {1462-2920}, support = {PICT 2018 N&#xb0; 2545 PRESTAMO BID//Agencia Nacional de Promoci&#xf3;n de la Investigaci&#xf3;n, el Desarrollo Tecnol&#xf3;gico y la Innovaci&#xf3;n/ ; PIUNT A618/2//Universidad Nacional de Tucum&#xe1;n/ ; }, mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; *Micrococcus/genetics ; *Conjugation, Genetic ; Evolution, Molecular ; Phylogeny ; Open Reading Frames ; DNA, Bacterial/genetics ; Base Composition ; }, abstract = {Actinobacteria have frequently been reported in the Andean Puna, including strains of the genus Micrococcus. These strains demonstrate resistance to high levels of UV radiation, arsenic, and multiple antibiotics, and possess large linear plasmids. A comparative analysis of the sequences and putative functions of these plasmids was conducted. The presence of large regions with high sequence identity (exceeding 30 kb in total) in all three studied Micrococcus megaplasmids indicates a clear evolutionary link among these elements. Genes related to essential plasmid functions were primarily found within these conserved regions, while genes associated with resistance to metals and antibiotics resided in accessory regions. Moreover, the abundance of open reading frames related to transposition and recombination, along with local deviations from the average GC content, provides evidence for the mosaic nature and considerable genetic plasticity of these plasmids. This study presents evidence of a common ancestor for linear plasmids in Micrococcus and suggests that horizontal gene transfer likely occurs frequently within Andean lakes, providing the native microbial community with a beneficial gene pool to withstand extreme conditions. Additionally, the successful transfer of the linear plasmid pLMA1 by a DNase-insensitive, conjugation-type mechanism and its potential use as a genetic vector is demonstrated.}, }
@article {pmid39777461, year = {2025}, author = {Blanchais, C and Pages, C and Campos, M and Boubekeur, K and Contarin, R and Orlando, M and Siguier, P and Laaberki, MH and Cornet, F and Charpentier, X and Rousseau, P}, title = {Interplay between the Xer recombination system and the dissemination of antibioresistance in Acinetobacter baumannii.}, journal = {Nucleic acids research}, volume = {53}, number = {1}, pages = {}, pmid = {39777461}, issn = {1362-4962}, support = {//University of Toulouse III Paul Sabatier/ ; ANR-AAPG2021-InXS//Agence Nationale de la Recherche/ ; ANR-11-LABX-0048//LabEx Ecofect/ ; ANR-11-IDEX-0007//Universit&#xe9; de Lyon/ ; EQU202303016268//Fondation pour la Recherche M&#xe9;dicale/ ; ANR-AAPG2021-InXS//Agence Nationale de la Recherche/ ; }, mesh = {*Acinetobacter baumannii/genetics/drug effects ; *Plasmids/genetics ; *Recombination, Genetic ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Recombinases/metabolism/genetics ; Escherichia coli/genetics/drug effects ; }, abstract = {Antibiotic-resistant infections are a pressing clinical challenge. Plasmids are known to accelerate the emergence of resistance by facilitating horizontal gene transfer of antibiotic resistance genes between bacteria. We explore this question in Acinetobacter baumannii, a globally emerging nosocomial pathogen responsible for a wide range of infections with a worrying accumulation of resistance, particularly involving plasmids. In this species, plasmids of the Rep_3 family harbor antibiotic resistance genes within variable regions flanked by potential site-specific recombination sites recognized by the XerCD recombinase. We first show that the Xer system of A. baumannii functions as described in Escherichia coli, resolving chromosome dimers at the dif site and recombining plasmid-carried sites. However, the multiple Xer recombination sites found in Rep_3 plasmids do not allow excision of plasmid fragments. Rather, they recombine to cointegrate plasmids, which could then evolve to exchange genes. Cointegrates represent a significant fraction of the plasmid population and their formation is controlled by the sequence of recombination sites, which determines the compatibility between recombination sites. We conclude that plasmids in A. baumannii frequently recombine by Xer recombination, allowing a high level of yet controlled plasticity in the acquisition and combination of antibiotic resistance genes.}, }
@article {pmid39776180, year = {2025}, author = {Shimuta, K and Ohama, Y and Ito, S and Hoshina, S and Takahashi, H and Igawa, G and Dorin Yamamoto, M and Akeda, Y and Ohnishi, M}, title = {Emergence of ceftriaxone-resistant Neisseria gonorrhoeae through horizontal gene transfer among Neisseria spp.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiaf008}, pmid = {39776180}, issn = {1537-6613}, abstract = {OBJECTIVES: It has been suggested that the emergence of ceftriaxone-resistant strains of Neisseria gonorrhoeae involves the incorporation of the penA gene from commensal Neisseria spp. that are resistant to ceftriaxone. However, the mechanism of this mosaic penA generation is unknown.<br><br>METHODS: We obtained 10 strains of commensal Neisseria spp. showing ceftriaxone MIC >0.5 mg/L. The similarity of the penA gene region of these commensal Neisseria spp. strains and some ceftriaxone-resistant N. gonorrhoeae strains was investigated. To obtain transformants, commensal Neisseria spp., Neisseria lactamica, gDNA was used as donor DNA and a N. gonorrhoeae strain as the recipient.<br><br>RESULTS: The sequence similarity in certain regions of penA-murE between some of the commensal Neisseria spp. strains and the N. gonorrhoeae FC428 strain was very high. The sequence of these regions was very similar among some ceftriaxone-resistant strains of Neisseria spp. The PenA of the transformants matched the full PenA 60 of the original FC428 strain. Furthermore, our findings indicated that the source of resistance could have been a penA fragment derived from Neisseria spp. that originally carried the same sequence.<br><br>CONCLUSIONS: We suggest that FC428 developed ceftriaxone resistance by acquiring part of the penA-murE gene region from N. lactamica through horizontal gene transfer. The ceftriaxone-resistant N. lactamica shown here may also have emerged by acquiring part of penA from other Neisseria spp. From this work, our data provide insights into the understanding of the mechanism underlying the evolution of drug-resistant gonorrhea-causing strains.}, }
@article {pmid39772912, year = {2025}, author = {Figueroa, D and Ruiz, D and Tellini, N and De Chiara, M and Kessi-Pérez, EI and Martínez, C and Liti, G and Querol, A and Guillamón, JM and Salinas, F}, title = {Optogenetic control of horizontally acquired genes prevent stuck fermentations in yeast.}, journal = {Microbiology spectrum}, volume = {13}, number = {2}, pages = {e0179424}, pmid = {39772912}, issn = {2165-0497}, support = {1210955//ANID | Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico (FONDECYT)/ ; 11220533//ANID | Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico (FONDECYT)/ ; 1201104//ANID | Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico (FONDECYT)/ ; ID24I10027//ANID | Fondo de Fomento al Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico (FONDEF)/ ; ID21I10198//ANID | Fondo de Fomento al Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico (FONDEF)/ ; ICN17_022//Agencia Nacional de Investigaci&#xf3;n y Desarrollo (ANID)/ ; 21200745//Agencia Nacional de Investigaci&#xf3;n y Desarrollo (ANID)/ ; }, mesh = {*Fermentation/genetics ; *Saccharomyces cerevisiae/genetics/metabolism ; Wine/microbiology ; *Optogenetics/methods ; Nitrogen/metabolism ; *Gene Transfer, Horizontal ; Gene Expression Regulation, Fungal ; Vitis/microbiology ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; }, abstract = {Nitrogen limitations in the grape must be the main cause of stuck fermentations during the winemaking process. In Saccharomyces cerevisiae, a genetic segment known as region A, which harbors 12 protein-coding genes, was acquired horizontally from a phylogenetically distant yeast species. This region is mainly present in the genome of wine yeast strains, carrying genes that have been associated with nitrogen utilization. Despite the putative importance of region A in yeast fermentation, its contribution to the fermentative process is largely unknown. In this work, we used a wine yeast strain to evaluate the contribution of region A to the fermentation process. To do this, we first sequenced the genome of the wine yeast strain using long-read sequencing and determined that region A is present in a single copy. We then implemented an optogenetic system in this wine yeast strain to precisely regulate the expression of each gene, generating a collection of 12 strains that allow for light-activated gene expression. To evaluate the role of these genes during fermentation, we assayed this collection using microculture and fermentation experiments in synthetic must with varying amounts of nitrogen concentration. Our results show that changes in gene expression for genes within this region can impact growth parameters and fermentation rate. We additionally found that the expression of various genes in region A is necessary to complete the fermentation process and prevent stuck fermentations under low nitrogen conditions. Altogether, our optogenetics-based approach demonstrates the importance of region A in completing fermentation under nitrogen-limited conditions.IMPORTANCEStuck fermentations due to limited nitrogen availability in grape must represent one of the main problems in the winemaking industry. Nitrogen limitation in grape must reduces yeast biomass and fermentation rate, resulting in incomplete fermentations with high levels of residual sugar, undesired by-products, and microbiological instability. Here, we used an optogenetic approach to demonstrate that expression of genes within region A is necessary to complete fermentations under low nitrogen availability. Overall, our results suggest that region A is a genetic signature for adaptation to low nitrogen conditions.}, }
@article {pmid39771135, year = {2024}, author = {Li, Z and Yuan, D}, title = {Metagenomic Analysis Reveals the Effects of Microplastics on Antibiotic Resistance Genes in Sludge Anaerobic Digestion.}, journal = {Toxics}, volume = {12}, number = {12}, pages = {}, pmid = {39771135}, issn = {2305-6304}, support = {No. 52170097//the National Natural Science Foundation of China/ ; }, abstract = {Sewage sludge is recognized as both a source and a reservoir for antibiotic resistance genes (ARGs). Within an anaerobic digestion (AD) system, the presence of microplastics (MPs) has been observed to potentially facilitate the proliferation of these ARGs. Understanding the influence of MPs on microbial behavior and horizontal gene transfer (HGT) within the AD system is crucial for effectively managing the dissemination of ARGs in the environment. This study utilized metagenomic approaches to analyze the dynamics of various types of ARGs and potential microbial mechanisms under exposure to MPs during the AD process. The findings indicated that MPs in the AD process can enhance the proliferation of ARGs, with the extent of this enhancement increasing with the dosage of MPs: polyethylene (PE), polyethylene terephthalate (PET), and polylactic acid (PLA) MPs increased the abundance of ARGs in the anaerobic digestion system by up to 29.90%, 18.64%, and 14.15%, respectively. Additionally, the presence of MPs increased the relative abundance of mobile genetic elements (MGEs) during the AD process. Network correlation analysis further revealed that plasmids represent the predominant category of MGEs involved in the HGT of ARGs. Propionibacterium and Alicycliphilus were identified as the primary potential hosts for these ARGs. The results of gene function annotation indicated that exposure to MPs led to an increased the relative abundance of genes related to the production of reactive oxygen species (ROS), alterations in membrane permeability, ATP synthesis, and the secretion of extracellular polymeric substances (EPS). These genes play crucial roles in influencing the HGT of ARGs.}, }
@article {pmid39770765, year = {2024}, author = {Cangioli, L and Tabacchioni, S and Visca, A and Fiore, A and Aprea, G and Ambrosino, P and Ercole, E and Sørensen, S and Mengoni, A and Bevivino, A}, title = {Genome Insights into Beneficial Microbial Strains Composing SIMBA Microbial Consortia Applied as Biofertilizers for Maize, Wheat and Tomato.}, journal = {Microorganisms}, volume = {12}, number = {12}, pages = {}, pmid = {39770765}, issn = {2076-2607}, support = {862695//European Union's Horizon 2020/ ; }, abstract = {For the safe use of microbiome-based solutions in agriculture, the genome sequencing of strains composing the inoculum is mandatory to avoid the spread of virulence and multidrug resistance genes carried by them through horizontal gene transfer to other bacteria in the environment. Moreover, the annotated genomes can enable the design of specific primers to trace the inoculum into the soil and provide insights into the molecular and genetic mechanisms of plant growth promotion and biocontrol activity. In the present work, the genome sequences of some members of beneficial microbial consortia that have previously been tested in greenhouse and field trials as promising biofertilizers for maize, tomato and wheat crops have been determined. Strains belong to well-known plant-growth-promoting bacterial genera such as Bacillus, Burkholderia, Pseudomonas and Rahnella. The genome size of strains ranged from 4.5 to 7.5 Mbp, carrying many genes spanning from 4402 to 6697, and a GC content of 0.04% to 3.3%. The annotation of the genomes revealed the presence of genes that are implicated in functions related to antagonism, pathogenesis and other secondary metabolites possibly involved in plant growth promotion and gene clusters for protection against oxidative damage, confirming the plant-growth-promoting (PGP) activity of selected strains. All the target genomes were found to possess at least 3000 different PGP traits, belonging to the categories of nitrogen acquisition, colonization for plant-derived substrate usage, quorum sensing response for biofilm formation and, to a lesser extent, bacterial fitness and root colonization. No genes putatively involved in pathogenesis were identified. Overall, our study suggests the safe application of selected strains as "plant probiotics" for sustainable agriculture.}, }
@article {pmid39770663, year = {2024}, author = {Ben Natan, M and Masasa, M and Shashar, N and Guttman, L}, title = {Antibiotic Resistance in Vibrio Bacteria Associated with Red Spotting Disease in Sea Urchin Tripneustes gratilla (Echinodermata).}, journal = {Microorganisms}, volume = {12}, number = {12}, pages = {}, pmid = {39770663}, issn = {2076-2607}, support = {3-0000-17701//The Israeli Ministry of Health/ ; }, abstract = {The red spotting disease harms sea urchins to the extent of mass mortality in the ocean and echinocultures, accompanied by environmental damage and economic losses. The current study emphasizes the antimicrobial resistance of three isolated bacteria, closely related to Vibrio harveyi, Vibrio owensii, and Vibrio fortis, associated with red spotting in the cultured sea urchin Tripneustes gratilla. In vitro trials examined the susceptibility of these bacterial isolates to various antibiotics. In addition, using an in silico examination, we revealed the arsenal of antimicrobial resistance genes in available genomes of various pathogenic Vibrio associated with diseases in sea urchins, fish, shellfish, and corals. These two approaches enabled the discussion of the similarities and differences between aquatic pathogenic Vibrio and their antibiotic resistance. Among them, we revealed a core resistance to tetracyclines and penams by the in vitro examined strains. At the same time, the in silico study also supported this core resistance by the presence of the adeF and CRP genes in the bacterial genomes. Nevertheless, variability and specific resistance were evident at the species and strain levels in the Vibrio bacteria and genomes. The in vitro trials highlighted the diverse resistance of the Vibrio harveyi-like isolate to all examined antibiotics, while the other two isolates were found susceptible to nitrofurantoin and sulfamethoxazole. The resistance of the Vibrio harveyi-like isolate could not have been obtained in the genome of the proposed relative of Vibrio harveyi VHJR7 that lacks the oqxA and oqxB genes, which enables such a resistance. A unique sensitivity of the Vibrio fortis-like isolate to erythromycin is proposed when compared to other isolated Vibrio and Vibrio genomes that seem capable of resisting this drug. According to the results, we propose nitrofurantoin or sulfamethoxazole for treating two of the red-spotting-associated isolates (Vibrio fortis and Vibrio owensii-like), but not Vibrio harveyi-like. We assume that a shared resistance to some antibiotics by Vibrios is gained by a horizontal gene transfer while previous exposures of a bacterial strain to a specific drug may induce the development of a unique resistance. Finally, we discuss the novel knowledge on antibiotic resistance in Vibrio from the current research in light of the potential risks when using drugs for disease control in aquaculture.}, }
@article {pmid39770308, year = {2024}, author = {Islam, MM and Jung, DE and Shin, WS and Oh, MH}, title = {Colistin Resistance Mechanism and Management Strategies of Colistin-Resistant Acinetobacter baumannii Infections.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {12}, pages = {}, pmid = {39770308}, issn = {2076-0817}, support = {Grant Nos. 2022R1F1A1071415 and NRF-RS-2023-00275307 and Grant No. 2019R1A6C1010033//National Research Foundation of Korea (NRF) funded by the Ministry of Education &amp; Basic Science Research Capacity Enhancement Project through Korea Basic Science Institute (National research Facilities and Equipment Center) grant funded by the Ministry o/ ; }, mesh = {*Acinetobacter baumannii/drug effects/genetics ; *Colistin/pharmacology/therapeutic use ; Humans ; *Acinetobacter Infections/drug therapy ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics/drug effects ; Drug Resistance, Bacterial/genetics/drug effects ; Animals ; }, abstract = {The emergence of antibiotic-resistant Acinetobacter baumannii (A. baumannii) is a pressing threat in clinical settings. Colistin is currently a widely used treatment for multidrug-resistant A. baumannii, serving as the last line of defense. However, reports of colistin-resistant strains of A. baumannii have emerged, underscoring the urgent need to develop alternative medications to combat these serious pathogens. To resist colistin, A. baumannii has developed several mechanisms. These include the loss of outer membrane lipopolysaccharides (LPSs) due to mutation of LPS biosynthetic genes, modification of lipid A (a constituent of LPSs) structure through the addition of phosphoethanolamine (PEtN) moieties to the lipid A component by overexpression of chromosomal pmrCAB operon genes and eptA gene, or acquisition of plasmid-encoded mcr genes through horizontal gene transfer. Other resistance mechanisms involve alterations of outer membrane permeability through porins, the expulsion of colistin by efflux pumps, and heteroresistance. In response to the rising threat of colistin-resistant A. baumannii, researchers have developed various treatment strategies, including antibiotic combination therapy, adjuvants to potentiate antibiotic activity, repurposing existing drugs, antimicrobial peptides, nanotechnology, photodynamic therapy, CRISPR/Cas, and phage therapy. While many of these strategies have shown promise in vitro and in vivo, further clinical trials are necessary to ensure their efficacy and widen their clinical applications. Ongoing research is essential for identifying the most effective therapeutic strategies to manage colistin-resistant A. baumannii. This review explores the genetic mechanisms underlying colistin resistance and assesses potential treatment options for this challenging pathogen.}, }
@article {pmid39766551, year = {2024}, author = {Li, R and Dai, H and Wang, W and Peng, R and Yu, S and Zhang, X and Huo, ZY and Yuan, Q and Luo, Y}, title = {Local Electric Field-Incorporated In-Situ Copper Ions Eliminating Pathogens and Antibiotic Resistance Genes in Drinking Water.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {12}, pages = {}, pmid = {39766551}, issn = {2079-6382}, support = {2022YFC3205400//National Key R&amp;D Program of China/ ; 42377436 &amp; 52200079//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND/OBJECTIVES: Pathogen inactivation and harmful gene destruction from water just before drinking is the last line of defense to protect people from waterborne diseases. However, commonly used disinfection methods, such as chlorination, ultraviolet irradiation, and membrane filtration, experience several challenges such as continuous chemical dosing, the spread of antibiotic resistance genes (ARGs), and intensive energy consumption.<br><br>METHODS: Here, we perform a simultaneous elimination of pathogens and ARGs in drinking water using local electric fields and in-situ generated trace copper ions (LEF-Cu) without external chemical dosing. A 100-&#x3bc;m thin copper wire placed in the center of a household water pipe can generate local electric fields and trace copper ions near its surface after an external low voltage is applied.<br><br>RESULTS: The local electric field rapidly damages the outer structure of microorganisms through electroporation, and the trace copper ions can effectively permeate the electroporated microorganisms, successfully damaging their nucleic acids. The LEF-Cu disinfection system achieved complete inactivation (>6 log removal) of Escherichia coli O157:H7, Pseudomonas aeruginosa PAO1, and bacteriophage MS2 in drinking water at 2 V for 2 min, with low energy consumption (10[-2] kWh/m[3]). Meanwhile, the system effectively damages both intracellular (0.54~0.64 log) and extracellular (0.5~1.09 log) ARGs and blocks horizontal gene transfer.<br><br>CONCLUSIONS: LEF-Cu disinfection holds promise for preventing horizontal gene transfer and providing safe drinking water for household applications.}, }
@article {pmid39766521, year = {2024}, author = {de Andrade, FCC and Carvalho, MF and Figueiredo, AMS}, title = {Survival Strategies of Staphylococcus aureus: Adaptive Regulation of the Anti-Restriction Gene ardA-H1 Under Stress Conditions.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {12}, pages = {}, pmid = {39766521}, issn = {2079-6382}, support = {443804/2018-4 and 307672/2019-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e tecnol&#xf3;gico (CNPq)/ ; E-26/210.875/2016, E-26/211.554/2019, E-26.200.952/2020, and E-26/203.941/2024//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa (FAPERJ)/ ; 001//Funda&#xe7;&#xe3;o Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior (CAPES)/ ; INV-007641/GATES/Bill &amp; Melinda Gates Foundation/United States ; }, abstract = {Background/Objective: The anti-restriction protein ArdA-H1, found in multiresistant Staphylococcus aureus (MRSA) strains from the ST239-SCCmecIII lineage, inhibits restriction-modification systems, fostering horizontal gene transfer (HGT) and supporting genetic adaptability and resistance. This study investigates the regulatory mechanisms controlling ardA-H1 expression in S. aureus under various stress conditions, including acidic pH, iron limitation, and vancomycin exposure, and explores the roles of the Agr quorum sensing system. Methods: The expression of ardA-H1 was analyzed in S. aureus strains exposed to environmental stressors using real-time quantitative reverse transcription PCR. Comparisons were made between Agr-functional and Agr-deficient strains. In addition, Agr inhibition was achieved using a heterologous Agr autoinducing peptide. Results: The Agr system upregulated ardA-H1 expression in acidic and iron-limited conditions. However, vancomycin induced ardA-H1 activation specifically in the Agr-deficient strain GV69, indicating that an alternative regulatory pathway controls ardA-H1 expression in the absence of agr. The vancomycin response in GV69 suggests that diminished quorum sensing may offer a survival advantage by promoting persistence and HGT-related adaptability. Conclusion: Overall, our findings provide new insights into the intricate relationships between quorum-sensing, stress responses, bacterial virulence, and genetic plasticity, enhancing our understanding of S. aureus adaptability in challenging environments.}, }
@article {pmid39765217, year = {2025}, author = {Niault, T and van Houte, S and Westra, E and Swarts, DC}, title = {Evolution and ecology of anti-defence systems in phages and plasmids.}, journal = {Current biology : CB}, volume = {35}, number = {1}, pages = {R32-R44}, doi = {10.1016/j.cub.2024.11.033}, pmid = {39765217}, issn = {1879-0445}, mesh = {*Plasmids/genetics ; *Bacteriophages/genetics/physiology ; *Bacteria/virology/genetics ; Archaea/genetics/virology ; Evolution, Molecular ; Biological Evolution ; Interspersed Repetitive Sequences ; }, abstract = {Prokaryotes (Bacteria and Archaea) encode a highly diversified arsenal of defence systems that protect them against mobile genetic elements, such as phages and plasmids. In turn, mobile genetic elements encode anti-defence systems that allow them to escape the activity of these defence systems. This has resulted in an evolutionary arms race in which defence systems and anti-defence systems evolve and adapt continuously, driving intriguing innovation and enormous diversification on both sides. Over 150 prokaryotic defence systems have been identified to date. Anti-defence systems are known for only a subset of these, but more are being discovered at a steady rate. Despite an increasing understanding of the highly diverse molecular mechanisms of anti-defence systems, their diverse evolutionary origins, the selective pressures they are subjected to, and their ecological importance and implications often remain obscure. In this review, we describe the diverse strategies that phage and plasmid anti-defence systems employ to escape host defence systems. We explore the evolutionary origins of anti-defence systems and describe different factors that exert selective pressure, affecting their maintenance and diversification. We describe how, in turn, defence systems themselves evolved to act upon anti-defence mechanisms, thereby adding a new layer to the co-evolutionary battle between prokaryotes and their mobile genetic elements. We discuss how the continuous selective pressures found in dynamic microbial communities promote the retention and diversification of these anti-defence systems. Finally, we consider the ecological implications for both hosts and their mobile genetic elements, noting how the balance of defence and anti-defence strategies can shape microbial community composition, influence horizontal gene transfer, and impact ecosystem stability.}, }
@article {pmid39763003, year = {2025}, author = {Feng, Y and Lu, X and Zhao, J and Li, H and Xu, J and Li, Z and Wang, M and Peng, Y and Tian, T and Yuan, G and Zhang, Y and Liu, J and Zhang, M and Zhu La, AT and Qu, G and Mu, Y and Guo, W and Wu, Y and Zhang, Y and Wang, D and Hu, Y and Kan, B}, title = {Regional antimicrobial resistance gene flow among the One Health sectors in China.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {3}, pmid = {39763003}, issn = {2049-2618}, support = {2022YFC2303900//National Key Research and Development Program of China/ ; 22193064//major projects of the National Natural Science Foundation of China/ ; }, mesh = {Humans ; China ; *Gene Transfer, Horizontal ; *One Health ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; *Anti-Bacterial Agents/pharmacology ; *Gene Flow ; Feces/microbiology ; Drug Resistance, Bacterial/genetics ; Food Microbiology ; Metagenomics/methods ; Genes, Bacterial/genetics ; }, abstract = {BACKGROUND: Antimicrobial resistance poses a significant threat to global health, with its spread intricately linked across human, animal, and environmental sectors. Revealing the antimicrobial resistance gene (ARG) flow among the One Health sectors is essential for better control of antimicrobial resistance.<br><br>RESULTS: In this study, we investigated regional ARG transmission among humans, food, and the environment in Dengfeng, Henan Province, China by combining large-scale metagenomic sequencing with culturing of resistant bacterial isolates in 592 samples. A total of 40 ARG types and 743 ARG subtypes were identified, with a predominance of multidrug resistance genes. Compared with microbes from human fecal samples, those from food and environmental samples showed a significantly higher load of ARGs. We revealed that dietary habits and occupational exposure significantly affect ARG abundance. Pseudomonadota, particularly Enterobacteriaceae, were identified as the main ARG carriers shaping the resistome. The resistome in food samples was found more affected by mobile genetic elements (MGEs), whereas in environmental samples, it was more associated with the microbial composition. We evidenced that horizontal gene transfer (HGT) mediated by plasmids and phages, together with strain transmission, particularly those associated with the Enterobacteriaceae members, drive regional ARG flow. Lifestyle, dietary habits, and occupational exposure are all correlated with ARG dissemination and flies and food are important potential sources of ARGs to humans. The widespread mobile carbapenemase gene, OXA-347, carried by non-Enterobacteriaceae bacteria in the human gut microbiota, requires particular attention. Finally, we showed that machine learning models based on microbiome profiles were effective in predicting the presence of carbapenem-resistant strains, suggesting a valuable approach for AMR surveillance.<br><br>CONCLUSIONS: Our study provides a full picture of regional ARG transmission among the One Health sectors in a county-level city in China, which facilitates a better understanding of the complex routes of ARG transmission and highlights new points of focus for AMR surveillance and control. Video Abstract.}, }
@article {pmid39760498, year = {2025}, author = {Peirano, G and Pitout, JDD}, title = {Rapidly spreading Enterobacterales with OXA-48-like carbapenemases.}, journal = {Journal of clinical microbiology}, volume = {63}, number = {2}, pages = {e0151524}, pmid = {39760498}, issn = {1098-660X}, mesh = {*beta-Lactamases/genetics/metabolism ; Humans ; *Bacterial Proteins/genetics/metabolism ; *Enterobacteriaceae Infections/epidemiology/microbiology/transmission ; *Enterobacteriaceae/enzymology/genetics/isolation &amp; purification/drug effects ; Anti-Bacterial Agents/pharmacology ; Klebsiella pneumoniae/enzymology/genetics ; Escherichia coli/enzymology/genetics ; Plasmids ; Gene Transfer, Horizontal ; }, abstract = {Enterobacterales (mostly Klebsiella pneumoniae, Escherichia coli) with OXA-48-like carbapenemases (e.g., OXA-48, -181, -232, -244) are undermining the global efficiency of carbapenem therapy. In the Middle East, North Africa, and some European countries, OXA-48-like carbapenemases are the most common types of carbapenemases among Enterobacterales. Currently, OXA-48 is endemic in the Middle East, North Africa, Spain, France, and Belgium; OXA-181 is endemic in Sub-Saharan Africa and the Indian Subcontinent, while OXA-232 has been increasing in the Indian Subcontinent. European countries (e.g., Germany, Denmark, Switzerland, France) are experiencing community outbreaks with E. coli ST38 that produce OXA-244, and these strains have been introduced into Norwegian, Polish, and Czech hospitals. The global ascendancy of OXA-48-like genes is due to the combination of carbapenemases with horizontal spread through promiscuous plasmids (e.g., IncL, IncX3, ColE2) and vertical spread with certain high-risk multidrug-resistant clones (e.g., K. pneumoniae ST14, ST15, ST147, ST307; E. coli ST38, ST410). This is a powerful "gene survival strategy" that has assisted with the survival of OXA-48-like genes in different environments including the community setting. The laboratory diagnosis is complex; therefore, bacteria with "difficult to detect" variants (e.g., OXA-244, OXA-484) are likely underreported and are spreading silently "beneath the radar" in hospital and community settings. K. pneumoniae and E. coli with OXA-48-like carbapenemases are forces to be reckoned with.}, }
@article {pmid39756571, year = {2025}, author = {Heneghan, PG and Salzberg, LI and Wolfe, KH}, title = {Zymocin-like killer toxin gene clusters in the nuclear genomes of filamentous fungi.}, journal = {Fungal genetics and biology : FG &amp; B}, volume = {176}, number = {}, pages = {103957}, doi = {10.1016/j.fgb.2024.103957}, pmid = {39756571}, issn = {1096-0937}, mesh = {*Multigene Family ; Phylogeny ; *Genome, Fungal ; *Mycotoxins/genetics ; Chitinases/genetics ; Fusarium/genetics ; *Ribonucleases/genetics ; Saccharomyces cerevisiae/genetics ; *Fungi/genetics ; Colletotrichum/genetics ; Killer Factors, Yeast ; }, abstract = {Zymocin-like killer toxins are anticodon nucleases secreted by some budding yeast species, which kill competitor yeasts by cleaving tRNA molecules. They are encoded by virus-like elements (VLEs), cytosolic linear DNA molecules that are also called killer plasmids. To date, toxins of this type have been found only in budding yeast species (Saccharomycotina). Here, we show that the nuclear genomes of many filamentous fungi (Pezizomycotina) contain small clusters of genes coding for a zymocin-like ribonuclease (γ-toxin), a chitinase (toxin α/β-subunit), and in some cases an immunity protein. The γ-toxins from Fusarium oxysporum and Colletotrichum siamense abolished growth when expressed intracellularly in S. cerevisiae. Phylogenetic analysis of glycoside hydrolase 18 (GH18) domains shows that the chitinase genes in the gene clusters are members of the previously described C-II subgroup of Pezizomycotina chitinases. We propose that the Pezizomycotina gene clusters originated by integration of a yeast-like VLE into the nuclear genome, but this event must have been ancient because (1) phylogenetically, the Pezizomycotina C-II chitinases and the Saccharomycotina VLE-encoded toxin α/β subunit chitinases are sister clades with neither of them nested inside the other, and (2) many of the Pezizomycotina toxin cluster genes contain introns, whereas VLEs do not. One of the toxin gene clusters in Fusarium graminearum is a locus that has previously been shown to be under diversifying selection in North American populations of this plant pathogen. We also show that two genera of agaric mushrooms (Basidiomycota) have acquired toxin gene clusters by horizontal transfers from different Pezizomycotina donors.}, }
@article {pmid39754881, year = {2025}, author = {Li, X and Zhang, Z and Liu, H and Wen, H and Wang, Q}, title = {The fate of intracellular and extracellular antibiotic resistance genes during ultrafiltration-ultraviolet-chlorination in a full-scale wastewater treatment plant.}, journal = {Journal of hazardous materials}, volume = {486}, number = {}, pages = {137088}, doi = {10.1016/j.jhazmat.2024.137088}, pmid = {39754881}, issn = {1873-3336}, mesh = {*Ultraviolet Rays ; Halogenation ; Ultrafiltration ; *Wastewater/microbiology ; Disinfection/methods ; *Genes, Bacterial ; *Drug Resistance, Microbial/genetics ; *Water Purification/methods ; Waste Disposal, Fluid/methods ; }, abstract = {Effluent from wastewater treatment plants (WWTPs) is recognized as a significant source of antibiotic resistance genes (ARGs) in the environment. Advanced treatment processes such as ultrafiltration (UF), ultraviolet (UV) light disinfection, and chlorination have emerged as promising approaches for ARG removal. However, the efficacy of sequential disinfection processes, such as UF-UV-chlorination on intracellular (iARGs) and extracellular ARGs (eARGs), remains largely unknown. This study investigates the impact of this sequential disinfection process on the fate of iARGs, eARGs, and a crucial mobile genetic element (intI1) within a full-scale WWTP. Our findings revealed that the UF-UV-chlorination process effectively reduced the overall absolute abundance of detected ARGs in the effluent by 1.93 log, and intI1 by 0.86 log, compared to secondary effluent. The majority of these removals was achieved due to the UF and UV disinfection, while chlorination showed negligible impact on the absolute abundance of ARGs in the final effluent. Notably, five genera were identified as potential hosts for intI1 and eight iARGs, including aac(6')-Ib-cr, drfA1, sul1, sul2, ermB, mefA, tetA, and tetX, suggesting a high potential for horizontal gene transfer involving these ARGs. Overall, this study demonstrated that UF-UV-chlorination is a highly effective method for reducing ARGs in effluent from WWTPs.}, }
@article {pmid39752084, year = {2025}, author = {Heiss, J and Huson, DH and Steel, M}, title = {Transformations to Simplify Phylogenetic Networks.}, journal = {Bulletin of mathematical biology}, volume = {87}, number = {2}, pages = {20}, pmid = {39752084}, issn = {1522-9602}, support = {23-UOC-003//Marsden Fund/ ; }, mesh = {*Phylogeny ; *Mathematical Concepts ; *Models, Genetic ; Biological Evolution ; Evolution, Molecular ; }, abstract = {The evolutionary relationships between species are typically represented in the biological literature by rooted phylogenetic trees. However, a tree fails to capture ancestral reticulate processes, such as the formation of hybrid species or lateral gene transfer events between lineages, and so the history of life is more accurately described by a rooted phylogenetic network. Nevertheless, phylogenetic networks may be complex and difficult to interpret, so biologists sometimes prefer a tree that summarises the central tree-like trend of evolution. In this paper, we formally investigate methods for transforming an arbitrary phylogenetic network into a tree (on the same set of leaves) and ask which ones (if any) satisfy a simple consistency condition. This consistency condition states that if we add additional species into a phylogenetic network (without otherwise changing this original network) then transforming this enlarged network into a rooted phylogenetic tree induces the same tree on the original set of species as transforming the original network. We show that the LSA (lowest stable ancestor) tree method satisfies this consistency property, whereas several other commonly used methods (and a new one we introduce) do not. We also briefly consider transformations that convert arbitrary phylogenetic networks to another simpler class, namely normal networks.}, }
@article {pmid39750749, year = {2025}, author = {Molari, M and Shaw, LP and Neher, RA}, title = {Quantifying the Evolutionary Dynamics of Structure and Content in Closely Related E. coli Genomes.}, journal = {Molecular biology and evolution}, volume = {42}, number = {1}, pages = {}, pmid = {39750749}, issn = {1537-1719}, support = {/WT_/Wellcome Trust/United Kingdom ; //Sir Henry Wellcome Postdoctoral Fellow/ ; 220422/Z/20/Z//Wellcome/ ; //University of Basel/ ; }, mesh = {*Escherichia coli/genetics ; *Evolution, Molecular ; *Genome, Bacterial ; Phylogeny ; Synteny ; }, abstract = {Bacterial genomes primarily diversify via gain, loss, and rearrangement of genetic material in their flexible accessory genome. Yet the dynamics of accessory genome evolution are very poorly understood, in contrast to the core genome where diversification is readily described by mutations and homologous recombination. Here, we tackle this problem for the case of very closely related genomes. We comprehensively describe genome evolution within n=222 genomes of Escherichia coli ST131, which likely shared a common ancestor around 100 years ago. After removing putative recombinant diversity, the total length of the phylogeny is 6,000 core genome substitutions. Within this diversity, we find 22 modifications to core genome synteny and estimate around 2,000 structural changes within the accessory genome, i.e. one structural change for every three core genome substitutions. Sixty-three percent of loci with structural diversity could be resolved into individual gain and loss events with 10-fold more gains than losses, demonstrating a dominance of gains due to insertion sequences and prophage integration. Our results suggest the majority of synteny changes and insertions in our dataset are likely deleterious and only persist for a short time before being removed by purifying selection.}, }
@article {pmid39749146, year = {2024}, author = {Chaves, CRS and Salamandane, A and Vieira, EJF and Salamandane, C}, title = {Antibiotic Resistance in Fermented Foods Chain: Evaluating the Risks of Emergence of Enterococci as an Emerging Pathogen in Raw Milk Cheese.}, journal = {International journal of microbiology}, volume = {2024}, number = {}, pages = {2409270}, pmid = {39749146}, issn = {1687-918X}, abstract = {Fermented foods, particularly fermented dairy products, offer significant health benefits but also present serious concerns. Probiotic bacteria, such as lactic acid bacteria (LAB), found in these foods have been strongly linked to the selection and dissemination of antibiotic resistance genes (ARGs). This study aims to examine the potential risks associated with fermented foods, despite their importance in human nutrition, by analyzing the entire production chain from raw material acquisition to storage. Focusing on cheese production as a key fermented food, the study will investigate various aspects, including dairy farm management, milk acquisition, milk handling, and the application of good manufacturing practices (GMP) and good hygiene practices (GHP) in cheese production. The findings of this review highlight that ARGs found in LAB are similar to those observed in hygiene indicator bacteria like E. coli and pathogens like S. aureus. The deliberate use of antibiotics in dairy farms and the incorrect use of disinfectants in cheese factories contribute to the prevalence of antibiotic-resistant bacteria in cheeses. Cheese factories, with their high frequency of horizontal gene transfer, are environments where the microbiological diversity of raw milk can enhance ARG transfer. The interaction between the raw milk microbiota and other environmental microbiotas, facilitated by cross-contamination, increases metabolic communication between bacteria, further promoting ARG transfer. Understanding these bacterial and ARG interactions is crucial to ensure food safety for consumers.}, }
@article {pmid39747694, year = {2025}, author = {Hsu, TY and Nzabarushimana, E and Wong, D and Luo, C and Beiko, RG and Langille, M and Huttenhower, C and Nguyen, LH and Franzosa, EA}, title = {Profiling lateral gene transfer events in the human microbiome using WAAFLE.}, journal = {Nature microbiology}, volume = {10}, number = {1}, pages = {94-111}, pmid = {39747694}, issn = {2058-5276}, support = {R24DK110499//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; K23DK125838//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; T32CA009001//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; Career Development Award//Crohn's and Colitis Foundation (Crohn's &amp; Colitis Foundation)/ ; T32 CA009001/CA/NCI NIH HHS/United States ; U54DE023798//U.S. Department of Health &amp; Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; Research Scholars Award//American Gastroenterological Association (AGA)/ ; }, mesh = {Humans ; *Gene Transfer, Horizontal ; *Microbiota/genetics ; Phylogeny ; Metagenome/genetics ; Algorithms ; *Bacteria/genetics/classification ; Metagenomics/methods ; *Computational Biology/methods ; }, abstract = {Lateral gene transfer (LGT), also known as horizontal gene transfer, facilitates genomic diversification in microbial populations. While previous work has surveyed LGT in human-associated microbial isolate genomes, the landscape of LGT arising in personal microbiomes is not well understood, as there are no widely adopted methods to characterize LGT from complex communities. Here we developed, benchmarked and validated a computational algorithm (WAAFLE or Workflow to Annotate Assemblies and Find LGT Events) to profile LGT from assembled metagenomes. WAAFLE prioritizes specificity while maintaining high sensitivity for intergenus LGT. Applying WAAFLE to >2,000 human metagenomes from diverse body sites, we identified >100,000 high-confidence previously uncharacterized LGT (~2 per microbial genome-equivalent). These were enriched for mobile elements, as well as restriction-modification functions associated with the destruction of foreign DNA. LGT frequency was influenced by biogeography, phylogenetic similarity of involved pairs (for example, Fusobacterium periodonticum and F. nucleatum) and donor abundance. These forces manifest as networks in which hub taxa donate unequally with phylogenetic neighbours. Our findings suggest that human microbiome LGT may be more ubiquitous than previously described.}, }
@article {pmid39742307, year = {2024}, author = {Lian, ZH and Salam, N and Tan, S and Yuan, Y and Li, MM and Li, YX and Liu, ZT and Hu, CJ and Lv, AP and OuYang, YT and Lu, CY and Zhang, JY and Chen, Y and Chen, LB and Luo, ZH and Ma, B and Hua, ZS and Jiao, JY and Li, WJ and Liu, L}, title = {Metagenomic analysis sheds light on the mixotrophic lifestyle of bacterial phylum Zhuqueibacterota.}, journal = {iMeta}, volume = {3}, number = {6}, pages = {e249}, pmid = {39742307}, issn = {2770-596X}, abstract = {Zhuqueibacterota is a novel bacterial phylum proposed based on hot spring metagenomes and public metagenome-assembled genomes, classified within the Fibrobacterota-Chlorobiota-Bacteroidota superphylum. This globally distributed phylum consists of one class and five orders, with the majority of its members being facultative anaerobes. Notably, the order Zhuqueibacterales utilizes hydrogen as an electron donor for carbon fixation through the Calvin Benson Bassham cycle. Phylogenetic and metabolic analyses reveal the phylum's key role in the carbon cycle, with frequent horizontal gene transfer events influencing its evolutionary trajectory.}, }
@article {pmid39740178, year = {2024}, author = {Zahir, A and Okorie, PA and Nwobasi, VN and David, EI and Nwankwegu, RO and Azi, F}, title = {Harnessing Microbial Signal Transduction Systems in Natural and Synthetic Consortia for Biotechnological Applications.}, journal = {Biotechnology and applied biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1002/bab.2707}, pmid = {39740178}, issn = {1470-8744}, abstract = {Signal transduction is crucial for communication and cellular response in microbial communities. Consortia rely on it for effective communication, responding to changing environmental conditions, establishing community structures, and performing collective behaviors. Microbial signal transduction can be through quorum sensing (QS), two-component signal transduction systems, biofilm formation, nutrient sensing, chemotaxis, horizontal gene transfer stress response, and so forth. The consortium uses small signaling molecules in QS to regulate gene expression and coordinate intercellular communication and behaviors. Biofilm formation allows cells to adhere and aggregate, promoting species interactions and environmental stress resistance. Chemotaxis enables directional movement toward or away from chemical gradients, promoting efficient resource utilization and community organization within the consortium. In recent years, synthetic microbial consortia have gained attention for their potential applications in biotechnology and bioremediation. Understanding signal transduction in natural and synthetic microbial consortia is important for gaining insights into community dynamics, evolution, and ecological function. It can provide strategies for biotechnological innovation for enhancing biosensors, biodegradation, bioenergy efficiency, and waste reduction. This review provides compelling insight that will advance our understanding of microbial signal transduction dynamics and its role in orchestrating microbial interactions, which facilitate coordination, cooperation, gene expression, resource allocation, and trigger specific responses that determine community success.}, }
@article {pmid39737801, year = {2024}, author = {Singh, S and Selvakumar, S and Swaminathan, P}, title = {In silico targeting of AmpC beta-lactamases in Enterobacter cloacae: unveiling Piperenol B as a potent antimicrobial lead.}, journal = {Journal of biomolecular structure &amp; dynamics}, volume = {}, number = {}, pages = {1-18}, doi = {10.1080/07391102.2024.2446661}, pmid = {39737801}, issn = {1538-0254}, abstract = {Antimicrobial Resistance poses a major threat to human health worldwide. Microorganisms develop multi-drug resistance due to intrinsic factors, evolutionary chromosomal alterations, and horizontal gene transfer. Enterobacter cloacae, a common nosocomial bacterium, can cause various infections and is classified as multidrug-resistant. This species produces AmpC enzymes, serine beta-lactamases that hydrolyze beta-lactam antibiotics by cleaving their beta-lactam ring, contributing to its resistance. Traditionally, many phytoconstituents have been used for their antibacterial properties against microorganisms. This study explores phytocompounds to mitigate the effects of beta-lactamase enzymes. In this study, we selected 12592 phytoconstituents with antibacterial properties from Dr. Duke's Ethnobotanical and Phytochemical Database for the virtual screening process. Initial hits were selected based on highest docking scores and then filtered using the ADMET property. Among these, a promising compound Piperenol B showed the highest docking score of -9.1 kcal/mol. A 240 ns molecular dynamics simulation showed that Piperenol B maintained stable conformation and showed consistent results in multiple runs with AmpC protein. Piperenol B complex had a binding free energy score of -61.75 ± 8.0 kJ/mol, whereas the known AmpC inhibitor Clavulanic acid showed -46.64 ± 3.2 kJ/mol. Non-covalent contacts in protein-ligand interactions and specific subunit interfaces were examined using the Protein Contacts Atlas. The STRING database was used to construct the Protein-Protein interaction for AmpC and its interacting proteins. The findings of this study suggested that Piperenol B could be an effective inhibitor of the targeted AmpC protein in Enterobacter cloacae which requires validation in in vitro studies.}, }
@article {pmid39736215, year = {2025}, author = {Wang, Y and Ge, J and Xian, W and Tang, Z and Xue, B and Yu, J and Yao, YF and Liu, H and Qiu, J and Liu, X}, title = {Phosphorylation of the prokaryotic histone-like protein H-NS modulates bacterial virulence in Salmonella Typhimurium.}, journal = {Microbiological research}, volume = {292}, number = {}, pages = {128041}, doi = {10.1016/j.micres.2024.128041}, pmid = {39736215}, issn = {1618-0623}, mesh = {*Salmonella typhimurium/pathogenicity/genetics/metabolism ; Phosphorylation ; *Bacterial Proteins/metabolism/genetics ; Virulence/genetics ; Gene Expression Regulation, Bacterial ; *DNA-Binding Proteins/metabolism/genetics ; *Histones/metabolism ; Type III Secretion Systems/metabolism/genetics ; Humans ; Protein Processing, Post-Translational ; Salmonella Infections/microbiology ; }, abstract = {H-NS is a prokaryotic histone-like protein that binds to bacterial chromosomal DNA with important regulatory roles in gene expression. Unlike histone proteins, hitherto post-translational modifications of H-NS are still largely uncharacterized, especially in bacterial pathogens. Salmonella Typhimurium is a primary enteric pathogen and its virulence is mainly dependent on specialized type III secretion systems (T3SSs), which were evolutionarily acquired via horizontal gene transfer. Previous studies have shown that H-NS plays a critical role in silencing foreign T3SS genes. Here, we found that H-NS is phosphorylated at multiple residues in S. Typhimurium, including S45, Y61, S78, S84, T86, and T106. Notably, we demonstrated that phosphorylation of H-NS S78 promotes its dissociation from DNA via a mechanism dependent on dimer formation, thereby leading to transcriptional activation of target genes. Functionally, phosphoryl-H-NS contributes to the expression of T3SS-associated proteins and hence increases bacterial virulence during infection. Therefore, our study reveals a novel mechanism by which covalent modifications of prokaryotic histone-like proteins regulate bacterial virulence of an important human pathogen.}, }
@article {pmid39733752, year = {2025}, author = {Feng, B and Chen, J and Wang, C and Wang, P and You, G and Lin, J and Gao, H}, title = {Removal of ofloxacin and inhibition of antibiotic resistance gene spread during the aerobic biofilm treatment of rural domestic sewage through the micro-nano aeration technology.}, journal = {Journal of hazardous materials}, volume = {486}, number = {}, pages = {137020}, doi = {10.1016/j.jhazmat.2024.137020}, pmid = {39733752}, issn = {1873-3336}, mesh = {*Biofilms ; *Ofloxacin/isolation &amp; purification/metabolism ; *Anti-Bacterial Agents ; *Sewage/microbiology ; *Water Pollutants, Chemical/metabolism ; Aerobiosis ; Biodegradation, Environmental ; *Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; }, abstract = {Micro-nano aeration (MNA) has great potential for emerging contaminant removal. However, the mechanism of antibiotic removal and antibiotic resistance gene (ARG) spread, and the impact of the different aeration conditions remain unclear. This study investigated the adsorption and biodegradation of ofloxacin (OFL) and the spread of ARGs in aerobic biofilm systems under MNA and conventional aeration (CVA) conditions. Results showed that the MNA increased OFL removal by 17.27 %-40.54 % and decreased total ARG abundance by 36.37 %-54.98 %, compared with CVA. MNA-induced biofilm rough morphology, high zeta potential, and reduced extracellular polymeric substance (EPS) secretion enhanced OFL adsorption. High dissolved oxygen and temperature, induced by MNA-enriched aerobic bacteria and their carrying OFL-degrading genes, enhanced OFL biodegradation. MNA inhibited the enrichment of ARG host bacteria, which acquired ARGs possibly via horizontal gene transfer (HGT). Functional profiles involved in the HGT process, including reactive oxygen species production, membrane permeability, mobile genetic elements (MGEs), adenosine triphosphate synthesis, and EPS secretion, were down-regulated by MNA, inhibiting ARG spread. Partial least-squares path modeling revealed that MGEs might be the main factor inhibiting ARG spread. This study provides insights into the mechanisms by which MNA enhances antibiotic removal and inhibits ARG spread in aerobic biofilm systems.}, }
@article {pmid39733355, year = {2024}, author = {Kumar, G and Balakrishna, K and Mukhopadhyay, C and Kalwaje Eshwara, V}, title = {Characterization and comparative analysis of antimicrobial resistance in Escherichia coli from hospital and municipal wastewater treatment plants.}, journal = {Journal of water and health}, volume = {22}, number = {12}, pages = {2276-2288}, pmid = {39733355}, issn = {1477-8920}, support = {Intramural Fund//Manipal Academy of Higher Education/ ; }, mesh = {*Escherichia coli/drug effects/genetics/isolation &amp; purification ; *Wastewater/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Integrons ; Hospitals ; Drug Resistance, Bacterial ; Waste Disposal, Fluid ; }, abstract = {The spread of antimicrobial resistance (AMR) poses global health threats, with wastewater treatment plants (WWTPs) as hotspots for its development. Horizontal gene transfer facilitates acquisition of resistance genes, particularly through integrons in Escherichia coli. Our study investigates E. coli isolates from hospital and municipal WWTPs, focusing on integrons, their temporal correlation and phenotypic and molecular characterization of AMR. Samples from hospital and municipal WWTPs were collected over two seasons, pre-monsoon (March-May) and post-monsoon (December-February). From the hospital (hWWTP) and municipal (mWWTP) influents, 45 and 172 E. coli isolates were obtained, respectively. E. coli from hWWTP exhibited significantly higher resistance rates than mWWTP to most tested antimicrobials except tetracycline. The hWWTP isolates showed a higher prevalence (86.7%) of multidrug resistance (MDR) compared with mWWTP (48.3%). The proportion of MDR isolates from mWWTP nearly doubled in the post-monsoon season. Integron positivity was 17.7% (hWWTP) and 19.7% (mWWTP) with common gene cassettes conferring resistance to trimethoprim and aminoglycosides. Phylogroup analysis showed a predominance of group A in hWWTP and group B1 in mWWTP. The study highlights the role of hospital and municipal wastewater in disseminating AMR, with high rates of MDR E. coli and class 1 integrons detected.}, }
@article {pmid39731890, year = {2025}, author = {Zhang, Y and Zhu, D and Zhou, S and Gong, H and Dai, X}, title = {Antibiotic resistome during two-stage partial nitritation/anammox process for sludge anaerobic digestion reject water treatment.}, journal = {Journal of hazardous materials}, volume = {486}, number = {}, pages = {136967}, doi = {10.1016/j.jhazmat.2024.136967}, pmid = {39731890}, issn = {1873-3336}, mesh = {*Sewage/microbiology ; Anaerobiosis ; *Drug Resistance, Microbial/genetics ; *Water Purification/methods ; *Waste Disposal, Fluid/methods ; Genes, Bacterial ; Bioreactors ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Anaerobic digestion (AD) reject water serves as a significant reservoir for antibiotic resistance genes (ARGs), underscoring the importance of understanding ARGs dynamics during treatment processes. Partial nitritation /anammox (PN/A) has become an increasingly adopted process, while comprehensive investigation on ARG behavior within this system, especially in full-scale, remains limited. This study explores the distribution of ARGs in a full-scale two-stage PN/A system, with an anaerobic/anoxic/oxic (AAO) system for comparison. The sludge in partial nitritation (PN) stage exhibited higher ARG abundance (0.82 copy/cell) compared to that in anammox stage (0.21-0.26 copy/cell). In anammox sludge samples, 95.8-99.1 % of the mobile genetic elements (MGEs) were identified as tnpA, while the PN stage showing greater diversity. Some ARGs co-occur in the same contigs, and some of these ARGs belong to different ARGs types, which is related to multi-antibiotic resistance, with the highest frequency observed in the PN stage. The abundance of contigs with ARG-MGE co-occurrence, suggesting the possibility of horizontal gene transfer (HGT), was most prevalent in the AAO system. Potential ARG hosts were identified by metagenomic binning, and some functional bacteria, like Nitrosomonas, were regarded as ARGs host. This study offers a comprehensive analysis of the complexities of ARGs distribution within full-scale two-stage PN/A systems treating AD reject water.}, }
@article {pmid39731837, year = {2025}, author = {Yang, R and Tang, J and Niu, J and Hou, B and Zhang, L}, title = {Dissemination mechanisms of unique antibiotic resistance genes from flowback water to soil revealed by combined Illumina and Nanopore sequencing.}, journal = {Water research}, volume = {273}, number = {}, pages = {123030}, doi = {10.1016/j.watres.2024.123030}, pmid = {39731837}, issn = {1879-2448}, mesh = {*Soil Microbiology ; *Drug Resistance, Microbial/genetics ; Soil/chemistry ; Nanopore Sequencing ; }, abstract = {As a byproduct of shale gas extraction, flowback water (FW) is produced in large quantities globally. Due to the unique interactions between pollutants and microorganisms, FW always harbor multiple antibiotic resistance genes (ARGs) that have been confirmed in our previous findings, potentially serving as a point source for ARGs released into the environment. However, whether ARGs in FW can disseminate or integrate into the environmental resistome remains unclear. In this study, unique ARGs from FW were identified, and the ARG profiles in soil and FW-spiked soil were compared using a combination of Illumina and Nanopore sequencing. The results indicated that the total abundance of the soil resistome increased by 30.8 % in soil contaminated with FW. Of this increase, 11.1 % was attributable to the integration of exogenous ARGs from FW into the soil resistome. Sequence alignment at the gene level further confirmed the successful integration of 20 unique ARG sequences classified as multidrug and vancomycin resistance genes into the soil resistome. These 20 ARG sequences were detected only in the FW. Multiple lines of evidence indicated that horizontal gene transfer dominated ARG dissemination in soil contaminated by FW. This conclusion is supported by the discrepancy between changes in mobile ARGs and host abundance, the upregulation of oxidative stress-related genes (SOD1 and SOD2) and the SOS response (lexA and recA), as well as the upregulation of genes related to quorum sensing (virD4, virB9, and virB3) and naked DNA uptake (pilD, pilT, and pilQ).}, }
@article {pmid39731060, year = {2024}, author = {Shen, SP and Lin, HC and Chen, JF and Wang, HS and Huang, YY and Hsia, KC and Lin, JH and Kuo, YW and Li, CM and Hsu, YC and Tsai, SY and Ho, HH}, title = {Assessment of the safety and gut microbiota modulation ability of an infant formula containing Bifidobacterium animalis ssp. lactis CP-9 or Lactobacillus salivarius AP-32 and the effects of the formula on infant growth outcomes: insights from a four-month clinical study in infants under two months old.}, journal = {BMC pediatrics}, volume = {24}, number = {1}, pages = {840}, pmid = {39731060}, issn = {1471-2431}, mesh = {Humans ; *Infant Formula ; *Gastrointestinal Microbiome ; *Probiotics ; Infant ; Male ; Female ; *Bifidobacterium animalis ; *Ligilactobacillus salivarius ; Infant, Newborn ; Child Development ; Milk, Human/microbiology ; }, abstract = {BACKGROUND: Breast milk is a natural treasure for infants, and its microbiota contains a rich array of bacterial species. When breastfeeding is not possible, infant formula with probiotics can be used as a sole source or as a breast milk supplement. The main aim of this study was to evaluate the growth outcomes and tolerance of infants consuming an infant formula containing Bifidobacterium animalis ssp. lactis CP-9 (B. animalis CP-9) or Lactobacillus salivarius AP-32 (L. salivarius AP-32), which were isolated from breast milk and the guts of healthy infants. The safety of these strains in terms of antibiotic resistance and their ability to modulate the gut microbiota were also evaluated.<br><br>METHODS: One hundred eighty healthy infants were included in this study and separated into three groups: the control group, the L. salivarius AP-32 group, and the B. animalis CP-9 group. In this clinical study, adverse events, growth effects, and the incidence of allergies and gastrointestinal disorders in infants consuming infant formula containing B. animalis CP-9 or L. salivarius AP-32 were evaluated. Finally, the impact of the probiotic infant formula on the gut microbiota was elucidated via next-generation sequencing (NGS) analysis.<br><br>RESULTS: The 4-month interventional study revealed that body weight, recumbent length, and head circumference were similar among the three groups. No adverse events related to the intervention were observed. The microbiota composition was more diverse on day 0 and became more uniform by month 4. B. animalis CP-9 and L. salivarius AP-32 were found to be susceptible to streptomycin, tetracycline, erythromycin, clindamycin, chloramphenicol, and ampicillin.<br><br>CONCLUSIONS: The use of infant formula containing B. animalis CP-9 and L. salivarius AP-32 was considered safe and well tolerated, with no adverse events observed during the study. While these strains showed low antibiotic resistance and no immediate concerns related to antibiotic resistance genes, further research is needed to comprehensively assess their long-term safety and efficacy and the potential risk of horizontal gene transfer in broader contexts.<br><br>TRIAL REGISTRATION: The trial was registered with the US Library of Medicine (clinicaltrials.gov) with the number NCT03993301 on 20/06/2019.}, }
@article {pmid39730778, year = {2025}, author = {Cotta, SR and Dias, ACF and Mendes, R and Andreote, FD}, title = {Role of horizontal gene transfer and cooperation in rhizosphere microbiome assembly.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {56}, number = {1}, pages = {225-236}, pmid = {39730778}, issn = {1678-4405}, support = {2018/24049-2//Fapesp/ ; 485116/2013-8//CNPq/ ; 405163/2018-5//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {*Gene Transfer, Horizontal ; *Rhizosphere ; *Microbiota/genetics ; *Soil Microbiology ; *Bacteria/genetics/metabolism/classification ; }, abstract = {Microbes employ a variety of mechanisms, encompassing chemical signaling (e.g., quorum-sensing molecules) and genetic processes like horizontal gene transfer (HGT), to engage in interactions. HGT, in particular, holds a pivotal role as it facilitates the generation of metabolic diversity, thus directly or indirectly influencing microorganisms' interactions and functioning within their habitat. In this study, we investigate the correlations between enhanced metabolic diversity through HGT and cooperative behavior in the rhizosphere. Despite the potential drawbacks of cooperative behavior, which renders it susceptible to exploitation by cheaters based on evolutionary theory, HGT emerges as a mitigating factor. It serves as a valuable and adaptive tool for survival in competitive environments, notably the rhizosphere. By initiating a comprehensive discussion on these processes combined, we anticipate achieving a profound understanding of the rhizosphere microbiome, ultimately enhancing soil microbiology management and the exploitation of this ecological niche.}, }
@article {pmid39729844, year = {2025}, author = {Ku, H and Kelk, D and Bauer, DC and Sidhu, JPS}, title = {Phage-plasmid hybrids as vectors for antibiotic resistance in environmental Escherichia coli.}, journal = {The Science of the total environment}, volume = {959}, number = {}, pages = {178157}, doi = {10.1016/j.scitotenv.2024.178157}, pmid = {39729844}, issn = {1879-1026}, mesh = {*Escherichia coli/genetics/virology/drug effects ; *Plasmids/genetics ; *Bacteriophages/genetics ; Anti-Bacterial Agents ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Virulence Factors/genetics ; }, abstract = {This study investigated the potential role of phages in the dissemination of antimicrobial resistance genes (ARGs) and virulence factor genes (VFGs) in Escherichia coli (E. coli). A comprehensive in silico analysis of 18,410 phage sequences retrieved from the National Center for Biotechnology Information database (NCBI) revealed distinct carriage patterns for ARGs and VFGs between lytic, temperate, and chronic phage types. Notably, 57 temperate phages carried ARGs, particularly associated with multidrug and aminoglycoside resistance. Temperate phages (8.97 %, 635/7081) and chronic phages (8.09 %, 14/173) exhibited a significantly higher prevalence of VFGs (Chi-Square, p ≤ 0.05), particularly associated with exotoxin-related genes, compared to lytic phages (0.05 %, 6/11,156). This underscores the role phages play as reservoirs and potential vectors for the dissemination of ARGs and VFGs in bacteria. Our environmental E. coli isolates (n = 60) were found to carry 179 intact prophages containing polymyxin, macrolide, tetracycline, and multidrug resistance genes as well as various VFGs. This study documents the presence of phage-plasmids (P-Ps) in environmental E. coli isolates, offering new insights into horizontal gene transfer (HGT) mechanisms. Notably, the blaCTX-M-15 gene, associated with beta-lactam resistance, was identified in two P-Ps, suggesting a potentially novel route for the dissemination of beta-lactam resistance. The diverse replicon types observed in P-Ps suggest a broader integration capacity compared to traditional plasmids, potentially enabling the blaCTX-M-15 gene dissemination across diverse bacterial species. This study provides valuable insights into the multifaceted role of phages in shaping the antimicrobial resistance landscape. Further research is necessary to fully understand the intricate mechanisms underlying phage-mediated ARG and VFG dissemination.}, }
@article {pmid39729729, year = {2025}, author = {Wang, M and Yao, Y and Yang, Y and Zhu, D and Wang, M and Jia, R and Chen, S and Zhao, X and Yang, Q and Wu, Y and Zhang, S and Huang, J and Ou, X and Tian, B and Sun, D and Zhang, L and Yu, Y and He, Y and Wu, Z and Cheng, A and Liu, M}, title = {The characterization of outer membrane vesicles (OMVs) and their role in mediating antibiotic-resistance gene transfer through natural transformation in Riemerella anatipestifer.}, journal = {Poultry science}, volume = {104}, number = {2}, pages = {104730}, pmid = {39729729}, issn = {1525-3171}, mesh = {*Riemerella/genetics/drug effects/physiology ; *Gene Transfer, Horizontal ; Poultry Diseases/microbiology ; Animals ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Ducks ; Flavobacteriaceae Infections/veterinary/microbiology ; }, abstract = {Riemerella anatipestifer (R. anatipestifer, RA) is the etiological agent of duck serositis, an acute multisystemic disease in ducks that is globally distributed and causes serious economic losses in the duck industry. Despite exhibiting multidrug resistance, the transmission mechanism of its antibiotic resistance genes (ARGs) remains incompletely identified. To contribute to addressing this gap, in this study, outer membrane vesicles (OMVs) from the RA strain CH-1 were isolated and characterized to investigate their involvement in ARG transfer in RA. Sequencing and data analysis revealed that RA CH-1 OMVs had ∼2.04 Mb genomic size, representing 88.3 % of the RA CH-1 genomic length. Proteomic analysis showed that OMVs contained 577 proteins, representing 27.2 % of the bacterial proteins. Subsequent investigations demonstrated that OMVs from antibiotic-resistant strains transferred ARG fragments and plasmids to the sensitive strain RA ATCC11845, relying on the natural transformation system, and the transformants exhibited corresponding resistance. Overall, OMV-mediated horizontal transfer of ARGs serving as a significant mechanism for acquiring multiple resistance genes in R. anatipestifer.}, }
@article {pmid39729001, year = {2024}, author = {Elbir, H}, title = {Updating the Relationship Between the Threshold Value of Average Nucleotide Identity and Digital DNA-DNA Hybridization for Reliable Taxonomy of Corynebacterium.}, journal = {Veterinary sciences}, volume = {11}, number = {12}, pages = {}, pmid = {39729001}, issn = {2306-7381}, abstract = {Currently, bacterial classification at the species level relies on the 95-96% average nucleotide identity (ANI) value that is known to be equivalent to a 70% digital DNA-DNA hybridization (dDDH) value. However, during the routine identification of bacteria in the uteri of camels with a history of conception failure, we found that four out of the seven strains (2298A, 2569A, 2652, 2571B, 1103A, 2571A, and 335C) could not be assigned to any valid Corynebacterium species. Furthermore, a 70% dDDH value did not correspond to a 95-96% ANI value in strain 2569A. Thus, we aimed to classify these strains and explain the mechanisms underlying gene repertoire diversity and the disagreement we found between the ANI and dDDH cutoff values. For this study, we extracted information from the genomes of 150 Corynebacterium-type species and seven sequenced genomes of uterine Corynebacterium isolates. We found that the 96.67% OrthoANI value should be used in place of the generally accepted 95-96% ANI threshold in order to obtain an equivalent 70% dDDH value. Phylogenomic analysis determined the evolutionary position of each uterine strain. Then, strains 2652 and 2571B were classified as C. camporealensis based on the ANI value (98.44% and 98.72%) and dDDH value (85.8% and 88.5%). Strain 2569A had a 96.58% ANI and a 69.4% dDDH value and was classified as C. urogenitale. The strains 335C, 1103A, 2571A, and 2298A were classified as novel Corynebacterium based on the ANI value (77.12, 94.01%, 94.26%, and 94.03%) and dDDH value (21.3%, 54.1%, 54.9%, and 51.3%), respectively. Genes for menaquinone biosynthesis and the saturation of chains were detected in uterine strains and their closely related type strains. Gene gain predominates as a source of variation in the gene repertoire. Most of these genes are gained by horizontal gene transfer, driven by genomic islands and prophage. In summary, we refined the ANI cutoff value for an accurate diagnosis of Corynebacterium. Moreover, we clarified the mechanism underlying the diversity of the gene repertoire and expanded the number of Corynebacterium species isolated from the camel uterus.}, }
@article {pmid39727166, year = {2025}, author = {}, title = {Correction to 'GutMetaNet: an integrated database for exploring horizontal gene transfer and functional redundancy in the human gut microbiome'.}, journal = {Nucleic acids research}, volume = {53}, number = {1}, pages = {}, doi = {10.1093/nar/gkae1307}, pmid = {39727166}, issn = {1362-4962}, }
@article {pmid39727139, year = {2024}, author = {Wang, Q and Qiu, JH and Sun, Y and Ni, N and Sun, SJ and Li, XL and Yang, SJ and Liu, YR and Cui, YY}, title = {[Research progress on the effect of estuary microplastics on antibiotic resistance genes].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {35}, number = {10}, pages = {2916-2924}, doi = {10.13287/j.1001-9332.202410.028}, pmid = {39727139}, issn = {1001-9332}, mesh = {*Microplastics ; *Water Pollutants, Chemical/analysis ; *Estuaries ; Biofilms/drug effects/growth &amp; development ; Drug Resistance, Microbial/genetics ; Environmental Monitoring ; Gene Transfer, Horizontal ; }, abstract = {Estuaries are transitional zones between rivers and marine environments, with intensive human activities. Pollutants pose a threat to the ecological systems of estuaries. Among these pollutants, microplastics and antibiotic resistant genes have gained significant attention due to their potential impacts on estuarine organisms and human health. Microplastics can form unique biofilms, adsorb pollutants from the surrounding environment, and provide potential hosts for antibiotic resistant genes, with positive consequence on horizontal gene transfer of antibiotic resistance. We provided an overview of the pollution status of microplastics and antibiotic resistant genes in estua-rine areas, with a particular emphasis on the influence of biofilms formed on microplastics on the enrichment, transport, and transfer of antibiotic resistant genes. We also highlighted the limitations in current research, regarding microplastic sampling, analysis methods, and inconsistent reporting units. Furthermore, we proposed prospects for the biodegradation of microplastics and potential risk assessment of microplastic biofilms.}, }
@article {pmid39725890, year = {2024}, author = {Javier-López, R and Geliashvili, N and Birkeland, NK}, title = {Comparative genomics of Fervidobacterium: a new phylogenomic landscape of these wide-spread thermophilic anaerobes.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1248}, pmid = {39725890}, issn = {1471-2164}, support = {328955//Norges Forskningsr&#xe5;d/ ; 328955//Norges Forskningsr&#xe5;d/ ; 862555//ERA-NET Cofund on Food Systems and Climate (FOSC)/ ; 862555//ERA-NET Cofund on Food Systems and Climate (FOSC)/ ; 862555//ERA-NET Cofund on Food Systems and Climate (FOSC)/ ; CPEA-LT-2017/10061//Norwegian Directorate for Higher Education and Skills/ ; CPEA-LT-2017/10061//Norwegian Directorate for Higher Education and Skills/ ; }, mesh = {*Phylogeny ; *Genome, Bacterial ; *Genomics ; RNA, Ribosomal, 16S/genetics ; Base Composition ; }, abstract = {BACKGROUND: Fervidobacterium is a genus of thermophilic anaerobic Gram-negative rod-shaped bacteria belonging to the phylum Thermotogota. They can grow through fermentation on a wide range of sugars and protein-rich substrates. Some can also break down feather keratin, which has significant biotechnological potential. Fervidobacteria genomes have undergone several horizontal gene transfer events, sharing DNA with unrelated microbial taxa. Despite increasing biotechnological and evolutionary interest in this genus, only seven species have been described to date. Here, we present and describe six new and complete Fervidobacterium genomes, including the type strains Fervidobacterium gondwanense CBS-1[ T], F. islandicum H-21[ T] and F. thailandense FC2004[T], one novel isolate from Georgia (strain GSH) and two strains (DSM 21710 and DSM 13770) that have not been previously described along with an evolutionary and phylogenomic analysis of the genus.<br><br>RESULTS: The complete genomes were around 2&#xa0;Mb with approximately 2,000 CDS identified and annotated in each of them and a G&#x2009;+&#x2009;C content ranging from 38.9&#xa0;mol% to 45.8&#xa0;mol%. Phylogenomic comparisons of all currently available Fervidobacterium genomes, including OrthoANI and TYGS analyses, as well as a phylogenetic analysis based on the 16S rRNA gene, identified six species and nine subspecies clusters across the genus, with a consistent topology and a distant and separately branching species, Fervidobacterium thailandense. F. thailandense harbored the highest number of transposases, CRISPR clusters, pseudo genes and horizontally transferred regions The pan genome of the genus showed that 44% of the genes belong to the cloud pangenome, with most of the singletons found also in F. thailandense.<br><br>CONCLUSIONS: The additional genome sequences described in this work and the comparison with all available Fervidobacterium genome sequences provided new insights into the evolutionary history of this genus and supported a phylogenetic reclassification. The phylogenomic results from OrthoANI and TYGS analyses revealed that F. riparium and F. gondwanense belong to the same genome species, and includes Fervidobacterium sp. 13770, while "F. pennivorans" strain DYC belongs to a separate genome species, whereas Fervidobacterium sp. 21710 and Fervidobacterium sp. GSH within the Fervidobacterium pennivorans clade represent two subspecies. F. changbaicum is reclassified as F. islandicum.}, }
@article {pmid39725200, year = {2025}, author = {Song, M and Wang, K and Xie, Y and Wen, X and Tu, Y and Teng, T and Luo, C and Zhang, D}, title = {Impacts of anthropogenic disturbances on antibiotic resistomes in biological soil crusts on the Qinghai-Tibetan Plateau.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {367}, number = {}, pages = {125582}, doi = {10.1016/j.envpol.2024.125582}, pmid = {39725200}, issn = {1873-6424}, mesh = {*Soil Microbiology ; Tibet ; *Environmental Monitoring ; *Anti-Bacterial Agents ; *Drug Resistance, Microbial/genetics ; *Anthropogenic Effects ; Soil/chemistry ; China ; Humans ; }, abstract = {Biological soil crusts (BSCs) are the main landscape on the Qinghai-Tibetan Plateau and an ecological indicator of human disturbance. Information about antibiotic resistomes in BSCs on the Qinghai-Tibetan Plateau can provide baseline for the risk assessment and management of resistomes and yet to be explored. This work investigated the profiles and geographic patterns of antibiotic resistomes in BSCs along the Lhasa River and their response to anthropogenic activities for the first time. Various antibiotic resistance genes (ARGs) were widely distributed in BSCs, but had relatively lower detection frequency and abundance comparing to soils from human disturbed sites. ARGs profiles in BSCs were separated by altitude from 3860 to 3880 m, possibly attributing to the difference in anthropogenic activities. Above 3860 m, resistomes exhibited lower abundance including total ARGs, aadA, blaSFO and tnpA-04 owing to the rare human activities; at human disturbed sites with altitude <3860 m, the detection frequency and relative abundance of tetG02, oprJ, qacEdelta1-01, and ARGs with the mechanism of efflux pump were higher and viewed as potential indicators of human activities. Anthropogenic activities potentially promoted the horizontal gene transfer of ARGs in BSCs at human disturbed sites from co-occurrence network analysis. Our findings provided fundamental information of antibiotic resistomes in BSCs on the Qinghai-Tibetan Plateau, and unraveled possible mechanisms of human disturbance in shaping antibiotic resistomes.}, }
@article {pmid39724227, year = {2024}, author = {Shahid, U and Hooi, SL and Lim, SY and Mohd Aris, A and Khor, BC and Ayub, Q and Tan, HS}, title = {Metagenomic surveillance of microbial community and antibiotic resistant genes associated with Malaysian wastewater during the COVID-19 pandemic.}, journal = {Current genetics}, volume = {71}, number = {1}, pages = {1}, pmid = {39724227}, issn = {1432-0983}, mesh = {*Wastewater/microbiology ; *COVID-19/epidemiology ; Malaysia/epidemiology ; *Metagenomics/methods ; *SARS-CoV-2/genetics ; Humans ; Drug Resistance, Microbial/genetics ; Pandemics ; Microbiota/genetics ; Metagenome ; Bacteria/genetics/classification/drug effects ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; }, abstract = {Wastewater is a reservoir of pathogens and hotspots for disseminating antibiotic resistance genes across species. The metagenomic surveillance of wastewater provides insight into the native microbial community, antibiotic-resistance genes (ARGs) and mobile genetic elements. t. The COVID-19 pandemic has caused wider dissemination of ARGs and resistant bacteria in wastewater. Although immensely significant, no research has been performed on the Malaysian wastewater microbial community and ARGs or their correlation with COVID-19 infections. This study utilised a 16S metagenomics approach to characterise the microbial community in Malaysian wastewater during high and low-case phases of the pandemic. Bacteria belonging to Bacteriodales, Bacillales, Actinomycetales and opportunistic pathogens-Arcobacters, Flavobacteria, and Campylobacterales, Neisseriales, were enriched during higher COVID-19 pandemic (active cases). Additionally, copy number profiling of ARGs in water samples showed the prevalence of elements conferring resistance to antibiotics like sulphonamides, cephalosporins, and colistin. The high prevalence of intI1 and other ion-based transporters in samples highlights an extensive risk of horizontal gene transfer to previously susceptible species. Our study emphasises the importance of wastewater surveillance in understanding microbial community dynamics and ARG dissemination, particularly during public health crises like the COVID-19 pandemic.}, }
@article {pmid39724170, year = {2025}, author = {Farrell, AA and Nesbø, CL and Zhaxybayeva, O}, title = {Bacterial Growth Temperature as a Horizontally Acquired Polygenic Trait.}, journal = {Genome biology and evolution}, volume = {17}, number = {1}, pages = {}, pmid = {39724170}, issn = {1759-6653}, support = {//Dartmouth Fellowship/ ; }, mesh = {*Gene Transfer, Horizontal ; *Bacteria/genetics/classification ; *Temperature ; *Multifactorial Inheritance ; Phylogeny ; Evolution, Molecular ; Genome, Bacterial ; Adaptation, Physiological/genetics ; }, abstract = {Evolutionary events leading to organismal preference for a specific growth temperature, as well as genes whose products are needed for a proper function at that temperature, are poorly understood. Using 64 bacteria from phylum Thermotogota as a model system, we examined how optimal growth temperature changed throughout Thermotogota history. We inferred that Thermotogota's last common ancestor was a thermophile and that some Thermotogota evolved the mesophilic and hyperthermophilic lifestyles secondarily. By modeling gain and loss of genes throughout Thermotogota history and by reconstructing their phylogenies, we demonstrated that adaptations to lower and higher growth temperature involve both the acquisition of necessary genes and loss of unnecessary genes. Via a pangenome-wide association study, we correlated presence/absence of 68 genes with specific optimal growth temperature intervals. While some of these genes are poorly characterized, most are involved in metabolism of amino acids, nucleotides, carbohydrates, and lipids, as well as in signal transduction and regulation of transcription. Most of the 68 genes have a history of horizontal gene transfer with other bacteria and archaea that often grow at similar temperatures, suggesting that parallel acquisitions of genes likely promote independent adaptations of different Thermotogota species to specific growth temperatures.}, }
@article {pmid39723821, year = {2025}, author = {Sanchez, VA and Renner, T and Baker, LJ and Hendry, TA}, title = {Genome evolution following an ecological shift in nectar-dwelling Acinetobacter.}, journal = {mSphere}, volume = {10}, number = {1}, pages = {e0101024}, pmid = {39723821}, issn = {2379-5042}, mesh = {*Acinetobacter/genetics/classification ; *Genome, Bacterial ; *Plant Nectar/metabolism ; Phylogeny ; *Evolution, Molecular ; Ecosystem ; Gene Transfer, Horizontal ; }, abstract = {UNLABELLED: The bacterial genus Acinetobacter includes species found in environmental habitats like soil and water, as well as taxa adapted to be host-associated or pathogenic. High genetic diversity may allow for this habitat flexibility, but the specific genes underlying switches between habitats are poorly understood. One lineage of Acinetobacter has undergone a substantial habitat change by evolving from a presumed soil-dwelling ancestral state to thrive in floral nectar. Here, we compared the genomes of floral-dwelling and pollinator-associated Acinetobacter, including newly described species, with genomes from relatives found in other environments to determine the genomic changes associated with this ecological shift. Following one evolutionary origin of floral nectar adaptation, nectar-dwelling Acinetobacter taxa have undergone reduction in genome size compared with relatives and have experienced dynamic gene gains and losses as they diversified. Gene content changes suggest a shift to metabolism of monosaccharides rather than diverse carbohydrates, and scavenging of nitrogen sources, which we predict to be beneficial in nectar environments. Gene gains appear to result from duplication events, evolutionary divergence, and horizontal gene transfer. Most notably, nectar-dwelling Acinetobacter acquired the ability to degrade pectin from plant pathogens, and the genes underlying this ability have duplicated and are under selection within the clade. We hypothesize that this ability was a key trait for adaptation to floral nectar, as it could improve access to nutrients in the nutritionally unbalanced habitat of nectar. These results identify the genomic changes and traits coinciding with a dramatic habitat switch from soil to floral nectar.<br><br>IMPORTANCE: Many bacteria, including the genus Acinetobacter, commonly evolve to exploit new habitats. However, the genetic changes that underlie habitat switches are often unknown. Floral nectar is home to specialized microbes that can grow in this nutritionally unbalanced habitat. Several specialized Acinetobacter species evolved from soil-dwelling relatives to become common and abundant in floral nectar. Here, we investigate the genomic adaptations required to successfully colonize a novel habitat like floral nectar. We performed comparative genomics analyses between nectar-dwelling Acinetobacter and Acinetobacter species from other environments, like soil and water. We find that although gene loss coincided with the switch to living in nectar, gains of specific genes from other bacteria may have been particularly important for this ecological change. Acinetobacter living in nectar gained genes for degrading pectin, a plant polysaccharide, which may improve access to nutrients in their environment. These findings shed light on how evolutionary novelty evolves in bacteria.}, }
@article {pmid39721637, year = {2025}, author = {Zhou, JZ and Sun, QN and Li, A and Wang, XJ and Zhao, JF}, title = {[Simultaneous Removal of Antibiotic-resistant Bacteria, Genes, and Inhibition of Horizontal Transfer using Vis-rGO-CNCF-enhanced Peroxymonosulfate Activation Process].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {46}, number = {1}, pages = {305-317}, doi = {10.13227/j.hjkx.202401171}, pmid = {39721637}, issn = {0250-3301}, mesh = {*Graphite/chemistry ; *Drug Resistance, Bacterial/genetics ; Peroxides/chemistry ; Copper/chemistry ; Gene Transfer, Horizontal ; Ferric Compounds/chemistry ; Anti-Bacterial Agents/pharmacology/chemistry ; Water Purification/methods ; Bacteria/genetics/drug effects ; Oxidation-Reduction ; Drug Resistance, Microbial/genetics ; }, abstract = {As emerging contaminants, antibiotic-resistant bacteria （ARBs） and antibiotic-resistant genes （ARGs） pose a serious threat to human health and ecological security. Here, a reduced graphene oxide and g-C3N4 co-doped copper ferrite （rGO-CNCF） were synthesized. The composite material was characterized using XRD, FTIR, XPS, SEM-EDS, TEM, and DRS analysis methods, and a visible-light-assisted rGO-CNCF-activated PMS system was constructed for the removal of ARB and ARGs in water. The results showed that the complete inactivation of 8.01 log SA-ARB could be achieved within 30 min when the catalyst dosage was 0.2 g·L[-1], The PMS dosage was 0.3 g·L[-1], and the initial pH value of the solution was 7.0. The Vis-rGO-CNCF/PMS system was able to effectively reduce the horizontal transfer of SA-ARGs, and this system had a good destructive ability for intracellular and extracellular SA-ARGs. The destruction ability of the advanced oxidation process for the two pollutants together, SMT and SA-ARB, was maintained at a high level. This system could destroy the cell membrane structure of resistant bacteria, causing cell fragmentation, and quenching experiments showed that singlet oxygen （[1]O2） played a major role in the system. This study can provide a promising method for controlling ARB and ARG pollution in water and controlling the horizontal transfer of ARGs.}, }
@article {pmid39719706, year = {2025}, author = {Zhang, AN and Gaston, JM and Cárdenas, P and Zhao, S and Gu, X and Alm, EJ}, title = {CRISPR-Cas spacer acquisition is a rare event in human gut microbiome.}, journal = {Cell genomics}, volume = {5}, number = {1}, pages = {100725}, pmid = {39719706}, issn = {2666-979X}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *CRISPR-Cas Systems/genetics ; Gene Transfer, Horizontal/genetics ; Bacteriophages/genetics ; Bifidobacterium longum/genetics ; Metagenome/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Genome, Bacterial/genetics ; }, abstract = {Host-parasite relationships drive the evolution of both parties. In microbe-phage dynamics, CRISPR functions as an adaptive defense mechanism, updating immunity via spacer acquisition. Here, we investigated these interactions within the human gut microbiome, uncovering low frequencies of spacer acquisition at an average rate of one spacer every ∼2.9 point mutations using isolates' whole genomes and ∼2.7 years using metagenome time series. We identified a highly prevalent CRISPR array in Bifidobacterium longum spreading via horizontal gene transfer (HGT), with six spacers found in various genomic regions in 15 persons from the United States and Europe. These spacers, targeting two prominent Bifidobacterium phages, comprised 76% of spacer occurrence of all spacers targeting these phages in all B. longum populations. This result suggests that HGT of an entire CRISPR-Cas system introduced three times more spacers than local CRISPR-Cas acquisition in B. longum. Overall, our findings identified key ecological and evolutionary factors in prokaryote adaptive immunity.}, }
@article {pmid39718247, year = {2025}, author = {Santos, PKF and de Souza Araujo, N and Françoso, E and Werren, JH and Kapheim, KM and Arias, MC}, title = {The genome of the solitary bee Tetrapedia diversipes (Hymenoptera, Apidae).}, journal = {G3 (Bethesda, Md.)}, volume = {15}, number = {2}, pages = {}, pmid = {39718247}, issn = {2160-1836}, support = {001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 306932/2016-4//CNPq - Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 2013/12530-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (FAPESP)/ ; DEB1257053//USNSF/ ; }, mesh = {Animals ; Bees/genetics/microbiology ; *Genome, Insect ; Genomics/methods ; Molecular Sequence Annotation ; Phylogeny ; Gene Transfer, Horizontal ; Wolbachia/genetics ; DNA Transposable Elements ; }, abstract = {Tetrapedia diversipes is a Neotropical solitary bee commonly found in trap-nests, known for its morphological adaptations for floral oil collection and prepupal diapause during the cold and dry season. Here, we present the genome assembly of T. diversipes (332 Mbp), comprising 2,575 scaffolds, with 15,028 predicted protein-coding genes. Repetitive elements constitute 38.68% of the genome, notably Class II transposable elements. An investigation into lateral gene transfers identified a low frequency (0.037%) of nuclear copies of mitochondrial DNA and 18 candidate regions from bacterial origins. Furthermore, the annotation of 3 scaffolds reveals the presence of the Wolbachia endosymbiont genome, confirming the infection by 2 strains in T. diversipes populations. This genome contributes valuable insights into Neotropical bee genomics, offering a resource for comparative studies and enhancing our understanding of the molecular basis of solitary bee adaptations and interactions.}, }
@article {pmid39717269, year = {2024}, author = {Zhang, S and Shu, Y and Yang, Z and Zhong, Z and Wang, M and Jia, R and Chen, S and Liu, M and Zhu, D and Zhao, X and Wu, Y and Yang, Q and Huang, J and Ou, X and Sun, D and Tian, B and Wu, Z and He, Y and Cheng, A}, title = {Decoding the enigma: unveiling the transmission characteristics of waterfowl-associated bla NDM-5-positive Escherichia coli in select regions of China.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1501594}, pmid = {39717269}, issn = {1664-302X}, abstract = {Escherichia coli (E. coli) serves as a critical indicator microorganism for assessing the prevalence and dissemination of antibiotic resistance, notably harboring various antibiotic-resistant genes (ARGs). Among these, the emergence of the bla NDM gene represents a significant threat to public health, especially since carbapenem antibiotics are vital for treating severe infections caused by Gram-negative bacteria. This study aimed to characterize the antibiotic resistance features of bla NDM-5-positive E. coli strains isolated from waterfowl in several regions of China and elucidate the dissemination patterns of the bla NDM-5 gene. We successfully isolated 103 bla NDM-5-positive E. coli strains from 431 intestinal fecal samples obtained from waterfowl across five provincial-level units in China, with all strains exhibiting multidrug resistance (MDR). Notably, the bla NDM-5 gene was identified on plasmids, which facilitate efficient and stable horizontal gene transfer (HGT). Our adaptability assays indicated that while the bla NDM-5-positive plasmid imposed a fitness cost on the host bacteria, the NDM-5 protein was successfully induced and purified, exhibiting significant enzymatic activity. One strain, designated DY51, exhibited a minimum inhibitory concentration (MIC) for imipenem of 4 mg/L, which escalated to 512 mg/L following exposure to increasing imipenem doses. This altered strain demonstrated stable resistance to imipenem alongside improved adaptability, correlating with elevated relative expression levels of the bla NDM-5 and overexpression of efflux pumps. Collectively, this study highlights the horizontal dissemination of the bla NDM-5 plasmid among E. coli strains, confirms the associated fitness costs, and provides insights into the mechanisms underlying the stable increase in antibiotic resistance to imipenem. These findings offer a theoretical framework for understanding the dissemination dynamics of bla NDM-5 in E. coli, which is essential for developing effective strategies to combat carbapenem antibiotic resistance.}, }
@article {pmid39716502, year = {2025}, author = {Zheng, J and Li, YY and Lu, YS and Wang, D and Liu, C and Peng, HL and Shi, CH and Xie, KZ and Zhang, K and Sun, LL and Zhou, CM and Gu, WJ}, title = {Impact of different continuous fertilizations on the antibiotic resistome associated with a subtropical triple-cropping system over one decade.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {367}, number = {}, pages = {125564}, doi = {10.1016/j.envpol.2024.125564}, pmid = {39716502}, issn = {1873-6424}, mesh = {*Fertilizers ; *Soil Microbiology ; *Agriculture/methods ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents ; Soil/chemistry ; Manure ; Chickens ; Animals ; Zea mays ; Crops, Agricultural ; }, abstract = {The prevalence of antibiotic resistance genes (ARGs) in agricultural soils has garnered significant attention. However, the long-term impacts of various nitroge (N)-substitution fertilization regimes on the distribution of soil ARGs and their dominant drivers in a subtropical triple-cropping system remain largely unexplored. This study employed a metagenomic approach to analyze soil ARGs, microbial communities, mobile genetic elements (MGEs), and viruses from a maize-maize-cabbage rotation field experiment with five different fertilization regimes. Soil samples were collected in 2012 and 2021. A total of 615 unique ARG subtypes were identified, with multidrug, bacitracin, and rifamycin resistance genes being the most abundant. Notably, ARG types. the continuous application of fresh chicken manure (CM) over 10 years significantly increased both the count of unique ARG subtypes and the total ARG abundance compared to other fertilization regimes, such as inorganic fertilizer and composted chicken manure. Specifically, the abundance of genes associated with antibiotic target replacement (e.g., sul1 and sul2) in the CM-treated soil rose by 8.83-fold from 2021 to 2012. Our random forest analysis revealed that the abundance of three MGEs (QacEdelta, plasmids, and IstB), two viral families (Myoviridae and Podoviridae), two bacterial phyla (Chloroflexi and Planctomycetes), and two environmental factors (pH and soil organic matter (SOM)) significantly influenced the distribution of ARGs. Furthermore, variance decomposition analysis underscored the critical roles of the three MGEs and the two viral families in the dissemination of ARGs, suggesting that horizontal gene transfer (HGT) may play a key role in ARG spread. These findings enhance our understanding of how different fertilization practices influence ARG dissemination in subtropical triple-cropping agroecosystems over the long term and provide valuable insights for optimizing fertilization management strategies.}, }
@article {pmid39710145, year = {2025}, author = {Tavares, RDS and Tacão, M and Henriques, I}, title = {Integrons are key players in the spread of beta-lactamase-encoding genes.}, journal = {International journal of antimicrobial agents}, volume = {65}, number = {3}, pages = {107421}, doi = {10.1016/j.ijantimicag.2024.107421}, pmid = {39710145}, issn = {1872-7913}, mesh = {*Integrons/genetics ; *beta-Lactamases/genetics ; Humans ; *Bacteria/genetics/drug effects/enzymology ; Anti-Bacterial Agents/pharmacology ; beta-Lactam Resistance/genetics ; *Gene Transfer, Horizontal ; }, abstract = {Integrons mediate the acquisition and expression of gene cassettes (GCs). The production of beta-lactamases (BLs) is the most relevant mechanism of beta-lactams resistance. To explore the role of integrons in BL genes dissemination, sequences and metadata were retrieved from the INTEGRALL database and a literature review performed. Integrons (mostly class 1) carrying ≥1 BL-encoding genes (n = 1981) were detected in 37 bacterial genera and encoded BLs from 18 families. A total of 159 BL-encoding gene cassettes (BLGCs) were identified, representing all Ambler classes, with blaOXA-, blaVIM- and blaIMP-carrying integrons the most prevalent. blaGES, blaBEL and most metallo-BLs were exclusively associated with integrons. BL genes from 13 families were identified as genes captured by ISCR1 in complex integrons (n = 234), namely blaNDM, blaCTX-M and blaTEM. Frequently co-detected GCs encoded resistance to all major classes of antibiotics, namely aminoglycosides, phenicols and trimethoprim. Most BLGCs encoded resistance to carbapenems (n = 90) and Pseudomonas aeruginosa was the most frequent host. Most bla-carrying integrons were from clinical contexts and wastewater was the richest environmental compartment. The frequent association of BLs and integrons indicates a significant role in dissemination of beta-lactams resistance. Considering that integrons are (i) low-cost structures often associated with other mobile elements, and (ii) often carry multiple GCs (interchangeable according to environmental stimuli), the association of BL genes with integrons should always be considered a risk factor for the spread of beta-lactam resistance when performing surveillance and epidemiological studies. Further studies monitoring prevalence and diversity of integrons, particularly across non-clinical environments, will draw a more comprehensive picture of integron-associated dissemination of beta-lactams resistance.}, }
@article {pmid39708795, year = {2025}, author = {Tarnopol, RL and Tamsil, JA and Cinege, G and Ha, JH and Verster, KI and Ábrahám, E and Magyar, LB and Kim, BY and Bernstein, SL and Lipinszki, Z and Andó, I and Whiteman, NK}, title = {Experimental horizontal transfer of phage-derived genes to Drosophila confers innate immunity to parasitoids.}, journal = {Current biology : CB}, volume = {35}, number = {3}, pages = {514-529.e7}, pmid = {39708795}, issn = {1879-0445}, support = {R35 GM119816/GM/NIGMS NIH HHS/United States ; T32 GM132022/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Gene Transfer, Horizontal ; *Immunity, Innate/genetics ; *Wasps/physiology ; *Drosophila melanogaster/genetics/immunology/parasitology ; *Bacteriophages/genetics ; }, abstract = {Metazoan parasites have played a major role in shaping innate immunity in animals. Insect hosts and parasitoid wasps are excellent models for illuminating how animal innate immune systems have evolved to neutralize these enemies. One such strategy relies on symbioses between insects and intracellular bacteria that express phage-encoded toxins. In some cases, the genes that encode these toxins have been horizontally transferred to the genomes of the insects. Here, we used genome editing in Drosophila melanogaster to recapitulate the evolution of two toxin genes-cytolethal distending toxin B (cdtB) and apoptosis inducing protein of 56kDa (aip56)-that were horizontally transferred likely from phages of endosymbiotic bacteria to insects millions of years ago. We found that a cdtB::aip56 fusion gene (fusionB), which is conserved in D. ananassae subgroup species, dramatically promoted fly survival and suppressed parasitoid wasp development when heterologously expressed in D. melanogaster immune tissues. We found that FusionB was a functional nuclease and was secreted into the host hemolymph where it targeted the parasitoid embryo's serosal tissue. Although the mechanism of toxicity remains unknown, when expressed ubiquitously, fusionB resulted in delayed development of late-stage fly larvae and eventually killed pupating flies. These results point to the salience of regulatory constraint in mitigating autoimmunity during the domestication process following horizontal transfer. Our findings demonstrate how horizontal gene transfer can instantly provide new, potent innate immune modules in animals.}, }
@article {pmid39708598, year = {2025}, author = {Sun, D and Shi, X and Shen, Y and Liu, Y and Luo, S and Jin, Y and Zhai, W and Liu, L and Deng, Z and Sun, C and Liu, D and Yang, X and Xie, Y and Krüger-Haker, H and Wu, C and Schwarz, S and Shen, J and Chen, Y and Ma, S and Wang, Y}, title = {Comparative efficacy of anaerobic digestion systems in removing antimicrobial resistance genes from swine wastewater.}, journal = {Journal of hazardous materials}, volume = {485}, number = {}, pages = {136868}, doi = {10.1016/j.jhazmat.2024.136868}, pmid = {39708598}, issn = {1873-3336}, mesh = {Animals ; *Wastewater/microbiology ; Swine ; Anaerobiosis ; *Waste Disposal, Fluid/methods ; Bioreactors ; *Genes, Bacterial ; Anti-Bacterial Agents ; *Drug Resistance, Microbial/genetics ; Sewage/microbiology ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Swine farm wastewater is a major reservoir of antimicrobial resistance genes (ARGs). Anaerobic digestion (AD), widely implemented in farms, has been extensively studied for ARG removal. However, a comparative study on ARG removal efficiency across the four principal AD systems - up-flow anaerobic sludge blanket (UASB), continuous stirred tank reactor (CSTR), buried biogas digester (BBD), and septic tank (SPT) - is lacking. Herein, we employed metagenomic sequencing, ultra-performance liquid chromatography-tandem mass spectrometry, as well as atomic absorption spectrometry/atomic fluorescence spectrophotometry, and revealed that UASB and CSTR achieved higher removal efficiencies for both ARGs (67% and 57%) and antibiotic residues (100% and 90%) compared to BBD and SPT. Acinetobacter, Escherichia, Pseudomonas and Streptococcus were the primary ARG hosts, comprising over 65% of the total abundance in influent samples. UASB and CSTR systems demonstrated superior removal efficiencies for both mobile genetic elements (MGEs) and antibiotic residues, both of which had essential impacts on ARG profiles. In addition, heavy metals might contribute to variation in ARGs through horizontal gene transfer. Collectively, the variation in microbial communities and better removal of both MGEs and antibiotic residues contribute to the remarkable ARG removal efficiency of UASB and CSTR, therefore, advocating for the widespread adoption of these two AD systems in swine farms.}, }
@article {pmid39706477, year = {2025}, author = {Bientz, L and Guyet, U and Guiraud, J and Metifiot, M and Moulieras, M and Aillerie, S and Coulange-Mayonnove, L and Boureima-Abdou, B and Groppi, A and Nikolski, M and Bébéar, C and Pereyre, S and Dubois, V}, title = {Mobilization of an ICEclc-Like Element as a Potential Mechanism for the Spread of IMP-13 Carbapenemase in Pseudomonas aeruginosa.}, journal = {Journal of global antimicrobial resistance}, volume = {41}, number = {}, pages = {44-51}, doi = {10.1016/j.jgar.2024.12.006}, pmid = {39706477}, issn = {2213-7173}, mesh = {*Pseudomonas aeruginosa/genetics/drug effects/enzymology/isolation &amp; purification ; *beta-Lactamases/genetics ; *Bacterial Proteins/genetics ; Humans ; Anti-Bacterial Agents/pharmacology ; Pseudomonas Infections/microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Microbial Sensitivity Tests ; Retrospective Studies ; *Interspersed Repetitive Sequences ; Carbapenems/pharmacology ; }, abstract = {Carbapenem-resistant Pseudomonas aeruginosa is a global public health concern. IMP-13 is a carbapenemase that was described for the first time in 2001 but is often underestimated due to poor hydrolysis of carbapenems and a lack of molecular detection. The aim of this study was to characterize the genetic support of blaIMP-13 in P. aeruginosa and to assess the ability of mobile genetic elements to disseminate this resistance. A retrospective analysis conducted between 2010 and 2020 revealed eight multiresistant P. aeruginosa isolates by their production of the carbapenemase IMP-13 in Bordeaux. Additionally, three of the studied isolates exhibited high-level resistance to imipenem and imipenem-relebactam that was linked to an insertion sequence in the oprD gene. Successful mating was achieved, and transconjugants and parental clinical isolate genomes were sequenced. All clinical isolates were found to be ST621 strains. The data revealed that blaIMP-13 was carried on an Integrative and Conjugative Element (ICEclc-like) of 88,589 bp with a 62% GC content harboring 85 CDSs, and was inserted at the tRNA[Gly] locus PA0729.1. The ICE was identical in the eight studied clinical isolates and in all the ST621 strains found in the databases. The conjugation rate was low, at approximately 10[-8] transconjugants per donor and ICE transfer appeared to mobilize some adjacent parental genes located immediately downstream of the ICE. In conclusion, these results suggest that even if the spread of blaIMP-13 is mainly due to an epidemic ST621 clone, the mobilization of a blaIMP-13-carrying ICEclc-like element is possible and should not be underestimated.}, }
@article {pmid39706021, year = {2025}, author = {Dinesh, R and Sreena, CP and Sheeja, TE and Srinivasan, V and Subila, KP and Sona, C and Kumar, IPV and Anusree, M and Alagupalamuthirsolai, M and Jayarajan, K and Sajith, V}, title = {Co-resistance is the dominant mechanism of co-selection and dissemination of antibiotic resistome in nano zinc oxide polluted soil.}, journal = {Journal of hazardous materials}, volume = {485}, number = {}, pages = {136885}, doi = {10.1016/j.jhazmat.2024.136885}, pmid = {39706021}, issn = {1873-3336}, mesh = {*Zinc Oxide/toxicity ; *Soil Pollutants/toxicity ; Soil Microbiology ; *Anti-Bacterial Agents/pharmacology ; *Metal Nanoparticles/toxicity ; Genes, Bacterial ; Bacteria/genetics/drug effects ; *Drug Resistance, Microbial/genetics ; Microbiota/drug effects ; Gene Transfer, Horizontal ; *Drug Resistance, Bacterial/genetics ; }, abstract = {The broader soil bacterial community responses at ecotoxicologically relevant levels of nano ZnO (nZnO) focussing on co-selection of antibiotic resistance (AR) were investigated. nZnO imposed a stronger influence than the bulk counterpart (bZnO) on antibiotic resistance genes (ARGs) with multidrug resistance (MDR) systems being predominant (63 % of total ARGs). Proliferation of biomarker ARGs especially for last resort antibiotic like vancomycin was observed and Streptomyces hosted multiple ARGs. nZnO was the major driver of the resistome with efflux systems dominating the AR mechanism. Environmental risk associated with nZnO was mediated through metal driven co-selection of ARGs and their probable transfer to eukaryotic hosts through horizontal gene transfer (HGT) via mobile genetic elements (MGEs). Novel resistance genes tetA, mdtA, int and tnpA validated in our study can be used as biomarkers for rapid detection of nZnO toxicity in soils. qRT-PCR validation of resistome in the rhizosphere soil microbiome of turmeric indicated that Zn levels decreased by 16 % compared to bulk soil with 80 % bioaccumulation in rhizomes at 1000 mg Zn kg[-1] and subsequent down regulation of ARGs. Expression of key biosynthetic genes for curcumin in turmeric rhizomes showed an increase up to 500 mg Zn kg[-1] as nZnO. Validation of co-selection phenomenon in microcosm with 10 mg kg[-1] tetracycline without added Zn indicated 20 % upregulation of Zn resistance genes (ZRGs) like czcA, yiip and zntA.}, }
@article {pmid39699696, year = {2024}, author = {Yagisawa, F and Fujiwara, T and Yamashita, S and Hirooka, S and Tamashiro, K and Izumi, J and Kanesaki, Y and Onuma, R and Misumi, O and Nakamura, S and Yoshikawa, H and Kuroiwa, H and Kuroiwa, T and Miyagishima, SY}, title = {A fusion protein of polyphosphate kinase 1 (PPK1) and a Nudix hydrolase is involved in inorganic polyphosphate accumulation in the unicellular red alga Cyanidioschyzon merolae.}, journal = {Plant molecular biology}, volume = {115}, number = {1}, pages = {9}, pmid = {39699696}, issn = {1573-5028}, support = {22K06299//Japan Society for the Promotion of Science/ ; 22K06396//Japan Society for the Promotion of Science/ ; 22K15166//Japan Society for the Promotion of Science/ ; 22H02657//Japan Society for the Promotion of Science/ ; 24H00579//Japan Society for the Promotion of Science/ ; JPMJMI22E1//JST-Mirai Program/ ; NIG-JOINT 68A2024//National Institute of Genetics/ ; S1311017//Ministry of Education, Culture, Sports, Science and Technology/ ; Spatiotemporal Genomics Project//University of the Ryukyus/ ; Researcher exchange promotion program//Research Organization of Information and Systems/ ; }, mesh = {*Rhodophyta/genetics/enzymology/metabolism ; *Polyphosphates/metabolism ; *Phosphotransferases (Phosphate Group Acceptor)/metabolism/genetics ; *Phylogeny ; *Nudix Hydrolases ; Pyrophosphatases/metabolism/genetics ; Recombinant Fusion Proteins/metabolism/genetics ; }, abstract = {Inorganic polyphosphate (polyP) is a linear polymer of phosphate that plays various roles in cells, including in phosphate and metal homeostasis. Homologs of the vacuolar transporter chaperone 4 (VTC4), catalyzing polyP synthesis in many eukaryotes, are absent in red algae, which are among the earliest divergent plant lineages. We identified homologs of polyphosphate kinase 1 (PPK1), a conserved polyP synthase in bacteria, in 42 eukaryotic genomes, including 31 species detected in this study and 12 species of red algae. Phylogenetic analysis suggested that most eukaryotic PPK1 homologs originated from horizontal gene transfer from a prokaryote to a plant before the divergence of red algae and Viridiplantae. In red algae, the homologs were fused to a nucleoside diphosphate-linked moiety X (Nudix) hydrolase of the diphosphoinositol polyphosphate phosphohydrolase (DIPP) family. We characterized the fusion protein CmPPK1 in the unicellular red alga Cyanidioschyzon merolae, which has been used in studies on basic features of eukaryotes. In the knockout strain ∆CmPPK1, polyP was undetectable, suggesting a primary role for CmPPK1 in polyP synthesis. In addition, ∆CmPPK1 showed altered metal balance. Mutations in the catalytically important residues of the Nudix hydrolase domain (NHD) either increased or decreased polyP contents. Both high and low polyP NHD mutants were susceptible to phosphate deprivation, indicating that adequate NHD function is necessary for normal phosphate starvation responses. The results reveal the unique features of PPK1 in red algae and promote further investigation of polyP metabolism and functions in red algae and eukaryotic evolution.}, }
@article {pmid39696916, year = {2025}, author = {Prabhu, C and Satyaprasad, AU and Deekshit, VK}, title = {Understanding Bacterial Resistance to Heavy Metals and Nanoparticles: Mechanisms, Implications, and Challenges.}, journal = {Journal of basic microbiology}, volume = {65}, number = {2}, pages = {e2400596}, doi = {10.1002/jobm.202400596}, pmid = {39696916}, issn = {1521-4028}, support = {//This work was funded by the Indian Council of Medical Research (grant no. AMR/DHR/GIA/3/ECD-II/2020)./ ; }, mesh = {*Metals, Heavy/pharmacology ; *Nanoparticles ; *Bacteria/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology ; Humans ; *Drug Resistance, Bacterial ; Drug Resistance, Multiple, Bacterial ; }, abstract = {Antimicrobial resistance is a global health problem as it contributes to high mortality rates in several infectious diseases. To address this issue, engineered nanoparticles/nano-formulations of antibiotics have emerged as a promising strategy. Nanoparticles are typically defined as materials with dimensions up to 100 nm and are made of different materials such as inorganic particles, lipids, polymers, etc. They are widely dispersed in the environment through various consumer products, and their clinical applications are diverse, ranging from contrast agents in imaging to carriers for gene and drug delivery. Nanoparticles can also act as antimicrobial agents either on their own or in combination with traditional antibiotics to produce synergistic effects, earning them the label of "next-generation therapeutics." They have also shown great effectiveness against multidrug-resistant pathogens responsible for nosocomial infections. However, overexposure or prolonged exposure to sublethal doses of nanoparticles can promote the development of resistance in human pathogens. The resistance can arise from various factors such as genetic mutation, horizontal gene transfer, production of reactive oxygen species, changes in the outer membrane of bacteria, efflux-induced resistance, cross-resistance from intrinsic antibiotic resistance determinants, plasmid-mediated resistance, and many more. Continuous exposure to nanoparticles can also transform an antibiotic-susceptible bacterial pathogen into multidrug resistance. Considering all these, the current review focuses on the mode of action of different heavy metals and nanoparticles and possible mechanisms through which bacteria attain resistance towards these heavy metals and nanoparticles.}, }
@article {pmid39696539, year = {2024}, author = {Pianezza, R and Haider, A and Kofler, R}, title = {GenomeDelta: detecting recent transposable element invasions without repeat library.}, journal = {Genome biology}, volume = {25}, number = {1}, pages = {315}, pmid = {39696539}, issn = {1474-760X}, support = {P35093//Austrian Science Fund (FWF)/ ; }, mesh = {*DNA Transposable Elements ; Animals ; *Drosophila melanogaster/genetics ; Software ; Ascomycota/genetics ; Gene Library ; }, abstract = {We present GenomeDelta, a novel tool for identifying sample-specific sequences, such as recent transposable element (TE) invasions, without requiring a repeat library. GenomeDelta compares high-quality assemblies with short-read data to detect sequences absent from the short reads. It is applicable to both model and non-model organisms and can identify recent TE invasions, spatially heterogeneous sequences, viral insertions, and hotizontal gene transfers. GenomeDelta was validated with simulated and real data and used to discover three recent TE invasions in Drosophila melanogaster and a novel TE with geographic variation in Zymoseptoria tritici.}, }
@article {pmid39695425, year = {2024}, author = {Yu, L and Zhao, Y and Zhang, S and Ni, W and Zhang, L and Xue, C and Wang, P and Zhang, X}, title = {Antimicrobial resistance and virulence factors analysis of a multidrug-resistant Acinetobacter baumannii isolated from chickens using whole-genome sequencing.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {526}, pmid = {39695425}, issn = {1471-2180}, support = {32202810//National Natural Science Foundation of China/ ; ZR2022QC115//Natural Science Foundation of Shandong Province/ ; }, mesh = {Animals ; *Chickens/microbiology ; *Acinetobacter baumannii/genetics/drug effects/pathogenicity/isolation &amp; purification ; *Virulence Factors/genetics ; *Drug Resistance, Multiple, Bacterial/genetics ; *Whole Genome Sequencing ; *Acinetobacter Infections/microbiology/veterinary ; *Genome, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; *Poultry Diseases/microbiology ; Microbial Sensitivity Tests ; Virulence/genetics ; Plasmids/genetics ; }, abstract = {Multidrug-resistant (MDR) Acinetobacter baumannii (A. baumannii) is currently recognized not only as a significant nosocomial pathogen but also is an emerging bacterial infection in food-producing animals, posing a critical threat to global health. However, this is a hindrance to detailed bioinformatic studies of MDR A. baumannii of chicken origin due to the lack of its complete genome sequence. Here, we report whole-genome sequencing analysis of MDR A. baumannii Y03 isolated from chickens. The Y03 genome consists of 1 circular chromosome and 4 circular plasmids, The Y03 chromosome harbors 41 antimicrobial resistance genes conferring resistance to major classes of antibiotics, including β-lactams, phenicols, macrolides, lincosamides, aminoglycosides, and nitrofurans, as well as 135 virulence factors involved in effector delivery system, immune modulation, adherence, stress survival, biofilm, exotoxin, and nutritional/metabolic factor. The in vivo infection experiments certificated that Y03 was virulent to chickens. Meanwhile, we used PCR amplification method to detect 10 antimicrobial resistance genes including abeM, adeB, adeH, adeK, blaapmC, blaOXA-90, catB9, macB, folP, and parE, as well as 14 virulence genes including lpxC, pilO, fimT, ompA, basA, bauA, gspL, csu, pgaC, plc2, tssA, tviB, bap, and vgrG. Whole-genome sequencing analysis revealed that Y03 contained 46 horizontal gene transfer elements, including 11 genomic islands, 30 transposons, and 5 prophages, as well as 518 mutations associated with reduced virulence and 44 mutations resulting in loss of pathogenicity. Furthermore, there were 22 antibiotic targets and 28 lethal mutations on the Y03 chromosome that could be used as potential targets to prevent, control, and treat infections caused by MDR A. baumannii Y03. Therefore, this study contributes to the development of strategies for the prevention, control, and treatment of A. baumannii infections and their spread in chickens.}, }
@article {pmid39694196, year = {2025}, author = {Panigrahi, M and Rajawat, D and Nayak, SS and Jain, K and Nayak, A and Rajput, AS and Sharma, A and Dutt, T}, title = {A comprehensive review on genomic insights and advanced technologies for mastitis prevention in dairy animals.}, journal = {Microbial pathogenesis}, volume = {199}, number = {}, pages = {107233}, doi = {10.1016/j.micpath.2024.107233}, pmid = {39694196}, issn = {1096-1208}, mesh = {Animals ; *Mastitis, Bovine/prevention &amp; control/genetics ; *Genomics/methods ; Female ; Cattle ; *Dairying/methods ; Milk ; Proteomics ; }, abstract = {Mastitis is a multi-etiological disease that significantly impacts milk production and reproductive efficiency. It is highly prevalent in dairy populations subjected to intensive selection for higher milk yield and where inbreeding is common. The issue is amplified by climate change and poor hygiene management, making disease control challenging. Key obstacles include antibiotic resistance, maximum residue levels, horizontal gene transfer, and limited success in breeding for resistance. Predictive genomics offers a promising solution for mastitis prevention by identifying genetic traits linked with susceptibility to mastitis. This review compiles the research and findings on genomics and its allied approaches, such as pan-genomics, epigenetics, proteomics, and transcriptomics, for diagnosing, understanding, and treating mastitis. In dairy production, artificial intelligence (AI), particularly deep learning (DL) techniques like convolutional neural networks (CNNs), has demonstrated significant potential to enhance milk production and improve farm profitability. It highlights the integration of advanced technologies like machine learning (ML), CRISPR, and pan-genomics to improve our knowledge of mastitis epidemiology, pathogen evolution, and the development of more effective diagnostic, preventive and therapeutic strategies for dairy herds. Genomic advancements provide critical insights into the complexities of mastitis, offering new avenues for understanding its dynamics. Integrating these findings with key predisposing factors can drive targeted prevention and more effective disease management.}, }
@article {pmid39693608, year = {2025}, author = {Laidlaw, A and Blondin-Brosseau, M and Shay, J and Dussault, F and Rao, M and Petronella, N and Tamber, S}, title = {Variation in plasmid conjugation among nontyphoidal Salmonella enterica serovars.}, journal = {Canadian journal of microbiology}, volume = {71}, number = {}, pages = {1-14}, doi = {10.1139/cjm-2024-0164}, pmid = {39693608}, issn = {1480-3275}, mesh = {*Plasmids/genetics ; *Salmonella enterica/genetics/drug effects/classification ; *Conjugation, Genetic ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Humans ; Serogroup ; Animals ; Salmonella Infections/microbiology ; }, abstract = {Conjugation is a complex phenomenon involving multiple plasmid, bacterial, and environmental factors. Here we describe an IncI1 plasmid encoding multidrug antibiotic resistance to aminoglycosides, sulfonamides, and third-generation cephalosporins. This plasmid is widespread geographically among animal, human, and environmental sectors. We present data on the transmissibility of this plasmid from Salmonella enterica ser. Kentucky into 40 strains of S. enterica (10 strains each from serovars Enteritidis, Heidelberg, Infantis, and Typhimurium). Thirty seven out of 40 strains were able to take up the plasmid. Rates of conjugation were variable between strains ranging from 10[-8] to 10[-4]. Overall, serovars Enteritidis and Typhimurium demonstrated the highest rates of conjugation, followed by Heidelberg, and then Infantis. No relationships were observed between the recipient cell surface and rate of conjugation. Recipient cell numbers correlated positively with conjugation rate and strains with high conjugation rates had marginally but significantly higher growth parameters compared to strains that took up the plasmid at lower frequencies. Environmental conditions known to impact cell growth, such as temperature, nutrient availability, and the presence of antibiotics, had a modulating effect on conjugation. Collectively, these results will further understanding of plasmid transmission dynamics in Salmonella, which is a critical first step towards the development of mitigation strategies.}, }
@article {pmid39692564, year = {2024}, author = {Sloan, DB and Broz, AK and Kuster, SA and Muthye, V and Peñafiel-Ayala, A and Marron, JR and Lavrov, DV and Brieba, LG}, title = {Expansion of the MutS gene family in plants.}, journal = {The Plant cell}, volume = {}, number = {}, pages = {}, doi = {10.1093/plcell/koae277}, pmid = {39692564}, issn = {1532-298X}, support = {R35 GM148134/GM/NIGMS NIH HHS/United States ; }, abstract = {The widely distributed MutS gene family functions in recombination, DNA repair, and protein translation. Multiple evolutionary processes have expanded this gene family in plants relative to other eukaryotes. Here, we investigate the origins and functions of these plant-specific genes. Cyanobacterial-like MutS1 and MutS2 genes were ancestrally gained via plastid endosymbiotic gene transfer. MutS1 was subsequently lost in seed plants, whereas MutS2 was duplicated in Viridiplantae (i.e., land plants and green algae). Viridiplantae also have two anciently duplicated copies of the eukaryotic MSH6 gene and acquired MSH1 via horizontal gene transfer - potentially from a nucleocytovirus. Despite sharing a name, "plant MSH1" is not directly related to the MSH1 gene in some fungi and animals, which may be an ancestral eukaryotic gene acquired via mitochondrial endosymbiosis and subsequently lost in most eukaryotes. There has been substantial progress in understanding the functions of plant MSH1 and MSH6 genes, but the cyanobacterial-like MutS1 and MutS2 genes remain uncharacterized. Known functions of bacterial homologs and predicted protein structures, including fusions to diverse nuclease domains, provide hypotheses about potential molecular mechanisms. Because most plant-specific MutS proteins are mitochondrial and/or plastid-targeted, the expansion of this family has played a large role in shaping plant organelle genetics.}, }
@article {pmid39690351, year = {2024}, author = {Ullah, H and Hassan, SHA and Yang, Q and Salama, ES and Liu, P and Li, X}, title = {Dynamic interaction of antibiotic resistance between plant microbiome and organic fertilizers: sources, dissemination, and health risks.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {41}, number = {1}, pages = {4}, pmid = {39690351}, issn = {1573-0972}, support = {lzujbky-2024-ey12//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Animals ; Humans ; Agriculture/methods ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/drug effects/genetics/classification ; Drug Resistance, Bacterial/drug effects/genetics ; *Fertilizers/analysis ; Gene Transfer, Horizontal ; *Manure/microbiology ; *Microbiota/drug effects ; *Plants/microbiology ; Sewage/microbiology ; Soil/chemistry ; *Soil Microbiology ; Wastewater/chemistry/microbiology ; }, abstract = {Antibiotic resistance is a global health problem driven by the irrational use of antibiotics in different areas (such as agriculture, animal farming, and human healthcare). Sub-lethal concentrations of antibiotic residues impose selective pressure on environmental, plant-associated, and human microbiome leading to the emergence of antibiotic-resistant bacteria (ARB). This review summarizes all sources of antibiotic resistance in agricultural soils (including manure, sewage sludge, wastewater, hospitals/pharmaceutical industry, and bioinoculants). The factors (such as the physicochemical properties of soil, root exudates, concentration of antibiotic exposure, and heavy metals) that facilitate the transmission of resistance in plant microbiomes are discussed. Potential solutions for effective measures and control of antibiotic resistance in the environment are also hypothesized. Manure exhibits the highest antibiotics load, followed by hospital and municipal WW. Chlortetracycline, tetracycline, and sulfadiazine have the highest concentrations in the manure. Antibiotic resistance from organic fertilizers is transmitted to the plant microbiome via horizontal gene transfer (HGT). Plant microbiomes serve as transmission routes of ARB and ARGS to humans. The ingestion of ARB leads to human health risks (such as ineffectiveness of medication, increased morbidity, and mortality).}, }
@article {pmid39689477, year = {2025}, author = {Li, S and Wang, K and Wang, D and Wang, H and Zhao, H and Pu, J and Wang, K and Li, C}, title = {Distribution and environmental dissemination of antibiotic resistance genes in poultry farms and surrounding ecosystems.}, journal = {Poultry science}, volume = {104}, number = {1}, pages = {104665}, pmid = {39689477}, issn = {1525-3171}, mesh = {Animals ; RNA, Ribosomal, 16S/analysis/genetics ; *Bacteria/genetics/drug effects/isolation &amp; purification ; Farms ; Soil Microbiology ; *Drug Resistance, Microbial/genetics ; *Ecosystem ; Anti-Bacterial Agents/pharmacology ; *Chickens ; Animal Husbandry ; Microbiota ; *Genes, Bacterial ; *Drug Resistance, Bacterial/genetics ; Cloaca/microbiology ; }, abstract = {Antibiotic resistance poses a significant threat to human and animal health worldwide, with farms serving as crucial reservoirs of Antibiotic Resistance Genes (ARGs) and Antibiotic-resistant bacteria. However, the distribution of ARGs in poultry farms and their transmission patterns in the environment remain poorly understood. This study collected samples of aerosol microorganisms, cloacal matter, soil, and vegetables from poultry farms and surrounding environments at three different distances. We used 16S rRNA gene sequencing and HT-qPCR to analyze the characteristics of aerosol microbial communities and the abundance of ARGs. At the phylum level, Proteobacteria, Firmicutes, and Bacteroidetes were dominant in cloacal samples, aerosol samples, and vegetable samples, while Proteobacteria Actinobacteriota and Acidobacteria dominated soil. Pseudomonas was dominant in cloacal samples at the genus level, whereas Fusobacterium was prevalent in soil. The diversity and richness of bacterial communities were more similar between cloacal samples than those observed between either sample type compared with soil. Our results showed that tetracycline and aminoglycoside ARG relative abundance was high across all sample types but significantly increased within feces/air compared to soils/vegetables. Association analysis revealed five potential host genera for ARG/MGE presence among various microbiota populations studied here. Our findings confirm that farms are important sources for the environmental dissemination of pathogens and ARGs.}, }
@article {pmid39688393, year = {2025}, author = {Lurie-Weinberger, MN and Bychenko-Banyas, D and Mor, M and Laviad-Shitrit, S and Kaplan, E and Rakovitsky, N and Keren-Paz, A and Ben-Zvi, C and Carmeli, Y}, title = {In vivo interspecies dissemination of IncM2-type blaNDM-1 carrying plasmid.}, journal = {Microbiology spectrum}, volume = {13}, number = {2}, pages = {e0039924}, pmid = {39688393}, issn = {2165-0497}, mesh = {*beta-Lactamases/genetics/metabolism ; *Plasmids/genetics ; *Klebsiella pneumoniae/genetics/drug effects/enzymology/isolation &amp; purification ; Humans ; *Escherichia coli/genetics/drug effects/enzymology/isolation &amp; purification ; Drug Resistance, Multiple, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Male ; Klebsiella Infections/microbiology ; Gene Transfer, Horizontal ; Female ; Microbial Sensitivity Tests ; Enterobacteriaceae Infections/microbiology ; Bacterial Proteins/genetics ; Middle Aged ; Aged ; }, abstract = {The gastrointestinal tract is a unique ecological niche with a high abundance of various Enterobacterales in close proximity. This allows the exchange of mobile genetic elements that carry resistance determinants. In the hospital setting, resistant organisms are prevalent and selective antibiotic pressure is high, providing a supportive platform for interspecies dissemination of resistance. Seven New Delhi metallo-beta-lactamase(NDM) positive and one NDM-negative bacteria were sent for WGS followed by bioinformatics analysis. Here, we describe three separate cases of patients simultaneously colonized by two NDM producing-species (Escherichia coli and Klebsiella pneumoniae), in which we documented interspecies dissemination of the blaNDM-1 by an 87,450 bp IncM2 type multi-drug resistance plasmid (here named pNCICAN_NDM-01_21-il). This plasmid was found to be highly conjugative. Our results underline the risk of interspecies horizontal plasmid dissemination. Such events may cause the emergence of high-risk clones, as well as lead to under-recognized multi-species outbreaks.IMPORTANCEConjugative, carbapenemase-carrying multidrug-resistant plasmids that can move between species of clinically relevant Enterobacterales pose a great risk to patients' health, especially when they spread inside a medical institution. Yet, most institutions monitor bacteria according to species and are at risk of missing plasmid-driven outbreaks. Thus, this work indicates that plasmid surveillance is an important tool for infection control.}, }
@article {pmid39686544, year = {2024}, author = {Stott, C and Diop, A and Raymann, K and Bobay, LM}, title = {Co-evolution and Gene Transfers Drive Speciation Patterns in Host-Associated Bacteria.}, journal = {Molecular biology and evolution}, volume = {41}, number = {12}, pages = {}, pmid = {39686544}, issn = {1537-1719}, support = {R01 GM132137/GM/NIGMS NIH HHS/United States ; DEB-2344788//National Science Foundation/ ; R01GM132137/NH/NIH HHS/United States ; DEB-1831730//National Science Foundation NSF/ ; }, mesh = {*Gene Transfer, Horizontal ; Animals ; Bees/microbiology/genetics ; *Genetic Speciation ; Bacteria/genetics ; Gastrointestinal Microbiome ; Host Microbial Interactions/genetics ; Symbiosis ; Homologous Recombination ; Evolution, Molecular ; }, abstract = {Microbial communities that maintain symbiotic relationships with animals evolve by adapting to the specific environmental niche provided by their host, yet understanding their patterns of speciation remains challenging. Whether bacterial speciation occurs primarily through allopatric or sympatric processes remains an open question. In addition, patterns of DNA transfers, which are pervasive in bacteria, are more constrained in a closed host-gut system. Eusocial bees have co-evolved with their specialized microbiota for over 85 million years, constituting a simple and valuable system to study the complex dynamics of host-associated microbial interactions. Here, we studied the patterns of speciation and evolution of seven specialized gut bacteria from three clades of eusocial bee species: western honey bees, eastern honey bees, and bumblebees. We conducted genomic analyses to infer species delineation relative to the patterns of homologous recombination (HR), and horizontal gene transfer (HGT). The studied bacteria presented various modes of evolution and speciation relative to their hosts, but some trends were consistent across all of them. We observed a clear interruption of HR between bacteria inhabiting different bee hosts, which is consistent with a mechanism of allopatric speciation, but we also identified interruptions of HR within hosts, suggesting recent or ongoing sympatric speciation. In contrast to HR, we observed that HGT events were not constrained by species borders. Overall, our findings show that in host-associated bacterial populations, patterns of HR and HGT have different impacts on speciation patterns, which are driven by both allopatric and sympatric speciation processes.}, }
@article {pmid39684674, year = {2024}, author = {Wiśniewski, P and Chajęcka-Wierzchowska, W and Zadernowska, A}, title = {High-Pressure Processing Influences Antibiotic Resistance Gene Transfer in Listeria monocytogenes Isolated from Food and Processing Environments.}, journal = {International journal of molecular sciences}, volume = {25}, number = {23}, pages = {}, pmid = {39684674}, issn = {1422-0067}, support = {2018/29/B/NZ9/00645 (OPUS-15)//National Science Center/ ; }, mesh = {*Listeria monocytogenes/genetics/drug effects ; *Food Microbiology ; *Anti-Bacterial Agents/pharmacology ; Food Handling/methods ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; Pressure ; Daucus carota/microbiology/genetics ; }, abstract = {The study aimed to assess the high-pressure processing (HPP) impact on antibiotic resistance gene transfer in L. monocytogenes from food and food processing environments, both in vitro (in microbiological medium) and in situ (in carrot juice), using the membrane filter method. Survival, recovery, and frequency of antibiotic resistance gene transfer analyses were performed by treating samples with HPP at different pressures (200 MPa and 400 MPa). The results showed that the higher pressure (400 MPa) had a significant effect on increasing the transfer frequency of genes such as fosX, encoding fosfomycin resistance, and tet_A1, tet_A3, tetC, responsible for tetracycline resistance, both in vitro and in situ. In contrast, the Lde gene (the gene encoding ciprofloxacin resistance) was not transferred under any conditions. In the food matrix (carrot juice), greater variability in results was observed, suggesting that food matrices may have a protective effect on bacteria and modify HPP efficacy. In general, an increase in MIC values for antibiotics was noted in transconjugants compared to donors. Genotypic analysis of transconjugants showed differences in genetic structure, especially after exposure to 400 MPa pressure, indicating genotypic changes induced by pressure stress. The study confirms the possibility of antibiotic resistance genes transfer in the food environment, even from strains showing initial susceptibility to antibiotics carrying so-called silent antibiotic resistance genes, highlighting the public health risk of the potential spread of antibiotic-resistant strains through the food chain. The findings suggest that high-pressure processing can increase and decrease the frequency of resistance gene transfer depending on the strain, antibiotic combination, and processing conditions.}, }
@article {pmid39671179, year = {2024}, author = {Chen, X and Urban, JM and Wurlitzer, J and Wei, X and Han, J and E O'Connor, S and Rudolf, JD and Köllner, TG and Chen, F}, title = {Canonical terpene synthases in arthropods: Intraphylum gene transfer.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {51}, pages = {e2413007121}, pmid = {39671179}, issn = {1091-6490}, mesh = {Animals ; *Alkyl and Aryl Transferases/genetics/metabolism ; *Gene Transfer, Horizontal ; *Arthropods/genetics/enzymology ; *Phylogeny ; Male ; Female ; Evolution, Molecular ; Terpenes/metabolism ; }, abstract = {Insects employ terpenoids for communication both within and between species. While terpene synthases derived from isoprenyl diphosphate synthase have been shown to catalyze terpenoid biosynthesis in some insects, canonical terpene synthases (TPS) commonly found in plants, fungi, and bacteria were previously unidentified in insects. This study reveals the presence of TPS genes in insects, likely originating via horizontal gene transfer from noninsect arthropods. By examining 361 insect genomes, we identified TPS genes in five species of the Sciaridae family (fungus gnats). Additionally, TPS genes were found in Collembola (springtails) and Acariformes (mites) among diverse noninsect arthropods. Selected TPS enzymes from Sciaridae, Collembola, and Acariformes display monoterpene, sesquiterpene, and/or diterpene synthase activities. Through comprehensive protein database search and phylogenetic analysis, the TPS genes in Sciaridae were found to be most closely related to those in Acariformes, suggesting transfer of TPS genes from Acariformes to Sciaridae. In the model Sciaridae Bradysia coprophila, all five TPS genes are most highly expressed in adult males, suggesting a sex- and developmental stage-specific role of their terpenoid products. The finding of TPS genes in insects and their possible evolutionary origin through intraphylum gene transfer within arthropods sheds light on metabolic innovation in insects.}, }
@article {pmid39670763, year = {2025}, author = {Dalia, TN and Dalia, AB}, title = {SbcB facilitates natural transformation in Vibrio cholerae in an exonuclease-independent manner.}, journal = {Journal of bacteriology}, volume = {207}, number = {1}, pages = {e0041924}, pmid = {39670763}, issn = {1098-5530}, support = {R35 GM128674/GM/NIGMS NIH HHS/United States ; R35GM128674//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, mesh = {*Vibrio cholerae/genetics/enzymology/metabolism ; *Bacterial Proteins/metabolism/genetics ; *Gene Transfer, Horizontal ; *Transformation, Bacterial ; *Exonucleases/metabolism/genetics ; Rec A Recombinases/metabolism/genetics ; }, abstract = {UNLABELLED: Natural transformation (NT) is a conserved mechanism of horizontal gene transfer in bacterial species. During this process, DNA is taken up into the cytoplasm where it can be integrated into the host genome by homologous recombination. We have previously shown that some cytoplasmic exonucleases inhibit NT by degrading ingested DNA prior to its successful recombination. However, one exonuclease, SbcB, counterintuitively promotes NT in Vibrio cholerae. Here, through a systematic analysis of the distinct steps of NT, we show that SbcB acts downstream of DNA uptake into the cytoplasm, but upstream of recombinational branch migration. Through mutational analysis, we show that SbcB promotes NT in a manner that does not rely on its exonuclease activity. Finally, we provide genetic evidence that SbcB directly interacts with the primary bacterial recombinase, RecA. Together, these data advance our molecular understanding of horizontal gene transfer in V. cholerae and reveal that SbcB promotes homologous recombination during NT in a manner that does not rely on its canonical exonuclease activity.<br><br>IMPORTANCE: Horizontal gene transfer by natural transformation contributes to the spread of antibiotic resistance and virulence factors in bacterial species. Here, we study how one protein, SbcB, helps facilitate this process in the facultative bacterial pathogen Vibrio cholerae. SbcB is a well-known for its exonuclease activity (i.e., the ability to degrade the ends of linear DNA). Through this study, we uncover that while SbcB is important for natural transformation, it does not facilitate this process using its exonuclease activity. Thus, this work helps further our understanding of the molecular events required for this conserved evolutionary process and uncovers a function for SbcB beyond its canonical exonuclease activity.}, }
@article {pmid39668116, year = {2025}, author = {Fagerquist, CK and Shi, Y and Park, J}, title = {Colicin Immunity Proteins of Pathogenic Bacteria Detected by Antibiotic-Induced SOS Response, Plasmid Sequencing, MALDI-TOF-TOF Mass Spectrometry, and Top-Down Proteomic Analysis.}, journal = {Rapid communications in mass spectrometry : RCM}, volume = {39}, number = {5}, pages = {e9964}, doi = {10.1002/rcm.9964}, pmid = {39668116}, issn = {1097-0231}, support = {ARS project number 0500-00093-001-00-D//USDA-ARS/ ; USDA-ARS project numbers: 2030-42000-055-000-D//USDA-ARS/ ; 0500-00093-001-00-D//USDA-ARS/ ; 2030-42000-055-000-D//USDA-ARS/ ; }, mesh = {*Colicins/genetics/chemistry ; *Proteomics/methods ; *Plasmids/genetics ; *Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; *Anti-Bacterial Agents/pharmacology ; *SOS Response, Genetics ; Escherichia coli Proteins/genetics ; Shiga-Toxigenic Escherichia coli/genetics ; Sequence Analysis, DNA ; }, abstract = {RATIONALE: Plasmids can play a major role in the survival of pathogenic bacteria. Plasmids are acquired through horizontal gene transfer resulting in their spread across various strains, species and genera of bacteria. Colicins are bacterial protein toxins expressed by plasmid genes and released against co-located bacterial competitors.<br><br>METHODS: Three Shiga toxin-producing E.&#x2009;coli (STEC), whose genomes were sequenced previously, were analyzed using a combination of antibiotic induction, MALDI-TOF-TOF mass spectrometry, top-down proteomic analysis, and small plasmid sequencing. Protein biomarkers were identified using in-house software that matches protein mass and fragment ions of backbone cleavage by the aspartic acid effect. Predicted in silico protein structures assisted in the interpretation of protein ion fragmentation.<br><br>RESULTS: In addition to proteomic identification of phage-encoded Shiga toxin, we were able to identify plasmid-encoded immunity proteins for colicin D and E3. The genes for these plasmid-encoded proteins were not found in the previous genomic sequencing. However, resequencing of these strains for small plasmids revealed the genes to be present on 7-8&#x2009;kb sized plasmids. Upstream of the colicin/immunity genes was an inverted repeat of the SOS/LexA box that represses gene expression until antibiotic challenge.<br><br>CONCLUSIONS: Our top-down proteomic method demonstrates that it is possible to screen putative pathogenic bacteria (whose genomes have been sequenced in full, in part or not at all) for the presence of phage- and plasmid-encoded toxin and colicin genes under SOS control. Small plasmid sequencing confirmed the presence of colicin/immunity genes (and their regulatory control) suggested from induction and top-down proteomic analysis.}, }
@article {pmid39667859, year = {2025}, author = {Pham, VD and Gerlinsky, M and Lettrari, S and Gänzle, MG}, title = {Evolution and ecology of C30 carotenoid synthesis in Lactobacillaceae and application of pigmented lactobacilli in pasta production.}, journal = {Food microbiology}, volume = {127}, number = {}, pages = {104688}, doi = {10.1016/j.fm.2024.104688}, pmid = {39667859}, issn = {1095-9998}, mesh = {*Carotenoids/metabolism ; *Fermentation ; *Phylogeny ; *Flour/microbiology/analysis ; Lactobacillaceae/metabolism/genetics/classification/isolation &amp; purification ; Triticum/microbiology ; Food Microbiology ; Pigmentation ; Bacterial Proteins/genetics/metabolism ; Color ; }, abstract = {Pasta is a staple food in many parts of the world. A bright yellow colour of pasta is preferred by consumers. However, the colour is easily degraded during pasta processing. In a sourdough used for pasta production, we identified the pigmented Fructilactobacillus spp. FUA 3913, which represents a novel species that remains to be described ,and carries genes for the carotenoid-producing enzymes CrtM and CrtN in its genome. HPLC and spectral analysis identified the carotenoid as 4,4'-diaponeurosporene which is also produced by other lactobacilli expressing CrtM and CrtN. The topology of the CrtM/N trees does not match the phylogeny of the organisms, indicating that the enzymes were acquired by horizontal gene transfer. Pigmentation is frequent in insect-associated lactobacilli and lactobacilli that are part of the phyllosphere. Pigmented heterofermentative lactobacilli may enhance the yellow colour of durum semolina pasta by two mechanisms, first, by producing carotenoids and second, by preventing lipoxygenase-mediated degradation of durum carotenoids during dough mixing and extrusion. The comparison of the influence of fermentation with the non-pigmented, homofermentative Lactiplantibacillus plantarum, the non-pigmented heterofermentative Fructilactobacillus sanfranciscensis and the pigmented, heterofermentative Fructilactobacillus spp. FUA3913 indicated that inhibition of lipid oxidation is more relevant for the colour of pasta. In summary, our study provides novel insights into the evolution of C30 carotenoid and ecology of lactobacilli, and documents the use of pigmented lactobacilli to enhance the yellow colour of fermented foods.}, }
@article {pmid39667662, year = {2025}, author = {Sandmann, G}, title = {Origin and evolution of yeast carotenoid pathways.}, journal = {Biochimica et biophysica acta. Molecular and cell biology of lipids}, volume = {1870}, number = {2}, pages = {159586}, doi = {10.1016/j.bbalip.2024.159586}, pmid = {39667662}, issn = {1879-2618}, mesh = {*Carotenoids/metabolism ; *Evolution, Molecular ; *Yeasts/metabolism/genetics ; }, abstract = {Carotenoid pathways exist in nature in all domains. Comparison of the genes involved and their distribution allowed the elucidation of the origin and evolution of carotenoid biosynthesis from an early common ancestor of prokaryotes to Bacteria and Archaea. From the latter domain, carotenogenic genes are inherited by fungi as the only phylum of Eukarya. Carotenoid biosynthesis in the algal-plant lineage emerged independently by endosymbiotic gene transfer from an engulfed carotenogenic cyanobacterium. The early set of carotenogenic genes included crtB of phytoene synthase, the desaturase gene crtI, and the lycopene cyclase gene crtYcd for the synthesis of β-carotene. This carotenoid is further metabolised either to zeaxanthin and retinal due to the presence of crtZ and ccd or elongated to a C50 carotenoids by the crtEb gene product. The diversified pathways, especially in bacteria and fungi, result from gene modifications altering the substrate and product specificities of the corresponding enzymes or from the acquisition of novel genes. This was highlighted in more detail for the carotenoid pathways in the red yeasts of Basidiomycota leading to torularhodin, 2'-plectaniaxanthin, and astaxanthin.}, }
@article {pmid39660924, year = {2025}, author = {Christel, S and Carrell, AA and Hochanadel, LH and Villalobos Solis, MI and Abraham, PE and Jawdy, SS and Chaves, JE and Engle, NL and Berhane, T-K and Yao, T and Chen, J-G and Muchero, W and Tschaplinski, TJ and Cregger, MA and Michener, JK}, title = {Catabolic pathway acquisition by rhizosphere bacteria readily enables growth with a root exudate component but does not affect root colonization.}, journal = {mBio}, volume = {16}, number = {1}, pages = {e0301624}, pmid = {39660924}, issn = {2150-7511}, support = {//U.S. Department of Energy (DOE)/ ; }, mesh = {*Rhizosphere ; *Plant Roots/microbiology ; *Gene Transfer, Horizontal ; *Pseudomonas/metabolism/genetics ; *Soil Microbiology ; Metabolic Networks and Pathways/genetics ; Benzyl Alcohols/metabolism ; Plant Exudates/metabolism ; }, abstract = {Horizontal gene transfer (HGT) is a fundamental evolutionary process that plays a key role in bacterial evolution. The likelihood of a successful transfer event is expected to depend on the precise balance of costs and benefits resulting from pathway acquisition. Most experimental analyses of HGT have focused on phenotypes that have large fitness benefits under appropriate selective conditions, such as antibiotic resistance. However, many examples of HGT involve phenotypes that are predicted to provide smaller benefits, such as the ability to catabolize additional carbon sources. We have experimentally simulated the consequences of one such HGT event in the laboratory, studying the effects of transferring a pathway for catabolism of the plant-derived aromatic compound salicyl alcohol between rhizosphere isolates from the Pseudomonas genus. We find that pathway acquisition enables rapid catabolism of salicyl alcohol with only minor disruptions to the existing metabolic and regulatory networks of the new host. However, this new catabolic potential does not confer a measurable fitness advantage during competitive growth in the rhizosphere. We conclude that the phenotype of salicyl alcohol catabolism is readily transferable but is selectively neutral under environmentally relevant conditions. We propose that this condition is common and that HGT of many pathways will be self-limiting because the selective benefits are small.IMPORTANCEHorizontal gene transfer (HGT) is a key process in microbial evolution, but the factors limiting HGT are poorly understood. Aside from the rather unique scenario of antibiotic resistance, the evolutionary benefits of pathway acquisition are still unclear. To experimentally test the effects of pathway acquisition, we transferred a pathway for catabolism of a plant-derived aromatic compound between soil bacteria isolated from the roots of poplar trees and determined the resulting phenotypic and fitness effects. We found that pathway acquisition allowed bacteria to grow using the plant-derived compound in the laboratory, but that this new phenotype did not provide an advantage when the bacteria were reinoculated onto plant roots. These results suggest that the benefits of pathway acquisition may be small when measured under ecologically-relevant conditions. From an engineering perspective, efforts to alter microbial community composition in situ by manipulating catabolic pathways or nutrient availability will be challenging when gaining access to a new niche does not provide a benefit.}, }
@article {pmid39660283, year = {2024}, author = {Fang, L and Chen, R and Li, C and Sun, J and Liu, R and Shen, Y and Guo, X}, title = {The association between the genetic structures of commonly incompatible plasmids in Gram-negative bacteria, their distribution and the resistance genes.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1472876}, pmid = {39660283}, issn = {2235-2988}, mesh = {*Plasmids/genetics ; *Gram-Negative Bacteria/genetics/drug effects ; *Gene Transfer, Horizontal ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Incompatible plasmids play a crucial role in the horizontal transfer of antibiotic resistance in bacteria, particularly in Gram-negative bacteria, and have thus attracted considerable attention in the field of microbiological research. In the 1970s, these plasmids, housing an array of resistance genes and genetic elements, were predominantly discovered. They exhibit a broad presence in diverse host bacteria, showcasing diversity in geographic distribution and the spectrum of antibiotic resistance genes. The complex genetic structure of plasmids further accelerates the accumulation of resistance genes in Gram-negative bacteria. This article offers a comprehensive review encompassing the discovery process, host distribution, geographic prevalence, carried resistance genes, and the genetic structure of different types incompatible plasmids, including IncA, IncC, IncF, IncL, IncM, IncH, and IncP. It serves as a valuable reference for enhancing our understanding of the role of these different types of plasmids in bacterial evolution and the dissemination of antibiotic resistance.}, }
@article {pmid39655960, year = {2025}, author = {Tian, Q and Ye, H and Zhou, X and Wang, J and Zhang, L and Sun, W and Duan, C and Fan, M and Zhou, W and Bi, C and Ye, Q and Wong, A}, title = {Evaluating the health risk of probiotic supplements from the perspective of antimicrobial resistance.}, journal = {Microbiology spectrum}, volume = {13}, number = {1}, pages = {e0001924}, pmid = {39655960}, issn = {2165-0497}, support = {SpF2021002//Wenzhou-Kean University Student Partnering with Faculty (SpF) research program/ ; SpF2021029//Wenzhou-Kean University Student Partnering with Faculty (SpF) research program/ ; }, mesh = {*Probiotics/administration &amp; dosage/pharmacology ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Dietary Supplements ; Drug Resistance, Bacterial/genetics ; Streptomycin/pharmacology ; Caco-2 Cells ; Escherichia coli/drug effects/genetics ; Enterococcus faecalis/drug effects/genetics ; Microbial Sensitivity Tests ; Staphylococcus aureus/drug effects/genetics ; Erythromycin/pharmacology ; }, abstract = {UNLABELLED: Antimicrobial resistance remains a public health threat. Probiotics harboring antimicrobial resistant genes (ARGs) have, in recent years, been considered a potential health risk. Studies conducted on probiotics from increasingly popular health supplements have raised the possibility of transmitting ARGs to commensals in the human gut, concomitantly establishing a reservoir of ARGs and risking acquisition by opportunistic pathogens. Building on our previous study that reported multiple antibiotic resistance in probiotics of health supplements, in this research, we have attempted to detect their ARGs that may account for resistant phenotypes. ARGs responsible for tetracycline, macrolide, aminoglycoside, and glycopeptide resistance were prevalent in probiotics. Through laboratory adaptive evolution studies, we also show that streptomycin-adapted probiotics gained resistance to erythromycin, tetracycline, and doxycycline more effectively than non-adapted ones. When co-incubated with Enterococcus faecalis, Escherichia coli, or Staphylococcus aureus on Caco-2 and/or HCT-116 cells, streptomycin resistance was transferred from the adapted probiotics to generate transconjugants at frequencies comparable to or higher than that of other studies conducted through filter mating. Consistently, ARGs conferring resistance to streptomycin (aadA) and erythromycin [erm(B)-1] were detected in E. coli and S. aureus transconjugants, respectively, after co-incubation with streptomycin-adapted probiotics on Caco-2 cells. aadA and erm(B)-1 were both detected in E. faecalis transconjugant after the same co-incubation on HCT-116 cells. Our data and future comparative genomics and metagenomics studies conducted on animal models and in healthy, immunocompromised, and/or antibiotic-treated human cohorts will contribute to a more comprehensive understanding of probiotic consumption, application, and safety.<br><br>IMPORTANCE: Probiotics are becoming increasingly popular, with promising applications in food and medicine, but the risk of transferring ARGs to disease-causing bacteria has raised concerns. Our study detected ARGs in probiotics of health supplements conferring resistance to tetracycline, macrolide, aminoglycoside, and glycopeptide drugs. Streptomycin-adapted probiotics also gained resistance to other antibiotics more effectively than non-adapted ones. Importantly, we showed that streptomycin resistance could be transferred to other bacteria after co-incubation with probiotics on human intestinal cells. ARGs responsible for erythromycin and streptomycin resistance, which were initially absent in the recipient bacteria, were also detected in the transconjugants. Our data build the foundation for future studies that will be conducted on animal models and in humans and leveraging advanced metagenomics approaches to clarify the long-term health risk of probiotic consumption.}, }
@article {pmid39653497, year = {2024}, author = {St Leger, RJ}, title = {The evolution of complex Metarhizium-insect-plant interactions.}, journal = {Fungal biology}, volume = {128}, number = {8 Pt B}, pages = {2513-2528}, doi = {10.1016/j.funbio.2024.01.001}, pmid = {39653497}, issn = {1878-6146}, mesh = {*Metarhizium/genetics/pathogenicity/physiology ; Animals ; *Insecta/microbiology ; *Plants/microbiology ; Gene Transfer, Horizontal ; Symbiosis ; Biological Evolution ; Host Specificity ; Host-Pathogen Interactions ; }, abstract = {Metarhizium species interact with plants, insects, and microbes within a diffuse coevolutionary framework that benefits soil health, biodiversity, and plant growth. The insect host ranges of these fungi vary greatly. Specialization to a narrow host range usually occurs in the tropics with its stable insect populations, and is characterized by the rapid evolution of existing protein sequences, sexual recombination, and small genomes. Host-generalists are associated with temperate regions and ephemeral insect populations. Their mutualistic plant-colonizing lifestyle increases survival when insects are rare, while facultative entomopathogenicity feeds both the fungi and plants when insects are common. Generalists have lost meiosis and associated genome defense mechanisms, enabling gene duplications to diversify functions related to plant colonization and host exploitation. Horizontal gene transfer events via transposons have also contributed to host range changes, while parasexuality combines beneficial mutations within individual clones of generalists. There is also a lot of genetic variation in insect populations and both pathogen virulence and insect immunity are linked with variations in stress responses. Thus, susceptibility to generalists can vary due to non-specific resistance to multiple stressors, multipurpose physical and chemical barriers, and heterogeneity in physiological and behavioral factors, such as sleep.}, }
@article {pmid39647412, year = {2024}, author = {He, T and Xie, J and Jin, L and Zhao, J and Zhang, X and Liu, H and Li, XD}, title = {Seasonal dynamics of the phage-bacterium linkage and associated antibiotic resistome in airborne PM2.5 of urban areas.}, journal = {Environment international}, volume = {194}, number = {}, pages = {109155}, doi = {10.1016/j.envint.2024.109155}, pmid = {39647412}, issn = {1873-6750}, mesh = {*Bacteriophages/genetics ; *Particulate Matter ; China ; *Bacteria/genetics/drug effects ; *Seasons ; Humans ; Air Microbiology ; Cities ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Air Pollutants/analysis ; Metagenomics ; Drug Resistance, Bacterial/genetics ; Microbiota ; }, abstract = {Inhalable microorganisms in airborne fine particulate matter (PM2.5), including bacteria and phages, are major carriers of antibiotic resistance genes (ARGs) with strong ecological linkages and potential health implications for urban populations. A full-spectrum study on ARG carriers and phage-bacterium linkages will shed light on the environmental processes of antibiotic resistance from airborne dissemination to the human lung microbiome. Our metagenomic study reveals the seasonal dynamics of phage communities in PM2.5, their impacts on clinically important ARGs, and potential implications for the human respiratory microbiome in selected cities of China. Gene-sharing network comparisons show that air harbours a distinct phage community connected to human- and water-associated viromes, with 57 % of the predicted hosts being potential bacterial pathogens. The ARGs of common antibiotics, e.g., peptide and tetracycline, dominate both the antibiotic resistome associated with bacteria and phages in PM2.5. Over 60 % of the predicted hosts of vARG-carrying phages are potential bacterial pathogens, and about 67 % of these hosts have not been discovered as direct carriers of the same ARGs. The profiles of ARG-carrying phages are distinct among urban sites, but show a significant enrichment in abundance, diversity, temperate lifestyle, and matches of CRISPR (short for 'clustered regularly interspaced short palindromic repeats') to identified bacterial genomes in winter and spring. Moreover, phages putatively carry 52 % of the total mobile genetic element (MGE)-ARG pairs with a unique 'flu season' pattern in urban areas. This study highlights the role that phages play in the airborne dissemination of ARGs and their delivery of ARGs to specific opportunistic pathogens in human lungs, independent of other pathways of horizontal gene transfer. Natural and anthropogenic stressors, particularly wind speed, UV index, and level of ozone, potentially explained over 80 % of the seasonal dynamics of phage-bacterial pathogen linkages on antibiotic resistance. Therefore, understanding the phage-host linkages in airborne PM2.5, the full-spectrum of antibiotic resistomes, and the potential human pathogens involved, will be of benefit to protect human health in urban areas.}, }
@article {pmid39644844, year = {2025}, author = {Liu, X and Fan, Q and Li, F and Wu, C and Yi, S and Lu, H and Wu, Y and Liu, Y and Tian, J}, title = {Assessing foodborne health risks from dietary exposure to antibiotic resistance genes and opportunistic pathogens in three types of vegetables: An in vitro simulation of gastrointestinal digestion.}, journal = {Journal of hazardous materials}, volume = {484}, number = {}, pages = {136731}, doi = {10.1016/j.jhazmat.2024.136731}, pmid = {39644844}, issn = {1873-3336}, mesh = {*Vegetables/microbiology ; Risk Assessment ; Humans ; *Dietary Exposure ; Genes, Bacterial ; Digestion ; Bacteria/genetics ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Foodborne health risks posed by antibiotic resistant genes (ARGs) and pathogenic bacteria have garnered increasing global attention. However, the patterns of their propagation and reduction, as well as the resulting health risks in the human gastrointestinal tract, remain unknown. We employed leafy vegetables (water spinach), solanaceous vegetables (pepper), and root vegetables (radish) to investigate the propagation and reduction patterns of ARGs and pathogenic bacteria within an in vitro simulated digestion system. This system mimicked the soil-vegetable-stomach-small intestine (SVSTI) transmission chain. We found that kan, oqxA, and multidrug resistance genes were enriched by 1.10-fold, 11.2-fold, and 2.21-fold, respectively, along the transmission chain. The succession of bacterial communities and horizontal gene transfer mediated by intl1 were identified as the primary drivers of ARG accumulation. Notably, certain pathogenic bacteria (Bacillus cereus, Klebsiella pneumoniae) accumulated in the intestinal environment. According to our proposed health risk assessment system, Bacillus species, as potential ARG hosts, and multidrug ARGs are at a higher risk of exposure to intestinal environment through the transmission chain. Our findings highlight the significant health risks associated with the intake of ARGs and pathogenic bacteria carried by vegetables, emphasizing an urgent need to implement effective biological control measures in vegetable production and consumption.}, }
@article {pmid39642748, year = {2025}, author = {Lin, H and Diarra, MS and Jia, G and Zhao, X}, title = {Detection of plasmids in Salmonella from poultry and investigating the potential horizontal transfer of antimicrobial resistance and virulence genes: PLASMID TRANSFER OF RESISTANCE AND VIRULENCE.}, journal = {Poultry science}, volume = {104}, number = {1}, pages = {104591}, pmid = {39642748}, issn = {1525-3171}, mesh = {*Plasmids/genetics ; Animals ; *Salmonella/genetics/pathogenicity/drug effects ; *Gene Transfer, Horizontal ; *Poultry Diseases/microbiology ; Virulence/genetics ; *Salmonella Infections, Animal/microbiology ; *Drug Resistance, Bacterial/genetics ; Chickens ; Anti-Bacterial Agents/pharmacology ; Poultry ; }, abstract = {Antimicrobial resistance genes (ARGs) and virulence genes (VGs) have been widely reported in Salmonella which are major foodborne pathogens from poultry. This study assessed the replicon typing and conjugative ability of plasmids from poultry-derived Salmonella as well as ARGs and VGs carried by these plasmids using an in silico approach. Both PlasmidFinder 2.1 and VRprofile2 were employed to detect plasmids in Salmonella sequences downloaded from the National Center for Biotechnology Information (NCBI) Reference Sequences (RefSeq) database, and then oriTfinder was used to determine the conjugative ability of plasmids. The ARGs and VGs on plasmids were identified by both VRprofile2 and oriTfinder. The phenotypes of ARGs were predicted by ResFinder 4.1 and oriTfinder, while the phenotypes of virulence were predicted by oriTfinder and VRprofile2. We identified 183 plasmid sequences from 309 downloaded sequences. Among them, 77 (42.1 %) plasmids were conjugative, 25 (13.7 %) mobilizable, and 81 (44.3 %) non-mobilizable. Fifty-one plasmids (27.9 %) contained multi-replicons. One hundred and five plasmids carried 58 ARGs, belonging to 12 classes. The most prevalent ARG groups in plasmids were the aminoglycoside, β-lactam, sulfonamide, and tetracycline groups. In addition, 49 plasmids carried 36 different VGs belonging to 13 gene classes. The most prevalent VG groups were the adhesin, type III secretion system, and resistance to complement killing groups. The detected high percentage of conjugative plasmids and existence of many multiple replicons suggest possible high rates of plasmid-mediated horizontal gene transfer (HGT) events. Detection of previously unreported plasmid-borne VG (fdeC) from Salmonella in poultry calls for more vigilant monitoring.}, }
@article {pmid39642232, year = {2024}, author = {Urquhart, AS and Gluck-Thaler, E and Vogan, AA}, title = {Gene acquisition by giant transposons primes eukaryotes for rapid evolution via horizontal gene transfer.}, journal = {Science advances}, volume = {10}, number = {49}, pages = {eadp8738}, pmid = {39642232}, issn = {2375-2548}, mesh = {*Gene Transfer, Horizontal ; *DNA Transposable Elements/genetics ; *Evolution, Molecular ; Phylogeny ; Eukaryota/genetics ; Fungi/genetics ; Multigene Family ; Genome, Fungal ; }, abstract = {Horizontal gene transfer (HGT) disseminates genetic information between species and is a powerful mechanism of adaptation. Yet, we know little about its underlying drivers in eukaryotes. Giant Starship transposons have been implicated as agents of fungal HGT, providing an unprecedented opportunity to reveal the evolutionary parameters behind this process. Here, we characterize the ssf gene cluster, which contributes to formaldehyde resistance, and use it to demonstrate how mobile element evolution shapes fungal adaptation. We found that ssf clusters have been acquired by various distantly related Starships, which each exhibit multiple instances of horizontal transfer across fungal species (at least nine events, including between different taxonomic orders). Many ssf clusters have subsequently integrated into their host's genome, illustrating how Starships shape the evolutionary trajectory of fungal hosts beyond any single transfer. Our results demonstrate the key role Starships play in mediating rapid and repeated adaptation via HGT, elevating the importance of mobile element evolution in eukaryotic biology.}, }
@article {pmid39642107, year = {2024}, author = {Wingfield, BD and Wingfield, MJ}, title = {Gene transfer between fungal species triggers repeated coffee wilt disease outbreaks.}, journal = {PLoS biology}, volume = {22}, number = {12}, pages = {e3002901}, pmid = {39642107}, issn = {1545-7885}, mesh = {*Plant Diseases/microbiology ; *Gene Transfer, Horizontal ; *Disease Outbreaks ; Coffea/microbiology ; Coffee/microbiology ; DNA Transposable Elements/genetics ; }, abstract = {Two outbreaks of coffee wilt disease have devastated African coffee production. A PLOS Biology study suggests that horizontal gene transfer via large Starship transposons between 2 fungal species played a key role in the repeated emergence of the disease.}, }
@article {pmid39642000, year = {2024}, author = {Villavicencio, F and Albán, V and Satán, C and Quintana, H and Enríquez, W and Jaramillo, K and Flores, F and Arisqueta, L}, title = {Salmonella enterica Serovar Infantis KPC-2 Producer: First Isolate Reported in Ecuador.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {30}, number = {12}, pages = {502-508}, doi = {10.1089/mdr.2024.0072}, pmid = {39642000}, issn = {1931-8448}, mesh = {Ecuador ; *Anti-Bacterial Agents/pharmacology ; *beta-Lactamases/genetics ; *Salmonella enterica/drug effects/genetics ; Humans ; *Microbial Sensitivity Tests ; *Plasmids ; *Whole Genome Sequencing ; Serogroup ; Salmonella Infections/microbiology/drug therapy ; Gene Transfer, Horizontal ; Drug Resistance, Multiple, Bacterial/genetics ; }, abstract = {Antimicrobial resistance is currently considered a public health threat. Carbapenems are antimicrobials for hospital use, and Enterobacterales resistant to these β-lactams have spread alarmingly in recent years, especially those that cause health care-associated infections. The blaKPC gene is considered one of the most important genetic determinants disseminated by plasmids, promoting horizontal gene transfer. This study describes, for the first time in Ecuador, and worldwide, the presence of a blaKPC-2 gene in an isolate of Salmonella enterica serovar Infantis from a clinical sample. Through whole-genome sequencing, we characterized the genetic determinants of antimicrobial resistance in this Salmonella ST-32 strain. Our results showed the presence of several resistance genes, including blaCTX-M-65, and a conjugative plasmid Kpn-WC17-007-03 that may be responsible for the horizontal transference of these resistance mechanisms.}, }
@article {pmid39640918, year = {2024}, author = {Baede, VO and Jlassi, O and Lesiczka, PM and Younsi, H and Jansen, HJ and Dachraoui, K and Segobola, J and Ben Said, M and Veneman, WJ and Dirks, RP and Sprong, H and Zhioua, E}, title = {Similarities between Ixodes ricinus and Ixodes inopinatus genomes and horizontal gene transfer from their endosymbionts.}, journal = {Current research in parasitology &amp; vector-borne diseases}, volume = {6}, number = {}, pages = {100229}, pmid = {39640918}, issn = {2667-114X}, abstract = {The taxa Ixodes ricinus and Ixodes inopinatus are sympatric in Tunisia. The genetics underlying their morphological differences are unresolved. In this study, ticks collected in Jouza-Amdoun, Tunisia, were morphologically identified and sequenced using Oxford Nanopore Technologies. Three complete genome assemblies of I. inopinatus and three of I. ricinus with BUSCO scores of ∼98% were generated, including the reconstruction of mitochondrial genomes and separation of both alleles of the TRPA1, TROSPA and calreticulin genes. Deep sequencing allowed the first descriptions of complete bacterial genomes for "Candidatus Midichloria mitochondrii", Rickettsia helvetica and R. monacensis from North Africa, and the discovery of extensive integration of parts of the Spiroplasma ixodetis and "Ca. M. mitochondrii" into the nuclear genome of these ticks. Phylogenetic analyses of the mitochondrial genome, the nuclear genes, and symbionts showed differentiation between Tunisian and Dutch ticks, but high genetic similarities between Tunisian I. ricinus and I. inopinatus. Subtraction of the genome assemblies identified the presence of some unique sequences, which could not be confirmed when screening a larger batch of I. ricinus and I. inopinatus ticks using PCR. Our findings yield compelling evidence that I. inopinatus is genetically highly similar, if not identical, to sympatric I. ricinus. Defined morphological differences might be caused by extrinsic factors such as micro-climatic conditions or bloodmeal composition. Our findings support the existence of different lineages of I. ricinus as well of its symbionts/pathogens from geographically dispersed locations.}, }
@article {pmid39637834, year = {2024}, author = {Peck, LD and Llewellyn, T and Bennetot, B and O'Donnell, S and Nowell, RW and Ryan, MJ and Flood, J and Rodríguez de la Vega, RC and Ropars, J and Giraud, T and Spanu, PD and Barraclough, TG}, title = {Horizontal transfers between fungal Fusarium species contributed to successive outbreaks of coffee wilt disease.}, journal = {PLoS biology}, volume = {22}, number = {12}, pages = {e3002480}, pmid = {39637834}, issn = {1545-7885}, mesh = {*Plant Diseases/microbiology ; *Fusarium/genetics/pathogenicity/isolation &amp; purification ; *Gene Transfer, Horizontal ; *Coffea/microbiology/genetics ; *Genome, Fungal/genetics ; Phylogeny ; Disease Outbreaks ; Host Specificity ; }, abstract = {Outbreaks of fungal diseases have devastated plants and animals throughout history. Over the past century, the repeated emergence of coffee wilt disease caused by the fungal pathogen Fusarium xylarioides severely impacted coffee production across sub-Saharan Africa. To improve the disease management of such pathogens, it is crucial to understand their genetic structure and evolutionary potential. We compared the genomes of 13 historic strains spanning 6 decades and multiple disease outbreaks to investigate population structure and host specialisation. We found that F. xylarioides comprised at least 4 distinct lineages: 1 host-specific to Coffea arabica, 1 to C. canephora var. robusta, and 2 historic lineages isolated from various Coffea species. The presence/absence of large genomic regions across populations, the higher genetic similarities of these regions between species than expected based on genome-wide divergence and their locations in different loci in genomes across populations showed that horizontal transfers of effector genes from members of the F. oxysporum species complex contributed to host specificity. Multiple transfers into F. xylarioides populations matched different parts of the F. oxysporum mobile pathogenicity chromosome and were enriched in effector genes and transposons. Effector genes in this region and other carbohydrate-active enzymes important in the breakdown of plant cell walls were shown by transcriptomics to be highly expressed during infection of C. arabica by the fungal arabica strains. Widespread sharing of specific transposons between F. xylarioides and F. oxysporum, and the correspondence of a putative horizontally transferred regions to a Starship (large mobile element involved in horizontal gene transfers in fungi), reinforce the inference of horizontal transfers and suggest that mobile elements were involved. Our results support the hypothesis that horizontal gene transfers contributed to the repeated emergence of coffee wilt disease.}, }
@article {pmid39637801, year = {2025}, author = {Zhang, S and Zheng, S and Gong, Y and Wang, Y and Wei, Q and Zhu, Y and Liu, L and Wu, R and Du, S}, title = {Does the herbicide napropamide exhibit enantioselective effects across genus plasmid transfer from Escherichia coli to Bacillus subtilis?.}, journal = {Journal of hazardous materials}, volume = {484}, number = {}, pages = {136704}, doi = {10.1016/j.jhazmat.2024.136704}, pmid = {39637801}, issn = {1873-3336}, mesh = {*Herbicides/chemistry/pharmacology/toxicity ; *Escherichia coli/genetics/drug effects ; *Bacillus subtilis/genetics/drug effects ; *Plasmids/genetics ; Stereoisomerism ; Molecular Docking Simulation ; Conjugation, Genetic/drug effects ; Gene Transfer, Horizontal/drug effects ; }, abstract = {The dissemination of plasmid-borne antibiotic resistance genes (ARGs) into the environment is an urgent concern. However, the enantioselective effects of herbicides on plasmid conjugation among bacterial genera and their underlying mechanisms remain unclear. This study demonstrates for the first time that the herbicide napropamide (NAP), commonly used in vegetable fields, exhibits a concentration-dependent effect on the transfer efficiency of the pBE2R plasmid from Escherichia coli to Bacillus subtilis. Notably, at a concentration of 5 mg L[-1], R-NAP increased transfer efficiency by threefold compared to the S-enantiomer. Scanning electron microscopy revealed that R-NAP caused less structural damage to bacteria than S-NAP but more effectively reduced cell wall components (lipopolysaccharides and peptidoglycan) in donor and recipient bacteria, increasing reactive oxygen species levels and membrane permeability. Transcriptomic analysis indicated that NAP enantiomers altered the expression of genes related to membrane transport activity and transposons. Cross-domain network analysis identified yieK, ygeH, and ydbL as key genes mediating conjugation transfer. Molecular docking results showed that NAP likely interacts hydrophobically with the active sites of the proteins encoded by these genes. In conclusion, herbicides like R-NAP should be carefully managed in fields irrigated with livestock manure to mitigate the risk of ARG transfer and accumulation in crops.}, }
@article {pmid39637780, year = {2025}, author = {Huang, C and Cui, M and Li, T and Zheng, C and Qiu, M and Shan, M and Li, B and Zhang, L and Yu, Y and Fang, H}, title = {Migration of fungicides, antibiotics and resistome in the soil-lettuce system.}, journal = {Journal of hazardous materials}, volume = {484}, number = {}, pages = {136725}, doi = {10.1016/j.jhazmat.2024.136725}, pmid = {39637780}, issn = {1873-3336}, mesh = {*Fungicides, Industrial/analysis ; *Anti-Bacterial Agents/pharmacology/analysis ; *Soil Microbiology ; *Lactuca/microbiology ; *Soil Pollutants/analysis ; Bacteria/genetics/drug effects ; Gene Transfer, Horizontal ; Genes, Bacterial ; }, abstract = {The emergence and spread of antibiotic resistance genes (ARGs) have become a serious issue in global agricultural production. However, understanding how these ARGs spread across different spatial scales, especially when exposed to both pesticides and antibiotics, has remained a challenge. Here, metagenomic assembly and binning methodologies were used to determine the spread pathway of ARGs in the soil-lettuce system under individual and combined exposure of fungicides (carbendazim and pyraclostrobin) and antibiotics (chlortetracycline and ciprofloxacin). These agrochemicals not only facilitated the spread of ARGs from soil to lettuce but also significantly elevated the risk of developing multi-antibiotic resistance among bacteria, especially to some antibiotic types (i.e. sulfonamide, aminoglycoside, quinolone, and tetracycline). ARGs could be migrated through distinct pathways, including both vertical and horizontal gene transfer, with plasmids playing a crucial role in facilitating the horizontal gene transfer. These transfer pathways have enabled key pathogenic bacteria belonging to the genera Acinetobacter, Pseudomonas, and Pantoea to acquire resistance and remain recalcitrant, posing the potential risk to crop health and food safety. In summary, our findings highlighted that fungicide and antibiotic could drive upward migration of ARGs in the soil-lettuce system and reduced the quality safety of agricultural products.}, }
@article {pmid39636264, year = {2024}, author = {Romanov, KA and O'Connor, TJ}, title = {Legionella pneumophila, a Rosetta stone to understanding bacterial pathogenesis.}, journal = {Journal of bacteriology}, volume = {206}, number = {12}, pages = {e0032424}, pmid = {39636264}, issn = {1098-5530}, support = {R21 AI119580/AI/NIAID NIH HHS/United States ; 1R21AI166238//HHS | National Institutes of Health (NIH)/ ; 1R01A1163273//HHS | National Institutes of Health (NIH)/ ; 1R01AI125402//HHS | National Institutes of Health (NIH)/ ; 1R21AI119580//HHS | National Institutes of Health (NIH)/ ; R01 AI125402/AI/NIAID NIH HHS/United States ; }, mesh = {*Legionella pneumophila/pathogenicity/genetics/physiology ; Humans ; *Host-Pathogen Interactions ; *Legionnaires' Disease/microbiology ; *Virulence Factors/genetics/metabolism ; Amoeba/microbiology ; Animals ; Host Specificity ; Virulence ; }, abstract = {Legionella pneumophila is an environmentally acquired pathogen that causes respiratory disease in humans. While the discovery of L. pneumophila is relatively recent compared to other bacterial pathogens, over the past 50 years, L. pneumophila has emerged as a powerhouse for studying host-pathogen interactions. In its natural habitat of fresh water, L. pneumophila interacts with a diverse array of protozoan hosts and readily evolve to expand their host range. This has led to the accumulation of the most extensive arsenal of secreted virulence factors described for a bacterial pathogen and their ability to infect humans. Within amoebae and human alveolar macrophages, the bacteria replicate within specialized membrane-bound compartments, establishing L. pneumophila as a model for studying intracellular vacuolar pathogens. In contrast, the virulence factors required for intracellular replication are specifically tailored to individual host cells types, allowing the pathogen to adapt to variation between disparate niches. The broad host range of this pathogen, combined with the extensive diversity and genome plasticity across the Legionella genus, has thus established this bacterium as an archetype to interrogate pathogen evolution, functional genomics, and ecology. In this review, we highlight the features of Legionella that establish them as a versatile model organism, new paradigms in bacteriology and bacterial pathogenesis resulting from the study of Legionella, as well as current and future questions that will undoubtedly expand our understanding of the complex and intricate biology of the microbial world.}, }
@article {pmid39631624, year = {2025}, author = {Chen, W and Li, Z and Zheng, J and Wang, D and Gao, S and Zhou, W and Shen, H and Zhang, Y and Cao, X}, title = {A comprehensive analysis of the epidemiological and genomic characteristics of global Serratia Marcescens.}, journal = {Journal of global antimicrobial resistance}, volume = {40}, number = {}, pages = {81-89}, doi = {10.1016/j.jgar.2024.11.013}, pmid = {39631624}, issn = {2213-7173}, mesh = {*Serratia marcescens/genetics/drug effects/classification/isolation &amp; purification ; Humans ; *Serratia Infections/epidemiology/microbiology ; Phylogeny ; *Genome, Bacterial ; Genomics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; beta-Lactamases/genetics ; Bacterial Proteins/genetics ; Drug Resistance, Bacterial/genetics ; Global Health ; }, abstract = {BACKGROUND: Serratia marcescens outbreaks present significant challenges in clinical treatment, necessitating a deeper understanding of its epidemiological and genomic traits.<br><br>OBJECTIVE: To analyse the epidemiological and genomic characteristics of S. marcescens at a global scale.<br><br>METHODS: High-quality genomes of S. marcescens were retrieved from NCBI and annotated using Prodigal. Antibiotic resistance genes (ARGs) were identified via Blastn, sequence types (STs) were determined with a proprietary tool, and phylogenetic analysis was conducted to explore evolutionary relationships.<br><br>RESULTS: The study analysed genomes from 33 countries, with major contributions from the USA (27.8%), UK (15.3%), Italy (14.7%), and Japan (10.7%). Human clinical samples accounted for 73.5% of the isolates, primarily from blood (44.8%) and sputum (19.3%). Eleven ARGs were identified, with sde being the most prevalent. Carbapenemase genes included blaSME, blaKPC, and blaNDM-1, though co-occurrence in individual strains was absent. Novel ARGs, including armA, rmtC, and fosA7.2, were reported. Among 855 genomes with identified STs, ST366, ST367, ST365, and ST423 were most common. Phylogenetic analysis highlighted significant genetic diversity and distinct evolutionary lineages.<br><br>CONCLUSION: Temporal analysis showed a genome peak in 2019, underscoring the global prevalence and adaptability of S. marcescens. The distribution of ARGs across diverse STs emphasizes horizontal gene transfer as a key driver of resistance. Judicious antibiotic use is essential to mitigate further resistance.}, }
@article {pmid39631390, year = {2025}, author = {Feyissa, BA and de Becker, EM and Salesse-Smith, CE and Shu, M and Zhang, J and Yates, TB and Xie, M and De, K and Gotarkar, D and Chen, MSS and Jawdy, SS and Carper, DL and Barry, K and Schmutz, J and Weston, DJ and Abraham, PE and Tsai, CJ and Morrell-Falvey, JL and Taylor, G and Chen, JG and Tuskan, GA and Long, SP and Burgess, SJ and Muchero, W}, title = {An orphan gene BOOSTER enhances photosynthetic efficiency and plant productivity.}, journal = {Developmental cell}, volume = {60}, number = {5}, pages = {723-734.e7}, doi = {10.1016/j.devcel.2024.11.002}, pmid = {39631390}, issn = {1878-1551}, mesh = {*Photosynthesis/genetics ; *Populus/genetics/growth &amp; development/metabolism ; Arabidopsis/genetics/metabolism/growth &amp; development ; Gene Expression Regulation, Plant ; Genome-Wide Association Study ; Ribulose-Bisphosphate Carboxylase/genetics/metabolism ; Plants, Genetically Modified ; *Genes, Plant ; Biomass ; *Plant Proteins/genetics/metabolism ; Plastids/metabolism/genetics ; }, abstract = {Organelle-to-nucleus DNA transfer is an ongoing process playing an important role in the evolution of eukaryotic life. Here, genome-wide association studies (GWAS) of non-photochemical quenching parameters in 743 Populus trichocarpa accessions identified a nuclear-encoded genomic region associated with variation in photosynthesis under fluctuating light. The identified gene, BOOSTER (BSTR), comprises three exons, two with apparent endophytic origin and the third containing a large fragment of plastid-encoded Rubisco large subunit. Higher expression of BSTR facilitated anterograde signaling between nucleus and plastid, which corresponded to enhanced expression of Rubisco, increased photosynthesis, and up to 35% greater plant height and 88% biomass in poplar accessions under field conditions. Overexpression of BSTR in Populus tremula × P. alba achieved up to a 200% in plant height. Similarly, Arabidopsis plants heterologously expressing BSTR gained up to 200% in biomass and up to 50% increase in seed.}, }
@article {pmid39631158, year = {2025}, author = {Wang, Y and Liu, X and Huang, C and Han, W and Gu, P and Jing, R and Yang, Q}, title = {Antibiotic resistance genes and virulence factors in the plastisphere in wastewater treatment plant effluent: Health risk quantification and driving mechanism interpretation.}, journal = {Water research}, volume = {271}, number = {}, pages = {122896}, doi = {10.1016/j.watres.2024.122896}, pmid = {39631158}, issn = {1879-2448}, mesh = {*Wastewater/microbiology ; *Drug Resistance, Microbial/genetics ; *Virulence Factors ; Waste Disposal, Fluid ; Biofilms ; Water Pollutants, Chemical ; Risk Assessment ; }, abstract = {Microplastics (MPs) are ubiquitous in wastewater treatment plants (WWTPs) and provide a unique niche for the spread of pollutants. To date, risk assessments and driving mechanisms of pathogens, antibiotic resistance genes (ARGs), and virulence factors (VFs) in the plastisphere are still lacking. Here, the microbiota, ARGs, VFs, their potential health risks, and biologically driving mechanisms on polythene (PE), polyethylene terephthalate (PET), poly (butyleneadipate-co-terephthalate) and polylactic acid blends (PBAT/PLA), PLA MPs, and gravel in WWTP effluent were investigated. The results showed that plastisphere and gravel biofilm harbored more distinctive microorganisms, promoting the uniqueness of pathogens, ARGs, and VFs compared to WWTP effluent. The abundance of major pathogens, ARGs, and VFs in the plastisphere was 1.01-1.35 times higher than that in the effluent. The high health risk of ARGs (HRA) calculated by fully considering the abundance, clinical relevance, pathogenicity, accessibility and mobility, and the high proportion of resistance contigs with mobile genetic elements confirmed that the plastisphere posed the highest potential health risk. Candidatus Microthrix and Candidatus Promineifilum were the essential hosts of ARGs and VFs in the plastisphere and gravel biofilm, respectively. High metabolic activity such as amino acid metabolism and biosynthesis of secondary metabolites, and highly expressed key genes increased the synthesis of ARGs and VFs. The primary mechanisms driving ARG enrichment in the plastisphere were enhanced microbial metabolic activity, increased frequency of horizontal gene transfer, heightened antibiotic inactivation and efflux, and reduced cell permeability. This study provided new insights into the ARGs, VFs, and health risks of the plastisphere and emphasized the importance of strict control of wastewater discharge.}, }
@article {pmid39630207, year = {2025}, author = {Markert, EX and Severe, L and Severe, K and Twing, KI and Ward, LM}, title = {Genomes of novel Serratia strains from suburban soil.}, journal = {Microbiology resource announcements}, volume = {14}, number = {1}, pages = {e0086624}, pmid = {39630207}, issn = {2576-098X}, abstract = {Here, we present genomes of three strains of Serratia initially isolated from suburban soil-one strain of S. ureilytica and two strains of S. quinivorans-resistant to multiple classes of antibiotics. This expands the genomic sampling of a group relevant to the ecosystem and human health.}, }
@article {pmid39628168, year = {2024}, author = {Gu, JY and Li, WY and Zhou, Y and Zhang, GS}, title = {[Environmental Pollution and Extraction Methods of Extracellular Antibiotic Resistance Genes in Water].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {45}, number = {12}, pages = {7041-7048}, doi = {10.13227/j.hjkx.202401087}, pmid = {39628168}, issn = {0250-3301}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/isolation &amp; purification/drug effects ; China ; *Drug Resistance, Bacterial/genetics ; Environmental Monitoring ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Water Microbiology ; }, abstract = {Antibiotics are widely used to treat diseases such as bacterial infections. However, the abuse of antibiotics has led to the spread of antibiotic resistant bacteria and intracellular and extracellular antibiotic resistance genes, making China one of the countries with the highest incidence of antibiotic resistance and thus threatening public health. Extracellular antibiotic resistance genes, as one of the novel environmental pollutants, could exist in water for a long time and could be transmitted between different bacteria through horizontal gene transfer, resulting in the spread of antibiotic resistance. At present, due to the limitation of enrichment and recovery methods, the in-depth studies of extracellular antibiotic resistance genes in water have been rarely reported. Thus, it is impossible to carry out effective supervision and risk assessments. Based on literature analysis and investigation, the pollution sources, current situations, and characteristics of extracellular antibiotic resistance genes in water are expounded. Meanwhile, the advantages and disadvantages of their enrichment and recovery methods are compared and analyzed and the enrichment and recovery methods are verified and discussed through practical cases. These provide theoretical reference for studies such as examining extracellular antibiotic resistance genes in water on their transmission and provide a technical basis for antibiotic resistance control and health risk assessments of extracellular antibiotic resistance genes.}, }
@article {pmid39626640, year = {2025}, author = {Magyar, LB and Ábrahám, E and Lipinszki, Z and Tarnopol, RL and Whiteman, NK and Varga, V and Hultmark, D and Andó, I and Cinege, G}, title = {Pore-Forming Toxin-Like Proteins in the Anti-Parasitoid Immune Response of Drosophila.}, journal = {Journal of innate immunity}, volume = {17}, number = {1}, pages = {10-28}, pmid = {39626640}, issn = {1662-8128}, support = {R35 GM119816/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Pore Forming Cytotoxic Proteins/genetics/metabolism ; *Wasps/immunology ; *Drosophila/immunology/parasitology/genetics ; *Drosophila Proteins/genetics/metabolism ; *Hemolysin Proteins/genetics/metabolism ; Gene Transfer, Horizontal ; Phylogeny ; Immunity, Innate ; Hemocytes/immunology ; Hemolymph/metabolism ; Bacterial Toxins/genetics ; }, abstract = {INTRODUCTION: Species of the ananassae subgroup of Drosophilidae are highly resistant to parasitoid wasp infections. We have previously shown that the genes encoding cytolethal distending toxin B (CdtB) and the apoptosis inducing protein of 56 kDa (AIP56) were horizontally transferred to these fly species from prokaryotes and are now instrumental in the anti-parasitoid immune defense of Drosophila ananassae. Here we describe a new family of genes, which encode proteins with hemolysin E domains, heretofore only identified in prokaryotes. Hemolysin E proteins are pore-forming toxins, important virulence factors of bacteria.<br><br>METHODS: Bioinformatical, transcriptional, and protein expressional studies were used.<br><br>RESULTS: The hemolysin E-like genes have a scattered distribution among the genomes of species belonging to several different monophyletic lineages in the family Drosophilidae. We detected structural homology with the bacterial Hemolysin E toxins and showed that the origin of the D. ananassae hemolysin E-like genes (hl1-38) is consistent with prokaryotic horizontal gene transfer. These genes encode humoral factors, secreted into the hemolymph by the fat body and hemocytes. Their expression is induced solely by parasitoid infection and the proteins bind to the developing parasitoids.<br><br>CONCLUSIONS: Hemolysin E-like proteins acquired by horizontal gene transfer and expressed by the primary immune organs may contribute to the elimination of parasitoids, as novel humoral factors in Drosophila innate immunity.}, }
@article {pmid39621811, year = {2024}, author = {Wright, RCT and Wood, AJ and Bottery, MJ and Muddiman, KJ and Paterson, S and Harrison, E and Brockhurst, MA and Hall, JPJ}, title = {A chromosomal mutation is superior to a plasmid-encoded mutation for plasmid fitness cost compensation.}, journal = {PLoS biology}, volume = {22}, number = {12}, pages = {e3002926}, pmid = {39621811}, issn = {1545-7885}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Plasmids/genetics ; *Pseudomonas fluorescens/genetics ; *Mutation ; *Chromosomes, Bacterial/genetics ; *Genetic Fitness ; Gene Transfer, Horizontal ; Evolution, Molecular ; }, abstract = {Plasmids are important vectors of horizontal gene transfer in microbial communities but can impose a burden on the bacteria that carry them. Such plasmid fitness costs are thought to arise principally from conflicts between chromosomal- and plasmid-encoded molecular machineries, and thus can be ameliorated by compensatory mutations (CMs) that reduce or resolve the underlying causes. CMs can arise on plasmids (i.e., plaCM) or on chromosomes (i.e., chrCM), with contrasting predicted effects upon plasmid success and subsequent gene transfer because plaCM can also reduce fitness costs in plasmid recipients, whereas chrCM can potentially ameliorate multiple distinct plasmids. Here, we develop theory and a novel experimental system to directly compare the ecological effects of plaCM and chrCM that arose during evolution experiments between Pseudomonas fluorescens SBW25 and its sympatric mercury resistance megaplasmid pQBR57. We show that while plaCM was predicted to succeed under a broader range of parameters in mathematical models, chrCM dominated in our experiments, including conditions with numerous recipients, due to a more efficacious mechanism of compensation, and advantages arising from transmission of costly plasmids to competitors (plasmid "weaponisation"). We show analytically the presence of a mixed Rock-Paper-Scissors (RPS) regime for CMs, driven by trade-offs with horizontal transmission, that offers one possible explanation for the observed failure of plaCM to dominate even in competition against an uncompensated plasmid. Our results reveal broader implications of plasmid-bacterial evolution for plasmid ecology, demonstrating the importance of specific compensatory mutations for resistance gene spread. One consequence of the superiority of chrCM over plaCM is the likely emergence in microbial communities of compensated bacteria that can act as "hubs" for plasmid accumulation and dissemination.}, }
@article {pmid39621273, year = {2025}, author = {Hancks, DC}, title = {An Evolutionary Framework Exploiting Virologs and Their Host Origins to Inform Poxvirus Protein Functions.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2860}, number = {}, pages = {257-272}, pmid = {39621273}, issn = {1940-6029}, mesh = {Animals ; Humans ; Evolution, Molecular ; Genome, Viral ; Host Specificity/genetics ; Host-Pathogen Interactions/genetics ; Open Reading Frames/genetics ; *Poxviridae/genetics/physiology ; Poxviridae Infections/virology/veterinary ; *Viral Proteins/genetics/metabolism ; }, abstract = {Poxviruses represent evolutionary successful infectious agents. As a family, poxviruses can infect a wide variety of species including humans, fish, and insects. While many other viruses are species-specific, an individual poxvirus species is often capable of infecting diverse hosts and cell types. For example, the prototypical poxvirus, vaccinia, is well known to infect numerous human cell types but can also infect cells from divergent hosts like frog neurons. Notably, poxvirus infections result in both detrimental human and animal diseases. The most infamous disease linked to a poxvirus is smallpox caused by variola virus. Poxviruses are large double-stranded DNA viruses, which uniquely replicate in the cytoplasm of cells. The model poxvirus genome encodes ~200 nonoverlapping protein-coding open reading frames (ORFs). Poxvirus gene products impact various biological processes like the production of virus particles, the host range of infectivity, and disease pathogenesis. In addition, poxviruses and their gene products have biomedical application with several species commonly engineered for use as vaccines and oncolytic virotherapy. Nevertheless, we still have an incomplete understanding of the functions associated with many poxvirus genes. In this chapter, we outline evolutionary insights that can complement ongoing studies of poxvirus gene functions and biology, which may serve to elucidate new molecular activities linked to this biomedically relevant class of viruses.}, }
@article {pmid39617215, year = {2025}, author = {Zuccarotto, A and Sollitto, M and Leclère, L and Panzella, L and Gerdol, M and Leone, S and Castellano, I}, title = {Molecular evolution of ovothiol biosynthesis in animal life reveals diversity of the natural antioxidant ovothiols in Cnidaria.}, journal = {Free radical biology &amp; medicine}, volume = {227}, number = {}, pages = {117-128}, doi = {10.1016/j.freeradbiomed.2024.11.037}, pmid = {39617215}, issn = {1873-4596}, mesh = {Animals ; *Antioxidants/metabolism ; *Evolution, Molecular ; *Cnidaria/genetics/metabolism ; Phylogeny ; Transcriptome ; }, abstract = {Sulfoxide synthase OvoA is the key enzyme involved in the biosynthesis of ovothiols (OSHs), secondary metabolites endowed with unique antioxidant properties. Understanding the evolution of such enzymes and the diversity of their metabolites should reveal fundamental mechanisms governing redox signaling and environmental adaptation. "Early-branching" animals such as Cnidaria display unique molecular diversity and symbiotic relationships responsible for the biosynthesis of natural products, however, they have been neglected in previous research on antioxidants and OSHs. In this work, we have integrated genome and transcriptome mining with biochemical analyses to study the evolution and diversification of OSHs biosynthesis in cnidarians. By tracing the history of the ovoA gene, we inferred its loss in the latest common ancestor of Medusozoa, followed by the acquisition of a unique ovoB/ovoA chimaeric gene in Hydrozoa, likely through a horizontal gene transfer from dinoflagellate donors. While Anthozoa (corals and anemones), bearing canonical ovoA genes, produced a striking variety of OSHs (A, B, and C), the multifunctional enzyme in Hydrozoa was related to OSH B biosynthesis, as shown in Clytia hemisphaerica. Surprisingly, the ovoA-lacking jellyfish Aurelia aurita and Pelagia noctiluca also displayed OSHs, and we provided evidence of their incorporation from external sources. Finally, transcriptome mining revealed ovoA conserved expression pattern during larval development from Cnidaria to more evolved organisms and its regulation by external stimuli, such as UV exposure. The results of our study shed light on the origin and diversification of OSH biosynthesis in basal animals and highlight the importance of redox-active molecules from ancient metazoans as cnidarians to vertebrates.}, }
@article {pmid39615392, year = {2025}, author = {Zhao, C and Suyamud, B and Yuan, Y and Ghosh, S and Xu, X and Hu, J}, title = {Effect of non-antibiotic factors on conjugative transfer of antibiotic resistance genes in aquaculture water.}, journal = {Journal of hazardous materials}, volume = {483}, number = {}, pages = {136701}, doi = {10.1016/j.jhazmat.2024.136701}, pmid = {39615392}, issn = {1873-3336}, mesh = {Aquaculture ; *Conjugation, Genetic/drug effects ; *Gene Transfer, Horizontal/drug effects ; *Drug Resistance, Bacterial/genetics ; Oxolinic Acid/pharmacology ; Genes, Bacterial ; Reactive Oxygen Species/metabolism ; Hydrogen Peroxide/pharmacology ; *Water Microbiology ; Plasmids/genetics ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects ; }, abstract = {Aquaculture water with antibiotic resistance genes (ARGs) is escalating due to the horizontal gene transfer. Non-antibiotic stressors specifically found, including those from fishery feed and disinfectants, are potential co-selectors. However, the mechanisms underlying this process remains unclear. Intragenus and intergenus conjugative transfer systems of the antibiotic-resistant plasmid RP4 were established to examine conjugative transfer frequency under exposure to five widely used non-antibiotic factors in aquaculture water: iodine, oxolinic acid, NO2-N, NO3-N and H2O2 and four different recipient bacteria: E. coli HB101, Citrobacter portucalensis SG1, Vibrio harveyi and Vibrio alginolyticus. The study found that low concentrations of non-antibiotic factors significantly promoted conjugative transfer, whereas high concentrations inhibited it. Moreover, the conjugation transfer efficiencies were significantly different with different bacterial species within (E. coli HB101 ∼ 10[-3] %) or cross genera (C. portucalensis SG1 ∼10[-5] %, V. harveyi ∼1 %). Besides, excessive exposure concentrations inhibited the expression of related genes and the generation of reactive oxygen species (ROS). Regulation of multiple related genes and ROS-induced SOS responses are common primary mechanisms. However, the mechanisms of non-antibiotic factors differ from those of standard antibiotics, with direct changes in cell membrane permeability potentially playing a dominant role. Additionally, variations among non-antibiotic factors and the specific characteristics of bacterial species contribute to differences in conjugation mechanisms. Notably, this study found that non-antibiotic factors could increase the frequency of intergeneric conjugation beyond that of intrageneric conjugation. Furthermore, non-antibiotic factors influenced by multiple transport systems may raise the risk of unintended cross-resistance, significantly amplifying the potential for resistance gene spread. This study underscores the significance of non-antibiotic factors in the propagation of ARGs, highlighting their role in advancing aquaculture development and protecting human health.}, }
@article {pmid39611838, year = {2025}, author = {Liu, F and Wang, S-H and Cheewangkoon, R and Zhao, R-L}, title = {Uneven distribution of prokaryote-derived horizontal gene transfer in fungi: a lifestyle-dependent phenomenon.}, journal = {mBio}, volume = {16}, number = {1}, pages = {e0285524}, pmid = {39611838}, issn = {2150-7511}, support = {2022YFD1200600//MOST | National Key Research and Development Program of China (NKPs)/ ; KFJ-BRP-009//biological resources programme, chinese academy of sciences/ ; 221111110600//Henan Province key research and development project/ ; }, mesh = {*Gene Transfer, Horizontal ; *Fungi/genetics/classification ; *Phylogeny ; *Genome, Fungal ; *Bacteria/genetics/classification ; Evolution, Molecular ; Symbiosis/genetics ; }, abstract = {UNLABELLED: Horizontal gene transfer (HGT) in fungi is less understood despite its significance in prokaryotes. In this study, we systematically searched for HGT events in 829 representative fungal genomes. Using a combination of sequence similarity and phylogeny-based approaches, we detected 20,093 prokaryotic-derived transferred genes across 750 fungal genomes, via 8,815 distinct HGT events. Notably, our analysis revealed that eight lifestyle-related traits significantly influence HGT diversity in fungi. For instance, parasites exhibited the highest estimated number of HGT-acquired genes, followed by saprotrophs, with symbionts showing the lowest. HGT-acquired genes were predominantly associated with metabolism and cellular functions and underwent purifying selection. Moreover, horizontally transferred genes with introns have significantly higher expression levels compared to intron-lacking genes, suggesting a probable role of intron gains in the adaptation of HGT-acquired genes. Overall, our findings highlight the influence of lifestyle on HGT diversity in fungi and underscore the substantial contribution of HGT to fungal adaptation.<br><br>IMPORTANCE: This study sheds new light on the role of horizontal gene transfer (HGT) in fungi, an area that has remained relatively unexplored compared to its well-established prevalence in bacteria. By analyzing 829 fungal genomes, we identified over 20,000 genes that fungi acquired from prokaryotes, revealing the significant impact of HGT on fungal evolution. Our findings highlight that fungal lifestyle traits, such as being parasitic or saprotrophic, play a key role in determining the extent of HGT, with parasites showing the highest gene acquisition rates. We also uncovered unique patterns of HGT occurrence based on fungal morphology and reproduction. Importantly, genes with introns, which are more highly expressed, appear to play a crucial role in fungal adaptation. This research deepens our understanding of how HGT contributes to the metabolic diversity and ecological success of fungi, and it underscores the broader significance of gene transfer in shaping fungal evolution.}, }
@article {pmid39611587, year = {2024}, author = {Sayid, R and van den Hurk, AWM and Rothschild-Rodriguez, D and Herrema, H and de Jonge, PA and Nobrega, FL}, title = {Characteristics of phage-plasmids and their impact on microbial communities.}, journal = {Essays in biochemistry}, volume = {68}, number = {5}, pages = {583-592}, pmid = {39611587}, issn = {1744-1358}, support = {AUF 5188//Amsterdam University Fund/ ; PhD fellowship//Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers (ACS)/ ; //Bowel Research UK (BRUK)/ ; Aspasia premium (015.017.050)//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)/ ; BB/T008768/1//Biotechnology and Biological Sciences Research Council (BBSRC)/ ; Black Futures Research Studentship//University of Southampton (University of Southampton UK)/ ; }, mesh = {*Bacteriophages/physiology ; *Plasmids/genetics ; *Bacteria/virology/genetics ; *Microbiota ; CRISPR-Cas Systems ; }, abstract = {Bacteria host various foreign genetic elements, most notably plasmids and bacteriophages (or phages). Historically, these two classes were seen as separate, but recent research has shown considerable interplay between them. Phage-plasmids (P-Ps) exhibit characteristics of both phages and plasmids, allowing them to exist extrachromosomally within bacterial hosts as plasmids, but also to infect and lyse bacteria as phages. This dual functionality enables P-Ps to utilize the modes of transmission of both phage and plasmids, facilitating the rapid dissemination of genetic material, including antibiotic resistance and virulence genes, throughout bacterial populations. Additionally, P-Ps have been found to encode toxin-antitoxin and CRISPR-Cas adaptive immune systems, which enhance bacterial survival under stress and provide immunity against other foreign genetic elements. Despite a growing body of literature on P-Ps, large gaps remain in our understanding of their ecological roles and environmental prevalence. This review aims to synthesise existing knowledge and identify research gaps on the impacts of P-Ps on microbial communities.}, }
@article {pmid39611041, year = {2024}, author = {Liu, L and Lian, ZH and Lv, AP and Salam, N and Zhang, JC and Li, MM and Sun, WM and Tan, S and Luo, ZH and Gao, L and Yuan, Y and Ming, YZ and OuYang, YT and Li, YX and Liu, ZT and Hu, CJ and Chen, Y and Hua, ZS and Shu, WS and Hedlund, BP and Li, WJ and Jiao, JY}, title = {Insights into chemoautotrophic traits of a prevalent bacterial phylum CSP1-3, herein Sysuimicrobiota.}, journal = {National science review}, volume = {11}, number = {11}, pages = {nwae378}, pmid = {39611041}, issn = {2053-714X}, abstract = {Candidate bacterial phylum CSP1-3 has not been cultivated and is poorly understood. Here, we analyzed 112 CSP1-3 metagenome-assembled genomes and showed they are likely facultative anaerobes, with 3 of 5 families encoding autotrophy through the reductive glycine pathway (RGP), Wood-Ljungdahl pathway (WLP) or Calvin-Benson-Bassham (CBB), with hydrogen or sulfide as electron donors. Chemoautotrophic enrichments from hot spring sediments and fluorescence in situ hybridization revealed enrichment of six CSP1-3 genera, and both transcribed genes and DNA-stable isotope probing were consistent with proposed chemoautotrophic metabolisms. Ancestral state reconstructions showed that the ancestors of phylum CSP1-3 may have been acetogens that were autotrophic via the RGP, whereas the WLP and CBB were acquired by horizontal gene transfer. Our results reveal that CSP1-3 is a widely distributed phylum with the potential to contribute to the cycling of carbon, sulfur and nitrogen. The name Sysuimicrobiota phy. nov. is proposed.}, }
@article {pmid39608506, year = {2025}, author = {Chetri, S}, title = {Escherichia coli: An arduous voyage from commensal to Antibiotic-resistance.}, journal = {Microbial pathogenesis}, volume = {198}, number = {}, pages = {107173}, doi = {10.1016/j.micpath.2024.107173}, pmid = {39608506}, issn = {1096-1208}, mesh = {Humans ; *Virulence Factors/genetics ; *Anti-Bacterial Agents/pharmacology ; *Escherichia coli Infections/microbiology/drug therapy ; *Escherichia coli/genetics/drug effects/pathogenicity ; Animals ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Gastrointestinal Microbiome/drug effects ; Drug Resistance, Multiple, Bacterial/genetics ; Virulence/genetics ; Symbiosis ; }, abstract = {Escherichia coli (E. coli), a normal intestinal microbiota is one of the most common pathogen known for infecting urinary tract, wound, lungs, bone marrow, blood system and brain. Irrational and overuse of commercially available antibiotics is the most imperative reason behind the emergence of the life threatening infections caused due to antibiotic resistant pathogens. The World Health Organization (WHO) identified antimicrobial resistance (AMR) as one of the 10 biggest public health threats of our time. This harmless commensal can acquire a range of mobile genetic elements harbouring genes coding for virulence factors becoming highly versatile human pathogens causing severe intestinal and extra intestinal diseases. Although, E. coli has been the most widely studied micro-organism, it never ceases to astound us with its ability to open up new research avenues and reveal cutting-edge survival mechanisms in diverse environments that impact human and surrounding environment. This review aims to summarize and highlight persistent research gaps in the field, including: (i) the transfer of resistant genes among bacterial species in diverse environments, such as those associated with humans and animals; (ii) the development of resistance mechanisms against various classes of antibiotics, including quinolones, tetracyclines, etc., in addition to β-lactams; and (iii) the relationship between resistance and virulence factors for understanding how virulence factors and resistance interact to gain a better grasp of how resistance mechanisms impact an organism's capacity to spread illness and interact with the host's defences. Moreover, this review aims to offer a thorough overview, exploring the history and factors contributing to antimicrobial resistance (AMR), the different reported pathotypes, and their links to virulence in both humans and animals. It will also examine their prevalence in various contexts, including food, environmental, and clinical settings. The objective is to deliver a more informative and current analysis, highlighting the evolution from microbiota (historical context) to sophisticated diseases caused by highly successful pathogens. Developing more potent tactics to counteract antibiotic resistance in E. coli requires filling in these gaps. By bridging these gaps, we can strengthen our capacity to manage and prevent resistance, which will eventually enhance public health and patient outcomes.}, }
@article {pmid39606649, year = {2024}, author = {Qing, Y and Zou, Z and Jiang, G and Qin, L and Liu, K and Liu, Z}, title = {A global perspective on the abundance, diversity and mobility of antibiotic resistance genes in Escherichia coli.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1442159}, pmid = {39606649}, issn = {2297-1769}, abstract = {INTRODUCTION: Escherichia coli (E. coli), a ubiquitous opportunistic pathogen, poses a growing threat to human health due to the increasing prevalence of antibiotic resistance. However, a comprehensive understanding of the global distribution, diversity, and transmission of antibiotic resistance genes (ARGs) in E. coli remains lacking, hindering effective strategies to combat resistance.<br><br>METHODS: In this study, we analyzed 94,762 E. coli genome sequences obtained from the NCBI database using advanced bioinformatics tools. ARGs were identified by comparing sequences against a custom ARG database using BLAST. Mobile genetic element (MGE)-associated ARGs were identified by matching with ISfinder databases. Global distribution of ARGs was analyzed by clustering mobile ARG sequences with 99% genetic similarity.<br><br>RESULTS: Our analysis revealed that 50.51% of the E. coli genome sequences contained ARGs, totaling 301,317 identified ARG sequences. These ARGs were categorized into 12 major classes and 229 subtypes. Notably, ARGs associated with multi-drug resistance (MDR), &#x3b2;-lactams, macrolide-lincosamide-streptogramins (MLS), tetracyclines, and aminoglycosides were particularly abundant, with the subtypes mdtK, macB, and ampC being especially prevalent. Additionally, significant differences in ARG abundance and diversity were observed across countries, with higher diversity found in high-income nations. Furthermore, 9.28% of the ARG sequences were linked to MGEs, accounting for 98.25% of all ARG subtypes. Notably, 4.20% of mobile ARGs were identified in over 20 countries, with &#x3b2;-lactam and aminoglycoside ARGs being the most widespread.<br><br>DISCUSSION: This study provides a comprehensive overview of the global distribution and transmission of ARGs in E. coli. The high abundance of MDR and &#x3b2;-lactam-related ARGs, along with their widespread transmission across countries, highlights the urgent need for global surveillance and control measures. Furthermore, the strong association between ARGs and MGEs underscores the role of horizontal gene transfer in the spread of resistance. The observed variations in ARG diversity between countries suggest that socioeconomic factors, such as healthcare infrastructure and antibiotic usage patterns, significantly influence ARG prevalence. These findings are crucial for informing global strategies to mitigate the spread of antibiotic resistance and improve public health outcomes.}, }
@article {pmid39606646, year = {2024}, author = {Wang, Z and Sun, M and Guo, S and Wang, Y and Meng, L and Shi, J and Geng, C and Han, D and Fu, X and Xue, J and Ma, H and Liu, K}, title = {Detection of drug resistance in Escherichia coli from calves with diarrhea in the Tongliao region: an analysis of multidrug-resistant strains.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1466690}, pmid = {39606646}, issn = {2297-1769}, abstract = {INTRODUCTION: Escherichia coli is a major pathogen responsible for calf diarrhea, which has been exacerbated by the irrational and unscientific use of antimicrobial drugs, leading to significant drug resistance.<br><br>METHODS: This study focused on the isolation and identification of E. coli from calf diarrhea samples in the Tongliao area of China. Isolation was conducted using selective media, Gram staining, and 16S rRNA sequencing. The minimum inhibitory concentration (MIC) of E. coli was determined through the microbroth dilution method. Additionally, the presence of antibiotic-resistant genes was detected, and multidrug-resistant strains were selected for whole-genome sequencing (WGS).<br><br>RESULTS: The results revealed that all 40 isolated strains of E. coli exhibited resistance to sulfadiazine sodium, enrofloxacin, and ciprofloxacin, with 90% of the strains being susceptible to polymyxin B. Notably, strains 11, 23, and 24 demonstrated severe resistance. The detection rates of the antibiotic resistance genes TEM-1, TEM-206, strA, strB, qacH, and blaCTX were 100%, indicating a high prevalence of these genes. Moreover, the majority of strains carried antibiotic resistance genes consistent with their resistance phenotypes. WGS of strains 11, 23, and 24 revealed genome sizes of 4,897,185&#x2009;bp, 4,920,234&#x2009;bp, and 4,912,320&#x2009;bp, respectively. These strains carried two, one, and two plasmids, respectively. The prediction of antibiotic resistance genes showed a substantial number of these genes within the genomes, with strain 24 harboring the highest number, totaling 77 subspecies containing 88 antibiotic resistance genes.<br><br>DISCUSSION: In conclusion, all 40 isolated strains of E. coli from calf diarrhea in this study were multidrug-resistant, exhibiting a broad distribution of antibiotic resistance genes and mobile components. This poses a significant risk of horizontal gene transfer, highlighting the critical situation of antibiotic resistance in this region.}, }
@article {pmid39605964, year = {2024}, author = {Jia, J and Liu, Q and Zhao, E and Li, X and Xiong, X and Wu, C}, title = {Biofilm formation on microplastics and interactions with antibiotics, antibiotic resistance genes and pathogens in aquatic environment.}, journal = {Eco-Environment &amp; Health}, volume = {3}, number = {4}, pages = {516-528}, pmid = {39605964}, issn = {2772-9850}, abstract = {Microplastics (MPs) in aquatic environments easily support biofilm development, which can interact with other environmental pollutants and act as harbors for microorganisms. Recently, numerous studies have investigated the fate and behavior of MP biofilms in aquatic environments, highlighting their roles in the spread of pathogens and antibiotic resistance genes (ARGs) to aquatic organisms and new habitats. The prevalence and effects of MP biofilms in aquatic environments have been extensively investigated in recent decades, and their behaviors in aquatic environments need to be synthesized systematically with updated information. This review aims to reveal the development of MP biofilm and its interactions with antibiotics, ARGs, and pathogens in aquatic environments. Recent research has shown that the adsorption capabilities of MPs to antibiotics are enhanced after the biofilm formation, and the adsorption of biofilms to antibiotics is biased towards chemisorption. ARGs and microorganisms, especially pathogens, are selectively enriched in biofilms and significantly different from those in surrounding waters. MP biofilm promotes the propagation of ARGs through horizontal gene transfer (HGT) and vertical gene transfer (VGT) and induces the emergence of antibiotic-resistant pathogens, resulting in increased threats to aquatic ecosystems and human health. Some future research needs and strategies in this review are also proposed to better understand the antibiotic resistance induced by MP biofilms in aquatic environments.}, }
@article {pmid39605872, year = {2024}, author = {Kettlewell, R and Jones, C and Felton, TW and Lagator, M and Gifford, DR}, title = {Insights into durability against resistance from the antibiotic nitrofurantoin.}, journal = {npj antimicrobials and resistance}, volume = {2}, number = {1}, pages = {41}, pmid = {39605872}, issn = {2731-8745}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {Nitrofurantoin has shown exceptional durability against resistance over 70 years of use. This longevity stems from factors such as rapid achievement of therapeutic concentrations, multiple physiological targets against bacteria, low risk of horizontal gene transfer, and the need to acquire multiple mutations to achieve resistance. These combined features limit resistance emergence and spread of nitrofurantoin resistance. We propose nitrofurantoin as an exemplar for developing other durable treatments.}, }
@article {pmid39603126, year = {2025}, author = {Zhao, W and Zhang, B and Zheng, S and Yan, W and Yu, X and Ye, C}, title = {High temperatures promote antibiotic resistance genes conjugative transfer under residual chlorine: Mechanisms and risks.}, journal = {Journal of hazardous materials}, volume = {483}, number = {}, pages = {136675}, doi = {10.1016/j.jhazmat.2024.136675}, pmid = {39603126}, issn = {1873-3336}, mesh = {*Chlorine ; *Hot Temperature ; *Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; *Conjugation, Genetic/drug effects ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects ; *Gene Transfer, Horizontal ; }, abstract = {The impact of residual chlorine on the dissemination of antibiotic resistance during the distribution and storage of water has become a critical concern. However, the influence of rising temperatures attributed to global warming on this process remains ambiguous, warranting further investigation. This study investigated the effects of different temperatures (17, 27, 37, and 42°C) on the conjugative transfer of antibiotic resistance genes (ARGs) under residual chlorine (0, 0.1, 0.3, and 0.5 mg/L). The results indicated that high temperatures significantly increased the conjugative transfer frequency of ARGs in intra-species under residual chlorine. Compared to 17°C, the transfer frequencies at 27°C, 37°C, and 42°C increased by 1.07-2.43, 1.20-4.80, and 1.24-2.82 times, respectively. The promoting effect of high temperatures was mainly due to the generation of reactive oxygen species, the triggered SOS response, and the formation of pilus channels. Transcriptomic analysis demonstrated that higher temperature stimulates the electron transport chain, thereby enhancing ATP production and facilitating the processes of conjugative, as confirmed by inhibitor validation. Additionally, rising temperatures similarly promoted the frequency of conjugative transfer in inter-species and communities under residual chlorine. These further highlighted the risk of antibiotic resistance spread in extreme and prolonged high-temperature events. The increased risk of antibiotic resistance in the process of drinking water transmission under the background of climate warming is emphasized.}, }
@article {pmid39602248, year = {2024}, author = {Dai, L and Wu, Z and Sahin, O and Zhao, S and Yu, EW and Zhang, Q}, title = {Mutation-based mechanism and evolution of the potent multidrug efflux pump RE-CmeABC in Campylobacter.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {51}, pages = {e2415823121}, pmid = {39602248}, issn = {1091-6490}, support = {R01 AI140669/AI/NIAID NIH HHS/United States ; R01AI140669//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; }, mesh = {*Campylobacter jejuni/genetics/metabolism ; *Evolution, Molecular ; *Drug Resistance, Multiple, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; *Bacterial Proteins/genetics/metabolism ; *Mutation ; *Membrane Transport Proteins/genetics/metabolism ; Campylobacter/genetics/metabolism ; Humans ; Campylobacter Infections/microbiology ; Promoter Regions, Genetic ; Amino Acid Substitution ; }, abstract = {The resistance-nodulation-cell division (RND) superfamily of multidrug efflux systems are important players in mediating antibiotic resistance in gram-negative pathogens. Campylobacter jejuni, a major enteric pathogen, utilizes an RND-type transporter system, CmeABC, as the primary mechanism for extrusion of various antibiotics. Recently, a functionally potent variant of CmeABC (named RE-CmeABC) emerged in clinical Campylobacter isolates, conferring enhanced resistance to multiple antibiotic classes. Despite the clinical importance of RE-CmeABC, the molecular mechanisms for its functional gain and its evolutionary trajectory remain unknown. Here, we demonstrated that amino acid substitutions in RE-CmeB (inner membrane transporter), but not in RE-CmeA (periplasmic protein) and RE-CmeC (outer membrane protein), in conjunction with a nucleotide mutation in the promoter region of the efflux operon, are responsible for the functional gain of the multidrug efflux system. We also showed that RE-cmeABC is emerging globally and distributed in genetically diverse C. jejuni strains, suggesting its possible spread by horizontal gene transfer. Notably, many of RE-cmeABC harboring isolates were associated with the human host including strains from large disease outbreaks, indicating the clinical relevance and significance of RE-CmeABC. Evolutionary analysis indicated that RE-cmeB likely originated from Campylobacter coli, but its expansion mainly occurred in C. jejuni, possibly driven by antibiotic selection pressure. Additionally, RE-cmeB, but not RE-cmeA and RE-cmeC, experienced a selective sweep and was progressing to be fixed during evolution. Together, these results identify a mutation-based mechanism for functional gain in RE-CmeABC and reveal the key role of RE-CmeB in facilitating Campylobacter adaptation to antibiotic selection.}, }
@article {pmid39599864, year = {2024}, author = {Richards, VA and Ferrell, BD and Polson, SW and Wommack, KE and Fuhrmann, JJ}, title = {Soybean Bradyrhizobium spp. Spontaneously Produce Abundant and Diverse Temperate Phages in Culture.}, journal = {Viruses}, volume = {16}, number = {11}, pages = {}, pmid = {39599864}, issn = {1999-4915}, support = {P20 GM103446/GM/NIGMS NIH HHS/United States ; S10 OD028725/OD/NIH HHS/United States ; 1736030//National Science Foundation/ ; }, mesh = {*Bradyrhizobium/virology ; *Glycine max/virology/microbiology ; *Bacteriophages/isolation &amp; purification/genetics/classification/physiology/ultrastructure ; Lysogeny ; Genome, Viral ; Symbiosis ; Microscopy, Electron, Transmission ; }, abstract = {Soybean bradyrhizobia (Bradyrhizobium spp.) are symbiotic root-nodulating bacteria that fix atmospheric nitrogen for the host plant. The University of Delaware Bradyrhizobium Culture Collection (UDBCC; 353 accessions) was created to study the diversity and ecology of soybean bradyrhizobia. Some UDBCC accessions produce temperate (lysogenic) bacteriophages spontaneously under routine culture conditions without chemical or other apparent inducing agents. Spontaneous phage production may promote horizontal gene transfer and shape bacterial genomes and associated phenotypes. A diverse subset (n = 98) of the UDBCC was examined for spontaneously produced virus-like particles (VLPs) using epifluorescent microscopy, with a majority (69%) producing detectable VLPs (>1 × 10[7] mL[-1]) in laboratory culture. Phages from the higher-producing accessions (>2.0 × 10[8] VLP mL[-1]; n = 44) were examined using transmission electron microscopy. Diverse morphologies were observed, including various tail types and lengths, capsid sizes and shapes, and the presence of collars or baseplates. In many instances, putative extracellular vesicles of a size similar to virions were also observed. Three of the four species examined (B. japonicum, B. elkanii, and B. diazoefficiens) produced apparently tailless phages. All species except B. ottawaense also produced siphovirus-like phages, while all but B. diazoefficiens additionally produced podovirus-like phages. Myovirus-like phages were restricted to B. japonicum and B. elkanii. At least three strains were polylysogens, producing up to three distinct morphotypes. These observations suggest spontaneously produced phages may play a significant role in the ecology and evolution of soybean bradyrhizobia.}, }
@article {pmid39599778, year = {2024}, author = {Yoxsimer, AM and Offenberg, EG and Katzer, AW and Bell, MA and Massengill, RL and Kingsley, DM}, title = {Genomic Sequence of the Threespine Stickleback Iridovirus (TSIV) from Wild Gasterosteus aculeatus in Stormy Lake, Alaska.}, journal = {Viruses}, volume = {16}, number = {11}, pages = {}, pmid = {39599778}, issn = {1999-4915}, support = {R01 GM124330/GM/NIGMS NIH HHS/United States ; Investigator/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; *Phylogeny ; Alaska ; *Smegmamorpha/virology ; *Genome, Viral ; *Fish Diseases/virology ; *Open Reading Frames ; *Iridovirus/genetics/classification/isolation &amp; purification ; *Lakes/virology ; DNA Virus Infections/veterinary/virology ; Genomics/methods ; DNA, Viral/genetics ; }, abstract = {The threespine stickleback iridovirus (TSIV), a double-stranded DNA virus, was the first megalocytivirus detected in wild North American fishes. We report a second occurrence of TSIV in threespine stickleback (Gasterosteus aculeatus) from Stormy Lake, Alaska, and assemble a nearly complete genome of TSIV. The 115-kilobase TSIV genome contains 94 open reading frames (ORFs), with 91 that share homology with other known iridoviruses. We identify three ORFs that likely originate from recent lateral gene transfers from a eukaryotic host and one ORF with homology to B22 poxvirus proteins that likely originated from a lateral gene transfer between viruses. Phylogenetic analysis of 24 iridovirus core genes and pairwise sequence identity analysis support TSIV as a divergent sister taxon to other megalocytiviruses and a candidate for a novel species designation. Screening of stickleback collected from Stormy Lake before and after a 2012 rotenone treatment to eliminate invasive fish shows 100% positivity for TSIV in the two years before treatment (95% confidence interval: 89-100% prevalence) and 0% positivity for TSIV in 2024 after treatment (95% confidence interval: 0 to 3.7% prevalence), suggesting that the rotenone treatment and subsequent crash and reestablishment of the stickleback population is associated with loss of TSIV.}, }
@article {pmid39599474, year = {2024}, author = {McDonald, NL and Wareham, DW and Bean, DC}, title = {Aeromonas and mcr-3: A Critical Juncture for Transferable Polymyxin Resistance in Gram-Negative Bacteria.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {11}, pages = {}, pmid = {39599474}, issn = {2076-0817}, mesh = {Humans ; *Aeromonas/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacterial Proteins/genetics ; *Colistin/pharmacology/therapeutic use ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Escherichia coli Proteins/genetics ; Gene Transfer, Horizontal ; Gram-Negative Bacteria/drug effects/genetics ; *Gram-Negative Bacterial Infections/microbiology/drug therapy ; Microbial Sensitivity Tests ; Phylogeny ; *Polymyxins/pharmacology/therapeutic use ; Transferases (Other Substituted Phosphate Groups) ; }, abstract = {Polymyxin antibiotics B and colistin are considered drugs of last resort for the treatment of multi-drug and carbapenem-resistant Gram-negative bacteria. With the emergence and dissemination of multi-drug resistance, monitoring the use and resistance to polymyxins imparted by mobilised colistin resistance genes (mcr) is becoming increasingly important. The Aeromonas genus is widely disseminated throughout the environment and serves as a reservoir of mcr-3, posing a significant risk for the spread of resistance to polymyxins. Recent phylogenetic studies and the identification of insertion elements associated with mcr-3 support the notion that Aeromonas spp. may be the evolutionary origin of the resistance gene. Furthermore, mcr-3-related genes have been shown to impart resistance in naïve E. coli and can increase the polymyxin MIC by up to 64-fold (with an MIC of 64 mg/L) in members of Aeromonas spp. This review will describe the genetic background of the mcr gene, the epidemiology of mcr-positive isolates, and the relationship between intrinsic and transferable mcr resistance genes, focusing on mcr-3 and mcr-3-related genes.}, }
@article {pmid39597557, year = {2024}, author = {Shah, Y and Kafaie, S}, title = {Evaluating Sequence Alignment Tools for Antimicrobial Resistance Gene Detection in Assembly Graphs.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597557}, issn = {2076-2607}, abstract = {Antimicrobial resistance (AMR) is an escalating global health threat, often driven by the horizontal gene transfer (HGT) of resistance genes. Detecting AMR genes and understanding their genomic context within bacterial populations is crucial for mitigating the spread of resistance. In this study, we evaluate the performance of three sequence alignment tools-Bandage, SPAligner, and GraphAligner-in identifying AMR gene sequences from assembly and de Bruijn graphs, which are commonly used in microbial genome assembly. Efficiently identifying these genes allows for the detection of neighboring genetic elements and possible HGT events, contributing to a deeper understanding of AMR dissemination. We compare the performance of the tools both qualitatively and quantitatively, analyzing the precision, computational efficiency, and accuracy in detecting AMR-related sequences. Our analysis reveals that Bandage offers the most precise and efficient identification of AMR gene sequences, followed by GraphAligner and SPAligner. The comparison includes evaluating the similarity of paths returned by each tool and measuring output accuracy using a modified edit distance metric. These results highlight Bandage's potential for contributing to the accurate identification and study of AMR genes in bacterial populations, offering important insights into resistance mechanisms and potential targets for mitigating AMR spread.}, }
@article {pmid39597512, year = {2024}, author = {Banerji, A and Brinkman, NE and Davis, B and Franklin, A and Jahne, M and Keely, SP}, title = {Food Webs and Feedbacks: The Untold Ecological Relevance of Antimicrobial Resistance as Seen in Harmful Algal Blooms.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597512}, issn = {2076-2607}, abstract = {Antimicrobial resistance (AMR) has long been framed as an epidemiological and public health concern. Its impacts on the environment are unclear. Yet, the basis for AMR is altered cell physiology. Just as this affects how microbes interact with antimicrobials, it can also affect how they interact with their own species, other species, and their non-living environment. Moreover, if the microbes are globally notorious for causing landscape-level environmental issues, then these effects could alter biodiversity and ecosystem function on a grand scale. To investigate these possibilities, we compiled peer-reviewed literature from the past 20 years regarding AMR in toxic freshwater cyanobacterial harmful algal blooms (HABs). We examined it for evidence of AMR affecting HAB frequency, severity, or persistence. Although no study within our scope was explicitly designed to address the question, multiple studies reported AMR-associated changes in HAB-forming cyanobacteria (and co-occurring microbes) that pertained directly to HAB timing, toxicity, and phase, as well as to the dynamics of HAB-afflicted aquatic food webs. These findings highlight the potential for AMR to have far-reaching environmental impacts (including the loss of biodiversity and ecosystem function) and bring into focus the importance of confronting complex interrelated issues such as AMR and HABs in concert, with interdisciplinary tools and perspectives.}, }
@article {pmid39596782, year = {2024}, author = {Mendoza-Guido, B and Barrantes, K and Rodríguez, C and Rojas-Jimenez, K and Arias-Andres, M}, title = {The Impact of Urban Pollution on Plasmid-Mediated Resistance Acquisition in Enterobacteria from a Tropical River.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {11}, pages = {}, pmid = {39596782}, issn = {2079-6382}, support = {C1455, C2650, C3509//Vicerrector&#xed;a de Investigaci&#xf3;n of the Universidad de Costa Rica/ ; SIA 0483-21//Universidad Nacional, Costa Rica/ ; Proyecto Plasmidoma//Consejo Nacional de Rectores (CONARE), Costa Rica/ ; }, abstract = {Background: The exposure of environmental bacteria to contaminants in aquatic ecosystems accelerates the dissemination of antibiotic-resistance genes (ARGs) through horizontal gene transfer (HGT). Methods: In this study, we sampled three locations along a contamination gradient of a polluted river, focusing on isolating Enterobacteria from the surface waters to investigate the relationship between urban pollution and antibiotic resistance. The genomes of 15 isolates (5 per site) were sequenced to identify plasmid-borne ARGs and their association with resistance phenotypes. Results: Isolates from the site with the highest contamination (Site 3) showeda larger number of ARGs, plasmids, and resistance phenotypes. Notably, one of the isolates analyzed, E. coli A231-12, exhibited phenotypic resistance to seven antibiotics, presumably conferred by a single plasmid carrying 12 ARGs. Comparative analysis of this plasmid revealed its close evolutionary relationship with another IncH plasmid hosted by Salmonella enterica, underscoring its high ARG burden in the aquatic environment. Other plasmids identified in our isolates carried sul and dfrA genes, conferring resistance to trimethoprim/sulfamethoxazole, a commonly prescribed antibiotic combination in clinical settings. Conclusions: These results highlight the critical need to expand research on the link between pollution and plasmid-mediated antimicrobial resistance in aquatic ecosystems, which can act as reservoirs of ARGs.}, }
@article {pmid39596781, year = {2024}, author = {Ifedinezi, OV and Nnaji, ND and Anumudu, CK and Ekwueme, CT and Uhegwu, CC and Ihenetu, FC and Obioha, P and Simon, BO and Ezechukwu, PS and Onyeaka, H}, title = {Environmental Antimicrobial Resistance: Implications for Food Safety and Public Health.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {11}, pages = {}, pmid = {39596781}, issn = {2079-6382}, abstract = {Antimicrobial resistance (AMR) is a serious global health issue, aggravated by antibiotic overuse and misuse in human medicine, animal care, and agriculture. This study looks at the different mechanisms that drive AMR, such as environmental contamination, horizontal gene transfer, and selective pressure, as well as the severe implications of AMR for human and animal health. This study demonstrates the need for concerted efforts across the scientific, healthcare, agricultural, and policy sectors to control the emergence of AMR. Some crucial strategies discussed include developing antimicrobial stewardship (AMS) programs, encouraging targeted narrow-spectrum antibiotic use, and emphasizing the significance of strict regulatory frameworks and surveillance systems, like the Global Antimicrobial Resistance and Use Surveillance System (GLASS) and the Access, Watch, and Reserve (AWaRe) classification. This study also emphasizes the need for national and international action plans in combating AMR and promotes the One Health strategy, which unifies environmental, animal, and human health. This study concludes that preventing the spread of AMR and maintaining the effectiveness of antibiotics for future generations requires a comprehensive, multidisciplinary, and internationally coordinated strategy.}, }
@article {pmid39596258, year = {2024}, author = {Dec, M and Nowak, T and Webster, J and Wódz, K}, title = {Serotypes, Antimicrobial Susceptibility, and Potential Mechanisms of Resistance Gene Transfer in Erysipelothrix rhusiopathiae Strains from Waterfowl in Poland.}, journal = {International journal of molecular sciences}, volume = {25}, number = {22}, pages = {}, pmid = {39596258}, issn = {1422-0067}, mesh = {Animals ; Poland ; *Erysipelothrix/genetics ; *Serogroup ; *Anti-Bacterial Agents/pharmacology ; *Geese/microbiology ; Ducks/microbiology ; Microbial Sensitivity Tests ; Erysipelothrix Infections/microbiology/genetics ; Multilocus Sequence Typing ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Drug Resistance, Multiple, Bacterial/genetics ; }, abstract = {Erysipelas is a significant problem in the waterfowl farming in Poland, and information on the characteristics of the Erysipelothrix rhusiopathiae strains causing this disease is limited. In this study, we determined the serotypes, antimicrobial susceptibility, and potential mechanisms of resistance gene transfer in E. rhusiopathiae isolates (n = 60) from domestic geese and ducks. We also developed a multiplex PCR for the detection of resistance genes. The antimicrobial susceptibility of the isolates was assessed using the broth microdilution method. Resistance genes, integrative conjugative element (ICE)-specific genes, phage-specific genes, and serotype determinants were detected by PCR. Multilocus sequence typing (MLST) was performed for selected resistant strains. The comparative analyses included 260 E. rhusiopathiae strains whose whole genome sequences (WGSs) are publicly available. E. rhusiopathiae isolates represented 7 serotypes, among which serotypes 5 (38.3%) and 1b (28.3%) were the most common. All strains were susceptible to β-lactams, and the vast majority of them were resistant to tetracycline (85%) and enrofloxacin (80%). The percentages of isolates resistant to other antimicrobials used ranged from 3.3% to 16.7%. Ten isolates (16.7%) were found to be multidrug resistant (MDR). The genotypic resistance profiles of the E. rhusiopathiae strains corresponded to their phenotypic resistance, and the amplification patterns obtained using the 10-plex PCR developed in this study were fully consistent with the results of single PCRs. The most prevalent resistance gene was tetM. In enrofloxacin-resistant strains, nonsynonymous mutations in the gyrA and parC genes were identified. The presence of ICE-specific genes was confirmed in resistant strains, and in MDR isolates of serotype 8 that represented sequence type (ST) 113, prophage DNA (Javan630-like) linked to the lsaE gene was additionally detected. The results indicate that β-lactam antibiotics should be the first choice for the treatment of waterfowl erysipelas in Poland. ICEs, including a transposon from the Tn916/Tn1545 family, and bacteriophages are most likely responsible for the transfer of resistance genes in E. rhusiopathiae.}, }
@article {pmid39592962, year = {2024}, author = {Mane, A and Sanderson, H and White, AP and Zaheer, R and Beiko, R and Chauve, C}, title = {Plaseval: a framework for comparing and evaluating plasmid detection tools.}, journal = {BMC bioinformatics}, volume = {25}, number = {1}, pages = {365}, pmid = {39592962}, issn = {1471-2105}, mesh = {*Plasmids/genetics/metabolism ; Software ; Genome, Bacterial ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Plasmids play a major role in the transfer of antimicrobial resistance (AMR) genes among bacteria via horizontal gene transfer. The identification of plasmids in short-read assemblies is a challenging problem and a very active research area. Plasmid binning aims at detecting, in a draft genome assembly, groups (bins) of contigs likely to originate from the same plasmid. Several methods for plasmid binning have been developed recently, such as PlasBin-flow, HyAsP, gplas, MOB-suite, and plasmidSPAdes. This motivates the problem of evaluating the performances of plasmid binning methods, either against a given ground truth or between them.<br><br>RESULTS: We describe PlasEval, a novel method aimed at comparing the results of plasmid binning tools. PlasEval computes a dissimilarity measure between two sets of plasmid bins, that can originate either from two plasmid binning tools, or from a plasmid binning tool and a ground truth set of plasmid bins. The PlasEval dissimilarity accounts for the contig content of plasmid bins, the length of contigs and is repeat-aware. Moreover, the dissimilarity score computed by PlasEval is broken down into several parts, that allows to understand qualitative differences between the compared sets of plasmid bins. We illustrate the use of PlasEval by benchmarking four recently developed plasmid binning tools-PlasBin-flow, HyAsP, gplas, and MOB-recon-on a data set of 53 E. coli bacterial genomes.<br><br>CONCLUSION: Analysis of the results of plasmid binning methods using PlasEval shows that their behaviour varies significantly. PlasEval can be used to decide which specific plasmid binning method should be used for a specific dataset. The disagreement between different methods also suggests that the problem of plasmid binning on short-read contigs requires further research. We believe that PlasEval can prove to be an effective tool in this regard. PlasEval is publicly available at https://github.com/acme92/PlasEval.}, }
@article {pmid39592922, year = {2024}, author = {Das, VA and Gautam, B and Yadav, PK and Varadwaj, PK and Wadhwa, G and Singh, S}, title = {Computational approach to identify novel genomic features conferring high fitness in Bacillus atrophaeus CNY01 and Bacillus velezensis AK-0 associated with plant growth promotion (PGP) in apple.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {1127}, pmid = {39592922}, issn = {1471-2229}, mesh = {*Bacillus/genetics/physiology ; *Malus/microbiology/genetics ; *Genome, Bacterial ; Genetic Fitness ; Genomics/methods ; Genomic Islands ; Computational Biology/methods ; }, abstract = {A comparative genomic analysis approach provides valuable information about genetic variations and evolutionary relationships among microorganisms, aiding not only in the identification of functional genes responsible for traits such as pathogenicity, antibiotic resistance, and metabolic capabilities but also in enhancing our understanding of microbial genomic diversity and their ecological roles, such as supporting plant growth promotion, thereby enabling the development of sustainable strategies for agriculture. We used two strains from different Bacillus species, Bacillus velezensis AK-0 and Bacillus atrophaeus CNY01, which have previously been reported to have PGP activity in apple, and performed comparative genomic analysis to understand their evolutionary process and obtain a mechanistic understanding of their plant growth-promoting activity. We identified genomic features such as mobile genetic elements (MGEs) that encode key proteins involved in the survival, adaptation and growth of these bacterial strains. The presence of genomic islands and intact prophage DNA in Bacillus atrophaeus CNY01 and Bacillus velezensis AK-0 suggests that horizontal gene transfer has contributed to their diversification and acquisition of adaptive traits, enhancing their evolutionary advantage. We also identified novel DNA motifs that are associated with key physiological processes and metabolic pathways.}, }
@article {pmid39591316, year = {2024}, author = {Jafari Jozani, R and Khallawi, MFHA and Trott, D and Petrovski, K and Low, WY and Hemmatzadeh, F}, title = {Unravelling Antimicrobial Resistance in Mycoplasma hyopneumoniae: Genetic Mechanisms and Future Directions.}, journal = {Veterinary sciences}, volume = {11}, number = {11}, pages = {}, pmid = {39591316}, issn = {2306-7381}, support = {2021/0025//Australian Pork (APL)/ ; }, abstract = {Antimicrobial resistance (AMR) in Mycoplasma hyopneumoniae, the causative agent of Enzootic Pneumonia in swine, poses a significant challenge to the swine industry. This review focuses on the genetic foundations of AMR in M. hyopneumoniae, highlighting the complexity of resistance mechanisms, including mutations, horizontal gene transfer, and adaptive evolutionary processes. Techniques such as Whole Genome Sequencing (WGS) and multiple-locus variable number tandem repeats analysis (MLVA) have provided insights into the genetic diversity and resistance mechanisms of M. hyopneumoniae. The study underscores the role of selective pressures from antimicrobial use in driving genomic variations that enhance resistance. Additionally, bioinformatic tools utilizing machine learning algorithms, such as CARD and PATRIC, can predict resistance traits, with PATRIC predicting 7 to 12 AMR genes and CARD predicting 0 to 3 AMR genes in 24 whole genome sequences available on NCBI. The review advocates for a multidisciplinary approach integrating genomic, phenotypic, and bioinformatics data to combat AMR effectively. It also elaborates on the need for refining genotyping methods, enhancing resistance prediction accuracy, and developing standardized antimicrobial susceptibility testing procedures specific to M. hyopneumoniae as a fastidious microorganism. By leveraging contemporary genomic technologies and bioinformatics resources, the scientific community can better manage AMR in M. hyopneumoniae, ultimately safeguarding animal health and agricultural productivity. This comprehensive understanding of AMR mechanisms will be beneficial in the adaptation of more effective treatment and management strategies for Enzootic Pneumonia in swine.}, }
@article {pmid39590772, year = {2024}, author = {Cui, H and Lu, J and Ding, W and Zhang, W}, title = {Genomic Features and Antimicrobial Activity of Phaeobacter inhibens Strains from Marine Biofilms.}, journal = {Marine drugs}, volume = {22}, number = {11}, pages = {}, pmid = {39590772}, issn = {1660-3397}, mesh = {*Biofilms/drug effects ; *Rhodobacteraceae/genetics ; *Phylogeny ; *Genome, Bacterial ; *Anti-Bacterial Agents/pharmacology ; *Tropolone/pharmacology/analogs &amp; derivatives ; Multigene Family ; Aquatic Organisms ; Vibrio/genetics/drug effects ; Genomics/methods ; Animals ; }, abstract = {Members of the genus Phaeobacter are widely distributed in the marine environment and are known for their ability to produce tropodithietic acid (TDA). Studies investigating the genomic and metabolic features of Phaeobacter strains from marine biofilms are sparse. Here, we analyze the complete genomes of 18 Phaeobacter strains isolated from biofilms on subtidal stones, with the aim of determining their potential to synthesize secondary metabolites. Based on whole-genome comparison and average nucleotide identity calculation, the isolated bacteria are classified as novel strains of Phaeobacter inhibens. Further analysis reveals a total of 153 biosynthetic gene clusters, which are assigned to 32 gene cluster families with low similarity to previously published ones. Complete TDA clusters are identified in 14 of the 18 strains, while in the other 4 strains the TDA clusters are rather incomplete and scattered across different chromosome and plasmid locations. Phylogenetic analysis suggests that their presence or absence may be potentially attributed to horizontal gene transfer. High-performance liquid chromatography-mass spectrometry analysis demonstrates the production of TDA in all the examined strains. Furthermore, the Phaeobacter strains have strong antibacterial activity against the pathogenic strain Vibrio owensii ems001, which is associated with acute hepatopancreatic necrosis in South American white shrimp. Altogether, this study ameliorates our knowledge of marine biofilm-associated Phaeobacter and offers new avenues for exploiting marine antimicrobial agents.}, }
@article {pmid39589125, year = {2024}, author = {Zhang, Z and Tong, M and Ding, W and Liu, S and Jong, M-C and Radwan, AA and Cai, Z and Zhou, J}, title = {Changes in the diversity and functionality of viruses that can bleach healthy coral.}, journal = {mSphere}, volume = {9}, number = {12}, pages = {e0081624}, pmid = {39589125}, issn = {2379-5042}, mesh = {*Anthozoa/virology/microbiology ; Animals ; *Microbiota/genetics ; *Viruses/genetics/classification ; *Metagenomics ; Bacteria/genetics/classification/virology/isolation &amp; purification ; Symbiosis ; Bacteriophages/genetics/physiology/classification/isolation &amp; purification ; }, abstract = {UNLABELLED: Coral microbiomes play a crucial role in maintaining the health and functionality of holobionts. Disruption in the equilibrium of holobionts, including bacteria, fungi, and archaea, can result in the bleaching of coral. However, little is known about the viruses that can infect holobionts in coral, especially bacteriophages. Here, we employed a combination of amplicon and metagenomic analyses on Acropora muricata and Galaxea astreata to investigate the diversity and functionality of viruses in healthy and bleached corals. Analysis showed that the alpha diversity of holobionts (bacteria, eukaryotes, zooxanthellae, and lysogenic and lytic viruses) was higher in bleached corals than that in healthy corals. Meanwhile, bleached corals exhibited a relatively higher abundance of specific viral classes, including Revtraviricetes, Arfiviricetes, Faserviricetes, Caudoviricetes, Herviviricetes, and Tectiliviricetes; moreover, we found that the expression levels of functional genes involved in carbon and sulfur metabolism were enriched. An increase in Vibrio abundance has been reported as a notable factor in coral bleaching; our analysis also revealed an increased abundance of Vibrio in bleached coral. Finally, bleached corals contained a higher abundance of Vibrio phages and encoded more virulence factor genes to increase the competitiveness of Vibrio after coral bleaching. In conclusion, we attempted to understand the causes of coral bleaching from the perspective of phage-bacteria-coral tripartite interaction.<br><br>IMPORTANCE: Viruses, especially bacteriophages, outnumber other microorganisms by approximately 10-fold and represent the most abundant members of coral holobionts. Corals represent a model system for the study of symbiosis, the influence of viruses on organisms inhabiting healthy coral reef, the role of rapid horizontal gene transfer, and the expression of auxiliary metabolic genes. However, the least studied component of coral holobiont are viruses. Therefore, there is a critical need to investigate the viral community of viruses, and their functionality, in healthy and bleached coral. Here, we compared the composition and functionality of viruses in healthy and bleached corals and found that viruses may participate in the induction of coral bleaching by enhancing the expression of virulence genes and other auxiliary metabolic functions.}, }
@article {pmid39587099, year = {2024}, author = {Sheikh, S and Fu, CJ and Brown, MW and Baldauf, SL}, title = {The Acrasis kona genome and developmental transcriptomes reveal deep origins of eukaryotic multicellular pathways.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {10197}, pmid = {39587099}, issn = {2041-1723}, support = {VR 2017-04351//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2100888//National Science Foundation (NSF)/ ; }, mesh = {*Transcriptome ; *Dictyostelium/genetics/growth &amp; development ; Genome, Protozoan ; Amoeba/genetics ; Phylogeny ; Gene Transfer, Horizontal ; Protozoan Proteins/genetics/metabolism ; Proteome/metabolism/genetics ; Genome ; }, abstract = {Acrasids are amoebae with the capacity to form multicellular fruiting bodies in a process known as aggregative multicellularity (AGM). This makes acrasids the only known example of multicellularity among the earliest branches of eukaryotes (the former Excavata). Here, we report the Acrasis kona genome sequence plus transcriptomes from pre-, mid- and post-developmental stages. The genome is rich in novelty and genes with strong signatures of horizontal transfer, and multigene families encode nearly half of the amoeba's predicted proteome. Development in A. kona appears molecularly simple relative to the AGM model, Dictyostelium discoideum. However, the acrasid also differs from the dictyostelid in that it does not appear to be starving during development. Instead, developing A. kona appears to be very metabolically active, does not induce autophagy and does not up-regulate its proteasomal genes. Together, these observations strongly suggest that starvation is not essential for AGM development. Nonetheless, development in the two amoebae appears to employ remarkably similar pathways for signaling, motility and, potentially, construction of an extracellular matrix surrounding the developing cell mass. Much of this similarity is also shared with animal development, suggesting that much of the basic tool kit for multicellular development arose early in eukaryote evolution.}, }
@article {pmid39581358, year = {2025}, author = {Fischer, K and Jordbræk, SV and Olsen, S and Bockwoldt, M and Schwacke, R and Usadel, B and Krause, K}, title = {Taken to extremes: Loss of plastid rpl32 in Streptophyta and Cuscuta's unconventional solution for its replacement.}, journal = {Molecular phylogenetics and evolution}, volume = {204}, number = {}, pages = {108243}, doi = {10.1016/j.ympev.2024.108243}, pmid = {39581358}, issn = {1095-9513}, mesh = {Phylogeny ; *Plastids/genetics ; Gene Transfer, Horizontal ; *Streptophyta/genetics/classification ; *Cuscuta/genetics/classification ; *Evolution, Molecular ; *Ribosomal Proteins/genetics ; Sequence Analysis, DNA ; }, abstract = {The evolution of plant genomes is riddled with exchanges of genetic material within one plant (endosymbiotic gene transfer/EGT) and between unrelated plants (horizontal gene transfer/HGT). These exchanges have left their marks on plant genomes. Parasitic plants with their special evolutionary niche provide ample examples for these processes because they are under a reduced evolutionary pressure to maintain autotrophy and thus to conserve their plastid genomes. On the other hand, the close physical connections with different hosts enabled them to acquire genetic material from other plants. Based on an analysis of an extensive dataset including the parasite Cuscuta campestris and other parasitic plant species, we identified a unique evolutionary history of rpl32 genes coding for an essential plastid ribosomal subunit in Cuscuta. Our analysis suggests that the gene was most likely sequestered by HGT from a member of the Oxalidales order serving as host to an ancestor of the Cuscuta subgenus Grammica. Oxalidales had suffered an ancestral EGT of rpl32 predating the evolution of the genus Cuscuta. The HGT subsequently relieved the plastid rpl32 from its evolutionary constraint and led to its loss from the plastid genome. The HGT-based acquisition in Cuscuta is supported by a high sequence similarity of the mature L32 protein between species of the subgenus Grammica and representatives of the Oxalidales, and by a surprisingly conserved transit peptide, whose functionality in Cuscuta was experimentally verified. The findings are discussed in view of an overall pattern of EGT events for plastid ribosomal subunits in Streptophyta.}, }
@article {pmid39581254, year = {2025}, author = {Xu, F and Xiang, Q and Xu, ML and Carter, LJ and Du, WC and Zhu, CW and Ai, FX and Yin, Y and Ji, R and Guo, HY}, title = {Elevated CO2 alters antibiotic resistome in soil amended with sulfamethazine via chemical-organic fertilization.}, journal = {Environmental research}, volume = {264}, number = {Pt 2}, pages = {120416}, doi = {10.1016/j.envres.2024.120416}, pmid = {39581254}, issn = {1096-0953}, mesh = {*Sulfamethazine ; *Soil Microbiology ; *Fertilizers/analysis ; *Carbon Dioxide ; *Soil/chemistry ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial/drug effects ; Bacteria/drug effects/genetics ; }, abstract = {Rising antimicrobial resistance (AMR) is an enormous challenge for global healthcare systems. The effects of elevated CO2 (eCO2) on AMR are poorly characterized. Using a free-air CO2 enrichment system and high-throughput qPCR arrays, we investigated the response of soil antibiotic resistome and bacterial communities to eCO2 (ambient + 200 ppm) in soils amended with sulfamethazine (SMZ) at 0.1 and 1 mg kg[-1] via chemical-organic fertilizer (COL, COH). Results showed that under ambient condition, COH significantly enhanced the diversity of high-risk antibiotic resistance genes (ARGs), relative abundance of low risk ARGs, unassessed ARGs and total ARGs compared to COL. Nevertheless, eCO2 mitigated the effects of COH, with no significant difference found between COL and COH on the above high risk, low risk, unassessed and total ARGs. Meanwhile, eCO2 decreased the relative abundance of spcN, ermA, olec, oprD, sulA-olP, tetB, tetT and vanXD in COL, and alleviated the enrichment of pikR2, ampC, lunC, oprD and pncA caused by the application of SMZ at 1 mg kg[-1]. Correlation and network analysis illustrated that changes of certain bacteria biomarkers and horizontal gene transfer of integrase gene were associated with the altered response of ARGs abundance to eCO2. This study adds knowledge of the potential risk of antibiotic resistance in agricultural exposure scenarios under increasing CO2 concentration.}, }
@article {pmid39581077, year = {2024}, author = {Guernier-Cambert, V and Trachsel, J and Atkinson, B and Oladeinde, A and Anderson, CL and Bearson, SMD and Monson, MS and Looft, T}, title = {Tetracycline resistance gene transfer from Escherichia coli donors to Salmonella Heidelberg in chickens is impacted by the genetic context of donors.}, journal = {Veterinary microbiology}, volume = {299}, number = {}, pages = {110294}, doi = {10.1016/j.vetmic.2024.110294}, pmid = {39581077}, issn = {1873-2542}, mesh = {Animals ; *Chickens/microbiology ; *Escherichia coli/genetics/drug effects ; *Gene Transfer, Horizontal ; *Salmonella Infections, Animal/microbiology ; *Salmonella enterica/genetics/drug effects ; *Poultry Diseases/microbiology ; *Tetracycline Resistance/genetics ; Anti-Bacterial Agents/pharmacology ; Cecum/microbiology ; Tetracycline/pharmacology ; Conjugation, Genetic ; Plasmids/genetics ; }, abstract = {Chicken ceca are a rich source of bacteria, including zoonotic pathogens such as Salmonella enterica. The microbiota includes strains/species carrying antimicrobial resistance genes and horizontal transfer of resistance determinants between species may increase the risk to public health and farming systems. Possible sources of these antimicrobial resistance donors - the eggshell carrying bacteria from the hen vertically transmitted to the offspring, or the barn environment where chicks are hatched and raised - has been little explored. In this study, we used Salmonella enterica serovar Heidelberg to evaluate if layer chicks raised in different environments (using combinations of sterilized or non-sterile eggs placed in sterilized isolation chambers or non-sterile rooms) acquired transferable tetracycline resistance genes from surrounding bacteria, especially Escherichia coli. Two-day old chicks were challenged with an antibiotic-susceptible S. Heidelberg strain SH2813nal[R] and Salmonella recovered from the cecum of birds at different timepoints to test the in vivo acquisition of tetracycline resistance. Tetracycline-resistant E. coli isolates recovered from birds from the in vivo experiment were used to test the in vitro transfer of tetracycline resistance genes from E. coli to Salmonella. Even though Salmonella SH2813nal[R] colonized the 2-day old chicks after oral challenge, tetracycline-resistant Salmonella transconjugants were not recovered, as previously observed. In vitro experiments provided similar results. We discuss several hypotheses that might explain the absence of transconjugants in vitro and in vivo, despite the presence of diverse plasmids in the recovered E. coli. The factors that can inhibit/promote antimicrobial resistance transfers to Salmonella for different plasmid types need further exploration.}, }
@article {pmid39577948, year = {2024}, author = {Sheng, H and Zhao, L and Suo, J and Yang, Q and Cao, C and Chen, J and Cui, G and Fan, Y and Ma, Y and Huo, S and Wu, X and Yang, T and Cui, X and Chen, S and Cui, S and Yang, B}, title = {Niche-specific evolution and gene exchange of Salmonella in retail pork and chicken.}, journal = {Food research international (Ottawa, Ont.)}, volume = {197}, number = {Pt 2}, pages = {115299}, doi = {10.1016/j.foodres.2024.115299}, pmid = {39577948}, issn = {1873-7145}, mesh = {Animals ; *Chickens/microbiology ; *Salmonella/genetics ; Swine ; *Food Microbiology ; China ; *Pork Meat/microbiology ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; Meat/microbiology ; Drug Resistance, Bacterial/genetics ; Genetic Variation ; Red Meat/microbiology ; }, abstract = {Salmonella exhibits extensive genetic diversity, facilitated by horizontal gene transfer occurring within and between species, playing a pivotal role in this diversification. Nevertheless, most studies focus on clinical and farm animal isolates, and research on the pangenome dynamics of Salmonella isolates from retail stage of the animal food supply chain is limited. Here, we investigated the genomes of 950 Salmonella isolates recovered from retail chicken and pork meats in seven provinces and one municipality of China in 2018. We observed a strong correlation between Salmonella sublineage diversity and the accessory genome with meat type, revealing reduced diversity associated with increased resistance. Importantly, genes associated with antibiotic, biocide, and heavy metal resistance were unevenly distributed in Salmonella from retail chicken and pork. Pork Salmonella isolates showed a higher prevalence of copper and silver resistance genes, while chicken Salmonella isolates displayed a significant predominance of genetic determinants associated with cephalosporin and ciprofloxacin resistance. Moreover, co-occurrence patterns of resistance determinants and their interaction with mobile genetic elements also correlated with meat type. In summary, our findings shed light on how Salmonella achieves their ecological niche success driven by evolution and gene changes in the retail stage of the animal food supply chain.}, }
@article {pmid39577842, year = {2024}, author = {Whangsuk, W and Dulyayangkul, P and Loprasert, S and Dubbs, JM and Vattanaviboon, P and Mongkolsuk, S}, title = {Re-sensitization of imipenem-resistant Pseudomonas aeruginosa and restoration of cephalosporins susceptibility in Enterobacteriaceae by recombinant Esterase B.}, journal = {Letters in applied microbiology}, volume = {77}, number = {12}, pages = {}, doi = {10.1093/lambio/ovae118}, pmid = {39577842}, issn = {1472-765X}, support = {//Thailand Science Research and Innovation/ ; 49892/4759806//Chulabhorn Research Institute/ ; }, mesh = {*Pseudomonas aeruginosa/genetics/drug effects/enzymology ; *Anti-Bacterial Agents/pharmacology ; *Cephalosporins/pharmacology ; *Microbial Sensitivity Tests ; *Imipenem/pharmacology ; Enterobacteriaceae/genetics/drug effects/enzymology ; Bacterial Proteins/genetics/metabolism ; Esterases/genetics/metabolism ; Bacterial Outer Membrane Proteins/genetics/metabolism ; Recombinant Proteins/genetics/metabolism ; Drug Resistance, Bacterial ; Escherichia coli/genetics/drug effects ; Plasmids/genetics ; }, abstract = {Sphingobium sp. SM42 Esterase B (EstB) is an enzyme with a dual function in degrading dibutyl phthalate and catalyzing the cleavage of the C-S bond in C3-sidechains of the dihydrothiazine ring of cephalosporins, generating more active β-lactam derivatives. Global prokaryotic genome analysis revealed the existence of a gene identical to estB in Pseudomonas aeruginosa strain PS1 suggesting a horizontal gene transfer event involving estB. To investigate the effect of ectopic expression of EstB in the periplasm of P. aeruginosa and several Enterobacteriaceae on antibiotic susceptibility levels, plasmid, pEstB, carrying a recombinant EstB fused with the signal peptide from Escherichia coli outer membrane protein A (OmpA) for periplasmic localization was constructed. The expression of EstB in the periplasm of P. aeruginosa and the Enterobacteriaceae: E. coli, Klebsiella pneumoniae, and Salmonella enterica serovar Typhi, increased susceptibility to carbapenems and cephalosporins. EstB reversed the imipenem resistance of P. aeruginosa ΔmexS and restored the changes in susceptibility to cephalosporins conferred by the downregulation of the outer membrane proteins, OmpK35 and OmpK36, in K. pneumoniae ΔramR-ompK36 to wild-type level. The introduction of EstB to the periplasmic space of Gram-negative bacteria can increase carbapenem and cephalosporin susceptibility.}, }
@article {pmid39577583, year = {2024}, author = {Yu, K and He, B and Xiong, J and Kan, P and Sheng, H and Zhi, S and Zhu, DZ and Yao, Z}, title = {Deciphering basic and key traits of bio-pollutants in a long-term reclaimed water headwater urban stream.}, journal = {The Science of the total environment}, volume = {957}, number = {}, pages = {177696}, doi = {10.1016/j.scitotenv.2024.177696}, pmid = {39577583}, issn = {1879-1026}, mesh = {*Environmental Monitoring ; *Rivers/microbiology/chemistry ; Water Pollutants, Chemical/analysis ; Waste Disposal, Fluid/methods ; Acinetobacter baumannii/genetics ; China ; Drug Resistance, Microbial/genetics ; }, abstract = {Reclaimed water has been recognized as a stable water resource for ecological replenishment in riverine environment. However, information about the bio-pollutants spatial and temporal distributions and the associated risk in this environment remains insufficient. Herein, the bio-pollutant profile in a long-term reclaimed water headwater urban stream, including antibiotic resistance genes (ARGs), mobile genetic elements and pathogens, were revealed by metagenomics. Notably, the temporal variation in bio-pollutant levels exceeded spatial fluctuations, possibly due to the varied rainfall intensity. Specially, multidrug resistance genes and Acinetobacter baumannii (A. baumannii) were the dominant ARGs and pathogens, respectively, exhibiting higher abundance in the dry season, especially in the downstream of the receiving point, where the bio-risk also peaked. A. baumannii and Ralstonia solanacearum were found to be the main plasmids contributors inducing the horizontal gene transfer process in this stream. Overall, A. baumannii contributed over 50 % bio-risk values in most samples, indicating that it was the "overlord" in this headwater urban stream. This study revealed characteristics of bio-pollutants in a typical long-term reclaimed water headwater urban stream, highlighting the superiority of A. baumannii in bio-pollutants, which should be a key consideration in the bio-pollutants surveillance for reclaimed waters.}, }
@article {pmid39575680, year = {2025}, author = {Wang, H and Xu, Z and Zhang, Z and Zhong, B}, title = {Horizontal transposon transfer during plant terrestrialization.}, journal = {Journal of integrative plant biology}, volume = {67}, number = {1}, pages = {15-18}, doi = {10.1111/jipb.13809}, pmid = {39575680}, issn = {1744-7909}, support = {32122010//National Natural Science Foundation of China/ ; 32370228//National Natural Science Foundation of China/ ; }, mesh = {*Gene Transfer, Horizontal/genetics ; *DNA Transposable Elements/genetics ; *Plants/genetics ; Retroelements/genetics ; }, abstract = {During the move to land, plants acquired transposable elements by horizontal transfer from bacteria and fungi and land plants have many long non-coding RNAs derived from retrotransposons acquired by horizontal transposon transfer, including some that are highly expressed and involved in the response to drought stress and abscisic acid.}, }
@article {pmid39575186, year = {2024}, author = {Verma, T and Hendiani, S and Carbajo, C and Andersen, SB and Hammarlund, EU and Burmølle, M and Sand, KK}, title = {Recurrence and propagation of past functions through mineral facilitated horizontal gene transfer.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1449094}, pmid = {39575186}, issn = {1664-302X}, abstract = {Horizontal gene transfer is one of the most important drivers of bacterial evolution. Transformation by uptake of extracellular DNA is traditionally not considered to be an effective mode of gene acquisition, simply because extracellular DNA is degraded in a matter of days when it is suspended in e.g. seawater. Recently the age span of stored DNA was increased to at least 2 Ma. Here, we show that Acinetobacter baylyi can incorporate 60 bp DNA fragments adsorbed to common sedimentary minerals and that the transformation frequencies scale with mineral surface properties. Our work highlights that ancient environmental DNA can fuel the evolution of contemporary bacteria. In contrast to heritable stochastic mutations, the processes by which bacteria acquire new genomic material during times of increased stress and needs, indicate a non-random mechanism that may propel evolution in a non-stochastic manner.}, }
@article {pmid39572773, year = {2024}, author = {Hoffmann, L}, title = {Finding the sweet spot in the deep ocean.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1544}, pmid = {39572773}, issn = {2399-3642}, abstract = {‘Candidatus Endonucleobacter’ infects the nuclei of deep-sea mussels but it was unknown how they can prevent apoptosis of the host. A new study by Porras and colleagues, published in Nature Microbiology, suggests that the bacterium upregulates host-derived apoptosis inhibitors and genes for digesting sugars, lipids and amino acids acquired through horizontal gene transfer from the mussels.}, }
@article {pmid39571737, year = {2025}, author = {Jing, T and Yang, J and Pan, J and Liu, X and Yang, X and Farhan, M and Su, H and Ma, X and Zhang, S}, title = {A near-complete genome reveals the population evolution of the cotton-melon aphid Aphis gossypii.}, journal = {Insect biochemistry and molecular biology}, volume = {176}, number = {}, pages = {104215}, doi = {10.1016/j.ibmb.2024.104215}, pmid = {39571737}, issn = {1879-0240}, mesh = {Animals ; *Aphids/genetics ; *Genome, Insect ; Male ; Female ; Telomere/genetics ; }, abstract = {The cotton-melon aphid Aphis gossypii Glover is a severe pest worldwide. Interhaplotype genomic variation can be used as a starting point to analyze the adaptability of Ap. gossypii. In this study, we utilized long-read PacBio HiFi sequencing and HiC scaffolding techniques to assemble a near telomere-to-telomere gap-free genome assembly of Hap4. The assembly had two gaps totaling 321.24 Mb. We characterized five telomeric repetitive regions (GGTTA)n, including the four found at the 3' end of the chromosomes, and obtained new structural information about the telomeres. Due to the improved sequencing technology, we also identified more than 55.03 Mb of repetitive DNA in the genome assembly of Hap4, which contributed significantly to the increase in genome size compared to that of Hap1 and Hap3. Most of the additional repetitive DNA content was located on the X chromosome, and the tandem repeat sequence occupied 16.8% of the X chromosome length. The Hap4 assembly showed that the X chromosome exhibited a greater abundance of AT-rich satDNA arrays (11 satDNA arrays longer than 100 kb) than that observed in the autosomes (A1 and A2 harboured 3 and 1 satDNA arrays). We detected presence-absence variations, insertions, and deletions events between Hap1, Hap3, and Hap4 Ap. gossypii, which had significant effects on gene expression. Additionally, we identified a male-specific glyceraldehyde-3-phosphate dehydrogenase of fungal origin in all strains of Ap. gossypii. This comprehensive genome assembly provides valuable insights into the structural characteristics of highly repetitive regions and allows comparative genomic analyses that facilitate our understanding of Ap. gossypii's adaptation and diversification.}, }
@article {pmid39571576, year = {2024}, author = {Denoeud, F and Godfroy, O and Cruaud, C and Heesch, S and Nehr, Z and Tadrent, N and Couloux, A and Brillet-Guéguen, L and Delage, L and Mckeown, D and Motomura, T and Sussfeld, D and Fan, X and Mazéas, L and Terrapon, N and Barrera-Redondo, J and Petroll, R and Reynes, L and Choi, SW and Jo, J and Uthanumallian, K and Bogaert, K and Duc, C and Ratchinski, P and Lipinska, A and Noel, B and Murphy, EA and Lohr, M and Khatei, A and Hamon-Giraud, P and Vieira, C and Avia, K and Akerfors, SS and Akita, S and Badis, Y and Barbeyron, T and Belcour, A and Berrabah, W and Blanquart, S and Bouguerba-Collin, A and Bringloe, T and Cattolico, RA and Cormier, A and Cruz de Carvalho, H and Dallet, R and De Clerck, O and Debit, A and Denis, E and Destombe, C and Dinatale, E and Dittami, S and Drula, E and Faugeron, S and Got, J and Graf, L and Groisillier, A and Guillemin, ML and Harms, L and Hatchett, WJ and Henrissat, B and Hoarau, G and Jollivet, C and Jueterbock, A and Kayal, E and Knoll, AH and Kogame, K and Le Bars, A and Leblanc, C and Le Gall, L and Ley, R and Liu, X and LoDuca, ST and Lopez, PJ and Lopez, P and Manirakiza, E and Massau, K and Mauger, S and Mest, L and Michel, G and Monteiro, C and Nagasato, C and Nègre, D and Pelletier, E and Phillips, N and Potin, P and Rensing, SA and Rousselot, E and Rousvoal, S and Schroeder, D and Scornet, D and Siegel, A and Tirichine, L and Tonon, T and Valentin, K and Verbruggen, H and Weinberger, F and Wheeler, G and Kawai, H and Peters, AF and Yoon, HS and Hervé, C and Ye, N and Bapteste, E and Valero, M and Markov, GV and Corre, E and Coelho, SM and Wincker, P and Aury, JM and Cock, JM}, title = {Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems.}, journal = {Cell}, volume = {187}, number = {24}, pages = {6943-6965.e39}, doi = {10.1016/j.cell.2024.10.049}, pmid = {39571576}, issn = {1097-4172}, mesh = {*Phaeophyceae/genetics ; *Ecosystem ; *Phylogeny ; *Genomics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome/genetics ; }, abstract = {Brown seaweeds are keystone species of coastal ecosystems, often forming extensive underwater forests, and are under considerable threat from climate change. In this study, analysis of multiple genomes has provided insights across the entire evolutionary history of this lineage, from initial emergence, through later diversification of the brown algal orders, down to microevolutionary events at the genus level. Emergence of the brown algal lineage was associated with a marked gain of new orthologous gene families, enhanced protein domain rearrangement, increased horizontal gene transfer events, and the acquisition of novel signaling molecules and key metabolic pathways, the latter notably related to biosynthesis of the alginate-based extracellular matrix, and halogen and phlorotannin biosynthesis. We show that brown algal genome diversification is tightly linked to phenotypic divergence, including changes in life cycle strategy and zoid flagellar structure. The study also showed that integration of large viral genomes has had a significant impact on brown algal genome content throughout the emergence of the lineage.}, }
@article {pmid39568508, year = {2024}, author = {Mukherjee, K and Moroz, LL}, title = {Evolution of g-type lysozymes in metazoa: insights into immunity and digestive adaptations.}, journal = {Frontiers in cell and developmental biology}, volume = {12}, number = {}, pages = {1487920}, pmid = {39568508}, issn = {2296-634X}, abstract = {Exploring the evolutionary dynamics of lysozymes is critical for advancing our knowledge of adaptations in immune and digestive systems. Here, we characterize the distribution of a unique class of lysozymes known as g-type, which hydrolyze key components of bacterial cell walls. Notably, ctenophores, and choanoflagellates (the sister group of Metazoa), lack g-type lysozymes. We reveal a mosaic distribution of these genes, particularly within lophotrochozoans/spiralians, suggesting the horizontal gene transfer events from predatory myxobacteria played a role in their acquisition, enabling specialized dietary and defensive adaptations. We further identify two major groups of g-type lysozymes based on their widespread distribution in gastropods. Despite their sequence diversity, these lysozymes maintain conserved structural integrity that is crucial for enzymatic activity, underscoring independent evolutionary pathways where g-type lysozymes have developed functionalities typically associated with different lysozyme types in other species. Specifically, using Aplysia californica as a reference species, we identified three distinct g-type lysozyme genes: two are expressed in organs linked to both feeding and defense, and the third exhibits broader distribution, likely associated with immune functions. These findings advance our understanding of the evolutionary dynamics shaping the recruitment and mosaic functional diversification of these enzymes across metazoans, offering new insights into ecological physiology and physiological evolution as emerging fields.}, }
@article {pmid39566460, year = {2025}, author = {Xia, L and Wang, J and Chen, M and Li, G and Wang, W and An, T}, title = {Biofilm formation mechanisms of mixed antibiotic-resistant bacteria in water: Bacterial interactions and horizontal transfer of antibiotic-resistant plasmids.}, journal = {Journal of hazardous materials}, volume = {481}, number = {}, pages = {136554}, doi = {10.1016/j.jhazmat.2024.136554}, pmid = {39566460}, issn = {1873-3336}, mesh = {*Biofilms/drug effects/growth &amp; development ; *Plasmids/genetics ; *Gene Transfer, Horizontal ; *Escherichia coli/drug effects/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Water Microbiology ; Bacteria/drug effects/genetics/metabolism ; Microbial Interactions ; }, abstract = {Over 95 % of bacteria on water supply pipeline surfaces exist in biofilms, which are hotspots for antibiotic resistance gene (ARG) transmission. This study established mixed biofilm culture systems on a metal iron substrate using Escherichia coli: antibiotic-sensitive bacteria (ASB) and antibiotic-resistant bacteria (ARB). The growth rate and extracellular polymeric substances (EPS) content of mixed biofilm surpassed single-species biofilms due to synergistic interactions among different bacteria. However, the composition of mixed biofilms formed by ASB and ARB became unstable after 72 h, linked to reduced polysaccharide proportions in EPS and inter-bacterial competition. The bacterial composition and conjugative transfer frequency of ARGs in mixed biofilms indicate that biofilm formation significantly enhances horizontal transfer of ARGs. Notably, the conjugative transfer frequency of the mixed biofilm formed by two ARB increased 100-fold within five days. In contrast, the conjugative transfer frequency in the mixed biofilm formed by ASB and ARB was unstable; inter-bacterial competition led to plasmid loss associated with horizontal transfer of ARGs, ultimately resulting in biofilm shedding. Furthermore, genes associated with ARG transfer and biofilm growth up-regulated by 1.5 - 6 and 2 - 7 times, respectively, in mixed biofilm. These findings highlight a mutually reinforcing relationship between biofilm formation and horizontal ARG transmission, with significant environmental implications.}, }
@article {pmid39565221, year = {2025}, author = {Molano, LG and Hirsch, P and Hannig, M and Müller, R and Keller, A}, title = {The PLSDB 2025 update: enhanced annotations and improved functionality for comprehensive plasmid research.}, journal = {Nucleic acids research}, volume = {53}, number = {D1}, pages = {D189-D196}, pmid = {39565221}, issn = {1362-4962}, support = {//European Commission/ ; 466168626//DFG/ ; }, mesh = {*Plasmids/genetics ; *Molecular Sequence Annotation ; *Databases, Genetic ; Bacteria/genetics ; Software ; Artificial Intelligence ; Gene Transfer, Horizontal ; }, abstract = {Plasmids are extrachromosomal DNA molecules in bacteria and archaea, playing critical roles in horizontal gene transfer, antibiotic resistance, and pathogenicity. Since its first release in 2018, our database on plasmids, PLSDB, has significantly grown and enhanced its content and scope. From 34 513 records contained in the 2021 version, PLSDB now hosts 72 360 entries. Designed to provide life scientists with convenient access to extensive plasmid data and to support computer scientists by offering curated datasets for artificial intelligence (AI) development, this latest update brings more comprehensive and accurate information for plasmid research, with interactive visualization options. We enriched PLSDB by refining the identification and classification of plasmid host ecosystems and host diseases. Additionally, we incorporated annotations for new functional structures, including protein-coding genes and biosynthetic gene clusters. Further, we enhanced existing annotations, such as antimicrobial resistance genes and mobility typing. To accommodate these improvements and to host the increase plasmid sets, the webserver architecture and underlying data structures of PLSDB have been re-reconstructed, resulting in decreased response times and enhanced visualization of features while ensuring that users have access to a more efficient and user-friendly interface. The latest release of PLSDB is freely accessible at https://www.ccb.uni-saarland.de/plsdb2025.}, }
@article {pmid39565095, year = {2024}, author = {Bulka, O and Mahadevan, R and Edwards, EA}, title = {Pangenomic insights into Dehalobacter evolution and acquisition of functional genes for bioremediation.}, journal = {Microbial genomics}, volume = {10}, number = {11}, pages = {}, pmid = {39565095}, issn = {2057-5858}, mesh = {*Biodegradation, Environmental ; *Phylogeny ; *Genome, Bacterial ; Evolution, Molecular ; Bacterial Proteins/genetics/metabolism ; Genomics ; Gene Transfer, Horizontal ; Metagenome ; }, abstract = {Dehalobacter is a genus of organohalide-respiring bacteria that is recognized for its fastidious growth using reductive dehalogenases (RDases). In the SC05 culture, however, a Dehalobacter population also mineralizes dichloromethane (DCM) produced by chloroform dechlorination using the mec cassette, just downstream of its active RDase. A closed genome of this DCM-mineralizing lineage has previously evaded assembly. Here, we present the genomes of two novel Dehalobacter strains, each of which was assembled from the metagenome of a distinct subculture from SC05. A pangenomic analysis of the Dehalobacter genus, including RDase synteny and phylogenomics, reveals at least five species of Dehalobacter based on average nucleotide identity, RDase and core gene synteny, as well as differential functional genes. An integration hotspot is also pinpointed in the Dehalobacter genome, in which many recombinase islands have accumulated. This nested recombinase island encodes the active RDase and mec cassette in both SC05 Dehalobacter genomes, indicating the transfer of key functional genes between species of Dehalobacter. Horizontal gene transfer between these two novel Dehalobacter strains has implications for the evolutionary history within the SC05 subcultures and of the Dehalobacter genus as a whole, especially regarding adaptation to anthropogenic chemicals.}, }
@article {pmid39564482, year = {2024}, author = {Huang, CJ and Wu, TL and Wu, YL and Wang, RS and Lin, YC}, title = {Comparative genomic analysis uncovered phylogenetic diversity, evolution of virulence factors, and horizontal gene transfer events in tomato bacterial spot Xanthomonas euvesicatoria.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1487917}, pmid = {39564482}, issn = {1664-302X}, abstract = {INTRODUCTION: Bacterial spot, caused by diverse xanthomonads classified into four lineages within three species, poses a significant threat to global pepper and tomato production. In Taiwan, tomato bacterial spot xanthomonads phylogenetically related to an atypical Xanthomonas euvesicatoria pv. perforans (Xep) strain NI1 from Nigeria were found.<br><br>METHODS: To investigate the genetic structure of Taiwanese Xep strains and determine the phylogenetic position of the atypical strains, we completed high-quality, gap-free, circularized genomes of seven Taiwanese Xep strains and performed comparative genomic analyses with genomes of X. euvesicatoria pathovars. Average nucleotide identity, core genome analysis, and phylogenomic analysis were conducted.<br><br>RESULTS: Three sequenced strains were identified as typical Xep, while four clustered with the atypical strain NI1, forming a distinct genomovar within X. euvesicatoria, proposed as X. euvesicatoria genomovar taiwanensis (Xet). This new lineage likely originated in Taiwan and spread to Nigeria through global seed trade. At the genomovar level, chromosomes remained conserved among Taiwanese strains, while plasmids likely contributed to bacterial virulence, avirulence, and field fitness. Gap-free genomes revealed associations between the evolution of type III effectors, horizontal gene transfer events, plasmid diversity, and recombination.<br><br>DISCUSSION: This study highlights the critical roles of horizontal gene transfer and plasmids in shaping the genetic makeup, evolution, and environmental adaptation of plant pathogenic xanthomonads. The identification of a new genomovar, X. euvesicatoria genomovar taiwanensis, provides insights into the diversity and global spread of bacterial spot pathogens through seed trade.}, }
@article {pmid39562586, year = {2024}, author = {Goh, YX and Anupoju, SMB and Nguyen, A and Zhang, H and Ponder, M and Krometis, LA and Pruden, A and Liao, J}, title = {Evidence of horizontal gene transfer and environmental selection impacting antibiotic resistance evolution in soil-dwelling Listeria.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {10034}, pmid = {39562586}, issn = {2041-1723}, mesh = {*Gene Transfer, Horizontal ; *Soil Microbiology ; *Listeria/genetics/drug effects ; *Phylogeny ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Genome, Bacterial/genetics ; Evolution, Molecular ; Selection, Genetic ; }, abstract = {Soil is an important reservoir of antibiotic resistance genes (ARGs) and understanding how corresponding environmental changes influence their emergence, evolution, and spread is crucial. The soil-dwelling bacterial genus Listeria, including L. monocytogenes, the causative agent of listeriosis, serves as a key model for establishing this understanding. Here, we characterize ARGs in 594 genomes representing 19 Listeria species that we previously isolated from soils in natural environments across the United States. Among the five putatively functional ARGs identified, lin, which confers resistance to lincomycin, is the most prevalent, followed by mprF, sul, fosX, and norB. ARGs are predominantly found in Listeria sensu stricto species, with those more closely related to L. monocytogenes tending to harbor more ARGs. Notably, phylogenetic and recombination analyses provide evidence of recent horizontal gene transfer (HGT) in all five ARGs within and/or across species, likely mediated by transformation rather than conjugation and transduction. In addition, the richness and genetic divergence of ARGs are associated with environmental conditions, particularly soil properties (e.g., aluminum and magnesium) and surrounding land use patterns (e.g., forest coverage). Collectively, our data suggest that recent HGT and environmental selection play a vital role in the acquisition and diversification of bacterial ARGs in natural environments.}, }
@article {pmid39562577, year = {2024}, author = {Chen, Y and Wang, W and Zhang, S and Zhao, Y and Feng, L and Zhu, C}, title = {Assembly and analysis of the complete mitochondrial genome of Carya illinoinensis to provide insights into the conserved sequences of tRNA genes.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {28571}, pmid = {39562577}, issn = {2045-2322}, support = {32001344//the National Natural Science Foundation of China/ ; 32001344//the National Natural Science Foundation of China/ ; 32001344//the National Natural Science Foundation of China/ ; 32001344//the National Natural Science Foundation of China/ ; 32001344//the National Natural Science Foundation of China/ ; 32001344//the National Natural Science Foundation of China/ ; BK20200290//the Natural Science Foundation of Jiangsu Province, China/ ; BK20200290//the Natural Science Foundation of Jiangsu Province, China/ ; BK20200290//the Natural Science Foundation of Jiangsu Province, China/ ; BK20200290//the Natural Science Foundation of Jiangsu Province, China/ ; BK20200290//the Natural Science Foundation of Jiangsu Province, China/ ; BK20200290//the Natural Science Foundation of Jiangsu Province, China/ ; }, mesh = {*Carya/classification/genetics ; *Genome, Mitochondrial ; *Genome, Plant ; *RNA, Transfer/chemistry/genetics ; *Conserved Sequence ; Phylogeny ; RNA Folding ; Sequence Analysis, DNA ; Codon Usage ; RNA Editing ; Gene Transfer, Horizontal ; Fagus/genetics ; }, abstract = {Carya illinoinensis is an economically important nut tree, and its chloroplast (cp.) genome has been reported; however, its mitochondrial (mt) genome remains unknown. In the present study, we assembled the first mt genome of C. illinoinensis. The circular mt genome of C. illinoinensis is 495,205 bp long, with 37 protein-coding genes(PCGs), 24 tRNA genes, and 3 rRNA genes. All the tRNAs could be folded into typical cloverleaf secondary structures, with lengths of 58-88 bp. A conserved U-U-C-x-A-x2 consensus nucleotide sequence was discovered in the Ψ-loops of tRNA sequences. In addition, 447 dispersed repeats were detected, as well as found 482 RNA editing sites and 9,960 codons in the mt genome. Furthermore, a total of 27 DNA sequences with a length of 43,277 bp were transferred from the cp. to the mt genome, and eight integrated cp-derived genes (trnL-CAA, trnV-GAC, trnD-GUC, trnW-CCA, trnN-GUU, trnH-GUG, trnM-CAU, and rps7) were identified. We also obtained 1,086 hits, including 364.023 kp of nuclear genome sequences, that were transferred to the mt genome. To determine the evolutionary position of C. illinoinensis, we conducted a phylogenetic analysis of the mitogenomes of C. illinoinensis and 14 other taxa. The results strongly suggested that C. illinoinensis and Fagus sylvatica formed a single clade with 100% bootstrap support. This study sequenced comprehensive data on the C. illinoinensis mitochondrial genome and provided insights into the conserved sequences of tRNA genes, which could facilitate evolutionary research in other Carya trees in the future.}, }
@article {pmid39555914, year = {2024}, author = {Ulrich, NJ and Miller, SR}, title = {Integration of horizontally acquired light-harvesting genes into an ancestral regulatory network in the cyanobacterium Acaryochloris marina MBIC11017.}, journal = {mBio}, volume = {15}, number = {12}, pages = {e0242324}, pmid = {39555914}, issn = {2150-7511}, support = {NNA15BB04A//National Aeronautics and Space Administration (NASA)/ ; //Montana Space Grant Consortium (MSGC)/ ; }, mesh = {*Gene Transfer, Horizontal ; *Cyanobacteria/genetics/metabolism ; *Gene Regulatory Networks ; *Phycocyanin/genetics/metabolism ; Evolution, Molecular ; Light-Harvesting Protein Complexes/genetics/metabolism ; Chlorophyll/metabolism ; Gene Expression Regulation, Bacterial ; Bacterial Proteins/genetics/metabolism ; Transcriptome ; Light ; }, abstract = {The acquisition of new capabilities by horizontal gene transfer (HGT) shapes the distribution of traits during microbial diversification. In the Chlorophyll (Chl) d-producing cyanobacterium Acaryochloris marina, the genes involved in the production and disassembly of the light-harvesting phycobiliprotein phycocyanin (PC) were lost in the A. marina common ancestor but then subsequently regained via HGT in A. marina strain MBIC11017. However, it remains unknown how the HGT-acquired PC genes in MBIC11017 have been reintegrated into its existing regulatory network after tens of millions of years since their loss. Here, we investigated potential mechanisms of regulatory assimilation of PC genes by comparing the transcriptomes of A. marina strain MBIC11017 and a PC-lacking close relative under both low irradiance far-red light and high irradiance white light. We found that PC assembly and degradation processes have been re-assimilated into a conserved ancestral response to high light. Further, we identified putative regulatory elements that were likely co-transferred with PC genes and could be recognized by A. marina's pre-existing light response machinery. This study offers insights into how HGT-acquired genes can be reintegrated into an existing transcriptional regulatory network that has evolved in their absence.IMPORTANCEHorizontal gene transfer, the asymmetric movement of genetic information between donor and recipient organisms, is an important mechanism for acquiring new traits. In order for newly acquired gene content to be retained, it must be integrated into the genetic repertoire and regulatory networks of the recipient cell. In a strain of the Chlorophyll d-producing cyanobacterium Acaryochloris marina, the recent reacquisition of the genes required to produce the light-harvesting pigment phycocyanin offers a rare opportunity to understand the mechanisms underlying the regulatory assimilation of an acquired complex trait in bacteria. The significance in our research is in characterizing how an ancestrally lost, complex trait can be reintegrated into a conserved regulatory network, even after millions of years.}, }
@article {pmid39552541, year = {2024}, author = {Singh, CK and Sodhi, KK}, title = {Targeting bioinformatics tools to study the dissemination and spread of antibiotic resistant genes in the environment and clinical settings.}, journal = {Critical reviews in microbiology}, volume = {}, number = {}, pages = {1-19}, doi = {10.1080/1040841X.2024.2429603}, pmid = {39552541}, issn = {1549-7828}, abstract = {Antibiotic resistance has expanded as a result of the careless use of antibiotics in the medical field, the food industry, agriculture, and other industries. By means of genetic recombination between commensal and pathogenic bacteria, the microbes obtain antibiotic resistance genes (ARGs). In bacteria, horizontal gene transfer (HGT) is the main mechanism for acquiring ARGs. With the development of high-throughput sequencing, ARG sequence analysis is now feasible and widely available. Preventing the spread of AMR in the environment requires the implementation of ARGs mapping. The metagenomic technique, in particular, has helped in identifying antibiotic resistance within microbial communities. Due to the exponential growth of experimental and clinical data, significant investments in computer capacity, and advancements in algorithmic techniques, the application of machine learning (ML) algorithms to the problem of AMR has attracted increasing attention over the past five years. The review article sheds a light on the application of bioinformatics for the antibiotic resistance monitoring. The most advanced tool currently being employed to catalog the resistome of various habitats are metagenomics and metatranscriptomics. The future lies in the hands of artificial intelligence (AI) and machine learning (ML) methods, to predict and optimize the interaction of antibiotic-resistant compounds with target proteins.}, }
@article {pmid39551215, year = {2024}, author = {Bierge, P and Sánchez-Osuna, M and Duarte, B and Gómez-Sánchez, I and Espasa, M and Freitas, AR and Peixe, L and Gasch, O and Pich, OQ and Novais, C}, title = {Diverse genomic and epidemiological landscapes of redundant pbp5 genes in Enterococcus spp.: Insights into plasmid mobilization, ampicillin susceptibility, and environmental interactions.}, journal = {The Science of the total environment}, volume = {957}, number = {}, pages = {177562}, doi = {10.1016/j.scitotenv.2024.177562}, pmid = {39551215}, issn = {1879-1026}, mesh = {*Ampicillin/pharmacology ; *Plasmids/genetics ; Anti-Bacterial Agents/pharmacology ; Enterococcus/genetics/drug effects ; Phylogeny ; Bacterial Proteins/genetics ; Humans ; }, abstract = {Genetic redundancy in bacteria plays a crucial role in enhancing adaptability and accelerating evolution in response to selective pressures, particularly those associated with rapid environmental changes. Aminopenicillins like ampicillin are important therapeutic options for Enterococcus infections in both humans and animals, with resistance mostly associated with pbp5 gene mutations or overexpression. While the occurrence of redundant pbp5 genes has been occasionally reported, the advantages for the host bacteria have not been explored in detail. During a whole-genome sequencing project of Enterococcus faecium from bacteremic patients, we identified an ST592 strain (Efm57) with redundant pbp5 genes. This presented an opportunity to investigate the prevalence and implications of multiple pbp5 acquisitions in diverse Enterococcus species across various sources, geographical regions, and timeframes. The analysis of 618 complete Enterococcus genomes from public databases revealed that 3.2 % harbored redundant pbp5 genes, located on chromosomes or plasmids across different species from diverse epidemiological backgrounds. The proteins encoded by these genes showed homologies ranging from 51.1 % to 97.5 % compared to native copies. Phylogenetic analysis grouped redundant PBP5 amino acid sequences into three distinct clades, with insertion sequences (mostly IS6-like) facilitating their recent spread to diverse plasmids with varying genetic backbones. The presence of multiple antibiotic resistance genes on pbp5-plasmids, including those conferring resistance to linezolid, underscores their involvement in co-selection and recombination events with other clinically-relevant antibiotics. Conjugation experiments confirmed the transferability of a specific 24 kb pbp5-plasmid from the Efm57 strain. This plasmid was associated with higher minimum inhibitory concentrations of ampicillin and conferred bacteria growth advantages at 22 °C. In conclusion, the widespread distribution of redundant pbp5 genes among Enterococcus spp. highlights the complex interplay between genetic mobility, environmental factors, and multidrug resistance in overlapping ecosystems emphasizing the importance of understanding these dynamics to mitigate antibiotic resistance spread within the One Health framework.}, }
@article {pmid39550371, year = {2024}, author = {Yang, JX and Peng, Y and Yu, QY and Yang, JJ and Zhang, YH and Zhang, HY and Adams, CA and Willing, CE and Wang, C and Li, QS and Han, XG and Gao, C}, title = {Gene horizontal transfers and functional diversity negatively correlated with bacterial taxonomic diversity along a nitrogen gradient.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {128}, pmid = {39550371}, issn = {2055-5008}, mesh = {*Soil Microbiology ; Soil/chemistry ; *Nitrogen/metabolism/pharmacology ; *Biodiversity ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/metabolism ; Metagenome ; *Gene Transfer, Horizontal/drug effects ; }, abstract = {Horizontal gene transfer (HGT) mediated diversification is a critical force driving evolutionary and ecological processes. However, how HGT might relate to anthropogenic activity such as nitrogen addition, and its subsequent effect on functional diversity and cooccurrence networks remain unknown. Here we approach this knowledge gap by blending bacterial 16S rRNA gene amplicon and shotgun metagenomes from a platform of cessation of nitrogen additions and continuous nitrogen additions. We found that bacterial HGT events, functional genes, and virus diversities increased whereas bacterial taxonomic diversity decreased by nitrogen additions, resulting in a counterintuitive strong negative association between bacterial taxonomic and functional diversities. Nitrogen additions, especially the ceased one, complexified the cooccurrence network by increasing the contribution of vitamin B12 auxotrophic Acidobacteria, indicating cross-feeding. These findings advance our perceptions of the causes and consequences of the diversification process in community ecology.}, }
@article {pmid39549700, year = {2024}, author = {Siozios, S and Nadal-Jimenez, P and Azagi, T and Sprong, H and Frost, CL and Parratt, SR and Taylor, G and Brettell, L and Liew, KC and Croft, L and King, KC and Brockhurst, MA and Hypša, V and Novakova, E and Darby, AC and Hurst, GDD}, title = {Genome dynamics across the evolutionary transition to endosymbiosis.}, journal = {Current biology : CB}, volume = {34}, number = {24}, pages = {5659-5670.e7}, doi = {10.1016/j.cub.2024.10.044}, pmid = {39549700}, issn = {1879-0445}, mesh = {*Symbiosis/genetics ; *Genome, Bacterial ; Biological Evolution ; Gene Transfer, Horizontal ; Evolution, Molecular ; Enterobacteriaceae/genetics/physiology ; }, abstract = {Endosymbiosis-where a microbe lives and replicates within a host-is an important contributor to organismal function that has accelerated evolutionary innovations and catalyzed the evolution of complex life. The evolutionary processes associated with transitions to endosymbiosis, however, are poorly understood. Here, we leverage the wide diversity of host-associated lifestyles of the genus Arsenophonus to reveal the complex evolutionary processes that occur during the transition to a vertically transmitted endosymbiotic lifestyle from strains maintained solely by horizontal (infectious) transmission. We compared the genomes of 38 strains spanning diverse lifestyles from horizontally transmitted pathogens to obligate interdependent endosymbionts. Among culturable strains, we observed those with vertical transmission had larger genome sizes than closely related horizontally transmitting counterparts, consistent with evolutionary innovation and the rapid gain of new functions. Increased genome size was a consequence of prophage and plasmid acquisition, including a cargo of type III effectors, alongside the concomitant loss of CRISPR-Cas genome defense systems, enabling mobile genetic element expansion. Persistent endosymbiosis was also associated with loss of type VI secretion, which we hypothesize to be a consequence of reduced microbe-microbe competition. Thereafter, the transition to endosymbiosis with strict vertical inheritance was associated with the expected relaxation of purifying selection, gene pseudogenization, metabolic degradation, and genome reduction. We argue that reduced phage predation in endosymbiotic niches drives the loss of genome defense systems driving rapid genome expansion upon the adoption of endosymbiosis and vertical transmission. This remodeling enables rapid horizontal gene transfer-mediated evolutionary innovation and precedes the reductive evolution traditionally associated with adaptation to endosymbiosis.}, }
@article {pmid39545400, year = {2025}, author = {Stern, DB and Raborn, RT and Lovett, SP and Boise, NR and Carrasquilla, L and Enke, S and Radune, D and Woodruff, DL and Wahl, KL and Rosovitz, MJ}, title = {Novel Toxin Biosynthetic Gene Cluster in Harmful Algal Bloom-Causing Heteroscytonema crispum: Insights into the Origins of Paralytic Shellfish Toxins.}, journal = {Genome biology and evolution}, volume = {17}, number = {1}, pages = {}, pmid = {39545400}, issn = {1759-6653}, support = {//Battelle National Biodefense Institute/ ; /DHS/DHS/United States ; //Science and Technology Directorate/ ; //National Biodefense Analysis and Countermeasures Center/ ; //Federally Funded Research and Development Center/ ; }, mesh = {*Harmful Algal Bloom ; *Multigene Family ; *Cyanobacteria/genetics/metabolism ; *Saxitoxin/genetics/biosynthesis ; *Phylogeny ; Marine Toxins/genetics/biosynthesis ; Dinoflagellida/genetics/metabolism ; Genome, Bacterial ; Gene Transfer, Horizontal ; }, abstract = {Caused by both eukaryotic dinoflagellates and prokaryotic cyanobacteria, harmful algal blooms are events of severe ecological, economic, and public health consequence, and their incidence has become more common of late. Despite coordinated research efforts to identify and characterize the genomes of harmful algal bloom-causing organisms, the genomic basis and evolutionary origins of paralytic shellfish toxins produced by harmful algal blooms remain at best incomplete. The paralytic shellfish toxin saxitoxin has an especially complex genomic architecture and enigmatic phylogenetic distribution, spanning dinoflagellates and multiple cyanobacterial genera. Using filtration and extraction techniques to target the desired cyanobacteria from nonaxenic culture, coupled with a combination of short- and long-read sequencing, we generated a reference-quality hybrid genome assembly for Heteroscytonema crispum UTEX LB 1556, a freshwater, paralytic shellfish toxin-producing cyanobacterium thought to have the largest known genome in its phylum. We report a complete, novel biosynthetic gene cluster for the paralytic shellfish toxin saxitoxin. Leveraging this biosynthetic gene cluster, we find support for the hypothesis that paralytic shellfish toxin production has appeared in divergent Cyanobacteria lineages through widespread and repeated horizontal gene transfer. This work demonstrates the utility of long-read sequencing and metagenomic assembly toward advancing our understanding of paralytic shellfish toxin biosynthetic gene cluster diversity and suggests a mechanism for the origin of paralytic shellfish toxin biosynthetic genes.}, }
@article {pmid39542384, year = {2024}, author = {Wang, J and Wu, Y and Zhu, L and Guo, K and Gao, S and Dong, Y}, title = {Genomic evolution and patterns of horizontal gene transfer in Papilio.}, journal = {Genomics}, volume = {116}, number = {6}, pages = {110956}, doi = {10.1016/j.ygeno.2024.110956}, pmid = {39542384}, issn = {1089-8646}, mesh = {*Gene Transfer, Horizontal ; *Butterflies/genetics ; Animals ; *Evolution, Molecular ; Phylogeny ; ATP-Binding Cassette Transporters/genetics ; }, abstract = {The Papilio genus, known for its ecological and phenotypic diversity, is a valuable model for evolutionary studies. This study conducted a comparative genomic analysis of 11 Papilio species, revealing species-specific gene family expansions, including the UDP-glucosyltransferase 2 gene associated with insect detoxification, particularly expanding in Papilio polyxenes. Our analysis also revealed 199 horizontal gene transfer (HGT) acquired genes from 76 microbial species, with Pseudomonadota and Bacillota as common HGT donors across these genomes. Furthermore, we examined the evolutionary patterns of nine ABC transporter subfamilies, uncovering potential links between gene family evolution and environmental adaptation. This study provides new insights into evolutionary relationships and genomic adaptations within the Papilio genus, contributing to broader butterfly evolutionary research.}, }
@article {pmid39542270, year = {2024}, author = {Yuan, S and Jin, G and Cui, R and Wang, X and Wang, M and Chen, Z}, title = {Transmission and control strategies of antimicrobial resistance from the environment to the clinic: A holistic review.}, journal = {The Science of the total environment}, volume = {957}, number = {}, pages = {177461}, doi = {10.1016/j.scitotenv.2024.177461}, pmid = {39542270}, issn = {1879-1026}, mesh = {Humans ; *Gene Transfer, Horizontal ; Drug Resistance, Bacterial ; Anti-Bacterial Agents ; Drug Resistance, Microbial ; Antimicrobial Stewardship ; }, abstract = {The environment serves as a significant reservoir of antimicrobial resistance (AMR) microbes and genes and is increasingly recognized as key source of clinical AMR. Modern human activities impose an additional burden on environmental AMR, promoting its transmission to clinical setting and posing a serious threat to human health and welfare. Therefore, a comprehensive review of AMR transmission from the environment to the clinic, along with proposed effective control strategies, is crucial. This review systematically summarized current research on the transmission of environmental AMR to clinical settings. Furthermore, the transmission pathways, horizontal gene transfer (HGT) mechanisms, as well as the influential drivers including triple planetary crisis that may facilitate AMR transfer from environmental species to clinical pathogens are highlighted. In response to the growing trend of AMR transmission, we propose insightful mitigation strategies under the One Health framework, integrating advanced surveillance and tracking technologies, interdisciplinary knowledge, multisectoral interventions, alongside multiple antimicrobial use and stewardship approaches to tacking development and spread of AMR.}, }
@article {pmid39541852, year = {2025}, author = {Wang, Q and Wang, M and Yang, Q and Feng, L and Zhang, H and Wang, R and Wang, R}, title = {The role of bacteriophages in facilitating the horizontal transfer of antibiotic resistance genes in municipal wastewater treatment plants.}, journal = {Water research}, volume = {268}, number = {Pt B}, pages = {122776}, doi = {10.1016/j.watres.2024.122776}, pmid = {39541852}, issn = {1879-2448}, mesh = {*Bacteriophages/genetics ; *Gene Transfer, Horizontal ; *Wastewater ; Drug Resistance, Microbial/genetics ; Waste Disposal, Fluid ; Plasmids/genetics ; Bacteria/virology/genetics ; }, abstract = {Bacteriophages play integral roles in the ecosystem; however, their precise involvement in horizontal gene transfer and the spread of antibiotic resistance genes (ARGs) are not fully understood. In this study, a coculture system involving consortia of bacteriophages and multidrug-resistant bacteria from an aerobic tank in a municipal wastewater treatment plant (WWTP) was established to investigate the functions of bacteriophages in ARG transfer and spread. The results of the cocultivation of the MRB and bacteriophage consortia indicated that the bacterial community remained stable throughout the whole process, but the addition of bacteriophages significantly increased ARG abundance, especially in bacteriophage DNA. Nine out of the 11 identified ARGs significantly increased, indicating that more bacteriophage particles carried ARGs in the system after cocultivation. In addition, 686 plasmids were detected during cocultivation, of which only 3.36 % were identified as conjugative plasmids, which is significantly lower than the proportion found among previously published plasmids (25.2 %, totaling 14,029 plasmids). Our findings revealed that bacteriophages may play important roles in the horizontal transfer of ARGs through both bacteriophage-mediated conduction and an increase in extracellular ARGs; however, conjugative transfer may not be the main mechanism by which multidrug-resistant bacteria acquire and spread ARGs. Unlike in most previous reports, a coculture system of diverse bacteria and bacteriophages was established in this study to assess bacteriophage functions in ARG transfer and dissemination in the environment, overcoming the limitations associated with the isolation of bacteria and bacteriophages, as well as the specificity of bacteriophage hosts.}, }
@article {pmid39541851, year = {2025}, author = {Wang, F and Huang, W and Chen, J and Luo, Y and Cao, J and Fang, F and Liu, X and Wu, Y and Luo, J}, title = {Non-antibiotic disinfectant synchronously interferes methane production and antibiotic resistance genes propagation during sludge anaerobic digestion: Activation of microbial adaptation and reconfiguration of bacteria-archaea synergies.}, journal = {Water research}, volume = {268}, number = {Pt B}, pages = {122773}, doi = {10.1016/j.watres.2024.122773}, pmid = {39541851}, issn = {1879-2448}, mesh = {*Sewage/microbiology ; *Methane ; Anaerobiosis ; *Disinfectants/pharmacology ; *Bacteria/drug effects/metabolism ; *Archaea/genetics/drug effects ; *Drug Resistance, Microbial/genetics ; Bioreactors ; Waste Disposal, Fluid ; }, abstract = {Waste activated sludge (WAS) presents both resource recovery potential and pollution risks, making its efficient treatment challenging. Anaerobic digestion is broadly recognized as a green and sustainable approach to WAS treatment, whose efficiency is easily impacted by the exogeneous pollutants in WAS. However, the impact of polyhexamethylene guanidine (PHMG), as a widely-used non-antibiotic disinfectant, on WAS digestion under semi-continuous flow conditions remains unclear. In this study, CH4 production decreased from 16.1 mL/g volatile suspended solids (VSS) in the control to 13.2 mL/g VSS and 0.3 mL/g VSS under low and high PHMG exposure, respectively, while PHMG increased the number of antibiotic resistance gene (ARG) copies per bacterium by 4.6-12.7 %. Molecular docking analysis revealed that PHMG could spontaneously bind to and disintegrate WAS (binding energy:2.35 and -9.62 kcal/mol), increasing the likelihood of microbial exposure to PHMG. This led to an increase in bacterial abundance and a reduction in archaeal populations, resulting in bacterial dominance in ecological niches. The network topology index in PHMG-treated reactors was consistently lower than in the control, with a higher proportion of negatively correlated links, indicating a more antagonistic relationship between bacteria and archaea. Consequently, PHMG significantly interfered with key genes involved in CH4 biosynthesis (e.g., mch and mtd). Interestingly, methanogenic activity and archaeal chemotaxis (e.g., rfk and cheA) partially recovered under low PHMG exposure due to archaeal adaptation through quorum sensing and two-component systems. However, this adaptation process also contributed to the propagation of ARGs through horizontal gene transfer, facilitated by the enhancement of mobile genetic elements and ARGs hosts. These findings confirm the ecological risks of PHMG and highlight the need for effective WAS disposal strategies.}, }
@article {pmid39540883, year = {2024}, author = {Garcia, LE and Sanchez-Puerta, MV}, title = {Mitochondrial Splicing Efficiency Is Lower in Holoparasites Than in Free-Living Plants.}, journal = {Plant &amp; cell physiology}, volume = {65}, number = {12}, pages = {2018-2029}, doi = {10.1093/pcp/pcae120}, pmid = {39540883}, issn = {1471-9053}, mesh = {*RNA Splicing ; *Mitochondria/genetics/metabolism ; *Introns/genetics ; Gene Transfer, Horizontal ; Magnoliopsida/genetics/parasitology ; Evolution, Molecular ; Plants/genetics/parasitology ; }, abstract = {Mitochondria play a crucial role in eukaryotic organisms, housing their own genome with genes vital for oxidative phosphorylation. Coordination between nuclear and mitochondrial genomes is pivotal for organelle gene expression. Splicing, editing and processing of mitochondrial transcripts are regulated by nuclear-encoded factors. Splicing efficiency (SEf) of the many group II introns present in plant mitochondrial genes is critical for mitochondrial function since a splicing defect or splicing deficiency can severely impact plant growth and development. This study investigates SEf in free-living and holoparasitic plants, focusing on 25 group II introns from 15 angiosperm species. Our comparative analyses reveal distinctive splicing patterns with holoparasites exhibiting significantly lower SEf, potentially linked to their unique evolutionary trajectory. Given the preponderance of horizontal gene transfer (HGT) in parasitic plants, we investigated the effect of HGT on SEf, such as the presence of foreign introns or foreign nuclear-encoded splicing factors. Contrary to expectations, the SEf reductions do not correlate with HGT events, suggesting that other factors are at play, such as the loss of photosynthesis or the transition to a holoparasitic lifestyle. The findings of this study broaden our understanding of the molecular evolution in parasitic plants and shed light on the multifaceted factors influencing organelle gene expression.}, }
@article {pmid39535289, year = {2024}, author = {Vanhout, Z and Abdellati, S and Gestels, Z and De Baetselier, I and de Block, T and Vanbaelen, T and Manoharan-Basil, SS and Kenyon, C}, title = {Macrolide resistance is pervasive in oral streptococci in the Belgian general population: a cross-sectional survey.}, journal = {Journal of medical microbiology}, volume = {73}, number = {11}, pages = {}, doi = {10.1099/jmm.0.001932}, pmid = {39535289}, issn = {1473-5644}, mesh = {Humans ; Belgium/epidemiology ; *Anti-Bacterial Agents/pharmacology ; *Microbial Sensitivity Tests ; Child ; Cross-Sectional Studies ; *Macrolides/pharmacology ; *Drug Resistance, Bacterial ; Female ; Adult ; Male ; *Streptococcal Infections/microbiology/epidemiology ; Child, Preschool ; *Streptococcus/drug effects/genetics/isolation &amp; purification ; Mouth/microbiology ; Azithromycin/pharmacology ; Middle Aged ; Adolescent ; Young Adult ; Parents ; Prevalence ; Infant ; }, abstract = {Background. Commensal streptococci are common inhabitants of the oral microbiome and regulate its structure and function in beneficial ways for human health. They can, however, also be opportunistic pathogens and act as a reservoir of resistance genes that can be passed on to other bacteria, including pathogens. Little is known about the prevalence of these commensals in parents and their children and their antimicrobial susceptibilities in the Belgian general population.Gap Statement. The macrolide susceptibility of commensal oral Streptococci in Belgium is unknown.Methods. We assessed the prevalence and azithromycin susceptibility of commensal streptococcal species in the parents (n=38) and children (n=50) of 35 families in Belgium.Results. The most frequently detected taxonomic grouping was Streptococcus mitis/oralis, which was detected in 78/181 (43.1%) of the children's isolates and 66/128 (51.6%) of the parents' isolates. Of the 311 isolates collected in this study, 282 isolates (90.7%) had an azithromycin MIC value greater than the breakpoint of 0.25 mg l[-1] and 146 isolates (46.9%) had azithromycin MICs greater than 2 mg l[-1]. There was no difference in the azithromycin MIC distribution of all streptococcal isolates between children and parents. All individuals were colonized by streptococci with azithromycin MICs greater than 0.25 mg l[-1], and 87.5% of individuals had streptococci with MICs greater than 2 mg l[-1].Interpretation. The most prevalent species identified in both age groups was S. mitis/oralis. All individuals harboured streptococci with macrolide resistance. This highlights the need for additional antimicrobial stewardship initiatives to reduce the consumption of macrolides in the general population.}, }
@article {pmid39535230, year = {2024}, author = {van Westerhoven, AC and Dijkstra, J and Aznar Palop, JL and Wissink, K and Bell, J and Kema, GHJ and Seidl, MF}, title = {Frequent genetic exchanges revealed by a pan-mitogenome graph of a fungal plant pathogen.}, journal = {mBio}, volume = {15}, number = {12}, pages = {e0275824}, pmid = {39535230}, issn = {2150-7511}, support = {AG-5797//Bill and Melinda Gates Foundation (GF)/ ; }, mesh = {*Genome, Mitochondrial/genetics ; *Fusarium/genetics/classification ; *Recombination, Genetic ; Evolution, Molecular ; Phylogeny ; Gene Transfer, Horizontal ; Genome, Fungal ; Plant Diseases/microbiology ; Genetic Variation ; }, abstract = {Mitochondria are present in almost all eukaryotic lineages. The mitochondrial genomes (mitogenomes) evolve separately from nuclear genomes, and they can therefore provide relevant insights into the evolution of their host species. Fusarium oxysporum is a major fungal plant pathogen that is assumed to reproduce clonally. However, horizontal chromosome transfer between strains can occur through heterokaryon formation, and recently, signs of sexual recombination have been observed. Similarly, signs of recombination in F. oxysporum mitogenomes challenged the prevailing assumption of clonal reproduction in this species. Here, we construct, to our knowledge, the first fungal pan-mitogenome graph of nearly 500 F. oxysporum mitogenome assemblies to uncover the variation and evolution. In general, the gene order of fungal mitogenomes is not well conserved, yet the mitogenome of F. oxysporum and related species are highly colinear. We observed two strikingly contrasting regions in the F. oxysporum pan-mitogenome, comprising a highly conserved core mitogenome and a long variable region (6-16 kb in size), of which we identified three distinct types. The pan-mitogenome graph reveals that only five intron insertions occurred in the core mitogenome and that the long variable regions drive the difference between mitogenomes. Moreover, we observed that their evolution is neither concurrent with the core mitogenome nor with the nuclear genome. Our large-scale analysis of long variable regions uncovers frequent recombination between mitogenomes, even between strains that belong to different taxonomic clades. This challenges the common assumption of incompatibility between genetically diverse F. oxysporum strains and provides new insights into the evolution of this fungal species.IMPORTANCEInsights into plant pathogen evolution is essential for the understanding and management of disease. Fusarium oxysporum is a major fungal pathogen that can infect many economically important crops. Pathogenicity can be transferred between strains by the horizontal transfer of pathogenicity chromosomes. The fungus has been thought to evolve clonally, yet recent evidence suggests active sexual recombination between related isolates, which could at least partially explain the horizontal transfer of pathogenicity chromosomes. By constructing a pan-genome graph of nearly 500 mitochondrial genomes, we describe the genetic variation of mitochondria in unprecedented detail and demonstrate frequent mitochondrial recombination. Importantly, recombination can occur between genetically diverse isolates from distinct taxonomic clades and thus can shed light on genetic exchange between fungal strains.}, }
@article {pmid39527185, year = {2024}, author = {Kim, K and Islam, MM and Bang, S and Kim, J and Lee, CY and Lee, JC and Shin, M}, title = {H-NS is a Transcriptional Repressor of the CRISPR-Cas System in Acinetobacter baumannii ATCC 19606.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {62}, number = {11}, pages = {999-1012}, pmid = {39527185}, issn = {1976-3794}, support = {2022R1A2C2010683//Ministry of Science and ICT, South Korea/ ; }, mesh = {*Acinetobacter baumannii/genetics/metabolism ; *CRISPR-Cas Systems ; *Promoter Regions, Genetic ; *Bacterial Proteins/genetics/metabolism ; *Gene Expression Regulation, Bacterial ; DNA-Binding Proteins/genetics/metabolism ; Repressor Proteins/genetics/metabolism ; CRISPR-Associated Proteins/metabolism/genetics ; }, abstract = {Acinetobacter baumannii is a multidrug-resistant opportunistic pathogen primarily associated with hospital-acquired infections. The bacterium can gain multidrug resistance through several mechanisms, including horizontal gene transfer. A CRISPR-Cas system including several Cas genes could restrict the horizontal gene transfer. However, the molecular mechanism of CRISPR- Cas transcriptional regulation remains unclear. We identified a type I-F CRISPR-Cas system in A. baumannii ATCC 19606[T] standard strain based on sequence analysis. We focused on the transcriptional regulation of Cas3, a key protein of the CRISPR-Cas system. We performed a DNA affinity chromatography-pulldown assay to identify transcriptional regulators of the Cas3 promoter. We identified several putative transcriptional factors, such as H-NS, integration host factor, and HU, that can bind to the promoter region of Cas3. We characterized AbH-NS using size exclusion chromatography and cross-linking experiments and demonstrated that the Cas3 promoter can be regulated by AbH-NS in a concentration-dependent manner via an in vitro transcription assay. CRISPR-Cas expression levels in wild-type and hns mutant strains in the early stationary phase were examined by qPCR and β-galactosidase assay. We found that H-NS can act as a repressor of Cas3. Our transformation efficiency results indicated that the hns mutation decreased the transformation efficiency, while the Cas3 mutation increased it. We report the existence and characterization of the CRISPR-Cas system in A. baumannii 19606[T] and demonstrate that AbH-NS is a transcriptional repressor of CRISPR-Cas-related genes in A. baumannii.}, }
@article {pmid39526401, year = {2025}, author = {Jiang, Y and Wang, Y and Che, L and Yang, S and Zhang, X and Lin, Y and Shi, Y and Zou, N and Wang, S and Zhang, Y and Zhao, Z and Li, SC}, title = {GutMetaNet: an integrated database for exploring horizontal gene transfer and functional redundancy in the human gut microbiome.}, journal = {Nucleic acids research}, volume = {53}, number = {D1}, pages = {D772-D782}, pmid = {39526401}, issn = {1362-4962}, support = {20220814183301001//Shenzhen Science and Technology Program/ ; }, mesh = {*Gene Transfer, Horizontal ; Humans ; *Gastrointestinal Microbiome/genetics ; *Databases, Genetic ; Metagenome/genetics ; Metagenomics/methods ; Bacteria/genetics/classification ; }, abstract = {Metagenomic studies have revealed the critical roles of complex microbial interactions, including horizontal gene transfer (HGT) and functional redundancy (FR), in shaping the gut microbiome's functional capacity and resilience. However, the lack of comprehensive data integration and systematic analysis approaches has limited the in-depth exploration of HGT and FR dynamics across large-scale gut microbiome datasets. To address this gap, we present GutMetaNet (https://gutmetanet.deepomics.org/), a first-of-its-kind database integrating extensive human gut microbiome data with comprehensive HGT and FR analyses. GutMetaNet contains 21 567 human gut metagenome samples with whole-genome shotgun sequencing data related to various health conditions. Through systematic analysis, we have characterized the taxonomic profiles and FR profiles, and identified 14 636 HGT events using a shared reference genome database across the collected samples. These HGT events have been curated into 8049 clusters, which are annotated with categorized mobile genetic elements, including transposons, prophages, integrative mobilizable elements, genomic islands, integrative conjugative elements and group II introns. Additionally, GutMetaNet incorporates automated analyses and visualizations for the HGT events and FR, serving as an efficient platform for in-depth exploration of the interactions among gut microbiome taxa and their implications for human health.}, }
@article {pmid39521804, year = {2024}, author = {Jerlström-Hultqvist, J and Gallot-Lavallée, L and Salas-Leiva, DE and Curtis, BA and Záhonová, K and Čepička, I and Stairs, CW and Pipaliya, S and Dacks, JB and Archibald, JM and Roger, AJ}, title = {A unique symbiosome in an anaerobic single-celled eukaryote.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {9726}, pmid = {39521804}, issn = {2041-1723}, support = {12188//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 5782//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 12188//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 12188//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; RES0043758//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en G&#xe9;nie du Canada)/ ; RES0046091//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en G&#xe9;nie du Canada)/ ; FRN-142349//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Sant&#xe9; du Canada)/ ; }, mesh = {*Symbiosis ; Anaerobiosis ; In Situ Hybridization, Fluorescence ; Eukaryota/genetics/metabolism ; Phylogeny ; Gene Transfer, Horizontal ; Microscopy, Electron, Scanning ; }, abstract = {Symbiotic relationships between eukaryotes and prokaryotes played pivotal roles in the evolution of life and drove the emergence of specialized symbiotic structures in animals, plants and fungi. The host-evolved symbiotic structures of microbial eukaryotes - the vast majority of such hosts in nature - remain largely unstudied. Here we describe highly structured symbiosomes within three free-living anaerobic protists (Anaeramoeba spp.). We dissect this symbiosis using complete genome sequencing and transcriptomics of host and symbiont cells coupled with fluorescence in situ hybridization, and 3D reconstruction using focused-ion-beam scanning electron microscopy. The emergence of the symbiosome is underpinned by expansion of gene families encoding regulators of membrane trafficking and phagosomal maturation and extensive bacteria-to-eukaryote lateral transfer. The symbionts reside deep within a symbiosomal membrane network that enables metabolic syntrophy by precisely positioning sulfate-reducing bacteria alongside host hydrogenosomes. Importantly, the symbionts maintain connections to the Anaeramoeba plasma membrane, blurring traditional boundaries between ecto- and endosymbiosis.}, }
@article {pmid39518977, year = {2024}, author = {Traglia, GM and Pasteran, F and Moheb, S and Akhtar, U and Gonzalez, S and Maldonado, C and Furtado, N and Mohamed, A and Escalante, J and Tuttobene, MR and Quillen, A and Fontan, C and Albornoz, E and Corso, A and Bonomo, RA and Rao, GG and Tolmasky, ME and Ramirez, MS}, title = {Insights into Acinetobacter baumannii AMA205's Unprecedented Antibiotic Resistance.}, journal = {International journal of molecular sciences}, volume = {25}, number = {21}, pages = {}, pmid = {39518977}, issn = {1422-0067}, support = {R01 AI100560/AI/NIAID NIH HHS/United States ; SC3GM125556 to MSR, R01AI100560, R01AI063517, R01AI072219 to RAB, and 2R15 AI047115 to MET/GF/NIH HHS/United States ; R01 AI072219/AI/NIAID NIH HHS/United States ; R01 AI063517/AI/NIAID NIH HHS/United States ; SC3 GM125556/GM/NIGMS NIH HHS/United States ; R15 AI047115/AI/NIAID NIH HHS/United States ; }, mesh = {*Acinetobacter baumannii/genetics/drug effects ; Humans ; *beta-Lactamases/genetics/metabolism ; *Acinetobacter Infections/microbiology/drug therapy ; *Anti-Bacterial Agents/pharmacology ; COVID-19/virology ; Bacterial Proteins/genetics/metabolism ; Drug Resistance, Multiple, Bacterial/genetics ; Microbial Sensitivity Tests ; Gene Transfer, Horizontal ; SARS-CoV-2/drug effects/genetics ; Genome, Bacterial ; Argentina ; Virulence Factors/genetics ; }, abstract = {The rise of antibiotic-resistant bacteria in clinical settings has become a significant global concern. Among these bacteria, Acinetobacter baumannii stands out due to its remarkable ability to acquire resistance genes and persist in hospital environments, leading to some of the most challenging infections. Horizontal gene transfer (HGT) plays a crucial role in the evolution of this pathogen. The A. baumannii AMA205 strain, belonging to sequence type ST79, was isolated from a COVID-19 patient in Argentina in 2021. This strain's antimicrobial resistance profile is notable as it harbors multiple resistance genes, some of which had not been previously described in this species. The AmpC family β-lactamase blaCMY-6, commonly found in Enterobacterales, had never been detected in A. baumannii before. Furthermore, this is the first ST79 strain known to carry the carbapenemase blaNDM-1 gene. Other acquired resistance genes include the carbapenemase blaOXA-23, further complicating treatment. Susceptibility testing revealed high resistance to most antibiotic families, including cefiderocol, with significant contributions from blaCMY-6 and blaNDM-1 genes to the cephalosporin and carbapenem resistance profiles. The A. baumannii AMA205 genome also contains genetic traits coding for 111 potential virulence factors, such as the iron-uptake system and biofilm-associated proteins. This study underscores A. baumannii's ability to acquire multiple resistance genes and highlights the need for alternative therapies and effective antimicrobial stewardship to control the spread of these highly resistant strains.}, }
@article {pmid39516559, year = {2024}, author = {Ares-Arroyo, M and Nucci, A and Rocha, EPC}, title = {Expanding the diversity of origin of transfer-containing sequences in mobilizable plasmids.}, journal = {Nature microbiology}, volume = {9}, number = {12}, pages = {3240-3253}, pmid = {39516559}, issn = {2058-5276}, mesh = {*Plasmids/genetics ; *Escherichia coli/genetics ; *Conjugation, Genetic ; *Klebsiella pneumoniae/genetics ; *Acinetobacter baumannii/genetics/classification ; Computational Biology/methods ; Gene Transfer, Horizontal ; Replication Origin/genetics ; DNA, Bacterial/genetics/chemistry ; }, abstract = {Conjugative plasmids are important drivers of bacterial evolution. Most plasmids lack genes for conjugation and characterized origins of transfer (oriT), which has hampered our understanding of plasmid mobility. Here we used bioinformatic analyses to characterize occurrences of known oriT families across 38,057 plasmids, confirming that most conjugative and mobilizable plasmids lack identifiable oriTs. Recognizable oriT sequences tend to be intergenic, upstream of relaxase genes and specifically associated with relaxase types. We used these criteria to develop a computational method to search for and identify 21 additional families of oriT-containing sequences in plasmids from the pathogens Escherichia coli, Klebsiella pneumoniae and Acinetobacter baumannii. Sequence analyses found 3,072 occurrences of these oriT-containing sequences across 2,976 plasmids, many of which encoded antimicrobial resistance genes. Six candidate oriT-containing sequences were validated experimentally and were shown to facilitate conjugation in E. coli. These findings expand our understanding of plasmid mobility.}, }
@article {pmid39515144, year = {2024}, author = {Luo, Y and Xu, T and Li, B and Liu, F and Wu, B and Dobson, PS and Yin, H and Chen, Z and Qiu, Y and Huang, X}, title = {The effects of small plastic particles on antibiotic resistance gene transfer revealed by single cell and community level analysis.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {136271}, doi = {10.1016/j.jhazmat.2024.136271}, pmid = {39515144}, issn = {1873-3336}, mesh = {*Escherichia coli/drug effects/genetics ; *Polystyrenes/toxicity/chemistry ; *Particle Size ; Microplastics/toxicity ; Gene Transfer, Horizontal ; Sewage/microbiology ; Single-Cell Analysis ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics/drug effects ; Plastics/toxicity ; Anti-Bacterial Agents/pharmacology/toxicity ; }, abstract = {Small plastic particles with sizes comparable to bacterial cells, widely exist in environment. However, their effects on antibiotic resistance gene (ARG) dissemination remain unclear. Using polystyrene (PS) particles (0.2 µm, 2 µm, 5 µm, 10 µm, 15 µm, 20 µm) as models, conjugative transfer of ARGs between the donor E. coli and different recipients (E. coli or sludge bacterial community) was investigated. Compared to the pure strain, the sludge bacterial community exposed to PS particles showed higher transfer frequencies (1.67 to 14.31 times the blank control). The transfer frequencies first decreased and then increased with particle size, and plastics similar in size to bacteria (e.g., 2 µm) appear to be a transitional zone with minimal impact on ARG transmission. Furthermore, using microfluidics, in-situ observation at single cell level found that 2 µm plastics can act as barriers between donor and recipient bacteria inhibiting growth, but conjugation events mostly occurred around them. Conversely, nanoplastics (e.g., 0.2 µm) and larger microplastics (e.g., 20 µm) significantly promote conjugation, mainly due to increased reactive oxygen species production and cell membrane permeability, or facilitating bacterial adhesion and biofilm formation, respectively. This study aids in assessing environmental risks of small plastic particles on ARG dissemination.}, }
@article {pmid39511299, year = {2024}, author = {Hu, Y and Duan, G and Yan, H and Guo, Y and Chang, J and Zhou, M and Yan, S and Li, W and Ruan, C and Gao, S}, title = {Discovery of the first Tn630 member and the closest homolog of IS630 from viruses.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {27081}, pmid = {39511299}, issn = {2045-2322}, support = {2024-KF-03//the Open Project of Qinghai Key Laboratory of Qinghai-Tibet Plateau Biological Resources/ ; }, mesh = {*DNA Transposable Elements/genetics ; Phylogeny ; Viruses/genetics ; Bacteria/genetics/virology ; Animals ; Host Specificity/genetics ; }, abstract = {IS630/Tc1/mariner (ITm) represents the most widely distributed superfamily of DNA transposons in nature. Currently, bioinformatics research on ITm members primarily involves collecting data of existing and emerging members and organizing them into new groups or families. In the present study, our survey revealed that Tc1 and IS630 members have a broad host range, spanning across all six biological kingdoms (bacteria, fungi, plantae, animalia, archaea and protista) and viruses. The primary discoveries include the first Tn630 member-Tn630-NC1 and the closest homolog of IS630 from viruses-Tc1-C#1. By incorporating our discoveries into existing knowledge, we proposed a model to elucidate the formation of composite transposons. Organization of Tc1 and IS630 members into groups across biological kingdoms facilitates data collection for future research, particularly on their horizontal transfer between different kingdoms. The formation of composite transposons may result from asymmetric of terminal inverted repeats. IS630 should be merged with Tc1 into a single family IS630/Tc1. Furthermore, IS630 and its homologs constitute a valuable resource for studying horizontal gene transfer between gut bacteria and phages, opening up new avenues for research in this field.}, }
@article {pmid39510298, year = {2024}, author = {Song, J and Huang, Z and Gao, Y and Wang, W and Guo, G and Duan, Y and Zhou, S and Tang, Z}, title = {Metagenomic insight into the enrichment of antibiotic resistance genes in activated sludge upon exposure to nanoplastics.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {363}, number = {Pt 2}, pages = {125260}, doi = {10.1016/j.envpol.2024.125260}, pmid = {39510298}, issn = {1873-6424}, mesh = {*Sewage/microbiology ; *Drug Resistance, Microbial/genetics ; Metagenomics ; Bacteria/genetics/drug effects ; Gene Transfer, Horizontal ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; Water Pollutants, Chemical/toxicity ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Activated sludge is an important reservoir for the co-occurring emerging contaminants including nanoplastics (NPs) and antibiotic resistance genes (ARGs). However, the impacts and potential mechanisms of NPs on the fate of ARGs in activated sludge are not fully understood. Herein, we used metagenomic approach to investigate the responses of ARGs, host bacteria, mobile genetic elements (MGEs), and functional genes to polystyrene (PS) NPs at environmentally relevant (0.5 mg/L) and high stress concentrations (50 mg/L) in activated sludge. The results showed that 0.5 and 50 mg/L PS NPs increased the relative abundance of ARGs in the activated sludge by 58.68% and 46.52%, respectively (p < 0.05). Host tracking analysis elucidated that the hosts of ARGs were significantly enriched by PS NPs (p < 0.05), with Proteobacteria being the predominant host bacteria. Additionally, the occurrence of new ARGs hosts and the enrichment of MGEs and functional genes (i.e., genes related to SOS response, cell membrane permeability, and secretion system, etc.) indicated that PS NPs promoted horizontal gene transfer (HGT) of ARGs. Finally, path modeling analysis revealed that the proliferation of ARGs caused by PS NPs was primarily attributed to the enhancement of HGT and the enrichment of host bacteria. Our findings contribute to a comprehensive understanding of the spread risk of ARGs in activated sludge under NPs pollution.}, }
@article {pmid39510271, year = {2024}, author = {Xiong, J and Hu, S and Xu, Z and Li, C and Li, Z and Li, S and Ma, Y and Ren, X and Huang, B and Pan, X}, title = {Different paths, same destination: Bisphenol A and its substitute induce the conjugative transfer of antibiotic resistance genes.}, journal = {Chemosphere}, volume = {368}, number = {}, pages = {143625}, doi = {10.1016/j.chemosphere.2024.143625}, pmid = {39510271}, issn = {1879-1298}, mesh = {*Benzhydryl Compounds/toxicity ; *Phenols/toxicity ; *Escherichia coli/drug effects/genetics ; *Conjugation, Genetic ; Gene Transfer, Horizontal ; Drug Resistance, Microbial/genetics ; Sulfones/toxicity ; Plasmids/genetics ; Reactive Oxygen Species/metabolism ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/toxicity/pharmacology ; }, abstract = {Antibiotic resistance genes are primarily spread through horizontal gene transfer in aquatic environments. Bisphenols, which are widely used in industry, are pervasive contaminants in such environments. This study investigated how environmentally relevant concentrations of bisphenol A and its substitute (bisphenol S, Bisphenol AP and Bisphenol AF) affect the spread of antibiotic resistance genes among Escherichia coli. As a result, bisphenol A and its three substitutes were found to promote the RP4 plasmid-mediated conjugative transfer of antibiotic resistance genes with different promotive efficiency. Particularly, bisphenol A and bisphenol S were found to induce more than double the incidence of conjugation at 0.1 nmol/L concentration. They therefore were selected as model compounds to investigate the involved mechanisms. Surprisingly, both slightly inhibited bacterial activity, but there was no significant increase in cell death. Bisphenols exposure changed the polymeric substances excreted by the bacteria, increased the permeability of their cell membranes, induced the secretion of antioxidant enzymes and generated reactive oxygen species. They also affected the expression of genes related to conjugative transfer by upregulating replication and DNA transfer genes and downregulating global regulatory genes. It should be noted that gene expression levels were higher in the BPS-exposed group than in the BPA-exposed group. The synthesis of bacterial metabolites and functional components was also significantly affected by bisphenols exposure. This research has helped to clarify the potential health risks of bisphenol contamination of aquatic environments.}, }
@article {pmid39508585, year = {2024}, author = {Androsiuk, L and Maane, S and Tal, S}, title = {CRISPR spacers acquired from plasmids primarily target backbone genes, making them valuable for predicting potential hosts and host range.}, journal = {Microbiology spectrum}, volume = {12}, number = {12}, pages = {e0010424}, pmid = {39508585}, issn = {2165-0497}, abstract = {In recent years, there has been a surge in metagenomic studies focused on identifying plasmids in environmental samples. Although these studies have unearthed numerous novel plasmids, enriching our understanding of their environmental roles, a significant gap remains: the scarcity of information regarding the bacterial hosts of these newly discovered plasmids. Furthermore, even when plasmids are identified within bacterial isolates, the reported host is typically limited to the original isolate, with no insights into alternative hosts or the plasmid's potential host range. Given that plasmids depend on hosts for their existence, investigating plasmids without the knowledge of potential hosts offers only a partial perspective. This study introduces a method for identifying potential hosts and host ranges for plasmids through alignment with CRISPR spacers. To validate the method, we compared the PLSDB plasmids database with the CRISPR spacers database, yielding host predictions for 46% of the plasmids. When compared with reported hosts, our predictions achieved 84% concordance at the family level and 99% concordance at the phylum level. Moreover, the method frequently identified multiple potential hosts for a plasmid, thereby enabling predictions of alternative hosts and the host range. Notably, we found that CRISPR spacers predominantly target plasmid backbone genes while sparing functional genes, such as those linked to antibiotic resistance, aligning with our hypothesis that CRISPR spacers are acquired from plasmid-specific regions rather than insertion elements from diverse sources. Finally, we illustrate the network of connections among different bacterial taxa through plasmids, revealing potential pathways for horizontal gene transfer.IMPORTANCEPlasmids are notorious for their role in distributing antibiotic resistance genes, but they may also carry and distribute other environmentally important genes. Since plasmids are not free-living entities and rely on host bacteria for survival and propagation, predicting their hosts is essential. This study presents a method for predicting potential hosts for plasmids and offers insights into the potential paths for spreading functional genes between different bacteria. Understanding plasmid-host relationships is crucial for comprehending the ecological and clinical impact of plasmids and implications for various biological processes.}, }
@article {pmid39506544, year = {2024}, author = {Choufa, C and Gascht, P and Leblond, H and Gauthier, A and Vos, M and Bontemps, C and Leblond, P}, title = {Conjugation Mediates Large-Scale Chromosomal Transfer in Streptomyces Driving Diversification of Antibiotic Biosynthetic Gene Clusters.}, journal = {Molecular biology and evolution}, volume = {41}, number = {11}, pages = {}, pmid = {39506544}, issn = {1537-1719}, support = {//French National Research Agency/ ; ANR-11-LABX-0002//Investissements d'Avenir program/ ; //R&#xe9;gion Grand Est/ ; }, mesh = {*Streptomyces/genetics/metabolism ; *Multigene Family ; *Gene Transfer, Horizontal ; *Chromosomes, Bacterial/genetics ; *Conjugation, Genetic ; *Anti-Bacterial Agents/biosynthesis ; }, abstract = {Streptomyces are ubiquitous soil-dwelling bacteria with large, linear genomes that are of special importance as a source of metabolites used in human and veterinary medicine, agronomy, and industry. Conjugative elements (actinomycetes integrative and conjugative elements, AICEs) are the main drivers of Streptomyces Horizontal Gene Transfer. AICE transfer has long been known to be accompanied by mobilization of chromosomal DNA. However, the magnitude of DNA transfer, or the localization of acquired DNA across their linear chromosome, has remained undetermined. We here show that conjugative crossings in sympatric strains of Streptomyces result in the large-scale, genome-wide distributed replacement of up to one-third of the recipient chromosome, a phenomenon for which we propose the name "Streptomyces Chromosomal Transfer" (SCT). Such chromosome blending results in the acquisition, loss, and hybridization of Specialized Metabolite Biosynthetic Gene Clusters, leading to a novel metabolic arsenal in exconjugant offspring. Harnessing conjugation-mediated specialized metabolite biosynthesis gene cluster diversification holds great promise in the discovery of new bioactive compounds including antibiotics.}, }
@article {pmid39504695, year = {2025}, author = {Liu, M and Su, X and Yuan, J and Yang, X and Chen, Y and Xu, Q and Huang, X and Xu, J and He, Y}, title = {Unravelling the processes involved in biodegradation of chlorinated organic pollutant: From microbial community to isolated organohalide degraders.}, journal = {Water research}, volume = {268}, number = {Pt B}, pages = {122730}, doi = {10.1016/j.watres.2024.122730}, pmid = {39504695}, issn = {1879-2448}, mesh = {*Biodegradation, Environmental ; Bacteria/metabolism/genetics ; Hydrocarbons, Chlorinated/metabolism ; Microbiota ; }, abstract = {Hundreds of studies have demonstrated the bioremediation of chlorinated organic pollutants (COPs) in flooded environments. However, the role of specific functional strains in degrading COPs under complex media such as wetlands is still unclear. Here, we focused on the microbial characteristics of COP-polluted sediments, identified the bacteria responsible for degradation and conducted a genomic analysis of these bacteria. Four strains were obtained and identified as Petrimonas sulfuriphila PET, Robertmurraya sp. CYTO, Hungatella sp. CloS1 and Enterococcus avium PseS3, respectively. They were capable of degrading a typical COP, γ-hexachlorocyclohexane (γ-HCH). The residual γ-HCH concentrations were 58.8 % (PET), 45.6 % (CYTO), 60.2 % (CloS1), and 69.3 % (PseS3) of its initial value, respectively. Strain PET, CYTO and CloS1 could degrade γ-HCH to its dehalogenation product chlorobenzene. Each strain harbors genes annotated to the pathway of halogenated organic matter degradation (e.g. 2-haloacid dehalogenase) and cobalamin biosynthesis, which are involved in the degradation of COPs. Comparative genomic analysis of the four strains and other classical organohalide-respiring bacteria (e.g. Dehalococcoides mccartyi and Sulfurospirillum multivorans DSM 12446) showed that they share orthologous clusters related to the cobalamin biosynthetic process (GO:0009236). VB12 was also detected in the culture systems of the four strains, further highlighting the importance of cobalamin in COPs degradation. In the genome of the four strains, some genes were annotated to the halogenated organic matter degradation and cobalamin biosynthesis pathway within horizontal gene transfer (HGT) regions. This further indicated that microorganisms carrying these genes can adapt faster to pollution stress through HGT. Together, these findings revealed the co-evolution mechanism of functional strains and may provide novel insights into improved bioremediation strategies for COP-polluted complex media based on generalist organochlorine-degrading bacteria.}, }
@article {pmid39503503, year = {2024}, author = {Werner Lass, S and Smith, BE and Camphire, S and Eutsey, RA and Prentice, JA and Yerneni, SS and Arun, A and Bridges, AA and Rosch, JW and Conway, JF and Campbell, P and Hiller, NL}, title = {Pneumococcal extracellular vesicles mediate horizontal gene transfer via the transformation machinery.}, journal = {mSphere}, volume = {9}, number = {12}, pages = {e0072724}, pmid = {39503503}, issn = {2379-5042}, support = {//Shurl and Kay Curci Foundation (SKCF)/ ; T32 GM133353/GM/NIGMS NIH HHS/United States ; 5T32GM133353-04//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; S10 OD025009/CD/ODCDC CDC HHS/United States ; S10 OD025009/OD/NIH HHS/United States ; //NSF | National Science Foundation Graduate Research Fellowship Program (GRFP)/ ; }, mesh = {*Gene Transfer, Horizontal ; *Extracellular Vesicles/metabolism/genetics ; *Streptococcus pneumoniae/genetics ; *Transformation, Bacterial ; *DNA, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; Humans ; }, abstract = {Bacterial cells secrete extracellular vesicles (EVs), the function of which is a matter of intense investigation. Here, we show that the EVs secreted by the human pathogen Streptococcus pneumoniae (pneumococcus) are associated with bacterial DNA on their surface and can deliver this DNA to the transformation machinery of competent cells. These findings suggest that EVs contribute to gene transfer in Gram-positive bacteria and, in doing so, may promote the spread of drug resistance genes in the population.IMPORTANCEThis work extends our understanding of horizontal gene transfer and the roles of extracellular vesicles in pneumococcus. This bacterium serves as the model for transformation, a process by which bacteria can take up naked DNA from the environment. Here, we show that extracellular vesicles secreted by the pneumococcus have DNA on their surface and that this DNA can be imported by the transformation machinery, facilitating gene transfer. Understanding EV-mediated gene transfer may provide new avenues to manage the spread of antibiotic drug resistance.}, }
@article {pmid39500921, year = {2024}, author = {Stewart, RD and Oluwalana-Sanusi, AE and Munzeiwa, WA and Magoswana, L and Chaukura, N}, title = {Profiling the bacterial microbiome diversity and assessing the potential to detect antimicrobial resistance bacteria in wastewater in Kimberley, South Africa.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {26867}, pmid = {39500921}, issn = {2045-2322}, mesh = {*Wastewater/microbiology ; South Africa ; *Microbiota/genetics ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/classification/isolation &amp; purification/drug effects ; RNA, Ribosomal, 16S/genetics ; Anti-Bacterial Agents/pharmacology ; Phylogeny ; }, abstract = {Wastewater treatment plants (WWTPs) are hotspots for pathogens, and can facilitate horizontal gene transfer, potentially releasing harmful genetic material and antimicrobial resistance genes into the environment. Little information exists on the composition and behavior of microbes in WWTPs, especially in developing countries. This study used environmental DNA (eDNA) techniques to examine the microbiome load of wastewater from WWTPs. The DNA was isolated from wastewater samples collected from the treatment trains of three WWTPs in Kimberley, South Africa, and the microbial diversity and composition was compared through 16 S rRNA gene sequencing. The microbes detected were of the Kingdom Bacteria, and of these, 48.27% were successfully identified to genus level. The majority of reads from the combined bacterial data fall within the class Gammaproteobacteria, which is known to adversely impact ecological and human health. Arcobacteraceae constituted 19% of the bacterial reads, which is expected as this family is widespread in aquatic environments. Interestingly, the most abundant bacterial group was Bacteroides, which contain a variety of antibiotic-resistant members. Overall, various antibiotic-resistant taxa were detected in the wastewater, indicating a concerning level of antibiotic resistance within the bacterial community. Therefore, eDNA analysis can be a valuable tool in monitoring and assessing the bacterial microbiome in wastewater, thus providing important information for the optimization and improvement of wastewater treatment systems and mitigate public health risks.}, }
@article {pmid39500447, year = {2024}, author = {Fagunwa, OE and Ashiru-Oredope, D and Gilmore, BF and Doherty, S and Oyama, LB and Huws, SA}, title = {Climate change as a challenge for pharmaceutical storage and tackling antimicrobial resistance.}, journal = {The Science of the total environment}, volume = {956}, number = {}, pages = {177367}, doi = {10.1016/j.scitotenv.2024.177367}, pmid = {39500447}, issn = {1879-1026}, mesh = {*Climate Change ; Drug Storage ; Anti-Infective Agents ; Humans ; Drug Resistance, Microbial ; }, abstract = {The rise of antimicrobial resistance (AMR) remains a pressing global health challenge. Infections that were once easily treatable with first-line antimicrobials are becoming increasingly difficult to manage. This shift directly threatens the wellness of humans, animals, plants, and the environment. While the AMR crisis can be attributed to a myriad of factors, including lack of infection prevention and control measures, over-prescription of antimicrobials, patient non-compliance, and the misuse of antimicrobials, one aspect that has garnered less attention is the role of storage conditions of these medicines. The way medications, particularly antimicrobials, are transported and stored until the point of use can influence their efficacy and, subsequently, may impact the development of resistant microbial strains. This review delves deeper into the often-overlooked domain of climate change (CC) and antimicrobial storage practices and the potential effects. Inappropriate storage conditions, such as exposure to extreme temperatures, humidity or light, can degrade the potency of antimicrobials. When these compromised medicines are administered to patients or animals alike, they may not effectively eradicate the targeted pathogens, leading to partial survival of the pathogens. These surviving pathogens, having been exposed to sub-lethal doses, are more likely to evolve and develop resistance mechanisms. The review discusses the mechanism underlying this and underscores the implications of antimicrobial storage practices in relation to two of the most pressing global health challenges: AMR and CC. The review also presents specific case studies and highlights the importance of monitoring storage practices and supply chain surveillance. Furthermore, the importance of deploying genomic tools to understand the potential impact of storage conditions on the development of AMR is discussed, and antimicrobial storage highlighted as a crucial part of comprehensive strategies in the fight against AMR.}, }
@article {pmid39500253, year = {2024}, author = {Zhang, G and Ren, R and Yan, X and Zhang, H and Zhu, Y}, title = {Effects of microplastics on dissipation of oxytetracycline and its relevant resistance genes in soil without and with Serratia marcescens: Comparison between biodegradable and conventional microplastics.}, journal = {Ecotoxicology and environmental safety}, volume = {287}, number = {}, pages = {117235}, doi = {10.1016/j.ecoenv.2024.117235}, pmid = {39500253}, issn = {1090-2414}, mesh = {*Oxytetracycline/toxicity ; *Serratia marcescens/drug effects/genetics ; *Soil Pollutants/toxicity ; *Soil Microbiology ; *Biodegradation, Environmental ; *Microplastics/toxicity ; Soil/chemistry ; Anti-Bacterial Agents/toxicity ; Drug Resistance, Bacterial/genetics ; }, abstract = {The biodegradable (polybutylene adipate terephthalate: PBAT) and conventional (polyethylene: PE) microplastics (MPs) at 0.5 %, 1 %, and 2 % dosages (w/w) were added into soils with and without Serratia marcescens ZY01 (ZY01, a tet-host strain) to understand their different effects on the dissipation of oxytetracycline (OTC) and tet. The results showed that the dosages of PBAT MP exhibited different inhibition degrees of OTC biodegradation in soils regardless of ZY01, while the dosages of PE MP did not change the enhancement degree of OTC biodegradation in soils without ZY01. These differences were due to the higher adsorption capacity of OTC on PBAT MP and the stronger toxicity of PBAT MP to microorganisms. Besides soil organic matter, pH and total phosphorus were important factors regulating specific tet-host bacteria in soils with MPs (e.g., the nitrogen-cycling bacteria Steroidobacter and Nitrospira) and MPs + ZY01 (e.g., the phosphorus-cycling bacteria Saccharimonadales and Haliangium), respectively. Regardless of ZY01, a stronger selective harboring of tet-host bacteria in PE MP treatments than PBAT MP treatments was observed at the MP dosage of 1 % (w/w), while the opposite trend was true at the MP dosages of 0.5 % and 2 % (w/w). Some specific genera belonging to Actinobacteriota strongly associated with the class 1 integron-integrase gene (intI1), playing a critical role in the horizontal gene transfer of tet in soils especially for the co-existence of MPs and ZY01. This study will be helpful for understanding on how biodegradable and conventional MPs as hotspots affect the environmental behavior of antibiotics and ARGs in soil.}, }
@article {pmid39499398, year = {2024}, author = {Fu, J and Zhang, P and Yin, X and Zhu, L and Zong, G and Zhong, C and Cao, G}, title = {A scientific research training programme for teaching biomedical students to identify the horizontal transfer of antibiotic resistance genes.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, pmid = {39499398}, issn = {1874-9356}, support = {SDYAL2022135//the Course Construction Project of Shandong Province/ ; }, abstract = {Worldwide prevalence of multi-antibiotic resistant bacteria is rapidly increasing, and the education of undergraduates and graduates about antibiotic resistance and its associated horizontal gene transfer is critical in the general effort to confront the spread of antibiotic resistance. In this study, a deeper understanding of antibiotic resistance and horizontal gene transfer was achieved by biomedical undergraduate students through a scientific research programme. The enthusiasm of students to participate in the training programme was very high, and results revealed that each student could identify the antibiotic resistance integrative and conjugative element from the Stenotrophomonas maltophilia MER1 genome. Each student could also draw the phylogenetic relationship of the antibiotic resistance integrative and conjugative element. In addition, students proved the horizontal transfer of antibiotic resistance genes from S. maltophilia MER1 to Escherichia coli strain 25DN through conjugation and PCR assays. Each group of students was able to obtain the expected results, indicating that the outcome of the scientific research programme was highly reproducible. This programme improved the theoretical knowledge about antibiotic resistance and horizontal gene transfer and the research skills of biomedical sciences students. Through this programme, students learned that antibiotic resistance genes can be horizontally transferred among different bacteria, laying a solid foundation for students to value the importance of the appropriate use of antibiotics in their future work and life.}, }
@article {pmid39498151, year = {2024}, author = {Dias, YJM and Dezordi, FZ and Wallau, GDL}, title = {EEfinder, a general purpose tool for identification of bacterial and viral endogenized elements in eukaryotic genomes.}, journal = {Computational and structural biotechnology journal}, volume = {23}, number = {}, pages = {3662-3668}, pmid = {39498151}, issn = {2001-0370}, abstract = {Horizontal gene transfer is a phenomenon of genetic material transmission between species with no parental relationship. It has been characterized among several major branches of life, including among prokaryotes, viruses and eukaryotes. The characterization of endogenous elements derived from viruses or bacteria provides a snapshot of past host-pathogen interactions and coevolution as well as reference information to remove false positive results from metagenomic studies. Currently there is a lack of general purpose standardized tools for endogenous elements screening which limits reproducibility and hinder comparative analysis between studies. Here we describe EEfinder, a new general purpose tool for identification and classification of endogenous elements derived from viruses or bacteria found in eukaryotic genomes. The tool was developed to include six common steps performed in this type of analysis: data cleaning, similarity search through sequence alignment, filtering candidate elements, taxonomy assignment, merging of truncated elements and flanks extraction. We evaluated the sensitivity of EEfinder to identify endogenous elements through comparative analysis using data from the literature and showed that EEfinder automatically detected 97 % of the EVEs compared to published results obtained by manual curation and detected an almost exact full integration of a Wolbachia genome described using wet-lab experiments. Therefore, EEfinder can effectively and systematically identify endogenous elements with bacterial/viral origin integrated in eukaryotic genomes. EEfinder is publicly available on https://github.com/WallauBioinfo/EEfinder.}, }
@article {pmid39498132, year = {2024}, author = {Abe, K and Yahara, H and Nakao, R and Yamaguchi, T and Akeda, Y}, title = {A simple and cost-effective transformation system for Porphyromonas gingivalis via natural competence.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1476171}, pmid = {39498132}, issn = {1664-302X}, abstract = {Porphyromonas gingivalis is a major oral bacterial pathogen responsible for severe periodontal diseases. Numerous studies have used genetic approaches to elucidate the molecular mechanisms underlying its pathogenicity. Typically, electroporation and conjugation are utilized for mutagenesis of P. gingivalis; however, these techniques require specialized equipment such as high-voltage electroporators, conjugative plasmids and donor strains. In this study, we present a simple, cost-effective transformation method for P. gingivalis without any special equipment by exploiting its natural DNA competence. P. gingivalis ATCC 33277 was grown to the early-exponential phase and mixed with a donor DNA cassette. This mixture was then spotted onto a BHI-HM blood-agar plate and incubated for one day to promote colony biofilm formation. The resulting colony biofilm was suspended in a liquid medium and spread onto antibiotic-containing agar plates. Transformants appeared within 4 to 5 days, achieving a maximum efficiency of 7.7 × 10[6] CFU/μg. Although we optimized the transformation conditions using a representative strain ATCC 33277, but the method was also effective for other P. gingivalis strains, W83 and TDC60. Additionally, we discovered that deletion of PGN_0421 or PGN_0519, encoding putative ComEA and ComEC, abolished competency, indicating that these gene products are essential for the natural competence.}, }
@article {pmid39497365, year = {2024}, author = {Qu, S and Zhang, Y and Weng, L and Shan, X and Cheng, P and Li, Q and Li, L}, title = {The role of bacterial extracellular vesicles in promoting antibiotic resistance.}, journal = {Critical reviews in microbiology}, volume = {}, number = {}, pages = {1-18}, doi = {10.1080/1040841X.2024.2423159}, pmid = {39497365}, issn = {1549-7828}, abstract = {The burgeoning proliferation of infections attributed to multidrug-resistant (MDR) bacterial pathogens is profoundly undermining conventional chemotherapeutic modalities, portending a grave menace to global public health. The propagation of drug resistance among bacteria is fundamentally facilitated by bacterial interactions, with extracellular vesicles (EVs) assuming a critical role in interbacterial communication. Here, we briefly delineate the methodologies for isolation, extraction, and characterization of EVs from both Gram-negative and Gram-positive bacterial origins. We further investigate assorted methodologies to augment EV production, embracing physical stimulation, chemical elicitation, and genetic engineering. Moreover, we expound on the pivotal involvement of EVs in the facilitation of bacterial drug resistance proliferation and anticipate future trajectories of research and application potential. This overview of EV-mediated novel mechanisms of horizontal gene transfer implicated in antibiotic resistance among bacteria aims to obstruct the transmission conduits of bacterial drug resistance and thus fortify public health integrity.}, }
@article {pmid39494898, year = {2024}, author = {Priya, S and Rossbach, S and Eng, T and Lin, H-H and Andeer, PF and Mortimer, JC and Northen, TR and Mukhopadhyay, A}, title = {Assessing horizontal gene transfer in the rhizosphere of Brachypodium distachyon using fabricated ecosystems (EcoFABs).}, journal = {Applied and environmental microbiology}, volume = {90}, number = {11}, pages = {e0150524}, pmid = {39494898}, issn = {1098-5336}, support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; }, mesh = {*Gene Transfer, Horizontal ; *Rhizosphere ; *Brachypodium/genetics/microbiology ; *Pseudomonas putida/genetics ; *Plasmids/genetics ; *Soil Microbiology ; Ecosystem ; Plant Roots/microbiology ; Burkholderia/genetics ; Microbiota ; }, abstract = {Horizontal gene transfer (HGT) is a major process by which genes are transferred between microbes in the rhizosphere. However, examining HGT remains challenging due to the complexity of mimicking conditions within the rhizosphere. Fabricated ecosystems (EcoFABs) have been used to investigate several complex processes in plant-associated environments. Here we show that EcoFABs are efficient tools to examine and measure HGT frequency in the rhizosphere. We provide the first demonstration of gene transfer via a triparental conjugation system in the Brachypodium distachyon rhizosphere in an EcoFAB using Pseudomonas putida KT2440 as both donor and recipient bacterial strain with the donor containing a mobilizable and non-self-transmissible plasmid. We observed that the frequency of plasmid transfer in the rhizosphere is potentially dependent on the plant developmental stage and the composition and amount of root exudates. The frequency of plasmid transfer also increased with higher numbers of donor cells. We demonstrate the transfer of plasmid from P. putida to another B. distachyon root colonizer, Burkholderia sp. OAS925, showing HGT within a rhizosphere microbial community. Environmental stresses also influenced the rate and efficiency of HGT in the rhizosphere between different species and genera. This study provides a robust workflow to evaluate transfer of engineered plasmids in the rhizosphere when such plasmids are potentially introduced in a field or other plant-associated environments.IMPORTANCEWe report the use of EcoFABs to investigate the HGT process in a rhizosphere environment. It highlights the potential of EcoFABs in recapitulating the dynamic rhizosphere conditions as well as their versatility in studying plant-microbe interactions. This study also emphasizes the importance of studying the parameters impacting the HGT frequency. Several factors such as plant developmental stages, nutrient conditions, number of donor cells, and environmental stresses influence gene transfer within the rhizosphere microbial community. This study paves the way for future investigations into understanding the fate and movement of engineered plasmids in a field environment.}, }
@article {pmid39494882, year = {2024}, author = {Oke, MT and Martz, K and Mocăniță, M and Knezevic, S and D'Costa, VM}, title = {Analysis of Acinetobacter P-type type IV secretion system-encoding plasmid diversity uncovers extensive secretion system conservation and diverse antibiotic resistance determinants.}, journal = {Antimicrobial agents and chemotherapy}, volume = {68}, number = {12}, pages = {e0103824}, pmid = {39494882}, issn = {1098-6596}, support = {PJ4-175369,PJT-178191//Canadian Government | Canadian Institutes of Health Research (CIHR)/ ; }, mesh = {*Plasmids/genetics ; *Type IV Secretion Systems/genetics ; *Anti-Bacterial Agents/pharmacology ; Humans ; *Drug Resistance, Multiple, Bacterial/genetics ; Gene Transfer, Horizontal ; Acinetobacter/genetics/drug effects ; Acinetobacter baumannii/genetics/drug effects ; Bacterial Proteins/genetics ; beta-Lactamases/genetics ; Acinetobacter Infections/microbiology ; Microbial Sensitivity Tests ; Phylogeny ; }, abstract = {Acinetobacter baumannii is globally recognized as a multi-drug-resistant pathogen of critical concern due to its capacity for horizontal gene transfer and resistance to antibiotics. Phylogenetically diverse Acinetobacter species mediate human infection, including many considered as important emerging pathogens. While globally recognized as a pathogen of concern, pathogenesis mechanisms are poorly understood. P-type type IV secretion systems (T4SSs) represent important drivers of pathogen evolution, responsible for horizontal gene transfer and secretion of proteins that mediate host-pathogen interactions, contributing to pathogen survival, antibiotic resistance, virulence, and biofilm formation. Genes encoding a P-type T4SS were previously identified on plasmids harboring the carbapenemase gene blaNDM-1 in several clinically problematic Acinetobacter; however, their prevalence among the genus, geographical distribution, the conservation of T4SS proteins, and full capacity for resistance genes remain unclear. Using systematic analyses, we show that these plasmids belong to a group of 53 P-type T4SS-encoding plasmids in 20 established Acinetobacter species, the majority of clinical relevance, including diverse A. baumannii sequence types and one strain of Providencia rettgeri. The strains were globally distributed in 14 countries spanning five continents, and the conjugative operon's T4SS proteins were highly conserved in most plasmids. A high proportion of plasmids harbored resistance genes, with 17 different genes spanning seven drug classes. Collectively, this demonstrates that P-type T4SS-encoding plasmids are more widespread among the Acinetobacter genus than previously anticipated, including strains of both clinical and environmental importance. This research provides insight into the spread of resistance genes among Acinetobacter and highlights a group of plasmids of importance for future surveillance.}, }
@article {pmid39493848, year = {2024}, author = {Yang, Y and Zhang, H and Zhao, R and Qiu, X and Ye, J and Lu, W and Li, Q and Wu, G}, title = {Distribution diversity and expression regulation of class 1 integron promoters in clinical isolates of Morganella morganii.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1459162}, pmid = {39493848}, issn = {1664-302X}, abstract = {BACKGROUND: Morganella morganii is an emerging nosocomial opportunistic pathogen with increasing multidrug resistance. Antibiotic resistance, driven primarily by the horizontal transfer of resistance genes, has become a global health crisis. Integrons, mobile genetic elements, are now understood to facilitate the transfer of these genes, contributing to the rapid proliferation of resistant strains. Understanding the regulatory role of integrons in drug resistance gene expression is crucial for developing novel strategies to combat this pressing public health issue.<br><br>OBJECTIVE: To investigate the distribution of promoter types in the variable regions of class 1 integrons isolated from clinical isolates of M. morganii and their regulatory role in the expression of downstream drug resistance gene cassettes.<br><br>METHODS: Ninety seven clinical isolates of M. morganii were screened for the presence of class 1 integrons (intI1) using polymerase chain reaction (PCR). Gene cassettes within the variable regions of positive isolates were characterized, and the gene cassette promoter Pc variants and downstream auxiliary promoter P2 were identified. Enterobacterial repetitive intergenic consensus (ERIC)-PCR was employed for homology analysis. Recombinant plasmids containing different variable region promoters and gene cassettes were constructed to evaluate drug resistance genes and integrase (intI1) expression levels using reverse transcription-quantitative PCR (RT-qPCR) and antimicrobial susceptibility testing.<br><br>RESULTS: Of the clinical isolates, 28.9% (n&#x2009;=&#x2009;28/97) were positive for class 1 integrons. 24.7% (n&#x2009;=&#x2009;24/97) of these isolates carried gene cassettes encoding resistance to aminoglycosides and trimethoprim. Three Pc promoter types (PcH1, PcS, and PcW) were identified, while all P2 promoters were inactive with a 14-base pair spacing between the -35 and -10 regions. ERIC-PCR analysis classified the integron-positive strains into 6 genotypes, with high consistency in promoter types and gene cassettes within each genotype. RT-qPCR and antimicrobial susceptibility testing demonstrated that strong promoters significantly enhanced the expression of downstream drug resistance gene cassettes compared to weak promoters. Additionally, RT-qPCR revealed a negative correlation between intI1 expression and Pc promoter strength.<br><br>CONCLUSION: Class 1 integrons are prevalent in M. morganii. The promoter types within these integrons are diverse, and promoter strength is closely linked to downstream gene cassette expression. Integron-positive strains exhibit high homology, suggesting horizontal gene transfer and dissemination in clinical settings.}, }
@article {pmid39492387, year = {2023}, author = {Duan, Z and Zhu, Y and Xia, H and Huang, K and Peng, L}, title = {A novel strategy for eliminating antibiotic resistance genes during fertilization of dewatered sludge by earthworms: Vermicomposting practice using Chinese herbal residues derived from Lianhua Qingwen as a bulking material.}, journal = {Journal of environmental management}, volume = {349}, number = {}, pages = {119444}, doi = {10.1016/j.jenvman.2023.119444}, pmid = {39492387}, issn = {1095-8630}, abstract = {Vermicomposting is a sustainable sludge recycling technology that utilizes an eco-friendly composting using earthworms and microorganisms. However, a high abundance of antibiotic resistance genes (ARGs) remains in dewatered sludge that is not satisfactorily eliminated by vermicomposting. Chinese herbs have played a major role in curing many diseases in East Asia, leading to a large amount of Chinese herbal residues (CHRs) are difficult to dispose of. The present study investigated the feasibility of CHRs on the ARGs reduction in dewatered sludge during vermicomposting. The CHRs derived from Lianhua Qingwen were added separately to sludge with weight ratios of 0%, 10%, 30%, and 50%; sludge was then vermicomposted for 30 days. The results showed that co-vermicomposting of sludge and CHRs is a feasible strategy. The CHR treatments significantly (P < 0.05) decreased antibiotic concentration and bacterial population by 23.64%-49.68% and 42.58%-93.07%, respectively, compared to counterpart. Compared to the control, the CHR addition lowered the absolute abundances of macrolide, tetracycline, and sulfonamide ARGs by 42.69%-85.15%, 22.03%-75.24%, and 23.59%-90.66%, respectively. In addition, sludge containing 30% CHRs showed significant (P < 0.05) elimination of intⅠ-1 and tnpA-4 genes with abundance reductions of 71.40% and 52.33%, respectively, relative to the control. This study suggests that the CHRs can effectively reduce ARGs content in sludge by decreasing the bacterial population and horizontal gene transfer capacity during vermicomposting.}, }
@article {pmid39491810, year = {2025}, author = {Pereira, AB and Marano, M and Bathala, R and Zaragoza, RA and Neira, A and Samano, A and Owoyemi, A and Casola, C}, title = {Orphan genes are not a distinct biological entity.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {47}, number = {1}, pages = {e2400146}, pmid = {39491810}, issn = {1521-1878}, support = {//Texas A&amp;M AgriLife Research/ ; 1019860//USDA National Institute of Food and Agriculture/ ; //Texas&#xa0;A&amp;M&#xa0;Forest Service/ ; }, mesh = {*Evolution, Molecular ; *Phylogeny ; Animals ; Humans ; DNA Transposable Elements/genetics ; Gene Transfer, Horizontal/genetics ; Genome/genetics ; }, abstract = {The genome sequencing revolution has revealed that all species possess a large number of unique genes critical for trait variation, adaptation, and evolutionary innovation. One widely used approach to identify such genes consists of detecting protein-coding sequences with no homology in other genomes, termed orphan genes. These genes have been extensively studied, under the assumption that they represent valid proxies for species-specific genes. Here, we critically evaluate taxonomic, phylogenetic, and sequence evolution evidence showing that orphan genes belong to a range of evolutionary ages and thus cannot be assigned to a single lineage. Furthermore, we show that the processes generating orphan genes are substantially more diverse than generally thought and include horizontal gene transfer, transposable element domestication, and overprinting. Thus, orphan genes represent a heterogeneous collection of genes rather than a single biological entity, making them unsuitable as a subject for meaningful investigation of gene evolution and phenotypic innovation.}, }
@article {pmid39487157, year = {2024}, author = {Wardi, M and Lemkhente, Z and Alla, AA and Slimani, N and Abali, M and Idaghdour, Y and Belmouden, A}, title = {Resistome analysis of wastewater treatment plants in Agadir city, Morocco, using a metagenomics approach.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {26328}, pmid = {39487157}, issn = {2045-2322}, mesh = {*Wastewater/microbiology ; Morocco ; *Metagenomics/methods ; Anti-Bacterial Agents/pharmacology ; Water Purification/methods ; Bacteria/genetics/drug effects ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; }, abstract = {Water scarcity has evolved into a pressing global issue, significantly impacting numerous regions worldwide. The use of treated wastewater stands out as a promising solution to this problem. However, the proliferation of various contaminants, primarily Antimicrobial Resistance Genes (ARGs), poses a significant challenge to its safe and sustainable use. In this study, we assessed the composition and abundance of 373 ARGs, corresponding to 31 different classes of antibiotics, in six wastewater treatment plants (WWTP) in Agadir city of Morocco. Influent and effluent samples were collected during the months of February and July in 2020, in addition to samples from the Atlantic Ocean. In total, 223 ARGs were uncovered, highlighting in particular resistance to aminoglycoside, macrolide lincosamide, beta-lactamase, chloramphenicol, sulfonamide, tetracycline, and other antibiotics. The mechanisms of action of these ARGs were mainly antibiotic inactivation, antibiotic target alteration, efflux pump and cellular protection. Mobile genetic elements (MGEs) were detected at high levels their co-occurrence with ARGs highlights their involvement in the acquisition and transmission of ARGs in microbial communities through horizontal gene transfer. While many wastewater treatment methods effectively reduce a large proportion of gene material and pathogens, a substantial fraction of ARGs and other contaminants persist in treated wastewater. This persistence poses potential risks to both human health and the environment, warranting the need of more effective treatment strategies.}, }
@article {pmid39484419, year = {2025}, author = {Dalia, TN and Machouri, M and Lacrouts, C and Fauconnet, Y and Guerois, R and Andreani, J and Radicella, JP and Dalia, AB}, title = {DprA recruits ComM to facilitate recombination during natural transformation in Gram-negative bacteria.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.10.21.619469}, pmid = {39484419}, issn = {2692-8205}, abstract = {UNLABELLED: Natural transformation (NT) represents one of the major modes of horizontal gene transfer in bacterial species. During NT, cells can take up free DNA from the environment and integrate it into their genome by homologous recombination. While NT has been studied for >90 years, the molecular details underlying this recombination remain poorly understood. Recent work has demonstrated that ComM is an NT-specific hexameric helicase that promotes recombinational branch migration in Gram-negative bacteria. How ComM is loaded onto the post-synaptic recombination intermediate during NT, however, remains unclear. Another NT-specific recombination mediator protein that is ubiquitously conserved in both Gram-positive and Gram-negative bacteria is DprA. Here, we uncover that DprA homologs in Gram-negative species contain a C-terminal winged helix domain that is predicted to interact with ComM by AlphaFold. Using Helicobacter pylori and Vibrio cholerae as model systems, we demonstrate that ComM directly interacts with the DprA winged-helix domain, and that this interaction is critical for DprA to recruit ComM to the recombination site to promote branch migration during NT. These results advance our molecular understanding of recombination during this conserved mode of horizontal gene transfer. Furthermore, they demonstrate how structural modeling can help uncover unexpected interactions between well-studied proteins to provide deep mechanistic insight into the molecular coordination required for their activity.<br><br>SIGNIFICANCE STATEMENT: Bacteria can acquire novel traits like antibiotic resistance and virulence through horizontal gene transfer by natural transformation. During this process, cells take up free DNA from the environment and integrate it into their genome by homologous recombination. Many of the molecular details underlying this process, however, remain incompletely understood. In this study, we identify a new protein-protein interaction between ComM and DprA, two factors that promote homologous recombination during natural transformation in Gram-negative species. Through a combination of bioinformatics, structural modeling, cell biological assays, and complementary genetic approaches, we demonstrate that this interaction is required for DprA to recruit ComM to the site of homologous recombination.}, }
@article {pmid39488185, year = {2024}, author = {Guo, J and Jin, X and Zhou, Y and Gao, B and Li, Y and Zhou, Y}, title = {Microplastic and antibiotics in waters: Interactions and environmental risks.}, journal = {Journal of environmental management}, volume = {371}, number = {}, pages = {123125}, doi = {10.1016/j.jenvman.2024.123125}, pmid = {39488185}, issn = {1095-8630}, mesh = {*Anti-Bacterial Agents/chemistry ; *Microplastics/toxicity ; *Water Pollutants, Chemical/chemistry ; Adsorption ; Drug Resistance, Microbial/genetics ; Water/chemistry ; Environmental Monitoring ; }, abstract = {Antibiotics (ATs) are ubiquitously detected in natural waters worldwide, and their tendency to co-migrate with microplastics (MPs) post-adsorption leads to heightened environmental risk. Research on the adsorption of ATs on MPs and their subsequent effects on the environmental risks is gaining significant attention globally. This adsorption process predominantly occurs through hydrophobic forces, hydrogen bonds, and electrostatic interactions and is influenced by various environmental factors. The interaction between MPs and ATs exhibited varying degrees of efficiency across different pH levels and ionic strengths. Furthermore, this paper outlines the environmental risks associated with the co-presence of MPs and ATs in aquatic environments, emphasizing the potential effect of MPs on the distribution of antibiotic resistance genes (ARGs) and related environmental risks. The potential hazards posed by MPs and ATs in aquatic systems warrant serious consideration. Future research should concentrate on the adsorption of ATs/ARGs on MPs under real environmental conditions, horizontal gene transfer on MPs, as well as biofilm formation and agglomeration behavior on MPs that needs to be emphasized.}, }
@article {pmid39488061, year = {2025}, author = {Zhao, Y and Zhang, J and Zheng, Y and Shi, J and Hu, Z and Xie, H and Guo, Z and Liang, S and Wu, H}, title = {Overlooked dissemination risks of antimicrobial resistance through green tide proliferation.}, journal = {Water research}, volume = {268}, number = {Pt B}, pages = {122714}, doi = {10.1016/j.watres.2024.122714}, pmid = {39488061}, issn = {1879-2448}, mesh = {*Seawater/microbiology ; Drug Resistance, Microbial/genetics ; Eutrophication ; Bacteria/drug effects/genetics ; Drug Resistance, Bacterial/genetics ; Ulva ; Gene Transfer, Horizontal ; }, abstract = {Green tides, particularly those induced by Enteromorpha, pose significant environmental challenges, exacerbated by climate change, coastal eutrophication, and other anthropogenic impacts. More concerningly, these blooms may influence the spread of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) within ecosystems. However, the manner in which Enteromorpha blooms affect the distribution and spread of antimicrobial resistance (AMR) remains uncertain. This study investigated ARG profiles, dynamic composition, and associated health risks within the Enteromorpha phycosphere and surrounding seawater in typical bays (Jiaozhou, Aoshan, and Lingshan) in the South Yellow Sea. The Enteromorpha phycosphere exhibited significantly higher ARG abundance (p < 0.05) but lower diversity compared to the surrounding seawater. Source-tracking and metagenomic analyses revealed that the phycosphere was the main contributor to the resistome of surrounding seawater. Moreover, resistant pathogens, especially ESKAPE pathogens, with horizontal gene transfer (HGT) potential, were more abundant in the phycosphere than in the surrounding seawater. The phycosphere released high-risk ARGs to the surrounding seawater during Enteromorpha blooms, posing serious health and ecological AMR risks in marine environments. This study highlights the significant role of Enteromorpha blooms in ARG spread and associated risks, urging a reassessment of AMR burden from a public health perspective.}, }
@article {pmid39486342, year = {2025}, author = {Dai, S and Han, Z and Liu, S and Wang, Y and Zhang, Y and Yang, M}, title = {Bacterial hosts and horizontal transfer characteristics of clinically important tet(X)-variant genes in municipal wastewater treatment plants using epicPCR-directed cultivation strategy.}, journal = {Water research}, volume = {268}, number = {Pt B}, pages = {122658}, doi = {10.1016/j.watres.2024.122658}, pmid = {39486342}, issn = {1879-2448}, mesh = {*Wastewater/microbiology ; Gene Transfer, Horizontal ; Polymerase Chain Reaction ; Bacteria/genetics ; Sewage/microbiology ; Genes, Bacterial ; Anti-Bacterial Agents ; Enterobacteriaceae/genetics ; Waste Disposal, Fluid ; }, abstract = {Mobile tet(X)-variant genes confer resistance to a wide range of tetracyclines, including the antibiotic of last-resort, tigecycline, raising significant concerns regarding their potential spread cross-environmental dissemination. However, the bacterial hosts and environmental spread of these genes remain poorly understood. Herein, a retrospective study unveiled the prevalence of tet(X)-variant genes (ranging from tet(X3) to tet(X6)) in activated sludge samples from five municipal wastewater treatment plants (WWTPs) from 2013 to 2021. Among these variants, tet(X4) exhibited the highest detection frequency (100 %) and abundance [(2.48 ± 3.07) × 10[7] copies/g dry weight] with an increasing trend. An epicPCR-directed cultivation strategy was proposed to facilitate the targeted isolation of tet(X4)-carrying bacterial hosts in activated sludge. This strategy involves the identification of bacterial host profiles using epicPCR and subsequent selective isolating target bacteria. Enterobacteriaceae emerged as the primary bacterial host for tet(X4), alongside previously unreported genera like Providencia, Advenella, and Moheibacter. Subsequent selective isolation of the most abundant Enterobacteriaceae based on the epicPCR-informed host spectrum yielded 39 tet(X4)-carrying Escherichia coli strains from the WWTP. Whole genome sequencing of tet(X4)-positive strains revealed that plasmid-mediated horizontal gene transfer is the primary mechanism driving tet(X4) dissemination. Plasmids including IncFIA(HI1)/IncHI1A/IncHI1B(R27) and IncX1, commonly reported in various clinical and animal settings, were identified as the predominant carriers of tet(X4). E. coli strains harbouring tet(X4) in the WWTP showed substantial genetic similarity to strains from hospital and animal sources, underscoring concerns about the potential risk of across diverse sectors. This study provided the first glimpse of the presence of mobile tet(X)-variants in WWTPs, and highlighted the promise of the epicPCR-directed cultivation strategy for exploring bacterial hosts of clinically important ARGs in different habitats from a One Health perspective.}, }
@article {pmid39481662, year = {2024}, author = {Liu, W and Wang, Z and Huang, Y and Liu, Y and Li, R and Wang, M and Zhang, H and Meng, C and Xiao, X}, title = {Acetylshikonin reduces the spread of antibiotic resistance via plasmid conjugation.}, journal = {International journal of antimicrobial agents}, volume = {64}, number = {6}, pages = {107370}, doi = {10.1016/j.ijantimicag.2024.107370}, pmid = {39481662}, issn = {1872-7913}, mesh = {*Plasmids/genetics ; *Conjugation, Genetic ; Animals ; *Anti-Bacterial Agents/pharmacology ; Mice ; Drug Resistance, Bacterial/genetics/drug effects ; Microbial Sensitivity Tests ; Escherichia coli/drug effects/genetics ; Escherichia coli Proteins/genetics ; Anthraquinones/pharmacology ; Female ; }, abstract = {The plasmid-mediated conjugative transfer of antibiotic resistance genes (ARGs) stands out as the primary driver behind the dissemination of antimicrobial resistance (AMR). Developing effective inhibitors that target conjugative transfer represents an potential strategy for addressing the issue of AMR. Here, we studied the effect of acetylshikonin (ASK), a botanical derivative, on plasmid conjugation. The conjugative transfer of RP4-7 plasmid inter and intra species was notably reduced by ASK. The conjugation process of IncI2 and IncX4 plasmids harbouring the mobile colistin resistance gene (mcr-1), IncX4 and IncX3 plasmids containing the carbapenem resistance gene (blaNDM-5), and IncFI and IncFII plasmids possessing the tetracycline resistance gene [tet(X4)] were also reduced by ASK. Importantly, the conjugative transfer frequency of mcr-1 positive IncI2 plasmid in mouse peritoneal conjugation model and gut conjugation model was reduced by ASK. The mechanism investigation showed that ASK disrupted the functionality of the bacterial cell membrane. Furthermore, the proton motive force (PMF) was dissipated. In addition, ASK blocked the electron transmission in bacteria's electron transport chain (ETC) through disturbing the quinone interaction, resulting in an insufficient energy supply for conjugation. Collectively, ASK is a potential conjugative transfer inhibitor, providing novel strategies to prevent the spread of AMR.}, }
@article {pmid39481552, year = {2024}, author = {Zhao, X and Qiao, Q and Qin, X and Zhao, P and Li, X and Xie, J and Zhai, F and Li, Y}, title = {Viral community and antibiotic resistance genes carried by virus in soil microbial fuel cells.}, journal = {The Science of the total environment}, volume = {955}, number = {}, pages = {177260}, doi = {10.1016/j.scitotenv.2024.177260}, pmid = {39481552}, issn = {1879-1026}, mesh = {*Soil Microbiology ; *Bioelectric Energy Sources ; *Drug Resistance, Microbial/genetics ; Soil/chemistry ; Gene Transfer, Horizontal ; Viruses/genetics ; }, abstract = {Soil microbial fuel cells (MFCs) can control the horizontal transfer of antibiotic resistance genes (ARGs) by reducing the abundance of mobile genetic elements. However, little is known about the effect of soil MFCs on the horizontal transfer pathway of ARGs transduced by viruses. In this study, the average abundance of ARGs in soil MFCs was 11 % lower than that in the open-circuit control. Lower virus abundance in soil MFCs suggested less detriment of microbial communities. The structure of the viral community was respectively shifted by the introduction of electrodes and the stimulation of biocurrent, especially for the top three viral genera Oslovirus, Tequatrovirus and Incheonvrus in soil. The ARGs aac(6)-I, cat chloramphenicol acetyltransferase, qnrA and vanY were found as the highest health risk (Rank I), and their total abundance showed the lowest in MFCs, with a decrease of 91-99 % compared to the controls. As the main carrier of ARGs, the abundance of Caudoviricetes showed a significant positive correlation with ARGs. Viral integrase was identified respectively coexisting with arnA and vanR (Rank III) in the same contig, which might aggravate their horizontal transfer. Proteobacteria was the main host of viruses carrying ARGs, which exhibited the lowest abundance in the soil MFC. The genus Pseudomonas was the host of viruses carrying ARGs, whose amount reduced by soil MFCs. This study provides an insight into the bioelectrochemical control of ARGs horizontal transfer.}, }
@article {pmid39476778, year = {2025}, author = {Li, J and Sun, Y and Zhang, Q and Liu, S and Liu, P and Zhang, XX}, title = {Unveiling the potential role of virus-encoded polyphosphate kinases in enhancing phosphorus removal in activated sludge systems.}, journal = {Water research}, volume = {268}, number = {Pt A}, pages = {122678}, doi = {10.1016/j.watres.2024.122678}, pmid = {39476778}, issn = {1879-2448}, mesh = {*Viral Proteins/genetics/metabolism ; Phylogeny ; *Viruses/classification/enzymology/genetics ; Bacteria/classification/enzymology/genetics ; Water Purification ; Genetic Variation ; *Phosphotransferases (Phosphate Group Acceptor)/chemistry/genetics/metabolism ; Models, Molecular ; Protein Structure, Tertiary ; Sequence Analysis, Protein ; Sewage/virology ; }, abstract = {While microbial phosphate removal in activated sludge (AS) systems has been extensively studied, the role of viruses in this process remains largely unexplored. In this study, we identified 149 viral auxiliary metabolic genes associated with phosphorus cycling from 2,510 viral contigs (VCs) derived from AS systems. Notably, polyphosphate kinase 1 (ppk1) and polyphosphate kinase 2 (ppk2) genes, which are primarily responsible for phosphate removal, were found in five unclassified VCs. These genes exhibited conserved protein structures and active catalytic sites, indicating a pivotal role of viruses in enhancing phosphorus removal. Phylogenetic analysis demonstrated a close relationship between viral ppk genes and their bacterial counterparts, suggesting the occurrence of horizontal gene transfer. Furthermore, experimental assays validated that viral ppk genes enhanced host phosphate removal capabilities. VCs carrying ppk genes were observed across diverse ecological and geographical contexts, suggesting their potential to bolster host functions in varied environmental and nutrient settings, spanning natural and engineered systems. These findings uncover a previously underappreciated mechanism by which viruses enhance phosphate removal in wastewater treatment plants. Overall, our study highlights the potential for leveraging virus-encoded genes to improve the efficiency of biological phosphorus removal processes, offering new insights into the microbial ecology of AS systems and the role of viruses in biogeochemical cycling.}, }
@article {pmid39475308, year = {2024}, author = {Schrago, CG and Mello, B}, title = {Challenges in Assembling the Dated Tree of Life.}, journal = {Genome biology and evolution}, volume = {16}, number = {10}, pages = {}, pmid = {39475308}, issn = {1759-6653}, mesh = {*Phylogeny ; Evolution, Molecular ; Gene Transfer, Horizontal ; }, abstract = {The assembly of a comprehensive and dated Tree of Life (ToL) remains one of the most formidable challenges in evolutionary biology. The complexity of life's history, involving both vertical and horizontal transmission of genetic information, defies its representation by a simple bifurcating phylogeny. With the advent of genome and metagenome sequencing, vast amounts of data have become available. However, employing this information for phylogeny and divergence time inference has introduced significant theoretical and computational hurdles. This perspective addresses some key methodological challenges in assembling the dated ToL, namely, the identification and classification of homologous genes, accounting for gene tree-species tree mismatch due to population-level processes along with duplication, loss, and horizontal gene transfer, and the accurate dating of evolutionary events. Ultimately, the success of this endeavor requires new approaches that integrate knowledge databases with optimized phylogenetic algorithms capable of managing complex evolutionary models.}, }
@article {pmid39474943, year = {2024}, author = {Sharma, P and Kishore, A and Singh, M}, title = {Single-use polyethylene terephthalate bottle-derived nanoplastics propagate antibiotic resistance in bacteria via transformation and outer membrane vesicle secretion.}, journal = {Nanoscale}, volume = {16}, number = {46}, pages = {21360-21378}, doi = {10.1039/d4nr02613f}, pmid = {39474943}, issn = {2040-3372}, mesh = {*Polyethylene Terephthalates/chemistry ; *Escherichia coli/drug effects/metabolism ; Microplastics/chemistry ; Gene Transfer, Horizontal ; Drug Resistance, Microbial/drug effects ; Plasmids/metabolism ; Nanoparticles/chemistry ; Drug Resistance, Bacterial/drug effects ; Bacterial Outer Membrane/metabolism/drug effects ; Transformation, Bacterial ; }, abstract = {Plastic pollution arising from single-use plastic bottles (SUPBs) and containers leads to the formation of micro/nanoplastics (NPs). These NPs raise concerns due to their potential toxicity and interactions with microorganisms. In various environments, including our digestive system, both microorganisms and plastics coexist. The interactions between these NPs and microorganisms can have far-reaching consequences, potentially affecting the ecosystems and human health. Therefore, understanding these interactions is crucial for addressing the challenges posed by plastic pollution. This study investigated the role of NPs in propagating antibiotic resistance (AR), specifically through outer membrane vesicles (OMVs), which is a mechanism that has not been fully explored to date in terms of NPs' effects. To explore this, NPs were synthesized using polyethylene terephthalate (PET) SUPBs, mimicking the natural chemical composition of environmental nanoplastics, unlike previous studies, which used pure PET, polystyrene (PS) or other pure plastic materials. The resulting PET bottle-derived nanoplastics (PBNPs), which exhibited diverse shapes and sizes (50-850 nm), were found to facilitate horizontal gene transfer (HGT) through transformation and outer membrane vesicles (OMVs), enabling the transport of plasmids among bacteria. In transformation, PBNPs physically carried plasmids across the bacterial membrane. In another scenario, PBNPs induced oxidative stress and bacterial surface damage, which led to the upregulation of stress response-associated genes and the escalation of OMV secretion in E. coli. This novel pathway highlights how PBNPs contribute to AR gene dissemination, potentially exacerbating the global antibiotic resistance crisis. Furthermore, PBNPs mediate cross-species gene transfer from E. coli to Lactobacillus acidophilus, underscoring their impact on diverse microorganisms, including those in the human gut. Our findings suggest that nanoplastics may be an unrecognized contributor to the rising tide of antibiotic resistance, with significant consequences for human health and the environment. Molecular analyses revealed the upregulated expression of genes associated with stress response and OMV secretion, offering deeper insights into the biological mechanisms affected by PBNPs. This study offers crucial insights into the interactions of NPs and microorganisms for developing strategies to address the ecological and health implications of nanoplastic contamination.}, }
@article {pmid39472795, year = {2024}, author = {Andriyanov, P and Zhurilov, P and Menshikova, A and Tutrina, A and Yashin, I and Kashina, D}, title = {Large-scale genomic analysis of Elizabethkingia anophelis.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1015}, pmid = {39472795}, issn = {1471-2164}, mesh = {*Flavobacteriaceae/genetics ; *Genome, Bacterial ; *Phylogeny ; *Genomics/methods ; Gene Transfer, Horizontal ; Humans ; Flavobacteriaceae Infections/microbiology ; Animals ; Drug Resistance, Bacterial/genetics ; }, abstract = {The recent emergence of Elizabethkingia anophelis as a human pathogen is a major concern for global public health. This organism has the potential to cause severe infections and has inherent antimicrobial resistance. The potential for widespread outbreaks and rapid global spread highlights the critical importance of understanding the biology and transmission dynamics of this infectious agent. We performed a large-scale analysis of available 540 E. anophelis, including one novel strain isolated from raw milk and sequenced in this study. Pan-genome analysis revealed an open and diverse pan-genome in this species, characterized by the presence of many accessory genes. This suggests that the species has a high level of adaptability and can thrive in a variety of environments. Phylogenetic analysis has also revealed a complex population structure, with limited source-lineage correlation. We identified diverse antimicrobial resistance factors, including core-genome and accessory ones often associated with mobile genetic elements within specific lineages. Mobilome analysis revealed a dynamic landscape primarily composed of genetic islands, integrative and conjugative elements, prophage elements, and small portion of plasmids emphasizing a complex mechanism of horizontal gene transfer. Our study underscores the adaptability of E. anophelis, characterized by a diverse range of antimicrobial resistance genes, putative virulence factors, and genes enhancing fitness. This adaptability is also supported by the organism's ability to acquire genetic material through horizontal gene transfer, primarily facilitated by mobile genetic elements such as integrative and conjugative elements (ICEs). The potential for rapid evolution of this emerging pathogen poses a significant challenge to public health efforts.}, }
@article {pmid39471530, year = {2025}, author = {Qi, H and Lv, J and Liao, J and Jin, J and Ren, Y and Tao, Y and Wang, D and Alvarez, PJJ and Yu, P}, title = {Metagenomic insights into microalgae-bacterium-virus interactions and viral functions in phycosphere facing environmental fluctuations.}, journal = {Water research}, volume = {268}, number = {Pt A}, pages = {122676}, doi = {10.1016/j.watres.2024.122676}, pmid = {39471530}, issn = {1879-2448}, mesh = {*Microalgae/virology ; Bacteria/genetics ; Metagenomics ; Phylogeny ; Symbiosis ; Gene Transfer, Horizontal ; Viruses/genetics ; }, abstract = {Despite the ecological and biotechnological significance of microalgae-bacterium symbionts, the response of host-virus interactions to external environmental fluctuations and the role of viruses in phycosphere remain largely unexplored. Herein, we employed algal-bacterial granular sludge (ABGS) with varying light intensity and organic carbon loading to investigate the mechanisms of microalgae-bacterium-virus symbionts in response to environmental fluctuations. Metagenomics revealed that enhanced light intensity decreased the diversity of microalgae, so did the diversity of symbiotic bacteria and viruses. As carbon sources decreased, bacteria prompted horizontal gene transfer in phycosphere by 12.76 %-157.40 %, increased the proportion of oligotrophs as keystone species (0.00 % vs 14.29 %) as well as viruses using oligotrophs as hosts (18.52 % vs 25.00 %). Furthermore, virus-carried auxiliary metabolic genes (AMGs) and biosynthetic gene clusters (BGCs) encoding vitamin B12 synthesis (e.g., cobS), antioxidation (e.g., queC), and microbial aggregation (e.g., cysE). Additionally, phylogenetic and similarity analysis further revealed the evolutionary origin and potential horizontal transfer of the AMGs and BGCs, which could potentially enhance the adaptability of bacteria and eukaryotic microalgae. Overall, our research demonstrates that environmental fluctuations have cascading effects on the microalgae-bacteria-virus interactions, and emphasizes the important role of viruses in maintaining the stability of the phycosphere symbiotic community.}, }
@article {pmid39470278, year = {2024}, author = {Scherff, N and Rothgänger, J and Weniger, T and Mellmann, A and Harmsen, D}, title = {Real-time plasmid transmission detection pipeline.}, journal = {Microbiology spectrum}, volume = {12}, number = {12}, pages = {e0210024}, pmid = {39470278}, issn = {2165-0497}, abstract = {UNLABELLED: The spread of antimicrobial resistance among bacteria by horizontal plasmid transmissions poses a major challenge for clinical microbiology. Here, we evaluate a new real-time plasmid transmission detection pipeline implemented in the SeqSphere[+] (Ridom GmbH, Münster, Germany) software. Within the pipeline, a local Mash plasmid database is created, and Mash searches with a distance threshold of 0.001 are used to trigger plasmid transmission early warning alerts (EWAs). Clonal transmissions are detected using core-genome multi-locus sequence typing allelic differences. The tools MOB-suite, NCBI AMRFinderPlus, CGE MobileElementFinder, pyGenomeViz, and MUMmer, integrated in SeqSphere+, are used to characterize plasmids and for visual pairwise plasmid comparisons, respectively. We evaluated the pipeline using published hybrid assemblies (Oxford Nanopore Technology/Illumina) of a surveillance and outbreak data set with plasmid transmissions. To emulate prospective usage, samples were imported in chronological order of sampling date. Different combinations of the user-adjustable parameters sketch size (1,000 vs 10,000) and plasmid size correction were tested, and discrepancies between resulting clusters were analyzed with Quast. When using a sketch size of 1,000 with size correction turned on, the SeqSphere[+] pipeline agreed with the published data and produced the same clonal and carbapenemase-carrying plasmid clusters. EWAs were in the correct chronological order. In summary, the developed pipeline presented here is suitable for integration into clinical microbiology settings with limited bioinformatics knowledge due to its automated analyses and alert system, which are combined with the GUI-based SeqSphere[+] platform. Thus, with its integrated sample database, (near) real-time plasmid transmission detection is within reach in bacterial routine-diagnostic settings when long-read sequencing is employed.<br><br>IMPORTANCE: Plasmid-mediated spread of antimicrobial resistance is a major challenge for clinical microbiology, and monitoring of potential plasmid transmissions is essential to combat further dissemination. Whole-genome sequencing is often used to surveil nosocomial transmissions but usually limited to the detection of clonal transmissions (based on chromosomal markers). Recent advances in long-read sequencing technologies enable full reconstruction of plasmids and the detection of very similar plasmids, but so far, easy-to-use bioinformatic tools for this purpose have been missing. Here, we present an evaluation of an innovative real-time plasmid transmission detection pipeline. It is integrated into the GUI-based SeqSphere[+] software, which already offers core-genome multi-locus sequence typing-based pathogen outbreak detection. It requires very limited bioinformatics knowledge, and its database, automated analyses, and alert system make it well suited for prospective clinical application.}, }
@article {pmid39467614, year = {2024}, author = {Gobbo, A and Fraiture, MA and Van Poelvoorde, L and De Keersmaecker, SCJ and Garcia-Graells, C and Van Hoorde, K and Verhaegen, B and Huwaert, A and Maloux, H and Hutse, V and Ceyssens, PJ and Roosens, N}, title = {Strategy to develop and validate digital droplet PCR methods for global antimicrobial resistance wastewater surveillance.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {96}, number = {11}, pages = {e11145}, doi = {10.1002/wer.11145}, pmid = {39467614}, issn = {1554-7531}, support = {//Sciensano (contract NAP-AMR)/ ; }, mesh = {*Wastewater/microbiology ; Real-Time Polymerase Chain Reaction/methods ; Environmental Monitoring/methods ; Polymerase Chain Reaction/methods ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; }, abstract = {According to World Health Organization (WHO), antimicrobial resistance (AMR) is currently one of the world's top 10 health threats, causing infections to become difficult or impossible to treat, increasing the risk of disease spread, severe illness, disability, and death. Accurate surveillance is a key component in the fight against AMR. Wastewater is progressively becoming a new player in AMR surveillance, with the promise of a cost-effective real-time tracking of global AMR profiles in specific regions. One of the most useful analytical methods for wastewater surveillance is currently based on real-time PCR (qPCR) and digital droplet PCR (ddPCR) technologies. As stated in the EU Wastewater Treatment Directive proposal, methodological standardization, including a workflow for method development and validation, will play a crucial role in global monitoring of AMR in wastewater. However, according to our knowledge, there are currently no qPCR and ddPCR methods for AMR surveillance available that have been validated according to international standard performance criteria. Therefore, this study proposes a workflow for the development and validation of PCR-based methods for a harmonized and global AMR surveillance, including the construction of specific sequence databases and microbial collections for an efficient method development and method specificity evaluation. Following this strategy, we have developed and validated four duplex ddPCR methods responding to international standard performance criteria, focusing on seven AMR genes (ARG's), including extended spectrum beta-lactam (blaCTX-M), carbapenem (blaKPC-2/3), tetracycline (tet(M)), erythromycin (erm(B)), vancomycin (vanA), sulfonamide (sul2), and aminoglycoside (aac(3)-IV), as well as one indicator of antibiotic (multi-) resistance and horizontal gene transfer, named the class I integron (intl1). The performance of these ddPCR methods was successfully assessed for their specificity, as no false-positive and false-negative results were observed. These ddPCR methods were also considered to be highly sensitive as showing a limit of detection below 25 copies of the targets. In addition, their applicability was confirmed using 14 wastewater samples collected from two Belgian water resource recovery facilities. The proposed study represents therefore a step forward to reinforce method harmonization in the context of the global AMR surveillance in wastewater. PRACTITIONER POINTS: In the context of wastewater surveillance, no PCR-based methods for global AMR monitoring are currently validated according to international standards. Consequently, we propose a workflow to develop and validate PCR-based methods for a harmonized and global AMR surveillance. This workflow resulted here in four duplex ddPCR methods targeting seven ARGs and one general indicator for mobilizable resistance genes. The applicability of these validated ddPCR methods was confirmed on 14 wastewater samples from two Belgian water resource recovery facilities.}, }
@article {pmid39460620, year = {2025}, author = {Zhu, Q and Chen, Q and Gao, S and Li, Z and Zhou, H and Cui, Z and Fan, G and Liu, X and Wu, X and Ma, J and Kan, B and Hu, S and Wu, L and Lu, X}, title = {PIPdb: a comprehensive plasmid sequence resource for tracking the horizontal transfer of pathogenic factors and antimicrobial resistance genes.}, journal = {Nucleic acids research}, volume = {53}, number = {D1}, pages = {D169-D178}, pmid = {39460620}, issn = {1362-4962}, support = {2021YFF0703805//National Key Research and Development Program of China/ ; XDB0830000//Chinese Academy of Sciences/ ; 2022YFC2602301//National Key Research and Development Program of China/ ; 22193064//National Natural Science Foundation of China/ ; SRPG22007//Self-supporting Program of Guangzhou National Laboratory/ ; }, mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; *Virulence Factors/genetics ; *Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; Humans ; Databases, Genetic ; Genome, Bacterial ; }, abstract = {Plasmids, as independent genetic elements, carrying resistance or virulence genes and transfer them among different pathogens, posing a significant threat to human health. Under the 'One Health' approach, it is crucial to control the spread of plasmids carrying such genes. To achieve this, a comprehensive characterization of plasmids in pathogens is essential. Here we present the Plasmids in Pathogens Database (PIPdb), a pioneering resource that includes 792 964 plasmid segment clusters (PSCs) derived from 1 009 571 assembled genomes across 450 pathogenic species from 110 genera. To our knowledge, PIPdb is the first database specifically dedicated to plasmids in pathogenic bacteria, offering detailed multi-dimensional metadata such as collection date, geographical origin, ecosystem, host taxonomy, and habitat. PIPdb also provides extensive functional annotations, including plasmid type, insertion sequences, integron, oriT, relaxase, T4CP, virulence factors genes, heavy metal resistance genes and antibiotic resistance genes. The database features a user-friendly interface that facilitates studies on plasmids across diverse host taxa, habitats, and ecosystems, with a focus on those carrying antimicrobial resistance genes (ARGs). We have integrated online tools for plasmid identification and annotation from assembled genomes. Additionally, PIPdb includes a risk-scoring system for identifying potentially high-risk plasmids. The PIPdb web interface is accessible at https://nmdc.cn/pipdb.}, }
@article {pmid39459963, year = {2024}, author = {Pu, F and Zhang, N and Pang, J and Zeng, N and Baloch, FB and Li, Z and Li, B}, title = {Deciphering the Genetic Architecture of Staphylococcus warneri Prophage vB_G30_01: A Comprehensive Molecular Analysis.}, journal = {Viruses}, volume = {16}, number = {10}, pages = {}, pmid = {39459963}, issn = {1999-4915}, support = {31271818//National Natural Science Foundation of China/ ; 2023-01//International Cooperation Project of Universities in Liaoning Province/ ; 2022030673-JH5/104//Liaoning Province Rural Science and Technology Special Action Project/ ; 22-319-2-13//Shenyang Science and Technology Project/ ; 202108857002//China Scholarship Council/ ; }, mesh = {*Genome, Viral ; *Staphylococcus/virology/genetics ; *Prophages/genetics/physiology ; *Phylogeny ; *Host Specificity ; *Open Reading Frames ; *Staphylococcus Phages/genetics/classification/physiology/ultrastructure ; *Lysogeny ; DNA, Viral/genetics ; Genomics/methods ; }, abstract = {The current knowledge of Staphylococcus warneri phages is limited, with few genomes sequenced and characterized. In this study, a prophage, vB_G30_01, isolated from Staphylococcus warneri G30 was characterized and evaluated for its lysogenic host range. The phage was studied using transmission electron microscopy and a host range. The phage genome was sequenced and characterized in depth, including phylogenetic and taxonomic analyses. The linear dsDNA genome of vB_G30_01 contains 67 predicted open reading frames (ORFs), classifying it within Bronfenbrennervirinae. With a total of 10 ORFs involved in DNA replication-related and transcriptional regulator functions, vB_G30_01 may play a role in the genetics and transcription of a host. Additionally, vB_G30_01 possesses a complete set of genes related to host lysogeny and lysis, implying that vB_G30_01 may influence the survival and adaptation of its host. Furthermore, a comparative genomic analysis reveals that vB_G30_01 shares high genomic similarity with other Staphylococcus phages and is relatively closely related to those of Exiguobacterium and Bacillus, which, in combination with the cross-infection assay, suggests possible cross-species infection capabilities. This study enhances the understanding of Staphylococcus warneri prophages, providing insights into phage-host interactions and potential horizontal gene transfer.}, }
@article {pmid39458330, year = {2024}, author = {Dixson, JD and Vumma, L and Azad, RK}, title = {An Analysis of Combined Molecular Weight and Hydrophobicity Similarity between the Amino Acid Sequences of Spike Protein Receptor Binding Domains of Betacoronaviruses and Functionally Similar Sequences from Other Virus Families.}, journal = {Microorganisms}, volume = {12}, number = {10}, pages = {}, pmid = {39458330}, issn = {2076-2607}, abstract = {Recently, we proposed a new method, based on protein profiles derived from physicochemical dynamic time warping (PCDTW), to functionally/structurally classify coronavirus spike protein receptor binding domains (RBD). Our method, as used herein, uses waveforms derived from two physicochemical properties of amino acids (molecular weight and hydrophobicity (MWHP)) and is designed to reach into the twilight zone of homology, and therefore, has the potential to reveal structural/functional relationships and potentially homologous relationships over greater evolutionary time spans than standard primary sequence alignment-based techniques. One potential application of our method is inferring deep evolutionary relationships such as those between the RBD of the spike protein of betacoronaviruses and functionally similar proteins found in other families of viruses, a task that is extremely difficult, if not impossible, using standard multiple alignment-based techniques. Here, we applied PCDTW to compare members of four divergent families of viruses to betacoronaviruses in terms of MWHP physicochemical similarity of their RBDs. We hypothesized that some members of the families Arteriviridae, Astroviridae, Reoviridae (both from the genera rotavirus and orthoreovirus considered separately), and Toroviridae would show greater physicochemical similarity to betacoronaviruses in protein regions similar to the RBD of the betacoronavirus spike protein than they do to other members of their respective taxonomic groups. This was confirmed to varying degrees in each of our analyses. Three arteriviruses (the glycoprotein-2 sequences) clustered more closely with ACE2-binding betacoronaviruses than to other arteriviruses, and a clade of 33 toroviruses was found embedded within a clade of non-ACE2-binding betacoronaviruses, indicating potentially shared structure/function of RBDs between betacoronaviruses and members of other virus clades.}, }
@article {pmid39455017, year = {2024}, author = {Zhou, Y and Yang, Y and Wu, C and Zhou, P and Gao, H and Wang, B and Zhao, H and Xu, Y and Yu, F}, title = {LuxS/AI-2 system facilitates the dissemination of antibiotic-resistant plasmids in Klebsiella pneumoniae.}, journal = {International journal of antimicrobial agents}, volume = {64}, number = {6}, pages = {107361}, doi = {10.1016/j.ijantimicag.2024.107361}, pmid = {39455017}, issn = {1872-7913}, mesh = {*Klebsiella pneumoniae/genetics/drug effects ; *Plasmids/genetics ; *Bacterial Proteins/genetics/metabolism ; *Carbon-Sulfur Lyases/genetics ; *Conjugation, Genetic ; *Quorum Sensing/genetics ; Homoserine/analogs &amp; derivatives/metabolism ; Lactones/metabolism/pharmacology ; Gene Expression Regulation, Bacterial ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Plasmid conjugation is a central mechanism driving the dissemination of antibiotic resistance in Klebsiella pneumoniae. However, the conjugative operon requires specific stimuli for activation. Identifying signals and elucidating the underlying mechanisms is crucial in combating plasmid spread. This study uncovers a key mechanism promoting the dissemination of high-risk plasmids, including IncFII, IncX3, and IncX4 types, in K. pneumoniae. In this study, increased donor density significantly enhanced conjugation, and transcript levels of both conjugation and AI-2 quorum sensing genes were markedly upregulated. Mutating the luxS and lsrR genes in K. pneumoniae 1678 decreased plasmid conjugation efficiency in the 1678ΔluxS mutant, and significantly increased plasmid conjugation efficiency in the 1678ΔlsrR mutant. RT-qPCR and β-galactosidase assays showed that LsrR represses transcription of relaxosome and T4CP genes, whereas AI-2 (synthesised by LuxS) activates their expression. AlphaFold 3 docking models indicate that LsrR may bind directly to IncX plasmid relaxase promoters, inhibiting their expression. Adding external AI-2 signals revealed no effect on plasmid conjugation when LsrR was absent, confirming the dependence of AI-2 signals on LsrR repression. In conclusion, AI-2-mediated signalling enhances donor density effects on plasmid conjugation by de-repressing LsrR-mediated suppression.}, }
@article {pmid39454331, year = {2024}, author = {Wang, Y and Ren, Z and Wu, Y and Li, Y and Han, S}, title = {Antibiotic resistance genes transfer risk: Contributions from soil erosion and sedimentation activities, agricultural cycles, and soil chemical contamination.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {136227}, doi = {10.1016/j.jhazmat.2024.136227}, pmid = {39454331}, issn = {1873-3336}, mesh = {*Agriculture ; *Soil Pollutants/toxicity/analysis ; *Drug Resistance, Microbial/genetics ; *Soil/chemistry ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/toxicity ; Soil Microbiology ; Geologic Sediments/chemistry ; }, abstract = {The transfer of antibiotic resistance genes (ARGs) pose environmental risks that are influenced by soil activity and pollution. Soil erosion and sedimentation accelerate degradation and migration, thereby affecting soil distribution and contamination. This study quantified the vertical and horizontal transfer capabilities of ARGs and simulated soil environments under various scenarios, such as erosion, agricultural cycles, and chemical pollution. The results showed that slope, runoff, and sediment volume significantly affected soil erosion and ARG transfer risks. The response of environmental factors to the transfer risk of ARGs is as follows: the promotion effect of soil deposition (average: 21.41 %) is significantly greater than the inhibitory effect of soil erosion (average: -11.31 %); the planting period (average: -64.654) is greater than the harvest period (average: -56.225); the response to soil chemical pollution is: the impact of phosphate fertilizer residues, antibiotics, and pesticide pollution is more significant. This study constructed a vertical and horizontal transfer system of ARGs in soil erosion and sedimentation environments and proposed a response analysis method for the impact of factors, such as soil erosion and sedimentation activities, agricultural cycles, and soil chemical pollution, on ARGs transfer capabilities.}, }
@article {pmid39453690, year = {2024}, author = {Toppings, N and Marshall, M and Smirnova, AV and Sheremet, A and Pasala, AS and Nwosu, FC and Hepburn, M and Lewis, I and Coleman, NV and Dunfield, PF}, title = {Ethylene and epoxyethane metabolism in methanotrophic bacteria: comparative genomics and physiological studies using Methylohalobius crimeensis.}, journal = {Microbial genomics}, volume = {10}, number = {10}, pages = {}, pmid = {39453690}, issn = {2057-5858}, mesh = {*Ethylenes/metabolism ; *Multigene Family ; *Genomics/methods ; Oxidation-Reduction ; Methane/metabolism ; Phylogeny ; Epoxy Compounds/metabolism ; Oxygenases/genetics/metabolism ; Genome, Bacterial ; Bacterial Proteins/genetics/metabolism ; Methylococcaceae/genetics/metabolism ; }, abstract = {The genome of the methanotrophic bacterium Methylohalobius crimeensis strain 10Ki contains a gene cluster that encodes a putative coenzyme-M (CoM)-dependent pathway for oxidation of epoxyethane, based on homology to genes in bacteria that grow on ethylene and propylene as sole substrates. An alkene monooxygenase was not detected in the M. crimeensis genome, so epoxyethane is likely produced from co-oxidation of ethylene by the methane monooxygenase enzyme. Similar gene clusters were detected in about 10% of available genomes from aerobic methanotrophic bacteria, primarily strains grown from rice paddies and other wetlands. The sparse occurrence of the gene cluster across distant phylogenetic groups suggests that multiple lateral gene transfer events have occurred in methanotrophs. In support of this, the gene cluster in M. crimeensis was detected within a large genomic island predicted using multiple methods. Growth studies, reverse transcription-quantitative PCR (RT-qPCR) and proteomics were performed to examine the expression of these genes in M. crimeensis. Growth and methane oxidation activity were completely inhibited by the addition of >0.5% (v/v) ethylene to the headspace of cultures, but at 0.125% and below, the inhibition was only partial, and ethylene was gradually oxidized. The etnE gene encoding epoxyalkane:CoM transferase was strongly upregulated in ethylene-exposed cells based on RT-qPCR. Proteomics analysis confirmed that EtnE and nine other proteins encoded in the same gene cluster became much more predominant after cells were exposed to ethylene. The results suggest that ethylene is strongly inhibitory to M. crimeensis, but the bacterium responds to ethylene exposure by expressing an epoxide oxidation system similar to that used by bacteria that grow on alkenes. In the obligate methanotroph M. crimeensis, this system does not facilitate growth on ethylene but likely alleviates toxicity of epoxyethane formed through ethylene co-oxidation by particulate methane monooxygenase. The presence of predicted epoxide detoxification systems in several other wetland methanotrophs suggests that co-oxidation of ambient ethylene presents a stress for methanotrophic bacteria in these environments and that epoxyethane removal has adaptive value.}, }
@article {pmid39452755, year = {2024}, author = {Sabin, SJ and Beesley, CA and Marston, CK and Paisie, TK and Gulvik, CA and Sprenger, GA and Gee, JE and Traxler, RM and Bell, ME and McQuiston, JR and Weiner, ZP}, title = {Investigating Anthrax-Associated Virulence Genes among Archival and Contemporary Bacillus cereus Group Genomes.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {10}, pages = {}, pmid = {39452755}, issn = {2076-0817}, mesh = {*Bacillus cereus/genetics/pathogenicity ; *Virulence Factors/genetics ; *Genome, Bacterial/genetics ; *Anthrax/microbiology ; Virulence/genetics ; *Phylogeny ; Humans ; Whole Genome Sequencing ; Bacillus anthracis/genetics/pathogenicity ; }, abstract = {Bacillus anthracis causes anthrax through virulence factors encoded on two plasmids. However, non-B. anthracis organisms within the closely related, environmentally ubiquitous Bacillus cereus group (BCG) may cause an anthrax-like disease in humans through the partial adoption of anthrax-associated virulence genes, challenging the definition of anthrax disease. To elucidate these phenomena and their evolutionary past, we performed whole-genome sequencing on non-anthracis BCG isolates, including 93 archival (1967-2003) and 5 contemporary isolates (2019-2023). We produced annotated genomic assemblies and performed a pan-genome analysis to identify evidence of virulence gene homology and virulence gene acquisition by linear inheritance or horizontal gene transfer. At least one anthrax-associated virulence gene was annotated in ten isolates. Most homologous sequences in archival isolates showed evidence of pseudogenization and subsequent gene loss. The presence or absence of accessory genes, including anthrax-associated virulence genes, aligned with the phylogenetic structure of the BCG core genome. These findings support the hypothesis that anthrax-associated virulence genes were inherited from a common ancestor in the BCG and were retained or lost across different lineages, and contribute to a growing body of work informing public health strategies related to anthrax surveillance and identification.}, }
@article {pmid39452226, year = {2024}, author = {Durocher, AF and Paquet, VE and St-Laurent, RE and Duchaine, C and Charette, SJ}, title = {Impact of Predation by Ciliate Tetrahymena borealis on Conjugation in Aeromonas salmonicida subsp. salmonicida.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {10}, pages = {}, pmid = {39452226}, issn = {2079-6382}, support = {539024-2019//Natural Sciences and Engineering Research Council/ ; }, abstract = {BACKGROUND/OBJECTIVES: Antibiotic resistance gene (ARG) spread is driven by horizontal gene transfer (HGT). Ciliated protozoa may contribute to this process, as their predation has been shown to facilitate HGT in certain bacteria. Here, this phenomenon was further investigated using A. salmonicida subsp. salmonicida. This fish pathogen bears an extensive and dynamic plasmidome, suggesting a high potential for HGT.<br><br>METHODS: A. salmonicida strains carrying one of three conjugative plasmids bearing ARGs (pSN254b, pRAS1b or pAsa4b) were cocultured with a recipient, either A. salmonicida, E. coli or A. hydrophila. Conjugation rates were assessed in the presence and absence of the ciliate Tetrahymena borealis. PCR genotyping confirmed the acquisition of the conjugative plasmids and was used to verify the mobilization of other plasmids.<br><br>RESULTS: The basal rate of conjugation observed was high. Under the conditions studied, ciliate predation did not appear to influence the conjugation rate, except at higher proportions of ciliates, which typically hampered conjugation. Microscopy revealed that most bacteria were digested in these conditions. PCR screening demonstrated that small mobilizable plasmids from A. salmonicida (pAsa1, pAsa2, pAsa3, and pAsal1) were acquired by the recipients along with the conjugative plasmids, with a slight effect of the ciliates in some donor/recipient cell combination.<br><br>CONCLUSIONS: These results highlight how A. salmonicida can conjugate efficiently with different species and how complex its relationship with ciliates is.}, }
@article {pmid39452131, year = {2024}, author = {Xiong, Z and Zhang, W and Yin, H and Wan, J and Wu, Z and Gao, Y}, title = {Diversity and Evolution of NLR Genes in Citrus Species.}, journal = {Biology}, volume = {13}, number = {10}, pages = {}, pmid = {39452131}, issn = {2079-7737}, support = {32060615//National Natural Science Foundation of China/ ; jxsq2020102134//Double Thousand Plan of Jiangxi Province/ ; }, abstract = {NLR genes are crucial components of the effector-triggered immunity (ETI) system, responsible for recognizing pathogens and initiating immune responses. Although NLR genes in many plant species have been extensively studied, the diversity of NLR genes in citrus remains largely unknown. Our analysis revealed significant variations in the copy numbers of NLR genes among these species. Gene duplication and recombination were identified as the major driving forces behind this diversity. Additionally, horizontal gene transfer (HGT) emerged as the principal mechanism responsible for the increase in NLR gene copy number in A. buxifolia. The citrus NLR genes were classified into four categories: TIR-NBS-LRR (TNL), CC-NBS-LRR (CNL), RPW8-NBS-LRR (RNL), and NL. Our findings indicate that TNL, RNL, and CNL genes originated from NL genes through the acquisition of TIR and RPW8 domains, along with CC motifs, followed by the random loss of corresponding domains. Phylogenetic analysis suggested that citrus NLR genes originated alongside the species and underwent adaptive evolution, potentially playing crucial roles in the global colonization of citrus. This study provides important insights into the diversity of citrus NLR genes and serves as a foundational dataset for future research aimed at breeding disease-resistant citrus varieties.}, }
@article {pmid39450285, year = {2024}, author = {Agudo, R and Reche, MP}, title = {Revealing antibiotic resistance's ancient roots: insights from pristine ecosystems.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1445155}, pmid = {39450285}, issn = {1664-302X}, abstract = {The prevailing belief that antibiotic resistance mechanisms emerged with human antibiotic use has been challenged. Evidence indicates that some antibiotic resistance genes (ARGs) have a long evolutionary history, predating the advent of antibiotics in human medicine, thereby demonstrating that resistance is an ancient phenomenon. Despite extensive surveys of resistance elements in environments impacted by human activity, limited data are available from remote and pristine habitats. This minireview aims to compile the most relevant research on the origins and evolution of ARGs in these habitats, which function as reservoirs for ancient resistance mechanisms. These studies indicate that ancient ARGs functionally similar to modern resistance genes, highlighting the general role of natural antimicrobial substances in fostering the evolution and exchange of diverse resistance mechanisms through horizontal gene transfer over time. This minireview underscores that antibiotic resistance was present in ancestral microbial communities and emphasizes the ecological role of antibiotics and resistance determinants. Understanding ancient ARGs is crucial for predicting and managing the evolution of antibiotic resistance. Thus, these insights provide a foundational basis for developing new antibiotics and strategies for microbial resistance management.}, }
@article {pmid39448149, year = {2025}, author = {Fang, M and Yuan, Y and Fox, EM and Wu, K and Tian, X and Zhang, L and Feng, H and Li, R and Bai, L and Wang, X and Yang, Z and Zhang, R and Wang, J}, title = {Prevalence and genomic characteristics of becAB-carrying Clostridium perfringens strains.}, journal = {Food microbiology}, volume = {125}, number = {}, pages = {104640}, doi = {10.1016/j.fm.2024.104640}, pmid = {39448149}, issn = {1095-9998}, mesh = {*Clostridium perfringens/genetics/classification/isolation &amp; purification ; *Clostridium Infections/microbiology/epidemiology/veterinary ; China/epidemiology ; Prevalence ; Humans ; *Bacterial Toxins/genetics ; Animals ; Genome, Bacterial ; Plasmids/genetics ; Genomics ; Phylogeny ; }, abstract = {Clostridium perfringens, as a foodborne pathogen, can cause various intestinal diseases in both humans and animals according to its repertoire of toxins. In recent years, a multitude of studies have highlighted its threat to infants and young children. C. perfringens carries numerous toxins, with the newly identified BEC toxin confirmed as the second toxin to cause diarrheal illness, after CPE. However, the global dissemination of C. perfringens strains carrying becAB genes, which encode BEC toxins, has not been extensively studied. Following epidemiological surveillance of the prevalence of C. perfringens from different sources in various provinces of China, we identified two becAB-carrying strains and one strain carrying a sequence similar to becAB from distinct provinces and sources. When combined with genomic analysis of other becAB-carrying C. perfringens strains from public databases, we found that becAB was present in strains from different lineages. Our analysis of the plasmid and genetic environment corroborates previous findings on becAB-carrying strains, confirming that it currently achieves horizontal transmission through one type of evolutionarily conserved Pcp plasmid. This study provides a comprehensive analysis of the prevalence and transmission patterns of the newly emerged toxin gene locus, becAB, in C. perfringens. Despite the relatively low identification rate of becAB-carrying strains, their potential impact requires ongoing surveillance and investigation of their features, particularly their antimicrobial resistance.}, }
@article {pmid39446960, year = {2024}, author = {Li, L and Ge, Z and Liu, S and Zheng, K and Li, Y and Chen, K and Fu, Y and Lei, X and Cui, Z and Wang, Y and Huang, J and Liu, Y and Duan, M and Sun, Z and Chen, J and Li, L and Shen, P and Wang, G and Chen, J and Li, R and Li, C and Yang, Z and Ning, Y and Luo, A and Chen, B and Seim, I and Liu, X and Wang, F and Yao, Y and Guo, F and Yang, M and Liu, CH and Fan, G and Wang, L and Yang, D and Zhang, L}, title = {Multi-omics landscape and molecular basis of radiation tolerance in a tardigrade.}, journal = {Science (New York, N.Y.)}, volume = {386}, number = {6720}, pages = {eadl0799}, doi = {10.1126/science.adl0799}, pmid = {39446960}, issn = {1095-9203}, mesh = {Animals ; DNA Damage ; *DNA Repair ; Gene Transfer, Horizontal ; Genome ; Mitochondrial Proteins/metabolism/genetics ; Multiomics ; NAD/metabolism ; Poly (ADP-Ribose) Polymerase-1/metabolism/genetics ; Proteome ; *Radiation Tolerance/genetics ; *Tardigrada/genetics/metabolism/radiation effects ; *Transcriptome ; }, abstract = {Tardigrades are captivating organisms known for their resilience in extreme environments, including ultra-high-dose radiation, but the underlying mechanisms of this resilience remain largely unknown. Using genome, transcriptome, and proteome analysis of Hypsibius henanensis sp. nov., we explored the molecular basis contributing to radiotolerance in this organism. A putatively horizontally transferred gene, DOPA dioxygenase 1 (DODA1), responds to radiation and confers radiotolerance by synthesizing betalains-a type of plant pigment with free radical-scavenging properties. A tardigrade-specific radiation-induced disordered protein, TRID1, facilitates DNA damage repair through a mechanism involving phase separation. Two mitochondrial respiratory chain complex assembly proteins, BCS1 and NDUFB8, accumulate to accelerate nicotinamide adenine dinucleotide (NAD[+]) regeneration for poly(adenosine diphosphate-ribosyl)ation (PARylation) and subsequent poly(adenosine diphosphate-ribose) polymerase 1 (PARP1)-mediated DNA damage repair. These three observations expand our understanding of mechanisms of tardigrade radiotolerance.}, }
@article {pmid39446952, year = {2024}, author = {Sheahan, ML and Flores, K and Coyne, MJ and García-Bayona, L and Chatzidaki-Livanis, M and Holst, AQ and Smith, RC and Sundararajan, A and Barquera, B and Comstock, LE}, title = {A ubiquitous mobile genetic element changes the antagonistic weaponry of a human gut symbiont.}, journal = {Science (New York, N.Y.)}, volume = {386}, number = {6720}, pages = {414-420}, doi = {10.1126/science.adj9504}, pmid = {39446952}, issn = {1095-9203}, support = {R01 AI093771/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Bacteroides fragilis/genetics ; Conjugation, Genetic ; *Gastrointestinal Microbiome/genetics ; *Gene Transfer, Horizontal ; Genetic Fitness ; Genome, Bacterial ; *Interspersed Repetitive Sequences ; *Symbiosis ; *Type VI Secretion Systems/genetics ; *DNA, Bacterial/genetics ; }, abstract = {DNA transfer is ubiquitous in the human gut microbiota, especially among species of the order Bacteroidales. In silico analyses have revealed hundreds of mobile genetic elements shared between these species, yet little is known about the phenotypes they encode, their effects on fitness, or pleiotropic consequences for the recipient's genome. In this work, we show that acquisition of a ubiquitous integrative conjugative element (ICE) encoding a type VI secretion system (T6SS) shuts down the native T6SS of Bacteroides fragilis. Despite inactivating this T6SS, ICE acquisition increases the fitness of the B. fragilis transconjugant over its progenitor by arming it with the new T6SS. DNA transfer causes the strain to change allegiances so that it no longer targets ecosystem members with the same element yet is armed for communal defense.}, }
@article {pmid39443865, year = {2024}, author = {Xiong, Y and Lei, X and Xiong, Y and Liu, Y and Dong, Z and Zhao, J and Yu, Q and Ma, X}, title = {Factors contributing to organelle genomes size variation and the intracellular DNA transfer in Polygonaceae.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {994}, pmid = {39443865}, issn = {1471-2164}, support = {32271753//National Natural Science Foundation of China/ ; 2022YFQ0076//Sichuan Province regional innovation cooperation project/ ; 2023YFSY0012//Cooperation project of provincial college, and provincial school/ ; }, mesh = {*Genome, Mitochondrial ; *Genome, Chloroplast ; *Polygonaceae/genetics ; *Genome Size ; *Phylogeny ; Evolution, Molecular ; Genome, Plant ; Gene Transfer, Horizontal ; }, abstract = {The use of complete organelle genomes, including chloroplast and mitochondrial genomes, is a powerful molecular method for studying biological evolution and gene transfer. However, in the case of Polygonaceae, an important family with numerous edible, medicinal, and ornamental species, the mitochondrial genomes of only three species have been sequenced and analyzed. In this study, we present the mitochondrial and chloroplast genomes of two important Tibetan medicinal plants, Bistorta viviparum and B. macrophyllum. All the organelle genomes are assembled into a single circular structure and contain a common set of 32 protein-coding genes (PCGs). Some genes such as rps2 and ndhF were found to have high nucleotide polymorphism (Pi) in the chloroplast genomes, while cox1, mttB and rps12 showed pronounced Pi values in the mitochondrial genomes. Furthermore, our analysis revealed that most chloroplast genes and mitochondrial PCGs in Polygonaceae plants are under purifying selection. However, a few genes, including the chloroplast gene psaJ and the mitochondrial genes ccmFc, atp8 and nad4, showed positive selection in certain Polygonaceae plants, as indicated by a Ka/Ks ratio greater than one. Structural variation analysis revealed a wealth of differences between the mitochondrial genomes of five Polygonaceae species, with a particularly notable large-scale inversion observed between Reynoutria japonica and Fallopia aubertii. Furthermore, an analysis of the homologous sequences in the chloroplast and mitochondrial genomes revealed that the rps7 has been transferred from the chloroplast to the mitochondrial genome in all five Polygonaceae species. Finally, ecological niche models were constructed for B. viviparum and B. macrophyllum, indicating that mean annual temperature and altitude are the main climatic factors influencing the distribution of both species. Although the current distribution of B. viviparum is significantly wider than that of B. macrophyllum, projections suggest that the optimal growth ranges of both species will expand in the future, with B. macrophyllum potentially exceeding B. viviparum. This study not only contributes to the plastid genome database for Polygonaceae plants, but also provides theoretical insights into the adaptive evolution of these plants.}, }
@article {pmid39441990, year = {2024}, author = {Uppal, S and Waterworth, SC and Nick, A and Vogel, H and Flórez, LV and Kaltenpoth, M and Kwan, JC}, title = {Repeated horizontal acquisition of lagriamide-producing symbionts in Lagriinae beetles.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39441990}, issn = {1751-7370}, support = {ERC CoG 819585//European Research Council through an ERC Consolidator/ ; 1845890//National Science Foundation/ ; }, mesh = {Animals ; *Symbiosis ; *Coleoptera/microbiology ; *Burkholderia/genetics/metabolism/classification/physiology ; Phylogeny ; Metagenomics ; Genome, Bacterial ; Gene Transfer, Horizontal ; }, abstract = {Microbial symbionts associate with multicellular organisms on a continuum from facultative associations to mutual codependency. In the oldest intracellular symbioses there is exclusive vertical symbiont transmission, and co-diversification of symbiotic partners over millions of years. Such symbionts often undergo genome reduction due to low effective population sizes, frequent population bottlenecks, and reduced purifying selection. Here, we describe multiple independent acquisition events of closely related defensive symbionts followed by genome erosion in a group of Lagriinae beetles. Previous work in Lagria villosa revealed the dominant genome-eroded symbiont of the genus Burkholderia produces the antifungal compound lagriamide, protecting the beetle's eggs and larvae from antagonistic fungi. Here, we use metagenomics to assemble 11 additional genomes of lagriamide-producing symbionts from 7 different host species within Lagriinae from 5 countries, to unravel the evolutionary history of this symbiotic relationship. In each host, we detected one dominant genome-eroded Burkholderia symbiont encoding the lagriamide biosynthetic gene cluster. However, we did not find evidence for host-symbiont co-diversification or for monophyly of the lagriamide-producing symbionts. Instead, our analyses support a single ancestral acquisition of the gene cluster followed by at least four independent symbiont acquisitions and subsequent genome erosion in each lineage. By contrast, a clade of plant-associated relatives retained large genomes but secondarily lost the lagriamide gene cluster. Our results, therefore, reveal a dynamic evolutionary history with multiple independent symbiont acquisitions characterized by a high degree of specificity and highlight the importance of the specialized metabolite lagriamide for the establishment and maintenance of this defensive symbiosis.}, }
@article {pmid39441515, year = {2024}, author = {Cardoso, EM and Dea Lindner, J and Ferreira, FA}, title = {Genomic analysis of Salmonella Heidelberg isolated from the Brazilian poultry farms.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {55}, number = {4}, pages = {4129-4137}, pmid = {39441515}, issn = {1678-4405}, mesh = {Animals ; Brazil ; *Salmonella Infections, Animal/microbiology ; Chickens/microbiology ; *Poultry Diseases/microbiology ; *Genome, Bacterial ; Virulence Factors/genetics ; Anti-Bacterial Agents/pharmacology ; Farms ; Polymorphism, Single Nucleotide ; *Salmonella enterica/genetics/isolation &amp; purification/drug effects/classification ; Phylogeny ; Genomics ; *Salmonella/genetics/isolation &amp; purification/classification ; Genomic Islands ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; }, abstract = {The rapid expansion of broiler chicken production in Brazil has presented significant sanitation challenges within the poultry industry. Among these challenges, Salmonella enterica subsp. enterica serotype Heidelberg stands as a contributor to global salmonellosis outbreaks. This study analyzed 13 draft genomes of Salmonella Heidelberg isolated from the pre-slaughter broiler chickens farms in Brazil. By conducting in silico analysis of these genomes, the study investigated genome similarity based on single nucleotide polymorphisms (SNPs) and identified genes encoding resistance to antimicrobials, sanitizers, and virulence factors. Furthermore, mobile genetic elements (MGE) were identified to assess their potential role in propagating genes through horizontal gene transfer. A risk classification was also applied based on the resistomes. The genomes revealed a high prevalence of genes conferring resistance to aminoglycosides, fosfomycin, sulfonamides, tetracycline, and genes linked to quaternary ammonium resistance. The study also uncovered six Salmonella pathogenicity islands (SPI) and over 100 genes encoding virulence factors. The association of MGE with antibiotic-resistant genes sul2 and blaCMY-2 raised concerns about the potential transfer to other bacteria, posing a substantial risk for spreading resistance mechanisms according to established risk protocols. Additionally, SNP analysis indicated close phylogenetic relationships among some isolates, suggesting a common origin. This study enhances our understanding of Salmonella Heidelberg strains by identifying key risk factors for transmission and revealing the association between resistance genes and MGEs. This insight provides a foundation for developing and implementing effective control, monitoring, and treatment strategies in the poultry industry.}, }
@article {pmid39441253, year = {2024}, author = {Varshith, MR and Ghosh Dastidar, R and Shrilaxmi, MS and Bhattacharya, R and Jha, S and Choudhary, S and Varny, E and Carvalho, RA and John, L and Sundaramoorthy, V and Smith, CM and Damerla, RR and Herai, RH and Biswas, SR and Lal, PB and Mukhopadhyay, C and Ghosh Dastidar, S}, title = {Virulome and phylogenomic profiling of a novel Burkholderia pseudomallei strain from an Indian clinical isolate.}, journal = {Molecular genetics and genomics : MGG}, volume = {299}, number = {1}, pages = {98}, pmid = {39441253}, issn = {1617-4623}, support = {102. IFD/SAN/2549/2019-20 Dated 29-10-2019//Department of Biotechnology, Ramalingaswami re-entry Fellowship/ ; }, mesh = {*Burkholderia pseudomallei/genetics/isolation &amp; purification/pathogenicity ; Humans ; *Melioidosis/microbiology ; *Virulence Factors/genetics ; India ; *Phylogeny ; Genome, Bacterial/genetics ; Genomic Islands/genetics ; Whole Genome Sequencing/methods ; Virulence/genetics ; }, abstract = {Highly pathogenic Burkholderia pseudomallei is the causative agent of melioidosis, a neglected tropical disease endemic in Southeast Asian tropical region. This bacterium encompasses diverse virulence factors which further undergo dynamic gene-expression flux as it transits through distinct environmental niches within the host which may lead to manifestation of differential clinical symptoms. B. pseudomallei, is classified as a Tier 1 select agent in the United States and regarded as a risk group 3 organism in India with the potential to be used as bioweapon. Considering these facts, it is vital to uncover both physiological and genetic heterogeneity of B. pseudomallei, particularly to identify any novel virulence factors that may contribute to pathogenicity. B. pseudomallei strain CM000113 was isolated from a clinical case in India, characterized it for its physiological, biochemical, and prominently genetic traits through WGS. It has a type 2 morphotype with faster doubling time and high biofilm producing capacity as compared to Pseudomonas aeruginosa. The genome size is 7.3 Mbp and it is phylogenetically close to B. pseudomallei strain Mahidol 1106a and Burkholderia mallei Turkey 2. We observed genetic heterogeneity, as key virulence factors that were identified shows sequence dissimilarity with reference strains. Additionally, presence of genomic islands, harbouring two virulence factors, GmhA and GmhB2, associated with pathogenesis indicates possibility of horizontal gene transfer. These results emphasize the need for an extensive study focusing the genome of B. pseudomallei and its associated heterogeneity, to identify molecular biomarkers aiding to develop point-of-care diagnostic kits for early diagnosis of melioidosis.}, }
@article {pmid39441081, year = {2025}, author = {Li, Y and Feng, X and Chen, X and Yang, S and Zhao, Z and Chen, Y and Li, SC}, title = {PlasmidScope: a comprehensive plasmid database with rich annotations and online analytical tools.}, journal = {Nucleic acids research}, volume = {53}, number = {D1}, pages = {D179-D188}, pmid = {39441081}, issn = {1362-4962}, support = {32061160472//NSFC-RGC Joint Research Scheme/ ; 32300527//National Natural Science Foundation of China/ ; 2022A1515110784//Guangdong Basic and Applied Basic Research Foundation/ ; 20220814183301001//Shenzhen Science and Technology Program/ ; }, mesh = {*Plasmids/genetics ; *Molecular Sequence Annotation ; *Databases, Genetic ; Software ; Internet ; Bacteria/genetics ; CRISPR-Cas Systems ; }, abstract = {Plasmids are extrachromosomal genetic molecules that replicate independent of chromosomes in bacteria, archaea, and eukaryotic organisms. They contain diverse functional elements and are capable of horizontal gene transfer among hosts. While existing plasmid databases have archived plasmid sequences isolated from individual microorganisms or natural environments, there is a need for a comprehensive, standardized, and annotated plasmid database to address the vast accumulation of plasmid sequences. Here, we propose PlasmidScope (https://plasmid.deepomics.org/), a plasmid database offering comprehensive annotations, automated online analysis, and interactive visualization. PlasmidScope harbors a substantial collection of 852 600 plasmids curated from 10 repositories. Along with consolidated background information, PlasmidScope utilizes 12 state-of-the-art tools and provides comprehensive annotations for the curated plasmids, covering genome completeness, topological structure, mobility, host source, tRNA, tmRNA, signal peptides, transmembrane proteins and CRISPR/Cas systems. PlasmidScope offers diverse functional annotations for its 25 231 059 predicted genes from 9 databases as well as corresponding protein structures predicted by ESMFold. In addition, PlasmidScope integrates online analytical modules and interactive visualization, empowering researchers to delve into the complexities of plasmids.}, }
@article {pmid39437930, year = {2024}, author = {Da, YM and Yang, XR and Li, MJ and Li, SS and Gao, ZP and Zhang, Y and Su, JQ and Zhou, GW}, title = {Promotion of antibiotic-resistant genes dissemination by the micro/nanoplastics in the gut of snail Achatina fulica.}, journal = {The Science of the total environment}, volume = {955}, number = {}, pages = {176829}, doi = {10.1016/j.scitotenv.2024.176829}, pmid = {39437930}, issn = {1879-1026}, mesh = {Animals ; *Snails ; *Gastrointestinal Microbiome/drug effects ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Nanoparticles ; Microplastics ; Water Pollutants, Chemical ; RNA, Ribosomal, 16S ; }, abstract = {Terrestrial animal intestines are hotspots for the enrichment of micro/nano plastics (M/NPs) and antibiotic-resistant genes (ARGs). However, little is known about the further impact of M/NPs on the spread of ARGs in animal guts. This study investigates the role of M/NPs (polystyrene) with varying particle sizes (0.082, 42, and 182 μm), concentrations (10 and 100 mg/L), and exposure durations (4 and 16 days) in the ARGs dissemination via conjugation in the edible snail (Achatina fulica) gut. Combination of qPCR with 16S rRNA-based sequencing, we found that PS exposure caused intestinal cell impairment and shifts in the gut microbial community of snails. Conjugation rate increased with PS particle sizes in the snail gut. After 4 days of exposure, significantly higher conjugation rates were observed in the gut exposed to 100 mg/L PS compared to 10 mg/L, however, this trend reversed after 16 days. Consistently, the abundances of conjugation relevant genes trfA and trbB shared similar trends to the conjugation ratios in the snail gut after PS exposure. Transconjugant diversity was much lower in 10 mg/L PS groups than in 100 mg/L PS treatments. Therefore, this study suggests that the presence of M/NPs would complicate management of ARG spread. The selection pressure exerted by M/NPs may sustain or even amplify the spread of ARGs in the gut of terrestrial animals even in the absence of antibiotics. It highlights the necessity of avoiding M/NPs intake as a part of comprehensive strategy for cubing ARG dissemination in the gut of animals.}, }
@article {pmid39437688, year = {2024}, author = {Zhang, B and Hu, X and Zhao, D and Wang, Y and Qu, J and Tao, Y and Kang, Z and Yu, H and Zhang, J and Zhang, Y}, title = {Harnessing microbial biofilms in soil ecosystems: Enhancing nutrient cycling, stress resilience, and sustainable agriculture.}, journal = {Journal of environmental management}, volume = {370}, number = {}, pages = {122973}, doi = {10.1016/j.jenvman.2024.122973}, pmid = {39437688}, issn = {1095-8630}, mesh = {*Biofilms ; *Agriculture/methods ; *Soil/chemistry ; *Soil Microbiology ; *Ecosystem ; Nutrients/metabolism ; }, abstract = {Soil ecosystems are complex networks of microorganisms that play pivotal roles in nutrient cycling, stress resilience, and the provision of ecosystem services. Among these microbial communities, soil biofilms, and complex aggregations of microorganisms embedded within extracellular polymeric substances (EPS) exert significant influence on soil health and function. This review delves into the dynamics of soil biofilms, highlighting their structural intricacies and the mechanisms by which they facilitate nutrient cycling, and discusses how biofilms enhance the degradation of pollutants through the action of extracellular enzymes and horizontal gene transfer, contributing to soil detoxification and fertility. Furthermore, the role of soil biofilms in stress resilience is underscored, as they form symbiotic relationships with plants, bolstering their growth and resistance to environmental stressors. The review also explores the ecological functions of biofilms in enhancing soil structure stability by promoting aggregate formation, which is crucial for water retention and aeration. By integrating these insights, we aim to provide a comprehensive understanding of the multifaceted benefits of biofilms in soil ecosystems. This knowledge is essential for developing strategies to manipulate soil biofilms to improve agricultural productivity and ecological sustainability. This review also identifies research gaps and emphasizes the need for practical applications of biofilms in sustainable agriculture.}, }
@article {pmid39436807, year = {2024}, author = {Koleva, DT and Bengochea, AW and Mellor, SB and Ochoa-Fernandez, R and Nelson, DR and Møller, BL and Gillam, EMJ and Sørensen, M}, title = {Sequence diversity in the monooxygenases involved in oxime production in plant defense and signaling: a conservative revision in the nomenclature of the highly complex CYP79 family.}, journal = {The Plant journal : for cell and molecular biology}, volume = {120}, number = {3}, pages = {1236-1256}, doi = {10.1111/tpj.17044}, pmid = {39436807}, issn = {1365-313X}, support = {//Villum Fonden/ ; CF19-0301//Carlsbergfondet/ ; CF20-0352//Carlsbergfondet/ ; NNF21OC0071074//Novo Nordisk Fonden/ ; }, mesh = {*Cytochrome P-450 Enzyme System/genetics/metabolism ; *Phylogeny ; *Oximes/metabolism ; Plant Proteins/genetics/metabolism ; Signal Transduction ; Plants/enzymology/genetics ; Evolution, Molecular ; Substrate Specificity ; Amino Acid Sequence ; }, abstract = {Cytochrome P450 monooxygenases of the CYP79 family catalyze conversion of specific amino acids into oximes feeding into a variety of metabolic plant pathways. Here we present an extensive phylogenetic tree of the CYP79 family built on carefully curated sequences collected across the entire plant kingdom. Based on a monophyletic origin of the P450s, a set of evolutionarily distinct branches was identified. Founded on the functionally characterized CYP79 sequences, sequence features of the individual substrate recognition sites (SRSs) were analyzed. Co-evolving amino acid residues were identified using co-evolutionary sequence analysis. SRS4 possesses a specific sequence pattern when tyrosine is a substrate. Except for the CYP79Cs and CYP79Fs, substrate preferences toward specific amino acids could not be assigned to specific subfamilies. The highly diversified CYP79 tree, reflecting recurrent independent evolution of CYP79s, may relate to the different roles of oximes in different plant species. The sequence differences across individual CYP79 subfamilies may facilitate the in vivo orchestration of channeled metabolic pathways based on altered surface charge domains of the CYP79 protein. Alternatively, they may serve to optimize dynamic interactions with oxime metabolizing enzymes to enable optimal ecological interactions. The outlined detailed curation of the CYP79 sequences used for building the phylogenetic tree made it appropriate to make a conservative phylogenetic tree-based revision of the naming of the sequences within this highly complex cytochrome P450 family. The same approach may be used in other complex P450 subfamilies. The detailed phylogeny of the CYP79 family will enable further exploration of the evolution of function in these enzymes.}, }
@article {pmid39433770, year = {2024}, author = {Yoon, EJ and Choi, YJ and Won, D and Choi, JR and Jeong, SH}, title = {Klebsiella pneumoniae, a human-dog shuttle organism for the genes of CTX-M ESBL.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {24725}, pmid = {39433770}, issn = {2045-2322}, support = {2019ER540402//Korea Disease Control and Prevention Agency/ ; }, mesh = {*Klebsiella pneumoniae/genetics/drug effects/isolation &amp; purification ; *beta-Lactamases/genetics ; Humans ; Animals ; Dogs ; *Plasmids/genetics ; *Escherichia coli/genetics/drug effects ; *Klebsiella Infections/microbiology ; Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; Genome, Bacterial ; Escherichia coli Infections/microbiology/veterinary ; }, abstract = {Antimicrobials reserved for human medicines are permitted for companion animals and it is important to understand multidrug-resistant pathogens recovered from companion animals in terms of epidemiological correlation with human pathogens and possibility of transmission to human-beings. Seventeen of each CTX-M-type extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-EC) and Klebsiella pneumoniae (ESBL-KP) canine isolates were assessed. Entire genomes of the 34 isolates were sequenced. Plasmid transfer and relative growth rates were assessed at differed temperature conditions indicating the body temperature of dogs, that of human-beings, and environment. ESBL-ECs were clonally diverse, while ESBL-KPs were not. The ESBL-ECs carried the blaCTX-M-15 gene in plasmids and the blaCTX-M-14-like gene either in chromosomes or in plasmids. The ESBL-KPs possessed the blaCTX-M-15 gene in plasmids (n = 15). One of the isolates carried another blaCTX-M-15 gene in a chromosome simultaneously and the other isolate had an additional blaCTX-M-9 gene-harbouring plasmid, together. Two ESBL-KP isolates carried the blaCTX-M-14 gene in plasmids. Plasmid transfer ESBL-EC to K. pneumoniae was efficient and the differed biological costs by temperature was much more in ESBL-EC than in ESBL-KP. Intersectoral dissemination of ESBL-ECs occurred mainly by horizontal gene transfer, while that of ESBL-KPs occurred by clonal dissemination.}, }
@article {pmid39431893, year = {2024}, author = {Kim, DH and Seo, H and Jung, S and Kim, B-J}, title = {Global prevalence of Mycobacterium massiliense strains with recombinant rpoB genes (Rec-Mas) horizontally transferred from Mycobacterium abscessus: two major types, dominant circulating clone 7 and MLST ST46 sequence type.}, journal = {Microbiology spectrum}, volume = {12}, number = {12}, pages = {e0193524}, pmid = {39431893}, issn = {2165-0497}, abstract = {UNLABELLED: Mycobacterium abscessus is a group of emerging antimicrobial-resistant nontuberculous mycobacteria that causes severe lung disease in infected patients globally. Recently, molecular epidemiology studies have indicated that horizontal gene transfer (HGT) events in the rpoB gene are prevalent between M. abscessus subspecies. To determine the global prevalence of M. abscessus strains subjected to rpoB HGT, we performed phylogenetic inference using a 711-bp rpoB sequence extracted from 1,786 M. abscessus isolates for which the whole-genome sequence was publicly available. Our data showed that a total of 74 isolates (4.1%) from 1,786 strains are subject to rpoB HGT, which is more prevalent than strains with hsp65 HGT (19 isolates from 1,786, 1.1%). Most of these (69 isolates) belong to two major groups of Mycobacterium massiliense, of which the rpoB gene is horizontally transferred from M. abscessus (Rec-mas), dominant circulating clone 7 (DCC7) (44 isolates) and ST46 type by multilocus sequence typing (25 isolates). The Rec-mas strains of the two groups have distinct geographical patient distributions, of which the former is mainly distributed in the United States, while the latter is prevalent in Asia. Our further genome-based analysis indicated that the ST46 type is a novel DCC candidate of M. massiliense that is responsible for dissemination between noncystic fibrosis patients in Asia. In conclusion, our global phylogenetic analysis revealed two major Rec-mas clones with distinct geographical distributions, namely, DCC7 and ST46. This study provides insights into the genetic clustering and person-to-person transmission of globally dominant and area-specific strains harboring the HGT rpoB gene.<br><br>IMPORTANCE: Horizontal gene transfer (HGT) events play a pivotal role in the evolution of Mycobacterium abscessus into dominant circulating clones (DCCs), which is capable of causing patient-to-patient transmission. In particular, HGT of the rpoB gene between strains of different subspecies of M. abscessus could also compromise differentiation between strains of M. abscessus. Here, for the first time, using 1,786 M. abscessus genome sequences, we evaluated the global prevalence of M. abscessus strains subjected to rpoB HGT. We found a greater prevalence of M. abscessus subjected to rpoB HGT than to those subjected to hsp65 HGT, which is mainly due to two Rec-mas clones, dominant circulating clone 7 and ST46, which are responsible for dissemination between non-CF patients in Asia. Our data highlight the importance of rpoB HGT in the evolution of M. abscessus, particularly Mycobacterium massiliense, into virulent DCC clones.}, }
@article {pmid39431819, year = {2024}, author = {Qian, Y and Lai, L and Cheng, M and Fang, H and Fan, D and Zylstra, GJ and Huang, X}, title = {Identification, characterization, and distribution of novel amidase gene aphA in sphingomonads conferring resistance to amphenicol antibiotics.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {11}, pages = {e0151224}, pmid = {39431819}, issn = {1098-5336}, support = {42277016//MOST | National Natural Science Foundation of China (NSFC)/ ; 41977119//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {*Anti-Bacterial Agents/pharmacology ; *Thiamphenicol/analogs &amp; derivatives/pharmacology ; *Amidohydrolases/genetics/metabolism ; *Bacterial Proteins/genetics/metabolism ; Sphingomonadaceae/genetics/enzymology/drug effects ; Chloramphenicol/pharmacology ; Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; }, abstract = {Amphenicol antibiotics, such as chloramphenicol (CHL), thiamphenicol (TAP), and florfenicol (Ff), are high-risk emerging pollutants. Their extensive usage in aquaculture, livestock, and poultry farming has led to an increase in bacterial antibiotic resistance and facilitated the spread of resistance genes. Yet, limited research has been conducted on the co-resistance of CHL, TAP, and Ff. Herein, a novel amidase AphA was identified from a pure cultured strain that can concurrently mediate the hydrolytic inactivation of CHL, TAP, and Ff, yielding products p-nitrophenylserinol, thiamphenicol amine (TAP-amine), and florfenicol amine (Ff-amine), respectively. The antibacterial activity of these antibiotic hydrolysates exhibited a significant reduction or complete loss in comparison to the parent compounds. Notably, AphA shared less than 26% amino acid sequence identity with previously reported enzymes and exhibited high conservation within the sphingomonad species. Through enzymatic kinetic analysis, the AphA exhibited markedly superior affinity and catalytic activity toward Ff in comparison to CHL and TAP. Site-directed mutagenesis analysis revealed the indispensability of catalytic triad residues, particularly serine 153 and histidine 277, in forming crucial hydrogen bonds essential for AphA's hydrolytic activity. Comparative genomic analysis showed that aphA genes in some species are closely adjacent to various transposable elements, indicating that there is a high potential risk of horizontal gene transfer (HGT). This study established a hydrolysis resistance mechanism of amphenicol antibiotics in sphingomonads, which offers theoretical guidance and a novel marker gene for assessing the prevalent risk of amphenicol antibiotics in the environment.IMPORTANCEAmphenicol antibiotics are pervasive emerging contaminants that present a substantial threat to ecological systems. Few studies have elucidated resistance genes or mechanisms that can act on CHL, TAP, and Ff simultaneously. The results of this study fill this knowledge gap and identify a novel amidase AphA from the bacterium Sphingobium yanoikuyae B1, which mediates three typical amphenicol antibiotic inactivation, and the molecular mechanism is elucidated. The diverse types of transposable elements were identified in the flanking regions of the aphA gene, indicating the risk of horizontal transfer of this antibiotic resistance genes (ARG). These findings offer new insights into the bacterial resistance to amphenicol antibiotics. The gene reported herein can be utilized as a novel genetic diagnostic marker for monitoring the environmental fate of amphenicol antibiotics, thereby enriching risk assessment efforts within the context of antibiotic resistance.}, }
@article {pmid39430728, year = {2025}, author = {Zhang, Y and Xue, B and Mao, Y and Chen, X and Yan, W and Wang, Y and Wang, Y and Liu, L and Yu, J and Zhang, X and Chao, S and Topp, E and Zheng, W and Zhang, T}, title = {High-throughput single-cell sequencing of activated sludge microbiome.}, journal = {Environmental science and ecotechnology}, volume = {23}, number = {}, pages = {100493}, pmid = {39430728}, issn = {2666-4984}, abstract = {Wastewater treatment plants (WWTPs) represent one of biotechnology's largest and most critical applications, playing a pivotal role in environmental protection and public health. In WWTPs, activated sludge (AS) plays a major role in removing contaminants and pathogens from wastewater. While metagenomics has advanced our understanding of microbial communities, it still faces challenges in revealing the genomic heterogeneity of cells, uncovering the microbial dark matter, and establishing precise links between genetic elements and their host cells as a bulk method. These issues could be largely resolved by single-cell sequencing, which can offer unprecedented resolution to show the unique genetic information. Here we show the high-throughput single-cell sequencing to the AS microbiome. The single-amplified genomes (SAGs) of 15,110 individual cells were clustered into 2,454 SAG bins. We find that 27.5% of the genomes in the AS microbial community represent potential novel species, highlighting the presence of microbial dark matter. Furthermore, we identified 1,137 antibiotic resistance genes (ARGs), 10,450 plasmid fragments, and 1,343 phage contigs, with shared plasmid and phage groups broadly distributed among hosts, indicating a high frequency of horizontal gene transfer (HGT) within the AS microbiome. Complementary analysis using 1,529 metagenome-assembled genomes from the AS samples allowed for the taxonomic classification of 98 SAG bins, which were previously unclassified. Our study establishes the feasibility of single-cell sequencing in characterizing the AS microbiome, providing novel insights into its ecological dynamics, and deepening our understanding of HGT processes, particularly those involving ARGs. Additionally, this valuable tool could monitor the distribution, spread, and pathogenic hosts of ARGs both within AS environments and between AS and other environments, which will ultimately contribute to developing a health risk evaluation system for diverse environments within a One Health framework.}, }
@article {pmid39427888, year = {2024}, author = {Wang, S and Li, W and Xi, B and Cao, L and Huang, C}, title = {Mechanisms and influencing factors of horizontal gene transfer in composting system: A review.}, journal = {The Science of the total environment}, volume = {955}, number = {}, pages = {177017}, doi = {10.1016/j.scitotenv.2024.177017}, pmid = {39427888}, issn = {1879-1026}, mesh = {*Gene Transfer, Horizontal ; *Composting/methods ; Drug Resistance, Microbial/genetics ; Quorum Sensing ; Bacteria/genetics ; Soil Microbiology ; }, abstract = {Organic solid wastes such as livestock manure and sewage sludge are important sources and repositories of antibiotic resistance genes (ARGs). Composting, a solid waste treatment technology, has demonstrated efficacy in degrading various antibiotics and reducing ARGs. However, some recalcitrant ARGs (e.g., sul1, sul2) will enrich during the composting maturation period. These ARGs persist in compost products and spread through horizontal gene transfer (HGT). We analyzed the reasons behind the increase of ARGs during the maturation phase. It was found that the proliferation of ARG-host bacteria and HGT process play an important role. This article revealed that microbial physiological responses, environmental factors, pollutants, and quorum sensing (QS) can all influence the HGT process in composting systems. We examined the influence of these factors on HGT in the compost system and summarized potential mechanisms by analyzing the alterations in microbial communities. We comprehensively summarized the HGT hazards that these factors may present in composting systems. Finally, we summarized methods to inhibit HGT in compost, such as using additives, quorum sensing inhibitors (QSIs), microbial inoculation, and predicting HGT events. Overall, the HGT mechanism and driving force in complex composting systems are still insufficiently studied. In view of the current situation, using predictions to assess the risk of HGT in composting may be advisable.}, }
@article {pmid39426452, year = {2024}, author = {Jaffer, YD and Abdolahpur Monikh, F and Uli, K and Grossart, HP}, title = {Tire wear particles enhance horizontal gene transfer of antibiotic resistance genes in aquatic ecosystems.}, journal = {Environmental research}, volume = {263}, number = {Pt 3}, pages = {120187}, doi = {10.1016/j.envres.2024.120187}, pmid = {39426452}, issn = {1096-0953}, mesh = {*Gene Transfer, Horizontal ; *Escherichia coli/drug effects/genetics ; *Pseudomonas/genetics/drug effects ; Microplastics/toxicity ; Lakes/microbiology ; Drug Resistance, Microbial/genetics ; Ecosystem ; Water Pollutants, Chemical/toxicity/analysis ; }, abstract = {Microplastics (MPs) have introduced new surfaces for biofilm development and gene exchange among bacteria. We investigated Tire Wear Particles (TWPs) for their involvement in horizontal gene transfer (HGT), particularly in relation to associated metals in the matrices of TWPs. We employed red-fluorescently tagged E. coli strain as a donor with green-fluorescently tagged, broad-host-range plasmid pKJK5, resistant to trimethoprim. As a recipient, we utilized Pseudomonas sp. and a natural lake microbial community. HGT activity on TWPs was determined and compared with that on polystyrene (PS) (with and without metals), and chitosan, which was used as a natural surface. Exposure to TWPs significantly enhanced HGT frequency of antibiotic resistance gene (ARG) from donor to recipient compared to PS and chitosan, and metals of TWPs further promoted HGT. HGT frequency on TWPs with Pseudomonas sp. was found to be 10[-3] at 30 °C. in the lake community, it was similarly high already at 25 °C suggesting a higher permissiveness of the natural microbial community towards ARG at lower temperatures. This study sheds light on the potential impact of TWPs in promoting HGT, forming the basis for health risk assessments of TWPs and more generally of MP pollution in various aquatic ecosystems.}, }
@article {pmid39423639, year = {2024}, author = {Xu, Y and Li, H and Ding, Y and Zhang, D and Liu, W}, title = {How nanoscale plastics facilitate the evolution of antibiotic resistance?.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {136157}, doi = {10.1016/j.jhazmat.2024.136157}, pmid = {39423639}, issn = {1873-3336}, mesh = {*Serratia marcescens/drug effects/genetics/metabolism ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Plastics/chemistry ; Gene Transfer, Horizontal ; Nanoparticles/chemistry ; Drug Resistance, Microbial/genetics ; }, abstract = {The plastic can enhance the proliferation of antibiotic resistance genes (ARGs), however, the effect of nanoplastics (NPLs) on bacterial antibiotic resistance has not been clearly explained. Herein, we explored the effects and mechanisms of NPLs of different sizes (200 and 600 nm) on the evolution of antibiotic resistance in Serratia marcescens. The results indicated that the evolution of bacterial antibiotic resistance could be promoted under NPLs exposure, which the median of relative abundance of ARGs was 1.11-1.46 times compared to the treatment without NPLs. Transcriptomic analysis showed that the larger size of NPLs mainly increased the permeability of bacterial cell membranes to efflux antibiotics, thus potentiating antibiotic resistance. While, the smaller NPLs is more than that, its enhanced the expression of antibiotic resistance by modulating bacterial metabolic processes. The genome SNP analysis found that the NPLs could cause the genetic mutation occurrence to alter the membrane transport and metabolism processes, and it increased at a size of 200 nm more than at 600 nm NPLs. Importantly, we demonstrated that the horizontal transfer of ARGs was augmented due to the NPLs could dock to bacterial surface proteins and pull their movement to contact with other bacteria (binding energy of membrane proteins: -8.54 kcal/mol), especially the smaller size. It suggests that NPLs will also contribute to the proliferation of ARGs in the environment. This study provides data for understanding the risk of bacterial resistance.}, }
@article {pmid39423563, year = {2024}, author = {Gomberg, AF and Grossman, AD}, title = {It's complicated: relationships between integrative and conjugative elements and their bacterial hosts.}, journal = {Current opinion in microbiology}, volume = {82}, number = {}, pages = {102556}, pmid = {39423563}, issn = {1879-0364}, support = {R35 GM148343/GM/NIGMS NIH HHS/United States ; }, mesh = {*Conjugation, Genetic ; *Bacteria/genetics/metabolism ; *DNA Transposable Elements/genetics ; Chromosomes, Bacterial/genetics ; Gene Transfer, Horizontal ; }, abstract = {Integrative and conjugative elements (ICEs) are typically found integrated in a bacterial host chromosome. They can excise, replicate, and transfer from cell to cell. Many contain genes that confer phenotypes to host cells, including antibiotic resistances, specialized metabolisms, phage defense, and symbiosis or pathogenesis determinants. Recent studies revealed that at least three ICEs (ICEclc, Tn916, and TnSmu1) cause growth arrest or death of host cells upon element activation. This review highlights the complex interactions between ICEs and their hosts, including the recent examples of the significant costs to host cells. We contrast two examples of killing, ICEclc and Tn916, in which killing, respectively, benefits or impairs conjugation and emphasize the importance of understanding the impacts of ICE-host relationships on conjugation. ICEs are typically only active in a small fraction of cells in a population, and we discuss how phenotypes normally occurring in a small subset of host cells can be uncovered.}, }
@article {pmid39417646, year = {2024}, author = {Wang, Q and Geng, L and Gao, Z and Sun, Y and Li, X and Sun, S and Luo, Y}, title = {Microalgae Enhances the Adaptability of Epiphytic Bacteria to Sulfamethoxazole Stress and Proliferation of Antibiotic Resistance Genes Mediated by Integron.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {43}, pages = {19397-19407}, doi = {10.1021/acs.est.4c04925}, pmid = {39417646}, issn = {1520-5851}, mesh = {*Microalgae/drug effects ; *Sulfamethoxazole/pharmacology ; *Drug Resistance, Microbial/genetics ; *Bacteria/drug effects/genetics/metabolism ; Integrons ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The transmission of ARGs in the microalgae-associated epiphytic bacteria remains unclear under antibiotic exposure, apart from altering the microbial community structure. In this study, Chlorella vulgaris cocultured with bacteria screened from surface water was examined to explore the spread of ARGs in the presence of sulfamethoxazole (SMX). The extracellular polymers released by Chlorella vulgaris could reduce antibiotic-induced collateral damage to bacteria, thus increasing the diversity of the microalgae-associated epiphytic bacteria. The abundances of sul1 and intI1 in the phycosphere at 1 mg/L SMX dose increased by 290 and 28 times, respectively. Metagenomic sequencing further confirmed that SMX bioaccumulation stimulated the horizontal transfer of sul1 mediated by intI1 in the microalgae-associated epiphytic bacteria, while reactive oxygen species (ROS)-mediated oxidative stress induced the SOS response and thus enhanced the transformation of sul1 in the J group. This is the first study to verify that microalgae protect bacteria from antibiotic damage and hinder the spread of ARGs mediated by SOS response, while the transfer of ARGs mediated by integron is promoted due to the bioaccumulation of SMX in the phycosphere. The results contribute to present comprehensive understanding of the risk of ARG proliferation by the presence of emerging contaminants residues in river.}, }
@article {pmid39417302, year = {2024}, author = {Li, J and Fang, W and Li, C and Cui, M and Qian, L and Jiang, Z and Jiang, Y and Shi, L and Xie, X and Guo, H and Li, P and Dong, Y and Xiu, W and Wang, Y and Wang, Y}, title = {Dissimilatory Iodate-Reducing Microorganisms Contribute to the Enrichment of Iodine in Groundwater.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {43}, pages = {19255-19265}, doi = {10.1021/acs.est.4c04455}, pmid = {39417302}, issn = {1520-5851}, mesh = {*Groundwater/microbiology ; *Iodates/metabolism ; *Iodine/metabolism ; China ; }, abstract = {Iodate reduction by dissimilatory iodate-reducing microorganisms (DIRMs) plays a crucial role in the biogeochemical cycling of iodine on Earth. However, the occurrence and distribution of DIRMs in iodine-rich groundwater remain unclear. In this study, we isolated the dissimilatory iodate-reducing bacteriumAzonexus hydrophilusstrain NCP973 from a geogenic high-iodine groundwater of China for the first time. The analysis of genome, transcriptome, and heterologous expression revealed that strain NCP973 uses the dissimilatory iodate-reducing enzyme IdrABP1P2 to reduce dissolved or in situ sediment-bound iodate to iodide. The location of IdrABP1P2 in the conjugative plasmid of strain NCP973 implies that IdrABP1P2 could be spread by horizontal gene transfer and allow the recipient microorganisms to participate in the enrichment of iodide in aquifers. Based on the global iodine-rich groundwater metagenomes and genomes, the identification of idrA showed that phylogenetically diverse DIRMs are widely distributed not only in geogenic high-iodine groundwater of China but also in radionuclide-contaminated groundwater of USA as well as in subsurface cavern waters in Germany and Italy. Moreover, the abundance of idrA was found to be higher in groundwater with a relatively high iodine content. Collectively, these results suggest that terrestrial iodine-affected groundwater systems are another important habitat for DIRMs in addition to marine environments, and their activity in aquifers triggers the mobilization and enrichment of iodine in groundwater worldwide.}, }
@article {pmid39416196, year = {2024}, author = {Heredia, AG and Grossman, AD}, title = {Regulation of the SOS response and homologous recombination by an integrative and conjugative element.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39416196}, issn = {2692-8205}, support = {R35 GM122538/GM/NIGMS NIH HHS/United States ; R35 GM148343/GM/NIGMS NIH HHS/United States ; }, abstract = {Integrative and conjugative elements (ICEs) are mobile genetic elements that transfer between bacteria and influence host physiology and promote evolution. ICEBs1 of Bacillus subtilis modulates the host DNA damage response by reducing RecA filament formation. We found that the two ICEBs1-encoded proteins, RamT and RamA that modulate the SOS response in donors also function in recipient cells to inhibit both the SOS response and homologous recombination following transfer of the element. Expression of RamT and RamA caused a decrease in binding of the host single strand binding protein SsbA to ssDNA. We found that RamA interacted with PcrA, the host DNA translocase that functions to remove RecA from DNA, likely functioning to modulate the SOS response and recombination by stimulating PcrA activity. These findings reveal how ICEBs1 can modulate key host processes, including the SOS response and homologous recombination, highlighting the complex interplay between mobile genetic elements and their bacterial hosts in adaptation and evolution.}, }
@article {pmid39416164, year = {2024}, author = {McKeithen-Mead, S and Anderson, ME and García-Heredia, A and Grossman, AD}, title = {Activation and modulation of the host response to DNA damage by an integrative and conjugative element.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39416164}, issn = {2692-8205}, support = {R01 GM050895/GM/NIGMS NIH HHS/United States ; R35 GM122538/GM/NIGMS NIH HHS/United States ; R35 GM148343/GM/NIGMS NIH HHS/United States ; T32 GM007287/GM/NIGMS NIH HHS/United States ; }, abstract = {Mobile genetic elements help drive horizontal gene transfer and bacterial evolution. Conjugative elements and temperate bacteriophages can be stably maintained in host cells. They can alter host physiology and regulatory responses and typically carry genes that are beneficial to their hosts. We found that ICEBs1, an integrative and conjugative element of Bacillus subtilis, inhibits the host response to DNA damage (the SOS response). Activation of ICEBs1 before DNA damage reduced host cell lysis that was caused by SOS-mediated activation of two resident prophages. Further, activation of ICEBs1 itself activated the SOS response in a subpopulation of cells, and this activation was attenuated by the functions of the ICEBs1 genes ydcT and yddA (now ramT and ramA, for RecA modulator). Double mutant analyses indicated that RamA functions to inhibit and RamT functions to both inhibit and activate the SOS response. Both RamT and RamA caused a reduction in RecA filaments, one of the early steps in activation of the SOS response. We suspect that there are several different mechanisms by which mobile genetic elements that generate ssDNA during their lifecycle inhibit the host SOS response and RecA function, as RamT and RamA differ from the known SOS inhibitors encoded by conjugative elements.}, }
@article {pmid39415115, year = {2024}, author = {Bao, D and Chen, L and Shen, W and Xu, X and Zhu, L and Wang, Y and Wu, Y and He, X and Zhu, F and Li, H}, title = {Genomic epidemiology of ceftriaxone-resistant non-typhoidal Salmonella enterica strain in China.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {974}, pmid = {39415115}, issn = {1471-2164}, support = {LQ24H200003//Zhejiang Provincial Natural Science Foundation of China/ ; 2023KY414//Zhejiang Provincial Medical and Health Science and Technology Plan/ ; 2024KY1441//Zhejiang Provincial Medical and Health Science and Technology Plan/ ; }, mesh = {*Ceftriaxone/pharmacology ; China/epidemiology ; *Salmonella enterica/genetics/drug effects ; Humans ; *Salmonella Infections/microbiology/epidemiology/drug therapy ; *Plasmids/genetics ; *Anti-Bacterial Agents/pharmacology ; *Phylogeny ; Drug Resistance, Multiple, Bacterial/genetics ; Multilocus Sequence Typing ; Microbial Sensitivity Tests ; Molecular Epidemiology ; }, abstract = {Non-typhoidal Salmonella (NTS) is one of the top causes of diarrhea worldwide. Ceftriaxone is commonly recommended as the initial treatment option for Salmonella infections due to its antibacterial effectiveness. The objective of this study was to investigate the molecular epidemiological characteristics of NTS and to compare the phenotypic and genotypic profiles of antimicrobial resistance in multidrug-resistant Salmonella strains by sequencing 329 NTS strains collected from a county-level hospital between 2018 and 2021. Multi-locus sequence typing (MLST), antimicrobial resistance genes and plasmid types were identified by BacWGSTdb 2.0 webserver. Phylogenetic analysis of all NTS strains was carried out using Snippy and Gubbins software. The transferability of ceftriaxone resistant plasmids was confirmed through plasmid conjugation assays, and verified by S1-PFGE-Southern blot assays. The predominant serotypes among all NTS strains were Typhimurium (161/329), Enteritidis (49/329) and London (45/329). The most common sequence type observed was ST34 (86/329), followed by ST19 (72/329) and ST11 (47/329). The antimicrobial resistance of Salmonella to a wide range of antimicrobials showed an overall increase. Out of these 37 (11.24%) ceftriaxone-resistant strains, with the majority of them (33/37) being blaCTX-M. The predominant plasmid types identified were IncHI2 (14/21) and IncI1 (6/21), ranging in size from 70 kb to 360 kb. The conjugation efficiency was calculated with the high conjugation efficiency of 1.1 × 10[- 5] to 9.3 × 10[- 2]. The strains varied widely, ranging from 3 to 45,024 single nucleotide polymorphisms (SNPs). There are close linkages observed among the predominant lineage, with an average of 78 SNPs between each pair of ST34 strains. The findings contribute to our understanding of the transmission and resistance mechanisms of multidrug-resistant Salmonella, thereby facilitating the development of effective control strategies.}, }
@article {pmid39414627, year = {2024}, author = {Aggarwal, T and Kondabagil, K}, title = {Proteome-scale structural prediction of the giant Marseillevirus reveals conserved folds and putative homologs of the hypothetical proteins.}, journal = {Archives of virology}, volume = {169}, number = {11}, pages = {222}, pmid = {39414627}, issn = {1432-8798}, support = {CRG/2023/00131//Science and Engineering Research Board/ ; 58/14/11/2020-BRNS/37188//Board of Research in Nuclear Sciences/ ; BT/PR35928/BRB/10/1979/2021//Department of Biotechnology, Ministry of Science and Technology, India/ ; }, mesh = {*Proteome ; *Viral Proteins/genetics/chemistry ; *Genome, Viral/genetics ; Protein Folding ; Amino Acid Sequence ; Computational Biology/methods ; Giant Viruses/genetics/classification/chemistry ; Protein Conformation ; }, abstract = {A significant proportion of the highly divergent and novel proteins of giant viruses are termed "hypothetical" due to the absence of detectable homologous sequences in the existing databases. The quality of genome and proteome annotations often relies on the identification of signature sequences and motifs in order to assign putative functions to the gene products. These annotations serve as the first set of information for researchers to develop workable hypotheses for further experimental research. The structure-function relationship of proteins suggests that proteins with similar functions may also exhibit similar folding patterns. Here, we report the first proteome-wide structure prediction of the giant Marseillevirus. We use AlphaFold-predicted structures and their comparative analysis with the experimental structures in the PDB database to preliminarily annotate the viral proteins. Our work highlights the conservation of structural folds in proteins with highly divergent sequences and reveals potentially paralogous relationships among them. We also provide evidence for gene duplication and fusion as contributing factors to giant viral genome expansion and evolution. With the easily accessible AlphaFold and other advanced bioinformatics tools for high-confidence de novo structure prediction, we propose a combined sequence and predicted-structure-based proteome annotation approach for the initial characterization of novel and complex organisms or viruses.}, }
@article {pmid39414103, year = {2024}, author = {Zhao, W and Ye, C and Li, J and Yu, X}, title = {Increased risk of antibiotic resistance in surface water due to global warming.}, journal = {Environmental research}, volume = {263}, number = {Pt 2}, pages = {120149}, doi = {10.1016/j.envres.2024.120149}, pmid = {39414103}, issn = {1096-0953}, mesh = {*Global Warming ; Water Microbiology ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; Drug Resistance, Microbial/genetics ; }, abstract = {As the pace of global warming accelerates, so do the threats to human health, urgent priority among them being antibiotic-resistant infections. In the context of global warming, this review summarises the direct and indirect effects of rising surface water temperatures on the development of bacterial antibiotic resistance. First, the resistance of typical pathogens such as E. coli increased with average temperature. This is not only related to increased bacterial growth rate and horizontal gene transfer frequency at high temperatures but also heat shock responses and cumulative effects. Secondly, the acceleration of bacterial growth indirectly promotes antibiotic residues in surface water, which is conducive to the growth and spread of resistant bacteria. Furthermore, the cascading effects of global warming, including the release of nutrients into the water and the resulting increase of bacteria and algae, indirectly promote the improvement of resistance. Water treatment processes exposed to high temperatures also increase the risk of resistance in surface water. The fitness costs of antibiotic resistance under these dynamic conditions are also discussed, concluding the relationship between various factors and resistance persistence. It was expected to provide a comprehensive basis for mitigating antibiotic resistance in the face of global warming.}, }
@article {pmid39412865, year = {2024}, author = {Bartlett, KV and Luo, TL and Ong, AC and Maybank, RA and Stribling, W and Thompson, B and Powell, A and Kwak, YI and Bennett, JW and Lebreton, F and Mc Gann, PT}, title = {Tn4661-mediated transfer of bla CTX-M-15 from Klebsiella michiganensis to an outbreak clone of Pseudomonas aeruginosa.}, journal = {Microbial genomics}, volume = {10}, number = {10}, pages = {}, pmid = {39412865}, issn = {2057-5858}, mesh = {*beta-Lactamases/genetics ; *Pseudomonas aeruginosa/genetics/drug effects/isolation &amp; purification ; Humans ; *Disease Outbreaks ; *Plasmids/genetics ; *Pseudomonas Infections/microbiology/epidemiology ; Klebsiella/genetics/isolation &amp; purification/drug effects ; DNA Transposable Elements ; Gene Transfer, Horizontal ; }, abstract = {Carriage of CTX-M-type extended-spectrum β-lactamase (ESBL) is rare in Pseudomonas aeruginosa. During routine surveillance of an endemic ST-621 P. aeruginosa at a large hospital, isolate MRSN 100690 carrying bla CTX-M-15 was cultured from a patient (P2). This was the first detection of this ESBL in the endemic ST-621 lineage. All 1 488 bacterial isolates collected from the same facility in the 12 months prior to the incidence of 100 690 were screened for the presence of bla CTX-M-15. A set of 183 isolates was identified, in which corresponding patient metadata was evaluated for spatiotemporal overlaps with P2. The resulting three isolates, along with 100 690, were long-read sequenced using the Oxford Nanopore MinION platform to determine a potential donor of bla CTX-M-15. The screen revealed a single Klebsiella michiganensis isolate, MRSN 895358, which carried an IncA/C2 plasmid harbouring bla CTX-M-15. Notably, the patient harbouring 895358, P1, occupied the same hospital room as P2 9 months prior. Genomic alignment revealed that both isolates shared an identical 80.8 kb region containing the IncA/C2 plasmid replicon and bla CTX-M-15. This region was plasmid bound in 895 358, but chromosomally bound in 100 690 due to Tn4661-mediated transposition. ESBL bla CTX-M-15 was acquired and subsequently integrated into the chromosome of a ST-621 P. aeruginosa, likely initiated by plasmid transfer from a K. michiganensis strain.}, }
@article {pmid39411937, year = {2024}, author = {Sekar, G and Bahot, A and Bansode, M and Phadnis, A and Sarode, SC and Sharma, NK}, title = {Potentiation of Tumor Hallmarks by the Loss of GULO, a Vitamin C Biosynthesis Gene in Humans.}, journal = {Current molecular medicine}, volume = {}, number = {}, pages = {}, doi = {10.2174/0115665240328074241003110326}, pmid = {39411937}, issn = {1875-5666}, abstract = {Vitamin C plays a significant role in various physiological functions. Humans depend on external sources of vitamin C due to the loss of the L-gulono-γ-lactone oxidase (GULO) gene that contributes to the synthesis of vitamin C. During the evolutionary loss of the GULO gene, physical, chemical, and biological factors were different from the present environmental settings. Besides the evolutionary genetic loss of the GULO gene, there is a gap in the insightful discussion on the potential implications of the non-functional GULO gene towards the predisposition of humans to cancer that faces hostile and carcinogenic environments. Various methods by which vitamin C modulates cellular processes related to cancer, including DNA repair, epigenetic changes, and redox balance, are discussed. Furthermore, we present experimental and clinical evidence indicating that vitamin C deficiency promotes tumor growth, metastasis, and therapy resistance, emphasizing its potential as a cancer phenotypic modulator. Therapeutic implications of restoring vitamin C levels in cancer treatment range from improving the efficacy of conventional medicines to exploiting metabolic vulnerabilities in tumors. The relevance of assessing vitamin C status in cancer patients and the basis for additional research into vitamin C supplementation as an adjuvant therapy is emphasized. This paper presents a comprehensive overview of the implications associated with the functional deficiency of the GULO gene in human subjects exhibiting diverse tumor hallmarks, encompassing ECM remodeling, hypoxia, epigenetic reprogramming, oxidative stress, and drug responsiveness.}, }
@article {pmid39411151, year = {2024}, author = {Meza-Padilla, I and McConkey, BJ and Nissimov, JI}, title = {Structural models predict a significantly higher binding affinity between the NblA protein of cyanophage Ma-LMM01 and the phycocyanin of Microcystis aeruginosa NIES-298 compared to the host homolog.}, journal = {Virus evolution}, volume = {10}, number = {1}, pages = {veae082}, pmid = {39411151}, issn = {2057-1577}, abstract = {Horizontal gene transfer events between viruses and hosts are widespread across the virosphere. In cyanophage-host systems, such events often involve the transfer of genes involved in photosynthetic processes. The genome of the lytic cyanophage Ma-LMM01 infecting the toxic, bloom-forming, freshwater Microcystis aeruginosa NIES-298 contains a homolog of the non-bleaching A (nblA) gene, which was probably transferred from a cyanobacterial host. The function of the NblA protein is to disassemble phycobilisomes, cyanobacterial light-harvesting complexes that can comprise up to half of the cellular soluble protein content. NblA thus plays an essential dual role in cyanobacteria: it protects the cell from high-light intensities and increases the intracellular nitrogen pool under nutrient limitation. NblA has previously been shown to interact with phycocyanin, one of the main components of phycobilisomes. Using structural modeling and protein-protein docking, we show that the NblA dimer of Ma-LMM01 is predicted to have a significantly higher binding affinity for M. aeruginosa NIES-298 phycocyanin (αβ)6 hexamers, compared to the host homolog. Protein-protein docking suggests that the viral NblA structural model is able to bind deeper into the phycocyanin groove. The main structural difference between the virus and host NblA appears to be an additional α-helix near the N-terminus of the viral NblA, which interacts with the inside of the phycocyanin groove and could thus be considered partly responsible for this deeper binding. Interestingly, phylogenetic analyses indicate that this longer nblA was probably acquired from a different Microcystis host. Based on infection experiments and previous findings, we propose that a higher binding affinity of the viral NblA to the host phycocyanin may represent a selective advantage for the virus, whose infection cycle requires an increased phycobilisome degradation rate that is not fulfilled by the NblA of the host.}, }
@article {pmid39405618, year = {2025}, author = {Tan, Y and Yu, P and Yu, Z and Xuan, F and Zhu, L}, title = {Deciphering defense system modulating bacteria-mobile genetic elements symbiosis in microbial aggregates under elevated hydraulic stress.}, journal = {Water research}, volume = {268}, number = {Pt A}, pages = {122590}, doi = {10.1016/j.watres.2024.122590}, pmid = {39405618}, issn = {1879-2448}, mesh = {*Bacteria/genetics ; *Symbiosis ; Bioreactors ; Interspersed Repetitive Sequences ; Sewage/microbiology ; Biofilms ; Gene Transfer, Horizontal ; Plasmids/genetics ; }, abstract = {Bacterial defense systems are under strong evolutionary pressures to defend against mobile genetic elements (MGEs), yet their distribution in microbial aggregates in engineered systems remains largely unexplored. Herein, we investigated the bacterial defensome and MGEs within activated sludge flocs (AS) and membrane-attached biofilm (MF) in a full-scale membrane bioreactor. Similar distribution pattern of bacterial defense systems (63 types) was observed in prokaryotic genome in AS and MF, including RM system (∼40 %), Cas system (∼18 %) and TA-Abi system (∼28 %), exhibiting a dependency on the genome size and bacterial taxonomy in microbial aggregates under elevated hydraulic stress (MF). In contrast to plasmid and provirus, which carried defense systems (22 types) similar to their associated hosts, virome (61 %) carried novel defense systems (40 types) absent in their associated hosts. With 54 % of which involved in MGEs geneflow network, 69 % of high quality bacterial genome bins were associated with horizontal gene transfer (HGT), facilitating the exchange of mobile core functional genes. This potentially conferred competitive advantages to hosts through habitat-specific payload genes related to biotic defense, antibiotic resistance, and nitrogen metabolism. The longer growth cycle and varied defense gene density suggested the potential defense redundancy and trade-off of metabolic expense and immunity in bacterial host-MGE symbionts. Furthermore, enhanced cooperative network modules of cross-feeding and defense were observed in the MF, potentially helped the symbiotic microbial communities in coping with hostile conditions under elevated hydraulic stress. These findings shed light on the dynamics of bacterial defense systems in host-MGE coevolution and provide new perspectives of microbial aggregates manipulation for ecological and engineering application.}, }
@article {pmid39404847, year = {2024}, author = {Bethke, JH and Kimbrel, J and Jiao, Y and Ricci, D}, title = {Toxin-Antitoxin Systems Reflect Community Interactions Through Horizontal Gene Transfer.}, journal = {Molecular biology and evolution}, volume = {41}, number = {10}, pages = {}, pmid = {39404847}, issn = {1537-1719}, mesh = {*Gene Transfer, Horizontal ; *Toxin-Antitoxin Systems/genetics ; *Plasmids/genetics ; Bacteria/genetics ; }, abstract = {Bacterial evolution through horizontal gene transfer (HGT) reflects their community interactions. In this way, HGT networks do well at mapping community interactions, but offer little toward controlling them-an important step in the translation of synthetic strains into natural contexts. Toxin-antitoxin (TA) systems serve as ubiquitous and diverse agents of selection; however, their utility is limited by their erratic distribution in hosts. Here we examine the heterogeneous distribution of TAs as a consequence of their mobility. By systematically mapping TA systems across a 10,000 plasmid network, we find HGT communities have unique and predictable TA signatures. We propose these TA signatures arise from plasmid competition and have further potential to signal the degree to which plasmids, hosts, and phage interact. To emphasize these relationships, we construct an HGT network based solely on TA similarity, framing specific selection markers in the broader context of bacterial communities. This work both clarifies the evolution of TA systems and unlocks a common framework for manipulating community interactions through TA compatibility.}, }
@article {pmid39404832, year = {2024}, author = {Díaz-Martínez, C and Bolívar, A and Mercanoglu Taban, B and Kanca, N and Pérez-Rodríguez, F}, title = {Exploring the antibiotic resistance of Listeria monocytogenes in food environments - a review.}, journal = {Critical reviews in microbiology}, volume = {}, number = {}, pages = {1-24}, doi = {10.1080/1040841X.2024.2412007}, pmid = {39404832}, issn = {1549-7828}, abstract = {Listeria monocytogenes, a resilient bacterium in diverse food conditions, such as refrigeration, reduced water activity and low pH, poses a significant threat to the food industry and public health. In recent years, it has been documented an increase in the antibiotic resistance of zoonotic pathogens, including L. monocytogenes. This review provides new insight into the molecular mechanisms involved in both intrinsic and acquired antibiotic resistance of L. monocytogenes with an emphasis on the effect of different environmental and food-related factors. It also explores the relationship of these resistance mechanisms with virulence factors. An analysis of literature data (2009-2021) was conducted to investigate statistically and graphically potential associations between specific antibiotic resistance patterns in the pathogen and food categories using an unbiased variance analysis. The results evidenced that food type had an influence on the antibiotic resistance profiles of L. monocytogenes, with meat and vegetables being the food categories exhibiting the most prevalent profiles. The frequent detection of resistance to ampicillin, penicillin, and tetracycline (non-intrinsic resistances) indicates that specific processing conditions along the food chain may induce them. Many questions remain about the impact of food chain factors (e.g. thermal treatments, cold chain, preservatives, etc.) and food type (low pH, reduced water activity, etc.) on the antibiotic resistance patterns of the pathogen, particularly concerning food-related sources, the resistance mechanisms involved (e.g. cross-protection, horizontal gene transfer, etc.), and the evolutionary processes of antibiotic-resistant microbial populations. Metagenomics, in addition to other -omics technologies (metabolomics and transcriptomics), allows a better understanding of the processes involved in the acquisition of resistance.}, }
@article {pmid39402773, year = {2025}, author = {Dunmyre, A and Vinayamohan, P and Locke, SR and Cheng, TY and Schaffner, V and Habing, G}, title = {Characterisation of Antimicrobial Resistance in Special-Fed Veal Production Environments.}, journal = {Zoonoses and public health}, volume = {72}, number = {1}, pages = {75-83}, pmid = {39402773}, issn = {1863-2378}, support = {//U.S. Department of Agriculture/ ; 018- 68003-27466//National Institute of Food and Agriculture/ ; //USDA National Institute of Food and Agriculture/ ; //Agricultural and Food Research Initiative Competitive Program/ ; 2018-68003-27466//Agriculture Economics and Rural Communities/ ; }, mesh = {Animals ; *Escherichia coli/drug effects ; Cattle ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial ; Animal Husbandry ; Abattoirs ; Escherichia coli Infections/veterinary/microbiology/epidemiology ; Drug Resistance, Multiple, Bacterial ; }, abstract = {INTRODUCTION: Antimicrobial resistance (AMR) is one of the leading public health threats globally. AMR genes can be transferred between bacteria through lateral gene transfer, and AMR organisms can spread through environments by contaminated water, agriculture and animals. Thus, widespread environmental dissemination of bacteria and lateral gene transfer facilitate AMR transmission pathways. Farm environments in dairy and calf production are known to harbour AMR bacteria that pose a risk for food contamination and to workers in direct or indirect contact with animals. Escherichia coli is present in farm environments and is known to participate in lateral gene transfer, providing a good marker of resistance genes in each environment.<br><br>METHODS: In this study, E. coli from nine cohorts of calves was isolated at different time points from nine barns, nine trailers and one slaughterhouse environment in a single special-fed veal calf production facility. The antimicrobial susceptibility to 15 antimicrobials, classified as highly or critically important by the World Health Organization, was characterised for E. coli isolates using Kirby-Bauer disk diffusion.<br><br>RESULTS: The highest proportion of isolates showing multidrug resistance was present in barn environments (51.7%), where calves were housed from their arrival at <&#x2009;2&#x2009;weeks of age until they were transported to slaughter. Additionally, 15 E. coli isolates were resistant to 11 of the 15 antimicrobials tested. Trailer and slaughterhouse environments had greater prevalence of resistance after accommodating calves, including resistance to third-generation cephalosporins.<br><br>CONCLUSION: These data highlight the importance of calf environments in the dissemination of resistant bacteria and gives insight into where interventions could be most effective in combatting antimicrobial-resistant bacteria that could infect humans and livestock.}, }
@article {pmid39401218, year = {2024}, author = {Mazzamurro, F and Chirakadavil, JB and Durieux, I and Poiré, L and Plantade, J and Ginevra, C and Jarraud, S and Wilharm, G and Charpentier, X and P C Rocha, E}, title = {Intragenomic conflicts with plasmids and chromosomal mobile genetic elements drive the evolution of natural transformation within species.}, journal = {PLoS biology}, volume = {22}, number = {10}, pages = {e3002814}, pmid = {39401218}, issn = {1545-7885}, mesh = {*Plasmids/genetics ; *Interspersed Repetitive Sequences/genetics ; *Legionella pneumophila/genetics ; Humans ; Acinetobacter baumannii/genetics ; Phylogeny ; Evolution, Molecular ; Chromosomes, Bacterial/genetics ; Transformation, Bacterial ; Gene Transfer, Horizontal ; }, abstract = {Natural transformation is the only mechanism of genetic exchange controlled by the recipient bacteria. We quantified its rates in 786 clinical strains of the human pathogens Legionella pneumophila (Lp) and 496 clinical and environmental strains of Acinetobacter baumannii (Ab). The analysis of transformation rates in the light of phylogeny revealed they evolve by a mixture of frequent small changes and a few large quick jumps across 6 orders of magnitude. In standard conditions close to half of the strains of Lp and a more than a third in Ab are below the detection limit and thus presumably non-transformable. Ab environmental strains tend to have higher transformation rates than the clinical ones. Transitions to non-transformability were frequent and usually recent, suggesting that they are deleterious and subsequently purged by natural selection. Accordingly, we find that transformation decreases genetic linkage in both species, which might accelerate adaptation. Intragenomic conflicts with chromosomal mobile genetic elements (MGEs) and plasmids could explain these transitions and a GWAS confirmed systematic negative associations between transformation and MGEs: plasmids and other conjugative elements in Lp, prophages in Ab, and transposable elements in both. In accordance with the hypothesis of modulation of transformation rates by genetic conflicts, transformable strains have fewer MGEs in both species and some MGEs inactivate genes implicated in the transformation with heterologous DNA (in Ab). Innate defense systems against MGEs are associated with lower transformation rates, especially restriction-modification systems. In contrast, CRISPR-Cas systems are associated with higher transformation rates suggesting that adaptive defense systems may facilitate cell protection from MGEs while preserving genetic exchanges by natural transformation. Ab and Lp have different lifestyles, gene repertoires, and population structure. Nevertheless, they exhibit similar trends in terms of variation of transformation rates and its determinants, suggesting that genetic conflicts could drive the evolution of natural transformation in many bacteria.}, }
@article {pmid39395971, year = {2024}, author = {Li, Z and Ran, Z and Xiao, X and Yan, C and Xu, J and Tang, M and An, M}, title = {Comparative analysis of the whole mitochondrial genomes of four species in sect. Chrysantha (Camellia L.), endemic taxa in China.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {955}, pmid = {39395971}, issn = {1471-2229}, support = {2022&#xff08;072&#xff09;//Guizhou Provincial Basic Research Program (Natural Science)/ ; 32360101//National Natural Science Foundation of China/ ; 31960043//National Natural Science Foundation of China/ ; }, mesh = {*Genome, Mitochondrial ; China ; *Camellia/genetics ; Phylogeny ; RNA Editing ; Genome, Plant ; Base Composition ; }, abstract = {BACKGROUND: The sect. Chrysantha Chang of plants with yellow flowers of Camellia species as the "Queen of the Tea Family", most of these species are narrowly distributed endemics of China and are currently listed Grde-II in National Key Protected Wild Plant of China. They are commercially important plants with horticultural medicinal and scientific research value. However, the study of the sect. Chrysantha species genetics are still in its infancy, to date, the mitochondrial genome in sect. Chrysantha has been still unexplored.<br><br>RESULTS: In this study, we provide a comprehensive assembly and annotation of the mitochondrial genomes for four species within the sect. Chrysantha. The results showed that the mitochondrial genomes were composed of closed-loop DNA molecules with sizes ranging from 850,836&#xa0;bp (C. nitidissima) to 1,098,121&#xa0;bp (C. tianeensis) with GC content of 45.71-45.78% and contained 48-58 genes, including 28-37 protein-coding genes, 17-20 tRNA genes and 2 rRNA genes. We also examined codon usage, sequence repeats, RNA editing and selective pressure in the four species. Then, we performed a comprehensive comparison of their basic structures, GC contents, codon preferences, repetitive sequences, RNA editing sites, Ka/Ks ratios, haplotypes, and RNA editing sites. The results showed that these plants differ little in gene type and number. C. nitidissima has the greatest variety of genes, while C. tianeensis has the greatest loss of genes. The Ka/Ks values of the atp6 gene in all four plants were greater than 1, indicating positive selection. And the codons ending in A and T were highly used. In addition, the RNA editing sites differed greatly in number, type, location, and efficiency. Twelve, six, five, and twelve horizontal gene transfer (HGT) fragments were found in C. tianeensis, Camellia huana, Camellia liberofilamenta, and C. nitidissima, respectively. The phylogenetic tree clusters the four species of sect. Chrysantha plants into one group, and C. huana and C. liberofilamenta have closer affinities.<br><br>CONCLUSIONS: In this study, the mitochondrial genomes of four sect. Chrysantha plants were assembled and annotated, and these results contribute to the development of new genetic markers, DNA barcode databases, genetic improvement and breeding, and provide important references for scientific research, population genetics, and kinship identification of sect. Chrysantha plants.}, }
@article {pmid39395498, year = {2024}, author = {Hou, H and Zou, D and Shi, W and Wang, Y and Ma, D and Wang, Y and Li, Q and Gao, Y and Gao, B}, title = {Localized heating coupling with radical oxidation eliminating antibiotic resistance genes (ARGs) in interfacial photothermal Fenton-like disinfection process.}, journal = {The Science of the total environment}, volume = {955}, number = {}, pages = {176779}, doi = {10.1016/j.scitotenv.2024.176779}, pmid = {39395498}, issn = {1879-1026}, mesh = {*Disinfection/methods ; *Hydrogen Peroxide/chemistry ; *Oxidation-Reduction ; *Drug Resistance, Microbial/genetics ; Escherichia coli/drug effects ; Iron/chemistry ; Anti-Bacterial Agents/pharmacology/chemistry ; Reactive Oxygen Species/metabolism ; }, abstract = {Conventional oxidative disinfection processes are inefficient in eliminating intracellular antibiotic resistance genes (iARGs) due to the barrier of the cell membrane and the competitive reaction of cellular constituents within antibiotic-resistant bacteria (ARB), resulting in the widespread prevalence of ARGs in recycled water. This study presented the first application of localized heating coupling with advanced oxidation to destroy the resistant Escherichia coli cells and improved subsequent iARGs (blaTEM-1) degradation in a novel photothermal Fenton-like disinfection process. The Fe-Mn@CNT microfiltration membrane, comprising carbon nanotubes wrapped with Fe and Mn nanoparticles (Fe-Mn@CNT), was employed as a nanomaterial for photothermal conversion and H2O2 activation. The highly efficient absorption of full-spectrum photons by CNTs enabled the Fe-Mn@CNT membrane to concentrate light to generate localized intense heat, resulting in the destruction of ARB nearby, and the subsequent release of iARGs. Interfacial heat favored Fe-Mn-induced H2O2 activation, leading to the production of more ·OH, which in turn promoted the oxidation for ARG degradation and ARB cell damage. The results of the acetylcysteine quenching experiments indicated that interfacial heating and radical oxidation-induced accumulation of intracellular reactive oxygen species contributed to the elimination of about 1-log iARGs through direct attack. The integrity of the cell membrane, the morphology of ARB and the variation of i/e ARG copy numbers were observed to reveal that the introduction of interfacial heating aggravated the cell lysis and accelerated the iARGs release, resulting in the inactivation of 7.27-log ARB and the elimination of 4.64-log iARGs and 2.23-log eARGs. Localized heating coupling with ·OH oxidation achieved a 143 % increase in iARGs removal compared to the conventional Fenton-like oxidation. The interfacial photothermal Fenton-like disinfection process exhibited remarkable material stability, robust disinfection performance, and effective suppression of horizontal gene transfer, underscoring its immense potential to mitigate the risk of ARG dissemination in reclaimed water systems.}, }
@article {pmid39387591, year = {2024}, author = {Zhang, M and Yin, Z and Chen, B and Yu, Z and Liang, J and Tian, X and Li, D and Deng, X and Peng, L}, title = {Investigation of Citrobacter freundii clinical isolates in a Chinese hospital during 2020-2022 revealed genomic characterization of an extremely drug-resistant C. freundii ST257 clinical strain GMU8049 co-carrying blaNDM-1 and a novel blaCMY variant.}, journal = {Microbiology spectrum}, volume = {12}, number = {11}, pages = {e0425423}, pmid = {39387591}, issn = {2165-0497}, support = {2023A1515220222//the Guangdong Basic and Applied Basic Research Foundation: Provincal-Enterprise Joint Fund/ ; 2024SRP134//Research Ability Enhancement Program of Guangzhou Medical University/ ; 2022A1515012504//the National Science Foundation of Guangdong Province/ ; }, mesh = {*Citrobacter freundii/genetics/drug effects/isolation &amp; purification/enzymology ; *beta-Lactamases/genetics ; Humans ; *Drug Resistance, Multiple, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; *Microbial Sensitivity Tests ; China ; *Plasmids/genetics ; *Whole Genome Sequencing ; *Enterobacteriaceae Infections/microbiology ; Genome, Bacterial/genetics ; Genomics ; Hospitals ; Azabicyclo Compounds/pharmacology ; Bacterial Proteins/genetics/metabolism ; Ceftazidime/pharmacology ; }, abstract = {The emergence of multidrug-resistant Citrobacter freundii poses a significant threat to public health. C. freundii isolates were collected from clinical patients in a Chinese hospital during 2020-2022. An unusual strain, GMU8049, was not susceptible to any of the antibiotics tested, including the novel β-lactam/β-lactamase inhibitor combination ceftazidime-avibactam. Whole-genome sequencing (WGS) revealed that GMU8049 harbors a circular chromosome belonging to the rare ST257 and an IncX3 resistance plasmid. Genomic analysis revealed the coexistence of two β-lactamase genes, including plasmid-mediated blaNDM-1 and chromosomal blaCMY encoding a novel CMY variant, combined with an outer membrane porin deficiency, which may account for the extreme resistance to β-lactams. Conjugation experiment confirmed that the blaNDM-1 resistance gene located on pGMU8049 could be successfully transferred to Escherichia coli EC600. The novel CMY variant had an amino acid substitution at position 106 (N106S) compared to the closely related CMY-51. Additionally, a GMU8049-specific truncation in an OmpK37 variant that produces a premature stop codon. Moreover, a variety of chromosome-located efflux pump coding genes and virulence-related genes were also identified. Analysis of strain GMU8049 in the context of other C. freundii strains reveals an open pan-genome and the presence of mobile genetic elements that can mediate horizontal gene transfer of antimicrobial resistance and virulence genes. Our work provides comprehensive insights into the genetic mechanisms of highly resistant C. freundii, highlighting the importance of genomic surveillance of this opportunistic pathogen as a high-risk population for emerging resistance and pathogenicity.IMPORTANCEEmerging pathogens exhibiting multi-, extremely, and pan-drug resistance are a major concern for hospitalized patients and the healthcare community due to limited antimicrobial treatment options and the potential for spread. Genomic technologies have enabled clinical surveillance of emerging pathogens and modeling of the evolution and transmission of antimicrobial resistance and virulence. Here, we report the genomic characterization of an extremely drug-resistant ST257 Citrobacter freundii clinical isolate. Genomic analysis of GMU8049 with a rare ST type and unusual phenotypes can provide information on how this extremely resistant clinical isolate has evolved, including the acquisition of blaNDM-1 via the IncX3 plasmid and accumulation through chromosomal mutations leading to a novel CMY variant and deficiency of the outer membrane porin OmpK37. Our work highlights that the emergence of extremely resistant C. freundii poses a significant challenge to the treatment of clinical infections. Therefore, great efforts must be made to specifically monitor this opportunistic pathogen.}, }
@article {pmid39394251, year = {2024}, author = {Hossain, M and Aslan, B and Hatoum-Aslan, A}, title = {Tandem mobilization of anti-phage defenses alongside SCCmec elements in staphylococci.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {8820}, pmid = {39394251}, issn = {2041-1723}, support = {R01 AI173022/AI/NIAID NIH HHS/United States ; R01AI 173022-01//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; 1020298//Burroughs Wellcome Fund (BWF)/ ; }, mesh = {*Genomic Islands/genetics ; Staphylococcus/genetics ; Recombinases/metabolism/genetics ; Methicillin Resistance/genetics ; Staphylococcus Phages/genetics ; Gene Transfer, Horizontal ; Methicillin-Resistant Staphylococcus aureus/genetics ; Bacteriophages/genetics/physiology ; Chromosomes, Bacterial/genetics ; }, abstract = {Recent research has identified multiple immune systems that bacteria use to protect themselves from viral infections. However, little is known about the mechanisms by which these systems horizontally spread, especially among bacterial pathogens. Here, we investigate antiviral defenses in staphylococci, opportunistic pathogens that constitute leading causes of antibiotic-resistant infections. We show that these organisms harbor a variety of anti-phage defenses encoded within or near SCC (staphylococcal cassette chromosome) mec cassettes, mobile genomic islands that confer methicillin resistance. Importantly, we demonstrate that SCCmec-encoded recombinases mobilize not only SCCmec, but also tandem SCC-like cassettes enriched in genes coding for diverse defense systems. Further, we show that phage infection stimulates cassette mobilization (i.e. excision and circularization). Thus, our findings indicate that SCC/SCCmec cassettes not only spread antibiotic resistance but can also play a role in mobilizing anti-phage defenses.}, }
@article {pmid39394195, year = {2024}, author = {Chu, J and Choi, J and Ji, SK and Park, C and Jung, SH and Park, SH and Lee, DG}, title = {An outbreak of blaKPC-4- and blaVIM-1-producing Klebsiella pneumoniae and Klebsiella variicola at a single hospital in South Korea.}, journal = {Antimicrobial resistance and infection control}, volume = {13}, number = {1}, pages = {123}, pmid = {39394195}, issn = {2047-2994}, support = {HI22C0226//Korea Health Industry Development Institute/Republic of Korea ; 2021R1A2C1009867//National Research Foundation of Korea/ ; }, mesh = {Humans ; *beta-Lactamases/genetics/metabolism ; *Disease Outbreaks ; *Klebsiella pneumoniae/genetics/isolation &amp; purification ; Republic of Korea/epidemiology ; *Klebsiella Infections/epidemiology/microbiology/transmission ; *Klebsiella/genetics ; *Plasmids/genetics ; Cross Infection/microbiology/epidemiology ; Bacterial Proteins/genetics/metabolism ; Hospitals ; Whole Genome Sequencing ; Gene Transfer, Horizontal ; Female ; Anti-Bacterial Agents/pharmacology ; Male ; }, abstract = {BACKGROUND: The dissemination of Klebsiella spp. producing multiple carbapenemases has been increasingly recognized. Between July 2019 and August 2021, ten patients were found to carry Klebsiella spp. co-harboring blaKPC-4 and blaVIM-1 across multiple wards at a Korean hospital, and one isolate was recovered from a hand-washing sink, more than a year after the outbreak. This study aimed to investigate the outbreak and conduct a genomic study of these isolates.<br><br>METHODS: Whole-genome sequencing, including long-read sequencing, was performed to analyze plasmid structures and mobile genetic elements (MGEs). Bioinformatics analyses were performed to trace clonal transmission chains and horizontal gene transfer.<br><br>RESULTS: The findings suggested that the inter-ward spread of Klebsiella spp. seemed to be facilitated by healthcare worker contact or patient movement. Of the nine isolates collected (eight clinical and one environmental), seven (including the environmental isolate) were identified as K. pneumoniae (ST3680) and two were K. variicola (single-locus variant of ST5252). These isolates showed high genetic relatedness within their species and harbored the IncHI5B plasmid carrying both blaKPC-4 and blaVIM-1 (pKPCVIM.1). On this plasmid, blaVIM-1 was located in the Class 1 integron associated with IS1326::IS1353 (In2), and Tn4401b carrying blaKPC-4 was inserted into IS1326::IS1353, creating a novel MGE construct (In2_blaVIM-1-Tn4401b_blaKPC-4).<br><br>CONCLUSION: The hospital-wide spread of blaKPC-4 and blaVIM-1 was facilitated by clonal spread and horizontal plasmid transfer. The persistence of this strain in the hospital sink suggests a potential reservoir of the strain. Understanding the transmission mechanisms of persistent pathogens is important for improving infection control strategies in hospitals.}, }
@article {pmid39393940, year = {2024}, author = {Hall, JPJ}, title = {Loading and unloading plasmid cargoes.}, journal = {Trends in microbiology}, volume = {32}, number = {12}, pages = {1150-1152}, doi = {10.1016/j.tim.2024.09.012}, pmid = {39393940}, issn = {1878-4380}, mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; *Bacteria/genetics/metabolism ; Chromosomes, Bacterial/genetics ; }, abstract = {Plasmids are vehicles for horizontal gene transfer between cells, but they also exchange genes with associated chromosomes in a process termed 'intracellular mobility'. I discuss a recent article by Kadibalban et al. mapping such plasmid-chromosomal sequence similarities across diverse bacteria.}, }
@article {pmid39389705, year = {2024}, author = {Zhen, Q and Wang, X and Cheng, X and Fang, W}, title = {Remediation of toxic metal and metalloid pollution with plant symbiotic fungi.}, journal = {Advances in applied microbiology}, volume = {129}, number = {}, pages = {171-187}, doi = {10.1016/bs.aambs.2024.04.001}, pmid = {39389705}, issn = {0065-2164}, mesh = {*Plants/microbiology ; *Symbiosis ; *Biodegradation, Environmental ; *Metalloids/metabolism/toxicity ; *Soil Pollutants/metabolism/toxicity ; *Fungi/metabolism/genetics ; *Mycorrhizae/metabolism/physiology ; Endophytes/metabolism/physiology/isolation &amp; purification/genetics ; Metals/metabolism/toxicity ; Soil Microbiology ; }, abstract = {Anthropogenic activities have dramatically accelerated the release of toxic metal(loid)s into soil and water, which can be subsequently accumulated in plants and animals, threatening biodiversity, human health, and food security. Compared to physical and chemical remediation, bioremediation of metal(loid)-polluted soil using plants and/or plant symbiotic fungi is usually low-cost and environmentally friendly. Mycorrhizal fungi and endophytic fungi are two major plant fungal symbionts. Mycorrhizal fungi can immobilize metal(loid)s via constitutive mechanisms, including intracellular sequestration with vacuoles and vesicles and extracellular immobilization by cell wall components and extracellular polymeric substances such as glomalin. Mycorrhizal fungi can improve the efficacy of phytoremediation by promoting plant symplast and apoplast pathways. Endophytic fungi also use constitutive cellular components to immobilize metal(loid)s and to reduce the accumulation of metal(loid)s in plants by modifying plant physiological status. However, a specific mechanism for the removal of methylmercury pollution was recently discovered in the endophytic fungi Metarhizium, which could be acquired from bacteria via horizontal gene transfer. In contrast to mycorrhizal fungi that are obligate biotrophs, some endophytic fungi, such as Metarhizium and Trichoderma, can be massively and cost-effectively produced, so they seem to be well-placed for remediation of metal(loid)-polluted soil on a large scale.}, }
@article {pmid39389327, year = {2025}, author = {Narain Singh, D and Pandey, P and Shankar Singh, V and Kumar Tripathi, A}, title = {Evidence for high-risk pollutants and emerging microbial contaminants at two major bathing ghats of the river Ganga using high-resolution mass spectrometry and metagenomics.}, journal = {Gene}, volume = {933}, number = {}, pages = {148991}, doi = {10.1016/j.gene.2024.148991}, pmid = {39389327}, issn = {1879-0038}, mesh = {*Rivers/microbiology/chemistry ; *Metagenomics/methods ; *Wastewater/microbiology ; Bacteria/genetics/isolation &amp; purification/classification ; Water Pollutants, Chemical/analysis ; India ; Mass Spectrometry/methods ; Environmental Monitoring/methods ; Water Microbiology ; }, abstract = {An efficient wastewater treatment plant is imperative to limit the entry of emerging pollutants (EPs) and emerging microbial contaminants (EMCs) in the river ecosystem. The detection of emerging EPs in aquatic environments is challenging due to complex sample preparation methods, and the need for sophisticated accurate analytical tools. In Varanasi (India), the river Ganga holds immense significance as a holy river but is consistently polluted with municipal (MWW) and hospital wastewater (HWW). We developed an efficient method for untargeted detection of EPs in the water samples using High-resolution mass spectrometry (HRMS), and identified 577 and 670 chemicals (or chemical components) in the water samples from two major bathing ghats, Assi Ghat (AG) and Dashashwamedh Ghat (DG), respectively. The presence of EPs of different categories viz chemicals from research labs, diagnostic labs, lifestyle and industrial chemicals, toxins, flavor and food additives indicated the unsafe disposal of MWW and HWW or inefficient wastewater treatment plants (WWTPs). Besides, shotgun metagenomic analysis depicted the presence of bacteria associated with MWW viz Cloacibacterium normanse, Sphaerotilus natans (sewage fungi), E. coli, and Prevotella. Also, the presence of human pathogens Arcobacter, Polynucleobacter, Pseudomonas, Klebsiella, Aeromonas, Acinetobacter, Vibrio, and Campylobacter suggests the discharge of HWW. EPs are linked to the development, and transmission of antimicrobial resistance (AMR). Occurrence of antibiotic resistance genes (ARGs), plasmid-borne β-lactamases, aminoglycoside transferases, and ARGs associated with integrons, transposons and plasmids viz mcr-3 gene that confer resistance to colistin, the last resort of antibiotics confirmed the presence of emerging microbial contaminants. Subsequent genome reconstruction studies showed the presence of uncultivable ARB and transmission of ARGs through horizontal gene transfer. This study can be used to monitor the health of aquatic bodies as well as the efficiency of WWTPs and raise an urgent need for efficient WWTPs to safeguard the river, Ganga.}, }
@article {pmid39386473, year = {2024}, author = {Dalia, TN and Dalia, AB}, title = {SbcB facilitates natural transformation in Vibrio cholerae in an exonuclease-independent manner.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.09.25.615017}, pmid = {39386473}, issn = {2692-8205}, abstract = {UNLABELLED: Natural transformation (NT) is a conserved mechanism of horizontal gene transfer in bacterial species. During this process, DNA is taken up into the cytoplasm where it can be integrated into the host genome by homologous recombination. We have previously shown that some cytoplasmic exonucleases inhibit NT by degrading ingested DNA prior to its successful recombination. However, one exonuclease, SbcB, counterintuitively promotes NT in Vibrio cholerae . Here, through a systematic analysis of the distinct steps of NT, we show that SbcB acts downstream of DNA uptake into the cytoplasm, but upstream of recombinational branch migration. Through mutational analysis, we show that SbcB promotes NT in a manner that does not rely on its exonuclease activity. Finally, we provide genetic evidence that SbcB directly interacts with the primary bacterial recombinase, RecA. Together, these data advance our molecular understanding of horizontal gene transfer in V. cholerae , and reveal that SbcB promotes homologous recombination during NT in a manner that does not rely on its canonical exonuclease activity.<br><br>IMPORTANCE: Horizontal gene transfer by natural transformation contributes to the spread of antibiotic resistance and virulence factors in bacterial species. Here, we study how one protein, SbcB, helps facilitate this process in the facultative bacterial pathogen Vibrio cholerae . SbcB is a well-known for its exonuclease activity (i . e ., the ability to degrade the ends of linear DNA). Through this study we uncover that while SbcB is important for natural transformation, it does not facilitate this process using its exonuclease activity. Thus, this work helps further our understanding of the molecular events required for this conserved evolutionary process, and uncovers a function for SbcB beyond its canonical exonuclease activity.}, }
@article {pmid39385022, year = {2024}, author = {Samuel, B and Mittelman, K and Croitoru, SY and Ben Haim, M and Burstein, D}, title = {Diverse anti-defence systems are encoded in the leading region of plasmids.}, journal = {Nature}, volume = {635}, number = {8037}, pages = {186-192}, pmid = {39385022}, issn = {1476-4687}, mesh = {*Conjugation, Genetic ; CRISPR-Cas Systems/genetics ; DNA, Single-Stranded/genetics ; *Escherichia coli/genetics/immunology ; Gene Transfer, Horizontal ; *Plasmids/genetics ; Promoter Regions, Genetic/genetics ; SOS Response, Genetics/genetics ; }, abstract = {Plasmids are major drivers of gene mobilization by means of horizontal gene transfer and play a key role in spreading antimicrobial resistance among pathogens[1,2]. Despite various bacterial defence mechanisms such as CRISPR-Cas, restriction-modification systems and SOS-response genes that prevent the invasion of mobile genetic elements[3], plasmids robustly transfer within bacterial populations through conjugation[4,5]. Here we show that the leading region of plasmids, the first to enter recipient cells, is a hotspot for an extensive repertoire of anti-defence systems, encoding anti-CRISPR, anti-restriction, anti-SOS and other counter-defence proteins. We further identified in the leading region a prevalence of promoters known to allow expression from single-stranded DNA[6], potentially facilitating rapid protection against bacterial immunity during the early stages of plasmid establishment. We demonstrated experimentally the importance of anti-defence gene localization in the leading region for efficient conjugation. These results indicate that focusing on the leading region of plasmids could lead to the discovery of diverse anti-defence genes. Combined, our findings show a new facet of plasmid dissemination and provide theoretical foundations for developing efficient conjugative delivery systems for natural microbial communities.}, }
@article {pmid39384008, year = {2024}, author = {Gentile, A and Di Stasio, L and Oliva, G and Vigliotta, G and Cicatelli, A and Guarino, F and Nissim, WG and Labra, M and Castiglione, S}, title = {Antibiotic resistance in urban soils: Dynamics and mitigation strategies.}, journal = {Environmental research}, volume = {263}, number = {Pt 2}, pages = {120120}, doi = {10.1016/j.envres.2024.120120}, pmid = {39384008}, issn = {1096-0953}, mesh = {*Drug Resistance, Microbial/genetics ; *Soil Microbiology ; *Soil/chemistry ; *Anti-Bacterial Agents/pharmacology ; Cities ; Soil Pollutants/toxicity ; Humans ; }, abstract = {Antibiotic resistance (AR) is a critical global health issue with significant clinical and economic implications. AR occurs when microorganisms develop mechanisms to withstand the effects of antibiotics, reducing treatment efficacy and increasing the risk of mortality and healthcare costs. While the connection between antibiotic use in clinical and agricultural settings and the emergence of AR is well-established, the role of urban soils as reservoirs and spreaders of AR is underexplored. This review examines the complex dynamics of AR in urban soils, highlighting the various sources of antibiotics, including domestic wastewater, industrial effluents, urban agricultural practices, but also microplastics and domestic animal excrements. The selective pressure exerted by these anthropogenic sources promotes the proliferation of antibiotic-resistant bacteria, particularly through horizontal gene transfer, which facilitates the transmission of resistance genes among soil microorganisms in urban environments. About that, the presence of antibiotics in urban soils poses a significant threat to public health by potentially transferring resistance genes to human pathogens through multiple pathways, including direct contact, food consumption, and water ingestion. Furthermore, AR in urban soils disrupts microbial community dynamics, impacting soil fertility, plant growth, and overall environmental quality. Therefore, this review aims to address gaps in understanding AR in urban soils, offering insights into its implications for human health and ecosystem integrity. By identifying these gaps and suggesting evidence-based strategies, this review proposes valid and sustainable solutions to mitigate and counteract the spread of AR in urban environments.}, }
@article {pmid39383948, year = {2024}, author = {Rao, M and Teixeira, JS and Flint, A and Tamber, S}, title = {Hazard Characterization of Antibiotic-resistant Aeromonas spp. Isolated from Mussel and Oyster Shellstock Available for Retail Purchase in Canada.}, journal = {Journal of food protection}, volume = {87}, number = {11}, pages = {100374}, doi = {10.1016/j.jfp.2024.100374}, pmid = {39383948}, issn = {1944-9097}, mesh = {*Aeromonas/isolation &amp; purification/drug effects ; Animals ; Canada ; *Anti-Bacterial Agents/pharmacology ; *Bivalvia/microbiology ; Humans ; *Ostreidae/microbiology ; Shellfish/microbiology ; Microbial Sensitivity Tests ; Drug Resistance, Bacterial ; Food Microbiology ; Food Contamination/analysis ; }, abstract = {Surveillance and monitoring of foods for the presence of antimicrobial-resistant (AMR) bacteria are required to assess the risks these bacteria pose to human health. Frequently consumed raw or lightly cooked, live bivalve shellfish such as mussels and oysters can be a source of exposure to AMR bacteria. This study sought to determine the prevalence of third-generation cephalosporin (3GC) and carbapenem-resistant bacteria in live mussel and oyster shellstock available for retail purchase through the course of one calendar year. Just over half of the 180 samples (52%) tested positive for the presence of 3GC-resistant bacteria belonging to thirty distinct bacterial species. Speciation of the isolates was carried out using the Bruker MALDI Biotyper. Serratia spp., Aeromonas spp., and Rahnella spp. were the most frequently isolated groups of bacteria. Antibiotic resistance testing confirmed reduced susceptibility for 3GCs and/or carbapenems in 15 of the 29 Aeromonas isolates. Based on AMR patterns, and species identity, a subset of ten Aeromonas strains was chosen for further characterization by whole genome sequence analysis. Genomic analysis revealed the presence of multiple antibiotic resistance and virulence genes. A number of mobile genetic elements were also identified indicating the potential for horizontal gene transfer. Differences in gene detection by the bioinformatic tools and databases used (ResFinder. CARD RGI, PlasmidFinder, and MobSuite) are discussed. This study highlights the strengths and limitations of using genomics tools to perform hazard characterization of diverse foodborne bacterial species.}, }
@article {pmid39383803, year = {2025}, author = {Xiang, Y and Song, X and Yang, Y and Deng, S and Fu, L and Yang, C and Chen, M and Pu, J and Zhang, H and Chai, H}, title = {Comammox rather than AOB dominated the efficient autotrophic nitrification-denitrification process in an extremely oxygen-limited environment.}, journal = {Water research}, volume = {268}, number = {Pt A}, pages = {122572}, doi = {10.1016/j.watres.2024.122572}, pmid = {39383803}, issn = {1879-2448}, mesh = {*Nitrification ; *Denitrification ; *Oxygen/metabolism ; *Autotrophic Processes ; *Ammonia/metabolism ; *Bacteria/metabolism/genetics ; *RNA, Ribosomal, 16S/genetics ; Nitrogen/metabolism ; Oxidation-Reduction ; Bioreactors/microbiology ; }, abstract = {The discovery of complete ammonia oxidizer (comammox) has challenged the traditional understanding of the two-step nitrification process. However, their functions in the oxygen-limited autotrophic nitrification-denitrification (OLAND) process remain unclear. In this study, OLAND was achieved using comammox-dominated nitrifying bacteria in an extremely oxygen-limited environment with a dissolved oxygen concentrations of 0.05 mg/L. The ammonia removal efficiency exceeded 97 %, and the total nitrogen removal efficiency reached 71 % when sodium bicarbonate was used as the carbon source. The pseudo-first- and second-order models were found to best fit the ammonia removal processes under low and high loads, respectively, suggesting distinct ammonia removal pathways. Full-length 16S rRNA gene sequencing and metagenomic results revealed that comammox-dominated under different oxygen levels, in conjunction with anammox and heterotrophic denitrifiers. The abundance of enzymes involved in energy metabolism indicates the coexistence of anammox and autotrophic nitrification-heterotrophic denitrification pathways. The binning results showed that comammox bacteria engaged in horizontal gene transfer with nitrifiers, anammox bacteria, and denitrifiers to adapt to an obligate environments. Therefore, this study demonstrated that comammox, anammox, and heterotrophic denitrifiers play important roles in the OLAND process and provide a reference for further reducing aeration energy in the autotrophic nitrogen removal process.}, }
@article {pmid39376581, year = {2024}, author = {Du, Y and Qian, C and Li, X and Zheng, X and Huang, S and Yin, Z and Chen, T and Pan, L}, title = {Unveiling intraspecific diversity and evolutionary dynamics of the foodborne pathogen Bacillus paranthracis through high-quality pan-genome analysis.}, journal = {Current research in food science}, volume = {9}, number = {}, pages = {100867}, pmid = {39376581}, issn = {2665-9271}, abstract = {Understanding the evolutionary dynamics of foodborne pathogens throughout host-associated habitats is of utmost importance. Bacterial pan-genomes, as dynamic entities, are strongly influenced by ecological lifestyles. As a phenotypically diverse species in the Bacillus cereus group, Bacillus paranthracis is recognized as an emerging foodborne pathogen and a probiotic simultaneously. This poorly understood species is a suitable study model for adaptive pan-genome evolution. In this study, we determined the biogeographic distribution, abundance, genetic diversity, and genotypic profiles of key genetic elements of B. paranthracis. Metagenomic read recruitment analyses demonstrated that B. paranthracis members are globally distributed and abundant in host-associated habitats. A high-quality pan-genome of B. paranthracis was subsequently constructed to analyze the evolutionary dynamics involved in ecological adaptation comprehensively. The open pan-genome indicated a flexible gene repertoire with extensive genetic diversity. Significant divergences in the phylogenetic relationships, functional enrichment, and degree of selective pressure between the different components demonstrated different evolutionary dynamics between the core and accessory genomes driven by ecological forces. Purifying selection and gene loss are the main signatures of evolutionary dynamics in B. paranthracis pan-genome. The plasticity of the accessory genome is characterized by horizontal gene transfer (HGT), massive gene losses, and weak purifying or positive selection, which might contribute to niche-specific adaptation. In contrast, although the core genome dominantly undergoes purifying selection, its association with HGT and positively selected mutations indicates its potential role in ecological diversification. Furthermore, host fitness-related dynamics are characterized by the loss of secondary metabolite biosynthesis gene clusters (BGCs) and CAZyme-encoding genes and the acquisition of antimicrobial resistance (AMR) and virulence genes via HGT. This study offers a case study of pan-genome evolution to investigate the ecological adaptations reflected by biogeographical characteristics, thereby advancing the understanding of intraspecific diversity and evolutionary dynamics of foodborne pathogens.}, }
@article {pmid39375624, year = {2024}, author = {Männer, L and Schell, T and Spies, J and Galià-Camps, C and Baranski, D and Ben Hamadou, A and Gerheim, C and Neveling, K and Helfrich, EJN and Greve, C}, title = {Chromosome-level genome assembly of the sacoglossan sea slug Elysia timida (Risso, 1818).}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {941}, pmid = {39375624}, issn = {1471-2164}, mesh = {Animals ; *Gastropoda/genetics ; *Molecular Sequence Annotation ; *Genome ; *Chromosomes/genetics ; Genomics/methods ; }, abstract = {BACKGROUND: Sequencing and annotating genomes of non-model organisms helps to understand genome architecture, the genetic processes underlying species traits, and how these genes have evolved in closely-related taxa, among many other biological processes. However, many metazoan groups, such as the extremely diverse molluscs, are still underrepresented in the number of sequenced and annotated genomes. Although sequencing techniques have recently improved in quality and quantity, molluscs are still neglected due to difficulties in applying standardized protocols for obtaining genomic data.<br><br>RESULTS: In this study, we present the chromosome-level genome assembly and annotation of the sacoglossan sea slug&#xa0;species Elysia timida, known for its ability to store the chloroplasts of its food algae. In particular, by optimizing the long-read and chromosome conformation capture library preparations, the genome assembly was performed using PacBio HiFi and Arima HiC data. The scaffold and contig N50s, at 41.8&#xa0;Mb and 1.92&#xa0;Mb, respectively, are approximately 30-fold and fourfold higher compared to other published sacoglossan genome assemblies. Structural annotation resulted in 19,904 protein-coding genes, which are more contiguous and complete compared to publicly available annotations of Sacoglossa with respect to metazoan BUSCOs. We found no evidence for horizontal gene transfer (HGT), i.e. no photosynthetic genes encoded in the sacoglossan nucleus genome. However, we detected genes encoding polyketide synthases in E. timida, indicating that polypropionates are produced. HPLC-MS/MS analysis confirmed the presence of a large number of polypropionates, including known and yet uncharacterised compounds.<br><br>CONCLUSIONS: We can show that our methodological approach helps to obtain a high-quality genome assembly even for a "difficult-to-sequence" organism, which may facilitate genome sequencing in molluscs. This will enable a better understanding of complex biological processes in molluscs, such as functional kleptoplasty in Sacoglossa, by significantly improving the quality of genome assemblies and annotations.}, }
@article {pmid39373502, year = {2025}, author = {Liu, G and Li, X and Guan, J and Tai, C and Weng, Y and Chen, X and Ou, HY}, title = {oriTDB: a database of the origin-of-transfer regions of bacterial mobile genetic elements.}, journal = {Nucleic acids research}, volume = {53}, number = {D1}, pages = {D163-D168}, pmid = {39373502}, issn = {1362-4962}, support = {2023YFC2307103//National Key Research and Development Program of China/ ; 32070572//National Natural Science Foundation of China/ ; SHDC2022CRD039//Shanghai Hospital Development Center Foundation/ ; GWV1-11.2-XD01//Talent Program on Public Health System Construction of Shanghai/ ; 20240818//Shanghai Jiao Tong University School of Medicine/ ; }, mesh = {*Interspersed Repetitive Sequences ; Gene Transfer, Horizontal ; Plasmids/genetics ; Conjugation, Genetic ; Bacteria/genetics/classification ; Databases, Genetic ; Genome, Bacterial ; Bacterial Proteins/genetics/metabolism ; Databases, Nucleic Acid ; DNA, Bacterial/genetics ; }, abstract = {Conjugation and mobilization are two important pathways of horizontal transfer of bacterial mobile genetic elements (MGEs). The origin-of-transfer (oriT) region is crucial for this process, serving as a recognition site for relaxase and containing the DNA nicking site (nic site), which initiates the conjugation or mobilization. Here, we present a database of the origin-of-transfer regions of bacterial MGEs, oriTDB (https://bioinfo-mml.sjtu.edu.cn/oriTDB2/). Incorporating data from text mining and genome analysis, oriTDB comprises 122 experimentally validated and 22 927 predicted oriTs within bacterial plasmids, Integrative and Conjugative Elements, and Integrative and Mobilizable Elements. Additionally, oriTDB includes details about associated relaxases, auxiliary proteins, type IV coupling proteins, and a gene cluster encoding the type IV secretion system. The database also provides predicted secondary structures of oriT sequences, dissects oriT regions into pairs of inverted repeats, nic sites, and their flanking conserved sequences, and offers an interactive visual representation. Furthermore, oriTDB includes an enhanced oriT prediction pipeline, oriTfinder2, which integrates a functional annotation module for cargo genes in bacterial MGEs. This resource is intended to support research on bacterial conjugative or mobilizable elements and promote an understanding of their cargo gene functions.}, }
@article {pmid39368562, year = {2024}, author = {Hu, JC and Han, M and Yan, RY and Hua, MM and Li, J and Shen, H and Cao, XL}, title = {Mobile genetic elements contributing to horizontal gene transfer of blaNDM among Escherichia coli in the community setting.}, journal = {Microbial pathogenesis}, volume = {196}, number = {}, pages = {106996}, doi = {10.1016/j.micpath.2024.106996}, pmid = {39368562}, issn = {1096-1208}, mesh = {*Gene Transfer, Horizontal ; Humans ; *Escherichia coli/genetics/drug effects/isolation &amp; purification ; *beta-Lactamases/genetics ; *Interspersed Repetitive Sequences/genetics ; *Anti-Bacterial Agents/pharmacology ; *Whole Genome Sequencing ; China/epidemiology ; *Feces/microbiology ; *Plasmids/genetics ; Microbial Sensitivity Tests ; Phylogeny ; Carbapenem-Resistant Enterobacteriaceae/genetics/isolation &amp; purification ; Escherichia coli Proteins/genetics ; Escherichia coli Infections/microbiology/epidemiology ; Citrobacter freundii/genetics/drug effects/isolation &amp; purification ; Genotype ; Carbapenems/pharmacology ; Klebsiella/genetics/drug effects/enzymology ; }, abstract = {OBJECTIVE: To investigate the distribution of carbapenem-resistant Enterobacterales (CRE) in the community and to describe the genomic characteristics.<br><br>METHODS: CRE screened from fecal samples in healthy people at the health examination center of a tertiary hospital in China underwent Whole genome sequencing (WGS) to analyze genotypic characteristics of CRE. The flanking DNA sequence of blaNDM-5 and mcr1.1 genes were analyzed by Gcluster software.<br><br>RESULTS: A total of 7187 fecal samples were screened, and CRE carriage was detected in 0.4&#xa0;% of the sampled population. In total, 30 Escherichia coli, one Citrobacter freundii and one Klebsiella aerogene were screened. The 30 carbapenem-resistant Escherichia coli (CREC) isolates displayed slight resistance to amikacin (13.3&#xa0;%) and aztreonam (20.0&#xa0;%). All the CRE isolates contained blaNDM, and blaNDM-5 (84.4&#xa0;%) was the most common one. B1 (n&#xa0;=&#xa0;11) and A (n&#xa0;=&#xa0;7) were predominant phylogroups. Furthermore, 34 distinct plasmid replicons, 67 different VFs, 22 distinct STs, 17 different FimH types, 26 O:H serotypes as well as 74 MGEs including 61 insertion sequences and 13 transposons were identified. The flanking DNA sequence analysis of blaNDM-5 and mcr1.1 genes indicates the key role of horizontal transfer of blaNDM-5 in the CRE development evidenced by diverse STs and phylogenetic tree.<br><br>CONCLUSION: E. coli was the most predominant CRE isolates in community setting, and blaNDM (blaNDM-5) was the main CH&#x3b2;L encoding genes. The high prevalence of ARGs was associated with high resistance to commonly used antimicrobials. Besides, the genetic diversity of these isolates suggested the key role of blaNDM horizontal transfer in the CRE development. Thus, active screening of blaNDM in communities is particularly important for the prevention and control of CRE.}, }
@article {pmid39368190, year = {2024}, author = {Jiao, P and Zhou, Y and Zhang, X and Jian, H and Zhang, XX and Ma, L}, title = {Mechanisms of horizontal gene transfer and viral contribution to the fate of intracellular and extracellular antibiotic resistance genes in anaerobic digestion supplemented with conductive materials under ammonia stress.}, journal = {Water research}, volume = {267}, number = {}, pages = {122549}, doi = {10.1016/j.watres.2024.122549}, pmid = {39368190}, issn = {1879-2448}, mesh = {*Gene Transfer, Horizontal ; *Ammonia ; Anaerobiosis ; *Drug Resistance, Microbial/genetics ; Sewage ; }, abstract = {The addition of conductive materials (CMs) is an effective strategy for mitigating ammonia inhibition during anaerobic digestion (AD). However, the introduction of CMs can result in increased antibiotic resistance genes (ARGs) pollution, potentially facilitated by enhanced horizontal gene transfer (HGT). The complex dynamics of intracellular and extracellular ARGs (iARGs/eARGs) and the mechanisms underlying their transfer, mediated by CMs, in ammonia-stressed AD systems remain unclear. In this study, we investigated the effects of three commonly used CMs-nano magnetite (Mag), nano zero-valent iron (nZVI), and granular activated carbon (GAC)-on the fate of iARGs and eARGs during the AD of waste activated sludge under ammonia stress. The results revealed an unexpected enrichment of iARGs by 1.5 %-10.9 % and a reduction of eARGs by 14.1 %-25.2 % in CM-supplemented AD. This discrepancy in the dynamics of iARGs and eARGs may be attributed to changes in microbial hosts and the horizontal transfer of ARGs. Notably, CMs activated prophages within antibiotic-resistant bacteria (ARB) and their symbiotic partners involved in vitamin B12 provision, leading to the lysis of ARB and the subsequent release of eARGs for transformation. Additionally, the abundance of potentially mobile ARGs, which co-occurred with mobile genetic elements, increased by 56.6 %-134.5 % with CM addition, highlighting an enhanced potential for the HGT of ARGs. Specifically, Mag appeared to promote both transformation and conjugation processes, while nZVI only promoted conjugation. Moreover, none of the three CMs had any discernible impact on transduction. GAC proved superior to both nano Mag and nZVI in controlling the enrichment of iARGs, reducing eARGs, and limiting HGTs simultaneously. Overall, these findings provide novel insights into the role of viruses and the mechanisms of ARG spread in CM-assisted AD, offering valuable information for developing strategies to mitigate ARG pollution in practical applications.}, }
@article {pmid39368156, year = {2024}, author = {Zhou, Y and Zhang, G and Zhang, D and Zhu, N and Bo, J and Meng, X and Chen, Y and Qin, Y and Liu, H and Li, W}, title = {Microplastic biofilms promote the horizontal transfer of antibiotic resistance genes in estuarine environments.}, journal = {Marine environmental research}, volume = {202}, number = {}, pages = {106777}, doi = {10.1016/j.marenvres.2024.106777}, pmid = {39368156}, issn = {1879-0291}, mesh = {*Biofilms/drug effects ; *Gene Transfer, Horizontal ; *Microplastics/toxicity ; *Estuaries ; *Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Bacteria/genetics/drug effects ; Water Pollutants, Chemical/toxicity ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology/toxicity ; }, abstract = {As emerging pollutants, microplastics can aggregate microorganisms on their surfaces and form biofilms, enriching antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Consequently, microplastic biofilms have become a focal point of research. Horizontal gene transfer is one of the primary mechanisms by which bacteria acquire antibiotic resistance, with much of the research focusing on suspended bacteria. However, microplastic biofilms, as hotspots for horizontal gene transfer, also merit significant investigation. This study primarily explored and compared the frequency of ARG conjugative transfer between suspended bacteria and microplastic biofilms. The results demonstrated that, compared to suspended bacteria, microplastic biofilms enhanced the frequency of ARG conjugative transfer by 7.2-19.6 times. Among them, biofilms on polyethylene microplastics showed the strongest promotion of conjugation. After the formation of microplastic biofilms, there was a significant increase in bacterial density within the biofilms, which raised the collision frequency of donor and recipient bacteria. Then microplastic biofilms facilitated the gene expression levels of outer membrane proteins, enhanced bacterial gene transfer capabilities, promoted the synthesis of conjugative pili, accelerated the formation of conjugative pairing systems, and elevated the expression levels of genes related to DNA replication and transfer systems, thereby enhancing the conjugative transfer of ARGs within microplastic biofilms. Among different types of microplastic biofilms, polyethylene biofilms exhibited the highest bacterial density, thus showing the highest frequency of ARG conjugation. This study highlights the risks associated with ARG conjugative transfer following the formation of microplastic biofilms and provides insights into the risks of microplastic and antibiotic resistance propagation in estuarine environments.}, }
@article {pmid39366749, year = {2024}, author = {Leclerc, L and Mattick, J and Burns, BP and Sassera, D and Hotopp, JD and Lo, N}, title = {Metatranscriptomics provide insights into the role of the symbiont Midichloria mitochondrii in Ixodes ticks.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {12}, pages = {}, pmid = {39366749}, issn = {1574-6941}, support = {//The Linnean Society of New South Wales/ ; //University of New South Wales/ ; }, mesh = {*Ixodes/microbiology/genetics ; Animals ; *Symbiosis ; *Transcriptome ; Gene Transfer, Horizontal ; Nymph/microbiology/growth &amp; development/genetics ; Gene Expression Profiling ; }, abstract = {Ticks are important vectors of bacterial, viral, and protozoan pathogens of humans and animals worldwide. Candidatus Midichloria mitochondrii is a highly abundant bacterial endosymbiont found in many tick species, including two medically important ticks respectively found in Europe and Australia, Ixodes ricinus and Ixodes holocyclus. The present study aimed to determine the symbiont's biological role by identifying lateral gene transfer (LGT) events, characterizing the transcriptome, and performing differential expression analyses. Metatranscriptomic data revealed that M. mitochondrii species in I. ricinus and I. holocyclus were equipped with the metabolic potential and were actively transcribing the genes for several important roles including heme, biotin and folate synthesis, oxidative stress response, osmotic regulation, and ATP production in microaerobic conditions. Differential expression analyses additionally showed an upregulation in stringent response and DNA repair genes in M. mitochondrii of I. holocyclus nymphs compared to adults. Low rates of differential expression suggest the symbiont may lack global gene regulation, as observed in other endosymbionts. Moreover, the identification of an LGT event and the proposed specialization of the M. mitochondrii strains, mIxholo1 and mIxholo2, for different I. holocyclus life stages highlight the complex interactions between M. mitochondrii and their tick hosts.}, }
@article {pmid39366703, year = {2024}, author = {Gomez-Simmonds, A and Annavajhala, MK and Seeram, D and Hokunson, TW and Park, H and Uhlemann, AC}, title = {Genomic epidemiology of carbapenem-resistant Enterobacterales at a New York City hospital over a 10-year period reveals complex plasmid-clone dynamics and evidence for frequent horizontal transfer of bla KPC.}, journal = {Genome research}, volume = {34}, number = {11}, pages = {1895-1907}, pmid = {39366703}, issn = {1549-5469}, support = {K99 AI163348/AI/NIAID NIH HHS/United States ; P30 DK132710/DK/NIDDK NIH HHS/United States ; R01 AI116939/AI/NIAID NIH HHS/United States ; K24 AI183182/AI/NIAID NIH HHS/United States ; K23 AI137316/AI/NIAID NIH HHS/United States ; R01 AI175414/AI/NIAID NIH HHS/United States ; U54 DK104309/DK/NIDDK NIH HHS/United States ; }, mesh = {*Plasmids/genetics ; *beta-Lactamases/genetics ; Humans ; *Gene Transfer, Horizontal ; *Bacterial Proteins/genetics ; *Carbapenems/pharmacology ; New York City/epidemiology ; Carbapenem-Resistant Enterobacteriaceae/genetics ; Enterobacteriaceae Infections/microbiology/epidemiology/transmission ; Klebsiella pneumoniae/genetics/drug effects ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; Molecular Epidemiology ; Multilocus Sequence Typing ; }, abstract = {Transmission of carbapenem-resistant Enterobacterales (CRE) in hospitals has been shown to occur through complex, multifarious networks driven by both clonal spread and horizontal transfer mediated by plasmids and other mobile genetic elements. We performed nanopore long-read sequencing on CRE isolates from a large urban hospital system to determine the overall contribution of plasmids to CRE transmission and identify specific plasmids implicated in the spread of bla KPC (the Klebsiella pneumoniae carbapenemase [KPC] gene). Six hundred and five CRE isolates collected between 2009 and 2018 first underwent Illumina sequencing for genome-wide genotyping; 435 bla KPC-positive isolates were then successfully nanopore sequenced to generate hybrid assemblies including circularized bla KPC-harboring plasmids. Phylogenetic analysis and Mash clustering were used to define putative clonal and plasmid transmission clusters, respectively. Overall, CRE isolates belonged to 96 multilocus sequence types (STs) encoding bla KPC on 447 plasmids which formed 54 plasmid clusters. We found evidence for clonal transmission in 66% of CRE isolates, over half of which belonged to four clades comprising K. pneumoniae ST258. Plasmid-mediated acquisition of bla KPC occurred in 23%-27% of isolates. While most plasmid clusters were small, several plasmids were identified in multiple different species and STs, including a highly promiscuous IncN plasmid and an IncF plasmid putatively spreading bla KPC from ST258 to other clones. Overall, this points to both the continued dominance of K. pneumoniae ST258 and the dissemination of bla KPC across clones and species by diverse plasmid backbones. These findings support integrating long-read sequencing into genomic surveillance approaches to detect the hitherto silent spread of carbapenem resistance driven by mobile plasmids.}, }
@article {pmid39367299, year = {2024}, author = {Wang, J and Liu, X and Zhang, M and Liu, R}, title = {The mitochondrial genome of Lavandula angustifolia Mill. (Lamiaceae) sheds light on its genome structure and gene transfer between organelles.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {929}, pmid = {39367299}, issn = {1471-2164}, support = {No. 2022BCA022//Hubei Province key research and development project/ ; }, mesh = {*Genome, Mitochondrial ; *Lavandula/genetics ; *Phylogeny ; RNA, Transfer/genetics ; Organelles/genetics ; Gene Transfer, Horizontal ; RNA Editing ; Molecular Sequence Annotation ; Genome, Plant ; Evolution, Molecular ; }, abstract = {BACKGROUND: Lavandula angustifolia holds importance as an aromatic plant with extensive applications spanning the fragrance, perfume, cosmetics, aromatherapy, and spa sectors. Beyond its aesthetic and sensory applications, this plant offers medicinal benefits as a natural herbal remedy and finds use in household cleaning products. While extensive genomic data, inclusive of plastid and nuclear genomes, are available for this species, researchers have yet to characterize its mitochondrial genome. This gap in knowledge hampers deeper understanding of the genome organization and its evolutionary significance.<br><br>RESULTS: Through the course of this study, we successfully assembled and annotated the mitochondrial genome of L. angustifolia, marking a first in this domain. This assembled genome encompasses 61 genes, which comprise 34 protein-coding genes, 24 transfer RNA genes, and three ribosomal RNA genes. We identified a chloroplast sequence insertion into the mitogenome, which spans a length of 10,645&#xa0;bp, accounting for 2.94% of the mitogenome size. Within these inserted sequences, there are seven intact tRNA genes (trnH-GUG, trnW-CCA, trnD-GUC, trnS-GGA, trnN-GUU, trnT-GGU, trnP-UGG) and four complete protein-coding genes (psbA, rps15, petL, petG) of chloroplast derivation. Additional discoveries include 88 microsatellites, 15 tandem repeats, 74 palindromic repeats, and 87 forward long repeats. An RNA editing analysis highlighted an elevated count of editing sites in the cytochrome c oxidase genes, notably ccmB with 34 editing sites, ccmFN with 32, and ccmC with 29. All protein-coding genes showed evidence of cytidine-to-uracil conversion. A phylogenetic analysis, utilizing common protein-coding genes from 23 Lamiales species, yielded a tree with consistent topology, supported by high confidence values.<br><br>CONCLUSIONS: Analysis of the current mitogenome resource revealed its typical circular genome structure. Notably, sequences originally from the chloroplast genome were found within the mitogenome, pointing to the occurrence of horizontal gene transfer between organelles. This assembled mitogenome stands as a valuable resource for subsequent studies on mitogenome structures, their evolution, and molecular biology.}, }
@article {pmid39366964, year = {2024}, author = {Kawaichi, S and Kotoky, R and Fiutowski, J and Rotaru, AE}, title = {Adaptation of a methanogen to Fe[0] corrosion via direct contact.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {100}, pmid = {39366964}, issn = {2055-5008}, support = {ERC CoG 101045149//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; UFM 5229-00010B//Uddannelses- og Forskningsministeriet (Ministry of Higher Education and Science)/ ; }, mesh = {*Methanococcus/genetics/metabolism ; Corrosion ; *Adaptation, Physiological ; *Hydrogenase/genetics/metabolism ; Gene Transfer, Horizontal ; Methane/metabolism ; Iron/metabolism ; }, abstract = {Due to unique genomic adaptations, Methanococcus maripaludis Mic1c10 is highly corrosive when in direct contact with Fe[0]. A critical adaptation involves increased glycosylation of an extracellular [NiFe]-hydrogenase, facilitating its anchoring to cell surface proteins. Corrosive strains adapt to the constructed environment via horizontal gene transfer while retaining ancestral genes important for intraspecies competition and surface attachment. This calls for a reevaluation of how the built environment impacts methane cycling.}, }
@article {pmid39365569, year = {2024}, author = {Gniewosz, M and Andrzejczak-Grządko, S}, title = {[Characterization of KPC-type drug resistance in bacteria].}, journal = {Postepy biochemii}, volume = {70}, number = {3}, pages = {315-324}, doi = {10.18388/pb.2021_555}, pmid = {39365569}, issn = {0032-5422}, mesh = {*beta-Lactamases/genetics/metabolism ; *Bacterial Proteins/genetics/metabolism ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Humans ; Carbapenems/pharmacology ; Bacteria/genetics/drug effects ; Gene Transfer, Horizontal ; }, abstract = {One of the main problems of modern medicine is the phenomenon of drug resistance. Inappropriate use of antibiotics is considered to be the most important reason for the emergence of new resistance mechanisms in microorganisms. Carbapenems, which belong to the β-lactams, are considered the most effective group of antimicrobial agents. Unfortunately, as a result of prolonged exposure to the aforementioned drugs, bacteria have developed several mechanisms for survival. The most important of these is the production of hydrolytic enzymes (carbapenemases), which cleave the β-lactam ring and inactivate the antibiotics. The mentioned enzymes are encoded by blaKPC genes, which are located in so-called mobile genetic elements (i.e. plasmids and transposons). Such localization is associated with their ease of transfer between different bacterial species in the process of horizontal gene transfer.}, }
@article {pmid39364782, year = {2024}, author = {Bellinazzo, F and Nadal Bigas, J and Hogers, RAH and Kodde, J and van der Wal, F and Kokkinopoulou, P and Duijts, KTM and Angenent, GC and van Dijk, ADJ and van Velzen, R and Immink, RGH}, title = {Evolutionary origin and functional investigation of the widely conserved plant PEBP gene STEPMOTHER OF FT AND TFL1 (SMFT).}, journal = {The Plant journal : for cell and molecular biology}, volume = {120}, number = {4}, pages = {1410-1420}, doi = {10.1111/tpj.17057}, pmid = {39364782}, issn = {1365-313X}, support = {//KAVB Productgroep Tulp/ ; //Stimuflori/ ; VICI16129//NWO/ ; ALWGR.2017.008//NWO/ ; VICI192033//NWO/ ; }, mesh = {*Evolution, Molecular ; *Phosphatidylethanolamine Binding Protein/genetics/metabolism ; *Phylogeny ; Plant Proteins/genetics/metabolism ; Gene Transfer, Horizontal ; Arabidopsis/genetics/metabolism ; Arabidopsis Proteins/genetics/metabolism ; }, abstract = {Genes of the family PHOSPHATIDYLETHANOLAMINE-BINDING PROTEINS (PEBP) have been intensely studied in plants for their role in cell (re)programming and meristem differentiation. Recently, sporadic reports of the presence of a new type of PEBP in plants became available, highly similar to the YY-PEBPs of prokaryotes. A comprehensive investigation of their spread, origin, and function revealed conservation across the plant kingdom. The YY-PEBP clade in plants seems to have resulted from a single Horizontal Gene Transfer (HGT) episode from a prokaryotic organism to an ancestral streptophyte. YY-PEBPs are also present in other eukaryotes, such as certain fungi, diatoms, and rotifers, and these cases derive from independent HGT events. Reciprocally, the occurrence of the eukaryotic CETS/RKIP type PEBPs (CR-PEBPs) was noticed in bacteria of the genus Nocardia, showing that HGT has occurred as well from eukaryotes to prokaryotes. Based on these observations, we propose that the current model of the PEBP family in plants needs to be updated with the clade STEPMOTHER OF FT AND TFL1 (SMFT). SMFT genes not only share high sequence conservation but also show specific expression in homologous plant structures that serve as propagules. Functional analysis of Arabidopsis smft mutant lines pointed to a function for this gene in regulating seed germination, both concerning primary dormancy release and in response to adverse high-temperature conditions. Overall, our study reveals an increasing complexity in the evolutionary history of the PEBP gene family, unlocking new potential in understanding the evolution and functional spectrum of these important key regulatory genes.}, }
@article {pmid39360841, year = {2024}, author = {Smith, AC and Shrivastava, A and Cartee, JC and Bélanger, M and Sharpe, S and Lewis, J and Budionno, S and Gomez, R and Khubbar, MK and ,  and Pham, CD and Gernert, KM and Schmerer, MW and Raphael, BH and Learner, ER and Kersh, EN and Joseph, SJ}, title = {Whole-genome sequencing resolves biochemical misidentification of Neisseria species from urogenital specimens.}, journal = {Journal of clinical microbiology}, volume = {62}, number = {11}, pages = {e0070424}, pmid = {39360841}, issn = {1098-660X}, mesh = {Humans ; *Whole Genome Sequencing ; *Neisseria gonorrhoeae/genetics/classification/isolation &amp; purification ; *Genome, Bacterial/genetics ; *Gonorrhea/microbiology/diagnosis ; Neisseria meningitidis/genetics/isolation &amp; purification/classification ; Urogenital System/microbiology ; Gene Transfer, Horizontal ; Male ; Female ; Diagnostic Errors ; }, abstract = {Neisseria meningitidis (Nm) and Neisseria gonorrhoeae (Ng) are human pathogens that sometimes occupy the same anatomical niche. Ng, the causative agent of gonorrhea, infects 87 million individuals annually worldwide and is an urgent threat due to increasing drug resistance. Ng is a pathogen of the urogenital tract and may infect the oropharyngeal or rectal site, often asymptomatically. Conversely, Nm is an opportunistic pathogen. While often a commensal in the oropharyngeal tract, it is also the leading cause of bacterial meningitis with 1.2 million cases globally, causing significant morbidity and mortality. Horizontal gene transfer (HGT) is likely to occur between Ng and Nm due to their shared anatomical niches and genetic similarity, which poses challenges for accurate detection and treatment. Routine surveillance through the Gonococcal Isolate Surveillance Project and Strengthening the U.S. Response to Resistant Gonorrhea detected six concerning urogenital Neisseria isolates with contradicting species identification in Milwaukee (MIL). While all six isolates were positive for Ng using nucleic acid amplification testing (NAAT) and matrix-assisted laser desorption/ionization time of flight identified the isolates as Ng, two biochemical tests, Gonochek-II and API NH, classified them as Nm. To address this discrepancy, we performed whole-genome sequencing (WGS) using Illumina MiSeq on all isolates and employed various bioinformatics tools. Species detection analysis using BMScan, which uses WGS data, identified all isolates as Ng. Furthermore, Kraken revealed over 98% of WGS reads mapped to the Ng genome and <1% to Nm. Recombination analysis identified putative HGT in all MIL isolates within the γ-glutamyl transpeptidase (ggt) gene, a key component in the biochemical tests used to differentiate between Nm and Ng. Further analysis identified Nm as the source of HGT event. Specifically, the active Nm ggt gene replaced the Ng pseudogenes, ggt1 and ggt2. Together, this study demonstrates that closely related Neisseria species sharing a niche underwent HGT, which led to the misidentification of species following biochemical testing. Importantly, NAAT accurately detected Ng. The misidentification highlights the importance of using WGS to continually evaluate diagnostic or bacterial identification tests.}, }
@article {pmid39360838, year = {2024}, author = {Ott, L and Smith, C and Mellata, M}, title = {Dietary zinc supplementation inhibits bacterial plasmid conjugation in vitro by regulating plasmid replication (rep) and transfer (tra) genes.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {10}, pages = {e0148024}, pmid = {39360838}, issn = {1098-5336}, support = {IOW05679//USDA | National Institute of Food and Agriculture (NIFA)/ ; IOW05700//U.S. Department of Agriculture (USDA)/ ; IOW04202//U.S. Department of Agriculture (USDA)/ ; }, mesh = {*Plasmids/genetics ; *Zinc/pharmacology ; *Dietary Supplements ; *Escherichia coli/genetics/drug effects ; *Conjugation, Genetic ; Animals ; Humans ; Gene Transfer, Horizontal ; Escherichia coli Proteins/genetics ; }, abstract = {Humans use dietary supplements for several intended effects, such as supplementing malnutrition. While these compounds have been developed for host end benefits, their ancillary impact on the gut microbiota remains unclear. The human gut has been proposed as a reservoir for the prevalent lateral transfer of antimicrobial resistance and virulence genes in bacteria through plasmid conjugation. Here, we studied the effect of dietary zinc supplements on the incidence of plasmid conjugation in vitro. Supplement effects were analyzed through standardized broth conjugation assays. The avian pathogenic Escherichia coli (APEC) strain APEC-O2-211 was a donor of the multidrug resistance plasmid pAPEC-O2-211A-ColV, and the human commensal isolate E. coli HS-4 was the plasmid-free recipient. Bacterial strains were standardized and mixed 1:1 and supplemented 1:10 with water, or zinc derived from either commercial zinc supplements or zinc gluconate reagent at varying concentrations. We observed a significant reduction in donors, recipients, and transconjugant populations in conjugations supplemented with zinc, with a dose-dependent relationship. Additionally, we observed a significant reduction (P < 0.05) in log conjugation efficiency in zinc-treated reactions. Upregulation of the mRNA for the plasmid replication initiation gene repA and the subset of transfer genes M, J, E, K, B, P, C, W, U, N, F, Q, D, I, and X was observed. Furthermore, we observed a downregulation of the conjugal propilin gene traA and the entry exclusion gene traS. This study demonstrates the effect of dietary zinc supplements on the conjugal transfer of a multidrug resistance plasmid between pathogenic and commensal bacteria during in vitro conditions.IMPORTANCEThis study identifies dietary zinc supplementation as a potential novel intervention for mitigating the emergence of multidrug resistance in bacteria, thus preventing antibiotic treatment failure and death in patients and animals. Further studies are required to determine the applicability of this approach in an in vivo model.}, }
@article {pmid39359630, year = {2024}, author = {Wang, Y and Chen, P and Lin, Q and Zuo, L and Li, L}, title = {Endophytic bacteria with allelopathic potential regulate gene expression and metabolite production in host Casuarina equisetifolia.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1435440}, pmid = {39359630}, issn = {1664-462X}, abstract = {INTRODUCTION: Casuarina equisetifolia is a common protective forest in coastal areas. However, artificial C. equisetifolia forests cannot self-renew, mainly due to the accumulation of allelochemicals. Endophytic bacteria may alleviate the root growth inhibition caused by allelochemicals in C. equisetifolia seedlings. B. amyloliquefaciens and B. aryabhattai were endophytic bacteria with strong allelopathy in C. equisetifolia root. The allelopathy mechanism of these two endophytes and their interaction with C. equisetifolia remains to be studied.<br><br>METHODS: Whole-genome sequencing of B. amyloliquefaciens and B. aryabhattai isolated from the roots of allelochemical-accumulating C. equisetifolia was performed using Illumina Hiseq and PacBio single-molecule sequencing platforms. Sterile seedlings of C. equisetifolia were treated with either individual or mixed bacterial cultures through root drenching. Transcriptional and metabolomics analyses were conducted after 3 days of infection.<br><br>RESULTS AND DISCUSSION: Whole-genome sequencing of Bacillus aryabhattai and Bacillus amyloliquefaciens showed that the two strains contained various horizontal gene transfer elements such as insertion sequence, prophage and transposon. In addition, these two strains also contain numerous genes related to the synthesis and catabolism of allelochemicals. After these two strains of bacteria were individually or mixed infected with C. equisetifolia, metabolomics and transcriptomic analysis of C. equisetifolia showed the 11 important secondary metabolite biosynthesis among them alkaloids biosynthesis, phenylpropanoid and terpenes biosynthesis and related genes were putatively regulated. Correlation analysis revealed that 48 differentially expressed genes had strong positive correlations with 42 differential metabolites, and 48 differentially expressed genes had strong negative correlations with 36 differential metabolites. For example, CMBL gene showed positive correlations with the allelochemical (-)-Catechin gallate, while Bp10 gene showed negative correlations with (-)-Catechin gallate.<br><br>CONCLUSION: The intergenerational accumulation of allelochemicals may induce horizontal gene transfer in endogenic bacteria of Casuarina equisetifolia root. Endophytic Bacillus plays an allelopathic role by assisting the host in regulating gene expression and the production and/or variety of allelochemicals. This comprehensive study sheds light on the intricate genetic and metabolic interactions between Bacillus endophytes and C. equisetifolia. These findings provide insights into endophyte-mediated allelopathy and its potential uses in plant biology and forest sustainability.}, }
@article {pmid39357349, year = {2024}, author = {Zhang, K and Gao, J and Lu, T and Wang, Y and Zhang, J and An, J and Xu, H}, title = {Evolution of microbial community and resistance genes in denitrification system under single and combined exposure to benzethonium chloride and methylparaben.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {136010}, doi = {10.1016/j.jhazmat.2024.136010}, pmid = {39357349}, issn = {1873-3336}, mesh = {*Parabens/toxicity ; *Denitrification/drug effects ; *Water Pollutants, Chemical/toxicity ; *Benzethonium/toxicity ; Microbiota/drug effects ; Sewage/microbiology ; Wastewater ; Genes, Bacterial/drug effects ; Gene Transfer, Horizontal ; }, abstract = {Benzethonium chloride (BZC) and methylparaben (MeP) are commonly added into cosmetics as preservatives, which are frequently detected in wastewater treatment plants. Different response patterns of denitrification system were proposed under single and combined exposure to BZC and MeP (0, 0.5, 5 mg/L) by evaluating system performance, functional genes, extracellular polymeric substance (EPS), cytotoxicity, microbial community structure and resistance genes (RGs). The inhibition effect of BZC on denitrification system was stronger than MeP, and the co-exposure of BZC and MeP showed synergistic effect, enhancing the inhibition effect of BZC single exposure. BZC and/or MeP could promote the diffusion of RGs in sludge, including intracellular RGs (si-RGs) and extracellular RGs (se-RGs). Moreover, the single exposure of BZC and co-exposure of BZC and MeP increased the dissemination risks of RGs in water (w-RGs). IntI1 and tnpA-04, mobile genetic elements (MGEs), correlated positively with diverse RGs from different fractions. Notably, the spread of RGs through horizontal gene transfer mediated by MGEs and the flow of si-RGs into extracellular and water were observed in this study.}, }
@article {pmid39352766, year = {2024}, author = {Ling, X and Gu, X and Shen, Y and Fu, C and Zhou, Y and Yin, Y and Gao, Y and Zhu, Y and Lou, Y and Zheng, M}, title = {Comparative genomic analysis of Acanthamoeba from different sources and horizontal transfer events of antimicrobial resistance genes.}, journal = {mSphere}, volume = {9}, number = {10}, pages = {e0054824}, pmid = {39352766}, issn = {2379-5042}, mesh = {*Acanthamoeba/genetics/classification/microbiology ; *Gene Transfer, Horizontal ; *Phylogeny ; Humans ; *Acanthamoeba Keratitis/parasitology/microbiology ; Genomics ; Genome, Protozoan ; Genetic Variation ; Whole Genome Sequencing ; Drug Resistance/genetics ; }, abstract = {UNLABELLED: Acanthamoeba species are among the most common free-living amoeba and ubiquitous protozoa, mainly distributed in water and soil, and cause Acanthamoeba keratitis (AK) and severe visual impairment in patients. Although several studies have reported genomic characteristics of Acanthamoeba, limited sample sizes and sources have resulted in an incomplete understanding of the genetic diversity of Acanthamoeba from different sources. While endosymbionts exert a significant influence on the phenotypes of Acanthamoeba, including pathogenicity, virulence, and drug resistance, the species diversity and functional characterization remain largely unexplored. Herein, our study sequenced and analyzed the whole genomes of 19 Acanthamoeba pathogenic strains that cause AK, and by integrating publicly available genomes, we sampled 29 Acanthamoeba strains from ocular, environmental, and other sources. Combined pan-genomic and comparative functional analyses revealed genetic differences and evolutionary relationships among the different sources of Acanthamoeba, as well as classification into multiple functional groups, with ocular isolates in particular showing significant differences that may account for differences in pathogenicity. Phylogenetic and rhizome gene mosaic analyses of ocular Acanthamoeba strains suggested that genomic exchanges between Acanthamoeba and endosymbionts, particularly potential antimicrobial resistance genes trafficking including the adeF, amrA, and amrB genes exchange events, potentially contribute to Acanthamoeba drug resistance. In conclusion, this study elucidated the adaptation of Acanthamoeba to different ecological niches and the influence of gene exchange on the evolution of ocular Acanthamoeba genome, guiding the clinical diagnosis and treatment of AK and laying a theoretical groundwork for developing novel therapeutic approaches.<br><br>IMPORTANCE: Acanthamoeba causes a serious blinding keratopathy, Acanthamoeba keratitis, which is currently under-recognized by clinicians. In this study, we analyzed 48 strains of Acanthamoeba using a whole-genome approach, revealing differences in pathogenicity and function between strains of different origins. Horizontal transfer events of antimicrobial resistance genes can help provide guidance as potential biomarkers for the treatment of specific Acanthamoeba keratitis cases.}, }
@article {pmid39350642, year = {2024}, author = {Saha, S and Kanaujia, SP}, title = {Decoding Substrate Selectivity of an Archaeal RlmCD-like Methyltransferase Through Its Salient Traits.}, journal = {Biochemistry}, volume = {63}, number = {19}, pages = {2477-2492}, doi = {10.1021/acs.biochem.4c00401}, pmid = {39350642}, issn = {1520-4995}, mesh = {Substrate Specificity ; *Archaeal Proteins/metabolism/genetics/chemistry ; *Methyltransferases/metabolism/chemistry/genetics ; Pyrococcus horikoshii/enzymology/genetics ; Models, Molecular ; Crystallography, X-Ray ; S-Adenosylmethionine/metabolism ; Amino Acid Sequence ; }, abstract = {5-Methyluridine (m[5]U) rRNA modifications frequently occur at U747 and U1939 (Escherichia coli numbering) in domains II and IV of the 23S rRNA in Gram-negative bacteria, with the help of S-adenosyl-l-methionine (SAM)-dependent rRNA methyltransferases (MTases), RlmC and RlmD, respectively. In contrast, Gram-positive bacteria utilize a single SAM-dependent rRNA MTase, RlmCD, to modify both corresponding sites. Notably, certain archaea, specifically within the Thermococcales group, have been found to possess two genes encoding SAM-dependent archaeal (tRNA and rRNA) m[5]U (Arm[5]U) MTases. Among these, a tRNA-specific Arm[5]U MTase (PabTrmU54) has already been characterized. This study focused on the structural and functional characterization of the rRNA-specific Arm[5]U MTase from the hyperthermophilic archaeon Pyrococcus horikoshii (PhRlmCD). An in-depth structural examination revealed a dynamic hinge movement induced by the replacement of the iron-sulfur cluster with disulfide bonds, obstructing the substrate-binding site. It revealed distinctive characteristics of PhRlmCD, including elongated positively charged loops in the central domain and rotational variations in the TRAM domain, which influence substrate selectivity. Additionally, the results suggested that two potential mini-rRNA fragments interact in a similar manner with PhRlmCD at a positively charged cleft at the interface of domains and facilitate dual MTase activities akin to the protein RlmCD. Altogether, these observations showed that Arm[5]U MTases originated from horizontal gene transfer events, most likely from Gram-positive bacteria.}, }
@article {pmid39348487, year = {2024}, author = {Ishida, JK and Costa, EC}, title = {What we know so far and what we can expect next: A molecular investigation of plant parasitism.}, journal = {Genetics and molecular biology}, volume = {47Suppl 1}, number = {Suppl 1}, pages = {e20240051}, pmid = {39348487}, issn = {1415-4757}, abstract = {The review explores parasitic plants' evolutionary success and adaptability, highlighting their widespread occurrence and emphasizing the role of an invasive organ called haustorium in nutrient acquisition from hosts. It discusses the genetic and physiological adaptations that facilitate parasitism, including horizontal gene transfer, and the impact of environmental factors like climate change on these relationships. It addresses the need for further research into parasitic plants' genomes and interactions with their hosts to better predict environmental changes' impacts.}, }
@article {pmid39348416, year = {2024}, author = {Mayfield, JA and Raman, S and Ramnarine, AK and Mishra, VK and Huang, AD and Dudoit, S and Buter, J and Cheng, TY and Young, DC and Nair, YM and Ouellet, IG and Griebel, BT and Ma, S and Sherman, DR and Mallet, L and Rhee, KY and Minnaard, AJ and Branch Moody, D}, title = {Mycobacteria that cause tuberculosis have retained ancestrally acquired genes for the biosynthesis of chemically diverse terpene nucleosides.}, journal = {PLoS biology}, volume = {22}, number = {9}, pages = {e3002813}, pmid = {39348416}, issn = {1545-7885}, support = {U19 AI162598/AI/NIAID NIH HHS/United States ; U19 AI162584/AI/NIAID NIH HHS/United States ; DP2 AI164249/AI/NIAID NIH HHS/United States ; R01 AI165573/AI/NIAID NIH HHS/United States ; R01 AI146194/AI/NIAID NIH HHS/United States ; }, mesh = {*Mycobacterium tuberculosis/metabolism/genetics ; *Tuberculosis/microbiology ; *Terpenes/metabolism ; Humans ; *Nucleosides/metabolism ; Adenosine/metabolism/analogs &amp; derivatives ; Lipidomics/methods ; Mass Spectrometry ; Bacterial Proteins/metabolism/genetics ; Genes, Bacterial ; Lipids ; }, abstract = {Mycobacterium tuberculosis (Mtb) releases the unusual terpene nucleoside 1-tuberculosinyladenosine (1-TbAd) to block lysosomal function and promote survival in human macrophages. Using conventional approaches, we found that genes Rv3377c and Rv3378c, but not Rv3376, were necessary for 1-TbAd biosynthesis. Here, we introduce linear models for mass spectrometry (limms) software as a next-generation lipidomics tool to study the essential functions of lipid biosynthetic enzymes on a whole-cell basis. Using limms, whole-cell lipid profiles deepened the phenotypic landscape of comparative mass spectrometry experiments and identified a large family of approximately 100 terpene nucleoside metabolites downstream of Rv3378c. We validated the identity of previously unknown adenine-, adenosine-, and lipid-modified tuberculosinol-containing molecules using synthetic chemistry and collisional mass spectrometry, including comprehensive profiling of bacterial lipids that fragment to adenine. We tracked terpene nucleoside genotypes and lipid phenotypes among Mycobacterium tuberculosis complex (MTC) species that did or did not evolve to productively infect either human or nonhuman mammals. Although 1-TbAd biosynthesis genes were thought to be restricted to the MTC, we identified the locus in unexpected species outside the MTC. Sequence analysis of the locus showed nucleotide usage characteristic of plasmids from plant-associated bacteria, clarifying the origin and timing of horizontal gene transfer to a pre-MTC progenitor. The data demonstrated correlation between high level terpene nucleoside biosynthesis and mycobacterial competence for human infection, and 2 mechanisms of 1-TbAd biosynthesis loss. Overall, the selective gain and evolutionary retention of tuberculosinyl metabolites in modern species that cause human TB suggest a role in human TB disease, and the newly discovered molecules represent candidate disease-specific biomarkers.}, }
@article {pmid39343406, year = {2024}, author = {Lin, L and Sun, M and Pan, X and Zhang, W and Yang, Y and Yang, Y}, title = {Absence of synergistic effects between microplastics and copper ions on the spread of antibiotic resistance genes within aquatic bacteria at the community level.}, journal = {The Science of the total environment}, volume = {954}, number = {}, pages = {176591}, doi = {10.1016/j.scitotenv.2024.176591}, pmid = {39343406}, issn = {1879-1026}, mesh = {*Copper/toxicity ; *Microplastics/toxicity ; *Water Pollutants, Chemical/toxicity ; *Bacteria/drug effects/genetics ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; }, abstract = {Microplastics and copper ions (Cu[2+]) are favorable in accelerating the propagation of antibiotic resistance genes (ARGs) in the plastisphere, however, their combined effects on the ARG spread within the bacterial community of the natural environment were less understood. The influence of microplastic types and Cu[2+] concentrations on the horizontal gene transfer (HGT) of ARGs mediated by RP4 plasmid within natural bacterial communities in aquatic environments was investigated. Both biodegradable polybutylene succinate (PBS) and non-biodegradable polyvinyl chloride (PVC) microplastics significantly enhanced the transfer of ARGs, with PBS showing a significant higher effect compared to PVC. Cu[2+] also increased transconjugation rates at environmentally relevant concentrations (5 μg L[-1]), but higher levels (50 μg L[-1]) lead to decreased rates due to severe bacterial cell membrane damage. The transconjugation rates in the presence of both microplastics and Cu[2+] were lower than the sum of their individual effects, indicating no synergistic effects between them on transconjugation. Proteobacteria dominated the composition of transconjugates for all the treatment. Transmission electron microscope images and reactive oxygen species production in bacterial cells indicated that the increased contact frequency due to extracellular polymeric substances, combined with enhanced membrane permeability induced by microplastics and Cu[2+], accounted for the increasing transconjugation rates. The study provides valuable insight into the potential effects of microplastics and heavy metals on the spread of ARGs from donors to bacterial communities in natural environments.}, }
@article {pmid39343112, year = {2024}, author = {Tao, Y and Zeng, Z and Deng, Y and Zhang, M and Wang, F and Wang, Y}, title = {Phylogeny and evolution of dissimilatory sulfite reduction in prokaryotes.}, journal = {Molecular phylogenetics and evolution}, volume = {201}, number = {}, pages = {108208}, doi = {10.1016/j.ympev.2024.108208}, pmid = {39343112}, issn = {1095-9513}, mesh = {*Phylogeny ; *Sulfites/metabolism ; *Oxidation-Reduction ; *Evolution, Molecular ; Bacteria/genetics/classification/metabolism ; Gene Transfer, Horizontal ; Archaea/genetics/classification/metabolism ; Prokaryotic Cells/classification/metabolism ; Sequence Analysis, DNA ; }, abstract = {Sulfate is the second most common nonmetallic ion in modern oceans, as its concentration dramatically increased alongside tectonic activity and atmospheric oxidation in the Proterozoic. Microbial sulfate/sulfite metabolism, involving organic carbon or hydrogen oxidation, is linked to sulfur and carbon biogeochemical cycles. However, the coevolution of microbial sulfate/sulfite metabolism and Earth's history remains unclear. Here, we conducted a comprehensive phylogenetic analysis to explore the evolutionary history of the dissimilatory sulfite reduction (Dsr) pathway. The phylogenies of the Dsr-related genes presented similar branching patterns but also some incongruencies, indicating the complex origin and evolution of Dsr. Among these genes, dsrAB is the hallmark of sulfur-metabolizing prokaryotes. Our detailed analyses suggested that the evolution of dsrAB was shaped by vertical inheritance and multiple horizontal gene transfer events and that selection pressure varied across distinct lineages. Dated phylogenetic trees indicated that key evolutionary events of dissimilatory sulfur-metabolizing prokaryotes were related to the Great Oxygenation Event (2.4-2.0 Ga) and several geological events in the "Boring Billion" (1.8-0.8 Ga), including the fragmentation of the Columbia supercontinent (approximately 1.6 Ga), the rapid increase in marine sulfate (1.3-1.2 Ga), and the Neoproterozoic glaciation event (approximately 1.0 Ga). We also proposed that the voluminous iron formations (approximately 1.88 Ga) might have induced the metabolic innovation of iron reduction. In summary, our study provides new insights into Dsr evolution and a systematic view of the coevolution of dissimilatory sulfur-metabolizing prokaryotes and the Earth's environment.}, }
@article {pmid39343029, year = {2024}, author = {Fernie, AR and de Vries, S and de Vries, J}, title = {Evolution of plant metabolism: the state-of-the-art.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {379}, number = {1914}, pages = {20230347}, pmid = {39343029}, issn = {1471-2970}, mesh = {*Plants/metabolism/genetics ; Biological Evolution ; Metabolic Networks and Pathways/genetics ; Evolution, Molecular ; }, abstract = {Immense chemical diversity is one of the hallmark features of plants. This chemo-diversity is mainly underpinned by a highly complex and biodiverse biochemical machinery. Plant metabolic enzymes originated and were inherited from their eukaryotic and prokaryotic ancestors and further diversified by the unprecedentedly high rates of gene duplication and functionalization experienced in land plants. Unlike prokaryotic microbes, which display frequent horizontal gene transfer events and multiple inputs of energy and organic carbon, land plants predominantly rely on organic carbon generated from CO2 and have experienced relatively few gene transfers during their recent evolutionary history. As such, plant metabolic networks have evolved in a stepwise manner using existing networks as a starting point and under various evolutionary constraints. That said, until recently, the evolution of only a handful of metabolic traits had been extensively investigated and as such, the evolution of metabolism has received a fraction of the attention of, the evolution of development, for example. Advances in metabolomics and next-generation sequencing have, however, recently led to a deeper understanding of how a wide range of plant primary and specialized (secondary) metabolic pathways have evolved both as a consequence of natural selection and of domestication and crop improvement processes. This article is part of the theme issue 'The evolution of plant metabolism'.}, }
@article {pmid39339889, year = {2024}, author = {Arhab, Y and Pestova, TV and Hellen, CUT}, title = {Translation of Overlapping Open Reading Frames Promoted by Type 2 IRESs in Avian Calicivirus Genomes.}, journal = {Viruses}, volume = {16}, number = {9}, pages = {}, pmid = {39339889}, issn = {1999-4915}, support = {5 R01 GM097014//NIH (NIGMS)/ ; 5 R35 GM122602//NIH (NIGMS)/ ; }, mesh = {*Open Reading Frames ; *Genome, Viral ; Animals ; *Internal Ribosome Entry Sites/genetics ; *Caliciviridae/genetics ; *Protein Biosynthesis ; RNA, Viral/genetics ; 5' Untranslated Regions/genetics ; Ribosomes/metabolism/genetics ; }, abstract = {Caliciviruses have positive-sense RNA genomes, typically with short 5'-untranslated regions (5'UTRs) that precede the long open reading frame 1 (ORF1). Exceptionally, some avian caliciviruses have long 5'UTRs containing a picornavirus-like internal ribosomal entry site (IRES), which was likely acquired by horizontal gene transfer. Here, we identified numerous additional avian calicivirus genomes with IRESs, predominantly type 2, and determined that many of these genomes contain a ~200-300 codon-long ORF (designated ORF1*) that overlaps the 5'-terminal region of ORF1. The activity of representative type 2 IRESs from grey teal calicivirus (GTCV) and Caliciviridae sp. isolate yc-13 (RaCV1) was confirmed by in vitro translation. Toeprinting showed that in cell-free extracts and in vitro reconstituted reactions, ribosomal initiation complexes assembled on the ORF1* initiation codon and at one or two AUG codons in ORF1 at the 3'-border and/or downstream of the IRES. Initiation at all three sites required eIF4A and eIF4G, which bound to a conserved region of the IRES; initiation on the ORF1* and principal ORF1 initiation codons involved eIF1/eIF1A-dependent scanning from the IRES's 3'-border. Initiation on these IRESs was enhanced by the IRES trans-acting factors (ITAFs) Ebp1/ITAF45, which bound to the apical subdomain Id of the IRES, and PTB (GTCV) or PCBP2 (RaCV1).}, }
@article {pmid39338985, year = {2024}, author = {Sung, K and Nawaz, M and Park, M and Chon, J and Khan, SA and Alotaibi, K and Khan, AA}, title = {Comprehensive Genomic Analysis of Uropathogenic E. coli: Virulence Factors, Antimicrobial Resistance, and Mobile Genetic Elements.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {9}, pages = {}, pmid = {39338985}, issn = {2076-0817}, support = {E0770601//United States Food and Drug Administration/ ; }, mesh = {*Uropathogenic Escherichia coli/genetics/drug effects/pathogenicity ; Humans ; *Virulence Factors/genetics ; *Escherichia coli Infections/microbiology/drug therapy ; *Anti-Bacterial Agents/pharmacology ; *Interspersed Repetitive Sequences/genetics ; *Drug Resistance, Multiple, Bacterial/genetics ; Genome, Bacterial ; Genomics/methods ; Urinary Tract Infections/microbiology/drug therapy ; Genomic Islands/genetics ; Whole Genome Sequencing ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Female ; Male ; }, abstract = {Our whole-genome sequencing analysis of sixteen uropathogenic E. coli isolates revealed a concerning picture of multidrug resistance and potentially virulent bacteria. All isolates belonged to four distinct clonal groups, with the highly prevalent ST131 lineage being associated with extensive antibiotic resistance and virulence factors. Notably, all isolates exhibited multidrug resistance, with some resistant to as many as 12 antibiotics. Fluoroquinolone resistance stemmed primarily from efflux pumps and mutations in gyrase and topoisomerase genes. Additionally, we identified genes encoding resistance to extended-spectrum cephalosporins, trimethoprim/sulfamethoxazole, and various heavy metals. The presence of diverse plasmids and phages suggests the potential for horizontal gene transfer and the dissemination of virulence factors. All isolates harbored genomic islands containing virulence factors associated with adhesion, biofilm formation, and invasion. Genes essential for iron acquisition, flagella biosynthesis, secretion systems, and toxin production were also prevalent. Adding further complexity to understanding the isolates' genetic makeup, we identified CRISPR-Cas systems. This study underscores the need for continued genomic surveillance in understanding the pathogenic mechanisms and resistance profiles of uropathogenic E. coli to aid in developing targeted therapeutic strategies.}, }
@article {pmid39338594, year = {2024}, author = {Oliveira, M and Antunes, W and Mota, S and Madureira-Carvalho, &#xc1; and Dinis-Oliveira, RJ and Dias da Silva, D}, title = {An Overview of the Recent Advances in Antimicrobial Resistance.}, journal = {Microorganisms}, volume = {12}, number = {9}, pages = {}, pmid = {39338594}, issn = {2076-2607}, support = {UIDP/04378/2020, UIDB/04378/2020, LA/P/0140/2020, UIDB/50006//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; }, abstract = {Antimicrobial resistance (AMR), frequently considered a major global public health threat, requires a comprehensive understanding of its emergence, mechanisms, advances, and implications. AMR's epidemiological landscape is characterized by its widespread prevalence and constantly evolving patterns, with multidrug-resistant organisms (MDROs) creating new challenges every day. The most common mechanisms underlying AMR (i.e., genetic mutations, horizontal gene transfer, and selective pressure) contribute to the emergence and dissemination of new resistant strains. Therefore, mitigation strategies (e.g., antibiotic stewardship programs-ASPs-and infection prevention and control strategies-IPCs) emphasize the importance of responsible antimicrobial use and surveillance. A One Health approach (i.e., the interconnectedness of human, animal, and environmental health) highlights the necessity for interdisciplinary collaboration and holistic strategies in combating AMR. Advancements in novel therapeutics (e.g., alternative antimicrobial agents and vaccines) offer promising avenues in addressing AMR challenges. Policy interventions at the international and national levels also promote ASPs aiming to regulate antimicrobial use. Despite all of the observed progress, AMR remains a pressing concern, demanding sustained efforts to address emerging threats and promote antimicrobial sustainability. Future research must prioritize innovative approaches and address the complex socioecological dynamics underlying AMR. This manuscript is a comprehensive resource for researchers, policymakers, and healthcare professionals seeking to navigate the complex AMR landscape and develop effective strategies for its mitigation.}, }
@article {pmid39338472, year = {2024}, author = {Gonzalez, V and Abarca-Hurtado, J and Arancibia, A and Claverías, F and Guevara, MR and Orellana, R}, title = {Novel Insights on Extracellular Electron Transfer Networks in the Desulfovibrionaceae Family: Unveiling the Potential Significance of Horizontal Gene Transfer.}, journal = {Microorganisms}, volume = {12}, number = {9}, pages = {}, pmid = {39338472}, issn = {2076-2607}, support = {11190863//ANID/Fondecyt/ ; 1211977//ANID/Fondecyt/ ; PAI79170091//ANID/ ; FOVI 230154//ANID/ ; Milenio-NCN2023_054//ANID/ ; Scholarship 21231799/2023//ANID/ ; }, abstract = {Some sulfate-reducing bacteria (SRB), mainly belonging to the Desulfovibrionaceae family, have evolved the capability to conserve energy through microbial extracellular electron transfer (EET), suggesting that this process may be more widespread than previously believed. While previous evidence has shown that mobile genetic elements drive the plasticity and evolution of SRB and iron-reducing bacteria (FeRB), few have investigated the shared molecular mechanisms related to EET. To address this, we analyzed the prevalence and abundance of EET elements and how they contributed to their differentiation among 42 members of the Desulfovibrionaceae family and 23 and 59 members of Geobacteraceae and Shewanellaceae, respectively. Proteins involved in EET, such as the cytochromes PpcA and CymA, the outer membrane protein OmpJ, and the iron-sulfur cluster-binding CbcT, exhibited widespread distribution within Desulfovibrionaceae. Some of these showed modular diversification. Additional evidence revealed that horizontal gene transfer was involved in the acquiring and losing of critical genes, increasing the diversification and plasticity between the three families. The results suggest that specific EET genes were widely disseminated through horizontal transfer, where some changes reflected environmental adaptations. These findings enhance our comprehension of the evolution and distribution of proteins involved in EET processes, shedding light on their role in iron and sulfur biogeochemical cycling.}, }
@article {pmid39337307, year = {2024}, author = {Zhang, J and Zhu, S and Sun, J and Liu, Y}, title = {Bisphenol S Promotes the Transfer of Antibiotic Resistance Genes via Transformation.}, journal = {International journal of molecular sciences}, volume = {25}, number = {18}, pages = {}, pmid = {39337307}, issn = {1422-0067}, support = {BE2023332//Key R&amp;D Program of Jiangsu Province (Modern Agriculture)/ ; ZDYF2024SHFZ050//Science and Technology special fund of Hainan Province/ ; }, mesh = {*Phenols ; *Escherichia coli/genetics/drug effects ; *Sulfones/pharmacology ; *Plasmids/genetics ; Reactive Oxygen Species/metabolism ; Transformation, Bacterial ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; Benzhydryl Compounds ; Citric Acid Cycle/drug effects/genetics ; }, abstract = {The antibiotic resistance crisis has seriously jeopardized public health and human safety. As one of the ways of horizontal transfer, transformation enables bacteria to acquire exogenous genes naturally. Bisphenol compounds are now widely used in plastics, food, and beverage packaging, and have become a new environmental pollutant. However, their potential relationship with the spread of antibiotic resistance genes (ARGs) in the environment remains largely unexplored. In this study, we aimed to assess whether the ubiquitous bisphenol S (BPS) could promote the transformation of plasmid-borne ARGs. Using plasmid pUC19 carrying the ampicillin resistance gene as an extracellular ARG and model microorganism E. coli DH5α as the recipient, we established a transformation system. Transformation assays revealed that environmentally relevant concentrations of BPS (0.1-10 μg/mL) markedly enhanced the transformation frequency of plasmid-borne ARGs into E. coli DH5α up to 2.02-fold. Fluorescent probes and transcript-level analyses suggest that BPS stimulated increased reactive oxygen species (ROS) production, activated the SOS response, induced membrane damage, and increased membrane fluidity, which weakened the barrier for plasmid transfer, allowing foreign DNA to be more easily absorbed. Moreover, BPS stimulates ATP supply by activating the tricarboxylic acid (TCA) cycle, which promotes flagellar motility and expands the search for foreign DNA. Overall, these findings provide important insight into the role of bisphenol compounds in facilitating the horizontal spread of ARGs and emphasize the need to monitor the residues of these environmental contaminants.}, }
@article {pmid39336804, year = {2024}, author = {Opazo-Capurro, A and Xanthopoulou, K and Arazo Del Pino, R and González-Muñoz, P and Matus-Köhler, M and Amsteins-Romero, L and Jerez-Olate, C and Hormazábal, JC and Vera, R and Aguilera, F and Fuller, S and Higgins, PG and González-Rocha, G}, title = {Co-Occurrence of Two Plasmids Encoding Transferable blaNDM-1 and tet(Y) Genes in Carbapenem-Resistant Acinetobacter bereziniae.}, journal = {Genes}, volume = {15}, number = {9}, pages = {}, pmid = {39336804}, issn = {2073-4425}, support = {FONDECYT 1220708//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; FONDECYT Iniciacion 11190602//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; FONDEQUIP EQM200056//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; }, mesh = {*Plasmids/genetics ; *Acinetobacter/genetics/drug effects ; *beta-Lactamases/genetics ; Humans ; *Carbapenems/pharmacology ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Microbial Sensitivity Tests ; Acinetobacter Infections/microbiology/drug therapy/epidemiology ; Bacterial Proteins/genetics ; Whole Genome Sequencing ; COVID-19 ; }, abstract = {Acinetobacter bereziniae has emerged as a significant human pathogen, acquiring multiple antibiotic resistance genes, including carbapenemases. This study focuses on characterizing the plasmids harboring the blaNDM-1 and tet(Y) genes in two carbapenem-resistant A. bereziniae isolates (UCO-553 and UCO-554) obtained in Chile during the COVID-19 pandemic. Methods: Antibiotic susceptibility testing was conducted on UCO-553 and UCO-554. Both isolates underwent whole-genome sequencing to ascertain their sequence type (ST), core genome multilocus sequence-typing (cgMLST) profile, antibiotic resistance genes, plasmids, and mobile genetic elements. Conjugation experiments were performed for both isolates. Results: Both isolates exhibited broad resistance, including resistance to carbapenems, third-generation cephalosporins, fluoroquinolones, tetracycline, cotrimoxazole, and aminoglycosides. Both isolates belong to sequence type ST[PAS]1761, with a difference of 17 out of 2984 alleles. Each isolate carried a 47,274 bp plasmid with blaNDM-1 and aph(3')-VI genes and two highly similar plasmids: a 35,184 bp plasmid with tet(Y), sul2, aph(6)-Id, and aph(3″)-Ib genes, and a 6078 bp plasmid containing the ant(2″)-Ia gene. Quinolone-resistance mutations were identified in the gyrA and parC genes of both isolates. Importantly, blaNDM-1 was located within a Tn125 transposon, and tet(Y) was embedded in a Tn5393 transposon. Conjugation experiments successfully transferred blaNDM-1 and tet(Y) into the A. baumannii ATCC 19606 strain, indicating the potential for horizontal gene transfer. Conclusions: This study highlights the critical role of plasmids in disseminating resistance genes in A. bereziniae and underscores the need for the continued genomic surveillance of this emerging pathogen. The findings emphasize the importance of monitoring A. bereziniae for its potential to cause difficult-to-treat infections and its capacity to spread resistance determinants against clinically significant antibiotics.}, }
@article {pmid39335078, year = {2024}, author = {Tarrah, A and Zhang, D and Darvishzadeh, P and LaPointe, G}, title = {The Contribution of Dairy Bedding and Silage to the Dissemination of Genes Coding for Antimicrobial Resistance: A Narrative Review.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {9}, pages = {}, pmid = {39335078}, issn = {2079-6382}, abstract = {Antimicrobial resistance (AMR) is a concern in the dairy industry. Recent studies have indicated that bedding serves as a reservoir for antimicrobial-resistant bacteria and antimicrobial-resistance genes (ARGs), while silage has been proposed as another possible source. The impact of AMR in dairy farming can be significant, resulting in decreased productivity and economic losses for farmers. Several studies have highlighted the safety implications of AMR bacteria and genes in bedding and silage, emphasizing the need for further research on how housing, bedding, and silage management affect AMR in farm environments. Exposure to sub-lethal concentrations of antibiotics, such as those from contaminated bedding and silage, can prompt bacteria to develop resistance mechanisms. Thus, even if antimicrobial usage is diminished, ARGs may be maintained in the dairy farm environment. By implementing proactive measures to tackle AMR in dairy farming, we can take steps to preserve the health and productivity of dairy cattle while also protecting public health. This involves addressing the prudent use of antibiotics during production and promoting animal welfare, hygiene, and management practices in bedding and farm environments to minimize the risk of AMR development and spread. This narrative review compiles the growing research, positioning the contribution of bedding and silage to the prevalence and dissemination of AMR, which can elicit insights for researchers and policymakers.}, }
@article {pmid39334999, year = {2024}, author = {Mitchell, TM and Ho, T and Salinas, L and VanderYacht, T and Walas, N and Trueba, G and Graham, JP}, title = {Analysis of Antibiotic Resistance Genes (ARGs) across Diverse Bacterial Species in Shrimp Aquaculture.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {9}, pages = {}, pmid = {39334999}, issn = {2079-6382}, abstract = {There is little information available on antibiotic resistance (ABR) within shrimp aquaculture environments. The aim of this study was to investigate the presence of antibiotic resistance genes (ARGs) in shrimp farming operations in Atacames, Ecuador. Water samples (n = 162) and shrimp samples (n = 54) were collected from three shrimp farming operations. Samples were cultured and a subset of isolates that grew in the presence of ceftriaxone, a third-generation cephalosporin, were analyzed using whole-genome sequencing (WGS). Among the sequenced isolates (n = 44), 73% of the isolates contained at least one ARG and the average number of ARGs per isolate was two, with a median of 3.5 ARGs. Antibiotic resistance genes that confer resistance to the β-lactam class of antibiotics were observed in 65% of the sequenced isolates from water (20/31) and 54% of the isolates from shrimp (7/13). We identified 61 different ARGs across the 44 sequenced isolates, which conferred resistance to nine antibiotic classes. Over half of all sequenced isolates (59%, n = 26) carried ARGs that confer resistance to more than one class of antibiotics. ARGs for certain antibiotic classes were more common, including beta-lactams (26 ARGs); aminoglycosides (11 ARGs); chloramphenicol (three ARGs); and trimethoprim (four ARGs). Sequenced isolates consisted of a diverse array of bacterial orders and species, including Escherichia coli (48%), Klebsiella pneumoniae (7%), Aeromonadales (7%), Pseudomonadales (16%), Enterobacter cloacae (2%), and Citrobacter freundii (2%). Many ARGs were shared across diverse species, underscoring the risk of horizontal gene transfer in these environments. This study indicated the widespread presence of extended-spectrum β-lactamase (ESBL) genes in shrimp aquaculture, including blaCTX-M, blaSHV, and blaTEM genes. Increased antibiotic resistance surveillance of shrimp farms and identification of aquaculture operation-level risk factors, such as antibiotic use, will likely be important for mitigating the spread of ARGs of clinical significance.}, }
@article {pmid39334992, year = {2024}, author = {Liu, L and Zou, X and Cheng, Y and Li, H and Zhang, X and Yuan, Q}, title = {Contrasting Dynamics of Intracellular and Extracellular Antibiotic Resistance Genes in Response to Nutrient Variations in Aquatic Environments.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {9}, pages = {}, pmid = {39334992}, issn = {2079-6382}, support = {No. 42377436 and 42177348//National Natural Science Foundation of China/ ; 2022YFC3205400//China National Key R&amp;D Program/ ; }, abstract = {The propagation of antibiotic resistance in environments, particularly aquatic environments that serve as primary pathways for antibiotic resistance genes (ARGs), poses significant health risks. The impact of nutrients, as key determinants of bacterial growth and metabolism, on the propagation of ARGs, particularly extracellular ARGs (eARGs), remains poorly understood. In this study, we collected microorganisms from the Yangtze River and established a series of microcosms to investigate how variations in nutrient levels and delivery frequency affect the relative abundance of intracellular ARGs (iARGs) and eARGs in bacterial communities. Our results show that the relative abundance of 7 out of 11 representative eARGs in water exceeds that of iARGs, while 8 iARGs dominate in biofilms. Notably, iARGs and eARGs consistently exhibited opposite responses to nutrient variation. When nutrient levels increased, iARGs in the water also increased, with the polluted group (COD = 333.3 mg/L, COD:N:P = 100:3:0.6, m/m) and the eutrophic group (COD = 100 mg/L, COD:N:P = 100:25:5, m/m) showing 1.2 and 3.2 times higher levels than the normal group (COD = 100 mg/L, COD:N:P = 100:10:2, m/m), respectively. In contrast, eARGs decreased by 6.7% and 8.4% in these groups. On the other hand, in biofilms, higher nutrient levels led to an increase in eARGs by 1.5 and 1.7 times, while iARGs decreased by 17.5% and 50.1% in the polluted and eutrophic groups compared to the normal group. Moreover, while increasing the frequency of nutrient delivery (from 1 time/10 d to 20 times/10 d) generally did not favor iARGs in either water or biofilm, it selectively enhanced eARGs in both. To further understand these dynamics, we developed an ARGs-nutrient model by integrating the Lotka-Volterra and Monod equations. The results highlight the complex interplay of bacterial growth, nutrient availability, and mechanisms such as horizontal gene transfer and secretion influencing ARGs' propagation, driving the opposite trend between these two forms of ARGs. This contrasting response between iARGs and eARGs contributes to a dynamic balance that stabilizes bacterial resistance levels amid nutrient fluctuations. This study offers helpful implications regarding the persistence of bacterial resistance in the environment.}, }
@article {pmid39329926, year = {2024}, author = {Syed, K}, title = {Ferredoxins: Functions, Evolution, Potential Applications, and Challenges of Subtype Classification.}, journal = {Current issues in molecular biology}, volume = {46}, number = {9}, pages = {9659-9673}, pmid = {39329926}, issn = {1467-3045}, abstract = {Ferredoxins are proteins found in all biological kingdoms and are involved in essential biological processes including photosynthesis, lipid metabolism, and biogeochemical cycles. Ferredoxins are classified into different groups based on the iron-sulfur (Fe-S) clusters that they contain. A new subtype classification and nomenclature system, based on the spacing between amino acids in the Fe-S binding motif, has been proposed in order to better understand ferredoxins' biological diversity and evolutionary linkage across different organisms. This new classification system has revealed an unparalleled diversity between ferredoxins and has helped identify evolutionarily linked ferredoxins between species. The current review provides the latest insights into ferredoxin functions and evolution, and the new subtype classification, outlining their potential biotechnological applications and the future challenges in streamlining the process.}, }
@article {pmid39328914, year = {2024}, author = {Yan, J and Doublet, B and Wiedemann, A}, title = {Trends in horizontal gene transfer research in Salmonella antimicrobial resistance: a bibliometric analysis.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1439664}, pmid = {39328914}, issn = {1664-302X}, abstract = {Horizontal gene transfer (HGT) favors the acquisition and spread of antimicrobial resistance (AMR) genes in Salmonella, making it a major public health concern. We performed a bibliometric analysis to provide the current landscape of HGT in research on Salmonella AMR and identify emerging trends and potential research directions for the future. Data were collected from the Web of Science Core Collection and limited to articles and reviews published between 1999 and 2024 in English. VOSviewer 1.6.19 and CiteSpace 6.2.R1 software were used to conduct bibliometric analysis and visualize co-occurring keywords. A total of 1,467 publications were retrieved for analysis. American researchers contributed the most articles (n = 310). In the meantime, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement have the highest citation/publication rate of 85.6. Recent studies have focused on the application of whole genome sequencing (WGS), Salmonella quinolone and colistin resistance, and the biocontrol of Salmonella AMR. These findings provide new insights into the role of HGT and help identify new targets for controlling the spread of AMR in Salmonella populations.}, }
@article {pmid39327210, year = {2025}, author = {García-Lozano, M and Salem, H}, title = {Microbial bases of herbivory in beetles.}, journal = {Trends in microbiology}, volume = {33}, number = {2}, pages = {151-163}, doi = {10.1016/j.tim.2024.08.004}, pmid = {39327210}, issn = {1878-4380}, mesh = {Animals ; *Coleoptera/microbiology/physiology ; *Herbivory/physiology ; Gene Transfer, Horizontal ; Symbiosis ; Bacteria/genetics/metabolism ; *Microbiota ; }, abstract = {The ecological radiation of herbivorous beetles is among the most successful in the animal kingdom. It coincided with the rise and diversification of flowering plants, requiring beetles to adapt to a nutritionally imbalanced diet enriched in complex polysaccharides and toxic secondary metabolites. In this review, we explore how beetles overcame these challenges by coopting microbial genes, enzymes, and metabolites, through both horizontal gene transfer (HGT) and symbiosis. Recent efforts revealed the functional convergence governing both processes and the unique ways in which microbes continue to shape beetle digestion, development, and defense. The development of genetic and experimental tools across a diverse set of study systems has provided valuable mechanistic insights into how microbes spurred metabolic innovation and facilitated an herbivorous transition in beetles.}, }
@article {pmid39326418, year = {2024}, author = {Liu, Y and Miao, B and Li, W and Hu, X and Bai, F and Abuduresule, Y and Liu, Y and Zheng, Z and Wang, W and Chen, Z and Zhu, S and Feng, X and Cao, P and Ping, W and Yang, R and Dai, Q and Liu, F and Tian, C and Yang, Y and Fu, Q}, title = {Bronze Age cheese reveals human-Lactobacillus interactions over evolutionary history.}, journal = {Cell}, volume = {187}, number = {21}, pages = {5891-5900.e8}, doi = {10.1016/j.cell.2024.08.008}, pmid = {39326418}, issn = {1097-4172}, mesh = {Humans ; *Cheese/microbiology ; *Lactobacillus/genetics ; Kefir/microbiology ; History, Ancient ; Phylogeny ; China ; Biological Evolution ; Fermentation ; Asia, Eastern ; }, abstract = {Despite the long history of consumption of fermented dairy, little is known about how the fermented microbes were utilized and evolved over human history. Here, by retrieving ancient DNA of Bronze Age kefir cheese (∼3,500 years ago) from the Xiaohe cemetery, we explored past human-microbial interactions. Although it was previously suggested that kefir was spread from the Northern Caucasus to Europe and other regions, we found an additional spreading route of kefir from Xinjiang to inland East Asia. Over evolutionary history, the East Asian strains gained multiple gene clusters with defensive roles against environmental stressors, which can be a result of the adaptation of Lactobacillus strains to various environmental niches and human selection. Overall, our results highlight the role of past human activities in shaping the evolution of human-related microbes, and such insights can, in turn, provide a better understanding of past human behaviors.}, }
@article {pmid39324609, year = {2024}, author = {Liu, QH and Yuan, L and Li, ZH and Leung, KMY and Sheng, GP}, title = {Natural Organic Matter Enhances Natural Transformation of Extracellular Antibiotic Resistance Genes in Sunlit Water.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {40}, pages = {17990-17998}, doi = {10.1021/acs.est.4c08211}, pmid = {39324609}, issn = {1520-5851}, mesh = {*Drug Resistance, Microbial/genetics ; *Sunlight ; Anti-Bacterial Agents/pharmacology ; Reactive Oxygen Species/metabolism ; }, abstract = {Antibiotic resistance genes (ARGs) as emerging environmental contaminants exacerbate the risk of spreading antibiotic resistance. Natural organic matter (NOM) is ubiquitous in aquatic environments and plays a crucial role in biogeochemical cycles. However, its impact on the dissemination of extracellular antibiotic resistance genes (eARGs) under sunlight exposure remains elusive. This study reveals that environmentally relevant levels of NOM (0.1-20 mg/L) can significantly enhance the natural transformation frequency of the model bacterium Acinetobacter baylyi ADP1 by up to 7.6-fold under simulated sunlight. Similarly, this enhancement was consistently observed in natural water and wastewater systems. Further mechanism analysis revealed that reactive oxygen species (ROS) generated by NOM under sunlight irradiation, primarily singlet oxygen and hydroxyl radicals, play a crucial role in this process. These ROS induce intracellular oxidative stress and elevated cellular membrane permeability, thereby indirectly boosting ATP production and enhancing cell competence of extracellular DNA uptake and integration. Our findings highlight a previously underestimated role of natural factors in the dissemination of eARGs within aquatic ecosystems and deepen our understanding of the complex interplay between NOM, sunlight, and microbes in environmental water bodies. This underscores the importance of developing comprehensive strategies to mitigate the spread of antibiotic resistance in aquatic environments.}, }
@article {pmid39322056, year = {2024}, author = {Chen, J and Lin, Y and Zhu, Y and Zhang, Y and Qian, Q and Chen, C and Xie, S}, title = {Spatiotemporal profiles and underlying mechanisms of the antibiotic resistome in two water-diversion lakes.}, journal = {Environmental research}, volume = {263}, number = {Pt 1}, pages = {120051}, doi = {10.1016/j.envres.2024.120051}, pmid = {39322056}, issn = {1096-0953}, mesh = {*Lakes/microbiology ; China ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Seasons ; Drug Resistance, Microbial/genetics ; Spatio-Temporal Analysis ; Environmental Monitoring ; Bacteria/drug effects/genetics ; Drug Resistance, Bacterial/genetics ; }, abstract = {Human-induced interventions have altered the local characteristics of the lake ecosystems through changes in hydraulic exchange, which in turn impacts the ecological processes of antibiotic resistance genes (ARGs) in the lakes. However, the current understanding of the spatiotemporal patterns and driving factors of ARGs in water-diversion lakes is still seriously insufficient. In the present study, we investigated antibiotic resistome in the main regulation and storage hubs, namely Nansi Lake and Dongping Lake, of the eastern part of the South-to-North Water Diversion project in Shandong Province (China) using a metagenomic-based approach. A total of 653 ARG subtypes belonging to 25 ARG types were detected with a total abundance of 0.125-0.390 copies/cell, with the dominance of bacitracin, multidrug, and macrolide-lincosamide streptogramin resistance genes. The ARG compositions were sensitive to seasonal variation and also interfered by artificial regulation structures along the way. Human pathogenic bacteria such as Acinetobacter calcoaceticus, Acinetobacter lwoffii, Klebsiella pneumoniae, along with the multidrug resistance genes they carried, were the focus of risk control in the two studied lakes, especially in summer. Plasmids were the key mobile genetic elements (MGEs) driving the horizontal gene transfer of ARGs, especially multidrug and sulfonamide resistance genes. The null model revealed that stochastic process was the main driver of ecological drift for ARGs in the lakes. The partial least squares structural equation model further determined that seasonal changes of pH and temperature drove a shift in the bacterial community, which in turn shaped the profile of ARGs by altering the composition of MGEs, antibacterial biocide- and metal-resistance genes (BMGs), and virulence factor genes (VFGs). Our results highlighted the importance of seasonal factors in determining the water transfer period. These findings can aid in a deeper understanding of the spatiotemporal variations of ARGs in lakes and their driving factors, offering a scientific basis for antibiotic resistance management.}, }
@article {pmid39321940, year = {2024}, author = {Wang, P and Li, L and Zhang, Y and Ren, D and Feng, Y and Li, X and Wu, D and Xie, B and Ma, J}, title = {Triclosan facilitates the dissemination of antibiotic resistance genes during anaerobic digestion: Focusing on horizontal transfer and microbial response.}, journal = {Bioresource technology}, volume = {413}, number = {}, pages = {131522}, doi = {10.1016/j.biortech.2024.131522}, pmid = {39321940}, issn = {1873-2976}, mesh = {*Triclosan/pharmacology ; Anaerobiosis ; *Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Bioreactors ; }, abstract = {The present study aims to investigate the mechanism by which triclosan influences the dissemination of antibiotic resistance genes (ARGs) during the whole anaerobic digestion process. qPCR and metagenomic analyses revealed that triclosan facilitated ARGs dissemination in a dose- and time-dependent manner. Furthermore, integrons exhibited a significant correlation with the majority of quantified ARGs, and various ARGs were frequently linked on integron gene cassettes. Microbial community and redundancy analyses indicated that triclosan altered the components of dominant ARGs hosts Firmicutes, Synergistetes and Bacteroidetes. Path modeling analysis confirmed integrons were the main driving force for facilitating ARGs dissemination. The promoted ARGs dissemination may be associated with the increased reactive oxygen species generation, cell membrane permeability, close-connected the ARGs transfer related regulatory proteins induced by triclosan. This study broadens the understanding of triclosan facilitates ARGs dissemination through anaerobic treatment, the strategies for preventing potential risks should be proposed in practice.}, }
@article {pmid39321479, year = {2024}, author = {Rong, L and Wu, L and Zong, L and Wang, W and Xiao, Y and Yang, C and Pan, H and Zou, X}, title = {Evolution of the Black solider fly larvae gut antibiotic resistome during kitchen waste disposal.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {135878}, doi = {10.1016/j.jhazmat.2024.135878}, pmid = {39321479}, issn = {1873-3336}, mesh = {Animals ; *Larva/drug effects ; *Gastrointestinal Microbiome/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; Refuse Disposal ; Gene Transfer, Horizontal ; Diptera/genetics/microbiology/drug effects ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; }, abstract = {Kitchen waste (KW) is an important reservoir of antibiotic resistance genes (ARGs). Black solider fly larvae (BSFL) are extensively employed in KW disposal, closely linking to their robust gut microbes. However, antibiotic resistome in BSFL gut during the KW disposal processes and the mechanism remain unclear. In the present study, the antibiotic resistome in BSFL gut within the 12 days KW disposal processes were investigated. Results showed that, ARGs abundance initially increased and subsequently decreased, the five most prevalent core ARG classes were tetracycline, aminoglycoside, cephalosporin, lincosamide and multidrug. A total of 7 MGE types were observed and the horizontal gene transfer (HGT) of ARGs was predominantly mediated by plasmids. Host microbes were mainly categorized into Proteobacteria (98.12 %) and their assemblies were mainly classified into the deterministic processes. To elucidate the driving mechanisms, the mantel test and the structural equation model (SEM) were developed. Results indicated that microbial functions (0.912, p < 0.0001) and microbial community (1.014, p = 0.036), consistently showed very significant relationships with the patterns of ARGs, which presented higher direct effects than indirect effects. Overall, this study makes an initial contribution to a more deepgoing comprehension of the gut antibiotic resistome of BSFL during KW disposal.}, }
@article {pmid39319368, year = {2024}, author = {Pierpont, CL and Baroch, JJ and Church, MJ and Miller, SR}, title = {Idiosyncratic genome evolution of the thermophilic cyanobacterium Synechococcus at the limits of phototrophy.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39319368}, issn = {1751-7370}, support = {IOS-1755407//National Science Foundation/ ; }, mesh = {*Synechococcus/genetics ; *Genome, Bacterial ; *Evolution, Molecular ; *Phylogeny ; Phototrophic Processes ; Gene Transfer, Horizontal ; Thermotolerance/genetics ; Hot Temperature ; }, abstract = {Thermophilic microorganisms are expected to have smaller cells and genomes compared with mesophiles, a higher proportion of horizontally acquired genes, and distinct nucleotide and amino acid composition signatures. Here, we took an integrative approach to investigate these apparent correlates of thermophily for Synechococcus A/B cyanobacteria, which include the most heat-tolerant phototrophs on the planet. Phylogenomics confirmed a unique origin of different thermotolerance ecotypes, with low levels of continued gene flow between ecologically divergent but overlapping populations, which has shaped the distribution of phenotypic traits along these geothermal gradients. More thermotolerant strains do have smaller genomes, but genome reduction is associated with a decrease in community richness and metabolic diversity, rather than with cell size. Horizontal gene transfer played only a limited role during Synechococcus evolution, but, the most thermotolerant strains have acquired a Thermus tRNA modification enzyme that may stabilize translation at high temperatures. Although nucleotide base composition was not associated with thermotolerance, we found a general replacement of aspartate with glutamate, as well as a dramatic remodeling of amino acid composition at the highest temperatures that substantially differed from previous predictions. We conclude that Synechococcus A/B genome diversification largely does not conform to the standard view of temperature adaptation. In addition, carbon fixation was more thermolabile than photosynthetic oxygen evolution for the most thermotolerant strains compared with less tolerant lineages. This suggests that increased flow of reducing power generated during the light reactions to an electron sink(s) beyond carbon dioxide has emerged during temperature adaptation of these bacteria.}, }
@article {pmid39316921, year = {2024}, author = {Liu, Z and Feng, L and Li, B and Lü, C and Sun, J and Giannakis, S}, title = {Crouching bacteria, hidden tetA genes in natural waters: Intracellular damage via double persulfate activation (UVA/Fe[2+]/PDS) effectively alleviates the spread of antibiotic resistance.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {135854}, doi = {10.1016/j.jhazmat.2024.135854}, pmid = {39316921}, issn = {1873-3336}, mesh = {*Ultraviolet Rays ; *Sulfates/chemistry ; Drug Resistance, Bacterial/genetics/drug effects ; Anti-Bacterial Agents/pharmacology/chemistry/toxicity ; Escherichia coli/drug effects/genetics ; Iron/chemistry ; Gene Transfer, Horizontal ; Bacteria/drug effects/genetics ; Water Microbiology ; Rivers/chemistry/microbiology ; Peroxides ; }, abstract = {In this study, we elucidated the chemical and biological inactivation mechanisms of peroxydisulfate (PDS) activated by UVA and Fe[2+] (UVA/Fe[2+]/PDS) in wild-type antibiotic-resistant bacteria (ARB) isolated from a river in Inner Mongolia. Among the screened wild-type ARB, the relative abundance of unidentified Enterobacteriaceae, Stenotrophomonas, and Ralstonia was high. A ratio of 1:1 for Fe[2+] and PDS under 18 W·m[-2] UVA radiation (sunny days) completely inactivated the environmental ARB isolates. In the macro view of the inactivation process, Fe[2+] first activates PDS rapidly, and later the UVA energy accumulated starts to activate PDS; HO• then becomes the main active species at a rate-limiting step. From a micro perspective, damage to the cell wall, intracellular proteins, inactivation of antioxidant enzymes, and genetic material degradation are the inactivation series of events by UVA/Fe[2+]/PDS, contributing to the 97.8 % inactivation of ARB at the initial stage. No regrowth of sublethal ARBs was observed. The transfer of tetracycline resistance genes from ARB to lab E. coli was evaluated by horizontal gene transfer (HGT), in which no HGT occurred when ARB was eliminated by UVA/Fe[2+]/PDS. Moreover, the sulfate and iron residuals in the effluents of treated water were lower than the drinking water standards. In summary, PDS, UVA, and Fe[2+] activation effectively inactivated wild ARB with a low concentration of reagents, while inhibiting their regrowth and spread of resistance due to the contribution of intracellular inactivation pathways.}, }
@article {pmid39316269, year = {2024}, author = {Wang, L and Yu, L and Cai, B}, title = {Characteristics of tetracycline antibiotic resistance gene enrichment and migration in soil-plant system.}, journal = {Environmental geochemistry and health}, volume = {46}, number = {11}, pages = {427}, pmid = {39316269}, issn = {1573-2983}, support = {LH2023C088//the Natural Science Foundation of Heilongjiang Province of China/ ; LH2023C088//the Natural Science Foundation of Heilongjiang Province of China/ ; LH2023C088//the Natural Science Foundation of Heilongjiang Province of China/ ; HST2022TR002//the Scientific Research Project on Ecological Environmental Protection in Heilongjiang Province/ ; HST2022TR002//the Scientific Research Project on Ecological Environmental Protection in Heilongjiang Province/ ; HST2022TR002//the Scientific Research Project on Ecological Environmental Protection in Heilongjiang Province/ ; 2023SYSJJ15//2023 Open Fund Subjects of the Key Laboratory of Agro-ecological Safety in Hebei Province Project/ ; 2023SYSJJ15//2023 Open Fund Subjects of the Key Laboratory of Agro-ecological Safety in Hebei Province Project/ ; 2023SYSJJ15//2023 Open Fund Subjects of the Key Laboratory of Agro-ecological Safety in Hebei Province Project/ ; }, mesh = {*Soil Microbiology ; *Soil Pollutants ; *Tetracycline Resistance/genetics ; *Gene Transfer, Horizontal ; Plants/microbiology ; Humans ; Bacteria/genetics/drug effects ; Soil/chemistry ; Tetracycline/pharmacology ; }, abstract = {Tetracycline Resistance Genes (TRGs) have received widespread attention in recent years, as they are a novel environmental pollutant that can rapidly accumulate and migrate in soil plant systems through horizontal gene transfer (HGT), posing a potential threat to food safety and public health. This article systematically reviews the pollution sources, enrichment, and migration characteristics of TRGs in soil. The main sources of TRGs include livestock manure and contaminated wastewater, especially in intensive farming environments where TRGs pollution is more severe. In soil, TRGs diffuse horizontally between bacteria and migrate to plant tissues through mechanisms such as plasmid conjugation, integron mediation, and phage transduction. The migration of TRGs is not limited to the soil interior, and increasing evidence suggests that they can also enter the plant system through plant root absorption and the HGT pathway of endophytic bacteria, ultimately accumulating in plant roots, stems, leaves, fruits, and other parts. This process has a direct impact on human health, especially when TRGs are found in crops such as vegetables, which may be transmitted to the human body through the food chain. In addition, this article also deeply analyzed various factors that affect the migration of TRGs, including the residual level of tetracycline in soil, the type and concentration of microorganisms, heavy metal pollution, and the presence of new pollutants such as microplastics. These factors significantly affect the enrichment rate and migration mode of TRGs in soil. In addition, two technologies that can effectively eliminate TRGs in livestock breeding environments were introduced, providing reference for healthy agricultural production. The article concludes by summarizing the shortcomings of current research on TRGs, particularly the limited understanding of TRG migration pathways and their impact mechanisms. Future research should focus on revealing the migration mechanisms of TRGs in soil plant systems and developing effective control and governance measures to reduce the environmental transmission risks of TRGs and ensure the safety of ecosystems and human health.}, }
@article {pmid39312572, year = {2024}, author = {Gonçalves, C and Harrison, MC and Steenwyk, JL and Opulente, DA and LaBella, AL and Wolters, JF and Zhou, X and Shen, XX and Groenewald, M and Hittinger, CT and Rokas, A}, title = {Diverse signatures of convergent evolution in cactus-associated yeasts.}, journal = {PLoS biology}, volume = {22}, number = {9}, pages = {e3002832}, pmid = {39312572}, issn = {1545-7885}, support = {R01 AI153356/AI/NIAID NIH HHS/United States ; T32 HG002760/HG/NHGRI NIH HHS/United States ; }, mesh = {*Cactaceae/microbiology/genetics ; Phylogeny ; Yeasts/genetics ; Genome, Fungal/genetics ; Biological Evolution ; Evolution, Molecular ; Phenotype ; Gene Transfer, Horizontal ; Thermotolerance/genetics ; Ascomycota/genetics/pathogenicity ; Machine Learning ; }, abstract = {Many distantly related organisms have convergently evolved traits and lifestyles that enable them to live in similar ecological environments. However, the extent of phenotypic convergence evolving through the same or distinct genetic trajectories remains an open question. Here, we leverage a comprehensive dataset of genomic and phenotypic data from 1,049 yeast species in the subphylum Saccharomycotina (Kingdom Fungi, Phylum Ascomycota) to explore signatures of convergent evolution in cactophilic yeasts, ecological specialists associated with cacti. We inferred that the ecological association of yeasts with cacti arose independently approximately 17 times. Using a machine learning-based approach, we further found that cactophily can be predicted with 76% accuracy from both functional genomic and phenotypic data. The most informative feature for predicting cactophily was thermotolerance, which we found to be likely associated with altered evolutionary rates of genes impacting the cell envelope in several cactophilic lineages. We also identified horizontal gene transfer and duplication events of plant cell wall-degrading enzymes in distantly related cactophilic clades, suggesting that putatively adaptive traits evolved independently through disparate molecular mechanisms. Notably, we found that multiple cactophilic species and their close relatives have been reported as emerging human opportunistic pathogens, suggesting that the cactophilic lifestyle-and perhaps more generally lifestyles favoring thermotolerance-might preadapt yeasts to cause human disease. This work underscores the potential of a multifaceted approach involving high-throughput genomic and phenotypic data to shed light onto ecological adaptation and highlights how convergent evolution to wild environments could facilitate the transition to human pathogenicity.}, }
@article {pmid39309771, year = {2024}, author = {Westerström, P and Gabrielsen Ås, C and Bak Dragsted, U}, title = {Characterising virulence in a nontoxigenic non-O1/non-O139 Vibrio cholerae isolate imported from Vietnam.}, journal = {Heliyon}, volume = {10}, number = {18}, pages = {e37205}, pmid = {39309771}, issn = {2405-8440}, abstract = {Vibrio cholerae is a major human pathogen that can cause life-threatening acute diarrhea. V. cholerae are classified according to O-antigen polysaccharide outer membrane properties, where the serotypes O1 and O139 are strains that cause pandemics and epidemics while non-O1/non-O139 usually cause mild disease. The dynamic evolution of V. cholerae involves acquisition of new virulence factors through horizontal gene transfer and formerly nontoxigenic serogroups are increasingly being reported to cause severe forms of human disease. In this study we have serotyped one isolate (ST588-CPH) of imported V. cholerae from Vietnam to Denmark and performed whole genome sequencing to identify known virulence genes and furthermore studied the pattern of virulence in closely related pathogenic strains of V. cholerae. ST558-CPH was found to be a non-O1/non-O139 strain. Initial analysis from the whole genome sequencing gave a 96,6 % match to the O139-specific wbfZ gene, but in a second analysis with a higher identification threshold, the wbfZ gene was absent. We suggest a "de novo" display of a database misannotation, which explains the conflicting results. The MLST analysis revealed that the isolate belongs to the nontoxigenic non-O1/non-O139 sequence type ST558. ST558 has recently been reported as a sequence type forming a cluster of ST's that should be monitored, as it has shown to have virulence causing moderate to severe illness. Our analysis of virulence genes identified MakA, a recently discovered toxin, which seems to be generally present in both toxigenic and nontoxigenic strains.}, }
@article {pmid39308980, year = {2024}, author = {Mendoza, H and Lamb, EA and Thomas, J and Tavares, DG and Schroeder, LA and Müller, C and Agrawal, N and Schirawski, J and Perlin, MH}, title = {Comparative mitogenomic analysis of Sporisorium reilianum f. sp. zeae suggests recombination events during its evolutionary history.}, journal = {Frontiers in physiology}, volume = {15}, number = {}, pages = {1264359}, pmid = {39308980}, issn = {1664-042X}, abstract = {INTRODUCTION: Modern understanding of the concept of genetic diversity must include the study of both nuclear and organellar DNA, which differ greatly in terms of their structure, organization, gene content and distribution. This study comprises an analysis of the genetic diversity of the smut fungus Sporisorium reilianum f. sp. zeae from a mitochondrial perspective.<br><br>METHODS: Whole-genome sequencing data was generated from biological samples of S. reilianum collected from different geographical regions. Multiple sequence alignment and gene synteny analysis were performed to further characterize genetic diversity in the context of mitogenomic polymorphisms.<br><br>RESULTS: Mitochondria of strains collected in China contained unique sequences. The largest unique sequence stretch encompassed a portion of cox1, a mitochondrial gene encoding one of the subunits that make up complex IV of the mitochondrial electron transport chain. This unique sequence had high percent identity to the mitogenome of the related species Sporisorium scitamineum and Ustilago bromivora.<br><br>DISCUSSION: The results of this study hint at potential horizontal gene transfer or mitochondrial genome recombination events during the evolutionary history of basidiomycetes. Additionally, the distinct polymorphic region detected in the Chinese mitogenome provides the ideal foundation to develop a diagnostic method to discern between mitotypes and enhance knowledge on the genetic diversity of this organism.}, }
@article {pmid39306135, year = {2024}, author = {Wang, B and Farhan, MHR and Yuan, L and Sui, Y and Chu, J and Yang, X and Li, Y and Huang, L and Cheng, G}, title = {Transfer dynamics of antimicrobial resistance among gram-negative bacteria.}, journal = {The Science of the total environment}, volume = {954}, number = {}, pages = {176347}, doi = {10.1016/j.scitotenv.2024.176347}, pmid = {39306135}, issn = {1879-1026}, mesh = {*Gram-Negative Bacteria/drug effects ; *Drug Resistance, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; Interspersed Repetitive Sequences ; Bacteriophages/physiology ; Plasmids/genetics ; }, abstract = {Antimicrobial resistance (AMR) in gram-negative bacteria (GNBs) is a significant global health concern, exacerbated by mobile genetic elements (MGEs). This review examines the transfer of antibiotic resistance genes (ARGs) within and between different species of GNB facilitated by MGEs, focusing on the roles of plasmids and phages. The impact of non-antibiotic chemicals, environmental factors affecting ARG transfer frequency, and underlying molecular mechanisms of bacterial resistance evolution are also discussed. Additionally, the study critically assesses the impact of fitness costs and compensatory evolution driven by MGEs in host organisms, shedding light on the transfer frequency of ARGs and host evolution within ecosystems. Overall, this comprehensive review highlights the factors and mechanisms influencing ARG movement among diverse GNB species and underscores the importance of implementing holistic One-Health strategies to effectively address the escalating public health challenges associated with AMR.}, }
@article {pmid39305601, year = {2024}, author = {Wang, F and Hu, Z and Wang, W and Wang, J and Xiao, Y and Shi, J and Wang, C and Mai, W and Li, G and An, T}, title = {Selective enrichment of high-risk antibiotic resistance genes and priority pathogens in freshwater plastisphere: Unique role of biodegradable microplastics.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {135901}, doi = {10.1016/j.jhazmat.2024.135901}, pmid = {39305601}, issn = {1873-3336}, mesh = {*Microplastics/toxicity ; *Drug Resistance, Microbial/genetics ; *Fresh Water/microbiology ; Water Pollutants, Chemical/toxicity ; Biofilms/drug effects ; Bacteria/genetics/drug effects ; Genes, Bacterial ; Virulence Factors/genetics ; Polyhydroxyalkanoates ; Polyesters/metabolism ; Microbiota/drug effects/genetics ; Biodegradation, Environmental ; Biodegradable Plastics ; }, abstract = {Microplastics (MPs) has been concerned as emerging vectors for spreading antibiotic resistance and pathogenicity in aquatic environments, but the role of biodegradable MPs remains largely unknown. Herein, field in-situ incubation method combined with metagenomic sequencing were employed to reveal the dispersal characteristics of microbial community, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and virulence factors (VFs) enriched by MPs biofilms. Results showed that planktonic microbes were more prone to enrich on biodegradable MPs (i.e., polyhydroxyalkanoate and polylactic acid) than non-biodegradable MPs (i.e., polystyrene, polypropylene and polyethylene). Distinctive microbial communities were assembled on biodegradable MPs, and the abundances of ARGs, MGEs, and VFs on biofilms of biodegradable MPs were much higher than that of non-biodegradable MPs. Notably, network analysis showed that the biodegradable MPs selectively enriched pathogens carrying ARGs, VFs and MGEs concurrently, suggesting a strong potential risks of co-spreading antibiotic resistance and pathogenicity through horizontal gene transfer. According to WHO priority list of Antibiotic Resistant Pathogens (ARPs) and ARGs health risk assessment framework, the highest abundances of Priority 1 ARPs and Rank I risk ARGs were found on polylactic acid and polyhydroxyalkanoate, respectively. These findings elucidate the unique and critical role of biodegradable MPs for selective enrichment of high-risk ARGs and priority pathogens in freshwater environments.}, }
@article {pmid39305593, year = {2024}, author = {Shen, Y and Zhang, B and Yao, Y and Wang, H and Chen, Z and Hao, A and Guo, P}, title = {Insights into the interactions of plant-associated bacteria and their role in the transfer of antibiotic resistance genes from soil to plant.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {135881}, doi = {10.1016/j.jhazmat.2024.135881}, pmid = {39305593}, issn = {1873-3336}, mesh = {*Soil Microbiology ; *Rhizosphere ; *Bacteria/genetics/metabolism/classification ; *Plant Roots/microbiology ; Plants/microbiology ; Microbiota ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Plant Shoots/microbiology/growth &amp; development ; Gene Transfer, Horizontal ; }, abstract = {This study discussed the role of plant-associated microbiome in regulating ARG transfer in soil-plant systems. Results showed that target ARGs in plants were mainly derived from rhizosphere soil. Cooperative interactions among bacteria in rhizosphere soil, plant-roots, plant-shoots, and soil-roots-shoots systems occurred during ARG transfer. The number of modules and keystone taxa identified as positively correlated with ARG transfer in rhizosphere soil, roots, and shoots was 3 and 49, 3 and 41, 2 and 5, respectively. Among these modules, module 3 in roots was significantly positively correlated with module 3 in rhizosphere soils and module 2 in shoots, indicating that module 3 in roots played central hub roles in ARG transfer from rhizosphere soil to roost and shoots. This may be because module 3 in roots increased cell motility and xenobiotics biodegradation and metabolism. These keystone taxa mainly belonged to Proteobacteria that can carry ARGs to transfer in soil-plant systems, especially Clostridium-sensu_stricito and Pseudomonas in rhizosphere soil carried ARGs into the shoot. Additionally, they promoted ARG transfer by increasing plant biomass, net photosynthetic rate and water use efficiency. The findings helped reveal the mechanism of plant-associated bacterial interactions and provided understanding for potential risks of ARG transfer from soil to plants.}, }
@article {pmid39304531, year = {2024}, author = {Umar, M and Merlin, TS and Puthiyedathu Sajeevan, T}, title = {Genomic insights into symbiosis and host adaptation of sponge-associated novel bacterium, Rossellomorea orangium sp. nov.}, journal = {FEMS microbiology letters}, volume = {371}, number = {}, pages = {}, doi = {10.1093/femsle/fnae074}, pmid = {39304531}, issn = {1574-6968}, support = {BT/PR41474/NDB/39/760/2020//Higher Education Department, Government of Kerala/ ; 1422/2021/HEDN//Performance Linked Encouragement for Academic Studies and Endeavour (PLEASE)/ ; CUSAT/PL(UGC).A1/2314/2023//Rashtriya Uchchatar Shiksha Abhiyan/ ; //Kerala State Council for Science, Technology and Environment/ ; //University Grants Commission India/ ; }, mesh = {*Symbiosis ; *Porifera/microbiology ; Animals ; *Genome, Bacterial ; *Phylogeny ; Genomics ; Multigene Family ; Adaptation, Physiological ; Flavobacteriaceae/genetics/classification ; Secondary Metabolism ; Gene Transfer, Horizontal ; }, abstract = {Sponge-associated microorganisms play vital roles in marine sponge ecology. This study presents a genomic investigation of Rossellomorea sp. MCCB 382, isolated from Stelletta sp., reveals insights into its adaptations and symbiotic roles. Phylogenomic study and Overall Genomic Relatedness Index (OGRI) classify MCCB 382 as a novel species, Rossellomorea orangium sp. nov. The genome encodes numerous carbohydrate metabolism enzymes (CAZymes), likely aiding nutrient cycling in the sponge host. Unique eukaryotic-like protein domains hint at potential mechanisms of symbiosis. Defence mechanisms include CRISPR, restriction-modification systems, DNA phosphorothioation, toxin-antitoxin systems, and heavy metal and multidrug resistance genes, indicating adaptation to challenging marine environments. Unlike obligate mutualists, MCCB 382 shows no genome reduction. Furthermore, the presence of mobile genetic elements, horizontal gene transfer, and prophages suggest genetic versatility, implying flexible metabolic potential and capacity for rapid adaptation and symbiosis shifts. MCCB 382 possesses six biosynthetic gene clusters for secondary metabolites, including both type II and III polyketide synthases (PKS), terpenes, (NRPS), NRPS-independent-siderophore, and lassopeptide. Further genome mining using BiGScape revealed four distinct gene cluster families, T2PKS, NRPS-independent-siderophore, lasso peptide, and terpene, presenting opportunities for novel compound elucidation. Our study reveals a symbiotic lifestyle of MCCB 382 with the host sponge, highlighting symbiont factors that aid in establishing and sustaining this relationship. This is the pioneering genomic characterization of a novel Rossellomorea sp. within the sponge Stelletta sp. holobiont.}, }
@article {pmid39304387, year = {2024}, author = {Vos, M and Buckling, A and Kuijper, B and Eyre-Walker, A and Bontemps, C and Leblond, P and Dimitriu, T}, title = {Why do mobile genetic elements transfer DNA of their hosts?.}, journal = {Trends in genetics : TIG}, volume = {40}, number = {11}, pages = {927-938}, doi = {10.1016/j.tig.2024.07.008}, pmid = {39304387}, issn = {0168-9525}, mesh = {*Gene Transfer, Horizontal/genetics ; *Interspersed Repetitive Sequences/genetics ; Selection, Genetic/genetics ; DNA Transposable Elements/genetics ; Bacteria/genetics ; }, abstract = {The prokaryote world is replete with mobile genetic elements (MGEs) - self-replicating entities that can move within and between their hosts. Many MGEs not only transfer their own DNA to new hosts but also transfer host DNA located elsewhere on the chromosome in the process. This could potentially lead to indirect benefits to the host when the resulting increase in chromosomal variation results in more efficient natural selection. We review the diverse ways in which MGEs promote the transfer of host DNA and explore the benefits and costs to MGEs and hosts. In many cases, MGE-mediated transfer of host DNA might not be selected for because of a sex function, but evidence of MGE domestication suggests that there may be host benefits of MGE-mediated sex.}, }
@article {pmid39304140, year = {2024}, author = {Qi, Q and Ghaly, TM and Rajabal, V and Russell, DH and Gillings, MR and Tetu, SG}, title = {Vegetable phylloplane microbiomes harbour class 1 integrons in novel bacterial hosts and drive the spread of chlorite resistance.}, journal = {The Science of the total environment}, volume = {954}, number = {}, pages = {176348}, doi = {10.1016/j.scitotenv.2024.176348}, pmid = {39304140}, issn = {1879-1026}, mesh = {*Integrons/genetics ; *Microbiota/drug effects/genetics ; *Vegetables/microbiology ; Chlorides ; Drug Resistance, Bacterial/genetics ; Bacteria/genetics/drug effects ; Gene Transfer, Horizontal ; }, abstract = {Bacterial hosts in vegetable phylloplanes carry mobile genetic elements, such as plasmids and transposons that are associated with integrons. These mobile genetic elements and their cargo genes can enter human microbiomes via consumption of fresh agricultural produce, including uncooked vegetables. This presents a risk of acquiring antimicrobial resistance genes from uncooked vegetables. To better understand horizontal gene transfer of class 1 integrons in these compartments, we applied epicPCR, a single-cell fusion-PCR surveillance technique, to link the class 1 integron integrase (intI1) gene with phylogenetic markers of their bacterial hosts. Ready-to-eat salads carried class 1 integrons from the phyla Bacteroidota and Pseudomonadota, including four novel genera that were previously not known to be associated with intI1. We whole-genome sequenced Pseudomonas and Erwinia hosts of pre-clinical class 1 integrons that are embedded in Tn402-like transposons. The proximal gene cassette in these integrons was identified as a chlorite dismutase gene cassette, which we showed experimentally to confer chlorite resistance. Chlorine-derived compounds such as acidified sodium chlorite and chloride dioxide are used to disinfectant raw vegetables in food processing facilities, suggesting selection for chlorite resistance in phylloplane integrons. The spread of integrons conferring chlorite resistance has the potential to exacerbate integron-mediated antimicrobial resistance (AMR) via co-selection of chlorite resistance and AMR, thus highlighting the importance of monitoring chlorite residues in agricultural produce. These results demonstrate the strength of combining epicPCR and culture-based isolation approaches for identifying hosts and dissecting the molecular ecology of class 1 integrons.}, }
@article {pmid39303860, year = {2024}, author = {Yong, Y and Hu, S and Zhong, M and Wen, Y and Zhou, Y and Ma, R and Jiang, X and Zhang, Q}, title = {Horizontal gene transfer from chloroplast to mitochondria of seagrasses in the yellow-Bohai seas.}, journal = {Genomics}, volume = {116}, number = {5}, pages = {110940}, doi = {10.1016/j.ygeno.2024.110940}, pmid = {39303860}, issn = {1089-8646}, mesh = {*Gene Transfer, Horizontal ; Genome, Mitochondrial ; Chloroplasts/genetics ; Genome, Chloroplast ; Alismatales/genetics/metabolism ; Phylogeny ; Mitochondria/genetics/metabolism ; }, abstract = {Seagrasses are ideal for studying plant adaptation to marine environments. In this study, the mitochondrial (mt) and chloroplast (cp) genomes of Ruppia sinensis were sequenced. The results showed an extensive gene loss in seagrasses, including a complete loss of cp-rpl19 genes in Zosteraceae, most cp-ndh genes in Hydrocharitaceae, and mt-rpl and mt-rps genes in all seagrasses, except for the mt-rpl16 gene in Phyllospadix iwatensis. Notably, most ribosomal protein genes were lost in the mt and cp genomes. The deleted cp genes were not transferred to the mt genomes through horizontal gene transfer. Additionally, a significant DNA transfer between seagrass organelles was found, with the mt genomes of Zostera containing numerous sequences from the cp genome. Rearrangement analyses revealed an unreported inversion of the cp genome in R. sinensis. Moreover, four positively selected genes (atp8, nad5, atp4, and ccmFn) and five variable regions (matR, atp4, atp8, rps7, and ccmFn) were identified.}, }
@article {pmid39303615, year = {2024}, author = {Li, X and Cai, S and Xu, M}, title = {Nanoscale zero-valent iron alleviated horizontal transfer of antibiotic resistance genes in soil: The important role of extracellular polymeric substances.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {135902}, doi = {10.1016/j.jhazmat.2024.135902}, pmid = {39303615}, issn = {1873-3336}, mesh = {*Iron/chemistry/metabolism ; *Soil Microbiology ; *Gene Transfer, Horizontal ; *Extracellular Polymeric Substance Matrix/metabolism ; *Soil Pollutants ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; Tetracycline/pharmacology ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; }, abstract = {Extracellular polymeric substances (EPS) are tightly related to the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs), but often neglected in soil. In this study, nanoscale zero-valent iron (nZVI) was utilized for attenuation of ARGs in contaminated soil, with an emphasis on its effects on EPS secretion and HGT. Results showed during soil microbe cultivation exposed to tetracycline, more EPS was secreted and significant increase of tet was observed due to facilitated HGT. Notably, copies of EPS-tet accounted for 71.39 % of the total tet, implying vital effects of EPS on ARGs proliferation. When co-exposed to nZVI, EPS secretion was decreased by 38.36-71.46 %, for that nZVI could alleviate the microbial oxidative stress exerted by tetracycline resulting in downregulation of genes expression related to the c-di-GMP signaling system. Meanwhile, the abundance of EPS-tet was obviously reduced from 7.04 to 5.12-6.47 log unit, directly causing decrease of total tet from 7.19 to 5.68-6.69 log unit. For the reduced tet, it was mainly due to decreased EPS secretion induced by nZVI resulting in inhibition of HGT especially transformation of the EPS-tet. This work gives an inspiration for attenuation of ARGs dissemination in soil through an EPS regulation strategy.}, }
@article {pmid39301187, year = {2024}, author = {Xu, M and Ke, H and Zang, Y and Gou, H and Yang, D and Shi, K and Zhang, K and Li, Y and Jiang, Z and Chu, P and Zhai, S and Li, C}, title = {Outer membrane vesicles secreted from Actinobacillus pleuropneumoniae isolate disseminating the floR resistance gene to Enterobacteriaceae.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1467847}, pmid = {39301187}, issn = {1664-302X}, abstract = {Actinobacillus pleuropneumoniae, a significant respiratory pig pathogen, is causing substantial losses in the global swine industry. The resistance spectrum of A. pleuropneumoniae is expanding, and multidrug resistance is a severe issue. Horizontal gene transfer (HGT) plays a crucial role in the development of the bacterial genome by facilitating the dissemination of resistance determinants. However, the horizontal transfer of resistance genes via A. pleuropneumoniae-derived outer membrane vesicles (OMVs) has not been previously reported. In this study, we used Illumina NovaSeq and PacBio SequeI sequencing platforms to determine the whole genome sequence of A. pleuropneumoniae GD2107, a multidrug-resistant (MDR) isolate from China. We detected a plasmid in the isolate named pGD2107-1; the plasmid was 5,027 bp in size with 7 putative open reading frames (ORF) and included the floR resistance genes. The carriage of resistance genes in A. pleuropneumoniae OMVs was identified using a polymerase chain reaction (PCR) assay, and then we thoroughly evaluated the influence of OMVs on the horizontal transfer of drug-resistant plasmids. The transfer of the plasmid to recipient bacteria via OMVs was confirmed by PCR. In growth competition experiments, all recipients carrying the pGD2107-1 plasmid exhibited a fitness cost compared to the corresponding original recipients. This study revealed that OMVs could mediate interspecific horizontal transfer of the resistance plasmid pGD2107-1 into Escherichia coli recipient strains and significantly enhance the resistance of the transformants. In summary, A. pleuropneumoniae-OMVs play the pivotal role of vectors for dissemination of the floR gene spread and may contribute to more antimicrobial resistance gene transfer in other Enterobacteriaceae.}, }
@article {pmid39299886, year = {2024}, author = {Urquhart, A and Vogan, AA and Gluck-Thaler, E}, title = {Starships: a new frontier for fungal biology.}, journal = {Trends in genetics : TIG}, volume = {40}, number = {12}, pages = {1060-1073}, doi = {10.1016/j.tig.2024.08.006}, pmid = {39299886}, issn = {0168-9525}, mesh = {*DNA Transposable Elements/genetics ; *Genome, Fungal/genetics ; *Evolution, Molecular ; *Fungi/genetics ; Gene Transfer, Horizontal/genetics ; Symbiosis/genetics ; }, abstract = {Transposable elements (TEs) are semiautonomous genetic entities that proliferate in genomes. We recently discovered the Starships, a previously hidden superfamily of giant TEs found in a diverse subphylum of filamentous fungi, the Pezizomycotina. Starships are unlike other eukaryotic TEs because they have evolved mechanisms for both mobilizing entire genes, including those encoding conditionally beneficial phenotypes, and for horizontally transferring between individuals. We argue that Starships have unrivaled capacity to engage their fungal hosts as genetic parasites and mutualists, revealing unexplored terrain for investigating the ecoevolutionary dynamics of TE-eukaryote interactions. We build on existing models of fungal genome evolution by conceptualizing Starships as a distinct genomic compartment whose dynamics profoundly shape fungal biology.}, }
@article {pmid39296779, year = {2024}, author = {Thomy, J and Sanchez, F and Prioux, C and Yau, S and Xu, Y and Mak, J and Sun, R and Piganeau, G and Yung, CCM}, title = {Unveiling Prasinovirus diversity and host specificity through targeted enrichment in the South China Sea.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae109}, pmid = {39296779}, issn = {2730-6151}, abstract = {Unicellular green picophytoplankton from the Mamiellales order are pervasive in marine ecosystems and susceptible to infections by prasinoviruses, large double-stranded DNA viruses within the Nucleocytoviricota phylum. We developed a double-stranded DNA virus enrichment and shotgun sequencing method, and successfully assembled 80 prasinovirus genomes from 43 samples in the South China Sea. Our research delivered the first direct estimation of 94% accuracy in correlating genome similarity to host range. Stirkingly, our analyses uncovered unexpected host-switching across diverse algal lineages, challenging the existing paradigms of host-virus co-speciation and revealing the dynamic nature of viral evolution. We also detected six instances of horizontal gene transfer between prasinoviruses and their hosts, including a novel alternative oxidase. Additionally, diversifying selection on a major capsid protein suggests an ongoing co-evolutionary arms race. These insights not only expand our understanding of prasinovirus genomic diversity but also highlight the intricate evolutionary mechanisms driving their ecological success and shaping broader virus-host interactions in marine environments.}, }
@article {pmid39294579, year = {2024}, author = {Shabbir, MAB and Shamim, M and Tahir, AH and Sattar, A and Qin, W and Ahmad, W and Ahmad, W and Khan, FA and Ashraf, MA}, title = {Potential of ZnO nanoparticles for multi-drug resistant Escherichia coli having CRISPR-Cas from poultry market in Lahore.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {355}, pmid = {39294579}, issn = {1471-2180}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *CRISPR-Cas Systems ; *Drug Resistance, Multiple, Bacterial/genetics ; *Escherichia coli/genetics/drug effects ; *Escherichia coli Infections/microbiology/veterinary ; Microbial Sensitivity Tests ; Nanoparticles ; Poultry/microbiology ; *Poultry Diseases/microbiology ; *Zinc Oxide/pharmacology ; }, abstract = {BACKGROUND AND OBJECTIVES: Apart from known factors such as irrational use of antibiotics and horizontal gene transfer, it is now reported that clustered regularly interspaced short palindromic repeats (CRISPR) are also associated with increased antimicrobial resistance. Hence, it is critical to explore alternatives to antibiotics to control economic losses. Therefore, the present study aimed to determine not only the association of CRISPR-Cas system with antibiotic resistance but also the potential of Zinc Oxide nanoparticles (ZnO-NPs) for avian pathogenic Escherichia coli (APEC) isolated from poultry market Lahore.<br><br>MATERIALS AND METHODS: Samples (n&#x2009;=&#x2009;100) were collected from live bird markets of Lahore, and isolates were confirmed as Escherichia coli (E. coli) using the Remel One fast kit, and APEC was identified using PCR. The antibiotic resistance pattern in APEC was determined using the minimum inhibitory concentration (MIC), followed by genotypic confirmation of antibiotic-resistant genes using the PCR. The CRISPR-Cas system was also identified in multidrug-resistant (MDR) isolates, and its association with antibiotics was determined using qRT-PCR. The potential of ZnO-NPs was evaluated for multidrug-resistant (MDR) isolates by MIC.<br><br>RESULTS: All isolates of APEC were resistant to nalidixic acid, whereas 95% were resistant to chloramphenicol and 89% were resistant to streptomycin. Nineteen MDR APEC were found in the present study and the CRISPR-Cas system was detected in all of these MDR isolates. In addition, an increased expression of CRISPR-related genes was observed in the standard strain and MDR isolates of APEC.&#xa0;ZnO-NPs inhibited the growth of resistant isolates.<br><br>CONCLUSIONS: The findings showed the presence of the CRISPR-Cas system in MDR strains of APEC, along with the potential of ZnO-NPs for a possible solution to proceed. This highlights the importance of regulating antimicrobial resistance in poultry to reduce potential health consequences.}, }
@article {pmid39293438, year = {2024}, author = {Zhang, ZJ and Cole, CG and Coyne, MJ and Lin, H and Dylla, N and Smith, RC and Pappas, TE and Townson, SA and Laliwala, N and Waligurski, E and Ramaswamy, R and Woodson, C and Burgo, V and Little, JC and Moran, D and Rose, A and McMillin, M and McSpadden, E and Sundararajan, A and Sidebottom, AM and Pamer, EG and Comstock, LE}, title = {Comprehensive analyses of a large human gut Bacteroidales culture collection reveal species- and strain-level diversity and evolution.}, journal = {Cell host &amp; microbe}, volume = {32}, number = {10}, pages = {1853-1867.e5}, pmid = {39293438}, issn = {1934-6069}, support = {P01 CA023766/CA/NCI NIH HHS/United States ; T32 GM144292/GM/NIGMS NIH HHS/United States ; U01 AI124275/AI/NIAID NIH HHS/United States ; R01 AI093771/AI/NIAID NIH HHS/United States ; R01 AI042135/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Phylogeny ; *Genome, Bacterial ; Bacteroidetes/genetics/classification/isolation &amp; purification ; Gene Transfer, Horizontal ; Genetic Variation ; Metabolomics ; Evolution, Molecular ; DNA, Bacterial/genetics ; Genomics ; Sequence Analysis, DNA ; }, abstract = {Species of the Bacteroidales order are among the most abundant and stable bacterial members of the human gut microbiome, with diverse impacts on human health. We cultured and sequenced the genomes of 408 Bacteroidales isolates from healthy human donors representing nine genera and 35 species and performed comparative genomic, gene-specific, metabolomic, and horizontal gene transfer analyses. Families, genera, and species could be grouped based on many distinctive features. We also observed extensive DNA transfer between diverse families, allowing for shared traits and strain evolution. Inter- and intra-species diversity is also apparent in the metabolomic profiling studies. This highly characterized and diverse Bacteroidales culture collection with strain-resolved genomic and metabolomic analyses represents a valuable resource to facilitate informed selection of strains for microbiome reconstitution.}, }
@article {pmid39288183, year = {2024}, author = {Tuffet, R and Carvalho, G and Godeux, AS and Mazzamurro, F and Rocha, EPC and Laaberki, MH and Venner, S and Charpentier, X}, title = {Manipulation of natural transformation by AbaR-type islands promotes fixation of antibiotic resistance in Acinetobacter baumannii.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {39}, pages = {e2409843121}, pmid = {39288183}, issn = {1091-6490}, support = {ANR-20-CE12-0004//Agence Nationale de la Recherche (ANR)/ ; ANR-11-LABX-0048//Agence Nationale de la Recherche (ANR)/ ; PhD grant//VetAgro Sup (VetAgro-Sup)/ ; 80|PRIME//Centre National de la Recherche Scientifique (CNRS)/ ; }, mesh = {*Acinetobacter baumannii/genetics/drug effects ; *Genomic Islands ; Drug Resistance, Multiple, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; Transformation, Bacterial ; Polymorphism, Single Nucleotide ; Bacterial Proteins/genetics/metabolism ; }, abstract = {The opportunistic pathogen Acinetobacter baumannii, carries variants of A. baumannii resistance islands (AbaR)-type genomic islands conferring multidrug resistance. Their pervasiveness in the species has remained enigmatic. The dissemination of AbaRs is intricately linked to their horizontal transfer via natural transformation, a process through which bacteria can import and recombine exogenous DNA, effecting allelic recombination, genetic acquisition, and deletion. In experimental populations of the closely related pathogenic Acinetobacter nosocomialis, we quantified the rates at which these natural transformation events occur between individuals. When integrated into a model of population dynamics, they lead to the swift removal of AbaRs from the population, contrasting with the high prevalence of AbaRs in genomes. Yet, genomic analyses show that nearly all AbaRs specifically disrupt comM, a gene encoding a helicase critical for natural transformation. We found that such disruption impedes gene acquisition, and deletion, while moderately impacting acquisition of single nucleotide polymorphism. A mathematical evolutionary model demonstrates that AbaRs inserted into comM gain a selective advantage over AbaRs inserted in sites that do not inhibit or completely inhibit transformation, in line with the genomic observations. The persistence of AbaRs can be ascribed to their integration into a specific gene, diminishing the likelihood of their removal from the bacterial genome. This integration preserves the acquisition and elimination of alleles, enabling the host bacterium-and thus its AbaR-to adapt to unpredictable environments and persist over the long term. This work underscores how manipulation of natural transformation by mobile genetic elements can drive the prevalence of multidrug resistance.}, }
@article {pmid39287446, year = {2024}, author = {Contarin, R and Drapeau, A and François, P and Madec, J-Y and Haenni, M and Dordet-Frisoni, E}, title = {The interplay between mobilome and resistome in Staphylococcus aureus.}, journal = {mBio}, volume = {15}, number = {10}, pages = {e0242824}, pmid = {39287446}, issn = {2150-7511}, support = {//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE)/ ; //Agence Nationale de S&#xe9;curit&#xe9; Sanitaire de l'Alimentation, de l'Environnement et du Travail (ANSES)/ ; }, mesh = {*Staphylococcus aureus/genetics/drug effects ; Humans ; *Staphylococcal Infections/microbiology ; Animals ; *Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences ; *Plasmids/genetics ; *Genome, Bacterial ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; DNA Transposable Elements ; Drug Resistance, Multiple, Bacterial/genetics ; Genes, Bacterial/genetics ; }, abstract = {Antibiotic resistance genes (ARGs) in Staphylococcus aureus can disseminate vertically through successful clones, but also horizontally through the transfer of genes conveyed by mobile genetic elements (MGEs). Even though underexplored, MGE/ARG associations in S. aureus favor the emergence of multidrug-resistant clones, which are challenging therapeutic success in both human and animal health. This study investigated the interplay between the mobilome and the resistome of more than 10,000 S. aureus genomes from human and animal origin. The analysis revealed a remarkable diversity of MGEs and ARGs, with plasmids and transposons being the main carriers of ARGs. Numerous MGE/ARG associations were identified, suggesting that MGEs play a critical role in the dissemination of resistance. A high degree of similarity was observed in MGE/ARG associations between human and animal isolates, highlighting the potential for unrestricted spread of ARGs between hosts. Our results showed that in parallel to clonal expansion, MGEs and their associated ARGs can spread across different strain types sequence types (STs), favoring the evolution of these clones and their adaptation in selective environments. The high variability of MGE/ARG associations within individual STs and their spread across several STs highlight the crucial role of MGEs in shaping the S. aureus resistome. Overall, this study provides valuable insights into the complex interplay between MGEs and ARGs in S. aureus, emphasizing the need to elucidate the mechanisms governing the epidemic success of MGEs, particularly those implicated in ARG transfer.IMPORTANCEThe research presented in this article highlights the importance of understanding the interactions between mobile genetic elements (MGEs) and antibiotic resistance genes (ARGs) carried by Staphylococcus aureus, a versatile bacterium that can be both a harmless commensal and a dangerous pathogen for humans and animals. S. aureus has a great capacity to acquire and disseminate ARGs, enabling efficient adaption to various environmental or clinical conditions. By analyzing a large data set of S. aureus genomes, we highlighted the substantial role of MGEs, particularly plasmids and transposons, in disseminating ARGs within and between S. aureus populations, bypassing host barriers. Given that multidrug-resistant S. aureus strains are classified as a high-priority pathogen by global health organizations, this knowledge is crucial for understanding the complex dynamics of transmission of antibiotic resistance in this species.}, }
@article {pmid39287432, year = {2024}, author = {Nwokocha, GC and Ghosh, A and Grove, A}, title = {Regulation of bacterial virulence genes by PecS family transcription factors.}, journal = {Journal of bacteriology}, volume = {206}, number = {10}, pages = {e0030224}, pmid = {39287432}, issn = {1098-5530}, support = {MCB-2153410//National Science Foundation (NSF)/ ; }, mesh = {*Gene Expression Regulation, Bacterial ; *Transcription Factors/genetics/metabolism ; *Bacterial Proteins/genetics/metabolism ; Virulence/genetics ; Virulence Factors/genetics/metabolism ; }, abstract = {Bacterial plant pathogens adjust their gene expression programs in response to environmental signals and host-derived compounds. This ensures that virulence genes or genes encoding proteins, which promote bacterial fitness in a host environment, are expressed only when needed. Such regulation is in the purview of transcription factors, many of which belong to the ubiquitous multiple antibiotic resistance regulator (MarR) protein family. PecS proteins constitute a subset of this large protein family. PecS has likely been distributed by horizontal gene transfer, along with the divergently encoded efflux pump PecM, suggesting its integration into existing gene regulatory networks. Here, we discuss the roles of PecS in the regulation of genes associated with virulence and fitness of bacterial plant pathogens. A comparison of phenotypes and differential gene expression associated with the disruption of pecS shows that functional consequences of PecS integration into existing transcriptional networks are highly variable, resulting in distinct PecS regulons. Although PecS universally binds to the pecS-pecM intergenic region to repress the expression of both genes, binding modes differ. A particularly relaxed sequence preference appears to apply for Dickeya dadantii PecS, perhaps to optimize its integration as a global regulator and regulate genes ancestral to the acquisition of pecS-pecM. Even inducing ligands for PecS are not universally conserved. It appears that PecS function has been optimized to match the unique regulatory needs of individual bacterial species and that its roles must be appreciated in the context of the regulatory networks into which it was recruited.}, }
@article {pmid39287139, year = {2024}, author = {Pu, L and Shamir, R}, title = {4CAC: 4-class classifier of metagenome contigs using machine learning and assembly graphs.}, journal = {Nucleic acids research}, volume = {52}, number = {19}, pages = {e94}, pmid = {39287139}, issn = {1362-4962}, support = {1339/18//Israel Science Foundation/ ; //Edmond J. Safra Center for Bioinformatics at Tel-Aviv University/ ; //Planning &amp; Budgeting Committee/ ; //Council for Higher Education/ ; }, mesh = {*Machine Learning ; *Metagenome/genetics ; Bacteria/genetics/classification ; Plasmids/genetics ; Archaea/genetics/classification ; Software ; Metagenomics/methods ; Viruses/genetics/classification ; Contig Mapping/methods ; Algorithms ; }, abstract = {Microbial communities usually harbor a mix of bacteria, archaea, plasmids, viruses and microeukaryotes. Within these communities, viruses, plasmids, and microeukaryotes coexist in relatively low abundance, yet they engage in intricate interactions with bacteria. Moreover, viruses and plasmids, as mobile genetic elements, play important roles in horizontal gene transfer and the development of antibiotic resistance within microbial populations. However, due to the difficulty of identifying viruses, plasmids, and microeukaryotes in microbial communities, our understanding of these minor classes lags behind that of bacteria and archaea. Recently, several classifiers have been developed to separate one or more minor classes from bacteria and archaea in metagenome assemblies. However, these classifiers often overlook the issue of class imbalance, leading to low precision in identifying the minor classes. Here, we developed a classifier called 4CAC that is able to identify viruses, plasmids, microeukaryotes, and prokaryotes simultaneously from metagenome assemblies. 4CAC generates an initial four-way classification using several sequence length-adjusted XGBoost models and further improves the classification using the assembly graph. Evaluation on simulated and real metagenome datasets demonstrates that 4CAC substantially outperforms existing classifiers and combinations thereof on short reads. On long reads, it also shows an advantage unless the abundance of the minor classes is very low. 4CAC runs 1-2 orders of magnitude faster than the other classifiers. The 4CAC software is available at https://github.com/Shamir-Lab/4CAC.}, }
@article {pmid39282498, year = {2024}, author = {Jiang, C and Yang, J and Xiao, G and Xiao, N and Hu, J and Yang, Y and Sun, Z and Li, Y}, title = {The ISVsa3-ORF2-abh-tet(X4) circular intermediate-mediated transmission of tigecycline resistance in Escherichia coli isolates from duck farms.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1444031}, pmid = {39282498}, issn = {2235-2988}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; China ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; *Ducks/microbiology ; *Escherichia coli/genetics/drug effects/isolation &amp; purification ; *Escherichia coli Infections/veterinary/microbiology ; Escherichia coli Proteins/genetics ; *Farms ; Feces/microbiology ; Gene Transfer, Horizontal ; Genotype ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Plasmids/genetics ; Poultry Diseases/microbiology ; *Tigecycline/pharmacology ; *Whole Genome Sequencing ; }, abstract = {Tigecycline is a last-resort drug used to treat serious infections caused by multidrug-resistant bacteria. tet(X4) is a recently discovered plasmid-mediated tigecycline resistance gene that confers high-level resistance to tigecycline and other tetracyclines. Since the first discovery of tet(X4) in 2019, it has spread rapidly worldwide, and as a consequence, tigecycline has become increasingly ineffective in the clinical treatment of multidrug-resistant infections. In this study, we identified and analyzed tet(X4)-positive Escherichia coli isolates from duck farms in Hunan Province, China. In total, 976 samples were collected from nine duck farms. Antimicrobial susceptibility testing and whole-genome sequencing (WGS) were performed to establish the phenotypes and genotypes of tet(X4)-positive isolates. In addition, the genomic characteristics and transferability of tet(X4) were determined based on bioinformatics analysis and conjugation. We accordingly detected an E. coli strain harboring tet(X4) and seven other resistance genes in duck feces. Multi-locus sequence typing analysis revealed that this isolate belonged to a new clone, and subsequent genetic analysis indicated that tet(X4) was carried in a 4608-bp circular intermediate, flanked by ISVsa3-ORF2-abh elements. Moreover, it exhibited transferability to E. coli C600 with a frequency of 10[-5]. The detection of tet(X4)-harboring E, coli strains on duck farms enhances our understanding of tigecycline resistance dynamics. The transferable nature of the circular intermediate of tet(X4) contributing to the spread of tigecycline resistance genes poses a substantial threat to healthcare. Consequently, vigilant monitoring and proactive measures are necessary to prevent their spread.}, }
@article {pmid39278585, year = {2024}, author = {Yang, B and Sun, J and Zhu, S and Wang, Z and Liu, Y}, title = {Exposure to bisphenol compounds accelerates the conjugative transfer of antibiotic resistance plasmid.}, journal = {Environmental research}, volume = {263}, number = {Pt 1}, pages = {120002}, doi = {10.1016/j.envres.2024.120002}, pmid = {39278585}, issn = {1096-0953}, mesh = {*Phenols/toxicity ; *Plasmids/genetics ; Animals ; *Gene Transfer, Horizontal ; Mice ; Benzhydryl Compounds/toxicity ; Conjugation, Genetic/drug effects ; Drug Resistance, Microbial/genetics ; Endocrine Disruptors/toxicity ; }, abstract = {Antimicrobial resistance poses the most formidable challenge to public health, with plasmid-mediated horizontal gene transfer playing a pivotal role in its global spread. Bisphenol compounds (BPs), a group of environmental contaminants with endocrine-disrupting properties, are extensively used in various plastic products and can be transmitted to food. However, the impact of BPs on the plasmid-mediated horizontal transfer of antibiotic resistance genes (ARGs) has not yet been elucidated. Herein, we demonstrate that BPs could promote the conjugative transfer frequency of RP4-7 and clinically multidrug-resistant plasmids. Furthermore, the promoting effect of BPs on the plasmid transfer was also confirmed in a murine model. Microbial diversity analysis of transconjugants indicated an increase in α diversity in the BPAF-treated group, along with the declined richness of some beneficial bacteria and elevated richness of Faecalibaculum rodentium, which might serve as an intermediate repository for resistance plasmids. The underlying mechanisms driving the enhanced conjugative transfer upon BPAF treatment include exacerbated oxidative stress, disrupted membrane homeostasis, augmented energy metabolism, and the increased expression of conjugation-related genes. Collectively, our findings highlight the potential risk associated with the exacerbated dissemination of AMR both in vitro and in vivo caused by BPs exposure.}, }
@article {pmid39277355, year = {2024}, author = {Gao, Y and Guo, Y and Wang, L and Guo, L and Shi, B and Zhu, L and Wang, J and Kim, YM and Wang, J}, title = {Tebuconazole exacerbates co-occurrence and horizontal transfer of antibiotic resistance genes.}, journal = {Pesticide biochemistry and physiology}, volume = {204}, number = {}, pages = {106026}, doi = {10.1016/j.pestbp.2024.106026}, pmid = {39277355}, issn = {1095-9939}, mesh = {*Triazoles/toxicity/pharmacology ; *Gene Transfer, Horizontal ; *Fungicides, Industrial/toxicity/pharmacology ; *Biofilms/drug effects ; Drug Resistance, Microbial/genetics ; Plasmids/genetics ; Genes, Bacterial ; }, abstract = {As one of the most widely used pesticides in the global fungicide market, tebuconazole has become heavily embedded in soil along with antibiotic resistance genes (ARGs). However, it remains unclear whether the selective pressure produced by tebuconazole affects ARGs and their horizontal transfer. In this experiment, we simulated a tebuconazole-contaminated soil ecosystem and observed changes in the abundance of ARGs and mobile genetic element (MGEs) due to tebuconazole exposure. We also established a plasmid RP4-mediated conjugative transfer system to investigate in depth the impact of tebuconazole on the horizontal transfer of ARGs and its mechanism of action. The results showed that under tebuconazole treatment at concentrations ranging from 0 to 10 mg/L, there was a gradual increase in the frequency of plasmid conjugative transfer, peaking at 10 mg/L which was 7.93 times higher than that of the control group, significantly promoting horizontal transfer of ARGs. Further analysis revealed that the conjugative transfer system under tebuconazole stress exhibited strong ability to form biofilm, and the conjugative transfer frequency ratio of biofilm to planktonic bacteria varied with the growth cycle of biofilm. Additionally, scanning electron microscopy and flow cytometry demonstrated increased cell membrane permeability in both donor and recipient bacteria under tebuconazole stress, accompanied by upregulation of ompA gene expression controlling cell membrane permeability. Furthermore, enzyme activity assays indicated significant increases in CAT, SOD activity, and GSH content in recipient bacteria under tebuconazole stress. Moreover, expression levels of transmembrane transporter gene trfAp as well as genes involved in oxidative stress and SOS response were found to be correlated with the frequency of plasmid conjugative transfer.}, }
@article {pmid39276831, year = {2024}, author = {Li, C and Zhang, Y and Shi, W and Peng, Y and Han, Y and Jiang, S and Dong, X and Zhang, R}, title = {Viral diversity within marine biofilms and interactions with corrosive microbes.}, journal = {Environmental research}, volume = {263}, number = {Pt 1}, pages = {119991}, doi = {10.1016/j.envres.2024.119991}, pmid = {39276831}, issn = {1096-0953}, mesh = {*Biofilms/growth &amp; development ; Corrosion ; Bacteria/genetics ; Viruses/genetics/classification ; Phylogeny ; Metagenome ; Archaea/virology/genetics ; }, abstract = {In marine environments, a wide variety of microbes like bacteria, and archaea influence on the corrosion of materials. Viruses are widely distributed in biofilms among these microbes and may affect the corrosion process through interactions with key corrosive prokaryotes. However, understanding of the viral communities within biofilms and their interactions with corrosive microbes remains is limited. To improve this knowledge gap, 53 metagenomes were utilized to investigate the diversity of viruses within biofilms on 8 different materials and their interactions with corrosive microbes. Notably, the viruses within biofilms predominantly belonged to Caudoviricetes, and phylogenetic analysis of Caudoviricetes and protein-sharing networks with other environments revealed the presence of numerous novel viral clades in biofilms. The virus‒host linkages revealed a close association between viruses and corrosive microbes in biofilms. This means that viruses may modulate host corrosion-related metabolism through auxiliary metabolic genes. It was observed that the virus could enhance host resistance to metals and antibiotics via horizontal gene transfer. Interestingly, viruses could protect themselves from host antiviral systems through anti-defense systems. This study illustrates the diversity of viruses within biofilms formed on materials and the intricate interactions between viruses and corrosive microbes, showing the potential roles of viruses in corrosive biofilms.}, }
@article {pmid39270765, year = {2024}, author = {Bjornson, S and Verbruggen, H and Upham, NS and Steenwyk, JL}, title = {Reticulate evolution: Detection and utility in the phylogenomics era.}, journal = {Molecular phylogenetics and evolution}, volume = {201}, number = {}, pages = {108197}, doi = {10.1016/j.ympev.2024.108197}, pmid = {39270765}, issn = {1095-9513}, mesh = {*Phylogeny ; Genomics ; Gene Transfer, Horizontal ; Hybridization, Genetic ; Genetic Speciation ; Models, Genetic ; Biological Evolution ; Evolution, Molecular ; Animals ; }, abstract = {Phylogenomics has enriched our understanding that the Tree of Life can have network-like or reticulate structures among some taxa and genes. Two non-vertical modes of evolution - hybridization/introgression and horizontal gene transfer - deviate from a strictly bifurcating tree model, causing non-treelike patterns. However, these reticulate processes can produce similar patterns to incomplete lineage sorting or recombination, potentially leading to ambiguity. Here, we present a brief overview of a phylogenomic workflow for inferring organismal histories and compare methods for distinguishing modes of reticulate evolution. We discuss how the timing of coalescent events can help disentangle introgression from incomplete lineage sorting and how horizontal gene transfer events can help determine the relative timing of speciation events. In doing so, we identify pitfalls of certain methods and discuss how to extend their utility across the Tree of Life. Workflows, methods, and future directions discussed herein underscore the need to embrace reticulate evolutionary patterns for understanding the timing and rates of evolutionary events, providing a clearer view of life's history.}, }
@article {pmid39270668, year = {2024}, author = {Aserse, AA and Nimusiima, J and Tumuhairwe, JB and Yli-Halla, M and Lindström, K}, title = {Phylogenetic diversity of Rhizobium species recovered from nodules of common beans (Phaseolus vulgaris L.) in fields in Uganda: R. phaseoli, R. etli, and R. hidalgonense.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {11}, pages = {}, pmid = {39270668}, issn = {1574-6941}, support = {319&#x2009;874//Academy of Finland/ ; 0116947-3//Finnish Cultural Foundation/ ; }, mesh = {*Phylogeny ; *Rhizobium/genetics/classification/isolation &amp; purification ; Uganda ; *Phaseolus/microbiology ; *Root Nodules, Plant/microbiology ; Symbiosis ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Genetic Variation ; Bacterial Proteins/genetics ; Rec A Recombinases/genetics ; }, abstract = {A total of 75 bacterial isolates were obtained from nodules of beans cultivated across 10 sites in six agro-ecological zones in Uganda. Using recA gene sequence analysis, 66 isolates were identified as members of the genus Rhizobium, while 9 were related to Agrobacterium species. In the recA gene tree, most Rhizobium strains were classified into five recognized species. Phylogenetic analysis based on six concatenated sequences (recA-rpoB-dnaK-glnII-gyrB-atpD) placed 32 representative strains into five distinct Rhizobium species, consistent with the species groups observed in the recA gene tree: R. phaseoli, R. etli, R. hidalgonense, R. ecuadorense, and R. sophoriradicis, with the first three being the predominant. The rhizobial strains grouped into three nodC subclades within the symbiovar phaseoli clade, encompassing strains from distinct phylogenetic groups. This pattern reflects the conservation of symbiotic genes, likely acquired through horizontal gene transfer among diverse rhizobial species. The 32 representative strains formed symbiotic relationships with host beans, while the Agrobacterium strains did not form nodules and lacked symbiotic genes. Multivariate analysis revealed that species distribution was influenced by the environmental factors of the sampling sites, emphasizing the need to consider these factors in future effectiveness studies to identify effective nitrogen-fixing strains for specific locations.}, }
@article {pmid39269515, year = {2024}, author = {Amara, Y and Mahjoubi, M and Souissi, Y and Cherif, H and Naili, I and ElHidri, D and Kadidi, I and Mosbah, A and Masmoudi, AS and Cherif, A}, title = {Tapping into haloalkaliphilic bacteria for sustainable agriculture in treated wastewater: insights into genomic fitness and environmental adaptation.}, journal = {Antonie van Leeuwenhoek}, volume = {118}, number = {1}, pages = {1}, pmid = {39269515}, issn = {1572-9699}, support = {No 688320//European Union's Horizon 2020, MADFORWATER/ ; No 688320//European Union's Horizon 2020, MADFORWATER/ ; No 688320//European Union's Horizon 2020, MADFORWATER/ ; No 688320//European Union's Horizon 2020, MADFORWATER/ ; }, mesh = {*Wastewater/microbiology ; *Phylogeny ; *Soil Microbiology ; *RNA, Ribosomal, 16S/genetics ; Salinity ; Rhizosphere ; Bacteria/genetics/classification/isolation &amp; purification/metabolism ; Agriculture/methods ; Tunisia ; Adaptation, Physiological ; Olea/microbiology ; Genome, Bacterial ; }, abstract = {The increasing salinity and alkalinity of soils pose a global challenge, particularly in arid regions such as Tunisia, where about 50% of lands are sensitive to soil salinization. Anthropogenic activities, including the use of treated wastewater (TWW) for irrigation, exacerbate these issues. Haloalkaliphilic bacteria, adapted to TWW conditions and exhibiting plant-growth promotion (PGP) and biocontrol traits, could offer solutions. In this study, 24 haloalkaliphilic bacterial strains were isolated from rhizosphere sample of olive tree irrigated with TWW for more than 20 years. The bacterial identification using 16S rRNA gene sequencing showed that the haloalkaliphilic isolates, capable of thriving in high salinity and alkaline pH, were primarily affiliated to Bacillota (Oceanobacillus and Staphylococcus). Notably, these strains exhibited biofertilization and enzyme production under both normal and saline conditions. Traits such as phosphate solubilization, and the production of exopolysaccharide, siderophore, ammonia, and hydrogen cyanide were observed. The strains also demonstrated enzymatic activities, including protease, amylase, and esterase. Four selected haloalkaliphilic PGPR strains displayed antifungal activity against Alternaria terricola, with three showing tolerances to heavy metals and pesticides. The strain Oceanobacillus picturea M4W.A2 was selected for genome sequencing. Phylogenomic analyses indicated that the extreme environmental conditions probably influenced the development of specific adaptations in M4W.A2 strain, differentiating it from other Oceanobacillus picturae strains. The presence of the key genes associated with plant growth promotion, osmotic and oxidative stress tolerance, antibiotic and heavy metals resistance hinted the functional capabilities might help the strain M4W.A2 to thrive in TWW-irrigated soils. By demonstrating this connection, we aim to improve our understanding of genomic fitness to stressed environments. Moreover, the identification of gene duplication and horizontal gene transfer events through mobile genetic elements allow the comprehension of these adaptation dynamics. This study reveals that haloalkaliphilc bacteria from TWW-irrigated rhizosphere exhibit plant-growth promotion and biocontrol traits, with genomic adaptations enabling their survival in high salinity and alkaline conditions, offering potential solutions for soil salinization issues.}, }
@article {pmid39268957, year = {2024}, author = {Yang, P and Li, J and Lv, M and He, P and Song, G and Shan, B and Yang, X}, title = {Molecular Epidemiology and Horizontal Transfer Mechanism of optrA-Carrying Linezolid-Resistant Enterococcus faecalis.}, journal = {Polish journal of microbiology}, volume = {73}, number = {3}, pages = {349-362}, pmid = {39268957}, issn = {2544-4646}, mesh = {*Enterococcus faecalis/genetics/drug effects ; *Linezolid/pharmacology ; *Gene Transfer, Horizontal ; *Anti-Bacterial Agents/pharmacology ; Humans ; *Gram-Positive Bacterial Infections/microbiology/epidemiology ; China/epidemiology ; Bacterial Proteins/genetics/metabolism ; Molecular Epidemiology ; Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; Drug Resistance, Multiple, Bacterial/genetics ; Whole Genome Sequencing ; Conjugation, Genetic ; }, abstract = {The aim of this work was to provide a theoretical and scientific basis for the treatment, prevention, and control of clinical drug-resistant bacterial infections by studying the molecular epidemiology and horizontal transfer mechanism of optrA-carrying linezolid-resistant Enterococcus faecalis strains (LREfs) that were clinically isolated in a tertiary hospital in Kunming, China. Non-repetitive LREfs retained in a tertiary A hospital in Kunming, China. The strains were identified by Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The transferability and horizontal transfer mechanism of optrA gene were analyzed using polymerase chain reaction (PCR), whole-genome sequencing (WGS), and conjugation experiments. A total of 39 LREfs strains were collected, and all of them were multi-drug resistant. There were 30 LREfs strains (76.9%) carrying the optrA gene, The cfr, poxtA genes and mutations in the 23S rRNA gene were not detected. The conjugation experiments showed that only three of 10 randomly selected optrA-carrying LREfs were successfully conjugated with JH2-2. Further analysis of one successfully conjugated strain revealed that the optrA gene, located in the donor bacterium, formed the IS1216E-erm(A)-optrA-fexA-IS1216E transferable fragment under the mediation of the mobile genetic element (MGE) IS1216E, which was then transferred to the recipient bacterium via horizontal plasmid transfer. Carrying the optrA gene is the primary resistance mechanism of LREfs strains. The optrA gene could carry the erm(A) and fexA genes to co-transfer among E. faecalis. MGEs such as insertion sequence IS1216E play an important role in the horizontal transfer of the optrA gene.}, }
@article {pmid39268528, year = {2024}, author = {Riva, F and Dechesne, A and Eckert, EM and Riva, V and Borin, S and Mapelli, F and Smets, BF and Crotti, E}, title = {Conjugal plasmid transfer in the plant rhizosphere in the One Health context.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1457854}, pmid = {39268528}, issn = {1664-302X}, abstract = {INTRODUCTION: Horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) is one of the primary routes of antimicrobial resistance (AMR) dissemination. In the One Health context, tracking the spread of mobile genetic elements (MGEs) carrying ARGs in agri-food ecosystems is pivotal in understanding AMR diffusion and estimating potential risks for human health. So far, little attention has been devoted to plant niches; hence, this study aimed to evaluate the conjugal transfer of ARGs to the bacterial community associated with the plant rhizosphere, a hotspot for microbial abundance and activity in the soil. We simulated a source of AMR determinants that could enter the food chain via plants through irrigation.<br><br>METHODS: Among the bacterial strains isolated from treated wastewater, the strain Klebsiella variicola EEF15 was selected as an ARG donor because of the relevance of Enterobacteriaceae in the AMR context and the One Health framework. The strain ability to recolonize lettuce, chosen as a model for vegetables that were consumed raw, was assessed by a rifampicin resistant mutant. K. variicola EEF15 was genetically manipulated to track the conjugal transfer of the broad host range plasmid pKJK5 containing a fluorescent marker gene to the natural rhizosphere microbiome obtained from lettuce plants. Transconjugants were sorted by fluorescent protein expression and identified through 16S rRNA gene amplicon sequencing.<br><br>RESULTS AND DISCUSSION: K. variicola EEF15 was able to colonize the lettuce rhizosphere and inhabit its leaf endosphere 7 days past bacterial administration. Fluorescence stereomicroscopy revealed plasmid transfer at a frequency of 10[-3]; cell sorting allowed the selection of the transconjugants. The conjugation rates and the strain's ability to colonize the plant rhizosphere and leaf endosphere make strain EEF15::lacI[q]-pLpp-mCherry-gm[R] with pKJK5::Plac::gfp an interesting candidate to study ARG spread in the agri-food ecosystem. Future studies taking advantage of additional environmental donor strains could provide a comprehensive snapshot of AMR spread in the One Health context.}, }
@article {pmid39266980, year = {2024}, author = {Wu, H and Dongchen, W and Li, Y and Brown, SE and Wei, S and Lin, C and Mao, Z and Liu, Z}, title = {Mitogenomes comparison of 3 species of Asparagus L shedding light on their functions due to domestication and adaptative evolution.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {857}, pmid = {39266980}, issn = {1471-2164}, support = {202305A0350012//Yunnan Basic Research Program/ ; 202305A0350012//Yunnan Basic Research Program/ ; 202305A0350012//Yunnan Basic Research Program/ ; 202305A0350012//Yunnan Basic Research Program/ ; 202305A0350012//Yunnan Basic Research Program/ ; 32360089//National Natural Science Foundation of China/ ; 32360089//National Natural Science Foundation of China/ ; 202101BD070001-027//Yunnan Agricultural joint Fund-key project/ ; }, mesh = {*Asparagus Plant/genetics ; *Genome, Mitochondrial ; *Phylogeny ; *Domestication ; *Evolution, Molecular ; RNA Editing ; Gene Transfer, Horizontal ; Genome, Chloroplast ; }, abstract = {BACKGROUND: Asparagus L., widely distributed in the old world is a genus under Asparagaceae, Asparagales. The species of the genus were mainly used as vegetables, traditional medicines as well as ornamental plants. However, the evolution and functions of mitochondrial (Mt) genomes (mitogenomes) remains largely unknown. In this study, the typical herbal medicine A. taliensis and ornamental plant A. setaceus were used to assemble and annotate the mitogenomes, and the resulting mitogenomes were further compared with published mitogenome of A. officinalis for the analysis of their functions in the context of domestication and adaptative evolution.<br><br>RESULTS: The mitochondrial genomes of both A. taliensis and A. setaceus were assembled as complete circular ones. The phylogenetic trees based on conserved protein-coding genes of Mt genomes and whole chloroplast (Cp) genomes showed that, the phylogenetic relationship of the sampled 13 species of Asparagus L. were not exactly consistent. The collinear analyses between the nuclear (Nu) and Mt genomes confirmed the existence of mutual horizontal genes transfers (HGTs) between Nu and Mt genomes within these species. Based on RNAseq data, the Mt RNA editing were predicted and atp1 and ccmB RNA editing of A. taliensis were further confirmed by DNA sequencing. Simultaneously homologous search found 5 Nu coding gene families including pentatricopeptide-repeats (PPRs) involved in Mt RNA editing. Finally, the Mt genome variations, gene expressions and mutual HGTs between Nu and Mt were detected with correlation to the growth and developmental phenotypes respectively. The results suggest that, both Mt and Nu genomes co-evolved and maintained the Mt organella replication and energy production through TCA and oxidative phosphorylation .<br><br>CONCLUSION: The assembled and annotated complete mitogenomes of both A. taliensis and A. setaceus provide valuable information for their phylogeny and concerted action of Nu and Mt genomes to maintain the energy production system of Asparagus L. in the context of domestication and adaptation to environmental niches.}, }
@article {pmid39266188, year = {2024}, author = {Ali, N and Vora, C and Mathuria, A and Kataria, N and Mani, I}, title = {Advances in CRISPR-Cas systems for gut microbiome.}, journal = {Progress in molecular biology and translational science}, volume = {208}, number = {}, pages = {59-81}, doi = {10.1016/bs.pmbts.2024.07.008}, pmid = {39266188}, issn = {1878-0814}, mesh = {*CRISPR-Cas Systems/genetics ; Humans ; *Gastrointestinal Microbiome/genetics ; Animals ; Gene Editing ; Probiotics/therapeutic use ; }, abstract = {CRISPR-Cas technology has revolutionized microbiome research by enabling precise genetic manipulation of microbial communities. This review explores its diverse applications in gut microbiome studies, probiotic development, microbiome diagnostics, pathogen targeting, and microbial community engineering. Engineered bacteriophages and conjugative probiotics exemplify CRISPR-Cas's capability for targeted bacterial manipulation, offering promising strategies against antibiotic-resistant infections and other gut-related disorders. CRISPR-Cas systems also enhance probiotic efficacy by improving stress tolerance and colonization in the gastrointestinal tract. CRISPR-based techniques in diagnostics enable early intervention by enabling fast and sensitive pathogen identification. Furthermore, CRISPR-mediated gene editing allows tailored modification of microbial populations, mitigating risks associated with horizontal gene transfer and enhancing environmental and health outcomes. Despite its transformative potential, ethical and regulatory challenges loom large, demanding robust frameworks to guide its responsible application. This chapter highlights CRISPR-Cas's pivotal role in advancing microbiome research toward personalized medicine and microbial therapeutics while emphasizing the imperative of balanced ethical deliberations and comprehensive regulatory oversight.}, }
@article {pmid39266183, year = {2024}, author = {Mathuria, A and Vora, C and Ali, N and Mani, I}, title = {Advances in CRISPR-Cas systems for human bacterial disease.}, journal = {Progress in molecular biology and translational science}, volume = {208}, number = {}, pages = {19-41}, doi = {10.1016/bs.pmbts.2024.07.013}, pmid = {39266183}, issn = {1878-0814}, mesh = {*CRISPR-Cas Systems/genetics ; Humans ; *Bacterial Infections/microbiology/genetics ; Gene Editing ; Bacteria/genetics ; }, abstract = {Prokaryotic adaptive immune systems called CRISPR-Cas systems have transformed genome editing by allowing for precise genetic alterations through targeted DNA cleavage. This system comprises CRISPR-associated genes and repeat-spacer arrays, which generate RNA molecules that guide the cleavage of invading genetic material. CRISPR-Cas is classified into Class 1 (multi-subunit effectors) and Class 2 (single multi-domain effectors). Its applications span combating antimicrobial resistance (AMR), targeting antibiotic resistance genes (ARGs), resensitizing bacteria to antibiotics, and preventing horizontal gene transfer (HGT). CRISPR-Cas3, for example, effectively degrades plasmids carrying resistance genes, providing a precise method to disarm bacteria. In the context of ESKAPE pathogens, CRISPR technology can resensitize bacteria to antibiotics by targeting specific resistance genes. Furthermore, in tuberculosis (TB) research, CRISPR-based tools enhance diagnostic accuracy and facilitate precise genetic modifications for studying Mycobacterium tuberculosis. CRISPR-based diagnostics, leveraging Cas endonucleases' collateral cleavage activity, offer highly sensitive pathogen detection. These advancements underscore CRISPR's transformative potential in addressing AMR and enhancing infectious disease management.}, }
@article {pmid39264185, year = {2024}, author = {Magar, S and Kolte, V and Sharma, G and Govindarajan, S}, title = {Exploring pangenomic diversity and CRISPR-Cas evasion potential in jumbo phages: a comparative genomics study.}, journal = {Microbiology spectrum}, volume = {12}, number = {10}, pages = {e0420023}, pmid = {39264185}, issn = {2165-0497}, support = {/WT_/Wellcome Trust/United Kingdom ; //DST-INSPIRE Faculty Grant/ ; IA/E/19/1/504958//Wellcome Trust DBT India Alliance (India Alliance)/ ; CRG/2020/003295//DST | Science and Engineering Research Board (SERB)/ ; }, mesh = {*Genomics ; *Genetic Variation ; *CRISPR-Cas Systems ; *Bacteriophages/genetics ; *Genome, Viral ; Molecular Sequence Annotation ; Viral Proteins/genetics ; Phylogeny ; Genes, Viral ; Gene Regulatory Networks ; *Immune Evasion/genetics ; }, abstract = {UNLABELLED: Jumbo phages are characterized by their remarkably large-sized genome and unique life cycles. Jumbo phages belonging to Chimalliviridae family protect the replicating phage DNA from host immune systems like CRISPR-Cas and restriction-modification system through a phage nucleus structure. Several recent studies have provided new insights into jumbo phage infection biology, but the pan-genome diversity of jumbo phages and their relationship with CRISPR-Cas targeting beyond Chimalliviridae are not well understood. In this study, we used pan-genome analysis to identify orthologous gene families shared among 331 jumbo phages with complete genomes. We show that jumbo phages lack a universally conserved set of core genes but identified seven "soft-core genes" conserved in over 50% of these phages. These genes primarily govern DNA-related activities, such as replication, repair, or nucleotide synthesis. Jumbo phages exhibit a wide array of accessory and unique genes, underscoring their genetic diversity. Phylogenetic analyses of the soft-core genes revealed frequent horizontal gene transfer events between jumbo phages, non-jumbo phages, and occasionally even giant eukaryotic viruses, indicating a polyphyletic evolutionary nature. We categorized jumbo phages into 11 major viral clusters (VCs) spanning 130 sub-clusters, with the majority being multi-genus jumbo phage clusters. Moreover, through the analysis of hallmark genes related to CRISPR-Cas targeting, we predict that many jumbo phages can evade host immune systems using both known and yet-to-be-identified mechanisms. In summary, our study enhances our understanding of jumbo phages, shedding light on their pan-genome diversity and remarkable genome protection capabilities.<br><br>IMPORTANCE: Jumbo phages are large bacterial viruses known for more than 50 years. However, only in recent years, a significant number of complete genome sequences of jumbo phages have become available. In this study, we employed comparative genomic approaches to investigate the genomic diversity and genome protection capabilities of the 331 jumbo phages. Our findings revealed that jumbo phages exhibit high genetic diversity, with only a few genes being relatively conserved across jumbo phages. Interestingly, our data suggest that jumbo phages employ yet-to-be-identified strategies to protect their DNA from the host immune system, such as CRISPR-Cas.}, }
@article {pmid39264161, year = {2024}, author = {Matsumoto, S and Kishida, K and Nonoyama, S and Sakai, K and Tsuda, M and Nagata, Y and Ohtsubo, Y}, title = {Evolution of the Tn4371 ICE family: traR-mediated coordination of cargo gene upregulation and horizontal transfer.}, journal = {Microbiology spectrum}, volume = {12}, number = {10}, pages = {e0060724}, pmid = {39264161}, issn = {2165-0497}, support = {K-2016-004//Institute for Fermentation, Osaka (IFO)/ ; 19H02865//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 22H02233//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 22K19124//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 19K15725//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; }, mesh = {*Gene Transfer, Horizontal ; *DNA Transposable Elements/genetics ; *Gene Expression Regulation, Bacterial ; Bacterial Proteins/genetics/metabolism ; Evolution, Molecular ; Operon ; Up-Regulation ; Conjugation, Genetic ; }, abstract = {ICEKKS102Tn4677 carries a bph operon for the mineralization of polychlorinated biphenyls (PCBs)/biphenyl and belongs to the Tn4371 ICE (integrative and conjugative element) family. In this study, we investigated the role of the traR gene in ICE transfer. The traR gene encodes a LysR-type transcriptional regulator, which is conserved in sequence, positioning, and directional orientation among Tn4371 family ICEs. The traR belongs to the bph operon, and its overexpression on solid medium resulted in modest upregulation of traG (threefold), marked upregulation of xis (80-fold), enhanced ICE excision and, most notably, ICE transfer frequency. We propose the evolutional roles of traR, which upon insertion to its current position, might have connected the cargo gene activation and ICE transfer. This property of ICE, i.e., undergoing transfer under environmental conditions that lead to cargo gene activation, would instantly confer fitness advantages to bacteria newly acquiring this ICE, thereby resulting in efficient dissemination of the Tn4371 family ICEs.IMPORTANCEOnly ICEKKS102Tn4677 is proven to transfer among the widely disseminating Tn4371 family integrative and conjugative elements (ICEs) from β and γ-proteobacteria. We showed that the traR gene in ICEKKS102Tn4677, which is conserved in the ICE family with fixed location and direction, is co-transcribed with the cargo gene and activates ICE transfer. We propose that capturing of traR by an ancestral ICE to the current position established the Tn4371 family of ICEs. Our findings provide insights into the evolutionary processes that led to the widespread distribution of the Tn4371 family of ICEs across bacterial species.}, }
@article {pmid39260133, year = {2024}, author = {Xu, Q and Xie, M and Yang, X and Liu, X and Ye, L and Chen, K and Chan, EW and Chen, S}, title = {Conjugative transmission of virulence plasmid in Klebsiella pneumoniae mediated by a novel IncN-like plasmid.}, journal = {Microbiological research}, volume = {289}, number = {}, pages = {127896}, doi = {10.1016/j.micres.2024.127896}, pmid = {39260133}, issn = {1618-0623}, mesh = {*Klebsiella pneumoniae/genetics/pathogenicity ; *Plasmids/genetics ; Animals ; *Klebsiella Infections/microbiology/transmission ; Virulence/genetics ; *Conjugation, Genetic ; Mice ; *Virulence Factors/genetics ; *Drug Resistance, Multiple, Bacterial/genetics ; Gene Transfer, Horizontal ; Interleukin-1beta/genetics ; Phagocytosis ; Disease Models, Animal ; Macrophages/microbiology ; Female ; Humans ; Type IV Secretion Systems/genetics ; }, abstract = {Klebsiella pneumoniae (Kp) is increasingly recognized as a reservoir for a range of antibiotic resistance genes and a pathogen that frequently causes severe infections in both hospital and community settings. In this study, we have identified a novel mechanism of conjugative transfer of a non-conjugative virulence plasmid through the formation of a fusion plasmid between the virulence plasmid and a novel 59,162 bp IncN- plasmid. This plasmid was found to be a multidrug-resistance (MDR) plasmid and carried a T4SS cluster, which greatly facilitated the efficient horizontal transfer of the fusion plasmid between Kp strains. The fused virulence plasmid conferred the resistance of serum killing and macrophage phagocytosis to the transconjugants. Importantly, this plasmid was shown to be essential for Kp virulence in a mouse model. Mechanistic analysis revealed that the virulence factors encoded by this virulence plasmid contributed to resistance to in vivo clearance and induced a high level of proinflammatory cytokine IL-1β, which acts as an inducer for more neutrophil recruitment. The transmission of the fusion plasmid in Kp has the potential to convert it into both MDR and hypervirulent Kp, accelerating its evolution, and posing a serious threat to human health. The findings of this study provide new insights into the rapid evolution of MDR and hypervirulent Kp in recent years.}, }
@article {pmid39258299, year = {2024}, author = {Song, W and Li, C and Lu, Y and Shen, D and Jia, Y and Huo, Y and Piao, W and Jin, H}, title = {Chlomito: a novel tool for precise elimination of organelle genome contamination from nuclear genome assembly.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1430443}, pmid = {39258299}, issn = {1664-462X}, abstract = {INTRODUCTION: Accurate reference genomes are fundamental to understanding biological evolution, biodiversity, hereditary phenomena and diseases. However, many assembled nuclear chromosomes are often contaminated by organelle genomes, which will mislead bioinformatic analysis, and genomic and transcriptomic data interpretation.<br><br>METHODS: To address this issue, we developed a tool named Chlomito, aiming at precise identification and elimination of organelle genome contamination from nuclear genome assembly. Compared to conventional approaches, Chlomito utilized new metrics, alignment length coverage ratio (ALCR) and sequencing depth ratio (SDR), thereby effectively distinguishing true organelle genome sequences from those transferred into nuclear genomes via horizontal gene transfer (HGT).<br><br>RESULTS: The accuracy of Chlomito was tested using sequencing data from Plum, Mango and Arabidopsis. The results confirmed that Chlomito can accurately detect contigs originating from the organelle genomes, and the identified contigs covered most regions of the organelle reference genomes, demonstrating efficiency and precision of Chlomito. Considering user convenience, we further packaged this method into a Docker image, simplified the data processing workflow.<br><br>DISCUSSION: Overall, Chlomito provides an efficient, accurate and convenient method for identifying and removing contigs derived from organelle genomes in genomic assembly data, contributing to the improvement of genome assembly quality.}, }
@article {pmid39255666, year = {2024}, author = {Li, Y and Zheng, Q and Lu, Y and Qiao, Y and Guo, H and Ma, Q and Zhou, J and Li, H and Wang, T}, title = {Water temperature disturbance alters the conjugate transfer of antibiotic resistance genes via affecting ROS content and intercellular aggregation.}, journal = {Journal of hazardous materials}, volume = {479}, number = {}, pages = {135762}, doi = {10.1016/j.jhazmat.2024.135762}, pmid = {39255666}, issn = {1873-3336}, mesh = {*Reactive Oxygen Species/metabolism ; *Temperature ; *Plasmids/genetics ; Drug Resistance, Microbial/genetics ; Water/chemistry ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Gene Transfer, Horizontal ; Escherichia coli/genetics/drug effects ; Drug Resistance, Bacterial/genetics ; Cell Membrane Permeability/drug effects ; Water Microbiology ; }, abstract = {Spread of antibiotic resistance genes (ARGs) in aquatic ecosystems poses a significant global challenge to public health. The potential effects of water temperature perturbation induced by specific water environment changes on ARGs transmission are still unclear. The conjugate transfer of plasmid-mediated ARGs under water temperature perturbation was investigated in this study. The conjugate transfer frequency (CTF) was only 7.16 × 10[-7] at a constant water temperature of 5 °C, and it reached 2.18 × 10[-5] at 30 °C. Interestingly, compared to the constant 5 °C, the water temperature perturbations (cooling and warming models between 5-30 °C) significantly promoted the CTF. Intracellular reactive oxygen species was a dominant factor, which not only directly affected the CTF of ARGs, but also functioned indirectly via influencing the cell membrane permeability and cell adhesion. Compared to the constant 5 °C, water temperature perturbations significantly elevated the gene expression associated with intercellular contact, cell membrane permeability, oxidative stress responses, and energy driven force for CTF. Furthermore, based on the mathematical model predictions, the stabilization times of acquiring plasmid maintenance were shortened to 184 h and 190 h under cooling and warming model, respectively, thus the water temperature perturbations promoted the ARGs transmission in natural conditions compared with the constant low temperature conditions.}, }
@article {pmid39254330, year = {2024}, author = {Lee, E and Priutt, E and Woods, S and Quick, A and King, S and McLellan, LK and Shields, RC}, title = {Genomic analysis of conjugative and chromosomally integrated mobile genetic elements in oral streptococci.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {10}, pages = {e0136024}, pmid = {39254330}, issn = {1098-5336}, support = {R01 DE033403/DE/NIDCR NIH HHS/United States ; R03 DE029882/DE/NIDCR NIH HHS/United States ; R03DE029882//HHS | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; R01DE033403//HHS | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; }, mesh = {*Interspersed Repetitive Sequences ; *Conjugation, Genetic ; *Streptococcus/genetics ; *Genome, Bacterial ; *Mouth/microbiology ; Genomics ; Chromosomes, Bacterial/genetics ; Humans ; }, abstract = {This study aimed to investigate the diversity of conjugative and chromosomally integrated mobile genetic elements (cciMGEs) within six oral streptococci species. cciMGEs, including integrative and conjugative elements (ICEs) and integrative and mobilizable elements (IMEs), are stably maintained on the host cell chromosome; however, under certain conditions, they are able to excise, form extrachromosomal circles, and transfer via a conjugation apparatus. Many cciMGEs encode "cargo" functions that aid survival in new niches and evolve new antimicrobial resistance or virulence properties, whereas others have been shown to influence host bacterial physiology. Here, using a workflow employing preexisting bioinformatics tools, we analyzed 551 genomes for the presence of cciMGEs across six common health- and disease-associated oral streptococci. We identified 486 cciMGEs, 173 of which were ICEs and 233 of which were IMEs. The cciMGEs were diverse in size, cargo genes, and relaxase types. We identified several novel relaxase proteins and a widespread IME carrying a small multidrug resistance transporter. Additionally, we provide evidence that several of the bioinformatically predicted cciMGEs encoded within various Streptococcus mutans strains are capable of excision and circularization, a critical step for cciMGE conjugative transfer. These findings highlight the significance and potential impact of MGEs in shaping the genetic landscape, pathogenicity, and antimicrobial resistance profiles of the oral microbiota.IMPORTANCEOral streptococci are important players in the oral microbiome, influencing both health and disease states within dental bacterial communities. Evolutionary adaptation, shaped in a major part by the horizontal transfer of genes, is essential for their survival in the oral cavity and within new environments. Conjugation is a significant driver of horizontal gene transfer; however, there is limited information regarding this process in oral bacteria. This study utilizes publicly available genome sequences to identify conjugative and chromosomally integrated mobile genetic elements (cciMGEs) across several species of oral streptococci and presents the preliminary characterization of these elements. Our findings significantly enhance our understanding of the mobile genomic landscape of oral streptococci critical for human health, with valuable insights into how cciMGEs might influence the survival and pathogenesis of these bacteria in the oral microbiome.}, }
@article {pmid39253440, year = {2025}, author = {Frail, S and Steele-Ogus, M and Doenier, J and Moulin, SLY and Braukmann, T and Xu, S and Yeh, E}, title = {Genomes of nitrogen-fixing eukaryotes reveal a non-canonical model of organellogenesis.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39253440}, issn = {2692-8205}, support = {S10 OD030441/OD/NIH HHS/United States ; T32 AI007328/AI/NIAID NIH HHS/United States ; T32 GM007276/GM/NIGMS NIH HHS/United States ; }, abstract = {Endosymbiotic gene transfer and import of host-encoded proteins are considered hallmarks of organelles necessary for stable integration of two cells. However, newer endosymbiotic models have challenged the origin and timing of such genetic integration during organellogenesis. Epithemia diatoms contain diazoplasts, obligate endosymbionts that are closely related to recently-described nitrogen-fixing organelles and share similar function as integral cell compartments. We report genomic analyses of two species which are highly divergent but share a common ancestor at the origin of the endosymbiosis. We found minimal evidence of genetic integration in E.clementina: nonfunctional diazoplast-to-nucleus DNA transfers and 6 host-encoded proteins of unknown function in the diazoplast proteome, far fewer than detected in other recently-acquired endosymbionts designated organelles. Epithemia diazoplasts are a valuable counterpoint to existing organellogenesis models, demonstrating that endosymbionts can function as integral compartments absent significant genetic integration. The minimal genetic integration makes diazoplasts valuable blueprints for bioengineering endosymbiotic compartments de novo.}, }
@article {pmid39249569, year = {2024}, author = {Ruhal, R and Sahu, A and Koujalagi, T and Das, A and Prasanth, H and Kataria, R}, title = {Biofilm-specific determinants of enterococci pathogen.}, journal = {Archives of microbiology}, volume = {206}, number = {10}, pages = {397}, pmid = {39249569}, issn = {1432-072X}, support = {NA//VIT University/ ; NA//VIT University/ ; NA//VIT University/ ; NA//VIT University/ ; NA//VIT University/ ; NA//VIT University/ ; }, mesh = {*Enterococcus/genetics/metabolism ; *Biofilms ; Gene Expression Regulation, Bacterial ; *Gram-Positive Bacterial Infections/epidemiology/microbiology/physiopathology ; Bacterial Adhesion/genetics ; Adhesins, Bacterial/genetics/metabolism ; Polysaccharides, Bacterial/metabolism ; Gene Transfer, Horizontal ; }, abstract = {Amongst all Enterococcus spp., E. faecalis and E. faecium are most known notorious pathogen and their biofilm formation has been associated with endocarditis, oral, urinary tract, and wound infections. Biofilm formation involves a pattern of initial adhesion, microcolony formation, and mature biofilms. The initial adhesion and microcolony formation involve numerous surface adhesins e.g. pili Ebp and polysaccharide Epa. The mature biofilms are maintained by eDNA, It's worth noting that phage-mediated dispersal plays a prominent role. Further, the involvement of peptide pheromones in regulating biofilm maintenance sets it apart from other pathogens and facilitating the horizontal transfer of resistance genes. The role of fsr based regulation by regulating gelE expression is also discussed. Thus, we provide a concise overview of the significant determinants at each stage of Enterococcus spp. biofilm formation. These elements could serve as promising targets for antibiofilm strategies.}, }
@article {pmid39248569, year = {2024}, author = {Hassan, J and Hinenoya, A and Hatanaka, N and Awasthi, SP and Manjunath, GB and Rahman, N and Yamate, J and Nakamura, S and Motooka, D and Nagita, A and Faruque, SM and Yamasaki, S}, title = {A plasmid-mediated type III secretion system associated with invasiveness and diarrheagenicity of Providencia rustigianii.}, journal = {mBio}, volume = {15}, number = {10}, pages = {e0229724}, pmid = {39248569}, issn = {2150-7511}, support = {20K07483//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; }, mesh = {*Providencia/genetics/metabolism/pathogenicity ; *Plasmids/genetics ; Humans ; *Type III Secretion Systems/genetics/metabolism ; Animals ; HeLa Cells ; *Bacterial Toxins/genetics/metabolism ; *Enterobacteriaceae Infections/microbiology ; Rabbits ; Diarrhea/microbiology ; Genome, Bacterial ; Whole Genome Sequencing ; Virulence Factors/genetics ; Virulence/genetics ; Conjugation, Genetic ; Gene Transfer, Horizontal ; }, abstract = {We have recently described a clinical isolate of Providencia rustigianii strain JH-1 carrying the genes for cytolethal distending toxin (CDT) in a conjugative plasmid. A cdtB mutant of strain JH-1, which lost CDT activity, was still found to retain invasiveness and diarrheagenicity. The strain was subjected to phenotypic and genetic analyses including whole genome sequencing (WGS) to explore the genetic determinants of the observed invasiveness and diarrheagenic properties. Analysis and annotation of WGS data revealed the presence of two distinct type III secretion systems (T3SS) in strain JH-1, one of which was located on the chromosome designated as cT3SS (3,992,833 bp) and the other on a mega-plasmid designated as pT3SS (168,819 bp). Comparative genomic analysis revealed that cT3SS is generally conserved in Providencia spp. but pT3SS was limited to a subset of Providencia spp., carrying cdt genes. Strain JH-1 was found to invade HeLa cells and induce fluid accumulation with characteristic pathological lesions in rabbit ileal loops. Remarkably, these phenomena were associated with the pT3SS but not cT3SS. The plasmid could be transferred by conjugation from strain JH-1 to other strains of P. rustigianii, Providencia rettgeri, and Escherichia coli with concomitant transfer of these virulence properties. This is the first report of a functional and mobile T3SS in P. rustigianii and its association with invasiveness and diarrheagenicity of this bacterium. These data suggest that P. rustigianii and other CDT-producing Providencia strains might carry T3SS and exert their diarrheagenic effect by exploiting the T3SS nano-machinery.IMPORTANCEThe precise mechanism of virulence of Providencia rustigianii is unclear, although some strains produce cytolethal distending toxin as a putative virulence factor. We have detected the presence of a type III secretion system (T3SS) for the first time on a plasmid in a P. rustigianii strain. Plasmid-mediated T3SS seems to be directly involved in virulence of P. rustigianii and may serve as a means of horizontal transfer of T3SS genes. Our results may have implication in understanding the mechanism of emergence of new pathogenic strains of P. rustigianii.}, }
@article {pmid39248479, year = {2024}, author = {Glen, KA and Lamont, IL}, title = {Characterization of acquired β-lactamases in Pseudomonas aeruginosa and quantification of their contributions to resistance.}, journal = {Microbiology spectrum}, volume = {12}, number = {10}, pages = {e0069424}, pmid = {39248479}, issn = {2165-0497}, support = {//University of Otago (Te Whare W&#x101;nanga o Ot&#x101;go)/ ; }, mesh = {*Pseudomonas aeruginosa/drug effects/genetics/enzymology ; *beta-Lactamases/genetics/metabolism ; *Anti-Bacterial Agents/pharmacology ; *Microbial Sensitivity Tests ; *Carbapenems/pharmacology ; *Pseudomonas Infections/microbiology/drug therapy ; *beta-Lactam Resistance/genetics ; Humans ; beta-Lactams/pharmacology ; Bacterial Proteins/genetics/metabolism ; Plasmids/genetics ; Cephalosporins/pharmacology ; }, abstract = {Pseudomonas aeruginosa is a highly problematic opportunistic pathogen that causes a range of different infections. Infections are commonly treated with β-lactam antibiotics, including cephalosporins, monobactams, penicillins, and carbapenems, with carbapenems regarded as antibiotics of last resort. Isolates of P. aeruginosa can contain horizontally acquired bla genes encoding β-lactamase enzymes, but the extent to which these contribute to β-lactam resistance in this species has not been systematically quantified. The overall aim of this research was to address this knowledge gap by quantifying the frequency of β-lactamase-encoding genes in P. aeruginosa and by determining the effects of β-lactamases on susceptibility of P. aeruginosa to β-lactams. Genome analysis showed that β-lactamase-encoding genes are present in 3% of P. aeruginosa but are enriched in carbapenem-resistant isolates (35%). To determine the substrate antibiotics, 10 β-lactamases were expressed from an integrative plasmid in the chromosome of P. aeruginosa reference strain PAO1. The β-lactamases reduced susceptibility to a variety of clinically used antibiotics, including carbapenems (meropenem, imipenem), penicillins (ticarcillin, piperacillin), cephalosporins (ceftazidime, cefepime), and a monobactam (aztreonam). Different enzymes acted on different β-lactams. β-lactamases encoded by the genomes of P. aeruginosa clinical isolates had similar effects to the enzymes expressed in strain PAO1. Genome engineering was used to delete β-lactamase-encoding genes from three carbapenem-resistant clinical isolates and increased susceptibility to substrate β-lactams. Our findings demonstrate that acquired β-lactamases play an important role in β-lactam resistance in P. aeruginosa, identifying substrate antibiotics for a range of enzymes and quantifying their contributions to resistance.IMPORTANCEPseudomonas aeruginosa is an extremely problematic pathogen, with isolates that are resistant to the carbapenem class of β-lactam antibiotics being in critical need of new therapies. Genes encoding β-lactamase enzymes that degrade β-lactam antibiotics can be present in P. aeruginosa, including carbapenem-resistant isolates. Here, we show that β-lactamase genes are over-represented in carbapenem-resistant isolates, indicating their key role in resistance. We also show that different β-lactamases alter susceptibility of P. aeruginosa to different β-lactam antibiotics and quantify the effects of selected enzymes on β-lactam susceptibility. This research significantly advances the understanding of the contributions of acquired β-lactamases to antibiotic resistance, including carbapenem resistance, in P. aeruginosa and by implication in other species. It has potential to expedite development of methods that use whole genome sequencing of infecting bacteria to inform antibiotic treatment, allowing more effective use of antibiotics, and facilitate the development of new antibiotics.}, }
@article {pmid39245329, year = {2024}, author = {Zhang, F and Li, Z and Liu, X and Li, Z and Lei, Z and Zhao, J and Zhang, Y and Wu, Y and Yang, X and Lu, B}, title = {In-host intra- and inter-species transfer of blaKPC-2 and blaNDM-1 in Serratia marcescens and its local and global epidemiology.}, journal = {International journal of antimicrobial agents}, volume = {64}, number = {5}, pages = {107327}, doi = {10.1016/j.ijantimicag.2024.107327}, pmid = {39245329}, issn = {1872-7913}, mesh = {*Serratia marcescens/genetics/drug effects/isolation &amp; purification ; *beta-Lactamases/genetics ; Humans ; *Serratia Infections/microbiology/epidemiology ; *Gene Transfer, Horizontal ; *Plasmids/genetics ; *Whole Genome Sequencing ; Microbial Sensitivity Tests ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Phylogeny ; Providencia/genetics/drug effects ; Drug Resistance, Multiple, Bacterial/genetics ; }, abstract = {OBJECTIVES: The aim of this study was to investigate interspecies transfer of resistance gene blaNDM-1 and intraspecies transfer of resistance gene blaKPC-2 in Serratia marcescens, and explore the epidemical and evolutionary characteristics of carbapenemase-producing S. marcescens (CPSM) regionally and globally.<br><br>METHODS: Interspecies and intraspecies transfer of blaKPC-2- or blaNDM-1 were identified by antimicrobial susceptibility testing, plasmid conjugation and curing, discovery of transposable units (TUs), outer membrane vesicles (OMVs), qPCR, whole-genome sequencing (WGS) and bioinformatic analysis. The genomic evolution of CPSM strains was explored by cgSNP and maximum-likelihood phylogenetic tree.<br><br>RESULTS: CPSM S50079 strain, co-carrying blaKPC-2 and blaNDM-1 on one plasmid, was isolated from the blood of a patient with acute pancreatitis and could generate TUs carrying either blaKPC-2 or blaNDM-1. The interspecies transfer of blaNDM-1-carrying plasmid from Providencia rettgeri P50213, producing the identical blaNDM-1-carrying TUs, to S. marcescens S50079K, an S50079 variant via plasmid curing, was identified through blaNDM-1-harbouring plasmid conjugation and OMVs transfer. Moreover, the intraspecies transfer of blaKPC-2, mediated by IS26 from plasmid to chromosome in S50079, was also identified. In another patient, who underwent lung transplantation, interspecies transfer of blaNDM-1 carried by IncX3 plasmid was identified among S. marcescens and Citrobacter freundii as well as Enterobacter hormaechei via plasmid transfer. Furthermore, 11 CPSM from 349 non-repetitive S. marcescens strains were identified in the same hospital, and clonal dissemination, with carbapenemase evolution from blaKPC-2 to both blaKPC-2 and blaNDM-1, was found in the 8 CPSM across 4 years. Finally, the analysis of 236 global CPSM from 835 non-repetitive S. marcescens genomes, retrieved from the NCBI database, revealed long-term spread and evolution worldwide, and would cause the convergence of more carbapenemase genes.<br><br>CONCLUSIONS: Interspecies transfer of resistance gene blaNDM-1 and intraspecies transfer of resistance gene blaKPC-2 in CPSM were identified. Nosocomial and global dissemination of CPSM were revealed and more urgent surveillance was acquired.}, }
@article {pmid39243547, year = {2024}, author = {Hu, RG and Yang, L and Wang, LY and Yang, YL and Li, HJ and Yang, BT and Kang, YH and Liang, ZL and Cong, W}, title = {Unveiling the pathogenic and multidrug-resistant profiles of Vibrio alfacsensis: A potential identified threat in turbot (Scophthalmus maximus) aquaculture.}, journal = {Journal of hazardous materials}, volume = {479}, number = {}, pages = {135729}, doi = {10.1016/j.jhazmat.2024.135729}, pmid = {39243547}, issn = {1873-3336}, mesh = {Animals ; *Flatfishes/microbiology ; *Vibrio/drug effects/genetics/pathogenicity ; *Aquaculture ; *Fish Diseases/microbiology ; *Drug Resistance, Multiple, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; Vibrio Infections/microbiology/veterinary ; Phylogeny ; Virulence ; Microbial Sensitivity Tests ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Vibrio alfacsensis is traditionally seen as an environmental symbiont within its genus, with no detailedly documented pathogenicity in marine aquaculture to date. This study delves into the largely unexplored pathogenic potential and emerging antibiotic resistance of V. alfacsensis. The VA-1 strain, isolated from recirculating aquaculture system (RAS) effluent of cultured turbot (Scophthalmus maximus), underwent comprehensive analysis including biochemical identification, antibiotic susceptibility testing and reinfection trials. The results confirmed VA-1's pathogenicity and significant multiple antibiotic resistance. VA-1 could induce systemic infection in turbot, with symptoms like kidney enlargement, exhibiting virulence comparable to known Vibrio pathogens, with an LD50 around 2.36 × 10[6] CFU/fish. VA-1's remarkable resistance phenotype (14/22) suggested potential for genetic exchange and resistance factor acquisition in aquaculture environments. Phylogenetic analysis based on 16S rDNA sequences and whole-genome sequencing has firmly placed VA-1 within the V. alfacsensis clade, while genome-wide analysis highlights its similarity and diversity in relation to strains from across the globe. VA-1 contained numerous replicons, indicating the possibility for the spread of resistance and virulence genes. This study suggests V. alfacsensis may acquire and transfer pathogenic and resistant traits through horizontal gene transfer, a likelihood intensified by changing environmental and aquaculture conditions, highlighting the need for vigilant pathogen monitoring and new non-antibiotic treatments.}, }
@article {pmid39243538, year = {2024}, author = {Lin, L and Li, L and Yang, X and Hou, L and Wu, D and Wang, B and Ma, B and Liao, X and Yan, X and Gad, M and Su, J and Liu, Y and Liu, K and Hu, A}, title = {Unnoticed antimicrobial resistance risk in Tibetan cities unveiled by sewage metagenomic surveillance: Compared to the eastern Chinese cities.}, journal = {Journal of hazardous materials}, volume = {479}, number = {}, pages = {135730}, doi = {10.1016/j.jhazmat.2024.135730}, pmid = {39243538}, issn = {1873-3336}, mesh = {*Sewage/microbiology ; Tibet ; China ; *Cities ; *Metagenomics ; Drug Resistance, Microbial/genetics ; Bacteria/genetics/drug effects ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; }, abstract = {Sewage surveillance is a cost-effective tool for assessing antimicrobial resistance (AMR) in urban populations. However, research on sewage AMR in remote areas is still limited. Here, we used shotgun metagenomic sequencing to profile antibiotic resistance genes (ARGs) and ARG-carrying pathogens (APs) across 15 cities in Tibetan Plateau (TP) and the major cities in eastern China. Notable regional disparities in sewage ARG composition were found, with a significantly higher ARG abundance in TP (2.97 copies/cell). A total of 542 and 545 APs were identified in sewage from TP and the East, respectively, while more than 40 % carried mobile genetic elements (MGEs). Moreover, 65 MGEs-carrying APs were identified as World Health Organization (WHO) priority-like bacterial and fungal pathogens. Notably, a fungal zoonotic pathogen, Enterocytozoon bieneusi, was found for the first time to carry a nitroimidazole resistance gene (nimJ). Although distinct in AP compositions, the relative abundances of APs were comparable in these two regions. Furthermore, sewage in TP was found to be comparable to the cities in eastern China in terms of ARG mobility and AMR risks. These findings provide insights into ARGs and APs distribution in Chinese sewage and stress the importance of AMR surveillance and management strategies in remote regions.}, }
@article {pmid39242818, year = {2024}, author = {Porras, M&#xc1;G and Assié, A and Tietjen, M and Violette, M and Kleiner, M and Gruber-Vodicka, H and Dubilier, N and Leisch, N}, title = {An intranuclear bacterial parasite of deep-sea mussels expresses apoptosis inhibitors acquired from its host.}, journal = {Nature microbiology}, volume = {9}, number = {11}, pages = {2877-2891}, pmid = {39242818}, issn = {2058-5276}, support = {340535//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; Gottfried Wilhelm Leibniz Prize//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Heisenberggrant GR 5028/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; OIA 1934844//National Science Foundation (NSF)/ ; IOS 2003107//National Science Foundation (NSF)/ ; }, mesh = {Animals ; *Phylogeny ; *Apoptosis ; *Gene Transfer, Horizontal ; Bivalvia/microbiology/parasitology ; Cell Nucleus/metabolism ; Transcriptome ; Bacteroidetes/genetics/metabolism ; Apoptosis Regulatory Proteins/genetics/metabolism ; }, abstract = {A limited number of bacteria are able to colonize the nuclei of eukaryotes. 'Candidatus Endonucleobacter' infects the nuclei of deep-sea mussels, where it replicates to ≥80,000 bacteria per nucleus and causes nuclei to swell to 50 times their original size. How these parasites are able to replicate and avoid apoptosis is not known. Dual RNA-sequencing transcriptomes of infected nuclei isolated using laser-capture microdissection revealed that 'Candidatus Endonucleobacter' does not obtain most of its nutrition from nuclear DNA or RNA. Instead, 'Candidatus Endonucleobacter' upregulates genes for importing and digesting sugars, lipids, amino acids and possibly mucin from its host. It likely prevents apoptosis of host cells by upregulating 7-13 inhibitors of apoptosis, proteins not previously seen in bacteria. Comparative phylogenetic analyses revealed that 'Ca. Endonucleobacter' acquired inhibitors of apoptosis through horizontal gene transfer from their hosts. Horizontal gene transfer from eukaryotes to bacteria is assumed to be rare, but may be more common than currently recognized.}, }
@article {pmid39236811, year = {2024}, author = {Sun, Z and Hong, W and Xue, C and Dong, N}, title = {A comprehensive review of antibiotic resistance gene contamination in agriculture: Challenges and AI-driven solutions.}, journal = {The Science of the total environment}, volume = {953}, number = {}, pages = {175971}, doi = {10.1016/j.scitotenv.2024.175971}, pmid = {39236811}, issn = {1879-1026}, mesh = {*Agriculture/methods ; *Drug Resistance, Microbial/genetics ; Artificial Intelligence ; Anti-Bacterial Agents ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; Wastewater/microbiology ; Animals ; }, abstract = {Since their discovery, the prolonged and widespread use of antibiotics in veterinary and agricultural production has led to numerous problems, particularly the emergence and spread of antibiotic-resistant bacteria (ARB). In addition, other anthropogenic factors accelerate the horizontal transfer of antibiotic resistance genes (ARGs) and amplify their impact. In agricultural environments, animals, manure, and wastewater are the vectors of ARGs that facilitate their spread to the environment and humans via animal products, water, and other environmental pathways. Therefore, this review comprehensively analyzed the current status, removal methods, and future directions of ARGs on farms. This article 1) investigates the origins of ARGs on farms, the pathways and mechanisms of their spread to surrounding environments, and various strategies to mitigate their spread; 2) determines the multiple factors influencing the abundance of ARGs on farms, the pathways through which ARGs spread from farms to the environment, and the effects and mechanisms of non-antibiotic factors on the spread of ARGs; 3) explores methods for controlling ARGs in farm wastes; and 4) provides a comprehensive summary and integration of research across various fields, proposing that in modern smart farms, emerging technologies can be integrated through artificial intelligence to control or even eliminate ARGs. Moreover, challenges and future research directions for controlling ARGs on farms are suggested.}, }
@article {pmid39236533, year = {2024}, author = {Yuan, Q and Li, W and Goh, SG and Chen, SL and Ng, OT and He, Y and Gin, KY}, title = {Genetic traits and transmission of antimicrobial resistance characteristics of cephalosporin resistant Escherichia coli in tropical aquatic environments.}, journal = {Journal of hazardous materials}, volume = {479}, number = {}, pages = {135707}, doi = {10.1016/j.jhazmat.2024.135707}, pmid = {39236533}, issn = {1873-3336}, mesh = {*Escherichia coli/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology ; Singapore ; Tropical Climate ; Water Microbiology ; Gene Transfer, Horizontal ; Wastewater/microbiology ; Cephalosporins/pharmacology ; Sewage/microbiology ; Drug Resistance, Bacterial/genetics ; Humans ; Cephalosporin Resistance/genetics ; Aquaculture ; }, abstract = {This study investigates the genetic traits and transmission mechanisms of cephalosporin-resistant Escherichia coli in tropical aquatic environments in Singapore. From 2016 to 2020, monthly samples were collected from wastewater treatment plants, marine niches, community sewage, beaches, reservoirs, aquaculture farms, and hospitals, yielding 557 isolates that were analyzed for antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) using genomic methods. Findings reveal significant genotypic similarities between environmental and hospital-derived strains, particularly the pandemic E. coli ST131. Environmental strains exhibited high levels of intrinsic resistance mechanisms, including mutations in porins and efflux pumps, with key ARGs such as CMY-2 and NDM-9 predominantly carried by MGEs, which facilitate horizontal gene transfer. Notably, pathogenic EPEC and EHEC strains were detected in community sewage and aquaculture farms, posing substantial public health risks. This underscores the critical role of these environments as reservoirs for multidrug-resistant pathogens and emphasizes the interconnectedness of human activities and environmental health.}, }
@article {pmid39236354, year = {2024}, author = {Brdová, D and Ruml, T and Viktorová, J}, title = {Mechanism of staphylococcal resistance to clinically relevant antibiotics.}, journal = {Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy}, volume = {77}, number = {}, pages = {101147}, doi = {10.1016/j.drup.2024.101147}, pmid = {39236354}, issn = {1532-2084}, mesh = {*Anti-Bacterial Agents/pharmacology/therapeutic use ; Humans ; *Staphylococcal Infections/drug therapy/microbiology ; *Staphylococcus aureus/drug effects ; Drug Resistance, Bacterial ; Microbial Sensitivity Tests ; Animals ; }, abstract = {Staphylococcus aureus, a notorious pathogen with versatile virulence, poses a significant challenge to current antibiotic treatments due to its ability to develop resistance mechanisms against a variety of clinically relevant antibiotics. In this comprehensive review, we carefully dissect the resistance mechanisms employed by S. aureus against various antibiotics commonly used in clinical settings. The article navigates through intricate molecular pathways, elucidating the mechanisms by which S. aureus evades the therapeutic efficacy of antibiotics, such as β-lactams, vancomycin, daptomycin, linezolid, etc. Each antibiotic is scrutinised for its mechanism of action, impact on bacterial physiology, and the corresponding resistance strategies adopted by S. aureus. By synthesising the knowledge surrounding these resistance mechanisms, this review aims to serve as a comprehensive resource that provides a foundation for the development of innovative therapeutic strategies and alternative treatments for S. aureus infections. Understanding the evolving landscape of antibiotic resistance is imperative for devising effective countermeasures in the battle against this formidable pathogen.}, }
@article {pmid39235659, year = {2025}, author = {Fu, Y and Fu, Z and Yu, J and Wang, H and Zhang, Y and Liu, M and Wang, X and Yu, W and Han, F}, title = {Biochemical Characterization of Hyaluronate Lyase CpHly8 from an Intestinal Microorganism Clostridium perfringens G1121.}, journal = {Applied biochemistry and biotechnology}, volume = {197}, number = {2}, pages = {771-792}, pmid = {39235659}, issn = {1559-0291}, support = {2022QNLM030003-1//Qingdao Marine Science and Technology Center/ ; ZR2019ZD18//Natural Science Foundation of Shandong Province/ ; 2018YFC0311105//Shandong Province Technology Innovation Guidance Program/ ; 22-3-6-gjxm-5-gx//Science &amp; Technology Development Project of Qingdao/ ; 21-1-6-gjxm-27-gx//Science &amp; Technology Development Project of Qingdao/ ; 20-11-6-64-gx//Science &amp; Technology Development Project of Qingdao/ ; }, mesh = {*Clostridium perfringens/enzymology/genetics ; *Polysaccharide-Lyases/metabolism/genetics/chemistry ; Animals ; *Hyaluronic Acid/metabolism ; Mice ; *Intestines/microbiology ; *Bacterial Proteins/metabolism/chemistry/genetics ; Hydrogen-Ion Concentration ; }, abstract = {Hyaluronic acid (HA) is an important component of extracellular matrices (ECM) and a linear polysaccharide involved in various physiological and pathological processes within the biological system. Several pathogens exploit HA degradation within the extracellular matrix to facilitate infection. While many intestinal microorganisms play significant roles in HA utilization in the human body, there remains a scarcity of related studies. This paper addressed this gap by screening intestinal microorganisms capable of degrading HA, resulting in the isolation of Clostridium perfringens G1121, which had been demonstrated the ability to degrade HA. Subsequent genome sequencing and analysis of C. perfringens G1121 revealed its utilization of the polysaccharide utilization loci of HA (PULHA), which was obtained by horizontal gene transfer. The PULHA contains a sequence encoding a hyaluronic acid-specific degradation enzyme designated CpHly8, belonging to polysaccharide lyase family 8. The specific activity of CpHly8 towards HA was 142.98 U/mg, with the optimum reaction temperature and pH observed at 50℃ and 6.0, respectively. The final product of HA degradation by CpHly8 was unsaturated hyaluronic acid disaccharide. Moreover, subcutaneous diffusion experiments with trypan blue in mice revealed that CpHly8 effectively promoted subcutaneous diffusion and sustained its effects long-term, suggesting its potential application as an adjunct in drug delivery. Overall, our study enriches our understanding of intestinal microbial degradation of HA, provides new evidence for horizontal gene transfer among intestinal microorganisms, and confirms that CpHly8 is a promising candidate for intestinal microbial hyaluronidase.}, }
@article {pmid39235644, year = {2024}, author = {Jaswal, R and Dubey, H and Kiran, K and Rawal, H and Kumar, G and Rajarammohan, S and Deshmukh, R and Sonah, H and Prasad, P and Bhardwaj, SC and Gupta, N and Sharma, TR}, title = {Identification and functional characterization of the npc-2-like domain containing rust effector protein that suppresses cell death in plants.}, journal = {Molecular biology reports}, volume = {51}, number = {1}, pages = {962}, pmid = {39235644}, issn = {1573-4978}, mesh = {*Plant Diseases/microbiology ; *Phylogeny ; *Cell Death ; *Fungal Proteins/metabolism/genetics ; Nicotiana/microbiology/metabolism/genetics ; Basidiomycota/pathogenicity/metabolism/genetics ; Puccinia/pathogenicity/metabolism ; Protein Domains ; Molecular Docking Simulation ; Onions/microbiology/metabolism/genetics ; }, abstract = {The MD-2-related lipid-recognition (ML/Md-2) domain is a lipid/sterol-binding domain that are involved in sterol transfer and innate immunity in eukaryotes. Here we report a genome-wide survey of this family, identifying 84 genes in 30 fungi including plant pathogens. All the studied species were found to have varied ML numbers, and expansion of the family was observed in Rhizophagus irregularis (RI) with 33 genes. The molecular docking studies of these proteins with cholesterol derivatives indicate lipid-binding functional conservation across the animal and fungi kingdom. The phylogenetic studies among eukaryotic ML proteins showed that Puccinia ML members are more closely associated with animal (insect) npc2 proteins than other fungal ML members. One of the candidates from leaf rust fungus Puccinia triticina, Pt5643 was PCR amplified and further characterized using various studies such as qRT-PCR, subcellular localization studies, yeast functional complementation, signal peptide validation, and expression studies. The Pt5643 exhibits the highest expression on the 5th day post-infection (dpi). The confocal microscopy of Pt5643 in onion epidermal cells and N. benthamiana shows its location in the cytoplasm and nucleus. The functional complementation studies of Pt5643 in npc2 mutant yeast showed its functional similarity to the eukaryotic/yeast npc2 gene. Furthermore, the overexpression of Pt5643 also suppressed the BAX, NEP1, and H2O2-induced program cell death in Nicotiana species and yeast. Altogether the present study reports the novel function of ML domain proteins in plant fungal pathogens and their possible role as effector molecules in host defense manipulation.}, }
@article {pmid39235595, year = {2024}, author = {Xu, R and Huang, C and Yang, B and Wang, S and Zhong, T and Ma, L and Shang, Q and Zhang, M and Chu, Z and Liu, X}, title = {Influence of Two-Dimensional Black Phosphorus on the Horizontal Transfer of Plasmid-Mediated Antibiotic Resistance Genes: Promotion or Inhibition?.}, journal = {Current microbiology}, volume = {81}, number = {10}, pages = {344}, pmid = {39235595}, issn = {1432-0991}, support = {52070063//National Natural Science Foundation of China/ ; 2308085Y38//Science Fund for Distinguished Young Scholars of Anhui Province/ ; 21-22RC30//Hefei University/ ; }, mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; *Phosphorus/metabolism ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Conjugation, Genetic ; Escherichia coli/genetics/drug effects ; Nanostructures ; Bacterial Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial/drug effects ; Bacteria/genetics/drug effects ; }, abstract = {The problem of bacterial resistance caused by antibiotic abuse is seriously detrimental to global human health and ecosystem security. The two-dimensional nanomaterial (2D) such as black phosphorus (BP) is recently expected to become a new bacterial inhibitor and has been widely used in the antibacterial field due to its specific physicochemical properties. Nevertheless, the effects of 2D-BP on the propagation of antibiotic resistance genes (ARGs) in environments and the relevant mechanisms are not clear. Herein, we observed that the sub-inhibitory concentrations of 2D-BP dramatically increased the conjugative transfer of ARGs mediated by the RP4 plasmid up to 2.6-fold at the 125 mg/L exposure level compared with the untreated bacterial cells. Nevertheless, 2D-BP with the inhibitory concentration caused a dramatic decrease in the conjugative frequency. The phenotypic changes revealed that the increase of the conjugative transfer caused by 2D-BP exposure were attributed to the excessive reactive oxygen species and oxidative stress, and increased bacterial cell membrane permeability. The genotypic evidence demonstrated that 2D-BP affecting the horizontal gene transfer of ARGs was probably through the upregulation of mating pair formation genes (trbBp and traF) and DNA transfer and replication genes (trfAp and traJ), as well as the downregulation of global regulatory gene expression (korA, korB, and trbA). In summary, the changes in the functional and regulatory genes in the conjugative transfer contributed to the stimulation of conjugative transfer. This research aims to broaden our comprehension of how nanomaterials influence the dissemination of ARGs by elucidating their effects and mechanisms.}, }
@article {pmid39233522, year = {2024}, author = {Lee, JH and Tareen, AR and Kim, NH and Jeong, C and Kang, B and Lee, G and Kim, DW and Zahra, R and Lee, SH}, title = {Comparative Genomic Analyses of E. coli ST2178 Strains Originated from Wild Birds in Pakistan.}, journal = {Journal of microbiology and biotechnology}, volume = {34}, number = {10}, pages = {2041-2048}, pmid = {39233522}, issn = {1738-8872}, mesh = {Animals ; Pakistan ; *Phylogeny ; *Escherichia coli/genetics/isolation &amp; purification/classification ; *Birds/microbiology ; *Genome, Bacterial ; *Virulence Factors/genetics ; *Feces/microbiology ; *Plasmids/genetics ; *Escherichia coli Infections/microbiology/veterinary ; *Animals, Wild/microbiology ; *Genomics ; Humans ; Drug Resistance, Multiple, Bacterial/genetics ; Gene Transfer, Horizontal ; Interspersed Repetitive Sequences/genetics ; Whole Genome Sequencing ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The emergence and spread of multidrug-resistance (MDR) pathogenic Escherichia coli due to horizontal gene transfer of antibiotic resistance genes (ARGs) and virulence factors (VFs) is a global health concern, particularly in developing countries. While numerous studies have focused on major sequence types (STs), the implication of minor STs in ARG dissemination and their pathogenicity remains crucial. In this study, two E. coli strains (PEC1011 and PEC1012) were isolated from wild bird feces in Pakistan and identified as ST2178 based on their complete genome sequences. To understand this minor ST, 204 genome assemblies of ST2178 were comparatively analyzed with the isolates' genomes. The phylogenetic analyses revealed five subclades of ST2178. Subclade E strains were predominantly isolated from human specimens, whereas subclades A and B strains including strains PEC1011 and PEC1012, respectively, were frequently isolated from animal. Mobile genetic elements (MGEs) exhibited the positive correlation with ARGs but not with VFs in this ST. Plasmid-borne ARGs exhibited higher correlation with plasmid-borne MGEs, indicating the role of diverse mobile plasmid structures in ARG transmission. Subclade E exhibited diverse plasmid-borne ARG repertoires correlated with MGEs, marking it as a critical surveillance target. In the case of VFs, they exhibited phylogeny-dependent profiles. Strain PEC1012 harbored various plasmid-borne ARGs, which are similar with conserved ARG repertoires in subclade A. The presence of unique ARG insertion in pPEC1012 highlights the importance of subclade A in ARG dissemination. This study comprehensively elucidates the landscape of ST2178, identifying critical phylogenetic subclades and their characteristics in ARG and VF occurrence.}, }
@article {pmid39233087, year = {2024}, author = {Kong, F and Qi, Z and Tong, H and Ren, N and You, S}, title = {Case study on the relationship between transmission of antibiotic resistance genes and microbial community under freeze-thaw cycle on cold-region dairy farm.}, journal = {The Science of the total environment}, volume = {952}, number = {}, pages = {175989}, doi = {10.1016/j.scitotenv.2024.175989}, pmid = {39233087}, issn = {1879-1026}, mesh = {*Soil Microbiology ; *Dairying ; *Drug Resistance, Microbial/genetics ; *Freezing ; *Microbiota/genetics/drug effects ; Farms ; Gene Transfer, Horizontal ; Genes, Bacterial ; China ; Environmental Monitoring ; }, abstract = {Freeze-thaw cycle (FTC) is a naturally occurring phenomenon in high-latitude terrestrial ecosystems, which may exert influence on distribution and evolution of microbial community in the soil. The relationship between transmission of antibiotic resistance genes (ARGs) and microbial community was investigated upon the case study on the soil of cold-region dairy farm under seasonal FTC. The results demonstrated that 37 ARGs underwent decrease in the abundance of blaTEM from 80.4 % for frozen soil to 71.7 % for thawed soil, and that sul2 from 8.8 % for frozen soil to 6.5 % for thawed soil, respectively. Antibiotic deactivation was identified to be closely related to the highest relative abundance of blaTEM, and the spread of sulfonamide resistance genes (SRGs) occurred mainly via target modification. Firmicutes in frozen soil were responsible for dominating the abundance of ARGs by suppressing the native bacteria under starvation effect in cold regions, and then underwent horizontal gene transfer (HGT) among native bacteria through mobile genetic elements (MGEs). The TRB-C (32.6-49.1 %) and tnpA-06 (0.27-7.5 %) were significantly increased in frozen soil, while Int3 (0.67-10.6 %) and tnpA-04 (11.1-19.4 %) were up-regulated in thawed soil. Moreover, the ARGs in frozen soil primarily underwent HGT through MGEs, i.e. TRB-C and tnpA-06, with increased number of Firmicutes serving as carrier. The case study not only demonstrated relationship between transmission of ARGs and microbial community in the soil under practically relevant FTC condition, but also emphasized the importance for formulating better strategies for preventing FTC-induced ARGs in dairy farm in cold regions.}, }
@article {pmid39231787, year = {2024}, author = {Baqar, Z and Sinwat, N and Prathan, R and Chuanchuen, R}, title = {Meat ducks as carriers of antimicrobial-resistant Escherichia coli harboring transferable R plasmids.}, journal = {Journal of veterinary science}, volume = {25}, number = {5}, pages = {e62}, pmid = {39231787}, issn = {1976-555X}, support = {N42A660897/NRCT/National Research Council of Thailand/Thailand ; }, mesh = {Animals ; *Ducks ; *Escherichia coli/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology ; Plasmids/genetics ; Drug Resistance, Bacterial/genetics ; Escherichia coli Infections/veterinary/microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Poultry Diseases/microbiology ; Microbial Sensitivity Tests ; R Factors/genetics ; Gene Transfer, Horizontal ; }, abstract = {IMPORTANCE: Antimicrobial resistance (AMR) is a serious public health threat. AMR bacteria and their resistance determinants in food can be transmitted to humans through the food chain and by direct contact and disseminate directly to the environment.<br><br>OBJECTIVE: This study examined the AMR characteristics and transferable R plasmids in Escherichia coli isolated from meat ducks raised in an open-house system.<br><br>METHODS: One hundred seventy-seven (n = 177) commensal E. coli were examined for their antimicrobial susceptibilities and horizontal resistance transfer. The plasmids were examined by PCR-based plasmid replicon typing (PBRT) and plasmid multi-locus sequence typing (pMLST).<br><br>RESULTS: The highest resistance rate was found against ampicillin (AMP, 83.0%) and tetracycline (TET, 81.9%), and most isolates exhibited multidrug resistance (MDR) (86.4%). The R plasmids were conjugally transferred when TET (n = 4), AMP (n = 3), and chloramphenicol (n = 3) were used as a selective pressure. The three isolates transferred resistance genes either in AMP or TET. The blaCTX-M1 gene resided on conjugative plasmids. Five replicon types were identified, of which Inc FrepB was most common in the donors (n = 13, 38.4%) and transconjugants (n = 16, 31.2%). Subtyping F plasmids revealed five distinct replicons combinations, including F47:A-:B- (n = 2), F29:A-:B23 (n = 1), F29:A-:B- (n = 1), F18:A-B:- (n = 1), and F4:A-:B- (n = 1). The chloramphenicol resistance was significantly correlated with the other AMR phenotypes (p < 0.05).<br><br>CONCLUSIONS AND RELEVANCE: The meat ducks harbored MDR E. coli and played an important role in the environmental dissemination of AMR bacteria and its determinants. This confirms AMR as a health issue, highlighting the need for routine AMR monitoring and surveillance of meat ducks.}, }
@article {pmid39226958, year = {2024}, author = {Cedeño-Muñoz, JS and Aransiola, SA and Reddy, KV and Ranjit, P and Victor-Ekwebelem, MO and Oyedele, OJ and Pérez-Almeida, IB and Maddela, NR and Rodríguez-Díaz, JM}, title = {Antibiotic resistant bacteria and antibiotic resistance genes as contaminants of emerging concern: Occurrences, impacts, mitigations and future guidelines.}, journal = {The Science of the total environment}, volume = {952}, number = {}, pages = {175906}, doi = {10.1016/j.scitotenv.2024.175906}, pmid = {39226958}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents ; *Bacteria/genetics/drug effects ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Environmental Monitoring ; Environmental Restoration and Remediation/methods ; }, abstract = {Antibiotic resistance, driven by the proliferation of antibiotic resistance genes (ARGs) and antibiotic resistance bacteria (ARBs), has emerged as a pressing global health concern. Antimicrobial resistance is exacerbated by the widespread use of antibiotics in agriculture, aquaculture, and human medicine, leading to their accumulation in various environmental compartments such as soil, water, and sediments. The presence of ARGs in the environment, particularly in municipal water, animal husbandry, and hospital environments, poses significant risks to human health, as they can be transferred to potential human pathogens. Current remediation strategies, including the use of pyroligneous acid, coagulants, advanced oxidation, and bioelectrochemical systems, have shown promising results in reducing ARGs and ARBs from soil and water. However, these methods come with their own set of challenges, such as the need for elevated base levels in UV-activated persulfate and the long residence period required for photocatalysts. The future of combating antibiotic resistance lies in the development of standardized monitoring techniques, global collaboration, and the exploration of innovative remediation methods. Emphasis on combination therapies, advanced oxidation processes, and monitoring horizontal gene transfer can pave the way for a comprehensive approach to mitigate the spread of antibiotic resistance in the environment.}, }
@article {pmid39224035, year = {2025}, author = {Chopra, A and Bhuvanagiri, G and Natu, K and Chopra, A}, title = {Role of CRISPR-Cas systems in periodontal disease pathogenesis and potential for periodontal therapy: A review.}, journal = {Molecular oral microbiology}, volume = {40}, number = {1}, pages = {1-16}, pmid = {39224035}, issn = {2041-1014}, mesh = {Humans ; *CRISPR-Cas Systems ; *Periodontal Diseases/therapy/microbiology ; *Gene Editing/methods ; Biofilms ; Bacteria/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats ; Gene Transfer, Horizontal ; Virulence/genetics ; Periodontitis/therapy/microbiology ; Genetic Therapy/methods ; }, abstract = {Clustered regularly interspaced short palindromic repeats (CRISPRs) are DNA sequences capable of editing a host genome sequence. CRISPR and its specific CRISPR-associated (Cas) protein complexes have been adapted for various applications. These include activating or inhibiting specific genetic sequences or acting as molecular scissors to cut and modify the host DNA precisely. CRISPR-Cas systems are also naturally present in many oral bacteria, where they aid in nutrition, biofilm formation, inter- and intraspecies communication (quorum sensing), horizontal gene transfer, virulence, inflammation modulation, coinfection, and immune response evasion. It even functions as an adaptive immune system, defending microbes against invading viruses and foreign genetic elements from other bacteria by targeting and degrading their DNA. Recently, CRISPR-Cas systems have been tested as molecular editing tools to manipulate specific genes linked with periodontal disease (such as periodontitis) and as novel methods of delivering antimicrobial agents to overcome antimicrobial resistance. With the rapidly increasing role of CRISPR in treating inflammatory diseases, its application in periodontal disease is also becoming popular. Therefore, this review aims to discuss the different types of CRISPR-Cas in oral microbes and their role in periodontal disease pathogenesis and precision periodontal therapy.}, }
@article {pmid39223450, year = {2024}, author = {Valerio, F and Martel, C and Stefanescu, C and van Nouhuys, S and Kankare, M and Duplouy, A}, title = {Wolbachia strain diversity in a complex group of sympatric cryptic parasitoid wasp species.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {319}, pmid = {39223450}, issn = {1471-2180}, mesh = {Animals ; *Wolbachia/genetics/classification/isolation &amp; purification ; *Wasps/microbiology ; *Symbiosis ; *Phylogeny ; Sympatry ; Gene Transfer, Horizontal ; Genetic Variation ; Lepidoptera/microbiology/parasitology ; }, abstract = {BACKGROUND: Maternally-inherited symbionts can induce pre-mating and/or post-mating reproductive isolation between sympatric host lineages, and speciation, by modifying host reproductive phenotypes. The large parasitoid wasp genus Cotesia (Braconidae) includes a diversity of cryptic species, each specialized in parasitizing one to few related Lepidoptera host species. Here, we characterized the infection status of an assemblage of 21 Cotesia species from 15 countries by several microbial symbionts, as a first step toward investigating whether symbionts may provide a barrier to gene flow between these parasitoid host lineages.<br><br>RESULTS: The symbiotic microbes Arsenophonus, Cardinium, Microsporidium and Spiroplasma were not detected in the Cotesia wasps. However, the endosymbiotic bacterium Wolbachia was present in at least eight Cotesia species, and hence we concentrated on it upon screening additional DNA extracts and SRAs from NCBI. Some of the closely related Cotesia species carry similar Wolbachia strains, but most Wolbachia strains showed patterns of horizontal transfer between phylogenetically distant host lineages.<br><br>CONCLUSIONS: The lack of co-phylogenetic signal between Wolbachia and Cotesia suggests that the symbiont and hosts have not coevolved to an extent that would drive species divergence between the Cotesia host lineages. However, as the most common facultative symbiont of Cotesia species, Wolbachia may still function as a key-player in the biology of the parasitoid wasps. Its precise role in the evolution of this complex clade of cryptic species remains to be experimentally investigated.}, }
@article {pmid39222343, year = {2024}, author = {Lyulina, AS and Liu, Z and Good, BH}, title = {Linkage equilibrium between rare mutations.}, journal = {Genetics}, volume = {228}, number = {3}, pages = {}, pmid = {39222343}, issn = {1943-2631}, support = {R35 GM146949/GM/NIGMS NIH HHS/United States ; FG-2021-15708//Alfred P. Sloan Foundation/ ; R35GM146949/GM/NIGMS NIH HHS/United States ; }, mesh = {*Models, Genetic ; *Recombination, Genetic ; *Mutation ; *Selection, Genetic ; Genetic Linkage ; Genetic Drift ; Evolution, Molecular ; Gene Transfer, Horizontal ; }, abstract = {Recombination breaks down genetic linkage by reshuffling existing variants onto new genetic backgrounds. These dynamics are traditionally quantified by examining the correlations between alleles, and how they decay as a function of the recombination rate. However, the magnitudes of these correlations are strongly influenced by other evolutionary forces like natural selection and genetic drift, making it difficult to tease out the effects of recombination. Here, we introduce a theoretical framework for analyzing an alternative family of statistics that measure the homoplasy produced by recombination. We derive analytical expressions that predict how these statistics depend on the rates of recombination and recurrent mutation, the strength of negative selection and genetic drift, and the present-day frequencies of the mutant alleles. We find that the degree of homoplasy can strongly depend on this frequency scale, which reflects the underlying timescales over which these mutations occurred. We show how these scaling properties can be used to isolate the effects of recombination and discuss their implications for the rates of horizontal gene transfer in bacteria.}, }
@article {pmid39221153, year = {2024}, author = {Belay, WY and Getachew, M and Tegegne, BA and Teffera, ZH and Dagne, A and Zeleke, TK and Abebe, RB and Gedif, AA and Fenta, A and Yirdaw, G and Tilahun, A and Aschale, Y}, title = {Mechanism of antibacterial resistance, strategies and next-generation antimicrobials to contain antimicrobial resistance: a review.}, journal = {Frontiers in pharmacology}, volume = {15}, number = {}, pages = {1444781}, pmid = {39221153}, issn = {1663-9812}, abstract = {Antibacterial drug resistance poses a significant challenge to modern healthcare systems, threatening our ability to effectively treat bacterial infections. This review aims to provide a comprehensive overview of the types and mechanisms of antibacterial drug resistance. To achieve this aim, a thorough literature search was conducted to identify key studies and reviews on antibacterial resistance mechanisms, strategies and next-generation antimicrobials to contain antimicrobial resistance. In this review, types of resistance and major mechanisms of antibacterial resistance with examples including target site modifications, decreased influx, increased efflux pumps, and enzymatic inactivation of antibacterials has been discussed. Moreover, biofilm formation, and horizontal gene transfer methods has also been included. Furthermore, measures (interventions) taken to control antimicrobial resistance and next-generation antimicrobials have been discussed in detail. Overall, this review provides valuable insights into the diverse mechanisms employed by bacteria to resist the effects of antibacterial drugs, with the aim of informing future research and guiding antimicrobial stewardship efforts.}, }
@article {pmid39221073, year = {2024}, author = {Xie, X and Deng, X and Chen, L and Yuan, J and Chen, H and Wei, C and Liu, X and Wuertz, S and Qiu, G}, title = {Integrated genomics provides insights into the evolution of the polyphosphate accumulation trait of Ca. Accumulibacter.}, journal = {Environmental science and ecotechnology}, volume = {20}, number = {}, pages = {100353}, pmid = {39221073}, issn = {2666-4984}, abstract = {Candidatus Accumulibacter, a prominent polyphosphate-accumulating organism (PAO) in wastewater treatment, plays a crucial role in enhanced biological phosphorus removal (EBPR). The genetic underpinnings of its polyphosphate accumulation capabilities, however, remain largely unknown. Here, we conducted a comprehensive genomic analysis of Ca. Accumulibacter-PAOs and their relatives within the Rhodocyclaceae family, identifying 124 core genes acquired via horizontal gene transfer (HGT) at its least common ancestor. Metatranscriptomic analysis of an enrichment culture of Ca. Accumulibacter revealed active transcription of 44 of these genes during an EBPR cycle, notably including the polyphosphate kinase 2 (PPK2) gene instead of the commonly recognized polyphosphate kinase 1 (PPK1) gene. Intriguingly, the phosphate regulon (Pho) genes showed minimal transcriptions, pointing to a distinctive fact of Pho dysregulation, where PhoU, the phosphate signaling complex protein, was not regulating the high-affinity phosphate transport (Pst) system, resulting in continuous phosphate uptake. To prevent phosphate toxicity, Ca. Accumulibacter utilized the laterally acquired PPK2 to condense phosphate into polyphosphate, resulting in the polyphosphate-accumulating feature. This study provides novel insights into the evolutionary emergence of the polyphosphate-accumulating trait in Ca. Accumulibacter, offering potential advancements in understanding the PAO phenotype in the EBPR process.}, }
@article {pmid39219575, year = {2024}, author = {He, XY and Chen, JM and Li, ZZ}, title = {Complete organelle genomes of the threatened aquatic species Scheuchzeria palustris (Scheuchzeriaceae): Insights into adaptation and phylogenomic placement.}, journal = {Ecology and evolution}, volume = {14}, number = {9}, pages = {e70248}, pmid = {39219575}, issn = {2045-7758}, abstract = {Scheuchzeria palustris, the only species in the Scheuchzeriaceae family, plays a crucial role in methane production and transportation, influencing the global carbon cycle and maintaining ecosystem stability. However, it is now threatened by human activities and global warming. In this study, we generated new organelle genomes for S. palustris, with the plastome (pt) measuring 158,573 bp and the mitogenome (mt) measuring 420,724 bp. We predicted 296 RNA editing sites in mt protein-coding genes (PCGs) and 142 in pt-PCGs. Notably, abundant RNA editing sites in pt-PCGs likely originated from horizontal gene transfer between the plastome and mitogenome. Additionally, we identified positive selection signals in four mt-PCGs (atp4, ccmB, nad3, and sdh4) and one pt-PCG (rps7), which may contribute to the adaptation of S. palustris to low-temperature and high-altitude environments. Furthermore, we identified 35 mitochondrial plastid DNA (MTPT) segments totaling 58,479 bp, attributed to dispersed repeats near most MTPT. Phylogenetic trees reconstructed from mt- and pt-PCGs showed topologies consistent with the APG IV system. However, the conflicting position of S. palustris can be explained by significant differences in the substitution rates of its mt- and pt-PCGs (p < .001). In conclusion, our study provides vital genomic resources to support future conservation efforts and explores the adaptation mechanisms of S. palustris.}, }
@article {pmid39216666, year = {2024}, author = {Qiu, T and Shen, L and Guo, Y and Gao, M and Gao, H and Li, Y and Zhao, G and Wang, X}, title = {Impact of aeration rate on the transfer range of antibiotic-resistant plasmids during manure composting.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {361}, number = {}, pages = {124851}, doi = {10.1016/j.envpol.2024.124851}, pmid = {39216666}, issn = {1873-6424}, mesh = {*Manure ; *Plasmids/genetics ; *Composting/methods ; *Anti-Bacterial Agents/pharmacology ; Soil Microbiology ; Animals ; Pseudomonas putida/genetics ; Drug Resistance, Microbial/genetics ; }, abstract = {Conjugative plasmids are important vectors of mobile antibiotic resvistance genes (ARGs), facilitating their horizontal transfer within the environment. While composting is recognized as an effective method to reduce antibiotics and ARGs in animal manure, its impact on the bacterial host communities containing antibiotic-resistant plasmids remains unclear. In this study, we investigated the permissiveness of bacterial community during composting when challenged with multidrug-resistant conjugative RP4 plasmids, employing Pseudomonas putida as the donor strain. Ultimately, this represents the first exploration of the effects of aeration rates on the range of RP4 plasmid transfer hosts. Transconjugants were analyzed through fluorescent reporter gene-based fluorescence-activated cell sorting and Illumina sequencing. Overall, aeration rates were found to influence various physicochemical parameters of compost, including temperature, pH, total organic matter, total nitrogen, and potassium. Regarding RP4 plasmid host bacteria, the dominant phylum was determined to shift from Bacteroidetes in the raw material to Proteobacteria in the compost. Notably, a moderate-intensity aeration rate (0.05 L/min/L) was found to be more effective in reducing the diversity and richness of the RP4 plasmid host bacterial community. Following composting, the total percentage of dominant transconjugant-related genera decreased by 66.15-76.62%. Ultimately, this study determined that the aeration rate negatively impacts RP4 plasmid host abundance primarily through alterations to the environmental factors during composting. In summary, these findings enhance our understanding of plasmid host bacterial communities under varying composting aeration rates and offer novel insights into preventing the dissemination of ARGs from animal manure to farmland.}, }
@article {pmid39216410, year = {2024}, author = {Vissapragada, M and Addala, S and Aggunna, M and Sodasani, M and Grandhi, AVKS and Yedidi, RS}, title = {Leveraging the potential of bacterial lateral gene transfer in boosting the efficacy of an edible probiotic prototype yogurt vaccine for COVID-19.}, journal = {Biochemical and biophysical research communications}, volume = {734}, number = {}, pages = {150622}, doi = {10.1016/j.bbrc.2024.150622}, pmid = {39216410}, issn = {1090-2104}, mesh = {*Probiotics/administration &amp; dosage ; *Yogurt/microbiology ; Humans ; *COVID-19 Vaccines/immunology ; *SARS-CoV-2/immunology/genetics ; *COVID-19/prevention &amp; control ; *Spike Glycoprotein, Coronavirus/immunology/genetics ; Lactobacillus/genetics ; Gene Transfer, Horizontal ; Gastrointestinal Microbiome ; Escherichia coli/genetics ; Animals ; }, abstract = {Administration of coronavirus disease-2019 (COVID-19) vaccines with appropriate booster doses through painful injections under clinical supervision was challenging during the recent COVID-19 pandemic. As an alternative solution, we designed a safer, edible probiotic yogurt vaccine prototype (YoVac) that can be orally consumed by circumventing painful injections and clinical supervision. We hypothesized that YoVac prepared using Lactobacillus carrying an antigen coding gene (donor) can transfer the same to other bacteria (recipients) in the human gut microbiome (hgMb) through lateral gene transfer (LGT) for boosted antigen levels potentially triggering a robust immune response. In this study we confirmed the in vitro LGT efficiency of a plasmid (pRBD-Amp[r]) containing severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) spike protein-receptor binding domain (RBD) coding gene along with an ampicillin-resistance gene (selection marker) from the probiotic Lactobacillus (donor) cultured from homemade yogurt to E. coli and Helicobacter pylori (recipients). Both the donor and recipient bacteria not only exhibited ampicillin-resistance from pRBD-Amp[r] but also expressed RBD protein. Furthermore, Lactobacillus isolated from YoVac consistently showed the expression of RBD protein over a period of one month confirming the shelf life of our prototype stored at 4 °C. Taken together, our in vitro results provide a preliminary basis for the potential in vivo transfer of RBD coding gene from YoVac to other bacterial species in the hgMb through LGT and may potentially boost the vaccine dosage by delegating them.}, }
@article {pmid39216330, year = {2024}, author = {Fernández-Arévalo, U and Fuchs, J and Boll, M and Díaz, E}, title = {Transcriptional regulation of the anaerobic 3-hydroxybenzoate degradation pathway in Aromatoleum sp. CIB.}, journal = {Microbiological research}, volume = {288}, number = {}, pages = {127882}, doi = {10.1016/j.micres.2024.127882}, pmid = {39216330}, issn = {1618-0623}, mesh = {*Gene Expression Regulation, Bacterial ; Anaerobiosis ; *Hydroxybenzoates/metabolism ; *Multigene Family ; Bacterial Proteins/genetics/metabolism ; Promoter Regions, Genetic ; Metabolic Networks and Pathways/genetics ; Operon ; Transcription, Genetic ; Acyl Coenzyme A/metabolism/genetics ; Transcription Factors/metabolism/genetics ; Lignin/metabolism ; }, abstract = {Phenolic compounds are commonly found in anoxic environments, where they serve as both carbon and energy sources for certain anaerobic bacteria. The anaerobic breakdown of m-cresol, catechol, and certain lignin-derived compounds yields the central intermediate 3-hydroxybenzoate/3-hydroxybenzoyl-CoA. In this study, we have characterized the transcription and regulation of the hbd genes responsible for the anaerobic degradation of 3-hydroxybenzoate in the β-proteobacterium Aromatoleum sp. CIB. The hbd cluster is organized in three catabolic operons and a regulatory hbdR gene that encodes a dimeric transcriptional regulator belonging to the TetR family. HbdR suppresses the activity of the three catabolic promoters (PhbdN, PhbdE and PhbdH) by binding to a conserved palindromic operator box (ATGAATGAN4TCATTCAT). 3-Hydroxybenzoyl-CoA, the initial intermediate of the 3-hydroxybenzoate degradation pathway, along with benzoyl-CoA, serve as effector molecules that bind to HbdR inducing the expression of the hbd genes. Moreover, the hbd genes are subject to additional regulation influenced by the presence of non-aromatic carbon sources (carbon catabolite repression), and their expression is induced in oxygen-deprived conditions by the AcpR transcriptional activator. The prevalence of the hbd cluster among members of the Aromatoleum/Thauera bacterial group, coupled with its association with mobile genetic elements, suggests acquisition through horizontal gene transfer. These findings significantly enhance our understanding of the regulatory mechanisms governing the hbd gene cluster in bacteria, paving the way for further exploration into the anaerobic utilization/valorization of phenolic compounds derived from lignin.}, }
@article {pmid39214976, year = {2024}, author = {Yi, X and Liang, JL and Wen, P and Jia, P and Feng, SW and Liu, SY and Zhuang, YY and Guo, YQ and Lu, JL and Zhong, SJ and Liao, B and Wang, Z and Shu, WS and Li, JT}, title = {Giant viruses as reservoirs of antibiotic resistance genes.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {7536}, pmid = {39214976}, issn = {2041-1723}, mesh = {*Phylogeny ; *Giant Viruses/genetics ; *Genome, Viral/genetics ; Drug Resistance, Microbial/genetics ; Bacteriophages/genetics/isolation &amp; purification ; Anti-Bacterial Agents/pharmacology ; Metagenome/genetics ; Gene Transfer, Horizontal ; Trimethoprim/pharmacology ; Drug Resistance, Bacterial/genetics ; }, abstract = {Nucleocytoplasmic large DNA viruses (NCLDVs; also called giant viruses), constituting the phylum Nucleocytoviricota, can infect a wide range of eukaryotes and exchange genetic material with not only their hosts but also prokaryotes and phages. A few NCLDVs were reported to encode genes conferring resistance to beta‑lactam, trimethoprim, or pyrimethamine, suggesting that they are potential vehicles for the transmission of antibiotic resistance genes (ARGs) in the biome. However, the incidence of ARGs across the phylum Nucleocytoviricota, their evolutionary characteristics, their dissemination potential, and their association with virulence factors remain unexplored. Here, we systematically investigated ARGs of 1416 NCLDV genomes including those of almost all currently available cultured isolates and high-quality metagenome-assembled genomes from diverse habitats across the globe. We reveal that 39.5% of them carry ARGs, which is approximately 37 times higher than that for phage genomes. A total of 12 ARG types are encoded by NCLDVs. Phylogenies of the three most abundant NCLDV-encoded ARGs hint that NCLDVs acquire ARGs from not only eukaryotes but also prokaryotes and phages. Two NCLDV-encoded trimethoprim resistance genes are demonstrated to confer trimethoprim resistance in Escherichia coli. The presence of ARGs in NCLDV genomes is significantly correlated with mobile genetic elements and virulence factors.}, }
@article {pmid39214865, year = {2024}, author = {Fonseca, DR and Day, LA and Crone, KK and Costa, KC}, title = {An Extracellular, Ca[2+]-Activated Nuclease (EcnA) Mediates Transformation in a Naturally Competent Archaeon.}, journal = {Molecular microbiology}, volume = {122}, number = {4}, pages = {477-490}, doi = {10.1111/mmi.15311}, pmid = {39214865}, issn = {1365-2958}, support = {MCB-2148165//National Science Foundation/ ; }, mesh = {*Methanococcus/genetics/metabolism/enzymology ; *Calcium/metabolism ; *DNA, Single-Stranded/metabolism/genetics ; Archaeal Proteins/metabolism/genetics ; Endonucleases/metabolism/genetics ; Archaea/genetics/metabolism/enzymology ; DNA, Archaeal/genetics/metabolism ; }, abstract = {Transformation, the uptake of DNA directly from the environment, is a major driver of gene flow in microbial populations. In bacteria, DNA uptake requires a nuclease that processes dsDNA to ssDNA, which is subsequently transferred into the cell and incorporated into the genome. However, the process of DNA uptake in archaea is still unknown. Previously, we cataloged genes essential to natural transformation in Methanococcus maripaludis, but few homologs of bacterial transformation-associated genes were identified. Here, we characterize one gene, MMJJ_16440 (named here as ecnA), to be an extracellular nuclease. We show that EcnA is Ca[2+]-activated, present on the cell surface, and essential for transformation. While EcnA can degrade several forms of DNA, the highest activity was observed with ssDNA as a substrate. Activity was also observed with circular dsDNA, suggesting that EcnA is an endonuclease. This is the first biochemical characterization of a transformation-associated protein in a member of the archaeal domain and suggests that both archaeal and bacterial transformation initiate in an analogous fashion.}, }
@article {pmid39214042, year = {2024}, author = {Li, G and Long, TF and Zhou, SY and Xia, LJ and Gao, A and Wan, L and Diao, XY and He, YZ and Sun, RY and Yang, JT and Tang, SQ and Ren, H and Fang, LX and Liao, XP and Liu, YH and Chen, L and Sun, J}, title = {CRISPR-AMRtracker: A novel toolkit to monitor the antimicrobial resistance gene transfer in fecal microbiota.}, journal = {Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy}, volume = {77}, number = {}, pages = {101142}, doi = {10.1016/j.drup.2024.101142}, pmid = {39214042}, issn = {1532-2084}, mesh = {*Feces/microbiology ; Humans ; *CRISPR-Cas Systems/genetics ; *Drug Resistance, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; *Gene Transfer, Horizontal ; *Plasmids/genetics ; Animals ; Bacteria/genetics/drug effects ; RNA, Ribosomal, 16S/genetics ; Microbiota/drug effects/genetics ; Gastrointestinal Microbiome/drug effects/genetics ; Drug Resistance, Microbial/genetics ; }, abstract = {The spread of antibiotic resistance genes (ARGs), particularly those carried on plasmids, poses a major risk to global health. However, the extent and frequency of ARGs transfer in microbial communities among human, animal, and environmental sectors is not well understood due to a lack of effective tracking tools. We have developed a novel fluorescent tracing tool, CRISPR-AMRtracker, to study ARG transfer. It combines CRISPR/Cas9 fluorescence tagging, fluorescence-activated cell sorting, 16S rRNA gene sequencing, and microbial community analysis. CRISPR-AMRtracker integrates a fluorescent tag immediately downstream of ARGs, enabling the tracking of ARG transfer without compromising the host cell's antibiotic susceptibility, fitness, conjugation, and transposition. Notably, our experiments demonstrate that sfGFP-tagged plasmid-borne mcr-1 can transfer across diverse bacterial species within fecal samples. This innovative approach holds the potential to illuminate the dynamics of ARG dissemination and provide valuable insights to shape effective strategies in mitigating the escalating threat of antibiotic resistance.}, }
@article {pmid39213533, year = {2024}, author = {Zeng, Q and Wu, X and Song, M and Jiang, L and Zeng, Q and Qiu, R and Luo, C}, title = {Opposite Effects of Planting on Antibiotic Resistomes in Rhizosphere Soil with Different Sulfamethoxazole Levels.}, journal = {Journal of agricultural and food chemistry}, volume = {72}, number = {36}, pages = {19957-19965}, doi = {10.1021/acs.jafc.4c04258}, pmid = {39213533}, issn = {1520-5118}, mesh = {*Sulfamethoxazole/pharmacology/metabolism ; *Rhizosphere ; *Soil Microbiology ; *Glycine max/growth &amp; development/metabolism/chemistry/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification/drug effects/growth &amp; development ; Soil/chemistry ; Drug Resistance, Bacterial/genetics ; Plant Roots/microbiology/metabolism/chemistry/growth &amp; development ; Soil Pollutants/metabolism ; }, abstract = {Achieving consensus about the rhizosphere effect on soil antibiotic resistomes is challenging due to the variability in antibiotic concentrations, sources, and the elusory underlying mechanisms. Here, we characterized the antibiotic resistomes in both the rhizosphere and bulk soils of soybean plants grown in environments with varying levels of antibiotic contamination, using sulfamethoxazole (SMX) as a model compound. We also investigated the factors influencing resistome profiles. Soybean cultivation altered the structure of antibiotic-resistant genes (ARGs) and increased their absolute abundance. However, the rhizosphere effect on the relative abundance of ARGs was dependent on SMX concentrations. At low SMX levels, the rhizosphere effect was characterized by the inhibition of antibiotic-resistant bacteria (ARBs) and the promotion of sensitive bacteria. In contrast, at high SMX levels, the rhizosphere promoted the growth of ARBs and facilitated horizontal gene transfer of ARGs. This novel mechanism provides new insights into accurately assessing the rhizosphere effect on soil antibiotic resistomes.}, }
@article {pmid39213158, year = {2024}, author = {Ma, Y and Kan, A and Johnson, DR}, title = {Metabolic interactions control the transfer and spread of plasmid-encoded antibiotic resistance during surface-associated microbial growth.}, journal = {Cell reports}, volume = {43}, number = {9}, pages = {114653}, doi = {10.1016/j.celrep.2024.114653}, pmid = {39213158}, issn = {2211-1247}, mesh = {*Plasmids/metabolism/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Escherichia coli/genetics/metabolism/growth &amp; development ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; }, abstract = {Surface-associated microbial systems are hotspots for the spread of plasmid-encoded antibiotic resistance, but how surface association affects plasmid transfer and proliferation remains unclear. Surface association enables prolonged spatial proximities between different populations, which promotes plasmid transfer between them. However, surface association also fosters strong metabolic interactions between different populations, which can direct their spatial self-organization with consequences for plasmid transfer and proliferation. Here, we hypothesize that metabolic interactions direct the spatial self-organization of different populations and, in turn, regulate the spread of plasmid-encoded antibiotic resistance. We show that resource competition causes populations to spatially segregate, which represses plasmid transfer. In contrast, resource cross-feeding causes populations to spatially intermix, which promotes plasmid transfer. We further show that the spatial positionings that emerge from metabolic interactions determine the proliferation of plasmid recipients. Our results demonstrate that metabolic interactions are important regulators of both the transfer and proliferation of plasmid-encoded antibiotic resistance.}, }
@article {pmid39213152, year = {2024}, author = {Cordero, M and Jauffred, L}, title = {Following plasmid propagation in complex bacterial communities.}, journal = {Cell reports}, volume = {43}, number = {9}, pages = {114675}, doi = {10.1016/j.celrep.2024.114675}, pmid = {39213152}, issn = {2211-1247}, mesh = {*Plasmids/genetics/metabolism ; *Gene Transfer, Horizontal ; *Bacteria/genetics/metabolism ; Conjugation, Genetic ; }, abstract = {In this issue of Cell Reports, Ma et al.[1] identify causative regulatory links between self-organization in surface-attached bacterial colonies and the rate of horizontal gene transfers (conjugations) and subsequent selection of the newly arising population of recipient bacteria (transconjugants).}, }
@article {pmid39211246, year = {2024}, author = {Hughes Lago, C and Blackburn, D and Kinder Pavlicek, M and Threadgill, DS}, title = {Comparative Genomic Analysis of Campylobacter rectus and Closely Related Species.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.07.26.605372}, pmid = {39211246}, issn = {2692-8205}, abstract = {Campylobacter rectus is a gram-negative, anaerobic bacterium strongly associated with periodontitis. It also causes various extraoral infections and is linked to adverse pregnancy outcomes in humans and murine models. C. rectus and related oral Campylobacters have been termed "emerging Campylobacter species" because infections by these organisms are likely underreported. Previously, no comparative methods have been used to analyze more than single C. rectus strains and until recently, very few C. rectus genomes have been publicly available. More sequenced genomes and comparative analyses are needed to study the genomic features and pathogenicity of this species. We sequenced eight new C. rectus strains and used comparative methods to identify regions of interest. An emphasis was put on the type III flagellar secretion system (T3SS), type IV secretion system (T4SS), and type VI secretion system (T6SS) because these protein complexes are important for pathogenesis in other Campylobacter species. RAST, BV-BRC, and other bioinformatics tools were used to assemble, annotate, and compare these regions in the genomes. The pan-genome of C. rectus consists of 2670 genes with core and accessory genomes of 1429 and 1241 genes, respectively. All isolates analyzed in this study have T3SS and T6SS hallmark proteins, while five of the isolates are missing a T4SS system. Twenty-one prophage clusters were identified across the panel of isolates, including four that appear intact. Overall, significant genomic islands were found, suggesting regions in the genomes that underwent horizontal gene transfer. Additionally, the high frequency of CRISPR arrays and other repetitive elements has led to genome rearrangements across the strains, including in areas adjacent to secretion system gene clusters. This study describes the substantial diversity present among C. rectus isolates and highlights tools/assays that have been developed to permit functional genomic studies. Additionally, we have expanded the studies on C. showae T4SS since we have two new C. showae genomes to report. We also demonstrate that unlike C. rectus , C showae does not demonstrate evidence of intact T6SS except for the strain CAM. The only strain of sequenced C. massilensis has neither T4SS or T6SS.}, }
@article {pmid39211212, year = {2024}, author = {Marcarian, HQ and Sivakoses, A and Arias, AM and Ihedioha, O and Bishop, MC and Lee, BR and Bothwell, ALM}, title = {Renal cancer cells acquire immune surface protein through trogocytosis and horizontal gene transfer.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.08.07.607036}, pmid = {39211212}, issn = {2692-8205}, abstract = {Trogocytosis is an underappreciated phenomenon that shapes the immune microenvironment surrounding many types of solid tumors. The consequences of membrane-bound proteins being deposited from a donor immune cell to a recipient cancer cell via trogocytosis are still unclear. Here, we report that human clear cell renal carcinoma tumors stably express the lymphoid markers CD45, CD56, CD14, and CD16. Flow cytometry performed on fresh kidney tumors revealed consistent CD45 expression on tumor cells, as well as varying levels of the other markers mentioned previously. These results were consistent with our immunofluorescent analysis, which also revealed colocalization of lymphoid markers with carbonic anhydrase 9 (CAIX), a standard kidney tumor marker. RNA analysis showed a significant upregulation of genes typically associated with immune cells in tumor cells following trogocytosis. Finally, we show evidence of chromosomal DNA being transferred from immune cells to tumor cells during trogocytosis. This horizontal gene transfer has transcriptional consequences in the recipient tumor cell, resulting in a fusion phenotype that expressed both immune and cancer specific proteins. This work demonstrates a novel mechanism by which tumor cell protein expression is altered through the acquisition of surface membrane fragments and genomic DNA from infiltrating lymphocytes. These results alter the way in which we understand tumor-immune cell interactions and may reveal new insights into the mechanisms by which tumors develop. Additionally, further studies into trogocytosis will help push the field towards the next generation of immunotherapies and biomarkers for treating renal cell carcinoma and other types of cancers.}, }
@article {pmid39210455, year = {2024}, author = {Abdellati, S and Gestels, Z and Laumen, JGE and Van Dijck, C and De Baetselier, I and de Block, T and Van den Bossche, D and Vanbaelen, T and Kanesaka, I and Manoharan-Basil, SS and Kenyon, C}, title = {Antimicrobial susceptibility of commensal Neisseria spp. in parents and their children in Belgium: a cross-sectional survey.}, journal = {FEMS microbiology letters}, volume = {371}, number = {}, pages = {}, doi = {10.1093/femsle/fnae069}, pmid = {39210455}, issn = {1574-6968}, support = {PRESTIP//SOFI-B/ ; }, mesh = {Humans ; Belgium/epidemiology ; *Neisseria/drug effects/isolation &amp; purification/genetics ; Cross-Sectional Studies ; Child ; *Anti-Bacterial Agents/pharmacology ; Female ; Child, Preschool ; *Microbial Sensitivity Tests ; Male ; Adult ; *Parents ; Middle Aged ; Adolescent ; Drug Resistance, Bacterial ; Infant ; Oropharynx/microbiology ; Prevalence ; Young Adult ; }, abstract = {BACKGROUND: commensal Neisseria species are part of the oropharyngeal microbiome and play an important role in nitrate reduction and protecting against colonization by pathogenic bacteria. They do, however, also serve as a reservoir of antimicrobial resistance. Little is known about the prevalence of these species in the general population, how this varies by age and how antimicrobial susceptibility varies between species.<br><br>METHODS: we assessed the prevalence and antimicrobial susceptibility of commensal Neisseria species in the parents (n&#xa0;=&#xa0;38) and children (n&#xa0;=&#xa0;50) of 35 families in Belgium.<br><br>RESULTS: various commensal Neisseria (n&#xa0;=&#xa0;5) could be isolated from the participants. Most abundant were N. subflava and N. mucosa. Neisseria subflava was detected in 77 of 88 (87.5%) individuals and N. mucosa in 64 of 88 (72.7%). Neisseria mucosa was more prevalent in children [41/50 (82%)] than parents [23/38 (60.5%); P&#xa0;<&#xa0;.05], while N. bacilliformis was more prevalent in parents [7/36 (19.4%)] than children [2/50 (4%); P&#xa0;<&#xa0;.05]. Neisseria bacilliformis had high ceftriaxone minimum inhibitory concentrations (MICs; median MIC 0.5&#xa0;mg/l; IQR 0.38-0.75). The ceftriaxone MICs of all Neisseria isolates were higher in the parents than in the children. This could be explained by a higher prevalence of N. bacilliformis in the parents.<br><br>INTERPRETATION: the N. bacilliformis isolates had uniformly high ceftriaxone MICs which warrant further investigation.}, }
@article {pmid39208359, year = {2024}, author = {Ares-Arroyo, M and Coluzzi, C and Moura de Sousa, JA and Rocha, EPC}, title = {Hijackers, hitchhikers, or co-drivers? The mysteries of mobilizable genetic elements.}, journal = {PLoS biology}, volume = {22}, number = {8}, pages = {e3002796}, pmid = {39208359}, issn = {1545-7885}, mesh = {*Gene Transfer, Horizontal ; Interspersed Repetitive Sequences/genetics ; Bacteria/genetics ; Evolution, Molecular ; Genomic Islands ; Symbiosis/genetics ; Genome, Bacterial ; }, abstract = {Mobile genetic elements shape microbial gene repertoires and populations. Recent results reveal that many, possibly most, microbial mobile genetic elements require helpers to transfer between genomes, which we refer to as Hitcher Genetic Elements (hitchers or HGEs). They may be a large fraction of pathogenicity and resistance genomic islands, whose mechanisms of transfer have remained enigmatic for decades. Together with their helper elements and their bacterial hosts, hitchers form tripartite networks of interactions that evolve rapidly within a parasitism-mutualism continuum. In this emerging view of microbial genomes as communities of mobile genetic elements many questions arise. Which elements are being moved, by whom, and how? How often are hitchers costly hyper-parasites or beneficial mutualists? What is the evolutionary origin of hitchers? Are there key advantages associated with hitchers' lifestyle that justify their unexpected abundance? And why are hitchers systematically smaller than their helpers? In this essay, we start answering these questions and point ways ahead for understanding the principles, origin, mechanisms, and impact of hitchers in bacterial ecology and evolution.}, }
@article {pmid39207571, year = {2024}, author = {Smiatek, J}, title = {Principles of Molecular Evolution: Concepts from Non-equilibrium Thermodynamics for the Multilevel Theory of Learning.}, journal = {Journal of molecular evolution}, volume = {92}, number = {6}, pages = {703-719}, pmid = {39207571}, issn = {1432-1432}, mesh = {*Evolution, Molecular ; *Thermodynamics ; *Entropy ; *Mutation ; Models, Genetic ; Learning/physiology ; }, abstract = {We present a non-equilibrium thermodynamics approach to the multilevel theory of learning for the study of molecular evolution. This approach allows us to study the explicit time dependence of molecular evolutionary processes and their impact on entropy production. Interpreting the mathematical expressions, we can show that two main contributions affect entropy production of molecular evolution processes which can be identified as mutation and gene transfer effects. Accordingly, our results show that the optimal adaptation of organisms to external conditions in the context of evolutionary processes is driven by principles of minimum entropy production. Such results can also be interpreted as the basis of some previous postulates of the theory of learning. Although our macroscopic approach requires certain simplifications, it allows us to interpret molecular evolutionary processes using thermodynamic descriptions with reference to well-known biological processes.}, }
@article {pmid39207102, year = {2024}, author = {Zhang, W and Fan, Y and Deng, W and Chen, Y and Wang, S and Kang, S and Steenwyk, JL and Xiang, M and Liu, X}, title = {Characterization of genome-wide phylogenetic conflict uncovers evolutionary modes of carnivorous fungi.}, journal = {mBio}, volume = {15}, number = {10}, pages = {e0213324}, pmid = {39207102}, issn = {2150-7511}, support = {32020103001//MOST | National Natural Science Foundation of China (NSFC)/ ; 32200009//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {*Phylogeny ; *Genome, Fungal ; *Evolution, Molecular ; *Ascomycota/genetics/classification ; Animals ; Biological Evolution ; Nematoda/genetics/microbiology ; }, abstract = {Mass extinction has often paved the way for rapid evolutionary radiation, resulting in the emergence of diverse taxa within specific lineages. The emergence and diversification of carnivorous nematode-trapping fungi (NTF) in Ascomycota have been linked to the Permian-Triassic (PT) extinction, but the processes underlying NTF radiation remain unclear. We conducted phylogenomic analyses using 23 genomes that represent three NTF lineages, each employing distinct nematode traps-mechanical traps (Drechslerella spp.), three-dimensional (3D) adhesive traps (Arthrobotrys spp.), and two-dimensional (2D) adhesive traps (Dactylellina spp.), and the genome of one non-NTF species as the outgroup. These analyses revealed multiple mechanisms that likely contributed to the tempo of the NTF evolution and rapid radiation. The species tree of NTFs based on 2,944 single-copy orthologous genes suggested that Drechslerella emerged earlier than Arthrobotrys and Dactylellina. Extensive genome-wide phylogenetic discordance was observed, mainly due to incomplete lineage sorting (ILS) between lineages. Two modes of non-vertical evolution (introgression and horizontal gene transfer) also contributed to phylogenetic discordance. The ILS genes that are associated with hyphal growth and trap morphogenesis (e.g., those associated with the cell membrane system and polarized cell division) exhibited signs of positive selection.IMPORTANCEBy conducting a comprehensive phylogenomic analysis of 23 genomes across three NTF lineages, the research reveals how diverse evolutionary mechanisms, including ILS and non-vertical evolution (introgression and horizontal gene transfer), contribute to the swift diversification of NTFs. These findings highlight the complex evolutionary dynamics that drive the rapid radiation of NTFs, providing valuable insights into the processes underlying their diversity and adaptation.}, }
@article {pmid39206372, year = {2024}, author = {Kirk, A and Stavrinides, J}, title = {Distribution and comparative genomic analysis of antimicrobial gene clusters found in Pantoea.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1416674}, pmid = {39206372}, issn = {1664-302X}, abstract = {Members of the bacterial genus Pantoea produce a variety of antimicrobial products that are effective against plant, animal, and human pathogens. To date, little is known about the distribution and evolutionary history of these clusters. We surveyed the public databases for the 12 currently known antibiotic biosynthetic gene clusters found across Pantoea strains to determine their distribution. We show that some clusters, namely pantocin B, PNP-3, and PNP-4 are found strictly in Pantoea, while agglomerin, andrimid, AGA, dapdiamide, herbicolin, PNP-1, PNP-2, PNP-5, and pantocin A, are more broadly distributed in distantly related genera within Vibrionaceae, Pectobacteriaceae, Yersiniaceae, Morganellaceae, and Hafniaceae. We evaluated the evolutionary history of these gene clusters relative to a cpn60-based species tree, considering the flanking regions of each cluster, %GC, and presence of mobile genetic elements, and identified potential occurrences of horizontal gene transfer. Lastly, we also describe the biosynthetic gene cluster of pantocin B in the strain Pantoea agglomerans Eh318 more than 20 years after this antibiotic was first described.}, }
@article {pmid39203510, year = {2024}, author = {Lv, N and Ni, J and Fang, S and Liu, Y and Wan, S and Sun, C and Li, J and Zhou, A}, title = {Potential Convergence to Accommodate Pathogenicity Determinants and Antibiotic Resistance Revealed in Salmonella Mbandaka.}, journal = {Microorganisms}, volume = {12}, number = {8}, pages = {}, pmid = {39203510}, issn = {2076-2607}, support = {32260032//National Natural Science Foundation of China/ ; 32370143//National Natural Science Foundation of China/ ; 31800118//National Natural Science Foundation of China/ ; jxsq2019101054//Double Thousand Talents Plan of Jiangxi/ ; }, abstract = {Salmonella species are causal pathogens instrumental in human food-borne diseases. The pandemic survey related to multidrug resistant (MDR) Salmonella genomics enables the prevention and control of their dissemination. Currently, serotype Mbandaka is notorious as a multiple host-adapted non-typhoid Salmonella. However, its epidemic and MDR properties are still obscure, especially its genetic determinants accounting for virulence and MD resistance. Here, we aim to characterize the genetic features of a strain SMEH pertaining to Salmonella Mbandaka (S. Mbandaka), isolated from the patient's hydropericardium, using cell infections, a mouse model, antibiotic susceptibility test and comparative genomics. The antibiotic susceptibility testing showed that it could tolerate four antibiotics, including chloramphenicol, tetracycline, fisiopen and doxycycline by Kirby-Bauer (K-B) testing interpreted according to the Clinical and Laboratory Standards Institute (CLSI). Both the reproducibility in RAW 264.7 macrophages and invasion ability to infect HeLa cells with strain SMEH were higher than those of S. Typhimurium strain 14028S. In contrast, its attenuated virulence was determined in the survival assay using a mouse model. As a result, the candidate genetic determinants responsible for antimicrobial resistance, colonization/adaptability and their transferability were comparatively investigated, such as bacterial secretion systems and pathogenicity islands (SPI-1, SPI-2 and SPI-6). Moreover, collective efforts were made to reveal a potential role of the plasmid architectures in S. Mbandaka as the genetic reservoir to transfer or accommodate drug-resistance genes. Our findings highlight the essentiality of antibiotic resistance and risk assessment in S. Mbandaka. In addition, genomic surveillance is an efficient method to detect pathogens and monitor drug resistance. The genetic determinants accounting for virulence and antimicrobial resistance underscore the increasing clinical challenge of emerging MDR Mbandaka isolates, and provide insights into their prevention and treatment.}, }
@article {pmid39201699, year = {2024}, author = {Li, H and Liang, T and Liu, Y and Wang, P and Wang, S and Zhao, M and Zhang, Y}, title = {Exploring Mitochondrial Heterogeneity and Evolutionary Dynamics in Thelephora ganbajun through Population Genomics.}, journal = {International journal of molecular sciences}, volume = {25}, number = {16}, pages = {}, pmid = {39201699}, issn = {1422-0067}, support = {31870009//National Natural Science Foundation of China/ ; YNWR-QNBJ-2018-355//Top Young Talents Program of the Ten Thousand Talents Plan in Yunnan Province/ ; 2021KF009//YNCUB/ ; }, mesh = {*Genome, Mitochondrial ; *Evolution, Molecular ; Phylogeny ; Introns/genetics ; Mitochondria/genetics ; Basidiomycota/genetics ; DNA, Mitochondrial/genetics ; Genomics/methods ; Gene Transfer, Horizontal ; }, abstract = {Limited exploration in fungal mitochondrial genetics has uncovered diverse inheritance modes. The mitochondrial genomes are inherited uniparentally in the majority of sexual eukaryotes, our discovery of persistent mitochondrial heterogeneity within the natural population of the basidiomycete fungus Thelephora ganbajun represents a significant advance in understanding mitochondrial inheritance and evolution in eukaryotes. Here, we present a comprehensive analysis by sequencing and assembling the complete mitogenomes of 40 samples exhibiting diverse cox1 heterogeneity patterns from various geographical origins. Additionally, we identified heterogeneous variants in the nad5 gene, which, similar to cox1, displayed variability across multiple copies. Notably, our study reveals a distinct prevalence of introns and homing endonucleases in these heterogeneous genes. Furthermore, we detected potential instances of horizontal gene transfer involving homing endonucleases. Population genomic analyses underscore regional variations in mitochondrial genome composition among natural samples exhibiting heterogeneity. Thus, polymorphisms in heterogeneous genes, introns, and homing endonucleases significantly influence mitochondrial structure, structural variation, and evolutionary dynamics in this species. This study contributes valuable insights into mitochondrial genome architecture, population dynamics, and the evolutionary implications of mitochondrial heterogeneity in sexual eukaryotes.}, }
@article {pmid39200594, year = {2024}, author = {Habibi, N and Uddin, S and Behbehani, M and Mustafa, AS and Al-Fouzan, W and Al-Sarawi, HA and Safar, H and Alatar, F and Al Sawan, RMZ}, title = {Aerosol-Mediated Spread of Antibiotic Resistance Genes: Biomonitoring Indoor and Outdoor Environments.}, journal = {International journal of environmental research and public health}, volume = {21}, number = {8}, pages = {}, pmid = {39200594}, issn = {1660-4601}, mesh = {*Aerosols/analysis ; *Gene Transfer, Horizontal ; Humans ; Biological Monitoring ; Drug Resistance, Microbial/genetics ; Air Microbiology ; Air Pollution, Indoor/analysis ; Environmental Monitoring ; Anti-Bacterial Agents/analysis ; Drug Resistance, Bacterial/genetics ; }, abstract = {Antimicrobial resistance (AMR) has emerged as a conspicuous global public health threat. The World Health Organization (WHO) has launched the "One-Health" approach, which encourages the assessment of antibiotic resistance genes (ARGs) within an environment to constrain and alleviate the development of AMR. The prolonged use and overuse of antibiotics in treating human and veterinary illnesses, and the inability of wastewater treatment plants to remove them have resulted in elevated concentrations of these metabolites in the surroundings. Microbes residing within these settings acquire resistance under selective pressure and circulate between the air-land interface. Initial evidence on the indoor environments of wastewater treatment plants, hospitals, and livestock-rearing facilities as channels of AMR has been documented. Long- and short-range transport in a downwind direction disseminate aerosols within urban communities. Inhalation of such aerosols poses a considerable occupational and public health risk. The horizontal gene transfer (HGT) is another plausible route of AMR spread. The characterization of ARGs in the atmosphere therefore calls for cutting-edge research. In the present review, we provide a succinct summary of the studies that demonstrated aerosols as a media of AMR transport in the atmosphere, strengthening the need to biomonitor these pernicious pollutants. This review will be a useful resource for environmental researchers, healthcare practitioners, and policymakers to issue related health advisories.}, }
@article {pmid39200027, year = {2024}, author = {Milani, G and Cortimiglia, C and Belloso Daza, MV and Greco, E and Bassi, D and Cocconcelli, PS}, title = {Microplastic-Mediated Transfer of Tetracycline Resistance: Unveiling the Role of Mussels in Marine Ecosystems.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {8}, pages = {}, pmid = {39200027}, issn = {2079-6382}, support = {PE00000003//Italian Ministry of University and Research funded by the European Union - NextGenerationEU/ ; }, abstract = {The global threat of antimicrobial resistance (AMR) is exacerbated by the mobilization of antimicrobial resistance genes (ARGs) occurring in different environmental niches, including seawater. Marine environments serve as reservoirs for resistant bacteria and ARGs, further complicated by the ubiquity of microplastics (MPs). MPs can adsorb pollutants and promote bacterial biofilm formation, creating conditions favorable to the dissemination of ARGs. This study explores the dynamics of ARG transfer in the marine bivalve Mytilus galloprovincialis within a seawater model, focusing on the influence of polyethylene MPs on the mobilization of the Tn916-carrying tetM gene and plasmid-encoded ermB. Experiments revealed that biofilm formation on MPs by Enterococcus faecium and Listeria monocytogenes facilitated the transfer of the tetM resistance gene, but not the ermB gene. Furthermore, the presence of MPs significantly increased the conjugation frequency of tetM within mussels, indicating that MPs enhance the potential for ARG mobilization in marine environments. These findings highlight the role of MPs and marine organisms in ARG spread, underscoring the ecological and public health implications.}, }
@article {pmid39199982, year = {2024}, author = {Yao, Y and Imirzalioglu, C and Falgenhauer, L and Falgenhauer, J and Heinmüller, P and ,  and Domann, E and Chakraborty, T}, title = {Plasmid-Mediated Spread of Carbapenem Resistance in Enterobacterales: A Three-Year Genome-Based Survey.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {8}, pages = {}, pmid = {39199982}, issn = {2079-6382}, abstract = {The worldwide emergence and dissemination of carbapenem-resistant Gram-negative bacteria (CRGNB) is a challenging problem of antimicrobial resistance today. Outbreaks with CRGNB have severe consequences for both the affected healthcare settings as well as the patients with infection. Thus, bloodstream infections caused by metallo-ß-lactamase-producing Enterobacterales can often have clinical implications, resulting in high mortality rates due to delays in administering effective treatment and the limited availability of treatment options. The overall threat of CRGNB is substantial because carbapenems are used to treat infections caused by ESBL-producing Enterobacterales which also exist with high frequency within the same geographical regions. A genome-based surveillance of 589 CRGNB from 61 hospitals across the federal state Hesse in Germany was implemented using next-generation sequencing (NGS) technology to obtain a high-resolution landscape of carbapenem-resistant isolates over a three-year period (2017-2019). The study examined all reportable CRGNB isolates submitted by participating hospitals. This included isolates carrying known carbapenemases (435) together with carbapenem-resistant non-carbapenemase producers (154). Predominant carbapenemase producers included Klebsiella pneumoniae, Escherichia coli, Citrobacter freundii and Acinetobacter baumannii. Over 80% of 375 carbapenem-resistant determinants including KPC-, NDM-, VIM- and OXA-48-like ones detected in 520 Enterobacterales were plasmid-encoded, and half of these were dominated by a few incompatibility (Inc) types, viz., IncN, IncL/M, IncFII and IncF(K). Our results revealed that plasmids play an extraordinary role in the dissemination of carbapenem resistance in the heterogeneous CRGNB population. The plasmids were also associated with several multispecies dissemination events and local outbreaks throughout the study period, indicating the substantial role of horizontal gene transfer in carbapenemase spread. Furthermore, due to vertical and horizontal plasmid transfer, this can have an impact on implant-associated infections and is therefore important for antibiotic-loaded bone cement and drug-containing devices in orthopedic surgery. Future genomic surveillance projects should increase their focus on plasmid characterization.}, }
@article {pmid39198891, year = {2024}, author = {Tian, F and Wainaina, JM and Howard-Varona, C and Domínguez-Huerta, G and Bolduc, B and Gazitúa, MC and Smith, G and Gittrich, MR and Zablocki, O and Cronin, DR and Eveillard, D and Hallam, SJ and Sullivan, MB}, title = {Prokaryotic-virus-encoded auxiliary metabolic genes throughout the global oceans.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {159}, pmid = {39198891}, issn = {2049-2618}, support = {T32 GM141955/GM/NIGMS NIH HHS/United States ; ABI#1759874, ABI#2149505, OCE#1536989, OCE#1829831, and OCE#2019589//National Science Foundation/ ; #3790//Gordon and Betty Moore Foundation Investigator Award/ ; }, mesh = {*Oceans and Seas ; *Seawater/virology/microbiology ; Metagenomics ; Bacteria/genetics/classification/metabolism ; Viruses/genetics/classification/isolation &amp; purification ; Prokaryotic Cells/metabolism/virology ; Metagenome ; Metabolic Networks and Pathways/genetics ; Gene Transfer, Horizontal ; Phosphatidylethanolamines/metabolism ; }, abstract = {BACKGROUND: Prokaryotic microbes have impacted marine biogeochemical cycles for billions of years. Viruses also impact these cycles, through lysis, horizontal gene transfer, and encoding and expressing genes that contribute to metabolic reprogramming of prokaryotic cells. While this impact is difficult to quantify in nature, we hypothesized that it can be examined by surveying virus-encoded auxiliary metabolic genes (AMGs) and assessing their ecological context.<br><br>RESULTS: We systematically developed a global ocean AMG catalog by integrating previously described and newly identified AMGs and then placed this catalog into ecological and metabolic contexts relevant to ocean biogeochemistry. From 7.6 terabases of Tara Oceans paired prokaryote- and virus-enriched metagenomic sequence data, we increased known ocean virus populations to 579,904 (up 16%). From these virus populations, we then conservatively identified 86,913 AMGs that grouped into 22,779 sequence-based gene clusters, 7248 (~&#x2009;32%) of which were not previously reported. Using our catalog and modeled data from mock communities, we estimate that&#x2009;~&#x2009;19% of ocean virus populations carry at least one AMG. To understand AMGs in their metabolic context, we identified 340 metabolic pathways encoded by ocean microbes and showed that AMGs map to 128 of them. Furthermore, we identified metabolic "hot spots" targeted by virus AMGs, including nine pathways where most steps (&#x2265;&#x2009;0.75) were AMG-targeted (involved in carbohydrate, amino acid, fatty acid, and nucleotide metabolism), as well as other pathways where virus-encoded AMGs outnumbered cellular homologs (involved in lipid A phosphates, phosphatidylethanolamine, creatine biosynthesis, phosphoribosylamine-glycine ligase, and carbamoyl-phosphate synthase pathways).<br><br>CONCLUSIONS: Together, this systematically curated, global ocean AMG catalog and analyses provide a valuable resource and foundational observations to understand the role of viruses in modulating global ocean metabolisms and their biogeochemical implications. Video Abstract.}, }
@article {pmid39198572, year = {2024}, author = {Sastre-Dominguez, J and DelaFuente, J and Toribio-Celestino, L and Herencias, C and Herrador-Gómez, P and Costas, C and Hernández-García, M and Cantón, R and Rodríguez-Beltrán, J and Santos-Lopez, A and San Millan, A}, title = {Plasmid-encoded insertion sequences promote rapid adaptation in clinical enterobacteria.}, journal = {Nature ecology &amp; evolution}, volume = {8}, number = {11}, pages = {2097-2112}, pmid = {39198572}, issn = {2397-334X}, support = {PI23/01945//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; CD21/00115//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; PI21/01363//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; 101077809-HorizonGT//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; CP20/00154//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; 895671-REPLAY//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 757440-PLASREVOLUTION//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; LCF/BQ/PR22/11920001//"la Caixa" Foundation (Caixa Foundation)/ ; Research Grant 2022//European Society of Clinical Microbiology and Infectious Diseases (ESCMID)/ ; PI19/00749//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; 757440/ERC_/European Research Council/International ; }, mesh = {*Plasmids/genetics ; *DNA Transposable Elements/genetics ; *Enterobacteriaceae/genetics/physiology ; Adaptation, Physiological/genetics ; Enterobacteriaceae Infections/microbiology ; Humans ; Gene Transfer, Horizontal ; }, abstract = {Plasmids are extrachromosomal genetic elements commonly found in bacteria. They are known to fuel bacterial evolution through horizontal gene transfer, and recent analyses indicate that they can also promote intragenomic adaptations. However, the role of plasmids as catalysts of bacterial evolution beyond horizontal gene transfer is poorly explored. In this study, we investigated the impact of a widespread conjugative plasmid, pOXA-48, on the evolution of several multidrug-resistant clinical enterobacteria. Combining experimental and within-patient evolution analyses, we unveiled that plasmid pOXA-48 promotes bacterial evolution through the transposition of plasmid-encoded insertion sequence 1 (IS1) elements. Specifically, IS1-mediated gene inactivation expedites the adaptation rate of clinical strains in vitro and fosters within-patient adaptation in the gut microbiota. We deciphered the mechanism underlying the plasmid-mediated surge in IS1 transposition, revealing a negative feedback loop regulated by the genomic copy number of IS1. Given the overrepresentation of IS elements in bacterial plasmids, our findings suggest that plasmid-mediated IS1 transposition represents a crucial mechanism for swift bacterial adaptation.}, }
@article {pmid39198281, year = {2024}, author = {He, Z and Smets, BF and Dechesne, A}, title = {Mating Assay: Plating Below a Cell Density Threshold is Required for Unbiased Estimation of Plasmid Conjugation Frequency of RP4 Transfer Between E. coli Strains.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {109}, pmid = {39198281}, issn = {1432-184X}, support = {0236-00022B//Innovationsfonden/ ; 0236-00022B//Innovationsfonden/ ; 0236-00022B//Innovationsfonden/ ; PhD Scholarship//Sino-Danish Center/ ; PhD Scholarship//Sino-Danish Center/ ; }, mesh = {*Escherichia coli/genetics ; *Conjugation, Genetic ; *Plasmids/genetics ; Gene Transfer, Horizontal ; }, abstract = {Mating assays are common laboratory experiments for measuring the conjugation frequency, i.e. efficiency at which a plasmid transfers from a population of donor cells to a population of recipient cells. Selective plating remains a widely used quantification method to enumerate transconjugants at the end of such assays. However, conjugation frequencies may be inaccurately estimated because plasmid transfer can occur on transconjugant-selective plates rather than only during the intended mating duration. We investigated the influence of cell density on this phenomenon. We conducted mating experiments with IncPα plasmid RP4 harbored in Escherichia coli at a fixed cell density and mating conditions, inoculated a serial dilution of the mating mixture on transconjugant-selective plates or in transconjugant-selective broth, and compared the results to a model of cell-to-cell distance distribution. Our findings suggest that irrespective of the mating mode (liquid vs solid), the enumeration of transconjugants becomes significantly biased if the plated cell density exceeds 28 Colony Forming Unit (CFU)/mm[2] (or 1.68•10[5] CFU/standard 9 cm Petri dish). This threshold is determined with a 95% confidence interval of ± 4 CFU/mm[2] (± 2.46•10[4] CFU/standard 9 cm Petri dish). Liquid mating assays were more sensitive to this bias because the conjugation frequency of RP4 is several orders of magnitude lower in suspension compared to surface mating. Therefore, if selective plating is used, we recommend to plate at this density threshold and that negative controls are performed where donors and recipients are briefly mixed before plating at the same dilutions as for the actual mating assay. As an alternative, a liquid enumeration method can be utilized to increase the signal-to-noise ratio and allow for more accurate enumeration of transconjugants.}, }
@article {pmid39194517, year = {2024}, author = {Yang, X and Liu, Z and Zhang, Y and Shi, X and Wu, Z}, title = {Dinoflagellate-Bacteria Interactions: Physiology, Ecology, and Evolution.}, journal = {Biology}, volume = {13}, number = {8}, pages = {}, pmid = {39194517}, issn = {2079-7737}, support = {42106093 and 41976130//National Natural Science Foundation of China/ ; 2022T150706//China Postdoctoral Science Foundation/ ; GPCGD223103FG015F//Comprehensive Protection and Utilization Program for the Coastal Zone of Guangdong 534 Province (Revision)/ ; DD20230460, DD20230107, and DD20242792//Marine Geological Survey 535 Program of China Geological Survey/ ; }, abstract = {Dinoflagellates and heterotrophic bacteria are two major micro-organism groups within marine ecosystems. Their coexistence has led to a co-evolutionary relationship characterized by intricate interactions that not only alter their individual behaviors but also exert a significant influence on the broader biogeochemical cycles. Our review commenced with an analysis of bacterial populations, both free-living and adherent to dinoflagellate surfaces. Members of Alphaproteobacteria, Gammaproteobacteria, and the Cytophaga-Flavobacterium-Bacteroides group are repeatedly found to be associated with dinoflagellates, with representation by relatively few genera, such as Methylophaga, Marinobacter, and Alteromonas. These bacterial taxa engage with dinoflagellates in a limited capacity, involving nutrient exchange, the secretion of pathogenic substances, or participation in chemical production. Furthermore, the genomic evolution of dinoflagellates has been profoundly impacted by the horizontal gene transfer from bacteria. The integration of bacterial genes into dinoflagellates has been instrumental in defining their biological characteristics and nutritional strategies. This review aims to elucidate the nuanced interactions between dinoflagellates and their associated bacteria, offering a detailed perspective on their complex relationship.}, }
@article {pmid39194203, year = {2024}, author = {Allain, M and Morel-Journel, T and Condamine, B and Gibeaux, B and Gachet, B and Gschwind, R and Denamur, E and Landraud, L}, title = {IncC plasmid genome rearrangements influence the vertical and horizontal transmission tradeoff in Escherichia coli.}, journal = {Antimicrobial agents and chemotherapy}, volume = {68}, number = {10}, pages = {e0055424}, pmid = {39194203}, issn = {1098-6596}, support = {DEQ20161136698//Fondation pour la Recherche M&#xe9;dicale (FRM)/ ; }, mesh = {*Plasmids/genetics ; *Escherichia coli/genetics ; *Drug Resistance, Multiple, Bacterial/genetics ; *Conjugation, Genetic ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Escherichia coli Infections/microbiology/transmission ; }, abstract = {It has been shown that an evolutionary tradeoff between vertical (host growth rate) and horizontal (plasmid conjugation) transmissions contributes to global plasmid fitness. As conjugative IncC plasmids are important for the spread of multidrug resistance (MDR), in a broad range of bacterial hosts, we investigated vertical and horizontal transmissions of two multidrug-resistant IncC plasmids according to their backbones and MDR-region rearrangements, upon plasmid entry into a new host. We observed plasmid genome deletions after conjugation in three diverse natural Escherichia coli clinical strains, varying from null to high number depending on the plasmid, all occurring in the MDR region. The plasmid burden on bacterial fitness depended more on the strain background than on the structure of the MDR region, with deletions appearing to have no impact. Besides, we observed an increase in plasmid transfer rate, from ancestral host to new clinical recipient strains, when the IncC plasmid was rearranged. Finally, using a second set of conjugation experiments, we investigated the evolutionary tradeoff of the IncC plasmid during the critical period of plasmid establishment in E. coli K-12, by correlating the transfer rates of deleted or non-deleted IncC plasmids and their costs on the recipient strain. Plasmid deletions strongly improved conjugation efficiency with no negative growth effect. Our findings indicate that the flexibility of the MDR-region of the IncC plasmids can promote their dissemination, and provide diverse opportunities to capture new resistance genes. In a broader view, they suggest that the vertical-horizontal transmission tradeoff can be manipulated by the plasmid to improve its fitness.}, }
@article {pmid39193949, year = {2024}, author = {Kim, HJ and Koo, SH and Choi, Q}, title = {Horizontal Gene Transfer of blaNDM-5 Among Three Different Enterobacteriaceae Species Isolated from a Single Patient.}, journal = {Clinical laboratory}, volume = {70}, number = {8}, pages = {}, doi = {10.7754/Clin.Lab.2024.240309}, pmid = {39193949}, issn = {1433-6510}, mesh = {Humans ; *Gene Transfer, Horizontal ; *Microbial Sensitivity Tests ; *beta-Lactamases/genetics ; *Enterobacteriaceae/genetics/drug effects/isolation &amp; purification ; *Anti-Bacterial Agents/pharmacology ; *Plasmids/genetics ; Enterobacteriaceae Infections/microbiology/diagnosis/drug therapy ; Whole Genome Sequencing ; Escherichia coli/genetics/drug effects/isolation &amp; purification ; Klebsiella oxytoca/genetics/isolation &amp; purification/drug effects ; Citrobacter/genetics/isolation &amp; purification/drug effects ; }, abstract = {BACKGROUND: In this study, Escherichia coli, Klebsiella oxytoca, and Citrobacter amalonaticus carrying blaNDM-5 were isolated from a single patient.<br><br>METHODS: The antibiotic susceptibility of the isolates was evaluated by using E-test and agar dilution methods, and blaNDM-5 was identified in genomic and plasmid DNA by using polymerase chain reaction and sequencing. Whole genome sequencing and de novo assembly were used for species characterization, resistance gene identification, and plasmid analysis.<br><br>RESULTS: All three species had identical plasmids, which were similar to pEC463-NDM5, a plasmid harboring blaNDM-5. Transconjugation experiments confirmed the horizontal gene transfer of blaNDM-5, highlighting the need for a close monitoring of Enterobacteriaceae species harboring this gene.<br><br>CONCLUSIONS: This study conclusively demonstrates the propensity for horizontal gene transfer of blaNDM-5 among Enterobacteriaceae species, underlining the importance of vigilant monitoring to combat antibiotic resistance.}, }
@article {pmid39191402, year = {2024}, author = {Aoun, N and Georgoulis, SJ and Avalos, JK and Grulla, KJ and Miqueo, K and Tom, C and Lowe-Power, TM}, title = {A pangenomic atlas reveals eco-evolutionary dynamics that shape type VI secretion systems in plant-pathogenic Ralstonia.}, journal = {mBio}, volume = {15}, number = {10}, pages = {e0032324}, pmid = {39191402}, issn = {2150-7511}, support = {Hatch #1023861,Award# 1030618//USDA | National Institute of Food and Agriculture (NIFA)/ ; //Hellman Foundation (The Hellman Foundation)/ ; }, mesh = {*Type VI Secretion Systems/genetics/metabolism ; *Phylogeny ; *Genome, Bacterial ; *Ralstonia solanacearum/genetics/metabolism ; *Evolution, Molecular ; Plant Diseases/microbiology ; Bacterial Toxins/genetics/metabolism ; Burkholderiaceae/genetics/metabolism/classification ; Multigene Family ; Ralstonia/genetics/metabolism ; Genomics ; Gene Transfer, Horizontal ; }, abstract = {Soilborne Ralstonia solanacearum species complex (RSSC) pathogens disrupt microbial communities as they invade roots and fatally wilt plants. RSSC pathogens secrete antimicrobial toxins using a type VI secretion system (T6SS). To investigate how evolution and ecology have shaped the T6SS of these bacterial pathogens, we analyzed the T6SS gene content and architecture across the RSSC and their evolutionary relatives. Our analysis reveals that two ecologically similar Burkholderiaceae taxa, xylem-pathogenic RSSC and Paracidovorax, have convergently evolved to wield large arsenals of T6SS toxins. To understand the mechanisms underlying genomic enrichment of T6SS toxins, we compiled an atlas of 1,066 auxiliary T6SS toxin clusters ("aux" clusters) across 99 high-quality RSSC genomes. We classified 25 types of aux clusters with toxins that predominantly target lipids, nucleic acids, or unknown cellular substrates. The aux clusters were located in diverse genetic neighborhoods and had complex phylogenetic distributions, suggesting frequent horizontal gene flow. Phages and other mobile genetic elements account for most of the aux cluster acquisition on the chromosome but very little on the megaplasmid. Nevertheless, RSSC genomes were more enriched in aux clusters on the megaplasmid. Although the single, ancestral T6SS was broadly conserved in the RSSC, the T6SS has been convergently lost in atypical, non-soilborne lineages. Overall, our data suggest dynamic interplay between the lifestyle of RSSC lineages and the evolution of T6SSes with robust arsenals of toxins. This pangenomic atlas poises the RSSC as an emerging, tractable model to understand the role of the T6SS in shaping pathogen populations.IMPORTANCEWe explored the eco-evolutionary dynamics that shape the inter-microbial warfare mechanisms of a globally significant plant pathogen, the Ralstonia solanacearum species complex. We discovered that most Ralstonia wilt pathogens have evolved extensive and diverse repertoires of type VI secretion system-associated antimicrobial toxins. These expansive toxin arsenals potentially enhance the ability of Ralstonia pathogens to invade plant microbiomes, enabling them to rapidly colonize and kill their host plants. We devised a classification system to categorize the Ralstonia toxins. Interestingly, many of the toxin gene clusters are encoded on mobile genetic elements, including prophages, which may be mutualistic symbionts that enhance the inter-microbial competitiveness of Ralstonia wilt pathogens. Moreover, our findings suggest that the convergent loss of this multi-gene trait contributes to genome reduction in two vector-transmitted lineages of Ralstonia pathogens. Our findings demonstrate that the interplay between microbial ecology and pathogen lifestyle shapes the evolution of a genetically complex antimicrobial weapon.}, }
@article {pmid39191296, year = {2024}, author = {Xiao, Y and Qin, Y and Jiang, X and Gao, P}, title = {Effects of polypropylene microplastics on digestion performance, microbial community, and antibiotic resistance during microbial anaerobic digestion.}, journal = {Bioresource technology}, volume = {411}, number = {}, pages = {131358}, doi = {10.1016/j.biortech.2024.131358}, pmid = {39191296}, issn = {1873-2976}, mesh = {*Polypropylenes ; Anaerobiosis ; *Drug Resistance, Microbial/genetics ; *Microplastics ; Bioreactors ; Methane/metabolism ; Biodegradation, Environmental ; Bacteria/drug effects/genetics/metabolism ; }, abstract = {As an emerging pollutant, microplastics (MPs) have attracted increasing attention worldwide. The effects of polypropylene (PP) MPs on digestion performance, behaviors of dominant microbial communities, antibiotic resistance genes (ARGs) and mobile genetic elements in microbial anaerobic digesters were investigated. The results showed that the addition of PP-MPs to digesters led to an increase in methane production of 10.8% when 300 particles/g TSS of PP-MPs was introduced compared with that in digester not treated with PP-MPs. This increase was attributed to the enrichment of acetogens such as Syntrophobacter (42.0%), Syntrophorhabdus (27.0%), and Syntrophomonas (10.6%), and methanogens including Methanobacterium and Methanosaeta. tetX was highly enriched due to PP-MP exposure, whereas parC exhibited the greatest increase (35.5% - 222.7%). Horizontal gene transfer via ISCR1 and intI1 genes might play an important role in the spread of ARGs. Overall, these findings provide comprehensive insight into the ecological dynamics of PP-MPs during microbial anaerobic digestion.}, }
@article {pmid39191191, year = {2024}, author = {Middendorf, PS and Zomer, AL and Bergval, IL and Jacobs-Reitsma, WF and den Besten, HMW and Abee, T}, title = {Host associations of Campylobacter jejuni and Campylobacter coli isolates carrying the L-fucose or d-glucose utilization cluster.}, journal = {International journal of food microbiology}, volume = {425}, number = {}, pages = {110855}, doi = {10.1016/j.ijfoodmicro.2024.110855}, pmid = {39191191}, issn = {1879-3460}, mesh = {*Campylobacter coli/genetics/isolation &amp; purification/metabolism ; *Campylobacter jejuni/genetics/metabolism/isolation &amp; purification ; *Glucose/metabolism ; Humans ; *Fucose/metabolism ; Genome, Bacterial ; Gene Transfer, Horizontal ; Campylobacter Infections/microbiology/veterinary ; Multigene Family ; Finland ; Netherlands ; Bacterial Proteins/genetics/metabolism ; }, abstract = {Campylobacter was considered asaccharolytic, but is now known to carry saccharide metabolization pathways for L-fucose and d-glucose. We hypothesized that these clusters are beneficial for Campylobacter niche adaptation and may help establish human infection. We investigated the distribution of d-glucose and L-fucose clusters among ∼9600 C. jejuni and C. coli genomes of different isolation sources in the Netherlands, the United Kingdom, the United States of America and Finland. The L-fucose utilization cluster was integrated at the same location in all C. jejuni and C. coli genomes, and was flanked by the genes rpoB, rpoC, rspL, repsG and fusA, which are associated with functions in transcription as well as translation and in acquired drug resistance. In contrast, the flanking regions of the d-glucose utilization cluster were variable among the isolates, and integration sites were located within one of the three different 16S23S ribosomal RNA areas of the C. jejuni and C. coli genomes. In addition, we investigated whether acquisition of the L-fucose utilization cluster could be due to horizontal gene transfer between the two species and found three isolates for which this was the case: one C. jejuni isolate carrying a C. coli L-fucose cluster, and two C. coli isolates which carried a C. jejuni L-fucose cluster. Furthermore, L-fucose utilization cluster alignments revealed multiple frameshift mutations, most of which were commonly found in the non-essential genes for L-fucose metabolism, namely, Cj0484 and Cj0489. These findings support our hypothesis that the L-fucose cluster was integrated multiple times across the C. coli/C. jejuni phylogeny. Notably, association analysis using the C. jejuni isolates from the Netherlands showed a significant correlation between human C. jejuni isolates and C. jejuni isolates carrying the L-fucose utilization cluster. This correlation was even stronger when the Dutch isolates were combined with the isolates from the UK, the USA and Finland. No such correlations were observed for C. coli or for the d-glucose cluster for both species. This research provides insight into the spread and host associations of the L-fucose and d-glucose utilization clusters in C. jejuni and C. coli, and the potential benefits in human infection and/or proliferation in humans, conceivably after transmission from any reservoir.}, }
@article {pmid39191006, year = {2024}, author = {Zhao, H and Sun, Y and Cao, X and Waigi, MG and Liu, J}, title = {Effects and mechanisms of chlormequat on horizontal transfer of antibiotic resistance genes through plasmid-mediated conjugation in agro-ecosystems.}, journal = {Journal of hazardous materials}, volume = {479}, number = {}, pages = {135639}, doi = {10.1016/j.jhazmat.2024.135639}, pmid = {39191006}, issn = {1873-3336}, mesh = {*Plasmids/genetics ; *Oryza/microbiology/growth &amp; development/drug effects/genetics ; *Gene Transfer, Horizontal ; *Conjugation, Genetic ; *Escherichia coli/genetics/drug effects ; *Pseudomonas/genetics/drug effects/metabolism ; Pseudomonas putida/genetics/drug effects/metabolism ; Genes, Bacterial/drug effects ; Anti-Bacterial Agents/pharmacology ; Agriculture ; Drug Resistance, Bacterial/genetics/drug effects ; Drug Resistance, Microbial/genetics ; }, abstract = {Chlormequat (CCC) is widely used in agricultural production to increase the crop yield. However, the effects of CCC on transfer of ARGs in agricultural system are still unclear. In this study, using E.coli DH5α (carrying RP4 plasmid with Amp[R], Tet[R], Kan[R]) as the donor bacterium, E.coli HB101, endophytic Pseudomonas sp. Ph6 or rhizosphere Pseudomonas putida KT2440 as the recipient strain, three conjugative systems were designed to investigate the effects of CCC on ARG transfer. Meanwhile, hydroponics experiments were designed to study the ARG spread in the rice-nutrient solution system after CCC application. The results showed that CCC significantly promoted the RP4 conjugation by expanding cell membrane permeability and improving the relative transcription levels of trfAp, trbBp, traA and traL genes in RP4. Furthermore, the conjugation frequency between E. coli and Pseudomonas was much higher than that between E. coli cells. Compared with spraying foliage with 2500 mg·L[-1] of CCC, soaking seeds with 250 mg·L[-1] of CCC was more beneficial to the colonization of ARB in rice, and also increased the abundance of ARGs in rice cultivation system. These results remind that the use of CCC in agricultural production might promote the ARG transmission in agro-ecosystems; however, foliage spraying with 2500 mg·L[-1] of CCC could control its spread.}, }
@article {pmid39190937, year = {2024}, author = {Wen, AX and Herman, C}, title = {Horizontal gene transfer and beyond: the delivery of biological matter by bacterial membrane vesicles to host and bacterial cells.}, journal = {Current opinion in microbiology}, volume = {81}, number = {}, pages = {102525}, pmid = {39190937}, issn = {1879-0364}, support = {DP1 AI152073/AI/NIAID NIH HHS/United States ; }, mesh = {*Gene Transfer, Horizontal ; *Bacteria/genetics/metabolism ; *Extracellular Vesicles/metabolism ; Cell Membrane/metabolism ; }, abstract = {Membrane vesicles (MVs) are produced in all domains of life. In eukaryotes, extracellular vesicles have been shown to mediate the horizontal transfer of biological material between cells [1]. Therefore, bacterial MVs are also thought to mediate horizontal material transfer to host cells and other bacteria, especially in the context of cell stress. In this review, we discuss the mechanisms of bacterial MV production, evidence that their contents can be trafficked to host cells and other bacteria, and the biological relevance of horizontal material transfer by bacterial MVs.}, }
@article {pmid39190025, year = {2024}, author = {Alav, I and Pordelkhaki, P and Rodriguez-Navarro, J and Neo, O and Kessler, C and Awodipe, RJ and Cliffe, P and Pulavan, N and Marton, HL and Gibbons, S and Buckner, MMC}, title = {Natural products from food sources can alter the spread of antimicrobial resistance plasmids in Enterobacterales.}, journal = {Microbiology (Reading, England)}, volume = {170}, number = {8}, pages = {}, pmid = {39190025}, issn = {1465-2080}, mesh = {*Plasmids/genetics ; *Anti-Bacterial Agents/pharmacology ; *Klebsiella pneumoniae/drug effects/genetics ; *Escherichia coli/genetics/drug effects ; *beta-Lactamases/genetics/metabolism ; *Biological Products/pharmacology ; Drug Resistance, Bacterial/genetics ; Conjugation, Genetic ; Bacterial Proteins/genetics/metabolism ; Enterobacteriaceae/drug effects/genetics ; Microbial Sensitivity Tests ; Food Microbiology ; Gene Transfer, Horizontal ; }, abstract = {Antimicrobial resistance (AMR) poses a significant threat to global public health. Notably, resistance to carbapenem and extended-spectrum β-lactam antibiotics in Gram-negative bacteria is a major impediment to treating infections. Genes responsible for antibiotic resistance are frequently carried on plasmids, which can transfer between bacteria. Therefore, exploring strategies to prevent this transfer and the prevalence of AMR plasmids is timely and pertinent. Here, we show that certain natural product extracts and associated pure compounds can reduce the conjugation of AMR plasmids into new bacterial hosts. Using our established high-throughput fluorescence-based flow cytometry assay, we found that the natural products were more active in reducing transmission of the IncK extended-spectrum β-lactamase-encoding plasmid pCT in Escherichia coli EC958c, compared to Klebsiella pneumoniae Ecl8 carrying the IncFII carbapenemase-encoding plasmid pKpQIL. The exception was the natural product rottlerin, also active in K. pneumoniae. In classical conjugation assays, rottlerin also reduced the conjugation frequency of the IncFII bla NDM-1 carrying plasmid pCPE16_3 from a clinical K. pneumoniae isolate. Our data indicate that the natural products tested here, in their current molecular structure, reduced conjugation by a small amount, which is unlikely to achieve a large-scale reduction in AMR in bacterial populations. However, certain natural products like rottlerin could provide a foundation for further research into compounds with effective anti-plasmid activity.}, }
@article {pmid39189989, year = {2024}, author = {Brewer, TE and Wagner, A}, title = {Horizontal Gene Transfer of a key Translation Factor and its Role in Polyproline Proteome Evolution.}, journal = {Molecular biology and evolution}, volume = {41}, number = {9}, pages = {}, pmid = {39189989}, issn = {1537-1719}, mesh = {*Gene Transfer, Horizontal ; *Peptide Elongation Factors/genetics/metabolism ; *Evolution, Molecular ; *Peptides/metabolism/genetics ; *Proteome ; Bacteria/genetics/metabolism ; Phylogeny ; Bacterial Proteins/genetics/metabolism ; }, abstract = {Prolines cause ribosomes to stall during translation due to their rigid structure. This phenomenon occurs in all domains of life and is exacerbated at polyproline motifs. Such stalling can be eased by the elongation factor P (EF-P) in bacteria. We discovered a potential connection between the loss of ancestral EF-P, the appearance of horizontally transferred EF-P variants, and genomic signs of EF-P dysfunction. Horizontal transfer of the efp gene has occurred several times among bacteria and is associated with the loss of highly conserved polyproline motifs. In this study, we pinpoint cases of horizontal EF-P transfer among a diverse set of bacteria and examine genomic features associated with these events in the phyla Thermotogota and Planctomycetes. In these phyla, horizontal EF-P transfer is also associated with the loss of entire polyproline motif-containing proteins, whose expression is likely dependent on EF-P. In particular, three proteases (Lon, ClpC, and FtsH) and three tRNA synthetases (ValS, IleS1, and IleS2) appear highly sensitive to EF-P transfer. The conserved polyproline motifs within these proteins all reside within close proximity to ATP-binding-regions, some of which are crucial for their function. Our work shows that an ancient EF-P dysfunction has left genomic traces that persist to this day, although it remains unclear whether this dysfunction was strictly due to loss of ancestral EF-P or was related to the appearance of an exogenous variant. The latter possibility would imply that the process of "domesticating" a horizontally transferred efp gene can perturb the overall function of EF-P.}, }
@article {pmid39189956, year = {2024}, author = {Zheng, X and Huang, L}, title = {Diverse non-canonical electron bifurcating [FeFe]-hydrogenases of separate evolutionary origins in Hydrogenedentota.}, journal = {mSystems}, volume = {9}, number = {9}, pages = {e0099924}, pmid = {39189956}, issn = {2379-5077}, support = {SQ2021QZKK0302//Ministry of Science and Technology of the People's Republic of China (MOST)/ ; XDB42000000//CAS | Bureau of Development and Planning, Chinese Academy of Sciences (Bureau of Development and Planning, CAS)/ ; 42376238//MOST | National Natural Science Foundation of China (NSFC)/ ; 32393970//MOST | National Natural Science Foundation of China (NSFC)/ ; 91751000//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {*Hydrogenase/genetics/metabolism/chemistry ; *Phylogeny ; *Evolution, Molecular ; *Iron-Sulfur Proteins/genetics/metabolism ; Bacterial Proteins/genetics/metabolism/chemistry ; Bacteria/genetics/enzymology ; Genome, Bacterial ; Hydrogen/metabolism ; Gene Transfer, Horizontal ; }, abstract = {UNLABELLED: Hydrogenedentota, a globally distributed bacterial phylum-level lineage, is poorly understood. Here, we established a comprehensive genomic catalog of Hydrogenedentota, including a total of seven clades (or families) with 179 genomes, and explored the metabolic potential and evolutionary history of these organisms. We show that a single genome, especially those belonging to Clade 6, often encodes multiple hydrogenases with genomes in Clade 2, which rarely encode hydrogenases being the exception. Notably, most members of Hydrogenedentota contain a group A3 [FeFe]-hydrogenase (BfuABC) with a non-canonical electron bifurcation mechanism, in addition to substrate-level phosphorylation and electron transport-linked phosphorylation pathways, in energy conservation. Furthermore, we show that BfuABC from Hydrogenedentota fall into five sub-types. Phylogenetic analysis reveals five independent routes for the evolution of BfuABC homologs in Hydrogenedentota. We speculate that the five sub-types of BfuABC might be acquired from Bacillota (synonym Firmicutes) through separate horizontal gene transfer events. These data shed light on the diversity and evolution of bifurcating [FeFe]-hydrogenases and provide insight into the strategy of Hydrogenedentota to adapt to survival in various habitats.<br><br>IMPORTANCE: The phylum Hydrogenedentota is widely distributed in various environments. However, their physiology, ecology, and evolutionary history remain unknown, primarily due to the limited availability of the genomes and the lack of cultured representatives of the phylum. Our results have increased the knowledge of the genetic and metabolic diversity of these organisms and shed light on their diverse energy conservation strategies, especially those involving electron bifurcation with a non-canonical mechanism, which are likely responsible for their wide distribution. Besides, the organization and phylogenetic relationships of gene clusters coding for BfuABC in Hydrogenedentota provide valuable clues to the evolutionary history of group A3 electron bifurcating [FeFe]-hydrogenases.}, }
@article {pmid39189770, year = {2024}, author = {Kopejtka, K and Tomasch, J and Shivaramu, S and Saini, MK and Kaftan, D and Koblížek, M}, title = {Minimal transcriptional regulation of horizontally transferred photosynthesis genes in phototrophic bacterium Gemmatimonas phototrophica.}, journal = {mSystems}, volume = {9}, number = {9}, pages = {e0070624}, pmid = {39189770}, issn = {2379-5077}, support = {GX19-28778X//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky (GA&#x10c;R)/ ; CZ.02.01.01/00/22_008/0004624//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy/ ; }, mesh = {*Gene Transfer, Horizontal ; *Photosynthesis/genetics ; *Gene Expression Regulation, Bacterial/radiation effects ; Light ; Bacterial Proteins/genetics/metabolism ; Transcriptome ; }, abstract = {UNLABELLED: The first phototrophic member of the bacterial phylum Gemmatimonadota, Gemmatimonas phototrophica AP64[T], received all its photosynthesis genes via distant horizontal gene transfer from a purple bacterium. Here, we investigated how these acquired genes, which are tightly controlled by oxygen and light in the ancestor, are integrated into the regulatory system of its new host. G. phototrophica grew well under aerobic and semiaerobic conditions, with almost no difference in gene expression. Under aerobic conditions, the growth of G. phototrophica was optimal at 80 µmol photon m[-2] s[-1], while higher light intensities had an inhibitory effect. The transcriptome showed only a minimal response to the dark-light shift at optimal light intensity, while the exposure to a higher light intensity (200 µmol photon m[-2] s[-1]) induced already stronger but still transient changes in gene expression. Interestingly, a singlet oxygen defense was not activated under any conditions tested. Our results indicate that G. phototrophica possesses neither the oxygen-dependent repression of photosynthesis genes known from purple bacteria nor the light-dependent repression described in aerobic anoxygenic phototrophs. Instead, G. phototrophica has evolved as a low-light species preferring reduced oxygen concentrations. Under these conditions, the bacterium can safely employ its photoheterotrophic metabolism without the need for complex regulatory mechanisms.<br><br>IMPORTANCE: Horizontal gene transfer is one of the main mechanisms by which bacteria acquire new genes. However, it represents only the first step as the transferred genes have also to be functionally and regulatory integrated into the recipient's cellular machinery. Gemmatimonas phototrophica, a member of bacterial phylum Gemmatimonadota, acquired its photosynthesis genes via distant horizontal gene transfer from a purple bacterium. Thus, it represents a unique natural experiment, in which the entire package of photosynthesis genes was transplanted into a distant host. We show that G. phototrophica lacks the regulation of photosynthesis gene expressions in response to oxygen concentration and light intensity that are common in purple bacteria. This restricts its growth to low-light habitats with reduced oxygen. Understanding the regulation of horizontally transferred genes is important not only for microbial evolution but also for synthetic biology and the engineering of novel organisms, as these rely on the successful integration of foreign genes.}, }
@article {pmid39189747, year = {2024}, author = {Duchin Rapp, Y and Lipsman, V and Yuda, L and Kublanov, IV and Matsliyah, D and Segev, E}, title = {Algal exudates promote conjugation in marine Roseobacters.}, journal = {mBio}, volume = {15}, number = {10}, pages = {e0106224}, pmid = {39189747}, issn = {2150-7511}, mesh = {*Roseobacter/metabolism/genetics ; *Conjugation, Genetic ; *Gene Transfer, Horizontal ; Plasmids/genetics ; Aquatic Organisms/genetics/metabolism ; Type IV Secretion Systems/metabolism/genetics ; Seawater/microbiology ; }, abstract = {UNLABELLED: Horizontal gene transfer (HGT) is a pivotal mechanism driving bacterial evolution, conferring adaptability within dynamic marine ecosystems. Among HGT mechanisms, conjugation mediated by type IV secretion systems (T4SSs) plays a central role in the ecological success of marine bacteria. However, the conditions promoting conjugation events in the marine environment are not well-understood. Roseobacters, abundant marine bacteria commonly associated with algae, possess a multitude of T4SSs. Many Roseobacters are heterotrophic bacteria that rely on algal secreted compounds to support their growth. These compounds attract bacteria, facilitating colonization and attachment to algal cells. Algae and their metabolites bring bacteria into close proximity, potentially promoting bacterial HGT. Investigation across various Roseobacters revealed that algal exudates indeed enhance plasmid transfer through conjugation. While algal exudates do not influence the transcription of bacterial conjugative machinery genes, they promote bacterial attachment, potentially stabilizing proximity and facilitating HGT. Notably, under conditions where attachment is less advantageous, the impact of algal exudates on conjugation is reduced. These findings suggest that algae enhance bacterial conjugation primarily by fostering attachment and highlight the importance of studying bacterial HGT within the context of algal-bacterial interactions.<br><br>IMPORTANCE: This study explores how algal-bacterial interactions influence horizontal gene transfer (HGT) among marine bacteria. HGT, a key driver of bacterial evolution, is facilitated by conjugation mediated by type IV secretion systems (T4SSs). Through investigating Roseobacters, abundant marine bacteria often found to be associated with algae, the study reveals that algal exudates enhance plasmid transfer via conjugation. This enhancement is attributed to the promotion of bacterial attachment by algal compounds, emphasizing the role of algal-bacterial interactions in shaping genetic exchange within dynamic marine ecosystems. Understanding these mechanisms is crucial for elucidating bacterial adaptability and evolution in the marine environment.}, }
@article {pmid39189727, year = {2024}, author = {Xu, Y and Liu, B and Jiao, N and Liu, J and Chen, F}, title = {New evidence supports the prophage origin of RcGTA.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {9}, pages = {e0043424}, pmid = {39189727}, issn = {1098-5336}, support = {2020ZLYS04//Department of Science and Technology of Shandong Province ()/ ; 2018YFA0605800//Ministry of Science and Technology of the People's Republic of China (MOST)/ ; }, mesh = {*Prophages/genetics ; Rhodobacter capsulatus/virology/genetics ; Gene Transfer, Horizontal ; Genome, Viral ; Phylogeny ; Evolution, Molecular ; Methylobacterium/virology/genetics ; }, abstract = {Gene transfer agents (GTAs) are phage-like entities that package and transfer random host genome fragments between prokaryotes. RcGTA, produced by Rhodobacter capsulatus, is hypothesized to originate from a prophage ancestor. Most of the evidence supporting this hypothesis came from the finding of RcGTA-like genes in phages. More than 75% of the RcGTA genes have a phage homolog. However, only a few RcGTA homologs have been identified in a (pro)phage genome, leaving the hypothesis that GTAs evolved from prophages through gene loss with only weak evidence. We herein report the discovery of an inducible prophage (vB_MseS-P1) from a Mesorhizobium sediminum strain that contains the largest number (12) of RcGTA homologs found in a phage genome to date. We also identified three putative prophages and two prophage remnants harboring 12-14 RcGTA homologs in a Methylobacterium nodulans strain. The protein remote homology detection also revealed more RcGTA homologs from other phages than we previously thought. Moreover, the head-tail gene architecture of these newly discovered prophage-related elements closely resembles that of RcGTA. Furthermore, vB_MseS-P1 virions have structural proteins similar to RcGTA particles. Close phylogenetic relationships between certain prophage genes and RcGTA-like genes in Alphaproteobacteria further support the shared ancestry between RcGTA and prophages. Our findings provide new relatively direct evidence of the origin of RcGTA from a prophage progenitor.IMPORTANCEGTAs are important genetic elements in certain groups of bacteria and contribute to the genetic diversification, evolution, and ecological adaptation of bacteria. RcGTA, a common type of GTA, is known to package and transfer random fragments of the bacterial genome to recipient cells. However, the origin of RcGTA is still elusive. It has been hypothesized that RcGTA evolved from a prophage ancestor through gene loss. However, the few RcGTA homologs identified in a (pro)phage genome leave the hypothesis lacking direct evidence. This study uncovers the presence of a large number of RcGTA homologs in an inducible prophage and several putative prophages. The similar head-tail gene architecture and structural protein compositions of these newly discovered prophage-related elements and RcGTA further demonstrate an unprecedentedly observed close evolutionary relationship between prophages and RcGTA. Together, our findings provide more direct evidence supporting the origin of RcGTA from prophage.}, }
@article {pmid39187833, year = {2024}, author = {Yutin, N and Tolstoy, I and Mutz, P and Wolf, YI and Krupovic, M and Koonin, EV}, title = {DNA polymerase swapping in Caudoviricetes bacteriophages.}, journal = {Virology journal}, volume = {21}, number = {1}, pages = {200}, pmid = {39187833}, issn = {1743-422X}, support = {/LM/NLM NIH HHS/United States ; }, mesh = {*DNA-Directed DNA Polymerase/genetics ; *Phylogeny ; *Viral Proteins/genetics/metabolism ; Evolution, Molecular ; Genome, Viral ; Caudovirales/genetics/classification ; DNA, Viral/genetics ; Bacteriophages/genetics/enzymology/classification ; DNA Replication ; }, abstract = {BACKGROUND: Viruses with double-stranded (ds) DNA genomes in the realm Duplodnaviria share a conserved structural gene module but show a broad range of variation in their repertoires of DNA replication proteins. Some of the duplodnaviruses encode (nearly) complete replication systems whereas others lack (almost) all genes required for replication, relying on the host replication machinery. DNA polymerases (DNAPs) comprise the centerpiece of the DNA replication apparatus. The replicative DNAPs are classified into 4 unrelated or distantly related families (A-D), with the protein structures and sequences within each family being, generally, highly conserved. More than half of the duplodnaviruses encode a DNAP of family A, B or C. We showed previously that multiple pairs of closely related viruses in the order Crassvirales encode DNAPs of different families.<br><br>METHODS: Groups of phages in which DNAP swapping likely occurred were identified as subtrees of a defined depth in a comprehensive evolutionary tree of tailed bacteriophages that included phages with DNAPs of different families. The DNAP swaps were validated by constrained tree analysis that was performed on phylogenetic tree of large terminase subunits, and the phage genomes encoding swapped DNAPs were aligned using Mauve. The structures of the discovered unusual DNAPs were predicted using AlphaFold2.<br><br>RESULTS: We identified four additional groups of tailed phages in the class Caudoviricetes in which the DNAPs apparently were swapped on multiple occasions, with replacements occurring both between families A and B, or A and C, or between distinct subfamilies within the same family. The DNAP swapping always occurs "in situ", without changes in the organization of the surrounding genes. In several cases, the DNAP gene is the only region of substantial divergence between closely related phage genomes, whereas in others, the swap apparently involved neighboring genes encoding other proteins involved in phage genome replication. In addition, we identified two previously undetected, highly divergent groups of family A DNAPs that are encoded in some phage genomes along with the main DNAP implicated in genome replication.<br><br>CONCLUSIONS: Replacement of the DNAP gene by one encoding a DNAP of a different family occurred on many independent occasions during the evolution of different families of tailed phages, in some cases, resulting in very closely related phages encoding unrelated DNAPs. DNAP swapping was likely driven by selection for avoidance of host antiphage mechanisms targeting the phage DNAP that remain to be identified, and/or by selection against replicon incompatibility.}, }
@article {pmid39186748, year = {2024}, author = {Pradel, N and Bartoli, M and Koenen, M and Bale, N and Neumann-Schaal, M and Spröer, C and Bunk, B and Rohde, M and Pester, M and Spring, S}, title = {Description and genome analysis of a novel archaeon isolated from a syntrophic pyrite-forming enrichment culture and reclassification of Methanospirillum hungatei strains GP1 and SK as Methanospirillum purgamenti sp. nov.}, journal = {PloS one}, volume = {19}, number = {8}, pages = {e0308405}, pmid = {39186748}, issn = {1932-6203}, mesh = {*Methanospirillum/genetics/metabolism ; *Phylogeny ; *Genome, Archaeal ; Sulfides/metabolism ; Iron/metabolism ; RNA, Ribosomal, 16S/genetics ; Methane/metabolism ; }, abstract = {The archaeal isolate J.3.6.1-F.2.7.3T was obtained from an anaerobic enrichment culture, where it may play an important role in methane production during pyrite formation. The new isolate formed a species-level clade with Methanospirillum hungatei strains GP1 and SK, which is separate from the type strain JF-1T. Cultivation-independent surveys indicate the occurrence of this phylogenetic group in sediments and anaerobic digesters. The abundance of this clade appears to be negatively affected by high nitrogen loads, indicating a sensitivity to certain nitrogen compounds that is not known in M. hungatei JF-1T. The relatively large core genome of this Methanospirillum clade is indicative of niche specialization and efficient control of horizontal gene transfer. Genes for nitrogenase and F420-dependent secondary alcohol dehydrogenase contribute to the metabolic versatility of this lineage. Characteristics of the new isolate such as the ability to utilize 2-propanol as an electron donor or the requirement for acetate as a carbon source are found also in the strains GP1 and SK, but not in the type strain M. hungatei JF-1T. Based on the genomic differences to related species, a new species within the genus Methanospirillum is proposed with the name M. purgamenti sp. nov. The determined phenotypic characteristics support this proposal and indicate a metabolic adaptation to a separate ecological niche.}, }
@article {pmid39184916, year = {2024}, author = {Han, H and He, T and Wu, Y and He, T and Zhou, W}, title = {Multidimensional analysis of tumor stem cells: from biological properties, metabolic adaptations to immune escape mechanisms.}, journal = {Frontiers in cell and developmental biology}, volume = {12}, number = {}, pages = {1441081}, pmid = {39184916}, issn = {2296-634X}, abstract = {As a key factor in tumorigenesis, progression, recurrence and metastasis, the biological properties, metabolic adaptations and immune escape mechanisms of CSCs are the focus of current oncological research. CSCs possess self-renewal, multidirectional differentiation and tumorigenicity, and their mechanisms of action can be elucidated by the clonal evolution, hierarchical model and the dynamic CSCs model, of which the dynamic model is widely recognized due to its better explanation of the function and origin of CSCs. The origin hypothesis of CSCs involves cell-cell fusion, horizontal gene transfer, genomic instability and microenvironmental regulation, which together shape the diversity of CSCs. In terms of classification, CSCs include primary CSCs (pri-CSCs), precancerous stem cells (pre-CSCs), migratory CSCs (mig-CSCs), and chemo-radiotherapy-resistant CSCs (cr-CSCs and rr-CSCs), with each type playing a specific role in tumor progression. Surface markers of CSCs, such as CD24, CD34, CD44, CD90, CD133, CD166, EpCAM, and LGR5, offer the possibility of identifying, isolating, and targeting CSCs, but the instability and heterogeneity of their expression increase the difficulty of treatment. CSCs have adapted to their survival needs through metabolic reprogramming, showing the ability to flexibly switch between glycolysis and oxidative phosphorylation (OXPHOS), as well as adjustments to amino acid and lipid metabolism. The Warburg effect typifies their metabolic profiles, and altered glutamine and fatty acid metabolism further contributes to the rapid proliferation and survival of CSCs. CSCs are able to maintain their stemness by regulating the metabolic networks to maintain their stemness characteristics, enhance antioxidant defences, and adapt to therapeutic stress. Immune escape is another strategy for CSCs to maintain their survival, and CSCs can effectively evade immune surveillance through mechanisms such as up-regulating PD-L1 expression and promoting the formation of an immunosuppressive microenvironment. Together, these properties reveal the multidimensional complexity of CSCs, underscoring the importance of a deeper understanding of the biology of CSCs for the development of more effective tumor therapeutic strategies. In the future, therapies targeting CSCs will focus on precise identification of surface markers, intervention of metabolic pathways, and overcoming immune escape, with the aim of improving the relevance and efficacy of cancer treatments, and ultimately improving patient prognosis.}, }
@article {pmid39184814, year = {2024}, author = {Chen, N and Li, Y and Liang, X and Qin, K and Zhang, Y and Wang, J and Wu, Q and Gupta, TB and Ding, Y}, title = {Bacterial extracellular vesicle: A non-negligible component in biofilm life cycle and challenges in biofilm treatments.}, journal = {Biofilm}, volume = {8}, number = {}, pages = {100216}, pmid = {39184814}, issn = {2590-2075}, abstract = {Bacterial biofilms, especially those formed by pathogens, have been increasingly impacting human health. Bacterial extracellular vesicle (bEV), a kind of spherical membranous structure released by bacteria, has not only been reported to be a component of the biofilm matrix but also plays a non-negligible role in the biofilm life cycle. Nevertheless, a comprehensive overview of the bEVs functions in biofilms remains elusive. In this review, we summarize the biogenesis and distinctive features characterizing bEVs, and consolidate the current literature on their functions and proposed mechanisms in the biofilm life cycle. Furthermore, we emphasize the formidable challenges associated with vesicle interference in biofilm treatments. The primary objective of this review is to raise awareness regarding the functions of bEVs in the biofilm life cycle and lay the groundwork for the development of novel therapeutic strategies to control or even eliminate bacterial biofilms.}, }
@article {pmid39182428, year = {2024}, author = {Ando, S and Tanaka, R and Ito, H}, title = {Activity examination of plant Mg-dechelatase and its bacterial homolog in plants and in vitro.}, journal = {Plant physiology and biochemistry : PPB}, volume = {215}, number = {}, pages = {109073}, doi = {10.1016/j.plaphy.2024.109073}, pmid = {39182428}, issn = {1873-2690}, mesh = {*Bacterial Proteins/metabolism/genetics ; Chlorophyll/metabolism ; Plant Proteins/metabolism/genetics ; Chlorophyll A/metabolism ; Nicotiana/genetics/metabolism ; }, abstract = {Chlorophyll a serves as a photosynthetic pigment in plants. Its degradation is initiated by the extraction of the central Mg by the Mg-dechelatase enzyme, which is encoded by Stay-Green (SGR). Plant SGR is believed to be derived from bacterial SGR homolog obtained through horizontal gene transfer into photosynthetic eukaryotes. However, it is not known how the bacterial SGR homolog was modified to function in plants. To assess its adaptation mechanism in plants, a bacterial SGR homolog derived from the Anaerolineae bacterium SM23_63 was introduced into plants. It was found that the bacterial SGR homolog metabolized chlorophyll in plants. However, its chlorophyll catabolic activity was lower than that of plant SGR. Recombinant proteins of the bacterial SGR homolog exhibited higher activity than those of the plant SGR. The reduced chlorophyll catabolic activity of bacterial SGR homologs in plants may be associated with low hydrophobicity of the entrance to the catalytic site compared to that of plant SGR. This hinders the enzyme access to chlorophyll, which is localized in hydrophobic environments. This study offers insights into the molecular changes underlying the optimization of enzyme function.}, }
@article {pmid39180708, year = {2024}, author = {Witt, ASA and Carvalho, JVRP and Serafim, MSM and Arias, NEC and Rodrigues, RAL and Abrahão, JS}, title = {The GC% landscape of the Nucleocytoviricota.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {55}, number = {4}, pages = {3373-3387}, pmid = {39180708}, issn = {1678-4405}, support = {88882.348380/2010-1//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 405249/2022-5//Ministry of Science and Technology/ ; 406441/2022-7//Ministry of Science and Technology/ ; }, mesh = {Base Composition ; *Genome, Viral ; Phylogeny ; Evolution, Molecular ; Gene Transfer, Horizontal ; }, abstract = {Genomic studies on sequence composition employ various approaches, such as calculating the proportion of guanine and cytosine within a given sequence (GC% content), which can shed light on various aspects of the organism's biology. In this context, GC% can provide insights into virus-host relationships and evolution. Here, we present a comprehensive gene-by-gene analysis of 61 representatives belonging to the phylum Nucleocytoviricota, which comprises viruses with the largest genomes known in the virosphere. Parameters were evaluated not only based on the average GC% of a given viral species compared to the entire phylum but also considering gene position and phylogenetic history. Our results reveal that while some families exhibit similar GC% among their representatives (e.g., Marseilleviridae), others such as Poxviridae, Phycodnaviridae, and Mimiviridae have members with discrepant GC% values, likely reflecting adaptation to specific biological cycles and hosts. Interestingly, certain genes located at terminal regions or within specific genomic clusters show GC% values distinct from the average, suggesting recent acquisition or unique evolutionary pressures. Horizontal gene transfer and the presence of potential paralogs were also assessed in genes with the most discrepant GC% values, indicating multiple evolutionary histories. Taken together, to the best of our knowledge, this study represents the first global and gene-by-gene analysis of GC% distribution and profiles within genomes of Nucleocytoviricota members, highlighting their diversity and identifying potential new targets for future studies.}, }
@article {pmid39179660, year = {2024}, author = {Wang, S and Sun, S and Wang, Q and Chen, H and Guo, Y and Cai, M and Yin, Y and Ma, S and Wang, H}, title = {PathoTracker: an online analytical metagenomic platform for Klebsiella pneumoniae feature identification and outbreak alerting.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1038}, pmid = {39179660}, issn = {2399-3642}, support = {32141001//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81991533//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Klebsiella pneumoniae/genetics/isolation &amp; purification ; *Metagenomics/methods ; Humans ; *Disease Outbreaks ; *Klebsiella Infections/microbiology/epidemiology/diagnosis ; *Phylogeny ; China/epidemiology ; Nanopore Sequencing/methods ; Databases, Genetic ; Genome, Bacterial ; }, abstract = {Clinical metagenomics (CMg) Nanopore sequencing can facilitate infectious disease diagnosis. In China, sub-lineages ST11-KL64 and ST11-KL47 Carbapenem-resistant Klebsiella pneumoniae (CRKP) are widely prevalent. We propose PathoTracker, a specially compiled database and arranged method for strain feature identification in CMg samples and CRKP traceability. A database targeting high-prevalence horizontal gene transfer in CRKP strains and a ST11-only database for distinguishing two sub-lineages in China were created. To make the database user-friendly, facilitate immediate downstream strain feature identification from raw Nanopore metagenomic data, and avoid the need for phylogenetic analysis from scratch, we developed data analysis methods. The methods included pre-performed phylogenetic analysis, gene-isolate-cluster index and multilevel pan-genome database and reduced storage space by 10-fold and random-access memory by 52-fold compared with normal methods. PathoTracker can provide accurate and fast strain-level analysis for CMg data after 1 h Nanopore sequencing, allowing early warning of outbreaks. A user-friendly page (http://PathoTracker.pku.edu.cn/) was developed to facilitate online analysis, including strain-level feature, species identifications and phylogenetic analyses. PathoTracker proposed in this study will aid in the downstream analysis of CMg.}, }
@article {pmid39176446, year = {2024}, author = {Ahmed, M and Kayal, E and Lavrov, DV}, title = {Mitochondrial DNA of the Demosponge Acanthella acuta: Linear Architecture and Other Unique Features.}, journal = {Genome biology and evolution}, volume = {16}, number = {8}, pages = {}, pmid = {39176446}, issn = {1759-6653}, mesh = {*DNA, Mitochondrial/genetics ; Animals ; *Phylogeny ; *Introns ; *Open Reading Frames ; *Porifera/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; }, abstract = {While Acanthella acuta Schmidt 1862, a common demosponge found in the Mediterranean Sea and Atlantic Ocean, is morphologically similar to other sponges, its mitochondrial DNA (mtDNA) is unique within the class. In contrast to all other studied demosponges, the mtDNA of A. acuta is inferred to be linear and displays several unusual features such as inverted terminal repeats, group II introns in three mitochondrial genes, and two unique open reading frames (ORFs): one of which (ORF1535) combines a DNA polymerase domain with a DNA-directed RNA polymerase domain, while the second bears no discernible similarity to any reported sequences. The group II intron within the cox2 gene is the first such intron reported in an animal. Our phylogenetic analyses indicate that the cox1 intron is related to similar introns found in other demosponges, while the cox2 intron is likely not of animal origin. The two domains found within ORF1535 do not share a common origin and, along with the cox2 intron, were likely acquired by horizontal gene transfer. The findings of this paper open new avenues of exploration in the understanding of mtDNA linearization within Metazoa.}, }
@article {pmid39174812, year = {2024}, author = {Döcker, J and Linz, S and Wicke, K}, title = {Bounding the Softwired Parsimony Score of a Phylogenetic Network.}, journal = {Bulletin of mathematical biology}, volume = {86}, number = {10}, pages = {121}, pmid = {39174812}, issn = {1522-9602}, support = {XXXX//Marsden Fund/ ; }, mesh = {*Phylogeny ; *Models, Genetic ; *Mathematical Concepts ; Algorithms ; Evolution, Molecular ; Sequence Alignment/statistics &amp; numerical data ; }, abstract = {In comparison to phylogenetic trees, phylogenetic networks are more suitable to represent complex evolutionary histories of species whose past includes reticulation such as hybridisation or lateral gene transfer. However, the reconstruction of phylogenetic networks remains challenging and computationally expensive due to their intricate structural properties. For example, the small parsimony problem that is solvable in polynomial time for phylogenetic trees, becomes NP-hard on phylogenetic networks under softwired and parental parsimony, even for a single binary character and structurally constrained networks. To calculate the parsimony score of a phylogenetic network N, these two parsimony notions consider different exponential-size sets of phylogenetic trees that can be extracted from N and infer the minimum parsimony score over all trees in the set. In this paper, we ask: What is the maximum difference between the parsimony score of any phylogenetic tree that is contained in the set of considered trees and a phylogenetic tree whose parsimony score equates to the parsimony score of N? Given a gap-free sequence alignment of multi-state characters and a rooted binary level-k phylogenetic network, we use the novel concept of an informative blob to show that this difference is bounded by k + 1 times the softwired parsimony score of N. In particular, the difference is independent of the alignment length and the number of character states. We show that an analogous bound can be obtained for the softwired parsimony score of semi-directed networks, while under parental parsimony on the other hand, such a bound does not hold.}, }
@article {pmid39173632, year = {2024}, author = {Yang, XY and Shen, Z and Wang, C and Nakanishi, K and Fu, TM}, title = {DdmDE eliminates plasmid invasion by DNA-guided DNA targeting.}, journal = {Cell}, volume = {187}, number = {19}, pages = {5253-5266.e16}, pmid = {39173632}, issn = {1097-4172}, support = {R01 GM124320/GM/NIGMS NIH HHS/United States ; R01 GM138997/GM/NIGMS NIH HHS/United States ; }, mesh = {*Bacterial Proteins/metabolism/genetics ; DNA/metabolism ; DNA Helicases/metabolism ; DNA, Bacterial/metabolism/genetics ; Escherichia coli/genetics/metabolism ; *Gene Transfer, Horizontal ; Models, Molecular ; *Plasmids/metabolism/genetics ; }, abstract = {Horizontal gene transfer is a key driver of bacterial evolution, but it also presents severe risks to bacteria by introducing invasive mobile genetic elements. To counter these threats, bacteria have developed various defense systems, including prokaryotic Argonautes (pAgos) and the DNA defense module DdmDE system. Through biochemical analysis, structural determination, and in vivo plasmid clearance assays, we elucidate the assembly and activation mechanisms of DdmDE, which eliminates small, multicopy plasmids. We demonstrate that DdmE, a pAgo-like protein, acts as a catalytically inactive, DNA-guided, DNA-targeting defense module. In the presence of guide DNA, DdmE targets plasmids and recruits a dimeric DdmD, which contains nuclease and helicase domains. Upon binding to DNA substrates, DdmD transitions from an autoinhibited dimer to an active monomer, which then translocates along and cleaves the plasmids. Together, our findings reveal the intricate mechanisms underlying DdmDE-mediated plasmid clearance, offering fundamental insights into bacterial defense systems against plasmid invasions.}, }
@article {pmid39173362, year = {2024}, author = {Zhang, Y and Zuo, S and Zheng, Q and Yu, G and Wang, Y}, title = {Removal of antibiotic resistant bacteria and antibiotic resistance genes by an electrochemically driven UV/chlorine process for decentralized water treatment.}, journal = {Water research}, volume = {265}, number = {}, pages = {122298}, doi = {10.1016/j.watres.2024.122298}, pmid = {39173362}, issn = {1879-2448}, mesh = {*Water Purification/methods ; *Ultraviolet Rays ; *Chlorine/chemistry/pharmacology ; Escherichia coli/drug effects/genetics ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology/chemistry ; Bacteria ; Drug Resistance, Bacterial/genetics ; }, abstract = {The UV/chlorine (UV/Cl2) process is a developing advanced oxidation process and can efficiently remove antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). However, the transportation and storage of chlorine solutions limit the application of the UV/Cl2 process, especially for decentralized water treatment. To overcome the limitation, an electrochemically driven UV/Cl2 process (E-UV/Cl2) where Cl2 can be electrochemically produced in situ from anodic oxidation of chloride (Cl[-]) ubiquitously present in various water matrices was evaluated in this study. >5-log inactivation of the ARB (E. coli) was achieved within 5 s of the E-UV/Cl2 process, and no photoreactivation of the ARB was observed after the treatment. In addition to the ARB, intracellular and extracellular ARGs (tetA, sul1, sul2, and ermB) could be effectively degraded (e.g., log(C0/C) > 4 for i-ARGs) within 5 min of the E-UV/Cl2 process. Atomic force microscopy showed that the most of the i-ARGs were interrupted into short fragments (< 30 nm) during the E-UV/Cl2 process, which can thus effectively prevent the self-repair of i-ARGs and the horizontal gene transfer. Modelling results showed that the abatement efficiencies of i-ARG correlated positively with the exposures of •OH, Cl2[-]•, and ClO• during the E-UV/Cl2 process. Due to the short treatment time (5 min) required for ARB and ARG removal, insignificant concentrations of trihalomethanes (THMs) were generated during of the E-UV/Cl2 process, and the energy consumption (EEO) of ARG removal was ∼0.20‒0.27 kWh/m[3]-log, which is generally comparable to that of the UV/Cl2 process (0.18-0.23 kWh/m[3]-log). These results demonstrate that the E-UV/Cl2 process can provide a feasible and attractive alternative to the UV/Cl2 process for ARB and ARG removal in decentralized water treatment system.}, }
@article {pmid39172952, year = {2024}, author = {Zhou, W and Karan, KR and Gu, W and Klein, HU and Sturm, G and De Jager, PL and Bennett, DA and Hirano, M and Picard, M and Mills, RE}, title = {Somatic nuclear mitochondrial DNA insertions are prevalent in the human brain and accumulate over time in fibroblasts.}, journal = {PLoS biology}, volume = {22}, number = {8}, pages = {e3002723}, pmid = {39172952}, issn = {1545-7885}, support = {P30 AG072975/AG/NIA NIH HHS/United States ; U01 AG046152/AG/NIA NIH HHS/United States ; R01 AG066828/AG/NIA NIH HHS/United States ; U01 AG061356/AG/NIA NIH HHS/United States ; R01 AG017917/AG/NIA NIH HHS/United States ; P30 AG010161/AG/NIA NIH HHS/United States ; R21 HG011493/HG/NHGRI NIH HHS/United States ; P30 AG072931/AG/NIA NIH HHS/United States ; R01 AG015819/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; *DNA, Mitochondrial/genetics ; *Fibroblasts/metabolism ; *Brain/metabolism ; Male ; Female ; Cell Nucleus/metabolism ; Middle Aged ; Adult ; Aged ; Longevity/genetics ; Aging/physiology/genetics ; }, abstract = {The transfer of mitochondrial DNA into the nuclear genomes of eukaryotes (Numts) has been linked to lifespan in nonhuman species and recently demonstrated to occur in rare instances from one human generation to the next. Here, we investigated numtogenesis dynamics in humans in 2 ways. First, we quantified Numts in 1,187 postmortem brain and blood samples from different individuals. Compared to circulating immune cells (n = 389), postmitotic brain tissue (n = 798) contained more Numts, consistent with their potential somatic accumulation. Within brain samples, we observed a 5.5-fold enrichment of somatic Numt insertions in the dorsolateral prefrontal cortex (DLPFC) compared to cerebellum samples, suggesting that brain Numts arose spontaneously during development or across the lifespan. Moreover, an increase in the number of brain Numts was linked to earlier mortality. The brains of individuals with no cognitive impairment (NCI) who died at younger ages carried approximately 2 more Numts per decade of life lost than those who lived longer. Second, we tested the dynamic transfer of Numts using a repeated-measures whole-genome sequencing design in a human fibroblast model that recapitulates several molecular hallmarks of aging. These longitudinal experiments revealed a gradual accumulation of 1 Numt every ~13 days. Numtogenesis was independent of large-scale genomic instability and unlikely driven by cell clonality. Targeted pharmacological perturbations including chronic glucocorticoid signaling or impairing mitochondrial oxidative phosphorylation (OxPhos) only modestly increased the rate of numtogenesis, whereas patient-derived SURF1-mutant cells exhibiting mtDNA instability accumulated Numts 4.7-fold faster than healthy donors. Combined, our data document spontaneous numtogenesis in human cells and demonstrate an association between brain cortical somatic Numts and human lifespan. These findings open the possibility that mito-nuclear horizontal gene transfer among human postmitotic tissues produces functionally relevant human Numts over timescales shorter than previously assumed.}, }
@article {pmid39172793, year = {2024}, author = {Chen, X and Wang, M and Luo, L and Liu, X and An, L and Nie, Y and Wu, XL}, title = {The evolution of autonomy from two cooperative specialists in fluctuating environments.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {35}, pages = {e2317182121}, pmid = {39172793}, issn = {1091-6490}, support = {2018YFA0902100//MOST | National Key Research and Development Program of China (NKPs)/ ; 91951204//Data Center of Management Science, National Natural Science Foundation of China - Peking University (DCMS, NSFC-PKU)/ ; }, mesh = {*Naphthalenes/metabolism ; Gene Transfer, Horizontal ; Biological Evolution ; Symbiosis ; Microbial Consortia/genetics/physiology ; Genotype ; }, abstract = {From microbes to humans, organisms perform numerous tasks for their survival, including food acquisition, migration, and reproduction. A complex biological task can be performed by either an autonomous organism or by cooperation among several specialized organisms. However, it remains unclear how autonomy and cooperation evolutionarily switch. Specifically, it remains unclear whether and how cooperative specialists can repair deleted genes through direct genetic exchange, thereby regaining metabolic autonomy. Here, we address this question by experimentally evolving a mutualistic microbial consortium composed of two specialists that cooperatively degrade naphthalene. We observed that autonomous genotypes capable of performing the entire naphthalene degradation pathway evolved from two cooperative specialists and dominated the community. This evolutionary transition was driven by the horizontal gene transfer (HGT) between the two specialists. However, this evolution was exclusively observed in the fluctuating environment alternately supplied with naphthalene and pyruvate, where mutualism and competition between the two specialists alternated. The naphthalene-supplied environment exerted selective pressure that favors the expansion of autonomous genotypes. The pyruvate-supplied environment promoted the coexistence and cell density of the cooperative specialists, thereby increasing the likelihood of HGT. Using a mathematical model, we quantitatively demonstrate that environmental fluctuations facilitate the evolution of autonomy through HGT when the relative growth rate and carrying capacity of the cooperative specialists allow enhanced coexistence and higher cell density in the competitive environment. Together, our results demonstrate that cooperative specialists can repair deleted genes through a direct genetic exchange under specific conditions, thereby regaining metabolic autonomy.}, }
@article {pmid39168346, year = {2024}, author = {Li, J and Li, C and Han, Y and Yang, J and Hu, Y and Xu, H and Zhou, Y and Zuo, J and Tang, Y and Lei, C and Li, C and Wang, H}, title = {Bacterial membrane vesicles from swine farm microbial communities harboring and safeguarding diverse functional genes promoting horizontal gene transfer.}, journal = {The Science of the total environment}, volume = {951}, number = {}, pages = {175639}, doi = {10.1016/j.scitotenv.2024.175639}, pmid = {39168346}, issn = {1879-1026}, mesh = {*Gene Transfer, Horizontal ; Animals ; Swine ; Farms ; Microbiota ; Bacteria/genetics ; Feces/microbiology ; Drug Resistance, Microbial/genetics ; Wastewater/microbiology ; Drug Resistance, Bacterial/genetics ; Soil Microbiology ; Genes, Bacterial ; }, abstract = {Antibiotic resistance (AMR) poses a significant global health challenge, with swine farms recognized as major reservoirs of antibiotic resistance genes (ARGs). Recently, bacterial membrane vesicles (BMVs) have emerged as novel carriers mediating horizontal gene transfer. However, little is known about the ARGs carried by BMVs in swine farm environments and their transfer potential. This study investigated the distribution, sources, and microbiological origins of BMVs in three key microbial habitats of swine farms (feces, soil, and fecal wastewater), along with the ARGs and mobile genetic elements (MGEs) they harbor. Characterization of BMVs revealed particle sizes ranging from 20 to 500 nm and concentrations from 10[8] to 10[12] particles/g, containing DNA and proteins. Metagenomic sequencing identified BMVs predominantly composed of members of the Proteobacteria phyla, including Pseudomonadaceae, Moraxellaceae, and Enterobacteriaceae, carrying diverse functional genes encompassing resistance to 14 common antibiotics and 74,340 virulence genes. Notably, multidrug resistance, tetracycline, and chloramphenicol resistance genes were particularly abundant. Furthermore, BMVs harbored various MGEs, primarily plasmids, and demonstrated the ability to protect their DNA cargo from degradation and facilitate horizontal gene transfer, including the transmission of resistance genes. In conclusion, this study reveals widespread presence of BMVs carrying ARGs and potential virulence genes in swine farm feces, soil, and fecal wastewater. These findings not only provide new insights into the role of extracellular DNA in the environment but also highlight concerns regarding the gene transfer potential mediated by BMVs and associated health risks.}, }
@article {pmid39167960, year = {2024}, author = {Nasu, T and Maeda, S}, title = {Escherichia coli persisters in biofilm can perform horizontal gene transfer by transformation.}, journal = {Biochemical and biophysical research communications}, volume = {738}, number = {}, pages = {150549}, doi = {10.1016/j.bbrc.2024.150549}, pmid = {39167960}, issn = {1090-2104}, mesh = {*Biofilms/drug effects/growth &amp; development ; *Escherichia coli/genetics/drug effects ; *Gene Transfer, Horizontal ; *Plasmids/genetics ; *Transformation, Bacterial ; Ampicillin/pharmacology ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics/drug effects ; }, abstract = {Persisters represent a subset of cells that exhibit transient tolerance to antimicrobials. These persisters can withstand sudden exposure to antimicrobials, even as the majority of normal cells perish. In this study, we have demonstrated the capacity of ampicillin-tolerant and alkali-tolerant persisters to execute horizontal gene transfer via in situ transformation within biofilms. Air-solid biofilms, comprising two Escherichia coli populations each with a distinct plasmid, were formed on agar media. They were treated with lethal doses of ampicillin or NaOH for 24 h, followed by a 1-min glass-ball roll. This process led to a high frequency of horizontal plasmid transfer (10[-7]-10[-6] per cell) from dead cells to surviving persisters within the biofilms. Plasmid transfer was DNase-sensitive and also occurred by adding purified plasmid DNA to plasmid-free biofilms, demonstrating a transformation mechanism. This marks the first evidence of persisters' novel ability for horizontal gene transfer, via transformation.}, }
@article {pmid39166873, year = {2024}, author = {Kwan, S-Y and Sabotta, CM and Cruz, LR and Wong, MC and Ajami, NJ and McCormick, JB and Fisher-Hoch, SP and Beretta, L}, title = {Gut phageome in Mexican Americans: a population at high risk for metabolic dysfunction-associated steatotic liver disease and diabetes.}, journal = {mSystems}, volume = {9}, number = {9}, pages = {e0043424}, pmid = {39166873}, issn = {2379-5077}, support = {P50 CA217674/CA/NCI NIH HHS/United States ; UL1 TR000371/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; Male ; Female ; *Gastrointestinal Microbiome/genetics ; *Bacteriophages/genetics ; Middle Aged ; *Virome/genetics ; *Mexican Americans ; *Fatty Liver/genetics ; Cross-Sectional Studies ; Adult ; Diabetes Mellitus ; Feces/microbiology/virology ; Aged ; }, abstract = {Mexican Americans are disproportionally affected by metabolic dysfunction-associated steatotic liver disease (MASLD), which often co-occurs with diabetes. Despite extensive evidence on the causative role of the gut microbiome in MASLD, studies determining the involvement of the gut phageome are scarce. In this cross-sectional study, we characterized the gut phageome in Mexican Americans of South Texas by stool shotgun metagenomic sequencing of 340 subjects, concurrently screened for liver steatosis by transient elastography. Inter-individual variations in the phageome were associated with gender, country of birth, diabetes, and liver steatosis. The phage signatures for diabetes and liver steatosis were subsequently determined. Enrichment of Inoviridae was associated with both diabetes and liver steatosis. Diabetes was further associated with the enrichment of predominantly temperate Escherichia phages, some of which possessed virulence factors. Liver steatosis was associated with the depletion of Lactococcus phages r1t and BK5-T, and enrichment of the globally prevalent Crassvirales phages, including members of genus cluster IX (Burzaovirus coli, Burzaovirus faecalis) and VI (Kahnovirus oralis). The Lactococcus phages showed strong correlations and co-occurrence with Lactococcus lactis, while the Crassvirales phages, B. coli, B. faecalis, and UAG-readthrough crAss clade correlated and co-occurred with Prevotella copri. In conclusion, we identified the gut phageome signatures for two closely linked metabolic diseases with significant global burden. These phage signatures may have utility in risk modeling and disease prevention in this high-risk population, and identification of potential bacterial targets for phage therapy.IMPORTANCEPhages influence human health and disease by shaping the gut bacterial community. Using stool samples from a high-risk Mexican American population, we provide insights into the gut phageome changes associated with diabetes and liver steatosis, two closely linked metabolic diseases with significant global burden. Common to both diseases was an enrichment of Inoviridae, a group of phages that infect bacterial hosts chronically without lysis, allowing them to significantly influence bacterial growth, virulence, motility, biofilm formation, and horizontal gene transfer. Diabetes was additionally associated with the enrichment of Escherichia coli-infecting phages, some of which contained virulence factors. Liver steatosis was additionally associated with the depletion of Lactococcus lactis-infecting phages, and enrichment of Crassvirales phages, a group of virulent phages with high global prevalence and persistence across generations. These phageome signatures may have utility in risk modeling, as well as identify potential bacterial targets for phage therapy.}, }
@article {pmid39166856, year = {2024}, author = {Karpenko, A and Shelenkov, A and Manzeniuk, I and Kulikova, N and Gevorgyan, A and Mikhaylova, Y and Akimkin, V}, title = {Whole genome analysis of multidrug-resistant Escherichia coli isolate collected from drinking water in Armenia revealed the plasmid-borne mcr-1.1-mediated colistin resistance.}, journal = {Microbiology spectrum}, volume = {12}, number = {10}, pages = {e0075124}, pmid = {39166856}, issn = {2165-0497}, support = {075-15-2019-1666//Ministry of Science and Higher Education of the Russian Federation (Minobrnauki of Russia)/ ; }, mesh = {*Escherichia coli/genetics/drug effects/isolation &amp; purification ; *Drug Resistance, Multiple, Bacterial/genetics ; *Plasmids/genetics ; *Colistin/pharmacology ; *Anti-Bacterial Agents/pharmacology ; *Whole Genome Sequencing ; *Escherichia coli Proteins/genetics ; *Drinking Water/microbiology ; Humans ; Armenia ; Microbial Sensitivity Tests ; Genome, Bacterial/genetics ; Escherichia coli Infections/microbiology/veterinary ; Water Microbiology ; }, abstract = {UNLABELLED: The rate of polymyxin-resistant Enterobacteriaceae, as well as human and animal infections caused by them, is increasing worldwide, posing a high epidemiological threat since colistin represents a last-resort antibiotic to treat complicated infections. The study of environmental niches, in particular, aquatic ecosystems in terms of genome analysis of inhabiting antimicrobial-resistant (AMR) microorganisms as reservoirs of acquired resistance determinants (AMR genes), represents a specific concern from a One Health approach. Here, we present a phenotypic AMR analysis and molecular characterization of Escherichia coli isolate found in municipal drinking water after an accident in the water supply system of a residential building in Armenia in 2021. CrieF1144 E. coli isolate was resistant to ampicillin, ampicillin/sulbactam, cefuroxime, ciprofloxacin, levofloxacin, trimethoprim/sulfamethoxazole, colistin, and tigecycline, whereas whole genome sequencing (WGS) revealed blaTEM-1B, tet(A), and a combination of dfrA14 with sul1 resistance determinants, which corresponds well with phenotypic resistance above. Moreover, the multidrug-resistant isolate studied harbored mcr-1.1 gene on a conjugative 251 Kb IncHI2 plasmid, whose structure was determined using hybrid short- and long-reads assembly. CrieF1141_p1 plasmid carried all antimicrobial resistance genes revealed in the isolate and did not harbor any virulence determinants, so it could contribute to the spread of AMR genes in the bacterial population. Two copies of ISApl1 transposase-encoding element, which is likely to mediate mcr-1.1 gene mobilization, were revealed surrounding this gene in a plasmid.<br><br>IMPORTANCE: Evolutionary patterns of Escherichia coli show that they usually develop into highly pathogenic forms by acquiring fitness advantages such as antimicrobial resistance (AMR) and various virulence factors through horizontal gene transfer mediated by mobile elements. This has led to high prevalence of multidrug-resistant (MDR) strains, which highlights the relevancy of enhanced surveillance to monitor and prevent transmission of the MDR bacteria to human and animal populations. However, the limited number of reports regarding the whole genome sequencing (WGS) investigation of MDR E. coli strains isolated from drinking water and harboring mcr genes hampers the adoption of a comprehensive approach to address the relationship between environmental E. coli populations and human and veterinary infections. Our results highlight the relevance of analyzing the environment, especially water, as a part of the surveillance programs to understand the origins and dissemination of antimicrobial resistance within the One Health concept.}, }
@article {pmid39166427, year = {2024}, author = {Wu, JJ and Deng, QW and Qiu, YY and Liu, C and Lin, CF and Ru, YL and Sun, Y and Lai, J and Liu, LX and Shen, XX and Pan, R and Zhao, YP}, title = {Post-transfer adaptation of HGT-acquired genes and contribution to guanine metabolic diversification in land plants.}, journal = {The New phytologist}, volume = {244}, number = {2}, pages = {694-707}, doi = {10.1111/nph.20040}, pmid = {39166427}, issn = {1469-8137}, support = {32071484//National Natural Science Foundation of China/ ; 32200231//National Natural Science Foundation of China/ ; 32371691//National Natural Science Foundation of China/ ; LZ21C030003//Natural Science Foundation of Zhejiang Province/ ; LZ23C020002//Natural Science Foundation of Zhejiang Province/ ; LR23C140001//Natural Science Foundation of Zhejiang Province/ ; 2023000CC0010//Beijing Life Science Academy/ ; 226-2023-00021//Fundamental Research Funds for the Central Universities/ ; 2022YFD1401600//National Key Research and Development Program of China/ ; }, mesh = {*Gene Transfer, Horizontal ; *Embryophyta/genetics ; *Introns/genetics ; *Genes, Plant ; *Guanine/metabolism ; Phylogeny ; Adaptation, Physiological/genetics ; Genome, Plant ; Evolution, Molecular ; }, abstract = {Horizontal gene transfer (HGT) is a major driving force in the evolution of prokaryotic and eukaryotic genomes. Despite recent advances in distribution and ecological importance, the extensive pattern, especially in seed plants, and post-transfer adaptation of HGT-acquired genes in land plants remain elusive. We systematically identified 1150 foreign genes in 522 land plant genomes that were likely acquired via at least 322 distinct transfers from nonplant donors and confirmed that recent HGT events were unevenly distributed between seedless and seed plants. HGT-acquired genes evolved to be more similar to native genes in terms of average intron length due to intron gains, and HGT-acquired genes containing introns exhibited higher expression levels than those lacking introns, suggesting that intron gains may be involved in the post-transfer adaptation of HGT in land plants. Functional validation of bacteria-derived gene GuaD in mosses and gymnosperms revealed that the invasion of foreign genes introduced a novel bypass of guanine degradation and resulted in the loss of native pathway genes in some gymnosperms, eventually shaping three major types of guanine metabolism in land plants. We conclude that HGT has played a critical role in land plant evolution.}, }
@article {pmid39165128, year = {2024}, author = {Trost, K and Knopp, MR and Wimmer, JLE and Tria, FDK and Martin, WF}, title = {A universal and constant rate of gene content change traces pangenome flux to LUCA.}, journal = {FEMS microbiology letters}, volume = {371}, number = {}, pages = {}, pmid = {39165128}, issn = {1574-6968}, support = {101018894/ERC_/European Research Council/International ; 101018894/ERC_/European Research Council/International ; }, mesh = {*Bacteria/genetics/classification ; *Genome, Bacterial ; *Archaea/genetics/classification ; *Evolution, Molecular ; *Genome, Archaeal ; Gene Transfer, Horizontal ; Phylogeny ; }, abstract = {Prokaryotic genomes constantly undergo gene flux via lateral gene transfer, generating a pangenome structure consisting of a conserved core genome surrounded by a more variable accessory genome shell. Over time, flux generates change in genome content. Here, we measure and compare the rate of genome flux for 5655 prokaryotic genomes as a function of amino acid sequence divergence in 36 universally distributed proteins of the informational core (IC). We find a clock of gene content change. The long-term average rate of gene content flux is remarkably constant across all higher prokaryotic taxa sampled, whereby the size of the accessory genome-the proportion of the genome harboring gene content difference for genome pairs-varies across taxa. The proportion of species-level accessory genes per genome, varies from 0% (Chlamydia) to 30%-33% (Alphaproteobacteria, Gammaproteobacteria, and Clostridia). A clock-like rate of gene content change across all prokaryotic taxa sampled suggest that pangenome structure is a general feature of prokaryotic genomes and that it has been in existence since the divergence of bacteria and archaea.}, }
@article {pmid39163267, year = {2024}, author = {Kloub, L and Gosselin, S and Graf, J and Gogarten, JP and Bansal, MS}, title = {Investigating Additive and Replacing Horizontal Gene Transfers Using Phylogenies and Whole Genomes.}, journal = {Genome biology and evolution}, volume = {16}, number = {9}, pages = {}, pmid = {39163267}, issn = {1759-6653}, support = {1616514//National Science Foundation/ ; 8082-32000-006-00-D//United States Department of Agriculture/ ; }, mesh = {*Gene Transfer, Horizontal ; *Phylogeny ; *Genome, Bacterial ; Aeromonas/genetics ; Evolution, Molecular ; }, abstract = {Horizontal gene transfer (HGT) is fundamental to microbial evolution and adaptation. When a gene is horizontally transferred, it may either add itself as a new gene to the recipient genome (possibly displacing nonhomologous genes) or replace an existing homologous gene. Currently, studies do not usually distinguish between "additive" and "replacing" HGTs, and their relative frequencies, integration mechanisms, and specific roles in microbial evolution are poorly understood. In this work, we develop a novel computational framework for large-scale classification of HGTs as either additive or replacing. Our framework leverages recently developed phylogenetic approaches for HGT detection and classifies HGTs inferred between terminal edges based on gene orderings along genomes and phylogenetic relationships between the microbial species under consideration. The resulting method, called DART, is highly customizable and scalable and can classify a large fraction of inferred HGTs with high confidence and statistical support. Our application of DART to a large dataset of thousands of gene families from 103 Aeromonas genomes provides insights into the relative frequencies, functional biases, and integration mechanisms of additive and replacing HGTs. Among other results, we find that (i) the relative frequency of additive HGT increases with increasing phylogenetic distance, (ii) replacing HGT dominates at shorter phylogenetic distances, (iii) additive and replacing HGTs have strikingly different functional profiles, (iv) homologous recombination in flanking regions of a novel gene may be a frequent integration mechanism for additive HGT, and (v) phages and mobile genetic elements likely play an important role in facilitating additive HGT.}, }
@article {pmid39162532, year = {2024}, author = {Ito, Y and Hashimoto, Y and Suzuki, M and Kaneko, N and Yoshida, M and Nakayama, H and Tomita, H}, title = {The emergence of metronidazole-resistant Prevotella bivia harboring nimK gene in Japan.}, journal = {Microbiology spectrum}, volume = {12}, number = {10}, pages = {e0056224}, pmid = {39162532}, issn = {2165-0497}, support = {21KA1004,24KA1005//Japanese Ministry of Health, Labor and Welfare/ ; JP23fk0108604,JP24fk0108665//Japan Agency for Medical Research and Development (AMED)/ ; 22K07067//Ministry of Education, Culture, Sports, Science and Technology (MEXT)/ ; JP23gm1610003,JP23fk0108665,JP23wm0225029//Japan Agency for Medical Research and Development (AMED)/ ; 22K16368//Ministry of Education, Culture, Sports, Science and Technology (MEXT)/ ; }, mesh = {*Prevotella/genetics/drug effects/isolation &amp; purification ; *Metronidazole/pharmacology ; Humans ; Female ; *Anti-Bacterial Agents/pharmacology ; *Microbial Sensitivity Tests ; Japan ; *Drug Resistance, Bacterial/genetics ; *Bacteroidaceae Infections/microbiology ; Whole Genome Sequencing ; Aged ; Bacterial Proteins/genetics/metabolism ; DNA Transposable Elements/genetics ; Genome, Bacterial/genetics ; Interspersed Repetitive Sequences/genetics ; }, abstract = {UNLABELLED: We present the identification and characterization of the complete genome of metronidazole (MTZ)-resistant Prevotella bivia strain TOH-2715 [minimum inhibitory concentration (MIC): 8 mg/L], isolated from the urine of an elderly Japanese woman, as well as details of its mobile genetic elements (MGEs) containing antimicrobial resistance (AMR) genes and its relationship with other bacterial species determined using whole-genome sequencing (WGS) data. TOH-2715 possessed two chromosomes with putative MGEs containing AMR genes. Two AMR-related MGE regions were present in chromosome 2. MGE-region 1 (7,821 bp) included Tn6456, where nimK was located, and MGE-region 2 (58.8 Kbp) included the integrative and conjugative element (ICE), where tet(Q) and ermF were located. The genetic structure of the ICE of TOH-2715 was similar to that of CTnDOT-family transposons, where ermF and tet(Q) are located. A search of public databases revealed that nimK was present in Prevotella spp., including P. bivia, and was partially composed of a Tn6456-like element lacking the efflux transporter gene qacE and the Crp/Fnr family transcriptional regulator gene in some cases. Core ICE gene analysis showed that ICEs similar to that of TOH-2715 were present in Prevotella spp. and Bacteroides spp., suggesting horizontal gene transfer among anaerobes. This is the report of WGS analysis of an MTZ-resistant clinical strain of P. bivia (TOH-2715) with Tn6456 encoding nimK. Other submitted genomes have described the presence of nimK, but none of them have described MTZ resistance. Additionally, we described putative MGE regions containing the AMR gene within the genus Prevotella and among anaerobes, raising concerns about the future spread of nimK among anaerobes.<br><br>IMPORTANCE: Metronidazole (MTZ) is an important antimicrobial agent in anaerobic infections and is widely used in clinical settings. The rate of MTZ resistance in anaerobic bacteria has been increasing in recent years, and the nim gene (nitro-imidazole reductase) is one of the resistance mechanisms. Prevotella bivia is found in humans in the urinary tract and vagina and is known to cause infections in some cases. One of the nim genes, nimK, has recently been discovered in this species of bacteria, but there are no reports of antimicrobial resistance (AMR)-related regions in its whole genome level. In this study, we analyzed the AMR region of nimK-positive P. bivia derived from clinical specimens based on comparisons with other anaerobic genomes. P. bivia was found to be engaged in horizontal gene transfer with other anaerobic bacteria, and the future spread of the nimK gene is a concern.}, }
@article {pmid39162515, year = {2024}, author = {Wang, Z and Hülpüsch, C and Foesel, B and Traidl-Hoffmann, C and Reiger, M and Schloter, M}, title = {Genomic and functional divergence of Staphylococcus aureus strains from atopic dermatitis patients and healthy individuals: insights from global and local scales.}, journal = {Microbiology spectrum}, volume = {12}, number = {10}, pages = {e0057124}, pmid = {39162515}, issn = {2165-0497}, support = {//Helmholtz Munich Internal Funding/ ; }, mesh = {*Dermatitis, Atopic/microbiology/genetics ; *Staphylococcus aureus/genetics/classification/isolation &amp; purification ; Humans ; *Skin/microbiology ; Staphylococcal Infections/microbiology ; Genome, Bacterial/genetics ; Genomics ; Genetic Variation ; Phylogeny ; Gene Transfer, Horizontal ; Bacteriocins/genetics/metabolism ; }, abstract = {Atopic dermatitis (AD) is the most common chronic inflammatory skin disease worldwide and is characterized by a complex interplay with skin microbiota, with Staphylococcus aureus often abnormally more abundant in AD patients than in healthy individuals (HE). S. aureus harbors diverse strains with varied genetic compositions and functionalities, which exhibit differential connections with the severity of AD. However, the differences in S. aureus strains between AD and HE remain unclear, with most variations seen at a specific geographic level, implying spontaneous adaptations rather than systematic distinctions. This study presents genomic and functional differences between these S. aureus strains from AD and HE on both global and local levels. We observed reduced gene content diversity but increased functional variation in the global AD-associated strains. Two additional AD-dominant clusters emerged, with Cluster 1 enriched in transposases and Cluster 2 showcasing genes linked to adaptability and antibiotic resistance. Particularly, robust evidence illustrates that the lantibiotic operon of S. aureus, involved in the biosynthesis of lantibiotics, was acquired via horizontal gene transfer from environmental bacteria. Comparisons of the gene abundance profiles in functional categories also indicate limited zoonotic potential between human and animal isolates. Local analysis mirrored global gene diversity but showed distinct functional variations between AD and HE strains. Overall, this research provides foundational insights into the genomic evolution, adaptability, and antibiotic resistance of S. aureus, with significant implications for clinical microbiology.IMPORTANCEOur study uncovers significant genomic variations in Staphylococcus aureus strains associated with atopic dermatitis. We observed adaptive evolution tailored to the disease microenvironment, characterized by a smaller pan-genome than strains from healthy skin both on the global and local levels. Key functional categories driving strain diversification include "replication and repair" and "transporters," with transposases being pivotal. Interestingly, the local strains predominantly featured metal-related genes, whereas global ones emphasized antimicrobial resistances, signifying scale-dependent diversification nuances. We also pinpointed horizontal gene transfer events, indicating interactions between human-associated and environmental bacteria. These insights expand our comprehension of S. aureus's genetic adaptation in atopic dermatitis, yielding valuable implications for clinical approaches.}, }
@article {pmid39159726, year = {2024}, author = {Zhang, Y and Wang, N and Wan, J and Jousset, A and Jiang, G and Wang, X and Wei, Z and Xu, Y and Shen, Q}, title = {Exploring the antibiotic resistance genes removal dynamics in chicken manure by composting.}, journal = {Bioresource technology}, volume = {410}, number = {}, pages = {131309}, doi = {10.1016/j.biortech.2024.131309}, pmid = {39159726}, issn = {1873-2976}, mesh = {Animals ; *Manure/microbiology ; *Chickens ; *Composting ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Bacteria/genetics/drug effects ; Microbiota/drug effects ; Gene Transfer, Horizontal ; }, abstract = {Prolonged antibiotic usage in livestock farming leads to the accumulation of antibiotic resistance genes in animal manure. Composting has been shown as an effective way of removing antibiotic resistance from manures, but the specific mechanisms remain unclear. This study used time-series sampling and metagenomics to analyse the resistome types and their bacterial hosts in chicken manures. Composting significantly altered the physicochemical properties and microbiome composition, reduced antibiotic resistance genes by 65.71 %, mobile genetic elements by 68.15 % and horizontal gene transfer frequency. Source tracking revealed that Firmicutes, Actinobacteria, and Proteobacteria are the major bacterial hosts involved in the resistome and gene transfer events. Composting reduces the resistome risk by targeting pathogens such as Staphylococcus aureus. Structural equation modelling confirmed that composting reduces resistome risk by changing pH and pathogen abundance. This study demonstrates that composting is an effective strategy for mitigating resistome risk in chicken manure, thereby supporting the One Health initiative.}, }
@article {pmid39158311, year = {2024}, author = {Liu, H and Zheng, L and Fan, H and Pang, J}, title = {Genomic analysis of antibiotic resistance genes and mobile genetic elements in eight strains of nontyphoid Salmonella.}, journal = {mSystems}, volume = {9}, number = {9}, pages = {e0058624}, pmid = {39158311}, issn = {2379-5077}, support = {2022-JSYZ-13//The Second Phase of Jinshan Medical Personnel Training Program/ ; KFQM-27//Rehabilitation Medicine Talent Leading Program/ ; }, mesh = {Humans ; *Salmonella/genetics/drug effects/isolation &amp; purification ; *Interspersed Repetitive Sequences/genetics ; *Salmonella Infections/microbiology/epidemiology ; Anti-Bacterial Agents/pharmacology ; China/epidemiology ; Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; Gene Transfer, Horizontal ; Genome, Bacterial/genetics ; Plasmids/genetics ; Genomics ; Feces/microbiology ; }, abstract = {UNLABELLED: Nontyphoidal Salmonella (NTS) is the main etiological agent of human nontyphoidal salmonellosis. The aim of this study was to analyze the epidemiological characteristics and horizontal transfer mechanisms of antimicrobial resistance (AMR) genes from eight strains of NTS detected in Zhenjiang City, Jiangsu Province, China. Fecal samples from outpatients with food-borne diarrhea were collected in 2022. The NTS isolates were identified, and their susceptibility was tested with the Vitek 2 Compact system. The genomes of the NTS isolates were sequenced with the Illumina NovaSeq platform and Oxford Nanopore Technologies platform. The AMR genes and mobile genetic elements (MGEs) were predicted with the relevant open access resources. Eight strains of NTS were isolated from 153 specimens, and Salmonella Typhimurium ST19 was the most prevalent serotype. The AMR gene with the highest detection rate was AAC(6')-Iaa (10.5%) followed by TEM-1 (7.9%), sul2 (6.6%), and tet(A) (5.3%). Eleven MGEs carrying 34 AMR genes were identified on the chromosomes of 3 of the 8 NTS, including 3 resistance islands, 6 composite transposons (Tns), and 2 integrons. Eighteen plasmids carrying 40 AMR genes were detected in the 8 NTS strains, including 6 mobilizable plasmids, 3 conjugative plasmids, and 9 nontransferable plasmids, 7 of which carried 10 composite Tns and 3 integrons. This study provided a theoretical basis, from a genetic perspective, for the prevention and control of NTS resistance in Zhenjiang City.<br><br>IMPORTANCE: Human nontyphoidal salmonellosis is one of the common causes of bacterial food-borne illnesses, with significant social and economic impacts, especially those caused by invasive multidrug-resistant nontyphoidal Salmonella, which entails high morbidity and mortality. Antimicrobial resistance is mainly mediated by drug resistance genes, and mobile genetic elements play key roles in the capture, accumulation, and dissemination of antimicrobial resistance genes. Therefore, it is necessary to study the epidemiological characteristics and horizontal transfer mechanisms of antimicrobial resistance genes of nontyphoidal Salmonella to prevent the spread of multidrug-resistant nontyphoidal Salmonella.}, }
@article {pmid39158272, year = {2024}, author = {Upreti, C and Kumar, P and Durso, LM and Palmer, KL}, title = {CRISPR-Cas inhibits plasmid transfer and immunizes bacteria against antibiotic resistance acquisition in manure.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {9}, pages = {e0087624}, pmid = {39158272}, issn = {1098-5336}, support = {R01 AI116610/AI/NIAID NIH HHS/United States ; 58-3042-8-012//U.S. Department of Agriculture (USDA)/ ; R01AI116610//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; }, mesh = {*Plasmids/genetics ; *Enterococcus faecalis/genetics/drug effects ; *CRISPR-Cas Systems ; Animals ; *Manure/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; *Gene Transfer, Horizontal ; Humans ; Swine ; Cattle ; }, abstract = {The horizontal transfer of antibiotic resistance genes among bacteria is a pressing global issue. The bacterial defense system clustered regularly interspaced short palindromic repeats (CRISPR)-Cas acts as a barrier to the spread of antibiotic resistance plasmids, and CRISPR-Cas-based antimicrobials can be effective to selectively deplete antibiotic-resistant bacteria. While significant surveillance efforts monitor the spread of antibiotic-resistant bacteria in the clinical context, a major, often overlooked aspect of the issue is resistance emergence in agriculture. Farm animals are commonly treated with antibiotics, and antibiotic resistance in agriculture is on the rise. Yet, CRISPR-Cas efficacy has not been investigated in this setting. Here, we evaluate the prevalence of CRISPR-Cas in agricultural Enterococcus faecalis strains and its antiplasmid efficacy in an agricultural niche: manure. Analyzing 1,986 E. faecalis genomes from human and animal hosts, we show that the prevalence of CRISPR-Cas subtypes is similar between clinical and agricultural E. faecalis strains. Using plasmid conjugation assays, we found that CRISPR-Cas is a significant barrier against resistance plasmid transfer in manure. Finally, we used a CRISPR-based antimicrobial approach to cure resistant E. faecalis of erythromycin resistance, but this was limited by delivery efficiency of the CRISPR antimicrobial in manure. However, immunization of bacteria against resistance gene acquisition in manure was highly effective. Together, our results show that E. faecalis CRISPR-Cas is prevalent and effective in an agricultural setting and has the potential to be utilized for depleting antibiotic-resistant populations. Our work has broad implications for tackling antibiotic resistance in the increasingly relevant agricultural setting, in line with a One Health approach.IMPORTANCEAntibiotic resistance is a growing global health crisis in human and veterinary medicine. Previous work has shown technologies based on CRISPR-Cas-a bacterial defense system-to be effective in tackling antibiotic resistance. Here we test if CRISPR-Cas is present and effective in agricultural niches, specifically in the ubiquitously present bacterium, Enterococcus faecalis. We show that CRISPR-Cas is both prevalent and functional in manure and has the potential to be used to specifically kill bacteria carrying antibiotic resistance genes. This study demonstrates the utility of CRISPR-Cas-based strategies for control of antibiotic resistance in agricultural settings.}, }
@article {pmid39158107, year = {2024}, author = {Ming, Y and Abdullah Al, M and Zhang, D and Zhu, W and Liu, H and Cai, L and Yu, X and Wu, K and Niu, M and Zeng, Q and He, Z and Yan, Q}, title = {Insights into the evolutionary and ecological adaption strategies of nirS- and nirK-type denitrifying communities.}, journal = {Molecular ecology}, volume = {33}, number = {18}, pages = {e17507}, doi = {10.1111/mec.17507}, pmid = {39158107}, issn = {1365-294X}, support = {SML2020SP004//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2023SP237//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2021SP203//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2023SP205//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; 42377111//National Natural Science Foundation of China/ ; //Ocean Negative Carbon Emissions (ONCE) Program/ ; }, mesh = {*Denitrification/genetics ; *Nitrite Reductases/genetics ; China ; *Phylogeny ; *Metagenome/genetics ; Lakes/microbiology ; Bioreactors/microbiology ; Gene Transfer, Horizontal ; Microbiota/genetics ; Metagenomics ; Geologic Sediments/microbiology ; Bacteria/genetics/classification/metabolism ; Nitrogen/metabolism ; Adaptation, Physiological/genetics ; }, abstract = {Denitrification is a crucial process in the global nitrogen cycle, in which two functionally equivalent genes, nirS and nirK, catalyse the critical reaction and are usually used as marker genes. The nirK gene can function independently, whereas nirS requires additional genes to encode nitrite reductase and is more sensitive to environmental factors than nirK. However, the ecological differentiation mechanisms of those denitrifying microbial communities and their adaptation strategies to environmental stresses remain unclear. Here, we conducted metagenomic analysis for sediments and bioreactor samples from Lake Donghu, China. We found that nirS-type denitrifying communities had a significantly lower horizontal gene transfer frequency than that of nirK-type denitrifying communities, and nirS gene phylogeny was more congruent with taxonomy than that of nirK gene. Metabolic reconstruction of metagenome-assembled genomes further revealed that nirS-type denitrifying communities have robust metabolic systems for energy conservation, enabling them to survive under environmental stresses. Nevertheless, nirK-type denitrifying communities seemed to adapt to oxygen-limited environments with the ability to utilize various carbon and nitrogen compounds. Thus, this study provides novel insights into the ecological differentiation mechanism of nirS and nirK-type denitrifying communities, as well as the regulation of the global nitrogen cycle and greenhouse gas emissions.}, }
@article {pmid39153565, year = {2024}, author = {Yang, C and Yan, S and Zhang, B and Yao, X and Mo, J and Rehman, F and Guo, J}, title = {Spatiotemporal distribution of the planktonic microbiome and antibiotic resistance genes in a typical urban river contaminated by macrolide antibiotics.}, journal = {Environmental research}, volume = {262}, number = {Pt 1}, pages = {119808}, doi = {10.1016/j.envres.2024.119808}, pmid = {39153565}, issn = {1096-0953}, mesh = {*Rivers/microbiology/chemistry ; *Microbiota/drug effects ; *Macrolides/analysis ; *Anti-Bacterial Agents/pharmacology/analysis ; *Plankton/drug effects/genetics ; *Drug Resistance, Microbial/genetics ; *Water Pollutants, Chemical/analysis ; Environmental Monitoring ; Genes, Bacterial ; Bacteria/genetics/drug effects/classification ; }, abstract = {The widespread application of macrolide antibiotics has caused antibiotic resistance pollution, threatening the river ecological health. In this study, five macrolide antibiotics (azithromycin, clarithromycin, roxithromycin, erythromycin, and anhydro erythromycin A) were monitored in the Zao River across three hydrological periods (April, July, and December). Simultaneously, the changes in antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and planktonic bacterial communities were determined using metagenomic sequencing. A clear pollution gradient was observed for azithromycin and roxithromycin, with the concentrations in the dry season surpassing those in other seasons. The highest concentration was observed for azithromycin (1.36 μg/L). The abundance of MLS resistance genes increased along the Zao River during the dry season, whereas the opposite trend was obtained during the wet season. A significant correlation between the levels of MLS resistance genes and macrolide antibiotics was identified during the dry season. Notably, compared with the reference site, the abundance of transposase in the effluent from wastewater treatment plants (WWTPs) was significantly elevated in both dry and wet seasons, whereas the abundance of insertion sequences (IS) and plasmids declined during the dry season. The exposure to wastewater containing macrolide antibiotics altered the diversity of planktonic bacterial communities. The bacterial host for ARGs appeared to be Pseudomonas, primarily associated with multidrug subtypes. Moreover, the ARG subtypes were highly correlated with MGEs (transposase and istA). The partial least-squares path model (PLS-PM) demonstrated a positive correlation between the abundance of MGEs and ARGs, indicating the significance of horizontal gene transfer (HGT) in the dissemination of ARGs within the Zao River. Environmental variables, such as TN and NO3[-]-N, were significantly correlated with the abundance of MGEs, ARGs, and bacteria. Collectively, our findings could provide insights into the shift patterns of the microbiome and ARGs across the contamination gradient of AZI and ROX in the river.}, }
@article {pmid39153075, year = {2024}, author = {Panickar, A and Manoharan, A and Anbarasu, A and Ramaiah, S}, title = {Respiratory tract infections: an update on the complexity of bacterial diversity, therapeutic interventions and breakthroughs.}, journal = {Archives of microbiology}, volume = {206}, number = {9}, pages = {382}, pmid = {39153075}, issn = {1432-072X}, support = {IRIS ID: 2021-11889//Indian Council of Medical Research/ ; }, mesh = {*Respiratory Tract Infections/microbiology/drug therapy ; Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria/genetics/drug effects/classification ; Drug Resistance, Bacterial ; Bacterial Infections/microbiology/drug therapy ; Virulence ; }, abstract = {Respiratory tract infections (RTIs) have a significant impact on global health, especially among children and the elderly. The key bacterial pathogens Streptococcus pneumoniae, Haemophilus influenzae, Klebsiella pneumoniae, Staphylococcus aureus and non-fermenting Gram Negative bacteria such as Acinetobacter baumannii and Pseudomonas aeruginosa are most commonly associated with RTIs. These bacterial pathogens have evolved a diverse array of resistance mechanisms through horizontal gene transfer, often mediated by mobile genetic elements and environmental acquisition. Treatment failures are primarily due to antimicrobial resistance and inadequate bacterial engagement, which necessitates the development of alternative treatment strategies. To overcome this, our review mainly focuses on different virulence mechanisms and their resulting pathogenicity, highlighting different therapeutic interventions to combat resistance. To prevent the antimicrobial resistance crisis, we also focused on leveraging the application of artificial intelligence and machine learning to manage RTIs. Integrative approaches combining mechanistic insights are crucial for addressing the global challenge of antimicrobial resistance in respiratory infections.}, }
@article {pmid39149034, year = {2024}, author = {Kadkhoda, H and Gholizadeh, P and Samadi Kafil, H and Ghotaslou, R and Pirzadeh, T and Ahangarzadeh Rezaee, M and Nabizadeh, E and Feizi, H and Aghazadeh, M}, title = {Role of CRISPR-Cas systems and anti-CRISPR proteins in bacterial antibiotic resistance.}, journal = {Heliyon}, volume = {10}, number = {14}, pages = {e34692}, pmid = {39149034}, issn = {2405-8440}, abstract = {The emergence and development of antibiotic resistance in bacteria is a serious threat to global public health. Antibiotic resistance genes (ARGs) are often located on mobile genetic elements (MGEs). They can be transferred among bacteria by horizontal gene transfer (HGT), leading to the spread of drug-resistant strains and antibiotic treatment failure. CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated genes) is one of the many strategies bacteria have developed under long-term selection pressure to restrict the HGT. CRISPR-Cas systems exist in about half of bacterial genomes and play a significant role in limiting the spread of antibiotic resistance. On the other hand, bacteriophages and other MGEs encode a wide range of anti-CRISPR proteins (Acrs) to counteract the immunity of the CRISPR-Cas system. The Acrs could decrease the CRISPR-Cas system's activity against phages and facilitate the acquisition of ARGs and virulence traits for bacteria. This review aimed to assess the relationship between the CRISPR-Cas systems and Acrs with bacterial antibiotic resistance. We also highlighted the CRISPR technology and Acrs to control and prevent antibacterial resistance. The CRISPR-Cas system can target nucleic acid sequences with high accuracy and reliability; therefore, it has become a novel gene editing and gene therapy tool to prevent the spread of antibiotic resistance. CRISPR-based approaches may pave the way for developing smart antibiotics, which could eliminate multidrug-resistant (MDR) bacteria and distinguish between pathogenic and beneficial microorganisms. Additionally, the engineered anti-CRISPR gene-containing phages in combination with antibiotics could be used as a cutting-edge treatment approach to reduce antibiotic resistance.}, }
@article {pmid39148687, year = {2024}, author = {Santos, AJDC and Dias, RS and da Silva, CHM and Vidigal, PMP and de Sousa, MP and da Silva, CC and de Paula, SO}, title = {Genomic analysis of Oceanotoga teriensis strain UFV_LIMV02, a multidrug-resistant thermophilic bacterium isolated from an offshore oil reservoir.}, journal = {Access microbiology}, volume = {6}, number = {8}, pages = {}, pmid = {39148687}, issn = {2516-8290}, abstract = {Bacteria of the species Oceanotoga teriensis belong to the family Petrotogaceae, are Gram-negative bacilli, are moderately thermophilic and are included in the group of thiosulfate-reducing bacteria, being capable of significantly accelerating corrosion in metallic structures. However, no in-depth study on the genome, antibiotic resistance and mobile elements has been carried out so far. In this work, the isolation, phenotypic and genotypic characterization of the multi-resistant O. teriensis UFV_LIMV02 strain was carried out, from water samples from an offshore oil extraction platform in Rio de Janeiro (Brazil). We determined that the isolate has a genome of 2 812 778 bp in size, with 26 % GC content, organized into 34 contigs. Genomic annotation using Rapid Annotation using Subsystem Technology revealed the presence of genes related to resistance to antibiotics and heavy metals. By evaluating the antimicrobial resistance of the isolate using the disc diffusion technique, resistance was verified for the classes of antibiotics, beta-lactams, fluoroquinolones, aminoglycosides, sulfonamides, lincosamides and rifamycins, a total of 14 antibiotics. The search for genomic islands, prophages and defence systems against phage infection revealed the presence of five genomic islands in its genome, containing genes related to resistance to heavy metals and antibiotics, most of which are efflux pumps and several transposases. No prophage was found in its genome; however, nine different defence systems against phage infection were detected. When analysing the clustered regularly interspaced short palindromic repeat (CRISPR) systems, four CRISPR arrays, classified as types I-B and III-B, with 272 spacers, can provide the strain with immunity to different mobile genetic elements and bacteriophage infection. The results found in this study show that the isolate UFV_LIVM02 is an environmental bacterium, resistant to different classes of antibiotics, and that the proteins encoded by the predicted genomic islands may be associated with the development of greater resistance to antibiotics and heavy metals. They provide evidence that environmental bacteria found in offshore oil exploration residues may pose a risk for the spread of antibiotic resistance genes. More comprehensive studies on the microbial community present in oil waste are needed to assess the risks of horizontal gene transfer.}, }
@article {pmid39147525, year = {2024}, author = {Wu, Q and Li, W and Kwok, LY and Lv, H and Sun, J and Sun, Z}, title = {Regional variation and adaptive evolution in Bifidobacterium pseudocatenulatum: Insights into genomic and functional diversity in human gut.}, journal = {Food research international (Ottawa, Ont.)}, volume = {192}, number = {}, pages = {114840}, doi = {10.1016/j.foodres.2024.114840}, pmid = {39147525}, issn = {1873-7145}, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Phylogeny ; *Genome, Bacterial ; *Bifidobacterium pseudocatenulatum/genetics/metabolism ; Genetic Variation ; Genomics ; Diet ; }, abstract = {Bifidobacterium pseudocatenulatum is a prevalent gut microbe in humans of all ages and plays a crucial role in host health. However, its adaptive evolutionary characteristics remain poorly understood. This study analyzed the genome of 247 B. pseudocatenulatum isolates from Chinese, Vietnamese, Japanese and other region populations using population genomics and functional genomics. Our findings revealed high genetic heterogeneity and regional clustering within B. pseudocatenulatum isolates. Significant differences were observed in genome characteristics, phylogeny, and functional genes. Specifically, Chinese and Vietnamese isolates exhibited a higher abundance of genes involved in the metabolism of plant-derived carbohydrates (GH13, GH43, and GH5 enzyme families), aligning with the predominantly vegetable-, wheat- and fruit-based diets of these populations. Additionally, we found widespread transmission of antibiotic resistance genes (tetO and tetW) through mobile genetic elements, such as genomic islands (GIs), resulting in substantial intra-regional differences. Our findings highlight distinct adaptive evolution in B. pseudocatenulatum driven by gene specialization, possibly in response to regional variations in diet and lifestyle. This study sheds light on bifidobacteria colonization mechanisms in the host gut. IMPORTANCE: Gut microbiota, as a key link in the gut-brain axis, helps to maintain the health of the organism, among which, Bifidobacterium pseudocatenulatum (B. pseudocatenulatum) is an important constituent member of the gut microbiota, which plays an important role in maintaining the balance of gut microbiota. The probiotic properties of B. pseudocatenulatum have been widely elaborated, and in order to excavate its evolutionary features at the genomic level, here we focused on the genetic background and evolutionary mechanism of the B. pseudocatenulatum genomes isolated from the intestinal tracts of different populations. Ultimately, based on the phylogenetic tree, we found that B. pseudocatenulatum has high genetic diversity and regional clustering phenomenon, in which plant-derived carbohydrate metabolism genes (GH13, GH43, GH5) showed significant regional differences, and this genetic differentiation drove the adaptive evolution, which likely shaped by diet and lifestyle.}, }
@article {pmid39144201, year = {2024}, author = {Pramanik, S and Sil, AK}, title = {Anti-foam cell activity of metabolites of a bacterium isolated from yogurt.}, journal = {Food science and biotechnology}, volume = {33}, number = {11}, pages = {2597-2610}, pmid = {39144201}, issn = {2092-6456}, abstract = {UNLABELLED: Existing literature documents the beneficial effects of probiotics against atherosclerosis, a major cause of human death. However, it suffers from a serious limitation due to horizontal gene transfer. Therefore, currently, efforts are targeted to examine the beneficial effects of metabolites obtained from probiotics. In this context, the current study isolated a bacterium from yogurt and investigated the effect of its metabolites on foam cell formation, a key event for developing atherosclerosis. Results showed that the cell-free conditioned medium (CM) of this isolate and di-chloro methane extract of CM (CME) not only prevented the formation but also reduced the level of preformed foam cells. To understand the mechanism, the GC-MS study revealed the presence of compounds known to exert anti-atherogenic activities like anti-oxidant, anti-NF-κB, and lipolytic activities. Consistently, CME exhibited substantial anti-oxidant and anti-NF-κB activity. In conclusion, metabolites of this bacterium have anti-atherogenic activities and thus have therapeutic potential.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10068-023-01515-7.}, }
@article {pmid39141729, year = {2024}, author = {Lai, S and Wang, H and Bork, P and Chen, WH and Zhao, XM}, title = {Long-read sequencing reveals extensive gut phageome structural variations driven by genetic exchange with bacterial hosts.}, journal = {Science advances}, volume = {10}, number = {33}, pages = {eadn3316}, pmid = {39141729}, issn = {2375-2548}, mesh = {*Bacteriophages/genetics ; Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteria/virology/genetics ; *Gene Transfer, Horizontal ; Metagenomics/methods ; Genetic Variation ; Virome/genetics ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; }, abstract = {Genetic variations are instrumental for unraveling phage evolution and deciphering their functional implications. Here, we explore the underlying fine-scale genetic variations in the gut phageome, especially structural variations (SVs). By using virome-enriched long-read metagenomic sequencing across 91 individuals, we identified a total of 14,438 nonredundant phage SVs and revealed their prevalence within the human gut phageome. These SVs are mainly enriched in genes involved in recombination, DNA methylation, and antibiotic resistance. Notably, a substantial fraction of phage SV sequences share close homology with bacterial fragments, with most SVs enriched for horizontal gene transfer (HGT) mechanism. Further investigations showed that these SV sequences were genetic exchanged between specific phage-bacteria pairs, particularly between phages and their respective bacterial hosts. Temperate phages exhibit a higher frequency of genetic exchange with bacterial chromosomes and then virulent phages. Collectively, our findings provide insights into the genetic landscape of the human gut phageome.}, }
@article {pmid39141706, year = {2024}, author = {Souque, C and González Ojeda, I and Baym, M}, title = {From Petri Dishes to Patients to Populations: Scales and Evolutionary Mechanisms Driving Antibiotic Resistance.}, journal = {Annual review of microbiology}, volume = {78}, number = {1}, pages = {361-382}, doi = {10.1146/annurev-micro-041522-102707}, pmid = {39141706}, issn = {1545-3251}, support = {T32 GM008313/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects ; *Evolution, Molecular ; *Drug Resistance, Bacterial/genetics ; Bacterial Infections/microbiology/drug therapy ; }, abstract = {Tackling the challenge created by antibiotic resistance requires understanding the mechanisms behind its evolution. Like any evolutionary process, the evolution of antimicrobial resistance (AMR) is driven by the underlying variation in a bacterial population and the selective pressures acting upon it. Importantly, both selection and variation will depend on the scale at which resistance evolution is considered (from evolution within a single patient to the host population level). While laboratory experiments have generated fundamental insights into the mechanisms underlying antibiotic resistance evolution, the technological advances in whole genome sequencing now allow us to probe antibiotic resistance evolution beyond the lab and directly record it in individual patients and host populations. Here we review the evolutionary forces driving antibiotic resistance at each of these scales, highlight gaps in our current understanding of AMR evolution, and discuss future steps toward evolution-guided interventions.}, }
@article {pmid39141562, year = {2024}, author = {Karan, J and Mandal, S and Khan, G and Arya, H and Samhita, L}, title = {Enhanced Extraction of Low-Molecular Weight DNA from Wastewater for Comprehensive Assessment of Antimicrobial Resistance.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {209}, pages = {}, doi = {10.3791/66899}, pmid = {39141562}, issn = {1940-087X}, mesh = {*Wastewater/microbiology/chemistry ; Polyethylene Glycols/chemistry ; Molecular Weight ; DNA, Bacterial/genetics/isolation &amp; purification ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; }, abstract = {Environmental surveillance is recognized as an important tool for assessing public health in the post-pandemic era. Water, in particular wastewater, has emerged as the source of choice to sample pathogen burdens in the environment. Wastewater from open drains and community water treatment plants is a reservoir of both pathogens and antimicrobial resistance (AMR) genes, and frequently comes in contact with humans. While there are many methods of tracking AMR from water, isolating good-quality DNA at high yields from heterogeneous samples remains a challenge. To compensate, sample volumes often need to be high, creating practical constraints. Additionally, environmental DNA is frequently fragmented, and the sources of AMR (plasmids, phages, linear DNA) consist of low-molecular-weight DNA. Yet, few extraction processes have focused on methods for high-yield extraction of linear and low-molecular-weight DNA. Here, a simple method for high-yield linear DNA extraction from small volumes of wastewater using the precipitation properties of polyethylene glycol (PEG) is reported. This study makes a case for increasing overall DNA yields from water samples collected for metagenomic analyses by enriching the proportion of linear DNA. In addition, enhancing low-molecular-weight DNA overcomes the current problem of under-sampling environmental AMR due to a focus on high-molecular-weight and intracellular DNA. This method is expected to be particularly useful when extracellular DNA exists but at low concentrations, such as with effluents from treatment plants. It should also enhance the environmental sampling of AMR gene fragments that spread through horizontal gene transfer.}, }
@article {pmid39139006, year = {2024}, author = {Rao, Y and Wang, Y and Zhang, H and Wang, Y and He, Q and Yuan, X and Guo, J and Chen, H}, title = {A Strategy of Killing Two Birds With One Stone for Blocking Drug Resistance Spread With Engineered Bdellovibrio bacteriovorus.}, journal = {Advanced materials (Deerfield Beach, Fla.)}, volume = {36}, number = {41}, pages = {e2406910}, doi = {10.1002/adma.202406910}, pmid = {39139006}, issn = {1521-4095}, support = {21935008//National Natural Science Foundation of China/ ; SKJY2021042//Livelihood Technology Project of Suzhou/ ; 23KJA150008//Jiangsu Province Higher Education Natural Science Research Major Project/ ; //Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; }, mesh = {*Bdellovibrio bacteriovorus ; *Anti-Bacterial Agents/pharmacology/chemistry ; Pseudomonas aeruginosa/drug effects ; Biofilms/drug effects ; Cerium/chemistry/pharmacology ; Drug Resistance, Bacterial/drug effects ; Animals ; Kanamycin/pharmacology ; Dopamine/metabolism ; Polymers/chemistry/pharmacology ; Plasmids/metabolism/genetics ; DNA Cleavage/drug effects ; Indoles ; }, abstract = {Drug-resistant pathogens significantly threaten human health and life. Simply killing drug-resistant pathogens cannot effectively eliminate their threat since the drug-resistant genes (DRGs) released from dead drug-resistant pathogens are difficult to eliminate and can further spread via horizontal gene transfer, leading to the spread of drug resistance. The development of antibacterial materials with sterilization and DRGs cleavage activities is highly crucial. Herein, a living system, Ce-PEA@Bdello, is fabricated with bacterial killing and DRGs cleavage activities for blocking bacterial drug resistance dissemination by engineered Bdellovibrio bacteriovorus (Bdello). Ce-PEA@Bdello is obtained by engineering Bdello with dopamine and a multinuclear cerium (IV) complex. Ce-PEA@Bdello can penetrate and eliminate kanamycin-resistant P. aeruginosa (Kan[R]) biofilms via the synergistic effect of predatory Bdello and photothermal polydopamine under near-infrared light. Additionally, the DNase-mimicking ability of Ce-PEA@Bdello endows it with genome and plasmid DNA cleavage ability. An in vivo study reveals that Ce-PEA@Bdello can eliminate P. aeruginosa (Kan[R]) and cleave DRGs in scald/burn infected wounds to block the spread of drug resistance and accelerate wound healing. This bioactive system constructed from natural living materials offers a promising means for blocking the spread of drug resistance.}, }
@article {pmid39138294, year = {2024}, author = {York, A}, title = {Targeting the spread of antimicrobial resistance plasmids.}, journal = {Nature reviews. Microbiology}, volume = {22}, number = {10}, pages = {595}, pmid = {39138294}, issn = {1740-1534}, mesh = {*Plasmids/genetics ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Bacteria/drug effects/genetics ; Gene Transfer, Horizontal ; }, }
@article {pmid39135654, year = {2024}, author = {Winter, M and Vos, M and Buckling, A and Johnsen, PJ and Harms, K}, title = {Effect of chemotherapeutic agents on natural transformation frequency in Acinetobacter baylyi.}, journal = {Access microbiology}, volume = {6}, number = {7}, pages = {}, pmid = {39135654}, issn = {2516-8290}, abstract = {Natural transformation is the ability of a bacterial cell to take up extracellular DNA which is subsequently available for recombination into the chromosome (or maintenance as an extrachromosomal element). Like other mechanisms of horizontal gene transfer, natural transformation is a significant driver for the dissemination of antimicrobial resistance. Recent studies have shown that many pharmaceutical compounds such as antidepressants and anti-inflammatory drugs can upregulate transformation frequency in the model species Acinetobacter baylyi. Chemotherapeutic compounds have been shown to increase the abundance of antimicrobial resistance genes and increase colonization rates of potentially pathogenic bacteria in patient gastrointestinal tracts, indicating an increased risk of infection and providing a pool of pathogenicity or resistance genes for transformable commensal bacteria. We here test for the effect of six cancer chemotherapeutic compounds on A. baylyi natural transformation frequency, finding two compounds, docetaxel and daunorubicin, to significantly decrease transformation frequency, and daunorubicin to also decrease growth rate significantly. Enhancing our understanding of the effect of chemotherapeutic compounds on the frequency of natural transformation could aid in preventing the horizontal spread of antimicrobial resistance genes.}, }
@article {pmid39132438, year = {2024}, author = {Liu, H and Fan, S and Zhang, X and Yuan, Y and Zhong, W and Wang, L and Wang, C and Zhou, Z and Zhang, S and Geng, Y and Peng, G and Wang, Y and Zhang, K and Yan, Q and Luo, Y and Shi, K and Zhong, Z}, title = {Antibiotic-resistant characteristics and horizontal gene transfer ability analysis of extended-spectrum β-lactamase-producing Escherichia coli isolated from giant pandas.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1394814}, pmid = {39132438}, issn = {2297-1769}, abstract = {Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (ESBL-EC) is regarded as one of the most important priority pathogens within the One Health interface. However, few studies have investigated the occurrence of ESBL-EC in giant pandas, along with their antibiotic-resistant characteristics and horizontal gene transfer abilities. In this study, we successfully identified 12 ESBL-EC strains (8.33%, 12/144) out of 144 E. coli strains which isolated from giant pandas. We further detected antibiotic resistance genes (ARGs), virulence-associated genes (VAGs) and mobile genetic elements (MGEs) among the 12 ESBL-EC strains, and the results showed that 13 ARGs and 11 VAGs were detected, of which bla CTX-M (100.00%, 12/12, with 5 variants observed) and papA (83.33%, 10/12) were the most prevalent, respectively. And ISEcp1 (66.67%, 8/12) and IS26 (66.67%, 8/12) were the predominant MGEs. Furthermore, horizontal gene transfer ability analysis of the 12 ESBL-EC showed that all bla CTX-M genes could be transferred by conjugative plasmids, indicating high horizontal gene transfer ability. In addition, ARGs of rmtB and sul2, VAGs of papA, fimC and ompT, MGEs of ISEcp1 and IS26 were all found to be co-transferred with bla CTX-M. Phylogenetic analysis clustered these ESBL-EC strains into group B2 (75.00%, 9/12), D (16.67%, 2/12), and B1 (8.33%, 1/12), and 10 sequence types (STs) were identified among 12 ESBL-EC (including ST48, ST127, ST206, ST354, ST648, ST1706, and four new STs). Our present study showed that ESBL-EC strains from captive giant pandas are reservoirs of ARGs, VAGs and MGEs that can co-transfer with bla CTX-M via plasmids. Transmissible ESBL-EC strains with high diversity of resistance and virulence elements are a potential threat to humans, animals and surrounding environment.}, }
@article {pmid39128935, year = {2024}, author = {Wang, W and Ge, Q and Wen, J and Zhang, H and Guo, Y and Li, Z and Xu, Y and Ji, D and Chen, C and Guo, L and Xu, M and Shi, C and Fan, G and Xie, C}, title = {Horizontal gene transfer and symbiotic microorganisms regulate the adaptive evolution of intertidal algae, Porphyra sense lato.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {976}, pmid = {39128935}, issn = {2399-3642}, support = {42176117//National Natural Science Foundation of China (National Science Foundation of China)/ ; U21A20265//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32100514//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Gene Transfer, Horizontal ; *Symbiosis/genetics ; *Porphyra/microbiology/genetics ; Adaptation, Physiological/genetics ; Phylogeny ; Biological Evolution ; }, abstract = {Intertidal algae may adapt to environmental challenges by acquiring genes from other organisms and relying on symbiotic microorganisms. Here, we obtained a symbiont-free and chromosome-level genome of Pyropia haitanensis (47.2 Mb), a type of intertidal algae, by using multiple symbiont screening methods. We identified 286 horizontal gene transfer (HGT) genes, 251 of which harbored transposable elements (TEs), reflecting the importance of TEs for facilitating the transfer of genes into P. haitanensis. Notably, the bulked segregant analysis revealed that two HGT genes, sirohydrochlorin ferrochelatase and peptide-methionine (R)-S-oxide reductase, play a significant role in the adaptation of P. haitanensis to heat stress. Besides, we found Pseudomonas, Actinobacteria, and Bacteroidetes are the major taxa among the symbiotic bacteria of P. haitanensis (nearly 50% of the HGT gene donors). Among of them, a heat-tolerant actinobacterial strain (Saccharothrix sp.) was isolated and revealed to be associated with the heat tolerance of P. haitanensis through its regulatory effects on the genes involved in proline synthesis (proC), redox homeostasis (ggt), and protein folding (HSP20). These findings contribute to our understanding of the adaptive evolution of intertidal algae, expanding our knowledge of the HGT genes and symbiotic microorganisms to enhance their resilience and survival in challenging intertidal environments.}, }
@article {pmid39127705, year = {2024}, author = {Park, H and Bulzu, PA and Shabarova, T and Kavagutti, VS and Ghai, R and Kasalický, V and Jezberová, J}, title = {Uncovering the genomic basis of symbiotic interactions and niche adaptations in freshwater picocyanobacteria.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {150}, pmid = {39127705}, issn = {2049-2618}, support = {20&#x2011;12496X//Grantov&#xe1; Agentura Cesk&#xe9; Republiky (GA&#x10c;R)/ ; 20&#x2011;12496X//Grantov&#xe1; Agentura Cesk&#xe9; Republiky (GA&#x10c;R)/ ; 23-05081S//Grantov&#xe1; Agentura Cesk&#xe9; Republiky (GA&#x10c;R)/ ; 19-23261S//Grantov&#xe1; Agentura Cesk&#xe9; Republiky (GA&#x10c;R)/ ; 20&#x2011;12496X//Grantov&#xe1; Agentura Cesk&#xe9; Republiky (GA&#x10c;R)/ ; 19-23261S//Grantov&#xe1; Agentura Cesk&#xe9; Republiky (GA&#x10c;R)/ ; 19-23261S//Grantov&#xe1; Agentura Cesk&#xe9; Republiky (GA&#x10c;R)/ ; }, mesh = {*Symbiosis ; *Fresh Water/microbiology ; *Genome, Bacterial ; *Phylogeny ; *Cyanobacteria/genetics/classification ; Adaptation, Physiological/genetics ; Europe ; Ecosystem ; Gene Transfer, Horizontal ; Genomics ; }, abstract = {BACKGROUND: Picocyanobacteria from the genera Prochlorococcus, Synechococcus, and Cyanobium are the most widespread photosynthetic organisms in aquatic ecosystems. However, their freshwater populations remain poorly explored, due to uneven and insufficient sampling across diverse inland waterbodies.<br><br>RESULTS: In this study, we present 170 high-quality genomes of freshwater picocyanobacteria from non-axenic cultures collected across Central Europe. In addition, we recovered 33 genomes of their potential symbiotic partners affiliated with four genera, Pseudomonas, Mesorhizobium, Acidovorax, and Hydrogenophaga. The genomic basis of symbiotic interactions involved heterotrophs benefiting from picocyanobacteria-derived nutrients while providing detoxification of ROS. The global abundance patterns of picocyanobacteria revealed ecologically significant ecotypes, associated with trophic status, temperature, and pH as key environmental factors. The adaptation of picocyanobacteria in (hyper-)eutrophic waterbodies could be attributed to their colonial lifestyles and CRISPR-Cas systems. The prevailing CRISPR-Cas subtypes in picocyanobacteria were I-G and I-E, which appear to have been acquired through horizontal gene transfer from other bacterial phyla.<br><br>CONCLUSIONS: Our findings provide novel insights into the population diversity, ecology, and evolutionary strategies of the most widespread photoautotrophs within freshwater ecosystems. Video Abstract.}, }
@article {pmid39125965, year = {2024}, author = {Sadowska-Bartosz, I and Bartosz, G}, title = {Antioxidant Defense in the Toughest Animals on the Earth: Its Contribution to the Extreme Resistance of Tardigrades.}, journal = {International journal of molecular sciences}, volume = {25}, number = {15}, pages = {}, pmid = {39125965}, issn = {1422-0067}, mesh = {Animals ; *Tardigrada/metabolism/genetics ; *Antioxidants/metabolism ; Oxidative Stress ; Earth, Planet ; Trehalose/metabolism ; }, abstract = {Tardigrades are unique among animals in their resistance to dehydration, mainly due to anhydrobiosis and tun formation. They are also very resistant to high-energy radiation, low and high temperatures, low and high pressure, and various chemical agents, Interestingly, they are resistant to ionizing radiation both in the hydrated and dehydrated states to a similar extent. They are able to survive in the cosmic space. Apparently, many mechanisms contribute to the resistance of tardigrades to harmful factors, including the presence of trehalose (though not common to all tardigrades), heat shock proteins, late embryogenesis-abundant proteins, tardigrade-unique proteins, DNA repair proteins, proteins directly protecting DNA (Dsup and TDR1), and efficient antioxidant system. Antioxidant enzymes and small-molecular-weight antioxidants are an important element in the tardigrade resistance. The levels and activities of many antioxidant proteins is elevated by anhydrobiosis and UV radiation; one explanation for their induction during dehydration is provided by the theory of "preparation for oxidative stress", which occurs during rehydration. Genes coding for some antioxidant proteins are expanded in tardigrades; some genes (especially those coding for catalases) were hypothesized to be of bacterial origin, acquired by horizontal gene transfer. An interesting antioxidant protein found in tardigrades is the new Mn-dependent peroxidase.}, }
@article {pmid39125866, year = {2024}, author = {Cheng, X and Liu, X and Jordan, KW and Yu, J and Whitworth, RJ and Park, Y and Chen, MS}, title = {Frequent Acquisition of Glycoside Hydrolase Family 32 (GH32) Genes from Bacteria via Horizontal Gene Transfer Drives Adaptation of Invertebrates to Diverse Sources of Food and Living Habitats.}, journal = {International journal of molecular sciences}, volume = {25}, number = {15}, pages = {}, pmid = {39125866}, issn = {1422-0067}, mesh = {*Gene Transfer, Horizontal ; *Glycoside Hydrolases/genetics/metabolism ; Animals ; *Bacteria/genetics/enzymology ; *Phylogeny ; Invertebrates/genetics ; Adaptation, Physiological/genetics ; Ecosystem ; Evolution, Molecular ; }, abstract = {Glycoside hydrolases (GHs, also called glycosidases) catalyze the hydrolysis of glycosidic bonds in polysaccharides. Numerous GH genes have been identified from various organisms and are classified into 188 families, abbreviated GH1 to GH188. Enzymes in the GH32 family hydrolyze fructans, which are present in approximately 15% of flowering plants and are widespread across microorganisms. GH32 genes are rarely found in animals, as fructans are not a typical carbohydrate source utilized in animals. Here, we report the discovery of 242 GH32 genes identified in 84 animal species, ranging from nematodes to crabs. Genetic analyses of these genes indicated that the GH32 genes in various animals were derived from different bacteria via multiple, independent horizontal gene transfer events. The GH32 genes in animals appear functional based on the highly conserved catalytic blades and triads in the active center despite the overall low (35-60%) sequence similarities among the predicted proteins. The acquisition of GH32 genes by animals may have a profound impact on sugar metabolism for the recipient organisms. Our results together with previous reports suggest that the acquired GH32 enzymes may not only serve as digestive enzymes, but also may serve as effectors for manipulating host plants, and as metabolic enzymes in the non-digestive tissues of certain animals. Our results provide a foundation for future studies on the significance of horizontally transferred GH32 genes in animals. The information reported here enriches our knowledge of horizontal gene transfer, GH32 functions, and animal-plant interactions, which may result in practical applications. For example, developing crops via targeted engineering that inhibits GH32 enzymes could aid in the plant's resistance to animal pests.}, }
@article {pmid39125715, year = {2024}, author = {Bucka-Kolendo, J and Kiousi, DE and Dekowska, A and Mikołajczuk-Szczyrba, A and Karadedos, DM and Michael, P and Galanis, A and Sokołowska, B}, title = {Exploration of Alicyclobacillus spp. Genome in Search of Antibiotic Resistance.}, journal = {International journal of molecular sciences}, volume = {25}, number = {15}, pages = {}, pmid = {39125715}, issn = {1422-0067}, mesh = {*Alicyclobacillus/genetics/drug effects ; *Genome, Bacterial ; *Microbial Sensitivity Tests ; *Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Guaiacol/pharmacology/analogs &amp; derivatives ; }, abstract = {The study investigates the antibiotic resistance (AR) profiles and genetic determinants in three strains of guaiacol-producing Alicyclobacillus spp. isolated from orchard soil and pears. Their phenotypic characteristics, such as spore formation; resistance to different factors, including drugs or disinfectants; or production of off-flavor compounds, can affect the taste and aroma of spoiled products. Food and beverages are potential vectors for the transfer of antibiotic resistance genes, which is a growing health concern; thus, microorganisms in food and beverages should not be a potential source of drug resistance to consumers. Whole-genome sequencing (WGS) was utilized to identify antibiotic resistance genes, metabolic pathways, and elements associated with guaiacol and halophenol production. Minimum inhibitory concentration (MIC) testing revealed that all strains were susceptible to eight out of nine tested antibiotics (ampicillin, gentamycin, kanamycin, streptomycin, clindamycin, tetracycline, chloramphenicol, and vancomycin) but exhibited high resistance to erythromycin. Analysis indicated that the erythromycin resistance gene, ribosomal RNA small subunit methyltransferase A (RsmA), was intrinsic and likely acquired through horizontal gene transfer (HGT). The comprehensive genomic analysis provides insights into the molecular mechanisms of antibiotic resistance in Alicyclobacillus spp., highlighting the potential risk of these bacteria as vectors for antibiotic resistance genes in the food chain. This study expands the understanding of the genetic makeup of these spoilage bacteria and their role in antimicrobial resistance dissemination.}, }
@article {pmid39122691, year = {2024}, author = {Williams, SK and Jerlström Hultqvist, J and Eglit, Y and Salas-Leiva, DE and Curtis, B and Orr, RJS and Stairs, CW and Atalay, TN and MacMillan, N and Simpson, AGB and Roger, AJ}, title = {Extreme mitochondrial reduction in a novel group of free-living metamonads.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {6805}, pmid = {39122691}, issn = {2041-1723}, support = {FRN-142349//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Sant&#xe9; du Canada)/ ; }, mesh = {*Mitochondria/metabolism/genetics ; *Phylogeny ; *Proteome/metabolism/genetics ; Transcriptome ; Eukaryota/genetics/metabolism/classification ; Gene Transfer, Horizontal ; Iron-Sulfur Proteins/metabolism/genetics ; }, abstract = {Metamonads are a diverse group of heterotrophic microbial eukaryotes adapted to living in hypoxic environments. All metamonads but one harbour metabolically altered 'mitochondrion-related organelles' (MROs) with reduced functions, however the degree of reduction varies. Here, we generate high-quality draft genomes, transcriptomes, and predicted proteomes for five recently discovered free-living metamonads. Phylogenomic analyses placed these organisms in a group we name the 'BaSk' (Barthelonids+Skoliomonads) clade, a deeply branching sister group to the Fornicata, a phylum that includes parasitic and free-living flagellates. Bioinformatic analyses of gene models shows that these organisms are predicted to have extremely reduced MRO proteomes in comparison to other free-living metamonads. Loss of the mitochondrial iron-sulfur cluster assembly system in some organisms in this group appears to be linked to the acquisition in their common ancestral lineage of a SUF-like minimal system Fe/S cluster pathway by lateral gene transfer. One of the isolates, Skoliomonas litria, appears to have lost all other known MRO pathways. No proteins were confidently assigned to the predicted MRO proteome of this organism suggesting that the organelle has been lost. The extreme mitochondrial reduction observed within this free-living anaerobic protistan clade demonstrates that mitochondrial functions may be completely lost even in free-living organisms.}, }
@article {pmid39121985, year = {2024}, author = {Yan, Y and Lu, H and Liang, X and Xu, T and Yan, S and Yu, Y and Wang, Y}, title = {The virulence plasmid associated with AHPND in shrimp appears to have originated from Vibrio owensii through a process of homologous recombination of parental plasmids and the transposable insertion of two large fragments.}, journal = {Journal of invertebrate pathology}, volume = {206}, number = {}, pages = {108173}, doi = {10.1016/j.jip.2024.108173}, pmid = {39121985}, issn = {1096-0805}, mesh = {*Vibrio/genetics/pathogenicity ; Animals ; *Plasmids/genetics ; Virulence/genetics ; *Penaeidae/microbiology ; *Homologous Recombination ; Vibrio Infections/veterinary/microbiology ; Phylogeny ; DNA Transposable Elements ; }, abstract = {Acute hepatopancreatic necrosis disease (AHPND) is a highly contagious and lethal disease of shrimp caused by Vibrio strains carrying the virulence plasmid (pAHPND) containing the pirAB virulence genes. Through analysis of plasmid sequence similarity, clustering, and phylogeny, a horizontal transfer element similar to IS91 was discovered within the pAHPND plasmid. Additionally, two distinct clades of plasmids related to pAHPND (designated as pAHPND-r1 and pAHPND-r2) were identified, which may serve as potential parental plasmids for pAHPND. The available evidence, including the difference in G+C content between the plasmid and its host, codon usage preference, and plasmid recombination event prediction, suggests that the formation of the pAHPND plasmid in the Vibrio owensii strain was likely due to the synergistic effect of the recombinase RecA and the associated proteins RecBCD on the pAHPND-r1 and pAHPND-r2, resulting in the recombination and formation of the precursor plasmid for pAHPND (pre-pAHPND). The emergence of pAHPND was found to be a result of successive insertions of the horizontal transfer elements of pirAB-Tn903 and IS91-like segment, which led to the deletion of one third of the pre-pAHPND. This plasmid was then able to spread horizontally to other Vibrio strains, contributing to the epidemics of AHPND. These findings shed light on previously unknown mechanisms involved in the emergence of pAHPND and improve our understanding of the disease's spread.}, }
@article {pmid39119206, year = {2024}, author = {Zaer-Anaqz, Z and Khakvar, R and Mohammadi, SA and Bannazadeh Baghi, H and Koolivand, D}, title = {Physicochemical Characterization of Novel Bacteriophages of Pseudomonas syringe from Northwest Iran.}, journal = {PHAGE (New Rochelle, N.Y.)}, volume = {5}, number = {2}, pages = {99-106}, pmid = {39119206}, issn = {2641-6549}, abstract = {Bacterial canker, caused by Pseudomonas syringae, is a devastating disease of stone fruit trees worldwide. The bacterium has a broad host range and a high capacity for adaptation and dissemination, owing to its high mutation rate and horizontal gene transfer. Traditional control methods based on copper compounds and antibiotics have resulted in the development of resistance in the bacterial population. Thus, alternative approaches are needed, such as phage therapy. This study aimed to characterize the physicochemical and biological properties of novel Pseudomonas syringae pv. syringae (Pss)-specific phages isolated from the soils of northwestern Iran. Seventy-five phage isolates were obtained, and their host range was determined against various bacterial pathogens. Five phages exhibiting the highest lytic activity against Pss and a narrow host range were selected for subsequent analysis. The stability of the selected phages was assessed under different conditions such as ultraviolet irradiation, temperature, pH, NaCl concentration, and chloroform exposure. The selected phages demonstrated significant effectiveness in vivo, exerting substantial suppression on the population of Pss. This reduction was observed for both individual phages and when the phages were utilized as a mixture. The findings indicate that phages have the potential to be used as biocontrol agents in agriculture.}, }
@article {pmid39119203, year = {2024}, author = {Delesalle, VA and Ankeriasniemi, RE and Lewis, CM and Mody, JM and Roy, AM and Sarvis, WA and Vo, DD and Walsh, AE and Zappia, RJ}, title = {Introducing Casbah, Kronus, and MmasiCarm, Members of the Mycobacteriophage Subcluster B3.}, journal = {PHAGE (New Rochelle, N.Y.)}, volume = {5}, number = {2}, pages = {84-90}, pmid = {39119203}, issn = {2641-6549}, abstract = {BACKGROUND: As part of a large science education effort, bacteriophages that lyse Mycobacterium smegmatis mc[2]155 continue to be discovered.<br><br>MATERIALS AND METHODS: Phages were isolated from soil samples from urban sites in the Northeastern United States. Their genomes were sequenced, assembled, and bioinformatically compared.<br><br>RESULTS: Three lytic siphoviruses belonging to subcluster B3 with high similarity to each other and other B3 mycobacteriophages were isolated. These phages contain double-stranded DNA genomes (68,754 to 69,495 bp) with high GC content (67.4-67.5%) and 102-104 putative protein coding genes. Notable features include a HicA-like toxin and 33 genes exclusive to subcluster B3. One phage had an intein in its terminase sequence.<br><br>CONCLUSIONS: Genomic analyses of these phages provide insights into genome evolution and horizontal gene transfer (HGT). The networks for HGT are apparently vast and gene specific. Interestingly, a number of genes are found in both B3 and Gordonia DR phages.}, }
@article {pmid39117207, year = {2024}, author = {Erler, T and Droop, F and Lübbert, C and Knobloch, JK and Carlsen, L and Papan, C and Schwanz, T and Zweigner, J and Dengler, J and Hoffmann, M and Mutters, NT and Savin, M}, title = {Analysing carbapenemases in hospital wastewater: Insights from intracellular and extracellular DNA using qPCR and digital PCR.}, journal = {The Science of the total environment}, volume = {950}, number = {}, pages = {175344}, doi = {10.1016/j.scitotenv.2024.175344}, pmid = {39117207}, issn = {1879-1026}, mesh = {*Wastewater/microbiology ; *beta-Lactamases/genetics ; *Real-Time Polymerase Chain Reaction ; *Bacterial Proteins/genetics ; DNA, Bacterial ; Germany ; Environmental Monitoring/methods ; Hospitals ; Polymerase Chain Reaction/methods ; }, abstract = {The widespread dissemination of carbapenem-resistant bacteria in wastewater systems, particularly from clinical sources, poses a significant public health risk. This study assessed the concentrations and distributions of extracellular DNA (exDNA) and intracellular DNA (iDNA) harboring carbapenemase genes in wastewater from six tertiary care hospitals in Germany. We collected a total of 36 samples, comprising six biological replicates from each hospital, and analysed them using quantitative real-time PCR (qPCR) and digital PCR (dPCR). The analysis targeted seven carbapenemase genes: blaNDM, blaKPC, blaIMP, blaVIM, blaOXA-23-like, blaOXA-48-like, and blaOXA-58-like across both DNA fractions. Our results revealed significant variability in the concentrations of exDNA and iDNA across the sampling sites, with iDNA typically present at higher concentrations. Using NanoDrop One spectrophotometry and the Qubit dsDNA kit, exDNA concentrations ranged from 2.7 to 7.7 ng/mL, while Qubit recorded lower values between 1.1 and 4.0 ng/mL. Conversely, iDNA concentrations were markedly higher, spanning from 42.3 to 191.7 ng/mL with NanoDrop and 12.0 to 46.5 ng/mL with Qubit, highlighting the variability between DNA types and quantification methods. Despite its lower concentrations, exDNA comprised up to 18.2 % of total DNA, highlighting its potential role in the horizontal transfer of antimicrobial resistance genes (ARGs). The study detected target ARGs in both DNA fractions at all sites, with notable differences in their concentrations; iDNA consistently exhibited higher levels of ARGs, with the highest concentrations reaching 10.57 ± 0.20 log gene copies per liter (GC/L) for blaVIM in iDNA and 6.96 ± 0.72 log GC/L for blaIMP in exDNA. dPCR demonstrated greater sensitivity than qPCR, especially effective for detecting low-abundance targets like blaOXA-23-like in the exDNA fraction. Additionally, qPCR's susceptibility to inhibition and contamination emphasizes the superior robustness of dPCR. This research highlights the need for improved monitoring and the implementation of advanced treatment technologies to mitigate ARG dissemination in wastewater.}, }
@article {pmid39113256, year = {2024}, author = {Hossain, AKMZ and Chowdhury, AMMA}, title = {Understanding the Evolution and Transmission Dynamics of Antibiotic Resistance Genes: A Comprehensive Review.}, journal = {Journal of basic microbiology}, volume = {64}, number = {10}, pages = {e2400259}, doi = {10.1002/jobm.202400259}, pmid = {39113256}, issn = {1521-4028}, mesh = {*Gene Transfer, Horizontal ; *Anti-Bacterial Agents/pharmacology ; Humans ; *Bacteria/genetics/drug effects ; *Evolution, Molecular ; Bangladesh ; Plasmids/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; Bacterial Infections/microbiology/drug therapy/transmission ; Public Health ; }, abstract = {Antibiotic resistance poses a formidable challenge to global public health, necessitating comprehensive understanding and strategic interventions. This review explores the evolution and transmission dynamics of antibiotic resistance genes, with a focus on Bangladesh. The indiscriminate use of antibiotics, compounded by substandard formulations and clinical misdiagnosis, fuels the emergence and spread of resistance in the country. Studies reveal high resistance rates among common pathogens, emphasizing the urgent need for targeted interventions and rational antibiotic use. Molecular assessments uncover a diverse array of antibiotic resistance genes in environmental reservoirs, highlighting the complex interplay between human activities and resistance dissemination. Horizontal gene transfer mechanisms, particularly plasmid-mediated conjugation, facilitate the exchange of resistance determinants among bacterial populations, driving the evolution of multidrug-resistant strains. The review discusses clinical implications, emphasizing the interconnectedness of environmental and clinical settings in resistance dynamics. Furthermore, bioinformatic and experimental evidence elucidates novel mechanisms of resistance gene transfer, underscoring the dynamic nature of resistance evolution. In conclusion, combating antibiotic resistance requires a multifaceted approach, integrating surveillance, stewardship, and innovative research to preserve the efficacy of antimicrobial agents and safeguard public health.}, }
@article {pmid39107250, year = {2024}, author = {Barragan, AC and Latorre, SM and Malmgren, A and Harant, A and Win, J and Sugihara, Y and Burbano, HA and Kamoun, S and Langner, T}, title = {Multiple Horizontal Mini-chromosome Transfers Drive Genome Evolution of Clonal Blast Fungus Lineages.}, journal = {Molecular biology and evolution}, volume = {41}, number = {8}, pages = {}, pmid = {39107250}, issn = {1537-1719}, support = {//Gatsby Charitable Foundation/ ; UKRI-BBSRC//UK Research and Innovation Biotechnology and Biological Sciences Research Council/ ; /ERC_/European Research Council/International ; 743165//BLASTOFF/ ; 101077853//PANDEMIC/ ; RSWF\R1\191011//Royal Society/ ; }, mesh = {*Gene Transfer, Horizontal ; *Evolution, Molecular ; Chromosomes, Fungal/genetics ; Ascomycota/genetics ; Plant Diseases/microbiology ; Genome, Fungal ; }, abstract = {Crop disease pandemics are often driven by asexually reproducing clonal lineages of plant pathogens that reproduce asexually. How these clonal pathogens continuously adapt to their hosts despite harboring limited genetic variation, and in absence of sexual recombination remains elusive. Here, we reveal multiple instances of horizontal chromosome transfer within pandemic clonal lineages of the blast fungus Magnaporthe (Syn. Pyricularia) oryzae. We identified a horizontally transferred 1.2Mb accessory mini-chromosome which is remarkably conserved between M. oryzae isolates from both the rice blast fungus lineage and the lineage infecting Indian goosegrass (Eleusine indica), a wild grass that often grows in the proximity of cultivated cereal crops. Furthermore, we show that this mini-chromosome was horizontally acquired by clonal rice blast isolates through at least nine distinct transfer events over the past three centuries. These findings establish horizontal mini-chromosome transfer as a mechanism facilitating genetic exchange among different host-associated blast fungus lineages. We propose that blast fungus populations infecting wild grasses act as genetic reservoirs that drive genome evolution of pandemic clonal lineages that afflict cereal crops.}, }
@article {pmid39106433, year = {2024}, author = {Tan, Y and Aravind, L and Zhang, D}, title = {Genomic Underpinnings of Cytoplasmic Incompatibility: CIF Gene-Neighborhood Diversification Through Extensive Lateral Transfers and Recombination in Wolbachia.}, journal = {Genome biology and evolution}, volume = {16}, number = {8}, pages = {}, pmid = {39106433}, issn = {1759-6653}, support = {//Saint Louis University/ ; //Intramural Research Program of the NIH/ ; /LM/NLM NIH HHS/United States ; }, mesh = {*Wolbachia/genetics ; *Gene Transfer, Horizontal ; *Recombination, Genetic ; Evolution, Molecular ; Phylogeny ; Genome, Bacterial ; Cytoplasm/genetics ; Animals ; Bacterial Proteins/genetics ; }, abstract = {Cytoplasmic incompatibility (CI), a non-Mendelian genetic phenomenon, involves the manipulation of host reproduction by Wolbachia, a maternally transmitted alphaproteobacterium. The underlying mechanism is centered around the CI Factor (CIF) system governed by two genes, cifA and cifB, where cifB induces embryonic lethality, and cifA counteracts it. Recent investigations have unveiled intriguing facets of this system, including diverse cifB variants, prophage association in specific strains, copy number variation, and rapid component divergence, hinting at a complex evolutionary history. We utilized comparative genomics to systematically classify CIF systems, analyze their locus structure and domain architectures, and reconstruct their diversification and evolutionary trajectories. Our new classification identifies ten distinct CIF types, featuring not just versions present in Wolbachia, but also other intracellular bacteria, and eukaryotic hosts. Significantly, our analysis of CIF loci reveals remarkable variability in gene composition and organization, encompassing an array of diverse endonucleases, variable toxin domains, deubiquitinating peptidases (DUBs), prophages, and transposons. We present compelling evidence that the components within the loci have been diversifying their sequences and domain architectures through extensive, independent lateral transfers and interlocus recombination involving gene conversion. The association with diverse transposons and prophages, coupled with selective pressures from host immunity, likely underpins the emergence of CIF loci as recombination hotspots. Our investigation also posits the origin of CifB-REase domains from mobile elements akin to CR (Crinkler-RHS-type) effectors and Tribolium Medea1 factor, which is linked to another non-Mendelian genetic phenomenon. This comprehensive genomic analysis offers novel insights into the molecular evolution and genomic foundations of Wolbachia-mediated host reproductive control.}, }
@article {pmid39103341, year = {2024}, author = {Hu, K and Chou, CW and Wilke, CO and Finkelstein, IJ}, title = {Distinct horizontal transfer mechanisms for type I and type V CRISPR-associated transposons.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {6653}, pmid = {39103341}, issn = {2041-1723}, support = {R01 GM124141/GM/NIGMS NIH HHS/United States ; R01GM088344//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R01 GM088344/GM/NIGMS NIH HHS/United States ; F-1808//Welch Foundation/ ; R01GM124141//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, mesh = {*DNA Transposable Elements/genetics ; *Escherichia coli/genetics/metabolism ; *CRISPR-Cas Systems ; *Clustered Regularly Interspaced Short Palindromic Repeats ; *Gene Transfer, Horizontal ; *CRISPR-Associated Proteins/metabolism/genetics ; Escherichia coli Proteins/genetics/metabolism ; }, abstract = {CASTs use both CRISPR-associated proteins and Tn7-family transposons for RNA-guided vertical and horizontal transmission. CASTs encode minimal CRISPR arrays but can't acquire new spacers. Here, we report that CASTs can co-opt defense-associated CRISPR arrays for horizontal transmission. A bioinformatic analysis shows that CASTs co-occur with defense-associated CRISPR systems, with the highest prevalence for type I-B and type V CAST sub-types. Using an E. coli quantitative transposition assay and in vitro reconstitution, we show that CASTs can use CRISPR RNAs from these defense systems. A high-resolution structure of the type I-F CAST-Cascade in complex with a type III-B CRISPR RNA reveals that Cas6 recognizes direct repeats via sequence-independent π - π interactions. In addition to using heterologous CRISPR arrays, type V CASTs can also transpose via an unguided mechanism, even when the S15 co-factor is over-expressed. Over-expressing S15 and the trans-activating CRISPR RNA or a single guide RNA reduces, but does not abrogate, off-target integration for type V CASTs. Our findings suggest that some CASTs may exploit defense-associated CRISPR arrays and that this fact must be considered when porting CASTs to heterologous bacterial hosts. More broadly, this work will guide further efforts to engineer the activity and specificity of CASTs for gene editing applications.}, }
@article {pmid39103039, year = {2024}, author = {Zhang, H and Xu, L and Hou, X and Li, Y and Niu, L and Zhang, J and Wang, X}, title = {Ketoprofen promotes the conjugative transfer of antibiotic resistance among antibiotic resistant bacteria in natural aqueous environments.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {360}, number = {}, pages = {124676}, doi = {10.1016/j.envpol.2024.124676}, pmid = {39103039}, issn = {1873-6424}, mesh = {*Ketoprofen/pharmacology ; *Gene Transfer, Horizontal ; Conjugation, Genetic ; Escherichia coli/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Water Pollutants, Chemical/toxicity ; Anti-Inflammatory Agents, Non-Steroidal/pharmacology ; }, abstract = {The emergence and spread of antibiotic resistance in the environment pose a serious threat to global public health. It is acknowledged that non-antibiotic stresses, including disinfectants, pharmaceuticals and organic pollutants, play a crucial role in horizontal transmission of antibiotic resistance genes (ARGs). Despite the widespread presence of non-steroidal anti-inflammatory drugs (NSAIDs), notably in surface water, their contributions to the transfer of ARGs have not been systematically explored. Furthermore, previous studies have primarily concentrated on model strains to investigate whether contaminants promote the conjugative transfer of ARGs, leaving the mechanisms of ARG transmission among antibiotic resistant bacteria in natural aqueous environments under the selective pressures of non-antibiotic contaminants remains unclear. In this study, the Escherichia coli (E. coli) K12 carrying RP4 plasmid was used as the donor strain, indigenous strain Aeromonas veronii containing rifampicin resistance genes in Taihu Lake, and E. coli HB101 were used as receptor strains to establish inter-genus and intra-genus conjugative transfer systems, examining the conjugative transfer frequency under the stress of ketoprofen. The results indicated that ketoprofen accelerated the environmental spread of ARGs through several mechanisms. Ketoprofen promoted cell-to-cell contact by increasing cell surface hydrophobicity and reducing cell surface charge, thereby mitigating cell-to-cell repulsion. Furthermore, ketoprofen induced increased levels of reactive oxygen species (ROS) production, activated the DNA damage-induced response (SOS), and enhanced cell membrane permeability, facilitating ARG transmission in intra-genus and inter-genus systems. The upregulation of outer membrane proteins, oxidative stress, SOS response, mating pair formation (Mpf) system, and DNA transfer and replication (Dtr) system related genes, as well as the inhibition of global regulatory genes, all contributed to higher transfer efficiency under ketoprofen treatment. These findings served as an early warning for a comprehensive assessment of the roles of NSAIDs in the spread of antibiotic resistance in natural aqueous environments.}, }
@article {pmid39102038, year = {2024}, author = {Olanrewaju, OS and Molale-Tom, LG and Bezuidenhout, CC}, title = {Genomic diversity, antibiotic resistance, and virulence in South African Enterococcus faecalis and Enterococcus lactis isolates.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {40}, number = {10}, pages = {289}, pmid = {39102038}, issn = {1573-0972}, mesh = {South Africa ; *Genome, Bacterial ; *Enterococcus faecalis/genetics/drug effects/pathogenicity/isolation &amp; purification ; Virulence/genetics ; *Genetic Variation ; *Anti-Bacterial Agents/pharmacology ; *Virulence Factors/genetics ; Humans ; Drug Resistance, Bacterial/genetics ; Genomic Islands/genetics ; Gram-Positive Bacterial Infections/microbiology ; Enterococcus/genetics/drug effects/pathogenicity/isolation &amp; purification/classification ; Phylogeny ; Gene Transfer, Horizontal ; Genomics ; Microbial Sensitivity Tests ; }, abstract = {This study presents the empirical findings of an in-depth genomic analysis of Enterococcus faecalis and Enterococcus lactis isolates from South Africa. It offers valuable insights into their genetic characteristics and their significant implications for public health. The study uncovers nuanced variations in the gene content of these isolates, despite their similar GC contents, providing a comprehensive view of the evolutionary diversity within the species. Genomic islands are identified, particularly in E. faecalis, emphasizing its propensity for horizontal gene transfer and genetic diversity, especially in terms of antibiotic resistance genes. Pangenome analysis reveals the existence of a core genome, accounting for a modest proportion of the total genes, with 2157 core genes, 1164 shell genes, and 4638 cloud genes out of 7959 genes in 52 South African E. faecalis genomes (2 from this study, 49 south Africa genomes downloaded from NCBI, and E. faecalis reference genome). Detecting large-scale genomic rearrangements, including chromosomal inversions, underscores the dynamic nature of bacterial genomes and their role in generating genetic diversity. The study uncovers an array of antibiotic resistance genes, with trimethoprim, tetracycline, glycopeptide, and multidrug resistance genes prevalent, raising concerns about the effectiveness of antibiotic treatment. Virulence gene profiling unveils a diverse repertoire of factors contributing to pathogenicity, encompassing adhesion, biofilm formation, stress resistance, and tissue damage. These empirical findings provide indispensable insights into these bacteria's genomic dynamics, antibiotic resistance mechanisms, and virulence potential, underlining the pressing need to address antibiotic resistance and implement robust control measures.}, }
@article {pmid39101807, year = {2024}, author = {Dhurve, G and Behera, SR and Kodetham, G and Siddavattam, D}, title = {Outer membrane vesicles of Acinetobacter baumannii DS002 carry circular DNA similar to bovine meat and milk factors (BMMFs) and SPHINX 2.36 and probably play a role in interdomain lateral gene transfer.}, journal = {Microbiology spectrum}, volume = {12}, number = {9}, pages = {e0081724}, pmid = {39101807}, issn = {2165-0497}, mesh = {Animals ; Mice ; *Plasmids/genetics ; *Acinetobacter baumannii/genetics/metabolism ; Cattle ; *Gene Transfer, Horizontal ; *DNA, Circular/genetics/metabolism ; Bacterial Outer Membrane/metabolism ; Female ; Bacteriophages/genetics/physiology ; Meat/microbiology ; Milk/microbiology ; Acinetobacter Infections/microbiology ; Extracellular Vesicles/metabolism ; Mice, Inbred BALB C ; DNA, Bacterial/genetics ; }, abstract = {UNLABELLED: The discovery of Replication Competent Circular DNA molecules in mammalian cells and tissues is being linked to debilitating diseases, such as multiple sclerosis (MS), bovine spongiform encephalopathy (BSE), and colorectal cancer (CRC). These circular DNA molecules, otherwise known as bovine meat and milk factors (BMMFs) and Slow Progressive Hidden INfections of variable (X) latency (SPHINX), bear significant (80%) sequence similarity with the plasmids of Acinetobacter baumannii strains. Nanostructures, such as bacterial outer membrane vesicles (OMVs) serve as vehicles for transporting biomolecular cargo and have the potential to facilitate interkingdom lateral mobility of DNA. Strengthening the proposed hypothesis, this study demonstrates that OMVs derived from A. baumannii DS002 carrying four plasmids and genome (pTS236) of phage, AbDs1, successfully reached different parts of the body, including the central nervous system, following the injection of fluorescein isothiocyanate (FITC)-labeled OMVs into experimental mice. Out of the four OMV-associated plasmids, three (pTS4586, pTS9900, and pTS134338) were identified within the lumen, and the fourth one (pTS11291) was found on the surface of OMVs. In addition to the indigenous plasmids, the phage-encoded protein, Orf96, anchored on the surface of the OMVs by establishing a strong interaction with the OMV-associated porin, OmpA. Intriguingly, a subset of labeled OMVs, when incubated with Neuro2A cells, translocated across the membrane and reached to the cytoplasmic space of the cells. Collectively, the experimental evidence presented herein underscores the promising potential of OMVs as vehicles for delivering molecular cargo containing plasmids and phage genomes to diverse mammalian tissues and cells.<br><br>IMPORTANCE: Several independent studies have demonstrated the existence of replication competent circular DNA molecules of bacterial and viral origin in mammalian cells and tissues. However, studies about their origin and lateral mobility to mammalian cells are scarce. Our work describes the existence of circular DNA, similar to that of DNA molecules identified in mammalian cells, OMVs derived from soil isolate of A. baumannii DS002. Furthermore, the work also provides visual evidence that demonstrates the passage of labeled OMVs to different organs of experimental mice within hours after intravenously administering OMVs into experimental mice. Some of the labeled OMVs have even crossed the membrane of Neuro2A, suggesting the existence of interkingdom horizontal mobility between bacteria and mammals.}, }
@article {pmid39101574, year = {2024}, author = {Rappaport, HB and Oliverio, AM}, title = {Lessons from Extremophiles: Functional Adaptations and Genomic Innovations across the Eukaryotic Tree of Life.}, journal = {Genome biology and evolution}, volume = {16}, number = {8}, pages = {}, pmid = {39101574}, issn = {1759-6653}, mesh = {Adaptation, Physiological/genetics ; *Eukaryota/genetics ; Evolution, Molecular ; *Extremophiles/genetics ; Genome ; Genomics ; Phylogeny ; }, abstract = {From hydrothermal vents, to glaciers, to deserts, research in extreme environments has reshaped our understanding of how and where life can persist. Contained within the genomes of extremophilic organisms are the blueprints for a toolkit to tackle the multitude of challenges of survival in inhospitable environments. As new sequencing technologies have rapidly developed, so too has our understanding of the molecular and genomic mechanisms that have facilitated the success of extremophiles. Although eukaryotic extremophiles remain relatively understudied compared to bacteria and archaea, an increasing number of studies have begun to leverage 'omics tools to shed light on eukaryotic life in harsh conditions. In this perspective paper, we highlight a diverse breadth of research on extremophilic lineages across the eukaryotic tree of life, from microbes to macrobes, that are collectively reshaping our understanding of molecular innovations at life's extremes. These studies are not only advancing our understanding of evolution and biological processes but are also offering a valuable roadmap on how emerging technologies can be applied to identify cellular mechanisms of adaptation to cope with life in stressful conditions, including high and low temperatures, limited water availability, and heavy metal habitats. We shed light on patterns of molecular and organismal adaptation across the eukaryotic tree of life and discuss a few promising research directions, including investigations into the role of horizontal gene transfer in eukaryotic extremophiles and the importance of increasing phylogenetic diversity of model systems.}, }
@article {pmid39100236, year = {2024}, author = {Bhattacharya, A and Aluquin, A and Kennedy, DA}, title = {Exceptions to the rule: When does resistance evolution not undermine antibiotic therapy in human bacterial infections?.}, journal = {Evolution letters}, volume = {8}, number = {4}, pages = {478-493}, pmid = {39100236}, issn = {2056-3744}, support = {R01 GM140459/GM/NIGMS NIH HHS/United States ; }, abstract = {The use of antibiotics to treat bacterial infections often imposes strong selection for antibiotic resistance. However, the prevalence of antibiotic resistance varies greatly across different combinations of pathogens and drugs. What underlies this variation? Systematic reviews, meta-analyses, and literature surveys capable of integrating data across many studies have tried to answer this question, but the vast majority of these studies have focused only on cases where resistance is common or problematic. Yet much could presumably be learned from the cases where resistance is infrequent or absent. Here we conducted a literature survey and a systematic review to study the evolution of antibiotic resistance across a wide range of pathogen-by-drug combinations (57 pathogens and 53 antibiotics from 15 drug classes). Using Akaike information criterion-based model selection and model-averaged parameter estimation we explored 14 different factors posited to be associated with resistance evolution. We find that the most robust predictors of high resistance are nosocomial transmission (i.e., hospital-acquired pathogens) and indirect transmission (e.g., vector-, water-, air-, or vehicle-borne pathogens). While the former was to be expected based on prior studies, the positive correlation between high resistance frequencies and indirect transmission is, to our knowledge, a novel insight. The most robust predictor of low resistance is zoonosis from wild animal reservoirs. We also found partial support that resistance was associated with pathogen type, horizontal gene transfer, commensalism, and human-to-human transmission. We did not find support for correlations between resistance and environmental reservoirs, mechanisms of drug action, and global drug use. This work explores the relative explanatory power of various pathogen and drug factors on resistance evolution, which is necessary to identify priority targets of stewardship efforts to slow the spread of drug-resistant pathogens.}, }
@article {pmid39100235, year = {2024}, author = {Ciach, MA and Pawłowska, J and Górecki, P and Muszewska, A}, title = {The interkingdom horizontal gene transfer in 44 early diverging fungi boosted their metabolic, adaptive, and immune capabilities.}, journal = {Evolution letters}, volume = {8}, number = {4}, pages = {526-538}, pmid = {39100235}, issn = {2056-3744}, abstract = {Numerous studies have been devoted to individual cases of horizontally acquired genes in fungi. It has been shown that such genes expand the hosts' metabolic capabilities and contribute to their adaptations as parasites or symbionts. Some studies have provided an extensive characterization of the horizontal gene transfer (HGT) in Dikarya. However, in the early diverging fungi (EDF), a similar characterization is still missing. In order to fill this gap, we have designed a computational pipeline to obtain a statistical sample of reliable HGT events with a low false discovery rate. We have analyzed 44 EDF proteomes and identified 829 xenologs in fungi ranging from Chytridiomycota to Mucoromycota. We have identified several patterns and statistical properties of EDF HGT. We show that HGT is driven by bursts of gene exchange and duplication, resulting in highly divergent numbers and molecular properties of xenologs between fungal lineages. Ancestrally aquatic fungi are generally more likely to acquire foreign genetic material than terrestrial ones. Endosymbiotic bacteria can be a source of useful xenologs, as exemplified by NOD-like receptors transferred to Mortierellomycota. Closely related fungi have similar rates of intronization of xenologs. Posttransfer gene fusions and losses of protein domains are common and may influence the encoded proteins' functions. We argue that there is no universal approach for HGT identification and inter- and intra-kingdom transfers require tailored identification methods. Our results help to better understand how and to what extent HGT has shaped the metabolic, adaptive, and immune capabilities of fungi.}, }
@article {pmid39098155, year = {2024}, author = {Wang, H and Gao, J and Ren, H and Zhao, Y and Wang, Y and An, J and Chen, H and Wang, Q}, title = {Whatever does not kill them makes them stronger: Using quaternary ammonia antimicrobials to alleviate the inhibition of ammonia oxidation under perfluorooctanoic acid stress.}, journal = {Water research}, volume = {263}, number = {}, pages = {122171}, doi = {10.1016/j.watres.2024.122171}, pmid = {39098155}, issn = {1879-2448}, mesh = {*Ammonia/metabolism ; *Fluorocarbons ; *Caprylates/pharmacology ; *Oxidation-Reduction ; Sewage ; Anti-Infective Agents/pharmacology ; Water Pollutants, Chemical ; Bacteria/metabolism/drug effects ; Nitrification ; }, abstract = {Perfluorooctanoic acid (PFOA), benzalkyl dimethylammonium compounds (BAC) and antibiotic resistance genes (ARGs) have negative effects on biological sewage treatment. The performance of nitrification systems under stress of PFOA (0.1-5 mg/L) or/and BAC (0.2-10 mg/L) was explored during 84-day experiments using four sequencing batch reactors, in this study. Low (0.1 mg/L) concentration PFOA had a positive influence on ammonia removal, while medium and high (2 and 5 mg/L) concentrations PFOA caused severe inhibition. Meanwhile, PFOA stress resulted in the enrichment of ARGs in water (w-ARGs). BAC (0-10 mg/L) had no obvious influence on ammonia removal. However, BAC promoted the reduction of ARGs and the bacterial community was the main participator (48.07%) for the spread of ARGs. Interestingly, the joint stress of PFOA and BAC increased the ammonia-oxidizing bacteria (AOB) activity from 5.81 ± 0.19 and 6.05 ± 0.79 mg N/(g MLSS·h) to 7.09 ± 0.87 and 7.23 ± 0.29 mg N/(g MLSS·h) in medium and high concentrations, compared to single stress of PFOA, which was observed for the first time. BAC could reduce bioavailability of PFOA through competitive adsorption and decreasing sludge hydrophobicity by the lower β-Sheet and α-Helix in tightly bound protein. Furthermore, the joint stress of PFOA and BAC was able to intensify the proliferation of w-ARGs and extracellular ARGs in sludge, and developed the most active horizontal gene transfer mediated by intl1 compared to single stress of PFOA or BAC. The batch tests verified the detoxification capacity of BAC on nitrification under 2.5 mg/L PFOA (48 h exposing), and the maximum alleviation of AOB activity was achieved at BAC and PFOA mass ratio of 2:1. In summary, BAC could be used to alleviate the inhibition of PFOA on ammonia oxidation, providing an efficient and sustainable approach in wastewater treatment.}, }
@article {pmid39096995, year = {2024}, author = {Tian, J and Xu, L and Sun, JQ}, title = {Taxonomic characterization and comparative genomic analysis of a novel Devosia species revealed that phenolic acid-degrading traits are ubiquitous in the Devosia genus.}, journal = {Environmental research}, volume = {261}, number = {}, pages = {119724}, doi = {10.1016/j.envres.2024.119724}, pmid = {39096995}, issn = {1096-0953}, mesh = {*Hydroxybenzoates/metabolism ; Hyphomicrobiaceae/genetics/metabolism ; Soil Microbiology ; Genome, Bacterial ; Genomics ; Phylogeny ; Rhizosphere ; Biodegradation, Environmental ; }, abstract = {Phenolic acids (PAs) are widely distributed allelochemicals in various environments. To better understand the fate of PAs in environments, a halotolerant PAs-degrading bacterium (named strain RR2S18[T]) isolated from rhizosphere soil was identified as a novel species of Devosia, named Devosia rhizosphaerae sp. nov. The strain initially degraded PAs into central ring-fission intermediates (protocatechuic acid) using the CoA-dependent non-β-oxidation pathway. The produced ring-fission intermediates were then consecutively degraded by an ortho-cleavage reaction and the β-ketoadipic acid pathway. A comparative genomics analysis of 62 Devosia strains revealed that PAs-degrading genes were ubiquitous in their genomes, indicating that PAs degradation is universal among members of this genus. The analysis also suggested that the genes involved in CoA-dependent non-β-oxidation are inherent to Devosia strains, while those involved in ring-fission and β-ketoadipic acid pathways were obtained by horizontal gene transfer.}, }
@article {pmid39096644, year = {2024}, author = {Wu, Q and Wu, GG and Pan, KN and Wang, XP and Li, HY and Tian, Z and Jin, RC and Fan, NS}, title = {Beta-blocker drives the conjugative transfer of multidrug resistance genes in pure and complex biological systems.}, journal = {Journal of hazardous materials}, volume = {477}, number = {}, pages = {135403}, doi = {10.1016/j.jhazmat.2024.135403}, pmid = {39096644}, issn = {1873-3336}, mesh = {*Metoprolol ; *Plasmids/genetics ; *Conjugation, Genetic/drug effects ; Drug Resistance, Multiple, Bacterial/genetics/drug effects ; Adrenergic beta-Antagonists/pharmacology ; Gene Transfer, Horizontal ; Bacteria/genetics/drug effects/metabolism ; Anti-Bacterial Agents/pharmacology ; Genes, MDR/genetics ; Microbiota/drug effects ; }, abstract = {Drug resistance poses a high risk to human health. Extensive use of non-antibiotic drugs contributes to antibiotic resistance genes (ARGs) transfer. However, how they affect the spread of broad-host plasmids in complex biological systems remains unknown. This study investigated the effect of metoprolol on the transfer frequency and host range of ARGs in both intrageneric and intergeneric pure culture systems, as well as in anammox microbiome. The results showed that environmental concentrations of metoprolol significantly promoted the intrageneric and intergeneric conjugative transfer. Initially, metoprolol induced excessive oxidative stress, resulting in high cell membrane permeability and bacterial SOS response. Meanwhile, more pili formation increased the adhesion and contact between bacteria, and the abundance of conjugation-related genes also increased significantly. Activation of the electron transport chain provided more ATP for this energy-consuming process. The underlying mechanism was further verified in the complex anammox conjugative system. Metoprolol induced the enrichment of ARGs and mobile genetic elements. The enhanced bacterial interaction and energy generation facilitated the high conjugative transfer frequency of ARGs. In addition, plasmid-borne ARGs tended to transfer to opportunistic pathogens. This work raises public concerns about the health and ecological risks of non-antibiotic drugs.}, }
@article {pmid39095425, year = {2024}, author = {Landa, CR and Ariza-Mateos, A and Briones, C and Perales, C and Wagner, A and Domingo, E and Gómez, J}, title = {Adapting the rhizome concept to an extended definition of viral quasispecies and the implications for molecular evolution.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {17914}, pmid = {39095425}, issn = {2045-2322}, mesh = {*Rhizome/virology ; *Evolution, Molecular ; *Quasispecies/genetics ; *Phylogeny ; RNA Viruses/genetics/classification ; Gene Transfer, Horizontal ; Mutation ; Genome, Viral ; }, abstract = {The rhizome concept proposed by Gilles Deleuze and Félix Guattari offers a novel perspective on the organization and interdependence of complex constellations of heterogeneous entities, their mapping and their ruptures. The emphasis of the present study is placed on the dynamics of contacts and communication among such entities that arise from experimentation, without any favored hierarchy or origin. When applied to biological evolution, the rhizome concept integrates all types of heterogeneity resulting from "symbiotic" relationships among living beings (or their genomic material), horizontal genetic transfer, recombination and mutation, and breaks away from the approach that gives rise to the phylogenetic tree of life. It has already been applied to describe the dynamics and evolution of RNA viruses. Thus, here we introduce a novel framework for the interpretation the viral quasispecies concept, which explains the evolution of RNA virus populations as the result of dynamic interconnections and multifaceted interdependence between highly heterogeneous viral sequences and its inherently heterogeneous host cells. The rhizome network perspective underlines even further the medical implications of the broad mutant spectra of viruses that are in constant flow, given the multiple pathways they have available for fitness loss and gain.}, }
@article {pmid39095161, year = {2025}, author = {Guo, Z and Tang, X and Wang, W and Luo, Z and Zeng, Y and Zhou, N and Yu, Z and Wang, D and Song, B and Zhou, C and Xiong, W}, title = {The photo-based treatment technology simultaneously removes resistant bacteria and resistant genes from wastewater.}, journal = {Journal of environmental sciences (China)}, volume = {148}, number = {}, pages = {243-262}, doi = {10.1016/j.jes.2024.01.005}, pmid = {39095161}, issn = {1001-0742}, mesh = {*Wastewater/chemistry ; *Waste Disposal, Fluid/methods ; Bacteria ; Disinfection/methods ; Drug Resistance, Bacterial/genetics ; Ultraviolet Rays ; Water Purification/methods ; }, abstract = {Because of the recent widespread usage of antibiotics, the acquisition and dissemination of antibiotic-resistance genes (ARGs) were prevalent in the majority of habitats. Generally, the biological wastewater treatment processes used in wastewater treatment plants have a limited efficiencies of antibiotics resistant bacteria (ARB) disinfection and ARGs degradation and even promote the proliferation of ARGs. Problematically, ARB and ARGs in effluent pose potential risks if they are not further treated. Photocatalytic oxidation is considered a promising disinfection technology, where the photocatalytic process generates many free radicals that enhance the interaction between light and deoxyribonucleic acid (DNA) for ARB elimination and subsequent degradation of ARGs. This review aims to illustrate the progress of photocatalytic oxidation technology for removing antibiotics resistant (AR) from wastewater in recent years. We discuss the sources and transfer of ARGs in wastewater. The overall removal efficiencies of ultraviolet radiation (UV)/chlorination, UV/ozone, UV/H2O2, and UV/sulfate-radical based system for ARB and ARGs, as well as the experimental parameters and removal mechanisms, are systematically discussed. The contribution of photocatalytic materials based on TiO2 and g-C3N4 to the inactivation of ARB and degradation of ARGs is highlighted, producing many free radicals to attack ARB and ARGs while effectively limiting the horizontal gene transfer (HGT) in wastewater. Finally, based on the reviewed studies, future research directions are proposed to realize specific photocatalytic oxidation technology applications and overcome current challenges.}, }
@article {pmid39093595, year = {2024}, author = {Wu, J and Meng, L and Gaïa, M and Hikida, H and Okazaki, Y and Endo, H and Ogata, H}, title = {Gene Transfer Among Viruses Substantially Contributes to Gene Gain of Giant Viruses.}, journal = {Molecular biology and evolution}, volume = {41}, number = {8}, pages = {}, pmid = {39093595}, issn = {1537-1719}, support = {18H02279//JSPS/KAKENHI/ ; JPMJSP2110//JST SPRING/ ; 2022-26//Institute for Chemical Research, Kyoto University/ ; }, mesh = {*Gene Transfer, Horizontal ; *Giant Viruses/genetics ; Evolution, Molecular ; Phylogeny ; Genome, Viral ; Gene Duplication ; }, abstract = {The phylum Nucleocytoviricota comprises a diverse group of double-stranded DNA viruses that display a wide range of gene repertoires. Although these gene repertoires determine the characteristics of individual viruses, the evolutionary processes that have shaped the gene repertoires of extant viruses since their common ancestor are poorly characterized. In this study, we aimed to address this gap in knowledge by using amalgamated likelihood estimation, a probabilistic tree reconciliation method that infers evolutionary scenarios by distinguishing origination, gene duplications, virus-to-virus horizontal gene transfer (vHGT), and gene losses. We analyzed over 4,700 gene families from 195 genomes spanning all known viral orders. The evolutionary reconstruction suggests a history of extensive gene gains and losses during the evolution of these viruses, notably with vHGT contributing to gene gains at a comparable level to duplications and originations. The vHGT frequently occurred between phylogenetically closely related viruses, as well as between distantly related viruses with an overlapping host range. We observed a pattern of massive gene duplications that followed vHGTs for gene families that was potentially related to host range control and virus-host arms race. These results suggest that vHGT represents a previously overlooked, yet important, evolutionary force that integrates the evolutionary paths of multiple viruses and affects shaping of Nucleocytoviricota virus gene repertoires.}, }
@article {pmid39089095, year = {2024}, author = {Zhuang, M and Yan, W and Xiong, Y and Wu, Z and Cao, Y and Sanganyado, E and Siame, BA and Chen, L and Kashi, Y and Leung, KY}, title = {Horizontal plasmid transfer promotes antibiotic resistance in selected bacteria in Chinese frog farms.}, journal = {Environment international}, volume = {190}, number = {}, pages = {108905}, doi = {10.1016/j.envint.2024.108905}, pmid = {39089095}, issn = {1873-6750}, mesh = {Animals ; *Plasmids/genetics ; China ; *Gene Transfer, Horizontal ; *Bacteria/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Farms ; Drug Resistance, Bacterial/genetics ; Rana catesbeiana/microbiology/genetics ; Drug Resistance, Microbial/genetics ; Microbiota/genetics ; }, abstract = {The emergence and dissemination of antibiotic resistance genes (ARGs) in the ecosystem are global public health concerns. One Health emphasizes the interconnectivity between different habitats and seeks to optimize animal, human, and environmental health. However, information on the dissemination of antibiotic resistance genes (ARGs) within complex microbiomes in natural habitats is scarce. We investigated the prevalence of antibiotic resistant bacteria (ARB) and the spread of ARGs in intensive bullfrog (Rana catesbeiana) farms in the Shantou area of China. Antibiotic susceptibilities of 361 strains, combined with microbiome analyses, revealed Escherichia coli, Edwardsiella tarda, Citrobacter and Klebsiella sp. as prevalent multidrug resistant bacteria on these farms. Whole genome sequencing of 95 ARB identified 250 large plasmids that harbored a wide range of ARGs. Plasmid sequences and sediment metagenomes revealed an abundance of tetA, sul1, and aph(3″)-Ib ARGs. Notably, antibiotic resistance (against 15 antibiotics) highly correlated with plasmid-borne rather than chromosome-borne ARGs. Based on sequence similarities, most plasmids (62%) fell into 32 distinct groups, indicating a potential for horizontal plasmid transfer (HPT) within the frog farm microbiome. HPT was confirmed in inter- and intra-species conjugation experiments. Furthermore, identical mobile ARGs, flanked by mobile genetic elements (MGEs), were found in different locations on the same plasmid, or on different plasmids residing in the same or different hosts. Our results suggest a synergy between MGEs and HPT to facilitate ARGs dissemination in frog farms. Mining public databases retrieved similar plasmids from different bacterial species found in other environmental niches globally. Our findings underscore the importance of HPT in mediating the spread of ARGs in frog farms and other microbiomes of the ecosystem.}, }
@article {pmid39086116, year = {2024}, author = {Yang, Q and Li, L and Zhao, G and Cui, Q and Gong, X and Ying, L and Yang, T and Fu, M and Shen, Z}, title = {Characterization of a multiresistance optrA- and lsa(E)-harbouring unconventional circularizable structure in Streptococcus suis.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {79}, number = {10}, pages = {2528-2533}, doi = {10.1093/jac/dkae250}, pmid = {39086116}, issn = {1460-2091}, support = {2022YFC2303900//National Key Research and Development Program of China/ ; 32141001//National Natural Science Foundation of China/ ; }, mesh = {*Streptococcus suis/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Multiple, Bacterial/genetics ; *Microbial Sensitivity Tests ; *Multigene Family ; *Conjugation, Genetic/genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Genomic Islands/genetics ; Lincosamides/pharmacology ; Pleuromutilins ; Diterpenes/pharmacology ; Polycyclic Compounds ; Streptococcal Infections/microbiology ; Genes, Bacterial ; Streptogramin A/pharmacology ; }, abstract = {OBJECTIVES: To identify novel genetic elements facilitating the horizontal transfer of the oxazolidinone/phenicol resistance gene optrA and the pleuromutilin-lincosamide-streptogramin A resistance gene lsa(E) in Streptococcus suis.<br><br>METHODS: The complete genomes of S. suis HB18 and two transconjugants were obtained using both the Illumina and Nanopore platforms. MICs were determined by broth microdilution. Inverse PCR was performed to identify circular forms of the novel unconventional circularizable structure (UCS), genomic island (GI) and integrative and conjugative element (ICE). Conjugation experiments assessed the transferability of optrA and lsa(E) genes in S. suis.<br><br>RESULTS: S. suis HB18 carried a multiresistance gene cluster optrA-lsa(E)-lnu(B)-aphA-aadE-spw. This gene cluster, flanked by intact and truncated erm(B) in the same orientation, resided on a novel ICESsuHB18. Inverse PCR revealed the existence of a novel UCS, named UCS-optrA&#x200a;+&#x200a;lsa(E), which could excise the gene cluster optrA-lsa(E)-lnu(B)-aphA-aadE-spw and one copy of erm(B) from ICESsuHB18. Two transconjugants with different characteristics were obtained. In transconjugant T-JH-GI, UCS-optrA&#x200a;+&#x200a;lsa(E) excised from ICESsuHB18 inserted into the erm(B)-positive GI, designated GISsuHB18, generating the novel GISsuHB18-1. Meanwhile, in T-JH-ICE, genetic rearrangement events occurred in ICESsuHB18 and GISsuHB18, forming the novel ICESsuHB18-1.<br><br>CONCLUSIONS: This is the first report demonstrating the functionally active UCS-optrA&#x200a;+&#x200a;lsa(E) excising from ICESsuHB18 and inserting into the erm(B)-positive GISsuHB18 during the conjugation process. The location of optrA and lsa(E) on a multiresistance UCS enhances its persistence and dissemination.}, }
@article {pmid39082809, year = {2024}, author = {Kanno, K and Kuriki, R and Yasuno, Y and Shinada, T and Ito, T and Hemmi, H}, title = {Archaeal mevalonate pathway in the uncultured bacterium Candidatus Promineifilum breve belonging to the phylum Chloroflexota.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {8}, pages = {e0110624}, pmid = {39082809}, issn = {1098-5336}, support = {18K19170,19H04651, 20H02899, 23K18109, 23H02126.//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; }, mesh = {*Mevalonic Acid/metabolism ; Archaea/genetics/metabolism/classification/enzymology ; Chloroflexi/genetics/metabolism/enzymology/classification ; Metabolic Networks and Pathways/genetics ; Phylogeny ; Escherichia coli/genetics/metabolism ; }, abstract = {The archaeal mevalonate pathway is a recently discovered modified version of the eukaryotic mevalonate pathway. This pathway is widely conserved in archaea, except for some archaeal lineages possessing the eukaryotic or other modified mevalonate pathways. Although the pathway seems almost exclusive to the domain Archaea, the whole set of homologous genes of the pathway is found in the metagenome-assembled genome sequence of an uncultivated bacterium, Candidatus Promineifilum breve, of the phylum Chloroflexota. To prove the existence of the archaea-specific pathway in the domain Bacteria, we confirmed the activities of the enzymes specific to the pathway, phosphomevalonate dehydratase and anhydromevalonate phosphate decarboxylase, because only these two enzymes are absent in closely related Chloroflexota bacteria that possess a different type of modified mevalonate pathway. The activity of anhydromevalonate phosphate decarboxylase was evaluated by carotenoid production via the archaeal mevalonate pathway reconstituted in Escherichia coli cells, whereas that of phosphomevalonate dehydratase was confirmed by an in vitro assay using the recombinant enzyme after purification and iron-sulfur cluster reconstruction. Phylogenetic analyses of some mevalonate pathway-related enzymes suggest an evolutionary route for the archaeal mevalonate pathway in Candidatus P. breve, which probably involves horizontal gene transfer events.IMPORTANCEThe recent discovery of various modified mevalonate pathways in microorganisms, such as archaea and Chloroflexota bacteria, has shed light on the complexity of the evolution of metabolic pathways, including those involved in primary metabolism. The fact that the archaeal mevalonate pathway, which is almost exclusive to the domain Archaea, exists in a Chloroflexota bacterium provides valuable insights into the molecular evolution of the mevalonate pathways and associated enzymes. Putative genes probably involved in the archaeal mevalonate pathway have also been found in the metagenome-assembled genomes of Chloroflexota bacteria. Such genes can contribute to metabolic engineering for the bioproduction of valuable isoprenoids because the archaeal mevalonate pathway is known to be an energy-saving metabolic pathway that consumes less ATP than other mevalonate pathways do.}, }
@article {pmid39080678, year = {2024}, author = {Rajput, M and Pandey, M and Dixit, R and Shukla, VK}, title = {Is cross-species horizontal gene transfer responsible for gallbladder carcinogenesis.}, journal = {World journal of surgical oncology}, volume = {22}, number = {1}, pages = {201}, pmid = {39080678}, issn = {1477-7819}, mesh = {Humans ; *Gene Transfer, Horizontal ; *Gallbladder Neoplasms/genetics/pathology/virology ; Carcinogenesis/genetics ; RNA, Antisense/genetics ; Gene Expression Regulation, Neoplastic ; Transcriptome ; }, abstract = {BACKGROUND: Cross-species horizontal gene transfer (HGT) involves the transfer of genetic material between different species of organisms. In recent years, mounting evidence has emerged that cross-species HGT does take place and may play a role in the development and progression of diseases.<br><br>METHODS: Transcriptomic data obtained from patients with gallbladder cancer (GBC)&#xa0;was assessed for the differential expression of antisense RNAs (asRNAs). The Basic Local Alignment Search Tool (BLAST) was used for&#xa0;cross-species analysis with viral, bacterial, fungal, and ancient human genomes to elucidate the evolutionary cross species origins of these differential asRNAs. Functional enrichment analysis and text mining were conducted and a network of asRNAs targeting mRNAs was constructed to understand the function of differential asRNAs better.<br><br>RESULTS: A total of 17 differentially expressed antisense RNAs (asRNAs) were identified in gallbladder cancer tissue&#xa0;compared to that of normal gallbladder. BLAST analysis of 15 of these asRNAs (AFAP1-AS1, HMGA2-AS1, MNX1-AS1, SLC2A1-AS1, BBOX1-AS1, ELFN1-AS1, TRPM2-AS, DNAH17-AS1, DCST1-AS1, VPS9D1-AS1, MIR1-1HG-AS1, HAND2-AS1, PGM5P4-AS1, PGM5P3-AS1, and MAGI2-AS) showed varying degree of similarities with bacterial and viral genomes, except for UNC5B-AS1 and SOX21-AS1, which were conserved during evolution. Two of these 15&#xa0;asRNAs, (VPS9D1-AS1 and SLC2A1-AS1) exhibited a high degree of similarity with viral genomes (Chikungunya virus, Human immunodeficiency virus 1, Stealth virus 1, and Zika virus) and bacterial genomes including (Staphylococcus sp., Bradyrhizobium sp., Pasteurella multocida sp., and, Klebsiella pneumoniae sp.), indicating potential HGT during evolution.<br><br>CONCLUSION: The results provide novel evidence supporting the hypothesis that differentially expressed asRNAs in GBC exhibit varying sequence similarity with bacterial, viral, and ancient human genomes, indicating a potential shared evolutionary origin. These non-coding genes are enriched with methylation and were found to be associated with cancer-related pathways, including the P53 and PI3K-AKT signaling pathways, suggesting their possible involvement in tumor development.}, }
@article {pmid39079455, year = {2025}, author = {Russell, SL and Penunuri, G and Condon, C}, title = {Diverse genetic conflicts mediated by molecular mimicry and computational approaches to detect them.}, journal = {Seminars in cell &amp; developmental biology}, volume = {165}, number = {}, pages = {1-12}, doi = {10.1016/j.semcdb.2024.07.001}, pmid = {39079455}, issn = {1096-3634}, support = {R00 GM135583/GM/NIGMS NIH HHS/United States ; T32 HG012344/HG/NHGRI NIH HHS/United States ; }, mesh = {*Molecular Mimicry/genetics ; Humans ; Animals ; Computational Biology/methods ; }, abstract = {In genetic conflicts between intergenomic and selfish elements, driver and killer elements achieve biased survival, replication, or transmission over sensitive and targeted elements through a wide range of molecular mechanisms, including mimicry. Driving mechanisms manifest at all organismal levels, from the biased propagation of individual genes, as demonstrated by transposable elements, to the biased transmission of genomes, as illustrated by viruses, to the biased transmission of cell lineages, as in cancer. Targeted genomes are vulnerable to molecular mimicry through the conserved motifs they use for their own signaling and regulation. Mimicking these motifs enables an intergenomic or selfish element to control core target processes, and can occur at the sequence, structure, or functional level. Molecular mimicry was first appreciated as an important phenomenon more than twenty years ago. Modern genomics technologies, databases, and machine learning approaches offer tremendous potential to study the distribution of molecular mimicry across genetic conflicts in nature. Here, we explore the theoretical expectations for molecular mimicry between conflicting genomes, the trends in molecular mimicry mechanisms across known genetic conflicts, and outline how new examples can be gleaned from population genomic datasets. We discuss how mimics involving short sequence-based motifs or gene duplications can evolve convergently from new mutations. Whereas, processes that involve divergent domains or fully-folded structures occur among genomes by horizontal gene transfer. These trends are largely based on a small number of organisms and should be reevaluated in a general, phylogenetically independent framework. Currently, publicly available databases can be mined for genotypes driving non-Mendelian inheritance patterns, epistatic interactions, and convergent protein structures. A subset of these conflicting elements may be molecular mimics. We propose approaches for detecting genetic conflict and molecular mimicry from these datasets.}, }
@article {pmid39078126, year = {2024}, author = {Ai, C and Cui, P and Liu, C and Wu, J and Xu, Y and Liang, X and Yang, Q and Tang, X and Zhou, S and Liao, H and Friman, V-P}, title = {Viral and thermal lysis facilitates transmission of antibiotic resistance genes during composting.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {8}, pages = {e0069524}, pmid = {39078126}, issn = {1098-5336}, mesh = {*Composting ; Gene Transfer, Horizontal ; Manure/microbiology/virology ; Soil Microbiology ; Bacteria/genetics/drug effects ; Animals ; Metagenome ; Cattle ; Hot Temperature ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; Microbiota ; Bacteriophages/genetics/physiology ; }, abstract = {UNLABELLED: While the distribution of extracellular ARGs (eARGs) in the environment has been widely reported, the factors governing their release remain poorly understood. Here, we combined multi-omics and direct experimentation to test whether the release and transmission of eARGs are associated with viral lysis and heat during cow manure composting. Our results reveal that the proportion of eARGs increased 2.7-fold during composting, despite a significant and concomitant reduction in intracellular ARG abundances. This relative increase of eARGs was driven by composting temperature and viral lysis of ARG-carrying bacteria based on metagenome-assembled genome (MAG) analysis. Notably, thermal lysis of mesophilic bacteria carrying ARGs was a key factor in releasing eARGs at the thermophilic phase, while viral lysis played a relatively stronger role during the non-thermal phase of composting. Furthermore, MAG-based tracking of ARGs in combination with direct transformation experiments demonstrated that eARGs released during composting pose a potential transmission risk. Our study provides bioinformatic and experimental evidence of the undiscovered role of temperature and viral lysis in co-driving the spread of ARGs in compost microbiomes via the horizontal transfer of environmentally released DNA.<br><br>IMPORTANCE: The spread of antibiotic resistance genes (ARGs) is a critical global health concern. Understanding the factors influencing the release of extracellular ARGs (eARGs) is essential for developing effective strategies. In this study, we investigated the association between viral lysis, heat, and eARG release during composting. Our findings revealed a substantial increase in eARGs despite reduced intracellular ARG abundance. Composting temperature and viral lysis were identified as key drivers, with thermal lysis predominant during the thermophilic phase and viral lysis during non-thermal phases. Moreover, eARGs released during composting posed a transmission risk through horizontal gene transfer. This study highlights the significance of temperature and phage lysis in ARG spread, providing valuable insights for mitigating antibiotic resistance threats.}, }
@article {pmid39073917, year = {2024}, author = {Gao, L and Liu, L and Lv, AP and Fu, L and Lian, ZH and Nunoura, T and Hedlund, BP and Xu, QY and Wu, D and Yang, J and Ali, M and Li, MM and Liu, YH and Antunes, A and Jiang, HC and Cheng, L and Jiao, JY and Li, WJ and Fang, BZ}, title = {Reversed oxidative TCA (roTCA) for carbon fixation by an Acidimicrobiia strain from a saline lake.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39073917}, issn = {1751-7370}, support = {2022B0202110001//Key-Area Research and Development Program of Guangdong Province/ ; 92251302//National Natural Science Foundation of China/ ; 2022D01A154//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2021FY100900//National Science and Technology Fundamental Resources Investigation Program of China/ ; 2022xjkk1200//Third Xinjiang Scientific Expedition Program/ ; }, mesh = {*Lakes/microbiology ; *Carbon Cycle ; *Phylogeny ; Oxidation-Reduction ; Citric Acid Cycle ; Chemoautotrophic Growth ; }, abstract = {Acidimicrobiia are widely distributed in nature and suggested to be autotrophic via the Calvin-Benson-Bassham (CBB) cycle. However, direct evidence of chemolithoautotrophy in Acidimicrobiia is lacking. Here, we report a chemolithoautotrophic enrichment from a saline lake, and the subsequent isolation and characterization of a chemolithoautotroph, Salinilacustristhrix flava EGI L10123T, which belongs to a new Acidimicrobiia family. Although strain EGI L10123T is autotrophic, neither its genome nor Acidimicrobiia metagenome-assembled genomes from the enrichment culture encode genes necessary for the CBB cycle. Instead, genomic, transcriptomic, enzymatic, and stable-isotope probing data hinted at the activity of the reversed oxidative TCA (roTCA) coupled with the oxidation of sulfide as the electron donor. Phylogenetic analysis and ancestral character reconstructions of Acidimicrobiia suggested that the essential CBB gene rbcL was acquired through multiple horizontal gene transfer events from diverse microbial taxa. In contrast, genes responsible for sulfide- or hydrogen-dependent roTCA carbon fixation were already present in the last common ancestor of extant Acidimicrobiia. These findings imply the possibility of roTCA carbon fixation in Acidimicrobiia and the ecological importance of Acidimicrobiia. Further research in the future is necessary to confirm whether these characteristics are truly widespread across the clade.}, }
@article {pmid39073766, year = {2024}, author = {González-Pinto, L and Alonso-García, I and Blanco-Martín, T and Camacho-Zamora, P and Fraile-Ribot, PA and Outeda-García, M and Lasarte-Monterrubio, C and Guijarro-Sánchez, P and Maceiras, R and Moya, B and Juan, C and Vázquez-Ucha, JC and Beceiro, A and Oliver, A and Bou, G and Arca-Suárez, J}, title = {Impact of chromosomally encoded resistance mechanisms and transferable β-lactamases on the activity of cefiderocol and innovative β-lactam/β-lactamase inhibitor combinations against Pseudomonas aeruginosa.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {79}, number = {10}, pages = {2591-2597}, pmid = {39073766}, issn = {1460-2091}, support = {//European Union/ ; //Merck Sharp &amp; Dohme/ ; //Investigator Initiated Studies Program/ ; CB21/13/00055//Centro de Investigaci&#xf3;n Biom&#xe9;dica en Red de Enfermedades Infecciosas/ ; //Spanish Network of Research in Infectious Diseases/ ; //National Plan for Scientific Research, Development and Technological Innovation 2013-2016/ ; //ISCIII-General Subdirection of Assessment and Promotion of the Research-European Regional Development Fund/ ; //Axencia Galega de Innovaci&#xf3;n/ ; IN607D2021/12//Conseller&#xed;a de Innovaci&#xf3;n, Conseller&#xed;a de Econom&#xed;a, Emprego e Industria/ ; PI21/00704//ISCIII/ ; CM21/00076//R&#xed;o Hortega program/ ; IN606B-2022/009//Xunta de Galicia/ ; JR21/00026//Juan Rod&#xe9;s program/ ; }, mesh = {*Pseudomonas aeruginosa/drug effects/genetics/enzymology ; *Cephalosporins/pharmacology ; *Microbial Sensitivity Tests ; *beta-Lactamase Inhibitors/pharmacology ; *beta-Lactamases/genetics/metabolism ; *Anti-Bacterial Agents/pharmacology ; *Azabicyclo Compounds/pharmacology ; *Drug Combinations ; *Cefiderocol ; Cyclooctanes/pharmacology ; Tazobactam/pharmacology ; beta-Lactams/pharmacology ; Humans ; beta-Lactam Resistance/genetics ; Ceftazidime/pharmacology ; Pseudomonas Infections/microbiology/drug therapy ; Gene Transfer, Horizontal ; Chromosomes, Bacterial/genetics ; }, abstract = {OBJECTIVES: We aimed to compare the stability of the newly developed β-lactams (cefiderocol) and β-lactam/β-lactamase inhibitor combinations (ceftazidime/avibactam, ceftolozane/tazobactam, aztreonam/avibactam, cefepime/taniborbactam, cefepime/zidebactam, imipenem/relebactam, meropenem/vaborbactam, meropenem/nacubactam and meropenem/xeruborbactam) against the most clinically relevant mechanisms of mutational and transferable β-lactam resistance in Pseudomonas aeruginosa.<br><br>METHODS: We screened a collection of 61 P. aeruginosa PAO1 derivatives. Eighteen isolates displayed the most relevant mechanisms of mutational resistance to &#x3b2;-lactams. The other 43 constructs expressed transferable &#x3b2;-lactamases from genes cloned in pUCP-24. MICs were determined by reference broth microdilution.<br><br>RESULTS: Cefiderocol and imipenem/relebactam exhibited excellent in vitro activity against all of the mutational resistance mechanisms studied. Aztreonam/avibactam, cefepime/taniborbactam, cefepime/zidebactam, meropenem/vaborbactam, meropenem/nacubactam and meropenem/xeruborbactam proved to be more vulnerable to mutational events, especially to overexpression of efflux operons. The agents exhibiting the widest spectrum of activity against transferable &#x3b2;-lactamases were aztreonam/avibactam and cefepime/zidebactam, followed by cefepime/taniborbactam, cefiderocol, meropenem/xeruborbactam and meropenem/nacubactam. However, some MBLs, particularly NDM enzymes, may affect their activity. Combined production of certain enzymes (e.g. NDM-1) with increased MexAB-OprM-mediated efflux and OprD deficiency results in resistance to almost all agents tested, including last options such as aztreonam/avibactam and cefiderocol.<br><br>CONCLUSIONS: Cefiderocol and new &#x3b2;-lactam/&#x3b2;-lactamase inhibitor combinations show promising and complementary in vitro activity against mutational and transferable P. aeruginosa &#x3b2;-lactam resistance. However, the combined effects of efflux pumps, OprD deficiency and efficient &#x3b2;-lactamases could still result in the loss of all therapeutic options. Resistance surveillance, judicious use of new agents and continued drug development efforts are encouraged.}, }
@article {pmid39071422, year = {2024}, author = {Robinson, LR and McDevitt, CJ and Regan, MR and Quail, SL and Wadsworth, CB}, title = {In vitro evolution of ciprofloxacin resistance in Neisseria commensals and derived mutation population dynamics in natural Neisseria populations.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39071422}, issn = {2692-8205}, support = {R15 AI174182/AI/NIAID NIH HHS/United States ; }, abstract = {Commensal Neisseria are members of a healthy human oropharyngeal microbiome; however, they also serve as a reservoir of antimicrobial resistance for their pathogenic relatives. Despite their known importance as sources of novel genetic variation for pathogens, we still do not understand the full suite of resistance mutations commensal species can harbor. Here, we use in vitro selection to assess the mutations that emerge in response to ciprofloxacin selection in commensal Neisseria by passaging 4 replicates of 4 different species in the presence of a selective antibiotic gradient for 20 days; then categorized derived mutations with whole genome sequencing. 10/16 selected cells lines across the 4 species evolved ciprofloxacin resistance (≥ 1 ug/ml); with resistance-contributing mutations primarily emerging in DNA gyrase subunit A and B (gyrA and gyrB), topoisomerase IV subunits C and E (parC and parE), and the multiple transferable efflux pump repressor (mtrR). Of note, these derived mutations appeared in the same loci responsible for ciprofloxacin reduced susceptibility in the pathogenic Neisseria, suggesting conserved mechanisms of resistance across the genus. Additionally, we tested for zoliflodacin cross-resistance in evolved strain lines and found 6 lineages with elevated zoliflodacin minimum inhibitory concentrations. Finally, to interrogate the likelihood of experimentally derived mutations emerging and contributing to resistance in natural Neisseria, we used a population-based approach and identified GyrA 91I as a substitution circulating within commensal Neisseria populations and ParC 85C in a single gonococcal isolate. Small clusters of gonococcal isolates had commensal-like alleles at parC and parE, indicating recent cross-species recombination events.}, }
@article {pmid39071318, year = {2024}, author = {Sloan, DB and Broz, AK and Kuster, SA and Muthye, V and Peñafiel-Ayala, A and Marron, JR and Lavrov, DV and Brieba, LG}, title = {Expansion of the MutS Gene Family in Plants.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39071318}, issn = {2692-8205}, support = {R35 GM148134/GM/NIGMS NIH HHS/United States ; T32 GM132057/GM/NIGMS NIH HHS/United States ; }, abstract = {The MutS gene family is distributed across the tree of life and is involved in recombination, DNA repair, and protein translation. Multiple evolutionary processes have expanded the set of MutS genes in plants relative to other eukaryotes. Here, we investigate the origins and functions of these plant-specific genes. Land plants, green algae, red algae, and glaucophytes share cyanobacterial-like MutS1 and MutS2 genes that presumably were gained via plastid endosymbiotic gene transfer. MutS1 was subsequently lost in some taxa, including seed plants, whereas MutS2 was duplicated in Viridiplantae (i.e., land plants and green algae) with widespread retention of both resulting paralogs. Viridiplantae also have two anciently duplicated copies of the eukaryotic MSH6 gene (i.e., MSH6 and MSH7) and acquired MSH1 via horizontal gene transfer - potentially from a nucleocytovirus. Despite sharing the same name, "plant MSH1" is not directly related to the gene known as MSH1 in some fungi and animals, which may be an ancestral eukaryotic gene acquired via mitochondrial endosymbiosis and subsequently lost in most eukaryotic lineages. There has been substantial progress in understanding the functions of MSH1 and MSH6/MSH7 in plants, but the roles of the cyanobacterial-like MutS1 and MutS2 genes remain uncharacterized. Known functions of bacterial homologs and predicted protein structures, including fusions to diverse nuclease domains, provide hypotheses about potential molecular mechanisms. Because most plant-specific MutS proteins are targeted to the mitochondria and/or plastids, the expansion of this family appears to have played a large role in shaping plant organelle genetics.}, }
@article {pmid39071313, year = {2024}, author = {Yang, XY and Shen, Z and Wang, C and Nakanishi, K and Fu, TM}, title = {DdmDE eliminates plasmid invasion by DNA-guided DNA targeting.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.07.20.604412}, pmid = {39071313}, issn = {2692-8205}, abstract = {Horizontal gene transfer is a key driver of bacterial evolution, but it also presents severe risks to bacteria by introducing invasive mobile genetic elements. To counter these threats, bacteria have developed various defense systems, including prokaryotic Argonautes (pAgo) and the D NA D efense M odule DdmDE system. Through biochemical analysis, structural determination, and in vivo plasmid clearance assays, we elucidate the assembly and activation mechanisms of DdmDE, which eliminates small, multicopy plasmids. We demonstrate that DdmE, a pAgo-like protein, acts as a catalytically inactive, DNA-guided, DNA-targeting defense module. In the presence of guide DNA, DdmE targets plasmids and recruits a dimeric DdmD, which contains nuclease and helicase domains. Upon binding to DNA substrates, DdmD transitions from an autoinhibited dimer to an active monomer, which then translocates along and cleaves the plasmids. Together, our findings reveal the intricate mechanisms underlying DdmDE-mediated plasmid clearance, offering fundamental insights into bacterial defense systems against plasmid invasions.}, }
@article {pmid39067739, year = {2024}, author = {Chen, X and Song, X and Liang, Y and Wang, F and Pan, C and Wei, Z}, title = {Evaluation of the potential horizontal gene transfer ability during chicken manure and pig manure composting.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {360}, number = {}, pages = {124621}, doi = {10.1016/j.envpol.2024.124621}, pmid = {39067739}, issn = {1873-6424}, mesh = {Animals ; *Manure ; *Chickens ; *Composting ; Swine ; *Gene Transfer, Horizontal ; Bacteria/genetics ; Soil Microbiology ; }, abstract = {Resistance genes have been identified as emerging pollutants due to their ability to rapidly spread in the environment through horizontal gene transfer (HGT). Microbial community serves as the pivotal factor influencing the frequency of HGT during manure composting. However, the characteristics of HGT in microbial community from different types of manure were unclear. Therefore, this study aimed to evaluate the potential risk of HGT in bacterial community through the co-composting of chicken manure and pig manure in different proportions. The experimental results showed that the abundance of sulfonamide antibiotic resistance genes and integrase genes was higher during pig manure composting than those during chicken manure composting. In addition, the addition of pig manure also increased resistance genes abundance during chicken manure composting. These results suggested that the potential HGT risk was greater during pig manure composting. Furthermore, microbial analysis of co-composting suggested that bacterial community of pig manure was more competitive and adaptable than that of chicken manure. Ultimately, statistical analysis indicated that compared to chicken manure composting, the potential ability of HGT was greater during pig manure composting. This study provided the vital theoretical support and scientific guidance for mitigating the HGT risk during manure composting.}, }
@article {pmid39067603, year = {2024}, author = {Liu, M and Kasuga, I}, title = {Impact of chlorine disinfection on intracellular and extracellular antimicrobial resistance genes in wastewater treatment and water reclamation.}, journal = {The Science of the total environment}, volume = {949}, number = {}, pages = {175046}, doi = {10.1016/j.scitotenv.2024.175046}, pmid = {39067603}, issn = {1879-1026}, mesh = {*Chlorine ; *Wastewater/microbiology ; *Waste Disposal, Fluid/methods ; *Disinfection/methods ; Disinfectants ; Genes, Bacterial ; Water Purification/methods ; Drug Resistance, Bacterial/genetics ; Bacteria/drug effects/genetics ; Drug Resistance, Microbial/genetics ; }, abstract = {Wastewater treatment plants and water reclamation facilities are reservoirs of antimicrobial resistance genes (ARGs). These ARGs are not limited solely to intracellular DNA (inARGs) but include extracellular DNA (exARGs) present in wastewater. The release of exARGs from cells can be exacerbated by treatment processes, including chlorine disinfection, which disrupts bacterial cells. Given the potential for exARGs to drive horizontal gene transfer and contribute to the proliferation of antimicrobial resistance, it is imperative to recognize these fractions as emerging environmental pollutants. In this study, we conducted a comprehensive year-long assessment of both inARGs and exARGs, further differentiating between dissolved exARGs (Dis_exARGs) and exARGs adsorbed onto particulate matter (Ads_exARGs), within a full-scale wastewater treatment and water reclamation facility. The results revealed that Ads_exARGs comprised up to 30 % of the total ARGs in raw sewage with high biomass content. Generally, treatments at low and high doses of chlorine increased the abundance of Dis_exARGs and Ads_exARGs. The fate of ARG levels that varied depending on the type of ARGs suggested variations in the susceptibility of the host bacteria to chlorination. Moreover, co-occurrence of several potential opportunistic pathogenic bacteria and ARGs were observed. Therefore, we propose higher doses of chlorination as a prerequisite for the effective removal of inARGs and exARGs.}, }
@article {pmid39066295, year = {2024}, author = {Li, W and Tahiri, N}, title = {Host-Virus Cophylogenetic Trajectories: Investigating Molecular Relationships between Coronaviruses and Bat Hosts.}, journal = {Viruses}, volume = {16}, number = {7}, pages = {}, pmid = {39066295}, issn = {1999-4915}, support = {326911//Fonds de recherche du Qu&#xe9;bec/ ; RGPIN-2022-04322//Natural Sciences and Engineering Research Council/ ; }, mesh = {*Chiroptera/virology ; Animals ; *Phylogeny ; *Coronavirus/genetics/classification/physiology ; Evolution, Molecular ; Host-Pathogen Interactions/genetics ; Spike Glycoprotein, Coronavirus/genetics/metabolism ; Host Specificity ; Coronavirus Infections/virology ; }, abstract = {Bats, with their virus tolerance, social behaviors, and mobility, are reservoirs for emerging viruses, including coronaviruses (CoVs) known for genetic flexibility. Studying the cophylogenetic link between bats and CoVs provides vital insights into transmission dynamics and host adaptation. Prior research has yielded valuable insights into phenomena such as host switching, cospeciation, and other dynamics concerning the interaction between CoVs and bats. Nonetheless, a distinct gap exists in the current literature concerning a comparative cophylogenetic analysis focused on elucidating the contributions of sequence fragments to the co-evolution between hosts and viruses. In this study, we analyzed the cophylogenetic patterns of 69 host-virus connections. Among the 69 host-virus links examined, 47 showed significant cophylogeny based on ParaFit and PACo analyses, affirming strong associations. Focusing on two proteins, ORF1ab and spike, we conducted a comparative analysis of host and CoV phylogenies. For ORF1ab, the specific window ranged in multiple sequence alignment (positions 520-680, 770-870, 2930-3070, and 4910-5080) exhibited the lowest Robinson-Foulds (RF) distance (i.e., 84.62%), emphasizing its higher contribution in the cophylogenetic association. Similarly, within the spike region, distinct window ranges (positions 0-140, 60-180, 100-410, 360-550, and 630-730) displayed the lowest RF distance at 88.46%. Our analysis identified six recombination regions within ORF1ab (positions 360-1390, 550-1610, 680-1680, 700-1710, 2060-3090, and 2130-3250), and four within the spike protein (positions 10-510, 50-560, 170-710, and 230-730). The convergence of minimal RF distance regions with combination regions robustly affirms the pivotal role of recombination in viral adaptation to host selection pressures. Furthermore, horizontal gene transfer reveals prominent instances of partial gene transfer events, occurring not only among variants within the same host species but also crossing host species boundaries. This suggests a more intricate pattern of genetic exchange. By employing a multifaceted approach, our comprehensive strategy offers a nuanced understanding of the intricate interactions that govern the co-evolutionary dynamics between bat hosts and CoVs. This deeper insight enhances our comprehension of viral evolution and adaptation mechanisms, shedding light on the broader dynamics that propel viral diversity.}, }
@article {pmid39061350, year = {2024}, author = {Drane, K and Sheehan, M and Whelan, A and Ariel, E and Kinobe, R}, title = {The Role of Wastewater Treatment Plants in Dissemination of Antibiotic Resistance: Source, Measurement, Removal and Risk Assessment.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {7}, pages = {}, pmid = {39061350}, issn = {2079-6382}, support = {2256.95982.2331//Townsville City Council, Townsville Australia/ ; }, abstract = {Antibiotic Resistance Genes (ARGs) are contaminants of emerging concern with marked potential to impact public and environmental health. This review focusses on factors that influence the presence, abundance, and dissemination of ARGs within Wastewater Treatment Plants (WWTPs) and associated effluents. Antibiotic-Resistant Bacteria (ARB) and ARGs have been detected in the influent and the effluent of WWTPs worldwide. Different levels of wastewater treatment (primary, secondary, and tertiary) show different degrees of removal efficiency of ARGs, with further differences being observed when ARGs are captured as intracellular or extracellular forms. Furthermore, routinely used molecular methodologies such as quantitative polymerase chain reaction or whole genome sequencing may also vary in resistome identification and in quantifying ARG removal efficiencies from WWTP effluents. Additionally, we provide an overview of the One Health risk assessment framework, as well as future strategies on how WWTPs can be assessed for environmental and public health impact.}, }
@article {pmid39061343, year = {2024}, author = {Fahy, S and O'Connor, JA and Sleator, RD and Lucey, B}, title = {From Species to Genes: A New Diagnostic Paradigm.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {7}, pages = {}, pmid = {39061343}, issn = {2079-6382}, abstract = {Molecular diagnostics has the potential to revolutionise the field of clinical microbiology. Microbial identification and nomenclature have, for too long, been restricted to phenotypic characterisation. However, this species-level view fails to wholly account for genetic heterogeneity, a result of lateral gene transfer, mediated primarily by mobile genetic elements. This genetic promiscuity has helped to drive virulence development, stress adaptation, and antimicrobial resistance in several important bacterial pathogens, complicating their detection and frustrating our ability to control them. We argue that, as clinical microbiologists at the front line, we must embrace the molecular technologies that allow us to focus specifically on the genetic elements that cause disease rather than the bacterial species that express them. This review focuses on the evolution of microbial taxonomy since the introduction of molecular sequencing, the role of mobile genetic elements in antimicrobial resistance, the current and emerging assays in clinical laboratories, and the comparison of phenotypic versus genotypic analyses. In essence, it is time now to refocus from species to genes as part of a new diagnostic paradigm.}, }
@article {pmid39061274, year = {2024}, author = {Ghazawi, A and Anes, F and Mouftah, S and Elbediwi, M and Baig, A and Alketbi, M and Almazrouei, F and Alhashmi, M and Alzarooni, N and Manzoor, A and Habib, I and Strepis, N and Nabi, A and Khan, M}, title = {Genomic Study of High-Risk Clones of Enterobacter hormaechei Collected from Tertiary Hospitals in the United Arab Emirates.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {7}, pages = {}, pmid = {39061274}, issn = {2079-6382}, support = {G00004620 and G00004164//United Arab Emirates University/ ; }, abstract = {Enterobacter hormaechei has emerged as a significant pathogen within healthcare settings due to its ability to develop multidrug resistance (MDR) and survive in hospital environments. This study presents a genome-based analysis of carbapenem-resistant Enterobacter hormaechei isolates from two major hospitals in the United Arab Emirates. Eight isolates were subjected to whole-genome sequencing (WGS), revealing extensive resistance profiles including the blaNDM-1, blaOXA-48, and blaVIM-4 genes. Notably, one isolate belonging to ST171 harbored dual carbapenemase genes, while five isolates exhibited colistin resistance without mcr genes. The presence of the type VI secretion system (T6SS), various adhesins, and virulence genes contributes to the virulence and competitive advantage of the pathogen. Additionally, our isolates (87.5%) possessed ampC β-lactamase genes, predominantly blaACT genes. The genomic context of blaNDM-1, surrounded by other resistance genes and mobile genetic elements, highlights the role of horizontal gene transfer (HGT) in the spread of resistance. Our findings highlight the need for rigorous surveillance, strategic antibiotic stewardship, and hospital-based WGS to manage and mitigate the spread of these highly resistant and virulent pathogens. Accurate identification and monitoring of Enterobacter cloacae complex (ECC) species and their resistance mechanisms are crucial for effective infection control and treatment strategies.}, }
@article {pmid39060998, year = {2024}, author = {Seth-Smith, H and Bommana, S and Dean, D and Read, TD and Marti, H}, title = {Chlamydia suis undergoes interclade recombination promoting Tet-island exchange.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {724}, pmid = {39060998}, issn = {1471-2164}, support = {323530_177579//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; }, mesh = {*Chlamydia/genetics ; *Recombination, Genetic ; *Phylogeny ; *Tetracycline Resistance/genetics ; *Genomic Islands ; Animals ; Swine ; Gene Transfer, Horizontal ; Genome, Bacterial ; }, abstract = {BACKGROUND: The obligate intracellular bacterial family Chlamydiaceae comprises a number of different species that cause disease in various vertebrate hosts including humans. Chlamydia suis, primarily found in the gastrointestinal tract of pigs, is the only species of the Chlamydiaceae family to have naturally gained tetracycline resistance (TetR), through a genomic island (Tet-island), integrated into the middle of chromosomal invasin-like gene inv. Previous studies have hypothesised that the uptake of the Tet-island from a host outside the Chlamydiaceae family was a unique event, followed by spread among C. suis through homologous recombination. In vitro recombination studies have shown that Tet-island exchange between C. suis strains is possible. Our aim in this study was to gain a deeper understanding of the interclade recombination of the Tet-island, among currently circulating C. suis field strains compared to in vitro-generated recombinants, using published whole genome sequences of C. suis field strains (n = 35) and in vitro-generated recombinants (n = 63).<br><br>RESULTS: We found that the phylogeny of inv better reflected the phylogeny of the Tet-island than that of the whole genome, supporting recombination rather than site-specific insertion as the means of transfer. There were considerable differences between the distribution of recombinations within in vitro-generated strains compared to that within the field strains. These differences are likely because in vitro-generated recombinants were selected for a tetracycline and rifamycin/rifampicin resistant background, leading to the largest peak of recombination across the Tet-island. Finally, we found that interclade recombinations across the Tet-island were more variable in length downstream of the Tet-island than upstream.<br><br>CONCLUSIONS: Our study supports the hypothesis that the occurrence of TetR strains in both clades of C. suis came about through interclade recombination after a single ancestral horizontal gene transfer event.}, }
@article {pmid39058093, year = {2024}, author = {Peñil-Celis, A and Tagg, KA and Webb, HE and Redondo-Salvo, S and Francois Watkins, L and Vielva, L and Griffin, C and Kim, JY and Folster, JP and Garcillan-Barcia, MP and de la Cruz, F}, title = {Mobile genetic elements define the non-random structure of the Salmonella enterica serovar Typhi pangenome.}, journal = {mSystems}, volume = {9}, number = {8}, pages = {e0036524}, pmid = {39058093}, issn = {2379-5077}, support = {PID2020-117923GB-I00 MCIN/AEI/10.13039/501100011033//Ministerio de Ciencia e Innovaci&#xf3;n (MCIN)/ ; PID2020-117923GB-I00 MCIN/AEI/10.13039/501100011033//Ministerio de Ciencia e Innovaci&#xf3;n (MCIN)/ ; Contracts No. 75D30119C06679 and 75D30121C11978//HHS | Centers for Disease Control and Prevention (CDC)/ ; DI-17-09164//Ministerio de Econom&#xed;a y Competitividad (MEC)/ ; }, mesh = {*Salmonella typhi/genetics ; *Genome, Bacterial/genetics ; *Interspersed Repetitive Sequences/genetics ; Plasmids/genetics ; Evolution, Molecular ; Humans ; Phylogeny ; Typhoid Fever/microbiology/epidemiology ; }, abstract = {Bacterial relatedness measured using select chromosomal loci forms the basis of public health genomic surveillance. While approximating vertical evolution through this approach has proven exceptionally valuable for understanding pathogen dynamics, it excludes a fundamental dimension of bacterial evolution-horizontal gene transfer. Incorporating the accessory genome is the logical remediation and has recently shown promise in expanding epidemiological resolution for enteric pathogens. Employing k-mer-based Jaccard index analysis, and a novel genome length distance metric, we computed pangenome (i.e., core and accessory) relatedness for the globally important pathogen Salmonella enterica serotype Typhi (Typhi), and graphically express both vertical (homology-by-descent) and horizontal (homology-by-admixture) evolutionary relationships in a reticulate network of over 2,200 U.S. Typhi genomes. This analysis revealed non-random structure in the Typhi pangenome that is driven predominantly by the gain and loss of mobile genetic elements, confirming and expanding upon known epidemiological patterns, revealing novel plasmid dynamics, and identifying avenues for further genomic epidemiological exploration. With an eye to public health application, this work adds important biological context to the rapidly improving ways of analyzing bacterial genetic data and demonstrates the value of the accessory genome to infer pathogen epidemiology and evolution.IMPORTANCEGiven bacterial evolution occurs in both vertical and horizontal dimensions, inclusion of both core and accessory genetic material (i.e., the pangenome) is a logical step toward a more thorough understanding of pathogen dynamics. With an eye to public, and indeed, global health relevance, we couple contemporary tools for genomic analysis with decades of research on mobile genetic elements to demonstrate the value of the pangenome, known and unknown, annotated, and hypothetical, for stratification of Salmonella enterica serovar Typhi (Typhi) populations. We confirm and expand upon what is known about Typhi epidemiology, plasmids, and antimicrobial resistance dynamics, and offer new avenues of exploration to further deduce Typhi ecology and evolution, and ultimately to reduce the incidence of human disease.}, }
@article {pmid39056664, year = {2024}, author = {Aguirre-Carvajal, K and Munteanu, CR and Armijos-Jaramillo, V}, title = {Database Bias in the Detection of Interdomain Horizontal Gene Transfer Events in Pezizomycotina.}, journal = {Biology}, volume = {13}, number = {7}, pages = {}, pmid = {39056664}, issn = {2079-7737}, support = {PRG.BIO.23.14.01//Universidad de Las Am&#xe9;ricas/ ; }, abstract = {Horizontal gene transfer (HGT) is a widely acknowledged phenomenon in prokaryotes for generating genetic diversity. However, the impact of this process in eukaryotes, particularly interdomain HGT, is a topic of debate. Although there have been observed biases in interdomain HGT detection, little exploration has been conducted on the effects of imbalanced databases. In our study, we conducted experiments to assess how different databases affect the detection of interdomain HGT using proteomes from the Pezizomycotina fungal subphylum as our focus group. Our objective was to simulate the database imbalance commonly found in public biological databases, where bacterial and eukaryotic sequences are unevenly represented, and demonstrate that an increase in uploaded eukaryotic sequences leads to a decrease in predicted HGTs. For our experiments, four databases with varying proportions of eukaryotic sequences but consistent proportions of bacterial sequences were utilized. We observed a significant reduction in detected interdomain HGT candidates as the proportion of eukaryotes increased within the database. Our data suggest that the imbalance in databases bias the interdomain HGT detection and highlights challenges associated with confirming the presence of interdomain HGT among Pezizomycotina fungi and potentially other groups within Eukarya.}, }
@article {pmid39053184, year = {2024}, author = {Checcucci, A and Buscaroli, E and Modesto, M and Luise, D and Blasioli, S and Scarafile, D and Di Vito, M and Bugli, F and Trevisi, P and Braschi, I and Mattarelli, P}, title = {The swine waste resistome: Spreading and transfer of antibiotic resistance genes in Escherichia coli strains and the associated microbial communities.}, journal = {Ecotoxicology and environmental safety}, volume = {283}, number = {}, pages = {116774}, doi = {10.1016/j.ecoenv.2024.116774}, pmid = {39053184}, issn = {1090-2414}, mesh = {Animals ; *Escherichia coli/genetics/drug effects ; Swine ; *Manure/microbiology ; *Gene Transfer, Horizontal ; *Integrons/genetics ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Microbiota/drug effects ; Drug Resistance, Microbial/genetics ; }, abstract = {The overuse of antimicrobials in livestock farming has led to the development of resistant bacteria and the spread of antibiotic-resistant genes (ARGs) among animals. When manure containing these antibiotics is applied to agricultural fields, it creates a selective pressure that promotes the acquisition of ARGs by bacteria, primarily through horizontal gene transfer. Most research on ARGs focuses on their role in clinical antibiotic resistance and their transfer from environmental sources to bacteria associated with humans, such as Escherichia coli. The study investigates the spread of antibiotic-resistant genes (ARGs) through class 1 integrons in 27 Escherichia coli strains from pig manure. It focuses on six common ARGs (ermB, cmlA, floR, qnrS, tetA, and TEM) and the class 1 integron gene, assessing their prevalence in manure samples from three pig farms. The study found correlations and anticorrelations among these genes, indicating a predisposition of the integron in spreading certain ARGs. Specifically, cmlA and tetA genes were positively correlated with each other and negatively with int1, suggesting they are not transferred via Int1. Farm B had the highest int1 counts and a higher abundance of the TEM gene, but lower levels of cmlA and tetA genes. The results underscore the complexity of predicting ARG spread in agricultural environments and the associated health risks to humans through the food chain. The study's results offer valuable insights into the antibiotic-resistant genes (ARGs) profile in swine livestock, potentially aiding in the development of methods to trace ARGs in the environment.}, }
@article {pmid39052705, year = {2024}, author = {Wan, Y and Myall, AC and Boonyasiri, A and Bolt, F and Ledda, A and Mookerjee, S and Weiße, AY and Getino, M and Turton, JF and Abbas, H and Prakapaite, R and Sabnis, A and Abdolrasouli, A and Malpartida-Cardenas, K and Miglietta, L and Donaldson, H and Gilchrist, M and Hopkins, KL and Ellington, MJ and Otter, JA and Larrouy-Maumus, G and Edwards, AM and Rodriguez-Manzano, J and Didelot, X and Barahona, M and Holmes, AH and Jauneikaite, E and Davies, F}, title = {Integrated Analysis of Patient Networks and Plasmid Genomes to Investigate a Regional, Multispecies Outbreak of Carbapenemase-Producing Enterobacterales Carrying Both blaIMP and mcr-9 Genes.}, journal = {The Journal of infectious diseases}, volume = {230}, number = {1}, pages = {e159-e170}, pmid = {39052705}, issn = {1537-6613}, support = {MRF-145-0004-TPG-AVISO/MRF/MRF/United Kingdom ; PSN109//Imperial College London/ ; //National Institute for Health Research/ ; //Imperial Health Charity/ ; EP/N014529///EPSRC Centre for Mathematics of Precision Healthcare/ ; M683//Stoneygate Trust/ ; /WT_/Wellcome Trust/United Kingdom ; //UK Health Security Agency/ ; //Imperial Biomedical Research Centre/ ; MR/T005254/1/MRC_/Medical Research Council/United Kingdom ; //NIHR Health Protection Research Unit/ ; //NIHR Health Protection Research Unit in Genomics and Enabling Data/ ; //Faculty of Medicine, Siriraj Hospital, Mahidol University/ ; NIHR200915//University of Oxford/ ; //Rosetrees Trust/ ; }, mesh = {Humans ; *Plasmids/genetics ; *beta-Lactamases/genetics ; *Enterobacteriaceae Infections/epidemiology/microbiology/transmission ; *Disease Outbreaks ; *Bacterial Proteins/genetics ; London/epidemiology ; Anti-Bacterial Agents/pharmacology ; Phylogeny ; Genome, Bacterial ; Male ; Female ; Middle Aged ; Microbial Sensitivity Tests ; Adult ; Enterobacteriaceae/genetics/drug effects ; Aged ; Carbapenem-Resistant Enterobacteriaceae/genetics/isolation &amp; purification ; Colistin/pharmacology ; }, abstract = {BACKGROUND: Carbapenemase-producing Enterobacterales (CPE) are challenging in healthcare, with resistance to multiple classes of antibiotics. This study describes the emergence of imipenemase (IMP)-encoding CPE among diverse Enterobacterales species between 2016 and 2019 across a London regional network.<br><br>METHODS: We performed a network analysis of patient pathways, using electronic health records, to identify contacts between IMP-encoding CPE-positive patients. Genomes of IMP-encoding CPE isolates were overlaid with patient contacts to imply potential transmission events.<br><br>RESULTS: Genomic analysis of 84 Enterobacterales isolates revealed diverse species (predominantly Klebsiella spp, Enterobacter spp, and Escherichia coli); 86% (72 of 84) harbored an IncHI2 plasmid carrying blaIMP and colistin resistance gene mcr-9 (68 of 72). Phylogenetic analysis of IncHI2 plasmids identified 3 lineages showing significant association with patient contacts and movements between 4 hospital sites and across medical specialties, which was missed in initial investigations.<br><br>CONCLUSIONS: Combined, our patient network and plasmid analyses demonstrate an interspecies, plasmid-mediated outbreak of blaIMPCPE, which remained unidentified during standard investigations. With DNA sequencing and multimodal data incorporation, the outbreak investigation approach proposed here provides a framework for real-time identification of key factors causing pathogen spread. Plasmid-level outbreak analysis reveals that resistance spread may be wider than suspected, allowing more interventions to stop transmission within hospital networks.SummaryThis was an investigation, using integrated pathway networks and genomics methods, of the emergence of imipenemase-encoding carbapenemase-producing Enterobacterales among diverse Enterobacterales species between 2016 and 2019 in patients across a London regional hospital network, which was missed on routine investigations.}, }
@article {pmid39052112, year = {2024}, author = {Li, H and Liu, B and Li, M and Shen, M}, title = {Livestock and poultry breeding farms as a fixed and underestimated source of antibiotic resistance genes.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {37}, pages = {49916-49931}, pmid = {39052112}, issn = {1614-7499}, mesh = {Animals ; *Poultry ; *Livestock ; *Drug Resistance, Microbial/genetics ; *Farms ; Anti-Bacterial Agents/pharmacology ; Animal Husbandry ; Drug Resistance, Bacterial/genetics ; }, abstract = {The excessive use of antibiotics, disinfectants, and drugs in livestock and poultry breeding has resulted in a rise in the presence of antibiotic resistance genes (ARGs). Antibiotic-resistant bacteria (ARB) and ARGs have been widely found in animal feces, farm wastewater, and farm air. ARGs can not only spread across media through adsorption and migration, but also transfer resistance across bacterial genera through horizontal gene transfer. Livestock breeding has become a fixed and unavoidable source of ARGs in the environment. Existing technologies for controlling ARGs, such as composting, disinfection, and sewage treatment, are not efficient in removing ARB and ARGs from waste. Furthermore, the remaining ARGs still possess a strong capacity for dissemination. At present, antibiotics used in animal husbandry are difficult to replace in a short period of time. The growth and potential risks of resistance genes in livestock and poultry breeding sources in the receiving environment are not yet clear. In this paper, we summarize the current situation of ARGs in the livestock and poultry breeding environment. We also explain the key environmental processes, main influencing factors, and corresponding ecological risks associated with ARGs in this environment. The advantages and disadvantages of current technologies for the removal of ARGs are primarily discussed. There is a particular emphasis on clarifying the spatiotemporal evolution patterns and environmental process mechanisms of ARGs, as well as highlighting the importance and urgency of developing efficient pollution control technologies.}, }
@article {pmid39052074, year = {2024}, author = {Allman, ES and Baños, H and Garrote-Lopez, M and Rhodes, JA}, title = {Identifiability of Level-1 Species Networks from Gene Tree Quartets.}, journal = {Bulletin of mathematical biology}, volume = {86}, number = {9}, pages = {110}, pmid = {39052074}, issn = {1522-9602}, support = {P20 GM103395/GM/NIGMS NIH HHS/United States ; DMS-2331660//National Science Foundation/ ; P20GM103395//Foundation for the National Institutes of Health/ ; DMS-2051760//National Science Foundation/ ; }, mesh = {*Phylogeny ; *Mathematical Concepts ; *Models, Genetic ; *Gene Transfer, Horizontal ; Evolution, Molecular ; Genetic Speciation ; Gene Regulatory Networks ; Computer Simulation ; Hybridization, Genetic ; }, abstract = {When hybridization or other forms of lateral gene transfer have occurred, evolutionary relationships of species are better represented by phylogenetic networks than by trees. While inference of such networks remains challenging, several recently proposed methods are based on quartet concordance factors-the probabilities that a tree relating a gene sampled from the species displays the possible 4-taxon relationships. Building on earlier results, we investigate what level-1 network features are identifiable from concordance factors under the network multispecies coalescent model. We obtain results on both topological features of the network, and numerical parameters, uncovering a number of failures of identifiability related to 3-cycles in the network. Addressing these identifiability issues is essential for designing statistically consistent inference methods.}, }
@article {pmid39047887, year = {2024}, author = {Wu, X and Jia, W and Fang, Z and Sun, H and Wang, G and Liu, L and Zheng, M and Chen, G}, title = {Cyanobacteria mediate the dissemination of bacterial antibiotic resistance through conjugal transfer.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {359}, number = {}, pages = {124592}, doi = {10.1016/j.envpol.2024.124592}, pmid = {39047887}, issn = {1873-6424}, mesh = {*Drug Resistance, Bacterial/genetics ; *Microcystis/genetics ; *Gene Transfer, Horizontal ; *Cyanobacteria/genetics ; Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; Genes, Bacterial ; Bacteria/genetics/drug effects ; }, abstract = {Cyanobacterial blooms are expanding world-wide in freshwater and marine environments, and can cause serious ecological and environmental issues, which also contribute to the spread of antibiotic resistance genes (ARGs). However, the mechanistic understanding of cyanobacteria-mediated resistance dynamics is not fully elucidated yet. We selected Microcystis aeruginosa as a model cyanobacteria to illustrate how cyanobacteria mediate the evolution and transfer processes of bacterial antibiotic resistance. The results show that the presence of cyanobacteria significantly decreased the abundance of antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs) by 3%-99% and 2%-18%, respectively. In addition, it clearly altered bacterial community structure, with the dominant genera evolving from Acinetobacter (27%) and Enterobacter (42%) to Porphyrobacter (59%). The abundance of ARGs positively correlated with Proteobacteria and Firmicutes, rather than Cyanobacteria, and Bacteroidetes. In the presence of cyanobacteria, the transfer events of bacterial resistance genes via conjugation were found to decrease by 10%-89% (p < 0.05). Surprisingly, we found an extradentary high transfer frequency (about 0.1) for the ARGs via plasmid conjugation from the bacteria into M. aeruginosa population. It confirmed the role of cyanobacterial population as the competent hosts to facilitate ARGs spreading. Our findings provide valuable information on the risk evaluation of ARGs caused by cyanobacterial blooms in aquatic environments, key for the protection and assessment of aquatic environmental quality.}, }
@article {pmid39044460, year = {2024}, author = {Roulet, ME and Ceriotti, LF and Gatica-Soria, L and Sanchez-Puerta, MV}, title = {Horizontally transferred mitochondrial DNA tracts become circular by microhomology-mediated repair pathways.}, journal = {The New phytologist}, volume = {243}, number = {6}, pages = {2442-2456}, doi = {10.1111/nph.19984}, pmid = {39044460}, issn = {1469-8137}, support = {PICT2020-01018//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; 06/A092-T1//Secretar&#xed;a de Investigaci&#xf3;n, Internacionales y Posgrado, Universidad Nacional de Cuyo/ ; }, mesh = {*Gene Transfer, Horizontal ; *DNA, Mitochondrial/genetics ; *Phylogeny ; *DNA, Circular/genetics ; DNA Repair/genetics ; Genome, Mitochondrial/genetics ; }, abstract = {The holoparasitic plant Lophophytum mirabile exhibits remarkable levels of mitochondrial horizontal gene transfer (HGT). Gathering comparative data from other individuals and host plants can provide insights into the HGT process. We sequenced the mitochondrial genome (mtDNA) from individuals of two species of Lophophytum and from mimosoid hosts. We applied a stringent phylogenomic approach to elucidate the origin of the whole mtDNAs, estimate the timing of the transfers, and understand the molecular mechanisms involved. Ancestral and recent HGT events replaced and enlarged the multichromosomal mtDNA of Lophophytum spp., with the foreign DNA ascending to 74%. A total of 14 foreign mitochondrial chromosomes originated from continuous regions in the host mtDNA flanked by short direct repeats. These foreign tracts are circularized by microhomology-mediated repair pathways and replicate independently until they are lost or they eventually recombine with other chromosomes. The foreign noncoding chromosomes are variably present in the population and likely evolve by genetic drift. We present the 'circle-mediated HGT' model in which foreign mitochondrial DNA tracts become circular and are maintained as plasmid-like molecules. This model challenges the conventional belief that foreign DNA must be integrated into the recipient genome for successful HGT.}, }
@article {pmid39042422, year = {2024}, author = {Alves, J and Dry, I and White, JH and Dryden, DTF and Lynskey, NN}, title = {Generation of tools for expression and purification of the phage-encoded Type I restriction enzyme inhibitor, Ocr.}, journal = {Microbiology (Reading, England)}, volume = {170}, number = {7}, pages = {}, pmid = {39042422}, issn = {1465-2080}, mesh = {*Recombinant Proteins/genetics/metabolism/isolation &amp; purification ; Viral Proteins/genetics/metabolism ; Bacteriophages/genetics/enzymology ; Streptococcus pyogenes/genetics/enzymology/metabolism ; Transformation, Bacterial ; Deoxyribonucleases, Type I Site-Specific/metabolism/genetics ; Gene Expression ; Escherichia coli/genetics/metabolism ; }, abstract = {DNA manipulation is an essential tool in molecular microbiology research that is dependent on the ability of bacteria to take up and preserve foreign DNA by horizontal gene transfer. This process can be significantly impaired by the activity of bacterial restriction modification systems; bacterial operons comprising paired enzymatic activities that protectively methylate host DNA, while cleaving incoming unmodified foreign DNA. Ocr is a phage-encoded protein that inhibits Type I restriction modification systems, the addition of which significantly improves bacterial transformation efficiency. We recently established an improved and highly efficient transformation protocol for the important human pathogen group A Streptococcus using commercially available recombinant Ocr protein, manufacture of which has since been discontinued. In order to ensure the continued availability of Ocr protein within the research community, we have generated tools and methods for in-house Ocr production and validated the activity of the purified recombinant protein.}, }
@article {pmid39039821, year = {2024}, author = {Bohl, V and Mogk, A}, title = {When the going gets tough, the tough get going-Novel bacterial AAA+ disaggregases provide extreme heat resistance.}, journal = {Environmental microbiology}, volume = {26}, number = {7}, pages = {e16677}, doi = {10.1111/1462-2920.16677}, pmid = {39039821}, issn = {1462-2920}, support = {MO970/7-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Bacterial Proteins/metabolism/genetics ; HSP70 Heat-Shock Proteins/metabolism/genetics ; Thermotolerance ; Hot Temperature ; Bacteria/genetics/metabolism ; Endopeptidase Clp/metabolism/genetics ; Heat-Shock Proteins/metabolism/genetics ; Heat-Shock Response ; }, abstract = {Heat stress can lead to protein misfolding and aggregation, potentially causing cell death due to the loss of essential proteins. Bacteria, being particularly exposed to environmental stress, are equipped with disaggregases that rescue these aggregated proteins. The bacterial Hsp70 chaperone DnaK and the ATPase associated with diverse cellular activities protein ClpB form the canonical disaggregase in bacteria. While this combination operates effectively during physiological heat stress, it is ineffective against massive aggregation caused by temperature-based sterilization protocols used in the food industry and clinics. This leaves bacteria unprotected against these thermal processes. However, bacteria that can withstand extreme, man-made stress conditions have emerged. These bacteria possess novel ATPase associated with diverse cellular activities disaggregases, ClpG and ClpL, which are key players in extreme heat resistance. These disaggregases, present in selected Gram-negative or Gram-positive bacteria, respectively, function superiorly by exhibiting increased thermal stability and enhanced threading power compared to DnaK/ClpB. This enables ClpG and ClpL to operate at extreme temperatures and process large and tight protein aggregates, thereby contributing to heat resistance. The genes for ClpG and ClpL are often encoded on mobile genomic islands or conjugative plasmids, allowing for their rapid spread among bacteria via horizontal gene transfer. This threatens the efficiency of sterilization protocols. In this review, we describe the various bacterial disaggregases identified to date, characterizing their commonalities and the specific features that enable these novel disaggregases to provide stress protection against extreme stress conditions.}, }
@article {pmid39039101, year = {2024}, author = {Brown, CL and Maile-Moskowitz, A and Lopatkin, AJ and Xia, K and Logan, LK and Davis, BC and Zhang, L and Vikesland, PJ and Pruden, A}, title = {Author Correction: Selection and horizontal gene transfer underlie microdiversity-level heterogeneity in resistance gene fate during wastewater treatment.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {6166}, doi = {10.1038/s41467-024-50577-6}, pmid = {39039101}, issn = {2041-1723}, }
@article {pmid39038713, year = {2024}, author = {Sun, B and Bai, Z and Li, R and Song, M and Zhang, J and Wang, J and Zhuang, X}, title = {Efficient elimination of antibiotic resistome in livestock manure by semi-permeable membrane covered hyperthermophilic composting.}, journal = {Bioresource technology}, volume = {407}, number = {}, pages = {131134}, doi = {10.1016/j.biortech.2024.131134}, pmid = {39038713}, issn = {1873-2976}, mesh = {*Manure/microbiology ; *Composting/methods ; Animals ; *Membranes, Artificial ; *Drug Resistance, Microbial/genetics ; *Livestock ; Chickens ; Anti-Bacterial Agents/pharmacology ; Permeability ; Interspersed Repetitive Sequences ; }, abstract = {Livestock manure is a hotspot for antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), and an important contributor to antibiotic resistance in non-clinical settings. This study investigated the effectiveness and potential mechanisms of a novel composting technology, semi-permeable membrane covered hyperthermophilic composting (smHTC), in removal of ARGs and MGEs in chicken manure. Results showed that smHTC was more efficient in removal of ARGs and MGEs (92% and 93%) compared to conventional thermophilic composting (cTC) (76% and 92%). The efficient removal in smHTC is attributed to direct or indirect negative effects caused by the high temperature, including reducing the involvement of bio-available heavy metals (HMs) in co-selection processes of antibiotic resistance, decreasing the bacterial abundance and diversity, suppressing the horizontal gene transfer and killing potential ARGs hosts. Overall, smHTC can efficiently remove the resistome in livestock manure, reducing the risk to crops and humans from ARGs residues in compost products.}, }
@article {pmid39038196, year = {2024}, author = {Mori, BA and Coutu, C and Erlandson, MA and Hegedus, DD}, title = {Exploring the contribution of the salivary gland and midgut to digestion in the swede midge (Contarinia nasturtii) through a genomics-guided approach.}, journal = {Archives of insect biochemistry and physiology}, volume = {116}, number = {3}, pages = {e22135}, doi = {10.1002/arch.22135}, pmid = {39038196}, issn = {1520-6327}, support = {//Alberta Canola Producers Commission/ ; //Alberta Barley Commission/ ; //Alberta Wheat Commission/ ; 545088//NSERC Industrial Research Chair/ ; RGPIN-2021-02479//NSERC/ ; //Agriculture &amp; Agri-Food Canada Genomics Research and Development Initiative/ ; //Alberta Pulse Growers Commission/ ; }, mesh = {Animals ; *Salivary Glands/metabolism/enzymology ; *Larva/genetics/metabolism/growth &amp; development ; *Diptera/genetics/enzymology/metabolism ; Transcriptome ; Digestion ; Genomics ; Gastrointestinal Tract/metabolism ; Insect Proteins/metabolism/genetics ; }, abstract = {The larvae of Contarinia nasturtii (Kieffer) (Diptera: Cecidomyiidae), the swede midge, targets the meristem of brassica crops where they induce the formation of galls and disrupt seed and vegetable production. Previously, we examined the salivary gland transcriptome of newly-hatched first instar larvae as they penetrated the host and initiated gall formation. Here we examine the salivary gland and midgut transcriptome of third instar larvae and provide evidence for cooperative nutrient acquisition beginning with secretion of enzymes and feeding facilitators followed by gastrointestinal digestion. Sucrose, presumably obtained from the phloem, appeared to be a major nutrient source as several α-glucosidases (sucrases, maltases) and β-fructofuranosidases (invertases) were identified. Genes encoding β-fructofuranosidases/invertases were among the most highly expressed in both tissues and represented two distinct gene families that may have originated via horizontal gene transfer from bacteria. The importance of the phloem as a nutrient source is underscored by the expression of genes encoding regucalcin and ARMET (arginine-rich mutated in early stages of tumor) which interfere with calcium signalling and prevent sieve tube occlusion. Lipids, proteins, and starch appear to serve as a secondary nutrient sources. Genes encoding enzymes involved in the detoxification of glucosinolates (myrosinases, arylsulfatases, and glutathione-S-transferases) were expressed indicative of Brassicaceae host specialization. The midgut expressed simple peritrophins and mucins typical of those found in Type II peritrophic matrices, the first such description for a gall midge.}, }
@article {pmid39038013, year = {2024}, author = {Berg, A and Berntsson, RP and Barandun, J}, title = {Nematocida displodere mechanosensitive ion channel of small conductance 2 assembles into a unique 6-channel super-structure in vitro.}, journal = {PloS one}, volume = {19}, number = {7}, pages = {e0301951}, pmid = {39038013}, issn = {1932-6203}, mesh = {*Ion Channels/metabolism/chemistry/genetics ; *Cryoelectron Microscopy ; Animals ; Caenorhabditis elegans/metabolism/genetics ; Microsporidia/metabolism/genetics ; Mechanotransduction, Cellular ; }, abstract = {Mechanosensitive ion channels play an essential role in reacting to environmental signals and sustaining cell integrity by facilitating ion flux across membranes. For obligate intracellular pathogens like microsporidia, adapting to changes in the host environment is crucial for survival and propagation. Despite representing a eukaryote of extreme genome reduction, microsporidia have expanded the gene family of mechanosensitive ion channels of small conductance (mscS) through repeated gene duplication and horizontal gene transfer. All microsporidian genomes characterized to date contain mscS genes of both eukaryotic and bacterial origin. Here, we investigated the cryo-electron microscopy structure of the bacterially derived mechanosensitive ion channel of small conductance 2 (MscS2) from Nematocida displodere, an intracellular pathogen of Caenorhabditis elegans. MscS2 is the most compact MscS-like channel known and assembles into a unique superstructure in vitro with six heptameric MscS2 channels. Individual MscS2 channels are oriented in a heterogeneous manner to one another, resembling an asymmetric, flexible six-way cross joint. Finally, we show that microsporidian MscS2 still forms a heptameric membrane channel, however the extreme compaction suggests a potential new function of this MscS-like protein.}, }
@article {pmid39037483, year = {2024}, author = {de Carvalho, A and Giambiagi-deMarval, M and Rossi, CC}, title = {Mammaliicoccus sciuri's Pan-Immune System and the Dynamics of Horizontal Gene Transfer Among Staphylococcaceae: a One-Health CRISPR Tale.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {62}, number = {9}, pages = {775-784}, pmid = {39037483}, issn = {1976-3794}, support = {408564/2023-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 304839/2022-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; E-26/010.000172/2016; 010.00128/2016; E-26.210.875/2016//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; 101056/2018; 001463/2019; 211.554/2019; 201.071/2020//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; 200.895/2021//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; E-26/204.925/2022//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; APQ-03498-22//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; 23038.002486/2018-26//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; }, mesh = {*Gene Transfer, Horizontal ; *CRISPR-Cas Systems ; Humans ; Animals ; *One Health ; Genome, Bacterial ; Virulence/genetics ; Phylogeny ; }, abstract = {Recently emancipated from the Staphylococcus genus due to genomic differences, Mammaliicoccus sciuri, previously classified as an occasional pathogen, emerges as a significant player in the landscape of resistance gene dissemination among Staphylococcaceae. Despite its classification, its role remained enigmatic. In this study, we delved into the genomic repertoire of M. sciuri to unravel its contribution to resistance and virulence gene transfer in the context of One Health. Through comprehensive analysis of publicly available genomes, we unveiled a diverse pan-immune system adept at defending against exogenous genetic elements, yet concurrently fostering horizontal gene transfer (HGT). Specifically, exploration of CRISPR-Cas systems, with spacer sequences as molecular signatures, elucidated a global dissemination pattern spanning environmental, animal, and human hosts. Notably, we identified the integration of CRISPR-Cas systems within SCCmecs (Staphylococcal Cassette Chromosome mec), harboring key genes associated with pathogenicity and resistance, especially the methicillin resistance gene mecA, suggesting a strategic adaptation to outcompete other mobile genetic elements. Our findings underscored M. sciuri's active engagement in HGT dynamics and evolutionary trajectories within Staphylococcaceae, emphasizing its central role in shaping microbial communities and highlighting the significance of understanding its implications in the One Health framework, an interdisciplinary approach that recognizes the interconnectedness of human, animal, and environmental health to address global health challenges.}, }
@article {pmid39035534, year = {2024}, author = {Gheorghe-Barbu, I and Surleac, M and Barbu, IC and Paraschiv, S and Bănică, LM and Rotaru, LI and Vrâncianu, CO and Niță Lazăr, M and Oțelea, D and Chifiriuc, MC}, title = {Decoding the resistome, virulome and mobilome of clinical versus aquatic Acinetobacter baumannii in southern Romania.}, journal = {Heliyon}, volume = {10}, number = {13}, pages = {e33372}, pmid = {39035534}, issn = {2405-8440}, abstract = {Acinetobacter baumannii, a notorious opportunistic pathogen, presents a formidable challenge in both clinical and environmental fields due to its resilience and ability to acquire resistance. This study undertook a comprehensive analysis of 183 A. baumannii isolates collected between 2019 and 2022 from intra-hospital infections (IHI), hospital sewages (Hs), wastewater treatment plants (WWTP), and adjacent river waters from two Southern cities, focusing on their resistome, virulome, and mobilome through isolation on chromogenic media, identification by MALDI-TOF-MS and antibiotic susceptibility testing by disk diffusion) followed by genotypic characterization [Whole Genome Sequencing (WGS), 3rd generation sequencing through the MinION (ONT) platform, pangenome description, and respectively horizontal gene transfer through conjugation assays]. Our findings reveal significant genomic plasticity and the prevalence of high-risk international clones, underlining the potential of these isolates to act as reservoirs for antibiotic resistance genes (ARGs) that could be dynamically exchanged between clinical and environmental settings through mobile genetic elements (MGEs) such as the pMAL1 plasmids and the critical role of WWTPs in the persistence and spread of A. baumannii. Moreover, our study presents the first report of the co-occurrence of bla OXA-23 and bla OXA-72 in A. baumannii ST2 clone. Thus, our research underscores the necessity for integrated surveillance and targeted interventions across healthcare and environmental sectors to mitigate the risk posed by this adaptable pathogen.}, }
@article {pmid39030691, year = {2024}, author = {Gan, D and Lin, Z and Zeng, L and Deng, H and Walsh, TR and Zhou, S and Yang, QE}, title = {Housefly gut microbiomes as a reservoir and facilitator for the spread of antibiotic resistance.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39030691}, issn = {1751-7370}, support = {//Science Foundation of Fujian Province/ ; //Outstanding Young Research Talents Program of Fujian Agriculture and Forestry University/ ; //National Science Foundation of China/ ; //National Key R&amp;D Program of China/ ; }, mesh = {*Houseflies/microbiology ; *Gastrointestinal Microbiome ; Animals ; *Plasmids/genetics ; Escherichia coli/genetics/drug effects ; RNA, Ribosomal, 16S/genetics ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; }, abstract = {Arthropods, such as houseflies, play a significant role in the dissemination of antimicrobial resistance (AMR); however, their impact has often been overlooked in comparison to other AMR vectors. Understanding the contribution of arthropods to the spread of AMR is critical for implementing robust policies to mitigate the spread of AMR across One Health sectors, affecting animals and environmental habitats as well as humans. In this study, we investigated the in situ transfer of a gfp-labelled AMR plasmid (IncA/C carrying an mcr-8 gene, pA/C_MCR-8) in the gut microbiota of houseflies (Musca domestica) by applying single-cell sorting, 16S rRNA gene amplicon sequencing and whole-genome sequencing. Our findings demonstrate that the pA/C_MCR-8-positive Escherichia coli donor strain is capable of colonizing the gut microbiome of houseflies and persists in the housefly intestine for 5 days; however, no transfer was detectable above the detection threshold of 10-5 per cell. The conjugative plasmid pA/C_MCR-8 demonstrated a high transfer frequency ranging from 4.1 × 10-3 to 5.0 × 10-3 per cell in vitro and exhibited transfer across various bacterial phyla, primarily encompassing Pseudomonadota and Bacillota. Phylogenic analysis has revealed that Providencia stuartii, a human opportunistic pathogen, is a notable recipient of pA/C_MCR-8. The conjugation assays further revealed that newly formed P. stuartii transconjugants readily transfer pA/C_MCR-8 to other clinically relevant pathogens (e.g. Klebsiella pneumoniae). Our findings indicate the potential transfer of AMR plasmids from houseflies to human opportunistic pathogens and further support the adoption of a One Health approach in developing infection control policies that address AMR across clinical settings.}, }
@article {pmid39030685, year = {2024}, author = {Echeveste Medrano, MJ and Leu, AO and Pabst, M and Lin, Y and McIlroy, SJ and Tyson, GW and van Ede, J and Sánchez-Andrea, I and Jetten, MSM and Jansen, R and Welte, CU}, title = {Osmoregulation in freshwater anaerobic methane-oxidizing archaea under salt stress.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39030685}, issn = {1751-7370}, support = {VI.Vidi.223.012//NWO-VIDI/ ; FT190100211//Australian Research Council/ ; 854088//ERC/ ; 024.002.002//NWO/ ; }, mesh = {*Methane/metabolism ; *Fresh Water/microbiology ; Anaerobiosis ; *Archaea/metabolism/genetics/classification ; *Salt Stress ; *Phylogeny ; *Osmoregulation ; Oxidation-Reduction ; }, abstract = {Climate change-driven sea level rise threatens freshwater ecosystems and elicits salinity stress in microbiomes. Methane emissions in these systems are largely mitigated by methane-oxidizing microorganisms. Here, we characterized the physiological and metabolic response of freshwater methanotrophic archaea to salt stress. In our microcosm experiments, inhibition of methanotrophic archaea started at 1%. However, during gradual increase of salt up to 3% in a reactor over 12 weeks, the culture continued to oxidize methane. Using gene expression profiles and metabolomics, we identified a pathway for salt-stress response that produces the osmolyte of anaerobic methanotrophic archaea: N(ε)-acetyl-β-L-lysine. An extensive phylogenomic analysis on N(ε)-acetyl-β-L-lysine-producing enzymes revealed that they are widespread across both bacteria and archaea, indicating a potential horizontal gene transfer and a link to BORG extrachromosomal elements. Physicochemical analysis of bioreactor biomass further indicated the presence of sialic acids and the consumption of intracellular polyhydroxyalkanoates in anaerobic methanotrophs during salt stress.}, }
@article {pmid39029947, year = {2024}, author = {Azizpour, A and Balaji, A and Treangen, TJ and Segarra, S}, title = {Graph-based self-supervised learning for repeat detection in metagenomic assembly.}, journal = {Genome research}, volume = {34}, number = {9}, pages = {1468-1476}, pmid = {39029947}, issn = {1549-5469}, mesh = {*Metagenomics/methods ; *Supervised Machine Learning ; Repetitive Sequences, Nucleic Acid ; Neural Networks, Computer ; Sequence Analysis, DNA/methods ; Algorithms ; Metagenome ; }, abstract = {Repetitive DNA (repeats) poses significant challenges for accurate and efficient genome assembly and sequence alignment. This is particularly true for metagenomic data, in which genome dynamics such as horizontal gene transfer, gene duplication, and gene loss/gain complicate accurate genome assembly from metagenomic communities. Detecting repeats is a crucial first step in overcoming these challenges. To address this issue, we propose GraSSRep, a novel approach that leverages the assembly graph's structure through graph neural networks (GNNs) within a self-supervised learning framework to classify DNA sequences into repetitive and nonrepetitive categories. Specifically, we frame this problem as a node classification task within a metagenomic assembly graph. In a self-supervised fashion, we rely on a high-precision (but low-recall) heuristic to generate pseudolabels for a small proportion of the nodes. We then use those pseudolabels to train a GNN embedding and a random forest classifier to propagate the labels to the remaining nodes. In this way, GraSSRep combines sequencing features with predefined and learned graph features to achieve state-of-the-art performance in repeat detection. We evaluate our method using simulated and synthetic metagenomic data sets. The results on the simulated data highlight GraSSRep's robustness to repeat attributes, demonstrating its effectiveness in handling the complexity of repeated sequences. Additionally, experiments with synthetic metagenomic data sets reveal that incorporating the graph structure and the GNN enhances the detection performance. Finally, in comparative analyses, GraSSRep outperforms existing repeat detection tools with respect to precision and recall.}, }
@article {pmid39028534, year = {2024}, author = {da Rosa, EEB and Kremer, FS}, title = {The mobilome landscape of biocide-resistance in Brazilian ESKAPE isolates.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {55}, number = {4}, pages = {3603-3616}, pmid = {39028534}, issn = {1678-4405}, support = {Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; }, mesh = {*Disinfectants/pharmacology ; Brazil ; Humans ; *Drug Resistance, Bacterial/genetics ; Genome, Bacterial ; Computational Biology ; Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; Whole Genome Sequencing ; *Bacteria/drug effects/genetics/isolation &amp; purification ; }, abstract = {The increasing frequency of antibiotic-resistant bacteria is a constant threat to global human health. Therefore, the pathogens of the ESKAPE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, and Enterobacter spp.) are among the most relevant causes of hospital infections responsible for millions of deaths every year. However, little has been explored about the danger of microorganisms resistant to biocides such as antiseptics and disinfectants. Widely used in domestic, industrial, and hospital environments, these substances reach the environment and can cause selective pressure for resistance genes and induce cross-resistance to antibiotics, further aggravating the problem. Therefore, it is necessary to use innovative and efficient strategies to monitor the spread of genes related to resistance to biocides. Whole genome sequencing and bioinformatics analysis aiming to search for sequences encoding resistance mechanisms are essential to help monitor and combat these pathogens. Thus, this work describes the construction of a bioinformatics tool that integrates different databases to identify gene sequences that may confer some resistance advantage about biocides. Furthermore, the tool analyzed all the genomes of Brazilian ESKAPE isolates deposited at NCBI and found a series of different genes related to resistance to benzalkonium chloride, chlorhexidine, and triclosan, which were the focus of this work. As a result, the presence of resistance genes was identified in different types of biological samples, environments, and hosts. Regarding mobile genetic elements (MGEs), around 52% of isolates containing genes related to resistance to these compounds had their genes identified in plasmids, and 48.7% in prophages. These data show that resistance to biocides can be a silent, underestimated danger spreading across different environments and, therefore, requires greater attention.}, }
@article {pmid39025839, year = {2024}, author = {Nowell, RW and Rodriguez, F and Hecox-Lea, BJ and Mark Welch, DB and Arkhipova, IR and Barraclough, TG and Wilson, CG}, title = {Bdelloid rotifers deploy horizontally acquired biosynthetic genes against a fungal pathogen.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {5787}, pmid = {39025839}, issn = {2041-1723}, support = {R01GM111917//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; NE/M01651X/1//RCUK | Natural Environment Research Council (NERC)/ ; R21AG046899//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; NE/J01933X/1//RCUK | Natural Environment Research Council (NERC)/ ; R01 GM111917/GM/NIGMS NIH HHS/United States ; R21 AG046899/AG/NIA NIH HHS/United States ; LTF-733-2010//European Molecular Biology Organization (EMBO)/ ; NE/S010866/1//RCUK | Natural Environment Research Council (NERC)/ ; }, mesh = {*Gene Transfer, Horizontal ; Animals ; *Rotifera/genetics/metabolism ; Biosynthetic Pathways/genetics ; Peptide Synthases/genetics/metabolism ; Polyketides/metabolism ; Phylogeny ; Multigene Family ; }, abstract = {Coevolutionary antagonism generates relentless selection that can favour genetic exchange, including transfer of antibiotic synthesis and resistance genes among bacteria, and sexual recombination of disease resistance alleles in eukaryotes. We report an unusual link between biological conflict and DNA transfer in bdelloid rotifers, microscopic animals whose genomes show elevated levels of horizontal gene transfer from non-metazoan taxa. When rotifers were challenged with a fungal pathogen, horizontally acquired genes were over twice as likely to be upregulated as other genes - a stronger enrichment than observed for abiotic stressors. Among hundreds of upregulated genes, the most markedly overrepresented were clusters resembling bacterial polyketide and nonribosomal peptide synthetases that produce antibiotics. Upregulation of these clusters in a pathogen-resistant rotifer species was nearly ten times stronger than in a susceptible species. By acquiring, domesticating, and expressing non-metazoan biosynthetic pathways, bdelloids may have evolved to resist natural enemies using antimicrobial mechanisms absent from other animals.}, }
@article {pmid39021167, year = {2024}, author = {Barcan, AS and Barcan, RA and Vamanu, E}, title = {Genomic Insights into Bacterial Antimicrobial Resistance Transmission and Mitigation Strategies.}, journal = {Current pharmaceutical biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.2174/0113892010304596240629102419}, pmid = {39021167}, issn = {1873-4316}, abstract = {The rapid emergence and global spread of antimicrobial resistance in recent years have raised significant concerns about the future of modern medicine. Superbugs and multidrugresistant bacteria have become endemic in many parts of the world, raising the specter of untreatable infections. The overuse and misuse of antimicrobials over the past 80 years have undoubtedly contributed to the development of antimicrobial resistance, placing immense pressure on healthcare systems worldwide. Nonetheless, the molecular mechanisms underlying antimicrobial resistance in bacteria have existed since ancient times. Some of these mechanisms and processes have served as the precursors of current resistance determinants, highlighting the ongoing arms race between bacteria and their antimicrobial adversaries. Moreover, the environment harbors many putative resistance genes, yet we cannot still predict which of these genes will emerge and manifest as pathogenic resistance phenotypes. The presence of antibiotics in natural habitats, even at sub-inhibitory concentrations, may provide selective pressures that favor the emergence of novel antimicrobial resistance apparatus and, thus, underscores the need for a comprehensive understanding of the factors driving the persistence and spread of antimicrobial resistance. As the development of antimicrobial strategies that evade resistance is urgently needed, a clear perception of these critical factors could ultimately pave the way for the design of innovative therapeutic targets.}, }
@article {pmid39012117, year = {2024}, author = {Zalewska, M and Błażejewska, A and Gawor, J and Adamska, D and Goryca, K and Szeląg, M and Kalinowski, P and Popowska, M}, title = {A newly identified IncY plasmid from multi-drug-resistant Escherichia coli isolated from dairy cattle feces in Poland.}, journal = {Microbiology spectrum}, volume = {12}, number = {8}, pages = {e0087724}, pmid = {39012117}, issn = {2165-0497}, support = {2017/25/Z/NZ7/03026//National Science Centre, Poland/ ; }, mesh = {Animals ; Cattle ; *Plasmids/genetics ; *Escherichia coli/genetics/drug effects/isolation &amp; purification ; *Drug Resistance, Multiple, Bacterial/genetics ; Poland ; *Anti-Bacterial Agents/pharmacology ; *Feces/microbiology ; *Gene Transfer, Horizontal ; Whole Genome Sequencing ; Escherichia coli Infections/microbiology/veterinary ; Microbial Sensitivity Tests ; }, abstract = {UNLABELLED: Comprehensive whole-genome sequencing was performed on two multi-drug-resistant Escherichia coli strains isolated from cattle manure from a typical dairy farm in Poland in 2020. The identified strains are resistant to beta-lactams, aminoglycosides, tetracyclines, trimethoprim/sulfamethoxazole, and fluoroquinolones. The complete sequences of the harbored plasmids revealed antibiotic-resistance genes located within many mobile genetic elements (e.g., insertional sequences or transposons) and genes facilitating conjugal transfer or promoting horizontal gene transfer. These plasmids are hitherto undescribed. Similar plasmids have been identified, but not in Poland. The identified plasmids carried resistance genes, including the tetracycline resistance gene tet(A), aph family aminoglycoside resistance genes aph(3″)-lb and aph (6)-ld, beta-lactam resistance genes blaTEM-1 and blaCTX-M-15, sulfonamide resistance gene sul2, fluoroquinolone resistance gene qnrS1, and the trimethoprim resistance gene dfrA14. The characterized resistance plasmids were categorized into the IncY incompatibility group, indicating a high possibility for dissemination among the Enterobacteriaceae. While similar plasmids (99% identity) have been found in environmental and clinical samples, none have been identified in farm animals. These findings are significant within the One Health framework, as they underline the potential for antimicrobial-resistant E. coli from livestock and food sources to be transmitted to humans and vice versa. It highlights the need for careful monitoring and strategies to limit the spread of antibiotic resistance in the One Health approach.<br><br>IMPORTANCE: This study reveals the identification of new strains of antibiotic-resistant Escherichia coli in cattle manure from a dairy farm in Poland, offering critical insights into the spread of drug resistance. Through whole-genome sequencing, researchers discovered novel plasmids within these bacteria, which carry genes resistant to multiple antibiotics. These findings are particularly alarming, as these plasmids can transfer between different bacterial species, potentially escalating the spread of antibiotic resistance. This research underscores the vital connection between the health of humans, animals, and the environment, emphasizing the concept of One Health. It points to the critical need for global vigilance and strategies to curb the proliferation of antibiotic resistance. By showcasing the presence of these strains and their advanced resistance mechanisms, the study calls for enhanced surveillance and preventive actions in both agricultural practices and healthcare settings to address the imminent challenge of antibiotic-resistant bacteria.}, }
@article {pmid39012101, year = {2024}, author = {Duran-Bedolla, J and Téllez-Sosa, J and Bocanegra-Ibarias, P and Schilmann, A and Bravo-Romero, S and Reyna-Flores, F and Villa-Reyes, T and Barrios-Camacho, H}, title = {Citrobacter spp. and Enterobacter spp. as reservoirs of carbapenemase blaNDM and blaKPC resistance genes in hospital wastewater.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {8}, pages = {e0116524}, pmid = {39012101}, issn = {1098-5336}, support = {001//CONAGUA/ ; }, mesh = {*Wastewater/microbiology ; *beta-Lactamases/genetics ; *Bacterial Proteins/genetics ; *Hospitals ; *Citrobacter/genetics/enzymology/drug effects/isolation &amp; purification ; *Enterobacter/genetics/drug effects/isolation &amp; purification/enzymology ; Anti-Bacterial Agents/pharmacology ; Mexico ; }, abstract = {UNLABELLED: Antibiotic resistance has emerged as a global threat to public health, generating a growing interest in investigating the presence of antibiotic-resistant bacteria in environments influenced by anthropogenic activities. Wastewater treatment plants in hospital serve as significant reservoirs of antimicrobial-resistant bacteria, where a favorable environment is established, promoting the proliferation and transfer of resistance genes among different bacterial species. In our study, we isolated a total of 243 strains from 5 hospital wastewater sites in Mexico, belonging to 21 distinct Gram-negative bacterial species. The presence of β-lactamase was detected in 46.9% (114/243) of the isolates, which belonging to the Enterobacteriaceae family. We identified a total of 169 β-lactamase genes; blaTEM in 33.1%, blaCTX-M in 25.4%, blaKPC in 25.4%, blaNDM 8.8%, blaSHV in 5.3%, and blaOXA-48 in 1.1% distributed in 12 different bacteria species. Among the 114 of the isolates, 50.8% were found to harbor at least one carbapenemase and were discharged into the environment. The carbapenemase blaKPC was found in six Citrobacter spp. and E. coli, while blaNDM was detected in two distinct Enterobacter spp. and E. coli. Notably, blaNDM-1 was identified in a 110 Kb IncFII conjugative plasmid in E. cloacae, E. xiangfangensis, and E. coli within the same hospital wastewater. In conclusion, hospital wastewater showed the presence of Enterobacteriaceae carrying a high frequency of carbapenemase blaKPC and blaNDM. We propose that hospital wastewater serves as reservoirs for resistance mechanism within bacterial communities and creates an optimal environment for the exchange of this resistance mechanism among different bacterial strains.<br><br>IMPORTANCE: The significance of this study lies in its findings regarding the prevalence and diversity of antibiotic-resistant bacteria and genes identified in hospital wastewater in Mexico. The research underscores the urgent need for enhanced surveillance and prevention strategies to tackle the escalating challenge of antibiotic resistance, particularly evident through the elevated frequencies of carbapenemase genes such as blaKPC and blaNDM within the Enterobacteriaceae family. Moreover, the identification of these resistance genes on conjugative plasmids highlights the potential for widespread transmission via horizontal gene transfer. Understanding the mechanisms of antibiotic resistance in hospital wastewater is crucial for developing targeted interventions aimed at reducing transmission, thereby safeguarding public health and preserving the efficacy of antimicrobial therapies.}, }
@article {pmid39011898, year = {2024}, author = {Yuan, W and Yu, J and Li, Z}, title = {Rapid functional activation of horizontally transferred eukaryotic intron-containing genes in the bacterial recipient.}, journal = {Nucleic acids research}, volume = {52}, number = {14}, pages = {8344-8355}, pmid = {39011898}, issn = {1362-4962}, support = {2020YFA0908000//National Key Research and Development Program of China/ ; TSBICIP-CXRC-001//Tianjin Synthetic Biotechnology Innovation Capacity Improvement Project/ ; 2060302//The ability establishment of sustainable use for valuable Chinese medicine resources/ ; }, mesh = {*Gene Transfer, Horizontal ; *Introns/genetics ; *Escherichia coli/genetics ; Genes, Bacterial ; Escherichia coli Proteins/genetics/metabolism ; }, abstract = {Horizontal gene transfer has occurred across all domains of life and contributed substantially to the evolution of both prokaryotes and eukaryotes. Previous studies suggest that many horizontally transferred eukaryotic genes conferred selective advantages to bacterial recipients, but how these eukaryotic genes evolved into functional bacterial genes remained unclear, particularly how bacteria overcome the expressional barrier posed by eukaryotic introns. Here, we first confirmed that the presence of intron would inactivate the horizontally transferred gene in Escherichia coli even if this gene could be efficiently transcribed. Subsequent large-scale genetic screens for activation of gene function revealed that activation events could rapidly occur within several days of selective cultivation. Molecular analysis of activation events uncovered two distinct mechanisms how bacteria overcome the intron barrier: (i) intron was partially deleted and the resulting stop codon-removed mutation led to one intact foreign protein or (ii) intron was intactly retained but it mediated the translation initiation and the interaction of two split small proteins (derived from coding sequences up- and downstream of intron, respectively) to restore gene function. Our findings underscore the likelihood that horizontally transferred eukaryotic intron-containing genes could rapidly acquire functionality if they confer a selective advantage to the prokaryotic recipient.}, }
@article {pmid39010965, year = {2024}, author = {Jinnai, M and Yamaguchi, T and Minh, DTN and Hoang, ON and Le Thi, H and Thanh, PN and Hoai, PH and Do, PN and Van, CD and Kumeda, Y and Hase, A and Nakayama, T}, title = {Edible river fish-derived extended-spectrum β-lactamase (ESBL)-producing Enterobacterales harboring transferable plasmids encoding bla CTX-M-15, bla CTX-M-27, and bla CTX-M-55.}, journal = {One health (Amsterdam, Netherlands)}, volume = {18}, number = {}, pages = {100685}, pmid = {39010965}, issn = {2352-7714}, abstract = {Transmission of extended-spectrum β-lactamase (ESBL) genes has increased the global prevalence of ESBL-producing bacteria, especially in developing countries. Human infection with these bacteria may be food-mediated but has not been fully elucidated. Therefore, we aimed to examine ESBL-producing bacteria in edible river fish and elucidate their potential for horizontal gene transfer. A total of 173 ESBL-producing Enterobacterales were isolated (Escherichia coli [n = 87], Klebsiella pneumoniae [n = 52], Enterobacter cloacae complex [n = 18], Citrobacter freundii complex [n = 14], Atlantibacter hermannii [n = 1] and Serratia fonticola [n = 1]) from 56 of 80 fish intestinal contents sampled. Among the bacterial bla CTX-M genotypes, bla CTX-M-55 was the most predominant, followed by bla CTX-M-15, bla CTX-M-27, and bla CTX-M-65. Furthermore, we found that ESBL-producing Enterobacterales were able to transfer their bla CTX-M genes to E. coli. In summary, our results suggest that ESBL-producing Enterobacterales transfer bla CTX-M to indigenous gut E. coli in humans, following the consumption of contaminated fish.}, }
@article {pmid39007976, year = {2024}, author = {Zalewska, M and Błażejewska, A and Gawor, J and Adamska, D and Goryca, K and Szeląg, M and Kalinowski, P and Popowska, M}, title = {The IncC and IncX1 resistance plasmids present in multi-drug resistant Escherichia coli strains isolated from poultry manure in Poland.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {35}, pages = {47727-47741}, pmid = {39007976}, issn = {1614-7499}, support = {2017/25/Z/NZ7/03026//Narodowym Centrum Nauki/ ; }, mesh = {Animals ; *Escherichia coli/genetics/drug effects ; Poland ; *Plasmids ; *Drug Resistance, Multiple, Bacterial/genetics ; *Manure/microbiology ; *Anti-Bacterial Agents/pharmacology ; Poultry ; Chickens ; }, abstract = {The study describes the whole-genome sequencing of two antibiotic-resistant representative Escherichia coli strains, isolated from poultry manure in 2020. The samples were obtained from a commercial chicken meat production facility in Poland. The antibiotic resistance profile was characterized by co-resistance to β-lactam antibiotics, aminoglycosides, and fluoroquinolones. The three identified resistance plasmids (R-plasmids), pECmdr13.2, pECmdr13.3, and pECmdr14.1, harbored various genes conferring resistance to tetracyclines (tetR[A]) for, aminoglycoside (aph, aac, and aad families), β-lactam (blaCMY-2, blaTEM-176), sulfonamide (sul1, sul2), fluoroquinolone (qnrS1), and phenicol (floR). These plasmids, which have not been previously reported in Poland, were found to carry IS26 insertion elements, the intI1-integrase gene, and conjugal transfer genes, facilitating horizontal gene transfer. Plasmids pECmdr13.2 and pECmdr14.1 also possessed a mercury resistance gene operon related to transposon Tn6196; this promotes plasmid persistence even without antibiotic selection pressure due to co-selection mechanisms such as co-resistance. The chicken manure-derived plasmids belonged to the IncX1 (narrow host range) and IncC (broad host range) incompatibility groups. Similar plasmids have been identified in various environments, clinical isolates, and farm animals, including cattle, swine, and poultry. This study holds significant importance for the One Health approach, as it highlights the potential for antibiotic-resistant bacteria from livestock and food sources, particularly E. coli, to transfer through the food chain to humans and vice versa.}, }
@article {pmid39001714, year = {2024}, author = {Williams, TA and Davin, AA and Szánthó, LL and Stamatakis, A and Wahl, NA and Woodcroft, BJ and Soo, RM and Eme, L and Sheridan, PO and Gubry-Rangin, C and Spang, A and Hugenholtz, P and Szöllősi, GJ}, title = {Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39001714}, issn = {1751-7370}, support = {GBMF9741//Gordon and Betty Moore Foundation/ ; 714774//European Union's Horizon 2020 Research and Innovation Programme/ ; /ERC_/European Research Council/International ; 947317//European Union's Horizon 2020 Research and Innovation Programme/ ; 735929LPI//Simons Foundation/ ; FL150100038//Australian Research Council Laureate Fellowship/ ; 812811//Simons Foundation/ ; 101087081//European Union's Horizon Europe ERA Chair Program/ ; URF150571//Royal Society University Research Fellowship/ ; }, mesh = {*Phylogeny ; *Archaea/genetics/classification ; Bacteria/genetics/classification ; Evolution, Molecular ; Genome, Bacterial ; Symbiosis ; Ecology ; }, abstract = {In recent years, phylogenetic reconciliation has emerged as a promising approach for studying microbial ecology and evolution. The core idea is to model how gene trees evolve along a species tree and to explain differences between them via evolutionary events including gene duplications, transfers, and losses. Here, we describe how phylogenetic reconciliation provides a natural framework for studying genome evolution and highlight recent applications including ancestral gene content inference, the rooting of species trees, and the insights into metabolic evolution and ecological transitions they yield. Reconciliation analyses have elucidated the evolution of diverse microbial lineages, from Chlamydiae to Asgard archaea, shedding light on ecological adaptation, host-microbe interactions, and symbiotic relationships. However, there are many opportunities for broader application of the approach in microbiology. Continuing improvements to make reconciliation models more realistic and scalable, and integration of ecological metadata such as habitat, pH, temperature, and oxygen use offer enormous potential for understanding the rich tapestry of microbial life.}, }
@article {pmid38992783, year = {2024}, author = {Klimov, PB and Hubert, J and Erban, T and Alejandra Perotti, M and Braig, HR and Flynt, A and He, Q and Cui, Y}, title = {Genomic and metagenomic analyses of the domestic mite Tyrophagus putrescentiae identify it as a widespread environmental contaminant and a host of a basal, mite-specific Wolbachia lineage (supergroup Q).}, journal = {International journal for parasitology}, volume = {54}, number = {13}, pages = {661-674}, doi = {10.1016/j.ijpara.2024.07.001}, pmid = {38992783}, issn = {1879-0135}, mesh = {Animals ; *Wolbachia/genetics/isolation &amp; purification ; *Phylogeny ; Metagenomics ; Genomics ; Symbiosis ; Acaridae/genetics ; Environmental Pollutants ; Mites/microbiology/genetics ; }, abstract = {Tyrophagus putrescentiae (mould mite) is a global, microscopic trophic generalist that commonly occurs in various human-created habitats, causing allergies and damaging stored food. Its ubiquity and extraordinary ability to penetrate research samples or cultures through air currents or by active walking through tights spaces (such as treads of screw caps) may lead to sample contamination and introduction of its DNA to research materials in the laboratory. This prompts a thorough investigation into potential sequence contamination in public genomic databases. The trophic success of T. putrescentiae is primarily attributed to the symbiotic bacteria housed in specialized internal mite structures, facilitating adaptation to varied nutritional niches. However, recent work suggests that horizontal transfer of bacterial/fungal genes related to nutritional functionality may also contribute to the mite's trophic versatility. This aspect requires independent confirmation. Additionally, T. putrescentiae harbors an uncharacterized and genetically divergent bacterium, Wolbachia, displaying blocking and microbiome-modifying effects. The phylogenomic position and supergroup assignment of this bacterium are unknown. Here, we sequenced and assembled the T. putrescentiae genome, analyzed its microbiome, and performed detailed phylogenomic analyses of the mite-specific Wolbachia. We show that T. putrescentiae DNA is a substantial source of contamination of research samples. Its DNA may inadvertently be co-extracted with the DNA of the target organism, eventually leading to sequence contamination in public databases. We identified a diversity of bacterial species associated with T. putrescentiae, including those capable of rapidly developing antibiotic resistance, such as Escherichia coli. Despite the presence of diverse bacterial communities in T. putrescentiae, we did not detect any recent horizontal gene transfers in this mite species and/or in astigmatid (domestic) mites in general. Our phylogenomic analysis of Wolbachia recovered a basal, mite-specific lineage (supergroup Q) represented by two Wolbachia spp. from the mould mite and a gall-inducing plant mite. Fluorescence in situ hybridization confirmed the presence of Wolbachia inside the mould mite. The discovery of an early derivative Wolbachia lineage (supergroup Q) in two phylogenetically unrelated and ecologically dissimilar mites suggests that this endosymbiotic bacterial lineage formed a long-term association with mites. This finding provides a unique insight into the early evolution and host associations of Wolbachia. Further discoveries of Wolbachia diversity in acariform mites are anticipated.}, }
@article {pmid38992444, year = {2024}, author = {Soni, K and Jyoti, K and Kumar, A and Chandra, R}, title = {Coexistence of multidrug resistance and ESBL encoding genes - blaTEM, blaSHV, and blaCTX-M; its amplification and dispersion in the environment via municipal wastewater treatment plant.}, journal = {Chemosphere}, volume = {362}, number = {}, pages = {142829}, doi = {10.1016/j.chemosphere.2024.142829}, pmid = {38992444}, issn = {1879-1298}, mesh = {*Wastewater/microbiology ; *beta-Lactamases/genetics ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Waste Disposal, Fluid ; Bacteria/genetics/drug effects ; Genes, Bacterial ; Gene Transfer, Horizontal ; }, abstract = {Municipal wastewater treatment plants (MWWTPs) are a global source of antibiotic resistance genes (ARGs), collecting wastewater from a variety of sources, including hospital wastewater, domestic wastewater, runoff from agricultural and livestock farms, etc. These sources are contaminated with organic and inorganic pollutants, ARGs and antibiotic-resistant bacteria (ARB). Such pollutants aided eutrophication and encouraged bacterial growth. During bacterial growth horizontal gene transfer (HGT) and vertical gene transfer (VGT) of ARGs and extended-spectrum β-lactamase (ESBL) encoding genes may facilitate, resulting in the spread of antibiotic resistance exponentially. The current study investigated the prevalence of multidrug resistance (MDR) and ESBL encoding genes in various treatment units of MWWTP and their spread in the environment. A total of three sampling sites (BUT, BRO, and BFB) were chosen, and 33 morphologically distinct bacterial colonies were isolated. 14 of the 33 isolates tested positive for antibiotic resistance and were further tested for the coexistence of MDR and ESBL production. The selected 14 isolates showed the highest resistance to trimethoprim (85.71%), followed by ciprofloxacin, azithromycin, and ampicillin (71.42%), tetracycline (57.14%), and vancomycin, gentamicin, and colistin sulphate (50%). A total of 9 isolates (64.28%) were phenotypically positive for ESBL production (BUT2, BUT3, BUT5, BRO1, BRO2, BRO3, BRO4, BRO5 and BFB1). The molecular detection of ESBL encoding genes, i.e. blaTEM, blaSHV, and blaCTX-M was carried out. The most prevalent gene was blaTEM (69.23%), followed by blaSHV (46.15%), and blaCTX-M (23.07%). In this study, 9 isolates (64.28%) out of 14 showed the coexistence of MDR and ESBL encoding genes, namely BUT3, BUT4, BUT5, BUT6, BUT7, BRO1, BRO2, BRO4, and BFB1. The coexistence of ESBL encoding genes and resistance to other antibiotic classes exacerbates human health and the environment.}, }
@article {pmid38992349, year = {2024}, author = {Nazir, R and Du, S and Shen, JP and Hu, HW and Wang, JT and He, JZ}, title = {Effect of meddling ARBs on ARGs dynamics in fungal infested soil and their selective dispersal along spatially distant mycelial networks.}, journal = {The Science of the total environment}, volume = {947}, number = {}, pages = {174594}, doi = {10.1016/j.scitotenv.2024.174594}, pmid = {38992349}, issn = {1879-1026}, mesh = {*Soil Microbiology ; *Fungi/physiology ; Bacteria/drug effects ; Soil/chemistry ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; }, abstract = {During the recent times, environmental antibiotic resistance genes (ARGs) and their potential transfer to other bacterial hosts of pathogenic importance are of serious concern. However, the dissemination strategies of such ARGs are largely unknown. We tested that saprotrophic soil fungi differentially enriched antibiotic resistant bacteria (ARBs) and subsequently contributed in spatial distribution of selective ARGs. Wafergen qPCR analysis of 295 different ARGs was conducted for manure treated pre-sterilized soil incubated or not with selected bacterial-fungal consortia. The qPCR assay detected unique ARGs specifically found in the mycosphere of ascomycetous and basidiomycetous fungi. Both fungi exerted potentially different selection pressures on ARBs, resulting in different patterns of ARGs dissemination (to distant places) along their respective growing fungal highways. The relative abundance of mobile genetic elements (MGEs) was significantly decreased along fungal highways compared to the respective inoculation points. Moreover, the decrease in MGEs and ARGs (along fungal highways) was more prominent over time which depicts the continuous selection pressure of growing fungi on ARBs for enrichment of particular ARGs in mycosphere. Such data also indicate the potential role of saprotrophic soil fungi to facilitate horizontal gene transfer within mycospheric environmental settings. Our study, therefore, advocates to emphasize the future investigations for such (bacteria-fungal) interactive microbial consortia for potential (spatial) dissemination of resistance determinants which may ultimately increase the exposure risks of ARGs.}, }
@article {pmid38990885, year = {2024}, author = {Windels, A and Franceus, J and Pleiss, J and Desmet, T}, title = {CANDy: Automated analysis of domain architectures in carbohydrate-active enzymes.}, journal = {PloS one}, volume = {19}, number = {7}, pages = {e0306410}, pmid = {38990885}, issn = {1932-6203}, mesh = {*Protein Domains ; Glycoside Hydrolases/chemistry/metabolism/genetics ; Catalytic Domain ; Software ; Carbohydrate Metabolism ; Carbohydrates/chemistry ; Animals ; }, abstract = {Carbohydrate-active enzymes (CAZymes) can be found in all domains of life and play a crucial role in metabolic and physiological processes. CAZymes often possess a modular structure, comprising not only catalytic domains but also associated domains such as carbohydrate-binding modules (CBMs) and linker domains. By exploring the modular diversity of CAZy families, catalysts with novel properties can be discovered and further insight in their biological functions and evolutionary relationships can be obtained. Here we present the carbohydrate-active enzyme domain analysis tool (CANDy), an assembly of several novel scripts, tools and databases that allows users to analyze the domain architecture of all protein sequences in a given CAZy family. CANDy's usability is shown on glycoside hydrolase family 48, a small yet underexplored family containing multi-domain enzymes. Our analysis reveals the existence of 35 distinct domain assemblies, including eight known architectures, with the remaining assemblies awaiting characterization. Moreover, we substantiate the occurrence of horizontal gene transfer from prokaryotes to insect orthologs and provide evidence for the subsequent removal of auxiliary domains, likely through a gene fission event. CANDy is available at https://github.com/PyEED/CANDy.}, }
@article {pmid38987681, year = {2024}, author = {Elgayar, FA and Gouda, MK and Badran, AA and El Halfawy, NM}, title = {Pathogenomics analysis of high-risk clone ST147 multidrug-resistant Klebsiella pneumoniae isolated from a patient in Egypt.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {256}, pmid = {38987681}, issn = {1471-2180}, mesh = {*Klebsiella pneumoniae/genetics/drug effects/isolation &amp; purification/classification ; Humans ; Egypt ; *Drug Resistance, Multiple, Bacterial/genetics ; *Klebsiella Infections/microbiology/epidemiology ; *Anti-Bacterial Agents/pharmacology ; *Microbial Sensitivity Tests ; *Virulence Factors/genetics ; *Whole Genome Sequencing ; *Genome, Bacterial/genetics ; beta-Lactamases/genetics ; Bacterial Proteins/genetics ; Plasmids/genetics ; }, abstract = {BACKGROUND: The emergence of multi-drug-resistant Klebsiella pneumoniae (MDR-KP) represents a serious clinical health concern. Antibiotic resistance and virulence interactions play a significant role in the pathogenesis of K. pneumoniae infections. Therefore, tracking the clinical resistome and virulome through monitoring antibiotic resistance genes (ARG) and virulence factors in the bacterial genome using computational analysis tools is critical for predicting the next epidemic.<br><br>METHODS: In the current study, one hundred extended spectrum &#x3b2;-lactamase (ESBL)-producing clinical isolates were collected from Mansoura University Hospital, Egypt, in a six-month period from January to June 2022. One isolate was selected due to the high resistance phenotype, and the genetic features of MDR-KP recovered from hospitalized patient were investigated. Otherwise, the susceptibility to 25 antimicrobials was determined using the DL Antimicrobial Susceptibility Testing (AST) system. Whole genome sequencing (WGS) using Illumina NovaSeq 6000 was employed to provide genomic insights into K. pneumoniae WSF99 clinical isolate.<br><br>RESULTS: The isolate K. pneumoniae WSF99 was phenotypically resistant to the antibiotics under investigation via antibiotic susceptibility testing. WGS analysis revealed that WSF99 total genome length was 5.7&#xa0;Mb with an estimated 5,718 protein-coding genes and a G&#x2009;+&#x2009;C content of 56.98&#xa0;mol%. Additionally, the allelic profile of the WSF99 isolate was allocated to the high-risk clone ST147. Furthermore, diverse antibiotic resistance genes were determined in the genome that explain the high-level resistance phenotypes. Several &#x3b2;-lactamase genes, including blaCTX-M-15, blaTEM-1, blaTEM-12, blaSHV-11, blaSHV-67, and blaOXA-9, were detected in the WSF99 isolate. Moreover, a single carbapenemase gene, blaNDM-5, was predicted in the genome, positioned within a mobile cassette. In addition, other resistance genes were predicted in the genome including, aac(6')-Ib, aph(3')-VI, sul1, sul2, fosA, aadA, arr-2, qnrS1, tetA and tetC. Four plasmid replicons CoIRNAI, IncFIB(K), IncFIB(pQil), and IncR were predicted in the genome. The draft genome analysis revealed the occurrence of genetic mobile elements positioned around the ARGs, suggesting the ease of dissemination via horizontal gene transfer.<br><br>CONCLUSIONS: This study reports a comprehensive pathogenomic analysis of MDR-KP isolated from a hospitalized patient. These findings could be relevant for future studies investigating the diversity of antimicrobial resistance and virulence in Egypt.}, }
@article {pmid38986507, year = {2024}, author = {Irusan, D and Akshay, SD and Shetty, VP and Karunasagar, I and Deekshit, VK and Rohit, A}, title = {Analysis of mcr family of colistin resistance genes in Gram-negative isolates from a tertiary care hospital in India.}, journal = {Journal of applied microbiology}, volume = {135}, number = {7}, pages = {}, doi = {10.1093/jambio/lxae172}, pmid = {38986507}, issn = {1365-2672}, support = {AMR/DHR/GIA/3/ECD-II/2020//ICMR/ ; }, mesh = {*Colistin/pharmacology ; India ; *Tertiary Care Centers ; *Anti-Bacterial Agents/pharmacology ; Humans ; *Microbial Sensitivity Tests ; *Gram-Negative Bacteria/genetics/drug effects/isolation &amp; purification ; Drug Resistance, Multiple, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; Gram-Negative Bacterial Infections/microbiology ; Plasmids/genetics ; Bacterial Proteins/genetics ; Escherichia coli/genetics/drug effects/isolation &amp; purification ; Acinetobacter baumannii/genetics/drug effects/isolation &amp; purification ; Pseudomonas aeruginosa/genetics/drug effects/isolation &amp; purification ; }, abstract = {AIM: Colistin serves as the drug of last resort for combating numerous multidrug-resistant (MDR) Gram-negative infections. Its efficacy is hampered by the prevalent issue of colistin resistance, which severely limits treatment options for critically ill patients. Identifying resistance genes is crucial for controlling resistance spread, with horizontal gene transfer being the primary mechanism among bacteria. This study aimed to assess the prevalence of plasmid-mediated mcr genes associated with colistin resistance in Gram-negative bacteria, utilizing both genotypic and phenotypic tests.<br><br>METHODS AND RESULTS: The clinical isolates (n&#xa0;=&#xa0;913) were obtained from a tertiary care center in Chennai, India. Colistin resistance was seen among Gram-negative isolates. These strains underwent screening for mcr-1, mcr-3, mcr-4, and mcr-5 genes via conventional PCR. Additionally, mcr-positive isolates were confirmed through Sanger sequencing and phenotypic testing. The bacterial isolates predominantly comprised Klebsiella pneumoniae (62.43%), Escherichia coli (19.71%), Pseudomonas aeruginosa (10.73%), and Acinetobacter baumannii (4.81%), along with other species. All isolates exhibited multidrug resistance to three or more antibiotic classes. Colistin resistance, determined via broth microdilution (BMD) using CLSI guidelines, was observed in 13.08% of the isolates studied. Notably, mcr-5 was detected in K. pneumoniae in PCR, despite its absence in Sanger sequencing and phenotypic tests (including the combined-disk test, colistin MIC in the presence of EDTA, and Zeta potential assays). This finding underscores the importance of employing multiple diagnostic approaches to accurately identify colistin resistance mechanisms.}, }
@article {pmid38986416, year = {2024}, author = {Chi, W and Zou, Y and Qiu, T and Shi, W and Tang, L and Xu, M and Wu, H and Luan, X}, title = {Horizontal gene transfer plays a crucial role in the development of antibiotic resistance in an antibiotic-free shrimp farming system.}, journal = {Journal of hazardous materials}, volume = {476}, number = {}, pages = {135150}, doi = {10.1016/j.jhazmat.2024.135150}, pmid = {38986416}, issn = {1873-3336}, mesh = {*Gene Transfer, Horizontal ; Animals ; *Aquaculture ; *Penaeidae/microbiology/genetics ; Drug Resistance, Microbial/genetics ; Plasmids/genetics ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects ; Genes, Bacterial ; Wastewater/microbiology ; Drug Resistance, Bacterial/genetics ; }, abstract = {Antibiotic selective pressure in aquaculture systems often results in the antibiotic resistance genes (ARGs) proliferation. Nonetheless, a paucity of data exists concerning the mechanisms of ARGs development in aquaculture systems without the influences of antibiotics. This study utilized metagenomic approaches to elucidate the dynamics and transfer mechanisms of ARGs throughout the aquaculture of Pacific white shrimp. A marked change in the resistome was observed throughout the aquaculture without antibiotics. The total ARGs relative abundance increased from 0.05 to 0.33 by day 90 of cultivation, with even higher in mixed wastewater (0.44). Both bacterial communities and mobile genetic elements play pivotal roles in the development of ARGs. Metagenome-assembled genomes showed enrichment of environmentally intrinsic ARGs on chromosomes including macB and mdtK. The plasmid-mediated horizontal transfer was recognized as a principal factor contributing to the rise of ARGs, particularly for tetG and floR, and this led to an escalation of resistance risk, peaking at a risks core of 35.43 on day 90. This study demonstrates that horizontal gene transfer plays a crucial role in ARGs development without antibiotic pressure, which can provide a theoretical foundation for controlling ARGs proliferation in aquaculture systems.}, }
@article {pmid38983623, year = {2024}, author = {Chin, HS and Ravi Varadharajulu, N and Lin, ZH and Chen, WY and Zhang, ZH and Arumugam, S and Lai, CY and Yu, SS}, title = {Isolation, molecular identification, and genomic analysis of Mangrovibacter phragmitis strain ASIOC01 from activated sludge harboring the bioremediation prowess of glycerol and organic pollutants in high-salinity.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1415723}, pmid = {38983623}, issn = {1664-302X}, abstract = {The physiological and genotypic characteristics of Mangrovibacter (MGB) remain largely unexplored, including their distribution and abundance within ecosystems. M. phragmitis (MPH) ASIOC01 was successfully isolated from activated sludge (AS), which was pre-enriched by adding 1,3-dichloro-2-propanol and 3-chloro-1,2-propanediol as carbon sources. The new isolate, MPH ASIOC01, exhibited resilience in a medium containing sodium chloride concentration up to 11% (with optimal growth observed at 3%) and effectively utilizing glycerol as their sole carbon source. However, species delimitation of MGBs remains challenging due to high 16S rRNA sequence similarity (greater than 99% ANI) among different MGBs. In contrast, among the housekeeping gene discrepancies, the tryptophan synthase beta chain gene can serve as a robust marker for fast species delimitation among MGBs. Furthermore, the complete genome of MPH ASIOC01 was fully sequenced and circlized as a single contig using the PacBio HiFi sequencing method. Comparative genomics revealed genes potentially associated with various phenotypic features of MGBs, such as nitrogen-fixing, phosphate-solubilizing, cellulose-digesting, Cr-reducing, and salt tolerance. Computational analysis suggested that MPH ASIOC01 may have undergone horizontal gene transfer events, possibly contributing unique traits such as antibiotic resistance. Finally, our findings also disclosed that the introduction of MPH ASIOC01 into AS can assist in the remediation of wastewater chemical oxygen demand, which was evaluated using gas chromatograph-mass spectrometry. To the best of our knowledge, this study offers the most comprehensive understanding of the phenotypic and genotypic features of MGBs to date.}, }
@article {pmid38980659, year = {2024}, author = {Poddar, BJ and Khardenavis, AA}, title = {Genomic Insights into the Landfill Microbial Community: Denitrifying Activity Supporting One-Carbon Utilization.}, journal = {Applied biochemistry and biotechnology}, volume = {196}, number = {12}, pages = {8866-8891}, pmid = {38980659}, issn = {1559-0291}, support = {EMR/2016/006589//SERB, New Delhi/ ; }, mesh = {*Denitrification ; Carbon/metabolism ; Waste Disposal Facilities ; Nitrates/metabolism ; Genome, Bacterial ; Methane/metabolism ; Enterobacter cloacae/genetics/metabolism/enzymology ; Genomics ; Bacillus subtilis/genetics/metabolism/enzymology ; Phylogeny ; Bacillus/genetics/metabolism/enzymology ; }, abstract = {In spite of the developments in understanding of denitrifying methylotrophy in the recent years, challenges still exist in unravelling the overall biochemistry of nitrate-dependent methane oxidation in novel or poorly characterized/not-yet-cultured bacteria. In the present study, landfill site was mined for novel C1-carbon-metabolizing bacteria which can use nitrate/nitrite as an electron acceptor. A high-throughput rapid plate assay identified three bacterial isolates with eminent ability for nitrate-dependent methane metabolism under anaerobic conditions. Taxonomic identification by whole-genome sequence-based overall genome relatedness indices accurately assigned the isolates AAK_M13, AAK_M29, and AAK_M39 at the species level to Enterobacter cloacae, Bacillus subtilis, and Bacillus halotolerans, respectively. Several genes encoding sub-components involved in alcohol utilization and denitrification pathways, such as adh, fdh, fdo, nar, nir, and nor, were identified in all the genomes. Though no gene clusters encoding MMO/AMO were annotated, sequencing of PCR amplicons revealed similarity with pMMO/AMO gene using translated nucleotide sequence of strains AAK_M29 and AAK_M39, while strain AAK_M13 showed similarity with XRE family transcriptional regulator. This suggests the horizontal gene transfer and/or presence of a truncated version of a housekeeping enzyme encoded by genes exhibiting partial sequence similarity with pMMO genes that mimicked its function at greenhouse gas emission sites. Owing to lack of conclusive evidence for presence of methane metabolism genes in the selected isolates, further experiment was performed to validate their nitrate-dependent methane oxidation capacities. Bacillus subtilis AAK_M29, Bacillus halotolerans AAK_M39, and Enterobacter cloacae AAK_M13 could oxidize 60%, 75%, and 85% of the added methane respectively accompanied by high nitrate reduction (56-62%) thus supporting the correlation between these two activities. The remarkable ability of these isolates for nitrate-dependent methane metabolism has highlighted their role in ecological contribution and biotechnological potential to serve as methane and nitrate sinks in the landfill sites.}, }
@article {pmid38977308, year = {2024}, author = {Vakirlis, N and Kupczok, A}, title = {Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins.}, journal = {Genome research}, volume = {34}, number = {6}, pages = {888-903}, pmid = {38977308}, issn = {1549-5469}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Evolution, Molecular ; *Species Specificity ; Base Composition ; Phylogeny ; }, abstract = {Species-specific genes, also known as orphans, are ubiquitous across life's domains. In prokaryotes, species-specific orphan genes (SSOGs) are mostly thought to originate in external elements such as viruses followed by horizontal gene transfer, whereas the scenario of native origination, through rapid divergence or de novo, is mostly dismissed. However, quantitative evidence supporting either scenario is lacking. Here, we systematically analyzed genomes from 4644 human gut microbiome species and identified more than 600,000 unique SSOGs, representing an average of 2.6% of a given species' pangenome. These sequences are mostly rare within each species yet show signs of purifying selection. Overall, SSOGs use optimal codons less frequently, and their proteins are more disordered than those of conserved genes (i.e., non-SSOGs). Importantly, across species, the GC content of SSOGs closely matches that of conserved ones. In contrast, the ∼5% of SSOGs that share similarity to known viral sequences have distinct characteristics, including lower GC content. Thus, SSOGs with similarity to viruses differ from the remaining SSOGs, contrasting an external origination scenario for most of them. By examining the orthologous genomic region in closely related species, we show that a small subset of SSOGs likely evolved natively de novo and find that these genes also differ in their properties from the remaining SSOGs. Our results challenge the notion that external elements are the dominant source of prokaryotic genetic novelty and will enable future studies into the biological role and relevance of species-specific genes in the human gut.}, }
@article {pmid38975782, year = {2024}, author = {Price, CTD and Hanford, HE and Al-Quadan, T and Santic, M and Shin, CJ and Da'as, MSJ and Abu Kwaik, Y}, title = {Amoebae as training grounds for microbial pathogens.}, journal = {mBio}, volume = {15}, number = {8}, pages = {e0082724}, pmid = {38975782}, issn = {2150-7511}, support = {R01 AI140195/AI/NIAID NIH HHS/United States ; R01AI140195//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; }, mesh = {*Amoeba/virology/microbiology ; Animals ; Humans ; Symbiosis ; Gene Transfer, Horizontal ; Biological Evolution ; Host-Pathogen Interactions ; }, abstract = {Grazing of amoebae on microorganisms represents one of the oldest predator-prey dynamic relationships in nature. It represents a genetic "melting pot" for an ancient and continuous multi-directional inter- and intra-kingdom horizontal gene transfer between amoebae and its preys, intracellular microbial residents, endosymbionts, and giant viruses, which has shaped the evolution, selection, and adaptation of microbes that evade degradation by predatory amoeba. Unicellular phagocytic amoebae are thought to be the ancient ancestors of macrophages with highly conserved eukaryotic processes. Selection and evolution of microbes within amoeba through their evolution to target highly conserved eukaryotic processes have facilitated the expansion of their host range to mammals, causing various infectious diseases. Legionella and environmental Chlamydia harbor an immense number of eukaryotic-like proteins that are involved in ubiquitin-related processes or are tandem repeats-containing proteins involved in protein-protein and protein-chromatin interactions. Some of these eukaryotic-like proteins exhibit novel domain architecture and novel enzymatic functions absent in mammalian cells, such as ubiquitin ligases, likely acquired from amoebae. Mammalian cells and amoebae may respond similarly to microbial factors that target highly conserved eukaryotic processes, but mammalian cells may undergo an accidental response to amoeba-adapted microbial factors. We discuss specific examples of microbes that have evolved to evade amoeba predation, including the bacterial pathogens- Legionella, Chlamydia, Coxiella, Rickettssia, Francisella, Mycobacteria, Salmonella, Bartonella, Rhodococcus, Pseudomonas, Vibrio, Helicobacter, Campylobacter, and Aliarcobacter. We also discuss the fungi Cryptococcus, and Asperigillus, as well as amoebae mimiviruses/giant viruses. We propose that amoeba-microbe interactions will continue to be a major "training ground" for the evolution, selection, adaptation, and emergence of microbial pathogens equipped with unique pathogenic tools to infect mammalian hosts. However, our progress will continue to be highly dependent on additional genomic, biochemical, and cellular data of unicellular eukaryotes.}, }
@article {pmid38971740, year = {2024}, author = {Bhat, A and Sharma, R and Desigan, K and Lucas, MM and Mishra, A and Bowers, RM and Woyke, T and Epstein, B and Tiffin, P and Pueyo, JJ and Paape, T}, title = {Horizontal gene transfer of the Mer operon is associated with large effects on the transcriptome and increased tolerance to mercury in nitrogen-fixing bacteria.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {247}, pmid = {38971740}, issn = {1471-2180}, support = {Quantitative Plant Science Initiative (QPSI)//U.S. Department of Energy/ ; Quantitative Plant Science Initiative (QPSI)//U.S. Department of Energy/ ; Quantitative Plant Science Initiative (QPSI)//U.S. Department of Energy/ ; Quantitative Plant Science Initiative (QPSI)//U.S. Department of Energy/ ; 3092-53000-001-00D//U.S. Department of Agriculture/ ; 3092-53000-001-00D//U.S. Department of Agriculture/ ; }, mesh = {*Gene Transfer, Horizontal ; *Mercury/metabolism/toxicity ; *Operon ; *Transcriptome ; *Symbiosis ; Nitrogen-Fixing Bacteria/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Nitrogen Fixation ; Rhizobium leguminosarum/genetics/metabolism ; Soil Microbiology ; }, abstract = {BACKGROUND: Mercury (Hg) is highly toxic and has the potential to cause severe health problems for humans and foraging animals when transported into edible plant parts. Soil rhizobia that form symbiosis with legumes may possess mechanisms to prevent heavy metal translocation from roots to shoots in plants by exporting metals from nodules or compartmentalizing metal ions inside nodules. Horizontal gene transfer has potential to confer immediate de novo adaptations to stress. We used comparative genomics of high quality de novo assemblies to identify structural differences in the genomes of nitrogen-fixing rhizobia that were isolated from a mercury (Hg) mine site that show high variation in their tolerance to Hg.<br><br>RESULTS: Our analyses identified multiple structurally conserved merA homologs in the genomes of Sinorhizobium medicae and Rhizobium leguminosarum but only the strains that possessed a Mer operon exhibited 10-fold increased tolerance to Hg. RNAseq analysis revealed nearly all genes in the Mer operon were significantly up-regulated in response to Hg stress in free-living conditions and in nodules. In both free-living and nodule environments, we found the Hg-tolerant strains with a Mer operon exhibited the fewest number of differentially expressed genes (DEGs) in the genome, indicating a rapid and efficient detoxification of Hg from the cells that reduced general stress responses to the Hg-treatment. Expression changes in S. medicae while in bacteroids showed that both rhizobia strain and host-plant tolerance affected the number of DEGs. Aside from Mer operon genes, nif genes which are involved in nitrogenase activity in S. medicae showed significant up-regulation in the most Hg-tolerant strain while inside the most Hg-accumulating host-plant. Transfer of a plasmid containing the Mer operon from the most tolerant strain to low-tolerant strains resulted in an immediate increase in Hg tolerance, indicating that the Mer operon is able to confer hyper tolerance to Hg.<br><br>CONCLUSIONS: Mer operons have not been previously reported in nitrogen-fixing rhizobia. This study demonstrates a pivotal role of the Mer operon in effective mercury detoxification and hypertolerance in nitrogen-fixing rhizobia. This finding has major implications not only for soil bioremediation, but also host plants growing in mercury contaminated soils.}, }
@article {pmid38971360, year = {2024}, author = {Zhang, W and Geng, J and Sun, M and Jiang, C and Lin, H and Chen, H and Yang, Y}, title = {Distinct species turnover patterns shaped the richness of antibiotic resistance genes on eight different microplastic polymers.}, journal = {Environmental research}, volume = {259}, number = {}, pages = {119562}, doi = {10.1016/j.envres.2024.119562}, pmid = {38971360}, issn = {1096-0953}, mesh = {*Microplastics/toxicity ; Drug Resistance, Microbial/genetics ; Bacteria/genetics/drug effects ; Genes, Bacterial ; }, abstract = {Elucidating the formation mechanism of plastisphere antibiotic resistance genes (ARGs) on different polymers is necessary to understand the ecological risks of plastisphere ARGs. Here, we explored the turnover and assembly mechanism of plastisphere ARGs on 8 different microplastic polymers (4 biodegradable (bMPs) and 4 non-biodegradable microplastics (nMPs)) by metagenomic sequencing. Our study revealed the presence of 479 ARGs with abundance ranging from 41.37 to 58.17 copies/16S rRNA gene in all plastispheres. These ARGs were predominantly multidrug resistance genes. The richness of plastisphere ARGs on different polymers had a significant correlation with the contribution of species turnover to plastisphere ARGs β diversity. Furthermore, polymer type was the most critical factor affecting the composition of plastisphere ARGs. More opportunistic pathogens carrying diverse ARGs on BMPs (PBAT, PBS, and PHA) with higher horizontal gene transfer potential may further magnify the ecological risks and human health threats. For example, the opportunistic pathogens Riemerella anatipestifer, Vibrio campbellii, and Vibrio cholerae are closely related to human production and life, which were the important potential hosts of many plastisphere ARGs and mobile genetic elements on BMPs. Thus, we emphasize the urgency of developing the formation mechanism of plastisphere ARGs and the necessity of controlling BMPs and ARG pollution, especially BMPs, with ever-increasing usage in daily life.}, }
@article {pmid38969684, year = {2024}, author = {Salem, S and Abdelsalam, NA and Shata, AH and Mouftah, SF and Cobo-Díaz, JF and Osama, D and Atteya, R and Elhadidy, M}, title = {Unveiling the microevolution of antimicrobial resistance in selected Pseudomonas aeruginosa isolates from Egyptian healthcare settings: A genomic approach.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {15500}, pmid = {38969684}, issn = {2045-2322}, support = {CRP/EGY22-03//CRP-ICGEB grant/ ; }, mesh = {*Pseudomonas aeruginosa/genetics/drug effects/isolation &amp; purification ; Egypt/epidemiology ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Microbial Sensitivity Tests ; Pseudomonas Infections/microbiology/epidemiology ; Biofilms/drug effects/growth &amp; development ; Whole Genome Sequencing/methods ; Genomics/methods ; Genome, Bacterial ; Evolution, Molecular ; Drug Resistance, Bacterial/genetics ; Multilocus Sequence Typing ; Polymorphism, Single Nucleotide ; Drug Resistance, Multiple, Bacterial/genetics ; Phylogeny ; }, abstract = {The incidence of Pseudomonas aeruginosa infections in healthcare environments, particularly in low-and middle-income countries, is on the rise. The purpose of this study was to provide comprehensive genomic insights into thirteen P. aeruginosa isolates obtained from Egyptian healthcare settings. Phenotypic analysis of the antimicrobial resistance profile and biofilm formation were performed using minimum inhibitory concentration and microtiter plate assay, respectively. Whole genome sequencing was employed to identify sequence typing, resistome, virulome, and mobile genetic elements. Our findings indicate that 92.3% of the isolates were classified as extensively drug-resistant, with 53.85% of these demonstrating strong biofilm production capabilities. The predominant clone observed in the study was ST773, followed by ST235, both of which were associated with the O11 serotype. Core genome multi-locus sequence typing comparison of these clones with global isolates suggested their potential global expansion and adaptation. A significant portion of the isolates harbored Col plasmids and various MGEs, all of which were linked to antimicrobial resistance genes. Single nucleotide polymorphisms in different genes were associated with the development of antimicrobial resistance in these isolates. In conclusion, this pilot study underscores the prevalence of extensively drug-resistant P. aeruginosa isolates and emphasizes the role of horizontal gene transfer facilitated by a diverse array of mobile genetic elements within various clones. Furthermore, specific insertion sequences and mutations were found to be associated with antibiotic resistance.}, }
@article {pmid38968733, year = {2024}, author = {Li, Y and Zhang, S and Chen, Z and Huang, W and Liu, Q and Fang, H and Chi, B and Yang, N and Zhang, Q}, title = {Deciphering the impact of organic loading rate and digestate recirculation on the occurrence patterns of antibiotics and antibiotic resistance genes in dry anaerobic digestion of kitchen waste.}, journal = {Water research}, volume = {261}, number = {}, pages = {122005}, doi = {10.1016/j.watres.2024.122005}, pmid = {38968733}, issn = {1879-2448}, mesh = {*Anti-Bacterial Agents/pharmacology ; Anaerobiosis ; *Drug Resistance, Microbial/genetics ; *Bioreactors ; Waste Disposal, Fluid ; }, abstract = {Organic loading rate (OLR) is crucial for determining the stability of dry anaerobic digestion (AD). Digestate recirculation contributes to reactor stability and enhances methane production. Nevertheless, the understanding of how OLR and digestate recirculation affect the abundance and diversity of antibiotics and antibiotic resistance genes (ARGs), as well as the mechanisms involved in the dissemination of ARGs, remains limited. This study thoroughly investigated this critical issue through a long-term pilot-scale experiment. The metabolome analyses revealed the enrichment of various antibiotics, such as aminoglycoside, tetracycline, and macrolide, under low OLR conditions (OLR ≤ 4.0 g·VS/L·d) and the reactor instability. Antibiotics abundance decreased by approximately 19.66-31.69 % during high OLR operation (OLR ≥ 6.0 g·VS/L·d) with digestate recirculation. The metagenome analyses demonstrated that although low OLR promoted reactor stability, it facilitated the proliferation of antibiotic-resistant bacteria, such as Pseudomonas, and triggered functional profiles related to ATP generation, oxidative stress response, EPS secretion, and cell membrane permeability, thereby facilitating horizontal gene transfer (HGT) of ARGs. However, under stable operation at an OLR of 6.0 g·VS/L·d, there was a decrease in ARGs abundance but a notable increase in human pathogenic bacteria (HPB) and mobile genetic elements (MGEs). Subsequently, during reactor instability, the abundance of ARGs and HPB increased. Notably, during digestate recirculation at OLR levels of 6.0 and 7.0 g·VS/L·d, the process attenuated the risk of ARGs spread by reducing the diversity of ARGs hosts, minimizing interactions among ARGs hosts, ARGs, and MGEs, and weakening functional profiles associated with HGT of ARGs. Overall, digestate recirculation aids in reducing the abundance of antibiotics and ARGs under high OLR conditions. These findings provide advanced insights into how OLR and digestate recirculation affect the occurrence patterns of antibiotics and ARGs in dry AD.}, }
@article {pmid38965531, year = {2024}, author = {Babajanyan, SG and Garushyants, SK and Wolf, YI and Koonin, EV}, title = {Microbial diversity and ecological complexity emerging from environmental variation and horizontal gene transfer in a simple mathematical model.}, journal = {BMC biology}, volume = {22}, number = {1}, pages = {148}, pmid = {38965531}, issn = {1741-7007}, support = {Intramural Research Program//U.S. National Library of Medicine/ ; }, mesh = {*Gene Transfer, Horizontal ; *Microbiota/genetics ; Biodiversity ; Symbiosis/genetics ; Models, Theoretical ; Models, Biological ; }, abstract = {BACKGROUND: Microbiomes are generally characterized by high diversity of coexisting microbial species and strains, and microbiome composition typically remains stable across a broad range of conditions. However, under fixed conditions, microbial ecology conforms with the exclusion principle under which two populations competing for the same resource within the same niche cannot coexist because the less fit population inevitably goes extinct. Therefore, the long-term persistence of microbiome diversity calls for an explanation.<br><br>RESULTS: To explore the conditions for stabilization of microbial diversity, we developed a simple mathematical model consisting of two competing populations that could exchange a single gene allele via horizontal gene transfer (HGT). We found that, although in a fixed environment, with unbiased HGT, the system obeyed the exclusion principle, in an oscillating environment, within large regions of the phase space bounded by the rates of reproduction and HGT, the two populations coexist. Moreover, depending on the parameter combination, all three major types of symbiosis were obtained, namely, pure competition, host-parasite relationship, and mutualism. In each of these regimes, certain parameter combinations provided for synergy, that is, a greater total abundance of both populations compared to the abundance of the winning population in the fixed environment.<br><br>CONCLUSIONS: The results of this modeling study show that basic phenomena that are universal in microbial communities, namely, environmental variation and HGT, provide for stabilization and persistence of microbial diversity, and emergence of ecological complexity.}, }
@article {pmid38964677, year = {2024}, author = {Xu, G and Yang, S}, title = {Evolution of orphan and atypical histidine kinases and response regulators for microbial signaling diversity.}, journal = {International journal of biological macromolecules}, volume = {275}, number = {Pt 1}, pages = {133635}, doi = {10.1016/j.ijbiomac.2024.133635}, pmid = {38964677}, issn = {1879-0003}, mesh = {*Histidine Kinase/genetics/metabolism ; *Evolution, Molecular ; *Phylogeny ; *Signal Transduction/genetics ; Bacterial Proteins/genetics/metabolism/chemistry ; Bacteria/genetics/enzymology ; Gene Transfer, Horizontal ; }, abstract = {Two-component signaling systems (TCS) are the predominant means of microbes for sensing and responding to environmental stimuli. Typically, TCS is comprised of a sensor histidine kinase (HK) and a cognate response regulator (RR), which might have coevolved together. They usually involve the phosphoryl transfer signaling mechanism. However, there are also some orphan and atypical HK and RR homologs, and their evolutionary origins are still not very clear. They are not associated with cognate pairs or lack the conserved residues for phosphoryl transfer, but they could receive or respond to signals from other regulators. The objective of this study is to reveal the evolutionary history of these orphan and atypical HK and RR homologs. Structural, domain, sequence, and phylogenetic analyses indicated that their evolution process might undergo gene duplication, divergence, and domain shuffling. Meanwhile, lateral gene transfer might also be involved for their gene distribution. Evolution of orphan and atypical HK and RR homologs have increased their signaling diversity, which could be helpful for microbial adaption in complex environments.}, }
@article {pmid38964571, year = {2024}, author = {Xu, C and Hu, C and Li, F and Liu, W and Xu, Y and Shi, D}, title = {Antibiotic resistance genes risks in relation to host pathogenicity and mobility in a typical hospital wastewater treatment process.}, journal = {Environmental research}, volume = {259}, number = {}, pages = {119554}, doi = {10.1016/j.envres.2024.119554}, pmid = {38964571}, issn = {1096-0953}, mesh = {*Wastewater/microbiology ; *Hospitals ; Waste Disposal, Fluid ; Bacteria/genetics/drug effects/pathogenicity ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; }, abstract = {Hospital wastewaters (HWWs) serve as critical reservoirs for disseminating antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB). However, the dynamics and noteworthy shifts of ARGs and their associated pathogenicity, mobility, and resistome risks during HWWs treatment processes remain poorly understood. Utilizing metagenomic sequencing and assembly, we identified 817 ARG subtypes conferring resistance to 20 classes of antibiotics across 18 HWW samples from influent to effluent. Genes encoding resistance to multidrug, aminoglycoside and beta_lactam were the most prevalent ARG types, reflecting patterns observed in clinical settings. On-site treatment efforts decreased the relative abundance of ARGs by 77.4% from influent to secondary sedimentation, whereas chlorine disinfection significantly increased their abundance in the final effluent. Deterministic processes primarily drove the taxonomic assembly, with Proteobacteria being the most abundant phylum and serving as the primary host for 15 ARG types. Contig-based analysis further revealed 114 pathogenic ARB, with Escherichia coli, Pseudomonas alcaligenes, and Pseudomonas aeruginosa exhibiting multidrug-resistant. The contributions of host bacteria and pathogenic ARB varied throughout wastewater treatment. In addition, 7.10%-31.0 % ARGs were flanked by mobile genetic elements (MGEs), predominantly mediated by transposase (74.1%). Notably, tnpA exhibited the highest potential for ARG dissemination, frequently co-occurring with beta-lactam resistance genes (35.2%). Considering ARG profiles, pathogenic hosts, and transferability, raw influent exhibited the highest antibiotic resistome risk index (ARRI), followed by the final effluent. Chlorine disinfection exacerbated resistome risks by inducing potential pathogenic ARB and mobile ARGs, posing threats to the receiving environment. This study delineates ARG occurrence patterns, highlights mechanisms of ARG carriage and horizontal gene transfer, and provides insights for assessing resistance risks and prioritizing interventions in clinical settings.}, }
@article {pmid38964386, year = {2024}, author = {Shi, J and Sun, C and An, T and Jiang, C and Mei, S and Lv, B}, title = {Unraveling the effect of micro/nanoplastics on the occurrence and horizontal transfer of environmental antibiotic resistance genes: Advances, mechanisms and future prospects.}, journal = {The Science of the total environment}, volume = {947}, number = {}, pages = {174466}, doi = {10.1016/j.scitotenv.2024.174466}, pmid = {38964386}, issn = {1879-1026}, mesh = {*Gene Transfer, Horizontal ; *Drug Resistance, Microbial/genetics ; *Microplastics ; Anti-Bacterial Agents ; Bacteria/drug effects ; Genes, Bacterial ; }, abstract = {Microplastics can not only serve as vectors of antibiotic resistance genes (ARGs), but also they and even nanoplastics potentially affect the occurrence of ARGs in indigenous environmental microorganisms, which have aroused great concern for the development of antibiotic resistance. This article specifically reviews the effects of micro/nanoplastics (concentration, size, exposure time, chemical additives) and their interactions with other pollutants on environmental ARGs dissemination. The changes of horizontal genes transfer (HGT, i.e., conjugation, transformation and transduction) of ARGs caused by micro/nanoplastics were also summarized. Further, this review systematically sums up the mechanisms of micro/nanoplastics regulating HGT process of ARGs, including reactive oxygen species production, cell membrane permeability, transfer-related genes expression, extracellular polymeric substances production, and ARG donor-recipient adsorption/contaminants adsorption/biofilm formation. The underlying mechanisms in changes of bacterial communities induced by micro/nanoplastics were also discussed as it was an important factor for structuring the profile of ARGs in the actual environment, including causing environmental stress, providing carbon sources, forming biofilms, affecting pollutants distribution and environmental factors. This review contributes to a systematical understanding of the potential risks of antibiotic resistance dissemination caused by micro/nanoplastics and provokes thinking about perspectives for future research and the management of micro/nanoplastics and plastics.}, }
@article {pmid38964320, year = {2024}, author = {Kadibalban, AS and Landan, G and Dagan, T}, title = {The extent and characteristics of DNA transfer between plasmids and chromosomes.}, journal = {Current biology : CB}, volume = {34}, number = {14}, pages = {3189-3200.e5}, doi = {10.1016/j.cub.2024.06.030}, pmid = {38964320}, issn = {1879-0445}, mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; *Chromosomes, Bacterial/genetics ; Bacteria/genetics ; DNA, Bacterial/genetics ; }, abstract = {Plasmids are extrachromosomal genetic elements that reside in prokaryotes. The acquisition of plasmids encoding beneficial traits can facilitate short-term survival in harsh environmental conditions or long-term adaptation of new ecological niches. Due to their ability to transfer between cells, plasmids are considered agents of gene transfer. Nonetheless, the frequency of DNA transfer between plasmids and chromosomes remains understudied. Using a novel approach for detection of homologous loci between genome pairs, we uncover gene sharing with the chromosome in 1,974 (66%) plasmids residing in 1,016 (78%) taxonomically diverse isolates. The majority of homologous loci correspond to mobile elements, which may be duplicated in the host chromosomes in tens of copies. Neighboring shared genes often encode similar functional categories, indicating the transfer of multigene functional units. Rare transfer events of antibiotics resistance genes are observed mainly with mobile elements. The frequent erosion of sequence similarity in homologous regions indicates that the transferred DNA is often devoid of function. DNA transfer between plasmids and chromosomes thus generates genetic variation that is akin to workings of endosymbiotic gene transfer in eukaryotic evolution. Our findings imply that plasmid contribution to gene transfer most often corresponds to transfer of the plasmid entity rather than transfer of protein-coding genes between plasmids and chromosomes.}, }
@article {pmid38963857, year = {2024}, author = {Weimann, A and Dinan, AM and Ruis, C and Bernut, A and Pont, S and Brown, K and Ryan, J and Santos, L and Ellison, L and Ukor, E and Pandurangan, AP and Krokowski, S and Blundell, TL and Welch, M and Blane, B and Judge, K and Bousfield, R and Brown, N and Bryant, JM and Kukavica-Ibrulj, I and Rampioni, G and Leoni, L and Harrison, PT and Peacock, SJ and Thomson, NR and Gauthier, J and Fothergill, JL and Levesque, RC and Parkhill, J and Floto, RA}, title = {Evolution and host-specific adaptation of Pseudomonas aeruginosa.}, journal = {Science (New York, N.Y.)}, volume = {385}, number = {6704}, pages = {eadi0908}, doi = {10.1126/science.adi0908}, pmid = {38963857}, issn = {1095-9203}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Cystic Fibrosis/microbiology ; Evolution, Molecular ; Gene Transfer, Horizontal ; Host Adaptation ; Host Specificity ; Macrophages/microbiology/immunology ; *Pseudomonas aeruginosa/genetics/pathogenicity ; *Pseudomonas Infections/microbiology ; Host-Pathogen Interactions ; }, abstract = {The major human bacterial pathogen Pseudomonas aeruginosa causes multidrug-resistant infections in people with underlying immunodeficiencies or structural lung diseases such as cystic fibrosis (CF). We show that a few environmental isolates, driven by horizontal gene acquisition, have become dominant epidemic clones that have sequentially emerged and spread through global transmission networks over the past 200 years. These clones demonstrate varying intrinsic propensities for infecting CF or non-CF individuals (linked to specific transcriptional changes enabling survival within macrophages); have undergone multiple rounds of convergent, host-specific adaptation; and have eventually lost their ability to transmit between different patient groups. Our findings thus explain the pathogenic evolution of P. aeruginosa and highlight the importance of global surveillance and cross-infection prevention in averting the emergence of future epidemic clones.}, }
@article {pmid38962965, year = {2024}, author = {Diamant, I and Adani, B and Sylman, M and Rahav, G and Gal-Mor, O}, title = {The transcriptional regulation of the horizontally acquired iron uptake system, yersiniabactin and its contribution to oxidative stress tolerance and pathogenicity of globally emerging salmonella strains.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2369339}, pmid = {38962965}, issn = {1949-0984}, mesh = {Animals ; *Oxidative Stress ; *Iron/metabolism ; Mice ; *Bacterial Proteins/genetics/metabolism ; *Gene Expression Regulation, Bacterial ; *Salmonella enterica/genetics/metabolism/pathogenicity ; Virulence/genetics ; Phenols/metabolism ; Thiazoles/metabolism ; Humans ; Salmonella Infections/microbiology ; Gene Transfer, Horizontal ; Female ; Virulence Factors/genetics/metabolism ; Plasmids/genetics ; }, abstract = {The bacterial species Salmonella enterica (S. enterica) is a highly diverse pathogen containing more than 2600 distinct serovars, which can infect a wide range of animal and human hosts. Recent global emergence of multidrug resistant strains, from serovars Infantis and Muenchen is associated with acquisition of the epidemic megaplasmid, pESI that augments antimicrobial resistance and pathogenicity. One of the main pESI's virulence factors is the potent iron uptake system, yersiniabactin encoded by fyuA, irp2-irp1-ybtUTE, ybtA, and ybtPQXS gene cluster. Here we show that yersiniabactin, has an underappreciated distribution among different S. enterica serovars and subspecies, integrated in their chromosome or carried by different conjugative plasmids, including pESI. While the genetic organization and the coding sequence of the yersiniabactin genes are generally conserved, a 201-bp insertion sequence upstream to ybtA, was identified in pESI. Despite this insertion, pESI-encoded yersiniabactin is regulated by YbtA and the ancestral Ferric Uptake Regulator (Fur), which binds directly to the ybtA and irp2 promoters. Furthermore, we show that yersiniabactin genes are specifically induced during the mid-late logarithmic growth phase and in response to iron-starvation or hydrogen peroxide. Concurring, yersiniabactin was found to play a previously unknown role in oxidative stress tolerance and to enhance intestinal colonization of S. Infantis in mice. These results indicate that yersiniabactin contributes to Salmonella fitness and pathogenicity in vivo and is likely to play a role in the rapid dissemination of pESI among globally emerging Salmonella lineages.}, }
@article {pmid38962322, year = {2024}, author = {Sobh, G and Araj, GF and Finianos, M and Sourenian, T and Hrabak, J and Pappagianitsis, CC and Chaar, ME and Bitar, I}, title = {Molecular characterization of carbapenem and ceftazidime-avibactam-resistant Enterobacterales and horizontal spread of bla NDM-5 gene at a Lebanese medical center.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1407246}, pmid = {38962322}, issn = {2235-2988}, mesh = {*Ceftazidime/pharmacology ; *Azabicyclo Compounds/pharmacology ; Humans ; Lebanon ; *beta-Lactamases/genetics/metabolism ; *Klebsiella pneumoniae/genetics/drug effects ; *Whole Genome Sequencing ; *Anti-Bacterial Agents/pharmacology ; *Escherichia coli/genetics/drug effects ; *Carbapenems/pharmacology ; *Drug Resistance, Multiple, Bacterial/genetics ; *Drug Combinations ; Plasmids/genetics ; Microbial Sensitivity Tests ; Gene Transfer, Horizontal ; Genome, Bacterial ; Carbapenem-Resistant Enterobacteriaceae/genetics/drug effects/isolation &amp; purification ; Bacterial Proteins/genetics/metabolism ; Tertiary Care Centers ; }, abstract = {INTRODUCTION: In the battle against multidrug-resistant bacterial infections, ceftazidime- avibactam (CZA) stands as a pivotal defense, particularly against carbapenemresistant (CR) Gram-negative pathogens. However, the rise in resistance against this drug poses a significant threat to its effectiveness, highlighting the critical need for in-depth studies about its resistance mechanisms.<br><br>METHODS: This research focuses on the genomic characterization of CR- and CZA-resistant Escherichia coli (n=26) and Klebsiella pneumoniae (n=34) strains, harboring the blaNDM and/or blaOXA-48-like genes, at a major Lebanese tertiary care medical center, using whole genome sequencing (WGS).<br><br>RESULTS: Our findings revealed a notable prevalence of blaNDM in all K. pneumoniae strains isolates, with 27 of these also harboring blaOXA-48. On the other hand, E. coli strains predominantly carried the blaNDM-5 gene. Whole genome sequencing (WGS) identified a predominance of ST383 among K. pneumoniae strains, which possessed a multi-replicon IncFIB-IncHI1B plasmid harboring the blaNDM-5. Additionally, various Inc group plasmids in K. pneumoniae across multiple sequence types were found to carry the blaNDM. Similarly, diverse STs of E. coli were observed to carry blaNDM-5 on different plasmids.<br><br>DISCUSSION: The study underscores NDM carbapenemases as a paramount resistance mechanism in Lebanon,jeopardizing critical last-resort treatments. It also illuminates the role of varied sequence types and mobile genetic elements in the spread of NDM resistance,stressing the urgent need for strategies to mitigate this threat, especially in nosocomial infections.}, }
@article {pmid38961341, year = {2024}, author = {Yang, Y and Zhou, P and Tian, D and Wang, W and Zhou, Y and Jiang, X}, title = {CRISPR-Cas3 and type I restriction-modification team up against blaKPC-IncF plasmid transfer in Klebsiella pneumoniae.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {240}, pmid = {38961341}, issn = {1471-2180}, support = {82102439//National Natural Science Foundation of China/ ; 82202564//National Natural Science Foundation of China/ ; 82172315//National Natural Science Foundation of China/ ; 22YF1437500//Shanghai Sailing Program/ ; }, mesh = {*Klebsiella pneumoniae/genetics ; *Plasmids/genetics ; *CRISPR-Cas Systems ; *Conjugation, Genetic ; beta-Lactamases/genetics ; DNA Restriction-Modification Enzymes/genetics ; China ; Klebsiella Infections/microbiology ; Gene Transfer, Horizontal ; Humans ; Genome, Bacterial/genetics ; }, abstract = {OBJECTIVE: We explored whether the Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas and restriction-modification (R-M) systems are compatible and act together to resist plasmid attacks.<br><br>METHODS: 932 global whole-genome sequences from GenBank, and 459 K. pneumoniae isolates from six provinces of China, were collected to investigate the co-distribution of CRISPR-Cas, R-M systems, and blaKPC plasmid. Conjugation and transformation assays were applied to explore the anti-plasmid function of CRISPR and R-M systems.<br><br>RESULTS: We found a significant inverse correlation between the presence of CRISPR and R-M systems and blaKPC plasmids in K. pneumoniae, especially when both systems cohabited in one host. The multiple matched recognition sequences of both systems in blaKPC-IncF plasmids (97%) revealed that they were good targets for both systems. Furthermore, the results of conjugation assay demonstrated that CRISPR-Cas and R-M systems in K. pneumoniae could effectively hinder blaKPC plasmid invasion. Notably, CRISPR-Cas and R-M worked together to confer a 4-log reduction in the acquisition of blaKPC plasmid in conjugative events, exhibiting robust synergistic anti-plasmid immunity.<br><br>CONCLUSIONS: Our results indicate the synergistic role of CRISPR and R-M in regulating horizontal gene transfer in K. pneumoniae and rationalize the development of antimicrobial strategies that capitalize on the immunocompromised status of KPC-KP.}, }
@article {pmid38960277, year = {2025}, author = {Li, W and Wang, Y and Zhao, K and Xu, L and Shi, T and Ma, B and Lv, X}, title = {Host-virus coevolution drives soil microbial function succession along a millennium land reclamation chronosequence.}, journal = {Journal of advanced research}, volume = {71}, number = {}, pages = {297-306}, doi = {10.1016/j.jare.2024.06.022}, pmid = {38960277}, issn = {2090-1224}, mesh = {*Soil Microbiology ; Metagenome ; *Host Microbial Interactions/genetics ; Virome/genetics ; Gene Transfer, Horizontal ; *DNA Viruses/genetics ; Soil/chemistry ; }, abstract = {INTRODUCTION: Gene exchange between viruses and hosts plays an important role in driving virus-host coevolution, enabling adaptation of both viruses and hosts to environmental changes. However, the mechanisms and functional significance of virus-host gene exchanges over long-term scales remain largely unexplored.<br><br>OBJECTIVE: The present study aimed to gain insights into the role of viruses in virus-host interactions and coevolution by monitoring virome dynamics along a millennium-long land reclamation chronosequence.<br><br>METHODS: We collected 24 soil samples from 8 stages of a millennium-long land reclamation chronosequence, including non-reclamation, and reclamation periods of 10, 50, 100, 300, 500, 700, and 1000&#xa0;years. We characterized their metagenomes, and identified DNA viruses within these metagenomes.<br><br>RESULTS: Our findings reveal a significant shift in viral community composition after 50&#xa0;years of land reclamation, but soil viral diversity reached a stable phase approximately 300&#xa0;years after the initial reclamation. Analysis of the virus-host network showed a scale-free degree distribution and a reduction in complexity over time, with generalist viruses emerging as key facilitators of horizontal gene transfer.<br><br>CONCLUSION: These findings highlight the integral role of viruses, especially generalist types, in mediating gene exchanges between viruses and hosts, thereby influencing the coevolutionary dynamics in soil ecosystems over significant timescales. This study offers novel insights into long-term virus-host interactions, showing how the virome responds to environmental changes, driving shifts in various microbial functions in reclaimed land.}, }
@article {pmid38949703, year = {2024}, author = {Saula, AY and Knight, G and Bowness, R}, title = {Within-Host Mathematical Models of Antibiotic Resistance.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2833}, number = {}, pages = {79-91}, pmid = {38949703}, issn = {1940-6029}, mesh = {*Bacteria/genetics/drug effects ; Humans ; *Gene Transfer, Horizontal ; Drug Resistance, Microbial/genetics ; Models, Theoretical ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Host-Pathogen Interactions/genetics ; }, abstract = {Mathematical models have been used to study the spread of infectious diseases from person to person. More recently studies are developing within-host modeling which provides an understanding of how pathogens-bacteria, fungi, parasites, or viruses-develop, spread, and evolve inside a single individual and their interaction with the host's immune system.Such models have the potential to provide a more detailed and complete description of the pathogenesis of diseases within-host and identify other influencing factors that may not be detected otherwise. Mathematical models can be used to aid understanding of the global antibiotic resistance (ABR) crisis and identify new ways of combating this threat.ABR occurs when bacteria respond to random or selective pressures and adapt to new environments through the acquisition of new genetic traits. This is usually through the acquisition of a piece of DNA from other bacteria, a process called horizontal gene transfer (HGT), the modification of a piece of DNA within a bacterium, or through. Bacteria have evolved mechanisms that enable them to respond to environmental threats by mutation, and horizontal gene transfer (HGT): conjugation; transduction; and transformation. A frequent mechanism of HGT responsible for spreading antibiotic resistance on the global scale is conjugation, as it allows the direct transfer of mobile genetic elements (MGEs). Although there are several MGEs, the most important MGEs which promote the development and rapid spread of antimicrobial resistance genes in bacterial populations are plasmids and transposons. Each of the resistance-spread-mechanisms mentioned above can be modeled allowing us to understand the process better and to define strategies to reduce resistance.}, }
@article {pmid38948848, year = {2024}, author = {Lv, C and Abdullah, M and Chen, W and Zhou, N and Cheng, Z and Chen, Y and Li, M and Simpson, KW and Elsaadi, A and Zhu, Y and Lipkin, SM and Chang, YF}, title = {Genomic characterization of Escherichia coli harbor a polyketide synthase (pks) island associated with colorectal cancer (CRC) development.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.06.16.599199}, pmid = {38948848}, issn = {2692-8205}, abstract = {The E. coli strain harboring the polyketide synthase (Pks) island encodes the genotoxin colibactin, a secondary metabolite reported to have severe implications for human health and for the progression of colorectal cancer. The present study involved whole-genome-wide comparison and phylogenetic analysis of pks harboring E. coli isolates to gain insight into the distribution and evolution of these organism. Fifteen E. coli strains isolated from patients with ulcerative colitis were sequenced, 13 of which harbored pks islands. In addition, 2,654 genomes from the public database were also screened for pks harboring E. coli genomes, 158 of which were pks -positive isolates. Whole-genome-wide comparison and phylogenetic analysis revealed that 171 (158+13) pks -positive isolates belonged to phylogroup B2, and most of the isolates associated to sequence types ST73 and ST95. One isolate from an ulcerative colitis (UC) patient was of the sequence type ST8303. The maximum likelihood tree based on the core genome of pks -positive isolates revealed horizontal gene transfer across sequence types and serotypes. Virulome and resistome analyses revealed the preponderance of virulence genes and a reduced number of antimicrobial genes in Pks -positive isolates. This study strongly contributes to understanding the evolution of pks islands in E. coli .}, }
@article {pmid38947372, year = {2024}, author = {Gómez-Gaviria, M and Contreras-López, LM and Aguilera-Domínguez, JI and Mora-Montes, HM}, title = {Strategies of Pharmacological Repositioning for the Treatment of Medically Relevant Mycoses.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {2641-2658}, pmid = {38947372}, issn = {1178-6973}, abstract = {Fungal infections represent a worldwide concern for public health, due to their prevalence and significant increase in cases each year. Among the most frequent mycoses are those caused by members of the genera Candida, Cryptococcus, Aspergillus, Histoplasma, Pneumocystis, Mucor, and Sporothrix, which have been treated for years with conventional antifungal drugs, such as flucytosine, azoles, polyenes, and echinocandins. However, these microorganisms have acquired the ability to evade the mechanisms of action of these drugs, thus hindering their treatment. Among the most common evasion mechanisms are alterations in sterol biosynthesis, modifications of drug transport through the cell wall and membrane, alterations of drug targets, phenotypic plasticity, horizontal gene transfer, and chromosomal aneuploidies. Taking into account these problems, some research groups have sought new therapeutic alternatives based on drug repositioning. Through repositioning, it is possible to use existing pharmacological compounds for which their mechanism of action is already established for other diseases, and thus exploit their potential antifungal activity. The advantage offered by these drugs is that they may be less prone to resistance. In this article, a comprehensive review was carried out to highlight the most relevant repositioning drugs to treat fungal infections. These include antibiotics, antivirals, anthelmintics, statins, and anti-inflammatory drugs.}, }
@article {pmid38946899, year = {2024}, author = {Ji, J and Zhu, Y and Zhao, F and Zhang, J and Yao, B and Zhu, M and Yu, Y and Zhang, J and Fu, Y}, title = {Co-colonization of different species harboring KPC or NDM carbapenemase in the same host gut: insight of resistance evolution by horizontal gene transfer.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1416454}, pmid = {38946899}, issn = {1664-302X}, abstract = {INTRODUCTION: The dissemination of carbapenem-resistant Enterobacteriales (CRE) in nosocomial settings is primarily associated with the horizontal transfer of plasmids. However, limited research has focused on the in-host transferability of carbapenem resistance. In this study, ten isolates were collected from gut specimens of five individuals, each hosting two different species, including Escherichia coli, Klebsiella pneumoniae, Klebsiella aerogenes, Enterobacter cloacae, or Citrobacter koseri.<br><br>METHODS: Species identification and antimicrobial susceptibility were determined by MALDI-TOF MS and broth microdilution method. Carbapenemase genes were detected and localized using PCR, S1-PFGE and southern blot. The transferability of carbapenemase genes between species was investigated through filter mating experiments, and the genetic contexts of the plasmids were analyzed using whole genome sequencing.<br><br>RESULTS AND DISCUSSION: Our results revealed that each of the ten isolates harbored a carbapenemase gene, including bla NDM-5, bla NDM-1, or bla KPC-2, on a plasmid. Five different plasmids were successfully transferred to recipient cells of E. coli, K. pneumoniae or A. baumannii by transconjugation. The genetic contexts of the carbapenemase gene were remarkably similar between the two CRE isolates from each individual. This study highlights the potential for interspecies plasmid transmission in human gut, emphasizing the colonization of CRE as a significant risk factor for the dissemination of carbapenemase genes within the host. These findings underscore the need for appropriate intestinal CRE screening and colonization prevention.}, }
@article {pmid38944065, year = {2024}, author = {Marchetti, A and Orlando, M and Bombardi, L and Fusco, S and Mangiagalli, M and Lotti, M}, title = {Evolutionary history and activity towards oligosaccharides and polysaccharides of GH3 glycosidases from an Antarctic marine bacterium.}, journal = {International journal of biological macromolecules}, volume = {275}, number = {Pt 1}, pages = {133449}, doi = {10.1016/j.ijbiomac.2024.133449}, pmid = {38944065}, issn = {1879-0003}, mesh = {*Glycoside Hydrolases/metabolism/genetics/chemistry ; Substrate Specificity ; *Oligosaccharides/metabolism ; Antarctic Regions ; *Evolution, Molecular ; Polysaccharides/metabolism/chemistry ; Phylogeny ; Marinomonas/enzymology/genetics ; Aquatic Organisms/enzymology ; Enzyme Stability ; Catalytic Domain ; Hydrolysis ; }, abstract = {Glycoside hydrolases (GHs) are pivotal in the hydrolysis of the glycosidic bonds of sugars, which are the main carbon and energy sources. The genome of Marinomonas sp. ef1, an Antarctic bacterium, contains three GHs belonging to family 3. These enzymes have distinct architectures and low sequence identity, suggesting that they originated from separate horizontal gene transfer events. M-GH3_A and M-GH3_B, were found to differ in cold adaptation and substrate specificity. M-GH3_A is a bona fide cold-active enzyme since it retains 20 % activity at 10 °C and exhibits poor long-term thermal stability. On the other hand, M-GH3_B shows mesophilic traits with very low activity at 10 °C (< 5 %) and higher long-term thermal stability. Substrate specificity assays highlight that M-GH3_A is a promiscuous β-glucosidase mainly active on cellobiose and cellotetraose, whereas M-GH3_B is a β-xylosidase active on xylan and arabinoxylan. Structural analysis suggests that such functional differences are due to their differently shaped active sites. The active site of M-GH3_A is wider but has a narrower entrance compared to that of M-GH3_B. Genome-based prediction of metabolic pathways suggests that Marinomonas sp. ef1 can use monosaccharides derived from the GH3-catalyzed hydrolysis of oligosaccharides either as a carbon source or for producing osmolytes.}, }
@article {pmid38942826, year = {2024}, author = {Boukouvala, S and Kontomina, E and Olbasalis, I and Patriarcheas, D and Tzimotoudis, D and Arvaniti, K and Manolias, A and Tsatiri, MA and Basdani, D and Zekkas, S}, title = {Insights into the genomic and functional divergence of NAT gene family to serve microbial secondary metabolism.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {14905}, pmid = {38942826}, issn = {2045-2322}, support = {3712//Hellenic Foundation for Research and Innovation (H.F.R.I.)/ ; MIS-5000432//State Scholarships Foundation (&#x399;&#x39a;&#x3a5;)/ ; }, mesh = {*Multigene Family ; *Secondary Metabolism/genetics ; *Bacteria/genetics/metabolism ; Archaea/genetics/metabolism ; Phylogeny ; Arylamine N-Acetyltransferase/genetics/metabolism ; Fungi/genetics ; Genomics/methods ; Gene Transfer, Horizontal ; }, abstract = {Microbial NAT enzymes, which employ acyl-CoA to acylate aromatic amines and hydrazines, have been well-studied for their role in xenobiotic metabolism. Some homologues have also been linked to secondary metabolism, but this function of NAT enzymes is not as well-known. For this comparative study, we surveyed sequenced microbial genomes to update the list of formally annotated NAT genes, adding over 4000 new sequences (mainly bacterial, but also archaeal, fungal and protist) and portraying a broad but not universal distribution of NATs in the microbiocosmos. Localization of NAT sequences within microbial gene clusters was not a rare finding, and this association was evident across all main types of biosynthetic gene clusters (BGCs) implicated in secondary metabolism. Interrogation of the MIBiG database for experimentally characterized clusters with NAT genes further supports that secondary metabolism must be a major function for microbial NAT enzymes and should not be overlooked by researchers in the field. We also show that NAT sequences can be associated with bacterial plasmids potentially involved in horizontal gene transfer. Combined, our computational predictions and MIBiG literature findings reveal the extraordinary functional diversification of microbial NAT genes, prompting further research into their role in predicted BGCs with as yet uncharacterized function.}, }
@article {pmid38942024, year = {2024}, author = {Harder, CB and Miyauchi, S and Virágh, M and Kuo, A and Thoen, E and Andreopoulos, B and Lu, D and Skrede, I and Drula, E and Henrissat, B and Morin, E and Kohler, A and Barry, K and LaButti, K and Salamov, A and Lipzen, A and Merényi, Z and Hegedüs, B and Baldrian, P and Stursova, M and Weitz, H and Taylor, A and Koriabine, M and Savage, E and Grigoriev, IV and Nagy, LG and Martin, F and Kauserud, H}, title = {Extreme overall mushroom genome expansion in Mycena s.s. irrespective of plant hosts or substrate specializations.}, journal = {Cell genomics}, volume = {4}, number = {7}, pages = {100586}, pmid = {38942024}, issn = {2666-979X}, mesh = {*Genome, Fungal/genetics ; *Agaricales/genetics ; Phylogeny ; DNA Transposable Elements/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Plants/microbiology/genetics ; }, abstract = {Mycena s.s. is a ubiquitous mushroom genus whose members degrade multiple dead plant substrates and opportunistically invade living plant roots. Having sequenced the nuclear genomes of 24 Mycena species, we find them to defy the expected patterns for fungi based on both their traditionally perceived saprotrophic ecology and substrate specializations. Mycena displayed massive genome expansions overall affecting all gene families, driven by novel gene family emergence, gene duplications, enlarged secretomes encoding polysaccharide degradation enzymes, transposable element (TE) proliferation, and horizontal gene transfers. Mainly due to TE proliferation, Arctic Mycena species display genomes of up to 502 Mbp (2-8× the temperate Mycena), the largest among mushroom-forming Agaricomycetes, indicating a possible evolutionary convergence to genomic expansions sometimes seen in Arctic plants. Overall, Mycena show highly unusual, varied mosaic-like genomic structures adaptable to multiple lifestyles, providing genomic illustration for the growing realization that fungal niche adaptations can be far more fluid than traditionally believed.}, }
@article {pmid38942019, year = {2024}, author = {Mason, B and Hayward, DC and Moya, A and Cooke, I and Sorenson, A and Brunner, R and Andrade, N and Huerlimann, R and Bourne, DG and Schaeffer, P and Grinblat, M and Ravasi, T and Ueda, N and Tang, SL and Ball, EE and Miller, DJ}, title = {Microbiome manipulation by corals and other Cnidaria via quorum quenching.}, journal = {Current biology : CB}, volume = {34}, number = {14}, pages = {3226-3232.e5}, doi = {10.1016/j.cub.2024.05.073}, pmid = {38942019}, issn = {1879-0445}, mesh = {Animals ; *Anthozoa/microbiology/immunology/physiology ; *Quorum Sensing ; *Microbiota ; Cnidaria/physiology/genetics ; Coral Reefs ; Acyl-Butyrolactones/metabolism ; }, abstract = {A dynamic mucous layer containing numerous micro-organisms covers the surface of corals and has multiple functions including both removal of sediment and "food gathering."[1] It is likely to also act as the primary barrier to infection; various proteins and compounds with antimicrobial activity have been identified in coral mucus, though these are thought to be largely or exclusively of microbial origin. As in Hydra,[2] anti-microbial peptides (AMPs) are likely to play major roles in regulating the microbiomes of corals.[3][,][4] Some eukaryotes employ a complementary but less obvious approach to manipulate their associated microbiome by interfering with quorum signaling, effectively preventing bacteria from coordinating gene expression across a population. Our investigation of immunity in the reef-building coral Acropora millepora,[5] however, led to the discovery of a coral gene referred to here as AmNtNH1 that can inactivate a range of acyl homoserine lactones (AHLs), common bacterial quorum signaling molecules, and is induced on immune challenge of adult corals and expressed during the larval settlement process. Closely related proteins are widely distributed within the Scleractinia (hard corals) and some other cnidarians, with multiple paralogs in Acropora, but their closest relatives are bacterial, implying that these are products of one or more lateral gene transfer events post-dating the cnidarian-bilaterian divergence. The deployment by corals of genes used by bacteria to compete with other bacteria reflects a mechanism of microbiome manipulation previously unknown in Metazoa but that may apply more generally.}, }
@article {pmid38941922, year = {2024}, author = {Li, B and Ni, S and Liu, Y and Lin, J and Wang, X}, title = {The histone-like nucleoid-structuring protein encoded by the plasmid pMBL6842 regulates both plasmid stability and host physiology of Pseudoalteromonas rubra SCSIO 6842.}, journal = {Microbiological research}, volume = {286}, number = {}, pages = {127817}, doi = {10.1016/j.micres.2024.127817}, pmid = {38941922}, issn = {1618-0623}, mesh = {*Plasmids/genetics ; *Bacterial Proteins/genetics/metabolism ; *Gene Expression Regulation, Bacterial ; *Pseudoalteromonas/genetics/metabolism ; DNA-Binding Proteins/genetics/metabolism ; Gene Transfer, Horizontal ; Conjugation, Genetic ; Histones/metabolism/genetics ; }, abstract = {Plasmids orchestrate bacterial adaptation across diverse environments and facilitate lateral gene transfer within bacterial communities. Their presence can perturb host metabolism, creating a competitive advantage for plasmid-free cells. Plasmid stability hinges on efficient replication and partition mechanisms. While plasmids commonly encode histone-like nucleoid-structuring (H-NS) family proteins, the precise influence of plasmid-encoded H-NS proteins on stability remains elusive. In this study, we examined the conjugative plasmid pMBL6842, harboring the hns gene, and observed its positive regulation of parAB transcription, critical for plasmid segregation. Deletion of hns led to rapid plasmid loss, which was remedied by hns complementation. Further investigations unveiled adverse effects of hns overexpression on the bacterial host. Transcriptome analysis revealed hns's role in regulating numerous bacterial genes, impacting both host growth and swimming motility in the presence of the hns gene. Therefore, our study unveils the multifaceted roles of H-NS in both plasmid stability and host physiology, underscoring its biological significance and paving the way for future inquiries into the involvement of H-NS in horizontal gene transfer events.}, }
@article {pmid38940556, year = {2024}, author = {Sun, W-S and Torrens, G and Ter Beek, J and Cava, F and Berntsson, RP-A}, title = {Breaking barriers: pCF10 type 4 secretion system relies on a self-regulating muramidase to modulate the cell wall.}, journal = {mBio}, volume = {15}, number = {8}, pages = {e0048824}, pmid = {38940556}, issn = {2150-7511}, support = {2016-03599//Vetenskapsr&#xe5;det (VR)/ ; 2018-02823//Vetenskapsr&#xe5;det (VR)/ ; 2018-05882//Vetenskapsr&#xe5;det (VR)/ ; SMK-1869//Kempestiftelserna (Kempe Foundations)/ ; SMK2062//Kempestiftelserna (Kempe Foundations)/ ; }, mesh = {*Cell Wall/metabolism ; *Type IV Secretion Systems/metabolism/genetics ; *Enterococcus faecalis/genetics/enzymology/metabolism ; *Muramidase/metabolism/genetics ; Plasmids/genetics ; Bacterial Proteins/metabolism/genetics ; Conjugation, Genetic ; Catalytic Domain ; }, abstract = {Conjugative type 4 secretion systems (T4SSs) are the main driver for the spread of antibiotic resistance genes and virulence factors in bacteria. To deliver the DNA substrate to recipient cells, it must cross the cell envelopes of both donor and recipient bacteria. In the T4SS from the enterococcal conjugative plasmid pCF10, PrgK is known to be the active cell wall degrading enzyme. It has three predicted extracellular hydrolase domains: metallo-peptidase (LytM), soluble lytic transglycosylase (SLT), and cysteine, histidine-dependent amidohydrolases/peptidases (CHAP). Here, we report the structure of the LytM domain and show that its active site is degenerate and lacks the active site metal. Furthermore, we show that only the predicted SLT domain is functional in vitro and that it unexpectedly has a muramidase instead of a lytic transglycosylase activity. While we did not observe any peptidoglycan hydrolytic activity for the LytM or CHAP domain, we found that these domains downregulated the SLT muramidase activity. The CHAP domain was also found to be involved in PrgK dimer formation. Furthermore, we show that PrgK interacts with PrgL, which likely targets PrgK to the rest of the T4SS. The presented data provides important information for understanding the function of Gram-positive T4SSs.IMPORTANCEAntibiotic resistance is a large threat to human health and is getting more prevalent. One of the major contributors to the spread of antibiotic resistance among different bacteria is type 4 secretion systems (T4SS). However, mainly T4SSs from Gram-negative bacteria have been studied in detail. T4SSs from Gram-positive bacteria, which stand for more than half of all hospital-acquired infections, are much less understood. The significance of our research is in identifying the function and regulation of a cell wall hydrolase, a key component of the pCF10 T4SS from Enterococcus faecalis. This system is one of the best-studied Gram-positive T4SSs, and this added knowledge aids in our understanding of horizontal gene transfer in E. faecalis as well as other medically relevant Gram-positive bacteria.}, }
@article {pmid38940543, year = {2024}, author = {Jian, J and Wang, Z and Chen, C and Workman, CT and Fang, X and Larsen, TO and Guo, J and Sonnenschein, EC}, title = {Two high-quality Prototheca zopfii genomes provide new insights into their evolution as obligate algal heterotrophs and their pathogenicity.}, journal = {Microbiology spectrum}, volume = {12}, number = {8}, pages = {e0414823}, pmid = {38940543}, issn = {2165-0497}, mesh = {*Prototheca/genetics/pathogenicity ; *Heterotrophic Processes ; Phylogeny ; Genome, Plastid ; Evolution, Molecular ; Photosynthesis/genetics ; Genome, Plant ; }, abstract = {UNLABELLED: The majority of the nearly 10,000 described species of green algae are photoautotrophs; however, some species have lost their ability to photosynthesize and become obligate heterotrophs that rely on parasitism for survival. Two high-quality genomes of the heterotrophic algae Prototheca zopfii Pz20 and Pz23 were obtained using short- and long-read genomic as well as transcriptomic data. The genome sizes were 31.2 Mb and 31.3 Mb, respectively, and contig N50 values of 1.99 Mb and 1.26 Mb. Although P. zopfii maintained its plastid genome, the transition to heterotrophy led to a reduction in both plastid and nuclear genome size, including the loss of photosynthesis-related genes from both the nuclear and plastid genomes and the elimination of genes encoding for carotenoid oxygenase and pheophorbide an oxygenase. The loss of genes, including basic leucine-zipper (bZIP) transcription factors, flavin adenine dinucleotide-linked oxidase, and helicase, could have played a role in the transmission of autotrophy to heterotrophs and in the processes of abiotic stress resistance and pathogenicity. A total of 66 (1.37%) and 73 (1.49%) genes were identified as potential horizontal gene transfer events in the two P. zopfii genomes, respectively. Genes for malate synthase and isocitrate lyase, which are horizontally transferred from bacteria, may play a pivotal role in carbon and nitrogen metabolism as well as the pathogenicity of Prototheca and non-photosynthetic organisms. The two high-quality P. zopfii genomes provide new insights into their evolution as obligate heterotrophs and pathogenicity.<br><br>IMPORTANCE: The genus Prototheca, characterized by its heterotrophic nature and pathogenicity, serves as an exemplary model for investigating pathobiology. The limited understanding of the protothecosis infectious disease is attributed to the lack of genomic resources. Using HiFi long-read sequencing, both nuclear and plastid genomes were generated for two strains of P. zopfii. The findings revealed a concurrent reduction in both plastid and nuclear genome size, accompanied by the loss of genes associated with photosynthesis, carotenoid oxygenase, basic leucine-zipper (bZIP) transcription factors, and others. The analysis of horizontal gene transfer revealed the presence of 1.37% and 1.49% bacterial genes, including malate synthase and isocitrate lyase, which play crucial roles in carbon and nitrogen metabolism, as well as pathogenicity and obligate heterotrophy. The two high-quality P. zopfii genomes represent valuable resources for investigating their adaptation and evolution as obligate heterotrophs, as well as for developing future prevention and treatment strategies against protothecosis.}, }
@article {pmid38940156, year = {2024}, author = {Curry, KD and Yu, FB and Vance, SE and Segarra, S and Bhaya, D and Chikhi, R and Rocha, EPC and Treangen, TJ}, title = {Reference-free structural variant detection in microbiomes via long-read co-assembly graphs.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {Suppl 1}, pages = {i58-i67}, pmid = {38940156}, issn = {1367-4811}, support = {//Department of Energy Joint Genome Institute/ ; P01 AI152999/AI/NIAID NIH HHS/United States ; //National Institute of Allergy and Infectious Diseases/ ; //Department of Energy/ ; P01-AI152999/GF/NIH HHS/United States ; //European Union's Horizon 2020/ ; 2023333162//NSF/ ; //Office of Science/ ; //Carnegie Institution for Science/ ; //Ken Kennedy Institute Recruiting/ ; EF-2126387//MIM Universal Rules of Live/ ; //Rice University Wagoner Foreign Study Scholarship/ ; IIS-2239114//NSF/ ; 872539//Marie Sk&#x142;odowska-Curie/ ; //NSF/ ; }, mesh = {*Microbiota/genetics ; *Metagenome ; *Genome, Bacterial ; Metagenomics/methods ; Gene Transfer, Horizontal ; Bacteria/genetics ; Algorithms ; }, abstract = {MOTIVATION: The study of bacterial genome dynamics is vital for understanding the mechanisms underlying microbial adaptation, growth, and their impact on host phenotype. Structural variants (SVs), genomic alterations of 50 base pairs or more, play a pivotal role in driving evolutionary processes and maintaining genomic heterogeneity within bacterial populations. While SV detection in isolate genomes is relatively straightforward, metagenomes present broader challenges due to the absence of clear reference genomes and the presence of mixed strains. In response, our proposed method rhea, forgoes reference genomes and metagenome-assembled genomes (MAGs) by encompassing all metagenomic samples in a series (time or other metric) into a single co-assembly graph. The log fold change in graph coverage between successive samples is then calculated to call SVs that are thriving or declining.<br><br>RESULTS: We show rhea to outperform existing methods for SV and horizontal gene transfer (HGT) detection in two simulated mock metagenomes, particularly as the simulated reads diverge from reference genomes and an increase in strain diversity is incorporated. We additionally demonstrate use cases for rhea on series metagenomic data of environmental and fermented food microbiomes to detect specific sequence alterations between successive time and temperature samples, suggesting host advantage. Our approach leverages previous work in assembly graph structural and coverage patterns to provide versatility in studying SVs across diverse and poorly characterized microbial communities for more comprehensive insights into microbial gene flux.<br><br>rhea is open source and available at: https://github.com/treangenlab/rhea.}, }
@article {pmid38936370, year = {2024}, author = {Yu, T and Xu, X and Liu, Y and Wang, X and Wu, S and Qiu, Z and Liu, X and Pan, X and Gu, C and Wang, S and Dong, L and Li, W and Yao, X}, title = {Multi-omics signatures reveal genomic and functional heterogeneity of Cutibacterium acnes in normal and diseased skin.}, journal = {Cell host &amp; microbe}, volume = {32}, number = {7}, pages = {1129-1146.e8}, doi = {10.1016/j.chom.2024.06.002}, pmid = {38936370}, issn = {1934-6069}, mesh = {Humans ; *Skin/microbiology ; *Dermatitis, Atopic/microbiology/genetics ; *Keratinocytes/microbiology ; *Acne Vulgaris/microbiology ; *Propionibacterium acnes/genetics ; Genomics ; Genome, Bacterial ; Staphylococcus epidermidis/genetics ; Transcriptome ; Virulence Factors/genetics ; Propionibacteriaceae/genetics ; Metabolome ; Metabolomics ; Microbiota/genetics ; Multiomics ; }, abstract = {Cutibacterium acnes is the most abundant bacterium of the human skin microbiome since adolescence, participating in both skin homeostasis and diseases. Here, we demonstrate individual and niche heterogeneity of C. acnes from 1,234 isolate genomes. Skin disease (atopic dermatitis and acne) and body site shape genomic differences of C. acnes, stemming from horizontal gene transfer and selection pressure. C. acnes harbors characteristic metabolic functions, fewer antibiotic resistance genes and virulence factors, and a more stable genome compared with Staphylococcus epidermidis. Integrated genome, transcriptome, and metabolome analysis at the strain level unveils the functional characteristics of C. acnes. Consistent with the transcriptome signature, C. acnes in a sebum-rich environment induces toxic and pro-inflammatory effects on keratinocytes. L-carnosine, an anti-oxidative stress metabolite, is up-regulated in the C. acnes metabolome from atopic dermatitis and attenuates skin inflammation. Collectively, our study reveals the joint impact of genes and the microenvironment on C. acnes function.}, }
@article {pmid38936366, year = {2024}, author = {Garric, S and Ratin, M and Marie, D and Foulon, V and Probert, I and Rodriguez, F and Six, C}, title = {Impaired photoacclimation in a kleptoplastidic dinoflagellate reveals physiological limits of early stages of endosymbiosis.}, journal = {Current biology : CB}, volume = {34}, number = {14}, pages = {3064-3076.e5}, doi = {10.1016/j.cub.2024.05.066}, pmid = {38936366}, issn = {1879-0445}, mesh = {*Dinoflagellida/physiology/genetics ; *Symbiosis ; *Photosynthesis ; *Plastids/genetics/metabolism ; Phycoerythrin/metabolism/genetics ; Cryptophyta/genetics/physiology ; Light ; }, abstract = {Dinophysis dinoflagellates are predators of Mesodinium ciliates, from which they retain only the plastids of cryptophyte origin. The absence of nuclear photosynthetic cryptophyte genes in Dinophysis raises intriguing physiological and evolutionary questions regarding the functional dynamics of these temporary kleptoplastids within a foreign cellular environment. In an experimental setup including two light conditions, the comparative analysis with Mesodinium rubrum and the cryptophyte Teleaulax amphioxeia revealed that Dinophysis acuminata possessed a smaller and less dynamic functional photosynthetic antenna for green light, a function performed by phycoerythrin. We showed that the lack of the cryptophyte nucleus prevented the synthesis of the phycoerythrin α subunit, thereby hindering the formation of a complete phycoerythrin in Dinophysis. In particular, biochemical analyses showed that Dinophysis acuminata synthesized a poorly stable, incomplete phycoerythrin composed of chromophorylated β subunits, with impaired performance. We show that, consequently, a continuous supply of new plastids is crucial for growth and effective photoacclimation in this organism. Transcriptome analyses revealed that all examined strains of Dinophysis spp. have acquired the cryptophyte pebA and pebB genes through horizontal gene transfer, suggesting a potential ability to synthesize the phycobilin pigments bound to the cryptophyte phycoerythrin. By emphasizing that a potential long-term acquisition of the cryptophyte plastid relies on establishing genetic independence for essential functions such as light harvesting, this study highlights the intricate molecular challenges inherent in the enslavement of organelles and the processes involved in the diversification of photosynthetic organisms through endosymbiosis.}, }
@article {pmid38936185, year = {2024}, author = {Hu, CJ and Lv, YQ and Xian, WD and Jiao, JY and Lian, ZH and Tan, S and Li, MM and Luo, ZH and Liu, ZT and Lv, AP and Liu, L and Ali, M and Liu, WQ and Li, WJ}, title = {Multi-omics insights into the function and evolution of sodium benzoate biodegradation pathway in Benzoatithermus flavus gen. nov., sp. nov. from hot spring.}, journal = {Journal of hazardous materials}, volume = {476}, number = {}, pages = {135017}, doi = {10.1016/j.jhazmat.2024.135017}, pmid = {38936185}, issn = {1873-3336}, mesh = {*Sodium Benzoate/metabolism ; *Biodegradation, Environmental ; *Hot Springs/microbiology ; *Phylogeny ; Water Pollutants, Chemical/metabolism ; Multiomics ; }, abstract = {Biodegradation stands as an eco-friendly and effective approach for organic contaminant remediation. However, research on microorganisms degrading sodium benzoate contaminants in extreme environments remains limited. In this study, we report to display the isolation of a novel hot spring enriched cultures with sodium benzoate (400 mg/L) as the sole carbon source. The results revealed that the phylum Pseudomonadota was the potential sodium benzoate degrader and a novel genus within the family Geminicoccaceae of this phylum. The isolated strain was named Benzoatithermus flavus SYSU G07066[T] and was isolated from HNT-2 hot spring samples. Genomic analysis revealed that SYSU G07066[T] carried benABC genes and physiological experiments indicated the ability to utilize sodium benzoate as a sole carbon source for growth, which was further confirmed by transcriptomic data with expression of benABC. Phylogenetic analysis suggested that Horizontal Gene Transfer (HGT) plays a significant role in acquiring sodium benzoate degradation capability among prokaryotes, and SYSU G07066[T] might have acquired benABC genes through HGT from the family Acetobacteraceae. The discovery of the first microorganism with sodium benzoate degradation function from a hot spring enhances our understanding of the diverse functions within the family Geminicoccaceae. This study unearths the first novel genus capable of efficiently degrading sodium benzoate and its evolution history at high temperatures, holding promising industrial applications, and provides a new perspective for further exploring the application potential of hot spring "microbial dark matter".}, }
@article {pmid38936038, year = {2024}, author = {Wang, F and Huang, W and Zhang, M and Zhang, Q and Luo, Y and Chen, J and Su, Y and Huang, H and Fang, F and Luo, J}, title = {Disinfectant polyhexamethylene guanidine triggered simultaneous efflux pump antibiotic- and metal-resistance genes propagation during sludge anaerobic digestion.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {357}, number = {}, pages = {124453}, doi = {10.1016/j.envpol.2024.124453}, pmid = {38936038}, issn = {1873-6424}, mesh = {*Sewage/microbiology ; *Disinfectants/toxicity/pharmacology ; *Guanidines/toxicity ; Gene Transfer, Horizontal ; Metals/toxicity ; Anaerobiosis ; Drug Resistance, Microbial/genetics ; Bacteria/genetics/drug effects ; Anti-Bacterial Agents/pharmacology/toxicity ; Waste Disposal, Fluid ; Drug Resistance, Bacterial/genetics ; }, abstract = {The environmental transmission of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) exerted devastating threats to global public health, and their interactions with other emerging contaminants (ECs) have raised increasing concern. This study investigated that the abundances of ARGs and MRGs with the predominant type of efflux pump were simultaneously increased (8.4-59.1%) by disinfectant polyhexamethylene guanidine (PHMG) during waste activated sludge (WAS) anaerobic digestion. The aggregation of the same microorganisms (i.e., Hymenobacter and Comamonas) and different host bacteria (i.e., Azoarcus and Thauera) were occurred upon exposure to PHMG, thereby increasing the co-selection and propagation of MRGs and ARGs by vertical gene transfer. Moreover, PHMG enhanced the process of horizontal gene transfer (HGT), facilitating their co-transmission by the same mobile genetic elements (20.2-223.7%). Additionally, PHMG up-regulated the expression of critical genes (i.e., glnB, trpG and gspM) associated with the HGT of ARGs and MRGs (i.e., two-component regulatory system and quorum sensing) and exocytosis system (i.e., bacterial secretion system). Structural equation model analysis further verified that the key driver for the simultaneous enrichment of ARGs and MRGs under PHMG stress was microbial community structure. The study gives new insights into the aggravated environmental risks and mechanisms of ECs in sludge digestion system, providing guidance for subsequent regulation and control of ECs.}, }
@article {pmid38936019, year = {2024}, author = {Liu, Y and Song, X and Hou, X and Wang, Y and Cao, X}, title = {Effect of Mn-HA on ARGs and MRGs in nitrogen-culturing sludge.}, journal = {Journal of environmental management}, volume = {365}, number = {}, pages = {121615}, doi = {10.1016/j.jenvman.2024.121615}, pmid = {38936019}, issn = {1095-8630}, mesh = {*Sewage/microbiology ; *Nitrogen/metabolism ; *Manganese ; Drug Resistance, Microbial/genetics ; Denitrification ; Bacteria/metabolism/genetics ; Metagenomics ; }, abstract = {The simultaneous escalation in ARGs (antibiotic resistance genes) and MRGs (metal resistance genes) further complicates the intricate network of factors contributing to the proliferation of microbial resistance. Manganese, which has been reported to affect the resistance of bacteria to antibiotics and metals, plays a vital role in microbial nitrogen metabolism. Moreover, nitrifying and denitrifying populations are potential hosts for ARGs. In this study, manganese was introduced in its prevalent organic chelated form in the environment (Manganese humus chelates, Mn-HA) to a N metabolism sludge to explore the effect of manganese on MRGs and ARGs dissemination. Metagenomics results revealed that manganese availability enhances nitrogen metabolism, while a decrease in ARGs was noted which may be attributed to the inhibition of horizontal gene transfer (HGT), reflected in the reduced integrase -encoded gene int. Population analysis revealed that nitrifier and denitrifier genus harbor MRGs and ARGs, indicating that nitrifier and denitrifier are hosts of MRGs and ARGs. This raises the question of whether the prevalence of ARGs is always increased in metal-contained environments.}, }
@article {pmid38935608, year = {2024}, author = {Randriantseheno, LN and Andrianaivoarimanana, V and Pizarro-Cerdá, J and Wagner, DM and Rajerison, M}, title = {Review of genotyping methods for Yersinia pestis in Madagascar.}, journal = {PLoS neglected tropical diseases}, volume = {18}, number = {6}, pages = {e0012252}, pmid = {38935608}, issn = {1935-2735}, mesh = {*Yersinia pestis/genetics/classification/isolation &amp; purification ; Madagascar/epidemiology ; *Plague/microbiology/epidemiology ; Humans ; Animals ; Genotype ; Genotyping Techniques/methods ; }, abstract = {BACKGROUND: Plague, a zoonotic disease caused by Yersinia pestis, was responsible for 3 historical human pandemics that killed millions of people. It remains endemic in rodent populations in Africa, Asia, North America, and South America but human plague is rare in most of these locations. However, human plague is still highly prevalent in Madagascar, which typically records a significant part of all annual global cases. This has afforded an opportunity to study contemporary human plague in detail using various typing methods for Y. pestis.<br><br>AIM: This review aims to summarize the methods that have been used to type Y. pestis in Madagascar along with the major discoveries that have been made using these approaches.<br><br>METHODS: Pubmed and Google Scholar were used to search for the keywords: "typing Yersinia pestis Madagascar," "evolution Yersinia pestis Madagascar," and "diversity Yersinia pestis Madagascar." Eleven publications were relevant to our topic and further information was retrieved from references cited in those publications.<br><br>RESULTS: The history of Y. pestis typing in Madagascar can be divided in 2 periods: the pre-genomics and genomics eras. During the pre-genomics era, ribotyping, direct observation of plasmid content and plasmid restriction fragment length polymorphisms (RFLP) were employed but only revealed a limited amount of diversity among Malagasy Y. pestis strains. Extensive diversity only started to be revealed in the genomics era with the use of clustered regularly interspaced palindromic repeats (CRISPR), multiple-locus variable number tandem repeats (VNTR) analysis (MLVA), and single-nucleotide polymorphisms (SNPs) discovered from whole genome sequences. These higher-resolution genotyping methods have made it possible to highlight the distribution and persistence of genotypes in the different plague foci of Madagascar (Mahajanga and the Central and Northern Highlands) by genotyping strains from the same locations across years, to detect transfers between foci, to date the emergence of genotypes, and even to document the transmission of antimicrobial resistant (AMR) strains during a pneumonic plague outbreak. Despite these discoveries, there still remain topics that deserve to be explored, such as the contribution of horizontal gene transfer to the evolution of Malagasy Y. pestis strains and the evolutionary history of Y. pestis in Madagascar.<br><br>CONCLUSIONS: Genotyping of Y. pestis has yielded important insights on plague in Madagascar, particularly since the advent of whole-genome sequencing (WGS). These include a better understanding of plague persistence in the environment, antimicrobial AMR and multi-drug resistance in Y. pestis, and the person-to-person spread of pneumonic plague. Considering that human plague is still a significant public health threat in Madagascar, these insights can be useful for controlling and preventing human plague in Madagascar and elsewhere, and also are relevant for understanding the historical pandemics and the possible use of Y. pestis as a biological weapon.}, }
@article {pmid38935220, year = {2024}, author = {Parra, B and Lutz, VT and Brøndsted, L and Carmona, JL and Palomo, A and Nesme, J and Van Hung Le, V and Smets, BF and Dechesne, A}, title = {Characterization and Abundance of Plasmid-Dependent Alphatectivirus Bacteriophages.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {85}, pmid = {38935220}, issn = {1432-184X}, support = {101026675//European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant/ ; 002200000279//VRID Postdoctorado from Vicerrector&#xed;a de Investigaci&#xf3;n y Desarrollo, Universidad de Concepci&#xf3;n/ ; P-PhanFARE (23046)//Villum Fonden/ ; }, mesh = {*Plasmids/genetics ; *Wastewater/virology/microbiology ; *Bacteriophages/genetics/isolation &amp; purification/physiology/classification ; Genome, Viral ; Escherichia coli/virology/genetics ; Host Specificity ; Pseudomonas putida/virology/genetics ; Salmonella enterica/virology/genetics ; Phylogeny ; }, abstract = {Antimicrobial resistance (AMR) is a major public health threat, exacerbated by the ability of bacteria to rapidly disseminate antimicrobial resistance genes (ARG). Since conjugative plasmids of the incompatibility group P (IncP) are ubiquitous mobile genetic elements that often carry ARG and are broad-host-range, they are important targets to prevent the dissemination of AMR. Plasmid-dependent phages infect plasmid-carrying bacteria by recognizing components of the conjugative secretion system as receptors. We sought to isolate plasmid-dependent phages from wastewater using an avirulent strain of Salmonella enterica carrying the conjugative IncP plasmid pKJK5. Irrespective of the site, we only obtained bacteriophages belonging to the genus Alphatectivirus. Eleven isolates were sequenced, their genomes analyzed, and their host range established using S. enterica, Escherichia coli, and Pseudomonas putida carrying diverse conjugative plasmids. We confirmed that Alphatectivirus are abundant in domestic and hospital wastewater using culture-dependent and culture-independent approaches. However, these results are not consistent with their low or undetectable occurrence in metagenomes. Therefore, overall, our results emphasize the importance of performing phage isolation to uncover diversity, especially considering the potential of plasmid-dependent phages to reduce the spread of ARG carried by conjugative plasmids, and to help combat the AMR crisis.}, }
@article {pmid38934605, year = {2024}, author = {Burcham, ZM}, title = {Comparative genomic analysis of an emerging Pseudomonadaceae member, Thiopseudomonas alkaliphila.}, journal = {Microbiology spectrum}, volume = {12}, number = {8}, pages = {e0415723}, pmid = {38934605}, issn = {2165-0497}, support = {//University of Tennessee, Knoxville (UT)/ ; }, mesh = {*Genome, Bacterial/genetics ; *Genomics ; *Phylogeny ; Humans ; Animals ; Gene Transfer, Horizontal ; Prophages/genetics ; }, abstract = {Thiopseudomonas alkaliphila, an organism recently classified within the Pseudomonadaceae family, has been detected in diverse sources such as human tissues, animal guts, industrial fermenters, and decomposition environments, suggesting a diverse ecological role. However, a large knowledge gap exists in how T. alkaliphila functions. In this comparative genomic analysis, adaptations indicative of habitat specificity among strains and genomic similarity to known opportunistic pathogens are revealed. Genomic investigation reveals a core metabolic utilization of multiple oxidative and non-oxidative catabolic pathways, suggesting adaptability to varied environments and carbon sources. The genomic repertoire of T. alkaliphila includes secondary metabolites, such as antimicrobials and siderophores, indicative of its involvement in microbial competition and resource acquisition. Additionally, the presence of transposases, prophages, plasmids, and Clustered Regularly Interspaced Short Palindromic Repeats-Cas systems in T. alkaliphila genomes suggests mechanisms for horizontal gene transfer and defense against viral predation. This comprehensive genomic analysis expands our understanding on the ecological functions, community interactions, and potential virulence of T. alkaliphila, while emphasizing its adaptability and diverse capabilities across environmental and host-associated ecosystems.IMPORTANCEAs the microbial world continues to be explored, new organisms will emerge with beneficial and/or pathogenetic impact. Thiopseudomonas alkaliphila is a species originally isolated from clinical human tissue and fluid samples but has not been attributed to disease. Since its classification, T. alkaliphila has been found in animal guts, animal waste, decomposing remains, and biogas fermentation reactors. This is the first study to provide an in-depth view of the metabolic potential of publicly available genomes belonging to this species through a comparative genomics and draft pangenome calculation approach. It was found that T. alkaliphila is metabolically versatile and likely adapts to diverse energy sources and environments, which may make it useful for bioremediation and in industrial settings. A range of virulence factors and antibiotic resistances were also detected, suggesting T. alkaliphila may operate as an undescribed opportunistic pathogen.}, }
@article {pmid38930473, year = {2024}, author = {Otero-Olarra, JE and Díaz-Cárdenas, G and Aguilera-Arreola, MG and Curiel-Quesada, E and Pérez-Valdespino, A}, title = {Aeromonas trota Is Highly Refractory to Acquire Exogenous Genetic Material.}, journal = {Microorganisms}, volume = {12}, number = {6}, pages = {}, pmid = {38930473}, issn = {2076-2607}, abstract = {Aeromonas trota is sensitive to most antibiotics and the sole species of this genus susceptible to ampicillin. This susceptibility profile could be related to its inability to acquire exogenous DNA. In this study, A. trota isolates were analyzed to establish their capacity to incorporate foreign DNA. Fourteen strains were identified as A. trota by multilocus phylogenetic analysis (MLPA). Minimal inhibitory concentrations of antibiotics (MIC) were assessed, confirming the susceptibility to most antibiotics tested. To explore their capacity to be transformed, A. trota strains were used as recipients in different horizontal transfer assays. Results showed that around fifty percent of A. trota strains were able to incorporate pBAMD1-2 and pBBR1MCS-3 plasmids after conjugal transfer. In all instances, conjugation frequencies were very low. Interestingly, several isoforms of plasmid pBBR1MCS-3 were observed in transconjugants. Strains could not receive pAr-32, a native plasmid from A. salmonicida. A. trota strains were unable to receive DNA by means of electroporation, natural transformation or vesiduction. These results confirm that A. trota species are extremely refractory to horizontal gene transfer, which could be associated to plasmid instability resulting from oligomerization or to the presence of defense systems against exogenous genetic material in their genomes. To explain the poor results of horizontal gene transfer (HGT), selected genomes were sequenced and analyzed, revealing the presence of defense systems, which could prevent the stable incorporation of exogenous DNA in A. trota.}, }
@article {pmid38927231, year = {2024}, author = {Amábile-Cuevas, CF and Lund-Zaina, S}, title = {Non-Canonical Aspects of Antibiotics and Antibiotic Resistance.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {6}, pages = {}, pmid = {38927231}, issn = {2079-6382}, abstract = {The understanding of antibiotic resistance, one of the major health threats of our time, is mostly based on dated and incomplete notions, especially in clinical contexts. The "canonical" mechanisms of action and pharmacodynamics of antibiotics, as well as the methods used to assess their activity upon bacteria, have not changed in decades; the same applies to the definition, acquisition, selective pressures, and drivers of resistance. As a consequence, the strategies to improve antibiotic usage and overcome resistance have ultimately failed. This review gathers most of the "non-canonical" notions on antibiotics and resistance: from the alternative mechanisms of action of antibiotics and the limitations of susceptibility testing to the wide variety of selective pressures, lateral gene transfer mechanisms, ubiquity, and societal factors maintaining resistance. Only by having a "big picture" view of the problem can adequate strategies to harness resistance be devised. These strategies must be global, addressing the many aspects that drive the increasing prevalence of resistant bacteria aside from the clinical use of antibiotics.}, }
@article {pmid38927226, year = {2024}, author = {Gestels, Z and Abdellati, S and Kenyon, C and Manoharan-Basil, SS}, title = {Ciprofloxacin Concentrations 100-Fold Lower than the MIC Can Select for Ciprofloxacin Resistance in Neisseria subflava: An In Vitro Study.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {6}, pages = {}, pmid = {38927226}, issn = {2079-6382}, support = {Unknown//PRESTIP/ ; }, abstract = {Neisseria gonorrhoeae can acquire antimicrobial resistance (AMR) through horizontal gene transfer (HGT) from other Neisseria spp. such as commensals like Neisseria subflava. Low doses of antimicrobials in food could select for AMR in N. subflava, which could then be transferred to N. gonorrhoeae. In this study, we aimed to determine the lowest concentration of ciprofloxacin that can induce ciprofloxacin resistance (minimum selection concentration-MSC) in a N. subflava isolate (ID-Co000790/2, a clinical isolate collected from a previous community study conducted at ITM). In this study, Neisseria subflava was serially passaged on gonococcal (GC) medium agar plates containing ciprofloxacin concentrations ranging from 1:100 to 1:10,000 below its ciprofloxacin MIC (0.006 µg/mL) for 6 days. After 6 days of serial passaging at ciprofloxacin concentrations of 1/100th of the MIC, 24 colonies emerged on the plate containing 0.06 µg/mL ciprofloxacin, which corresponds to the EUCAST breakpoint for N. gonorrhoeae. Their ciprofloxacin MICs were between 0.19 to 0.25 µg/mL, and whole genome sequencing revealed a missense mutation T91I in the gyrA gene, which has previously been found to cause reduced susceptibility to fluoroquinolones. The N. subflava MSCde novo was determined to be 0.06 ng/mL (0.00006 µg/mL), which is 100×-fold lower than the ciprofloxacin MIC. The implications of this finding are that the low concentrations of fluoroquinolones found in certain environmental samples, such as soil, river water, and even the food we eat, may be able to select for ciprofloxacin resistance in N. subflava.}, }
@article {pmid38927197, year = {2024}, author = {Yaikhan, T and Suwannasin, S and Singkhamanan, K and Chusri, S and Pomwised, R and Wonglapsuwan, M and Surachat, K}, title = {Genomic Characterization of Multidrug-Resistant Enterobacteriaceae Clinical Isolates from Southern Thailand Hospitals: Unraveling Antimicrobial Resistance and Virulence Mechanisms.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {6}, pages = {}, pmid = {38927197}, issn = {2079-6382}, support = {B13F670075//the NSRF via the Program Management Unit for Human Resources &amp; Institutional Development, Research Innovation/ ; //the Postdoctoral Fellowship from Prince of Songkla University/ ; B13F660074//the NSRF via the Program Management Unit for Human Resources &amp; Institutional Development, Research and Innovation/ ; }, abstract = {The emergence and spread of antimicrobial resistance (AMR) among Enterobacteriaceae pose significant threats to global public health. In this study, we conducted a short-term surveillance effort in Southern Thailand hospitals to characterize the genomic diversity, AMR profiles, and virulence factors of Enterobacteriaceae strains. We identified 241 carbapenem-resistant Enterobacteriaceae, of which 12 were selected for whole-genome sequencing (WGS) and genome analysis. The strains included Proteus mirabilis, Serratia nevei, Klebsiella variicola, Klebsiella aerogenes, Klebsiella indica, Klebsiella grimontii, Phytobacter ursingii, Phytobacter palmae, Kosakonia spp., and Citrobacter freundii. The strains exhibited high levels of multidrug resistance, including resistance to carbapenem antibiotics. Whole-genome sequencing revealed a diverse array of antimicrobial resistance genes (ARGs), with strains carrying genes for ß-lactamase, efflux pumps, and resistance to other antibiotic classes. Additionally, stress response, metal tolerance, and virulence-associated genes were identified, highlighting the adaptability and pathogenic potential of these strains. A plasmid analysis identified several plasmid replicons, including IncA/C2, IncFIB(K), and Col440I, as well as several plasmids identical to those found globally, indicating the potential for the horizontal gene transfer of ARGs. Importantly, this study also identified a novel species of Kosakonia spp. PSU27, adding to the understanding of the genetic diversity and resistance mechanisms of Enterobacteriaceae in Southern Thailand. The results reported in this study highlight the critical importance of implementing effective antimicrobial management programs and developing innovative treatment approaches to urgently tackle AMR.}, }
@article {pmid38927185, year = {2024}, author = {Peng, J and Feng, J and Ji, H and Kong, X and Hong, J and Zhu, L and Qian, H}, title = {Emergence of Rarely Reported Extensively Drug-Resistant Salmonella Enterica Serovar Paratyphi B among Patients in East China.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {6}, pages = {}, pmid = {38927185}, issn = {2079-6382}, support = {National Major S&amp;T Projects(2018ZX10714-002)//Ministry of Science and Technology of the People's Republic of China/ ; Ym2023040//Jiangsu Preventive Medicine Association/ ; }, abstract = {BACKGROUND: In recent years, global concern over increasing multidrug resistance (MDR) among various Salmonella serotypes has grown significantly. However, reports on MDR Salmonella Paratyphi B remain scarce, let alone the extensively drug-resistant (XDR) strains.<br><br>METHODS: In this retrospective study, we investigated the isolates of Salmonella Paratyphi B in Jiangsu Province over the past decade and carried out antimicrobial susceptibility tests, then the strains were sequenced and bioinformatics analyses were performed.<br><br>RESULTS: 27 Salmonella Paratyphi B strains were identified, of which the predominant STs were ST42 (11), ST86 (10), and ST2814 (5). Among these strains, we uncovered four concerning XDR Salmonella Paratyphi B ST2814 strains (4/5) which were previously unreported. These alarmingly resistant isolates showed resistance to all three major antibiotic classes for Salmonella treatment and even the last resort treatment tigecycline. Bioinformatics analysis revealed high similarity between the plasmids harbored by these XDR strains and diverse Salmonella serotypes and Escherichia coli from China and neighboring regions. Notably, these four plasmids carried the ramAp gene responsible for multiple antibiotic resistance by regulating the AcrAB-TolC pump, predominantly originating from China. Additionally, a distinct MDR ST42(1/11) strain with an ICE on chromosome was also identified. Furthermore, phylogenetic analysis of global ST42/ST2814 isolates highlighted the regional specificity of these strains, with Jiangsu isolates clustering together with domestic isolates and XDR ST2814 forming a distinct branch, suggesting adaptation to local antibiotic pressures.<br><br>CONCLUSIONS: This research underscores the pressing need for closely monitoring the MDR/XDR Salmonella Paratyphi B, particularly the emerging ST2814 strains in Jiangsu Province, to effectively curb its spread and protect public health. Moreover, surveillance should be strengthened across different ecological niches and genera to track resistance genes and horizontal gene transfer elements under the concept of "ONE HEALTH".}, }
@article {pmid38926391, year = {2024}, author = {Brown, CL and Maile-Moskowitz, A and Lopatkin, AJ and Xia, K and Logan, LK and Davis, BC and Zhang, L and Vikesland, PJ and Pruden, A}, title = {Selection and horizontal gene transfer underlie microdiversity-level heterogeneity in resistance gene fate during wastewater treatment.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {5412}, pmid = {38926391}, issn = {2041-1723}, support = {1545756//National Science Foundation (NSF)/ ; 2004751//National Science Foundation (NSF)/ ; 2125798//National Science Foundation (NSF)/ ; 4813//Water Research Foundation (WRF)/ ; }, mesh = {*Gene Transfer, Horizontal ; *Sewage/microbiology ; *Wastewater/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/classification/metabolism ; Water Purification/methods ; Metagenomics/methods ; Drug Resistance, Microbial/genetics ; Waste Disposal, Fluid/methods ; Drug Resistance, Bacterial/genetics ; Selection, Genetic ; }, abstract = {Activated sludge is the centerpiece of biological wastewater treatment, as it facilitates removal of sewage-associated pollutants, fecal bacteria, and pathogens from wastewater through semi-controlled microbial ecology. It has been hypothesized that horizontal gene transfer facilitates the spread of antibiotic resistance genes within the wastewater treatment plant, in part because of the presence of residual antibiotics in sewage. However, there has been surprisingly little evidence to suggest that sewage-associated antibiotics select for resistance at wastewater treatment plants via horizontal gene transfer or otherwise. We addressed the role of sewage-associated antibiotics in promoting antibiotic resistance using lab-scale sequencing batch reactors fed field-collected wastewater, metagenomic sequencing, and our recently developed bioinformatic tool Kairos. Here, we found confirmatory evidence that fluctuating levels of antibiotics in sewage are associated with horizontal gene transfer of antibiotic resistance genes, microbial ecology, and microdiversity-level differences in resistance gene fate in activated sludge.}, }
@article {pmid38922012, year = {2024}, author = {Kerek, &#xc1; and Németh, V and Szabó, &#xc1; and Papp, M and Bányai, K and Kardos, G and Kaszab, E and Bali, K and Nagy, Z and Süth, M and Jerzsele, &#xc1;}, title = {Monitoring Changes in the Antimicrobial-Resistance Gene Set (ARG) of Raw Milk and Dairy Products in a Cattle Farm, from Production to Consumption.}, journal = {Veterinary sciences}, volume = {11}, number = {6}, pages = {}, pmid = {38922012}, issn = {2306-7381}, support = {RRF-2.3.1-21-2022-00001//National Recovery Fund/ ; }, abstract = {Raw milk and dairy products can serve as potential vectors for transmissible bacterial, viral and protozoal diseases, alongside harboring antimicrobial-resistance genes. This study monitors the changes in the antimicrobial-resistance gene pool in raw milk and cheese, from farm to consumer, utilizing next-generation sequencing. Five parallel sampling runs were conducted to assess the resistance gene pool, as well as phage or plasmid carriage and potential mobility. In terms of taxonomic composition, in raw milk the Firmicutes phylum made up 41%, while the Proteobacteria phylum accounted for 58%. In fresh cheese, this ratio shifted to 93% Firmicutes and 7% Proteobacteria. In matured cheese, the composition was 79% Firmicutes and 21% Proteobacteria. In total, 112 antimicrobial-resistance genes were identified. While a notable reduction in the resistance gene pool was observed in the freshly made raw cheese compared to the raw milk samples, a significant growth in the resistance gene pool occurred after one month of maturation, surpassing the initial gene frequency. Notably, the presence of extended-spectrum beta-lactamase (ESBL) genes, such as OXA-662 (100% coverage, 99.3% identity) and OXA-309 (97.1% coverage, 96.2% identity), raised concerns; these genes have a major public health relevance. In total, nineteen such genes belonging to nine gene families (ACT, CMY, EC, ORN, OXA, OXY, PLA, RAHN, TER) have been identified. The largest number of resistance genes were identified against fluoroquinolone drugs, which determined efflux pumps predominantly. Our findings underscore the importance of monitoring gene pool variations throughout the product pathway and the potential for horizontal gene transfer in raw products. We advocate the adoption of a new approach to food safety investigations, incorporating next-generation sequencing techniques.}, }
@article {pmid38920383, year = {2024}, author = {Rakibova, Y and Dunham, DT and Seed, KD and Freddolino, L}, title = {Nucleoid-associated proteins shape the global protein occupancy and transcriptional landscape of a clinical isolate of Vibrio cholerae.}, journal = {mSphere}, volume = {9}, number = {7}, pages = {e0001124}, pmid = {38920383}, issn = {2379-5042}, support = {2018257700//National Science Foundation (NSF)/ ; R01AI127652//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01 AI127652/AI/NIAID NIH HHS/United States ; AI134678//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R35 GM128637/GM/NIGMS NIH HHS/United States ; R01 AI134678/AI/NIAID NIH HHS/United States ; }, mesh = {*Bacterial Proteins/genetics/metabolism ; *Vibrio cholerae/genetics/pathogenicity/metabolism ; *Gene Expression Regulation, Bacterial ; *Cholera/microbiology ; DNA-Binding Proteins/genetics/metabolism ; Humans ; Transcription, Genetic ; Virulence ; Virulence Factors/genetics ; Gene Transfer, Horizontal ; }, abstract = {UNLABELLED: Vibrio cholerae, the causative agent of the diarrheal disease cholera, poses an ongoing health threat due to its wide repertoire of horizontally acquired elements (HAEs) and virulence factors. New clinical isolates of the bacterium with improved fitness abilities, often associated with HAEs, frequently emerge. The appropriate control and expression of such genetic elements is critical for the bacteria to thrive in the different environmental niches they occupy. H-NS, the histone-like nucleoid structuring protein, is the best-studied xenogeneic silencer of HAEs in gamma-proteobacteria. Although H-NS and other highly abundant nucleoid-associated proteins (NAPs) have been shown to play important roles in regulating HAEs and virulence in model bacteria, we still lack a comprehensive understanding of how different NAPs modulate transcription in V. cholerae. By obtaining genome-wide measurements of protein occupancy and active transcription in a clinical isolate of V. cholerae, harboring recently discovered HAEs encoding for phage defense systems, we show that a lack of H-NS causes a robust increase in the expression of genes found in many HAEs. We further found that TsrA, a protein with partial homology to H-NS, regulates virulence genes primarily through modulation of H-NS activity. We also identified few sites that are affected by TsrA independently of H-NS, suggesting TsrA may act with diverse regulatory mechanisms. Our results demonstrate how the combinatorial activity of NAPs is employed by a clinical isolate of an important pathogen to regulate recently discovered HAEs.<br><br>IMPORTANCE: New strains of the bacterial pathogen Vibrio cholerae, bearing novel horizontally acquired elements (HAEs), frequently emerge. HAEs provide beneficial traits to the bacterium, such as antibiotic resistance and defense against invading bacteriophages. Xenogeneic silencers are proteins that help bacteria harness new HAEs and silence those HAEs until they are needed. H-NS is the best-studied xenogeneic silencer; it is one of the nucleoid-associated proteins (NAPs) in gamma-proteobacteria and is responsible for the proper regulation of HAEs within the bacterial transcriptional network. We studied the effects of H-NS and other NAPs on the HAEs of a clinical isolate of V. cholerae. Importantly, we found that H-NS partners with a small and poorly characterized protein, TsrA, to help domesticate new HAEs involved in bacterial survival and in causing disease. A proper understanding of the regulatory state in emerging isolates of V. cholerae will provide improved therapies against new isolates of the pathogen.}, }
@article {pmid38918632, year = {2024}, author = {Mei, Z and Wang, F and Bhosle, A and Dong, D and Mehta, R and Ghazi, A and Zhang, Y and Liu, Y and Rinott, E and Ma, S and Rimm, EB and Daviglus, M and Willett, WC and Knight, R and Hu, FB and Qi, Q and Chan, AT and Burk, RD and Stampfer, MJ and Shai, I and Kaplan, RC and Huttenhower, C and Wang, DD}, title = {Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes.}, journal = {Nature medicine}, volume = {30}, number = {8}, pages = {2265-2276}, pmid = {38918632}, issn = {1546-170X}, support = {K99 DK119412/DK/NIDDK NIH HHS/United States ; R01NR01999//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01 MD011389/MD/NIMHD NIH HHS/United States ; U01 CA152904/CA/NCI NIH HHS/United States ; N01HC65235/HL/NHLBI NIH HHS/United States ; R01AG077489//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; N01HC65234/HL/NHLBI NIH HHS/United States ; R01 NR019992/NR/NINR NIH HHS/United States ; P30 DK046200/DK/NIDDK NIH HHS/United States ; N01HC65237/HL/NHLBI NIH HHS/United States ; R01 AG077489/AG/NIA NIH HHS/United States ; RF1 AG083764/AG/NIA NIH HHS/United States ; R01 HL035464/HL/NHLBI NIH HHS/United States ; P30DK046200//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R00DK119412//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R24 DK110499/DK/NIDDK NIH HHS/United States ; R00 DK119412/DK/NIDDK NIH HHS/United States ; R24DK110499//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; R01 CA202704/CA/NCI NIH HHS/United States ; P01 CA055075/CA/NCI NIH HHS/United States ; 209933838//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 897161//American Heart Association (American Heart Association, Inc.)/ ; U01 CA176726/CA/NCI NIH HHS/United States ; U01 CA167552/CA/NCI NIH HHS/United States ; N01HC65236/HL/NHLBI NIH HHS/United States ; P30 DK111022/DK/NIDDK NIH HHS/United States ; N01HC65233/HL/NHLBI NIH HHS/United States ; R35 CA253185/CA/NCI NIH HHS/United States ; R01 HL060712/HL/NHLBI NIH HHS/United States ; }, mesh = {*Diabetes Mellitus, Type 2/microbiology/genetics ; Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenome/genetics ; *Phylogeny ; Cohort Studies ; Male ; Middle Aged ; Female ; China/epidemiology ; Dysbiosis/microbiology ; United States/epidemiology ; Israel/epidemiology ; Europe/epidemiology ; }, abstract = {The association of gut microbial features with type 2 diabetes (T2D) has been inconsistent due in part to the complexity of this disease and variation in study design. Even in cases in which individual microbial species have been associated with T2D, mechanisms have been unable to be attributed to these associations based on specific microbial strains. We conducted a comprehensive study of the T2D microbiome, analyzing 8,117 shotgun metagenomes from 10 cohorts of individuals with T2D, prediabetes, and normoglycemic status in the United States, Europe, Israel and China. Dysbiosis in 19 phylogenetically diverse species was associated with T2D (false discovery rate < 0.10), for example, enriched Clostridium bolteae and depleted Butyrivibrio crossotus. These microorganisms also contributed to community-level functional changes potentially underlying T2D pathogenesis, for example, perturbations in glucose metabolism. Our study identifies within-species phylogenetic diversity for strains of 27 species that explain inter-individual differences in T2D risk, such as Eubacterium rectale. In some cases, these were explained by strain-specific gene carriage, including loci involved in various mechanisms of horizontal gene transfer and novel biological processes underlying metabolic risk, for example, quorum sensing. In summary, our study provides robust cross-cohort microbial signatures in a strain-resolved manner and offers new mechanistic insights into T2D.}, }
@article {pmid38918467, year = {2024}, author = {Grodner, B and Shi, H and Farchione, O and Vill, AC and Ntekas, I and Diebold, PJ and Wu, DT and Chen, CY and Kim, DM and Zipfel, WR and Brito, IL and De Vlaminck, I}, title = {Spatial mapping of mobile genetic elements and their bacterial hosts in complex microbiomes.}, journal = {Nature microbiology}, volume = {9}, number = {9}, pages = {2262-2277}, pmid = {38918467}, issn = {2058-5276}, support = {DP2 AI138242/AI/NIAID NIH HHS/United States ; 1DP2AI138242//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R33 CA235302/CA/NCI NIH HHS/United States ; S10 OD018516/OD/NIH HHS/United States ; 1R33CA235302//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; S10OD018516//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; }, mesh = {*Biofilms/growth &amp; development ; *Microbiota/genetics ; *In Situ Hybridization, Fluorescence/methods ; *Bacteriophages/genetics ; *Bacteria/genetics/virology/classification ; *Interspersed Repetitive Sequences/genetics ; Humans ; *Plasmids/genetics ; *Prophages/genetics ; *Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; Mouth/microbiology ; }, abstract = {The exchange of mobile genetic elements (MGEs) facilitates the spread of functional traits including antimicrobial resistance within bacterial communities. Tools to spatially map MGEs and identify their bacterial hosts in complex microbial communities are currently lacking, limiting our understanding of this process. Here we combined single-molecule DNA fluorescence in situ hybridization (FISH) with multiplexed ribosomal RNA-FISH to enable simultaneous visualization of both MGEs and bacterial taxa. We spatially mapped bacteriophage and antimicrobial resistance (AMR) plasmids and identified their host taxa in human oral biofilms. This revealed distinct clusters of AMR plasmids and prophage, coinciding with densely packed regions of host bacteria. Our data suggest spatial heterogeneity in bacterial taxa results in heterogeneous MGE distribution within the community, with MGE clusters resulting from horizontal gene transfer hotspots or expansion of MGE-carrying strains. Our approach can help advance the study of AMR and phage ecology in biofilms.}, }
@article {pmid38917629, year = {2024}, author = {Liu, F and Shen, Y and Hou, Y and Wu, J and Ting, Y and Nie, C and Tong, M}, title = {Elimination of representative antibiotic-resistant bacteria, antibiotic resistance genes and ciprofloxacin from water via photoactivation of periodate using FeS2.}, journal = {Journal of hazardous materials}, volume = {476}, number = {}, pages = {134982}, doi = {10.1016/j.jhazmat.2024.134982}, pmid = {38917629}, issn = {1873-3336}, mesh = {*Ciprofloxacin/pharmacology ; *Anti-Bacterial Agents/pharmacology/chemistry ; *Ferrous Compounds/chemistry/pharmacology ; *Drug Resistance, Bacterial/genetics ; Sunlight ; Disinfection/methods ; Water Purification/methods ; Escherichia coli/drug effects/genetics ; Water Pollutants, Chemical ; Water Microbiology ; Bacteria/drug effects/genetics/metabolism/radiation effects ; Gene Transfer, Horizontal ; }, abstract = {The propagation of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) induced by the release of antibiotics poses great threats to ecological safety and human health. In this study, periodate (PI)/FeS2/simulated sunlight (SSL) system was employed to remove representative ARB, ARGs and antibiotics in water. 1 × 10[7] CFU mL[-1] of gentamycin-resistant Escherichia coli was effectively disinfected below limit of detection in PI/FeS2/SSL system under different water matrix and in real water samples. Sulfadiazine-resistant Pseudomonas and Gram-positive Bacillus subtilis could also be efficiently sterilized. Theoretical calculation showed that (110) facet was the most reactive facet on FeS2 to activate PI for the generation of reactive species (·OH, ·O2[-], h[+] and Fe(IV)=O) to damage cell membrane and intracellular enzyme defense system. Both intracellular and extracellular ARGs could be degraded and the expression levels of multidrug resistance-related genes were downregulated during the disinfection process. Thus, horizontal gene transfer (HGT) of ARB was inhibited. Moreover, PI/FeS2/SSL system could disinfect ARB in a continuous flow reactor and in an enlarged reactor under natural sunlight irradiation. PI/FeS2/SSL system could also effectively degrade the HGT-promoting antibiotic (ciprofloxacin) via hydroxylation and ring cleavage process. Overall, PI/FeS2/SSL exhibited great promise for the elimination of antibiotic resistance from water.}, }
@article {pmid38915079, year = {2024}, author = {Wu, CS and Wang, RJ and Chaw, SM}, title = {Integration of large and diverse angiosperm DNA fragments into Asian Gnetum mitogenomes.}, journal = {BMC biology}, volume = {22}, number = {1}, pages = {140}, pmid = {38915079}, issn = {1741-7007}, support = {No. 2022B1111040003//Guangdong Provincial Key R&amp;D Programme/ ; }, mesh = {*Phylogeny ; *Gene Transfer, Horizontal ; *Genome, Mitochondrial ; *Gnetum/genetics ; DNA, Plant/genetics ; Evolution, Molecular ; Magnoliopsida/genetics ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT) events have rarely been reported in gymnosperms. Gnetum is a gymnosperm genus comprising 25‒35 species sympatric with angiosperms in West African, South American, and Southeast Asian rainforests. Only a single acquisition of an angiosperm mitochondrial intron has been documented to date in Asian Gnetum mitogenomes. We wanted to develop a more comprehensive understanding of frequency and fragment length distribution of such events as well as their evolutionary history in this genus.<br><br>RESULTS: We sequenced and assembled mitogenomes from five Asian Gnetum species. These genomes vary remarkably in size and foreign DNA content. We identified 15 mitochondrion-derived and five plastid-derived (MTPT) foreign genes. Our phylogenetic analyses strongly indicate that these foreign genes were transferred from diverse eudicots-mostly from the Rubiaceae genus Coptosapelta and ten genera of Malpighiales. This indicates that Asian Gnetum has experienced multiple independent HGT events. Patterns of sequence evolution strongly suggest DNA-mediated transfer between mitochondria as the primary mechanism giving rise to these HGT events. Most Asian Gnetum species are lianas and often entwined with sympatric angiosperms. We therefore propose that close apposition of Gnetum and angiosperm stems presents opportunities for interspecific cell-to-cell contact through friction and wounding, leading to HGT.<br><br>CONCLUSIONS: Our study reveals that multiple HGT events have resulted in massive amounts of angiosperm mitochondrial DNA integrated into Asian Gnetum mitogenomes. Gnetum and its neighboring angiosperms are often entwined with each other, possibly accounting for frequent HGT between these two phylogenetically remote lineages.}, }
@article {pmid38914331, year = {2024}, author = {Haffiez, N and Kalantar, E and Zakaria, BS and Azizi, SMM and Farner, JM and Dhar, BR}, title = {Impact of aging of primary and secondary polystyrene nanoplastics on the transmission of antibiotic resistance genes in anaerobic digestion.}, journal = {The Science of the total environment}, volume = {947}, number = {}, pages = {174213}, doi = {10.1016/j.scitotenv.2024.174213}, pmid = {38914331}, issn = {1879-1026}, mesh = {Anaerobiosis ; *Polystyrenes ; *Sewage/microbiology ; *Drug Resistance, Microbial/genetics ; Microplastics/toxicity ; Waste Disposal, Fluid/methods ; Water Pollutants, Chemical/analysis/toxicity ; Bioreactors/microbiology ; }, abstract = {Sewage sludge is a significant reservoir of nano/microplastics (NPs/MPs) and antibiotic resistance genes (ARGs). Research has revealed that NPs/MPs may exert an inhibitory effect on anaerobic digestion (AD) of sludge. Moreover, NPs/MPs can influence microbial community diversity and composition, potentially increasing ARGs dissemination. The morphological changes to NPs/MPs surface due to aging contribute to modifying hydrophobic properties. To date, there is limited comprehension regarding how various surface properties of NPs influence ARGs dissemination during AD. This study investigated the impact of primary aged/non-aged and secondary aged/non-aged polystyrene nanoplastics (PSNPs) on ARGs and mobile genetic elements (MGEs) propagation during AD. The findings indicated that the UV-aging process resulted in surface oxidation and distinct morphological characteristics in both primary and secondary PSNPs, while the surface oxidation effect was more pronounced in the secondary aged PSNPs. High concentrations (150 μg/L) of primary and secondary PSNPs inhibited methane production, with secondary PSNPs causing greater inhibition by 16 to 20 % compared to control. In contrast, low concentration (25 μg/L) had negligible or slightly positive effects on methane production. PSNPs at 150 μg/L reduced total VFA concentration, indicating an inhibitory effect on the fermentation step in the AD process. Primary and secondary PSNPs exhibited changes in EPS characteristics. ARGs abundance was enriched in reactors amended with PSNPs, with the highest abundance of 8.54 × 10[5] copies/g sludge observed in the secondary aged PSNPs (150 μg/L) reactor. Reactors exposed to aged PSNPs exhibited a relatively higher abundance of ARGs compared to reactors exposed to non-aged PSNPs. Exposure to PSNPs increased the microbial community diversity within the digesters and triggered the enrichment of Comamonadaceae and Syntrophaceae, belonging to Proteobacteria phylum. On the other hand, archaeal communities tended to shift towards hydrogenotrophic methanogens in PSNPs reactors. The correlation analysis showed that Comamonadaceae were positively correlated with the majority of ARGs and intl1. A positive correlation was observed between MGEs and most ARGs, suggesting that the increased proliferation of ARGs under PSNPs exposure may be linked to the abundance of MGEs, which in turn promotes the growth of hosts carrying ARGs. These findings suggest that aged and non-aged NPs could substantially impact the spread of ARGs and MGEs, which also led to notable alterations in the composition of the microbial community. Overall, this study provides valuable insights into the multifaceted impacts of PSNPs with various characteristics on AD processes, microbial communities, and ARGs proliferation, highlighting the urgent need for comprehensive assessments of NPs pollutants in the environment.}, }
@article {pmid38913753, year = {2024}, author = {Maier, JL and Gin, C and Callahan, B and Sheriff, EK and Duerkop, BA and Kleiner, M}, title = {Pseudo-pac site sequences used by phage P22 in generalized transduction of Salmonella.}, journal = {PLoS pathogens}, volume = {20}, number = {6}, pages = {e1012301}, pmid = {38913753}, issn = {1553-7374}, support = {R01 AI141479/AI/NIAID NIH HHS/United States ; R35 GM138362/GM/NIGMS NIH HHS/United States ; }, mesh = {*Bacteriophage P22/genetics ; *Salmonella typhimurium/virology/genetics ; Transduction, Genetic ; Gene Transfer, Horizontal ; Genome, Bacterial ; DNA Packaging ; }, abstract = {Salmonella enterica Serovar Typhimurium (Salmonella) and its bacteriophage P22 are a model system for the study of horizontal gene transfer by generalized transduction. Typically, the P22 DNA packaging machinery initiates packaging when a short sequence of DNA, known as the pac site, is recognized on the P22 genome. However, sequences similar to the pac site in the host genome, called pseudo-pac sites, lead to erroneous packaging and subsequent generalized transduction of Salmonella DNA. While the general genomic locations of the Salmonella pseudo-pac sites are known, the sequences themselves have not been determined. We used visualization of P22 sequencing reads mapped to host Salmonella genomes to define regions of generalized transduction initiation and the likely locations of pseudo-pac sites. We searched each genome region for the sequence with the highest similarity to the P22 pac site and aligned the resulting sequences. We built a regular expression (sequence match pattern) from the alignment and used it to search the genomes of two P22-susceptible Salmonella strains-LT2 and 14028S-for sequence matches. The final regular expression successfully identified pseudo-pac sites in both LT2 and 14028S that correspond with generalized transduction initiation sites in mapped read coverages. The pseudo-pac site sequences identified in this study can be used to predict locations of generalized transduction in other P22-susceptible hosts or to initiate generalized transduction at specific locations in P22-susceptible hosts with genetic engineering. Furthermore, the bioinformatics approach used to identify the Salmonella pseudo-pac sites in this study could be applied to other phage-host systems.}, }
@article {pmid38911822, year = {2024}, author = {Banerjee, P and Eulenstein, O and Friedberg, I}, title = {Discovering genomic islands in unannotated bacterial genomes using sequence embedding.}, journal = {Bioinformatics advances}, volume = {4}, number = {1}, pages = {vbae089}, pmid = {38911822}, issn = {2635-0041}, abstract = {MOTIVATION: Genomic islands (GEIs) are clusters of genes in bacterial genomes that are typically acquired by horizontal gene transfer. GEIs play a crucial role in the evolution of bacteria by rapidly introducing genetic diversity and thus helping them adapt to changing environments. Specifically of interest to human health, many GEIs contain pathogenicity and antimicrobial resistance genes. Detecting GEIs is, therefore, an important problem in biomedical and environmental research. There have been many previous studies for computationally identifying GEIs. Still, most of these studies rely on detecting anomalies in the unannotated nucleotide sequences or on a fixed set of known features on annotated nucleotide sequences.<br><br>RESULTS: Here, we present TreasureIsland, which uses a new unsupervised representation of DNA sequences to predict GEIs. We developed a high-precision boundary detection method featuring an incremental fine-tuning of GEI borders, and we evaluated the accuracy of this framework using a new comprehensive reference dataset, Benbow. We show that TreasureIsland's accuracy rivals other GEI predictors, enabling efficient and faster identification of GEIs in unannotated bacterial genomes.<br><br>TreasureIsland is available under an MIT license at: https://github.com/FriedbergLab/GenomicIslandPrediction.}, }
@article {pmid38910035, year = {2025}, author = {Zarlenga, DS and Hoberg, EP and Thompson, P and Rosenthal, B}, title = {Trichinella: Becoming a parasite.}, journal = {Veterinary parasitology}, volume = {333}, number = {}, pages = {110220}, doi = {10.1016/j.vetpar.2024.110220}, pmid = {38910035}, issn = {1873-2550}, mesh = {Animals ; *Biological Evolution ; Climate Change ; Gene Transfer, Horizontal ; Host-Parasite Interactions ; *Phylogeny ; *Trichinella/genetics/classification/physiology ; Trichinellosis/parasitology ; }, abstract = {Phylogenetic evidence indicates that free-living nematodes gave rise to parasitic nematodes where parasitism evolved independently at least 15 times. The high level of genetic and biological diversity among parasites dictates an equally high level of diversity in the transition to parasitism. We previously hypothesized that horizontal gene transfer (HGT) played an important role in the evolution of parasitism among early ancestors of Trichinella, mediated by an interplay of ecological and evolutionary pathways that contributed to persistence and diversification. We propose that host selection may have been associated with the metabolism of ammonia and engender a new paradigm whereby the reprogrammed nurse cell is capable of generating cyanate thereby enabling the importance of the Trichinella cyanase in the longevity of the cell. Parasites and parasitism have revealed considerable resilience against a backdrop of climate change and environmental perturbation. Here we provide a putative link between key periods in the evolution of Trichinella and major geological and climatological events dating back 500 million years. A useful lens for exploring such ideas, the Stockholm Paradigm, integrates Ecological Fitting (a foundation for host colonization and diversification), the Oscillation Hypothesis (recurring shifts between trends in generalization and specialization relative to host range), the Geographic Mosaic Theory of Coevolution (microevolutionary co-adaptive processes), and the Taxon Pulse Hypothesis (alternating events of biotic expansion i.e., exploitation in evolutionary and ecological time). Here we examine how one or more of these interactive theories, in a phylogenetic-historical context and in conjunction with HGT, may help explain the scope and depth of diversity among Trichinella genotypes.}, }
@article {pmid38908181, year = {2024}, author = {Wu, Y and Niu, Q and Liu, Y and Zheng, X and Long, M and Chen, Y}, title = {Chlorinated organophosphorus flame retardants induce the propagation of antibiotic resistance genes in sludge fermentation systems: Insight of chromosomal mutation and microbial traits.}, journal = {Journal of hazardous materials}, volume = {476}, number = {}, pages = {134971}, doi = {10.1016/j.jhazmat.2024.134971}, pmid = {38908181}, issn = {1873-3336}, mesh = {*Flame Retardants/toxicity ; *Sewage/microbiology ; *Fermentation ; *Mutation ; Organophosphorus Compounds/toxicity/chemistry ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; Molecular Docking Simulation ; Genes, Bacterial ; Gene Transfer, Horizontal ; Bacteria/genetics/drug effects/metabolism ; Organophosphates/toxicity ; Chromosomes, Bacterial/genetics ; }, abstract = {Waste activated sludge (WAS) is a critical reservoir for antibiotic resistance genes (ARGs) due to the prevalent misuse of antibiotics. Horizontal gene transfer (HGT) is the primary mechanism for ARGs spread through mobile genetic elements (MGEs). However, the role of non-antibiotic organophosphorus flame retardants (Cl-OFRs) in ARG transmission in the WAS fermentation system remains unclear. This study examines the effects of tris(2-chloroethyl) phosphate (TCEP), a representative Cl-OFR, on ARG dynamics in WAS fermentation using molecular docking and metagenomic analysis. The results showed a 33.4 % increase in ARG abundance in the presence of TCEP. Interestingly, HGT did not appear to be the primary mechanism of ARG dissemination under TCEP stress, as evidenced by a 2.51 % decrease in MGE abundance. TCEP binds to sludge through hydrogen bonds with a binding energy of - 3.6 kJ/mol, leading to microbial damage and an increase in the proportion of non-viable cells. This interaction prompts a microbial shift toward Firmicutes with thick cell walls, which are significant ARG carriers. Additionally, TCEP induces chromosomal mutations through oxidative stress and the SOS response, contributing to ARG formation. Microorganisms also develop multidrug resistance mechanisms to expel TCEP and mitigate its toxicity. This study provides a comprehensive understanding of Cl-OFRs effects on the ARGs fates in WAS fermentation system and offers guidance for the safe and efficient treatment of Cl-OFRs and WAS.}, }
@article {pmid38906294, year = {2024}, author = {Yao, S and Yu, J and Zhang, T and Xie, J and Yan, C and Ni, X and Guo, B and Cui, C}, title = {Comprehensive analysis of distribution characteristics and horizontal gene transfer elements of blaNDM-1-carrying bacteria.}, journal = {The Science of the total environment}, volume = {946}, number = {}, pages = {173907}, doi = {10.1016/j.scitotenv.2024.173907}, pmid = {38906294}, issn = {1879-1026}, mesh = {*beta-Lactamases/genetics ; *Gene Transfer, Horizontal ; Bacteria/genetics ; Anti-Bacterial Agents/pharmacology ; Plasmids/genetics ; }, abstract = {The worldwide dissemination of New Delhi metallo-β-lactamase-1 (NDM-1), which mediates resistance to almost all clinical β-lactam antibiotics, is a major public health problem. The global distribution, species, sources, and potential transfer risk of blaNDM-1-carrying bacteria are unclear. Results of a comprehensive analysis of literature in 2010-2022 showed that a total of 6002 blaNDM-1 carrying bacteria were widely distributed around 62 countries with a high trend in the coastal areas. Opportunistic pathogens or pathogens like Klebsiella sp., Escherichia sp., Acinetobacter sp. and Pseudomonas sp. were the four main species indicating the potential microbial risk. Source analysis showed that 86.45 % of target bacteria were isolated from the source of hospital (e.g., Hospital patients and wastewater) and little from surface water (5.07 %) and farms (3.98 %). A plasmid-encoded blaNDM-1Acinetobacter sp. with the resistance mechanisms of antibiotic efflux pump, antibiotic target change and antibiotic degradation was isolated from the wastewater of a typical tertiary hospital. Insertion sequences (IS3 and IS30) located in the adjacent 5 kbp of blaNDM-1-bleMBL gene cluster indicating the transposon-mediated horizontal gene transfer risk. These results showed that the worldwide spread of blaNDM-1-carrying bacteria and its potential horizontal gene transfer risk deserve good control.}, }
@article {pmid38905247, year = {2024}, author = {Mohamed, DS and Abd El-Baky, RM and El-Mokhtar, MA and Ghanem, SK and Yahia, R and Alqahtani, AM and Abourehab, MAS and Ahmed, EF}, title = {Influence of selected non-antibiotic pharmaceuticals on antibiotic resistance gene transfer in Escherichia coli.}, journal = {PloS one}, volume = {19}, number = {6}, pages = {e0304980}, pmid = {38905247}, issn = {1932-6203}, mesh = {*Escherichia coli/drug effects/genetics ; *Gene Transfer, Horizontal ; *Plasmids/genetics ; Metoclopramide/pharmacology ; Microbial Sensitivity Tests ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics/drug effects ; Conjugation, Genetic ; Drug Resistance, Microbial/genetics/drug effects ; }, abstract = {BACKGROUND: Antibiotic resistance genes (ARGs) transfer rapidly among bacterial species all over the world contributing to the aggravation of antibiotic resistance crisis. Antibiotics at sub-inhibitory concentration induce horizontal gene transfer (HRT) between bacteria, especially through conjugation. The role of common non-antibiotic pharmaceuticals in the market in disseminating antibiotic resistance is not well studied.<br><br>OBJECTIVES: In this work, we indicated the effect of some commonly used non-antibiotic pharmaceuticals including antiemetic (metoclopramide HCl) and antispasmodics (hyoscine butyl bromide and tiemonium methyl sulfate) on the plasmid-mediated conjugal transfer of antibiotic resistance genes between pathogenic E. coli in the gastric intestinal tract (GIT).<br><br>METHODS: Broth microdilution assay was used to test the antibacterial activity of the tested non-antibiotic pharmaceuticals. A conjugation mating system was applied in presence of the studied non-antibiotic pharmaceuticals to test their effect on conjugal transfer frequency. Plasmid extraction and PCR were performed to confirm the conjugation process. Transmission electron microscopy (TEM) was used for imaging the effect of non-antibiotic pharmaceuticals on bacterial cells.<br><br>RESULTS: No antibacterial activity was reported for the used non-antibiotic pharmaceuticals. Plasmid-mediated conjugal transfer between isolates was induced by metoclopramide HCl but suppressed by hyoscine butyl bromide. Tiemonium methylsulfate slightly promoted conjugal transfer. Aggregation between cells and periplasmic bridges was clear in the case of metoclopramide HCl while in presence of hyoscine butyl bromide little affinity was observed.<br><br>CONCLUSION: This study indicates the contribution of non-antibiotic pharmaceuticals to the dissemination and evolution of antibiotic resistance at the community level. Metoclopramide HCl showed an important role in the spread of antibiotic resistance.}, }
@article {pmid38904756, year = {2024}, author = {Kaur, J and Verma, H and Kaur, J and Lata, P and Dhingra, GG and Lal, R}, title = {In Silico Analysis of the Phylogenetic and Physiological Characteristics of Sphingobium indicum B90A: A Hexachlorocyclohexane-Degrading Bacterium.}, journal = {Current microbiology}, volume = {81}, number = {8}, pages = {233}, pmid = {38904756}, issn = {1432-0991}, mesh = {*Phylogeny ; *Sphingomonadaceae/genetics/metabolism/classification ; *Genome, Bacterial ; *Hexachlorocyclohexane/metabolism ; *Computer Simulation ; *Biodegradation, Environmental ; Genomic Islands ; Gene Transfer, Horizontal ; }, abstract = {The study focuses on the in silico genomic characterization of Sphingobium indicum B90A, revealing a wealth of genes involved in stress response, carbon monoxide oxidation, β-carotene biosynthesis, heavy metal resistance, and aromatic compound degradation, suggesting its potential as a bioremediation agent. Furthermore, genomic adaptations among nine Sphingomonad strains were explored, highlighting shared core genes via pangenome analysis, including those related to the shikimate pathway and heavy metal resistance. The majority of genes associated with aromatic compound degradation, heavy metal resistance, and stress response were found within genomic islands across all strains. Sphingobium indicum UT26S exhibited the highest number of genomic islands, while Sphingopyxis alaskensis RB2256 had the maximum fraction of its genome covered by genomic islands. The distribution of lin genes varied among the strains, indicating diverse genetic responses to environmental pressures. Additionally, in silico evidence of horizontal gene transfer (HGT) between plasmids pSRL3 and pISP3 of the Sphingobium and Sphingomonas genera, respectively, has been provided. The manuscript offers novel insights into strain B90A, highlighting its role in horizontal gene transfer and refining evolutionary relationships among Sphingomonad strains. The discovery of stress response genes and the czcABCD operon emphasizes the potential of Sphingomonads in consortia development, supported by genomic island analysis.}, }
@article {pmid38904697, year = {2024}, author = {Bhattacharjee, A and Singh, AK}, title = {Delineating the Acquired Genetic Diversity and Multidrug Resistance in Alcaligenes from Poultry Farms and Nearby Soil.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {62}, number = {7}, pages = {511-523}, pmid = {38904697}, issn = {1976-3794}, support = {OLP-2035//Council for Scientific and Industrial Research/ ; OLP-2081//Council for Scientific and Industrial Research/ ; GPP-0423//DST-SERB/ ; }, mesh = {Animals ; *Drug Resistance, Multiple, Bacterial/genetics ; *Poultry/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Soil Microbiology ; *Farms ; Microbial Sensitivity Tests ; Genetic Variation ; Whole Genome Sequencing ; Genomic Islands ; Alcaligenes faecalis/genetics/isolation &amp; purification/drug effects ; Genome, Bacterial ; Feces/microbiology ; Gram-Negative Bacterial Infections/microbiology/veterinary ; }, abstract = {Alcaligenes faecalis is one of the most important and clinically significant environmental pathogens, increasing in importance due to its isolation from soil and nosocomial environments. The Gram-negative soil bacterium is associated with skin endocarditis, bacteremia, dysentery, meningitis, endophthalmitis, urinary tract infections, and pneumonia in patients. With emerging antibiotic resistance in A. faecalis, it has become crucial to understand the origin of such resistance genes within this clinically significant environmental and gut bacterium. In this research, we studied the impact of antibiotic overuse in poultry and its effect on developing resistance in A. faecalis. We sampled soil and faecal materials from five poultry farms, performed whole genome sequencing &amp; analysis and identified four strains of A. faecalis. Furthermore, we characterized the genes in the genomic islands of A. faecalis isolates. We found four multidrug-resistant A. faecalis strains that showed resistance against vancomycin (MIC >1000 μg/ml), ceftazidime (50 μg/ml), colistin (50 μg/ml) and ciprofloxacin (50 μg/ml). From whole genome comparative analysis, we found more than 180 resistance genes compared to the reference sequence. Parts of our assembled contigs were found to be similar to different bacteria which included pbp1A and pbp2 imparting resistance to amoxicillin originally a part of Helicobacter and Bordetella pertussis. We also found the Mycobacterial insertion element IS6110 in the genomic islands of all four genomes. This prominent insertion element can be transferred and induce resistance to other bacterial genomes. The results thus are crucial in understanding the transfer of resistance genes in the environment and can help in developing regimes for antibiotic use in the food and poultry industry.}, }
@article {pmid38903782, year = {2024}, author = {Ott, LC and Mellata, M}, title = {Short-chain fatty acids inhibit bacterial plasmid transfer through conjugation in vitro and in ex vivo chicken tissue explants.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1414401}, pmid = {38903782}, issn = {1664-302X}, abstract = {The animal gut acts as a potent reservoir for spreading and maintaining conjugative plasmids that confer antimicrobial resistance (AMR), fitness, and virulence attributes. Interventions that inhibit the continued emergence and expansion of AMR and virulent strains in agricultural and clinical environments are greatly desired. This study aims to determine the presence and efficacy of short-chain fatty acids (SCFA) inhibitory effects on the conjugal transfer of AMR plasmids. In vitro broth conjugations were conducted between donor Escherichia coli strains carrying AMP plasmids and the plasmid-less Escherichia coli HS-4 recipient strain. Conjugations were supplemented with ddH2O or SCFAs at 1, 0.1, 0.01, or 0.001 molar final concentration. The addition of SCFAs completely inhibited plasmid transfer at 1 and 0.1 molar and significantly (p < 0.05) reduced transfer at 0.01 molar, regardless of SCFA tested. In explant models for the chicken ceca, either ddH2O or a final concentration of 0.025 M SCFAs were supplemented to the explants infected with donor and recipient E. coli. In every SCFA tested, significant decreases in transconjugant populations compared to ddH2O-treated control samples were observed with minimal effects on donor and recipient populations. Finally, significant reductions in transconjugants for plasmids of each incompatibility type (IncP1ε, IncFIβ, and IncI1) tested were detected. This study demonstrates for the first time the broad inhibition ability of SCFAs on bacterial plasmid transfer and eliminates AMR with minimal effect on bacteria. Implementing interventions that increase the concentrations of SCFAs in the gut may be a viable method to reduce the risk, incidence, and rate of AMR emergence in agricultural and human environments.}, }
@article {pmid38903098, year = {2024}, author = {Sastre-Dominguez, J and DelaFuente, J and Toribio-Celestino, L and Herencias, C and Herrador-Gomez, P and Costas, C and Hernandez-Garcia, M and Canton, R and Rodriguez-Beltran, J and Santos-Lopez, A and San Millan, A}, title = {Plasmid-encoded insertion sequences promote rapid adaptation in clinical enterobacteria.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.03.01.582297}, pmid = {38903098}, issn = {2692-8205}, abstract = {Plasmids are extrachromosomal genetic elements commonly found in bacteria. Plasmids are known to fuel bacterial evolution through horizontal gene transfer (HGT), but recent analyses indicate that they can also promote intragenomic adaptations. However, the role of plasmids as catalysts of bacterial evolution beyond HGT remains poorly explored. In this study, we investigate the impact of a widespread conjugative plasmid, pOXA-48, on the evolution of various multidrug-resistant clinical enterobacteria. Combining experimental and within-patient evolution analyses, we unveil that plasmid pOXA-48 promotes bacterial evolution through the transposition of plasmid-encoded insertion sequence 1 (IS1) elements. Specifically, IS1-mediated gene inactivations expedite the adaptation rate of clinical strains in vitro and foster within-patient adaptation in the gut microbiota. We decipher the mechanism underlying the plasmid-mediated surge in IS1 transposition, revealing a negative feedback loop regulated by the genomic copy number of IS1. Given the overrepresentation of IS elements in bacterial plasmids, our findings propose that plasmid-mediated IS transposition represents a crucial mechanism for swift bacterial adaptation.}, }
@article {pmid38902796, year = {2024}, author = {Chaudhari, NM and Pérez-Carrascal, OM and Overholt, WA and Totsche, KU and Küsel, K}, title = {Genome streamlining in Parcubacteria transitioning from soil to groundwater.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {41}, pmid = {38902796}, issn = {2524-6372}, abstract = {BACKGROUND: To better understand the influence of habitat on the genetic content of bacteria, with a focus on members of Candidate Phyla Radiation (CPR) bacteria, we studied the effects of transitioning from soil via seepage waters to groundwater on genomic composition of ultra-small Parcubacteria, the dominating CPR class in seepage waters, using genome resolved metagenomics.<br><br>RESULTS: Bacterial metagenome-assembled genomes (MAGs), (318 total, 32 of Parcubacteria) were generated from seepage waters and compared directly to groundwater counterparts. The estimated average genome sizes of members of major phyla Proteobacteria, Bacteroidota and Cand. Patescibacteria (Candidate Phyla Radiation - CPR bacteria) were significantly higher in soil-seepage water as compared to their groundwater counterparts. Seepage water Parcubacteria (Paceibacteria) exhibited 1.18-fold greater mean genome size and 2-fold lower mean proportion of pseudogenes than those in groundwater. Bacteroidota and Proteobacteria also showed a similar trend of reduced genomes in groundwater compared to seepage. While exploring gene loss and adaptive gains in closely related CPR lineages in groundwater, we identified a membrane protein, and a lipoglycopeptide resistance gene unique to a seepage Parcubacterium genome. A nitrite reductase gene was also identified and was unique to the groundwater Parcubacteria genomes, likely acquired from other planktonic microbes via horizontal gene transfer.<br><br>CONCLUSIONS: Overall, our data suggest that bacteria in seepage waters, including ultra-small Parcubacteria, have significantly larger genomes and higher metabolic enrichment than their groundwater counterparts, highlighting possible genome streamlining of the latter in response to habitat selection in an oligotrophic environment.}, }
@article {pmid38901473, year = {2024}, author = {Walt, HK and Ahn, SJ and Hoffmann, FG}, title = {Horizontally transferred glycoside hydrolase 26 may aid hemipteran insects in plant tissue digestion.}, journal = {Molecular phylogenetics and evolution}, volume = {198}, number = {}, pages = {108134}, doi = {10.1016/j.ympev.2024.108134}, pmid = {38901473}, issn = {1095-9513}, mesh = {Animals ; *Gene Transfer, Horizontal ; *Hemiptera/genetics/enzymology/classification ; *Phylogeny ; *Glycoside Hydrolases/genetics ; Plants/genetics/classification ; }, abstract = {Glycoside hydrolases are enzymes that break down complex carbohydrates into simple sugars by catalyzing the hydrolysis of glycosidic bonds. There have been multiple instances of adaptive horizontal gene transfer of genes belonging to various glycoside hydrolase families from microbes to insects, as glycoside hydrolases can metabolize constituents of the carbohydrate-rich plant cell wall. In this study, we characterize the horizontal transfer of a gene from the glycoside hydrolase family 26 (GH26) from bacteria to insects of the order Hemiptera. Our phylogenies trace the horizontal gene transfer to the common ancestor of the superfamilies Pentatomoidea and Lygaeoidea, which include stink bugs and seed bugs. After horizontal transfer, the gene was assimilated into the insect genome as indicated by the gain of an intron, and a eukaryotic signal peptide. Subsequently, the gene has undergone independent losses and expansions in copy number in multiple lineages, suggesting an adaptive role of GH26s in some insects. Finally, we measured tissue-level gene expression of multiple stink bugs and the large milkweed bug using publicly available RNA-seq datasets. We found that the GH26 genes are highly expressed in tissues associated with plant digestion, especially in the principal salivary glands of the stink bugs. Our results are consistent with the hypothesis that this horizontally transferred GH26 was co-opted by the insect to aid in plant tissue digestion and that this HGT event was likely adaptive.}, }
@article {pmid38896653, year = {2024}, author = {Elliott, JFK and McLeod, DV and Taylor, TB and Westra, ER and Gandon, S and Watson, BNJ}, title = {Conditions for the spread of CRISPR-Cas immune systems into bacterial populations.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38896653}, issn = {1751-7370}, support = {BB/T008741/1//Biotechnology and Biological Sciences Research Council SWBio DTP/ ; DH150169//Royal Society Dorothy Hodgkin Fellowship/ ; NE/S001921/1//Natural Environment Research Council/ ; BB/X010600/1//Biotechnology and Biological Sciences Research Council Discovery Fellowship/ ; }, mesh = {*CRISPR-Cas Systems ; *Bacteriophages/genetics ; *Bacteria/genetics/virology/classification ; Pseudomonas aeruginosa/virology/genetics/immunology ; Gene Transfer, Horizontal ; Clustered Regularly Interspaced Short Palindromic Repeats ; }, abstract = {Bacteria contain a wide variety of innate and adaptive immune systems which provide protection to the host against invading genetic material, including bacteriophages (phages). It is becoming increasingly clear that bacterial immune systems are frequently lost and gained through horizontal gene transfer. However, how and when new immune systems can become established in a bacterial population have remained largely unstudied. We developed a joint epidemiological and evolutionary model that predicts the conditions necessary for the spread of a CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) immune system into a bacterial population lacking this system. We found that whether bacteria carrying CRISPR-Cas will spread (increase in frequency) into a bacterial population depends on the abundance of phages and the difference in the frequency of phage resistance mechanisms between bacteria carrying a CRISPR-Cas immune system and those not (denoted as ${f}_{\Delta }$). Specifically, the abundance of cells carrying CRISPR-Cas will increase if there is a higher proportion of phage resistance (either via CRISPR-Cas immunity or surface modification) in the CRISPR-Cas-possessing population than in the cells lacking CRISPR-Cas. We experimentally validated these predictions in a model using Pseudomonas aeruginosa PA14 and phage DMS3vir. Specifically, by varying the initial ratios of different strains of bacteria that carry alternative forms of phage resistance, we confirmed that the spread of cells carrying CRISPR-Cas through a population can be predicted based on phage density and the relative frequency of resistance phenotypes. Understanding which conditions promote the spread of CRISPR-Cas systems helps to predict when and where these defences can become established in bacterial populations after a horizontal gene transfer event, both in ecological and clinical contexts.}, }
@article {pmid38896471, year = {2024}, author = {Lerminiaux, N and Mitchell, R and Katz, K and Fakharuddin, K and McGill, E and Mataseje, L}, title = {Plasmid genomic epidemiology of carbapenem-hydrolysing class D β-lactamase (CDHL)-producing Enterobacterales in Canada, 2010-2021.}, journal = {Microbial genomics}, volume = {10}, number = {6}, pages = {}, pmid = {38896471}, issn = {2057-5858}, mesh = {*beta-Lactamases/genetics ; *Plasmids/genetics ; Canada/epidemiology ; Humans ; *Carbapenems/pharmacology ; *Whole Genome Sequencing ; *Bacterial Proteins/genetics ; *Enterobacteriaceae Infections/microbiology/epidemiology ; Enterobacteriaceae/genetics/drug effects/classification ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; Cross Infection/microbiology/epidemiology ; }, abstract = {Carbapenems are last-resort antibiotics for treatment of infections caused by multidrug-resistant Enterobacterales, but carbapenem resistance is a rising global threat due to the acquisition of carbapenemase genes. Oxacillinase-48 (bla OXA-48)-type carbapenemases are increasing in abundance in Canada and elsewhere; these genes are frequently found on mobile genetic elements and are associated with specific transposons. This means that alongside clonal dissemination, bla OXA-48-type genes can spread through plasmid-mediated horizontal gene transfer. We applied whole genome sequencing to characterize 249 bla OXA-48-type-producing Enterobacterales isolates collected by the Canadian Nosocomial Infection Surveillance Program from 2010 to 2021. Using a combination of short- and long-read sequencing, we obtained 70 complete and circular bla OXA-48-type-encoding plasmids. Using MOB-suite, four major plasmids clustered were identified, and we further estimated a plasmid cluster for 91.9 % (147/160) of incomplete bla OXA-48-type-encoding contigs. We identified different patterns of carbapenemase mobilization across Canada, including horizontal transmission of bla OXA-181/IncX3 plasmids (75/249, 30.1 %) and bla OXA-48/IncL/M plasmids (47/249, 18.9 %), and both horizontal transmission and clonal transmission of bla OXA-232 for Klebsiella pneumoniae ST231 on ColE2-type/ColKP3 plasmids (25/249, 10.0 %). Our findings highlight the diversity of OXA-48-type plasmids and indicate that multiple plasmid clusters and clonal transmission have contributed to bla OXA-48-type spread and persistence in Canada.}, }
@article {pmid38896033, year = {2024}, author = {Huang, B and Xiao, Y and Zhang, Y}, title = {Asgard archaeal selenoproteome reveals a roadmap for the archaea-to-eukaryote transition of selenocysteine incorporation machinery.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38896033}, issn = {1751-7370}, support = {32270680//National Natural Science Foundation of China/ ; 2023SHIBS0003//Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions/ ; }, mesh = {*Selenocysteine/metabolism/genetics ; *Archaea/genetics/metabolism/classification ; *Selenoproteins/genetics/metabolism ; *Eukaryota/genetics/classification/metabolism ; Genome, Archaeal ; Proteome ; Codon, Terminator/genetics ; Archaeal Proteins/genetics/metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal ; Phylogeny ; }, abstract = {Selenocysteine (Sec) is encoded by the UGA codon that normally functions as a stop signal and is specifically incorporated into selenoproteins via a unique recoding mechanism. The translational recoding of UGA as Sec is directed by an unusual RNA structure, the SECIS element. Although archaea and eukaryotes adopt similar Sec encoding machinery, the SECIS elements have no similarities to each other with regard to sequence and structure. We analyzed >400 Asgard archaeal genomes to examine the occurrence of both Sec encoding system and selenoproteins in this archaeal superphylum, the closest prokaryotic relatives of eukaryotes. A comprehensive map of Sec utilization trait has been generated, providing the most detailed understanding of the use of this nonstandard amino acid in Asgard archaea so far. By characterizing the selenoproteomes of all organisms, several selenoprotein-rich phyla and species were identified. Most Asgard archaeal selenoprotein genes possess eukaryotic SECIS-like structures with varying degrees of diversity. Moreover, euryarchaeal SECIS elements might originate from Asgard archaeal SECIS elements via lateral gene transfer, indicating a complex and dynamic scenario of the evolution of SECIS element within archaea. Finally, a roadmap for the transition of eukaryotic SECIS elements from archaea was proposed, and selenophosphate synthetase may serve as a potential intermediate for the generation of ancestral eukaryotic SECIS element. Our results offer new insights into a deeper understanding of the evolution of Sec insertion machinery.}, }
@article {pmid38895488, year = {2024}, author = {Ellison, TJ and Ellison, CK}, title = {DNA binding is rate-limiting for natural transformation.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38895488}, issn = {2692-8205}, support = {R35 GM150916/GM/NIGMS NIH HHS/United States ; }, abstract = {Bacteria take up environmental DNA using dynamic appendages called type IV pili (T4P) to elicit horizontal gene transfer in a process called natural transformation. Natural transformation is widespread amongst bacteria yet determining how different factors universally contribute to or limit this process across species has remained challenging. Here we show that Acinetobacter baylyi, the most naturally transformable species, is highly transformable due to its ability to robustly bind nonspecific DNA via a dedicated orphan minor pilin, FimT. We show that, compared to its homologues, A. baylyi FimT contains multiple positively charged residues that additively promote DNA binding efficiency. Expression of A. baylyi FimT in a closely related Acinetobacter pathogen is sufficient to substantially improve its capacity for natural transformation, demonstrating that T4P-DNA binding is a rate-limiting step in this process. These results demonstrate the importance of T4P-DNA binding efficiency in driving natural transformation, establishing a key factor limiting horizontal gene transfer.}, }
@article {pmid38895396, year = {2025}, author = {Chang, TH and Pourtois, JD and Haddock, NL and Furkuawa, D and Kelly, KE and Amanatullah, DF and Burgener, E and Milla, C and Banaei, N and Bollyky, PL}, title = {Prophages are Infrequently Associated With Antibiotic Resistance in Pseudomonas aeruginosa Clinical Isolates.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.06.02.595912}, pmid = {38895396}, issn = {2692-8205}, support = {R01 HL148184/HL/NHLBI NIH HHS/United States ; }, abstract = {UNLABELLED: Lysogenic bacteriophages can integrate their genome into the bacterial chromosome in the form of a prophage and can promote genetic transfer between bacterial strains in vitro . However, the contribution of lysogenic phages to the incidence of antimicrobial resistance (AMR) in clinical settings is poorly understood. Here, in a set of 186 clinical isolates of Pseudomonas aeruginosa collected from respiratory cultures from 82 patients with cystic fibrosis (CF), we evaluate the links between prophage counts and both genomic and phenotypic resistance to six anti-pseudomonal antibiotics: tobramycin, colistin, ciprofloxacin, meropenem, aztreonam, and piperacillin-tazobactam. We identified 239 different prophages in total. We find that P. aeruginosa isolates contain on average 3.06 +/- 1.84 (SD) predicted prophages. We find no significant association between the number of prophages per isolate and the minimum inhibitory concentration (MIC) for any of these antibiotics. We then investigate the relationship between particular prophages and AMR. We identify a single lysogenic phage associated with phenotypic resistance to the antibiotic tobramycin and, consistent with this association, we observe that AMR genes associated with resistance to tobramycin are more likely to be found when this prophage is present. However we find that they are not encoded directly on prophage sequences. Additionally, we identify a single prophage statistically associated with ciprofloxacin resistance but do not identify any genes associated with ciprofloxacin phenotypic resistance. These findings suggest that prophages are only infrequently associated with the AMR genes in clinical isolates of P. aeruginosa .<br><br>IMPORTANCE: Antibiotic-resistant infections of Pseudomonas aeruginosa , a leading pathogen in patients with Cystic Fibrosis (CF) are a global health threat. While lysogenic bacteriophages are known to facilitate horizontal gene transfer, their role in promoting antibiotic resistance in clinical settings remains poorly understood. In our analysis of 186 clinical isolates of P. aeruginosa from CF patients, we find that prophage abundance does not predict phenotypic resistance to key antibiotics but that specific prophages are infrequently associated with tobramycin resistance genes. In addition, we do not find antimicrobial resistance (AMR) genes encoded directly on prophages. These results highlight that while phages can be associated with AMR, phage-mediated AMR transfer may be rare in clinical isolates and difficult to identify. This work is important for future efforts on mitigating AMR in Cystic Fibrosis and other vulnerable populations affected by Pseudomonas aeruginosa infections and advances our understanding of bacterial-phage dynamics in clinical infections.}, }
@article {pmid38895369, year = {2024}, author = {Klein, JA and Predeus, AV and Greissl, AR and Clark-Herrera, MM and Cruz, E and Cundiff, JA and Haeberle, AL and Howell, M and Lele, A and Robinson, DJ and Westerman, TL and Wrande, M and Wright, SJ and Green, NM and Vallance, BA and McClelland, M and Mejia, A and Goodman, AG and Elfenbein, JR and Knodler, LA}, title = {Pathogenic diversification of the gut commensal Providencia alcalifaciens via acquisition of a second type III secretion system.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.06.07.595826}, pmid = {38895369}, issn = {2692-8205}, abstract = {Providencia alcalifaciens is a Gram-negative bacterium found in a wide variety of water and land environments and organisms. It has been isolated as part of the gut microbiome of animals and insects, as well as from stool samples of patients with diarrhea. Specific P. alcalifaciens strains encode gene homologs of virulence factors found in other pathogenic members of the same Enterobacterales order, such as Salmonella enterica serovar Typhimurium and Shigella flexneri. Whether these genes are also pathogenic determinants in P. alcalifaciens is not known. Here we have used P. alcalifaciens 205/92, a clinical isolate, with in vitro and in vivo infection models to investigate P. alcalifaciens -host interactions at the cellular level. Our particular focus was the role of two type III secretion systems (T3SS) belonging to the Inv-Mxi/Spa family. T3SS 1b is widespread in Providencia spp. and encoded on the chromosome. T3SS 1a is encoded on a large plasmid that is present in a subset of P. alcalifaciens strains, which are primarily isolates from diarrheal patients. Using a combination of electron and fluorescence microscopy and gentamicin protection assays we show that P. alcalifaciens 205/92 is internalized into eukaryotic cells, rapidly lyses its internalization vacuole and proliferates in the cytosol. This triggers caspase-4 dependent inflammasome responses in gut epithelial cells. The requirement for the T3SS 1a in entry, vacuole lysis and cytosolic proliferation is host-cell type specific, playing a more prominent role in human intestinal epithelial cells as compared to macrophages. In a bovine ligated intestinal loop model, P. alcalifaciens colonizes the intestinal mucosa, inducing mild epithelial damage with negligible fluid accumulation. No overt role for T3SS 1a or T3SS 1b was seen in the calf infection model. However, T3SS 1b was required for the rapid killing of Drosophila melanogaster . We propose that the acquisition of two T3SS by horizontal gene transfer has allowed P. alcalifaciens to diversify its host range, from a highly virulent pathogen of insects to an opportunistic gastrointestinal pathogen of animals.}, }
@article {pmid38891015, year = {2024}, author = {Zhou, H and Lu, Z and Liu, X and Bie, X and Xue, F and Tang, S and Feng, Q and Cheng, Y and Yang, J}, title = {Environmentally Relevant Concentrations of Tetracycline Promote Horizontal Transfer of Antimicrobial Resistance Genes via Plasmid-Mediated Conjugation.}, journal = {Foods (Basel, Switzerland)}, volume = {13}, number = {11}, pages = {}, pmid = {38891015}, issn = {2304-8158}, support = {32272295//National Natural Science Foundation of China/ ; BE2022684//Jiangsu Provincial Key Research and Development Program/ ; KJ2024017//the Science and Technology Project of Jiangsu Provincial Administration for Market Regulation/ ; }, abstract = {The ubiquitous presence of antimicrobial-resistant organisms and antimicrobial resistance genes (ARGs) constitutes a major threat to global public safety. Tetracycline (TET) is a common antimicrobial agent that inhibits bacterial growth and is frequently detected in aquatic environments. Although TET may display coselection for resistance, limited knowledge is available on whether and how it might influence plasmid-mediated conjugation. Subinhibitory concentrations (3.9-250 ng/mL) of TET promoted horizontal gene transfer (HGT) via the mobilizable plasmid pVP52-1 from the donor Vibrio parahaemolyticus NJIFDCVp52 to the recipient Escherichia coli EC600 by 1.47- to 3.19-fold. The transcription levels of tetracycline resistance genes [tetA, tetR(A)], conjugation-related genes (traA, traD), outer membrane protein genes (ompA, ompK, ompV), reactive oxygen species (ROS)-related genes (oxyR, rpoS), autoinducer-2 (AI-2) synthesis gene (luxS), and SOS-related genes (lexA, recA) in the donor and recipient were significantly increased. Furthermore, the overproduced intracellular ROS generation and increased cell membrane permeability under TET exposure stimulated the conjugative transfer of ARGs. Overall, this study provides important insights into the contributions of TET to the spread of antimicrobial resistance.}, }
@article {pmid38888367, year = {2024}, author = {Li, X and Gallardo, O and August, E and Dassa, B and Court, DL and Stavans, J and Arbel-Goren, R}, title = {Stability and gene strand bias of lambda prophages and chromosome organization in Escherichia coli.}, journal = {mBio}, volume = {15}, number = {7}, pages = {e0207823}, pmid = {38888367}, issn = {2150-7511}, support = {//NIH Intramural Research Program/ ; //Kushner Fellowship/ ; //Siegfried and Irma Ullman Professorial Chair/ ; }, mesh = {*Escherichia coli/genetics/virology ; *Bacteriophage lambda/genetics/physiology ; *Chromosomes, Bacterial/genetics ; *Lysogeny/genetics ; Virus Integration ; Gene Transfer, Horizontal ; Genomic Instability ; Repressor Proteins/genetics/metabolism ; Prophages/genetics/physiology ; In Situ Hybridization, Fluorescence ; Viral Regulatory and Accessory Proteins ; }, abstract = {Temperate phage-mediated horizontal gene transfer is a potent driver of genetic diversity in the evolution of bacteria. Most lambdoid prophages in Escherichia coli are integrated into the chromosome with the same orientation with respect to the direction of chromosomal replication, and their location on the chromosome is far from homogeneous. To better understand these features, we studied the interplay between lysogenic and lytic states of phage lambda in both native and inverted integration orientations at the wild-type integration site as well as at other sites on the bacterial chromosome. Measurements of free phage released by spontaneous induction showed that the stability of lysogenic states is affected by location and orientation along the chromosome, with stronger effects near the origin of replication. Competition experiments and range expansions between lysogenic strains with opposite orientations and insertion loci indicated that there are no major differences in growth. Moreover, measurements of the level of transcriptional bursts of the cI gene coding for the lambda phage repressor using single-molecule fluorescence in situ hybridization resulted in similar levels of transcription for both orientations and prophage location. We postulate that the preference for a given orientation and location is a result of a balance between the maintenance of lysogeny and the ability to lyse.IMPORTANCEThe integration of genetic material of temperate bacterial viruses (phages) into the chromosomes of bacteria is a potent evolutionary force, allowing bacteria to acquire in one stroke new traits and restructure the information in their chromosomes. Puzzlingly, this genetic material is preferentially integrated in a particular orientation and at non-random sites on the bacterial chromosome. The work described here reveals that the interplay between the maintenance of the stability of the integrated phage, its ability to excise, and its localization along the chromosome plays a key role in setting chromosomal organization in Escherichia coli.}, }
@article {pmid38884912, year = {2024}, author = {Libante, V and Dechêne-Tempier, M and Leblond-Bourget, N and Payot, S}, title = {Detection and Quantification of Conjugative Transfer of Mobile Genetic Elements Carrying Antibiotic Resistance Genes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2815}, number = {}, pages = {79-91}, pmid = {38884912}, issn = {1940-6029}, mesh = {*Conjugation, Genetic ; *Interspersed Repetitive Sequences/genetics ; Gene Transfer, Horizontal ; Streptococcus suis/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Polymerase Chain Reaction/methods ; Genes, Bacterial ; }, abstract = {Multidrug resistance, due to acquired antimicrobial resistance genes, is increasingly reported in the zoonotic pathogen Streptococcus suis. Most of these resistance genes are carried by chromosomal Mobile Genetic Elements (MGEs), in particular, Integrative and Conjugative Elements (ICEs) and Integrative and Mobilizable Elements (IMEs). ICEs and IMEs frequently form tandems or nested composite elements, which make their identification difficult. To evaluate their mobility, it is necessary to (i) select the suitable donor-recipient pairs for mating assays, (ii) do PCR excision tests to confirm that the genetic element is able to excise from the chromosome as a circular intermediate, and (iii) evaluate the transfer of the genetic element by conjugation by doing mating assays. In addition to a dissemination of resistance genes between S. suis strains, MGEs can lead to a spreading of resistance genes in the environment and toward pathogenic bacteria. This propagation had to be considered in a One Health perspective.}, }
@article {pmid38884260, year = {2024}, author = {Wang, S and Jiang, Y and Che, L and Wang, RH and Li, SC}, title = {Enhancing insights into diseases through horizontal gene transfer event detection from gut microbiome.}, journal = {Nucleic acids research}, volume = {52}, number = {14}, pages = {e61}, pmid = {38884260}, issn = {1362-4962}, support = {20220814183301001//Shenzhen Science and Technology Program/ ; 9667242//Applied Research/ ; 9440262//Hong Kong Innovation and Technology Fund/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Gene Transfer, Horizontal ; *Metagenomics/methods ; Colorectal Neoplasms/genetics/microbiology ; Diarrhea/microbiology/genetics ; Bacteria/genetics/classification ; }, abstract = {Horizontal gene transfer (HGT) phenomena pervade the gut microbiome and significantly impact human health. Yet, no current method can accurately identify complete HGT events, including the transferred sequence and the associated deletion and insertion breakpoints from shotgun metagenomic data. Here, we develop LocalHGT, which facilitates the reliable and swift detection of complete HGT events from shotgun metagenomic data, delivering an accuracy of 99.4%-verified by Nanopore data-across 200 gut microbiome samples, and achieving an average F1 score of 0.99 on 100 simulated data. LocalHGT enables a systematic characterization of HGT events within the human gut microbiome across 2098 samples, revealing that multiple recipient genome sites can become targets of a transferred sequence, microhomology is enriched in HGT breakpoint junctions (P-value = 3.3e-58), and HGTs can function as host-specific fingerprints indicated by the significantly higher HGT similarity of intra-personal temporal samples than inter-personal samples (P-value = 4.3e-303). Crucially, HGTs showed potential contributions to colorectal cancer (CRC) and acute diarrhoea, as evidenced by the enrichment of the butyrate metabolism pathway (P-value = 3.8e-17) and the shigellosis pathway (P-value = 5.9e-13) in the respective associated HGTs. Furthermore, differential HGTs demonstrated promise as biomarkers for predicting various diseases. Integrating HGTs into a CRC prediction model achieved an AUC of 0.87.}, }
@article {pmid38882494, year = {2024}, author = {Xu, X and Feng, Q and Zhang, T and Gao, Y and Cheng, Q and Zhang, W and Wu, Q and Xu, K and Li, Y and Nguyen, N and Taft, DH and Mills, DA and Lemay, DG and Zhu, W and Mao, S and Zhang, A and Xu, K and Liu, J}, title = {Infant age inversely correlates with gut carriage of resistance genes, reflecting modifications in microbial carbohydrate metabolism during early life.}, journal = {iMeta}, volume = {3}, number = {2}, pages = {e169}, pmid = {38882494}, issn = {2770-596X}, abstract = {The infant gut microbiome is increasingly recognized as a reservoir of antibiotic resistance genes, yet the assembly of gut resistome in infants and its influencing factors remain largely unknown. We characterized resistome in 4132 metagenomes from 963 infants in six countries and 4285 resistance genes were observed. The inherent resistome pattern of healthy infants (N = 272) could be distinguished by two stages: a multicompound resistance phase (Months 0-7) and a tetracycline-mupirocin-β-lactam-dominant phase (Months 8-14). Microbial taxonomy explained 40.7% of the gut resistome of healthy infants, with Escherichia (25.5%) harboring the most resistance genes. In a further analysis with all available infants (N = 963), we found age was the strongest influencer on the resistome and was negatively correlated with the overall resistance during the first 3 years (p < 0.001). Using a random-forest approach, a set of 34 resistance genes could be used to predict age (R [2] = 68.0%). Leveraging microbial host inference analyses, we inferred the age-dependent assembly of infant resistome was a result of shifts in the gut microbiome, primarily driven by changes in taxa that disproportionately harbor resistance genes across taxa (e.g., Escherichia coli more frequently harbored resistance genes than other taxa). We performed metagenomic functional profiling and metagenomic assembled genome analyses whose results indicate that the development of gut resistome was driven by changes in microbial carbohydrate metabolism, with an increasing need for carbohydrate-active enzymes from Bacteroidota and a decreasing need for Pseudomonadota during infancy. Importantly, we observed increased acquired resistance genes over time, which was related to increased horizontal gene transfer in the developing infant gut microbiome. In summary, infant age was negatively correlated with antimicrobial resistance gene levels, reflecting a composition shift in the gut microbiome, likely driven by the changing need for microbial carbohydrate metabolism during early life.}, }
@article {pmid38880617, year = {2024}, author = {Miyoshi, SI and Amako, K and Muraoka, M and Morinaga, H and Ueba, S}, title = {Mobile genetic elements associated with utilization of dichloromethane and methanol as energy sources in Cupriavidus metallidurans.}, journal = {Journal of microorganism control}, volume = {29}, number = {2}, pages = {55-65}, doi = {10.4265/jmc.29.2_55}, pmid = {38880617}, issn = {2758-6391}, mesh = {*Methanol/metabolism ; *Cupriavidus/genetics/metabolism/drug effects ; *Methylene Chloride/metabolism ; *Interspersed Repetitive Sequences/genetics ; Energy Metabolism/drug effects/genetics ; Genome, Bacterial/genetics ; Gene Transfer, Horizontal ; }, abstract = {Cupriavidus metallidurans strain PD11 isolated from laboratory waste drainage can use C1 compounds, such as dichloromethane (DCM) and methanol, as a sole carbon and energy source. However, strain CH34 (a type-strain) cannot grow in the medium supplemented with DCM. In the present study, we aimed to unravel the genetic elements underlying the utilization of C1 compounds by strain PD11. The genome subtraction approach indicated that only strain PD11 had several genes highly homologous to those of Herminiimonas arsenicoxydans strain ULPAs1. Moreover, a series of polymerase chain reaction (PCR) to detect the orthologs of H. arsenicoxydans genes and the comparative study of the genomes of three strains revealed that the 87.9 kb DNA fragment corresponding to HEAR1959 to HEAR2054 might be horizontally transferred to strain PD11. The 87.9 kb DNA fragment identified was found to contain three genes whose products were putatively involved in the metabolism of formaldehyde, a common intermediate of DCM and methanol. In addition, reverse transcription PCR analysis showed that all three genes were significantly expressed when strain PD11 was cultivated in the presence of DCM or methanol. These findings suggest that strain PD11 can effectively utilize the C1 compounds because of transfer of the mobile genetic elements from other bacterial species, for instance, from H. arsenicoxydans.}, }
@article {pmid38880337, year = {2024}, author = {Sugimoto, TN and Jouraku, A and Mitsuhashi, W}, title = {Search for genes gained by horizontal gene transfer in an entomopoxvirus, with special reference to the analysis of the transfer of an ABC transporter gene.}, journal = {Virus research}, volume = {347}, number = {}, pages = {199418}, pmid = {38880337}, issn = {1872-7492}, mesh = {*Gene Transfer, Horizontal ; Animals ; *ATP-Binding Cassette Transporters/genetics/metabolism ; *Open Reading Frames ; *Entomopoxvirinae/genetics ; Coleoptera/virology/genetics ; Phylogeny ; Genes, Viral ; Genome, Viral ; Evolution, Molecular ; Viral Proteins/genetics/metabolism ; }, abstract = {Although it is generally believed that large DNA viruses capture genes by horizontal gene transfer (HGT), the detailed manner of such transfer has not been fully elucidated. Here, we searched for genes in the coleopteran entomopoxvirus (EV) Anomala cuprea entomopoxvirus (ACEV) that might have been gained by ACEV by HGT. We classified the potential source organisms for HGT into three categories: the host A. cuprea; other organisms, including viruses unrelated to EVs; and organisms with uncertain host attribution. Of the open reading frames (ORFs) of the ACEV genome, 2.1 % were suggested to have been gained from the host by ACEV or its recent ancestor via HGT; 8.7 % were possibly from organisms other than the host, and 3.7 % were possibly from the third category of organisms via HGT. The analysis showed that ACEV contains some interesting ORFs obtained by HGT, including a large ATP-binding cassette protein (ABC transporter) ORF and a tenascin ORF (IDs ACV025 and ACV123, respectively). We then performed a detailed analysis of the HGT of the ACEV large ABC transporter ORF-the largest of the ACEV ORFs. mRNA sequences obtained by RNA-seq from fat bodies-sites of ACEV replication-and midgut tissues-sites of initial infection-of the virus's host A. cuprea larvae were subjected to BLAST analysis. One type of ABC transporter ORF from the fat bodies and two types from the midgut tissues, one of which was identical to that in the fat bodies, had the greatest identity to the ABC transporter ORF of ACEV. The two types from the host had high levels of identity to each other (approximately 95 % nucleotide sequence identity), strongly suggesting that the host ABC transporter group consisting of the two types was the origin of ACV025. We then determined the sequence (12,381 bp) containing a full-length gene of the A. cuprea ABC transporter. It turned out to be a transcription template for the abovementioned mRNA found in both tissues. In addition, we determined a large part (ca. 6.9 kb) of the template sequence for the mRNA found only in the midgut tissues. The results showed that the ACEV ABC transporter ORF is missing parts corresponding to introns of the host ABC transporter genes, indicating that the ORF was likely acquired by HGT in the form of mRNA. The presence of definite duplicated sequences adjacent to the ACEV ABC transporter genes-a sign of LINE-1 retrotransposon-mediated HGT-was not observed. An approximately 2-month ACV025 transcription experiment suggested that the transporter sequence is presumed to be continuously functional. The amino acid sequence of ACV025 suggests that its product might function in the regulation of phosphatide in the host-cell membranes.}, }
@article {pmid38878503, year = {2024}, author = {Hu, Q and Zhang, L and Yang, R and Tang, J and Dong, G}, title = {Quaternary ammonium biocides promote conjugative transfer of antibiotic resistance gene in structure- and species-dependent manner.}, journal = {Environment international}, volume = {189}, number = {}, pages = {108812}, doi = {10.1016/j.envint.2024.108812}, pmid = {38878503}, issn = {1873-6750}, mesh = {*Disinfectants/pharmacology ; *Quaternary Ammonium Compounds/pharmacology ; *Escherichia coli/drug effects/genetics ; *Conjugation, Genetic ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; }, abstract = {The linkage between biocides and antibiotic resistance has been widely suggested in laboratories and various environments. However, the action mechanism of biocides on antibiotic resistance genes (ARGs) spread is still unclear. Thus, 6 quaternary ammonium biocides (QACs) with different bonded substituents or alkyl chain lengths were selected to assess their effects on the conjugation transfer of ARGs in this study. Two conjugation models with the same donor (E. coli DH5α (RP4)) into two receptors, E. coli MG1655 and pathogenic S. sonnei SE6-1, were constructed. All QACs were found to significantly promote intra- and inter-genus conjugative transfer of ARGs, and the frequency was highly impacted by their structure and receptors. At the same environmental exposure level (4 × 10[-1] mg/L), didecyl dimethyl ammonium chloride (DDAC (C10)) promoted the most frequency of conjugative transfer, while benzathine chloride (BEC) promoted the least. With the same donor, the enhanced frequency of QACs of intra-transfer is higher than inter-transfer. Then, the acquisition mechanisms of two receptors were further determined using biochemical combined with transcriptome analysis. For the recipient E. coli, the promotion of the intragenus conjugative transfer may be associated with increased cell membrane permeability, reactive oxygen species (ROS) production and proton motive force (PMF)-induced enhancement of flagellar motility. Whereas, the increase of cell membrane permeability and decreased flagellar motility due to PMF disruption but encouraged biofilm formation, maybe the main reasons for promoting intergenus conjugative transfer in the recipient S. sonnei. As one pathogenic bacterium, S. sonnei was first found to acquire ARGs by biocide exposure.}, }
@article {pmid38878444, year = {2024}, author = {Li, W and Zeng, J and Zheng, N and Ge, C and Li, Y and Yao, H}, title = {Polyvinyl chloride microplastics in the aquatic environment enrich potential pathogenic bacteria and spread antibiotic resistance genes in the fish gut.}, journal = {Journal of hazardous materials}, volume = {475}, number = {}, pages = {134817}, doi = {10.1016/j.jhazmat.2024.134817}, pmid = {38878444}, issn = {1873-3336}, mesh = {Animals ; *Microplastics/toxicity ; *Polyvinyl Chloride ; *Water Pollutants, Chemical/toxicity ; *Oxytetracycline/toxicity ; *Carps/microbiology ; *Anti-Bacterial Agents/pharmacology/toxicity ; Gastrointestinal Microbiome/drug effects ; Bacteria/drug effects/genetics ; Sulfamethazine/toxicity ; Genes, Bacterial/drug effects ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics/drug effects ; }, abstract = {Microplastics and antibiotics coexist in aquatic environments, especially in freshwater aquaculture areas. However, as the second largest production of polyvinyl chloride (PVC) in the world, the effects of co-exposure to microplastics particles and antibiotics on changes in antibiotic resistance gene (ARG) profiles and the microbial community structure of aquatic organism gut microorganisms are poorly understood. Therefore, in this study, carp (Cyprinus carpio) were exposed to single or combined PVC microplastic contamination and oxytetracycline (OTC) or sulfamethazine (SMZ) for 8 weeks. PVC microplastics can enrich potential pathogenic bacteria, such as Enterobacter and Acinetobacter, among intestinal microorganisms. The presence of PVC microplastics enhanced the selective enrichment and dissemination risk of ARGs. PVC microplastics combined with OTC (OPVC) treatment significantly increased the abundance of tetracycline resistance genes (1.40-fold) compared with that in the OTC exposure treatment, revealing an obvious co-selection effect. However, compared with those in the control group, the total abundance of ARGs and MGEs in the OPVC treatment groups were significantly lower, which was correlated with the reduced abundances of the potential host Enterobacter. Overall, our results emphasized the diffusion and spread of ARGs are more influenced by PVC microplastics than by antibiotics, which may lead to antibiotic resistance in aquaculture.}, }
@article {pmid38878442, year = {2024}, author = {Ma, Y and Xu, S and Huang, Y and Du, J and Wang, J and Gao, B and Song, J and Ma, S and Jia, H and Zhan, S}, title = {The mechanism differences between sulfadiazine degradation and antibiotic resistant bacteria inactivation by iron-based graphitic biochar and peroxydisulfate system.}, journal = {Journal of hazardous materials}, volume = {475}, number = {}, pages = {134907}, doi = {10.1016/j.jhazmat.2024.134907}, pmid = {38878442}, issn = {1873-3336}, mesh = {*Charcoal/chemistry ; *Sulfadiazine/chemistry ; *Anti-Bacterial Agents/chemistry/pharmacology ; *Iron/chemistry/metabolism ; *Graphite/chemistry ; *Sulfates/chemistry/metabolism ; Water Pollutants, Chemical/chemistry ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Bacteria/metabolism/drug effects/genetics ; Water Purification/methods ; Peroxides/chemistry ; }, abstract = {In this study, the activation of peroxydisulfate (PS) by K2FeO4-activation biochar (KFeB) and acid-picking K2FeO4-activation biochar (AKFeB) was investigated to reveal the mechanism differences between iron site and graphitic structure in sulfadiazine (SDZ) degradation and ARB inactivation, respectively. KFeB/PS and AKFeB/PS systems had similar degradation property towards SDZ, but only KFeB/PS system showed excellent bactericidal property. The mechanism study demonstrated that dissolved SDZ was degraded through electron transfer pathway mediated by graphitic structure, while suspended ARB was inactivated through free radicals generated by iron-activated PS, accompanied by excellent removal on antibiotic resistance genes (ARGs). The significant decrease in conjugative transfer frequency indicated the reduced horizontal gene transfer risk of ARGs after treatment with KFeB/PS system. Transcriptome data suggested that membrane protein channel disruption and adenosine triphosphate synthesis inhibition were key reasons for conjugative transfer frequency reduction. Continuous flow reactor of KFeB/PS system can efficiently remove antibiotics and ARB, implying the potential application in practical wastewater purification. In conclusion, this study provides novel insights for classified and collaborative control of antibiotics and ARB by carbon-based catalysts driven persulfate advanced oxidation technology.}, }
@article {pmid38878435, year = {2024}, author = {Zhang, X and Ma, L and Zhang, XX}, title = {Neglected risks of enhanced antimicrobial resistance and pathogenicity in anaerobic digestion during transition from thermophilic to mesophilic.}, journal = {Journal of hazardous materials}, volume = {475}, number = {}, pages = {134886}, doi = {10.1016/j.jhazmat.2024.134886}, pmid = {38878435}, issn = {1873-3336}, mesh = {Anaerobiosis ; *Drug Resistance, Bacterial/genetics ; Temperature ; Methane/metabolism ; Bacteria/genetics/pathogenicity/metabolism/drug effects ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Virulence Factors/genetics ; Gene Transfer, Horizontal ; Enterobacteriaceae/genetics/pathogenicity/drug effects/metabolism ; Genes, Bacterial ; }, abstract = {Minimization of antibiotic resistance genes (ARGs) and potential pathogenic antibiotic-resistant bacteria (PARB) during anaerobic digestion (AD) is significantly impacted by temperature. However, knowledge on how ARGs and PARB respond to temperature transition from thermophilic to mesophilic is limited. Here, we combined metagenomic-based with culture-based approaches and revealed the risks of antimicrobial resistance and pathogenicity during transition from 55 °C to 35 °C for AD, with strategies of sharp (ST, one-step by 20 °C/d) and mild (MT, step-wise by 1 °C/d). Results indicated a lower decrease in methane production with MT (by 38.9%) than ST (by 88.8%). Phenotypic assays characterized a significant propagation of multi-resistant lactose-fermenting Enterobacteriaceae and indicator pathogens after both transitions, especially via ST. Further genomic evidence indicated a significant increase of ARGs (29.4-fold), virulence factor genes (1.8-fold) and PARB (65.3-fold) after ST, while slight enrichment via MT. Bacterial succession and enhanced horizontal transfer mediated by mobile genetic elements promoted ARG propagation in AD during transition, which was synchronously exacerbated through horizontal transfer mechanisms mediated by cellular physiological responses (oxidative stress, membrane permeability, bacterial conjugation and transformation) and co-selection mechanisms of biomethanation metabolic functions (acidogenesis and acetogenesis). This study reveals temperature-dependent resistome and pathogenicity development in AD, facilitating microbial risk control.}, }
@article {pmid38878434, year = {2024}, author = {Chen, MM and Zhang, YQ and Cheng, LC and Zhao, FJ and Wang, P}, title = {Photoaged nanoplastics with multienzyme-like activities significantly shape the horizontal transfer of antibiotic resistance genes.}, journal = {Journal of hazardous materials}, volume = {475}, number = {}, pages = {134884}, doi = {10.1016/j.jhazmat.2024.134884}, pmid = {38878434}, issn = {1873-3336}, mesh = {*Gene Transfer, Horizontal ; *Escherichia coli/genetics/drug effects ; *Plasmids/genetics ; *Reactive Oxygen Species/metabolism ; Nanoparticles/chemistry/toxicity ; Drug Resistance, Microbial/genetics ; Polystyrenes/chemistry ; Sunlight ; Drug Resistance, Bacterial/genetics ; Oxidoreductases/genetics/metabolism ; }, abstract = {Nanoplastics (NPs), identified as emerging pollutants, pose a great risk to environment and global public health, exerting profound influences on the prevalence and dissemination of antibiotic resistance genes (ARGs). Despite evidence suggesting that nano-sized plastic particles can facilitate the horizontal gene transfer (HGT) of ARGs, it is imperative to explore strategies for inhibiting the transfer of ARGs. Currently, limited information exists regarding the characteristics of environmentally aged NPs and their impact on ARGs propagation. Herein, we investigated the impact of photo-aged NPs on the transfer of ARG-carrying plasmids into Escherichia coli (E. coli) cells. Following simulated sunlight irradiation, photo-aged nano-sized polystyrene plastics (PS NPs) exhibited multiple enzyme-like activities, including peroxidase (POD) and oxidase (OXD), leading to a burst of reactive oxygen species (ROS). At relatively low concentrations (0.1, 1 μg/mL), both pristine and aged PS NPs facilitated the transfer of pUC19 and pHSG396 plasmids within E. coli due to moderate ROS production and enhanced cell membrane permeability. Intriguingly, at relatively high concentrations (5, 10 μg/mL), aged PS NPs significantly suppressed plasmids transformation. The non-unidirectional impact of aged PS NPs involved the overproduction of ROS (•OH and •O2[-]) via nanozyme activity, directly degrading ARGs and damaging plasmid structure. Additionally, oxidative damage to bacteria resulted from the presence of much toxic free radicals, causing physical damage to cell membranes, reduction of the SOS response and restriction of adenosine-triphosphate (ATP) supply, ultimately leading to inactivation of recipient cells. This study unveils the intrinsic multienzyme-like activity of environmentally aged NPs, highlighting their potential to impede the transfer and dissemination of ARGs.}, }
@article {pmid38878274, year = {2024}, author = {Vidal-Quist, JC and Ortego, F and Rombauts, S and Hernández-Crespo, P}, title = {The genome-wide response of Dermatophagoides pteronyssinus to cystatin A, a peptidase inhibitor from human skin, sheds light on its digestive physiology and allergenicity.}, journal = {Insect molecular biology}, volume = {33}, number = {6}, pages = {662-677}, doi = {10.1111/imb.12931}, pmid = {38878274}, issn = {1365-2583}, mesh = {Animals ; *Dermatophagoides pteronyssinus/immunology ; *Cystatin A/metabolism/genetics ; Antigens, Dermatophagoides/immunology ; Arthropod Proteins/genetics/metabolism/immunology ; Digestion ; Humans ; Allergens/immunology ; Skin/metabolism/immunology ; }, abstract = {The digestive physiology of house dust mites (HDMs) is particularly relevant for their allergenicity since many of their allergens participate in digestion and are excreted into faecal pellets, a main source of exposure for allergic subjects. To gain insight into the mite dietary digestion, the genome of the HDM Dermatophagoides pteronyssinus was screened for genes encoding peptidases (n = 320), glycosylases (n = 77), lipases and esterases (n = 320), peptidase inhibitors (n = 65) and allergen-related proteins (n = 52). Basal gene expression and transcriptional responses of mites to dietary cystatin A, a cysteine endopeptidase inhibitor with previously shown antinutritional effect on mites, were analysed by RNAseq. The ingestion of cystatin A resulted in significant regulation of different cysteine endopeptidase and glycosylase genes. One Der p 1-like and two cathepsin B-like cysteine endopeptidase genes of high basal expression were induced, which suggests their prominent role in proteolytic digestion together with major allergen Der p 1. A number of genes putatively participating in the interaction of mites with their microbiota and acquired by horizontal gene transfer were repressed, including genes encoding the peptidase Der p 38, two 1,3-beta-glucanases, a lysozyme and a GH19 chitinase. Finally, the disruption of mite digestion resulted in the regulation of up to 17 allergen and isoallergen genes. Altogether, our results shed light on the putative role of specific genes in digestion and illustrate the connection between the digestive physiology of HDM and allergy.}, }
@article {pmid38876022, year = {2024}, author = {Sivalingam, P and Sabatino, R and Sbaffi, T and Corno, G and Fontaneto, D and Borgomaneiro, G and Rogora, M and Crotti, E and Mapelli, F and Borin, S and Pilar, AL and Eckert, EM and Di Cesare, A}, title = {Anthropogenic pollution may enhance natural transformation in water, favouring the spread of antibiotic resistance genes.}, journal = {Journal of hazardous materials}, volume = {475}, number = {}, pages = {134885}, doi = {10.1016/j.jhazmat.2024.134885}, pmid = {38876022}, issn = {1873-3336}, mesh = {*Wastewater/microbiology ; Drug Resistance, Microbial/genetics ; Lakes/microbiology ; Genes, Bacterial/drug effects ; Water Pollution ; Water Microbiology ; Microbiota/drug effects ; Anti-Bacterial Agents/pharmacology ; Plasmids/genetics ; Drug Resistance, Bacterial/genetics ; Bacteria/drug effects/genetics/classification ; }, abstract = {Aquatic ecosystems are crucial in the antimicrobial resistance cycle. While intracellular DNA has been extensively studied to understand human activity's impact on antimicrobial resistance gene (ARG) dissemination, extracellular DNA is frequently overlooked. This study examines the effect of anthropogenic water pollution on microbial community diversity, the resistome, and ARG dissemination. We analyzed intracellular and extracellular DNA from wastewater treatment plant effluents and lake surface water by shotgun sequencing. We also conducted experiments to evaluate anthropogenic pollution's effect on transforming extracellular DNA (using Gfp-plasmids carrying ARGs) within a natural microbial community. Chemical analysis showed treated wastewater had higher anthropogenic pollution-related parameters than lake water. The richness of microbial community, antimicrobial resistome, and high-risk ARGs was greater in treated wastewaters than in lake waters both for intracellular and extracellular DNA. Except for the high-risk ARGs, richness was significantly higher in intracellular than in extracellular DNA. Several ARGs were associated with mobile genetic elements and located on plasmids. Furthermore, Gfp-plasmid transformation within a natural microbial community was enhanced by anthropogenic pollution levels. Our findings underscore anthropogenic pollution's pivotal role in shaping microbial communities and their antimicrobial resistome. Additionally, it may facilitate ARG dissemination through extracellular DNA plasmid uptake.}, }
@article {pmid38871331, year = {2024}, author = {Wang, X and Li, J and Pan, X}, title = {How micro-/nano-plastics influence the horizontal transfer of antibiotic resistance genes - A review.}, journal = {The Science of the total environment}, volume = {944}, number = {}, pages = {173881}, doi = {10.1016/j.scitotenv.2024.173881}, pmid = {38871331}, issn = {1879-1026}, mesh = {*Gene Transfer, Horizontal ; *Plastics ; *Drug Resistance, Microbial/genetics ; *Microplastics ; }, abstract = {Plastic debris such as microplastics (MPs) and nanoplastics (NPTs), along with antibiotic resistance genes (ARGs), are pervasive in the environment and are recognized as significant global health and ecological concerns. Micro-/nano-plastics (MNPs) have been demonstrated to favor the spread of ARGs by enhancing the frequency of horizontal gene transfer (HGT) through various pathways. This paper comprehensively and systematically reviews the current study with focus on the influence of plastics on the HGT of ARGs. The critical role of MNPs in the HGT of ARGs has been well illustrated in sewage sludge, livestock farms, constructed wetlands and landfill leachate. A summary of the performed HGT assay and the underlying mechanism of plastic-mediated transfer of ARGs is presented in the paper. MNPs could facilitate or inhibit HGT of ARGs, and their effects depend on the type, size, and concentration. This review provides a comprehensive insight into the effects of MNPs on the HGT of ARGs, and offers suggestions for further study. Further research should attempt to develop a standard HGT assay and focus on investigating the impact of different plastics, including the oligomers they released, under real environmental conditions on the HGT of ARGs.}, }
@article {pmid38871190, year = {2024}, author = {Skalny, M and Rokowska, A and Szuwarzynski, M and Gajewska, M and Dziewit, L and Bajda, T}, title = {Nanoscale surface defects of goethite governing DNA adsorption process and formation of the Goethite-DNA conjugates.}, journal = {Chemosphere}, volume = {362}, number = {}, pages = {142602}, doi = {10.1016/j.chemosphere.2024.142602}, pmid = {38871190}, issn = {1879-1298}, mesh = {*Iron Compounds/chemistry ; Adsorption ; *Minerals/chemistry ; *DNA/chemistry ; Porosity ; Particle Size ; }, abstract = {In urbanized areas, extracellular DNA (exDNA) is suspected of carrying genes with undesirable traits like virulence genes (VGs) or antibiotic resistance genes (ARGs), which can spread through horizontal gene transfer (HGT). Hence, it is crucial to develop novel approaches for the mitigation of exDNA in the environment. Our research explores the role of goethite, a common iron mineral with high adsorption capabilities, in exDNA adsorption processes. We compare well-crystalline, semi-crystalline, and nano goethites with varying particle sizes to achieve various specific surface areas (SSAs) (18.7-161.6 m[2]/g) and porosities. We conducted batch adsorption experiments using DNA molecules of varying chain lengths (DNA sizes: <11 Kb, <6 Kb, and <3 Kb) and assessed the impact of Ca[2+] and biomacromolecules on the adsorption efficacy and mechanisms. Results show that porosity and pore structure significantly influence DNA adsorption capacity. Goethite with well-developed meso- and macroporosity demonstrated enhanced DNA adsorption. The accumulation of DNA on the goethite interface led to substantial aggregation in the system, thus the formation of DNA-goethite conjugates, indicating the bridging between mineral particles. DNA chain length, the presence of Ca[2+], and the biomacromolecule matrix also affected the adsorption capacity and mechanism. Interactions between DNA and positively charged biomacromolecules or Ca[2+] led to DNA compaction, allowing greater DNA accumulation in pores. However, a high concentration of biomacromolecules led to the saturation of the goethite surface, inhibiting DNA adsorption. AFM imaging of goethite particles after adsorption suggested the formation of the DNA multilayer. The study advances understanding of the environmental behavior of exDNA and its interaction with iron oxyhydroxides, offering insights into developing more effective methods for ARGs removal in wastewater treatment plants. By manipulating the textural properties of goethite, it's possible to enhance exDNA removal, potentially reducing the spread of biocontamination in urban and industrial environments.}, }
@article {pmid38870897, year = {2024}, author = {Kennedy, NW and Comstock, LE}, title = {Mechanisms of bacterial immunity, protection, and survival during interbacterial warfare.}, journal = {Cell host &amp; microbe}, volume = {32}, number = {6}, pages = {794-803}, pmid = {38870897}, issn = {1934-6069}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; R01 AI093771/AI/NIAID NIH HHS/United States ; T32 DK007074/DK/NIDDK NIH HHS/United States ; }, mesh = {*Bacteria/immunology/genetics ; *Bacterial Toxins/metabolism/immunology ; Gene Transfer, Horizontal ; Humans ; Microbial Viability ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/metabolism/genetics ; }, abstract = {Most bacteria live in communities, often with closely related strains and species with whom they must compete for space and resources. Consequently, bacteria have acquired or evolved mechanisms to antagonize competitors through the production of antibacterial toxins. Similar to bacterial systems that combat phage infection and mechanisms to thwart antibiotics, bacteria have also acquired and evolved features to protect themselves from antibacterial toxins. Just as there is a large body of research identifying and characterizing antibacterial proteins and toxin delivery systems, studies of bacterial mechanisms to resist and survive assault from competitors' weapons have also expanded tremendously. Emerging data are beginning to reveal protective processes and mechanisms that are as diverse as the toxins themselves. Protection against antibacterial toxins can be acquired by horizontal gene transfer, receptor or target alteration, induction of protective functions, physical barriers, and other diverse processes. Here, we review recent studies in this rapidly expanding field.}, }
@article {pmid38870889, year = {2024}, author = {Zhang, P and Wang, Y and Lin, H and Liang, J and Wang, J and Bai, Y and Qu, J and Wang, A}, title = {Bacterial evolution in Biofiltration of drinking water treatment plant: Different response of phage and plasmid to varied water sources.}, journal = {Water research}, volume = {259}, number = {}, pages = {121887}, doi = {10.1016/j.watres.2024.121887}, pmid = {38870889}, issn = {1879-2448}, mesh = {*Plasmids ; *Drinking Water/microbiology ; *Water Purification ; *Bacteriophages/genetics ; *Bacteria ; Filtration ; Gene Transfer, Horizontal ; Groundwater ; }, abstract = {Biofiltration in drinking water treatment (BDWT) are popular as it holds promise as an alternative to chemical treatments, yet our understanding of the key drivers and trends underlying bacterial evolution within this process remains limited. While plasmids and phages are recognized as the main vectors of horizontal gene transfer (HGT), their roles in shaping bacterial evolution in BDWT remain largely unknown. Here we leverage global metagenomic data to unravel the primary forces driving bacterial evolution in BDWT. Our results revealed that the primary vector of HGT varies depending on the type of source water (groundwater and surface water). Both plasmids and phages accelerated bacterial evolution in BDWT by enhancing genetic diversity within species, but they drove contrasting evolutionary trends in functional redundancy in different source water types. Specifically, trends towards and away from functional redundancy (indicated as gene-protein ratio) were observed in surface-water and groundwater biofilters, respectively. Virulent phages drove bacterial evolution through synergistic interactions with bacterial species capable of natural transformation and with certain natural compounds that disrupt bacterial cytoplasmic membranes. Genes relating to water purification (such as Mn(II)-oxidizing genes), microbial risks (antibiotic resistance genes), and chemical risk (polycyclic aromatic hydrocarbons) were enriched via HGT in BDWT, highlighting the necessity for heighted focus on these useful and risky objects. Overall, these discoveries enhance our understanding of bacterial evolution in BDWT and have implications for the optimization of water treatment strategies.}, }
@article {pmid38867468, year = {2024}, author = {Qi, L and Wang, W and Fang, L and Li, J and Qi, L and Wang, D and Liu, J and Xiao, Y and Zhou, W and Fang, X}, title = {DNA Molecular Glue Assisted Bacterial Conjugative Transfer.}, journal = {Chemistry (Weinheim an der Bergstrasse, Germany)}, volume = {30}, number = {52}, pages = {e202401399}, doi = {10.1002/chem.202401399}, pmid = {38867468}, issn = {1521-3765}, support = {2022YFA1304500,2022YFC3401003//the National Key Scientific Program of China/ ; Nos. 21735006//National Natural Science Foundation of China/ ; Nos.21890742//National Natural Science Foundation of China/ ; }, mesh = {*Escherichia coli/genetics ; *Conjugation, Genetic ; *DNA, Single-Stranded/chemistry ; Click Chemistry ; Gene Transfer, Horizontal ; Oligonucleotides/chemistry ; }, abstract = {Bacterial conjugation, a commonly used method to horizontally transfer functional genes from donor to recipient strains, plays an important role in the genetic manipulation of bacteria for basic research and industrial production. Successful conjugation depends on the donor-recipient cell recognition and a tight mating junction formation. However, the efficiency of conjugative transfer is usually very low. In this work, we developed a new technique that employed DNA molecule "glue" to increase the match frequency and the interaction stability between the donor and recipient cells. We used two E. coli strains, ETZ and BL21, as a model system, and modified them with the complementary ssDNA oligonucleotides by click chemistry. The conjugation efficiency of the modified bacteria was improved more than 4 times from 10 %-46 %. This technique is simple and generalizable as it only relies on the active amino groups on the bacterial surface. It is expected to have broad applications in constructing engineered bacteria.}, }
@article {pmid38861577, year = {2024}, author = {Elsen, S and Simon, V and Attrée, I}, title = {Cross-regulation and cross-talk of conserved and accessory two-component regulatory systems orchestrate Pseudomonas copper resistance.}, journal = {PLoS genetics}, volume = {20}, number = {6}, pages = {e1011325}, pmid = {38861577}, issn = {1553-7404}, mesh = {*Copper/metabolism ; *Pseudomonas/genetics/metabolism ; *Gene Expression Regulation, Bacterial ; *Operon/genetics ; *Bacterial Proteins/genetics/metabolism ; Drug Resistance, Bacterial/genetics ; Signal Transduction/genetics ; }, abstract = {Bacteria use diverse strategies and molecular machinery to maintain copper homeostasis and to cope with its toxic effects. Some genetic elements providing copper resistance are acquired by horizontal gene transfer; however, little is known about how they are controlled and integrated into the central regulatory network. Here, we studied two copper-responsive systems in a clinical isolate of Pseudomonas paraeruginosa and deciphered the regulatory and cross-regulation mechanisms. To do so, we combined mutagenesis, transcriptional fusion analyses and copper sensitivity phenotypes. Our results showed that the accessory CusRS two-component system (TCS) responds to copper and activates both its own expression and that of the adjacent nine-gene operon (the pcoA2 operon) to provide resistance to elevated levels of extracellular copper. The same locus was also found to be regulated by two core-genome-encoded TCSs-the copper-responsive CopRS and the zinc-responsive CzcRS. Although the target palindromic sequence-ATTCATnnATGTAAT-is the same for the three response regulators, transcriptional outcomes differ. Thus, depending on the operon/regulator pair, binding can result in different activation levels (from none to high), with the systems demonstrating considerable plasticity. Unexpectedly, although the classical CusRS and the noncanonical CopRS TCSs rely on distinct signaling mechanisms (kinase-based vs. phosphatase-based), we discovered cross-talk in the absence of the cognate sensory kinases. This cross-talk occurred between the proteins of these two otherwise independent systems. The cusRS-pcoA2 locus is part of an Integrative and Conjugative Element and was found in other Pseudomonas strains where its expression could provide copper resistance under appropriate conditions. The results presented here illustrate how acquired genetic elements can become part of endogenous regulatory networks, providing a physiological advantage. They also highlight the potential for broader effects of accessory regulatory proteins through interference with core regulatory proteins.}, }
@article {pmid38853947, year = {2024}, author = {Wendt, G and Collins, JJ}, title = {Horizontal gene transfer of a functional cki homolog in the human pathogen Schistosoma mansoni.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38853947}, issn = {2692-8205}, support = {HHSN272201700014C/AI/NIAID NIH HHS/United States ; R01 AI121037/AI/NIAID NIH HHS/United States ; R01 AI150776/AI/NIAID NIH HHS/United States ; }, abstract = {Schistosomes are parasitic flatworms responsible for the neglected tropical disease schistosomiasis, causing devastating morbidity and mortality in the developing world. The parasites are protected by a skin-like tegument, and maintenance of this tegument is controlled by a schistosome ortholog of the tumor suppressor TP53. To understand mechanistically how p53-1 controls tegument production, we identified a cyclin dependent kinase inhibitor homolog (cki) that was co-expressed with p53-1. RNA interference of cki resulted in a hyperproliferation phenotype, that, in combination with p53-1 RNA interference yielded abundant tumor-like growths, indicating that cki and p53-1 are bona fide tumor suppressors in Schistosoma mansoni. Interestingly, cki homologs are widely present throughout parasitic flatworms but evidently absent from their free-living ancestors, suggesting this cki homolog came from an ancient horizontal gene transfer event. This in turn implies that the evolution of parasitism in flatworms may have been aided by a highly unusual means of metazoan genetic inheritance.}, }
@article {pmid38843310, year = {2024}, author = {Coelho, MA and David-Palma, M and Shea, T and Bowers, K and McGinley-Smith, S and Mohammad, AW and Gnirke, A and Yurkov, AM and Nowrousian, M and Sun, S and Cuomo, CA and Heitman, J}, title = {Comparative genomics of the closely related fungal genera Cryptococcus and Kwoniella reveals karyotype dynamics and suggests evolutionary mechanisms of pathogenesis.}, journal = {PLoS biology}, volume = {22}, number = {6}, pages = {e3002682}, pmid = {38843310}, issn = {1545-7885}, support = {R01 AI039115/AI/NIAID NIH HHS/United States ; R01 AI050113/AI/NIAID NIH HHS/United States ; U19 AI110818/AI/NIAID NIH HHS/United States ; U54 HG003067/HG/NHGRI NIH HHS/United States ; }, mesh = {*Cryptococcus/genetics/pathogenicity/classification ; *Chromosomes, Fungal/genetics ; *Genome, Fungal ; *Karyotype ; *Genomics/methods ; *Evolution, Molecular ; Phylogeny ; Synteny ; Centromere/genetics ; Cryptococcosis/microbiology ; Humans ; }, abstract = {In exploring the evolutionary trajectories of both pathogenesis and karyotype dynamics in fungi, we conducted a large-scale comparative genomic analysis spanning the Cryptococcus genus, encompassing both global human fungal pathogens and nonpathogenic species, and related species from the sister genus Kwoniella. Chromosome-level genome assemblies were generated for multiple species, covering virtually all known diversity within these genera. Although Cryptococcus and Kwoniella have comparable genome sizes (about 19.2 and 22.9 Mb) and similar gene content, hinting at preadaptive pathogenic potential, our analysis found evidence of gene gain (via horizontal gene transfer) and gene loss in pathogenic Cryptococcus species, which might represent evolutionary signatures of pathogenic development. Genome analysis also revealed a significant variation in chromosome number and structure between the 2 genera. By combining synteny analysis and experimental centromere validation, we found that most Cryptococcus species have 14 chromosomes, whereas most Kwoniella species have fewer (11, 8, 5, or even as few as 3). Reduced chromosome number in Kwoniella is associated with formation of giant chromosomes (up to 18 Mb) through repeated chromosome fusion events, each marked by a pericentric inversion and centromere loss. While similar chromosome inversion-fusion patterns were observed in all Kwoniella species with fewer than 14 chromosomes, no such pattern was detected in Cryptococcus. Instead, Cryptococcus species with less than 14 chromosomes showed reductions primarily through rearrangements associated with the loss of repeat-rich centromeres. Additionally, Cryptococcus genomes exhibited frequent interchromosomal translocations, including intercentromeric recombination facilitated by transposons shared between centromeres. Overall, our findings advance our understanding of genetic changes possibly associated with pathogenicity in Cryptococcus and provide a foundation to elucidate mechanisms of centromere loss and chromosome fusion driving distinct karyotypes in closely related fungal species, including prominent global human pathogens.}, }
@article {pmid38842312, year = {2024}, author = {Klepa, MS and diCenzo, GC and Hungria, M}, title = {Comparative genomic analysis of Bradyrhizobium strains with natural variability in the efficiency of nitrogen fixation, competitiveness, and adaptation to stressful edaphoclimatic conditions.}, journal = {Microbiology spectrum}, volume = {12}, number = {7}, pages = {e0026024}, pmid = {38842312}, issn = {2165-0497}, support = {465133/2014-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; 043/2019//Funda&#xe7;&#xe3;o Arauc&#xe1;ria-STI/ ; RGPIN-2020-07000//Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; //Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior (CAPES)/ ; FR71100//Mitacs (Mitacs Canada)/ ; }, mesh = {*Bradyrhizobium/genetics/classification/isolation &amp; purification ; *Nitrogen Fixation/genetics ; Brazil ; *Phylogeny ; *Glycine max/microbiology ; *Symbiosis/genetics ; *Genome, Bacterial ; Genetic Variation ; Adaptation, Physiological/genetics ; Root Nodules, Plant/microbiology ; Soil Microbiology ; Genomics ; }, abstract = {Bradyrhizobium is known for fixing atmospheric nitrogen in symbiosis with agronomically important crops. This study focused on two groups of strains, each containing eight natural variants of the parental strains, Bradyrhizobium japonicum SEMIA 586 (=CNPSo 17) or Bradyrhizobium diazoefficiens SEMIA 566 (=CNPSo 10). CNPSo 17 and CNPSo 10 were used as commercial inoculants for soybean crops in Brazil at the beginning of the crop expansion in the southern region in the 1960s-1970s. Variants derived from these parental strains were obtained in the late 1980s through a strain selection program aimed at identifying elite strains adapted to a new cropping frontier in the central-western Cerrado region, with a higher capacity of biological nitrogen fixation (BNF) and competitiveness. Here, we aimed to detect genetic variations possibly related to BNF, competitiveness for nodule occupancy, and adaptation to the stressful conditions of the Brazilian Cerrado soils. High-quality genome assemblies were produced for all strains. The core genome phylogeny revealed that strains of each group are closely related, as confirmed by high average nucleotide identity values. However, variants accumulated divergences resulting from horizontal gene transfer, genomic rearrangements, and nucleotide polymorphisms. The B. japonicum group presented a larger pangenome and a higher number of nucleotide polymorphisms than the B. diazoefficiens group, possibly due to its longer adaptation time to the Cerrado soil. Interestingly, five strains of the B. japonicum group carry two plasmids. The genetic variability found in both groups is discussed considering the observed differences in their BNF capacity, competitiveness for nodule occupancy, and environmental adaptation.IMPORTANCEToday, Brazil is a global leader in the study and use of biological nitrogen fixation with soybean crops. As Brazilian soils are naturally void of soybean-compatible bradyrhizobia, strain selection programs were established, starting with foreign isolates. Selection searched for adaptation to the local edaphoclimatic conditions, higher efficiency of nitrogen fixation, and strong competitiveness for nodule occupancy. We analyzed the genomes of two parental strains of Bradyrhizobium japonicum and Bradyrhizobium diazoefficiens and eight variant strains derived from each parental strain. We detected two plasmids in five strains and several genetic differences that might be related to adaptation to the stressful conditions of the soils of the Brazilian Cerrado biome. We also detected genetic variations in specific regions that may impact symbiotic nitrogen fixation. Our analysis contributes to new insights into the evolution of Bradyrhizobium, and some of the identified differences may be applied as genetic markers to assist strain selection programs.}, }
@article {pmid38839049, year = {2024}, author = {Middlebrook, EA and Katani, R and Fair, JM}, title = {OrthoPhyl-streamlining large-scale, orthology-based phylogenomic studies of bacteria at broad evolutionary scales.}, journal = {G3 (Bethesda, Md.)}, volume = {14}, number = {8}, pages = {}, pmid = {38839049}, issn = {2160-1836}, support = {//Defense Threat Reduction Agency/ ; 89233218CNA000001//Los Alamos National Laboratory/ ; }, mesh = {*Phylogeny ; *Genome, Bacterial ; *Genomics/methods ; *Software ; Bacteria/genetics/classification ; Computational Biology/methods ; Evolution, Molecular ; }, abstract = {There are a staggering number of publicly available bacterial genome sequences (at writing, 2.0 million assemblies in NCBI's GenBank alone), and the deposition rate continues to increase. This wealth of data begs for phylogenetic analyses to place these sequences within an evolutionary context. A phylogenetic placement not only aids in taxonomic classification but informs the evolution of novel phenotypes, targets of selection, and horizontal gene transfer. Building trees from multi-gene codon alignments is a laborious task that requires bioinformatic expertise, rigorous curation of orthologs, and heavy computation. Compounding the problem is the lack of tools that can streamline these processes for building trees from large-scale genomic data. Here we present OrthoPhyl, which takes bacterial genome assemblies and reconstructs trees from whole genome codon alignments. The analysis pipeline can analyze an arbitrarily large number of input genomes (>1200 tested here) by identifying a diversity-spanning subset of assemblies and using these genomes to build gene models to infer orthologs in the full dataset. To illustrate the versatility of OrthoPhyl, we show three use cases: E. coli/Shigella, Brucella/Ochrobactrum and the order Rickettsiales. We compare trees generated with OrthoPhyl to trees generated with kSNP3 and GToTree along with published trees using alternative methods. We show that OrthoPhyl trees are consistent with other methods while incorporating more data, allowing for greater numbers of input genomes, and more flexibility of analysis.}, }
@article {pmid38830804, year = {2024}, author = {Dadeh Amirfard, K and Moriyama, M and Suzuki, S and Sano, D}, title = {Effect of environmental factors on conjugative transfer of antibiotic resistance genes in aquatic settings.}, journal = {Journal of applied microbiology}, volume = {135}, number = {6}, pages = {}, doi = {10.1093/jambio/lxae129}, pmid = {38830804}, issn = {1365-2672}, support = {16H01782//KAKENHI/ ; }, mesh = {*Gene Transfer, Horizontal ; *Anti-Bacterial Agents/pharmacology ; *Conjugation, Genetic ; *Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; Water Microbiology ; Escherichia coli/genetics/drug effects ; Genes, Bacterial ; Acinetobacter/genetics/drug effects ; Biofilms/drug effects ; }, abstract = {Antimicrobial-resistance genes (ARGs) are spread among bacteria by horizontal gene transfer, however, the effect of environmental factors on the dynamics of the ARG in water environments has not been very well understood. In this systematic review, we employed the regression tree algorithm to identify the environmental factors that facilitate/inhibit the transfer of ARGs via conjugation in planktonic/biofilm-formed bacterial cells based on the results of past relevant research. Escherichia coli strains were the most studied genus for conjugation experiments as donor/recipient in the intra-genera category. Conversely, Pseudomonas spp., Acinetobacter spp., and Salmonella spp. were studied primarily as recipients across inter-genera bacteria. The conjugation efficiency (ce) was found to be highly dependent on the incubation period. Some antibiotics, such as nitrofurantoin (at ≥0.2 µg ml-1) and kanamycin (at ≥9.5 mg l-1) as well as metallic compounds like mercury (II) chloride (HgCl2, ≥3 µmol l-1), and vanadium (III) chloride (VCl3, ≥50 µmol l-1) had enhancing effect on conjugation. The highest ce value (-0.90 log10) was achieved at 15°C-19°C, with linoleic acid concentrations <8 mg l-1, a recognized conjugation inhibitor. Identifying critical environmental factors affecting ARG dissemination in aquatic environments will accelerate strategies to control their proliferation and combat antibiotic resistance.}, }
@article {pmid38830497, year = {2024}, author = {Zhang, X and Li, P and Wang, J and Fu, D and Zhao, B and Dong, W and Liu, Y}, title = {Comparative genomic and phylogenetic analyses of mitochondrial genomes of hawthorn (Crataegus spp.) in Northeast China.}, journal = {International journal of biological macromolecules}, volume = {272}, number = {Pt 1}, pages = {132795}, doi = {10.1016/j.ijbiomac.2024.132795}, pmid = {38830497}, issn = {1879-0003}, mesh = {*Crataegus/genetics/classification ; *Genome, Mitochondrial/genetics ; *Phylogeny ; China ; Genomics/methods ; Genome, Plant ; }, abstract = {Hawthorn (Crataegus spp.) plants are major sources of health food and medicines. Twenty species and seven variations of Crataegus are present in China. A variety of unique Crataegus species was found in their natural distribution in northeast China. In the present study, we assembled and annotated the mitochondrial genomes of five Crataegus species from northeastern China. The sizes of the newly sequenced mitochondrial genomes ranged from 245,907 bp to 410,837 bp. A total of 45-55 genes, including 12-19 transfer RNA genes, three ribosomal RNA genes, and 29-33 protein-coding genes (PCGs) were encoded by these mitochondrial genomes. Seven divergent hotspot regions were identified by comparative analyses: atp6, nad3, ccmFN, matR, nad1, nad5, and rps1. The most conserved genes among the Crataegus species, according to the whole-genome correlation analysis, were nad1, matR, nad5, ccmFN, cox1, nad4, trnQ-TTG, trnK-TTT, trnE-TTC, and trnM-CAT. Horizontal gene transfer between organellar genomes was common in Crataegus plants. Based on the phylogenetic trees of mitochondrial PCGs, C. maximowiczii, C. maximowiczii var. ninganensis, and C. bretschneideri shared similar maternal relationships. This study improves Crataegus mitochondrial genome resources and offers important insights into the taxonomy and species identification of this genus.}, }
@article {pmid38830094, year = {2024}, author = {Attah, V and Milner, DS and Fang, Y and Yan, X and Leonard, G and Heitman, J and Talbot, NJ and Richards, TA}, title = {Duplication and neofunctionalization of a horizontally transferred xyloglucanase as a facet of the Red Queen coevolutionary dynamic.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {24}, pages = {e2218927121}, pmid = {38830094}, issn = {1091-6490}, support = {R01 AI039115/AI/NIAID NIH HHS/United States ; PLP-2014-147//Leverhulme Trust/ ; URF/R/191005//Royal Society (The Royal Society)/ ; }, mesh = {*Gene Transfer, Horizontal ; *Glycoside Hydrolases/metabolism/genetics ; *Phylogeny ; Phytophthora/pathogenicity/genetics ; Plant Diseases/microbiology/parasitology ; Evolution, Molecular ; Gene Duplication ; }, abstract = {Oomycete protists share phenotypic similarities with fungi, including the ability to cause plant diseases, but branch in a distant region of the tree of life. It has been suggested that multiple horizontal gene transfers (HGTs) from fungi-to-oomycetes contributed to the evolution of plant-pathogenic traits. These HGTs are predicted to include secreted proteins that degrade plant cell walls, a barrier to pathogen invasion and a rich source of carbohydrates. Using a combination of phylogenomics and functional assays, we investigate the diversification of a horizontally transferred xyloglucanase gene family in the model oomycete species Phytophthora sojae. Our analyses detect 11 xyloglucanase paralogs retained in P. sojae. Using heterologous expression in yeast, we show consistent evidence that eight of these paralogs have xyloglucanase function, including variants with distinct protein characteristics, such as a long-disordered C-terminal extension that can increase xyloglucanase activity. The functional variants analyzed subtend a phylogenetic node close to the fungi-to-oomycete transfer, suggesting the horizontally transferred gene was a bona fide xyloglucanase. Expression of three xyloglucanase paralogs in Nicotiana benthamiana triggers high-reactive oxygen species (ROS) generation, while others inhibit ROS responses to bacterial immunogens, demonstrating that the paralogs differentially stimulate pattern-triggered immunity. Mass spectrometry of detectable enzymatic products demonstrates that some paralogs catalyze the production of variant breakdown profiles, suggesting that secretion of variant xyloglucanases increases efficiency of xyloglucan breakdown as well as diversifying the damage-associated molecular patterns released. We suggest that this pattern of neofunctionalization and the variant host responses represent an aspect of the Red Queen host-pathogen coevolutionary dynamic.}, }
@article {pmid38827508, year = {2024}, author = {Tang, N and Wei, D and Zeng, Y and Zhang, G and Wang, C and Feng, J and Song, Y}, title = {Understanding the rapid spread of antimicrobial resistance genes mediated by IS26.}, journal = {mLife}, volume = {3}, number = {1}, pages = {101-109}, pmid = {38827508}, issn = {2770-100X}, abstract = {Insertion sequences (ISs) promote the transmission of antimicrobial resistance genes (ARGs) across bacterial populations. However, their contributions and dynamics during the transmission of resistance remain unclear. In this study, we selected IS26 as a representative transposable element to decipher the relationship between ISs and ARGs and to investigate their transfer features and transmission trends. We retrieved 2656 translocatable IS 26 -bounded units with ARGs (tIS26-bUs-ARGs) in complete bacterial genomes from the NCBI RefSeq database. In total, 124 ARGs spanning 12 classes of antibiotics were detected, and the average contribution rate of IS26 to these genes was 41.2%. We found that IS 26 -bounded units (IS26-bUs) mediated extensive ARG dissemination within the bacteria of the Gammaproteobacteria class, showing strong transfer potential between strains, species, and even phyla. The IS26-bUs expanded in bacterial populations over time, and their temporal expansion trend was significantly correlated with antibiotic usage. This wide dissemination could be due to the nonspecific target site preference of IS26. Finally, we experimentally confirmed that the introduction of a single copy of IS26 could lead to the formation of a composite transposon mediating the transmission of "passenger" genes. These observations extend our knowledge of the IS26 and provide new insights into the mediating role of ISs in the dissemination of antibiotic resistance.}, }
@article {pmid38823616, year = {2024}, author = {Peng, J and Wang, D and He, P and Wei, P and Zhang, L and Lan, W and Zhang, X and Guan, J and Chen, Y and Li, W and Zheng, Y and Li, Y and Chen, W and Zhao, Z and Jiang, L and Zhou, L}, title = {Seasonal dynamics of antibiotic resistance genes and mobile genetic elements in a subtropical coastal ecosystem: Implications for environmental health risks.}, journal = {Environmental research}, volume = {257}, number = {}, pages = {119298}, doi = {10.1016/j.envres.2024.119298}, pmid = {38823616}, issn = {1096-0953}, mesh = {*Seasons ; China ; *Ecosystem ; *Drug Resistance, Microbial/genetics ; Interspersed Repetitive Sequences ; Environmental Health ; Microbiota/drug effects ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Antibiotic resistance poses a considerable global public health concern, leading to heightened rates of illness and mortality. However, the impact of seasonal variations and environmental factors on the health risks associated with antibiotic resistance genes (ARGs) and their assembly mechanisms is not fully understood. Based on metagenomic sequencing, this study investigated the antibiotic resistome, mobile genetic elements (MGEs), and microbiomes in a subtropical coastal ecosystem of the Beibu Gulf, China, over autumn and winter, and explored the factors influencing seasonal changes in ARG and MGE abundance and diversity. Results indicated that ARG abundance and diversity were higher in winter than in autumn, with beta-lactam and multidrug resistance genes being the most diverse and abundant, respectively. Similarly, MGE abundance and diversity increased in winter and were strongly correlated with ARGs. In contrast, more pronounced associations between microbial communities, especially archaea, and the antibiotic resistome were observed in autumn than in winter. The co-occurrence network identified multiple interactions between MGEs and various multidrug efflux pumps in winter, suggesting a potential for ARG dissemination. Multivariate correlation analyses and path modeling indicated that environmental factors driving microbial community changes predominantly influenced antibiotic resistome assembly in autumn, while the relative importance of MGEs increased significantly in winter. These findings suggest an elevated health risk associated with antimicrobial resistance in the Beibu Gulf during winter, attributed to the dissemination of ARGs by horizontal gene transfer. The observed seasonal variations highlight the dynamic nature of antibiotic resistance dissemination in coastal ecosystems, emphasizing the need for comprehensive surveillance and management measures to address the growing threat of antimicrobial resistance in vulnerable environments.}, }
@article {pmid38823494, year = {2024}, author = {Tang, C and Shen, S and Yang, W and Shi, Q and Ding, L and Han, R and Hu, F}, title = {Dynamic evolution of ceftazidime-avibactam resistance from a single patient through the IncX3_NDM-5 plasmid transfer and blaKPC mutation.}, journal = {International journal of antimicrobial agents}, volume = {64}, number = {2}, pages = {107228}, doi = {10.1016/j.ijantimicag.2024.107228}, pmid = {38823494}, issn = {1872-7913}, mesh = {*Ceftazidime/pharmacology ; *Azabicyclo Compounds/pharmacology ; *Drug Combinations ; *Plasmids/genetics ; Humans ; *Klebsiella pneumoniae/genetics/drug effects ; *beta-Lactamases/genetics ; *Anti-Bacterial Agents/pharmacology ; *Microbial Sensitivity Tests ; *Enterobacter cloacae/genetics/drug effects ; *Mutation ; *Drug Resistance, Multiple, Bacterial/genetics ; Escherichia coli/genetics/drug effects ; Klebsiella Infections/microbiology/drug therapy ; Bacterial Proteins/genetics ; Gene Transfer, Horizontal ; Carbapenem-Resistant Enterobacteriaceae/genetics/drug effects ; }, abstract = {The rapid dissemination of carbapenem-resistant Enterobacterales (CRE) especially carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a great threat to global public health. Ceftazidime-avibactam, a novel β-lactam/β-lactamase inhibitor combination, has been widely used due to its excellent antibacterial activity against KPC-producing K. pneumoniae. However, several resistance mechanisms have been reported since its use. Here, we conducted a series of in vitro experiments to reveal and demonstrate the dynamic evolution of ceftazidime-avibactam resistance including interspecies IncX3_NDM-5 plasmid transfer between Enterobacter cloacae and K. pneumoniae and blaKPC mutation from blaKPC-2 to blaKPC-33. Through the analysis of conjugation frequency and fitness cost, the IncX3_NDM-5 plasmid in this study showed strong transmissibility and stability in E. coli EC600 and clinical strain K. pneumoniae 5298 as recipient strain. With increasing ceftazidime-avibactam concentration, the conjugation frequency remained at 10[-3]-10[-5], while the mutation frequency of K. pneumoniae 5298 was 10[-6]-10[-8] at the same concentration. Further plasmid analysis (the IncX3_NDM plasmid from this study and other 658 plasmids from the NCBI database) revealed the diverse origin and genetic structure of blaNDM-5 carrying plasmids. E. coli (42.9%), China (43.9%), IncX3 (66.6%) are the most common strains, regions, and Inc types respectively. By analysing of genetic environment detected in IncX3 plasmids, the dominant structures (168/258, 65.1%) were identified: ISKox3-IS26-blaNDM-5-IS5-ISAba125-Tn3000-Tn3. In additon, several structural variations were found in the core gene structure. In conclusion, the high fitness and transmissibility of the IncX3_NDM-5 plasmids were noteworthy. More importantly, the diverse ceftazidime-avibactam resistance mechanisms including blaNDM-5 tranfer and blaKPC-2 mutation highlighted the importance of the continuous monitoring of antimicrobial susceptibility and carbapenemases subtype during ceftazidime-avibactam treatment.}, }
@article {pmid38820540, year = {2024}, author = {Morel-Letelier, I and Yuen, B and Kück, AC and Camacho-García, YE and Petersen, JM and Lara, M and Leray, M and Eisen, JA and Osvatic, JT and Gros, O and Wilkins, LGE}, title = {Adaptations to nitrogen availability drive ecological divergence of chemosynthetic symbionts.}, journal = {PLoS genetics}, volume = {20}, number = {5}, pages = {e1011295}, pmid = {38820540}, issn = {1553-7404}, support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; S10 OD010786/OD/NIH HHS/United States ; }, mesh = {*Symbiosis/genetics ; Animals ; *Phylogeny ; *Nitrogen Fixation/genetics ; *Nitrogen/metabolism ; *Bivalvia/microbiology/genetics ; *Gene Transfer, Horizontal ; Bacteria/genetics/classification/metabolism ; Adaptation, Physiological/genetics ; Genome, Bacterial ; Caribbean Region ; Panama ; }, abstract = {Bacterial symbionts, with their shorter generation times and capacity for horizontal gene transfer (HGT), play a critical role in allowing marine organisms to cope with environmental change. The closure of the Isthmus of Panama created distinct environmental conditions in the Tropical Eastern Pacific (TEP) and Caribbean, offering a "natural experiment" for studying how closely related animals evolve and adapt under environmental change. However, the role of bacterial symbionts in this process is often overlooked. We sequenced the genomes of endosymbiotic bacteria in two sets of sister species of chemosymbiotic bivalves from the genera Codakia and Ctena (family Lucinidae) collected on either side of the Isthmus, to investigate how differing environmental conditions have influenced the selection of symbionts and their metabolic capabilities. The lucinid sister species hosted different Candidatus Thiodiazotropha symbionts and only those from the Caribbean had the genetic potential for nitrogen fixation, while those from the TEP did not. Interestingly, this nitrogen-fixing ability did not correspond to symbiont phylogeny, suggesting convergent evolution of nitrogen fixation potential under nutrient-poor conditions. Reconstructing the evolutionary history of the nifHDKT operon by including other lucinid symbiont genomes from around the world further revealed that the last common ancestor (LCA) of Ca. Thiodiazotropha lacked nif genes, and populations in oligotrophic habitats later re-acquired the nif operon through HGT from the Sedimenticola symbiont lineage. Our study suggests that HGT of the nif operon has facilitated niche diversification of the globally distributed Ca. Thiodiazotropha endolucinida species clade. It highlights the importance of nitrogen availability in driving the ecological diversification of chemosynthetic symbiont species and the role that bacterial symbionts may play in the adaptation of marine organisms to changing environmental conditions.}, }
@article {pmid38819554, year = {2024}, author = {Hellmuth, M and Stadler, PF}, title = {The Theory of Gene Family Histories.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2802}, number = {}, pages = {1-32}, pmid = {38819554}, issn = {1940-6029}, mesh = {*Phylogeny ; *Multigene Family ; *Gene Transfer, Horizontal ; *Evolution, Molecular ; Models, Genetic ; Computational Biology/methods ; }, abstract = {Most genes are part of larger families of evolutionary-related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene family histories, i.e., the precise dating of evolutionary events relative to phylogenetic tree of the underlying species has remained a challenging topic despite their importance as a basis for detailed investigations into adaptation and functional evolution of individual members of the gene family. The identification of orthologs, moreover, is a particularly important subproblem of the more general setting considered here. In the last few years, an extensive body of mathematical results has appeared that tightly links orthology, a formal notion of best matches among genes, and horizontal gene transfer. The purpose of this chapter is to broadly outline some of the key mathematical insights and to discuss their implication for practical applications. In particular, we focus on tree-free methods, i.e., methods to infer orthology or horizontal gene transfer as well as gene trees, species trees, and reconciliations between them without using a priori knowledge of the underlying trees or statistical models for the inference of phylogenetic trees. Instead, the initial step aims to extract binary relations among genes.}, }
@article {pmid38818268, year = {2023}, author = {Konstantinidis, KT}, title = {Sequence-discrete species for prokaryotes and other microbes: A historical perspective and pending issues.}, journal = {mLife}, volume = {2}, number = {4}, pages = {341-349}, pmid = {38818268}, issn = {2770-100X}, abstract = {Whether prokaryotes, and other microorganisms, form distinct clusters that can be recognized as species remains an issue of paramount theoretical as well as practical consequence in identifying, regulating, and communicating about these organisms. In the past decade, comparisons of thousands of genomes of isolates and hundreds of metagenomes have shown that prokaryotic diversity may be predominantly organized in such sequence-discrete clusters, albeit organisms of intermediate relatedness between the identified clusters are also frequently found. Accumulating evidence suggests, however, that the latter "intermediate" organisms show enough ecological and/or functional distinctiveness to be considered different species. Notably, the area of discontinuity between clusters often-but not always-appears to be around 85%-95% genome-average nucleotide identity, consistently among different taxa. More recent studies have revealed remarkably similar diversity patterns for viruses and microbial eukaryotes as well. This high consistency across taxa implies a specific mechanistic process that underlies the maintenance of the clusters. The underlying mechanism may be a substantial reduction in the efficiency of homologous recombination, which mediates (successful) horizontal gene transfer, around 95% nucleotide identity. Deviations from the 95% threshold (e.g., species showing lower intraspecies diversity) may be caused by ecological differentiation that imposes barriers to otherwise frequent gene transfer. While this hypothesis that clusters are driven by ecological differentiation coupled to recombination frequency (i.e., higher recombination within vs. between groups) is appealing, the supporting evidence remains anecdotal. The data needed to rigorously test the hypothesis toward advancing the species concept are also outlined.}, }
@article {pmid38817968, year = {2024}, author = {Zhao, Y and Ding, WJ and Xu, L and Sun, JQ}, title = {A comprehensive comparative genomic analysis revealed that plant growth promoting traits are ubiquitous in strains of Stenotrophomonas.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1395477}, pmid = {38817968}, issn = {1664-302X}, abstract = {Stenotrophomonas strains, which are often described as plant growth promoting (PGP) bacteria, are ubiquitous in many environments. A total of 213 genomes of strains of Stenotrophomonas were analyzed using comparative genomics to better understand the ecological roles of these bacteria in the environment. The pan-genome of the 213 strains of Stenotrophomonas consists of 27,186 gene families, including 710 core gene families, 11,039 unique genes and 15,437 accessory genes. Nearly all strains of Stenotrophomonas harbor the genes for GH3-family cellulose degradation and GH2- and GH31-family hemicellulose hydrolase, as well as intact glycolysis and tricarboxylic acid cycle pathways. These abilities suggest that the strains of this genus can easily obtain carbon and energy from the environment. The Stenotrophomonas strains can respond to oxidative stress by synthesizing catalase, superoxide dismutase, methionine sulfoxide reductase, and disulfide isomerase, as well as managing their osmotic balance by accumulating potassium and synthesizing compatible solutes, such as betaine, trehalose, glutamate, and proline. Each Stenotrophomonas strain also contains many genes for resistance to antibiotics and heavy metals. These genes that mediate stress tolerance increase the ability of Stenotrophomonas strains to survive in extreme environments. In addition, many functional genes related to attachment and plant colonization, growth promotion and biocontrol were identified. In detail, the genes associated with flagellar assembly, motility, chemotaxis and biofilm formation enable the strains of Stenotrophomonas to effectively colonize host plants. The presence of genes for phosphate-solubilization and siderophore production and the polyamine, indole-3-acetic acid, and cytokinin biosynthetic pathways confer the ability to promote plant growth. These strains can produce antimicrobial compounds, chitinases, lipases and proteases. Each Stenotrophomonas genome contained 1-9 prophages and 17-60 genomic islands, and the genes related to antibiotic and heavy metal resistance and the biosynthesis of polyamines, indole-3-acetic acid, and cytokinin may be acquired by horizontal gene transfer. This study demonstrates that strains of Stenotrophomonas are highly adaptable for different environments and have strong potential for use as plant growth-promoting bacteria.}, }
@article {pmid38817813, year = {2023}, author = {Li, L and Zhang, T}, title = {Roadmap to tackle antibiotic resistance in the environment under the One Health framework.}, journal = {mLife}, volume = {2}, number = {3}, pages = {224-228}, pmid = {38817813}, issn = {2770-100X}, abstract = {Antibiotic resistance has been recognized as a major challenge worldwide for humans. "One Health" has been recognized as a key concept for containment of antibiotic resistance. Under the framework, the role of the environment in the development of antibiotic resistance genes (ARGs) has become increasingly obvious. Despite numerous efforts, response to antibiotic resistance is considered to be inadequate, which is probably due to the lack of a clear roadmap. Here, we propose a "One Health" roadmap to combat antibiotic resistance in the environment through (1) understanding environmental resistome. The environmental gene pool has long been recognized as the single largest reservoir of both known and novel ARGs. (2) Standardizing ARG quantification. Systematic joint efforts based on standardized quantification are urgently needed to understand the true tempospatial profiles of the environmental resistome. (3) Identifying mechanisms of resistome development. Horizontal gene transfer and co-selection have been recognized as the two main mechanisms contributing to the environmental resistome. (4) Establishing a risk-assessment framework. The first critical step for large-scale cost-effective targeted ARG management in the environment is the risk assessment to identify the priority ARGs for control. (5) Formulating regulatory standards. By correlating the environmental ARG profile with public health, we may identify the indicator ARGs that can be integrated into current environmental quality standards. (6) Developing control strategies. Systematic analysis of available control technologies is required to identify the most feasible ones to curtail the spread of ARGs in the environment. The proposed roadmap under the "One Health" framework provides a guide to tackle antibiotic resistance in the environment.}, }
@article {pmid38816863, year = {2024}, author = {Pontes, A and Paraíso, F and Silva, M and Lagoas, C and Aires, A and Brito, PH and Rosa, CA and Lachance, MA and Sampaio, JP and Gonçalves, C and Gonçalves, P}, title = {Extensive remodeling of sugar metabolism through gene loss and horizontal gene transfer in a eukaryotic lineage.}, journal = {BMC biology}, volume = {22}, number = {1}, pages = {128}, pmid = {38816863}, issn = {1741-7007}, support = {UIDB/04378/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; LA/P/0140/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PTDC/BIA-EVL/1100/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PTDC/BIA-EVL/0604/2021//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2023.09581.CPCA.A1//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2022.15871.CPCA.A2//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/04378/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; LA/P/0140/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PTDC/BIA-EVL/1100/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PTDC/BIA-EVL/0604/2021//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2023.09581.CPCA.A1//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2022.15871.CPCA.A2//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; #406564/2022-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 0457499/2014-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 313088/2020-9//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 408733/2021//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; #406564/2022-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; CNPq process numbers 0457499/2014-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 313088/2020-9//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 408733/2021//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; APQ-01525-14//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; APQ-02552-15//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; APQ-01525-14//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; APQ-02552-15//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; }, mesh = {*Gene Transfer, Horizontal ; Phylogeny ; Carbohydrate Metabolism/genetics ; Sugars/metabolism ; Evolution, Molecular ; Genome, Fungal ; }, abstract = {BACKGROUND: In yeasts belonging to the subphylum Saccharomycotina, genes encoding components of the main metabolic pathways, like alcoholic fermentation, are usually conserved. However, in fructophilic species belonging to the floral Wickerhamiella and Starmerella genera (W/S clade), alcoholic fermentation was uniquely shaped by events of gene loss and horizontal gene transfer (HGT).<br><br>RESULTS: Because HGT and gene losses were first identified when only eight W/S-clade genomes were available, we collected publicly available genome data and sequenced the genomes of 36 additional species. A total of 63 genomes, representing most of the species described in the clade, were included in the analyses. Firstly, we inferred the phylogenomic tree of the clade and inspected the genomes for the presence of HGT-derived genes involved in fructophily and alcoholic fermentation. We predicted nine independent HGT events and several instances of secondary loss pertaining to both pathways. To investigate the possible links between gene loss and acquisition events and evolution of sugar metabolism, we conducted phenotypic characterization of 42 W/S-clade species including estimates of sugar consumption rates and fermentation byproduct formation. In some instances, the reconciliation of genotypes and phenotypes yielded unexpected results, such as the discovery of fructophily in the absence of the cornerstone gene (FFZ1) and robust alcoholic fermentation in the absence of the respective canonical pathway.<br><br>CONCLUSIONS: These observations suggest that reinstatement of alcoholic fermentation in the W/S clade triggered a surge of innovation that goes beyond the utilization of xenologous enzymes, with fructose metabolism playing a key role.}, }
@article {pmid38813783, year = {2024}, author = {Wolyniak, MJ and Frazier, RH and Gemborys, PK and Loehr, HE}, title = {Malate dehydrogenase: a story of diverse evolutionary radiation.}, journal = {Essays in biochemistry}, volume = {68}, number = {2}, pages = {213-220}, pmid = {38813783}, issn = {1744-1358}, support = {//Hampden-Sydney College Office of Undergraduate Research/ ; }, mesh = {*Malate Dehydrogenase/metabolism/genetics ; *Evolution, Molecular ; Bacteria/enzymology/genetics ; Phylogeny ; Archaea/genetics/enzymology ; Symbiosis ; Humans ; Eukaryota/enzymology/genetics ; Gene Transfer, Horizontal ; }, abstract = {Malate dehydrogenase (MDH) is a ubiquitous enzyme involved in cellular respiration across all domains of life. MDH's ubiquity allows it to act as an excellent model for considering the history of life and how the rise of aerobic respiration and eukaryogenesis influenced this evolutionary process. Here, we present the diversity of the MDH family of enzymes across bacteria, archaea, and eukarya, the relationship between MDH and lactate dehydrogenase (LDH) in the formation of a protein superfamily, and the connections between MDH and endosymbiosis in the formation of mitochondria and chloroplasts. The development of novel and powerful DNA sequencing techniques has challenged some of the conventional wisdom underlying MDH evolution and suggests a history dominated by gene duplication, horizontal gene transfer, and cryptic endosymbiosis events and adaptation to a diverse range of environments across all domains of life over evolutionary time. The data also suggest a superfamily of proteins that do not share high levels of sequential similarity but yet retain strong conservation of core function via key amino acid residues and secondary structural components. As DNA sequencing and 'big data' analysis techniques continue to improve in the life sciences, it is likely that the story of MDH will continue to refine as more examples of superfamily diversity are recovered from nature and analyzed.}, }
@article {pmid38811160, year = {2024}, author = {Breidenstein, A and Lamy, A and Bader, CP and Sun, WS and Wanrooij, PH and Berntsson, RP}, title = {PrgE: an OB-fold protein from plasmid pCF10 with striking differences to prototypical bacterial SSBs.}, journal = {Life science alliance}, volume = {7}, number = {8}, pages = {}, pmid = {38811160}, issn = {2575-1077}, mesh = {*Plasmids/genetics ; *DNA-Binding Proteins/metabolism/genetics/chemistry ; *Bacterial Proteins/genetics/metabolism/chemistry ; *Enterococcus faecalis/genetics/metabolism ; *DNA, Single-Stranded/metabolism/genetics ; Protein Binding ; Conjugation, Genetic/genetics ; Type IV Secretion Systems/genetics/metabolism ; Models, Molecular ; Gene Transfer, Horizontal ; DNA, Bacterial/genetics/metabolism ; }, abstract = {A major pathway for horizontal gene transfer is the transmission of DNA from donor to recipient cells via plasmid-encoded type IV secretion systems (T4SSs). Many conjugative plasmids encode for a single-stranded DNA-binding protein (SSB) together with their T4SS. Some of these SSBs have been suggested to aid in establishing the plasmid in the recipient cell, but for many, their function remains unclear. Here, we characterize PrgE, a proposed SSB from the Enterococcus faecalis plasmid pCF10. We show that PrgE is not essential for conjugation. Structurally, it has the characteristic OB-fold of SSBs, but it has very unusual DNA-binding properties. Our DNA-bound structure shows that PrgE binds ssDNA like beads on a string supported by its N-terminal tail. In vitro studies highlight the plasticity of PrgE oligomerization and confirm the importance of the N-terminus. Unlike other SSBs, PrgE binds both double- and single-stranded DNA equally well. This shows that PrgE has a quaternary assembly and DNA-binding properties that are very different from the prototypical bacterial SSB, but also different from eukaryotic SSBs.}, }
@article {pmid38810941, year = {2024}, author = {Zhang, Y and Liu, M and Zhang, J and Wu, J and Hong, L and Zhu, L and Long, J}, title = {Large-scale comparative analysis reveals phylogenomic preference of blaNDM-1 and blaKPC-2 transmission among Klebsiella pneumoniae.}, journal = {International journal of antimicrobial agents}, volume = {64}, number = {2}, pages = {107225}, doi = {10.1016/j.ijantimicag.2024.107225}, pmid = {38810941}, issn = {1872-7913}, mesh = {*beta-Lactamases/genetics ; *Klebsiella pneumoniae/genetics/drug effects/classification ; *Klebsiella Infections/transmission/microbiology/epidemiology ; Humans ; *Phylogeny ; Genome, Bacterial ; Anti-Bacterial Agents/pharmacology ; Virulence Factors/genetics ; Microbial Sensitivity Tests ; Carbapenems/pharmacology ; }, abstract = {blaNDM-1 and blaKPC-2 are responsible for the global increase in carbapenem-resistant Klebsiella pneumoniae, posing a great challenge to public health. However, the impact of phylogenetic factors on the dissemination of blaNDM-1 and blaKPC-2 is not yet fully understood. This study established a global dataset of 4051 blaNDM-1+ and 10,223 blaKPC-2+ K. pneumoniae genomes, and compared their transmission modes on a global scale. The results showed that blaNDM-1+ K. pneumoniae genomes exhibited a broader geographical distribution and higher sequence type (ST) richness than blaKPC-2+ genomes, indicating higher transmissibility of the blaNDM-1 gene. Furthermore, blaNDM-1+ genomes displayed significant differences in ST lineage, antibiotic resistance gene composition, virulence gene composition and genetic environments compared with blaKPC-2+ genomes, suggesting distinct dissemination mechanisms. blaNDM-1+ genomes were predominantly associated with ST147 and ST16, whereas blaKPC-2+ genomes were mainly found in ST11 and ST258. Significantly different accessory genes were identified between blaNDM-1+ and blaKPC-2+ genomes. The preference for blaKPC-2 distribution across certain countries, ST lineages and genetic environments underscores vertical spread as the primary mechanism driving the expansion of blaKPC-2. In contrast, blaNDM-1+ genomes did not display such a strong preference, confirming that the dissemination of blaNDM-1 mainly depends on horizontal gene transfer. Overall, this study demonstrates different phylogenetic drivers for the dissemination of blaNDM-1 and blaKPC-2, providing new insights into their global transmission dynamics.}, }
@article {pmid38808732, year = {2024}, author = {He, J and Yang, Z and Wang, M and Jia, R and Chen, S and Liu, M and Zhao, X and Yang, Q and Wu, Y and Zhang, S and Huang, J and Ou, X and Sun, D and Tian, B and He, Y and Wu, Z and Cheng, A and Zhu, D}, title = {Integrative and conjugative elements of Pasteurella multocida: Prevalence and signatures in population evolution.}, journal = {Virulence}, volume = {15}, number = {1}, pages = {2359467}, pmid = {38808732}, issn = {2150-5608}, mesh = {*Pasteurella multocida/genetics/classification ; *Gene Transfer, Horizontal ; Animals ; *Phylogeny ; *Pasteurella Infections/microbiology/epidemiology/transmission ; *Genome, Bacterial ; DNA Transposable Elements ; Conjugation, Genetic ; Evolution, Molecular ; Poultry/microbiology ; Prevalence ; High-Throughput Nucleotide Sequencing ; }, abstract = {Pasteurella multocida (P. multocida) is a bacterial pathogen responsible for a range of infections in humans and various animal hosts, causing significant economic losses in farming. Integrative and conjugative elements (ICEs) are important horizontal gene transfer elements, potentially enabling host bacteria to enhance adaptability by acquiring multiple functional genes. However, the understanding of ICEs in P. multocida and their impact on the transmission of this pathogen remains limited. In this study, 42 poultry-sourced P. multocida genomes obtained by high-throughput sequencing together with 393 publicly available P. multocida genomes were used to analyse the horizontal transfer of ICEs. Eighty-two ICEs were identified in P. multocida, including SXT/R391 and Tn916 subtypes, as well as three subtypes of ICEHin1056 family, with the latter being widely prevalent in P. multocida and carrying multiple resistance genes. The correlations between insertion sequences and resistant genes in ICEs were also identified, and some ICEs introduced the carbapenem gene blaOXA-2 and the bleomycin gene bleO to P. multocida. Phylogenetic and collinearity analyses of these bioinformatics found that ICEs in P. multocida were transmitted vertically and horizontally and have evolved with host specialization. These findings provide insight into the transmission and evolution mode of ICEs in P. multocida and highlight the importance of understanding these elements for controlling the spread of antibiotic resistance.}, }
@article {pmid38808121, year = {2024}, author = {Haimlich, S and Fridman, Y and Khandal, H and Savaldi-Goldstein, S and Levy, A}, title = {Widespread horizontal gene transfer between plants and bacteria.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae073}, pmid = {38808121}, issn = {2730-6151}, abstract = {Plants host a large array of commensal bacteria that interact with the host. The growth of both bacteria and plants is often dependent on nutrients derived from the cognate partners, and the bacteria fine-tune host immunity against pathogens. This ancient interaction is common in all studied land plants and is critical for proper plant health and development. We hypothesized that the spatial vicinity and the long-term relationships between plants and their microbiota may promote cross-kingdom horizontal gene transfer (HGT), a phenomenon that is relatively rare in nature. To test this hypothesis, we analyzed the Arabidopsis thaliana genome and its extensively sequenced microbiome to detect events of horizontal transfer of full-length genes that transferred between plants and bacteria. Interestingly, we detected 75 unique genes that were horizontally transferred between plants and bacteria. Plants and bacteria exchange in both directions genes that are enriched in carbohydrate metabolism functions, and bacteria transferred to plants genes that are enriched in auxin biosynthesis genes. Next, we provided a proof of concept for the functional similarity between a horizontally transferred bacterial gene and its Arabidopsis homologue in planta. The Arabidopsis DET2 gene is essential for biosynthesis of the brassinosteroid phytohormones, and loss of function of the gene leads to dwarfism. We found that expression of the DET2 homologue from Leifsonia bacteria of the Actinobacteria phylum in the Arabidopsis det2 background complements the mutant and leads to normal plant growth. Together, these data suggest that cross-kingdom HGT events shape the metabolic capabilities and interactions between plants and bacteria.}, }
@article {pmid38806321, year = {2024}, author = {Craske, MW and Wilson, JS and Fogg, PCM}, title = {Gene transfer agents: structural and functional properties of domesticated viruses.}, journal = {Trends in microbiology}, volume = {32}, number = {12}, pages = {1200-1211}, doi = {10.1016/j.tim.2024.05.002}, pmid = {38806321}, issn = {1878-4380}, mesh = {*Gene Transfer, Horizontal ; *Bacteriophages/genetics/physiology ; Rhodobacter capsulatus/virology/genetics/metabolism ; Archaea/virology/genetics ; Bacteria/virology/genetics/metabolism ; Evolution, Molecular ; DNA, Viral/genetics ; }, abstract = {Horizontal exchange of DNA between bacteria and archaea is prevalent and has major potential implications for genome evolution, plasticity, and population fitness. Several transfer mechanisms have been identified, including gene transfer agents (GTAs). GTAs are intricately regulated domesticated viruses that package host DNA into virus-like capsids and transfer this DNA throughout the bacterial community. Several important advances have recently been made in our understanding of these unusual particles. In this review, we highlight some of these findings, primarily for the model GTA produced by Rhodobacter capsulatus but also for newly identified GTA producers. We provide key insights into these important genetic elements, including the differences between GTAs from their ancestral bacteriophages, their regulation and control, and their elusive evolutionary function.}, }
@article {pmid38802023, year = {2024}, author = {Ji, W and Ma, J and Zheng, Z and Al-Herrawy, AZ and Xie, B and Wu, D}, title = {Algae blooms with resistance in fresh water: Potential interplay between Microcystis and antibiotic resistance genes.}, journal = {The Science of the total environment}, volume = {940}, number = {}, pages = {173528}, doi = {10.1016/j.scitotenv.2024.173528}, pmid = {38802023}, issn = {1879-1026}, mesh = {*Microcystis/genetics/physiology ; *Drug Resistance, Microbial/genetics ; *Microcystins ; *Fresh Water/microbiology ; Eutrophication ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; }, abstract = {Microcystis, a type of cyanobacteria known for producing microcystins (MCs), is experiencing a global increase in blooms. They have been recently recognized as potential contributors to the widespread of antibiotic resistance genes (ARGs). By reviewing approximately 150 pieces of recent studies, a hypothesis has been formulated suggesting that significant fluctuations in MCs concentrations and microbial community structure during Microcystis blooms could influence the dynamics of waterborne ARGs. Among all MCs, microcystin-LR (MC-LR) is the most widely distributed worldwide, notably abundant in reservoirs during summer. MCs inhibit protein phosphatases or increase reactive oxygen species (ROS), inducing oxidative stresses, enhancing membrane permeability, and causing DNA damage. This further enhances selective pressures and horizontal gene transfer (HGT) chances of ARGs. The mechanisms by which Microcystis regulates ARG dissemination have been systematically organized for the first time, focusing on the secretion of MCs and the alterations of bacterial community structure. However, several knowledge gaps remain, particularly concerning how MCs interfere with the electron transport chain and how Microcystis facilitates HGT of ARGs. Concurrently, the predominance of Microcystis forming the algal microbial aggregates is considered a hotspot for preserving and transferring ARGs. Yet, Microcystis can deplete the nutrients from other taxa within these aggregates, thereby reducing the density of ARG-carrying bacteria. Therefore, further studies are needed to explore the 'symbiotic - competitive' relationships between Microcystis and ARG-hosting bacteria under varied nutrient conditions. Addressing these knowledge gaps is crucial to understand the impacts of the algal aggregates on dynamics of waterborne antibiotic resistome, and underscores the need for effective control of Microcystis to curb the spread of antibiotic resistance. Constructed wetlands and photocatalysis represent advantageous strategies for halting the spread of ARGs from the perspective of Microcystis blooms, as they can effectively control Microcystis and MCs while maintaining the stability of aquatic ecosystem.}, }
@article {pmid38789482, year = {2024}, author = {Puginier, C and Libourel, C and Otte, J and Skaloud, P and Haon, M and Grisel, S and Petersen, M and Berrin, JG and Delaux, PM and Dal Grande, F and Keller, J}, title = {Phylogenomics reveals the evolutionary origins of lichenization in chlorophyte algae.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {4452}, pmid = {38789482}, issn = {2041-1723}, mesh = {*Lichens/genetics/microbiology ; *Phylogeny ; *Symbiosis/genetics ; *Chlorophyta/genetics ; Gene Transfer, Horizontal ; Evolution, Molecular ; Biological Evolution ; Transcriptome ; Glycoside Hydrolases/genetics/metabolism ; Genomics ; }, abstract = {Mutualistic symbioses have contributed to major transitions in the evolution of life. Here, we investigate the evolutionary history and the molecular innovations at the origin of lichens, which are a symbiosis established between fungi and green algae or cyanobacteria. We de novo sequence the genomes or transcriptomes of 12 lichen algal symbiont (LAS) and closely related non-symbiotic algae (NSA) to improve the genomic coverage of Chlorophyte algae. We then perform ancestral state reconstruction and comparative phylogenomics. We identify at least three independent gains of the ability to engage in the lichen symbiosis, one in Trebouxiophyceae and two in Ulvophyceae, confirming the convergent evolution of the lichen symbioses. A carbohydrate-active enzyme from the glycoside hydrolase 8 (GH8) family was identified as a top candidate for the molecular-mechanism underlying lichen symbiosis in Trebouxiophyceae. This GH8 was acquired in lichenizing Trebouxiophyceae by horizontal gene transfer, concomitantly with the ability to associate with lichens fungal symbionts (LFS) and is able to degrade polysaccharides found in the cell wall of LFS. These findings indicate that a combination of gene family expansion and horizontal gene transfer provided the basis for lichenization to evolve in chlorophyte algae.}, }
@article {pmid38789462, year = {2024}, author = {Wranne, MS and Karami, N and Kk, S and Jaén-Luchoro, D and Yazdanshenas, S and Lin, YL and Kabbinale, A and Flach, CF and Westerlund, F and Åhrén, C}, title = {Comparison of CTX-M encoding plasmids present during the early phase of the ESBL pandemic in western Sweden.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {11880}, pmid = {38789462}, issn = {2045-2322}, support = {C4A 2020-02518//V&#xe4;stra G&#xf6;talandsregionen/ ; ALF-965000//V&#xe4;stra G&#xf6;talandsregionen/ ; 2021-00922//Svenska Forskningsr&#xe5;det Formas/ ; 634890//EU Horizon 2020 program BeyondSeq/ ; }, mesh = {Sweden/epidemiology ; *Plasmids/genetics ; *beta-Lactamases/genetics ; *Escherichia coli/genetics ; Humans ; Pandemics ; Escherichia coli Infections/epidemiology/microbiology ; Gene Transfer, Horizontal ; Escherichia coli Proteins/genetics ; Whole Genome Sequencing ; }, abstract = {Plasmids encoding blaCTX-M genes have greatly shaped the evolution of E. coli producing extended-spectrum beta-lactamases (ESBL-E. coli) and adds to the global threat of multiresistant bacteria by promoting horizontal gene transfer (HGT). Here we screened the similarity of 47 blaCTX-M -encoding plasmids, from 45 epidemiologically unrelated and disperse ESBL-E. coli strains, isolated during the early phase (2009-2014) of the ESBL pandemic in western Sweden. Using optical DNA mapping (ODM), both similar and rare plasmids were identified. As many as 57% of the plasmids formed five ODM-plasmid groups of at least three similar plasmids per group. The most prevalent type (28%, IncIl, pMLST37) encoded blaCTX-M-15 (n = 10), blaCTX-M-3 (n = 2) or blaCTX-M-55 (n = 1). It was found in isolates of various sequence types (STs), including ST131. This could indicate ongoing local HGT as whole-genome sequencing only revealed similarities with a rarely reported, IncIl plasmid. The second most prevalent type (IncFII/FIA/FIB, F1:A2:B20) harboring blaCTX-M-27, was detected in ST131-C1-M27 isolates, and was similar to plasmids previously reported for this subclade. The results also highlight the need for local surveillance of plasmids and the importance of temporospatial epidemiological links so that detection of a prevalent plasmid is not overestimated as a potential plasmid transmission event in outbreak investigations.}, }
@article {pmid38788585, year = {2024}, author = {Liu, T and Lee, S and Kim, M and Fan, P and Boughton, RK and Boucher, C and Jeong, KC}, title = {A study at the wildlife-livestock interface unveils the potential of feral swine as a reservoir for extended-spectrum β-lactamase-producing Escherichia coli.}, journal = {Journal of hazardous materials}, volume = {473}, number = {}, pages = {134694}, doi = {10.1016/j.jhazmat.2024.134694}, pmid = {38788585}, issn = {1873-3336}, support = {R01 AI141810/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Escherichia coli/genetics/drug effects/enzymology ; *beta-Lactamases/genetics/metabolism ; *Animals, Wild/microbiology ; Swine ; *Disease Reservoirs/microbiology ; Cattle ; Gene Transfer, Horizontal ; Livestock/microbiology ; Drug Resistance, Bacterial ; Escherichia coli Infections/microbiology/veterinary ; }, abstract = {Wildlife is known to serve as carriers and sources of antimicrobial resistance (AMR). Due to their unrestricted movements and behaviors, they can spread antimicrobial resistant bacteria among livestock, humans, and the environment, thereby accelerating the dissemination of AMR. Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae is one of major concerns threatening human and animal health, yet transmission mechanisms at the wildlife-livestock interface are not well understood. Here, we investigated the mechanisms of ESBL-producing bacteria spreading across various hosts, including cattle, feral swine, and coyotes in the same habitat range, as well as from environmental samples over a two-year period. We report a notable prevalence and clonal dissemination of ESBL-producing E. coli in feral swine and coyotes, suggesting their persistence and adaptation within wildlife hosts. In addition, in silico studies showed that horizontal gene transfer, mediated by conjugative plasmids and insertion sequences elements, may play a key role in spreading the ESBL genes among these bacteria. Furthermore, the shared gut resistome of cattle and feral swine suggests the dissemination of antibiotic resistance genes at the wildlife-livestock interface. Taken together, our results suggest that feral swine may serve as a reservoir of ESBL-producing E. coli.}, }
@article {pmid38788579, year = {2024}, author = {Zhou, CS and Cao, GL and Liu, BF and Liu, W and Ma, WL and Ren, NQ}, title = {Deciphering the reduction of antibiotic resistance genes (ARGs) during medium-chain fatty acids production from waste activated sludge: Driven by inhibition of ARGs transmission and shift of microbial community.}, journal = {Journal of hazardous materials}, volume = {473}, number = {}, pages = {134676}, doi = {10.1016/j.jhazmat.2024.134676}, pmid = {38788579}, issn = {1873-3336}, mesh = {*Sewage/microbiology ; *Fatty Acids/metabolism ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/drug effects/metabolism ; Microbiota/drug effects ; Gene Transfer, Horizontal ; Genes, Bacterial ; Waste Disposal, Fluid/methods ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Medium-chain fatty acids (MCFAs) production from waste activated sludge (WAS) by chain extension (CE) is a promising technology. However, the effects and mechanisms of CE process on the fate of antibiotic resistance genes (ARGs) remain unclear. In this study, the results showed that the removal efficiency of ARGs was 81.15 % in CE process, suggesting its efficacy in reducing environmental risks. Further, the observed decrease in mobile genetic elements (MGEs) indicated that CE process restricted the horizontal gene transfer (HGT). Complementing this, the increase in soluble organic matters and extracellular 16 S rDNA confirmed that MCFAs production caused bacterial damage. Decreased intracellular ARGs and increased extracellular ARGs further revealed that MCFAs production impaired ARGs hosts, thereby limiting the vertical gene transfer (VGT) of ARGs. Shift of microbial community combined with co-occurrence network analysis demonstrated that functional bacteria without host potential for ARGs were enriched, but potential ARGs and MGEs hosts decreased, showing the role of functional bacterial phylogeny and selection pressure of MCFAs in reducing ARGs. Finally, partial least squares path model was used to systematic verify the mechanism of ARGs removal in CE process, which was attributed to the inhibition of ARGs transmission (HGT and VGT) and shift of microbial community.}, }
@article {pmid38786183, year = {2024}, author = {Sabtcheva, S and Stoikov, I and Ivanov, IN and Donchev, D and Lesseva, M and Georgieva, S and Teneva, D and Dobreva, E and Christova, I}, title = {Genomic Characterization of Carbapenemase-Producing Enterobacter hormaechei, Serratia marcescens, Citrobacter freundii, Providencia stuartii, and Morganella morganii Clinical Isolates from Bulgaria.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {5}, pages = {}, pmid = {38786183}, issn = {2079-6382}, abstract = {Carbapenemase-producing Enterobacter spp. Serratia marcescens, Citrobacter freundii, Providencia spp., and Morganella morganii (CP-ESCPM) are increasingly identified as causative agents of nosocomial infections but are still not under systematic genomic surveillance. In this study, using a combination of whole-genome sequencing and conjugation experiments, we sought to elucidate the genomic characteristics and transferability of resistance genes in clinical CP-ESCPM isolates from Bulgaria. Among the 36 sequenced isolates, NDM-1 (12/36), VIM-4 (11/36), VIM-86 (8/36), and OXA-48 (7/36) carbapenemases were identified; two isolates carried both NDM-1 and VIM-86. The majority of carbapenemase genes were found on self-conjugative plasmids. IncL plasmids were responsible for the spread of OXA-48 among E. hormaechei, C. freundii, and S. marcescens. IncM2 plasmids were generally associated with the spread of NDM-1 in C. freundii and S. marcescens, and also of VIM-4 in C. freundii. IncC plasmids were involved in the spread of the recently described VIM-86 in P. stuartii isolates. IncC plasmids carrying blaNDM-1 and blaVIM-86 were observed too. blaNDM-1 was also detected on IncX3 in S. marcescens and on IncT plasmid in M. morganii. The significant resistance transfer rates we observed highlight the role of the ESCPM group as a reservoir of resistance determinants and stress the need for strengthening infection control measures.}, }
@article {pmid38786161, year = {2024}, author = {Lamichhane, J and Choi, BI and Stegman, N and Fontes Noronha, M and Wolfe, AJ}, title = {Macrolide Resistance in the Aerococcus urinae Complex: Implications for Integrative and Conjugative Elements.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {5}, pages = {}, pmid = {38786161}, issn = {2079-6382}, support = {Pathnostics//Pathnostics/ ; }, abstract = {The recognition of the Aerococcus urinae complex (AUC) as an emerging uropathogen has led to growing concerns due to a limited understanding of its disease spectrum and antibiotic resistance profiles. Here, we investigated the prevalence of macrolide resistance within urinary AUC isolates, shedding light on potential genetic mechanisms. Phenotypic testing revealed a high rate of macrolide resistance: 45%, among a total of 189 urinary AUC isolates. Genomic analysis identified integrative and conjugative elements (ICEs) as carriers of the macrolide resistance gene ermA, suggesting horizontal gene transfer as a mechanism of resistance. Furthermore, comparison with publicly available genomes of related pathogens revealed high ICE sequence homogeneity, highlighting the potential for cross-species dissemination of resistance determinants. Understanding mechanisms of resistance is crucial for developing effective surveillance strategies and improving antibiotic use. Furthermore, the findings underscore the importance of considering the broader ecological context of resistance dissemination, emphasizing the need for community-level surveillance to combat the spread of antibiotic resistance within the urinary microbiome.}, }
@article {pmid38786130, year = {2024}, author = {Monecke, S and Burgold-Voigt, S and Braun, SD and Diezel, C and Liebler-Tenorio, EM and Müller, E and Nassar, R and Reinicke, M and Reissig, A and Senok, A and Ehricht, R}, title = {Characterisation of PVL-Positive Staphylococcus argenteus from the United Arab Emirates.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {5}, pages = {}, pmid = {38786130}, issn = {2079-6382}, support = {13GW0456//Federal Ministry of Education and Research/ ; 13N15717//Federal Ministry of Education and Research/ ; }, abstract = {Staphylococcus argenteus is a recently described staphylococcal species that is related to Staphylococcus aureus but lacks the staphyloxanthin operon. It is able to acquire both resistance markers such as the SCCmec elements and mobile genetic elements carrying virulence-associated genes from S. aureus. This includes those encoding the Panton-Valentine leukocidin (PVL), which is associated mainly with severe and/or recurrent staphylococcal skin and soft tissue infections. Here, we describe the genome sequences of two PVL-positive, mecA-negative S. argenteus sequence type (ST) 2250 isolates from the United Arab Emirates in detail. The isolates were found in a dental clinic in the United Arab Emirates (UAE). Both were sequenced using Oxford Nanopore Technology (ONT). This demonstrated the presence of temperate bacteriophages in the staphylococcal genomes, including a PVL prophage. It was essentially identical to the published sequence of phiSa2wa_st78 (GenBank NC_055048), a PVL phage from an Australian S. aureus clonal complex (CC) 88 isolate. Besides the PVL prophage, one isolate carried another prophage and the second isolate carried two additional prophages, whereby the region between these two prophages was inverted. This "flipped" region comprised about 1,083,000 bp, or more than a third of the strain's genome, and it included the PVL prophage. Prophages were induced by Mitomycin C treatment and subjected to transmission electron microscopy (TEM). This yielded, in accordance to the sequencing results, one or, respectively, two distinct populations of icosahedral phages. It also showed prolate phages which presumptively might be identified as the PVL phage. This observation highlights the significance bacteriophages have as agents of horizontal gene transfer as well as the need for monitoring emerging staphylococcal strains, especially in cosmopolitan settings such as the UAE.}, }
@article {pmid38783378, year = {2024}, author = {Brattig, N and Bergquist, R and Vienneau, D and Zhou, XN}, title = {Geography and health: role of human translocation and access to care.}, journal = {Infectious diseases of poverty}, volume = {13}, number = {1}, pages = {37}, pmid = {38783378}, issn = {2049-9957}, mesh = {Humans ; *Health Services Accessibility ; Animals ; *Zoonoses/epidemiology ; COVID-19/transmission/epidemiology ; Communicable Diseases/epidemiology/transmission ; SARS-CoV-2 ; Geography ; }, abstract = {Natural, geographical barriers have historically limited the spread of communicable diseases. This is no longer the case in today's interconnected world, paired with its unprecedented environmental and climate change, emphasising the intersection of evolutionary biology, epidemiology and geography (i.e. biogeography). A total of 14 articles of the special issue entitled "Geography and health: role of human translocation and access to care" document enhanced disease transmission of diseases, such as malaria, leishmaniasis, schistosomiasis, COVID-19 (Severe acute respiratory syndrome corona 2) and Oropouche fever in spite of spatiotemporal surveillance. High-resolution satellite images can be used to understand spatial distributions of transmission risks and disease spread and to highlight the major avenue increasing the incidence and geographic range of zoonoses represented by spill-over transmission of coronaviruses from bats to pigs or civets. Climate change and globalization have increased the spread and establishment of invasive mosquitoes in non-tropical areas leading to emerging outbreaks of infections warranting improved physical, chemical and biological vector control strategies. The translocation of pathogens and their vectors is closely connected with human mobility, migration and the global transport of goods. Other contributing factors are deforestation with urbanization encroaching into wildlife zones. The destruction of natural ecosystems, coupled with low income and socioeconomic status, increase transmission probability of neglected tropical and zoonotic diseases. The articles in this special issue document emerging or re-emerging diseases and surveillance of fever symptoms. Health equity is intricately connected to accessibility to health care and the targeting of healthcare resources, necessitating a spatial approach. Public health comprises successful disease management integrating spatial surveillance systems, including access to sanitation facilities. Antimicrobial resistance caused, e.g. by increased use of antibiotics in health, agriculture and aquaculture, or acquisition of resistance genes, can be spread by horizontal gene transfer. This editorial reviews the key findings of this 14-article special issue, identifies important gaps relevant to our interconnected world and makes a number of specific recommendations to mitigate the transmission risks of infectious diseases in the post-COVID-19 pandemic era.}, }
@article {pmid38783210, year = {2024}, author = {Han, D and Ma, S and He, C and Yang, Y and Li, P and Lu, L}, title = {Unveiling the genetic architecture and transmission dynamics of a novel multidrug-resistant plasmid harboring blaNDM-5 in E. Coli ST167: implications for antibiotic resistance management.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {178}, pmid = {38783210}, issn = {1471-2180}, support = {2022B1154//Health Projects of Zhongshan City/ ; 2018B1081//Health Projects of Zhongshan City/ ; }, mesh = {*Plasmids/genetics ; *Escherichia coli/genetics/drug effects ; *Drug Resistance, Multiple, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; *beta-Lactamases/genetics ; Humans ; *Escherichia coli Infections/microbiology/transmission ; *Microbial Sensitivity Tests ; China ; Gene Transfer, Horizontal ; Carbapenems/pharmacology ; }, abstract = {BACKGROUND: The emergence of multidrug-resistant (MDR) Escherichia coli strains poses significant challenges in clinical settings, particularly when these strains harbor New Delhi metallo-ß-lactamase (NDM) gene, which confer resistance to carbapenems, a critical class of last-resort antibiotics. This study investigates the genetic characteristics and implications of a novel blaNDM-5-carrying plasmid pNDM-5-0083 isolated from an E. coli strain GZ04-0083 from clinical specimen in Zhongshan, China.<br><br>RESULTS: Phenotypic and genotypic evaluations confirmed that the E. coli ST167 strain GZ04-0083 is a multidrug-resistant organism, showing resistance to diverse classes of antibiotics including &#xdf;-lactams, carbapenems, fluoroquinolones, aminoglycosides, and sulfonamides, while maintaining susceptibility to monobactams. Investigations involving S1 pulsed-field gel electrophoresis, Southern blot analysis, and conjugation experiments, alongside genomic sequencing, confirmed the presence of the blaNDM-5 gene within a 146-kb IncFIB plasmid pNDM-5-0083. This evidence underscores a significant risk for the horizontal transfer of resistance genes among bacterial populations. Detailed annotations of genetic elements-such as resistance genes, transposons, and insertion sequences-and comparative BLAST analyses with other blaNDM-5-carrying plasmids, revealed a unique architectural configuration in the pNDM-5-0083. The MDR region of this plasmid shares a conserved gene arrangement (repA-IS15DIV-blaNDM-5-bleMBL-IS91-suI2-aadA2-dfrA12) with three previously reported plasmids, indicating a potential for dynamic genetic recombination and evolution within the MDR region. Additionally, the integration of virulence factors, including the iro and sit gene clusters and enolase, into its genetic architecture poses further therapeutic challenges by enhancing the strain's pathogenicity through improved host tissue colonization, immune evasion, and increased infection severity.<br><br>CONCLUSIONS: The detailed identification and characterization of pNDM-5-0083 enhance our understanding of the mechanisms facilitating the spread of carbapenem resistance. This study illuminates the intricate interplay among various genetic elements within the novel blaNDM-5-carrying plasmid, which are crucial for the stability and mobility of resistance genes across bacterial populations. These insights highlight the urgent need for ongoing surveillance and the development of effective strategies to curb the proliferation of antibiotic resistance.}, }
@article {pmid38783209, year = {2024}, author = {Gevin, M and Latifi, A and Talla, E}, title = {The modular architecture of sigma factors in cyanobacteria: a framework to assess their diversity and understand their evolution.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {512}, pmid = {38783209}, issn = {1471-2164}, support = {ANR-21-CE20-0025-01//Agence Nationale de la Recherche/ ; ANR-21-CE20-0025-01//Agence Nationale de la Recherche/ ; ANR-21-CE20-0025-01//Agence Nationale de la Recherche/ ; }, mesh = {*Sigma Factor/genetics/metabolism ; *Evolution, Molecular ; *Cyanobacteria/genetics/metabolism ; *Phylogeny ; Bacterial Proteins/genetics/metabolism ; Genetic Variation ; }, abstract = {BACKGROUND: Bacterial RNA polymerase holoenzyme requires sigma70 factors to start transcription by identifying promoter elements. Cyanobacteria possess multiple sigma70 factors to adapt to a wide variety of ecological niches. These factors are grouped into two categories: primary sigma factor initiates transcription of housekeeping genes during normal growth conditions, while alternative sigma factors initiate transcription of specific genes under particular conditions. However, the present classification does not consider the modular organization of their structural domains, introducing therefore multiple functional and structural biases. A comprehensive analysis of this protein family in cyanobacteria is needed to address these limitations.<br><br>RESULTS: We investigated the structure and evolution of sigma70 factors in cyanobacteria, analyzing their modular architecture and variation among unicellular, filamentous, and heterocyst-forming morphotypes. 4,193 sigma70 homologs were found with 59 distinct modular patterns, including six essential and 29 accessory domains, such as DUF6596. 90% of cyanobacteria typically have 5 to 17 sigma70 homologs and this number likely depends on the strain morphotype, the taxonomic order and the genome size. We classified sigma70 factors into 12 clans and 36 families. According to taxonomic orders and phenotypic traits, the number of homologs within the 14 main families was variable, with the A.1 family including the primary sigma factor since this family was found in all cyanobacterial species. The A.1, A.5, C.1, E.1, J.1, and K.1 families were found to be key sigma families that distinguish heterocyst-forming strains. To explain the diversification and evolution of sigma70, we propose an evolutionary scenario rooted in the diversification of a common ancestor of the A1 family. This scenario is characterized by evolutionary events including domain losses, gains, insertions, and modifications. The high occurrence of the DUF6596 domain in bacterial sigma70 proteins, and its association with the highest prevalence observed in Actinobacteria, suggests that this domain might be important for sigma70 function. It also implies that the domain could have emerged in Actinobacteria and been transferred through horizontal gene transfer.<br><br>CONCLUSION: Our analysis provides detailed insights into the modular domain architecture of sigma70, introducing a novel robust classification. It also proposes an evolutionary scenario explaining their diversity across different taxonomical orders.}, }
@article {pmid38781445, year = {2024}, author = {Vuruputoor, VS and Starovoitov, A and Cai, Y and Liu, Y and Rahmatpour, N and Hedderson, TA and Wilding, N and Wegrzyn, JL and Goffinet, B}, title = {Crossroads of assembling a moss genome: navigating contaminants and horizontal gene transfer in the moss Physcomitrellopsis africana.}, journal = {G3 (Bethesda, Md.)}, volume = {14}, number = {7}, pages = {}, pmid = {38781445}, issn = {2160-1836}, support = {DEB-0919284//US National Science Foundation/ ; }, mesh = {*Gene Transfer, Horizontal ; *Bryopsida/genetics ; *Genome, Plant ; *Phylogeny ; Genomics/methods ; Molecular Sequence Annotation ; }, abstract = {The first chromosome-scale reference genome of the rare narrow-endemic African moss Physcomitrellopsis africana (P. africana) is presented here. Assembled from 73 × Oxford Nanopore Technologies (ONT) long reads and 163 × Beijing Genomics Institute (BGI)-seq short reads, the 414 Mb reference comprises 26 chromosomes and 22,925 protein-coding genes [Benchmarking Universal Single-Copy Ortholog (BUSCO) scores: C:94.8% (D:13.9%)]. This genome holds 2 genes that withstood rigorous filtration of microbial contaminants, have no homolog in other land plants, and are thus interpreted as resulting from 2 unique horizontal gene transfers (HGTs) from microbes. Further, P. africana shares 176 of the 273 published HGT candidates identified in Physcomitrium patens (P. patens), but lacks 98 of these, highlighting that perhaps as many as 91 genes were acquired in P. patens in the last 40 million years following its divergence from its common ancestor with P. africana. These observations suggest rather continuous gene gains via HGT followed by potential losses during the diversification of the Funariaceae. Our findings showcase both dynamic flux in plant HGTs over evolutionarily "short" timescales, alongside enduring impacts of successful integrations, like those still functionally maintained in extant P. africana. Furthermore, this study describes the informatic processes employed to distinguish contaminants from candidate HGT events.}, }
@article {pmid38777914, year = {2024}, author = {Zhang, F and Shi, X and Xu, J and Yuan, W and Li, Z}, title = {Tandem gene duplication selected by activation of horizontally transferred gene in bacteria.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {340}, pmid = {38777914}, issn = {1432-0614}, support = {2020YFA0908000//The National Key R&amp;D Program of China/ ; TSBICIP-CXRC-001//Tianjin Synthetic Biotechnology Innovation Capacity Improvement Project/ ; 2060302//Key project at central government level: The ability establishment of sustainable use for valuable Chinese medicine resource/ ; }, mesh = {*Gene Duplication ; *Gene Transfer, Horizontal ; *Escherichia coli/genetics/metabolism ; *Plasmids/genetics ; Bacteria/genetics/metabolism ; Gene Dosage ; Recombination, Genetic ; }, abstract = {Horizontal gene transfer occurs frequently in bacteria, but the mechanism driving activation and optimization of the expression of horizontally transferred genes (HTGs) in new recipient strains is not clear. Our previous study found that spontaneous tandem DNA duplication resulted in rapid activation of HTGs. Here, we took advantage of this finding to develop a novel technique for tandem gene duplication, named tandem gene duplication selected by activation of horizontally transferred gene in bacteria (TDAH), in which tandem duplication was selected by the activation of horizontally transferred selectable marker gene. TDAH construction does not contain any reported functional elements based on homologous or site-specific recombination and DNA amplification. TDAH only contains an essential selectable marker for copy number selection and 9-bp-microhomology border sequences for precise illegitimate recombination. One transformation and 3 days were enough to produce a high-copy strain, so its procedure is simple and fast. Without subsequent knockout of the endogenous recombination system, TDAH could also generate the relatively stable high-copy tandem duplication for plasmid-carried and genome-integrated DNA. TDAH also showed an excellent capacity for increase gene expression and worked well in different industrial bacteria. We also applied TDAH to select the optimal high copy number of ribA for vitamin B2 production in E. coli; the yield was improved by 3.5 times and remained stable even after 12 subcultures. TDAH is a useful tool for recombinant protein production and expression optimization of biosynthetic pathways. KEY POINTS: • We develop a novel and efficient technique (TDAH) for tandem gene duplication in bacterium. TDAH is based on the mechanism of HTG rapid activation. TDAH does not contain any reported functional elements based on homologous recombination and DNA amplification. TDAH only contains an essential selectable marker for copy number selection, so its construction and procedure are very simple and fast. • TDAH is the first reported selected and stable tandem-gene-duplication technique in which the selected high-copy plasmid-carried and genome-integrated DNA could remain stable without the subsequent knockout of recombination system. • TDAH showed an excellent capacity for regulating gene expression and worked well in different industrial bacteria, indicating it is a useful tool for recombinant protein production and expression optimization of biosynthetic pathways. • TDAH was applied to select the optimal high copy number of ribA for vitamin B2 production in E. coli; the yield was improved by 3.5-fold and remained stable even after 12 subcultures.}, }
@article {pmid38772228, year = {2024}, author = {Xu, M and Gao, P and Gao, Y and Xiong, SJ and Chen, HQ and Shen, XX}, title = {Impacts of microplastic type on the fate of antibiotic resistance genes and horizontal gene transfer mechanism during anaerobic digestion.}, journal = {Journal of environmental management}, volume = {360}, number = {}, pages = {121090}, doi = {10.1016/j.jenvman.2024.121090}, pmid = {38772228}, issn = {1095-8630}, mesh = {*Gene Transfer, Horizontal ; *Drug Resistance, Microbial/genetics ; *Microplastics ; Anaerobiosis ; *Sewage/microbiology ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Microplastics (MPs) and antibiotic resistance genes (ARGs) are important pollutants in waste activated sludge (WAS), but their interactions during anaerobic digestion (AD) still need to be further explored. This study investigated variations in ARGs, mobile genetic elements (MGEs), and host bacteria during AD under the pressure of polyamide (PA), polyethylene (PE), and polypropylene (PP). The results showed that the MPs increased methane production by 11.7-35.5%, and decreased ARG abundance by 5.6-24.6%. Correlation analysis showed that the decrease of MGEs (plasmid, prophage, etc.) promoted the decrease of the abundance of multidrug, aminoglycoside and tetracycline resistance genes. Metagenomic annotation revealed that the reduction of key host bacteria (Arenimonas, Lautropia, etc.) reduced the abundance of major ARGs (rsmA, rpoB2, etc.). Moreover, PP MPs contributed to a reduction in the abundance of functional genes related to the production of reactive oxygen species, ATP synthesis, and cell membrane permeability, which was conducive to reducing the potential for horizontal gene transfer of ARGs. These findings provide insights into the treatment of organic waste containing MPs.}, }
@article {pmid38772218, year = {2024}, author = {Kang, J and Zhang, C and Wan, S and Li, W and Zhao, W and Li, L and Shang, Y and Du, XD and Liu, D and Yao, H}, title = {Prevalence and characterization of aminoglycoside resistance gene aph(2")-If-carrying Campylobacter jejuni.}, journal = {International journal of food microbiology}, volume = {419}, number = {}, pages = {110747}, doi = {10.1016/j.ijfoodmicro.2024.110747}, pmid = {38772218}, issn = {1879-3460}, mesh = {*Campylobacter jejuni/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; *Aminoglycosides/pharmacology ; Animals ; *Phylogeny ; *Anti-Bacterial Agents/pharmacology ; *Multilocus Sequence Typing ; *Campylobacter Infections/microbiology/veterinary/epidemiology ; Whole Genome Sequencing ; Humans ; Prevalence ; China ; Food Microbiology ; Microbial Sensitivity Tests ; }, abstract = {Campylobacter jejuni is recognized as a significant foodborne pathogen, and recent studies have indicated a rising trend of aminoglycosides resistance gene aph(2″)-If among C. jejuni isolates from food-producing animals in China. However, systematic information about aph(2″)-If-positive C. jejuni from food-producing animals and other sources worldwide based on whole-genome analysis remains a knowledge gap. In this study, we aimed to analyze the worldwide distribution, genetic environment and phylogenetic tree of aph(2″)-If by utilizing Whole Genome Sequencing (WGS) data obtained, coupled with information in the GenBank database. A total of 160C. jejuni isolates in the GenBank database and 14C. jejuni isolates in our laboratory carrying aph(2″)-If gene were performed for further analysis. WGS analysis revealed the global distribution of aph(2″)-If among C. jejuni from 6 countries. Multilocus Sequence Typing(MLST) results indicated that 70 STs were involved in the dissemination of aph(2″)-If, with ST10086 being the predominant ST. Whole-genome Multilocus Sequence Typing(wg-MLST) analysis according to times, countries, and origins of C. jejuni isolation further demonstrated a close relationship between aph(2″)-If carrying C. jejuni isolates from farm and food. The findings also revealed the existence of 32 distinct types of genetic environments surrounding aph(2″)-If among these isolates. Notably, Type 30, characterized by the arrangement ISsag10-deoD-ant(9)-hp-hp-aph(2″)-If, emerged as the predominant genetic environment. In conclusion, our analysis provides the inaugural perspective on the worldwide distribution of aph(2″)-If. This resistance gene demonstrates horizontal transferability and regional diffusion in a clonal pattern. The close association observed among aph(2″)-If-positive C. jejuni strains isolated from poultry, food, and clinical environments underscores the potential for zoonotic transmission from these isolates.}, }
@article {pmid38771049, year = {2024}, author = {Muñoz-Gutiérrez, I and Cantu, L and Shanahan, J and Girguis, M and de la Cruz, M and Mota-Bravo, L}, title = {Cryptic environmental conjugative plasmid recruits a novel hybrid transposon resulting in a new plasmid with higher dispersion potential.}, journal = {mSphere}, volume = {9}, number = {6}, pages = {e0025224}, pmid = {38771049}, issn = {2379-5042}, support = {T34 GM136498/GM/NIGMS NIH HHS/United States ; GM136498//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, mesh = {*Plasmids/genetics ; *DNA Transposable Elements/genetics ; *Escherichia coli/genetics/drug effects ; *Conjugation, Genetic ; *Anti-Bacterial Agents/pharmacology ; Lakes/microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; }, abstract = {UNLABELLED: Cryptic conjugative plasmids lack antibiotic-resistance genes (ARGs). These plasmids can capture ARGs from the vast pool of the environmental metagenome, but the mechanism to recruit ARGs remains to be elucidated. To investigate the recruitment of ARGs by a cryptic plasmid, we sequenced and conducted mating experiments with Escherichia coli SW4848 (collected from a lake) that has a cryptic IncX (IncX4) plasmid and an IncF (IncFII/IncFIIB) plasmid with five genes that confer resistance to aminoglycosides (strA and strB), sulfonamides (sul2), tetracycline [tet(A)], and trimethoprim (dfrA5). In a conjugation experiment, a novel hybrid Tn21/Tn1721 transposon of 22,570 bp (designated Tn7714) carrying the five ARG mobilized spontaneously from the IncF plasmid to the cryptic IncX plasmid. The IncF plasmid was found to be conjugative when it was electroporated into E. coli DH10B (without the IncX plasmid). Two parallel conjugations with the IncF and the new IncX (carrying the novel Tn7714 transposon) plasmids in two separate E. coli DH10B as donors and E. coli J53 as the recipient revealed that the conjugation rate of the new IncX plasmid (with the novel Tn7714 transposon and five ARGs) is more than two orders of magnitude larger than the IncF plasmid. For the first time, this study shows experimental evidence that cryptic environmental plasmids can capture and transfer transposons with ARGs to other bacteria, creating novel multidrug-resistant conjugative plasmids with higher dispersion potential.<br><br>IMPORTANCE: Cryptic conjugative plasmids are extrachromosomal DNA molecules without antibiotic-resistance genes (ARGs). Environmental bacteria carrying cryptic plasmids with a high conjugation rate threaten public health because they can capture clinically relevant ARGs and rapidly spread them to pathogenic bacteria. However, the mechanism to recruit ARG by cryptic conjugative plasmids in environmental bacteria has not been observed experimentally. Here, we document the first translocation of a transposon with multiple clinically relevant ARGs to a cryptic environmental conjugative plasmid. The new multidrug-resistant conjugative plasmid has a conjugation rate that is two orders of magnitude higher than the original plasmid that carries the ARG (i.e., the new plasmid from the environment can spread ARG more than two orders of magnitude faster). Our work illustrates the importance of studying the mobilization of ARGs in environmental bacteria. It sheds light on how cryptic conjugative plasmids recruit ARGs, a phenomenon at the root of the antibiotic crisis.}, }
@article {pmid38771034, year = {2024}, author = {Chong, TN and Shapiro, L}, title = {Bacterial cell differentiation enables population level survival strategies.}, journal = {mBio}, volume = {15}, number = {6}, pages = {e0075824}, pmid = {38771034}, issn = {2150-7511}, support = {R35 GM118071/GM/NIGMS NIH HHS/United States ; //Chan Zuckerberg Initiative (CZI)/ ; R35-GM118071//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, mesh = {*Bacteria/genetics ; Bacterial Physiological Phenomena ; Cell Differentiation ; Adaptation, Physiological ; Microbial Viability ; Signal Transduction ; }, abstract = {Clonal reproduction of unicellular organisms ensures the stable inheritance of genetic information. However, this means of reproduction lacks an intrinsic basis for genetic variation, other than spontaneous mutation and horizontal gene transfer. To make up for this lack of genetic variation, many unicellular organisms undergo the process of cell differentiation to achieve phenotypic heterogeneity within isogenic populations. Cell differentiation is either an inducible or obligate program. Induced cell differentiation can occur as a response to a stimulus, such as starvation or host cell invasion, or it can be a stochastic process. In contrast, obligate cell differentiation is hardwired into the organism's life cycle. Whether induced or obligate, bacterial cell differentiation requires the activation of a signal transduction pathway that initiates a global change in gene expression and ultimately results in a morphological change. While cell differentiation is considered a hallmark in the development of multicellular organisms, many unicellular bacteria utilize this process to implement survival strategies. In this review, we describe well-characterized cell differentiation programs to highlight three main survival strategies used by bacteria capable of differentiation: (i) environmental adaptation, (ii) division of labor, and (iii) bet-hedging.}, }
@article {pmid38770060, year = {2024}, author = {Tamayo-Leiva, J and Alcorta, J and Sepúlveda, F and Fuentes-Alburquenque, S and Arroyo, JI and González-Pastor, JE and Díez, B}, title = {Structure and dispersion of the conjugative mobilome in surface ocean bacterioplankton.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae059}, pmid = {38770060}, issn = {2730-6151}, abstract = {Mobile genetic elements (MGEs), collectively referred to as the "mobilome", can have a significant impact on the fitness of microbial communities and therefore on ecological processes. Marine MGEs have mainly been associated with wide geographical and phylogenetic dispersal of adaptative traits. However, whether the structure of this mobilome exhibits deterministic patterns in the natural community is still an open question. The aim of this study was to characterize the structure of the conjugative mobilome in the ocean surface bacterioplankton by searching the publicly available marine metagenomes from the TARA Oceans survey, together with molecular markers, such as relaxases and type IV coupling proteins of the type IV secretion system (T4SS). The T4SS machinery was retrieved in more abundance than relaxases in the surface marine bacterioplankton. Moreover, among the identified MGEs, mobilizable elements were the most abundant, outnumbering self-conjugative sequences. Detection of a high number of incomplete T4SSs provides insight into possible strategies related to trans-acting activity between MGEs, and accessory functions of the T4SS (e.g. protein secretion), allowing the host to maintain a lower metabolic burden in the highly dynamic marine system. Additionally, the results demonstrate a wide geographical dispersion of MGEs throughout oceanic regions, while the Southern Ocean appears segregated from other regions. The marine mobilome also showed a high similarity of functions present in known plasmid databases. Moreover, cargo genes were mostly related to DNA processing, but scarcely associated with antibiotic resistance. Finally, within the MGEs, integrative and conjugative elements showed wider marine geographic dispersion than plasmids.}, }
@article {pmid38769479, year = {2024}, author = {Talat, A and Khan, F and Khan, AU}, title = {Genome analyses of colistin-resistant high-risk blaNDM-5 producing Klebsiella pneumoniae ST147 and Pseudomonas aeruginosa ST235 and ST357 in clinical settings.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {174}, pmid = {38769479}, issn = {1471-2180}, mesh = {*Klebsiella pneumoniae/genetics/drug effects/isolation &amp; purification ; *Pseudomonas aeruginosa/genetics/drug effects/isolation &amp; purification ; *Colistin/pharmacology ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Whole Genome Sequencing ; *Microbial Sensitivity Tests ; *Pseudomonas Infections/microbiology ; *Drug Resistance, Multiple, Bacterial/genetics ; *Genome, Bacterial/genetics ; *Klebsiella Infections/microbiology ; Gene Transfer, Horizontal ; India ; beta-Lactamases/genetics ; Plasmids/genetics ; }, abstract = {BACKGROUND: Colistin is a last-resort antibiotic used in extreme cases of multi-drug resistant (MDR) Gram-negative bacterial infections. Colistin resistance has increased in recent years and often goes undetected due to the inefficiency of predominantly used standard antibiotic susceptibility tests (AST). To address this challenge, we aimed to detect the prevalence of colistin resistance strains through both Vitek®2 and broth micro-dilution. We investigated 1748 blood, tracheal aspirate, and pleural fluid samples from the Intensive Care Unit (ICU), Neonatal Intensive Care Unit (NICU), and Tuberculosis and Respiratory Disease centre (TBRD) in an India hospital. Whole-genome sequencing (WGS) of extremely drug-resitant (XDR) and pan-drug resistant (PDR) strains revealed the resistance mechanisms through the Resistance Gene Identifier (RGI.v6.0.0) and Snippy.v4.6.0. Abricate.v1.0.1, PlasmidFinder.v2.1, MobileElementFinder.v1.0.3 etc. detected virulence factors, and mobile genetic elements associated to uncover the pathogenecity and the role of horizontal gene transfer (HGT).<br><br>RESULTS: This study reveals compelling insights into colistin resistance among global high-risk clinical isolates: Klebsiella pneumoniae ST147 (16/20), Pseudomonas aeruginosa ST235 (3/20), and ST357 (1/20). Vitek&#xae;2 found 6 colistin-resistant strains (minimum inhibitory concentrations, MIC&#x2009;=&#x2009;4&#x2009;&#x3bc;g/mL), while broth microdilution identified 48 (MIC&#x2009;=&#x2009;32-128&#x2009;&#x3bc;g/mL), adhering to CLSI guidelines. Despite the absence of mobile colistin resistance (mcr) genes, mechanisms underlying colistin resistance included mgrB deletion, phosphoethanolamine transferases arnT, eptB, ompA, and mutations in pmrB (T246A, R256G) and eptA (V50L, A135P, I138V, C27F) in K. pneumoniae. P. aeruginosa harbored phosphoethanolamine transferases basS/pmrb, basR, arnA, cprR, cprS, alongside pmrB (G362S), and parS (H398R) mutations. Both strains carried diverse clinically relevant antimicrobial resistance genes (ARGs), including plasmid-mediated blaNDM-5 (K. pneumoniae ST147) and chromosomally mediated blaNDM-1 (P. aeruginosa ST357).<br><br>CONCLUSION: The global surge in MDR, XDR and PDR bacteria necessitates last-resort antibiotics such as colistin. However, escalating resistance, particularly to colistin, presents a critical challenge. Inefficient colistin resistance detection methods, including Vitek2, alongside limited surveillance resources, accentuate the need for improved strategies. Whole-genome sequencing revealed alarming colistin resistance among K. pneumoniae and P. aeruginosa in an Indian hospital. The identification of XDR and PDR strains underscores urgency for enhanced surveillance and infection control. SNP analysis elucidated resistance mechanisms, highlighting the complexity of combatting resistance.}, }
@article {pmid38767750, year = {2024}, author = {S, V and T, J and E, AP and A, MHA}, title = {Antibiotic resistance of heterotrophic bacteria from the sediments of adjoining high Arctic fjords, Svalbard.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {55}, number = {3}, pages = {2371-2383}, pmid = {38767750}, issn = {1678-4405}, mesh = {*Geologic Sediments/microbiology ; Arctic Regions ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; *Anti-Bacterial Agents/pharmacology ; Svalbard ; *Drug Resistance, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Microbial Sensitivity Tests ; Estuaries ; Phylogeny ; Heterotrophic Processes ; }, abstract = {Antibiotic resistance bacteria (ARB) and antibiotic resistance genes (ARGs) are now considered major global threats. The Kongsfjorden and Krossfjorden are the interlinked fjords in the Arctic that are currently experiencing the effects of climate change and receiving input of pollutants from distant and regional sources. The present study focused on understanding the prevalence of antibiotic resistance of retrievable heterotrophic bacteria from the sediments of adjacent Arctic fjords Kongsfjorden and Krossfjorden. A total of 237 bacterial isolates were tested against 16 different antibiotics. The higher resistance observed towards Extended Spectrum β-lactam antibiotic (ESBL) includes ceftazidime (45.56%) followed by trimethoprim (27%) and sulphamethizole (24.05%). The extent of resistance was meagre against tetracycline (2.53%) and gentamycin (2.95%). The 16S rRNA sequencing analysis identified that Proteobacteria (56%) were the dominant antibiotic resistant phyla, followed by Firmicutes (35%), Actinobacteria (8%) and Bacteroidetes. The dominant resistant bacterial isolates are Bacillus cereus (10%), followed by Alcaligenes faecalis (6.47%), Cytobacillus firmus (5.75%) Salinibacterium sp. (5%) and Marinobacter antarcticus (5%). Our study reveals the prevalence of antibiotic resistance showed significant differences in both the inner and outer fjords of Kongsfjorden and Krossfjorden (p < 0.05). This may be the input of antibiotic resistance bacteria released into the fjords from the preserved permafrost due to the melting of glaciers, horizontal gene transfer, and human influence in the Arctic region act as a selection pressure for the development and dissemination of more antibiotic resistant bacteria in Arctic fjords.}, }
@article {pmid38765968, year = {2025}, author = {Mancuso, CP and Baker, JS and Qu, E and Tripp, AD and Balogun, IO and Lieberman, TD}, title = {Intraspecies warfare restricts strain coexistence in human skin microbiomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38765968}, issn = {2692-8205}, support = {DP2 GM140922/GM/NIGMS NIH HHS/United States ; }, abstract = {Determining why only a fraction of encountered or applied strains engraft in a given person's microbiome is crucial for understanding and engineering these communities. Previous work has established that metabolic competition can restrict colonization success in vivo, but the relevance of bacterial warfare in preventing commensal engraftment has been less explored. Here, we demonstrate that intraspecies warfare presents a significant barrier to strain coexistence in the human skin microbiome by profiling 14,884 pairwise interactions between Staphylococcus epidermidis isolates cultured from eighteen people from six families. We find that intraspecies antagonisms are abundant, mechanistically diverse, independent of strain relatedness, and consistent with rapid evolution via horizontal gene transfer. Critically, these antagonisms are significantly depleted among strains residing on the same person relative to random assemblages, indicating a significant in vivo role. Together, our results emphasize that accounting for intraspecies warfare may be essential to the design of long-lasting probiotic therapeutics.}, }
@article {pmid38765680, year = {2024}, author = {Tan, BSY and Mohan, L and Watthanaworawit, W and Ngamprasertchai, T and Nosten, FH and Ling, C and Bifani, P}, title = {Detection of florfenicol resistance in opportunistic Acinetobacter spp. infections in rural Thailand.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1368813}, pmid = {38765680}, issn = {1664-302X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {Florfenicol (Ff) is an antimicrobial agent belonging to the class amphenicol used for the treatment of bacterial infections in livestock, poultry, and aquaculture (animal farming). It inhibits protein synthesis. Ff is an analog of chloramphenicol, an amphenicol compound on the WHO essential medicine list that is used for the treatment of human infections. Due to the extensive usage of Ff in animal farming, zoonotic pathogens have developed resistance to this antimicrobial agent. There are numerous reports of resistance genes from organisms infecting or colonizing animals found in human pathogens, suggesting a possible exchange of genetic materials. One of these genes is floR, a gene that encodes for an efflux pump that removes Ff from bacterial cells, conferring resistance against amphenicol, and is often associated with mobile genetic elements and other resistant determinants. In this study, we analyzed bacterial isolates recovered in rural Thailand from patients and environmental samples collected for disease monitoring. Whole genome sequencing was carried out for all the samples collected. Speciation and genome annotation was performed revealing the presence of the floR gene in the bacterial genome. The minimum inhibitory concentration (MIC) was determined for Ff and chloramphenicol. Chromosomal and phylogenetic analyses were performed to investigate the acquisition pattern of the floR gene. The presence of a conserved floR gene in unrelated Acinetobacter spp. isolated from human bacterial infections and environmental samples was observed, suggesting multiple and independent inter-species genetic exchange of drug-resistant determinants. The floR was found to be in the variable region containing various mobile genetic elements and other antibiotic resistance determinants; however, no evidence of HGT could be found. The floR gene identified in this study is chromosomal for all isolates. The study highlights a plausible impact of antimicrobials used in veterinary settings on human health. Ff shares cross-resistance with chloramphenicol, which is still in use in several countries. Furthermore, by selecting for floR-resistance genes, we may be selecting for and facilitating the zoonotic and reverse zoonotic exchange of other flanking resistance markers between human and animal pathogens or commensals with detrimental public health consequences.}, }
@article {pmid38760381, year = {2024}, author = {Nguyen, Q and Nguyen, YTP and Ha, TT and Tran, DTN and Voong, PV and Chau, V and Nguyen, PLN and Le, NTQ and Nguyen, LPH and Nguyen, TTN and Trinh, TV and Carrique-Mas, JJ and Baker, S and Thwaites, G and Rabaa, MA and Choisy, M and Chung, HT and Pham, DT}, title = {Genomic insights unveil the plasmid transfer mechanism and epidemiology of hypervirulent Klebsiella pneumoniae in Vietnam.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {4187}, pmid = {38760381}, issn = {2041-1723}, support = {222983/Z/21/Z//Wellcome Trust (Wellcome)/ ; 0010734//Oxford University | John Fell Fund, University of Oxford (John Fell OUP Research Fund)/ ; }, mesh = {*Klebsiella pneumoniae/genetics/pathogenicity/isolation &amp; purification ; Vietnam/epidemiology ; Humans ; *Plasmids/genetics ; *Klebsiella Infections/epidemiology/microbiology ; *Phylogeny ; *Whole Genome Sequencing ; Virulence/genetics ; Adult ; Female ; Gene Transfer, Horizontal ; Male ; Genome, Bacterial ; Middle Aged ; Anti-Bacterial Agents/pharmacology ; Child ; Genomics ; Drug Resistance, Bacterial/genetics ; }, abstract = {Hypervirulent Klebsiella pneumoniae (hvKp) is a significant cause of severe invasive infections in Vietnam, yet data on its epidemiology, population structure and dynamics are scarce. We screened hvKp isolates from patients with bloodstream infections (BSIs) at a tertiary infectious diseases hospital in Vietnam and healthy individuals, followed by whole genome sequencing and plasmid analysis. Among 700 BSI-causing Kp strains, 100 (14.3%) were hvKp. Thirteen hvKp isolates were identified from 350 rectal swabs of healthy adults; none from 500 rectal swabs of healthy children. The hvKp isolates were genetically diverse, encompassing 17 sequence types (STs), predominantly ST23, ST86 and ST65. Among the 113 hvKp isolates, 14 (12.6%) carried at least one antimicrobial resistance (AMR) gene, largely mediated by IncFII, IncR, and IncA/C plasmids. Notably, the acquisition of AMR conjugative plasmids facilitated horizontal transfer of the non-conjugative virulence plasmid between K. pneumoniae strains. Phylogenetic analysis demonstrated hvKp isolates from BSIs and human carriage clustered together, suggesting a significant role of intestinal carriage in hvKp transmission. Enhanced surveillance is crucial to understand the factors driving intestinal carriage and hvKp transmission dynamics for informing preventive measures. Furthermore, we advocate the clinical use of our molecular assay for diagnosing hvKp infections to guide effective management.}, }
@article {pmid38756985, year = {2024}, author = {Roughgarden, J}, title = {Lytic/Lysogenic Transition as a Life-History Switch.}, journal = {Virus evolution}, volume = {10}, number = {1}, pages = {veae028}, pmid = {38756985}, issn = {2057-1577}, abstract = {The transition between lytic and lysogenic life cycles is the most important feature of the life-history of temperate viruses. To explain this transition, an optimal life-history model is offered based a discrete-time formulation of phage/bacteria population dynamics that features infection of bacteria by Poisson sampling of virions from the environment. The time step is the viral latency period. In this model, density-dependent viral absorption onto the bacterial surface produces virus/bacteria coexistence and density dependence in bacterial growth is not needed. The formula for the transition between lytic and lysogenic phases is termed the 'fitness switch'. According to the model, the virus switches from lytic to lysogenic when its population grows faster as prophage than as virions produced by lysis of the infected cells, and conversely for the switch from lysogenic to lytic. A prophage that benefits the bacterium it infects automatically incurs lower fitness upon exiting the bacterial genome, resulting in its becoming locked into the bacterial genome in what is termed here as a 'prophage lock'. The fitness switch qualitatively predicts the ecogeographic rule that environmental enrichment leads to microbialization with a concomitant increase in lysogeny, fluctuating environmental conditions promote virus-mediated horizontal gene transfer, and prophage-containing bacteria can integrate into the microbiome of a eukaryotic host forming a functionally integrated tripartite holobiont. These predictions accord more with the 'Piggyback-the-Winner' hypothesis than with the 'Kill-the-Winner' hypothesis in virus ecology.}, }
@article {pmid38756231, year = {2024}, author = {Pobeguts, OV and Galaymina, MA and Sikamov, KV and Urazaeva, DR and Avshalumov, AS and Mikhailycheva, MV and Babenko, VV and Smirnov, IP and Gorbachev, AY}, title = {Unraveling the adaptive strategies of Mycoplasma hominis through proteogenomic profiling of clinical isolates.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1398706}, pmid = {38756231}, issn = {2235-2988}, mesh = {Humans ; *Mycoplasma hominis/genetics/metabolism ; *Proteogenomics ; *Mycoplasma Infections/microbiology ; *Adaptation, Physiological ; Biofilms/growth &amp; development ; Genome, Bacterial ; Phenotype ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics/metabolism ; Drug Resistance, Bacterial/genetics ; }, abstract = {INTRODUCTION: Mycoplasma hominis (M. hominis) belongs to the class Mollicutes, characterized by a very small genome size, reduction of metabolic pathways, including transcription factors, and the absence of a cell wall. Despite this, they adapt well not only to specific niches within the host organism but can also spread throughout the body, colonizing various organs and tissues. The adaptation mechanisms of M. hominis, as well as their regulatory pathways, are poorly understood. It is known that, when adapting to adverse conditions, Mycoplasmas can undergo phenotypic switches that may persist for several generations.<br><br>METHODS: To investigate the adaptive properties of M. hominis related to survival in the host, we conducted a comparative phenotypic and proteogenomic analysis of eight clinical isolates of M. hominis obtained from patients with urogenital infections and the laboratory strain H-34.<br><br>RESULTS: We have shown that clinical isolates differ in phenotypic features from the laboratory strain, form biofilms more effectively and show resistance to ofloxacin. The comparative proteogenomic analysis revealed that, unlike the laboratory strain, the clinical isolates possess several features related to stress survival: they switch carbon metabolism, activating the energetically least advantageous pathway of nucleoside utilization, which allows slowing down cellular processes and transitioning to a starvation state; they reconfigure the repertoire of membrane proteins; they have integrative conjugative elements in their genomes, which are key mediators of horizontal gene transfer. The upregulation of the methylating subunit of the restriction-modification (RM) system type I and the additional components of RM systems found in clinical isolates suggest that DNA methylation may play a role in regulating the adaptation mechanisms of M. hominis in the host organism. It has been shown that based on the proteogenomic profile, namely the genome sequence, protein content, composition of the RM systems and additional subunits HsdM, HsdS and HsdR, composition and number of transposable elements, as well as the sequence of the main variable antigen Vaa, we can divide clinical isolates into two phenotypes: typical colonies (TC), which have a high growth rate, and atypical (aTC) mini-colonies, which have a slow growth rate and exhibit properties similar to persisters.<br><br>DISCUSSION: We believe that the key mechanism of adaptation of M. hominis in the host is phenotypic restructuring, leading to a slowing down cellular processes and the formation of small atypical colonies. This is due to a switch in carbon metabolism and activation the pathway of nucleoside utilization. We hypothesize that DNA methylation may play a role in regulating this switch.}, }
@article {pmid38755134, year = {2024}, author = {Fujino, T and Sonoda, R and Higashinagata, T and Mishiro-Sato, E and Kano, K and Murakami, H}, title = {Ser/Leu-swapped cell-free translation system constructed with natural/in vitro transcribed-hybrid tRNA set.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {4143}, pmid = {38755134}, issn = {2041-1723}, support = {23H05456//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 21K05270//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; }, mesh = {*Cell-Free System ; *Protein Biosynthesis ; *Escherichia coli/genetics/metabolism ; RNA, Transfer, Leu/genetics/metabolism ; RNA, Transfer, Ser/metabolism/genetics ; Genetic Code ; RNA, Transfer/genetics/metabolism ; Green Fluorescent Proteins/metabolism/genetics ; Protein Engineering/methods ; Transcription, Genetic ; Anticodon/genetics/metabolism ; }, abstract = {The Ser/Leu-swapped genetic code can act as a genetic firewall, mitigating biohazard risks arising from horizontal gene transfer in genetically modified organisms. Our prior work demonstrated the orthogonality of this swapped code to the standard genetic code using a cell-free translation system comprised of 21 in vitro transcribed tRNAs. In this study, to advance this system for protein engineering, we introduce a natural/in vitro transcribed-hybrid tRNA set. This set combines natural tRNAs from Escherichia coli (excluding Ser, Leu, and Tyr) and in vitro transcribed tRNAs, encompassing anticodon-swapped tRNA[Ser]GAG and tRNA[Leu]GGA. This approach reduces the number of in vitro transcribed tRNAs required from 21 to only 4. In this optimized system, the production of a model protein, superfolder green fluorescent protein, increases to 3.5-fold. With this hybrid tRNA set, the Ser/Leu-swapped cell-free translation system will stand as a potent tool for protein production with reduced biohazard concerns in future biological endeavors.}, }
@article {pmid38755022, year = {2024}, author = {Figueroa, W and Cazares, D and Cazares, A}, title = {Phage-plasmids: missed links between mobile genetic elements.}, journal = {Trends in microbiology}, volume = {32}, number = {7}, pages = {622-623}, doi = {10.1016/j.tim.2024.04.014}, pmid = {38755022}, issn = {1878-4380}, mesh = {*Bacteriophages/genetics ; *Plasmids/genetics ; *Interspersed Repetitive Sequences ; *Bacteria/genetics/virology ; Gene Transfer, Horizontal ; Gene Flow ; Evolution, Molecular ; }, abstract = {Phages and plasmids are discrete mobile genetic elements (MGEs) with critical roles in gene dissemination across bacteria but limited scope for exchanging DNA between them. By investigating recent gene-sharing events, Pfeifer and Rocha describe how the hybrid elements phage-plasmids (P-Ps) promote gene flow between MGE types and evolve into new ones.}, }
@article {pmid38754503, year = {2024}, author = {Wei, L and Han, Y and Zheng, J and Xu, X and Zhu, L}, title = {Accelerated dissemination of antibiotic resistant genes via conjugative transfer driven by deficient denitrification in biochar-based biofiltration systems.}, journal = {The Science of the total environment}, volume = {934}, number = {}, pages = {173268}, doi = {10.1016/j.scitotenv.2024.173268}, pmid = {38754503}, issn = {1879-1026}, mesh = {*Denitrification ; *Charcoal/chemistry ; *Gene Transfer, Horizontal ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents ; Filtration/methods ; Waste Disposal, Fluid/methods ; Wastewater/microbiology ; Biofilms ; }, abstract = {Biofiltration systems harbored and disseminated antibiotic resistance genes (ARGs), when confronting antibiotic-contained wastewater. Biochar, a widely used environmental remediation material, can mitigate antibiotic stress on adjoining microbes by lowering the availability of sorbed antibiotics, and enhance the attachment of denitrifiers. Herein, bench-scale biofiltration systems, packed with commercial biochars, were established to explore the pivotal drivers affecting ARG emergence. Results showed that biofiltration columns, achieving higher TN removal and denitrification capacity, showed a significant decrease in ARG accumulation (p < 0.05). The relative abundance of ARGs (0.014 ± 0.0008) in the attached biofilms decreased to 1/5-folds of that in the control group (0.065 ± 0.004). Functional analysis indicated ARGs' accumulation was less attributed to ARG activation or horizontal gene transfer (HGT) driven by sorbed antibiotics. Most denitrifiers, like Bradyrhizobium, Geothrix, etc., were found to be enriched and host ARGs. Nitrosative stress from deficient denitrification was demonstrated to be the dominant driver for affecting ARG accumulation and dissemination. Metagenomic and metaproteomic analysis revealed that nitrosative stress promoted the conjugative HGT of ARGs mainly via increasing the transmembrane permeability and enhancing the amino acid transport and metabolism, such as cysteine, methionine, and valine metabolism. Overall, this study highlighted the risks of deficient denitrification in promoting ARG transfer and transmission in biofiltration systems and natural ecosystems.}, }
@article {pmid38754416, year = {2024}, author = {Benz, F and Camara-Wilpert, S and Russel, J and Wandera, KG and Čepaitė, R and Ares-Arroyo, M and Gomes-Filho, JV and Englert, F and Kuehn, JA and Gloor, S and Mestre, MR and Cuénod, A and Aguilà-Sans, M and Maccario, L and Egli, A and Randau, L and Pausch, P and Rocha, EPC and Beisel, CL and Madsen, JS and Bikard, D and Hall, AR and Sørensen, SJ and Pinilla-Redondo, R}, title = {Type IV-A3 CRISPR-Cas systems drive inter-plasmid conflicts by acquiring spacers in trans.}, journal = {Cell host &amp; microbe}, volume = {32}, number = {6}, pages = {875-886.e9}, doi = {10.1016/j.chom.2024.04.016}, pmid = {38754416}, issn = {1934-6069}, mesh = {*CRISPR-Cas Systems ; *Plasmids/genetics ; *Klebsiella pneumoniae/genetics ; *Conjugation, Genetic ; Clustered Regularly Interspaced Short Palindromic Repeats ; Gene Transfer, Horizontal ; Bacteriophages/genetics ; Bacterial Proteins/genetics/metabolism ; }, abstract = {Plasmid-encoded type IV-A CRISPR-Cas systems lack an acquisition module, feature a DinG helicase instead of a nuclease, and form ribonucleoprotein complexes of unknown biological functions. Type IV-A3 systems are carried by conjugative plasmids that often harbor antibiotic-resistance genes and their CRISPR array contents suggest a role in mediating inter-plasmid conflicts, but this function remains unexplored. Here, we demonstrate that a plasmid-encoded type IV-A3 system co-opts the type I-E adaptation machinery from its host, Klebsiella pneumoniae (K. pneumoniae), to update its CRISPR array. Furthermore, we reveal that robust interference of conjugative plasmids and phages is elicited through CRISPR RNA-dependent transcriptional repression. By silencing plasmid core functions, type IV-A3 impacts the horizontal transfer and stability of targeted plasmids, supporting its role in plasmid competition. Our findings shed light on the mechanisms and ecological function of type IV-A3 systems and demonstrate their practical efficacy for countering antibiotic resistance in clinically relevant strains.}, }
@article {pmid38753980, year = {2024}, author = {He, Z and Dechesne, A and Schreiber, F and Zhu, YG and Larsson, DGJ and Smets, BF}, title = {Understanding Stimulation of Conjugal Gene Transfer by Nonantibiotic Compounds: How Far Are We?.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {21}, pages = {9017-9030}, doi = {10.1021/acs.est.3c06060}, pmid = {38753980}, issn = {1520-5851}, mesh = {*Conjugation, Genetic ; Reactive Oxygen Species/metabolism ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; }, abstract = {A myriad of nonantibiotic compounds is released into the environment, some of which may contribute to the dissemination of antimicrobial resistance by stimulating conjugation. Here, we analyzed a collection of studies to (i) identify patterns of transfer stimulation across groups and concentrations of chemicals, (ii) evaluate the strength of evidence for the proposed mechanisms behind conjugal stimulation, and (iii) examine the plausibility of alternative mechanisms. We show that stimulatory nonantibiotic compounds act at concentrations from 1/1000 to 1/10 of the minimal inhibitory concentration for the donor strain but that stimulation is always modest (less than 8-fold). The main proposed mechanisms for stimulation via the reactive oxygen species/SOS cascade and/or an increase in cell membrane permeability are not unequivocally supported by the literature. However, we identify the reactive oxygen species/SOS cascade as the most likely mechanism. This remains to be confirmed by firm molecular evidence. Such evidence and more standardized and high-throughput conjugation assays are needed to create technologies and solutions to limit the stimulation of conjugal gene transfer and contribute to mitigating global antibiotic resistance.}, }
@article {pmid38752994, year = {2024}, author = {Ortiz Charneco, G and McDonnell, B and Kelleher, P and Buivydas, A and Dashko, S and de Waal, PP and van Rijswijck, I and van Peij, NNME and Mahony, J and Van Sinderen, D}, title = {Plasmid-mediated horizontal gene mobilisation: Insights from two lactococcal conjugative plasmids.}, journal = {Microbial biotechnology}, volume = {17}, number = {5}, pages = {e14421}, pmid = {38752994}, issn = {1751-7915}, support = {//dsm-firmenich, Taste, Texture &amp; Health/ ; 12/RC/2273/SFI_/Science Foundation Ireland/Ireland ; 17/SP/4678/SFI_/Science Foundation Ireland/Ireland ; }, mesh = {*Plasmids/genetics ; *Conjugation, Genetic ; *Gene Transfer, Horizontal ; Bacterial Proteins/genetics/metabolism ; Lactococcus lactis/genetics ; }, abstract = {The distinct conjugation machineries encoded by plasmids pNP40 and pUC11B represent the most prevalent plasmid transfer systems among lactococcal strains. In the current study, we identified genetic determinants that underpin pNP40- and pUC11B-mediated, high-frequency mobilisation of other, non-conjugative plasmids. The mobilisation frequencies of the smaller, non-conjugative plasmids and the minimal sequences required for their mobilisation were determined, owing to the determination of the oriT sequences of both pNP40 and pUC11B, which allowed the identification of similar sequences in some of the non-conjugative plasmids that were shown to promote their mobilisation. Furthermore, the auxiliary gene mobC, two distinct functional homologues of which are present in several plasmids harboured by the pNP40- and pUC11B-carrying host strains, was observed to confer a high-frequency mobilisation phenotype. These findings provide mechanistic insights into how lactococcal conjugative plasmids achieve conjugation and promote mobilisation of non-conjugative plasmids. Ultimately, these insights would be harnessed to optimise conjugation and mobilisation strategies for the rapid and predictable development of robust and technologically improved strains.}, }
@article {pmid38752745, year = {2024}, author = {Tomasch, J and Kopejtka, K and Shivaramu, S and Mujakić, I and Koblížek, M}, title = {On the evolution of chromosomal regions with high gene strand bias in bacteria.}, journal = {mBio}, volume = {15}, number = {6}, pages = {e0060224}, pmid = {38752745}, issn = {2150-7511}, support = {GX19-28778X//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky (GA&#x10c;R)/ ; }, mesh = {*Chromosomes, Bacterial/genetics ; *Evolution, Molecular ; *DNA Replication ; Bacteria/genetics/classification ; Genome, Bacterial ; Gene Transfer, Horizontal ; DNA, Bacterial/genetics ; }, abstract = {On circular bacterial chromosomes, the majority of genes are coded on the leading strand. This gene strand bias (GSB) ranges from up to 85% in some Bacillota to a little more than 50% in other phyla. The factors determining the extent of the strand bias remain to be found. Here, we report that species in the phylum Gemmatimonadota share a unique chromosome architecture, distinct from neighboring phyla: in a conserved 600-kb region around the terminus of replication, almost all genes were located on the leading strands, while on the remaining part of the chromosome, the strand preference was more balanced. The high strand bias (HSB) region harbors the rRNA clusters, core, and highly expressed genes. Selective pressure for reduction of collisions with DNA replication to minimize detrimental mutations can explain the conservation of essential genes in this region. Repetitive and mobile elements are underrepresented, suggesting reduced recombination frequency by structural isolation from other parts of the chromosome. We propose that the HSB region forms a distinct chromosomal domain. Gemmatimonadota chromosomes evolved mainly by expansion through horizontal gene transfer and duplications outside of the ancient high strand bias region. In support of our hypothesis, we could further identify two Spiroplasma strains on a similar evolutionary path.IMPORTANCEOn bacterial chromosomes, a preferred location of genes on the leading strand has evolved to reduce conflicts between replication and transcription. Despite a vast body of research, the question why bacteria show large differences in their gene strand bias is still not solved. The discovery of "hybrid" chromosomes in different phyla, including Gemmatimonadota, in which a conserved high strand bias is found exclusively in a region at ter, points toward a role of nucleoid structure, additional to replication, in the evolution of strand preferences. A fine-grained structural analysis of the ever-increasing number of available bacterial genomes could help to better understand the forces that shape the sequential and spatial organization of the cell's information content.}, }
@article {pmid38750628, year = {2024}, author = {Mrnjavac, N and Nagies, FSP and Wimmer, JLE and Kapust, N and Knopp, MR and Trost, K and Modjewski, L and Bremer, N and Mentel, M and Esposti, MD and Mizrahi, I and Allen, JF and Martin, WF}, title = {The radical impact of oxygen on prokaryotic evolution-enzyme inhibition first, uninhibited essential biosyntheses second, aerobic respiration third.}, journal = {FEBS letters}, volume = {598}, number = {14}, pages = {1692-1714}, pmid = {38750628}, issn = {1873-3468}, support = {101018894//H2020 European Research Council/ ; MA 1426/21-1//Deutsche Forschungsgemeinschaft/ ; 1/0457/24//Scientific Grant Agency of the Ministry of Education of the Slovak Republic (VEGA)/ ; 2476/2-1//German-Israeli Project Cooperation (DIP)/ ; 1426/23-1//German-Israeli Project Cooperation (DIP)/ ; 101018894/ERC_/European Research Council/International ; 96742//Volkswagen Foundation/ ; }, mesh = {*Oxygen/metabolism ; Aerobiosis ; Phylogeny ; Prokaryotic Cells/metabolism ; Evolution, Molecular ; Oxidation-Reduction ; Enzymes/metabolism/genetics ; }, abstract = {Molecular oxygen is a stable diradical. All O2-dependent enzymes employ a radical mechanism. Generated by cyanobacteria, O2 started accumulating on Earth 2.4 billion years ago. Its evolutionary impact is traditionally sought in respiration and energy yield. We mapped 365 O2-dependent enzymatic reactions of prokaryotes to phylogenies for the corresponding 792 protein families. The main physiological adaptations imparted by O2-dependent enzymes were not energy conservation, but novel organic substrate oxidations and O2-dependent, hence O2-tolerant, alternative pathways for O2-inhibited reactions. Oxygen-dependent enzymes evolved in ancestrally anaerobic pathways for essential cofactor biosynthesis including NAD[+], pyridoxal, thiamine, ubiquinone, cobalamin, heme, and chlorophyll. These innovations allowed prokaryotes to synthesize essential cofactors in O2-containing environments, a prerequisite for the later emergence of aerobic respiratory chains.}, }
@article {pmid38747597, year = {2024}, author = {Stindt, KR and McClean, MN}, title = {Tuning interdomain conjugation to enable in situ population modification in yeasts.}, journal = {mSystems}, volume = {9}, number = {6}, pages = {e0005024}, pmid = {38747597}, issn = {2379-5077}, support = {R01 AI154940/AI/NIAID NIH HHS/United States ; P30CA014520//University of Wisconsin Carbone Cancer Center (UWCCC)/ ; P30 CA014520/CA/NCI NIH HHS/United States ; R35 GM128873/GM/NIGMS NIH HHS/United States ; 135AAI9593//Wisconsin Alumni Research Foundation (WARF)/ ; R35GM128873//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; T32 GM130550/GM/NIGMS NIH HHS/United States ; T32GM130550//Molecular Biophysics Training Grant/ ; R01AI154940//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; }, mesh = {*Saccharomyces cerevisiae/genetics ; *Escherichia coli/genetics/metabolism ; Conjugation, Genetic ; }, abstract = {The ability to modify and control natural and engineered microbiomes is essential for biotechnology and biomedicine. Fungi are critical members of most microbiomes, yet technology for modifying the fungal members of a microbiome has lagged far behind that for bacteria. Interdomain conjugation (IDC) is a promising approach, as DNA transfer from bacterial cells to yeast enables in situ modification. While such genetic transfers have been known to naturally occur in a wide range of eukaryotes and are thought to contribute to their evolution, IDC has been understudied as a technique to control fungal or fungal-bacterial consortia. One major obstacle to the widespread use of IDC is its limited efficiency. In this work, we manipulated metabolic and physical interactions between genetically tractable Escherichia coli and Saccharomyces cerevisiae to control the incidence of IDC. We test the landscape of population interactions between the bacterial donors and yeast recipients to find that bacterial commensalism leads to maximized IDC, both in culture and in mixed colonies. We demonstrate the capacity of cell-to-cell binding via mannoproteins to assist both IDC incidence and bacterial commensalism in culture and model how these tunable controls can predictably yield a range of IDC outcomes. Furthermore, we demonstrate that these controls can be utilized to irreversibly alter a recipient yeast population, by both "rescuing" a poor-growing recipient population and collapsing a stable population via a novel IDC-mediated CRISPR/Cas9 system.IMPORTANCEFungi are important but often unaddressed members of most natural and synthetic microbial communities. This work highlights opportunities for modifying yeast microbiome populations through bacterial conjugation. While conjugation has been recognized for its capacity to deliver engineerable DNA to a range of cells, its dependence on cell contact has limited its efficiency. Here, we find "knobs" to control DNA transfer, by engineering the metabolic dependence between bacterial donors and yeast recipients and by changing their ability to physically adhere to each other. Importantly, we functionally validate these "knobs" by irreversibly altering yeast populations. We use these controls to "rescue" a failing yeast population, demonstrate the capacity of conjugated CRISPR/Cas9 to depress or collapse populations, and show that conjugation can be easily interrupted by disrupting cell-to-cell binding. These results offer building blocks toward in situ mycobiome editing, with significant implications for clinical treatments of fungal pathogens and other fungal system engineering.}, }
@article {pmid38746121, year = {2024}, author = {García-Bayona, L and Said, N and Coyne, MJ and Flores, K and Elmekki, NM and Sheahan, ML and Camacho, AG and Hutt, K and Yildiz, FH and Kovács, &#xc1;T and Waldor, MK and Comstock, LE}, title = {A pervasive large conjugative plasmid mediates multispecies biofilm formation in the intestinal microbiota increasing resilience to perturbations.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.04.29.590671}, pmid = {38746121}, issn = {2692-8205}, support = {K99 AI167064/AI/NIAID NIH HHS/United States ; P30 DK042086/DK/NIDDK NIH HHS/United States ; R00 AI167064/AI/NIAID NIH HHS/United States ; R25 GM109439/GM/NIGMS NIH HHS/United States ; }, abstract = {Although horizontal gene transfer is pervasive in the intestinal microbiota, we understand only superficially the roles of most exchanged genes and how the mobile repertoire affects community dynamics. Similarly, little is known about the mechanisms underlying the ability of a community to recover after a perturbation. Here, we identified and functionally characterized a large conjugative plasmid that is one of the most frequently transferred elements among Bacteroidales species and is ubiquitous in diverse human populations. This plasmid encodes both an extracellular polysaccharide and fimbriae, which promote the formation of multispecies biofilms in the mammalian gut. We use a hybridization-based approach to visualize biofilms in clarified whole colon tissue with unprecedented 3D spatial resolution. These biofilms increase bacterial survival to common stressors encountered in the gut, increasing strain resiliency, and providing a rationale for the plasmid's recent spread and high worldwide prevalence.}, }
@article {pmid38743630, year = {2024}, author = {Dewar, AE and Hao, C and Belcher, LJ and Ghoul, M and West, SA}, title = {Bacterial lifestyle shapes pangenomes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {21}, pages = {e2320170121}, pmid = {38743630}, issn = {1091-6490}, support = {834164/ERC_/European Research Council/International ; 834164//EC | ERC | HORIZON EUROPE European Research Council (ERC)/ ; }, mesh = {*Genome, Bacterial ; *Bacteria/genetics/classification ; *Phylogeny ; }, abstract = {Pangenomes vary across bacteria. Some species have fluid pangenomes, with a high proportion of genes varying between individual genomes. Other species have less fluid pangenomes, with different genomes tending to contain the same genes. Two main hypotheses have been suggested to explain this variation: differences in species' bacterial lifestyle and effective population size. However, previous studies have not been able to test between these hypotheses because the different features of lifestyle and effective population size are highly correlated with each other, and phylogenetically conserved, making it hard to disentangle their relative importance. We used phylogeny-based analyses, across 126 bacterial species, to tease apart the causal role of different factors. We found that pangenome fluidity was lower in i) host-associated compared with free-living species and ii) host-associated species that are obligately dependent on a host, live inside cells, and are more pathogenic and less motile. In contrast, we found no support for the competing hypothesis that larger effective population sizes lead to more fluid pangenomes. Effective population size appears to correlate with pangenome variation because it is also driven by bacterial lifestyle, rather than because of a causal relationship.}, }
@article {pmid38742878, year = {2024}, author = {Mies, US and Hervé, V and Kropp, T and Platt, K and Sillam-Dussès, D and Šobotník, J and Brune, A}, title = {Genome reduction and horizontal gene transfer in the evolution of Endomicrobia-rise and fall of an intracellular symbiosis with termite gut flagellates.}, journal = {mBio}, volume = {15}, number = {6}, pages = {e0082624}, pmid = {38742878}, issn = {2150-7511}, support = {//Max-Planck-Institut f&#xfc;r Terrestrische Mikrobiologie (MPI for Terrestrial Microbiology)/ ; SFB 987//Deutsche Forschungsgemeinschaft (DFG)/ ; }, mesh = {Animals ; *Isoptera/microbiology/parasitology ; *Symbiosis ; *Gene Transfer, Horizontal ; *Gastrointestinal Microbiome ; *Phylogeny ; *Genome, Bacterial ; *Bacteria/genetics/classification ; Evolution, Molecular ; Metagenome ; }, abstract = {Bacterial endosymbionts of eukaryotic hosts typically experience massive genome reduction, but the underlying evolutionary processes are often obscured by the lack of free-living relatives. Endomicrobia, a family-level lineage of host-associated bacteria in the phylum Elusimicrobiota that comprises both free-living representatives and endosymbionts of termite gut flagellates, are an excellent model to study evolution of intracellular symbionts. We reconstructed 67 metagenome-assembled genomes (MAGs) of Endomicrobiaceae among more than 1,700 MAGs from the gut microbiota of a wide range of termites. Phylogenomic analysis confirmed a sister position of representatives from termites and ruminants, and allowed to propose eight new genera in the radiation of Endomicrobiaceae. Comparative genome analysis documented progressive genome erosion in the new genus Endomicrobiellum, which comprises all flagellate endosymbionts characterized to date. Massive gene losses were accompanied by the acquisition of new functions by horizontal gene transfer, which led to a shift from a glucose-based energy metabolism to one based on sugar phosphates. The breakdown of glycolysis and many anabolic pathways for amino acids and cofactors in several subgroups was compensated by the independent acquisition of new uptake systems, including an ATP/ADP antiporter, from other gut microbiota. The putative donors are mostly flagellate endosymbionts from other bacterial phyla, including several, hitherto unknown lineages of uncultured Alphaproteobacteria, documenting the importance of horizontal gene transfer in the convergent evolution of these intracellular symbioses. The loss of almost all biosynthetic capacities in some lineages of Endomicrobiellum suggests that their originally mutualistic relationship with flagellates is on its decline.IMPORTANCEUnicellular eukaryotes are frequently colonized by bacterial and archaeal symbionts. A prominent example are the cellulolytic gut flagellates of termites, which harbor diverse but host-specific bacterial symbionts that occur exclusively in termite guts. One of these lineages, the so-called Endomicrobia, comprises both free-living and endosymbiotic representatives, which offers the unique opportunity to study the evolutionary processes underpinning the transition from a free-living to an intracellular lifestyle. Our results revealed a progressive gene loss in energy metabolism and biosynthetic pathways, compensated by the acquisition of new functions via horizontal gene transfer from other gut bacteria, and suggest the eventual breakdown of an initially mutualistic symbiosis. Evidence for convergent evolution of unrelated endosymbionts reflects adaptations to the intracellular environment of termite gut flagellates.}, }
@article {pmid38741889, year = {2024}, author = {Carrera Páez, LC and Olivier, M and Gambino, AS and Poklepovich, T and Aguilar, AP and Quiroga, MP and Centrón, D}, title = {Sporadic clone Escherichia coli ST615 as a vector and reservoir for dissemination of crucial antimicrobial resistance genes.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1368622}, pmid = {38741889}, issn = {2235-2988}, mesh = {*Escherichia coli/genetics/drug effects ; *Plasmids/genetics ; Humans ; *Escherichia coli Infections/microbiology ; *beta-Lactamases/genetics ; *Gene Transfer, Horizontal ; *Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; Escherichia coli Proteins/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Microbial Sensitivity Tests ; Latin America ; Drug Resistance, Bacterial/genetics ; }, abstract = {There is scarce information concerning the role of sporadic clones in the dissemination of antimicrobial resistance genes (ARGs) within the nosocomial niche. We confirmed that the clinical Escherichia coli M19736 ST615 strain, one of the first isolates of Latin America that harbors a plasmid with an mcr-1 gene, could receive crucial ARG by transformation and conjugation using as donors critical plasmids that harbor bla CTX-M-15, bla KPC-2, bla NDM-5, bla NDM-1, or aadB genes. Escherichia coli M19736 acquired bla CTX-M-15, bla KPC-2, bla NDM-5, bla NDM-1, and aadB genes, being only blaNDM-1 maintained at 100% on the 10th day of subculture. In addition, when the evolved MDR-E. coli M19736 acquired sequentially bla CTX-M-15 and bla NDM-1 genes, the maintenance pattern of the plasmids changed. In addition, when the evolved XDR-E. coli M19736 acquired in an ulterior step the paadB plasmid, a different pattern of the plasmid's maintenance was found. Interestingly, the evolved E. coli M19736 strains disseminated simultaneously the acquired conjugative plasmids in different combinations though selection was ceftazidime in all cases. Finally, we isolated and characterized the extracellular vesicles (EVs) from the native and evolved XDR-E. coli M19736 strains. Interestingly, EVs from the evolved XDR-E. coli M19736 harbored bla CTX-M-15 though the pDCAG1-CTX-M-15 was previously lost as shown by WGS and experiments, suggesting that EV could be a relevant reservoir of ARG for susceptible bacteria. These results evidenced the genetic plasticity of a sporadic clone of E. coli such as ST615 that could play a relevant transitional link in the clinical dynamics and evolution to multidrug/extensively/pandrug-resistant phenotypes of superbugs within the nosocomial niche by acting simultaneously as a vector and reservoir of multiple ARGs which later could be disseminated.}, }
@article {pmid38741746, year = {2024}, author = {Ghaly, TM and Gillings, MR and Rajabal, V and Paulsen, IT and Tetu, SG}, title = {Horizontal gene transfer in plant microbiomes: integrons as hotspots for cross-species gene exchange.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1338026}, pmid = {38741746}, issn = {1664-302X}, abstract = {Plant microbiomes play important roles in plant health and fitness. Bacterial horizontal gene transfer (HGT) can influence plant health outcomes, driving the spread of both plant growth-promoting and phytopathogenic traits. However, community dynamics, including the range of genetic elements and bacteria involved in this process are still poorly understood. Integrons are genetic elements recently shown to be abundant in plant microbiomes, and are associated with HGT across broad phylogenetic boundaries. They facilitate the spread of gene cassettes, small mobile elements that collectively confer a diverse suite of adaptive functions. Here, we analysed 5,565 plant-associated bacterial genomes to investigate the prevalence and functional diversity of integrons in this niche. We found that integrons are particularly abundant in the genomes of Pseudomonadales, Burkholderiales, and Xanthomonadales. In total, we detected nearly 9,000 gene cassettes, and found that many could be involved in plant growth promotion or phytopathogenicity, suggesting that integrons might play a role in bacterial mutualistic or pathogenic lifestyles. The rhizosphere was enriched in cassettes involved in the transport and metabolism of diverse substrates, suggesting that they may aid in adaptation to this environment, which is rich in root exudates. We also found that integrons facilitate cross-species HGT, which is particularly enhanced in the phyllosphere. This finding may provide an ideal opportunity to promote plant growth by fostering the spread of genes cassettes relevant to leaf health. Together, our findings suggest that integrons are important elements in plant microbiomes that drive HGT, and have the potential to facilitate plant host adaptation.}, }
@article {pmid38741126, year = {2024}, author = {Blanco-Melo, D and Campbell, MA and Zhu, H and Dennis, TPW and Modha, S and Lytras, S and Hughes, J and Gatseva, A and Gifford, RJ}, title = {A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus fossil record.}, journal = {Genome biology}, volume = {25}, number = {1}, pages = {120}, pmid = {38741126}, issn = {1474-760X}, support = {MC_UU_12014/12/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; *Vertebrates/genetics/virology ; *Genome ; *Fossils ; *Phylogeny ; Evolution, Molecular ; Humans ; Gene Transfer, Horizontal ; Viruses/genetics ; Genomics/methods ; Endogenous Retroviruses/genetics ; DNA Transposable Elements ; }, abstract = {BACKGROUND: Genomic regions that remain poorly understood, often referred to as the dark genome, contain a variety of functionally relevant and biologically informative features. These include endogenous viral elements (EVEs)-virus-derived sequences that can dramatically impact host biology and serve as a virus fossil record. In this study, we introduce a database-integrated genome screening (DIGS) approach to investigate the dark genome in silico, focusing on EVEs found within vertebrate genomes.<br><br>RESULTS: Using DIGS on 874 vertebrate genomes, we uncover approximately 1.1 million EVE sequences, with over 99% originating from endogenous retroviruses or transposable elements that contain EVE DNA. We show that the remaining 6038 sequences represent over a thousand distinct horizontal gene transfer events across 10 virus families, including some that have not previously been reported as EVEs. We explore the genomic and phylogenetic characteristics of non-retroviral EVEs and determine their rates of acquisition during vertebrate evolution. Our study uncovers novel virus diversity, broadens knowledge of virus distribution among vertebrate hosts, and provides new insights into the ecology and evolution of vertebrate viruses.<br><br>CONCLUSIONS: We comprehensively catalog and analyze EVEs within 874 vertebrate genomes, shedding light on the distribution, diversity, and long-term evolution of viruses and reveal their extensive impact on vertebrate genome evolution. Our results demonstrate the power of linking a relational database management system to a similarity search-based screening pipeline for in silico exploration of the dark genome.}, }
@article {pmid38738821, year = {2024}, author = {Liao, L and Qin, Q and Yi, D and Lai, Q and Cong, B and Zhang, H and Shao, Z and Zhang, J and Chen, B}, title = {Evolution and adaptation of terrestrial plant-associated Plantibacter species into remote marine environments.}, journal = {Molecular ecology}, volume = {33}, number = {12}, pages = {e17385}, doi = {10.1111/mec.17385}, pmid = {38738821}, issn = {1365-294X}, support = {2022YFC2807501//National Key Research and Development Program of China/ ; 2023YFC2812600//National Key Research and Development Program of China/ ; 41976224//National Natural Science Foundation of China/ ; }, mesh = {*Gene Transfer, Horizontal ; Plants/microbiology/genetics ; Microbiota/genetics ; Phylogeny ; Adaptation, Physiological/genetics ; Genome, Bacterial/genetics ; Ecosystem ; Atlantic Ocean ; Biological Evolution ; Seawater/microbiology ; }, abstract = {Microbes are thought to be distributed and circulated around the world, but the connection between marine and terrestrial microbiomes remains largely unknown. We use Plantibacter, a representative genus associated with plants, as our research model to investigate the global distribution and adaptation of plant-related bacteria in plant-free environments, particularly in the remote Southern Ocean and the deep Atlantic Ocean. The marine isolates and their plant-associated relatives shared over 98% whole-genome average nucleotide identity (ANI), indicating recent divergence and ongoing speciation from plant-related niches to marine environments. Comparative genomics revealed that the marine strains acquired new genes via horizontal gene transfer from non-Plantibacter species and refined existing genes through positive selection to improve adaptation to new habitats. Meanwhile, marine strains retained the ability to interact with plants, such as modifying root system architecture and promoting germination. Furthermore, Plantibacter species were found to be widely distributed in marine environments, revealing an unrecognized phenomenon that plant-associated microbiomes have colonized the ocean, which could serve as a reservoir for plant growth-promoting microbes. This study demonstrates the presence of an active reservoir of terrestrial plant growth-promoting bacteria in remote marine systems and advances our understanding of the microbial connections between plant-associated and plant-free environments at the genome level.}, }
@article {pmid38736754, year = {2024}, author = {Singh, H and Gibb, B and Abdi, R}, title = {Abundance and diversity of methicillin-resistant bacteria from bathroom surfaces at workplaces using CHROMagar media, 16S, and dnaJ gene sequence typing.}, journal = {International journal of molecular epidemiology and genetics}, volume = {15}, number = {2}, pages = {12-21}, pmid = {38736754}, issn = {1948-1756}, abstract = {University campus communities consist of dynamic and diverse human populations originated from different regions of the country or the world. Their national/global movement to and from campus may contribute to the spread and buildup of methicillin-resistant (MR) bacteria, including MR Staphylococci (MRS) on high-touch surfaces, sinks, and toilets. However, studies on MR bacteria contamination of surfaces, sinks, and toilets are scarce in workplaces outside of healthcare settings. Hence, little is known whether university communities contaminate campus bathrooms by MR bacteria. This study evaluated the abundance, identity, and phylogenetics of MR bacteria grown on CHROMagar MRSA media from bathrooms at workplaces. We collected 21 sink and 21 toilet swab samples from 10 buildings on campus and cultured them on CHROMagar MRSA media, extracted DNA from MR bacteria colonies, sequenced PCR products of 16S and dnaJ primers, determined the sequence identities by BLAST search, and constructed a phylogenetic tree. Of 42 samples, 57.1% (24/42) harbored MR bacteria. MR bacteria were more prevalent on the sink (61.9%) than in the toilet (52.2%) and in male bathrooms (54.2%) than in female bathrooms (41.7%). The colony count on the bathroom surfaces of 42 samples varied in that 42.9% (18/42), 33.3, 14.3, and 9.5% of samples harbored 0, 100, and > 1000 MR bacteria colonies, respectively. Of MR bacteria sequenced, BLAST search and phylogenetic analysis showed that Staphylococcus accounted for 60% of the MR bacteria and the rest were non-Staphylococci. Of Staphylococcus carrying MR (n = 15), 53.3% were S. hemolyticus followed by S. lugdunensis (26.7%), S. epidermidis (8%), and a newly discovered S. borealis in 2020 (4%). Of non-Staphylococci MR bacteria, 20% accounted for Sphingomonas koreensis. Campus bathrooms serve as a reservoir for diverse bacteria carrying MR, which pose a direct risk of infection and a potential source of horizontal gene transfer. To reduce the health risk posed by MR bacteria in high traffic areas such as bathrooms additional environmental monitoring and improved decontamination practices are needed.}, }
@article {pmid38733792, year = {2024}, author = {Musat, F and Kjeldsen, KU and Rotaru, AE and Chen, SC and Musat, N}, title = {Archaea oxidizing alkanes through alkyl-coenzyme M reductases.}, journal = {Current opinion in microbiology}, volume = {79}, number = {}, pages = {102486}, doi = {10.1016/j.mib.2024.102486}, pmid = {38733792}, issn = {1879-0364}, mesh = {*Alkanes/metabolism ; *Archaea/enzymology/genetics/metabolism ; *Oxidation-Reduction ; *Oxidoreductases/metabolism/genetics ; *Phylogeny ; Electron Transport ; Archaeal Proteins/metabolism/genetics/chemistry ; Gene Transfer, Horizontal ; Bacteria/enzymology/genetics/metabolism/classification ; }, abstract = {This review synthesizes recent discoveries of novel archaea clades capable of oxidizing higher alkanes, from volatile ones like ethane to longer-chain alkanes like hexadecane. These archaea, termed anaerobic multicarbon alkane-oxidizing archaea (ANKA), initiate alkane oxidation using alkyl-coenzyme M reductases, enzymes similar to the methyl-coenzyme M reductases of methanogenic and anaerobic methanotrophic archaea (ANME). The polyphyletic alkane-oxidizing archaea group (ALOX), encompassing ANME and ANKA, harbors increasingly complex alkane degradation pathways, correlated with the alkane chain length. We discuss the evolutionary trajectory of these pathways emphasizing metabolic innovations and the acquisition of metabolic modules via lateral gene transfer. Additionally, we explore the mechanisms by which archaea couple alkane oxidation with the reduction of electron acceptors, including electron transfer to partner sulfate-reducing bacteria (SRB). The phylogenetic and functional constraints that shape ALOX-SRB associations are also discussed. We conclude by highlighting the research needs in this emerging research field and its potential applications in biotechnology.}, }
@article {pmid40078307, year = {2024}, author = {Salman, S and Umar, Z and Xiao, Y}, title = {Current epidemiologic features and health dynamics of ESBL-producing Escherichia coli in China.}, journal = {Biosafety and health}, volume = {6}, number = {1}, pages = {40-49}, pmid = {40078307}, issn = {2590-0536}, abstract = {Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (E. coli) are widespread in China, with occurrences documented in humans, animals, and the environment. The dissemination of ESBL-producing E. coli is likely facilitated by the widespread use of antibiotics in human and animal agriculture, the presence of antibiotic-resistant bacteria (ARBs) in animal feces, and close human-animal interactions. Plasmids, particularly those belonging to incompatibility (Inc) group, such as IncF, IncI, and IncH families, play a vital role in facilitating the horizontal gene transfer of ESBL genes across various sectors, from humans to animals and the environment. IS26 and IS1 elements also significantly influences the mobilization and evolution of antibiotic-resistance genes (ARGs), contributing to the spread of ESBL-producing E. coli. bla CTX-M-14, bla CTX-15, and bla CTX-M-55 are prevalent in ESBL-producing E. coli across the three domains and are often found in conjunction with other ARGs. Considering these challenges, it is imperative to take proactive measures to prevent the further spread of ARBs. This includes the judicious and responsible use of antibiotics and efforts to minimize contact with animal feces. Sector-specific strategies should be developed to effectively educate and engage relevant personnel in tackling this multifaceted problem. These efforts are vital to combat the dissemination of ESBL-producing E. coli and preserve public health.}, }
@article {pmid39295911, year = {2023}, author = {Panwar, S and Kumari, S and Verma, J and Bakshi, S and Narendrakumar, L and Paul, D and Das, B}, title = {Toxin-linked mobile genetic elements in major enteric bacterial pathogens.}, journal = {Gut microbiome (Cambridge, England)}, volume = {4}, number = {}, pages = {e5}, pmid = {39295911}, issn = {2632-2897}, abstract = {One of the fascinating outcomes of human microbiome studies adopting multi-omics technology is its ability to decipher millions of microbial encoded functions in the most complex and crowded microbial ecosystem, including the human gastrointestinal (GI) tract without cultivating the microbes. It is well established that several functions that modulate the human metabolism, nutrient assimilation, immunity, infections, disease severity and therapeutic efficacy of drugs are mostly of microbial origins. In addition, these microbial functions are dynamic and can disseminate between microbial taxa residing in the same ecosystem or other microbial ecosystems through horizontal gene transfer. For clinicians and researchers alike, understanding the toxins, virulence factors and drug resistance traits encoded by the microbes associated with the human body is of utmost importance. Nevertheless, when such traits are genetically linked with mobile genetic elements (MGEs) that make them transmissible, it creates an additional burden to public health. This review mainly focuses on the functions of gut commensals and the dynamics and crosstalk between commensal and pathogenic bacteria in the gut. Also, the review summarises the plethora of MGEs linked with virulence genes present in the genomes of various enteric bacterial pathogens, which are transmissible among other pathogens and commensals.}, }
@article {pmid40166126, year = {2025}, author = {Zhang, Y and Zhang, B and Ahmed, I and Zhang, H and He, Y}, title = {Profiles and natural drivers of antibiotic resistome in multiple environmental media in penguin-colonized area in Antarctica.}, journal = {Fundamental research}, volume = {5}, number = {1}, pages = {269-281}, pmid = {40166126}, issn = {2667-3258}, abstract = {Profiles and driving mechanisms of antibiotic resistome in the polar region are important for exploring the natural evolution of antibiotic resistance genes (ARGs). Here, we evaluated the profiles of antibiotic resistome in multiple media on Inexpressible Island, Terra Nova Bay, Antarctica. Average concentrations of ARGs in intracellular DNA (iARGs) among water (3.98 × 10[6] copies/L), soil (3.41 × 10[7] copies/kg), and penguin guano (7.04 × 10[7] copies/kg) were higher than those of ARGs in extracellular DNA (eARGs) among water (1.99 × 10[4] copies/L), soil (1.75 × 10[6] copies/kg), and penguin guano (8.02 × 10[6] copies/kg). It was indicated that the transmission of ARGs across different media occurs with around 77.8% of iARGs from soil and 86.7% of iARGs from penguins observed in water, and 80.7% of iARGs and 56.7% of eARGs from penguins found in soil. Annual inputs of ARGs from Adélie penguins on Inexpressible Island have increased since 1983. Bacitracin, multidrug, and aminoglycoside resistance genes were the main ARGs among water, soil, and penguin guano. Primary medium-risk ARGs associated with human pathogenic bacteria were multidrug resistance genes, and main low-risk ARGs associated with mobile genetic elements (MGEs) were aminoglycoside resistance genes. Antibiotic-resistant bacteria (ARB) from soil and penguins were more phylogenetically related to aquatic antibiotic-resistant mesophiles than aquatic antibiotic-resistant psychrophiles. MGEs, ARB, bacterial diversities, antibiotics, and metals could explain total ARGs between water and soil. Intracellular MGEs were the most significant in-situ driver of iARGs in water, reflecting that horizontal gene transfer could facilitate the spread of ARGs in water. Penguins were important ex-situ drivers of environmental antibiotic resistome, which was linked with risky ARGs between water and soil. These findings highlight the major roles of natural drivers (e.g., MGEs and penguins) in shaping environmental antibiotic resistome in polar areas, improving our understanding of the evolution of environmental microbiome.}, }
@article {pmid38818484, year = {2022}, author = {Zhou, Z and Liu, Y and Anantharaman, K and Li, M}, title = {The expanding Asgard archaea invoke novel insights into Tree of Life and eukaryogenesis.}, journal = {mLife}, volume = {1}, number = {4}, pages = {374-381}, pmid = {38818484}, issn = {2770-100X}, abstract = {The division of organisms on the Tree of Life into either a three-domain (3D) tree or a two-domain (2D) tree has been disputed for a long time. Ever since the discovery of Archaea by Carl Woese in 1977 using 16S ribosomal RNA sequence as the evolutionary marker, there has been a great advance in our knowledge of not only the growing diversity of Archaea but also the evolutionary relationships between different lineages of living organisms. Here, we present this perspective to summarize the progress of archaeal diversity and changing notion of the Tree of Life. Meanwhile, we provide the latest progress in genomics/physiology-based discovery of Asgard archaeal lineages as the closest relative of Eukaryotes. Furthermore, we propose three major directions for future research on exploring the "next one" closest Eukaryote relative, deciphering the function of archaeal eukaryotic signature proteins and eukaryogenesis from both genomic and physiological aspects, and understanding the roles of horizontal gene transfer, viruses, and mobile elements in eukaryogenesis.}, }
@article {pmid39816412, year = {2022}, author = {Arredondo-Hernandez, R and Siebe, C and Castillo-Rojas, G and Ponce de León, S and López-Vidal, Y}, title = {The synergistic interaction of systemic inflammation, dysbiosis and antimicrobial resistance promotes growth restriction in children with acute severe malnutrition: An emphasis on Escherichia coli.}, journal = {Frontiers in antibiotics}, volume = {1}, number = {}, pages = {1001717}, pmid = {39816412}, issn = {2813-2467}, abstract = {A healthy development is denied to millions of children worldwide as harsh life conditions manifest themselves in an altered inflammation-prone microbiome crosstalk environment. Keynote of this tragedy is that insufficient nutritious amino acid blocks lipids-intake to sustain diverse microbiota, and promotes the generalist strategy followed by Escherichia coli -besides other proteobacteria- of shifting gut metabolism, subverting the site specificity of first immune reaction. Furthermore, it could be hypothesized that selective success lies in their ability to induce inflammation, since this phenomenon also fuels horizontal gene transfer (HGT). In this review, we dilucidate how immune mechanisms of environmental enteric dysfunction affect overgrowth restriction, infectious morbidity rate, and acquired lifelong risks among severe acute malnourished children. Also, despite acknowledging complexities of antimicrobial resistant enrichment, we explore and speculate over the links between virulence regulation and HGT as an indissociable part in the quest for new inflammatory niches by open genome bacteria, particularly when both collide in the most vulnerable.}, }
@article {pmid38818326, year = {2022}, author = {Da Cunha, V and Gaïa, M and Forterre, P}, title = {The expanding Asgard archaea and their elusive relationships with Eukarya.}, journal = {mLife}, volume = {1}, number = {1}, pages = {3-12}, pmid = {38818326}, issn = {2770-100X}, abstract = {The discovery of Asgard archaea and the exploration of their diversity over the last 6 years have deeply impacted the scientific community working on eukaryogenesis, rejuvenating an intense debate on the topology of the universal tree of life (uTol). Here, we discuss how this debate is impacted by two recent publications that expand the number of Asgard lineages and eukaryotic signature proteins (ESPs). We discuss some of the main difficulties that can impair the phylogenetic reconstructions of the uTol and suggest that the debate about its topology is not settled. We notably hypothesize the existence of horizontal gene transfers between ancestral Asgards and proto-eukaryotes that could result in the observed abnormal behaviors of some Asgard ESPs and universal marker proteins. This hypothesis is relevant regardless of the scenario considered regarding eukaryogenesis. It implies that the Asgards were already diversified before the last eukaryotic common ancestor and shared the same biotopes with proto-eukaryotes. We suggest that some Asgards might be still living in symbiosis today with modern Eukarya.}, }
@article {pmid38733104, year = {2024}, author = {Quiñonero-Coronel, MDM and Devos, DP and Garcillán-Barcia, MP}, title = {Specificities and commonalities of the Planctomycetes plasmidome.}, journal = {Environmental microbiology}, volume = {26}, number = {5}, pages = {e16638}, doi = {10.1111/1462-2920.16638}, pmid = {38733104}, issn = {1462-2920}, support = {9733//Moore-Simons Project on the Origin of the Eukaryotic Cell/ ; FPU20/04579//Ministerio de Universidades/ ; PID2020-117923GB-I0//Ministerio de Ciencia e Innovaci&#xf3;n/ ; }, mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; Bacteria/genetics/classification ; Bacterial Proteins/genetics ; Conjugation, Genetic ; Phylogeny ; Planctomycetales/genetics ; Evolution, Molecular ; Replication Origin/genetics ; }, abstract = {Plasmids, despite their critical role in antibiotic resistance and modern biotechnology, are understood in only a few bacterial groups in terms of their natural ecological dynamics. The bacterial phylum Planctomycetes, known for its unique molecular and cellular biology, has a largely unexplored plasmidome. This study offers a thorough exploration of the diversity of natural plasmids within Planctomycetes, which could serve as a foundation for developing various genetic research tools for this phylum. Planctomycetes plasmids encode a broad range of biological functions and appear to have coevolved significantly with their host chromosomes, sharing many homologues. Recent transfer events of insertion sequences between cohabiting chromosomes and plasmids were also observed. Interestingly, 64% of plasmid genes are distantly related to either chromosomally encoded genes or have homologues in plasmids from other bacterial groups. The planctomycetal plasmidome is composed of 36% exclusive proteins. Most planctomycetal plasmids encode a replication initiation protein from the Replication Protein A family near a putative iteron-containing replication origin, as well as active type I partition systems. The identification of one conjugative and three mobilizable plasmids suggests the occurrence of horizontal gene transfer via conjugation within this phylum. This comprehensive description enhances our understanding of the plasmidome of Planctomycetes and its potential implications in antibiotic resistance and biotechnology.}, }
@article {pmid38728817, year = {2024}, author = {Wen, X and Xu, J and Worrich, A and Li, X and Yuan, X and Ma, B and Zou, Y and Wang, Y and Liao, X and Wu, Y}, title = {Priority establishment of soil bacteria in rhizosphere limited the spread of tetracycline resistance genes from pig manure to soil-plant systems based on synthetic communities approach.}, journal = {Environment international}, volume = {187}, number = {}, pages = {108732}, doi = {10.1016/j.envint.2024.108732}, pmid = {38728817}, issn = {1873-6750}, mesh = {*Manure/microbiology ; Animals ; *Soil Microbiology ; Swine ; *Rhizosphere ; *Tetracycline Resistance/genetics ; Arabidopsis/microbiology/genetics ; Bacteria/genetics ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The spread of antibiotic resistance genes (ARGs) in agroecosystems through the application of animal manure is a global threat to human and environmental health. However, the adaptability and colonization ability of animal manure-derived bacteria determine the spread pathways of ARG in agroecosystems, which have rarely been studied. Here, we performed an invasion experiment by creating a synthetic communities (SynCom) with ten isolates from pig manure and followed its assembly during gnotobiotic cultivation of a soil-Arabidopsis thaliana (A. thaliana) system. We found that Firmicutes in the SynCom were efficiently filtered out in the rhizosphere, thereby limiting the entry of tetracycline resistance genes (TRGs) into the plant. However, Proteobacteria and Actinobacteria in the SynCom were able to establish in all compartments of the soil-plant system thereby spreading TRGs from manure to soil and plant. The presence of native soil bacteria prevented the establishment of manure-borne bacteria and effectively reduced the spread of TRGs. Achromobacter mucicolens and Pantoea septica were the main vectors for the entry of tetA into plants. Furthermore, doxycycline stress promoted the horizontal gene transfer (HGT) of the conjugative resistance plasmid RP4 within the SynCom in A. thaliana by upregulating the expression of HGT-related mRNAs. Therefore, this study provides evidence for the dissemination pathways of ARGs in agricultural systems through the invasion of manure-derived bacteria and HGT by conjugative resistance plasmids and demonstrates that the priority establishment of soil bacteria in the rhizosphere limited the spread of TRGs from pig manure to soil-plant systems.}, }
@article {pmid38727238, year = {2024}, author = {Lee, D-H and Lee, K and Kim, Y-S and Cha, C-J}, title = {Comprehensive genomic landscape of antibiotic resistance in Staphylococcus epidermidis.}, journal = {mSystems}, volume = {9}, number = {6}, pages = {e0022624}, pmid = {38727238}, issn = {2379-5077}, support = {2016001350004//Ministry of Environment (MOE)/ ; NRF-2023R1A2C1003654//National Research Foundation of Korea (NRF)/ ; }, mesh = {*Staphylococcus epidermidis/genetics/drug effects/isolation &amp; purification ; *Genome, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Genomics ; Humans ; Genes, Bacterial/genetics ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Bacterial Proteins/genetics ; Plasmids/genetics ; }, abstract = {UNLABELLED: Staphylococcus epidermidis, a common commensal bacterium found on human skin, can cause infections in clinical settings, and the presence of antibiotic resistance genes (ARGs) impedes the treatment of S. epidermidis infections. However, studies characterizing the ARGs in S. epidermidis with regard to genomic and ecological diversities are limited. Thus, we performed a comprehensive and comparative analysis of 405 high-quality S. epidermidis genomes, including those of 35 environmental isolates from the Han River, to investigate the genomic diversity of antibiotic resistance in this pathogen. Comparative genomic analysis revealed the prevalence of ARGs in S. epidermidis genomes associated with multi-locus sequence types. The genes encoding dihydrofolate reductase (dfrC) and multidrug efflux pump (norA) were genome-wide core ARGs. β-Lactam class ARGs were also highly prevalent in the S. epidermidis genomes, which was consistent with the resistance phenotype observed in river isolates. Furthermore, we identified chloramphenicol acetyltransferase genes (cat) in the plasmid-like sequences of the six river isolates, which have not been reported previously in S. epidermidis genomes. These genes were identical to those harbored by the Enterococcus faecium plasmids and associated with the insertion sequence 6 family transposases, homologous to those found in Staphylococcus aureus plasmids, suggesting the possibility of horizontal gene transfer between these Gram-positive pathogens. Comparison of the ARG and virulence factor profiles between S. epidermidis and S. aureus genomes revealed that these two species were clearly distinguished, suggesting genomic demarcation despite ecological overlap. Our findings provide a comprehensive understanding of the genomic diversity of antibiotic resistance in S. epidermidis.<br><br>IMPORTANCE: A comprehensive understanding of the antibiotic resistance gene (ARG) profiles of the skin commensal bacterium and opportunistic pathogen Staphylococcus epidermidis needs to be documented from a genomic point of view. Our study encompasses a comparative analysis of entire S. epidermidis genomes from various habitats, including those of 35 environmental isolates from the Han River sequenced in this study. Our results shed light on the distribution and diversity of ARGs within different S. epidermidis multi-locus sequence types, providing valuable insights into the ecological and genetic factors associated with antibiotic resistance. A comparison between S. epidermidis and Staphylococcus aureus revealed marked differences in ARG and virulence factor profiles, despite their overlapping ecological niches.}, }
@article {pmid38723713, year = {2024}, author = {Na, IY and Seo, J and Jin, Y and Ko, KS}, title = {Whole-plasmid analysis of NDM-1-producing Acinetobacter seifertii isolate and its fitness in several Acinetobacter species.}, journal = {Journal of global antimicrobial resistance}, volume = {38}, number = {}, pages = {223-226}, doi = {10.1016/j.jgar.2024.05.003}, pmid = {38723713}, issn = {2213-7173}, mesh = {*Acinetobacter/genetics/drug effects/isolation &amp; purification/enzymology ; *beta-Lactamases/genetics ; *Plasmids/genetics ; Humans ; *Microbial Sensitivity Tests ; Republic of Korea ; *Anti-Bacterial Agents/pharmacology ; *Acinetobacter Infections/microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Gene Transfer, Horizontal ; Genotype ; Carbapenems/pharmacology ; Conjugation, Genetic ; }, abstract = {OBJECTIVES: The aim of this study was to characterize an NDM-1-producing Acinetobacter seifertii isolates from a patient in South Korea.<br><br>METHODS: Antibiotic susceptibility testing and genotyping using multigene sequencing were performed and whole plasmid sequences were determined.<br><br>RESULTS: The genotype of A. seifertii was ST1899 and was resistant to ceftazidime, trimethoprim-sulfamethoxazole, and piperacillin-tazobactam, in addition to carbapenem. blaNDM-1 was surrounded by the ISAba125 insertion sequence within the structure of Tn125 in the 47 kb-sized plasmid. The plasmid exhibited a structure similar to that of other plasmids of diverse Acinetobacter sp. found worldwide. Transconjugation and the growth curve indicated that the plasmid was adapted to A. seifertii rather than other closely related Acinetobacter sp.<br><br>CONCLUSIONS: Acquisition of carbapenem resistance by horizontal transfer of the blaNDM-1-carrying plasmid from another Acinetobacter species was found with no growth defect.}, }
@article {pmid38721599, year = {2024}, author = {Yang, Z and Chai, Z and Wang, X and Zhang, Z and Zhang, F and Kang, F and Liu, W and Ren, H and Jin, Y and Yue, J}, title = {Comparative genomic analysis provides insights into the genetic diversity and pathogenicity of the genus Brucella.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1389859}, pmid = {38721599}, issn = {1664-302X}, abstract = {Some Brucella spp. are important pathogens. According to the latest prokaryotic taxonomy, the Brucella genus consists of facultative intracellular parasitic Brucella species and extracellular opportunistic or environmental Brucella species. Intracellular Brucella species include classical and nonclassical types, with different species generally exhibiting host preferences. Some classical intracellular Brucella species can cause zoonotic brucellosis, including B. melitensis, B. abortus, B. suis, and B. canis. Extracellular Brucella species comprise opportunistic or environmental species which belonged formerly to the genus Ochrobactrum and thus nowadays renamed as for example Brucella intermedia or Brucella anthropi, which are the most frequent opportunistic human pathogens within the recently expanded genus Brucella. The cause of the diverse phenotypic characteristics of different Brucella species is still unclear. To further investigate the genetic evolutionary characteristics of the Brucella genus and elucidate the relationship between its genomic composition and prediction of phenotypic traits, we collected the genomic data of Brucella from the NCBI Genome database and conducted a comparative genomics study. We found that classical and nonclassical intracellular Brucella species and extracellular Brucella species exhibited differences in phylogenetic relationships, horizontal gene transfer and distribution patterns of mobile genetic elements, virulence factor genes, and antibiotic resistance genes, showing the close relationship between the genetic variations and prediction of phenotypic traits of different Brucella species. Furthermore, we found significant differences in horizontal gene transfer and the distribution patterns of mobile genetic elements, virulence factor genes, and antibiotic resistance genes between the two chromosomes of Brucella, indicating that the two chromosomes had distinct dynamics and plasticity and played different roles in the survival and evolution of Brucella. These findings provide new directions for exploring the genetic evolutionary characteristics of the Brucella genus and could offer new clues to elucidate the factors influencing the phenotypic diversity of the Brucella genus.}, }
@article {pmid38717818, year = {2024}, author = {Nair, S and Barker, CR and Bird, M and Greig, DR and Collins, C and Painset, A and Chattaway, M and Pickard, D and Larkin, L and Gharbia, S and Didelot, X and Ribeca, P}, title = {Presence of phage-plasmids in multiple serovars of Salmonella enterica.}, journal = {Microbial genomics}, volume = {10}, number = {5}, pages = {}, pmid = {38717818}, issn = {2057-5858}, mesh = {*Plasmids/genetics ; *Salmonella enterica/virology/genetics ; *Serogroup ; Salmonella Infections/microbiology ; Bacteriophages/genetics/classification ; Salmonella Phages/genetics/classification ; Humans ; Phylogeny ; Gene Transfer, Horizontal ; Retrospective Studies ; }, abstract = {Evidence is accumulating in the literature that the horizontal spread of antimicrobial resistance (AMR) genes mediated by bacteriophages and bacteriophage-like plasmid (phage-plasmid) elements is much more common than previously envisioned. For instance, we recently identified and characterized a circular P1-like phage-plasmid harbouring a bla CTX-M-15 gene conferring extended-spectrum beta-lactamase (ESBL) resistance in Salmonella enterica serovar Typhi. As the prevalence and epidemiological relevance of such mechanisms has never been systematically assessed in Enterobacterales, in this study we carried out a follow-up retrospective analysis of UK Salmonella isolates previously sequenced as part of routine surveillance protocols between 2016 and 2021. Using a high-throughput bioinformatics pipeline we screened 47 784 isolates for the presence of the P1 lytic replication gene repL, identifying 226 positive isolates from 25 serovars and demonstrating that phage-plasmid elements are more frequent than previously thought. The affinity for phage-plasmids appears highly serovar-dependent, with several serovars being more likely hosts than others; most of the positive isolates (170/226) belonged to S. Typhimurium ST34 and ST19. The phage-plasmids ranged between 85.8 and 98.2 kb in size, with an average length of 92.1 kb; detailed analysis indicated a high amount of diversity in gene content and genomic architecture. In total, 132 phage-plasmids had the p0111 plasmid replication type, and 94 the IncY type; phylogenetic analysis indicated that both horizontal and vertical gene transmission mechanisms are likely to be involved in phage-plasmid propagation. Finally, phage-plasmids were present in isolates that were resistant and non-resistant to antimicrobials. In addition to providing a first comprehensive view of the presence of phage-plasmids in Salmonella, our work highlights the need for a better surveillance and understanding of phage-plasmids as AMR carriers, especially through their characterization with long-read sequencing.}, }
@article {pmid38717786, year = {2024}, author = {Zhang, Y and Wang, J and Yu, J}, title = {PSA: an effective method for predicting horizontal gene transfers through parsimonious phylogenetic networks.}, journal = {Cladistics : the international journal of the Willi Hennig Society}, volume = {40}, number = {4}, pages = {443-455}, doi = {10.1111/cla.12578}, pmid = {38717786}, issn = {1096-0031}, support = {NJYT24036//2024 Youth Science and Technology Talent Development Project (Youth Science and Technology Talents) of Education Department of Inner Mongolia Autonomous Region of China/ ; NMGIRT2318//University Youth Science and Technology Talent Development Project (Innovation Group Development Plan) of Inner Mongolia A. R. of China/ ; 2022MS01002//Natural Science Foundation of Inner Mongolia Province/ ; 12002175//National Natural Science Foundation of China/ ; 62002181//National Natural Science Foundation of China/ ; 62061035//National Natural Science Foundation of China/ ; }, mesh = {*Gene Transfer, Horizontal ; *Phylogeny ; *Algorithms ; Models, Genetic ; Evolution, Molecular ; Computer Simulation ; }, abstract = {Horizontal gene transfer (HGT) from one organism to another, according to some researchers, can be abundant in the evolution of species. A phylogenetic network is a network structure that describes the HGTs among species. Several studies have proposed methods to construct phylogenetic networks to predict HGTs based on parsimony values. Existing definitions of parsimony values for a phylogenetic network are based on the assumption that each gene site or segment evolves independently along different trees in the network. However, in the current study, we define a novel parsimony value, denoted the p definition, for phylogenetic networks, considering that a gene as a whole typically evolves along a tree. Using Simulated Annealing, a new method called the Phylogeny with Simulated Annealing (PSA) algorithm is proposed to search for an optimal network based on the p definition. The PSA method is tested on the simulated data. The results reveal that the parsimonious networks constructed using PSA can better represent the evolutionary relationships of species involving HGTs. Additionally, the HGTs predicted using PSA are more accurate than those predicted using other methods. The PSA algorithm is publicly accessible at http://github.com/imustu/sap.}, }
@article {pmid38716477, year = {2024}, author = {Cheewapat, R and Redkimned, J and Lekuthai, S and Kitti, T and Tasanapak, K and Thanwisai, A and Sitthisak, S and Sornda, T and Impheng, H and Onsurathum, S and Leungtongkam, U and Lamlertthon, S and Kucharoenphaibul, S and Wongwigkarn, J and Singkum, P and Chanchaithong, P and Thummeepak, R}, title = {Genomic Landscape Reveals Chromosomally-Mediated Antimicrobial Resistome and Virulome of a High-Risk International Clone II Acinetobacter baumannii AB073 from Thailand.}, journal = {Global health, epidemiology and genomics}, volume = {2024}, number = {}, pages = {8872463}, pmid = {38716477}, issn = {2054-4200}, mesh = {*Acinetobacter baumannii/genetics/drug effects ; Thailand/epidemiology ; *Acinetobacter Infections/microbiology/epidemiology/drug therapy ; Humans ; Genome, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; Drug Resistance, Multiple, Bacterial/genetics ; Carbapenems/pharmacology ; Virulence/genetics ; }, abstract = {This study utilized integrative bioinformatics' tools together with phenotypic assays to understand the whole-genome features of a carbapenem-resistant international clone II Acinetobacter baumannii AB073. Overall, we found the isolate to be resistant to seven antibiotic classes, penicillins, β-lactam/β-lactamase inhibitor combinations, cephalosporins, carbapenems, aminoglycosides, fluoroquinolones, and folate pathway antagonists. These resistance phenotypes are related to various chromosomal-located antibiotic resistance determinants involved in different mechanisms such as reduced permeability, antibiotic target protection, antibiotic target alteration, antibiotic inactivation, and antibiotic efflux. IC2 A. baumannii AB073 could not transfer antibiotic resistance by conjugation experiments. Likewise, mobilome analysis found that AB073 did not carry genetic determinants involving horizontal gene transfer. Moreover, this isolate also carried multiple genes associated with the ability of iron uptake, biofilm formation, immune invasion, virulence regulations, and serum resistance. In addition, the genomic epidemiological study showed that AB073-like strains were successful pathogens widespread in various geographic locations and clinical sources. In conclusion, the comprehensive analysis demonstrated that AB073 contained multiple genomic determinants which were important characteristics to classify this isolate as a successful international clone II obtained from Thailand.}, }
@article {pmid38714248, year = {2024}, author = {Wang, S and Tian, R and Bi, Y and Meng, F and Zhang, R and Wang, C and Wang, D and Liu, L and Zhang, B}, title = {A review of distribution and functions of extracellular DNA in the environment and wastewater treatment systems.}, journal = {Chemosphere}, volume = {359}, number = {}, pages = {142264}, doi = {10.1016/j.chemosphere.2024.142264}, pmid = {38714248}, issn = {1879-1298}, mesh = {*Wastewater ; DNA, Environmental/analysis ; Biofilms ; Biodiversity ; Environmental Monitoring/methods ; Gene Transfer, Horizontal ; Waste Disposal, Fluid/methods ; }, abstract = {Extracellular DNA refers to DNA fragments existing outside the cell, originating from various cell release mechanisms, including active secretion, cell lysis, and phage-mediated processes. Extracellular DNA serves as a vital environmental biomarker, playing crucial ecological and environmental roles in water bodies. This review is summarized the mechanisms of extracellular DNA release, including pathways involving cell lysis, extracellular vesicles, and type IV secretion systems. Then, the extraction and detection methods of extracellular DNA from water, soil, and biofilm are described and analyzed. Finally, we emphasize the role of extracellular DNA in microbial community systems, including its significant contributions to biofilm formation, biodiversity through horizontal gene transfer, and electron transfer processes. This review offers a comprehensive insight into the sources, distribution, functions, and impacts of extracellular DNA within aquatic environments, aiming to foster further exploration and understanding of extracellular DNA dynamics in aquatic environments as well as other environments.}, }
@article {pmid38714231, year = {2024}, author = {Wang, YL and Ikuma, K and Brown, AMV and Deonarine, A}, title = {Global survey of hgcA-carrying genomes in marine and freshwater sediments: Insights into mercury methylation processes.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {352}, number = {}, pages = {124117}, doi = {10.1016/j.envpol.2024.124117}, pmid = {38714231}, issn = {1873-6424}, mesh = {*Geologic Sediments/chemistry/microbiology ; *Mercury/metabolism ; Methylation ; *Water Pollutants, Chemical/metabolism ; *Fresh Water ; Methylmercury Compounds/metabolism ; Seawater/chemistry/microbiology ; Bacteria/genetics/metabolism ; Metagenome ; }, abstract = {Mercury (Hg) methylation is a microbially mediated process that produces methylmercury (MeHg), a bioaccumulative neurotoxin. A highly conserved gene pair, hgcAB, is required for Hg methylation, which provides a basis for identifying Hg methylators and evaluating their genomic composition. In this study, we conducted a large-scale omics analysis in which 281 metagenomic freshwater and marine sediment samples from 46 geographic locations across the globe were queried. Specific objectives were to examine the prevalence of Hg methylators, to identify horizontal gene transfer (HGT) events involving hgcAB within Hg methylator communities, and to identify associations between hgcAB and microbial biochemical functions/genes. Hg methylators from the phyla Desulfobacterota and Bacteroidota were dominant in both freshwater and marine sediments while Firmicutes and methanogens belonging to Euryarchaeota were identified only in freshwater sediments. Novel Hg methylators were found in the Phycisphaerae and Planctomycetia classes within the phylum Planctomycetota, including potential hgcA-carrying anammox metagenome-assembled genomes (MAGs) from Candidatus Brocadiia. HGT of hgcA and hgcB were identified in both freshwater and marine methylator communities. Spearman's correlation analysis of methylator genomes suggested that in addition to sulfide, thiosulfate, sulfite, and ammonia may be important parameters for Hg methylation processes in sediments. Overall, our results indicated that the biochemical drivers of Hg methylation vary between marine and freshwater sites, lending insight into the influence of environmental perturbances, such as a changing climate, on Hg methylation processes.}, }
@article {pmid38712952, year = {2024}, author = {Fidopiastis, PM and Childs, C and Esin, JJ and Stellern, J and Darin, A and Lorenzo, A and Mariscal, VT and Lorenz, J and Gopan, V and McAnulty, S and Visick, KL}, title = {Corrected and republished from: "Vibrio fischeri Possesses Xds and Dns Nucleases That Differentially Influence Phosphate Scavenging, Aggregation, Competence, and Symbiotic Colonization of Squid".}, journal = {Applied and environmental microbiology}, volume = {90}, number = {6}, pages = {e0032824}, pmid = {38712952}, issn = {1098-5336}, support = {R35 GM130355/GM/NIGMS NIH HHS/United States ; }, mesh = {*Aliivibrio fischeri/genetics/physiology/enzymology ; *Decapodiformes/microbiology ; Animals ; *Symbiosis ; *Phosphates/metabolism ; *Bacterial Proteins/metabolism/genetics ; Deoxyribonucleases/metabolism/genetics ; }, abstract = {Cells of Vibrio fischeri colonize the light organ of Euprymna scolopes, providing the squid bioluminescence in exchange for nutrients and protection. The bacteria encounter DNA-rich mucus throughout their transition to a symbiotic lifestyle, leading us to hypothesize a role for nuclease activity in the colonization process. In support of this, we detected abundant extracellular nuclease activity in growing cells of V. fischeri. To discover the gene(s) responsible for this activity, we screened a V. fischeri transposon mutant library for nuclease-deficient strains. Interestingly, only one strain, whose transposon insertion mapped to nuclease gene VF_1451, showed a complete loss of nuclease activity in our screens. A database search revealed that VF_1451 is homologous to the nuclease-encoding gene xds in Vibrio cholerae. However, V. fischeri strains lacking xds eventually revealed slight nuclease activity on plates upon prolonged incubation. This led us to hypothesize that a second secreted nuclease, identified through a database search as VF_0437, a homolog of V. cholerae dns, might be responsible for the residual nuclease activity. Here, we show that Xds and/or Dns are involved in essential aspects of V. fischeri biology, including natural transformation, aggregation, and phosphate scavenging. Furthermore, strains lacking either nuclease were outcompeted by the wild type for squid colonization. Understanding the specific role of nuclease activity in the squid colonization process represents an intriguing area of future research.IMPORTANCEFrom soil and water to host-associated secretions such as mucus, environments that bacteria inhabit are awash in DNA. Extracellular DNA (eDNA) is a nutritious resource that microbes dedicate significant energy to exploit. Calcium binds eDNA to promote cell-cell aggregation and horizontal gene transfer. eDNA hydrolysis impacts the construction of and dispersal from biofilms. Strategies in which pathogens use nucleases to avoid phagocytosis or disseminate by degrading host secretions are well-documented; significantly less is known about nucleases in mutualistic associations. This study describes the role of nucleases in the mutualism between Vibrio fischeri and its squid host Euprymna scolopes. We find that nuclease activity is an important determinant of colonization in V. fischeri, broadening our understanding of how microbes establish and maintain beneficial associations.}, }
@article {pmid38712904, year = {2024}, author = {Muelbaier, H and Arthen, F and Collins, G and Hickler, T and Hohberg, K and Lehmitz, R and Pauchet, Y and Pfenninger, M and Potapov, A and Romahn, J and Schaefer, I and Scheu, S and Schneider, C and Ebersberger, I and Bálint, M}, title = {Genomic evidence for the widespread presence of GH45 cellulases among soil invertebrates.}, journal = {Molecular ecology}, volume = {33}, number = {20}, pages = {e17351}, doi = {10.1111/mec.17351}, pmid = {38712904}, issn = {1365-294X}, support = {LOEWE/1/10/519/03/03.001(0014)/52//Landes-Offensive zur Entwicklung Wissenschaftlich-&#xf6;konomischer Exzellenz (LOEWE)/ ; BA 4843/4-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Animals ; *Phylogeny ; *Soil/chemistry ; *Invertebrates/genetics/enzymology ; *Cellulases/genetics/metabolism ; Lignin/metabolism ; Mites/genetics/enzymology ; Cellulose/metabolism ; Genomics ; }, abstract = {Lignocellulose is a major component of vascular plant biomass. Its decomposition is crucial for the terrestrial carbon cycle. Microorganisms are considered primary decomposers, but evidence increases that some invertebrates may also decompose lignocellulose. We investigated the taxonomic distribution and evolutionary origins of GH45 hydrolases, important enzymes for the decomposition of cellulose and hemicellulose, in a collection of soil invertebrate genomes. We found that these genes are common in springtails and oribatid mites. Phylogenetic analysis revealed that cellulase genes were acquired early in the evolutionary history of these groups. Domain architectures and predicted 3D enzyme structures indicate that these cellulases are functional. Patterns of presence and absence of these genes across different lineages prompt further investigation into their evolutionary and ecological benefits. The ubiquity of cellulase genes suggests that soil invertebrates may play a role in lignocellulose decomposition, independently or in synergy with microorganisms. Understanding the ecological and evolutionary implications might be crucial for understanding soil food webs and the carbon cycle.}, }
@article {pmid38712252, year = {2024}, author = {Buck, CB and Welch, N and Belford, AK and Varsani, A and Pastrana, DV and Tisza, MJ and Starrett, GJ}, title = {Widespread Horizontal Gene Transfer Among Animal Viruses.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38712252}, issn = {2692-8205}, abstract = {The initial objective of this study was to shed light on the evolution of small DNA tumor viruses by analyzing de novo assemblies of publicly available deep sequencing datasets. The survey generated a searchable database of contig snapshots representing more than 100,000 Sequence Read Archive records. Using modern structure-aware search tools, we iteratively broadened the search to include an increasingly wide range of other virus families. The analysis revealed a surprisingly diverse range of chimeras involving different virus groups. In some instances, genes resembling known DNA-replication modules or known virion protein operons were paired with unrecognizable sequences that structural predictions suggest may represent previously unknown replicases and novel virion architectures. Discrete clades of an emerging group called adintoviruses were discovered in datasets representing humans and other primates. As a proof of concept, we show that the contig database is also useful for discovering RNA viruses and candidate archaeal phages. The ancillary searches revealed additional examples of chimerization between different virus groups. The observations support a gene-centric taxonomic framework that should be useful for future virus-hunting efforts.}, }
@article {pmid38710287, year = {2024}, author = {Zuo, Y and Yang, J and Zhang, H and Li, L and Luo, J and Lv, Y and Yuan, M and Yang, K}, title = {Genome comparison of long-circulating field CnmeGV isolates from the same region.}, journal = {Virus research}, volume = {345}, number = {}, pages = {199390}, pmid = {38710287}, issn = {1872-7492}, mesh = {*Genome, Viral ; Animals ; *Genetic Variation ; Phylogeny ; China ; Granulovirus/genetics/classification/isolation &amp; purification ; Whole Genome Sequencing ; Oryza/virology ; Tandem Repeat Sequences/genetics ; Plant Diseases/virology ; Recombination, Genetic ; }, abstract = {Cnaphalocrocis medinalis granulovirus (CnmeGV), belonging to Betabaculovirus cnamedinalis, can infect the rice pest, the rice leaf roller. In 1979, a CnmeGV isolate, CnmeGV-EP, was collected from Enping County, China. In 2014, we collected another CnmeGV isolate, CnmeGV-EPDH3, at the same location and obtained the complete virus genome sequence using Illumina and ONT sequencing technologies. By combining these two virus isolates, we updated the genome annotation of CnmeGV and conducted an in-depth analysis of its genome features. CnmeGV genome contains abundant tandem repeat sequences, and the repeating units in the homologous regions (hrs) exhibit overlapping and nested patterns. The genetic variations within EPDH3 population show the high stability of CnmeGV genome, and tandem repeats are the only region of high genetic variation in CnmeGV genome replication. Some defective viral genomes formed by recombination were found within the population. Comparison analysis of the two virus isolates collected from Enping showed that the proteins encoded by the CnmeGV-specific genes were less conserved relative to the baculovirus core genes. At the genomic level, there are a large number of SNPs and InDels between the two virus isolates, especially in and around the bro genes and hrs. Additionally, we discovered that CnmeGV acquired a segment of non-ORF sequence from its host, which does not provide any new proteins but rather serves as redundant genetic material integrated into the viral genome. Furthermore, we observed that the host's transposon piggyBac has inserted into some virus genes. Together, dsDNA viruses could acquire non-coding genetic material from their hosts to expand the size of their genomes. These findings provide new insights into the evolution of dsDNA viruses.}, }
@article {pmid38710286, year = {2024}, author = {Zhao, F and Wang, J}, title = {Another piece of puzzle for the human microbiome: the gut virome under dietary modulation.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {51}, number = {10}, pages = {983-996}, doi = {10.1016/j.jgg.2024.04.013}, pmid = {38710286}, issn = {1673-8527}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Virome/genetics ; *Diet ; Bacteriophages/genetics/physiology ; Bacteria/genetics/classification/virology ; Gene Transfer, Horizontal ; Viruses/genetics ; }, abstract = {The virome is the most abundant and highly variable microbial consortium in the gut. Because of difficulties in isolating and culturing gut viruses and the lack of reference genomes, the virome has remained a relatively elusive aspect of the human microbiome. In recent years, studies on the virome have accumulated growing evidence showing that the virome is diet-modulated and widely involved in regulating health. Here, we review the responses of the gut virome to dietary intake and the potential health implications, presenting changes in the gut viral community and preferences of viral members to particular diets. We further discuss how viral-bacterial interactions and phage lifestyle shifts shape the gut microbiota. We also discuss the specific functions conferred by diet on the gut virome and bacterial community in the context of horizontal gene transfer, as well as the import of new viral members along with the diet. Collating these studies will expand our understanding of the dietary regulation of the gut virome and inspire dietary interventions and health maintenance strategies targeting the gut microbiota.}, }
@article {pmid38707295, year = {2024}, author = {Cochran, JP and Zhang, L and Parrott, BB and Seaman, JC}, title = {Plasmid size determines adsorption to clay and breakthrough in a saturated sand column.}, journal = {Heliyon}, volume = {10}, number = {9}, pages = {e29679}, pmid = {38707295}, issn = {2405-8440}, abstract = {Horizontal gene transfer (HGT) is a major factor in the spread of antibiotic resistant genes (ARG). Transformation, one mode of HGT, involves the acquisition and expression of extracellular DNA (eDNA). eDNA in soils is degraded rapidly by extracellular nucleases. However, if bound to a clay particle, eDNA can persist for long periods of time without losing its transformation ability. To better understand the mechanism of eDNA persistence in soil, this experiment assessed the effects of 1) clay mineralogy, 2) mixed salt solution, 3) plasmid size on DNA adsorption to clay and 4) breakthrough behavior of three differently sized plasmids in an environmentally relevant solution. Batch test methods were used to determine adsorption trends of three differently sized DNA plasmids, pUC19, pBR322, and pTYB21, to several pure clay minerals, goethite (α-FeOOH), illite, and kaolinite, and one environmental soil sample. Results show not all sorbents have equal adsorption capacity based on surface area with adsorption capacities decreasing from goethite > illite = kaolinite > bulk soil, and low ionic strength solutions will likely not significantly alter sorption trends. Additionally, plasmid DNA size (i.e., length) was shown to be a significant predictor of adsorption efficiency and that size affects DNA breakthrough, with breakthroughs occurring later with larger plasmids. Given that DNA persistence is linked to its adsorption to soil constituents and breakthrough, eDNA size is likely an important contributor to the spread of ARG within natural microbial communities.}, }
@article {pmid38705616, year = {2024}, author = {Bui, QTN and Kim, HS and Ki, JS}, title = {Polyphyletic origin of saxitoxin biosynthesis genes in the marine dinoflagellate Alexandrium revealed by comparative transcriptomics.}, journal = {Harmful algae}, volume = {134}, number = {}, pages = {102620}, doi = {10.1016/j.hal.2024.102620}, pmid = {38705616}, issn = {1878-1470}, mesh = {*Dinoflagellida/genetics/metabolism ; *Saxitoxin/genetics/biosynthesis ; *Phylogeny ; *Transcriptome ; Gene Expression Profiling ; Evolution, Molecular ; }, abstract = {The marine dinoflagellate Alexandrium is known to form harmful algal blooms, and at least 14 species within the genus can produce saxitoxins (STXs). STX biosynthesis genes (sxt) are individually revealed in toxic dinoflagellates; however, the evolutionary history remains controversial. Herein, we determined the transcriptome sequences of toxic Alexandrium (A. catenella and A. pacificum) and non-toxic Alexandrium (A. fraterculus and A. fragae) and characterized their sxt by focusing on evolutionary events and STX production. Comparative transcriptome analysis revealed higher homology of the sxt in toxic Alexandrium than in non-toxic species. Notably, non-toxic Alexandrium spp. were found to have lost two sxt core genes, namely sxtA4 and sxtG. Expression levels of 28 transcripts related to eight sxt core genes showed that sxtA, sxtG, and sxtI were relatively high (>1.5) in the toxic group compared to the non-toxic group. In contrast, the non-toxic group showed high expression levels in sxtU (1.9) and sxtD (1.7). Phylogenetic tree comparisons revealed distinct evolutionary patterns between 28S rDNA and sxtA, sxtB, sxtI, sxtD, and sxtU. However, similar topology was observed between 28S rDNA, sxtS, and sxtH/T. In the sxtB and sxtI phylogeny trees, toxic Alexandrium and cyanobacteria were clustered together, separating from non-toxic species. These suggest that Alexandrium may acquire sxt genes independently via horizontal gene transfer from toxic cyanobacteria and other multiple sources, demonstrating monocistronic transcripts of sxt in dinoflagellates.}, }
@article {pmid38705297, year = {2024}, author = {Xu, Q and Ali, S and Afzal, M and Nizami, AS and Han, S and Dar, MA and Zhu, D}, title = {Advancements in bacterial chemotaxis: Utilizing the navigational intelligence of bacteria and its practical applications.}, journal = {The Science of the total environment}, volume = {931}, number = {}, pages = {172967}, doi = {10.1016/j.scitotenv.2024.172967}, pmid = {38705297}, issn = {1879-1026}, mesh = {*Chemotaxis ; *Bacterial Physiological Phenomena ; *Bacteria ; Biodegradation, Environmental ; }, abstract = {The fascinating world of microscopic life unveils a captivating spectacle as bacteria effortlessly maneuver through their surroundings with astonishing accuracy, guided by the intricate mechanism of chemotaxis. This review explores the complex mechanisms behind this behavior, analyzing the flagellum as the driving force and unraveling the intricate signaling pathways that govern its movement. We delve into the hidden costs and benefits of this intricate skill, analyzing its potential to propagate antibiotic resistance gene while shedding light on its vital role in plant colonization and beneficial symbiosis. We explore the realm of human intervention, considering strategies to manipulate bacterial chemotaxis for various applications, including nutrient cycling, algal bloom and biofilm formation. This review explores the wide range of applications for bacterial capabilities, from targeted drug delivery in medicine to bioremediation and disease control in the environment. Ultimately, through unraveling the intricacies of bacterial movement, we can enhance our comprehension of the intricate web of life on our planet. This knowledge opens up avenues for progress in fields such as medicine, agriculture, and environmental conservation.}, }
@article {pmid38704526, year = {2024}, author = {Kobakhidze, S and Koulouris, S and Kakabadze, N and Kotetishvili, M}, title = {Genetic recombination-mediated evolutionary interactions between phages of potential industrial importance and prophages of their hosts within or across the domains of Escherichia, Listeria, Salmonella, Campylobacter, and Staphylococcus.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {155}, pmid = {38704526}, issn = {1471-2180}, mesh = {*Prophages/genetics ; *Recombination, Genetic ; Campylobacter/virology/genetics ; Staphylococcus/virology/genetics ; Gene Transfer, Horizontal ; Bacteriophages/genetics/physiology/classification ; Listeria/virology/genetics ; Salmonella/virology/genetics ; Evolution, Molecular ; Bacteria/virology/genetics ; }, abstract = {BACKGROUND: The in-depth understanding of the role of lateral genetic transfer (LGT) in phage-prophage interactions is essential to rationalizing phage applications for human and animal therapy, as well as for food and environmental safety. This in silico study aimed to detect LGT between phages of potential industrial importance and their hosts.<br><br>METHODS: A large array of genetic recombination detection algorithms, implemented in SplitsTree and RDP4, was applied to detect LGT between various Escherichia, Listeria, Salmonella, Campylobacter, Staphylococcus, Pseudomonas, and Vibrio phages and their hosts. PHASTER and RAST were employed respectively to identify prophages across the host genome and to annotate LGT-affected genes with unknown functions. PhageAI was used to gain deeper insights into the life cycle history of recombined phages.<br><br>RESULTS: The split decomposition inferences (bootstrap values: 91.3-100; fit: 91.433-100), coupled with the Phi (0.0-2.836E-12) and RDP4 (P being well below 0.05) statistics, provided strong evidence for LGT between certain Escherichia, Listeria, Salmonella, and Campylobacter virulent phages and prophages of their hosts. The LGT events entailed mainly the phage genes encoding for hypothetical proteins, while some of these genetic loci appeared to have been affected even by intergeneric recombination in specific E. coli and S. enterica virulent phages when interacting with their host prophages. Moreover, it is shown that certain L. monocytogenes virulent phages could serve at least as the donors of the gene loci, involved in encoding for the basal promoter specificity factor, for L. monocytogenes. In contrast, the large genetic clusters were determined to have been simultaneously exchanged by many S. aureus prophages and some Staphylococcus temperate phages proposed earlier as potential therapeutic candidates (in their native or modified state). The above genetic clusters were found to encompass multiple genes encoding for various proteins, such as e.g., phage tail proteins, the capsid and scaffold proteins, holins, and transcriptional terminator proteins.<br><br>CONCLUSIONS: It is suggested that phage-prophage interactions, mediated by LGT (including intergeneric recombination), can have a far-reaching impact on the co-evolutionary trajectories of industrial phages and their hosts especially when excessively present across microbially rich environments.}, }
@article {pmid38704005, year = {2024}, author = {Lv, B and Jiang, C and Han, Y and Wu, D and Jin, L and Zhu, G and An, T and Shi, J}, title = {Diverse bacterial hosts and potential risk of antibiotic resistomes in ship ballast water revealed by metagenomic binning.}, journal = {Environmental research}, volume = {253}, number = {}, pages = {119056}, doi = {10.1016/j.envres.2024.119056}, pmid = {38704005}, issn = {1096-0953}, mesh = {*Ships ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; Metagenomics ; Water Microbiology ; Anti-Bacterial Agents/pharmacology ; Metagenome ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; }, abstract = {Ship ballast water promoting the long-range migration of antibiotic resistance genes (ARGs) has raised a great concern. This study attempted to reveal ARGs profile in ballast water and decipher their hosts and potential risk using metagenomic approaches. In total, 710 subtypes across 26 ARG types were identified among the ballast water samples from 13 ships of 11 countries and regions, and multidrug resistance genes were the most dominant ARGs. The composition of ARGs were obviously different across samples, and only 5% of the ARG subtypes were shared by all samples. Procrustes analysis showed the bacterial community contributed more than the mobile genetic elements (MGEs) in shaping the antibiotic resistome. Further, 79 metagenome-assembled genomes (46 genera belong to four phyla) were identified as ARG hosts, with predominantly affiliated with the Proteobacteria. Notably, potential human pathogens (Alcaligenes, Mycolicibacterium, Rhodococcus and Pseudomonas) were also recognized as the ARG hosts. Above 30% of the ARGs hosts contained the MGEs simultaneously, supporting a pronounced horizontal gene transfer capability. A total of 43 subtypes (six percent of overall ARGs) of ARGs were assessed with high-risk, of which 23 subtypes belonged to risk Rank I (including rsmA, ugd, etc.) and 20 subtypes to the risk Rank II (including aac(6)-I, sul1, etc.). In addition, antibiotic resistance risk index indicated the risk of ARGs in ballast water from choke points of maritime trade routes was significantly higher than that from other regions. Overall, this study offers insights for risk evaluation and management of antibiotic resistance in ballast water.}, }
@article {pmid38700770, year = {2024}, author = {Zhang, Y and Ji, Y and Tang, X and Chen, M and Su, J}, title = {Spread of plasmids carrying antibiotic resistance genes in soil-lettuce-snail food chain.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {23}, pages = {34295-34308}, pmid = {38700770}, issn = {1614-7499}, support = {41701564//National Natural Science Foundation of China/ ; SNG201613//Science and Technology Program of Suzhou/ ; }, mesh = {*Plasmids/genetics ; *Soil Microbiology ; *Drug Resistance, Microbial/genetics ; Animals ; *Food Chain ; Snails ; Soil/chemistry ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Fertilization can change the composition of antibiotic resistance genes(ARGs) and their host bacteria in agricultural fields, while complex microbial activities help ARGs into crops and transmit them to humans through agricultural products.Therefore, this study constructed a farmland food chain with soil-lettuce-snail as a typical structure, added genetically engineered Pseudomonas fluorescens containing multidrug-resistant plasmid RP4 to track its spread in the farmland food chain, and used different fertilization methods to explore its influence on the spread and diffusion of ARGs and intl1 in the farmland food chain. It was found that exogenous Pseudomonas can enter plants from soil and pass into snails' intestines, and there is horizontal gene transfer phenomenon of RP4 plasmid in bacteria. At different interfaces of the constructed food chain, the addition of exogenous drug-resistant bacteria had different effects on the total abundance of ARGs and intl1. Fertilization, especially manure, not only promoted the spread of Pseudomonas aeruginosa and the transfer of RP4 plasmid levels, but also significantly increased the total abundance of ARGs and intl1 at all interfaces of the constructed food chain. The main ARGs host bacteria in the constructed food chain include Proteobacteria, Bacteroides, and Firmicutes, while Flavobacterium of Bacteroides is the unique potential host bacteria of RP4 plasmid. In conclusion, this study provides a reference for the risk assessment of ARGs transmitted to the human body through the food chain, and has important practical significance to reduce the antibiotic resistance contamination of agricultural products and ensure the safety of vegetable basket.}, }
@article {pmid38698002, year = {2024}, author = {Da Silva Morais, E and Grimaud, GM and Warda, A and Stanton, C and Ross, P}, title = {Genome plasticity shapes the ecology and evolution of Phocaeicola dorei and Phocaeicola vulgatus.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {10109}, pmid = {38698002}, issn = {2045-2322}, support = {101054719/ERC_/European Research Council/International ; BACtheWINNER, Project No. 101054719/ERC_/European Research Council/International ; }, mesh = {*Phylogeny ; *Genome, Bacterial ; Humans ; Gastrointestinal Microbiome/genetics ; Gene Transfer, Horizontal ; Evolution, Molecular ; Genomics/methods ; Bacteroidetes/genetics ; }, abstract = {Phocaeicola dorei and Phocaeicola vulgatus are very common and abundant members of the human gut microbiome and play an important role in the infant gut microbiome. These species are closely related and often confused for one another; yet, their genome comparison, interspecific diversity, and evolutionary relationships have not been studied in detail so far. Here, we perform phylogenetic analysis and comparative genomic analyses of these two Phocaeicola species. We report that P. dorei has a larger genome yet a smaller pan-genome than P. vulgatus. We found that this is likely because P. vulgatus is more plastic than P. dorei, with a larger repertoire of genetic mobile elements and fewer anti-phage defense systems. We also found that P. dorei directly descends from a clade of P. vulgatus¸ and experienced genome expansion through genetic drift and horizontal gene transfer. Overall, P. dorei and P. vulgatus have very different functional and carbohydrate utilisation profiles, hinting at different ecological strategies, yet they present similar antimicrobial resistance profiles.}, }
@article {pmid38696408, year = {2024}, author = {Aldaihani, R and Heath, LS}, title = {Investigating the nature of prokaryotic genomic island locations within a genome.}, journal = {PloS one}, volume = {19}, number = {5}, pages = {e0301172}, pmid = {38696408}, issn = {1932-6203}, mesh = {*Genomic Islands ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Genome, Archaeal ; Replication Origin/genetics ; Prokaryotic Cells/metabolism ; }, abstract = {Horizontal gene transfer (HGT) is a powerful evolutionary force that considerably shapes the structure of prokaryotic genomes and is associated with genomic islands (GIs). A GI is a DNA segment composed of transferred genes that can be found within a prokaryotic genome, obtained through HGT. Much research has focused on detecting GIs in genomes, but here we pursue a new course, which is identifying possible preferred locations of GIs in the prokaryotic genome. Here, we identify the locations of the GIs within prokaryotic genomes to examine patterns in those locations. Prokaryotic GIs were analyzed according to the genome structure that they are located in, whether it be a circular or a linear genome. The analytical investigations employed are: (1) studying the GI locations in relation to the origin of replication (oriC); (2) exploring the distances between GIs; and (3) determining the distribution of GIs across the genomes. For each of the investigations, the analysis was performed on all of the GIs in the data set. Moreover, to void bias caused by the distribution of the genomes represented, the GIs in one genome from each species and the GIs of the most frequent species are also analyzed. Overall, the results showed that there are preferred sites for the GIs in the genome. In the linear genomes, these sites are usually located in the oriC region and terminus region, while in the circular genomes, they are located solely in the terminus region. These results also showed that the distance distribution between the GIs is almost exponential, which proves that GIs have preferred sites within genomes. The oriC and termniuns are preferred sites for the GIs and a possible natural explanation for this could be connected to the content of the oriC region. Moreover, the content of the GIs in terms of its protein families was studied and the results demonstrated that the majority of frequent protein families are close to identical in each section.}, }
@article {pmid38695851, year = {2024}, author = {Fang, L and Li, M and Zhang, J and Jia, C and Qiang, Y and He, X and Liu, T and Zhou, Q and Luo, D and Han, Y and Li, Z and Liu, W and Yang, Y and Liu, J and Liu, Z}, title = {Chromosome-level genome assembly of Pedicularis kansuensis illuminates genome evolution of facultative parasitic plant.}, journal = {Molecular ecology resources}, volume = {24}, number = {5}, pages = {e13966}, doi = {10.1111/1755-0998.13966}, pmid = {38695851}, issn = {1755-0998}, support = {CCPTZX2023N04//National Grassland Technology Innovation Center (Preparatory) of China/ ; 32201463//National Natural Science Foundation of China/ ; 32071862//National Natural Science Foundation of China/ ; 2023-NK-147//Qinghai Province Talented Scientists Responsibility System Project/ ; }, mesh = {*Genome, Plant/genetics ; *Gene Transfer, Horizontal ; *Pedicularis/genetics ; *Evolution, Molecular ; Genome Size ; Phylogeny ; Chromosomes, Plant/genetics ; Retroelements/genetics ; Tibet ; }, abstract = {Parasitic plants have a heterotrophic lifestyle, in which they withdraw all or part of their nutrients from their host through the haustorium. Despite the release of many draft genomes of parasitic plants, the genome evolution related to the parasitism feature of facultative parasites remains largely unknown. In this study, we present a high-quality chromosomal-level genome assembly for the facultative parasite Pedicularis kansuensis (Orobanchaceae), which invades both legume and grass host species in degraded grasslands on the Qinghai-Tibet Plateau. This species has the largest genome size compared with other parasitic species, and expansions of long terminal repeat retrotransposons accounting for 62.37% of the assembly greatly contributed to the genome size expansion of this species. A total of 42,782 genes were annotated, and the patterns of gene loss in P. kansuensis differed from other parasitic species. We also found many mobile mRNAs between P. kansuensis and one of its host species, but these mobile mRNAs could not compensate for the functional losses of missing genes in P. kansuensis. In addition, we identified nine horizontal gene transfer (HGT) events from rosids and monocots, as well as one single-gene duplication events from HGT genes, which differ distinctly from that of other parasitic species. Furthermore, we found evidence for HGT through transferring genomic fragments from phylogenetically remote host species. Taken together, these findings provide genomic insights into the evolution of facultative parasites and broaden our understanding of the diversified genome evolution in parasitic plants and the molecular mechanisms of plant parasitism.}, }
@article {pmid38695606, year = {2024}, author = {Wang, X-Q and Du, K and Chen, C and Hou, P and Li, W-F and Chen, Y and Li, Q and Zhou, C-Z}, title = {Profiling the interplay and coevolution of Microcystis aeruginosa and cyanosiphophage Mic1.}, journal = {Microbiology spectrum}, volume = {12}, number = {6}, pages = {e0029824}, pmid = {38695606}, issn = {2165-0497}, support = {32000112//MOST | National Natural Science Foundation of China (NSFC)/ ; U19A2020//MOST | National Natural Science Foundation of China (NSFC)/ ; 2018YFA0903100//Ministry of Science and Technology of the People's Republic of China (MOST)/ ; WK2070000195//MOE | Fundamental Research Funds for the Central Universities (Fundamental Research Fund for the Central Universities)/ ; }, mesh = {*Microcystis/virology/genetics/metabolism ; *Bacteriophages/genetics/physiology ; China ; Transcriptome ; Lakes/microbiology/virology ; Genome, Viral/genetics ; Evolution, Molecular ; }, abstract = {UNLABELLED: The cyanosiphophage Mic1 specifically infects the bloom-forming Microcystis aeruginosa FACHB 1339 from Lake Chaohu, China. Previous genomic analysis showed that its 92,627 bp double-stranded DNA genome consists of 98 putative open reading frames, 63% of which are of unknown function. Here, we investigated the transcriptome dynamics of Mic1 and its host using RNA sequencing. In the early, middle, and late phases of the 10 h lytic cycle, the Mic1 genes are sequentially expressed and could be further temporally grouped into two distinct clusters in each phase. Notably, six early genes, including gp49 that encodes a TnpB-like transposase, immediately reach the highest transcriptional level in half an hour, representing a pioneer cluster that rapidly regulates and redirects host metabolism toward the phage. An in-depth analysis of the host transcriptomic profile in response to Mic1 infection revealed significant upregulation of a polyketide synthase pathway and a type III-B CRISPR system, accompanied by moderate downregulation of the photosynthesis and key metabolism pathways. The constant increase of phage transcripts and relatively low replacement rate over the host transcripts indicated that Mic1 utilizes a unique strategy to gradually take over a small portion of host metabolism pathways after infection. In addition, genomic analysis of a less-infective Mic1 and a Mic1-resistant host strain further confirmed their dynamic interplay and coevolution via the frequent horizontal gene transfer. These findings provide insights into the mutual benefit and symbiosis of the highly polymorphic cyanobacteria M. aeruginosa and cyanophages.<br><br>IMPORTANCE: The highly polymorphic Microcystis aeruginosa is one of the predominant bloom-forming cyanobacteria in eutrophic freshwater bodies and is infected by diverse and abundant cyanophages. The presence of a large number of defense systems in M. aeruginosa genome suggests a dynamic interplay and coevolution with the cyanophages. In this study, we investigated the temporal gene expression pattern of Mic1 after infection and the corresponding transcriptional responses of its host. Moreover, the identification of a less-infective Mic1 and a Mic1-resistant host strain provided the evolved genes in the phage-host coevolution during the multiple-generation cultivation in the laboratory. Our findings enrich the knowledge on the interplay and coevolution of M. aeruginosa and its cyanophages and lay the foundation for the future application of cyanophage as a potential eco-friendly and bio-safe agent in controlling the succession of harmful cyanobacterial blooms.}, }
@article {pmid38695519, year = {2024}, author = {Garrido, V and Arrieta-Gisasola, A and Migura-García, L and Laorden, L and Grilló, MJ}, title = {Multidrug resistance in Salmonella isolates of swine origin: mobile genetic elements and plasmids associated with cephalosporin resistance with potential transmission to humans.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {5}, pages = {e0026424}, pmid = {38695519}, issn = {1098-5336}, support = {IIQ14061.RI1//Direcci&#xf3;n General de Industria, Energia y Proyectos Estrategicos S3, Gobierno de Navarra (Department of Industry of the Government of Navarra)/ ; PA20/03//Centres de Recerca de Catalunya (CERCA)/ ; Grant PIF-19/290//Basque Country University (UPV/EHU)/ ; }, mesh = {Animals ; Swine/microbiology ; *Plasmids/genetics ; *Salmonella/genetics/drug effects/isolation &amp; purification ; *Interspersed Repetitive Sequences ; *Drug Resistance, Multiple, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; Humans ; Cephalosporin Resistance/genetics ; Salmonella Infections, Animal/microbiology ; Spain ; Swine Diseases/microbiology ; Cephalosporins/pharmacology ; Gene Transfer, Horizontal ; }, abstract = {The emergence of foodborne Salmonella strains carrying antimicrobial resistance (AMR) in mobile genetic elements (MGE) is a significant public health threat in a One Health context requiring continuous surveillance. Resistance to ciprofloxacin and cephalosporins is of particular concern. Since pigs are a relevant source of foodborne Salmonella for human beings, we studied transmissible AMR genes and MGE in a collection of 83 strains showing 9 different serovars and 15 patterns of multidrug resistant (MDR) previously isolated from pigs raised in the conventional breeding system of Northern Spain. All isolates were susceptible to ciprofloxacin and three isolates carried blaCMY-2 or blaCTX-M-9 genes responsible for cefotaxime resistance. Filter mating experiments showed that the two plasmids carrying blaCTX-M-9 were conjugative while that carrying blaCMY-2 was self-transmissible by transformation. Whole-genome sequencing and comparative analyses were performed on the isolates and plasmids. The IncC plasmid pSB109, carrying blaCMY-2, was similar to one found in S. Reading from cattle, indicating potential horizontal transfer between serovars and animal sources. The IncHI2 plasmids pSH102 in S. Heidelberg and pSTM45 in S. Typhimurium ST34, carrying blaCTX-M-9, shared similar backbones and two novel "complex class 1 integrons" containing different AMR and heavy metal genes. Our findings emphasize the importance of sequencing techniques to identify emerging AMR regions in conjugative and stable plasmids from livestock production. The presence of MGE carrying clinically relevant AMR genes raises public health concerns, requiring monitoring to mitigate the emergence of bacteria carrying AMR genes and subsequent spread through animals and food.IMPORTANCEThe emergence of foodborne Salmonella strains carrying antimicrobial resistance (AMR) in mobile genetic elements (MGE) is a significant public health threat in a One Health context. Since pigs are a relevant source of foodborne Salmonella for humans, in this study, we investigate different aspects of AMR in a collection of 83 Salmonella showing nine different serovars and 15 patterns of multidrug resistant (MDR) isolated from pigs raised in the conventional breeding system. Our findings emphasize the importance of sequencing techniques to identify emerging AMR regions in conjugative and stable plasmids from livestock production. The presence of MGE carrying clinically relevant AMR genes raises public health concerns, requiring monitoring to mitigate the emergence of bacteria carrying AMR genes and subsequent spread through animals and food.}, }
@article {pmid38695111, year = {2024}, author = {Van Etten, J and Stephens, TG and Chille, E and Lipzen, A and Peterson, D and Barry, K and Grigoriev, IV and Bhattacharya, D}, title = {Diverse fates of ancient horizontal gene transfers in extremophilic red algae.}, journal = {Environmental microbiology}, volume = {26}, number = {5}, pages = {e16629}, doi = {10.1111/1462-2920.16629}, pmid = {38695111}, issn = {1462-2920}, support = {80NSSC19K0462/NASA/NASA/United States ; 80NSSC19K1542/NASA/NASA/United States ; }, mesh = {*Gene Transfer, Horizontal ; *Rhodophyta/genetics ; *Extremophiles/genetics ; *Arsenic/metabolism ; Mercury/metabolism ; Stress, Physiological/genetics ; Inactivation, Metabolic/genetics ; Evolution, Molecular ; }, abstract = {Horizontal genetic transfer (HGT) is a common phenomenon in eukaryotic genomes. However, the mechanisms by which HGT-derived genes persist and integrate into other pathways remain unclear. This topic is of significant interest because, over time, the stressors that initially favoured the fixation of HGT may diminish or disappear. Despite this, the foreign genes may continue to exist if they become part of a broader stress response or other pathways. The conventional model suggests that the acquisition of HGT equates to adaptation. However, this model may evolve into more complex interactions between gene products, a concept we refer to as the 'Integrated HGT Model' (IHM). To explore this concept further, we studied specialized HGT-derived genes that encode heavy metal detoxification functions. The recruitment of these genes into other pathways could provide clear examples of IHM. In our study, we exposed two anciently diverged species of polyextremophilic red algae from the Galdieria genus to arsenic and mercury stress in laboratory cultures. We then analysed the transcriptome data using differential and coexpression analysis. Our findings revealed that mercury detoxification follows a 'one gene-one function' model, resulting in an indivisible response. In contrast, the arsH gene in the arsenite response pathway demonstrated a complex pattern of duplication, divergence and potential neofunctionalization, consistent with the IHM. Our research sheds light on the fate and integration of ancient HGTs, providing a novel perspective on the ecology of extremophiles.}, }
@article {pmid38694799, year = {2024}, author = {Zhang, Y and Xue, G and Wang, F and Zhang, J and Xu, L and Yu, C}, title = {The impact of antibiotic exposure on antibiotic resistance gene dynamics in the gut microbiota of inflammatory bowel disease patients.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1382332}, pmid = {38694799}, issn = {1664-302X}, abstract = {BACKGROUND: While antibiotics are commonly used to treat inflammatory bowel disease (IBD), their widespread application can disturb the gut microbiota and foster the emergence and spread of antibiotic resistance. However, the dynamic changes to the human gut microbiota and direction of resistance gene transmission under antibiotic effects have not been clearly elucidated.<br><br>METHODS: Based on the Human Microbiome Project, a total of 90 fecal samples were collected from 30 IBD patients before, during and after antibiotic treatment. Through the analysis workflow of metagenomics, we described the dynamic process of changes in bacterial communities and resistance genes pre-treatment, during and post-treatment. We explored potential consistent relationships between gut microbiota and resistance genes, and established gene transmission networks among species before and after antibiotic use.<br><br>RESULTS: Exposure to antibiotics can induce alterations in the composition of the gut microbiota in IBD patients, particularly a reduction in probiotics, which gradually recovers to a new steady state after cessation of antibiotics. Network analyses revealed intra-phylum transfers of resistance genes, predominantly between taxonomically close organisms. Specific resistance genes showed increased prevalence and inter-species mobility after antibiotic cessation.<br><br>CONCLUSION: This study demonstrates that antibiotics shape the gut resistome through selective enrichment and promotion of horizontal gene transfer. The findings provide insights into ecological processes governing resistance gene dynamics and dissemination upon antibiotic perturbation of the microbiota. Optimizing antibiotic usage may help limit unintended consequences like increased resistance in gut bacteria during IBD management.}, }
@article {pmid38694026, year = {2024}, author = {Reem, A and Almansoob, S and Senan, AM and Kumar Raj, A and Shah, R and Kumar Shrewastwa, M and Kumal, JPP}, title = {Pseudomonas aeruginosa and related antibiotic resistance genes as indicators for wastewater treatment.}, journal = {Heliyon}, volume = {10}, number = {9}, pages = {e29798}, pmid = {38694026}, issn = {2405-8440}, abstract = {This review aims to examine the existence of Pseudomonas aeruginosa (P. aeruginosa) and their antibiotic resistance genes (ARGs) in aquatic settings and the alternative treatment ways. P. aeruginosa in a various aquatic environment have been identified as contaminants with impacts on human health and the environment. P. aeruginosa resistance to multiple antibiotics, such as sulfamethoxazole, ciprofloxacin, quinolone, trimethoprim, tetracycline, vancomycin, as well as specific antibiotic resistance genes including sul1, qnrs, blaVIM, blaTEM, blaCTX, blaAIM-1, tetA, ampC, blaVIM. The development of resistance can occur naturally, through mutations, or via horizontal gene transfer facilitated by sterilizing agents. In addition, an overview of the current knowledge on inactivation of Pseudomonas aeruginosa and ARG and the mechanisms of action of various disinfection processes in water and wastewater (UV chlorine processes, catalytic oxidation, Fenton reaction, and ozonation) is given. An overview of the effects of nanotechnology and the resulting wetlands is also given.}, }
@article {pmid38693917, year = {2024}, author = {Filgueiras, JPC and Zámocký, M and Turchetto-Zolet, AC}, title = {Unraveling the evolutionary origin of the P5CS gene: a story of gene fusion and horizontal transfer.}, journal = {Frontiers in molecular biosciences}, volume = {11}, number = {}, pages = {1341684}, pmid = {38693917}, issn = {2296-889X}, abstract = {The accumulation of proline in response to the most diverse types of stress is a widespread defense mechanism. In prokaryotes, fungi, and certain unicellular eukaryotes (green algae), the first two reactions of proline biosynthesis occur through two distinct enzymes, γ-glutamyl kinase (GK E.C. 2.7.2.11) and γ-glutamyl phosphate reductase (GPR E.C. 1.2.1.41), encoded by two different genes, ProB and ProA, respectively. Plants, animals, and a few unicellular eukaryotes carry out these reactions through a single bifunctional enzyme, the Δ[1]-pyrroline-5-carboxylate synthase (P5CS), which has the GK and GPR domains fused. To better understand the origin and diversification of the P5CS gene, we use a robust phylogenetic approach with a broad sampling of the P5CS, ProB and ProA genes, including species from all three domains of life. Our results suggest that the collected P5CS genes have arisen from a single fusion event between the ProA and ProB gene paralogs. A peculiar fusion event occurred in an ancestral eukaryotic lineage and was spread to other lineages through horizontal gene transfer. As for the diversification of this gene family, the phylogeny of the P5CS gene in plants shows that there have been multiple independent processes of duplication and loss of this gene, with the duplications being related to old polyploidy events.}, }
@article {pmid38693486, year = {2024}, author = {Rork, AM and Bala, AS and Renner, T}, title = {Dynamic evolution of the mTHF gene family associated with primary metabolism across life.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {432}, pmid = {38693486}, issn = {1471-2164}, mesh = {*Evolution, Molecular ; *Phylogeny ; *Methylenetetrahydrofolate Dehydrogenase (NADP)/genetics/metabolism ; *Multigene Family ; Archaea/genetics/metabolism ; Eukaryota/genetics/metabolism ; Metabolic Networks and Pathways/genetics ; Gene Transfer, Horizontal ; }, abstract = {BACKGROUND: The folate cycle of one-carbon (C1) metabolism, which plays a central role in the biosynthesis of nucleotides and amino acids, demonstrates the significance of metabolic adaptation. We investigated the evolutionary history of the methylenetetrahydrofolate dehydrogenase (mTHF) gene family, one of the main drivers of the folate cycle, across life.<br><br>RESULTS: Through comparative genomic and phylogenetic analyses, we found that several lineages of Archaea lacked domains vital for folate cycle function such as the mTHF catalytic and NAD(P)-binding domains of FolD. Within eukaryotes, the mTHF gene family diversified rapidly. For example, several duplications have been observed in lineages including the Amoebozoa, Opisthokonta, and Viridiplantae. In a common ancestor of Opisthokonta, FolD and FTHFS underwent fusion giving rise to the gene MTHFD1, possessing the domains of both genes.<br><br>CONCLUSIONS: Our evolutionary reconstruction of the mTHF gene family associated with a primary metabolic pathway reveals dynamic evolution, including gene birth-and-death, gene fusion, and potential horizontal gene transfer events and/or amino acid convergence.}, }
@article {pmid38692276, year = {2024}, author = {Li, C and Li, CQ and Chen, ZB and Liu, BQ and Sun, X and Wei, KH and Li, CY and Luan, JB}, title = {Wolbachia symbionts control sex in a parasitoid wasp using a horizontally acquired gene.}, journal = {Current biology : CB}, volume = {34}, number = {11}, pages = {2359-2372.e9}, doi = {10.1016/j.cub.2024.04.035}, pmid = {38692276}, issn = {1879-0445}, mesh = {Animals ; *Wolbachia/physiology/genetics ; *Wasps/physiology/microbiology/genetics ; *Symbiosis/genetics ; Female ; Male ; *Gene Transfer, Horizontal ; Parthenogenesis/genetics ; Insect Proteins/genetics/metabolism ; Sex Determination Processes/genetics ; }, abstract = {Host reproduction can be manipulated by bacterial symbionts in various ways. Parthenogenesis induction is the most effective type of reproduction manipulation by symbionts for their transmission. Insect sex is determined by regulation of doublesex (dsx) splicing through transformer2 (tra2) and transformer (tra) interaction. Although parthenogenesis induction by symbionts has been studied since the 1970s, its underlying molecular mechanism is unknown. Here we identify a Wolbachia parthenogenesis-induction feminization factor gene (piff) that targets sex-determining genes and causes female-producing parthenogenesis in the haplodiploid parasitoid Encarsia formosa. We found that Wolbachia elimination repressed expression of female-specific dsx and enhanced expression of male-specific dsx, which led to the production of wasp haploid male offspring. Furthermore, we found that E. formosa tra is truncated and non-functional, and Wolbachia has a functional tra homolog, termed piff, with an insect origin. Wolbachia PIFF can colocalize and interact with wasp TRA2. Moreover, Wolbachia piff has coordinated expression with tra2 and dsx of E. formosa. Our results demonstrate the bacterial symbiont Wolbachia has acquired an insect gene to manipulate the host sex determination cascade and induce parthenogenesis in wasps. This study reveals insect-to-bacteria horizontal gene transfer drives the evolution of animal sex determination systems, elucidating a striking mechanism of insect-microbe symbiosis.}, }
@article {pmid38692255, year = {2024}, author = {Li, H and Wang, Q and Wang, Y and Liu, Y and Zhou, J and Wang, T and Zhu, L and Guo, J}, title = {EDTA enables to alleviate impacts of metal ions on conjugative transfer of antibiotic resistance genes.}, journal = {Water research}, volume = {257}, number = {}, pages = {121659}, doi = {10.1016/j.watres.2024.121659}, pmid = {38692255}, issn = {1879-2448}, mesh = {*Edetic Acid/pharmacology/chemistry ; *Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Plasmids ; Metals, Heavy/chemistry ; Escherichia coli/drug effects/genetics ; Metals ; Ions ; }, abstract = {Various heavy metals are reported to be able to accelerate horizontal transfer of antibiotic resistance genes (ARGs). In real water environmental settings, ubiquitous complexing agents would affect the environmental behaviors of heavy metal ions due to the formation of metal-organic complexes. However, little is known whether the presence of complexing agents would change horizontal gene transfer due to heavy metal exposure. This study aimed to fill this gap by investigating the impacts of a typical complexing agent ethylenediaminetetraacetic acid (EDTA) on the conjugative transfer of plasmid-mediated ARGs induced by a range of heavy metal ions. At the environmentally relevant concentration (0.64 mg L[-1]) of metal ions, all the tested metal ions (Mg[2+], Ca[2+], Co[2+], Pb[2+], Ni[2+], Cu[2+], and Fe[3+]) promoted conjugative transfer of ARGs, while an inhibitory effect was observed at a relatively higher concentration (3.20 mg L[-1]). In contrast, EDTA (0.64 mg L[-1]) alleviated the effects of metal ions on ARGs conjugation transfer, evidenced by 11 %-66 % reduction in the conjugate transfer frequency. Molecular docking and dynamics simulations disclosed that this is attributed to the stronger binding of metal ions with the lipids in cell membranes. Under metal-EDTA exposure, gene expressions related to oxidative stress response, cell membrane permeability, intercellular contact, energy driving force, mobilization, and channels of plasmid transfer were suppressed compared with the metal ions exposure. This study offers insights into the alleviation mechanisms of complexing agents on ARGs transfer induced by free metal ions.}, }
@article {pmid38692150, year = {2024}, author = {Cai, Y and Chen, C and Sun, T and Li, G and Wang, W and Zhao, H and An, T}, title = {Mariculture waters as yet another hotbed for the creation and transfer of new antibiotic-resistant pathogenome.}, journal = {Environment international}, volume = {187}, number = {}, pages = {108704}, doi = {10.1016/j.envint.2024.108704}, pmid = {38692150}, issn = {1873-6750}, mesh = {*Aquaculture ; *Bacteria/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology ; *RNA, Ribosomal, 16S/genetics ; China ; Water Microbiology ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Drug Resistance, Microbial/genetics ; Metagenomics ; }, abstract = {With the rapid growth of aquaculture globally, large amounts of antibiotics have been used to treat aquatic disease, which may accelerate induction and spread of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in aquaculture environments. Herein, metagenomic and 16S rRNA analyses were used to analyze the potentials and co-occurrence patterns of pathogenome (culturable and unculturable pathogens), antibiotic resistome (ARGs), and mobilome (mobile genetic elements (MGEs)) from mariculture waters near 5000 km coast of South China. Total 207 species of pathogens were identified, with only 10 culturable species. Furthermore, more pathogen species were detected in mariculture waters than those in coastal waters, and mariculture waters were prone to become reservoirs of unculturable pathogens. In addition, 913 subtypes of 21 ARG types were also identified, with multidrug resistance genes as the majority. MGEs including plasmids, integrons, transposons, and insertion sequences were abundantly present in mariculture waters. The co-occurrence network pattern between pathogenome, antibiotic resistome, and mobilome suggested that most of pathogens may be potential multidrug resistant hosts, possibly due to high frequency of horizontal gene transfer. These findings increase our understanding of mariculture waters as reservoirs of antibiotic resistome and mobilome, and as yet another hotbed for creation and transfer of new antibiotic-resistant pathogenome.}, }
@article {pmid38689039, year = {2024}, author = {Shepherd, MJ and Fu, T and Harrington, NE and Kottara, A and Cagney, K and Chalmers, JD and Paterson, S and Fothergill, JL and Brockhurst, MA}, title = {Ecological and evolutionary mechanisms driving within-patient emergence of antimicrobial resistance.}, journal = {Nature reviews. Microbiology}, volume = {22}, number = {10}, pages = {650-665}, pmid = {38689039}, issn = {1740-1534}, mesh = {Humans ; *Bacteria/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; *Gene Transfer, Horizontal ; *Bacterial Infections/microbiology/drug therapy ; Evolution, Molecular ; Mutation ; }, abstract = {The ecological and evolutionary mechanisms of antimicrobial resistance (AMR) emergence within patients and how these vary across bacterial infections are poorly understood. Increasingly widespread use of pathogen genome sequencing in the clinic enables a deeper understanding of these processes. In this Review, we explore the clinical evidence to support four major mechanisms of within-patient AMR emergence in bacteria: spontaneous resistance mutations; in situ horizontal gene transfer of resistance genes; selection of pre-existing resistance; and immigration of resistant lineages. Within-patient AMR emergence occurs across a wide range of host niches and bacterial species, but the importance of each mechanism varies between bacterial species and infection sites within the body. We identify potential drivers of such differences and discuss how ecological and evolutionary analysis could be embedded within clinical trials of antimicrobials, which are powerful but underused tools for understanding why these mechanisms vary between pathogens, infections and individuals. Ultimately, improving understanding of how host niche, bacterial species and antibiotic mode of action combine to govern the ecological and evolutionary mechanism of AMR emergence in patients will enable more predictive and personalized diagnosis and antimicrobial therapies.}, }
@article {pmid38688912, year = {2024}, author = {Yang, QE and Ma, X and Li, M and Zhao, M and Zeng, L and He, M and Deng, H and Liao, H and Rensing, C and Friman, VP and Zhou, S and Walsh, TR}, title = {Evolution of triclosan resistance modulates bacterial permissiveness to multidrug resistance plasmids and phages.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {3654}, pmid = {38688912}, issn = {2041-1723}, support = {32100150//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42277436//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Triclosan/pharmacology ; *Plasmids/genetics ; *Klebsiella pneumoniae/drug effects/genetics/virology ; *Bacteriophages/genetics/physiology ; Drug Resistance, Multiple, Bacterial/genetics ; Mutation ; Gene Transfer, Horizontal ; Whole Genome Sequencing ; Evolution, Molecular ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The horizontal transfer of plasmids has been recognized as one of the key drivers for the worldwide spread of antimicrobial resistance (AMR) across bacterial pathogens. However, knowledge remain limited about the contribution made by environmental stress on the evolution of bacterial AMR by modulating horizontal acquisition of AMR plasmids and other mobile genetic elements. Here we combined experimental evolution, whole genome sequencing, reverse genetic engineering, and transcriptomics to examine if the evolution of chromosomal AMR to triclosan (TCS) disinfectant has correlated effects on modulating bacterial pathogen (Klebsiella pneumoniae) permissiveness to AMR plasmids and phage susceptibility. Herein, we show that TCS exposure increases the evolvability of K. pneumoniae to evolve TCS-resistant mutants (TRMs) by acquiring mutations and altered expression of several genes previously associated with TCS and antibiotic resistance. Notably, nsrR deletion increases conjugation permissiveness of K. pneumoniae to four AMR plasmids, and enhances susceptibility to various Klebsiella-specific phages through the downregulation of several bacterial defense systems and changes in membrane potential with altered reactive oxygen species response. Our findings suggest that unrestricted use of TCS disinfectant imposes a dual impact on bacterial antibiotic resistance by augmenting both chromosomally and horizontally acquired AMR mechanisms.}, }
@article {pmid38688811, year = {2024}, author = {Szczepankowska, AK and Łobocka, M}, title = {Exploring the role of phage plasmids in gene transfers.}, journal = {Trends in genetics : TIG}, volume = {40}, number = {7}, pages = {555-557}, doi = {10.1016/j.tig.2024.04.011}, pmid = {38688811}, issn = {0168-9525}, mesh = {Bacteria/genetics/virology ; *Bacteriophages/genetics ; *Gene Transfer, Horizontal/genetics ; *Plasmids/genetics ; }, abstract = {Bacteriophages and plasmids drive horizontal gene transfer (HGT) in bacteria. Phage-plasmids (P-Ps) are hybrids of plasmid and phages. Pfeifer and Rocha recently demonstrated that P-Ps can serve as intermediates in gene exchanges between these two types of elements, identified categories of preferentially transferred genes, and reconstructed gene flows involving phage P1-like P-Ps.}, }
@article {pmid38683832, year = {2024}, author = {Guillén-Chable, F and Valdez Iuit, JO and Avila Castro, LA and Rosas, C and Merino, E and Rodríguez-Escamilla, Z and Martínez-Núñez, MA}, title = {Geographical distribution of mobile genetic elements in microbial communities along the Yucatan coast.}, journal = {PloS one}, volume = {19}, number = {4}, pages = {e0301642}, pmid = {38683832}, issn = {1932-6203}, mesh = {*Interspersed Repetitive Sequences/genetics ; *Gene Transfer, Horizontal ; *Microbiota/genetics ; Mexico ; Bacteria/genetics/classification ; Proteobacteria/genetics ; }, abstract = {Horizontal gene transfer (HGT) is a well-documented strategy used by bacteria to enhance their adaptability to challenging environmental conditions. Through HGT, a group of conserved genetic elements known as mobile genetic elements (MGEs) is disseminated within bacterial communities. MGEs offer numerous advantages to the host, increasing its fitness by acquiring new functions that help bacteria contend with adverse conditions, including exposure to heavy metal and antibiotics. This study explores MGEs within microbial communities along the Yucatan coast using a metatranscriptomics approach. Prior to this research, nothing was known about the coastal Yucatan's microbial environmental mobilome and HGT processes between these bacterial communities. This study reveals a positive correlation between MGEs and antibiotic resistance genes (ARGs) along the Yucatan coast, with higher MGEs abundance in more contaminated sites. The Proteobacteria and Firmicutes groups exhibited the highest number of MGEs. It's important to highlight that the most abundant classes of MGEs might not be the ones most strongly linked to ARGs, as observed for the recombination/repair class. This work presents the first geographical distribution of the environmental mobilome in Yucatan Peninsula mangroves.}, }
@article {pmid38683670, year = {2024}, author = {Ferrari, E and Di Benedetto, G and Firrincieli, A and Presentato, A and Frascari, D and Cappelletti, M}, title = {Unravelling the role of the group 6 soluble di-iron monooxygenase (SDIMO) SmoABCD in alkane metabolism and chlorinated alkane degradation.}, journal = {Microbial biotechnology}, volume = {17}, number = {5}, pages = {e14453}, pmid = {38683670}, issn = {1751-7915}, mesh = {*Alkanes/metabolism ; *Mixed Function Oxygenases/metabolism/genetics ; Genetic Complementation Test ; Mutagenesis, Insertional ; Biotransformation ; DNA Transposable Elements ; Hydrocarbons, Chlorinated/metabolism ; }, abstract = {Soluble di-iron monooxygenases (SDIMOs) are multi-component enzymes catalysing the oxidation of various substrates. These enzymes are characterized by high sequence and functional diversity that is still not well understood despite their key role in biotechnological processes including contaminant biodegradation. In this study, we analysed a mutant of Rhodoccocus aetherivorans BCP1 (BCP1-2.10) characterized by a transposon insertion in the gene smoA encoding the alpha subunit of the plasmid-located SDIMO SmoABCD. The mutant BCP1-2.10 showed a reduced capacity to grow on propane, lost the ability to grow on butane, pentane and n-hexane and was heavily impaired in the capacity to degrade chloroform and trichloroethane. The expression of the additional SDIMO prmABCD in BCP1-2.10 probably allowed the mutant to partially grow on propane and to degrade it, to some extent, together with the other short-chain n-alkanes. The complementation of the mutant, conducted by introducing smoABCD in the genome as a single copy under a constitutive promoter or within a plasmid under a thiostreptone-inducible promoter, allowed the recovery of the alkanotrophic phenotype as well as the capacity to degrade chlorinated n-alkanes. The heterologous expression of smoABCD allowed a non-alkanotrophic Rhodococcus strain to grow on pentane and n-hexane when the gene cluster was introduced together with the downstream genes encoding alcohol and aldehyde dehydrogenases and a GroEL chaperon. BCP1 smoA gene was shown to belong to the group 6 SDIMOs, which is a rare group of monooxygenases mostly present in Mycobacterium genus and in a few Rhodococcus strains. SmoABCD originally evolved in Mycobacterium and was then acquired by Rhodococcus through horizontal gene transfer events. This work extends the knowledge of the biotechnologically relevant SDIMOs by providing functional and evolutionary insights into a group 6 SDIMO in Rhodococcus and demonstrating its key role in the metabolism of short-chain alkanes and degradation of chlorinated n-alkanes.}, }
@article {pmid38683013, year = {2024}, author = {Taylor, AJ and Yahara, K and Pascoe, B and Ko, S and Mageiros, L and Mourkas, E and Calland, JK and Puranen, S and Hitchings, MD and Jolley, KA and Kobras, CM and Bayliss, S and Williams, NJ and van Vliet, AHM and Parkhill, J and Maiden, MCJ and Corander, J and Hurst, LD and Falush, D and Keim, P and Didelot, X and Kelly, DJ and Sheppard, SK}, title = {Epistasis, core-genome disharmony, and adaptation in recombining bacteria.}, journal = {mBio}, volume = {15}, number = {6}, pages = {e0058124}, pmid = {38683013}, issn = {2150-7511}, support = {MR/L015080/1//UKRI | Medical Research Council (MRC)/ ; 088786/C/09/Z//Wellcome Trust (WT)/ ; 2022/23//Cowden Endowment for Food Microbiology/ ; FS101087//Food Standards Agency (FSA)/ ; /WT_/Wellcome Trust/United Kingdom ; BB/S014497/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; MR/M501608/1//UKRI | Medical Research Council (MRC)/ ; }, mesh = {*Epistasis, Genetic ; *Genome, Bacterial ; *Gene Transfer, Horizontal ; *Campylobacter jejuni/genetics ; *Recombination, Genetic ; *Campylobacter coli/genetics ; Evolution, Molecular ; Adaptation, Physiological/genetics ; Adaptation, Biological/genetics ; }, abstract = {Recombination of short DNA fragments via horizontal gene transfer (HGT) can introduce beneficial alleles, create genomic disharmony through negative epistasis, and create adaptive gene combinations through positive epistasis. For non-core (accessory) genes, the negative epistatic cost is likely to be minimal because the incoming genes have not co-evolved with the recipient genome and are frequently observed as tightly linked cassettes with major effects. By contrast, interspecific recombination in the core genome is expected to be rare because disruptive allelic replacement is likely to introduce negative epistasis. Why then is homologous recombination common in the core of bacterial genomes? To understand this enigma, we take advantage of an exceptional model system, the common enteric pathogens Campylobacter jejuni and C. coli that are known for very high magnitude interspecies gene flow in the core genome. As expected, HGT does indeed disrupt co-adapted allele pairings, indirect evidence of negative epistasis. However, multiple HGT events enable recovery of the genome's co-adaption between introgressing alleles, even in core metabolism genes (e.g., formate dehydrogenase). These findings demonstrate that, even for complex traits, genetic coalitions can be decoupled, transferred, and independently reinstated in a new genetic background-facilitating transition between fitness peaks. In this example, the two-step recombinational process is associated with C. coli that are adapted to the agricultural niche.IMPORTANCEGenetic exchange among bacteria shapes the microbial world. From the acquisition of antimicrobial resistance genes to fundamental questions about the nature of bacterial species, this powerful evolutionary force has preoccupied scientists for decades. However, the mixing of genes between species rests on a paradox: 0n one hand, promoting adaptation by conferring novel functionality; on the other, potentially introducing disharmonious gene combinations (negative epistasis) that will be selected against. Taking an interdisciplinary approach to analyze natural populations of the enteric bacteria Campylobacter, an ideal example of long-range admixture, we demonstrate that genes can independently transfer across species boundaries and rejoin in functional networks in a recipient genome. The positive impact of two-gene interactions appears to be adaptive by expanding metabolic capacity and facilitating niche shifts through interspecific hybridization. This challenges conventional ideas and highlights the possibility of multiple-step evolution of multi-gene traits by interspecific introgression.}, }
@article {pmid38682189, year = {2024}, author = {Almatroudi, A}, title = {Investigating Biofilms: Advanced Methods for Comprehending Microbial Behavior and Antibiotic Resistance.}, journal = {Frontiers in bioscience (Landmark edition)}, volume = {29}, number = {4}, pages = {133}, doi = {10.31083/j.fbl2904133}, pmid = {38682189}, issn = {2768-6698}, mesh = {*Biofilms/drug effects/growth &amp; development ; Humans ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; Extracellular Polymeric Substance Matrix/metabolism ; Bacteria/genetics/drug effects/metabolism ; }, abstract = {Biofilms, which consist of microorganisms enclosed in an extracellular polymeric material (EPS), hold immense importance in the fields of environmental research, industry, and medicine. They play a significant role in ecosystem dynamics and stability, but they also pose issues such as biofouling, corrosion, and pollution. Biofilms in medical environments are linked to persistent infections and elevated healthcare expenses. The EPS matrix plays a crucial role in maintaining the structural integrity and antibiotic resistance of these structures. The research primarily investigates the role of the EPS matrix in facilitating horizontal gene transfer among biofilm communities, with a particular emphasis on EPS and its impact on this process. The process is recognized as a pivotal mechanism in the emergence of antibiotic resistance, underscoring the crucial function of EPS in the dynamics of biofilms. The analysis also highlights the significant financial constraints caused by biofilms in several industries. Biofilm-associated infections in the healthcare sector result in escalated treatment expenses and extended hospitalization periods. In an industrial context, biofilms have a role in increasing maintenance expenses and product contamination, emphasizing the need for efficient management solutions. This review presents the most recent progress in biofilm research, emphasizing the utilization of sophisticated imaging tools and molecular methodologies. In addition to conventional imaging techniques, the research explores the utilization of sophisticated molecular tools, such as DNA and RNA sequencing, in conjunction with proteomics. These approaches are essential for assessing the genetic and metabolic mechanisms that regulate biofilm development and antibiotic resistance. The review underscores the significance of employing an interdisciplinary methodology in the study of biofilms. By incorporating a range of approaches, such as sophisticated imaging and molecular analysis, a comprehensive understanding of biofilm dynamics may be achieved. This approach also opens up possibilities for developing novel solutions to address the negative impacts of biofilms on health, industry, and the environment.}, }
@article {pmid38678226, year = {2024}, author = {Alexa, EA and Cobo-Díaz, JF and Renes, E and O Callaghan, TF and Kilcawley, K and Mannion, D and Skibinska, I and Ruiz, L and Margolles, A and Fernández-Gómez, P and Alvarez-Molina, A and Puente-Gómez, P and Crispie, F and López, M and Prieto, M and Cotter, PD and Alvarez-Ordóñez, A}, title = {The detailed analysis of the microbiome and resistome of artisanal blue-veined cheeses provides evidence on sources and patterns of succession linked with quality and safety traits.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {78}, pmid = {38678226}, issn = {2049-2618}, support = {818368//European Commission under the European Union&#xb4;s Horizon 2020 research and innovation program/ ; 818368//European Commission under the European Union&#xb4;s Horizon 2020 research and innovation program/ ; 818368//European Commission under the European Union&#xb4;s Horizon 2020 research and innovation program/ ; 818368//European Commission under the European Union&#xb4;s Horizon 2020 research and innovation program/ ; 818368//European Commission under the European Union&#xb4;s Horizon 2020 research and innovation program/ ; AGL2016-78085-P//Ministry of Science and Innovation of the Spanish Government/ ; AGL2016-78085-P//Ministry of Science and Innovation of the Spanish Government/ ; AGL2016-78085-P//Ministry of Science and Innovation of the Spanish Government/ ; }, mesh = {*Cheese/microbiology/standards ; *Food Microbiology ; *Microbiota/physiology ; Gene Transfer, Horizontal/genetics ; Metagenome/genetics ; Drug Resistance, Microbial/genetics ; }, abstract = {BACKGROUND: Artisanal cheeses usually contain a highly diverse microbial community which can significantly impact their quality and safety. Here, we describe a detailed longitudinal study assessing the impact of ripening in three natural caves on the microbiome and resistome succession across three different producers of Cabrales blue-veined cheese.<br><br>RESULTS: Both the producer and cave in which cheeses were ripened significantly influenced the cheese microbiome. Lactococcus and the former Lactobacillus genus, among other taxa, showed high abundance in cheeses at initial stages of ripening, either coming from the raw material, starter culture used, and/or the environment of processing plants. Along cheese ripening in caves, these taxa were displaced by other bacteria, such as Tetragenococcus, Corynebacterium, Brevibacterium, Yaniella, and Staphylococcus, predominantly originating from cave environments (mainly food contact surfaces), as demonstrated by source-tracking analysis, strain analysis at read level, and the characterization of 613 metagenome-assembled genomes. The high abundance of Tetragenococcus koreensis and Tetragenococcus halophilus detected in cheese has not been found previously in cheese metagenomes. Furthermore, Tetragenococcus showed a high level of horizontal gene transfer with other members of the cheese microbiome, mainly with Lactococcus and Staphylococcus, involving genes related to carbohydrate metabolism functions. The resistome analysis revealed that raw milk and the associated processing environments are a rich reservoir of antimicrobial resistance determinants, mainly associated with resistance to aminoglycosides, tetracyclines, and &#x3b2;-lactam antibiotics and harbored by aerobic gram-negative bacteria of high relevance from a safety point of view, such as Escherichia coli, Salmonella enterica, Acinetobacter, and Klebsiella pneumoniae, and that the displacement of most raw milk-associated taxa by cave-associated taxa during ripening gave rise to a significant decrease in the load of ARGs and, therefore, to a safer end product.<br><br>CONCLUSION: Overall, the cave environments represented an important source of non-starter microorganisms which may play a relevant role in the quality and safety of the end products. Among them, we have identified novel taxa and taxa not previously regarded as being dominant components of the cheese microbiome (Tetragenococcus spp.), providing very valuable information for the authentication of this protected designation of origin artisanal cheese. Video Abstract.}, }
@article {pmid38678007, year = {2024}, author = {Wang, X and Tang, Y and Yue, X and Wang, S and Yang, K and Xu, Y and Shen, Q and Friman, VP and Wei, Z}, title = {The role of rhizosphere phages in soil health.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {5}, pages = {}, pmid = {38678007}, issn = {1574-6941}, support = {2022YFC3501501//National Key Research and Development Program of China/ ; 42325704//National Natural Science Foundation of China/ ; //Nanjing Agricultural University/ ; }, mesh = {*Soil Microbiology ; *Rhizosphere ; *Bacteriophages/genetics ; *Microbiota ; *Bacteria/virology/genetics ; Gene Transfer, Horizontal ; Plants/microbiology/virology ; Ecosystem ; }, abstract = {While the One Health framework has emphasized the importance of soil microbiomes for plant and human health, one of the most diverse and abundant groups-bacterial viruses, i.e. phages-has been mostly neglected. This perspective reviews the significance of phages for plant health in rhizosphere and explores their ecological and evolutionary impacts on soil ecosystems. We first summarize our current understanding of the diversity and ecological roles of phages in soil microbiomes in terms of nutrient cycling, top-down density regulation, and pathogen suppression. We then consider how phages drive bacterial evolution in soils by promoting horizontal gene transfer, encoding auxiliary metabolic genes that increase host bacterial fitness, and selecting for phage-resistant mutants with altered ecology due to trade-offs with pathogen competitiveness and virulence. Finally, we consider challenges and avenues for phage research in soil ecosystems and how to elucidate the significance of phages for microbial ecology and evolution and soil ecosystem functioning in the future. We conclude that similar to bacteria, phages likely play important roles in connecting different One Health compartments, affecting microbiome diversity and functions in soils. From the applied perspective, phages could offer novel approaches to modulate and optimize microbial and microbe-plant interactions to enhance soil health.}, }
@article {pmid38669903, year = {2024}, author = {Liu, H and Al-Dhabi, NA and Jiang, H and Liu, B and Qing, T and Feng, B and Ma, T and Tang, W and Zhang, P}, title = {Toward nitrogen recovery: Co-cultivation of microalgae and bacteria enhances the production of high-value nitrogen-rich cyanophycin.}, journal = {Water research}, volume = {256}, number = {}, pages = {121624}, doi = {10.1016/j.watres.2024.121624}, pmid = {38669903}, issn = {1879-2448}, mesh = {*Nitrogen/metabolism ; *Microalgae/metabolism ; Bacteria/metabolism ; Bioreactors ; Waste Disposal, Fluid/methods ; Wastewater ; Bacterial Proteins ; }, abstract = {The algal-bacterial wastewater treatment process has been proven to be highly efficient in removing nutrients and recovering nitrogen (N). However, the recovery of the valuable N-rich biopolymer, cyanophycin, remains limited. This research explored the synthesis mechanism and recovery potential of cyanophycin within two algal-bacterial symbiotic reactors. The findings reveal that the synergy between algae and bacteria enhances the removal of N and phosphorus. The crude contents of cyanophycin in the algal-bacterial consortia reached 115 and 124 mg/g of mixed liquor suspended solids (MLSS), respectively, showing an increase of 11.7 %-20.4 % (p < 0.001) compared with conventional activated sludge. Among the 170 metagenome-assembled genomes (MAGs) analyzed, 50 were capable of synthesizing cyanophycin, indicating that cyanophycin producers are common in algal-bacterial systems. The compositions of cyanophycin producers in the two algal-bacterial reactors were affected by different lighting initiation time. The study identified two intracellular synthesis pathways for cyanophycin. Approximately 36 MAGs can synthesize cyanophycin de novo using ammonium and glucose, while the remaining 14 MAGs require exogenous arginine for production. Notably, several MAGs with high abundance are capable of assimilating both nitrate and ammonium into cyanophycin, demonstrating a robust N utilization capability. This research also marks the first identification of potential horizontal gene transfer of the cyanophycin synthase encoding gene (cphA) within the wastewater microbial community. This suggests that the spread of cphA could expand the population of cyanophycin producers. The study offers new insights into recycling the high-value N-rich biopolymer cyanophycin, contributing to the advancement of wastewater resource utilization.}, }
@article {pmid38664322, year = {2024}, author = {Vincent, J and Tenore, A and Mattei, MR and Frunzo, L}, title = {Modelling Plasmid-Mediated Horizontal Gene Transfer in Biofilms.}, journal = {Bulletin of mathematical biology}, volume = {86}, number = {6}, pages = {63}, pmid = {38664322}, issn = {1522-9602}, support = {861088//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; }, mesh = {*Biofilms/growth &amp; development ; *Gene Transfer, Horizontal ; *Plasmids/genetics ; *Mathematical Concepts ; *Models, Biological ; *Models, Genetic ; Conjugation, Genetic ; Anti-Bacterial Agents/pharmacology ; }, abstract = {In this study, we present a mathematical model for plasmid spread in a growing biofilm, formulated as a nonlocal system of partial differential equations in a 1-D free boundary domain. Plasmids are mobile genetic elements able to transfer to different phylotypes, posing a global health problem when they carry antibiotic resistance factors. We model gene transfer regulation influenced by nearby potential receptors to account for recipient-sensing. We also introduce a promotion function to account for trace metal effects on conjugation, based on literature data. The model qualitatively matches experimental results, showing that contaminants like toxic metals and antibiotics promote plasmid persistence by favoring plasmid carriers and stimulating conjugation. Even at higher contaminant concentrations inhibiting conjugation, plasmid spread persists by strongly inhibiting plasmid-free cells. The model also replicates higher plasmid density in biofilm's most active regions.}, }
@article {pmid38658529, year = {2024}, author = {Xie, O and Zachreson, C and Tonkin-Hill, G and Price, DJ and Lacey, JA and Morris, JM and McDonald, MI and Bowen, AC and Giffard, PM and Currie, BJ and Carapetis, JR and Holt, DC and Bentley, SD and Davies, MR and Tong, SYC}, title = {Overlapping Streptococcus pyogenes and Streptococcus dysgalactiae subspecies equisimilis household transmission and mobile genetic element exchange.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {3477}, pmid = {38658529}, issn = {2041-1723}, support = {/WT_/Wellcome Trust/United Kingdom ; 206194/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Streptococcus pyogenes/genetics/isolation &amp; purification/classification ; *Streptococcal Infections/transmission/microbiology ; Humans ; *Streptococcus/genetics/isolation &amp; purification ; *Interspersed Repetitive Sequences/genetics ; *Gene Transfer, Horizontal ; Australia ; Genome, Bacterial/genetics ; Female ; Male ; Child ; Family Characteristics ; Adult ; Child, Preschool ; Adolescent ; Longitudinal Studies ; Drug Resistance, Bacterial/genetics ; Young Adult ; }, abstract = {Streptococcus dysgalactiae subspecies equisimilis (SDSE) and Streptococcus pyogenes share skin and throat niches with extensive genomic homology and horizontal gene transfer (HGT) possibly underlying shared disease phenotypes. It is unknown if cross-species transmission interaction occurs. Here, we conduct a genomic analysis of a longitudinal household survey in remote Australian First Nations communities for patterns of cross-species transmission interaction and HGT. Collected from 4547 person-consultations, we analyse 294 SDSE and 315 S. pyogenes genomes. We find SDSE and S. pyogenes transmission intersects extensively among households and show that patterns of co-occurrence and transmission links are consistent with independent transmission without inter-species interference. We identify at least one of three near-identical cross-species mobile genetic elements (MGEs) carrying antimicrobial resistance or streptodornase virulence genes in 55 (19%) SDSE and 23 (7%) S. pyogenes isolates. These findings demonstrate co-circulation of both pathogens and HGT in communities with a high burden of streptococcal disease, supporting a need to integrate SDSE and S. pyogenes surveillance and control efforts.}, }
@article {pmid38658407, year = {2024}, author = {Kuwata, K and Sato-Takabe, Y and Nakai, R and Sugimura, Y and Tazato, N and Kunihiro, T and Morohoshi, S and Iwataki, M and Hamasaki, K and Shiozaki, T}, title = {Novel aerobic anoxygenic phototrophic bacterium Jannaschia pagri sp. nov., isolated from seawater around a fish farm.}, journal = {Antonie van Leeuwenhoek}, volume = {117}, number = {1}, pages = {70}, pmid = {38658407}, issn = {1572-9699}, support = {80635839//MEXT Grants-in-Aid for Young Scientists/ ; JP19H04263//JSPS KAKENHI/ ; }, mesh = {*Phylogeny ; *Seawater/microbiology ; RNA, Ribosomal, 16S/genetics ; Japan ; Aquaculture ; DNA, Bacterial/genetics ; Photosynthesis ; Bacterial Typing Techniques ; Aerobiosis ; Animals ; Bacteriochlorophyll A/analysis ; }, abstract = {The genus Jannaschia is one of the representatives of aerobic anoxygenic phototrophic (AAP) bacteria, which is a strictly aerobic bacterium, producing a photosynthetic pigment bacteriochlorophyll (BChl) a. However, a part of the genus Jannaschia members have not been confirmed the photosynthetic ability. The partly presence of the ability in the genus Jannaschia could suggest the complexity of evolutionary history for anoxygenic photosynthesis in the genus, which is expected as gene loss and/or horizontal gene transfer. Here a novel AAP bacterium designated as strain AI_62[T] (= DSM 115720[ T] = NBRC 115938[ T]), was isolated from coastal seawater around a fish farm in the Uwa Sea, Japan. Its closest relatives were identified as Jannaschia seohaensis SMK-146[ T] (95.6% identity) and J. formosa 12N15[T] (94.6% identity), which have been reported to produce BChl a. The genomic characteristic of strain AI_62[T] clearly showed the possession of the anoxygenic photosynthesis related gene sets. This could be a useful model organism to approach the evolutionary mystery of anoxygenic photosynthesis in the genus Jannaschia. Based on a comprehensive consideration of both phylogenetic and phenotypic characteristics, we propose the classification of a novel species within the genus Jannaschia, designated as Jannaschia pagri sp. nov. The type strain for this newly proposed species is AI_62[T] (= DSM 115720[ T] = NBRC 115938[ T]).}, }
@article {pmid38657817, year = {2024}, author = {Gong, W and Guo, L and Huang, C and Xie, B and Jiang, M and Zhao, Y and Zhang, H and Wu, Y and Liang, H}, title = {A systematic review of antibiotics and antibiotic resistance genes (ARGs) in mariculture wastewater: Antibiotics removal by microalgal-bacterial symbiotic system (MBSS), ARGs characterization on the metagenomic.}, journal = {The Science of the total environment}, volume = {930}, number = {}, pages = {172601}, doi = {10.1016/j.scitotenv.2024.172601}, pmid = {38657817}, issn = {1879-1026}, mesh = {*Wastewater/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; *Microalgae/genetics/physiology ; Waste Disposal, Fluid/methods ; Bacteria ; Metagenomics ; Aquaculture ; Water Pollutants, Chemical/analysis ; Symbiosis ; Genes, Bacterial ; }, abstract = {Antibiotic residues in mariculture wastewater seriously affect the aquatic environment. Antibiotic Resistance Genes (ARGs) produced under antibiotic stress flow through the environment and eventually enter the human body, seriously affecting human health. Microalgal-bacterial symbiotic system (MBSS) can remove antibiotics from mariculture and reduce the flow of ARGs into the environment. This review encapsulates the present scenario of mariculture wastewater, the removal mechanism of MBSS for antibiotics, and the biomolecular information under metagenomic assay. When confronted with antibiotics, there was a notable augmentation in the extracellular polymeric substances (EPS) content within MBSS, along with a concurrent elevation in the proportion of protein (PN) constituents within the EPS, which limits the entry of antibiotics into the cellular interior. Quorum sensing stimulates the microorganisms to produce biological responses (DNA synthesis - for adhesion) through signaling. Oxidative stress promotes gene expression (coupling, conjugation) to enhance horizontal gene transfer (HGT) in MBSS. The microbial community under metagenomic detection is dominated by aerobic bacteria in the bacterial-microalgal system. Compared to aerobic bacteria, anaerobic bacteria had the significant advantage of decreasing the distribution of ARGs. Overall, MBSS exhibits remarkable efficacy in mitigating the challenges posed by antibiotics and resistant genes from mariculture wastewater.}, }
@article {pmid38651513, year = {2025}, author = {Gomathinayagam, S and Kodiveri Muthukaliannan, G}, title = {Dynamics of antibiotic resistance genes in plasmids and bacteriophages.}, journal = {Critical reviews in microbiology}, volume = {51}, number = {2}, pages = {219-228}, doi = {10.1080/1040841X.2024.2339262}, pmid = {38651513}, issn = {1549-7828}, mesh = {*Plasmids/genetics ; *Bacteriophages/genetics ; *Bacteria/genetics/virology/drug effects ; Gene Transfer, Horizontal ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Prophages/genetics ; }, abstract = {This brief review explores the intricate interplay between bacteriophages and plasmids in the context of antibiotic resistance gene (ARG) dissemination. Originating from studies in the late 1950s, the review traces the evolution of knowledge regarding extrachromosomal factors facilitating horizontal gene transfer and adaptation in bacteria. Analyzing the gene repertoires of plasmids and bacteriophages, the study highlights their contributions to bacterial evolution and adaptation. While plasmids encode essential and accessory genes influencing host characteristics, bacteriophages carry auxiliary metabolic genes (AMGs) that augment host metabolism. The debate on phages carrying ARGs is explored through a critical evaluation of various studies, revealing contrasting findings from researchers. Additionally, the review addresses the interplay between prophages and plasmids, underlining their similarities and divergences. Based on the available literature evidence, we conclude that plasmids generally encode ARGs while bacteriophages typically do not contain ARGs. But extra-chromosomaly present prophages with plasmid characteristics can encode and disseminate ARGs.}, }
@article {pmid38648967, year = {2024}, author = {Se, J and Xie, Y and Ma, Q and Zhu, L and Fu, Y and Xu, X and Shen, C and Nannipieri, P}, title = {Drying-wetting cycle enhances stress resistance of Escherichia coli O157:H7 in a model soil.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {350}, number = {}, pages = {123988}, doi = {10.1016/j.envpol.2024.123988}, pmid = {38648967}, issn = {1873-6424}, mesh = {*Escherichia coli O157/physiology ; *Soil Microbiology ; *Soil/chemistry ; Stress, Physiological ; Proteomics ; }, abstract = {Outbreaks of Escherichia coli (E. coli) O157:H7 in farms are often triggered by heavy rains and flooding. Most cells die with the decreasing of soil moisture, while few cells enter a dormant state and then resuscitate after rewetting. The resistance of dormant cells to stress has been extensively studied, whereas the molecular mechanisms of the cross-resistance development of the resuscitated cells are poorly known. We performed a comparative proteomic analysis on O157:H7 before and after undergoing soil dry-wet alternation. A differential expression of 820 proteins was identified in resuscitated cells compared to exponential-phase cells, as determined by proteomics analysis. The GO and KEGG pathway enrichment analyses revealed that up-regulated proteins were associated with oxidative phosphorylation, glycolysis/gluconeogenesis, the citrate cycle (TCA cycle), aminoacyl-tRNA biosynthesis, ribosome activity, and transmembrane transporters, indicating increased energy production and protein synthesis in resuscitated O157:H7. Moreover, proteins related to acid, osmotic, heat, oxidative, antibiotic stress and horizontal gene transfer efficiency were up-regulated, suggesting a potential improvement in stress resistance. Subsequent validation experiments demonstrated that the survival rates of the resuscitated cells were 476.54 and 7786.34 times higher than the exponential-phase cells, with pH levels of 1.5 and 2.5, respectively. Similarly, resuscitated cells showed higher survival rates under osmotic stress, with 7.5%, 15%, and 30% NaCl resulting in survival rates that were 460.58, 1974.55, and 3475.31 times higher. Resuscitated cells also exhibited increased resistance to heat stress, with survival rates 69.64 and 139.72 times higher at 55 °C and 90 °C, respectively. Furthermore, the horizontal gene transfer (HGT) efficiency of resuscitated cells was significantly higher (153.12-fold) compared to exponential phase cells. This study provides new insights into bacteria behavior under changing soil moisture and this may explain O157:H7 outbreaks following rainfall and flooding, as the dry-wet cycle promotes stress cross-resistance development.}, }
@article {pmid38647527, year = {2024}, author = {Ruhluel, D and Fisher, L and Barton, TE and Leighton, H and Kumar, S and Amores Morillo, P and O'Brien, S and Fothergill, JL and Neill, DR}, title = {Secondary messenger signalling influences Pseudomonas aeruginosa adaptation to sinus and lung environments.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38647527}, issn = {1751-7370}, support = {//UK Cystic Fibrosis Trust/ ; SRC 022//Strategic Research Centre/ ; //CF Foundation/ ; 204457/Z/16/Z//Wellcome and Royal Society Sir Henry Dale/ ; /WT_/Wellcome Trust/United Kingdom ; NC/S001700/1/NC3RS_/National Centre for the Replacement, Refinement and Reduction of Animals in Research/United Kingdom ; NC/S00100/1//NC3Rs/ ; }, mesh = {*Pseudomonas aeruginosa/genetics/physiology/metabolism ; *Pseudomonas Infections/microbiology ; *Adaptation, Physiological ; *Biofilms/growth &amp; development ; Animals ; Lung/microbiology ; Fimbriae, Bacterial/genetics/metabolism ; Second Messenger Systems ; Cystic Fibrosis/microbiology ; Mice ; Humans ; Anti-Bacterial Agents/pharmacology ; Cyclic GMP/metabolism/analogs &amp; derivatives ; Mutation ; Phenotype ; }, abstract = {Pseudomonas aeruginosa is a cause of chronic respiratory tract infections in people with cystic fibrosis (CF), non-CF bronchiectasis, and chronic obstructive pulmonary disease. Prolonged infection allows the accumulation of mutations and horizontal gene transfer, increasing the likelihood of adaptive phenotypic traits. Adaptation is proposed to arise first in bacterial populations colonizing upper airway environments. Here, we model this process using an experimental evolution approach. Pseudomonas aeruginosa PAO1, which is not airway adapted, was serially passaged, separately, in media chemically reflective of upper or lower airway environments. To explore whether the CF environment selects for unique traits, we separately passaged PAO1 in airway-mimicking media with or without CF-specific factors. Our findings demonstrated that all airway environments-sinus and lungs, under CF and non-CF conditions-selected for loss of twitching motility, increased resistance to multiple antibiotic classes, and a hyper-biofilm phenotype. These traits conferred increased airway colonization potential in an in vivo model. CF-like conditions exerted stronger selective pressures, leading to emergence of more pronounced phenotypes. Loss of twitching was associated with mutations in type IV pili genes. Type IV pili mediate surface attachment, twitching, and induction of cAMP signalling. We additionally identified multiple evolutionary routes to increased biofilm formation involving regulation of cyclic-di-GMP signalling. These included the loss of function mutations in bifA and dipA phosphodiesterase genes and activating mutations in the siaA phosphatase. These data highlight that airway environments select for traits associated with sessile lifestyles and suggest upper airway niches support emergence of phenotypes that promote establishment of lung infection.}, }
@article {pmid38643972, year = {2024}, author = {Kogay, R and Wolf, YI and Koonin, EV}, title = {Defence systems and horizontal gene transfer in bacteria.}, journal = {Environmental microbiology}, volume = {26}, number = {4}, pages = {e16630}, pmid = {38643972}, issn = {1462-2920}, support = {Z01 LM000073/ImNIH/Intramural NIH HHS/United States ; }, mesh = {*Gene Transfer, Horizontal/genetics ; *Bacteria/classification/genetics ; Interspersed Repetitive Sequences/genetics ; CRISPR-Cas Systems/genetics ; Lysogeny/genetics ; Species Specificity ; Evolution, Molecular ; }, abstract = {Horizontal gene transfer (HGT) is a fundamental process in prokaryotic evolution, contributing significantly to diversification and adaptation. HGT is typically facilitated by mobile genetic elements (MGEs), such as conjugative plasmids and phages, which often impose fitness costs on their hosts. However, a considerable number of bacterial genes are involved in defence mechanisms that limit the propagation of MGEs, suggesting they may actively restrict HGT. In our study, we investigated whether defence systems limit HGT by examining the relationship between the HGT rate and the presence of 73 defence systems across 12 bacterial species. We discovered that only six defence systems, three of which were different CRISPR-Cas subtypes, were associated with a reduced gene gain rate at the species evolution scale. Hosts of these defence systems tend to have a smaller pangenome size and fewer phage-related genes compared to genomes without these systems. This suggests that these defence mechanisms inhibit HGT by limiting prophage integration. We hypothesize that the restriction of HGT by defence systems is species-specific and depends on various ecological and genetic factors, including the burden of MGEs and the fitness effect of HGT in bacterial populations.}, }
@article {pmid38643216, year = {2024}, author = {Bartoš, O and Chmel, M and Swierczková, I}, title = {The overlooked evolutionary dynamics of 16S rRNA revises its role as the "gold standard" for bacterial species identification.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {9067}, pmid = {38643216}, issn = {2045-2322}, support = {MO1012//Ministry of Defence, Czech Republic/ ; }, mesh = {RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Biological Evolution ; Sequence Analysis, DNA ; }, abstract = {The role of 16S rRNA has been and largely remains crucial for the identification of microbial organisms. Although 16S rRNA could certainly be described as one of the most studied sequences ever, the current view of it remains somewhat ambiguous. While some consider 16S rRNA to be a variable marker with resolution power down to the strain level, others consider them to be living fossils that carry information about the origin of domains of cellular life. We show that 16S rRNA is clearly an evolutionarily very rigid sequence, making it a largely unique and irreplaceable marker, but its applicability beyond the genus level is highly limited. Interestingly, it seems that the evolutionary rigidity is not driven by functional constraints of the sequence (RNA-protein interactions), but rather results from the characteristics of the host organism. Our results suggest that, at least in some lineages, Horizontal Gene Transfer (HGT) within genera plays an important role for the evolutionary non-dynamics (stasis) of 16S rRNA. Such genera exhibit an apparent lack of diversification at the 16S rRNA level in comparison to the rest of a genome. However, why it is limited specifically and solely to 16S rRNA remains enigmatic.}, }
@article {pmid38642082, year = {2024}, author = {Singh, CK and Sodhi, KK and Shree, P and Nitin, V}, title = {Heavy Metals as Catalysts in the Evolution of Antimicrobial Resistance and the Mechanisms Underpinning Co-selection.}, journal = {Current microbiology}, volume = {81}, number = {6}, pages = {148}, pmid = {38642082}, issn = {1432-0991}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; *Metals, Heavy ; Bacteria/genetics ; *Environmental Pollutants ; }, abstract = {The menace caused by antibiotic resistance in bacteria is acknowledged on a global scale. Concerns over the same are increasing because of the selection pressure exerted by a huge number of different antimicrobial agents, including heavy metals. Heavy metals are non-metabolizable and recalcitrant to degradation, therefore the bacteria can expel the pollutants out of the system and make it less harmful via different mechanisms. The selection of antibiotic-resistant bacteria may be influenced by heavy metals present in environmental reservoirs. Through co-resistance and cross-resistance processes, the presence of heavy metals in the environment can act as co-selecting agents, hence increasing resistance to both heavy metals and antibiotics. The horizontal gene transfer or mutation assists in the selection of mutant bacteria resistant to the polluted environment. Hence, bioremediation and biodegradation are sustainable methods for the natural clean-up of pollutants. This review sheds light on the occurrence of metal and antibiotic resistance in the environment via the co-resistance and cross-resistance mechanisms underpinning co-selection emphasizing the dearth of studies that specifically examine the method of co-selection in clinical settings. Furthermore, it is advised that future research incorporate both culture- and molecular-based methodologies to further our comprehension of the mechanisms underlying bacterial co- and cross-resistance to antibiotics and heavy metals.}, }
@article {pmid38641304, year = {2024}, author = {Sha, G and Wu, Z and Chen, T and Zhang, G and Shen, J and Zhao, X and Wang, L}, title = {Mechanisms for more efficient antibiotics and antibiotic resistance genes removal during industrialized treatment of over 200 tons of tylosin and spectinomycin mycelial dregs by integrated meta-omics.}, journal = {Bioresource technology}, volume = {401}, number = {}, pages = {130715}, doi = {10.1016/j.biortech.2024.130715}, pmid = {38641304}, issn = {1873-2976}, mesh = {*Tylosin/pharmacology ; *Anti-Bacterial Agents/pharmacology ; *Fermentation ; *Spectinomycin/pharmacology ; Mycelium/drug effects ; Drug Resistance, Microbial/genetics/drug effects ; Biodegradation, Environmental ; Genes, Bacterial ; }, abstract = {To mitigate the environmental risks posed by the accumulation of antibiotic mycelial dregs (AMDs), this study first attempted over 200 tons of mass production fermentation (MP) using tylosin and spectinomycin mycelial dregs alongside pilot-scale fermentation (PS) for comparison, utilizing the integrated-omics and qPCR approaches. Co-fermentation results showed that both antibiotics were effectively removed in all treatments, with an average removal rate of 92%. Antibiotic resistance gene (ARG)-related metabolic pathways showed that rapid degradation of antibiotics was associated with enzymes that inactivate macrolides and aminoglycosides (e.g., K06979, K07027, K05593). Interestingly, MP fermentations with optimized conditions had more efficient ARGs removal because homogenization permitted faster microbial succession, with more stable removal of antibiotic resistant bacteria and mobile genetic elements. Moreover, Bacillus reached 75% and secreted antioxidant enzymes that might inhibit horizontal gene transfer of ARGs. The findings confirmed the advantages of MP fermentation and provided a scientific basis for other AMDs.}, }
@article {pmid38641198, year = {2024}, author = {Ouzounis, CA}, title = {The Net of Life, a short story: Intricate patterns of gene flows across hundreds of extant genomes, all the way to LUCA.}, journal = {Bio Systems}, volume = {239}, number = {}, pages = {105199}, doi = {10.1016/j.biosystems.2024.105199}, pmid = {38641198}, issn = {1872-8324}, mesh = {Animals ; Humans ; *Evolution, Molecular ; *Gene Flow ; Gene Transfer, Horizontal ; *Genome/genetics ; Models, Genetic ; Phylogeny ; }, abstract = {Over the past quarter-century, the field of evolutionary biology has been transformed by the emergence of complete genome sequences and the conceptual framework known as the 'Net of Life.' This paradigm shift challenges traditional notions of evolution as a tree-like process, emphasizing the complex, interconnected network of gene flow that may blur the boundaries between distinct lineages. In this context, gene loss, rather than horizontal gene transfer, is the primary driver of gene content, with vertical inheritance playing a principal role. The 'Net of Life' not only impacts our understanding of genome evolution but also has profound implications for classification systems, the rapid appearance of new traits, and the spread of diseases. Here, we explore the core tenets of the 'Net of Life' and its implications for genome-scale phylogenetic divergence, providing a comprehensive framework for further investigations in evolutionary biology.}, }
@article {pmid38641137, year = {2024}, author = {De, R and Jani, M and Azad, RK}, title = {DICEP: An integrative approach to augmenting genomic island detection.}, journal = {Journal of biotechnology}, volume = {388}, number = {}, pages = {49-58}, doi = {10.1016/j.jbiotec.2024.04.011}, pmid = {38641137}, issn = {1873-4863}, mesh = {*Genomic Islands/genetics ; *Genome, Bacterial/genetics ; Bacteria/genetics ; Genomics/methods ; Phylogeny ; Software ; Computational Biology/methods ; }, abstract = {Mobilization of clusters of genes called genomic islands (GIs) across bacterial lineages facilitates dissemination of traits, such as, resistance against antibiotics, virulence or hypervirulence, and versatile metabolic capabilities. Robust delineation of GIs is critical to understanding bacterial evolution that has a vast impact on different life forms. Methods for identification of GIs exploit different evolutionary features or signals encoded within the genomes of bacteria, however, the current state-of-the-art in GI detection still leaves much to be desired. Here, we have taken a combinatorial approach that accounted for GI specific features such as compositional bias, aberrant phyletic pattern, and marker gene enrichment within an integrative framework to delineate GIs in bacterial genomes. Our GI prediction tool, DICEP, was assessed on simulated genomes and well-characterized bacterial genomes. DICEP compared favorably with current GI detection tools on real and synthetic datasets.}, }
@article {pmid38641096, year = {2024}, author = {Liu, Y and Chu, K and Hua, Z and Li, Q and Lu, Y and Ye, F and Dong, Y and Li, X}, title = {Dynamics of antibiotic resistance genes in the sediments of a water-diversion lake and its human exposure risk behaviour.}, journal = {The Science of the total environment}, volume = {929}, number = {}, pages = {172563}, doi = {10.1016/j.scitotenv.2024.172563}, pmid = {38641096}, issn = {1879-1026}, mesh = {*Drug Resistance, Microbial/genetics ; Lakes/microbiology ; Environmental Monitoring/methods ; Humans ; *Environmental Exposure/statistics &amp; numerical data ; Geologic Sediments/microbiology ; Water Pollution/statistics &amp; numerical data ; Spatio-Temporal Analysis ; Gene Transfer, Horizontal ; China ; }, abstract = {The dynamics and exposure risk behaviours of antibiotic resistance genes (ARGs) in the sediments of water-diversion lakes remain poorly understood. In this study, spatiotemporal investigations of ARG profiles in sediments targeting non-water (NWDP) and water diversion periods (WDP) were conducted in Luoma Lake, a typical water-diversion lake, and an innovative dynamics-based risk assessment framework was constructed to evaluate ARG exposure risks to local residents. ARGs in sediments were significantly more abundant in the WDP than in the NWDP, but there was no significant variation in their spatial distribution in either period. Moreover, the pattern of ARG dissemination in sediments was unchanged between the WDP and NWDP, with horizontal gene transfer (HGT) and vertical gene transfer (VGT) contributing to ARG dissemination in both periods. However, water diversion altered the pattern in lake water, with HGT and VGT in the NWDP but only HGT in the WDP, which were critical pathways for the dissemination of ARGs. The significantly lower ARG sediment-water partition coefficient in the WDP indicated that water diversion could shift the fate of ARGs and facilitate their aqueous partitioning. Risk assessment showed that all age groups faced a higher human exposure risk of ARGs (HERA) in the WDP than in the NWDP, with the 45-59 age group having the highest risk. Furthermore, HERA increased overall with the bacterial carrying capacity in the local environment and peaked when the carrying capacity reached three (NWDP) or four (WDP) orders of magnitude higher than the observed bacterial population. HGT and VGT promoted, whereas ODF covering gene mutation and loss mainly reduced HERA in the lake. As the carrying capacity increased, the relative contribution of ODF to HERA remained relatively stable, whereas the dominant mechanism of HERA development shifted from HGT to VGT.}, }
@article {pmid38640666, year = {2024}, author = {Xie, S and Hamid, N and Zhang, T and Zhang, Z and Peng, L}, title = {Unraveling the nexus: Microplastics, antibiotics, and ARGs interactions, threats and control in aquaculture - A review.}, journal = {Journal of hazardous materials}, volume = {471}, number = {}, pages = {134324}, doi = {10.1016/j.jhazmat.2024.134324}, pmid = {38640666}, issn = {1873-3336}, mesh = {*Aquaculture ; *Microplastics/toxicity ; *Anti-Bacterial Agents ; *Water Pollutants, Chemical/analysis ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Wastewater/chemistry ; }, abstract = {In recent years, aquaculture has expanded rapidly to address food scarcity and provides high-quality aquatic products. However, this growth has led to the release of significant effluents, containing emerging contaminants like antibiotics, microplastics (MPs), and antibiotic resistance genes (ARGs). This study investigated the occurrence and interactions of these pollutants in aquaculture environment. Combined pollutants, such as MPs and coexisting adsorbents, were widespread and could include antibiotics, heavy metals, resistance genes, and pathogens. Elevated levels of chemical pollutants on MPs could lead to the emergence of resistance genes under selective pressure, facilitated by bacterial communities and horizontal gene transfer (HGT). MPs acted as vectors, transferring pollutants into the food web. Various technologies, including membrane technology, coagulation, and advanced oxidation, have been trialed for pollutants removal, each with its benefits and drawbacks. Future research should focus on ecologically friendly treatment technologies for emerging contaminants in aquaculture wastewater. This review provided insights into understanding and addressing newly developing toxins, aiming to develop integrated systems for effective aquaculture wastewater treatment.}, }
@article {pmid38638913, year = {2024}, author = {Liu, F and Luo, Y and Xu, T and Lin, H and Qiu, Y and Li, B}, title = {Current examining methods and mathematical models of horizontal transfer of antibiotic resistance genes in the environment.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1371388}, pmid = {38638913}, issn = {1664-302X}, abstract = {The increasing prevalence of antibiotic resistance genes (ARGs) in the environment has garnered significant attention due to their health risk to human beings. Horizontal gene transfer (HGT) is considered as an important way for ARG dissemination. There are four general routes of HGT, including conjugation, transformation, transduction and vesiduction. Selection of appropriate examining methods is crucial for comprehensively understanding characteristics and mechanisms of different HGT ways. Moreover, combined with the results obtained from different experimental methods, mathematical models could be established and serve as a powerful tool for predicting ARG transfer dynamics and frequencies. However, current reviews of HGT for ARG spread mainly focus on its influencing factors and mechanisms, overlooking the important roles of examining methods and models. This review, therefore, delineated four pathways of HGT, summarized the strengths and limitations of current examining methods, and provided a comprehensive summing-up of mathematical models pertaining to three main HGT ways of conjugation, transformation and transduction. Finally, deficiencies in current studies were discussed, and proposed the future perspectives to better understand and assess the risks of ARG dissemination through HGT.}, }
@article {pmid38638826, year = {2024}, author = {Nasrollahian, S and Graham, JP and Halaji, M}, title = {A review of the mechanisms that confer antibiotic resistance in pathotypes of E. coli.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1387497}, pmid = {38638826}, issn = {2235-2988}, mesh = {Humans ; *Escherichia coli/genetics ; *Escherichia coli Infections/drug therapy ; Microbial Sensitivity Tests ; Anti-Bacterial Agents/pharmacology/therapeutic use ; beta-Lactamases/genetics ; Drug Resistance, Microbial ; }, abstract = {The dissemination of antibiotic resistance in Escherichia coli poses a significant threat to public health worldwide. This review provides a comprehensive update on the diverse mechanisms employed by E. coli in developing resistance to antibiotics. We primarily focus on pathotypes of E. coli (e.g., uropathogenic E. coli) and investigate the genetic determinants and molecular pathways that confer resistance, shedding light on both well-characterized and recently discovered mechanisms. The most prevalent mechanism continues to be the acquisition of resistance genes through horizontal gene transfer, facilitated by mobile genetic elements such as plasmids and transposons. We discuss the role of extended-spectrum β-lactamases (ESBLs) and carbapenemases in conferring resistance to β-lactam antibiotics, which remain vital in clinical practice. The review covers the key resistant mechanisms, including: 1) Efflux pumps and porin mutations that mediate resistance to a broad spectrum of antibiotics, including fluoroquinolones and aminoglycosides; 2) adaptive strategies employed by E. coli, including biofilm formation, persister cell formation, and the activation of stress response systems, to withstand antibiotic pressure; and 3) the role of regulatory systems in coordinating resistance mechanisms, providing insights into potential targets for therapeutic interventions. Understanding the intricate network of antibiotic resistance mechanisms in E. coli is crucial for the development of effective strategies to combat this growing public health crisis. By clarifying these mechanisms, we aim to pave the way for the design of innovative therapeutic approaches and the implementation of prudent antibiotic stewardship practices to preserve the efficacy of current antibiotics and ensure a sustainable future for healthcare.}, }
@article {pmid38626826, year = {2024}, author = {Zhang, J and Zhao, L and Wang, W and Zhang, Q and Wang, XT and Xing, DF and Ren, NQ and Lee, DJ and Chen, C}, title = {Large language model for horizontal transfer of resistance gene: From resistance gene prevalence detection to plasmid conjugation rate evaluation.}, journal = {The Science of the total environment}, volume = {931}, number = {}, pages = {172466}, doi = {10.1016/j.scitotenv.2024.172466}, pmid = {38626826}, issn = {1879-1026}, mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; Conjugation, Genetic ; Drug Resistance, Bacterial/genetics ; Pseudomonas/genetics ; }, abstract = {The burgeoning issue of plasmid-mediated resistance genes (ARGs) dissemination poses a significant threat to environmental integrity. However, the prediction of ARGs prevalence is overlooked, especially for emerging ARGs that are potentially evolving gene exchange hotspot. Here, we explored to classify plasmid or chromosome sequences and detect resistance gene prevalence by using DNABERT. Initially, the DNABERT fine-tuned in plasmid and chromosome sequences followed by multilayer perceptron (MLP) classifier could achieve 0.764 AUC (Area under curve) on external datasets across 23 genera, outperforming 0.02 AUC than traditional statistic-based model. Furthermore, Escherichia, Pseudomonas single genera based model were also be trained to explore its predict performance to ARGs prevalence detection. By integrating K-mer frequency attributes, our model could boost the performance to predict the prevalence of ARGs in an external dataset in Escherichia with 0.0281-0.0615 AUC and Pseudomonas with 0.0196-0.0928 AUC. Finally, we established a random forest model aimed at forecasting the relative conjugation transfer rate of plasmids with 0.7956 AUC, drawing on data from existing literature. It identifies the plasmid's repression status, cellular density, and temperature as the most important factors influencing transfer frequency. With these two models combined, they provide useful reference for quick and low-cost integrated evaluation of resistance gene transfer, accelerating the process of computer-assisted quantitative risk assessment of ARGs transfer in environmental field.}, }
@article {pmid38626743, year = {2024}, author = {Sewell, HL and Criddle, CS and Woo, SG and Kim, S and Müller, JA and Kaster, AK}, title = {Pseudomonas stutzeri KC carries the pdt genes for carbon tetrachloride degradation on an integrative and conjugative element.}, journal = {Microbial physiology}, volume = {}, number = {}, pages = {}, doi = {10.1159/000538783}, pmid = {38626743}, issn = {2673-1673}, abstract = {Pseudomonas stutzeri KC can rapidly degrade carbon tetrachloride (CCl4) to CO2 by a fortuitous reaction with pyridine-2,6-bis(thiocarboxylic acid), a metal chelator encoded by pdt genes. These genes were first identified after a spontaneous mutant, strain CTN1, lost the ability to degrade CCl4. Here we report the complete genome of strain KC and show that these pdt genes are located on an integrative and conjugative element (ICE), designated ICEPsstKC. Comparative genome analyses revealed homologues of pdt genes in genomes of members of other gammaproteobacterial orders. Discrepancies between the tree topologies of the deduced pdt gene products and the host phylogeny based on 16S rRNA provided evidence for horizontal gene transfer (HGT) in several sequenced strains of these orders. In addition to ICEPsstKC, HGT may be have been facilitated by other mobile genetic elements, as indicated by the location of the pdt gene cluster adjacent to fragments of other ICEs and prophages in several genome assemblies. We could here show that the majority of cells from the culture collection DSMZ had lost the ICE. The presence of the pdt gene cluster on mobile genetic elements has important implications for the bioremediation of CCl4 for bioremediation of CCl4 and needs consideration when selecting suitable strains.}, }
@article {pmid38618896, year = {2024}, author = {Peng, X and Zhou, J and Lan, Z and Tan, R and Chen, T and Shi, D and Li, H and Yang, Z and Zhou, S and Jin, M and Li, JW and Yang, D}, title = {Carbonaceous particulate matter promotes the horizontal transfer of antibiotic resistance genes.}, journal = {Environmental science. Processes &amp; impacts}, volume = {26}, number = {5}, pages = {915-927}, doi = {10.1039/d3em00547j}, pmid = {38618896}, issn = {2050-7895}, mesh = {*Particulate Matter/analysis ; *Gene Transfer, Horizontal ; *Air Pollutants/analysis ; Drug Resistance, Microbial/genetics ; Particle Size ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; }, abstract = {There is growing concern about the transfer of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in airborne particulate matter. In this study, we investigated the effects of various types of carbonaceous particulate matter (CPM) on the transfer of ARGs in vitro. The results showed that CPM promoted the transfer of ARGs, which was related to the concentration and particle size. Compared with the control group, the transfer frequency was 95.5, 74.7, 65.4, 14.7, and 3.8 times higher in G (graphene), CB (carbon black), NGP (nanographite powder), GP1.6 (graphite powder 1.6 micron), and GP45 (graphite powder 45 micron) groups, respectively. Moreover, the transfer frequency gradually increased with the increase in CPM concentration, while there was a negative relationship between the CPM particle size and conjugative transfer frequency. In addition, the results showed that CPM could promote the transfer of ARGs by increasing ROS, as well as activating the SOS response and expression of conjugative transfer-related genes (trbBp, trfAp, korA, kroB, and trbA). These findings are indicative of the potential risk of CPM for the transfer of ARGs in the environment, enriching our understanding of environmental pollution and further raising awareness of environmental protection.}, }
@article {pmid38618705, year = {2024}, author = {Sarkar, S and Anyaso-Samuel, S and Qiu, P and Datta, S}, title = {Multiblock partial least squares and rank aggregation: Applications to detection of bacteriophages associated with antimicrobial resistance in the presence of potential confounding factors.}, journal = {Statistics in medicine}, volume = {43}, number = {13}, pages = {2527-2546}, doi = {10.1002/sim.10058}, pmid = {38618705}, issn = {1097-0258}, mesh = {*Bacteriophages/genetics ; Humans ; Least-Squares Analysis ; Metagenomics/methods ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Drug Resistance, Microbial/genetics ; Confounding Factors, Epidemiologic ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Microbiota/drug effects ; }, abstract = {Urban environments, characterized by bustling mass transit systems and high population density, host a complex web of microorganisms that impact microbial interactions. These urban microbiomes, influenced by diverse demographics and constant human movement, are vital for understanding microbial dynamics. We explore urban metagenomics, utilizing an extensive dataset from the Metagenomics &amp; Metadesign of Subways &amp; Urban Biomes (MetaSUB) consortium, and investigate antimicrobial resistance (AMR) patterns. In this pioneering research, we delve into the role of bacteriophages, or "phages"-viruses that prey on bacteria and can facilitate the exchange of antibiotic resistance genes (ARGs) through mechanisms like horizontal gene transfer (HGT). Despite their potential significance, existing literature lacks a consensus on their significance in ARG dissemination. We argue that they are an important consideration. We uncover that environmental variables, such as those on climate, demographics, and landscape, can obscure phage-resistome relationships. We adjust for these potential confounders and clarify these relationships across specific and overall antibiotic classes with precision, identifying several key phages. Leveraging machine learning tools and validating findings through clinical literature, we uncover novel associations, adding valuable insights to our comprehension of AMR development.}, }
@article {pmid38617843, year = {2024}, author = {Guinet, B and Leobold, M and Herniou, EA and Bloin, P and Burlet, N and Bredlau, J and Navratil, V and Ravallec, M and Uzbekov, R and Kester, K and Gundersen Rindal, D and Drezen, JM and Varaldi, J and Bézier, A}, title = {A novel and diverse family of filamentous DNA viruses associated with parasitic wasps.}, journal = {Virus evolution}, volume = {10}, number = {1}, pages = {veae022}, pmid = {38617843}, issn = {2057-1577}, abstract = {Large dsDNA viruses from the Naldaviricetes class are currently composed of four viral families infecting insects and/or crustaceans. Since the 1970s, particles described as filamentous viruses (FVs) have been observed by electronic microscopy in several species of Hymenoptera parasitoids but until recently, no genomic data was available. This study provides the first comparative morphological and genomic analysis of these FVs. We analyzed the genomes of seven FVs, six of which were newly obtained, to gain a better understanding of their evolutionary history. We show that these FVs share all genomic features of the Naldaviricetes while encoding five specific core genes that distinguish them from their closest relatives, the Hytrosaviruses. By mining public databases, we show that FVs preferentially infect Hymenoptera with parasitoid lifestyle and that these viruses have been repeatedly integrated into the genome of many insects, particularly Hymenoptera parasitoids, overall suggesting a long-standing specialization of these viruses to parasitic wasps. Finally, we propose a taxonomical revision of the class Naldaviricetes in which FVs related to the Leptopilina boulardi FV constitute a fifth family. We propose to name this new family, Filamentoviridae.}, }
@article {pmid38617331, year = {2024}, author = {Lyulina, AS and Liu, Z and Good, BH}, title = {Linkage equilibrium between rare mutations.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38617331}, issn = {2692-8205}, support = {R35 GM146949/GM/NIGMS NIH HHS/United States ; }, abstract = {Recombination breaks down genetic linkage by reshuffling existing variants onto new genetic backgrounds. These dynamics are traditionally quantified by examining the correlations between alleles, and how they decay as a function of the recombination rate. However, the magnitudes of these correlations are strongly influenced by other evolutionary forces like natural selection and genetic drift, making it difficult to tease out the effects of recombination. Here we introduce a theoretical framework for analyzing an alternative family of statistics that measure the homoplasy produced by recombination. We derive analytical expressions that predict how these statistics depend on the rates of recombination and recurrent mutation, the strength of negative selection and genetic drift, and the present-day frequencies of the mutant alleles. We find that the degree of homoplasy can strongly depend on this frequency scale, which reflects the underlying timescales over which these mutations occurred. We show how these scaling properties can be used to isolate the effects of recombination, and discuss their implications for the rates of horizontal gene transfer in bacteria.}, }
@article {pmid38615644, year = {2024}, author = {Fu, X and Gao, J and Wang, Q and Chen, H and Liu, Y and Zeng, L and Yuan, Y and Xu, H}, title = {Mechanisms on the removal of gram-negative/positive antibiotic resistant bacteria and inhibition of horizontal gene transfer by ferrate coupled with peroxydisulfate or peroxymonosulfate.}, journal = {Journal of hazardous materials}, volume = {470}, number = {}, pages = {134254}, doi = {10.1016/j.jhazmat.2024.134254}, pmid = {38615644}, issn = {1873-3336}, mesh = {*Peroxides/chemistry ; *Gene Transfer, Horizontal ; *Iron/chemistry ; Water Purification/methods ; Escherichia coli/drug effects/genetics ; Drug Resistance, Bacterial/genetics ; Disinfection/methods ; Sulfates/chemistry ; Anti-Bacterial Agents/pharmacology/chemistry ; Bacillus/genetics/drug effects/metabolism ; }, abstract = {The existence of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) has been a global public environment and health issue. Due to the different cell structures, gram-positive/negative ARB exhibit various inactivation mechanisms in water disinfection. In this study, a gram-negative ARB Escherichia coli DH5α (E. coli DH5α) was used as a horizontal gene transfer (HGT) donor, while a gram-positive ARB Bacillus as a recipient. To develop an efficient and engineering applicable method in water disinfection, ARB and ARGs removal efficiency of Fe(VI) coupled peroxydisulfate (PDS) or peroxymonosulfate (PMS) was compared, wherein hydroxylamine (HA) was added as a reducing agent. The results indicated that Fe(VI)/PMS/HA showed higher disinfection efficiency than Fe(VI)/PDS/HA. When the concentration of each Fe(VI), PMS, HA was 0.48 mM, 5.15 log E. coli DH5α and 3.57 log Bacillus lost cultivability, while the proportion of recovered cells was 0.0017 % and 0.0566 %, respectively, and HGT was blocked. Intracellular tetA was reduced by 2.49 log. Fe(IV) and/or Fe(V) were proved to be the decisive reactive species. Due to the superiority of low cost as well as high efficiency and practicality, Fe(VI)/PMS/HA has significant application potential in ARB, ARGs removal and HGT inhibition, offering a new insight for wastewater treatment.}, }
@article {pmid38609370, year = {2024}, author = {Quinones-Olvera, N and Owen, SV and McCully, LM and Marin, MG and Rand, EA and Fan, AC and Martins Dosumu, OJ and Paul, K and Sanchez Castaño, CE and Petherbridge, R and Paull, JS and Baym, M}, title = {Diverse and abundant phages exploit conjugative plasmids.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {3197}, pmid = {38609370}, issn = {2041-1723}, support = {T32 GM135014/GM/NIGMS NIH HHS/United States ; R35 GM133700/GM/NIGMS NIH HHS/United States ; }, mesh = {*Bacteriophages/genetics ; Wastewater ; Biological Evolution ; Biotechnology ; Cell Membrane ; }, abstract = {Phages exert profound evolutionary pressure on bacteria by interacting with receptors on the cell surface to initiate infection. While the majority of phages use chromosomally encoded cell surface structures as receptors, plasmid-dependent phages exploit plasmid-encoded conjugation proteins, making their host range dependent on horizontal transfer of the plasmid. Despite their unique biology and biotechnological significance, only a small number of plasmid-dependent phages have been characterized. Here we systematically search for new plasmid-dependent phages targeting IncP and IncF plasmids using a targeted discovery platform, and find that they are common and abundant in wastewater, and largely unexplored in terms of their genetic diversity. Plasmid-dependent phages are enriched in non-canonical types of phages, and all but one of the 65 phages we isolated were non-tailed, and members of the lipid-containing tectiviruses, ssDNA filamentous phages or ssRNA phages. We show that plasmid-dependent tectiviruses exhibit profound differences in their host range which is associated with variation in the phage holin protein. Despite their relatively high abundance in wastewater, plasmid-dependent tectiviruses are missed by metaviromic analyses, underscoring the continued importance of culture-based phage discovery. Finally, we identify a tailed phage dependent on the IncF plasmid, and find related structural genes in phages that use the orthogonal type 4 pilus as a receptor, highlighting the evolutionarily promiscuous use of these distinct contractile structures by multiple groups of phages. Taken together, these results indicate plasmid-dependent phages play an under-appreciated evolutionary role in constraining horizontal gene transfer via conjugative plasmids.}, }
@article {pmid38608575, year = {2024}, author = {Xu, Z and Hu, S and Zhao, D and Xiong, J and Li, C and Ma, Y and Li, S and Huang, B and Pan, X}, title = {Molybdenum disulfide nanosheets promote the plasmid-mediated conjugative transfer of antibiotic resistance genes.}, journal = {Journal of environmental management}, volume = {358}, number = {}, pages = {120827}, doi = {10.1016/j.jenvman.2024.120827}, pmid = {38608575}, issn = {1095-8630}, mesh = {*Molybdenum/chemistry ; *Plasmids/genetics ; *Disulfides/chemistry ; *Escherichia coli/genetics/drug effects ; *Drug Resistance, Microbial/genetics ; Conjugation, Genetic ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; }, abstract = {The environmental safety of nanoscale molybdenum disulfide (MoS2) has attracted considerable attention, but its influence on the horizontal migration of antibiotic resistance genes and the ecological risks entailed have not been reported. This study addressed the influence of exposure to MoS2 at different concentrations up to 100 mg/L on the conjugative transfer of antibiotic resistance genes carried by RP4 plasmids with two strains of Escherichia coli. As a result, MoS2 facilitated RP4 plasmid-mediated conjugative transfer in a dose-dependent manner. The conjugation of RP4 plasmids was enhanced as much as 7-fold. The promoting effect is mainly attributable to increased membrane permeability, oxidative stress induced by reactive oxygen species, changes in extracellular polymer secretion and differential expression of the genes involved in horizontal gene transfer. The data highlight the distinct dose dependence of the conjugative transfer of antibiotic resistance genes and the need to improve awareness of the ecological and health risks of nanoscale transition metal dichalcogenides.}, }
@article {pmid38608246, year = {2024}, author = {Yi, S and Zhou, K and Xu, X}, title = {Characterization of erm(B)-Carrying Integrative and Conjugative Elements Transferred from Streptococcus anginosus to Other Streptococci and Enterococci.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {30}, number = {6}, pages = {243-253}, doi = {10.1089/mdr.2023.0342}, pmid = {38608246}, issn = {1931-8448}, mesh = {*Streptococcus anginosus/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology ; *Gene Transfer, Horizontal ; *Enterococcus/genetics/drug effects ; *Conjugation, Genetic ; Streptococcus/genetics/drug effects ; Microbial Sensitivity Tests ; Humans ; Bacterial Proteins/genetics ; Drug Resistance, Bacterial/genetics ; }, abstract = {Integrative and conjugative elements (ICEs) are important vectors of lateral gene transfer and contribute to the evolution of bacterial pathogens. However, studies on the transfer among species and the physiological consequences of ICEs are rare. The objective of this study was to investigate the cross-species transferability of newly identified erm(B)-carried ICE in Streptococcus anginosus San95 and its physiological consequences after transfer. The erm(B)-carried ICE, characterized by a triple serine integrase module, integrated into hsdM genes, thus designated ICESan95_hsdM. Analysis of ICESan95_hsdM revealed 32 additional ICESan95-like ICEs in the available NCBI genome (n = 24) and sequence of clinical isolates (n = 8). Polymerase chain reaction (PCR) was used to evaluate the 467 clinical isolates, of which 84 were positive for core genes (integrase, relaxase, and T4SS genes) of ICESan95_hsdM. Cross-species transfer experiments demonstrated that ICESan95_hsdM could transfer from S. anginosus to different streptococcal and enterococcal recipients. Growth and competitive culture assays showed acquisition of ICESan95_hsdM incurred no fitness cost. Our work discovered a group of ICEs in Streptococci and Enterococci. For the first time, we demonstrated the broad cross-species transferability to different species or genera of ICEs with no fitness cost that enables commensal S. anginosus to deliver antimicrobial resistance genes to other streptococci and enterococci.}, }
@article {pmid38605260, year = {2024}, author = {Rafiq, MS and Shabbir, MA and Raza, A and Irshad, S and Asghar, A and Maan, MK and Gondal, MA and Hao, H}, title = {CRISPR-Cas System: A New Dawn to Combat Antibiotic Resistance.}, journal = {BioDrugs : clinical immunotherapeutics, biopharmaceuticals and gene therapy}, volume = {38}, number = {3}, pages = {387-404}, pmid = {38605260}, issn = {1179-190X}, support = {32172914//the National Natural Science Foundation of China/ ; 2021YFD1800600//Key Technology Research and Development Program of Shandong Province/ ; . 2662022DKYJC005//the Fundamental Research Funds for the Central Universities/ ; }, mesh = {*CRISPR-Cas Systems ; Humans ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacterial Infections/drug therapy ; Plasmids/genetics ; }, abstract = {Antimicrobial resistance (AMR) can potentially harm global public health. Horizontal gene transfer (HGT), which speeds up the emergence of AMR and increases the burden of drug resistance in mobile genetic elements (MGEs), is the primary method by which AMR genes are transferred across bacterial pathogens. New approaches are urgently needed to halt the spread of bacterial diseases and antibiotic resistance. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), an RNA-guided adaptive immune system, protects prokaryotes from foreign DNA like plasmids and phages. This approach may be essential in limiting horizontal gene transfer and halting the spread of antibiotic resistance. The CRISPR-Cas system has been crucial in identifying and understanding resistance mechanisms and developing novel therapeutic approaches. This review article investigates the CRISPR-Cas system's potential as a tool to combat bacterial AMR. Antibiotic-resistant bacteria can be targeted and eliminated by the CRISPR-Cas system. It has been proven to be an efficient method for removing carbapenem-resistant plasmids and regaining antibiotic susceptibility. The CRISPR-Cas system has enormous potential as a weapon against bacterial AMR. It precisely targets and eliminates antibiotic-resistant bacteria, facilitates resistance mechanism identification, and offers new possibilities in diagnostics and therapeutics.}, }
@article {pmid38605009, year = {2024}, author = {Zorea, A and Pellow, D and Levin, L and Pilosof, S and Friedman, J and Shamir, R and Mizrahi, I}, title = {Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {3147}, pmid = {38605009}, issn = {2041-1723}, support = {866530//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; ISF 1947/19//Israel Science Foundation (ISF)/ ; }, mesh = {Humans ; *Ecosystem ; Plasmids/genetics ; Bacteria/genetics ; Anti-Bacterial Agents ; Gene Transfer, Horizontal ; *Inflammatory Bowel Diseases/genetics ; }, abstract = {Plasmids are pivotal in driving bacterial evolution through horizontal gene transfer. Here, we investigated 3467 human gut microbiome samples across continents and disease states, analyzing 11,086 plasmids. Our analyses reveal that plasmid dispersal is predominantly stochastic, indicating neutral processes as the primary driver of their wide distribution. We find that only 20-25% of plasmid DNA is being selected in various disease states, constraining its distribution across hosts. Selective pressures shape specific plasmid segments with distinct ecological functions, influenced by plasmid mobilization lifestyle, antibiotic usage, and inflammatory gut diseases. Notably, these elements are more commonly shared within groups of individuals with similar health conditions, such as Inflammatory Bowel Disease (IBD), regardless of geographic location across continents. These segments contain essential genes such as iron transport mechanisms- a distinctive gut signature of IBD that impacts the severity of inflammation. Our findings shed light on mechanisms driving plasmid dispersal and selection in the human gut, highlighting their role as carriers of vital gene pools impacting bacterial hosts and ecosystem dynamics.}, }
@article {pmid38604355, year = {2024}, author = {Yin, Z and Liang, J and Zhang, M and Chen, B and Yu, Z and Tian, X and Deng, X and Peng, L}, title = {Pan-genome insights into adaptive evolution of bacterial symbionts in mixed host-microbe symbioses represented by human gut microbiota Bacteroides cellulosilyticus.}, journal = {The Science of the total environment}, volume = {927}, number = {}, pages = {172251}, doi = {10.1016/j.scitotenv.2024.172251}, pmid = {38604355}, issn = {1879-1026}, mesh = {*Symbiosis ; *Gastrointestinal Microbiome/genetics ; *Bacteroides/genetics/physiology ; Humans ; *Genome, Bacterial ; Evolution, Molecular ; Gene Transfer, Horizontal ; }, abstract = {Animal hosts harbor diverse assemblages of microbial symbionts that play crucial roles in the host's lifestyle. The link between microbial symbiosis and host development remains poorly understood. In particular, little is known about the adaptive evolution of gut bacteria in host-microbe symbioses. Recently, symbiotic relationships have been categorized as open, closed, or mixed, reflecting their modes of inter-host transmission and resulting in distinct genomic features. Members of the genus Bacteroides are the most abundant human gut microbiota and possess both probiotic and pathogenic potential, providing an excellent model for studying pan-genome evolution in symbiotic systems. Here, we determined the complete genome of an novel clinical strain PL2022, which was isolated from a blood sample and performed pan-genome analyses on a representative set of Bacteroides cellulosilyticus strains to quantify the influence of the symbiotic relationship on the evolutionary dynamics. B. cellulosilyticus exhibited correlated genomic features with both open and closed symbioses, suggesting a mixed symbiosis. An open pan-genome is characterized by abundant accessory gene families, potential horizontal gene transfer (HGT), and diverse mobile genetic elements (MGEs), indicating an innovative gene pool, mainly associated with genomic islands and plasmids. However, massive parallel gene loss, weak purifying selection, and accumulation of positively selected mutations were the main drivers of genome reduction in B. cellulosilyticus. Metagenomic read recruitment analyses showed that B. cellulosilyticus members are globally distributed and active in human gut habitats, in line with predominant vertical transmission in the human gut. However, existence and/or high abundance were also detected in non-intestinal tissues, other animal hosts, and non-host environments, indicating occasional horizontal transmission to new niches, thereby creating arenas for the acquisition of novel genes. This case study of adaptive evolution under a mixed host-microbe symbiosis advances our understanding of symbiotic pan-genome evolution. Our results highlight the complexity of genetic evolution in this unusual intestinal symbiont.}, }
@article {pmid38601936, year = {2024}, author = {Ortañez, J and Degnan, PH}, title = {Tracking and characterization of a novel conjugative transposon identified by shotgun transposon mutagenesis.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1241582}, pmid = {38601936}, issn = {1664-302X}, abstract = {The horizontal transfer of mobile genetic elements (MGEs) is an essential process determining the functional and genomic diversity of bacterial populations. MGEs facilitate the exchange of fitness determinant genes like antibiotic resistance and virulence factors. Various computational methods exist to identify potential MGEs, but confirming their ability to transfer requires additional experimental approaches. Here, we apply a transposon (Tn) mutagenesis technique for confirming mobilization without the need for targeted mutations. Using this method, we identified two MGEs, including a previously known conjugative transposon (CTn) called BoCTn found in Bacteroides ovatus and a novel CTn, PvCTn, identified in Phocaeicola vulgatus. In addition, Tn mutagenesis and subsequent genetic deletion enabled our characterization of a helix-turn-helix motif gene, BVU3433 which negatively regulates the conjugation efficiency of PvCTn in vitro. Furthermore, our transcriptomics data revealed that BVU3433 plays a crucial role in the repression of PvCTn genes, including genes involved in forming complete conjugation machinery [Type IV Secretion System (T4SS)]. Finally, analysis of individual strain genomes and community metagenomes identified the widespread prevalence of PvCTn-like elements with putative BVU3433 homologs among human gut-associated bacteria. In summary, this Tn mutagenesis mobilization method (TMMM) enables observation of transfer events in vitro and can ultimately be applied in vivo to identify a broader diversity of functional MGEs that may underly the transfer of important fitness determinants.}, }
@article {pmid38601791, year = {2024}, author = {Babiker, A and Lohsen, S and Van Riel, J and Hjort, K and Weiss, DS and Andersson, DI and Satola, S}, title = {Heteroresistance to piperacillin/tazobactam in Klebsiella pneumoniae is mediated by increased copy number of multiple β-lactamase genes.}, journal = {JAC-antimicrobial resistance}, volume = {6}, number = {2}, pages = {dlae057}, pmid = {38601791}, issn = {2632-1823}, support = {U19 AI158080/AI/NIAID NIH HHS/United States ; UM1 AI104681/AI/NIAID NIH HHS/United States ; }, abstract = {BACKGROUND: Piperacillin/tazobactam is a β-lactam/β-lactamase inhibitor combination with a broad spectrum of activity that is often used as empirical and/or targeted therapy among hospitalized patients. Heteroresistance (HR) is a form of antibiotic resistance in which a minority population of resistant cells coexists with a majority susceptible population that has been found to be a cause of antibiotic treatment failure in murine models.<br><br>OBJECTIVES: To determine the prevalence of HR and mechanisms of HR to piperacillin/tazobactam among Klebsiella pneumoniae bloodstream infection (BSI) isolates.<br><br>MATERIALS: From July 2018 to June 2021, K. pneumoniae piperacillin/tazobactam-susceptible BSI isolates were collected from two tertiary hospitals in Atlanta, GA, USA. Only first isolates from each patient per calendar year were included. Population analysis profiling (PAP) and WGS were performed to identify HR and its mechanisms.<br><br>RESULTS: Among 423 K. pneumoniae BSI isolates collected during the study period, 6% (25/423) were found to be HR with a subpopulation surviving above the breakpoint. WGS of HR isolates grown in the presence of piperacillin/tazobactam at concentrations 8-fold that of the MIC revealed copy number changes of plasmid-located &#x3b2;-lactamase genes blaCTX-M-15, blaSHV33, blaOXA-1 and blaTEM-1 by tandem gene amplification or plasmid copy number increase.<br><br>CONCLUSIONS: Prevalence of HR to piperacillin/tazobactam among bloodstream isolates was substantial. The HR phenotype appears to be caused by tandem amplification of &#x3b2;-lactamase genes found on plasmids or plasmid copy number increase. This raises the possibility of dissemination of HR through horizontal gene transfer and requires further study.}, }
@article {pmid38601688, year = {2024}, author = {Ma, X and Yin, Z and Li, H and Guo, J}, title = {Roles of herbivorous insects salivary proteins.}, journal = {Heliyon}, volume = {10}, number = {7}, pages = {e29201}, pmid = {38601688}, issn = {2405-8440}, abstract = {The intricate relationship between herbivorous insects and plants has evolved over millions of years, central to this dynamic interaction are salivary proteins (SPs), which mediate key processes ranging from nutrient acquisition to plant defense manipulation. SPs, sourced from salivary glands, intestinal regurgitation or acquired through horizontal gene transfer, exhibit remarkable functional versatility, influencing insect development, behavior, and adhesion mechanisms. Moreover, SPs play pivotal roles in modulating plant defenses, to induce or inhibit plant defenses as elicitors or effectors. In this review, we delve into the multifaceted roles of SPs in herbivorous insects, highlighting their diverse impacts on insect physiology and plant responses. Through a comprehensive exploration of SP functions, this review aims to deepen our understanding of plant-insect interactions and foster advancements in both fundamental research and practical applications in plant-insect interactions.}, }
@article {pmid38599270, year = {2024}, author = {Thibodeau, AJ and Barret, M and Mouchet, F and Nguyen, VX and Pinelli, E}, title = {The potential contribution of aquatic wildlife to antibiotic resistance dissemination in freshwater ecosystems: A review.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {350}, number = {}, pages = {123894}, doi = {10.1016/j.envpol.2024.123894}, pmid = {38599270}, issn = {1873-6424}, mesh = {Animals ; *Fresh Water ; *Ecosystem ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; Bacteria/drug effects/genetics ; Fishes/microbiology ; Environmental Monitoring ; Water Pollutants, Chemical ; Gene Transfer, Horizontal ; Aquatic Organisms/genetics ; Animals, Wild/microbiology ; Drug Resistance, Bacterial/genetics ; }, abstract = {Antibiotic resistance (AR) is one of the major health threats of our time. The presence of antibiotics in the environment and their continuous release from sewage treatment plants, chemical manufacturing plants and animal husbandry, agriculture and aquaculture, result in constant selection pressure on microbial organisms. This presence leads to the emergence, mobilization, horizontal gene transfer and a selection of antibiotic resistance genes, resistant bacteria and mobile genetic elements. Under these circumstances, aquatic wildlife is impacted in all compartments, including freshwater organisms with partially impermeable microbiota. In this narrative review, recent advancements in terms of occurrence of antibiotics and antibiotic resistance genes in sewage treatment plant effluents source compared to freshwater have been examined, occurrence of antibiotic resistance in wildlife, as well as experiments on antibiotic exposure. Based on this current state of knowledge, we propose the hypothesis that freshwater aquatic wildlife may play a crucial role in the dissemination of antibiotic resistance within the environment. Specifically, we suggest that organisms with high bacterial density tissues, which are partially isolated from the external environment, such as fishes and amphibians, could potentially be reservoirs and amplifiers of antibiotic resistance in the environment, potentially favoring the increase of the abundance of antibiotic resistance genes and resistant bacteria. Potential avenues for further research (trophic transfer, innovative exposure experiment) and action (biodiversity eco-engineering) are finally proposed.}, }
@article {pmid38598950, year = {2024}, author = {Lei, L and Chen, N and Chen, Z and Zhao, Y and Lin, H and Li, X and Hu, W and Zhang, H and Shi, J and Luo, Y}, title = {Dissemination of antibiotic resistance genes from aboveground sources to groundwater in livestock farms.}, journal = {Water research}, volume = {256}, number = {}, pages = {121584}, doi = {10.1016/j.watres.2024.121584}, pmid = {38598950}, issn = {1879-2448}, mesh = {*Groundwater/microbiology ; Animals ; *Livestock ; *Drug Resistance, Microbial/genetics ; Farms ; Swine ; China ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Wastewater/microbiology ; Drug Resistance, Bacterial/genetics ; }, abstract = {Antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are prevalent in various environments on livestock farms, including livestock waste, soil, and groundwater. Contamination of groundwater by ARB and ARGs in livestock farms is a growing concern as it may have potentially huge risks to human health. However, the source of groundwater-borne ARB and ARGs in animal farms remains largely unknown. In this study, different types of samples including groundwater and its potential contamination sources from aboveground (pig feces, wastewater, and soil) from both working and abandoned swine feedlots in southern China were collected and subjected to metagenomic sequencing and ARB isolation. The source tracking based on metagenomic analysis revealed that 56-95 % of ARGs in groundwater was attributable to aboveground sources. Using metagenomic assembly, we found that 45 ARGs predominantly conferring resistance to aminoglycosides, sulfonamides, and tetracyclines could be transferred from the aboveground sources to groundwater, mostly through plasmid-mediated horizontal gene transfer. Furthermore, the full-length nucleotide sequences of sul1, tetA, and TEM-1 detected in ARB isolates exhibited the close evolutionary relationships between aboveground sources and groundwater. Some isolated strains of antibiotic-resistant Pseudomonas spp. from aboveground sources and groundwater had the high similarity (average nucleotide identity > 99 %). Notably, the groundwater-borne ARGs were identified as mainly carried by bacterial pathogens, potentially posing risks to human and animal health. Overall, this study underscores the dissemination of ARGs from aboveground sources to groundwater in animal farms and associated risks.}, }
@article {pmid38598855, year = {2024}, author = {Hsieh, SC and Peters, JE}, title = {Natural and Engineered Guide RNA-Directed Transposition with CRISPR-Associated Tn7-Like Transposons.}, journal = {Annual review of biochemistry}, volume = {93}, number = {1}, pages = {139-161}, pmid = {38598855}, issn = {1545-4509}, support = {R01 GM129118/GM/NIGMS NIH HHS/United States ; R35 GM152260/GM/NIGMS NIH HHS/United States ; }, mesh = {*DNA Transposable Elements/genetics ; *CRISPR-Cas Systems ; *RNA, Guide, CRISPR-Cas Systems/genetics/metabolism ; *Transposases/metabolism/genetics ; Gene Editing/methods ; Bacteria/genetics ; Plasmids/metabolism/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats ; }, abstract = {CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated nuclease) defense systems have been naturally coopted for guide RNA-directed transposition on multiple occasions. In all cases, cooption occurred with diverse elements related to the bacterial transposon Tn7. Tn7 tightly controls transposition; the transposase is activated only when special targets are recognized by dedicated target-site selection proteins. Tn7 and the Tn7-like elements that coopted CRISPR-Cas systems evolved complementary targeting pathways: one that recognizes a highly conserved site in the chromosome and a second pathway that targets mobile plasmids capable of cell-to-cell transfer. Tn7 and Tn7-like elements deliver a single integration into the site they recognize and also control the orientation of the integration event, providing future potential for use as programmable gene-integration tools. Early work has shown that guide RNA-directed transposition systems can be adapted to diverse hosts, even within microbial communities, suggesting great potential for engineering these systems as powerful gene-editing tools.}, }
@article {pmid38598457, year = {2024}, author = {Gao, X and Xu, L and Zhong, T and Song, X and Zhang, H and Liu, X and Jiang, Y}, title = {The proliferation of antibiotic resistance genes (ARGs) and microbial communities in industrial wastewater treatment plant treating N,N-dimethylformamide (DMF) by AAO process.}, journal = {PloS one}, volume = {19}, number = {4}, pages = {e0299740}, pmid = {38598457}, issn = {1932-6203}, mesh = {*Anti-Bacterial Agents/pharmacology ; Dimethylformamide ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; *Microbiota/genetics ; Cell Proliferation ; }, abstract = {The excessive use of antibiotics has resulted in the contamination of the environment with antibiotic resistance genes (ARGs), posing a significant threat to public health. Wastewater treatment plants (WWTPs) are known to be reservoirs of ARGs and considered to be hotspots for horizontal gene transfer (HGT) between bacterial communities. However, most studies focused on the distribution and dissemination of ARGs in hospital and urban WWTPs, and little is known about their fate in industrial WWTPs. In this study, collected the 15 wastewater samples containing N,N-dimethylformamide (DMF) from five stages of the anaerobic anoxic aerobic (AAO) process in an industrial WWTPs. The findings revealed a stepwise decrease in DMF and chemical oxygen demand (COD) content with the progression of treatment. However, the number and abundances of ARGs increase in the effluents of biological treatments. Furthermore, the residues of DMF and the treatment process altered the structure of the bacterial community. The correlation analysis indicated that the shift in bacterial community structures might be the main driver for the dynamics change of ARGs. Interestingly, observed that the AAO process may acted as a microbial source and increased the total abundance of ARGs instead of attenuating it. Additionally, found that non-pathogenic bacteria had higher ARGs abundance than pathogenic bacteria in effluents. The study provides insights into the microbial community structure and the mechanisms that drive the variation in ARGs abundance in industrial WWTPs.}, }
@article {pmid38598029, year = {2024}, author = {Ramnarine, SDBJ and Jayaraman, J and Ramsubhag, A}, title = {Crucifer Lesion-Associated Xanthomonas Strains Show Multi-Resistance to Heavy Metals and Antibiotics.}, journal = {Current microbiology}, volume = {81}, number = {5}, pages = {136}, pmid = {38598029}, issn = {1432-0991}, support = {CRP.5.APR17.45//University of the West Indies, St. Augustine Campus/ ; }, mesh = {Animals ; Humans ; *Anti-Bacterial Agents/pharmacology ; Copper ; *Metals, Heavy/toxicity ; Ampicillin ; Chloramphenicol ; }, abstract = {Copper resistance in phytopathogens is a major challenge to crop production globally and is known to be driven by excessive use of copper-based pesticides. However, recent studies have shown co-selection of multiple heavy metal and antibiotic resistance genes in bacteria exposed to heavy metal and xenobiotics, which may impact the epidemiology of plant, animal, and human diseases. In this study, multi-resistance to heavy metals and antibiotics were evaluated in local Xanthomonas campestris pv. campestris (Xcc) and co-isolated Xanthomonas melonis (Xmel) strains from infected crucifer plants in Trinidad. Resistance to cobalt, cadmium, zinc, copper, and arsenic (V) was observed in both Xanthomonas species up to 25 mM. Heavy metal resistance (HMR) genes were found on a small plasmid-derived locus with ~ 90% similarity to a Stenotrophomonas spp. chromosomal locus and a X. perforans pLH3.1 plasmid. The co-occurrence of mobile elements in these regions implies their organization on a composite transposon-like structure. HMR genes in Xcc strains showed the lowest similarity to references, and the cus and ars operons appear to be unique among Xanthomonads. Overall, the similarity of HMR genes to Stenotrophomonas sp. chromosomal genomes suggest their origin in this genus or a related organism and subsequent spread through lateral gene transfer events. Further resistome characterization revealed the presence of small multidrug resistance (SMR), multidrug resistance (MDR) efflux pumps, and bla (Xcc) genes for broad biocide resistance in both species. Concurrently, resistance to antibiotics (streptomycin, kanamycin, tetracycline, chloramphenicol, and ampicillin) up to 1000 µg/mL was confirmed.}, }
@article {pmid38597658, year = {2024}, author = {Schmid, N and Brandt, D and Walasek, C and Rolland, C and Wittmann, J and Fischer, D and Müsken, M and Kalinowski, J and Thormann, K}, title = {An autonomous plasmid as an inovirus phage satellite.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {5}, pages = {e0024624}, pmid = {38597658}, issn = {1098-5336}, mesh = {*Plasmids/genetics ; *Shewanella/virology/genetics ; Inovirus/genetics ; Satellite Viruses/genetics ; Genome, Viral ; Bacteriophages/genetics/classification/isolation &amp; purification ; }, abstract = {Bacterial viruses (phages) are potent agents of lateral gene transfer and thus are important drivers of evolution. A group of mobile genetic elements, referred to as phage satellites, exploits phages to disseminate their own genetic material. Here, we isolated a novel member of the family Inoviridae, Shewanella phage Dolos, along with an autonomously replicating plasmid, pDolos. Dolos causes a chronic infection in its host Shewanella oneidensis by phage production with only minor effects on the host cell proliferation. When present, plasmid pDolos hijacks Dolos functions to be predominantly packaged into phage virions and released into the environment and, thus, acts as a phage satellite. pDolos can disseminate further genetic material encoding, e.g., resistances or fluorophores to host cells sensitive to Dolos infection. Given the rather simple requirements of a plasmid for takeover of an inovirus and the wide distribution of phages of this group, we speculate that similar phage-satellite systems are common among bacteria.IMPORTANCEPhage satellites are mobile genetic elements, which hijack phages to be transferred to other host cells. The vast majority of these phage satellites integrate within the host's chromosome, and they all carry remaining phage genes. Here, we identified a novel phage satellite, pDolos, which uses an inovirus for dissemination. pDolos (i) remains as an autonomously replicating plasmid within its host, (ii) does not carry recognizable phage genes, and (iii) is smaller than any other phage satellites identified so far. Thus, pDolos is the first member of a new class of phage satellites, which resemble natural versions of phagemids.}, }
@article {pmid38593892, year = {2024}, author = {Zheng, B and Wang, G and Qu, Z and Hu, J and Bao, Z and Wang, M}, title = {Glycosaminoglycan lyase: A new competition between bacteria and the pacific white shrimp Litopenaeus vannamei.}, journal = {Developmental and comparative immunology}, volume = {156}, number = {}, pages = {105177}, doi = {10.1016/j.dci.2024.105177}, pmid = {38593892}, issn = {1879-0089}, mesh = {Animals ; *Penaeidae/immunology/microbiology/genetics ; *Vibrio parahaemolyticus/physiology ; *Phylogeny ; *Gene Transfer, Horizontal ; Arthropod Proteins/genetics/metabolism ; Hepatopancreas/microbiology/immunology/metabolism ; Bacteria ; Immunity, Innate/genetics ; Polysaccharide-Lyases/genetics/metabolism ; Vibrio Infections/immunology ; }, abstract = {Horizontal gene transfer (HGT) is an important evolutionary force in the formation of prokaryotic and eukaryotic genomes. In recent years, many HGT genes horizontally transferred from prokaryotes to eukaryotes have been reported, and most of them are present in arthropods. The Pacific white shrimp Litopenaeus vannamei, an important economic species of arthropod, has close relationships with bacteria, providing a platform for horizontal gene transfer (HGT). In this study, we analyzed bacteria-derived HGT based on a high-quality genome of L. vannamei via a homology search and phylogenetic analysis, and six HGT genes were identified. Among these six horizontally transferred genes, we found one gene (LOC113799989) that contains a bacterial chondroitinase AC structural domain and encodes an unknown glycosaminoglycan (GAG) lyase in L. vannamei. The real-time quantitative PCR results showed that the mRNA expression level of LOC113799989 was highest in the hepatopancreas and heart, and after stimulation by Vibrio parahaemolyticus, its mRNA expression level was rapidly up-regulated within 12 h. Furthermore, after injecting si-RNA and stimulation by V. parahaemolyticus, we found that the experimental group had a higher cumulative mortality rate in 48 h than the control group, indicating that the bacteria-derived GAG lyase can reduce the mortality of shrimp with respect to infection by V. parahaemolyticus and might be related to the resistance of shrimp to bacterial diseases. Our findings contribute to the study of the function of GAGs and provide new insights into GAG-related microbial pathogenesis and host defense mechanisms in arthropods.}, }
@article {pmid38593473, year = {2024}, author = {Paul, B and Siddaramappa, S}, title = {Comparative analysis of the diversity of trinucleotide repeats in bacterial genomes.}, journal = {Genome}, volume = {67}, number = {8}, pages = {281-291}, doi = {10.1139/gen-2023-0097}, pmid = {38593473}, issn = {1480-3321}, mesh = {*Genome, Bacterial ; *Trinucleotide Repeats ; Humans ; Genetic Variation ; Bacteria/genetics/classification ; }, abstract = {The human gut is the most favorable niche for microbial populations, and few studies have explored the possibilities of horizontal gene transfer between host and pathogen. Trinucleotide repeat (TNR) expansion in humans can cause more than 40 neurodegenerative diseases. Further, TNRs are a type of microsatellite that resides on coding regions can contribute to the synthesis of homopolymeric amino acids. Hence, the present study aims to estimate the occurrence and diversity of TNRs in bacterial genomes available in the NCBI Genome database. Genome-wide analyses revealed that several bacterial genomes contain different types of uninterrupted TNRs. It was found that TNRs are abundant in the genomes of Alcaligenes faecalis, Mycoplasma gallisepticum, Mycoplasma genitalium, Sorangium cellulosum, and Thermus thermophilus. Interestingly, the genome of Bacillus thuringiensis strain YBT-1518 contained 169 uninterrupted ATT repeats. The genome of Leclercia adecarboxylata had 46 uninterrupted CAG repeats, which potentially translate into polyglutamine. In some instances, the TNRs were present in genes that potentially encode essential functions. Similar occurrences in human genes are known to cause genetic disorders. Further analysis of the occurrence of TNRs in bacterial genomes is likely to provide a better understanding of mismatch repair, genetic disorders, host-pathogen interaction, and homopolymeric amino acids.}, }
@article {pmid38591887, year = {2024}, author = {Ng, WL and Rego, EH}, title = {A nucleoid-associated protein is involved in the emergence of antibiotic resistance by promoting the frequent exchange of the replicative DNA polymerase in Mycobacterium smegmatis.}, journal = {mSphere}, volume = {9}, number = {5}, pages = {e0012224}, pmid = {38591887}, issn = {2379-5042}, support = {R01 AI148255/AI/NIAID NIH HHS/United States ; 100000875//Pew Charitable Trusts (PCT)/ ; 100014185//Searle Scholars Program (SSP)/ ; }, mesh = {*Mycobacterium smegmatis/genetics/drug effects/metabolism/enzymology ; *DNA Replication ; *DNA-Directed DNA Polymerase/genetics/metabolism ; *Bacterial Proteins/genetics/metabolism ; *Drug Resistance, Bacterial/genetics ; DNA-Binding Proteins/genetics/metabolism ; Antigens, Bacterial ; }, abstract = {UNLABELLED: Antibiotic resistance in Mycobacterium tuberculosis exclusively originates from chromosomal mutations, either during normal DNA replication or under stress, when the expression of error-prone DNA polymerases increases to repair damaged DNA. To bypass DNA lesions and catalyze error-prone DNA synthesis, translesion polymerases must be able to access the DNA, temporarily replacing the high-fidelity replicative polymerase. The mechanisms that govern polymerase exchange are not well understood, especially in mycobacteria. Here, using a suite of quantitative fluorescence imaging techniques, we discover that in Mycobacterium smegmatis, as in other bacterial species, the replicative polymerase, DnaE1, exchanges at a timescale much faster than that of DNA replication. Interestingly, this fast exchange rate depends on an actinobacteria-specific nucleoid-associated protein (NAP), Lsr2. In cells missing lsr2, DnaE1 exchanges less frequently, and the chromosome is replicated more faithfully. Additionally, in conditions that damage DNA, cells lacking lsr2 load the complex needed to bypass DNA lesions less effectively and, consistently, replicate with higher fidelity but exhibit growth defects. Together, our results show that Lsr2 promotes dynamic flexibility of the mycobacterial replisome, which is critical for robust cell growth and lesion repair in conditions that damage DNA.<br><br>IMPORTANCE: Unlike many other pathogens, Mycobacterium tuberculosis has limited ability for horizontal gene transfer, a major mechanism for developing antibiotic resistance. Thus, the mechanisms that facilitate chromosomal mutagenesis are of particular importance in mycobacteria. Here, we show that Lsr2, a nucleoid-associated protein, has a novel role in DNA replication and mutagenesis in the model mycobacterium Mycobacterium smegmatis. We find that Lsr2 promotes the fast exchange rate of the replicative DNA polymerase, DnaE1, at the replication fork and is important for the effective loading of the DnaE2-ImuA'-ImuB translesion complex. Without lsr2, M. smegmatis replicates its chromosome more faithfully and acquires resistance to rifampin at a lower rate, but at the cost of impaired survival to DNA damaging agents. Together, our work establishes Lsr2 as a potential factor in the emergence of mycobacterial antibiotic resistance.}, }
@article {pmid38591882, year = {2024}, author = {Xing, Y and Clark, JR and Chang, JD and Zulk, JJ and Chirman, DM and Piedra, F-A and Vaughan, EE and Hernandez Santos, HJ and Patras, KA and Maresso, AW}, title = {Progress toward a vaccine for extraintestinal pathogenic E. coli (ExPEC) II: efficacy of a toxin-autotransporter dual antigen approach.}, journal = {Infection and immunity}, volume = {92}, number = {5}, pages = {e0044023}, pmid = {38591882}, issn = {1098-5522}, support = {U19 AI144297/AI/NIAID NIH HHS/United States ; U19 AI157981/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Extraintestinal Pathogenic Escherichia coli/genetics/immunology ; *Escherichia coli Infections/prevention &amp; control/microbiology/immunology ; Mice ; *Hemolysin Proteins/immunology/genetics ; *Escherichia coli Proteins/genetics/immunology ; *Escherichia coli Vaccines/immunology ; Antigens, Bacterial/immunology/genetics ; Female ; Virulence Factors/genetics/immunology ; Type V Secretion Systems/immunology/genetics ; Disease Models, Animal ; Humans ; }, abstract = {Extraintestinal pathogenic Escherichia coli (ExPEC) is a leading cause of worldwide morbidity and mortality, the top cause of antimicrobial-resistant (AMR) infections, and the most frequent cause of life-threatening sepsis and urinary tract infections (UTI) in adults. The development of an effective and universal vaccine is complicated by this pathogen's pan-genome, its ability to mix and match virulence factors and AMR genes via horizontal gene transfer, an inability to decipher commensal from pathogens, and its intimate association and co-evolution with mammals. Using a pan virulome analysis of >20,000 sequenced E. coli strains, we identified the secreted cytolysin α-hemolysin (HlyA) as a high priority target for vaccine exploration studies. We demonstrate that a catalytically inactive pure form of HlyA, expressed in an autologous host using its own secretion system, is highly immunogenic in a murine host, protects against several forms of ExPEC infection (including lethal bacteremia), and significantly lowers bacterial burdens in multiple organ systems. Interestingly, the combination of a previously reported autotransporter (SinH) with HlyA was notably effective, inducing near complete protection against lethal challenge, including commonly used infection strains ST73 (CFT073) and ST95 (UTI89), as well as a mixture of 10 of the most highly virulent sequence types and strains from our clinical collection. Both HlyA and HlyA-SinH combinations also afforded some protection against UTI89 colonization in a murine UTI model. These findings suggest recombinant, inactive hemolysin and/or its combination with SinH warrant investigation in the development of an E. coli vaccine against invasive disease.}, }
@article {pmid38591037, year = {2024}, author = {Giermasińska-Buczek, K and Gawor, J and Stefańczyk, E and Gągała, U and Żuchniewicz, K and Rekosz-Burlaga, H and Gromadka, R and Łobocka, M}, title = {Interaction of bacteriophage P1 with an epiphytic Pantoea agglomerans strain-the role of the interplay between various mobilome elements.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1356206}, pmid = {38591037}, issn = {1664-302X}, abstract = {P1 is a model, temperate bacteriophage of the 94 kb genome. It can lysogenize representatives of the Enterobacterales order. In lysogens, it is maintained as a plasmid. We tested P1 interactions with the biocontrol P. agglomerans L15 strain to explore the utility of P1 in P. agglomerans genome engineering. A P1 derivative carrying the Tn9 (cm[R]) transposon could transfer a plasmid from Escherichia coli to the L15 cells. The L15 cells infected with this derivative formed chloramphenicol-resistant colonies. They could grow in a liquid medium with chloramphenicol after adaptation and did not contain prophage P1 but the chromosomally inserted cm[R] marker of P1 Tn9 (cat). The insertions were accompanied by various rearrangements upstream of the Tn9 cat gene promoter and the loss of IS1 (IS1L) from the corresponding region. Sequence analysis of the L15 strain genome revealed a chromosome and three plasmids of 0.58, 0.18, and 0.07 Mb. The largest and the smallest plasmid appeared to encode partition and replication incompatibility determinants similar to those of prophage P1, respectively. In the L15 derivatives cured of the largest plasmid, P1 with Tn9 could not replace the smallest plasmid even if selected. However, it could replace the smallest and the largest plasmid of L15 if its Tn9 IS1L sequence driving the Tn9 mobility was inactivated or if it was enriched with an immobile kanamycin resistance marker. Moreover, it could develop lytically in the L15 derivatives cured of both these plasmids. Clearly, under conditions of selection for P1, the mobility of the P1 selective marker determines whether or not the incoming P1 can outcompete the incompatible L15 resident plasmids. Our results demonstrate that P. agglomerans can serve as a host for bacteriophage P1 and can be engineered with the help of this phage. They also provide an example of how antibiotics can modify the outcome of horizontal gene transfer in natural environments. Numerous plasmids of Pantoea strains appear to contain determinants of replication or partition incompatibility with P1. Therefore, P1 with an immobile selective marker may be a tool of choice in curing these strains from the respective plasmids to facilitate their functional analysis.}, }
@article {pmid38587657, year = {2024}, author = {Gidhi, A and Jha, SK and Kumar, M and Mukhopadhyay, K}, title = {The F-box protein encoding genes of the leaf-rust fungi Puccinia triticina: genome-wide identification, characterization and expression dynamics during pathogenesis.}, journal = {Archives of microbiology}, volume = {206}, number = {5}, pages = {209}, pmid = {38587657}, issn = {1432-072X}, mesh = {Phylogeny ; Puccinia ; *Basidiomycota/genetics ; *F-Box Proteins/genetics ; }, abstract = {The F-box proteins in fungi perform diverse functions including regulation of cell cycle, circadian clock, development, signal transduction and nutrient sensing. Genome-wide analysis revealed 10 F-box genes in Puccinia triticina, the causal organism for the leaf rust disease in wheat and were characterized using in silico approaches for revealing phylogenetic relationships, gene structures, gene ontology, protein properties, sequence analysis and gene expression studies. Domain analysis predicted functional domains like WD40 and LRR at C-terminus along with the obvious presence of F-box motif in N-terminus. MSA showed amino acid replacements, which might be due to nucleotide substitution during replication. Phylogenetic analysis revealed the F-box proteins with similar domains to be clustered together while some sequences were spread out in different clades, which might be due to functional diversity. The clustering of Puccinia triticina GG705409 with Triticum aestivum TaAFB4/TaAFB5 in a single clade suggested the possibilities of horizontal gene transfer during the coevolution of P. triticina and wheat. Gene ontological annotation categorized them into three classes and were functionally involved in protein degradation through the protein ubiquitination pathway. Protein-protein interaction network revealed F-box proteins to interact with other components of the SCF complex involved in protein ubiquitination. Relative expression analysis of five F-box genes in a time course experiment denoted their involvement in leaf rust susceptible wheat plants. This study provides information on structure elucidation of F-box proteins of a basidiomycetes plant pathogenic fungi and their role during pathogenesis.}, }
@article {pmid38587426, year = {2024}, author = {Bessen, DE and Beall, BW and Hayes, A and Huang, W and DiChiara, JM and Velusamy, S and Tettelin, H and Jolley, KA and Fallon, JT and Chochua, S and Alobaidallah, MSA and Higgs, C and Barnett, TC and Steemson, JT and Proft, T and Davies, MR}, title = {Recombinational exchange of M-fibril and T-pilus genes generates extensive cell surface diversity in the global group A Streptococcus population.}, journal = {mBio}, volume = {15}, number = {5}, pages = {e0069324}, pmid = {38587426}, issn = {2150-7511}, support = {R21 AI156226/AI/NIAID NIH HHS/United States ; R01 AI173565/AI/NIAID NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; R03 AI148983/AI/NIAID NIH HHS/United States ; }, mesh = {*Streptococcus pyogenes/genetics/classification ; *Genetic Variation ; Humans ; *Genotype ; Recombination, Genetic ; Bacterial Outer Membrane Proteins/genetics ; Fimbriae Proteins/genetics ; Gene Transfer, Horizontal ; Antigens, Bacterial/genetics ; Streptococcal Infections/microbiology/epidemiology ; Impetigo/microbiology/epidemiology ; Pharyngitis/microbiology ; Fimbriae, Bacterial/genetics ; Carrier Proteins ; }, abstract = {Among genes present in all group A streptococci (GAS), those encoding M-fibril and T-pilus proteins display the highest levels of sequence diversity, giving rise to the two primary serological typing schemes historically used to define strain. A new genotyping scheme for the pilin adhesin and backbone genes is developed and, when combined with emm typing, provides an account of the global GAS strain population. Cluster analysis based on nucleotide sequence similarity assigns most T-serotypes to discrete pilin backbone sequence clusters, yet the established T-types correspond to only half the clusters. The major pilin adhesin and backbone sequence clusters yield 98 unique combinations, defined as "pilin types." Numerous horizontal transfer events that involve pilin or emm genes generate extensive antigenic and functional diversity on the bacterial cell surface and lead to the emergence of new strains. Inferred pilin genotypes applied to a meta-analysis of global population-based collections of pharyngitis and impetigo isolates reveal highly significant associations between pilin genotypes and GAS infection at distinct ecological niches, consistent with a role for pilin gene products in adaptive evolution. Integration of emm and pilin typing into open-access online tools (pubmlst.org) ensures broad utility for end-users wanting to determine the architecture of M-fibril and T-pilus genes from genome assemblies.IMPORTANCEPrecision in defining the variant forms of infectious agents is critical to understanding their population biology and the epidemiology of associated diseases. Group A Streptococcus (GAS) is a global pathogen that causes a wide range of diseases and displays a highly diverse cell surface due to the antigenic heterogeneity of M-fibril and T-pilus proteins which also act as virulence factors of varied functions. emm genotyping is well-established and highly utilized, but there is no counterpart for pilin genes. A global GAS collection provides the basis for a comprehensive pilin typing scheme, and online tools for determining emm and pilin genotypes are developed. Application of these tools reveals the expansion of structural-functional diversity among GAS via horizontal gene transfer, as evidenced by unique combinations of surface protein genes. Pilin and emm genotype correlations with superficial throat vs skin infection provide new insights on the molecular determinants underlying key ecological and epidemiological trends.}, }
@article {pmid38585972, year = {2024}, author = {Marin, MG and Wippel, C and Quinones-Olvera, N and Behruznia, M and Jeffrey, BM and Harris, M and Mann, BC and Rosenthal, A and Jacobson, KR and Warren, RM and Li, H and Meehan, CJ and Farhat, MR}, title = {Analysis of the limited M. tuberculosis accessory genome reveals potential pitfalls of pan-genome analysis approaches.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.03.21.586149}, pmid = {38585972}, issn = {2692-8205}, support = {R01 AI155765/AI/NIAID NIH HHS/United States ; T15 LM007092/LM/NLM NIH HHS/United States ; }, abstract = {Pan-genome analysis is a fundamental tool for studying bacterial genome evolution; however, the variety of methods used to define and measure the pan-genome poses challenges to the interpretation and reliability of results. To quantify sources of bias and error related to common pan-genome analysis approaches, we evaluated different approaches applied to curated collection of 151 Mycobacterium tuberculosis (Mtb) isolates. Mtb is characterized by its clonal evolution, absence of horizontal gene transfer, and limited accessory genome, making it an ideal test case for this study. Using a state-of-the-art graph-genome approach, we found that a majority of the structural variation observed in Mtb originates from rearrangement, deletion, and duplication of redundant nucleotide sequences. In contrast, we found that pan-genome analyses that focus on comparison of coding sequences (at the amino acid level) can yield surprisingly variable results, driven by differences in assembly quality and the softwares used. Upon closer inspection, we found that coding sequence annotation discrepancies were a major contributor to inflated Mtb accessory genome estimates. To address this, we developed panqc, a software that detects annotation discrepancies and collapses nucleotide redundancy in pan-genome estimates. When applied to Mtb and E. coli pan-genomes, panqc exposed distinct biases influenced by the genomic diversity of the population studied. Our findings underscore the need for careful methodological selection and quality control to accurately map the evolutionary dynamics of a bacterial species.}, }
@article {pmid38585963, year = {2024}, author = {Maier, JL and Gin, C and Callahan, B and Sheriff, EK and Duerkop, BA and Kleiner, M}, title = {Pseudo-pac site sequences used by phage P22 in generalized transduction of Salmonella.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38585963}, issn = {2692-8205}, support = {R01 AI141479/AI/NIAID NIH HHS/United States ; R35 GM138362/GM/NIGMS NIH HHS/United States ; }, abstract = {Salmonella enterica Serovar Typhimurium (Salmonella) and its bacteriophage P22 are a model system for the study of horizontal gene transfer by generalized transduction. Typically, the P22 DNA packaging machinery initiates packaging when a short sequence of DNA, known as the pac site, is recognized on the P22 genome. However, sequences similar to the pac site in the host genome, called pseudo-pac sites, lead to erroneous packaging and subsequent generalized transduction of Salmonella DNA. While the general genomic locations of the Salmonella pseudo-pac sites are known, the sequences themselves have not been determined. We used visualization of P22 sequencing reads mapped to host Salmonella genomes to define regions of generalized transduction initiation and the likely locations of pseudo-pac sites. We searched each genome region for the sequence with the highest similarity to the P22 pac site and aligned the resulting sequences. We built a regular expression (sequence match pattern) from the alignment and used it to search the genomes of two P22-susceptible Salmonella strains- LT2 and 14028S- for sequence matches. The final regular expression successfully identified pseudo-pac sites in both LT2 and 14028S that correspond with generalized transduction initiation sites in mapped read coverages. The pseudo-pac site sequences identified in this study can be used to predict locations of generalized transduction in other P22-susceptible hosts or to initiate generalized transduction at specific locations in P22-susceptible hosts with genetic engineering. Furthermore, the bioinformatics approach used to identify the Salmonella pseudo-pac sites in this study could be applied to other phage-host systems.}, }
@article {pmid38579360, year = {2024}, author = {Whitfield, GB and Brun, YV}, title = {The type IVc pilus: just a Tad different.}, journal = {Current opinion in microbiology}, volume = {79}, number = {}, pages = {102468}, doi = {10.1016/j.mib.2024.102468}, pmid = {38579360}, issn = {1879-0364}, mesh = {*Fimbriae, Bacterial/metabolism/genetics/physiology ; Caulobacter crescentus/genetics/metabolism/physiology ; Bacteria/genetics/metabolism ; Bacterial Adhesion/genetics ; Gene Transfer, Horizontal ; Fimbriae Proteins/genetics/metabolism ; Bacterial Proteins/metabolism/genetics ; Myxococcus xanthus/genetics/physiology/metabolism ; }, abstract = {Bacteria utilize type IV pili (T4P) to interact with their environment, where they facilitate processes including motility, adherence, and DNA uptake. T4P require multisubunit, membrane-spanning nanomachines for assembly. The tight adherence (Tad) pili are an Archaea-derived T4P subgroup whose machinery exhibits significant mechanistic and architectural differences from bacterial type IVa and IVb pili. Most Tad biosynthetic genes are encoded in a single locus that is widespread in bacteria due to facile acquisition via horizontal gene transfer. These loci experience extensive structural rearrangements, including the acquisition of novel regulatory or biosynthetic genes, which fine-tune their function. This has permitted their integration into many different bacterial lifestyles, including the Caulobacter crescentus cell cycle, Myxococcus xanthus predation, and numerous plant and mammalian pathogens and symbionts.}, }
@article {pmid38578105, year = {2024}, author = {Darby, EM and Moran, RA and Holden, E and Morris, T and Harrison, F and Clough, B and McInnes, RS and Schneider, L and Frickel, EM and Webber, MA and Blair, JMA}, title = {Differential development of antibiotic resistance and virulence between Acinetobacter species.}, journal = {mSphere}, volume = {9}, number = {5}, pages = {e0010924}, pmid = {38578105}, issn = {2379-5042}, support = {/WT_/Wellcome Trust/United Kingdom ; 222386/Z/21/Z//Wellcome Trust (WT)/ ; }, mesh = {*Acinetobacter/genetics/drug effects/pathogenicity ; Virulence/genetics ; *Acinetobacter Infections/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Biofilms/drug effects/growth &amp; development ; *Microbial Sensitivity Tests ; Animals ; Humans ; Drug Resistance, Bacterial/genetics ; Acinetobacter baumannii/genetics/drug effects/pathogenicity ; Mice ; Gene Transfer, Horizontal ; United Kingdom ; Female ; Plasmids/genetics ; }, abstract = {UNLABELLED: The two species that account for most cases of Acinetobacter-associated bacteremia in the United Kingdom are Acinetobacter lwoffii, often a commensal but also an emerging pathogen, and Acinetobacter baumannii, a well-known antibiotic-resistant species. While these species both cause similar types of human infection and occupy the same niche, A. lwoffii (unlike A. baumannii) has thus far remained susceptible to antibiotics. Comparatively little is known about the biology of A. lwoffii, and this is the largest study on it conducted to date, providing valuable insights into its behaviour and potential threat to human health. This study aimed to explain the antibiotic susceptibility, virulence, and fundamental biological differences between these two species. The relative susceptibility of A. lwoffii was explained as it encoded fewer antibiotic resistance and efflux pump genes than A. baumannii (9 and 30, respectively). While both species had markers of horizontal gene transfer, A. lwoffii encoded more DNA defense systems and harbored a far more restricted range of plasmids. Furthermore, A. lwoffii displayed a reduced ability to select for antibiotic resistance mutations, form biofilm, and infect both in vivo and in in vitro models of infection. This study suggests that the emerging pathogen A. lwoffii has remained susceptible to antibiotics because mechanisms exist to make it highly selective about the DNA it acquires, and we hypothesize that the fact that it only harbors a single RND system restricts the ability to select for resistance mutations. This provides valuable insights into how development of resistance can be constrained in Gram-negative bacteria.<br><br>IMPORTANCE: Acinetobacter lwoffii is often a harmless commensal but is also an emerging pathogen and is the most common cause of Acinetobacter-derived bloodstream infections in England and Wales. In contrast to the well-studied and often highly drug-resistant A. baumannii, A. lwoffii has remained susceptible to antibiotics. This study explains why this organism has not evolved resistance to antibiotics. These new insights are important to understand why and how some species develop antibiotic resistance, while others do not, and could inform future novel treatment strategies.}, }
@article {pmid38574109, year = {2024}, author = {Samson, S and Lord, &#xc9; and Makarenkov, V}, title = {Assessing the emergence time of SARS-CoV-2 zoonotic spillover.}, journal = {PloS one}, volume = {19}, number = {4}, pages = {e0301195}, pmid = {38574109}, issn = {1932-6203}, mesh = {Animals ; Humans ; SARS-CoV-2/genetics ; Phylogeny ; *Chiroptera ; Pangolins/genetics ; *COVID-19/epidemiology ; Bayes Theorem ; Zoonoses/epidemiology ; }, abstract = {Understanding the evolution of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) and its relationship to other coronaviruses in the wild is crucial for preventing future virus outbreaks. While the origin of the SARS-CoV-2 pandemic remains uncertain, mounting evidence suggests the direct involvement of the bat and pangolin coronaviruses in the evolution of the SARS-CoV-2 genome. To unravel the early days of a probable zoonotic spillover event, we analyzed genomic data from various coronavirus strains from both human and wild hosts. Bayesian phylogenetic analysis was performed using multiple datasets, using strict and relaxed clock evolutionary models to estimate the occurrence times of key speciation, gene transfer, and recombination events affecting the evolution of SARS-CoV-2 and its closest relatives. We found strong evidence supporting the presence of temporal structure in datasets containing SARS-CoV-2 variants, enabling us to estimate the time of SARS-CoV-2 zoonotic spillover between August and early October 2019. In contrast, datasets without SARS-CoV-2 variants provided mixed results in terms of temporal structure. However, they allowed us to establish that the presence of a statistically robust clade in the phylogenies of gene S and its receptor-binding (RBD) domain, including two bat (BANAL) and two Guangdong pangolin coronaviruses (CoVs), is due to the horizontal gene transfer of this gene from the bat CoV to the pangolin CoV that occurred in the middle of 2018. Importantly, this clade is closely located to SARS-CoV-2 in both phylogenies. This phylogenetic proximity had been explained by an RBD gene transfer from the Guangdong pangolin CoV to a very recent ancestor of SARS-CoV-2 in some earlier works in the field before the BANAL coronaviruses were discovered. Overall, our study provides valuable insights into the timeline and evolutionary dynamics of the SARS-CoV-2 pandemic.}, }
@article {pmid38572613, year = {2024}, author = {Moore, KA and Petersen, AP and Zierden, HC}, title = {Microorganism-derived extracellular vesicles: emerging contributors to female reproductive health.}, journal = {Nanoscale}, volume = {16}, number = {17}, pages = {8216-8235}, doi = {10.1039/d3nr05524h}, pmid = {38572613}, issn = {2040-3372}, mesh = {*Extracellular Vesicles/metabolism ; Female ; Humans ; *Vagina/microbiology/metabolism ; *Microbiota ; *Reproductive Health ; Bacteria/metabolism ; }, abstract = {Extracellular vesicles (EVs) are cell-derived nanoparticles that carry small molecules, nucleic acids, and proteins long distances in the body facilitating cell-cell communication. Microorganism-derived EVs mediate communication between parent cells and host cells, with recent evidence supporting their role in biofilm formation, horizontal gene transfer, and suppression of the host immune system. As lipid-bound bacterial byproducts, EVs demonstrate improved cellular uptake and distribution in vivo compared to cell-free nucleic acids, proteins, or small molecules, allowing these biological nanoparticles to recapitulate the effects of parent cells and contribute to a range of human health outcomes. Here, we focus on how EVs derived from vaginal microorganisms contribute to gynecologic and obstetric outcomes. As the composition of the vaginal microbiome significantly impacts women's health, we discuss bacterial EVs from both healthy and dysbiotic vaginal microbiota. We also examine recent work done to evaluate the role of EVs from common vaginal bacterial, fungal, and parasitic pathogens in pathogenesis of female reproductive tract disease. We highlight evidence for the role of EVs in women's health, gaps in current knowledge, and opportunities for future work. Finally, we discuss how leveraging the innate interactions between microorganisms and mammalian cells may establish EVs as a novel therapeutic modality for gynecologic and obstetric indications.}, }
@article {pmid38568420, year = {2024}, author = {Hamrick, GS and Maddamsetti, R and Son, HI and Wilson, ML and Davis, HM and You, L}, title = {Programming Dynamic Division of Labor Using Horizontal Gene Transfer.}, journal = {ACS synthetic biology}, volume = {13}, number = {4}, pages = {1142-1151}, doi = {10.1021/acssynbio.3c00615}, pmid = {38568420}, issn = {2161-5063}, support = {R01 EB031869/EB/NIBIB NIH HHS/United States ; }, mesh = {*Microbial Consortia ; Gene Transfer, Horizontal ; *Microbiota ; Metabolic Engineering ; Genomics ; }, abstract = {The metabolic engineering of microbes has broad applications, including biomanufacturing, bioprocessing, and environmental remediation. The introduction of a complex, multistep pathway often imposes a substantial metabolic burden on the host cell, restraining the accumulation of productive biomass and limiting pathway efficiency. One strategy to alleviate metabolic burden is the division of labor (DOL) in which different subpopulations carry out different parts of the pathway and work together to convert a substrate into a final product. However, the maintenance of different engineered subpopulations is challenging due to competition and convoluted interstrain population dynamics. Through modeling, we show that dynamic division of labor (DDOL), which we define as the DOL between indiscrete populations capable of dynamic and reversible interchange, can overcome these limitations and enable the robust maintenance of burdensome, multistep pathways. We propose that DDOL can be mediated by horizontal gene transfer (HGT) and use plasmid genomics to uncover evidence that DDOL is a strategy utilized by natural microbial communities. Our work suggests that bioengineers can harness HGT to stabilize synthetic metabolic pathways in microbial communities, enabling the development of robust engineered systems for deployment in a variety of contexts.}, }
@article {pmid38568247, year = {2024}, author = {Fu, S and Iqbal, B and Li, G and Alabbosh, KF and Khan, KA and Zhao, X and Raheem, A and Du, D}, title = {The role of microbial partners in heavy metal metabolism in plants: a review.}, journal = {Plant cell reports}, volume = {43}, number = {4}, pages = {111}, pmid = {38568247}, issn = {1432-203X}, support = {BK20220030//Open Project of the Carbon Peak and Carbon Neutrality Technology Innovation Foundation of Jiangsu Province/ ; 32271587//National Natural Science Foundation of China/ ; 3235041400//National Natural Science Foundation of China/ ; 18JDG039//Senior Talent Foundation of Jiangsu University/ ; RGP2/360/44//Deanship of Scientific Research at King Khalid University Saudi Arabia for funding this work through Large Groups Project/ ; }, mesh = {*Herb-Drug Interactions ; *Metals, Heavy/toxicity ; Protein Processing, Post-Translational ; Soil ; }, abstract = {Heavy metal pollution threatens plant growth and development as well as ecological stability. Here, we synthesize current research on the interplay between plants and their microbial symbionts under heavy metal stress, highlighting the mechanisms employed by microbes to enhance plant tolerance and resilience. Several key strategies such as bioavailability alteration, chelation, detoxification, induced systemic tolerance, horizontal gene transfer, and methylation and demethylation, are examined, alongside the genetic and molecular basis governing these plant-microbe interactions. However, the complexity of plant-microbe interactions, coupled with our limited understanding of the associated mechanisms, presents challenges in their practical application. Thus, this review underscores the necessity of a more detailed understanding of how plants and microbes interact and the importance of using a combined approach from different scientific fields to maximize the benefits of these microbial processes. By advancing our knowledge of plant-microbe synergies in the metabolism of heavy metals, we can develop more effective bioremediation strategies to combat the contamination of soil by heavy metals.}, }
@article {pmid38565359, year = {2024}, author = {Medeiros, P and Canato, D and Braz, ASK and Paulino, LC}, title = {Phylogenetic analyses reveal insights into interdomain horizontal gene transfer of microbial lipases.}, journal = {Molecular phylogenetics and evolution}, volume = {195}, number = {}, pages = {108069}, doi = {10.1016/j.ympev.2024.108069}, pmid = {38565359}, issn = {1095-9513}, mesh = {Humans ; Phylogeny ; *Gene Transfer, Horizontal ; *Evolution, Molecular ; Bacteria/genetics ; Gene Duplication ; }, abstract = {Microbial lipases play a pivotal role in a wide range of biotechnological processes and in the human skin microbiome. However, their evolution remains poorly understood. Accessing the evolutionary process of lipases could contribute to future applications in health and biotechnology. We investigated genetic events associated with the evolutionary trajectory of the microbial family LIP lipases. Using phylogenetic analysis, we identified two distinct horizontal gene transfer (HGT) events from Bacteria to Fungi. Further analysis of human cutaneous mycobiome members such as the lipophilic Malassezia yeasts and CUG-Ser-1 clade (including Candida sp. and other microorganisms associated with cutaneous mycobiota) revealed recent evolutionary processes, with multiple gene duplication events. The Lid region of fungal lipases, crucial for substrate interaction, exhibits varying degrees of conservation among different groups. Our findings suggest the adaptability of the fungal LIP family in various genetic and metabolic contexts and its potential role in niche exploration.}, }
@article {pmid38565354, year = {2024}, author = {Li, X and Chen, T and Ren, Q and Lu, J and Cao, S and Liu, C and Li, Y}, title = {Phages in sludge from the A/O wastewater treatment process play an important role in the transmission of ARGs.}, journal = {The Science of the total environment}, volume = {926}, number = {}, pages = {172111}, doi = {10.1016/j.scitotenv.2024.172111}, pmid = {38565354}, issn = {1879-1026}, mesh = {Humans ; Swine ; Animals ; Sewage/microbiology ; Wastewater ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; *Bacteriophages/genetics ; Drug Resistance, Microbial/genetics ; *Water Purification ; }, abstract = {Phages can influence the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) through transduction, but their profiles and effects on the transmission of ARGs are unclear, especially in complex swine sludge. In this study, we investigated the characterization of phage and ARG profiles in sludge generated from anoxic/oxic (A/O) wastewater treatment processes on swine farms using metagenomes and viromes. The results demonstrated that 205-221 subtypes of ARGs could be identified in swine sludge, among which sul1, tet(M), and floR were the dominant ARGs, indicating that sludge is an important reservoir of ARGs, especially in sludge (S) tanks. The greater abundance of mobile genetic elements (MGEs) in the S tank could significantly contribute to the greater abundance of ARGs there compared to the anoxic (A) and oxic (O) tanks (P < 0.05). However, when we compared the abundances of ARGs and MGEs in the A and O tanks, we observed opposite significant differences (P < 0.05), suggesting that MGEs are not the only factor influencing the abundance of ARGs. The high proportion of lysogenic phages in sludge from the S tank can also have a major impact on the ARG profile. Siphoviridae, Myoviridae, and Podoviridae were the dominant phage families in sludge, and a network diagram of bacteria-ARG-phages revealed that dominant phages and bacteria acted simultaneously as potential hosts for ARGs, which may have led to phage-mediated HGT of ARGs. Therefore, the risk of phage-mediated HGT of ARGs cannot be overlooked.}, }
@article {pmid38564675, year = {2024}, author = {Lehman, SS and Verhoeve, VI and Driscoll, TP and Beckmann, JF and Gillespie, JJ}, title = {Metagenome diversity illuminates the origins of pathogen effectors.}, journal = {mBio}, volume = {15}, number = {5}, pages = {e0075923}, pmid = {38564675}, issn = {2150-7511}, support = {R21 AI156762/AI/NIAID NIH HHS/United States ; R21 AI166832/AI/NIAID NIH HHS/United States ; }, mesh = {*Metagenome ; *Rickettsia/genetics/classification ; *Phylogeny ; *Genome, Bacterial ; Evolution, Molecular ; Rickettsiales/genetics/classification ; Genetic Variation ; Type IV Secretion Systems/genetics/metabolism ; Gene Transfer, Horizontal ; Humans ; Bacterial Proteins/genetics/metabolism ; }, abstract = {Recent metagenome-assembled genome (MAG) analyses have profoundly impacted Rickettsiology systematics. The discovery of basal lineages (novel families Mitibacteraceae and Athabascaceae) with predicted extracellular lifestyles exposed an evolutionary timepoint for the transition to host dependency, which seemingly occurred independent of mitochondrial evolution. Notably, these basal rickettsiae carry the Rickettsiales vir homolog (rvh) type IV secretion system and purportedly use rvh to kill congener microbes rather than parasitize host cells as described for later-evolving rickettsial pathogens. MAG analysis also substantially increased diversity for the genus Rickettsia and delineated a sister lineage (the novel genus Tisiphia) that stands to inform on the emergence of human pathogens from protist and invertebrate endosymbionts. Herein, we probed Rickettsiales MAG and genomic diversity for the distribution of Rickettsia rvh effectors to ascertain their origins. A sparse distribution of most Rickettsia rvh effectors outside of Rickettsiaceae lineages illuminates unique rvh evolution from basal extracellular species and other rickettsial families. Remarkably, nearly every effector was found in multiple divergent forms with variable architectures, indicating profound roles for gene duplication and recombination in shaping effector repertoires in Rickettsia pathogens. Lateral gene transfer plays a prominent role in shaping the rvh effector landscape, as evinced by the discovery of many effectors on plasmids and conjugative transposons, as well as pervasive effector gene exchange between Rickettsia and Legionella species. Our study exemplifies how MAGs can yield insight into pathogen effector origins, particularly how effector architectures might become tailored to the discrete host cell functions of different eukaryotic hosts.IMPORTANCEWhile rickettsioses are deadly vector-borne human diseases, factors distinguishing Rickettsia pathogens from the innumerable bevy of environmental rickettsial endosymbionts remain lacking. Recent metagenome-assembled genome (MAG) studies revealed evolutionary timepoints for rickettsial transitions to host dependency. The rvh type IV secretion system was likely repurposed from congener killing in basal extracellular species to parasitizing host cells in later-evolving pathogens. Our analysis of MAG diversity for over two dozen rvh effectors unearthed their presence in some non-pathogens. However, most effectors were found in multiple divergent forms with variable architectures, indicating gene duplication and recombination-fashioned effector repertoires of Rickettsia pathogens. Lateral gene transfer substantially shaped pathogen effector arsenals, evinced by the discovery of effectors on plasmids and conjugative transposons, as well as pervasive effector gene exchanges between Rickettsia and Legionella species. Our study exemplifies how MAGs yield insight into pathogen effector origins and evolutionary processes tailoring effectors to eukaryotic host cell biology.}, }
@article {pmid38561802, year = {2024}, author = {Lanoizelet, M and Elkhoury Youhanna, C and Roure, A and Darras, S}, title = {Molecular control of cellulosic fin morphogenesis in ascidians.}, journal = {BMC biology}, volume = {22}, number = {1}, pages = {74}, pmid = {38561802}, issn = {1741-7007}, support = {Emergence 2021//Sorbonne Universit&#xe9;/ ; DBM2020//Institut des sciences biologiques/ ; DBM2022//Institut des sciences biologiques/ ; }, mesh = {Animals ; *Urochordata/genetics ; Morphogenesis/genetics ; Epidermis ; Peripheral Nervous System ; Larva/genetics ; Cellulose ; }, abstract = {BACKGROUND: The tunicates form a group of filter-feeding marine animals closely related to vertebrates. They share with them a number of features such as a notochord and a dorsal neural tube in the tadpole larvae of ascidians, one of the three groups that make tunicates. However, a number of typical chordate characters have been lost in different branches of tunicates, a diverse and fast-evolving phylum. Consequently, the tunic, a sort of exoskeleton made of extracellular material including cellulose secreted by the epidermis, is the unifying character defining the tunicate phylum. In the larva of ascidians, the tunic differentiates in the tail into a median fin (with dorsal and ventral extended blades) and a caudal fin.<br><br>RESULTS: Here we have performed experiments in the ascidian Phallusia mammillata to address the molecular control of tunic 3D morphogenesis. We have demonstrated that the tail epidermis medio-lateral patterning essential for peripheral nervous system specification also controls tunic elongation into fins. More specifically, when tail epidermis midline identity was abolished by BMP signaling inhibition, or CRISPR/Cas9 inactivation of the transcription factor coding genes Msx or Klf1/2/4/17, median fin did not form. We postulated that this genetic program should regulate effectors of tunic secretion. We thus analyzed the expression and regulation in different ascidian species of two genes acquired by horizontal gene transfer (HGT) from bacteria, CesA coding for a cellulose synthase and Gh6 coding for a cellulase. We have uncovered an unexpected dynamic history of these genes in tunicates and high levels of variability in gene expression and regulation among ascidians. Although, in Phallusia, Gh6 has a regionalized expression in the epidermis compatible with an involvement in fin elongation, our functional studies indicate a minor function during caudal fin formation only.<br><br>CONCLUSIONS: Our study constitutes an important step in the study of the integration of HGT-acquired genes into developmental networks and a cellulose-based morphogenesis of extracellular material in animals.}, }
@article {pmid38561223, year = {2024}, author = {LeBleu, VS and Kanasaki, K and Lovisa, S and Alge, JL and Kim, J and Chen, Y and Teng, Y and Gerami-Naini, B and Sugimoto, H and Kato, N and Revuelta, I and Grau, N and Sleeman, JP and Taduri, G and Kizu, A and Rafii, S and Hochedlinger, K and Quaggin, SE and Kalluri, R}, title = {Genetic reprogramming with stem cells regenerates glomerular epithelial podocytes in Alport syndrome.}, journal = {Life science alliance}, volume = {7}, number = {6}, pages = {}, pmid = {38561223}, issn = {2575-1077}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; R01 DK055001/DK/NIDDK NIH HHS/United States ; T32 DK007760/DK/NIDDK NIH HHS/United States ; T32 HL007374/HL/NHLBI NIH HHS/United States ; }, mesh = {Mice ; Animals ; *Nephritis, Hereditary/genetics/metabolism ; *Podocytes/metabolism ; Collagen Type IV/genetics/metabolism ; Glomerular Basement Membrane/metabolism ; Stem Cells/metabolism ; }, abstract = {Glomerular filtration relies on the type IV collagen (ColIV) network of the glomerular basement membrane, namely, in the triple helical molecules containing the α3, α4, and α5 chains of ColIV. Loss of function mutations in the genes encoding these chains (Col4a3, Col4a4, and Col4a5) is associated with the loss of renal function observed in Alport syndrome (AS). Precise understanding of the cellular basis for the patho-mechanism remains unknown and a specific therapy for this disease does not currently exist. Here, we generated a novel allele for the conditional deletion of Col4a3 in different glomerular cell types in mice. We found that podocytes specifically generate α3 chains in the developing glomerular basement membrane, and that its absence is sufficient to impair glomerular filtration as seen in AS. Next, we show that horizontal gene transfer, enhanced by TGFβ1 and using allogenic bone marrow-derived mesenchymal stem cells and induced pluripotent stem cells, rescues Col4a3 expression and revive kidney function in Col4a3-deficient AS mice. Our proof-of-concept study supports that horizontal gene transfer such as cell fusion enables cell-based therapy in Alport syndrome.}, }
@article {pmid38560215, year = {2024}, author = {Comba-González, NB and Chaves-Moreno, D and Santamaría-Vanegas, J and Montoya-Castaño, D}, title = {A pan-genomic assessment: Delving into the genome of the marine epiphyte Bacillus altitudinis strain 19_A and other very close Bacillus strains from multiple environments.}, journal = {Heliyon}, volume = {10}, number = {7}, pages = {e27820}, pmid = {38560215}, issn = {2405-8440}, abstract = {Marine macroalgae are the habitat of epiphytic bacteria and provide several conditions for a beneficial biological interaction to thrive. Although Bacillus is one of the most abundant epiphytic genera, genomic information on marine macroalgae-associated Bacillus species remains scarce. In this study, we further investigated our previously published genome of the epiphytic strain Bacillus altitudinis 19_A to find features that could be translated to potential metabolites produced by this microorganism, as well as genes that play a role in its interaction with its macroalgal host. To achieve this goal, we performed a pan-genome analysis of Bacillus sp. and a codon bias assessment, including the genome of the strain Bacillus altitudinis 19_A and 29 complete genome sequences of closely related Bacillus strains isolated from soil, marine environments, plants, extreme environments, air, and food. This genomic analysis revealed that Bacillus altitudinis 19_A possessed unique genes encoding proteins involved in horizontal gene transfer, DNA repair, transcriptional regulation, and bacteriocin biosynthesis. In this comparative analysis, codon bias was not associated with the habitat of the strains studied. Some accessory genes were identified in the Bacillus altitudinis 19_A genome that could be related to its epiphytic lifestyle, as well as gene clusters for the biosynthesis of a sporulation-killing factor and a bacteriocin, showing their potential as a source of antimicrobial peptides. Our results provide a comprehensive view of the Bacillus altitudinis 19_A genome to understand its adaptation to the marine environment and its potential as a producer of bioactive compounds.}, }
@article {pmid38555673, year = {2024}, author = {Sun, H and Chang, H and Zhu, Y and Li, X and Yang, X and Zhou, X and Wu, D and Ding, J and Liu, Y}, title = {Strong suppression of silver nanoparticles on antibiotic resistome in anammox process.}, journal = {Journal of hazardous materials}, volume = {470}, number = {}, pages = {134128}, doi = {10.1016/j.jhazmat.2024.134128}, pmid = {38555673}, issn = {1873-3336}, mesh = {*Silver/chemistry/pharmacology ; *Metal Nanoparticles/chemistry/toxicity ; *Drug Resistance, Microbial/genetics/drug effects ; Anti-Bacterial Agents/pharmacology/chemistry ; Gene Transfer, Horizontal ; Sewage/microbiology ; Nitrogen/chemistry/metabolism ; Bacteria/drug effects/genetics/metabolism ; Anaerobiosis ; Microbiota/drug effects ; Oxidation-Reduction ; }, abstract = {This study comprehensively deciphered the effect of silver nanoparticles (AgNPs) on anammox flocculent sludge, including nitrogen removal performance, microbial community structure, functional enzyme abundance, antibiotic resistance gene (ARGs) dissemination, and horizontal gene transfer (HGT) mechanisms. After long-term exposure to 0-2.5 mg/L AgNPs for 200 cycles, anammox performance significantly decreased (P < 0.05), while the relative abundances of dominant Ca. Kuenenia and anammox-related enzymes (hzsA, nirK) increased compared to the control (P < 0.05). For antibiotic resistome, ARG abundance hardly changed with 0-0.5 mg/L AgNPs but decreased by approximately 90% with 1.5-2.5 mg/L AgNPs. More importantly, AgNPs effectively inhibited MGE-mediated HGT of ARGs. Additionally, structural equation model (SEM) disclosed the underlying relationship between AgNPs, the antibiotic resistome, and the microbial community. Overall, AgNPs suppressed the anammox-driven nitrogen cycle, regulated the microbial community, and prevented the spread of ARGs in anammox flocs. This study provides a theoretical baseline for an advanced understanding of the ecological roles of nanoparticles and resistance elements in engineered ecosystems.}, }
@article {pmid38554973, year = {2024}, author = {Song, H and Yoo, JS and Unno, T}, title = {Discerning the dissemination mechanisms of antibiotic resistance genes through whole genome sequencing of extended-spectrum beta-lactamase (ESBL)-producing E. coli isolated from veterinary clinics and farms in South Korea.}, journal = {The Science of the total environment}, volume = {926}, number = {}, pages = {172068}, doi = {10.1016/j.scitotenv.2024.172068}, pmid = {38554973}, issn = {1879-1026}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Escherichia coli ; Farms ; *Escherichia coli Infections/microbiology ; Hospitals, Animal ; beta-Lactamases/genetics ; Drug Resistance, Microbial ; Republic of Korea ; Plasmids/genetics ; Whole Genome Sequencing ; }, abstract = {Extended-spectrum beta-lactamase (ESBL)-producing bacteria are resistant to most beta-lactams, including third-generation cephalosporins, limiting the treatment methods against the infections they cause. In this study, we performed whole genome sequencing of ESBL-producing E. coli to determine the mechanisms underlying the dissemination of antibiotic resistance genes. We analyzed 141 ESBL-producing isolates which had been collected from 16 veterinary clinics and 16 farms in South Korea. Long- and short-read sequencing platforms were used to obtain high-quality assemblies. The results showed that blaCTX-M is the dominant ESBL gene type found in South Korea. The spread of blaCTX-M appears to have been facilitated by both clonal spread between different host species and conjugation. Most blaCTX-M genes were found associated with diverse mobile genetic elements that may contribute to the chromosomal integration of the genes. Diverse incompatibility groups of blaCTX-M-harboring plasmids were also observed, which allows their spread among a variety of bacteria. Comprehensive whole genome sequence analysis was useful for the identification of the most prevalent types of ESBL genes and their dissemination mechanisms. The results of this study suggest that the propagation of ESBL genes can occur through clonal spread and plasmid-mediated dissemination, and that suitable action plans should be developed to prevent further propagation of these genes.}, }
@article {pmid38554512, year = {2024}, author = {Qin, J and Qi, X and Li, Y and Tang, Z and Zhang, X and Ru, S and Xiong, JQ}, title = {Bisphenols can promote antibiotic resistance by inducing metabolic adaptations and natural transformation.}, journal = {Journal of hazardous materials}, volume = {470}, number = {}, pages = {134149}, doi = {10.1016/j.jhazmat.2024.134149}, pmid = {38554512}, issn = {1873-3336}, mesh = {*Phenols/toxicity/metabolism ; *Acinetobacter/drug effects/genetics/metabolism ; *Benzhydryl Compounds/toxicity/metabolism ; Animals ; Plasmids ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Water Pollutants, Chemical/toxicity/metabolism ; Adaptation, Physiological ; Plasticizers/toxicity ; Anti-Bacterial Agents/pharmacology/toxicity ; *Sulfones ; }, abstract = {Whether bisphenols, as plasticizers, can influence bacterial uptake of antibiotic resistance genes (ARGs) in natural environment, as well as the underlying mechanism remains largely unknown. Our results showed that four commonly used bisphenols (bisphenol A, S, F, and AF) at their environmental relative concentrations can significantly promote transmission of ARGs by 2.97-3.56 times in Acinetobacter baylyi ADP1. Intriguingly, we observed ADP1 acquired resistance by integrating plasmids uptake and cellular metabolic adaptations other than through reactive oxygen species mediated pathway. Metabolic adaptations including upregulation of capsules polysaccharide biosynthesis and intracellularly metabolic enzymes, which enabled formation of thicker capsules for capturing free plasmids, and degradation of accumulated compounds. Simultaneously, genes encoding DNA uptake and translocation machinery were incorporated to enhance natural transformation of antibiotic resistance carrying plasmids. We further exposed aquatic fish to bisphenols for 120 days to monitor their long-term effects in aquatic environment, which showed that intestinal bacteria communities were dominated by a drug resistant microbiome. Our study provides new insight into the mechanism of enhanced natural transformation of ARGs by bisphenols, and highlights the investigations for unexpectedly-elevated antibiotic-resistant risks by structurally related environmental chemicals.}, }
@article {pmid38552150, year = {2024}, author = {Howard-Varona, C and Lindback, MM and Fudyma, JD and Krongauz, A and Solonenko, NE and Zayed, AA and Andreopoulos, WB and Olson, HM and Kim, YM and Kyle, JE and Glavina Del Rio, T and Adkins, JN and Tfaily, MM and Paul, S and Sullivan, MB and Duhaime, MB}, title = {Environment-specific virocell metabolic reprogramming.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38552150}, issn = {1751-7370}, support = {2149505//NSF Advances in Biological Informatics/ ; DE-AC05-76RL0-1830//U.S. Department of Energy/ ; //Joint Genome Institute/ ; //U.S. Department of Energy/ ; 1536989//National Science Foundation/ ; //University of Michigan/ ; 034//C-CoMP/ ; //Department of Energy/ ; T32 AI112542/AI/NIAID NIH HHS/United States ; 2055455//NSF Polar Programs/ ; 1-T32-AI-112542//National Institutes of Health (NIH)/National Institute of Allergy and Infectious Diseases (NIAID)/ ; //Facilities Integrating Collaborations for User Science/ ; 3790//Gordon and Betty Moore Foundation/ ; //EMSL/ ; //Office of Science/ ; DGE1256260//NSF Graduate Research Fellowship/ ; DE-AC02-05CH11231//Biological and Environmental Research/ ; C-CoMP NSF-STC 2019589//NSF Center for Chemical Currencies of a Microbial Planet/ ; //Environmental Molecular Sciences Laboratory/ ; DE-SC0020173//Office of Biological and Environmental Research/ ; }, mesh = {*Bacteriophages/genetics/physiology ; Proteomics ; Phosphates/metabolism ; Metabolomics ; Systems Biology ; Transcriptome ; Metabolic Reprogramming ; }, abstract = {Viruses impact microbial systems through killing hosts, horizontal gene transfer, and altering cellular metabolism, consequently impacting nutrient cycles. A virus-infected cell, a "virocell," is distinct from its uninfected sister cell as the virus commandeers cellular machinery to produce viruses rather than replicate cells. Problematically, virocell responses to the nutrient-limited conditions that abound in nature are poorly understood. Here we used a systems biology approach to investigate virocell metabolic reprogramming under nutrient limitation. Using transcriptomics, proteomics, lipidomics, and endo- and exo-metabolomics, we assessed how low phosphate (low-P) conditions impacted virocells of a marine Pseudoalteromonas host when independently infected by two unrelated phages (HP1 and HS2). With the combined stresses of infection and nutrient limitation, a set of nested responses were observed. First, low-P imposed common cellular responses on all cells (virocells and uninfected cells), including activating the canonical P-stress response, and decreasing transcription, translation, and extracellular organic matter consumption. Second, low-P imposed infection-specific responses (for both virocells), including enhancing nitrogen assimilation and fatty acid degradation, and decreasing extracellular lipid relative abundance. Third, low-P suggested virocell-specific strategies. Specifically, HS2-virocells regulated gene expression by increasing transcription and ribosomal protein production, whereas HP1-virocells accumulated host proteins, decreased extracellular peptide relative abundance, and invested in broader energy and resource acquisition. These results suggest that although environmental conditions shape metabolism in common ways regardless of infection, virocell-specific strategies exist to support viral replication during nutrient limitation, and a framework now exists for identifying metabolic strategies of nutrient-limited virocells in nature.}, }
@article {pmid38551849, year = {2024}, author = {Masuda, T and Mareš, J and Shiozaki, T and Inomura, K and Fujiwara, A and Prášil, O}, title = {Crocosphaera watsonii - A widespread nitrogen-fixing unicellular marine cyanobacterium.}, journal = {Journal of phycology}, volume = {60}, number = {3}, pages = {604-620}, doi = {10.1111/jpy.13450}, pmid = {38551849}, issn = {1529-8817}, support = {23-06593S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; JP23H02301//Japan Society for the Promotion of Science/ ; JPMJPR23GA//JST, PRESTO/ ; }, mesh = {*Cyanobacteria/genetics/metabolism/physiology ; *Nitrogen Fixation ; *Phylogeny ; }, abstract = {Crocosphaera watsonii is a unicellular N2-fixing (diazotrophic) cyanobacterium observed in tropical and subtropical oligotrophic oceans. As a diazotroph, it can be a source of bioavailable nitrogen (N) to the microbial community in N-limited environments, and this may fuel primary production in the regions where it occurs. Crocosphaera watsonii has been the subject of intense study, both in culture and in field populations. Here, we summarize the current understanding of the phylogenetic and physiological diversity of C. watsonii, its distribution, and its ecological niche. Analysis of the relationships among the individual Crocosphaera species and related free-living and symbiotic lineages of diazotrophs based on the nifH gene have shown that the C. watsonii group holds a basal position and that its sequence is more similar to Rippkaea and Zehria than to other Crocosphaera species. This finding warrants further scrutiny to determine if the placement is related to a horizontal gene transfer event. Here, the nifH UCYN-B gene copy number from a recent synthesis effort was used as a proxy for relative C. watsonii abundance to examine patterns of C. watsonii distribution as a function of environmental factors, like iron and phosphorus concentration, and complimented with a synthesis of C. watsonii physiology. Furthermore, we have summarized the current knowledge of C. watsonii with regards to N2 fixation, photosynthesis, and quantitative modeling of physiology. Because N availability can limit primary production, C. watsonii is widely recognized for its importance to carbon and N cycling in ocean ecosystems, and we conclude this review by highlighting important topics for further research on this important species.}, }
@article {pmid38548766, year = {2024}, author = {Pratt, CJ and Meili, CH and Jones, AL and Jackson, DK and England, EE and Wang, Y and Hartson, S and Rogers, J and Elshahed, MS and Youssef, NH}, title = {Anaerobic fungi in the tortoise alimentary tract illuminate early stages of host-fungal symbiosis and Neocallimastigomycota evolution.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {2714}, pmid = {38548766}, issn = {2041-1723}, support = {2029478//National Science Foundation (NSF)/ ; 2029478//National Science Foundation (NSF)/ ; }, mesh = {Humans ; Animals ; *Neocallimastigomycota/genetics/metabolism ; *Turtles/genetics ; Phylogeny ; Anaerobiosis ; Symbiosis/genetics ; Mammals ; Fungi/genetics ; }, abstract = {Anaerobic gut fungi (AGF, Neocallimastigomycota) reside in the alimentary tract of herbivores. While their presence in mammals is well documented, evidence for their occurrence in non-mammalian hosts is currently sparse. Culture-independent surveys of AGF in tortoises identified a unique community, with three novel deep-branching genera representing >90% of sequences in most samples. Representatives of all genera were successfully isolated under strict anaerobic conditions. Transcriptomics-enabled phylogenomic and molecular dating analyses indicated an ancient, deep-branching position in the AGF tree for these genera, with an evolutionary divergence time estimate of 104-112 million years ago (Mya). Such estimates push the establishment of animal-Neocallimastigomycota symbiosis from the late to the early Cretaceous. Further, tortoise-associated isolates (T-AGF) exhibited limited capacity for plant polysaccharides metabolism and lacked genes encoding several carbohydrate-active enzyme (CAZyme) families. Finally, we demonstrate that the observed curtailed degradation capacities and reduced CAZyme repertoire is driven by the paucity of horizontal gene transfer (HGT) in T-AGF genomes, compared to their mammalian counterparts. This reduced capacity was reflected in an altered cellulosomal production capacity in T-AGF. Our findings provide insights into the phylogenetic diversity, ecological distribution, evolutionary history, evolution of fungal-host nutritional symbiosis, and dynamics of genes acquisition in Neocallimastigomycota.}, }
@article {pmid38546735, year = {2024}, author = {Klose, SM and Legione, AR and Bushell, RN and Browning, GF and Vaz, PK}, title = {Unveiling genome plasticity and a novel phage in Mycoplasma felis: Genomic investigations of four feline isolates.}, journal = {Microbial genomics}, volume = {10}, number = {3}, pages = {}, pmid = {38546735}, issn = {2057-5858}, mesh = {Cats ; Animals ; Horses ; Australia ; Genomics ; *Mycoplasma/genetics ; *Felis ; *Bacteriophages ; }, abstract = {Mycoplasma felis has been isolated from diseased cats and horses, but to date only a single fully assembled genome of this species, of an isolate from a horse, has been characterized. This study aimed to characterize and compare the completely assembled genomes of four clinical isolates of M. felis from three domestic cats, assembled with the aid of short- and long-read sequencing methods. The completed genomes encoded a median of 759 ORFs (range 743-777) and had a median average nucleotide identity of 98.2 % with the genome of the available equid origin reference strain. Comparative genomic analysis revealed the occurrence of multiple horizontal gene transfer events and significant genome reassortment. This had resulted in the acquisition or loss of numerous genes within the Australian felid isolate genomes, encoding putative proteins involved in DNA transfer, metabolism, DNA replication, host cell interaction and restriction modification systems. Additionally, a novel mycoplasma phage was detected in one Australian felid M. felis isolate by genomic analysis and visualized using cryo-transmission electron microscopy. This study has highlighted the complex genomic dynamics in different host environments. Furthermore, the sequences obtained in this work will enable the development of new diagnostic tools, and identification of future infection control and treatment options for the respiratory disease complex in cats.}, }
@article {pmid38543613, year = {2024}, author = {Mei, L and Song, Y and Liu, X and Li, K and Guo, X and Liu, L and Liu, Y and Kozlakidis, Z and Cheong, IH and Wang, D and Wei, Q}, title = {Characterization and Implications of IncP-2A Plasmid pMAS152 Harboring Multidrug Resistance Genes in Extensively Drug-Resistant Pseudomonas aeruginosa.}, journal = {Microorganisms}, volume = {12}, number = {3}, pages = {}, pmid = {38543613}, issn = {2076-2607}, support = {001/WHO_/World Health Organization/International ; }, abstract = {Bacterial antimicrobial resistance (AMR) poses a significant global public health challenge. The escalation of AMR is primarily attributed to the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs), often facilitated by plasmids. This underscores the critical need for a comprehensive understanding of the resistance mechanisms and transmission dynamics of these plasmids. In this study, we utilized in vitro drug sensitivity testing, conjugation transfer assays, and whole-genome sequencing to investigate the resistance mechanism of an extensively drug-resistant (XDR) Pseudomonas aeruginosa clinical isolate, MAS152. We specifically focused on analyzing the drug-resistant plasmid pMAS152 it harbors and its potential for widespread dissemination. Bioinformatics analysis revealed that MAS152 carries a distinct IncpP-2A plasmid, pMAS152, characterized by a 44.8 kb multidrug resistance (MDR) region. This region houses a 16S rRNA methyltransferase (16S-RMTase) gene, rmtB, conferring high-level resistance to aminoglycoside antibiotics. Notably, this region also contains an extended-spectrum β-Lactamase (ESBL) gene, blaPER-1, and an efflux pump operon, tmexCD-oprJ, which mediate resistance to β-Lactams and quinolone antibiotics, respectively. Such a combination of ARGs, unprecedented in reported plasmids, could significantly undermine the effectiveness of first-line antibiotics in treating P. aeruginosa infections. Investigation into the genetic environment of the MDR region suggests that Tn2 and IS91 elements may be instrumental in the horizontal transfer of rmtB. Additionally, a complex Class I integron with an ISCR1 structure, along with TnAs1, seems to facilitate the horizontal transfer of blaPER-1. The conjugation transfer assay, coupled with the annotation of conjugation-related genes and phylogenetic analysis, indicates that the plasmid pMAS152 functions as a conjugative plasmid, with other genus Pseudomonas species as potential hosts. Our findings provide vital insights into the resistance mechanisms and transmission potential of the XDR P. aeruginosa isolate MAS152, underlining the urgent need for novel strategies to combat the spread of AMR. This study highlights the complex interplay of genetic elements contributing to antibiotic resistance and underscores the importance of continuous surveillance of emerging ARGs in clinical isolates.}, }
@article {pmid38543545, year = {2024}, author = {Skwor, T and Jones, DC and Cahak, C and Newton, RJ}, title = {First Report and Characterization of a Plasmid-Encoded blaSFO-1 in a Multi-Drug-Resistant Aeromonas hydrophila Clinical Isolate.}, journal = {Microorganisms}, volume = {12}, number = {3}, pages = {}, pmid = {38543545}, issn = {2076-2607}, abstract = {Antibiotic resistance remains one of the most pressing public health issues facing the world today. At the forefront of this battle lies the ever-increasing identification of extended-spectrum beta-lactamases and carbapenemases within human pathogens, conferring resistance towards broad-spectrum and last-resort antimicrobials. This study was prompted due to the identification of a pathogenic Aeromonas hydrophila isolate (strain MAH-4) collected from abdominal fluid, which presented a robust resistance pattern against second-, third-, and fourth-generation cephalosporins, ertapenem, ciprofloxacin, gentamicin, levofloxacin and moxifloxacin, and beta lactam/beta-lactamase inhibitor combinations. Whole genome sequencing was performed and identified a 328 kb plasmid (pMAH4) encoding 10 antibiotic resistance genes, including blaSFO-1, blaTEM-1, and blaOXA-1 of A. hydrophia MAH-4. This is the first report of beta-lactamase SFO-1 within a clinical strain of Aeromonas. Due to the remarkable sequence identity of pMAH4 to plasmids associated with Enterobacterales genera like Klebsiella and the extensive capabilities of Aeromonas for horizontal gene transfer, our identification of a clinical isolate encoding SFO-1 on a plasmid suggests antibiotic resistance gene mobility between Enterobacterales and non-Enterobacterales species.}, }
@article {pmid38542054, year = {2024}, author = {Barathan, M and Ng, SL and Lokanathan, Y and Ng, MH and Law, JX}, title = {Unseen Weapons: Bacterial Extracellular Vesicles and the Spread of Antibiotic Resistance in Aquatic Environments.}, journal = {International journal of molecular sciences}, volume = {25}, number = {6}, pages = {}, pmid = {38542054}, issn = {1422-0067}, support = {DIP-2023-011//National University of Malaysia/ ; FF-2021-518//Faculty of Medicine, Universiti Kebangsaan Malaysia/ ; }, mesh = {*Ecosystem ; Bacteria/genetics ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Drug Resistance, Multiple, Bacterial ; *Extracellular Vesicles ; Genes, Bacterial ; }, abstract = {This paper sheds light on the alarming issue of antibiotic resistance (ABR) in aquatic environments, exploring its detrimental effects on ecosystems and public health. It examines the multifaceted role of antibiotic use in aquaculture, agricultural runoff, and industrial waste in fostering the development and dissemination of resistant bacteria. The intricate interplay between various environmental factors, horizontal gene transfer, and bacterial extracellular vesicles (BEVs) in accelerating the spread of ABR is comprehensively discussed. Various BEVs carrying resistance genes like blaCTX-M, tetA, floR, and sul/I, as well as their contribution to the dominance of multidrug-resistant bacteria, are highlighted. The potential of BEVs as both a threat and a tool in combating ABR is explored, with promising strategies like targeted antimicrobial delivery systems and probiotic-derived EVs holding significant promise. This paper underscores the urgency of understanding the intricate interplay between BEVs and ABR in aquatic environments. By unraveling these unseen weapons, we pave the way for developing effective strategies to mitigate the spread of ABR, advocating for a multidisciplinary approach that includes stringent regulations, enhanced wastewater treatment, and the adoption of sustainable practices in aquaculture.}, }
@article {pmid38539090, year = {2024}, author = {Kumar, G and Balakrishna, K and Mukhopadhyay, C and Kalwaje Eshwara, V}, title = {Comparison of integron mediated antimicrobial resistance in clinical isolates of Escherichia coli from urinary and bacteremic sources.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {102}, pmid = {38539090}, issn = {1471-2180}, mesh = {Humans ; *Escherichia coli ; Anti-Bacterial Agents/pharmacology ; Integrons/genetics ; *Escherichia coli Infections/microbiology ; Drug Resistance, Bacterial/genetics ; }, abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a global threat driven mainly by horizontal gene transfer (HGT) mechanisms through mobile genetic elements (MGEs) including integrons. The variable region (VR) of an integron can acquire or excise gene cassettes (GCs) that confer resistance to antibiotics based on the selection pressure. Escherichia coli plays a significant role in the genetic transfer of resistance determinants to other Gram-negative bacteria. Current study is aimed to detect and compare integron-mediated resistance in clinical isolates of E. coli. Unique isolates of E. coli from urine or blood cultures were studied for their antimicrobial resistance patterns and integrons were detected using polymerase chain reaction assays followed by Sanger sequencing of GCs.<br><br>RESULTS: During the study period, a total of 470 E. coli isolates were obtained, 361 (76.8%) from urinary and 109 (23.1%) from bacteremic sources. Class 1 integrons were detected in 66 (18.2%) and 26 (23.8%) isolates respectively. Urinary isolates of E. coli harbouring Class 1 integrons demonstrated significantly higher rates of resistance (p&#x2009;<&#x2009;0.05) for most antibiotics (12/16, 75%) compared to integron negative isolates. Although not statistically significant, similar differences were observed in bacteremic isolates. Among the urinary isolates, 27 (40.9%) had a VR, in which the most common GC array detected was DfrA17-AadA5 (n&#x2009;=&#x2009;14), followed by DfrA5 (n&#x2009;=&#x2009;4) and DfrA12 (n&#x2009;=&#x2009;3). Among bacteremic isolates, only 4 (15.3%) had a VR, all of which were carrying DfrA17. The detected GC array correlated with the respective isolates' phenotypic resistance patterns.<br><br>CONCLUSION: We found a strong correlation between integron positivity and trimethoprim resistance among E. coli from urinary sources. Although higher rates of resistance were observed in bacteremic isolates, they mostly carried empty integrons.}, }
@article {pmid38538528, year = {2024}, author = {Chiquito-Contreras, CJ and Meza-Menchaca, T and Guzmán-López, O and Vásquez, EC and Ricaño-Rodríguez, J}, title = {Molecular Insights into Plant-Microbe Interactions: A Comprehensive Review of Key Mechanisms.}, journal = {Frontiers in bioscience (Elite edition)}, volume = {16}, number = {1}, pages = {9}, doi = {10.31083/j.fbe1601009}, pmid = {38538528}, issn = {1945-0508}, mesh = {*Ecosystem ; *Epigenesis, Genetic ; Plants ; Symbiosis ; Bacteria ; }, abstract = {In most ecosystems, plants establish complex symbiotic relationships with organisms, such as bacteria and fungi, which significantly influence their health by promoting or inhibiting growth. These relationships involve biochemical exchanges at the cellular level that affect plant physiology and have evolutionary implications, such as species diversification, horizontal gene transfer, symbiosis and mutualism, environmental adaptation, and positive impacts on community structure and biodiversity. For these reasons, contemporary research, moving beyond observational studies, seeks to elucidate the molecular basis of these interactions; however, gaps in knowledge remain. This is particularly noticeable in understanding how plants distinguish between beneficial and antagonistic microorganisms. In light of the above, this literature review aims to address some of these gaps by exploring the key mechanisms in common interspecies relationships. Thus, our study presents novel insights into these evolutionary archetypes, focusing on the antibiosis process and microbial signaling, including chemotaxis and quorum sensing. Additionally, it examined the biochemical basis of endophytism, pre-mRNA splicing, and transcriptional plasticity, highlighting the roles of transcription factors and epigenetic regulation in the functions of the interacting organisms. These findings emphasize the importance of understanding these confluences in natural environments, which are crucial for future theoretical and practical applications, such as improving plant nutrition, protecting against pathogens, developing transgenic crops, sustainable agriculture, and researching disease mechanisms. It was concluded that because of the characteristics of the various biomolecules involved in these biological interactions, there are interconnected molecular networks in nature that give rise to different ecological scaffolds. These networks integrate a myriad of functionally organic units that belong to various kingdoms. This interweaving underscores the complexity and multidisciplinary integration required to understand plant-microbe interactions at the molecular level. Regarding the limitations inherent in this study, it is recognized that researchers face significant obstacles. These include technical difficulties in experimentation and fieldwork, as well as the arduous task of consolidating and summarizing findings for academic articles. Challenges range from understanding complex ecological and molecular dynamics to unbiased and objective interpretation of diverse and ever-changing literature.}, }
@article {pmid38537404, year = {2024}, author = {Cui, J and Dong, Y and Chen, Q and Zhang, C and He, K and Hu, G and He, D and Yuan, L}, title = {Horizontal transfer characterization of ColV plasmids in blaCTX-M-bearing avian Escherichia coli.}, journal = {Poultry science}, volume = {103}, number = {5}, pages = {103631}, pmid = {38537404}, issn = {1525-3171}, mesh = {*Escherichia coli/genetics/drug effects ; Animals ; *Escherichia coli Infections/veterinary/microbiology ; *Gene Transfer, Horizontal ; *Poultry Diseases/microbiology ; *Plasmids/genetics ; *Chickens ; *beta-Lactamases/genetics/metabolism ; Drug Resistance, Multiple, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Extended-spectrum-β-lactamases (ESBLs)-producing Escherichia coli conferred resistance to most β-lactams, except for carbapenems. To date, the transmission mechanism of blaCTX-M, as the most common ESBLs subtype, in E. coli has received sustained attention around the worldwide, but the research on the pathogenicity of blaCTX-M-bearing E. coli is still scarce. The aims of this study were to discern the spread characteristics of ColV (encoding colicin V) plasmids in blaCTX-M-positive E. coli. The multi-drug resistance traits, phylogroups, and ColV plasmid profilings were screened in 76 blaCTX-M-positive E. coli. Thereafter, the genetic profiles of E. coli G12 and GZM7 were determined by whole genome sequencing, conjugation and S1-pulsed-field gel electrophoresis. The median lethal dose was analyzed in E. coli G12 and TG12A, the ColV-plasmid transconjugant of G12. Of all 76 blaCTX-M-bearing E. coli, 67.11% exhibited resistance to at least 2 drugs in addition to ceftiofur, 14.47% carried ColV-positive plasmids, and 53.95% were phylogroup C. Further studies demonstrated that the blaCTX-M-bearing E. coli G12 was assigned to the predominant lineage O78:H4-ST117 of phylogroup G. In addition, its ColV-positive plasmid simultaneously carried multiple resistance genes, and could be independently transferred to confer partial pathogenicity on its host by plasmid mating. E. coli GZM7 was O53:H9-ST23 of phylogroup C, which belonged to another representative lineage of APEC (avian pathogenic E. coli). Its ColV-positive plasmid could complete conjugation with the help of the other coexisting-resistance conjugative plasmid, although it failed to transfer alone. Our findings highlight the flexibly horizontal transfer of ColV plasmids along with multidrug-resistant genes among blaCTX-M-bearing E. coli poses a threat to poultry health and food safety, which contributes to elucidate the concept of "One Health" and deserves particular concern.}, }
@article {pmid38536216, year = {2024}, author = {Dechêne-Tempier, M and de Boisséson, C and Lucas, P and Bougeard, S and Libante, V and Marois-Créhan, C and Payot, S}, title = {Virulence genes, resistome and mobilome of Streptococcus suis strains isolated in France.}, journal = {Microbial genomics}, volume = {10}, number = {3}, pages = {}, pmid = {38536216}, issn = {2057-5858}, mesh = {Humans ; Animals ; Swine ; *Streptococcus suis ; Virulence ; France ; Virulence Factors ; DNA ; }, abstract = {Streptococcus suis is a leading cause of infection in pigs, causing extensive economic losses. In addition, it can also infect wild fauna, and can be responsible for severe infections in humans. Increasing antimicrobial resistance (AMR) has been described in S. suis worldwide and most of the AMR genes are carried by mobile genetic elements (MGEs). This contributes to their dissemination by horizontal gene transfer. A collection of 102 strains isolated from humans, pigs and wild boars in France was subjected to whole genome sequencing in order to: (i) study their genetic diversity, (ii) evaluate their content in virulence-associated genes, (iii) decipher the mechanisms responsible for their AMR and their association with MGEs, and (iv) study their ability to acquire extracellular DNA by natural transformation. Analysis by hierarchical clustering on principal components identified a few virulence-associated factors that distinguish invasive CC1 strains from the other strains. A plethora of AMR genes (n=217) was found in the genomes. Apart from the frequently reported erm(B) and tet(O) genes, more recently described AMR genes were identified [vga(F)/sprA, vat(D)]. Modifications in PBPs/MraY and GyrA/ParC were detected in the penicillin- and fluoroquinolone-resistant isolates respectively. New AMR gene-MGE associations were detected. The majority of the strains have the full set of genes required for competence, i.e for the acquisition of extracellular DNA (that could carry AMR genes) by natural transformation. Hence the risk of dissemination of these AMR genes should not be neglected.}, }
@article {pmid38534711, year = {2024}, author = {Li, Q and Li, J and He, T and Ji, X and Wei, R and Yu, M and Wang, R}, title = {Sub-MIC Antibiotics Modulate Productions of Outer Membrane Vesicles in Tigecycline-Resistant Escherichia coli.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {3}, pages = {}, pmid = {38534711}, issn = {2079-6382}, support = {32102728//National Natural Science Foundation of China/ ; ZX(21)1224//Exploration and Disruptive Innovation Projects of Jiangsu Academy of Agricultural Sciences/ ; GJFP20230305//National Agricultural Product Quality and Safety Risk Assessment/ ; }, abstract = {Antimicrobial resistance (AMR) has been recognized as one of the most important crises affecting global human health in the 21st century. Tigecycline is one of the last resort antibiotics for treating severe infections caused by multi-drug resistant Enterobacteriaceae. However, the mobile resistance gene tet(X4), which could mediate high-level tigecycline resistance, was discovered in 2019. The outer membrane vesicle (OMV) has been recognized as a new route for horizontal gene transfer; antimicrobial resistant bacteria also have the ability to secret OMVs, while little is known about the impact of antibiotics on the secretion and characteristics of OMVs from tigecycline resistant bacteria till now. This study aimed to investigate the effects of antibiotics on the production and traits of a tigecycline resistant Escherichia coli strain of 47EC. The results showed that sub-inhibitory (1/2 MIC or 1/4 MIC) concentrations of gentamicin, meropenem, ceftazidime, chloramphenicol, tigecycline, ciprofloxacin, polymycin, rifaximin and mitomycin C could significantly increase the secretion of OMVs (0.713 ± 0.05~6.333 ± 0.15 mg/mL) from E. coli 47EC compared to the respective untreated control (0.709 ± 0.03 mg/mL). In addition, the particle sizes of OMVs were generally larger, and the zeta potential were lower in the antibiotics-treated groups than those of the antibiotic-free group. The copy numbers of the tigecycline resistance gene of tet(X4) in the OMVs of most antimicrobial-treated groups were higher than that of the control group. Moreover, transcriptome analysis on ciprofloxacin-treated E. coli 47EC indicated that the SOS response and prophage activation might participate in the ciprofloxacin-induced OMV formation. In conclusion, the clinical application of antibiotics in treating bacterial infections, especially multi-drug resistant bacteria, might lead to the increased secretion of bacterial OMVs and the enrichment of antimicrobial-resistant genes in the OMVs.}, }
@article {pmid38534448, year = {2024}, author = {Duwor, S and Brites, D and Mäser, P}, title = {Phylogenetic Analysis of Pyruvate-Ferredoxin Oxidoreductase, a Redox Enzyme Involved in the Pharmacological Activation of Nitro-Based Prodrugs in Bacteria and Protozoa.}, journal = {Biology}, volume = {13}, number = {3}, pages = {}, pmid = {38534448}, issn = {2079-7737}, abstract = {The present frontrunners in the chemotherapy of infections caused by protozoa are nitro-based prodrugs that are selectively activated by PFOR-mediated redox reactions. This study seeks to analyze the distribution of PFOR in selected protozoa and bacteria by applying comparative genomics to test the hypothesis that PFOR in eukaryotes was acquired through horizontal gene transfer (HGT) from bacteria. Furthermore, to identify other putatively acquired genes, proteome-wide and gene enrichment analyses were used. A plausible explanation for the patchy occurrence of PFOR in protozoa is based on the hypothesis that bacteria are potential sources of genes that enhance the adaptation of protozoa in hostile environments. Comparative genomics of Entamoeba histolytica and the putative gene donor, Desulfovibrio vulgaris, identified eleven candidate genes for HGT involved in intermediary metabolism. If these results can be reproduced in other PFOR-possessing protozoa, it would provide more validated evidence to support the horizontal transfer of pfor from bacteria.}, }
@article {pmid38533399, year = {2024}, author = {Peng, D and Wang, Z and Tian, J and Wang, W and Guo, S and Dai, X and Yin, H and Li, L}, title = {Phyllosphere bacterial community dynamics in response to bacterial wildfire disease: succession and interaction patterns.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1331443}, pmid = {38533399}, issn = {1664-462X}, abstract = {Plants interact with complex microbial communities in which microorganisms play different roles in plant development and health. While certain microorganisms may cause disease, others promote nutrient uptake and resistance to stresses through a variety of mechanisms. Developing plant protection measures requires a deeper comprehension of the factors that influence multitrophic interactions and the organization of phyllospheric communities. High-throughput sequencing was used in this work to investigate the effects of climate variables and bacterial wildfire disease on the bacterial community's composition and assembly in the phyllosphere of tobacco (Nicotiana tabacum L.). The samples from June (M1), July (M2), August (M3), and September (M4) formed statistically separate clusters. The assembly of the whole bacterial population was mostly influenced by stochastic processes. PICRUSt2 predictions revealed genes enriched in the M3, a period when the plant wildfire disease index reached climax, were associated with the development of the wildfire disease (secretion of virulence factor), the enhanced metabolic capacity and environmental adaption. The M3 and M4 microbial communities have more intricate molecular ecological networks (MENs), bursting with interconnections within a densely networked bacterial population. The relative abundances of plant-beneficial and antagonistic microbes Clostridiales, Bacillales, Lactobacillales, and Sphingobacteriales, showed significant decrease in severally diseased sample (M3) compared to the pre-diseased samples (M1/M2). Following the results of MENs, we further test if the correlating bacterial pairs within the MEN have the possibility to share functional genes and we have unraveled 139 entries of such horizontal gene transfer (HGT) events, highlighting the significance of HGT in shaping the adaptive traits of plant-associated bacteria across the MENs, particularly in relation to host colonization and pathogenicity.}, }
@article {pmid38530969, year = {2024}, author = {Nasser, F and Gaudreau, A and Lubega, S and Zaker, A and Xia, X and Mer, AS and D'Costa, VM}, title = {Characterization of the diversity of type IV secretion system-encoding plasmids in Acinetobacter.}, journal = {Emerging microbes &amp; infections}, volume = {13}, number = {1}, pages = {2320929}, pmid = {38530969}, issn = {2222-1751}, mesh = {Humans ; *Type IV Secretion Systems ; Escherichia coli/genetics ; Plasmids ; Anti-Bacterial Agents/pharmacology ; *Acinetobacter baumannii ; beta-Lactamases/genetics ; Microbial Sensitivity Tests ; Drug Resistance, Multiple, Bacterial/genetics ; }, abstract = {The multi-drug resistant pathogen Acinetobacter baumannii has gained global attention as an important clinical challenge. Owing to its ability to survive on surfaces, its capacity for horizontal gene transfer, and its resistance to front-line antibiotics, A. baumannii has established itself as a successful pathogen. Bacterial conjugation is a central mechanism for pathogen evolution. The epidemic multidrug-resistant A. baumannii ACICU harbours a plasmid encoding a Type IV Secretion System (T4SS) with homology to the E. coli F-plasmid, and plasmids with homologous gene clusters have been identified in several A. baumannii sequence types. However the genetic and host strain diversity, global distribution, and functional ability of this group of plasmids is not fully understood. Using systematic analysis, we show that pACICU2 belongs to a group of almost 120 T4SS-encoding plasmids within four different species of Acinetobacter and one strain of Klebsiella pneumoniae from human and environmental origin, and globally distributed across 20 countries spanning 4 continents. Genetic diversity was observed both outside and within the T4SS-encoding cluster, and 47% of plasmids harboured resistance determinants, with two plasmids harbouring eleven. Conjugation studies with an extensively drug-resistant (XDR) strain showed that the XDR plasmid could be successfully transferred to a more divergent A. baumanii, and transconjugants exhibited the resistance phenotype of the plasmid. Collectively, this demonstrates that these T4SS-encoding plasmids are globally distributed and more widespread among Acinetobacter than previously thought, and that they represent an important potential reservoir for future clinical concern.}, }
@article {pmid38529905, year = {2024}, author = {Crowley, C and Selvaraj, A and Hariharan, A and Healy, CM and Moran, GP}, title = {Fusobacterium nucleatum subsp. polymorphum recovered from malignant and potentially malignant oral disease exhibit heterogeneity in adhesion phenotypes and adhesin gene copy number, shaped by inter-subspecies horizontal gene transfer and recombination-derived mosaicism.}, journal = {Microbial genomics}, volume = {10}, number = {3}, pages = {}, pmid = {38529905}, issn = {2057-5858}, mesh = {Humans ; *Mosaicism ; Phylogeny ; *Gene Transfer, Horizontal ; Fusobacterium/genetics ; Phenotype ; Gene Dosage ; }, abstract = {Fusobacterium nucleatum is an anaerobic commensal of the oral cavity associated with periodontitis and extra-oral diseases, including colorectal cancer. Previous studies have shown an increased relative abundance of this bacterium associated with oral dysplasia or within oral tumours. Using direct culture, we found that 75 % of Fusobacterium species isolated from malignant or potentially malignant oral mucosa were F. nucleatum subsp. polymorphum. Whole genome sequencing and pangenome analysis with Panaroo was carried out on 76 F. nucleatum subsp. polymorphum genomes. F. nucleatum subsp. polymorphum was shown to possesses a relatively small core genome of 1604 genes in a pangenome of 7363 genes. Phylogenetic analysis based on the core genome shows the isolates can be separated into three main clades with no obvious genotypic associations with disease. Isolates recovered from healthy and diseased sites in the same patient are generally highly related. A large repertoire of adhesins belonging to the type V secretion system (TVSS) could be identified with major variation in repertoire and copy number between strains. Analysis of intergenic recombination using fastGEAR showed that adhesin complement is shaped by horizontal gene transfer and recombination. Recombination events at TVSS adhesin genes were not only common between lineages of subspecies polymorphum, but also between different subspecies of F. nucleatum. Strains of subspecies polymorphum with low copy numbers of TVSS adhesin encoding genes tended to have the weakest adhesion to oral keratinocytes. This study highlights the genetic heterogeneity of F. nucleatum subsp. polymorphum and provides a new framework for defining virulence in this organism.}, }
@article {pmid38527381, year = {2024}, author = {Ferilli, F and Lione, G and Gonthier, P and Turina, M and Forgia, M}, title = {First detection of mycoviruses in Gnomoniopsis castaneae suggests a putative horizontal gene transfer event between negative-sense and double-strand RNA viruses.}, journal = {Virology}, volume = {594}, number = {}, pages = {110057}, doi = {10.1016/j.virol.2024.110057}, pmid = {38527381}, issn = {1096-0341}, mesh = {*Fungal Viruses/genetics ; Double Stranded RNA Viruses/genetics ; Gene Transfer, Horizontal ; Genome, Viral ; Plant Diseases ; Phylogeny ; *RNA Viruses/genetics ; *Viruses/genetics ; RNA, Viral/genetics ; RNA, Double-Stranded/genetics ; *Ascomycota ; }, abstract = {Gnomoniopsis castaneae is an ascomycetous fungus mainly known as a major pathogen of chestnut causing nut rots, although it is often found as an endophyte in chestnut tissues. To date, no virus has been reported as associated with to this fungus. Here, a collection of G. castaneae isolates from several European countries was screened to detect mycoviruses infecting the fungus: for the first time we report the identification and prevalence of mitovirus Gnomoniopsis castaneae mitovirus 1 (GcMV1) and the chrysovirus Gnomoniopsis castaneae chrysovirus 1 (GcCV1). Interestingly, we provide evidence supporting a putative horizontal gene transfer between members of the phyla Negarnaviricota and Duplornaviricota: a small putative protein of unknown function encoded on the RNA3 of GcCV1 (Chrysoviridae) has homologs in the genome of viruses of the family Mymonaviridae.}, }
@article {pmid38521802, year = {2024}, author = {Asad, A and Jahan, I and Munni, MA and Begum, R and Mukta, MA and Saif, K and Faruque, SN and Hayat, S and Islam, Z}, title = {Multidrug-resistant conjugative plasmid carrying mphA confers increased antimicrobial resistance in Shigella.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {6947}, pmid = {38521802}, issn = {2045-2322}, support = {D43 TW010540/TW/FIC NIH HHS/United States ; K43 TW011447/TW/FIC NIH HHS/United States ; K43TW011447/TW/FIC NIH HHS/United States ; NIH FIC TW010540/TW/FIC NIH HHS/United States ; }, mesh = {Child ; Humans ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Dysentery, Bacillary/drug therapy/epidemiology ; Macrolides/pharmacology/therapeutic use ; Drug Resistance, Bacterial/genetics ; *Shigella ; Azithromycin/pharmacology/therapeutic use ; Ciprofloxacin/pharmacology/therapeutic use ; Ceftriaxone/pharmacology ; Microbial Sensitivity Tests ; Protein Synthesis Inhibitors/pharmacology ; Plasmids/genetics ; }, abstract = {Shigellosis remains a common gastrointestinal disease mostly in children < 5 years of age in developing countries. Azithromycin (AZM), a macrolide, is currently the first-line treatment for shigellosis in Bangladesh; ciprofloxacin (CIP) and ceftriaxone (CRO) are also used frequently. We aimed to evaluate the current epidemiology of antimicrobial resistance (AMR) and mechanism(s) of increasing macrolide resistance in Shigella in Bangladesh. A total of 2407 clinical isolates of Shigella from 2009 to 2016 were studied. Over the study period, Shigella sonnei was gradually increasing and become predominant (55%) over Shigella flexneri (36%) by 2016. We used CLSI-guided epidemiological cut-off value (ECV) for AZM in Shigella to set resistance breakpoints (zone-diameter ≤ 15 mm for S. flexneri and ≤ 11 mm for S. sonnei). Between 2009 and 2016, AZM resistance increased from 22% to approximately 60%, CIP resistance increased by 40%, and CRO resistance increased from zero to 15%. The mphA gene was the key macrolide resistance factor in Shigella; a 63MDa conjugative middle-range plasmid was harboring AZM and CRO resistance factors. Our findings show that, especially after 2014, there has been a rapid increase in resistance to the three most effective antibiotics. The rapid spread of macrolide (AZM) resistance genes among Shigella are driven by horizontal gene transfer rather than direct lineage.}, }
@article {pmid38521276, year = {2024}, author = {Liu, Q and Peng, Y and Liao, J and Liu, X and Peng, J and Wang, JH and Shao, Z}, title = {Broad-spectrum hydrocarbon-degrading microbes in the global ocean metagenomes.}, journal = {The Science of the total environment}, volume = {926}, number = {}, pages = {171746}, doi = {10.1016/j.scitotenv.2024.171746}, pmid = {38521276}, issn = {1879-1026}, mesh = {*Metagenome ; Hydrocarbons/metabolism ; Bacteria/genetics/metabolism ; Biodegradation, Environmental ; Oceans and Seas ; *Petroleum/metabolism ; }, abstract = {Understanding the diversity and functions of hydrocarbon-degrading microorganisms in marine environments is crucial for both advancing knowledge of biogeochemical processes and improving bioremediation methods. In this study, we leveraged nearly 20,000 metagenome-assembled genomes (MAGs), recovered from a wide array of marine samples across the global oceans, to map the diversity of aerobic hydrocarbon-degrading microorganisms. A broad bacterial diversity was uncovered, with a notable preference for degrading aliphatic hydrocarbons over aromatic ones, primarily within Proteobacteria and Actinobacteriota. Three types of broad-spectrum hydrocarbon-degrading bacteria were identified for their ability to degrade various hydrocarbons and possession of multiple copies of hydrocarbon biodegradation genes. These bacteria demonstrate extensive metabolic versatility, aiding their survival and adaptability in diverse environmental conditions. Evidence of gene duplication and horizontal gene transfer in these microbes suggested a potential enhancement in the diversity of hydrocarbon-degrading bacteria. Positive correlations were observed between the abundances of hydrocarbon-degrading genes and environmental parameters such as temperature (-5 to 35 °C) and salinity (20 to 42 PSU). Overall, our findings offer valuable insights into marine hydrocarbon-degrading microorganisms and suggest considerations for selecting microbial strains for oil pollution remediation.}, }
@article {pmid38519541, year = {2024}, author = {Baker, BA and Gutiérrez-Preciado, A and Rodríguez Del Río, &#xc1; and McCarthy, CGP and López-García, P and Huerta-Cepas, J and Susko, E and Roger, AJ and Eme, L and Moreira, D}, title = {Expanded phylogeny of extremely halophilic archaea shows multiple independent adaptations to hypersaline environments.}, journal = {Nature microbiology}, volume = {9}, number = {4}, pages = {964-975}, pmid = {38519541}, issn = {2058-5276}, support = {787904//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 803151//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, mesh = {Phylogeny ; *Salinity ; Archaea/genetics ; *Euryarchaeota/genetics ; Metagenome ; }, abstract = {Extremely halophilic archaea (Haloarchaea, Nanohaloarchaeota, Methanonatronarchaeia and Halarchaeoplasmatales) thrive in saturating salt concentrations where they must maintain osmotic equilibrium with their environment. The evolutionary history of adaptations enabling salt tolerance remains poorly understood, in particular because the phylogeny of several lineages is conflicting. Here we present a resolved phylogeny of extremely halophilic archaea obtained using improved taxon sampling and state-of-the-art phylogenetic approaches designed to cope with the strong compositional biases of their proteomes. We describe two uncultured lineages, Afararchaeaceae and Asbonarchaeaceae, which break the long branches at the base of Haloarchaea and Nanohaloarchaeota, respectively. We obtained 13 metagenome-assembled genomes (MAGs) of these archaea from metagenomes of hypersaline aquatic systems of the Danakil Depression (Ethiopia). Our phylogenomic analyses including these taxa show that at least four independent adaptations to extreme halophily occurred during archaeal evolution. Gene-tree/species-tree reconciliation suggests that gene duplication and horizontal gene transfer played an important role in this process, for example, by spreading key genes (such as those encoding potassium transporters) across extremely halophilic lineages.}, }
@article {pmid38518756, year = {2024}, author = {Gàlvez-Morante, A and Guéguen, L and Natsidis, P and Telford, MJ and Richter, DJ}, title = {Dollo Parsimony Overestimates Ancestral Gene Content Reconstructions.}, journal = {Genome biology and evolution}, volume = {16}, number = {4}, pages = {}, pmid = {38518756}, issn = {1759-6653}, support = {/ERC_/European Research Council/International ; 949745/ERC_/European Research Council/International ; }, mesh = {Phylogeny ; Likelihood Functions ; *Evolution, Molecular ; }, abstract = {Ancestral reconstruction is a widely used technique that has been applied to understand the evolutionary history of gain and loss of gene families. Ancestral gene content can be reconstructed via different phylogenetic methods, but many current and previous studies employ Dollo parsimony. We hypothesize that Dollo parsimony is not appropriate for ancestral gene content reconstruction inferences based on sequence homology, as Dollo parsimony is derived from the assumption that a complex character cannot be regained. This premise does not accurately model molecular sequence evolution, in which false orthology can result from sequence convergence or lateral gene transfer. The aim of this study is to test Dollo parsimony's suitability for ancestral gene content reconstruction and to compare its inferences with a maximum likelihood-based approach that allows a gene family to be gained more than once within a tree. We first compared the performance of the two approaches on a series of artificial data sets each of 5,000 genes that were simulated according to a spectrum of evolutionary rates without gene gain or loss, so that inferred deviations from the true gene count would arise only from errors in orthology inference and ancestral reconstruction. Next, we reconstructed protein domain evolution on a phylogeny representing known eukaryotic diversity. We observed that Dollo parsimony produced numerous ancestral gene content overestimations, especially at nodes closer to the root of the tree. These observations led us to the conclusion that, confirming our hypothesis, Dollo parsimony is not an appropriate method for ancestral reconstruction studies based on sequence homology.}, }
@article {pmid38517978, year = {2024}, author = {Sheinman, M and Arndt, PF and Massip, F}, title = {Modeling the mosaic structure of bacterial genomes to infer their evolutionary history.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {13}, pages = {e2313367121}, pmid = {38517978}, issn = {1091-6490}, mesh = {Phylogeny ; *Models, Genetic ; *Genome, Bacterial/genetics ; Genomics/methods ; Bacteria/genetics ; Evolution, Molecular ; }, abstract = {The chronology and phylogeny of bacterial evolution are difficult to reconstruct due to a scarce fossil record. The analysis of bacterial genomes remains challenging because of large sequence divergence, the plasticity of bacterial genomes due to frequent gene loss, horizontal gene transfer, and differences in selective pressure from one locus to another. Therefore, taking advantage of the rich and rapidly accumulating genomic data requires accurate modeling of genome evolution. An important technical consideration is that loci with high effective mutation rates may diverge beyond the detection limit of the alignment algorithms used, biasing the genome-wide divergence estimates toward smaller divergences. In this article, we propose a novel method to gain insight into bacterial evolution based on statistical properties of genome comparisons. We find that the length distribution of sequence matches is shaped by the effective mutation rates of different loci, by the horizontal transfers, and by the aligner sensitivity. Based on these inputs, we build a model and show that it accounts for the empirically observed distributions, taking the Enterobacteriaceae family as an example. Our method allows to distinguish segments of vertical and horizontal origins and to estimate the time divergence and exchange rate between any pair of taxa from genome-wide alignments. Based on the estimated time divergences, we construct a time-calibrated phylogenetic tree to demonstrate the accuracy of the method.}, }
@article {pmid38511257, year = {2025}, author = {Fogg, PCM}, title = {Gene transfer agents: The ambiguous role of selfless viruses in genetic exchange and bacterial evolution.}, journal = {Molecular microbiology}, volume = {123}, number = {2}, pages = {124-131}, pmid = {38511257}, issn = {1365-2958}, support = {/WT_/Wellcome Trust/United Kingdom ; BB/V016288/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 109363/Z/15/A/WT_/Wellcome Trust/United Kingdom ; 109363/Z/15/A//Royal Society/ ; }, mesh = {*Gene Transfer, Horizontal/genetics ; *Bacteriophages/genetics ; *Bacteria/genetics/virology ; Evolution, Molecular ; }, abstract = {Gene transfer agents (GTAs) are genetic elements derived from ancestral bacteriophages that have become domesticated by the host. GTAs are present in diverse prokaryotic organisms, where they can facilitate horizontal gene transfer under certain conditions. Unlike typical bacteriophages, GTAs do not exhibit any preference for the replication or transfer of the genes encoding them; instead, they exhibit a remarkable capacity to package chromosomal, and sometimes extrachromosomal, DNA into virus-like capsids and disseminate it to neighboring cells. Because GTAs resemble defective prophages, identification of novel GTAs is not trivial. The detection of candidates relies on the genetic similarity to known GTAs, which has been fruitful in α-proteobacterial lineages but challenging in more distant bacteria. Here we consider several fundamental questions: What is the true prevalence of GTAs in prokaryote genomes? Given there are high costs for GTA production, what advantage do GTAs provide to the bacterial host to justify their maintenance? How is the bacterial chromosome recognized and processed for inclusion in GTA particles? This article highlights the challenges in comprehensively understanding GTAs' prevalence, function and DNA packaging method. Going forward, broad study of atypical GTAs and use of ecologically relevant conditions are required to uncover their true impact on bacterial chromosome evolution.}, }
@article {pmid38510031, year = {2024}, author = {Liu, X and Zhao, H and Wong, A}, title = {Accounting for the health risk of probiotics.}, journal = {Heliyon}, volume = {10}, number = {6}, pages = {e27908}, pmid = {38510031}, issn = {2405-8440}, abstract = {Probiotics have long been associated with a myriad of health benefits, so much so that their adverse effects whether mild or severe, are often neglected or overshadowed by the enormous volume of articles describing their beneficial effects in the current literature. Recent evidence has demonstrated several health risks of probiotics that warrant serious reconsideration of their applications and further investigations. This review aims to highlight studies that report on how probiotics might cause opportunistic systemic and local infections, detrimental immunological effects, metabolic disturbance, allergic reactions, and facilitating the spread of antimicrobial resistance. To offer a recent account of the literature, articles within the last five years were prioritized. The narration of these evidence was based on the nature of the studies in the following order of preference: clinical studies or human samples, in vivo or animal models, in situ, in vitro and/or in silico. We hope that this review will inform consumers, food scientists, and medical practitioners, on the health risks, while also encouraging research that will focus on and clarify the adverse effects of probiotics.}, }
@article {pmid38508537, year = {2024}, author = {Yang, W and Tang, C and Shen, S and Shi, Q and Hu, F}, title = {Spread and evolution of blaKPC-plasmid between Serratia marcescens and Klebsiella pneumoniae.}, journal = {International journal of antimicrobial agents}, volume = {63}, number = {5}, pages = {107149}, doi = {10.1016/j.ijantimicag.2024.107149}, pmid = {38508537}, issn = {1872-7913}, mesh = {*Serratia marcescens/genetics/drug effects/isolation &amp; purification/enzymology ; *Klebsiella pneumoniae/genetics/drug effects ; Humans ; *Plasmids/genetics ; *Microbial Sensitivity Tests ; *beta-Lactamases/genetics ; *Serratia Infections/microbiology/epidemiology ; *Anti-Bacterial Agents/pharmacology ; *Klebsiella Infections/microbiology/epidemiology ; *Whole Genome Sequencing ; Ceftazidime/pharmacology ; Drug Combinations ; Drug Resistance, Multiple, Bacterial/genetics ; Azabicyclo Compounds/pharmacology ; Sputum/microbiology ; Evolution, Molecular ; Gene Transfer, Horizontal ; Carbapenems/pharmacology ; }, abstract = {OBJECTIVES: blaKPC-carrying Enterobacterales have post great challenges to global healthcare systems. In this study, we reported the evolution and spread of blaKPC between Serratia marcescens and Klebsiella pneumoniae.<br><br>METHODS: Four S. marcescens and one K. pneumoniae strains were isolated from the sputum samples of the patient. Antimicrobial susceptibility tests and whole genome sequencing were performed to investigate the phenotype &amp; genotype of strains. Conjugation assays, cloning experiment and kinetic parameters measuring were performed to explore the spread and antimicrobial resistance mechanisms.<br><br>RESULTS: The evolution and transmission of blaKPC-2 occurred during the treatment of ceftazidime-avibactam and trimethoprim-sulfamethoxazole. Analysis of the antimicrobial susceptibility and genetic profiles of the clinical strains showed that blaKPC-2 evolved into blaKPC-71 and blaKPC-44, together with resistance to ceftazidime-avibactam and carbapenems susceptibility recovery under antimicrobial pressure. Cloning and expression of blaKPC-44 &amp; blaKPC-71 in E. coli DH5&#x3b1; showed that KPC-44 and KPC-71 resulted in a 64&#x223c;128-fold increase in the MIC value for ceftazidime-avibactam. Meanwhile, the kinetic assays also showed that the enzyme activity of KPC-44 and KPC-71 towards carbapenems was destroyed and couldn't be inhibited by avibactam. Based on the conjugation assay and whole genome sequence analyses, we provided evolutionary insights into the transmission pathway trace of blaKPC-bearing plasmids between S. marcescens and K. pneumoniae.<br><br>CONCLUSIONS: Mixed-species co-infection is one of the risk factors leading to the spread of plasmids carrying carbapenem-resistant genes, and increased surveillance of multidrug-resistant Enterobacterales is urgently needed.}, }
@article {pmid38507447, year = {2024}, author = {Kehlet-Delgado, H and Montoya, AP and Jensen, KT and Wendlandt, CE and Dexheimer, C and Roberts, M and Torres Martínez, L and Friesen, ML and Griffitts, JS and Porter, SS}, title = {The evolutionary genomics of adaptation to stress in wild rhizobium bacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {13}, pages = {e2311127121}, pmid = {38507447}, issn = {1091-6490}, support = {IOS-1755454//National Science Foundation (NSF)/ ; DEB-1943239//National Science Foundation (NSF)/ ; }, mesh = {Humans ; *Rhizobium/genetics ; Nickel ; *Metals, Heavy/toxicity ; Genomics ; Soil ; }, abstract = {Microbiota comprise the bulk of life's diversity, yet we know little about how populations of microbes accumulate adaptive diversity across natural landscapes. Adaptation to stressful soil conditions in plants provides seminal examples of adaptation in response to natural selection via allelic substitution. For microbes symbiotic with plants however, horizontal gene transfer allows for adaptation via gene gain and loss, which could generate fundamentally different evolutionary dynamics. We use comparative genomics and genetics to elucidate the evolutionary mechanisms of adaptation to physiologically stressful serpentine soils in rhizobial bacteria in western North American grasslands. In vitro experiments demonstrate that the presence of a locus of major effect, the nre operon, is necessary and sufficient to confer adaptation to nickel, a heavy metal enriched to toxic levels in serpentine soil, and a major axis of environmental soil chemistry variation. We find discordance between inferred evolutionary histories of the core genome and nreAXY genes, which often reside in putative genomic islands. This suggests that the evolutionary history of this adaptive variant is marked by frequent losses, and/or gains via horizontal acquisition across divergent rhizobium clades. However, different nre alleles confer distinct levels of nickel resistance, suggesting allelic substitution could also play a role in rhizobium adaptation to serpentine soil. These results illustrate that the interplay between evolution via gene gain and loss and evolution via allelic substitution may underlie adaptation in wild soil microbiota. Both processes are important to consider for understanding adaptive diversity in microbes and improving stress-adapted microbial inocula for human use.}, }
@article {pmid38506281, year = {2024}, author = {Adeyelu, OO and Essien, EN and Adebote, V and Ajayi, A and Essiet, UU and Adeleye, AI and Smith, SI}, title = {Antimicrobial resistance genetic determinants and susceptibility profile of Pseudomonas aeruginosa isolated from clinical samples in a tertiary hospital in Ogun State, Nigeria.}, journal = {Transactions of the Royal Society of Tropical Medicine and Hygiene}, volume = {118}, number = {7}, pages = {474-476}, doi = {10.1093/trstmh/trae012}, pmid = {38506281}, issn = {1878-3503}, mesh = {*Pseudomonas aeruginosa/genetics/drug effects/isolation &amp; purification ; Humans ; *Pseudomonas Infections/microbiology/epidemiology ; *Microbial Sensitivity Tests ; *Tertiary Care Centers ; *Anti-Bacterial Agents/pharmacology ; *beta-Lactamases/genetics ; Nigeria/epidemiology ; *Plasmids/genetics ; Female ; Integrons/genetics ; Male ; Adult ; Drug Resistance, Multiple, Bacterial/genetics ; Middle Aged ; beta-Lactams/pharmacology ; Drug Resistance, Bacterial/genetics ; }, abstract = {BACKGROUND: Genetic determinants are known to promote antibiotic resistance through horizontal gene transfer.<br><br>METHODS: We molecularly characterized integrons, plasmid replicon types and metallo-&#x3b2;-lactamase-encoding genes of 38 Pseudomonas aeruginosa strains isolated from clinical samples.<br><br>RESULTS: The P. aeruginosa isolates displayed high resistance (97.4%) to &#x3b2;-lactams. Seventeen (44.74%) of them possessed plasmids. Of the 17 isolates that possessed plasmids, 11 (64.7%) of them harboured IncFIA plasmid replicon type, while 6 (35.3%), 5 (29.4%) and 5 (29.4%) were of the IncFIB, IncF and IncW types, respectively. The intI1 gene was detected in 19 (50%) of the isolates. The blaNDM-A, blaNDM-B and blaVIM genes were detected in 14 (35.9%), 4 (10.3%) and 5 (12.8%) of the isolates, respectively.<br><br>CONCLUSIONS: High resistance to &#x3b2;-lactams was observed among P. aeruginosa strains of clinical origin in this study. They possessed transmissible genetic elements indicating the potential for continuous dissemination, thus continuous surveillance is advocated.}, }
@article {pmid38504610, year = {2024}, author = {Tekle, YI and Tefera, H}, title = {A Small Genome amidst the Giants: Evidence of Genome Reduction in a Small Tubulinid Free-Living Amoeba.}, journal = {Genome biology and evolution}, volume = {16}, number = {3}, pages = {}, pmid = {38504610}, issn = {1759-6653}, support = {R15 GM116103/GM/NIGMS NIH HHS/United States ; 1R15GM116103-02/NH/NIH HHS/United States ; }, mesh = {*Amoeba/genetics ; Phylogeny ; Genome ; *Amoebozoa/genetics ; Genomics ; }, abstract = {This study investigates the genomic characteristics of Echinamoeba silvestris, a small-sized amoeba within the Tubulinea clade of the Amoebozoa supergroup. Despite Tubulinea's significance in various fields, genomic data for this clade have been scarce. E. silvestris presents the smallest free-living amoeba genome within Tubulinea and Amoebozoa to date. Comparative analysis reveals intriguing parallels with parasitic lineages in terms of genome size and predicted gene numbers, emphasizing the need to understand the consequences of reduced genomes in free-living amoebae. Functional categorization of predicted genes in E. silvestris shows similar percentages of ortholog groups to other amoebae in various categories, but a distinctive feature is the extensive gene contraction in orphan (ORFan) genes and those involved in biological processes. Notably, among the few genes that underwent expansion, none are related to cellular components, suggesting adaptive processes that streamline biological processes and cellular components for efficiency and energy conservation. Additionally, our investigation into noncoding and repetitive elements sheds light on the evolution of genome size in amoebae, with E. silvestris distinguished by low percentage of repetitive elements. Furthermore, the analysis reveals that E. silvestris has the lowest mean number of introns per gene among the species studied, providing further support for its observed compact genome. Overall, this research underscores the diversity within Tubulinea, highlights knowledge gaps in Amoebozoa genomics, and positions E. silvestris as a valuable addition to genomic data sets, prompting further exploration of complexities in Amoebozoa diversity and genome evolution.}, }
@article {pmid38498548, year = {2024}, author = {Bernabeu, M and Manzano-Morales, S and Gabaldón, T}, title = {On the impact of incomplete taxon sampling on the relative timing of gene transfer events.}, journal = {PLoS biology}, volume = {22}, number = {3}, pages = {e3002460}, pmid = {38498548}, issn = {1545-7885}, mesh = {Phylogeny ; *Gene Flow ; *Biological Evolution ; Gene Transfer, Horizontal ; }, abstract = {A recent study questioned the use of branch length methods to assess the relative timing of horizontal gene transfers because of the effects of so-called "ghost" lineages. This Formal Comment discusses key considerations regarding the potential effect of missing lineages when assessing relative timing of evolutionary events.}, }
@article {pmid38497713, year = {2024}, author = {Tang, X-F and Sun, Y-F and Liang, Y-S and Yang, K-Y and Chen, P-T and Li, H-S and Huang, Y-H and Pang, H}, title = {Metabolism, digestion, and horizontal transfer: potential roles and interaction of symbiotic bacteria in the ladybird beetle Novius pumilus and their prey Icerya aegyptiaca.}, journal = {Microbiology spectrum}, volume = {12}, number = {5}, pages = {e0295523}, pmid = {38497713}, issn = {2165-0497}, support = {2023YFD1400600//National Key Research and Development Program of China/ ; 32172472//National Natural Science Foundation of China/ ; 31970439//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Coleoptera/microbiology ; *Symbiosis ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Gene Transfer, Horizontal ; Phylogeny ; Female ; Microbiota ; }, abstract = {In this study, we first time sequenced and analyzed the 16S rRNA gene data of predator ladybird beetles Novius pumilus and globally distributed invasive pest Icerya aegyptiaca at different stages, and combined data with bacterial genome sequences in N. pumilus to explored the taxonomic distribution, alpha and beta diversity, differentially abundant bacteria, co-occurrence network, and putative functions of their microbial community. Our finding revealed that Candidatus Walczuchella, which exhibited a higher abundance in I. aegyptiaca, possessed several genes in essential amino acid biosynthesis and seemed to perform roles in providing nutrients to the host, similar to other obligate symbionts in scale insects. Lactococcus, Serratia, and Pseudomonas, more abundant in N. pumilus, were predicted to have genes related to hydrocarbon, fatty acids, and chitin degradation, which may assist their hosts in digesting the wax shell covering the scale insects. Notably, our result showed that Lactococcus had relatively higher abundances in adults and eggs compared to other stages in N. pumilus, indicating potential vertical transmission. Additionally, we found that Arsenophonus, known to influence sex ratios in whitefly and wasp, may also function in I. aegyptiaca, probably by influencing nutrient metabolism as it similarly had many genes corresponding to vitamin B and essential amino acid biosynthesis. Also, we observed a potential horizontal transfer of Arsenophonus between the scale insect and its predator, with a relatively high abundance in the ladybirds compared to other bacteria from the scale insects.IMPORTANCEThe composition and dynamic changes of microbiome in different developmental stages of ladybird beetles Novius pumilus with its prey Icerya aegyptiaca were detected. We found that Candidatus Walczuchella, abundant in I. aegyptiaca, probably provide nutrients to their host based on their amino acid biosynthesis-related genes. Abundant symbionts in N. pumilus, including Lactococcus, Serratia, and Pseudophonus, may help the host digest the scale insects with their hydrocarbon, fatty acid, and chitin degrading-related genes. A key endosymbiont Arsenophonus may play potential roles in the nutrient metabolisms and sex determination in I. aegyptiaca, and is possibly transferred from the scale insect to the predator.}, }
@article {pmid38497640, year = {2024}, author = {Wang, P and Du, X and Zhao, Y and Wang, W and Cai, T and Tang, K and Wang, X}, title = {Combining CRISPR/Cas9 and natural excision for the precise and complete removal of mobile genetic elements in bacteria.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {4}, pages = {e0009524}, pmid = {38497640}, issn = {1098-5336}, support = {32070175//MOST | National Natural Science Foundation of China (NSFC)/ ; 42188102//MOST | National Natural Science Foundation of China (NSFC)/ ; 91951203//MOST | National Natural Science Foundation of China (NSFC)/ ; 2022YFC3103600//MOST | National Key Research and Development Program of China (NKPs)/ ; 2019BT02Y262//Local Innovative and Research Teams Project of Guangdong Pearl River Talents Program/ ; 2021345//Youth Innovation Promotion Association of the Chinese Academy of Sciences (CAS YIPA)/ ; }, mesh = {*CRISPR-Cas Systems ; *RNA, Guide, CRISPR-Cas Systems ; Bacteria/genetics ; Genomic Islands ; Gene Transfer, Horizontal ; Plasmids/genetics ; Interspersed Repetitive Sequences ; }, abstract = {Horizontal gene transfer, facilitated by mobile genetic elements (MGEs), is an adaptive evolutionary process that contributes to the evolution of bacterial populations and infectious diseases. A variety of MGEs not only can integrate into the bacterial genome but also can survive or even replicate like plasmids in the cytoplasm, thus requiring precise and complete removal for studying their strategies in benefiting host cells. Existing methods for MGE removal, such as homologous recombination-based deletion and excisionase-based methods, have limitations in effectively eliminating certain MGEs. To overcome these limitations, we developed the Cas9-NE method, which combines the CRISPR/Cas9 system with the natural excision of MGEs. In this approach, a specialized single guide RNA (sgRNA) element is designed with a 20-nucleotide region that pairs with the MGE sequence. This sgRNA is expressed from a plasmid that also carries the Cas9 gene. By utilizing the Cas9-NE method, both the integrative and circular forms of MGEs can be precisely and completely eliminated through Cas9 cleavage, generating MGE-removed cells. We have successfully applied the Cas9-NE method to remove four representative MGEs, including plasmids, prophages, and genomic islands, from Vibrio strains. This new approach not only enables various investigations on MGEs but also has significant implications for the rapid generation of strains for commercial purposes.IMPORTANCEMobile genetic elements (MGEs) are of utmost importance for bacterial adaptation and pathogenicity, existing in various forms and multiple copies within bacterial cells. Integrated MGEs play dual roles in bacterial hosts, enhancing the fitness of the host by delivering cargo genes and potentially modifying the bacterial genome through the integration/excision process. This process can lead to alterations in promoters or coding sequences or even gene disruptions at integration sites, influencing the physiological functions of host bacteria. Here, we developed a new approach called Cas9-NE, allowing them to maintain the natural sequence changes associated with MGE excision. Cas9-NE allows the one-step removal of integrated and circular MGEs, addressing the challenge of eliminating various MGE forms efficiently. This approach simplifies MGE elimination in bacteria, expediting research on MGEs.}, }
@article {pmid38494146, year = {2024}, author = {Xu, H and Tan, C and Li, C and Li, J and Han, Y and Tang, Y and Lei, C and Wang, H}, title = {ESBL-Escherichia coli extracellular vesicles mediate bacterial resistance to β-lactam and mediate horizontal transfer of blaCTX-M-55.}, journal = {International journal of antimicrobial agents}, volume = {63}, number = {5}, pages = {107145}, doi = {10.1016/j.ijantimicag.2024.107145}, pmid = {38494146}, issn = {1872-7913}, mesh = {*Escherichia coli/drug effects/genetics ; *Extracellular Vesicles/metabolism ; *Gene Transfer, Horizontal ; *beta-Lactamases/genetics/metabolism ; *beta-Lactams/pharmacology ; *beta-Lactam Resistance/genetics ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; Escherichia coli Infections/microbiology ; Animals ; }, abstract = {OBJECTIVES: Extracellular vesicles (EVs) have become the focus of research as an emerging method of horizontal gene transfer. In recent years, studies on the association between EVs and the spread of bacterial resistance have emerged, but there is a lack of research on the role of EVs secreted by extended-spectrum β-lactamase (ESBL)-producing Escherichia coli in the spread of β-lactam resistance. Therefore, the aim of this study was to investigate the role of EVs in the transmission of β-lactam resistance.<br><br>METHODS: In this study, the role of EVs in the transmission of &#x3b2;-lactam resistance in E. coli was evaluated by the EVs-mediated bacterial resistance to &#x3b2;-lactam antibiotics test and the EVs-mediated blaCTX-M-55 transfer experiments using EVs secreted by ESBL-E. coli.<br><br>RESULTS: The results showed that ESBL-EVs were protective against &#x3b2;-lactam antibiotic-susceptible bacteria, and this protective effect was dependent on the integrity of the EVs and showed dose- and time-dependent effects. At the same time, ESBL-EVs can also mediate the horizontal transmission of blaCTX-M-55, and EVs-mediated gene transfer is selective, preferring to transfer in more closely related species.<br><br>CONCLUSIONS: In this study, we demonstrated the important role of EVs in the transmission of &#x3b2;-lactam resistance in chicken ESBL-E. coli, and evaluated the risk of EVs-mediated horizontal gene transfer, which provided a theoretical basis for elucidating the mechanism of EVs-mediated resistance transmission.}, }
@article {pmid38493856, year = {2024}, author = {You, Z and Wang, C and Yang, X and Liu, Z and Guan, Y and Mu, J and Shi, H and Zhao, Z}, title = {Effects of eutrophication on the horizontal transfer of antibiotic resistance genes in microalgal-bacterial symbiotic systems.}, journal = {Environmental research}, volume = {251}, number = {Pt 2}, pages = {118692}, doi = {10.1016/j.envres.2024.118692}, pmid = {38493856}, issn = {1096-0953}, mesh = {*Gene Transfer, Horizontal ; *Microalgae/genetics/drug effects ; *Eutrophication ; *Symbiosis ; *Bacteria/genetics/drug effects ; *Drug Resistance, Microbial/genetics ; Chlorella/genetics/drug effects ; Nitrogen ; }, abstract = {Overloading of nutrients such as nitrogen causes eutrophication of freshwater bodies. The spread of antibiotic resistance genes (ARGs) poses a threat to ecosystems. However, studies on the enrichment and spread of ARGs from increased nitrogen loading in algal-bacterial symbiotic systems are limited. In this study, the transfer of extracellular kanamycin resistance (KR) genes from large (RP4) small (pEASY-T1) plasmids into the intracellular and extracellular DNA (iDNA, eDNA) of the inter-algal environment of Chlorella pyrenoidosa was investigated, along with the community structure of free-living (FL) and particle-attached (PA) bacteria under different nitrogen source concentrations (0-2.5 g/L KNO3). The results showed that KR gene abundance in the eDNA adsorbed on solid particles (D-eDNA) increased initially and then decreased with increasing nitrogen concentration, while the opposite was true for the rest of the free eDNA (E-eDNA). Medium nitrogen concentrations promoted the transfer of extracellular KR genes into the iDNA attached to algal microorganisms (A-iDNA), eDNA attached to algae (B-eDNA), and the iDNA of free microorganisms (C-iDNA); high nitrogen contributed to the transfer of KR genes into C-iDNA. The highest percentage of KR genes was found in B-eDNA with RP4 plasmid treatment (66.2%) and in C-iDNA with pEASY-T1 plasmid treatment (86.88%). In addition, dissolved oxygen (DO) significantly affected the bacterial PA and FL community compositions. Nephelometric turbidity units (NTU) reflected the abundance of ARGs in algae. Proteobacteria, Cyanobacteria, Bacteroidota, and Actinobacteriota were the main potential hosts of ARGs. These findings provide new insights into the distribution and dispersal of ARGs in the phytoplankton inter-algal environment.}, }
@article {pmid38486809, year = {2024}, author = {Novikova, PV and Bhanu Busi, S and Probst, AJ and May, P and Wilmes, P}, title = {Functional prediction of proteins from the human gut archaeome.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycad014}, pmid = {38486809}, issn = {2730-6151}, abstract = {The human gastrointestinal tract contains diverse microbial communities, including archaea. Among them, Methanobrevibacter smithii represents a highly active and clinically relevant methanogenic archaeon, being involved in gastrointestinal disorders, such as inflammatory bowel disease and obesity. Herein, we present an integrated approach using sequence and structure information to improve the annotation of M. smithii proteins using advanced protein structure prediction and annotation tools, such as AlphaFold2, trRosetta, ProFunc, and DeepFri. Of an initial set of 873 481 archaeal proteins, we found 707 754 proteins exclusively present in the human gut. Having analysed archaeal proteins together with 87 282 994 bacterial proteins, we identified unique archaeal proteins and archaeal-bacterial homologs. We then predicted and characterized functional domains and structures of 73 unique and homologous archaeal protein clusters linked the human gut and M. smithii. We refined annotations based on the predicted structures, extending existing sequence similarity-based annotations. We identified gut-specific archaeal proteins that may be involved in defense mechanisms, virulence, adhesion, and the degradation of toxic substances. Interestingly, we identified potential glycosyltransferases that could be associated with N-linked and O-glycosylation. Additionally, we found preliminary evidence for interdomain horizontal gene transfer between Clostridia species and M. smithii, which includes sporulation Stage V proteins AE and AD. Our study broadens the understanding of archaeal biology, particularly M. smithii, and highlights the importance of considering both sequence and structure for the prediction of protein function.}, }
@article {pmid38485028, year = {2024}, author = {Liu, H and Zhang, Z and Li, X and Zhou, T and Wang, Z and Li, J and Li, Y and Wang, Q}, title = {Temperature-phased anaerobic sludge digestion effectively removes antibiotic resistance genes in a full-scale wastewater treatment plant.}, journal = {The Science of the total environment}, volume = {924}, number = {}, pages = {171555}, doi = {10.1016/j.scitotenv.2024.171555}, pmid = {38485028}, issn = {1879-1026}, mesh = {*Sewage/microbiology ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Anaerobiosis ; Temperature ; Drug Resistance, Microbial/genetics ; *Water Purification ; Digestion ; }, abstract = {Sludge is a major by-product and the final reservoir of antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs). Temperature-phased anaerobic digestion (TPAD), consisting of thermophilic anaerobic digestion (AD) (55 °C) and mesophilic AD processes (37 °C), has been implemented in WWTPs for sludge reduction while improving the biomethane production. However, the impact of TPAD on the ARGs' fate is still undiscovered in lab-scale experiments and full-scale WWTPs. This study, for the first time, investigated the fate of ARGs during the TPAD process across three seasons in a full-size WWTP. Ten typical ARGs and one integrase gene of class 1 integron (intI1) involving ARGs horizontal gene transfer were examined in sludge before and after each step of the TPAD process. TPAD reduced aac(6')-Ib-cr, blaTEM, drfA1, sul1, sul2, ermb, mefA, tetA, tetB and tetX by 87.3-100.0 %. TPAD reduced the overall average absolute abundance of targeted ARGs and intI1 by 92.39 % and 92.50 %, respectively. The abundance of targeted ARGs in sludge was higher in winter than in summer and autumn before and after TPAD. During the TPAD processes, thermophilic AD played a major role in the removal of ARGs, contributing to >60 % removal of ARGs, while the subsequent mesophilic AD contributed to a further 31 % removal of ARGs. The microbial community analysis revealed that thermophilic AD reduced the absolute abundance of ARGs hosts, antibiotic resistant bacteria. In addition, thermophilic AD reduced the abundance of the intI1, while the intI1 did not reproduce during the mesophilic AD, also contributing to a decline in the absolute abundance of ARGs in TPAD. This study demonstrates that TPAD can effectively reduce the abundance of ARGs in sludge, which will suppress the transmission of ARGs from sludge into the natural environment and deliver environmental and health benefits to our society.}, }
@article {pmid38478693, year = {2024}, author = {Keith, M and Park de la Torriente, A and Chalka, A and Vallejo-Trujillo, A and McAteer, SP and Paterson, GK and Low, AS and Gally, DL}, title = {Predictive phage therapy for Escherichia coli urinary tract infections: Cocktail selection for therapy based on machine learning models.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {12}, pages = {e2313574121}, pmid = {38478693}, issn = {1091-6490}, support = {BBS/E/D/20002173//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, mesh = {Humans ; Animals ; Escherichia coli/genetics ; *Phage Therapy ; *Escherichia coli Infections/microbiology ; *Bacteriophages/genetics ; Anti-Bacterial Agents/pharmacology ; *Urinary Tract Infections/drug therapy ; }, abstract = {This study supports the development of predictive bacteriophage (phage) therapy: the concept of phage cocktail selection to treat a bacterial infection based on machine learning (ML) models. For this purpose, ML models were trained on thousands of measured interactions between a panel of phage and sequenced bacterial isolates. The concept was applied to Escherichia coli associated with urinary tract infections. This is an important common infection in humans and companion animals from which multidrug-resistant (MDR) bloodstream infections can originate. The global threat of MDR infection has reinvigorated international efforts into alternatives to antibiotics including phage therapy. E. coli exhibit extensive genome-level variation due to horizontal gene transfer via phage and plasmids. Associated with this, phage selection for E. coli is difficult as individual isolates can exhibit considerable variation in phage susceptibility due to differences in factors important to phage infection including phage receptor profiles and resistance mechanisms. The activity of 31 phage was measured on 314 isolates with growth curves in artificial urine. Random Forest models were built for each phage from bacterial genome features, and the more generalist phage, acting on over 20% of the bacterial population, exhibited F1 scores of >0.6 and could be used to predict phage cocktails effective against previously untested strains. The study demonstrates the potential of predictive ML models which integrate bacterial genomics with phage activity datasets allowing their use on data derived from direct sequencing of clinical samples to inform rapid and effective phage therapy.}, }
@article {pmid38477539, year = {2024}, author = {Shang, Y and Zhang, Y and Wang, R and Peng, Y and Ding, B and Liu, Y and Li, C and Feng, L and Liu, H and Yang, C and Tang, Y}, title = {Deciphering the molecular and functional basis of TMexCD1: the plasmid-encoded efflux pump of resistance-nodulation-division superfamily.}, journal = {Antimicrobial agents and chemotherapy}, volume = {68}, number = {4}, pages = {e0167823}, pmid = {38477539}, issn = {1098-6596}, support = {2021YFC2101500//National Key Research and Development Program of China/ ; 42077214//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Animals ; *Escherichia coli/genetics/metabolism ; *Escherichia coli Proteins/metabolism ; Anti-Bacterial Agents/chemistry ; Molecular Docking Simulation ; Drug Resistance, Multiple, Bacterial/genetics ; Multidrug Resistance-Associated Proteins/genetics ; Microbial Sensitivity Tests ; }, abstract = {Horizontal gene transfer has been demonstrated to be an important driver for the emergency of multidrug-resistant pathogens. Recently, a transferable gene cluster tmexCD1-toprJ1 of the resistance-nodulation-division (RND) superfamily was identified in the plasmids of animal-derived Klebsiella pneumoniae strains, with a higher efflux capacity for various drugs than the Escherichia coli AcrAB-TolC homolog system. In this study, we focused on the differences in the inner membrane pump of these two systems and identified some key residues that contribute to the robust efflux activity of the TMexCD1 system. With the aid of homologous modeling and molecular docking, eight residues from the proximal binding pocket (PBP) and nine from the distal binding pocket (DBP) were selected and subjected to site-directed mutagenesis. Several of them, such as S134, I139, D181, and A290, were shown to be important for substrate binding in the DBP region, and all residues in PBP and DBP showed certain substrate preferences. Apart from the conservative switch loop (L613-623[TMexD1]) previously identified in the E. coli AcrB (EcAcrB), a relatively unconservative loop (L665-675[TMexD1]) at the bottom of PBP was proposed as a critical element for the robust activity of TMexD1, due to variations at sites E669, G670, N673, and S674 compared to EcAcrAB, and the significantly altered efflux activity due to their mutations. The conservation and flexibility of these key factors can contribute to the evolution of the RND efflux pumps and thus serve as potential targets for developing inhibitors to block the widespread of the TMexCD1 system.}, }
@article {pmid38471323, year = {2024}, author = {Li, J and Liao, Q and Wang, Y and Wang, X and Liu, J and Zha, R and He, JZ and Zhang, M and Zhang, W}, title = {Involvement of functional metabolism promotes the enrichment of antibiotic resistome in drinking water: Based on the PICRUSt2 functional prediction.}, journal = {Journal of environmental management}, volume = {356}, number = {}, pages = {120544}, doi = {10.1016/j.jenvman.2024.120544}, pmid = {38471323}, issn = {1095-8630}, mesh = {*Anti-Bacterial Agents/pharmacology/analysis ; *Drinking Water ; Genes, Bacterial ; Angiotensin Receptor Antagonists/analysis ; Nitrites/analysis ; Drug Resistance, Microbial/genetics ; Angiotensin-Converting Enzyme Inhibitors/analysis ; Nitrogen/analysis ; }, abstract = {Biofilters are the important source and sink of antibiotic resistance genes (ARGs) and antibiotic resistance bacteria (ARB) in the drinking water. Current studies generally ascribed the prevalence of BAR in biofilter from the perspective of gene behavior, i.e. horizontal gene transfer (HGT), little attentions have been paid on the ARGs carrier- ARB. In this study, we proposed the hypothesis that ARB participating in pollutant metabolism processes and becoming dominant is an important way for the enrichment of ARGs. To verify this, the antibiotic resistome and bacterial functional metabolic pathways of a sand filter was profiled using heterotrophic bacterial plate counting method (HPC), high-throughput qPCR, Illumina Hiseq sequencing and PICRUSt2 functional prediction. The results illustrated a significant leakage of ARB in the effluent of the sand filter with an average absolute abundance of approximately 10[2]-10[3] CFU/mL. Further contribution analysis revealed that the dominant genera, such as Acinetobacter spp., Aeromonas spp., Elizabethkingia spp., and Bacillus spp., were primary ARGs hosts, conferring resistance to multiple antibiotics including sulfamethoxazole, tetracycline and β-lactams. Notably, these ARGs hosts were involved in nitrogen metabolism, including extracellular nitrate/nitrite transport and nitrite reduction, which are crucial in nitrification and denitrification in biofilters. For example, Acinetobacter spp., the dominant bacteria in the filter (relative abundance 69.97 %), contributed the majority of ARGs and 53.79 % of nitrite reduction function. That is, ARB can predominate by participating in the nitrogen metabolism pathways, facilitating the enrichment of ARGs. These findings provide insights into the stable presence of ARGs in biofilters from a functional metabolism perspective, offering a significant supplementary to the mechanisms of the emergence, maintenance, and transmission of BARin drinking water.}, }
@article {pmid38470054, year = {2024}, author = {Beck, C and Krusche, J and Notaro, A and Walter, A and Kränkel, L and Vollert, A and Stemmler, R and Wittmann, J and Schaller, M and Slavetinsky, C and Mayer, C and De Castro, C and Peschel, A}, title = {Wall teichoic acid substitution with glucose governs phage susceptibility of Staphylococcus epidermidis.}, journal = {mBio}, volume = {15}, number = {4}, pages = {e0199023}, pmid = {38470054}, issn = {2150-7511}, support = {ID 246807620, ID 410190180, ID 39083813//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Humans ; *Staphylococcus epidermidis/genetics/metabolism ; Staphylococcus aureus/genetics ; Coagulase/metabolism ; Glucose/metabolism ; Teichoic Acids/metabolism ; Staphylococcus/metabolism ; Staphylococcus Phages/genetics ; DNA/metabolism ; Cell Wall/metabolism ; *Staphylococcal Infections/metabolism ; }, abstract = {The species- and clone-specific susceptibility of Staphylococcus cells for bacteriophages is governed by the structures and glycosylation patterns of wall teichoic acid (WTA) glycopolymers. The glycosylation-dependent phage-WTA interactions in the opportunistic pathogen Staphylococcus epidermidis and in other coagulase-negative staphylococci (CoNS) have remained unknown. We report a new S. epidermidis WTA glycosyltransferase TagE whose deletion confers resistance to siphoviruses such as ΦE72 but enables binding of otherwise unbound podoviruses. S. epidermidis glycerolphosphate WTA was found to be modified with glucose in a tagE-dependent manner. TagE is encoded together with the enzymes PgcA and GtaB providing uridine diphosphate-activated glucose. ΦE72 transduced several other CoNS species encoding TagE homologs, suggesting that WTA glycosylation via TagE is a frequent trait among CoNS that permits interspecies horizontal gene transfer. Our study unravels a crucial mechanism of phage-Staphylococcus interaction and horizontal gene transfer, and it will help in the design of anti-staphylococcal phage therapies.IMPORTANCEPhages are highly specific for certain bacterial hosts, and some can transduce DNA even across species boundaries. How phages recognize cognate host cells remains incompletely understood. Phages infecting members of the genus Staphylococcus bind to wall teichoic acid (WTA) glycopolymers with highly variable structures and glycosylation patterns. How WTA is glycosylated in the opportunistic pathogen Staphylococcus epidermidis and in other coagulase-negative staphylococci (CoNS) species has remained unknown. We describe that S. epidermidis glycosylates its WTA backbone with glucose, and we identify a cluster of three genes responsible for glucose activation and transfer to WTA. Their inactivation strongly alters phage susceptibility patterns, yielding resistance to siphoviruses but susceptibility to podoviruses. Many different CoNS species with related glycosylation genes can exchange DNA via siphovirus ΦE72, suggesting that glucose-modified WTA is crucial for interspecies horizontal gene transfer. Our finding will help to develop antibacterial phage therapies and unravel routes of genetic exchange.}, }
@article {pmid38466360, year = {2024}, author = {Kim, YH and Lee, DH and Seo, HS and Eun, SH and Lee, DS and Choi, YK and Lee, SH and Kim, TY}, title = {Genome-based taxonomic identification and safety assessment of an Enterococcus strain isolated from a homemade dairy product.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {27}, number = {5}, pages = {1513-1525}, pmid = {38466360}, issn = {1618-1905}, mesh = {*Enterococcus/genetics/isolation &amp; purification/classification/drug effects/pathogenicity ; *Genome, Bacterial ; *Virulence Factors/genetics ; *Anti-Bacterial Agents/pharmacology ; *Whole Genome Sequencing ; *Cheese/microbiology ; Food Microbiology ; Republic of Korea ; Virulence/genetics ; Drug Resistance, Bacterial/genetics ; Dairy Products/microbiology ; Microbial Sensitivity Tests ; }, abstract = {The aim of this study was to explore the taxonomic identification and evaluate the safety of a bacterium, Enterococcus lactis IDCC 2105, isolated from homemade cheese in Korea, using whole genome sequence (WGS) analysis. It sought to identify the species level of this Enterococcus spp., assess its antibiotic resistance, and evaluate its virulence potential. WGS analysis confirmed the bacterial strain IDCC 2105 as E. lactis and identified genes responsible for resistance to erythromycin and clindamycin, specifically msrC, and eatAv, which are chromosomally located, indicating a minimal risk for horizontal gene transfer. The absence of plasmids in E. lactis IDCC 2105 further diminishes the likelihood of resistance gene dissemination. Additionally, our investigation into seven virulence factors, including hemolysis, platelet aggregation, biofilm formation, hyaluronidase, gelatinase, ammonia production, and β-glucuronidase activity, revealed no detectable virulence traits. Although bioinformatic analysis suggested the presence of collagen adhesion genes acm and scm, these were not corroborated by phenotypic virulence assays. Based on these findings, E. lactis IDCC 2105 presents as a safe strain for potential applications, contributing valuable information on its taxonomy, antibiotic resistance profile, and lack of virulence factors, supporting its use in food products.}, }
@article {pmid38463488, year = {2024}, author = {Simón, D and Ramos, N and Lamolle, G and Musto, H}, title = {Two decades ago, giant viruses were discovered: the fall of an old paradigm.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1356711}, pmid = {38463488}, issn = {1664-302X}, }
@article {pmid38458877, year = {2024}, author = {Wilson, CG and Pieszko, T and Nowell, RW and Barraclough, TG}, title = {Recombination in bdelloid rotifer genomes: asexuality, transfer and stress.}, journal = {Trends in genetics : TIG}, volume = {40}, number = {5}, pages = {422-436}, doi = {10.1016/j.tig.2024.02.001}, pmid = {38458877}, issn = {0168-9525}, mesh = {Animals ; *Rotifera/genetics/physiology ; *Gene Transfer, Horizontal/genetics ; *Recombination, Genetic ; *Stress, Physiological/genetics ; Reproduction, Asexual/genetics ; Genome/genetics ; Genome, Helminth ; Phylogeny ; Male ; }, abstract = {Bdelloid rotifers constitute a class of microscopic animals living in freshwater habitats worldwide. Several strange features of bdelloids have drawn attention: their ability to tolerate desiccation and other stresses, a lack of reported males across the clade despite centuries of study, and unusually high numbers of horizontally acquired, non-metazoan genes. Genome sequencing is transforming our understanding of their lifestyle and its consequences, while in turn providing wider insights about recombination and genome organisation in animals. Many questions remain, not least how to reconcile apparent genomic signatures of sex with the continued absence of reported males, why bdelloids have so many horizontally acquired genes, and how their remarkable ability to survive stress interacts with recombination and other genomic processes.}, }
@article {pmid38457521, year = {2024}, author = {Colombi, E and Bertels, F and Doulcier, G and McConnell, E and Pichugina, T and Sohn, KH and Straub, C and McCann, HC and Rainey, PB}, title = {Rapid dissemination of host metabolism-manipulating genes via integrative and conjugative elements.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {11}, pages = {e2309263121}, pmid = {38457521}, issn = {1091-6490}, support = {MAU1709//Royal Society of New Zealand | Marsden Fund (Royal Society of New Zealand Marsden Fund)/ ; SFB1182 Project C4//Deutsche Forschungsgemeinschaft (DFG)/ ; }, mesh = {Phylogeny ; *Conjugation, Genetic ; *Gene Transfer, Horizontal/genetics ; Biological Evolution ; DNA Transposable Elements/genetics ; }, abstract = {Integrative and conjugative elements (ICEs) are self-transmissible mobile elements that transfer functional genetic units across broad phylogenetic distances. Accessory genes shuttled by ICEs can make significant contributions to bacterial fitness. Most ICEs characterized to date encode readily observable phenotypes contributing to symbiosis, pathogenicity, and antimicrobial resistance, yet the majority of ICEs carry genes of unknown function. Recent observations of rapid acquisition of ICEs in a pandemic lineage of Pseudomonas syringae pv. actinidae led to investigation of the structural and functional diversity of these elements. Fifty-three unique ICE types were identified across the P. syringae species complex. Together they form a distinct family of ICEs (PsICEs) that share a distant relationship to ICEs found in Pseudomonas aeruginosa. PsICEs are defined by conserved backbone genes punctuated by an array of accessory cargo genes, are highly recombinogenic, and display distinct evolutionary histories compared to their bacterial hosts. The most common cargo is a recently disseminated 16-kb mobile genetic element designated Tn6212. Deletion of Tn6212 did not alter pathogen growth in planta, but mutants displayed fitness defects when grown on tricarboxylic acid (TCA) cycle intermediates. RNA-seq analysis of a set of nested deletion mutants showed that a Tn6212-encoded LysR regulator has global effects on chromosomal gene expression. We show that Tn6212 responds to preferred carbon sources and manipulates bacterial metabolism to maximize growth.}, }
@article {pmid38453913, year = {2024}, author = {Hayashi, N and Lai, Y and Fuerte-Stone, J and Mimee, M and Lu, TK}, title = {Cas9-assisted biological containment of a genetically engineered human commensal bacterium and genetic elements.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {2096}, pmid = {38453913}, issn = {2041-1723}, support = {R25 GM109439/GM/NIGMS NIH HHS/United States ; R35 GM147478/GM/NIGMS NIH HHS/United States ; T32 GM007183/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *CRISPR-Cas Systems/genetics ; *Containment of Biohazards ; Genetic Engineering ; Bacteria/genetics ; Thymidine ; }, abstract = {Sophisticated gene circuits built by synthetic biology can enable bacteria to sense their environment and respond predictably. Engineered biosensing bacteria outfitted with such circuits can potentially probe the human gut microbiome to prevent, diagnose, or treat disease. To provide robust biocontainment for engineered bacteria, we devised a Cas9-assisted auxotrophic biocontainment system combining thymidine auxotrophy, an Engineered Riboregulator (ER) for controlled gene expression, and a CRISPR Device (CD). The CD prevents the engineered bacteria from acquiring thyA via horizontal gene transfer, which would disrupt the biocontainment system, and inhibits the spread of genetic elements by killing bacteria harboring the gene cassette. This system tunably controlled gene expression in the human gut commensal bacterium Bacteroides thetaiotaomicron, prevented escape from thymidine auxotrophy, and blocked transgene dissemination. These capabilities were validated in vitro and in vivo. This biocontainment system exemplifies a powerful strategy for bringing genetically engineered microorganisms safely into biomedicine.}, }
@article {pmid38453092, year = {2024}, author = {Wang, YC and Mao, Y and Fu, HM and Wang, J and Weng, X and Liu, ZH and Xu, XW and Yan, P and Fang, F and Guo, JS and Shen, Y and Chen, YP}, title = {New insights into functional divergence and adaptive evolution of uncultured bacteria in anammox community by complete genome-centric analysis.}, journal = {The Science of the total environment}, volume = {924}, number = {}, pages = {171530}, doi = {10.1016/j.scitotenv.2024.171530}, pmid = {38453092}, issn = {1879-1026}, mesh = {*Anaerobic Ammonia Oxidation ; Oxidation-Reduction ; *Sewage/microbiology ; Bacteria/genetics/metabolism ; Nitrogen/metabolism ; Bioreactors/microbiology ; }, abstract = {Anaerobic ammonium-oxidation (anammox) bacteria play a crucial role in global nitrogen cycling and wastewater nitrogen removal, but they share symbiotic relationships with various other microorganisms. Functional divergence and adaptive evolution of uncultured bacteria in anammox community remain underexplored. Although shotgun metagenomics based on short reads has been widely used in anammox research, metagenome-assembled genomes (MAGs) are often discontinuous and highly contaminated, which limits in-depth analyses of anammox communities. Here, for the first time, we performed Pacific Biosciences high-fidelity (HiFi) long-read sequencing on the anammox granule sludge sample from a lab-scale bioreactor, and obtained 30 accurate and complete metagenome-assembled genomes (cMAGs). These cMAGs were obtained by selecting high-quality circular contigs from initial assemblies of long reads generated by HiFi sequencing, eliminating the need for Illumina short reads, binning, and reassembly. One new anammox species affiliated with Candidatus Jettenia and three species affiliated with novel families were found in this anammox community. cMAG-centric analysis revealed functional divergence in general and nitrogen metabolism among the anammox community members, and they might adopt a cross-feeding strategy in organic matter, cofactors, and vitamins. Furthermore, we identified 63 mobile genetic elements (MGEs) and 50 putative horizontal gene transfer (HGT) events within these cMAGs. The results suggest that HGT events and MGEs related to phage and integration or excision, particularly transposons containing tnpA in anammox bacteria, might play important roles in the adaptive evolution of this anammox community. The cMAGs generated in the present study could be used to establish of a comprehensive database for anammox bacteria and associated microorganisms. These findings highlight the advantages of HiFi sequencing for the studies of complex mixed cultures and advance the understanding of anammox communities.}, }
@article {pmid38452676, year = {2024}, author = {Xie, X and Chen, B and Zhu, S and Yang, R and Yuan, K and Yang, Y and Chen, R and Lin, L and Chen, B}, title = {Comparative analysis of characteristics of antibiotic resistomes between Arctic soils and representative contaminated samples using metagenomic approaches.}, journal = {Journal of hazardous materials}, volume = {469}, number = {}, pages = {133943}, doi = {10.1016/j.jhazmat.2024.133943}, pmid = {38452676}, issn = {1873-3336}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; Soil ; Bacteria/genetics ; Ampicillin ; }, abstract = {Antibiotic resistance is one of the most concerned global health issues. However, comprehensive profiles of antibiotic resistance genes (ARGs) in various environmental settings are still needed to address modern antibiotic resistome. Here, Arctic soils and representative contaminated samples from ARG pollution sources were analyzed using metagenomic approaches. The diversity and abundance of ARGs in Arctic soils were significantly lower than those in contaminated samples (p < 0.01). ARG profiles in Arctic soils were featured with the dominance of vanF, ceoB, and bacA related to multidrug and bacitracin, whereas those from ARG pollution sources were characterized by prevalent resistance to anthropogenic antibiotics such as sulfonamides, tetracyclines, and beta-lactams. Mobile genetic elements (MGEs) were found in all samples, and their abundance and relatedness to ARGs were both lower in Arctic soils than in polluted samples. Significant relationships between bacterial communities and ARGs were observed (p < 0.01). Cultural bacteria in Arctic soils had clinically-concerned resistance to erythromycin, vancomycin, ampicillin, etc., but ARGs relevant to those antibiotics were undetectable in their genomes. Our results suggested that Arctic environment could be an important reservoir of novel ARGs, and antibiotic stresses could cause ARG pollution via horizontal gene transfer and enrichment of resistant bacteria.}, }
@article {pmid38449530, year = {2024}, author = {Franceus, J and Rivas-Fernández, JP and Lormans, J and Rovira, C and Desmet, T}, title = {Evolution of Phosphorylase Activity in an Ancestral Glycosyltransferase.}, journal = {ACS catalysis}, volume = {14}, number = {5}, pages = {3103-3114}, pmid = {38449530}, issn = {2155-5435}, abstract = {The reconstruction of ancestral sequences can offer a glimpse into the fascinating process of molecular evolution by exposing the adaptive pathways that shape the proteins found in nature today. Here, we track the evolution of the carbohydrate-active enzymes responsible for the synthesis and turnover of mannogen, a critical carbohydrate reserve in Leishmania parasites. Biochemical characterization of resurrected enzymes demonstrated that mannoside phosphorylase activity emerged in an ancestral bacterial mannosyltransferase, and later disappeared in the process of horizontal gene transfer and gene duplication in Leishmania. By shuffling through plausible historical sequence space in an ancestral mannosyltransferase, we found that mannoside phosphorylase activity could be toggled on through various combinations of mutations at positions outside of the active site. Molecular dynamics simulations showed that such mutations can affect loop rigidity and shield the active site from water molecules that disrupt key interactions, allowing α-mannose 1-phosphate to adopt a catalytically productive conformation. These findings highlight the importance of subtle distal mutations in protein evolution and suggest that the vast collection of natural glycosyltransferases may be a promising source of engineering templates for the design of tailored phosphorylases.}, }
@article {pmid38448399, year = {2024}, author = {Haudiquet, M and Le Bris, J and Nucci, A and Bonnin, RA and Domingo-Calap, P and Rocha, EPC and Rendueles, O}, title = {Capsules and their traits shape phage susceptibility and plasmid conjugation efficiency.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {2032}, pmid = {38448399}, issn = {2041-1723}, support = {ANR 18 CE12 0001 01 ENCAPSULATION//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR 16 CE15 0022 03 PREDIRES//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-10-LABX-62- IBEID//Agence Nationale de la Recherche (French National Research Agency)/ ; PIA/ANR-16- CONV-0005//Agence Nationale de la Recherche (French National Research Agency)/ ; EQU201903007835//Fondation pour la Recherche M&#xe9;dicale (Foundation for Medical Research in France)/ ; }, mesh = {Phenotype ; Plasmids/genetics ; Serogroup ; *Genome, Bacterial ; *Bacteriophages/genetics ; }, abstract = {Bacterial evolution is affected by mobile genetic elements like phages and conjugative plasmids, offering new adaptive traits while incurring fitness costs. Their infection is affected by the bacterial capsule. Yet, its importance has been difficult to quantify because of the high diversity of confounding mechanisms in bacterial genomes such as anti-viral systems and surface receptor modifications. Swapping capsule loci between Klebsiella pneumoniae strains allowed us to quantify their impact on plasmid and phage infection independently of genetic background. Capsule swaps systematically invert phage susceptibility, revealing serotypes as key determinants of phage infection. Capsule types also influence conjugation efficiency in both donor and recipient cells, a mechanism shaped by capsule volume and conjugative pilus structure. Comparative genomics confirmed that more permissive serotypes in the lab correspond to the strains acquiring more conjugative plasmids in nature. The least capsule-sensitive pili (F-like) are the most frequent in the species' plasmids, and are the only ones associated with both antibiotic resistance and virulence factors, driving the convergence between virulence and antibiotics resistance in the population. These results show how traits of cellular envelopes define slow and fast lanes of infection by mobile genetic elements, with implications for population dynamics and horizontal gene transfer.}, }
@article {pmid38447655, year = {2024}, author = {Shi, X and Shen, Z and Shao, B and Shen, J and Wu, Y and Wang, S}, title = {Antibiotic resistance genes profile in the surface sediments of typical aquaculture areas across 15 major lakes in China.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {347}, number = {}, pages = {123709}, doi = {10.1016/j.envpol.2024.123709}, pmid = {38447655}, issn = {1873-6424}, mesh = {Humans ; *Lakes/microbiology ; *Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Aquaculture ; China ; Anti-Bacterial Agents/pharmacology/analysis ; }, abstract = {Aquatic farming is considered as a major source of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) for the natural environment of the lakes. ARB and ARGs in the natural environment have increased quickly because of the human activities. Here, we have profiled the diversity and abundance of ARGs in sediments from the typical aquaculture areas around 15 major lakes in China using PCR and qPCR, and further assessed the risk factor shaping the occurrence and distribution of ARGs. And class 1, 2 and 3 integrons were initially detected by PCR with specific primers. ARGs were widely distributed in the lakes: Weishan Lake and Poyang Lake showed high diversity of ARGs, followed by Dongting Lake, Chao Lake and Tai Lake. Generally, the ARGs in the Middle-Lower Yangtze Plain were more abundant than those in the Qinghai-Tibet Plateau. Tetracycline resistance genes (tet(C), tet(A) &amp; tet(M)) were prominent in sediments, and the next was AmpC β-lactamase gene group BIL/LAT/CMY, and the last was the genes resistance to aminoglycoside (strA-strB). Partial least squares path modeling analysis (PLS-PMA) revealed that livestock had a significant direct effect on the distribution of ARGs in lakes, and population might indirectly influence the profiles of ARGs by affecting the scale of livestock and aquaculture. The detectable rate of class 1, 2 and 3 integrons were 80%, 100% and 46.67%, respectively. The prevalence of integrons might play a key role in promoting more frequent horizontal gene transfer (HGT) events, resulting in the environmental mobilization and dissemination of ARGs between bacteria.}, }
@article {pmid38447371, year = {2024}, author = {Wang, Y and Zhang, Z and Kang, J and Chen, B and Hong, W and Lv, B and Wang, T and Qian, H}, title = {Phages in different habitats and their ability to carry antibiotic resistance genes.}, journal = {Journal of hazardous materials}, volume = {469}, number = {}, pages = {133941}, doi = {10.1016/j.jhazmat.2024.133941}, pmid = {38447371}, issn = {1873-3336}, mesh = {Humans ; *Bacteriophages/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Ecosystem ; Biodiversity ; Genes, Bacterial ; }, abstract = {As the most abundant organisms on Earth, phages play a key role in the evolution of bacterial antibiotic resistance. Although previous studies have demonstrated the molecular mechanisms of horizontal gene transfer mediated by mobile genetic elements, our understanding of the intertwined relationships between antibiotic resistance genes (ARGs) and phages is limited. In this study, we analysed 2781 metagenomic samples to reveal the composition and species interactions of phage communities in different habitats as well as their capacity to carry ARGs with health risks. The composition of phage communities varies in different habitats and mainly depends on environmental conditions. Terrestrial habitats display more complex and robust interactions between phages than aquatic and human-associated habitats, resulting in the highest biodiversity of phages. Several types of phages in certain taxa (4.95-7.67%, mainly belonging to Caudoviricetes) have the capacity to carry specific ARGs and display a high potential risk to human health, especially in human-associated habitats. Overall, our results provide insights into the assembly mechanisms of phage communities and their effects on the dissemination of antibiotic resistance.}, }
@article {pmid38445859, year = {2024}, author = {Sharma, DK and Rajpurohit, YS}, title = {Multitasking functions of bacterial extracellular DNA in biofilms.}, journal = {Journal of bacteriology}, volume = {206}, number = {4}, pages = {e0000624}, pmid = {38445859}, issn = {1098-5530}, support = {RBA4031//DAE | Bhabha Atomic Research Centre (BARC)/ ; }, mesh = {Humans ; DNA, Bacterial/genetics ; *Ecosystem ; *Biofilms ; Bacteria/genetics ; Extracellular Matrix ; }, abstract = {Bacterial biofilms are intricate ecosystems of microbial communities that adhere to various surfaces and are enveloped by an extracellular matrix composed of polymeric substances. Within the context of bacterial biofilms, extracellular DNA (eDNA) originates from cell lysis or is actively secreted, where it exerts a significant influence on the formation, stability, and resistance of biofilms to environmental stressors. The exploration of eDNA within bacterial biofilms holds paramount importance in research, with far-reaching implications for both human health and the environment. An enhanced understanding of the functions of eDNA in biofilm formation and antibiotic resistance could inspire the development of strategies to combat biofilm-related infections and improve the management of antibiotic resistance. This comprehensive review encapsulates the latest discoveries concerning eDNA, encompassing its origins, functions within bacterial biofilms, and significance in bacterial pathogenesis.}, }
@article {pmid38443606, year = {2024}, author = {Dmitrijeva, M and Tackmann, J and Matias Rodrigues, JF and Huerta-Cepas, J and Coelho, LP and von Mering, C}, title = {A global survey of prokaryotic genomes reveals the eco-evolutionary pressures driving horizontal gene transfer.}, journal = {Nature ecology &amp; evolution}, volume = {8}, number = {5}, pages = {986-998}, pmid = {38443606}, issn = {2397-334X}, support = {51NF40_180575//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 310030-192569//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 2018SHZDZX01//Science and Technology Commission of Shanghai Municipality (Shanghai Municipal Science and Technology Commission)/ ; }, mesh = {*Gene Transfer, Horizontal ; *Bacteria/genetics ; Genome, Bacterial ; Ecosystem ; Archaea/genetics ; Genome, Archaeal ; Evolution, Molecular ; }, abstract = {Horizontal gene transfer, the exchange of genetic material through means other than reproduction, is a fundamental force in prokaryotic genome evolution. Genomic persistence of horizontally transferred genes has been shown to be influenced by both ecological and evolutionary factors. However, there is limited availability of ecological information about species other than the habitats from which they were isolated, which has prevented a deeper exploration of ecological contributions to horizontal gene transfer. Here we focus on transfers detected through comparison of individual gene trees to the species tree, assessing the distribution of gene-exchanging prokaryotes across over a million environmental sequencing samples. By analysing detected horizontal gene transfer events, we show distinct functional profiles for recent versus old events. Although most genes transferred are part of the accessory genome, genes transferred earlier in evolution tend to be more ubiquitous within present-day species. We find that co-occurring, interacting and high-abundance species tend to exchange more genes. Finally, we show that host-associated specialist species are most likely to exchange genes with other host-associated specialist species, whereas species found across different habitats have similar gene exchange rates irrespective of their preferred habitat. Our study covers an unprecedented scale of integrated horizontal gene transfer and environmental information, highlighting broad eco-evolutionary trends.}, }
@article {pmid38442604, year = {2024}, author = {Zhang, Y and Li, W and Wu, Y and Tian, X and Li, G and Zhou, Y and Sun, J and Liao, X and Liu, Y and Wang, Y and Yu, Y}, title = {Chitosan oligosaccharide accelerates the dissemination of antibiotic resistance genes through promoting conjugative plasmid transfer.}, journal = {Journal of hazardous materials}, volume = {469}, number = {}, pages = {133922}, doi = {10.1016/j.jhazmat.2024.133922}, pmid = {38442604}, issn = {1873-3336}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Escherichia coli/genetics ; *Chitosan/pharmacology ; Drug Resistance, Bacterial/genetics ; Plasmids/genetics ; Gene Transfer, Horizontal ; Oligosaccharides/pharmacology ; }, abstract = {The dissemination of antibiotic resistance genes (ARGs), especially via plasmid-mediated horizontal gene transfer, poses a pervasive threat to global health. Chitosan-oligosaccharide (COS) is extensively utilized in medicine, plant and animal husbandry. However, their impact on microflora implies the potential to exert selective pressure on plasmid transfer. To explore the role of COS in facilitating the dissemination of ARGs via plasmid conjugation, we established in vitro mating models. The addition of COS to conjugation mixtures significantly enhanced the transfer of RP4 plasmid and mcr-1 positive IncX4 plasmid in both intra- and inter-specific. Phenotypic and transcriptome analysis revealed that COS enhanced intercellular contact by neutralizing cell surface charge and increasing cell surface hydrophobicity. Additionally, COS increased membrane permeability by inhibiting the Tol-Pal system, thereby facilitating plasmid conjugative transfer. Furthermore, COS served as the carbon source and was metabolized by E. coli, providing energy for plasmid conjugation through regulating the expression of ATPase and global repressor factor-related genes in RP4 plasmid. Overall, these findings improve our awareness of the potential risks associated with the presence of COS and the spread of bacterial antibiotic resistance, emphasizing the need to establish guidelines for the prudent use of COS and its discharge into the environment.}, }
@article {pmid38441061, year = {2024}, author = {Gschwind, R and Petitjean, M and Fournier, C and Lao, J and Clermont, O and Nordmann, P and Mellmann, A and Denamur, E and Poirel, L and Ruppé, E}, title = {Inter-phylum circulation of a beta-lactamase-encoding gene: a rare but observable event.}, journal = {Antimicrobial agents and chemotherapy}, volume = {68}, number = {4}, pages = {e0145923}, pmid = {38441061}, issn = {1098-6596}, support = {FNS-407240_177381/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {Humans ; *Escherichia coli ; beta-Lactamases/genetics/metabolism ; *Escherichia coli Infections/microbiology ; Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; }, abstract = {Beta-lactamase-mediated degradation of beta-lactams is the most common mechanism of beta-lactam resistance in Gram-negative bacteria. Beta-lactamase-encoding genes can be transferred between closely related bacteria, but spontaneous inter-phylum transfers (between distantly related bacteria) have never been reported. Here, we describe an extended-spectrum beta-lactamase (ESBL)-encoding gene (blaMUN-1) shared between the Pseudomonadota and Bacteroidota phyla. An Escherichia coli strain was isolated from a patient in Münster (Germany). Its genome was sequenced. The ESBL-encoding gene (named blaMUN-1) was cloned, and the corresponding enzyme was characterized. The distribution of the gene among bacteria was investigated using the RefSeq Genomes database. The frequency and relative abundance of its closest homolog in the global microbial gene catalog (GMGC) were analyzed. The E. coli strain exhibited two distinct morphotypes. Each morphotype possessed two chromosomal copies of the blaMUN-1 gene, with one morphotype having two additional copies located on a phage-plasmid p0111. Each copy was located within a 7.6-kb genomic island associated with mobility. blaMUN-1 encoded for an extended-spectrum Ambler subclass A2 beta-lactamase with 43.0% amino acid identity to TLA-1. blaMUN-1 was found in species among the Bacteroidales order and in Sutterella wadsworthensis (Pseudomonadota). Its closest homolog in GMGC was detected frequently in human fecal samples. This is, to our knowledge, the first reported instance of inter-phylum transfer of an ESBL-encoding gene, between the Bacteroidota and Pseudomonadota phyla. Although the gene was frequently detected in the human gut, inter-phylum transfer was rare, indicating that inter-phylum barriers are effective in impeding the spread of ESBL-encoding genes, but not entirely impenetrable.}, }
@article {pmid38436469, year = {2024}, author = {van der Gulik, PTS and Hoff, WD and Speijer, D}, title = {The contours of evolution: In defence of Darwin's tree of life paradigm.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {46}, number = {5}, pages = {e2400012}, doi = {10.1002/bies.202400012}, pmid = {38436469}, issn = {1521-1878}, mesh = {Animals ; *Biological Evolution ; *Gene Transfer, Horizontal ; *Phylogeny ; }, abstract = {Both the concept of a Darwinian tree of life (TOL) and the possibility of its accurate reconstruction have been much criticized. Criticisms mostly revolve around the extensive occurrence of lateral gene transfer (LGT), instances of uptake of complete organisms to become organelles (with the associated subsequent gene transfer to the nucleus), as well as the implications of more subtle aspects of the biological species concept. Here we argue that none of these criticisms are sufficient to abandon the valuable TOL concept and the biological realities it captures. Especially important is the need to conceptually distinguish between organismal trees and gene trees, which necessitates incorporating insights of widely occurring LGT into modern evolutionary theory. We demonstrate that all criticisms, while based on important new findings, do not invalidate the TOL. After considering the implications of these new insights, we find that the contours of evolution are best represented by a TOL.}, }
@article {pmid38436262, year = {2024}, author = {Harmer, CJ and Hall, RM}, title = {IS26 and the IS26 family: versatile resistance gene movers and genome reorganizers.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {88}, number = {2}, pages = {e0011922}, pmid = {38436262}, issn = {1098-5557}, support = {GNT1194879//DHAC | National Health and Medical Research Council (NHMRC)/ ; }, mesh = {*DNA Transposable Elements/genetics ; *Gram-Negative Bacteria/genetics ; Genome, Bacterial ; Drug Resistance, Bacterial/genetics ; Transposases/metabolism/genetics ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; }, abstract = {SUMMARYIn Gram-negative bacteria, the insertion sequence IS26 is highly active in disseminating antibiotic resistance genes. IS26 can recruit a gene or group of genes into the mobile gene pool and support their continued dissemination to new locations by creating pseudo-compound transposons (PCTs) that can be further mobilized by the insertion sequence (IS). IS26 can also enhance expression of adjacent potential resistance genes. IS26 encodes a DDE transposase but has unique properties. It forms cointegrates between two separate DNA molecules using two mechanisms. The well-known copy-in (replicative) route generates an additional IS copy and duplicates the target site. The recently discovered and more efficient and targeted conservative mechanism requires an IS in both participating molecules and does not generate any new sequence. The unit of movement for PCTs, known as a translocatable unit or TU, includes only one IS26. TU formed by homologous recombination between the bounding IS26s can be reincorporated via either cointegration route. However, the targeted conservative reaction is key to generation of arrays of overlapping PCTs seen in resistant pathogens. Using the copy-in route, IS26 can also act on a site in the same DNA molecule, either inverting adjacent DNA or generating an adjacent deletion plus a circular molecule carrying the DNA segment lost and an IS copy. If reincorporated, these circular molecules create a new PCT. IS26 is the best characterized IS in the IS26 family, which includes IS257/IS431, ISSau10, IS1216, IS1006, and IS1008 that are also implicated in spreading resistance genes in Gram-positive and Gram-negative pathogens.}, }
@article {pmid38435906, year = {2024}, author = {Satija, K and Anjankar, VP}, title = {Molecular Characterization of Multidrug-Resistant Shigella flexneri.}, journal = {Cureus}, volume = {16}, number = {1}, pages = {e53276}, pmid = {38435906}, issn = {2168-8184}, abstract = {Due to their propensity for causing diarrheal illnesses and their rising susceptibility to antimicrobials, Shigella infections constitute a serious threat to global public health. This extensive study explores the frequency, antibiotic resistance, genetic evolution, and effects of Shigella infections on vulnerable groups. The research covers a wide range of geographical areas and sheds information on how the prevalence of Shigella species is evolving. Shigella strain antimicrobial resistance patterns are thoroughly examined. Multidrug resistance (MDR) has been found to often occur in investigations, especially when older antimicrobials are used. The improper use of antibiotics in China is blamed for the quick emergence of resistance, and variations in resistance rates have been seen across different geographical areas. Shigella strains' genetic makeup can be used to identify emerging trends and horizontal gene transfer's acquisition of resistance genes. Notably, S. sonnei exhibits the capacity to obtain resistance genes from nearby bacteria, increasing its capacity for infection. The study also emphasizes the difficulties in accurately serotyping Shigella strains due to inconsistencies between molecular and conventional serology. These results highlight the necessity of reliable diagnostic methods for monitoring Shigella infections. In conclusion, this study emphasizes how dynamic Shigella infections are, with varying patterns of occurrence, changing resistance landscapes, and genetic adaptability. In addition to tackling the rising problem of antibiotic resistance in Shigella infections, these findings are essential for guiding efforts for disease surveillance, prevention, and treatment.}, }
@article {pmid38434434, year = {2024}, author = {Xiao, Y and Zhang, S and Li, H and Teng, K and Wu, S and Liu, Y and Yu, F and He, Z and Li, L and Li, L and Meng, D and Yin, H and Wang, Y}, title = {Metagenomic insights into the response of soil microbial communities to pathogenic Ralstonia solanacearum.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1325141}, pmid = {38434434}, issn = {1664-462X}, abstract = {Understanding the response of soil microbial communities to pathogenic Ralstonia solanacearum is crucial for preventing bacterial wilt outbreaks. In this study, we investigated the soil physicochemical and microbial community to assess their impact on the pathogenic R.solanacearum through metagenomics. Our results revealed that certain archaeal taxa were the main contributors influencing the health of plants. Additionally, the presence of the pathogen showed a strong negative correlation with soil phosphorus levels, while soil phosphorus was significantly correlated with bacterial and archaeal communities. We found that the network of microbial interactions in healthy plant rhizosphere soils was more complex compared to diseased soils. The diseased soil network had more linkages, particularly related to the pathogen occurrence. Within the network, the family Comamonadaceae, specifically Ramlibacter_tataouinensis, was enriched in healthy samples and showed a significantly negative correlation with the pathogen. In terms of archaea, Halorubrum, Halorussus_halophilus (family: Halobacteriaceae), and Natronomonas_pharaonis (family: Haloarculaceae) were enriched in healthy plant rhizosphere soils and showed negative correlations with R.solanacearum. These findings suggested that the presence of these archaea may potentially reduce the occurrence of bacterial wilt disease. On the other hand, Halostagnicola_larseniia and Haloterrigena_sp._BND6 (family: Natrialbaceae) had higher relative abundance in diseased plants and exhibited significantly positive correlations with R.solanacearum, indicating their potential contribution to the pathogen's occurrence. Moreover, we explored the possibility of functional gene sharing among the correlating bacterial pairs within the Molecular Ecological Network. Our analysis revealed 468 entries of horizontal gene transfer (HGT) events, emphasizing the significance of HGT in shaping the adaptive traits of plant-associated bacteria, particularly in relation to host colonization and pathogenicity. Overall, this work revealed key factors, patterns and response mechanisms underlying the rhizosphere soil microbial populations. The findings offer valuable guidance for effectively controlling soil-borne bacterial diseases and developing sustainable agriculture practices.}, }
@article {pmid38431762, year = {2024}, author = {Huang, HJ and Li, LL and Ye, ZX and Lu, JB and Lou, YH and Wei, ZY and Sun, ZT and Chen, JP and Li, JM and Zhang, CX}, title = {Salivary proteins potentially derived from horizontal gene transfer are critical for salivary sheath formation and other feeding processes.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {257}, pmid = {38431762}, issn = {2399-3642}, support = {32001987//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; *Gene Transfer, Horizontal ; Insect Proteins/genetics/metabolism ; *Heteroptera/genetics/metabolism ; Salivary Proteins and Peptides/genetics/metabolism ; }, abstract = {Herbivorous insects employ an array of salivary proteins to aid feeding. However, the mechanisms behind the recruitment and evolution of these genes to mediate plant-insect interactions remain poorly understood. Here, we report a potential horizontal gene transfer (HGT) event from bacteria to an ancestral bug of Eutrichophora. The acquired genes subsequently underwent duplications and evolved through co-option. We annotated them as horizontal-transferred, Eutrichophora-specific salivary protein (HESPs) according to their origin and function. In Riptortus pedestris (Coreoidea), all nine HESPs are secreted into plants during feeding. The RpHESP4 to RpHESP8 are recently duplicated and found to be indispensable for salivary sheath formation. Silencing of RpHESP4-8 increases the difficulty of R. pedestris in probing the soybean, and the treated insects display a decreased survivability. Although silencing the other RpHESPs does not affect the salivary sheath formation, negative effects are also observed. In Pyrrhocoris apterus (Pyrrhocoroidea), five out of six PaHESPs are secretory salivary proteins, with PaHESP3 being critical for insect survival. The PaHESP5, while important for insects, no longer functions as a salivary protein. Our results provide insight into the potential origin of insect saliva and shed light on the evolution of salivary proteins.}, }
@article {pmid38431327, year = {2024}, author = {Wiśniewski, P and Zakrzewski, A and Chajęcka-Wierzchowska, W and Zadernowska, A}, title = {Possibility of transfer and activation of 'silent' tetracycline resistance genes among Enterococcus faecalis under high-pressure processing.}, journal = {Food microbiology}, volume = {120}, number = {}, pages = {104481}, doi = {10.1016/j.fm.2024.104481}, pmid = {38431327}, issn = {1095-9998}, mesh = {*Enterococcus faecalis/genetics ; *Tetracycline Resistance/genetics ; Anti-Bacterial Agents/pharmacology ; Tetracycline/pharmacology ; Tetracyclines/pharmacology ; Microbial Sensitivity Tests ; }, abstract = {In this study, the tetracycline resistance of Enterococcus faecalis strains isolated from food was determined and molecular analyses of the resistance background were performed by determining the frequency of selected tetracycline resistance genes. In addition, the effect of high-pressure stress (400 and 500 MPa) on the expression of selected genes encoding tetracycline resistance was determined, as well as changes in the frequency of transfer of these genes in isolates showing sensitivity to tetracyclines. In our study, we observed an increase in the expression of genes encoding tetracyclines, especially the tet(L) gene, mainly under 400 MPa pressure. The study confirmed the possibility of transferring genes encoding tetracyclines such as tet(M), tet(L), tet(K), tet(W) and tet(O) by horizontal gene transfer in both control strains and exposed to high-pressure. Exposure of the strains to 400 MPa pressure had a greater effect on the possibility of gene transfer and expression than the application of a higher-pressure. To our knowledge, this study for the first time determined the effect of high-pressure stress on the expression of selected genes encoding tetracycline resistance, as well as the possibility and changes in the frequency of transfer of these genes in Enterococcus faecalis isolates showing sensitivity to tetracyclines and possessing silent genes. Due to the observed possibility of increased expression of some of the genes encoding tetracycline resistance and the possibility of their spread by horizontal gene transfer to other microorganisms in the food environment, under the influence of high-pressure processing in strains phenotypically susceptible to this antibiotic, it becomes necessary to monitor this ability in isolates derived from foods.}, }
@article {pmid38428395, year = {2024}, author = {Fogarty, EC and Schechter, MS and Lolans, K and Sheahan, ML and Veseli, I and Moore, RM and Kiefl, E and Moody, T and Rice, PA and Yu, MK and Mimee, M and Chang, EB and Ruscheweyh, HJ and Sunagawa, S and Mclellan, SL and Willis, AD and Comstock, LE and Eren, AM}, title = {A cryptic plasmid is among the most numerous genetic elements in the human gut.}, journal = {Cell}, volume = {187}, number = {5}, pages = {1206-1222.e16}, pmid = {38428395}, issn = {1097-4172}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; R35 GM133420/GM/NIGMS NIH HHS/United States ; RC2 DK122394/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Bacteria/genetics ; Bacteroidetes/genetics ; Feces/microbiology ; *Metagenome ; *Plasmids/genetics ; *Gastrointestinal Tract ; }, abstract = {Plasmids are extrachromosomal genetic elements that often encode fitness-enhancing features. However, many bacteria carry "cryptic" plasmids that do not confer clear beneficial functions. We identified one such cryptic plasmid, pBI143, which is ubiquitous across industrialized gut microbiomes and is 14 times as numerous as crAssphage, currently established as the most abundant extrachromosomal genetic element in the human gut. The majority of mutations in pBI143 accumulate in specific positions across thousands of metagenomes, indicating strong purifying selection. pBI143 is monoclonal in most individuals, likely due to the priority effect of the version first acquired, often from one's mother. pBI143 can transfer between Bacteroidales, and although it does not appear to impact bacterial host fitness in vivo, it can transiently acquire additional genetic content. We identified important practical applications of pBI143, including its use in identifying human fecal contamination and its potential as an alternative approach to track human colonic inflammatory states.}, }
@article {pmid38427560, year = {2024}, author = {Workman, RE and Stoltzfus, MJ and Keith, NC and Euler, CW and Bondy-Denomy, J and Modell, JW}, title = {Anti-CRISPR proteins trigger a burst of CRISPR-Cas9 expression that enhances phage defense.}, journal = {Cell reports}, volume = {43}, number = {3}, pages = {113849}, pmid = {38427560}, issn = {2211-1247}, support = {R35 GM142731/GM/NIGMS NIH HHS/United States ; }, mesh = {*Bacteriophages/physiology ; CRISPR-Cas Systems/genetics ; Bacteria/metabolism ; Lysogeny ; Viral Proteins/genetics/metabolism ; }, abstract = {CRISPR-Cas immune systems provide bacteria with adaptive immunity against bacteriophages, but they are often transcriptionally repressed to mitigate auto-immunity. In some cases, CRISPR-Cas expression increases in response to a phage infection, but the mechanisms of induction are largely unknown, and it is unclear whether induction occurs strongly and quickly enough to benefit the bacterial host. In S. pyogenes, Cas9 is both an immune effector and auto-repressor of CRISPR-Cas expression. Here, we show that phage-encoded anti-CRISPR proteins relieve Cas9 auto-repression and trigger a rapid increase in CRISPR-Cas levels during a single phage infective cycle. As a result, fewer cells succumb to lysis, leading to a striking survival benefit after multiple rounds of infection. CRISPR-Cas induction also reduces lysogeny, thereby limiting a route for horizontal gene transfer. Altogether, we show that Cas9 is not only a CRISPR-Cas effector and repressor but also a phage sensor that can mount an anti-anti-CRISPR transcriptional response.}, }
@article {pmid38421146, year = {2024}, author = {Wong, TKF and Cherryh, C and Rodrigo, AG and Hahn, MW and Minh, BQ and Lanfear, R}, title = {MAST: Phylogenetic Inference with Mixtures Across Sites and Trees.}, journal = {Systematic biology}, volume = {73}, number = {2}, pages = {375-391}, pmid = {38421146}, issn = {1076-836X}, support = {DP200103151//Australian Research Council Discovery Project/ ; DEB-1936187//National Science Foundation/ ; //Chan-Zuckerberg Initiative Grant/ ; //Moore-Simons Foundation/ ; }, mesh = {*Phylogeny ; *Classification/methods ; Models, Genetic ; Computer Simulation ; Software ; Animals ; }, abstract = {Hundreds or thousands of loci are now routinely used in modern phylogenomic studies. Concatenation approaches to tree inference assume that there is a single topology for the entire dataset, but different loci may have different evolutionary histories due to incomplete lineage sorting (ILS), introgression, and/or horizontal gene transfer; even single loci may not be treelike due to recombination. To overcome this shortcoming, we introduce an implementation of a multi-tree mixture model that we call mixtures across sites and trees (MAST). This model extends a prior implementation by Boussau et al. (2009) by allowing users to estimate the weight of each of a set of pre-specified bifurcating trees in a single alignment. The MAST model allows each tree to have its own weight, topology, branch lengths, substitution model, nucleotide or amino acid frequencies, and model of rate heterogeneity across sites. We implemented the MAST model in a maximum-likelihood framework in the popular phylogenetic software, IQ-TREE. Simulations show that we can accurately recover the true model parameters, including branch lengths and tree weights for a given set of tree topologies, under a wide range of biologically realistic scenarios. We also show that we can use standard statistical inference approaches to reject a single-tree model when data are simulated under multiple trees (and vice versa). We applied the MAST model to multiple primate datasets and found that it can recover the signal of ILS in the Great Apes, as well as the asymmetry in minor trees caused by introgression among several macaque species. When applied to a dataset of 4 Platyrrhine species for which standard concatenated maximum likelihood (ML) and gene tree approaches disagree, we observe that MAST gives the highest weight (i.e., the largest proportion of sites) to the tree also supported by gene tree approaches. These results suggest that the MAST model is able to analyze a concatenated alignment using ML while avoiding some of the biases that come with assuming there is only a single tree. We discuss how the MAST model can be extended in the future.}, }
@article {pmid38417645, year = {2024}, author = {Jeong, GJ and Khan, F and Tabassum, N and Cho, KJ and Kim, YM}, title = {Bacterial extracellular vesicles: Modulation of biofilm and virulence properties.}, journal = {Acta biomaterialia}, volume = {178}, number = {}, pages = {13-23}, doi = {10.1016/j.actbio.2024.02.029}, pmid = {38417645}, issn = {1878-7568}, mesh = {Humans ; Virulence ; *Biofilms ; Bacteria/metabolism ; Virulence Factors/metabolism ; Polysaccharides ; DNA ; *Nucleic Acids ; Disease Progression ; Lipids ; }, abstract = {Microbial pathogens cause persistent infections by forming biofilms and producing numerous virulence factors. Bacterial extracellular vesicles (BEVs) are nanostructures produced by various bacterial species vital for molecular transport. BEVs include various components, including lipids (glycolipids, LPS, and phospholipids), nucleic acids (genomic DNA, plasmids, and short RNA), proteins (membrane proteins, enzymes, and toxins), and quorum-sensing signaling molecules. BEVs play a major role in forming extracellular polymeric substances (EPS) in biofilms by transporting EPS components such as extracellular polysaccharides, proteins, and extracellular DNA. BEVs have been observed to carry various secretory virulence factors. Thus, BEVs play critical roles in cell-to-cell communication, biofilm formation, virulence, disease progression, and resistance to antimicrobial treatment. In contrast, BEVs have been shown to impede early-stage biofilm formation, disseminate mature biofilms, and reduce virulence. This review summarizes the current status in the literature regarding the composition and role of BEVs in microbial infections. Furthermore, the dual functions of BEVs in eliciting and suppressing biofilm formation and virulence in various microbial pathogens are thoroughly discussed. This review is expected to improve our understanding of the use of BEVs in determining the mechanism of biofilm development in pathogenic bacteria and in developing drugs to inhibit biofilm formation by microbial pathogens. STATEMENT OF SIGNIFICANCE: Bacterial extracellular vesicles (BEVs) are nanostructures formed by membrane blebbing and explosive cell lysis. It is essential for transporting lipids, nucleic acids, proteins, and quorum-sensing signaling molecules. BEVs play an important role in the formation of the biofilm's extracellular polymeric substances (EPS) by transporting its components, such as extracellular polysaccharides, proteins, and extracellular DNA. Furthermore, BEVs shield genetic material from nucleases and thermodegradation by packaging it during horizontal gene transfer, contributing to the transmission of bacterial adaptation determinants like antibiotic resistance. Thus, BEVs play a critical role in cell-to-cell communication, biofilm formation, virulence enhancement, disease progression, and drug resistance. In contrast, BEVs have been shown to prevent early-stage biofilm, disperse mature biofilm, and reduce virulence characteristics.}, }
@article {pmid38417454, year = {2024}, author = {Kfoury, B and Rodrigues, WFC and Kim, SJ and Brandizzi, F and Del-Bem, LE}, title = {Multiple horizontal gene transfer events have shaped plant glycosyl hydrolase diversity and function.}, journal = {The New phytologist}, volume = {242}, number = {2}, pages = {809-824}, doi = {10.1111/nph.19595}, pmid = {38417454}, issn = {1469-8137}, support = {Serra-1812-26691//Instituto Serrapilheira/ ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; DE-FG02-91ER20021//Chemical Sciences, Geosciences, and Biosciences Division/ ; DE-SC0018409//Great Lakes Bioenergy Research Center/ ; MICL02598//AgBioResearch, Michigan State University/ ; }, mesh = {Humans ; *Hydrolases ; Phylogeny ; *Gene Transfer, Horizontal/genetics ; Evolution, Molecular ; Plants/genetics ; }, abstract = {Plant glycosyl hydrolases (GHs) play a crucial role in selectively breaking down carbohydrates and glycoconjugates during various cellular processes, such as reserve mobilization, pathogen defense, and modification/disassembly of the cell wall. In this study, we examined the distribution of GH genes in the Archaeplastida supergroup, which encompasses red algae, glaucophytes, and green plants. We identified that the GH repertoire expanded from a few tens of genes in early archaeplastidians to over 400 genes in modern angiosperms, spanning 40 GH families in land plants. Our findings reveal that major evolutionary transitions were accompanied by significant changes in the GH repertoire. Specifically, we identified at least 23 GH families acquired by green plants through multiple horizontal gene transfer events, primarily from bacteria and fungi. We found a significant shift in the subcellular localization of GH activity during green plant evolution, with a marked increase in extracellular-targeted GH proteins associated with the diversification of plant cell wall polysaccharides and defense mechanisms against pathogens. In conclusion, our study sheds light on the macroevolutionary processes that have shaped the GH repertoire in plants, highlighting the acquisition of GH families through horizontal transfer and the role of GHs in plant adaptation and defense mechanisms.}, }
@article {pmid38415983, year = {2024}, author = {Zhang, M and Yang, B and Shi, J and Wang, Z and Liu, Y}, title = {Host defense peptides mitigate the spread of antibiotic resistance in physiologically relevant condition.}, journal = {Antimicrobial agents and chemotherapy}, volume = {68}, number = {4}, pages = {e0126123}, pmid = {38415983}, issn = {1098-6596}, support = {32222084, 32172907//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Animals ; Cattle ; Humans ; *Conjugation, Genetic ; Plasmids/genetics ; Drug Resistance, Microbial ; *Genes, Bacterial ; Gene Transfer, Horizontal ; Antimicrobial Cationic Peptides/pharmacology ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Antibiotic resistance represents a significant challenge to public health and human safety. The primary driver behind the dissemination of antibiotic resistance is the horizontal transfer of plasmids. Current conjugative transfer assay is generally performed in a standardized manner, ignoring the effect of the host environment. Host defense peptides (HDPs) possess a wide range of biological targets and play an essential role in the innate immune system. Herein, we reveal that sub-minimum inhibitory concentrations of HDPs facilitate the conjugative transfer of RP4-7 plasmid in the Luria Broth medium, and this observation is reversed in the RPMI medium, designed to simulate the host environment. Out of these HDPs, indolicidin (Ind), a cationic tridecapeptide from bovine neutrophils, significantly inhibits the conjugation of multidrug resistance plasmids in a dose-dependent manner, including blaNDM- and tet(X4)-bearing plasmids. We demonstrate that the addition of Ind to RPMI medium as the incubation substrate downregulates the expression of conjugation-related genes. In addition, Ind weakens the tricarboxylic acid cycle, impedes the electron transport chain, and disrupts the proton motive force, consequently diminishing the synthesis of adenosine triphosphate and limiting the energy supply. Our findings highlight the importance of the host-like environments for the development of horizontal transfer inhibitors and demonstrate the potential of HDPs in preventing the spread of resistance plasmids.}, }
@article {pmid38415839, year = {2024}, author = {Sun, L and David, KT and Wolters, JF and Karlen, SD and Gonçalves, C and Opulente, DA and LaBella, AL and Groenewald, M and Zhou, X and Shen, XX and Rokas, A and Hittinger, CT}, title = {Functional and Evolutionary Integration of a Fungal Gene With a Bacterial Operon.}, journal = {Molecular biology and evolution}, volume = {41}, number = {4}, pages = {}, pmid = {38415839}, issn = {1537-1719}, support = {R01 AI153356/AI/NIAID NIH HHS/United States ; /NH/NIH HHS/United States ; }, mesh = {*Operon ; *Enterobactin/metabolism/genetics ; *Phylogeny ; *Evolution, Molecular ; Siderophores/metabolism/genetics ; Genes, Fungal ; Saccharomycetales/genetics/metabolism ; Gene Transfer, Horizontal ; }, abstract = {Siderophores are crucial for iron-scavenging in microorganisms. While many yeasts can uptake siderophores produced by other organisms, they are typically unable to synthesize siderophores themselves. In contrast, Wickerhamiella/Starmerella (W/S) clade yeasts gained the capacity to make the siderophore enterobactin following the remarkable horizontal acquisition of a bacterial operon enabling enterobactin synthesis. Yet, how these yeasts absorb the iron bound by enterobactin remains unresolved. Here, we demonstrate that Enb1 is the key enterobactin importer in the W/S-clade species Starmerella bombicola. Through phylogenomic analyses, we show that ENB1 is present in all W/S clade yeast species that retained the enterobactin biosynthetic genes. Conversely, it is absent in species that lost the ent genes, except for Starmerella stellata, making this species the only cheater in the W/S clade that can utilize enterobactin without producing it. Through phylogenetic analyses, we infer that ENB1 is a fungal gene that likely existed in the W/S clade prior to the acquisition of the ent genes and subsequently experienced multiple gene losses and duplications. Through phylogenetic topology tests, we show that ENB1 likely underwent horizontal gene transfer from an ancient W/S clade yeast to the order Saccharomycetales, which includes the model yeast Saccharomyces cerevisiae, followed by extensive secondary losses. Taken together, these results suggest that the fungal ENB1 and bacterial ent genes were cooperatively integrated into a functional unit within the W/S clade that enabled adaptation to iron-limited environments. This integrated fungal-bacterial circuit and its dynamic evolution determine the extant distribution of yeast enterobactin producers and cheaters.}, }
@article {pmid38413855, year = {2024}, author = {Wang, H and Xia, F and Xia, Y and Li, J and Hu, Y and Deng, Y and Zou, M}, title = {Pangenome analysis of Shewanella xiamenensis revealed important genetic traits concerning genetic diversity, pathogenicity and antibiotic resistance.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {216}, pmid = {38413855}, issn = {1471-2164}, support = {No. 2023JJ30942//Natural Science Foundation of&#xa0;Hunan Province/ ; }, mesh = {Animals ; Humans ; *Genome, Bacterial ; Virulence/genetics ; Phylogeny ; Drug Resistance, Microbial ; *Genetic Variation ; *Shewanella ; }, abstract = {BACKGROUND: Shewanella xiamenensis, widely distributed in natural environments, has long been considered as opportunistic pathogen. Recently, significant changes in the resistance spectrum have been observed in S. xiamenensis, due to acquired antibiotic resistance genes. Therefore, a pan-genome analysis was conducted to illuminate the genomic changes in S. xiamenensis.<br><br>RESULTS: Phylogenetic analysis revealed three major clusters and three singletons, among which close relationship between several strains was discovered, regardless of their host and niches. The "open" genomes with diversity of accessory and strain-specific genomes took advantage towards diversity environments. The purifying selection pressure was the main force on genome evolution, especially in conservative genes. Only 53 gene families were under positive selection pressure. Phenotypic resistance analysis revealed 21 strains were classified as multi-drug resistance (MDR). Ten types of antibiotic resistance genes and two heavy metal resistance operons were discovered in S. xiamenensis. Mobile genetic elements and horizontal gene transfer increased genome diversity and were closely related to MDR strains. S. xiamenensis carried a variety of virulence genes and macromolecular secretion systems, indicating their important roles in pathogenicity and adaptability. Type IV secretion system was discovered in 15 genomes with various sequence structures, indicating it was originated from different donors through horizontal gene transfer.<br><br>CONCLUSIONS: This study provided with a detailed insight into the changes in the pan-genome of S. xiamenensis, highlighting its capability to acquire new mobile genetic elements and resistance genes for its adaptation to environment and pathogenicity to human and animals.}, }
@article {pmid38412971, year = {2024}, author = {Dewar, AE and Belcher, LJ and Scott, TW and West, SA}, title = {Genes for cooperation are not more likely to be carried by plasmids.}, journal = {Proceedings. Biological sciences}, volume = {291}, number = {2017}, pages = {20232549}, pmid = {38412971}, issn = {1471-2954}, mesh = {Plasmids/genetics ; *Genome, Bacterial ; *Bacteria/genetics ; Genomics ; Gene Transfer, Horizontal ; }, abstract = {Cooperation is prevalent across bacteria, but risks being exploited by non-cooperative cheats. Horizontal gene transfer, particularly via plasmids, has been suggested as a mechanism to stabilize cooperation. A key prediction of this hypothesis is that genes which are more likely to be transferred, such as those on plasmids, should be more likely to code for cooperative traits. Testing this prediction requires identifying all genes for cooperation in bacterial genomes. However, previous studies used a method which likely misses some of these genes for cooperation. To solve this, we used a new genomics tool, SOCfinder, which uses three distinct modules to identify all kinds of genes for cooperation. We compared where these genes were located across 4648 genomes from 146 bacterial species. In contrast to the prediction of the hypothesis, we found no evidence that plasmid genes are more likely to code for cooperative traits. Instead, we found the opposite-that genes for cooperation were more likely to be carried on chromosomes. Overall, the vast majority of genes for cooperation are not located on plasmids, suggesting that the more general mechanism of kin selection is sufficient to explain the prevalence of cooperation across bacteria.}, }
@article {pmid38412361, year = {2024}, author = {Crippen, TL and Sullivan, JP and Anderson, RC}, title = {Bacterial proximity effects on the transfer of antibiotic resistance genes within the alimentary tract of yellow mealworm larvae.}, journal = {Journal of economic entomology}, volume = {117}, number = {2}, pages = {417-426}, doi = {10.1093/jee/toae019}, pmid = {38412361}, issn = {1938-291X}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; *Tenebrio/genetics/microbiology ; Larva ; Plasmids ; Bacteria/genetics ; Insecta/genetics ; Drug Resistance, Microbial ; Escherichia coli/genetics ; }, abstract = {The arthropod intestinal tract and other anatomical parts naturally carry microorganisms. Some of which are pathogens, secrete toxins, or carry transferable antibiotic-resistance genes. The risks associated with the production and consumption of edible arthropods are dependent on indigenous microbes, as well as microbes introduced during the processes of rearing. This mass arthropod production puts individual arthropods in close proximity, which increases the possibility of their exposure to antibiotic-resistant bacteria carried by bacteria from fellow insects, industry workers, or rearing hardware and substrates. The purpose of this study was to determine if the alimentary tract of the yellow mealworm provided an environment permitting horizontal gene transfer between bacteria. The effect of the concentration of bacterial exposure was also assessed. Antibiotic resistance gene transfer between marker Salmonella Lignières (Enterobacterales: Enterobacteriaceae) and Escherichia coli (Migula) (Enterobacterales: Enterobacteriaceae) introduced into the larval gut demonstrated that the nutrient-rich environment of the yellow mealworm gut provided favorable conditions for the transfer of antibiotic resistance genes. Conjugation frequencies were similar across inoculum concentrations; however, transconjugant production correlated positively to increased exposure concentration. The lowest concentration of bacterial exposure required enrichment to detect and thus may have been approaching a threshold level for the 2 bacteria to colocate within the expanse of the larval gut. While many factors can affect this transfer, the simple factor of the proximity of donor and recipient bacteria, as defined by the concentration of bacteria within the volume of the insect gut, likely primarily contributed to the efficiency of antibiotic gene transfer.}, }
@article {pmid38410456, year = {2024}, author = {Kogay, R and Wolf, YI and Koonin, EV}, title = {Defense systems and horizontal gene transfer in bacteria.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38410456}, issn = {2692-8205}, abstract = {Horizontal gene transfer (HGT) is a fundamental process in the evolution of prokaryotes, making major contributions to diversification and adaptation. Typically, HGT is facilitated by mobile genetic elements (MGEs), such as conjugative plasmids and phages that generally impose fitness costs on their hosts. However, a substantial fraction of bacterial genes is involved in defense mechanisms that limit the propagation of MGEs, raising the possibility that they can actively restrict HGT. Here we examine whether defense systems curb HGT by exploring the connections between HGT rate and the presence of 73 defense systems in 12 bacterial species. We found that only 6 defense systems, 3 of which are different CRISPR-Cas subtypes, are associated with the reduced gene gain rate on the scale of species evolution. The hosts of such defense systems tend to have a smaller pangenome size and harbor fewer phage-related genes compared to genomes lacking these systems, suggesting that these defense mechanisms inhibit HGT by limiting the integration of prophages. We hypothesize that restriction of HGT by defense systems is species-specific and depends on various ecological and genetic factors, including the burden of MGEs and fitness effect of HGT in bacterial populations.}, }
@article {pmid38402936, year = {2024}, author = {Rzymski, P and Gwenzi, W and Poniedziałek, B and Mangul, S and Fal, A}, title = {Climate warming, environmental degradation and pollution as drivers of antibiotic resistance.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {346}, number = {}, pages = {123649}, doi = {10.1016/j.envpol.2024.123649}, pmid = {38402936}, issn = {1873-6424}, mesh = {Humans ; *Plastics ; Environmental Pollution ; Drug Resistance, Microbial/genetics ; Bacteria ; Metals ; Anti-Bacterial Agents/pharmacology ; *Pesticides ; Genes, Bacterial ; }, abstract = {Antibiotic resistance is a major challenge to public health, but human-caused environmental changes have not been widely recognized as its drivers. Here, we provide a comprehensive overview of the relationships between environmental degradation and antibiotic resistance, demonstrating that the former can potentially fuel the latter with significant public health outcomes. We describe that (i) global warming favors horizontal gene transfer, bacterial infections, the spread of drug-resistant pathogens due to water scarcity, and the release of resistance genes with wastewater; (ii) pesticide and metal pollution act as co-selectors of antibiotic resistance mechanisms; (iii) microplastics create conditions promoting and spreading antibiotic resistance and resistant bacteria; (iv) changes in land use, deforestation, and environmental pollution reduce microbial diversity, a natural barrier to antibiotic resistance spread. We argue that management of antibiotic resistance must integrate environmental goals, including mitigation of further increases in the Earth's surface temperature, better qualitative and quantitative protection of water resources, strengthening of sewage infrastructure and improving wastewater treatment, counteracting the microbial diversity loss, reduction of pesticide and metal emissions, and plastic use, and improving waste recycling. These actions should be accompanied by restricting antibiotic use only to clinically justified situations, developing novel treatments, and promoting prophylaxis. It is pivotal for health authorities and the medical community to adopt the protection of environmental quality as a part of public health measures, also in the context of antibiotic resistance management.}, }
@article {pmid38399658, year = {2024}, author = {Ishola, OA and Kublik, S and Durai Raj, AC and Ohnmacht, C and Schulz, S and Foesel, BU and Schloter, M}, title = {Comparative Metagenomic Analysis of Bacteriophages and Prophages in Gnotobiotic Mouse Models.}, journal = {Microorganisms}, volume = {12}, number = {2}, pages = {}, pmid = {38399658}, issn = {2076-2607}, support = {Helmholtz Munich Allergy Program//Helmholtz Munich Allergy Program/ ; }, abstract = {Gnotobiotic murine models are important to understand microbiota-host interactions. Despite the role of bacteriophages as drivers for microbiome structure and function, there is no information about the structure and function of the gut virome in gnotobiotic models and the link between bacterial and bacteriophage/prophage diversity. We studied the virome of gnotobiotic murine Oligo-MM12 (12 bacterial species) and reduced Altered Schaedler Flora (ASF, three bacterial species). As reference, the virome of Specific Pathogen-Free (SPF) mice was investigated. A metagenomic approach was used to assess prophages and bacteriophages in the guts of 6-week-old female mice. We identified a positive correlation between bacteria diversity, and bacteriophages and prophages. Caudoviricetes (82.4%) were the most prominent class of phages in all samples with differing relative abundance. However, the host specificity of bacteriophages belonging to class Caudoviricetes differed depending on model bacterial diversity. We further studied the role of bacteriophages in horizontal gene transfer and microbial adaptation to the host's environment. Analysis of mobile genetic elements showed the contribution of bacteriophages to the adaptation of bacterial amino acid metabolism. Overall, our results implicate virome "dark matter" and interactions with the host system as factors for microbial community structure and function which determine host health. Taking the importance of the virome in the microbiome diversity and horizontal gene transfer, reductions in the virome might be an important factor driving losses of microbial biodiversity and the subsequent dysbiosis of the gut microbiome.}, }
@article {pmid38399642, year = {2024}, author = {Lerner, A and Benzvi, C and Vojdani, A}, title = {The Potential Harmful Effects of Genetically Engineered Microorganisms (GEMs) on the Intestinal Microbiome and Public Health.}, journal = {Microorganisms}, volume = {12}, number = {2}, pages = {}, pmid = {38399642}, issn = {2076-2607}, abstract = {Gut luminal dysbiosis and pathobiosis result in compositional and biodiversified alterations in the microbial and host co-metabolites. The primary mechanism of bacterial evolution is horizontal gene transfer (HGT), and the acquisition of new traits can be achieved through the exchange of mobile genetic elements (MGEs). Introducing genetically engineered microbes (GEMs) might break the harmonized balance in the intestinal compartment. The present objectives are: 1. To reveal the role played by the GEMs' horizontal gene transfers in changing the landscape of the enteric microbiome eubiosis 2. To expand on the potential detrimental effects of those changes on the human genome and health. A search of articles published in PubMed/MEDLINE, EMBASE, and Scielo from 2000 to August 2023 using appropriate MeSH entry terms was performed. The GEMs' horizontal gene exchanges might induce multiple human diseases. The new GEMs can change the long-term natural evolution of the enteric pro- or eukaryotic cell inhabitants. The worldwide regulatory authority's safety control of GEMs is not enough to protect public health. Viability, biocontainment, and many other aspects are only partially controlled and harmful consequences for public health should be avoided. It is important to remember that prevention is the most cost-effective strategy and primum non nocere should be the focus.}, }
@article {pmid38397005, year = {2024}, author = {Valenzuela, JA and Vázquez, L and Rodríguez, J and Flórez, AB and Vasek, OM and Mayo, B}, title = {Phenotypic, Technological, Safety, and Genomic Profiles of Gamma-Aminobutyric Acid-Producing Lactococcus lactis and Streptococcus thermophilus Strains Isolated from Cow's Milk.}, journal = {International journal of molecular sciences}, volume = {25}, number = {4}, pages = {}, pmid = {38397005}, issn = {1422-0067}, support = {PID2022-141271NB-I00//Agencia Estatal de Investigaci&#xf3;n/ ; }, mesh = {Animals ; Milk/microbiology ; *Lactococcus lactis/genetics ; Streptococcus thermophilus/genetics ; gamma-Aminobutyric Acid ; *Lactobacillales ; Genomics ; Fermentation ; *Cheese/microbiology ; }, abstract = {Gamma-aminobutyric acid (GABA)-producing lactic acid bacteria (LAB) can be used as starters in the development of GABA-enriched functional fermented foods. In this work, four GABA-producing strains each of Lactococcus lactis and Streptococcus thermophilus species were isolated from cow's milk, and their phenotypic, technological, and safety profiles determined. Genome analysis provided genetic support for the majority of the analyzed traits, namely, GABA production, growth in milk, and the absence of genes of concern. The operon harboring the glutamate decarboxylase gene (gadB) was chromosomally encoded in all strains and showed the same gene content and gene order as those reported, respectively, for L. lactis and S. thermophilus. In the latter species, the operon was flanked (as in most strains of this species) by complete or truncated copies of insertion sequences (IS), suggesting recent acquisition through horizontal gene transfer. The genomes of three L. lactis and two S. thermophilus strains showed a gene encoding a caseinolytic proteinase (PrtP in L. lactis and PrtS in S. thermophilus). Of these, all but one grew in milk, forming a coagulum of good appearance and an appealing acidic flavor and taste. They also produced GABA in milk supplemented with monosodium glutamate. Two L. lactis strains were identified as belonging to the biovar. diacetylactis, utilized citrate from milk, and produced significant amounts of acetoin. None of the strains showed any noticeable antibiotic resistance, nor did their genomes harbor transferable antibiotic resistance genes or genes involved in toxicity, virulence, or pathogenicity. Altogether these results suggest that all eight strains may be considered candidates for use as starters or components of mixed LAB cultures for the manufacture of GABA-enriched fermented dairy products.}, }
@article {pmid38394997, year = {2024}, author = {Wang, H and Wu, P and Xiong, L and Kim, HS and Kim, JH and Ki, JS}, title = {Nuclear genome of dinoflagellates: Size variation and insights into evolutionary mechanisms.}, journal = {European journal of protistology}, volume = {93}, number = {}, pages = {126061}, doi = {10.1016/j.ejop.2024.126061}, pmid = {38394997}, issn = {1618-0429}, mesh = {Humans ; Phylogeny ; *Dinoflagellida/genetics ; Genome/genetics ; Biological Evolution ; DNA ; }, abstract = {Recent progress in high-throughput sequencing technologies has dramatically increased availability of genome data for prokaryotes and eukaryotes. Dinoflagellates have distinct chromosomes and a huge genome size, which make their genomic analysis complicated. Here, we reviewed the nuclear genomes of core dinoflagellates, focusing on the genome and cell size. Till now, the genome sizes of several dinoflagellates (more than 25) have been measured by certain methods (e.g., flow cytometry), showing a range of 3-250 pg of genomic DNA per cell. In contrast to their relatively small cell size, their genomes are huge (about 1-80 times the human haploid genome). In the present study, we collected the genome and cell size data of dinoflagellates and compared their relationships. We found that dinoflagellate genome size exhibits a positive correlation with cell size. On the other hand, we recognized that the genome size is not correlated with phylogenetic relatedness. These may be caused by genome duplication, increased gene copy number, repetitive non-coding DNA, transposon expansion, horizontal gene transfer, organelle-to-nucleus gene transfer, and/or mRNA reintegration into the genome. Ultimate verification of these factors as potential causative mechanisms would require sequencing of more dinoflagellate genomes in the future.}, }
@article {pmid38394893, year = {2024}, author = {Chen, T and Mo, C and Yuan, Y and Li, S and Wu, Y and Liao, X and Yang, Y}, title = {Short-, long-read metagenome and virome reveal the profile of phage-mediated ARGs in anoxic-oxic processes for swine wastewater treatment.}, journal = {Journal of hazardous materials}, volume = {468}, number = {}, pages = {133789}, doi = {10.1016/j.jhazmat.2024.133789}, pmid = {38394893}, issn = {1873-3336}, mesh = {Animals ; Swine ; *Anti-Bacterial Agents/pharmacology ; Metagenome ; Wastewater ; *Bacteriophages/genetics ; Virome ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Genes, Bacterial ; }, abstract = {Phages are among the most widely spread viruses, but their profiles and the antibiotic resistance genes (ARGs) they carry in swine wastewater remain underexplored. The present study investigated the distribution characteristics of phages and their ARG risk in anoxic/oxic (A/O) wastewater treatment processes of swine farms using short- and long-read metagenome and virome. The results demonstrated that the virome could extract more phage sequences than the total metagenome; thus, it was more suited for studying phages in wastewater settings. Intriguingly, phages had significantly lower abundance of ARG than ARGs harbored by total microorganisms (P < 0.01). Eleven ARGs co-occurred with phages and bacteria (R > 0.6 and P < 0.05), with Siphoviridae being the phage co-occurring with the most ARGs (5). Horizontal gene transfer (HGT) events were observed between Proteobacteria and the major phyla except for Bacteroidota. Furthermore, there were prophage sequences and ARGs on the same contig in bacterial MAGs. These data strongly demonstrate that phages promote horizontal transfer of ARG between bacterial hosts in A/O processes for swine wastewater treatment. Therefore, the risk of phage-mediated horizontal transfer of ARGs cannot be overlooked despite the low abundance of phage ARGs (pARG).}, }
@article {pmid38393159, year = {2024}, author = {Jiang, YN and Tamiya-Ishitsuka, H and Aoi, R and Okabe, T and Yokota, A and Noda, N}, title = {MazEF Homologs in Symbiobacterium thermophilum Exhibit Cross-Neutralization with Non-Cognate MazEFs.}, journal = {Toxins}, volume = {16}, number = {2}, pages = {}, pmid = {38393159}, issn = {2072-6651}, support = {KAKENHI JP19K06555//Japan Society for the Promotion of Science/ ; }, mesh = {*Escherichia coli Proteins/genetics ; *Bacterial Toxins/genetics/metabolism ; Escherichia coli/genetics ; *Lactobacillales/metabolism ; Endoribonucleases/metabolism ; Ribonucleotides ; Bacterial Proteins/genetics/metabolism ; DNA-Binding Proteins/genetics ; *Clostridiales ; }, abstract = {Toxin-antitoxin systems are preserved by nearly every prokaryote. The type II toxin MazF acts as a sequence-specific endoribonuclease, cleaving ribonucleotides at specific sequences that vary from three to seven bases, as has been reported in different host organisms to date. The present study characterized the MazEF module (MazEF-sth) conserved in the Symbiobacterium thermophilum IAM14863 strain, a Gram-negative syntrophic bacterium that can be supported by co-culture with multiple bacteria, including Bacillus subtilis. Based on a method combining massive parallel sequencing and the fluorometric assay, MazF-sth was determined to cleave ribonucleotides at the UACAUA motif, which is markedly similar to the motifs recognized by MazF from B. subtilis (MazF-bs), and by several MazFs from Gram-positive bacteria. MazF-sth, with mutations at conserved amino acid residues Arg29 and Thr52, lost most ribonuclease activity, indicating that these residues that are crucial for MazF-bs also play significant roles in MazF-sth catalysis. Further, cross-neutralization between MazF-sth and the non-cognate MazE-bs was discovered, and herein, the neutralization mechanism is discussed based on a protein-structure simulation via AlphaFold2 and multiple sequence alignment. The conflict between the high homology shared by these MazF amino acid sequences and the few genetic correlations among their host organisms may provide evidence of horizontal gene transfer.}, }
@article {pmid38391535, year = {2024}, author = {Yaikhan, T and Chukamnerd, A and Singkhamanan, K and Nokchan, N and Chintakovid, N and Chusri, S and Pomwised, R and Wonglapsuwan, M and Surachat, K}, title = {Genomic Characterization of Mobile Genetic Elements Associated with Multidrug-Resistant Acinetobacter Non-baumannii Species from Southern Thailand.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {2}, pages = {}, pmid = {38391535}, issn = {2079-6382}, support = {MED6601319S//the National Science, Research and Innovation Fund (NSRF) and Prince of Songkla University, Thailand/ ; }, abstract = {This study investigated the genetic diversity, antimicrobial resistance profiles, and virulence characteristics of Acinetobacter non-baumannii isolates obtained from four hospitals in southern Thailand. Clinical data, genome information, and average nucleotide identity (ANI) were analyzed for eight isolates, revealing diverse genetic profiles and novel sequence types (STs). Minimum spanning tree analysis indicated potential clonal spread of certain STs across different geographic regions. Antimicrobial resistance genes (ARGs) were detected in all isolates, with a high prevalence of genes conferring resistance to carbapenems, highlighting the challenge of antimicrobial resistance in Acinetobacter spp. infections. Mobile genetic elements (MGEs) carrying ARGs were also identified, emphasizing the role of horizontal gene transfer in spreading resistance. Evaluation of virulence-associated genes revealed a diverse range of virulence factors, including those related to biofilm formation and antibiotic resistance. However, no direct correlation was found between virulence-associated genes in Acinetobacter spp. and specific clinical outcomes, such as infection severity or patient mortality. This complexity suggests that factors beyond gene presence may influence disease progression and outcomes. This study emphasizes the importance of continued surveillance and molecular epidemiological studies to combat the spread of multidrug-resistant (MDR) Acinetobacter non-baumannii strains. The findings provide valuable insights into the epidemiology and genetic characteristics of this bacteria in southern Thailand, with implications for infection control and antimicrobial management efforts.}, }
@article {pmid38384862, year = {2024}, author = {Wu, Z and Solís-Lemus, C}, title = {Ultrafast learning of four-node hybridization cycles in phylogenetic networks using algebraic invariants.}, journal = {Bioinformatics advances}, volume = {4}, number = {1}, pages = {vbae014}, pmid = {38384862}, issn = {2635-0041}, abstract = {MOTIVATION: The abundance of gene flow in the Tree of Life challenges the notion that evolution can be represented with a fully bifurcating process which cannot capture important biological realities like hybridization, introgression, or horizontal gene transfer. Coalescent-based network methods are increasingly popular, yet not scalable for big data, because they need to perform a heuristic search in the space of networks as well as numerical optimization that can be NP-hard. Here, we introduce a novel method to reconstruct phylogenetic networks based on algebraic invariants. While there is a long tradition of using algebraic invariants in phylogenetics, our work is the first to define phylogenetic invariants on concordance factors (frequencies of four-taxon splits in the input gene trees) to identify level-1 phylogenetic networks under the multispecies coalescent model.<br><br>RESULTS: Our novel hybrid detection methodology is optimization-free as it only requires the evaluation of polynomial equations, and as such, it bypasses the traversal of network space, yielding a computational speed at least 10 times faster than the fastest-to-date network methods. We illustrate our method's performance on simulated and real data from the genus Canis.<br><br>We present an open-source publicly available Julia package PhyloDiamond.jl available at https://github.com/solislemuslab/PhyloDiamond.jl with broad applicability within the evolutionary community.}, }
@article {pmid38382161, year = {2024}, author = {Mori, Y and Yamashita, E and Nakagawa, A and Matsuzawa, T and Inagaki, M and Aiba, Y and Tanaka, S and Hatori, S and Ayami, M and Takeda, S}, title = {Determination of the three-dimensional structure of bacteriophage Mu(-) tail fiber and its characterization.}, journal = {Virology}, volume = {593}, number = {}, pages = {110017}, doi = {10.1016/j.virol.2024.110017}, pmid = {38382161}, issn = {1096-0341}, mesh = {*Bacteriophage mu/chemistry/genetics ; *Bacteriophages/genetics ; Viral Tail Proteins/genetics ; }, abstract = {Bacteriophage Mu is a temperate phage known to infect various species of Enterobacteria, playing a role in bacterial mutation induction and horizontal gene transfer. The phage possesses two types of tail fibers important for host recognition, which enable it to expand its range of hosts. The alternate tail fibers are formed through the action of genes 49-50 or 52-51, allowing the Mu phage to recognize different surfaces of host cells. In a previous study, we presented the X-ray crystal structure of the C-terminal lipopolysaccharide (LPS)-binding domain of gene product (gp) 49, one of the subunits comprising the Mu tail fiber. In this study, we have determined the structure of the alternative tail fiber subunit, gp52, and compared it with other tail fibers. The results revealed that Mu phage employs different structural motifs for two individual tail fibers for recognizing different hosts.}, }
@article {pmid38381581, year = {2024}, author = {Aggarwal, R and Mahajan, P and Pandiya, S and Bajaj, A and Verma, SK and Yadav, P and Kharat, AS and Khan, AU and Dua, M and Johri, AK}, title = {Antibiotic resistance: a global crisis, problems and solutions.}, journal = {Critical reviews in microbiology}, volume = {50}, number = {5}, pages = {896-921}, doi = {10.1080/1040841X.2024.2313024}, pmid = {38381581}, issn = {1549-7828}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/drug effects/genetics ; Bacterial Infections/microbiology/drug therapy ; Drug Resistance, Bacterial ; }, abstract = {Healthy state is priority in today's world which can be achieved using effective medicines. But due to overuse and misuse of antibiotics, a menace of resistance has increased in pathogenic microbes. World Health Organization (WHO) has announced ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) as the top priority pathogens as these have developed resistance against certain antibiotics. To combat such a global issue, it is utmost important to identify novel therapeutic strategies/agents as an alternate to such antibiotics. To name certain antibiotic adjuvants including: inhibitors of beta-lactamase, efflux pumps and permeabilizers for outer membrane can potentially solve the antibiotic resistance problems. In this regard, inhibitors of lytic domain of lytic transglycosylases provide a novel way to not only act as an alternate to antibiotics but also capable of restoring the efficiency of previously resistant antibiotics. Further, use of bacteriophages is another promising strategy to deal with antibiotic resistant pathogens. Taking in consideration the alternatives of antibiotics, a green synthesis nanoparticle-based therapy exemplifies a good option to combat microbial resistance. As horizontal gene transfer (HGT) in bacteria facilitates the evolution of new resistance strains, therefore identifying the mechanism of resistance and development of inhibitors against it can be a novel approach to combat such problems. In our perspective, host-directed therapy (HDT) represents another promising strategy in combating antimicrobial resistance (AMR). This approach involves targeting specific factors within host cells that pathogens rely on for their survival, either through replication or persistence. As many new drugs are under clinical trials it is advisable that more clinical data and antimicrobial stewardship programs should be conducted to fully assess the clinical efficacy and safety of new therapeutic agents.}, }
@article {pmid38381035, year = {2024}, author = {Unitt, A and Maiden, M and Harrison, O}, title = {Characterizing the diversity and commensal origins of penA mosaicism in the genus Neisseria.}, journal = {Microbial genomics}, volume = {10}, number = {2}, pages = {}, pmid = {38381035}, issn = {2057-5858}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; Mosaicism ; Neisseria/genetics ; Neisseria gonorrhoeae/genetics ; *Neisseria meningitidis ; *Gonorrhea ; }, abstract = {Mosaic penA alleles formed through horizontal gene transfer (HGT) have been instrumental to the rising incidence of ceftriaxone-resistant gonococcal infections. Although interspecies HGT of regions of the penA gene between Neisseria gonorrhoeae and commensal Neisseria species has been described, knowledge concerning which species are the most common contributors to mosaic penA alleles is limited, with most studies examining only a small number of alleles. Here, we investigated the origins of recombinant penA alleles through in silico analyses that incorporated 1700 penA alleles from 35 513 Neisseria isolates, comprising 15 different Neisseria species. We identified Neisseria subflava and Neisseria cinerea as the most common source of recombinant sequences in N. gonorrhoeae penA. This contrasted with Neisseria meningitidis penA, for which the primary source of recombinant DNA was other meningococci, followed by Neisseria lactamica. Additionally, we described the distribution of polymorphisms implicated in antimicrobial resistance in penA, and found that these are present across the genus. These results provide insight into resistance-related changes in the penA gene across human-associated Neisseria species, illustrating the importance of genomic surveillance of not only the pathogenic Neisseria, but also of the oral niche-associated commensals from which these pathogens are sourcing key genetic variation.}, }
@article {pmid38378896, year = {2024}, author = {Pfeifer, E and Rocha, EPC}, title = {Phage-plasmids promote recombination and emergence of phages and plasmids.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {1545}, pmid = {38378896}, issn = {2041-1723}, mesh = {*Bacteriophages/genetics ; Plasmids/genetics ; Prophages/genetics ; Gene Transfer, Horizontal/genetics ; }, abstract = {Phages and plasmids are regarded as distinct types of mobile genetic elements that drive bacterial evolution by horizontal gene transfer. However, the distinction between both types is blurred by the existence of elements known as prophage-plasmids or phage-plasmids, which transfer horizontally between cells as viruses and vertically within cellular lineages as plasmids. Here, we study gene flow between the three types of elements. We show that the gene repertoire of phage-plasmids overlaps with those of phages and plasmids. By tracking recent recombination events, we find that phage-plasmids exchange genes more frequently with plasmids than with phages, and that direct gene exchange between plasmids and phages is less frequent in comparison. The results suggest that phage-plasmids can mediate gene flow between plasmids and phages, including exchange of mobile element core functions, defense systems, and antibiotic resistance. Moreover, a combination of gene transfer and gene inactivation may result in the conversion of elements. For example, gene loss turns P1-like phage-plasmids into integrative prophages or into plasmids (that are no longer phages). Remarkably, some of the latter have acquired conjugation-related functions to became mobilisable by conjugation. Thus, our work indicates that phage-plasmids can play a key role in the transfer of genes across mobile elements within their hosts, and can act as intermediates in the conversion of one type of element into another.}, }
@article {pmid38376265, year = {2024}, author = {Saini, P and Bandsode, V and Singh, A and Mendem, SK and Semmler, T and Alam, M and Ahmed, N}, title = {Genomic insights into virulence, antimicrobial resistance, and adaptation acumen of Escherichia coli isolated from an urban environment.}, journal = {mBio}, volume = {15}, number = {3}, pages = {e0354523}, pmid = {38376265}, issn = {2150-7511}, support = {AMR/257/2021/ECD-II//ICMR/ ; IoE by MoE [F11/9/2019-U3A]//UoH/ ; //GAT-B Fellowship/ ; (PMRF-ID 3702547) MoE//Prime ministers Research Fellowship/ ; }, mesh = {Animals ; Humans ; *Escherichia coli/genetics ; Virulence/genetics ; Anti-Bacterial Agents/pharmacology ; *Escherichia coli Infections/microbiology ; Drug Resistance, Bacterial ; Genomics ; Soil ; Water ; }, abstract = {UNLABELLED: Populations of common commensal bacteria such as Escherichia coli undergo genetic changes by the acquisition of certain virulence and antimicrobial resistance (AMR) encoding genetic elements leading to the emergence of pathogenic strains capable of surviving in the previously uninhabited or protected niches. These bacteria are also reported to be prevalent in the environment where they survive by adopting various recombination strategies to counter microflora of the soil and water, under constant selection pressure(s). In this study, we performed molecular characterization, phenotypic AMR analysis, and whole genome sequencing (WGS) of E. coli (n = 37) isolated from soil and surface water representing the urban and peri-urban areas. The primary aim of this study was to understand the genetic architecture and pathogenic acumen exhibited by environmental E. coli. WGS-based analysis entailing resistome and virulome profiling indicated the presence of various virulence (adherence, iron uptake, and toxins) and AMR encoding genes, including blaNDM-5 in the environmental isolates. A majority of our isolates belonged to phylogroup B1 (73%). A few isolates in our collection were of sequence type(s) (ST) 58 and 224 that could have emerged recently as clonal lineages and might pose risk of infection/transmission. Mobile genetic elements (MGEs) such as plasmids (predominantly) of the IncF family, prophages, pipolins, and insertion elements such as IS1 and IS5 were also observed to exist, which may presumably aid in the propagation of genes encoding resistance against antimicrobial drugs. The observed high prevalence of MGEs associated with multidrug resistance in pathogenic E. coli isolates belonging to the phylogroup B1 underscores the need for extended surveillance to keep track of and prevent the transmission of the bacterium to certain vulnerable human and animal populations.<br><br>IMPORTANCE: Evolutionary patterns of E. coli bacteria convey that they evolve into highly pathogenic forms by acquiring fitness advantages, such as AMR, and various virulence factors through the horizontal gene transfer (HGT)-mediated acquisition of MGEs. However, limited research on the genetic profiles of environmental E. coli, particularly from India, hinders our understanding of their transition to pathogenic forms and impedes the adoption of a comprehensive approach to address the connection between environmentally dwelling E. coli populations and human and veterinary public health. This study focuses on high-resolution genomic analysis of the environmental E. coli isolates aiming to understand the genetic similarities and differences among isolates from different environmental niches and uncover the survival strategies employed by these bacteria to thrive in their surroundings. Our approach involved molecular characterization of environmental samples using PCR-based DNA fingerprinting and subsequent WGS analysis. This multidisciplinary approach is likely to provide valuable insights into the understanding of any potential spill-over to human and animal populations and locales. Investigating these environmental isolates has significant potential for developing epidemiological strategies against transmission and understanding niche-specific evolutionary patterns.}, }
@article {pmid38374083, year = {2024}, author = {Fox, BW and Helf, MJ and Burkhardt, RN and Artyukhin, AB and Curtis, BJ and Palomino, DF and Schroeder, AF and Chaturbedi, A and Tauffenberger, A and Wrobel, CJJ and Zhang, YK and Lee, SS and Schroeder, FC}, title = {Evolutionarily related host and microbial pathways regulate fat desaturation in C. elegans.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {1520}, pmid = {38374083}, issn = {2041-1723}, support = {P40 OD010440/OD/NIH HHS/United States ; R35 GM131877/GM/NIGMS NIH HHS/United States ; T32 GM138826/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Caenorhabditis elegans/metabolism ; *Caenorhabditis elegans Proteins/metabolism ; PPAR alpha/metabolism ; Escherichia coli/genetics/metabolism ; Fatty Acids/metabolism ; Cyclopropanes/metabolism ; }, abstract = {Fatty acid desaturation is central to metazoan lipid metabolism and provides building blocks of membrane lipids and precursors of diverse signaling molecules. Nutritional conditions and associated microbiota regulate desaturase expression, but the underlying mechanisms have remained unclear. Here, we show that endogenous and microbiota-dependent small molecule signals promote lipid desaturation via the nuclear receptor NHR-49/PPARα in C. elegans. Untargeted metabolomics of a β-oxidation mutant, acdh-11, in which expression of the stearoyl-CoA desaturase FAT-7/SCD1 is constitutively increased, revealed accumulation of a β-cyclopropyl fatty acid, becyp#1, that potently activates fat-7 expression via NHR-49. Biosynthesis of becyp#1 is strictly dependent on expression of cyclopropane synthase by associated bacteria, e.g., E. coli. Screening for structurally related endogenous metabolites revealed a β-methyl fatty acid, bemeth#1, which mimics the activity of microbiota-dependent becyp#1 but is derived from a methyltransferase, fcmt-1, that is conserved across Nematoda and likely originates from bacterial cyclopropane synthase via ancient horizontal gene transfer. Activation of fat-7 expression by these structurally similar metabolites is controlled by distinct mechanisms, as microbiota-dependent becyp#1 is metabolized by a dedicated β-oxidation pathway, while the endogenous bemeth#1 is metabolized via α-oxidation. Collectively, we demonstrate that evolutionarily related biosynthetic pathways in metazoan host and associated microbiota converge on NHR-49/PPARα to regulate fat desaturation.}, }
@article {pmid38373236, year = {2024}, author = {Zhao, S and Rogers, MJ and Ding, C and Xu, G and He, J}, title = {Interspecies Mobility of Organohalide Respiration Gene Clusters Enables Genetic Bioaugmentation.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {9}, pages = {4214-4225}, doi = {10.1021/acs.est.3c09171}, pmid = {38373236}, issn = {1520-5851}, mesh = {Ecosystem ; Bacteria/genetics ; *Environmental Pollutants ; Respiration ; Multigene Family ; Biodegradation, Environmental ; *Chloroflexi ; }, abstract = {Anthropogenic organohalide pollutants pose a severe threat to public health and ecosystems. In situ bioremediation using organohalide respiring bacteria (OHRB) offers an environmentally friendly and cost-efficient strategy for decontaminating organohalide-polluted sites. The genomic structures of many OHRB suggest that dehalogenation traits can be horizontally transferred among microbial populations, but their occurrence among anaerobic OHRB has not yet been demonstrated experimentally. This study isolates and characterizes a novel tetrachloroethene (PCE)-dechlorinating Sulfurospirillum sp. strain SP, distinguishing itself among anaerobic OHRB by showcasing a mechanism essential for horizontal dissemination of reductive dehalogenation capabilities within microbial populations. Its genetic characterization identifies a unique plasmid (pSULSP), harboring reductive dehalogenase and de novo corrinoid biosynthesis operons, functions critical to organohalide respiration, flanked by mobile elements. The active mobility of these elements was demonstrated through genetic analyses of spontaneously emerging nondehalogenating variants of strain SP. More importantly, bioaugmentation of nondehalogenating microcosms with pSULSP DNA triggered anaerobic PCE dechlorination in taxonomically diverse bacterial populations. Our results directly support the hypothesis that exposure to anthropogenic organohalide pollutants can drive the emergence of dehalogenating microbial populations via horizontal gene transfer and demonstrate a mechanism by which genetic bioaugmentation for remediation of organohalide pollutants could be achieved in anaerobic environments.}, }
@article {pmid38372324, year = {2024}, author = {Lehnert, T and Gijs, MAM}, title = {Microfluidic systems for infectious disease diagnostics.}, journal = {Lab on a chip}, volume = {24}, number = {5}, pages = {1441-1493}, doi = {10.1039/d4lc00117f}, pmid = {38372324}, issn = {1473-0189}, mesh = {Humans ; Microfluidics ; Ecosystem ; *Viruses ; *Communicable Diseases/diagnosis ; Point-of-Care Systems ; }, abstract = {Microorganisms, encompassing both uni- and multicellular entities, exhibit remarkable diversity as omnipresent life forms in nature. They play a pivotal role by supplying essential components for sustaining biological processes across diverse ecosystems, including higher host organisms. The complex interactions within the human gut microbiota are crucial for metabolic functions, immune responses, and biochemical signalling, particularly through the gut-brain axis. Viruses also play important roles in biological processes, for example by increasing genetic diversity through horizontal gene transfer when replicating inside living cells. On the other hand, infection of the human body by microbiological agents may lead to severe physiological disorders and diseases. Infectious diseases pose a significant burden on global healthcare systems, characterized by substantial variations in the epidemiological landscape. Fast spreading antibiotic resistance or uncontrolled outbreaks of communicable diseases are major challenges at present. Furthermore, delivering field-proven point-of-care diagnostic tools to the most severely affected populations in low-resource settings is particularly important and challenging. New paradigms and technological approaches enabling rapid and informed disease management need to be implemented. In this respect, infectious disease diagnostics taking advantage of microfluidic systems combined with integrated biosensor-based pathogen detection offers a host of innovative and promising solutions. In this review, we aim to outline recent activities and progress in the development of microfluidic diagnostic tools. Our literature research mainly covers the last 5 years. We will follow a classification scheme based on the human body systems primarily involved at the clinical level or on specific pathogen transmission modes. Important diseases, such as tuberculosis and malaria, will be addressed more extensively.}, }
@article {pmid38370577, year = {2023}, author = {Yuan, C and An, T and Li, X and Zou, J and Lin, Z and Gu, J and Hu, R and Fang, Z}, title = {Genomic analysis of Ralstonia pickettii reveals the genetic features for potential pathogenicity and adaptive evolution in drinking water.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1272636}, pmid = {38370577}, issn = {1664-302X}, abstract = {Ralstonia pickettii, the most critical clinical pathogen of the genus Ralstonia, has been identified as a causative agent of numerous harmful infections. Additionally, Ralstonia pickettii demonstrates adaptability to extreme environmental conditions, such as those found in drinking water. In this study, we conducted a comprehensive genomic analysis to investigate the genomic characteristics related to potential pathogenicity and adaptive evolution in drinking water environments of Ralstonia pickettii. Through phylogenetic analysis and population genetic analysis, we divided Ralstonia pickettii into five Groups, two of which were associated with drinking water environments. The open pan-genome with a large and flexible gene repertoire indicated a high genetic plasticity. Significant differences in functional enrichment were observed between the core- and pan-genome of different groups. Diverse mobile genetic elements (MGEs), extensive genomic rearrangements, and horizontal gene transfer (HGT) events played a crucial role in generating genetic diversity. In drinking water environments, Ralstonia pickettii exhibited strong adaptability, and the acquisition of specific adaptive genes was potentially facilitated by genomic islands (GIs) and HGT. Furthermore, environmental pressures drove the adaptive evolution of Ralstonia pickettii, leading to the accumulation of unique mutations in key genes. These mutations may have a significant impact on various physiological functions, particularly carbon metabolism and energy metabolism. The presence of virulence-related elements associated with macromolecular secretion systems, virulence factors, and antimicrobial resistance indicated the potential pathogenicity of Ralstonia pickettii, making it capable of causing multiple nosocomial infections. This study provides comprehensive insights into the potential pathogenicity and adaptive evolution of Ralstonia pickettii in drinking water environments from a genomic perspective.}, }
@article {pmid38368718, year = {2024}, author = {Wang, T and Xu, Y and Ling, W and Mosa, A and Liu, S and Lin, Z and Wang, H and Hu, X}, title = {Dissemination of antibiotic resistance genes is regulated by iron oxides: Insight into the influence on bacterial transformation.}, journal = {Environment international}, volume = {185}, number = {}, pages = {108499}, doi = {10.1016/j.envint.2024.108499}, pmid = {38368718}, issn = {1873-6750}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Transformation, Bacterial ; Escherichia coli/genetics ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Soil/chemistry ; Oxides ; Iron ; Soil Microbiology ; Manure/microbiology ; *Ferric Compounds ; }, abstract = {The transportation of antibiotic resistance genes (ARGs) in manure-soil-plant continuums poses risks to human health. Horizontal gene transfer, particularly for bacterial transformation, is an important way for ARG dissemination. As crucial components in soils, iron oxides impacted the fates of various abiotic and biotic contaminants due to their active properties. However, whether they can influence the transformation of ARGs is unknown, which waits to be figured out to boost the assessment and control of ARG spread risks. In this study, we have investigated the effects of goethite, hematite, and magnetite (0-250 mg/L, with sizes < 100 nm and > 100 nm) on the transfer of ampicillin resistance genes to Escherichia coli cells. At lower iron oxide concentrations, the transformation of ARGs was first facilitated (transformation frequency reached up to 3.38-fold higher), but the facilitating effects gradually weakened and eventually disappeared as concentrations further increased. Particle size and iron oxide type were not the universal determinants controlling the transformation. At lower concentrations, iron oxides interacted with proteins and phospholipids in E. coli envelope structures, and induced the overgeneration of intracellular reactive oxygen species. Consequently, they led to pore formation and permeability enhancement on the cell membrane, thus promoting the transformation. The facilitation was also associated with the carrier-like effect of iron oxides for antibiotic resistance plasmids. At higher concentrations, the weakened facilitations were attributed to the aggregation of iron oxides. In this study, we highlight the crucial roles of the concentrations (contents) of iron oxides on the dissemination of ARGs in soils; this study may serve as a reference for ARG pollution control in future agricultural production.}, }
@article {pmid38368638, year = {2024}, author = {Zheng, W and Teng, X and Jiang, T and Tang, W and Jiang, L and Zhu, H and Yu, X and Chen, G and Wang, J and Zhang, J and Qu, M and Zhang, X}, title = {Genome analysis of a novel avian atadenovirus reveals a possible horizontal gene transfer.}, journal = {Virology}, volume = {593}, number = {}, pages = {109999}, doi = {10.1016/j.virol.2024.109999}, pmid = {38368638}, issn = {1096-0341}, mesh = {Animals ; *Atadenovirus/genetics ; Genome, Viral ; Phylogeny ; Gene Transfer, Horizontal ; Adenoviridae/genetics ; *Aviadenovirus/genetics ; Birds ; *Adenoviridae Infections/genetics ; }, abstract = {We report the discovery and characterization of a novel adenovirus, Zoothera dauma adenovirus (ZdAdV), from a wild bird species, Zoothera dauma (Scaly thrush). This new atadenovirus was discovered by metagenomic sequencing without virus cultivation. Analyses of the full genome sequence revealed that this new virus is a distinct member of the genus Atadenovirus and represents a novel species. ZdAdV has a genome of 34,760 bp with 28 predicted genes and 39% GC content. ZdAdV is the first atadenovirus to contain ORF19, a gene previously found only in aviadenoviruses. Phylogenetic analysis of ORF19 suggests that it was acquired by ZdAdV through horizontal gene transfer from an aviadenovirus. By analyzing all orthologous genes of aviadenovirus, mastadenovirus, atadenovirus, and siadenovirus, we also found potential horizontal gene transfer for the E4 gene in Pigeon aviadenovirus B. Our study widens our knowledge concerning the genetic diversity and evolutionary history of atadenoviruses and their potential for cross-species transmission.}, }
@article {pmid38367442, year = {2024}, author = {Liu, Q and Jia, J and Hu, H and Li, X and Zhao, Y and Wu, C}, title = {Nitrogen and phosphorus limitations promoted bacterial nitrate metabolism and propagation of antibiotic resistome in the phycosphere of Auxenochlorella pyrenoidosa.}, journal = {Journal of hazardous materials}, volume = {468}, number = {}, pages = {133786}, doi = {10.1016/j.jhazmat.2024.133786}, pmid = {38367442}, issn = {1873-3336}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Nitrates ; Genes, Bacterial ; Nitrogen/pharmacology ; Bacteria/genetics ; }, abstract = {Despite that nitrogen (N) and phosphorus (P) play critical roles in the lifecycle of microalgae, how N and P further affect the distribution of bacteria and antibiotic resistance genes (ARGs) in the phycosphere is still poorly understood. In this study, the effects of N and P on the distribution of ARGs in the phycosphere of Auxenochlorella pyrenoidosa were investigated. Results showed that the growth and chlorophyll synthesis of microalgae were inhibited when N or P was limited, regardless of the N/P ratios, but the extracellular polymeric substances content and nitrate assimilation efficiency were enhanced in contrast. Metagenomic sequencing revealed that N or P limitation resulted in the recruitment of specific bacteria that highly contribute to the nitrate metabolism in the phycosphere. Besides, N or P limitation promoted the propagation of phycosphere ARGs, primarily through horizontal gene transfer mediated by mobile genetic elements. The enrichment of specific bacteria induced by changes in the algal physiology also contributed to the ARGs proliferation under nutrient limitation. Our results demonstrated that the reduction of algal cells caused by nutrient limitation could promote the propagation of ARGs, which provides new insights into the occurrence and spread of ARGs in the phycosphere.}, }
@article {pmid38366574, year = {2024}, author = {Ko, I and Kranse, OP and Senatori, B and Eves-van den Akker, S}, title = {A Critical Appraisal of DNA Transfer from Plants to Parasitic Cyst Nematodes.}, journal = {Molecular biology and evolution}, volume = {41}, number = {2}, pages = {}, pmid = {38366574}, issn = {1537-1719}, support = {//British Society for Plant Pathology/ ; 125034/359149/3//University of Cambridge/ ; BB/R011311/1//BBSRC/ ; EP/X024008/1//UKRI/ ; }, mesh = {Animals ; *Plants/genetics ; DNA ; Genomics ; *Tylenchoidea/genetics ; Plant Diseases/parasitology ; }, abstract = {Plant-parasitic nematodes are one of the most economically important pests of crops. It is widely accepted that horizontal gene transfer-the natural acquisition of foreign genes in parasitic nematodes-contributes to parasitism. However, an apparent paradox has emerged from horizontal gene transfer analyses: On the one hand, distantly related organisms with very dissimilar genetic structures (i.e. bacteria), and only transient interactions with nematodes as far as we know, dominate the list of putative donors, while on the other hand, considerably more closely related organisms (i.e. the host plant), with similar genetic structure (i.e. introns) and documented long-term associations with nematodes, are rare among the list of putative donors. Given that these nematodes ingest cytoplasm from a living plant cell for several weeks, there seems to be a conspicuous absence of plant-derived cases. Here, we used comparative genomic approaches to evaluate possible plant-derived horizontal gene transfer events in plant parasitic nematodes. Our evidence supports a cautionary message for plant-derived horizontal gene transfer cases in the sugar beet cyst nematode, Heterodera schachtii. We propose a 4-step model for horizontal gene transfer from plant to parasite in order to evaluate why the absence of plant-derived horizontal gene transfer cases is observed. We find that the plant genome is mobilized by the nematode during infection, but that uptake of the said "mobilome" is the first major barrier to horizontal gene transfer from host to nematode. These results provide new insight into our understanding of the prevalence/role of nucleic acid exchange in the arms race between plants and plant parasites.}, }
@article {pmid38366248, year = {2024}, author = {Zhao, D and Zhang, S and Chen, J and Zhao, J and An, P and Xiang, H}, title = {Members of the class Candidatus Ordosarchaeia imply an alternative evolutionary scenario from methanogens to haloarchaea.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38366248}, issn = {1751-7370}, support = {92251302//National Natural Science Foundation of China/ ; CAM202202//Central Asian Drug Discovery and Development Center of Chinese Academy of Sciences/ ; }, mesh = {Phylogeny ; *Methane/metabolism ; *Euryarchaeota/metabolism ; Archaea ; Metagenome ; }, abstract = {The origin of methanogenesis can be traced to the common ancestor of non-DPANN archaea, whereas haloarchaea (or Halobacteria) are believed to have evolved from a methanogenic ancestor through multiple evolutionary events. However, due to the accelerated evolution and compositional bias of proteins adapting to hypersaline habitats, Halobacteria exhibit substantial evolutionary divergence from methanogens, and the identification of the closest methanogen (either Methanonatronarchaeia or other taxa) to Halobacteria remains a subject of debate. Here, we obtained five metagenome-assembled genomes with high completeness from soda-saline lakes on the Ordos Plateau in Inner Mongolia, China, and we proposed the name Candidatus Ordosarchaeia for this novel class. Phylogenetic analyses revealed that Ca. Ordosarchaeia is firmly positioned near the median position between the Methanonatronarchaeia and Halobacteria-Hikarchaeia lineages. Functional predictions supported the transitional status of Ca. Ordosarchaeia with the metabolic potential of nonmethanogenic and aerobic chemoheterotrophy, as did remnants of the gene sequences of methylamine/dimethylamine/trimethylamine metabolism and coenzyme M biosynthesis. Based on the similarity of the methyl-coenzyme M reductase genes mcrBGADC in Methanonatronarchaeia with the phylogenetically distant methanogens, an alternative evolutionary scenario is proposed, in which Methanonatronarchaeia, Ca. Ordosarchaeia, Ca. Hikarchaeia, and Halobacteria share a common ancestor that initially lost mcr genes. However, certain members of Methanonatronarchaeia subsequently acquired mcr genes through horizontal gene transfer from distantly related methanogens. This hypothesis is supported by amalgamated likelihood estimation, phylogenetic analysis, and gene arrangement patterns. Altogether, Ca. Ordosarchaeia genomes clarify the sisterhood of Methanonatronarchaeia with Halobacteria and provide new insights into the evolution from methanogens to haloarchaea.}, }
@article {pmid38366209, year = {2024}, author = {Wang, X and Zhang, H and Yu, S and Li, D and Gillings, MR and Ren, H and Mao, D and Guo, J and Luo, Y}, title = {Inter-plasmid transfer of antibiotic resistance genes accelerates antibiotic resistance in bacterial pathogens.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38366209}, issn = {1751-7370}, support = {41831287//Key Projects of the National Natural Science Foundation of China/ ; 2020YFC1806904//National Key R&amp;D Program of China/ ; 31870351//National Natural Science Foundation of China/ ; }, mesh = {*Anti-Bacterial Agents/pharmacology ; Plasmids/genetics ; Drug Resistance, Microbial/genetics ; *Bacteria/genetics ; Genes, Bacterial ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; }, abstract = {Antimicrobial resistance is a major threat for public health. Plasmids play a critical role in the spread of antimicrobial resistance via horizontal gene transfer between bacterial species. However, it remains unclear how plasmids originally recruit and assemble various antibiotic resistance genes (ARGs). Here, we track ARG recruitment and assembly in clinically relevant plasmids by combining a systematic analysis of 2420 complete plasmid genomes and experimental validation. Results showed that ARG transfer across plasmids is prevalent, and 87% ARGs were observed to potentially transfer among various plasmids among 8229 plasmid-borne ARGs. Interestingly, recruitment and assembly of ARGs occur mostly among compatible plasmids within the same bacterial cell, with over 88% of ARG transfers occurring between compatible plasmids. Integron and insertion sequences drive the ongoing ARG acquisition by plasmids, especially in which IS26 facilitates 63.1% of ARG transfer events among plasmids. In vitro experiment validated the important role of IS26 involved in transferring gentamicin resistance gene aacC1 between compatible plasmids. Network analysis showed four beta-lactam genes (blaTEM-1, blaNDM-4, blaKPC-2, and blaSHV-1) shuffling among 1029 plasmids and 45 clinical pathogens, suggesting that clinically alarming ARGs transferred accelerate the propagation of antibiotic resistance in clinical pathogens. ARGs in plasmids are also able to transmit across clinical and environmental boundaries, in terms of the high-sequence similarities of plasmid-borne ARGs between clinical and environmental plasmids. This study demonstrated that inter-plasmid ARG transfer is a universal mechanism for plasmid to recruit various ARGs, thus advancing our understanding of the emergence of multidrug-resistant plasmids.}, }
@article {pmid38366199, year = {2024}, author = {Takeuchi, N and Fullmer, MS and Maddock, DJ and Poole, AM}, title = {The Constructive Black Queen hypothesis: new functions can evolve under conditions favouring gene loss.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38366199}, issn = {1751-7370}, support = {22-UOA-250//Royal Society of New Zealand Marsden Fund/ ; //School of Biological Sciences Academic Leaders' Fund, University of Auckland/ ; //Faculty of Science Faculty Research Development Fund, University of Auckland/ ; }, mesh = {*Prokaryotic Cells ; *Multigene Family ; Evolution, Molecular ; }, abstract = {Duplication is a major route for the emergence of new gene functions. However, the emergence of new gene functions via this route may be reduced in prokaryotes, as redundant genes are often rapidly purged. In lineages with compact, streamlined genomes, it thus appears challenging for novel function to emerge via duplication and divergence. A further pressure contributing to gene loss occurs under Black Queen dynamics, as cheaters that lose the capacity to produce a public good can instead acquire it from neighbouring producers. We propose that Black Queen dynamics can favour the emergence of new function because, under an emerging Black Queen dynamic, there is high gene redundancy spread across a community of interacting cells. Using computational modelling, we demonstrate that new gene functions can emerge under Black Queen dynamics. This result holds even if there is deletion bias due to low duplication rates and selection against redundant gene copies resulting from the high cost associated with carrying a locus. However, when the public good production costs are high, Black Queen dynamics impede the fixation of new functions. Our results expand the mechanisms by which new gene functions can emerge in prokaryotic systems.}, }
@article {pmid38365845, year = {2024}, author = {Maddamsetti, R and Yao, Y and Wang, T and Gao, J and Huang, VT and Hamrick, GS and Son, HI and You, L}, title = {Duplicated antibiotic resistance genes reveal ongoing selection and horizontal gene transfer in bacteria.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {1449}, pmid = {38365845}, issn = {2041-1723}, support = {R01 AI125604/AI/NIAID NIH HHS/United States ; R01 GM098642/GM/NIGMS NIH HHS/United States ; R01 EB031869/EB/NIBIB NIH HHS/United States ; }, mesh = {Humans ; *Genes, Bacterial/genetics ; *Gene Transfer, Horizontal/genetics ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Horizontal gene transfer (HGT) and gene duplication are often considered as separate mechanisms driving the evolution of new functions. However, the mobile genetic elements (MGEs) implicated in HGT can copy themselves, so positive selection on MGEs could drive gene duplications. Here, we use a combination of modeling and experimental evolution to examine this hypothesis and use long-read genome sequences of tens of thousands of bacterial isolates to examine its generality in nature. Modeling and experiments show that antibiotic selection can drive the evolution of duplicated antibiotic resistance genes (ARGs) through MGE transposition. A key implication is that duplicated ARGs should be enriched in environments associated with antibiotic use. To test this, we examined the distribution of duplicated ARGs in 18,938 complete bacterial genomes with ecological metadata. Duplicated ARGs are highly enriched in bacteria isolated from humans and livestock. Duplicated ARGs are further enriched in an independent set of 321 antibiotic-resistant clinical isolates. Our findings indicate that duplicated genes often encode functions undergoing positive selection and horizontal gene transfer in microbial communities.}, }
@article {pmid38365256, year = {2024}, author = {Holert, J and Borker, A and Nübel, LL and Daniel, R and Poehlein, A and Philipp, B}, title = {Bacteria use a catabolic patchwork pathway of apparently recent origin for degradation of the synthetic buffer compound TRIS.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38365256}, issn = {1751-7370}, support = {//German Research Foundation/ ; //BioAug/ ; //University of M&#xfc;nster/ ; INST 211/646--1 FUGG//German Research Foundation/ ; }, mesh = {*Pseudomonas putida/genetics/metabolism ; Pseudomonas/genetics/metabolism ; Multigene Family ; Oxidation-Reduction ; Metabolic Networks and Pathways/genetics ; }, abstract = {The synthetic buffer compound TRIS (2-amino-2-(hydroxymethyl)propane-1,3-diol) is used in countless applications, and no detailed information on its degradation has been published so far. Herein, we describe the discovery of a complete bacterial degradation pathway for TRIS. By serendipity, a Pseudomonas strain was isolated from sewage sludge that was able to grow with TRIS as only carbon and nitrogen source. Genome and transcriptome analyses revealed two adjacent gene clusters embedded in a mobile genetic element on a conjugative plasmid to be involved in TRIS degradation. Heterologous gene expression revealed cluster I to encode a TRIS uptake protein, a TRIS alcohol dehydrogenase, and a TRIS aldehyde dehydrogenase, catalyzing the oxidation of TRIS into 2-hydroxymethylserine. Gene cluster II encodes a methylserine hydroxymethyltransferase (mSHMT) and a d-serine dehydratase that plausibly catalyze the conversion of 2-hydroxymethylserine into pyruvate. Conjugational plasmid transfer into Pseudomonas putida KT2440 enabled this strain to grow with TRIS and with 2-hydromethylserine, demonstrating that the complete TRIS degradation pathway can be transmitted by horizontal gene transfer. Subsequent enrichments from wastewater purification systems led to the isolation of further TRIS-degrading bacteria from the Pseudomonas and Shinella genera carrying highly similar TRIS degradation gene clusters. Our data indicate that TRIS degradation evolved recently via gene recruitment and enzyme adaptation from multiple independent metabolic pathways, and database searches suggest that the TRIS degradation pathway is now globally distributed. Overall, our study illustrates how engineered environments can enhance the emergence of new microbial metabolic pathways in short evolutionary time scales.}, }
@article {pmid38365232, year = {2024}, author = {Zheng, Y and Wang, B and Gao, P and Yang, Y and Xu, B and Su, X and Ning, D and Tao, Q and Li, Q and Zhao, F and Wang, D and Zhang, Y and Li, M and Winkler, MH and Ingalls, AE and Zhou, J and Zhang, C and Stahl, DA and Jiang, J and Martens-Habbena, W and Qin, W}, title = {Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38365232}, issn = {1751-7370}, support = {548565//Simons Postdoctoral Fellowship in Marine Microbial Ecology/ ; //Florida Agricultural Experiment Station Hatch project/ ; //National Natural Science Foundation of China/ ; 2020Z01//Shanghai Sheshan National Geophysical Observatory/ ; 20200925173954005//Stable Support Plan Program of Shenzhen Natural Science Fund/ ; ZDSYS201802081843490//Southern University of Science and Technology/ ; //Shenzhen Key Laboratory of Marine Archaea Geo-Omics/ ; 2020KCXTD023//the Innovation Team Project of Universities/ ; //National Natural Science Foundation of China/ ; //Fundamental Research Funds for the Central Universities of China/ ; 92051114//National Natural Science Foundation of China/ ; }, mesh = {*Archaea ; *Ammonia/metabolism ; Ecosystem ; RNA, Ribosomal, 16S/genetics/metabolism ; Oxidation-Reduction ; Phylogeny ; Soil ; Soil Microbiology ; }, abstract = {Ammonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant archaea on Earth, widely distributed in marine, terrestrial, and geothermal ecosystems. However, the genomic diversity, biogeography, and evolutionary process of AOA populations in subsurface environments are vastly understudied compared to those in marine and soil systems. Here, we report a novel AOA order Candidatus (Ca.) Nitrosomirales which forms a sister lineage to the thermophilic Ca. Nitrosocaldales. Metagenomic and 16S rRNA gene-read mapping demonstrates the abundant presence of Nitrosomirales AOA in various groundwater environments and their widespread distribution across a range of geothermal, terrestrial, and marine habitats. Terrestrial Nitrosomirales AOA show the genetic capacity of using formate as a source of reductant and using nitrate as an alternative electron acceptor. Nitrosomirales AOA appear to have acquired key metabolic genes and operons from other mesophilic populations via horizontal gene transfer, including genes encoding urease, nitrite reductase, and V-type ATPase. The additional metabolic versatility conferred by acquired functions may have facilitated their radiation into a variety of subsurface, marine, and soil environments. We also provide evidence that each of the four AOA orders spans both marine and terrestrial habitats, which suggests a more complex evolutionary history for major AOA lineages than previously proposed. Together, these findings establish a robust phylogenomic framework of AOA and provide new insights into the ecology and adaptation of this globally abundant functional guild.}, }
@article {pmid38365231, year = {2024}, author = {Kolan, D and Cattan-Tsaushu, E and Enav, H and Freiman, Z and Malinsky-Rushansky, N and Ninio, S and Avrani, S}, title = {Tradeoffs between phage resistance and nitrogen fixation drive the evolution of genes essential for cyanobacterial heterocyst functionality.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38365231}, issn = {1751-7370}, support = {//Israel Water Authority/ ; 1386/20//Israel Science Foundation/ ; }, mesh = {Nitrogen Fixation/genetics ; *Bacteriophages/genetics ; Phylogeny ; *Nostoc/genetics ; Nitrogen ; }, abstract = {Harmful blooms caused by diazotrophic (nitrogen-fixing) Cyanobacteria are becoming increasingly frequent and negatively impact aquatic environments worldwide. Cyanophages (viruses infecting Cyanobacteria) can potentially regulate cyanobacterial blooms, yet Cyanobacteria can rapidly acquire mutations that provide protection against phage infection. Here, we provide novel insights into cyanophage:Cyanobacteria interactions by characterizing the resistance to phages in two species of diazotrophic Cyanobacteria: Nostoc sp. and Cylindrospermopsis raciborskii. Our results demonstrate that phage resistance is associated with a fitness tradeoff by which resistant Cyanobacteria have reduced ability to fix nitrogen and/or to survive nitrogen starvation. Furthermore, we use whole-genome sequence analysis of 58 Nostoc-resistant strains to identify several mutations associated with phage resistance, including in cell surface-related genes and regulatory genes involved in the development and function of heterocysts (cells specialized in nitrogen fixation). Finally, we employ phylogenetic analyses to show that most of these resistance genes are accessory genes whose evolution is impacted by lateral gene transfer events. Together, these results further our understanding of the interplay between diazotrophic Cyanobacteria and their phages and suggest that a tradeoff between phage resistance and nitrogen fixation affects the evolution of cell surface-related genes and of genes involved in heterocyst differentiation and nitrogen fixation.}, }
@article {pmid38361819, year = {2024}, author = {Zhang, S and Yang, C and Qiu, Y and Liao, R and Xuan, Z and Ren, F and Dong, Y and Xie, X and Han, Y and Wu, D and Ramos-González, PL and Freitas-Astúa, J and Yang, H and Zhou, C and Cao, M}, title = {Conserved untranslated regions of multipartite viruses: Natural markers of novel viral genomic components and tags of viral evolution.}, journal = {Virus evolution}, volume = {10}, number = {1}, pages = {veae004}, pmid = {38361819}, issn = {2057-1577}, abstract = {Viruses with split genomes are classified as being either segmented or multipartite based on whether their genomic segments occur within a single virion or across different virions. Despite variations in number and sequence during evolution, the genomic segments of many viruses are conserved within the untranslated regions (UTRs). In this study, we present a methodology that combines RNA sequencing with iterative BLASTn of UTRs (https://github.com/qq371260/Iterative-blast-v.1.0) to identify new viral genomic segments. Some novel multipartite-like viruses related to the phylum Kitrinoviricota were annotated using sequencing data from field plant samples and public databases. We identified potentially plant-infecting jingmen-related viruses (order Amarillovirales) and jivi-related viruses (order Martellivirales) with at least six genomic components. The number of RNA molecules associated with a genome of the novel viruses in the families Closteroviridae, Kitaviridae, and Virgaviridae within the order Martellivirales reached five. Several of these viruses seem to represent new taxa at the subgenus, genus, and family levels. The diversity of novel genomic components and the multiple duplication of proteins or protein domains within single or multiple genomic components emphasize the evolutionary roles of genetic recombination (horizontal gene transfer), reassortment, and deletion. The relatively conserved UTRs at the genome level might explain the relationships between monopartite and multipartite viruses, as well as how subviral agents such as defective RNAs and satellite viruses can coexist with their helper viruses.}, }
@article {pmid38352454, year = {2024}, author = {Curry, KD and Yu, FB and Vance, SE and Segarra, S and Bhaya, D and Chikhi, R and Rocha, EPC and Treangen, TJ}, title = {Reference-free Structural Variant Detection in Microbiomes via Long-read Coassembly Graphs.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38352454}, issn = {2692-8205}, support = {P01 AI152999/AI/NIAID NIH HHS/United States ; }, abstract = {Bacterial genome dynamics are vital for understanding the mechanisms underlying microbial adaptation, growth, and their broader impact on host phenotype. Structural variants (SVs), genomic alterations of 10 base pairs or more, play a pivotal role in driving evolutionary processes and maintaining genomic heterogeneity within bacterial populations. While SV detection in isolate genomes is relatively straightforward, metagenomes present broader challenges due to absence of clear reference genomes and presence of mixed strains. In response, our proposed method rhea, forgoes reference genomes and metagenome-assembled genomes (MAGs) by encompassing a single metagenome coassembly graph constructed from all samples in a series. The log fold change in graph coverage between subsequent samples is then calculated to call SVs that are thriving or declining throughout the series. We show rhea to outperform existing methods for SV and horizontal gene transfer (HGT) detection in two simulated mock metagenomes, which is particularly noticeable as the simulated reads diverge from reference genomes and an increase in strain diversity is incorporated. We additionally demonstrate use cases for rhea on series metagenomic data of environmental and fermented food microbiomes to detect specific sequence alterations between subsequent time and temperature samples, suggesting host advantage. Our innovative approach leverages raw read patterns rather than references or MAGs to include all sequencing reads in analysis, and thus provide versatility in studying SVs across diverse and poorly characterized microbial communities for more comprehensive insights into microbial genome dynamics.}, }
@article {pmid38351266, year = {2024}, author = {Arbulu, S and Kjos, M}, title = {Revisiting the Multifaceted Roles of Bacteriocins : The Multifaceted Roles of Bacteriocins.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {41}, pmid = {38351266}, issn = {1432-184X}, support = {101029099//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; 296906//Norges Forskningsr&#xe5;d/ ; }, mesh = {*Bacteriocins/pharmacology ; Biofilms ; Bacteria ; Peptides ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Bacteriocins are gene-encoded antimicrobial peptides produced by bacteria. These peptides are heterogeneous in terms of structure, antimicrobial activities, biosynthetic clusters, and regulatory mechanisms. Bacteriocins are widespread in nature and may contribute to microbial diversity due to their capacity to target specific bacteria. Primarily studied as food preservatives and therapeutic agents, their function in natural settings is however less known. This review emphasizes the ecological significance of bacteriocins as multifunctional peptides by exploring bacteriocin distribution, mobility, and their impact on bacterial population dynamics and biofilms.}, }
@article {pmid38349402, year = {2024}, author = {Neil, B and Cheney, GL and Rosenzweig, JA and Sha, J and Chopra, AK}, title = {Antimicrobial resistance in aeromonads and new therapies targeting quorum sensing.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {205}, pmid = {38349402}, issn = {1432-0614}, support = {R21 AI135453/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Quorum Sensing ; Drug Resistance, Bacterial ; Agriculture ; *Cross Infection ; }, abstract = {Aeromonas species (spp.) are well-known fish pathogens, several of which have been recognized as emerging human pathogens. The organism is capable of causing a wide spectrum of diseases in humans, ranging from gastroenteritis, wound infections, and septicemia to devastating necrotizing fasciitis. The systemic form of infection is often fatal, particularly in patients with underlying chronic diseases. Indeed, recent trends demonstrate rising numbers of hospital-acquired Aeromonas infections, especially in immuno-compromised individuals. Additionally, Aeromonas-associated antibiotic resistance is an increasing challenge in combating both fish and human infections. The acquisition of antibiotic resistance is related to Aeromonas' innate transformative properties including its ability to share plasmids and integron-related gene cassettes between species and with the environment. As a result, alternatives to antibiotic treatments are desperately needed. In that vein, many treatments have been proposed and studied extensively in the fish-farming industry, including treatments that target Aeromonas quorum sensing. In this review, we discuss current strategies targeting quorum sensing inhibition and propose that such studies empower the development of novel chemotherapeutic approaches to combat drug-resistant Aeromonas spp. infections in humans. KEY POINTS: • Aeromonas notoriously acquires and maintains antimicrobial resistance, making treatment options limited. • Quorum sensing is an essential virulence mechanism in Aeromonas infections. • Inhibiting quorum sensing can be an effective strategy in combating Aeromonas infections in animals and humans.}, }
@article {pmid38349154, year = {2024}, author = {Vargas-Gastélum, L and Romer, AS and Ghotbi, M and Dallas, JW and Alexander, NR and Moe, KC and McPhail, KL and Neuhaus, GF and Shadmani, L and Spatafora, JW and Stajich, JE and Tabima, JF and Walker, DM}, title = {Herptile gut microbiomes: a natural system to study multi-kingdom interactions between filamentous fungi and bacteria.}, journal = {mSphere}, volume = {9}, number = {3}, pages = {e0047523}, pmid = {38349154}, issn = {2379-5042}, mesh = {Bacteria/genetics ; Fungi/genetics ; *Gastrointestinal Microbiome ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Animals ; }, abstract = {Reptiles and amphibians (herptiles) are some of the most endangered and threatened species on the planet and numerous conservation strategies are being implemented with the goal of ensuring species recovery. Little is known, however, about the gut microbiome of wild herptiles and how it relates to the health of these populations. Here, we report results from the gut microbiome characterization of both a broad survey of herptiles, and the correlation between the fungus Basidiobolus, and the bacterial community supported by a deeper, more intensive sampling of Plethodon glutinosus, known as slimy salamanders. We demonstrate that bacterial communities sampled from frogs, lizards, and salamanders are structured by the host taxonomy and that Basidiobolus is a common and natural component of these wild gut microbiomes. Intensive sampling of multiple hosts across the ecoregions of Tennessee revealed that geography and host:geography interactions are strong predictors of distinct Basidiobolus operational taxonomic units present within a given host. Co-occurrence analyses of Basidiobolus and bacterial community diversity support a correlation and interaction between Basidiobolus and bacteria, suggesting that Basidiobolus may play a role in structuring the bacterial community. We further the hypothesis that this interaction is advanced by unique specialized metabolism originating from horizontal gene transfer from bacteria to Basidiobolus and demonstrate that Basidiobolus is capable of producing a diversity of specialized metabolites including small cyclic peptides.IMPORTANCEThis work significantly advances our understanding of biodiversity and microbial interactions in herptile microbiomes, the role that fungi play as a structural and functional members of herptile gut microbiomes, and the chemical functions that structure microbiome phenotypes. We also provide an important observational system of how the gut microbiome represents a unique environment that selects for novel metabolic functions through horizontal gene transfer between fungi and bacteria. Such studies are needed to better understand the complexity of gut microbiomes in nature and will inform conservation strategies for threatened species of herpetofauna.}, }
@article {pmid38347627, year = {2024}, author = {Behling, AH and Wilson, BC and Ho, D and Cutfield, WS and Vatanen, T and O'Sullivan, JM}, title = {Horizontal gene transfer after faecal microbiota transplantation in adolescents with obesity.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {26}, pmid = {38347627}, issn = {2049-2618}, mesh = {Adolescent ; Humans ; Fecal Microbiota Transplantation/methods ; Gene Transfer, Horizontal ; *Pediatric Obesity ; *Microbiota ; *Gastrointestinal Microbiome/genetics ; Bacteria/genetics ; Feces/microbiology ; Treatment Outcome ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT) describes the transmission of DNA outside of direct ancestral lineages. The process is best characterised within the bacterial kingdom and can enable the acquisition of genetic traits that support bacterial adaptation to novel niches. The adaptation of bacteria to novel niches has particular relevance for faecal microbiota transplantation (FMT), a therapeutic procedure which aims to resolve gut-related health conditions of individuals, through transplanted gut microbiota from healthy donors.<br><br>RESULTS: Three hundred eighty-one stool metagenomic samples from a placebo-controlled FMT trial for obese adolescents (the Gut Bugs Trial) were analysed for HGT, using two complementary methodologies. First, all putative HGT events, including historical HGT signatures, were quantified using the bioinformatics application WAAFLE. Second, metagenomic assembly and gene clustering were used to assess and quantify donor-specific genes transferred to recipients following the intervention. Both methodologies found no difference between the level of putative HGT events in the gut microbiomes of FMT and placebo recipients, post-intervention. HGT events facilitated by engrafted donor species in the FMT recipient gut at 6&#xa0;weeks post-intervention were identified and characterised. Bacterial strains contributing to this subset of HGT events predominantly belonged to the phylum Bacteroidetes. Engraftment-dependent horizontally transferred genes were retained within recipient microbiomes at 12 and 26&#xa0;weeks post-intervention.<br><br>CONCLUSION: Our study suggests that novel microorganisms introduced into the recipient gut following FMT have no impact on the basal rate of HGT within the human gut microbiome. Analyses of further FMT studies are required to assess the generalisability of this conclusion across different FMT study designs and for the treatment of different gut-related conditions. Video Abstract.}, }
@article {pmid38344902, year = {2024}, author = {Macesic, N and Dennis, A and Hawkey, J and Vezina, B and Wisniewski, JA and Cottingham, H and Blakeway, LV and Harshegyi, T and Pragastis, K and Badoordeen, GZ and Bass, P and Stewardson, AJ and Dennison, A and Spelman, DW and Jenney, AWJ and Peleg, AY}, title = {Genomic investigation of multispecies and multivariant blaNDM outbreak reveals key role of horizontal plasmid transmission.}, journal = {Infection control and hospital epidemiology}, volume = {45}, number = {6}, pages = {709-716}, pmid = {38344902}, issn = {1559-6834}, mesh = {Humans ; *beta-Lactamases/genetics ; *Plasmids/genetics ; *Disease Outbreaks ; Male ; Female ; Middle Aged ; Aged ; Australia/epidemiology ; Whole Genome Sequencing ; Adult ; Enterobacteriaceae Infections/epidemiology/transmission/microbiology ; Gene Transfer, Horizontal ; Aged, 80 and over ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Genome, Bacterial ; }, abstract = {OBJECTIVES: New Delhi metallo-β-lactamases (NDMs) are major contributors to the spread of carbapenem resistance globally. In Australia, NDMs were previously associated with international travel, but from 2019 we noted increasing incidence of NDM-positive clinical isolates. We investigated the clinical and genomic epidemiology of NDM carriage at a tertiary-care Australian hospital from 2016 to 2021.<br><br>METHODS: We identified 49 patients with 84 NDM-carrying isolates in an institutional database, and we collected clinical data from electronic medical record. Short- and long-read whole genome sequencing was performed on all isolates. Completed genome assemblies were used to assess the genetic setting of blaNDM genes and to compare NDM plasmids.<br><br>RESULTS: Of 49 patients, 38 (78%) were identified in 2019-2021 and only 11 (29%) of 38 reported prior travel, compared with 9 (82%) of 11 in 2016-2018 (P = .037). In patients with NDM infection, the crude 7-day mortality rate was 0% and the 30-day mortality rate was 14% (2 of 14 patients). NDMs were noted in 41 bacterial strains (ie, species and sequence type combinations). Across 13 plasmid groups, 4 NDM variants were detected: blaNDM-1, blaNDM-4, blaNDM-5, and blaNDM-7. We noted a change from a diverse NDM plasmid repertoire in 2016-2018 to the emergence of conserved blaNDM-1 IncN and blaNDM-7 IncX3 epidemic plasmids, with interstrain spread in 2019-2021. These plasmids were noted in 19 (50%) of 38 patients and 35 (51%) of 68 genomes in 2019-2021.<br><br>CONCLUSIONS: Increased NDM case numbers were due to local circulation of 2 epidemic plasmids with extensive interstrain transfer. Our findings underscore the challenges of outbreak detection when horizontal transmission of plasmids is the primary mode of spread.}, }
@article {pmid38341975, year = {2024}, author = {Li, Z and Guo, X and Liu, B and Huang, T and Liu, R and Liu, X}, title = {Metagenome sequencing reveals shifts in phage-associated antibiotic resistance genes from influent to effluent in wastewater treatment plants.}, journal = {Water research}, volume = {253}, number = {}, pages = {121289}, doi = {10.1016/j.watres.2024.121289}, pmid = {38341975}, issn = {1879-2448}, mesh = {*Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Wastewater ; Metagenome ; Drug Resistance, Microbial/genetics ; *Water Purification ; }, abstract = {Antibiotic resistance poses a significant threat to global health, and the microbe-rich activated sludge environment may contribute to the dissemination of antibiotic resistance genes (ARGs). ARGs spread across various bacterial populations via multiple dissemination routes, including horizontal gene transfer mediated by bacteriophages (phages). However, the potential role of phages in spreading ARGs in wastewater treatment systems remains unclear. This study characterized the core resistome, mobile genetic elements (MGEs), and virus-associated ARGs (vir_ARGs) in influents (Inf) and effluents (Eff) samples from nine WWTPs in eastern China. The abundance of ARGs in the Inf samples was higher than that in the Eff samples. A total of 21 core ARGs were identified, accounting for 38.70 %-83.70 % of the different samples. There was an increase in MGEs associated with phage-related processes from influents to effluents (from 12.68 % to 21.10 %). These MGEs showed strong correlations in relative abundance and composition with the core ARGs in the Eff samples. Across the Inf and Eff samples, 58 unique vir_ARGs were detected, with the Eff samples exhibiting higher diversity of vir_ARGs than the Inf samples. Statistical analyses indicated a robust relationship between core ARG profile, MGEs associated with phage-related processes, and vir_ARG composition in the Eff samples. Additionally, the co-occurrence of MGEs and ARGs in viral genomes was observed, ranging from 22.73 % to 68.75 %. This co-occurrence may exacerbate the persistence and spread of ARGs within WWTPs. The findings present new information on the changes in core ARGs, MGEs, and phage-associated ARGs from influents to effluents in WWTPs and provide new insights into the role of phage-associated ARGs in these systems.}, }
@article {pmid38340701, year = {2024}, author = {Liu, Z and Heng, S and Dai, Q and Gao, Y and Han, Y and Hu, L and Liu, Y and Lu, X and Zhen, G}, title = {Simultaneous removal of antibiotic resistance genes and improved dewatering ability of waste activated sludge by Fe(II)-activated persulfate oxidation.}, journal = {Water research}, volume = {253}, number = {}, pages = {121265}, doi = {10.1016/j.watres.2024.121265}, pmid = {38340701}, issn = {1879-2448}, mesh = {*Sewage/chemistry ; *Anti-Bacterial Agents ; Waste Disposal, Fluid/methods ; Drug Resistance, Microbial/genetics ; Oxidation-Reduction ; Water/chemistry ; Ferrous Compounds/chemistry ; }, abstract = {Waste activated sludge properties vary widely with different regions due to the difference in living standards and geographical distribution, making a big challenge to developing a universally effective sludge dewatering technique. The Fe(II)-activated persulfate (S2O8[2-]) oxidation process shows excellent ability to disrupt sludge cells and extracellular polymeric substances (EPS), and release bound water from sludge flocs. In this study, the discrepancies in the physicochemical characteristics of sludge samples from seven representative cities in China (e.g., dewaterability, EPS composition, surface charge, microbial community, relative abundance of antibiotic resistance genes (ARGs), etc.) were investigated, and the role of Fe(II)-S2O8[2-] oxidation in enhancing removal of antibiotic resistance genes and dewatering ability were explored. The results showed significant differences between the EPS distribution and chemical composition of sludge samples due to different treatment processes, effluent sources, and regions. The Fe(II)-S2O8[2-] oxidation pretreatment had a good enhancement of sludge dewatering capacity (up to 76 %). Microbial analysis showed that the microbial community in each sludge varied significantly depending on the types of wastewater, the wastewater treatment processes, and the regions, but Fe(II)-S2O8[2-] oxidation was able to attack and rupture the sludge zoogloea indiscriminately. Genetic analysis further showed that a considerable number of ARGs were detected in all of these sludge samples and that Fe(II)-S2O8[2-] oxidation was effective in removing ARGs by higher than 90 %. The highly active radicals (e.g., SO4[-]·, ·OH) produced in this process caused drastic damage to sludge microbial cells and DNA stability while liberating the EPS/cell-bound water. Co-occurrence network analysis highlighted a positive correlation between population distribution and ARGs abundance, while variations in microbial communities were linked to regional differences in living standards and level of economic development. Despite these variations, the Fe(II)-S2O8[2-] oxidation consistently achieved excellent performance in both ARGs removal and sludge dewatering. The significant modularity of associations between different microbial communities also confirms its ability to reduce horizontal gene transfer (HGT) by scavenging microbes.}, }
@article {pmid38338856, year = {2024}, author = {Zhao, Z and Li, Y and Zhai, JW and Liu, ZJ and Li, MH}, title = {Organelle Genomes of Epipogium roseum Provide Insight into the Evolution of Mycoheterotrophic Orchids.}, journal = {International journal of molecular sciences}, volume = {25}, number = {3}, pages = {}, pmid = {38338856}, issn = {1422-0067}, support = {2023YFD1000500//the National Key Research and Development Program of China/ ; 72202200205//the Forestry Peak Discipline Construction Project of Fujian Agriculture and Forestry University/ ; }, mesh = {Phylogeny ; Plastids ; *Genome, Plastid ; *Orchidaceae/genetics ; Asia ; Evolution, Molecular ; }, abstract = {Epipogium roseum, commonly known as one of the ghost orchids due to its rarity and almost transparent color, is a non-photosynthetic and fully mycoheterotrophic plant. Given its special nutritional strategies and evolutionary significance, the mitogenome was first characterized, and three plastomes sampled from Asia were assembled. The plastomes were found to be the smallest among Orchidaceae, with lengths ranging from 18,339 to 19,047 bp, and exhibited high sequence variety. For the mitogenome, a total of 414,552 bp in length, comprising 26 circular chromosomes, were identified. A total of 54 genes, including 38 protein-coding genes, 13 tRNA genes, and 3 rRNA genes, were annotated. Multiple repeat sequences spanning a length of 203,423 bp (45.47%) were discovered. Intriguingly, six plastid regions via intracellular gene transfer and four plastid regions via horizontal gene transfer to the mitogenome were observed. The phylogenomics, incorporating 90 plastomes and 56 mitogenomes, consistently revealed the sister relationship of Epipogium and Gastrodia, with a bootstrap percentage of 100%. These findings shed light on the organelle evolution of Orchidaceae and non-photosynthetic plants.}, }
@article {pmid38337962, year = {2024}, author = {Zhang, J and Wang, J and Zhu, C and Singh, RP and Chen, W}, title = {Chickpea: Its Origin, Distribution, Nutrition, Benefits, Breeding, and Symbiotic Relationship with Mesorhizobium Species.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {3}, pages = {}, pmid = {38337962}, issn = {2223-7747}, support = {31970006//National Nature Science Foundation of China/ ; Yuzutong[2023]No.11//Central Plains youth top talent project/ ; }, abstract = {Chickpea (Cicer arietinum L.), encompassing the desi and kabuli varieties, is a beloved pulse crop globally. Its cultivation spans over fifty countries, from the Indian subcontinent and southern Europe to the Middle East, North Africa, the Americas, Australia, and China. With a rich composition of carbohydrates and protein, constituting 80% of its dry seed mass, chickpea is also touted for its numerous health benefits, earning it the title of a 'functional food'. In the past two decades, research has extensively explored the rhizobial diversity associated with chickpea and its breeding in various countries across Europe, Asia, and Oceania, aiming to understand its impact on the sustainable yield and quality of chickpea crops. To date, four notable species of Mesorhizobium-M. ciceri, M. mediterraneum, M. muleiense, and M. wenxiniae-have been reported, originally isolated from chickpea root nodules. Other species, such as M. amorphae, M. loti, M. tianshanense, M. oportunistum, M. abyssinicae, and M. shonense, have been identified as potential symbionts of chickpea, possibly acquiring symbiotic genes through lateral gene transfer. While M. ciceri and M. mediterraneum are widely distributed and studied across chickpea-growing regions, they remain absent in China, where M. muleiense and M. wenxiniae are the sole rhizobial species associated with chickpea. The geographic distribution of chickpea rhizobia is believed to be influenced by factors such as genetic characteristics, competitiveness, evolutionary adaptation to local soil conditions, and compatibility with native soil microbes. Inoculating chickpea with suitable rhizobial strains is crucial when introducing the crop to new regions lacking indigenous chickpea rhizobia. The introduction of a novel chickpea variety, coupled with the effective use of rhizobia for inoculation, offers the potential not only to boost the yield and seed quality of chickpeas, but also to enhance crop productivity within rotation and intercropped systems involving chickpea and other crops. Consequently, this advancement holds the promise to drive forward the cause of sustainable agriculture on a global scale.}, }
@article {pmid38335841, year = {2024}, author = {Qiu, X and Wang, B and Ren, S and Liu, X and Wang, Y}, title = {Regulation of quorum sensing for the manipulation of conjugative transfer of antibiotic resistance genes in wastewater treatment system.}, journal = {Water research}, volume = {253}, number = {}, pages = {121222}, doi = {10.1016/j.watres.2024.121222}, pmid = {38335841}, issn = {1879-2448}, mesh = {*Quorum Sensing ; *Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Escherichia coli ; Plasmids ; Gene Transfer, Horizontal ; *Benzaldehydes ; }, abstract = {The emergence and transmission of antibiotic resistance genes (ARGs) through plasmid-mediated conjugation has become a significant worldwide public health threat. Biofilms are widely recognized as the primary reservoirs for ARGs, providing favorable conditions for horizontal gene transfer. Quorum sensing (QS) plays a critical role in bacterial biofilm formation, which further influences the spread of bacterial resistance. In this study, we examined the effects of vanillin, a QS inhibitor (QSI), at subinhibitory concentrations (sub-MICs) ranging from 0 - 0.1 g/L, on the transfer of ARGs between Escherichia coli and Pseudomonas aeruginosa. Our findings indicated that vanillin at sub-MICs inhibited the conjugative transfer frequency of the RP4 plasmid. This inhibition was supported by the downregulation of plasmid transfer genes. The suppression of conjugation can mainly be attributed to the inhibition of biofilm formation, the synthesis of extracellular polymeric substances (EPS), and the secretion of virulence factors, all of which are regulated by the bacterial QS system. On the other hand, the levels of ROS and cell membrane permeability were not primary explanations for this phenomenon. Furthermore, vanillin also reduced the conjugative transfer frequency of ARGs in wastewater effluent, providing a potential approach to alleviate bacterial resistance in water environments. These findings underscore the regulatory role of QSI in controlling ARGs transfer and have significant implications for manipulating the dissemination of bacterial resistance in the environment.}, }
@article {pmid38330161, year = {2024}, author = {Li, Q and Chan, YB and Galtier, N and Scornavacca, C}, title = {The Effect of Copy Number Hemiplasy on Gene Family Evolution.}, journal = {Systematic biology}, volume = {73}, number = {2}, pages = {355-374}, doi = {10.1093/sysbio/syae007}, pmid = {38330161}, issn = {1076-836X}, support = {ANR-19-CE45-0012//Agence Nationale de la Recherche/ ; }, mesh = {*Evolution, Molecular ; *Models, Genetic ; *Gene Dosage ; Gene Duplication ; Multigene Family ; Phylogeny ; Classification/methods ; Computer Simulation ; }, abstract = {The evolution of gene families is complex, involving gene-level evolutionary events such as gene duplication, horizontal gene transfer, and gene loss, and other processes such as incomplete lineage sorting (ILS). Because of this, topological differences often exist between gene trees and species trees. A number of models have been recently developed to explain these discrepancies, the most realistic of which attempts to consider both gene-level events and ILS. When unified in a single model, the interaction between ILS and gene-level events can cause polymorphism in gene copy number, which we refer to as copy number hemiplasy (CNH). In this paper, we extend the Wright-Fisher process to include duplications and losses over several species, and show that the probability of CNH for this process can be significant. We study how well two unified models-multilocus multispecies coalescent (MLMSC), which models CNH, and duplication, loss, and coalescence (DLCoal), which does not-approximate the Wright-Fisher process with duplication and loss. We then study the effect of CNH on gene family evolution by comparing MLMSC and DLCoal. We generate comparable gene trees under both models, showing significant differences in various summary statistics; most importantly, CNH reduces the number of gene copies greatly. If this is not taken into account, the traditional method of estimating duplication rates (by counting the number of gene copies) becomes inaccurate. The simulated gene trees are also used for species tree inference with the summary methods ASTRAL and ASTRAL-Pro, demonstrating that their accuracy, based on CNH-unaware simulations calibrated on real data, may have been overestimated.}, }
@article {pmid38329938, year = {2024}, author = {Liu, Z and Good, BH}, title = {Dynamics of bacterial recombination in the human gut microbiome.}, journal = {PLoS biology}, volume = {22}, number = {2}, pages = {e3002472}, pmid = {38329938}, issn = {1545-7885}, support = {R35 GM146949/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Bacteria/genetics ; Gene Transfer, Horizontal/genetics ; }, abstract = {Horizontal gene transfer (HGT) is a ubiquitous force in microbial evolution. Previous work has shown that the human gut is a hotspot for gene transfer between species, but the more subtle exchange of variation within species-also known as recombination-remains poorly characterized in this ecosystem. Here, we show that the genetic structure of the human gut microbiome provides an opportunity to measure recent recombination events from sequenced fecal samples, enabling quantitative comparisons across diverse commensal species that inhabit a common environment. By analyzing recent recombination events in the core genomes of 29 human gut bacteria, we observed widespread heterogeneities in the rates and lengths of transferred fragments, which are difficult to explain by existing models of ecological isolation or homology-dependent recombination rates. We also show that natural selection helps facilitate the spread of genetic variants across strain backgrounds, both within individual hosts and across the broader population. These results shed light on the dynamics of in situ recombination, which can strongly constrain the adaptability of gut microbial communities.}, }
@article {pmid38326975, year = {2024}, author = {Ma, D and Xu, J and Wu, M and Zhang, R and Hu, Z and Ji, CA and Wang, Y and Zhang, Z and Yu, R and Liu, X and Yang, L and Li, G and Shen, D and Liu, M and Yang, Z and Zhang, H and Wang, P and Zhang, Z}, title = {Phenazine biosynthesis protein MoPhzF regulates appressorium formation and host infection through canonical metabolic and noncanonical signaling function in Magnaporthe oryzae.}, journal = {The New phytologist}, volume = {242}, number = {1}, pages = {211-230}, pmid = {38326975}, issn = {1469-8137}, support = {R03 AI156254/AI/NIAID NIH HHS/United States ; R21 AI168867/AI/NIAID NIH HHS/United States ; }, mesh = {Fungal Proteins/genetics/metabolism ; *Magnaporthe ; *Oryza/metabolism ; Phenazines/metabolism ; Plant Diseases/genetics ; *Ascomycota ; }, abstract = {Microbe-produced secondary metabolite phenazine-1-carboxylic acid (PCA) facilitates pathogen virulence and defense mechanisms against competitors. Magnaporthe oryzae, a causal agent of the devastating rice blast disease, needs to compete with other phyllosphere microbes and overcome host immunity for successful colonization and infection. However, whether M. oryzae produces PCA or it has any other functions remains unknown. Here, we found that the MoPHZF gene encodes the phenazine biosynthesis protein MoPhzF, synthesizes PCA in M. oryzae, and regulates appressorium formation and host virulence. MoPhzF is likely acquired through an ancient horizontal gene transfer event and has a canonical function in PCA synthesis. In addition, we found that PCA has a role in suppressing the accumulation of host-derived reactive oxygen species (ROS) during infection. Further examination indicated that MoPhzF recruits both the endoplasmic reticulum membrane protein MoEmc2 and the regulator of G-protein signaling MoRgs1 to the plasma membrane (PM) for MoRgs1 phosphorylation, which is a critical regulatory mechanism in appressorium formation and pathogenicity. Collectively, our studies unveiled a canonical function of MoPhzF in PCA synthesis and a noncanonical signaling function in promoting appressorium formation and host infection.}, }
@article {pmid38323496, year = {2024}, author = {Sabino, YNV and de Melo, MD and da Silva, GC and Mantovani, HC}, title = {Unraveling the diversity and dissemination dynamics of antimicrobial resistance genes in Enterobacteriaceae plasmids across diverse ecosystems.}, journal = {Journal of applied microbiology}, volume = {135}, number = {2}, pages = {}, doi = {10.1093/jambio/lxae028}, pmid = {38323496}, issn = {1365-2672}, support = {//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; //Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; //Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; }, mesh = {Animals ; Humans ; *Enterobacteriaceae/genetics ; *Anti-Bacterial Agents/pharmacology ; Phylogeny ; Ecosystem ; Drug Resistance, Bacterial/genetics ; Plasmids/genetics ; Escherichia coli/genetics ; }, abstract = {AIM: The objective of this study was to investigate the antimicrobial resistance genes (ARGs) in plasmids of Enterobacteriaceae from soil, sewage, and feces of food-producing animals and humans.<br><br>METHODS AND RESULTS: The plasmid sequences were obtained from the NCBI database. For the identification of ARG, comprehensive antibiotic resistance database (CARD), and ResFinder were used. Gene conservation and evolution were investigated using DnaSP v.6. The transfer potential of the plasmids was evaluated using oriTfinder and a MOB-based phylogenetic tree was reconstructed using Fastree. We identified a total of 1064 ARGs in all plasmids analyzed, conferring resistance to 15 groups of antibiotics, mostly aminoglycosides, beta-lactams, and sulfonamides. The greatest number of ARGs per plasmid was found in enterobacteria from chicken feces. Plasmids from Escherichia coli carrying multiple ARGs were found in all ecosystems. Some of the most abundant genes were shared among all ecosystems, including aph(6)-Id, aph(3'')-Ib, tet(A), and sul2. A high level of sequence conservation was found among these genes, and tet(A) and sul2 are under positive selective pressure. Approximately 62% of the plasmids carrying at least one ARG were potentially transferable. Phylogenetic analysis indicated a potential co-evolution of Enterobacteriaceae plasmids in nature.<br><br>CONCLUSION: The high abundance of Enterobacteriaceae plasmids from diverse ecosystems carrying ARGs reveals their widespread distribution and importance.}, }
@article {pmid38321476, year = {2024}, author = {López Sánchez, A and Lafond, M}, title = {Predicting horizontal gene transfers with perfect transfer networks.}, journal = {Algorithms for molecular biology : AMB}, volume = {19}, number = {1}, pages = {6}, pmid = {38321476}, issn = {1748-7188}, abstract = {BACKGROUND: Horizontal gene transfer inference approaches are usually based on gene sequences: parametric methods search for patterns that deviate from a particular genomic signature, while phylogenetic methods use sequences to reconstruct the gene and species trees. However, it is well-known that sequences have difficulty identifying ancient transfers since mutations have enough time to erase all evidence of such events. In this work, we ask whether character-based methods can predict gene transfers. Their advantage over sequences is that homologous genes can have low DNA similarity, but still have retained enough important common motifs that allow them to have common character traits, for instance the same functional or expression profile. A phylogeny that has two separate clades that acquired the same character independently might indicate the presence of a transfer even in the absence of sequence similarity.<br><br>OUR CONTRIBUTIONS: We introduce perfect transfer networks, which are phylogenetic networks that can explain the character diversity of a set of taxa under the assumption that characters have unique births, and that once a character is gained it is rarely lost. Examples of such traits include transposable elements, biochemical markers and emergence of organelles, just to name a few. We study the differences between our model and two similar models: perfect phylogenetic networks and ancestral recombination networks. Our goals are to initiate a study on the structural and algorithmic properties of perfect transfer networks. We then show that in polynomial time, one can decide whether a given network is a valid explanation for a set of taxa, and show how, for a given tree, one can add transfer edges to it so that it explains a set of taxa. We finally provide lower and upper bounds on the number of transfers required to explain a set of taxa, in the worst case.}, }
@article {pmid38321410, year = {2024}, author = {Orel, N and Fadeev, E and Herndl, GJ and Turk, V and Tinta, T}, title = {Recovering high-quality bacterial genomes from cross-contaminated cultures: a case study of marine Vibrio campbellii.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {146}, pmid = {38321410}, issn = {1471-2164}, mesh = {Animals ; *Ecosystem ; Sequence Analysis, DNA ; RNA, Ribosomal, 16S/genetics ; *Vibrio/genetics ; Genome, Bacterial ; Phylogeny ; }, abstract = {BACKGROUND: Environmental monitoring of bacterial pathogens is critical for disease control in coastal marine ecosystems to maintain animal welfare and ecosystem function and to prevent significant economic losses. This requires accurate taxonomic identification of environmental bacterial pathogens, which often cannot be achieved by commonly used genetic markers (e.g., 16S rRNA gene), and an understanding of their pathogenic potential based on the information encoded in their genomes. The decreasing costs of whole genome sequencing (WGS), combined with newly developed bioinformatics tools, now make it possible to unravel the full potential of environmental pathogens, beyond traditional microbiological approaches. However, obtaining a high-quality bacterial genome, requires initial cultivation in an axenic culture, which is a bottleneck in environmental microbiology due to cross-contamination in the laboratory or isolation of non-axenic strains.<br><br>RESULTS: We applied WGS to determine the pathogenic potential of two Vibrio isolates from coastal seawater. During the analysis, we identified cross-contamination of one of the isolates and decided to use this dataset to evaluate the possibility of bioinformatic contaminant removal and recovery of bacterial genomes from a contaminated culture. Despite the contamination, using an appropriate bioinformatics workflow, we were able to obtain high quality and highly identical genomes (Average Nucleotide Identity value 99.98%) of one of the Vibrio isolates from both the axenic and the contaminated culture. Using the assembled genome, we were able to determine that this isolate belongs to a sub-lineage of Vibrio campbellii associated with several diseases in marine organisms. We also found that the genome of the isolate contains a novel Vibrio plasmid associated with bacterial defense mechanisms and horizontal gene transfer, which may offer a competitive advantage to this putative pathogen.<br><br>CONCLUSIONS: Our study shows that, using state-of-the-art bioinformatics tools and a sufficient sequencing effort, it is possible to obtain high quality genomes of the bacteria of interest and perform in-depth genomic analyses even in the case of a contaminated culture. With the new isolate and its complete genome, we are providing new insights into the genomic characteristics and functional potential of this sub-lineage of V. campbellii. The approach described here also highlights the possibility of recovering complete bacterial genomes in the case of non-axenic cultures or obligatory co-cultures.}, }
@article {pmid38315121, year = {2024}, author = {Han, K and Li, J and Yang, D and Zhuang, Q and Zeng, H and Rong, C and Yue, J and Li, N and Gu, C and Chen, L and Chen, C}, title = {Detecting horizontal gene transfer with metagenomics co-barcoding sequencing.}, journal = {Microbiology spectrum}, volume = {12}, number = {3}, pages = {e0360223}, pmid = {38315121}, issn = {2165-0497}, support = {2021YFF0703805//MOST | National Key Research and Development Program of China (NKPs)/ ; 82102447//MOST | National Natural Science Foundation of China (NSFC)/ ; DFL20191801//Beijing Hospital Authority/ ; Z201100005520040//Beijing Municipal Science and Technology Commission, Adminitrative Commission of Zhongguancun Science Park/ ; QML20230701//Beijing Hospitals Authority Youth Programme/ ; }, mesh = {Animals ; Humans ; Mice ; *Gene Transfer, Horizontal ; *Metagenomics/methods ; Computational Biology/methods ; Metagenome ; Bacteria/genetics ; DNA ; }, abstract = {Horizontal gene transfer (HGT) is the process through which genetic information is transferred between different genomes and that played a crucial role in bacterial evolution. HGT can enable bacteria to rapidly acquire antibiotic resistance and bacteria that have acquired resistance is spreading within the microbiome. Conventional methods of characterizing HGT patterns include short-read metagenomic sequencing (short-reads mNGS), long-read sequencing, and single-cell sequencing. These approaches present several limitations, such as short-read fragments, high amounts of input DNA, and sequencing costs, respectively. Here, we attempt to circumvent present limitations to detect HGT by developing a metagenomics co-barcode sequencing workflow (MECOS) and applying it to the human and mouse gut microbiomes. In addition to that, we have over 10-fold increased contig length compared to short-reads mNGS; we also obtained exceeding 30 million paired reads with co-barcode information. Applying the novel bioinformatic pipeline, we integrated this co-barcoding information and the context information from long reads, and observed over 50-fold HGT events after we corrected the potential wrong HGT events. Specifically, we detected approximately 3,000 HGT blocks in individual samples, encompassing ~6,000 genes and ~100 taxonomic groups, including loci conferring tetracycline resistance through ribosomal protection. MECOS provides a valuable tool for investigating HGT and advance our understanding on the evolution of natural microbial communities within hosts.IMPORTANCEIn this study, to better identify horizontal gene transfer (HGT) in individual samples, we introduce a new co-barcoding sequencing system called metagenomics co-barcoding sequencing (MECOS), which has three significant improvements: (i) long DNA fragment extraction, (ii) a special transposome insertion, (iii) hybridization of DNA to barcode beads, and (4) an integrated bioinformatic pipeline. Using our approach, we have over 10-fold increased contig length compared to short-reads mNGS, and observed over 50-fold HGT events after we corrected the potential wrong HGT events. Our results indicate the presence of approximately 3,000 HGT blocks, involving roughly 6,000 genes and 100 taxonomic groups in individual samples. Notably, these HGT events are predominantly enriched in genes that confer tetracycline resistance via ribosomal protection. MECOS is a useful tool for investigating HGT and the evolution of natural microbial communities within hosts, thereby advancing our understanding of microbial ecology and evolution.}, }
@article {pmid38313259, year = {2024}, author = {Babajanyan, SG and Garushyants, SK and Wolf, YI and Koonin, EV}, title = {Microbial diversity and ecological complexity emerging from environmental variation and horizontal gene transfer in a simple mathematical model.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38313259}, issn = {2692-8205}, abstract = {Microbiomes are generally characterized by high diversity of coexisting microbial species and strains that remains stable within a broad range of conditions. However, under fixed conditions, microbial ecology conforms with the exclusion principle under which two populations competing for the same resource within the same niche cannot coexist because the less fit population inevitably goes extinct. To explore the conditions for stabilization of microbial diversity, we developed a simple mathematical model consisting of two competing populations that could exchange a single gene allele via horizontal gene transfer (HGT). We found that, although in a fixed environment, with unbiased HGT, the system obeyed the exclusion principle, in an oscillating environment, within large regions of the phase space bounded by the rates of reproduction and HGT, the two populations coexist. Moreover, depending on the parameter combination, all three major types of symbiosis obtained, namely, pure competition, host-parasite relationship and mutualism. In each of these regimes, certain parameter combinations provided for synergy, that is, a greater total abundance of both populations compared to the abundance of the winning population in the fixed environments. These findings show that basic phenomena that are universal in microbial communities, environmental variation and HGT, provide for stabilization of microbial diversity and ecological complexity.}, }
@article {pmid38310066, year = {2024}, author = {Stein, AM and Biller, SJ}, title = {An ocean of diffusible information.}, journal = {Trends in genetics : TIG}, volume = {40}, number = {3}, pages = {209-210}, doi = {10.1016/j.tig.2024.01.007}, pmid = {38310066}, issn = {0168-9525}, mesh = {*DNA/genetics ; Bacteria/genetics ; *Extracellular Vesicles/genetics ; Gene Transfer, Horizontal/genetics ; Oceans and Seas ; }, abstract = {In the ocean, free-living bacteria exist in a dilute world where direct physical interactions between cells are relatively rare. How then do they exchange genetic information via horizontal gene transfer (HGT)? Lücking et al. have explored the world of marine 'protected extracellular DNA' (peDNA), and find that extracellular vesicles (EVs) are likely to play an important role.}, }
@article {pmid38309275, year = {2024}, author = {Roisné-Hamelin, F and Liu, HW and Taschner, M and Li, Y and Gruber, S}, title = {Structural basis for plasmid restriction by SMC JET nuclease.}, journal = {Molecular cell}, volume = {84}, number = {5}, pages = {883-896.e7}, doi = {10.1016/j.molcel.2024.01.009}, pmid = {38309275}, issn = {1097-4164}, mesh = {*DNA/metabolism ; Plasmids/genetics ; *Endonucleases ; Prokaryotic Cells ; Cell Cycle Proteins/metabolism ; }, abstract = {DNA loop-extruding SMC complexes play crucial roles in chromosome folding and DNA immunity. Prokaryotic SMC Wadjet (JET) complexes limit the spread of plasmids through DNA cleavage, yet the mechanisms for plasmid recognition are unresolved. We show that artificial DNA circularization renders linear DNA susceptible to JET nuclease cleavage. Unlike free DNA, JET cleaves immobilized plasmid DNA at a specific site, the plasmid-anchoring point, showing that the anchor hinders DNA extrusion but not DNA cleavage. Structures of plasmid-bound JetABC reveal two presumably stalled SMC motor units that are drastically rearranged from the resting state, together entrapping a U-shaped DNA segment, which is further converted to kinked V-shaped cleavage substrate by JetD nuclease binding. Our findings uncover mechanical bending of residual unextruded DNA as molecular signature for plasmid recognition and non-self DNA elimination. We moreover elucidate key elements of SMC loop extrusion, including the motor direction and the structure of a DNA-holding state.}, }
@article {pmid38309246, year = {2024}, author = {Banks, EJ and Le, TBK}, title = {Co-opting bacterial viruses for DNA exchange: structure and regulation of gene transfer agents.}, journal = {Current opinion in microbiology}, volume = {78}, number = {}, pages = {102431}, doi = {10.1016/j.mib.2024.102431}, pmid = {38309246}, issn = {1879-0364}, mesh = {*Rhodobacter capsulatus/genetics ; *Bacteriophages/genetics ; Bacteria/genetics ; DNA ; Gene Transfer, Horizontal ; DNA, Bacterial/genetics ; }, abstract = {Horizontal gene transfer occurs via a range of mechanisms, including transformation, conjugation and bacteriophage transduction. Gene transfer agents (GTAs) are an alternative, less-studied route for interbacterial DNA exchange. Encoded within bacterial or archaeal genomes, GTAs assemble into phage-like particles that selflessly package and transmit host DNA to recipient bacteria. Several unique features distinguish GTAs from canonical phages such as an inability to self-replicate, thus producing non-infectious particles. GTAs are also deeply integrated into the physiology of the host cell and are maintained under tight host-regulatory control. Recent advances in understanding the structure and regulation of GTAs have provided further insights into a DNA transfer mechanism that is proving increasingly widespread across the bacterial tree of life.}, }
@article {pmid38306427, year = {2024}, author = {Yang, Z and Guo, Z and Gong, C and Xia, J and Hu, Y and Zhong, J and Yang, X and Xie, W and Wang, S and Wu, Q and Ye, W and Liu, B and Zhou, X and Turlings, TCJ and Zhang, Y}, title = {Two horizontally acquired bacterial genes steer the exceptionally efficient and flexible nitrogenous waste cycling in whiteflies.}, journal = {Science advances}, volume = {10}, number = {5}, pages = {eadi3105}, pmid = {38306427}, issn = {2375-2548}, mesh = {Animals ; *Hemiptera/genetics/metabolism/microbiology ; Genes, Bacterial ; Plants/genetics ; Nitrogen/metabolism ; }, abstract = {Nitrogen is an essential element for all life on earth. Nitrogen metabolism, including excretion, is essential for growth, development, and survival of plants and animals alike. Several nitrogen metabolic processes have been described, but the underlying molecular mechanisms are unclear. Here, we reveal a unique process of nitrogen metabolism in the whitefly Bemisia tabaci, a global pest. We show that it has acquired two bacterial uricolytic enzyme genes, B. tabaci urea carboxylase (BtUCA) and B. tabaci allophanate hydrolase (BtAtzF), through horizontal gene transfer. These genes operate in conjunction to not only coordinate an efficient way of metabolizing nitrogenous waste but also control B. tabaci's exceptionally flexible nitrogen recycling capacity. Its efficient nitrogen processing explains how this important pest can feed on a vast spectrum of plants. This finding provides insight into how the hijacking of microbial genes has allowed whiteflies to develop a highly economic and stable nitrogen metabolism network and offers clues for pest management strategies.}, }
@article {pmid38305416, year = {2024}, author = {Phillips, D and Noble, D}, title = {Reply from Daniel Phillips and Denis Noble.}, journal = {The Journal of physiology}, volume = {602}, number = {11}, pages = {2669-2672}, doi = {10.1113/JP286224}, pmid = {38305416}, issn = {1469-7793}, }
@article {pmid38304712, year = {2024}, author = {Chen, P and Wang, S and Li, H and Qi, X and Hou, Y and Ma, T}, title = {Comparative genomic analyses of Cutibacterium granulosum provide insights into genomic diversity.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1343227}, pmid = {38304712}, issn = {1664-302X}, abstract = {Cutibacterium granulosum, a commensal bacterium found on human skin, formerly known as Propionibacterium granulosum, rarely causes infections and is generally considered non-pathogenic. Recent research has revealed the transferability of the multidrug-resistant plasmid pTZC1 between C. granulosum and Cutibacterium acnes, the latter being an opportunistic pathogen in surgical site infections. However, there is a noticeable lack of research on the genome of C. granulosum, and the genetic landscape of this species remains largely uncharted. We investigated the genomic features and evolutionary structure of C. granulosum by analyzing a total of 30 Metagenome-Assembled Genomes (MAGs) and isolate genomes retrieved from public databases, as well as those generated in this study. A pan-genome of 6,077 genes was identified for C. granulosum. Remarkably, the 'cloud genes' constituted 62.38% of the pan-genome. Genes associated with mobilome: prophages, transposons [X], defense mechanisms [V] and replication, recombination and repair [L] were enriched in the cloud genome. Phylogenomic analysis revealed two distinct mono-clades, highlighting the genomic diversity of C. granulosum. The genomic diversity was further confirmed by the distribution of Average Nucleotide Identity (ANI) values. The functional profiles analysis of C. granulosum unveiled a wide range of potential Antibiotic Resistance Genes (ARGs) and virulence factors, suggesting its potential tolerance to various environmental challenges. Subtype I-E of the CRISPR-Cas system was the most abundant in these genomes, a feature also detected in C. acnes genomes. Given the widespread distribution of C. granulosum strains within skin microbiome, our findings make a substantial contribution to our broader understanding of the genetic diversity, which may open new avenues for investigating the mechanisms and treatment of conditions such as acne vulgaris.}, }
@article {pmid38299814, year = {2024}, author = {Yu, S and Ma, Q and Huang, J and Liu, Y and Li, J and Wang, Y and Gong, T and Zhang, Q and Zou, J and Li, Y}, title = {SMU_1361c regulates the oxidative stress response of Streptococcus mutans.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {2}, pages = {e0187123}, pmid = {38299814}, issn = {1098-5336}, support = {2022NSFSC1482//Sichuan Science and Technology Program/ ; 2023NSFSC1509//Sichuan Science and Technology Program/ ; 82170947//MOST | National Natural Science Foundation of China (NSFC)/ ; 32170046//MOST | National Natural Science Foundation of China (NSFC)/ ; RD-02-202402//Fundamental Research Funds for the Central Universities, Research and Develop Program, West China Hospital of Stomatology Sichuan University/ ; RD-02-202406//Fundamental Research Funds for the Central Universities, Research and Develop Program, West China Hospital of Stomatology Sichuan University/ ; RCDWJS2023-10//Research Funding from West China School/Hospital of Stomatology Sichuan University/ ; }, mesh = {Humans ; *Streptococcus mutans/metabolism ; Bacterial Proteins/genetics/metabolism ; *Dental Caries ; Biofilms ; Oxidative Stress ; Tetracyclines ; Deoxyribonuclease I/metabolism ; }, abstract = {Dental caries is the most common chronic infectious disease around the world and disproportionately affects the marginalized socioeconomic group. Streptococcus mutans, considered a primary etiological agent of caries, depends on the coordinated physiological response to tolerate the oxidative stress generated by commensal species within dental plaque, which is a critical aspect of its pathogenicity. Here, we identified and characterized a novel tetracycline repressor family regulator, SMU_1361c, which appears to be acquired by the bacteria via horizontal gene transfer. Surprisingly, smu_1361c functions as a negative transcriptional regulator to regulate gene expression outside its operon and is involved in the oxidative stress response of S. mutans. The smu_1361c overexpression strain UA159/pDL278-1361c was more susceptible to oxidative stress and less competitive against hydrogen peroxide generated by commensal species Streptococcus gordonii and Streptococcus sanguinis. Transcriptomics analysis revealed that smu_1361c overexpression resulted in the significant downregulation of 22 genes, mainly belonging to three gene clusters responsible for the oxidative stress response. The conversed DNA binding motif of SMU_1361c was determined by electrophoretic mobility shift and DNase I footprinting assay with purified SMU_1361c protein; therefore, smu_1361c is directly involved in gene transcription related to the oxidative stress response. Crucially, our finding provides a new understanding of how S. mutans deals with the oxidative stress that is required for pathogenesis and will facilitate the development of new and improved therapeutic approaches for dental caries.IMPORTANCEStreptococcus mutans is the major organism associated with the development of dental caries, which globally is the most common chronic disease. To persist and survive in biofilms, S. mutans must compete with commensal species that occupy the same ecological niche. Here, we uncover a novel molecular mechanism of how tetracycline repressor family regulator smu_1361c is involved in the oxidative stress response through transcriptomics analysis, electrophoretic mobility shift assay, and DNase I footprinting assay. Furthermore, we demonstrated that smu_1361c mediates S. mutans sensitivity to oxidative stress and competitiveness with commensal streptococci. Therefore, this study has revealed a previously unknown regulation between smu_1361c and genes outside its operon and demonstrated the importance of smu_1361c in the oxidative stress response and the fitness of S. mutans within the plaque biofilms, which can be exploited as a new therapy to modulate ecological homeostasis and prevent dental caries.}, }
@article {pmid38296951, year = {2024}, author = {Bálint, B and Merényi, Z and Hegedüs, B and Grigoriev, IV and Hou, Z and Földi, C and Nagy, LG}, title = {ContScout: sensitive detection and removal of contamination from annotated genomes.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {936}, pmid = {38296951}, issn = {2041-1723}, support = {758161//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; LP2019-13/2019//Magyar Tudom&#x00E1;nyos Akad&#x00E9;mia (Hungarian Academy of Sciences)/ ; }, mesh = {*Genome ; *Genomics ; Phylogeny ; Biological Evolution ; Metagenomics ; Evolution, Molecular ; }, abstract = {Contamination of genomes is an increasingly recognized problem affecting several downstream applications, from comparative evolutionary genomics to metagenomics. Here we introduce ContScout, a precise tool for eliminating foreign sequences from annotated genomes. It achieves high specificity and sensitivity on synthetic benchmark data even when the contaminant is a closely related species, outperforms competing tools, and can distinguish horizontal gene transfer from contamination. A screen of 844 eukaryotic genomes for contamination identified bacteria as the most common source, followed by fungi and plants. Furthermore, we show that contaminants in ancestral genome reconstructions lead to erroneous early origins of genes and inflate gene loss rates, leading to a false notion of complex ancestral genomes. Taken together, we offer here a tool for sensitive removal of foreign proteins, identify and remove contaminants from diverse eukaryotic genomes and evaluate their impact on phylogenomic analyses.}, }
@article {pmid38295970, year = {2024}, author = {Wei, J and Luo, J and Peng, T and Zhou, P and Zhang, J and Yang, F}, title = {Comparative genomic analysis and functional investigations for MCs catabolism mechanisms and evolutionary dynamics of MCs-degrading bacteria in ecology.}, journal = {Environmental research}, volume = {248}, number = {}, pages = {118336}, doi = {10.1016/j.envres.2024.118336}, pmid = {38295970}, issn = {1096-0953}, mesh = {Humans ; *Ecosystem ; Microcystins ; Biodegradation, Environmental ; *Sphingomonadaceae/genetics/metabolism ; Genomics ; }, abstract = {Microcystins (MCs) significantly threaten the ecosystem and public health. Biodegradation has emerged as a promising technology for removing MCs. Many MCs-degrading bacteria have been identified, including an indigenous bacterium Sphingopyxis sp. YF1 that could degrade MC-LR and Adda completely. Herein, we gained insight into the MCs biodegradation mechanisms and evolutionary dynamics of MCs-degrading bacteria, and revealed the toxic risks of the MCs degradation products. The biochemical characteristics and genetic repertoires of strain YF1 were explored. A comparative genomic analysis was performed on strain YF1 and six other MCs-degrading bacteria to investigate their functions. The degradation products were investigated, and the toxicity of the intermediates was analyzed through rigorous theoretical calculation. Strain YF1 might be a novel species that exhibited versatile substrate utilization capabilities. Many common genes and metabolic pathways were identified, shedding light on shared functions and catabolism in the MCs-degrading bacteria. The crucial genes involved in MCs catabolism mechanisms, including mlr and paa gene clusters, were identified successfully. These functional genes might experience horizontal gene transfer events, suggesting the evolutionary dynamics of these MCs-degrading bacteria in ecology. Moreover, the degradation products for MCs and Adda were summarized, and we found most of the intermediates exhibited lower toxicity to different organisms than the parent compound. These findings systematically revealed the MCs catabolism mechanisms and evolutionary dynamics of MCs-degrading bacteria. Consequently, this research contributed to the advancement of green biodegradation technology in aquatic ecology, which might protect human health from MCs.}, }
@article {pmid38295006, year = {2024}, author = {Anantharajah, A and Goormaghtigh, F and Nguvuyla Mantu, E and Güler, B and Bearzatto, B and Momal, A and Werion, A and Hantson, P and Kabamba-Mukadi, B and Van Bambeke, F and Rodriguez-Villalobos, H and Verroken, A}, title = {Long-term intensive care unit outbreak of carbapenemase-producing organisms associated with contaminated sink drains.}, journal = {The Journal of hospital infection}, volume = {143}, number = {}, pages = {38-47}, doi = {10.1016/j.jhin.2023.10.010}, pmid = {38295006}, issn = {1532-2939}, mesh = {Adult ; Humans ; *Cross Infection/epidemiology/prevention &amp; control ; beta-Lactamases/genetics ; Bacterial Proteins/genetics ; Disease Outbreaks ; Anti-Bacterial Agents ; *Disinfectants ; Intensive Care Units ; }, abstract = {BACKGROUND: Between 2018 and 2022, a Belgian tertiary care hospital faced a growing issue with acquiring carbapenemase-producing organisms (CPO), mainly VIM-producing P. aeruginosa (PA-VIM) and NDM-producing Enterobacterales (CPE-NDM) among hospitalized patients in the adult intensive care unit (ICU).<br><br>AIM: To investigate this ICU long-term CPO outbreak involving multiple species and a persistent environmental reservoir.<br><br>METHODS: Active case finding, environmental sampling, whole-genome sequencing (WGS) analysis of patient and environmental strains, and implemented control strategies were described in this study.<br><br>FINDINGS: From 2018 to 2022, 37 patients became colonized or infected with PA-VIM and/or CPE-NDM during their ICU stay. WGS confirmed the epidemiological link between clinical and environmental strains collected from the sink drains with clonal strain dissemination and horizontal gene transfer mediated by plasmid conjugation and/or transposon jumps. Environmental disinfection by quaternary ammonium-based disinfectant and replacement of contaminated equipment failed to eradicate environmental sources. Interestingly, efflux pump genes conferring resistance to quaternary ammonium compounds were widespread in the isolates. As removing sinks was not feasible, a combination of a foaming product degrading the biofilm and foaming disinfectant based on peracetic acid and hydrogen peroxide has been evaluated and has so far prevented recolonization of the proximal sink drain by CPO.<br><br>CONCLUSION: The persistence in the hospital environment of antibiotic- and disinfectant-resistant bacteria with the ability to transfer mobile genetic elements poses a serious threat to ICU patients with a risk of shifting towards an endemicity scenario. Innovative strategies are needed to address persistent environmental reservoirs and prevent CPO transmission.}, }
@article {pmid38290350, year = {2024}, author = {Wen, X and Chen, M and Ma, B and Xu, J and Zhu, T and Zou, Y and Liao, X and Wang, Y and Worrich, A and Wu, Y}, title = {Removal of antibiotic resistance genes during swine manure composting is strongly impaired by high levels of doxycycline residues.}, journal = {Waste management (New York, N.Y.)}, volume = {177}, number = {}, pages = {76-85}, doi = {10.1016/j.wasman.2024.01.037}, pmid = {38290350}, issn = {1879-2456}, mesh = {Animals ; Swine ; *Doxycycline ; Anti-Bacterial Agents/pharmacology ; *Composting ; Manure ; Drug Resistance, Microbial/genetics ; Livestock ; }, abstract = {Antibiotic resistance genes (ARGs) are emerging pollutants that enter the farm and surrounding environment via the manure of antibiotic-treated animals. Pretreatment of livestock manure by composting decreases ARGs abundance, but how antibiotic residues affect ARGs removal efficiency remains poorly understood. Here, we explored the fate of the resistome under different doxycycline residue levels during aerobic swine manure composting. Metagenomic sequencing showed that the presence of high levels of doxycycline generally had a higher abundance of tetracycline ARGs, and their dominant host bacteria of Firmicutes, especially Clostridium and Streptococcus, also had limited elimination in composting under high levels of doxycycline stress. Moreover, high levels of doxycycline impaired the removal of the total ARGs number in finished composts, with a removal rate of 51.74 % compared to 63.70 % and 71.52 % for the control and low-level doxycycline manure, respectively. Horizontal gene transfer and strengthened correlations among the bacterial community fostered ARGs preservation at high doxycycline levels during composting. In addition, ARGs carried by both plasmids and chromosomes, such as multidrug ARGs, showed wide host characteristics and rebound during compost maturation. Compared with chromosomes, a greater variety of ARGs on plasmids suggested that the majority of ARGs were characterized by horizontal mobility during composting, and the cross-host characteristics of ARGs during composting deserve further attention. This study provided deep insight into the fate of ARGs under residual antibiotic stress during manure composting and reminded the associated risk for environmental and public health.}, }
@article {pmid38289113, year = {2024}, author = {Abdulkadir, N and Saraiva, JP and Zhang, J and Stolte, S and Gillor, O and Harms, H and Rocha, U}, title = {Genome-centric analyses of 165 metagenomes show that mobile genetic elements are crucial for the transmission of antimicrobial resistance genes to pathogens in activated sludge and wastewater.}, journal = {Microbiology spectrum}, volume = {12}, number = {3}, pages = {e0291823}, pmid = {38289113}, issn = {2165-0497}, support = {VH-NG-1248 Micro' Big Data'//Helmholtz Association ()/ ; 460129525//Deutsche Forschungsgemeinschaft (DFG)/ ; 91717355//German Academic Exchange Service (DAAD)/ ; }, mesh = {Animals ; Humans ; *Wastewater ; Sewage/microbiology ; Anti-Bacterial Agents/pharmacology ; Metagenome ; Genes, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; Bacteria ; *Microbiota ; Interspersed Repetitive Sequences ; }, abstract = {UNLABELLED: Wastewater is considered a reservoir of antimicrobial resistance genes (ARGs), where the abundant antimicrobial-resistant bacteria and mobile genetic elements facilitate horizontal gene transfer. However, the prevalence and extent of these phenomena in different taxonomic groups that inhabit wastewater are still not fully understood. Here, we determined the presence of ARGs in metagenome-assembled genomes (MAGs) and evaluated the risks of MAG-carrying ARGs in potential human pathogens. The potential of these ARGs to be transmitted horizontally or vertically was also determined. A total of 5,916 MAGs (completeness >50%, contamination <10%) were recovered, covering 68 phyla and 279 genera. MAGs were dereplicated into 1,204 genome operational taxonomic units (gOTUs) as a proxy for species (average nucleotide identity >0.95). The dominant ARG classes detected were bacitracin, multi-drug, macrolide-lincosamide-streptogramin (MLS), glycopeptide, and aminoglycoside, and 10.26% of them were located on plasmids. The main hosts of ARGs belonged to Escherichia, Klebsiella, Acinetobacter, Gresbergeria, Mycobacterium, and Thauera. Our data showed that 253 MAGs carried virulence factor genes (VFGs) divided into 44 gOTUs, of which 45 MAGs were carriers of ARGs, indicating that potential human pathogens carried ARGs. Alarmingly, the MAG assigned as Escherichia coli contained 159 VFGs, of which 95 were located on chromosomes and 10 on plasmids. In addition to shedding light on the prevalence of ARGs in individual genomes recovered from activated sludge and wastewater, our study demonstrates a workflow that can identify antimicrobial-resistant pathogens in complex microbial communities.<br><br>IMPORTANCE: Antimicrobial resistance (AMR) threatens the health of humans, animals, and natural ecosystems. In our study, an analysis of 165 metagenomes from wastewater revealed antibiotic-targeted alteration, efflux, and inactivation as the most prevalent AMR mechanisms. We identified several genera correlated with multiple ARGs, including Klebsiella, Escherichia, Acinetobacter, Nitrospira, Ottowia, Pseudomonas, and Thauera, which could have significant implications for AMR transmission. The abundance of bacA, mexL, and aph(3")-I in the genomes calls for their urgent management in wastewater. Our approach could be applied to different ecosystems to assess the risk of potential pathogens containing ARGs. Our findings highlight the importance of managing AMR in wastewater and can help design measures to reduce the transmission and evolution of AMR in these systems.}, }
@article {pmid38288414, year = {2023}, author = {Kuo, LY and Su, HJ and Koubínová, D and Xie, PJ and Whitehouse, C and Ebihara, A and Grant, JR}, title = {Organellar phylogenomics of Ophioglossaceae fern genera.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1294716}, pmid = {38288414}, issn = {1664-462X}, abstract = {Previous phylogenies showed conflicting relationships among the subfamilies and genera within the fern family Ophioglossaceae. However, their classification remains unsettled where contrasting classifications recognize four to 15 genera. Since these treatments are mostly based on phylogenetic evidence using limited, plastid-only loci, a phylogenomic understanding is actually necessary to provide conclusive insight into the systematics of the genera. In this study, we have therefore compiled datasets with the broadest sampling of Ophioglossaceae genera to date, including all fifteen currently recognized genera, especially for the first time the South African endemic genus Rhizoglossum. Notably, our comprehensive phylogenomic matrix is based on both plastome and mitogenome genes. Inferred from the coding sequences of 83 plastid and 37 mitochondrial genes, a strongly supported topology for these subfamilies is presented, and is established by analyses using different partitioning approaches and substitution models. At the generic level, most relationships are well resolved except for few within the subfamily Ophioglossoideae. With this new phylogenomic scheme, key morphological and genomic changes were further identified along this backbone. In addition, we confirmed numerous horizontally transferred (HGT) genes in the genera Botrypus, Helminthostachys, Mankyua, Sahashia, and Sceptridium. These HGT genes are most likely located in mitogenomes and are predominately donated from angiosperm Santalales or non-Ophioglossaceae ferns. By our in-depth searches of the organellar genomes, we also provided phylogenetic overviews for the plastid and mitochondrial MORFFO genes found in these Ophioglossaceae ferns.}, }
@article {pmid38286289, year = {2024}, author = {Hazra, M and Watts, JEM and Williams, JB and Joshi, H}, title = {An evaluation of conventional and nature-based technologies for controlling antibiotic-resistant bacteria and antibiotic-resistant genes in wastewater treatment plants.}, journal = {The Science of the total environment}, volume = {917}, number = {}, pages = {170433}, doi = {10.1016/j.scitotenv.2024.170433}, pmid = {38286289}, issn = {1879-1026}, mesh = {Humans ; *Wastewater ; Anti-Bacterial Agents/analysis ; Genes, Bacterial ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Bacteria/genetics ; Soil ; Water ; *Water Purification ; }, abstract = {Antibiotic resistance is a globally recognized health concern which leads to longer hospital stays, increased morbidity, increased mortality, and higher medical costs. Understanding how antibiotic resistance persists and exchanges in environmental systems like soil, water, and wastewater are critically important for understanding the emergence of pathogens with new resistance profiles and the subsequent exposure of people who indirectly/directly come in contact with these pathogens. There are concerns about the widespread application of prophylactic antibiotics in the clinical and agriculture sectors, as well as chemicals/detergents used in food and manufacturing industries, especially the quaternary ammonium compounds which have been found responsible for the generation of resistant genes in water and soil. The rates of horizontal gene transfer increase where there is a lack of proper water/wastewater infrastructure, high antibiotic manufacturing industries, or endpoint users - such as hospitals and intensive agriculture. Conventional wastewater treatment technologies are often inefficient in the reduction of ARB/ARGs and provide the perfect combination of conditions for the development of antibiotic resistance. The wastewater discharged from municipal facilities may therefore be enriched with bacterial communities/pathogens and provide a suitable environment (due to the presence of nutrients and other pollutants) to enhance the transfer of antibiotic resistance. However, facilities with tertiary treatment (either traditional/emerging technologies) provide higher rates of reduction. This review provides a synthesis of the current understanding of wastewater treatment and antibiotic resistance, examining the drivers that may accelerate their possible transmission to a different environment, and highlighting the need for tertiary technologies used in treatment plants for the reduction of resistant bacteria/genes.}, }
@article {pmid38285528, year = {2024}, author = {Wu, Y and Zhang, L}, title = {Computing the Bounds of the Number of Reticulations in a Tree-Child Network That Displays a Set of Trees.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {31}, number = {4}, pages = {345-359}, doi = {10.1089/cmb.2023.0309}, pmid = {38285528}, issn = {1557-8666}, mesh = {*Phylogeny ; *Algorithms ; Models, Genetic ; Evolution, Molecular ; Computational Biology/methods ; Computer Simulation ; Gene Transfer, Horizontal ; }, abstract = {Phylogenetic network is an evolutionary model that uses a rooted directed acyclic graph (instead of a tree) to model an evolutionary history of species in which reticulate events (e.g., hybrid speciation or horizontal gene transfer) occurred. Tree-child network is a kind of phylogenetic network with structural constraints. Existing approaches for tree-child network reconstruction can be slow for large data. In this study, we present several computational approaches for bounding from below the number of reticulations in a tree-child network that displays a given set of rooted binary phylogenetic trees. In addition, we also present some theoretical results on bounding from above the number of reticulations. Through simulation, we demonstrate that the new lower bounds on the reticulation number for tree-child networks can practically be computed for large tree data. The bounds can provide estimates of reticulation for relatively large data.}, }
@article {pmid38281357, year = {2024}, author = {Kang, Y and Wang, J and Li, Z}, title = {Meta-analysis addressing the characterization of antibiotic resistome in global hospital wastewater.}, journal = {Journal of hazardous materials}, volume = {466}, number = {}, pages = {133577}, doi = {10.1016/j.jhazmat.2024.133577}, pmid = {38281357}, issn = {1873-3336}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Wastewater ; Genes, Bacterial ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; }, abstract = {Hospital wastewater (HWW) is a significant environmental reservoir of antibiotic resistance genes (ARGs). However, currently, no comprehensive understanding exists of the antibiotic resistome in global HWW. In this study, we attempted to address this knowledge gap through an in silico reanalysis of publicly accessible global HWW metagenomic data. We reanalyzed ARGs in 338 HWW samples from 13 countries in Africa, Asia, and Europe. In total, 2420 ARG subtypes belonging to 30 ARG types were detected, dominated by multidrug, beta-lactam, and aminoglycoside resistance genes. ARG composition in Europe differed from that in Asia and Africa. Notably, the ARGs presented co-occurrence with mobile genetic elements (MGEs), metal resistance genes (MRGs), and human bacterial pathogens (HBP), indicating a potential dissemination risk of ARGs in the HWW. Multidrug resistance genes presented co-occurrence with MGEs, MRGs, and HBP, is particularly pronounced. The abundance of contigs that contained ARG, contigs that contained ARG and HBP, contigs that contained ARG and MGE, contigs that contained ARG and MRG were used for health and transmission risk assessment of antibiotic resistome and screened out 40 high risk ARGs in the global HWW. This study first provides a comprehensive characterization and risk of the antibiotic resistome in global HWW.}, }
@article {pmid38280843, year = {2024}, author = {Zhu, S and Hong, J and Wang, T}, title = {Horizontal gene transfer is predicted to overcome the diversity limit of competing microbial species.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {800}, pmid = {38280843}, issn = {2041-1723}, mesh = {*Ecosystem ; *Gene Transfer, Horizontal ; Biodiversity ; }, abstract = {Natural microbial ecosystems harbor substantial diversity of competing species. Explaining such diversity is challenging, because in classic theories it is extremely infeasible for a large community of competing species to stably coexist in homogeneous environments. One important aspect mostly overlooked in these theories, however, is that microbes commonly share genetic materials with their neighbors through horizontal gene transfer (HGT), which enables the dynamic change of species growth rates due to the fitness effects of the mobile genetic elements (MGEs). Here, we establish a framework of species competition by accounting for the dynamic gene flow among competing microbes. Combining theoretical derivation and numerical simulations, we show that in many conditions HGT can surprisingly overcome the biodiversity limit predicted by the classic model and allow the coexistence of many competitors, by enabling dynamic neutrality of competing species. In contrast with the static neutrality proposed by previous theories, the diversity maintained by HGT is highly stable against random perturbations of microbial fitness. Our work highlights the importance of considering gene flow when addressing fundamental ecological questions in the world of microbes and has broad implications for the design and engineering of complex microbial consortia.}, }
@article {pmid38280464, year = {2024}, author = {Kim, H and Yoo, K}, title = {Marine plastisphere selectively enriches microbial assemblages and antibiotic resistance genes during long-term cultivation periods.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {344}, number = {}, pages = {123450}, doi = {10.1016/j.envpol.2024.123450}, pmid = {38280464}, issn = {1873-6424}, mesh = {Humans ; *Plastics ; *Anti-Bacterial Agents/pharmacology ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; Drug Resistance, Microbial/genetics ; Microplastics ; Bacteria ; Genes, Bacterial ; Polyethylene ; }, abstract = {Several studies have focused on identifying and quantifying suspended plastics in surface and subsurface seawater. Microplastics (MPs) have attracted attention as carriers of antibiotic resistance genes (ARGs) in the marine environment. Plastispheres, specific biofilms on MP, can provide an ideal niche to spread more widely through horizontal gene transfer (HGT), thereby increasing risks to ecosystems and human health. However, the microbial communities formed on different plastic types and ARG abundances during exposure time in natural marine environments remain unclear. Four types of commonly used MPs (polyethylene (PE), polypropylene (PP), polystyrene (PS), and polyvinyl chloride (PVC)) were periodically cultured (46, 63, and 102 d) in a field-based marine environment to study the co-selection of ARGs and microbial communities in marine plastispheres. After the first 63 d of incubation (p < 0.05), the initial 16S rRNA gene abundance of microorganisms in the plastisphere increased significantly, and the biomass subsequently decreased. These results suggest that MPs can serve as vehicles for various microorganisms to travel to different environments and eventually provide a niche for a variety of microorganisms. Additionally, the qPCR results showed that MPs selectively enriched ARGs. In particular, tetA, tetQ, sul1, and qnrS were selectively enriched in the PVC-MPs. The abundances of intl1, a mobile genetic element, was measured in all MP types for 46 d (5.22 × 10[-5] ± 8.21 × 10[-6] copies/16s rRNA gene copies), 63 d (5.90 × 10[-5] ± 2.49 × 10[-6] copies/16s rRNA gene copies), and 102 d (4.00 × 10[-5] ± 5.11 × 10[-6] copies/16s rRNA gene copies). Network analysis indicated that ARG profiles co-occurred with key biofilm-forming bacteria. This study suggests that the selection of ARGs and their co-occurring bacteria in MPs could potentially accelerate their transmission through HGT in natural marine plastics.}, }
@article {pmid38277437, year = {2024}, author = {Goldstein, SA and Elde, NC}, title = {Recurrent viral capture of cellular phosphodiesterases that antagonize OAS-RNase L.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {5}, pages = {e2312691121}, pmid = {38277437}, issn = {1091-6490}, support = {F32 AI152341/AI/NIAID NIH HHS/United States ; R35 GM134936/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Phosphoric Diester Hydrolases/genetics/metabolism ; Phylogeny ; *Middle East Respiratory Syndrome Coronavirus ; Mammals/metabolism ; Diethylstilbestrol/*analogs &amp; derivatives ; *Endoribonucleases ; *Rotavirus ; }, abstract = {Phosphodiesterases (PDEs) encoded by viruses are putatively acquired by horizontal transfer of cellular PDE ancestor genes. Viral PDEs inhibit the OAS-RNase L antiviral pathway, a key effector component of the innate immune response. Although the function of these proteins is well-characterized, the origins of these gene acquisitions are less clear. Phylogenetic analysis revealed at least five independent PDE acquisition events by ancestral viruses. We found evidence that PDE-encoding genes were horizontally transferred between coronaviruses belonging to different genera. Three clades of viruses within Nidovirales: merbecoviruses (MERS-CoV), embecoviruses (HCoV-OC43), and toroviruses encode independently acquired PDEs, and a clade of rodent alphacoronaviruses acquired an embecovirus PDE via recent horizontal transfer. Among rotaviruses, the PDE of rotavirus A was acquired independently from rotavirus B and G PDEs, which share a common ancestor. Conserved motif analysis suggests a link between all viral PDEs and a similar ancestor among the mammalian AKAP7 proteins despite low levels of sequence conservation. Additionally, we used ancestral sequence reconstruction and structural modeling to reveal that sequence and structural divergence are not well-correlated among these proteins. Specifically, merbecovirus PDEs are as structurally divergent from the ancestral protein and the solved structure of human AKAP7 PDE as they are from each other. In contrast, comparisons of rotavirus B and G PDEs reveal virtually unchanged structures despite evidence for loss of function in one, suggesting impactful changes that lie outside conserved catalytic sites. These findings highlight the complex and volatile evolutionary history of viral PDEs and provide a framework to facilitate future studies.}, }
@article {pmid38276173, year = {2023}, author = {Lücking, D and Alarcón-Schumacher, T and Erdmann, S}, title = {Distribution and Implications of Haloarchaeal Plasmids Disseminated in Self-Encoded Plasmid Vesicles.}, journal = {Microorganisms}, volume = {12}, number = {1}, pages = {}, pmid = {38276173}, issn = {2076-2607}, support = {Max-Planck Research Group Archaeal Virology//Max-Planck Society/ ; 98 190//Volkswagen Foundation/ ; }, abstract = {Even though viruses and plasmids are both drivers of horizontal gene transfer, they differ fundamentally in their mode of transfer. Virus genomes are enclosed in virus capsids and are not dependent on cell-to-cell contacts for their dissemination. In contrast, the transfer of plasmids most often requires physical contact between cells. However, plasmid pR1SE of Halorubrum lacusprofundi is disseminated between cells, independent of cell-cell contacts, in specialized membrane vesicles that contain plasmid proteins. In this study, we searched for pR1SE-like elements in public databases and a metagenomics dataset from Australian salt lakes and identified 40 additional pR1SE-like elements in hypersaline environments worldwide. Herein, these elements are named apHPVs (archaeal plasmids of haloarchaea potentially transferred in plasmid vesicles). They share two sets of closely related proteins with conserved synteny, strongly indicating an organization into different functional clusters. We find that apHPVs, besides transferring themselves, have the potential to transfer large fragments of DNA between host cells, including virus defense systems. Most interestingly, apHPVs likely play an important role in the evolution of viruses and plasmids in haloarchaea, as they appear to recombine with both of them. This further supports the idea that plasmids and viruses are not distinct but closely related mobile genetic elements.}, }
@article {pmid38275928, year = {2024}, author = {Gong, J and Zeng, X and Xu, J and Zhang, D and Dou, X and Lin, J and Wang, C}, title = {Genomic Characterization of a Plasmid-Free and Highly Drug-Resistant Salmonella enterica Serovar Indiana Isolate in China.}, journal = {Veterinary sciences}, volume = {11}, number = {1}, pages = {}, pmid = {38275928}, issn = {2306-7381}, support = {31772758//National Natural Science 291 Foundation of China/ ; CX(23)3005//Jiangsu agricultural science and technology 292 innovation fund/ ; }, abstract = {The emergence of multi-drug resistant (MDR) Salmonella enterica serovar Indiana (S. Indiana) strains in China is commonly associated with the presence of one or more resistance plasmids harboring integrons pivotal in acquiring antimicrobial resistance (AMR). This study aims to elucidate the genetic makeup of this plasmid-free, highly drug-resistant S. Indiana S1467 strain. Genomic sequencing was performed using Illumina HiSeq 2500 sequencer and PacBio RS II System. Prodigal software predicted putative protein-coding sequences while BLASTP analysis was conducted. The S1467 genome comprises a circular 4,998,300 bp chromosome with an average GC content of 51.81%, encompassing 4709 open reading frames (ORFs). Fifty-four AMR genes were identified, conferring resistance across 16 AMR categories, aligning closely with the strain's antibiotic susceptibility profile. Genomic island prediction unveiled an approximately 51 kb genomic island housing a unique YeeVU toxin-antitoxin system (TAS), a rarity in Salmonella species. This suggests that the AMR gene cluster on the S1467 genomic island may stem from the integration of plasmids originating from other Enterobacteriaceae. This study contributes not only to the understanding of the genomic characteristics of a plasmid-free, highly drug-resistant S. Indiana strain but also sheds light on the intricate mechanisms underlying antimicrobial resistance. The implications of our findings extend to the broader context of horizontal gene transfer between bacterial species, emphasizing the need for continued surveillance and research to address the evolving challenges posed by drug-resistant pathogens.}, }
@article {pmid38273225, year = {2024}, author = {Liu, D and Zhang, Z and Hao, Y and Li, M and Yu, H and Zhang, X and Mi, H and Cheng, L and Zhao, Y}, title = {Decoding the complete organelle genomic architecture of Stewartia gemmata: an early-diverging species in Theaceae.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {114}, pmid = {38273225}, issn = {1471-2164}, support = {21HASTIT040//Program for Science &amp; Technology Innovation Talents in Universities of Henan Province/ ; 21HASTIT040//Program for Science &amp; Technology Innovation Talents in Universities of Henan Province/ ; 212102110447//Scientific and Technological Project in Henan Province/ ; 212102110447//Scientific and Technological Project in Henan Province/ ; Qian-Jiao-Ji [2023]007//Key Laboratory of Functional Agriculture within Guizhou Province's Higher Education Institutions/ ; Qian-Jiao-Ji [2023]007//Key Laboratory of Functional Agriculture within Guizhou Province's Higher Education Institutions/ ; }, mesh = {Phylogeny ; *Theaceae/genetics ; Genomics ; Codon/genetics ; Chloroplasts/genetics ; RNA, Transfer/genetics ; Tea ; *Genome, Chloroplast ; }, abstract = {BACKGROUND: Theaceae, comprising 300 + species, holds significance in biodiversity, economics, and culture, notably including the globally consumed tea plant. Stewartia gemmata, a species of the earliest diverging tribe Stewartieae, is critical to offer insights into Theaceae's origin and evolutionary history.<br><br>RESULT: We sequenced the complete organelle genomes of Stewartia gemmata using short/long reads sequencing technologies. The chloroplast genome (158,406&#xa0;bp) exhibited a quadripartite structure including the large single-copy region (LSC), a small single-copy region (SSC), and a pair of inverted repeat regions (IRs); 114 genes encoded 80 proteins, 30 tRNAs, and four rRNAs. The mitochondrial genome (681,203&#xa0;bp) exhibited alternative conformations alongside a monocyclic structure: 61 genes encoding 38 proteins, 20 tRNAs, three rRNAs, and RNA editing-impacting genes, including ATP6, RPL16, COX2, NAD4L, NAD5, NAD7, and RPS1. Comparative analyses revealed frequent recombination events and apparent rRNA gene gains and losses in the mitochondrial genome of Theaceae. In organelle genomes, the protein-coding genes exhibited a strong A/U bias at codon endings; ENC-GC3 analysis implies selection-driven codon bias. Transposable elements might facilitate interorganelle sequence transfer. Phylogenetic analysis confirmed Stewartieae's early divergence within Theaceae, shedding light on organelle genome characteristics and evolution in Theaceae.<br><br>CONCLUSIONS: We studied the detailed characterization of organelle genomes, including genome structure, composition, and repeated sequences, along with the identification of lateral gene transfer (LGT) events and complexities. The discovery of a large number of repetitive sequences and simple sequence repeats (SSRs) has led to new insights into molecular phylogenetic markers. Decoding the Stewartia gemmata organellar genome provides valuable genomic resources for further studies in tea plant phylogenomics and evolutionary biology.}, }
@article {pmid38271287, year = {2024}, author = {Harada, R and Hirakawa, Y and Yabuki, A and Kim, E and Yazaki, E and Kamikawa, R and Nakano, K and Eliáš, M and Inagaki, Y}, title = {Encyclopedia of Family A DNA Polymerases Localized in Organelles: Evolutionary Contribution of Bacteria Including the Proto-Mitochondrion.}, journal = {Molecular biology and evolution}, volume = {41}, number = {2}, pages = {}, pmid = {38271287}, issn = {1537-1719}, support = {18KK0203//Japan Society for Promotion of Sciences projects/ ; 21-19664S//Czech Science Foundation/ ; //National Institute for Environmental Studies/ ; //Ministry of Education, Culture, Sports, Science and Technology/ ; //National Institute of Genetics/ ; //University of Tsukuba/ ; }, mesh = {*Organelles/genetics ; Phylogeny ; DNA-Directed DNA Polymerase/genetics ; Plastids/genetics ; Mitochondria ; *Cyanobacteria/genetics ; Symbiosis ; }, abstract = {DNA polymerases synthesize DNA from deoxyribonucleotides in a semiconservative manner and serve as the core of DNA replication and repair machinery. In eukaryotic cells, there are 2 genome-containing organelles, mitochondria, and plastids, which were derived from an alphaproteobacterium and a cyanobacterium, respectively. Except for rare cases of genome-lacking mitochondria and plastids, both organelles must be served by nucleus-encoded DNA polymerases that localize and work in them to maintain their genomes. The evolution of organellar DNA polymerases has yet to be fully understood because of 2 unsettled issues. First, the diversity of organellar DNA polymerases has not been elucidated in the full spectrum of eukaryotes. Second, it is unclear when the DNA polymerases that were used originally in the endosymbiotic bacteria giving rise to mitochondria and plastids were discarded, as the organellar DNA polymerases known to date show no phylogenetic affinity to those of the extant alphaproteobacteria or cyanobacteria. In this study, we identified from diverse eukaryotes 134 family A DNA polymerase sequences, which were classified into 10 novel types, and explored their evolutionary origins. The subcellular localizations of selected DNA polymerases were further examined experimentally. The results presented here suggest that the diversity of organellar DNA polymerases has been shaped by multiple transfers of the PolI gene from phylogenetically broad bacteria, and their occurrence in eukaryotes was additionally impacted by secondary plastid endosymbioses. Finally, we propose that the last eukaryotic common ancestor may have possessed 2 mitochondrial DNA polymerases, POP, and a candidate of the direct descendant of the proto-mitochondrial DNA polymerase I, rdxPolA, identified in this study.}, }
@article {pmid38267392, year = {2024}, author = {Zhang, J and Lu, T and Song, Y and Rocha, UND and Liu, J and Nikolausz, M and Wei, Y and Richnow, HH}, title = {Viral Communities Contribute More to the Lysis of Antibiotic-Resistant Bacteria than the Transduction of Antibiotic Resistance Genes in Anaerobic Digestion Revealed by Metagenomics.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {5}, pages = {2346-2359}, pmid = {38267392}, issn = {1520-5851}, mesh = {*Anti-Bacterial Agents/pharmacology ; Anaerobiosis ; Angiotensin Receptor Antagonists ; Genes, Bacterial ; Angiotensin-Converting Enzyme Inhibitors ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; *Bacteriophages/genetics ; Metagenomics ; }, abstract = {Ecological role of the viral community on the fate of antibiotic resistance genes (ARGs) (reduction vs proliferation) remains unclear in anaerobic digestion (AD). Metagenomics revealed a dominance of Siphoviridae and Podoviridae among 13,895 identified viral operational taxonomic units (vOTUs) within AD, and only 21 of the vOTUs carried ARGs, which only accounted for 0.57 ± 0.43% of AD antibiotic resistome. Conversely, ARGs locating on plasmids and integrative and conjugative elements accounted for above 61.0%, indicating a substantial potential for conjugation in driving horizontal gene transfer of ARGs within AD. Virus-host prediction based on CRISPR spacer, tRNA, and homology matches indicated that most viruses (80.2%) could not infect across genera. Among 480 high-quality metagenome assembly genomes, 95 carried ARGs and were considered as putative antibiotic-resistant bacteria (pARB). Furthermore, lytic phages of 66 pARBs were identified and devoid of ARGs, and virus/host abundance ratios with an average value of 71.7 indicated extensive viral activity and lysis. The infectivity of lytic phage was also elucidated through laboratory experiments concerning changes of the phage-to-host ratio, pH, and temperature. Although metagenomic evidence for dissemination of ARGs by phage transduction was found, the higher proportion of lytic phages infecting pARBs suggested that the viral community played a greater role in reducing ARB numbers than spreading ARGs in AD.}, }
@article {pmid38266895, year = {2024}, author = {Zhang, C and You, Z and Li, S and Zhang, C and Zhao, Z and Zhou, D}, title = {NO3[-] as an electron acceptor elevates antibiotic resistance gene and human bacterial pathogen risks in managed aquifer recharge (MAR): A comparison with O2.}, journal = {Environmental research}, volume = {248}, number = {}, pages = {118277}, doi = {10.1016/j.envres.2024.118277}, pmid = {38266895}, issn = {1096-0953}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; Electrons ; Bacteria ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Oxygen ; *Groundwater/microbiology ; }, abstract = {Managed aquifer recharge (MAR) stands out as a promising strategy for ensuring water resource sustainability. This study delves into the comparative impact of nitrate (NO3[-]) and oxygen (O2) as electron acceptors in MAR on water quality and safety. Notably, NO3[-], acting as an electron acceptor, has the potential to enrich denitrifying bacteria, serving as hosts for antibiotic resistance genes (ARGs) and enriching human bacterial pathogens (HBPs) compared to O2. However, a direct comparison between NO3[-] and O2 remains unexplored. This study assessed risks in MAR effluent induced by NO3[-] and O2, alongside the presence of the typical refractory antibiotic sulfamethoxazole. Key findings reveal that NO3[-] as an electron acceptor resulted in a 2 times reduction in dissolved organic carbon content compared to O2, primarily due to a decrease in soluble microbial product production. Furthermore, NO3[-] significantly enriched denitrifying bacteria, the primary hosts of major ARGs, by 747%, resulting in a 66% increase in the overall abundance of ARGs in the effluent of NO3[-] MAR compared to O2. This escalation was predominantly attributed to horizontal gene transfer mechanisms, as evidenced by a notable 78% increase in the relative abundance of mobile ARGs, alongside a minor 27% rise in chromosomal ARGs. Additionally, the numerous denitrifying bacteria enriched under NO3[-] influence also belong to the HBP category, resulting in a significant 114% increase in the abundance of all HBPs. The co-occurrence of ARGs and HBPs was also observed to intensify under NO3[-] influence. Thus, NO3[-] as an electron acceptor in MAR elevates ARG and HBP risks compared to O2, potentially compromising groundwater quality and safety.}, }
@article {pmid38263430, year = {2024}, author = {Keeling, PJ}, title = {Horizontal gene transfer in eukaryotes: aligning theory with data.}, journal = {Nature reviews. Genetics}, volume = {25}, number = {6}, pages = {416-430}, pmid = {38263430}, issn = {1471-0064}, mesh = {*Gene Transfer, Horizontal ; Eukaryota/genetics ; Symbiosis/genetics ; Eukaryotic Cells/metabolism ; Animals ; Phagocytosis/genetics ; Archaea/genetics ; Evolution, Molecular ; Models, Genetic ; }, abstract = {Horizontal gene transfer (HGT), or lateral gene transfer, is the non-sexual movement of genetic information between genomes. It has played a pronounced part in bacterial and archaeal evolution, but its role in eukaryotes is less clear. Behaviours unique to eukaryotic cells - phagocytosis and endosymbiosis - have been proposed to increase the frequency of HGT, but nuclear genomes encode fewer HGTs than bacteria and archaea. Here, I review the existing theory in the context of the growing body of data on HGT in eukaryotes, which suggests that any increased chance of acquiring new genes through phagocytosis and endosymbiosis is offset by a reduced need for these genes in eukaryotes, because selection in most eukaryotes operates on variation not readily generated by HGT.}, }
@article {pmid38262510, year = {2024}, author = {Sajjad, W and Ilahi, N and Haq, A and Shang, Z and Nabi, G and Rafiq, M and Bahadur, A and Banerjee, A and Kang, S}, title = {Bacteria populating freshly appeared supraglacial lake possess metals and antibiotic-resistant genes.}, journal = {Environmental research}, volume = {247}, number = {}, pages = {118288}, doi = {10.1016/j.envres.2024.118288}, pmid = {38262510}, issn = {1096-0953}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Lakes/microbiology ; Metals ; }, abstract = {Antibiotic resistance (AR) has been extensively studied in natural habitats and clinical applications. AR is mainly reported with the use and misuse of antibiotics; however, little is known about its presence in antibiotic-free remote supraglacial lake environments. This study evaluated bacterial strains isolated from supraglacial lake debris and meltwater in Dook Pal Glacier, northern Pakistan, for antibiotic-resistant genes (ARGs) and metal-tolerant genes (MTGs) using conventional PCR. Several distinct ARGs were reported in the bacterial strains isolated from lake debris (92.5%) and meltwater (100%). In lake debris, 57.5% of isolates harbored the blaTEM gene, whereas 58.3% of isolates in meltwater possessed blaTEM and qnrA each. Among the ARGs, qnrA was dominant in debris isolates (19%), whereas in meltwater isolates, qnrA (15.2%) and blaTEM (15.2%) were dominant. ARGs were widely distributed among the bacterial isolates and different bacteria shared similar types of ARGs. Relatively greater number of ARGs were reported in Gram-negative bacterial strains. In addition, 92.5% of bacterial isolates from lake debris and 83.3% of isolates from meltwater harbored MTGs. Gene copA was dominant in meltwater isolates (50%), whereas czcA was greater in debris bacterial isolates (45%). Among the MTGs, czcA (18.75%) was dominant in debris strains, whereas copA (26.0%) was greater in meltwater isolates. This presents the co-occurrence and co-selection of MTGs and ARGs in a freshly appeared supraglacial lake. The same ARGs and MTGs were present in different bacteria, exhibiting horizontal gene transfer (HGT). Both positive and negative correlations were determined between ARGs and MTGs. The research provides insights into the existence of MTGs and ARGs in bacterial strains isolated from remote supraglacial lake environments, signifying the need for a more detailed study of bacteria harboring ARGs and MTGs in supraglacial lakes.}, }
@article {pmid38261993, year = {2024}, author = {Teyssonniere, EM and Shichino, Y and Mito, M and Friedrich, A and Iwasaki, S and Schacherer, J}, title = {Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast.}, journal = {Nucleic acids research}, volume = {52}, number = {5}, pages = {2434-2445}, pmid = {38261993}, issn = {1362-4962}, support = {S10 OD018174/OD/NIH HHS/United States ; S10 OD018174/CD/ODCDC CDC HHS/United States ; 772505/ERC_/European Research Council/International ; }, mesh = {Humans ; *Saccharomyces cerevisiae/genetics ; *Transcriptome ; Gene Expression Profiling ; Ribosomes/genetics ; Genetic Background ; Genetic Variation ; }, abstract = {Gene expression is known to vary among individuals, and this variability can impact the phenotypic diversity observed in natural populations. While the transcriptome and proteome have been extensively studied, little is known about the translation process itself. Here, we therefore performed ribosome and transcriptomic profiling on a genetically and ecologically diverse set of natural isolates of the Saccharomyces cerevisiae yeast. Interestingly, we found that the Euclidean distances between each profile and the expression fold changes in each pairwise isolate comparison were higher at the transcriptomic level. This observation clearly indicates that the transcriptional variation observed in the different isolates is buffered through a phenomenon known as post-transcriptional buffering at the translation level. Furthermore, this phenomenon seemed to have a specific signature by preferentially affecting essential genes as well as genes involved in complex-forming proteins, and low transcribed genes. We also explored the translation of the S. cerevisiae pangenome and found that the accessory genes related to introgression events displayed similar transcription and translation levels as the core genome. By contrast, genes acquired through horizontal gene transfer events tended to be less efficiently translated. Together, our results highlight both the extent and signature of the post-transcriptional buffering.}, }
@article {pmid38261836, year = {2024}, author = {Kaur, J and Kaur, J}, title = {Comparative genomics of seven genomes of genus Idiomarina reveals important halo adaptations and genes for stress response.}, journal = {3 Biotech}, volume = {14}, number = {2}, pages = {40}, pmid = {38261836}, issn = {2190-572X}, abstract = {UNLABELLED: The genus Idiomarina consists of halophilic and/or haloalkaliphilic organisms. We compared the complete genomes of seven strains of the genus Idiomarina to investigate its adaptation to saline environment. A total of 1,313 core genes related to salinity tolerance, stress response, antibiotic resistance genes, virulence factors, and drug targets were found. Comparative genomics revealed various genes involved in halo adaptations of these organisms, including transporters and influx or efflux systems for elements such as Fe, Cu, Zn, Pb, and Cd. In agreement with their isolation sources (such as hydrothermal vents and marine sediments) and environments abundant in heavy metals, various resistance proteins and transporters associated with metal tolerance were also identified. These included copper resistance proteins, zinc uptake transcriptional repressor Zur, MerC domain-containing protein, Cd(II)/Pb(II)-responsive transcriptional regulator, Co/Zn/Cd efflux system protein, and mercuric transporter. Interestingly, we observed that the carbohydrate metabolism pathways were incomplete in all the strains and transporters used for absorption of small sugars were also not found in them. Also, the presence of higher proportion of genes involved in protein metabolism than carbohydrate metabolism indicates that proteinaceous substrates act as the major food substrates for these bacterial strains than carbohydrates. Genomic islands were detected in some species, highlighting the role of horizontal gene transfer for acquisition in novel genes. Genomic rearrangements in terms of partially palindromic regions were detected in all strains. To our knowledge, this is the first comprehensive comparative genomics study among the genus Idiomarina revealing unique genomic features within bacterial species inhabiting different ecological niches.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-023-03887-3.}, }
@article {pmid38259350, year = {2024}, author = {Allman, ES and Baños, H and Garrote-Lopez, M and Rhodes, JA}, title = {IDENTIFIABILITY OF LEVEL-1 SPECIES NETWORKS FROM GENE TREE QUARTETS.}, journal = {ArXiv}, volume = {}, number = {}, pages = {}, pmid = {38259350}, issn = {2331-8422}, support = {P20 GM103395/GM/NIGMS NIH HHS/United States ; }, abstract = {When hybridization or other forms of lateral gene transfer have occurred, evolutionary relationships of species are better represented by phylogenetic networks than by trees. While inference of such networks remains challenging, several recently proposed methods are based on quartet concordance factors - the probabilities that a tree relating a gene sampled from the species displays the possible 4-taxon relationships. Building on earlier results, we investigate what level-1 network features are identifiable from concordance factors under the network multispecies coalescent model. We obtain results on both topological features of the network, and numerical parameters, uncovering a number of failures of identifiability related to 3-cycles in the network.}, }
@article {pmid38257923, year = {2024}, author = {Monecke, S and Braun, SD and Collatz, M and Diezel, C and Müller, E and Reinicke, M and Cabal Rosel, A and Feßler, AT and Hanke, D and Loncaric, I and Schwarz, S and Cortez de Jäckel, S and Ruppitsch, W and Gavier-Widén, D and Hotzel, H and Ehricht, R}, title = {Molecular Characterization of Chimeric Staphylococcus aureus Strains from Waterfowl.}, journal = {Microorganisms}, volume = {12}, number = {1}, pages = {}, pmid = {38257923}, issn = {2076-2607}, support = {13GW0456//Federal Ministry of Education and Research/ ; }, abstract = {Staphylococcus aureus is a versatile pathogen that does not only occur in humans but also in various wild and domestic animals, including several avian species. When characterizing S. aureus isolates from waterfowl, isolates were identified as atypical CC133 by DNA microarray analysis. They differed from previously sequenced CC133 strains in the presence of the collagen adhesin gene cna; some also showed a different capsule type and a deviant spa type. Thus, they were subjected to whole-genome sequencing. This revealed multiple insertions of large regions of DNA from other S. aureus lineages into a CC133-derived backbone genome. Three distinct strains were identified based on the size and extent of these inserts. One strain comprised two small inserts of foreign DNA up- and downstream of oriC; one of about 7000 nt or 0.25% originated from CC692 and the other, at ca. 38,000 nt or 1.3% slightly larger one was of CC522 provenance. The second strain carried a larger CC692 insert (nearly 257,000 nt or 10% of the strain's genome), and its CC522-derived insert was also larger, at about 53,500 nt or 2% of the genome). The third strain carried an identical CC692-derived region (in which the same mutations were observed as in the second strain), but it had a considerably larger CC522-like insertion of about 167,000 nt or 5.9% of the genome. Both isolates of the first, and two out of four isolates of the second strain also harbored a hemolysin-beta-integrating prophage carrying "bird-specific" virulence factors, ornithine cyclodeaminase D0K6J8 and a putative protease D0K6J9. Furthermore, isolates had two different variants of SCC elements that lacked mecA/mecC genes. These findings highlight the role of horizontal gene transfer in the evolution of S. aureus facilitated by SCC elements, by phages, and by a yet undescribed mechanism for large-scale exchange of core genomic DNA.}, }
@article {pmid38253827, year = {2024}, author = {Musiyiwa, K and Simbanegavi, TT and Marumure, J and Makuvara, Z and Chaukura, N and Gwenzi, W}, title = {The soil-microbe-plant resistome: A focus on the source-pathway-receptor continuum.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {9}, pages = {12666-12682}, pmid = {38253827}, issn = {1614-7499}, mesh = {Humans ; *Genes, Bacterial ; *Soil/chemistry ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Anti-Bacterial Agents ; Soil Microbiology ; }, abstract = {The One World, One Health concept implies that antibiotic resistance (AR) in the soil-microbe-plant resistome is intricately linked to the human resistome. However, the literature is mainly confined to sources and types of AR in soils or microbes, but comprehensive reviews tracking AR in the soil-microbe-plant resistome are limited. The present review applies the source-pathway-receptor concept to understand the sources, behaviour, and health hazards of the soil-microbe-plant resistome. The results showed that the soil-microbe-plant system harbours various antibiotic-resistance genes (ARGs), antibiotic-resistant bacteria (ARB), and mobile genetic elements (MGEs). Anthropogenic sources and drivers include soil application of solid waste, wastewater, biosolids, and industrial waste. Water-, wind-, and human-driven processes and horizontal gene transfer circulate AR in the soil-microbe-plant resistome. The AR in bulk soil, soil components that include soil microorganisms, soil meso- and macro-organisms, and possible mechanisms of AR transfer to soil components and ultimately to plants are discussed. The health risks of the soil-microbe-plant resistome are less studied, but potential impacts include (1) the transfer of AR to previously susceptible organisms and other resistomes, including the human resistome. Overall, the study tracks the behaviour and health risks of AR in the soil-plant system. Future research should focus on (1) ecological risks of AR at different levels of biological organization, (2) partitioning of AR among various phases of the soil-plant system, (3) physico-chemical parameters controlling the fate of AR, and (4) increasing research from low-income regions particularly Africa as most of the available literature is from developed countries.}, }
@article {pmid38253607, year = {2024}, author = {Lehmkuhl, J and Schneider, JS and Werth, KLV and Scherff, N and Mellmann, A and Kampmeier, S}, title = {Role of membrane vesicles in the transmission of vancomycin resistance in Enterococcus faecium.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {1895}, pmid = {38253607}, issn = {2045-2322}, mesh = {*Enterococcus faecium/genetics ; Vancomycin Resistance/genetics ; Vancomycin/pharmacology ; *Vancomycin-Resistant Enterococci/genetics ; Membranes ; }, abstract = {Clonal transmission and horizontal gene transfer (HGT) contribute to the spread of vancomycin-resistant enterococci (VRE) in global healthcare. Our study investigated vesiduction, a HGT mechanism via membrane vesicles (MVs), for vanA and vanB genes that determine vancomycin resistance. We isolated MVs for VRE of different sequence types (STs) and analysed them by nanoparticle tracking analysis. Selected MV samples were subjected to DNA sequence analysis. In resistance transfer experiments, vancomycin-susceptible enterococci were exposed to MVs and bacterial supernatants of VRE. Compared to bacteria grown in lysogeny broth (MVs/LB), cultivation under vancomycin stress (MVs/VAN) resulted in increased particle concentrations of up to 139-fold (ST80). As a key finding, we could show that VRE isolates of ST80 and ST117 produced remarkably more vesicles at subinhibitory antibiotic concentrations (approx. 9.2 × 10[11] particles/ml for ST80 and 2.4 × 10[11] particles/ml for ST117) than enterococci of other STs (range between 1.8 × 10[10] and 5.3 × 10[10] particles/ml). In those MV samples, the respective resistance genes vanA and vanB were completely verifiable using sequence analysis. Nevertheless, no vancomycin resistance transfer via MVs to vancomycin-susceptible Enterococcus faecium was phenotypically detectable. However, our results outline the potential of future research on ST-specific MV properties, promising new insights into VRE mechanisms.}, }
@article {pmid38251876, year = {2024}, author = {Wang, Y and Unnikrishnan, M and Ramsey, B and El Andlosy, D and Keeley, AT and Murphy, CJ and Gruebele, M}, title = {In-Cell Association of a Bioorthogonal Tubulin.}, journal = {Biomacromolecules}, volume = {25}, number = {2}, pages = {1282-1290}, doi = {10.1021/acs.biomac.3c01253}, pmid = {38251876}, issn = {1526-4602}, mesh = {Humans ; *Tubulin/chemistry ; *Bacterial Proteins/chemistry ; Microtubules/chemistry ; }, abstract = {Studies of proteins from one organism in another organism's cells have shown that such exogenous proteins stick more, pointing toward coevolution of the cytoplasm and protein surface to minimize stickiness. Here we flip this question around by asking whether exogenous proteins can assemble efficiently into their target complexes in a non-native cytoplasm. We use as our model system the assembly of BtubA and BtubB from Prosthecobacter hosted in human U-2 OS cells. BtubA and B evolved from eukaryotic tubulins after horizontal gene transfer, but they have low surface sequence identity with the homologous human tubulins and do not respond to tubulin drugs such as nocodazole. In U-2 OS cells, BtubA and B assemble efficiently into dimers compared to in vitro, and the wild-type BtubA and B proteins subsequently are able to form microtubules as well. We find that generic crowding effects (Ficoll 70 in vitro) contribute significantly to efficient dimer assembly when compared to sticking interactions (U-2 OS cell lysate in vitro), consistent with the notion that a generic mechanism such as crowding can be effective at driving assembly of exogenous proteins, even when protein-cytoplasm quinary structure and sticking have been modified in a non-native cytoplasm. A simple Monte Carlo model of in vitro and in-cell interactions, treating BtubA and B as sticky dipoles in a matrix of sticky or nonsticky crowders, rationalizes all the experimental trends with two adjustable parameters and reveals nucleation as the likely mechanism for the time-scale separation between dimer- and tubule formation in-cell and in vitro.}, }
@article {pmid38251331, year = {2023}, author = {Vasconcelos, PC and Leite, EL and Saraiva, MMS and Ferrari, RG and Cibulski, SP and Silva, NMV and Freitas Neto, OC and Givisiez, PEN and Vieira, RFC and Oliveira, CJB}, title = {Genomic Analysis of a Community-Acquired Methicillin-Resistant Staphylococcus aureus Sequence Type 1 Associated with Caprine Mastitis.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {1}, pages = {}, pmid = {38251331}, issn = {2076-0817}, support = {Finance code 001//Coordena&#xe7;&#xe3;o de Aperfeicoamento de Pessoal de N&#xed;vel Superior/ ; CT-INFRA//Financiadora de Estudos e Projetos/ ; 313678/2020-0//Conselho Nacional de Pesquisa e P&#xf3;s-gradua&#xe7;&#xe3;o em Direito/ ; }, mesh = {*Methicillin-Resistant Staphylococcus aureus/genetics/drug effects/isolation &amp; purification ; Animals ; *Goats/microbiology ; *Mastitis/microbiology/epidemiology ; *Staphylococcal Infections/microbiology/epidemiology ; Female ; *Goat Diseases/microbiology/epidemiology/transmission ; *Phylogeny ; *Community-Acquired Infections/microbiology/epidemiology ; Brazil/epidemiology ; Anti-Bacterial Agents/pharmacology ; Virulence Factors/genetics ; Genome, Bacterial/genetics ; Milk/microbiology ; Whole Genome Sequencing ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Genomics ; Polymorphism, Single Nucleotide/genetics ; }, abstract = {This study aimed to investigate the genomic and epidemiological features of a methicillin-resistant Staphylococcus aureus sequence type 1 (MRSA ST1) strain associated with caprine subclinical mastitis. An S. aureus strain was isolated from goat's milk with subclinical mastitis in Paraiba, Northeastern Brazil, by means of aseptic procedures and tested for antimicrobial susceptibility using the disk-diffusion method. Whole genome sequencing was performed using the Illumina MiSeq platform. After genome assembly and annotation, in silico analyses, including multilocus sequence typing (MLST), antimicrobial resistance and stress-response genes, virulence factors, and plasmids detection were performed. A comparative SNP-based phylogenetic analysis was performed using publicly available MRSA genomes. The strain showed phenotypic resistance to cefoxitin, penicillin, and tetracycline and was identified as sequence type 1 (ST1) and spa type 128 (t128). It harbored the SCCmec type IVa (2B), as well as the lukF-PV and lukS-PV genes. The strain was phylogenetically related to six community-acquired MRSA isolates (CA-MRSA) strains associated with human clinical disease in North America, Europe, and Australia. This is the first report of a CA-MRSA strain associated with milk in the Americas. The structural and epidemiologic features reported in the MRSA ST1 carrying a mecA-SCCmec type IVa suggest highly complex mechanisms of horizontal gene transfer in MRSA. The SNP-based phylogenetic analysis suggests a zooanthroponotic transmission, i.e., a strain of human origin.}, }
@article {pmid38240570, year = {2024}, author = {Kogay, R and Zhaxybayeva, O}, title = {Co-evolution of gene transfer agents and their alphaproteobacterial hosts.}, journal = {Journal of bacteriology}, volume = {206}, number = {2}, pages = {e0039823}, pmid = {38240570}, issn = {1098-5530}, mesh = {Humans ; *Bacteria/genetics ; Archaea/genetics ; DNA ; *Alphaproteobacteria/genetics ; Gene Transfer, Horizontal ; }, abstract = {Gene transfer agents (GTAs) are enigmatic elements that resemble small viruses and are known to be produced during nutritional stress by some bacteria and archaea. The production of GTAs is regulated by quorum sensing, under which a small fraction of the population acts as GTA producers, while the rest becomes GTA recipients. In contrast to canonical viruses, GTAs cannot propagate themselves because they package pieces of the producing cell's genome. In alphaproteobacteria, GTAs are mostly vertically inherited and reside in their hosts' genomes for hundreds of millions of years. While GTAs' ability to transfer genetic material within a population and their long-term preservation suggest an increased fitness of GTA-producing microbes, the associated benefits and type of selection that maintains GTAs are poorly understood. By comparing rates of evolutionary change in GTA genes to the rates in gene families abundantly present across 293 alphaproteobacterial genomes, we detected 59 gene families that likely co-evolve with GTA genes. These gene families are predominantly involved in stress response, DNA repair, and biofilm formation. We hypothesize that biofilm formation enables the physical proximity of GTA-producing cells, limiting GTA-derived benefits only to a group of closely related cells. We further conjecture that the population structure of biofilm-forming sub-populations ensures that the trait of GTA production is maintained despite the inevitable rise of "cheating" genotypes. Because release of GTA particles kills the producing cell, maintenance of GTAs is an exciting example of social evolution in a microbial population.IMPORTANCEGene transfer agents (GTAs) are viruses domesticated by some archaea and bacteria as vehicles for carrying pieces of the host genome. Produced under certain environmental conditions, GTA particles can deliver DNA to neighboring, closely related cells. The function of GTAs remains uncertain. While making GTAs is suicidal for a cell, GTA-encoding genes are widespread in genomes of alphaproteobacteria. Such GTA persistence implies functional benefits but raises questions about how selection maintains this lethal trait. By showing that GTA genes co-evolve with genes involved in stress response, DNA repair, and biofilm formation, we provide support for the hypothesis that GTAs facilitate DNA exchange during the stress conditions and present a model for how GTAs persist in biofilm-forming bacterial populations despite being lethal.}, }
@article {pmid38238664, year = {2024}, author = {Peng, M and Lin, W and Zhou, A and Jiang, Z and Zhou, F and Wang, Z}, title = {High genetic diversity and different type VI secretion systems in Enterobacter species revealed by comparative genomics analysis.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {26}, pmid = {38238664}, issn = {1471-2180}, support = {32200094//National Natural Science Foundation of China/ ; PT012201//Hubei Key Laboratory of Biological Resources Protection and Utilization (Hubei Minzu University)/ ; 2022CFB674//Natural Science Foundation of Hubei Province/ ; }, mesh = {Humans ; *Type VI Secretion Systems/genetics ; Enterobacter/genetics ; Bacterial Proteins/genetics ; Genomics ; Virulence Factors/genetics ; Genetic Variation ; }, abstract = {The human-pathogenic Enterobacter species are widely distributed in diverse environmental conditions, however, the understanding of the virulence factors and genetic variations within the genus is very limited. In this study, we performed comparative genomics analysis of 49 strains originated from diverse niches and belonged to eight Enterobacter species, in order to further understand the mechanism of adaption to the environment in Enterobacter. The results showed that they had an open pan-genome and high genomic diversity which allowed adaptation to distinctive ecological niches. We found the number of secretion systems was the highest among various virulence factors in these Enterobacter strains. Three types of T6SS gene clusters including T6SS-A, T6SS-B and T6SS-C were detected in most Enterobacter strains. T6SS-A and T6SS-B shared 13 specific core genes, but they had different gene structures, suggesting they probably have different biological functions. Notably, T6SS-C was restricted to E. cancerogenus. We detected a T6SS gene cluster, highly similar to T6SS-C (91.2%), in the remote related Citrobacter rodenitum, suggesting that this unique gene cluster was probably acquired by horizontal gene transfer. The genomes of Enterobacter strains possess high genetic diversity, limited number of conserved core genes, and multiple copies of T6SS gene clusters with differentiated structures, suggesting that the origins of T6SS were not by duplication instead by independent acquisition. These findings provide valuable information for better understanding of the functional features of Enterobacter species and their evolutionary relationships.}, }
@article {pmid38237429, year = {2024}, author = {Bernabeu, M and Cabello-Yeves, E and Flores, E and Samarra, A and Kimberley Summers, J and Marina, A and Collado, MC}, title = {Role of vertical and horizontal microbial transmission of antimicrobial resistance genes in early life: insights from maternal-infant dyads.}, journal = {Current opinion in microbiology}, volume = {77}, number = {}, pages = {102424}, doi = {10.1016/j.mib.2023.102424}, pmid = {38237429}, issn = {1879-0364}, mesh = {Infant ; Humans ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; *Gastrointestinal Microbiome/genetics ; *Microbiota/genetics ; Gene Transfer, Horizontal ; }, abstract = {Early life represents a critical window for metabolic, cognitive and immune system development, which is influenced by the maternal microbiome as well as the infant gut microbiome. Antibiotic exposure, mode of delivery and breastfeeding practices modulate the gut microbiome and the reservoir of antibiotic resistance genes (ARGs). Vertical and horizontal microbial gene transfer during early life and the mechanisms behind these transfers are being uncovered. In this review, we aim to provide an overview of the current knowledge on the transfer of antibiotic resistance in the mother-infant dyad through vertical and horizontal transmission and to highlight the main gaps and challenges in this area.}, }
@article {pmid38237397, year = {2024}, author = {Yu, Z and Wang, Q and Pinilla-Redondo, R and Madsen, JS and Clasen, KAD and Ananbeh, H and Olesen, AK and Gong, Z and Yang, N and Dechesne, A and Smets, B and Nesme, J and Sørensen, SJ}, title = {Horizontal transmission of a multidrug-resistant IncN plasmid isolated from urban wastewater.}, journal = {Ecotoxicology and environmental safety}, volume = {271}, number = {}, pages = {115971}, doi = {10.1016/j.ecoenv.2024.115971}, pmid = {38237397}, issn = {1090-2414}, mesh = {*Wastewater ; *Anti-Bacterial Agents/analysis ; Plasmids/genetics ; Drug Resistance, Microbial/genetics ; Water ; Genes, Bacterial ; }, abstract = {Wastewater treatment plants (WWTPs) are considered reservoirs of antibiotic resistance genes (ARGs). Given that plasmid-mediated horizontal gene transfer plays a critical role in disseminating ARGs in the environment, it is important to inspect the transfer potential of transmissible plasmids to have a better understanding of whether these mobile ARGs can be hosted by opportunistic pathogens and should be included in One Health's considerations. In this study, we used a fluorescent-reporter-gene based exogenous isolation approach to capture extended-spectrum beta-lactamases encoding mobile determinants from sewer microbiome samples that enter an urban water system (UWS) in Denmark. After screening and sequencing, we isolated a ∼73 Kbp IncN plasmid (pDK_DARWIN) that harboured and expressed multiple ARGs. Using a dual fluorescent reporter gene system, we showed that this plasmid can transfer into resident urban water communities. We demonstrated the transfer of pDK_DARWIN to microbiome members of both the sewer (in the upstream UWS compartment) and wastewater treatment (in the downstream UWS compartment) microbiomes. Sequence similarity search across curated plasmid repositories revealed that pDK_DARWIN derives from an IncN backbone harboured by environmental and nosocomial Enterobacterial isolates. Furthermore, we searched for pDK_DARWIN sequence matches in UWS metagenomes from three countries, revealing that this plasmid can be detected in all of them, with a higher relative abundance in hospital sewers compared to residential sewers. Overall, this study demonstrates that this IncN plasmid is prevalent across Europe and an efficient vector capable of disseminating multiple ARGs in the urban water systems.}, }
@article {pmid38234769, year = {2024}, author = {Coelho, MA and David-Palma, M and Shea, T and Bowers, K and McGinley-Smith, S and Mohammad, AW and Gnirke, A and Yurkov, AM and Nowrousian, M and Sun, S and Cuomo, CA and Heitman, J}, title = {Comparative genomics of Cryptococcus and Kwoniella reveals pathogenesis evolution and contrasting karyotype dynamics via intercentromeric recombination or chromosome fusion.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38234769}, issn = {2692-8205}, support = {R37 AI039115/AI/NIAID NIH HHS/United States ; U54 HG003067/HG/NHGRI NIH HHS/United States ; R01 AI039115/AI/NIAID NIH HHS/United States ; R01 AI050113/AI/NIAID NIH HHS/United States ; U19 AI110818/AI/NIAID NIH HHS/United States ; }, abstract = {A large-scale comparative genomic analysis was conducted for the global human fungal pathogens within the Cryptococcus genus, compared to non-pathogenic Cryptococcus species, and related species from the sister genus Kwoniella. Chromosome-level genome assemblies were generated for multiple species of both genera, resulting in a dataset encompassing virtually all of their known diversity. Although Cryptococcus and Kwoniella have comparable genome sizes (about 19.2 and 22.9 Mb) and similar gene content, hinting at pre-adaptive pathogenic potential, our analysis found evidence in pathogenic Cryptococcus species of specific examples of gene gain (via horizontal gene transfer) and gene loss, which might represent evolutionary signatures of pathogenic development. Genome analysis also revealed a significant variation in chromosome number and structure between the two genera. By combining synteny analysis and experimental centromere validation, we found that most Cryptococcus species have 14 chromosomes, whereas most Kwoniella species have fewer (11, 8, 5 or even as few as 3). Reduced chromosome number in Kwoniella is associated with formation of giant chromosomes (up to 18 Mb) through repeated chromosome fusion events, each marked by a pericentric inversion and centromere loss. While similar chromosome inversion-fusion patterns were observed in all Kwoniella species with fewer than 14 chromosomes, no such pattern was detected in Cryptococcus. Instead, Cryptococcus species with less than 14 chromosomes, underwent chromosome reductions primarily through rearrangements associated with the loss of repeat-rich centromeres. Additionally, Cryptococcus genomes exhibited frequent interchromosomal translocations, including intercentromeric recombination facilitated by transposons shared between centromeres. Taken together, our findings advance our understanding of genomic changes possibly associated with pathogenicity in Cryptococcus and provide a foundation to elucidate mechanisms of centromere loss and chromosome fusion driving distinct karyotypes in closely related fungal species, including prominent global human pathogens.}, }
@article {pmid38229742, year = {2024}, author = {Ward, KT and Williams, APL and Blair, CA and Chatterjee, AM and Karthikeyan, A and Roper, AS and Kellogg, CN and Steed, PR and Wolfe, AL}, title = {Amine Basicity of Quinoline ATP Synthase Inhibitors Drives Antibacterial Activity against Pseudomonas aeruginosa.}, journal = {ACS medicinal chemistry letters}, volume = {15}, number = {1}, pages = {149-155}, pmid = {38229742}, issn = {1948-5875}, support = {R15 AI163474/AI/NIAID NIH HHS/United States ; }, abstract = {Pseudomonas aeruginosa (PA), a Gram-negative pathogen, is a common cause of nosocomial infections, especially in immunocompromised and cystic fibrosis patients. PA is intrinsically resistant to many currently prescribed antibiotics due to its tightly packed, anionic lipopolysaccharide outer membrane, efflux pumps, and ability to form biofilms. PA can acquire additional resistance through mutation and horizontal gene transfer. PA ATP synthase is an attractive target for antibiotic development because it is essential for cell survival even under fermentation conditions. Previously, we developed two lead quinoline compounds that were capable of selectively inhibiting PA ATP synthase and acting as antibacterial agents against multidrug-resistant PA. Herein we conduct a structure-activity relationship analysis of the lead compounds through the synthesis and evaluation of 18 quinoline derivatives. These compounds function as new antibacterial agents while providing insight into the balance of physical properties needed to promote cellular entry while maintaining PA ATP synthase inhibition.}, }
@article {pmid38226780, year = {2024}, author = {Tokuda, M and Shintani, M}, title = {Microbial evolution through horizontal gene transfer by mobile genetic elements.}, journal = {Microbial biotechnology}, volume = {17}, number = {1}, pages = {e14408}, pmid = {38226780}, issn = {1751-7915}, support = {JP19H02869//Japan Society for the Promotion of Science/ ; JP19H05686//Japan Society for the Promotion of Science/ ; JP22J12723//Japan Society for the Promotion of Science/ ; JP23H02124//Japan Society for the Promotion of Science/ ; L-2023-1-002//Institute for Fermentation, Osaka/ ; //National University Corporation Shizuoka University, Japan/ ; 2023-RIGST-23104//Institute of Green Science and Technology Fund for Research Project Support/ ; //Ohsumi Frontier Science Foundation/ ; JP21wm0225008//Japan Agency for Medical Research and Development/ ; JP21wm0325022//Japan Agency for Medical Research and Development/ ; }, mesh = {*Interspersed Repetitive Sequences ; Gene Transfer, Horizontal ; Plasmids/genetics ; Bacteria/genetics ; *Bacteriophages/genetics ; Anti-Bacterial Agents ; }, abstract = {Mobile genetic elements (MGEs) are crucial for horizontal gene transfer (HGT) in bacteria and facilitate their rapid evolution and adaptation. MGEs include plasmids, integrative and conjugative elements, transposons, insertion sequences and bacteriophages. Notably, the spread of antimicrobial resistance genes (ARGs), which poses a serious threat to public health, is primarily attributable to HGT through MGEs. This mini-review aims to provide an overview of the mechanisms by which MGEs mediate HGT in microbes. Specifically, the behaviour of conjugative plasmids in different environments and conditions was discussed, and recent methodologies for tracing the dynamics of MGEs were summarised. A comprehensive understanding of the mechanisms underlying HGT and the role of MGEs in bacterial evolution and adaptation is important to develop strategies to combat the spread of ARGs.}, }
@article {pmid38220083, year = {2024}, author = {Ormsby, MJ and Woodford, L and Quilliam, RS}, title = {Can plastic pollution drive the emergence and dissemination of novel zoonotic diseases?.}, journal = {Environmental research}, volume = {246}, number = {}, pages = {118172}, doi = {10.1016/j.envres.2024.118172}, pmid = {38220083}, issn = {1096-0953}, mesh = {Animals ; Humans ; *Plastics ; *Environmental Pollution ; Zoonoses/epidemiology ; Agriculture ; Biofilms ; }, abstract = {As the volume of plastic in the environment increases, so too does human interactions with plastic pollution. Similarly, domestic, feral, and wild animals are increasingly interacting with plastic pollution, highlighting the potential for contamination of plastic wastes with animal faeces, urine, saliva, and blood. Substantial evidence indicates that once in the environment, plastics rapidly become colonised by microbial biofilm (the so-called 'plastisphere), which often includes potentially harmful microbial pathogens (including pathogens that are zoonotic in nature). Climate change, increased urbanisation, and the intensification of agriculture, mean that the three-way interactions between humans, animals, and plastic pollution are becoming more frequent, which is significant as almost 60% of emerging human infectious diseases during the last century have been zoonotic. Here, we critically review the potential for contaminated environmental plastics to facilitate the evolution of novel pathogenic strains of microorganisms, and the subsequent role of plastic pollution in the cyclical dissemination of zoonotic pathogens. As the interactions between humans, animals, and plastic pollution continues to grow, and the volume of plastics entering the environment increases, there is clearly an urgent need to better understand the role of plastic waste in facilitating zoonotic pathogen evolution and dissemination, and the effect this can have on environmental and human health.}, }
@article {pmid38220012, year = {2024}, author = {Fang, Q and Pan, X}, title = {A systematic review of antibiotic resistance driven by metal-based nanoparticles: Mechanisms and a call for risk mitigation.}, journal = {The Science of the total environment}, volume = {916}, number = {}, pages = {170080}, doi = {10.1016/j.scitotenv.2024.170080}, pmid = {38220012}, issn = {1879-1026}, mesh = {*Metal Nanoparticles ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Risk Assessment ; Gene Transfer, Horizontal ; }, abstract = {Elevations in antibiotic resistance genes (ARGs) are due not only to the antibiotic burden, but also to numerous environmental pressures (e.g., pesticides, metal ions, or psychotropic pharmaceuticals), which have led to an international public health emergency. Metal-based nanoparticles (MNPs) poison bacteria while propelling nanoresistance at ambient or sub-lethal concentrations, acting as a wide spectrum germicidal agent. Awareness of MNPs driven antibiotic resistance has created a surge of investigation into the molecule mechanisms of evolving and spreading environmental antibiotic resistome. Co-occurrence of MNPs resistance and antibiotic resistance emerge in environmental pathogens and benign microbes may entail a crucial outcome for human health. In this review we expound on the systematic mechanism of ARGs proliferation under the stress of MNPs, including reactive oxygen species (ROS) induced mutation, horizontal gene transfer (HGT) relevant genes regulation, nano-property, quorum sensing, and biofilm formation and highlighting on the momentous contribution of nanoparticle released ion. As antibiotic resistance pattern alteration is closely knit with the mediate activation of nanoparticle in water, soil, manure, or sludge habitats, we have proposed a virulence and evolution based antibiotic resistance risk assessment strategy for MNP contaminated areas and discussed practicable approaches that call for risk management in critical environmental compartments.}, }
@article {pmid38218181, year = {2024}, author = {Peterson, A and Baskett, C and Ratcliff, WC and Burnetti, A}, title = {Transforming yeast into a facultative photoheterotroph via expression of vacuolar rhodopsin.}, journal = {Current biology : CB}, volume = {34}, number = {3}, pages = {648-654.e3}, doi = {10.1016/j.cub.2023.12.044}, pmid = {38218181}, issn = {1879-0445}, mesh = {*Saccharomyces cerevisiae/metabolism ; *Rhodopsin/metabolism ; Phylogeny ; Vacuoles/metabolism ; Chlorophyll ; }, abstract = {Phototrophic metabolism, the capture of light for energy, was a pivotal biological innovation that greatly increased the total energy available to the biosphere. Chlorophyll-based photosynthesis is the most familiar phototrophic metabolism, but retinal-based microbial rhodopsins transduce nearly as much light energy as chlorophyll does,[1] via a simpler mechanism, and are found in far more taxonomic groups. Although this system has apparently spread widely via horizontal gene transfer,[2][,][3][,][4] little is known about how rhodopsin genes (with phylogenetic origins within prokaryotes[5][,][6]) are horizontally acquired by eukaryotic cells with complex internal membrane architectures or the conditions under which they provide a fitness advantage. To address this knowledge gap, we sought to determine whether Saccharomyces cerevisiae, a heterotrophic yeast with no known evolutionary history of phototrophy, can function as a facultative photoheterotroph after acquiring a single rhodopsin gene. We inserted a rhodopsin gene from Ustilago maydis,[7] which encodes a proton pump localized to the vacuole, an organelle normally acidified via a V-type rotary ATPase, allowing the rhodopsin to supplement heterotrophic metabolism. Probes of the physiology of modified cells show that they can deacidify the cytoplasm using light energy, demonstrating the ability of rhodopsins to ameliorate the effects of starvation and quiescence. Further, we show that yeast-bearing rhodopsins gain a selective advantage when illuminated, proliferating more rapidly than their non-phototrophic ancestor or rhodopsin-bearing yeast cultured in the dark. These results underscore the ease with which rhodopsins may be horizontally transferred even in eukaryotes, providing novel biological function without first requiring evolutionary optimization.}, }
@article {pmid38217904, year = {2024}, author = {Lin, D and Xu, JY and Wang, L and Du, S and Zhu, D}, title = {Long-term application of organic fertilizer prompting the dispersal of antibiotic resistance genes and their health risks in the soil plastisphere.}, journal = {Environment international}, volume = {183}, number = {}, pages = {108431}, doi = {10.1016/j.envint.2024.108431}, pmid = {38217904}, issn = {1873-6750}, mesh = {Humans ; *Soil ; *Anti-Bacterial Agents/pharmacology ; Fertilizers/analysis ; Genes, Bacterial ; Plastics ; Manure/microbiology ; Soil Microbiology ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; }, abstract = {Microplastic (MP) pollution is a rapidly growing global environmental concern that has led to the emergence of a new environmental compartment, the plastisphere, which is a hotspot for the accumulation of antibiotic resistance genes (ARGs) and human bacterial pathogens (HBPs). However, studies on the effects of long-term organic fertilizer application on the dispersal of ARGs and virulence factor genes (VFGs) in the plastisphere of farmland soil have been limited. Here, we performed a field culture experiment by burying nylon bags filled with MPs in paddy soil that had been treated with different fertilizers for over 30 years to explore the changes of ARGs and VFGs in soil plastisphere. Our results show that the soil plastisphere amplified the ARG and VFG pollution caused by organic fertilization by 1.5 and 1.4 times, respectively. And it also led to a 2.7-fold increase in the risk of horizontal gene transfer. Meanwhile, the plastisphere tended to promote deterministic process in the community assembly of HBPs, with an increase of 1.4 times. Network analysis found a significant correlation between ARGs, VFGs, and bacteria in plastisphere. Correlation analysis highlight the important role of mobile genetic elements (MGEs) and bacterial communities in shaping the abundance of ARGs and VFGs, respectively. Our findings provide new insights into the health risk associated with the soil plastisphere due ARGs and VFGs derived from organic fertilizers.}, }
@article {pmid38216797, year = {2024}, author = {Iqbal, S and Begum, F}, title = {Identification and characterization of integrated prophages and CRISPR-Cas system in Bacillus subtilis RS10 genome.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {55}, number = {1}, pages = {537-542}, pmid = {38216797}, issn = {1678-4405}, mesh = {Prophages/genetics ; Bacillus subtilis/genetics ; CRISPR-Cas Systems ; *Bacteriophages/genetics ; *Bacillus ; }, abstract = {Bacteriophages have been extensively investigated due to their prominent role in the virulence and resistance of pathogenic bacteria. However, little attention has been given to the non-pathogenic Bacillus phages, and their role in the ecological bacteria genome is overlooked. In the present study, we characterized two Bacillus phages with a linear DNA genome of 33.6 kb with 44.83% GC contents and 129.3 kb with 34.70% GC contents. A total of 46 and 175 putative coding DNA sequences (CDS) were identified in prophage 1 (P1) and prophage 2 (P2), respectively, with no tRNA genes. Comparative genome sequence analysis revealed that P1 shares eight CDS with phage Jimmer 2 (NC-041976), and phage Osiris (NC-028969), and six with phage phi CT9441A (NC-029022). On the other hand, P2 showed high similarity with Bacill_SPbeta_NC_001884 and Bacillus phage phi 105. Further, genome analysis indicates several horizontal gene transfer events in both phages during the evolution process. In addition, we detected two CRISPR-Cas systems for the first time in B. subtilis. The identified CRISPR system consists of 24 and 25 direct repeats and integrase coding genes, while the cas gene which encodes Cas protein involved in the cleavage of a target sequence is missing. These findings will expand the current knowledge of soil phages as well as help to develop a new perspective for investigating more ecological phages to understand their role in bacterial communities and diversity.}, }
@article {pmid38215844, year = {2024}, author = {Zhuang, X and Fan, H and Li, X and Dong, Y and Wang, S and Zhao, B and Wu, S}, title = {Transfer and accumulation of antibiotic resistance genes and bacterial pathogens in the mice gut due to consumption of organic foods.}, journal = {The Science of the total environment}, volume = {915}, number = {}, pages = {169842}, doi = {10.1016/j.scitotenv.2023.169842}, pmid = {38215844}, issn = {1879-1026}, mesh = {Animals ; Mice ; *Food, Organic ; *Genes, Bacterial ; RNA, Ribosomal, 16S ; Angiotensin Receptor Antagonists/pharmacology ; Angiotensin-Converting Enzyme Inhibitors/pharmacology ; Bacteria/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Integrases/genetics/pharmacology ; }, abstract = {Over the last few decades, organic food demand has grown largely because of increasing personal health concerns. Organic farming introduces antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) into foods. However, potential effects of organic foods on the gut microbiome and ARGs have been overlooked. Using high-throughput quantitative PCR and 16S rRNA high-throughput sequencing technology, we examined 132 ARGs from major classes, eight transposase genes, universal class I integron-integrase gene (intI), clinical class I integron-integrase gene (cintI), and the bacterial community in mouse gut after 8 weeks with an either organic or inorganic lettuce and wheat diet. A total of 8 types of major ARGs and 10 mobile genetic elements (MGEs) were detected in mice gut, including tetracycline, multidrug, sulfonamide, aminoglycoside, beta-lactamase, chloramphenicol, MLSB and vancomycin resistance genes. We found that abundance and diversity of ARGs, mobile gene elements, and potential ARB in the gut increased with time after consumption of organic foods, whereas no significant changes were observed in inorganic treated groups. Moreover, MGEs, including IS613, Tp614 and tnpA_03 were found to play an important role in regulating ARG profiles in the gut microbiome following consumption of organic foods. Importantly, feeding organic food increased the relative abundance of the potentially antibiotic-resistant pathogens, Bacteroides and Streptococcus. Our results confirm that there is an increasing risk of ARGs and ARB in the gut microbiome, which highlights the importance of organic food industries taking into account the potential accumulation and transmission of ARGs as a risk factor.}, }
@article {pmid38214578, year = {2024}, author = {Christinaki, AC and Myridakis, AI and Kouvelis, VN}, title = {Genomic insights into the evolution and adaptation of secondary metabolite gene clusters in fungicolous species Cladobotryum mycophilum ATHUM6906.}, journal = {G3 (Bethesda, Md.)}, volume = {14}, number = {4}, pages = {}, pmid = {38214578}, issn = {2160-1836}, support = {19620//Hellenic Foundation for Research and Innovation/ ; }, mesh = {*Genome, Fungal ; *Hypocreales/genetics ; Genomics ; Multigene Family ; }, abstract = {Mycophilic or fungicolous fungi can be found wherever fungi exist since they are able to colonize other fungi, which occupy a diverse range of habitats. Some fungicolous species cause important diseases on Basidiomycetes, and thus, they are the main reason for the destruction of mushroom cultivations. Nonetheless, despite their ecological significance, their genomic data remain limited. Cladobotryum mycophilum is one of the most aggressive species of the genus, destroying the economically important Agaricus bisporus cultivations. The 40.7 Mb whole genome of the Greek isolate ATHUM6906 is assembled in 16 fragments, including the mitochondrial genome and 2 small circular mitochondrial plasmids, in this study. This genome includes a comprehensive set of 12,282 protein coding, 56 rRNA, and 273 tRNA genes. Transposable elements, CAZymes, and pathogenicity related genes were also examined. The genome of C. mycophilum contained a diverse arsenal of genes involved in secondary metabolism, forming 106 biosynthetic gene clusters, which renders this genome as one of the most BGC abundant among fungicolous species. Comparative analyses were performed for genomes of species of the family Hypocreaceae. Some BGCs identified in C. mycophilum genome exhibited similarities to clusters found in the family Hypocreaceae, suggesting vertical heritage. In contrast, certain BGCs showed a scattered distribution among Hypocreaceae species or were solely found in Cladobotryum genomes. This work provides evidence of extensive BGC losses, horizontal gene transfer events, and formation of novel BGCs during evolution, potentially driven by neutral or even positive selection pressures. These events may increase Cladobotryum fitness under various environmental conditions and potentially during host-fungus interaction.}, }
@article {pmid38214507, year = {2024}, author = {Charubin, K and Hill, JD and Papoutsakis, ET}, title = {DNA transfer between two different species mediated by heterologous cell fusion in Clostridium coculture.}, journal = {mBio}, volume = {15}, number = {2}, pages = {e0313323}, pmid = {38214507}, issn = {2150-7511}, support = {P20 GM103446/GM/NIGMS NIH HHS/United States ; S10 OD016361/OD/NIH HHS/United States ; }, mesh = {*Clostridium acetobutylicum/genetics/metabolism ; Coculture Techniques ; Cell Fusion ; Clostridium/genetics ; DNA/metabolism ; RNA/metabolism ; }, abstract = {Prokaryotic evolution is driven by random mutations and horizontal gene transfer (HGT). HGT occurs via transformation, transduction, or conjugation. We have previously shown that in syntrophic cocultures of Clostridium acetobutylicum and Clostridium ljungdahlii, heterologous cell fusion leads to a large-scale exchange of proteins and RNA between the two organisms. Here, we present evidence that heterologous cell fusion facilitates the exchange of DNA between the two organisms. Using selective subculturing, we isolated C. acetobutylicum cells which acquired and integrated into their genome portions of plasmid DNA from a plasmid-carrying C. ljungdahlii strain. Limiting-dilution plating and DNA methylation data based on PacBio Single-Molecule Real Time (SMRT) sequencing support the existence of hybrid C. acetobutylicum/C. ljungdahlii cells. These findings expand our understanding of multi-species microbiomes, their survival strategies, and evolution.IMPORTANCEInvestigations of natural multispecies microbiomes and synthetic microbial cocultures are attracting renewed interest for their potential application in biotechnology, ecology, and medical fields. Previously, we have shown the syntrophic coculture of C. acetobutylicum and C. ljungdahlii undergoes heterologous cell-to-cell fusion, which facilitates the exchange of cytoplasmic protein and RNA between the two organisms. We now show that heterologous cell fusion between the two Clostridium organisms can facilitate the exchange of DNA. By applying selective pressures to this coculture system, we isolated clones of wild-type C. acetobutylicum which acquired the erythromycin resistance (erm) gene from the C. ljungdahlii strain carrying a plasmid with the erm gene. Single-molecule real-time sequencing revealed that the erm gene was integrated into the genome in a mosaic fashion. Our data also support the persistence of hybrid C. acetobutylicum/C. ljungdahlii cells displaying hybrid DNA-methylation patterns.}, }
@article {pmid38206425, year = {2024}, author = {Tartik, M}, title = {The priority of yeast to select among various DNA options to repair genome breaks by homologous recombination.}, journal = {Molecular biology reports}, volume = {51}, number = {1}, pages = {99}, pmid = {38206425}, issn = {1573-4978}, support = {BAP FEF.2019.00.0//Bing&#xf6;l &#xdc;niversitesi/ ; }, mesh = {Animals ; *Saccharomyces cerevisiae/genetics ; DNA ; Homologous Recombination/genetics ; *Fractures, Bone ; Gene Regulatory Networks ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT) is considered an important mechanism to contribute to the evolution of bacteria, plants, and animals by allowing the movement of genetic material between organisms, in difference to vertical inheritance. Thereby it can also play a significant role in spreading traits like antibiotic resistance among bacteria and virulence factors between pathogens. During the HGT, organisms take up free DNA from the environment and incorporate it into their genomes. Although HGT is known to be carried out by many organisms, there is limited information on how organisms select which genetic material for horizontal transfer. Here we have investigated the preference priority of Saccharomyces cerevisiae between different options of gene source presented under certain stress conditions to repair a double-strand break (DSB) in DNA via HR.<br><br>RESULTS: Each genetic module was designed with appropriate sequences being homologous for two sides of the DSB, which is important for yeast to repair the fracture with HR. S. cerevisiae made a random selection between two heterologous T1 (44%) and T2 (56%) modules to repair DSB. Interestingly, yeast corrected the DNA break only with the T3 module (almost 100%) when the homologous T3 module was an option for the selection. It seems that S. cerevisiae tends to prefer T3 over alternatives to fix DSBs when it exists among the options.<br><br>CONCLUSIONS: It seems that S. cerevisiae have a preference for priority to select a particular one under certain conditions when it has various DNA options to repair a DSB in its genome, further studies are required to support our findings.}, }
@article {pmid38193726, year = {2024}, author = {Li, H and Cai, L and Wang, L and Wang, Y and Xu, J and Zhang, R}, title = {The structure and assembly mechanisms of T4-like cyanophages community in the South China Sea.}, journal = {Microbiology spectrum}, volume = {12}, number = {2}, pages = {e0200223}, pmid = {38193726}, issn = {2165-0497}, support = {41861144018, 42188102//MOST | National Natural Science Foundation of China (NSFC)/ ; 42206133//MOST | National Natural Science Foundation of China (NSFC)/ ; LYG20220003//Lianyungang Postdoctoral Research Funding Program/ ; }, mesh = {Phylogeny ; Ecosystem ; *Bacteriophages/genetics ; Capsid Proteins/genetics ; Capsid ; *Cyanobacteria ; }, abstract = {Marine ecosystems contain an immense diversity of phages, many of which infect cyanobacteria (cyanophage) that are largely responsible for primary productivity. To characterize the genetic diversity and biogeographic distribution of the marine T4-like cyanophage community in the northern South China Sea, the T4-like cyanophage portal protein gene (g20) was amplified. Phylogenetic analysis revealed that marine T4-like cyanophages were highly diverse, with g20 operational taxonomic units being affiliated with five defined clades (Clusters I-V). Cluster II had a wide geographic distribution, Cluster IV was the most abundant in the open sea, and Cluster I was dominant in coastal shelf environments. Our results showed T4-like cyanophages (based on g20) community was generally shaped via heterogeneous selection. Highly variable environmental factors (such as salinity and temperature) can heterogeneously select different cyanophage communities. Nevertheless, the dominant drivers of the T4-like cyanophage community based on the g20 and g23 (T4-like phage major capsid protein gene) were different, probably due to different coverages by the primer sets. Furthermore, the community assembly processes of T4-like cyanophages were affected by host traits (abundance and distribution), viral traits (latent period, burst size, and host range), and environmental properties (temperature and salinity).IMPORTANCECyanophages are abundant and ubiquitous in the oceans, altering population structures and evolution of cyanobacteria, which account for a large portion of global carbon fixation, through host mortality, horizontal gene transfer, and the modulation of host metabolism. However, little is known about the biogeography and ecological drivers that shape the cyanophage community. Here, we use g20 and g23 genes to examine the biogeographic patterns and the assembly mechanisms of T4-like cyanophage community in the northern part of the South China Sea. The different coverages of primer sets might lead to the different dominant drivers of T4-like cyanophage community based on g20 and g23 genes. Our results showed that characteristics of viral traits (latent period, burst size, and host range) and host traits (abundance and distribution) were found to either limit or enhance the biogeographic distribution of T4-like cyanophages. Overall, both virus and host properties are critical to consider when determining rules of community assembly for viruses.}, }
@article {pmid38193706, year = {2024}, author = {Han, X and Zhou, J and Yu, L and Shao, L and Cai, S and Hu, H and Shi, Q and Wang, Z and Hua, X and Jiang, Y and Yu, Y}, title = {Genome sequencing unveils blaKPC-2-harboring plasmids as drivers of enhanced resistance and virulence in nosocomial Klebsiella pneumoniae.}, journal = {mSystems}, volume = {9}, number = {2}, pages = {e0092423}, pmid = {38193706}, issn = {2379-5077}, support = {32141001//MOST | National Natural Science Foundation of China (NSFC)/ ; 82272373//MOST | National Natural Science Foundation of China (NSFC)/ ; 2018YFE0102100//MOST | National Key Research and Development Program of China (NKPs)/ ; LY22H190001//MOST | NSFC | NSFC-Zhejiang Joint Fund | | Natural Science Foundation of Zhejiang Province (ZJNSF)/ ; 2021C03179//MOST | NSFC | NSFC-Zhejiang Joint Fund | Science and Technology Department of Zhejiang Province ()/ ; 2021C03055//MOST | NSFC | NSFC-Zhejiang Joint Fund | Science and Technology Department of Zhejiang Province ()/ ; }, mesh = {Humans ; Klebsiella pneumoniae/genetics ; Klebsiella/genetics ; *Klebsiella Infections/drug therapy ; *Cross Infection/epidemiology ; Virulence/genetics ; beta-Lactamases/genetics ; Anti-Bacterial Agents/pharmacology ; Plasmids/genetics ; Carbapenems/pharmacology ; }, abstract = {The threat posed by Klebsiella pneumoniae in healthcare settings has worsened due to the evolutionary advantages conferred by blaKPC-2-harboring plasmids (pKPC-2). However, the specific evolutionary pathway of nosocomial K. pneumoniae carrying pKPC-2 and its transmission between patients and healthcare environments are not yet well understood. Between 1 August and 31 December 2019, 237 ST11 KPC-2-producing-carbapenem-resistant K. pneumoniae (CRKP) (KPC-2-CRKP) were collected from patient or ward environments in an intensive care unit and subjected to Illumina sequencing, of which 32 strains were additionally selected for Nanopore sequencing to obtain complete plasmid sequences. Bioinformatics analysis, conjugation experiments, antimicrobial susceptibility tests, and virulence assays were performed to identify the evolutionary characteristics of pKPC-2. The pKPC-2 plasmids were divided into three subgroups with distinct evolutionary events, including Tn3-mediated plasmid homologous recombination, IS26-mediated horizontal gene transfer, and dynamic duplications of antibiotic resistance genes (ARGs). Surprisingly, the incidence rates of multicopy blaKPC-2, blaSHV-12, and blaCTX-M-65 were quite high (ranging from 27.43% to 67.01%), and strains negative for extended-spectrum β-lactamase tended to develop multicopy blaKPC-2. Notably, the presence of multicopy blaSHV-12 reduced sensitivity to ceftazidime/avibactam (CZA), and the relative expression level of blaSHV-12 in the CZA-resistant group was 6.12 times higher than that in the sensitive group. Furthermore, a novel hybrid pKPC-2 was identified, presenting enhanced virulence levels and decreased susceptibility to CZA. This study emphasizes the notable prevalence of multicopy ARGs and provides a comprehensive insight into the intricate and diverse evolutionary pathways of resistant plasmids that disseminate among patients and healthcare environments.IMPORTANCEThis study is based on a CRKP screening program between patients and ward environments in an intensive care unit, describing the pKPC-2 (blaKPC-2-harboring plasmids) population structure and evolutionary characteristics in clinical settings. Long-read sequencing was performed in genetically closely related strains, enabling the high-resolution analysis of evolution pathway between or within pKPC-2 subgroups. We revealed the extremely high rates of multicopy antibiotic resistance genes (ARGs) in clinical settings and its effect on resistance profile toward novel β-lactam/β-lactamase inhibitor combinations, which belongs to the last line treatment choices toward CRKP infection. A novel hybrid pKPC-2 carrying CRKP with enhanced resistance and virulence level was captured during its clonal spread between patients and ward environment. These evidences highlight the threat of pKPC-2 to CRKP treatment and control. Thus, surveillance and timely disinfection in clinical settings should be practiced to prevent transmission of CRKP carrying threatful pKPC-2. And rational use of antibiotics should be called for to prevent inducing of pKPC-2 evolution, especially the multicopy ARGs.}, }
@article {pmid38192262, year = {2024}, author = {Schuster, CD and Salvatore, F and Moens, L and Martí, MA}, title = {Globin phylogeny, evolution and function, the newest update.}, journal = {Proteins}, volume = {92}, number = {6}, pages = {720-734}, doi = {10.1002/prot.26659}, pmid = {38192262}, issn = {1097-0134}, mesh = {*Globins/genetics/chemistry/metabolism ; *Phylogeny ; *Evolution, Molecular ; Humans ; Bacteria/genetics/metabolism ; Animals ; Archaea/genetics/metabolism ; Protein Domains ; Gene Transfer, Horizontal ; }, abstract = {Our globin census update allows us to refine our vision of globin origin, evolution, and structure to function relationship in the context of the currently accepted tree of life. The modern globin domain originates as a single domain, three-over-three α-helical folded structure before the diversification of the kingdoms of life (Bacteria, Archaea, Eukarya). Together with the diversification of prokaryotes, three monophyletic globin families (M, S, and T) emerged, most likely in Proteobacteria and Actinobacteria, displaying specific sequence and structural features, and spread by vertical and horizontal gene transfer, most probably already present in the last universal common ancestor (LUCA). Non-globin domains were added, and eventually lost again, creating multi-domain structures in key branches of M- (FHb and Adgb) and the vast majority of S globins, which with their coevolved multi-domain architectures, have predominantly "sensor" functions. Single domain T-family globins diverged into four major groups and most likely display functions related to reactive nitrogen and oxygen species (RNOS) chemistry, as well as oxygen storage/transport which drives the evolution of its major branches with their characteristic key distal residues (B10, E11, E7, and G8). M-family evolution also lead to distinctive major types (FHb and Fgb, Ngb, Adgb, GbX vertebrate Gbs), and shows the shift from high oxygen affinity controlled by TyrB10-Gln/AsnE11 likely related to RNOS chemistry in microorganisms, to a moderate oxygen affinity storage/transport function controlled by hydrophobic B10/E11-HisE7 in multicellular animals.}, }
@article {pmid38187688, year = {2024}, author = {Wolff, R and Garud, NR}, title = {Pervasive selective sweeps across human gut microbiomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38187688}, issn = {2692-8205}, support = {R35 GM151023/GM/NIGMS NIH HHS/United States ; }, abstract = {The human gut microbiome is composed of a highly diverse consortia of species which are continually evolving within and across hosts. The ability to identify adaptations common to many human gut microbiomes would not only reveal shared selection pressures across hosts, but also key drivers of functional differentiation of the microbiome that may affect community structure and host traits. However, to date there has not been a systematic scan for adaptations that have spread across human gut microbiomes. Here, we develop a novel selection scan statistic named the integrated Linkage Disequilibrium Score (iLDS) that can detect the spread of adaptive haplotypes across host microbiomes via migration and horizontal gene transfer. Specifically, iLDS leverages signals of hitchhiking of deleterious variants with the beneficial variant. Application of the statistic to ~30 of the most prevalent commensal gut species from 24 populations around the world revealed more than 300 selective sweeps across species. We find an enrichment for selective sweeps at loci involved in carbohydrate metabolism-potentially indicative of adaptation to features of host diet-and we find that the targets of selection significantly differ between Westernized and non-Westernized populations. Underscoring the potential role of diet in driving selection, we find a selective sweep absent from non-Westernized populations but ubiquitous in Westernized populations at a locus known to be involved in the metabolism of maltodextrin, a synthetic starch that has recently become a widespread component of Western diets. In summary, we demonstrate that selective sweeps across host microbiomes are a common feature of the evolution of the human gut microbiome, and that targets of selection may be strongly impacted by host diet.}, }
@article {pmid38185239, year = {2024}, author = {Zhu, X and Wang, X and Wang, F and Tian, X and Pang, J}, title = {The integrative and conjugative element ICECiPOL15 mediates horizontal transfer of β-lactam resistance gene in Chryseobacterium indoltheticum POL15.}, journal = {Journal of global antimicrobial resistance}, volume = {36}, number = {}, pages = {223-229}, doi = {10.1016/j.jgar.2023.12.028}, pmid = {38185239}, issn = {2213-7173}, mesh = {*Chryseobacterium ; beta-Lactam Resistance ; Genomics ; Drug Resistance, Multiple, Bacterial/genetics ; }, abstract = {OBJECTIVES: The dissemination of antibiotic resistance genes (ARGs) from the environment, including agricultural sources, is of increasing concern. In this study, we examined the antibiotic resistance profile and genomic sequence of a strain of Chryseobacterium indoltheticum obtained from an agricultural location.<br><br>METHODS: The multidrug-resistant bacterial strain POL15 was isolated from the wastewater of a livestock farm in China. Whole-genome sequencing was performed followed by bioinformatics analyses to identify integrative and conjugative elements (ICEs) and ARGs. Mating assays were performed to analyse ICE transferability.<br><br>RESULTS: Whole-genome sequencing and annotation showed that the genome of POL15 encodes ARGs. Additionally, an ICE named ICECiPOL15, which carries a class C &#x3b2;-lactamase-encoding gene blaAQU, was identified in the POL15 genome. Genes encoding an integrase, an excisionase, a relaxase, a type IV coupling protein and conjugative transposon proteins involved in a type IV secretion system were also identified in ICECiPOL15. Sequence alignment revealed that ICECiPOL15 might have evolved from other Chryseobacterium species. The horizontal transferability of ICECiPOL15 was demonstrated by mating experiments between C. indoltheticum POL15 and Escherichia coli DL21.<br><br>CONCLUSIONS: This study represents the first characterization of a mobilizable antibiotic resistance ICE in a species of C. indoltheticum and provides evidence that C. indoltheticum strains could be important reservoirs and vehicles for ARGs on livestock farms.}, }
@article {pmid38182626, year = {2024}, author = {Rühlemann, MC and Bang, C and Gogarten, JF and Hermes, BM and Groussin, M and Waschina, S and Poyet, M and Ulrich, M and Akoua-Koffi, C and Deschner, T and Muyembe-Tamfum, JJ and Robbins, MM and Surbeck, M and Wittig, RM and Zuberbühler, K and Baines, JF and Leendertz, FH and Franke, A}, title = {Functional host-specific adaptation of the intestinal microbiome in hominids.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {326}, pmid = {38182626}, issn = {2041-1723}, support = {261376515//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 244372499//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 261376515//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 390884018//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {Animals ; *Hominidae ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Pan troglodytes ; Pan paniscus ; }, abstract = {Fine-scale knowledge of the changes in composition and function of the human gut microbiome compared that of our closest relatives is critical for understanding the evolutionary processes underlying its developmental trajectory. To infer taxonomic and functional changes in the gut microbiome across hominids at different timescales, we perform high-resolution metagenomic-based analyzes of the fecal microbiome from over two hundred samples including diverse human populations, as well as wild-living chimpanzees, bonobos, and gorillas. We find human-associated taxa depleted within non-human apes and patterns of host-specific gut microbiota, suggesting the widespread acquisition of novel microbial clades along the evolutionary divergence of hosts. In contrast, we reveal multiple lines of evidence for a pervasive loss of diversity in human populations in correlation with a high Human Development Index, including evolutionarily conserved clades. Similarly, patterns of co-phylogeny between microbes and hosts are found to be disrupted in humans. Together with identifying individual microbial taxa and functional adaptations that correlate to host phylogeny, these findings offer insights into specific candidates playing a role in the diverging trajectories of the gut microbiome of hominids. We find that repeated horizontal gene transfer and gene loss, as well as the adaptation to transient microaerobic conditions appear to have played a role in the evolution of the human gut microbiome.}, }
@article {pmid38181725, year = {2024}, author = {Jiang, YL and Zhou, CZ}, title = {Multiple masks of a Shigella podophage.}, journal = {Structure (London, England : 1993)}, volume = {32}, number = {1}, pages = {1-2}, doi = {10.1016/j.str.2023.12.002}, pmid = {38181725}, issn = {1878-4186}, support = {2018YFA0903100//Ministry of Science and Technology of China/ ; U19A2020//National Natural Science Foundation of China/ ; 2020452//Youth Innovation Promotion Association of Chinese Academy of Sciences/ ; }, mesh = {*Shigella/virology ; *Bacteriophages/ultrastructure ; }, abstract = {In this issue of Structure, Subramanian et al. present the cryo-EM structure of Shigella podophage HRP29, which possesses a T7-like tail complex surrounded by six P22/Sf6-like tailspikes and two unique decoration proteins. These colorful masks of HRP29 record the frequent events of horizontal gene transfer during evolution.}, }
@article {pmid38181593, year = {2024}, author = {Zhang, C and Li, S and Sun, H and Li, X and Fu, L and Zhang, C and Sun, S and Zhou, D}, title = {Assessing the impact of low organic loading on effluent safety in wastewater treatment: Insights from an activated sludge reactor study.}, journal = {Journal of hazardous materials}, volume = {465}, number = {}, pages = {133083}, doi = {10.1016/j.jhazmat.2023.133083}, pmid = {38181593}, issn = {1873-3336}, mesh = {Humans ; *Wastewater ; Sewage/microbiology ; Disinfection/methods ; Nitrogen ; *Water Purification/methods ; }, abstract = {In this study, an organic loading (OL) of 300 mg/(L d) was set as the relative normal condition (OL-300), while 150 mg/(L d) was chosen as the condition reflecting excessively low organic loading (OL-150) to thoroughly assess the associated risks in the effluent of the biological wastewater treatment process. Compared with OL-300, OL-150 did not lead to a significant decrease in dissolved organic carbon (DOC) concentration, but it did improve dissolved organic nitrogen (DON) levels by ∼63 %. Interestingly, the dissolved organic matter (DOM) exhibited higher susceptibility to transformation into chlorinated disinfection by-products (Cl-DBPs) in OL-150, resulting in an increase in the compound number of Cl-DBPs by ∼16 %. Additionally, OL-150 induced nutrient stress, which promoted engendered human bacterial pathogens (HBPs) survival by ∼32 % and led to ∼51 % increase in the antibiotic resistance genes (ARGs) abundance through horizontal gene transfer (HGT). These findings highlight the importance of carefully considering the potential risks associated with low organic loading strategies in wastewater treatment processes.}, }
@article {pmid38180978, year = {2024}, author = {Schilcher, K and Severn, MM and Jenul, C and Avina, YC and Keogh, RA and Horswill, AR}, title = {The Staphylococcus aureus CamS lipoprotein is a repressor of toxin production that shapes host-pathogen interaction.}, journal = {PLoS biology}, volume = {22}, number = {1}, pages = {e3002451}, pmid = {38180978}, issn = {1545-7885}, support = {I01 BX002711/BX/BLRD VA/United States ; P01 AI083211/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Staphylococcus aureus/genetics ; Lipoproteins/genetics ; *Staphylococcal Infections ; Host-Pathogen Interactions ; Cell Adhesion Molecules ; Cytotoxins ; Peptides ; }, abstract = {Lipoproteins of the opportunistic pathogen Staphylococcus aureus play a crucial role in various cellular processes and host interactions. Consisting of a protein and a lipid moiety, they support nutrient acquisition and anchor the protein to the bacterial membrane. Recently, we identified several processed and secreted small linear peptides that derive from the secretion signal sequence of S. aureus lipoproteins. Here, we show, for the first time, that the protein moiety of the S. aureus lipoprotein CamS has a biological role that is distinct from its associated linear peptide staph-cAM373. The small peptide was shown to be involved in interspecies horizontal gene transfer, the primary mechanism for the dissemination of antibiotic resistance among bacteria. We provide evidence that the CamS protein moiety is a potent repressor of cytotoxins, such as α-toxin and leukocidins. The CamS-mediated suppression of toxin transcription was reflected by altered disease severity in in vivo infection models involving skin and soft tissue, as well as bloodstream infections. Collectively, we have uncovered the role of the protein moiety of the staphylococcal lipoprotein CamS as a previously uncharacterized repressor of S. aureus toxin production, which consequently regulates virulence and disease outcomes. Notably, the camS gene is conserved in S. aureus, and we also demonstrated the muted transcriptional response of cytotoxins in 2 different S. aureus lineages. Our findings provide the first evidence of distinct biological functions of the protein moiety and its associated linear peptide for a specific lipoprotein. Therefore, lipoproteins in S. aureus consist of 3 functional components: a lipid moiety, a protein moiety, and a small linear peptide, with putative different biological roles that might not only determine the outcome of host-pathogen interactions but also drive the acquisition of antibiotic resistance determinants.}, }
@article {pmid38178191, year = {2024}, author = {Mahillon, M and Brodard, J and Dubuis, N and Gugerli, P and Blouin, AG and Schumpp, O}, title = {Mixed infection of ITPase-encoding potyvirid and secovirid in Mercurialis perennis: evidences for a convergent euphorbia-specific viral counterstrike.}, journal = {Virology journal}, volume = {21}, number = {1}, pages = {6}, pmid = {38178191}, issn = {1743-422X}, mesh = {Inosine Triphosphatase ; *Euphorbia ; Phylogeny ; *Coinfection ; *RNA Viruses/genetics ; Nucleotides/genetics ; *Potyviridae/genetics ; *Plant Viruses/genetics ; Plants/genetics ; *Nucleic Acids ; RNA, Viral/genetics ; Genome, Viral ; }, abstract = {BACKGROUND: In cellular organisms, inosine triphosphate pyrophosphatases (ITPases) prevent the incorporation of mutagenic deaminated purines into nucleic acids. These enzymes have also been detected in the genomes of several plant RNA viruses infecting two euphorbia species. In particular, two ipomoviruses produce replicase-associated ITPases to cope with high concentration of non-canonical nucleotides found in cassava tissues.<br><br>METHOD: Using high-throughput RNA sequencing on the wild euphorbia species Mercurialis perennis, two new members of the families Potyviridae and Secoviridae were identified. Both viruses encode for a putative ITPase, and were found in mixed infection with a new partitivirid. Following biological and genomic characterization of these viruses, the origin and function of the phytoviral ITPases were investigated.<br><br>RESULTS: While the potyvirid was shown to be pathogenic, the secovirid and partitivirid could not be transmitted. The secovirid was found belonging to a proposed new Comovirinae genus tentatively named "Mercomovirus", which also accommodates other viruses identified through transcriptome mining, and for which an asymptomatic pollen-associated lifestyle is suspected. Homology and phylogenetic analyses inferred that the ITPases encoded by the potyvirid and secovirid were likely acquired through independent horizontal gene transfer events, forming lineages distinct from the enzymes found in cassava ipomoviruses. Possible origins from cellular organisms are discussed for these proteins. In parallel, the endogenous ITPase of M. perennis was predicted to encode for a C-terminal nuclear localization signal, which appears to be conserved among the ITPases of euphorbias but absent in other plant families. This subcellular localization is in line with the idea that nucleic acids remain protected in the nucleus, while deaminated nucleotides accumulate in the cytoplasm where they act as antiviral molecules.<br><br>CONCLUSION: Three new RNA viruses infecting M. perennis are described, two of which encoding for ITPases. These enzymes have distinct origins, and are likely required by viruses to circumvent high level of cytoplasmic non-canonical nucleotides. This putative plant defense mechanism has emerged early in the evolution of euphorbias, and seems to specifically target certain groups of RNA viruses infecting perennial hosts.}, }
@article {pmid38177692, year = {2024}, author = {Nguyen, ANT and Gorrell, R and Kwok, T and Connallon, T and McDonald, MJ}, title = {Horizontal gene transfer facilitates the molecular reverse-evolution of antibiotic sensitivity in experimental populations of H. pylori.}, journal = {Nature ecology &amp; evolution}, volume = {8}, number = {2}, pages = {315-324}, pmid = {38177692}, issn = {2397-334X}, mesh = {Humans ; *Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; *Helicobacter pylori/genetics ; Evolution, Molecular ; Models, Theoretical ; }, abstract = {Reversing the evolution of traits harmful to humans, such as antimicrobial resistance, is a key ambition of applied evolutionary biology. A major impediment to reverse evolution is the relatively low spontaneous mutation rates that revert evolved genotypes back to their ancestral state. However, the repeated re-introduction of ancestral alleles by horizontal gene transfer (HGT) could make reverse evolution likely. Here we evolve populations of an antibiotic-resistant strain of Helicobacter pylori in growth conditions without antibiotics while introducing an ancestral antibiotic-sensitive allele by HGT. We evaluate reverse evolution using DNA sequencing and find that HGT facilitates the molecular reverse evolution of the antibiotic resistance allele, and that selection for high rates of HGT drives the evolution of increased HGT rates in low-HGT treatment populations. Finally, we use a theoretical model and carry out simulations to infer how the fitness costs of antibiotic resistance, rates of HGT and effects of genetic drift interact to determine the probability and predictability of reverse evolution.}, }
@article {pmid38176647, year = {2024}, author = {Mawla, GD and Kamal, SM and Cao, LY and Purhonen, P and Hebert, H and Sauer, RT and Baker, TA and Römling, U}, title = {The membrane-cytoplasmic linker defines activity of FtsH proteases in Pseudomonas aeruginosa clone C.}, journal = {The Journal of biological chemistry}, volume = {300}, number = {2}, pages = {105622}, pmid = {38176647}, issn = {1083-351X}, support = {R01 AI016892/AI/NIAID NIH HHS/United States ; R35 GM141517/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; *ATP-Dependent Proteases/chemistry/metabolism ; *Bacterial Proteins/metabolism ; Endopeptidases/metabolism ; Membrane Proteins/metabolism ; Peptide Hydrolases/metabolism ; *Pseudomonas aeruginosa/metabolism ; }, abstract = {Pandemic Pseudomonas aeruginosa clone C strains encode two inner-membrane associated ATP-dependent FtsH proteases. PaftsH1 is located on the core genome and supports cell growth and intrinsic antibiotic resistance, whereas PaftsH2, a xenolog acquired through horizontal gene transfer from a distantly related species, is unable to functionally replace PaftsH1. We show that purified PaFtsH2 degrades fewer substrates than PaFtsH1. Replacing the 31-amino acid-extended linker region of PaFtsH2 spanning from the C-terminal end of the transmembrane helix-2 to the first seven highly divergent residues of the cytosolic AAA+ ATPase module with the corresponding region of PaFtsH1 improves hybrid-enzyme substrate processing in vitro and enables PaFtsH2 to substitute for PaFtsH1 in vivo. Electron microscopy indicates that the identity of this linker sequence influences FtsH flexibility. We find membrane-cytoplasmic (MC) linker regions of PaFtsH1 characteristically glycine-rich compared to those from FtsH2. Consequently, introducing three glycines into the membrane-proximal end of PaFtsH2's MC linker is sufficient to elevate its activity in vitro and in vivo. Our findings establish that the efficiency of substrate processing by the two PaFtsH isoforms depends on MC linker identity and suggest that greater linker flexibility and/or length allows FtsH to degrade a wider spectrum of substrates. As PaFtsH2 homologs occur across bacterial phyla, we hypothesize that FtsH2 is a latent enzyme but may recognize specific substrates or is activated in specific contexts or biological niches. The identity of such linkers might thus play a more determinative role in the functionality of and physiological impact by FtsH proteases than previously thought.}, }
@article {pmid38172677, year = {2024}, author = {Choi, DG and Baek, JH and Han, DM and Khan, SA and Jeon, CO}, title = {Comparative pangenome analysis of Enterococcus faecium and Enterococcus lactis provides new insights into the adaptive evolution by horizontal gene acquisitions.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {28}, pmid = {38172677}, issn = {1471-2164}, support = {Graduate Research Scholarship in 2018//Chung-Ang University/ ; PJ01710102//Rural Development Administration/ ; 2018R1A5A1025077//Ministry of Science and ICT, South Korea/ ; }, mesh = {Animals ; Humans ; *Enterococcus faecium ; Phylogeny ; Enterococcus ; Genomics ; Anti-Bacterial Agents ; }, abstract = {BACKGROUND: Enterococcus faecium and E. lactis are phylogenetically closely related lactic acid bacteria that are ubiquitous in nature and are known to be beneficial or pathogenic. Despite their considerable industrial and clinical importance, comprehensive studies on their evolutionary relationships and genomic, metabolic, and pathogenic traits are still lacking. Therefore, we conducted comparative pangenome analyses using all available dereplicated genomes of these species.<br><br>RESULTS: E. faecium was divided into two subclades: subclade I, comprising strains derived from humans, animals, and food, and the more recent phylogenetic subclade II, consisting exclusively of human-derived strains. In contrast, E. lactis strains, isolated from diverse sources including foods, humans, animals, and the environment, did not display distinct clustering based on their isolation sources. Despite having similar metabolic features, noticeable genomic differences were observed between E. faecium subclades I and II, as well as E. lactis. Notably, E. faecium subclade II strains exhibited significantly larger genome sizes and higher gene counts compared to both E. faecium subclade I and E. lactis strains. Furthermore, they carried a higher abundance of antibiotic resistance, virulence, bacteriocin, and mobile element genes. Phylogenetic analysis of antibiotic resistance and virulence genes suggests that E. faecium subclade II strains likely acquired these genes through horizontal gene transfer, facilitating their effective adaptation in response to antibiotic use in humans.<br><br>CONCLUSIONS: Our study offers valuable insights into the adaptive evolution of E. faecium strains, enabling their survival as pathogens in the human environment through horizontal gene acquisitions.}, }
@article {pmid38169326, year = {2024}, author = {Yarus, M}, title = {Ordering events in a developing genetic code.}, journal = {RNA biology}, volume = {21}, number = {1}, pages = {1-8}, pmid = {38169326}, issn = {1555-8584}, mesh = {Codon ; *Evolution, Molecular ; *Genetic Code ; Anticodon ; Models, Genetic ; }, abstract = {Preexisting partial genetic codes can fuse to evolve towards the complete Standard Genetic Code (SGC). Such code fusion provides a path of 'least selection', readily generating precursor codes that resemble the SGC. Consequently, such least selections produce the SGC via minimal, thus rapid, change. Optimal code evolution therefore requires delayed wobble. Early wobble encoding slows code evolution, very specifically diminishing the most likely SGC precursors: near-complete, accurate codes which are the products of code fusions. In contrast: given delayed wobble, the SGC can emerge from a truncation selection/evolutionary radiation based on proficient fused coding.}, }
@article {pmid38169168, year = {2024}, author = {Li, S and Duan, G and Xi, Y and Chu, Y and Li, F and Ho, SH}, title = {Insights into the role of extracellular polymeric substances (EPS) in the spread of antibiotic resistance genes.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {343}, number = {}, pages = {123285}, doi = {10.1016/j.envpol.2023.123285}, pmid = {38169168}, issn = {1873-6424}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Wastewater ; Extracellular Polymeric Substance Matrix ; Genes, Bacterial ; Sewage ; Drug Resistance, Microbial/genetics ; }, abstract = {Antibiotic resistance genes (ARG) are prevalent in aquatic environments. Discharge from wastewater treatment plants is an important point source of ARG release into the environment. It has been reported that biological treatment processes may enhance rather than remove ARG because of their presence in sludge. Attenuation of ARG in biotechnological processes has been studied in depth, showing that many microorganisms can secrete complex extracellular polymeric substances (EPS). These EPS can serve as multifunctional elements of microbial communities, involving aspects, such as protection, structure, recognition, adhesion, and physiology. These aspects can influence the interaction between microbial cells and extracellular ARG, as well as the uptake of extracellular ARG by microbial cells, thus changing the transformative capability of extracellular ARG. However, it remains unclear whether EPS can affect horizontal ARG transfer, which is one of the main processes of ARG dissemination. In light of this knowledge gap, this review provides insight into the role of EPS in the transmission of ARGs; furthermore, the mechanism of ARG spread is analyzed, and the molecular compositions and functional properties of EPS are summarized; also, how EPS influence ARG mitigation is addressed, and factors impacting how EPS facilitate ARG during wastewater treatment are summarized. This review provides comprehensive insights into the role of EPS in controlling the transport and fate of ARG during biodegradation processes at the mechanistic level.}, }
@article {pmid38168155, year = {2023}, author = {Lass, SW and Camphire, S and Smith, BE and Eutsey, RA and Prentice, JA and Yerneni, SS and Arun, A and Bridges, AA and Rosch, JW and Conway, JF and Campbell, P and Hiller, NL}, title = {Pneumococcal Extracellular Vesicles Mediate Horizontal Gene Transfer via the Transformation Machinery.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38168155}, issn = {2692-8205}, support = {S10 OD025009/OD/NIH HHS/United States ; T32 GM133353/GM/NIGMS NIH HHS/United States ; }, abstract = {Bacterial cells secrete extracellular vesicles (EVs), the function of which is a matter of intense investigation. Here, we show that the EVs secreted by the human pathogen Streptococcus pneumoniae (pneumococcus) are associated with bacterial DNA on their surface and can deliver this DNA to the transformation machinery of competent cells. These findings suggest that EVs contribute to gene transfer in Gram-positive bacteria, and in doing so, may promote the spread of drug resistance genes in the population.}, }
@article {pmid38167305, year = {2024}, author = {Klose, SM and Legione, AR and Monotti, I and Bushell, RN and Sugiyama, T and Browning, GF and Vaz, PK}, title = {Genomic characterization of Mycoplasma edwardii isolated from a dog bite induced cat wound reveals multiple horizontal gene transfer events and loss of the CRISPR/Cas system.}, journal = {Journal of medical microbiology}, volume = {73}, number = {1}, pages = {}, doi = {10.1099/jmm.0.001788}, pmid = {38167305}, issn = {1473-5644}, mesh = {Dogs ; Cats ; Animals ; *Mycoplasma Infections/veterinary/microbiology ; CRISPR-Cas Systems ; Gene Transfer, Horizontal ; *Mycoplasma/genetics ; Genomics ; }, abstract = {A domestic short hair cat (Felis catus) suffering from a purulent wound infection resulting from a dog bite was sampled for bacterial culture and isolation as the wound had been unresponsive to prolonged antimicrobial treatment. A mycoplasma was isolated from the wound. Whole genome sequencing of the isolate was performed using short-read Illumina and long-read Oxford Nanopore chemistry, and the organism was identified as Mycoplasma edwardii. Comparison of the genome sequence of the isolate to a reference M. edwardii genome sequence (canid isolate) identified the loss of several key bacterial factors involved in genome editing, as well the insertion of several novel ORFs most closely related to those found in other canine mycoplasmas, specifically Mycoplasma canis, M. cynos, M. molare and M. maculosa. This is only the second known report of disease caused by M. edwardii in a non-canid species, and the first report of it infecting and causing clinical disease in a cat.}, }
@article {pmid38164507, year = {2024}, author = {Tuji, A and Ogiso-Tanaka, E and Yamaguchi, H}, title = {Complete Genome Sequence of Annamia dubia, filamentous colony-making Chroococcales with the analysis of FraC gene influencing filament integrity.}, journal = {Journal of genomics}, volume = {12}, number = {}, pages = {1-5}, pmid = {38164507}, issn = {1839-9940}, abstract = {The complete genome of Annamia dubia was sequenced. The genome size is 4.02 Mbp, including 3886286 bp circular chromosome and four circular plasmids (31516, 42453, 38085 and 24903 bp). It included 3718 protein-coding sequences, 45 tRNA genes, three sets of rRNA genes, a microcystin biosynthesis gene cluster and six CRISPR (clustered regularly interspaced short palindromic repeat). Annamia is the only one genus in the Chroococcales that makes filamentous colonies. FraC and FraG were identified in the genome. These genes are required for the integrity of cell junctions and influencing filament integrity and are thought to be related to colony formation. These genes are first reported from Chroococcales, and may play a significant role in the colony formation of this species. In the phylogenetic tree of the FraC gene, A. dubia was located in the basal position of Oscillatoriales. The GC ratio of FraC gene of A. dubia is very low from the genome and the FraC gene of Microcoleaceae. The presence of these genes in the basal region and the low GC ratio suggests that the FraC gene in this species was introduced by horizontal gene transfer. Since the filamentous colony is a fundamental and important taxonomic feature for the classification of cyanobacteria, the possibility of horizontal transmission of genes involved in filamentous cyanobacterial colonies is an important discovery for the classification of cyanobacteria.}, }
@article {pmid38163572, year = {2024}, author = {Gaviria-Cantin, T and Fernández-Coll, L and Vargas, AF and Jiménez, CJ and Madrid, C and Balsalobre, C}, title = {Expression of accessory genes in Salmonella requires the presence of the Gre factors.}, journal = {Genomics}, volume = {116}, number = {1}, pages = {110777}, doi = {10.1016/j.ygeno.2023.110777}, pmid = {38163572}, issn = {1089-8646}, mesh = {*Salmonella typhimurium/genetics/metabolism ; Plasmids ; Virulence/genetics ; *Bacterial Proteins/genetics/metabolism ; }, abstract = {Genomic studies with Salmonella enterica serovar Typhimurium reveal a crucial role of horizontal gene transfer (HGT) in the acquisition of accessory cellular functions involved in host-interaction. Many virulence genes are located in genomic islands, plasmids and prophages. GreA and GreB proteins, Gre factors, interact transiently with the RNA polymerase alleviating backtracked complexes during transcription elongation. The overall effect of Gre factors depletion in Salmonella expression profile was studied. Both proteins are functionally redundant since only when both Gre factors were depleted a major effect in gene expression was detected. Remarkably, the accessory gene pool is particularly sensitive to the lack of Gre factors, with 18.6% of accessory genes stimulated by the Gre factors versus 4.4% of core genome genes. Gre factors involvement is particularly relevant for the expression of genes located in genomic islands. Our data reveal that Gre factors are required for the expression of accessory genes.}, }
@article {pmid38159121, year = {2024}, author = {Wang, HM and Hu, GR and Luo, WY and Li, FL}, title = {The horizontal gene transfer of perchlorate reduction genomic island in three bacteria from an ecological niche.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {22}, pmid = {38159121}, issn = {1432-0614}, mesh = {Phylogeny ; Oxidation-Reduction ; *Perchlorates ; *Genomic Islands ; Gene Transfer, Horizontal ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Oxidoreductases/genetics ; Ecosystem ; Transposases/genetics ; }, abstract = {Three new strains of dissimilatory perchlorate-reducing bacteria (DPRB), QD19-16, QD1-5, and P3-1, were isolated from an active sludge. Phylogenetic trees based on 16S rRNA genes indicated that QD19-16, QD1-5, and P3-1 belonged to Brucella, Acidovorax, and Citrobacter, respectively, expanding the distribution of DPRB in the Proteobacteria. The three strains were gram-negative and facultative anaerobes with rod-shaped cells without flagella, which were 1.0-1.6 μm long and 0.5-0.6 μm wide. The three DPRB strains utilized similar broad spectrum of electron donors and acceptors and demonstrated a similar capability to reduce perchlorate within 6 days. The enzyme activity of perchlorate reductase in QD19-16 toward chlorate was higher than that toward perchlorate. The high sequence similarity of the perchlorate reductase operon and chlorite dismutase genes in the perchlorate reduction genomic islands (PRI) of the three strains implied that they were monophyletic origin from a common ancestral PRI. Two transposase genes (tnp1 and tnp2) were found in the PRIs of strain QD19-16 and QD1-5, but were absent in the strain P3-1 PRI. The presence of fragments of IR sequences in the P3-1 PRI suggested that P3-1 PRI had previously contained these two tnp genes. Therefore, it is plausible to suggest that a common ancestral PRI transferred across the strains Brucella sp. QD19-16, Acidovorax sp. QD1-5, and Citrobacter sp. P3-1 through horizontal gene transfer, facilitated by transposases. These results provided a direct evidence of horizontal gene transfer of PRI that could jump across phylogenetically unrelated bacteria through transposase. KEY POINTS: • Three new DPRB strains can effectively remove high concentration of perchlorate. • The PRIs of three DPRB strains are acquired from a single ancestral PRI. • PRIs are incorporated into different bacteria genome through HGT by transposase.}, }
@article {pmid38157363, year = {2023}, author = {Wedage, WMM and Harischandra, IN and Weerasena, OVDSJ and De Silva, BGDNK}, title = {Genetic diversity and phylogeography of Phlebotomus argentipes (Diptera: Psychodidae, Phlebotominae), using COI and ND4 mitochondrial gene sequences.}, journal = {PloS one}, volume = {18}, number = {12}, pages = {e0296286}, pmid = {38157363}, issn = {1932-6203}, mesh = {Animals ; *Psychodidae/genetics ; *Phlebotomus/genetics ; Phylogeography ; Phylogeny ; Genes, Mitochondrial ; *Leishmaniasis, Cutaneous/genetics ; Sri Lanka ; Genetic Variation ; }, abstract = {BACKGROUND: Phlebotomus argentipes complex is the primary vector for cutaneous leishmaniasis, a burgeoning health concern in contemporary Sri Lanka, where effective vector control is important for proper disease management. Understanding the genetic diversity of the P. argentipes population in Sri Lanka is vital before implementing a successful vector control program. Various studies have indicated that genetic divergence, caused by genetic drift or selection, can significantly influence the vector capacity of arthropod species. To devise innovative control strategies for P. argentipes, exploring genetic diversity and phylogeography can offer valuable insights into vector competence, key genetic trait transfer, and impact on disease epidemiology. The primary objective is to analyze the genetic diversity and phylogeography of the P. argentipes complex in Sri Lanka, based on two mitochondrial genomic regions in modern representatives of P. argentipes populations.<br><br>METHODOLOGY: A total of 159 P. argentipes specimens were collected from five endemic areas of cutaneous leishmaniasis and identified morphologically. Two mitochondrial regions (Cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit 4 (ND4) were amplified using the total DNA and subsequently sequenced. Partial sequences of those mitochondrial genes were utilized to analyze genetic diversity indices and to explore phylogenetic and phylogeographic relationships.<br><br>PRINCIPAL FINDINGS: Among five sampling locations, the highest genetic diversity for COI and ND4 was observed in Hambantota (Hd-0.749, &#x3c0;-0.00417) and Medirigiriya (Hd-0.977, &#x3c0;-0.01055), respectively. Phylogeographic analyses conducted using COI sequences and GenBank retrieved sequences demonstrated a significant divergence of P. argentipes haplotypes found in Sri Lanka. Results revealed that they have evolved from the Indian ancestral haplotype due to historical- geographical connections of the Indian subcontinent with Sri Lanka.<br><br>CONCLUSIONS: Utilizing high-mutation-rate mitochondrial genes, such as ND4, can enhance the accuracy of genetic variability analysis in P. argentipes populations in Sri Lanka. The phylogeographical analysis of COI gene markers in this study provides insights into the historical geographical relationship between India and P. argentipes in Sri Lanka. Both COI and ND4 genes exhibited consistent genetic homogeneity in P. argentipes in Sri Lanka, suggesting minimal impact on gene flow. This homogeneity also implies the potential for horizontal gene transfer across populations, facilitating the transmission of genes associated with traits like insecticide resistance. This dynamic undermines disease control efforts reliant on vector control strategies.}, }
@article {pmid38156017, year = {2023}, author = {Liu, Q and Chen, Y and Xu, XW}, title = {Genomic insight into strategy, interaction and evolution of nitrifiers in metabolizing key labile-dissolved organic nitrogen in different environmental niches.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1273211}, pmid = {38156017}, issn = {1664-302X}, abstract = {Ammonia-oxidizing archaea (AOA) and bacteria (AOB), nitrite-oxidizing bacteria (NOB), and complete ammonia oxidizers (comammox) are responsible for nitrification in nature; however, some groups have been reported to utilize labile-dissolved organic nitrogen (LDON) for satisfying nitrogen demands. To understand the universality of their capacity of LDON metabolism, we collected 70 complete genomes of AOA, AOB, NOB, and comammox from typical environments for exploring their potentials in the metabolism of representative LDON (urea, polyamines, cyanate, taurine, glycine betaine, and methylamine). Genomic analyses showed that urea was the most popular LDON used by nitrifiers. Each group harbored unique urea transporter genes (AOA: dur3 and utp, AOB: utp, and NOB and comammox: urtABCDE and utp) accompanied by urease genes ureABC. The differentiation in the substrate affinity of these transporters implied the divergence of urea utilization efficiency in nitrifiers, potentially driving them into different niches. The cyanate transporter (cynABD and focA/nirC) and degradation (cynS) genes were detected mostly in NOB, indicating their preference for a wide range of nitrogen substrates to satisfy high nitrogen demands. The lack of genes involved in the metabolism of polyamines, taurine, glycine betaine, and methylamines in most of nitrifiers suggested that they were not able to serve as a source of ammonium, only if they were degraded or oxidized extracellularly as previously reported. The phylogenetic analyses assisted with comparisons of GC% and the Codon Adaptation Index between target genes and whole genomes of nitrifiers implied that urea metabolic genes dur3 and ureC in AOA evolved independently from bacteria during the transition from Thaumarchaeota to AOA, while utp in terrestrial AOA was acquired from bacteria via lateral gene transfer (LGT). Cyanate transporter genes cynS and focA/nirC detected only in a terrestrial AOA Candidadus Nitrsosphaera gargensis Ga9.2 could be gained synchronously with Nitrospira of NOB by an ancient LGT. Our results indicated that LDON utilization was a common feature in nitrifiers, but metabolic potentials were different among nitrifiers, possibly being intensely interacted with their niches, survival strategies, and evolutions.}, }
@article {pmid38153127, year = {2024}, author = {Gucwa, K and Wons, E and Wisniewska, A and Jakalski, M and Dubiak, Z and Kozlowski, LP and Mruk, I}, title = {Lethal perturbation of an Escherichia coli regulatory network is triggered by a restriction-modification system's regulator and can be mitigated by excision of the cryptic prophage Rac.}, journal = {Nucleic acids research}, volume = {52}, number = {6}, pages = {2942-2960}, pmid = {38153127}, issn = {1362-4962}, support = {UMO-2019/35/B/NZ2/00701//National Science Center (Poland)/ ; //University of Gdansk, Poland/ ; }, mesh = {*Escherichia coli/genetics/metabolism ; Prophages/genetics/metabolism ; *Escherichia coli Proteins/genetics/metabolism ; Transcription Factors/genetics/metabolism ; DNA Restriction-Modification Enzymes/metabolism ; }, abstract = {Bacterial gene regulatory networks orchestrate responses to environmental challenges. Horizontal gene transfer can bring in genes with regulatory potential, such as new transcription factors (TFs), and this can disrupt existing networks. Serious regulatory perturbations may even result in cell death. Here, we show the impact on Escherichia coli of importing a promiscuous TF that has adventitious transcriptional effects within the cryptic Rac prophage. A cascade of regulatory network perturbations occurred on a global level. The TF, a C regulatory protein, normally controls a Type II restriction-modification system, but in E. coli K-12 interferes with expression of the RacR repressor gene, resulting in de-repression of the normally-silent Rac ydaT gene. YdaT is a prophage-encoded TF with pleiotropic effects on E. coli physiology. In turn, YdaT alters expression of a variety of bacterial regulons normally controlled by the RcsA TF, resulting in deficient lipopolysaccharide biosynthesis and cell division. At the same time, insufficient RacR repressor results in Rac DNA excision, halting Rac gene expression due to loss of the replication-defective Rac prophage. Overall, Rac induction appears to counteract the lethal toxicity of YdaT. We show here that E. coli rewires its regulatory network, so as to minimize the adverse regulatory effects of the imported C TF. This complex set of interactions may reflect the ability of bacteria to protect themselves by having robust mechanisms to maintain their regulatory networks, and/or suggest that regulatory C proteins from mobile operons are under selection to manipulate their host's regulatory networks for their own benefit.}, }
@article {pmid38148908, year = {2023}, author = {Valenzuela, X and Hedman, H and Villagomez, A and Cardenas, P and Eisenberg, JNS and Levy, K and Zhang, L and Trueba, G}, title = {Distribution of blaCTX-M-gene variants in E. coli from different origins in Ecuador.}, journal = {Medicine in microecology}, volume = {18}, number = {}, pages = {}, pmid = {38148908}, issn = {2590-0978}, support = {K01 AI103544/AI/NIAID NIH HHS/United States ; R01 AI050038/AI/NIAID NIH HHS/United States ; R01 AI137679/AI/NIAID NIH HHS/United States ; R01 AI167989/AI/NIAID NIH HHS/United States ; }, abstract = {The increasing abundance of extended spectrum (β-lactamase (ESBL) genes in E. coli, and other commensal and pathogenic bacteria, endangers the utility of third or more recent generation cephalosporins, which are major tools for fighting deadly infections. The role of domestic animals in the transmission of ESBL carrying bacteria has been recognized, especially in low- and middle-income countries, however the horizontal gene transfer of these genes is difficult to assess. Here we investigate blaCTX-M gene diversity (and flanking nucleotide sequences) in E. coli from chicken and humans, in an Ecuadorian rural community and from chickens in another location in Ecuador. The blaCTX-M associated sequences in isolates from humans and chickens in the same remote community showed greater similarity than those found in E. coli in a chicken industrial operation 200 km away. Our study may provide evidence of blaCTX-M transfer between chickens and humans in the community.}, }
@article {pmid38147751, year = {2024}, author = {Xu, JY and Ding, J and Du, S and Zhu, D}, title = {Tire particles and its leachates: Impact on antibiotic resistance genes in coastal sediments.}, journal = {Journal of hazardous materials}, volume = {465}, number = {}, pages = {133333}, doi = {10.1016/j.jhazmat.2023.133333}, pmid = {38147751}, issn = {1873-3336}, mesh = {*Plastics ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Genes, Bacterial ; }, abstract = {Tire particles (TPs), a significant group of microplastics, can be discharged into the coastal environments in various ways. However, our understanding of how TPs impact the antibiotic resistance and pathogenic risks of microorganisms in coastal sediments remains limited. In this study, we used metagenomics to investigate how TPs and their leachates could affect the prevalence of antibiotic resistance genes (ARGs), virulence factor genes (VFGs), and their potential risks to the living creatures such as soil invertebrates and microorganisms in the coastal sediments. We discovered that TP addition significantly increased the abundance and diversity of ARGs and VFGs in coastal sediments, with raw TPs displayed higher impacts than TP leachates and TPs after leaching on ARGs and VFGs. With increasing TP exposure concentrations, the co-occurrence frequency of ARGs and mobile genetic elements (MGEs) in the same contig also increased, suggesting that TPs could enhance the dispersal risk of ARGs. Our metagenome-based binning analysis further revealed that exposure to TPs increased the abundance of potentially pathogenic antibiotic-resistant bacteria (PARB). In addition, chemical additives of TP leachates (e.g., Zn and N-cyclohexylformamide) significantly affected the changes of ARGs in the pore water. In summary, our study provides novel insights into the adverse effects of TP pollutions on aggravating the dissemination and pathogenic risks of ARGs and PARB in the coastal environment.}, }
@article {pmid38147560, year = {2024}, author = {Beavan, AJS and Domingo-Sananes, MR and McInerney, JO}, title = {Contingency, repeatability, and predictability in the evolution of a prokaryotic pangenome.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {1}, pages = {e2304934120}, pmid = {38147560}, issn = {1091-6490}, support = {BB/Y513374/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, mesh = {Bacteria/genetics ; *Escherichia coli/genetics ; Evolution, Molecular ; *Genome, Bacterial/genetics ; Phylogeny ; Prokaryotic Cells ; }, abstract = {Pangenomes exhibit remarkable variability in many prokaryotic species, much of which is maintained through the processes of horizontal gene transfer and gene loss. Repeated acquisitions of near-identical homologs can easily be observed across pangenomes, leading to the question of whether these parallel events potentiate similar evolutionary trajectories, or whether the remarkably different genetic backgrounds of the recipients mean that postacquisition evolutionary trajectories end up being quite different. In this study, we present a machine learning method that predicts the presence or absence of genes in the Escherichia coli pangenome based on complex patterns of the presence or absence of other accessory genes within a genome. Our analysis leverages the repeated transfer of genes through the E. coli pangenome to observe patterns of repeated evolution following similar events. We find that the presence or absence of a substantial set of genes is highly predictable from other genes alone, indicating that selection potentiates and maintains gene-gene co-occurrence and avoidance relationships deterministically over long-term bacterial evolution and is robust to differences in host evolutionary history. We propose that at least part of the pangenome can be understood as a set of genes with relationships that govern their likely cohabitants, analogous to an ecosystem's set of interacting organisms. Our findings indicate that intragenomic gene fitness effects may be key drivers of prokaryotic evolution, influencing the repeated emergence of complex gene-gene relationships across the pangenome.}, }
@article {pmid38145799, year = {2024}, author = {Souguir, M and Châtre, P and Drapeau, A and Azaiez, S and Hmidi, I and Ncir, S and Lupo, A and Madec, JY and Haenni, M and Mansour, W}, title = {CTX-M-15/27-positive Escherichia coli and VIM-2-producing Pseudomonas putida in free-living pigeons (Columba livia) in Tunisia.}, journal = {Journal of global antimicrobial resistance}, volume = {36}, number = {}, pages = {70-75}, doi = {10.1016/j.jgar.2023.12.013}, pmid = {38145799}, issn = {2213-7173}, mesh = {Animals ; Humans ; Columbidae/genetics ; Escherichia coli ; *Pseudomonas putida/genetics ; Multilocus Sequence Typing ; Tunisia/epidemiology ; Phylogeny ; beta-Lactamases/genetics ; *Anti-Infective Agents ; }, abstract = {OBJECTIVES: Wild birds are vectors of antimicrobial resistance. Birds living in close contact with humans or other animals, like feral pigeons (Columba livia), might be especially prone to acquire resistance genes such as those encoding extended-spectrum beta-lactamases (ESBLs) and carbapenemases.<br><br>METHODS: Cloacal samples (n = 206) of free-living feral pigeons (C. livia) were collected in Sousse and Monastir, Tunisia. Antimicrobial susceptibility profiles were determined by disc-diffusion, and resistant isolates were short- and long-read whole-genome sequenced. Sequence analysis was performed using tools of the Centre for Genomic Epidemiology, and Phylogenetic analysis was performed based on the core-genome MLST.<br><br>RESULTS: Fourteen (14/206, 6.8%) pigeons harboured Enterobacterales resistant to last-generations cephalosporins, of which 10 were CTX-M-15- or CTX-M-27-producers, while two (1.0%) carried a VIM-2-producing Pseudomonas putida. Positive pigeons lived on four different livestock farms. Three STs (ST206, ST5584, ST8149) were identified among E. coli, of which ST5584 and ST8149 were found in two different farms. Genetic diversity was also observed in Enterobacter cloacae and P. putida isolates. The blaCTX-M-27 genes were chromosomally encoded, while the blaCTX-M-15 genes were carried on highly similar IncF/F-:A-:B53 plasmids. The blaVIM-2 gene was located on a class 1 integron co-harbouring several resistance genes.<br><br>CONCLUSION: Pigeons living on livestock farms carried clinically important resistance genes encoding ESBLs and carbapenemases. Our results evidenced that both clonal (ST8149 and ST5584) and plasmidic (IncF/F-:A-:B53) transfers played a role in the spread of resistance genes among pigeons. Further studies are needed to identify factors favouring the transfer and persistence of resistance genes within the pigeon communities.}, }
@article {pmid38145364, year = {2024}, author = {Gong, C and Guo, Z and Hu, Y and Yang, Z and Xia, J and Yang, X and Xie, W and Wang, S and Wu, Q and Ye, W and Zhou, X and Turlings, TCJ and Zhang, Y}, title = {A Horizontally Transferred Plant Fatty Acid Desaturase Gene Steers Whitefly Reproduction.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {11}, number = {10}, pages = {e2306653}, pmid = {38145364}, issn = {2198-3844}, support = {CAAS-ASTIP-IVFCAAS//Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences/ ; 788949//European Research Council Advanced/ ; 32221004//Innovative Research Group Project of the National Natural Science Foundation of China/ ; 2021YFD1400600//Key Technologies Research and Development Program/ ; CARS-23//Earmarked Fund for China Agriculture Research System/ ; //Beijing Key Laboratory for Pest Control and Sustainable Cultivation of Vegetables/ ; }, mesh = {Animals ; *Fatty Acid Desaturases/genetics ; *Hemiptera/genetics ; Drosophila melanogaster ; Fatty Acids, Unsaturated ; Stearoyl-CoA Desaturase ; Reproduction ; }, abstract = {Polyunsaturated fatty acids (PUFAs) are essential nutrients for all living organisms. PUFA synthesis is mediated by Δ12 desaturases in plants and microorganisms, whereas animals usually obtain PUFAs through their diet. The whitefly Bemisia tabaci is an extremely polyphagous agricultural pest that feeds on phloem sap of many plants that do not always provide them with sufficient PUFAs. Here, a plant-derived Δ12 desaturase gene family BtFAD2 is characterized in B. tabaci and it shows that the BtFAD2-9 gene enables the pest to synthesize PUFAs, thereby significantly enhancing its fecundity. The role of BtFAD2-9 in reproduction is further confirmed by transferring the gene to Drosophila melanogaster, which also increases the fruit fly's reproduction. These findings reveal an extraordinary evolutionary scenario whereby a phytophagous insect acquired a family of plant genes that enables it to synthesize essential nutrients, thereby lessening its nutritional dependency and allowing it to feed and reproduce on many host plants.}, }
@article {pmid38145107, year = {2023}, author = {Dabbaghie, F and Srikakulam, SK and Marschall, T and Kalinina, OV}, title = {PanPA: generation and alignment of panproteome graphs.}, journal = {Bioinformatics advances}, volume = {3}, number = {1}, pages = {vbad167}, pmid = {38145107}, issn = {2635-0041}, abstract = {MOTIVATION: Compared to eukaryotes, prokaryote genomes are more diverse through different mechanisms, including a higher mutation rate and horizontal gene transfer. Therefore, using a linear representative reference can cause a reference bias. Graph-based pangenome methods have been developed to tackle this problem. However, comparisons in DNA space are still challenging due to this high diversity. In contrast, amino acid sequences have higher similarity due to evolutionary constraints, whereby a single amino acid may be encoded by several synonymous codons. Coding regions cover the majority of the genome in prokaryotes. Thus, panproteomes present an attractive alternative leveraging the higher sequence similarity while not losing much of the genome in non-coding regions.<br><br>RESULTS: We present PanPA, a method that takes a set of multiple sequence alignments of protein sequences, indexes them, and builds a graph for each multiple sequence alignment. In the querying step, it can align DNA or amino acid sequences back to these graphs. We first showcase that PanPA generates correct alignments on a panproteome from 1350 Escherichia coli. To demonstrate that panproteomes allow comparisons at longer phylogenetic distances, we compare DNA and protein alignments from 1073 Salmonella enterica assemblies against E.coli reference genome, pangenome, and panproteome using BWA, GraphAligner, and PanPA, respectively; with PanPA aligning around 22% more sequences. We also aligned a DNA short-reads whole genome sequencing (WGS) sample from S.enterica against the E.coli reference with BWA and the panproteome with PanPA, where PanPA was able to find alignment for 68% of the reads compared to 5% with BWA.<br><br>PanPA is available at https://github.com/fawaz-dabbaghieh/PanPA.}, }
@article {pmid38143074, year = {2023}, author = {Kurushima, J}, title = {[Mechanism of high-frequent horizontal gene transfer in Gram positive bacterial pathogens].}, journal = {Nihon saikingaku zasshi. Japanese journal of bacteriology}, volume = {78}, number = {4}, pages = {179-187}, doi = {10.3412/jsb.78.179}, pmid = {38143074}, issn = {1882-4110}, mesh = {*Gene Transfer, Horizontal ; Plasmids/genetics ; Gram-Positive Bacteria/genetics ; Enterococcus faecalis/genetics ; *Anti-Infective Agents ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; }, abstract = {Horizontal gene transfer through transconjugation and natural transformation plays a major role in the spread of antimicrobial resistance. Although the phenomenon of genetic element transmission has long been known, the rapid increase in the number of antimicrobial resistant bacteria in recent years and the accompanying accumulation of genomic information have revealed that horizontal gene transfer contributes to genome plasticity in various ways. The author reported the molecular mechanism of the antimicrobial activity of the accessory factor bacteriocin encoded by the junctional transfer plasmid of Enterococcus faecalis, a representative Gram-positive opportunistic pathogen that is concerned as highly antimicrobial resistant, and found diversity in the selfimmune system based on epidemiological studies. In addition, the author established a technique to visualize and quantify genomic recombination by natural transformation in Streptococcus pneumoniae which is also one of the most concerns for antimicrobial resistance and vaccine escape, at single cells level resolution in real time. Focuses on outcome from these research, this paper introduces the molecular mechanisms that promote horizontal gene transmission and the prospects for their technological application.}, }
@article {pmid38142651, year = {2024}, author = {Ni, B and Zhang, TL and Cai, TG and Xiang, Q and Zhu, D}, title = {Effects of heavy metal and disinfectant on antibiotic resistance genes and virulence factor genes in the plastisphere from diverse soil ecosystems.}, journal = {Journal of hazardous materials}, volume = {465}, number = {}, pages = {133335}, doi = {10.1016/j.jhazmat.2023.133335}, pmid = {38142651}, issn = {1873-3336}, mesh = {Soil ; Anti-Bacterial Agents/pharmacology ; Ecosystem ; *Disinfectants/pharmacology ; *Metals, Heavy ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Environmental Pollutants ; Soil Microbiology ; }, abstract = {Antibiotic-resistance genes (ARGs) are world-wide contaminants posing potential health risks. Quaternary ammonium compounds (QACs) and heavy metals can apply selective pressure on antibiotic resistance. However, there is a lack of evidence regarding their coupled effect on changes in ARGs and virulence factor genes (VFGs) in various soil types and their plastispheres. Herein, we conducted a microcosm experiment to explore the abundances and profiles of ARGs and VFGs in soil plastispheres from three distinct types of soils amended with Cu and disinfectants. The plastispheres enriched the ARGs' abundance compared to soils and stimulated the coupling effect of combined pollutants on promoting the abundances of ARGs and VFGs. Horizontal gene transfer inevitably accelerates the propagation of ARGs and VFGs in plastispheres under pollutant stress. In plastispheres, combined exposure to disinfectants and Cu increased some potential pathogens' relative abundances. Moreover, the combined effect of disinfectants and Cu on ARGs and VFGs changed with soil type in plastispheres, emphasising the necessity to incorporate soil type considerations into health risk assessments for ARGs and VFGs. Overall, this study highlights the high health risks of ARGs under the selective pressure of combined pollutants in plastispheres and provides valuable insights for future risk assessments related to antibiotic resistance.}, }
@article {pmid38141819, year = {2024}, author = {Veloo, ACM and Boiten, KE and Hendrickx, APA and van Prehn, J and Rossen, JWA}, title = {Horizontal gene transfer of a cfiA element between two different Bacteroides species within a clinical specimen.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {30}, number = {4}, pages = {554-555}, doi = {10.1016/j.cmi.2023.12.022}, pmid = {38141819}, issn = {1469-0691}, mesh = {Humans ; *Bacteroides/genetics ; *Gene Transfer, Horizontal ; Anti-Bacterial Agents ; Meropenem ; Bacterial Proteins/genetics ; beta-Lactamases/genetics ; Microbial Sensitivity Tests ; }, }
@article {pmid38136990, year = {2023}, author = {Skoog, EJ and Fournier, GP and Bosak, T}, title = {Assessing the Influence of HGT on the Evolution of Stress Responses in Microbial Communities from Shark Bay, Western Australia.}, journal = {Genes}, volume = {14}, number = {12}, pages = {}, pmid = {38136990}, issn = {2073-4425}, support = {327126//Simons Foundation/ ; 344707//Simons Foundation/ ; }, mesh = {Western Australia ; *Bays ; Gene Transfer, Horizontal ; *Microbiota ; Metagenome ; }, abstract = {Pustular microbial mats in Shark Bay, Western Australia, are modern analogs of microbial systems that colonized peritidal environments before the evolution of complex life. To understand how these microbial communities evolved to grow and metabolize in the presence of various environmental stresses, the horizontal gene transfer (HGT) detection tool, MetaCHIP, was used to identify the horizontal transfer of genes related to stress response in 83 metagenome-assembled genomes from a Shark Bay pustular mat. Subsequently, maximum-likelihood phylogenies were constructed using these genes and their most closely related homologs from other environments in order to determine the likelihood of these HGT events occurring within the pustular mat. Phylogenies of several stress-related genes-including those involved in response to osmotic stress, oxidative stress and arsenic toxicity-indicate a potentially long history of HGT events and are consistent with these transfers occurring outside of modern pustular mats. The phylogeny of a particular osmoprotectant transport gene reveals relatively recent adaptations and suggests interactions between Planctomycetota and Myxococcota within these pustular mats. Overall, HGT phylogenies support a potentially broad distribution in the relative timing of the HGT events of stress-related genes and demonstrate ongoing microbial adaptations and evolution in these pustular mat communities.}, }
@article {pmid38136957, year = {2023}, author = {Qin, Y and Qu, B and Lee, B}, title = {Propidium Monoazide-Treated, Cell-Direct, Quantitative PCR for Detecting Viable Chloramphenicol-Resistant Escherichia coli and Corynebacterium glutamicum Cells.}, journal = {Genes}, volume = {14}, number = {12}, pages = {}, pmid = {38136957}, issn = {2073-4425}, support = {20014752//Ministry of Trade, Industry and Energy/ ; }, mesh = {*Escherichia coli/genetics ; *Corynebacterium glutamicum/genetics ; Real-Time Polymerase Chain Reaction/methods ; Ecosystem ; DNA ; }, abstract = {With the rapid development and commercialization of industrial genetically modified microorganisms (GMMs), public concerns regarding their potential effects are on the rise. It is imperative to promptly monitor the unintended release of viable GMMs into wastewater, the air, and the surrounding ecosystems to prevent the risk of horizontal gene transfer to native microorganisms. In this study, we have developed a method that combines propidium monoazide (PMA) with a dual-plex quantitative PCR (qPCR) approach based on TaqMan probes. This method targets the chloramphenicol-resistant gene (CmR) along with the endogenous genes D-1-deoxyxylulose 5-phosphate synthase (dxs) and chromosomal replication initiator protein (dnaA). It allows for the direct quantitative detection of viable genetically modified Escherichia coli and Corynebacterium glutamicum cells, eliminating the requirement for DNA isolation. The dual-plex qPCR targeting CmR/dxs and CmR/dnaA demonstrated excellent performance across various templates, including DNA, cultured cells, and PMA-treated cells. Repeatability and precision, defined as RSDr% and bias%, respectively, were calculated and found to fall within the acceptable limits specified by the European Network of GMO Laboratories (ENGL). Through PMA-qPCR assays, we determined the detection limits for viable chloramphenicol-resistant E. coli and C. glutamicum strains to be 20 and 51 cells, respectively, at a 95% confidence level. Notably, this method demonstrated superior sensitivity compared to Enzyme-Linked Immunosorbent Assay (ELISA), which has a detection limit exceeding 1000 viable cells for both GM bacterial strains. This approach offers the potential to accurately and efficiently detect viable cells of GMMs, providing a time-saving and cost-effective solution.}, }
@article {pmid38136751, year = {2023}, author = {Golikova, MV and Alieva, KN and Strukova, EN and Kondratieva, DA and Petrova, NF and Petrova, MA and Zinner, SH}, title = {Comparative Meropenem Pharmacodynamics and Emergence of Resistance against Carbapenem-Susceptible Non-Carbapenemase-Producing and Carbapenemase-Producing Enterobacterales: A Pharmacodynamic Study in a Hollow-Fiber Infection Model.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {12}, pages = {}, pmid = {38136751}, issn = {2079-6382}, support = {23-25-00525//Russian Science Foundation/ ; }, abstract = {Resistance to carbapenems has become a problem due to Klebsiella pneumoniae (K. pneumoniae), harboring carbapenemases. Among them, there are isolates that are recognized as carbapenem-susceptible; however, these carbapenemase-producing strains with low meropenem minimal inhibitory concentrations (MICs) may pose a threat to public health. We aimed to investigate the impact of the ability to produce carbapenemases by a bacterial isolate on the effectiveness of meropenem in the hollow-fiber infection model. K. pneumoniae and Escherichia coli (E. coli) strains with equal meropenem MICs but differing in their ability to produce carbapenemases were used in pharmacodynamic simulations with meropenem. In addition to standard MIC determination, we assessed the MICs against tested strains at high inoculum density to test if the inoculum effect occurs. According to pharmacodynamic data, the carbapenemase-producing strains were characterized with a relatively decreased meropenem effectiveness compared to non-producers. Meanwhile, the effect of meropenem perfectly correlated with the meropenem exposure expressed as the DOSE/MIC ratio when high-inoculum (HI) MICs but not standard-inoculum (SI) MICs were used for regression analysis. It could be concluded that meropenem-susceptible carbapenemase-producing strains may not respond to meropenem therapy; the antibiotic inoculum effect (IE) may have a prognostic value to reveal the meropenem-susceptible Enterobacterales that harbor carbapenemase genes.}, }
@article {pmid38135742, year = {2023}, author = {Fang, Z and Xu, M and Shen, S and Sun, W and Yu, Q and Wu, Q and Xiang, L and Weng, Q}, title = {Prediction and characterization of prophages of Stenotrophomonas maltophilia reveals a remarkable phylogenetic diversity of prophages.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {22941}, pmid = {38135742}, issn = {2045-2322}, support = {U1812401//Joint Fund of the National Natural Science Foundation of China and the Karst Science Research Center of Guizhou Province/ ; }, mesh = {*Prophages/genetics ; Phylogeny ; *Stenotrophomonas maltophilia/genetics ; Genomics ; Gene Transfer, Horizontal ; }, abstract = {Prophages, which enables bacterial hosts to acquire novel traits, and increase genetic variation and evolutionary innovation, are considered to be one of the greatest drivers of bacterial diversity and evolution. Stenotrophomonas maltophilia is widely distributed and one of the most important multidrug resistant bacteria in hospitals. However, the distribution and genetic diversity of S. maltophilia prophages have not been elucidated. In this study, putative prophages were predicted in S. maltophilia genomes by using virus prediction tools, and the genetic diversity and phylogeny of S. maltophilia and the prophages they harbor were further analyzed. A total of 356 prophage regions were predicted from 88 S. maltophilia genomes. Among them, 144 were intact prophages, but 77.09% of the intact prophages did not match any known phage sequences in the public database. The number of prophage carried by S. maltophilia is related to its host habitat and is an important factor affecting the size of the host genome, but it is not related to the genetic diversity of the prophage. The prediction of auxiliary genes encoded by prophage showed that antibiotic resistance genes was not predicted for any of the prophages except for one questionable prophage, while 53 virulence genes and 169 carbohydrate active enzymes were predicted from 11.24 and 44.1% prophages, respectively. Most of the prophages (72.29%) mediated horizontal gene transfer of S. maltophilia genome, but only involved in 6.25% of the horizontal gene transfer events. In addition, CRISPR prediction indicated 97.75% S. maltophilia strains contained the CRISPR-Cas system containing 818 spacer sequences. However, these spacer sequences did not match any known S. maltophilia phages, and only a few S. maltophilia prophages. Comparative genomic analysis revealed a highly conserved and syntenic organization with genomic rearrangement between the prophages and the known related S. maltophilia phages. Our results indicate a high prevalence and genetic diversity of prophages in the genome of S. maltophilia, as well as the presence of a large number of uncharacterized phages. It provides an important complement to understanding the diversity and biological characteristics of phages, as well as the interactions and evolution between bacteria and phages.}, }
@article {pmid38135225, year = {2024}, author = {Wang, M and Wang, C and Yang, J and Liu, X and Xie, B and Ren, P and Kong, X and Fu, Y}, title = {Biochar induces different responses of intracellular and extracellular antibiotic resistance genes and suppresses horizontal transfer during lincomycin fermentation dregs composting.}, journal = {Bioresource technology}, volume = {394}, number = {}, pages = {130227}, doi = {10.1016/j.biortech.2023.130227}, pmid = {38135225}, issn = {1873-2976}, mesh = {*Anti-Bacterial Agents/pharmacology ; Lincomycin/pharmacology ; *Composting ; Fermentation ; Escherichia coli/genetics ; Genes, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; *Charcoal ; }, abstract = {This study aims to indicate the influence of biochar on extracellular and intracellular ARGs (e/iARGs) variation and proliferation during lincomycin fermentation dregs (LFDs) compost. Biochar addition made iARGs keep reducing but eARGs increase to the maximum at the middle thermophilic phase and reduce at the end of the compost. Compared to control 3.15-log and 5.42-log reduction of iARGs and eARGs were observed, respectively. Biochar addition, bacterial community, and MGEs were the major contributors to iARGs and eARGs removal, with the contribution percentages of 38.4%, 31.0%, 23.7%, and 27.2%, 29.1%, and 34.9%, respectively. Moreover, biochar significantly inhibited eARGs transformation and RP4 plasmid conjugative transfer among E. coli DH5α and Pseudomonas aeruginosa HLS-6. The underlying mechanism involved in broken cell membranes of bacteria, and altered expression of oxidative stress genes and save our souls (SOS) response-related genes. The results indicated that biochar addition in composting could limit the dissemination of ARGs.}, }
@article {pmid38135177, year = {2024}, author = {Mukherjee, A and Kizziah, JL and Hawkins, NC and Nasef, MO and Parker, LK and Dokland, T}, title = {Structure of the Portal Complex from Staphylococcus aureus Pathogenicity Island 1 Transducing Particles In Situ and In Isolation.}, journal = {Journal of molecular biology}, volume = {436}, number = {4}, pages = {168415}, pmid = {38135177}, issn = {1089-8638}, support = {P30 CA013148/CA/NCI NIH HHS/United States ; R01 AI083255/AI/NIAID NIH HHS/United States ; S10 OD024978/OD/NIH HHS/United States ; U24 GM116789/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Capsid Proteins/chemistry ; Cryoelectron Microscopy ; *Genomic Islands ; *Staphylococcus aureus/genetics/pathogenicity/virology ; *Staphylococcus Phages/genetics ; Virulence Factors/genetics ; Transduction, Genetic ; DNA Packaging ; Nucleic Acid Conformation ; }, abstract = {Staphylococcus aureus is an important human pathogen, and the prevalence of antibiotic resistance is a major public health concern. The evolution of pathogenicity and resistance in S. aureus often involves acquisition of mobile genetic elements (MGEs). Bacteriophages play an especially important role, since transduction represents the main mechanism for horizontal gene transfer. S. aureus pathogenicity islands (SaPIs), including SaPI1, are MGEs that carry genes encoding virulence factors, and are mobilized at high frequency through interactions with specific "helper" bacteriophages, such as 80α, leading to packaging of the SaPI genomes into virions made from structural proteins supplied by the helper. Among these structural proteins is the portal protein, which forms a ring-like portal at a fivefold vertex of the capsid, through which the DNA is packaged during virion assembly and ejected upon infection of the host. We have used high-resolution cryo-electron microscopy to determine structures of the S. aureus bacteriophage 80α portal itself, produced by overexpression, and in situ in the empty and full SaPI1 virions, and show how the portal interacts with the capsid. These structures provide a basis for understanding portal and capsid assembly and the conformational changes that occur upon DNA packaging and ejection.}, }
@article {pmid38134694, year = {2024}, author = {Fang, Y and Chen, C and Cui, B and Zhou, D}, title = {Nanoscale zero-valent iron alleviate antibiotic resistance risk during managed aquifer recharge (MAR) by regulating denitrifying bacterial network.}, journal = {Journal of hazardous materials}, volume = {465}, number = {}, pages = {133238}, doi = {10.1016/j.jhazmat.2023.133238}, pmid = {38134694}, issn = {1873-3336}, mesh = {Iron ; Bacteria ; Anti-Bacterial Agents ; *Groundwater ; Drug Resistance, Microbial ; *Water Pollutants, Chemical ; }, abstract = {The frequent occurrence of antibiotics in reclaimed water is concerning, in the case of managed aquifer recharge (MAR), it inevitably hinders further water purification and accelerates the evolutionary resistance in indigenous bacteria. In this study, we constructed two column reactors and nanoscale zero-valent iron (nZVI) amendment was applied for its effects on water quality variation, microbial community succession, and antibiotic resistance genes (ARGs) dissemination, deciphered the underlying mechanism of resistance risk reduction. Results showed that nZVI was oxidized to iron oxides in the sediment column, and total effluent iron concentration was within permissible limits. nZVI enhanced NO3[-]-N removal by 15.5% through enriching denitrifying bacteria and genes, whereas made no effects on oxacillin (OXA) removal. In addition, nZVI exhibited a pivotal impact on ARGs and plasmids decreasing. Network analysis elucidated that the diversity and richness of ARG host declined with nZVI amendment. Denitrifying bacteria play a key role in suppressing horizontal gene transfer (HGT). The underlying mechanisms of inhibited HGT included the downregulated SOS response, the inhibited Type-Ⅳ secretion system and the weakened driving force. This study afforded vital insights into ARG spread control, providing a reference for future applications of nZVI in MAR.}, }
@article {pmid38134686, year = {2024}, author = {Zhang, J and Lu, K and Zhu, L and Li, N and Lin, D and Cheng, Y and Wang, M}, title = {Inhibition of quorum sensing serves as an effective strategy to mitigate the risks of human bacterial pathogens in soil.}, journal = {Journal of hazardous materials}, volume = {465}, number = {}, pages = {133272}, doi = {10.1016/j.jhazmat.2023.133272}, pmid = {38134686}, issn = {1873-3336}, mesh = {Humans ; *Quorum Sensing ; *Biofilms ; Soil ; Bacteria ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The coexistence of antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and virulence factor genes (VFGs) in human bacterial pathogens (HBPs) increases their risks to ecological security and human health and no effective strategy is available. Herein, we demonstrated two typical quorum sensing (QS) interfering agents, 4-nitropyridine-N-oxide (4-NPO, a QS inhibitor) and Acylase Ⅰ (a quorum quenching (QQ) enzyme), effectively decreased the abundance of HBPs by 48.30% and 72.54%, respectively, which was accompanied by the reduction of VFGs, ARGs, and MGEs. The decrease in QS signals mediated by QS interfering agents disturbed bacterial communication and inhibited biofilm formation. More importantly, QS interfering agents reduced the intra-species and inter-species conjugation frequencies among bacteria, considerably inhibiting the dissemination of ARGs and VFGs via horizontal gene transfer. Furthermore, the QS interfering agents did not significantly affect the metabolic function of other nonpathogenic microorganisms in the soil. Collectively, our study provides an effective and eco-friendly strategy to mitigate the risks of HBPs in soil.}, }
@article {pmid38133813, year = {2023}, author = {Seethalakshmi, PS and Prabhakaran, A and Kiran, GS and Selvin, J}, title = {Genomic insights into plasmid-mediated antimicrobial resistance in the bacterium Bhargavaea beijingensis strain PS04.}, journal = {Archives of microbiology}, volume = {206}, number = {1}, pages = {33}, pmid = {38133813}, issn = {1432-072X}, support = {BT/IN/Indo-UK/AMR-Env/02/JS/2020-21//Department of Biotechnology, Ministry of Science and Technology, India/ ; }, mesh = {Plasmids/genetics ; *Drug Resistance, Bacterial/genetics ; Bacteria/genetics ; Genomics ; *Anti-Bacterial Agents/pharmacology ; Humans ; Planococcaceae ; Soil ; }, abstract = {The dissemination of antimicrobial-resistant bacteria through environment is a major health concern for public health. Pathogenic bacteria in natural environment can mediate the transfer of antimicrobial-resistant genes via horizontal gene transfer to naturally occurring bacteria in the soil. Bhargavaea beijingensis is a Gram-negative bacterium that is commonly found in soil and water. In recent years, there has been an emergence of antibiotic-resistant strains of environmental bacteria, which pose a significant threat to human health. One mechanism of antibiotic resistance in bacteria is through the acquisition of plasmids, which can carry genes that confer resistance to various antibiotics. In this study, a novel plasmid of repUS12 replicon type was identified in the strain PS04 of B. beijingensis, which carried the ermT and tet(L) genes, encoding resistance to macrolides, lincosamides, and tetracycline. The plasmid was found to be the first of its kind in B. beijingensis and was thought to have been acquired through horizontal gene transfer. The emergence of plasmid-mediated resistance in B. beijingensis highlights the need for continued surveillance and monitoring of antibiotic resistance in environmental bacteria.}, }
@article {pmid38133341, year = {2023}, author = {Zell, R and Groth, M and Selinka, L and Selinka, HC}, title = {Exploring the Diversity of Plant-Associated Viruses and Related Viruses in Riverine Freshwater Samples Collected in Berlin, Germany.}, journal = {Pathogens (Basel, Switzerland)}, volume = {12}, number = {12}, pages = {}, pmid = {38133341}, issn = {2076-0817}, abstract = {Plant-infecting RNA viruses from 30 families and floating genera, as well as a great number of uncultured as yet-unclassified plant-associated viruses have been described. Even so, the plant RNA virosphere is still underexplored. RNA extracted from enriched virus particles of 50 L water samples from the Teltow Canal and the Havel River in Berlin, Germany, was sequenced using Illumina next-generation sequencing. Sequences were searched for plant viruses with BLAST and DIAMOND. Phylogenetic analyses were conducted with IQ-TREE 2. Altogether, 647 virus sequences greater than 1 kb were detected and further analyzed. These data revealed the presence of accepted and novel viruses related to Albetovirus, Alphaflexiviridae, Aspiviridae, Bromoviridae, Endornaviridae, Partitiviridae, Potyviridae, Solemoviridae, Tombusviridae and Virgaviridae. The vast majority of the sequences were novel and could not be taxonomically assigned. Several tombus- and endorna-like viruses make use of alternative translation tables that suggest unicellular green algae, ciliates, or diplomonades as their hosts. The identification of 27 albeto-like satellite viruses increases available sequence data five-fold. Sixteen new poty-like viruses align with other poty-like viruses in a link that combines the Astroviridae and Potyviridae families. Further, the identification of viruses with peptidase A6-like and peptidase A21-like capsid proteins suggests horizontal gene transfer in the evolution of these viruses.}, }
@article {pmid38132959, year = {2023}, author = {Entfellner, E and Baumann, KBL and Edwards, C and Kurmayer, R}, title = {High Structural Diversity of Aeruginosins in Bloom-Forming Cyanobacteria of the Genus Planktothrix as a Consequence of Multiple Recombination Events.}, journal = {Marine drugs}, volume = {21}, number = {12}, pages = {}, pmid = {38132959}, issn = {1660-3397}, support = {P 32193/FWF_/Austrian Science Fund FWF/Austria ; P32193//FWF Austrian Science Fund/ ; DOC [Doktorand/inn/enprogramm]//Austrian Academy of Sciences/ ; P24070//FWF Austrian Science Fund/ ; }, mesh = {Planktothrix ; *Cyanobacteria/genetics ; Microcystins/genetics ; *Microcystis ; Fresh Water ; Recombination, Genetic ; }, abstract = {Many compounds produced by cyanobacteria act as serine protease inhibitors, such as the tetrapeptides aeruginosins (Aer), which are found widely distributed. The structural diversity of Aer is intriguingly high. However, the genetic basis of this remains elusive. In this study, we explored the genetic basis of Aer synthesis among the filamentous cyanobacteria Planktothrix spp. In total, 124 strains, isolated from diverse freshwater waterbodies, have been compared regarding variability within Aer biosynthesis genes and the consequences for structural diversity. The high structural variability could be explained by various recombination processes affecting Aer synthesis, above all, the acquisition of accessory enzymes involved in post synthesis modification of the Aer peptide (e.g., halogenases, glycosyltransferases, sulfotransferases) as well as a large-range recombination of Aer biosynthesis genes, probably transferred from the bloom-forming cyanobacterium Microcystis. The Aer structural composition differed between evolutionary Planktothrix lineages, adapted to either shallow or deep waterbodies of the temperate climatic zone. Thus, for the first time among bloom-forming cyanobacteria, chemical diversification of a peptide family related to eco-evolutionary diversification has been described. It is concluded that various Aer peptides resulting from the recombination event act in chemical defense, possibly as a replacement for microcystins.}, }
@article {pmid38131669, year = {2024}, author = {Hofstaedter, CE and Chandler, CE and Met, CM and Gillespie, JJ and Harro, JM and Goodlett, DR and Rasko, DA and Ernst, RK}, title = {Divergent Pseudomonas aeruginosa LpxO enzymes perform site-specific lipid A 2-hydroxylation.}, journal = {mBio}, volume = {15}, number = {2}, pages = {e0282323}, pmid = {38131669}, issn = {2150-7511}, support = {R01 AI104895/AI/NIAID NIH HHS/United States ; U19 AI110820/AI/NIAID NIH HHS/United States ; R21 AI146773/AI/NIAID NIH HHS/United States ; T32 AI162579/AI/NIAID NIH HHS/United States ; R21 AI156762/AI/NIAID NIH HHS/United States ; R01 AI147314/AI/NIAID NIH HHS/United States ; R21 AI166832/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Animals ; Mice ; Pseudomonas aeruginosa/metabolism ; Lipid A/metabolism ; Persistent Infection ; Laurates/metabolism ; Hydroxylation ; *Cystic Fibrosis/microbiology ; *Pseudomonas Infections/microbiology ; *Dioxygenases/metabolism ; }, abstract = {Pseudomonas aeruginosa can survive in a myriad of environments, partially due to modifications of its lipid A, the membrane anchor of lipopolysaccharide. We previously demonstrated that divergent late acyltransferase paralogs, HtrB1 and HtrB2, add acyloxyacyl laurate to lipid A 2- and 2'-acyl chains, respectively. The genome of P. aeruginosa also has genes which encode two dioxygenase enzymes, LpxO1 and LpxO2, that individually hydroxylate a specific secondary laurate. LpxO1 acts on the 2'-acyloxyacyl laurate (added by HtrB2), whereas LpxO2 acts on the 2-acyloxyacyl laurate (added by HtrB1) in a site-specific manner. Furthermore, while both enzyme pairs are evolutionarily linked, phylogenomic analysis suggests the LpxO1/HtrB2 enzyme pair as being of ancestral origin, present throughout the Pseudomonas lineage, whereas the LpxO2/HtrB1 enzyme pair likely arose via horizontal gene transfer and has been retained in P. aeruginosa over time. Using a murine pulmonary infection model, we showed that both LpxO1 and LpxO2 enzymes are functional in vivo, as direct analysis of in vivo lipid A structure from bronchoalveolar lavage fluid revealed 2-hydroxylated lipid A. Gene expression analysis reveals increased lpxO2 but unchanged lpxO1 expression in vivo, suggesting differential regulation of these enzymes during infection. We also demonstrate that loss-of-function mutations arise in lpxO1 and lpxO2 during chronic lung infection in people with cystic fibrosis (CF), indicating a potential role for pathogenesis and airway adaptation. Collectively, our study characterizes lipid A 2-hydroxylation during P. aeruginosa airway infection that is regulated by two distinct lipid A dioxygenase enzymes.IMPORTANCEPseudomonas aeruginosa is an opportunistic pathogen that causes severe infection in hospitalized and chronically ill individuals. During infection, P. aeruginosa undergoes adaptive changes to evade host defenses and therapeutic interventions, increasing mortality and morbidity. Lipid A structural alteration is one such change that P. aeruginosa isolates undergo during chronic lung infection in CF. Investigating genetic drivers of this lipid A structural variation is crucial in understanding P. aeruginosa adaptation during infection. Here, we describe two lipid A dioxygenases with acyl-chain site specificity, each with different evolutionary origins. Further, we show that loss of function in these enzymes occurs in CF clinical isolates, suggesting a potential pathoadaptive phenotype. Studying these bacterial adaptations provides insight into selection pressures of the CF airway on P. aeruginosa phenotypes that persist during chronic infection. Understanding these adaptive changes may ultimately provide clinicians better control over bacterial populations during chronic infection.}, }
@article {pmid38128981, year = {2024}, author = {Carusi, J and Kabuki, DY and de Seixas Pereira, PM and Cabral, L}, title = {Aeromonas spp. in drinking water and food: Occurrence, virulence potential and antimicrobial resistance.}, journal = {Food research international (Ottawa, Ont.)}, volume = {175}, number = {}, pages = {113710}, doi = {10.1016/j.foodres.2023.113710}, pmid = {38128981}, issn = {1873-7145}, mesh = {Animals ; Humans ; *Aeromonas ; Virulence/genetics ; Anti-Bacterial Agents/pharmacology ; *Drinking Water ; Base Composition ; Drug Resistance, Bacterial ; Phylogeny ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; *Anti-Infective Agents ; }, abstract = {Aeromonas sp. is a Gram-negative, non-spore-forming, rod-shaped, oxidase-positive, facultative anaerobic bacterium and a natural contaminant found in aquatic environments. Some species can invade, colonize, and damage host cells due to the presence of virulence factors, such as flagella, elastase, hemolysins, aerolysins, adhesins, enterotoxins, phospholipases and lipases, that lead to pathogenic activities. Consequently, can cause many health disorders that range from gastrointestinal problems, enteric infections, and ulcers to hemorrhagic septicemia. Aeromonas has been isolated and identified from a variety of sources, including drinking water and ready-to-eat foods (fish, meat, fresh vegetables, dairy products, and others). Some species of this opportunistic pathogen are resistant to several commercial antibiotics, including some used as a last resort for treatment, which represents a major challenge in the clinical segment. Antimicrobial resistance can be attributed to the indiscriminate use of antibiotics by society in aquaculture and horticulture. In addition, antibiotic resistance is attributed to plasmid transfer between microorganisms and horizontal gene transfer. This review aimed to (i) verify the occurrence of Aeromonas species in water and food intended for human consumption; (ii) identify the methods used to detect Aeromonas species; (iii) report on the virulence genes carried by different species; and (iv) report on the antimicrobial resistance of this genus in the last 5 years of research. Additionally, we present the existence of Aeromonas spp. resistant to antimicrobials in food and drinking water represents a potential threat to public health.}, }
@article {pmid38124028, year = {2023}, author = {Naidoo, N and Zishiri, OT}, title = {Comparative genomics analysis and characterization of Shiga toxin-producing Escherichia coli O157:H7 strains reveal virulence genes, resistance genes, prophages and plasmids.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {791}, pmid = {38124028}, issn = {1471-2164}, mesh = {Virulence/genetics ; *Prophages/genetics ; Plasmids/genetics ; *Escherichia coli O157/genetics ; Genomics ; }, abstract = {Escherichia coli O157:H7 is a foodborne pathogen that has been linked to global disease outbreaks. These diseases include hemorrhagic colitis and hemolytic uremic syndrome. It is vital to know the features that make this strain pathogenic to understand the development of disease outbreaks. In the current study, a comparative genomic analysis was carried out to determine the presence of structural and functional features of O157:H7 strains obtained from 115 National Center for Biotechnology Information database. These strains of interest were analysed in the following programs: BLAST Ring Image Generator, PlasmidFinder, ResFinder, VirulenceFinder, IslandViewer 4 and PHASTER. Five strains (ECP19-198, ECP19-798, F7508, F8952, H2495) demonstrated a great homology with Sakai because of a few regions missing. Five resistant genes were identified, however, Macrolide-associated resistance gene mdf(A) was commonly found in all genomes. Majority of the strains (97%) were positive for 15 of the virulent genes (espA, espB, espF, espJ, gad, chuA, eae, iss, nleA, nleB, nleC, ompT, tccP, terC and tir). The plasmid analysis demonstrated that the IncF group was the most prevalent in the strains analysed. The prophage and genomic island analysis showed a distribution of bacteriophages and genomic islands respectively. The results indicated that structural and functional features of the many O157:H7 strains differ and may be a result of obtaining mobile genetic elements via horizontal gene transfer. Understanding the evolution of O157:H7 strains pathogenicity in terms of their structural and functional features will enable the development of detection and control of transmission strategies.}, }
@article {pmid38114770, year = {2023}, author = {Toh, SI and Elaine Keisha, J and Wang, YL and Pan, YC and Jhu, YH and Hsiao, PY and Liao, WT and Chen, PY and Ko, TM and Chang, CY}, title = {Discovery and characterization of genes conferring natural resistance to the antituberculosis antibiotic capreomycin.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {1282}, pmid = {38114770}, issn = {2399-3642}, support = {111-2113-M-002-025//Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)/ ; }, mesh = {*Capreomycin/pharmacology ; *Anti-Bacterial Agents/pharmacology/metabolism ; Bacteria/genetics ; Genes, Bacterial ; Immunity, Innate ; }, abstract = {Metagenomic-based studies have predicted an extraordinary number of potential antibiotic-resistance genes (ARGs). These ARGs are hidden in various environmental bacteria and may become a latent crisis for antibiotic therapy via horizontal gene transfer. In this study, we focus on a resistance gene cph, which encodes a phosphotransferase (Cph) that confers resistance to the antituberculosis drug capreomycin (CMN). Sequence Similarity Network (SSN) analysis classified 353 Cph homologues into five major clusters, where the proteins in cluster I were found in a broad range of actinobacteria. We examine the function and antibiotics targeted by three putative resistance proteins in cluster I via biochemical and protein structural analysis. Our findings reveal that these three proteins in cluster I confer resistance to CMN, highlighting an important aspect of CMN resistance within this gene family. This study contributes towards understanding the sequence-structure-function relationships of the phosphorylation resistance genes that confer resistance to CMN.}, }
@article {pmid38113741, year = {2024}, author = {Zhang, B and Zhang, J and Wang, Y and Qu, J and Jiang, Z and Zhang, X and Tao, Y and Wang, Y and Kang, Z and Han, S and Zhang, J and Zhang, Y}, title = {Biodegradation of atrazine with biochar-mediated functional bacterial biofilm: Construction, characterization and mechanisms.}, journal = {Journal of hazardous materials}, volume = {465}, number = {}, pages = {133237}, doi = {10.1016/j.jhazmat.2023.133237}, pmid = {38113741}, issn = {1873-3336}, mesh = {*Atrazine/chemistry ; Biodegradation, Environmental ; *Soil Pollutants/metabolism ; *Herbicides/metabolism ; Soil/chemistry ; Bacteria/metabolism ; Biofilms ; Soil Microbiology ; *Charcoal ; }, abstract = {The abuse and residue of herbicides in the black soil area had seriously affected the soil structure, function and crop growth, posing severe threats to agricultural soil environment and public health. Given the limitation of routine microbial remediation, innovative and eco-friendly functional bacterial biofilm which could adapt under adverse conditions was developed on the biochar to investigate its enhanced bioremediation and metabolic characteristics of typical herbicide atrazine. Results revealed that the atrazine degrading strain Acinetobacter lwoffii had competitive advantage in soil indigenous microorganisms and formed dense biofilms on the biochar which was beneficial to cell viability maintenance and aggregations. Metatranscriptomics and RT-qPCR analysis demonstrated that the biochar-mediated biofilm improved the frequency of intercellular communications through quorum sensing and two-component signal regulation systems, and enhanced the atrazine biodegradation efficiency through horizontal gene transfer in co-metabolism mode, providing important scientific basis for the biological remediation of farmland soil non-point source pollution.}, }
@article {pmid38112751, year = {2023}, author = {Gould, AL and Henderson, JB}, title = {Comparative genomics of symbiotic Photobacterium using highly contiguous genome assemblies from long read sequences.}, journal = {Microbial genomics}, volume = {9}, number = {12}, pages = {}, pmid = {38112751}, issn = {2057-5858}, support = {DP5 OD026405/OD/NIH HHS/United States ; }, mesh = {Animals ; *Photobacterium/genetics ; *Symbiosis ; DNA, Bacterial/genetics ; Genomics ; Genome, Bacterial ; }, abstract = {This study presents the assembly and comparative genomic analysis of luminous Photobacterium strains isolated from the light organs of 12 fish species using Oxford Nanopore Technologies (ONT) sequencing. The majority of assemblies achieved chromosome-level continuity, consisting of one large (>3 Mbp) and one small (~1.5 Mbp) contig, with near complete BUSCO scores along with varying plasmid sequences. Leveraging this dataset, this study significantly expanded the available genomes for P. leiognathi and its subspecies P. 'mandapamensis', enabling a comparative genomic analysis between the two lineages. An analysis of the large and small chromosomes unveiled distinct patterns of core and accessory genes, with a larger fraction of the core genes residing on the large chromosome, supporting the hypothesis of secondary chromosome evolution from megaplasmids in Vibrionaceae. In addition, we discovered a proposed new species, Photobacterium acropomis sp. nov., isolated from an acropomatid host, with an average nucleotide identify (ANI) of 93 % compared to the P. leiognathi and P. 'mandapamensis' strains. A comparison of the P. leiognathi and P. 'mandapamensis' lineages revealed minimal differences in gene content, yet highlighted the former's larger genome size and potential for horizontal gene transfer. An investigation of the lux-rib operon, responsible for light production, indicated congruence between the presence of luxF and host family, challenging its role in differentiating P. 'mandapamensis' from P. leiognathi. Further insights were derived from the identification of metabolic differences, such as the presence of the NADH:quinone oxidoreductase respiratory complex I in P. leiognathi as well as variations in the type II secretion system (T2S) genes between the lineages, potentially impacting protein secretion and symbiosis. In summary, this study advances our understanding of Photobacterium genome evolution, highlighting subtle differences between closely related lineages, specifically P. leiognathi and P. 'mandapamensis'. These findings highlight the benefit of long read sequencing for bacterial genome assembly and pangenome analysis and provide a foundation for exploring early bacterial speciation processes of these facultative light organ symbionts.}, }
@article {pmid38112433, year = {2024}, author = {Ding, Y and Jiang, X and Wu, J and Wang, Y and Zhao, L and Pan, Y and Xi, Y and Zhao, G and Li, Z and Zhang, L}, title = {Synergistic horizontal transfer of antibiotic resistance genes and transposons in the infant gut microbial genome.}, journal = {mSphere}, volume = {9}, number = {1}, pages = {e0060823}, pmid = {38112433}, issn = {2379-5042}, support = {Grant No. 82172320//MOST | National Natural Science Foundation of China (NSFC)/ ; Grant No. 2022M711915//China Postdoctoral Science Foundation (China Postdoctoral Foundation Project)/ ; Grant No. ZR2022QC169//Shandong Provincial Natural Science Foundation/ ; //TaiShan Industrial Experts Program tscy20190612/ ; //Shandong University Outstanding Young Scholars Program/ ; }, mesh = {Infant ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Escherichia coli/genetics ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Genome, Microbial ; }, abstract = {Transposons, plasmids, bacteriophages, and other mobile genetic elements facilitate horizontal gene transfer in the gut microbiota, allowing some pathogenic bacteria to acquire antibiotic resistance genes (ARGs). Currently, the relationship between specific ARGs and specific transposons in the comprehensive infant gut microbiome has not been elucidated. In this study, ARGs and transposons were annotated from the Unified Human Gastrointestinal Genome (UHGG) and the Early-Life Gut Genomes (ELGG). Association rules mining was used to explore the association between specific ARGs and specific transposons in UHGG, and the robustness of the association rules was validated using the external database in ELGG. Our results suggested that ARGs and transposons were more likely to be relevant in infant gut microbiota compared to adult gut microbiota, and nine robust association rules were identified, among which Klebsiella pneumoniae, Enterobacter hormaechei_A, and Escherichia coli_D played important roles in this association phenomenon. The emphasis of this study is to investigate the synergistic transfer of specific ARGs and specific transposons in the infant gut microbiota, which can contribute to the study of microbial pathogenesis and the ARG dissemination dynamics.IMPORTANCEThe transfer of transposons carrying antibiotic resistance genes (ARGs) among microorganisms accelerates antibiotic resistance dissemination among infant gut microbiota. Nonetheless, it is unclear what the relationship between specific ARGs and specific transposons within the infant gut microbiota. K. pneumoniae, E. hormaechei_A, and E. coli_D were identified as key players in the nine robust association rules we discovered. Meanwhile, we found that infant gut microorganisms were more susceptible to horizontal gene transfer events about specific ARGs and specific transposons than adult gut microorganisms. These discoveries could enhance the understanding of microbial pathogenesis and the ARG dissemination dynamics within the infant gut microbiota.}, }
@article {pmid38105949, year = {2024}, author = {Shropshire, JD and Conner, WR and Vanderpool, D and Hoffmann, AA and Turelli, M and Cooper, BS}, title = {Rapid host switching of Wolbachia and even more rapid turnover of their phages and incompatibility-causing loci.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38105949}, issn = {2692-8205}, support = {R35 GM124701/GM/NIGMS NIH HHS/United States ; }, abstract = {About half of all insect species carry maternally inherited Wolbachia alphaproteobacteria, making Wolbachia the most common endosymbionts known in nature. Often Wolbachia spread to high frequencies within populations due to cytoplasmic incompatibility (CI), a Wolbachia-induced sperm modification caused by prophage-associated genes (cifs) that kill embryos without Wolbachia. Several Wolbachia variants also block viruses, including wMel from Drosophila melanogaster when transinfected into the mosquito Aedes aegypti. CI enables the establishment and stable maintenance of pathogen-blocking wMel in natural Ae. aegypti populations. These transinfections are reducing dengue disease incidence on multiple continents. While it has long been known that closely related Wolbachia occupy distantly related hosts, the timing of Wolbachia host switching and molecular evolution has not been widely quantified. We provide a new, conservative calibration for Wolbachia chronograms based on examples of co-divergence of Wolbachia and their insect hosts. Synthesizing publicly available and new genomic data, we use our calibration to demonstrate that wMel-like variants separated by only about 370,000 years have naturally colonized holometabolous dipteran and hymenopteran insects that diverged approximately 350 million years ago. Data from Wolbachia variants closely related to those currently dominant in D. melanogaster and D. simulans illustrate that cifs are rapidly acquired and lost among Wolbachia genomes, on a time scale of 10[4]-10[5] years. This turnover occurs with and without the Wovirus prophages that contain them, with closely related cifs found in distantly related phages and distantly related cifs found in closely related phages. We present evidence for purifying selection on CI rescue function and on particular Cif protein domains. Our results quantify the tempo and mode of rapid host switching and horizontal gene transfer that underlie the spread and diversity of Wolbachia sampled from diverse host species. The wMel variants we highlight from hosts in different climates may offer new options for broadening Wolbachia-based biocontrol of diseases and pests.}, }
@article {pmid38101014, year = {2024}, author = {Zhang, S and Cui, L and Zhao, Y and Xie, H and Song, M and Wu, H and Hu, Z and Liang, S and Zhang, J}, title = {The critical role of microplastics in the fate and transformation of sulfamethoxazole and antibiotic resistance genes within vertical subsurface-flow constructed wetlands.}, journal = {Journal of hazardous materials}, volume = {465}, number = {}, pages = {133222}, doi = {10.1016/j.jhazmat.2023.133222}, pmid = {38101014}, issn = {1873-3336}, mesh = {*Anti-Bacterial Agents ; *Sulfamethoxazole ; Microplastics ; Plastics ; Wastewater ; Waste Disposal, Fluid/methods ; Wetlands ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; }, abstract = {Constructed wetlands (CWs) are reservoirs of microplastics (MPs) in the environment. However, knowledge about the impact of MPs on antibiotic removal and the fate of antibiotic resistance genes (ARGs) is limited. We focused on sulfamethoxazole (SMX) as a representative compound to examine the effects of MPs on SMX removal and the proliferation and dissemination of two SMX-related ARGs (sul1 and sul2) in vertical subsurface-flow CW (VFCW) microcosm. The presence of MPs in the substrate was found to enhance the proliferation of microorganisms owing to the large specific surface area of the MPs and the release of dissolved organic carbon (DOC) on MP surfaces, which resulted in a high SMX removal ranging from 97.80 % to 99.80 %. However, the presence of MPs promoted microbial interactions and the horizontal gene transfer (HGT) of ARGs, which led to a significant increase in the abundances of sul1 and sul2 of 68.47 % and 17.20 %, respectively. It is thus imperative to implement rigorous monitoring strategies for MPs to mitigate their potential ecological hazards.}, }
@article {pmid38099617, year = {2024}, author = {Schwarzerova, J and Zeman, M and Babak, V and Jureckova, K and Nykrynova, M and Varga, M and Weckwerth, W and Dolejska, M and Provaznik, V and Rychlik, I and Cejkova, D}, title = {Detecting horizontal gene transfer among microbiota: an innovative pipeline for identifying co-shared genes within the mobilome through advanced comparative analysis.}, journal = {Microbiology spectrum}, volume = {12}, number = {1}, pages = {e0196423}, pmid = {38099617}, issn = {2165-0497}, support = {GA22-16786S//Czech Science Foundation/ ; 206/2023/FVHE//Internal Grant Agency of the University of Veterinary Sciences Brno/ ; }, mesh = {Animals ; Swine ; *Gene Transfer, Horizontal ; *Microbiota ; Genome, Bacterial ; Anti-Bacterial Agents ; Bacteria/genetics ; Genes, Bacterial ; }, abstract = {Horizontal gene transfer (HGT) is a key driver in the evolution of bacterial genomes. The acquisition of genes mediated by HGT may enable bacteria to adapt to ever-changing environmental conditions. Long-term application of antibiotics in intensive agriculture is associated with the dissemination of antibiotic resistance genes among bacteria with the consequences causing public health concern. Commensal farm-animal-associated gut microbiota are considered the reservoir of the resistance genes. Therefore, in this study, we identified known and not-yet characterized mobilized genes originating from chicken and porcine fecal samples using our innovative pipeline followed by network analysis to provide appropriate visualization to support proper interpretation.}, }
@article {pmid38098417, year = {2023}, author = {Chen, R and Cheng, JH and Tang, XY}, title = {[Characteristics of Antibiotic Resistance Genes Distribution in Different Types of Agricultural Land Soils in Highly Cultivated Hilly Areas].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {44}, number = {12}, pages = {6947-6954}, doi = {10.13227/j.hjkx.202210109}, pmid = {38098417}, issn = {0250-3301}, mesh = {*Soil ; *Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Soil Microbiology ; Drug Resistance, Microbial/genetics ; Vegetables ; Manure ; }, abstract = {To characterize the distribution of antibiotic resistance genes(ARGs) in different types of agricultural soil in highly cultivated hilly areas, the abundance and diversity of ARGs in vegetable, orchard, and arable soils were analyzed in this study. The results showed that 70 ARGs and four mobile genetic elements(MGEs) were detected in all soil samples, with β-lactam cphA-01 being the most abundant genes in the agricultural soils. In vegetable and orchard soils, the main ARG subtypes were cphA-01 and cmx(A) genes, whereas the mexF and aacC genes were predominant in cropland soils. The relative abundance and diversity of soil ARGs showed that cropland<vegetable land<orchard, which was related to the nutrient conditions of different agricultural soils. Similarly, the relative abundance and diversity of MGEs were lowest in cropland, whereas their highest values were detected in vegetable and orchard soils, respectively. The significant positive correlation(P<0.05) between the abundance of soil MGEs and ARGs suggests that horizontal gene transfer may facilitate the spread of antibiotic resistance in the agricultural soils in highly cultivated hilly areas.}, }
@article {pmid38098126, year = {2023}, author = {Elsayed, SW and Elghaish, RA and Badr, E and Mouftah, SF and Saif, NA and Naga, IS and Shata, AH and Pascoe, B and Sheppard, SK and Elhadidy, M}, title = {Recombination-mediated dissemination of Methicillin-resistant S. aureus clonal complex 1 in the Egyptian health care settings.}, journal = {Annals of clinical microbiology and antimicrobials}, volume = {22}, number = {1}, pages = {109}, pmid = {38098126}, issn = {1476-0711}, mesh = {Humans ; *Methicillin-Resistant Staphylococcus aureus ; Methicillin Resistance/genetics ; Egypt/epidemiology ; Linezolid/pharmacology ; Pilot Projects ; *Staphylococcal Infections/epidemiology/drug therapy ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Clone Cells ; Recombination, Genetic ; Delivery of Health Care ; Microbial Sensitivity Tests ; }, abstract = {BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) is a rapidly evolving pathogen that is frequently associated with outbreaks and sustained epidemics. This study investigated the population structure, resistome, virulome, and the correlation between antimicrobial resistance determinants with phenotypic resistance profiles of 36 representative hospital-acquired MRSA isolates recovered from hospital settings in Egypt.<br><br>RESULTS: The community-acquired MRSA lineage, clonal complex 1 (CC1) was the most frequently detected clone, followed by three other globally disseminated clones, CC121, CC8, and CC22. Most isolates carried SCCmec type V and more than half of isolates demonstrated multi-drug resistant phenotypes. Resistance to linezolid, a last resort antibiotic for treating multidrug resistant MRSA, was observed in 11.11% of the isolates belonging to different genetic backgrounds. Virulome analysis indicated that most isolates harboured a large pool of virulence factors and toxins. Genes encoding aureolysin, gamma hemolysins, and serine proteases were the most frequently detected virulence encoding genes. CC1 was observed to have a high pool of AMR resistance determinants including cfr, qacA, and qacB genes, which are involved in linezolid and quaternary ammonium compounds resistance, as well as high content of virulence-related genes, including both of the PVL toxin genes. Molecular clock analysis revealed that CC1 had the greatest frequency of recombination (compared to mutation) among the four major clones, supporting the role of horizontal gene transfer in modulating AMR and hypervirulence in this clone.<br><br>CONCLUSIONS: This pilot study provided evidence on the dissemination success of CA-MRSA clone CC1 among Egyptian hospitals. Co-detection of multiple AMR and virulence genes in this lineage pose a broad public health risk, with implications for successful treatment. The results of this study, together with other surveillance studies in Egypt, should be used to develop strategies for controlling MRSA infections in Egyptian health-care settings.}, }
@article {pmid38095456, year = {2024}, author = {Røder, HL and Christidi, E and Amador, CI and Music, S and Olesen, AK and Svensson, B and Madsen, JS and Herschend, J and Kreft, J-U and Burmølle, M}, title = {Flagellar interference with plasmid uptake in biofilms: a joint experimental and modeling study.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {1}, pages = {e0151023}, pmid = {38095456}, issn = {1098-5336}, support = {11-106246//Independent Research Fund Denmark/ ; 10098, 35906//Villum Fonden (Villum Foundation)/ ; N62909-18-2179//DOD | USN | ONR | Office of Naval Research Global (ONRG)/ ; 34434//Villum Fonden (Villum Foundation)/ ; //Darwin Trust of Edinburgh (Darwin Trust)/ ; NC/R001707/1/NC3RS_/National Centre for the Replacement, Refinement and Reduction of Animals in Research/United Kingdom ; //Velux Fonden (Velux Foundations)/ ; NC/K000683/1/NC3RS_/National Centre for the Replacement, Refinement and Reduction of Animals in Research/United Kingdom ; }, mesh = {Plasmids ; *Xanthomonas/genetics ; Biofilms ; Drug Resistance, Microbial ; Gene Transfer, Horizontal ; Conjugation, Genetic ; *Pseudomonas putida/genetics ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Plasmid conjugation is a key facilitator of horizontal gene transfer (HGT), and plasmids encoding antibiotic resistance drive the increasing prevalence of antibiotic resistance. In natural, engineered, and clinical environments, bacteria often grow in protective biofilms. Therefore, a better understanding of plasmid transfer in biofilms is needed. Our aim was to investigate plasmid transfer in a biofilm-adapted wrinkly colony mutant of Xanthomonas retroflexus (XRw) with enhanced matrix production and reduced motility. We found that XRw biofilms had an increased uptake of the broad host-range IncP-1ϵ plasmid pKJK5 compared to the wild type (WT). Proteomics revealed fewer flagellar-associated proteins in XRw, suggesting that flagella were responsible for reducing plasmid uptake. This was confirmed by the higher plasmid uptake of non-flagellated fliM mutants of the X. retroflexus wrinkly mutant as well as the wild type. Moreover, testing several flagellar mutants of Pseudomonas putida suggested that the flagellar effect was more general. We identified seven mechanisms with the potential to explain the flagellar effect and simulated them in an individual-based model. Two mechanisms could thus be eliminated (increased distances between cells and increased lag times due to flagella). Another mechanism identified as viable in the modeling was eliminated by further experiments. The possibility of steric hindrance of pilus movement and binding by flagella, reducing the frequency of contact and thus plasmid uptake, proved viable, and the three other viable mechanisms had a reduced probability of plasmid transfer in common. Our findings highlight the important yet complex effects of flagella during bacterial conjugation in biofilms.IMPORTANCEBiofilms are the dominant form of microbial life and bacteria living in biofilms are markedly different from their planktonic counterparts, yet the impact of the biofilm lifestyle on horizontal gene transfer (HGT) is still poorly understood. Horizontal gene transfer by conjugative plasmids is a major driver in bacterial evolution and adaptation, as exemplified by the troubling spread of antibiotic resistance. To either limit or promote plasmid prevalence and dissemination, we need a better understanding of plasmid transfer between bacterial cells, especially in biofilms. Here, we identified a new factor impacting the transfer of plasmids, flagella, which are required for many types of bacterial motility. We show that their absence or altered activity can lead to enhanced plasmid uptake in two bacterial species, Xanthomonas retroflexus and Pseudomonas putida. Moreover, we demonstrate the utility of mathematical modeling to eliminate hypothetical mechanisms.}, }
@article {pmid38088550, year = {2024}, author = {Salinas, L and Cárdenas, P and Graham, JP and Trueba, G}, title = {IS26 drives the dissemination of bla CTX-M genes in an Ecuadorian community.}, journal = {Microbiology spectrum}, volume = {12}, number = {1}, pages = {e0250423}, pmid = {38088550}, issn = {2165-0497}, support = {R01 AI135118/AI/NIAID NIH HHS/United States ; R01 AI167989/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Child ; Humans ; *Escherichia coli Infections/epidemiology ; Plasmids/genetics ; Ecuador ; Escherichia coli/genetics ; *Anti-Infective Agents ; Animals, Domestic/genetics ; beta-Lactamases/genetics ; Microbial Sensitivity Tests ; }, abstract = {The horizontal gene transfer events are the major contributors to the current spread of CTX-M-encoding genes, the most common extended-spectrum β-lactamase (ESBL), and many clinically crucial antimicrobial resistance (AMR) genes. This study presents evidence of the critical role of IS26 transposable element for the mobility of bla CTX-M gene among Escherichia coli isolates from children and domestic animals in the community. We suggest that the nucleotide sequences of IS26-bla CTX-M could be used to study bla CTX-M transmission between humans, domestic animals, and the environment, because understanding of the dissemination patterns of AMR genes is critical to implement effective measures to slow down the dissemination of these clinically important genes.}, }
@article {pmid38086386, year = {2023}, author = {Amrofell, MB and Rengarajan, S and Vo, ST and Ramirez Tovar, ES and LoBello, L and Dantas, G and Moon, TS}, title = {Engineering E. coli strains using antibiotic-resistance-gene-free plasmids.}, journal = {Cell reports methods}, volume = {3}, number = {12}, pages = {100669}, pmid = {38086386}, issn = {2667-2375}, support = {R01 AT009741/AT/NCCIH NIH HHS/United States ; }, mesh = {Animals ; Mice ; *Anti-Bacterial Agents/pharmacology ; *Escherichia coli/genetics ; Plasmids/genetics ; Drug Resistance, Microbial/genetics ; Cloning, Molecular ; }, abstract = {We created a generalizable pipeline for antibiotic-resistance-gene-free plasmid (ARGFP)-based cloning using a dual auxotrophic- and essential-gene-based selection strategy. We use auxotrophic selection to construct plasmids in engineered E. coli DH10B cloning strains and both auxotrophic- and essential-gene-based selection to (1) select for recombinant strains and (2) maintain a plasmid in E. coli Nissle 1917, a common chassis for engineered probiotic applications, and E. coli MG1655, the laboratory "wild-type" E. coli strain. We show that our approach has comparable efficiency to that of antibiotic-resistance-gene-based cloning. We also show that the double-knockout Nissle and MG1655 strains are simple to transform with plasmids of interest. Notably, we show that the engineered Nissle strains are amenable to long-term plasmid maintenance in repeated culturing as well as in the mouse gut, demonstrating the potential for broad applications while minimizing the risk of antibiotic resistance spread via horizontal gene transfer.}, }
@article {pmid38085089, year = {2024}, author = {Zhang, T and Mu, Y and Gao, Y and Tang, Y and Mao, S and Liu, J}, title = {Fecal microbial gene transfer contributes to the high-grain diet-induced augmentation of aminoglycoside resistance in dairy cattle.}, journal = {mSystems}, volume = {9}, number = {1}, pages = {e0081023}, pmid = {38085089}, issn = {2379-5077}, support = {32372904//MOST | National Natural Science Foundation of China (NSFC)/ ; RENCAI2023008//MOST | NSFC | National Science Fund for Distinguished Young Scholars (National Science Foundation for Distinguished Young Scholars)/ ; BK20210402//JST | Natural Science Foundation of Jiangsu Province (Jiangsu Natural Science Foundation)/ ; }, mesh = {Animals ; Cattle ; Female ; *Aminoglycosides/pharmacology ; Anti-Bacterial Agents/pharmacology ; Diet/veterinary ; Genes, Microbial ; *Lactation ; }, abstract = {A high-grain (HG) diet can rapidly lower the rumen pH and thus modify the gastrointestinal microbiome in dairy cattle. Although the prevalence of antibiotic resistance is strongly linked with the gut microbiome, the influences of HG diet on animals' gut resistome remain largely unexplored. Here, we examined the impact and mechanism of an HG diet on the fecal resistome in dairy cattle by metagenomically characterizing the gut microbiome. Eight lactating Holstein cattle were randomly allocated into two groups and fed either a conventional (CON) or HG diet for 3 weeks. The fecal microbiome and resistome were significantly altered in dairy cattle from HG, demonstrating an adaptive response that peaks at day 14 after the dietary transition. Importantly, we determined that feeding an HG diet specifically elevated the prevalence of resistance to aminoglycosides (0.11 vs 0.24 RPKG, P < 0.05). This diet-induced resistance increase is interrelated with the disproportional propagation of microbes in Lachnospiraceae, indicating a potential reservoir of aminoglycosides resistance. We further showed that the prevalence of acquired resistance genes was also modified by introducing a different diet, likely due to the augmented frequency of lateral gene transfer (LGT) in microbes (CON vs HG: 254 vs 287 taxa) such as Lachnospiraceae. Consequently, we present that diet transition is associated with fecal resistome modification in dairy cattle and an HG diet specifically enriched aminoglycosides resistance that is likely by stimulating microbial LGT.IMPORTANCEThe increasing prevalence of antimicrobial resistance is one of the most severe threats to public health, and developing novel mitigation strategies deserves our top priority. High-grain (HG) diet is commonly applied in dairy cattle to enhance animals' performance to produce more high-quality milk. We present that despite such benefits, the application of an HG diet is correlated with an elevated prevalence of resistance to aminoglycosides, and this is a combined effect of the expansion of antibiotic-resistant bacteria and increased frequency of lateral gene transfer in the fecal microbiome of dairy cattle. Our results provided new knowledge in a typically ignored area by showing an unexpected enrichment of antibiotic resistance under an HG diet. Importantly, our findings laid the foundation for designing potential dietary intervention strategies to lower the prevalence of antibiotic resistance in dairy production.}, }
@article {pmid38081548, year = {2024}, author = {Wan, S and Zhou, A and Chen, R and Fang, S and Lu, J and Lv, N and Wang, C and Gao, J and Li, J and Wu, W}, title = {Metagenomics next-generation sequencing (mNGS) reveals emerging infection induced by Klebsiella pneumoniaeniae.}, journal = {International journal of antimicrobial agents}, volume = {63}, number = {2}, pages = {107056}, doi = {10.1016/j.ijantimicag.2023.107056}, pmid = {38081548}, issn = {1872-7913}, mesh = {Humans ; Male ; Aged ; *Klebsiella ; *Klebsiella Infections/drug therapy ; Carbapenems/pharmacology/therapeutic use ; Klebsiella pneumoniae ; Anti-Bacterial Agents/pharmacology/therapeutic use ; High-Throughput Nucleotide Sequencing ; }, abstract = {OBJECTIVES: The increasing emergence of hypervirulent Klebsiella pneumoniae (hv-Kp) and carbapenem-resistant K. pneumoniae (CR-Kp) is a serious and substantial public health problem. The use of the last resort antimicrobials, tigecycline and polymyxin to combat infections is complicated by the expanding repertoire of newly-identified CR-hvKp. The transmission and co-occurrence of the corresponding antimicrobial resistance and virulence determinants are largely unknown. The aim of this study was to investigate the dissemination and dynamics of CR-Kp and its antibiotic resistance in a hospitalised patient.<br><br>METHODS: Metagenomic next-generation sequencing (mNGS) was conducted for different specimens collected from an elderly male hospitalised patient. CR-Kp strains were examined using antibiotic susceptibility and string testing. Antimicrobial and virulence genes were annotated using whole-genome sequencing (WGS).<br><br>RESULTS: A clinical case of a patient infected with a variety of CR-Kp isolates was reported. The co-occurrence of KPC-2 and NDM-1 in the patient was revealed. The CR-Kp isolates, such as BALF2, and Sputum T1 and T3, were classified into ST11 and ST147, respectively. The genetic signature (iuc operon) of hypervirulence was identified in strain T1, although string testing indicated its intermediate virulence.<br><br>CONCLUSIONS: In this study, multiple infections of CR-Kp isolates were revealed by mNGS, and their dissemination was attributed to plasmid variations, mgrB inactivation and integrative conjugative elements (ICEs). Furthermore, the finding indicated one likely convergence to form CR-hvKp, different from acquisition of carbapenem-resistance determinants in hvKp. A combination of mNGS and WGS is beneficial for clinical diagnosis and anti-infection therapy, and facilitates a better understanding of genetic variants conferring antimicrobial and virulence properties.}, }
@article {pmid38079200, year = {2023}, author = {Piña-Iturbe, A and Hoppe-Elsholz, G and Suazo, ID and Kalergis, AM and Bueno, SM}, title = {Subinhibitory antibiotic concentrations promote the excision of a genomic island carried by the globally spread carbapenem-resistant Klebsiella pneumoniae sequence type 258.}, journal = {Microbial genomics}, volume = {9}, number = {12}, pages = {}, pmid = {38079200}, issn = {2057-5858}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Klebsiella pneumoniae ; Phylogeny ; Genomic Islands/genetics ; Carbapenems/pharmacology ; }, abstract = {The ICEKp258.2 genomic island (GI) has been proposed as an important factor for the emergence and success of the globally spread carbapenem-resistant Klebsiella pneumoniae sequence type (ST) 258. However, a characterization of this horizontally acquired element is lacking. Using bioinformatic and experimental approaches, we found that ICEKp258.2 is not confined to ST258 and ST512, but also carried by ST3795 strains and emergent invasive multidrug-resistant pathogens from ST1519. We also identified several ICEKp258.2-like GIs spread among different K. pneumoniae STs, other Klebsiella species and even other pathogen genera, uncovering horizontal gene transfer events between different STs and bacterial genera. Also, the comparative and phylogenetic analyses of the ICEKp258.2-like GIs revealed that the most closely related ICEKp258.2-like GIs were harboured by ST11 strains. Importantly, we found that subinhibitory concentrations of antibiotics used in treating K. pneumoniae infections can induce the excision of this GI and modulate its gene expression. Our findings provide the basis for the study of ICEKp258.2 and its role in the success of K. pneumoniae ST258. They also highlight the potential role of antibiotics in the spread of ICEKp258.2-like GIs among bacterial pathogens.}, }
@article {pmid38078984, year = {2023}, author = {Yang, X and Sui, X and Liu, Q and Wang, H and Sun, H and Bai, X and Xiong, Y}, title = {Characterization of the novel temperate Escherichia coli phage phiStx2k.}, journal = {Archives of virology}, volume = {169}, number = {1}, pages = {5}, pmid = {38078984}, issn = {1432-8798}, support = {82072254//National Nature Science Foundation of China/ ; }, mesh = {*Escherichia coli/genetics ; Coliphages/genetics ; *Bacteriophages/genetics ; }, abstract = {A novel temperate phage, phiStx2k, was induced from a clinical Escherichia coli isolate producing Shiga toxin (Stx) 2k. The phage particles have an icosahedral head (50 nm in diameter) and a long non-contractile tail (149 nm long). The phage genome consists of 46,647 bp of double-stranded DNA with an average G + C content of 51%. Genome sequence comparisons suggested that phiStx2k represents a new genus in the class Caudoviricetes. phiStx2k was capable of converting non-Stx-producing E. coli strains to Stx producers. These results expand our knowledge on the characteristics of Stx phages and highlight the potential risks of the emergence of Stx-producing strains or novel pathogens via horizontal gene transfer.}, }
@article {pmid38078732, year = {2024}, author = {Lages, MA and do Vale, A and Lemos, ML and Balado, M}, title = {Remodulation of bacterial transcriptome after acquisition of foreign DNA: the case of irp-HPI high-pathogenicity island in Vibrio anguillarum.}, journal = {mSphere}, volume = {9}, number = {1}, pages = {e0059623}, pmid = {38078732}, issn = {2379-5042}, support = {PID2019-103891RJ-100//Ministerio de Ciencia e Innovaci&#xf3;n (MCIN)/ ; PID2019-103891RJ-100//Agencia Estatal de Investigaci&#xf3;n (AEI)/ ; PID2021-122732OB-C21//Ministerio de Ciencia e Innovaci&#xf3;n (MCIN)/ ; PID2021-122732OB-C21//Agencia Estatal de Investigaci&#xf3;n (AEI)/ ; FEMS-GO-2019-600//Federation of European Microbiological Societies (FEMS)/ ; 2021.02251.CEECIND/CP1663/CT0016//COMPETE 2020 FEDER/ ; }, mesh = {Humans ; *Genomic Islands/genetics ; Transcriptome ; Lipopolysaccharides ; *Vibrio/genetics ; DNA ; *Organophosphorus Compounds ; }, abstract = {The high-pathogenicity island irp-HPI is widespread in Vibrionaceae and encodes the siderophore piscibactin, as well as the regulator PbtA that is essential for its expression. In this work, we aim to study whether PbtA directly interacts with irp-HPI promoters. Furthermore, we hypothesize that PbtA, and thereby the acquisition of irp-HPI island, may also influence the expression of other genes elsewhere in the bacterial genome. To address this question, an RNAseq analysis was conducted to identify differentially expressed genes after pbtA deletion in Vibrio anguillarum RV22 genetic background. The results showed that PbtA not only modulates the irp-HPI genes but also modulates the expression of a plethora of V. anguillarum core genome genes, inducing nitrate, arginine, and sulfate metabolism, T6SS1, and quorum sensing, while repressing lipopolysaccharide (LPS) production, MARTX toxin, and major porins such as OmpV and ChiP. The direct binding of the C-terminal domain of PbtA to piscibactin promoters (PfrpA and PfrpC), quorum sensing (vanT), LPS transporter wza, and T6SS structure- and effector-encoding genes was demonstrated by electrophoretic mobility shift assay (EMSA). The results provide valuable insights into the regulatory mechanisms underlying the expression of irp-HPI island and its impact on Vibrios transcriptome, with implications in pathogenesis.IMPORTANCEHorizontal gene transfer enables bacteria to acquire traits, such as virulence factors, thereby increasing the risk of the emergence of new pathogens. irp-HPI genomic island has a broad dissemination in Vibrionaceae and is present in numerous potentially pathogenic marine bacteria, some of which can infect humans. Previous works showed that certain V. anguillarum strains exhibit an expanded host range plasticity and heightened virulence, a phenomenon linked to the acquisition of the irp-HPI genomic island. The present work shows that this adaptive capability is likely achieved through comprehensive changes in the transcriptome of the bacteria and that these changes are mediated by the master regulator PbtA encoded within the irp-HPI element. Our results shed light on the broad implications of horizontal gene transfer in bacterial evolution, showing that the acquired DNA can directly mediate changes in the expression of the core genome, with profounds implications in pathogenesis.}, }
@article {pmid38077655, year = {2023}, author = {Mbewana Ntshanka, NG and Msagati, TAM}, title = {Trends and Progress on Antibiotic-Resistant Mycobacterium tuberculosis and Genes in relation to Human Immunodeficiency Virus.}, journal = {The Canadian journal of infectious diseases &amp; medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale}, volume = {2023}, number = {}, pages = {6659212}, pmid = {38077655}, issn = {1712-9532}, abstract = {Human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS) and tuberculosis (TB) are among the infectious diseases that cause high rates of mortality worldwide. The epidemiology of antibiotic resistance in correlation to people that live with TB and HIV has not been thoroughly investigated particularly in South Africa. Numerous cases of multidrug-resistant TB (MDR-TB) and extensively drug-resistant TB (XDR-TB) have been announced immensely worldwide. The spread and control of the MDR-TB pandemic due to unsuccessful treatment is one of the most serious public issues of concern, and this challenge is of international interest. Despite all measures that have been executed to overcome the challenge of MDR-TB in recent decades, the global MDR-TB trends have kept on accelerating with more and more people becoming victims. This is attributed to the abuse, misuse, and overuse of different antibacterial agents in human medicine, animal farms, and agricultural activities which serve as a wellspring for the evolution of antimicrobial resistance within the population. Over and above, the impetuous evolution, mutation, and the transfer of resistant genes via horizontal gene transfer are well-known contributive factors towards the antimicrobial resistance problem. Among the public health concerns in the world currently is the ever-increasing problem of antibiotic resistance which outpaces the progress of newly developed antimicrobials. The propagation of antimicrobial resistance (AMR) is even more amplified in areas where the pressure of antimicrobial resistant pathogens is elevated, and hence the population with ubiquitous HIV and AIDS is considered the hotspot. This review therefore aims to give in-depth coverage on the trends and the progress on the development of TB and HIV-resistant strains, highlight strategies to solve the problem, and accentuate the repercussions of the COVID-19 epidemic on the AMR.}, }
@article {pmid38075892, year = {2023}, author = {Wolters, JF and LaBella, AL and Opulente, DA and Rokas, A and Hittinger, CT}, title = {Mitochondrial genome diversity across the subphylum Saccharomycotina.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1268944}, pmid = {38075892}, issn = {1664-302X}, support = {R01 AI153356/AI/NIAID NIH HHS/United States ; T32 HG002760/HG/NHGRI NIH HHS/United States ; }, abstract = {INTRODUCTION: Eukaryotic life depends on the functional elements encoded by both the nuclear genome and organellar genomes, such as those contained within the mitochondria. The content, size, and structure of the mitochondrial genome varies across organisms with potentially large implications for phenotypic variance and resulting evolutionary trajectories. Among yeasts in the subphylum Saccharomycotina, extensive differences have been observed in various species relative to the model yeast Saccharomyces cerevisiae, but mitochondrial genome sampling across many groups has been scarce, even as hundreds of nuclear genomes have become available.<br><br>METHODS: By extracting mitochondrial assemblies from existing short-read genome sequence datasets, we have greatly expanded both the number of available genomes and the coverage across sparsely sampled clades.<br><br>RESULTS: Comparison of 353 yeast mitochondrial genomes revealed that, while size and GC content were fairly consistent across species, those in the genera Metschnikowia and Saccharomyces trended larger, while several species in the order Saccharomycetales, which includes S. cerevisiae, exhibited lower GC content. Extreme examples for both size and GC content were scattered throughout the subphylum. All mitochondrial genomes shared a core set of protein-coding genes for Complexes III, IV, and V, but they varied in the presence or absence of mitochondrially-encoded canonical Complex I genes. We traced the loss of Complex I genes to a major event in the ancestor of the orders Saccharomycetales and Saccharomycodales, but we also observed several independent losses in the orders Phaffomycetales, Pichiales, and Dipodascales. In contrast to prior hypotheses based on smaller-scale datasets, comparison of evolutionary rates in protein-coding genes showed no bias towards elevated rates among aerobically fermenting (Crabtree/Warburg-positive) yeasts. Mitochondrial introns were widely distributed, but they were highly enriched in some groups. The majority of mitochondrial introns were poorly conserved within groups, but several were shared within groups, between groups, and even across taxonomic orders, which is consistent with horizontal gene transfer, likely involving homing endonucleases acting as selfish elements.<br><br>DISCUSSION: As the number of available fungal nuclear genomes continues to expand, the methods described here to retrieve mitochondrial genome sequences from these datasets will prove invaluable to ensuring that studies of fungal mitochondrial genomes keep pace with their nuclear counterparts.}, }
@article {pmid38075610, year = {2023}, author = {Alexyuk, P and Alexyuk, M and Moldakhanov, Y and Berezin, V and Bogoyavlenskiy, A}, title = {Draft genome sequences data of Mammaliicoccus lentus isolated from horse farm soil.}, journal = {Data in brief}, volume = {51}, number = {}, pages = {109752}, pmid = {38075610}, issn = {2352-3409}, abstract = {Mammallicoccus lentus is a member of the commensal microflora of the Staphylococcaceae family, which colonizes the skin of several species of farm animals, including poultry and dairy animals (Huber et al., 2011; Zhang et al., 2009). The study of the members of the Staphylococcaceae family, such as the Mammaliicoccus genus, isolated from various sources is of great importance for agriculture and public health as contributes to the accumulation of knowledge and understanding of the mechanisms of antibiotic resistance gene transmission among bacterial pathogens. This thesis is supported by recent studies showing that some members of the Mammallicoccus genus serve as a reservoir of virulence and antibiotic resistance genes and may also be a source of horizontal gene transfer (Saraiva et al., 2021). Here, we present a draft genome sequence of Mammallicoccus lentus strain PVZ.22 from a horse farm soil sample. The sequencing was performed on the Illumina MiSeq platform. The genome was assembled using the Geneious software package. The genome contains 2,802,282 bp with a total of 2805 genes, 8 perfect and 12 strict AMR genes and 58 tRNAs genes.}, }
@article {pmid38071466, year = {2024}, author = {Chowdhury, AR and Mukherjee, D and Chatterjee, R and Chakravortty, D}, title = {Defying the odds: Determinants of the antimicrobial response of Salmonella Typhi and their interplay.}, journal = {Molecular microbiology}, volume = {121}, number = {2}, pages = {213-229}, doi = {10.1111/mmi.15209}, pmid = {38071466}, issn = {1365-2958}, support = {//ASTRA Chair Professorship and TATA Innovation fellowship funds/ ; //CSIR-SRF fellowship/ ; //DBT-IISc Partnership Program/ ; DAE0195//Department of Atomic Energy, Government of India/ ; //Department of Biotechnology (DBT)/ ; //IISc fellowship/ ; //Ministry of Science and Technology; Department of Science and Technology (DST)/ ; }, mesh = {Humans ; Salmonella typhi/genetics ; *Typhoid Fever/drug therapy/microbiology ; Anti-Bacterial Agents/pharmacology ; *Salmonella Infections/drug therapy ; DNA ; Microbial Sensitivity Tests ; }, abstract = {Salmonella Typhi, the invasive serovar of S. enterica subspecies enterica, causes typhoid fever in healthy human hosts. The emergence of antibiotic-resistant strains has consistently challenged the successful treatment of typhoid fever with conventional antibiotics. Antimicrobial resistance (AMR) in Salmonella is acquired either by mutations in the genomic DNA or by acquiring extrachromosomal DNA via horizontal gene transfer. In addition, Salmonella can form a subpopulation of antibiotic persistent (AP) cells that can survive at high concentrations of antibiotics. These have reduced the effectiveness of the first and second lines of antibiotics used to treat Salmonella infection. The recurrent and chronic carriage of S. Typhi in human hosts further complicates the treatment process, as a remarkable shift in the immune response from pro-inflammatory Th1 to anti-inflammatory Th2 is observed. Recent studies have also highlighted the overlap between AP, persistent infection (PI) and AMR. These incidents have revealed several areas of research. In this review, we have put forward a timeline for the evolution of antibiotic resistance in Salmonella and discussed the different mechanisms of the same availed by the pathogen at the genotypic and phenotypic levels. Further, we have presented a detailed discussion on Salmonella antibiotic persistence (AP), PI, the host and bacterial virulence factors that can influence PI, and how both AP and PI can lead to AMR.}, }
@article {pmid38070340, year = {2024}, author = {La Manna, P and De Carluccio, M and Oliva, G and Vigliotta, G and Rizzo, L}, title = {Urban wastewater disinfection by iron chelates mediated solar photo-Fenton: Effects on seven pathogens and antibiotic resistance transfer potential.}, journal = {Water research}, volume = {249}, number = {}, pages = {120966}, doi = {10.1016/j.watres.2023.120966}, pmid = {38070340}, issn = {1879-2448}, mesh = {*Wastewater ; *Escherichia coli ; Iron/pharmacology ; Disinfection/methods ; Hydrogen Peroxide/pharmacology ; Sunlight ; Drug Resistance, Microbial ; Iron Chelating Agents/pharmacology ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The effects of solar photo-Fenton (SPF) process mediated by the iron chelate Fe[3+] imminodisuccinic acid (Fe:IDS) on both the inactivation of seven relevant pathogens and the potential for antibiotic resistance transfer (degradation of antibiotic resistance genes (ARGs) and after treatment regrowth), in real secondary treated urban wastewater, were investigated for the first time. A comparison with results obtained by sunlight/H2O2 process and Fe[3+] ethylenediaminedisuccinic acid (Fe:EDDS) SPF was also carried out. ARGs were quantified by polymerase chain reaction (PCR) in samples before and after (3 h) the treatment. The persistence of the selected pathogens and ARGs was also evaluated in regrowth tests (72 h) under environmentally mimicking conditions. Fe:IDS SPF resulted to be more effective (from 1.4 log removal for Staphylococcus spp. to 4.3 log removal for Escherichia coli) than Fe:EDDS SPF (from 0.8 log removal for Pseudomonas aeruginosa to 2.0 log removal for Total coliphages) and sunlight/H2O2 (from 1.2 log removal for Clostridium perfringens to 3.3 log removal for E. coli) processes for the seven pathogens investigated. Potential pathogens regrowth was also severely affected, as no substantial regrowth was observed, both in presence and absence of catalase. A similar trend was observed for ARGs removal too (until 0.001 fold change expression for qnrS after 3 h). However, a poor effect and a slight increase in fold change was observed after treatment especially for gyrA, mefA and intl1. Overall, the effect of the investigated processes on ARGs was found to be ARG dependent. Noteworthy, coliphages can regrow after sunlight/H2O2 treatment unlike SPF processes, increasing the risk of antibiotic resistance transfer by transduction mechanism. In conclusion, Fe:IDS SPF is an attractive solution for tertiary treatment of urban wastewater in small wastewater treatment plants as it can provide effective disinfection and a higher protection against antibiotic resistance transfer than the other investigated processes.}, }
@article {pmid38069672, year = {2023}, author = {Li, Z and Xue, AZ and Maeda, GP and Li, Y and Nabity, PD and Moran, NA}, title = {Phylloxera and Aphids Show Distinct Features of Genome Evolution Despite Similar Reproductive Modes.}, journal = {Molecular biology and evolution}, volume = {40}, number = {12}, pages = {}, pmid = {38069672}, issn = {1537-1719}, support = {R35 GM131738/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Male ; *Aphids/genetics ; X Chromosome/genetics ; Parthenogenesis/genetics ; Reproduction ; Evolution, Molecular ; }, abstract = {Genomes of aphids (family Aphididae) show several unusual evolutionary patterns. In particular, within the XO sex determination system of aphids, the X chromosome exhibits a lower rate of interchromosomal rearrangements, fewer highly expressed genes, and faster evolution at nonsynonymous sites compared with the autosomes. In contrast, other hemipteran lineages have similar rates of interchromosomal rearrangement for autosomes and X chromosomes. One possible explanation for these differences is the aphid's life cycle of cyclical parthenogenesis, where multiple asexual generations alternate with 1 sexual generation. If true, we should see similar features in the genomes of Phylloxeridae, an outgroup of aphids which also undergoes cyclical parthenogenesis. To investigate this, we generated a chromosome-level assembly for the grape phylloxera, an agriculturally important species of Phylloxeridae, and identified its single X chromosome. We then performed synteny analysis using the phylloxerid genome and 30 high-quality genomes of aphids and other hemipteran species. Unexpectedly, we found that the phylloxera does not share aphids' patterns of chromosome evolution. By estimating interchromosomal rearrangement rates on an absolute time scale, we found that rates are elevated for aphid autosomes compared with their X chromosomes, but this pattern does not extend to the phylloxera branch. Potentially, the conservation of X chromosome gene content is due to selection on XO males that appear in the sexual generation. We also examined gene duplication patterns across Hemiptera and uncovered horizontal gene transfer events contributing to phylloxera evolution.}, }
@article {pmid38069639, year = {2023}, author = {Jeong, DE and Sundrani, S and Hall, RN and Krupovic, M and Koonin, EV and Fire, AZ}, title = {DNA Polymerase Diversity Reveals Multiple Incursions of Polintons During Nematode Evolution.}, journal = {Molecular biology and evolution}, volume = {40}, number = {12}, pages = {}, pmid = {38069639}, issn = {1537-1719}, support = {R35 GM130366/GM/NIGMS NIH HHS/United States ; R35GM130366/GM/NIGMS NIH HHS/United States ; /NH/NIH HHS/United States ; /LM/NLM NIH HHS/United States ; }, mesh = {Humans ; Animals ; Phylogeny ; DNA Transposable Elements ; DNA-Directed DNA Polymerase/genetics ; *Viruses/genetics ; *Nematoda/genetics ; }, abstract = {Polintons are double-stranded DNA, virus-like self-synthesizing transposons widely found in eukaryotic genomes. Recent metagenomic discoveries of Polinton-like viruses are consistent with the hypothesis that Polintons invade eukaryotic host genomes through infectious viral particles. Nematode genomes contain multiple copies of Polintons and provide an opportunity to explore the natural distribution and evolution of Polintons during this process. We performed an extensive search of Polintons across nematode genomes, identifying multiple full-length Polinton copies in several species. We provide evidence of both ancient Polinton integrations and recent mobility in strains of the same nematode species. In addition to the major nematode Polinton family, we identified a group of Polintons that are overall closely related to the major family but encode a distinct protein-primed DNA polymerase B (pPolB) that is related to homologs from a different group of Polintons present outside of the Nematoda. Phylogenetic analyses on the pPolBs support the evolutionary scenarios in which these extrinsic pPolBs that seem to derive from Polinton families present in oomycetes and molluscs replaced the canonical pPolB in subsets of Polintons found in terrestrial and marine nematodes, respectively, suggesting interphylum horizontal gene transfers. The pPolBs of the terrestrial nematode and oomycete Polintons share a unique feature, an insertion of an HNH nuclease domain, whereas the pPolBs in the marine nematode Polintons share an insertion of a VSR nuclease domain with marine mollusc pPolBs. We hypothesize that horizontal gene transfer occurs among Polintons from widely different but cohabiting hosts.}, }
@article {pmid38064674, year = {2023}, author = {Liang, H and Mower, JP and Chia, CP}, title = {Functional Prokaryotic-Like Deoxycytidine Triphosphate Deaminases and Thymidylate Synthase in Eukaryotic Social Amoebae: Vertical, Endosymbiotic, or Horizontal Gene Transfer?.}, journal = {Molecular biology and evolution}, volume = {40}, number = {12}, pages = {}, pmid = {38064674}, issn = {1537-1719}, mesh = {DCMP Deaminase/genetics/metabolism ; Gene Transfer, Horizontal ; Escherichia coli/genetics/metabolism ; *Amoeba/metabolism ; Thymidylate Synthase/genetics ; *Dictyostelium ; Deoxycytidine Monophosphate ; }, abstract = {The de novo synthesis of deoxythymidine triphosphate uses several pathways: gram-negative bacteria use deoxycytidine triphosphate deaminase to convert deoxycytidine triphosphate into deoxyuridine triphosphate, whereas eukaryotes and gram-positive bacteria instead use deoxycytidine monophosphate deaminase to transform deoxycytidine monophosphate to deoxyuridine monophosphate. It is then unusual that in addition to deoxycytidine monophosphate deaminases, the eukaryote Dictyostelium discoideum has 2 deoxycytidine triphosphate deaminases (Dcd1Dicty and Dcd2Dicty). Expression of either DcdDicty can fully rescue the slow growth of an Escherichia coli dcd knockout. Both DcdDicty mitigate the hydroxyurea sensitivity of a Schizosaccharomyces pombe deoxycytidine monophosphate deaminase knockout. Phylogenies show that Dcd1Dicty homologs may have entered the common ancestor of the eukaryotic groups of Amoebozoa, Obazoa, Metamonada, and Discoba through an ancient horizontal gene transfer from a prokaryote or an ancient endosymbiotic gene transfer from a mitochondrion, followed by horizontal gene transfer from Amoebozoa to several other unrelated groups of eukaryotes. In contrast, the Dcd2Dicty homologs were a separate horizontal gene transfer from a prokaryote or a virus into either Amoebozoa or Rhizaria, followed by a horizontal gene transfer between them. ThyXDicty, the D. discoideum thymidylate synthase, another enzyme of the deoxythymidine triphosphate biosynthesis pathway, was suggested previously to be acquired from the ancestral mitochondria or by horizontal gene transfer from alpha-proteobacteria. ThyXDicty can fully rescue the E. coli thymidylate synthase knockout, and we establish that it was obtained by the common ancestor of social amoebae not from mitochondria but from a bacterium. We propose horizontal gene transfer and endosymbiotic gene transfer contributed to the enzyme diversity of the deoxythymidine triphosphate synthesis pathway in most social amoebae, many Amoebozoa, and other eukaryotes.}, }
@article {pmid38064485, year = {2023}, author = {Culbertson, EM and Levin, TC}, title = {Eukaryotic CD-NTase, STING, and viperin proteins evolved via domain shuffling, horizontal transfer, and ancient inheritance from prokaryotes.}, journal = {PLoS biology}, volume = {21}, number = {12}, pages = {e3002436}, pmid = {38064485}, issn = {1545-7885}, support = {R00 AI139344/AI/NIAID NIH HHS/United States ; R35 GM150681/GM/NIGMS NIH HHS/United States ; S10 OD028483/OD/NIH HHS/United States ; }, mesh = {Humans ; Animals ; *Bacteria/genetics/metabolism ; *Bacterial Proteins/metabolism ; Biological Evolution ; Nucleotidyltransferases/genetics/metabolism ; Antiviral Agents ; Mammals/metabolism ; }, abstract = {Animals use a variety of cell-autonomous innate immune proteins to detect viral infections and prevent replication. Recent studies have discovered that a subset of mammalian antiviral proteins have homology to antiphage defense proteins in bacteria, implying that there are aspects of innate immunity that are shared across the Tree of Life. While the majority of these studies have focused on characterizing the diversity and biochemical functions of the bacterial proteins, the evolutionary relationships between animal and bacterial proteins are less clear. This ambiguity is partly due to the long evolutionary distances separating animal and bacterial proteins, which obscures their relationships. Here, we tackle this problem for 3 innate immune families (CD-NTases [including cGAS], STINGs, and viperins) by deeply sampling protein diversity across eukaryotes. We find that viperins and OAS family CD-NTases are ancient immune proteins, likely inherited since the earliest eukaryotes first arose. In contrast, we find other immune proteins that were acquired via at least 4 independent events of horizontal gene transfer (HGT) from bacteria. Two of these events allowed algae to acquire new bacterial viperins, while 2 more HGT events gave rise to distinct superfamilies of eukaryotic CD-NTases: the cGLR superfamily (containing cGAS) that has since diversified via a series of animal-specific duplications and a previously undefined eSMODS superfamily, which more closely resembles bacterial CD-NTases. Finally, we found that cGAS and STING proteins have substantially different histories, with STING protein domains undergoing convergent domain shuffling in bacteria and eukaryotes. Overall, our findings paint a picture of eukaryotic innate immunity as highly dynamic, where eukaryotes build upon their ancient antiviral repertoires through the reuse of protein domains and by repeatedly sampling a rich reservoir of bacterial antiphage genes.}, }
@article {pmid38063386, year = {2024}, author = {Parra, B and Cockx, B and Lutz, VT and Brøndsted, L and Smets, BF and Dechesne, A}, title = {Isolation and characterization of novel plasmid-dependent phages infecting bacteria carrying diverse conjugative plasmids.}, journal = {Microbiology spectrum}, volume = {12}, number = {1}, pages = {e0253723}, pmid = {38063386}, issn = {2165-0497}, support = {101026675//EC | Horizon Europe | Excellent Science | HORIZON EUROPE Marie Sklodowska-Curie Actions (MSCA)/ ; 230416//Villum Fonden (Villum Foundation)/ ; }, mesh = {Humans ; *Bacteriophages ; Anti-Bacterial Agents ; Plasmids/genetics ; Escherichia coli/genetics ; *Salmonella enterica/genetics ; Conjugation, Genetic ; }, abstract = {This work was undertaken because plasmid-dependent phages can reduce the prevalence of conjugative plasmids and can be leveraged to prevent the acquisition and dissemination of ARGs by bacteria. The two novel phages described in this study, Lu221 and Hi226, can infect Escherichia coli, Salmonella enterica, Kluyvera sp. and Enterobacter sp. carrying conjugative plasmids. This was verified with plasmids carrying resistance determinants and belonging to the most common plasmid families among Gram-negative pathogens. Therefore, the newly isolated phages could have the potential to help control the spread of ARGs and thus help combat the antimicrobial resistance crisis.}, }
@article {pmid38062354, year = {2023}, author = {Hochstedler-Kramer, BR and Ene, A and Putonti, C and Wolfe, AJ}, title = {Comparative genomic analysis of clinical Enterococcus faecalis distinguishes strains isolated from the bladder.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {752}, pmid = {38062354}, issn = {1471-2164}, support = {TL1 DK132769/DK/NIDDK NIH HHS/United States ; U2C DK129917/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Enterococcus faecalis/genetics ; *Genome, Bacterial ; DNA Transposable Elements/genetics ; Urinary Bladder ; Genomics ; Anti-Bacterial Agents ; Prophages/genetics ; }, abstract = {BACKGROUND: Enterococcus faecalis is the most commonly isolated enterococcal species in clinical infection. This bacterium is notorious for its ability to share genetic content within and outside of its species. With this increased proficiency for horizontal gene transfer, tremendous genomic diversity within this species has been identified. Many researchers have hypothesized E. faecalis exhibits niche adaptation to establish infections or colonize various parts of the human body. Here, we hypothesize that E. faecalis strains isolated from the human bladder will carry unique genomic content compared to clinical strains isolated from other sources.<br><br>RESULTS: This analysis includes comparison of 111 E. faecalis genomes isolated from bladder, urogenital, blood, and fecal samples. Phylogenomic comparison shows no association between isolation source and lineage; however, accessory genome comparison differentiates blood and bladder genomes. Further gene enrichment analysis identifies gene functions, virulence factors, antibiotic resistance genes, and plasmid-associated genes that are enriched or rare in bladder genomes compared to urogenital, blood, and fecal genomes. Using these findings as training data and 682 publicly available genomes as test data, machine learning classifiers successfully distinguished between bladder and non-bladder strains with high accuracy. Genes identified as important for this differentiation were often related to transposable elements and phage, including 3 prophage species found almost exclusively in bladder and urogenital genomes.<br><br>CONCLUSIONS: E. faecalis strains isolated from the bladder contain unique genomic content when compared to strains isolated from other body sites. This genomic diversity is most likely due to horizontal gene transfer, as evidenced by lack of phylogenomic clustering and enrichment of transposable elements and prophages. Investigation into how these enriched genes influence host-microbe interactions may elucidate gene functions required for successful bladder colonization and disease establishment.}, }
@article {pmid38059467, year = {2023}, author = {Ren, CY and Zhao, HP}, title = {Synthetic Nuclease-Producing Microbiome Achieves Efficient Removal of Extracellular Antibiotic Resistance Genes from Wastewater Effluent.}, journal = {Environmental science &amp; technology}, volume = {57}, number = {50}, pages = {21224-21234}, doi = {10.1021/acs.est.3c07974}, pmid = {38059467}, issn = {1520-5851}, mesh = {Humans ; *Anti-Bacterial Agents ; Wastewater ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; *Microbiota ; }, abstract = {Antibiotic resistance gene (ARG) transmission poses significant threats to human health. The effluent of wastewater treatment plants is demonstrated as a hotspot source of ARGs released into the environment. In this study, a synthetic microbiome containing nuclease-producing Deinococcus radiodurans was constructed to remove extracellular ARGs. Results of quantitative polymerase chain reaction (qPCR) showed significant reduction in plasmid RP4-associated ARGs (by more than 3 orders of magnitude) and reduction of indigenous ARG sul1 and mobile genetic element (MGE) intl1 (by more than 1 order of magnitude) in the synthetic microbiome compared to the control without D. radiodurans. Metagenomic analysis revealed a decrease in ARG and MGE diversity in extracellular DNA (eDNA) of the treated group. Notably, whereas eight antibiotic-resistant plasmids with mobility risk were detected in the control, only one was detected in the synthetic microbiome. The abundance of the nuclease encoding gene exeM, quantified by qPCR, indicated its enrichment in the synthetic microbiome, which ensures stable eDNA degradation even when D. radiodurans decreased. Moreover, intracellular ARGs and MGEs and pathogenic ARG hosts in the river receiving treated effluent were lower than those in the river receiving untreated effluent. Overall, this study presents a new approach for removing extracellular ARGs and further reducing the risk of ARG transmission in receiving rivers.}, }
@article {pmid38056093, year = {2024}, author = {Wang, M and Masoudi, A and Wang, C and Wu, C and Zhang, Z and Zhao, X and Liu, Y and Yu, Z and Liu, J}, title = {Impacts of net cages on pollutant accumulation and its consequence on antibiotic resistance genes (ARGs) dissemination in freshwater ecosystems: Insights for sustainable urban water management.}, journal = {Environment international}, volume = {183}, number = {}, pages = {108357}, doi = {10.1016/j.envint.2023.108357}, pmid = {38056093}, issn = {1873-6750}, mesh = {Humans ; *Genes, Bacterial ; Water ; *Environmental Pollutants ; Ecosystem ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Fresh Water ; Water Supply ; }, abstract = {There has been increasing interest in the role of human activities in disseminating antibiotic-resistance genes (ARGs) in aquatic ecosystems. However, the influence of pollutant accumulation on anthropogenic pollutant-ARG synergistic actions is limited. This study explored the association of net cages with the propagation of anthropogenic pollutants and their consequences for influencing the enrichment of ARGs using high-throughput metagenomic sequencing. We showed that net cages could substantially impact the ecology of freshwater systems by enhancing i) ARG diversity and the tendency for ARG-horizontal gene transfer and ii) the overlap of mobile genetic elements (MGEs) with biocide-metal resistance genes (BMRGs) and ARGs. These findings suggested that the cotransfer of these three genetic determinants would be favored in net cage plots and that nonantibiotic factors such as metal(loid)s, particularly iron (Fe), displayed robust selective pressures on ARGs exerted by the net cage. The resistome risk scores of net cage sediments and biofilms were higher than those from off-net cage plots, indicating that the net cage-origin antibiotic resistome should be of great concern. The combination of deterministic and stochastic processes acting on bacterial communities could explain the higher ARG variations in cage plots (8.2%) than in off-cage plots (3.4%). Moreover, MGEs and pollutants together explained 43.3% of the total variation in ARG communities, which was higher than that of off-cage plots (8.8%), considering pollutants, environmental variables, MGEs, and assembly processes. These findings will inform the development of policies and guidelines to more effectively limit the spread of antimicrobial resistance and achieve the goal of sustainability in freshwater systems in urban areas.}, }
@article {pmid38053766, year = {2023}, author = {Gisriel, CJ and Bryant, DA and Brudvig, GW and Cardona, T}, title = {Molecular diversity and evolution of far-red light-acclimated photosystem I.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1289199}, pmid = {38053766}, issn = {1664-462X}, support = {K99 GM140174/GM/NIGMS NIH HHS/United States ; MR/T017546/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {The need to acclimate to different environmental conditions is central to the evolution of cyanobacteria. Far-red light (FRL) photoacclimation, or FaRLiP, is an acclimation mechanism that enables certain cyanobacteria to use FRL to drive photosynthesis. During this process, a well-defined gene cluster is upregulated, resulting in changes to the photosystems that allow them to absorb FRL to perform photochemistry. Because FaRLiP is widespread, and because it exemplifies cyanobacterial adaptation mechanisms in nature, it is of interest to understand its molecular evolution. Here, we performed a phylogenetic analysis of the photosystem I subunits encoded in the FaRLiP gene cluster and analyzed the available structural data to predict ancestral characteristics of FRL-absorbing photosystem I. The analysis suggests that FRL-specific photosystem I subunits arose relatively late during the evolution of cyanobacteria when compared with some of the FRL-specific subunits of photosystem II, and that the order Nodosilineales, which include strains like Halomicronema hongdechloris and Synechococcus sp. PCC 7335, could have obtained FaRLiP via horizontal gene transfer. We show that the ancestral form of FRL-absorbing photosystem I contained three chlorophyll f-binding sites in the PsaB2 subunit, and a rotated chlorophyll a molecule in the A0B site of the electron transfer chain. Along with our previous study of photosystem II expressed during FaRLiP, these studies describe the molecular evolution of the photosystem complexes encoded by the FaRLiP gene cluster.}, }
@article {pmid38051116, year = {2024}, author = {Beltrán, L and Torsilieri, H and Patkowski, JB and Yang, JE and Casanova, J and Costa, TRD and Wright, ER and Egelman, EH}, title = {The mating pilus of E. coli pED208 acts as a conduit for ssDNA during horizontal gene transfer.}, journal = {mBio}, volume = {15}, number = {1}, pages = {e0285723}, pmid = {38051116}, issn = {2150-7511}, support = {P30 CA044579/CA/NCI NIH HHS/United States ; R35 GM122510/GM/NIGMS NIH HHS/United States ; U24 GM139168/GM/NIGMS NIH HHS/United States ; }, mesh = {*Escherichia coli/genetics/metabolism ; DNA, Bacterial/genetics/metabolism ; *Gene Transfer, Horizontal ; Conjugation, Genetic ; Fimbriae, Bacterial/genetics/metabolism ; Plasmids ; }, abstract = {Bacteria are constantly exchanging DNA, which constitutes horizontal gene transfer. While some of these occurs by a non-specific process called natural transformation, some occurs by a specific mating between a donor and a recipient cell. In specific conjugation, the mating pilus is extended from the donor cell to make contact with the recipient cell, but whether DNA is actually transferred through this pilus or by another mechanism involving the type IV secretion system complex without the pilus has been an open question. Using Escherichia coli, we show that DNA can be transferred through this pilus between a donor and a recipient cell that has not established a tight mating junction, providing a new picture for the role of this pilus.}, }
@article {pmid38047929, year = {2023}, author = {Kocsis, B}, title = {Hypervirulent Klebsiella pneumoniae: An update on epidemiology, detection and antibiotic resistance.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {70}, number = {4}, pages = {278-287}, doi = {10.1556/030.2023.02186}, pmid = {38047929}, issn = {1588-2640}, mesh = {Humans ; *Klebsiella pneumoniae ; Abscess/drug therapy ; *Klebsiella Infections/epidemiology/drug therapy ; Virulence/genetics ; Virulence Factors/genetics ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Drug Resistance, Microbial ; }, abstract = {Klebsiella pneumoniae is a major human pathogen as it is responsible for various infections. In the past years hypervirulent K. pneumoniae (hvKP) emerged and disseminated worldwide. In this review a summary will be given about epidemiology, detection and antibiotic resistance of hypervirulent K. pneumoniae. A common feature of hypervirulent K. pneumoniae is a combined expression of several virulence factors. A mucoviscosus phenotype, certain capsulare serotypes (e.g.: K1, K2, K28, K47, K63) together with additional genetic markers namely, magA, rmpA or iucABCD, are needed in combinations to achieve the hypervirulent pathotype. Plasmid coded virulence determinants are also detected, that indicates horizontal gene transfer of hypervirulence factors in K. pneumoniae.Interestingly, infections caused by hypervirulent K. pneumoniae occur usually in the community in otherwise healthy people, and during these infections multiple infection sites are detected. Clinical pictures include both invasive infections and local abscess formation. Pyogenic liver abscess is the most frequently reported clinical manifestation and abscess formation in brain, spleen and lung are also diagnosed. Additionally, meningitis, endophthalmitis, trombophlebitis, pneumonia can also develop.In the early reports, hypervirulent K. pneumoniae strains exhibited enhanced virulence but these were susceptible to commonly used antibiotics. However, recently KPC, VIM, NDM and OXA-48 carbapenemase producing hypervirulent K. pneumoniae strains are increasingly reported, furthermore, well-known high-risk K. pneumoniae clones (e.g.: ST11, ST147, ST307) can develop hypervirulent pathotype, that poses an even more alarming challenge.}, }
@article {pmid38047691, year = {2024}, author = {Nakabachi, A and Suzaki, T}, title = {Ultrastructure of the bacteriome and bacterial symbionts in the Asian citrus psyllid, Diaphorina citri.}, journal = {Microbiology spectrum}, volume = {12}, number = {1}, pages = {e0224923}, pmid = {38047691}, issn = {2165-0497}, support = {21687020, 26292174, 20H02998//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; }, mesh = {Animals ; *Hemiptera ; Bacteria/genetics ; Symbiosis ; }, abstract = {Omics analyses suggested a mutually indispensable tripartite association among the host D. citri and organelle-like bacteriome associates, Carsonella and Profftella, which are vertically transmitted through host generations. This relationship is based on the metabolic complementarity among these organisms, which is partly enabled by horizontal gene transfer between partners. However, little was known about the fine morphology of the symbionts and the bacteriome, the interface among these organisms. As a first step to address this issue, the present study performed transmission electron microscopy, which revealed previously unrecognized ultrastructures, including aggregations of ribosomes in Carsonella, numerous tubes and occasional protrusions of Profftella, apparently degrading Profftella, and host organelles with different abundance and morphology in distinct cell types. These findings provide insights into the behaviors of the symbionts and host cells to maintain the symbiotic relationship in D. citri.}, }
@article {pmid38045412, year = {2025}, author = {Lind, AL and McDonald, NA and Gerrick, ER and Bhatt, AS and Pollard, KS}, title = {Contiguous and complete assemblies of Blastocystis gut microbiome-associated protists reveal evolutionary diversification to host ecology.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38045412}, issn = {2692-8205}, support = {K22 AI173181/AI/NIAID NIH HHS/United States ; R01 AI143757/AI/NIAID NIH HHS/United States ; R01 AI148623/AI/NIAID NIH HHS/United States ; R01 HL160862/HL/NHLBI NIH HHS/United States ; }, abstract = {Blastocystis, an obligate host-associated protist, is the most common microbial eukaryote in the human gut and is widely distributed across vertebrate hosts. The evolutionary transition of Blastocystis from its free-living stramenopile ancestors to a radiation of host-associated organisms is poorly understood. To explore this, we cultured and sequenced eight strains representing the significant phylogenetic diversity of the genus using long-read, short-read, and Hi-C DNA sequencing, alongside gene annotation and RNA sequencing. Comparative genomic analyses revealed significant variation in gene content and genome structure across Blastocystis. Notably, three strains from herbivorous tortoises, phylogenetically distant from human subtypes, have markedly larger genomes with longer introns and intergenic regions, and retain canonical stop codons absent in the human-associated strains. Despite these genetic differences, all eight isolates exhibit gene losses linked to the reduced cellular complexity of Blastocystis, including losses of cilia and flagella genes, microtubule motor genes, and signal transduction genes. Isolates from herbivorous tortoises contained higher numbers of plant carbohydrate-metabolizing enzymes, suggesting that like gut bacteria, these protists ferment plant material in the host gut. We find evidence that some of these carbohydrate-metabolizing enzymes were horizontally acquired from bacteria, indicating that horizontal gene transfer is an ongoing process in Blastocystis that has contributed to host-related adaptation. Together, these results highlight substantial genetic and metabolic diversity within the Blastocystis genus, indicating different lineages of Blastocystis have varied ecological roles in the host gut.}, }
@article {pmid38045280, year = {2023}, author = {Sun, L and David, KT and Wolters, JF and Karlen, SD and Gonçalves, C and Opulente, DA and Leavitt LaBella, A and Groenewald, M and Zhou, X and Shen, XX and Rokas, A and Todd Hittinger, C}, title = {Functional and evolutionary integration of a fungal gene with a bacterial operon.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38045280}, issn = {2692-8205}, support = {R01 AI153356/AI/NIAID NIH HHS/United States ; }, abstract = {Siderophores are crucial for iron-scavenging in microorganisms. While many yeasts can uptake siderophores produced by other organisms, they are typically unable to synthesize siderophores themselves. In contrast, Wickerhamiella/Starmerella (W/S) clade yeasts gained the capacity to make the siderophore enterobactin following the remarkable horizontal acquisition of a bacterial operon enabling enterobactin synthesis. Yet, how these yeasts absorb the iron bound by enterobactin remains unresolved. Here, we demonstrate that Enb1 is the key enterobactin importer in the W/S-clade species Starmerella bombicola. Through phylogenomic analyses, we show that ENB1 is present in all W/S clade yeast species that retained the enterobactin biosynthetic genes. Conversely, it is absent in species that lost the ent genes, except for Starmerella stellata, making this species the only cheater in the W/S clade that can utilize enterobactin without producing it. Through phylogenetic analyses, we infer that ENB1 is a fungal gene that likely existed in the W/S clade prior to the acquisition of the ent genes and subsequently experienced multiple gene losses and duplications. Through phylogenetic topology tests, we show that ENB1 likely underwent horizontal gene transfer from an ancient W/S clade yeast to the order Saccharomycetales, which includes the model yeast Saccharomyces cerevisiae, followed by extensive secondary losses. Taken together, these results suggest that the fungal ENB1 and bacterial ent genes were cooperatively integrated into a functional unit within the W/S clade that enabled adaptation to iron-limited environments. This integrated fungal-bacterial circuit and its dynamic evolution determines the extant distribution of yeast enterobactin producers and cheaters.}, }
@article {pmid38044873, year = {2024}, author = {Shen, Z and Qin, J and Xiang, G and Chen, T and Nurxat, N and Gao, Q and Wang, C and Zhang, H and Liu, Y and Li, M}, title = {Outer membrane vesicles mediating horizontal transfer of the epidemic blaOXA-232 carbapenemase gene among Enterobacterales.}, journal = {Emerging microbes &amp; infections}, volume = {13}, number = {1}, pages = {2290840}, pmid = {38044873}, issn = {2222-1751}, mesh = {*beta-Lactamases/genetics/metabolism ; *Gene Transfer, Horizontal ; *Bacterial Proteins/genetics/metabolism ; Humans ; *Plasmids/genetics ; Klebsiella pneumoniae/genetics ; Enterobacteriaceae/genetics/enzymology ; Enterobacteriaceae Infections/microbiology/epidemiology ; Cross Infection/microbiology/epidemiology ; }, abstract = {OXA-232 is one of the most common OXA-48-like carbapenemase derivatives and is widely disseminated in nosocomial settings across countries. The blaOXA-232 gene is located on a 6-kb non-conjugative ColKP3-type plasmid, while the dissemination of blaOXA-232 into different Enterobacterales species and the polyclonal dissemination of OXA-232-producing K. pneumoniae revealed the horizontal transfer of blaOXA-232. However, it's still unclear how this non-conjugative ColKP3 plasmid could facilitate the mobilization of blaOXA-232. Here, we observed the in vivo intraspecies transfer of blaOXA-232 during a nosocomial outbreak of OXA-232-producing K. pneumoniae. We demonstrated the presence of ColKP3 OXA-232 plasmid in the outer membrane vesicles (OMVs) derived from clinical isolates, and OMVs could facilitate the horizontal transfer of blaOXA-232 among Enterobacterales. In contrast, for the most prevalent carbapenemase genes, including blaKPC-2 and blaNDM-1, though the presence of carbapenemase genes and plasmid backbones in the vesicular lumen was observed, OMVs couldn't promote effective transformation, probably due to the low copy number of plasmids in clinical isolates and the low number of plasmids loaded into vesicles. Conjugation assay revealed that the epidemic IncX3 NDM-1 and IncFII(pHN7A8)/IncR KPC-2 plasmids were conjugative and could be horizontally transferred via independent conjugation or with the help of a co-existent conjugative plasmid. For the large-size and low-copy number conjugative plasmids carrying carbapenemase genes, OMVs-mediated gene exchange may only serve as an alternative pathway for horizontal transfer. In conclusion, diverse mobilization strategies were employed by plasmids harbouring carbapenemase genes, and plasmids display a proper choice of mobility pathway due to their individual properties.}, }
@article {pmid38043355, year = {2024}, author = {Chen, Y and Yan, Z and Zhou, Y and Zhang, Y and Jiang, R and Wang, M and Yuan, S and Lu, G}, title = {Dynamic evolution of antibiotic resistance genes in plastisphere in the vertical profile of urban rivers.}, journal = {Water research}, volume = {249}, number = {}, pages = {120946}, doi = {10.1016/j.watres.2023.120946}, pmid = {38043355}, issn = {1879-2448}, mesh = {*Genes, Bacterial ; *Plastics ; Anti-Bacterial Agents/pharmacology ; Rivers ; Drug Resistance, Microbial/genetics ; Microplastics ; Polyesters ; Water ; }, abstract = {Microplastics (MPs) can vertically transport in the aquatic environment due to their aging and biofouling, forming distinct plastisphere in different water layers. However, even though MPs have been regarded as hotspots for antibiotic resistance genes (ARGs), little is known about the propagation and transfer of ARGs in plastisphere in waters, especially in the vertical profile. Therefore, this study investigated the dynamic responses and evolution of ARGs in different plastisphere distributed vertically in an urbanized river. The biofilm biomass in the polylactic acid (PLA) plastisphere was relatively higher than that in the polyethylene terephthalate (PET), showing depth-decay variations. The ARGs abundance in plastisphere were much higher than that in the surrounding waters, especially for the PLA. In the vertical profiles, the ARGs abundance in the PET plastisphere increased with water depths, while the highest abundance of ARGs in the PLA mostly appeared at intermediate waters. In the temporal dynamic, the ARGs abundance in plastisphere increased and then decreased, which may be dominated by the MP types at the initial periods. After long-term exposure, the influences of water depths seemed to be strengthened, especially in the PET plastisphere. Compared with surface waters, the microbiota attached in plastisphere in deep waters showed high species richness, strong diversity, and complex interactions, which was basically consistent with the changes of nutrient contents in different water layers. These vertical variations in microbiota and nutrients (e.g., nitrogen) may be responsible for the propagation of ARGs in plastisphere in deep waters. The host bacteria for ARGs in plastisphere was also developed as water depth increased, leading to an enrichment of ARGs in deep waters. In addition, the abundance of ARGs in plastisphere in bottom waters was positively correlated with the mobile genetic elements (MGEs) of intI1 and tnpA05, indicative of a frequent horizontal gene transfer of ARGs. Overall, water depth played a critical role in the propagation of ARGs in plastisphere, which should not be ignored in a long time series. This study provides new insights into the dynamic evolution of ARGs propagation in plastisphere under increasing global MPs pollution, especially in the vertical profile.}, }
@article {pmid38041553, year = {2024}, author = {Schmitz, M and Querques, I}, title = {DNA on the move: mechanisms, functions and applications of transposable elements.}, journal = {FEBS open bio}, volume = {14}, number = {1}, pages = {13-22}, pmid = {38041553}, issn = {2211-5463}, support = {//Branco Weiss Fellowship - Society in Science/ ; ALTF 296-2020//European Molecular Biology Organization/ ; //Federation of European Biochemical Societies/ ; //UZH Postdoc Grant/ ; }, mesh = {*DNA Transposable Elements/genetics ; Mutagenesis, Insertional ; *Bacteria/genetics ; CRISPR-Cas Systems/genetics ; Gene Transfer Techniques ; }, abstract = {Transposons are mobile genetic elements that have invaded all domains of life by moving between and within their host genomes. Due to their mobility (or transposition), transposons facilitate horizontal gene transfer in bacteria and foster the evolution of new molecular functions in prokaryotes and eukaryotes. As transposition can lead to detrimental genomic rearrangements, organisms have evolved a multitude of molecular strategies to control transposons, including genome defense mechanisms provided by CRISPR-Cas systems. Apart from their biological impacts on genomes, DNA transposons have been leveraged as efficient gene insertion vectors in basic research, transgenesis and gene therapy. However, the close to random insertion profile of transposon-based tools limits their programmability and safety. Despite recent advances brought by the development of CRISPR-associated genome editing nucleases, a strategy for efficient insertion of large, multi-kilobase transgenes at user-defined genomic sites is currently challenging. The discovery and experimental characterization of bacterial CRISPR-associated transposons (CASTs) led to the attractive hypothesis that these systems could be repurposed as programmable, site-specific gene integration technologies. Here, we provide a broad overview of the molecular mechanisms underpinning DNA transposition and of its biological and technological impact. The second focus of the article is to describe recent mechanistic and functional analyses of CAST transposition. Finally, current challenges and desired future advances of CAST-based genome engineering applications are briefly discussed.}, }
@article {pmid38039844, year = {2023}, author = {Harada, R and Inagaki, Y}, title = {Gleaning Euglenozoa-specific DNA polymerases in public single-cell transcriptome data.}, journal = {Protist}, volume = {174}, number = {6}, pages = {125997}, doi = {10.1016/j.protis.2023.125997}, pmid = {38039844}, issn = {1618-0941}, mesh = {*Euglenozoa ; Transcriptome ; DNA-Directed DNA Polymerase/genetics/metabolism ; *Euglenida ; }, abstract = {Multiple genes encoding family A DNA polymerases (famA DNAPs), which are evolutionary relatives of DNA polymerase I (PolI) in bacteria and phages, have been found in eukaryotic genomes, and many of these proteins are used mainly in organelles. Among members of the phylum Euglenozoa, distinct types of famA DNAP, PolIA, PolIBCD+, POP, and eugPolA, have been found. It is intriguing how the suite of famA DNAPs had been established during the evolution of Euglenozoa, but the DNAP data have not been sampled from the taxa that sufficiently represent the diversity of this phylum. In particular, little sequence data were available for basal branching species in Euglenozoa until recently. Thanks to the single-cell transcriptome data from symbiontids and phagotrophic euglenids, we have an opportunity to cover the "hole" in the repertory of famA DNAPs in the deep branches in Euglenozoa. The current study identified 16 new famA DNAP sequences in the transcriptome data from 33 phagotrophic euglenids and two symbiontids, respectively. Based on the new famA DNAP sequences, the updated diversity and evolution of famA DNAPs in Euglenozoa are discussed.}, }
@article {pmid38032214, year = {2023}, author = {Kubori, T}, title = {A two-component system serves as a central hub for connecting energy metabolism and plasmid dissemination in bacteria.}, journal = {mBio}, volume = {14}, number = {6}, pages = {e0247423}, pmid = {38032214}, issn = {2150-7511}, support = {//Takeda Science Foundation (TSF)/ ; }, mesh = {*Plasmids/genetics ; *Acinetobacter baumannii/genetics/metabolism ; *Energy Metabolism/genetics ; *Conjugation, Genetic ; Bacterial Proteins/genetics/metabolism ; Type IV Secretion Systems/genetics/metabolism ; Drug Resistance, Multiple, Bacterial/genetics ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; Gene Expression Regulation, Bacterial ; }, abstract = {Mobile genetic elements such as conjugative plasmids play a key role in the acquisition of antibiotic resistance by pathogenic bacteria. Resistance genes on plasmids can be transferred between bacteria using specialized conjugation machinery. Acinetobacter baumannii, the most common bacterium associated with nosocomial infections, harbors a large conjugative plasmid that encodes a type IV secretion system (T4SS). Feng et al. recently found that the A. baumannii T4SS is specialized for plasmid transfer, suggesting that it may be involved in multidrug resistance (Z. Feng, L. Wang, Q. Guan, X. Chu, and Z.-Q. Luo, mBio e02276-23, 2023, https://doi.org/10.1128/mbio.02276-23), T4SS-encoding genes are shown to be controlled by a versatile GacA/S two-component regulatory system. GacA/S is also found to regulate genes involved in central metabolism. The coordinated regulation of metabolism and plasmid conjugation may be a bacterial strategy for adapting to selective pressure from antibiotics.}, }
@article {pmid38032189, year = {2023}, author = {Zheng, Q and Li, L and Yin, X and Che, Y and Zhang, T}, title = {Is ICE hot? A genomic comparative study reveals integrative and conjugative elements as "hot" vectors for the dissemination of antibiotic resistance genes.}, journal = {mSystems}, volume = {8}, number = {6}, pages = {e0017823}, pmid = {38032189}, issn = {2379-5077}, support = {T21-705/20-N//Research Grants Council, University Grants Committee ()/ ; T21-705/20-N//Research Grants Council, University Grants Committee ()/ ; T21-705/20-N//Research Grants Council, University Grants Committee ()/ ; T21-705/20-N//Research Grants Council, University Grants Committee ()/ ; T21-705/20-N//Research Grants Council, University Grants Committee ()/ ; }, mesh = {*Anti-Bacterial Agents/pharmacology ; *Conjugation, Genetic ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal/genetics ; Genomics ; Phylogeny ; }, abstract = {Different from other extensively studied mobile genetic elements (MGEs) whose discoveries were initiated decades ago (1950s-1980s), integrative and conjugative elements (ICEs), a diverse array of more recently identified elements that were formally termed in 2002, have aroused increasing concern for their crucial contribution to the dissemination of antibiotic resistance genes (ARGs). However, the comprehensive understanding on ICEs' ARG profile across the bacterial tree of life is still blurred. Through a genomic study by comparison with two key MGEs, we, for the first time, systematically investigated the ARG profile as well as the host range of ICEs and also explored the MGE-specific potential to facilitate ARG propagation across phylogenetic barriers. These findings could serve as a theoretical foundation for risk assessment of ARGs mediated by distinct MGEs and further to optimize therapeutic strategies aimed at restraining antibiotic resistance crises.}, }
@article {pmid38031909, year = {2023}, author = {Kröger, C and Lerminiaux, NA and Ershova, AS and MacKenzie, KD and Kirzinger, MW and Märtlbauer, E and Perry, BJ and Cameron, ADS and Schauer, K}, title = {Plasmid-encoded lactose metabolism and mobilized colistin resistance (mcr-9) genes in Salmonella enterica serovars isolated from dairy facilities in the 1980s.}, journal = {Microbial genomics}, volume = {9}, number = {11}, pages = {}, pmid = {38031909}, issn = {2057-5858}, mesh = {*Colistin/pharmacology ; *Salmonella enterica/genetics ; Lactose ; Serogroup ; Drug Resistance, Bacterial/genetics ; Plasmids/genetics ; }, abstract = {Horizontal gene transfer by plasmids can confer metabolic capabilities that expand a host cell's niche. Yet, it is less understood whether the coalescence of specialized catabolic functions, antibiotic resistances and metal resistances on plasmids provides synergistic benefits. In this study, we report whole-genome assembly and phenotypic analysis of five Salmonella enterica strains isolated in the 1980s from milk powder in Munich, Germany. All strains exhibited the unusual phenotype of lactose-fermentation and encoded either of two variants of the lac operon. Surprisingly, all strains encoded the mobilized colistin resistance gene 9 (mcr-9), long before the first report of this gene in the literature. In two cases, the mcr-9 gene and the lac locus were linked within a large gene island that formed an IncHI2A-type plasmid in one strain but was chromosomally integrated in the other strain. In two other strains, the mcr-9 gene was found on a large IncHI1B/IncP-type plasmid, whereas the lac locus was encoded on a separate chromosomally integrated plasmidic island. The mcr-9 sequences were identical and genomic contexts could not explain the wide range of colistin resistances exhibited by the Salmonella strains. Nucleotide variants did explain phenotypic differences in motility and exopolysaccharide production. The observed linkage of mcr-9 to lactose metabolism, an array of heavy-metal detoxification systems, and other antibiotic resistance genes may reflect a coalescence of specialized phenotypes that improve the spread of colistin resistance in dairy facilities, much earlier than previously suspected.}, }
@article {pmid38013098, year = {2024}, author = {Fang, GY and Liu, XQ and Jiang, YJ and Mu, XJ and Huang, BW}, title = {Horizontal gene transfer in activated sludge enhances microbial antimicrobial resistance and virulence.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {168908}, doi = {10.1016/j.scitotenv.2023.168908}, pmid = {38013098}, issn = {1879-1026}, mesh = {*Sewage/microbiology ; Virulence/genetics ; *Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; Bacteria/genetics ; Virulence Factors/genetics ; }, abstract = {Activated sludge (AS) plays a vital role in removing organic pollutants and nutrients from wastewater. However, the risks posed by horizontal gene transfer (HGT) between bacteria in AS are still unclear. Here, a total of 478 high-quality non-redundant metagenome-assembled genomes (MAGs) were obtained. >50 % and 5 % of MAGs were involved in at least one HGT and recent HGT, respectively. Most of the transfers (82.4 %) of antimicrobial resistance genes (ARGs) occurred among the classes of Alphaproteobacteria and Gammaproteobacteria. The bacteria involved in the transfers of virulence factor genes (VFGs) mainly include Alphaproteobacteria (42.3 %), Bacteroidia (19.2 %), and Gammaproteobacteria (11.5 %). Moreover, the number of ARGs and VFGs in the classes of Alphaproteobacteria and Gammaproteobacteria was higher than that in other bacteria (P < 0.001). Mobile genetic elements were important contributors to ARGs and VFGs in AS bacteria. These results have implications for the management of antimicrobial resistance and virulence in activated sludge microorganisms.}, }
@article {pmid38012331, year = {2023}, author = {Zhu, H and Yu, J and Fu, Y and Mao, X and Yang, H}, title = {Two-Omics Probe on the Potential of Pseudomonas sp. GDMCC 1.1703 Under Phenol Stress.}, journal = {Current microbiology}, volume = {81}, number = {1}, pages = {21}, pmid = {38012331}, issn = {1432-0991}, support = {2019YFC1803801//Key Technologies Research and Development Program/ ; 2019YFC1803800//Key Technology Research and Development Program of Shandong/ ; }, mesh = {*Pseudomonas/metabolism ; *Phenol/metabolism ; RNA, Ribosomal, 16S/metabolism ; Base Sequence ; Bacteria/genetics ; Biodegradation, Environmental ; }, abstract = {Pseudomonas sp. harbors genetic diversity and readily adapts to environmental challenges, conferring upon it the ability to remediate. It is important to genetically determine the effects of bacterial application. The two-omics integration approach may shed more light on Pseudomonas isolates, filling the knowledge gap between genetic potential and dynamic function. In the present study, a strain from the Xi River was isolated using benzene-selective enrichment medium and phylogenetically identified as Pseudomonas sp. GDMCC 1.1703 by 16S rRNA gene sequencing. Its phenol degradability was optimally assessed at a rate of 45.7% (by statistics P < 0.05) in 12 h with a 200 mg/L concentration. Genomics and transcriptomics analyses were successively used to identify the genes and pathways responsible for phenol degradation. At least 42 genes were genomically identified to be involved in xenobiotic biodegradation. The degradative genes clustered into operons were hypothesized to have evolved through horizontal gene transfer. On the basis of genomic authentication, transcriptome analysis dynamically revealed that phenol degradation and responsive mechanisms were both upregulated as defense between the Ctrl (control) and PS (phenol-stressed) groups. Quantitative reverse transcription-PCR not only validated the key genes identified via RNA sequencing but also consistently confirmed the realistic intracellular expression. The approach of omics integration, which is effective in exploring the potential of isolates, will hopefully become an established method for determining the remediation potential of a candidate for development.}, }
@article {pmid38007474, year = {2023}, author = {Liu, Y and Brinkhoff, T and Berger, M and Poehlein, A and Voget, S and Paoli, L and Sunagawa, S and Amann, R and Simon, M}, title = {Metagenome-assembled genomes reveal greatly expanded taxonomic and functional diversification of the abundant marine Roseobacter RCA cluster.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {265}, pmid = {38007474}, issn = {2049-2618}, support = {TRR51//Deutsche Forschungsgemeinschaft/ ; TRR51//Deutsche Forschungsgemeinschaft/ ; TRR51//Deutsche Forschungsgemeinschaft/ ; TRR51//Deutsche Forschungsgemeinschaft/ ; TRR51//Deutsche Forschungsgemeinschaft/ ; 205321_184955//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 205321_184955//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 51NF40_180575//National Center of Competence in Research Quantum Science and Technology/ ; }, mesh = {*Roseobacter/genetics ; Seawater/microbiology ; Metagenome ; Phylogeny ; Oceans and Seas ; Metagenomics ; }, abstract = {BACKGROUND: The RCA (Roseobacter clade affiliated) cluster belongs to the family Roseobacteracea and represents a major Roseobacter lineage in temperate to polar oceans. Despite its prevalence and abundance, only a few genomes and one described species, Planktomarina temperata, exist. To gain more insights into our limited understanding of this cluster and its taxonomic and functional diversity and biogeography, we screened metagenomic datasets from the global oceans and reconstructed metagenome-assembled genomes (MAG) affiliated to this cluster.<br><br>RESULTS: The total of 82 MAGs, plus five genomes of isolates, reveal an unexpected diversity and novel insights into the genomic features, the functional diversity, and greatly refined biogeographic patterns of the RCA cluster. This cluster is subdivided into three genera: Planktomarina, Pseudoplanktomarina, and the most deeply branching Candidatus Paraplanktomarina. Six of the eight Planktomarina species have larger genome sizes (2.44-3.12 Mbp) and higher G&#x2009;+&#x2009;C contents (46.36-53.70%) than the four Pseudoplanktomarina species (2.26-2.72 Mbp, 42.22-43.72 G&#x2009;+&#x2009;C%). Cand. Paraplanktomarina is represented only by one species with a genome size of 2.40 Mbp and a G&#x2009;+&#x2009;C content of 45.85%. Three novel species of the genera Planktomarina and Pseudoplanktomarina are validly described according to the SeqCode nomenclature for prokaryotic genomes. Aerobic anoxygenic photosynthesis (AAP) is encoded in three Planktomarina species. Unexpectedly, proteorhodopsin (PR) is encoded in the other Planktomarina and all Pseudoplanktomarina species, suggesting that this light-driven proton pump is the most important mode of acquiring complementary energy of the RCA cluster. The Pseudoplanktomarina species exhibit differences in functional traits compared to Planktomarina species and adaptations to more resource-limited conditions. An assessment of the global biogeography of the different species greatly expands the range of occurrence and shows that the different species exhibit distinct biogeographic patterns. They partially reflect the genomic features of the species.<br><br>CONCLUSIONS: Our detailed MAG-based analyses shed new light on the diversification, environmental adaptation, and global biogeography of a major lineage of pelagic bacteria. The taxonomic delineation and validation by the SeqCode nomenclature of prominent genera and species of the RCA cluster may be a promising way for a refined taxonomic identification of major prokaryotic lineages and sublineages in marine and other prokaryotic communities assessed by metagenomics approaches. Video Abstract.}, }
@article {pmid38007076, year = {2024}, author = {Zhang, Z and Bo, L and Wang, S and Li, C and Zhang, X and Xue, B and Yang, X and He, X and Shen, Z and Qiu, Z and Zhao, C and Wang, J}, title = {Multidrug-resistant plasmid RP4 inhibits the nitrogen removal capacity of ammonia-oxidizing archaea, ammonia-oxidizing bacteria, and comammox in activated sludge.}, journal = {Environmental research}, volume = {242}, number = {}, pages = {117739}, doi = {10.1016/j.envres.2023.117739}, pmid = {38007076}, issn = {1096-0953}, mesh = {*Archaea/genetics/metabolism ; Sewage/microbiology ; Ammonia ; Nitrogen/metabolism ; Denitrification ; In Situ Hybridization, Fluorescence ; Oxidation-Reduction ; Bacteria/genetics/metabolism ; Plasmids/genetics ; *Betaproteobacteria/genetics/metabolism ; Anti-Bacterial Agents ; Phylogeny ; Soil Microbiology ; }, abstract = {In wastewater treatment plants (WWTPs), ammonia oxidation is primarily carried out by three types of ammonia oxidation microorganisms (AOMs): ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and comammox (CMX). Antibiotic resistance genes (ARGs), which pose an important public health concern, have been identified at every stage of wastewater treatment. However, few studies have focused on the impact of ARGs on ammonia removal performance. Therefore, our study sought to investigate the effect of the representative multidrug-resistant plasmid RP4 on the functional microorganisms involved in ammonia oxidation. Using an inhibitor-based method, we first evaluated the contributions of AOA, AOB, and CMX to ammonia oxidation in activated sludge, which were determined to be 13.7%, 41.1%, and 39.1%, respectively. The inhibitory effects of C2H2, C8H14, and 3,4-dimethylpyrazole phosphate (DMPP) were then validated by qPCR. After adding donor strains to the sludge, fluorescence in situ hybridization (FISH) imaging analysis demonstrated the co-localization of RP4 plasmids and all three AOMs, thus confirming the horizontal gene transfer (HGT) of the RP4 plasmid among these microorganisms. Significant inhibitory effects of the RP4 plasmid on the ammonia nitrogen consumption of AOA, AOB, and CMX were also observed, with inhibition rates of 39.7%, 36.2%, and 49.7%, respectively. Moreover, amoA expression in AOB and CMX was variably inhibited by the RP4 plasmid, whereas AOA amoA expression was not inhibited. These results demonstrate the adverse environmental effects of the RP4 plasmid and provide indirect evidence supporting plasmid-mediated conjugation transfer from bacteria to archaea.}, }
@article {pmid38006896, year = {2024}, author = {Yang, QE and Ma, X and Zeng, L and Wang, Q and Li, M and Teng, L and He, M and Liu, C and Zhao, M and Wang, M and Hui, D and Madsen, JS and Liao, H and Walsh, TR and Zhou, S}, title = {Interphylum dissemination of NDM-5-positive plasmids in hospital wastewater from Fuzhou, China: a single-centre, culture-independent, plasmid transmission study.}, journal = {The Lancet. Microbe}, volume = {5}, number = {1}, pages = {e13-e23}, doi = {10.1016/S2666-5247(23)00227-6}, pmid = {38006896}, issn = {2666-5247}, mesh = {Female ; Pregnancy ; Child ; Humans ; *Escherichia coli/genetics ; Wastewater ; RNA, Ribosomal, 16S/genetics ; Plasmids/genetics ; Bacteria/genetics ; Hospitals ; *Anti-Infective Agents ; }, abstract = {BACKGROUND: The global spread of plasmid-borne carbapenem resistance is an ongoing public health challenge; however, the nature of such horizontal gene transfer events among complex bacterial communities remains poorly understood. We examined the in-situ transfer of the globally dominant New Delhi metallo-β-lactamase (NDM)-5-positive IncX3 plasmid (denoted pX3_NDM-5) in hospital wastewater to simulate a real-world, One Health antimicrobial resistance context.<br><br>METHODS: For this transmission study, we tagged pX3_NDM-5 with the green fluorescent protein gene, gfp, using a CRISPR-based method and transferred the plasmid to a donor Escherichia coli strain. Bacteria were extracted from a hospital wastewater treatment plant (Fujian Provincial Maternity and Children's Hospital, Fuzhou, China) as the bacterial recipient community. We mixed this recipient community with the E coli donor strain carrying the gfp-tagged plasmid, both with and without sodium hypochlorite (NaClO) as an environmental stressor, and conducted several culture-based and culture-independent conjugation assays. The conjugation events were observed microscopically and quantified by fluorescence-activated cell sorting. We analysed the taxonomic composition of the sorted transconjugal pool by 16S rRNA gene amplicon sequencing and assessed the stability of the plasmid in the isolated transconjugants and its ability to transfer back to E coli.<br><br>FINDINGS: We show that the plasmid pX3_NDM-5 has a broad host range and can transfer across various bacterial phyla, including between Gram-negative and Gram-positive bacteria. Although environmental stress with NaClO did not affect the overall plasmid transfer frequency, it reduced the breadth of the transconjugant pool. The taxonomic composition of the transconjugal pool was distinct from that of the recipient communities, and environmental stress modulated the permissiveness of some operational taxonomic units towards the acquisition of pX3_NDM-5. Notably, pX3_NDM-5 transconjugants included the Gram-positive pathogen Enterococcus faecalis, and the plasmid could subsequently be reconjugated back to E coli. These findings suggest that E faecalis could act as a natural shuttle vector for the wide dissemination of pX3_NDM-5 plasmids.<br><br>INTERPRETATION: Our culture-independent conjugation model simulates natural environmental conditions and challenges the established theory that Gram-negative and Gram-positive bacteria rarely exchange clinically important plasmids. The data show that plasmids disseminate more widely across genera and phyla than previously thought. These findings have substantial implications when considering the spread of antimicrobial resistance across One Health sectors.<br><br>FUNDING: The Laboratory of Lingnan Modern Agriculture Project, the National Natural Science Foundation of China, the Natural Science Foundation of Fujian Province of China, and the Outstanding Young Research Talents Program of Fujian Agriculture and Forestry University.}, }
@article {pmid38006562, year = {2024}, author = {Serbus, LR}, title = {A Light in the Dark: Uncovering Wolbachia-Host Interactions Using Fluorescence Imaging.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2739}, number = {}, pages = {349-373}, pmid = {38006562}, issn = {1940-6029}, mesh = {Animals ; *Wolbachia/genetics ; *Arthropods/microbiology ; *Nematoda ; Symbiosis ; Optical Imaging ; }, abstract = {The success of microbial endosymbionts, which reside naturally within a eukaryotic "host" organism, requires effective microbial interaction with, and manipulation of, the host cells. Fluorescence microscopy has played a key role in elucidating the molecular mechanisms of endosymbiosis. For 30 years, fluorescence analyses have been a cornerstone in studies of endosymbiotic Wolbachia bacteria, focused on host colonization, maternal transmission, reproductive parasitism, horizontal gene transfer, viral suppression, and metabolic interactions in arthropods and nematodes. Fluorescence-based studies stand to continue informing Wolbachia-host interactions in increasingly detailed and innovative ways.}, }
@article {pmid38006561, year = {2024}, author = {Bordenstein, SR}, title = {Isolation of Phage WO Particles from Wolbachia-Infected Arthropods.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2739}, number = {}, pages = {337-348}, pmid = {38006561}, issn = {1940-6029}, mesh = {Animals ; *Arthropods ; *Wolbachia/genetics ; *Bacteriophages/genetics ; Prophages ; Myoviridae ; }, abstract = {Nearly all arthropod-associated Wolbachia contain intact and/or genomic remnants of phage WO, temperate bacteriophages that facilitate horizontal gene transfer, genomic rearrangement of the bacterial chromosome, and symbiotic interactions between Wolbachia and their arthropod hosts. Integrated prophage WO genomes produce active, lytic particles; but the lack of a cell-free culturing system for Wolbachia render them difficult to purify and study. This chapter describes polyethylene glycol (PEG) precipitation of phage particles from Wolbachia-infected arthropods, followed by confirmation of phage WO isolation and purification using electron microscopy and PCR.}, }
@article {pmid38005943, year = {2023}, author = {Loney, RE and Delesalle, VA and Chaudry, BE and Czerpak, M and Guffey, AA and Goubet-McCall, L and McCarty, M and Strine, MS and Tanke, NT and Vill, AC and Krukonis, GP}, title = {A Novel Subcluster of Closely Related Bacillus Phages with Distinct Tail Fiber/Lysin Gene Combinations.}, journal = {Viruses}, volume = {15}, number = {11}, pages = {}, pmid = {38005943}, issn = {1999-4915}, support = {52007540/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {*Bacillus Phages/genetics ; Genome, Viral ; *Bacteriophages/genetics ; Base Sequence ; Soil ; }, abstract = {Bacteriophages (phages) are the most numerous entities on Earth, but we have only scratched the surface of describing phage diversity. We isolated seven Bacillus subtilis phages from desert soil in the southwest United States and then sequenced and characterized their genomes. Comparative analyses revealed high nucleotide and amino acid similarity between these seven phages, which constitute a novel subcluster. Interestingly, the tail fiber and lysin genes of these phages seem to come from different origins and carry out slightly different functions. These genes were likely acquired by this subcluster of phages via horizontal gene transfer. In conjunction with host range assays, our data suggest that these phages are adapting to hosts with different cell walls.}, }
@article {pmid38005684, year = {2023}, author = {Khafizova, GV and Sierro, N and Ivanov, NV and Sokornova, SV and Polev, DE and Matveeva, TV}, title = {Nicotiana noctiflora Hook. Genome Contains Two Cellular T-DNAs with Functional Genes.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {22}, pages = {}, pmid = {38005684}, issn = {2223-7747}, support = {21-14-00050//Russian Science Foundation/ ; }, abstract = {Agrobacterium (Rhizobium)-mediated transformation leads to the formation of crown galls or hairy roots on infected plants. These effects develop due to the activity of T-DNA genes, gathered on a big plasmid, acquired from agrobacteria during horizontal gene transfer. However, a lot of plant species are known to contain such sequences, called cellular T-DNAs (cT-DNAs), and maintain normal phenotypes. Some of the genes remain intact, which leads to the conclusion of their functional role in plants. In this study, we present a comprehensive analysis of the cT-DNAs in the Nicotiana noctiflora Hook. genome, including gene expression and opine identification. Deep sequencing of the Nicotiana noctiflora genome revealed the presence of two different cT-DNAs, NnT-DNA1 and NnT-DNA2, which contain the intact genes iaaM, iaaH, acs, orf13, orf13a, and orf14. According to the expression analysis results, all these genes are most active in roots in comparison with other organs, which is consistent with data on cT-DNA gene expression in other plant species. We also used genetic engineering approaches and HPTLC and HPLC-MS methods to investigate the product of the acs gene (agrocinopine synthase), which turned out to be similar to agrocinopine A. Overall, this study expands our knowledge of cT-DNAs in plants and brings us closer to understanding their possible functions. Further research of cT-DNAs in different species and their functional implications could contribute to advancements in plant genetics and potentially unveil novel traits with practical applications in agriculture and other fields.}, }
@article {pmid38004737, year = {2023}, author = {Cai, T and Tang, H and Du, X and Wang, W and Tang, K and Wang, X and Liu, D and Wang, P}, title = {Genomic Island-Encoded Diguanylate Cyclase from Vibrio alginolyticus Regulates Biofilm Formation and Motility in Pseudoalteromonas.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, pmid = {38004737}, issn = {2076-2607}, support = {42188102, 91951203 and 32070175//the National Science Foundation of China/ ; 2022YFC3103600//the National Key R&amp;D Program of China/ ; 2021345//the Youth Innovation Promotion Association CAS/ ; 2019BT02Y262//the Local Innovative and Research Teams Project of Guangdong Pearl River Talents Program/ ; GJTD-2020-12//the K. C. Wong Education Foundation/ ; 2021B1212050023//the Science and Technology Planning Project of Guangdong Province of China/ ; }, abstract = {Many bacteria use the second messenger c-di-GMP to regulate exopolysaccharide production, biofilm formation, motility, virulence, and other phenotypes. The c-di-GMP level is controlled by the complex network of diguanylate cyclases (DGCs) and phosphodiesterases (PDEs) that synthesize and degrade c-di-GMP. In addition to chromosomally encoded DGCs, increasing numbers of DGCs were found to be located on mobile genetic elements. Whether these mobile genetic element-encoded DGCs can modulate the physiological phenotypes in recipient bacteria after horizontal gene transfer should be investigated. In our previous study, a genomic island encoding three DGC proteins (Dgc137, Dgc139, and Dgc140) was characterized in Vibrio alginolyticus isolated from the gastric cavity of the coral Galaxea fascicularis. Here, the effect of the three DGCs in four Pseudoalteromonas strains isolated from coral Galaxea fascicularis and other marine environments was explored. The results showed that when dgc137 is present rather than the three DGC genes, it obviously modulates biofilm formation and bacterial motility in these Pseudoalteromonas strains. Our findings implied that mobile genetic element-encoded DGC could regulate the physiological status of neighboring bacteria in a microbial community by modulating the c-di-GMP level after horizontal gene transfer.}, }
@article {pmid38004480, year = {2023}, author = {Muteeb, G and Rehman, MT and Shahwan, M and Aatif, M}, title = {Origin of Antibiotics and Antibiotic Resistance, and Their Impacts on Drug Development: A Narrative Review.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {16}, number = {11}, pages = {}, pmid = {38004480}, issn = {1424-8247}, support = {xxx//King Faisal University/ ; }, abstract = {Antibiotics have revolutionized medicine, saving countless lives since their discovery in the early 20th century. However, the origin of antibiotics is now overshadowed by the alarming rise in antibiotic resistance. This global crisis stems from the relentless adaptability of microorganisms, driven by misuse and overuse of antibiotics. This article explores the origin of antibiotics and the subsequent emergence of antibiotic resistance. It delves into the mechanisms employed by bacteria to develop resistance, highlighting the dire consequences of drug resistance, including compromised patient care, increased mortality rates, and escalating healthcare costs. The article elucidates the latest strategies against drug-resistant microorganisms, encompassing innovative approaches such as phage therapy, CRISPR-Cas9 technology, and the exploration of natural compounds. Moreover, it examines the profound impact of antibiotic resistance on drug development, rendering the pursuit of new antibiotics economically challenging. The limitations and challenges in developing novel antibiotics are discussed, along with hurdles in the regulatory process that hinder progress in this critical field. Proposals for modifying the regulatory process to facilitate antibiotic development are presented. The withdrawal of major pharmaceutical firms from antibiotic research is examined, along with potential strategies to re-engage their interest. The article also outlines initiatives to overcome economic challenges and incentivize antibiotic development, emphasizing international collaborations and partnerships. Finally, the article sheds light on government-led initiatives against antibiotic resistance, with a specific focus on the Middle East. It discusses the proactive measures taken by governments in the region, such as Saudi Arabia and the United Arab Emirates, to combat this global threat. In the face of antibiotic resistance, a multifaceted approach is imperative. This article provides valuable insights into the complex landscape of antibiotic development, regulatory challenges, and collaborative efforts required to ensure a future where antibiotics remain effective tools in safeguarding public health.}, }
@article {pmid38002987, year = {2023}, author = {Wang, B and Finazzo, M and Artsimovitch, I}, title = {Machine Learning Suggests That Small Size Helps Broaden Plasmid Host Range.}, journal = {Genes}, volume = {14}, number = {11}, pages = {}, pmid = {38002987}, issn = {2073-4425}, support = {R01 GM067153/GM/NIGMS NIH HHS/United States ; }, mesh = {*Host Specificity ; Plasmids/genetics ; *Bacteria/genetics ; beta-Lactamases/genetics ; Machine Learning ; }, abstract = {Plasmids mediate gene exchange across taxonomic barriers through conjugation, shaping bacterial evolution for billions of years. While plasmid mobility can be harnessed for genetic engineering and drug-delivery applications, rapid plasmid-mediated spread of resistance genes has rendered most clinical antibiotics useless. To solve this urgent and growing problem, we must understand how plasmids spread across bacterial communities. Here, we applied machine-learning models to identify features that are important for extending the plasmid host range. We assembled an up-to-date dataset of more than thirty thousand bacterial plasmids, separated them into 1125 clusters, and assigned each cluster a distribution possibility score, taking into account the host distribution of each taxonomic rank and the sampling bias of the existing sequencing data. Using this score and an optimized plasmid feature pool, we built a model stack consisting of DecisionTreeRegressor, EvoTreeRegressor, and LGBMRegressor as base models and LinearRegressor as a meta-learner. Our mathematical modeling revealed that sequence brevity is the most important determinant for plasmid spread, followed by P-loop NTPases, mobility factors, and β-lactamases. Ours and other recent results suggest that small plasmids may broaden their range by evading host defenses and using alternative modes of transfer instead of autonomous conjugation.}, }
@article {pmid38000736, year = {2024}, author = {Yao, N and Li, W and Hu, L and Fang, N}, title = {Do mould inhibitors alter the microbial community structure and antibiotic resistance gene profiles on textiles?.}, journal = {The Science of the total environment}, volume = {911}, number = {}, pages = {168808}, doi = {10.1016/j.scitotenv.2023.168808}, pmid = {38000736}, issn = {1879-1026}, mesh = {Humans ; *Genes, Bacterial ; Camphor ; Bacteria/genetics ; *Microbiota ; Drug Resistance, Microbial/genetics ; Fungi ; Textiles ; Naphthalenes/pharmacology ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Mould inhibitors are closely associated with human health and have been extensively applied to textiles to prevent mould and insect infestations. However, the impact of these mould inhibitors on the microbial community structure on textiles and antibiotic resistance gene (ARG) profiles remains largely unexplored. In this study, testing techniques, including high-throughput quantitative PCR and Illumina sequencing, were employed to analyse the effects of three types of mould inhibitors -para-dichlorobenzene (PDCB), naphthalene, and natural camphor balls-on the composition of microbial communities and ARG profiles. The microbial mechanisms underlying these effects were also investigated. The experiments revealed that PDCB reduced the diversity of bacterial communities on textiles, whereas naphthalene and natural camphor balls exerted relatively minor effects. In contrast with bacterial diversity, PDCB enhanced the diversity of fungal communities on textiles, but significantly reduced their abundance. Naphthalene had the least impact on fungal communities; however, it notably increased the relative abundance of Basidiomycota. All three types of mould inhibitors substantially altered ARG profiles. Potential mechanisms responsible for the alterations in ARG profiles include microbial community succession and horizontal gene transfer mediated by mobile genetic elements. PDCB prominently increased the abundance of ARGs, mainly attributable to the relative enrichment of potential hosts (including certain γ-Proteobacteria and Bacillales) for specific ARGs. Thus, this study has important implications for the selection of mould inhibitors, as well as the assessment of microbial safety in textiles.}, }
@article {pmid37999346, year = {2023}, author = {Marinacci, B and Krzyżek, P and Pellegrini, B and Turacchio, G and Grande, R}, title = {Latest Update on Outer Membrane Vesicles and Their Role in Horizontal Gene Transfer: A Mini-Review.}, journal = {Membranes}, volume = {13}, number = {11}, pages = {}, pmid = {37999346}, issn = {2077-0375}, abstract = {Outer membrane vesicles (OMVs) are spherical, lipid-based nano-structures, which are released by Gram-negative bacteria in both in vitro and in vivo conditions. The size and composition of OMVs depend on not only the producer bacterial species but also cells belonging to the same strain. The mechanism of vesicles' biogenesis has a key role in determining their cargo and the pattern of macromolecules exposed on their surface. Thus, the content of proteins, lipids, nucleic acids, and other biomolecules defines the properties of OMVs and their beneficial or harmful effects on human health. Many studies have provided evidence that OMVs can be involved in a plethora of biological processes, including cell-to-cell communication and bacteria-host interactions. Moreover, there is a growing body of literature supporting their role in horizontal gene transfer (HGT). During this process, OMVs can facilitate the spreading of genes involved in metabolic pathways, virulence, and antibiotic resistance, guaranteeing bacterial proliferation and survival. For this reason, a deeper understanding of this new mechanism of genetic transfer could improve the development of more efficient strategies to counteract infections sustained by Gram-negative bacteria. In line with this, the main aim of this mini-review is to summarize the latest evidence concerning the involvement of OMVs in HGT.}, }
@article {pmid37995998, year = {2024}, author = {Huang, B and Lv, X and Zheng, H and Yu, H and Zhang, Y and Zhang, C and Wang, J}, title = {Microbial organic fertilizer prepared by co-composting of Trichoderma dregs mitigates dissemination of resistance, virulence genes, and bacterial pathogens in soil and rhizosphere.}, journal = {Environmental research}, volume = {241}, number = {}, pages = {117718}, doi = {10.1016/j.envres.2023.117718}, pmid = {37995998}, issn = {1096-0953}, mesh = {*Composting ; Soil ; Fertilizers/analysis ; *Trichoderma/genetics ; Genes, Bacterial ; Rhizosphere ; Virulence ; Bacteria ; Anti-Bacterial Agents/pharmacology ; Manure/analysis/microbiology ; Soil Microbiology ; }, abstract = {The use of manure, mycelium dregs and other waste as organic fertilizer is the main source of antibiotic resistance genes (ARGs) and pathogens in farmland. Composting of waste may effectively remove ARGs and pathogens. However, the profiles and drivers of changes in metal resistance genes (MRGs), biocide resistance genes (BRGs), and virulence genes (VGs) in soil-crop rhizosphere systems after compost application remain largely unknown. Here, we prepared two kinds of microbial organic fertilizers (MOF) by using Trichoderma dregs (TDs) and organic fertilizer mixing method (MOF1) and TDs co-composting method (MOF2). The effects of different types and doses of MOF on resistance genes, VGs and pathogens in soil-rhizosphere system and their potential mechanisms were studied. The results showed that co-composting of TDs promoted the decomposition of organic carbon and decreased the absolute abundance of ARGs and mobile genetic elements (MGEs) by 53.4-65.0%. MOF1 application significantly increased the abundance and diversity of soil ARGs, BRGs, and VGs, while low and medium doses of MOF2 significantly decreased their abundance and diversity in soil and rhizosphere. Patterns of positive co-occurrence between MGEs and VGs/MRGs/BRGs/ARGs were observed through statistical analysis and gene arrangements. ARGs/MRGs reductions in MOF2 soil were directly driven by weakened horizontal gene transfer triggered by MGEs. Furthermore, MOF2 reduced soil BRGs/VGs levels by shifting bacterial communities (e.g., reduced bacterial host) or improving soil property. Our study provided new insights into the rational use of waste to minimize the spread of resistomes and VGs in soil.}, }
@article {pmid37988660, year = {2024}, author = {Zhang, M and Tong, X and Wang, W and Wang, J and Qu, W}, title = {Agarose biodegradation by deep-sea bacterium Vibrio natriegens WPAGA4 with the agarases through horizontal gene transfer.}, journal = {Journal of basic microbiology}, volume = {64}, number = {4}, pages = {e2300521}, doi = {10.1002/jobm.202300521}, pmid = {37988660}, issn = {1521-4028}, support = {2022C02040//"Pioneer" and "Leading Goose" R&amp;D Program of Zhejiang/ ; }, mesh = {Sepharose/metabolism ; *Bacterial Proteins/genetics/metabolism ; Gene Transfer, Horizontal ; Glycoside Hydrolases/metabolism ; *Vibrio/genetics ; }, abstract = {This study aimed to reveal the importance of horizontal gene transfer (HGT) for the agarose-degrading ability and the related degradation pathway of a deep-sea bacterium Vibrio natriegens WPAGA4, which was rarely reported in former works. A total of four agarases belonged to the GH50 family, including Aga3418, Aga3419, Aga3420, and Aga3472, were annotated and expressed in Escherichia coli cells. The agarose degradation products of Aga3418, Aga3420, and Aga3472 were neoagarobiose, while those of Aga3419 were neoagarobiose and neoagarotetraose. The RT-qPCR analysis showed that the expression level ratio of Aga3418, Aga3419, Aga3420, and Aga3472 was stable at about 1:1:1.5:2.5 during the degradation, which indicated the optimal expression level ratio of the agarases for agarose degradation by V. natriegens WPAGA4. Based on the genomic information, three of four agarases and other agarose-degrading related genes were in a genome island with a G + C content that was obviously lower than that of the whole genome of V. natriegens WPAGA4, indicating that these agarose-degrading genes were required through HGT. Our results demonstrated that the expression level ratio instead of the expression level itself of agarase genes was crucial for agarose degradation by V. natriegens WPAGA4, and HGT occurred in the deep-sea environment, thereby promoting the deep-sea carbon cycle and providing a reference for studying the evolution and transfer pathways of agar-related genes.}, }
@article {pmid37987191, year = {2023}, author = {Garbisu, C and Alkorta, I}, title = {A case for the importance of following antibiotic resistant bacteria throughout the soil food web.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {45}, number = {12}, pages = {e2300153}, doi = {10.1002/bies.202300153}, pmid = {37987191}, issn = {1521-1878}, support = {PID2020-116495RB-I00//MCIN/AEI/10.13039/501100011033/ ; IT1578-22//Basque Government/ ; //JRL Environmental Antibiotic Resistance/ ; }, mesh = {Animals ; *Soil ; *Bacteria/genetics ; Manure/microbiology ; Food Chain ; Ecosystem ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Anti-Bacterial Agents/pharmacology ; Soil Microbiology ; Genes, Bacterial ; }, abstract = {It is necessary to complement next-generation sequencing data on the soil resistome with theoretical knowledge provided by ecological studies regarding the spread of antibiotic resistant bacteria (ARB) in the abiotic and, especially, biotic fraction of the soil ecosystem. Particularly, when ARB enter agricultural soils as a consequence of the application of animal manure as fertilizer, from a microbial ecology perspective, it is important to know their fate along the soil food web, that is, throughout that complex network of feeding interactions among members of the soil biota that has crucial effects on species richness and ecosystem productivity and stability. It is critical to study how the ARB that enter the soil through the application of manure can reach other taxonomical groups (e.g., fungi, protists, nematodes, arthropods, earthworms), paying special attention to their presence in the gut microbiomes of mesofauna-macrofauna and to the possibilities for horizontal gene transfer of antibiotic resistant genes.}, }
@article {pmid37983489, year = {2023}, author = {Simmons, M and Horbelt, N and Sverko, T and Scoppola, E and Jackson, DJ and Harrington, MJ}, title = {Invasive mussels fashion silk-like byssus via mechanical processing of massive horizontally acquired coiled coils.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {48}, pages = {e2311901120}, pmid = {37983489}, issn = {1091-6490}, support = {RGPIN-2018-05243//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; CRC Tier 2 950-231953//Canada Research Chairs (Chaires de recherche du Canada)/ ; 528314512//Deutsche Forschungsgemeinschaft (DFG)/ ; }, mesh = {Animals ; Silk/chemistry ; Proteomics ; *Bivalvia/chemistry ; *Dreissena ; Protein Precursors/metabolism ; }, abstract = {Zebra and quagga mussels (Dreissena spp.) are invasive freshwater biofoulers that perpetrate devastating economic and ecological impact. Their success depends on their ability to anchor onto substrates with protein-based fibers known as byssal threads. Yet, compared to other mussel lineages, little is understood about the proteins comprising their fibers or their evolutionary history. Here, we investigated the hierarchical protein structure of Dreissenid byssal threads and the process by which they are fabricated. Unique among bivalves, we found that threads possess a predominantly β-sheet crystalline structure reminiscent of spider silk. Further analysis revealed unexpectedly that the Dreissenid thread protein precursors are mechanoresponsive α-helical proteins that are mechanically processed into β-crystallites during thread formation. Proteomic analysis of the byssus secretory organ and byssus fibers revealed a family of ultrahigh molecular weight (354 to 467 kDa) asparagine-rich (19 to 20%) protein precursors predicted to form α-helical coiled coils. Moreover, several independent lines of evidence indicate that the ancestral predecessor of these proteins was likely acquired via horizontal gene transfer. This chance evolutionary event that transpired at least 12 Mya has endowed Dreissenids with a distinctive and effective fiber formation mechanism, contributing significantly to their success as invasive species and possibly, inspiring new materials design.}, }
@article {pmid37982820, year = {2023}, author = {Cheatle Jarvela, AM and Wexler, JR}, title = {Advances in genome sequencing reveal changes in gene content that contribute to arthropod macroevolution.}, journal = {Development genes and evolution}, volume = {233}, number = {2}, pages = {59-76}, pmid = {37982820}, issn = {1432-041X}, mesh = {Animals ; *Arthropods/genetics ; Genome ; Genomics ; Base Sequence ; Evolution, Molecular ; Phylogeny ; }, abstract = {Current sequencing technology allows for the relatively affordable generation of highly contiguous genomes. Technological advances have made it possible for researchers to investigate the consequences of diverse sorts of genomic variants, such as gene gain and loss. With the extraordinary number of high-quality genomes now available, we take stock of how these genomic variants impact phenotypic evolution. We take care to point out that the identification of genomic variants of interest is only the first step in understanding their impact. Painstaking lab or fieldwork is still required to establish causal relationships between genomic variants and phenotypic evolution. We focus mostly on arthropod research, as this phylum has an impressive degree of phenotypic diversity and is also the subject of much evolutionary genetics research. This article is intended to both highlight recent advances in the field and also to be a primer for learning about evolutionary genetics and genomics.}, }
@article {pmid37982629, year = {2023}, author = {Tian, D and Zhao, M and Zheng, S and Jiang, X and Zhang, B}, title = {Involvement of Tn3 transposon in formation and transmission of hypervirulent and carbapenem-resistant Klebsiella pneumoniae.}, journal = {Microbiology spectrum}, volume = {11}, number = {6}, pages = {e0303823}, pmid = {37982629}, issn = {2165-0497}, support = {2022M721338//China Postdoctoral Science Foundation (China Postdoctoral Foundation Project)/ ; SDBX2022052//Shandong Postdoctoral Innovation Talents Support Program/ ; ZR2023QH215//Shandong Provincial Natural Science Foundation/ ; 2022KJ106//Project of Shandong Province Higher Educational Youth Innovation Science and Technology Program/ ; tsqn202306400//Tai Shan Young Scholar Foundation of Shandong Province/ ; }, mesh = {Humans ; Klebsiella pneumoniae ; Anti-Bacterial Agents/pharmacology ; Carbapenems/pharmacology ; Virulence/genetics ; Plasmids/genetics ; *Carbapenem-Resistant Enterobacteriaceae/genetics ; *Klebsiella Infections/microbiology ; }, abstract = {Carbapenem-resistant Klebsiella pneumoniae (CRKP) is resistant to most common antibiotics, becoming the most important and prevalent nosocomial opportunity pathogen. Besides, K. pneumoniae can also cause severe community-acquired infections, such as primary liver abscess and endophthalmitis. These pathogens are commonly referred to as hvKp. CRKP and hvKp have evolved separately, each occupying its own clonal lineage and exhibiting a variety of properties. Our study provides important insights into the evolutionary events related to the arousal of virulence and drug resistance in K. pneumoniae through plasmid transmission, mediated by Tn3 transposon. Our study also provides evidence that multiple mechanisms contribute to the successful transfer of non-conjugative virulence plasmid, and the involvement of transposons enhances the efficiency. A good knowledge of its transmission mechanisms is fundamental to finding effective strategies to combat these threatening pathogens. Transposons are widely present in bacteria, spreading resistance and virulence genes between the environment and humans. Therefore, emerging transposon-mediated hypervirulent and carbapenem-resistant pathogens should be highly valued.}, }
@article {pmid37981687, year = {2023}, author = {Chen, X and Wang, Z and Zhang, C and Hu, J and Lu, Y and Zhou, H and Mei, Y and Cong, Y and Guo, F and Wang, Y and He, K and Liu, Y and Li, F}, title = {Unraveling the complex evolutionary history of lepidopteran chromosomes through ancestral chromosome reconstruction and novel chromosome nomenclature.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {265}, pmid = {37981687}, issn = {1741-7007}, support = {2019FY100400//National Science &amp; Technology Fundamental Resources Investigation Program of China/ ; 2022YFD1401600//Key Technologies Research and Development Program/ ; LZ23C140002//Natural Science Foundation of Zhejiang Province/ ; LY22C140005//Natural Science Foundation of Zhejiang Province/ ; 32202366//National science foundation of China/ ; 32102271//National science foundation of China/ ; }, mesh = {Animals ; Female ; Male ; Geminin/genetics ; *Biological Evolution ; Genome ; Sex Chromosomes/genetics ; *Lepidoptera/genetics ; Evolution, Molecular ; }, abstract = {BACKGROUND: Lepidoptera is one of the most species-rich animal groups, with substantial karyotype variations among species due to chromosomal rearrangements. Knowledge of the evolutionary patterns of lepidopteran chromosomes still needs to be improved.<br><br>RESULTS: Here, we used chromosome-level genome assemblies of 185 lepidopteran insects to reconstruct an ancestral reference genome and proposed a new chromosome nomenclature. Thus, we renamed over 5000 extant chromosomes with this system, revealing the historical events of chromosomal rearrangements and their features. Additionally, our findings indicate that, compared with autosomes, the Z chromosome in Lepidoptera underwent a fast loss of conserved genes, rapid acquisition of lineage-specific genes, and a low rate of gene duplication. Moreover, we presented evidence that all available 67 W chromosomes originated from a common ancestor chromosome, with four neo-W chromosomes identified, including one generated by fusion with an autosome and three derived through horizontal gene transfer. We also detected nearly 4000 inter-chromosomal gene movement events. Notably, Geminin is transferred from the autosome to the Z chromosome. When located on the autosome, Geminin shows female-biased expression, but on the Z chromosome, it exhibits male-biased expression. This contributes to the sexual dimorphism of body size in silkworms.<br><br>CONCLUSIONS: Our study sheds light on the complex evolutionary history of lepidopteran chromosomes based on ancestral chromosome reconstruction and novel chromosome nomenclature.}, }
@article {pmid37980566, year = {2023}, author = {Lee, IPA and Eldakar, OT and Gogarten, JP and Andam, CP}, title = {Protocol for an agent-based model of recombination in bacteria playing a public goods game.}, journal = {STAR protocols}, volume = {4}, number = {4}, pages = {102733}, pmid = {37980566}, issn = {2666-1667}, mesh = {*Game Theory ; *Bacteria ; }, abstract = {Agent-based models are composed of individual agents coded for traits, such as cooperation and cheating, that interact in a virtual world based on defined rules. Here, we describe the use of an agent-based model of homologous recombination in bacteria playing a public goods game. We describe steps for software installation, setting model parameters, running and testing models, and visualization and statistical analysis. This protocol is useful in analyses of horizontal gene transfer, bacterial sociobiology, and game theory. For complete details on the use and execution of this protocol, please refer to Lee et al.[1].}, }
@article {pmid37980337, year = {2023}, author = {Yenew, B and Ghodousi, A and Diriba, G and Tesfaye, E and Cabibbe, AM and Amare, M and Moga, S and Alemu, A and Dagne, B and Sinshaw, W and Mollalign, H and Meaza, A and Tadesse, M and Gamtesa, DF and Abebaw, Y and Seid, G and Zerihun, B and Getu, M and Chiacchiaretta, M and Gaudin, C and Marceau, M and Didelot, X and Tolera, G and Abdella, S and Kebede, A and Getahun, M and Mehammed, Z and Supply, P and Cirillo, DM}, title = {A smooth tubercle bacillus from Ethiopia phylogenetically close to the Mycobacterium tuberculosis complex.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7519}, pmid = {37980337}, issn = {2041-1723}, support = {D43 TW009127/TW/FIC NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Mycobacterium tuberculosis ; Phylogeny ; Ethiopia ; *Tuberculosis/microbiology ; Africa, Eastern ; }, abstract = {The Mycobacterium tuberculosis complex (MTBC) includes several human- and animal-adapted pathogens. It is thought to have originated in East Africa from a recombinogenic Mycobacterium canettii-like ancestral pool. Here, we describe the discovery of a clinical tuberculosis strain isolated in Ethiopia that shares archetypal phenotypic and genomic features of M. canettii strains, but represents a phylogenetic branch much closer to the MTBC clade than to the M. canettii strains. Analysis of genomic traces of horizontal gene transfer in this isolate and previously identified M. canettii strains indicates a persistent albeit decreased recombinogenic lifestyle near the emergence of the MTBC. Our findings support that the MTBC emergence from its putative free-living M. canettii-like progenitor is evolutionarily very recent, and suggest the existence of a continuum of further extant derivatives from ancestral stages, close to the root of the MTBC, along the Great Rift Valley.}, }
@article {pmid37976849, year = {2024}, author = {Li, YJ and Yuan, Y and Tan, WB and Xi, BD and Wang, H and Hui, KL and Chen, JB and Zhang, YF and Wang, LF and Li, RF}, title = {Antibiotic resistance genes and heavy metals in landfill: A review.}, journal = {Journal of hazardous materials}, volume = {464}, number = {}, pages = {132395}, doi = {10.1016/j.jhazmat.2023.132395}, pmid = {37976849}, issn = {1873-3336}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; *Metals, Heavy ; Drug Resistance, Microbial/genetics ; Waste Disposal Facilities ; }, abstract = {Landfill is reservoir containing antibiotic resistance genes (ARGs) that pose a threat to human life and health. Heavy metals impose lasting effects on ARGs. This review investigated and analyzed the distribution, composition, and abundance of heavy metals and ARGs in landfill. The abundance ranges of ARGs detected in refuse and leachate were similar. The composition of ARG varied with sampling depth in refuse. ARG in leachate varies with the distribution of ARG in the refuse. The ARG of sulI was associated with 11 metals (Co, Pb, Mn, Zn, Cu, Cr, Ni, Sb, As, Cd, and Al). The effects of the total metal concentration on ARG abundance were masked by many factors. Low heavy metal concentrations showed positive effects on ARG diffusion; conversely, high heavy metal concentrations showed negative effects. Organic matter had a selective pressure effect on microorganisms and could provide energy for the diffusion of ARGs. Complexes of heavy metals and organic matter were common in landfill. Therefore, the hypothesis was proposed that organic matter and heavy metals have combined effects on the horizontal gene transfer (HGT) of ARGs during landfill stabilization. This work provides a new basis to better understand the HGT of ARGs in landfill.}, }
@article {pmid37976735, year = {2024}, author = {Gao, Y and Liu, J and Fang, Y and Xu, X and Wang, F and Tang, Y and Yin, D and Cookson, AL and Zhu, W and Mao, S and Zhong, R}, title = {Straw-based compost cultivation disproportionally contributes to the environmental persistence of antibiotic resistance from raw cattle manure to organic vegetables.}, journal = {Microbiological research}, volume = {278}, number = {}, pages = {127540}, doi = {10.1016/j.micres.2023.127540}, pmid = {37976735}, issn = {1618-0623}, mesh = {*Manure ; Drug Resistance, Microbial/genetics ; Metagenome ; Anti-Bacterial Agents/pharmacology ; *Composting ; Cattle ; Soil/chemistry ; Agaricus ; Animals ; Vegetables ; }, abstract = {Cattle manure, is a reservoir of antimicrobial resistance genes, but the mechanisms by which they migrate from farm to table remain obscure. Here, we chose Agaricus bisporus as a model vegetable to examine such migration and characterized the resistome in 112 metagenomes covering samples from raw manure, composting substrates, rhizosphere, and surfaces of mushrooms. A total of 1864 resistance genes, representing 113 unique mechanisms of resistance, were identified. Monensin treatment on beef specifically enriched fecal resistance genes within Moraxellaceae, but this effect did not persist in downstream mushrooms. Interestingly, we found that resistance genes were significantly more enriched on mushroom surfaces when cultivated with corn-based compost compared to rice and wheat, likely a result of the disproportional propagation of Pseudomonadaceae and varied ability of lateral gene transfer. Importantly, our sequence alignment together with genome-centric analysis observed that 89 resistance genes, mainly conferring resistance to drug and biocide (20.22%) and mercury (19.10%), were shared across all types of samples, indicating an efficient transmission of resistance in food production. Moreover, co-occurrence of genes conferring resistance to different compounds frequently occurred in parallel with microbial migration. Together, we present the influences of antibiotic treatment and straw-based composting on resistome along the mushroom production chain (from manure to straw-based compost, rhizosphere of compost cultivated mushroom and surface of mushroom) and highlighted the risks of resistance genes migration.}, }
@article {pmid37975503, year = {2023}, author = {Irby, I and Brown, SP}, title = {The social lives of viruses and other mobile genetic elements: a commentary on Leeks et al. 2023.}, journal = {Journal of evolutionary biology}, volume = {36}, number = {11}, pages = {1582-1586}, pmid = {37975503}, issn = {1420-9101}, support = {R21 AI156817/AI/NIAID NIH HHS/United States ; 5R21AI156817-02/NH/NIH HHS/United States ; }, mesh = {*Onions/genetics ; Gene Transfer, Horizontal ; Plasmids ; *Viruses/genetics ; Interspersed Repetitive Sequences ; }, abstract = {Illustration of life-histories of phages and plasmids through horizontal and vertical transmission (see Figure 1 for more information).}, }
@article {pmid37974331, year = {2024}, author = {Zhang, Y and Ding, N and Li, Y and Ouyang, M and Fu, P and Peng, Y and Tan, Y}, title = {Transcription factor FOXM1 specifies chromatin DNA to extracellular vesicles.}, journal = {Autophagy}, volume = {20}, number = {5}, pages = {1054-1071}, pmid = {37974331}, issn = {1554-8635}, mesh = {*Extracellular Vesicles/metabolism ; *Forkhead Box Protein M1/metabolism/genetics ; Humans ; *Chromatin/metabolism ; *DNA/metabolism ; *Autophagy/genetics ; Lysosomes/metabolism ; Microtubule-Associated Proteins/metabolism ; Protein Binding ; Cell Nucleus/metabolism ; Homeodomain Proteins/metabolism/genetics ; }, abstract = {Extracellular vesicle DNAs (evDNAs) hold significant diagnostic value for various diseases and facilitate transcellular transfer of genetic material. Our study identifies transcription factor FOXM1 as a mediator for directing chromatin genes or DNA fragments (termed FOXM1-chDNAs) to extracellular vesicles (EVs). FOXM1 binds to MAP1LC3/LC3 in the nucleus, and FOXM1-chDNAs, such as the DUX4 gene and telomere DNA, are designated by FOXM1 binding and translocated to the cytoplasm before being released to EVs through the secretory autophagy during lysosome inhibition (SALI) process involving LC3. Disrupting FOXM1 expression or the SALI process impairs FOXM1-chDNAs incorporation into EVs. FOXM1-chDNAs can be transmitted to recipient cells via EVs and expressed in recipient cells when they carry functional genes. This finding provides an example of how chromatin DNA fragments are specified to EVs by transcription factor FOXM1, revealing its contribution to the formation of evDNAs from nuclear chromatin. It provides a basis for further exploration of the roles of evDNAs in biological processes, such as horizontal gene transfer.Abbreviation: ATG5: autophagy related 5; CCFs: cytoplasmic chromatin fragments; ChIP: chromatin immunoprecipitation; cytoDNA: cytoplasmic DNA; CQ: chloroquine; FOXM1-DBD: FOXM1 DNA binding domain; DUX4:double homeobox 4; EVs: extracellular vesicles; evDNAs: extracellular vesicle DNAs; FOXM1: forkhead box M1; FOXM1-chDNAs: chromatin DNA fragments directed by FOXM1 to EVs; HGT: horizontal gene transfer; LC3-II: lipid modified LC3; LMNB1: lamin B1; LIR: LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MVBs: multivesicular bodies; M1-binding DNA: a linear DNA containing 72× FOXM1 binding sites; SALI: secretory autophagy during lysosome inhibition; siRNA: small interfering RNA; TetO-DUX4: TetO array-containing DUX4 DNA; TetO: tet operator; TetR: tet repressor.}, }
@article {pmid37974017, year = {2023}, author = {Thepmanee, O and Munkongwongsiri, N and Prachumwat, A and Saksmerprome, V and Jitrakorn, S and Sritunyalucksana, K and Vanichviriyakit, R and Chanarat, S and Jaroenlak, P and Itsathitphaisarn, O}, title = {Molecular and cellular characterization of four putative nucleotide transporters from the shrimp microsporidian Enterocytozoon hepatopenaei (EHP).}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {20008}, pmid = {37974017}, issn = {2045-2322}, mesh = {Animals ; *Microsporidia ; Nucleotides ; Phylogeny ; *Enterocytozoon/genetics ; *Penaeidae/parasitology ; }, abstract = {Microsporidia are obligate intracellular parasites that lost several enzymes required in energy production. The expansion of transporter families in these organisms enables them to hijack ATP from hosts. In this study, nucleotide transporters of the microsporidian Enterocytozoon hepatopenaei (EHP), which causes slow growth in economically valuable Penaeus shrimp, were characterized. Analysis of the EHP genome suggested the presence of four putative nucleotide transporter genes, namely EhNTT1, EhNTT2, EhNTT3, and EhNTT4. Sequence alignment revealed four charged amino acids that are conserved in previously characterized nucleotide transporters. Phylogenetic analysis suggested that EhNTT1, 3, and 4 were derived from one horizontal gene transfer event, which was independent from that of EhNTT2. Localization of EhNTT1 and EhNTT2 using immunofluorescence analysis revealed positive signals within the envelope of developing plasmodia and on mature spores. Knockdown of EhNTT2 by double administration of sequence specific double-stranded RNA resulted in a significant reduction in EHP copy numbers, suggesting that EhNTT2 is crucial for EHP replication in shrimp. Taken together, the insight into the roles of NTTs in microsporidian proliferation can provide the biological basis for the development of alternative control strategies for microsporidian infection in shrimp.}, }
@article {pmid37973843, year = {2023}, author = {Allard, N and Collette, A and Paquette, J and Rodrigue, S and Côté, JP}, title = {Systematic investigation of recipient cell genetic requirements reveals important surface receptors for conjugative transfer of IncI2 plasmids.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {1172}, pmid = {37973843}, issn = {2399-3642}, support = {5014521//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en G&#xe9;nie du Canada)/ ; 571440//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en G&#xe9;nie du Canada)/ ; 314063//Fonds de Recherche du Qu&#xe9;bec - Nature et Technologies (Quebec Fund for Research in Nature and Technology)/ ; }, mesh = {Plasmids/genetics ; *Escherichia coli/metabolism ; *Conjugation, Genetic ; Adhesins, Bacterial/genetics ; Gene Transfer, Horizontal ; }, abstract = {Bacterial conjugation is a major horizontal gene transfer mechanism. While the functions encoded by many conjugative plasmids have been intensively studied, the contribution of recipient chromosome-encoded genes remains largely unknown. Here, we analyzed the genetic requirement of recipient cells for conjugation of IncI2 plasmid TP114, which was recently shown to transfer at high rates in the gut microbiota. We performed transfer assays with ~4,000 single-gene deletion mutants of Escherichia coli. When conjugation occurs on a solid medium, we observed that recipient genes impairing transfer rates were not associated with a specific cellular function. Conversely, transfer assays performed in broth were largely dependent on the lipopolysaccharide biosynthesis pathway. We further identified specific structures in lipopolysaccharides used as recipient cell surface receptors by PilV adhesins associated with the type IVb accessory pilus of TP114. Our strategy is applicable to study other mobile genetic elements and understand important host cell factors for their dissemination.}, }
@article {pmid37972772, year = {2024}, author = {Xin, R and Zhang, Y and Zhang, K and Yang, Y and Ma, Y and Niu, Z}, title = {Investigation of the antimicrobial susceptibility patterns of marine cyanobacteria in Bohai Bay: Cyanobacteria may be important hosts of antibiotic resistance genes in marine environment.}, journal = {The Science of the total environment}, volume = {909}, number = {}, pages = {168516}, doi = {10.1016/j.scitotenv.2023.168516}, pmid = {37972772}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/pharmacology/analysis ; Genes, Bacterial ; Bays ; Drug Resistance, Microbial/genetics ; *Cyanobacteria/genetics ; }, abstract = {Marine cyanobacteria, as widely distributed and photosynthetically autotrophic bacteria in the ocean, may contribute to the global dissemination of antibiotic resistance genes (ARGs) and develop a different antimicrobial susceptibility pattern from heterotrophic bacteria and cyanobacteria from freshwater environments. However, studies on antimicrobial susceptibility and the carriage of ARGs in marine cyanobacteria are still very limited. In this study, the antibiotic resistance characteristics of cyanobacteria in nearshore waters were examined through field monitoring and laboratory investigations, which included PCR detection and ARG transformation. The results showed a positive correlation between marine cyanobacteria and some ARGs in the nearshore waters of Bohai Bay. Moreover, most screened cyanobacteria showed high minimum inhibitory concentration (MIC) values for polymyxins, tetracyclines, kanamycin, and sulfonamides, moderate MIC values for streptomycin, chloramphenicol, rifampicin, and norfloxacin, and low MIC values for roxithromycin and cephalosporins. The blaTEM, blaKPC, sul1, sul2, strA, tetA, tetB, tetC, tetM, mdfA, and intI1 genes were detected in the screened marine cyanobacteria. The highest detection rates were observed for blaTEM (93.3 %), sul1 (56.6 %), sul2 (90 %), and strA (73.3 %). The detection rate of tetA (33.3 %) was the highest among the tetracycline resistance genes, and mdfA, a multidrug-resistant pump gene with resistance to tetracycline, also showed a high detection level (23.3 %). Overall, most of the screened marine cyanobacteria were found to tolerate multiple antibiotics in seawater, and the condition of the ARGs carriage was serious. Furthermore, the screened marine Synechocystis sp. C12-2 demonstrated the ability to accept ARGs on the RP4 plasmid through natural transformation and showed reduced sensitivity to ampicillin, suggesting the possibility that some marine cyanobacteria could acquire ARGs from the environment through horizontal gene transfer. Thus, marine cyanobacteria may play an important role in the propagation of marine ARGs.}, }
@article {pmid37971327, year = {2023}, author = {Förster, M and Rathmann, I and Yüksel, M and Power, JJ and Maier, B}, title = {Genome-wide transformation reveals extensive exchange across closely related Bacillus species.}, journal = {Nucleic acids research}, volume = {51}, number = {22}, pages = {12352-12366}, pmid = {37971327}, issn = {1362-4962}, support = {CRC 1310//Deutsche Forschungsgemeinschaft/ ; //University of Cologne/ ; }, mesh = {*Bacillus/classification/genetics ; Bacillus subtilis/genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial/genetics ; Phylogeny ; *Transformation, Genetic ; }, abstract = {Bacterial transformation is an important mode of horizontal gene transfer that helps spread genetic material across species boundaries. Yet, the factors that pose barriers to genome-wide cross-species gene transfer are poorly characterized. Here, we develop a replacement accumulation assay to study the effects of genomic distance on transfer dynamics. Using Bacillus subtilis as recipient and various species of the genus Bacillus as donors, we find that the rate of orthologous replacement decreases exponentially with the divergence of their core genomes. We reveal that at least 96% of the B. subtilis core genes are accessible to replacement by alleles from Bacillus spizizenii. For the more distantly related Bacillus atrophaeus, gene replacement events cluster at genomic locations with high sequence identity and preferentially replace ribosomal genes. Orthologous replacement also creates mosaic patterns between donor and recipient genomes, rearranges the genome architecture, and governs gain and loss of accessory genes. We conclude that cross-species gene transfer is dominated by orthologous replacement of core genes which occurs nearly unrestricted between closely related species. At a lower rate, the exchange of accessory genes gives rise to more complex genome dynamics.}, }
@article {pmid37971255, year = {2023}, author = {Martínez-Alvarez, L and Ramond, J-B and Vikram, S and León-Sobrino, C and Maggs-Kölling, G and Cowan, DA}, title = {With a pinch of salt: metagenomic insights into Namib Desert salt pan microbial mats and halites reveal functionally adapted and competitive communities.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {12}, pages = {e0062923}, pmid = {37971255}, issn = {1098-5336}, support = {113308//National Research Foundation (NRF)/ ; }, mesh = {*Bacteria/genetics ; Desert Climate ; Soil Microbiology ; Sodium Chloride ; *Microbiota ; }, abstract = {The hyperarid Namib Desert is one of the oldest deserts on Earth. It contains multiple clusters of playas which are saline-rich springs surrounded by halite evaporites. Playas are of great ecological importance, and their indigenous (poly)extremophilic microorganisms are potentially involved in the precipitation of minerals such as carbonates and sulfates and have been of great biotechnological importance. While there has been a considerable amount of microbial ecology research performed on various Namib Desert edaphic microbiomes, little is known about the microbial communities inhabiting its multiple playas. In this work, we provide a comprehensive taxonomic and functional potential characterization of the microbial, including viral, communities of sediment mats and halites from two distant salt pans of the Namib Desert, contributing toward a better understanding of the ecology of this biome.}, }
@article {pmid37971242, year = {2023}, author = {Lerminiaux, N and Mitchell, R and Bartoszko, J and Davis, I and Ellis, C and Fakharuddin, K and Hota, SS and Katz, K and Kibsey, P and Leis, JA and Longtin, Y and McGeer, A and Minion, J and Mulvey, M and Musto, S and Rajda, E and Smith, SW and Srigley, JA and Suh, KN and Thampi, N and Tomlinson, J and Wong, T and Mataseje, L and , }, title = {Plasmid genomic epidemiology of blaKPC carbapenemase-producing Enterobacterales in Canada, 2010-2021.}, journal = {Antimicrobial agents and chemotherapy}, volume = {67}, number = {12}, pages = {e0086023}, pmid = {37971242}, issn = {1098-6596}, support = {//Public Health Agency of Canada (PHAC)/ ; }, mesh = {Humans ; Canada/epidemiology ; *beta-Lactamases/genetics/metabolism ; Plasmids/genetics ; Bacterial Proteins/genetics ; Klebsiella pneumoniae ; Anti-Bacterial Agents/pharmacology ; Carbapenems/pharmacology ; Genomics ; *Klebsiella Infections/epidemiology ; Microbial Sensitivity Tests ; }, abstract = {Carbapenems are considered last-resort antibiotics for the treatment of infections caused by multidrug-resistant Enterobacterales, but carbapenem resistance due to acquisition of carbapenemase genes is a growing threat that has been reported worldwide. Klebsiella pneumoniae carbapenemase (blaKPC) is the most common type of carbapenemase in Canada and elsewhere; it can hydrolyze penicillins, cephalosporins, aztreonam, and carbapenems and is frequently found on mobile plasmids in the Tn4401 transposon. This means that alongside clonal expansion, blaKPC can disseminate through plasmid- and transposon-mediated horizontal gene transfer. We applied whole genome sequencing to characterize the molecular epidemiology of 829 blaKPC carbapenemase-producing isolates collected by the Canadian Nosocomial Infection Surveillance Program from 2010 to 2021. Using a combination of short-read and long-read sequencing, we obtained 202 complete and circular blaKPC-encoding plasmids. Using MOB-suite, 10 major plasmid clusters were identified from this data set which represented 87% (175/202) of the Canadian blaKPC-encoding plasmids. We further estimated the genomic location of incomplete blaKPC-encoding contigs and predicted a plasmid cluster for 95% (603/635) of these. We identified different patterns of carbapenemase mobilization across Canada related to different plasmid clusters, including clonal transmission of IncF-type plasmids (108/829, 13%) in K. pneumoniae clonal complex 258 and novel repE(pEh60-7) plasmids (44/829, 5%) in Enterobacter hormaechei ST316, and horizontal transmission of IncL/M (142/829, 17%) and IncN-type plasmids (149/829, 18%) across multiple genera. Our findings highlight the diversity of blaKPC genomic loci and indicate that multiple, distinct plasmid clusters have contributed to blaKPC spread and persistence in Canada.}, }
@article {pmid37968548, year = {2024}, author = {Naidoo, Y and Pierneef, RE and Cowan, DA and Valverde, A}, title = {Characterization of the soil resistome and mobilome in Namib Desert soils.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {27}, number = {4}, pages = {967-975}, pmid = {37968548}, issn = {1618-1905}, mesh = {*Soil Microbiology ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; *Phylogeny ; *Desert Climate ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Metagenomics ; Gene Transfer, Horizontal ; Soil/chemistry ; Genes, Bacterial ; Interspersed Repetitive Sequences ; }, abstract = {The study of the soil resistome is important in understanding the evolution of antibiotic resistance and its dissemination between the clinic and the environment. However, very little is known about the soil resistome, especially of those from deserts. Here, we characterize the bacterial communities, using targeted sequencing of the 16S rRNA genes, and both the resistome and the mobilome in Namib Desert soils, using shotgun metagenomics. We detected a variety of antibiotic resistance genes (ARGs) that conferred resistance to antibiotics such as elfamycin, rifampicin, and fluoroquinolones, metal/biocide resistance genes (MRGs/BRGs) conferring resistance to metals such as arsenic and copper, and mobile genetic elements (MGEs) such as the ColE1-like plasmid. The presence of metal/biocide resistance genes in close proximity to ARGs indicated a potential for co-selection of resistance to antibiotics and metals/biocides. The co-existence of MGEs and horizontally acquired ARGs most likely contributed to a decoupling between bacterial community composition and ARG profiles. Overall, this study indicates that soil bacterial communities in Namib Desert soils host a diversity of resistance elements and that horizontal gene transfer, rather than host phylogeny, plays an essential role in their dynamics.}, }
@article {pmid37966605, year = {2024}, author = {Chu Yuan Kee, MJ and Chen, J}, title = {Phage Transduction of Staphylococcus aureus.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2738}, number = {}, pages = {263-275}, pmid = {37966605}, issn = {1940-6029}, mesh = {Humans ; *Lysogeny ; Transduction, Genetic ; Staphylococcus aureus/genetics ; Staphylococcus Phages/genetics ; Anti-Bacterial Agents ; *Staphylococcal Infections/microbiology ; Gene Transfer, Horizontal ; }, abstract = {Bacteriophage transduction is the major mechanism of horizontal gene transfer (HGT) among many bacteria. In Staphylococcus aureus, the phage-mediated acquisition of mobile genetic elements (MGEs) that encode virulence and antibiotic resistance genes largely contribute to its evolutionary adaptation and genetic plasticity. In molecular biology, generalized transduction is routinely used as a technique to manipulate and construct bacterial strains. Here, we describe optimized protocols for generalized transduction, applicable for the transfer of plasmid or chromosomal deoxyribonucleic acid (DNA) from donor to recipient S. aureus strains.}, }
@article {pmid37966239, year = {2023}, author = {Maccario, L and Silva, AF and Nesme, J and Amador, CI and Sørensen, SJ and Cooper, VS and Røder, HL}, title = {Draft genomes of seven isolates from Danish wastewater facilities belonging to Pseudomonas, Bacillus, Pseudochrobactrum, Brevundimonas, and Pandoraea.}, journal = {Microbiology resource announcements}, volume = {12}, number = {12}, pages = {e0052923}, pmid = {37966239}, issn = {2576-098X}, support = {794315//Horizon 2020 Framework Programme (H2020)/ ; 34434//Villum Fonden (Villum Foundation)/ ; 874735//EC | Horizon 2020 Framework Programme (H2020)/ ; }, abstract = {We report here seven draft genomes of bacterial strains from two Danish wastewater facilities, two of which might be characterized as a new group within the Pseudomonas and Pseudochrobactrum genera, respectively. These genomes will provide useful references for understanding bacterial interactions and horizontal gene transfer within bacterial communities.}, }
@article {pmid37965050, year = {2023}, author = {Kormos, A and Dimopoulos, G and Bier, E and Lanzaro, GC and Marshall, JM and James, AA}, title = {Conceptual risk assessment of mosquito population modification gene-drive systems to control malaria transmission: preliminary hazards list workshops.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {11}, number = {}, pages = {1261123}, pmid = {37965050}, issn = {2296-4185}, support = {R01 AI158615/AI/NIAID NIH HHS/United States ; R01 GM117321/GM/NIGMS NIH HHS/United States ; R21 AI168873/AI/NIAID NIH HHS/United States ; R01 AI170692/AI/NIAID NIH HHS/United States ; R01 AI162911/AI/NIAID NIH HHS/United States ; }, abstract = {The field-testing and eventual adoption of genetically-engineered mosquitoes (GEMs) to control vector-borne pathogen transmission will require them meeting safety criteria specified by regulatory authorities in regions where the technology is being considered for use and other locales that might be impacted. Preliminary risk considerations by researchers and developers may be useful for planning the baseline data collection and field research used to address the anticipated safety concerns. Part of this process is to identify potential hazards (defined as the inherent ability of an entity to cause harm) and their harms, and then chart the pathways to harm and evaluate their probability as part of a risk assessment. The University of California Malaria Initiative (UCMI) participated in a series of workshops held to identify potential hazards specific to mosquito population modification strains carrying gene-drive systems coupled to anti-parasite effector genes and their use in a hypothetical island field trial. The hazards identified were placed within the broader context of previous efforts discussed in the scientific literature. Five risk areas were considered i) pathogens, infections and diseases, and the impacts of GEMs on human and animal health, ii) invasiveness and persistence of GEMs, and interactions of GEMs with target organisms, iii) interactions of GEMs with non-target organisms including horizontal gene transfer, iv) impacts of techniques used for the management of GEMs and v) evolutionary and stability considerations. A preliminary hazards list (PHL) was developed and is made available here. This PHL is useful for internal project risk evaluation and is available to regulators at prospective field sites. UCMI project scientists affirm that the subsequent processes associated with the comprehensive risk assessment for the application of this technology should be driven by the stakeholders at the proposed field site and areas that could be affected by this intervention strategy.}, }
@article {pmid37963249, year = {2023}, author = {Goldlust, K and Ducret, A and Halte, M and Dedieu-Berne, A and Erhardt, M and Lesterlin, C}, title = {The F pilus serves as a conduit for the DNA during conjugation between physically distant bacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {47}, pages = {e2310842120}, pmid = {37963249}, issn = {1091-6490}, support = {FRM-EQU202103012587//Fondation pour la Recherche M&#xe9;dicale (FRM)/ ; ANR-18-CE35-0008//Agence Nationale de la Recherche (ANR)/ ; ANR-22-CE12-0032//Agence Nationale de la Recherche (ANR)/ ; no. 113_MC_GH_MEL-BER_Erhardt_HU//Berlin University Alliance (BUA)/ ; }, mesh = {*Escherichia coli/genetics ; *Genes, Bacterial ; Plasmids/genetics ; Fimbriae, Bacterial/genetics ; DNA, Bacterial/genetics ; Conjugation, Genetic ; DNA ; Gene Transfer, Horizontal ; }, abstract = {Horizontal transfer of F-like plasmids by bacterial conjugation is responsible for disseminating antibiotic resistance and virulence determinants among pathogenic Enterobacteriaceae species, a growing health concern worldwide. Central to this process is the conjugative F pilus, a long extracellular filamentous polymer that extends from the surface of plasmid donor cells, allowing it to probe the environment and make contact with the recipient cell. It is well established that the F pilus can retract to bring mating pair cells in tight contact before DNA transfer. However, whether DNA transfer can occur through the extended pilus has been a subject of active debate. In this study, we use live-cell microscopy to show that while most transfer events occur between cells in direct contact, the F pilus can indeed serve as a conduit for the DNA during transfer between physically distant cells. Our findings enable us to propose a unique model for conjugation that revises our understanding of the DNA transfer mechanism and the dissemination of drug resistance and virulence genes within complex bacterial communities.}, }
@article {pmid37959048, year = {2023}, author = {Qin, Y and Huang, W and Yang, J and Zhao, Y and Zhao, M and Xu, H and Zhang, M}, title = {The Antibiotic Resistome and Its Association with Bacterial Communities in Raw Camel Milk from Altay Xinjiang.}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {21}, pages = {}, pmid = {37959048}, issn = {2304-8158}, support = {2022D01C404//Natural Science Foundation of Xinjiang/ ; 2019Q002//Natural Science Foundation of Xinjiang/ ; 2022D01D42//Natural Science Foundation of Xinjiang/ ; }, abstract = {Raw camel milk is generally contaminated with varied microbiota, including antibiotic-resistant bacteria (ARB), that can act as a potential pathway for the spread of antibiotic resistance genes (ARGs). In this study, high-throughput quantitative PCR and 16S rRNA gene-based Illumine sequencing data were used to establish a comprehensive understanding of the antibiotic resistome and its relationship with the bacterial community in Bactrian camel milk from Xinjiang. A total of 136 ARGs and up to 1.33 × 10[8] total ARG copies per gram were identified, which predominantly encode resistance to β-lactamas and multidrugs. The ARGs' profiles were mainly explained by interactions between the bacteria community and physicochemical indicators (77.9%). Network analysis suggested that most ARGs exhibited co-occurrence with Corynebacterium, Leuconostoc and MGEs. Overall, raw camel milk serves as a reservoir for ARGs, which may aggravate the spread of ARGs through vertical and horizontal gene transfer in the food chain.}, }
@article {pmid37955258, year = {2024}, author = {Gong, P and Liu, H and Yu, T and Jiang, C and Gou, E and Guan, J and Chen, H and Kang, H}, title = {Evaluation of resistance risk in soil due to antibiotics during application of penicillin V fermentation residue.}, journal = {Environmental technology}, volume = {45}, number = {24}, pages = {5173-5181}, doi = {10.1080/09593330.2023.2283807}, pmid = {37955258}, issn = {1479-487X}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Soil Microbiology ; *Penicillin V ; Soil Pollutants/analysis ; Fermentation ; Drug Resistance, Microbial/genetics ; Soil/chemistry ; Genes, Bacterial ; Gene Transfer, Horizontal ; }, abstract = {The soil application of hydrothermally treated penicillin V fermentation residue (PFR) is attractive but challenged, due to the concern of the resistance risk in soil related to residual antibiotics. In this study, a lab-scale incubation experiment was conducted to investigate the influence of penicillin V on antibiotic resistance genes (ARGs) in PFR-amended soil via qPCR. The introduced penicillin V in soil could not be persistent, and its degradation occurred mainly within 2 days. The higher number of soil ARGs was detected under 108 mg/kg of penicillin V than lower contents (≤54 mg/kg). Additionally, the relative abundance of ARGs was higher in soil spiked with penicillin V than that in blank soil, and the great increase in the relative abundance of soil ARGs occurred earlier under 108 mg/kg of penicillin V than lower contents. The horizontal gene transfer might contribute to the shift of ARGs in PFR-amended soil. The results indicated that the residual penicillin V could cause the proliferation of soil ARGs and should be completely removed by hydrothermal treatment before soil application. The results of this study provide a comprehensive understanding of the resistance risk posed by penicillin V during the application of hydrothermally pretreated PFR.}, }
@article {pmid37953666, year = {2023}, author = {Pandey, T and Kalluraya, CA and Wang, B and Xu, T and Huang, X and Guang, S and Daugherty, MD and Ma, DK}, title = {Acquired stress resilience through bacteria-to-nematode interdomain horizontal gene transfer.}, journal = {The EMBO journal}, volume = {42}, number = {24}, pages = {e114835}, pmid = {37953666}, issn = {1460-2075}, support = {P40 OD010440/OD/NIH HHS/United States ; R35 GM133633/GM/NIGMS NIH HHS/United States ; R35 GM139618/GM/NIGMS NIH HHS/United States ; P40 OD010440/CD/ODCDC CDC HHS/United States ; }, mesh = {Animals ; Caenorhabditis elegans/metabolism ; Phylogeny ; Gene Transfer, Horizontal ; Rhamnose/metabolism ; *Resilience, Psychological ; *Nematoda ; Bacteria/genetics ; }, abstract = {Natural selection drives the acquisition of organismal resilience traits to protect against adverse environments. Horizontal gene transfer (HGT) is an important evolutionary mechanism for the acquisition of novel traits, including metazoan acquisitions in immunity, metabolic, and reproduction function via interdomain HGT (iHGT) from bacteria. Here, we report that the nematode gene rml-3 has been acquired by iHGT from bacteria and that it enables exoskeleton resilience and protection against environmental toxins in Caenorhabditis elegans. Phylogenetic analysis reveals that diverse nematode RML-3 proteins form a single monophyletic clade most similar to bacterial enzymes that biosynthesize L-rhamnose, a cell-wall polysaccharide component. C. elegans rml-3 is highly expressed during larval development and upregulated in developing seam cells upon heat stress and during the stress-resistant dauer stage. rml-3 deficiency impairs cuticle integrity, barrier functions, and nematode stress resilience, phenotypes that can be rescued by exogenous L-rhamnose. We propose that interdomain HGT of an ancient bacterial rml-3 homolog has enabled L-rhamnose biosynthesis in nematodes, facilitating cuticle integrity and organismal resilience to environmental stressors during evolution. These findings highlight a remarkable contribution of iHGT on metazoan evolution conferred by the domestication of a bacterial gene.}, }
@article {pmid37952399, year = {2023}, author = {Salter, C and Westrick, JA and Chaganti, SR and Birbeck, JA and Peraino, NJ and Weisener, CG}, title = {Elucidating microbial mechanisms of microcystin-LR degradation in Lake Erie beach sand through metabolomics and metatranscriptomics.}, journal = {Water research}, volume = {247}, number = {}, pages = {120816}, doi = {10.1016/j.watres.2023.120816}, pmid = {37952399}, issn = {1879-2448}, mesh = {Lakes/microbiology ; Microcystins/metabolism ; Sand ; *Cyanobacteria/metabolism ; *Microbiota ; Nitrogen/metabolism ; Ontario ; }, abstract = {As one of five Laurentian Great Lakes, Lake Erie ranks among the top freshwater drinking sources and ecosystems globally. Historical and current agriculture mismanagement and climate change sustains the environmental landscape for late summer cyanobacterial harmful algal blooms, and consequently, cyanotoxins such as microcystin (MC). Microcystin microbial degradation is a promising mitigation strategy, however the mechanisms controlling the breakdown of MCs in Lake Erie are not well understood. Pelee Island, Ontario, Canada is located in the western basin of Lake Erie and the bacterial community in the sand has demonstrated the capacity of metabolizing the toxin. Through a multi-omic approach, the metabolic, functional and taxonomical signatures of the Pelee Island microbial community during MC-LR degradation was investigated over a 48-hour period to comprehensively study the degradation mechanism. Cleavage of bonds surrounding nitrogen atoms and the upregulation of nitrogen deamination (dadA, alanine dehydrogenase, leucine dehydrogenase) and assimilation genes (glnA, gltB) suggests a targeted isolation of nitrogen by the microbial community for energy production. Methylotrophic pathways RuMP and H4MPT control assimilation and dissimilation of carbon, respectively and differential abundance of Methylophilales indicates an interconnected role through electron exchange of denitrification and methylotrophic pathways. The detected metabolites did not resolve a clear breakdown pathway, but rather the diversity of products in combination with taxonomic and functional results supports that a variety of strategies are applied, such as epoxidation, hydroxylation, and aromatic degradation. Annual repeated exposure to the toxin may have allowed the community to adaptatively establish a novel pathway through functional plasticity and horizontal gene transfer. The culmination of these results reveals the complexity of the Pelee Island sand community and supports a dynamic and cooperative metabolism between microbial species to achieve MC degradation.}, }
@article {pmid37951253, year = {2024}, author = {Kang, Y and Zhao, S and Cheng, H and Xu, W and You, R and Hu, J}, title = {The distribution profiles of tetracycline resistance genes in rice: Comparisons using four genotypes.}, journal = {The Science of the total environment}, volume = {908}, number = {}, pages = {168359}, doi = {10.1016/j.scitotenv.2023.168359}, pmid = {37951253}, issn = {1879-1026}, mesh = {Humans ; *Oryza/genetics ; Tetracycline Resistance/genetics ; Genes, Bacterial ; Tetracycline ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Genotype ; }, abstract = {The potential transmission of antibiotic resistance genes (ARGs) from the rhizosphere to plants and humans poses a significant concern. This study aims to investigate the distribution of tetracycline resistance genes (TRGs) in rice using four genotypes and identify the primary source of TRGs in grains. Quantitative polymerase chain reaction (qPCR) was employed to determine the abundance of seven TRGs and intI1 in four rice varieties and three partitions during the jointing and heading stages, respectively. The analysis of the bacterial community was conducted to elucidate the underlying mechanism of the profiles of TRGs. It was observed that tetZ was predominantly present in the rhizosphere and endoroot, whereas tetX became dominant in grains. The relative abundances of TRGs and intI1 exhibited significant variations across both the variety and partition. However, no significant differences were observed in grains, where the abundances of TRGs were several orders of magnitude lower compared to those in the rhizosphere. Nevertheless, the potential risk of the dissemination of TRGs to humans, particularly those carried by potential pathogens in grains, warrants attention. The increased likelihood of TRGs accumulation in the rhizosphere and endoroot of hybrid rice varieties, as opposed to japonica varieties, may be attributed to the heightened metabolic activities of their roots. The significant associations observed between intI1 and TRGs, coupled with the substantial alterations in potential hosts for intI1 across various treatments, indicate that intI1-mediated horizontal gene transfer plays a role in the diverse range of bacterial hosts for TRGs. The study also revealed that rhizosphere bacteria during the jointing stage serve as the primary contributors of TRGs in grains through the endoroot junction. The findings indicate that Japonica rice varieties exhibit superior control over TRGs compared to hybrid varieties, emphasizing the need for early interventions throughout the entire growth period of rice.}, }
@article {pmid37944236, year = {2024}, author = {Xiao, T and Chen, R and Cai, C and Yuan, S and Dai, X and Dong, B and Xu, Z}, title = {Abatement of antibiotics and resistance genes during catalytic ozonation enhanced sludge dewatering process: Synchronized in volume and hazardousness reduction.}, journal = {Journal of hazardous materials}, volume = {463}, number = {}, pages = {132912}, doi = {10.1016/j.jhazmat.2023.132912}, pmid = {37944236}, issn = {1873-3336}, mesh = {Sewage/microbiology ; Anti-Bacterial Agents/pharmacology ; Tetracycline ; Bacteria/genetics ; Genes, Bacterial ; Norfloxacin ; Ofloxacin ; *Oxytetracycline ; *Ozone ; }, abstract = {Based on the efficiency of the catalytic ozonation techniques (HDWS+O3 and MnFe2O4 @SBC+O3) in enhancing the sludge dewaterability, the effectiveness in synchronized abatement antibiotics and antibiotic resistance genes (ARGs) was conducted to determine. The results revealed that catalytic ozonation conditioning altered the distribution of target antibiotics (tetracycline (TC), oxytetracycline (OTC), norfloxacin (NOR), ofloxacin (OFL)) in the dewatered filtrate, the dewatered sludge cake and the extra-microcolony/cellular polymers (EMPS/ECPS) layers, achieving the redistribution from solid-phase adsorption to liquid-phase dissolution. The total degradation rate was over 90% for TC and OTC, 72-78% for NOR and OFL; the abatement efficiency of eleven ARGs reached 1.47-3.01 log and 1.64-3.59 log, respectively, and more than four eARGs were eliminated. The effective abatement of the absolute abundance of Mobile genetic elements (MGEs) (0.91-1.89 log) demonstrated that catalytic ozonation conditioning could also significantly inhibit horizontal gene transfer (HGT). The abundance of resistant bacteria was greatly reduced and the signal transduction of the typical ARGs host bacteria was inhibited. The highly reactive oxidation species (ROS) generated were responsible for the abatement of antibiotics and ARGs. These findings provided new insights into the sludge conditioning for ideal and synchronized reduction in volume and hazardousness by catalytic ozonation processes in sludge treatment.}, }
@article {pmid37940998, year = {2023}, author = {Schaller, D and Hartmann, T and Lafond, M and Stadler, PF and Wieseke, N and Hellmuth, M}, title = {Relative timing information and orthology in evolutionary scenarios.}, journal = {Algorithms for molecular biology : AMB}, volume = {18}, number = {1}, pages = {16}, pmid = {37940998}, issn = {1748-7188}, support = {RGPIN-2019-05817//Natural Sciences and Engineering Research Council of Canada/ ; 214087123//Deutsche Forschungsgemeinschaft/ ; }, abstract = {BACKGROUND: Evolutionary scenarios describing the evolution of a family of genes within a collection of species comprise the mapping of the vertices of a gene tree T to vertices and edges of a species tree S. The relative timing of the last common ancestors of two extant genes (leaves of T) and the last common ancestors of the two species (leaves of S) in which they reside is indicative of horizontal gene transfers (HGT) and ancient duplications. Orthologous gene pairs, on the other hand, require that their last common ancestors coincides with a corresponding speciation event. The relative timing information of gene and species divergences is captured by three colored graphs that have the extant genes as vertices and the species in which the genes are found as vertex colors: the equal-divergence-time (EDT) graph, the later-divergence-time (LDT) graph and the prior-divergence-time (PDT) graph, which together form an edge partition of the complete graph.<br><br>RESULTS: Here we give a complete characterization in terms of informative and forbidden triples that can be read off the three graphs and provide a polynomial time algorithm for constructing an evolutionary scenario that explains the graphs, provided such a scenario exists. While both LDT and PDT graphs are cographs, this is not true for the EDT graph in general. We show that every EDT graph is perfect. While the information about LDT and PDT graphs is necessary to recognize EDT graphs in polynomial-time for general scenarios, this extra information can be dropped in the HGT-free case. However, recognition of EDT graphs without knowledge of putative LDT and PDT graphs is NP-complete for general scenarios. In contrast, PDT graphs can be recognized in polynomial-time. We finally connect the EDT graph to the alternative definitions of orthology that have been proposed for scenarios with horizontal gene transfer. With one exception, the corresponding graphs are shown to be colored cographs.}, }
@article {pmid37938748, year = {2023}, author = {Zeldes, B and Poehlein, A and Jain, S and Baum, C and Daniel, R and Müller, V and Basen, M}, title = {DNA uptake from a laboratory environment drives unexpected adaptation of a thermophile to a minor medium component.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {2}, pmid = {37938748}, issn = {2730-6151}, support = {BA 5757/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 031B0857A//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 031B0857C//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 031B0857B//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; }, abstract = {DNA uptake is widespread among microorganisms and considered a strategy for rapid adaptation to new conditions. While both DNA uptake and adaptation are referred to in the context of natural environments, they are often studied in laboratories under defined conditions. For example, a strain of the thermophile Thermoanaerobacter kivui had been adapted to growth on high concentrations of carbon monoxide (CO). Unusual phenotypes of the CO-adapted strain prompted us to examine it more closely, revealing a horizontal gene transfer (HGT) event from another thermophile, Thermoanaerobacter sp. strain X514, being cultured in the same laboratory. The transferred genes conferred on T. kivui the ability to utilize trehalose, a trace component of the yeast-extract added to the media during CO-adaptation. This same HGT event simultaneously deleted a native operon for thiamine biosynthesis, which likely explains why the CO-adapted strain grows poorly without added vitamins. Attempts to replicate this HGT by providing T. kivui with genomic DNA from Thermoanaerobacter sp. strain X514 revealed that it is easily reproducible in the lab. This subtle form of "genome contamination" is difficult to detect, since the genome remains predominantly T. kivui, and no living cells from the original contamination remain. Unexpected HGT between two microorganisms as well as simultaneous adaptation to several conditions may occur often and unrecognized in laboratory environments, requiring caution and careful monitoring of phenotype and genotype of microorganisms that are naturally-competent for DNA uptake.}, }
@article {pmid37935916, year = {2023}, author = {An, T and Cai, Y and Li, G and Li, S and Wong, PK and Guo, J and Zhao, H}, title = {Prevalence and transmission risk of colistin and multidrug resistance in long-distance coastal aquaculture.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {115}, pmid = {37935916}, issn = {2730-6151}, support = {U1901210//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41425015//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42122056//&#xc9;cole Nationale d'Ing&#xe9;nieurs de Saint-Etienne (National Engineering School of Saint-&#xc9;tienne)/ ; }, abstract = {Due to the wide use of antibiotics, intensive aquaculture farms have been recognized as a significant reservoir of antibiotic resistomes. Although the prevalence of colistin resistance genes and multidrug-resistant bacteria (MDRB) has been documented, empirical evidence for the transmission of colistin and multidrug resistance between bacterial communities in aquaculture farms through horizontal gene transfer (HGT) is lacking. Here, we report the prevalence and transmission risk of colistin and multidrug resistance in 27 aquaculture water samples from 9 aquaculture zones from over 5000 km of subtropical coastlines in southern China. The colistin resistance gene mcr-1, mobile genetic element (MGE) intl1 and 13 typical antibiotic resistance genes (ARGs) were prevalent in all the aquaculture water samples. Most types of antibiotic (especially colistin) resistance are transmissible in bacterial communities based on evidence from laboratory conjugation and transformation experiments. Diverse MDRB were detected in most of the aquaculture water samples, and a strain with high-level colistin resistance, named Ralstonia pickettii MCR, was isolated. The risk of horizontal transfer of the colistin resistance of R. pickettii MCR through conjugation and transformation was low, but the colistin resistance could be steadily transmitted to offspring through vertical transfer. The findings have important implications for the future regulation of antibiotic use in aquaculture farms globally to address the growing threat posed by antibiotic resistance to human health.}, }
@article {pmid37934408, year = {2023}, author = {Martinez-Varela, A and Casas, G and Berrojalbiz, N and Lundin, D and Piña, B and Dachs, J and Vila-Costa, M}, title = {Metatranscriptomic responses and microbial degradation of background polycyclic aromatic hydrocarbons in the coastal Mediterranean and Antarctica.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {57}, pages = {119988-119999}, pmid = {37934408}, issn = {1614-7499}, support = {CTM2015-70535-P//Ministerio de Ciencia e Innovaci&#xf3;n/ ; CTM2015-65691-R//Ministerio de Ciencia e Innovaci&#xf3;n/ ; CEX2018-000794-S//Ministerio de Ciencia e Innovaci&#xf3;n/ ; 2017SGR800//Ag&#xe8;ncia de Gesti&#xf3; d'Ajuts Universitaris i de Recerca/ ; }, mesh = {*Polycyclic Aromatic Hydrocarbons/analysis ; Antarctic Regions ; Seawater ; *Microbiota ; *Alphaproteobacteria/metabolism ; Biodegradation, Environmental ; }, abstract = {Although microbial degradation is a key sink of polycyclic aromatic hydrocarbons (PAH) in surface seawaters, there is a dearth of field-based evidences of regional divergences in biodegradation and the effects of PAHs on site-specific microbial communities. We compared the magnitude of PAH degradation and its impacts in short-term incubations of coastal Mediterranean and the Maritime Antarctica microbiomes with environmentally relevant concentrations of PAHs. Mediterranean bacteria readily degraded the less hydrophobic PAHs, with rates averaging 4.72 ± 0.5 ng L h[-1]. Metatranscriptomic responses showed significant enrichments of genes associated to horizontal gene transfer, stress response, and PAH degradation, mainly harbored by Alphaproteobacteria. Community composition changed and increased relative abundances of Bacteroidota and Flavobacteriales. In Antarctic waters, there was no degradation of PAH, and minimal metatranscriptome responses were observed. These results provide evidence for factors such as geographic region, community composition, and pre-exposure history to predict PAH biodegradation in seawater.}, }
@article {pmid37931146, year = {2023}, author = {Kosterlitz, O and Grassi, N and Werner, B and McGee, RS and Top, EM and Kerr, B}, title = {Evolutionary "Crowdsourcing": Alignment of Fitness Landscapes Allows for Cross-species Adaptation of a Horizontally Transferred Gene.}, journal = {Molecular biology and evolution}, volume = {40}, number = {11}, pages = {}, pmid = {37931146}, issn = {1537-1719}, support = {R01 AI084918/AI/NIAID NIH HHS/United States ; }, mesh = {Genotype ; *Anti-Bacterial Agents ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genomics ; }, abstract = {Genes that undergo horizontal gene transfer (HGT) evolve in different genomic backgrounds. Despite the ubiquity of cross-species HGT, the effects of switching hosts on gene evolution remains understudied. Here, we present a framework to examine the evolutionary consequences of host-switching and apply this framework to an antibiotic resistance gene commonly found on conjugative plasmids. Specifically, we determined the adaptive landscape of this gene for a small set of mutationally connected genotypes in 3 enteric species. We uncovered that the landscape topographies were largely aligned with minimal host-dependent mutational effects. By simulating gene evolution over the experimentally gauged landscapes, we found that the adaptive evolution of the mobile gene in one species translated to adaptation in another. By simulating gene evolution over artificial landscapes, we found that sufficient alignment between landscapes ensures such "adaptive equivalency" across species. Thus, given adequate landscape alignment within a bacterial community, vehicles of HGT such as plasmids may enable a distributed form of genetic evolution across community members, where species can "crowdsource" adaptation.}, }
@article {pmid37930866, year = {2024}, author = {Camargo, AP and Call, L and Roux, S and Nayfach, S and Huntemann, M and Palaniappan, K and Ratner, A and Chu, K and Mukherjeep, S and Reddy, TBK and Chen, IA and Ivanova, NN and Eloe-Fadrosh, EA and Woyke, T and Baltrus, DA and Castañeda-Barba, S and de la Cruz, F and Funnell, BE and Hall, JPJ and Mukhopadhyay, A and Rocha, EPC and Stalder, T and Top, E and Kyrpides, NC}, title = {IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata.}, journal = {Nucleic acids research}, volume = {52}, number = {D1}, pages = {D164-D173}, pmid = {37930866}, issn = {1362-4962}, support = {MR/W02666X/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; *Metagenome ; Metadata ; Software ; Databases, Genetic ; Plasmids/genetics ; *Microbiota ; }, abstract = {Plasmids are mobile genetic elements found in many clades of Archaea and Bacteria. They drive horizontal gene transfer, impacting ecological and evolutionary processes within microbial communities, and hold substantial importance in human health and biotechnology. To support plasmid research and provide scientists with data of an unprecedented diversity of plasmid sequences, we introduce the IMG/PR database, a new resource encompassing 699 973 plasmid sequences derived from genomes, metagenomes and metatranscriptomes. IMG/PR is the first database to provide data of plasmid that were systematically identified from diverse microbiome samples. IMG/PR plasmids are associated with rich metadata that includes geographical and ecosystem information, host taxonomy, similarity to other plasmids, functional annotation, presence of genes involved in conjugation and antibiotic resistance. The database offers diverse methods for exploring its extensive plasmid collection, enabling users to navigate plasmids through metadata-centric queries, plasmid comparisons and BLAST searches. The web interface for IMG/PR is accessible at https://img.jgi.doe.gov/pr. Plasmid metadata and sequences can be downloaded from https://genome.jgi.doe.gov/portal/IMG_PR.}, }
@article {pmid37928655, year = {2023}, author = {Wang, Z and Zhang, N and Li, C and Shao, L}, title = {Diversity of antibiotic resistance genes in soils with four different fertilization treatments.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1291599}, pmid = {37928655}, issn = {1664-302X}, abstract = {Although the enrichment of resistance genes in soil has been explored in recent years, there are still some key questions to be addressed regarding the variation of ARG composition in soil with different fertilization treatments, such as the core ARGs in soil after different fertilization treatments, the correlation between ARGs and bacterial taxa, etc. For soils after different fertilization treatments, the distribution and combination of ARG in three typical fertilization methods (organic fertilizer alone, chemical fertilizer alone, and conventional fertilizer) and non-fertilized soils were investigated in this study using high-throughput fluorescence quantitative PCR (HT-qPCR) technique. The application of organic fertilizers significantly increased the abundance and quantity of ARGs and their subtypes in the soil compared to the non-fertilized soil, where sul1 was the ARGs specific to organic fertilizers alone and in higher abundance. The conventional fertilizer application also showed significant enrichment of ARGs, which indicated that manure addition often had a more decisive effect on ARGs in soil than chemical fertilizers, and three bacteria, Pseudonocardia, Irregularibacter, and Castllaniella, were the key bacteria affecting ARG changes in soil after fertilization. In addition, nutrient factors and heavy metals also affect the distribution of ARGs in soil and are positively correlated. This paper reveals the possible reasons for the increase in the number of total soil ARGs and their relative abundance under different fertilization treatments, which has positive implications for controlling the transmission of ARGs through the soil-human pathway.}, }
@article {pmid37923145, year = {2023}, author = {Geoffroy, F and Uecker, H}, title = {Limits to evolutionary rescue by conjugative plasmids.}, journal = {Theoretical population biology}, volume = {154}, number = {}, pages = {102-117}, doi = {10.1016/j.tpb.2023.10.001}, pmid = {37923145}, issn = {1096-0325}, mesh = {*Conjugation, Genetic ; Plasmids/genetics ; *Biological Evolution ; Gene Transfer, Horizontal ; Bacteria/genetics ; }, abstract = {Plasmids may carry genes coding for beneficial traits and thus contribute to adaptation of bacterial populations to environmental stress. Conjugative plasmids can horizontally transfer between cells, which a priori facilitates the spread of adaptive alleles. However, if the potential recipient cell is already colonized by another incompatible plasmid, successful transfer may be prevented. Competition between plasmids can thus limit horizontal transfer. Previous modeling has indeed shown that evolutionary rescue by a conjugative plasmid is hampered by incompatible resident plasmids in the population. If the rescue plasmid is a mutant variant of the resident plasmid, both plasmids transfer at the same rates. A high conjugation rate then has two, potentially opposing, effects - a direct positive effect on spread of the rescue plasmid and an increase in the fraction of resident plasmid cells. This raises the question whether a high conjugation rate always benefits evolutionary rescue. In this article, we systematically analyze three models of increasing complexity to disentangle the benefits and limits of increasing horizontal gene transfer in the presence of plasmid competition and plasmid costs. We find that the net effect can be positive or negative and that the optimal transfer rate is thus not always the highest one. These results can contribute to our understanding of the many facets of plasmid-driven adaptation and the wide range of transfer rates observed in nature.}, }
@article {pmid37923139, year = {2023}, author = {Arriaza, RH and Abiskaroon, B and Patel, M and Daneshian, L and Kluza, A and Snoeck, S and Watkins, MB and Hopkins, JB and Van Leeuwen, T and Grbic, M and Grbic, V and Borowski, T and Chruszcz, M}, title = {Structural and functional studies reveal the molecular basis of substrate promiscuity of a glycosyltransferase originating from a major agricultural pest.}, journal = {The Journal of biological chemistry}, volume = {299}, number = {12}, pages = {105421}, pmid = {37923139}, issn = {1083-351X}, support = {P30 GM138395/GM/NIGMS NIH HHS/United States ; }, mesh = {Genome ; *Glycosyltransferases/chemistry/genetics/metabolism ; Plants/parasitology ; Uridine Diphosphate ; Substrate Specificity ; *Tetranychidae/enzymology/genetics ; }, abstract = {The two-spotted spider mite, Tetranychus urticae, is a major cosmopolitan pest that feeds on more than 1100 plant species. Its genome contains an unprecedentedly large number of genes involved in detoxifying and transporting xenobiotics, including 80 genes that code for UDP glycosyltransferases (UGTs). These enzymes were acquired via horizontal gene transfer from bacteria after loss in the Chelicerata lineage. UGTs are well-known for their role in phase II metabolism; however, their contribution to host adaptation and acaricide resistance in arthropods, such as T. urticae, is not yet resolved. TuUGT202A2 (Tetur22g00270) has been linked to the ability of this pest to adapt to tomato plants. Moreover, it was shown that this enzyme can glycosylate a wide range of flavonoids. To understand this relationship at the molecular level, structural, functional, and computational studies were performed. Structural studies provided specific snapshots of the enzyme in different catalytically relevant stages. The crystal structure of TuUGT202A2 in complex with UDP-glucose was obtained and site-directed mutagenesis paired with molecular dynamic simulations revealed a novel lid-like mechanism involved in the binding of the activated sugar donor. Two additional TuUGT202A2 crystal complexes, UDP-(S)-naringenin and UDP-naringin, demonstrated that this enzyme has a highly plastic and open-ended acceptor-binding site. Overall, this work reveals the molecular basis of substrate promiscuity of TuUGT202A2 and provides novel insights into the structural mechanism of UGTs catalysis.}, }
@article {pmid37924893, year = {2024}, author = {Stevenson, EM and Buckling, A and Cole, M and Lindeque, PK and Murray, AK}, title = {Selection for antimicrobial resistance in the plastisphere.}, journal = {The Science of the total environment}, volume = {908}, number = {}, pages = {168234}, doi = {10.1016/j.scitotenv.2023.168234}, pmid = {37924893}, issn = {1879-1026}, mesh = {Animals ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Microplastics ; Plastics ; Commerce ; }, abstract = {Microplastics and antimicrobials are widespread contaminants that threaten global systems and frequently co-exist in the presence of human or animal pathogens. Whilst the impact of each of these contaminants has been studied in isolation, the influence of this co-occurrence in driving antimicrobial resistance (AMR)[1] in microplastic-adhered microbial communities, known as 'the Plastisphere', is not well understood. This review proposes the mechanisms by which interactions between antimicrobials and microplastics may drive selection for AMR in the Plastisphere. These include: 1) increased rates of horizontal gene transfer in the Plastisphere compared with free-living counterparts and natural substrate controls due to the proximity of cells, co-occurrence of environmental microplastics with AMR selective compounds and the sequestering of extracellular antibiotic resistance genes in the biofilm matrix. 2) An elevated AMR selection pressure in the Plastisphere due to the adsorbing of AMR selective or co-selective compounds to microplastics at concentrations greater than those found in surrounding mediums and potentially those adsorbed to comparator particles. 3) AMR selection pressure may be further elevated in the Plastisphere due to the incorporation of antimicrobial or AMR co-selective chemicals in the plastic matrix during manufacture. Implications for both ecological functioning and environmental risk assessments are discussed, alongside recommendations for further research.}, }
@article {pmid37917352, year = {2023}, author = {Rekadwad, BN and Shouche, YS and Jangid, K}, title = {Investigation of tRNA-based relatedness within the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) superphylum: a comparative analysis.}, journal = {Archives of microbiology}, volume = {205}, number = {12}, pages = {366}, pmid = {37917352}, issn = {1432-072X}, support = {PDFSS-2013-14-ST-MAH-4350//University Grants Commission/ ; }, mesh = {*Escherichia coli/genetics ; *RNA, Transfer/genetics/metabolism ; Verrucomicrobia/genetics ; Amino Acids/metabolism ; Planctomycetes ; Evolution, Molecular ; }, abstract = {The PVC superphylum is a diverse group of prokaryotes that require stringent growth conditions. RNA is a fascinating molecule to find evolutionary relatedness according to the RNA World Hypothesis. We conducted tRNA gene analysis to find evolutionary relationships in the PVC phyla. The analysis of genomic data (P = 9, V = 4, C = 8) revealed that the number of tRNA genes varied from 28 to 90 in Planctomycetes and Chlamydia, respectively. Verrucomicrobia has whole genomes and the longest scaffold (3 + 1), with tRNA genes ranging from 49 to 53 in whole genomes and 4 in the longest scaffold. Most tRNAs in the E. coli genome clustered with homologs, but approximately 43% clustered with tRNAs encoding different amino acids. Planctomyces, Akkermansia, Isosphaera, and Chlamydia were similar to E. coli tRNAs. In a phylum, tRNAs coding for different amino acids clustered at a range of 8 to 10%. Further analysis of these tRNAs showed sequence similarity with Cyanobacteria, Proteobacteria, Viridiplantae, Ascomycota and Basidiomycota (Eukaryota). This indicates the possibility of horizontal gene transfer or, otherwise, a different origin of tRNA in PVC bacteria. Hence, this work proves its importance for determining evolutionary relatedness and potentially identifying bacteria using tRNA. Thus, the analysis of these tRNAs indicates that primitive RNA may have served as the genetic material of LUCA before being replaced by DNA. A quantitative analysis is required to test these possibilities that relate the evolutionary significance of tRNA to the origin of life.}, }
@article {pmid37909761, year = {2023}, author = {Xedzro, C and Shimamoto, T and Yu, L and Zuo, H and Sugawara, Y and Sugai, M and Shimamoto, T}, title = {Emergence of colistin-resistant Enterobacter cloacae and Raoultella ornithinolytica carrying the phosphoethanolamine transferase gene, mcr-9, derived from vegetables in Japan.}, journal = {Microbiology spectrum}, volume = {11}, number = {6}, pages = {e0106323}, pmid = {37909761}, issn = {2165-0497}, support = {20202002//Cabinet Office, Government of Japan/ ; 22fk0108604j0002//Japan Agency for Medical Research and Development (AMED)/ ; 21HA2009//Japan Agency for Medical Research and Development (AMED)/ ; JP23fk0108664j0001//Japan Agency for Medical Research and Development (AMED)/ ; }, mesh = {Plasmids/genetics ; *Colistin/pharmacology ; Transferases/genetics ; Japan ; Drug Resistance, Bacterial/genetics ; *Enterobacter cloacae/genetics ; Vegetables/microbiology ; Anti-Bacterial Agents/pharmacology ; Enterobacteriaceae ; Microbial Sensitivity Tests ; }, abstract = {Plasmid-mediated mobile colistin-resistance genes have been recognized as a global threat because they jeopardize the efficacy of colistin in therapeutic practice. Here, we described the genetic features of two mcr-9.1-carrying Gram-negative bacteria with a colistin-resistant phenotype derived from vegetables in Japan. The colistin-resistant mcr-9.1, which has never been detected in vegetables, was located on a large plasmid in Enterobacter cloacae CST17-2 and Raoultella ornithinolytica CST129-1, suggesting a high chance of horizontal gene transfer. To the best of our knowledge, this is the first report of mcr-9 in R. ornithinolytica. This study indicates that fresh vegetables might be a potential source for the transmission of mcr-9 genes encoding resistance to frontline (colistin) and clinically relevant antimicrobials. The study also provides additional consideration for colistin use and the relevance of routine surveillance in epidemiological perspective to curb the continuous spread of mcr alleles.}, }
@article {pmid37909043, year = {2024}, author = {Subramanian, S and Bergland Drarvik, SM and Tinney, KR and Parent, KN}, title = {Cryo-EM structure of a Shigella podophage reveals a hybrid tail and novel decoration proteins.}, journal = {Structure (London, England : 1993)}, volume = {32}, number = {1}, pages = {24-34.e4}, pmid = {37909043}, issn = {1878-4186}, support = {R01 GM110185/GM/NIGMS NIH HHS/United States ; R35 GM140803/GM/NIGMS NIH HHS/United States ; U24 GM116789/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Cryoelectron Microscopy ; *Bacteriophages/chemistry ; *Shigella/metabolism ; Capsid Proteins/metabolism ; Capsid/chemistry ; Viral Tail Proteins/chemistry ; }, abstract = {There is a paucity of high-resolution structures of phages infecting Shigella, a human pathogen and a serious threat to global health. HRP29 is a Shigella podophage belonging to the Autographivirinae family, and has very low sequence identity to other known phages. Here, we resolved the structure of the entire HRP29 virion by cryo-EM. Phage HRP29 has a highly unusual tail that is a fusion of a T7-like tail tube and P22-like tailspikes mediated by interactions from a novel tailspike adaptor protein. Understanding phage tail structures is critical as they mediate hosts interactions. Furthermore, we show that the HRP29 capsid is stabilized by two novel, and essential decoration proteins, gp47 and gp48. Only one high resolution structure is currently available for Shigella podophages. The presence of a hybrid tail and an adapter protein suggests that it may be a product of horizontal gene transfer, and may be prevalent in other phages.}, }
@article {pmid37907163, year = {2024}, author = {Su, X and Qian, F and Bao, Y}, title = {The effect of bulk-biochar and nano-biochar amendment on the removal of antibiotic resistance genes in microplastic contaminated soil.}, journal = {Environmental research}, volume = {240}, number = {Pt 2}, pages = {117488}, doi = {10.1016/j.envres.2023.117488}, pmid = {37907163}, issn = {1096-0953}, mesh = {*Microplastics ; *Plastics ; Anti-Bacterial Agents ; Drug Resistance, Microbial ; Soil ; }, abstract = {Biochar amendment has significant benefits in removing antibiotic resistance genes (ARGs) in the soil. Nevertheless, there is little information on ARGs removal in microplastic contaminated soil. Herein, a 42-day soil microcosm experiment were carried out to study how two coconut shell biochars (bulk- and nano-size) eliminate soil ARGs with/without microplastic presence. The results showed that microplastic increased significantly the numbers and abundances of ARGs in soil at 14d of cultivation. And, two biochars amendment effectively inhibited soil ARGs spread whether or not microplastic was present, especially for nano-biochar which had more effective removal compared to bulk-biochar. However, microplastic weakened soil ARGs removal after applying same biochar. Two biochars removed ARGs through decreasing horizontal gene transfer (HGT) of ARGs, potential host-bacteria abundances, some bacteria crowding the eco-niche of hosts and promoting soil properties. The adverse effect of microplastic on ARGs removal was mainly caused by weakening mobile genetic elements (MGEs) removal, and by changing soil properties. Structural equation modeling (SEM) analysis indicated that biochar's effect on ARGs profile was changed by its size and microplastic presence through altering MGEs abundances. These results highlight that biochar amendment is still an effective method for ARGs removal in microplastic contaminated soil.}, }
@article {pmid37902330, year = {2023}, author = {Benigno, V and Carraro, N and Sarton-Lohéac, G and Romano-Bertrand, S and Blanc, DS and van der Meer, JR}, title = {Diversity and evolution of an abundant ICEclc family of integrative and conjugative elements in Pseudomonas aeruginosa.}, journal = {mSphere}, volume = {8}, number = {6}, pages = {e0051723}, pmid = {37902330}, issn = {2379-5042}, support = {310030_204897//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (SNF)/ ; }, mesh = {*Pseudomonas aeruginosa/genetics ; *Gene Transfer, Horizontal ; }, abstract = {Microbial populations swiftly adapt to changing environments through horizontal gene transfer. While the mechanisms of gene transfer are well known, the impact of environmental conditions on the selection of transferred gene functions remains less clear. We investigated ICEs, specifically the ICEclc-type, in Pseudomonas aeruginosa clinical isolates. Our findings revealed co-evolution between ICEs and their hosts, with ICE transfers occurring within strains. Gene functions carried by ICEs are positively selected, including potential virulence factors and heavy metal resistance. Comparison to publicly available P. aeruginosa genomes unveiled widespread antibiotic-resistance determinants within ICEclc clades. Thus, the ubiquitous ICEclc family significantly contributes to P. aeruginosa's adaptation and fitness in diverse environments.}, }
@article {pmid37901845, year = {2023}, author = {Li, L and Zhang, H and Meng, D and Yin, H}, title = {Transcriptomics of Lactobacillus paracasei: metabolism patterns and cellular responses under high-density culture conditions.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {11}, number = {}, pages = {1274020}, pmid = {37901845}, issn = {2296-4185}, abstract = {Lactobacillus paracasei has significant potential for development and application in the environmental field, particularly in addressing malodor pollution. This study aims to investigate the cellular response of L. paracasei B1 under high-density culture conditions. The selected strain has previously shown effective deodorizing and bacteriostatic abilities. Transcriptomics techniques are employed to dissect the nutrient metabolism pattern of L. paracasei B1 and its response mechanism under environmental stress. The study characterizes the functions of key differentially expressed genes during growth before and after optimizing the culture conditions. The optimization of fermentation culture conditions provides a suitable growth environment for L. paracasei B1, inducing an enhancement of its phosphotransferase system for sugar source uptake and maintaining high levels of glycolysis and pyruvate metabolism. Consequently, the strain is able to grow and multiply rapidly. Under acid stress conditions, glycolysis and pyruvate metabolism are inhibited, and L. paracasei B1 generates additional energy through aerobic respiration to meet the energy demand. The two-component system and quorum sensing play roles in the response and regulation of L. paracasei B1 to adverse environments. The strain mitigates oxygen stress damage through glutathione metabolism, cysteine and methionine metabolism, base excision repair, and purine and pyrimidine metabolism. Additionally, the strain enhances lysine synthesis, the alanine, aspartate, and glutamate metabolic pathways, and relies on the ABC transport system to accumulate amino acid-compatible solutes to counteract acid stress and osmotic stress during pH regulation. These findings establish a theoretical basis for the further development and application of L. paracasei B1 for its productive properties.}, }
@article {pmid37900760, year = {2023}, author = {Yan, XM and Zhou, SS and Liu, H and Zhao, SW and Tian, XC and Shi, TL and Bao, YT and Li, ZC and Jia, KH and Nie, S and Guo, JF and Kong, L and Porth, IM and Mao, JF}, title = {Unraveling the evolutionary dynamics of the TPS gene family in land plants.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1273648}, pmid = {37900760}, issn = {1664-462X}, abstract = {Terpenes and terpenoids are key natural compounds for plant defense, development, and composition of plant oil. The synthesis and accumulation of a myriad of volatile terpenoid compounds in these plants may dramatically alter the quality and flavor of the oils, which provide great commercial utilization value for oil-producing plants. Terpene synthases (TPSs) are important enzymes responsible for terpenic diversity. Investigating the differentiation of the TPS gene family could provide valuable theoretical support for the genetic improvement of oil-producing plants. While the origin and function of TPS genes have been extensively studied, the exact origin of the initial gene fusion event - it occurred in plants or microbes - remains uncertain. Furthermore, a comprehensive exploration of the TPS gene differentiation is still pending. Here, phylogenetic analysis revealed that the fusion of the TPS gene likely occurred in the ancestor of land plants, following the acquisition of individual C- and N- terminal domains. Potential mutual transfer of TPS genes was observed among microbes and plants. Gene synteny analysis disclosed a differential divergence pattern between TPS-c and TPS-e/f subfamilies involved in primary metabolism and those (TPS-a/b/d/g/h subfamilies) crucial for secondary metabolites. Biosynthetic gene clusters (BGCs) analysis suggested a correlation between lineage divergence and potential natural selection in structuring terpene diversities. This study provides fresh perspectives on the origin and evolution of the TPS gene family.}, }
@article {pmid37898203, year = {2024}, author = {Jian, J and Wu, Z and Silva-Núñez, A and Li, X and Zheng, X and Luo, B and Liu, Y and Fang, X and Workman, CT and Larsen, TO and Hansen, PJ and Sonnenschein, EC}, title = {Long-read genome sequencing provides novel insights into the harmful algal bloom species Prymnesium parvum.}, journal = {The Science of the total environment}, volume = {908}, number = {}, pages = {168042}, doi = {10.1016/j.scitotenv.2023.168042}, pmid = {37898203}, issn = {1879-1026}, mesh = {Animals ; *Harmful Algal Bloom ; *Haptophyta/genetics/metabolism ; Fishes ; }, abstract = {Prymnesium parvum is a toxin-producing haptophyte that causes harmful algal blooms worldwide, which are often associated with massive fish-kills and subsequent economic losses. In here, we present nuclear and plastid genome assemblies using PacBio HiFi long reads and DNBseq short reads for the two P. parvum strains UTEX 2797 and CCMP 3037, representing producers of type A prymnesins. Our results show that the P. parvum strains have a moderate haptophyte genome size of 97.56 and 107.32 Mb. The genome assemblies present one of highest contiguous assembled contig sequences to date consisting of 463 and 362 contigs with a contig N50 of 596.99 kb and 968.39 kb for strain UTEX 2797 and CCMP 3037, respectively. The assembled contigs of UTEX 2797 and CCMP 3037 were anchored to 34 scaffolds, with a scaffold N50 of 5.35 Mb and 3.61 Mb, respectively, accounting for 93.2 % and 97.9 % of the total length. Each plastid genome comprises a circular contig. A total of 20,578 and 19,426 protein-coding genes were annotated for UTEX 2797 and CCMP 3037. The expanded gene family analysis showed that starch and sucrose metabolism, sulfur metabolism, energy metabolism and ABC transporters are involved in the evolution of P. parvum. Polyketide synthase (PKS) genes responsible for the production of secondary metabolites such as prymnesins displayed different expression patterns under nutrient limitation. Overlap with repeats and horizontal gene transfer may be two contributing factors to the high number of PKS genes found in this species. The two high quality P. parvum genomes will serve as valuable resources for ecological, genetic, and toxicological studies of haptophytes that can be used to monitor and potentially manage harmful blooms of ichthyotoxic P. parvum in the future.}, }
@article {pmid37894729, year = {2023}, author = {Bravo, A and Moreno-Blanco, A and Espinosa, M}, title = {One Earth: The Equilibrium between the Human and the Bacterial Worlds.}, journal = {International journal of molecular sciences}, volume = {24}, number = {20}, pages = {}, pmid = {37894729}, issn = {1422-0067}, support = {PID2019-104553RB-C21//Spanish Ministry of Science and Innovation (MCIN/AEI/10.13039/501100011033)/ ; }, mesh = {Humans ; Animals ; Cattle ; *Bacteria/genetics ; Genes, Bacterial ; *Bacterial Infections/microbiology ; Drug Resistance, Microbial ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; }, abstract = {Misuse and abuse of antibiotics on humans, cattle, and crops have led to the selection of multi-resistant pathogenic bacteria, the most feared 'superbugs'. Infections caused by superbugs are progressively difficult to treat, with a subsequent increase in lethality: the toll on human lives is predicted to reach 10 million by 2050. Here we review three concepts linked to the growing resistance to antibiotics, namely (i) the Resistome, which refers to the collection of bacterial genes that confer resistance to antibiotics, (ii) the Mobilome, which includes all the mobile genetic elements that participate in the spreading of antibiotic resistance among bacteria by horizontal gene transfer processes, and (iii) the Nichome, which refers to the set of genes that are expressed when bacteria try to colonize new niches. We also discuss the strategies that can be used to tackle bacterial infections and propose an entente cordiale with the bacterial world so that instead of war and destruction of the 'fierce enemy' we can achieve a peaceful coexistence (the One Earth concept) between the human and the bacterial worlds. This, in turn, will contribute to microbial biodiversity, which is crucial in a globally changing climate due to anthropogenic activities.}, }
@article {pmid37894082, year = {2023}, author = {Anton, BP and Roberts, RJ}, title = {A Survey of Archaeal Restriction-Modification Systems.}, journal = {Microorganisms}, volume = {11}, number = {10}, pages = {}, pmid = {37894082}, issn = {2076-2607}, abstract = {When compared with bacteria, relatively little is known about the restriction-modification (RM) systems of archaea, particularly those in taxa outside of the haloarchaea. To improve our understanding of archaeal RM systems, we surveyed REBASE, the restriction enzyme database, to catalog what is known about the genes and activities present in the 519 completely sequenced archaeal genomes currently deposited there. For 49 (9.4%) of these genomes, we also have methylome data from Single-Molecule Real-Time (SMRT) sequencing that reveal the target recognition sites of the active m[6]A and m[4]C DNA methyltransferases (MTases). The gene-finding pipeline employed by REBASE is trained primarily on bacterial examples and so will look for similar genes in archaea. Nonetheless, the organizational structure and protein sequence of RM systems from archaea are highly similar to those of bacteria, with both groups acquiring systems from a shared genetic pool through horizontal gene transfer. As in bacteria, we observe numerous examples of "persistent" DNA MTases conserved within archaeal taxa at different levels. We experimentally validated two homologous members of one of the largest "persistent" MTase groups, revealing that methylation of C(m[5]C)WGG sites may play a key epigenetic role in Crenarchaea. Throughout the archaea, genes encoding m[6]A, m[4]C, and m[5]C DNA MTases, respectively, occur in approximately the ratio 4:2:1.}, }
@article {pmid37888586, year = {2023}, author = {Ortega-Balleza, JL and Guerrero, A and Castro-Escarpulli, G and Martínez-Vázquez, AV and Cruz-Hernández, MA and Luna-Santillana, EJ and Acosta-Cruz, E and Rodríguez-Sánchez, IP and Rivera, G and Bocanegra-García, V}, title = {Genomic Analysis of Multidrug-Resistant Escherichia coli Strains Isolated in Tamaulipas, Mexico.}, journal = {Tropical medicine and infectious disease}, volume = {8}, number = {10}, pages = {}, pmid = {37888586}, issn = {2414-6366}, abstract = {The global spread of antimicrobial resistance genes (ARGs) is a major public health concern. Mobile genetic elements (MGEs) are the main drivers of this spread by horizontal gene transfer (HGT). Escherichia coli is widespread in various environments and serves as an indicator for monitoring antimicrobial resistance (AMR). Therefore, the objective of this work was to evaluate the whole genome of multidrug-resistant E. coli strains isolated from human clinical, animal, and environmental sources. Four E. coli strains previously isolated from human urine (n = 2), retail meat (n = 1), and water from the Rio Grande River (n = 1) collected in northern Tamaulipas, Mexico, were analyzed. E. coli strains were evaluated for antimicrobial susceptibility, followed by whole genome sequencing and bioinformatic analysis. Several ARGs were detected, including blaCTX-M-15, blaOXA-1, blaTEM-1B, blaCMY-2, qnrB, catB3, sul2, and sul3. Additionally, plasmid replicons (IncFIA, IncFIB, IncFII, IncY, IncR, and Col) and intact prophages were also found. Insertion sequences (ISs) were structurally linked with resistance and virulence genes. Finally, these findings indicate that E. coli strains have a large repertoire of resistance determinants, highlighting a high pathogenic potential and the need to monitor them.}, }
@article {pmid37887056, year = {2023}, author = {Sandmann, G}, title = {Genes and Pathway Reactions Related to Carotenoid Biosynthesis in Purple Bacteria.}, journal = {Biology}, volume = {12}, number = {10}, pages = {}, pmid = {37887056}, issn = {2079-7737}, abstract = {In purple bacteria, the genes of the carotenoid pathways are part of photosynthesis gene clusters which were distributed among different species by horizontal gene transfer. Their close organisation facilitated the first-time cloning of carotenogenic genes and promoted the molecular investigation of spheroidene and spirilloxanthin biosynthesis. This review highlights the cloning of the spheroidene and spirilloxanthin pathway genes and presents the current knowledge on the enzymes involved in the carotenoid biosynthesis of purple sulphur and non-sulphur bacteria. Mostly, spheroidene or spirilloxanthin biosynthesis exists in purple non-sulphur bacteria but both pathways operate simultaneously in Rubrivivax gelatinosus. In the following years, genes from other bacteria including purple sulphur bacteria with an okenone pathway were cloned. The individual steps were investigated by kinetic studies with heterologously expressed pathway genes which supported the establishment of the reaction mechanisms. In particular, the substrate and product specificities revealed the sequential order of the speroidene and spiriloxanthin pathways as well as their interactions. Information on the enzymes involved revealed that the phytoene desaturase determines the type of pathway by the formation of different products. By selection of mutants with amino acid exchanges in the putative substrate-binding site, the neurosporene-forming phytoene desaturase could be changed into a lycopene-producing enzyme and vice versa. Concerning the oxygen groups in neurosporene and lycopene, the tertiary alcohol group at C1 is formed from water and not by oxygenation, and the C2 or C4 keto groups are inserted differently by an oxygen-dependent or oxygen-independent ketolation reaction, respectively.}, }
@article {pmid37886666, year = {2023}, author = {Arbé-Carton, K and Rey-Sogo, A and Santos-Fernández, N and Altube, O and Garbisu, C and Arana, L and Alkorta, I}, title = {Development of a high-throughput platform to measure plasmid transfer frequency.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1269732}, pmid = {37886666}, issn = {2235-2988}, mesh = {Plasmids/genetics ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial ; *Conjugation, Genetic ; Gene Transfer, Horizontal ; }, abstract = {Antibiotic resistance represents one of the greatest threats to global health. The spread of antibiotic resistance genes among bacteria occurs mostly through horizontal gene transfer via conjugation mediated by plasmids. This process implies a direct contact between a donor and a recipient bacterium which acquires the antibiotic resistance genes encoded by the plasmid and, concomitantly, the capacity to transfer the acquired plasmid to a new recipient. Classical assays for the measurement of plasmid transfer frequency (i.e., conjugation frequency) are often characterized by a high variability and, hence, they require many biological and technical replicates to reduce such variability and the accompanying uncertainty. In addition, classical conjugation assays are commonly tedious and time-consuming because they typically involve counting colonies on a large number of plates for the quantification of donors, recipients, and transconjugants (i.e., the bacteria that have received the genetic material by conjugation). Due to the magnitude of the antibiotic resistance problem, it is critical to develop reliable and rapid methods for the quantification of plasmid transfer frequency that allow the simultaneous analysis of many samples. Here, we present the development of a high-throughput, reliable, quick, easy, and cost-effective method to simultaneously accomplish and measure multiple conjugation events in 96-well plates, in which the quantification of donors, recipients, and transconjugants is estimated from the time required to reach a specific threshold value (OD600 value) in the bacterial growth curves. Our method successfully discriminates different plasmid transfer frequencies, yielding results that are equivalent to those obtained by a classical conjugation assay.}, }
@article {pmid37884245, year = {2023}, author = {Zhang, Z and Li, B and Chai, Z and Yang, Z and Zhang, F and Kang, F and Ren, H and Jin, Y and Yue, J}, title = {Evolution of the ability to evade host innate immune defense by Talaromyces marneffei.}, journal = {International journal of biological macromolecules}, volume = {253}, number = {Pt 8}, pages = {127597}, doi = {10.1016/j.ijbiomac.2023.127597}, pmid = {37884245}, issn = {1879-0003}, mesh = {Humans ; *Talaromyces/genetics ; Phylogeny ; *Mycoses/genetics/microbiology ; Immunity, Innate/genetics ; }, abstract = {Talaromyces (Penicillium) marneffei is an intracellular pathogenic fungus. Some strains of this fungus have been misidentified due to the similarity between Talaromyces and Penicillium. T. marneffei has mainly been found to afflict immunocompromised individuals, causing respiratory, skin, and systemic mycosis. Mp1p is a key virulence factor that can help T. marneffei evade clearance by the normally functioning immune system. Understanding how novel functions arise is an intriguing question in many fields of biology. Mp1p has two homologous domains (Mp1p-LBD1 and Mp1p-LBD2). Sequence similarity searches with Mp1p-LBD sequences revealed Mp1p homologs in many other pathogenic fungi. Integrated information on the taxonomic distribution, phylogenetic relationships, and sequence similarity of Mp1p domains revealed that the ancestor of Mp1p-LBDs was acquired through horizontal gene transfer (HGT). Additional evidence revealed that Mp1p homologs have undergone extensive gene duplications in T. marneffei. Mp1p might be a result of gene fusion following gene duplication. Furthermore, we propose a new method for identifying Talaromyces and identify 4 strains with misclassification errors. Our results characterize the evolutionary mechanism of T. marneffei evasion of host innate immune defense and clearly demonstrate the role of gene duplication and HGT in the evolution of host immune escape by T. marneffei.}, }
@article {pmid37883987, year = {2024}, author = {Parthasarathy, R and Wakefield, D and Santiago, FS and Kaakoush, NO and Tedla, N}, title = {Horizontal gene transfer and endogenous retroviruses as mechanisms for molecular mimicry.}, journal = {The Lancet. Microbe}, volume = {5}, number = {1}, pages = {e4-e5}, doi = {10.1016/S2666-5247(23)00316-6}, pmid = {37883987}, issn = {2666-5247}, mesh = {*Endogenous Retroviruses/genetics ; Molecular Mimicry ; Gene Transfer, Horizontal ; Amino Acid Sequence ; Gene Products, env/genetics ; }, }
@article {pmid37882558, year = {2023}, author = {Marti, H and Biggel, M and Shima, K and Onorini, D and Rupp, J and Charette, SJ and Borel, N}, title = {Chlamydia suis displays high transformation capacity with complete cloning vector integration into the chromosomal rrn-nqrF plasticity zone.}, journal = {Microbiology spectrum}, volume = {11}, number = {6}, pages = {e0237823}, pmid = {37882558}, issn = {2165-0497}, support = {323530_177579/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {Animals ; Humans ; Swine ; *Chlamydia/genetics ; Chlamydia trachomatis ; *Chlamydia Infections/microbiology ; Anti-Bacterial Agents ; Genetic Vectors ; }, abstract = {The obligate intracellular Chlamydia genus contains many pathogens with a negative impact on global health and economy. Despite recent progress, there is still a lack of genetic tools limiting our understanding of these complex bacteria. This study provides new insights into genetic manipulation of Chlamydia with the opportunistic porcine pathogen Chlamydia suis, the only chlamydial species naturally harboring an antibiotic resistance gene, originally obtained by horizontal gene transfer. C. suis is transmissible to humans, posing a potential public health concern. We report that C. suis can take up vectors that lack the native plasmid, a requirement for most chlamydial transformation systems described to date. Additionally, we show that C. trachomatis, the most common cause for bacterial sexually transmitted infections and infectious blindness worldwide, can be transformed with C. suis vectors. Finally, the chromosomal region that harbors the resistance gene of C. suis is highly susceptible to complete vector integration.}, }
@article {pmid37880110, year = {2024}, author = {Tanaka, E and Wajima, T and Ota, R and Uchiya, KI}, title = {The Association between Transformation Ability and Antimicrobial Resistant Potential in Haemophilus influenzae.}, journal = {Biological &amp; pharmaceutical bulletin}, volume = {47}, number = {1}, pages = {154-158}, doi = {10.1248/bpb.b23-00583}, pmid = {37880110}, issn = {1347-5215}, mesh = {Humans ; Haemophilus influenzae/genetics ; Anti-Bacterial Agents/pharmacology ; *Haemophilus Infections/drug therapy ; *Anti-Infective Agents ; *Quinolones ; Microbial Sensitivity Tests ; }, abstract = {The prevalence of quinolone low-susceptible Haemophilus influenzae has increased in Japan. Low quinolone susceptibility is caused by point mutations in target genes; however, it can also be caused by horizontal gene transfer via natural transformation. In this study, we examined whether this horizontal gene transfer could be associated with resistance to not only quinolones but also other antimicrobial agents. Horizontal transfer ability was quantified using the experimental transfer assay method for low quinolone susceptibility. Further, the association between horizontal transfer ability and resistance to β-lactams, the first-choice drugs for H. influenzae infection, was investigated. The transformation efficiency of 50 clinical isolates varied widely, ranging from 10[2] to 10[6] colony forming unit (CFU) of the colonies obtained by horizontal transfer assay. Efficiency was associated with β-lactam resistance caused by ftsI mutations, indicating that strains with high horizontal transfer ability acquired quinolone low-susceptibility as well as β-lactam resistance more easily. Strains with high transformation efficiency increased the transcript level of comA, suggesting that enhanced com operon was associated with a high DNA uptake ability. Overall, this study revealed that the transformation ability of H. influenzae was associated with multiple antimicrobial resistance. Increase in the number of strains with high horizontal transformation ability has raised concerns regarding the rapid spread of antimicrobial-resistant H. influenzae.}, }
@article {pmid37875161, year = {2023}, author = {Ribes-Navarro, A and Kabeya, N and Castro, LFC and Gomes-Dos-Santos, A and Fonseca, MM and Alberts-Hubatsch, H and Hontoria, F and Navarro, JC and Monroig, &#xd3;}, title = {Examination of gammarid transcriptomes reveals a widespread occurrence of key metabolic genes from epibiont bdelloid rotifers in freshwater species.}, journal = {Open biology}, volume = {13}, number = {10}, pages = {230196}, pmid = {37875161}, issn = {2046-2441}, mesh = {Fatty Acid Elongases/genetics/metabolism ; Phylogeny ; *Transcriptome ; *Fatty Acid Desaturases/genetics/metabolism ; Fatty Acids, Unsaturated ; Fresh Water ; }, abstract = {Previous data revealed the unexpected presence of genes encoding for long-chain polyunsaturated fatty acid (LC-PUFA) biosynthetic enzymes in transcriptomes from freshwater gammarids but not in marine species, even though closely related species were compared. This study aimed to clarify the origin and occurrence of selected LC-PUFA biosynthesis gene markers across all published gammarid transcriptomes. Through systematic searches, we confirmed the widespread occurrence of sequences from seven elongases and desaturases involved in LC-PUFA biosynthesis, in transcriptomes from freshwater gammarids but not marine species, and clarified that such occurrence is independent from the gammarid species and geographical origin. The phylogenetic analysis established that the retrieved elongase and desaturase sequences were closely related to bdelloid rotifers, confirming that multiple transcriptomes from freshwater gammarids contain contaminating rotifers' genetic material. Using the Adineta steineri genome, we investigated the genomic location and exon-intron organization of the elongase and desaturase genes, establishing they are all genome-anchored and, importantly, identifying instances of horizontal gene transfer. Finally, we provide compelling evidence demonstrating Bdelloidea desaturases and elongases enable these organisms to perform all the reactions for de novo biosynthesis of PUFA and, from them, LC-PUFA, an advantageous trait when considering the low abundance of these essential nutrients in freshwater environments.}, }
@article {pmid37875024, year = {2023}, author = {Wang, X and Qin, J and Xiang, G and Wang, C and Wang, Q and Qin, J and Wang, H and Shen, Z}, title = {Nosocomial dissemination of blaIMP-4 among Klebsiella pneumoniae by horizontal gene transfer and clonal spread: the epidemic IncN plasmids and the emerging high-risk IMP-4-producing ST101 clone.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {78}, number = {12}, pages = {2890-2894}, doi = {10.1093/jac/dkad326}, pmid = {37875024}, issn = {1460-2091}, support = {82272374//National Natural Science Foundation of China/ ; 22PJ1409600//Shanghai Pujiang Program/ ; RJTJ22-MS-018//Renji Hospital/ ; }, mesh = {Humans ; Child ; Klebsiella pneumoniae/genetics ; *Enterobacteriaceae Infections/microbiology ; Gene Transfer, Horizontal ; *Cross Infection/epidemiology/microbiology ; Prospective Studies ; China/epidemiology ; beta-Lactamases/genetics ; Plasmids/genetics ; Bacterial Proteins/genetics ; *Klebsiella Infections/epidemiology ; Microbial Sensitivity Tests ; Anti-Bacterial Agents ; }, abstract = {OBJECTIVES: To determine the genomic features of IMP-4-producing Klebsiella pneumoniae isolates recovered from paediatric patients and the transmission dynamics of blaIMP-4.<br><br>METHODS: IMP-producing K. pneumoniae isolates were collected from paediatric patients in Shanghai Children's Medical Center from 2013 to 2020. WGS was performed for all isolates, and the complete genomes of three IMP-4-producing isolates were generated. The distribution of blaIMP-4-harbouring plasmids was determined, and a conjugation assay was employed to investigate the horizontal transfer of blaIMP-4-harbouring plasmids.<br><br>RESULTS: We collected 21 blaIMP-carrying K. pneumoniae isolates, with IMP-4 (16/21, 76.2%) as the predominant subtype, followed by IMP-8 (n&#x200a;=&#x200a;3) and IMP-26 (n&#x200a;=&#x200a;2). IMP-4-producing isolates displayed a diverse population structure and all blaIMP-4 genes were located on plasmids, including IncN (n&#x200a;=&#x200a;9), IncHI5 (n&#x200a;=&#x200a;5), IncFII(K) (n&#x200a;=&#x200a;1) and IncFII(pKP91) (n&#x200a;=&#x200a;1), although only IncN plasmids were conjugative. Clonal transmission of ST101 strains carrying IncHI5 blaIMP-4-harbouring plasmids was observed, and the acquisition of blaIMP-4 by the international high-risk ST101 clone constituted a novel combination of ST101 clone and carbapenemase genes. Plasmid analysis demonstrated that the conjugal transfer of the IncHI5 blaIMP-4-harbouring plasmid might be blocked by the ST101 bacterial host.<br><br>CONCLUSIONS: The horizontal transfer of IncN plasmids and clonal spread of the international high-risk ST101 clone facilitated the nosocomial dissemination of blaIMP-4 among K. pneumoniae. The emerging IMP-4-producing ST101 clone displays diverse combinations of carbapenemase genes, and this clone could be a continually evolving threat and warrants prospective monitoring.}, }
@article {pmid37873201, year = {2023}, author = {Attah, V and Milner, DS and Fang, Y and Yan, X and Leonard, G and Heitman, J and Talbot, NJ and Richards, TA}, title = {Duplication and neofunctionalization of a horizontally-transferred xyloglucanase as a facet of the red queen co-evolutionary dynamic.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37873201}, issn = {2692-8205}, support = {R01 AI039115/AI/NIAID NIH HHS/United States ; }, abstract = {UNLABELLED: Oomycetes are heterotrophic protists that share phenotypic similarities with fungi, including the ability to cause plant diseases, but branch in a separate and distant region of the eukaryotic tree of life. It has been suggested that multiple horizontal gene transfers (HGTs) from fungi-to-oomycetes contributed to the evolution of plant-pathogenic traits. These HGTs are predicted to include secreted proteins that degrade plant cell walls. This is a key trait in the pathology of many oomycetes, as the plant cell wall represents a primary barrier to pathogen invasion and a rich source of carbohydrates. Many of the HGT gene families identified have undergone multiple rounds of duplication. Using a combination of phylogenomic analysis and functional assays, we investigate the diversification of a horizontally-transferred xyloglucanase gene family in the model oomycete species Phytophthora sojae. Our analyses detect 11 genes retained in P. sojae among a complex pattern of gene duplications and losses. Using a phenotype assay, based on heterologous expression in yeast, we show that eight of these paralogs have xyloglucanase function, including variants with distinct protein characteristics, such as a long-disordered C-terminal extension that can increase xyloglucanase activity. The functional xyloglucanase variants analysed subtend an ancestral node close to the fungi-oomycetes gene transfer, suggesting the horizontally-transferred gene was a bona fide xyloglucanase. Expression of xyloglucanase paralogs in Nicotiana benthamiana triggers distinct patterns of reactive oxygen species (ROS) generation, demonstrating that enzyme variants differentially stimulate pattern-triggered immunity in plants. Mass spectrometry of detectable enzymatic products demonstrates that some paralogs catalyze production of variant breakdown profiles, suggesting that secretion of multiple xyloglucanase variants increases efficiency of xyloglucan breakdown, as well as potentially diversifying the range of Damage-Associated Molecular Patterns (DAMPs) released during pathogen attack. We suggest that such patterns of protein neofunctionalization, and variant host responses, represent an aspect of the Red Queen host-pathogen co-evolutionary dynamic.<br><br>SIGNIFICANCE STATEMENT: The oomycetes are a diverse group of eukaryotic microbes that include some of the most devastating pathogens of plants. Oomycetes perceive, invade, and colonize plants in similar ways to fungi, in part because they acquired the genes to attack and feed on plants from fungi. These genes are predicted to be useful to oomycete plant pathogens because they have undergone multiple rounds of gene duplication. One key enzyme for attacking plant cell wall structures is called xyloglucanase. Xyloglucanase in the oomycetes has undergone multiple rounds of gene duplication, leading to variants including an enzyme with a C-terminal extension that increases activity. Some xyloglucanase variants trigger unique patterns of reactive oxygen species (ROS) in planta, and generate different profiles of cell wall breakdown products - such outcomes could act to mystify and increase the workload of the plant immune system, allowing successful pathogens to proliferate.}, }
@article {pmid37873187, year = {2023}, author = {Hamrick, GS and Maddamsetti, R and Son, HI and Wilson, ML and Davis, HM and You, L}, title = {Programming dynamic division of labor using horizontal gene transfer.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.10.03.560696}, pmid = {37873187}, issn = {2692-8205}, abstract = {The metabolic engineering of microbes has broad applications, including in biomanufacturing, bioprocessing, and environmental remediation. The introduction of a complex, multi-step pathway often imposes a substantial metabolic burden on the host cell, restraining the accumulation of productive biomass and limiting pathway efficiency. One strategy to alleviate metabolic burden is division of labor (DOL), in which different subpopulations carry out different parts of the pathway and work together to convert a substrate into a final product. However, the maintenance of different engineered subpopulations is challenging due to competition and convoluted inter-strain population dynamics. Through modeling, we show that dynamic division of labor (DDOL) mediated by horizontal gene transfer (HGT) can overcome these limitations and enable the robust maintenance of burdensome, multi-step pathways. We also use plasmid genomics to uncover evidence that DDOL is a strategy utilized by natural microbial communities. Our work suggests that bioengineers can harness HGT to stabilize synthetic metabolic pathways in microbial communities, enabling the development of robust engineered systems for deployment in a variety of contexts.}, }
@article {pmid37871361, year = {2023}, author = {Moussa, J and Nassour, E and Tahan, E and El Chaar, M and Jisr, T and Tokajian, S}, title = {Carbapenem resistance determinants and their transmissibility among clinically isolated Enterobacterales in Lebanon.}, journal = {Journal of infection and public health}, volume = {16}, number = {12}, pages = {1947-1953}, doi = {10.1016/j.jiph.2023.10.003}, pmid = {37871361}, issn = {1876-035X}, mesh = {Humans ; Lebanon/epidemiology ; *Carbapenems/pharmacology ; Imipenem ; Meropenem ; *Anti-Infective Agents ; }, abstract = {BACKGROUND: The occurrence of carbapenem-resistant bacterial infections has increased significantly over the years with Gram-negative bacteria exhibiting the broadest resistance range. In this study we aimed to investigate the genomic characteristics of clinical carbapenem-resistant Enterobacterales (CRE).<br><br>METHODS: Seventeen representative multi-drug resistant (MDR) isolates from a hospital setting showing high level of resistance to carbapenems (ertapenem, meropenem and imipenem) were chosen for further characterization through whole-genome sequencing. Resistance mechanisms and transferability of plasmids carrying carbapenemase-encoding genes were also determined in silico and through conjugative mating assays.<br><br>RESULTS: We detected 18 different &#x3b2;-lactamases, including four carbapenemases (blaNDM-1, blaNDM-5, blaNDM-7, blaOXA-48) on plasmids with different Inc groups. The combined results from PBRT and in silico replicon typing revealed 20 different replicons linked to plasmids ranging in size between 80 and 200&#xa0;kb. The most prevalent Inc groups were IncFIB(K) and IncM. OXA-48, detected on 76-kb IncM1 conjugable plasmid, was the most common carbapenemase. We also detected other conjugative plasmids with different carbapenemases confirming the role of horizontal gene transfer in the dissemination of antimicrobial resistance genes.<br><br>CONCLUSION: Our findings verified the continuing spread of carbapenemases in Enterobacterales and revealed the types of mobile elements circulating in a hospital setting and contributing to the spread of resistance determinants. The occurrence and transmission of plasmids carrying carbapenemase-encoding genes call for strengthening active surveillance and prevention efforts to control antimicrobial resistance dissemination in healthcare settings.}, }
@article {pmid37870180, year = {2023}, author = {Zhang, Q and Xu, N and Lei, C and Chen, B and Wang, T and Ma, Y and Lu, T and Penuelas, J and Gillings, M and Zhu, YG and Fu, Z and Qian, H}, title = {Metagenomic Insight into The Global Dissemination of The Antibiotic Resistome.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {10}, number = {33}, pages = {e2303925}, pmid = {37870180}, issn = {2198-3844}, support = {2022YFD1700400//National Key Research and Development Program of China/ ; 21976161//National Natural Science Foundation of China/ ; 22376187//National Natural Science Foundation of China/ ; 42307158//National Natural Science Foundation of China/ ; LZ23B070001//Natural Science Foundation of Zhejiang Province/ ; TED2021-132627B-I00//Department of Local Government, Sport and cultural industries/ ; }, mesh = {Animals ; Humans ; *Genes, Bacterial ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Metagenome/genetics ; Feces ; }, abstract = {The global crisis in antimicrobial resistance continues to grow. Estimating the risks of antibiotic resistance transmission across habitats is hindered by the lack of data on mobility and habitat-specificity. Metagenomic samples of 6092 are analyzed to delineate the unique core resistomes from human feces and seven other habitats. This is found that most resistance genes (≈85%) are transmitted between external habitats and human feces. This suggests that human feces are broadly representative of the global resistome and are potentially a hub for accumulating and disseminating resistance genes. The analysis found that resistance genes with ancient horizontal gene transfer (HGT) events have a higher efficiency of transfer across habitats, suggesting that HGT may be the main driver for forming unique but partly shared resistomes in all habitats. Importantly, the human fecal resistome is historically different and influenced by HGT and age. The most important routes of cross-transmission of resistance are from the atmosphere, buildings, and animals to humans. These habitats should receive more attention for future prevention of antimicrobial resistance. The study will disentangle transmission routes of resistance genes between humans and other habitats in a One Health framework and can identify strategies for controlling the ongoing dissemination and antibiotic resistance.}, }
@article {pmid37865329, year = {2024}, author = {Ye, C and Chen, C and Zhang, K and Feng, M and Yu, X}, title = {Solar/periodate inhibits ARGs transformation by degradation of DNA without damaging cell membrane.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {340}, number = {Pt 1}, pages = {122766}, doi = {10.1016/j.envpol.2023.122766}, pmid = {37865329}, issn = {1873-6424}, mesh = {*Genes, Bacterial ; *Anti-Bacterial Agents/pharmacology ; Wastewater ; Bacteria ; Disinfection/methods ; Cell Membrane ; Water ; }, abstract = {Antibiotic-resistant bacterial infections are a growing global threat to public health. Chlorine-based water disinfection and some advanced oxidation processes significantly increase the risk of ARGs release and transmission in the aquatic environment. Therefore, it is critical to develop or optimize disinfection methods to reduce the conversion and transmission of ARGs in natural water. This study investigated whether the solar/periodate (PI) system inhibited the natural transmission of ARGs and its mechanism. The results showed that solar/PI systems could effectively inhibit the propagation of ARGs in two simulated natural transformation systems, up to more than 100 times. By characterizing the cellular process of bacteria treated by the solar/PI system, we found that the solar/PI system could directly cause damage to DNA bases and its dual effect with almost no damage to the bacterial cell membrane, which was the main reason why this technology could inhibit natural transformation processes. Specifically, the inhibition effect of solar/PI on bacteria did not result in enhanced membrane permeability under appropriate PI dosage (<200 μM), which greatly reduced the risk of secondary contamination of eARGs released by traditional disinfection. Our findings could help improve existing disinfection strategies to ensure that antibiotic resistance is not spread in the natural water environment.}, }
@article {pmid37864197, year = {2023}, author = {Abante, J and Wang, PL and Salzman, J}, title = {DIVE: a reference-free statistical approach to diversity-generating and mobile genetic element discovery.}, journal = {Genome biology}, volume = {24}, number = {1}, pages = {240}, pmid = {37864197}, issn = {1474-760X}, support = {R35 GM139517/GM/NIGMS NIH HHS/United States ; }, mesh = {*Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences ; DNA Transposable Elements ; }, abstract = {Diversity-generating and mobile genetic elements are key to microbial and viral evolution and can result in evolutionary leaps. State-of-the-art algorithms to detect these elements have limitations. Here, we introduce DIVE, a new reference-free approach to overcome these limitations using information contained in sequencing reads alone. We show that DIVE has improved detection power compared to existing reference-based methods using simulations and real data. We use DIVE to rediscover and characterize the activity of known and novel elements and generate new biological hypotheses about the mobilome. Building on DIVE, we develop a reference-free framework capable of de novo discovery of mobile genetic elements.}, }
@article {pmid37863223, year = {2024}, author = {Jiménez-Volkerink, SN and Jordán, M and Smidt, H and Minguillón, C and Vila, J and Grifoll, M}, title = {Metagenomic insights into the microbial cooperative networks of a benz(a)anthracene-7,12-dione degrading community from a creosote-contaminated soil.}, journal = {The Science of the total environment}, volume = {907}, number = {}, pages = {167832}, doi = {10.1016/j.scitotenv.2023.167832}, pmid = {37863223}, issn = {1879-1026}, mesh = {Microbial Consortia ; Creosote ; Sand ; *Polycyclic Aromatic Hydrocarbons/metabolism ; Biodegradation, Environmental ; Carbon ; *Soil Pollutants/metabolism ; Soil Microbiology ; Soil ; }, abstract = {Genotoxicity of PAH-contaminated soils can eventually increase after bioremediation due to the formation and accumulation of polar transformation products, mainly oxygenated PAHs (oxy-PAHs). Biodegradation of oxy-PAHs has been described in soils, but information on the microorganisms and mechanisms involved is still scarce. Benz(a)anthracene-7,12-dione (BaAQ), a transformation product from benz(a)anthracene frequently detected in soils, presents higher genotoxic potential than its parent PAH. Here, using sand-in-liquid microcosms we identified a specialized BaAQ-degrading subpopulation in a PAH-contaminated soil. A BaAQ-degrading microbial consortium was obtained by enrichment in sand-in-liquid cultures with BaAQ as sole carbon source, and its metagenomic analysis identified members of Sphingobium, Stenotrophomonas, Pusillimonas, Olivibacter, Pseudomonas, Achromobacter, and Hyphomicrobiales as major components. The integration of data from metabolomic and metagenomic functional gene analyses of the consortium revealed that the BaAQ metabolic pathway was initiated by Baeyer-Villiger monooxygenases (BVMOs). The presence of plasmid pANTQ-1 in the metagenomic sequences, identified in a previous multi-omic characterization of a 9,10-anthraquinone-degrading isolate recovered from the same soil, suggested the occurrence of a horizontal gene transfer event. Further metagenomic analysis of the BaAQ-degrading consortium also provided insights into the potential roles and interactions within the consortium members. Several potential auxotrophies were detected, indicating that relevant nutritional interdependencies and syntrophic associations were taking place within the community members, not only to provide suitable carbon and energy sources, but also to supply essential nutrients and cofactors. Our work confirms the essential role that BVMO may play as a detoxification mechanism to mitigate the risk posed by oxy-PAH formation during bioremediation of contaminated soils.}, }
@article {pmid37863060, year = {2023}, author = {Mishina, T and Chiu, MC and Hashiguchi, Y and Oishi, S and Sasaki, A and Okada, R and Uchiyama, H and Sasaki, T and Sakura, M and Takeshima, H and Sato, T}, title = {Massive horizontal gene transfer and the evolution of nematomorph-driven behavioral manipulation of mantids.}, journal = {Current biology : CB}, volume = {33}, number = {22}, pages = {4988-4994.e5}, doi = {10.1016/j.cub.2023.09.052}, pmid = {37863060}, issn = {1879-0445}, mesh = {Animals ; *Mantodea ; Host-Parasite Interactions/genetics ; Behavior Control ; Gene Transfer, Horizontal ; *Parasites ; }, abstract = {To complete their life cycle, a wide range of parasites must manipulate the behavior of their hosts.[1] This manipulation is a well-known example of the "extended phenotype,[2]" where genes in one organism have phenotypic effects on another organism. Recent studies have explored the parasite genes responsible for such manipulation of host behavior, including the potential molecular mechanisms.[3][,][4] However, little is known about how parasites have acquired the genes involved in manipulating phylogenetically distinct hosts.[4] In a fascinating example of the extended phenotype, nematomorph parasites have evolved the ability to induce their terrestrial insect hosts to enter bodies of water, where the parasite then reproduces. Here, we comprehensively analyzed nematomorphs and their mantid hosts, focusing on the transcriptomic changes associated with host manipulations and sequence similarity between host and parasite genes to test molecular mimicry. The nematomorph's transcriptome changed during host manipulation, whereas no distinct changes were found in mantids. We then discovered numerous possible host-derived genes in nematomorphs, and these genes were frequently up-regulated during host manipulation. Our findings suggest a possible general role of horizontal gene transfer (HGT) in the molecular mechanisms of host manipulation, as well as in the genome evolution of manipulative parasites. The evidence of HGT between multicellular eukaryotes remains scarce but is increasing and, therefore, elucidating its mechanisms will advance our understanding of the enduring influence of HGT on the evolution of the web of life.}, }
@article {pmid37858689, year = {2023}, author = {Sajjad, W and Ali, B and Niu, H and Ilahi, N and Rafiq, M and Bahadur, A and Banerjee, A and Kang, S}, title = {High prevalence of antibiotic-resistant and metal-tolerant cultivable bacteria in remote glacier environment.}, journal = {Environmental research}, volume = {239}, number = {Pt 2}, pages = {117444}, doi = {10.1016/j.envres.2023.117444}, pmid = {37858689}, issn = {1096-0953}, mesh = {*Genes, Bacterial ; *Ice Cover/microbiology ; Prevalence ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Bacteria ; Anti-Bacterial Agents/pharmacology/analysis ; Metals/analysis ; Gram-Negative Bacteria/genetics ; Drug Resistance, Bacterial/genetics ; }, abstract = {Studies of antibiotic-resistant bacteria (ARB) have mainly originated from anthropic-influenced environments, with limited information from pristine environments. Remote cold environments are major reservoirs of ARB and have been determined in polar regions; however, their abundance in non-polar cold habitats is underexplored. This study evaluated antibiotics and metals resistance profiles, prevalence of antibiotic resistance genes (ARGs) and metals tolerance genes (MTGs) in 38 ARB isolated from the glacier debris and meltwater from Baishui Glacier No 1, China. Molecular identification displayed Proteobacteria (39.3%) predominant in debris, while meltwater was dominated by Actinobacteria (30%) and Proteobacteria (30%). Bacterial isolates exhibited multiple antibiotic resistance index values > 0.2. Gram-negative bacteria displayed higher resistance to antibiotics and metals than Gram-positive. PCR amplification exhibited distinct ARGs in bacteria dominated by β-lactam genes blaCTX-M (21.1-71.1%), blaACC (21.1-60.5%), tetracycline-resistant gene tetA (21.1-60.5%), and sulfonamide-resistant gene sulI (18.4-52.6%). Moreover, different MTGs were reported in bacterial isolates, including mercury-resistant merA (21.1-63.2%), copper-resistant copB (18.4-57.9%), chromium-resistant chrA (15.8-44.7%) and arsenic-resistant arsB (10.5-44.7%). This highlights the co-selection and co-occurrence of MTGs and ARGs in remote glacier environments. Different bacteria shared same ARGs, signifying horizontal gene transfer between species. Strong positive correlation among ARGs and MTGs was reported. Metals tolerance range exhibited that Gram-negative and Gram-positive bacteria clustered distinctly. Gram-negative bacteria were significantly tolerant to metals. Amino acid sequences of blaACC,blaCTX-M,blaSHV,blaampC,qnrA, sulI, tetA and blaTEM revealed variations. This study presents promising ARB, harboring ARGs with variations in amino acid sequences, highlighting the need to assess the transcriptome study of glacier bacteria conferring ARGs and MTGs.}, }
@article {pmid37856515, year = {2023}, author = {Johansson, MHK and Aarestrup, FM and Petersen, TN}, title = {Importance of mobile genetic elements for dissemination of antimicrobial resistance in metagenomic sewage samples across the world.}, journal = {PloS one}, volume = {18}, number = {10}, pages = {e0293169}, pmid = {37856515}, issn = {1932-6203}, mesh = {*Sewage/microbiology ; *Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; Bacteria/genetics ; Interspersed Repetitive Sequences/genetics ; }, abstract = {We are facing an ever-growing threat from increasing antimicrobial resistance (AMR) in bacteria. To mitigate this, we need a better understanding of the global spread of antimicrobial resistance genes (ARGs). ARGs are often spread among bacteria by horizontal gene transfer facilitated by mobile genetic elements (MGE). Here we use a dataset consisting of 677 metagenomic sequenced sewage samples from 97 countries or regions to study how MGEs are geographically distributed and how they disseminate ARGs worldwide. The ARGs, MGEs, and bacterial abundance were calculated by reference-based read mapping. We found systematic differences in the abundance of MGEs and ARGs, where some elements were prevalent on all continents while others had higher abundance in separate geographic areas. Different MGEs tended to be localized to temperate or tropical climate zones, while different ARGs tended to separate according to continents. This suggests that the climate is an important factor influencing the local flora of MGEs. MGEs were also found to be more geographically confined than ARGs. We identified several integrated MGEs whose abundance correlated with the abundance of ARGs and bacterial genera, indicating the ability to mobilize and disseminate these genes. Some MGEs seemed to be more able to mobilize ARGs and spread to more bacterial species. The host ranges of MGEs seemed to differ between elements, where most were associated with bacteria of the same family. We believe that our method could be used to investigate the population dynamics of MGEs in complex bacterial populations.}, }
@article {pmid37856455, year = {2023}, author = {Aubin, E and Llauro, C and Garrigue, J and Mirouze, M and Panaud, O and El Baidouri, M}, title = {Genome-wide analysis of horizontal transfer in non-model wild species from a natural ecosystem reveals new insights into genetic exchange in plants.}, journal = {PLoS genetics}, volume = {19}, number = {10}, pages = {e1010964}, pmid = {37856455}, issn = {1553-7404}, mesh = {*Ecosystem ; Pilot Projects ; *Genome, Plant/genetics ; Genomics ; Retroelements ; Phylogeny ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; }, abstract = {Horizontal transfer (HT) refers to the exchange of genetic material between divergent species by mechanisms other than reproduction. In recent years, several studies have demonstrated HTs in eukaryotes, particularly in the context of parasitic relationships and in model species. However, very little is known about HT in natural ecosystems, especially those involving non-parasitic wild species, and the nature of the ecological relationships that promote these HTs. In this work, we conducted a pilot study investigating HTs by sequencing the genomes of 17 wild non-model species from a natural ecosystem, the Massane forest, located in southern France. To this end, we developed a new computational pipeline called INTERCHANGE that is able to characterize HTs at the whole genome level without prior annotation and directly in the raw sequencing reads. Using this pipeline, we identified 12 HT events, half of which occurred between lianas and trees. We found that mainly low copy number LTR-retrotransposons from the Copia superfamily were transferred between these wild plant species, especially those of the Ivana and Ale lineages. This study revealed a possible new route for HTs between non-parasitic plants and provides new insights into the genomic characteristics of horizontally transferred DNA in plant genomes.}, }
@article {pmid37855620, year = {2023}, author = {Jia, C and Wang, Z and Huang, C and Teng, L and Zhou, H and An, H and Liao, S and Liu, Y and Huang, L and Tang, B and Yue, M}, title = {Mobilome-driven partitions of the resistome in Salmonella.}, journal = {mSystems}, volume = {8}, number = {6}, pages = {e0088323}, pmid = {37855620}, issn = {2379-5077}, mesh = {*Salmonella/drug effects/genetics ; *Drug Resistance, Bacterial ; }, abstract = {Antimicrobial resistance (AMR) has become a significant global challenge, with an estimated 10 million deaths annually by 2050. The emergence of AMR is mainly attributed to mobile genetic elements (MGEs or mobilomes), which accelerate wide dissemination among pathogens. The interaction between mobilomes and AMR genes (or resistomes) in Salmonella, a primary cause of diarrheal diseases that results in over 90 million cases annually, remains poorly understood. The available fragmented or incomplete genomes remain a significant limitation in investigating the relationship between AMR and MGEs. Here, we collected the most extensive closed Salmonella genomes (n = 1,817) from various sources across 58 countries. Notably, our results demonstrate that resistome transmission between Salmonella lineages follows a specific pattern of MGEs and is influenced by external drivers, including certain socioeconomic factors. Therefore, targeted interventions are urgently needed to mitigate the catastrophic consequences of Salmonella AMR.}, }
@article {pmid37855599, year = {2023}, author = {Feng, Z and Wang, L and Guan, Q and Chu, X and Luo, Z-Q}, title = {Acinetobacter baumannii coordinates central metabolism, plasmid dissemination, and virulence by sensing nutrient availability.}, journal = {mBio}, volume = {14}, number = {6}, pages = {e0227623}, pmid = {37855599}, issn = {2150-7511}, support = {YDZJ202201ZYTS025//Department of Science and Technology of Jilin Province ()/ ; }, mesh = {*Acinetobacter baumannii/genetics/metabolism/pathogenicity ; *Plasmids/genetics ; Virulence ; *Nutrients/metabolism ; *Gene Transfer, Horizontal ; Bacterial Proteins/genetics/metabolism ; Metabolic Networks and Pathways/genetics ; Conjugation, Genetic ; Gene Expression Regulation, Bacterial ; Humans ; }, abstract = {Plasmid conjugation is known to be an energy-expensive process, but our understanding of the molecular linkage between conjugation and metabolism is limited. Our finding reveals that Acinetobacter baumannii utilizes a two-component system to co-regulate metabolism, plasmid transfer, and virulence by sensing reaction intermediates of key metabolic pathways, which suggests that nutrient availability dictates not only bacterial proliferation but also horizontal gene transfer. The identification of Dot/Icm-like proteins as components of a conjugation system involved in the dissemination of antibiotic-resistance genes by A. baumannii has provided important targets for the development of agents capable of inhibiting virulence and the spread of anti-microbial-resistance genes in bacterial communities.}, }
@article {pmid37850911, year = {2023}, author = {Yee, W-X and Elsener, T and Cehovin, A and Maiden, MCJ and Tang, CM}, title = {Evolution and exchange of plasmids in pathogenic Neisseria.}, journal = {mSphere}, volume = {8}, number = {6}, pages = {e0044123}, pmid = {37850911}, issn = {2379-5042}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; Neisseria/genetics ; Doxycycline ; Microbial Sensitivity Tests ; Plasmids/genetics ; *Gonorrhea/microbiology ; Neisseria gonorrhoeae/genetics ; *Neisseria meningitidis/genetics ; }, abstract = {Horizontal gene transfer (HGT) is a major influence in driving the spread of antimicrobial resistance (AMR) in many bacteria. A conjugative plasmid which is widespread in Neisseria gonorrhoeae, pConj, prevented the use of tetracycline/doxycycline for treating gonococcal infection. Here, we show that pConj evolved in the related pathogen, Neisseria meningitidis, and has been acquired by the gonococcus from the meningococcus on multiple occasions. Following its initial acquisition, pConj spread to different gonococcal lineages; changes in the plasmid's conjugation machinery associated with another transfer event limit spread in the gonococcal populations. Our findings have important implications for the use of doxycycline to prevent bacterial sexually transmitted disease which is likely to exacerbate the spread of AMR through HGT in pathogenic bacteria.}, }
@article {pmid37850800, year = {2023}, author = {Giengkam, S and Kullapanich, C and Wongsantichon, J and Adcox, HE and Gillespie, JJ and Salje, J}, title = {Orientia tsutsugamushi: comprehensive analysis of the mobilome of a highly fragmented and repetitive genome reveals the capacity for ongoing lateral gene transfer in an obligate intracellular bacterium.}, journal = {mSphere}, volume = {8}, number = {6}, pages = {e0026823}, pmid = {37850800}, issn = {2379-5042}, support = {/WT_/Wellcome Trust/United Kingdom ; R21 AI156762/AI/NIAID NIH HHS/United States ; R21 AI166832/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Orientia tsutsugamushi/genetics/metabolism ; *Scrub Typhus/genetics/microbiology ; Gene Transfer, Horizontal ; Genome, Bacterial ; Longitudinal Studies ; }, abstract = {Obligate intracellular bacteria, or those only capable of growth inside other living cells, have limited opportunities for horizontal gene transfer with other microbes due to their isolated replicative niche. The human pathogen Ot, an obligate intracellular bacterium causing scrub typhus, encodes an unusually high copy number of a ~40 gene mobile genetic element that typically facilitates genetic transfer across microbes. This proliferated element is heavily degraded in Ot and previously assumed to be inactive. Here, we conducted a detailed analysis of this element in eight Ot strains and discovered two strains with at least one intact copy. This implies that the element is still capable of moving across Ot populations and suggests that the genome of this bacterium may be even more dynamic than previously appreciated. Our work raises questions about intracellular microbial evolution and sounds an alarm for gene-based efforts focused on diagnosing and combatting scrub typhus.}, }
@article {pmid37849012, year = {2023}, author = {Wei, Y and Gong, Z and Han, GZ}, title = {Plants acquired mitochondrial linear plasmids horizontally from fungi likely during the conquest of land.}, journal = {Mobile DNA}, volume = {14}, number = {1}, pages = {15}, pmid = {37849012}, issn = {1759-8753}, support = {31922001//National Natural Science Foundation of China/ ; }, abstract = {Mitochondrial linear plasmids have been sporadically reported in fungi and plants. Yet, much remains obscure about the diversity, distribution, and evolution of mitochondrial linear plasmids. Here, through phylogenomic analyses across 7,163 cellular organisms (including 991 plants), we find that mitochondrial linear plasmids are widely present in land plants and fungi. Phylogenetic analyses indicate that plants are likely to have acquired mitochondrial linear plasmids horizontally from fungi before or during the conquest of terrestrial environments by plants. Gene content analyses show that mitochondrial linear plasmids harbor a highly dynamic and promiscuous repertoire of genes. Our study refines the understanding of the origin and evolution of mitochondrial linear plasmids.}, }
@article {pmid37848554, year = {2023}, author = {Lücking, D and Mercier, C and Alarcón-Schumacher, T and Erdmann, S}, title = {Extracellular vesicles are the main contributor to the non-viral protected extracellular sequence space.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {112}, pmid = {37848554}, issn = {2730-6151}, support = {Max Planck Research Group Archaeal Virology//Max-Planck-Gesellschaft (Max Planck Society)/ ; Max Planck Research Group Archaeal Virology//Max-Planck-Gesellschaft (Max Planck Society)/ ; Max Planck Research Group Archaeal Virology//Max-Planck-Gesellschaft (Max Planck Society)/ ; Max Planck Research Group Archaeal Virology//Max-Planck-Gesellschaft (Max Planck Society)/ ; }, abstract = {Environmental virus metagenomes, commonly referred to as "viromes", are typically generated by physically separating virus-like particles (VLPs) from the microbial fraction based on their size and mass. However, most methods used to purify VLPs, enrich extracellular vesicles (EVs) and gene transfer agents (GTAs) simultaneously. Consequently, the sequence space traditionally referred to as a "virome" contains host-associated sequences, transported via EVs or GTAs. We therefore propose to call the genetic material isolated from size-fractionated (0.22 µm) and DNase-treated samples protected environmental DNA (peDNA). This sequence space contains viral genomes, DNA transduced by viruses and DNA transported in EVs and GTAs. Since there is no genetic signature for peDNA transported in EVs, GTAs and virus particles, we rely on the successful removal of contaminating remaining cellular and free DNA when analyzing peDNA. Using marine samples collected from the North Sea, we generated a thoroughly purified peDNA dataset and developed a bioinformatic pipeline to determine the potential origin of the purified DNA. This pipeline was applied to our dataset as well as existing global marine "viromes". Through this pipeline, we identified known GTA and EV producers, as well as organisms with actively transducing proviruses as the source of the peDNA, thus confirming the reliability of our approach. Additionally, we identified novel and widespread EV producers, and found quantitative evidence suggesting that EV-mediated gene transfer plays a significant role in driving horizontal gene transfer (HGT) in the world's oceans.}, }
@article {pmid37845226, year = {2023}, author = {Gonzalez-Serrano, R and Rosselli, R and Roda-Garcia, JJ and Martin-Cuadrado, AB and Rodriguez-Valera, F and Dunne, M}, title = {Distantly related Alteromonas bacteriophages share tail fibers exhibiting properties of transient chaperone caps.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {6517}, pmid = {37845226}, issn = {2041-1723}, mesh = {Humans ; *Bacteriophages/metabolism ; *Alteromonas/genetics/metabolism ; Molecular Chaperones/genetics/metabolism ; Carrier Proteins/metabolism ; Genome, Viral ; }, abstract = {The host recognition modules encoding the injection machinery and receptor binding proteins (RBPs) of bacteriophages are predisposed to mutation and recombination to maintain infectivity towards co-evolving bacterial hosts. In this study, we reveal how Alteromonas mediterranea schitovirus A5 shares its host recognition module, including tail fiber and cognate chaperone, with phages from distantly related families including Alteromonas myovirus V22. While the V22 chaperone is essential for producing active tail fibers, here we demonstrate production of functional A5 tail fibers regardless of chaperone co-expression. AlphaFold-generated models of tail fiber and chaperone pairs from phages A5, V22, and other Alteromonas phages reveal how amino acid insertions within both A5-like proteins results in a knob domain duplication in the tail fiber and a chaperone β-hairpin "tentacle" extension. These structural modifications are linked to differences in chaperone dependency between the A5 and V22 tail fibers. Structural similarity between the chaperones and intramolecular chaperone domains of other phage RBPs suggests an additional function of these chaperones as transient fiber "caps". Finally, our identification of homologous host recognition modules from morphologically distinct phages implies that horizontal gene transfer and recombination events between unrelated phages may be a more common process than previously thought among Caudoviricetes phages.}, }
@article {pmid37843655, year = {2023}, author = {Sudhakari, PA and Ramisetty, BCM}, title = {An Eco-evolutionary Model on Surviving Lysogeny Through Grounding and Accumulation of Prophages.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {3068-3081}, pmid = {37843655}, issn = {1432-184X}, mesh = {Humans ; Lysogeny ; Prophages/genetics ; Escherichia coli/genetics ; *Superinfection/genetics ; Wastewater ; *Bacteriophages/genetics ; Genome, Bacterial ; }, abstract = {Temperate phages integrate into the bacterial genomes propagating along with the bacterial genomes. Multiple phage elements, representing diverse prophages, are present in most bacterial genomes. The evolutionary events and the ecological dynamics underlying the accumulation of prophage elements in bacterial genomes have yet to be understood. Here, we show that the local wastewater had 7% of lysogens (hosting mitomycin C-inducible prophages), and they showed resistance to superinfection by their corresponding lysates. Genomic analysis of four lysogens and four non-lysogens revealed the presence of multiple prophages (belonging to Myoviridae and Siphoviridae) in both lysogens and non-lysogens. For large-scale comparison, 2180 Escherichia coli genomes isolated from various sources across the globe and 523 genomes specifically isolated from diverse wastewaters were analyzed. A total of 15,279 prophages were predicted among 2180 E. coli genomes and 2802 prophages among 523 global wastewater isolates, with a mean of ~ 5 prophages per genome. These observations indicate that most putative prophages are relics of past bacteria-phage conflicts; they are "grounded" prophages that cannot excise from the bacterial genome. Prophage distribution analysis based on the sequence homology suggested the random distribution of E. coli prophages within and between E. coli clades. The independent occurrence pattern of these prophages indicates extensive horizontal transfers across the genomes. We modeled the eco-evolutionary dynamics to reconstruct the events that could have resulted in the prophage accumulation accounting for infection, superinfection immunity, and grounding. In bacteria-phage conflicts, the bacteria win by grounding the prophage, which could confer superinfection immunity.}, }
@article {pmid37842006, year = {2023}, author = {López-Pérez, J and Otero, J and Sánchez-Osuna, M and Erill, I and Cortés, P and Llagostera, M}, title = {Impact of mutagenesis and lateral gene transfer processes in bacterial susceptibility to phage in food biocontrol and phage therapy.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1266685}, pmid = {37842006}, issn = {2235-2988}, mesh = {Animals ; *Bacteriophages/genetics ; *Salmonella Phages/genetics ; *Phage Therapy ; Chickens ; Gene Transfer, Horizontal ; Mutagenesis ; Bacteria ; }, abstract = {INTRODUCTION: The emergence of resistance and interference mechanisms to phage infection can hinder the success of bacteriophage-based applications, but the significance of these mechanisms in phage therapy has not been determined. This work studies the emergence of Salmonella isolates with reduced susceptibility to a cocktail of three phages under three scenarios: i) Salmonella cultures (LAB), ii) biocontrol of cooked ham slices as a model of food safety (FOOD), and iii) oral phage therapy in broilers (PT).<br><br>METHODS: S. Typhimurium ATCC 14028 RifR variants with reduced phage susceptibility were isolated from the three scenarios and conventional and molecular microbiology techniques were applied to study them.<br><br>RESULTS AND DISCUSSION: In LAB, 92% of Salmonella isolates lost susceptibility to all three phages 24 h after phage infection. This percentage was lower in FOOD, with 4.3% of isolates not susceptible to at least two of the three phages after seven days at 4&#xb0;C following phage treatment. In PT, 9.7% and 3.3 % of isolates from untreated and treated broilers, respectively, displayed some mechanism of interference with the life cycle of some of the phages. In LAB and FOOD scenarios, resistant variants carrying mutations in rfc and rfaJ genes involved in lipopolysaccharide synthesis (phage receptor) were identified. However, in PT, the significant decrease of EOP, ECOI, and burst size observed in isolates was prompted by lateral gene transfer of large IncI1 plasmids, which may encode phage defense mechanisms. These data indicate that the acquisition of specific conjugative plasmids has a stronger impact than mutagenesis on the emergence of reduced phage-susceptibility bacteria in certain environments. In spite of this, neither mechanism seems to significantly impair the success of Salmonella biocontrol and oral phage therapy.}, }
@article {pmid37841331, year = {2023}, author = {Asif, M and Li-Qun, Z and Zeng, Q and Atiq, M and Ahmad, K and Tariq, A and Al-Ansari, N and Blom, J and Fenske, L and Alodaini, HA and Hatamleh, AA}, title = {Comprehensive genomic analysis of Bacillus paralicheniformis strain BP9, pan-genomic and genetic basis of biocontrol mechanism.}, journal = {Computational and structural biotechnology journal}, volume = {21}, number = {}, pages = {4647-4662}, pmid = {37841331}, issn = {2001-0370}, abstract = {Many Bacillus species are essential antibacterial agents, but their antibiosis potential still needs to be elucidated to its full extent. Here, we isolated a soil bacterium, BP9, which has significant antibiosis activity against fungal and bacterial pathogens. BP9 improved the growth of wheat seedlings via active colonization and demonstrated effective biofilm and swarming activity. BP9 sequenced genome contains 4282 genes with a mean G-C content of 45.94% of the whole genome. A single copy concatenated 802 core genes of 28 genomes, and their calculated average nucleotide identity (ANI) discriminated the strain BP9 from Bacillus licheniformis and classified it as Bacillus paralicheniformis. Furthermore, a comparative pan-genome analysis of 40 B. paralicheniformis strains suggested that the genetic repertoire of BP9 belongs to open-type genome species. A comparative analysis of a pan-genome dataset using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Cluster of Orthologous Gene groups (COG) revealed the diversity of secondary metabolic pathways, where BP9 distinguishes itself by exhibiting a greater prevalence of loci associated with the metabolism and transportation of organic and inorganic substances, carbohydrate and amino acid for effective inhabitation in diverse environments. The primary secondary metabolites and their genes involved in synthesizing bacillibactin, fencing, bacitracin, and lantibiotics were identified as acquired through a recent Horizontal gene transfer (HGT) event, which contributes to a significant part of the strain`s antimicrobial potential. Finally, we report some genes essential for plant-host interaction identified in BP9, which reduce spore germination and virulence of multiple fungal and bacterial species. The effective colonization, diverse predicted metabolic pathways and secondary metabolites (antibiotics) suggest testing the suitability of strain BP9 as a potential bio-preparation in agricultural fields.}, }
@article {pmid37840734, year = {2023}, author = {Li, Y and Fan, Y and Ma, X and Wang, Y and Liu, J}, title = {Metagenomic survey reveals global distribution and evolution of microbial sialic acid catabolism.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1267152}, pmid = {37840734}, issn = {1664-302X}, abstract = {Sialic acids comprise a varied group of nine-carbon amino sugars found mostly in humans and other higher metazoans, playing major roles in cell interactions with external environments as well as other cells. Microbial sialic acid catabolism (SAC) has long been considered a virulence determinant, and appears to be mainly the purview of pathogenic and commensal bacterial species associated with eukaryotic hosts. Here, we used 2,521 (pre-)assembled metagenomes to evaluate the distribution of SAC in microbial communities from diverse ecosystems and human body parts. Our results demonstrated that microorganisms possessing SAC globally existed in non-host associated environments, although much less frequently than in mammal hosts. We also showed that the ecological significance and taxonomic diversity of microbial SAC have so far been largely underestimated. Phylogenetic analysis revealed a strong signal of horizontal gene transfer among distinct taxa and habitats, and also suggested a specific ecological pressure and a relatively independent evolution history in environmental communities. Our study expanded the known diversity of microbial SAC, and has provided the backbone for further studies on its ecological roles and potential pathogenesis.}, }
@article {pmid37838320, year = {2023}, author = {Wang, L and Hu, T and Li, Y and Zhao, Z and Zhu, M}, title = {Unraveling the interplay between antibiotic resistance genes and microbial communities in water and sediments of the intensive tidal flat aquaculture.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {339}, number = {}, pages = {122734}, doi = {10.1016/j.envpol.2023.122734}, pmid = {37838320}, issn = {1873-6424}, mesh = {*Anti-Bacterial Agents/pharmacology ; Water ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Aquaculture ; *Microbiota ; China ; }, abstract = {Tidal flats are formed valuably resources by the interaction of terrestrial and marine processes. Aquaculture on tidal flats has brought significant economic profits, but the over usage of antibiotics has resulted in the prevalence antibiotic resistance genes (ARGs) which pose serious threats to ecosystems. However, ARG abundances and bacterial community assemblies in the overlying water and sediments of tidal flat aquaculture areas have not been fully explored. Thus, antibiotic concentrations, ARG abundances, microbial communities and the influences of environmental factors in the Jiangsu tidal flat aquaculture ponds were investigated using high-throughput sequencing and qPCR. The concentrations of antibiotics at sampling ranged from not detectable to 2322.4 ng g[-1], and sulfamethazine and ciprofloxacin were the dominant antibiotics. The sul1 and sul2 abundances were highest and the ARG abundances were higher in sediment than in water. Meanwhile, bacterial community diversities and structures were significantly different (P < 0.05) between water and sediment samples. Network analysis identified Sphingomonadacear, Pseudomonas, and Xanthobacteraceae as potential ARG-carrying pathogens. A positive correlation between ARGs and intI1 indicated that horizontal gene transfer occurred in water, while antibiotics and TN significantly influenced ARG abundances in sediment. Neutral modeling showed that deterministic and stochastic processes contributed most to the bacterial community assemblies of water and sediment samples, respectively. This study comprehensively illustrates the prevalence of ARGs in intensive tidal flat aquaculture regions and provides an effective foundation for the management of antibiotics usage.}, }
@article {pmid37833945, year = {2023}, author = {Kuznetsova, MV and Pospelova, JS and Maslennikova, IL and Starčič Erjavec, M}, title = {Dual-Species Biofilms: Biomass, Viable Cell Ratio/Cross-Species Interactions, Conjugative Transfer.}, journal = {International journal of molecular sciences}, volume = {24}, number = {19}, pages = {}, pmid = {37833945}, issn = {1422-0067}, support = {No. 19-44-590014 r_a.//Goverment of Perm Krai/ ; AAAA-A19-119112290009-1//Russian Foundation for Basic Research/ ; }, mesh = {*Escherichia coli/genetics ; Biomass ; *Biofilms ; Plasmids/genetics ; Cell Communication ; }, abstract = {Biofilms as a form of adaptation are beneficial for bacterial survival and may be hot spots for horizontal gene transfer, including conjugation. The aim of this research was to characterize the biofilm biomass, viable cell ratios and conjugative transfer of the pOX38 plasmid, an F-plasmid derivative, from the Escherichia coli N4i pOX38 strain (donor) into a uropathogenic E. coli DL82 strain (recipient) within dual-species biofilms with one of the following opportunistic pathogenic bacteria: Klebsiella pneumoniae, Enterococcus faecalis or Pseudomonas aeruginosa. Dual-species biofilms of E. coli with K. pneumoniae or P. aeruginosa but not E. faecalis were more massive and possessed more exopolysaccharide matrix compared to single-species biofilms of donor and recipient cells. Correlation between biofilm biomass and exopolysaccharide matrix was rs = 0.888 in dual-species biofilms. In dual-species biofilm with E. faecalis the proportion of E. coli was the highest, while in the biofilm with P. aeruginosa and K. pneumoniae, the E. coli was less abundant. The conjugative frequencies of plasmid transfer in dual-species biofilms of E. coli with E. faecalis and P. aeruginosa were reduced. A decrease in conjugative frequency was also observed when cell-free supernatants (CFSs) of E. faecalis and P. aeruginosa were added to the E. coli conjugation mixture. Further, the activity of the autoinducer AI-2 in the CFSs of the E. coli conjugation mixture was reduced when bacteria or CFSs of E. faecalis and P. aeruginosa were added to the E. coli conjugation mixture. Hence, the intercellular and interspecies interactions in dual-species biofilms depend on the partners involved.}, }
@article {pmid37832298, year = {2023}, author = {Chu, K and Liu, Y and Hua, Z and Lu, Y and Ye, F}, title = {Spatio-temporal distribution and dynamics of antibiotic resistance genes in a water-diversion lake, China.}, journal = {Journal of environmental management}, volume = {348}, number = {}, pages = {119232}, doi = {10.1016/j.jenvman.2023.119232}, pmid = {37832298}, issn = {1095-8630}, mesh = {*Genes, Bacterial ; *Anti-Bacterial Agents/pharmacology ; Water ; Drug Resistance, Microbial/genetics ; China ; }, abstract = {The distribution and dynamics of antibiotic resistance genes (ARGs) in water-diversion lakes are poorly understood. In this study, two comparative in situ investigations of ARG profiles targeting water diversion (DP) and non-diversion periods (NDP) were conducted in Luoma Lake, a vital transfer node for the eastern route of the South-to-North Water Diversion Project in China. The results demonstrated significant spatiotemporal variations in ARG contamination and notable differences in the co-occurrence patterns of ARGs and bacterial communities between DP and NDP. Correlations among ARGs with the 16 S rRNA, and mobile genetic elements indicate that horizontal gene transfer (HGT) and vertical gene transfer (VGT) in NDP, but only HGT in DP, were the primary mechanisms of ARG proliferation and spread, implying that water diversion could be an essential control of the transfer pattern of ARGs in a lake environment. The null model analysis indicated that stochastic processes, with predominant driver of ecological drift in the lake mainly drove the assembly of ARGs. Partial least squares structural equation modeling was developed to analyze the causal effects of the factors in shaping ARG dynamics and identify the major driving forces in the DP and NDP.}, }
@article {pmid37832249, year = {2023}, author = {Wang, C and Yang, H and Liu, H and Zhang, XX and Ma, L}, title = {Anthropogenic contributions to antibiotic resistance gene pollution in household drinking water revealed by machine-learning-based source-tracking.}, journal = {Water research}, volume = {246}, number = {}, pages = {120682}, doi = {10.1016/j.watres.2023.120682}, pmid = {37832249}, issn = {1879-2448}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; *Drinking Water ; Drug Resistance, Microbial/genetics ; Machine Learning ; }, abstract = {Although the presence of antibiotic resistance genes (ARGs) in drinking water and their potential horizontal gene transfer to pathogenic microbes are known to pose a threat to human health, their pollution levels and potential anthropogenic sources are poorly understood. In this study, broad-spectrum ARG profiling combined with machine-learning-based source classification SourceTracker was performed to investigate the pollution sources of ARGs in household drinking water collected from 95 households in 47 cities of eight countries/regions. In total, 451 ARG subtypes belonging to 19 ARG types were detected with total abundance in individual samples ranging from 1.4 × 10[-4] to 1.5 × 10° copies per cell. Source tracking analysis revealed that many ARGs were highly contributed by anthropogenic sources (37.1%), mainly wastewater treatment plants. The regions with the highest detected ARG contribution from wastewater (∼84.3%) used recycled water as drinking water, indicating the need for better ARG control strategies to ensure safe water quality in these regions. Among ARG types, sulfonamide, rifamycin and tetracycline resistance genes were mostly anthropogenic in origin. The contributions of anthropogenic sources to the 20 core ARGs detected in all of the studied countries/regions varied from 36.6% to 84.1%. Moreover, the anthropogenic contribution of 17 potential mobile ARGs identified in drinking water was significantly higher than other ARGs, and metagenomic assembly revealed that these mobile ARGs were carried by diverse potential pathogens. These results indicate that human activities have exacerbated the constant input and transmission of ARGs in drinking water. Our further risk classification framework revealed three ARGs (sul1, sul2 and aadA) that pose the highest risk to public health given their high prevalence, anthropogenic sources and mobility, facilitating accurate monitoring and control of anthropogenic pollution in drinking water.}, }
@article {pmid37831481, year = {2023}, author = {Morgene, F and Rizoug Zeghlache, C and Feng, SY and Hauck, Y and Mirouze, N}, title = {Natural transformation and cell division delay in competent Staphylococcus aureus.}, journal = {Microbiology spectrum}, volume = {11}, number = {6}, pages = {e0280723}, pmid = {37831481}, issn = {2165-0497}, support = {ANR-18-CE35-0004//Agence Nationale de la Recherche (ANR)/ ; //China Scholarship Council (CSC)/ ; }, mesh = {Humans ; *Staphylococcus aureus/genetics/metabolism ; *Gene Transfer, Horizontal ; Bacteria/metabolism ; Bacterial Proteins/genetics/metabolism ; Cell Division ; }, abstract = {Natural transformation, considered one of the three main mechanisms leading to horizontal gene transfer in bacteria, is able to promote genomic plasticity and foster antibiotic resistance spreading. Conserved machinery and actors required to perform natural transformation have been shown to accumulate at different cellular localizations depending on the model organism considered. Here, we show in the human pathogen Staphylococcus aureus that DNA binding, uptake, and recombination are spatially and temporally coordinated to ensure S. aureus natural transformation. We also reveal that localization of natural transformation proteins occurs in the vicinity of the division septum allowing S. aureus competent cells to block cell division to ensure the success of natural transformation before the final constriction of the cytokinetic ring.}, }
@article {pmid37828802, year = {2024}, author = {Zhao, J and Feng, T and An, X and Chen, X and Han, N and Wang, J and Chang, G and Hou, X}, title = {Livestock grazing is associated with the gut microbiota and antibiotic resistance genes in sympatric plateau pika (Ochotona curzoniae).}, journal = {Integrative zoology}, volume = {19}, number = {4}, pages = {646-661}, doi = {10.1111/1749-4877.12778}, pmid = {37828802}, issn = {1749-4877}, support = {2019QZKK0501//Second Tibetan Plateau Scientific Expedition&#xa0;and Research Program (STEP)/ ; 32172436//National Natural Science Foundation of&#xa0;China/ ; 2022K-16//Science and Technology Program of Shaanxi Academy&#xa0;of Science/ ; 2019QZKK0501//Scond Tibetan Plateau Scientific Expedition and Research/ ; 32172436//National Natural Science Foundation of China/ ; 2022K-16//Science and Technology Program of Shaanxi Academy of Science/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Lagomorpha/genetics ; *Drug Resistance, Microbial/genetics ; Herbivory ; Bacteria/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Livestock/microbiology ; Genes, Bacterial ; }, abstract = {With the overuse of antibiotics in health care and animal husbandry, antibiotic resistance becomes a serious threat to public health. Antibiotic residues from veterinary medicine have increased the dissemination of antibiotic resistance genes (ARGs) by horizontal gene transfer globally, leading to the enrichment of ARGs in wildlife. Plateau pika (Ochotona curzoniae) is a small herbivore endemic to the Qinghai-Tibetan Plateau. Previous studies reveal that pika evolves a coprophagy behavior toward cohabitated yak, which makes the pika population a potential reservoir of ARGs. Yet, little is known about the resistome of pika under different grazing intensities. Here, we sampled the cecum content of pika from three different grazing intensity areas in the Qinghai-Tibetan Plateau to evaluate the effect of grazing on its gut microbiota and resistome. By using the 16S full-length amplicon and metagenomic sequencing, our study revealed that livestock grazing significantly altered the gut microbial community of plateau pika as compared to prohibited grazing areas. We found bacterial lineage Prevotellaceae, Lachnospirales, and RF39 increased in grazing areas. Analysis of the resistome revealed that pika from continuous grazing areas enriched a higher abundance of colistin (MCR) and streptogramin (vat) resistance genes. Moreover, we observed significant correlations between the gut microbial community, ARGs, and mobile genetic element profiles, hinting that pika gut microbiota was an important shaping force of the resistome. In future studies, the continuous monitoring of wildlife gut resistome and environmental antibiotic residues is imperative for a better understanding and for tackling the horizontal gene transfer of ARGs across the wildlife-livestock interface.}, }
@article {pmid37820728, year = {2023}, author = {Weiss, A and Wang, T and You, L}, title = {Promotion of plasmid maintenance by heterogeneous partitioning of microbial communities.}, journal = {Cell systems}, volume = {14}, number = {10}, pages = {895-905.e5}, pmid = {37820728}, issn = {2405-4720}, support = {R01 AI125604/AI/NIAID NIH HHS/United States ; R01 EB031869/EB/NIBIB NIH HHS/United States ; R01 GM098642/GM/NIGMS NIH HHS/United States ; }, mesh = {Plasmids/genetics ; *Microbiota/genetics ; Escherichia coli/genetics ; }, abstract = {Transferable plasmids play a critical role in shaping the functions of microbial communities. Previous studies suggested multiple mechanisms underlying plasmid persistence and abundance. Here, we focus on the interplay between heterogeneous community partitioning and plasmid fates. Natural microbiomes often experience partitioning that creates heterogeneous local communities with reduced population sizes and biodiversity. Little is known about how population partitioning affects the plasmid fate through the modulation of community structure. By modeling and experiments, we show that heterogeneous community partitioning can paradoxically promote the persistence of a plasmid that would otherwise not persist in a global community. Among the local communities created by partitioning, a minority will primarily consist of members able to transfer the plasmid fast enough to support its maintenance by serving as a local plasmid haven. Our results provide insights into plasmid maintenance and suggest a generalizable approach to modulate plasmid persistence for engineering and medical applications.}, }
@article {pmid37819078, year = {2023}, author = {Svet, L and Parijs, I and Isphording, S and Lories, B and Marchal, K and Steenackers, HP}, title = {Competitive interactions facilitate resistance development against antimicrobials.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {10}, pages = {e0115523}, pmid = {37819078}, issn = {1098-5336}, mesh = {*Anti-Infective Agents/pharmacology ; Biofilms ; Bacteria/genetics ; Phenotype ; Sulfathiazoles/pharmacology ; Anti-Bacterial Agents/pharmacology ; }, abstract = {While the evolution of antimicrobial resistance is well studied in free-living bacteria, information on resistance development in dense and diverse biofilm communities is largely lacking. Therefore, we explored how the social interactions in a duo-species biofilm composed of the brewery isolates Pseudomonas rhodesiae and Raoultella terrigena influence the adaptation to the broad-spectrum antimicrobial sulfathiazole. Previously, we showed that the competition between these brewery isolates enhances the antimicrobial tolerance of P. rhodesiae. Here, we found that this enhanced tolerance in duo-species biofilms is associated with a strongly increased antimicrobial resistance development in P. rhodesiae. Whereas P. rhodesiae was not able to evolve resistance against sulfathiazole in monospecies conditions, it rapidly evolved resistance in the majority of the duo-species communities. Although the initial presence of R. terrigena was thus required for P. rhodesiae to acquire resistance, the resistance mechanisms did not depend on the presence of R. terrigena. Whole genome sequencing of resistant P. rhodesiae clones showed no clear mutational hot spots. This indicates that the acquired resistance phenotype depends on complex interactions between low-frequency mutations in the genetic background of the strains. We hypothesize that the increased tolerance in duo-species conditions promotes resistance by enhancing the selection of partially resistant mutants and opening up novel evolutionary trajectories that enable such genetic interactions. This hypothesis is reinforced by experimentally excluding potential effects of increased initial population size, enhanced mutation rate, and horizontal gene transfer. Altogether, our observations suggest that the community mode of life and the social interactions therein strongly affect the accessible evolutionary pathways toward antimicrobial resistance.IMPORTANCEAntimicrobial resistance is one of the most studied bacterial properties due to its enormous clinical and industrial relevance; however, most research focuses on resistance development of a single species in isolation. In the present study, we showed that resistance evolution of brewery isolates can differ greatly between single- and mixed-species conditions. Specifically, we observed that the development of antimicrobial resistance in certain species can be significantly enhanced in co-culture as compared to the single-species conditions. Overall, the current study emphasizes the need of considering the within bacterial interactions in microbial communities when evaluating antimicrobial treatments and resistance evolution.}, }
@article {pmid37814055, year = {2023}, author = {Wang, Y and Gai, J and Hou, Q and Zhao, H and Shan, C and Guo, Z}, title = {Ultra-high-depth macrogenomic sequencing revealed differences in microbial composition and function between high temperature and medium-high temperature Daqu.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {39}, number = {12}, pages = {337}, pmid = {37814055}, issn = {1573-0972}, support = {2023//Science and technology plan project of Xinjiang Production and Construction Corps/ ; 2023//Science and technology plan project of Xinjiang Production and Construction Corps/ ; 2020kypytd009//Hubei university of arts and science cultivation fund for teachers' scientific research ability: technological innovation team/ ; }, mesh = {*Alcoholic Beverages/microbiology ; Temperature ; Bacteria/genetics ; *Microbiota ; Fermentation ; }, abstract = {Complex microorganisms in Daqu of different temperatures play a vital role in the taste, flavor and quality of Baijiu during fermentation. However, understanding the functional diversity of the whole microbial community between the Daqus of two different temperatures (high temperature Daqu, HD and medium-high temperature Daqu, MD) remains a major challenge. Here, a systematic study of the microbial diversity, functions as well as physiological and biochemical indexes of Daqu are described. The results revealed that the Daqu exhibited unique characteristics. In particular, the diversity of microorganisms in HD and MD was high, with 44 species including 14 novel species (Sphingomonas sp. is the main novel species) detected in all samples. Their profiles of carbohydrate-active enzymes and specific functional components supported the fact that these species were involved in flavor formation. The Daqu microbiome consisted of a high proportion of phage, providing evidence of phage infection/genome integration and horizontal gene transfer from phage to bacteria. Such processes would also regulate Daqu microbiomes and thus flavor quality. These results enrich current knowledge of Daqu and can be used to promote the development of Baijiu fermentation technology.}, }
@article {pmid37808307, year = {2023}, author = {Sharma, A and Singh, RN and Song, XP and Singh, RK and Guo, DJ and Singh, P and Verma, KK and Li, YR}, title = {Genome analysis of a halophilic Virgibacillus halodenitrificans ASH15 revealed salt adaptation, plant growth promotion, and isoprenoid biosynthetic machinery.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1229955}, pmid = {37808307}, issn = {1664-302X}, abstract = {Globally, due to widespread dispersion, intraspecific diversity, and crucial ecological components of halophilic ecosystems, halophilic bacteria is considered one of the key models for ecological, adaptative, and biotechnological applications research in saline environments. With this aim, the present study was to enlighten the plant growth-promoting features and investigate the systematic genome of a halophilic bacteria, Virgibacillus halodenitrificans ASH15, through single-molecule real-time (SMRT) sequencing technology. Results showed that strain ASH15 could survive in high salinity up to 25% (w/v) NaCl concentration and express plant growth-promoting traits such as nitrogen fixation, plant growth hormones, and hydrolytic enzymes, which sustain salt stress. The results of pot experiment revealed that strain ASH15 significantly enhanced sugarcane plant growth (root shoot length and weight) under salt stress conditions. Moreover, the sequencing analysis of the strain ASH15 genome exhibited that this strain contained a circular chromosome of 3,832,903 bp with an average G+C content of 37.54%: 3721 predicted protein-coding sequences (CDSs), 24 rRNA genes, and 62 tRNA genes. Genome analysis revealed that the genes related to the synthesis and transport of compatible solutes (glycine, betaine, ectoine, hydroxyectoine, and glutamate) confirm salt stress as well as heavy metal resistance. Furthermore, functional annotation showed that the strain ASH15 encodes genes for root colonization, biofilm formation, phytohormone IAA production, nitrogen fixation, phosphate metabolism, and siderophore production, which are beneficial for plant growth promotion. Strain ASH15 also has a gene resistance to antibiotics and pathogens. In addition, analysis also revealed that the genome strain ASH15 has insertion sequences and CRISPRs, which suggest its ability to acquire new genes through horizontal gene transfer and acquire immunity to the attack of viruses. This work provides knowledge of the mechanism through which V. halodenitrificans ASH15 tolerates salt stress. Deep genome analysis, identified MVA pathway involved in biosynthesis of isoprenoids, more precisely "Squalene." Squalene has various applications, such as an antioxidant, anti-cancer agent, anti-aging agent, hemopreventive agent, anti-bacterial agent, adjuvant for vaccines and drug carriers, and detoxifier. Our findings indicated that strain ASH15 has enormous potential in industries such as in agriculture, pharmaceuticals, cosmetics, and food.}, }
@article {pmid37806594, year = {2024}, author = {Li, N and Zheng, N and Pan, J and An, Q and Li, X and Sun, S and Chen, C and Zhu, H and Li, Z and Ji, Y}, title = {Distribution and major driving elements of antibiotic resistance genes in the soil-vegetable system under microplastic stress.}, journal = {The Science of the total environment}, volume = {906}, number = {}, pages = {167619}, doi = {10.1016/j.scitotenv.2023.167619}, pmid = {37806594}, issn = {1879-1026}, mesh = {*Vegetables ; *Microplastics ; Genes, Bacterial ; Soil ; Plastics ; Anti-Bacterial Agents/pharmacology ; Soil Microbiology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Lactuca ; Polyethylenes ; }, abstract = {Microplastics (MPs) and antibiotic resistance genes (ARGs) are both enriched in soil-vegetable systems as a consequence of the prolonged use of agricultural mulches. MPs can form unique bacterial communities and provide potential hosts for ARGs. Therefore, MPs stress may promote the spread of ARGs from soil to crops. Increasing ARGs pollution in soil-vegetable system. In our research, we investigated the distribution and major driving elements of antibiotic resistance genes in the soil-vegetable system under microplastic stress. The results showed that MPs treatment decreased the relative abundance of ARGs in non-rhizosphere soil. High concentrations of MPs promoted the enrichment of tetracycline antibiotic resistance genes in rhizosphere soil. MPs treatment promoted the enrichment of ARGs and mobile genetic elements (MGEs) in lettuce tissues, and the overall abundance of ARGs in root after 0.5 %, 1 %, and 2 % (w/w, dry weight) polyethylene (PE) administration was considerably higher compared to that in the untreated group (p < 0.05). At the same time, high PE concentrations promoted the spread of sulfa ARGs from root to leaf. MPs also impacted the bacterial communities in the soil-plant system, and the changes in ARGs as well as MGEs in each part of the soil-vegetable system were significantly correlated with the bacterial diversity index (p < 0.05). Correlation analysis and network analysis showed that bacterial communities and MGEs were the main drivers of ARGs variation in soil-lettuce systems.}, }
@article {pmid37805184, year = {2023}, author = {Roh, H and Kannimuthu, D}, title = {Comparative resistome analysis of Aeromonas species in aquaculture reveals antibiotic resistance patterns and phylogeographic distribution.}, journal = {Environmental research}, volume = {239}, number = {Pt 2}, pages = {117273}, doi = {10.1016/j.envres.2023.117273}, pmid = {37805184}, issn = {1096-0953}, mesh = {*Aeromonas/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial ; Aquaculture ; North America ; Genes, Bacterial ; }, abstract = {The overuse of antibiotics in aquaculture drives the emergence of multi-drug-resistant bacteria, and antibiotic-resistant genes (ARGs) can be disseminated to other bacteria through vertical- and horizontal gene transfer (VGT and HGT) under selective pressure. Profiling the antibiotic resistome and understanding the global distribution of ARGs constitutes the first step in developing a control strategy. Hence, this study utilized extensive genomic data from hundreds of Aeromonas strains in aquaculture to profile resistome patterns and explores their association with isolation year, country, and species characteristics. Overall, ∼400 Aeromonas genomes were used to predict the ARGs from A. salmonicida, A. hydrophila, A. veronii, A. media, and A. sobria. ARGs such as sul1, tet(A), and tet(D), which display a similar proportion of positive strains among species, were subjected to phylodynamic and phylogeographic analyses. More than a hundred ARGs were identified, some of which exhibited either species-specific or non-species-specific patterns. A. salmonicida and A. media were found to have a higher proportion of species-specific ARGs than other strains, which might lead to more distinct patterns of ARG acquisition. Overall, ∼25% of strains have either sul1, tet(A), or tet(D) gene(s), but no significant difference was observed in the proportion of positive strains by species. Phylogeographic analysis revealed that the abundant numbers of sul1, tet(A), and/or tet(D) introduced in a few East Asian and North American countries could spread to both adjacent and faraway countries. In recent years, the proportions of these ARGs have dramatically increased, particularly in strains sourced from aquatic environments, suggesting control is required of the overuse of antibiotics in aquaculture. The findings of this research offer significant insights into the global dissemination of ARGs.}, }
@article {pmid37804807, year = {2023}, author = {Xue, YM and Wang, YC and Lin, YT and Jiang, GY and Chen, R and Qin, RL and Jia, XQ and Wang, C}, title = {Engineering a Pseudomonas putida as living quorum quencher for biofilm formation inhibition, benzenes degradation, and environmental risk evaluation.}, journal = {Water research}, volume = {246}, number = {}, pages = {120690}, doi = {10.1016/j.watres.2023.120690}, pmid = {37804807}, issn = {1879-2448}, mesh = {*Sewage/microbiology ; *Pseudomonas putida/genetics ; Benzene ; Biofilms ; Quorum Sensing/physiology ; Bioreactors/microbiology ; }, abstract = {Bacterial communication interruption based on quorum quenching (QQ) has been proven its potential in biofilm formation inhibition and biofouling control. However, it would be more satisfying if QQ could be combined with the efficient degradation of contaminants in environmental engineering. In this study, we engineered a biofilm of Pseudomonas putida through introducing a QQ synthetic gene, which achieved both biofilm formation inhibition and efficient degradation of benzene series in wastewater. The aiiO gene introduced into the P. putida by heat shock method was highly expressed to produce QQ enzyme to degrade AHL-based signal molecules. The addition of this engineered P. putida reduced the AHLs concentration, quorum sensing gene expression, and connections of the microbial community network in activated sludge and therefore inhibited the biofilm formation. Meanwhile, the sodium benzoate degradation assay indicated an enhanced benzene series removal ability of the engineering bacteria on activated sludge. Besides, we also demonstrated a controllable environmental risk of this engineered bacteria through monitoring its abundance and horizontal gene transfer test. Overall, the results of this study suggest an alternative strategy to solve multiple environmental problems through genetic engineering means and provide support for the application of engineered bacteria in environmental biotechnology.}, }
@article {pmid37804524, year = {2023}, author = {Wang, YZ and Ye, YX and Lu, JB and Wang, X and Lu, HB and Zhang, ZL and Ye, ZX and Lu, YW and Sun, ZT and Chen, JP and Li, JM and Zhang, CX and Huang, HJ}, title = {Horizontally Transferred Salivary Protein Promotes Insect Feeding by Suppressing Ferredoxin-Mediated Plant Defenses.}, journal = {Molecular biology and evolution}, volume = {40}, number = {10}, pages = {}, pmid = {37804524}, issn = {1537-1719}, mesh = {Animals ; Ferredoxins/metabolism ; Plants/metabolism ; *Hemiptera/genetics ; Nicotiana/genetics/metabolism ; *Aphids/metabolism ; Salivary Proteins and Peptides/genetics ; }, abstract = {Herbivorous insects such as whiteflies, planthoppers, and aphids secrete abundant orphan proteins to facilitate feeding. Yet, how these genes are recruited and evolve to mediate plant-insect interaction remains unknown. In this study, we report a horizontal gene transfer (HGT) event from fungi to an ancestor of Aleyrodidae insects approximately 42 to 190 million years ago. BtFTSP1 is a salivary protein that is secreted into host plants during Bemisia tabaci feeding. It targets a defensive ferredoxin 1 in Nicotiana tabacum (NtFD1) and disrupts the NtFD1-NtFD1 interaction in plant cytosol, leading to the degradation of NtFD1 in a ubiquitin-dependent manner. Silencing BtFTSP1 has negative effects on B. tabaci feeding while overexpressing BtFTSP1 in N. tabacum benefits insects and rescues the adverse effect caused by NtFD1 overexpression. The association between BtFTSP1 and NtFD1 is newly evolved after HGT, with the homologous FTSP in its fungal donor failing to interact and destabilize NtFD1. Our study illustrates the important roles of horizontally transferred genes in plant-insect interactions and suggests the potential origin of orphan salivary genes.}, }
@article {pmid37803310, year = {2023}, author = {Kawabe, Y and Du, Q and Narita, TB and Bell, C and Schilde, C and Kin, K and Schaap, P}, title = {Emerging roles for diguanylate cyclase during the evolution of soma in dictyostelia.}, journal = {BMC ecology and evolution}, volume = {23}, number = {1}, pages = {60}, pmid = {37803310}, issn = {2730-7182}, support = {/WT_/Wellcome Trust/United Kingdom ; 100293/Z/12/Z/WT_/Wellcome Trust/United Kingdom ; BB/K000799/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Dictyostelium/genetics/metabolism ; Ammonia/metabolism ; Phosphorus-Oxygen Lyases/genetics/metabolism ; *Dictyosteliida/metabolism ; Oxygen/metabolism ; }, abstract = {BACKGROUND: Cyclic di-guanylate (c-di-GMP), synthesized by diguanylate cyclase, is a major second messenger in prokaryotes, where it triggers biofilm formation. The dictyostelid social amoebas acquired diguanylate cyclase (dgcA) by horizontal gene transfer. Dictyostelium discoideum (Ddis) in taxon group 4 uses c-di-GMP as a secreted signal to induce differentiation of stalk cells, the ancestral somatic cell type that supports the propagating spores. We here investigated how this role for c-di-GMP evolved in Dictyostelia by exploring dgcA function in the group 2 species Polysphondylium pallidum (Ppal) and in Polysphondylium violaceum (Pvio), which resides in a small sister clade to group 4.<br><br>RESULTS: Similar to Ddis, dgcA is upregulated after aggregation in Ppal and Pvio and predominantly expressed in the anterior region and stalks of emerging fruiting bodies. DgcA null mutants in Ppal and Pvio made fruiting bodies with very long and thin stalks and only few spores and showed delayed aggregation and larger aggregates, respectively. Ddis dgcA- cells cannot form stalks at all, but showed no aggregation defects. The long, thin stalks of Ppal and Pvio dgcA- mutants were also observed in acaA- mutants in these species. AcaA encodes adenylate cyclase A, which mediates the effects of c-di-GMP on stalk induction in Ddis. Other factors that promote stalk formation in Ddis are DIF-1, produced by the polyketide synthase StlB, low ammonia, facilitated by the ammonia transporter AmtC, and high oxygen, detected by the oxygen sensor PhyA (prolyl 4-hydroxylase). We deleted the single stlB, amtC and phyA genes in Pvio wild-type and dgcA- cells. Neither of these interventions affected stalk formation in Pvio wild-type and not or very mildly exacerbated the long thin stalk phenotype of Pvio dgcA- cells.<br><br>CONCLUSIONS: The study reveals a novel role for c-di-GMP in aggregation, while the reduced spore number in Pvio and Ppal dgcA- is likely an indirect effect, due to depletion of the cell pool by the extended stalk formation. The results indicate that in addition to c-di-GMP, Dictyostelia ancestrally used an as yet unknown factor for induction of stalk formation. The activation of AcaA by c-di-GMP is likely conserved throughout Dictyostelia.}, }
@article {pmid37801563, year = {2023}, author = {Liu, L and Zhang, QH and Li, RT}, title = {In Situ and Individual-Based Analysis of the Influence of Polystyrene Microplastics on Escherichia coli Conjugative Gene Transfer at the Single-Cell Level.}, journal = {Environmental science &amp; technology}, volume = {57}, number = {42}, pages = {15936-15944}, doi = {10.1021/acs.est.3c05476}, pmid = {37801563}, issn = {1520-5851}, mesh = {*Escherichia coli/genetics ; Plasmids ; *Microplastics ; Plastics ; Polystyrenes ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; }, abstract = {The impact of microplastic particles of micro- and nanometer sizes on microbial horizontal gene transfer (HGT) remains a controversial topic. Existing studies rely on traditional approaches, which analyze population behavior, leading to conflicting conclusions and a limited understanding. The present study addressed these limitations by employing a novel microfluidic chamber system for in situ visualization and precise quantification of the effects of different concentrations of polystyrene (PS) microbeads on microbial HGT at the single-cell level. The statistical analysis indicated no significant difference in the division times of both the donor and recipient bacteria across different PS microbead concentrations. However, as the concentration of PS microbeads increased from 0 to 2000 mg L[-1], the average conjugation frequency of Escherichia coli decreased from 0.028 ± 0.015 to 0.004 ± 0.003. Our observations from the microfluidic experiments revealed that 500 nm PS microbeads created a barrier effect on bacterial conjugative transfer. The presence of microbeads resulted in reduced contact and interaction between the donor and recipient strains, thereby causing a decrease in the conjugation transfer frequency. These findings were validated by an individual-based modeling framework parameterized by the data from the individual-level microfluidic experiments. Overall, this study offers a fresh perspective and strategy for investigating the risks associated with the dissemination of antibiotic resistance genes related to microplastics.}, }
@article {pmid37797823, year = {2024}, author = {Lagune, M and Kremer, L and Herrmann, JL}, title = {Mycobacterium abscessus, a complex of three fast-growing subspecies sharing virulence traits with slow-growing mycobacteria.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {30}, number = {6}, pages = {726-731}, doi = {10.1016/j.cmi.2023.08.036}, pmid = {37797823}, issn = {1469-0691}, mesh = {*Mycobacterium abscessus/genetics/pathogenicity/classification ; Humans ; *Virulence Factors/genetics ; Virulence/genetics ; *Mycobacterium Infections, Nontuberculous/microbiology ; Animals ; Genome, Bacterial ; Cystic Fibrosis/microbiology ; }, abstract = {BACKGROUND: Mycobacterium abscessus belongs to the largest group of mycobacteria, the rapid-growing saprophytic mycobacteria, and is one of the most difficult-to-treat opportunistic pathogen. Several features pertain to the high adaptability of M. abscessus to the host. These include the capacity to survive and persist within amoebae, to transition from a smooth to a rough morphotype that occurs during the course of the disease and to express of a wide array of virulence factors.<br><br>OBJECTIVES: The main objective of this narrative review consists to report major assets of M.&#xa0;abscessus that contribute to the virulence of these rapid-growing saprophytic mycobacteria. Strikingly, many of these determinants, whether they are from a mycobacterial origin or acquired by horizontal gene transfer, are known virulence factors found in slow-growing and strict pathogens for humans and animals.<br><br>SOURCES: In the light of recent published work in the field we attempted to highlight major features characterizing M. abscessus pathogenicity and to explain why this led to the emergence of this mycobacterial species in patients with cystic fibrosis.<br><br>CONTENT: M. abscessus genome plasticity, the smooth-to-rough transition, and the expression of a panel of enzymes associated with virulence in other bacteria are key players in M.&#xa0;abscessus virulence. In addition, the very large repertoire of lipid transporters, known as mycobacterial membrane protein large and small (MmpL and MmpS respectively), deeply influences the pathogenicity of M. abscessus, as exemplified here for some of them.<br><br>IMPLICATIONS: All these traits largely contribute to make M. abscessus a unique mycobacterium regarding to its pathophysiological processes, ranging from the early colonization steps to the establishment of severe and chronic pulmonary diseases.}, }
@article {pmid37797771, year = {2024}, author = {Liu, Q and Li, Y and Sun, Y and Xie, K and Zeng, Q and Hao, Y and Yang, Q and Pu, Y and Shi, S and Gong, Z}, title = {Deterioration of sludge characteristics and promotion of antibiotic resistance genes spread with the co-existing of polyvinylchloride microplastics and tetracycline in the sequencing batch reactor.}, journal = {The Science of the total environment}, volume = {906}, number = {}, pages = {167544}, doi = {10.1016/j.scitotenv.2023.167544}, pmid = {37797771}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Sewage ; Wastewater ; Microplastics ; Plastics ; Genes, Bacterial ; Tetracycline/pharmacology ; Phenol ; Phenols ; Drug Resistance, Microbial/genetics ; }, abstract = {With the continuous increase in microplastics (MPs) and tetracycline (TC) entering wastewater treatment plants (WWTPs) along with sewage, the co-existence of MPs and TC in the biological treatment of wastewater has attracted extensive attention. This study investigated the effect of 1 mg/L polyvinyl chloride (PVC) MPs and 100 ng/L TC co-existing on sequencing batch reactors (SBRs) (S2) treating phenol wastewater in contrast to the control with TC alone (S1). The phenol removal efficiency was significantly inhibited by the co-existence of PVC MPs and TC. Sludge characteristics were also distinctively influenced. The decreased zone sludge velocity (ZSV) and increased sludge volume index (SVI) indicated that the combined effect of PVC MPs and TC deteriorated sludge settleability, which had positive and negative linear correlations with extracellular polymeric substances (EPS) content and the protein (PN)/polysaccharide (PS) ratio, respectively. Moreover, the decreased and increased relative abundances of potential phenol-degraders and antibiotic resistance gene (ARG) carriers may elucidate the inhibition of phenol removal and promotion of ARGs propagation with the co-occurrence of PVC MPs and TC. In addition, the enhanced potential ARGs hosts, loss of the EPS protective effect, and increased membrane permeability induced by reactive oxygen species (ROS) jointly promoted ARGs dissemination in the co-existence of PVC MPs and TC. Notably, the co-occurrence of ARGs and mobile genetic element (MGEs) indicated that the co-existence of PVC MPs and TC promoted the spread of some transposase-associated ARGs mediated by horizontal gene transfer (HGT).}, }
@article {pmid37796811, year = {2023}, author = {Teixeira, M and Pillay, S and Urhan, A and Abeel, T}, title = {SHIP: identifying antimicrobial resistance gene transfer between plasmids.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {10}, pages = {}, pmid = {37796811}, issn = {1367-4811}, mesh = {*Anti-Bacterial Agents/pharmacology ; Phylogeny ; *Drug Resistance, Bacterial/genetics ; Plasmids/genetics ; Escherichia coli/genetics ; Integrons/genetics ; Gene Transfer, Horizontal ; }, abstract = {MOTIVATION: Plasmids are carriers for antimicrobial resistance (AMR) genes and can exchange genetic material with other structures, contributing to the spread of AMR. There is no reliable approach to identify the transfer of AMR genes across plasmids. This is mainly due to the absence of a method to assess the phylogenetic distance of plasmids, as they show large DNA sequence variability. Identifying and quantifying such transfer can provide novel insight into the role of small mobile elements and resistant plasmid regions in the spread of AMR.<br><br>RESULTS: We developed SHIP, a novel method to quantify plasmid similarity based on the dynamics of plasmid evolution. This allowed us to find conserved fragments containing AMR genes in structurally different and phylogenetically distant plasmids, which is evidence for lateral transfer. Our results show that regions carrying AMR genes are highly mobilizable between plasmids through transposons, integrons, and recombination events, and contribute to the spread of AMR. Identified transferred fragments include a multi-resistant complex class 1 integron in Escherichia coli and Klebsiella pneumoniae, and a region encoding tetracycline resistance transferred through recombination in Enterococcus faecalis.<br><br>The code developed in this work is available at https://github.com/AbeelLab/plasmidHGT.}, }
@article {pmid37796250, year = {2023}, author = {Jung, H and Lee, D and Lee, S and Kong, HJ and Park, J and Seo, YS}, title = {Comparative genomic analysis of Chryseobacterium species: deep insights into plant-growth-promoting and halotolerant capacities.}, journal = {Microbial genomics}, volume = {9}, number = {10}, pages = {}, pmid = {37796250}, issn = {2057-5858}, mesh = {*Chryseobacterium/genetics ; Phylogeny ; Comparative Genomic Hybridization ; Genomics ; Soil ; }, abstract = {Members of the genus Chryseobacterium have attracted great interest as beneficial bacteria that can promote plant growth and biocontrol. Given the recent risks of climate change, it is important to develop tolerance strategies for efficient applications of plant-beneficial bacteria in saline environments. However, the genetic determinants of plant-growth-promoting and halotolerance effects in Chryseobacterium have not yet been investigated at the genomic level. Here, a comparative genomic analysis was conducted with seven Chryseobacterium species. Phylogenetic and phylogenomic analyses revealed niche-specific evolutionary distances between soil and freshwater Chryseobacterium species, consistent with differences in genomic statistics, indicating that the freshwater bacteria have smaller genome sizes and fewer genes than the soil bacteria. Phosphorus- and zinc-cycling genes (required for nutrient acquisition in plants) were universally present in all species, whereas nitrification and sulphite reduction genes (required for nitrogen- and sulphur-cycling, respectively) were distributed only in soil bacteria. A pan-genome containing 6842 gene clusters was constructed, which reflected the general features of the core, accessory and unique genomes. Halotolerant species with an accessory genome shared a Kdp potassium transporter and biosynthetic pathways for branched-chain amino acids and the carotenoid lycopene, which are associated with countermeasures against salt stress. Protein-protein interaction network analysis was used to define the genetic determinants of Chryseobacterium salivictor NBC122 that reduce salt damage in bacteria and plants. Sixteen hub genes comprised the aromatic compound degradation and Por secretion systems, which are required to cope with complex stresses associated with saline environments. Horizontal gene transfer and CRISPR-Cas analyses indicated that C. salivictor NBC122 underwent more evolutionary events when interacting with different environments. These findings provide deep insights into genomic adaptation to dynamic interactions between plant-growth-promoting Chryseobacterium and salt stress.}, }
@article {pmid37793435, year = {2023}, author = {Raimondeau, P and Bianconi, ME and Pereira, L and Parisod, C and Christin, PA and Dunning, LT}, title = {Lateral gene transfer generates accessory genes that accumulate at different rates within a grass lineage.}, journal = {The New phytologist}, volume = {240}, number = {5}, pages = {2072-2084}, doi = {10.1111/nph.19272}, pmid = {37793435}, issn = {1469-8137}, support = {NE/T011025/1//Natural Environment Research Council/ ; NE/V000012/1//Natural Environment Research Council/ ; URF/R/180022//Royal Society/ ; }, mesh = {Humans ; Phylogeny ; *Poaceae/genetics ; *Gene Transfer, Horizontal ; Genome ; Evolution, Molecular ; }, abstract = {Lateral gene transfer (LGT) is the movement of DNA between organisms without sexual reproduction. The acquired genes represent genetic novelties that have independently evolved in the donor's genome. Phylogenetic methods have shown that LGT is widespread across the entire grass family, although we know little about the underlying dynamics. We identify laterally acquired genes in five de novo reference genomes from the same grass genus (four Alloteropsis semialata and one Alloteropsis angusta). Using additional resequencing data for a further 40 Alloteropsis individuals, we place the acquisition of each gene onto a phylogeny using stochastic character mapping, and then infer rates of gains and losses. We detect 168 laterally acquired genes in the five reference genomes (32-100 per genome). Exponential decay models indicate that the rate of LGT acquisitions (6-28 per Ma) and subsequent losses (11-24% per Ma) varied significantly among lineages. Laterally acquired genes were lost at a higher rate than vertically inherited loci (0.02-0.8% per Ma). This high turnover creates intraspecific gene content variation, with a preponderance of them occurring as accessory genes in the Alloteropsis pangenome. This rapid turnover generates standing variation that can ultimately fuel local adaptation.}, }
@article {pmid37792894, year = {2023}, author = {Pompei, S and Bella, E and Weitz, JS and Grilli, J and Lagomarsino, MC}, title = {Metacommunity structure preserves genome diversity in the presence of gene-specific selective sweeps under moderate rates of horizontal gene transfer.}, journal = {PLoS computational biology}, volume = {19}, number = {10}, pages = {e1011532}, pmid = {37792894}, issn = {1553-7358}, mesh = {Humans ; *Gene Transfer, Horizontal/genetics ; *Bacteria/genetics ; Biological Evolution ; Genome ; }, abstract = {The horizontal transfer of genes is fundamental for the eco-evolutionary dynamics of microbial communities, such as oceanic plankton, soil, and the human microbiome. In the case of an acquired beneficial gene, classic population genetics would predict a genome-wide selective sweep, whereby the genome spreads clonally within the community and together with the beneficial gene, removing genome diversity. Instead, several sources of metagenomic data show the existence of "gene-specific sweeps", whereby a beneficial gene spreads across a bacterial community, maintaining genome diversity. Several hypotheses have been proposed to explain this process, including the decreasing gene flow between ecologically distant populations, frequency-dependent selection from linked deleterious allelles, and very high rates of horizontal gene transfer. Here, we propose an additional possible scenario grounded in eco-evolutionary principles. Specifically, we show by a mathematical model and simulations that a metacommunity where species can occupy multiple patches, acting together with a realistic (moderate) HGT rate, helps maintain genome diversity. Assuming a scenario of patches dominated by single species, our model predicts that diversity only decreases moderately upon the arrival of a new beneficial gene, and that losses in diversity can be quickly restored. We explore the generic behaviour of diversity as a function of three key parameters, frequency of insertion of new beneficial genes, migration rates and horizontal transfer rates.Our results provides a testable explanation for how diversity can be maintained by gene-specific sweeps even in the absence of high horizontal gene transfer rates.}, }
@article {pmid37791787, year = {2023}, author = {Taton, A and Gilderman, TS and Ernst, DC and Omaga, CA and Cohen, LA and Rey-Bedon, C and Golden, JW and Golden, SS}, title = {Synechococcus elongatus Argonaute reduces natural transformation efficiency and provides immunity against exogenous plasmids.}, journal = {mBio}, volume = {14}, number = {5}, pages = {e0184323}, pmid = {37791787}, issn = {2150-7511}, support = {R01 GM118815/GM/NIGMS NIH HHS/United States ; R35 GM118290/GM/NIGMS NIH HHS/United States ; }, mesh = {*Synechococcus/genetics ; Plasmids/genetics ; *Circadian Clocks ; Genetic Engineering ; Bacterial Proteins/genetics ; }, abstract = {S. elongatus is an important cyanobacterial model organism for the study of its prokaryotic circadian clock, photosynthesis, and other biological processes. It is also widely used for genetic engineering to produce renewable biochemicals. Our findings reveal an SeAgo-based defense mechanism in S. elongatus against the horizontal transfer of genetic material. We demonstrate that deletion of the ago gene facilitates genetic studies and genetic engineering of S. elongatus.}, }
@article {pmid37788575, year = {2023}, author = {Coluzzi, C and Guillemet, M and Mazzamurro, F and Touchon, M and Godfroid, M and Achaz, G and Glaser, P and Rocha, EPC}, title = {Chance Favors the Prepared Genomes: Horizontal Transfer Shapes the Emergence of Antibiotic Resistance Mutations in Core Genes.}, journal = {Molecular biology and evolution}, volume = {40}, number = {10}, pages = {}, pmid = {37788575}, issn = {1537-1719}, mesh = {Plasmids ; *Escherichia coli/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; *Quinolones/pharmacology ; Mutation ; Gene Transfer, Horizontal ; }, abstract = {Bacterial lineages acquire novel traits at diverse rates in part because the genetic background impacts the successful acquisition of novel genes by horizontal transfer. Yet, how horizontal transfer affects the subsequent evolution of core genes remains poorly understood. Here, we studied the evolution of resistance to quinolones in Escherichia coli accounting for population structure. We found 60 groups of genes whose gain or loss induced an increase in the probability of subsequently becoming resistant to quinolones by point mutations in the gyrase and topoisomerase genes. These groups include functions known to be associated with direct mitigation of the effect of quinolones, with metal uptake, cell growth inhibition, biofilm formation, and sugar metabolism. Many of them are encoded in phages or plasmids. Although some of the chronologies may reflect epidemiological trends, many of these groups encoded functions providing latent phenotypes of antibiotic low-level resistance, tolerance, or persistence under quinolone treatment. The mutations providing resistance were frequent and accumulated very quickly. Their emergence was found to increase the rate of acquisition of other antibiotic resistances setting the path for multidrug resistance. Hence, our findings show that horizontal gene transfer shapes the subsequent emergence of adaptive mutations in core genes. In turn, these mutations further affect the subsequent evolution of resistance by horizontal gene transfer. Given the substantial gene flow within bacterial genomes, interactions between horizontal transfer and point mutations in core genes may be a key to the success of adaptation processes.}, }
@article {pmid37786731, year = {2023}, author = {Liao, J and Wei, X and Tao, K and Deng, G and Shu, J and Qiao, Q and Chen, G and Wei, Z and Fan, M and Saud, S and Fahad, S and Chen, S}, title = {Phenoloxidases: catechol oxidase - the temporary employer and laccase - the rising star of vascular plants.}, journal = {Horticulture research}, volume = {10}, number = {7}, pages = {uhad102}, pmid = {37786731}, issn = {2662-6810}, abstract = {Phenolics are vital for the adaptation of plants to terrestrial habitats and for species diversity. Phenoloxidases (catechol oxidases, COs, and laccases, LACs) are responsible for the oxidation and polymerization of phenolics. However, their origin, evolution, and differential roles during plant development and land colonization are unclear. We performed the phylogeny, domain, amino acids, compositional biases, and intron analyses to clarify the origin and evolution of COs and LACs, and analysed the structure, selective pressure, and chloroplast targeting to understand the species-dependent distribution of COs. We found that Streptophyta COs were not homologous to the Chlorophyta tyrosinases (TYRs), and might have been acquired by horizontal gene transfer from bacteria. COs expanded in bryophytes. Structural-functionality and selective pressure were partially responsible for the species-dependent retention of COs in embryophytes. LACs emerged in Zygnemaphyceae, having evolved from ascorbate oxidases (AAOs), and prevailed in the vascular plants and strongly expanded in seed plants. COs and LACs coevolved with the phenolic metabolism pathway genes. These results suggested that TYRs and AAOs were the first-stage phenoloxidases in Chlorophyta. COs might be the second key for the early land colonization. LACs were the third one (dominating in the vascular plants) and might be advantageous for diversified phenol substrates and the erect growth of plants. This work provided new insights into how phenoloxidases evolved and were devoted to plant evolution.}, }
@article {pmid37786723, year = {2023}, author = {Mukherjee, A and Kizziah, JL and Hawkins, NC and Nasef, MO and Parker, LK and Dokland, T}, title = {Structure of the portal complex from Staphylococcus aureus pathogenicity island 1 transducing particles in situ and in solution.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37786723}, issn = {2692-8205}, support = {R01 AI083255/AI/NIAID NIH HHS/United States ; S10 OD024978/OD/NIH HHS/United States ; U24 GM116789/GM/NIGMS NIH HHS/United States ; }, abstract = {Staphylococcus aureus is an important human pathogen, and the prevalence of antibiotic resistance is a major public health concern. The evolution of pathogenicity and resistance in S. aureus often involves acquisition of mobile genetic elements (MGEs). Bacteriophages play an especially important role, since transduction represents the main mechanism for horizontal gene transfer. S. aureus pathogenicity islands (SaPIs), including SaPI1, are MGEs that carry genes encoding virulence factors, and are mobilized at high frequency through interactions with specific "helper" bacteriophages, such as 80α, leading to packaging of the SaPI genomes into virions made from structural proteins supplied by the helper. Among these structural proteins is the portal protein, which forms a ring-like portal at a fivefold vertex of the capsid, through which the DNA is packaged during virion assembly and ejected upon infection of the host. We have used high-resolution cryo-electron microscopy to determine structures of the S. aureus bacteriophage 80α portal in solution and in situ in the empty and full SaPI1 virions, and show how the portal interacts with the capsid. These structures provide a basis for understanding portal and capsid assembly and the conformational changes that occur upon DNA packaging and ejection.}, }
@article {pmid37779688, year = {2023}, author = {González, D and Morales-Olavarria, M and Vidal-Veuthey, B and Cárdenas, JP}, title = {Insights into early evolutionary adaptations of the Akkermansia genus to the vertebrate gut.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1238580}, pmid = {37779688}, issn = {1664-302X}, abstract = {Akkermansia, a relevant mucin degrader from the vertebrate gut microbiota, is a member of the deeply branched Verrucomicrobiota, as well as the only known member of this phylum to be described as inhabitants of the gut. Only a few Akkermansia species have been officially described so far, although there is genomic evidence addressing the existence of more species-level variants for this genus. This niche specialization makes Akkermansia an interesting model for studying the evolution of microorganisms to their adaptation to the gastrointestinal tract environment, including which kind of functions were gained when the Akkermansia genus originated or how the evolutionary pressure functions over those genes. In order to gain more insight into Akkermansia adaptations to the gastrointestinal tract niche, we performed a phylogenomic analysis of 367 high-quality Akkermansia isolates and metagenome-assembled genomes, in addition to other members of Verrucomicrobiota. This work was focused on three aspects: the definition of Akkermansia genomic species clusters and the calculation and functional characterization of the pangenome for the most represented species; the evolutionary relationship between Akkermansia and their closest relatives from Verrucomicrobiota, defining the gene families which were gained or lost during the emergence of the last Akkermansia common ancestor (LAkkCA) and; the evaluation of the evolutionary pressure metrics for each relevant gene family of main Akkermansia species. This analysis found 25 Akkermansia genomic species clusters distributed in two main clades, divergent from their non-Akkermansia relatives. Pangenome analyses suggest that Akkermansia species have open pangenomes, and the gene gain/loss model indicates that genes associated with mucin degradation (both glycoside hydrolases and peptidases), (micro)aerobic metabolism, surface interaction, and adhesion were part of LAkkCA. Specifically, mucin degradation is a very ancestral innovation involved in the origin of Akkermansia. Horizontal gene transfer detection suggests that Akkermansia could receive genes mostly from unknown sources or from other Gram-negative gut bacteria. Evolutionary metrics suggest that Akkemansia species evolved differently, and even some conserved genes suffered different evolutionary pressures among clades. These results suggest a complex evolutionary landscape of the genus and indicate that mucin degradation could be an essential feature in Akkermansia evolution as a symbiotic species.}, }
@article {pmid37768051, year = {2023}, author = {Li, L and Liu, Z and Meng, D and Liu, Y and Liu, T and Jiang, C and Yin, H}, title = {Sequence similarity network and protein structure prediction offer insights into the evolution of microbial pathways for ferrous iron oxidation.}, journal = {mSystems}, volume = {8}, number = {5}, pages = {e0072023}, pmid = {37768051}, issn = {2379-5077}, support = {2022SK2076//KEY RESEARCH AND DEVELOPMENT OF HUNAN PROVINCE, CHINA/ ; }, mesh = {*Iron/metabolism ; *Ferrous Compounds/metabolism ; Artificial Intelligence ; Oxidation-Reduction ; Anaerobiosis ; }, abstract = {Microbial Fe(II) oxidation is a crucial process that harnesses and converts the energy available in Fe, contributing significantly to global element cycling. However, there are still many aspects of this process that remain unexplored. In this study, we utilized a combination of comparative genomics, sequence similarity network analysis, and artificial intelligence-driven structure modeling methods to address the lack of structural information on Fe(II) oxidation proteins and offer a comprehensive perspective on the evolution of Fe(II) oxidation pathways. Our findings suggest that several microbial Fe(II) oxidation pathways currently known may have originated within classes Gammaproteobacteria and Betaproteobacteria.}, }
@article {pmid37762674, year = {2023}, author = {Iasakov, T}, title = {Evolution End Classification of tfd Gene Clusters Mediating Bacterial Degradation of 2,4-Dichlorophenoxyacetic Acid (2,4-D).}, journal = {International journal of molecular sciences}, volume = {24}, number = {18}, pages = {}, pmid = {37762674}, issn = {1422-0067}, support = {23-24-00480//Russian Science Foundation (RSF)/ ; }, mesh = {Phylogeny ; Multigene Family ; *Alphaproteobacteria ; Catechols ; *Herbicides ; Phenoxyacetates ; 2,4-Dichlorophenoxyacetic Acid ; }, abstract = {The tfd (tfdI and tfdII) are gene clusters originally discovered in plasmid pJP4 which are involved in the bacterial degradation of 2,4-dichlorophenoxyacetic acid (2,4-D) via the ortho-cleavage pathway of chlorinated catechols. They share this activity, with respect to substituted catechols, with clusters tcb and clc. Although great effort has been devoted over nearly forty years to exploring the structural diversity of these clusters, their evolution has been poorly resolved to date, and their classification is clearly obsolete. Employing comparative genomic and phylogenetic approaches has revealed that all tfd clusters can be classified as one of four different types. The following four-type classification and new nomenclature are proposed: tfdI, tfdII, tfdIII and tfdIV(A,B,C). Horizontal gene transfer between Burkholderiales and Sphingomonadales provides phenomenal linkage between tfdI, tfdII, tfdIII and tfdIV type clusters and their mosaic nature. It is hypothesized that the evolution of tfd gene clusters proceeded within first (tcb, clc and tfdI), second (tfdII and tfdIII) and third (tfdIV(A,B,C)) evolutionary lineages, in each of which, the genes were clustered in specific combinations. Their clustering is discussed through the prism of hot spots and driving forces of various models, theories, and hypotheses of cluster and operon formation. Two hypotheses about series of gene deletions and displacements are also proposed to explain the structural variations across members of clusters tfdII and tfdIII, respectively. Taking everything into account, these findings reconstruct the phylogeny of tfd clusters, have delineated their evolutionary trajectories, and allow the contribution of various evolutionary processes to be assessed.}, }
@article {pmid37760664, year = {2023}, author = {Xia, X}, title = {Horizontal Gene Transfer and Drug Resistance Involving Mycobacterium tuberculosis.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {9}, pages = {}, pmid = {37760664}, issn = {2079-6382}, support = {RGPIN/2018-03878//Natural Sciences and Engineering Research Council/ ; }, abstract = {Mycobacterium tuberculosis (Mtb) acquires drug resistance at a rate comparable to that of bacterial pathogens that replicate much faster and have a higher mutation rate. One explanation for this rapid acquisition of drug resistance in Mtb is that drug resistance may evolve in other fast-replicating mycobacteria and then be transferred to Mtb through horizontal gene transfer (HGT). This paper aims to address three questions. First, does HGT occur between Mtb and other mycobacterial species? Second, what genes after HGT tend to survive in the recipient genome? Third, does HGT contribute to antibiotic resistance in Mtb? I present a conceptual framework for detecting HGT and analyze 39 ribosomal protein genes, 23S and 16S ribosomal RNA genes, as well as several genes targeted by antibiotics against Mtb, from 43 genomes representing all major groups within Mycobacterium. I also included mgtC and the insertion sequence IS6110 that were previously reported to be involved in HGT. The insertion sequence IS6110 shows clearly that the Mtb complex participates in HGT. However, the horizontal transferability of genes depends on gene function, as was previously hypothesized. HGT is not observed in functionally important genes such as ribosomal protein genes, rRNA genes, and other genes chosen as drug targets. This pattern can be explained by differential selection against functionally important and unimportant genes after HGT. Functionally unimportant genes such as IS6110 are not strongly selected against, so HGT events involving such genes are visible. For functionally important genes, a horizontally transferred diverged homologue from a different species may not work as well as the native counterpart, so the HGT event involving such genes is strongly selected against and eliminated, rendering them invisible to us. In short, while HGT involving the Mtb complex occurs, antibiotic resistance in the Mtb complex arose from mutations in those drug-targeted genes within the Mtb complex and was not gained through HGT.}, }
@article {pmid37760663, year = {2023}, author = {Al-Sarawi, HA and Habibi, N and Uddin, S and Jha, AN and Al-Sarawi, MA and Lyons, BP}, title = {Antibiotic Resistance Mediated by Escherichia coli in Kuwait Marine Environment as Revealed through Genomic Analysis.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {9}, pages = {}, pmid = {37760663}, issn = {2079-6382}, abstract = {Antibiotic-resistance gene elements (ARGEs) such as antibiotic-resistance genes (ARGs), integrons, and plasmids are key to the spread of antimicrobial resistance (AMR) in marine environments. Kuwait's marine area is vulnerable to sewage contaminants introduced by numerous storm outlets and indiscriminate waste disposal near recreational beaches. Therefore, it has become a significant public health issue and warrants immediate investigation. Coliforms, especially Gram-negative Escherichia coli, have been regarded as significant indicators of recent fecal pollution and carriers of ARGEs. In this study, we applied a genome-based approach to identify ARGs' prevalence in E. coli isolated from mollusks and coastal water samples collected in a previous study. In addition, we investigated the plasmids and intl1 (class 1 integron) genes coupled with the ARGs, mediating their spread within the Kuwait marine area. Whole-genome sequencing (WGS) identified genes resistant to the drug classes of beta-lactams (blaCMY-150, blaCMY-42, blaCTX-M-15, blaDHA-1, blaMIR-1, blaOKP-B-15, blaOXA-1, blaOXA-48, blaTEM-1B, blaTEM-35), trimethoprim (dfrA14, dfrA15, dfrA16, dfrA1, dfrA5, dfrA7), fluroquinolone (oqxA, oqxB, qnrB38, qnrB4, qnrS1), aminoglycoside (aadA2, ant(3'')-Ia, aph(3'')-Ib, aph(3')-Ia, aph(6)-Id), fosfomycin (fosA7, fosA_6, fosA, fosB1), sulfonamide (sul1, sul2, sul3), tetracycline (tet-A, tet-B), and macrolide (mph-A). The MFS-type drug efflux gene mdf-A is also quite common in E. coli isolates (80%). The plasmid ColRNAI was also found to be prevalent in E. coli. The integron gene intI1 and gene cassettes (GC) were reported to be in 36% and 33%, respectively, of total E. coli isolates. A positive and significant (p < 0.001) correlation was observed between phenotypic AMR-intl1 (r = 0.311) and phenotypic AMR-GC (r = 0.188). These findings are useful for the surveillance of horizontal gene transfer of AMR in the marine environments of Kuwait.}, }
@article {pmid37759643, year = {2023}, author = {Li, J and Cullis, C}, title = {Comparative Analysis of Tylosema esculentum Mitochondrial DNA Revealed Two Distinct Genome Structures.}, journal = {Biology}, volume = {12}, number = {9}, pages = {}, pmid = {37759643}, issn = {2079-7737}, support = {No Grant Number//Department of Biology, Case Western Reserve University./ ; }, abstract = {Tylosema esculentum, commonly known as the marama bean, is an underutilized legume with nutritious seeds, holding potential to enhance food security in southern Africa due to its resilience to prolonged drought and heat. To promote the selection of this agronomically valuable germplasm, this study assembled and compared the mitogenomes of 84 marama individuals, identifying variations in genome structure, single-nucleotide polymorphisms (SNPs), insertions/deletions (indels), heteroplasmy, and horizontal transfer. Two distinct germplasms were identified, and a novel mitogenome structure consisting of three circular molecules and one long linear chromosome was discovered. The structural variation led to an increased copy number of specific genes, nad5, nad9, rrnS, rrn5, trnC, and trnfM. The two mitogenomes also exhibited differences at 230 loci, with only one notable nonsynonymous substitution in the matR gene. Heteroplasmy was concentrated at certain loci on chromosome LS1 (OK638188). Moreover, the marama mitogenome contained an over 9 kb insertion of cpDNA, originating from chloroplast genomes, but had accumulated mutations and lost gene functionality. The evolutionary and comparative genomics analysis indicated that mitogenome divergence in marama might not be solely constrained by geographical factors. Additionally, marama, as a member from the Cercidoideae subfamily, tends to possess a more complete set of mitochondrial genes than Faboideae legumes.}, }
@article {pmid37759383, year = {2024}, author = {Hafez, M and Gourlie, R and McDonald, M and Telfer, M and Carmona, MA and Sautua, FJ and Moffat, CS and Moolhuijzen, PM and See, PT and Aboukhaddour, R}, title = {Evolution of the Toxb Gene in Pyrenophora tritici-repentis and Related Species.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {37}, number = {3}, pages = {327-337}, doi = {10.1094/MPMI-08-23-0114-FI}, pmid = {37759383}, issn = {0894-0282}, mesh = {Phylogeny ; *Fungal Proteins/genetics/metabolism ; *Ascomycota/genetics/metabolism ; Triticum/genetics/microbiology ; }, abstract = {Pyrenophora tritici-repentis (tan spot) is a destructive foliar pathogen of wheat with global impact. This ascomycete fungus possesses a highly plastic open pangenome shaped by the gain and loss of effector genes. This study investigated the allelic variations in the chlorosis-encoding gene ToxB across 422 isolates representing all identified pathotypes and worldwide origins. To gain better insights into ToxB evolution, we examined its presence and variability in other Pyrenophora spp. A ToxB haplotype network was constructed, revealing the evolutionary relationships of this gene (20 haplotypes) across four Pyrenophora species. Notably, toxb, the homolog of ToxB, was detected for the first time in the barley pathogen Pyrenophora teres. The ToxB/toxb genes display evidence of selection that is characterized by loss of function, duplication, and diverse mutations. Within the ToxB/toxb open reading frame, 72 mutations were identified, including 14 synonymous, 55 nonsynonymous, and 3 indel mutations. Remarkably, a, ∼5.6-kb Copia-like retrotransposon, named Copia-1_Ptr, was found inserted in the toxb gene of a race 3 isolate. This insert disrupted the ToxB gene's function, a first case of effector gene disruption by a transposable element in P. tritici-repentis. Additionally, a microsatellite with 25 nucleotide repeats (0 to 10) in the upstream region of ToxB suggested a potential mechanism influencing ToxB expression and regulation. Exploring ToxB-like protein distribution in other ascomycetes revealed the presence of ToxB-like proteins in 19 additional species, including the Leotiomycetes class for the first time. The presence/absence pattern of ToxB-like proteins defied species relatedness compared with a phylogenetic tree, suggesting a past horizontal gene transfer event during the evolution of the ToxB gene. [Formula: see text] Copyright © 2024 His Majesty the King in Right of Canada, as represented by the Minister of Agriculture and Agri-Food. This is an open access article distributed under the CC BY-NC-ND 4.0 International license.}, }
@article {pmid37757562, year = {2024}, author = {Sharma, M and Singh, DN and Uttam, G and Sharma, P and Meena, SA and Verma, AK and Negi, RK}, title = {Adaptive evolution of Sphingopyxis sp. MC4 conferred degradation potential for persistent β- and δ-Hexachlorocyclohexane (HCH) isomers.}, journal = {Journal of hazardous materials}, volume = {461}, number = {}, pages = {132545}, doi = {10.1016/j.jhazmat.2023.132545}, pmid = {37757562}, issn = {1873-3336}, mesh = {Ecosystem ; Hexachlorocyclohexane/metabolism ; *Sphingomonadaceae/genetics/metabolism ; *Pesticides/metabolism ; Biodegradation, Environmental ; }, abstract = {Hexachlorocyclohexane (HCH), an organochlorine pesticide imposes several harmful impacts on the ecosystem. β- and δ-isomers of HCH are highly toxic, persistent, and recalcitrant to biodegradation, slow and incomplete degradation of β- and δ- isomers have been reported in a few strains. We have isolated a strain designated as Sphingopyxis strain MC4 that can tolerate and degrade high concentrations of α-, β-, γ- and δ-HCH isomers. To date, no other Sphingopyxis strain has been reported to degrade β- and δ-isomers. To understand the underlying genetic makeup contributing to adaptations, the whole genome of strain MC4 was sequenced. Comparative genome analysis showed that strain MC4 harbors the complete pathway (lin genes) required for HCH degradation. Genetic footprints such as presence of lin genes on genomic islands, IS6100 elements in close proximity of lin genes, and synteny in lin flanking regions with other strains reflects the horizontal gene transfer in strain MC4. Positive selection and HGT drive the adaptive evolution of strain MC4 under the pressure of HCH contamination that it experienced in its surrounding niche. In silico analyses showed efficient binding of β- and δ-isomers with enzymes leading to rapid degradation that need further validation by cloning and biochemical experiments.}, }
@article {pmid37755994, year = {2023}, author = {Shikov, AE and Savina, IA and Nizhnikov, AA and Antonets, KS}, title = {Recombination in Bacterial Genomes: Evolutionary Trends.}, journal = {Toxins}, volume = {15}, number = {9}, pages = {}, pmid = {37755994}, issn = {2072-6651}, support = {075-15-2021-1055//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {Bacterial organisms have undergone homologous recombination (HR) and horizontal gene transfer (HGT) multiple times during their history. These processes could increase fitness to new environments, cause specialization, the emergence of new species, and changes in virulence. Therefore, comprehensive knowledge of the impact and intensity of genetic exchanges and the location of recombination hotspots on the genome is necessary for understanding the dynamics of adaptation to various conditions. To this end, we aimed to characterize the functional impact and genomic context of computationally detected recombination events by analyzing genomic studies of any bacterial species, for which events have been detected in the last 30 years. Genomic loci where the transfer of DNA was detected pertained to mobile genetic elements (MGEs) housing genes that code for proteins engaged in distinct cellular processes, such as secretion systems, toxins, infection effectors, biosynthesis enzymes, etc. We found that all inferences fall into three main lifestyle categories, namely, ecological diversification, pathogenesis, and symbiosis. The latter primarily exhibits ancestral events, thus, possibly indicating that adaptation appears to be governed by similar recombination-dependent mechanisms.}, }
@article {pmid37754684, year = {2023}, author = {Zhang, Y and Kitazumi, A and Liao, Y-T and de Los Reyes, BG and Wu, VCH}, title = {Metagenomic investigation reveals bacteriophage-mediated horizontal transfer of antibiotic resistance genes in microbial communities of an organic agricultural ecosystem.}, journal = {Microbiology spectrum}, volume = {11}, number = {5}, pages = {e0022623}, pmid = {37754684}, issn = {2165-0497}, support = {2030-42000-0055-000-D//USDA | Agricultural Research Service (ARS)/ ; }, mesh = {*Bacteriophages/genetics ; *Gene Transfer, Horizontal ; *Metagenomics ; *Agriculture ; *Bacteria/genetics/virology/drug effects ; *Microbiota/genetics ; Metagenome ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Ecosystem ; Drug Resistance, Bacterial/genetics ; Soil Microbiology ; }, abstract = {Antibiotic resistance has become a serious health concern worldwide. The potential impact of viruses, bacteriophages in particular, on spreading antibiotic resistance genes is still controversial due to the complexity of bacteriophage-bacterial interactions within diverse environments. In this study, we determined the microbiome profiles and the potential antibiotic resistance gene (ARG) transfer between bacterial and viral populations in different agricultural samples using a high-resolution analysis of the metagenomes. The results of this study provide compelling genetic evidence for ARG transfer through bacteriophage-bacteria interactions, revealing the inherent risks associated with bacteriophage-mediated ARG transfer across the agricultural microbiome.}, }
@article {pmid37754275, year = {2023}, author = {Ma, J and Zhao, H and Mo, S and Li, J and Ma, X and Tang, Y and Li, H and Liu, Z}, title = {Acquisition of Type I methyltransferase via horizontal gene transfer increases the drug resistance of Aeromonas veronii.}, journal = {Microbial genomics}, volume = {9}, number = {9}, pages = {}, pmid = {37754275}, issn = {2057-5858}, mesh = {*Gene Transfer, Horizontal ; *Aeromonas veronii/genetics ; *Methyltransferases/genetics ; Drug Resistance, Bacterial/genetics ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; Humans ; Genome, Bacterial ; Virulence/genetics ; Bacterial Proteins/genetics ; Gram-Negative Bacterial Infections/microbiology ; Animals ; DNA Methylation ; }, abstract = {Aeromonas veronii is an opportunistic pathogen that affects both fish and mammals, including humans, leading to bacteraemia, sepsis, meningitis and even death. The increasing virulence and drug resistance of A. veronii are of significant concern and pose a severe risk to public safety. The Type I restriction-modification (RM) system, which functions as a bacterial defence mechanism, can influence gene expression through DNA methylation. However, little research has been conducted to explore its origin, evolutionary path, and relationship to virulence and drug resistance in A. veronii. In this study, we analysed the pan-genome of 233 A. veronii strains, and the results indicated that it was 'open', meaning that A. veronii has acquired additional genes from other species. This suggested that A. veronii had the potential to adapt and evolve rapidly, which might have contributed to its drug resistance. One Type I methyltransferase (MTase) and two complete Type I RM systems were identified, namely AveC4I, AveC4II and AveC4III in A. veronii strain C4, respectively. Notably, AveC4I was exclusive to A. veronii C4. Phylogenetic analysis revealed that AveC4I was derived from horizontal gene transfer from Thiocystis violascens and exchanged genes with the human pathogen Comamonas kerstersii. Single molecule real-time sequencing was applied to identify the motif methylated by AveC4I, which was unique and not recognized by any reported MTases in the REBASE database. We also annotated the functions and pathways of the genes containing the motif, revealing that AveC4I may control drug resistance in A. veronii C4. Our findings provide new insight on the mechanisms underlying drug resistance in pathogenic bacteria. By identifying the specific genes and pathways affected by AveC4I, this study may aid in the development of new therapeutic approaches to combat A. veronii infections.}, }
@article {pmid37752971, year = {2023}, author = {Tekle, YI and Tran, H and Wang, F and Singla, M and Udu, I}, title = {Omics of an Enigmatic Marine Amoeba Uncovers Unprecedented Gene Trafficking from Giant Viruses and Provides Insights into Its Complex Life Cycle.}, journal = {Microbiology research}, volume = {14}, number = {2}, pages = {656-672}, pmid = {37752971}, issn = {2036-7473}, support = {R15 GM116103/GM/NIGMS NIH HHS/United States ; }, abstract = {Amoebozoa include lineages of diverse ecology, behavior, and morphology. They are assumed to encompass members with the largest genome sizes of all living things, yet genomic studies in the group are limited. Trichosphaerium, a polymorphic, multinucleate, marine amoeba with a complicated life cycle, has puzzled experts for over a century. In an effort to explore the genomic diversity and investigate extraordinary behavior observed among the Amoebozoa, we used integrated omics approaches to study this enigmatic marine amoeba. Omics data, including single-cell transcriptomics and cytological data, demonstrate that Trichosphaerium sp. possesses the complete meiosis toolkit genes. These genes are expressed in life stages of the amoeba including medium and large cells. The life cycle of Trichosphaerium sp. involves asexual processes via binary fission and multiple fragmentation of giant cells, as well as sexual-like processes involving genes implicated in sexual reproduction and polyploidization. These findings are in stark contrast to a life cycle previously reported for this amoeba. Despite the extreme morphological plasticity observed in Trichosphaerium, our genomic data showed that populations maintain a species-level intragenomic variation. A draft genome of Trichosphaerium indicates elevated lateral gene transfer (LGT) from bacteria and giant viruses. Gene trafficking in Trichosphaerium is the highest within Amoebozoa and among the highest in microbial eukaryotes.}, }
@article {pmid37752398, year = {2023}, author = {Liu, H and Shi, B and Liu, W and Wang, L and Zhu, L and Wang, J and Kim, YM and Wang, J}, title = {Effects of magnesium-modified biochar on antibiotic resistance genes and microbial communities in chicken manure composting.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {50}, pages = {108553-108564}, pmid = {37752398}, issn = {1614-7499}, support = {42277039//National Natural Science Foundation of China/ ; 42207026//National Natural Science Foundation of China/ ; ZR202111290386//Natural Science Foundation of Shandong Province/ ; }, mesh = {Animals ; Genes, Bacterial ; Manure/microbiology ; *Composting ; Chickens/genetics ; Magnesium ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Firmicutes ; Proteobacteria/genetics ; *Microbiota ; }, abstract = {Abatement of antibiotic resistance genes (ARGs) in livestock manure by composting has attracted attention. This study investigated the effect of adding magnesium-modified biochar (MBC) on ARGs and microbial communities in chicken manure composting. Twelve genes for tetracyclines, sulfonamides, and macrolides, and mobile genetic elements were measured in the compost pile. The results showed that after 45 days of the composting, the treatment groups of MBC had longer high temperature periods, significantly higher germination indices (GI) and lower phytotoxicity. There were four major dominant phyla (Firmicutes, Actinobacteriota, Proteobacteria, and Bacteroidota) in the compost. The abundance of Firmicutes decreased significantly during the compost cooling period; tetracycline resistance genes demonstrated an extremely significant positive correlation with Firmicutes, showing a trend of the same increase and decrease with composting time; tetT, tetO, tetM, tetW, ermB, and intI2 were reduced in the MBC group; the total abundance of resistance genes in the 2% MBC addition group was 0.67 times that of the control; Proteobacteria and Chloroflexi were also significantly lower than the other treatment groups. Most ARGs were significantly associated with mobile genetic elements (MGEs); MBC can reduce the spread and diffusion of ARGs by reducing the abundance of MGEs and inhibiting horizontal gene transfer (HGT).}, }
@article {pmid37748307, year = {2024}, author = {Gao, J and Xing, X and Cai, W and Li, Z and Shi, G and Chen, Y and Liang, H and Chen, C and Ma, K and Chen, J and Hu, C}, title = {Effect of micropollutants on disinfection byproducts and antibiotic resistance genes in drinking water in the process of biological activated carbon treatment.}, journal = {Journal of hazardous materials}, volume = {461}, number = {}, pages = {132304}, doi = {10.1016/j.jhazmat.2023.132304}, pmid = {37748307}, issn = {1873-3336}, mesh = {Disinfection ; *Drinking Water ; Charcoal ; Extracellular Polymeric Substance Matrix/chemistry ; Anti-Bacterial Agents ; *Water Purification ; *Water Pollutants, Chemical/toxicity/analysis ; *Disinfectants/pharmacology ; }, abstract = {The biofilm stress response of biological activated carbon (BAC) was investigated under prolonged exposure to sulfadiazine and 2,4-Dichlorophenoxyacetic acid, simulating complex emerging organic contaminants (EOCs) that are mainly involved in the formation of nitrogenous disinfection byproducts (N-DBPs) and antibiotic resistance genes (ARGs). Under trace complex EOCs condition (2 µg/L), N-DBP precursors and abundance of ARGs increased significantly in BAC effluent. The total formation potential of haloacetonitriles (HANs) and halonitromethanes (HNMs) was 751.47 ± 2.98 ng/L, which was much higher than the control group (440.67 ± 13.38 ng/L without EOCs). Similarly, the relative abundance of ARGs was more than twice that in the control group. The complex EOCs induce excessive extracellular polymeric substance secretion (EPS), thereby causing more N-DBP precursors and stronger horizontal gene transfer. Metagenome analysis revealed that functional amino acid and protein biosynthesis genes were overexpressed compared to the control group, causing more EPS to be secreted into the external environment. Complex EOCs promote Cobetia, Clostridium, and Streptomyces dominance, contributing to the production of N-DBP precursors and ARGs. For the first time, in addition to the direct hazards of the EOCs, this study successfully revealed the indirect water quality risks of complex EOCs from the microbial stress response during BAC treatment. Synergistic regulation of EOCs and microorganisms is important for tap water security.}, }
@article {pmid37746224, year = {2022}, author = {Schalamun, M and Schmoll, M}, title = {Trichoderma - genomes and genomics as treasure troves for research towards biology, biotechnology and agriculture.}, journal = {Frontiers in fungal biology}, volume = {3}, number = {}, pages = {1002161}, pmid = {37746224}, issn = {2673-6128}, support = {P 30893/FWF_/Austrian Science Fund FWF/Austria ; P 31464/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {The genus Trichoderma is among the best studied groups of filamentous fungi, largely because of its high relevance in applications from agriculture to enzyme biosynthesis to biofuel production. However, the physiological competences of these fungi, that led to these beneficial applications are intriguing also from a scientific and ecological point of view. This review therefore summarizes recent developments in studies of fungal genomes, updates on previously started genome annotation efforts and novel discoveries as well as efforts towards bioprospecting for enzymes and bioactive compounds such as cellulases, enzymes degrading xenobiotics and metabolites with potential pharmaceutical value. Thereby insights are provided into genomes, mitochondrial genomes and genomes of mycoviruses of Trichoderma strains relevant for enzyme production, biocontrol and mycoremediation. In several cases, production of bioactive compounds could be associated with responsible genes or clusters and bioremediation capabilities could be supported or predicted using genome information. Insights into evolution of the genus Trichoderma revealed large scale horizontal gene transfer, predominantly of CAZyme genes, but also secondary metabolite clusters. Investigation of sexual development showed that Trichoderma species are competent of repeat induced point mutation (RIP) and in some cases, segmental aneuploidy was observed. Some random mutants finally gave away their crucial mutations like T. reesei QM9978 and QM9136 and the fertility defect of QM6a was traced back to its gene defect. The Trichoderma core genome was narrowed down to 7000 genes and gene clustering was investigated in the genomes of multiple species. Finally, recent developments in application of CRISPR/Cas9 in Trichoderma, cloning and expression strategies for the workhorse T. reesei as well as the use genome mining tools for bioprospecting Trichoderma are highlighted. The intriguing new findings on evolution, genomics and physiology highlight emerging trends and illustrate worthwhile perspectives in diverse fields of research with Trichoderma.}, }
@article {pmid37745407, year = {2023}, author = {Gonçalves, C and Harrison, MC and Steenwyk, JL and Opulente, DA and LaBella, AL and Wolters, JF and Zhou, X and Shen, XX and Groenewald, M and Hittinger, CT and Rokas, A}, title = {Diverse signatures of convergent evolution in cacti-associated yeasts.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37745407}, issn = {2692-8205}, support = {R01 AI153356/AI/NIAID NIH HHS/United States ; T32 HG002760/HG/NHGRI NIH HHS/United States ; }, abstract = {Many distantly related organisms have convergently evolved traits and lifestyles that enable them to live in similar ecological environments. However, the extent of phenotypic convergence evolving through the same or distinct genetic trajectories remains an open question. Here, we leverage a comprehensive dataset of genomic and phenotypic data from 1,049 yeast species in the subphylum Saccharomycotina (Kingdom Fungi, Phylum Ascomycota) to explore signatures of convergent evolution in cactophilic yeasts, ecological specialists associated with cacti. We inferred that the ecological association of yeasts with cacti arose independently ~17 times. Using machine-learning, we further found that cactophily can be predicted with 76% accuracy from functional genomic and phenotypic data. The most informative feature for predicting cactophily was thermotolerance, which is likely associated with duplication and altered evolutionary rates of genes impacting the cell envelope in several cactophilic lineages. We also identified horizontal gene transfer and duplication events of plant cell wall-degrading enzymes in distantly related cactophilic clades, suggesting that putatively adaptive traits evolved through disparate molecular mechanisms. Remarkably, multiple cactophilic lineages and their close relatives are emerging human opportunistic pathogens, suggesting that the cactophilic lifestyle-and perhaps more generally lifestyles favoring thermotolerance-may preadapt yeasts to cause human disease. This work underscores the potential of a multifaceted approach involving high throughput genomic and phenotypic data to shed light onto ecological adaptation and highlights how convergent evolution to wild environments could facilitate the transition to human pathogenicity.}, }
@article {pmid37743870, year = {2023}, author = {Palanisamy, V and Bosilevac, JM and Barkhouse, DA and Velez, SE and Chitlapilly Dass, S}, title = {Shotgun-metagenomics reveals a highly diverse and communal microbial network present in the drains of three beef-processing plants.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1240138}, pmid = {37743870}, issn = {2235-2988}, mesh = {*Metagenomics ; *Microbiota/genetics ; *Biofilms/growth &amp; development ; Cattle ; Animals ; Red Meat/microbiology ; Bacteria/genetics/classification/isolation &amp; purification ; Food Handling/methods ; Food Microbiology ; Food-Processing Industry ; }, abstract = {BACKGROUND: Multi-species biofilms pose a problem in various environments, especially food-processing environments. The diversity of microorganisms in these biofilms plays a critical role in their integrity and protection against external biotic and abiotic factors. Compared to single-species biofilms, mixed-species biofilms are more resistant to various stresses, including antimicrobials like sanitizers. Therefore, understanding the microbiome composition and diversity in biofilms and their metabolic potential is a priority when developing intervention techniques to combat foodborne pathogens in food processing environments.<br><br>METHODS: This study aimed to describe and compare the microbiome profile of 75 drain biofilm samples obtained from five different locations (Hotscale, Hotbox, Cooler, Processing, &amp; Grind room) of three beef-processing plants (Plant A, B &amp; C) taken over two timepoints 2017-18 (T1) and 2021 (T2) by shotgun sequencing.<br><br>RESULTS: Core microbiome analysis found Pseudomonas, Psychrobacter, and Acinetobacter to be the top three prevalent genera among the plants and locations. Alpha diversity analysis demonstrated a high diversity of microbiome present in all the plants and locations across the time points. Functional analysis showed the high metabolic potential of the microbial community with abundance of genes in metabolism, cell-adhesion, motility, and quorum sensing. Moreover, Quaternary Ammonium Compound (QAC) resistance genes were also observed, this is significant as QAC sanitizers are commonly used in many food processing facilities. Multi-functional genes such as transposases, polymerases, permeases, flagellar proteins, and Mobile Genetic Elements (MGEs) were found suggesting these are dynamic microbial communities that work together to protect themselves against environmental stresses through multiple defense mechanisms.<br><br>CONCLUSION: This study provides a framework for understanding the collective microbial network spanning a beef processing system. The results can be used to develop intervention strategies to best control these highly communicative microbial networks.}, }
@article {pmid37742882, year = {2023}, author = {Gu, X}, title = {Genome distance and phylogenetic inference accommodating gene duplication, loss and new gene input.}, journal = {Molecular phylogenetics and evolution}, volume = {189}, number = {}, pages = {107916}, doi = {10.1016/j.ympev.2023.107916}, pmid = {37742882}, issn = {1095-9513}, mesh = {Phylogeny ; *Gene Duplication ; *Genome/genetics ; Biological Evolution ; Computer Simulation ; Evolution, Molecular ; }, abstract = {With the rapid growth of entire genome data, phylogenomics focuses on analyzing evolutionary histories and relationships of species, i.e., the tree of life. For decades it has been realized that the genome-wide phylogenetic inference can be approached based upon the dynamic pattern of gene content (the presence/absence of gene families), or extended gene content (absence, presence as a single-copy, or duplicates). Those methods, conceptually or technically, invoked the birth-and-death process to model the evolutionary process (gene duplication or gene loss. One common drawback is that the mechanism of new gene input, including de novo origin of new genes and the lateral gene transfer, has not been explicitly considered. In this paper, the author developed a new genome distance approach for genome phylogeny inference under the origin-birth-death stochastic process. The model takes gene duplication, gene loss and new gene input into account simultaneously. Computer simulations found that the two-genome approach is statistically difficult to distinguish between two proliferation parameters, i.e., the rate of gene duplication and the rate of new gene input. Nevertheless, it has also demonstrated the statistical feasibility for using the loss-genome distance to infer the genome phylogeny, which can avoid the large sampling problem. The strategy to study the universal tree of life was discussed and exemplified by an example.}, }
@article {pmid37741386, year = {2023}, author = {Shen, Y and Liu, Y and Du, Y and Wang, X and Guan, J and Jia, X and Xu, F and Song, Z and Gao, H and Zhang, B and Guo, P}, title = {Transfer of antibiotic resistance genes from soil to wheat: Role of host bacteria, impact on seed-derived bacteria, and affecting factors.}, journal = {The Science of the total environment}, volume = {905}, number = {}, pages = {167279}, doi = {10.1016/j.scitotenv.2023.167279}, pmid = {37741386}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Triticum ; Soil ; Genes, Bacterial ; Soil Microbiology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Seeds ; Manure/microbiology ; }, abstract = {The transfer of antibiotic resistance genes (ARGs) from soils to plants is poorly understood, especially the role of host bacteria in soils and its impact on seed-derived bacteria. Wheat (Triticum aestivum L.) was thus used to fill the gap by conducting pot experiments, with target ARGs and bacterial community analyzed. Results showed that the relative abundances of target ARGs gradually decreased during transfer of ARGs from the rhizosphere soil to root and shoot. Host bacteria in the rhizosphere soil were the primary source of ARGs in wheat. The 38, 21, and 19 potential host bacterial genera of target ARGs and intI1 in the rhizosphere soil, root, and shoot were identified, respectively, and they mainly belonged to phylum Proteobacteria. The abundance of ARGs carried by pathogenic Corynebacterium was reduced in sequence. During transfer of ARGs from the rhizosphere soil to root and shoot, some seed-derived bacteria and pathogenic Acinetobacter obtained ARGs through horizontal gene transfer and became potential host bacteria. Furthermore, total organic carbon, available nitrogen of the rhizosphere soil, water use efficiency, vapor pressure deficit, and superoxide dismutase of plants were identified as the key factors affecting potential host bacteria transfer in soils to wheat. This work provides important insights into transfer of ARGs and deepens our understanding of potential health risks of ARGs from soils to plants.}, }
@article {pmid37739550, year = {2023}, author = {Khambhati, K and Bhattacharjee, G and Gohil, N and Maurya, R and Singh, V}, title = {Exploring the potential of phage and their applications.}, journal = {Progress in molecular biology and translational science}, volume = {200}, number = {}, pages = {1-12}, doi = {10.1016/bs.pmbts.2023.04.001}, pmid = {37739550}, issn = {1878-0814}, mesh = {Humans ; *Bacteriophages ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Food ; Mutation ; }, abstract = {Antibiotic resistant microorganisms are significantly increasing due to horizontal gene transfer, mutation and overdose of antibiotics leading to serious health conditions globally. Several multidrug resistant microorganisms have shown resistance to even the last line of antibiotics making it very difficult to treat them. Besides using antibiotics, an alternative approach to treat such resistant bacterial pathogens through the use of bacteriophage (phage) was used in the early 1900s which however declined and vanished after the discovery of antibiotics. In recent times, phage has emerged and gained interest as an alternative approach to antibiotics to treat MDR pathogens. Phage can self-replicate by utilizing cellular machinery of bacterial host by following lytic and lysogenic life cycles and therefore suitable for rapid regeneration. Application of phage for detection of bacterial pathogens, elimination of bacteria, agents for controlling food spoilage, treating human disease and several others entitles phage as a futuristic antibacterial armamentarium.}, }
@article {pmid37739079, year = {2023}, author = {Wu, L and Wu, Q and Xu, J and Rong, L and Yu, X and Cai, C and Huang, X and Zou, X}, title = {Responses of antibiotic resistance genes in the enhanced biological phosphorus removal system under various antibiotics: Mechanisms and implications.}, journal = {The Science of the total environment}, volume = {905}, number = {}, pages = {167247}, doi = {10.1016/j.scitotenv.2023.167247}, pmid = {37739079}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Sewage/microbiology ; }, abstract = {The effects of antibiotics on the proliferation of antibiotic resistant genes (ARGs) in WWTPs have drawn great attention in recent years. The effects of antibiotics on ARGs in the enhanced biological phosphorus removal (EBPR) system and its mechanisms, however, are still not well understood. In this study, EBPR systems were constructed using activated sludge to investigate the effects of ten commonly detected antibiotics in the environment on the proliferation of ARGs and the mechanisms involved. The results showed that the total abundance of ARGs increased to varying degrees with the addition of different antibiotics (0.05 mmol/L), and the top 30 ARGs increased by 271.1 % to 370.0 %. Mobile genetic elements (MGEs), functional modules, and the bacteria community were consistently related to the changes in ARGs. Refractory antibiotics, in particular, have a stronger promoting effect on transduction in the EBPR system. The insertion sequence common region (ISCR) and transposon (Tnp) were identified as crucial factors in the proliferation of ARGs. Moreover, the risk of polyphosphate accumulating organisms (PAOs) carrying ARGs in the presence of antibiotics should not be ignored. Our findings emphasize the potential efficacy of employing strategies that target the reduction of MGEs, regulation of cellular communication, and management of microbial communities to effectively mitigate the risks associated with ARGs.}, }
@article {pmid37738943, year = {2023}, author = {Zhang, J and Xu, Z and Chu, W and Ju, F and Jin, W and Li, P and Xiao, R}, title = {Residual chlorine persistently changes antibiotic resistance gene composition and increases the risk of antibiotic resistance in sewer systems.}, journal = {Water research}, volume = {245}, number = {}, pages = {120635}, doi = {10.1016/j.watres.2023.120635}, pmid = {37738943}, issn = {1879-2448}, abstract = {During the COVID-19 pandemic, excessive amounts of disinfectants and their transformation products entered sewer systems worldwide, which was an extremely rare occurrence before. The stress of residual chlorine and disinfection by-products is not only likely to promote the spread of antibiotic resistance genes (ARGs), but also leads to the enrichment of chlorine-resistant bacteria that may also be resistant to antibiotics. Therefore, the potential impact of such discharge on ARG composition should be studied and the health risks should be assessed. Thus, this study combined high-throughput 16S rRNA gene amplicon sequencing and metagenomic analysis with long-term batch tests that involved two stages of stress and recovery to comprehensively evaluate the impact of residual chlorine on the microbial community and ARG compositions in sewer systems. The tests demonstrated that the disturbance of the microbial community structure by residual chlorine was reversible, but the change in ARG composition was persistent. This study found that vertical propagation and horizontal gene transfer jointly drove ARG composition succession in the biofilm, while the driving force was mainly horizontal gene transfer in the sediment. In this process, the biocide resistance gene (BRG) subtype chtR played an important role in promoting co-selection with ARGs through plasmids and integrative and conjugative elements. Moreover, it was further shown that the addition of sodium hypochlorite increased the risk of ARGs to human health, even after discontinuation of dosing, signifying that the impact was persistent. In general, this study strengthens the co-selection theory of ARGs and BRGs, and calls for improved disinfection strategies and more environmentally friendly disinfectants.}, }
@article {pmid37734313, year = {2024}, author = {Wang, YZ and An, XL and Fan, XT and Pu, Q and Li, H and Liu, WZ and Chen, Z and Su, JQ}, title = {Visible light-activated photosensitizer inhibits the plasmid-mediated horizontal gene transfer of antibiotic resistance genes.}, journal = {Journal of hazardous materials}, volume = {461}, number = {}, pages = {132564}, doi = {10.1016/j.jhazmat.2023.132564}, pmid = {37734313}, issn = {1873-3336}, mesh = {*Photosensitizing Agents/pharmacology ; *Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; Escherichia coli/genetics ; Plasmids/genetics ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; }, abstract = {Inhibition of plasmid transfer, including transformation and conjugation, is essential to prevent the spread of plasmid-encoded antimicrobial resistance. Photosensitizers have been successfully used in the treatment of serious infectious diseases, however, the effects of photosensitizers on the plasmid transfer are still elusive. In this study, we determined the transformation and conjugation efficiency of plasmid pUC19 and pRP4, respectively, when exposed to a photosensitizer (Visible Light-activated Rose Bengal, VLRB). The results showed that the activation of VLRB resulted in up to a 580-fold decrease in the transformation frequency of pUC19 and a 10-fold decrease in the conjugation frequency of pRP4 compared with the non-VLRB control. The inhibition of pUC19 transformation by VLRB exhibited a dose-dependent manner and was attributed to the changes in the plasmid conformation. The inhibition of pRP4 conjugation was associated with the generation of extracellular free radicals, induced oxidative stress, suppression of the mating pair formation gene (trbBp) and DNA transfer and replication gene (trfAp), and enhanced expression of the global regulatory genes (korA, korB, and trbA). These findings highlight the potential of visible light-activated photosensitizer for mitigating the dissemination of plasmid-encoded antibiotic resistance genes.}, }
@article {pmid37733747, year = {2023}, author = {Caygill, S and Dolan, L}, title = {ATP binding cassette transporters and uridine diphosphate glycosyltransferases are ancient protein families that evolved roles in herbicide resistance through exaptation.}, journal = {PloS one}, volume = {18}, number = {9}, pages = {e0287356}, pmid = {37733747}, issn = {1932-6203}, mesh = {*Glycosyltransferases/genetics ; *ATP-Binding Cassette Transporters/genetics ; Herbicide Resistance/genetics ; Phylogeny ; Amino Acid Sequence ; Plant Weeds ; }, abstract = {ATP-binding cassette (ABC) transporters actively transport various substances across membranes, while uridine diphosphate (UDP) glycosyltransferases (UGTs) are proteins that catalyse the chemical modification of various organic compounds. Both of these protein superfamilies have been associated with conferring herbicide resistance in weeds. Little is known about the evolutionary history of these protein families in the Archaeplastida. To infer the evolutionary histories of these protein superfamilies, we compared protein sequences collected from 10 species which represent distinct lineages of the Archaeplastida-the lineage including glaucophyte algae, rhodophyte algae, chlorophyte algae and the streptophytes-and generated phylogenetic trees. We show that ABC transporters were present in the last common ancestor of the Archaeplastida which lived 1.6 billion years ago, and the major clades identified in extant plants were already present then. Conversely, we only identified UGTs in members of the streptophyte lineage, which suggests a loss of these proteins in earlier diverging Archaeplastida lineages or arrival of UGTs into a common ancestor of the streptophyte lineage through horizontal gene transfer from a non-Archaeplastida eukaryote lineage. We found that within the streptophyte lineage, most diversification of the UGT protein family occurred in the vascular lineage, with 17 of the 20 clades identified in extant plants present only in vascular plants. Based on our findings, we conclude that ABC transporters and UGTs are ancient protein families which diversified during Archaeplastida evolution, which may have evolved for developmental functions as plants began to occupy new environmental niches and are now being selected to confer resistance to a diverse range of herbicides in weeds.}, }
@article {pmid37733635, year = {2023}, author = {Luo, T and Dai, X and Wei, W and Xu, Q and Ni, BJ}, title = {Microplastics Enhance the Prevalence of Antibiotic Resistance Genes in Anaerobic Sludge Digestion by Enriching Antibiotic-Resistant Bacteria in Surface Biofilm and Facilitating the Vertical and Horizontal Gene Transfer.}, journal = {Environmental science &amp; technology}, volume = {57}, number = {39}, pages = {14611-14621}, doi = {10.1021/acs.est.3c02815}, pmid = {37733635}, issn = {1520-5851}, mesh = {Humans ; *Sewage/microbiology ; *Microplastics ; Plastics ; Genes, Bacterial ; Anaerobiosis ; Gene Transfer, Horizontal ; Prevalence ; Angiotensin Receptor Antagonists ; Polyethylene ; Anti-Bacterial Agents/pharmacology ; Angiotensin-Converting Enzyme Inhibitors ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Digestion ; }, abstract = {Antibiotic resistance genes (ARGs) and microplastics (MPs) are recognized as emerging contaminants and threats to global human health. Despite both of them being significantly detected in their "hotspots", i.e., waste activated sludge (WAS), rare studies on how MPs affect ARGs and antibiotic-resistant bacteria (ARB) in anaerobic sludge digestion are available. Herein, the fate of ARGs and ARB after exposure to MPs of three dosages (10, 30, and 80 particles/g-TS), three polymer types (LDPE, PET, and PS), and three branching extents (LDPE, LLDPE, and HDPE) in anaerobic sludge digestion was investigated. Metagenomic results indicated that all variants of MPs resulted in an increase of the relative abundance of ARGs in the digester compared to the control. The abundance of ARGs demonstrated a dosage-dependent relationship within the range from 10 to 80 particles/g-TS, resulting in an increase from 4.5 to 27.9% compared to the control. Branching structure and polymer type influence ARG level in the sludge digester as well. Mechanism studies revealed that LDPE selectively enriched potential ARB and ARGs in the surface biofilm, possibly creating a favorable environment for ARB proliferation and ARG exchange. Furthermore, vertical transfer of ARGs was facilitated by LDPE through increasing bacterial cell proliferation accompanied by the enhancement of relevant functional genes. The elevated abundance of mobile genetic elements (MGEs) and ARGs-carrying plasmids also demonstrated that MGE-mediated horizontal transfer was promoted by LDPE at 80 particles/g-TS. This effect was compounded by increased oxidative stress, cell membrane permeability, and cell cohesion, collectively facilitating horizontal ARG transfer. Consequently, both vertical and horizontal transfer of ARGs could be concurrently promoted by LDPE an in anaerobic sludge digester.}, }
@article {pmid37732760, year = {2023}, author = {Wirth, NT and Rohr, K and Danchin, A and Nikel, PI}, title = {Recursive genome engineering decodes the evolutionary origin of an essential thymidylate kinase activity in Pseudomonas putida KT2440.}, journal = {mBio}, volume = {14}, number = {5}, pages = {e0108123}, pmid = {37732760}, issn = {2150-7511}, support = {NNF20CC0035580//Novo Nordisk Fonden (NNF)/ ; NNF18OC0034818//Novo Nordisk Fonden (NNF)/ ; NNF21OC0067996//Novo Nordisk Fonden (NNF)/ ; 814418//EC | H2020 | IL | LEIT | H2020 LEIT Biotechnology (BIOTEC)/ ; }, mesh = {*Pseudomonas putida/genetics/metabolism ; Genomic Islands ; Biotechnology ; }, abstract = {Investigating fundamental aspects of metabolism is vital for advancing our understanding of the diverse biochemical capabilities and biotechnological applications of bacteria. The origin of the essential thymidylate kinase function in the model bacterium Pseudomonas putida KT2440, seemingly interrupted due to the presence of a large genomic island that disrupts the cognate gene, eluded a satisfactory explanation thus far. This is a first-case example of an essential metabolic function, likely acquired by horizontal gene transfer, which "landed" in a locus encoding the same activity. As such, foreign DNA encoding an essential dNMPK could immediately adjust to the recipient host-instead of long-term accommodation and adaptation. Understanding how these functions evolve is a major biological question, and the work presented here is a decisive step toward this direction. Furthermore, identifying essential and accessory genes facilitates removing those deemed irrelevant in industrial settings-yielding genome-reduced cell factories with enhanced properties and genetic stability.}, }
@article {pmid37730038, year = {2023}, author = {Shen, M and Zhao, Y and Liu, S and Tao, S and Li, T and Long, H}, title = {Can microplastics and disinfectant resistance genes pose conceivable threats to water disinfection process?.}, journal = {The Science of the total environment}, volume = {905}, number = {}, pages = {167192}, doi = {10.1016/j.scitotenv.2023.167192}, pmid = {37730038}, issn = {1879-1026}, mesh = {*Disinfectants/analysis ; Disinfection ; Microplastics ; Plastics ; Water ; Bacteria/genetics ; }, abstract = {Microplastic pollution in the environment has aroused widespread concerns, however, the potential environmental risks caused by excessive use of disinfectants are still unknown. Disinfectants with doses below the threshold can enhance the communication of resistance genes in pathogenic microorganisms, promoting the development and spread of antimicrobial activity. Problematically, the intensification of microplastic pollution and the increase of disinfectant consumption will become a key driving force for the growth of disinfectant resistance bacteria (DRB) and disinfectant resistance genes (DRGs) in the environment. Disinfection plays a crucial role in ensuring water safety, however, the presence of microplastics and DRGs seriously disturb the water disinfection process. Microplastics can reduce the concentration of disinfectant in the local environment around microorganisms and improve their tolerance. Microorganisms can improve their resistance to disinfectants or generate resistance genes via phenotypic adaptation, gene mutations, and horizontal gene transfer. However, very limited information is available on the impact of DRB and DRGs on disinfection process. In this paper, the contribution of microplastics to the migration and transmission of DRGs was analyzed. The challenges posed by the presence of microplastics and DRGs on conventional disinfection were thoroughly discussed. The knowledge gaps faced by relevant current research and further research priorities have been proposed in order to provide a scientific basis in the future.}, }
@article {pmid37728942, year = {2023}, author = {Subirats, J and Sharpe, H and Tai, V and Fruci, M and Topp, E}, title = {Metagenome meta-analysis reveals an increase in the abundance of some multidrug efflux pumps and mobile genetic elements in chemically polluted environments.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {10}, pages = {e0104723}, pmid = {37728942}, issn = {1098-5336}, mesh = {Humans ; *Metagenome ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Interspersed Repetitive Sequences ; *Petroleum ; }, abstract = {Many human activities contaminate terrestrial and aquatic environments with numerous chemical pollutants that not only directly alter the environment but also affect microbial communities in ways that are potentially concerning to human health, such as selecting for the spread of antibiotic-resistance genes (ARGs) through horizontal gene transfer. In the present study, metagenomes available in the public domain from polluted (with antibiotics, with petroleum, with metal mining, or with coal-mining effluents) and unpolluted terrestrial and aquatic environments were compared to examine whether pollution has influenced the abundance and composition of ARGs and mobile elements, with specific focus on IS26 and class 1 integrons (intI1). When aggregated together, polluted environments had a greater relative abundance of ARGs than unpolluted environments and a greater relative abundance of IS26 and intI1. In general, chemical pollution, notably with petroleum, was associated with an increase in the prevalence of ARGs linked to multidrug efflux pumps. Included in the suite of efflux pumps were mexK, mexB, mexF, and mexW that are polyspecific and whose substrate ranges include multiple classes of critically important antibiotics. Also, in some instances, β-lactam resistance (TEM181 and OXA-541) genes increased, and genes associated with rifampicin resistance (RNA polymerases subunits rpoB and rpoB2) decreased in relative abundance. This meta-analysis suggests that different types of chemical pollution can enrich populations that carry efflux pump systems associated with resistance to multiple classes of medically critical antibiotics.IMPORTANCEThe United Nations has identified chemical pollution as being one of the three greatest threats to environmental health, through which the evolution of antimicrobial resistance, a seminally important public health challenge, may be favored. While this is a very plausible outcome of continued chemical pollution, there is little evidence or research evaluating this risk. The objective of the present study was to examine existing metagenomes from chemically polluted environments and evaluate whether there is evidence that pollution increases the relative abundance of genes and mobile genetic elements that are associated with antibiotic resistance. The key finding is that for some types of pollution, particularly in environments exposed to petroleum, efflux pumps are enriched, and these efflux pumps can confer resistance to multiple classes of medically important antibiotics that are typically associated with Pseudomonas spp. or other Gram-negative bacteria. This finding makes clear the need for more investigation on the impact of chemical pollution on the environmental reservoir of ARGs and their association with mobile genetic elements that can contribute to horizontal gene transfer events.}, }
@article {pmid37724865, year = {2023}, author = {Sabatino, R and Sbaffi, T and Sivalingam, P and Corno, G and Fontaneto, D and Di Cesare, A}, title = {Bacteriophages limitedly contribute to the antimicrobial resistome of microbial communities in wastewater treatment plants.}, journal = {Microbiology spectrum}, volume = {11}, number = {5}, pages = {e0110123}, pmid = {37724865}, issn = {2165-0497}, abstract = {Bacteriophages are known as players in the transmission of antimicrobial resistance genes (ARGs) by horizontal gene transfer. In this study, we characterized the bacteriophage community and the associated ARGs to estimate the potential for phages to spread ARGs in aquatic ecosystems analyzing the intra- and extracellular DNA isolated from two wastewater treatment plants (WWTPs) by shotgun metagenomics. We compared the phage antimicrobial resistome with the bacterial resistome and investigated the effect of the final disinfection treatment on the phage community and its resistome. Phage community was mainly composed by Siphoviridae and other members of the order Caudovirales. The final disinfection only marginally affected the composition of the phage community, and it was not possible to measure its effect on the antimicrobial resistome. Indeed, only three phage metagenome-assembled genomes (pMAGs) annotated as Siphoviridae, Padoviridae, and Myoviridae were positive for putative ARGs. Among the detected ARGs, i.e., dfrB6, rpoB mutants, and EF-Tu mutants, the first one was not annotated in the bacterial MAGs. Overall, these results demonstrate that bacteriophages limitedly contribute to the whole antimicrobial resistome. However, in order to obtain a comprehensive understanding of the antimicrobial resistome within a microbial community, the role of bacteriophages needs to be investigated. IMPORTANCE WWTPs are considered hotspots for the spread of ARGs by horizontal gene transfer. In this study, we evaluated the phage composition and the associated antimicrobial resistome by shotgun metagenomics of samples collected before and after the final disinfection treatment. Only a few bacteriophages carried ARGs. However, since one of the detected genes was not found in the bacterial metagenome-assembled genomes, it is necessary to investigate the phage community in order to gain a comprehensive overview of the antimicrobial resistome. This investigation could help assess the potential threats to human health.}, }
@article {pmid37724858, year = {2023}, author = {Derbyshire, KM and Salfinger, M}, title = {Plasmid-mediated drug resistance in mycobacteria: the tip of the iceberg?.}, journal = {Journal of clinical microbiology}, volume = {61}, number = {10}, pages = {e0062823}, pmid = {37724858}, issn = {1098-660X}, mesh = {Humans ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Mycobacterium chelonae/drug effects/genetics ; Macrolides/pharmacology ; Drug Resistance, Bacterial/genetics/drug effects ; Clarithromycin/therapeutic use ; *Mycobacterium/genetics/drug effects ; *Mycobacterium Infections, Nontuberculous/microbiology ; Nontuberculous Mycobacteria/isolation &amp; purification ; Chromosomes/drug effects ; }, abstract = {Macrolides, such as clarithromycin, are crucial in the treatment of nontuberculous mycobacteria (NTM). NTM are notoriously innately drug resistant, which has made the dependence on macrolides for their treatment even more important. Not surprisingly, resistance to macrolides has been documented in some NTM, including Mycobacterium avium and Mycobacterium abscessus, which are the two NTM species most often identified in clinical isolates. Resistance is mediated by point mutations in the 23S ribosomal RNA or by methylation of the rRNA by a methylase (encoded by an erm gene). Chromosomally encoded erm genes have been identified in many of the macrolide-resistant isolates, but not in Mycobacterium chelonae. Now, Brown-Elliott et al. (J Clin Microbiol 61:e00428-23, 2023, https://doi.org/10.1128/JCM.00428-23) describe the identification of a new erm variant, erm(55), which was found either on the chromosome or on a plasmid in highly macrolide-resistant clinical isolates of M. chelonae. The chromosomal erm(55) gene appears to be associated with mobile elements; one gene is within a putative transposon and the second is in a large (37 kb) insertion/deletion. The plasmid carrying erm(55) also encodes type IV and type VII secretion systems, which are often linked on large mycobacterial plasmids and are hypothesized to mediate plasmid transfer. While the conjugative transfer of the erm(55)-containing plasmid between NTM has yet to be demonstrated, the inferences are clear, as evidenced by the dissemination of plasmid-mediated drug resistance in other medically important bacteria. Here, we discuss the findings of Brown-Elliott et al., and the potential ramifications on treatment of NTM infections.}, }
@article {pmid37720149, year = {2023}, author = {Bhat, BA and Mir, RA and Qadri, H and Dhiman, R and Almilaibary, A and Alkhanani, M and Mir, MA}, title = {Integrons in the development of antimicrobial resistance: critical review and perspectives.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1231938}, pmid = {37720149}, issn = {1664-302X}, abstract = {Antibiotic resistance development and pathogen cross-dissemination are both considered essential risks to human health on a worldwide scale. Antimicrobial resistance genes (AMRs) are acquired, expressed, disseminated, and traded mainly through integrons, the key players capable of transferring genes from bacterial chromosomes to plasmids and their integration by integrase to the target pathogenic host. Moreover, integrons play a central role in disseminating and assembling genes connected with antibiotic resistance in pathogenic and commensal bacterial species. They exhibit a large and concealed diversity in the natural environment, raising concerns about their potential for comprehensive application in bacterial adaptation. They should be viewed as a dangerous pool of resistance determinants from the "One Health approach." Among the three documented classes of integrons reported viz., class-1, 2, and 3, class 1 has been found frequently associated with AMRs in humans and is a critical genetic element to serve as a target for therapeutics to AMRs through gene silencing or combinatorial therapies. The direct method of screening gene cassettes linked to pathogenesis and resistance harbored by integrons is a novel way to assess human health. In the last decade, they have witnessed surveying the integron-associated gene cassettes associated with increased drug tolerance and rising pathogenicity of human pathogenic microbes. Consequently, we aimed to unravel the structure and functions of integrons and their integration mechanism by understanding horizontal gene transfer from one trophic group to another. Many updates for the gene cassettes harbored by integrons related to resistance and pathogenicity are extensively explored. Additionally, an updated account of the assessment of AMRs and prevailing antibiotic resistance by integrons in humans is grossly detailed-lastly, the estimation of AMR dissemination by employing integrons as potential biomarkers are also highlighted. The current review on integrons will pave the way to clinical understanding for devising a roadmap solution to AMR and pathogenicity. Graphical AbstractThe graphical abstract displays how integron-aided AMRs to humans: Transposons capture integron gene cassettes to yield high mobility integrons that target res sites of plasmids. These plasmids, in turn, promote the mobility of acquired integrons into diverse bacterial species. The acquisitions of resistant genes are transferred to humans through horizontal gene transfer.}, }
@article {pmid37718237, year = {2023}, author = {You, L and Jin, H and Kwok, LY and Lv, R and Zhao, Z and Bilige, M and Sun, Z and Liu, W and Zhang, H}, title = {Intraspecific microdiversity and ecological drivers of lactic acid bacteria in naturally fermented milk ecosystem.}, journal = {Science bulletin}, volume = {68}, number = {20}, pages = {2405-2417}, doi = {10.1016/j.scib.2023.09.001}, pmid = {37718237}, issn = {2095-9281}, mesh = {Animals ; Milk/microbiology ; *Lactobacillales/genetics ; Lactobacillus/genetics ; Ecosystem ; Phylogeny ; *Lactobacillus delbrueckii/genetics ; *Lactococcus lactis ; }, abstract = {Traditional fermented milks are produced by inoculating technique, which selects well-adapted microorganisms that have been passed on through generations. Few reports have used naturally fermented milks as model ecosystems to investigate the mechanism of formation of intra-species microbial diversity. Here, we isolated and whole-genome-sequenced a total of 717 lactic acid bacterial isolates obtained from 12 independent naturally fermented milks collect from 12 regions across five countries. We further analyzed the within-sample intra-species phylogenies of 214 Lactobacillus helveticus isolates, 97 Lactococcus lactis subsp. lactis isolates, and 325 Lactobacillus delbrueckii subsp. bulgaricus isolates. We observed a high degree of intra-species genomic and functional gene diversity within-/between-sample(s). Single nucleotide polymorphism-based phylogenetic reconstruction revealed great within-sample intra-species heterogeneity, evolving from multiple lineages. Further phylogenetic reconstruction (presence-absence gene profile) revealed within-sample inter-clade functional diversity (based on carbohydrate-active enzyme- and peptidase-encoding genes) in all three investigated species/subspecies. By identifying and mapping clade-specific genes of intra-sample clades of the three species/subspecies to the respective fermented milk metagenome, we found extensive potential inter-/intra-species horizontal gene transfer events. Finally, the microbial composition of the samples is closely linked to the nucleotide diversity of the respective species/subspecies. Overall, our results contribute to the conservation of lactic acid bacteria resources, providing ecological insights into the microbial ecosystem of naturally fermented dairy products.}, }
@article {pmid37716694, year = {2023}, author = {Savin, M and Hammerl, JA and Hassa, J and Hembach, N and Kalinowski, J and Schwartz, T and Droop, F and Mutters, NT}, title = {Free-floating extracellular DNA (exDNA) in different wastewaters: Status quo on exDNA-associated antimicrobial resistance genes.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {337}, number = {}, pages = {122560}, doi = {10.1016/j.envpol.2023.122560}, pmid = {37716694}, issn = {1873-6424}, mesh = {*Wastewater ; Anti-Bacterial Agents ; Genes, Bacterial ; Waste Disposal, Fluid/methods ; RNA, Ribosomal, 16S ; Angiotensin Receptor Antagonists ; Drug Resistance, Bacterial/genetics ; Angiotensin-Converting Enzyme Inhibitors ; DNA ; *Ozone/analysis ; }, abstract = {Wastewater treatment plants (WWTPs) have been reported as major anthropogenic reservoirs for the spread of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) into the environment, worldwide. While most studies mainly focus on the intracellular DNA (iDNA), extracellular DNA (exDNA) accounting for a significant proportion of the total DNA in wastewater, was usually neglected. Following the One Health approach, this study focuses on wastewaters of municipal, clinical, and livestock origins (n = 45) that undergo different treatment processes (i.e., conventional activated sludge, ultrafiltration, and ozonation). Water samples were analysed for 12 ARGs as indicators of the different compartments associated with iDNA and exDNA by quantitative real-time PCR (qPCR). Taxonomic profiling of exDNA-fractions, obtained using nucleic acid adsorption particles, was conducted by sequencing the V3-V4 hypervariable regions of the 16S rRNA gene. Notified exDNA concentrations varied between on-site WWTPs and treatment stages, and ranged from 314.0 ± 70.2 ng/mL in untreated livestock wastewater down to 0.7 ± 0.1 ng/mL in effluents after ultrafiltration. In general, influents exhibited higher concentrations compared to effluents, while wastewater treated by advanced treatment processes (i.e., ultrafiltration and ozonation) showed the lowest exDNA concentrations. Despite the lower concentrations, free-floating exDNA accounted for up to 80.0 ± 5.8% of the total DNA in effluents. Target ARGs were more common in the iDNA (100%, n = 45/45), compared to the exDNA-fractions (51.1%, n = 23/45), whereas exDNA-ARGs were mostly detected in clinical and slaughterhouse wastewaters as well as in the municipal influents. Compared to the iDNA-ARGs, the concentrations of exDNA-ARGs were in general lower. Nevertheless, significant higher concentrations for exDNA-associated genes were measured in clinical wastewaters for blaNDM (4.07 ± 0.15 log gene copies (GC)/L) and blaVIM-2 (6.0 ± 0.2 log GC/L). Overall, our results suggest that depending on the origin of wastewater and its treatment methods, exDNA represents an important reservoir for ARGs, particularly in clinical wastewater.}, }
@article {pmid37716437, year = {2023}, author = {Rodríguez-Pallares, S and Mateo-Vargas, MA and Rodríguez-Iglesias, MA and Galán-Sánchez, F}, title = {Molecular characterization of consecutive isolates of OXA-48-producing Klebsiella pneumoniae: changes in the virulome using next-generation sequencing (NGS).}, journal = {Microbes and infection}, volume = {25}, number = {8}, pages = {105217}, doi = {10.1016/j.micinf.2023.105217}, pmid = {37716437}, issn = {1769-714X}, mesh = {Humans ; *Bacterial Proteins/genetics ; beta-Lactamases/genetics ; Klebsiella pneumoniae ; Multilocus Sequence Typing ; *Klebsiella Infections ; Virulence Factors/genetics ; Microbial Sensitivity Tests ; High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents/pharmacology/therapeutic use ; }, abstract = {Little is known about the clonality of consecutive OXA-48 producing-Klebsiella pneumoniae isolates from the same patient and the possibility of changes in their virulomes over time. We studied the molecular characteristics of twenty OXA-48-producing K. pneumoniae consecutive isolates from six patients using whole-genome sequencing. The genomes were screened for antimicrobial resistance and virulence factor genes and for replicon groups. MLST and SNPs analysis was performed. MLST analysis found 3 STs: ST11 (n = 13; 65.0%); ST4975 (n = 5, 25.0%); ST307 (n = 2; 10.0%). AcrAb efflux pump, siderophore enterobactin and rcsAB capsule synthesis regulator were detected in all sequenced isolates. The regulator of mucoid phenotype A (rmpA) and rmpA2 were not detected. Isolates also carried type 3 fimbriae (n = 19; 95.0%), yersiniabactin (n = 15; 75.0%) and type 1 fimbriae (7; 35.0%). Type 3 fimbriae and yersiniabactin were lost and recovered in consecutive isolates of two patients, probably acquired by horizontal gene transfer. Our findings reveal that recurrent infections are due to the same isolate, with an average of 2.69 SNPs per month, with different virulence profiles, and that the acquisition of virulence factor genes over time is possible.}, }
@article {pmid37715312, year = {2023}, author = {Xi, Y and Zhao, J and Zhang, J and Jin, Y and Yang, H and Duan, G and Chen, S and Long, J}, title = {Analysis of the features of 105 confirmed CRISPR loci in 487 Klebsiella variicola.}, journal = {Letters in applied microbiology}, volume = {76}, number = {9}, pages = {}, doi = {10.1093/lambio/ovad108}, pmid = {37715312}, issn = {1472-765X}, support = {2022M712859//China Postdoctoral Science Foundation/ ; 2018ZX10301407//National Science and Technology Specific Project of China/ ; }, mesh = {Humans ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Klebsiella/genetics ; Plasmids/genetics ; *Bacteriophages/genetics ; Klebsiella pneumoniae/genetics ; }, abstract = {Klebsiella variicola, an emerging human pathogen, poses a threat to public health. The horizontal gene transfer (HGT) of plasmids is an important driver of the emergence of multiple antibiotic-resistant K. variicola. Clustered regularly interspersed short palindromic repeats (CRISPR) coupled with CRISPR-associated genes (CRISPR/Cas) constitute an adaptive immune system in bacteria, and can provide acquired immunity against HGT. However, the information about the CRISPR/Cas system in K. variicola is still limited. In this study, 487 genomes of K. variicola obtained from the National Center for Biotechnology Information database were used to analyze the characteristics of CRISPR/Cas systems. Approximately 21.56% of genomes (105/487) harbor at least one confirmed CRISPR array. Three types of CRISPR/Cas systems, namely the type I-E, I-E*, and IV-A systems, were identified among 105 strains. Spacer origin analysis further revealed that approximately one-third of spacers significantly match plasmids or phages, which demonstrates the implication of CRISPR/Cas systems in controlling HGT. Moreover, spacers in K. variicola tend to target mobile genetic elements from K. pneumoniae. This finding provides new evidence of the interaction of K. variicola and K. pneumoniae during their evolution. Collectively, our results provide valuable insights into the role of CRISPR/Cas systems in K. variicola.}, }
@article {pmid37705515, year = {2023}, author = {Abdelbary, ER and Elsaghier, AM and Abd El-Baky, RM and Waly, NGFM and Ramadan, M and Abd-Elsamea, FS and Ali, ME and Alzahrani, HA and Salah, M}, title = {First Emergence of NDM-5 and OqxAB Efflux Pumps Among Multidrug-Resistant Klebsiella pneumoniae Isolated from Pediatric Patients in Assiut, Egypt.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {5965-5976}, pmid = {37705515}, issn = {1178-6973}, abstract = {INTRODUCTION: New Delhi metallo-β-lactamase (NDM)-producing K. pneumoniae poses a high risk, especially among Egyptian pediatric patients who consume carbapenems antibiotics very widely and without adequate diagnostic sources. In addition, presence of efflux pump genes such as OqxAB increases resistance against many groups of antimicrobials which exacerbates the problem faced for human health. This study aimed to determine NDM variants among K. pneumoniae strains isolated from pediatric patients in Egypt, analyze the presence of OqxAB genes, and molecular characterization of blaNDM-5-positive K. pneumoniae.<br><br>METHODS: Fifty-six K. pneumoniae&#xa0;isolates were recovered from pediatric patients, and tested for carbapenemase by modified carbapenem inactivation methods (mCIM) test. Minimum inhibitory concentrations of meropenem and colistin were determined by meropenem E-test strips and broth microdilution, respectively. PCR was used for the detection of the resistant genes (ESBL gene (blaCTX-M), carbapenemase genes (blaNDM, blaKPC) colistin resistant (mcr1, mcr2)) and genes for efflux pump (oqxA and oqxB). BlaNDM was sequenced. The effect of efflux pump in NDM-5-producing isolates was assessed by measuring MIC of ciprofloxacin and meropenem before and after exposure to the carbonyl cyanide 3-chlorophenylhydrazone (CCCP). The horizontal gene transfer ability of&#xa0;blaNDM-5 was determined using liquid mating assay and PCR-based replicon typing (PBRT) was done to determine the major plasmid incompatibility group.<br><br>RESULTS: Twenty-nine isolates were positive for blaNDM-1, nine isolates were positive for blaNDM-5, and 15 isolates were positive for blaKPC. There is a significant increase of meropenem MIC of NDM-5-positive isolates compared with NDM-1-positive isolates. In addition, 38 isolates were positive for CTX-M, and 15 isolates were positive for mcr1. Both OqxA and OqxB were detected in 26 isolates and 13 isolates were positive for OqxA while 11 isolates were positive for OqxB only. All NDM-5-producing isolates except one isolate could transfer their plasmids by conjugation to their corresponding transconjugants (E. coli J53). Plasmid replicon typing showed that FII was predominant in NDM-5-producing K. pneumoniae. Similar strains were found between the three isolates and similarity was also detected between the two isolates.<br><br>CONCLUSION: The highly resistant K. pneumoniae producing blaNDM-5 type was firstly isolated from pediatric patients. The association of efflux pump genes such as OqxAB is involved in resistance to ciprofloxacin. This highlighted the severity risk of&#xa0;blaNDM-5-positive&#xa0;K. pneumonia as it could transfer blaNDM-5 to other bacteria and has more resistance against carbapenems. This underlines the importance of continuous monitoring of infection control guidelines, and the urgent need for a national antimicrobial stewardship plan in Egyptian hospitals.}, }
@article {pmid37700871, year = {2023}, author = {Nasir, A and Caetano-Anollés, G and Claverie, JM}, title = {Editorial: Viruses, genetic exchange, and the tree of life, volume II.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1271181}, pmid = {37700871}, issn = {1664-302X}, }
@article {pmid37700035, year = {2023}, author = {Lin, X and Zhang, C and Han, R and Li, S and Peng, H and Zhou, X and Huang, L and Xu, Y}, title = {Oxytetracycline and heavy metals promote the migration of resistance genes in the intestinal microbiome by plasmid transfer.}, journal = {The ISME journal}, volume = {17}, number = {11}, pages = {2003-2013}, pmid = {37700035}, issn = {1751-7370}, mesh = {Animals ; Humans ; *Oxytetracycline/pharmacology ; *Gastrointestinal Microbiome ; Genes, Bacterial ; *Metals, Heavy/toxicity ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; *Microbiota ; Plasmids/genetics ; Gene Transfer, Horizontal ; }, abstract = {Horizontal gene transfer (HGT) has been considered the most important pathway to introduce antibiotic resistance genes (ARGs), which seriously threatens human health and biological security. The presence of ARGs in the aquatic environment and their effect on the intestinal micro-ecosystem of aquatic animals can occur easily. To investigate the HGT potential and rule of exogenous ARGs in the intestinal flora, a visual conjugative model was developed, including the donor of dual-fluorescent bacterium and the recipient of Xenopus tropicalis intestinal microbiome. Some common pollutants of oxytetracycline (OTC) and three heavy metals (Zn, Cu and Pb) were selected as the stressor. The multi-techniques of flow cytometry (FCM), scanning electron microscopy (SEM), atomic force microscopy (AFM), single-cell Raman spectroscopy with sorting (SCRSS) and indicator analysis were used in this study. The results showed that ARG transfer could occur more easily under stressors. Moreover, the conjugation efficiency mainly depended on the viability of the intestinal bacteria. The mechanisms of OTC and heavy metal stressing conjugation included the upregulation of ompC, traJ, traG and the downregulation of korA gene. Moreover, the enzymatic activities of SOD, CAT, GSH-PX increased and the bacterial surface appearance also changed. The predominant recipient was identified as Citrobacter freundi by SCRSS, in which the abundance and quantity of ARG after conjugation were higher than those before. Therefore, since the diversity of potential recipients in the intestine are very high, the migration of invasive ARGs in the microbiome should be given more attention to prevent its potential risks to public health.}, }
@article {pmid37697273, year = {2023}, author = {El-Sabeh, A and Mlesnita, AM and Munteanu, IT and Honceriu, I and Kallabi, F and Boiangiu, RS and Mihasan, M}, title = {Characterisation of the Paenarthrobacter nicotinovorans ATCC 49919 genome and identification of several strains harbouring a highly syntenic nic-genes cluster.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {536}, pmid = {37697273}, issn = {1471-2164}, support = {PN-III-P4-ID-PCE-2020-0656//Romanian Ministry of Education and Research/ ; PN-III-P4-ID-PCE-2020-0656//Romanian Ministry of Education and Research/ ; PN-III-P4-ID-PCE-2020-0656//Romanian Ministry of Education and Research/ ; PN-III-P4-ID-PCE-2020-0656//Romanian Ministry of Education and Research/ ; PN-III-P4-ID-PCE-2020-0656//Romanian Ministry of Education and Research/ ; }, mesh = {*Nicotine ; *Micrococcaceae ; Soil ; DNA ; }, abstract = {BACKGROUND: Paenarthrobacter nicotinovorans ATCC 49919 uses the pyridine-pathway to degrade nicotine and could provide a renewable source of precursors from nicotine-containing waste as well as a model for studying the molecular evolution of catabolic pathways and their spread by horizontal gene transfer via soil bacterial plasmids.<br><br>RESULTS: In the present study, the strain was sequenced using the Illumina NovaSeq 6000 and Oxford Nanopore Technology (ONT) MinION platforms. Following hybrid assembly with Unicycler, the complete genome sequence of the strain was obtained and used as reference for whole-genome-based phylogeny analyses. A total of 64 related genomes were analysed; five Arthrobacter strains showed both digital DNA-DNA hybridization and average nucleotide identity values over the species threshold when compared to P. nicotinovorans ATCC 49919. Five plasmids and two contigs belonging to Arthrobacter and Paenarthrobacter strains were shown to be virtually identical with the pAO1 plasmid of Paenarthrobacter nicotinovorans ATCC 49919. Moreover, a highly syntenic nic-genes cluster was identified on five plasmids, one contig and three chromosomes. The nic-genes cluster contains two major locally collinear blocks that appear to form a putative catabolic transposon. Although the origins of the nic-genes cluster and the putative transposon still elude us, we hypothesise here that the ATCC 49919 strain most probably evolved from Paenarthrobacter sp. YJN-D or a very closely related strain by acquiring the pAO1 megaplasmid and the nicotine degradation pathway.<br><br>CONCLUSIONS: The data presented here offers another snapshot into the evolution of plasmids harboured by Arthrobacter and Paenarthrobacter species and their role in the spread of metabolic traits by horizontal gene transfer among related soil bacteria.}, }
@article {pmid37693864, year = {2023}, author = {Doughty, EL and Liu, H and Moran, RA and Hua, X and Ba, X and Guo, F and Chen, X and Zhang, L and Holmes, M and van Schaik, W and McNally, A and Yu, Y}, title = {Endemicity and diversification of carbapenem-resistant Acinetobacter baumannii in an intensive care unit.}, journal = {The Lancet regional health. Western Pacific}, volume = {37}, number = {}, pages = {100780}, pmid = {37693864}, issn = {2666-6065}, support = {MR/S013660/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {BACKGROUND: Carbapenem-resistant Acinetobacter baumannii (CRAB) is a major public health concern globally. Often studied in the context of hospital outbreaks, little is known about the persistence and evolutionary dynamics of endemic CRAB populations.<br><br>METHODS: A three-month cross-sectional observational study was conducted in a 28-bed intensive care unit (ICU) in Hangzhou, China. A total of 5068 samples were collected from the hospital environment (n&#xa0;=&#xa0;3985), patients (n&#xa0;=&#xa0;964) and staff (n&#xa0;=&#xa0;119). CRAB isolates were obtained from 10.5% of these samples (n&#xa0;=&#xa0;532). All of these isolates, plus an additional 19 from clinical infections, were characterised through whole-genome sequencing.<br><br>FINDINGS: The ICU CRAB population was dominated by OXA-23-producing global clone 2 isolates (99.3% of all isolates) that could be divided into 20 distinct clusters, defined through genome sequencing. CRAB was persistently present in the ICU, driven by regular introductions of distinct clusters. The hospital environment was heavily contaminated, with CRAB isolated from bed units on 183/335 (54.6%) sampling occasions but from patients on only 72/299 (24.1%) occasions. CRAB was spread to adjacent bed units and rooms, and following re-location of patients within the ICU. We also observed three horizontal gene transfer events between CRAB strains in the ICU, involving three different plasmids.<br><br>INTERPRETATION: The epidemiology of CRAB in this setting contrasted with previously described clonal outbreaks in high-income countries, highlighting the importance of environmental CRAB reservoirs in ICU epidemiology and the unique challenges in containing the spread of CRAB in ICUs where this important multidrug-resistant pathogen is endemic.<br><br>FUNDING: This work was undertaken as part of the DETECTIVE research project funded by the Medical Research Council (MR/S013660/1), National Natural Science Foundation of China (81861138054, 32011530116, 31970128, 31770142), Zhejiang Province Medical Platform Backbone Talent Plan (2020RC075), and the National Key Research and Development Program of China grant (2018YFE0102100). W.v.S was also supported by a Wolfson Research Merit Award (WM160092).}, }
@article {pmid37693574, year = {2023}, author = {Fox, BW and Helf, MJ and Burkhardt, RN and Artyukhin, AB and Curtis, BJ and Palomino, DF and Chaturbedi, A and Tauffenberger, A and Wrobel, CJJ and Zhang, YK and Lee, SS and Schroeder, FC}, title = {Evolutionarily related host and microbial pathways regulate fat desaturation.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37693574}, issn = {2692-8205}, support = {P40 OD010440/OD/NIH HHS/United States ; R35 GM131877/GM/NIGMS NIH HHS/United States ; T32 GM138826/GM/NIGMS NIH HHS/United States ; }, abstract = {Fatty acid desaturation is central to metazoan lipid metabolism and provides building blocks of membrane lipids and precursors of diverse signaling molecules. Nutritional conditions and associated microbiota regulate desaturase expression[1-4], but the underlying mechanisms have remained unclear. Here, we show that endogenous and microbiota-dependent small molecule signals promote lipid desaturation via the nuclear receptor NHR-49/PPARα in C. elegans. Untargeted metabolomics of a β-oxidation mutant, acdh-11, in which expression of the stearoyl-CoA desaturase FAT-7/SCD1 is constitutively increased, revealed accumulation of a β-cyclopropyl fatty acid, becyp#1, that potently activates fat-7 expression via NHR-49. Biosynthesis of becyp#1 is strictly dependent on expression of cyclopropane synthase by associated bacteria, e.g., E. coli. Screening for structurally related endogenous metabolites revealed a β-methyl fatty acid, bemeth#1, whose activity mimics that of microbiota-dependent becyp#1, but is derived from a methyltransferase, fcmt-1, that is conserved across Nematoda and likely originates from bacterial cyclopropane synthase via ancient horizontal gene transfer. Activation of fat-7 expression by these structurally similar metabolites is controlled by distinct mechanisms, as microbiota-dependent becyp#1 is metabolized by a dedicated β-oxidation pathway, while the endogenous bemeth#1 is metabolized via α-oxidation. Collectively, we demonstrate that evolutionarily related biosynthetic pathways in metazoan host and associated microbiota converge on NHR-49/PPARα to regulate fat desaturation.}, }
@article {pmid37693541, year = {2023}, author = {Li, Z and Xue, AZ and Maeda, GP and Li, Y and Nabity, PD and Moran, NA}, title = {Phylloxera and aphids show distinct features of genome evolution despite similar reproductive modes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.08.28.555181}, pmid = {37693541}, issn = {2692-8205}, abstract = {Genomes of aphids (family Aphididae) show several unusual evolutionary patterns. In particular, within the XO sex determination system of aphids, the X chromosome exhibits a lower rate of interchromosomal rearrangements, fewer highly expressed genes, and faster evolution at nonsynonymous sites compared to the autosomes. In contrast, other hemipteran lineages have similar rates of interchromosomal rearrangement for autosomes and X chromosomes. One possible explanation for these differences is the aphid's life cycle of cyclical parthenogenesis, where multiple asexual generations alternate with one sexual generation. If true, we should see similar features in the genomes of Phylloxeridae, an outgroup of aphids which also undergoes cyclical parthenogenesis. To investigate this, we generated a chromosome-level assembly for the grape phylloxera, an agriculturally important species of Phylloxeridae, and identified its single X chromosome. We then performed synteny analysis using the phylloxerid genome and 30 high-quality genomes of aphids and other hemipteran species. Unexpectedly, we found that the phylloxera does not share aphids' patterns of chromosome evolution. By estimating interchromosomal rearrangement rates on an absolute time scale, we found that rates are elevated for aphid autosomes compared to their X chromosomes, but this pattern does not extend to the phylloxera branch. Potentially, the conservation of X chromosome gene content is due to selection on XO males that appear in the sexual generation. We also examined gene duplication patterns across Hemiptera and uncovered horizontal gene transfer events contributing to phylloxera evolution.}, }
@article {pmid37692203, year = {2023}, author = {Chang, H and Bai, J and Zhang, H and Huang, R and Chu, H and Wang, Q and Liu, H and Cheng, J and Jiang, H}, title = {Origin and evolution of the main starch biosynthetic enzymes.}, journal = {Synthetic and systems biotechnology}, volume = {8}, number = {3}, pages = {462-468}, pmid = {37692203}, issn = {2405-805X}, abstract = {Starch, a semi-crystalline energy storage form primarily found in plant plastids plays a crucial role in various food or no-food applications. Despite the starch biosynthetic pathway's main enzymes have been characterized, their origin and evolution remained a subject of debate. In this study, we conducted the comprehensive phylogenetic and structural analysis of three types of starch biosynthetic enzymes: starch synthase (SS), starch branching enzyme (SBE) and isoamylase-type debranching enzyme (ISA) from 51,151 annotated genomes. Our findings provide valuable insights into the possible scenario for the origin and evolution of the starch biosynthetic pathway. Initially, the ancestor of SBE can be traced back to an unidentified bacterium that existed before the formation of the last eukaryotic common ancestor (LECA) via horizontal gene transfer (HGT). This transfer event likely provided the eukaryote ancestor with the ability to synthesize glycogen. Furthermore, during the emergence of Archaeplastida, one clade of SS was transferred from Deltaproteobacteria by HGT, while ISA and the other clade of SS originated from Chlamydiae through endosymbiosis gene transfer (EGT). Both these transfer events collectively contributed to the establishment of the original starch biosynthetic pathway. Subsequently, after the divergence of Viridiplantae from Rhodophyta, all three enzymes underwent multiple duplications and N-terminus extension domain modifications, resulting in the formation of functionally specialized isoforms and ultimately leading to the complete starch biosynthetic pathway. By shedding light on the evolutionary origins of key enzymes involved in the starch biosynthetic pathway, this study provides important insights into the evolutionary events of plants.}, }
@article {pmid37690629, year = {2023}, author = {Haghjooy Javanmard, S and Rafiee, L and Bahri Najafi, M and Khorsandi, D and Hasan, A and Vaseghi, G and Makvandi, P}, title = {Microfluidic-based technologies in cancer liquid biopsy: Unveiling the role of horizontal gene transfer (HGT) materials.}, journal = {Environmental research}, volume = {238}, number = {Pt 1}, pages = {117083}, doi = {10.1016/j.envres.2023.117083}, pmid = {37690629}, issn = {1096-0953}, mesh = {Humans ; *Microfluidics ; *Neoplasms ; Gene Transfer, Horizontal ; Precision Medicine ; Liquid Biopsy ; DNA ; }, abstract = {Liquid biopsy includes the isolating and analysis of non-solid biological samples enables us to find new ways for molecular profiling, prognostic assessment, and better therapeutic decision-making in cancer patients. Despite the conventional theory of tumor development, a non-vertical transmission of DNA has been reported among cancer cells and between cancer and normal cells. The phenomenon referred to as horizontal gene transfer (HGT) has the ability to amplify the advancement of tumors by disseminating genes that encode molecules conferring benefits to the survival or metastasis of cancer cells. Currently, common liquid biopsy approaches include the analysis of extracellular vesicles (EVs) and tumor-free DNA (tfDNA) derived from primary tumors and their metastatic sites, which are well-known HGT mediators in cancer cells. Current technological and molecular advances expedited the high-throughput and high-sensitive HGT materials analyses by using new technologies, such as microfluidics in liquid biopsies. This review delves into the convergence of microfluidic-based technologies and the investigation of Horizontal Gene Transfer (HGT) materials in cancer liquid biopsy. The integration of microfluidics offers unprecedented advantages such as high sensitivity, rapid analysis, and the ability to analyze rare cell populations. These attributes are instrumental in detecting and characterizing CTCs, circulating nucleic acids, and EVs, which are carriers of genetic cargo that could potentially undergo HGT. The phenomenon of HGT in cancer has raised intriguing questions about its role in driving genomic diversity and acquired drug resistance. By leveraging microfluidic platforms, researchers have been able to capture and analyze individual cells or genetic material with enhanced precision, shedding light on the potential transfer of genetic material between cancer cells and surrounding stromal cells. Furthermore, the application of microfluidics in single-cell sequencing has enabled the elucidation of the genetic changes associated with HGT events, providing insights into the evolution of tumor genomes. This review also discusses the challenges and opportunities in studying HGT materials using microfluidic-based technologies. In conclusion, microfluidic-based technologies have significantly advanced the field of cancer liquid biopsy, enabling the sensitive and accurate detection of HGT materials. As the understanding of HGT's role in tumor evolution and therapy resistance continues to evolve, the synergistic integration of microfluidics and HGT research promises to provide valuable insights into cancer biology, with potential implications for precision oncology and therapeutic strategies.}, }
@article {pmid37689422, year = {2023}, author = {Hull, DM and Harrel, E and Harden, L and Thakur, S}, title = {Detection of resistance and virulence plasmids in Campylobacter coli and Campylobacter jejuni isolated from North Carolina food animal production, 2018-2019.}, journal = {Food microbiology}, volume = {116}, number = {}, pages = {104348}, doi = {10.1016/j.fm.2023.104348}, pmid = {37689422}, issn = {1095-9998}, mesh = {Animals ; Cattle ; Swine ; *Campylobacter coli/genetics ; *Campylobacter jejuni/genetics ; Virulence/genetics ; North Carolina ; Chickens ; *Campylobacter ; Virulence Factors/genetics ; Anti-Bacterial Agents/pharmacology ; Plasmids/genetics ; }, abstract = {Campylobacter remains the leading cause of bacterial foodborne illness in the U.S. and worldwide. Campylobacter plasmids may play a significant role in antimicrobial resistance (AMR) and virulence factor distribution, and potentially drive rapid adaptation. C. coli (n = 345) and C. jejuni (n = 199) isolates collected from live cattle, swine, turkey, and chickens, poultry carcasses at production, and retail meat in N.C. were analyzed to determine plasmid prevalence, extrachromosomal virulence and AMR genes, and the phylogeny of assembled plasmids. Putative plasmids ranging from <2 kb to 237kb were identified with virulence factors present in 66.1% (228/345) C. coli and 88.4% (176/199) C. jejuni plasmids (promoting adherence, invasion, exotoxin production, immune modulation, chemotaxis, mobility, and the type IV secretion system). AMR genes were identified in 21.2% (73/345) C. coli and 28.1% C. jejuni plasmids (conferring resistance to tetracyclines, aminoglycosides, beta-lactams, nucleosides, and lincosamides). Megaplasmids (>100 kb) were present in 25.7% (140/544) of the isolates and carried genes previously recognized to be involved with interspecies recombination. Our study highlights the extensive distribution and diversity of Campylobacter plasmids in food animal production and their role in the dissemination of biomedically important genes. Characterizing Campylobacter plasmids within the food animal production niche is important to understanding the epidemiology of potential emerging strains.}, }
@article {pmid37680975, year = {2023}, author = {Ashy, RA}, title = {Functional analysis of bacterial genes accidentally packaged in rhizospheric phageome of the wild plant species Abutilon fruticosum.}, journal = {Saudi journal of biological sciences}, volume = {30}, number = {10}, pages = {103789}, pmid = {37680975}, issn = {1319-562X}, abstract = {The study aimed to reveal the structure and function of phageome existing in soil rhizobiome of Abutilon fruticosum in order to detect accidentally-packaged bacterial genes that encode Carbohydrate-Active enZymes (or CAZymes) and those that confer antibiotic resistance (e.g., antibiotic resistance genes or ARGs). Highly abundant genes were shown to mainly exist in members of the genera Pseudomonas, Streptomyces, Mycobacterium and Rhodococcus. Enriched CAZymes belong to glycoside hydrolase families GH4, GH6, GH12, GH15 and GH43 and mainly function in D-glucose biosynthesis via 10 biochemical passages. Another enriched CAZyme, e.g., alpha-galactosidase, of the GH4 family is responsible for the wealth of different carbohydrate forms in rhizospheric soil sink of A. fruticosum. ARGs of this phageome include the soxR and OleC genes that participate in the "antibiotic efflux pump" resistance mechanism, the parY mutant gene that participates in the "antibiotic target alteration" mechanism and the arr-1, iri, and AAC(3)-Ic genes that participate in the "antibiotic inactivation" mechanism. It is claimed that the genera Streptomyces, which harbors phages with oleC and parY mutant genes, and Pseudomonas, which harbors phages with soxR and AAC(3)-Ic genes, are approaching multidrug resistance via newly disseminating phages. These ARGs inhibit many antibiotics including oleandomycin, tetracycline, rifampin and aminoglycoside. The study highlights the possibility of accidental packaging of these ARGs in soil phageome and the risk of their horizontal transfer to human gut pathogens through the food chain as detrimental impacts of soil phageome of A. fruticosum. The study also emphasizes the beneficial impacts of phageome on soil microbiome and plant interacting in storing carbohydrates in the soil sink for use by the two entities upon carbohydrate deprivation.}, }
@article {pmid37676703, year = {2023}, author = {Avontuur, JR and Wilken, PM and Palmer, M and Coetzee, MPA and Stępkowski, T and Venter, SN and Steenkamp, ET}, title = {Complex evolutionary history of photosynthesis in Bradyrhizobium.}, journal = {Microbial genomics}, volume = {9}, number = {9}, pages = {}, pmid = {37676703}, issn = {2057-5858}, mesh = {*Bradyrhizobium/genetics ; Photosynthesis/genetics ; }, abstract = {Bradyrhizobium comprises a diverse group of bacteria with various lifestyles. Although best known for their nodule-based nitrogen-fixation in symbiosis with legumes, a select group of bradyrhizobia are also capable of photosynthesis. This ability seems to be rare among rhizobia, and its origin and evolution in these bacteria remain a subject of substantial debate. Therefore, our aim here was to investigate the distribution and evolution of photosynthesis in Bradyrhizobium using comparative genomics and representative genomes from closely related taxa in the families Nitrobacteraceae, Methylobacteriaceae, Boseaceae and Paracoccaceae. We identified photosynthesis gene clusters (PGCs) in 25 genomes belonging to three different Bradyrhizobium lineages, notably the so-called Photosynthetic, B. japonicum and B. elkanii supergroups. Also, two different PGC architectures were observed. One of these, PGC1, was present in genomes from the Photosynthetic supergroup and in three genomes from a species in the B. japonicum supergroup. The second cluster, PGC2, was also present in some strains from the B. japonicum supergroup, as well as in those from the B. elkanii supergroup. PGC2 was largely syntenic to the cluster found in Rhodopseudomonas palustris and Tardiphaga . Bayesian ancestral state reconstruction unambiguously showed that the ancestor of Bradyrhizobium lacked a PGC and that it was acquired horizontally by various lineages. Maximum-likelihood phylogenetic analyses of individual photosynthesis genes also suggested multiple acquisitions through horizontal gene transfer, followed by vertical inheritance and gene losses within the different lineages. Overall, our findings add to the existing body of knowledge on Bradyrhizobium ’s evolution and provide a meaningful basis from which to explore how these PGCs and the photosynthesis itself impact the physiology and ecology of these bacteria.}, }
@article {pmid37670002, year = {2023}, author = {Natarajan, S and Pucker, B and Srivastava, S}, title = {Genomic and transcriptomic analysis of camptothecin producing novel fungal endophyte: Alternaria burnsii NCIM 1409.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {14614}, pmid = {37670002}, issn = {2045-2322}, mesh = {*Camptothecin ; *Endophytes ; Transcriptome ; Alternaria ; Genomics ; }, abstract = {Camptothecin is an important anticancer alkaloid produced by particular plant species. No suitable synthetic route has been established for camptothecin production yet, imposing a stress on plant-based production systems. Endophytes associated with these camptothecin-producing plants have been reported to also produce camptothecin and other high-value phytochemicals. A previous study identified a fungal endophyte Alternaria burnsii NCIM 1409, isolated from Nothapodytes nimmoniana, to be a sustainable producer of camptothecin. Our study provides key insights on camptothecin biosynthesis in this recently discovered endophyte. The whole genome sequence of A. burnsii NCIM 1409 was assembled and screened for biosynthetic gene clusters. Comparative studies with related fungi supported the identification of candidate genes involved in camptothecin synthesis and also helped to understand some aspects of the endophyte's defense against the toxic effects of camptothecin. No evidence for horizontal gene transfer of the camptothecin biosynthetic genes from the host plant to the endophyte was detected suggesting an independent evolution of the camptothecin biosynthesis in this fungus.}, }
@article {pmid37665285, year = {2024}, author = {Takahashi, T and Kim, H and Kim, HS and Kim, HS and Song, W and Kim, JS}, title = {Comparative Genomic Analysis of Staphylococcal Cassette Chromosome mec Type V Staphylococcus aureus Strains and Estimation of the Emergence of SCCmec V Clinical Isolates in Korea.}, journal = {Annals of laboratory medicine}, volume = {44}, number = {1}, pages = {47-55}, pmid = {37665285}, issn = {2234-3814}, mesh = {Humans ; Likelihood Functions ; *Methicillin-Resistant Staphylococcus aureus/genetics ; Phylogeny ; Staphylococcus aureus ; Genomics ; Staphylococcus ; Republic of Korea ; }, abstract = {BACKGROUND: Staphylococcal cassette chromosome mec type V (SCCmec V) methicillin-resistant Staphylococcus aureus (MRSA) has been recovered from patients and livestock. Using comparative genomic analyses, we evaluated the phylogenetic emergence of SCCmec V after transmission from overseas donor strains to Korean recipient strains.<br><br>METHODS: Sixty-three complete MRSA SCCmec V genomes (including six Korean clinical isolates) were used to construct a phylogenetic tree. Single-nucleotide polymorphisms were identified using Snippy, and a maximum-likelihood-based phylogenetic tree was constructed using RAxML. The possible emergence of the most common ancestor was estimated using BactDating. To estimate mecA horizontal gene transfer (HGT) events, Ranger-dtl was applied to 818 SCCmec V strains using publicly available whole-genome data.<br><br>RESULTS: The phylogenetic tree showed five major clades. German strains formed a major clade; their possible origin was traced to the 1980s. The emergence of Korean SCCmec V clinical isolates was traced to 2000-2010. mecA HGT events in Staphylococcus spp. were identified in seven strains. P7 (Hong Kong outbreak strain) served as the donor strain for two Korean sequence type (ST) 59 strains, whereas the other five recipient strains emerged from different SCCmec V donors.<br><br>CONCLUSIONS: Most Korean SCCmec V strains may have emerged during 2000-2010. A unique MRSA SCCmec V strain, ST72 (a Korean common type of community-associated MRSA), was also identified. The genomic dynamics of this clone with a zoonotic background should be monitored to accurately understand MRSA evolution.}, }
@article {pmid37664620, year = {2023}, author = {Mao, C and Li, Q and Komijani, M and Huang, J and Li, T}, title = {Metagenomic analysis reveals the dissemination mechanisms and risks of resistance genes in plateau lakes.}, journal = {iScience}, volume = {26}, number = {9}, pages = {107508}, pmid = {37664620}, issn = {2589-0042}, abstract = {Antibiotic resistance genes (ARGs) are emerging as environmental pollutants that can persist and disseminate in aquatic environments. Lakes, as important sources of freshwater, also serve as potential natural reservoirs of ARGs. In this study, we analyzed the distribution and potential risks of resistance genes in five typical freshwater lakes on the Yunnan-Guizhou Plateau. Our findings revealed that multidrug and MLS ARGs dominated in the studied lakes. Notably, while Lugu Lake exhibited higher abundance of ARGs, mobile genetic elements (MGEs), and metal resistance genes (MRGs), a greater resistome risk was observed in the eutrophic Xingyun Lake. The dissemination processes of ARGs and MRGs are primarily driven by microbial communities and the horizontal gene transfer via MGEs. Limnohabitans, Flavobacterium, and Acinetobacter were identified as key players in the dissemination of ARGs. Our study highlights the persistence of ARGs and provides valuable baseline data and risk assessment of ARGs in plateau freshwater lakes.}, }
@article {pmid37662302, year = {2023}, author = {Jeong, DE and Sundrani, S and Hall, RN and Krupovic, M and Koonin, EV and Fire, AZ}, title = {DNA polymerase diversity reveals multiple incursions of Polintons during nematode evolution.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.08.22.554363}, pmid = {37662302}, issn = {2692-8205}, abstract = {Polintons are dsDNA, virus-like self-synthesizing transposons widely found in eukaryotic genomes. Recent metagenomic discoveries of Polinton-like viruses are consistent with the hypothesis that Polintons invade eukaryotic host genomes through infectious viral particles. Nematode genomes contain multiple copies of Polintons and provide an opportunity to explore the natural distribution and evolution of Polintons during this process. We performed an extensive search of Polintons across nematode genomes, identifying multiple full-length Polinton copies in several species. We provide evidence of both ancient Polinton integrations and recent mobility in strains of the same nematode species. In addition to the major nematode Polinton family, we identified a group of Polintons that are overall closely related to the major family, but encode a distinct protein-primed B family DNA polymerase (pPolB) that is related to homologs from a different group of Polintons present outside of the Nematoda . Phylogenetic analyses on the pPolBs support the evolutionary scenarios in which these extrinsic pPolBs that seem to derive from Polinton families present in oomycetes and molluscs replaced the canonical pPolB in subsets of Polintons found in terrestrial and marine nematodes, respectively, suggesting inter-phylum horizontal gene transfers. The pPolBs of the terrestrial nematode and oomycete Polintons share a unique feature, an insertion of a HNH nuclease domain, whereas the pPolBs in the marine nematode Polintons share an insertion of a VSR nuclease domain with marine mollusc pPolBs. We hypothesize that horizontal gene transfer occurs among Polintons from widely different but cohabiting hosts.}, }
@article {pmid37662235, year = {2023}, author = {Pandey, T and Kalluraya, C and Wang, B and Xu, T and Huang, X and Guang, S and Daugherty, MD and Ma, DK}, title = {Acquired stress resilience through bacteria-to-nematode horizontal gene transfer.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37662235}, issn = {2692-8205}, support = {P40 OD010440/OD/NIH HHS/United States ; R35 GM133633/GM/NIGMS NIH HHS/United States ; R35 GM139618/GM/NIGMS NIH HHS/United States ; }, abstract = {Natural selection drives acquisition of organismal resilience traits to protect against adverse environments. Horizontal gene transfer (HGT) is an important evolutionary mechanism for the acquisition of novel traits, including metazoan acquisition of functions in immunity, metabolism, and reproduction via interdomain HGT (iHGT) from bacteria. We report that the nematode gene rml-3, which was acquired by iHGT from bacteria, enables exoskeleton resilience and protection against environmental toxins in C. elegans. Phylogenetic analysis reveals that diverse nematode RML-3 proteins form a single monophyletic clade most highly similar to bacterial enzymes that biosynthesize L-rhamnose to build cell wall polysaccharides. C. elegans rml-3 is regulated in developing seam cells by heat stress and stress-resistant dauer stage. Importantly, rml-3 deficiency impairs cuticle integrity, barrier functions and organismal stress resilience, phenotypes that are rescued by exogenous L-rhamnose. We propose that iHGT of an ancient bacterial rml-3 homolog enables L-rhamnose biosynthesis in nematodes that facilitates cuticle integrity and organismal resilience in adaptation to environmental stresses during evolution. These findings highlight the remarkable contribution of iHGT on metazoan evolution that is conferred by the domestication of bacterial genes.}, }
@article {pmid37662009, year = {2023}, author = {Li, Z and Zhou, X and Liao, D and Liu, R and Zhao, X and Wang, J and Zhong, Q and Zeng, Z and Peng, Y and Tan, Y and Yang, Z}, title = {Comparative genomics and DNA methylation analysis of Pseudomonas aeruginosa clinical isolate PA3 by single-molecule real-time sequencing reveals new targets for antimicrobials.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1180194}, pmid = {37662009}, issn = {2235-2988}, mesh = {*Pseudomonas aeruginosa/genetics ; DNA Methylation ; Phylogeny ; Genomics ; *Anti-Infective Agents ; DNA ; }, abstract = {INTRODUCTION: Pseudomonas aeruginosa (P.aeruginosa) is an important opportunistic pathogen with broad environmental adaptability and complex drug resistance. Single-molecule real-time (SMRT) sequencing technique has longer read-length sequences, more accuracy, and the ability to identify epigenetic DNA alterations.<br><br>METHODS: This study applied SMRT technology to sequence a clinical strain P. aeruginosa PA3 to obtain its genome sequence and methylation modification information. Genomic, comparative, pan-genomic, and epigenetic analyses of PA3 were conducted.<br><br>RESULTS: General genome annotations of PA3 were discovered, as well as information about virulence factors, regulatory proteins (RPs), secreted proteins, type II toxin-antitoxin (TA) pairs, and genomic islands. A genome-wide comparison revealed that PA3 was comparable to other P. aeruginosa strains in terms of identity, but varied in areas of horizontal gene transfer (HGT). Phylogenetic analysis showed that PA3 was closely related to P. aeruginosa 60503 and P. aeruginosa 8380. P. aeruginosa's pan-genome consists of a core genome of roughly 4,300 genes and an accessory genome of at least 5,500 genes. The results of the epigenetic analysis identified one main methylation sites, N6-methyladenosine (m6A) and 1 motif (CATNNNNNNNTCCT/AGGANNNNNNNATG). 16 meaningful methylated sites were picked. Among these, purH, phaZ, and lexA are of great significance playing an important role in the drug resistance and biological environment adaptability of PA3, and the targeting of these genes may benefit further antibacterial studies.<br><br>DISUCSSION: This study provided a detailed visualization and DNA methylation information of the PA3 genome and set a foundation for subsequent research into the molecular mechanism of DNA methyltransferase-controlled P. aeruginosa pathogenicity.}, }
@article {pmid37658677, year = {2023}, author = {Clark, JW}, title = {Genome evolution in plants and the origins of innovation.}, journal = {The New phytologist}, volume = {240}, number = {6}, pages = {2204-2209}, doi = {10.1111/nph.19242}, pmid = {37658677}, issn = {1469-8137}, support = {RPG-2019-004//Leverhulme Trust/ ; }, mesh = {*Plants/genetics ; *Evolution, Molecular ; Genome, Plant ; Gene Duplication ; Gene Transfer, Horizontal ; Phylogeny ; }, abstract = {Plant evolution has been characterised by a series of major novelties in their vegetative and reproductive traits that have led to greater complexity. Underpinning this diversification has been the evolution of the genome. When viewed at the scale of the plant kingdom, plant genome evolution has been punctuated by conspicuous instances of gene and whole-genome duplication, horizontal gene transfer and extensive gene loss. The periods of dynamic genome evolution often coincide with the evolution of key traits, demonstrating the coevolution of plant genomes and phenotypes at a macroevolutionary scale. Conventionally, plant complexity and diversity have been considered through the lens of gene duplication and the role of gene loss in plant evolution remains comparatively unexplored. However, in light of reductive evolution across multiple plant lineages, the association between gene loss and plant phenotypic diversity warrants greater attention.}, }
@article {pmid37657315, year = {2023}, author = {Zhao, Y and Hu, Z and Xie, H and Wu, H and Wang, Y and Xu, H and Liang, S and Zhang, J}, title = {Size-dependent promotion of micro(nano)plastics on the horizontal gene transfer of antibiotic resistance genes in constructed wetlands.}, journal = {Water research}, volume = {244}, number = {}, pages = {120520}, doi = {10.1016/j.watres.2023.120520}, pmid = {37657315}, issn = {1879-2448}, mesh = {*Gene Transfer, Horizontal ; *Wetlands ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Escherichia coli/genetics ; Polystyrenes ; }, abstract = {Constructed wetlands (CWs) have been identified as significant sources of micro(nano)plastics (MPs/NPs) and antibiotic resistance genes (ARGs) in aquatic environments. However, little is known about the impact of MPs/NPs exposure on horizontal gene transfer (HGT) of ARGs and shaping the corresponding ARG hosts' community. Herein, the contribution of polystyrene (PS) particles (control, 4 mm, 100 μm, and 100 nm) to ARG transfer was investigated by adding an engineered fluorescent Escherichia coli harboring RP4 plasmid-encoded ARGs into CWs. It was found MPs/NPs significantly promoted ARG transfer in a size-dependent manner in each CW medium (p < 0.05). The 100 μm-sized PS exhibited the most significant promotion of ARG transfer (p < 0.05), whereas 100 nm-sized PS induced limited promotion due to its inhibitory activity on microbes. The altered RP4-carrying bacterial communities suggested that MPs/NPs, especially 100 µm-PS, could recruit pathogenic and nitrifying bacteria to acquire ARGs. The increased sharing of RP4-carrying core bacteria in CW medium further suggested that ARGs can spread into CW microbiome using MPs/NPs as carriers. Overall, our results highlight the high risks of ARG dissemination induced by MPs/NPs exposure and emphasize the need for better control of plastic disposal to prevent the potential health threats.}, }
@article {pmid37653049, year = {2023}, author = {Johnson, ET and Bowman, MJ and Gomes, RP and Carneiro, LC and Dunlap, CA}, title = {Identification of 2,4-diacetylphloroglucinol production in the genus Chromobacterium.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {14292}, pmid = {37653049}, issn = {2045-2322}, mesh = {*Chromobacterium/genetics ; Phylogeny ; *Anti-Bacterial Agents/pharmacology ; Brazil ; Escherichia coli ; Pseudomonas ; }, abstract = {The compound 2,4-diacetylphloroglucinol (DAPG) is a broad-spectrum antibiotic that is primarily produced by Pseudomonas spp. DAPG plays an important role in the biocontrol disease suppressing activity of Pseudomonas spp. In the current study, we report the discovery of the DAPG biosynthetic cluster in strains of Chromobacterium vaccinii isolated from Brazilian aquatic environments and the distribution of the biosynthetic cluster in the Chromobacterium genus. Phylogenetic analysis of the phlD protein suggests the biosynthetic cluster probably entered the genus of Chromobacterium after a horizontal gene transfer event with a member of the Pseudomonas fluorescens group. We were able to detect trace amounts of DAPG in wild type cultures and confirm the function of the cluster with heterologous expression in Escherichia coli. In addition, we identified and verified the presence of other secondary metabolites in these strains. We also confirmed the ability of C. vaccinii strains to produce bioactive pigment violacein and bioactive cyclic depsipeptide FR900359. Both compounds have been reported to have antimicrobial and insecticidal activities. These compounds suggest strains of C. vaccinii should be further explored for their potential as biocontrol agents.}, }
@article {pmid37651790, year = {2023}, author = {Katsburg, M and Brombach, J and Hanke, D and Aubry, E and Lübke-Becker, A and Fulde, M}, title = {New variant strain of Streptococcus canis with Lancefield group C isolated from canine otitis externa.}, journal = {Veterinary microbiology}, volume = {285}, number = {}, pages = {109869}, doi = {10.1016/j.vetmic.2023.109869}, pmid = {37651790}, issn = {1873-2542}, mesh = {Dogs ; Animals ; *Streptococcal Infections/veterinary/microbiology ; *Otitis Externa/veterinary ; Streptococcus/genetics ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/veterinary ; *Dog Diseases/diagnosis/microbiology ; }, abstract = {Every basic course in microbiology teaches us, Streptococcus canis always tests positive for Lancefield group G. Surprisingly, we identified a strain of S. canis with Lancefield group C, cultured from a dog with otitis externa after lateral ear canal resection. Whole genome sequencing data and analysis points towards a horizontal gene transfer event between S. canis and S. dysgalactiae. Although these species are closely related, gene transfer in this region of the genome of S. canis has not been described before. The value of technologies as MALDI-TOF MS and sequencing in microbiological diagnostics will grow as more diverse streptococci arise that do not always conform anymore to the classical Lancefield group typing.}, }
@article {pmid37649002, year = {2023}, author = {Ye, J and Jin, L and Li, Y and Xu, H and Lin, Y and Zhou, T and Zheng, B and Wang, M and Wang, Z}, title = {Complete-genome sequencing and comparative genomic characterization of blaNDM-5 carrying Citrobacter freundii isolates from a patient with multiple infections.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {506}, pmid = {37649002}, issn = {1471-2164}, support = {82102457//the National Natural Science Foundation of China/ ; LQ22H200004//the Zhejiang Provincial Natural Science Foundation of China/ ; Y20210110//the Planned Science and Technology Project of Wenzhou/ ; 2019QD011//Start-up Funding for Talent Research Program in the First Affiliated Hospital of Wenzhou Medical University/ ; 2023RC046//the Zhejiang Provincial Science and Technology Plan Project of China/ ; 2022E10022//Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province/ ; }, mesh = {Humans ; *Citrobacter freundii/genetics ; Chromosome Mapping ; Conserved Sequence ; *Carbapenems/pharmacology/therapeutic use ; Escherichia coli ; Genomics ; }, abstract = {BACKGROUND: The emergence and wide spread of carbapenemase-producing Enterobacteriaceae (CPE) poses a growing threat to global public health. However, clinically derived carbapenemase-producing Citrobacter causing multiple infections has rarely been investigated. Here we first report the isolation and comparative genomics of two blaNDM-5 carrying Citrobacter freundii (C. freundii) isolates from a patient with bloodstream and urinary tract infections.<br><br>RESULTS: Antimicrobial susceptibility testing showed that both blaNDM-5 carrying C. freundii isolates were multidrug-resistant. Positive modified carbapenem inactivation method (mCIM) and EDTA-carbapenem inactivation method (eCIM) results suggested metallo-carbapenemase production. PCR and sequencing confirmed that both metallo-carbapenemase producers were blaNDM-5 positive. Genotyping and comparative genomics analyses revealed that both isolates exhibited a high level of genetic similarity. Plasmid analysis confirmed that the blaNDM-5 resistance gene is located on IncX3 plasmid with a length of 46,161 bp, and could successfully be transferred to the recipient Escherichia coli EC600 strain. A conserved structure sequence (ISAba125-IS5-blaNDM-5-trpF-IS26-umuD-ISKox3) was found in the upstream and downstream of the blaNDM-5 gene.<br><br>CONCLUSIONS: The data presented in this study showed that the conjugative blaNDM-5 plasmid possesses a certain ability to horizontal transfer. The dissemination of NDM-5-producing C. freundii isolates should be of close concern in future clinical surveillance. To our knowledge, this is the first study to characterize C. freundii strains carrying the blaNDM-5 gene from one single patient with multiple infections.}, }
@article {pmid37648730, year = {2023}, author = {Xiong, L and Li, Y and Yu, H and Wei, Y and Li, H and Ji, X}, title = {Whole genome analysis and cold adaptation strategies of Pseudomonas sivasensis W-6 isolated from the Napahai plateau wetland.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {14190}, pmid = {37648730}, issn = {2045-2322}, mesh = {*Wetlands ; *Bacteriophages ; Clustered Regularly Interspaced Short Palindromic Repeats ; Cold Temperature ; Pseudomonas/genetics ; }, abstract = {Microbial communities of wetlands play key roles in the earth's ecology and stability. To elucidate the cold adaptation mechanisms of bacteria in plateau wetlands, we conducted comparative genomic analyses of Pseudomonas sivasensis and closely related lineages. The genome of P. sivasensis W-6, a cold-adapted bacterium isolated from the Napahai plateau wetland, was sequenced and analyzed. The genome length was 6,109,123 bp with a G+C content of 59.5%. Gene prediction yielded 5360 protein-coding sequences, 70 tRNAs, 24 gene islands, and 2 CRISPR sequences. The isolate contained evidence of horizontal gene transfer events during its evolution. Two prophages were predicted and indicated that W-6 was a lysogen. The cold adaptation of the W-6 strain showed psychrophilic rather than psychrotrophic characteristics. Cold-adapted bacterium W-6 can utilize glycogen and trehalose as resources, associated with carbohydrate-active enzymes, and survive in a low-temperature environment. In addition, the cold-adapted mechanisms of the W-6 included membrane fluidity by changing the unsaturated fatty acid profile, the two-component regulatory systems, anti-sense transcription, the role played by rpsU genes in the translation process, etc. The genome-wide analysis of W-6 provided a deeper understanding of cold-adapted strategies of bacteria in environments. We elucidated the adaptive mechanism of the psychrophilic W-6 strain for survival in a cold environment, which provided a basis for further study on host-phage coevolution.}, }
@article {pmid37647945, year = {2023}, author = {Goodman, RN and Tansirichaiya, S and Roberts, AP}, title = {Development of pBACpAK entrapment vector derivatives to detect intracellular transfer of mobile genetic elements within chloramphenicol resistant bacterial isolates.}, journal = {Journal of microbiological methods}, volume = {213}, number = {}, pages = {106813}, doi = {10.1016/j.mimet.2023.106813}, pmid = {37647945}, issn = {1872-8359}, support = {MR/W030578/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Chloramphenicol/pharmacology ; *Escherichia coli ; Anti-Bacterial Agents/pharmacology ; Plasmids/genetics ; Interspersed Repetitive Sequences ; Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; }, abstract = {Antimicrobial resistance disseminates throughout bacterial populations via horizontal gene transfer, driven mainly by mobile genetic elements (MGEs). Entrapment vectors are key tools in determining MGE movement within a bacterial cell between different replicons or between sites within the same replicon. The pBACpAK entrapment vector has been previously used to study intracellular transfer in Gram-negative bacteria however since pBACpAK contains a chloramphenicol resistance gene, it cannot be used in bacterial isolates which are already resistant to chloramphenicol. Therefore, we developed new derivatives of the pBACpAK entrapment vector to determine intracellular transfer of MGEs in an Escherichia coli DH5α transconjugant containing the chloramphenicol resistance plasmid pD25466. The catA1 of pBACpAK was replaced by both mcr-1 in pBACpAK-COL and aph(3')-Ia in pBACpAK-KAN, allowing it to be used in chloramphenicol resistant strains. The plasmid constructs were verified and then used to transform the E. coli DH5α/pD25466 transconjugants in order to detect intracellular movement of the MGEs associated with the pD25466 plasmid. Here we report on the validation of the expanded suite of pBACpAK vectors which can be used to study the intracellular transfer of MGEs between, and within, replicons in bacteria with different antimicrobial resistance profiles.}, }
@article {pmid37645846, year = {2023}, author = {Youngblom, MA and Imhoff, MR and Smyth, LM and Mohamed, MA and Pepperell, CS}, title = {Portrait of a generalist bacterium: pathoadaptation, metabolic specialization and extreme environments shape diversity of Staphylococcus saprophyticus.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.08.18.553882}, pmid = {37645846}, issn = {2692-8205}, abstract = {UNLABELLED: Staphylococcus saprophyticus is a Gram-positive, coagulase-negative staphylococcus found in diverse environments including soil and freshwater, meat, and dairy foods. S. saprophyticus is also an important cause of urinary tract infections (UTIs) in humans, and mastitis in cattle. However, the genetic determinants of virulence have not yet been identified, and it remains unclear whether there are distinct sub-populations adapted to human and animal hosts. Using a diverse sample of S. saprophyticus isolates from food, animals, environmental sources, and human infections, we characterized the population structure and diversity of global populations of S. saprophyticus . We found that divergence of the two major clades of S. saprophyticus is likely facilitated by barriers to horizontal gene transfer (HGT) and differences in metabolism. Using genome-wide association study (GWAS) tools we identified the first Type VII secretion system (T7SS) described in S. saprophyticus and its association with bovine mastitis. Finally, we found that in general, strains of S. saprophyticus from different niches are genetically similar with the exception of built environments, which function as a 'sink' for S. saprophyticus populations. This work increases our understanding of the ecology of S. saprophyticus and of the genomics of bacterial generalists.<br><br>DATA SUMMARY: Raw sequencing data for newly sequenced S. saprophyticus isolates have been deposited to the NCBI SRA under the project accession PRJNA928770. A list of all genomes used in this work and their associated metadata are available in the supplementary material. Custom scripts used in the comparative genomics and GWAS analyses are available here: https://github.com/myoungblom/sapro_genomics .<br><br>IMPACT STATEMENT: It is not known whether human and cattle diseases caused by S. saprophyticus represent spillover events from a generalist adapted to survive in a range of environments, or whether the capacity to cause disease represents a specific adaptation. Seasonal cycles of S. saprophyticus UTIs and molecular epidemiological evidence suggest that these infections may be environmentally-acquired rather than via transmission from person to person. Using comparative genomics and genome wide association study tools, we found that S. saprophyticus appears adapted to inhabit a wide range of environments (generalist), with isolates from animals, food, natural environments and human infections being closely related. Bacteria that routinely switch environments, particularly between humans and animals, are of particular concern when it comes to the spread of antibiotic resistance from farm environments into human populations. This work provides a framework for comparative genomic analyses of bacterial generalists and furthers our understanding of how bacterial populations move between humans, animals, and the environment.}, }
@article {pmid37640834, year = {2023}, author = {van Dijk, B and Buffard, P and Farr, AD and Giersdorf, F and Meijer, J and Dutilh, BE and Rainey, PB}, title = {Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {90}, pmid = {37640834}, issn = {2730-6151}, abstract = {Microbial evolution is driven by rapid changes in gene content mediated by horizontal gene transfer (HGT). While mobile genetic elements (MGEs) are important drivers of gene flux, the nanobiome-the zoo of Darwinian replicators that depend on microbial hosts-remains poorly characterised. New approaches are necessary to increase our understanding beyond MGEs shaping individual populations, towards their impacts on complex microbial communities. A bioinformatic pipeline (xenoseq) was developed to cross-compare metagenomic samples from microbial consortia evolving in parallel, aimed at identifying MGE dissemination, which was applied to compost communities which underwent periodic mixing of MGEs. We show that xenoseq can distinguish movement of MGEs from demographic changes in community composition that otherwise confounds identification, and furthermore demonstrate the discovery of various unexpected entities. Of particular interest was a nanobacterium of the candidate phylum radiation (CPR) which is closely related to a species identified in groundwater ecosystems (Candidatus Saccharibacterium), and appears to have a parasitic lifestyle. We also highlight another prolific mobile element, a 313 kb plasmid hosted by a Cellvibrio lineage. The host was predicted to be capable of nitrogen fixation, and acquisition of the plasmid coincides with increased ammonia production. Taken together, our data show that new experimental strategies combined with bioinformatic analyses of metagenomic data stand to provide insight into the nanobiome as a driver of microbial community evolution.}, }
@article {pmid37634776, year = {2023}, author = {Zámocký, M and Ferianc, P}, title = {Discovering the deep evolutionary roots of serum amyloid A protein family.}, journal = {International journal of biological macromolecules}, volume = {252}, number = {}, pages = {126537}, doi = {10.1016/j.ijbiomac.2023.126537}, pmid = {37634776}, issn = {1879-0003}, mesh = {Animals ; *Serum Amyloid A Protein/genetics/metabolism ; Phylogeny ; *Bacteria/metabolism ; Genome, Bacterial ; Protein Isoforms/genetics ; }, abstract = {Deep evolutionary origin of the conserved animal serum amyloid A (SAA) apolipoprotein family leading to yet unknown highly similar SAA-like sequences occurring in certain bacterial genomes is demonstrated in this contribution. Horizontal gene transfer event of corresponding genes between gut bacteria and non-vertebrate animals was discovered in the reconstructed phylogenetic tree obtained with maximum likelihood and neighbor-joining methods, respectively. This detailed phylogeny based on totally 128 complete sequences comprised diverse serum amyloid A isoforms from various animal vertebrate and non-vertebrate phyla and also corresponding genes coding for highly similar proteins from animal gut bacteria. Typical largely conserved sequence motifs and a peculiar structural fold consisting mainly of four α-helices in a bundle within all reconstructed clades of the SAA protein family are discussed with respect to their supposed biological functions in various organisms that contain corresponding genes.}, }
@article {pmid37632379, year = {2023}, author = {Sabar, MA and Van Huy, T and Sugie, Y and Wada, H and Zhao, B and Matsuura, N and Ihara, M and Watanabe, T and Tanaka, H and Honda, R}, title = {Antimicrobial resistome and mobilome in the urban river affected by combined sewer overflows and wastewater treatment effluent.}, journal = {Journal of water and health}, volume = {21}, number = {8}, pages = {1032-1050}, doi = {10.2166/wh.2023.073}, pmid = {37632379}, issn = {1477-8920}, mesh = {Rivers ; *Anti-Infective Agents ; Anti-Bacterial Agents/pharmacology ; Macrolides ; *Microbiota ; }, abstract = {The dissemination of antimicrobial resistance in the environment is an emerging global health problem. Wastewater treatment effluent and combined sewer overflows (CSOs) are major sources of antimicrobial resistance in urban rivers. This study aimed to clarify the effect of municipal wastewater treatment effluent and CSO on antimicrobial resistance genes (ARGs), mobile gene elements, and the microbial community in an urban river. The ARG abundance per 16S-based microbial population in the target river was 0.37-0.54 and 0.030-0.097 during the CSO event and dry weather, respectively. During the CSO event, the antimicrobial resistome in the river shifted toward a higher abundance of ARGs to clinically important drug classes, including macrolide, fluoroquinolone, and β-lactam, whereas ARGs to sulfonamide and multidrug by efflux pump were relatively abundant in dry weather. The abundance of intI1 and tnpA genes were highly associated with the total ARG abundance, suggesting their potential application as an indicator for estimating resistome contamination. Increase of prophage during the CSO event suggested that impact of CSO has a greater potential for horizontal gene transfer (HGT) via transduction. Consequently, CSO not only increases the abundance of ARGs to clinically important antimicrobials but also possibly enhances potential of HGT in urban rivers.}, }
@article {pmid37632043, year = {2023}, author = {Kozlova, AP and Saksaganskaia, AS and Afonin, AM and Muntyan, VS and Vladimirova, ME and Dzyubenko, EA and Roumiantseva, ML}, title = {A Temperate Sinorhizobium Phage, AP-16-3, Closely Related to Phage 16-3: Mosaic Genome and Prophage Analysis.}, journal = {Viruses}, volume = {15}, number = {8}, pages = {}, pmid = {37632043}, issn = {1999-4915}, mesh = {Humans ; *Bacteriophages ; Prophages/genetics ; *Sinorhizobium ; *Siphoviridae ; Lysogeny ; }, abstract = {Soil Sinorhizobium phage AP-16-3, a strain phylogenetically close to Rhizobium phage 16-3, was isolated in a mountainous region of Dagestan, belonging to the origin of cultivated plants in the Caucasus, according to Vavilov N.I. The genome of phage AP-16-3 is 61 kbp in size and contains 62 ORFs, of which 42 ORFs have homologues in the genome of Rhizobium phage 16-3, which was studied in the 1960s-1980s. A search for Rhizobium phage 16-3-related sequences was performed in the genomes of modern strains of root nodule bacteria belonging to different species, genera, and families. A total of 43 prophages of interest were identified out of 437 prophages found in the genomes of 42 strains, of which 31 belonged to Sinorhizobium meliloti species. However, almost all of the mentioned prophages contained single ORFs, and only two prophages contained 51 and 39 ORFs homologous to phages related to 16-3. These prophages were detected in S. meliloti NV1.1.1 and Rh. leguminosarum OyaliB strains belonging to different genera; however, the similarity level of these two prophages did not exceed 14.7%. Analysis of the orphan genes in these prophages showed that they encoded predominantly virion structural elements, but also enzymes and an extensive group of hypothetical proteins belonging to the L, S, and E regions of viral genes of phage 16-3. The data obtained indicate that temperate phages related to 16-3 had high infectivity against nodule bacteria and participated in intragenomic recombination events involving other phages, and in horizontal gene transfer between rhizobia of different genera. According to the data obtained, it is assumed that the repetitive lysogenic cycle of temperate bacteriophages promotes the dissolution of the phage genetic material in the host bacterial genome, and radical updating of phage and host bacterial genomes takes place.}, }
@article {pmid37627664, year = {2023}, author = {Bonsaglia, ECR and Calvo, GH and Sordelli, DO and Silva, NCC and Rall, VLM and Casas, A and Buzzola, F}, title = {The Impact of Low-Level Benzalkonium Chloride Exposure on Staphylococcus spp. Strains and Control by Photoinactivation.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {8}, pages = {}, pmid = {37627664}, issn = {2079-6382}, support = {PICT2019-2883//Agencia Nacional de Promoci&#xf3;n de la Ciencia y Tecnolog&#xed;a (ANPCyT)/ ; PIP2021-11220200102843CO and PUE085//CONICET/ ; }, abstract = {Exposure of bacteria to low concentrations of biocides can facilitate horizontal gene transfer, which may lead to bacterial adaptive responses and resistance to antimicrobial agents. The emergence of antibacterial resistance not only poses a significant concern to the dairy industry but also adds to the complexity and cost of mastitis treatment. This study was aimed to evaluate how selective stress induced by benzalkonium chloride (BC) promotes antibiotic non-susceptibility in Staphylococcus spp. In addition, we investigated the efficacy of photodynamic inactivation (PDI) in both resistant and susceptible strains. The study determined the minimum inhibitory concentration (MIC) of BC using the broth microdilution method for different Staphylococcus strains. The experiments involved pairing strains carrying the qacA/qacC resistance genes with susceptible strains and exposing them to subinhibitory concentrations of BC for 72 h. The recovered isolates were tested for MIC BC and subjected to disc diffusion tests to assess changes in susceptibility patterns. The results demonstrated that subinhibitory concentrations of BC could select strains with reduced susceptibility and antibiotic resistance, particularly in the presence of S. pasteuri. The results of PDI mediated by toluidine blue (100 µM) followed by 60 min irradiation (total light dose of 2.5 J/cm[2]) were highly effective, showing complete inactivation for some bacterial strains and a reduction of up to 5 logs in others.}, }
@article {pmid37616556, year = {2023}, author = {Farrell, AA and Nesbø, CL and Zhaxybayeva, O}, title = {Early Divergence and Gene Exchange Highways in the Evolutionary History of Mesoaciditogales.}, journal = {Genome biology and evolution}, volume = {15}, number = {9}, pages = {}, pmid = {37616556}, issn = {1759-6653}, mesh = {Phylogeny ; *Biological Evolution ; *Bacteria ; Archaea ; Acclimatization ; }, abstract = {The placement of a nonhyperthermophilic order Mesoaciditogales as the earliest branching clade within the Thermotogota phylum challenges the prevailing hypothesis that the last common ancestor of Thermotogota was a hyperthermophile. Yet, given the long branch leading to the only two Mesoaciditogales described to date, the phylogenetic position of the order may be due to the long branch attraction artifact. By testing various models and applying data recoding in phylogenetic reconstructions, we observed that early branching of Mesoaciditogales within Thermotogota is strongly supported by the conserved marker genes assumed to be vertically inherited. However, based on the taxonomic content of 1,181 gene families and a phylogenetic analysis of 721 gene family trees, we also found that a substantial number of Mesoaciditogales genes are more closely related to species from the order Petrotogales. These genes contribute to coenzyme transport and metabolism, fatty acid biosynthesis, genes known to respond to heat and cold stressors, and include many genes of unknown functions. The Petrotogales comprise moderately thermophilic and mesophilic species with similar temperature tolerances to that of Mesoaciditogales. Our findings hint at extensive horizontal gene transfer (HGT) between, or parallel independent gene gains by, the two ecologically similar lineages and suggest that the exchanged genes may be important for adaptation to comparable temperature niches.}, }
@article {pmid37611393, year = {2023}, author = {Deng, WK and He, JL and Chen, JY and Wu, RT and Xing, SC and Liao, XD}, title = {Effects of microplastics on functional genes related to CH4 and N2O metabolism in bacteriophages during manure composting and its planting applications.}, journal = {Journal of hazardous materials}, volume = {460}, number = {}, pages = {132288}, doi = {10.1016/j.jhazmat.2023.132288}, pmid = {37611393}, issn = {1873-3336}, mesh = {*Composting ; *Greenhouse Gases ; Manure ; Microplastics ; Plastics ; *Bacteriophages/genetics ; Soil ; }, abstract = {Microplastics (MPs), as a new type of pollutant, widely exist in livestock and poultry breeding and agricultural soils. However, research on MPs pollution on greenhouse gas emissions in combined planting and breeding systems is lacking, especially from the perspective of phage horizontal gene transfer. Therefore, this paper explores the effects of MPs on functional genes related to CH4 and N2O metabolism in bacteriophages during manure composting and its planting applications. The results of the study indicated that the addition of MPs had an impact on both the physicochemical properties and microbial community structure of manure during the composting process and on the compost-applied rhizosphere soil of lactuca (Lactuca sativa). Specifically, on day 7 of composting, mcrA/pmoA and (nirS+nirK) levels in bacteria in the MP group significantly increased. Additionally, it was observed that the MP group had higher average temperatures during the high-temperature period of composting, which led to a rapid reduction in phages. However, the phage levels quickly recovered during the cooling period. Furthermore, the addition of MPs to the rhizosphere soil resulted in higher levels of nirK. These changes may affect greenhouse gas emissions.}, }
@article {pmid37610250, year = {2023}, author = {Zhao, Y and Kuang, W and An, Q and Li, J and Wang, Y and Deng, Z}, title = {Cryo-EM structures of African swine fever virus topoisomerase.}, journal = {mBio}, volume = {14}, number = {5}, pages = {e0122823}, pmid = {37610250}, issn = {2150-7511}, mesh = {Swine ; Animals ; *African Swine Fever Virus ; *African Swine Fever ; Cryoelectron Microscopy ; DNA Topoisomerases, Type II/genetics ; Catalytic Domain ; Saccharomyces cerevisiae/metabolism ; }, abstract = {African swine fever virus (ASFV) is a highly contagious virus that causes lethal hemorrhagic diseases known as African swine fever (ASF) with a case fatality rate of 100%. There is an urgent need to develop anti-ASFV drugs. We determine the first high-resolution structures of viral topoisomerase ASFV P1192R in both the closed and open C-gate forms. P1192R shows a similar overall architecture with eukaryotic and prokaryotic type II topoisomerases, which have been successful targets of many antimicrobials and anticancer drugs, with the most similarity to yeast topo II. P1192R also exhibits differences in the details of active site configuration, which are important to enzyme activity. These two structures offer useful structural information for antiviral drug design and provide structural evidence to support that eukaryotic type IIA topoisomerase likely originated from horizontal gene transfer from the virus.}, }
@article {pmid37609252, year = {2023}, author = {Hsu, TY and Nzabarushimana, E and Wong, D and Luo, C and Beiko, RG and Langille, M and Huttenhower, C and Nguyen, LH and Franzosa, EA}, title = {Profiling novel lateral gene transfer events in the human microbiome.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37609252}, issn = {2692-8205}, support = {K23 DK125838/DK/NIDDK NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; T32 CA009001/CA/NCI NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; }, abstract = {Lateral gene transfer (LGT) is an important mechanism for genome diversification in microbial populations, including the human microbiome. While prior work has surveyed LGT events in human-associated microbial isolate genomes, the scope and dynamics of novel LGT events arising in personal microbiomes are not well understood, as there are no widely adopted computational methods to detect, quantify, and characterize LGT from complex microbial communities. We addressed this by developing, benchmarking, and experimentally validating a computational method (WAAFLE) to profile novel LGT events from assembled metagenomes. Applying WAAFLE to >2K human metagenomes from diverse body sites, we identified >100K putative high-confidence but previously uncharacterized LGT events (~2 per assembled microbial genome-equivalent). These events were enriched for mobile elements (as expected), as well as restriction-modification and transport functions typically associated with the destruction of foreign DNA. LGT frequency was quantifiably influenced by biogeography, the phylogenetic similarity of the involved taxa, and the ecological abundance of the donor taxon. These forces manifest as LGT networks in which hub species abundant in a community type donate unequally with their close phylogenetic neighbors. Our findings suggest that LGT may be a more ubiquitous process in the human microbiome than previously described. The open-source WAAFLE implementation, documentation, and data from this work are available at http://huttenhower.sph.harvard.edu/waafle.}, }
@article {pmid37605076, year = {2023}, author = {Baig, MIR and Kadu, P and Bawane, P and Nakhate, KT and Yele, S and Ojha, S and Goyal, SN}, title = {Mechanisms of emerging resistance associated with non-antibiotic antimicrobial agents: a state-of-the-art review.}, journal = {The Journal of antibiotics}, volume = {76}, number = {11}, pages = {629-641}, pmid = {37605076}, issn = {1881-1469}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria ; *Anti-Infective Agents/pharmacology ; *Disinfectants/pharmacology ; Drug Resistance, Bacterial/genetics ; }, abstract = {Although the development of resistance by microorganisms to antimicrobial drugs has been recognized as a global public health concern, the contribution of various non-antibiotic antimicrobial agents to the development of antimicrobial resistance (AMR) remains largely neglected. The present review discusses various chemical substances and factors other than typical antibiotics, such as preservatives, disinfectants, biocides, heavy metals and improper chemical sterilization that contribute to the development of AMR. Furthermore, it encompasses the mechanisms like co-resistance and co-selection, horizontal gene transfer, changes in the composition and permeability of cell membrane, efflux pumps, transposons, biofilm formation and enzymatic degradation of antimicrobial chemicals which underlie the development of resistance to various non-antibiotic antimicrobial agents. In addition, the review addresses the resistance-associated changes that develops in microorganisms due to these agents, which ultimately contribute to the development of resistance to antibiotics. In order to prevent the indiscriminate use of chemical substances and create novel therapeutic agents to halt resistance development, a more holistic scientific approach might provide diversified views on crucial factors contributing to the persistence and spread of AMR. The review illustrates the common and less explored mechanisms contributing directly or indirectly to the development of AMR by non-antimicrobial agents that are commonly used.}, }
@article {pmid37595132, year = {2023}, author = {Kobayashi, N and Dang, TA and Pham, KTM and Gómez Luciano, LB and Van Vu, B and Izumitsu, K and Shimizu, M and Ikeda, KI and Li, WH and Nakayashiki, H}, title = {Horizontally Transferred DNA in the Genome of the Fungus Pyricularia oryzae is Associated With Repressive Histone Modifications.}, journal = {Molecular biology and evolution}, volume = {40}, number = {9}, pages = {}, pmid = {37595132}, issn = {1537-1719}, mesh = {*Histone Code ; Histones/genetics ; Phylogeny ; DNA ; *Ascomycota/genetics ; Triticum ; }, abstract = {Horizontal gene transfer (HGT) is a means of exchanging genetic material asexually. The process by which horizontally transferred genes are domesticated by the host genome is of great interest but is not well understood. In this study, we determined the telomere-to-telomere genome sequence of the wheat-infecting Pyricularia oryzae strain Br48. SNP analysis indicated that the Br48 strain is a hybrid of wheat- and Brachiaria-infecting strains by a sexual or parasexual cross. Comparative genomic analysis identified several megabase-scale "insertions" in the Br48 genome, some of which were possibly gained by HGT-related events from related species, such as P. pennisetigena or P. grisea. Notably, the mega-insertions often contained genes whose phylogeny is not congruent with the species phylogeny. Moreover, some of the genes have a close homolog even in distantly related organisms, such as basidiomycetes or prokaryotes, implying the involvement of multiple HGT events. Interestingly, the levels of the silent epigenetic marks H3K9me3 and H3K27me3 in a genomic region tended to be negatively correlated with the phylogenetic concordance of genes in the same region, suggesting that horizontally transferred DNA is preferentially targeted for epigenetic silencing. Indeed, the putative HGT-derived genes were activated when MoKmt6, the gene responsible for H3K27me3 modification, was deleted. Notably, these genes also tended to be up-regulated during infection, suggesting that they are now under host control and have contributed to establishing a fungal niche. In conclusion, this study suggests that epigenetic modifications have played an important role in the domestication of HGT-derived genes in the P. oryzae genome.}, }
@article {pmid37594001, year = {2023}, author = {Yang, C and Xiang, Y and Qiu, S}, title = {Resistance in Enteric Shigella and nontyphoidal Salmonella : emerging concepts.}, journal = {Current opinion in infectious diseases}, volume = {36}, number = {5}, pages = {360-365}, pmid = {37594001}, issn = {1473-6527}, mesh = {Humans ; *Azithromycin/pharmacology/therapeutic use ; Colistin ; *Shigella/genetics ; Salmonella/genetics ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Ciprofloxacin/pharmacology/therapeutic use ; }, abstract = {PURPOSE OF REVIEW: The emergence of globally resistant enteric Shigella and nontyphoidal Salmonella strains (NTS) has limited the selection of effective drugs, which has become a major challenge for the treatment of infections. The purpose of this review is to provide the current opinion on the antimicrobial-resistant enteric Shigella and nontyphoidal Salmonella .<br><br>RECENT FINDINGS: Enteric Shigella and NTS are resistant to almost all classes of antimicrobials in recent years. Those with co-resistance to ciprofloxacin, azithromycin and ceftriaxone, the first-line antibiotics for the treatment of infectious diarrhoea have emerged worldwide. Some of them have caused interregional and international spread by travel, trade, MSM, and polluted water sources. Several strains have even developed resistance to colistin, the last-resort antibiotic used for treatment of multidrug-resistant Gram-negative bacteria infections.<br><br>SUMMARY: The drug resistance of enteric Shigella and NTS is largely driven by the use of antibiotics and horizontal gene transfer of mobile genetic elements. These two species show various drug resistance patterns in different regions and serotypes. Hence treatment decisions for Shigella and Salmonella infections need to take into consideration prevalent antimicrobial drug resistance patterns. It is worth noting that the resistance genes such as blaCTX,mph, ermB , qnr and mcr , which can cause resistance to ciprofloxacin, cephalosporin, azithromycin and colistin are widespread because of transmission by IncFII, IncI1, IncI2 and IncB/O/K/Z plasmids. Therefore, continuous global monitoring of resistance in Shigella and Salmonella is imperative.}, }
@article {pmid37592233, year = {2023}, author = {Zhang, X and Xiao, L and Liu, J and Tian, Q and Xie, J}, title = {Trade-off in genome turnover events leading to adaptive evolution of Microcystis aeruginosa species complex.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {462}, pmid = {37592233}, issn = {1471-2164}, support = {32101368//National Natural Science Foundation of China/ ; 2022YFE0119600//National Key Research and Development Program of China/ ; }, mesh = {*Microcystis/genetics ; Genome-Wide Association Study ; *Bacteriophages ; Energy Metabolism ; Evolution, Molecular ; }, abstract = {BACKGROUND: Numerous studies in the past have expanded our understanding of the genetic differences of global distributed cyanobacteria that originated around billions of years ago, however, unraveling how gene gain and loss drive the genetic evolution of cyanobacterial species, and the trade-off of these evolutionary forces are still the central but poorly understood issues.<br><br>RESULTS: To delineate the contribution of gene flow in mediating the hereditary differentiation and shaping the microbial evolution, a global genome-wide study of bloom-forming cyanobacterium, Microcystis aeruginosa species complex, provided robust evidence for genetic diversity, reflected by enormous variation in gene repertoire among various strains. Mathematical extrapolation showed an 'open' microbial pan-genome of M. aeruginosa species, since novel genes were predicted to be introduced after new genomes were sequenced. Identification of numerous horizontal gene transfer's signatures in genome regions of interest suggested that genome expansion via transformation and phage-mediated transduction across bacterial lineage as an evolutionary route may contribute to the differentiation of Microcystis functions (e.g., carbohydrate metabolism, amino acid metabolism, and energy metabolism). Meanwhile, the selective loss of some dispensable genes at the cost of metabolic versatility is as a mean of adaptive evolution that has the potential to increase the biological fitness.<br><br>CONCLUSIONS: Now that the recruitment of novel genes was accompanied by a parallel loss of some other ones, a trade-off in gene content may drive the divergent differentiation of M. aeruginosa genomes. Our study provides a genetic framework for the evolution of M. aeruginosa species and illustrates their possible evolutionary patterns.}, }
@article {pmid37586197, year = {2023}, author = {Shen, C and He, M and Zhang, J and Liu, J and Su, J and Dai, J}, title = {Effects of the coexistence of antibiotics and heavy metals on the fate of antibiotic resistance genes in chicken manure and surrounding soils.}, journal = {Ecotoxicology and environmental safety}, volume = {263}, number = {}, pages = {115367}, doi = {10.1016/j.ecoenv.2023.115367}, pmid = {37586197}, issn = {1090-2414}, mesh = {Animals ; Female ; Anti-Bacterial Agents/pharmacology ; Chickens/genetics ; Manure/microbiology ; Soil/chemistry ; Genes, Bacterial ; *Metals, Heavy/analysis ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; *Chlortetracycline ; Soil Microbiology ; }, abstract = {Both heavy metals and antibiotics exert selection pressure on bacterial resistance, and as they are commonly co-contaminated in the environment, they may play a larger role in bacterial resistance. This study examined how breeding cycles affect antibiotic resistance genes (ARGs) in chicken manure and the surrounding topsoils at 20, 50, 100, 200, and 300 m from twelve typical laying hen farms in the Ningxia Hui Autonomous Region of northwest China. Six antibiotics, seven heavy metals, ten mobile genetic elements (MGEs), and microbial community affected the ARGs profile in chicken dung and soil samples. Tetracycline antibiotic residues were prevalent in chicken manure, as were relatively high content of aureomycin during each culture period. Zinc (Zn) content was highest among the seven heavy metals in chicken feces. Chicken dung also enriched aminoglycosides, MLSB, and tetracycline ARGs, notably during brooding and high production. The farm had a minimal influence on antibiotics in the surrounding soil, but its effect on ARGs and MGEs closer to the farm (50 m) was stronger, and several ARGs and MGEs increased with distance. Manure microbial composition differed dramatically throughout breeding cycles and sampling distances. ARGs were more strongly related with antibiotics and heavy metals in manure than soil, whereas MGEs were the reverse. Antibiotics, heavy metals, MGEs, and bacteria in manure accounted 12.28%, 22.25%, 0.74%, and 0.19% of ARGs composition variance, respectively, according to RDA and VPA. Bacteria (2.89%) and MGEs (2.82%) only affected soil ARGs composition. These findings showed that heavy metals and antibiotics are the main factors affecting faecal ARGs and bacteria and MGEs soil ARGs. This paper includes antibiotic resistance data for large-scale laying hen husbandry in northwest China and a theoretical framework for decreasing antibiotic resistance.}, }
@article {pmid37584599, year = {2023}, author = {Mi-Ichi, F and Tsugawa, H and Yoshida, H and Arita, M}, title = {Unique features of Entamoeba histolytica glycerophospholipid metabolism; has the E. histolytica lipid metabolism network evolved through gene loss and gain to enable parasitic life cycle adaptation?.}, journal = {mSphere}, volume = {8}, number = {5}, pages = {e0017423}, pmid = {37584599}, issn = {2379-5042}, mesh = {Animals ; Humans ; *Entamoeba histolytica/genetics ; *Parasites ; Lipid Metabolism ; Life Cycle Stages ; Glycerophospholipids/metabolism ; }, abstract = {Entamoeba histolytica, a protozoan parasite, causes amoebiasis, which is a global public health problem. During the life cycle of this parasite, the properties of the cell membrane are changed markedly. To clarify the mechanism of membrane lipid changes, we exploited state-of-the-art untargeted lipidomic analysis, and atypical features of glycerophospholipids, lysoglycerophospholipids, and sphingolipids were observed compared with human equivalents. Here, we overview an entire E. histolytica glycerophospholipid metabolic pathway based on re-evaluated whole lipidome and genome along with the results of metabolic labeling experiments. We also discuss whether the E. histolytica lipid metabolism network, including the glycerophospholipid metabolic pathway, has unique features necessary for parasitic life cycle adaptation through gene loss and/or gain, and raise important questions involving biochemistry, molecular cell biology, and physiology underlying this network. Answering these questions will advance the understanding of Entamoeba physiology and will provide potential targets to develop new anti-amoebiasis drugs.}, }
@article {pmid37584505, year = {2024}, author = {Boyer, C and Lefeuvre, P and Richard, D and Lobin, KK and Pruvost, O}, title = {Complete Genome Sequence of a Copper-Resistant Xanthomonas campestris pv. campestris Strain Isolated from Broccoli in Mauritius Suggests Adaptive Gene Gain Through Horizontal Gene Transfer.}, journal = {Phytopathology}, volume = {114}, number = {2}, pages = {328-333}, doi = {10.1094/PHYTO-05-23-0177-SC}, pmid = {37584505}, issn = {0031-949X}, mesh = {*Brassica ; Copper ; *Xanthomonas campestris/genetics ; Gene Transfer, Horizontal ; Mauritius ; Plant Diseases ; }, abstract = {Bacterial adaptation is facilitated by the presence of mobile genetic elements and horizontal gene transfer of genes, such as those coding for virulence factors or resistance to antimicrobial compounds. A hybrid assembly of Nanopore MinIon long-read and Illumina short-read data was produced from a copper-resistant Xanthomonas campestris pv. campestris strain isolated from symptomatic broccoli leaves in Mauritius. We obtained a 5.2-Mb high-quality chromosome and no plasmid. We found four genomic islands, three of which were characterized as integrative conjugative elements or integrative mobilizable elements. These genomic islands carried type III effectors and the copper resistance copLABMGF system involved in pathogenicity and environmental adaptation, respectively.}, }
@article {pmid37582866, year = {2023}, author = {}, title = {Horizontal gene transfer explains unusual traits of Armillaria fungi.}, journal = {Nature microbiology}, volume = {8}, number = {9}, pages = {1617-1618}, pmid = {37582866}, issn = {2058-5276}, mesh = {*Armillaria/genetics ; Gene Transfer, Horizontal ; Fungi/genetics ; }, }
@article {pmid37578142, year = {2023}, author = {Luo, G and Liang, B and Cui, H and Kang, Y and Zhou, X and Tao, Y and Lu, L and Fan, L and Guo, J and Wang, A and Gao, SH}, title = {Determining the Contribution of Micro/Nanoplastics to Antimicrobial Resistance: Challenges and Perspectives.}, journal = {Environmental science &amp; technology}, volume = {57}, number = {33}, pages = {12137-12152}, doi = {10.1021/acs.est.3c01128}, pmid = {37578142}, issn = {1520-5851}, mesh = {*Anti-Bacterial Agents ; *Drug Resistance, Bacterial/genetics ; Microplastics ; Plastics ; Gene Transfer, Horizontal ; }, abstract = {Microorganisms colonizing the surfaces of microplastics form a plastisphere in the environment, which captures miscellaneous substances. The plastisphere, owning to its inherently complex nature, may serve as a "Petri dish" for the development and dissemination of antibiotic resistance genes (ARGs), adding a layer of complexity in tackling the global challenge of both microplastics and ARGs. Increasing studies have drawn insights into the extent to which the proliferation of ARGs occurred in the presence of micro/nanoplastics, thereby increasing antimicrobial resistance (AMR). However, a comprehensive review is still lacking in consideration of the current increasingly scattered research focus and results. This review focuses on the spread of ARGs mediated by microplastics, especially on the challenges and perspectives on determining the contribution of microplastics to AMR. The plastisphere accumulates biotic and abiotic materials on the persistent surfaces, which, in turn, offers a preferred environment for gene exchange within and across the boundary of the plastisphere. Microplastics breaking down to smaller sizes, such as nanoscale, can possibly promote the horizontal gene transfer of ARGs as environmental stressors by inducing the overgeneration of reactive oxygen species. Additionally, we also discussed methods, especially quantitatively comparing ARG profiles among different environmental samples in this emerging field and the challenges that multidimensional parameters are in great necessity to systematically determine the antimicrobial dissemination risk in the plastisphere. Finally, based on the biological sequencing data, we offered a framework to assess the AMR risks of micro/nanoplastics and biocolonizable microparticles that leverage multidimensional AMR-associated messages, including the ARGs' abundance, mobility, and potential acquisition by pathogens.}, }
@article {pmid37577532, year = {2023}, author = {Wolters, JF and LaBella, AL and Opulente, DA and Rokas, A and Hittinger, CT}, title = {Mitochondrial Genome Diversity across the Subphylum Saccharomycotina.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37577532}, issn = {2692-8205}, support = {R01 AI153356/AI/NIAID NIH HHS/United States ; T32 HG002760/HG/NHGRI NIH HHS/United States ; }, abstract = {Eukaryotic life depends on the functional elements encoded by both the nuclear genome and organellar genomes, such as those contained within the mitochondria. The content, size, and structure of the mitochondrial genome varies across organisms with potentially large implications for phenotypic variance and resulting evolutionary trajectories. Among yeasts in the subphylum Saccharomycotina, extensive differences have been observed in various species relative to the model yeast Saccharomyces cerevisiae, but mitochondrial genome sampling across many groups has been scarce, even as hundreds of nuclear genomes have become available. By extracting mitochondrial assemblies from existing short-read genome sequence datasets, we have greatly expanded both the number of available genomes and the coverage across sparsely sampled clades. Comparison of 353 yeast mitochondrial genomes revealed that, while size and GC content were fairly consistent across species, those in the genera Metschnikowia and Saccharomyces trended larger, while several species in the order Saccharomycetales, which includes S. cerevisiae, exhibited lower GC content. Extreme examples for both size and GC content were scattered throughout the subphylum. All mitochondrial genomes shared a core set of protein-coding genes for Complexes III, IV, and V, but they varied in the presence or absence of mitochondrially-encoded canonical Complex I genes. We traced the loss of Complex I genes to a major event in the ancestor of the orders Saccharomycetales and Saccharomycodales, but we also observed several independent losses in the orders Phaffomycetales, Pichiales, and Dipodascales. In contrast to prior hypotheses based on smaller-scale datasets, comparison of evolutionary rates in protein-coding genes showed no bias towards elevated rates among aerobically fermenting (Crabtree/Warburg-positive) yeasts. Mitochondrial introns were widely distributed, but they were highly enriched in some groups. The majority of mitochondrial introns were poorly conserved within groups, but several were shared within groups, between groups, and even across taxonomic orders, which is consistent with horizontal gene transfer, likely involving homing endonucleases acting as selfish elements. As the number of available fungal nuclear genomes continues to expand, the methods described here to retrieve mitochondrial genome sequences from these datasets will prove invaluable to ensuring that studies of fungal mitochondrial genomes keep pace with their nuclear counterparts.}, }
@article {pmid37577448, year = {2023}, author = {Bonatelli, ML and Rohwerder, T and Popp, D and Liu, Y and Akay, C and Schultz, C and Liao, KP and Ding, C and Reemtsma, T and Adrian, L and Kleinsteuber, S}, title = {Recently evolved combination of unique sulfatase and amidase genes enables bacterial degradation of the wastewater micropollutant acesulfame worldwide.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1223838}, pmid = {37577448}, issn = {1664-302X}, abstract = {Xenobiotics often challenge the principle of microbial infallibility. One example is acesulfame introduced in the 1980s as zero-calorie sweetener, which was recalcitrant in wastewater treatment plants until the early 2010s. Then, efficient removal has been reported with increasing frequency. By studying acesulfame metabolism in alphaproteobacterial degraders of the genera Bosea and Chelatococcus, we experimentally confirmed the previously postulated route of two subsequent hydrolysis steps via acetoacetamide-N-sulfonate (ANSA) to acetoacetate and sulfamate. Genome comparison of wildtype Bosea sp. 100-5 and an acesulfame degradation-defective mutant revealed the involvement of two plasmid-borne gene clusters. The acesulfame-hydrolyzing sulfatase is strictly manganese-dependent and belongs to the metallo beta-lactamase family. In all degraders analyzed, it is encoded on a highly conserved gene cluster embedded in a composite transposon. The ANSA amidase, on the other hand, is an amidase signature domain enzyme encoded in another gene cluster showing variable length among degrading strains. Transposition of the sulfatase gene cluster between chromosome and plasmid explains how the two catabolic gene clusters recently combined for the degradation of acesulfame. Searching available genomes and metagenomes for the two hydrolases and associated genes indicates that the acesulfame plasmid evolved and spread worldwide in short time. While the sulfatase is unprecedented and unique for acesulfame degraders, the amidase occurs in different genetic environments and likely evolved for the degradation of other substrates. Evolution of the acesulfame degradation pathway might have been supported by the presence of structurally related natural and anthropogenic compounds, such as aminoacyl sulfamate ribonucleotide or sulfonamide antibiotics.}, }
@article {pmid37574851, year = {2023}, author = {Chandler, M and Ross, K and Varani, AM}, title = {The insertion sequence excision enhancer: A PrimPol-based primer invasion system for immobilizing transposon-transmitted antibiotic resistance genes.}, journal = {Molecular microbiology}, volume = {120}, number = {5}, pages = {658-669}, doi = {10.1111/mmi.15140}, pmid = {37574851}, issn = {1365-2958}, mesh = {Humans ; *DNA Transposable Elements/genetics ; *Anti-Bacterial Agents/pharmacology ; Regulatory Sequences, Nucleic Acid ; Bacteria/genetics ; Drug Resistance, Microbial ; DNA-Directed DNA Polymerase/genetics ; DNA Primase/genetics ; Multifunctional Enzymes/genetics ; }, abstract = {Evolutionary studies often identify genes that have been exchanged between different organisms and the phrase Lateral or Horizontal Gene Transfer is often used in this context. However, they rarely provide any mechanistic information concerning how these gene transfers might have occurred. With the astonishing increase in the number of sequences in public databases over the past two or three decades, identical antibiotic resistance genes have been identified in many different sequence contexts. One explanation for this would be that genes are initially transmitted by transposons which have subsequently decayed and can no longer be detected. Here, we provide an overview of a protein, IEE (Insertion Sequence Excision Enhancer) observed to facilitate high-frequency excision of IS629 from clinically important Escherichia coli O157:H7 and subsequently shown to affect a large class of bacterial insertion sequences which all transpose using the copy-out-paste-in transposition mechanism. Excision depends on both IEE and transposase indicating association with the transposition process itself. We review genetic and biochemical data and propose that IEE immobilizes genes carried by compound transposons by removing the flanking insertion sequence (IS) copies. The biochemical activities of IEE as a primase with the capacity to recognize DNA microhomologies and the observation that its effect appears restricted to IS families which use copy-out-paste-in transposition, suggests IS deletion occurs by abortive transposition involving strand switching (primer invasion) during the copy-out step. This reinforces the proposal made for understanding the widespread phenomenon loss of ISApl1 flanking mcr-1 in the compound transposon Tn6330 which we illustrate with a detailed model. This model also provides a convincing way to explain the high levels of IEE-induced precise IS excision.}, }
@article {pmid37567328, year = {2023}, author = {Andrade-Oliveira, AL and Lacerda-Rodrigues, G and Pereira, MF and Bahia, AC and Machado, EA and Rossi, CC and Giambiagi-deMarval, M}, title = {Tenebrio molitor as a model system to study Staphylococcus spp virulence and horizontal gene transfer.}, journal = {Microbial pathogenesis}, volume = {183}, number = {}, pages = {106304}, doi = {10.1016/j.micpath.2023.106304}, pmid = {37567328}, issn = {1096-1208}, mesh = {Animals ; Virulence/genetics ; *Tenebrio/microbiology ; Staphylococcus/genetics ; Staphylococcus aureus/genetics ; Gene Transfer, Horizontal ; Larva/microbiology ; }, abstract = {Invertebrates can provide a valuable alternative to traditional vertebrate animal models for studying bacterial and fungal infections. This study aimed to establish the larvae of the coleoptera Tenebrio molitor (mealworm) as an in vivo model for evaluating virulence and horizontal gene transfer between Staphylococcus spp. After identifying the best conditions for rearing T. molitor, larvae were infected with different Staphylococcus species, resulting in dose-dependent killing curves. All species tested killed the insects at higher doses, with S. nepalensis and S. aureus being the most and least virulent, respectively. However, only S. nepalensis was able to kill more than 50% of larvae 72 h post-infection at a low amount of 10[5] CFU. Staphylococcus infection also stimulated an increase in the concentration of hemocytes present in the hemolymph, which was proportional to the virulence. To investigate T. molitor's suitability as an in vivo model for plasmid transfer studies, we used S. aureus strains as donor and recipient of a plasmid containing the gentamicin resistance gene aac(6')-aph(2″). By inoculating larvae with non-lethal doses of each, we observed conjugation, and obtained transconjugant colonies with a frequency of 1.6 × 10[-5] per donor cell. This study demonstrates the potential of T. molitor larvae as a reliable and cost-effective model for analyzing the virulence of Staphylococcus and, for the first time, an optimal environment for the plasmid transfer between S. aureus carrying antimicrobial resistance genes.}, }
@article {pmid37565764, year = {2023}, author = {Yin, L and Wang, X and Xu, H and Yin, B and Wang, X and Zhang, Y and Li, X and Luo, Y and Chen, Z}, title = {Unrecognized risk of perfluorooctane sulfonate in promoting conjugative transfers of bacterial antibiotic resistance genes.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {9}, pages = {e0053323}, pmid = {37565764}, issn = {1098-5336}, mesh = {Humans ; *Escherichia coli/genetics ; Drug Resistance, Bacterial/genetics ; *Fluorocarbons/pharmacology ; Bacteria/genetics ; Anti-Bacterial Agents/pharmacology ; Soil ; Genes, Bacterial ; Plasmids/genetics ; Gene Transfer, Horizontal ; }, abstract = {Antibiotic resistance is a major global health crisis facing humanity, with horizontal gene transfer (HGT) as a principal dissemination mechanism in the natural and clinical environments. Perfluoroalkyl substances (PFASs) are emerging contaminants of global concern due to their high persistence in the environment and adverse effects on humans. However, it is unknown whether PFASs affect the HGT of bacterial antibiotic resistance. Using a genetically engineered Escherichia coli MG1655 as the donor of plasmid-encoded antibiotic resistance genes (ARGs), E. coli J53 and soil bacterial community as two different recipients, this study demonstrated that the conjugation frequency of ARGs between two E. coli strains was (1.45 ± 0.17) × 10[-5] and perfluorooctane sulfonate (PFOS) at environmentally relevant concentrations (2-50 μg L[-1]) increased conjugation transfer between E. coli strains by up to 3.25-fold. Increases in reactive oxygen species production, cell membrane permeability, biofilm formation capacity, and cell contact in two E. coli strains were proposed as major promotion mechanisms from PFOS exposure. Weighted gene co-expression network analysis of transcriptome data identified a series of candidate genes whose expression changes could contribute to the increase in conjugation transfer induced by PFOS. Furthermore, PFOS also generally increased the ARG transfer into the studied soil bacterial community, although the uptake ability of different community members of the plasmid either increased or decreased upon PFOS exposure depending on specific bacterial taxa. Overall, this study reveals an unrecognized risk of PFOS in accelerating the dissemination of antibiotic resistance. IMPORTANCE Perfluoroalkyl substances (PFASs) are emerging contaminants of global concern due to their high persistence in the environment and adverse health effects. Although the influence of environmental pollutants on the spread of antibiotic resistance, one of the biggest threats to global health, has attracted increasing attention in recent years, it is unknown whether environmental residues of PFASs affect the dissemination of bacterial antibiotic resistance. Considering PFASs, often called "forever" compounds, have significantly higher environmental persistence than most emerging organic contaminants, exploring the effect of PFASs on the spread of antibiotic resistance is more environmentally relevant and has essential ecological and health significance. By systematically examining the influence of perfluorooctane sulfonate on the antibiotic resistance gene conjugative transfer, not only at the single-strain level but also at the community level, this study has uncovered an unrecognized risk of PFASs in promoting conjugative transfers of bacterial antibiotic resistance genes, which could be incorporated into the risk assessment framework of PFASs.}, }
@article {pmid37561843, year = {2023}, author = {Cooper, RM and Wright, JA and Ng, JQ and Goyne, JM and Suzuki, N and Lee, YK and Ichinose, M and Radford, G and Ryan, FJ and Kumar, S and Thomas, EM and Vrbanac, L and Knight, R and Woods, SL and Worthley, DL and Hasty, J}, title = {Engineered bacteria detect tumor DNA.}, journal = {Science (New York, N.Y.)}, volume = {381}, number = {6658}, pages = {682-686}, pmid = {37561843}, issn = {1095-9203}, support = {R01 CA241728/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Humans ; Mice ; *Colorectal Neoplasms/diagnosis/genetics ; *DNA, Neoplasm/analysis ; Mutation ; *Acinetobacter/genetics ; *Cell-Free Nucleic Acids/analysis ; Bioengineering ; *Biosensing Techniques ; }, abstract = {Synthetic biology has developed sophisticated cellular biosensors to detect and respond to human disease. However, biosensors have not yet been engineered to detect specific extracellular DNA sequences and mutations. Here, we engineered naturally competent Acinetobacter baylyi to detect donor DNA from the genomes of colorectal cancer (CRC) cells, organoids, and tumors. We characterized the functionality of the biosensors in vitro with coculture assays and then validated them in vivo with sensor bacteria delivered to mice harboring colorectal tumors. We observed horizontal gene transfer from the tumor to the sensor bacteria in our mouse model of CRC. This cellular assay for targeted, CRISPR-discriminated horizontal gene transfer (CATCH) enables the biodetection of specific cell-free DNA.}, }
@article {pmid37557975, year = {2023}, author = {Weaver, RJ and McDonald, AE}, title = {Mitochondrial alternative oxidase across the tree of life: Presence, absence, and putative cases of lateral gene transfer.}, journal = {Biochimica et biophysica acta. Bioenergetics}, volume = {1864}, number = {4}, pages = {149003}, doi = {10.1016/j.bbabio.2023.149003}, pmid = {37557975}, issn = {1879-2650}, mesh = {Animals ; *Gene Transfer, Horizontal ; *Plant Proteins/genetics ; Oxidoreductases/genetics ; Mitochondria/genetics ; Plants ; Eukaryota/genetics ; }, abstract = {The alternative oxidase (AOX) is a terminal oxidase in the electron transport system that plays a role in mitochondrial bioenergetics. The past 20 years of research shows AOX has a wide yet patchy distribution across the tree of life. AOX has been suggested to have a role in stress tolerance, growth, and development in plants, but less is known about its function in other groups, including animals. In this study, we analyzed the taxonomic distribution of AOX across >2800 species representatives from prokaryotes and eukaryotes and developed a standardized workflow for finding and verifying the authenticity of AOX sequences. We found that AOX is limited to proteobacteria among prokaryotes, but is widely distributed in eukaryotes, with the highest prevalence in plants, fungi, and protists. AOX is present in many invertebrates, but is absent in others including most arthropods, and is absent from vertebrates. We found aberrant AOX sequences associated with some animal groups. Some of these aberrant AOXs were contaminants, but we also found putative cases of lateral gene transfer of AOX from fungi and protists to nematodes, springtails, fungus gnats, and rotifers. Our findings provide a robust and detailed analysis of the distribution of AOX and a method for identifying and verifying putative AOX sequences, which will be useful as more sequence data becomes available on public repositories.}, }
@article {pmid37557016, year = {2023}, author = {Veremeichik, GN and Gorpenchenko, TY and Rusapetova, TV and Brodovskaya, EV and Tchernoded, GK and Bulgakov, DV and Shkryl, YN and Bulgakov, VP}, title = {Auxin-dependent regulation of growth via rolB-induced modulation of the ROS metabolism in the long-term cultivated pRiA4-transformed Rubiacordifolia L. calli.}, journal = {Plant physiology and biochemistry : PPB}, volume = {202}, number = {}, pages = {107932}, doi = {10.1016/j.plaphy.2023.107932}, pmid = {37557016}, issn = {1873-2690}, mesh = {Reactive Oxygen Species/metabolism ; Indoleacetic Acids/pharmacology ; Plant Cells ; *Cell Culture Techniques/methods ; *Botany/methods ; Transformation, Genetic ; Agrobacterium ; Plant Growth Regulators/metabolism ; *Rubia/chemistry/metabolism ; Anthraquinones/metabolism ; }, abstract = {Gene transfer from Agrobacterium to plants is the best studied example of horizontal gene transfer (HGT) between prokaryotes and eukaryotes. The rol genes of A. rhizogenes (Rhizobium rhizogenes) provide uncontrolled root growth, or "hairy root" syndrome, the main diagnostic feature. In the present study, we investigated the stable pRiA4-transformed callus culture of Rubia cordifolia L. While untransformed callus cultures need PGRs (plant growth regulators) as an obligatory supplement, pRiA4 calli is able to achieve long-term PGR-free cultivation. For the first time, we described the pRiA4-transformed callus cultures' PGR-dependent ROS status, growth, and specialized metabolism. As we have shown, expression of the rolA and rolB but not the rolC genes is contradictory in a PGR-dependent manner. Moreover, a PGR-free pRiA4 transformed cell line is characterised as more anthraquinone (AQ) productive than an untransformed cell culture. These findings pertain to actual plant biotechnology: it could be the solution to troubles in choosing the best PGR combination for the cultivation of some rare, medicinal, and woody plants; wild-type Ri-plants and tissue cultures may become freed from legal controls on genetically modified organisms in the future. We propose possible PGR-dependent relationships between rolA and rolB as well as ROS signalling targets. The present study highlighted the high importance of the rolA gene in the regulation of combined rol gene effects and the large knowledge gap in rolA action.}, }
@article {pmid37550759, year = {2023}, author = {Pas, C and Latka, A and Fieseler, L and Briers, Y}, title = {Phage tailspike modularity and horizontal gene transfer reveals specificity towards E. coli O-antigen serogroups.}, journal = {Virology journal}, volume = {20}, number = {1}, pages = {174}, pmid = {37550759}, issn = {1743-422X}, mesh = {Humans ; Serogroup ; *Escherichia coli Infections/microbiology ; O Antigens/genetics/metabolism ; Gene Transfer, Horizontal ; Phylogeny ; *Shiga-Toxigenic Escherichia coli/genetics ; Feces/microbiology ; }, abstract = {BACKGROUND: The interaction between bacteriophages and their hosts is intricate and highly specific. Receptor-binding proteins (RBPs) of phages such as tail fibers and tailspikes initiate the infection process. These RBPs bind to diverse outer membrane structures, including the O-antigen, which is a serogroup-specific sugar-based component of the outer lipopolysaccharide layer of Gram-negative bacteria. Among the most virulent Escherichia coli strains is the Shiga toxin-producing E. coli (STEC) pathotype dominated by a subset of O-antigen serogroups.<br><br>METHODS: Extensive phylogenetic and structural analyses were used to identify and validate specificity correlations between phage RBP subtypes and STEC O-antigen serogroups, relying on the principle of horizontal gene transfer as main driver for RBP evolution.<br><br>RESULTS: We identified O-antigen specific RBP subtypes for seven out of nine most prevalent STEC serogroups (O26, O45, O103, O104, O111, O145 and O157) and seven additional E. coli serogroups (O2, O8, O16, O18, 4s/O22, O77 and O78). Eight phage genera (Gamaleya-, Justusliebig-, Kaguna-, Kayfuna-, Kutter-, Lederberg-, Nouzilly- and Uetakeviruses) emerged for their high proportion of serogroup-specific RBPs. Additionally, we reveal sequence motifs in the RBP region, potentially serving as recombination hotspots between lytic phages.<br><br>CONCLUSION: The results contribute to a better understanding of mosaicism of phage RBPs, but also demonstrate a method to identify and validate new RBP subtypes for current and future emerging serogroups.}, }
@article {pmid37550506, year = {2023}, author = {Sahu, N and Indic, B and Wong-Bajracharya, J and Merényi, Z and Ke, HM and Ahrendt, S and Monk, TL and Kocsubé, S and Drula, E and Lipzen, A and Bálint, B and Henrissat, B and Andreopoulos, B and Martin, FM and Bugge Harder, C and Rigling, D and Ford, KL and Foster, GD and Pangilinan, J and Papanicolaou, A and Barry, K and LaButti, K and Virágh, M and Koriabine, M and Yan, M and Riley, R and Champramary, S and Plett, KL and Grigoriev, IV and Tsai, IJ and Slot, J and Sipos, G and Plett, J and Nagy, LG}, title = {Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria.}, journal = {Nature microbiology}, volume = {8}, number = {9}, pages = {1668-1681}, pmid = {37550506}, issn = {2058-5276}, support = {758161/ERC_/European Research Council/International ; }, mesh = {*Armillaria/genetics/metabolism ; Biomass ; Gene Transfer, Horizontal ; Ecosystem ; Plants ; }, abstract = {The fungal genus Armillaria contains necrotrophic pathogens and some of the largest terrestrial organisms that cause tremendous losses in diverse ecosystems, yet how they evolved pathogenicity in a clade of dominantly non-pathogenic wood degraders remains elusive. Here we show that Armillaria species, in addition to gene duplications and de novo gene origins, acquired at least 1,025 genes via 124 horizontal gene transfer events, primarily from Ascomycota. Horizontal gene transfer might have affected plant biomass degrading and virulence abilities of Armillaria, and provides an explanation for their unusual, soft rot-like wood decay strategy. Combined multi-species expression data revealed extensive regulation of horizontally acquired and wood-decay related genes, putative virulence factors and two novel conserved pathogenicity-induced small secreted proteins, which induced necrosis in planta. Overall, this study details how evolution knitted together horizontally and vertically inherited genes in complex adaptive traits of plant biomass degradation and pathogenicity in important fungal pathogens.}, }
@article {pmid37549546, year = {2023}, author = {Ren, CY and Xu, QJ and Alvarez, PJJ and Zhu, L and Zhao, HP}, title = {Simultaneous antibiotic removal and mitigation of resistance induction by manganese bio-oxidation process.}, journal = {Water research}, volume = {244}, number = {}, pages = {120442}, doi = {10.1016/j.watres.2023.120442}, pmid = {37549546}, issn = {1879-2448}, mesh = {*Manganese ; *Anti-Bacterial Agents/pharmacology ; Escherichia coli/metabolism ; Oxidation-Reduction ; Oxides/metabolism ; Manganese Compounds/metabolism ; Tetracycline ; }, abstract = {Microbial degradation to remove residual antibiotics in wastewater is of growing interest. However, biological treatment of antibiotics may cause resistance dissemination by mutations and horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). In this study, a Mn(Ⅱ)-oxidizing bacterium (MnOB), Pseudomonas aeruginosa MQ2, simultaneously degraded antibiotics, decreased HGT, and mitigated antibiotic resistance mutation. Intracellular Mn(II) levels increased during manganese oxidation, and biogenic manganese oxides (BioMnOx, including Mn(II), Mn(III) and Mn(IV)) tightly coated the cell surface. Mn(II) bio-oxidation mitigated antibiotic resistance acquisition from an E. coli ARG donor and mitigated antibiotic resistance inducement by decreasing conjugative transfer and mutation, respectively. BioMnOx also oxidized ciprofloxacin (1 mg/L) and tetracycline (5 mg/L), respectively removing 93% and 96% within 24 h. Transcriptomic analysis revealed that two new multicopper oxidase and one peroxidase genes are involved in Mn(II) oxidation. Downregulation of SOS response, multidrug resistance and type Ⅳ secretion system related genes explained that Mn(II) and BioMnOx decreased HGT and mitigated resistance mutation by alleviating oxidative stress, which makes recipient cells more vulnerable to ARG acquisition and mutation. A manganese bio-oxidation based reactor was constructed and completely removed tetracycline with environmental concentration within 4-hour hydraulic retention time. Overall, this study suggests that Mn (II) bio-oxidation process could be exploited to control antibiotic contamination and mitigate resistance propagation during water treatment.}, }
@article {pmid37548082, year = {2023}, author = {Zackova Suchanova, J and Bilcke, G and Romanowska, B and Fatlawi, A and Pippel, M and Skeffington, A and Schroeder, M and Vyverman, W and Vandepoele, K and Kröger, N and Poulsen, N}, title = {Diatom adhesive trail proteins acquired by horizontal gene transfer from bacteria serve as primers for marine biofilm formation.}, journal = {The New phytologist}, volume = {240}, number = {2}, pages = {770-783}, doi = {10.1111/nph.19145}, pmid = {37548082}, issn = {1469-8137}, mesh = {*Diatoms/metabolism ; Adhesives/metabolism ; Gene Transfer, Horizontal ; Biofilms ; Bacteria ; }, abstract = {Biofilm-forming benthic diatoms are key primary producers in coastal habitats, where they frequently dominate sunlit intertidal substrata. The development of gliding motility in raphid diatoms was a key molecular adaptation that contributed to their evolutionary success. However, the structure-function correlation between diatom adhesives utilized for gliding and their relationship to the extracellular matrix that constitutes the diatom biofilm is unknown. Here, we have used proteomics, immunolocalization, comparative genomics, phylogenetics and structural homology analysis to investigate the evolutionary history and function of diatom adhesive proteins. Our study identified eight proteins from the adhesive trails of Craspedostauros australis, of which four form a new protein family called Trailins that contain an enigmatic Choice-of-Anchor A (CAA) domain, which was acquired through horizontal gene transfer from bacteria. Notably, the CAA-domain shares a striking structural similarity with one of the most widespread domains found in ice-binding proteins (IPR021884). Our work offers new insights into the molecular basis for diatom biofilm formation, shedding light on the function and evolution of diatom adhesive proteins. This discovery suggests that there is a transition in the composition of biomolecules required for initial surface colonization and those utilized for 3D biofilm matrix formation.}, }
@article {pmid37541538, year = {2023}, author = {Nielsen, TK and Winther-Have, CS and Thomsen, IM and Jackson, RW and Rabiey, M and Hennessy, RC and Bak, F and Kot, W and Nicolaisen, MH and Carstens, AB and Hansen, LH}, title = {Genetic rearrangements in Pseudomonas amygdali pathovar aesculi shape coronatine plasmids.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {113}, number = {}, pages = {105486}, doi = {10.1016/j.meegid.2023.105486}, pmid = {37541538}, issn = {1567-7257}, mesh = {*Pseudomonas/genetics/metabolism ; Plasmids/genetics ; *Virulence Factors/genetics/metabolism ; }, abstract = {Plant pathogenic Pseudomonas species use multiple classes of toxins and virulence factors during host infection. The genes encoding these pathogenicity factors are often located on plasmids and other mobile genetic elements, suggesting that they are acquired through horizontal gene transfer to confer an evolutionary advantage for successful adaptation to host infection. However, the genetic rearrangements that have led to mobilization of the pathogenicity genes are not fully understood. In this study, we have sequenced and analyzed the complete genome sequences of four Pseudomonas amygdali pv. aesculi (Pae), which infect European horse chestnut trees (Aesculus hippocastanum) and belong to phylogroup 3 of the P. syringae species complex. The four investigated genomes contain six groups of plasmids that all encode pathogenicity factors. Effector genes were found to be mostly associated with insertion sequence elements, suggesting that virulence genes are generally mobilized and potentially undergo horizontal gene transfer after transfer to a conjugative plasmid. We show that the biosynthetic gene cluster encoding the phytotoxin coronatine was recently transferred from a chromosomal location to a mobilizable plasmid that subsequently formed a co-integrate with a conjugative plasmid.}, }
@article {pmid37541493, year = {2023}, author = {Li, S and Li, X and Chang, H and Zhong, N and Ren, N and Ho, SH}, title = {Comprehensive insights into antibiotic resistance gene migration in microalgal-bacterial consortia: Mechanisms, factors, and perspectives.}, journal = {The Science of the total environment}, volume = {901}, number = {}, pages = {166029}, doi = {10.1016/j.scitotenv.2023.166029}, pmid = {37541493}, issn = {1879-1026}, abstract = {With the overuse of antibiotics, antibiotic resistance gene (ARG) prevalence is gradually increasing. ARGs are considered emerging contaminants that are broadly concentrated and dispersed in most aquatic environments. Recently, interest in microalgal-bacterial biotreatment of antibiotics has increased, as eukaryotes are not the primary target of antimicrobial drugs. Moreover, research has shown that microalgal-bacterial consortia can minimize the transmission of antibiotic resistance in the environment. Unfortunately, reviews surrounding the ARG migration mechanism in microalgal-bacterial consortia have not yet been performed. This review briefly introduces the migration of ARGs in aquatic environments. Additionally, an in-depth summary of horizontal gene transfer (HGT) between cyanobacteria and bacteria and from bacteria to eukaryotic microalgae is presented. Factors influencing gene transfer in microalgal-bacterial consortia are discussed systematically, including bacteriophage abundance, environmental conditions (temperature, pH, and nutrient availability), and other selective pressure conditions including nanomaterials, heavy metals, and pharmaceuticals and personal care products. Furthermore, considering that quorum sensing could be involved in DNA transformation by affecting secondary metabolites, current knowledge surrounding quorum sensing regulation of HGT of ARGs is summarized. In summary, this review gives valuable information to promote the development of practical and innovative techniques for ARG removal by microalgal-bacterial consortia.}, }
@article {pmid37537271, year = {2023}, author = {Lund, D and Coertze, RD and Parras-Moltó, M and Berglund, F and Flach, CF and Johnning, A and Larsson, DGJ and Kristiansson, E}, title = {Extensive screening reveals previously undiscovered aminoglycoside resistance genes in human pathogens.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {812}, pmid = {37537271}, issn = {2399-3642}, mesh = {Humans ; *Aminoglycosides/pharmacology ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology/metabolism ; Genome, Bacterial ; Escherichia coli/metabolism ; }, abstract = {Antibiotic resistance is a growing threat to human health, caused in part by pathogens accumulating antibiotic resistance genes (ARGs) through horizontal gene transfer. New ARGs are typically not recognized until they have become widely disseminated, which limits our ability to reduce their spread. In this study, we use large-scale computational screening of bacterial genomes to identify previously undiscovered mobile ARGs in pathogens. From ~1 million genomes, we predict 1,071,815 genes encoding 34,053 unique aminoglycoside-modifying enzymes (AMEs). These cluster into 7,612 families (<70% amino acid identity) of which 88 are previously described. Fifty new AME families are associated with mobile genetic elements and pathogenic hosts. From these, 24 of 28 experimentally tested AMEs confer resistance to aminoglycoside(s) in Escherichia coli, with 17 providing resistance above clinical breakpoints. This study greatly expands the range of clinically relevant aminoglycoside resistance determinants and demonstrates that computational methods enable early discovery of potentially emerging ARGs.}, }
@article {pmid37533411, year = {2023}, author = {Groisman, EA and Choi, J}, title = {Advancing evolution: Bacteria break down gene silencer to express horizontally acquired genes.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {45}, number = {10}, pages = {e2300062}, pmid = {37533411}, issn = {1521-1878}, support = {R01 AI049561/AI/NIAID NIH HHS/United States ; }, mesh = {*DNA-Binding Proteins/genetics ; *Bacterial Proteins/genetics/metabolism ; Bacteria/metabolism ; Salmonella typhimurium/genetics/metabolism ; DNA-Directed RNA Polymerases/genetics ; Gene Expression Regulation, Bacterial/genetics ; }, abstract = {Horizontal gene transfer advances bacterial evolution. To benefit from horizontally acquired genes, enteric bacteria must overcome silencing caused when the widespread heat-stable nucleoid structuring (H-NS) protein binds to AT-rich horizontally acquired genes. This ability had previously been ascribed to both anti-silencing proteins outcompeting H-NS for binding to AT-rich DNA and RNA polymerase initiating transcription from alternative promoters. However, we now know that pathogenic Salmonella enterica serovar Typhimurium and commensal Escherichia coli break down H-NS when this silencer is not bound to DNA. Curiously, both species use the same protease - Lon - to destroy H-NS in distinct environments. Anti-silencing proteins promote the expression of horizontally acquired genes without binding to them by displacing H-NS from AT-rich DNA, thus leaving H-NS susceptible to proteolysis and decreasing H-NS amounts overall. Conserved amino acid sequences in the Lon protease and H-NS cleavage site suggest that diverse bacteria degrade H-NS to exploit horizontally acquired genes.}, }
@article {pmid37533217, year = {2023}, author = {Shin, NR and Pauchet, Y}, title = {First evidence of a horizontally-acquired GH-7 cellobiohydrolase from a longhorned beetle genome.}, journal = {Archives of insect biochemistry and physiology}, volume = {114}, number = {2}, pages = {1-14}, doi = {10.1002/arch.22039}, pmid = {37533217}, issn = {1520-6327}, support = {//Max Planck Society/ ; PA2808/4-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Animals ; *Coleoptera/metabolism ; Cellulose 1,4-beta-Cellobiosidase/genetics/chemistry/metabolism ; Phylogeny ; Glycoside Hydrolases/genetics/metabolism ; Polysaccharides ; Cellulose ; }, abstract = {Xylophagous larvae of longhorned beetles (Coleoptera; Cerambycidae) efficiently break down polysaccharides of the plant cell wall, which make the bulk of their food, using a range of carbohydrate-active enzymes (CAZymes). In this study, we investigated the function and evolutionary history of the first identified example of insect-encoded members of glycoside hydrolase family 7 (GH7) derived from the Lamiinae Exocentrus adspersus. The genome of this beetle contained two genes encoding GH7 proteins located in tandem and flanked by transposable elements. Phylogenetic analysis revealed that the GH7 sequences of E. adspersus were closely related to those of Ascomycete fungi, suggesting that they were acquired through horizontal gene transfer (HGT) from fungi. However, they were more distantly related to those encoded by genomes of Crustacea and of protist symbionts of termites and cockroaches, supporting that the same enzyme family was recruited several times independently in Metazoa during the course of their evolution. The recombinant E. adspersus GH7 was found to primarily break down cellulose polysaccharides into cellobiose, indicating that it is a cellobiohydrolase, and could also use smaller cellulose oligomers as substrates. Additionally, the cellobiohydrolase activity was boosted by the presence of calcium chloride. Our findings suggest that the combination of GH7 cellobiohydrolases with other previously characterized endo-β-1,4-glucanases and β-glucosidases allows longhorned beetles like E. adspersus to efficiently break down cellulose into monomeric glucose.}, }
@article {pmid37531380, year = {2023}, author = {Pinder, C and Lebedinec, R and Levine, TP and Birch, M and Oliver, JD}, title = {Characterisation of putative class 1A DHODH-like proteins from Mucorales and dematiaceous mould species.}, journal = {PloS one}, volume = {18}, number = {8}, pages = {e0289441}, pmid = {37531380}, issn = {1932-6203}, mesh = {Dihydroorotate Dehydrogenase ; Saccharomyces cerevisiae/metabolism ; *Mucorales ; *Oxidoreductases Acting on CH-CH Group Donors/genetics/metabolism ; Pyrimidines/pharmacology ; }, abstract = {Olorofim is a new antifungal in clinical development which has a novel mechanism of action against dihydroorotate dehydrogenase (DHODH). DHODH form a ubiquitous family of enzymes in the de novo pyrimidine biosynthetic pathway and are split into class 1A, class 1B and class 2. Olorofim specifically targets the fungal class 2 DHODH present in a range of pathogenic moulds. The nature and number of DHODH present in many fungal species have not been addressed for large clades of this kingdom. Mucorales species do not respond to olorofim; previous work suggests they have only class 1A DHODH and so lack the class 2 target that olorofim inhibits. The dematiaceous moulds have mixed susceptibility to olorofim, yet previous analyses imply that they have class 2 DHODH. As this is at odds with their intermediate susceptibility to olorofim, we hypothesised that these pathogens may maintain a second class of DHODH, facilitating pyrimidine biosynthesis in the presence of olorofim. The aim of this study was to investigate the DHODH repertoire of clinically relevant species of Mucorales and dematiaceous moulds to further characterise these pathogens and understand variations in olorofim susceptibility. Using bioinformatic analysis, S. cerevisiae complementation and biochemical assays of recombinant protein, we provide the first evidence that two representative members of the Mucorales have only class 1A DHODH, substantiating a lack of olorofim susceptibility. In contrast, bioinformatic analyses initially suggested that seven dematiaceous species appeared to harbour both class 1A-like and class 2-like DHODH genes. However, further experimental investigation of the putative class 1A-like genes through yeast complementation and biochemical assays characterised them as dihydrouracil oxidases rather than DHODHs. These data demonstrate variation in dematiaceous mould olorofim susceptibility is not due to a secondary DHODH and builds on the growing picture of fungal dihydrouracil oxidases as an example of horizontal gene transfer.}, }
@article {pmid37526972, year = {2023}, author = {Winter, M and Harms, K and Johnsen, PJ and Buckling, A and Vos, M}, title = {Testing for the fitness benefits of natural transformation during community-embedded evolution.}, journal = {Microbiology (Reading, England)}, volume = {169}, number = {8}, pages = {}, pmid = {37526972}, issn = {1465-2080}, mesh = {*DNA ; DNA, Bacterial/genetics ; *Bacteria/genetics ; Transformation, Bacterial/genetics ; Adaptation, Physiological ; }, abstract = {Natural transformation is a process where bacteria actively take up DNA from the environment and recombine it into their genome or reconvert it into extra-chromosomal genetic elements. The evolutionary benefits of transformation are still under debate. One main explanation is that foreign allele and gene uptake facilitates natural selection by increasing genetic variation, analogous to meiotic sex. However, previous experimental evolution studies comparing fitness gains of evolved transforming- and isogenic non-transforming strains have yielded mixed support for the 'sex hypothesis.' Previous studies testing the sex hypothesis for natural transformation have largely ignored species interactions, which theory predicts provide conditions favourable to sex. To test for the adaptive benefits of bacterial transformation, the naturally transformable wild-type Acinetobacter baylyi and a transformation-deficient ∆comA mutant were evolved for 5 weeks. To provide strong and potentially fluctuating selection, A. baylyi was embedded in a community of five other bacterial species. DNA from a pool of different Acinetobacter strains was provided as a substrate for transformation. No effect of transformation ability on the fitness of evolved populations was found, with fitness increasing non-significantly in most treatments. Populations showed fitness improvement in their respective environments, with no apparent costs of adaptation to competing species. Despite the absence of fitness effects of transformation, wild-type populations evolved variable transformation frequencies that were slightly greater than their ancestor which potentially could be caused by genetic drift.}, }
@article {pmid37526649, year = {2023}, author = {Rodrigues, JA and Blankenship, HM and Cha, W and Mukherjee, S and Sloup, RE and Rudrik, JT and Soehnlen, M and Manning, SD}, title = {Pangenomic analyses of antibiotic-resistant Campylobacter jejuni reveal unique lineage distributions and epidemiological associations.}, journal = {Microbial genomics}, volume = {9}, number = {8}, pages = {}, pmid = {37526649}, issn = {2057-5858}, support = {U01 CK000510/CK/NCEZID CDC HHS/United States ; U01CK000510/ACL/ACL HHS/United States ; }, mesh = {Animals ; Cattle ; Anti-Bacterial Agents/pharmacology ; *Campylobacter jejuni/genetics ; *Campylobacter Infections/epidemiology ; Phylogeny ; Multilocus Sequence Typing ; }, abstract = {Application of whole-genome sequencing (WGS) to characterize foodborne pathogens has advanced our understanding of circulating genotypes and evolutionary relationships. Herein, we used WGS to investigate the genomic epidemiology of Campylobacter jejuni, a leading cause of foodborne disease. Among the 214 strains recovered from patients with gastroenteritis in Michigan, USA, 85 multilocus sequence types (STs) were represented and 135 (63.1 %) were phenotypically resistant to at least one antibiotic. Horizontally acquired antibiotic resistance genes were detected in 128 (59.8 %) strains and the genotypic resistance profiles were mostly consistent with the phenotypes. Core-gene phylogenetic reconstruction identified three sequence clusters that varied in frequency, while a neighbour-net tree detected significant recombination among the genotypes (pairwise homoplasy index P<0.01). Epidemiological analyses revealed that travel was a significant contributor to pangenomic and ST diversity of C. jejuni, while some lineages were unique to rural counties and more commonly possessed clinically important resistance determinants. Variation was also observed in the frequency of lineages over the 4 year period with chicken and cattle specialists predominating. Altogether, these findings highlight the importance of geographically specific factors, recombination and horizontal gene transfer in shaping the population structure of C. jejuni. They also illustrate the usefulness of WGS data for predicting antibiotic susceptibilities and surveillance, which are important for guiding treatment and prevention strategies.}, }
@article {pmid37517232, year = {2023}, author = {Zheng, Z and Huang, Y and Liu, L and Wang, L and Tang, J}, title = {Interaction between microplastic biofilm formation and antibiotics: Effect of microplastic biofilm and its driving mechanisms on antibiotic resistance gene.}, journal = {Journal of hazardous materials}, volume = {459}, number = {}, pages = {132099}, doi = {10.1016/j.jhazmat.2023.132099}, pmid = {37517232}, issn = {1873-3336}, mesh = {*Microplastics ; Plastics ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Drug Resistance, Microbial/genetics ; Biofilms ; *Environmental Pollutants ; }, abstract = {As two pollutants with similar transport pathways, microplastics (MPs) and antibiotics (ATs) inevitably co-exist in water environments, and their interaction has become a topic of intense research interest for scholars over the past few years. This paper comprehensively and systematically reviews the current interaction between MPs and ATs, in particular, the role played by biofilm developed MPs (microplastic biofilm). A summary of the formation process of microplastic biofilm and its unique microbial community structure is presented in the paper. The formation of microplastic biofilm can enhance the adsorption mechanisms of ATs on primary MPs. Moreover, microplastic biofilm system is a diverse and vast reservoir of genetic material, and this paper reviews the mechanisms by which microplastics with biofilm drive the production of antibiotic resistance genes (ARGs) and the processes that selectively enrich for more ARGs. Meanwhile, the enrichment of ARGs may lead to the development of microbial resistance and the gradual loss of the antimicrobial effect of ATs. The transfer pathways of ARGs affected by microplastic biofilm are outlined, and ARGs dependent transfer of antibiotic resistance bacteria (ARB) is mainly through horizontal gene transfer (HGT). Furthermore, the ecological implications of the interaction between microplastic biofilm and ATs and perspectives for future research are reviewed. This review contributes to a new insight into the aquatic ecological environmental risks and the fate of contaminants (MPs, ATs), and is of great significance for controlling the combined pollution of these two pollutants.}, }
@article {pmid37513735, year = {2023}, author = {Nath, J and De, J and Sur, S and Banerjee, P}, title = {Interaction of Microbes with Microplastics and Nanoplastics in the Agroecosystems-Impact on Antimicrobial Resistance.}, journal = {Pathogens (Basel, Switzerland)}, volume = {12}, number = {7}, pages = {}, pmid = {37513735}, issn = {2076-0817}, support = {2020-70020-33033//National Institute of Food and Agriculture/ ; 2022-70020-37590//National Institute of Food and Agriculture/ ; }, abstract = {Microplastics (MPs) and nanoplastics (NPs) are hotspots for the exchange of antimicrobial resistance genes (ARGs) between different bacterial taxa in the environment. Propagation of antimicrobial resistance (AMR) is a global public health issue that needs special attention concerning horizontal gene transfer (HGT) under micro-nano plastics (MNPs) pressure. Interactions between MNPs and microbes, or mere persistence of MNPs in the environment (either water or soil), influence microbial gene expressions, affecting autochthonous microbiomes, their resistomes, and the overall ecosystem. The adsorption of a range of co-contaminants on MNPs leads to the increased interaction of pollutants with microbes resulting in changes in AMR, virulence, toxin production, etc. However, accurately estimating the extent of MNP infestation in agroecosystems remains challenging. The main limitation in estimating the level of MNPs contamination in agroecosystems, surface and subsurface waters, or sediments is the lack of standardized protocols for extraction of MPs and analytical detection methods from complex high organic content matrices. Nonetheless, recent advances in MPs detection from complex matrices with high organic matter content are highly promising. This review aims to provide an overview of relevant information available to date and summarize the already existing knowledge about the mechanisms of MNP-microbe interactions including the different factors with influence on HGT and AMR. In-depth knowledge of the enhanced ARGs propagation in the environment under the influence of MNPs could raise the needed awareness, about future consequences and emergence of multidrug-resistant bacteria.}, }
@article {pmid37513616, year = {2023}, author = {Fan, X and Lu, Y and Zhao, Y and Miao, H and Qi, K and Wang, R}, title = {An Insight into the Exploration of Antibiotic Resistance Genes in Calorie Restricted Diet Fed Mice.}, journal = {Nutrients}, volume = {15}, number = {14}, pages = {}, pmid = {37513616}, issn = {2072-6643}, support = {7212143//Natural Science Foundation of Beijing/ ; 81803214, 81800750, 82003432//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Mice ; *Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; Caloric Restriction ; Manure/microbiology ; Drug Resistance, Microbial/genetics ; }, abstract = {Antibiotic resistance genes (ARGs) threaten the success of modern drugs against multidrug resistant infections. ARGs can be transferred to opportunistic pathogens by horizontal gene transfer (HGT). Many studies have investigated the characteristics of ARGs in various chemical stressors. Studies on the effects of dietary nutrition and dietary patterns on ARGs are rare. The study first demonstrated the effect of calorie restricted (CR) diet on the ARGs and mobile genetic elements (MGEs) in mouse feces and explored their relationship with gut microbiota and their functions. The results showed that the abundance of the total ARGs in mouse feces of the CR group increased, especially tetracycline ARGs (tetW-01). The abundance of the MLSB ARGs (ermB) decreased evidently in mouse feces of the CR group. In addition, the total abundance of MGEs decreased evidently in the CR group, especially tnpA-03. In the meantime, the abundance of Lactobacillus and Bifidobacterium in mouse feces of the CR group increased remarkably. The Spearman correlation analysis between gut microbiota and ARGs showed that several probiotics were significantly positively correlated with ARGs (tetW-01), which might be the main contribution to the increase in ARGs of the CR group.}, }
@article {pmid37513002, year = {2023}, author = {Gryganskyi, AP and Golan, J and Muszewska, A and Idnurm, A and Dolatabadi, S and Mondo, SJ and Kutovenko, VB and Kutovenko, VO and Gajdeczka, MT and Anishchenko, IM and Pawlowska, J and Tran, NV and Ebersberger, I and Voigt, K and Wang, Y and Chang, Y and Pawlowska, TE and Heitman, J and Vilgalys, R and Bonito, G and Benny, GL and Smith, ME and Reynolds, N and James, TY and Grigoriev, IV and Spatafora, JW and Stajich, JE}, title = {Sequencing the Genomes of the First Terrestrial Fungal Lineages: What Have We Learned?.}, journal = {Microorganisms}, volume = {11}, number = {7}, pages = {}, pmid = {37513002}, issn = {2076-2607}, support = {R01 AI039115/AI/NIAID NIH HHS/United States ; R01 AI050113/AI/NIAID NIH HHS/United States ; }, abstract = {The first genome sequenced of a eukaryotic organism was for Saccharomyces cerevisiae, as reported in 1996, but it was more than 10 years before any of the zygomycete fungi, which are the early-diverging terrestrial fungi currently placed in the phyla Mucoromycota and Zoopagomycota, were sequenced. The genome for Rhizopus delemar was completed in 2008; currently, more than 1000 zygomycete genomes have been sequenced. Genomic data from these early-diverging terrestrial fungi revealed deep phylogenetic separation of the two major clades-primarily plant-associated saprotrophic and mycorrhizal Mucoromycota versus the primarily mycoparasitic or animal-associated parasites and commensals in the Zoopagomycota. Genomic studies provide many valuable insights into how these fungi evolved in response to the challenges of living on land, including adaptations to sensing light and gravity, development of hyphal growth, and co-existence with the first terrestrial plants. Genome sequence data have facilitated studies of genome architecture, including a history of genome duplications and horizontal gene transfer events, distribution and organization of mating type loci, rDNA genes and transposable elements, methylation processes, and genes useful for various industrial applications. Pathogenicity genes and specialized secondary metabolites have also been detected in soil saprobes and pathogenic fungi. Novel endosymbiotic bacteria and viruses have been discovered during several zygomycete genome projects. Overall, genomic information has helped to resolve a plethora of research questions, from the placement of zygomycetes on the evolutionary tree of life and in natural ecosystems, to the applied biotechnological and medical questions.}, }
@article {pmid37512869, year = {2023}, author = {Zinno, P and Perozzi, G and Devirgiliis, C}, title = {Foodborne Microbial Communities as Potential Reservoirs of Antimicrobial Resistance Genes for Pathogens: A Critical Review of the Recent Literature.}, journal = {Microorganisms}, volume = {11}, number = {7}, pages = {}, pmid = {37512869}, issn = {2076-2607}, abstract = {Antimicrobial resistance (AMR) is a global and increasing threat to human health. Several genetic determinants of AMR are found in environmental reservoirs, including bacteria naturally associated with widely consumed fermented foods. Through the food chain, these bacteria can reach the gut, where horizontal gene transfer (HGT) can occur within the complex and populated microbial environment. Numerous studies on this topic have been published over the past decades, but a conclusive picture of the potential impact of the non-pathogenic foodborne microbial reservoir on the spread of AMR to human pathogens has not yet emerged. This review critically evaluates a comprehensive list of recent experimental studies reporting the isolation of AMR bacteria associated with fermented foods, focusing on those reporting HGT events, which represent the main driver of AMR spread within and between different bacterial communities. Overall, our analysis points to the methodological heterogeneity as a major weakness impairing determination or a causal relation between the presence of AMR determinants within the foodborne microbial reservoir and their transmission to human pathogens. The aim is therefore to highlight the main gaps and needs to better standardize future studies addressing the potential role of non-pathogenic bacteria in the spread of AMR.}, }
@article {pmid37512822, year = {2023}, author = {Di Pierro, F and Campedelli, I and De Marta, P and Fracchetti, F and Del Casale, A and Cavecchia, I and Matera, M and Cazzaniga, M and Bertuccioli, A and Guasti, L and Zerbinati, N}, title = {Bifidobacterium breve PRL2020: Antibiotic-Resistant Profile and Genomic Detection of Antibiotic Resistance Determinants.}, journal = {Microorganisms}, volume = {11}, number = {7}, pages = {}, pmid = {37512822}, issn = {2076-2607}, abstract = {Antibiotics are one of the greatest scientific achievements of modern medicine, but excessive use is creating challenges for the future of medicine. Antibiotic resistance (AR) is thought to cause changes in bowel habits and an increased risk of gastroenteritis, but it may also increase the risk of overweight, obesity, autoimmune and atopic diseases, and a low response to vaccines and cancer, likely mediated by antibiotic-induced gut dysbiosis. Probiotic add-on therapy could partially prevent antibiotic-induced gut dysbiosis, but their antibiotic sensitivity features likely limits this potential. The EFSA (European Food Safety Authority) guidelines consider the use of probiotics whose antibiotic-resistant profile could be transferable an important hazard. Recently, a strain of B. breve (PRL2020) has shown to be resistant to amoxicillin and amoxicillin-clavulanate (AC) by applying the microdilution protocol according EFSA guidelines. After verifying that horizontal gene transfer is unlikely to take place, this feature suggests its concomitant use with these specific antibiotics. The results of our tests demonstrated that the strain PRL2020 is indeed endowed with amoxicillin- and AC-resistant properties and that it is also insensitive to ampicillin. In-depth analysis of the annotated genome sequence of B. breve PRL2020 was employed to query the Comprehensive Antibiotic Resistance Database (CARD) using Resistance Gene Identifier (RGI) software (version 5.2.1). The similarity among the AR determinants found was studied through nucleotide sequence alignment, and it was possible to verify not only the absence of genes explaining these features in the flanking regions but also the presence of genetic sequences (rpoB and erm(X)) putatively responsible for rifampicin and erythromycin resistance. Both features are not phenotypically expressed, and for these antibiotics, the strain is within the EFSA limits. Analysis of the flanking regions of these genes revealed possible mobile elements upstream and downstream only in the case of the erm(X) gene, but the features of the Insertion Sequences (IS) are described as not to cause horizontal transfer. Our findings on strain PRL2020 demonstrate that its AR profile is compatible with antibiotics when taken with the aim of reducing the risk of dysbiosis.}, }
@article {pmid37511529, year = {2023}, author = {Kordiš, D and Turk, V}, title = {Origin and Early Diversification of the Papain Family of Cysteine Peptidases.}, journal = {International journal of molecular sciences}, volume = {24}, number = {14}, pages = {}, pmid = {37511529}, issn = {1422-0067}, support = {P1-0207, P1-0140, J1-2473//Slovenian Research Agency/ ; }, mesh = {*Papain/genetics/metabolism ; Cysteine/metabolism ; Evolution, Molecular ; Phylogeny ; Eukaryota/genetics ; Archaea/genetics ; *Cysteine Proteases/metabolism ; Peptide Hydrolases/metabolism ; }, abstract = {Peptidases of the papain family play a key role in protein degradation, regulated proteolysis, and the host-pathogen arms race. Although the papain family has been the subject of many studies, knowledge about its diversity, origin, and evolution in Eukaryota, Bacteria, and Archaea is limited; thus, we aimed to address these long-standing knowledge gaps. We traced the origin and expansion of the papain family with a phylogenomic analysis, using sequence data from numerous prokaryotic and eukaryotic proteomes, transcriptomes, and genomes. We identified the full complement of the papain family in all prokaryotic and eukaryotic lineages. Analysis of the papain family provided strong evidence for its early diversification in the ancestor of eukaryotes. We found that the papain family has undergone complex and dynamic evolution through numerous gene duplications, which produced eight eukaryotic ancestral paralogous C1A lineages during eukaryogenesis. Different evolutionary forces operated on C1A peptidases, including gene duplication, horizontal gene transfer, and gene loss. This study challenges the current understanding of the origin and evolution of the papain family and provides valuable insights into their early diversification. The findings of this comprehensive study provide guidelines for future structural and functional studies of the papain family.}, }
@article {pmid37511216, year = {2023}, author = {Kim, YK and Jo, S and Cheon, SH and Hong, JR and Kim, KJ}, title = {Ancient Horizontal Gene Transfers from Plastome to Mitogenome of a Nonphotosynthetic Orchid, Gastrodia pubilabiata (Epidendroideae, Orchidaceae).}, journal = {International journal of molecular sciences}, volume = {24}, number = {14}, pages = {}, pmid = {37511216}, issn = {1422-0067}, support = {NRF-2021R1A2C1013731//National Research Foundation of Korea/ ; NRF-2020R1A6A3A01100512//National Research Foundation of Korea/ ; }, mesh = {*Orchidaceae/genetics ; *Gastrodia/genetics ; *Genome, Mitochondrial ; Gene Transfer, Horizontal ; Phylogeny ; *Magnoliopsida/genetics ; }, abstract = {Gastrodia pubilabiata is a nonphotosynthetic and mycoheterotrophic orchid belonging to subfamily Epidendroideae. Compared to other typical angiosperm species, the plastome of G. pubilabiata is dramatically reduced in size to only 30,698 base pairs (bp). This reduction has led to the loss of most photosynthesis-related genes and some housekeeping genes in the plastome, which now only contains 19 protein coding genes, three tRNAs, and three rRNAs. In contrast, the typical orchid species contains 79 protein coding genes, 30 tRNAs, and four rRNAs. This study decoded the entire mitogenome of G. pubilabiata, which consisted of 44 contigs with a total length of 867,349 bp. Its mitogenome contained 38 protein coding genes, nine tRNAs, and three rRNAs. The gene content of G. pubilabiata mitogenome is similar to the typical plant mitogenomes even though the mitogenome size is twice as large as the typical ones. To determine possible gene transfer events between the plastome and the mitogenome individual BLASTN searches were conducted, using all available orchid plastome sequences and flowering plant mitogenome sequences. Plastid rRNA fragments were found at a high frequency in the mitogenome. Seven plastid protein coding gene fragments (ndhC, ndhJ, ndhK, psaA, psbF, rpoB, and rps4) were also identified in the mitogenome of G. pubilabiata. Phylogenetic trees using these seven plastid protein coding gene fragments suggested that horizontal gene transfer (HGT) from plastome to mitogenome occurred before losses of photosynthesis related genes, leading to the lineage of G. pubilabiata. Compared to species phylogeny of the lineage of orchid, it was estimated that HGT might have occurred approximately 30 million years ago.}, }
@article {pmid37508388, year = {2023}, author = {Zuber, NE and Fornasero, LV and Erdozain Bagolín, SA and Lozano, MJ and Sanjuán, J and Del Papa, MF and Lagares, A}, title = {Diversity, Genomics and Symbiotic Characteristics of Sinorhizobia That Nodulate Desmanthus spp. in Northwest Argentina.}, journal = {Biology}, volume = {12}, number = {7}, pages = {}, pmid = {37508388}, issn = {2079-7737}, support = {PICT-2019-01021//Ministerio de Ciencia Tecnololog&#xed;a e Innovaci&#xf3;n Productiva - MinCyT, Argentina/ ; PIP 2022-2024-11220210100367CO//Consejo Nacional de Investigaciones Cient&#xed;ficas y T&#xe9;cnicas - CONICET, Argentina/ ; ATN-RF-18786-RG//FONTAGRO/ ; }, abstract = {Desmanthus spp. are legumes with the ability to associate with diverse α-proteobacteria-a microsymbiont-in order to establish nitrogen-fixing root nodules. A previous investigation from our laboratory revealed that the main bacteria associated with Desmanthus paspalaceus in symbiosis in central Argentina (Province of Santa Fe) were quite diverse and belonged to the genera Rhizobium and Mesorhizobium. To achieve a more extensive view of the local microsymbionts associated with Desmanthus spp., we sampled three different sites in Jujuy and Salta, in northwest Argentina. Matrix-assisted Laser-Desorption-Ionization Time-of-Flight mass spectrometry (MALDI-TOF) typing, 16S-rDNA analysis, and genome sequencing demonstrated that the dominant root-nodule microsymbionts belonged to the genus Sinorhizobium, with some sequenced genomes related to Sinorhizobium mexicanum, Sinorhizobium chiapanecum, and Sinorhizobium psoraleae. An analysis of nodA and nodC markers indicated that, in some of the isolates, horizontal gene transfer appeared to be responsible for the lack of congruence between the phylogenies of the chromosome and of the symbiotic region. These results revealed diverse evolutionary strategies for reaching the current Desmanthus-microsymbiont diversity. What is remarkable beside their observed genetic diversity is that the tolerance profiles of these isolates to abiotic stresses (temperature, salt concentration, pH) were quite coincident with the separation of the sinorhizobia according to place of origin, suggesting possible ecoedaphic adaptations. This observation, together with the higher aerial dry-weight matter that some isolates generated in Desmanthus virgatus cv. Marc when compared to the biomass generated by the commercial strain Sinorhizobium terangae CB3126, distinguish the collected sinorhizobia as constituting valuable germplasm for evaluation in local fields to select for more efficient symbiotic pairs.}, }
@article {pmid37508321, year = {2023}, author = {Zaghen, F and Sora, VM and Meroni, G and Laterza, G and Martino, PA and Soggiu, A and Bonizzi, L and Zecconi, A}, title = {Epidemiology of Antimicrobial Resistance Genes in Staphyloccocus aureus Isolates from a Public Database in a One Health Perspective-Sample Characteristics and Isolates' Sources.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {7}, pages = {}, pmid = {37508321}, issn = {2079-6382}, support = {Programma di Sviluppo Rurale 2014-2020 Misura 16.1 project MOOH//FEASR/ ; 2017MZ5KWM_001 project "SAFE MILK: OMICS SCIENCE FOR MILK SAFETY AND QUALITY"//PRIN/ ; PSR2021 line 6 One Health Action Hub//University of Milan/ ; }, abstract = {Staphylococcus aureus is considered one of the most widespread bacterial pathogens for both animals and humans, being the causative agent of various diseases like food poisoning, respiratory tract infections, nosocomial bacteremia, and surgical site and cardiovascular infections in humans, as well as clinical and subclinical mastitis, dermatitis, and suppurative infections in animals. Thanks to their genetic flexibility, several virulent and drug-resistant strains have evolved mainly due to horizontal gene transfer and insurgence of point mutations. Infections caused by the colonization of such strains are particularly problematic due to frequently occurring antibiotic resistance, particulary methicillin-resistant S. aureus (MRSA), and are characterized by increased mortality, morbidity, and hospitalization rates compared to those caused by methicillin-sensitive S. aureus (MSSA). S. aureus infections in humans and animals are a prime example of a disease that may be managed by a One Health strategy. In fact, S. aureus is a significant target for control efforts due to its zoonotic potential, the frequency of its illnesses in both humans and animals, and the threat posed by S. aureus antibiotic resistance globally. The results of an epidemiological analysis on a worldwide public database (NCBI Pathogen Detection Isolate Browser; NPDIB) of 35,026 S. aureus isolates were described. We considered the diffusion of antibiotic resistance genes (ARGs), in both human and animal setting, and the results may be considered alarming. The result of this study allowed us to identify the presence of clusters with specific ARG patterns, and that these clusters are associated with different sources of isolation (e.g., human, non-human).}, }
@article {pmid37508250, year = {2023}, author = {Liu, S and Liu, B and Zhu, Y and Qiu, Y and Li, B}, title = {The Spatial-Temporal Effects of Bacterial Growth Substrates on Antibiotic Resistance Gene Spread in the Biofilm.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {7}, pages = {}, pmid = {37508250}, issn = {2079-6382}, support = {2020YFC19092-05, 2022YFC32031-04//Ministry of Science and Technology/ ; FRF-TP-20-011A3//Fundamental Research Funds for the Central Universities/ ; }, abstract = {Biofilm is considered as the hotspot of antibiotic resistance gene (ARG) dissemination. Bacterial growth substrates are important factors for biofilm formation, but its spatial-temporal effects on ARG spread in biofilm is still unclear. In this study, microfluidics combined with microscopic observation were used to reveal spatial-temporal effects of bacterial growth substrates on ARG transfer at real time. The initial horizontal gene transfer events were found to be independent of substrate levels. However, subsequent transfer processes varied greatly depending on the availability of growth substrates. The proportion of transconjugants was much higher (~12%) when observed in substrate-rich regions (under the channel) at 24 h, followed by an exponential decline, with the distance far from the channel. Furthermore, three-dimensional observation revealed that vertical gene transfer influenced by the concentrations of bacterial growth substrates was important for ARG spread in biofilm. The transfer frequency was 8.2 times higher in the high substrate concentration (50×) compared to low concentration (0.5×) in simulated sewage, underscoring the substantial impact of bacterial growth substrate variability on ARG dissemination. This study is helpful for in-depth understanding of ARG dissemination through biofilms and indicates that reducing pollutant emission is important for ARG control in the environment.}, }
@article {pmid37508224, year = {2023}, author = {Guidotti-Takeuchi, M and Melo, RT and Ribeiro, LNM and Dumont, CF and Ribeiro, RAC and Brum, BA and de Amorim Junior, TLIF and Rossi, DA}, title = {Interference with Bacterial Conjugation and Natural Alternatives to Antibiotics: Bridging a Gap.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {7}, pages = {}, pmid = {37508224}, issn = {2079-6382}, abstract = {Horizontal gene transfer (HGT) in food matrices has been investigated under conditions that favor gene exchange. However, the major challenge lies in determining the specific conditions pertaining to the adapted microbial pairs associated with the food matrix. HGT is primarily responsible for enhancing the microbial repertoire for the evolution and spread of antimicrobial resistance and is a major target for controlling pathogens of public health concern in food ecosystems. In this study, we investigated Salmonella Heidelberg (SH) and Escherichia coli (EC) regarding gene exchange under conditions mimicking the industrial environment, with the coproducts whey (SL) and chicken juice (CJ). The S. Heidelberg strain was characterized by antibiotic susceptibility standards and PCR to detect the blaTEM gene. A concentration of 0.39 mg/mL was determined to evaluate the anti-conjugation activity of nanostructured lipid nanocarriers (NLCs) of essential oils to mitigate β-lactam resistance gene transfer. The results showed that the addition of these coproducts promoted an increase of more than 3.5 (whey) and 2.5 (chicken juice) orders of magnitude in the conjugation process (p < 0.01), and NLCs of sage essential oil significantly reduced the conjugation frequency (CF) by 74.90, 90.6, and 124.4 times when compared to the transfers in the absence of coproducts and the presence of SL and CJ, respectively. For NLCs from olibanum essential oil, the decrease was 4.46-fold for conjugations without inhibitors and 3.12- and 11.3-fold in the presence of SL and CJ. NLCs associated with sage and olibanum essential oils effectively control the transfer of antibiotic resistance genes and are a promising alternative for use at industrial levels.}, }
@article {pmid37508213, year = {2023}, author = {Anyanwu, MU and Jaja, IF and Okpala, COR and Njoga, EO and Okafor, NA and Oguttu, JW}, title = {Mobile Colistin Resistance (mcr) Gene-Containing Organisms in Poultry Sector in Low- and Middle-Income Countries: Epidemiology, Characteristics, and One Health Control Strategies.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {7}, pages = {}, pmid = {37508213}, issn = {2079-6382}, abstract = {Mobile colistin resistance (mcr) genes (mcr-1 to mcr-10) are plasmid-encoded genes that threaten the clinical utility of colistin (COL), one of the highest-priority critically important antibiotics (HP-CIAs) used to treat infections caused by multidrug-resistant and extensively drug-resistant bacteria in humans and animals. For more than six decades, COL has been used largely unregulated in the poultry sector in low- and middle-income countries (LMICs), and this has led to the development/spread of mcr gene-containing bacteria (MGCB). The prevalence rates of mcr-positive organisms from the poultry sector in LMICs between January 1970 and May 2023 range between 0.51% and 58.8%. Through horizontal gene transfer, conjugative plasmids possessing insertion sequences (ISs) (especially ISApl1), transposons (predominantly Tn6330), and integrons have enhanced the spread of mcr-1, mcr-2, mcr-3, mcr-4, mcr-5, mcr-7, mcr-8, mcr-9, and mcr-10 in the poultry sector in LMICs. These genes are harboured by Escherichia, Klebsiella, Proteus, Salmonella, Cronobacter, Citrobacter, Enterobacter, Shigella, Providencia, Aeromonas, Raoultella, Pseudomonas, and Acinetobacter species, belonging to diverse clones. The mcr-1, mcr-3, and mcr-10 genes have also been integrated into the chromosomes of these bacteria and are mobilizable by ISs and integrative conjugative elements. These bacteria often coexpress mcr with virulence genes and other genes conferring resistance to HP-CIAs, such as extended-spectrum cephalosporins, carbapenems, fosfomycin, fluoroquinolone, and tigecycline. The transmission routes and dynamics of MGCB from the poultry sector in LMICs within the One Health triad include contact with poultry birds, feed/drinking water, manure, poultry farmers and their farm workwear, farming equipment, the consumption and sale of contaminated poultry meat/egg and associated products, etc. The use of pre/probiotics and other non-antimicrobial alternatives in the raising of birds, the judicious use of non-critically important antibiotics for therapy, the banning of nontherapeutic COL use, improved vaccination, biosecurity, hand hygiene and sanitization, the development of rapid diagnostic test kits, and the intensified surveillance of mcr genes, among others, could effectively control the spread of MGCB from the poultry sector in LMICs.}, }
@article {pmid37505810, year = {2023}, author = {Dewan, I and Uecker, H}, title = {A mathematician's guide to plasmids: an introduction to plasmid biology for modellers.}, journal = {Microbiology (Reading, England)}, volume = {169}, number = {7}, pages = {}, pmid = {37505810}, issn = {1465-2080}, mesh = {Humans ; Plasmids/genetics ; *Bacteria/genetics ; *Biology ; Gene Transfer, Horizontal ; }, abstract = {Plasmids, extrachromosomal DNA molecules commonly found in bacterial and archaeal cells, play an important role in bacterial genetics and evolution. Our understanding of plasmid biology has been furthered greatly by the development of mathematical models, and there are many questions about plasmids that models would be useful in answering. In this review, we present an introductory, yet comprehensive, overview of the biology of plasmids suitable for modellers unfamiliar with plasmids who want to get up to speed and to begin working on plasmid-related models. In addition to reviewing the diversity of plasmids and the genes they carry, their key physiological functions, and interactions between plasmid and host, we also highlight selected plasmid topics that may be of particular interest to modellers and areas where there is a particular need for theoretical development. The world of plasmids holds a great variety of subjects that will interest mathematical biologists, and introducing new modellers to the subject will help to expand the existing body of plasmid theory.}, }
@article {pmid37503831, year = {2023}, author = {Sanchez-Puerta, MV and Ceriotti, LF and Gatica-Soria, LM and Roulet, ME and Garcia, LE and Sato, HA}, title = {Invited Review Beyond parasitic convergence: unravelling the evolution of the organellar genomes in holoparasites.}, journal = {Annals of botany}, volume = {132}, number = {5}, pages = {909-928}, pmid = {37503831}, issn = {1095-8290}, support = {PICT2020-01018//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; 06/A092-T1//Universidad Nacional de Cuyo/ ; }, mesh = {*Magnoliopsida/genetics ; Plants/genetics ; *Genome, Mitochondrial/genetics ; Evolution, Molecular ; Plastids ; Phylogeny ; }, abstract = {BACKGROUND: The molecular evolution of organellar genomes in angiosperms has been studied extensively, with some lineages, such as parasitic ones, displaying unique characteristics. Parasitism has emerged 12 times independently in angiosperm evolution. Holoparasitism is the most severe form of parasitism, and is found in ~10 % of parasitic angiosperms. Although a few holoparasitic species have been examined at the molecular level, most reports involve plastomes instead of mitogenomes. Parasitic plants establish vascular connections with their hosts through haustoria to obtain water and nutrients, which facilitates the exchange of genetic information, making them more susceptible to horizontal gene transfer (HGT). HGT is more prevalent in the mitochondria than in the chloroplast or nuclear compartments.<br><br>SCOPE: This review summarizes current knowledge on the plastid and mitochondrial genomes of holoparasitic angiosperms, compares the genomic features across the different lineages, and discusses their convergent evolutionary trajectories and distinctive features. We focused on Balanophoraceae (Santalales), which exhibits extraordinary traits in both their organelles.<br><br>CONCLUSIONS: Apart from morphological similarities, plastid genomes of holoparasitic plants also display other convergent features, such as rampant gene loss, biased nucleotide composition and accelerated evolutionary rates. In addition, the plastomes of Balanophoraceae have extremely low GC and gene content, and two unexpected changes in the genetic code. Limited data on the mitochondrial genomes of holoparasitic plants preclude thorough comparisons. Nonetheless, no obvious genomic features distinguish them from the mitochondria of free-living angiosperms, except for a higher incidence of HGT. HGT appears to be predominant in holoparasitic angiosperms with a long-lasting endophytic stage. Among the Balanophoraceae, mitochondrial genomes exhibit disparate evolutionary paths with notable levels of heteroplasmy in Rhopalocnemis and unprecedented levels of HGT in Lophophytum. Despite their differences, these Balanophoraceae share a multichromosomal mitogenome, a feature also found in a few free-living angiosperms.}, }
@article {pmid37502928, year = {2023}, author = {Hu, K and Chia-Wei, C and Wilke, CO and Finkelstein, IJ}, title = {Distinct horizontal transfer mechanisms for type I and type V CRISPR-associated transposons.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37502928}, issn = {2692-8205}, support = {R01 GM088344/GM/NIGMS NIH HHS/United States ; R01 GM124141/GM/NIGMS NIH HHS/United States ; }, abstract = {CRISPR-associated transposons (CASTs) co-opt CRISPR-Cas proteins and Tn7-family transposons for RNA-guided vertical and horizontal transmission. CASTs encode minimal CRISPR arrays but can't acquire new spacers. Here, we show that CASTs instead co-opt defense-associated CRISPR arrays for horizontal transmission. A bioinformatic analysis shows that all CAST sub-types co-occur with defense-associated CRISPR-Cas systems. Using an E. coli quantitative transposition assay, we show that CASTs use CRISPR RNAs (crRNAs) from these defense systems for horizontal gene transfer. A high-resolution structure of the type I-F CAST-Cascade in complex with a type III-B crRNA reveals that Cas6 recognizes direct repeats via sequence-independent π - π interactions. In addition to using heterologous CRISPR arrays, type V CASTs can also transpose via a crRNA-independent unguided mechanism, even when the S15 co-factor is over-expressed. Over-expressing S15 and the trans-activating CRISPR RNA (tracrRNA) or a single guide RNA (sgRNA) reduces, but does not abrogate, off-target integration for type V CASTs. Exploiting new spacers in defense-associated CRISPR arrays explains how CASTs horizontally transfer to new hosts. More broadly, this work will guide further efforts to engineer the activity and specificity of CASTs for gene editing applications.}, }
@article {pmid37499542, year = {2023}, author = {Chen, X and Zhu, Y and Chen, J and Yan, S and Xie, S}, title = {Multi-omic profiling of a novel activated sludge strain Sphingobacterium sp. WM1 reveals the mechanism of tetracycline biodegradation and its merits of potential application.}, journal = {Water research}, volume = {243}, number = {}, pages = {120397}, doi = {10.1016/j.watres.2023.120397}, pmid = {37499542}, issn = {1879-2448}, mesh = {*Sewage/microbiology ; *Sphingobacterium/metabolism ; Multiomics ; Anti-Bacterial Agents/metabolism ; Tetracycline/metabolism ; Bacteria/metabolism ; Biodegradation, Environmental ; }, abstract = {As an emerging pollutant, the antibiotic tetracycline (TC) has been consistently detected in wastewater and activated sludge. Biodegradation represents a potentially crucial pathway to dissipate TC contamination. However, few efficient TC-degrading bacteria have been isolated and a comprehensive understanding of the molecular mechanisms underlying TC degradation is still lacking. In this study, a novel TC-degrading bacterium, designated as Sphingobacterium sp. WM1, was successfully isolated from activated sludge. Strain WM1 exhibited a remarkable performance in degrading 50 mg/L TC within 1 day under co-metabolic conditions. Genomic analysis of the strain WM1 unveiled the presence of three functional tetX genes. Unraveling the complex molecular mechanisms, transcriptome analysis highlighted the role of upregulated transmembrane transport and accelerated electron transport in facilitating TC degradation. Proteomics confirmed the up-regulation of proteins involved in cellular biosynthesis/metabolism and ribosomal processes. Crucially, the tetX gene-encoding protein showed a significant upregulation, indicating its role in TC degradation. Heterologous expression of the tetX gene resulted in TC dissipation from an initial 51.9 mg/L to 4.2 mg/L within 24 h. The degradation pathway encompassed TC hydroxylation, transforming into TP461 and subsequent metabolites, which effectively depleted TC's inhibitory activity. Notably, the tetX genes in strain WM1 showed limited potential for horizontal gene transfer. Collectively, strain WM1's potent TC degradation capacity signals a promise for enhancing TC clean-up strategies.}, }
@article {pmid37499413, year = {2023}, author = {Ma, R and Wang, J and Liu, Y and Wang, G and Yang, Y and Liu, Y and Kong, Y and Lin, J and Li, Q and Li, G and Yuan, J}, title = {Dynamics of antibiotic resistance genes and bacterial community during pig manure, kitchen waste, and sewage sludge composting.}, journal = {Journal of environmental management}, volume = {345}, number = {}, pages = {118651}, doi = {10.1016/j.jenvman.2023.118651}, pmid = {37499413}, issn = {1095-8630}, mesh = {Animals ; Swine ; *Anti-Bacterial Agents/pharmacology ; Sewage ; Tetracycline ; *Composting ; Manure/microbiology ; Genes, Bacterial ; Drug Resistance, Bacterial ; Macrolides ; Bacteria ; Sulfanilamide ; }, abstract = {Organic solid wastes (OSWs) are important reservoirs for antibiotic resistance genes (ARGs). Aerobic composting transforms OSWs into fertilizers. In this study, we investigated ARGs dynamics and their driving mechanisms in three OSW composts: pig manure (PM), kitchen waste (KC), and sewage sludge (SG). The dominant ARGs were different in each OSW, namely tetracycline, aminoglycoside, and macrolide resistance (PM); tetracyclines and aminoglycosides (KC); and sulfonamides (SG). ARGs abundance decreased in PM (71%) but increased in KC (5.9-fold) and SG (1.3-fold). Interestingly, the ARGs abundance was generally similar in all final composts, which was contributed to the similar bacterial community in final composts. In particular, sulfonamide and β-lactam resistant genes removed (100%) in PM, while sulfonamide in KC (38-fold) and tetracycline in SG (5-fold) increased the most. Additionally, ARGs abundance rebounded during the maturation period in all treatments. Firmicutes, Proteobacteria, and Actinobacteria were the main ARGs hosts. Several persistent and high-risk genes included tetW, aadA, aadE, tetX, strB, tetA, mefA, intl1, and intl2. The structural equation models showed ARGs removal was mainly affected by physicochemical parameters and bacterial communities in PM, the ARGs enrichment in KC composting correlated with increased mobile genetic elements (MGEs). In general, thermophilic aerobic composting can inhibit the vertical gene transfer (VGT) of pig manure and horizontal gene transfer (HGT) of sludge, but it increases the HGT of kitchen waste, resulting in a dramatic increase of ARGs in KC compost. More attention should be paid to the ARGs risk of kitchen waste composting.}, }
@article {pmid37495486, year = {2023}, author = {Soler-Bistué, A}, title = {Restriction-methylation systems regulate transformation in Acinetobacter baumannii.}, journal = {Trends in microbiology}, volume = {31}, number = {9}, pages = {879-881}, doi = {10.1016/j.tim.2023.07.009}, pmid = {37495486}, issn = {1878-4380}, mesh = {*Acinetobacter baumannii/genetics ; Methylation ; Anti-Bacterial Agents ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; }, abstract = {Antimicrobial resistance in Acinetobacter baumannii is a major concern. Natural transformation remains understudied as a horizontal gene transfer (HGT) mechanism for the spread of resistance genes. Recent work (Vesel et al.) reveals a profound impact of the state of donor DNA methylation with strong implications for HGT of resistance determinants in this worrisome pathogen.}, }
@article {pmid37494793, year = {2023}, author = {Wang, H and Xu, K and Wang, J and Feng, C and Chen, Y and Shi, J and Ding, Y and Deng, C and Liu, X}, title = {Microplastic biofilm: An important microniche that may accelerate the spread of antibiotic resistance genes via natural transformation.}, journal = {Journal of hazardous materials}, volume = {459}, number = {}, pages = {132085}, doi = {10.1016/j.jhazmat.2023.132085}, pmid = {37494793}, issn = {1873-3336}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Extracellular Polymeric Substance Matrix ; Plastics ; Microplastics ; Biofilms ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; }, abstract = {Microplastic (MP) biofilms provide a specific microniche for microbial life and are a potential hotspot for the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). Nevertheless, the acquisition of ARGs in MP biofilms via natural transformation mediated by extracellular DNA (eDNA) has been rarely explored. This study demonstrated that MP biofilms promoted the natural transformation of extracellular ARGs at the single-cell and multi-species levels, compared to natural substrate (NS) biofilms and bacterioplankton. The transformation frequency on MP biofilms was up to 1000-fold compare to that on NS. The small MPs and aged MPs enhanced the ARG transformation frequencies up to 77.16-fold and 32.05-fold, respectively, compared with the large MPs and pristine MPs. The transformation frequencies on MP biofilms were significantly positively correlated with the bacterial density and extracellular polymeric substance (EPS) content (P < 0.05). Furthermore, MPs significantly increased the expression of the biofilm formation related genes (motA and pgaA) and DNA uptake related genes (pilX and comA) compared to NS and bacterioplankton. The more transformants colonized on MPs contributed to the enhanced transformation frequencies at the community-wide level. Overall, eDNA-mediated transformation in MP biofilms may be an important path of ARG spread, which was promoted by heterogeneous biofilm.}, }
@article {pmid37486104, year = {2023}, author = {Hallal Ferreira Raro, O and Poirel, L and Tocco, M and Nordmann, P}, title = {Impact of veterinary antibiotics on plasmid-encoded antibiotic resistance transfer.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {78}, number = {9}, pages = {2209-2216}, pmid = {37486104}, issn = {1460-2091}, support = {/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {Animals ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Oxytetracycline/pharmacology ; Edaravone/pharmacology ; Reactive Oxygen Species ; Escherichia coli/genetics ; Plasmids/genetics ; Drug Resistance, Microbial ; Gene Transfer, Horizontal ; }, abstract = {OBJECTIVES: Resistance genes can be genetically transmitted and exchanged between commensal and pathogenic bacterial species, and in different compartments including the environment, or human and animal guts (One Health concept). The aim of our study was to evaluate whether subdosages of antibiotics administered in veterinary medicine could enhance plasmid transfer and, consequently, resistance gene exchange in gut microbiota.<br><br>METHODS: Conjugation frequencies were determined with Escherichia coli strains carrying IncL- (blaOXA-48) or IncI1-type (blaCTX-M-1) plasmids subjected to a series of subinhibitory concentrations of antibiotics used in veterinary medicine, namely amoxicillin, ceftiofur, apramycin, neomycin, enrofloxacin, colistin, erythromycin, florfenicol, lincomycin, oxytetracycline, sulfamethazine, tiamulin and the ionophore narasin. Treatments with subinhibitory dosages were performed with and without supplementation with the antioxidant edaravone, known as a mitigator of the inducibility effect of several antibiotics on plasmid conjugation frequency (PCF). Expression of SOS-response associated genes and fluorescence-based reactive oxygen species (ROS) detection assays were performed to evaluate the stress oxidative response.<br><br>RESULTS: Increased PCFs were observed for both strains when treating with florfenicol and oxytetracycline. Increased expression of the SOS-associated recA gene also occurred concomitantly, as well as increased ROS production. Addition of edaravone to the treatments reduced their PCF and also showed a decreasing effect on SOS and ROS responses for both plasmid scaffolds.<br><br>CONCLUSIONS: We showed here that some antibiotics used in veterinary medicine may induce transfer of plasmid-encoded resistance and therefore may contribute to the worldwide spread of antibiotic resistance genes.}, }
@article {pmid37485539, year = {2023}, author = {Li, L and Liu, Y and Xiao, Q and Xiao, Z and Meng, D and Yang, Z and Deng, W and Yin, H and Liu, Z}, title = {Dissecting the HGT network of carbon metabolic genes in soil-borne microbiota.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1173748}, pmid = {37485539}, issn = {1664-302X}, abstract = {The microbiota inhabiting soil plays a significant role in essential life-supporting element cycles. Here, we investigated the occurrence of horizontal gene transfer (HGT) and established the HGT network of carbon metabolic genes in 764 soil-borne microbiota genomes. Our study sheds light on the crucial role of HGT components in microbiological diversification that could have far-reaching implications in understanding how these microbial communities adapt to changing environments, ultimately impacting agricultural practices. In the overall HGT network of carbon metabolic genes in soil-borne microbiota, a total of 6,770 nodes and 3,812 edges are present. Among these nodes, phyla Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes are predominant. Regarding specific classes, Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Bacteroidia, Actinomycetia, Betaproteobacteria, and Clostridia are dominant. The Kyoto Encyclopedia of Genes and Genomes (KEGG) functional assignments of glycosyltransferase (18.5%), glycolysis/gluconeogenesis (8.8%), carbohydrate-related transporter (7.9%), fatty acid biosynthesis (6.5%), benzoate degradation (3.1%) and butanoate metabolism (3.0%) are primarily identified. Glycosyltransferase involved in cell wall biosynthesis, glycosylation, and primary/secondary metabolism (with 363 HGT entries), ranks first overwhelmingly in the list of most frequently identified carbon metabolic HGT enzymes, followed by pimeloyl-ACP methyl ester carboxylesterase, alcohol dehydrogenase, and 3-oxoacyl-ACP reductase. Such HGT events mainly occur in the peripheral functions of the carbon metabolic pathway instead of the core section. The inter-microbe HGT genetic traits in soil-borne microbiota genetic sequences that we recognized, as well as their involvement in the metabolism and regulation processes of carbon organic, suggest a pervasive and substantial effect of HGT on the evolution of microbes.}, }
@article {pmid37483384, year = {2023}, author = {Wang, M}, title = {Editorial: Antimicrobial resistance dissemination and horizontal gene transfer.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1240680}, pmid = {37483384}, issn = {2235-2988}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Bacteria/genetics ; }, }
@article {pmid37478933, year = {2023}, author = {Yan, Q and Xu, Y and Zhong, Z and Xu, Y and Lin, X and Cao, Z and Feng, G}, title = {Insights into antibiotic resistance-related changes in microbial communities, resistome and mobilome in paddy irrigated with reclaimed wastewater.}, journal = {The Science of the total environment}, volume = {900}, number = {}, pages = {165672}, doi = {10.1016/j.scitotenv.2023.165672}, pmid = {37478933}, issn = {1879-1026}, mesh = {*Wastewater ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology/analysis ; Soil ; *Microbiota ; Drug Resistance, Microbial/genetics ; }, abstract = {Reclaimed wastewater (reclaimed wastewater, RWW) from municipal wastewater treatment plants for paddy irrigation is a well-established practice to alleviate water scarcity. However, the reuse may result in the persistent exposure of the paddy to residual antibiotics in RWW. Continuous presence of even low-level antibiotics can exert selective pressure on microbiota, resulting in the proliferation and dissemination of antibiotic resistance genes (ARGs) in paddy. In this study, metagenomic analysis was applied to firstly deciphered the effects of residual antibiotics on microbiome and resistome in constructed mesocosm-scale paddy soils. The diversity and abundance of ARG have remarkably risen with the increasing antibiotic concentration in RWW. Network analysis revealed that 28 genera belonging to six phyla were considered as the potential ARG hosts, and their abundances were enhanced with increasing antibiotic concentrations. A partial least-squares path model indicated that the microbial community was the principal direct driver of the ARG abundance and the resistome alteration in paddy soil under long-term RWW irrigation. Microbes may acquire ARGs via horizontal gene transfer. IntI1 could play an essential role in the propagation and spread of ARGs. Functional analysis suggested that enhanced SOS response and T4SSs (Type IV secretion systems) modules could stimulate horizontal transfer potential and promote the ARG abundance. The obtained results provide a scientific decision for assessing the ecological risk of RWW application.}, }
@article {pmid37478352, year = {2023}, author = {Deng, Z and Chen, H and Wang, J and Zhang, N and Han, Z and Xie, Y and Zhang, X and Fang, X and Yu, H and Zhang, D and Yue, Z and Zhang, C}, title = {Marine Dehalogenator and Its Chaperones: Microbial Duties and Responses in 2,4,6-Trichlorophenol Dechlorination.}, journal = {Environmental science &amp; technology}, volume = {57}, number = {30}, pages = {11300-11312}, doi = {10.1021/acs.est.3c03738}, pmid = {37478352}, issn = {1520-5851}, abstract = {Marine environments contain diverse halogenated organic compounds (HOCs), both anthropogenic and natural, nourishing a group of versatile organohalide-respiring bacteria (OHRB). Here, we identified a novel OHRB (Peptococcaceae DCH) with conserved motifs but phylogenetically diverse reductive dehalogenase catalytic subunit (RdhAs) from marine enrichment culture. Further analyses clearly demonstrate the horizontal gene transfer of rdhAs among marine OHRB. Moreover, 2,4,6-trichlorophenol (TCP) was dechlorinated to 2,4-dichlorophenol and terminated at 4-chlorophenol in culture. Dendrosporobacter and Methanosarcina were the two dominant genera, and the constructed and verified metabolic pathways clearly demonstrated that the former provided various substrates for other microbes, while the latter drew nutrients, but might provide little benefit to microbial dehalogenation. Furthermore, Dendrosporobacter could readily adapt to TCP, and sporulation-related proteins of Dendrosporobacter were significantly upregulated in TCP-free controls, whereas other microbes (e.g., Methanosarcina and Aminivibrio) became more active, providing insights into how HOCs shape microbial communities. Additionally, sulfate could affect the dechlorination of Peptococcaceae DCH, but not debromination. Considering their electron accessibility and energy generation, the results clearly demonstrate that bromophenols are more suitable than chlorophenols for the enrichment of OHRB in marine environments. This study will greatly enhance our understanding of marine OHRB (rdhAs), auxiliary microbes, and microbial HOC adaptive mechanisms.}, }
@article {pmid37476668, year = {2023}, author = {Agarwal, V and Stubits, R and Nassrullah, Z and Dillon, MM}, title = {Pangenome insights into the diversification and disease specificity of worldwide Xanthomonas outbreaks.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1213261}, pmid = {37476668}, issn = {1664-302X}, abstract = {The bacterial genus Xanthomonas is responsible for disease outbreaks in several hundred plant species, many of them economically important crops. In the era of next-generation sequencing, thousands of strains from this genus have now been sequenced as part of isolated studies that focus on outbreak characterization, host range, diversity, and virulence factor identification. However, these data have not been synthesized and we lack a comprehensive phylogeny for the genus, with some species designations in public databases still relying on phenotypic similarities and representative sequence typing. The extent of genetic cohesiveness among Xanthomonas strains, the distribution of virulence factors across strains, and the impact of evolutionary history on host range across the genus are also poorly understood. In this study, we present a pangenome analysis of 1,910 diverse Xanthomonas genomes, highlighting their evolutionary relationships, the distribution of virulence-associated genes across strains, and rates of horizontal gene transfer. We find a number of broadly conserved classes of virulence factors and considerable diversity in the Type 3 Secretion Systems (T3SSs) and Type 3 Secreted Effector (T3SE) repertoires of different Xanthomonas species. We also use these data to re-assign incorrectly classified strains to phylogenetically informed species designations and find evidence of both monophyletic host specificity and convergent evolution of phylogenetically distant strains to the same host. Finally, we explore the role of recombination in maintaining genetic cohesion within the Xanthomonas genus as a result of both ancestral and recent recombination events. Understanding the evolutionary history of Xanthomonas species and the relationship of key virulence factors with host-specificity provides valuable insight into the mechanisms through which Xanthomonas species shift between hosts and will enable us to develop more robust resistance strategies against these highly virulent pathogens.}, }
@article {pmid37475746, year = {2023}, author = {Bhatia, RP and Kirit, HA and Lewis, CM and Sankaranarayanan, K and Bollback, JP}, title = {Evolutionary barriers to horizontal gene transfer in macrophage-associated Salmonella.}, journal = {Evolution letters}, volume = {7}, number = {4}, pages = {227-239}, pmid = {37475746}, issn = {2056-3744}, abstract = {Horizontal gene transfer (HGT) is a powerful evolutionary force facilitating bacterial adaptation and emergence of novel phenotypes. Several factors, including environmental ones, are predicted to restrict HGT, but we lack systematic and experimental data supporting these predictions. Here, we address this gap by measuring the relative fitness of 44 genes horizontally transferred from Escherichia coli to Salmonella enterica in infection-relevant environments. We estimated the distribution of fitness effects in each environment and identified that dosage-dependent effects across different environments are a significant barrier to HGT. The majority of genes were found to be deleterious. We also found longer genes had stronger negative fitness consequences than shorter ones, showing that gene length was negatively associated with HGT. Furthermore, fitness effects of transferred genes were found to be environmentally dependent. In summary, a substantial fraction of transferred genes had a significant fitness cost on the recipient, with both gene characteristics and the environment acting as evolutionary barriers to HGT.}, }
@article {pmid37475130, year = {2023}, author = {Yang, G and Cao, JM and Cui, HL and Zhan, XM and Duan, G and Zhu, YG}, title = {Artificial Sweetener Enhances the Spread of Antibiotic Resistance Genes During Anaerobic Digestion.}, journal = {Environmental science &amp; technology}, volume = {57}, number = {30}, pages = {10919-10928}, doi = {10.1021/acs.est.2c08673}, pmid = {37475130}, issn = {1520-5851}, mesh = {*Sweetening Agents/pharmacology ; Drug Resistance, Microbial/drug effects/genetics ; Anaerobiosis/drug effects ; Genes, Bacterial ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/pharmacology ; }, abstract = {Artificial sweeteners have been frequently detected in the feedstocks of anaerobic digestion. As these sweeteners can lead to the shift of anaerobic microbiota in the gut similar to that caused by antibiotics, we hypothesize that they may have an antibiotic-like impact on antibiotic resistance genes (ARGs) in anaerobic digestion. However, current understanding on this topic is scarce. This investigation aimed to examine the potential impact of acesulfame, a typical artificial sweetener, on ARGs in anaerobic digestion by using metagenomics sequencing and qPCR. It was found that acesulfame increased the number of detected ARG classes and the abundance of ARGs during anaerobic digestion. The abundance of typical mobile genetic elements (MGEs) and the number of potential hosts of ARGs also increased under acesulfame exposure, suggesting the enhanced potential of horizontal gene transfer of ARGs, which was further confirmed by the correlation analysis between absolute abundances of the targeted ARGs and MGEs. The increased horizontal dissemination of ARGs may be associated with the SOS response induced by the increased ROS production, and the increased cellular membrane permeability. These findings indicate that artificial sweeteners may accelerate ARG spread through digestate disposal, thus corresponding strategies should be considered to prevent potential risks in practice.}, }
@article {pmid37468904, year = {2023}, author = {Liu, B and Warnow, T}, title = {Weighted ASTRID: fast and accurate species trees from weighted internode distances.}, journal = {Algorithms for molecular biology : AMB}, volume = {18}, number = {1}, pages = {6}, pmid = {37468904}, issn = {1748-7188}, abstract = {BACKGROUND: Species tree estimation is a basic step in many biological research projects, but is complicated by the fact that gene trees can differ from the species tree due to processes such as incomplete lineage sorting (ILS), gene duplication and loss (GDL), and horizontal gene transfer (HGT), which can cause different regions within the genome to have different evolutionary histories (i.e., "gene tree heterogeneity"). One approach to estimating species trees in the presence of gene tree heterogeneity resulting from ILS operates by computing trees on each genomic region (i.e., computing "gene trees") and then using these gene trees to define a matrix of average internode distances, where the internode distance in a tree T between two species x and y is the number of nodes in T between the leaves corresponding to x and y. Given such a matrix, a tree can then be computed using methods such as neighbor joining. Methods such as ASTRID and NJst (which use this basic approach) are provably statistically consistent, very fast (low degree polynomial time) and have had high accuracy under many conditions that makes them competitive with other popular species tree estimation methods. In this study, inspired by the very recent work of weighted ASTRAL, we present weighted ASTRID, a variant of ASTRID that takes the branch uncertainty on the gene trees into account in the internode distance.<br><br>RESULTS: Our experimental study evaluating weighted ASTRID typically shows improvements in accuracy compared to the original (unweighted) ASTRID, and shows competitive accuracy against weighted ASTRAL, the state of the art. Our re-implementation of ASTRID also improves the runtime, with marked improvements on large datasets.<br><br>CONCLUSIONS: Weighted ASTRID is a new and very fast method for species tree estimation that typically improves upon ASTRID and has comparable accuracy to weighted ASTRAL, while remaining much faster. Weighted ASTRID is available at https://github.com/RuneBlaze/internode .}, }
@article {pmid37467272, year = {2023}, author = {Li, XL and Sun, Y and Yin, Y and Zhan, S and Wang, C}, title = {A bacterial-like Pictet-Spenglerase drives the evolution of fungi to produce β-carboline glycosides together with separate genes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {30}, pages = {e2303327120}, pmid = {37467272}, issn = {1091-6490}, mesh = {Animals ; Carbolines ; *Alkaloids ; Cytochrome P-450 Enzyme System/genetics ; Multigene Family ; Fungi/genetics ; *Beauveria/genetics ; }, abstract = {Diverse β-carboline (βC) alkaloids are produced by microbes, plants, and animals with myriad bioactivities and drug potentials. However, the biosynthetic mechanism of βCs remains largely elusive, especially regarding the hydroxyl and glucosyl modifications of βCs. Here, we report the presence of the bacterial-like Pictet-Spenglerase gene Fcs1 in the entomopathogenic Beauveria fungi that can catalyze the biosynthesis of the βC skeleton. The overexpression of Fcs1 in Beauveria bassiana led to the identification of six βC methyl glycosides, termed bassicarbosides (BCSs) A-F. We verified that the cytochrome P450 (CYP) genes adjacent to Fcs1 cannot oxidize βCs. Alternatively, the separated CYP684B2 family gene Fcs2 was identified to catalyze βC hydroxylation together with its cofactor gene Fcs3. The functional homologue of Fcs2 is only present in the Fcs1-containing fungi and highly similar to the Fcs1-connected yet nonfunctional CYP. Both evolved quicker than those from fungi without Fcs1 homologues. Finally, the paired methyl/glucosyl transferase genes were verified to mediate the production of BCSs from hydroxy-βCs. All these functionally verified genes are located on different chromosomes of Beauveria, which is in contrast to the typical content-clustered feature of fungal biosynthetic gene clusters (BGCs). We also found that the production of BCSs selectively contributed to fungal infection of different insect species. Our findings shed light on the biosynthetic mechanism of βC glycosides, including the identification of a βC hydroxylase. The results of this study also propose an evolving process of fungal BGC formation following the horizontal transfer of a bacterial gene to fungi.}, }
@article {pmid37467082, year = {2023}, author = {Jen, FE and Abrahams, JL and Schulz, BL and Lamelas, A and Pluschke, G and Jennings, MP}, title = {High-Frequency Changes in Pilin Glycosylation Patterns during Neisseria meningitidis Serogroup a Meningitis Outbreaks in the African Meningitis Belt.}, journal = {ACS infectious diseases}, volume = {9}, number = {8}, pages = {1451-1457}, pmid = {37467082}, issn = {2373-8227}, mesh = {Humans ; *Neisseria meningitidis/genetics ; Fimbriae Proteins/genetics ; Glycosylation ; Serogroup ; Disease Outbreaks ; *Meningitis ; Polysaccharides ; }, abstract = {In the meningitis belt of sub-Saharan Africa, there are cyclic meningococcal epidemics that coincide with clonal waves of Neisseria meningitidis carriage and invasive disease. In the framework of longitudinal colonization and disease studies in Ghana and Burkina Faso, meningococcal isolates belonging to the closely related hypervirulent A:ST-5, A:ST-7, and A:ST-2859 clones have been collected from 1998 to 2011 during meningococcal outbreaks. A comparative whole-genome sequencing study with 100 of these isolates identified the pilin glycosylation (pgl) locus as one hot spot of recombination. Frequent exchange of pgl genes in N. meningitidis by lateral gene transfer results in differences in the glycosylation patterns of pilin and other cell surface glycoproteins. In this study, we looked at both recombination and phase variation of the pgl genes of these clinical isolates and analyzed the glycan structures resulting from different pgl alleles and their variable expression. Our results indicate that the basal O-linked sugar of the glycans expressed by these isolates is masked by various additional mono- or disaccharide structures whose expression is highly variable due to the phase-variable expression of pgl genes. We also observed a distinct glycoform in two isolates with pgl loci that were modified by recombination. These data suggest that variation in N. meningitidis protein glycosylation could be crucial for bacterial adaptation to evade herd immunity in semi-immune populations. Investigating pilin glycosylation in N. meningitidis can shed light on the mechanisms by which this pathogen evades the host immune response, and may help identify potential targets for novel therapies and vaccines.}, }
@article {pmid37462915, year = {2024}, author = {Alav, I and Buckner, MMC}, title = {Non-antibiotic compounds associated with humans and the environment can promote horizontal transfer of antimicrobial resistance genes.}, journal = {Critical reviews in microbiology}, volume = {50}, number = {6}, pages = {993-1010}, pmid = {37462915}, issn = {1549-7828}, support = {MR/V009885/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Gene Transfer, Horizontal ; Humans ; *Plasmids/genetics ; *Bacteria/genetics/drug effects/metabolism ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Environmental Pollutants/metabolism ; Conjugation, Genetic ; }, abstract = {Horizontal gene transfer plays a key role in the global dissemination of antimicrobial resistance (AMR). AMR genes are often carried on self-transmissible plasmids, which are shared amongst bacteria primarily by conjugation. Antibiotic use has been a well-established driver of the emergence and spread of AMR. However, the impact of commonly used non-antibiotic compounds and environmental pollutants on AMR spread has been largely overlooked. Recent studies found common prescription and over-the-counter drugs, artificial sweeteners, food preservatives, and environmental pollutants, can increase the conjugative transfer of AMR plasmids. The potential mechanisms by which these compounds promote plasmid transmission include increased membrane permeability, upregulation of plasmid transfer genes, formation of reactive oxygen species, and SOS response gene induction. Many questions remain around the impact of most non-antibiotic compounds on AMR plasmid conjugation in clinical isolates and the long-term impact on AMR dissemination. By elucidating the role of routinely used pharmaceuticals, food additives, and pollutants in the dissemination of AMR, action can be taken to mitigate their impact by closely monitoring use and disposal. This review will discuss recent progress on understanding the influence of non-antibiotic compounds on plasmid transmission, the mechanisms by which they promote transfer, and the level of risk they pose.}, }
@article {pmid37461575, year = {2023}, author = {Asad, A and Jahan, I and Munni, MA and Begum, R and Mukta, MA and Saif, K and Faruque, SN and Hayat, S and Islam, Z}, title = {Increasing trend of antibiotic resistance in Shigella in Bangladesh: a plasmid-mediated transfer of mphA macrolide resistance gene.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {37461575}, issn = {2693-5015}, support = {D43 TW010540/TW/FIC NIH HHS/United States ; K43 TW011447/TW/FIC NIH HHS/United States ; }, abstract = {Shigellosis remains a common gastrointestinal disease mostly in children <5 years of age in developing countries. Azithromycin (AZM), a macrolide, is currently the first-line treatment for shigellosis in Bangladesh; ciprofloxacin (CIP) and ceftriaxone (CRO) are also used frequently. We aimed to evaluate the current epidemiology of antimicrobial resistance (AMR) and mechanism(s) of increasing macrolide resistance in Shigella in Bangladesh. A total of 2407 clinical isolates of Shigella from 2009 to 2016 were studied. Over the study period, Shigella sonnei was gradually increasing and become predominant (55%) over Shigella flexneri (36%) by 2016. We used CLSI-guided epidemiological cut-off value (ECV) for AZM in Shigella to set resistance breakpoints (zone-diameter ≤ 15 mm for S. flexneri and ≤ 11 mm for S. sonnei). Between 2009 and 2016, AZM resistance increased from 22% to approximately 60%, CIP resistance increased by 40%, and CRO resistance increased from zero to 15%. The mphA gene was the key macrolide resistance factor in Shigella; a 63MDa conjugative middle-range plasmid was harboring AZM and CRO resistance factors. Our findings show that, especially after 2014, there has been a rapid increase in resistance to the three most effective antibiotics. The rapid spread of macrolide (AZM) resistance genes among Shigella are driven by horizontal gene transfer rather than direct lineage.}, }
@article {pmid37460464, year = {2023}, author = {Morreale, DP and Porsch, EA and Kern, BK and St Geme, JW and Planet, PJ}, title = {Acquisition, co-option, and duplication of the rtx toxin system and the emergence of virulence in Kingella.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {4281}, pmid = {37460464}, issn = {2041-1723}, support = {R01 AI121015/AI/NIAID NIH HHS/United States ; R01 AI172841/AI/NIAID NIH HHS/United States ; T32 AI141393/AI/NIAID NIH HHS/United States ; }, mesh = {Phylogeny ; Virulence/genetics ; *Bacterial Toxins/genetics ; Kingella/genetics ; *Kingella kingae/genetics ; }, abstract = {The bacterial genus Kingella includes two pathogenic species, namely Kingella kingae and Kingella negevensis, as well as strictly commensal species. Both K. kingae and K. negevensis secrete a toxin called RtxA that is absent in the commensal species. Here we present a phylogenomic study of the genus Kingella, including new genomic sequences for 88 clinical isolates, genotyping of another 131 global isolates, and analysis of 52 available genomes. The phylogenetic evidence supports that the toxin-encoding operon rtxCA was acquired by a common ancestor of the pathogenic Kingella species, and that a preexisting type-I secretion system was co-opted for toxin export. Subsequent genomic reorganization distributed the toxin machinery across two loci, with 30-35% of K. kingae strains containing two copies of the rtxA toxin gene. The rtxA duplication is largely clonal and is associated with invasive disease. Assays with isogenic strains show that a single copy of rtxA is associated with reduced cytotoxicity in vitro. Thus, our study identifies key steps in the evolutionary transition from commensal to pathogen, including horizontal gene transfer, co-option of an existing secretion system, and gene duplication.}, }
@article {pmid37459818, year = {2023}, author = {Kelleher, ES}, title = {Jack of all trades versus master of one: how generalist versus specialist strategies of transposable elements relate to their horizontal transfer between lineages.}, journal = {Current opinion in genetics &amp; development}, volume = {81}, number = {}, pages = {102080}, pmid = {37459818}, issn = {1879-0380}, support = {R35 GM138112/GM/NIGMS NIH HHS/United States ; }, mesh = {*DNA Transposable Elements/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genomics ; }, abstract = {Transposable elements (TEs) are obligate genomic parasites, relying on host germline cells to ensure their replication and passage to future generations. While some TEs exhibit high fidelity to their host genome, being passed from parent to offspring through vertical transmission for millions of years, others frequently invade new and distantly related hosts through horizontal transfer. In this review, I highlight how the complexity of interactions between TE and host required for transposition may be an important determinant of horizontal transfer: with TEs with more complex regulatory requirements being less able to invade new host genomes.}, }
@article {pmid37452100, year = {2023}, author = {Koch, L}, title = {Maverick - top gun of horizontal gene transfer.}, journal = {Nature reviews. Genetics}, volume = {24}, number = {9}, pages = {586}, pmid = {37452100}, issn = {1471-0064}, }
@article {pmid37450185, year = {2023}, author = {Loret, S and Habib, B and Romain, P and Roba, A and Reboul, A}, title = {Prevention of horizontal transfer of laboratory plasmids to environmental bacteria: comparison of the effectiveness of a few disinfection approaches to degrade DNA.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {38}, pages = {89369-89380}, pmid = {37450185}, issn = {1614-7499}, support = {Grant Recipient/ Boutaina HABIB//UNamur GRant for Foreign PhD Students/ ; }, mesh = {*Disinfection/methods ; Wastewater ; Escherichia coli/genetics ; Laboratories ; Plasmids ; Bacteria/genetics ; DNA ; *Disinfectants/pharmacology ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; }, abstract = {The routine work of any molecular biology laboratory includes the daily use of microorganisms, including strains of E. coli, transformed with a variety of plasmids expressing at least one antibiotic resistance gene (ARG). Therefore, to avoid the accidental release of ARGs into environmental water, methods for disinfection of liquid laboratory waste must be effective in destroying nucleic acids. In support of this recommendation, the origin of replication of Enterobacteriaceae plasmids has been detected in strains of non-Enterobacteriaceae bacteria isolated from wastewater from laboratories and research institutes, suggesting that interspecific transfer of laboratory plasmids had occurred. Using quantitative polymerase chain reaction, we determined the decimal reduction value (D value, expressed as concentration of disinfectant or length of physical treatment) of several decontamination methods for their DNA degradation effect on cultures of E. coli Top10 transformed with a kanamycin resistant plasmid (pET28A + or pEGFP-C2). The estimated D values were 0.7 M for sulfuric acid, 6.3% for a commercial P3 disinfectant, 25 min for steam sterilization at 121 °C, and 49 min for disinfection by UVC. A 20-min treatment of bacteria cultures with a final concentration of 1-10% sodium hypochlorite was found to be ineffective in completely destroying a bacteria plasmid gene marker (coding for the pBR322 origin of replication). Residual DNA from NaClO-treated cells was 60%, while it decreased under 10% using the commercial disinfectant P3 diluted at 5%. As the degradation was incomplete in both cases, we recommend avoiding discharge of disinfected liquid waste to wastewater (even after chemical neutralization) without additional plasmid destruction treatment, to prevent horizontal transfer of laboratory ARGs to environmental bacteria.}, }
@article {pmid37445761, year = {2023}, author = {Xiao, Y and Zhang, Y and Xie, F and Olsen, RH and Shi, L and Li, L}, title = {Inhibition of Plasmid Conjugation in Escherichia coli by Targeting rbsB Gene Using CRISPRi System.}, journal = {International journal of molecular sciences}, volume = {24}, number = {13}, pages = {}, pmid = {37445761}, issn = {1422-0067}, mesh = {Humans ; *Escherichia coli/metabolism ; *RNA, Guide, CRISPR-Cas Systems ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Plasmids/genetics ; Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; }, abstract = {Bacterial conjugation constitutes a major horizontal gene transfer mechanism for the dissemination of antibiotic-resistant genes (ARGs) among human pathogens. The spread of ARGs can be halted or diminished by interfering with the conjugation process. In this study, we explored the possibility of using an rbsB gene as a single target to inhibit plasmid-mediated horizontal gene transfer in Escherichia coli by CRISPR interference (CRISPRi) system. Three single-guide RNAs (sgRNAs) were designed to target the rbsB gene. The transcriptional levels of the rbsB gene, the conjugation-related genes, and the conjugation efficiency in the CRISPRi strain were tested. We further explored the effect of the repressed expression of the rbsB gene on the quorum sensing (QS) system and biofilm formation. The results showed that the constructed CRISPRi system was effective in repressing the transcriptional level of the rbsB gene at a rate of 66.4%. The repressed expression of the rbsB gene resulted in the reduced conjugation rate of RP4 plasmid by 88.7%, which significantly inhibited the expression of the conjugation-related genes (trbBp, trfAp, traF and traJ) and increased the global regulator genes (korA, korB and trbA). The repressed rbsB gene expression reduced the depletion of autoinducer 2 signals (AI-2) by 12.8% and biofilm formation by a rate of 68.2%. The results of this study indicated the rbsB gene could be used as a universal target for the inhibition of conjugation. The constructed conjugative CRISPRi system has the potential to be used in ARG high-risk areas.}, }
@article {pmid37442321, year = {2023}, author = {van Hamelsveld, S and Kurenbach, B and Paull, DJ and Godsoe, WA and Ferguson, GC and Heinemann, JA}, title = {Indigenous food sources as vectors of Escherichia coli and antibiotic resistance.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {334}, number = {}, pages = {122155}, doi = {10.1016/j.envpol.2023.122155}, pmid = {37442321}, issn = {1873-6424}, mesh = {Animals ; Humans ; Anti-Bacterial Agents/pharmacology ; *Bivalvia ; Drug Resistance, Microbial ; *Escherichia coli ; Maori People ; Plasmids ; *Water Microbiology ; *Food Contamination ; }, abstract = {The contamination of surface waters by fecal bacteria, measured by the number of Escherichia coli, is a significant public health issue. When these bacteria are also resistant to antimicrobials, infections are more complicated to treat. While water is regularly tested at recreational sites, wild-harvested foods, known as mahinga kai by the indigenous Māori people of Aotearoa New Zealand, are commonly overlooked as a source of exposure to potential pathogens and antimicrobial resistance (AMR). We investigate two likely sources of risk from harvesting aquatic wild foods. The first is water contact, and the second is contact with/ingestion of the harvest. We used E. coli as a proxy for microbial water quality at harvesting sites. Two popular mahinga kai species were also harvested and assessed. We found antibiotic-resistant bacteria on watercress (Nasturtium officinale) and cockles (Austrovenus stutchburyi). One-third of E. coli isolates were conjugative donors of at least one resistance phenotype. Tank experiments were used to track the internalization of E. coli by Greenshell/lip mussels (Perna canaliculus). Greenshell mussels kept at environmentally relevant concentrations of E. coli were colonized to levels considered unsafe for human consumption in 24 h. Finally, we measured horizontal gene transfer between bacteria within the shellfish, what we termed 'intra-shellular' conjugation. The transmission frequency of plasmid RP4 was significantly higher in mussels than in water alone. Our results indicate that shellfish could promote the dissemination of antibiotic resistance. They highlight the need to limit or reduce human pathogenic bacteria where food is gathered.}, }
@article {pmid37440893, year = {2023}, author = {Brenner, E and Sreevatsan, S}, title = {Cold Cas: reevaluating the occurrence of CRISPR/Cas systems in Mycobacteriaceae.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1204838}, pmid = {37440893}, issn = {1664-302X}, support = {T15 LM009451/LM/NLM NIH HHS/United States ; }, abstract = {Bacterial CRISPR/Cas systems target foreign genetic elements such as phages and regulate gene expression by some pathogens, even in the host. The system is a marker for evolutionary history and has been used for inferences in Mycobacterium tuberculosis for 30 years. However, knowledge about mycobacterial CRISPR/Cas systems remains limited. It is believed that Type III-A Cas systems are exclusive to Mycobacterium canettii and the M. tuberculosis complex (MTBC) of organisms and that very few of the >200 diverse species of non-tuberculous mycobacteria (NTM) possess any CRISPR/Cas system. This study sought unreported CRISPR/Cas loci across NTM to better understand mycobacterial evolution, particularly in species phylogenetically near the MTBC. An analysis of available mycobacterial genomes revealed that Cas systems are widespread across Mycobacteriaceae and that some species contain multiple types. The phylogeny of Cas loci shows scattered presence in many NTM, with variation even within species, suggesting gains/losses of these loci occur frequently. Cas Type III-A systems were identified in pathogenic Mycobacterium heckeshornense and the geological environmental isolate Mycobacterium SM1. In summary, mycobacterial CRISPR/Cas systems are numerous, Type III-A systems are unreliable as markers for MTBC evolution, and mycobacterial horizontal gene transfer appears to be a frequent source of genetic variation.}, }
@article {pmid37440885, year = {2023}, author = {Verhaegen, M and Bergot, T and Liebana, E and Stancanelli, G and Streissl, F and Mingeot-Leclercq, MP and Mahillon, J and Bragard, C}, title = {On the use of antibiotics to control plant pathogenic bacteria: a genetic and genomic perspective.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1221478}, pmid = {37440885}, issn = {1664-302X}, abstract = {Despite growing attention, antibiotics (such as streptomycin, oxytetracycline or kasugamycin) are still used worldwide for the control of major bacterial plant diseases. This raises concerns on their potential, yet unknown impact on antibiotic and multidrug resistances and the spread of their genetic determinants among bacterial pathogens. Antibiotic resistance genes (ARGs) have been identified in plant pathogenic bacteria (PPB), with streptomycin resistance genes being the most commonly reported. Therefore, the contribution of mobile genetic elements (MGEs) to their spread among PPB, as well as their ability to transfer to other bacteria, need to be further explored. The only well-documented example of ARGs vector in PPB, Tn5393 and its highly similar variants (carrying streptomycin resistance genes), is concerning because of its presence outside PPB, in Salmonella enterica and Klebsiella pneumoniae, two major human pathogens. Although its structure among PPB is still relatively simple, in human- and animal-associated bacteria, Tn5393 has evolved into complex associations with other MGEs and ARGs. This review sheds light on ARGs and MGEs associated with PPB, but also investigates the potential role of antibiotic use in resistance selection in plant-associated bacteria.}, }
@article {pmid37440531, year = {2023}, author = {Gulay, A and Fournier, G and Smets, BF and Girguis, PR}, title = {Proterozoic Acquisition of Archaeal Genes for Extracellular Electron Transfer: A Metabolic Adaptation of Aerobic Ammonia-Oxidizing Bacteria to Oxygen Limitation.}, journal = {Molecular biology and evolution}, volume = {40}, number = {8}, pages = {}, pmid = {37440531}, issn = {1537-1719}, mesh = {Oxidation-Reduction ; *Ammonia/metabolism ; Electrons ; Phylogeny ; Oxygen ; Genes, Archaeal ; *Gammaproteobacteria/metabolism ; }, abstract = {Many aerobic microbes can utilize alternative electron acceptors under oxygen-limited conditions. In some cases, this is mediated by extracellular electron transfer (or EET), wherein electrons are transferred to extracellular oxidants such as iron oxide and manganese oxide minerals. Here, we show that an ammonia-oxidizer previously known to be strictly aerobic, Nitrosomonas communis, may have been able to utilize a poised electrode to maintain metabolic activity in anoxic conditions. The presence and activity of multiheme cytochromes in N. communis further suggest a capacity for EET. Molecular clock analysis shows that the ancestors of β-proteobacterial ammonia oxidizers appeared after Earth's atmospheric oxygenation when the oxygen levels were >10-4pO2 (present atmospheric level [PAL]), consistent with aerobic origins. Equally important, phylogenetic reconciliations of gene and species trees show that the multiheme c-type EET proteins in Nitrosomonas and Nitrosospira lineages were likely acquired by gene transfer from γ-proteobacteria when the oxygen levels were between 0.1 and 1 pO2 (PAL). These results suggest that β-proteobacterial EET evolved during the Proterozoic when oxygen limitation was widespread, but oxidized minerals were abundant.}, }
@article {pmid37439570, year = {2023}, author = {Diorio-Toth, L and Wallace, MA and Farnsworth, CW and Wang, B and Gul, D and Kwon, JH and Andleeb, S and Burnham, CD and Dantas, G}, title = {Intensive care unit sinks are persistently colonized with multidrug resistant bacteria and mobilizable, resistance-conferring plasmids.}, journal = {mSystems}, volume = {8}, number = {4}, pages = {e0020623}, pmid = {37439570}, issn = {2379-5077}, support = {F30 AI157161/AI/NIAID NIH HHS/United States ; R01 HD092414/HD/NICHD NIH HHS/United States ; U01 AI123394/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Drug Resistance, Multiple, Bacterial/genetics ; Prospective Studies ; Plasmids/genetics ; *Intensive Care Units ; Bacteria/genetics ; Anti-Bacterial Agents ; }, abstract = {Contamination of hospital sinks with microbial pathogens presents a serious potential threat to patients, but our understanding of sink colonization dynamics is largely based on infection outbreaks. Here, we investigate the colonization patterns of multidrug-resistant organisms (MDROs) in intensive care unit sinks and water from two hospitals in the USA and Pakistan collected over 27 months of prospective sampling. Using culture-based methods, we recovered 822 bacterial isolates representing 104 unique species and genomospecies. Genomic analyses revealed long-term colonization by Pseudomonas spp. and Serratia marcescens strains across multiple rooms. Nanopore sequencing uncovered examples of long-term persistence of resistance-conferring plasmids in unrelated hosts. These data indicate that antibiotic resistance (AR) in Pseudomonas spp. is maintained both by strain colonization and horizontal gene transfer (HGT), while HGT maintains AR within Acinetobacter spp. and Enterobacterales, independent of colonization. These results emphasize the importance of proactive, genomic-focused surveillance of built environments to mitigate MDRO spread. IMPORTANCE Hospital sinks are frequently linked to outbreaks of antibiotic-resistant bacteria. Here, we used whole-genome sequencing to track the long-term colonization patterns in intensive care unit (ICU) sinks and water from two hospitals in the USA and Pakistan collected over 27 months of prospective sampling. We analyzed 822 bacterial genomes, representing over 100 different species. We identified long-term contamination by opportunistic pathogens, as well as transient appearance of other common pathogens. We found that bacteria recovered from the ICU had more antibiotic resistance genes (ARGs) in their genomes compared to matched community spaces. We also found that many of these ARGs are harbored on mobilizable plasmids, which were found shared in the genomes of unrelated bacteria. Overall, this study provides an in-depth view of contamination patterns for common nosocomial pathogens and identifies specific targets for surveillance.}, }
@article {pmid37437616, year = {2023}, author = {Li, H and Wang, K and Xu, J and Wu, H and Ma, Y and Zou, R and Song, HL}, title = {Enhanced removal of antibiotic and antibiotic resistance genes by coupling biofilm electrode reactor and manganese ore substrate up-flow microbial fuel cell constructed wetland system.}, journal = {Chemosphere}, volume = {338}, number = {}, pages = {139461}, doi = {10.1016/j.chemosphere.2023.139461}, pmid = {37437616}, issn = {1879-1298}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Bioelectric Energy Sources/microbiology ; Manganese ; Wetlands ; Sulfadiazine ; Ciprofloxacin ; Bacteria/genetics ; Electrodes ; Biofilms ; Drug Resistance, Microbial/genetics ; }, abstract = {Manganese ore substrate up-flow microbial fuel cell constructed wetland (UCW-MFC(Mn)) as an innovative wastewater treatment technology for purifying antibiotics and electricity generation with few antibiotic resistance genes (ARGs) generation has attracted attention. However, antibiotic purifying effects should be further enhanced. In this study, a biofilm electrode reactor (BER) that needs direct current driving was powered by a Mn ore anode (UCW-MFC(Mn)) to form a coupled system without requiring direct-current source. Removal efficiencies of sulfadiazine (SDZ), ciprofloxacin (CIP) and the corresponding ARGs in the coupled system were compared with composite (BER was powered by direct-current source) and anaerobic systems (both of BER and UCW-MFC were in open circuit mode). The result showed that higher antibiotic removal efficiency (94% for SDZ and 99.1% for CIP) in the coupled system was achieved than the anaerobic system (88.5% for SDZ and 98.2% for CIP). Moreover, electrical stimulation reduced antibiotic selective pressure and horizontal gene transfer potential in BER, and UCW-MFC further reduced ARG abundances by strengthening the electro-adsorption of ARG hosts determined by Network analysis. Bacterial community diversity continuously decreased in BER while it increased in UCW-MFC, indicating that BER mitigated the toxicity of antibiotic. Degree of modularity, some functional bacteria (antibiotic degrading bacteria, fermentative bacteria and EAB), and P450 enzyme related to antibiotic and xenobiotics biodegradation genes were enriched in electric field existing UCW-MFC, accounting for the higher degradation efficiency. In conclusion, this study provided an effective strategy for removing antibiotics and ARGs in wastewater by operating a BER-UCW-MFC coupled system.}, }
@article {pmid37436868, year = {2023}, author = {Mondal, A and Bansal, MS}, title = {Generalizing the Domain-Gene-Species Reconciliation Framework to Microbial Genes and Domains.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {20}, number = {6}, pages = {3511-3522}, doi = {10.1109/TCBB.2023.3294480}, pmid = {37436868}, issn = {1557-9964}, mesh = {*Gene Duplication ; *Evolution, Molecular ; Phylogeny ; Algorithms ; Genes, Microbial ; Gene Transfer, Horizontal/genetics ; Models, Genetic ; }, abstract = {Protein domains play an important role in the function and evolution of many gene families. Previous studies have shown that domains are frequently lost or gained during gene family evolution. Yet, most computational approaches for studying gene family evolution do not account for domain-level evolution within genes. To address this limitation, a new three-level reconciliation framework, called the Domain-Gene-Species (DGS) reconciliation model, has been recently developed to simultaneously model the evolution of a domain family inside one or more gene families and the evolution of those gene families inside a species tree. However, the existing model applies only to multi-cellular eukaryotes where horizontal gene transfer is negligible. In this work, we generalize the existing DGS reconciliation model by allowing for the spread of genes and domains across species boundaries through horizontal transfer. We show that the problem of computing optimal generalized DGS reconciliations, though NP-hard, is approximable to within a constant factor, where the specific approximation ratio depends on the "event costs" used. We provide two different approximation algorithms for the problem and demonstrate the impact of the generalized framework using both simulated and real biological data. Our results show that our new algorithms result in highly accurate reconstructions of domain family evolution for microbes.}, }
@article {pmid37434470, year = {2023}, author = {Bucknell, AH and McDonald, MC}, title = {That's no moon, it's a Starship: Giant transposons driving fungal horizontal gene transfer.}, journal = {Molecular microbiology}, volume = {120}, number = {4}, pages = {555-563}, doi = {10.1111/mmi.15118}, pmid = {37434470}, issn = {1365-2958}, support = {//Royal Society of Biology/ ; //the School of Biosciences at the University of Birmingham/ ; }, abstract = {To date, most reports of horizontal gene transfer (HGT) in fungi rely on genome sequence data and are therefore an indirect measure of HGT after the event has occurred. However, a novel group of class II-like transposons known as Starships may soon alter this status quo. Starships are giant transposable elements that carry dozens of genes, some of which are host-beneficial, and are linked to many recent HGT events in the fungal kingdom. These transposons remain active and mobile in many fungal genomes and their transposition has recently been shown to be driven by a conserved tyrosine-recombinase called 'Captain'. This perspective explores some of the remaining unanswered questions about how these Starship transposons move, both within a genome and between different species. We seek to outline several experimental approaches that can be used to identify the genes essential for Starship-mediated HGT and draw links to other recently discovered giant transposons outside of the fungal kingdom.}, }
@article {pmid37434168, year = {2023}, author = {Li, KL and Nakashima, K and Hisata, K and Satoh, N}, title = {Expression and possible functions of a horizontally transferred glycosyl hydrolase gene, GH6-1, in Ciona embryogenesis.}, journal = {EvoDevo}, volume = {14}, number = {1}, pages = {11}, pmid = {37434168}, issn = {2041-9139}, abstract = {BACKGROUND: The Tunicata or Urochordata is the only animal group with the ability to synthesize cellulose directly and cellulose is a component of the tunic that covers the entire tunicate body. The genome of Ciona intestinalis type A contains a cellulose synthase gene, CesA, that it acquired via an ancient, horizontal gene transfer. CesA is expressed in embryonic epidermal cells and functions in cellulose production. Ciona CesA is composed of both a glycosyltransferase domain, GT2, and a glycosyl hydrolase domain, GH6, which shows a mutation at a key position and seems functionless. Interestingly, the Ciona genome contains a glycosyl hydrolase gene, GH6-1, in which the GH6 domain seems intact. This suggests expression and possible functions of GH6-1 during Ciona embryogenesis. Is GH6-1 expressed during embryogenesis? If so, in what tissues is the gene expressed? Does GH6-1 serve a function? If so, what is it? Answers to these questions may advance our understanding of evolution of this unique animal group.<br><br>RESULTS: Quantitative reverse transcription PCR and in situ hybridization revealed that GH6-1 is expressed in epidermis of tailbud embryos and in early swimming larvae, a pattern similar to that of CesA. Expression is downregulated at later stages and becomes undetectable in metamorphosed juveniles. The GH6-1 expression level is higher in the anterior-trunk region and caudal-tip regions of late embryos. Single-cell RNA sequencing analysis of the late tailbud stage showed that cells of three clusters with epidermal identity express GH6-1, and that some of them co-express CesA. TALEN-mediated genome editing was used to generate GH6-1 knockout Ciona larvae. Around half of TALEN-electroporated larvae showed abnormal development of adhesive papillae and altered distribution of surface cellulose. In addition, three-fourths of TALEN-electroporated animals failed to complete larval metamorphosis.<br><br>CONCLUSIONS: This study showed that tunicate GH6-1, a gene that originated by horizontal gene transfer of a prokaryote gene, is recruited into the ascidian genome, and that it is expressed and functions in epidermal cells of ascidian embryos. Although further research is required, this observation demonstrates that both CesA and GH6-1 are involved in tunicate cellulose metabolism, impacting tunicate morphology and ecology.}, }
@article {pmid37429971, year = {2023}, author = {Heo, S and Oh, SE and Lee, G and Lee, J and Ha, NC and Jeon, CO and Jeong, K and Lee, JH and Jeong, DW}, title = {Staphylococcus equorum plasmid pKS1030-3 encodes auxiliary biofilm formation and trans-acting gene mobilization systems.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {11108}, pmid = {37429971}, issn = {2045-2322}, mesh = {*Staphylococcus aureus ; *Staphylococcus/genetics ; Plasmids/genetics ; Biofilms ; }, abstract = {The foodborne bacterium Staphylococcus equorum strain KS1030 harbours plasmid pSELNU1, which encodes a lincomycin resistance gene. pSELNU1 undergoes horizontal transfer between bacterial strains, thus spreading antibiotic resistance. However, the genes required for horizontal plasmid transfer are not encoded in pSELNU1. Interestingly, a relaxase gene, a type of gene related to horizontal plasmid transfer, is encoded in another plasmid of S. equorum KS1030, pKS1030-3. The complete genome of pKS1030-3 is 13,583 bp long and encodes genes for plasmid replication, biofilm formation (the ica operon), and horizontal gene transfer. The replication system of pKS1030-3 possesses the replication protein-encoding gene repB, a double-stranded origin of replication, and two single-stranded origins of replication. The ica operon, relaxase gene, and a mobilization protein-encoding gene were detected in pKS1030-3 strain-specifically. When expressed in S. aureus RN4220, the ica operon and relaxase operon of pKS1030-3 conferred biofilm formation ability and horizontal gene transfer ability, respectively. The results of our analyses show that the horizontal transfer of pSELNU1 of S. equorum strain KS1030 depends on the relaxase encoded by pKS1030-3, which is therefore trans-acting. Genes encoded in pKS1030-3 contribute to important strain-specific properties of S. equorum KS1030. These results could contribute to preventing the horizontal transfer of antibiotic resistance genes in food.}, }
@article {pmid37428925, year = {2023}, author = {Walker, AA and Robinson, SD and Merritt, DJ and Cardoso, FC and Goudarzi, MH and Mercedes, RS and Eagles, DA and Cooper, P and Zdenek, CN and Fry, BG and Hall, DW and Vetter, I and King, GF}, title = {Horizontal gene transfer underlies the painful stings of asp caterpillars (Lepidoptera: Megalopygidae).}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {29}, pages = {e2305871120}, pmid = {37428925}, issn = {1091-6490}, mesh = {Animals ; Mice ; Gene Transfer, Horizontal ; *Moths/genetics ; *Bites and Stings ; Larva/genetics ; Venoms ; *Toxins, Biological ; Pain ; Mammals ; }, abstract = {Larvae of the genus Megalopyge (Lepidoptera: Zygaenoidea: Megalopygidae), known as asp or puss caterpillars, produce defensive venoms that cause severe pain. Here, we present the anatomy, chemistry, and mode of action of the venom systems of caterpillars of two megalopygid species, the Southern flannel moth Megalopyge opercularis and the black-waved flannel moth Megalopyge crispata. We show that megalopygid venom is produced in secretory cells that lie beneath the cuticle and are connected to the venom spines by canals. Megalopygid venoms consist of large aerolysin-like pore-forming toxins, which we have named megalysins, and a small number of peptides. The venom system differs markedly from those of previously studied venomous zygaenoids of the family Limacodidae, suggestive of an independent origin. Megalopygid venom potently activates mammalian sensory neurons via membrane permeabilization and induces sustained spontaneous pain behavior and paw swelling in mice. These bioactivities are ablated by treatment with heat, organic solvents, or proteases, indicating that they are mediated by larger proteins such as the megalysins. We show that the megalysins were recruited as venom toxins in the Megalopygidae following horizontal transfer of genes from bacteria to the ancestors of ditrysian Lepidoptera. Megalopygids have recruited aerolysin-like proteins as venom toxins convergently with centipedes, cnidarians, and fish. This study highlights the role of horizontal gene transfer in venom evolution.}, }
@article {pmid37427782, year = {2023}, author = {Tang, X and Shang, J and Ji, Y and Sun, Y}, title = {PLASMe: a tool to identify PLASMid contigs from short-read assemblies using transformer.}, journal = {Nucleic acids research}, volume = {51}, number = {15}, pages = {e83}, pmid = {37427782}, issn = {1362-4962}, mesh = {*Genome, Bacterial ; *Software ; Plasmids/genetics ; Metagenome ; Metagenomics/methods ; Sequence Analysis, DNA/methods ; }, abstract = {Plasmids are mobile genetic elements that carry important accessory genes. Cataloging plasmids is a fundamental step to elucidate their roles in promoting horizontal gene transfer between bacteria. Next generation sequencing (NGS) is the main source for discovering new plasmids today. However, NGS assembly programs tend to return contigs, making plasmid detection difficult. This problem is particularly grave for metagenomic assemblies, which contain short contigs of heterogeneous origins. Available tools for plasmid contig detection still suffer from some limitations. In particular, alignment-based tools tend to miss diverged plasmids while learning-based tools often have lower precision. In this work, we develop a plasmid detection tool PLASMe that capitalizes on the strength of alignment and learning-based methods. Closely related plasmids can be easily identified using the alignment component in PLASMe while diverged plasmids can be predicted using order-specific Transformer models. By encoding plasmid sequences as a language defined on the protein cluster-based token set, Transformer can learn the importance of proteins and their correlation through positionally token embedding and the attention mechanism. We compared PLASMe and other tools on detecting complete plasmids, plasmid contigs, and contigs assembled from CAMI2 simulated data. PLASMe achieved the highest F1-score. After validating PLASMe on data with known labels, we also tested it on real metagenomic and plasmidome data. The examination of some commonly used marker genes shows that PLASMe exhibits more reliable performance than other tools.}, }
@article {pmid37425999, year = {2023}, author = {Sun, D and Sun, X and Hu, Y and Yamaichi, Y}, title = {Editorial: Horizontal gene transfer mediated bacterial antibiotic resistance, volume II.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1221606}, pmid = {37425999}, issn = {1664-302X}, }
@article {pmid37425898, year = {2023}, author = {Culbertson, EM and Levin, TC}, title = {Eukaryotic antiviral immune proteins arose via convergence, horizontal transfer, and ancient inheritance.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37425898}, issn = {2692-8205}, support = {R00 AI139344/AI/NIAID NIH HHS/United States ; R35 GM150681/GM/NIGMS NIH HHS/United States ; S10 OD028483/OD/NIH HHS/United States ; }, abstract = {Animals use a variety of cell-autonomous innate immune proteins to detect viral infections and prevent replication. Recent studies have discovered that a subset of mammalian antiviral proteins have homology to anti-phage defense proteins in bacteria, implying that there are aspects of innate immunity that are shared across the Tree of Life. While the majority of these studies have focused on characterizing the diversity and biochemical functions of the bacterial proteins, the evolutionary relationships between animal and bacterial proteins are less clear. This ambiguity is partly due to the long evolutionary distances separating animal and bacterial proteins, which obscures their relationships. Here, we tackle this problem for three innate immune families (CD-NTases [including cGAS], STINGs, and Viperins) by deeply sampling protein diversity across eukaryotes. We find that Viperins and OAS family CD-NTases are truly ancient immune proteins, likely inherited since the last eukaryotic common ancestor and possibly longer. In contrast, we find other immune proteins that arose via at least four independent events of horizontal gene transfer (HGT) from bacteria. Two of these events allowed algae to acquire new bacterial viperins, while two more HGT events gave rise to distinct superfamilies of eukaryotic CD-NTases: the Mab21 superfamily (containing cGAS) which has diversified via a series of animal-specific duplications, and a previously undefined eSMODS superfamily, which more closely resembles bacterial CD-NTases. Finally, we found that cGAS and STING proteins have substantially different histories, with STINGs arising via convergent domain shuffling in bacteria and eukaryotes. Overall, our findings paint a picture of eukaryotic innate immunity as highly dynamic, where eukaryotes build upon their ancient antiviral repertoires through the reuse of protein domains and by repeatedly sampling a rich reservoir of bacterial anti-phage genes.}, }
@article {pmid37424546, year = {2023}, author = {Sharon, BM and Hulyalkar, NV and Zimmern, PE and Palmer, KL and De Nisco, NJ}, title = {Inter-species diversity and functional genomic analyses of closed genome assemblies of clinically isolated, megaplasmid-containing Enterococcus raffinosus Er676 and ATCC49464.}, journal = {Access microbiology}, volume = {5}, number = {6}, pages = {}, pmid = {37424546}, issn = {2516-8290}, support = {R01 AI116610/AI/NIAID NIH HHS/United States ; }, abstract = {Enterococcus raffinosus is an understudied member of its genus possessing a characteristic megaplasmid contributing to a large genome size. Although less commonly associated with human infection compared to other enterococci, this species can cause disease and persist in diverse niches such as the gut, urinary tract, blood and environment. Few complete genome assemblies have been published to date for E. raffinosus . In this study, we report the complete assembly of the first clinical urinary E. raffinosus strain, Er676, isolated from a postmenopausal woman with history of recurrent urinary tract infection. We additionally completed the assembly of clinical type strain ATCC49464. Comparative genomic analyses reveal inter-species diversity driven by large accessory genomes. The presence of a conserved megaplasmid indicates it is a ubiquitous and vital genetic feature of E. raffinosus . We find that the E. raffinosus chromosome is enriched for DNA replication and protein biosynthesis genes while the megaplasmid is enriched for transcription and carbohydrate metabolism genes. Prophage analysis suggests that diversity in the chromosome and megaplasmid sequences arises, in part, from horizontal gene transfer. Er676 demonstrated the largest genome size reported to date for E. raffinosus and the highest probability of human pathogenicity. Er676 also possesses multiple antimicrobial resistance genes, of which all but one are encoded on the chromosome, and has the most complete prophage sequences. Complete assembly and comparative analyses of the Er676 and ATCC49464 genomes provide important insight into the inter-species diversity of E. raffinosus that gives it its ability to colonize and persist in the human body. Investigating genetic factors that contribute to the pathogenicity of this species will provide valuable tools to combat diseases caused by this opportunistic pathogen.}, }
@article {pmid37424042, year = {2023}, author = {Wang, B and Xu, J and Wang, Y and Stirling, E and Zhao, K and Lu, C and Tan, X and Kong, D and Yan, Q and He, Z and Ruan, Y and Ma, B}, title = {Tackling Soil ARG-Carrying Pathogens with Global-Scale Metagenomics.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {10}, number = {26}, pages = {e2301980}, pmid = {37424042}, issn = {2198-3844}, support = {42090060//National Natural Science Foundation of China/ ; 42277283//National Natural Science Foundation of China/ ; 41991334//National Natural Science Foundation of China/ ; 2023C02004//Key R&amp;D Program of Zhejjiang Province/ ; 2023C02015//Key R&amp;D Program of Zhejjiang Province/ ; }, mesh = {*Soil ; *Metagenomics ; Ecosystem ; Soil Microbiology ; Anti-Bacterial Agents ; }, abstract = {Antibiotic overuse and the subsequent environmental contamination of residual antibiotics poses a public health crisis via an acceleration in the spread of antibiotic resistance genes (ARGs) through horizontal gene transfer. Although the occurrence, distribution, and driving factors of ARGs in soils have been widely investigated, little is known about the antibiotic resistance of soilborne pathogens at a global scale. To explore this gap, contigs from 1643 globally sourced metagnomes are assembled, yielding 407 ARG-carrying pathogens (APs) with at least one ARG; APs are detected in 1443 samples (sample detection rate of 87.8%). The richness of APs is greater in agricultural soils (with a median of 20) than in non-agricultural ecosystems. Agricultural soils possess a high prevalence of clinical APs affiliated with Escherichia, Enterobacter, Streptococcus, and Enterococcus. The APs detected in agricultural soils tend to coexist with multidrug resistance genes and bacA. A global map of soil AP richness is generated, where anthropogenic and climatic factors explained AP hot spots in East Asia, South Asia, and the eastern United States. The results herein advance this understanding of the global distribution of soil APs and determine regions prioritized to control soilborne APs worldwide.}, }
@article {pmid37410611, year = {2023}, author = {Shetty, VP and Akshay, SD and Rai, P and Deekshit, VK}, title = {Integrons as the potential targets for combating multidrug resistance in Enterobacteriaceae using CRISPR- Cas9 technique.}, journal = {Journal of applied microbiology}, volume = {134}, number = {7}, pages = {}, doi = {10.1093/jambio/lxad137}, pmid = {37410611}, issn = {1365-2672}, support = {AMR/DHR/GIA/3/ECD-II-2020//ICMR/ ; }, mesh = {*Enterobacteriaceae ; *Integrons ; CRISPR-Cas Systems ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple ; Drug Resistance, Multiple, Bacterial/genetics ; }, abstract = {The emergence of multi-drug resistance (MDR) to pan-drug resistance (PDR) in Enterobacteriaceae has made treatment extremely challenging. Genetic mutations and horizontal gene transfer (HGT) through mobile genetic elements (MGEs) were frequently associated mechanisms of drug resistance in pathogens. However, transposons, plasmids, and integrons transfer MDR genes in bacterium via HGT much faster. Integrons are dsDNA segment that plays a crucial role in the adaptation and evolution of bacteria. They contain multiple gene cassettes that code for antibiotic resistance determinants that are expressed by a single promoter (Pc). Integrons are the cause of drug resistance in Enterobacteriaceae. Although alternatives to antibiotics such as bacteriophages, phage proteins, antimicrobial peptides, and natural compounds have been widely used to treat MDR infections, there have been limited efforts to reverse the antibiotic resistance ability of bacteria. Thus, silencing the genes harboured on MGEs achieved by Gene Editing Techniques (GETs) might prevent the spread of MDR. One such GETs, which has a simple design, good repeatability, low cost, and high efficiency, is CRISPR- Cas9 system. Thus, this review is a first of the kind that focuses on utilizing the structure of an integron to make it an ideal target for GETs like CRISPR- Cas9 systems.}, }
@article {pmid37409977, year = {2023}, author = {Fan, Q and Zhang, J and Shi, H and Chang, S and Hou, F}, title = {Metagenomic Profiles of Yak and Cattle Manure Resistomes in Different Feeding Patterns before and after Composting.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {7}, pages = {e0064523}, pmid = {37409977}, issn = {1098-5336}, mesh = {Animals ; Humans ; Cattle ; *Genes, Bacterial ; *Composting ; Manure/microbiology ; Metagenomics ; Drug Resistance, Microbial/genetics ; Metals ; Anti-Bacterial Agents/pharmacology ; Livestock ; }, abstract = {Antibiotic resistance is a global threat to public health, with antibiotic resistance genes (ARGs) being one of the emerging contaminants; furthermore, animal manure is an important reservoir of biocide resistance genes (BRGs) and metal resistance genes (MRGs). However, few studies have reported differences in the abundance and diversity of BRGs and MRGs between different types of animal manure and the changes in BRGs and MRGs before and after composting. This study employed a metagenomics-based approach to investigate ARGs, BRGs, MRGs, and mobile genetic elements (MGEs) of yak and cattle manure before and after composting under grazing and intensive feeding patterns. The total abundances of ARGs, clinical ARGs, BRGs, MRGs, and MGEs were lower in the manure of grazing livestock than in the manure of the intensively fed group. After composting, the total abundances of ARGs, clinical ARGs, and MGEs in intensively fed livestock manure decreased, whereas those of ARGs, clinical ARGs, MRGs, and MGEs increased in grazing livestock manure. The synergy between MGEs mediated horizontal gene transfer and vertical gene transmission via host bacteria proliferation, which was the main driver that altered the abundance and diversity of ARGs, BRGs, and MRGs in livestock manure and compost. Additionally, tetQ, IS91, mdtF, and fabK were potential indicators for estimating the total abundance of clinical ARGs, BRGs, MRGs, and MGEs in livestock manure and compost. These findings suggest that grazing livestock manure can be directly discharged into the fields, whereas intensively fed livestock manure should be composted before returning to the field. IMPORTANCE The recent increase in the prevalence of antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), and metal resistance genes (MRGs) in livestock manure poses risks to human health. Composting is known to be a promising technology for reducing the abundance of resistance genes. This study investigated the differences and changes in the abundances of ARGs, BRGs, and MRGs between yak and cattle manure under grazing and intensive feeding patterns before and after composting. The results indicate that the feeding pattern significantly affected the abundances of resistance genes in livestock manure. Manure in intensive farming should be composted before being discharged into the field, while grazing livestock manure is not suitable for composting due to an increased number of resistance genes.}, }
@article {pmid37408640, year = {2023}, author = {Kumari, K and Rawat, V and Shadan, A and Sharma, PK and Deb, S and Singh, RP}, title = {In-depth genome and pan-genome analysis of a metal-resistant bacterium Pseudomonas parafulva OS-1.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1140249}, pmid = {37408640}, issn = {1664-302X}, abstract = {A metal-resistant bacterium Pseudomonas parafulva OS-1 was isolated from waste-contaminated soil in Ranchi City, India. The isolated strain OS-1 showed its growth at 25-45°C, pH 5.0-9.0, and in the presence of ZnSO4 (upto 5 mM). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain OS-1 belonged to the genus Pseudomonas and was most closely related to parafulva species. To unravel the genomic features, we sequenced the complete genome of P. parafulva OS-1 using Illumina HiSeq 4,000 sequencing platform. The results of average nucleotide identity (ANI) analysis indicated the closest similarity of OS-1 to P. parafulva PRS09-11288 and P. parafulva DTSP2. The metabolic potential of P. parafulva OS-1 based on Clusters of Othologous Genes (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) indicated a high number of genes related to stress protection, metal resistance, and multiple drug-efflux, etc., which is relatively rare in P. parafulva strains. Compared with other parafulva strains, P. parafulva OS-1 was found to have the unique β-lactam resistance and type VI secretion system (T6SS) gene. Additionally, its genomes encode various CAZymes such as glycoside hydrolases and other genes associated with lignocellulose breakdown, suggesting that strain OS-1 have strong biomass degradation potential. The presence of genomic complexity in the OS-1 genome indicates that horizontal gene transfer (HGT) might happen during evolution. Therefore, genomic and comparative genome analysis of parafulva strains is valuable for further understanding the mechanism of resistance to metal stress and opens a perspective to exploit a newly isolated bacterium for biotechnological applications.}, }
@article {pmid37406030, year = {2023}, author = {Rhoads, DD and Pummil, J and Ekesi, NS and Alrubaye, AAK}, title = {Horizontal transfer of probable chicken-pathogenicity chromosomal islands between Staphylococcus aureus and Staphylococcus agnetis.}, journal = {PloS one}, volume = {18}, number = {7}, pages = {e0283914}, pmid = {37406030}, issn = {1932-6203}, mesh = {Phylogeny ; Gene Transfer, Horizontal ; *Staphylococcus aureus/genetics ; Staphylococcus ; Female ; Cattle ; Virulence/genetics ; Humans ; Genomic Islands/genetics ; *Staphylococcal Infections/veterinary/genetics ; Animals ; Chickens/genetics ; }, abstract = {Staphylococcus agnetis is an emerging pathogen in chickens but has been most commonly isolated from sub-clinical mastitis in bovines. Previous whole-genome analyses for known virulence genes failed to identify determinants for the switch from mild ductal infections in cattle to severe infections in poultry. We now report identification of a family of 15 kbp, 17-19 gene mobile genetic elements (MGEs) specific to chicken osteomyelitis and dermatitis isolates of S. agnetis. These MGEs can be present in multiple copies per genome. The MGE has been vectored on a Staphylococcus phage that separately lysogenized two S. agnetis osteomyelitis strains. The S. agnetis genome from a broiler breeder case of ulcerative dermatitis contains 2 orthologs of this MGE, not associated with a prophage. BLASTn and phylogenetic analyses show that there are closely related intact MGEs found in genomes of S. aureus. The genome from a 1980s isolate from chickens in Ireland contains 3 copies of this MGE. More recent chicken isolates descended from that genome (Poland 2009, Oklahoma 2010, and Arkansas 2018) contain 2 to 4 related copies. Many of the genes of this MGE can be identified in disparate regions of the genomes of other chicken isolates of S. aureus. BLAST searches of the NCBI databases detect no similar MGEs outside of S. aureus and S. agnetis. These MGEs encode no proteins related to those produced by Staphylococcus aureus Pathogenicity Islands, which have been associated with the transition of S. aureus from human to chicken hosts. Other than mobilization functions, most of the genes in these new MGEs annotate as hypothetical proteins. The MGEs we describe appear to represent a new family of Chromosomal Islands (CIs) shared amongst S. agnetis and S. aureus. Further work is needed to understand the role of these CIs/MGEs in pathogenesis. Analysis of horizontal transfer of genetic elements between isolates and species of Staphylococci provides clues to evolution of host-pathogen interactions as well as revealing critical determinants for animal welfare and human diseases.}, }
@article {pmid37404190, year = {2023}, author = {Kosmopoulos, JC and Campbell, DE and Whitaker, RJ and Wilbanks, EG}, title = {Horizontal Gene Transfer and CRISPR Targeting Drive Phage-Bacterial Host Interactions and Coevolution in "Pink Berry" Marine Microbial Aggregates.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {7}, pages = {e0017723}, pmid = {37404190}, issn = {1098-5336}, support = {T32 DK077653-29//HHS | National Institutes of Health (NIH)/ ; }, mesh = {Humans ; *Bacteriophages/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats ; Gene Transfer, Horizontal ; Fruit ; Host Microbial Interactions ; }, abstract = {Bacteriophages (phages), which are viruses that infect bacteria, are the most abundant components of microbial communities and play roles in community dynamics and host evolution. However, the study of phage-host interactions is hindered by a paucity of model systems from natural environments. Here, we investigate phage-host interactions in the "pink berry" consortia, which are naturally occurring, low-diversity, macroscopic bacterial aggregates that are found in the Sippewissett Salt Marsh (Falmouth, MA, USA). We leverage metagenomic sequence data and a comparative genomics approach to identify eight compete phage genomes, infer their bacterial hosts from host-encoded clustered regularly interspaced short palindromic repeats (CRISPRs), and observe the potential evolutionary consequences of these interactions. Seven of the eight phages identified infect known pink berry symbionts, namely, Desulfofustis sp. PB-SRB1, Thiohalocapsa sp. PB-PSB1, and Rhodobacteraceae sp. A2, and they are largely divergent from known viruses. In contrast to the conserved bacterial community structure of pink berries, the distribution of these phages across aggregates is highly variable. Two phages persisted over a period of seven years with high sequence conservation, allowing us to identify gene gain and loss. Increased nucleotide variation in a conserved phage capsid gene that is commonly targeted by host CRISPR systems suggests that CRISPRs may drive phage evolution in pink berries. Finally, we identified a predicted phage lysin gene that was horizontally transferred to its bacterial host, potentially via a transposon intermediary. Taken together, our results demonstrate that pink berry consortia contain diverse and variable phages as well as provide evidence for phage-host coevolution via multiple mechanisms in a natural microbial system. IMPORTANCE Phages, which are viruses that infect bacteria, are important components of all microbial systems, in which they drive the turnover of organic matter by lysing host cells, facilitate horizontal gene transfer (HGT), and coevolve with their bacterial hosts. Bacteria resist phage infection, which is often costly or lethal, through a diversity of mechanisms. One of these mechanisms is CRISPR systems, which encode arrays of phage-derived sequences from past infections to block subsequent infection with related phages. Here, we investigate the bacteria and phage populations from a simple marine microbial community, known as "pink berries", found in salt marshes of Falmouth, Massachusetts, as a model of phage-host coevolution. We identify eight novel phages and characterize a case of putative CRISPR-driven phage evolution as well as an instance of HGT between a phage and its host, together suggesting that phages have large evolutionary impacts in a naturally occurring microbial community.}, }
@article {pmid37396349, year = {2023}, author = {Chen, F and Wang, D and Lu, T and Li, S}, title = {Identification of a novel type II-C Cas9 from the fish pathogen Flavobacterium psychrophilum.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1181303}, pmid = {37396349}, issn = {1664-302X}, abstract = {Flavobacterium psychrophilum is the causative agent of rainbow trout fry syndrome and bacterial cold-water disease in salmonid fish worldwide. As an important fish pathogen, F. psychrophilum is frequently exposed to multiple invading genetic elements in natural environments. Endonuclease Cas9 provides bacteria with adaptive interference against invading genetic elements. Previous studies revealed that several F. psychrophilum strains harbored a type II-C Cas9 called Fp1Cas9, but little is known about the potential role of this endonuclease against invading genetic elements. In this work, we identified a gene encoding a novel type II-C Cas9 called Fp2Cas9 from F. psychrophilum strain CN46. Through bacterial RNA sequencing, we demonstrated active transcription of both Fp2Cas9 and pre-crRNAs in strain CN46. Bioinformatics analysis further revealed that the transcription of Fp2Cas9 and pre-crRNAs was driven by a newly integrated promoter sequence and a promoter element embedded within each CRISPR repeat, respectively. To formally demonstrate that Fp2Cas9 and associated crRNAs yielded functional interference in strain CN46, a plasmid interference assay was performed, resulting in adaptive immunity to target DNA sequences in Flavobacterium bacteriophages. Phylogenetic analysis demonstrated that Fp2Cas9 was present only in several F. psychrophilum isolates. Phylogenetic analysis revealed that this novel endonuclease was probably acquired through horizontal gene transfer from the CRISPR-Cas9 system in an unidentified Flavobacterium species. Comparative genomics analysis further showed that the Fp2Cas9 was integrated into the type II-C CRISPR-Cas locus in strain CN38 instead of the original Fp1Cas9. Taken together, our results shed light on the origin and evolution of Fp2Cas9 gene and demonstrated that this novel endonuclease provided adaptive interference against bacteriophage infections.}, }
@article {pmid37395521, year = {2023}, author = {Meng, PQ and Zhang, Q and Ding, Y and Lin, JX and Chen, F}, title = {Evolutionary and Pan-genome Analysis of Three Important Black-pigmented Periodontal Pathogens.}, journal = {The Chinese journal of dental research}, volume = {26}, number = {2}, pages = {93-104}, doi = {10.3290/j.cjdr.b4128023}, pmid = {37395521}, issn = {1867-5646}, mesh = {*Prevotella/genetics/metabolism ; Phylogeny ; Prevotella intermedia/genetics/metabolism ; *Porphyromonas gingivalis/genetics/metabolism ; Prevotella nigrescens/genetics ; }, abstract = {OBJECTIVE: To analyse the pan-genome of three black-pigmented periodontal pathogens: Porphyromonas gingivalis, Prevotella intermedia and Prevotella nigrescens.<br><br>METHODS: Pan-genome analyses of 66, 33 and 5 publicly available whole-genome sequences of P. gingivalis, P. intermedia and P. nigrescens, respectively, were performed using Pan-genome Analysis Pipeline software (version 1.2.1; Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, PR China). Phylogenetic trees were constructed based on the entire pan-genome and single nucleotide polymorphisms within the core genome. The distribution and abundance of virulence genes in the core and dispensable genomes were also compared in the three species.<br><br>RESULTS: All three species possess an open pan-genome. The core genome of P. gingivalis, P. intermedia and P. nigrescens included 1001, 1514 and 1745 orthologous groups, respectively, which were mainly related to basic cellular functions such as metabolism. The dispensable genome of P. gingivalis, P. intermedia and P. nigrescens was composed of 2814, 2689 and 906 orthologous groups, respectively, and it was enriched in genes involved in pathogenicity or with unknown functions. Phylogenetic trees presented a clear separation of P. gingivalis, P. intermedia and P. nigrescens, verifying the reclassification of the black-pigmented species. Furthermore, the three species shared almost the same virulence factors involved in adhesion, proteolysis and evasion of host defences. Some of these virulence genes were conserved across species whereas others belonged to the dispensable genome, which might be acquired through horizontal gene transfer.<br><br>CONCLUSION: This study highlighted the usefulness of pan-genome analysis to infer evolutionary cues for black-pigmented species, indicating their homology and phylogenomic diversity.}, }
@article {pmid37395112, year = {2023}, author = {Lloyd, GS and Thomas, CM}, title = {Microbial Primer: The logic of bacterial plasmids.}, journal = {Microbiology (Reading, England)}, volume = {169}, number = {7}, pages = {}, doi = {10.1099/mic.0.001336}, pmid = {37395112}, issn = {1465-2080}, support = {BB/X512230/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Bacteria/genetics ; Conjugation, Genetic ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; *Logic ; Plasmids/genetics ; }, abstract = {This short primer is intended to give an overview of bacterial plasmids for those not yet familiar with these fascinating genetic elements. It covers their basic properties but does not attempt to cover the diversity of phenotypic properties that can be encoded by plasmids, and includes suggestions for further reading.}, }
@article {pmid37394915, year = {2023}, author = {Pereira, L and Dunning, LT}, title = {Extrachromosomal circular DNA as a vehicle to gene transfer in plants.}, journal = {Plant physiology}, volume = {193}, number = {1}, pages = {172-173}, pmid = {37394915}, issn = {1532-2548}, mesh = {*DNA, Circular/genetics ; Gene Transfer, Horizontal ; *Plants/genetics ; }, }
@article {pmid37394042, year = {2023}, author = {Mohammad Mirsoleimani Azizi, S and Zakaria, BS and Haffiez, N and Kumar, A and Ranjan Dhar, B}, title = {Pilot-scale investigation of conductive carbon cloth amendment for enhancing high-solids anaerobic digestion and mitigating antibiotic resistance.}, journal = {Bioresource technology}, volume = {385}, number = {}, pages = {129411}, doi = {10.1016/j.biortech.2023.129411}, pmid = {37394042}, issn = {1873-2976}, mesh = {*Carbon ; Anaerobiosis ; Electron Transport ; Drug Resistance, Microbial/genetics ; *Methane ; Bioreactors ; }, abstract = {This study examined the effectiveness of introducing conductive carbon cloth into a pilot-scale high-solids anaerobic digestion (HSAD) system. Adding carbon cloth increased methane production by 22 % and improved the maximum methane production rate by 39 %. Microbial community characterization indicated a possible direct interspecies electron transfer-based syntrophic association among microbes. Using carbon cloth also enhanced microbial richness, diversity, and evenness. Carbon cloth effectively reduced the total abundance of antibiotic resistance genes (ARGs) by 44.6 %, mainly by inhibiting horizontal gene transfer, as shown by the significant decrease in the relative abundance of integron genes (particularly intl1). The multivariate analysis further demonstrated strong correlations of intl1 with most of the targeted ARGs. These findings suggest that carbon cloth amendment can promote efficient methane production and attenuate the spread of ARGs in HSAD systems.}, }
@article {pmid37392596, year = {2023}, author = {Evans, D and Sundermann, A and Griffith, M and Rangachar Srinivasa, V and Mustapha, M and Chen, J and Dubrawski, A and Cooper, V and Harrison, L and Van Tyne, D}, title = {Empirically derived sequence similarity thresholds to study the genomic epidemiology of plasmids shared among healthcare-associated bacterial pathogens.}, journal = {EBioMedicine}, volume = {93}, number = {}, pages = {104681}, pmid = {37392596}, issn = {2352-3964}, mesh = {Humans ; *Anti-Bacterial Agents ; Plasmids/genetics ; Genomics ; Bacteria/genetics ; *Cross Infection/epidemiology ; Genome, Bacterial ; }, abstract = {BACKGROUND: Healthcare-associated bacterial pathogens frequently carry plasmids that contribute to antibiotic resistance and virulence. The horizontal transfer of plasmids in healthcare settings has been previously documented, but genomic and epidemiologic methods to study this phenomenon remain underdeveloped. The objectives of this study were to apply whole-genome sequencing to systematically resolve and track plasmids carried by nosocomial pathogens in a single hospital, and to identify epidemiologic links that indicated likely horizontal plasmid transfer.<br><br>METHODS: We performed an observational study of plasmids circulating among bacterial isolates infecting patients at a large hospital. We first examined plasmids carried by isolates sampled from the same patient over time and isolates that caused clonal outbreaks in the same hospital to develop thresholds with which horizontal plasmid transfer within a tertiary hospital could be inferred. We then applied those sequence similarity thresholds to perform a systematic screen of 3074 genomes of nosocomial bacterial isolates from a single hospital for the presence of 89 plasmids. We also collected and reviewed data from electronic health records for evidence of geotemporal links between patients infected with bacteria encoding plasmids of interest.<br><br>FINDINGS: Our analyses determined that 95% of analyzed genomes maintained roughly 95% of their plasmid genetic content and accumulated fewer than 15 SNPs per 100&#xa0;kb of plasmid sequence. Applying these similarity thresholds to identify horizontal plasmid transfer identified 45 plasmids that potentially circulated among clinical isolates. Ten highly preserved plasmids met criteria for geotemporal links associated with horizontal transfer. Several plasmids with shared backbones also encoded different additional mobile genetic element content, and these elements were variably present among the sampled clinical isolate genomes.<br><br>INTERPRETATION: Evidence suggests that the horizontal transfer of plasmids among nosocomial bacterial pathogens appears to be frequent within hospitals and can be monitored with whole genome sequencing and comparative genomics approaches. These approaches should incorporate both nucleotide identity and reference sequence coverage to study the dynamics of plasmid transfer in the hospital.<br><br>FUNDING: This research was supported by the US National Institute of Allergy and Infectious Disease (NIAID) and the University of Pittsburgh School of Medicine.}, }
@article {pmid37389331, year = {2023}, author = {Bromfield, ESP and Cloutier, S and Hynes, MF}, title = {Ensifer canadensis sp. nov. strain T173[T] isolated from Melilotus albus (sweet clover) in Canada possesses recombinant plasmid pT173b harbouring symbiosis and type IV secretion system genes apparently acquired from Ensifer medicae.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1195755}, pmid = {37389331}, issn = {1664-302X}, abstract = {A bacterial strain, designated T173[T], was previously isolated from a root-nodule of a Melilotus albus plant growing in Canada and identified as a novel Ensifer lineage that shared a clade with the non-symbiotic species, Ensifer adhaerens. Strain T173[T] was also previously found to harbour a symbiosis plasmid and to elicit root-nodules on Medicago and Melilotus species but not fix nitrogen. Here we present data for the genomic and taxonomic description of strain T173[T]. Phylogenetic analyses including the analysis of whole genome sequences and multiple locus sequence analysis (MLSA) of 53 concatenated ribosome protein subunit (rps) gene sequences confirmed placement of strain T173[T] in a highly supported lineage distinct from named Ensifer species with E. morelensis Lc04[T] as the closest relative. The highest digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values of genome sequences of strain T173[T] compared with closest relatives (35.7 and 87.9%, respectively) are well below the respective threshold values of 70% and 95-96% for bacterial species circumscription. The genome of strain T173[T] has a size of 8,094,229 bp with a DNA G + C content of 61.0 mol%. Six replicons were detected: a chromosome (4,051,102 bp) and five plasmids harbouring plasmid replication and segregation (repABC) genes. These plasmids were also found to possess five apparent conjugation systems based on analysis of TraA (relaxase), TrbE/VirB4 (part of the Type IV secretion system (T4SS)) and TraG/VirD4 (coupling protein). Ribosomal RNA operons encoding 16S, 23S, and 5S rRNAs that are usually restricted to bacterial chromosomes were detected on plasmids pT173d and pT173e (946,878 and 1,913,930 bp, respectively) as well as on the chromosome of strain T173[T]. Moreover, plasmid pT173b (204,278 bp) was found to harbour T4SS and symbiosis genes, including nodulation (nod, noe, nol) and nitrogen fixation (nif, fix) genes that were apparently acquired from E. medicae by horizontal transfer. Data for morphological, physiological and symbiotic characteristics complement the sequence-based characterization of strain T173[T]. The data presented support the description of a new species for which the name Ensifer canadensis sp. nov. is proposed with strain T173[T] (= LMG 32374[T] = HAMBI 3766[T]) as the species type strain.}, }
@article {pmid37384706, year = {2023}, author = {Widen, SA and Bes, IC and Koreshova, A and Pliota, P and Krogull, D and Burga, A}, title = {Virus-like transposons cross the species barrier and drive the evolution of genetic incompatibilities.}, journal = {Science (New York, N.Y.)}, volume = {380}, number = {6652}, pages = {eade0705}, doi = {10.1126/science.ade0705}, pmid = {37384706}, issn = {1095-9203}, mesh = {Animals ; *Caenorhabditis/genetics ; *Gene Transfer, Horizontal ; *Viruses/genetics ; *DNA Transposable Elements ; Genetic Vectors ; *Biological Evolution ; }, abstract = {Horizontal gene transfer, the movement of genetic material between species, has been reported across all major eukaryotic lineages. However, the underlying mechanisms of transfer and their impact on genome evolution are still poorly understood. While studying the evolutionary origin of a selfish element in the nematode Caenorhabditis briggsae, we discovered that Mavericks, ancient virus-like transposons related to giant viruses and virophages, are one of the long-sought vectors of horizontal gene transfer. We found that Mavericks gained a novel herpesvirus-like fusogen in nematodes, leading to the widespread exchange of cargo genes between extremely divergent species, bypassing sexual and genetic barriers spanning hundreds of millions of years. Our results show how the union between viruses and transposons causes horizontal gene transfer and ultimately genetic incompatibilities in natural populations.}, }
@article {pmid37384391, year = {2023}, author = {Römling, U and Cao, LY and Bai, FW}, title = {Evolution of cyclic di-GMP signalling on a short and long term time scale.}, journal = {Microbiology (Reading, England)}, volume = {169}, number = {6}, pages = {}, pmid = {37384391}, issn = {1465-2080}, mesh = {Humans ; *Signal Transduction ; *Second Messenger Systems ; Amino Acid Substitution ; Biofilms ; Gene Transfer, Horizontal ; }, abstract = {Diversifying radiation of domain families within specific lineages of life indicates the importance of their functionality for the organisms. The foundation for the diversifying radiation of the cyclic di-GMP signalling network that occurred within the bacterial kingdom is most likely based in the outmost adaptability, flexibility and plasticity of the system. Integrative sensing of multiple diverse extra- and intracellular signals is made possible by the N-terminal sensory domains of the modular cyclic di-GMP turnover proteins, mutations in the protein scaffolds and subsequent signal reception by diverse receptors, which eventually rewires opposite host-associated as well as environmental life styles including parallel regulated target outputs. Natural, laboratory and microcosm derived microbial variants often with an altered multicellular biofilm behaviour as reading output demonstrated single amino acid substitutions to substantially alter catalytic activity including substrate specificity. Truncations and domain swapping of cyclic di-GMP signalling genes and horizontal gene transfer suggest rewiring of the network. Presence of cyclic di-GMP signalling genes on horizontally transferable elements in particular observed in extreme acidophilic bacteria indicates that cyclic di-GMP signalling and biofilm components are under selective pressure in these types of environments. On a short and long term evolutionary scale, within a species and in families within bacterial orders, respectively, the cyclic di-GMP signalling network can also rapidly disappear. To investigate variability of the cyclic di-GMP signalling system on various levels will give clues about evolutionary forces and discover novel physiological and metabolic pathways affected by this intriguing second messenger signalling system.}, }
@article {pmid37379503, year = {2023}, author = {Duan, JL and Ma, JY and Sun, XD and Liu, XY and Wang, Y and Du, L and Xia, PF and Yuan, XZ}, title = {Bubbles Expand the Dissemination of Antibiotic Resistance in the Aquatic Environment.}, journal = {Environmental science &amp; technology}, volume = {57}, number = {27}, pages = {10079-10088}, doi = {10.1021/acs.est.3c02935}, pmid = {37379503}, issn = {1520-5851}, mesh = {Humans ; *Angiotensin Receptor Antagonists ; Pandemics ; Angiotensin-Converting Enzyme Inhibitors ; *COVID-19 ; Bacteria ; Drug Resistance, Microbial ; }, abstract = {Antibiotic resistance is a global health challenge, and the COVID-19 pandemic has amplified the urgency to understand its airborne transmission. The bursting of bubbles is a fundamental phenomenon in natural and industrial processes, with the potential to encapsulate or adsorb antibiotic-resistant bacteria (ARB). However, there is no evidence to date for bubble-mediated antibiotic resistance dissemination. Here, we show that bubbles can eject abundant bacteria to the air, form stable biofilms over the air-water interface, and provide opportunities for cell-cell contact that facilitates horizontal gene transfer at and over the air-liquid interface. The extracellular matrix (ECM) on bacteria can increase bubble attachment on biofilms, increase bubble lifetime, and, thus, produce abundant small droplets. We show through single-bubble probe atomic force microscopy and molecular dynamics simulations that hydrophobic interactions with polysaccharides control how the bubble interacts with the ECM. These results highlight the importance of bubbles and its physicochemical interaction with ECM in facilitating antibiotic resistance dissemination and fulfill the framework on antibiotic resistance dissemination.}, }
@article {pmid37378525, year = {2023}, author = {Tan, Q and Li, R and Liu, L and Wang, D and Dai, XF and Song, LM and Zhang, DD and Kong, ZQ and Klosterman, SJ and Usami, T and Subbarao, KV and Liang, WX and Chen, JY}, title = {Functional Characterization of Verticillium dahliae Race 3-Specific Gene VdR3e in Virulence and Elicitation of Plant Immune Responses.}, journal = {Microbiology spectrum}, volume = {11}, number = {4}, pages = {e0108323}, pmid = {37378525}, issn = {2165-0497}, mesh = {Virulence/genetics ; *Verticillium/genetics ; *Ascomycota ; Plant Immunity ; Virulence Factors/genetics/metabolism ; Plant Diseases/microbiology ; }, abstract = {Verticillium dahliae is a soilborne fungal pathogen that causes disease on many economically important crops. Based on the resistance or susceptibility of differential cultivars in tomato, isolates of V. dahliae are divided into three races. Avirulence (avr) genes within the genomes of the three races have also been identified. However, the functional role of the avr gene in race 3 isolates of V. dahliae has not been characterized. In this study, bioinformatics analysis showed that VdR3e, a cysteine-rich secreted protein encoded by the gene characterizing race 3 in V. dahliae, was likely obtained by horizontal gene transfer from the fungal genus Bipolaris. We demonstrate that VdR3e causes cell death by triggering multiple defense responses. In addition, VdR3e localized at the periphery of the plant cell and triggered immunity depending on its subcellular localization and the cell membrane receptor BAK1. Furthermore, VdR3e is a virulence factor and shows differential pathogenicity in race 3-resistant and -susceptible hosts. These results suggest that VdR3e is a virulence factor that can also interact with BAK1 as a pathogen-associated molecular pattern (PAMP) to trigger immune responses. IMPORTANCE Based on the gene-for-gene model, research on the function of avirulence genes and resistance genes has had an unparalleled impact on breeding for resistance in most crops against individual pathogens. The soilborne fungal pathogen, Verticillium dahliae, is a major pathogen on many economically important crops. Currently, avr genes of the three races in V. dahliae have been identified, but the function of avr gene representing race 3 has not been described. We investigated the characteristics of VdR3e-mediated immunity and demonstrated that VdR3e acts as a PAMP to activate a variety of plant defense responses and induce plant cell death. We also demonstrated that the role of VdR3e in pathogenicity was host dependent. This is the first study to describe the immune and virulence functions of the avr gene from race 3 in V. dahliae, and we provide support for the identification of genes mediating resistance against race 3.}, }
@article {pmid37374993, year = {2023}, author = {Caliskan-Aydogan, O and Alocilja, EC}, title = {A Review of Carbapenem Resistance in Enterobacterales and Its Detection Techniques.}, journal = {Microorganisms}, volume = {11}, number = {6}, pages = {}, pmid = {37374993}, issn = {2076-2607}, support = {1012975//United States Department of Agriculture/ ; 2022-67017-36982.//USDA-NIFA/ ; }, abstract = {Infectious disease outbreaks have caused thousands of deaths and hospitalizations, along with severe negative global economic impacts. Among these, infections caused by antimicrobial-resistant microorganisms are a major growing concern. The misuse and overuse of antimicrobials have resulted in the emergence of antimicrobial resistance (AMR) worldwide. Carbapenem-resistant Enterobacterales (CRE) are among the bacteria that need urgent attention globally. The emergence and spread of carbapenem-resistant bacteria are mainly due to the rapid dissemination of genes that encode carbapenemases through horizontal gene transfer (HGT). The rapid dissemination enables the development of host colonization and infection cases in humans who do not use the antibiotic (carbapenem) or those who are hospitalized but interacting with environments and hosts colonized with carbapenemase-producing (CP) bacteria. There are continuing efforts to characterize and differentiate carbapenem-resistant bacteria from susceptible bacteria to allow for the appropriate diagnosis, treatment, prevention, and control of infections. This review presents an overview of the factors that cause the emergence of AMR, particularly CRE, where they have been reported, and then, it outlines carbapenemases and how they are disseminated through humans, the environment, and food systems. Then, current and emerging techniques for the detection and surveillance of AMR, primarily CRE, and gaps in detection technologies are presented. This review can assist in developing prevention and control measures to minimize the spread of carbapenem resistance in the human ecosystem, including hospitals, food supply chains, and water treatment facilities. Furthermore, the development of rapid and affordable detection techniques is helpful in controlling the negative impact of infections caused by AMR/CRE. Since delays in diagnostics and appropriate antibiotic treatment for such infections lead to increased mortality rates and hospital costs, it is, therefore, imperative that rapid tests be a priority.}, }
@article {pmid37374909, year = {2023}, author = {Harris, M and Fasolino, T and Ivankovic, D and Davis, NJ and Brownlee, N}, title = {Genetic Factors That Contribute to Antibiotic Resistance through Intrinsic and Acquired Bacterial Genes in Urinary Tract Infections.}, journal = {Microorganisms}, volume = {11}, number = {6}, pages = {}, pmid = {37374909}, issn = {2076-2607}, abstract = {The overprescribing and misuse of antibiotics have led to the rapid development of multidrug-resistant bacteria, such as those that cause UTIs. UTIs are the most common outpatient infections and are mainly caused by Escherichia coli and Klebsiella spp., although some Gram-positive bacteria, such as Pseudomonas aeruginosa, have been isolated in many cases. The rise of antimicrobial-resistant bacteria is a major public health concern, as it is predicted to lead to increased healthcare costs and poor patient outcomes and is expected to be the leading cause of global mortality by 2050. Antibiotic resistance among bacterial species can arise from a myriad of factors, including intrinsic and acquired resistance mechanisms, as well as mobile genetic elements, such as transposons, integrons, and plasmids. Plasmid-mediated resistance is of major concern as drug-resistance genes can quickly and efficiently spread across bacterial species via horizontal gene transfer. The emergence of extended-spectrum β-lactamases (ESBLs) such as NDM-1, OXA, KPC, and CTX-M family members has conferred resistance to many commonly used antibiotics in the treatment of UTIs, including penicillins, carbapenems, cephalosporins, and sulfamethoxazole. This review will focus on plasmid-mediated bacterial genes, especially those that encode ESBLs, and how they contribute to antibiotic resistance. Early clinical detection of these genes in patient samples will provide better treatment options and reduce the threat of antibiotic resistance.}, }
@article {pmid37372483, year = {2023}, author = {Shymialevich, D and Wójcicki, M and Świder, O and Średnicka, P and Sokołowska, B}, title = {Characterization and Genome Study of a Newly Isolated Temperate Phage Belonging to a New Genus Targeting Alicyclobacillus acidoterrestris.}, journal = {Genes}, volume = {14}, number = {6}, pages = {}, pmid = {37372483}, issn = {2073-4425}, mesh = {*Alicyclobacillus/genetics ; *Bacteriophages/genetics ; Hot Temperature ; Temperature ; }, abstract = {The spoilage of juices by Alicyclobacillus spp. remains a serious problem in industry and leads to economic losses. Compounds such as guaiacol and halophenols, which are produced by Alicyclobacillus, create undesirable flavors and odors and, thus, decrease the quality of juices. The inactivation of Alicyclobacillus spp. constitutes a challenge because it is resistant to environmental factors, such as high temperatures, and active acidity. However, the use of bacteriophages seems to be a promising approach. In this study, we aimed to isolate and comprehensively characterize a novel bacteriophage targeting Alicyclobacillus spp. The Alicyclobacillus phage strain KKP 3916 was isolated from orchard soil against the Alicyclobacillus acidoterrestris strain KKP 3133. The bacterial host's range and the effect of phage addition at different rates of multiplicity of infections (MOIs) on the host's growth kinetics were determined using a Bioscreen C Pro growth analyzer. The Alicyclobacillus phage strain KKP 3916, retained its activity in a wide range of temperatures (from 4 °C to 30 °C) and active acidity values (pH from 3 to 11). At 70 °C, the activity of the phage decreased by 99.9%. In turn, at 80 °C, no activity against the bacterial host was observed. Thirty minutes of exposure to UV reduced the activity of the phages by almost 99.99%. Based on transmission-electron microscopy (TEM) and whole-genome sequencing (WGS) analyses, the Alicyclobacillus phage strain KKP 3916 was classified as a tailed bacteriophage. The genomic sequencing revealed that the newly isolated phage had linear double-stranded DNA (dsDNA) with sizes of 120 bp and 131 bp and 40.3% G+C content. Of the 204 predicted proteins, 134 were of unknown function, while the remainder were annotated as structural, replication, and lysis proteins. No genes associated with antibiotic resistance were found in the genome of the newly isolated phage. However, several regions, including four associated with integration into the bacterial host genome and excisionase, were identified, which indicates the temperate (lysogenic) life cycle of the bacteriophage. Due to the risk of its potential involvement in horizontal gene transfer, this phage is not an appropriate candidate for further research on its use in food biocontrol. To the best of our knowledge, this is the first article on the isolation and whole-genome analysis of the Alicyclobacillus-specific phage.}, }
@article {pmid37372055, year = {2023}, author = {Gheibzadeh, MS and Manyumwa, CV and Tastan Bishop, &#xd6; and Shahbani Zahiri, H and Parkkila, S and Zolfaghari Emameh, R}, title = {Genome Study of α-, β-, and γ-Carbonic Anhydrases from the Thermophilic Microbiome of Marine Hydrothermal Vent Ecosystems.}, journal = {Biology}, volume = {12}, number = {6}, pages = {}, pmid = {37372055}, issn = {2079-7737}, support = {737//National Institute of Genetic Engineering and Biotechnology/ ; M/75137//Ministry of Science, Research and Technology/ ; 111212//National Research Foundation/ ; }, abstract = {Carbonic anhydrases (CAs) are metalloenzymes that can help organisms survive in hydrothermal vents by hydrating carbon dioxide (CO2). In this study, we focus on alpha (α), beta (β), and gamma (γ) CAs, which are present in the thermophilic microbiome of marine hydrothermal vents. The coding genes of these enzymes can be transferred between hydrothermal-vent organisms via horizontal gene transfer (HGT), which is an important tool in natural biodiversity. We performed big data mining and bioinformatics studies on α-, β-, and γ-CA coding genes from the thermophilic microbiome of marine hydrothermal vents. The results showed a reasonable association between thermostable α-, β-, and γ-CAs in the microbial population of the hydrothermal vents. This relationship could be due to HGT. We found evidence of HGT of α- and β-CAs between Cycloclasticus sp., a symbiont of Bathymodiolus heckerae, and an endosymbiont of Riftia pachyptila via Integrons. Conversely, HGT of β-CA genes from the endosymbiont Tevnia jerichonana to the endosymbiont Riftia pachyptila was detected. In addition, Hydrogenovibrio crunogenus SP-41 contains a β-CA gene on genomic islands (GIs). This gene can be transferred by HGT to Hydrogenovibrio sp. MA2-6, a methanotrophic endosymbiont of Bathymodiolus azoricus, and a methanotrophic endosymbiont of Bathymodiolus puteoserpentis. The endosymbiont of R. pachyptila has a γ-CA gene in the genome. If α- and β-CA coding genes have been derived from other microorganisms, such as endosymbionts of T. jerichonana and Cycloclasticus sp. as the endosymbiont of B. heckerae, through HGT, the theory of the necessity of thermostable CA enzymes for survival in the extreme ecosystem of hydrothermal vents is suggested and helps the conservation of microbiome natural diversity in hydrothermal vents. These harsh ecosystems, with their integral players, such as HGT and endosymbionts, significantly impact the enrichment of life on Earth and the carbon cycle in the ocean.}, }
@article {pmid37369847, year = {2023}, author = {Steenwyk, JL and Li, Y and Zhou, X and Shen, XX and Rokas, A}, title = {Incongruence in the phylogenomics era.}, journal = {Nature reviews. Genetics}, volume = {24}, number = {12}, pages = {834-850}, pmid = {37369847}, issn = {1471-0064}, support = {R01 AI153356/AI/NIAID NIH HHS/United States ; }, mesh = {Phylogeny ; *Biological Evolution ; *Genome ; Evolution, Molecular ; Hybridization, Genetic ; }, abstract = {Genome-scale data and the development of novel statistical phylogenetic approaches have greatly aided the reconstruction of a broad sketch of the tree of life and resolved many of its branches. However, incongruence - the inference of conflicting evolutionary histories - remains pervasive in phylogenomic data, hampering our ability to reconstruct and interpret the tree of life. Biological factors, such as incomplete lineage sorting, horizontal gene transfer, hybridization, introgression, recombination and convergent molecular evolution, can lead to gene phylogenies that differ from the species tree. In addition, analytical factors, including stochastic, systematic and treatment errors, can drive incongruence. Here, we review these factors, discuss methodological advances to identify and handle incongruence, and highlight avenues for future research.}, }
@article {pmid37369704, year = {2023}, author = {Huang, J and Dai, X and Wu, Z and Hu, X and Sun, J and Tang, Y and Zhang, W and Han, P and Zhao, J and Liu, G and Wang, X and Mao, S and Wang, Y and Call, DR and Liu, J and Wang, L}, title = {Conjugative transfer of streptococcal prophages harboring antibiotic resistance and virulence genes.}, journal = {The ISME journal}, volume = {17}, number = {9}, pages = {1467-1481}, pmid = {37369704}, issn = {1751-7370}, mesh = {Animals ; *Prophages/genetics ; Virulence/genetics ; Streptococcus/genetics ; *Anti-Infective Agents ; Drug Resistance, Microbial ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; Plasmids ; Conjugation, Genetic ; }, abstract = {Prophages play important roles in the transduction of various functional traits, including virulence factors, but remain debatable in harboring and transmitting antimicrobial resistance genes (ARGs). Herein we characterize a prevalent family of prophages in Streptococcus, designated SMphages, which harbor twenty-five ARGs that collectively confer resistance to ten antimicrobial classes, including vanG-type vancomycin resistance locus and oxazolidinone resistance gene optrA. SMphages integrate into four chromosome attachment sites by utilizing three types of integration modules and undergo excision in response to phage induction. Moreover, we characterize four subtypes of Alp-related surface proteins within SMphages, the lethal effects of which are extensively validated in cell and animal models. SMphages transfer via high-frequency conjugation that is facilitated by integrative and conjugative elements from either donors or recipients. Our findings explain the widespread of SMphages and the rapid dissemination of ARGs observed in members of the Streptococcus genus.}, }
@article {pmid37368881, year = {2023}, author = {Tanabe, TS and Grosser, M and Hahn, L and Kümpel, C and Hartenfels, H and Vtulkin, E and Flegler, W and Dahl, C}, title = {Identification of a novel lipoic acid biosynthesis pathway reveals the complex evolution of lipoate assembly in prokaryotes.}, journal = {PLoS biology}, volume = {21}, number = {6}, pages = {e3002177}, pmid = {37368881}, issn = {1545-7885}, mesh = {*Thioctic Acid/genetics/metabolism ; Peptide Synthases/genetics/metabolism ; Phylogeny ; Bacterial Proteins/metabolism ; Sulfur ; }, abstract = {Lipoic acid is an essential biomolecule found in all domains of life and is involved in central carbon metabolism and dissimilatory sulfur oxidation. The machineries for lipoate assembly in mitochondria and chloroplasts of higher eukaryotes, as well as in the apicoplasts of some protozoa, are all of prokaryotic origin. Here, we provide experimental evidence for a novel lipoate assembly pathway in bacteria based on a sLpl(AB) lipoate:protein ligase, which attaches octanoate or lipoate to apo-proteins, and 2 radical SAM proteins, LipS1 and LipS2, which work together as lipoyl synthase and insert 2 sulfur atoms. Extensive homology searches combined with genomic context analyses allowed us to precisely distinguish between the new and established pathways and map them on the tree of life. This not only revealed a much wider distribution of lipoate biogenesis systems than expected, in particular, the novel sLpl(AB)-LipS1/S2 pathway, and indicated a highly modular nature of the enzymes involved, with unforeseen combinations, but also provided a new framework for the evolution of lipoate assembly. Our results show that dedicated machineries for both de novo lipoate biogenesis and scavenging from the environment were implemented early in evolution and that their distribution in the 2 prokaryotic domains was shaped by a complex network of horizontal gene transfers, acquisition of additional genes, fusions, and losses. Our large-scale phylogenetic analyses identify the bipartite archaeal LplAB ligase as the ancestor of the bacterial sLpl(AB) proteins, which were obtained by horizontal gene transfer. LipS1/S2 have a more complex evolutionary history with multiple of such events but probably also originated in the domain archaea.}, }
@article {pmid37368681, year = {2023}, author = {Boss, L and Kędzierska, B}, title = {Bacterial Toxin-Antitoxin Systems' Cross-Interactions-Implications for Practical Use in Medicine and Biotechnology.}, journal = {Toxins}, volume = {15}, number = {6}, pages = {}, pmid = {37368681}, issn = {2072-6651}, mesh = {*Bacterial Toxins/metabolism ; Prospective Studies ; *Toxin-Antitoxin Systems/genetics ; Bacteria/genetics/metabolism ; *Antitoxins/genetics ; Biotechnology ; Bacterial Proteins/genetics ; }, abstract = {Toxin-antitoxin (TA) systems are widely present in bacterial genomes. They consist of stable toxins and unstable antitoxins that are classified into distinct groups based on their structure and biological activity. TA systems are mostly related to mobile genetic elements and can be easily acquired through horizontal gene transfer. The ubiquity of different homologous and non-homologous TA systems within a single bacterial genome raises questions about their potential cross-interactions. Unspecific cross-talk between toxins and antitoxins of non-cognate modules may unbalance the ratio of the interacting partners and cause an increase in the free toxin level, which can be deleterious to the cell. Moreover, TA systems can be involved in broadly understood molecular networks as transcriptional regulators of other genes' expression or modulators of cellular mRNA stability. In nature, multiple copies of highly similar or identical TA systems are rather infrequent and probably represent a transition stage during evolution to complete insulation or decay of one of them. Nevertheless, several types of cross-interactions have been described in the literature to date. This implies a question of the possibility and consequences of the TA system cross-interactions, especially in the context of the practical application of the TA-based biotechnological and medical strategies, in which such TAs will be used outside their natural context, will be artificially introduced and induced in the new hosts. Thus, in this review, we discuss the prospective challenges of system cross-talks in the safety and effectiveness of TA system usage.}, }
@article {pmid37367481, year = {2023}, author = {Fakhar, AZ and Liu, J and Pajerowska-Mukhtar, KM and Mukhtar, MS}, title = {The Lost and Found: Unraveling the Functions of Orphan Genes.}, journal = {Journal of developmental biology}, volume = {11}, number = {2}, pages = {}, pmid = {37367481}, issn = {2221-3759}, support = {IOS-2038872//National Science Foundation/ ; }, abstract = {Orphan Genes (OGs) are a mysterious class of genes that have recently gained significant attention. Despite lacking a clear evolutionary history, they are found in nearly all living organisms, from bacteria to humans, and they play important roles in diverse biological processes. The discovery of OGs was first made through comparative genomics followed by the identification of unique genes across different species. OGs tend to be more prevalent in species with larger genomes, such as plants and animals, and their evolutionary origins remain unclear but potentially arise from gene duplication, horizontal gene transfer (HGT), or de novo origination. Although their precise function is not well understood, OGs have been implicated in crucial biological processes such as development, metabolism, and stress responses. To better understand their significance, researchers are using a variety of approaches, including transcriptomics, functional genomics, and molecular biology. This review offers a comprehensive overview of the current knowledge of OGs in all domains of life, highlighting the possible role of dark transcriptomics in their evolution. More research is needed to fully comprehend the role of OGs in biology and their impact on various biological processes.}, }
@article {pmid37367332, year = {2023}, author = {Fallon, AM and Carroll, EM}, title = {Virus-like Particles from Wolbachia-Infected Cells May Include a Gene Transfer Agent.}, journal = {Insects}, volume = {14}, number = {6}, pages = {}, pmid = {37367332}, issn = {2075-4450}, abstract = {Wolbachia are obligate intracellular bacteria that occur in insects and filarial worms. Strains that infect insects have genomes that encode mobile genetic elements, including diverse lambda-like prophages called Phage WO. Phage WO packages an approximately 65 kb viral genome that includes a unique eukaryotic association module, or EAM, that encodes unusually large proteins thought to mediate interactions between the bacterium, its virus, and the eukaryotic host cell. The Wolbachia supergroup B strain, wStri from the planthopper Laodelphax striatellus, produces phage-like particles that can be recovered from persistently infected mosquito cells by ultracentrifugation. Illumina sequencing, assembly, and manual curation of DNA from two independent preparations converged on an identical 15,638 bp sequence that encoded packaging, assembly, and structural proteins. The absence of an EAM and regulatory genes defined for Phage WO from the wasp, Nasonia vitripennis, was consistent with the possibility that the 15,638 bp sequence represents an element related to a gene transfer agent (GTA), characterized by a signature head-tail region encoding structural proteins that package host chromosomal DNA. Future investigation of GTA function will be supported by the improved recovery of physical particles, electron microscopic examination of potential diversity among particles, and rigorous examination of DNA content by methods independent of sequence assembly.}, }
@article {pmid37360531, year = {2023}, author = {Gaballa, A and Wiedmann, M and Carroll, LM}, title = {More than mcr: canonical plasmid- and transposon-encoded mobilized colistin resistance genes represent a subset of phosphoethanolamine transferases.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1060519}, pmid = {37360531}, issn = {2235-2988}, mesh = {Humans ; *Colistin/pharmacology ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Plasmids/genetics ; Transferases/genetics ; *Escherichia coli Proteins/genetics/metabolism ; Microbial Sensitivity Tests ; }, abstract = {Mobilized colistin resistance genes (mcr) may confer resistance to the last-resort antimicrobial colistin and can often be transmitted horizontally. mcr encode phosphoethanolamine transferases (PET), which are closely related to chromosomally encoded, intrinsic lipid modification PET (i-PET; e.g., EptA, EptB, CptA). To gain insight into the evolution of mcr within the context of i-PET, we identified 69,814 MCR-like proteins present across 256 bacterial genera (obtained by querying known MCR family representatives against the National Center for Biotechnology Information [NCBI] non-redundant protein database via protein BLAST). We subsequently identified 125 putative novel mcr-like genes, which were located on the same contig as (i) ≥1 plasmid replicon and (ii) ≥1 additional antimicrobial resistance gene (obtained by querying the PlasmidFinder database and NCBI's National Database of Antibiotic Resistant Organisms, respectively, via nucleotide BLAST). At 80% amino acid identity, these putative novel MCR-like proteins formed 13 clusters, five of which represented putative novel MCR families. Sequence similarity and a maximum likelihood phylogeny of mcr, putative novel mcr-like, and ipet genes indicated that sequence similarity was insufficient to discriminate mcr from ipet genes. A mixed-effect model of evolution (MEME) indicated that site- and branch-specific positive selection played a role in the evolution of alleles within the mcr-2 and mcr-9 families. MEME suggested that positive selection played a role in the diversification of several residues in structurally important regions, including (i) a bridging region that connects the membrane-bound and catalytic periplasmic domains, and (ii) a periplasmic loop juxtaposing the substrate entry tunnel. Moreover, eptA and mcr were localized within different genomic contexts. Canonical eptA genes were typically chromosomally encoded in an operon with a two-component regulatory system or adjacent to a TetR-type regulator. Conversely, mcr were represented by single-gene operons or adjacent to pap2 and dgkA, which encode a PAP2 family lipid A phosphatase and diacylglycerol kinase, respectively. Our data suggest that eptA can give rise to "colistin resistance genes" through various mechanisms, including mobilization, selection, and diversification of genomic context and regulatory pathways. These mechanisms likely altered gene expression levels and enzyme activity, allowing bona fide eptA to evolve to function in colistin resistance.}, }
@article {pmid37360032, year = {2023}, author = {Fleming, JF and Valero-Gracia, A and Struck, TH}, title = {Identifying and addressing methodological incongruence in phylogenomics: A review.}, journal = {Evolutionary applications}, volume = {16}, number = {6}, pages = {1087-1104}, pmid = {37360032}, issn = {1752-4571}, abstract = {The availability of phylogenetic data has greatly expanded in recent years. As a result, a new era in phylogenetic analysis is dawning-one in which the methods we use to analyse and assess our data are the bottleneck to producing valuable phylogenetic hypotheses, rather than the need to acquire more data. This makes the ability to accurately appraise and evaluate new methods of phylogenetic analysis and phylogenetic artefact identification more important than ever. Incongruence in phylogenetic reconstructions based on different datasets may be due to two major sources: biological and methodological. Biological sources comprise processes like horizontal gene transfer, hybridization and incomplete lineage sorting, while methodological ones contain falsely assigned data or violations of the assumptions of the underlying model. While the former provides interesting insights into the evolutionary history of the investigated groups, the latter should be avoided or minimized as best as possible. However, errors introduced by methodology must first be excluded or minimized to be able to conclude that biological sources are the cause. Fortunately, a variety of useful tools exist to help detect such misassignments and model violations and to apply ameliorating measurements. Still, the number of methods and their theoretical underpinning can be overwhelming and opaque. Here, we present a practical and comprehensive review of recent developments in techniques to detect artefacts arising from model violations and poorly assigned data. The advantages and disadvantages of the different methods to detect such misleading signals in phylogenetic reconstructions are also discussed. As there is no one-size-fits-all solution, this review can serve as a guide in choosing the most appropriate detection methods depending on both the actual dataset and the computational power available to the researcher. Ultimately, this informed selection will have a positive impact on the broader field, allowing us to better understand the evolutionary history of the group of interest.}, }
@article {pmid37358464, year = {2023}, author = {Binsker, U and Oelgeschläger, K and Neumann, B and Werner, G and Käsbohrer, A and Hammerl, JA}, title = {Genomic Evidence of mcr-1.26 IncX4 Plasmid Transmission between Poultry and Humans.}, journal = {Microbiology spectrum}, volume = {11}, number = {4}, pages = {e0101523}, pmid = {37358464}, issn = {2165-0497}, mesh = {Animals ; Humans ; *Colistin ; Escherichia coli ; Anti-Bacterial Agents/pharmacology ; Poultry ; *Escherichia coli Proteins/genetics ; Plasmids/genetics ; Genomics ; Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; }, abstract = {Colistin is still commonly used and misused in animal husbandry driving the evolution and dissemination of transmissible plasmid-mediated colistin resistance (mcr). mcr-1.26 is a rare variant and, so far, has only been detected in Escherichia coli obtained from a hospitalized patient in Germany in 2018. Recently, it was also notified in fecal samples from a pigeon in Lebanon. We report on the presence of 16 colistin-resistant, mcr-1.26-carrying extended-spectrum beta-lactamase (ESBL)-producing and commensal E. coli isolated from poultry samples in Germany, of which retail meat was the most common source. Short- and long-read genome sequencing and bioinformatic analyses revealed the location of mcr-1.26 exclusively on IncX4 plasmids. mcr-1.26 was identified on two different IncX4 plasmid types of 33 and 38 kb and was associated with an IS6-like element. Based on the genetic diversity of E. coli isolates, transmission of the mcr-1.26 resistance determinant is mediated by horizontal transfer of IncX4 plasmids, as confirmed by conjugation experiments. Notably, the 33-kb plasmid is highly similar to the plasmid reported for the human sample. Furthermore, we identified the acquisition of an additional beta-lactam resistance linked to a Tn2 transposon on the mcr-1.26 IncX4 plasmids of three isolates, indicating progressive plasmid evolution. Overall, all described mcr-1.26-carrying plasmids contain a highly conserved core genome necessary for colistin resistance development, transmission, replication, and maintenance. Variations in the plasmid sequences are mainly caused by the acquisition of insertion sequences and alteration in intergenic sequences or genes of unknown function. IMPORTANCE Evolutionary events causing the emergence of new resistances/variants are usually rare and challenging to predict. Conversely, common transmission events of widespread resistance determinants are quantifiable and predictable. One such example is the transmissible plasmid-mediated colistin resistance. The main determinant, mcr-1, has been notified in 2016 but has successfully established itself in multiple plasmid backbones in diverse bacterial species across all One Health sectors. So far, 34 variants of mcr-1 are described, of which some can be used for epidemiological tracing-back analysis to identify the origin and transmission dynamics of these genes. Here, we report the presence of the rare mcr-1.26 gene in E. coli isolated from poultry since 2014. Based on the temporal occurrence and high similarity of the plasmids between poultry and human isolates, our study provides first indications for poultry husbandry as the primary source of mcr-1.26 and its transmission between different niches.}, }
@article {pmid37353919, year = {2023}, author = {Frazão, N and Gordo, I}, title = {Ecotype formation and prophage domestication during gut bacterial evolution.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {45}, number = {8}, pages = {e2300063}, doi = {10.1002/bies.202300063}, pmid = {37353919}, issn = {1521-1878}, mesh = {Animals ; Prophages/genetics ; *Gastrointestinal Microbiome ; Domestication ; Ecotype ; Lysogeny ; *Bacteriophages/genetics ; Bacteria/genetics ; Mammals ; }, abstract = {How much bacterial evolution occurs in our intestines and which factors control it are currently burning questions. The formation of new ecotypes, some of which capable of coexisting for long periods of time, is highly likely in our guts. Horizontal gene transfer driven by temperate phages that can perform lysogeny is also widespread in mammalian intestines. Yet, the roles of mutation and especially lysogeny as key drivers of gut bacterial adaptation remain poorly understood. The mammalian gut contains hundreds of bacterial species, each with many strains and ecotypes, whose abundance varies along the lifetime of a host. A continuous high input of mutations and horizontal gene transfer events mediated by temperate phages drives that diversity. Future experiments to study the interaction between mutations that cause adaptation in microbiomes and lysogenic events with different costs and benefits will be key to understand the dynamic microbiomes of mammals. Also see the video abstract here: https://youtu.be/Zjqsiyb5Pk0.}, }
@article {pmid37350784, year = {2023}, author = {Fujihara, H and Hirose, J and Suenaga, H}, title = {Evolution of genetic architecture and gene regulation in biphenyl/PCB-degrading bacteria.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1168246}, pmid = {37350784}, issn = {1664-302X}, abstract = {A variety of bacteria in the environment can utilize xenobiotic compounds as a source of carbon and energy. The bacterial strains degrading xenobiotics are suitable models to investigate the adaptation and evolutionary processes of bacteria because they appear to have emerged relatively soon after the release of these compounds into the natural environment. Analyses of bacterial genome sequences indicate that horizontal gene transfer (HGT) is the most important contributor to the bacterial evolution of genetic architecture. Further, host bacteria that can use energy effectively by controlling the expression of organized gene clusters involved in xenobiotic degradation will have a survival advantage in harsh xenobiotic-rich environments. In this review, we summarize the current understanding of evolutionary mechanisms operative in bacteria, with a focus on biphenyl/PCB-degrading bacteria. We then discuss metagenomic approaches that are useful for such investigation.}, }
@article {pmid37348862, year = {2023}, author = {Moradigaravand, D and Li, L and Dechesne, A and Nesme, J and de la Cruz, R and Ahmad, H and Banzhaf, M and Sørensen, SJ and Smets, BF and Kreft, JU}, title = {Plasmid permissiveness of wastewater microbiomes can be predicted from 16S rRNA sequences by machine learning.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {7}, pages = {}, pmid = {37348862}, issn = {1367-4811}, support = {MR/P028195/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Wastewater ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Permissiveness ; Plasmids/genetics ; *Microbiota ; Gene Transfer, Horizontal ; }, abstract = {MOTIVATION: Wastewater treatment plants (WWTPs) harbor a dense and diverse microbial community. They constantly receive antimicrobial residues and resistant strains, and therefore provide conditions for horizontal gene transfer (HGT) of antimicrobial resistance (AMR) determinants. This facilitates the transmission of clinically important genes between, e.g. enteric and environmental bacteria, and vice versa. Despite the clinical importance, tools for predicting HGT remain underdeveloped.<br><br>RESULTS: In this study, we examined to which extent water cycle microbial community composition, as inferred by partial 16S rRNA gene sequences, can predict plasmid permissiveness, i.e. the ability of cells to receive a plasmid through conjugation, based on data from standardized filter mating assays using fluorescent bio-reporter plasmids. We leveraged a range of machine learning models for predicting the permissiveness for each taxon in the community, representing the range of hosts a plasmid is able to transfer to, for three broad host-range resistance IncP plasmids (pKJK5, pB10, and RP4). Our results indicate that the predicted permissiveness from the best performing model (random forest) showed a moderate-to-strong average correlation of 0.49 for pB10 [95% confidence interval (CI): 0.44-0.55], 0.43 for pKJK5 (0.95% CI: 0.41-0.49), and 0.53 for RP4 (0.95% CI: 0.48-0.57) with the experimental permissiveness in the unseen test dataset. Predictive phylogenetic signals occurred despite the broad host-range nature of these plasmids. Our results provide a framework that contributes to the assessment of the risk of AMR pollution in wastewater systems.<br><br>The predictive tool is available as an application at https://github.com/DaneshMoradigaravand/PlasmidPerm.}, }
@article {pmid37345922, year = {2023}, author = {Bosch, DE and Abbasian, R and Parajuli, B and Peterson, SB and Mougous, JD}, title = {Structural disruption of Ntox15 nuclease effector domains by immunity proteins protects against type VI secretion system intoxication in Bacteroidales.}, journal = {mBio}, volume = {14}, number = {4}, pages = {e0103923}, pmid = {37345922}, issn = {2150-7511}, support = {K08 AI159619/AI/NIAID NIH HHS/United States ; P30 GM124169/GM/NIGMS NIH HHS/United States ; R01 AI080609/AI/NIAID NIH HHS/United States ; S10 OD021832/OD/NIH HHS/United States ; }, mesh = {*Type VI Secretion Systems/metabolism/genetics ; *Bacterial Proteins/genetics/metabolism/chemistry/immunology ; Humans ; Gene Transfer, Horizontal ; }, abstract = {Bacteroidales use type VI secretion systems (T6SS) to competitively colonize and persist in the colon. We identify a horizontally transferred T6SS with Ntox15 family nuclease effector (Tde1) that mediates interbacterial antagonism among Bacteroidales, including several derived from a single human donor. Expression of cognate (Tdi1) or orphan immunity proteins in acquired interbacterial defense systems protects against Tde1-dependent attack. We find that immunity protein interaction induces a large effector conformational change in Tde nucleases, disrupting the active site and altering the DNA-binding site. Crystallographic snapshots of isolated Tde1, the Tde1/Tdi1 complex, and homologs from Phocaeicola vulgatus (Tde2/Tdi2) illustrate a conserved mechanism of immunity inserting into the central core of Tde, splitting the nuclease fold into two subdomains. The Tde/Tdi interface and immunity mechanism are distinct from all other polymorphic toxin-immunity interactions of known structure. Bacteroidales abundance has been linked to inflammatory bowel disease activity in prior studies, and we demonstrate that Tde and T6SS structural genes are each enriched in fecal metagenomes from ulcerative colitis subjects. Genetically mobile Tde1-encoding T6SS in Bacteroidales mediate competitive growth and may be involved in inflammatory bowel disease. Broad immunity is conferred by Tdi1 homologs through a fold-disrupting mechanism unique among polymorphic effector-immunity pairs of known structure. IMPORTANCE Bacteroidales are related to inflammatory bowel disease severity and progression. We identify type VI secretion system (T6SS) nuclease effectors (Tde) which are enriched in ulcerative colitis and horizontally transferred on mobile genetic elements. Tde-encoding T6SSs mediate interbacterial competition. Orphan and cognate immunity proteins (Tdi) prevent intoxication by multiple Tde through a new mechanism among polymorphic toxin systems. Tdi inserts into the effector central core, splitting Ntox15 into two subdomains and disrupting the active site. This mechanism may allow for evolutionary diversification of the Tde/Tdi interface as observed in colicin nuclease-immunity interactions, promoting broad neutralization of Tde by orphan Tdi. Tde-dependent T6SS interbacterial antagonism may contribute to Bacteroidales diversity in the context of ulcerative colitis.}, }
@article {pmid37339822, year = {2023}, author = {Arkhipova, IR and Yushenova, IA and Rodriguez, F}, title = {Shaping eukaryotic epigenetic systems by horizontal gene transfer.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {45}, number = {7}, pages = {e2200232}, pmid = {37339822}, issn = {1521-1878}, support = {R01 GM111917/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Eukaryota/genetics/metabolism ; *Gene Transfer, Horizontal ; DNA Methylation/genetics ; Epigenesis, Genetic ; Methyltransferases/genetics ; }, abstract = {DNA methylation constitutes one of the pillars of epigenetics, relying on covalent bonds for addition and/or removal of chemically distinct marks within the major groove of the double helix. DNA methyltransferases, enzymes which introduce methyl marks, initially evolved in prokaryotes as components of restriction-modification systems protecting host genomes from bacteriophages and other invading foreign DNA. In early eukaryotic evolution, DNA methyltransferases were horizontally transferred from bacteria into eukaryotes several times and independently co-opted into epigenetic regulatory systems, primarily via establishing connections with the chromatin environment. While C5-methylcytosine is the cornerstone of plant and animal epigenetics and has been investigated in much detail, the epigenetic role of other methylated bases is less clear. The recent addition of N4-methylcytosine of bacterial origin as a metazoan DNA modification highlights the prerequisites for foreign gene co-option into the host regulatory networks, and challenges the existing paradigms concerning the origin and evolution of eukaryotic regulatory systems.}, }
@article {pmid37339743, year = {2023}, author = {Takeuchi, N and Hamada-Zhu, S and Suzuki, H}, title = {Prophages and plasmids can display opposite trends in the types of accessory genes they carry.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {2001}, pages = {20231088}, pmid = {37339743}, issn = {1471-2954}, mesh = {*Prophages/genetics ; Plasmids ; Escherichia coli/genetics ; *Bacteriophages ; Virulence Factors/genetics ; Anti-Bacterial Agents ; }, abstract = {Mobile genetic elements (MGEs), such as phages and plasmids, often possess accessory genes encoding bacterial functions, facilitating bacterial evolution. Are there rules governing the arsenal of accessory genes MGEs carry? If such rules exist, they might be reflected in the types of accessory genes different MGEs carry. To test this hypothesis, we compare prophages and plasmids with respect to the frequencies at which they carry antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in the genomes of 21 pathogenic bacterial species using public databases. Our results indicate that prophages tend to carry VFGs more frequently than ARGs in three species, whereas plasmids tend to carry ARGs more frequently than VFGs in nine species, relative to genomic backgrounds. In Escherichia coli, where this prophage-plasmid disparity is detected, prophage-borne VFGs encode a much narrower range of functions than do plasmid-borne VFGs, typically involved in damaging host cells or modulating host immunity. In the species where the above disparity is not detected, ARGs and VFGs are barely found in prophages and plasmids. These results indicate that MGEs can differentiate in the types of accessory genes they carry depending on their infection strategies, suggesting a rule governing horizontal gene transfer mediated by MGEs.}, }
@article {pmid37337195, year = {2023}, author = {Zhang, Y and Miao, J and Zhang, N and Wang, X and Li, Z and Richard, OA and Li, B}, title = {The analysis of the function, diversity, and evolution of the Bacillus phage genome.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {170}, pmid = {37337195}, issn = {1471-2180}, mesh = {*Bacillus Phages/genetics ; Genome, Viral ; *Bacteriophages/genetics ; Prophages/genetics ; Mutation ; Evolution, Molecular ; }, abstract = {BACKGROUND: Phages play a pivotal role in the evolution of microbial populations. The interactions between phages and their hosts are complex and may vary in response to host physiology and environmental conditions. Here, we have selected the genomes of some representative Bacillus prophages and lysosomes from the NCBI database for evolutionary analysis. We explored their evolutionary relationships and analyzed the protein information encoded by hundreds of Bacillus phages.<br><br>RESULTS: We obtained the following conclusions: First, Bacillus phages carried some known functional gene fragments and a large number of unknown functional gene fragments, which might have an important impact on Bacillus populations, such as the formation of spores and biofilms and the transmission of virulence factors. Secondly, the Bacillus phage genome showed diversity, with a clear genome boundary between Bacillus prophages and Bacillus lytic phages. Furthermore, genetic mutations, sequence losses, duplications, and host-switching have occurred during the evolution of the Bacillus phage, resulting in low genome similarity between the Bacillus phages. Finally, the lysis module played an important influence on the process of Bacillus phage cross-species infestation.<br><br>CONCLUSIONS: This study systematically described their protein function, diversity, and genome evolution, and the results of this study provide a basis for evolutionary diversity, horizontal gene transfer and co-evolution with the host in Bacillus phages.}, }
@article {pmid37336594, year = {2023}, author = {Shafiq, M and Bilal, H and Permana, B and Xu, D and Cai, G and Li, X and Zeng, M and Yuan, Y and Jiao, X and Yao, F}, title = {Characterization of antibiotic resistance genes and mobile elements in extended-spectrum β-lactamase-producing Escherichia coli strains isolated from hospitalized patients in Guangdong, China.}, journal = {Journal of applied microbiology}, volume = {134}, number = {7}, pages = {}, doi = {10.1093/jambio/lxad125}, pmid = {37336594}, issn = {1365-2672}, support = {42150410383//National Natural Science Foundation of China/ ; 2020LKSFG03E//Li Ka Shing Foundation Cross-Disciplinary Research/ ; }, mesh = {Humans ; *Escherichia coli ; Anti-Bacterial Agents/pharmacology ; beta-Lactamases/genetics ; *Escherichia coli Infections/epidemiology ; Drug Resistance, Multiple, Bacterial/genetics ; }, abstract = {AIM: This study aimed to investigate the high-resolution phenotypic and genotypic characterization of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli strains isolated from hospitalized patients to explore the resistance genes and mobile genetic elements (MGEs) involved in horizontal dissemination.<br><br>METHODS: Between May and September 2021, a total of 216 ESBL-producing E. coli isolates were recovered from multiple departments. The identification of strains was performed using MALDI-TOF mass spectrometry and PCR, while antibiotic susceptibility testing was carried out using the Vitek 2 COMPACT system to determine resistance patterns, while PCR was used to detect different resistance genes and MGEs. In addition, a conjugation assay was performed to investigate the horizontal gene transfer of resistance genes. Selected isolates underwent whole-genome sequencing (WGS) using the Illumina MiSeq platform.<br><br>RESULTS: A total of 216 out of 409 E. coli isolates recovered from a tertiary hospital were observed to be ESBL-producing, giving a carriage rate of 52.8%, as determined by phenotypic screening. The most frequent sources of ESBL-producing E. coli isolates were urine (129/216, 59.72%) and blood (50/216, 23.14%). The most prevalent ESBL genes identified were blaCTX-M (60.18%), blaTEM (40.27%), and blaSHV (18.05%). Three E. coli isolates were found to carry the genes blaNDM, mcr-1, and fosA3 genes. The most prevalent MGEs were IS26 (95.37%), Int (87.03%), and IncFIB (76.85%). WGS analysis of eight MDR E. coli strains revealed that these isolates belonged to eight different sequence types (STs) and serotypes and were found to harbor multiple plasmid replicons and virulence factors.<br><br>CONCLUSION: This study highlights a high incidence of antibiotic resistance genes and MGEs associated with the dissemination of ESBLs and other resistance genes.}, }
@article {pmid37336333, year = {2023}, author = {Xia, Y and Zuo, S and Zheng, Y and Yang, W and Tang, X and Ke, X and Zhuo, Q and Yang, X and Li, Y and Liu, H and Fan, B}, title = {Extended one generation reproductive toxicity study and effect on gut flora of genetically modified rice rich in β-carotene in wistar rats.}, journal = {Reproductive toxicology (Elmsford, N.Y.)}, volume = {119}, number = {}, pages = {108424}, doi = {10.1016/j.reprotox.2023.108424}, pmid = {37336333}, issn = {1873-1708}, mesh = {Rats ; Animals ; Rats, Wistar ; *beta Carotene ; Plants, Genetically Modified/genetics/adverse effects ; *Gastrointestinal Microbiome ; Reproduction ; }, abstract = {To evaluate the reproductive toxicity of gene modified rice generated by introducing phytoene synthase (Psy) and bacterial phytoene desaturase (CrtI) from maize and Erwinia uredovora, Wistar rats were allocated into 3 groups and fed with Psy and CrtI gene modified rice mixture diet (GM group), non-gene modified rice mixture diet (non-GM group), and AIN-93 diet (Blank control group) from parental generation (F0) to the offsprings (F1). GM rice, Heijinmi (HJM) and Non-GM rice, Heishuai (HS), were both formulated into diets at ratios of 73.5% and 75.5% according to the AIN93 diet for rodent animals, respectively. Relative to the non-GM group, no biologically relevant differences were observed in GM group rats concerning reproductive performance such as fertility rate, gestation rate, mean duration, hormone level, and reproductive organ pathology. The developmental parameters results were not significantly different from the non-GM group such as body weight, food consumption, developmental neurotoxicity, behavior, hematology, and serum chemistry. In terms of immunotoxicity, the IgG indicators of offspring from the GM group improved in contrast with the non-GM group. Additional gut flora analysis of F0 generation rats resulted as that the treatment elicited an increased gut microflora diversity of F0 rats. And no horizontal gene transfer of Psy and CrtI genes in rats fed a GM rice HJM diet. In conclusion, we found no adverse effects related to GM rice in the extended one-generation reproductive toxicity study, indicating that GM rice is a safe alternative for its counterpart rice regarding reproductive toxicity.}, }
@article {pmid37333098, year = {2023}, author = {Grodner, B and Shi, H and Farchione, O and Vill, AC and Ntekas, I and Diebold, PJ and Zipfel, WR and Brito, IL and Vlaminck, I}, title = {Spatial Mapping of Mobile Genetic Elements and their Cognate Hosts in Complex Microbiomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37333098}, issn = {2692-8205}, support = {DP2 AI138242/AI/NIAID NIH HHS/United States ; R33 CA235302/CA/NCI NIH HHS/United States ; S10 OD018516/OD/NIH HHS/United States ; }, abstract = {The frequent exchange of mobile genetic elements (MGEs) between bacteria accelerates the spread of functional traits, including antimicrobial resistance, within the human microbiome. Yet, progress in understanding these intricate processes has been hindered by the lack of tools to map the spatial spread of MGEs in complex microbial communities, and to associate MGEs to their bacterial hosts. To overcome this challenge, we present an imaging approach that pairs single molecule DNA Fluorescence In Situ Hybridization (FISH) with multiplexed ribosomal RNA FISH, thereby enabling the simultaneous visualization of both MGEs and host bacterial taxa. We used this methodology to spatially map bacteriophage and antimicrobial resistance (AMR) plasmids in human oral biofilms, and we studied the heterogeneity in their spatial distributions and demonstrated the ability to identify their host taxa. Our data revealed distinct clusters of both AMR plasmids and prophage, coinciding with densely packed regions of host bacteria in the biofilm. These results suggest the existence of specialized niches that maintain MGEs within the community, possibly acting as local hotspots for horizontal gene transfer. The methods introduced here can help advance the study of MGE ecology and address pressing questions regarding antimicrobial resistance and phage therapy.}, }
@article {pmid37332513, year = {2022}, author = {Morson, N and Molenda, O and Picott, KJ and Richardson, RE and Edwards, EA}, title = {Long-term survival of Dehalococcoides mccartyi strains in mixed cultures under electron acceptor and ammonium limitation.}, journal = {FEMS microbes}, volume = {3}, number = {}, pages = {xtac021}, pmid = {37332513}, issn = {2633-6685}, abstract = {Few strains of Dehalococcoides mccartyi harbour and express the vinyl chloride reductase (VcrA) that catalyzes the dechlorination of vinyl chloride (VC), a carcinogenic soil and groundwater contaminant. The vcrA operon is found on a Genomic Island (GI) and, therefore, believed to participate in horizontal gene transfer (HGT). To try to induce HGT of the vcrA-GI, we blended two enrichment cultures in medium without ammonium while providing VC. We hypothesized that these conditions would select for a mutant strain of D. mccartyi that could both fix nitrogen and respire VC. However, after more than 4 years of incubation, we found no evidence for HGT of the vcrA-GI. Rather, we observed VC-dechlorinating activity attributed to the trichloroethene reductase TceA. Sequencing and protein modelling revealed a mutation in the predicted active site of TceA, which may have influenced substrate specificity. We also identified two nitrogen-fixing D. mccartyi strains in the KB-1 culture. The presence of multiple strains of D. mccartyi with distinct phenotypes is a feature of natural environments and certain enrichment cultures (such as KB-1), and may enhance bioaugmentation success. The fact that multiple distinct strains persist in the culture for decades and that we could not induce HGT of the vcrA-GI suggests that it is not as mobile as predicted, or that mobility is restricted in ways yet to be discovered to specific subclades of Dehalococcoides.}, }
@article {pmid37329912, year = {2023}, author = {Katsivelou, E and Perruchon, C and Karas, PA and Sarantidou, A and Pappa, E and Katsoula, A and Ligda, P and Sotiraki, S and Martin-Laurent, F and Vasileiadis, S and Karpouzas, DG}, title = {Accelerated dissipation, soil microbial toxicity and dispersal of antimicrobial resistance in soils repeatedly exposed to tiamulin, tilmicosin and sulfamethoxazole.}, journal = {The Science of the total environment}, volume = {893}, number = {}, pages = {164817}, doi = {10.1016/j.scitotenv.2023.164817}, pmid = {37329912}, issn = {1879-1026}, mesh = {*Soil/chemistry ; *Anti-Bacterial Agents/pharmacology ; Sulfamethoxazole/chemistry ; Manure/microbiology ; Soil Microbiology ; Ammonia/pharmacology ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; }, abstract = {The application of manures leads to the contamination of agricultural soils with veterinary antibiotics (VAs). These might exert toxicity on the soil microbiota and threaten environmental quality, and public health. We obtained mechanistic insights about the impact of three VAs, namely, sulfamethoxazole (SMX), tiamulin (TIA) and tilmicosin (TLM), on the abundance of key soil microbial groups, antibiotic resistance genes (ARGs) and class I integron integrases (intl1). In a microcosm study, we repeatedly treated two soils (differing in pH and VA dissipation capacity) with the studied VAs, either directly or via fortified manure. This application scheme resulted in accelerated dissipation of TIA, but not of SMX, and accumulation of TLM. Potential nitrification rates (PNR), and the abundance of ammonia-oxidizing microorganism (AOM) were reduced by SMX and TIA, but not by TLM. VAs strongly impacted the total prokaryotic and AOM communities, whereas manure addition was the main determinant of the fungal and protist communities. SMX stimulated sulfonamide resistance, while manure stimulated ARGs and horizontal gene transfer. Correlations identified opportunistic pathogens like Clostridia, Burkholderia-Caballeronia-Paraburkholderia, and Nocardioides as potential ARG reservoirs in soil. Our results provide unprecedented evidence about the effects of understudied VAs on soil microbiota and highlight risks posed by VA-contaminated manures. ENVIRONMENTAL IMPLICATION: The dispersal of veterinary antibiotics (VAs) through soil manuring enhances antimicrobial resistance (AMR) development and poses a threat to the environment and the public health. We provide insights about the impact of selected VAs on their: (i) microbially-mediated dissipation in soil; (ii) ecotoxicity on the soil microbial communities; (iii) capacity to stimulate AMR. Our results (i) demonstrate the effects of VAs and their application-mode on the bacterial, fungal, and protistan communities, and on the soil ammonia oxidizers; (ii) describe natural attenuation processes against VA dispersal, (iii) depict potential soil microbial AMR reservoirs, essential for the development of risk assessment strategies.}, }
@article {pmid37327521, year = {2023}, author = {Zhu, S and Yang, B and Wang, Z and Liu, Y}, title = {Augmented dissemination of antibiotic resistance elicited by non-antibiotic factors.}, journal = {Ecotoxicology and environmental safety}, volume = {262}, number = {}, pages = {115124}, doi = {10.1016/j.ecoenv.2023.115124}, pmid = {37327521}, issn = {1090-2414}, abstract = {The emergence and rapid spread of antibiotic resistance seriously compromise the clinical efficacy of current antibiotic therapies, representing a serious public health threat worldwide. Generally, drug-susceptible bacteria can acquire antibiotic resistance through genetic mutation or gene transfer, among which horizontal gene transfer (HGT) plays a dominant role. It is widely acknowledged that the sub-inhibitory concentrations of antibiotics are the key drivers in promoting the transmission of antibiotic resistance. However, accumulating evidence in recent years has shown that in addition to antibiotics, non-antibiotics can also accelerate the horizontal transfer of antibiotic resistance genes (ARGs). Nevertheless, the roles and potential mechanisms of non-antibiotic factors in the transmission of ARGs remain largely underestimated. In this review, we depict the four pathways of HGT and their differences, including conjugation, transformation, transduction and vesiduction. We summarize non-antibiotic factors accounting for the enhanced horizontal transfer of ARGs and their underlying molecular mechanisms. Finally, we discuss the limitations and implications of current studies.}, }
@article {pmid37325804, year = {2023}, author = {Woods, RJ and Barbosa, C and Koepping, L and Raygoza, JA and Mwangi, M and Read, AF}, title = {The evolution of antibiotic resistance in an incurable and ultimately fatal infection: A retrospective case study.}, journal = {Evolution, medicine, and public health}, volume = {11}, number = {1}, pages = {163-173}, pmid = {37325804}, issn = {2050-6201}, support = {K08 AI119182/AI/NIAID NIH HHS/United States ; }, abstract = {BACKGROUND AND OBJECTIVES: The processes by which pathogens evolve within a host dictate the efficacy of treatment strategies designed to slow antibiotic resistance evolution and influence population-wide resistance levels. The aim of this study is to describe the underlying genetic and phenotypic changes leading to antibiotic resistance within a patient who died as resistance evolved to available antibiotics. We assess whether robust patterns of collateral sensitivity and response to combinations existed that might have been leveraged to improve therapy.<br><br>METHODOLOGY: We used whole-genome sequencing of nine isolates taken from this patient over 279 days of a chronic infection with Enterobacter hormaechei, and systematically measured changes in resistance against five of the most relevant drugs considered for treatment.<br><br>RESULTS: The entirety of the genetic change is consistent with de novo mutations and plasmid loss events, without acquisition of foreign genetic material via horizontal gene transfer. The nine isolates fall into three genetically distinct lineages, with early evolutionary trajectories being supplanted by previously unobserved multi-step evolutionary trajectories. Importantly, although the population evolved resistance to all the antibiotics used to treat the infection, no single isolate was resistant to all antibiotics. Evidence of collateral sensitivity and response to combinations therapy revealed inconsistent patterns across this diversifying population.<br><br>CONCLUSIONS: Translating antibiotic resistance management strategies from theoretical and laboratory data to clinical situations, such as this, will require managing diverse population with unpredictable resistance trajectories.}, }
@article {pmid37323902, year = {2023}, author = {Nguyen, QH and Le, TTH and Nguyen, ST and Nguyen, KT and Quyen, DV and Hayer, J and Bañuls, AL and Tran, TTT}, title = {Large-scale analysis of putative plasmids in clinical multidrug-resistant Escherichia coli isolates from Vietnamese patients.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1094119}, pmid = {37323902}, issn = {1664-302X}, abstract = {INTRODUCTION: In the past decades, extended-spectrum beta-lactamase (ESBL)-producing and carbapenem-resistant (CR) Escherichia coli isolates have been detected in Vietnamese hospitals. The transfer of antimicrobial resistance (AMR) genes carried on plasmids is mainly responsible for the emergence of multidrug-resistant E. coli strains and the spread of AMR genes through horizontal gene transfer. Therefore, it is important to thoroughly study the characteristics of AMR gene-harboring plasmids in clinical multidrug-resistant bacterial isolates.<br><br>METHODS: The profiles of plasmid assemblies were determined by analyzing previously published whole-genome sequencing data of 751 multidrug-resistant E. coli isolates from Vietnamese hospitals in order to identify the risk of AMR gene horizontal transfer and dissemination.<br><br>RESULTS: The number of putative plasmids in isolates was independent of the sequencing coverage. These putative plasmids originated from various bacterial species, but mostly from the Escherichia genus, particularly E. coli species. Many different AMR genes were detected in plasmid contigs of the studied isolates, and their number was higher in CR isolates than in ESBL-producing isolates. Similarly, the blaKPC-2, blaNDM-5, blaOXA-1, blaOXA-48, and blaOXA-181 &#x3b2;-lactamase genes, associated with resistance to carbapenems, were more frequent in CR strains. Sequence similarity network and genome annotation analyses revealed high conservation of the &#x3b2;-lactamase gene clusters in plasmid contigs that carried the same AMR genes.<br><br>DISCUSSION: Our study provides evidence of horizontal gene transfer in multidrug-resistant E. coli isolates via conjugative plasmids, thus rapidly accelerating the emergence of resistant bacteria. Besides reducing antibiotic misuse, prevention of plasmid transmission also is essential to limit antibiotic resistance.}, }
@article {pmid37321361, year = {2023}, author = {Zhang, J and Huang, Z and Fu, W and Zhang, C and Zan, T and Nan, P and Li, L and Song, Z and Zhang, W and Yang, J and Wang, Y}, title = {Host shift promotes divergent evolution between closely related holoparasitic species.}, journal = {Molecular phylogenetics and evolution}, volume = {186}, number = {}, pages = {107842}, doi = {10.1016/j.ympev.2023.107842}, pmid = {37321361}, issn = {1095-9513}, mesh = {Humans ; Phylogeny ; *Orobanchaceae/genetics ; Genes, Plant ; *Genome, Plastid ; Repetitive Sequences, Nucleic Acid ; Gene Transfer, Horizontal ; }, abstract = {Distinct hosts have been hypothesized to possess the potential for affecting species differentiation and genome evolution of parasitic organisms. However, what host shift history is experienced by the closely related parasites and whether disparate evolution of their genomes occur remain largely unknown. Here, we screened horizontal gene transfer (HGT) events in a pair of sister species of holoparasitic Boschniakia (Orobanchaceae) having obligate hosts from distinct families to recall the former host-parasite associations and performed a comparative analysis to investigate the difference of their organelle genomes. Except those from the current hosts (Ericaceae and Betulaceae), we identified a number of HGTs from Rosaceae supporting the occurrence of unexpected ancient host shifts. Different hosts transfer functional genes which changed nuclear genomes of this sister species. Likewise, different donors transferred sequences to their mitogenomes, which vary in size due to foreign and repetitive elements rather than other factors found in other parasites. The plastomes are both severely reduced, and the degree of difference in reduction syndrome reaches the intergeneric level. Our findings provide new insights into the genome evolution of parasites adapting to different hosts and extend the mechanism of host shift promoting species differentiation to parasitic plant lineages.}, }
@article {pmid37317293, year = {2023}, author = {Shelenkov, A and Mikhaylova, Y and Voskanyan, S and Egorova, A and Akimkin, V}, title = {Whole-Genome Sequencing Revealed the Fusion Plasmids Capable of Transmission and Acquisition of Both Antimicrobial Resistance and Hypervirulence Determinants in Multidrug-Resistant Klebsiella pneumoniae Isolates.}, journal = {Microorganisms}, volume = {11}, number = {5}, pages = {}, pmid = {37317293}, issn = {2076-2607}, support = {075-15-2019-1666//the Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {Klebsiella pneumoniae, a member of the Enterobacteriaceae family, has become a dangerous pathogen accountable for a large fraction of the various infectious diseases in both clinical and community settings. In general, the K. pneumoniae population has been divided into the so-called classical (cKp) and hypervirulent (hvKp) lineages. The former, usually developing in hospitals, can rapidly acquire resistance to a wide spectrum of antimicrobial drugs, while the latter is associated with more aggressive but less resistant infections, mostly in healthy humans. However, a growing number of reports in the last decade have confirmed the convergence of these two distinct lineages into superpathogen clones possessing the properties of both, and thus imposing a significant threat to public health worldwide. This process is associated with horizontal gene transfer, in which plasmid conjugation plays a very important role. Therefore, the investigation of plasmid structures and the ways plasmids spread within and between bacterial species will provide benefits in developing prevention measures against these powerful pathogens. In this work, we investigated clinical multidrug-resistant K. pneumoniae isolates using long- and short-read whole-genome sequencing, which allowed us to reveal fusion IncHI1B/IncFIB plasmids in ST512 isolates capable of simultaneously carrying hypervirulence (iucABCD, iutA, prmpA, peg-344) and resistance determinants (armA, blaNDM-1 and others), and to obtain insights into their formation and transmission mechanisms. Comprehensive phenotypic, genotypic and phylogenetic analysis of the isolates, as well as of their plasmid repertoire, was performed. The data obtained will facilitate epidemiological surveillance of high-risk K. pneumoniae clones and the development of prevention strategies against them.}, }
@article {pmid37315610, year = {2023}, author = {Pires, J and Santos, R and Monteiro, S}, title = {Antibiotic resistance genes in bacteriophages from wastewater treatment plant and hospital wastewaters.}, journal = {The Science of the total environment}, volume = {892}, number = {}, pages = {164708}, doi = {10.1016/j.scitotenv.2023.164708}, pmid = {37315610}, issn = {1879-1026}, mesh = {*Wastewater ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Colistin ; *Bacteriophages/genetics ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Hospitals ; }, abstract = {Antibiotic resistant bacteria (ARB) are a major health risk caused particularly by anthropogenic activities. Acquisition of antibiotic resistances by bacteria is known to have happened before the discovery of antibiotics and can occur through different routes. Bacteriophages are thought to have an important contribution to the dissemination of antibiotic resistance genes (ARGs) in the environment. In this study, seven ARGs (blaTEM, blaSHV, blaCTX-M, blaCMY, mecA, vanA, and mcr-1) were investigated, in the bacteriophage fraction, in raw urban and hospital wastewaters. The genes were quantified in 58 raw wastewater samples collected at five WWTPs (n = 38) and hospitals (n = 20). All genes were detected in the phage DNA fraction, with the bla genes found in higher frequency. On the other hand, mecA and mcr-1 were the least frequently detected genes. Concentrations varied between 10[2] copies/L and 10[6] copies/L. The gene coding for the resistance to colistin (mcr-1), a last-resort antibiotic for the treatment of multidrug-resistant Gram-negative infections, was identified in raw urban and hospital wastewaters with positivity rates of 19 % and 10 %, respectively. ARGs patterns varied between hospital and raw urban wastewaters, and within hospitals and WWTP. This study suggests that phages are reservoirs of ARGs, and that ARGs (with particularly emphasis on resistance to colistin and vancomycin) in the phage fraction are already widely widespread in the environment with potential large implications for public health.}, }
@article {pmid37314210, year = {2023}, author = {Nguyen, M and Elmore, Z and Ihle, C and Moen, FS and Slater, AD and Turner, BN and Parrello, B and Best, AA and Davis, JJ}, title = {Predicting variable gene content in Escherichia coli using conserved genes.}, journal = {mSystems}, volume = {8}, number = {4}, pages = {e0005823}, pmid = {37314210}, issn = {2379-5077}, support = {75N93019C00076/AI/NIAID NIH HHS/United States ; }, mesh = {Escherichia coli/genetics ; Genome, Bacterial/genetics ; Plasmids ; *Escherichia coli Proteins/genetics ; *Anti-Infective Agents ; }, abstract = {Having the ability to predict the protein-encoding gene content of an incomplete genome or metagenome-assembled genome is important for a variety of bioinformatic tasks. In this study, as a proof of concept, we built machine learning classifiers for predicting variable gene content in Escherichia coli genomes using only the nucleotide k-mers from a set of 100 conserved genes as features. Protein families were used to define orthologs, and a single classifier was built for predicting the presence or absence of each protein family occurring in 10%-90% of all E. coli genomes. The resulting set of 3,259 extreme gradient boosting classifiers had a per-genome average macro F1 score of 0.944 [0.943-0.945, 95% CI]. We show that the F1 scores are stable across multi-locus sequence types and that the trend can be recapitulated by sampling a smaller number of core genes or diverse input genomes. Surprisingly, the presence or absence of poorly annotated proteins, including "hypothetical proteins" was accurately predicted (F1 = 0.902 [0.898-0.906, 95% CI]). Models for proteins with horizontal gene transfer-related functions had slightly lower F1 scores but were still accurate (F1s = 0.895, 0.872, 0.824, and 0.841 for transposon, phage, plasmid, and antimicrobial resistance-related functions, respectively). Finally, using a holdout set of 419 diverse E. coli genomes that were isolated from freshwater environmental sources, we observed an average per-genome F1 score of 0.880 [0.876-0.883, 95% CI], demonstrating the extensibility of the models. Overall, this study provides a framework for predicting variable gene content using a limited amount of input sequence data. IMPORTANCE Having the ability to predict the protein-encoding gene content of a genome is important for assessing genome quality, binning genomes from shotgun metagenomic assemblies, and assessing risk due to the presence of antimicrobial resistance and other virulence genes. In this study, we built a set of binary classifiers for predicting the presence or absence of variable genes occurring in 10%-90% of all publicly available E. coli genomes. Overall, the results show that a large portion of the E. coli variable gene content can be predicted with high accuracy, including genes with functions relating to horizontal gene transfer. This study offers a strategy for predicting gene content using limited input sequence data.}, }
@article {pmid37311294, year = {2023}, author = {Zhang, Q and Zhou, L and Zhao, Y and Gao, S and Yang, Y and Chen, Q and Li, W and Qi, Q and Dong, Q and Lei, J and Guo, X and Gao, Q and Yang, Y}, title = {Uncovering the virome and its interaction with antibiotic resistome during compost fertilization.}, journal = {Journal of hazardous materials}, volume = {457}, number = {}, pages = {131763}, doi = {10.1016/j.jhazmat.2023.131763}, pmid = {37311294}, issn = {1873-3336}, mesh = {Animals ; Swine ; *Anti-Bacterial Agents/pharmacology ; Virome ; Genes, Bacterial ; *Composting ; Manure/microbiology ; Soil ; Soil Microbiology ; Fertilization ; }, abstract = {Antibiotic resistance is a pressing global health issue, leading to increased illnesses and fatalities. The contribution of viruses to the acquisition, preservation, and dissemination of antibiotic resistance genes (ARGs) is not yet fully understood. By using a high-throughput functional gene-based microarray (GeoChip 5.0), this study examines the prevalence and relative abundance of bacteriophage and eukaryotic viral genes in swine manure, compost, compost-amended agricultural soil, and unamended soil from suburban regions of Beijing, China. Our findings reveal a significantly elevated presence of biomarker viral genes in compost-amended soils compared to unamended soils, suggesting potential health risks associated with compost fertilization. We also observed stronger ecological interactions between ARGs and viral genes in manure and compost than in soils. Network analysis identified arabinose efflux permeases and EmrB/QacA resistance genes, linked to CRISPR encoding sequences, as keystone nodes, indicating possible ARG acquisition via virus infections. Moreover, positive correlations were found between viral genes, antibiotic concentrations, and ARG diversity in manure, compost, and compost-amended soils, highlighting a likely pathway for virus-mediated ARG transfer. In summary, our results indicate that use of compost as a fertilizer in agricultural settings could facilitate the spread of ARGs through viral mechanisms, allowing for time-delayed genetic exchanges over broader temporal and spatial scales than ARGs within bacterial genomes.}, }
@article {pmid37310285, year = {2023}, author = {Cohen, H and Fridman, CM and Gerlic, M and Salomon, D}, title = {A Vibrio T6SS-Mediated Lethality in an Aquatic Animal Model.}, journal = {Microbiology spectrum}, volume = {11}, number = {4}, pages = {e0109323}, pmid = {37310285}, issn = {2165-0497}, mesh = {Animals ; Humans ; *Inflammasomes ; *Vibrio/genetics ; Eukaryota ; Virulence/genetics ; Phagocytes ; Mammals ; }, abstract = {Bacteria belonging to the genus Vibrio include many known and emerging pathogens. Horizontal gene transfer of pathogenicity islands is a major contributor to the emergence of new pathogenic Vibrio strains. Here, we use the brine shrimp Artemia salina as a model and show that the marine bacterium Vibrio proteolyticus uses a horizontally shared type VI secretion system, T6SS3, to intoxicate a eukaryotic host. Two T6SS3 effectors, which were previously shown to induce inflammasome-mediated pyroptotic cell death in mammalian phagocytic cells, contribute to this toxicity. Furthermore, we find a novel T6SS3 effector that also contributes to the lethality mediated by this system against Artemia salina. Therefore, our results reveal a T6SS that is shared among diverse vibrios and mediates host lethality, indicating that it can lead to the emergence of new pathogenic strains. IMPORTANCE The rise in sea surface temperature has been linked to the spread of bacteria belonging to the genus Vibrio and the human illnesses associated with them. Since vibrios often share virulence traits horizontally, a better understanding of their virulence potential and determinants can prepare us for new emerging pathogens. In this work, we showed that a toxin delivery system found in various vibrios mediates lethality in an aquatic animal. Taken together with previous reports showing that the same system induces inflammasome-mediated cell death in mammalian phagocytic cells, our findings suggest that this delivery system and its associated toxins may contribute to the emergence of pathogenic strains.}, }
@article {pmid37310275, year = {2023}, author = {Saati-Santamaría, Z}, title = {Global Map of Specialized Metabolites Encoded in Prokaryotic Plasmids.}, journal = {Microbiology spectrum}, volume = {11}, number = {4}, pages = {e0152323}, pmid = {37310275}, issn = {2165-0497}, mesh = {Humans ; *Bacteria/genetics ; Secondary Metabolism/genetics ; Plasmids/genetics ; *Multigene Family ; }, abstract = {Plasmids are the main mobile elements responsible for horizontal gene transfer (HGT) in microorganisms. These replicons extend the metabolic spectrum of their host cells by carrying functional genes. However, it is still unknown to what extent plasmids carry biosynthetic gene clusters (BGCs) related to the production of secondary or specialized metabolites (SMs). Here, we analyzed 9,183 microbial plasmids to unveil their potential to produce SMs, finding a large diversity of cryptic BGCs in a few varieties of prokaryotic host taxa. Some of these plasmids harbored 15 or more BGCs, and many others were exclusively dedicated to mobilizing BGCs. We found an occurrence pattern of BGCs within groups of homologous plasmids shared by a common taxon, mainly in host-associated microbes (e.g., Rhizobiales, Enterobacteriaceae members). Our results add to the knowledge of the ecological functions and potential industrial uses of plasmids and shed light on the dynamics and evolution of SMs in prokaryotes. IMPORTANCE Plasmids are mobile DNA elements that can be shared among microbial cells, and they are useful for bringing to fruition some microbial ecological traits. However, it is not known to what extent plasmids harbor genes related to the production of specialized/secondary metabolites (SMs). In microbes, these metabolites are frequently useful for defense purposes, signaling, etc. In addition, these molecules usually have biotechnological and clinical applications. Here, we analyzed the content, dynamics, and evolution of genes related to the production of SMs in >9,000 microbial plasmids. Our results confirm that some plasmids act as a reservoir of SMs. We also found that some families of biosynthetic gene clusters are exclusively present in some groups of plasmids shared among closely related microbes. Host-associated bacteria (e.g., plant and human microbes) harbor the majority of specialized metabolites encoded in plasmids. These results provide new knowledge about microbial ecological traits and might enable the discovery of novel metabolites.}, }
@article {pmid37307358, year = {2023}, author = {Marr, RA and Moore, J and Formby, S and Martiniuk, JT and Hamilton, J and Ralli, S and Konwar, K and Rajasundaram, N and Hahn, A and Measday, V}, title = {Whole genome sequencing of Canadian Saccharomyces cerevisiae strains isolated from spontaneous wine fermentations reveals a new Pacific West Coast Wine clade.}, journal = {G3 (Bethesda, Md.)}, volume = {13}, number = {8}, pages = {}, pmid = {37307358}, issn = {2160-1836}, mesh = {*Saccharomyces cerevisiae ; *Wine ; DNA Copy Number Variations ; Fermentation ; Phylogeny ; Canada ; Plant Breeding ; Whole Genome Sequencing ; }, abstract = {Vineyards in wine regions around the world are reservoirs of yeast with oenological potential. Saccharomyces cerevisiae ferments grape sugars to ethanol and generates flavor and aroma compounds in wine. Wineries place a high-value on identifying yeast native to their region to develop a region-specific wine program. Commercial wine strains are genetically very similar due to a population bottleneck and in-breeding compared to the diversity of S. cerevisiae from the wild and other industrial processes. We have isolated and microsatellite-typed hundreds of S. cerevisiae strains from spontaneous fermentations of grapes from the Okanagan Valley wine region in British Columbia, Canada. We chose 75 S. cerevisiae strains, based on our microsatellite clustering data, for whole genome sequencing using Illumina paired-end reads. Phylogenetic analysis shows that British Columbian S. cerevisiae strains cluster into 4 clades: Wine/European, Transpacific Oak, Beer 1/Mixed Origin, and a new clade that we have designated as Pacific West Coast Wine. The Pacific West Coast Wine clade has high nucleotide diversity and shares genomic characteristics with wild North American oak strains but also has gene flow from Wine/European and Ecuadorian clades. We analyzed gene copy number variations to find evidence of domestication and found that strains in the Wine/European and Pacific West Coast Wine clades have gene copy number variation reflective of adaptations to the wine-making environment. The "wine circle/Region B", a cluster of 5 genes acquired by horizontal gene transfer into the genome of commercial wine strains is also present in the majority of the British Columbian strains in the Wine/European clade but in a minority of the Pacific West Coast Wine clade strains. Previous studies have shown that S. cerevisiae strains isolated from Mediterranean Oak trees may be the living ancestors of European wine yeast strains. This study is the first to isolate S. cerevisiae strains with genetic similarity to nonvineyard North American Oak strains from spontaneous wine fermentations.}, }
@article {pmid37302657, year = {2023}, author = {Wu, T and Mao, H and Hai, D and Cheng, J and Fu, Y and Lin, Y and Jiang, D and Xie, J}, title = {Molecular characterization of a novel fungal alphaflexivirus reveals potential inter-species horizontal gene transfer.}, journal = {Virus research}, volume = {334}, number = {}, pages = {199151}, pmid = {37302657}, issn = {1872-7492}, mesh = {*Flexiviridae/genetics ; Phylogeny ; RNA, Viral/genetics ; Gene Transfer, Horizontal ; RNA-Dependent RNA Polymerase/genetics ; Ascomycota ; *RNA Viruses ; *Fungal Viruses ; Open Reading Frames ; Genome, Viral ; }, abstract = {Sclerotinia sclerotiorum is a notorious phytopathogenic fungus that harbors diverse mycoviruses. A novel positive-sense single-stranded RNA virus, Sclerotinia sclerotiorum alphaflexivirus 2 (SsAFV2), was isolated from the hypovirulent strain 32-9 of S. sclerotiorum, and its complete genome was determined. The SsAFV2 genome contains 7,162 nucleotides (nt), excluding the poly (A) structure, and is composed of four open reading frames (ORF1-4). ORF1 encodes a polyprotein that contains three conserved domains: methyltransferase, helicase, and RNA-dependent RNA polymerase (RdRp). The ORF3 putative encodes coat proteins (CP), with ORF2 and ORF4 encoding hypothetical proteins of unknown functions. Phylogenetic analysis revealed that SsAFV2 clustered with Botrytis virus X (BVX) based on multiple alignments of helicase, RdRp, and CP, but the methyltransferase of SsAFV2 was most closely related to Sclerotinia sclerotiorum alphaflexivirus 1, suggesting that SsAFV2 is a new member of the Botrexvirus genus within the Alphaflexiviridae family, and also revealed the occurrence of potential inter-species horizontal gene transfer events within the Botrexvirus genus during the evolutionary process. Our results contribute to the current knowledge regarding the evolution and divergence of Botrexviruses.}, }
@article {pmid37296404, year = {2023}, author = {Mehta, RS and Petit, RA and Read, TD and Weissman, DB}, title = {Detecting patterns of accessory genome coevolution in Staphylococcus aureus using data from thousands of genomes.}, journal = {BMC bioinformatics}, volume = {24}, number = {1}, pages = {243}, pmid = {37296404}, issn = {1471-2105}, support = {R01 AI139188/AI/NIAID NIH HHS/United States ; 214626/WT_/Wellcome Trust/United Kingdom ; AI139188/NH/NIH HHS/United States ; }, mesh = {Humans ; *Staphylococcus aureus/genetics ; Genome, Bacterial ; Virulence/genetics ; *Staphylococcal Infections/genetics/microbiology ; Anti-Bacterial Agents ; }, abstract = {Bacterial genomes exhibit widespread horizontal gene transfer, resulting in highly variable genome content that complicates the inference of genetic interactions. In this study, we develop a method for detecting coevolving genes from large datasets of bacterial genomes based on pairwise comparisons of closely related individuals, analogous to a pedigree study in eukaryotic populations. We apply our method to pairs of genes from the Staphylococcus aureus accessory genome of over 75,000 annotated gene families using a database of over 40,000 whole genomes. We find many pairs of genes that appear to be gained or lost in a coordinated manner, as well as pairs where the gain of one gene is associated with the loss of the other. These pairs form networks of rapidly coevolving genes, primarily consisting of genes involved in virulence, mechanisms of horizontal gene transfer, and antibiotic resistance, particularly the SCCmec complex. While we focus on gene gain and loss, our method can also detect genes that tend to acquire substitutions in tandem, or genotype-phenotype or phenotype-phenotype coevolution. Finally, we present the R package DeCoTUR that allows for the computation of our method.}, }
@article {pmid37294009, year = {2023}, author = {Manoharan-Basil, SS and Gestels, Z and Abdellati, S and Akomoneh, EA and Kenyon, C}, title = {Evidence of horizontal gene transfer within porB in 19 018 whole-genome Neisseria spp. isolates: a global phylogenetic analysis.}, journal = {Microbial genomics}, volume = {9}, number = {6}, pages = {}, pmid = {37294009}, issn = {2057-5858}, mesh = {Humans ; *Neisseria ; Phylogeny ; Gene Transfer, Horizontal ; *Gonorrhea ; Neisseria gonorrhoeae/genetics ; }, abstract = {The PorB porins are the major pore-forming proteins in the genus Neisseria . The trimeric PorB porins consist of 16 highly conserved transmembrane domains that form an amphipathic β-sheet connected by short periplasmic turns and eight extracellular hydrophilic loops. These loops are immunogenic and also play an important role in mediating antimicrobial influx. This study sought to (i) characterize the variations in Neisserial loop 3(355–438 bp) associated with intermediate resistance to penicillin/tetracycline and (ii) evaluate if there was evidence of horizontal gene transfer in any of the loops. We collated an integrated database consisting of 19 018 Neisseria spp. genomes – 17 882 Neisseria gonorrhoeae , 114 Neisseria meningitidis and 1022 commensal Neisseria spp. To identify the porB alleles, a gene-by-gene approach (chewBBACA) was employed. To evaluate the presence of recombination events, the Recombination Detection Programme (RDP4) was used. In total, 3885 porB alleles were detected. Paralogues were identified in 17 Neisseria isolates. Putative recombination was identified in loop regions. Intraspecies recombination among N. gonorrhoeae isolates and interspecies recombination between N. meningitidis and commensal Neisseria spp., and N. gonorrhoeae and N. lactamica were identified. Here, we present a large-scale study of 19 018 Neisseria isolates to describe recombination and variation in the porB gene. Importantly, we found putative recombination in loop regions between the pathogenic and non-pathogenic Neisseria spp. These findings suggest the need for pheno- and genotypic surveillance of antimicrobial susceptibility in commensal Neisseria spp. to prevent the emergence of AMR in the pathogenic Neisseria . This article contains data hosted by Microreact.}, }
@article {pmid37289828, year = {2023}, author = {Walsh, SK and Imrie, RM and Matuszewska, M and Paterson, GK and Weinert, LA and Hadfield, JD and Buckling, A and Longdon, B}, title = {The host phylogeny determines viral infectivity and replication across Staphylococcus host species.}, journal = {PLoS pathogens}, volume = {19}, number = {6}, pages = {e1011433}, pmid = {37289828}, issn = {1553-7374}, support = {BB/M009122/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /MRC_/Medical Research Council/United Kingdom ; 109385/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Bacteriophages/physiology ; Host Specificity ; Phylogeny ; Polymerase Chain Reaction ; *Staphylococcaceae/classification/virology ; Staphylococcus aureus/virology ; *Staphylococcus Phages/physiology ; Viral Plaque Assay ; Virus Replication ; }, abstract = {Virus host shifts, where a virus transmits to and infects a novel host species, are a major source of emerging infectious disease. Genetic similarity between eukaryotic host species has been shown to be an important determinant of the outcome of virus host shifts, but it is unclear if this is the case for prokaryotes where anti-virus defences can be transmitted by horizontal gene transfer and evolve rapidly. Here, we measure the susceptibility of 64 strains of Staphylococcaceae bacteria (48 strains of Staphylococcus aureus and 16 non-S. aureus species spanning 2 genera) to the bacteriophage ISP, which is currently under investigation for use in phage therapy. Using three methods-plaque assays, optical density (OD) assays, and quantitative (q)PCR-we find that the host phylogeny explains a large proportion of the variation in susceptibility to ISP across the host panel. These patterns were consistent in models of only S. aureus strains and models with a single representative from each Staphylococcaceae species, suggesting that these phylogenetic effects are conserved both within and among host species. We find positive correlations between susceptibility assessed using OD and qPCR and variable correlations between plaque assays and either OD or qPCR, suggesting that plaque assays alone may be inadequate to assess host range. Furthermore, we demonstrate that the phylogenetic relationships between bacterial hosts can generally be used to predict the susceptibility of bacterial strains to phage infection when the susceptibility of closely related hosts is known, although this approach produced large prediction errors in multiple strains where phylogeny was uninformative. Together, our results demonstrate the ability of bacterial host evolutionary relatedness to explain differences in susceptibility to phage infection, with implications for the development of ISP both as a phage therapy treatment and as an experimental system for the study of virus host shifts.}, }
@article {pmid37286020, year = {2023}, author = {Lapadula, WJ and Juri Ayub, M}, title = {Ribosome inactivating proteins in insects: HGT, gene expression, and functional implications.}, journal = {Gene}, volume = {877}, number = {}, pages = {147547}, doi = {10.1016/j.gene.2023.147547}, pmid = {37286020}, issn = {1879-0038}, mesh = {Animals ; Ribosome Inactivating Proteins/genetics/metabolism ; Gene Transfer, Horizontal ; Insecta/genetics ; Protein Biosynthesis ; RNA, Ribosomal ; *Ricin/chemistry/genetics/metabolism ; *Hemiptera/genetics/metabolism ; Plant Proteins/genetics ; }, abstract = {Ribosome-inactivating proteins (RIPs) are RNA N-glycosidases that depurinate an adenine residue in the conserved alpha-sarcin/ricin loop (SRL) of rRNA, inhibiting protein synthesis. Previously, we reported the existence of these toxins in insects, whose presence is restricted to mosquitoes from the Culicinae subfamily (e.g., Aedes aegypti) and whiteflies from the Aleyrodidae family (e.g., Bemisia tabaci). Both groups of genes are derived from two independent horizontal gene transfer (HGT) events and are evolving under purifying selection. Here, we report and characterize the occurrence of a third HGT event in the Sciaroidea superfamily, which supports the recurrent acquisition of RIP genes by insects. Transcriptomic experiments, available in databases, allowed us to describe the temporal and spatial expression profiles for these foreign genes in these organisms. Furthermore, we found that RIP expression is induced after infection with pathogens and provided, for the first time, transcriptomic evidence of parasite SRL depurination. This evidence suggests a possible role of these foreign genes as immune effectors in insects.}, }
@article {pmid37283901, year = {2023}, author = {Abubaker, KT and Anwar, KA}, title = {Antimicrobial susceptibility and integrons detection among extended-spectrum β-lactamase producing Enterobacteriaceae isolates in patients with urinary tract infection.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15429}, pmid = {37283901}, issn = {2167-8359}, mesh = {Humans ; Escherichia coli/genetics ; Integrons/genetics ; Cross-Sectional Studies ; beta-Lactamases/genetics ; Enterobacteriaceae/genetics ; Anti-Bacterial Agents/pharmacology ; *Urinary Tract Infections/drug therapy ; *Anti-Infective Agents ; }, abstract = {BACKGROUND: Integrons are bacterial mobile genetic components responsible for mediating the antibiotic resistance process by carrying and spreading antimicrobial resistance genes among bacteria through horizontal gene transfer.<br><br>OBJECTIVES: This cross-sectional hospital-based study aimed to find the prevalence of antibiotic resistance patterns and to detect integrons classes (I, II, and III) among bacterial isolates in patients with urinary tract infections (UTI) in Sulaimani, Iraq.<br><br>PATIENTS AND METHODS: Mid-stream urine samples (no. = 400) were collected from patients with UTI at three different Hospitals from Sulaimani, Iraq, between September 2021 to January 2022. Urine samples were cultured on various agar media, and grown bacteria were isolated. Antibiotic susceptibility test (AST) and an extended-spectrum &#x3b2;-lactamase (ESBL) screen were done for isolated bacteria. Then, integrons classes were screened using conventional PCR with gene sequencing and uploaded to the National Center for Biotechnology Information (NCBI).<br><br>RESULTS: The frequency rate of Enterobacteriaceae was 67.03% among positive urine cultures. E. coli (no. = 86) and Klebsiella pneumoniae (no. = 32) isolates were identified. The most sensitive antibiotics were the carbapenem group (85.3%) and nitrofurantoin (NFN) (64.2%), while the most resistant antibiotics were nalidixic acid (NA) and 3[rd] generation cephalosporin. The occurrence rate of ESBL was 56.6% with a predominance of class I integron (54.2%), then class II (15.8%) and no positive record for class III integron were observed.<br><br>CONCLUSION: Most bacterial isolates from patients with UTI produced class I and II integrons genes with favourable ESBL properties.}, }
@article {pmid37283060, year = {2023}, author = {Yang, L and Mai, G and Hu, Z and Zhou, H and Dai, L and Deng, Z and Ma, Y}, title = {Global transmission of broad-host-range plasmids derived from the human gut microbiome.}, journal = {Nucleic acids research}, volume = {51}, number = {15}, pages = {8005-8019}, pmid = {37283060}, issn = {1362-4962}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; Host Specificity ; Plasmids/genetics ; Bacteria/genetics ; Gene Transfer, Horizontal/genetics ; }, abstract = {Broad-host-range (BHR) plasmids in human gut bacteria are of considerable interest for their ability to mediate horizontal gene transfer (HGT) across large phylogenetic distance. However, the human gut plasmids, especially the BHR plasmids, remain largely unknown. Here, we identified the plasmids in the draft genomes of gut bacterial isolates from Chinese and American donors, resulting in 5372 plasmid-like clusters (PLCs), of which, 820 PLCs (comPLCs) were estimated with > 60% completeness genomes and only 155 (18.9%) were classified to known replicon types (n = 37). We observed that 175 comPLCs had a broad host range across distinct bacterial genera, of which, 71 were detected in at least two human populations of Chinese, American, Spanish, and Danish, and 13 were highly prevalent (>10%) in at least one human population. Haplotype analyses of two widespread PLCs demonstrated their spreading and evolutionary trajectory, suggesting frequent and recent exchanges of the BHR plasmids in environments. In conclusion, we obtained a large collection of plasmid sequences in human gut bacteria and demonstrated that a subset of the BHR plasmids can be transmitted globally, thus facilitating extensive HGT (e.g. antibiotic resistance genes) events. This study highlights the potential implications of the plasmids for global human health.}, }
@article {pmid37280593, year = {2023}, author = {Guo, X and Hu, X and Li, J and Shao, B and Wang, Y and Wang, L and Li, K and Lin, D and Wang, H and Gao, Z and Jiao, Y and Wen, Y and Ji, H and Ma, C and Ge, S and Jiang, W and Jin, X}, title = {The Sapria himalayana genome provides new insights into the lifestyle of endoparasitic plants.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {134}, pmid = {37280593}, issn = {1741-7007}, mesh = {*Genome, Mitochondrial ; Gene Transfer, Horizontal ; Plants/genetics ; Flowers/genetics ; Phylogeny ; }, abstract = {BACKGROUND: Sapria himalayana (Rafflesiaceae) is an endoparasitic plant characterized by a greatly reduced vegetative body and giant flowers; however, the mechanisms underlying its special lifestyle and greatly altered plant form remain unknown. To illustrate the evolution and adaptation of S. himalayasna, we report its de novo assembled genome and key insights into the molecular basis of its floral development, flowering time, fatty acid biosynthesis, and defense responses.<br><br>RESULTS: The genome of S. himalayana is&#x2009;~&#x2009;1.92&#xa0;Gb with 13,670 protein-coding genes, indicating remarkable gene loss (~&#x2009;54%), especially genes involved in photosynthesis, plant body, nutrients, and defense response. Genes specifying floral organ identity and controlling organ size were identified in S. himalayana and Rafflesia cantleyi, and showed analogous spatiotemporal expression patterns in both plant species. Although the plastid genome had been lost, plastids likely biosynthesize essential fatty acids and amino acids (aromatic amino acids and lysine). A set of credible and functional horizontal gene transfer (HGT) events (involving genes and mRNAs) were identified in the nuclear and mitochondrial genomes of S. himalayana, most of which were under purifying selection. Convergent HGTs in Cuscuta, Orobanchaceae, and S. himalayana were mainly expressed at the parasite-host interface. Together, these results suggest that HGTs act as a bridge between the parasite and host, assisting the parasite in acquiring nutrients from the host.<br><br>CONCLUSIONS: Our results provide new insights into the flower development process and endoparasitic lifestyle of Rafflesiaceae plants. The amount of gene loss in S. himalayana is consistent with the degree of reduction in its body plan. HGT events are common among endoparasites and play an important role in their lifestyle adaptation.}, }
@article {pmid37279941, year = {2023}, author = {Sheikh, S and Pánek, T and Gahura, O and Týč, J and Záhonová, K and Lukeš, J and Eliáš, M and Hashimi, H}, title = {A Novel Group of Dynamin-Related Proteins Shared by Eukaryotes and Giant Viruses Is Able to Remodel Mitochondria From Within the Matrix.}, journal = {Molecular biology and evolution}, volume = {40}, number = {6}, pages = {}, pmid = {37279941}, issn = {1537-1719}, mesh = {*Giant Viruses/genetics/metabolism ; Phylogeny ; Mitochondrial Proteins/genetics/metabolism ; Mitochondria/genetics/metabolism ; Dynamins/genetics/metabolism ; Saccharomyces cerevisiae/genetics ; }, abstract = {The diverse GTPases of the dynamin superfamily play various roles in the cell, as exemplified by the dynamin-related proteins (DRPs) Mgm1 and Opa1, which remodel the mitochondrial inner membrane in fungi and metazoans, respectively. Via an exhaustive search of genomic and metagenomic databases, we found previously unknown DRP types occurring in diverse eukaryotes and giant viruses (phylum Nucleocytoviricota). One novel DRP clade, termed MidX, combined hitherto uncharacterized proteins from giant viruses and six distantly related eukaryote taxa (Stramenopiles, Telonemia, Picozoa, Amoebozoa, Apusomonadida, and Choanoflagellata). MidX stood out because it was not only predicted to be mitochondria-targeted but also to assume a tertiary structure not observed in other DRPs before. To understand how MidX affects mitochondria, we exogenously expressed MidX from Hyperionvirus in the kinetoplastid Trypanosoma brucei, which lacks Mgm1 or Opa1 orthologs. MidX massively affected mitochondrial morphology from inside the matrix, where it closely associates with the inner membrane. This unprecedented mode of action contrasts to those of Mgm1 and Opa1, which mediate inner membrane remodeling in the intermembrane space. We speculate that MidX was acquired in Nucleocytoviricota evolution by horizontal gene transfer from eukaryotes and is used by giant viruses to remodel host mitochondria during infection. MidX's unique structure may be an adaptation for reshaping mitochondria from the inside. Finally, Mgm1 forms a sister group to MidX and not Opa1 in our phylogenetic analysis, throwing into question the long-presumed homology of these DRPs with similar roles in sister lineages.}, }
@article {pmid37279818, year = {2023}, author = {Wang, X and Zhang, L and Gu, J and Feng, Y and He, K and Jiang, H}, title = {Effects of soil solarization combined with manure-amended on soil ARGs and microbial communities during summer fallow.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {333}, number = {}, pages = {121950}, doi = {10.1016/j.envpol.2023.121950}, pmid = {37279818}, issn = {1873-6424}, mesh = {*Anti-Bacterial Agents/analysis ; Manure/analysis ; Genes, Bacterial ; Soil ; Drug Resistance, Microbial/genetics ; *Microbiota ; Soil Microbiology ; }, abstract = {Soil solarization (SS) is a technique for managing pathogens and weeds, which involves covering with transparent plastic to increase soil temperature during summer fallow (SF). However, SS also alters the diversity of bacterial communities. Therefore, during SF, various organic modifiers are used in combination with SS to improve its efficacy. Organic amendments may contain antibiotic resistance genes (ARGs). Greenhouse vegetable production (GVP) soils are vital to ensure food security and ecological balance. However, comprehensive study on the effects of SS combined with different types of manure on ARGs in GVP soils during SF remains unclear. Therefore, this study employed high-throughput qPCR to explore the effects of different organic amendments combined with SS on the abundance changes of ARGs and mobile genetic elements (MGEs) in GVP soils during SF. The abundance and diversity of ARGs and MGEs in GVP soils with different manure fertilization and SS decreased during SF. Horizontal gene transfer via MGEs (especially integrases 45.80%) induced by changes in environmental factors (NO3[-]-N 14.7% and NH4[+]-N) was the main factor responsible for the changes in ARGs. Proteobacteria (14.3%) and Firmicutes were the main potential hosts of ARGs. Network analysis suggested that Ornithinimicrobium, Idiomarina and Corynebacterium had positive correlations with aminoglycosides, MLSB, and tetracycline resistance genes. These results provide new insights to understand the fate of ARGs in the GVP soils by manure-amended combined with SS during SF, which may help to reduce the spread of ARGs.}, }
@article {pmid37278656, year = {2023}, author = {Huo, W and Price, VJ and Sharifi, A and Zhang, MQ and Palmer, KL}, title = {Enterococcus faecalis Strains with Compromised CRISPR-Cas Defense Emerge under Antibiotic Selection for a CRISPR-Targeted Plasmid.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {6}, pages = {e0012423}, pmid = {37278656}, issn = {1098-5336}, support = {R01 AI116610/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *CRISPR-Cas Systems ; *Anti-Bacterial Agents/pharmacology ; Enterococcus faecalis/genetics ; Plasmids/genetics ; Gastrointestinal Tract ; }, abstract = {Enterococcus faecalis is a Gram-positive bacterium that natively colonizes the human gastrointestinal tract and opportunistically causes life-threatening infections. Multidrug-resistant (MDR) E. faecalis strains have emerged that are replete with mobile genetic elements (MGEs). Non-MDR E. faecalis strains frequently possess CRISPR-Cas systems, which reduce the frequency of MGE acquisition. We demonstrated in previous studies that E. faecalis populations can transiently maintain both a functional CRISPR-Cas system and a CRISPR-Cas target. In this study, we used serial passage and deep sequencing to analyze these populations. In the presence of antibiotic selection for the plasmid, mutants with compromised CRISPR-Cas defense and enhanced ability to acquire a second antibiotic resistance plasmid emerged. Conversely, in the absence of selection, the plasmid was lost from wild-type E. faecalis populations but not E. faecalis populations that lacked the cas9 gene. Our results indicate that E. faecalis CRISPR-Cas can become compromised under antibiotic selection, generating populations with enhanced abilities to undergo horizontal gene transfer. IMPORTANCE Enterococcus faecalis is a leading cause of hospital-acquired infections and disseminator of antibiotic resistance plasmids among Gram-positive bacteria. We have previously shown that E. faecalis strains with an active CRISPR-Cas system can prevent plasmid acquisition and thus limit the transmission of antibiotic resistance determinants. However, CRISPR-Cas is not a perfect barrier. In this study, we observed populations of E. faecalis with transient coexistence of CRISPR-Cas and one of its plasmid targets. Our experimental data demonstrate that antibiotic selection results in compromised E. faecalis CRISPR-Cas function, thereby facilitating the acquisition of additional resistance plasmids by E. faecalis.}, }
@article {pmid37278068, year = {2023}, author = {Guinet, B and Lepetit, D and Charlat, S and Buhl, PN and Notton, DG and Cruaud, A and Rasplus, JY and Stigenberg, J and de Vienne, DM and Boussau, B and Varaldi, J}, title = {Endoparasitoid lifestyle promotes endogenization and domestication of dsDNA viruses.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {37278068}, issn = {2050-084X}, mesh = {Animals ; Female ; Biological Evolution ; DNA ; Domestication ; Genome, Viral ; *Viruses/genetics ; *Wasps/genetics ; }, abstract = {The accidental endogenization of viral elements within eukaryotic genomes can occasionally provide significant evolutionary benefits, giving rise to their long-term retention, that is, to viral domestication. For instance, in some endoparasitoid wasps (whose immature stages develop inside their hosts), the membrane-fusion property of double-stranded DNA viruses have been repeatedly domesticated following ancestral endogenizations. The endogenized genes provide female wasps with a delivery tool to inject virulence factors that are essential to the developmental success of their offspring. Because all known cases of viral domestication involve endoparasitic wasps, we hypothesized that this lifestyle, relying on a close interaction between individuals, may have promoted the endogenization and domestication of viruses. By analyzing the composition of 124 Hymenoptera genomes, spread over the diversity of this clade and including free-living, ecto, and endoparasitoid species, we tested this hypothesis. Our analysis first revealed that double-stranded DNA viruses, in comparison with other viral genomic structures (ssDNA, dsRNA, ssRNA), are more often endogenized and domesticated (that is, retained by selection) than expected from their estimated abundance in insect viral communities. Second, our analysis indicates that the rate at which dsDNA viruses are endogenized is higher in endoparasitoids than in ectoparasitoids or free-living hymenopterans, which also translates into more frequent events of domestication. Hence, these results are consistent with the hypothesis that the endoparasitoid lifestyle has facilitated the endogenization of dsDNA viruses, in turn, increasing the opportunities of domestications that now play a central role in the biology of many endoparasitoid lineages.}, }
@article {pmid37272817, year = {2023}, author = {Castellanos, A and Restrepo, L and Bajaña, L and Betancourt, I and Bayot, B and Reyes, A}, title = {Genomic and Evolutionary Features of Nine AHPND Positive Vibrio parahaemolyticus Strains Isolated from South American Shrimp Farms.}, journal = {Microbiology spectrum}, volume = {11}, number = {4}, pages = {e0485122}, pmid = {37272817}, issn = {2165-0497}, mesh = {Humans ; *Vibrio parahaemolyticus/genetics ; Plasmids/genetics ; *Toxins, Biological ; Genomics ; Aquaculture ; Necrosis ; }, abstract = {Vibrio parahaemolyticus is a bacterial pathogen that becomes lethal to Penaeus shrimps when acquiring the pVA1-type plasmid carrying the PirAB[vp] genes, causing acute hepatopancreatic necrosis disease (AHPND). This disease causes significant losses across the world, with outbreaks reported in Southeast Asia, Mexico, and South America. Virulence level and mortality differences have been reported in isolates from different locations, and whether this phenomenon is caused by plasmid-related elements or genomic-related elements from the bacteria remains unclear. Here, nine genomes of South American AHPND-causing V. parahaemolyticus (VPAHPND) isolates were assembled and analyzed using a comparative genomics approach at (i) whole-genome, (ii) secretion system, and (iii) plasmid level, and then included for a phylogenomic analysis with another 86 strains. Two main results were obtained from our analyses. First, all isolates contained pVA1-type plasmids harboring the toxin coding genes, and with high similarity with the prototypical sequence of Mexican-like origin, while phylogenomic analysis showed some level of heterogeneity with discrete clusters and wide diversity compared to other available genomes. Second, although a high genomic similarity was observed, variation in virulence genes and clusters was observed, which might be relevant in the expression of the disease. Overall, our results suggest that South American pathogenic isolates are derived from various genetic lineages which appear to have acquired the plasmid through horizontal gene transfer. Furthermore, pathogenicity seems to be a multifactorial trait where the degree of virulence could be altered by the presence or variations of several virulence factors. IMPORTANCE AHPND have caused losses of over $2.6 billion to the aquaculture industry around the world due to its high mortality rate in shrimp farming. The most common etiological agent is V. parahaemolyticus strains possessing the pVA1-type plasmid carrying the PirAB[vp] toxin. Nevertheless, complete understanding of the role of genetic elements and their impact in the virulence of this pathogen remains unclear. In this work, we analyzed nine South American AHPND-causing V. parahaemolyticus isolates at a genomic level, and assessed their evolutionary relationship with other 86 strains. We found that all our isolates were highly similar and possessed the Mexican-type plasmid, but their genomic content did not cluster with other Mexican strains, but instead were spread across all isolates. These results suggest that South American VPAHPND have different genetic backgrounds, and probably proceed from diverse geographical locations, and acquire the pVA1-type plasmid via horizontal gene transfer at different times.}, }
@article {pmid37271423, year = {2023}, author = {Feyereisen, R and Urban, JM and Nelson, DR}, title = {Aliens in the CYPome of the black fungus gnat, Bradysia coprophila.}, journal = {Insect biochemistry and molecular biology}, volume = {159}, number = {}, pages = {103965}, doi = {10.1016/j.ibmb.2023.103965}, pmid = {37271423}, issn = {1879-0240}, mesh = {Animals ; *Diptera/genetics ; Insecta ; *Insecticides ; Genome ; Fungi ; }, abstract = {The diverse cytochrome P450 enzymes of insects play essential physiological roles and also play important roles in the metabolism of environmental chemicals such as insecticides. We manually curated the complement of P450 (CYP) genes, or CYPome, of the black fungus gnat, Bradysia (Sciara) coprophila (Diptera, Sciaroidea), a species with a variable number of chromosomes. This CYPome carries two types of "alien" P450 genes. The first type of alien P450s was found among the 163 CYP genes of the core genome (autosomes and X). They consist of 28 sequences resulting from horizontal gene transfer, with closest sequences not found in insects, but in other arthropods, often Collembola. These genes are not contaminants, because they are expressed genes with introns, found in synteny with regular dipteran genes, also found in B. odoriphaga and B. hygida. Two such "alien" genes are representatives of CYP clans not otherwise found in insects, a CYP53 sequence related to fungal CYP53 genes, and a CYP19-like sequence similar to some collembolan sequences but of unclear origin. The second type of alien P450s are represented by 99 sequences from germline-restricted chromosomes (GRC). While most are P450 pseudogenes, 33 are apparently intact, with half being more closely related to P450s from Cecidomyiidae than from Sciaridae, thus supporting the hypothesis of a cross-family hybridization origin of the GRC.}, }
@article {pmid37270585, year = {2023}, author = {Liu, S and Zeng, J and Yu, H and Wang, C and Yang, Y and Wang, J and He, Z and Yan, Q}, title = {Antimony efflux underpins phosphorus cycling and resistance of phosphate-solubilizing bacteria in mining soils.}, journal = {The ISME journal}, volume = {17}, number = {8}, pages = {1278-1289}, pmid = {37270585}, issn = {1751-7370}, mesh = {Antimony/analysis/chemistry ; Soil/chemistry ; Phosphates/analysis ; Phosphorus/analysis ; Phylogeny ; Environmental Monitoring ; *Soil Pollutants/analysis ; *Metals, Heavy/analysis ; Bacteria/genetics ; *Microbiota ; China ; Soil Microbiology ; }, abstract = {Microorganisms play crucial roles in phosphorus (P) turnover and P bioavailability increases in heavy metal-contaminated soils. However, microbially driven P-cycling processes and mechanisms of their resistance to heavy metal contaminants remain poorly understood. Here, we examined the possible survival strategies of P-cycling microorganisms in horizontal and vertical soil samples from the world's largest antimony (Sb) mining site, which is located in Xikuangshan, China. We found that total soil Sb and pH were the primary factors affecting bacterial community diversity, structure and P-cycling traits. Bacteria with the gcd gene, encoding an enzyme responsible for gluconic acid production, largely correlated with inorganic phosphate (Pi) solubilization and significantly enhanced soil P bioavailability. Among the 106 nearly complete bacterial metagenome-assembled genomes (MAGs) recovered, 60.4% carried the gcd gene. Pi transportation systems encoded by pit or pstSCAB were widely present in gcd-harboring bacteria, and 43.8% of the gcd-harboring bacteria also carried the acr3 gene encoding an Sb efflux pump. Phylogenetic and potential horizontal gene transfer (HGT) analyses of acr3 indicated that Sb efflux could be a dominant resistance mechanism, and two gcd-harboring MAGs appeared to acquire acr3 through HGT. The results indicated that Sb efflux could enhance P cycling and heavy metal resistance in Pi-solubilizing bacteria in mining soils. This study provides novel strategies for managing and remediating heavy metal-contaminated ecosystems.}, }
@article {pmid37270161, year = {2023}, author = {Sharma, HK and Gupta, P and Nagpal, D and Mukherjee, M and Parmar, VS and Lather, V}, title = {Virtual screening and antimicrobial evaluation for identification of natural compounds as the prospective inhibitors of antibacterial drug resistance targets in Staphylococcus aureus.}, journal = {Fitoterapia}, volume = {168}, number = {}, pages = {105554}, doi = {10.1016/j.fitote.2023.105554}, pmid = {37270161}, issn = {1873-6971}, mesh = {Staphylococcus aureus ; *Methicillin-Resistant Staphylococcus aureus ; Thymol ; Eugenol/metabolism ; *Curcumin/metabolism ; Quercetin/pharmacology/metabolism ; *Berberine/metabolism ; Molecular Structure ; Anti-Bacterial Agents/pharmacology/chemistry ; Drug Resistance, Bacterial ; Microbial Sensitivity Tests ; }, abstract = {Infectious diseases have remained a burgeoning cause of death and disability since long. Staphylococcus aureus (S. aureus) is a severe bacterial pathogen causing nosocomial and community infections. It exhibits widespread resistance to antibiotics posing a significant threat to their efficacy. For combating this challenge, different strategies may include modifying existing antibiotics, developing new antibacterial agents, and combining treatments with resistance mechanism inhibitors. Resistance in S. aureus occurs through horizontal gene transfer or chromosomal mutations. Acquisition mechanisms involve enzymatic modification, efflux, target bypass, and drug displacement. Mutations can impact drug targets, activate efflux pumps, or alter cell wall composition to impede drug access. Overcoming S. aureus resistance requires innovative approaches to preserve antibiotic effectiveness. The present study involves the virtual screening of phytochemicals of diverse chemical classes from Zinc database against the antibiotic resistant targets of S. aureus like β-Lactamase, Penicillin Binding Protein 2a (PBP2a), Dihydrofolate reductase (DHFR), DNA gyrase, Multidrug ABC transporter SAV1866, Undecaprenyl diphosphate synthase (UPPS), etc. Thymol, eugenol, gallic acid, l-ascorbic acid, curcumin, berberine and quercetin were identified as potential molecules based on their docking score, binding interactions. These molecules were further analyzed for the ADMET and drug likeness properties using pkCSM, SwissADME and Qikprop tools. Further in vitro evaluation of these molecules against antibiotic-resistant strains of S. aureus, both alone and in combination with antibiotics revealed significant findings. Curcumin demonstrated the lowest MIC values (31.25-62.5 μg/ml) when tested individually. Thymol, berberine, and quercetin displayed MIC values within the range of 125-250 μg/ml, while eugenol and gallic acid exhibited MIC values ranging from 500 to 1000 μg/ml. Notably, thymol exhibited potent synergy with all four antibiotics against clinical isolates of S. aureus, with Fractional inhibitory concentration index (FICI) values consistently below 0.5, highlighting its exceptional antibacterial activity, especially in combination with amoxicillin.}, }
@article {pmid37270129, year = {2023}, author = {Xu, Y and Liu, Q and Meng, G and Dong, C}, title = {Horizontal gene transfer of Cccyt contributes to virulence of mycoparasite Calcarisporium cordycipiticola by interacting with a host heat shock protein.}, journal = {International journal of biological macromolecules}, volume = {242}, number = {Pt 4}, pages = {124927}, doi = {10.1016/j.ijbiomac.2023.124927}, pmid = {37270129}, issn = {1879-0003}, mesh = {Phylogeny ; Hypocreales ; Virulence/genetics ; *Gene Transfer, Horizontal ; *Heat-Shock Proteins/genetics ; }, abstract = {Horizontal gene transfer (HGT) is an important driving force for virulence evolution of pathogens, however, functions of these transferred genes are still not fully investigated. Here, an HGT effector, CcCYT was reported to contribute to virulence of a mycoparasite, Calcarisporium cordycipiticola to the host Cordyceps militaris, an important mushroom. Cccyt was predicted to be horizontally transferred from Actinobacteria ancestor by phylogenetic, synteny, GC content and codon usage pattern analyses. The transcript of Cccyt was sharply up-regulated at the early stage of infecting C. militaris. This effector was localized to the cell wall and contributed to the virulence of C. cordycipiticola without affecting its morphology, mycelial growth, conidiation, and resistance to abiotic stress. CcCYT can firstly bind the septa, and finally cytoplasm of the deformed hyphal cells of C. militaris. Pull-down assay coupled mass spectrometry revealed that proteins with which CcCYT interacted were related to protein process, folding and degradation. GST-Pull down assay confirmed that C. cordycipiticola effector CcCYT can interact with host protein CmHSP90 to inhibit the immune response of host. The results provided functional evidence that HGT is an important driving force for the virulence evolution and will be helpful for revealing the interaction between mycoparasite and mushroom host.}, }
@article {pmid37269713, year = {2023}, author = {Dai, X and Zhao, J and Sun, J and Chen, L and Han, P and Wang, X and Huang, J and Wang, L}, title = {ICESpsuAH0906, a novel optrA-carrying element conferring resistance to phenicols and oxazolidinones from Streptococcus parasuis, is transferable to Streptococcus suis.}, journal = {Veterinary microbiology}, volume = {283}, number = {}, pages = {109795}, doi = {10.1016/j.vetmic.2023.109795}, pmid = {37269713}, issn = {1873-2542}, mesh = {*Oxazolidinones ; Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents/pharmacology ; Animals ; *Streptococcus suis ; Streptococcus ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; }, abstract = {Streptococcus parasuis is a potential opportunistic zoonotic pathogen which is a close relative to Streptococcus suis, which exhibit extensive genetic exchange. The occurrence and dissemination of oxazolidinone resistance poses a severe threat to public health. However, such knowledge about the optrA gene in S. parasuis is limited. Herein, we characterized an optrA-positive multi-resistant S. parasuis isolate AH0906, in which the capsular polysaccharide locus exhibited a hybrid structure of S. suis serotype 11 and S. parasuis serotype 26. The optrA and erm(B) genes were co-located on a novel ICE of the ICESsuYZDH1 family, designated ICESpsuAH0906. IS1216E-optrA-carrying translocatable unit could be formed when excised from ICESpsuAH0906. ICESpsuAH0906 was found to be transferable from isolate AH0906 to Streptococcus suis P1/7RF at a relative high frequency of ∼ 10[-5]. Nonconservative integrations of ICESpsuAH0906 into the primary site SSU0877 and secondary site SSU1797 with 2-/4-nt imperfect direct repeats in recipient P1/7RF were observed. Upon transfer, the transconjugant displayed elevated MICs of the corresponding antimicrobial agents and performed a weak fitness cost when compared with the recipient strain. To our knowledge, it is the first description of the transfer of optrA in S. prarasuis and the first report of interspecies transfer of ICE with triplet serine integrases (of the ICESsuYZDH1 family). Considering the high transmission frequency of the ICEs and the extensive genetic exchange potential of S. parasuis with other streptococci, attention should be paid to the dissemination of the optrA gene from S. parasuis to clinically more important bacterial pathogens.}, }
@article {pmid37268165, year = {2024}, author = {Kameswaran, S and Gujjala, S and Zhang, S and Kondeti, S and Mahalingam, S and Bangeppagari, M and Bellemkonda, R}, title = {Quenching and quorum sensing in bacterial bio-films.}, journal = {Research in microbiology}, volume = {175}, number = {3}, pages = {104085}, doi = {10.1016/j.resmic.2023.104085}, pmid = {37268165}, issn = {1769-7123}, mesh = {*Quorum Sensing/genetics ; *Bacteria/genetics ; Biofilms ; Lactones ; }, abstract = {Quorum sensing (QS) is the ability of bacteria to monitor their population density and adjust gene expression accordingly. QS-regulated processes include host-microbe interactions, horizontal gene transfer, and multicellular behaviours (such as the growth and development of biofilm). The creation, transfer, and perception of bacterial chemicals known as autoinducers or QS signals are necessary for QS signalling (e.g. N-acylhomoserine lactones). Quorum quenching (QQ), another name for the disruption of QS signalling, comprises a wide range of events and mechanisms that are described and analysed in this study. In order to better comprehend the targets of the QQ phenomena that organisms have naturally developed and are currently being actively researched from practical perspectives, we first surveyed the diversity of QS-signals and QS-associated responses. Next, the mechanisms, molecular players, and targets related to QS interference are discussed, with a focus on natural QQ enzymes and compounds that function as QS inhibitors. To illustrate the processes and biological functions of QS inhibition in microbe-microbe and host-microbe interactions, a few QQ paradigms are described in detail. Finally, certain QQ techniques are offered as potential instruments in a variety of industries, including agriculture, medical, aquaculture, crop production, and anti-biofouling areas.}, }
@article {pmid37267763, year = {2023}, author = {Sun, S and Wang, Q and Wang, N and Yang, S and Qi, H}, title = {High-risk antibiotics positively correlated with antibiotic resistance genes in five typical urban wastewater.}, journal = {Journal of environmental management}, volume = {342}, number = {}, pages = {118296}, doi = {10.1016/j.jenvman.2023.118296}, pmid = {37267763}, issn = {1095-8630}, mesh = {Humans ; *Wastewater ; *Anti-Bacterial Agents/pharmacology/analysis ; Genes, Bacterial ; Ecosystem ; Drug Resistance, Microbial/genetics ; Pharmaceutical Preparations ; }, abstract = {Antibiotic resistance genes (ARGs) and antibiotic amount increased within close proximity to human dominated ecosystems. However, few studies assessed the distribution of antibiotics and ARGs in multiple ecosystems especially the different urban wastewater. In this study, the spatial distribution of ARGs and antibiotics across the urban wastewater included domestic, livestock, hospital, pharmaceutical wastewater, influent of the wastewater treatment plant (WWTP) in Northeast China. The q-PCR results showed that ARGs were most abundant in community wastewater and followed by WWTP influent, livestock wastewater, pharmaceutical wastewater and hospital wastewater. The ARG composition differed among the five ecotypes with qnrS was the dominant ARG subtypes in WWTP influent and community wastewater, while sul2 dominant in livestock, hospital, pharmaceutical wastewater. The concentration of antibiotics was closely related to the antibiotic usage and consumption data. In addition to the high concentration of azithromycin at all sampling points, more than half of the antibiotics in livestock wastewater were veterinary antibiotics. However, antibiotics that closely related to humankind such as roxithromycin and sulfamethoxazole accounted for a higher proportion in hospital wastewater (13.6%) and domestic sewage (33.6%), respectively. The ambiguous correlation between ARGs and their corresponding antibiotics was detected. However, antibiotics that exhibited high ecotoxic effects were closely and positively correlated with ARGs and the class 1 integrons (intI1), which indicated that high ecotoxic compounds might affect antimicrobial resistance of bacteria by mediating horizontal gene transfer of ARGs. The coupling mechanism between the ecological risk of antibiotics and bacterial resistance needed to be further studied, and thereby provided a new insight to study the impact of environmental pollutants on ARGs in various ecotypes.}, }
@article {pmid37267681, year = {2023}, author = {Carlsen, L and Büttner, H and Christner, M and Cordts, L and Franke, G and Hoffmann, A and Knobling, B and Lütgehetmann, M and Nakel, J and Werner, T and Knobloch, JK}, title = {Long time persistence and evolution of carbapenemase-producing Enterobacterales in the wastewater of a tertiary care hospital in Germany.}, journal = {Journal of infection and public health}, volume = {16}, number = {8}, pages = {1142-1148}, doi = {10.1016/j.jiph.2023.05.029}, pmid = {37267681}, issn = {1876-035X}, mesh = {Humans ; *Wastewater ; *Escherichia coli ; Tertiary Care Centers ; Bacterial Proteins/genetics ; beta-Lactamases/genetics ; Klebsiella pneumoniae/genetics ; Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; }, abstract = {BACKGROUND: Worldwide observations revealed increased frequencies of multi-resistant Enterobacterales and resistance genes in hospital wastewater compared to any other type of wastewater. Despite the description of clonal lineages possibly adapted to hospital wastewater, little is known about long term persistence as well as evolution of these lineages.<br><br>METHODS: In this study, wastewater isolates of different Enterobacterales species from a tertiary care hospital were investigated with 2.5 years distance. Whole Genome Sequencing (WGS) and resistance gene identification were performed for E. coli, C. freundii, S. marcescens, K. pneumoniae, K. oxytoca, and E. cloacae isolates (n&#xa0;=&#xa0;59), isolated in 2022 and compared with strains isolated from the same wastewater pipeline in 2019 (n&#xa0;=&#xa0;240).<br><br>RESULTS: Individual clonal lineages with highly related isolates could be identified in all species identified more than once in 2022 that appear to persist in the wastewater drainage. A common motif of all persistent clonal lineages was the carriage of mobile genetic elements encoding carbapenemase genes with hints for horizontal gene transfer in persistent clones in this environment observed over the 2.5-year period. Multiple plasmid replicons could be detected in both years. In 2022 isolates blaVIM-1 replaced blaOXA-48 as the most common carbapenemase gene compared to 2019. Interestingly, despite a similar abundance of carbapenemase genes (>80% of all isolates) at both time points genes encoding extended spectrum &#x3b2;-lactamases decreased over time.<br><br>CONCLUSIONS: This data indicates that hospital wastewater continuously releases genes encoding carbapenemases to the urban wastewater system. The evolution of the resident clones as well as the reasons for the selection advantage in this specific ecological niche needs to be further investigated in the future.}, }
@article {pmid37263036, year = {2023}, author = {Wu, C and Zhang, G and Zhang, K and Sun, J and Cui, Z and Guo, Y and Liu, H and Xu, W}, title = {Strong variation in sedimental antibiotic resistomes among urban rivers, estuaries and coastal oceans: Evidence from a river-connected coastal water ecosystem in northern China.}, journal = {Journal of environmental management}, volume = {342}, number = {}, pages = {118132}, doi = {10.1016/j.jenvman.2023.118132}, pmid = {37263036}, issn = {1095-8630}, mesh = {*Anti-Bacterial Agents/analysis ; *Estuaries ; Rivers/microbiology ; Genes, Bacterial ; Ecosystem ; Bacteria/genetics ; Oceans and Seas ; China ; Water ; }, abstract = {Sediment is thought to be a vital reservoir to spread antibiotic resistance genes (ARGs) among various natural environments. However, the spatial distribution patterns of the sedimental antibiotic resistomes around the Bohai Bay region, a river-connected coastal water ecosystem, are still poorly understood. The present study conducted a comprehensive investigation of ARGs among urban rivers (UR), estuaries (ES) and Bohai Bay (BHB) by metagenomic sequencing. Overall, a total of 169 unique ARGs conferring resistance to 15 antimicrobial classes were detected across all sediment samples. The Kruskal-Wallis test showed that the diversity and abundance of ARGs in the UR were all significantly higher than those in the ES and BHB (p < 0.05 and p < 0.01), revealing the distance dilution of the sedimental resistomes from the river to the ocean. Multidrug resistance genes contained most of the ARG subtypes, whereas rifamycin resistance genes were the most abundant ARGs in this region. Our study demonstrated that most antimicrobial resistomes were highly accumulated in urban river sediments, whereas beta-lactamase resistance genes (mainly PNGM-1) dramatically increased away from the estuary to the open ocean. The relative abundance of mobile genetic elements (MGEs) also gradually decreased from rivers to the coastal ocean, whereas the difference in pathogenic bacteria was not significant in the three classifications. Among MGEs, plasmids were recognized as the most important carriers to support the horizontal gene transfer of ARGs within and between species. According to co-occurrence networks, pathogenic Proteobacteria, Actinobacteria, and Bacteroidetes were recognized as potential and important hosts of ARGs. Heavy metals, pH and moisture content were all recognized as the vital environmental factors influencing the distribution of ARGs in sediment samples. Overall, the present study may help to understand the distribution patterns of ARGs at a watershed scale, and help to make effective policies to control the emergence, spread and evolution of different ARG subtypes in different habitats.}, }
@article {pmid37261234, year = {2023}, author = {Fatima, S and Ishaq, Z and Irfan, M and AlAsmari, AF and Achakzai, JK and Zaheer, T and Ali, A and Akbar, A}, title = {Whole-genome sequencing of multidrug resistance Salmonella Typhi clinical strains isolated from Balochistan, Pakistan.}, journal = {Frontiers in public health}, volume = {11}, number = {}, pages = {1151805}, pmid = {37261234}, issn = {2296-2565}, mesh = {Humans ; *Salmonella typhi/genetics ; Multilocus Sequence Typing ; Pakistan ; *Anti-Bacterial Agents/pharmacology ; Virulence Factors/genetics ; Whole Genome Sequencing ; Drug Resistance, Multiple ; }, abstract = {INTRODUCTION: Salmonella enterica serovar Typhi (S. Typhi) is a major cause of morbidity and mortality in developing countries, contributing significantly to the global disease burden.<br><br>METHODS: In this study, S. Typhi strains were isolated from 100 patients exhibiting symptoms of typhoid fever at a tertiary care hospital in Pakistan. Antimicrobial testing of all isolates was performed to determine the sensitivity and resistance pattern. Three MDR strains, namely QS194, QS430, and QS468, were subjected to whole genome sequencing for genomic characterization.<br><br>RESULTS AND DISCUSSION: MLST analysis showed that QS194, belonged to ST19, which is commonly associated with Salmonella enterica serovar typhimurium. In contrast, QS430 and QS468, belonged to ST1, a sequence type frequently associated with S. Typhi. PlasmidFinder identified the presence of IncFIB(S) and IncFII(S) plasmids in QS194, while IncQ1 was found in QS468. No plasmid was detected in QS430. CARD-based analysis showed that the strains were largely resistant to a variety of antibiotics and disinfecting agents/antiseptics, including fluoroquinolones, cephalosporins, monobactams, cephamycins, penams, phenicols, tetracyclines, rifamycins, aminoglycosides, etc. The S. Typhi strains possessed various virulence factors, such as Vi antigen, Agf/Csg, Bcf, Fim, Pef, etc. The sequencing data indicated that the strains had antibiotic resistance determinants and shared common virulence factors. Pangenome analysis of the selected S. Typhi strains identified 13,237 genes, with 3,611 being core genes, 2,093 shell genes, and 7,533 cloud genes. Genome-based typing and horizontal gene transfer analysis revealed that the strains had different evolutionary origins and may have adapted to distinct environments or host organisms. These findings provide important insights into the genetic characteristics of S. Typhi strains and their potential association with various ecological niches and host organisms.}, }
@article {pmid37258869, year = {2023}, author = {Abdelrazik, E and El-Hadidi, M}, title = {Tracking Antibiotic Resistance from the Environment to Human Health.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {289-301}, pmid = {37258869}, issn = {1940-6029}, mesh = {Humans ; *Bacteria/genetics ; Drug Resistance, Microbial/genetics ; *Anti-Bacterial Agents/pharmacology ; Genome, Bacterial ; Metagenome ; Genes, Bacterial ; Metagenomics ; }, abstract = {Antimicrobial resistance (AMR) is one of the threats to our world according to the World Health Organization (WHO). Resistance is an evolutionary dynamic process where host-associated microbes have to adapt to their stressful environments. AMR could be classified according to the mechanism of resistance or the biome where resistance takes place. Antibiotics are one of the stresses that lead to resistance through antibiotic resistance genes (ARGs). The resistome could be defined as the collection of all ARGs in an organism's genome or metagenome. Currently, there is a growing body of evidence supporting that the environment is the largest source of ARGs, but to what extent the environment does contribute to the antimicrobial resistance evolution is a matter of investigation. Monitoring the ARGs transfer route from the environment to humans and vice versa is a nature-to-nature feedback loop where you cannot set an accurate starting point of the evolutionary event. Thus, tracking resistome evolution and transfer to and from different biomes is crucial for the surveillance and prediction of the next resistance outbreak.Herein, we review the overlap between clinical and environmental resistomes and the available databases and computational analysis tools for resistome analysis through ARGs detection and characterization in bacterial genomes and metagenomes. Till this moment, there is no tool that can predict the resistance evolution and dynamics in a distinct biome. But, hopefully, by understanding the complicated relationship between the environmental and clinical resistome, we could develop tools that track the feedback loop from nature to nature in terms of evolution, mobilization, and transfer of ARGs.}, }
@article {pmid37257204, year = {2023}, author = {Chen, P and Yu, K and He, Y}, title = {The dynamics and transmission of antibiotic resistance associated with plant microbiomes.}, journal = {Environment international}, volume = {176}, number = {}, pages = {107986}, doi = {10.1016/j.envint.2023.107986}, pmid = {37257204}, issn = {1873-6750}, mesh = {Humans ; *Bacteria/genetics ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; *Microbiota ; Soil ; Anti-Bacterial Agents/pharmacology ; Soil Microbiology ; }, abstract = {Antibiotic resistance genes (ARGs) have been widely found and studied in soil and water environments. However, the propagation of ARGs in plant microbiomes has attracted insufficient attention. Plant microbiomes, especially the rhizosphere microorganisms, are closely connected with water, soil, and air, which allows ARGs to spread widely in ecosystems and pose a threat to human health after entering the human body with bacteria. Therefore, it is necessary to deeply understand and explore the dynamics and the transmission of ARGs in rhizosphere microorganisms and endophytes of plants. In this review, the transmission and influencing factors of ARGs in the microorganisms associated with plants, especially the influence of root exudates on plant microbiomes, are analyzed. Notably, the role of intrinsic genes of plants in determining root exudates and their potential effects on ARGs are proposed and analyzed. The important role of phyllosphere microorganisms and endophytes in the transmission of ARGs and co-resistance of antibiotics and other substances are also emphasized. The proliferation and transmission of ARGs associated with plant microbiomes addressed in this review is conducive to revealing the fate of ARGs in plant microorganisms and alleviating ARG pollution.}, }
@article {pmid37256324, year = {2023}, author = {Oliveira, GS and Lentz, SA and Wink, PL and Martins, AF}, title = {Molecular typing of mcr-1 Escherichia coli isolates from pigs and farm environment based on fumC and fimH alleles.}, journal = {Future microbiology}, volume = {18}, number = {}, pages = {481-488}, doi = {10.2217/fmb-2022-0173}, pmid = {37256324}, issn = {1746-0921}, mesh = {Animals ; Swine ; Escherichia coli ; Farms ; *Escherichia coli Infections/veterinary/genetics ; Alleles ; Phylogeny ; *Escherichia coli Proteins/genetics ; Multilocus Sequence Typing ; Anti-Bacterial Agents/pharmacology ; Colistin/pharmacology ; Microbial Sensitivity Tests ; Adhesins, Escherichia coli/genetics ; Fimbriae Proteins/genetics ; }, abstract = {Background: The dissemination of polymyxin resistance represents a significant threat to public health. Materials &amp; methods: Sequence-based typing was performed by 53 mcr-1 Escherichia coli isolates using fumC/fimH (CH) genes to characterize clones spreading from pig farming. Furthermore, 12 isolates had their whole genome sequenced for phylogenetic study. Results: The isolates were classified into 22 distinct CH types, and two novel CH types (CH41-1578 and CH4-1579) and one sequence type (ST12652) was also described. According to phylogenetic study, both multilocus sequence typing and CH methods grouped the isolates similarly. Conclusion: Our findings suggest that the dissemination of the mcr-1 gene in pig farming has occurred mainly by horizontal gene transfer, and CH typing proved to be a good tool to characterize E. coli clones.}, }
@article {pmid37254648, year = {2023}, author = {Rana, R and Jaiswal, G and Bansal, K and Patil, PB}, title = {Comparative genomics reveals the emergence of copper resistance in a non-pigmented Xanthomonas pathogen of grapevine.}, journal = {Environmental microbiology reports}, volume = {15}, number = {6}, pages = {716-726}, pmid = {37254648}, issn = {1758-2229}, support = {OLP0191-20//CSIR - Institute of Microbial Technology/ ; }, mesh = {*Copper/pharmacology ; *Xanthomonas/genetics ; Genomics ; Gene Transfer, Horizontal ; Plant Diseases/microbiology ; }, abstract = {Xanthomonas citri pv. viticola (Xcv) is the causal agent of bacterial canker in grapevine. The pathogen is restricted to India, where it was first reported in the 1970s, and Brazil. In the present study, we report the first complete genome sequence of Xcv LMG965, which is a reference pathotype strain. We also report genome sequences of additional isolates from India and comparative genome-based studies of isolates from Brazil. Apart from revealing the monophyletic origin of the pathovar, we could also confirm a common frameshift mutation in a gene that is part of the Xanthomonadin pigment biosynthetic gene cluster in all the isolates. The comparative study also revealed multiple intrinsic copper resistance-related genes in Brazilian isolates, suggesting intense selection, possibly because of heavy and indiscriminate usage of copper as an antimicrobial agent in the orchards. There is also the association of a Tn3-like transposase in the vicinity of the copper resistance genes, indicating a potential for rapid diversification through horizontal gene transfer events. The findings, along with genomic resources, will allow for systematic genetic and functional studies of Xcv.}, }
@article {pmid37252660, year = {2023}, author = {Tokuda, R and Iwabuchi, N and Kitazawa, Y and Nijo, T and Suzuki, M and Maejima, K and Oshima, K and Namba, S and Yamaji, Y}, title = {Potential mobile units drive the horizontal transfer of phytoplasma effector phyllogen genes.}, journal = {Frontiers in genetics}, volume = {14}, number = {}, pages = {1132432}, pmid = {37252660}, issn = {1664-8021}, abstract = {Phytoplasmas are obligate intracellular plant pathogenic bacteria that can induce phyllody, which is a type of abnormal floral organ development. Phytoplasmas possess phyllogens, which are effector proteins that cause phyllody in plants. Phylogenetic comparisons of phyllogen and 16S rRNA genes have suggested that phyllogen genes undergo horizontal transfer between phytoplasma species and strains. However, the mechanisms and evolutionary implications of this horizontal gene transfer are unclear. Here, we analyzed synteny in phyllogen flanking genomic regions from 17 phytoplasma strains that were related to six 'Candidatus' species, including three strains newly sequenced in this study. Many of the phyllogens were flanked by multicopy genes within potential mobile units (PMUs), which are putative transposable elements found in phytoplasmas. The multicopy genes exhibited two distinct patterns of synteny that correlated with the linked phyllogens. The low level of sequence identities and partial truncations found among these phyllogen flanking genes indicate that the PMU sequences are deteriorating, whereas the highly conserved sequences and functions (e.g., inducing phyllody) of the phyllogens suggest that the latter are important for phytoplasma fitness. Furthermore, although their phyllogens were similar, PMUs in strains related to 'Ca. P. asteris' were often located in different regions of the genome. These findings strongly indicate that PMUs drive the horizontal transfer of phyllogens among phytoplasma species and strains. These insights improve our understanding of how symptom-determinant genes have been shared among phytoplasmas.}, }
@article {pmid37251586, year = {2023}, author = {Scott, TW and West, SA and Dewar, AE and Wild, G}, title = {Is cooperation favored by horizontal gene transfer?.}, journal = {Evolution letters}, volume = {7}, number = {3}, pages = {113-120}, pmid = {37251586}, issn = {2056-3744}, support = {834164/ERC_/European Research Council/International ; }, abstract = {It has been hypothesized that horizontal gene transfer on plasmids can facilitate the evolution of cooperation, by allowing genes to jump between bacteria, and hence increase genetic relatedness at the cooperative loci. However, we show theoretically that horizontal gene transfer only appreciably increases relatedness when plasmids are rare, where there are many plasmid-free cells available to infect (many opportunities for horizontal gene transfer). In contrast, when plasmids are common, there are few opportunities for horizontal gene transfer, meaning relatedness is not appreciably increased, and so cooperation is not favored. Plasmids, therefore, evolve to be rare and cooperative, or common and noncooperative, meaning plasmid frequency and cooperativeness are never simultaneously high. The overall level of plasmid-mediated cooperation, given by the product of plasmid frequency and cooperativeness, is therefore consistently negligible or low.}, }
@article {pmid37250807, year = {2023}, author = {Mwakyoma, AA and Kidenya, BR and Minja, CA and Mushi, MF and Sandeman, A and Sabiti, W and Holden, MTG and Mshana, SE}, title = {Comparison of Horizontal blaCTX-M Gene Transfer via Conjugation among Extended Spectrum β-Lactamases Producing Escherichia coli Isolates from Patients with Urinary Tract Infection, Their Animals, and Environment.}, journal = {Archives of molecular biology and genetics}, volume = {2}, number = {1}, pages = {1-8}, pmid = {37250807}, issn = {2831-6754}, support = {MR/S004785/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {BACKGROUND: The dissemination of the extended spectrum β-lactamases (ESBL) producing E. coli poses a significant public health problem. Understanding the efficiency and frequency of horizontal gene transfer via conjugation of ESBL producing E. coli is imperative towards devising prevention and control measures. This study compared the frequencies and efficiencies of horizontal blaCTX-M gene transfer via conjugation among Escherichia coli isolates from urine and gastrointestinal tract (GIT) of patients with urinary tract infection (UTI), their animals and environment.<br><br>METHODS: Horizontal blaCTX-M gene transfer via conjugation by a broth mating experiment was performed using 50 confirmed ESBL producing E. coli isolates as donors and Escherichia coli J53 (F[-], met, pro, Az[r]), as the recipient. The transconjugants were detected and their frequencies and efficiencies of conjugation were measured and compared between ESBL producing E. coli isolates multi-sourced from urine, GIT, animals and environment. Antimicrobial susceptibility testing of all resulting transconjugants was performed. DNA was extracted from all transconjugants to confirm the presence and the acquisition of blaCTX-M gene.<br><br>RESULTS: Out of 50 ESBL producing E. coli isolates harboring blaCTX-M gene, 37 (74.0%) successfully exercised horizontal gene transfer through conjugation. All transconjugants were confirmed phenotypically and genotypically by PCR. Of note, all of the isolates from environment 100.0% (7/7) performed conjugation, exhibiting the highest transfer efficiency, followed by isolates from urine and animals, with the conjugation transfer efficiency of 77.8% (14/18) and 76.1% (10/13), respectively. The isolates from the environment conjugated with a significant more efficiency than those from the GIT [Two-sample test of proportions; p-value = 0.0119]. The overall conjugation transfer frequencies ranged from 0.4 &#xd7; 10[-14] - 5.5 &#xd7; 10[-11] per donor cells with the highest median conjugation transfer frequency observed among isolates from animal (3.23 &#xd7; 10[-12] [IQR: 0.70 &#xd7; 10[-12] - 7.22 &#xd7; 10[-12]]) followed by that of isolates from the environment (1.60 &#xd7; 10[-12] [IQR: 0.30 &#xd7; 10[-12] - 5.0 &#xd7; 10[-12]]).<br><br>CONCLUSION: ESBL producing E. coli from human, animals and environment exercises horizontal blaCTX-M gene transfer efficiently with the highest occurrence among isolates from the environment and animals. The antimicrobial resistance control and prevention strategies should be widened up to explore strategies to prevent horizontal AMR gene transfer.}, }
@article {pmid37246713, year = {2023}, author = {Jowsey, WJ and Morris, CRP and Hall, DA and Sullivan, JT and Fagerlund, RD and Eto, KY and Solomon, PD and Mackay, JP and Bond, CS and Ramsay, JP and Ronson, CW}, title = {DUF2285 is a novel helix-turn-helix domain variant that orchestrates both activation and antiactivation of conjugative element transfer in proteobacteria.}, journal = {Nucleic acids research}, volume = {51}, number = {13}, pages = {6841-6856}, pmid = {37246713}, issn = {1362-4962}, mesh = {Quorum Sensing/genetics ; Gene Transfer, Horizontal ; Transcriptional Activation ; Bacterial Proteins/genetics/metabolism ; Transcription Factors/metabolism ; *Conjugation, Genetic ; *Proteobacteria/genetics ; Mesorhizobium ; }, abstract = {Horizontal gene transfer is tightly regulated in bacteria. Often only a fraction of cells become donors even when regulation of horizontal transfer is coordinated at the cell population level by quorum sensing. Here, we reveal the widespread 'domain of unknown function' DUF2285 represents an 'extended-turn' variant of the helix-turn-helix domain that participates in both transcriptional activation and antiactivation to initiate or inhibit horizontal gene transfer. Transfer of the integrative and conjugative element ICEMlSymR7A is controlled by the DUF2285-containing transcriptional activator FseA. One side of the DUF2285 domain of FseA has a positively charged surface which is required for DNA binding, while the opposite side makes critical interdomain contacts with the N-terminal FseA DUF6499 domain. The QseM protein is an antiactivator of FseA and is composed of a DUF2285 domain with a negative surface charge. While QseM lacks the DUF6499 domain, it can bind the FseA DUF6499 domain and prevent transcriptional activation by FseA. DUF2285-domain proteins are encoded on mobile elements throughout the proteobacteria, suggesting regulation of gene transfer by DUF2285 domains is a widespread phenomenon. These findings provide a striking example of how antagonistic domain paralogues have evolved to provide robust molecular control over the initiation of horizontal gene transfer.}, }
@article {pmid37246198, year = {2023}, author = {Shafique, MS and Guo, W and Chen, X and Zhao, K and Liu, Y and Wang, C and Ji, Z}, title = {Genome resource of Xanthomonas oryzae pv. oryzae Chinese strain NE-8 causing bacterial blight of rice.}, journal = {Functional &amp; integrative genomics}, volume = {23}, number = {2}, pages = {189}, pmid = {37246198}, issn = {1438-7948}, support = {2019SLJ020378//China Scholarship council/ ; Y2022QC01//Central Public-interest Scientific Institution Basal Research Fund/ ; Y2022QC01//Central Public-interest Scientific Institution Basal Research Fund/ ; B21HJ0218//Hainan Yazhou-Bay Seed Laboratory/ ; B21HJ0218//Hainan Yazhou-Bay Seed Laboratory/ ; }, mesh = {Bacterial Proteins/genetics ; *Oryza/genetics/microbiology ; Plant Diseases/genetics/microbiology ; *Xanthomonas/genetics ; }, }
@article {pmid37243281, year = {2023}, author = {Arnau, V and Díaz-Villanueva, W and Mifsut Benet, J and Villasante, P and Beamud, B and Mompó, P and Sanjuan, R and González-Candelas, F and Domingo-Calap, P and Džunková, M}, title = {Inference of the Life Cycle of Environmental Phages from Genomic Signature Distances to Their Hosts.}, journal = {Viruses}, volume = {15}, number = {5}, pages = {}, pmid = {37243281}, issn = {1999-4915}, mesh = {*Bacteriophages/genetics ; Lysogeny ; Genomics ; Genome, Viral ; Bacteria/genetics ; Oligonucleotides ; }, abstract = {The environmental impact of uncultured phages is shaped by their preferred life cycle (lytic or lysogenic). However, our ability to predict it is very limited. We aimed to discriminate between lytic and lysogenic phages by comparing the similarity of their genomic signatures to those of their hosts, reflecting their co-evolution. We tested two approaches: (1) similarities of tetramer relative frequencies, (2) alignment-free comparisons based on exact k = 14 oligonucleotide matches. First, we explored 5126 reference bacterial host strains and 284 associated phages and found an approximate threshold for distinguishing lysogenic and lytic phages using both oligonucleotide-based methods. The analysis of 6482 plasmids revealed the potential for horizontal gene transfer between different host genera and, in some cases, distant bacterial taxa. Subsequently, we experimentally analyzed combinations of 138 Klebsiella pneumoniae strains and their 41 phages and found that the phages with the largest number of interactions with these strains in the laboratory had the shortest genomic distances to K. pneumoniae. We then applied our methods to 24 single-cells from a hot spring biofilm containing 41 uncultured phage-host pairs, and the results were compatible with the lysogenic life cycle of phages detected in this environment. In conclusion, oligonucleotide-based genome analysis methods can be used for predictions of (1) life cycles of environmental phages, (2) phages with the broadest host range in culture collections, and (3) potential horizontal gene transfer by plasmids.}, }
@article {pmid37239594, year = {2023}, author = {Tuvo, B and Scarpaci, M and Bracaloni, S and Esposito, E and Costa, AL and Ioppolo, M and Casini, B}, title = {Microplastics and Antibiotic Resistance: The Magnitude of the Problem and the Emerging Role of Hospital Wastewater.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {10}, pages = {}, pmid = {37239594}, issn = {1660-4601}, mesh = {Humans ; *Microplastics ; *Wastewater ; Plastics ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Hospitals ; }, abstract = {The role of microplastics (MPs) in the spread of antibiotic resistance genes (ARGs) is increasingly attracting global research attention due to their unique ecological and environmental effects. The ubiquitous use of plastics and their release into the environment by anthropic/industrial activities are the main sources for MP contamination, especially of water bodies. Because of their physical and chemical characteristics, MPs represent an ideal substrate for microbial colonization and formation of biofilm, where horizontal gene transfer is facilitated. In addition, the widespread and often injudicious use of antibiotics in various human activities leads to their release into the environment, mainly through wastewater. For these reasons, wastewater treatment plants, in particular hospital plants, are considered hotspots for the selection of ARGs and their diffusion in the environment. As a result, the interaction of MPs with drug-resistant bacteria and ARGs make them vectors for the transport and spread of ARGs and harmful microorganisms. Microplastic-associated antimicrobial resistance is an emerging threat to the environment and consequently for human health. More studies are required to better understand the interaction of these pollutants with the environment as well as to identify effective management systems to reduce the related risk.}, }
@article {pmid37239483, year = {2023}, author = {Alim, NTB and Koppenhöfer, S and Lang, AS and Beatty, JT}, title = {Extracellular Polysaccharide Receptor and Receptor-Binding Proteins of the Rhodobacter capsulatus Bacteriophage-like Gene Transfer Agent RcGTA.}, journal = {Genes}, volume = {14}, number = {5}, pages = {}, pmid = {37239483}, issn = {2073-4425}, mesh = {Carrier Proteins/metabolism ; Bacterial Proteins/genetics/metabolism ; *Rhodobacter capsulatus/genetics/metabolism ; *Bacteriophages/genetics ; Polysaccharides ; }, abstract = {A variety of prokaryotes produce a bacteriophage-like gene transfer agent (GTA), and the alphaproteobacterial Rhodobacter capsulatus RcGTA is a model GTA. Some environmental isolates of R. capsulatus lack the ability to acquire genes transferred by the RcGTA (recipient capability). In this work, we investigated the reason why R. capsulatus strain 37b4 lacks recipient capability. The RcGTA head spike fiber and tail fiber proteins have been proposed to bind extracellular oligosaccharide receptors, and strain 37b4 lacks a capsular polysaccharide (CPS). The reason why strain 37b4 lacks a CPS was unknown, as was whether the provision of a CPS to 37b4 would result in recipient capability. To address these questions, we sequenced and annotated the strain 37b4 genome and used BLAST interrogations of this genome sequence to search for homologs of genes known to be needed for R. capsulatus recipient capability. We also created a cosmid-borne genome library from a wild-type strain, mobilized the library into 37b4, and used the cosmid-complemented strain 37b4 to identify genes needed for a gain of function, allowing for the acquisition of RcGTA-borne genes. The relative presence of CPS around a wild-type strain, 37b4, and cosmid-complemented 37b4 cells was visualized using light microscopy of stained cells. Fluorescently tagged head spike fiber and tail fiber proteins of the RcGTA particle were created and used to measure the relative binding to wild-type and 37b4 cells. We found that strain 37b4 lacks recipient capability because of an inability to bind RcGTA; the reason it is incapable of binding is that it lacks CPS, and the absence of CPS is due to the absence of genes previously shown to be needed for CPS production in another strain. In addition to the head spike fiber, we found that the tail fiber protein also binds to the CPS.}, }
@article {pmid37239397, year = {2023}, author = {Dey, S and Gaur, M and Sykes, EME and Prusty, M and Elangovan, S and Dixit, S and Pati, S and Kumar, A and Subudhi, E}, title = {Unravelling the Evolutionary Dynamics of High-Risk Klebsiella pneumoniae ST147 Clones: Insights from Comparative Pangenome Analysis.}, journal = {Genes}, volume = {14}, number = {5}, pages = {}, pmid = {37239397}, issn = {2073-4425}, mesh = {Humans ; *beta-Lactamases/genetics ; Klebsiella pneumoniae/genetics ; Phylogeny ; Bayes Theorem ; *Klebsiella Infections/epidemiology/genetics/drug therapy ; }, abstract = {BACKGROUND: The high prevalence and rapid emergence of antibiotic resistance in high-risk Klebsiella pneumoniae (KP) ST147 clones is a global health concern and warrants molecular surveillance.<br><br>METHODS: A pangenome analysis was performed using publicly available ST147 complete genomes. The characteristics and evolutionary relationships among ST147 members were investigated through a Bayesian phylogenetic analysis.<br><br>RESULTS: The large number of accessory genes in the pangenome indicates genome plasticity and openness. Seventy-two antibiotic resistance genes were found to be linked with antibiotic inactivation, efflux, and target alteration. The exclusive detection of the blaOXA-232 gene within the ColKp3 plasmid of KP_SDL79 suggests its acquisition through horizontal gene transfer. The association of seventy-six virulence genes with the acrAB efflux pump, T6SS system and type I secretion system describes its pathogenicity. The presence of Tn6170, a putative Tn7-like transposon in KP_SDL79 with an insertion at the flanking region of the tnsB gene, establishes its transmission ability. The Bayesian phylogenetic analysis estimates ST147's initial divergence in 1951 and the most recent common ancestor for the entire KP population in 1621.<br><br>CONCLUSIONS: Present study highlights the genetic diversity and evolutionary dynamics of high-risk clones of K. pneumoniae. Further inter-clonal diversity studies will help us understand its outbreak more precisely and pave the way for therapeutic interventions.}, }
@article {pmid37237011, year = {2023}, author = {Negeri, AA and Mamo, H and Gahlot, DK and Gurung, JM and Seyoum, ET and Francis, MS}, title = {Characterization of plasmids carrying blaCTX-M genes among extra-intestinal Escherichia coli clinical isolates in Ethiopia.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {8595}, pmid = {37237011}, issn = {2045-2322}, mesh = {Humans ; Anti-Bacterial Agents ; beta-Lactamases/genetics ; *Escherichia coli/genetics ; *Escherichia coli Infections/epidemiology ; Ethiopia/epidemiology ; *Plasmids/genetics ; }, abstract = {CTX-Ms are encoded by blaCTX-M genes and are widely distributed extended-spectrum β-lactamases (ESBLs). They are the most important antimicrobial resistance (AMR) mechanism to β-lactam antibiotics in the Enterobacteriaceae. However, the role of transmissible AMR plasmids in the dissemination of blaCTX-M genes has scarcely been studied in Africa where the burden of AMR is high and rapidly spreading. In this study, AMR plasmid transmissibility, replicon types and addiction systems were analysed in CTX-M-producing Escherichia coli clinical isolates in Ethiopia with a goal to provide molecular insight into mechanisms underlying such high prevalence and rapid dissemination. Of 100 CTX-Ms-producing isolates obtained from urine (84), pus (10) and blood (6) from four geographically distinct healthcare settings, 75% carried transmissible plasmids encoding for CTX-Ms, with CTX-M-15 being predominant (n = 51). Single IncF plasmids with the combination of F-FIA-FIB (n = 17) carried the bulk of blaCTX-M-15 genes. In addition, IncF plasmids were associated with multiple addiction systems, ISEcp1 and various resistance phenotypes for non-cephalosporin antibiotics. Moreover, IncF plasmid carriage is associated with the international pandemic E. coli ST131 lineage. Furthermore, several CTX-M encoding plasmids were associated with serum survival of the strains, but less so with biofilm formation. Hence, both horizontal gene transfer and clonal expansion may contribute to the rapid and widespread distribution of blaCTX-M genes among E. coli populations in Ethiopian clinical settings. This information is relevant for local epidemiology and surveillance, but also for global understanding of the successful dissemination of AMR gene carrying plasmids.}, }
@article {pmid37236960, year = {2023}, author = {Wang, WJ and Yu, LM and Shao, MY and Jia, YT and Liu, LQ and Ma, XH and Zheng, Y and Liu, YF and Zhang, YZ and Luo, XX and Li, FM and Zheng, H}, title = {Research review on the pollution of antibiotic resistance genes in livestock and poultry farming environments.}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {34}, number = {5}, pages = {1415-1429}, doi = {10.13287/j.1001-9332.202305.032}, pmid = {37236960}, issn = {1001-9332}, mesh = {Animals ; Humans ; *Poultry/genetics ; *Anti-Bacterial Agents/pharmacology ; Livestock/genetics ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Agriculture ; }, abstract = {Increasingly serious pollution of antibiotic resistance genes (ARGs) caused by the abuse of antibiotics in livestock and poultry industry has raised worldwide concerns. ARGs could spread among various farming environmental media through adsorption, desorption, migration, and also could transfer into human gut microbiome by hori-zontal gene transfer (HGT), posing potential threats to public health. However, the comprehensive review on the pollution patterns, environmental behaviors, and control techniques of ARGs in livestock and poultry environments in view of One Health is still inadequate, resulting in the difficulties in effectively assessing ARGs transmission risk and developing the efficient control strategies. Here, we analyzed the pollution characteristics of typical ARGs in various countries, regions, livestock species, and environmental media, reviewed the critical environmental fate and influencing factors, control strategies, and the shortcomings of current researches about ARGs in the livestock and poultry farming industry combined with One Health philosophy. In particular, we addressed the importance and urgency of identifying the distribution characteristics and environmental process mechanisms of ARGs, and developing green and efficient ARG control means in livestock farming environments. We further proposed gaps and prospects for the future research. It would provide theoretical basis for the research on health risk assessment and technology exploitation of alleviating ARG pollution in livestock farming environment.}, }
@article {pmid37236388, year = {2023}, author = {Song, D and Tang, X and Tariq, A and Pan, K and Li, D}, title = {Regional distribution and migration potential of antibiotic resistance genes in croplands of Qinghai Tibet Plateau.}, journal = {Environmental research}, volume = {231}, number = {Pt 2}, pages = {116233}, doi = {10.1016/j.envres.2023.116233}, pmid = {37236388}, issn = {1096-0953}, mesh = {Tibet ; Anti-Bacterial Agents/pharmacology ; Ecosystem ; *Soil Pollutants/analysis ; *Metals, Heavy/analysis ; Soil/chemistry ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Soil Microbiology ; Crops, Agricultural ; }, abstract = {Agricultural activities have recently disturbed the ecosystem of the Qinghai-Tibet Plateau and the shift of antibiotic resistance genes (ARGs) in the different types of farmlands is not well understood, so more comprehensive ecological barrier management measures cannot be provided for the region. This research was performed to exploring ARG pollution in cropland soil on the Qinghai-Tibet Plateau to obtain information on the geographical and climatic factors shaping the ARG distribution. Based on high-throughput quantitative PCR (HT-qPCR) analysis, the ARG abundance in farmland ranged from 5.66 × 10[5] to 6.22 × 10[7] copies per gram of soil higher than previous research at soil and wetland in Qinghai-Tibet plateau, and it was higher in wheat and barley soils than in corn soil. The distribution of ARGs exhibited regional features as ARG abundance was adversely affected by mean annual precipitation and temperature with lower temperature and less rainfall at high altitude. According to network analysis and structural equation modeling (SEM), mobile genetic elements (MGEs) and heavy metals are the key drivers of ARG dissemination on the Qinghai-Tibet Plateau as they show negative relationship with ARGs, and selection copressure from heavy metals in cropland soil increases the horizontal gene transfer (HGT) potential of ARGs through synergistic selection effects, each contribution to the ARGs was 19% and 29% respectively. This research suggests the need to focus on controlling heavy metals and MGEs to constrain the dissemination of ARGs, as arable soil is already slightly contaminated by heavy metals.}, }
@article {pmid37232518, year = {2023}, author = {Burch, CL and Romanchuk, A and Kelly, M and Wu, Y and Jones, CD}, title = {Empirical Evidence That Complexity Limits Horizontal Gene Transfer.}, journal = {Genome biology and evolution}, volume = {15}, number = {6}, pages = {}, pmid = {37232518}, issn = {1759-6653}, mesh = {*Gene Transfer, Horizontal ; *Evolution, Molecular ; Genome, Bacterial ; Bacteria/genetics ; Prokaryotic Cells ; Escherichia coli/genetics ; }, abstract = {Horizontal gene transfer (HGT) is a major contributor to bacterial genome evolution, generating phenotypic diversity, driving the expansion of protein families, and facilitating the evolution of new phenotypes, new metabolic pathways, and new species. Comparative studies of gene gain in bacteria suggest that the frequency with which individual genes successfully undergo HGT varies considerably and may be associated with the number of protein-protein interactions in which the gene participates, that is, its connectivity. Two nonexclusive hypotheses have emerged to explain why transferability should decrease with connectivity: the complexity hypothesis (Jain R, Rivera MC, Lake JA. 1999. Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci U S A. 96:3801-3806.) and the balance hypothesis (Papp B, Pál C, Hurst LD. 2003. Dosage sensitivity and the evolution of gene families in yeast. Nature 424:194-197.). These hypotheses predict that the functional costs of HGT arise from a failure of divergent homologs to make normal protein-protein interactions or from gene misexpression, respectively. Here we describe genome-wide assessments of these hypotheses in which we used 74 existing prokaryotic whole genome shotgun libraries to estimate rates of horizontal transfer of genes from taxonomically diverse prokaryotic donors into Escherichia coli. We show that 1) transferability declines as connectivity increases, 2) transferability declines as the divergence between donor and recipient orthologs increases, and that 3) the magnitude of this negative effect of divergence on transferability increases with connectivity. These effects are particularly robust among the translational proteins, which span the widest range of connectivities. Whereas the complexity hypothesis explains all three of these observations, the balance hypothesis explains only the first one.}, }
@article {pmid37227565, year = {2023}, author = {Chettri, U and Nongkhlaw, M and Joshi, SR}, title = {Molecular Evidence for Occurrence of Heavy Metal and Antibiotic Resistance Genes Among Predominant Metal Tolerant Pseudomonas sp. and Serratia sp. Prevalent in the Teesta River.}, journal = {Current microbiology}, volume = {80}, number = {7}, pages = {226}, pmid = {37227565}, issn = {1432-0991}, support = {SR/FST/ LSI-666/2016(C)//Department of Science and Technology India/ ; F.4-7/2016/DRS-1 (SAP-II)//University Grants Commission India/ ; }, mesh = {*Anti-Bacterial Agents/pharmacology/metabolism ; Pseudomonas/genetics/metabolism ; Rivers ; Ecosystem ; Phylogeny ; *Metals, Heavy/pharmacology/metabolism ; Drug Resistance, Microbial ; Bacteria/genetics ; }, abstract = {Riverine ecosystems polluted by pharmaceutical and metal industries are potential incubators of bacteria with dual resistance to heavy metals and antibiotics. The processes of co-resistance and cross resistance that empower bacteria to negotiate these challenges, strongly endorse dangers of antibiotic resistance generated by metal stress. Therefore, investigation into the molecular evidence of heavy metal and antibiotic resistance genes was the prime focus of this study. The selected Pseudomonas and Serratia species isolates evinced by their minimum inhibitory concentration and multiple antibiotic resistance (MAR) index showed significant heavy metal tolerance and multi-antibiotic resistance capability, respectively. Consequently, isolates with higher tolerance for the most toxic metal cadmium evinced high MAR index value (0.53 for Pseudomonas sp., and 0.46 for Serratia sp.) in the present investigation. Metal tolerance genes belonging to PIB-type and resistance nodulation division family of proteins were evident in these isolates. The antibiotic resistance genes like mexB, mexF and mexY occurred in Pseudomonas isolates while sdeB genes were present in Serratia isolates. Phylogenetic incongruency and GC composition analysis of PIB-type genes suggested that some of these isolates had acquired resistance through horizontal gene transfer (HGT). Therefore, the Teesta River has become a reservoir for resistant gene exchange or movement via selective pressure exerted by metals and antibiotics. The resultant adaptive mechanisms and altered phenotypes are potential tools to track metal tolerant strains with clinically significant antibiotic resistance traits.}, }
@article {pmid37227251, year = {2023}, author = {Tonkin-Hill, G and Corander, J and Parkhill, J}, title = {Challenges in prokaryote pangenomics.}, journal = {Microbial genomics}, volume = {9}, number = {5}, pages = {}, pmid = {37227251}, issn = {2057-5858}, mesh = {Phylogeny ; *Evolution, Molecular ; *Prokaryotic Cells ; Bacteria/genetics ; Gene Transfer, Horizontal ; }, abstract = {Horizontal gene transfer (HGT) and the resulting patterns of gene gain and loss are a fundamental part of bacterial evolution. Investigating these patterns can help us to understand the role of selection in the evolution of bacterial pangenomes and how bacteria adapt to a new niche. Predicting the presence or absence of genes can be a highly error-prone process that can confound efforts to understand the dynamics of horizontal gene transfer. This review discusses both the challenges in accurately constructing a pangenome and the potential consequences errors can have on downstream analyses. We hope that by summarizing these issues researchers will be able to avoid potential pitfalls, leading to improved bacterial pangenome analyses.}, }
@article {pmid37221009, year = {2023}, author = {Shaferman, M and Gencel, M and Alon, N and Alasad, K and Rotblat, B and Serohijos, AWR and Alfonta, L and Bershtein, S}, title = {The Fitness Effects of Codon Composition of the Horizontally Transferred Antibiotic Resistance Genes Intensify at Sub-lethal Antibiotic Levels.}, journal = {Molecular biology and evolution}, volume = {40}, number = {6}, pages = {}, pmid = {37221009}, issn = {1537-1719}, mesh = {*Anti-Bacterial Agents/pharmacology ; Codon ; RNA, Messenger ; Drug Resistance, Microbial/genetics ; *Trimethoprim/pharmacology ; }, abstract = {The rampant variability in codon bias existing between bacterial genomes is expected to interfere with horizontal gene transfer (HGT), a phenomenon that drives bacterial adaptation. However, delineating the constraints imposed by codon bias on functional integration of the transferred genes is complicated by multiple genomic and functional barriers controlling HGT, and by the dependence of the evolutionary outcomes of HGT on the host's environment. Here, we designed an experimental system in which codon composition of the transferred genes is the only variable triggering fitness change of the host. We replaced Escherichia coli's chromosomal folA gene encoding dihydrofolate reductase, an essential enzyme that constitutes a target for trimethoprim, with combinatorial libraries of synonymous codons of folA genes from trimethoprim-sensitive Listeria grayi and trimethoprim-resistant Neisseria sicca. The resulting populations underwent selection at a range of trimethoprim concentrations, and the ensuing changes in variant frequencies were used to infer the fitness effects of the individual combinations of codons. We found that when HGT causes overstabilization of the 5'-end mRNA, the fitness contribution of mRNA folding stability dominates over that of codon optimality. The 5'-end overstabilization can also lead to mRNA accumulation outside of the polysome, thus preventing the decay of the foreign transcripts despite the codon composition-driven reduction in translation efficiency. Importantly, the fitness effects of mRNA stability or codon optimality become apparent only at sub-lethal levels of trimethoprim individually tailored for each library, emphasizing the central role of the host's environment in shaping the codon bias compatibility of horizontally transferred genes.}, }
@article {pmid37219457, year = {2023}, author = {Murthy, AC and Aleksanyan, N and Morton, GM and Toyoda, HC and Kalashyan, M and Chen, S and Ragucci, AE and Broulidakis, MP and Swerdlow, KJ and Bui, MNN and Muccioli, M and Berkmen, MB}, title = {Characterization of ConE, the VirB4 Homolog of the Integrative and Conjugative Element ICEBs1 of Bacillus subtilis.}, journal = {Journal of bacteriology}, volume = {205}, number = {6}, pages = {e0003323}, pmid = {37219457}, issn = {1098-5530}, mesh = {*Bacillus subtilis/genetics/metabolism ; *Conjugation, Genetic ; DNA, Bacterial/genetics/metabolism ; DNA Transposable Elements ; Bacterial Proteins/genetics/metabolism ; Adenosine Triphosphatases/genetics/metabolism ; Gene Transfer, Horizontal ; }, abstract = {Conjugation is a major form of horizontal gene transfer, contributing to bacterial evolution and the acquisition of new traits. During conjugation, a donor cell transfers DNA to a recipient through a specialized DNA translocation channel classified as a type IV secretion system (T4SS). Here, we focused on the T4SS of ICEBs1, an integrative and conjugative element in Bacillus subtilis. ConE, encoded by ICEBs1, is a member of the VirB4 family of ATPases, the most conserved component of T4SSs. ConE is required for conjugation and localizes to the cell membrane, predominantly at the cell poles. In addition to Walker A and B boxes, VirB4 homologs have conserved ATPase motifs C, D, and E. Here, we created alanine substitutions in five conserved residues within or near ATPase motifs in ConE. Mutations in all five residues drastically decreased conjugation frequency but did not affect ConE protein levels or localization, indicating that an intact ATPase domain is critical for DNA transfer. Purified ConE is largely monomeric with some oligomers and lacks enzymatic activity, suggesting that ATP hydrolysis may be regulated or require special solution conditions. Finally, we investigated which ICEBs1 T4SS components interact with ConE using a bacterial two-hybrid assay. ConE interacts with itself, ConB, and ConQ, but these interactions are not required to stabilize ConE protein levels and largely do not depend on conserved residues within the ATPase motifs of ConE. The structure-function characterization of ConE provides more insight into this conserved component shared by all T4SSs. IMPORTANCE Conjugation is a major form of horizontal gene transfer and involves the transfer of DNA from one bacterium to another through the conjugation machinery. Conjugation contributes to bacterial evolution by disseminating genes involved in antibiotic resistance, metabolism, and virulence. Here, we characterized ConE, a protein component of the conjugation machinery of the conjugative element ICEBs1 of the bacterium Bacillus subtilis. We found that mutations in the conserved ATPase motifs of ConE disrupt mating but do not alter ConE localization, self-interaction, or levels. We also explored which conjugation proteins ConE interacts with and whether these interactions contribute to stabilizing ConE. Our work contributes to the understanding of the conjugative machinery of Gram-positive bacteria.}, }
@article {pmid37218693, year = {2023}, author = {Bejenari, M and Sondergaard, TE and Sørensen, JL}, title = {6-MSA, a secondary metabolite distribution hub with multiple fungal destinations.}, journal = {Journal of applied microbiology}, volume = {134}, number = {6}, pages = {}, doi = {10.1093/jambio/lxad107}, pmid = {37218693}, issn = {1365-2672}, support = {NNF20OC0064343//Novo Nordisk Foundation/ ; }, mesh = {Humans ; *Patulin ; Multigene Family ; Bacteria/genetics ; Polyketide Synthases/genetics ; }, abstract = {6-methylsalicylic acid (6-MSA) is a small, simple polyketide produced by a broad spectrum of fungal species. Since fungi obtained the ability to synthesize 6-MSA from bacteria through a horizontal gene transfer event, it has developed into a multipurpose metabolic hub from where numerous complex compounds are produced. The most relevant metabolite from a human perspective is the small lactone patulin as it is one of the most potent mycotoxins. Other important end products derived from 6-MSA include the small quinone epoxide terreic acid and the prenylated yanuthones. The most advanced modification of 6-MSA is observed in the aculin biosynthetic pathway, which is mediated by a non-ribosomal peptide synthase and a terpene cyclase. In this short review, we summarize for the first time all the possible pathways that takes their onset from 6-MSA and provide a synopsis of the responsible gene clusters and derive the resulting biosynthetic pathways.}, }
@article {pmid37217185, year = {2023}, author = {Maruyama, M and Kagamoto, T and Matsumoto, Y and Onuma, R and Miyagishima, SY and Tanifuji, G and Nakazawa, M and Kashiyama, Y}, title = {Horizontally Acquired Nitrate Reductase Realized Kleptoplastic Photoautotrophy of Rapaza viridis.}, journal = {Plant &amp; cell physiology}, volume = {64}, number = {9}, pages = {1082-1090}, doi = {10.1093/pcp/pcad044}, pmid = {37217185}, issn = {1471-9053}, support = {18H03743 21H02273 21H02554 21K19240 21K19303//Japan Society for the Promotion of Science/ ; }, mesh = {Nitrate Reductase/genetics/metabolism ; *Nitrates/metabolism ; Phylogeny ; *Ammonium Compounds ; Nitrogen/metabolism ; }, abstract = {While photoautotrophic organisms utilize inorganic nitrogen as the nitrogen source, heterotrophic organisms utilize organic nitrogen and thus do not generally have an inorganic nitrogen assimilation pathway. Here, we focused on the nitrogen metabolism of Rapaza viridis, a unicellular eukaryote exhibiting kleptoplasty. Although belonging to the lineage of essentially heterotrophic flagellates, R. viridis exploits the photosynthetic products of the kleptoplasts and was therefore suspected to potentially utilize inorganic nitrogen. From the transcriptome data of R. viridis, we identified gene RvNaRL, which had sequence similarity to genes encoding nitrate reductases in plants. Phylogenetic analysis revealed that RvNaRL was acquired by a horizontal gene transfer event. To verify the function of the protein product RvNaRL, we established RNAi-mediated knock-down and CRISPR-Cas9-mediated knock-out experiments for the first time in R. viridis and applied them to this gene. The RvNaRL knock-down and knock-out cells exhibited significant growth only when ammonium was supplied. However, in contrast to the wild-type cells, no substantial growth was observed when nitrate was supplied. Such arrested growth in the absence of ammonium was attributed to impaired amino acid synthesis due to the deficiency of nitrogen supply from the nitrate assimilation pathway; this in turn resulted in the accumulation of excess photosynthetic products in the form of cytosolic polysaccharide grains, as observed. These results indicate that RvNaRL is certainly involved in nitrate assimilation by R. viridis. Thus, we inferred that R. viridis achieved its advanced kleptoplasty for photoautotrophy, owing to the acquisition of nitrate assimilation via horizontal gene transfer.}, }
@article {pmid37215039, year = {2023}, author = {Giengkam, S and Kullapanich, C and Wongsantichon, J and Adcox, HE and Gillespie, JJ and Salje, J}, title = {Orientia tsutsugamushi: analysis of the mobilome of a highly fragmented and repetitive genome reveals ongoing lateral gene transfer in an obligate intracellular bacterium.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37215039}, issn = {2692-8205}, support = {/WT_/Wellcome Trust/United Kingdom ; R21 AI156762/AI/NIAID NIH HHS/United States ; R21 AI166832/AI/NIAID NIH HHS/United States ; }, abstract = {The rickettsial human pathogen Orientia tsutsugamushi (Ot) is an obligate intracellular Gram-negative bacterium with one of the most highly fragmented and repetitive genomes of any organism. Around 50% of its ~2.3 Mb genome is comprised of repetitive DNA that is derived from the highly proliferated Rickettsiales amplified genetic element (RAGE). RAGE is an integrative and conjugative element (ICE) that is present in a single Ot genome in up to 92 copies, most of which are partially or heavily degraded. In this report, we analysed RAGEs in eight fully sequenced Ot genomes and manually curated and reannotated all RAGE-associated genes, including those encoding DNA mobilisation proteins, P-type (vir) and F-type (tra) type IV secretion system (T4SS) components, Ankyrin repeat- and tetratricopeptide repeat-containing effectors, and other piggybacking cargo. Originally, the heavily degraded Ot RAGEs led to speculation that they are remnants of historical ICEs that are no longer active. Our analysis, however, identified two Ot genomes harbouring one or more intact RAGEs with complete F-T4SS genes essential for mediating ICE DNA transfer. As similar ICEs have been identified in unrelated rickettsial species, we assert that RAGEs play an ongoing role in lateral gene transfer within the Rickettsiales. Remarkably, we also identified in several Ot genomes remnants of prophages with no similarity to other rickettsial prophages. Together these findings indicate that, despite their obligate intracellular lifestyle and host range restricted to mites, rodents and humans, Ot genomes are highly dynamic and shaped through ongoing invasions by mobile genetic elements and viruses.}, }
@article {pmid37213501, year = {2023}, author = {Huang, Y and Jiang, P and Liang, Z and Chen, R and Yue, Z and Xie, X and Guan, C and Fang, X}, title = {Assembly and analytical validation of a metagenomic reference catalog of human gut microbiota based on co-barcoding sequencing.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1145315}, pmid = {37213501}, issn = {1664-302X}, abstract = {Human gut microbiota is associated with human health and disease, and is known to have the second-largest genome in the human body. The microbiota genome is important for their functions and metabolites; however, accurate genomic access to the microbiota of the human gut is hindered due to the difficulty of cultivating and the shortcomings of sequencing technology. Therefore, we applied the stLFR library construction method to assemble the microbiota genomes and demonstrated that assembly property outperformed standard metagenome sequencing. Using the assembled genomes as references, SNP, INDEL, and HGT gene analyses were performed. The results demonstrated significant differences in the number of SNPs and INDELs among different individuals. The individual displayed a unique species variation spectrum, and the similarity of strains within individuals decreased over time. In addition, the coverage depth analysis of the stLFR method shows that a sequencing depth of 60X is sufficient for SNP calling. HGT analysis revealed that the genes involved in replication, recombination and repair, mobilome prophages, and transposons were the most transferred genes among different bacterial species in individuals. A preliminary framework for human gut microbiome studies was established using the stLFR library construction method.}, }
@article {pmid37213168, year = {2023}, author = {Youngblom, MA and Shockey, AC and Callaghan, MM and Dillard, JP and Pepperell, CS}, title = {The Gonococcal Genetic Island defines distinct sub-populations of Neisseria gonorrhoeae.}, journal = {Microbial genomics}, volume = {9}, number = {5}, pages = {}, pmid = {37213168}, issn = {2057-5858}, support = {R01 AI047958/AI/NIAID NIH HHS/United States ; R01 AI113287/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Neisseria gonorrhoeae/genetics ; DNA ; *Gonorrhea ; Type IV Secretion Systems/genetics ; Genomics ; }, abstract = {The incidence of gonorrhoea is increasing at an alarming pace, and therapeutic options continue to narrow as a result of worsening drug resistance. Neisseria gonorrhoeae is naturally competent, allowing the organism to adapt rapidly to selection pressures including antibiotics. A sub-population of N. gonorrhoeae carries the Gonococcal Genetic Island (GGI), which encodes a type IV secretion system (T4SS) that secretes chromosomal DNA. Previous research has shown that the GGI increases transformation efficiency in vitro, but the extent to which it contributes to horizontal gene transfer (HGT) during infection is unknown. Here we analysed genomic data from clinical isolates of N. gonorrhoeae to better characterize GGI+ and GGI- sub-populations and to delineate patterns of variation at the locus itself. We found the element segregating at an intermediate frequency (61%), and it appears to act as a mobile genetic element with examples of gain, loss, exchange and intra-locus recombination within our sample. We further found evidence suggesting that GGI+ and GGI- sub-populations preferentially inhabit distinct niches with different opportunities for HGT. Previously, GGI+ isolates were reported to be associated with more severe clinical infections, and our results suggest this could be related to metal-ion trafficking and biofilm formation. The co-segregation of GGI+ and GGI- isolates despite mobility of the element suggests that both niches inhabited by N. gonorrhoeae remain important to its overall persistence as has been demonstrated previously for cervical- and urethral-adapted sub-populations. These data emphasize the complex population structure of N. gonorrhoeae and its capacity to adapt to diverse niches.}, }
@article {pmid37213139, year = {2023}, author = {C Silva-de-Jesus, A and Rossi, CC and Pereira-Ribeiro, PM and Guaraldi, AL and Giambiagi-deMarval, M}, title = {Unusual carriage of virulence genes sasX/sesI/shsA by nosocomial Staphylococcus haemolyticus from Brazil.}, journal = {Future microbiology}, volume = {18}, number = {}, pages = {407-414}, doi = {10.2217/fmb-2022-0225}, pmid = {37213139}, issn = {1746-0921}, support = {23038.002486/2018-26//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 001463/2019, 010.00128/2016, 101056/2018, 200.895/2021, 201.071/2020, 211.554/2019, E-26/010.000172/2016//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; 305940/2018-0, PIBICUFRJ-CNPq 2020//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Humans ; Staphylococcus haemolyticus/genetics ; Virulence/genetics ; Brazil/epidemiology ; *Cross Infection/epidemiology ; *Staphylococcal Infections/epidemiology ; Staphylococcus epidermidis/genetics ; Hospitals ; Anti-Bacterial Agents ; }, abstract = {Background: Staphylococcus haemolyticus is an emerging threat in the nosocomial environment but only some virulence factors are known. Materials &amp; methods: The frequency of the sasX gene (or orthologues sesI/shsA), encoding an invasiveness-related surface-associated protein, in S. haemolyticus was detected in different hospitals in Rio de Janeiro. Results: 9.4% of strains were sasX/sesI/shsA-positive, some were in the context of the ΦSPβ-like prophage and devoid of CRISPR systems, indicating potential transferability of their virulence genes. Gene sequencing evidenced that Brazilian S. haemolyticus harbored sesI, instead of the usual sasX, while S. epidermidis had sasX instead of sesI, suggesting horizontal acquisition. Conclusion: The contexts of Brazilian sasX/sesI/shsA favor transfer, which is alarming given the difficulty in treating infections caused by S. haemolyticus.}, }
@article {pmid37210032, year = {2023}, author = {Yin, Y and Lou, T and Song, W and Wang, C and Wang, J}, title = {Production of medium chain fatty acids from antibiotic fermentation residuals pretreated by ionizing radiation: Elimination of antibiotic resistance genes.}, journal = {Bioresource technology}, volume = {382}, number = {}, pages = {129180}, doi = {10.1016/j.biortech.2023.129180}, pmid = {37210032}, issn = {1873-2976}, mesh = {*Anti-Bacterial Agents/pharmacology/metabolism ; Fermentation ; *Genes, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Radiation, Ionizing ; }, abstract = {The propagation of antibiotic resistance genes (ARGs) restricts the application of antibiotic fermentation residues (AFRs). This study investigated medium chain fatty acids (MCFA) production from AFRs, focusing on the effect of ionizing radiation pretreatment on the fates of ARGs. The results indicated that ionizing radiation pretreatment not only stimulated the MCFA production, but also inhibited the proliferation of ARGs. Radiation at 10-50 kGy decreased ARGs abundances by 0.6-21.1% at the end of fermentation process. Mobile genetic elements (MGEs) exhibited higher resistance to ionizing radiation, radiation over 30 kGy was required to suppress the proliferation of MGEs. Radiation at 50 kGy achieved an adequate inhibition to MGEs, and the degradation efficiency was 17.8-74.5% for different kinds of MGEs. This work suggested that ionizing radiation pretreatment could be a good option to ensure the safer application of AFRs by eliminating the ARGs and preventing the horizontal gene transfer of ARGs.}, }
@article {pmid37209559, year = {2023}, author = {Yuan, B and Zhang, Y and Zhang, Z and Lin, Z and Ma, Y and Sun, Y}, title = {Fluorescent tag reveals the potential mechanism of how indigenous soil bacteria affect the transfer of the wild fecal antibiotic resistance plasmid pKANJ7 in different habitat soils.}, journal = {Journal of hazardous materials}, volume = {455}, number = {}, pages = {131659}, doi = {10.1016/j.jhazmat.2023.131659}, pmid = {37209559}, issn = {1873-3336}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; *Drug Resistance, Microbial/genetics ; Ecosystem ; Genes, Bacterial ; Manure/microbiology ; Plasmids/genetics ; *Soil/chemistry ; *Soil Microbiology ; }, abstract = {Plasmids have increasingly become a point of concern since they act as a vital medium for the dissemination of antibiotic resistance genes (ARGs). Although indigenous soil bacteria are critical hosts for these plasmids, the mechanisms driving the transfer of antibiotic resistance plasmids (ARPs) have not been well researched. In this study, we tracked and visualized the colonization of the wild fecal antibiotic resistance plasmid pKANJ7 in indigenous bacteria of different habitat soils (unfertilized soil (UFS), chemical fertilized soil (CFS), and manure fertilized soil (MFS)). The results showed that plasmid pKANJ7 mainly transferred to the dominant genera in the soil and genera that were highly related to the donor. More importantly, plasmid pKANJ7 also transferred to intermediate hosts which aid in the survival and persistence of these plasmids in soil. Nitrogen levels also raised the plasmid transfer rate (14th day: UFS: 0.09%, CFS: 1.21%, MFS: 4.57%). Lastly, our structural equation model (SEM) showed that dominant bacteria shifts caused by nitrogen and loam were the major driver shaping the difference in the transfer of plasmid pKANJ7. Overall, our findings enhance the mechanistic understanding of indigenous soil bacteria's role in plasmid transfer and inform potential methods to prevent the transmission of plasmid-borne resistance in the environment.}, }
@article {pmid37204585, year = {2023}, author = {Lü, W and Ren, H and Ding, W and Li, H and Yao, X and Jiang, X}, title = {Rapid shifts in pond sediment microbiota in response to high ambient temperature in a water-sediment microcosm.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {29}, pages = {74358-74371}, doi = {10.1007/s11356-023-26823-7}, pmid = {37204585}, issn = {1614-7499}, support = {2017ZX07206//Major Science and Technology Program for Water Pollution Control and Treatment of China/ ; 41977322//National Natural Science Foundation of China/ ; 41907335//National Natural Science Foundation of China/ ; }, mesh = {*Ecosystem ; Temperature ; Ponds ; Hot Temperature ; *Microbiota ; Bacteria ; Climate Change ; Soil Microbiology ; }, abstract = {Unlike the extensive research on the response of soil microorganisms to high ambient temperature (HTA), the response of sediment microorganisms to HTA remains unclear. Understanding the response of sediment microorganisms to HTA is important to forecast their impacts on ecosystems and climate warming under projected climate change scenarios. Against the background of climate warming and frequent high ambient temperatures in summer, we conducted a laboratory incubation experiment to clarify the unique assembly characteristics of pond sediment bacterial communities at different temperatures (4, 10, 15, 25, 30 and 35 °C). The results showed that the structure and function of the microbial community in pond sediments at 35 °C were different from those under other temperatures; the microbial community structure at 35 °C had the most large modules and an average module size. Temperature and dissolved oxygen influenced the microbial community network modularity. The CO2 emission rates of pond sediments at 35 °C were significantly higher than those at other temperatures. At 35 °C, heterogeneous selection was the most important assembly process. Additionally, warming altered the microbial network structure and ecosystem functioning but not the microbial diversity or community composition, which may be related to horizontal gene transfer. Revealing the rapid response of pond sediment microorganisms to HTA is important for identifying their role in nutrient cycling and assessing the ecological impacts of climate warming and high ambient temperatures on inland water sediments.}, }
@article {pmid37201375, year = {2023}, author = {Huang, DQ and Wu, Q and Yang, JH and Jiang, Y and Li, ZY and Fan, NS and Jin, RC}, title = {Deciphering endogenous and exogenous regulations of anammox consortia in responding to lincomycin by multiomics: quorum sensing and CRISPR system.}, journal = {Water research}, volume = {239}, number = {}, pages = {120061}, doi = {10.1016/j.watres.2023.120061}, pmid = {37201375}, issn = {1879-2448}, mesh = {Animals ; Humans ; *Quorum Sensing ; *CRISPR-Cas Systems ; Lincomycin/pharmacology ; Multiomics ; Anaerobic Ammonia Oxidation ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The widespread use of antibiotics has created an antibiotic resistance genes (ARGs)-enriched environment, which causes high risks on human and animal health. Although antibiotics can be partially adsorbed and degraded in wastewater treatment processes, striving for a complete understanding of the microbial adaptive mechanism to antibiotic stress remains urgent. Combined with metagenomics and metabolomics, this study revealed that anammox consortia could adapt to lincomycin by spontaneously changing the preference for metabolite utilization and establishing interactions with eukaryotes, such as Ascomycota and Basidiomycota. Specifically, quorum sensing (QS) based microbial regulation and the ARGs transfer mediated by clustered regularly interspaced short palindromic repeats (CRISPR) system and global regulatory genes were the principal adaptive strategies. Western blotting results validated that Cas9 and TrfA were mainly responsible for the alteration of ARGs transfer pathway. These findings highlight the potential adaptative mechanism of microbes to antibiotic stress and fill gaps in horizontal gene transfer pathways in the anammox process, further facilitating the ARGs control through molecular and synthetic biology techniques.}, }
@article {pmid37196739, year = {2023}, author = {Zhang, W and Yu, C and Yin, S and Chang, X and Chen, K and Xing, Y and Yang, Y}, title = {Transmission and retention of antibiotic resistance genes (ARGs) in chicken and sheep manure composting.}, journal = {Bioresource technology}, volume = {382}, number = {}, pages = {129190}, doi = {10.1016/j.biortech.2023.129190}, pmid = {37196739}, issn = {1873-2976}, mesh = {Animals ; Sheep/genetics ; *Composting ; Chickens/genetics ; Genes, Bacterial/genetics ; Manure/microbiology ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; }, abstract = {Transmission of ARGs during composting with different feedstocks (i.e., sheep manure (SM), chicken manure (CM) and mixed manure (MM, SM:CM = 3:1 ratio) was studied by metagenomic sequencing. 53 subtypes of ARGs for 22 types of antibiotics were identified as commonly present in these compost mixes; among them, CM had higher abundance of ARGs, 1.69 times than that in SM, while the whole elimination rate of CM, MM and SM were 55.2%, 54.7% and 42.9%, respectively. More than 50 subtypes of ARGs (with 8.6%, 11.4% and 20.9% abundance in the initial stage in CM, MM and SM composting) were "diehard" ARGs, and their abundance grew significantly to 56.5%, 63.2% and 69.9% at the mature stage. These "diehard" ARGs were transferred from initial hosts of pathogenic and/or probiotic bacteria to final hosts of thermophilic bacteria, by horizontal gene transfer (HGT) via mobile gene elements (MGEs), and became rooted in composting products.}, }
@article {pmid37191574, year = {2023}, author = {Zhu, Q and Gao, S and Xiao, B and He, Z and Hu, S}, title = {Plasmer: an Accurate and Sensitive Bacterial Plasmid Prediction Tool Based on Machine Learning of Shared k-mers and Genomic Features.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0464522}, pmid = {37191574}, issn = {2165-0497}, mesh = {*Genomics/methods ; Plasmids/genetics ; *Genome, Bacterial ; Machine Learning ; }, abstract = {Identification of plasmids in bacterial genomes is critical for many factors, including horizontal gene transfer, antibiotic resistance genes, host-microbe interactions, cloning vectors, and industrial production. There are several in silico methods to predict plasmid sequences in assembled genomes. However, existing methods have evident shortcomings, such as unbalance in sensitivity and specificity, dependency on species-specific models, and performance reduction in sequences shorter than 10 kb, which has limited their scope of applicability. In this work, we proposed Plasmer, a novel plasmid predictor based on machine-learning of shared k-mers and genomic features. Unlike existing k-mer or genomic-feature based methods, Plasmer employs the random forest algorithm to make predictions using the percent of shared k-mers with plasmid and chromosome databases combined with other genomic features, including alignment E value and replicon distribution scores (RDS). Plasmer can predict on multiple species and has achieved an average the area under the curve (AUC) of 0.996 with accuracy of 98.4%. Compared to existing methods, tests of both sliding sequences and simulated and de novo assemblies have consistently shown that Plasmer has outperforming accuracy and stable performance across long and short contigs above 500 bp, demonstrating its applicability for fragmented assemblies. Plasmer also has excellent and balanced performance on both sensitivity and specificity (both >0.95 above 500 bp) with the highest F1-score, which has eliminated the bias on sensitivity or specificity that was common in existing methods. Plasmer also provides taxonomy classification to help identify the origin of plasmids. IMPORTANCE In this study, we proposed a novel plasmid prediction tool named Plasmer. Technically, unlike existing k-mer or genomic features-based methods, Plasmer is the first tool to combine the advantages of the percent of shared k-mers and the alignment score of genomic features. This has given Plasmer (i) evident improvement in performance compared to other methods, with the best F1-score and accuracy on sliding sequences, simulated contigs, and de novo assemblies; (ii) applicability for contigs above 500 bp with highest accuracy, enabling plasmid prediction in fragmented short-read assemblies; (iii) excellent and balanced performance between sensitivity and specificity (both >0.95 above 500 bp) with the highest F1-score, which eliminated the bias on sensitivity or specificity that commonly existed in other methods; and (iv) no dependency of species-specific training models. We believe that Plasmer provides a more reliable alternative for plasmid prediction in bacterial genome assemblies.}, }
@article {pmid37187278, year = {2023}, author = {Zhou, Q and Zhang, J and Fang, Q and Zhang, M and Wang, X and Zhang, D and Pan, X}, title = {Microplastic biodegradability dependent responses of plastisphere antibiotic resistance to simulated freshwater-seawater shift in onshore marine aquaculture zones.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {331}, number = {Pt 2}, pages = {121828}, doi = {10.1016/j.envpol.2023.121828}, pmid = {37187278}, issn = {1873-6424}, mesh = {*Microplastics ; *Anti-Bacterial Agents/pharmacology ; Plastics/pharmacology ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Fresh Water/microbiology ; Seawater/microbiology ; Aquaculture ; Water ; }, abstract = {MPs carrying ARGs can travel between freshwater and seawater due to intensive land-sea interaction in onshore marine aquaculture zones (OMAZ). However, the response of ARGs in plastisphere with different biodegradability to freshwater-seawater shift is still unknown. In this study, ARG dynamics and associated microbiota on biodegradable poly (butyleneadipate-co-terephthalate) (PBAT) and non-biodegradable polyethylene terephthalate (PET) MPs were investigated through a simulated freshwater-seawater shift. The results exhibited that freshwater-seawater shift significantly influenced ARG abundance in plastisphere. The relative abundance of most studied ARGs decreased rapidly in plastisphere after they entered seawater from freshwater but increased on PBAT after MPs entered freshwater from seawater. Besides, the high relative abundance of multi-drug resistance (MDR) genes occurred in plastisphere, and the co-change between most ARGs and mobile genetic elements indicated the role of horizontal gene transfer on ARG regulation. Proteobacteria was dominant phylum in plastisphere and the dominant genera, such as Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Afipia, Gemmobacter and Enhydrobacter, were significantly associated with qnrS, tet and MDR genes in plastisphere. Moreover, after MPs entered new water environment, the ARGs and microbiota genera in plastisphere changed significantly and tended to converge with those in receiving water. These results indicated that MP biodegradability and freshwater-seawater interaction influenced potential hosts and distributions of ARGs, of which biodegradable PBAT posed a high risk in ARG dissemination. This study would be helpful for understanding the impact of biodegradable MP pollution on spread of antibiotic resistance in OMAZ.}, }
@article {pmid37185344, year = {2023}, author = {Riccardi, C and Koper, P and Innocenti, G and diCenzo, GC and Fondi, M and Mengoni, A and Perrin, E}, title = {Independent origins and evolution of the secondary replicons of the class Gammaproteobacteria.}, journal = {Microbial genomics}, volume = {9}, number = {5}, pages = {}, pmid = {37185344}, issn = {2057-5858}, mesh = {Genome, Bacterial ; Plasmids/genetics ; Replicon/genetics ; *Sinorhizobium meliloti/genetics ; *Gammaproteobacteria/genetics ; }, abstract = {Multipartite genomes, consisting of more than one replicon, have been found in approximately 10 % of bacteria, many of which belong to the phylum Proteobacteria. Many aspects of their origin and evolution, and the possible advantages related to this type of genome structure, remain to be elucidated. Here, we performed a systematic analysis of the presence and distribution of multipartite genomes in the class Gammaproteobacteria, which includes several genera with diverse lifestyles. Within this class, multipartite genomes are mainly found in the order Alteromonadales (mostly in the genus Pseudoalteromonas) and in the family Vibrionaceae. Our data suggest that the emergence of secondary replicons in Gammaproteobacteria is rare and that they derive from plasmids. Despite their multiple origins, we highlighted the presence of evolutionary trends such as the inverse proportionality of the genome to chromosome size ratio, which appears to be a general feature of bacteria with multipartite genomes irrespective of taxonomic group. We also highlighted some functional trends. The core gene set of the secondary replicons is extremely small, probably limited to essential genes or genes that favour their maintenance in the genome, while the other genes are less conserved. This hypothesis agrees with the idea that the primary advantage of secondary replicons could be to facilitate gene acquisition through horizontal gene transfer, resulting in replicons enriched in genes associated with adaptation to different ecological niches. Indeed, secondary replicons are enriched both in genes that could promote adaptation to harsh environments, such as those involved in antibiotic, biocide and metal resistance, and in functional categories related to the exploitation of environmental resources (e.g. carbohydrates), which can complement chromosomal functions.}, }
@article {pmid37178001, year = {2023}, author = {Vesel, N and Iseli, C and Guex, N and Lemopoulos, A and Blokesch, M}, title = {DNA modifications impact natural transformation of Acinetobacter baumannii.}, journal = {Nucleic acids research}, volume = {51}, number = {11}, pages = {5661-5677}, pmid = {37178001}, issn = {1362-4962}, mesh = {*Acinetobacter baumannii/genetics ; DNA, Bacterial ; DNA Methylation ; *Drug Resistance, Bacterial ; DNA Restriction-Modification Enzymes ; }, abstract = {Acinetobacter baumannii is a dangerous nosocomial pathogen, especially due to its ability to rapidly acquire new genetic traits, including antibiotic resistance genes (ARG). In A. baumannii, natural competence for transformation, one of the primary modes of horizontal gene transfer (HGT), is thought to contribute to ARG acquisition and has therefore been intensively studied. However, knowledge regarding the potential role of epigenetic DNA modification(s) on this process remains lacking. Here, we demonstrate that the methylome pattern of diverse A. baumannii strains differs substantially and that these epigenetic marks influence the fate of transforming DNA. Specifically, we describe a methylome-dependent phenomenon that impacts intra- and inter-species DNA exchange by the competent A. baumannii strain A118. We go on to identify and characterize an A118-specific restriction-modification (RM) system that impairs transformation when the incoming DNA lacks a specific methylation signature. Collectively, our work contributes towards a more holistic understanding of HGT in this organism and may also aid future endeavors towards tackling the spread of novel ARGs. In particular, our results suggest that DNA exchanges between bacteria that share similar epigenomes are favored and could therefore guide future research into identifying the reservoir(s) of dangerous genetic traits for this multi-drug resistant pathogen.}, }
@article {pmid37177929, year = {2023}, author = {Lu, JW and Xu, CY and Hu, C and Liu, SR and Li, F}, title = {[Occurrence Characteristics of Microplastics and Metal Elements in the Surface Water of Huangpu River and Their Associations with Metal Resistance Genes].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {44}, number = {5}, pages = {2551-2561}, doi = {10.13227/j.hjkx.202206267}, pmid = {37177929}, issn = {0250-3301}, mesh = {*Microplastics ; Genes, Bacterial ; Plastics ; Rivers ; Water ; Metals ; *Mercury ; Anti-Bacterial Agents ; }, abstract = {Urban rivers have been regarded as the "hotspots" for microplastic (MPs) and metal contamination as they play important roles in pollution migration. However, as important sinks and sources of resistance genes, there has been little to no research investigating the associations between MPs, metal contaminations, and metal resistance genes (MRGs). Ten water samples were collected from the Huangpu River in situ; along with metal elements, MPs characteristics analyzed. Metal resistance genes and mobile genetic elements (MGEs) in waters and MPs were detected using metagenomic technology. As a result, the highest metal concentration was that of Sb in surface water (3.16±0.419) μg·L[-1]. The average abundance of MPs was (1.78±0.84) n·L[-1], and the peak levels located in industrial and densely populated areas, which was significantly higher than those in agricultural and low population density areas. Fibrous, small-size (<0.5 mm), and transparent polyethylene terephthalate (PET) were the largest contributors of MPs. Eighteen MRGs were detected in all the samples. The relative abundance of MRGs in water was 1.68±0.21. The most dominant MRGs subtypes were merR and ruvB, which are subtypes resistant to mercury and Multi_metals. Correlation analysis showed that chromium and nickel in waters were significantly positively associated with MRG-Cr, MRG-Ni, and Multi_metals resistance genes. For MPs particles, the relative abundance of MRGs was 1.63±0.53. The most dominant MRGs subtypes were merT-P and copB, which also belong to mercury-resistant and Multi_metals. The Multi_metals resistance gene, ctpC, cueA, czrA, kmtR, etc., had significant positive associations with Ni, Cr, and Sb in waters. Compared with water samples, MPs selectively enriched merT-P, copB, ziaA, sodA, and dmeF. Additionally, the co-occurrence patterns of MRGs and MGEs were explored based on network analysis. In water samples, the transposases (tnpA_1 and tnpA_2), integrase (qacEdelta), and insertion sequence (IS91) were the major contributors of the horizontal gene transfer (HGT) of specific MRGs. Multiple subtypes resistant to copper and Multi_metals resistance genes on MPs were positively associated with IncFIC(FII), Rep7, rep7, and rep13, which were subtypes of plasmids. The presence of MPs exerted a significant impact on HGT of specific MRGs mediated by plasmids.}, }
@article {pmid37173437, year = {2023}, author = {Feng, SY and Hauck, Y and Morgene, F and Mohammedi, R and Mirouze, N}, title = {The complex regulation of competence in Staphylococcus aureus under microaerobic conditions.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {512}, pmid = {37173437}, issn = {2399-3642}, mesh = {Humans ; *Staphylococcus aureus/genetics ; *Gene Expression Profiling ; }, abstract = {To perform natural transformation, one of the three main Horizontal Gene Transfer mechanisms, bacteria need to enter a physiological differentiated state called genetic competence. Interestingly, new bacteria displaying such aptitude are often discovered, and one of the latest is the human pathogen Staphylococcus aureus.Here, we show an optimized protocol, based on planktonic cells cultures, leading to a large percentage of the population activating the development of competence and a significant improvement of S. aureus natural transformation efficiencies. Taking advantage of these conditions, we perform transcriptomics analyses to characterize the regulon of each central competence regulator. SigH and ComK1 are both found essential for activating natural transformation genes but also important for activation or repression of peripheral functions. Even though ComK2 is not found important for the control of transformation genes, its regulon shows an important overlap with that of SigH and ComK1. Finally, we propose that microaerobic conditions, sensed by the SrrAB two-component system, are key to activate competence in S. aureus.}, }
@article {pmid37173063, year = {2023}, author = {Ayllón, MA and Vainio, EJ}, title = {Mycoviruses as a part of the global virome: Diversity, evolutionary links and lifestyle.}, journal = {Advances in virus research}, volume = {115}, number = {}, pages = {1-86}, doi = {10.1016/bs.aivir.2023.02.002}, pmid = {37173063}, issn = {1557-8399}, mesh = {*Fungal Viruses/genetics ; Phylogeny ; Virome ; *Viruses/genetics ; RNA, Double-Stranded ; *RNA Viruses/genetics ; RNA, Viral/genetics ; Genome, Viral ; }, abstract = {Knowledge of mycovirus diversity, evolution, horizontal gene transfer and shared ancestry with viruses infecting distantly related hosts, such as plants and arthropods, has increased vastly during the last few years due to advances in the high throughput sequencing methodologies. This also has enabled the discovery of novel mycoviruses with previously unknown genome types, mainly new positive and negative single-stranded RNA mycoviruses ((+) ssRNA and (-) ssRNA) and single-stranded DNA mycoviruses (ssDNA), and has increased our knowledge of double-stranded RNA mycoviruses (dsRNA), which in the past were thought to be the most common viruses infecting fungi. Fungi and oomycetes (Stramenopila) share similar lifestyles and also have similar viromes. Hypothesis about the origin and cross-kingdom transmission events of viruses have been raised and are supported by phylogenetic analysis and by the discovery of natural exchange of viruses between different hosts during virus-fungus coinfection in planta. In this review we make a compilation of the current information on the genome organization, diversity and taxonomy of mycoviruses, discussing their possible origins. Our focus is in recent findings suggesting the expansion of the host range of many viral taxa previously considered to be exclusively fungal, but we also address factors affecting virus transmissibility and coexistence in single fungal or oomycete isolates, as well as the development of synthetic mycoviruses and their use in investigating mycovirus replication cycles and pathogenicity.}, }
@article {pmid37172383, year = {2023}, author = {Liu, YJ and Li, ZH and He, YT and Yuan, L and Sheng, GP}, title = {Antibiotic resistomes in face-mask biofilm along an urban river: Multiple drivers and co-occurrence with human opportunistic pathogens.}, journal = {Journal of hazardous materials}, volume = {455}, number = {}, pages = {131587}, pmid = {37172383}, issn = {1873-3336}, mesh = {Humans ; *Genes, Bacterial ; Masks ; Rivers ; Anti-Bacterial Agents/pharmacology/analysis ; Pandemics ; *COVID-19 ; Water ; Biofilms ; }, abstract = {Discarded face masks from the global COVID-19 pandemic have contributed significantly to plastic pollution in surface water, whereas their potential as a reservoir for aquatic pollutants is not well understood. Herein, we conducted a field experiment along a human-impacted urban river, investigating the variations of antibiotic resistance genes (ARGs), pathogens, and water-borne contaminants in commonly-used face masks. Results showed that high-biomass biofilms formed on face masks selectively enriched more ARGs than stone biofilm (0.08-0.22 vs 0.07-0.15 copies/16 S rRNA gene copies) from bulk water, which mainly due to unique microbial communities, enhanced horizontal gene transfer, and selective pressure of accumulated contaminants based on redundancy analysis and variation partitioning analysis. Several human opportunistic pathogens (e.g., Acinetobacter, Escherichia-Shigella, Bacillus, and Klebsiella), which are considered potential ARG carriers, were also greatly concentrated in face-mask biofilms, imposing a potential threat to aquatic ecological environment and human health. Moreover, wastewater treatment plant effluents, as an important source of pollutants to urban rivers, further aggravated the abundances of ARGs and opportunistic pathogens in face-mask biofilms. Our findings demonstrated that discarded face masks provide a hotspot for the proliferation and spread of ARGs and pathogens in urban water, highlighting the urgent requirement for implementing stricter regulations in face mask disposal.}, }
@article {pmid37172034, year = {2023}, author = {Green, VE and Klancher, CA and Yamamoto, S and Dalia, AB}, title = {The molecular mechanism for carbon catabolite repression of the chitin response in Vibrio cholerae.}, journal = {PLoS genetics}, volume = {19}, number = {5}, pages = {e1010767}, pmid = {37172034}, issn = {1553-7404}, support = {R35 GM128674/GM/NIGMS NIH HHS/United States ; R01 GM130874/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Vibrio cholerae/genetics/metabolism ; Chitin/genetics/metabolism ; *Catabolite Repression/genetics ; Oligosaccharides/genetics/metabolism ; Gene Expression Regulation, Bacterial ; }, abstract = {Vibrio cholerae is a facultative pathogen that primarily occupies marine environments. In this niche, V. cholerae commonly interacts with the chitinous shells of crustacean zooplankton. As a chitinolytic microbe, V. cholerae degrades insoluble chitin into soluble oligosaccharides. Chitin oligosaccharides serve as both a nutrient source and an environmental cue that induces a strong transcriptional response in V. cholerae. Namely, these oligosaccharides induce the chitin sensor, ChiS, to activate the genes required for chitin utilization and horizontal gene transfer by natural transformation. Thus, interactions with chitin impact the survival of V. cholerae in marine environments. Chitin is a complex carbon source for V. cholerae to degrade and consume, and the presence of more energetically favorable carbon sources can inhibit chitin utilization. This phenomenon, known as carbon catabolite repression (CCR), is mediated by the glucose-specific Enzyme IIA (EIIAGlc) of the phosphoenolpyruvate-dependent phosphotransferase system (PTS). In the presence of glucose, EIIAGlc becomes dephosphorylated, which inhibits ChiS transcriptional activity by an unknown mechanism. Here, we show that dephosphorylated EIIAGlc interacts with ChiS. We also isolate ChiS suppressor mutants that evade EIIAGlc-dependent repression and demonstrate that these alleles no longer interact with EIIAGlc. These findings suggest that EIIAGlc must interact with ChiS to exert its repressive effect. Importantly, the ChiS suppressor mutations we isolated also relieve repression of chitin utilization and natural transformation by EIIAGlc, suggesting that CCR of these behaviors is primarily regulated through ChiS. Together, our results reveal how nutrient conditions impact the fitness of an important human pathogen in its environmental reservoir.}, }
@article {pmid37168121, year = {2023}, author = {Tao, S and Zhou, D and Chen, H and Li, N and Zheng, L and Fang, Y and Xu, Y and Jiang, Q and Liang, W}, title = {Analysis of genetic structure and function of clustered regularly interspaced short palindromic repeats loci in 110 Enterococcus strains.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1177841}, pmid = {37168121}, issn = {1664-302X}, abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR) and their CRISPR-associated proteins (Cas) are an adaptive immune system involved in specific defenses against the invasion of foreign mobile genetic elements, such as plasmids and phages. This study aims to analyze the gene structure and to explore the function of the CRISPR system in the Enterococcus genome, especially with regard to drug resistance. The whole genome information of 110 enterococci was downloaded from the NCBI database to analyze the distribution and the structure of the CRISPR-Cas system including the Cas gene, repeat sequences, and spacer sequence of the CRISPR-Cas system by bioinformatics methods, and to find drug resistance-related genes and analyze the relationship between them and the CRISPR-Cas system. Multilocus sequence typing (MLST) of enterococci was performed against the reference MLST database. Information on the drug resistance of Enterococcus was retrieved from the CARD database, and its relationship to the presence or absence of CRISPR was statistically analyzed. Among the 110 Enterococcus strains, 39 strains (35.45%) contained a complete CRISPR-Cas system, 87 CRISPR arrays were identified, and 62 strains contained Cas gene clusters. The CRISPR system in the Enterococcus genome was mainly type II-A (59.68%), followed by type II-C (33.87%). The phylogenetic analysis of the cas1 gene sequence was basically consistent with the typing of the CRISPR-Cas system. Of the 74 strains included in the study for MLST typing, only 19 (25.68%) were related to CRISPR-Cas typing, while the majority of the strains (74.32%) of MLST typing were associated with the untyped CRISPR system. Additionally, the CRISPR-Cas system may only be related to the carrying rate of some drug-resistant genes and the drug-resistant phenotype. In conclusion, the distribution of the enterococcus CRISPR-Cas system varies greatly among different species and the presence of CRISPR loci reduces the horizontal transfer of some drug resistance genes.}, }
@article {pmid37167868, year = {2023}, author = {Cai, P and Chen, Q and Du, W and Yang, S and Li, J and Cai, H and Zhao, X and Sun, W and Xu, N and Wang, J}, title = {Deciphering the dynamics of metal and antibiotic resistome profiles under different metal(loid) contamination levels.}, journal = {Journal of hazardous materials}, volume = {455}, number = {}, pages = {131567}, doi = {10.1016/j.jhazmat.2023.131567}, pmid = {37167868}, issn = {1873-3336}, mesh = {*Genes, Bacterial ; *Anti-Bacterial Agents/pharmacology ; Metals ; Drug Resistance, Microbial/genetics ; Sewage ; }, abstract = {Metal(loid) contaminations pose considerable threats to ecological security and public health, yet little is known about the dynamics of metal resistance genes (MRGs) and antibiotic resistance genes (ARGs) under different metal(loid) contamination levels. Here, we provided a systematic investigation of MRGs and ARGs in three zones (Zones I, II, and III) with different metal(loid) contamination levels across an abandoned sewage reservoir. More diverse MRGs and ARGs were detected from the high-contaminated Zone I and the moderate-contaminated Zone II, while the abundant MGEs (mobile genetic elements) potentially enhanced the horizontal gene transfer potential and the resistome diversity in Zone I. Particularly, resistome hosts represented by Thiobacillus, Ramlibacter, and Dyella were prevalent in Zone II, promoting the vertical gene transfer of MRGs and ARGs. The highest health risk of ARGs was predicted for Zone I (about 7.58% and 0.48% of ARGs classified into Rank I and Rank II, respectively), followed by Zone II (2.11% and 0%) and Zone III (0% and 0%). However, the ARGs co-occurring with MRGs might exhibit low proportions and low health risks (all were Rank IV) in the three zones. Overall, these findings uncovered the dynamic responses of resistomes and their hosts to different metal(loid) contamination levels, contributing to formulating accurate management and bioremediation countermeasures for various metal(loid) contaminated environments.}, }
@article {pmid37166501, year = {2023}, author = {Weber, M and Göpfert, B and von Wezyk, S and Savin-Hoffmeyer, M and Lipski, A}, title = {Correlation between Bacterial Cell Density and Abundance of Antibiotic Resistance on Milking Machine Surfaces Assessed by Cultivation and Direct qPCR Methods.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1676-1685}, pmid = {37166501}, issn = {1432-184X}, support = {41.2015.02//Ministry for Environment, Agriculture, Conservation and Consumer Protection of the State of North Rhine-Westphalia/ ; }, mesh = {Animals ; Cattle ; Female ; RNA, Ribosomal, 16S/genetics ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics ; Tetracycline ; Cloxacillin ; Drug Resistance, Microbial/genetics ; Cell Count ; Genes, Bacterial ; }, abstract = {The relative abundance of antibiotic-resistant bacteria and antibiotic-resistance genes was surveyed for different parts of a milking machine. A cultivation approach based on swab samples showed a highly diverse microbiota, harboring resistances against cloxacillin, ampicillin, penicillin, and tetracycline. This approach demonstrated a substantial cloxacillin resistance of numerous taxa within milking machine microbiota coming along with regular use of cloxacillin for dry-off therapy of dairy cows. For the less abundant tetracycline-resistant bacteria we found a positive correlation between microbial cell density and relative abundance of tetracycline-resistant microorganisms (R[2] = 0.73). This indicated an accelerated dispersion of resistant cells for sampling locations with high cell density. However, the direct quantification of the tetM gene from the swap samples by qPCR showed the reverse relation to bacterial density if normalized against the abundance of 16S rRNA genes (R[2] = 0.88). The abundance of 16S rRNA genes was analyzed by qPCR combined with a propidium monoazide treatment, which eliminates 16S rRNA gene signals in negative controls.}, }
@article {pmid37164096, year = {2023}, author = {Gao, Y and Luo, W and Zhang, H and Chen, Y and Li, Z and Wei, G and Chen, W}, title = {Enrichment of antibiotic resistance genes in roots is related to specific bacterial hosts and soil properties in two soil-plant systems.}, journal = {The Science of the total environment}, volume = {886}, number = {}, pages = {163933}, doi = {10.1016/j.scitotenv.2023.163933}, pmid = {37164096}, issn = {1879-1026}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; Soil/chemistry ; RNA, Ribosomal, 16S ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Soil Microbiology ; Endophytes ; }, abstract = {Soil microorganisms carrying antibiotic resistance genes (ARGs) can colonize plants as endophytes, posing a huge risk to human health. However, the distribution and transmission patterns of ARGs in different soil-plant systems are unclear. Here, we investigated the distribution of ARGs and the microbial communities in the soil-wheat and soil-cucumber systems by quantitative PCR (qPCR) and 16S rRNA gene sequencing. The results showed that the relative abundances of seven ARGs and intI1 in roots were higher than those of other samples in both soil-plant systems. Pseudomonas, Enterobacteriaceae, Rhizobiales and Gammaproteobacteria were dominant potential bacterial hosts of endophytic ARGs, with enrichment patterns similar to that of ARGs in roots. In addition, more ARGs were significantly positively correlated with intI1 in roots, indicating that ARGs may be more prone to horizontal gene transfer (HGT). Variation partitioning analysis (VPA) and structural equation models (SEM) revealed that the variations of ARGs were mainly directly affected by the HGT of intI1 and indirectly affected by soil properties in roots. These results demonstrated that root could have a strong proliferative effect on ARGs entering host plant endophytes. Overall, our findings enhanced the understanding distribution patterns of ARGs in different soil-plant systems, and provided an effective basis for developing measures to minimize the spread of ARGs.}, }
@article {pmid37158891, year = {2023}, author = {Tapia, SM and Macías, LG and Pérez-Torrado, R and Daroqui, N and Manzanares, P and Querol, A and Barrio, E}, title = {A novel aminotransferase gene and its regulator acquired in Saccharomyces by a horizontal gene transfer event.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {102}, pmid = {37158891}, issn = {1741-7007}, mesh = {*Transaminases ; *Saccharomyces/genetics ; Gene Transfer, Horizontal ; Phylogeny ; Saccharomyces cerevisiae ; Amino Acids ; Aminoisobutyric Acids ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT) is an evolutionary mechanism of adaptive importance, which has been deeply studied in wine S. cerevisiae strains, where those acquired genes conferred improved traits related to both transport and metabolism of the nutrients present in the grape must. However, little is known about HGT events that occurred in wild Saccharomyces yeasts and how they determine their phenotypes.<br><br>RESULTS: Through a comparative genomic approach among Saccharomyces species, we detected a subtelomeric segment present in the S. uvarum, S. kudriavzevii, and S. eubayanus species, belonging to the first species to diverge in the Saccharomyces genus, but absent in the other Saccharomyces species. The segment contains three genes, two of which were characterized, named DGD1 and DGD2. DGD1 encodes dialkylglicine decarboxylase, whose specific substrate is the non-proteinogenic amino acid 2-aminoisobutyric acid (AIB), a rare amino acid present in some antimicrobial peptides of fungal origin. DGD2 encodes putative zinc finger transcription factor, which is essential to induce the AIB-dependent expression of DGD1. Phylogenetic analysis showed that DGD1 and DGD2 are closely related to two adjacent genes present in Zygosaccharomyces.<br><br>CONCLUSIONS: The presented results show evidence of an early HGT event conferring new traits to the ancestor of the Saccharomyces genus that could be lost in the evolutionary more recent Saccharomyces species, perhaps due to loss of function during the colonization of new habitats.}, }
@article {pmid37156983, year = {2023}, author = {Calderón-Franco, D and van Loosdrecht, MCM and Abeel, T and Weissbrodt, DG}, title = {Catch me if you can: capturing microbial community transformation by extracellular DNA using Hi-C sequencing.}, journal = {Antonie van Leeuwenhoek}, volume = {116}, number = {7}, pages = {667-685}, pmid = {37156983}, issn = {1572-9699}, support = {15812//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; }, mesh = {*Wastewater ; Anti-Bacterial Agents/therapeutic use ; Plasmids/genetics ; DNA ; *Microbiota ; Gene Transfer, Horizontal ; Conjugation, Genetic ; }, abstract = {The transformation of environmental microorganisms by extracellular DNA is an overlooked mechanism of horizontal gene transfer and evolution. It initiates the acquisition of exogenous genes and propagates antimicrobial resistance alongside vertical and conjugative transfers. We combined mixed-culture biotechnology and Hi-C sequencing to elucidate the transformation of wastewater microorganisms with a synthetic plasmid encoding GFP and kanamycin resistance genes, in the mixed culture of chemostats exposed to kanamycin at concentrations representing wastewater, gut and polluted environments (0.01-2.5-50-100 mg L[-1]). We found that the phylogenetically distant Gram-negative Runella (102 Hi-C links), Bosea (35), Gemmobacter (33) and Zoogloea (24) spp., and Gram-positive Microbacterium sp. (90) were transformed by the foreign plasmid, under high antibiotic exposure (50 mg L[-1]). In addition, the antibiotic pressure shifted the origin of aminoglycoside resistance genes from genomic DNA to mobile genetic elements on plasmids accumulating in microorganisms. These results reveal the power of Hi-C sequencing to catch and surveil the transfer of xenogenetic elements inside microbiomes.}, }
@article {pmid37156401, year = {2023}, author = {Gartzonika, K and Politi, L and Mavroidi, A and Tsantes, AG and Spanakis, N and Priavali, E and Vrioni, G and Tsakris, A}, title = {High prevalence of clonally related ST182 NDM-1-producing Enterobacter cloacae complex clinical isolates in Greece.}, journal = {International journal of antimicrobial agents}, volume = {62}, number = {1}, pages = {106837}, doi = {10.1016/j.ijantimicag.2023.106837}, pmid = {37156401}, issn = {1872-7913}, mesh = {Humans ; Multilocus Sequence Typing ; *Enterobacter cloacae/genetics ; Greece/epidemiology ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Prevalence ; Phylogeny ; Retrospective Studies ; beta-Lactamases/genetics ; Carbapenems/pharmacology ; Plasmids/genetics ; Escherichia coli/genetics ; Microbial Sensitivity Tests ; }, abstract = {NDM-type metallo-β-lactamase (MBL)-producing Enterobacterales remain uncommon in the European region, especially among species other than Klebsiella pneumoniae and Escherichia coli. The aim of this study was to describe epidemiological and molecular characteristics of a widespread NDM-1-producing Enterobacter cloacae complex outbreak in Greece. Over a 6-year period (March 2016-March 2022), a retrospective study was conducted in a tertiary care Greek hospital. Ninety single-patient carbapenem-non-susceptible E. cloacae complex clinical isolates were recovered consecutively. The isolates were subjected to further investigation, including antimicrobial susceptibility testing and combined disc tests for carbapenemase production, polymerase chain reaction and sequencing for resistance genes, molecular fingerprinting by pulsed-field gel electrophoresis (PFGE), plasmid profiling, replicon typing, conjugation experiments, genotyping by multi-locus sequence typing (MLST), whole-genome sequencing and phylogenetic analysis. Phenotypic and molecular testing confirmed the presence of blaNDM-1 in 47 (52.2%) of the E. cloacae complex isolates. MLST analysis clustered all but four of the NDM-1 producers into a single MLST sequence type (ST182), whereas single isolates belonged to different sequence types (ST190, ST269, ST443 and ST743). PFGE analysis revealed that ST182 isolates were clustered into a single clonal type, with three subtypes, which differed from the clonal types detected among the remaining carbapenem non-susceptible E. cloacae complex isolates identified during the study period. All ST182 blaNDM-1-carrying isolates also harboured the blaACT-16 AmpC gene, while the blaESBL, blaOXA-1 and blaTEM-1 genes were detected in most cases. In all clonal isolates, the blaNDM-1 gene was located on an IncA/C-type plasmid, and flanked upstream by an ISAba125 element and downstream by bleMBL. Conjugation experiments failed to produce carbapenem-resistant transconjugants, indicating a low dynamic for horizontal gene transfer. Application of enforced infection control measures led to the absence of new NDM-positive cases for periods of time during the survey. This study represents the largest clonal outbreak of NDM-producing E. cloacae complex in Europe.}, }
@article {pmid37156383, year = {2023}, author = {Tyrrell, C and Do, TT and Leigh, RJ and Burgess, CM and Brennan, FP and Walsh, F}, title = {Differential impact of swine, bovine and poultry manure on the microbiome and resistome of agricultural grassland.}, journal = {The Science of the total environment}, volume = {886}, number = {}, pages = {163926}, doi = {10.1016/j.scitotenv.2023.163926}, pmid = {37156383}, issn = {1879-1026}, mesh = {Animals ; Cattle ; Swine ; *Genes, Bacterial ; Manure/analysis ; Poultry ; RNA, Ribosomal, 16S/genetics ; Grassland ; Drug Resistance, Microbial/genetics ; Soil Microbiology ; Agriculture ; *Microbiota ; Bacteria/genetics ; Anti-Bacterial Agents/pharmacology/analysis ; Soil ; Real-Time Polymerase Chain Reaction ; Poaceae ; }, abstract = {Land spreading of animal manure is an essential process in agriculture. Despite the importance of grassland in global food security the potential of the grass phyllosphere as a reservoir of antimicrobial resistance (AMR) is unknown. Additionally, the comparative risk associated with different manure sources is unclear. Due to the One Health nature of AMR there is an urgent need to fully understand the risk associated with AMR at the agriculture - environmental nexus. We performed a grassland field study to assess and compare the relative and temporal impact of bovine, swine and poultry manure application on the grass phyllosphere and soil microbiome and resistome over a period of four months, using 16S rRNA amplicon sequencing and high-throughput quantitative PCR (HT-qPCR). The soil and grass phyllosphere contained a diverse range of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs). Manure treatment was found to introduce ARGs belonging to clinically important antimicrobial classes, such as aminoglycoside and sulphonamide into grass and soil. Temporal analysis of ARGs and MGEs associated with manure treatment indicated ARGs patterns were similar across the different manure types in the manure treated soil and grass phyllosphere. Manure treatment resulted in the enrichment in members of the indigenous microbiota and the introduction of manure associated bacteria, with this impact extending past the recommended six-week exclusion period. However, these bacteria were in low relative abundance and manure treatment was not found to significantly impact the overall composition of the microbiome or resistome. This provides evidence that the current guidelines facilitate reduction of biological risk to livestock. Additionally, in soil and grass samples MGEs correlated with ARGs from clinically important antimicrobial classes, indicating the key role MGEs play in horizontal gene transfer in agricultural grassland. These results demonstrate the role of the grass phyllosphere as an under-studied sink of AMR.}, }
@article {pmid37155884, year = {2023}, author = {Kinsella, CM and van der Hoek, L}, title = {Vertebrate-tropism of a cressdnavirus lineage implicated by poxvirus gene capture.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {20}, pages = {e2303844120}, pmid = {37155884}, issn = {1091-6490}, mesh = {Animals ; Phylogeny ; *Poxviridae/genetics ; *Avipoxvirus/genetics ; Birds ; Tropism ; }, abstract = {Among cressdnaviruses, only the family Circoviridae is recognized to infect vertebrates, while many others have unknown hosts. Detection of virus-to-host horizontal gene transfer is useful for solving such virus-host relationships. Here, we extend this utility to an unusual case of virus-to-virus horizontal transfer, showing multiple ancient captures of cressdnavirus Rep genes by avipoxviruses-large dsDNA pathogens of birds and other saurians. As gene transfers must have occurred during virus coinfections, saurian hosts were implied for the cressdnavirus donor lineage. Surprisingly, phylogenetic analysis revealed that donors were not members of the vertebrate-infecting Circoviridae, instead belonging to a previously unclassified family that we name Draupnirviridae. While draupnirviruses still circulate today, we show that those in the genus Krikovirus infected saurian vertebrates at least 114 Mya, leaving endogenous viral elements inside snake, lizard, and turtle genomes throughout the Cretaceous Period. Endogenous krikovirus elements in some insect genomes and frequent detection in mosquitoes imply that spillover to vertebrates was arthropod mediated, while ancestral draupnirviruses likely infected protists before their emergence in animals. A modern krikovirus sampled from an avipoxvirus-induced lesion shows that their interaction with poxviruses is ongoing. Captured Rep genes in poxvirus genomes often have inactivated catalytic motifs, yet near-total presence across the Avipoxvirus genus, and evidence of both expression and purifying selection on them suggests currently unknown functions.}, }
@article {pmid37155541, year = {2023}, author = {Jiang, Y and Zhao, L and Li, JD and Sun, J and Miao, R and Shao, B and Wu, P}, title = {The universality of eAREs in animal feces suggesting that eAREs function possibly in horizontal gene transfer.}, journal = {Journal of advanced veterinary and animal research}, volume = {10}, number = {1}, pages = {103-112}, pmid = {37155541}, issn = {2311-7710}, abstract = {OBJECTIVES: This study aimed to pinpoint the universality of extracellular antimicrobial resistance elements (eAREs) and compare the contents of eAREs with those of intracellular AREs (iAREs) in animal feces, thus laying a foundation for the further analysis of the horizontal transfer of antimicrobial resistance genes (ARGs) in the animal guts.<br><br>MATERIALS AND METHODS: Extracellular DNAs were isolated from the fecal samples of Pavo cristatus (n = 18), Ursus thibetanus (n = 2), two breeds of broilers (n = 21 and 11, respectively), and from the contents of rabbit intestines (n = 5). eAREs were detected by PCR technology. iAREs in P. cristatus and broiler feces were also detected and compared with the corresponding eAREs. In addition, some gene cassettes of class 1 integrons were sequenced and analyzed.<br><br>RESULTS: The results showed that eAREs exist in animal feces and intestinal contents. In this study, different eAREs were detected from animal feces and intestinal contents, and tetA, tetB, sul1, sul2, class 1 integron, and IncFIB presented the highest detection rates. The detection rates of certain eAREs were significantly higher than those of parallel iAREs. The integral cassettes with intact structures were found in eAREs, and the cassettes carried ARGs.<br><br>CONCLUSIONS: The presented study here sheds light on the presence of eAREs in animal feces or guts, and eAREs may play an important role in the horizontal gene transfer of ARGs.}, }
@article {pmid37154532, year = {2023}, author = {Cai, L}, title = {Rethinking convergence in plant parasitism through the lens of molecular and population genetic processes.}, journal = {American journal of botany}, volume = {110}, number = {5}, pages = {e16174}, doi = {10.1002/ajb2.16174}, pmid = {37154532}, issn = {1537-2197}, mesh = {Phylogeny ; *Plants/genetics ; *Photosynthesis/genetics ; Genome, Plant ; Evolution, Molecular ; }, abstract = {The autotrophic lifestyle of photosynthetic plants has profoundly shaped their body plan, physiology, and gene repertoire. Shifts to parasitism and heterotrophy have evolved at least 12 times in more than 4000 species, and this transition has consequently left major evolutionary footprints among these parasitic lineages. Features that are otherwise rare at the molecular level and beyond have evolved repetitively, including reduced vegetative bodies, carrion-mimicking during reproduction, and the incorporation of alien genetic material. Here, I propose an integrated conceptual model, referred to as the funnel model, to define the general evolutionary trajectory of parasitic plants and provide a mechanistic explanation for their convergent evolution. This model connects our empirical understanding of gene regulatory networks in flowering plants with classical theories of molecular and population genetics. It emphasizes that the cascading effects brought about by the loss of photosynthesis may be a major force constraining the physiological capacity of parasitic plants and shaping their genomic landscapes. Here I review recent studies on the anatomy, physiology, and genetics of parasitic plants that lend support to this photosynthesis-centered funnel model. Focusing on nonphotosynthetic holoparasites, I elucidate how they may inevitably reach an evolutionary terminal status (i.e., extinction) and highlight the utility of a general, explicitly described and falsifiable model for future studies of parasitic plants.}, }
@article {pmid37152757, year = {2023}, author = {Nie, Z and Tang, K and Wang, W and Wang, P and Guo, Y and Wang, Y and Kao, SJ and Yin, J and Wang, X}, title = {Comparative genomic insights into habitat adaptation of coral-associated Prosthecochloris.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1138751}, pmid = {37152757}, issn = {1664-302X}, abstract = {Green sulfur bacteria (GSB) are a distinct group of anoxygenic phototrophic bacteria that are found in many ecological niches. Prosthecochloris, a marine representative genus of GSB, was found to be dominant in some coral skeletons. However, how coral-associated Prosthecochloris (CAP) adapts to diurnal changing microenvironments in coral skeletons is still poorly understood. In this study, three Prosthecochloris genomes were obtained through enrichment culture from the skeleton of the stony coral Galaxea fascicularis. These divergent three genomes belonged to Prosthecochloris marina and two genomes were circular. Comparative genomic analysis showed that between the CAP and non-CAP clades, CAP genomes possess specialized metabolic capacities (CO oxidation, CO2 hydration and sulfur oxidation), gas vesicles (vertical migration in coral skeletons), and cbb 3-type cytochrome c oxidases (oxygen tolerance and gene regulation) to adapt to the microenvironments of coral skeletons. Within the CAP clade, variable polysaccharide synthesis gene clusters and phage defense systems may endow bacteria with differential cell surface structures and phage susceptibility, driving strain-level evolution. Furthermore, mobile genetic elements (MGEs) or evidence of horizontal gene transfer (HGT) were found in most of the genomic loci containing the above genes, suggesting that MGEs play an important role in the evolutionary diversification between CAP and non-CAP strains and within CAP clade strains. Our results provide insight into the adaptive strategy and population evolution of endolithic Prosthecochloris strains in coral skeletons.}, }
@article {pmid37149187, year = {2023}, author = {Li, LG and Zhang, T}, title = {Plasmid-mediated antibiotic resistance gene transfer under environmental stresses: Insights from laboratory-based studies.}, journal = {The Science of the total environment}, volume = {887}, number = {}, pages = {163870}, doi = {10.1016/j.scitotenv.2023.163870}, pmid = {37149187}, issn = {1879-1026}, mesh = {Phylogeny ; *Plastics ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; *Environmental Pollutants ; Plasmids ; Gene Transfer, Horizontal ; Pharmaceutical Preparations ; }, abstract = {Although clinical settings play a major role in the current global dissemination of antibiotic resistance, once antibiotic resistance bacteria and genes are released into the environment, their fate will be subject to complex ecological processes. One of the processes prevalent in microbial communities - horizontal gene transfer - can largely facilitate the dissemination of antibiotic resistance genes (ARGs) across phylogenetic and ecological boundaries. Especially, plasmid transfer has aroused increasing concern as it has been proved a significant role in promoting ARG dissemination. As a multi-step process, plasmid transfer can be influenced by various factors, among which those stresses caused by environmental pollutants are important elements affecting the plasmid mediated ARG transfer in the environment. In fact, diverse traditional and emerging pollutants are continuously entering the environment nowadays, as evidenced by the global occurrence of pollutants like metals and pharmaceuticals in aquatic and terrestrial systems. It is therefore imperative to understand to what extent and in which way the plasmid mediated ARG dissemination can be influenced by these stresses. Over the past decades, numerous research endeavours have been made to understand the plasmid mediated ARG transfer under various environmental relevant pressures. In this review, progress and challenges of studies on environmental stress regulating plasmid mediated ARG dissemination will be discussed, with specific focus on emerging pollutants like antibiotics and non-antibiotic pharmaceuticals, metals and their nanoparticles, disinfectants and disinfection by-products, as well as the emerging particulate matter like microplastics. Despite the previous efforts, we are still lacking insights into the in situ plasmid transfer under environmental stresses, which can be addressed by future studies considering environmental relevant pollution status and multi-species microbial communities. We believe that future development of standardized high-throughput screening platforms will assist in rapidly identifying which pollutants enhance plasmid transfer and also which ones may block such gene transfer processes.}, }
@article {pmid37148762, year = {2023}, author = {Jiang, H and Zhang, L and Wang, X and Gu, J and Song, Z and Wei, S and Guo, H and Xu, L and Qian, X}, title = {Reductions in abundances of intracellular and extracellular antibiotic resistance genes by SiO2 nanoparticles during composting driven by mobile genetic elements.}, journal = {Journal of environmental management}, volume = {341}, number = {}, pages = {118071}, doi = {10.1016/j.jenvman.2023.118071}, pmid = {37148762}, issn = {1095-8630}, mesh = {Animals ; Swine ; Genes, Bacterial ; Silicon Dioxide ; *Composting ; Anti-Bacterial Agents/pharmacology ; Manure/microbiology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Livestock ; *Nanoparticles ; Interspersed Repetitive Sequences ; }, abstract = {Applying exogenous additives during the aerobic composting of livestock manure is effective for slowing down the spread of antibiotic resistance genes (ARGs) in the environment. Nanomaterials have received much attention because only low amounts need to be added and they have a high capacity for adsorbing pollutants. Intracellular ARGs (i-ARGs) and extracellular ARGs (e-ARGs) comprise the resistome in livestock manure but the effects of nanomaterials on the fates of these different fractions during composting are still unclear. Thus, we investigated the effects of adding SiO2 nanoparticles (SiO2NPs) at four levels (0 (CK), 0.5 (L), 1 (M), and 2 g/kg (H)) on i-ARGs, e-ARGs, and the bacterial community during composting. The results showed that i-ARGs represented the main fraction of ARGs during aerobic composting of swine manure, and their abundance was lowest under M. Compared with CK, M increased the removal rates of i-ARGs and e-ARGs by 17.9% and 100%, respectively. SiO2NPs enhanced the competition between ARGs hosts and non-hosts. M optimized the bacterial community by reducing the abundances of co-hosts (Clostridium_sensu_stricto_1, Terrisporobacter, and Turicibacter) of i-ARGs and e-ARGs (by 96.0% and 99.3%, respectively) and killing 49.9% of antibiotic-resistant bacteria. Horizontal gene transfer dominated by mobile genetic elements (MGEs) played a key role in the changes in the abundances of ARGs. i-intI1 and e-Tn916/1545 were key MGEs related closely to ARGs, and the maximum decreases of 52.8% and 100%, respectively, occurred under M, which mainly explained the decreased abundances of i-ARGs and e-ARGs. Our findings provide new insights into the distribution and main drivers of i-ARGs and e-ARGs, as well as demonstrating the possibility of adding 1 g/kg SiO2NPs to reduce the propagation of ARGs.}, }
@article {pmid37146969, year = {2023}, author = {Takada, H and Katoh, T and Sakanaka, M and Odamaki, T and Katayama, T}, title = {GH20 and GH84 β-N-acetylglucosaminidases with different linkage specificities underpin mucin O-glycan breakdown capability of Bifidobacterium bifidum.}, journal = {The Journal of biological chemistry}, volume = {299}, number = {6}, pages = {104781}, pmid = {37146969}, issn = {1083-351X}, mesh = {Animals ; *Acetylglucosaminidase/chemistry/metabolism ; *Bacterial Proteins/metabolism ; *Bifidobacterium bifidum/classification/enzymology/genetics ; *Mucins/metabolism ; Phylogeny ; Swine ; }, abstract = {Intestinal mucous layers mediate symbiosis and dysbiosis of host-microbe interactions. These interactions are influenced by the mucin O-glycan degrading ability of several gut microbes. The identities and prevalence of many glycoside hydrolases (GHs) involved in microbial mucin O-glycan breakdown have been previously reported; however, the exact mechanisms and extent to which these GHs are dedicated to mucin O-glycan degradation pathways warrant further research. Here, using Bifidobacterium bifidum as a model mucinolytic bacterium, we revealed that two β-N-acetylglucosaminidases belonging to the GH20 (BbhI) and GH84 (BbhIV) families play important roles in mucin O-glycan degradation. Using substrate specificity analysis of natural oligosaccharides and O-glycomic analysis of porcine gastric mucin (PGM) incubated with purified enzymes or B. bifidum carrying bbhI and/or bbhIV mutations, we showed that BbhI and BbhIV are highly specific for β-(1→3)- and β-(1→6)-GlcNAc linkages of mucin core structures, respectively. Interestingly, we found that efficient hydrolysis of the β-(1→3)-linkage by BbhI of the mucin core 4 structure [GlcNAcβ1-3(GlcNAcβ1-6)GalNAcα-O-Thr] required prior removal of the β-(1→6)-GlcNAc linkage by BbhIV. Consistent with this, inactivation of bbhIV markedly decreased the ability of B. bifidum to release GlcNAc from PGM. When combined with a bbhI mutation, we observed that the growth of the strain on PGM was reduced. Finally, phylogenetic analysis suggests that GH84 members may have gained diversified functions through microbe-microbe and host-microbe horizontal gene transfer events. Taken together, these data strongly suggest the involvement of GH84 family members in host glycan breakdown.}, }
@article {pmid37144438, year = {2023}, author = {Hu, X and Xu, Y and Liu, S and Gudda, FO and Ling, W and Qin, C and Gao, Y}, title = {Graphene Quantum Dots Nonmonotonically Influence the Horizontal Transfer of Extracellular Antibiotic Resistance Genes via Bacterial Transformation.}, journal = {Small (Weinheim an der Bergstrasse, Germany)}, volume = {19}, number = {37}, pages = {e2301177}, doi = {10.1002/smll.202301177}, pmid = {37144438}, issn = {1613-6829}, mesh = {Humans ; Anti-Bacterial Agents/pharmacology ; *Graphite/pharmacology ; *Quantum Dots ; Transformation, Bacterial ; Drug Resistance, Microbial/genetics ; Escherichia coli/genetics ; }, abstract = {Graphene quantum dots (GQDs) coexist with antibiotic resistance genes (ARGs) in the environment. Whether GQDs influence ARG spread needs investigation, since the resulting development of multidrug-resistant pathogens would threaten human health. This study investigates the effect of GQDs on the horizontal transfer of extracellular ARGs (i.e., transformation, a pivotal way that ARGs spread) mediated by plasmids into competent Escherichia coli cells. GQDs enhance ARG transfer at lower concentrations, which are close to their environmental residual concentrations. However, with further increases in concentration (closer to working concentrations needed for wastewater remediation), the effects of enhancement weaken or even become inhibitory. At lower concentrations, GQDs promote the gene expression related to pore-forming outer membrane proteins and the generation of intracellular reactive oxygen species, thus inducing pore formation and enhancing membrane permeability. GQDs may also act as carriers to transport ARGs into cells. These factors result in enhanced ARG transfer. At higher concentrations, GQD aggregation occurs, and aggregates attach to the cell surface, reducing the effective contact area of recipients for external plasmids. GQDs also form large agglomerates with plasmids and thus hindering ARG entrance. This study could promote the understanding of the GQD-caused ecological risks and benefit their safe application.}, }
@article {pmid37143068, year = {2023}, author = {Valach, M and Moreira, S and Petitjean, C and Benz, C and Butenko, A and Flegontova, O and Nenarokova, A and Prokopchuk, G and Batstone, T and Lapébie, P and Lemogo, L and Sarrasin, M and Stretenowich, P and Tripathi, P and Yazaki, E and Nara, T and Henrissat, B and Lang, BF and Gray, MW and Williams, TA and Lukeš, J and Burger, G}, title = {Recent expansion of metabolic versatility in Diplonema papillatum, the model species of a highly speciose group of marine eukaryotes.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {99}, pmid = {37143068}, issn = {1741-7007}, support = {BB/R016437/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Humans ; *Eukaryota/genetics ; Meiotic Prophase I ; Euglenozoa/genetics ; *Kinetoplastida/genetics ; Multigene Family ; Phylogeny ; }, abstract = {BACKGROUND: Diplonemid flagellates are among the most abundant and species-rich of known marine microeukaryotes, colonizing all habitats, depths, and geographic regions of the world ocean. However, little is known about their genomes, biology, and ecological role.<br><br>RESULTS: We present the first nuclear genome sequence from a diplonemid, the type species Diplonema papillatum. The&#x2009;~&#x2009;280-Mb genome assembly contains about 32,000 protein-coding genes, likely co-transcribed in groups of up to 100. Gene clusters are separated by long repetitive regions that include numerous transposable elements, which also reside within introns. Analysis of gene-family evolution reveals that the last common diplonemid ancestor underwent considerable metabolic expansion. D. papillatum-specific gains of carbohydrate-degradation capability were apparently acquired via horizontal gene transfer. The predicted breakdown of polysaccharides including pectin and xylan is at odds with reports of peptides being the predominant carbon source of this organism. Secretome analysis together with feeding experiments suggest that D. papillatum is predatory, able to degrade cell walls of live microeukaryotes, macroalgae, and water plants, not only for protoplast feeding but also for metabolizing cell-wall carbohydrates as an energy source. The analysis of environmental barcode samples shows that D. papillatum is confined to temperate coastal waters, presumably acting in bioremediation of eutrophication.<br><br>CONCLUSIONS: Nuclear genome information will allow systematic functional and cell-biology studies in D. papillatum. It will also serve as a reference for the highly diverse diplonemids and provide a point of comparison for studying gene complement evolution in the sister group of Kinetoplastida, including human-pathogenic taxa.}, }
@article {pmid37138596, year = {2023}, author = {Zhao, Y and Wei, HM and Yuan, JL and Xu, L and Sun, JQ}, title = {A comprehensive genomic analysis provides insights on the high environmental adaptability of Acinetobacter strains.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1177951}, pmid = {37138596}, issn = {1664-302X}, abstract = {Acinetobacter is ubiquitous, and it has a high species diversity and a complex evolutionary pattern. To elucidate the mechanism of its high ability to adapt to various environment, 312 genomes of Acinetobacter strains were analyzed using the phylogenomic and comparative genomics methods. It was revealed that the Acinetobacter genus has an open pan-genome and strong genome plasticity. The pan-genome consists of 47,500 genes, with 818 shared by all the genomes of Acinetobacter, while 22,291 are unique genes. Although Acinetobacter strains do not have a complete glycolytic pathway to directly utilize glucose as carbon source, most of them harbored the n-alkane-degrading genes alkB/alkM (97.1% of tested strains) and almA (96.7% of tested strains), which were responsible for medium-and long-chain n-alkane terminal oxidation reaction, respectively. Most Acinetobacter strains also have catA (93.3% of tested strains) and benAB (92.0% of tested strains) genes that can degrade the aromatic compounds catechol and benzoic acid, respectively. These abilities enable the Acinetobacter strains to easily obtain carbon and energy sources from their environment for survival. The Acinetobacter strains can manage osmotic pressure by accumulating potassium and compatible solutes, including betaine, mannitol, trehalose, glutamic acid, and proline. They respond to oxidative stress by synthesizing superoxide dismutase, catalase, disulfide isomerase, and methionine sulfoxide reductase that repair the damage caused by reactive oxygen species. In addition, most Acinetobacter strains contain many efflux pump genes and resistance genes to manage antibiotic stress and can synthesize a variety of secondary metabolites, including arylpolyene, β-lactone and siderophores among others, to adapt to their environment. These genes enable Acinetobacter strains to survive extreme stresses. The genome of each Acinetobacter strain contained different numbers of prophages (0-12) and genomic islands (GIs) (6-70), and genes related to antibiotic resistance were found in the GIs. The phylogenetic analysis revealed that the alkM and almA genes have a similar evolutionary position with the core genome, indicating that they may have been acquired by vertical gene transfer from their ancestor, while catA, benA, benB and the antibiotic resistance genes could have been acquired by horizontal gene transfer from the other organisms.}, }
@article {pmid37137974, year = {2023}, author = {Ikhimiukor, OO and Souza, SSR and Marcovici, MM and Nye, GJ and Gibson, R and Andam, CP}, title = {Leaky barriers to gene sharing between locally co-existing coagulase-negative Staphylococcus species.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {482}, pmid = {37137974}, issn = {2399-3642}, support = {R35 GM142924/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Coagulase/genetics ; Staphylococcus/genetics ; Plasmids ; *Bacteriophages ; }, abstract = {Coagulase-negative Staphylococcus (CoNS) are opportunistic pathogens implicated in many human and animal infections. The evolutionary history of CoNS remains obscure because of the historical lack of recognition for their clinical importance and poor taxonomic sampling. Here, we sequenced the genomes of 191 CoNS isolates representing 15 species sampled from diseased animals diagnosed in a veterinary diagnostic laboratory. We found that CoNS are important reservoirs of diverse phages, plasmids and mobilizable genes encoding antimicrobial resistance, heavy metal resistance, and virulence. Frequent exchange of DNA between certain donor-recipient partners suggests that specific lineages act as hubs of gene sharing. We also detected frequent recombination between CoNS regardless of their animal host species, indicating that ecological barriers to horizontal gene transfer can be surmounted in co-circulating lineages. Our findings reveal frequent but structured patterns of transfer that exist within and between CoNS species, which are driven by their overlapping ecology and geographical proximity.}, }
@article {pmid37133439, year = {2023}, author = {Tran, NN and Morrisette, T and Jorgensen, SCJ and Orench-Benvenutti, JM and Kebriaei, R}, title = {Current therapies and challenges for the treatment of Staphylococcus aureus biofilm-related infections.}, journal = {Pharmacotherapy}, volume = {43}, number = {8}, pages = {816-832}, doi = {10.1002/phar.2806}, pmid = {37133439}, issn = {1875-9114}, mesh = {Humans ; Staphylococcus aureus ; Biofilms ; *Staphylococcal Infections/drug therapy ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Community-Acquired Infections/drug therapy ; *Methicillin-Resistant Staphylococcus aureus/physiology ; Microbial Sensitivity Tests ; }, abstract = {Staphylococcus aureus is a major cause of nosocomial and community-acquired infections and contributes to significant increase in morbidity and mortality especially when associated with medical devices and in biofilm form. Biofilm structure provides a pathway for the enrichment of resistant and persistent phenotypes of S. aureus leading to relapse and recurrence of infection. Minimal diffusion of antibiotics inside biofilm structure leads to heterogeneity and distinct physiological activity. Additionally, horizontal gene transfer between cells in proximity adds to the challenges associated with eradication of biofilms. This narrative review focuses on biofilm-associated infections caused by S. aureus, the impact of environmental conditions on biofilm formation, interactions inside biofilm communities, and the clinical challenges that they present. Conclusively, potential solutions, novel treatment strategies, combination therapies, and reported alternatives are discussed.}, }
@article {pmid37126651, year = {2023}, author = {Akmal, M and Akatsuka, M and Nishiki, I and Yoshida, T}, title = {Resistance and genomic characterization of a plasmid pkh2101 harbouring erm(B) isolated from emerging fish pathogen Lactococcus garvieae serotype II in Japan.}, journal = {Journal of fish diseases}, volume = {46}, number = {8}, pages = {841-848}, doi = {10.1111/jfd.13793}, pmid = {37126651}, issn = {1365-2761}, support = {21H02287//Grants-in-Aid for Scientific Research from JSPS KAKENHI/ ; }, mesh = {Animals ; Japan ; Serogroup ; *Fish Diseases ; Plasmids/genetics ; Lactococcus/genetics ; Erythromycin ; Genomics ; }, abstract = {The emergence of antibiotic-resistant pathogenic strains of Lactococcus garvieae serotype II isolated from fish in Japan has become a growing concern in recent years. The data on drug susceptibility and its associated resistance mechanism are limited. Therefore, the present study was conducted to determine the minimum inhibitory concentrations (MICs) of chemotherapeutic agents against 98 pathogenic strains of emerging Lactococcus garvieae serotype II isolated from fish from six different prefectures in Japan from 2018 to 2021. The tested strains were resistant to erythromycin, lincomycin and tiamulin. PCR amplification revealed the presence of erm(B) in all erythromycin-resistant strains, while a conjugation experiment confirmed that these strains carried erm(B) that could be transferred to recipient Enterococcus faecalis OG1RF with frequencies from 10[-4] to 10[-6] per donor cells. Nucleotide sequencing of the representative isolated plasmid pkh2101 from an erythromycin-resistant strain showed that it was a 26,850 bp molecule with an average GC content of 33.49%, comprising 31 CDSs, 13 of which remained without any functional annotation. Comparative genomic analysis suggested that pkh2101 shared the highest similarity (97.57% identity) with the plasmid pAMbeta1, which was previously isolated clinically from Enterococcus faecalis DS-5. This study provides potential evidence that the plasmid harbouring erm(B) could be a source of antibiotic resistance transmission in emerging L. garvieae infection in aquaculture.}, }
@article {pmid37125932, year = {2023}, author = {Quan, J and Hu, H and Zhang, H and Meng, Y and Liao, W and Zhou, J and Han, X and Shi, Q and Zhao, D and Wang, Q and Jiang, Y and Yu, Y}, title = {Investigating Possible Interspecies Communication of Plasmids Associated with Transfer of Third-Generation Cephalosporin, Quinolone, and Colistin Resistance Between Simultaneously Isolated Escherichia Coli and Klebsiella Pneumoniae.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0355422}, pmid = {37125932}, issn = {2165-0497}, mesh = {Humans ; Escherichia coli/metabolism ; Colistin ; Klebsiella pneumoniae/metabolism ; Anti-Bacterial Agents/pharmacology ; *Quinolones ; *Coinfection ; Plasmids/genetics ; *Escherichia coli Proteins/genetics ; Cephalosporins/pharmacology ; Communication ; *Cross Infection ; Microbial Sensitivity Tests ; beta-Lactamases/genetics ; Drug Resistance, Bacterial/genetics ; *Klebsiella Infections ; }, abstract = {The coinfection process producing multiple species of pathogens provides a specific ecological niche for the exchange of genetic materials between pathogens, in which plasmids play a vital role in horizontal gene transfer, especially for drug resistance, but the underlying transfer pathway remains unclear. Interspecies communication of the plasmids associated with the transfer of third-generation cephalosporins, quinolones, and colistin resistance has been observed in simultaneously isolated Escherichia coli and Klebsiella pneumoniae from abdominal drainage following surgery. The MICs of antimicrobial agents were determined by the broth microdilution method. The complete chromosome and plasmid sequences were obtained by combining Illumina paired-end short reads and MinION long reads. S1-PFGE, southern blot analysis and conjugation assay confirmed the transferability of the mcr-1-harboring plasmid. Both the E. coli isolate EC15255 and K. pneumoniae isolate KP15255 from the same specimen presented multidrug resistance. Each of them harbored one chromosome and three plasmids, and two plasmids and their mediated resistance could be transferred to the recipient by conjugation. Comparison of their genome sequences suggested that several genetic communication events occurred between species, especially among their plasmids, such as whole-plasmid transfer, insertion, deletion, amplification, or inversion. Exchange of plasmids or the genetic elements they harbor plays a critical role in antimicrobial resistance gene transmission and poses a substantial threat to nosocomial infection control, necessitating the continued surveillance of multidrug resistant pathogens, especially during coinfection. IMPORTANCE The genome sequence of bacterial pathogens commonly provides a detailed clue of genetic communication among clones or even distinct species. The intestinal microecological environment is a representative ecological niche for genetic communication. However, it is still difficult to describe the details of horizontal gene transfer or other genetic events within them because the evidence in the genome sequence is incomplete and limited. In this study, the simultaneously isolated Escherichia coli and Klebsiella pneumoniae from a coinfection process provided an excellent example for observation of interspecies communication between the two genomes and the plasmids they harbor. A complete genome sequence acquired by combining the Illumina and MinION sequencing platforms facilitated the understanding of genetic communication events, such as whole-plasmid transfer, insertion, deletion, amplification, or inversion, which contribute to antimicrobial resistance gene transmission and are a substantial threat to nosocomial infection control.}, }
@article {pmid37125466, year = {2023}, author = {Castanheira, M and Mendes, RE and Gales, AC}, title = {Global Epidemiology and Mechanisms of Resistance of Acinetobacter baumannii-calcoaceticus Complex.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {76}, number = {Suppl 2}, pages = {S166-S178}, pmid = {37125466}, issn = {1537-6591}, mesh = {Humans ; *Acinetobacter baumannii/genetics ; Anti-Bacterial Agents/pharmacology ; *Acinetobacter calcoaceticus/genetics ; *Acinetobacter Infections/epidemiology ; *Acinetobacter ; *Bacteremia/epidemiology ; Drug Resistance, Multiple, Bacterial/genetics ; }, abstract = {Acinetobacter baumannii-calcoaceticus complex is the most commonly identified species in the genus Acinetobacter and it accounts for a large percentage of nosocomial infections, including bacteremia, pneumonia, and infections of the skin and urinary tract. A few key clones of A. baumannii-calcoaceticus are currently responsible for the dissemination of these organisms worldwide. Unfortunately, multidrug resistance is a common trait among these clones due to their unrivalled adaptive nature. A. baumannii-calcoaceticus isolates can accumulate resistance traits by a plethora of mechanisms, including horizontal gene transfer, natural transformation, acquisition of mutations, and mobilization of genetic elements that modulate expression of intrinsic and acquired genes.}, }
@article {pmid37121291, year = {2023}, author = {Kosterlitz, O and Huisman, JS}, title = {Guidelines for the estimation and reporting of plasmid conjugation rates.}, journal = {Plasmid}, volume = {126}, number = {}, pages = {102685}, doi = {10.1016/j.plasmid.2023.102685}, pmid = {37121291}, issn = {1095-9890}, mesh = {*Bacteria/genetics ; *Conjugation, Genetic/genetics ; *Gene Transfer, Horizontal/genetics ; *Plasmids/genetics ; Terminology as Topic ; *Research Design ; }, abstract = {Conjugation is a central characteristic of plasmid biology and an important mechanism of horizontal gene transfer in bacteria. However, there is little consensus on how to accurately estimate and report plasmid conjugation rates, in part due to the wide range of available methods. Given the similarity between approaches, we propose general reporting guidelines for plasmid conjugation experiments. These constitute best practices based on recent literature about plasmid conjugation and methods to measure conjugation rates. In addition to the general guidelines, we discuss common theoretical assumptions underlying existing methods to estimate conjugation rates and provide recommendations on how to avoid violating these assumptions. We hope this will aid the implementation and evaluation of conjugation rate measurements, and initiate a broader discussion regarding the practice of quantifying plasmid conjugation rates.}, }
@article {pmid37120693, year = {2023}, author = {Kuppa Baskaran, DK and Umale, S and Zhou, Z and Raman, K and Anantharaman, K}, title = {Metagenome-based metabolic modelling predicts unique microbial interactions in deep-sea hydrothermal plume microbiomes.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {42}, pmid = {37120693}, issn = {2730-6151}, abstract = {Deep-sea hydrothermal vents are abundant on the ocean floor and play important roles in ocean biogeochemistry. In vent ecosystems such as hydrothermal plumes, microorganisms rely on reduced chemicals and gases in hydrothermal fluids to fuel primary production and form diverse and complex microbial communities. However, microbial interactions that drive these complex microbiomes remain poorly understood. Here, we use microbiomes from the Guaymas Basin hydrothermal system in the Pacific Ocean to shed more light on the key species in these communities and their interactions. We built metabolic models from metagenomically assembled genomes (MAGs) and infer possible metabolic exchanges and horizontal gene transfer (HGT) events within the community. We highlight possible archaea-archaea and archaea-bacteria interactions and their contributions to the robustness of the community. Cellobiose, D-Mannose 1-phosphate, O2, CO2, and H2S were among the most exchanged metabolites. These interactions enhanced the metabolic capabilities of the community by exchange of metabolites that cannot be produced by any other community member. Archaea from the DPANN group stood out as key microbes, benefiting significantly as acceptors in the community. Overall, our study provides key insights into the microbial interactions that drive community structure and organisation in complex hydrothermal plume microbiomes.}, }
@article {pmid37120212, year = {2023}, author = {Ammoun, I and Kothe, CI and Mohellibi, N and Beal, C and Yaacoub, R and Renault, P}, title = {Lebanese fermented goat milk products: From tradition to meta-omics.}, journal = {Food research international (Ottawa, Ont.)}, volume = {168}, number = {}, pages = {112762}, doi = {10.1016/j.foodres.2023.112762}, pmid = {37120212}, issn = {1873-7145}, mesh = {Female ; Animals ; *Cultured Milk Products ; Ecosystem ; *Kefir ; *Lactococcus lactis ; Goats ; }, abstract = {Ambriss, Serdaleh and Labneh El Darff are traditional Lebanese products made from fermented goat's milk. A questionnaire completed by 50 producers of these products showed that they are prepared by periodic percolation either by milk or by Laban in amphora or goat skins during the lactation season. Production is carried out on a small scale and in a limited number of production units, often by elderly people, resulting in a real risk of disappearance of these products and loss of the corresponding microbial resources. In this study, 34 samples from 18 producers were characterized by culture-dependent and -independent analyses. The results obtained from these two methods were radically different, the latter revealing in Ambriss and Serdaleh the co-dominance of Lactobacillus kefiranofaciens, a fastidious-growing species, and Lactococcus lactis in a viable but not culturable state. Overall, their composition is reminiscent of kefir grains. Phylogenomic and functional analyses of the genomes of the key species Lb. kefiranofaciens have revealed differences from those found in kefir, particularly in their polysaccharide genes, which may explain the absence of grains. However, Labneh El Darff displayed a dominance of Lactobacillus delbrueckii, probably due to the addition of Laban. In addition, the study identified several zoonotic pathogens, including Streptococcus parasuis, which dominated in one sample. Metagenome-Assembled Genome (MAG) analysis indicated that this pathogen acquired lactose utilization genes through horizontal gene transfer. The contamination of the herd with Mycoplasmopsis agalactiae in the Chouf region was also revealed by MAG analysis of the Serdaleh samples. Antibiotic resistance genes were detected in most of the samples, particularly in the Serdaleh ones, where the dominant L. lactis strains possessed a plasmid with a multi-resistance island. Finally, this study paves the way for further analyses to shed light on the resilience of these ecosystems established in amphora or in goatskins and to improve hygiene practices for milk production.}, }
@article {pmid37120023, year = {2023}, author = {Adomako, MO and Yu, FH}, title = {Potential effects of micro- and nanoplastics on phyllosphere microorganisms and their evolutionary and ecological responses.}, journal = {The Science of the total environment}, volume = {884}, number = {}, pages = {163760}, doi = {10.1016/j.scitotenv.2023.163760}, pmid = {37120023}, issn = {1879-1026}, mesh = {*Microplastics ; Plastics ; Environmental Pollution ; *Microbiota ; Soil ; Plants ; }, abstract = {Plastic pollution is among the most urgent environmental and social challenges of the 21st century, and their influxes in the environment have altered critical growth drivers in all biomes, attracting global concerns. In particular, the consequences of microplastics on plants and their associated soil microorganisms have gained a large audience. On the contrary, how microplastics and nanoplastics (M/NPs) may influence the plant-associated microorganisms in the phyllosphere (i.e., the aboveground portion of plants) is nearly unknown. We, therefore, summarize evidence that may potentially connect M/NPs, plants, and phyllosphere microorganisms based on studies on other analogous contaminants such as heavy metals, pesticides, and nanoparticles. We show seven pathways that may link M/NPs into the phyllosphere environment, and provide a conceptual framework explaining the direct and indirect (soil legacy) effects of M/NPs on phyllosphere microbial communities. We also discuss the adaptive evolutionary and ecological responses, such as acquiring novel resistance genes via horizontal gene transfer and microbial degradation of plastics of the phyllosphere microbial communities, to M/NPs-induced threats. Finally, we highlight the global consequences (e.g., disruption of ecosystem biogeochemical cycling and impaired host-pathogen defense chemistry that can lead to reduced agricultural productivity) of altered plant-microbiome interactions in the phyllosphere in the context of a predicted surge of plastic production and conclude with pending questions for future research priorities. In conclusion, M/NPs are very likely to produce significant effects on phyllosphere microorganisms and mediate their evolutionary and ecological responses.}, }
@article {pmid37119017, year = {2023}, author = {Shin, NR and Okamura, Y and Kirsch, R and Pauchet, Y}, title = {Genome sequencing provides insights into the evolution of gene families encoding plant cell wall-degrading enzymes in longhorned beetles.}, journal = {Insect molecular biology}, volume = {32}, number = {5}, pages = {469-483}, doi = {10.1111/imb.12844}, pmid = {37119017}, issn = {1365-2583}, mesh = {Animals ; *Coleoptera/genetics ; Larva/genetics ; Base Sequence ; Genome ; Cell Wall/metabolism ; }, abstract = {With more than 36,000 species, the longhorned beetles (family Cerambycidae) are a mega-diverse lineage of mostly xylophagous insects, all of which are represented by the sole sequenced genome of the Asian longhorned beetle (Anoplophora glabripennis; Lamiinae). Their successful radiation has been linked to their ability to degrade plant cell wall components using a range of so-called plant cell wall-degrading enzymes (PCWDEs). Our previous analysis of larval gut transcriptomes demonstrated that cerambycid beetles horizontally acquired genes encoding PCWDEs from various microbial donors; these genes evolved through multiple duplication events to form gene families. To gain further insights into the evolution of these gene families during the Cerambycidae radiation, we assembled draft genomes for four beetle species belonging to three subfamilies using long-read nanopore sequencing. All the PCWDE-encoding genes we annotated from the corresponding larval gut transcriptomes were present in these draft genomes. We confirmed that the newly discovered horizontally acquired glycoside hydrolase family 7 (GH7), subfamily 26 of GH43 (GH43_26), and GH53 (all of which are absent from the A. glabripennis genome) were indeed encoded by these beetles' genome. Most of the PCWDE-encoding genes of bacterial origin gained introns after their transfer into the beetle genome. Altogether, we show that draft genome assemblies generated from nanopore long-reads offer meaningful information to the study of the evolution of gene families in insects. We anticipate that our data will support studies aiming to better understand the biology of the Cerambycidae and other beetles in general.}, }
@article {pmid37116631, year = {2023}, author = {Garcillán-Barcia, MP and Redondo-Salvo, S and de la Cruz, F}, title = {Plasmid classifications.}, journal = {Plasmid}, volume = {126}, number = {}, pages = {102684}, doi = {10.1016/j.plasmid.2023.102684}, pmid = {37116631}, issn = {1095-9890}, mesh = {Plasmids/genetics ; *Bacteria/genetics ; *Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; }, abstract = {Plasmids are universally present in bacteria and play key roles in the dissemination of genes such as antibiotic resistance determinants. Major concepts in Plasmid Biology derive from the efforts to classify plasmids. Here, we review the main plasmid classification systems, starting by phenotype-based methods, such as fertility inhibition and incompatibility, followed by schemes based on a single gene (replicon type and MOB class), and finishing with recently developed approaches that use genetic distances between whole plasmid sequences. A comparison of the latter highlights significant differences between them. We further discuss the need for an operational definition of plasmid species that reveals their biological features, akin to plasmid taxonomic units (PTUs).}, }
@article {pmid37115189, year = {2023}, author = {Salamzade, R and Cheong, JZA and Sandstrom, S and Swaney, MH and Stubbendieck, RM and Starr, NL and Currie, CR and Singh, AM and Kalan, LR}, title = {Evolutionary investigations of the biosynthetic diversity in the skin microbiome using lsaBGC.}, journal = {Microbial genomics}, volume = {9}, number = {4}, pages = {}, pmid = {37115189}, issn = {2057-5858}, support = {R35 GM137828/GM/NIGMS NIH HHS/United States ; U19 AI142720/AI/NIAID NIH HHS/United States ; }, mesh = {*Microbiota/genetics ; Metagenome ; Biological Evolution ; }, abstract = {Bacterial secondary metabolites, synthesized by enzymes encoded in biosynthetic gene clusters (BGCs), can underlie microbiome homeostasis and serve as commercialized products, which have historically been mined from a select group of taxa. While evolutionary approaches have proven beneficial for prioritizing BGCs for experimental characterization efforts to uncover new natural products, dedicated bioinformatics tools designed for comparative and evolutionary analysis of BGCs within focal taxa are limited. We thus developed lineage specific analysis of BGCs (lsaBGC; https://github.com/Kalan-Lab/lsaBGC) to aid exploration of microdiversity and evolutionary trends across homologous groupings of BGCs, gene cluster families (GCFs), in any bacterial taxa of interest. lsaBGC enables rapid and direct identification of GCFs in genomes, calculates evolutionary statistics and conservation for BGC genes, and builds a framework to allow for base resolution mining of novel variants through metagenomic exploration. Through application of the suite to four genera commonly found in skin microbiomes, we uncover new insights into the evolution and diversity of their BGCs. We show that the BGC of the virulence-associated carotenoid staphyloxanthin in Staphylococcus aureus is ubiquitous across the genus Staphylococcus . While one GCF encoding the biosynthesis of staphyloxanthin showcases evidence for plasmid-mediated horizontal gene transfer (HGT) between species, another GCF appears to be transmitted vertically amongst a sub-clade of skin-associated Staphylococcus . Further, the latter GCF, which is well conserved in S. aureus , has been lost in most Staphylococcus epidermidis , which is the most common Staphylococcus species on human skin and is also regarded as a commensal. We also identify thousands of novel single-nucleotide variants (SNVs) within BGCs from the Corynebacterium tuberculostearicum sp. complex, a narrow, multi-species clade that features the most prevalent Corynebacterium in healthy skin microbiomes. Although novel SNVs were approximately 10 times as likely to correspond to synonymous changes when located in the top five percentile of conserved sites, lsaBGC identified SNVs that defied this trend and are predicted to underlie amino acid changes within functionally key enzymatic domains. Ultimately, beyond supporting evolutionary investigations of BGCs, lsaBGC also provides important functionalities to aid efforts for the discovery or directed modification of natural products.}, }
@article {pmid37110299, year = {2023}, author = {Qi, Q and Kamruzzaman, M and Iredell, JR}, title = {A Streamlined Approach for Fluorescence Labelling of Low-Copy-Number Plasmids for Determination of Conjugation Frequency by Flow Cytometry.}, journal = {Microorganisms}, volume = {11}, number = {4}, pages = {}, pmid = {37110299}, issn = {2076-2607}, support = {G1145914//National Health and Medical Research Council/ ; }, abstract = {Bacterial conjugation plays a major role in the dissemination of antibiotic resistance and virulence traits through horizontal transfer of plasmids. Robust measurement of conjugation frequency of plasmids between bacterial strains and species is therefore important for understanding the transfer dynamics and epidemiology of conjugative plasmids. In this study, we present a streamlined experimental approach for fluorescence labelling of low-copy-number conjugative plasmids that allows plasmid transfer frequency during filter mating to be measured by flow cytometry. A blue fluorescent protein gene is inserted into a conjugative plasmid of interest using a simple homologous recombineering procedure. A small non-conjugative plasmid, which carries a red fluorescent protein gene with a toxin-antitoxin system that functions as a plasmid stability module, is used to label the recipient bacterial strain. This offers the dual advantage of circumventing chromosomal modifications of recipient strains and ensuring that the red fluorescent protein gene-bearing plasmid can be stably maintained in recipient cells in an antibiotic-free environment during conjugation. A strong constitutive promoter allows the two fluorescent protein genes to be strongly and constitutively expressed from the plasmids, thus allowing flow cytometers to clearly distinguish between donor, recipient, and transconjugant populations in a conjugation mix for monitoring conjugation frequencies more precisely over time.}, }
@article {pmid37110264, year = {2023}, author = {Vittorakis, E and Vică, ML and Zervaki, CO and Vittorakis, E and Maraki, S and Mavromanolaki, VE and Schürger, ME and Neculicioiu, VS and Papadomanolaki, E and Sinanis, T and Giannoulaki, G and Xydaki, E and Kastanakis, SG and Junie, LM}, title = {Examining the Prevalence and Antibiotic Susceptibility of S. aureus Strains in Hospitals: An Analysis of the pvl Gene and Its Co-Occurrence with Other Virulence Factors.}, journal = {Microorganisms}, volume = {11}, number = {4}, pages = {}, pmid = {37110264}, issn = {2076-2607}, abstract = {S. aureus is a pathogenic bacterium that causesinfections. Its virulence is due to surface components, proteins, virulence genes, SCCmec, pvl, agr, and SEs, which are low molecular weight superantigens. SEs are usually encoded by mobile genetic elements, and horizontal gene transfer accounts for their widespread presence in S. aureus. This study analyzed the prevalence of MRSA and MSSA strains of S. aureus in two hospitals in Greece between 2020-2022 and their susceptibility to antibiotics. Specimens collected were tested using the VITEK 2 system and the PCR technique to detect SCCmec types, agr types, pvl genes, and sem and seg genes. Antibiotics from various classes were also tested. This study examined the prevalence and resistance of S. aureus strains in hospitals. It found a high prevalence of MRSA and that the MRSA strains were more resistant to antibiotics. The study also identified the genotypes of the S. aureus isolates and the associated antibiotic resistances. This highlights the need for continued surveillance and effective strategies to combat the spread of MRSA in hospitals. This study examined the prevalence of the pvl gene and its co-occurrence with other genes in S. aureus strains, as well as their antibiotic susceptibility. The results showed that 19.15% of the isolates were pvl-positive and 80.85% were pvl-negative. The pvl gene co-existed with other genes, such as the agr and enterotoxin genes. The results could inform treatment strategies for S. aureus infections.}, }
@article {pmid37110261, year = {2023}, author = {Karnachuk, OV and Beletsky, AV and Rakitin, AL and Ikkert, OP and Avakyan, MR and Zyusman, VS and Napilov, A and Mardanov, AV and Ravin, NV}, title = {Antibiotic-Resistant Desulfovibrio Produces H2S from Supplements for Animal Farming.}, journal = {Microorganisms}, volume = {11}, number = {4}, pages = {}, pmid = {37110261}, issn = {2076-2607}, support = {Agreement &#x2116; 075-15-2021-1401, 03 November 2021//Ministry of Science and Higher Education of the Russian Fed-eration/ ; }, abstract = {Sulphate-reducing bacteria, primarily Desulfovibrio, are responsible for the active generation of H2S in swine production waste. The model species for sulphate reduction studies, Desulfovibrio vulgaris strain L2, was previously isolated from swine manure characterized by high rates of dissimilatory sulphate reduction. The source of electron acceptors in low-sulphate swine waste for the high rate of H2S formation remains uncertain. Here, we demonstrate the ability of the L2 strain to use common animal farming supplements including L-lysine-sulphate, gypsum and gypsum plasterboards as electron acceptors for H2S production. Genome sequencing of strain L2 revealed the presence of two megaplasmids and predicted resistance to various antimicrobials and mercury, which was confirmed in physiological experiments. Most of antibiotic resistance genes (ARG) are carried by two class 1 integrons located on the chromosome and on the plasmid pDsulf-L2-2. These ARGs, predicted to confer resistance to beta-lactams, aminoglycosides, lincosamides, sulphonamides, chloramphenicol and tetracycline, were probably laterally acquired from various Gammaproteobacteria and Firmicutes. Resistance to mercury is likely enabled by two mer operons also located on the chromosome and on pDsulf-L2-2 and acquired via horizontal gene transfer. The second megaplasmid, pDsulf-L2-1, encoded nitrogenase, catalase and type III secretion system suggesting close contact of the strain with intestinal cells in the swine gut. The location of ARGs on mobile elements allows us to consider D. vulgaris strain L2 as a possible vector transferring antimicrobials resistance determinants between the gut microbiote and microbial communities in environmental biotopes.}, }
@article {pmid37107701, year = {2023}, author = {Wu, L and Fan, P and Zhou, J and Li, Y and Xu, Z and Lin, Y and Wang, Y and Song, J and Yao, H}, title = {Gene Losses and Homology of the Chloroplast Genomes of Taxillus and Phacellaria Species.}, journal = {Genes}, volume = {14}, number = {4}, pages = {}, pmid = {37107701}, issn = {2073-4425}, mesh = {*Loranthaceae/genetics ; Phylogeny ; *Genome, Chloroplast ; Base Sequence ; }, abstract = {Research on the chloroplast genome of parasitic plants is limited. In particular, the homology between the chloroplast genomes of parasitic and hyperparasitic plants has not been reported yet. In this study, three chloroplast genomes of Taxillus (Taxillus chinensis, Taxillus delavayi, and Taxillus thibetensis) and one chloroplast genome of Phacellaria (Phacellaria rigidula) were sequenced and analyzed, among which T. chinensis is the host of P. rigidula. The chloroplast genomes of the four species were 119,941-138,492 bp in length. Compared with the chloroplast genome of the autotrophic plant Nicotiana tabacum, all of the ndh genes, three ribosomal protein genes, three tRNA genes and the infA gene were lost in the three Taxillus species. Meanwhile, in P. rigidula, the trnV-UAC gene and the ycf15 gene were lost, and only one ndh gene (ndhB) existed. The results of homology analysis showed that the homology between P. rigidula and its host T. chinensis was low, indicating that P. rigidula grows on its host T. chinensis but they do not share the chloroplast genome. In addition, horizontal gene transfer was not found between P. rigidula and its host T. chinensis. Several candidate highly variable regions in the chloroplast genomes of Taxillus and Phacellaria species were selected for species identification study. Phylogenetic analysis revealed that the species of Taxillus and Scurrula were closely related and supported that Scurrula and Taxillus should be treated as congeneric, while species in Phacellaria had a close relationship with that in Viscum.}, }
@article {pmid37104544, year = {2023}, author = {Brual, T and Effantin, G and Baltenneck, J and Attaiech, L and Grosbois, C and Royer, M and Cigna, J and Faure, D and Hugouvieux-Cotte-Pattat, N and Gueguen, E}, title = {A natural single nucleotide mutation in the small regulatory RNA ArcZ of Dickeya solani switches off the antimicrobial activities against yeast and bacteria.}, journal = {PLoS genetics}, volume = {19}, number = {4}, pages = {e1010725}, pmid = {37104544}, issn = {1553-7404}, mesh = {*Multigene Family/genetics ; *Point Mutation ; Genomics ; RNA, Bacterial/genetics/metabolism ; Polyketide Synthases/genetics ; *Antimicrobial Peptides/genetics/pharmacology ; Bacteria/drug effects ; Ascomycota/drug effects ; Dickeya/genetics/metabolism ; Gene Expression Regulation, Bacterial/genetics ; }, abstract = {The necrotrophic plant pathogenic bacterium Dickeya solani emerged in the potato agrosystem in Europe. All isolated strains of D. solani contain several large polyketide synthase/non-ribosomal peptide synthetase (PKS/NRPS) gene clusters. Analogy with genes described in other bacteria suggests that the clusters ooc and zms are involved in the production of secondary metabolites of the oocydin and zeamine families, respectively. A third cluster named sol was recently shown to produce an antifungal molecule. In this study, we constructed mutants impaired in each of the three secondary metabolite clusters sol, ooc, and zms to compare first the phenotype of the D. solani wild-type strain D s0432-1 with its associated mutants. We demonstrated the antimicrobial functions of these three PKS/NRPS clusters against bacteria, yeasts or fungi. The cluster sol, conserved in several other Dickeya species, produces a secondary metabolite inhibiting yeasts. Phenotyping and comparative genomics of different D. solani wild-type isolates revealed that the small regulatory RNA ArcZ plays a major role in the control of the clusters sol and zms. A single-point mutation, conserved in some Dickeya wild-type strains, including the D. solani type strain IPO 2222, impairs the ArcZ function by affecting its processing into an active form.}, }
@article {pmid37102089, year = {2023}, author = {Shao, M and Liu, L and Liu, B and Zheng, H and Meng, W and Liu, Y and Zhang, X and Ma, X and Sun, C and Luo, X and Li, F and Xing, B}, title = {Hormetic Effect of Pyroligneous Acids on Conjugative Transfer of Plasmid-mediated Multi-antibiotic Resistance Genes within Bacterial Genus.}, journal = {ACS environmental Au}, volume = {3}, number = {2}, pages = {105-120}, pmid = {37102089}, issn = {2694-2518}, abstract = {Spread of antibiotic resistance genes (ARGs) by conjugation poses great challenges to public health. Application of pyroligneous acids (PA) as soil amendments has been evidenced as a practical strategy to remediate pollution of ARGs in soils. However, little is known about PA effects on horizontal gene transfer (HGT) of ARGs by conjugation. This study investigated the effects of a woody waste-derived PA prepared at 450°C and its three distillation components (F1, F2, and F3) at different temperatures (98, 130, and 220°C) on conjugative transfer of plasmid RP4 within Escherichia coli. PA at relatively high amount (40-100 μL) in a 30-mL mating system inhibited conjugation by 74-85%, following an order of PA > F3 ≈ F2 ≈ F1, proving the hypothesis that PA amendments may mitigate soil ARG pollution by inhibiting HGT. The bacteriostasis caused by antibacterial components of PA, including acids, phenols, and alcohols, as well as its acidity (pH 2.81) contributed to the inhibited conjugation. However, a relatively low amount (10-20 μL) of PA in the same mating system enhanced ARG transfer by 26-47%, following an order of PA > F3 ≈ F2 > F1. The opposite effect at low amount is mainly attributed to the increased intracellular reactive oxygen species production, enhanced cell membrane permeability, increased extracellular polymeric substance contents, and reduced cell surface charge. Our findings highlight the hormesis (low-amount promotion and high-amount inhibition) of PA amendments on ARG conjugation and provide evidence for selecting an appropriate amount of PA amendment to control the dissemination of soil ARGs. Moreover, the promoted conjugation also triggers questions regarding the potential risks of soil amendments (e.g., PA) in the spread of ARGs via HGT.}, }
@article {pmid37099912, year = {2023}, author = {Sun, X and Kong, T and Huang, D and Chen, Z and Kolton, M and Yang, J and Huang, Y and Cao, Y and Gao, P and Yang, N and Li, B and Liu, H and Sun, W}, title = {Arsenic (As) oxidation by core endosphere microbiome mediates As speciation in Pteris vittata roots.}, journal = {Journal of hazardous materials}, volume = {454}, number = {}, pages = {131458}, doi = {10.1016/j.jhazmat.2023.131458}, pmid = {37099912}, issn = {1873-3336}, mesh = {*Arsenic/metabolism ; *Pteris/metabolism ; Plant Roots/metabolism ; Oxidation-Reduction ; Oxidoreductases/metabolism ; Biodegradation, Environmental ; *Soil Pollutants/metabolism ; }, abstract = {Pteris vittata is an arsenic(As)-hyperaccumulator that may be employed in phytoremediation of As-contaminated soils. P. vittata-associated microbiome are adapted to elevated As and may be important for host survival under stresses. Although P. vittata root endophytes could be critical for As biotransformation in planta, their compositions and metabolisms remain elusive. The current study aims to characterize the root endophytic community composition and As-metabolizing potentials in P. vittata. High As(III) oxidase gene abundances and rapid As(III) oxidation activity indicated that As(III) oxidation was the dominant microbial As-biotransformation processes compared to As reduction and methylization in P. vittata roots. Members of Rhizobiales were the core microbiome and the dominant As(III) oxidizers in P. vittata roots. Acquasition of As-metabolising genes, including both As(III) oxidase and As(V) detoxification reductase genes, through horizontal gene transfer was identified in a Saccharimonadaceae genomic assembly, which was another abundant population residing in P. vittata roots. Acquisition of these genes might improve the fitness of Saccharimonadaceae population to elevated As concentrations in P. vittata. Diverse plant growth promoting traits were encoded by the core root microbiome populations Rhizobiales. We propose that microbial As(III) oxidation and plant growth promotion are critical traits for P. vittata survival in hostile As-contaiminated sites.}, }
@article {pmid37098416, year = {2023}, author = {Gong, H and Huang, X and Zhu, W and Chen, J and Huang, Y and Zhao, Z and Weng, J and Che, Y and Wang, J and Wang, X}, title = {Pan-genome analysis of the Burkholderia gladioli PV. Cocovenenans reveal the extent of variation in the toxigenic gene cluster.}, journal = {Food microbiology}, volume = {113}, number = {}, pages = {104249}, doi = {10.1016/j.fm.2023.104249}, pmid = {37098416}, issn = {1095-9998}, mesh = {Humans ; *Burkholderia gladioli/genetics ; Bongkrekic Acid/analysis ; Multigene Family ; *Foodborne Diseases/microbiology ; }, abstract = {Burkholderia gladioli has been reported as the pathogen responsible for cases of foodborne illness in many countries. The poisonous bongkrekic acid (BA) produced by B. gladioli was linked to a gene cluster absent in non-pathogenic strains. The whole genome sequence of eight bacteria strains, which were screened from the collected 175 raw food and environmental samples, were assembled and analyzed to detect a significant association of 19 protein-coding genes with the pathogenic status. Except for the common BA synthesis-related gene, several other genes, including the toxin-antitoxin genes, were also absent in the non-pathogenic strains. The bacteria strains with the BA gene cluster were found to form a single cluster in the analysis of all B. gladioli genome assemblies for the variants in the gene cluster. Divergence of this cluster was detected in the analysis for both the flanking sequences and those of the whole genome level, which indicates its complex origin. Genome recombination was found to cause a precise sequence deletion in the gene cluster region, which was found to be predominant in the non-pathogenic strains indicating the possible effect of horizontal gene transfer. Our study provided new information and resources for understanding the evolution and divergence of the B. gladioli species.}, }
@article {pmid37098287, year = {2023}, author = {Nõlvak, H and Truu, M and Tiirik, K and Devarajan, AK and Peeb, A and Truu, J}, title = {The effect of synthetic silver nanoparticles on the antibiotic resistome and the removal efficiency of antibiotic resistance genes in a hybrid filter system treating municipal wastewater.}, journal = {Water research}, volume = {237}, number = {}, pages = {119986}, doi = {10.1016/j.watres.2023.119986}, pmid = {37098287}, issn = {1879-2448}, mesh = {*Wastewater ; Anti-Bacterial Agents/pharmacology/analysis ; Silver/analysis ; *Metal Nanoparticles ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Integrases/genetics ; Waste Disposal, Fluid/methods ; }, abstract = {Engineered nanoparticles, including silver nanoparticles (AgNPs), are released into the environment mainly through wastewater treatment systems. Knowledge of the impact of AgNPs on the abundance and removal efficiency of antibiotic resistance genes (ARGs) in wastewater treatment facilities, including constructed wetlands (CWs), is essential in the context of public health. This study evaluated the effect of increased (100-fold) collargol (protein-coated AgNPs) and ionic Ag[+] in municipal wastewater on the structure, abundance, and removal efficiency of the antibiotic resistome, integron-integrase genes, and pathogens in a hybrid CW using quantitative PCR and metagenomic approaches. The abundance of ARGs in wastewater and the removal efficiency of ARGs in the hybrid system were significantly affected by higher Ag concentrations, especially with collargol treatment, resulting in an elevated ARG discharge of system effluent into the environment. The accumulated Ag in the filters had a more profound effect on the absolute and relative abundance of ARGs in the treated water than the Ag content in the water. This study recorded significantly enhanced relative abundance values for tetracycline (tetA, tetC, tetQ), sulfonamide (sul1, sul2), and aminoglycoside (aadA) resistance genes, which are frequently found on mobile genetic elements in collargol- and, to a lesser extent, AgNO3-treated subsystems. Elevated plasmid and integron-integrase gene levels, especially intI1, in response to collargol presence indicated the substantial role of AgNPs in promoting horizontal gene transfer in the treatment system. The pathogenic segment of the prokaryotic community was similar to a typical sewage community, and strong correlations between pathogen and ARG proportions were recorded in vertical subsurface flow filters. Furthermore, the proportion of Salmonella enterica was positively related to the Ag content in these filter effluents. The effect of AgNPs on the nature and characteristics of prominent resistance genes carried by mobile genetic elements in CWs requires further investigation.}, }
@article {pmid37097444, year = {2023}, author = {Bibi, S and Weis, K and Kaur, A and Bhandari, R and Goss, E and Jones, JB and Potnis, N}, title = {A Brief Evaluation of a Copper Resistance Mobile Genetic Island in the Bacterial Leaf Spot Pathogen Xanthomonas euvesicatoria pv. perforans.}, journal = {Phytopathology}, volume = {113}, number = {8}, pages = {1394-1398}, doi = {10.1094/PHYTO-02-23-0077-SC}, pmid = {37097444}, issn = {0031-949X}, abstract = {Due to the continuous use of copper containing bactericides without effective alternative bactericides, copper resistance has become more prevalent in plant pathogens, including Xanthomonas euvesicatoria pv. perforans (formerly Xanthomonas perforans), a predominant cause of bacterial leaf spot disease of tomato and pepper in the Southeastern United States. Previously, reports of copper resistance have been associated with a large conjugative plasmid. However, we have characterized a copper resistance genomic island located within the chromosome of multiple X. euvesicatoria pv. perforans strains. The island is distinct from a previously described chromosomally encoded copper resistance island in X. vesicatoria strain XVP26. Computational analysis revealed the genomic island to contain multiple genes associated with genetic mobility, including both phage-related genes and transposase. Among copper-tolerant strains of X. euvesicatoria pv. perforans isolated from Florida, the majority of strains were found to have the copper resistance chromosomally encoded rather than plasmid borne. Our results suggest that this copper resistance island may have two modes of horizontal gene transfer and that chromosomally encoded copper resistance genes may provide a fitness advantage over plasmid-borne resistance.}, }
@article {pmid37097343, year = {2023}, author = {Francis, A and Steel, M}, title = {Labellable Phylogenetic Networks.}, journal = {Bulletin of mathematical biology}, volume = {85}, number = {6}, pages = {46}, pmid = {37097343}, issn = {1522-9602}, mesh = {Phylogeny ; *Evolution, Molecular ; *Models, Biological ; Models, Genetic ; Mathematical Concepts ; Algorithms ; }, abstract = {Phylogenetic networks are mathematical representations of evolutionary history that are able to capture both tree-like evolutionary processes (speciations) and non-tree-like 'reticulate' processes such as hybridization or horizontal gene transfer. The additional complexity that comes with this capacity, however, makes networks harder to infer from data, and more complicated to work with as mathematical objects. In this paper, we define a new, large class of phylogenetic networks, that we call labellable, and show that they are in bijection with the set of 'expanding covers' of finite sets. This correspondence is a generalisation of the encoding of phylogenetic forests by partitions of finite sets. Labellable networks can be characterised by a simple combinatorial condition, and we describe the relationship between this large class and other commonly studied classes. Furthermore, we show that all phylogenetic networks have a quotient network that is labellable.}, }
@article {pmid37095096, year = {2023}, author = {Ahmad, M and Prensky, H and Balestrieri, J and ElNaggar, S and Gomez-Simmonds, A and Uhlemann, AC and Traxler, B and Singh, A and Lopatkin, AJ}, title = {Tradeoff between lag time and growth rate drives the plasmid acquisition cost.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {2343}, pmid = {37095096}, issn = {2041-1723}, support = {R15 GM143694/GM/NIGMS NIH HHS/United States ; R35 GM148351/GM/NIGMS NIH HHS/United States ; R01 AI150152/AI/NIAID NIH HHS/United States ; }, mesh = {Plasmids ; *Bacteria/genetics ; *Gene Transfer, Horizontal ; }, abstract = {Conjugative plasmids drive genetic diversity and evolution in microbial populations. Despite their prevalence, plasmids can impose long-term fitness costs on their hosts, altering population structure, growth dynamics, and evolutionary outcomes. In addition to long-term fitness costs, acquiring a new plasmid introduces an immediate, short-term perturbation to the cell. However, due to the transient nature of this plasmid acquisition cost, a quantitative understanding of its physiological manifestations, overall magnitudes, and population-level implications, remains unclear. To address this, here we track growth of single colonies immediately following plasmid acquisition. We find that plasmid acquisition costs are primarily driven by changes in lag time, rather than growth rate, for nearly 60 conditions covering diverse plasmids, selection environments, and clinical strains/species. Surprisingly, for a costly plasmid, clones exhibiting longer lag times also achieve faster recovery growth rates, suggesting an evolutionary tradeoff. Modeling and experiments demonstrate that this tradeoff leads to counterintuitive ecological dynamics, whereby intermediate-cost plasmids outcompete both their low and high-cost counterparts. These results suggest that, unlike fitness costs, plasmid acquisition dynamics are not uniformly driven by minimizing growth disadvantages. Moreover, a lag/growth tradeoff has clear implications in predicting the ecological outcomes and intervention strategies of bacteria undergoing conjugation.}, }
@article {pmid37094448, year = {2023}, author = {Zhu, S and Yang, B and Jia, Y and Yu, F and Wang, Z and Liu, Y}, title = {Comprehensive analysis of disinfectants on the horizontal transfer of antibiotic resistance genes.}, journal = {Journal of hazardous materials}, volume = {453}, number = {}, pages = {131428}, doi = {10.1016/j.jhazmat.2023.131428}, pmid = {37094448}, issn = {1873-3336}, mesh = {Humans ; Anti-Bacterial Agents/pharmacology ; *Disinfectants/pharmacology ; Genes, Bacterial ; Pandemics ; *COVID-19 ; Drug Resistance, Microbial/genetics ; Guanidines ; Gene Transfer, Horizontal ; Plasmids/genetics ; }, abstract = {The propagation of antimicrobial resistance (AMR) is constantly paralyzing our healthcare systems. In addition to the pressure of antibiotic selection, the roles of non-antibiotic compounds in disseminating antibiotic resistance genes (ARGs) are a matter of great concerns. This study aimed to explore the impact of different disinfectants on the horizontal transfer of ARGs and their underlying mechanisms. First, the effects of different kinds of disinfectants on the conjugative transfer of RP4-7 plasmid were evaluated. Results showed that quaternary ammonium salt, organic halogen, alcohol and guanidine disinfectants significantly facilitated the conjugative transfer. Conversely, heavy-metals, peroxides and phenols otherwise displayed an inhibitory effect. Furthermore, we deciphered the mechanism by which guanidine disinfectants promoted conjugation, which includes increased cell membrane permeability, over-production of ROS, enhanced SOS response, and altered expression of conjugative transfer-related genes. More critically, we also revealed that guanidine disinfectants promoted bacterial energy metabolism by enhancing the activity of electron transport chain (ETC) and proton force motive (PMF), thus promoting ATP synthesis and flagellum motility. Overall, our findings reveal the promotive effects of disinfectants on the transmission of ARGs and highlight the potential risks caused by the massive use of guanidine disinfectants, especially during the COVID-19 pandemic.}, }
@article {pmid37093956, year = {2023}, author = {Baumdicker, F and Kupczok, A}, title = {Tackling the Pangenome Dilemma Requires the Concerted Analysis of Multiple Population Genetic Processes.}, journal = {Genome biology and evolution}, volume = {15}, number = {5}, pages = {}, pmid = {37093956}, issn = {1759-6653}, mesh = {Humans ; *Prokaryotic Cells ; *Gene Transfer, Horizontal ; Computer Simulation ; Mutation ; }, abstract = {The pangenome is the set of all genes present in a prokaryotic population. Most pangenomes contain many accessory genes of low and intermediate frequencies. Different population genetics processes contribute to the shape of these pangenomes, namely selection and fitness-independent processes such as gene transfer, gene loss, and migration. However, their relative importance is unknown and highly debated. Here, we argue that the debate around prokaryotic pangenomes arose due to the imprecise application of population genetics models. Most importantly, two different processes of horizontal gene transfer act on prokaryotic populations, which are frequently confused, despite their fundamentally different behavior. Genes acquired from distantly related organisms (termed here acquiring gene transfer) are most comparable to mutation in nucleotide sequences. In contrast, gene gain within the population (termed here spreading gene transfer) has an effect on gene frequencies that is identical to the effect of positive selection on single genes. We thus show that selection and fitness-independent population genetic processes affecting pangenomes are indistinguishable at the level of single gene dynamics. Nevertheless, population genetics processes are fundamentally different when considering the joint distribution of all accessory genes across individuals of a population. We propose that, to understand to which degree the different processes shaped pangenome diversity, the development of comprehensive models and simulation tools is mandatory. Furthermore, we need to identify summary statistics and measurable features that can distinguish between the processes, where considering the joint distribution of accessory genes across individuals of a population will be particularly relevant.}, }
@article {pmid37092000, year = {2023}, author = {Han, Z and Xu, S and Gao, T}, title = {Unexpected complex horizontal gene transfer in teleost fish.}, journal = {Current zoology}, volume = {69}, number = {2}, pages = {222-223}, pmid = {37092000}, issn = {1674-5507}, }
@article {pmid37091576, year = {2022}, author = {Varner, PM and Allemann, MN and Michener, JK and Gunsch, CK}, title = {The effect of bacterial growth strategies on plasmid transfer and naphthalene degradation for bioremediation.}, journal = {Environmental technology &amp; innovation}, volume = {28}, number = {}, pages = {}, pmid = {37091576}, issn = {2352-1864}, support = {P42 ES010356/ES/NIEHS NIH HHS/United States ; }, abstract = {Mobilizable plasmids are extra-chromosomal, circular DNA that have contributed to the rapid evolution of bacterial genomes and have been used in environmental, biotechnological, and medicinal applications. Degradative plasmids with genetic capabilities to degrade organic contaminants, such as polycyclic aromatic hydrocarbons (PAHs), have the potential to be useful for more environmentally friendly and cost-effective remediation technologies compared to existing physical remediation methods. Genetic bioaugmentation, the addition of catabolic genes into well-adapted communities via plasmid transfer (conjugation), is being explored as a remediation approach that is sustainable and long-lasting. Here, we explored the effect of the ecological growth strategies of plasmid donors and recipients on conjugation and naphthalene degradation of two PAH-degrading plasmids, pNL1 and NAH7. Overall, both pNL1 and NAH7 showed conjugation preferences towards a slow-growing ecological growth strategy, except when NAH7 was in a mixed synthetic community. These conjugation preferences were partially described by a combination of growth strategy, GC content, and phylogenetic relatedness. Further, removal of naphthalene via plasmid-mediated degradation was consistently higher in a community consisting of recipients with a slow-growing ecological growth strategy compared to a mixed community or a community consisting of fast-growing ecological growth strategy. Understanding plasmid conjugation and degradative preferences has the capacity to influence future remediation technology design and has broad implications in biomedical, environmental, and health fields.}, }
@article {pmid37087920, year = {2023}, author = {Zheng, CW and Luo, YH and Long, X and Gu, H and Cheng, J and Zhang, L and Lai, YJS and Rittmann, BE}, title = {The structure of biodegradable surfactants shaped the microbial community, antimicrobial resistance, and potential for horizontal gene transfer.}, journal = {Water research}, volume = {236}, number = {}, pages = {119944}, doi = {10.1016/j.watres.2023.119944}, pmid = {37087920}, issn = {1879-2448}, mesh = {*Surface-Active Agents/chemistry ; Anti-Bacterial Agents ; Cetrimonium/chemistry ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; *Anti-Infective Agents ; Quaternary Ammonium Compounds/chemistry ; }, abstract = {While most household surfactants are biodegradable in aerobic conditions, their biodegradability may obscure their environmental risks. The presence of surfactants in a biological treatment process can lead to the proliferation of antimicrobial-resistance genes (ARG) in the biomass. Surfactants can be cationic, anionic, or zwitterionic, and these different classes may have different effects on the proliferation ARG. Cationic hexadecyltrimethyl-ammonium (CTAB), anionic sodium dodecyl sulfate (SDS), and zwitterionic 3-(decyldimethylammonio)-propanesulfonate inner salt (DAPS) were used to represent the three classes of surfactants in domestic household clean-up products. This study focused on the removal of these surfactants by the O2-based Membrane Biofilm Reactor (O2-MBfR) for hotspot scenarios (∼1 mM) and how the three classes of surfactants affected the microbial community's structure and ARG. Given sufficient O2 delivery, the MBfR provided at least 98% surfactant removal. The presence and biodegradation for each surfactant uniquely shaped the biofilms' microbial communities and the presence of ARG. CTAB had by far the strongest impact and the higher ARG abundance. In particular, Pseudomonas and Stenotrophomonas, the two main genera in the biofilm treating CTAB, were highly correlated to the abundance of ARG for efflux pumps and antibiotic inactivation. CTAB also led to more functional genes relevant to the Type-IV secretion system and protection against oxidative stress, which also could encourage horizontal gene transfer. Our findings highlight that the biodegradation of quaternary ammonium surfactants, while beneficial, can pose public health concerns from its ability to promote the proliferation of ARG.}, }
@article {pmid37083586, year = {2023}, author = {Maphosa, S and Moleleki, LN and Motaung, TE}, title = {Bacterial secretion system functions: evidence of interactions and downstream implications.}, journal = {Microbiology (Reading, England)}, volume = {169}, number = {4}, pages = {}, pmid = {37083586}, issn = {1465-2080}, mesh = {*Bacterial Secretion Systems/genetics ; *Gram-Negative Bacteria/genetics ; Virulence ; Bacteria/genetics ; Virulence Factors ; Bacterial Proteins/genetics ; }, abstract = {Unprecedented insights into the biology and functions of bacteria have been and continue to be gained through studying bacterial secretion systems in isolation. This method, however, results in our understanding of the systems being primarily based on the idea that they operate independently, ignoring the subtleties of downstream interconnections. Gram-negative bacteria are naturally able to adapt to and navigate their frequently varied and dynamic surroundings, mostly because of the covert connections between secretion systems. Therefore, to comprehend some of the linked downstream repercussions for organisms that follow this discourse, it is vital to have mechanistic insights into how the intersecretion system functions in bacterial rivalry, virulence, and survival, among other things. To that purpose, this paper discusses a few key instances of molecular antagonistic and interdependent relationships between bacterial secretion systems and their produced functional products.}, }
@article {pmid37083356, year = {2023}, author = {Wu, J and Zhou, JH and Liu, DF and Wu, J and He, RL and Cheng, ZH and Li, HH and Li, WW}, title = {Phthalates Promote Dissemination of Antibiotic Resistance Genes: An Overlooked Environmental Risk.}, journal = {Environmental science &amp; technology}, volume = {57}, number = {17}, pages = {6876-6887}, doi = {10.1021/acs.est.2c09491}, pmid = {37083356}, issn = {1520-5851}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; *Bacteria/genetics ; Genes, Bacterial ; Plastics ; Gene Transfer, Horizontal ; }, abstract = {Plastics-microorganism interactions have aroused growing environmental and ecological concerns. However, previous studies concentrated mainly on the direct interactions and paid little attention to the ecotoxicology effects of phthalates (PAEs), a common plastic additive that is continuously released and accumulates in the environment. Here, we provide insights into the impacts of PAEs on the dissemination of antibiotic resistance genes (ARGs) among environmental microorganisms. Dimethyl phthalate (DMP, a model PAE) at environmentally relevant concentrations (2-50 μg/L) significantly boosted the plasmid-mediated conjugation transfer of ARGs among intrageneric, intergeneric, and wastewater microbiota by up to 3.82, 4.96, and 4.77 times, respectively. The experimental and molecular dynamics simulation results unveil a strong interaction between the DMP molecules and phosphatidylcholine bilayer of the cell membrane, which lowers the membrane lipid fluidity and increases the membrane permeability to favor transfer of ARGs. In addition, the increased reactive oxygen species generation and conjugation-associated gene overexpression under DMP stress also contribute to the increased gene transfer. This study provides fundamental knowledge of the PAE-bacteria interactions to broaden our understanding of the environmental and ecological risks of plastics, especially in niches with colonized microbes, and to guide the control of ARG environmental spreading.}, }
@article {pmid37079454, year = {2023}, author = {Gulliver, EL and Adams, V and Marcelino, VR and Gould, J and Rutten, EL and Powell, DR and Young, RB and D'Adamo, GL and Hemphill, J and Solari, SM and Revitt-Mills, SA and Munn, S and Jirapanjawat, T and Greening, C and Boer, JC and Flanagan, KL and Kaldhusdal, M and Plebanski, M and Gibney, KB and Moore, RJ and Rood, JI and Forster, SC}, title = {Extensive genome analysis identifies novel plasmid families in Clostridium perfringens.}, journal = {Microbial genomics}, volume = {9}, number = {4}, pages = {}, pmid = {37079454}, issn = {2057-5858}, mesh = {Humans ; *Clostridium perfringens ; *Bacterial Toxins/genetics ; Phylogeny ; Base Composition ; Sequence Analysis, DNA ; RNA, Ribosomal, 16S ; Plasmids/genetics ; }, abstract = {Globally, the anaerobic bacterium Clostridium perfringens causes severe disease in a wide array of hosts; however, C. perfringens strains are also carried asymptomatically. Accessory genes are responsible for much of the observed phenotypic variation and virulence within this species, with toxins frequently encoded on conjugative plasmids and many isolates carrying up to 10 plasmids. Despite this unusual biology, current genomic analyses have largely excluded isolates from healthy hosts or environmental sources. Accessory genomes, including plasmids, also have often been excluded from broader scale phylogenetic investigations. Here we interrogate a comprehensive collection of 464 C. perfringens genomes and identify the first putative non-conjugative enterotoxin (CPE)-encoding plasmids and a putative novel conjugative locus (Bcp) with sequence similarity to a locus reported from Clostridium botulinum. We sequenced and archived 102 new C. perfringens genomes, including those from rarely sequenced toxinotype B, C, D and E isolates. Long-read sequencing of 11 C. perfringens strains representing all toxinotypes (A-G) identified 55 plasmids from nine distinct plasmid groups. Interrogation of the 464 genomes in this collection identified 1045 plasmid-like contigs from the nine plasmid families, with a wide distribution across the C. perfringens isolates. Plasmids and plasmid diversity play an essential role in C. perfringens pathogenicity and broader biology. We have expanded the C. perfringens genome collection to include temporal, spatial and phenotypically diverse isolates including those carried asymptomatically in the gastrointestinal microbiome. This analysis has resulted in the identification of novel C. perfringens plasmids whilst providing a comprehensive understanding of species diversity.}, }
@article {pmid37078595, year = {2023}, author = {Botelho, J}, title = {Defense systems are pervasive across chromosomally integrated mobile genetic elements and are inversely correlated to virulence and antimicrobial resistance.}, journal = {Nucleic acids research}, volume = {51}, number = {9}, pages = {4385-4397}, pmid = {37078595}, issn = {1362-4962}, mesh = {*Anti-Bacterial Agents ; *Conjugation, Genetic ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Interspersed Repetitive Sequences ; Virulence/genetics ; *Bacteria/genetics ; *Archaea/genetics ; }, abstract = {Mobile genetic elements (MGEs) are key promoters of microbial evolution. These elements can be located extrachromosomally or integrated into the chromosome. Well-known examples of chromosomally integrated MGEs (ciMGEs) are integrative and conjugative/mobilizable elements (ICEs and IMEs), and most studies to date have focused on the biological mechanisms that shape their lifestyle. It is crucial to profile the diversity and understand their distribution across the microbial community, as the number of genome sequences increases exponentially. Herein, I scanned a collection of >20 000 bacterial and archaeal non-redundant genomes and found over 13 000 ciMGEs across multiple phyla, representing a massive increase in the number of ciMGEs available in public databases (<1000). Although ICEs are the most important ciMGEs for the accretion of defense systems, virulence, and antimicrobial resistance (AMR) genes, IMEs outnumbered ICEs. Moreover, defense systems, AMR, and virulence genes were negatively correlated in both ICEs and IMEs. Multiple ciMGEs form heterogeneous communities and challenge inter-phylum barriers. Finally, I observed that the functional landscape of ICEs was populated by uncharacterized proteins. Altogether, this study provides a comprehensive catalog of nucleotide sequences and associated metadata for ciMGEs from 34 phyla across the bacterial and archaeal domains.}, }
@article {pmid37072776, year = {2023}, author = {Hernández, M and Roy, S and Keevil, CW and Dumont, MG}, title = {Identification of diverse antibiotic resistant bacteria in agricultural soil with H2[18]O stable isotope probing combined with high-throughput sequencing.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {34}, pmid = {37072776}, issn = {2524-6372}, support = {NE/N02026X/1//Natural Environment Research Council/ ; NE/N02026X/1//Natural Environment Research Council/ ; }, abstract = {BACKGROUND: We aimed to identify bacteria able to grow in the presence of several antibiotics including the ultra-broad-spectrum antibiotic meropenem in a British agricultural soil by combining DNA stable isotope probing (SIP) with high throughput sequencing. Soil was incubated with cefotaxime, meropenem, ciprofloxacin and trimethoprim in [18]O-water. Metagenomes and the V4 region of the 16S rRNA gene from the labelled "heavy" and the unlabelled "light" SIP fractions were sequenced.<br><br>RESULTS: An increase of the 16S rRNA copy numbers in the "heavy" fractions of the treatments with [18]O-water compared with their controls was detected. The treatments resulted in differences in the community composition of bacteria. Members of the phyla Acidobacteriota (formally Acidobacteria) were highly abundant after two days of incubation with antibiotics. Pseudomonadota (formally Proteobacteria) including Stenotrophomonas were prominent after four days of incubation. Furthermore, a metagenome-assembled genome (MAG-1) from the genus Stenotrophomonas (90.7% complete) was retrieved from the heavy fraction. Finally, 11 antimicrobial resistance genes (ARGs) were identified in the unbinned-assembled heavy fractions, and 10 ARGs were identified in MAG-1. In comparison, only two ARGs from the unbinned-assembled light fractions were identified.<br><br>CONCLUSIONS: The results indicate that both non-pathogenic soil-dwelling bacteria as well as potential clinical pathogens are present in this agricultural soil and several ARGs were identified from the labelled communities, but it is still unclear if horizontal gene transfer between these groups can occur.}, }
@article {pmid37072330, year = {2023}, author = {Fokina, AS and Karyagina, AS and Rusinov, IS and Moshensky, DM and Spirin, SA and Alexeevski, AV}, title = {Evolution of Restriction-Modification Systems Consisting of One Restriction Endonuclease and Two DNA Methyltransferases.}, journal = {Biochemistry. Biokhimiia}, volume = {88}, number = {2}, pages = {253-261}, doi = {10.1134/S0006297923020086}, pmid = {37072330}, issn = {1608-3040}, mesh = {DNA Restriction Enzymes/genetics ; *DNA Restriction-Modification Enzymes/genetics ; Phylogeny ; *Methyltransferases/genetics ; DNA ; }, abstract = {Some restriction-modification systems contain two DNA methyltransferases. In the present work, we have classified such systems according to the families of catalytic domains present in the restriction endonucleases and both DNA methyltransferases. Evolution of the restriction-modification systems containing an endonuclease with a NOV_C family domain and two DNA methyltransferases, both with DNA_methylase family domains, was investigated in detail. Phylogenetic tree of DNA methyltransferases from the systems of this class consists of two clades of the same size. Two DNA methyltransferases of each restriction-modification system of this class belong to the different clades. This indicates independent evolution of the two methyltransferases. We detected multiple cross-species horizontal transfers of the systems as a whole, as well as the cases of gene transfer between the systems.}, }
@article {pmid37070987, year = {2023}, author = {Dai, X and Sun, J and Zhu, B and Lv, M and Chen, L and Chen, L and Wang, X and Huang, J and Wang, L}, title = {Various Mobile Genetic Elements Involved in the Dissemination of the Phenicol-Oxazolidinone Resistance Gene optrA in the Zoonotic Pathogen Streptococcus suis: a Nonignorable Risk to Public Health.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0487522}, pmid = {37070987}, issn = {2165-0497}, mesh = {Humans ; *Oxazolidinones ; *Streptococcus suis/genetics ; Public Health ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; Interspersed Repetitive Sequences ; }, abstract = {The rapid increase of phenicol-oxazolidinone (PhO) resistance in Streptococcus suis due to transferable resistance gene optrA is a matter of concern. However, genetic mechanisms for the dissemination of the optrA gene remain to be discovered. Here, we selected 33 optrA-positive S. suis isolates for whole-genome sequencing and analysis. The IS1216E element was present in 85% of the optrA-carrying contigs despite genetic variation observed in the flanking region. IS1216E-optrA-carrying segments could be inserted into larger mobile genetic elements (MGEs), including integrative and conjugative elements, plasmids, prophages, and antibiotic resistance-associated genomic islands. IS1216E-mediated circularization occurred to form the IS1216E-optrA-carrying translocatable units, suggesting a crucial role of IS1216E in optrA spreading. Three optrA-carrying MGEs (ICESsuAKJ47_SSU1797, plasmid pSH0918, and prophage ΦSsuFJSM5_rum) were successfully transferred via conjugation at different transfer frequencies. Interestingly, two types of transconjugants were observed due to the multilocus integration of ICESsuAKJ47 into an alternative SSU1943 attachment site along with the primary SSU1797 attachment site (type 1) or into the single SSU1797 attachment site (type 2). In addition, conjugative transfer of an optrA-carrying plasmid and prophage in streptococci was validated for the first time. Considering the abundance of MGEs in S. suis and the mobility of IS1216E-optrA-carrying translocatable units, attention should be paid to the potential risks to public health from the emergence and spread of PhO-resistant S. suis. IMPORTANCE Antimicrobial resistance to phenicols and oxazolidinones by the dissemination of the optrA gene leads to treatment failure in both veterinary and human medicine. However, information about the profile of these MGEs (mobilome) that carry optrA and their transferability in streptococci was limited, especially for the zoonotic pathogen S. suis. This study showed that the optrA-carrying mobilome in S. suis includes integrative and conjugative elements (ICEs), plasmids, prophages, and antibiotic resistance-associated genomic islands. IS1216E-mediated formation of optrA-carrying translocatable units played important roles in optrA spreading between types of MGEs, and conjugative transfer of various optrA-carrying MGEs (ICEs, plasmids, and prophages) further facilitated the transfer of optrA across strains, highlighting a nonignorable risk to public health of optrA dissemination to other streptococci and even to bacteria of other genera.}, }
@article {pmid37070984, year = {2023}, author = {Wu, HY and Wei, ZL and Shi, DY and Li, HB and Li, XM and Yang, D and Zhou, SQ and Peng, XX and Yang, ZW and Yin, J and Chen, TJ and Li, JW and Jin, M}, title = {Simulated Gastric Acid Promotes the Horizontal Transfer of Multidrug Resistance Genes across Bacteria in the Gastrointestinal Tract at Elevated pH Levels.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0482022}, pmid = {37070984}, issn = {2165-0497}, mesh = {Humans ; *Genes, MDR ; Reactive Oxygen Species ; *Angiotensin Receptor Antagonists/pharmacology ; Gastric Acid ; Angiotensin-Converting Enzyme Inhibitors/pharmacology ; Bacteria/genetics ; Anti-Bacterial Agents/pharmacology ; Intestines ; Hydrogen-Ion Concentration ; Gene Transfer, Horizontal ; Genes, Bacterial ; Plasmids ; }, abstract = {The assessment of factors that can promote the transmission of antibiotic resistance genes (ARGs) across bacteria in the gastrointestinal tract is in great demand to understand the occurrence of infections related to antibiotic-resistant bacteria (ARB) in humans. However, whether acid-resistant enteric bacteria can promote ARG transmission in gastric fluid under high-pH conditions remains unknown. This study assessed the effects of simulated gastric fluid (SGF) at different pH levels on the RP4 plasmid-mediated conjugative transfer of ARGs. Moreover, transcriptomic analysis, measurement of reactive oxygen species (ROS) levels, assessment of cell membrane permeability, and real-time quantitative assessment of the expression of key genes were performed to identify the underlying mechanisms. The frequency of conjugative transfer was the highest in SGF at pH 4.5. Antidepressant consumption and certain dietary factors further negatively impacted this situation, with 5.66-fold and 4.26-fold increases in the conjugative transfer frequency being noted upon the addition of sertraline and 10% glucose, respectively, compared with that in the control group without any additives. The induction of ROS generation, the activation of cellular antioxidant systems, increases in cell membrane permeability, and the promotion of adhesive pilus formation were factors potentially contributing to the increased transfer frequency. These findings indicate that conjugative transfer could be enhanced under certain circumstances in SGF at elevated pH levels, thereby facilitating ARG transmission in the gastrointestinal tract. IMPORTANCE The low pH of gastric acid kills unwanted microorganisms, in turn affecting their inhabitation in the intestine. Hence, studies on the factors that influence antibiotic resistance gene (ARG) propagation in the gastrointestinal tract and on the underlying mechanisms are limited. In this study, we constructed a conjugative transfer model in the presence of simulated gastric fluid (SGF) and found that SGF could promote the dissemination of ARGs under high-pH conditions. Furthermore, antidepressant consumption and certain dietary factors could negatively impact this situation. Transcriptomic analysis and a reactive oxygen species assay revealed the overproduction of reactive oxygen species as a potential mechanism by which SGF could promote conjugative transfer. This finding can help provide a comprehensive understanding of the bloom of antibiotic-resistant bacteria in the body and create awareness regarding the risk of ARG transmission due to certain diseases or an improper diet and the subsequent decrease in gastric acid levels.}, }
@article {pmid37071810, year = {2023}, author = {Paulat, NS and Storer, JM and Moreno-Santillán, DD and Osmanski, AB and Sullivan, KAM and Grimshaw, JR and Korstian, J and Halsey, M and Garcia, CJ and Crookshanks, C and Roberts, J and Smit, AFA and Hubley, R and Rosen, J and Teeling, EC and Vernes, SC and Myers, E and Pippel, M and Brown, T and Hiller, M and ,  and Rojas, D and Dávalos, LM and Lindblad-Toh, K and Karlsson, EK and Ray, DA}, title = {Chiropterans Are a Hotspot for Horizontal Transfer of DNA Transposons in Mammalia.}, journal = {Molecular biology and evolution}, volume = {40}, number = {5}, pages = {}, pmid = {37071810}, issn = {1537-1719}, support = {MR/T021985/1/MRC_/Medical Research Council/United Kingdom ; R01 HG002939/HG/NHGRI NIH HHS/United States ; R01 HG008742/HG/NHGRI NIH HHS/United States ; U24 HG010136/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; *DNA Transposable Elements/genetics ; *Chiroptera/genetics ; Gene Transfer, Horizontal ; Evolution, Molecular ; Mammals/genetics ; Phylogeny ; }, abstract = {Horizontal transfer of transposable elements (TEs) is an important mechanism contributing to genetic diversity and innovation. Bats (order Chiroptera) have repeatedly been shown to experience horizontal transfer of TEs at what appears to be a high rate compared with other mammals. We investigated the occurrence of horizontally transferred (HT) DNA transposons involving bats. We found over 200 putative HT elements within bats; 16 transposons were shared across distantly related mammalian clades, and 2 other elements were shared with a fish and two lizard species. Our results indicate that bats are a hotspot for horizontal transfer of DNA transposons. These events broadly coincide with the diversification of several bat clades, supporting the hypothesis that DNA transposon invasions have contributed to genetic diversification of bats.}, }
@article {pmid37065212, year = {2023}, author = {Wang, H and Cheng, H and Huang, B and Hu, X and Chen, Y and Zheng, L and Yang, L and Deng, J and Wang, Q}, title = {Characterization of resistance genes and plasmids from sick children caused by Salmonella enterica resistance to azithromycin in Shenzhen, China.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1116172}, pmid = {37065212}, issn = {2235-2988}, mesh = {Humans ; Child ; Azithromycin/pharmacology ; *Salmonella enterica/genetics ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Salmonella Infections/microbiology ; Salmonella/genetics ; Plasmids/genetics ; Microbial Sensitivity Tests ; Chloramphenicol/pharmacology ; Drug Resistance, Multiple, Bacterial ; }, abstract = {INTRODUCTION: Samonella is 1 of 4 key global causes of diarrhoeal diseases, sometimes it can be serious, especially for yong children. Due to the extensive resistance of salmonella serotypes to conventional first-line drugs, macrolides (such as azithromycin) have been designated as the most important antibiotics for the treatment of salmonella. Antimicrobial resistance is a major public health problem in the world, and the mechanism of azithromycin resistance is rarely studied.<br><br>METHODS: This study determined the azithromycin resistance and plasmids of Salmonella enterica isolates from children attending the Shenzhen Children's Hospital. The susceptibility of ampicillin (AMP), ciprofloxacin (CIP), ceftriaxone (CRO), sulfamethoxazole (SMZ), chloramphenicol (CL), and azithromycin (AZM) were detected and the genes and plasmids from azithromycin-resistant Salmonella were detected by Illumina hi-seq and Nanopore MinIone whole genome sequencing (WGS) using a map-based method, and the genomic background of these factors was evaluated using various bioinformatics tools.<br><br>RESULTS: In total, 15 strains of nontyphoid Salmonella strains that were isolated (including S. typhimurium, S.London, S. Goldcoast, and S.Stanley) demonstrated resistance to azithromycin (minimum inhibitory concentration,MIC from 32 to >256 &#xb5;g/mL), and the resistance rate was 3.08% (15/487). The sensitivity test to other antibiotics demonstrated 100% resistance to AMP, and the resistance to SMZ and CL was 86.7% and 80.0%, respectively. Through WGS analysis, all isolates were positive for a plasmid-encoded mphA gene. Plasmid incompatibility typing identified five IncFIB(K), five IncHI2/HI2A/Q1, two IncC, one IncHI2/HI2A/N, one IncR, one IncFII and one IncHI2/HI2A plasmids. Sequence analyses of plasmids revealed extensive homology to various plasmids or transposons in regions involved in plasmid replication/maintenance functions and/or in antibiotic resistance gene clusters.<br><br>CONCLUSION: mphA is the main gene involved in azithromycin, a macrolide, and resistance to Salmonella. It is usually located on plasmids and easily spreads, hence posing a great threat to the current treatment of Salmonella infection. The plasmid sequence similarities suggest that the plasmids acquired resistance genes from a variety of enterica bacteria and underscore the importance of a further understanding of horizontal gene transfer among enterica bacteria.}, }
@article {pmid37062264, year = {2023}, author = {Jin, C and Cao, J and Zhang, K and Zhang, X and Cao, Z and Zou, W}, title = {Promotion effects and mechanisms of molybdenum disulfide on the propagation of antibiotic resistance genes in soil.}, journal = {Ecotoxicology and environmental safety}, volume = {256}, number = {}, pages = {114913}, doi = {10.1016/j.ecoenv.2023.114913}, pmid = {37062264}, issn = {1090-2414}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Molybdenum/pharmacology ; Genes, Bacterial ; Soil ; Gene Transfer, Horizontal ; Drug Resistance, Microbial/genetics ; Escherichia coli ; Plasmids ; }, abstract = {The rapid development of nanotechnology has aroused considerable attentions toward understanding the effects of engineered nanomaterials (ENMs) on the propagation of antibiotic resistance. Molybdenum disulfide (MoS2) is an extensively used ENM and poses potential risks associated with environmental exposure; nevertheless, the role of MoS2 toward antibiotic resistance genes (ARGs) transfer remains largely unknown. Herein, it was discovered that MoS2 nanosheets accelerated the horizontal transfer of RP4 plasmid across Escherichia coli in a dose-dependent manner (0.5-10 mg/L), with the maximum transfer frequency 2.07-fold higher than that of the control. Integration of physiological, transcriptomics, and metabolomics analyses demonstrated that SOS response in bacteria was activated by MoS2 due to the elevation of oxidative damage, accompanied by cell membrane permeabilization. MoS2 promoted bacterial adhesion and intercellular contact via stimulating the secretion of extracellular polysaccharides. The ATP levels were maximally increased by 305.7 % upon exposure to MoS2, and the expression of plasmid transfer genes was up-regulated, contributing to the accelerated plasmid conjugation and increased ARG abundance in soil. Our findings highlight the roles of emerging ENMs (e.g., MoS2) in ARGs dissemination, which is significant for the safe applications and risk management of ENMs under the development scenarios of nanotechnology.}, }
@article {pmid37061654, year = {2023}, author = {Elbehery, AHA and Beason, E and Siam, R}, title = {Metagenomic profiling of antibiotic resistance genes in Red Sea brine pools.}, journal = {Archives of microbiology}, volume = {205}, number = {5}, pages = {195}, pmid = {37061654}, issn = {1432-072X}, support = {Faculty (Research) Support Grant//The American University in Cairo/ ; }, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; Indian Ocean ; *Drug Resistance, Bacterial/genetics ; Macrolides ; Genes, Bacterial ; }, abstract = {Antibiotic resistance (AR) is an alarming global health concern, causing an annual death rate of more than 35,000 deaths in the US. AR is a natural phenomenon, reported in several pristine environments. In this study, we report AR in pristine Red Sea deep brine pools. Antimicrobial resistance genes (ARGs) were detected for several drug classes with tetracycline and macrolide resistance being the most abundant. As expected, ARGs abundance increased in accordance with the level of human impact with pristine Red Sea samples having the lowest mean ARG level followed by estuary samples, while activated sludge samples showed a significantly higher ARG level. ARG hierarchical clustering grouped drug classes for which resistance was detected in Atlantis II Deep brine pool independent of the rest of the samples. ARG abundance was significantly lower in the Discovery Deep brine pool. A correlation between integrons and ARGs abundance in brine pristine samples could be detected, while insertion sequences and plasmids showed a correlation with ARGs abundance in human-impacted samples not seen in brine pristine samples. This suggests different roles of distinct mobile genetic elements (MGEs) in ARG distribution in pristine versus human-impacted sites. Additionally, we showed the presence of mobile antibiotic resistance genes in the Atlantis II brine pool as evidenced by the co-existence of integrases and plasmid replication proteins on the same contigs harboring predicted multidrug-resistant efflux pumps. This study addresses the role of non-pathogenic environmental bacteria as a silent reservoir for ARGs, and the possible horizontal gene transfer mechanism mediating ARG acquisition.}, }
@article {pmid37061183, year = {2023}, author = {Gilbert, C and Maumus, F}, title = {Sidestepping Darwin: horizontal gene transfer from plants to insects.}, journal = {Current opinion in insect science}, volume = {57}, number = {}, pages = {101035}, doi = {10.1016/j.cois.2023.101035}, pmid = {37061183}, issn = {2214-5753}, mesh = {Animals ; *Gene Transfer, Horizontal ; Insecta/genetics ; *Hemiptera/genetics ; Plants/genetics ; Bacteria ; }, abstract = {Horizontal transfer of genetic material (HT) is the passage of DNA between organisms by means other than reproduction. Increasing numbers of HT are reported in insects, with bacteria, fungi, plants, and insects acting as the main sources of these transfers. Here, we provide a detailed account of plant-to-insect HT events. At least 14 insect species belonging to 6 orders are known to have received plant genetic material through HT. One of them, the whitefly Bemisia tabaci (Middle East Asia Minor 1), concentrates most of these transfers, with no less than 28 HT events yielding 55 plant-derived genes in this species. Several plant-to-insect HT events reported so far involve gene families known to play a role in plant-parasite interactions. We highlight methodological approaches that may further help characterize these transfers. We argue that plant-to-insect HT is likely more frequent than currently appreciated and that in-depth studies of these transfers will shed new light on plant-insect interactions.}, }
@article {pmid37055994, year = {2023}, author = {Li, B and Jeon, MK and Li, X and Yan, T}, title = {Differential impacts of salinity on antibiotic resistance genes during cattle manure stockpiling are linked to mobility potentials revealed by metagenomic sequencing.}, journal = {Journal of hazardous materials}, volume = {445}, number = {}, pages = {130590}, doi = {10.1016/j.jhazmat.2022.130590}, pmid = {37055994}, issn = {1873-3336}, mesh = {Cattle ; Animals ; *Anti-Bacterial Agents/pharmacology ; *Manure/analysis ; Genes, Bacterial ; Salinity ; Drug Resistance, Microbial/genetics ; }, abstract = {Livestock manure is an important source of antibiotic resistance genes (ARGs), and its salinity level can change during stockpiling. To understand how the salinity changes affect the fate of ARGs, cattle manure was adjusted of salinity and stockpiled in laboratory microcosms at low (0.3% salt), moderate (3.0%) and high salinity levels (10.0%) for 44 days. Amongst the five ARGs (tetO, blaTEM, sul1, tetM, and ermB) and the first-class integrase (intI1) monitored by qPCR, the relative abundance of tetO and blaTEM exhibited no clear trend in response to salinity levels, while that of sul1, tetM, ermB and intI1 showed clear downward trends over time at the lower salinity levels (0.3% and 3%) but not at the high salinity level (10%). Metagenomic contig construction of cattle manure samples revealed that sul1, tetM and ermB genes were more likely to associate with mobile genetic elements (MGEs) than tetO and blaTEM, suggesting that their slower decay at higher salinity levels was either caused by horizontal gene transfer or co-selection of ARGs and osmotic stress resistant determinants. Further analysis of metagenomic contigs showed that osmotic stress resistance can also be located on MGEs or in conjunction with ARGs.}, }
@article {pmid37054673, year = {2023}, author = {Moura de Sousa, J and Lourenço, M and Gordo, I}, title = {Horizontal gene transfer among host-associated microbes.}, journal = {Cell host &amp; microbe}, volume = {31}, number = {4}, pages = {513-527}, doi = {10.1016/j.chom.2023.03.017}, pmid = {37054673}, issn = {1934-6069}, mesh = {*Gene Transfer, Horizontal ; Bacteria/genetics ; Biological Evolution ; *Microbiota/genetics ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Horizontal gene transfer is an important evolutionary force, facilitating bacterial diversity. It is thought to be pervasive in host-associated microbiomes, where bacterial densities are high and mobile elements are frequent. These genetic exchanges are also key for the rapid dissemination of antibiotic resistance. Here, we review recent studies that have greatly extended our knowledge of the mechanisms underlying horizontal gene transfer, the ecological complexities of a network of interactions involving bacteria and their mobile elements, and the effect of host physiology on the rates of genetic exchanges. Furthermore, we discuss other, fundamental challenges in detecting and quantifying genetic exchanges in vivo, and how studies have contributed to start overcoming these challenges. We highlight the importance of integrating novel computational approaches and theoretical models with experimental methods where multiple strains and transfer elements are studied, both in vivo and in controlled conditions that mimic the intricacies of host-associated environments.}, }
@article {pmid37052605, year = {2023}, author = {Calder, A and Snyder, LAS}, title = {Diversity of the type VI secretion systems in the Neisseria spp.}, journal = {Microbial genomics}, volume = {9}, number = {4}, pages = {}, pmid = {37052605}, issn = {2057-5858}, mesh = {Humans ; *Type VI Secretion Systems/genetics ; Bacterial Proteins/genetics/metabolism ; }, abstract = {Complete Type VI Secretion Systems were identified in the genome sequence data of Neisseria subflava isolates sourced from throat swabs of human volunteers. The previous report was the first to describe two complete Type VI Secretion Systems in these isolates, both of which were distinct in terms of their gene organization and sequence homology. Since publication of the first report, Type VI Secretion System subtypes have been identified in Neisseria spp. The characteristics of each type in N. subflava are further investigated here and in the context of the other Neisseria spp., including identification of the lineages containing the different types and subtypes. Type VI Secretion Systems use VgrG for delivery of toxin effector proteins; several copies of vgrG and associated effector / immunity pairs are present in Neisseria spp. Based on sequence similarity between strains and species, these core Type VI Secretion System genes, vgrG, and effector / immunity genes may diversify via horizontal gene transfer, an instrument for gene acquisition and repair in Neisseria spp.}, }
@article {pmid37052502, year = {2023}, author = {Tang, B and Yang, A and Liu, P and Wang, Z and Jian, Z and Chen, X and Yan, Q and Liang, X and Liu, W}, title = {Outer Membrane Vesicles Transmitting blaNDM-1 Mediate the Emergence of Carbapenem-Resistant Hypervirulent Klebsiella pneumoniae.}, journal = {Antimicrobial agents and chemotherapy}, volume = {67}, number = {5}, pages = {e0144422}, pmid = {37052502}, issn = {1098-6596}, mesh = {Humans ; Klebsiella pneumoniae ; Meropenem/pharmacology ; *Klebsiella Infections/drug therapy ; Carbapenems/pharmacology ; Anti-Bacterial Agents/pharmacology ; *Carbapenem-Resistant Enterobacteriaceae ; }, abstract = {Dissemination of hypervirulent and carbapenem-resistant Klebsiella pneumoniae (CRKP) has been reported worldwide, posing a serious threat to antimicrobial therapy and public health. Outer membrane vesicles (OMVs) act as vectors for the horizontal transfer of virulence and resistance genes. However, K. pneumoniae OMVs that transfer carbapenem resistance genes into hypervirulent K. pneumoniae (hvKP) have been insufficiently investigated. Therefore, this study investigates the transmission of the blaNDM-1 gene encoding resistance via OMVs released from CRKP and the potential mechanism responsible for the carbapenem-resistant hypervirulent K. pneumoniae (CR-hvKP) emergence. OMVs were isolated via ultracentrifugation from CRKP with or without meropenem selective pressure. OMVs were then used to transform classical K. pneumoniae (ckp) ATCC 10031, extended-spectrum β-lactamase (ESBL)-producing K. pneumoniae ATCC 700603, and hvKP NTUH-K2044. Our results showed that meropenem treatment resulted in changes in the number and diameter of OMVs secreted by CRKP. OMVs derived from CRKP mediated the transfer of blaNDM-1 to ckp and hvKP, thereby increasing the carbapenem MIC of transformants. Further experiments confirmed that NTUH-K2044 transformants exhibited hypervirulence. Our study demonstrates, for the first time, that OMVs derived from CRKP can carry blaNDM-1 and deliver resistance genes to other K. pneumoniae strains, even hvKP. The transfer of carbapenem genes into hypervirulent strains may promote the emergence and dissemination of CR-hvKP. This study elucidates a new mechanism underlying the formation of CR-hvKP.}, }
@article {pmid37047476, year = {2023}, author = {Msaddak, A and Mars, M and Quiñones, MA and Lucas, MM and Pueyo, JJ}, title = {Lupin, a Unique Legume That Is Nodulated by Multiple Microsymbionts: The Role of Horizontal Gene Transfer.}, journal = {International journal of molecular sciences}, volume = {24}, number = {7}, pages = {}, pmid = {37047476}, issn = {1422-0067}, support = {//Ministry of High Education and Scientific Research, Tunisia/ ; AGL2017-88381-R//Agencia Estatal de Investigaci&#xf3;n, AEI, Spain/ ; PID2021-125371OB-I00//Agencia Estatal de Investigaci&#xf3;n, AEI, Spain/ ; COOPB20610//Spanish National Research Council/ ; }, mesh = {*Fabaceae/genetics/microbiology ; *Lupinus/genetics/microbiology ; Root Nodules, Plant/microbiology ; Phylogeny ; Gene Transfer, Horizontal ; Health Promotion ; DNA, Bacterial/genetics ; Vegetables/genetics ; *Rhizobium/genetics ; *Bradyrhizobium/genetics ; Symbiosis/genetics ; Sequence Analysis, DNA ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Lupin is a high-protein legume crop that grows in a wide range of edaphoclimatic conditions where other crops are not viable. Its unique seed nutrient profile can promote health benefits, and it has been proposed as a phytoremediation plant. Most rhizobia nodulating Lupinus species belong to the genus Bradyrhizobium, comprising strains that are phylogenetically related to B. cytisi, B. hipponenese, B. rifense, B. iriomotense/B. stylosanthis, B. diazoefficiens, B. japonicum, B. canariense/B. lupini, and B. retamae/B. valentinum. Lupins are also nodulated by fast-growing bacteria within the genera Microvirga, Ochrobactrum, Devosia, Phyllobacterium, Agrobacterium, Rhizobium, and Neorhizobium. Phylogenetic analyses of the nod and nif genes, involved in microbial colonization and symbiotic nitrogen fixation, respectively, suggest that fast-growing lupin-nodulating bacteria have acquired their symbiotic genes from rhizobial genera other than Bradyrhizobium. Horizontal transfer represents a key mechanism allowing lupin to form symbioses with bacteria that were previously considered as non-symbiotic or unable to nodulate lupin, which might favor lupin's adaptation to specific habitats. The characterization of yet-unstudied Lupinus species, including microsymbiont whole genome analyses, will most likely expand and modify the current lupin microsymbiont taxonomy, and provide additional knowledge that might help to further increase lupin's adaptability to marginal soils and climates.}, }
@article {pmid37043515, year = {2023}, author = {Novelo, M and Dutra, HL and Metz, HC and Jones, MJ and Sigle, LT and Frentiu, FD and Allen, SL and Chenoweth, SF and McGraw, EA}, title = {Dengue and chikungunya virus loads in the mosquito Aedes aegypti are determined by distinct genetic architectures.}, journal = {PLoS pathogens}, volume = {19}, number = {4}, pages = {e1011307}, pmid = {37043515}, issn = {1553-7374}, support = {R01 AI143758/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Chikungunya virus/physiology ; *Aedes ; Mosquito Vectors ; *Chikungunya Fever ; *Dengue ; }, abstract = {Aedes aegypti is the primary vector of the arboviruses dengue (DENV) and chikungunya (CHIKV). These viruses exhibit key differences in their vector interactions, the latter moving more quicky through the mosquito and triggering fewer standard antiviral pathways. As the global footprint of CHIKV continues to expand, we seek to better understand the mosquito's natural response to CHIKV-both to compare it to DENV:vector coevolutionary history and to identify potential targets in the mosquito for genetic modification. We used a modified full-sibling design to estimate the contribution of mosquito genetic variation to viral loads of both DENV and CHIKV. Heritabilities were significant, but higher for DENV (40%) than CHIKV (18%). Interestingly, there was no genetic correlation between DENV and CHIKV loads between siblings. These data suggest Ae. aegypti mosquitoes respond to the two viruses using distinct genetic mechanisms. We also examined genome-wide patterns of gene expression between High and Low CHIKV families representing the phenotypic extremes of viral load. Using RNAseq, we identified only two loci that consistently differentiated High and Low families: a long non-coding RNA that has been identified in mosquito screens post-infection and a distant member of a family of Salivary Gland Specific (SGS) genes. Interestingly, the latter gene is also associated with horizontal gene transfer between mosquitoes and the endosymbiotic bacterium Wolbachia. This work is the first to link the SGS gene to a mosquito phenotype. Understanding the molecular details of how this gene contributes to viral control in mosquitoes may, therefore, also shed light on its role in Wolbachia.}, }
@article {pmid37037946, year = {2023}, author = {Yang, P and Zhu, X and Ning, K}, title = {Microbiome-based enrichment pattern mining has enabled a deeper understanding of the biome-species-function relationship.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {391}, pmid = {37037946}, issn = {2399-3642}, mesh = {*Copper ; Biological Evolution ; *Microbiota/genetics ; Soil ; Metagenome ; }, abstract = {Microbes live in diverse habitats (i.e. biomes), yet their species and genes were biome-specific, forming enrichment patterns. These enrichment patterns have mirrored the biome-species-function relationship, which is shaped by ecological and evolutionary principles. However, a grand picture of these enrichment patterns, as well as the roles of external and internal factors in driving these enrichment patterns, remain largely unexamined. In this work, we have examined the enrichment patterns based on 1705 microbiome samples from four representative biomes (Engineered, Gut, Freshwater, and Soil). Moreover, an "enrichment sphere" model was constructed to elucidate the regulatory principles behind these patterns. The driving factors for this model were revealed based on two case studies: (1) The copper-resistance genes were enriched in Soil biomes, owing to the copper contamination and horizontal gene transfer. (2) The flagellum-related genes were enriched in the Freshwater biome, due to high fluidity and vertical gene accumulation. Furthermore, this enrichment sphere model has valuable applications, such as in biome identification for metagenome samples, and in guiding 3D structure modeling of proteins. In summary, the enrichment sphere model aims towards creating a bluebook of the biome-species-function relationships and be applied in many fields.}, }
@article {pmid37037312, year = {2023}, author = {Wang, H and Min, C and Xia, F and Xia, Y and Tang, M and Li, J and Hu, Y and Zou, M}, title = {Metagenomic analysis reveals the short-term influences on conjugation of blaNDM-1 and microbiome in hospital wastewater by silver nanoparticles at environmental-related concentration.}, journal = {Environmental research}, volume = {228}, number = {}, pages = {115866}, doi = {10.1016/j.envres.2023.115866}, pmid = {37037312}, issn = {1096-0953}, mesh = {Wastewater ; Silver ; Metagenome ; *Metal Nanoparticles ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; *Microbiota ; Hospitals ; }, abstract = {Hospital wastewater contains large amounts of antibiotic-resistant bacteria and serves as an important reservoir for horizontal gene transfer (HGT). However, the response of the microbiome in hospital wastewater to silver remains unclear. In this study, the short-term impacts of silver on the microbiome in hospital wastewater were investigated by metagenome next-generation sequencing. The influence of silver on the conjugation of plasmid carrying blaNDM-1 was further examined. Our results showed that in hospital wastewater, high abundances of antibiotic resistance genes (ARGs) were detected. The distribution tendencies of certain ARG types on chromosomes or plasmids were different. Clinically important ARGs were identified in phage-like contigs, indicating potential transmission via transduction. Pseudomonadales, Enterobacterales, and Bacteroidales were the major ARG hosts. Mobile genetic elements were mainly detected in plasmids and associated with various types of ARGs. The binning approach identified 29 bins that were assigned to three phyla. Various ARGs and virulence factors were identified in 14 and 11 bins, respectively. MetaCHIP identified 49 HGT events. The transferred genes were annotated as ARGs, mobile genetic elements, and functional genes, and they mainly originated from donors belonging to Bacteroides and Pseudomonadales. In addition, 20 nm AgNPs reduced microbial diversity and enhanced the relative abundance of Acinetobacter. The changes induced by 20 nm AgNPs included increases in the abundances of ARGs and genes involved lipid metabolism pathway. Conjugation experiments showed that Ag[+] and 20 nm AgNPs caused 2.38-, 3.31-, 4.72-, and 4.57-fold and 1.46-, 1.61-, 3.86-, and 2.16-fold increases in conjugation frequencies of plasmid with blaNDM-1 at 0.1, 1, 10, and 100 μg/L, respectively. Our findings provide insight into the response of the microbiome in hospital wastewater to silver, emphasize the adaptation capability of Acinetobacter inhabiting hospitals against adverse environments, and highlight the promotion of silver for antibiotic resistance.}, }
@article {pmid37036996, year = {2023}, author = {Kalluraya, CA and Weitzel, AJ and Tsu, BV and Daugherty, MD}, title = {Bacterial origin of a key innovation in the evolution of the vertebrate eye.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {16}, pages = {e2214815120}, pmid = {37036996}, issn = {1091-6490}, support = {R35 GM133633/GM/NIGMS NIH HHS/United States ; T32 GM007240/GM/NIGMS NIH HHS/United States ; 1021386//Burroughs Wellcome Fund (BWF)/ ; 00032011//Pew Charitable Trusts (Pew)/ ; }, mesh = {Animals ; *Genes, Bacterial ; *Vertebrates/metabolism ; Eye Proteins/genetics ; Retinoids/metabolism ; Invertebrates/genetics ; Vision, Ocular/genetics ; }, abstract = {The vertebrate eye was described by Charles Darwin as one of the greatest potential challenges to a theory of natural selection by stepwise evolutionary processes. While numerous evolutionary transitions that led to the vertebrate eye have been explained, some aspects appear to be vertebrate specific with no obvious metazoan precursor. One critical difference between vertebrate and invertebrate vision hinges on interphotoreceptor retinoid-binding protein (IRBP, also known as retinol-binding protein, RBP3), which enables the physical separation and specialization of cells in the vertebrate visual cycle by promoting retinoid shuttling between cell types. While IRBP has been functionally described, its evolutionary origin has remained elusive. Here, we show that IRBP arose via acquisition of novel genetic material from bacteria by interdomain horizontal gene transfer (iHGT). We demonstrate that a gene encoding a bacterial peptidase was acquired prior to the radiation of extant vertebrates >500 Mya and underwent subsequent domain duplication and neofunctionalization to give rise to vertebrate IRBP. Our phylogenomic analyses on >900 high-quality genomes across the tree of life provided the resolution to distinguish contamination in genome assemblies from true instances of horizontal acquisition of IRBP and led us to discover additional independent transfers of the same bacterial peptidase gene family into distinct eukaryotic lineages. Importantly, this work illustrates the evolutionary basis of a key transition that led to the vertebrate visual cycle and highlights the striking impact that acquisition of bacterial genes has had on vertebrate evolution.}, }
@article {pmid37036995, year = {2023}, author = {Verster, KI and Cinege, G and Lipinszki, Z and Magyar, LB and Kurucz, &#xc9; and Tarnopol, RL and Ábrahám, E and Darula, Z and Karageorgi, M and Tamsil, JA and Akalu, SM and Andó, I and Whiteman, NK}, title = {Evolution of insect innate immunity through domestication of bacterial toxins.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {16}, pages = {e2218334120}, pmid = {37036995}, issn = {1091-6490}, support = {R35 GM119816/GM/NIGMS NIH HHS/United States ; T32 GM132022/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Domestication ; *Bacterial Toxins/metabolism ; Drosophila/genetics/metabolism ; Gene Transfer, Horizontal ; *Wasps/metabolism ; Immunity, Innate/genetics ; }, abstract = {Toxin cargo genes are often horizontally transferred by phages between bacterial species and are known to play an important role in the evolution of bacterial pathogenesis. Here, we show how these same genes have been horizontally transferred from phage or bacteria to animals and have resulted in novel adaptations. We discovered that two widespread bacterial genes encoding toxins of animal cells, cytolethal distending toxin subunit B (cdtB) and apoptosis-inducing protein of 56 kDa (aip56), were captured by insect genomes through horizontal gene transfer from bacteria or phages. To study the function of these genes in insects, we focused on Drosophila ananassae as a model. In the D. ananassae subgroup species, cdtB and aip56 are present as singular (cdtB) or fused copies (cdtB::aip56) on the second chromosome. We found that cdtB and aip56 genes and encoded proteins were expressed by immune cells, some proteins were localized to the wasp embryo's serosa, and their expression increased following parasitoid wasp infection. Species of the ananassae subgroup are highly resistant to parasitoid wasps, and we observed that D. ananassae lines carrying null mutations in cdtB and aip56 toxin genes were more susceptible to parasitoids than the wild type. We conclude that toxin cargo genes were captured by these insects millions of years ago and integrated as novel modules into their innate immune system. These modules now represent components of a heretofore undescribed defense response and are important for resistance to parasitoid wasps. Phage or bacterially derived eukaryotic toxin genes serve as macromutations that can spur the instantaneous evolution of novelty in animals.}, }
@article {pmid37036347, year = {2023}, author = {Lewis, AM and Willard, DJ and H Manesh, MJ and Sivabalasarma, S and Albers, SV and Kelly, RM}, title = {Stay or Go: Sulfolobales Biofilm Dispersal Is Dependent on a Bifunctional VapB Antitoxin.}, journal = {mBio}, volume = {14}, number = {2}, pages = {e0005323}, pmid = {37036347}, issn = {2150-7511}, support = {T32 GM133366/GM/NIGMS NIH HHS/United States ; 2T32GM008776/NH/NIH HHS/United States ; }, mesh = {*Antitoxins/metabolism ; Bacterial Proteins/metabolism ; *Bacterial Toxins/metabolism ; Sulfolobales ; Biofilms ; }, abstract = {A type II VapB14 antitoxin regulates biofilm dispersal in the archaeal thermoacidophile Sulfolobus acidocaldarius through traditional toxin neutralization but also through noncanonical transcriptional regulation. Type II VapC toxins are ribonucleases that are neutralized by their proteinaceous cognate type II VapB antitoxin. VapB antitoxins have a flexible tail at their C terminus that covers the toxin's active site, neutralizing its activity. VapB antitoxins also have a DNA-binding domain at their N terminus that allows them to autorepress not only their own promoters but also distal targets. VapB14 antitoxin gene deletion in S. acidocaldarius stunted biofilm and planktonic growth and increased motility structures (archaella). Conversely, planktonic cells were devoid of archaella in the ΔvapC14 cognate toxin mutant. VapB14 is highly conserved at both the nucleotide and amino acid levels across the Sulfolobales, extremely unusual for type II antitoxins, which are typically acquired through horizontal gene transfer. Furthermore, homologs of VapB14 are found across the Crenarchaeota, in some Euryarchaeota, and even bacteria. S. acidocaldarius vapB14 and its homolog in the thermoacidophile Metallosphaera sedula (Msed_0871) were both upregulated in biofilm cells, supporting the role of the antitoxin in biofilm regulation. In several Sulfolobales species, including M. sedula, homologs of vapB14 and vapC14 are not colocalized. Strikingly, Sulfuracidifex tepidarius has an unpaired VapB14 homolog and lacks a cognate VapC14, illustrating the toxin-independent conservation of the VapB14 antitoxin. The findings here suggest that a stand-alone VapB-type antitoxin was the product of selective evolutionary pressure to influence biofilm formation in these archaea, a vital microbial community behavior. IMPORTANCE Biofilms allow microbes to resist a multitude of stresses and stay proximate to vital nutrients. The mechanisms of entering and leaving a biofilm are highly regulated to ensure microbial survival, but are not yet well described in archaea. Here, a VapBC type II toxin-antitoxin system in the thermoacidophilic archaeon Sulfolobus acidocaldarius was shown to control biofilm dispersal through a multifaceted regulation of the archaeal motility structure, the archaellum. The VapC14 toxin degrades an RNA that causes an increase in archaella and swimming. The VapB14 antitoxin decreases archaella and biofilm dispersal by binding the VapC14 toxin and neutralizing its activity, while also repressing the archaellum genes. VapB14-like antitoxins are highly conserved across the Sulfolobales and respond similarly to biofilm growth. In fact, VapB14-like antitoxins are also found in other archaea, and even in bacteria, indicating an evolutionary pressure to maintain this protein and its role in biofilm formation.}, }
@article {pmid37036197, year = {2023}, author = {Mota-Bravo, L and Camps, M and Muñoz-Gutiérrez, I and Tatarenkov, A and Warner, C and Suarez, I and Cortés-Cortés, G}, title = {Detection of Horizontal Gene Transfer Mediated by Natural Conjugative Plasmids in E. coli.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {193}, pages = {}, doi = {10.3791/64523}, pmid = {37036197}, issn = {1940-087X}, mesh = {*Escherichia coli/genetics ; *Gene Transfer, Horizontal ; Conjugation, Genetic ; Plasmids/genetics ; Anti-Bacterial Agents ; }, abstract = {Conjugation represents one of the main mechanisms facilitating horizontal gene transfer in Gram-negative bacteria. This work describes methods for the study of the mobilization of naturally occurring conjugative plasmids, using two naturally-occurring plasmids as an example. These protocols rely on the differential presence of selectable markers in donor, recipient, and conjugative plasmid. Specifically, the methods described include 1) the identification of natural conjugative plasmids, 2) the quantification of conjugation rates in solid culture, and 3) the diagnostic detection of the antibiotic resistance genes and plasmid replicon types in transconjugant recipients by polymerase chain reaction (PCR). The protocols described here have been developed in the context of studying the evolutionary ecology of horizontal gene transfer, to screen for the presence of conjugative plasmids carrying antibiotic-resistance genes in bacteria found in the environment. The efficient transfer of conjugative plasmids observed in these experiments in culture highlights the biological relevance of conjugation as a mechanism promoting horizontal gene transfer in general and the spread of antibiotic resistance in particular.}, }
@article {pmid37033775, year = {2023}, author = {Alborzi, A and Hosseini, M and Bahrami, S and Ghorbanpoor, M and Tabandeh, M}, title = {Evaluation of hematological changes, oxidant/antioxidant status and immuno-logical responses in sheep and goats naturally infected with Linguatula serrata.}, journal = {Veterinary research forum : an international quarterly journal}, volume = {14}, number = {3}, pages = {161-167}, pmid = {37033775}, issn = {2008-8140}, abstract = {Linguatula serrata is a worldwide zoonotic food-borne parasite. The parasite is responsible for linguatulosis and poses a concern to human and animal health in endemic regions. This study investigated the hematological changes, oxidant/antioxidant status and immunological responses in goats and sheep naturally infected with L. serrata. Hematological changes, antioxidant enzymes and malondialdehyde (MDA) levels were measured. The level of inter-leukin-2 (IL-2), IL-4, IL-5, IL-10, and tumor necrosis factor alpha (TNF-α) mRNA expression was investigated in lymph nodes. According to the hemogram results, eosinophils were significantly increased in the infected goats and sheep, and Horizontal Gene Transfer (HGT), hematocrit (HCT), and mean corpuscular hemoglobin concentration (MCHC) were significantly decreased. The levels of MDA and the activity of glutathione peroxidase (GPx) were significantly higher in infected animals than in non-infected animals. However, the activity of superoxide dismutase (SOD) and catalase (CAT) was significantly lower in infected animals than in non-infected animals. A comparison of the cytokine mRNA expression in lymph nodes from infected and non-infected animals showed higher cytokine expression in the infected animals. Infection with L. serrata caused microcytic hypochromic and normocytic hypochromic anemia in goats and sheep. The inconsistent results of immunological changes were found in infected goats and sheep. In both animals, oxidative stress occurred and led to an increase in lipid peroxidation. L. serrata created a cytokine microenvironment biased towards the type 2 immune responses.}, }
@article {pmid37030228, year = {2023}, author = {Chen, J and Xia, H and Huang, K and Li, J and Xie, J}, title = {Earthworms restructure the distribution of extracellular antibiotics resistance genes of sludge by modifying the structure of extracellular polymeric substances during vermicomposting.}, journal = {Journal of hazardous materials}, volume = {452}, number = {}, pages = {131315}, doi = {10.1016/j.jhazmat.2023.131315}, pmid = {37030228}, issn = {1873-3336}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Sewage/chemistry ; Extracellular Polymeric Substance Matrix ; *Oligochaeta/genetics ; Genes, Bacterial ; }, abstract = {The role of earthworms in reducing the antibiotic resistance genes (ARGs) in sludge vermicompost remains unclear. The structure of extracellular polymeric substance (EPS) of sludge may be associated with the horizontal gene transfer behavior of ARGs in the vermicomposting of sludge. Therefore, this study aimed to investigate the effects of earthworms on the structural characteristics of EPS associated with the fate of ARGs in EPS during the vermicomposting of sludge. The results showed vermicomposting could diminish the abundance of ARGs and mobile genetic elements (MGEs) in the EPS of sludge by 47.93 % and 7.75 %, compared to the control, respectively. Relative to the control, vermicomposting also led to the reduction of MGEs abundances in the soluble EPS of 40.04 %, lightly bound EPS of 43.53 %, and tightly bound EPS of 70.49 %, respectively. The total abundances of certain ARGs dramatically diminished 95.37 % in tightly bound EPS of sludge during vermicomposting. In vermicomposting, the main influencing factor of ARGs distribution was the proteins in LB-EPS, accounting for 48.5 % of the variation. This study suggests that the earthworms lower the total abundances of ARGs by regulating the microbial community and modifying the microbial metabolic pathways associated with ARGs and MGEs in the EPS of sludge.}, }
@article {pmid37023995, year = {2023}, author = {Botts, RT and Page, DM and Bravo, JA and Brown, ML and Castilleja, CC and Guzman, VL and Hall, S and Henderson, JD and Kenney, SM and Lensink, ME and Paternoster, MV and Pyle, SL and Ustick, L and Walters-Laird, CJ and Top, EM and Cummings, DE}, title = {Polluted wetlands contain multidrug-resistance plasmids encoding CTX-M-type extended-spectrum β-lactamases.}, journal = {Plasmid}, volume = {126}, number = {}, pages = {102682}, pmid = {37023995}, issn = {1095-9890}, support = {R15 GM102995/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Plasmids/genetics ; *Escherichia coli/genetics ; Wetlands ; Anti-Bacterial Agents/pharmacology ; Cefotaxime/pharmacology ; Virulence Factors ; beta-Lactamases/genetics ; *Escherichia coli Infections ; Microbial Sensitivity Tests ; }, abstract = {While most detailed analyses of antibiotic resistance plasmids focus on those found in clinical isolates, less is known about the vast environmental reservoir of mobile genetic elements and the resistance and virulence factors they encode. We selectively isolated three strains of cefotaxime-resistant Escherichia coli from a wastewater-impacted coastal wetland. The cefotaxime-resistant phenotype was transmissible to a lab strain of E. coli after one hour, with frequencies as high as 10[-3] transconjugants per recipient. Two of the plasmids also transferred cefotaxime resistance to Pseudomonas putida, but these were unable to back-transfer this resistance from P. putida to E. coli. In addition to the cephalosporins, E. coli transconjugants inherited resistance to at least seven distinct classes of antibiotics. Complete nucleotide sequences revealed large IncF-type plasmids with globally distributed replicon sequence types F31:A4:B1 and F18:B1:C4 carrying diverse antibiotic resistance and virulence genes. The plasmids encoded extended-spectrum β-lactamases blaCTX-M-15 or blaCTX-M-55, each associated with the insertion sequence ISEc9, although in different local arrangements. Despite similar resistance profiles, the plasmids shared only one resistance gene in common, the aminoglycoside acetyltransferase aac(3)-IIe. Plasmid accessory cargo also included virulence factors involved in iron acquisition and defense against host immunity. Despite their sequence similarities, several large-scale recombination events were detected, including rearrangements and inversions. In conclusion, selection with a single antibiotic, cefotaxime, yielded conjugative plasmids conferring multiple resistance and virulence factors. Clearly, efforts to limit the spread of antibiotic resistance and virulence among bacteria must include a greater understanding of mobile elements in the natural and human-impacted environments.}, }
@article {pmid37023132, year = {2023}, author = {Urquhart, AS and Vogan, AA and Gardiner, DM and Idnurm, A}, title = {Starships are active eukaryotic transposable elements mobilized by a new family of tyrosine recombinases.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {15}, pages = {e2214521120}, pmid = {37023132}, issn = {1091-6490}, mesh = {*DNA Transposable Elements/genetics ; *Eukaryota/genetics ; Gene Transfer, Horizontal ; Recombinases/genetics ; Tyrosine/genetics ; Evolution, Molecular ; }, abstract = {Transposable elements in eukaryotic organisms have historically been considered "selfish," at best conferring indirect benefits to their host organisms. The Starships are a recently discovered feature in fungal genomes that are, in some cases, predicted to confer beneficial traits to their hosts and also have hallmarks of being transposable elements. Here, we provide experimental evidence that Starships are indeed autonomous transposons, using the model Paecilomyces variotii, and identify the HhpA "Captain" tyrosine recombinase as essential for their mobilization into genomic sites with a specific target site consensus sequence. Furthermore, we identify multiple recent horizontal gene transfers of Starships, implying that they jump between species. Fungal genomes have mechanisms to defend against mobile elements, which are frequently detrimental to the host. We discover that Starships are also vulnerable to repeat-induced point mutation defense, thereby having implications on the evolutionary stability of such elements.}, }
@article {pmid37022443, year = {2023}, author = {Stentz, R and Cheema, J and Philo, M and Carding, SR}, title = {A Possible Aquatic Origin of the Thiaminase TenA of the Human Gut Symbiont Bacteroides thetaiotaomicron.}, journal = {Journal of molecular evolution}, volume = {91}, number = {4}, pages = {482-491}, pmid = {37022443}, issn = {1432-1432}, support = {BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/CCG1860/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10355/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Humans ; Animals ; *Bacteroides thetaiotaomicron/metabolism ; Phylogeny ; Australia ; Thiamine/metabolism ; }, abstract = {TenA thiamin-degrading enzymes are commonly found in prokaryotes, plants, fungi and algae and are involved in the thiamin salvage pathway. The gut symbiont Bacteroides thetaiotaomicron (Bt) produces a TenA protein (BtTenA) which is packaged into its extracellular vesicles. An alignment of BtTenA protein sequence with proteins from different databases using the basic local alignment search tool (BLAST) and the generation of a phylogenetic tree revealed that BtTenA is related to TenA-like proteins not only found in a small number of intestinal bacterial species but also in some aquatic bacteria, aquatic invertebrates, and freshwater fish. This is, to our knowledge, the first report describing the presence of TenA-encoding genes in the genome of members of the animal kingdom. By searching metagenomic databases of diverse host-associated microbial communities, we found that BtTenA homologues were mostly represented in biofilms present on the surface of macroalgae found in Australian coral reefs. We also confirmed the ability of a recombinant BtTenA to degrade thiamin. Our study shows that BttenA-like genes which encode a novel sub-class of TenA proteins are sparingly distributed across two kingdoms of life, a feature of accessory genes known for their ability to spread between species through horizontal gene transfer.}, }
@article {pmid37022212, year = {2023}, author = {Tóth, AG and Judge, MF and Nagy, S&#xc1; and Papp, M and Solymosi, N}, title = {A survey on antimicrobial resistance genes of frequently used probiotic bacteria, 1901 to 2022.}, journal = {Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin}, volume = {28}, number = {14}, pages = {}, pmid = {37022212}, issn = {1560-7917}, mesh = {*Gram-Positive Bacteria/drug effects/genetics ; *Drug Resistance, Bacterial/genetics ; Probiotics ; Bifidobacterium animalis/drug effects/genetics ; Lactobacillales/drug effects/genetics ; Genome, Bacterial ; *Genes, Bacterial ; }, abstract = {BackgroundAntimicrobial resistance (AMR) is caused by AMR determinants, mainly genes (ARGs) in the bacterial genome. Bacteriophages, integrative mobile genetic elements (iMGEs) or plasmids can allow ARGs to be exchanged among bacteria by horizontal gene transfer (HGT). Bacteria, including bacteria with ARGs, can be found in food. Thus, it is conceivable that in the gastrointestinal tract, bacteria from the gut flora could take up ARGs from food.AimThe study objective was to gain insight into the ARG set carried by commonly used probiotic bacteria that may enter the human body with non-fermented foods, fermented foods, or probiotic dietary supplements (FFPs) and to assess ARG mobility.MethodsNext generation sequencing whole genome data from 579 isolates of 12 commonly employed probiotic bacterial species were collected from a public repository. Using bioinformatical tools, ARGs were analysed and linkage with mobile genetic elements assessed.ResultsResistance genes were found in eight bacterial species. The ratios of ARG positive/negative samples per species were: Bifidobacterium animalis (65/0), Lactiplantibacillus plantarum (18/194), Lactobacillus delbrueckii (1/40), Lactobacillus helveticus (2/64), Lactococcus lactis (74/5), Leucoconstoc mesenteroides (4/8), Levilactobacillus brevis (1/46), Streptococcus thermophilus (4/19). In 66% (112/169) of the ARG-positive samples, at least one ARG could be linked to plasmids or iMGEs. No bacteriophage-linked ARGs were found.ConclusionThe finding of potentially mobile ARGs in probiotic strains for human consumption raises awareness of a possibility of ARG HGT in the gastrointestinal tract. In addition to existing recommendations, screening FFP bacterial strains for ARG content and mobility characteristics might be considered.}, }
@article {pmid37020720, year = {2023}, author = {Liu, Q and Yang, LL and Xin, YH}, title = {Diversity of the genus Cryobacterium and proposal of 19 novel species isolated from glaciers.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1115168}, pmid = {37020720}, issn = {1664-302X}, abstract = {The bacterial genus Cryobacterium includes at present 14 species that live in cryospheric environments. In this study, we analyzed 101 genomes of Cryobacterium with pure cultures obtained from GenBank. They could be classified into 44 species based on average nucleotide identity (ANI) analysis, showing the diversity of Cryobacterium. Among these, 19 strains in our laboratory were isolated from the glacier samples in China. The pairwise ANI values of these 19 strains and known species were <95%, indicating that they represented 19 novel species. The comparative genomic analysis showed significant differences in gene content between the two groups with a maximum growth temperature (T max) of ≤ 20°C and a T max of >20°C. A comprehensive and robust phylogenetic tree, including 14 known species and 19 novel species, was constructed and showed five phylogenetic branches based on 265 concatenated single-copy gene sequences. The T max parameter had a strong phylogenetic signal, indicating that the temperature adaptation of Cryobacterium was largely through vertical transfer rather than horizontal gene transfer and was affected by selection. Furthermore, using polyphasic taxonomy combined with phylogenomic analysis, we proposed 19 novel species of the genus Cryobacterium by the following 19 names: Cryobacterium serini sp. nov., Cryobacterium lactosi sp. nov., Cryobacterium gelidum sp. nov., Cryobacterium suzukii sp. nov., Cryobacterium fucosi sp. nov., Cryobacterium frigoriphilum sp. nov., Cryobacterium cryoconiti sp. nov., Cryobacterium lyxosi sp. nov., Cryobacterium sinapicolor sp. nov., Cryobacterium sandaracinum sp. nov., Cryobacterium cheniae sp. nov., Cryobacterium shii sp. nov., Cryobacterium glucosi sp. nov., Cryobacterium algoritolerans sp. nov., Cryobacterium mannosilyticum sp. nov., Cryobacterium adonitolivorans sp. nov., Cryobacterium algoricola sp. nov., Cryobacterium tagatosivorans sp. nov., and Cryobacterium glaciale sp. nov. Overall, the taxonomy and genomic analysis can improve our knowledge of phenotypic diversity, genetic diversity, and evolutionary characteristics of Cryobacterium.}, }
@article {pmid37019751, year = {2023}, author = {Dart, E and Ahlgren, NA}, title = {New tRNA-targeting transposons that hijack phage and vesicles.}, journal = {Trends in genetics : TIG}, volume = {39}, number = {6}, pages = {433-435}, doi = {10.1016/j.tig.2023.03.004}, pmid = {37019751}, issn = {0168-9525}, mesh = {*Bacteriophages/genetics ; Gene Transfer, Horizontal/genetics ; *Cyanobacteria/genetics ; RNA, Transfer/genetics ; Genomic Islands ; }, abstract = {Genomic islands are hotspots for horizontal gene transfer (HGT) in bacteria, but, for Prochlorococcus, an abundant marine cyanobacterium, how these islands form has puzzled scientists. With the discovery of tycheposons, a new family of transposons, Hackl et al. provide evidence for elegant new mechanisms of gene rearrangement and transfer among Prochlorococcus and bacteria more broadly.}, }
@article {pmid37018030, year = {2023}, author = {Jerez, SA and Plaza, N and Bravo, V and Urrutia, IM and Blondel, CJ}, title = {Vibrio type III secretion system 2 is not restricted to the Vibrionaceae and encodes differentially distributed repertoires of effector proteins.}, journal = {Microbial genomics}, volume = {9}, number = {4}, pages = {}, pmid = {37018030}, issn = {2057-5858}, mesh = {Humans ; Type III Secretion Systems ; *Vibrionaceae ; Phylogeny ; *Vibrio Infections/microbiology ; *Vibrio parahaemolyticus/genetics ; }, abstract = {Vibrio parahaemolyticus is the leading cause of seafood-borne gastroenteritis worldwide. A distinctive feature of the O3:K6 pandemic clone, and its derivatives, is the presence of a second, phylogenetically distinct, type III secretion system (T3SS2) encoded within the genomic island VPaI-7. The T3SS2 allows the delivery of effector proteins directly into the cytosol of infected eukaryotic cells to subvert key host-cell processes, critical for V. parahaemolyticus to colonize and cause disease. Furthermore, the T3SS2 also increases the environmental fitness of V. parahaemolyticus in its interaction with bacterivorous protists; hence, it has been proposed that it contributed to the global oceanic spread of the pandemic clone. Several reports have identified T3SS2-related genes in Vibrio and non-Vibrio species, suggesting that the T3SS2 gene cluster is not restricted to the Vibrionaceae and can mobilize through horizontal gene transfer events. In this work, we performed a large-scale genomic analysis to determine the phylogenetic distribution of the T3SS2 gene cluster and its repertoire of effector proteins. We identified putative T3SS2 gene clusters in 1130 bacterial genomes from 8 bacterial genera, 5 bacterial families and 47 bacterial species. A hierarchical clustering analysis allowed us to define six T3SS2 subgroups (I-VI) with different repertoires of effector proteins, redefining the concepts of T3SS2 core and accessory effector proteins. Finally, we identified a subset of the T3SS2 gene clusters (subgroup VI) that lacks most T3SS2 effector proteins described to date and provided a list of 10 novel effector candidates for this subgroup through bioinformatic analysis. Collectively, our findings indicate that the T3SS2 extends beyond the family Vibrionaceae and suggest that different effector protein repertories could have a differential impact on the pathogenic potential and environmental fitness of each bacterium that has acquired the Vibrio T3SS2 gene cluster.}, }
@article {pmid37017542, year = {2023}, author = {Joglekar, P and Ferrell, BD and Jarvis, T and Haramoto, K and Place, N and Dums, JT and Polson, SW and Wommack, KE and Fuhrmann, JJ}, title = {Spontaneously Produced Lysogenic Phages Are an Important Component of the Soybean Bradyrhizobium Mobilome.}, journal = {mBio}, volume = {14}, number = {2}, pages = {e0029523}, pmid = {37017542}, issn = {2150-7511}, support = {P20 GM139760/GM/NIGMS NIH HHS/United States ; P20 GM103446/GM/NIGMS NIH HHS/United States ; }, mesh = {Glycine max ; *Bacteriophages/genetics ; *Bradyrhizobium/genetics ; Base Sequence ; Phylogeny ; Symbiosis ; }, abstract = {The ability of Bradyrhizobium spp. to nodulate and fix atmospheric nitrogen in soybean root nodules is critical to meeting humanity's nutritional needs. The intricacies of soybean bradyrhizobia-plant interactions have been studied extensively; however, bradyrhizobial ecology as influenced by phages has received somewhat less attention, even though these interactions may significantly impact soybean yield. In batch culture, four soybean bradyrhizobia strains, Bradyrhizobium japonicum S06B (S06B-Bj), B. japonicum S10J (S10J-Bj), Bradyrhizobium diazoefficiens USDA 122 (USDA 122-Bd), and Bradyrhizobium elkanii USDA 76[T] (USDA 76-Be), spontaneously (without apparent exogenous chemical or physical induction) produced tailed phages throughout the growth cycle; for three strains, phage concentrations exceeded cell numbers by ~3-fold after 48 h of incubation. Phage terminase large-subunit protein phylogeny revealed possible differences in phage packaging and replication mechanisms. Bioinformatic analyses predicted multiple prophage regions within each soybean bradyrhizobia genome, preventing accurate identification of spontaneously produced prophage (SPP) genomes. A DNA sequencing and mapping approach accurately delineated the boundaries of four SPP genomes within three of the soybean bradyrhizobia chromosomes and suggested that the SPPs were capable of transduction. In addition to the phages, S06B-Bj and USDA 76-Be contained three to four times more insertion sequences (IS) and large, conjugable, broad host range plasmids, both of which are known drivers of horizontal gene transfer (HGT) in soybean bradyrhizobia. These factors indicate that SPP along with IS and plasmids participate in HGT, drive bradyrhizobia evolution, and play an outsized role in bradyrhizobia ecology. IMPORTANCE Previous studies have shown that IS and plasmids mediate HGT of symbiotic nodulation (nod) genes in soybean bradyrhizobia; however, these events require close cell-to-cell contact, which could be limited in soil environments. Bacteriophage-assisted gene transduction through spontaneously produced prophages provides a stable means of HGT not limited by the constraints of proximal cell-to-cell contact. These phage-mediated HGT events may shape soybean bradyrhizobia population ecology, with concomitant impacts on soybean agriculture.}, }
@article {pmid37017538, year = {2023}, author = {Jonsdottir, I and Given, C and Penttinen, R and Jalasvuori, M}, title = {Preceding Host History of Conjugative Resistance Plasmids Affects Intra- and Interspecific Transfer Potential from Biofilm.}, journal = {mSphere}, volume = {8}, number = {3}, pages = {e0010723}, pmid = {37017538}, issn = {2379-5042}, support = {322204//Academy of Finland (AKA)/ ; 347531//Academy of Finland (AKA)/ ; }, mesh = {Plasmids/genetics ; *Anti-Bacterial Agents/pharmacology ; *Escherichia coli/genetics ; Bacteria/genetics ; beta-Lactams ; Klebsiella pneumoniae/genetics ; }, abstract = {Conjugative plasmids can confer antimicrobial resistance (AMR) to their host bacterium. The plasmids disperse even between distantly related host species, rescuing the host from otherwise detrimental effects of antibiotics. Little is known about the role of these plasmids in the spread of AMR during antibiotic treatment. One unstudied question is whether the past evolutionary history of a plasmid in a particular species creates host specificity in its rescue potential or if interspecific coevolution can improve interspecific rescues. To study this, we coevolved the plasmid RP4 under three different host settings; solely Escherichia coli or Klebsiella pneumoniae, or alternating between both of them. The ability of evolved plasmids in bacterial biofilm to rescue susceptible planktonic host bacteria of either the same or different species during beta-lactam treatment was tested. The interspecific coevolution seemed to decrease rescue potential for the RP4 plasmid, while the K. pneumoniae evolved plasmid became more host specific. Large deletion in the region encoding the mating pair formation (Tra2) apparatus was detected in the plasmids evolved with K. pneumoniae. This adaptation resulted in the exapted evolution of resistance against a plasmid-dependent bacteriophage PRD1. Further, previous studies have suggested that mutations in this region completely abolish the plasmid's ability to conjugate; however, our study shows it is not essential for conjugation but rather affects the host-specific conjugation efficiency. Overall, the results suggest that previous evolutionary history can result in the separation of host-specific plasmid lineages that may be further amplified by unselected exaptations such as phage resistance. IMPORTANCE Antimicrobial resistance (AMR) is a major global public health threat which can rapidly spread in microbial communities via conjugative plasmids. Here, we advance with evolutionary rescue via conjugation in a more natural setting, namely, biofilm, and incorporate a broad-host range plasmid RP4 to test whether intra- and interspecific host histories affect its transfer potential. Escherichia coli and Klebsiella pneumoniae hosts were seen to elicit different evolutionary influences on the RP4 plasmid, leading to clear differences in the rescue potential and underlining the significant role of the plasmid-host interactions in the spread of AMR. We also contradicted previous reports that established certain conjugal transfer genes of RP4 as essential. This work enhances the understanding of how plasmid host range evolve in different host settings and further, the potential effects it may have on the horizontal spread of AMR in complex environments such as biofilms.}, }
@article {pmid37014461, year = {2023}, author = {Talat, A and Miranda, C and Poeta, P and Khan, AU}, title = {Farm to table: colistin resistance hitchhiking through food.}, journal = {Archives of microbiology}, volume = {205}, number = {5}, pages = {167}, pmid = {37014461}, issn = {1432-072X}, support = {BT/PR40148/BTIS/137/20/2021//Department of Biotechnology, Ministry of Science and Technology, India/ ; }, mesh = {Animals ; Humans ; *Colistin/pharmacology ; Farms ; Chickens/microbiology ; Escherichia coli/genetics ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Poultry/microbiology ; *Escherichia coli Proteins/genetics ; Plasmids ; Microbial Sensitivity Tests ; }, abstract = {Colistin is a high priority, last-resort antibiotic recklessly used in livestock and poultry farms. It is used as an antibiotic for treating multi-drug resistant Gram-negative bacterial infections as well as a growth promoter in poultry and animal farms. The sub-therapeutic doses of colistin exert a selection pressure on bacteria leading to the emergence of colistin resistance in the environment. Colistin resistance gene, mcr are mostly plasmid-mediated, amplifying the horizontal gene transfer. Food products such as chicken, meat, pork etc. disseminate colistin resistance to humans through zoonotic transfer. The antimicrobial residues used in livestock and poultry often leaches to soil and water through faeces. This review highlights the recent status of colistin use in food-producing animals, its association with colistin resistance adversely affecting public health. The underlying mechanism of colistin resistance has been explored. The prohibition of over-the-counter colistin sales and as growth promoters for animals and broilers has exhibited effective stewardship of colistin resistance in several countries.}, }
@article {pmid37009500, year = {2023}, author = {Nodari, CS and Opazo-Capurro, A and Castillo-Ramirez, S and Mattioni Marchetti, V}, title = {Editorial: Mobile genetic elements as dissemination drivers of multidrug-resistant Gram-negative bacteria.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1180510}, pmid = {37009500}, issn = {2235-2988}, mesh = {*Drug Resistance, Multiple, Bacterial/genetics ; *Drug Resistance, Bacterial/genetics ; Gram-Negative Bacteria/genetics ; Interspersed Repetitive Sequences ; }, }
@article {pmid37007505, year = {2023}, author = {Apari, P and Földvári, G}, title = {Domestication and microbiome succession may drive pathogen spillover.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1102337}, pmid = {37007505}, issn = {1664-302X}, abstract = {Emerging infectious diseases have posed growing medical, social and economic threats to humanity. The biological background of pathogen spillover or host switch, however, still has to be clarified. Disease ecology finds pathogen spillovers frequently but struggles to explain at the molecular level. Contrarily, molecular biological traits of host-pathogen relationships with specific molecular binding mechanisms predict few spillovers. Here we aim to provide a synthetic explanation by arguing that domestication, horizontal gene transfer even between superkingdoms as well as gradual exchange of microbiome (microbiome succession) are essential in the whole scenario. We present a new perspective at the molecular level which can explain the observations of frequent pathogen spillover events at the ecological level. This proposed rationale is described in detail, along with supporting evidence from the peer-reviewed literature and suggestions for testing hypothesis validity. We also highlight the importance of systematic monitoring of virulence genes across taxonomical categories and in the whole biosphere as it helps prevent future epidemics and pandemics. We conclude that that the processes of domestication, horizontal gene transfer and microbial succession might be important mechanisms behind the many spillover events driven and accelerated by climate change, biodiversity loss and globalization.}, }
@article {pmid37004306, year = {2023}, author = {Deng, X and Yuan, J and Chen, L and Chen, H and Wei, C and Nielsen, PH and Wuertz, S and Qiu, G}, title = {CRISPR-Cas phage defense systems and prophages in Candidatus Accumulibacter.}, journal = {Water research}, volume = {235}, number = {}, pages = {119906}, doi = {10.1016/j.watres.2023.119906}, pmid = {37004306}, issn = {1879-2448}, mesh = {Prophages/genetics ; CRISPR-Cas Systems ; *Bacteriophages/genetics ; Phylogeny ; Wastewater ; *Betaproteobacteria ; }, abstract = {Candidatus Accumulibacter plays a major role in enhanced biological phosphorus removal (EBPR) from wastewater. Although bacteriophages have been shown to represent fatal threats to Ca. Accumulibacter organisms and thus interfere with the stability of the EBPR process, little is known about the ability of different Ca. Accumulibacter strains to resist phage infections. We conducted a systematic analysis of the occurrence and characteristics of clustered regularly interspaced short palindromic repeats and associated proteins (CRISPR-Cas) systems and prophages in Ca. Accumulibacter lineage members (43 in total, including 10 newly recovered genomes). Results indicate that 28 Ca. Accumulibacter genomes encode CRISPR-Cas systems. They were likely acquired via horizontal gene transfer, conveying a distinct adaptivity to phage predation to different Ca. Accumulibacter members. Major differences in the number of spacers show the unique phage resistance of these members. A comparison of the spacers in closely related Ca. Accumulibacter members from distinct geographical locations indicates that habitat isolation may have resulted in the acquisition of resistance to different phages by different Ca. Accumulibacter. Long-term operation of three laboratory-scale EBPR bioreactors revealed high relative abundances of Ca. Accumulibacter with CRISPSR-Cas systems. Their specific resistance to phages in these reactors was indicated by spacer analysis. Metatranscriptomic analyses showed the activation of the CRISPR-Cas system under both anaerobic and aerobic conditions. Additionally, 133 prophage regions were identified in 43 Ca. Accumulibacter genomes. Twenty-seven of them (in 19 genomes) were potentially active. Major differences in the occurrence of CRISPR-Cas systems and prophages in Ca. Accumulibacter will lead to distinct responses to phage predation. This study represents the first systematic analysis of CRISPR-Cas systems and prophages in the Ca. Accumulibacter lineage, providing new perspectives on the potential impacts of phages on Ca. Accumulibacter and EBPR systems.}, }
@article {pmid37002975, year = {2023}, author = {Stockdale, SR and Hill, C}, title = {Incorporating plasmid biology and metagenomics into a holistic model of the human gut microbiome.}, journal = {Current opinion in microbiology}, volume = {73}, number = {}, pages = {102307}, doi = {10.1016/j.mib.2023.102307}, pmid = {37002975}, issn = {1879-0364}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Plasmids/genetics ; *Microbiota/genetics ; Bacteria/genetics ; Metagenomics ; }, abstract = {The human gut microbiome is often described as the collection of bacteria, archaea, fungi, protists, and viruses associated with an individual, with no acknowledgement of the plasmid constituents. However, like viruses, plasmids are autonomous intracellular replicating entities that can influence the genotype and phenotype of their host and mediate trans-kingdom interactions. Plasmids are frequently noted as vehicles for horizontal gene transfer and for spreading antibiotic resistance, yet their multifaceted contribution to mutualistic and antagonistic interactions within the human microbiome and impact on human health is overlooked. In this review, we highlight the importance of plasmids and their biological properties as overlooked components of microbiomes. Subsequent human microbiome studies should include dedicated analyses of plasmids, particularly as a holistic understanding of human-microbial interactions is required before effective and safe interventions can be implemented to improve human well-being.}, }
@article {pmid37001724, year = {2023}, author = {Boiten, KE and Kuijper, EJ and Schuele, L and van Prehn, J and Bode, LGM and Maat, I and van Asten, SAV and Notermans, DW and Rossen, JWA and Veloo, ACM}, title = {Characterization of mobile genetic elements in multidrug-resistant Bacteroides fragilis isolates from different hospitals in the Netherlands.}, journal = {Anaerobe}, volume = {81}, number = {}, pages = {102722}, doi = {10.1016/j.anaerobe.2023.102722}, pmid = {37001724}, issn = {1095-8274}, mesh = {Humans ; Bacteroides fragilis/genetics ; Genes, Bacterial ; Netherlands ; *Bacterial Infections ; Interspersed Repetitive Sequences ; Anti-Bacterial Agents/pharmacology ; *Bacteroides Infections/epidemiology/microbiology ; Microbial Sensitivity Tests ; }, abstract = {OBJECTIVES: Five human clinical multidrug-resistant (MDR) Bacteroides fragilis isolates, including resistance to meropenem and metronidazole, were recovered at different hospitals in the Netherlands between 2014 and 2020 and sent to the anaerobic reference laboratory for full characterization.<br><br>METHODS: Isolates were recovered from a variety of clinical specimens from patients with unrelated backgrounds. Long- and short-read sequencing was performed, followed by a hybrid assembly to study the presence of mobile genetic elements (MGEs) and antimicrobial resistance genes (ARGs).<br><br>RESULTS: A cfxA gene was present on a transposon (Tn) similar to Tn4555 in two isolates. In two isolates a novel Tn was present with the cfxA gene. Four isolates harbored a nimE gene, located on a pBFS01_2 plasmid. One isolate contained a novel plasmid carrying a nimA gene with IS1168. The tetQ gene was present on novel conjugative transposons (CTns) belonging to the CTnDOT family. Two isolates harbored a novel plasmid with tetQ. Other ARGs in these isolates, but not on an MGE, were: cfiA, ermF, mef(EN2), and sul2. ARGs harboured differed between isolates and corresponded with the observed phenotypic resistance.<br><br>CONCLUSIONS: Novel CTns, Tns, and plasmids were encountered in the five MDR B.&#xa0;fragilis isolates, complementing our knowledge on MDR and horizontal gene transfer in anaerobic bacteria.}, }
@article {pmid36996986, year = {2023}, author = {Cheng, Y and Wang, X and Zhao, L and Zhang, X and Kong, Q and Li, H and You, X and Li, Y}, title = {Wheat straw pyrochar more efficiently decreased enantioselective uptake of dinotefuran by lettuce and dissemination of antibiotic resistance genes than hydrochar in an agricultural soil.}, journal = {The Science of the total environment}, volume = {880}, number = {}, pages = {163088}, doi = {10.1016/j.scitotenv.2023.163088}, pmid = {36996986}, issn = {1879-1026}, mesh = {Humans ; *Soil/chemistry ; Anti-Bacterial Agents/pharmacology ; Lactuca ; Triticum ; Ecosystem ; Stereoisomerism ; Drug Resistance, Microbial/genetics ; *Pesticides ; Bacteria/genetics ; Soil Microbiology ; Genes, Bacterial ; }, abstract = {Remediation of soils pollution caused by dinotefuran, a chiral pesticide, is indispensable for ensuring human food security. In comparison with pyrochar, the effect of hydrochar on enantioselective fate of dinotefuran, and antibiotic resistance genes (ARGs) profiles in the contaminated soils remain poorly understood. Therefore, wheat straw hydrochar (SHC) and pyrochar (SPC) were prepared at 220 and 500 °C, respectively, to investigate their effects and underlying mechanisms on enantioselective fate of dinotefuran enantiomers and metabolites, and soil ARG abundance in soil-plant ecosystems using a 30-day pot experiment planted with lettuce. SPC showed a greater reduction effect on the accumulation of R- and S-dinotefuran and metabolites in lettuce shoots than SHC. This was mainly resulted from the lowered soil bioavailability of R- and S-dinotefuran due to adsorption/immobilization by chars, together with the char-enhanced pesticide-degrading bacteria resulted from increased soil pH and organic matter content. Both SPC and SHC efficiently reduced ARG levels in soils, owing to lowered abundance of ARG-carrying bacteria and declined horizontal gene transfer induced by decreased dinotefuran bioavailability. The above results provide new insights for optimizing char-based sustainable technologies to mitigate pollution of dinotefuran and spread of ARGs in agroecosystems.}, }
@article {pmid36996977, year = {2023}, author = {Zhang, C and Wang, C and Zhao, X and Hakizimana, I}, title = {Effect of resistance difference on distribution of antibiotics in bacterial cell and conjugative gene transfer risks during electrochemical flow through reaction.}, journal = {The Science of the total environment}, volume = {878}, number = {}, pages = {163142}, doi = {10.1016/j.scitotenv.2023.163142}, pmid = {36996977}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Escherichia coli/genetics ; Genes, Bacterial ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Plasmids ; }, abstract = {The occurrences and spread of antibiotic resistance (AR) mediated by horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) in aquatic environment have been aggravated because of the abuse of antibiotics. While the pressure of different antibiotics is known to induce the spread of AR in bacteria, whether distribution of different antibiotics in cell structure could affect HGT risks is not clear. Here, a significant difference between the distribution of tetracycline hydrochloride (Tet) and sulfamethoxazole (Sul) in cell structure during electrochemical flow through reaction (EFTR) process was firstly reported. Meanwhile, EFTR treatment possessed excellent disinfection performance and consequently controlled the HGT risks. The intracellular Tet (iTet) was discharged through efflux pumps to increase the content of extracellular Tet (eTet) due to the resistance of donor E. coli DH5α under the selective pressure of Tet, declining the damage of donor and plasmid RP4. The HGT frequency was 8.18-fold increase compared with that by EFTR treatment alone. While the secretion of intracellular Sul (iSul) was inhibited by blocking the formation of efflux pumps to inactivate the donor under the Sul pressure, and the total content of iSul and adsorbed Sul (aSul) to be 1.36-fold higher than that of eSul. Therefore, the reactive oxygen species (ROS) generation and cell membrane permeability were improved to release ARGs, and •OH attacked plasmid RP4 in the EFTR process, inhibiting the HGT risks. This study advances the awareness of the interaction between distribution of different antibiotics in cell structure and the HGT risks in the EFTR process.}, }
@article {pmid36995244, year = {2023}, author = {Herviou, P and Balvay, A and Bellet, D and Bobet, S and Maudet, C and Staub, J and Alric, M and Leblond-Bourget, N and Delorme, C and Rabot, S and Denis, S and Payot, S}, title = {Transfer of the Integrative and Conjugative Element ICESt3 of Streptococcus thermophilus in Physiological Conditions Mimicking the Human Digestive Ecosystem.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0466722}, pmid = {36995244}, issn = {2165-0497}, mesh = {Animals ; Mice ; Humans ; *Streptococcus thermophilus/genetics ; Conjugation, Genetic ; Gastrointestinal Tract ; Gene Transfer, Horizontal ; *Microbiota ; }, abstract = {Metagenome analyses of the human microbiome suggest that horizontal gene transfer (HGT) is frequent in these rich and complex microbial communities. However, so far, only a few HGT studies have been conducted in vivo. In this work, three different systems mimicking the physiological conditions encountered in the human digestive tract were tested, including (i) the TNO gastro-Intestinal tract Model 1 (TIM-1) system (for the upper part of the intestine), (ii) the ARtificial COLon (ARCOL) system (to mimic the colon), and (iii) a mouse model. To increase the likelihood of transfer by conjugation of the integrative and conjugative element studied in the artificial digestive systems, bacteria were entrapped in alginate, agar, and chitosan beads before being placed in the different gut compartments. The number of transconjugants detected decreased, while the complexity of the ecosystem increased (many clones in TIM-1 but only one clone in ARCOL). No clone was obtained in a natural digestive environment (germfree mouse model). In the human gut, the richness and diversity of the bacterial community would offer more opportunities for HGT events to occur. In addition, several factors (SOS-inducing agents, microbiota-derived factors) that potentially increase in vivo HGT efficiency were not tested here. Even if HGT events are rare, expansion of the transconjugant clones can happen if ecological success is fostered by selecting conditions or by events that destabilize the microbial community. IMPORTANCE The human gut microbiota plays a key role in maintaining normal host physiology and health, but its homeostasis is fragile. During their transit in the gastrointestinal tract, bacteria conveyed by food can exchange genes with resident bacteria. New traits acquired by HGT (e.g., new catabolic properties, bacteriocins, antibiotic resistance) can impact the gut microbial composition and metabolic potential. We showed here that TIM-1, a system mimicking the upper digestive tract, is a useful tool to evaluate HGT events in conditions closer to the physiological ones. Another important fact pointed out in this work is that Enterococcus faecalis is a good candidate for foreign gene acquisition. Due to its high ability to colonize the gut and acquire mobile genetic elements, this commensal bacterium could serve as an intermediate for HGT in the human gut.}, }
@article {pmid36995224, year = {2023}, author = {Piscon, B and Pia Esposito, E and Fichtman, B and Samburski, G and Efremushkin, L and Amselem, S and Harel, A and Rahav, G and Zarrilli, R and Gal-Mor, O}, title = {The Effect of Outer Space and Other Environmental Cues on Bacterial Conjugation.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0368822}, pmid = {36995224}, issn = {2165-0497}, mesh = {*Conjugation, Genetic ; *Cues ; Plasmids ; Bacteria/genetics ; Gene Transfer, Horizontal ; }, abstract = {Bacterial conjugation is one of the most abundant horizontal gene transfer (HGT) mechanisms, playing a fundamental role in prokaryote evolution. A better understanding of bacterial conjugation and its cross talk with the environment is needed for a more complete understanding of HGT mechanisms and to fight the dissemination of malicious genes between bacteria. Here, we studied the effect of outer space, microgravity, and additional key environmental cues on transfer (tra) gene expression and conjugation efficiency, using the under studied broad-host range plasmid pN3, as a model. High resolution scanning electron microscopy revealed the morphology of the pN3 conjugative pili and mating pair formation during conjugation. Using a nanosatellite carrying a miniaturized lab, we studied pN3 conjugation in outer space, and used qRT-PCR, Western blotting and mating assays to determine the effect of ground physicochemical parameters on tra gene expression and conjugation. We showed for the first time that bacterial conjugation can occur in outer space and on the ground, under microgravity-simulated conditions. Furthermore, we demonstrated that microgravity, liquid media, elevated temperature, nutrient depletion, high osmolarity and low oxygen significantly reduce pN3 conjugation. Interestingly, under some of these conditions we observed an inverse correlation between tra gene transcription and conjugation frequency and found that induction of at least traK and traL can negatively affect pN3 conjugation frequency in a dose-dependent manner. Collectively, these results uncover pN3 regulation by various environmental cues and highlight the diversity of conjugation systems and the different ways in which they may be regulated in response to abiotic signals. IMPORTANCE Bacterial conjugation is a highly ubiquitous and promiscuous process, by which a donor bacterium transfers a large portion of genetic material to a recipient cell. This mechanism of horizontal gene transfer plays an important role in bacterial evolution and in the ability of bacteria to acquire resistance to antimicrobial drugs and disinfectants. Bacterial conjugation is a complex and energy-consuming process, that is tightly regulated and largely affected by various environmental signals sensed by the bacterial cell. Comprehensive knowledge about bacterial conjugation and the ways it is affected by environmental cues is required to better understand bacterial ecology and evolution and to find new effective ways to counteract the threating dissemination of antibiotic resistance genes between bacterial populations. Moreover, characterizing this process under stress or suboptimal growth conditions such as elevated temperatures, high salinity or in the outer space, may provide insights relevant to future habitat environmental conditions.}, }
@article {pmid36993299, year = {2023}, author = {Quinones-Olvera, N and Owen, SV and McCully, LM and Marin, MG and Rand, EA and Fan, AC and Martins Dosumu, OJ and Paul, K and Sanchez Castaño, CE and Petherbridge, R and Paull, JS and Baym, M}, title = {Diverse and abundant phages exploit conjugative plasmids.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {36993299}, issn = {2692-8205}, support = {R35 GM133700/GM/NIGMS NIH HHS/United States ; T32 GM135014/GM/NIGMS NIH HHS/United States ; }, abstract = {Phages exert profound evolutionary pressure on bacteria by interacting with receptors on the cell surface to initiate infection. While the majority of phages use chromosomally-encoded cell surface structures as receptors, plasmid-dependent phages exploit plasmid-encoded conjugation proteins, making their host range dependent on horizontal transfer of the plasmid. Despite their unique biology and biotechnological significance, only a small number of plasmid-dependent phages have been characterized. Here we systematically search for new plasmid-dependent phages targeting IncP and IncF plasmids using a targeted discovery platform, and find that they are common and abundant in wastewater, and largely unexplored in terms of their genetic diversity. Plasmid-dependent phages are enriched in non-canonical types of phages, and all but one of the 64 phages we isolated were non-tailed, and members of the lipid-containing tectiviruses, ssDNA filamentous phages or ssRNA phages. We show that plasmid-dependent tectiviruses exhibit profound differences in their host range which is associated with variation in the phage holin protein. Despite their relatively high abundance in wastewater, plasmid-dependent tectiviruses are missed by metaviromic analyses, underscoring the continued importance of culture-based phage discovery. Finally, we identify a tailed phage dependent on the IncF plasmid, and find related structural genes in phages that use the orthogonal type 4 pilus as a receptor, highlighting the promiscuous use of these distinct contractile structures by multiple groups of phages. Taken together, these results indicate plasmid-dependent phages play an under-appreciated evolutionary role in constraining horizontal gene transfer via conjugative plasmids.}, }
@article {pmid36990411, year = {2023}, author = {Sánchez-Arroyo, A and Plaza-Vinuesa, L and Rivas, BL and Mancheño, JM and Muñoz, R}, title = {The salicylate 1,2-dioxygenase from Pseudaminobacter salicylatoxidans DSM 6986[T] is a bifunctional enzyme that inactivates the mycotoxin ochratoxin A by a novel amidohydrolase activity.}, journal = {International journal of biological macromolecules}, volume = {237}, number = {}, pages = {124230}, doi = {10.1016/j.ijbiomac.2023.124230}, pmid = {36990411}, issn = {1879-0003}, mesh = {Phyllobacteriaceae ; Salicylates/chemistry ; Molecular Docking Simulation ; *Mycotoxins ; Phenylalanine ; *Dioxygenases/genetics ; }, abstract = {The salicylate 1,2-dioxygenase from the bacterium Pseudaminobacter salicylatoxidans DSM 6986[T] (PsSDO) is a versatile metalloenzyme that participates in the aerobic biodegradation of aromatic compounds, such as gentisates and salicylates. Surprisingly, and unrelated to this metabolic role, it has been reported that PsSDO may transform the mycotoxin ochratoxin A (OTA), a molecule that appears in numerous food products that results in serious biotechnological concern. In this work, we show that PsSDO, together with its dioxygenase activity, behaves as an amidohydrolase with a marked specificity for substrates containing a C-terminal phenylalanine residue, similar to OTA, although its presence is not an absolute requirement. This side chain would establish aromatic stacking interactions with the indole ring of Trp104. PsSDO hydrolysed the amide bond of OTA rendering the much less toxic ochratoxin α and L-β-phenylalanine. The binding mode of OTA and of a diverse set of synthetic carboxypeptidase substrates these substrates have been characterized by molecular docking simulations, which has permitted us to propose a catalytic mechanism of hydrolysis by PsSDO that, similarly to metallocarboxypeptidases, assumes a water-induced pathway following a general acid/base mechanism in which the side chain of Glu82 would provide the solvent nucleophilicity required for the enzymatic reaction. Since the PsSDO chromosomal region, absent in other Pseudaminobacter strains, contained a set of genes present in conjugative plasmids, it could have been acquired by horizontal gene transfer, probably from a Celeribacter strain.}, }
@article {pmid36989191, year = {2023}, author = {Rathnapala, JMSN and Ragab, W and Kawato, S and Furukawa, M and Nozaki, R and Kondo, H and Hirono, I}, title = {Genomic characterization and identification of virulence-related genes in Vibrio nigripulchritudo isolated from white leg shrimp Penaeus vannamei.}, journal = {Journal of fish diseases}, volume = {46}, number = {7}, pages = {779-790}, doi = {10.1111/jfd.13786}, pmid = {36989191}, issn = {1365-2761}, support = {//Japan Science and Technology Agency/ ; //Japan Society for the Promotion of Science London/ ; }, mesh = {Phylogeny ; Virulence/genetics ; Genomics ; Vibrio ; *Penaeidae ; *Fish Diseases ; Animals ; }, abstract = {Vibrio nigripulchritudo causes vibriosis in penaeid shrimps. Here, we used Illumina and Nanopore sequencing technologies to sequence the genomes of three of its strains (TUMSAT-V. nig1, TUMSAT-V. nig2, and TUMSAT-V. nig3) to explore opportunities for disease management. Putative virulence factors and mobile genetic elements were detected while evaluating the phylogenetic relationship of each isolated strain. The genomes consisted of two circular chromosomes (I and II) plus one or two plasmids. The size of chromosome I ranged from 4.02 to 4.07 Mb with an average GC content of 46%, while the number of predicted CDSs ranged from 3563 to 3644. The size of chromosome II ranged from 2.16 to 2.18 Mb, with an average GC content of 45.5%, and the number of predicted CDSs ranged from 1970 to 1987. Numerous virulence genes were identified related to adherence, antiphagocytosis, chemotaxis, motility, iron uptake, quorum sensing, secretion systems, and toxins in all three genomes. Higher numbers of prophages and genomic islands found in TUMSAT-V. nig1 suggest that the strain has experienced numerous horizontal gene transfer events. The presence of antimicrobial resistance genes suggests that the strains have multidrug resistance. Comparative genomic analysis showed that all three strains belonged to the same clade.}, }
@article {pmid36989040, year = {2023}, author = {Sanow, S and Kuang, W and Schaaf, G and Huesgen, P and Schurr, U and Roessner, U and Watt, M and Arsova, B}, title = {Molecular Mechanisms of Pseudomonas-Assisted Plant Nitrogen Uptake: Opportunities for Modern Agriculture.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {36}, number = {9}, pages = {536-548}, doi = {10.1094/MPMI-10-22-0223-CR}, pmid = {36989040}, issn = {0894-0282}, abstract = {Pseudomonas spp. make up 1.6% of the bacteria in the soil and are found throughout the world. More than 140 species of this genus have been identified, some beneficial to the plant. Several species in the family Pseudomonadaceae, including Azotobacter vinelandii AvOP, Pseudomonas stutzeri A1501, Pseudomonas stutzeri DSM4166, Pseudomonas szotifigens 6HT33bT, and Pseudomonas sp. strain K1 can fix nitrogen from the air. The genes required for these reactions are organized in a nitrogen fixation island, obtained via horizontal gene transfer from Klebsiella pneumoniae, Pseudomonas stutzeri, and Azotobacter vinelandii. Today, this island is conserved in Pseudomonas spp. from different geographical locations, which, in turn, have evolved to deal with different geo-climatic conditions. Here, we summarize the molecular mechanisms behind Pseudomonas-driven plant growth promotion, with particular focus on improving plant performance at limiting nitrogen (N) and improving plant N content. We describe Pseudomonas-plant interaction strategies in the soil, noting that the mechanisms of denitrification, ammonification, and secondary metabolite signaling are only marginally explored. Plant growth promotion is dependent on the abiotic conditions and differs at sufficient and deficient N. The molecular controls behind different plant responses are not fully elucidated. We suggest that superposition of transcriptome, proteome, and metabolome data and their integration with plant phenotype development through time will help fill these gaps. The aim of this review is to summarize the knowledge behind Pseudomonas-driven nitrogen fixation and to point to possible agricultural solutions. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.}, }
@article {pmid36988519, year = {2023}, author = {Low, WW and Seddon, C and Beis, K and Frankel, G}, title = {The Interaction of the F-Like Plasmid-Encoded TraN Isoforms with Their Cognate Outer Membrane Receptors.}, journal = {Journal of bacteriology}, volume = {205}, number = {4}, pages = {e0006123}, pmid = {36988519}, issn = {1098-5530}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Escherichia coli/genetics/metabolism ; *F Factor ; Amino Acid Sequence ; Conjugation, Genetic ; Plasmids/genetics ; Membrane Proteins/metabolism ; Protein Isoforms/genetics ; Bacterial Proteins/genetics/metabolism ; }, abstract = {Horizontal gene transfer via conjugation plays a major role in bacterial evolution. In F-like plasmids, efficient DNA transfer is mediated by close association between donor and recipient bacteria. This process, known as mating pair stabilization (MPS), is mediated by interactions between the plasmid-encoded outer membrane (OM) protein TraN in the donor and chromosomally-encoded OM proteins in the recipient. We have recently reported the existence of 7 TraN sequence types, which are grouped into 4 structural types, that we named TraNα, TraNβ, TraNγ, and TraNδ. Moreover, we have shown specific pairing between TraNα and OmpW, TraNβ and OmpK36 of Klebsiella pneumoniae, TraNγ and OmpA, and TraNδ and OmpF. In this study, we found that, although structurally similar, TraNα encoded by the Salmonella enterica pSLT plasmid (TraNα2) binds OmpW in both Escherichia coli and Citrobacter rodentium, while TraNα encoded by the R100-1 plasmid (TraNα1) only binds OmpW in E. coli. AlphaFold2 predictions suggested that this specificity is mediated by a single amino acid difference in loop 3 of OmpW, which we confirmed experimentally. Moreover, we show that single amino acids insertions into loop 3 of OmpK36 affect TraNβ-mediated conjugation efficiency of the K. pneumoniae resistance plasmid pKpQIL. Lastly, we report that TraNβ can also mediate MPS by binding OmpK35, making it the first TraN variant that can bind more than one OM protein in the recipient. Together, these data show that subtle sequence differences in the OM receptors can impact TraN-mediated conjugation efficiency. IMPORTANCE Conjugation plays a central role in the spread of antimicrobial resistance genes among bacterial pathogens. Efficient conjugation is mediated by formation of mating pairs via a pilus, followed by mating pair stabilization (MPS), mediated by tight interactions between the plasmid-encoded outer membrane protein (OMP) TraN in the donor (of which there are 7 sequence types grouped into the 4 structural isoforms α, β, γ, and δ), and an OMP receptor in the recipient (OmpW, OmpK36, OmpA, and OmpF, respectively). In this study, we found that subtle differences in OmpW and OmpK36 have significant consequences on conjugation efficiency and specificity, highlighting the existence of selective pressure affecting plasmid-host compatibility and the flow of horizontal gene transfer in bacteria.}, }
@article {pmid36985115, year = {2023}, author = {Gummalla, VS and Zhang, Y and Liao, YT and Wu, VCH}, title = {The Role of Temperate Phages in Bacterial Pathogenicity.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, pmid = {36985115}, issn = {2076-2607}, support = {2030-42000-0055-000-D//Agricultural Research Service/ ; }, abstract = {Bacteriophages are viruses that infect bacteria and archaea and are classified as virulent or temperate phages based on their life cycles. A temperate phage, also known as a lysogenic phage, integrates its genomes into host bacterial chromosomes as a prophage. Previous studies have indicated that temperate phages are beneficial to their susceptible bacterial hosts by introducing additional genes to bacterial chromosomes, creating a mutually beneficial relationship. This article reviewed three primary ways temperate phages contribute to the bacterial pathogenicity of foodborne pathogens, including phage-mediated virulence gene transfer, antibiotic resistance gene mobilization, and biofilm formation. This study provides insights into mechanisms of phage-bacterium interactions in the context of foodborne pathogens and provokes new considerations for further research to avoid the potential of phage-mediated harmful gene transfer in agricultural environments.}, }
@article {pmid36983453, year = {2023}, author = {Urquhart, AS and Idnurm, A}, title = {A Polyphasic Approach including Whole Genome Sequencing Reveals Paecilomyces paravariotii sp. nov. as a Cryptic Sister Species to P. variotii.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {3}, pages = {}, pmid = {36983453}, issn = {2309-608X}, abstract = {Whole genome sequencing is rapidly increasing phylogenetic resolution across many groups of fungi. To improve sequencing coverage in the genus Paecilomyces (Eurotiales), we report nine new Paecilomyces genomes representing five different species. Phylogenetic comparison between these genomes and those reported previously showed that Paecilomyces paravariotii is a distinct species from its close relative P. variotii. The independence of P. paravariotii is supported by analysis of overall gene identify (via BLAST), differences in secondary metabolism and an inability to form ascomata when paired with a fertile P. variotii strain of opposite mating type. Furthermore, whole genome sequencing resolves the P. formosus clade into three separate species, one of which lacked a valid name that is now provided.}, }
@article {pmid36982992, year = {2023}, author = {Liu, W and Huang, Y and Zhang, H and Liu, Z and Huan, Q and Xiao, X and Wang, Z}, title = {Factors and Mechanisms Influencing Conjugation In Vivo in the Gastrointestinal Tract Environment: A Review.}, journal = {International journal of molecular sciences}, volume = {24}, number = {6}, pages = {}, pmid = {36982992}, issn = {1422-0067}, support = {32273055//National Natural Science Foundation of China/ ; }, mesh = {Drug Resistance, Microbial ; *Intestines ; *Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; Plasmids/genetics ; Conjugation, Genetic ; }, abstract = {The emergence and spread of antibiotic resistance genes (ARGs) have imposed a serious threat on global public health. Horizontal gene transfer (HGT) via plasmids is mainly responsible for the spread of ARGs, and conjugation plays an important role in HGT. The conjugation process is very active in vivo and its effect on the spreading of ARGs may be underestimated. In this review, factors affecting conjugation in vivo, especially in the intestinal environment, are summarized. In addition, the potential mechanisms affecting conjugation in vivo are summarized from the perspectives of bacterial colonization and the conjugation process.}, }
@article {pmid36980919, year = {2023}, author = {Weltzer, ML and Wall, D}, title = {Social Diversification Driven by Mobile Genetic Elements.}, journal = {Genes}, volume = {14}, number = {3}, pages = {}, pmid = {36980919}, issn = {2073-4425}, support = {R35 GM140886/GM/NIGMS NIH HHS/United States ; }, mesh = {*Bacteria/genetics ; *Myxococcales/genetics ; Biological Evolution ; Genome ; Interspersed Repetitive Sequences/genetics ; }, abstract = {Social diversification in microbes is an evolutionary process where lineages bifurcate into distinct populations that cooperate with themselves but not with other groups. In bacteria, this is frequently driven by horizontal transfer of mobile genetic elements (MGEs). Here, the resulting acquisition of new genes changes the recipient's social traits and consequently how they interact with kin. These changes include discriminating behaviors mediated by newly acquired effectors. Since the producing cell is protected by cognate immunity factors, these selfish elements benefit from selective discrimination against recent ancestors, thus facilitating their proliferation and benefiting the host. Whether social diversification benefits the population at large is less obvious. The widespread use of next-generation sequencing has recently provided new insights into population dynamics in natural habitats and the roles MGEs play. MGEs belong to accessory genomes, which often constitute the majority of the pangenome of a taxon, and contain most of the kin-discriminating loci that fuel rapid social diversification. We further discuss mechanisms of diversification and its consequences to populations and conclude with a case study involving myxobacteria.}, }
@article {pmid36975806, year = {2023}, author = {Desingu, PA and Nagarajan, K and Sundaresan, NR}, title = {Unique Tandem Repeats in the Inverted Terminal Repeat Regions of Monkeypox Viruses.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0319922}, pmid = {36975806}, issn = {2165-0497}, abstract = {The genetic diversity, especially in noncoding regions between clade I, clade IIa, and clade IIb monkeypox viruses (MPXVs), is still not fully understood. Here, we report that unique 16-nucleotide-length tandem repeats in MPXVs viruses are located in the noncoding regions of inverted terminal repeats (ITR), and the copy number of this repeat is different among clade I, clade IIa, and clade IIb viruses. It is noteworthy that tandem repeats containing these specific sequences (AACTAACTTATGACTT) are only present in MPXVs and are not found in other poxviruses. Also, the tandem repeats containing these specific sequences (AACTAACTTATGACTT) do not correspond to the tandem repeats present in the human and rodent (mice and rat) genomes. On the other hand, some of the reported tandem repeats in the human and rodent (mice and rat) genomes are present in the clade IIb-B.1 lineage of MPXV. In addition, it is noteworthy that the genes flanking these tandem repeats are lost and gained compared between clade I, clade IIa, and clade IIb MPXV. IMPORTANCE The different groups of MPXVs contain unique tandem repeats with different copy numbers in the ITR regions, and these repeats may be likely to play a role in the genetic diversity of the virus. Clade IIb (B) MPXV contains 38 and 32 repeats similar to the Tandem repeats reported in the human and rodent genome, respectively. However, none of these 38 (human) and 32 (rodent) tandem repeats matched the tandem repeats (AACTAACTTATGACTT) found in the present study. Finally, when developing attenuated or modified MPXV vaccine strains, these repeats in noncoding genomic regions can be exploited to incorporate foreign proteins (adjuvants/other virus proteins/racking fluorescent proteins such as green fluorescent protein) to carry out studies such as vaccine production and virus pathogenesis.}, }
@article {pmid36964199, year = {2023}, author = {Kavagutti, VS and Chiriac, MC and Ghai, R and Salcher, MM and Haber, M}, title = {Isolation of phages infecting the abundant freshwater Actinobacteriota order 'Ca. Nanopelagicales'.}, journal = {The ISME journal}, volume = {17}, number = {6}, pages = {943-946}, pmid = {36964199}, issn = {1751-7370}, mesh = {*Bacteriophages ; Bacteria/genetics ; Gene Transfer, Horizontal ; Metagenome ; Fresh Water/microbiology ; Genome, Viral ; Phylogeny ; }, abstract = {Low-GC Actinobacteriota of the order 'Ca. Nanopelagicales' (also known as acI or hgcI clade) are abundant in freshwaters around the globe. Extensive predation pressure by phages has been assumed to be the reason for their high levels of microdiversity. So far, however, only a few metagenome-assembled phages have been proposed to infect them and no phages have been isolated. Taking advantage of recent advances in the cultivation of 'Ca. Nanopelagicales' we isolated a novel species of its genus 'Ca. Planktophila'. Using this isolate as bait, we cultivated the first two phages infecting this abundant bacterial order. Both genomes contained a whiB-like transcription factor and a RNA polymerase sigma-70 factor, which might aid in manipulating their host's metabolism. Both phages encoded a glycosyltransferase and one an anti-restriction protein, potential means to evade degradation of their DNA by nucleases present in the host genome. The two phage genomes shared only 6% of their genome with their closest relatives, with whom they form a previously uncultured family of actinophages within the Caudoviricetes. Read recruitment analyses against globally distributed metagenomes revealed the endemic distribution of this group of phages infecting 'Ca. Nanopelagicales'. The recruitment pattern against metagenomes from the isolation site and the modular distribution of shared genes between the two phages indicate high levels of horizontal gene transfer, likely mirroring the microdiversity of their host in the evolutionary arms race between host and phage.}, }
@article {pmid36961781, year = {2023}, author = {Belal, NA and Heath, LS}, title = {A complete theoretical framework for inferring horizontal gene transfers using partial order sets.}, journal = {PloS one}, volume = {18}, number = {3}, pages = {e0281824}, pmid = {36961781}, issn = {1932-6203}, mesh = {Phylogeny ; *Gene Transfer, Horizontal ; *Evolution, Molecular ; }, abstract = {We present a method for detecting horizontal gene transfer (HGT) using partial orders (posets). The method requires a poset for each species/gene pair, where we have a set of species S, and a set of genes G. Given the posets, the method constructs a phylogenetic tree that is compatible with the set of posets; this is done for each gene. Also, the set of posets can be derived from the tree. The trees constructed for each gene are then compared and tested for contradicting information, where a contradiction suggests HGT.}, }
@article {pmid36958858, year = {2023}, author = {Bird, SM and Ford, S and Thompson, CMA and Little, R and Hall, JPJ and Jackson, RW and Malone, J and Harrison, E and Brockhurst, MA}, title = {Compensatory mutations reducing the fitness cost of plasmid carriage occur in plant rhizosphere communities.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {4}, pages = {}, pmid = {36958858}, issn = {1574-6941}, support = {BB/R014884/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R014884/2/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R018154/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/J/000PR9797/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Rhizosphere ; Plasmids/genetics ; Mutation ; *Pseudomonas fluorescens/genetics ; }, abstract = {Plasmids drive bacterial evolutionary innovation by transferring ecologically important functions between lineages, but acquiring a plasmid often comes at a fitness cost to the host cell. Compensatory mutations, which ameliorate the cost of plasmid carriage, promote plasmid maintenance in simplified laboratory media across diverse plasmid-host associations. Whether such compensatory evolution can occur in more complex communities inhabiting natural environmental niches where evolutionary paths may be more constrained is, however, unclear. Here, we show a substantial fitness cost of carrying the large conjugative plasmid pQBR103 in Pseudomonas fluorescens SBW25 in the plant rhizosphere. This plasmid fitness cost could be ameliorated by compensatory mutations affecting the chromosomal global regulatory system gacA/gacS, which arose rapidly in plant rhizosphere communities and were exclusive to plasmid carriers. These findings expand our understanding of the importance of compensatory evolution in plasmid dynamics beyond simplified lab media. Compensatory mutations contribute to plasmid survival in bacterial populations living within complex microbial communities in their environmental niche.}, }
@article {pmid36958158, year = {2023}, author = {Saha, S and Xiong, JQ and Patil, SM and Ha, GS and Hoh, JK and Park, HK and Chung, W and Chang, SW and Khan, MA and Park, HB and Jeon, BH}, title = {Dissemination of sulfonamide resistance genes in digester microbiome during anaerobic digestion of food waste leachate.}, journal = {Journal of hazardous materials}, volume = {452}, number = {}, pages = {131200}, doi = {10.1016/j.jhazmat.2023.131200}, pmid = {36958158}, issn = {1873-3336}, mesh = {Anaerobiosis ; Food ; *Refuse Disposal ; *Microbiota/genetics ; Sewage/microbiology ; Bacteria/metabolism ; Sulfanilamide ; Anti-Bacterial Agents/metabolism ; *Chloroflexi ; Firmicutes ; Methane/metabolism ; Bioreactors ; }, abstract = {The preeminence of sulfonamide drug resistance genes in food waste (FW) and the increased utilization of high-strength organic FW in anaerobic digestion (AD) to enhance methane production have raised severe public health concerns in wastewater treatment plants worldwide. In this regard, the dissemination patterns of different sulfonamide resistance genes (sul1 and sul2) and their impact on the digester core microbiota during AD of FW leachate (FWL) were evaluated. The presence of various sulfonamide antibiotics (SAs) in FWL digesters improved the final methane yield by 37 % during AD compared with FWL digesters without SAs. Microbial population shifts towards hydrolytic, acidogenic, and acetogenic bacteria in the phyla Actinobacteriota, Bacteroidota, Chloroflexi, Firmicutes, Proteobacteria, and Synergistota occurred due to SA induced substrate digestion and absorption through active transport; butanoate, propanoate, and pyruvate metabolism; glycolysis; gluconeogenesis; the citrate cycle; and pentose phosphate pathway. The initial dominance of Methanosaeta (89-96 %) declined to 47-53 % as AD progressed and shifted towards Methanosarcina (40 %) in digesters with the highest SA concentrations at the end of AD. Dissemination of sul1 depended on class 1 integron gene (intl1)-based horizontal gene transfer to pathogenic members of Chloroflexi, Firmicutes, and Patescibacteria, whereas sul2 was transmitted to Synergistota independent of intl1. Low susceptibility and ability to utilize SAs during methanogenesis shielded methanogenic archaea against selection pressure, thus preventing them from interacting with sul or intl1 genes, thereby minimizing the risk of antibiotic resistance development. The observed emergence of cationic antimicrobial peptide, vancomycin, and β-lactam resistance in the core microbiota during AD of FWL in the presence of SAs suggests that multidrug resistance caused by bacterial transformation could lead to an increase in the environmental resistome through wastewater sludge treatment.}, }
@article {pmid36951100, year = {2023}, author = {Lin, H and Moody, ERR and Williams, TA and Moreau, JW}, title = {On the Origin and Evolution of Microbial Mercury Methylation.}, journal = {Genome biology and evolution}, volume = {15}, number = {4}, pages = {}, pmid = {36951100}, issn = {1759-6653}, mesh = {*Mercury ; *Methylmercury Compounds ; Methylation ; Phylogeny ; Bacteria/genetics ; Archaea/genetics ; }, abstract = {The origin of microbial mercury methylation has long been a mystery. Here, we employed genome-resolved phylogenetic analyses to decipher the evolution of the mercury-methylating gene, hgcAB, constrain the ancestral origin of the hgc operon, and explain the distribution of hgc in Bacteria and Archaea. We infer the extent to which vertical inheritance and horizontal gene transfer have influenced the evolution of mercury methylators and hypothesize that evolution of this trait bestowed the ability to produce an antimicrobial compound (MeHg+) on a potentially resource-limited early Earth. We speculate that, in response, the evolution of MeHg+-detoxifying alkylmercury lyase (encoded by merB) reduced a selective advantage for mercury methylators and resulted in widespread loss of hgc in Bacteria and Archaea.}, }
@article {pmid36950985, year = {2023}, author = {Ding, D and Wang, B and Zhang, X and Zhang, J and Zhang, H and Liu, X and Gao, Z and Yu, Z}, title = {The spread of antibiotic resistance to humans and potential protection strategies.}, journal = {Ecotoxicology and environmental safety}, volume = {254}, number = {}, pages = {114734}, doi = {10.1016/j.ecoenv.2023.114734}, pmid = {36950985}, issn = {1090-2414}, mesh = {Animals ; Humans ; *Bacteria/genetics ; *Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; }, abstract = {Antibiotic resistance is currently one of the greatest threats to human health. Widespread use and residues of antibiotics in humans, animals, and the environment can exert selective pressure on antibiotic resistance bacteria (ARB) and antibiotic resistance gene (ARG), accelerating the flow of antibiotic resistance. As ARG spreads to the population, the burden of antibiotic resistance in humans increases, which may have potential health effects on people. Therefore, it is critical to mitigate the spread of antibiotic resistance to humans and reduce the load of antibiotic resistance in humans. This review briefly described the information of global antibiotic consumption information and national action plans (NAPs) to combat antibiotic resistance and provided a set of feasible control strategies for the transmission of ARB and ARG to humans in three areas including (a) Reducing the colonization capacity of exogenous ARB, (b) Enhancing human colonization resistance and mitigating the horizontal gene transfer (HGT) of ARG, (c) Reversing ARB antibiotic resistance. With the hope of achieving interdisciplinary one-health prevention and control of bacterial resistance.}, }
@article {pmid36949816, year = {2023}, author = {Guzmán-Herrador, DL and Fernández-Gómez, A and Llosa, M}, title = {Recruitment of heterologous substrates by bacterial secretion systems for transkingdom translocation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1146000}, pmid = {36949816}, issn = {2235-2988}, mesh = {Humans ; *Bacterial Secretion Systems/genetics ; *Bacteria/metabolism ; Virulence ; Bacterial Proteins/genetics/metabolism ; Type IV Secretion Systems/metabolism ; }, abstract = {Bacterial secretion systems mediate the selective exchange of macromolecules between bacteria and their environment, playing a pivotal role in processes such as horizontal gene transfer or virulence. Among the different families of secretion systems, Type III, IV and VI (T3SS, T4SS and T6SS) share the ability to inject their substrates into human cells, opening up the possibility of using them as customized injectors. For this to happen, it is necessary to understand how substrates are recruited and to be able to engineer secretion signals, so that the transmembrane machineries can recognize and translocate the desired substrates in place of their own. Other factors, such as recruiting proteins, chaperones, and the degree of unfolding required to cross through the secretion channel, may also affect transport. Advances in the knowledge of the secretion mechanism have allowed heterologous substrate engineering to accomplish translocation by T3SS, and to a lesser extent, T4SS and T6SS into human cells. In the case of T4SS, transport of nucleoprotein complexes adds a bonus to its biotechnological potential. Here, we review the current knowledge on substrate recognition by these secretion systems, the many examples of heterologous substrate translocation by engineering of secretion signals, and the current and future biotechnological and biomedical applications derived from this approach.}, }
@article {pmid36949153, year = {2023}, author = {Wang, Q and Wei, S and Silva, AF and Madsen, JS}, title = {Cooperative antibiotic resistance facilitates horizontal gene transfer.}, journal = {The ISME journal}, volume = {17}, number = {6}, pages = {846-854}, pmid = {36949153}, issn = {1751-7370}, support = {794315/MCCC_/Marie Curie/United Kingdom ; }, mesh = {*Gene Transfer, Horizontal/drug effects/genetics ; *Drug Resistance, Microbial/drug effects/genetics ; Plasmids/drug effects/genetics ; beta-Lactamases/genetics/metabolism ; Genotype ; Conjugation, Genetic ; Chromosomes, Bacterial/genetics ; beta-Lactams/pharmacology ; Anti-Bacterial Agents/pharmacology ; *Bacteria/cytology/drug effects/genetics ; }, abstract = {The rise of β-lactam resistance among pathogenic bacteria, due to the horizontal transfer of plasmid-encoded β-lactamases, is a current global health crisis. Importantly, β-lactam hydrolyzation by β-lactamases, not only protects the producing cells but also sensitive neighboring cells cooperatively. Yet, how such cooperative traits affect plasmid transmission and maintenance is currently poorly understood. Here we experimentally show that KPC-2 β-lactamase expression and extracellular activity were higher when encoded on plasmids compared with the chromosome, resulting in the elevated rescue of sensitive non-producers. This facilitated efficient plasmid transfer to the rescued non-producers and expanded the potential plasmid recipient pool and the probability of plasmid transfer to new genotypes. Social conversion of non-producers by conjugation was efficient yet not absolute. Non-cooperative plasmids, not encoding KPC-2, were moderately more competitive than cooperative plasmids when β-lactam antibiotics were absent. However, in the presence of a β-lactam antibiotic, strains with non-cooperative plasmids were efficiently outcompeted. Moreover, plasmid-free non-producers were more competitive than non-producers imposed with the metabolic burden of a plasmid. Our results suggest that cooperative antibiotic resistance especially promotes the fitness of replicons that transfer horizontally such as conjugative plasmids.}, }
@article {pmid36949027, year = {2023}, author = {Tanaka, E and Wajima, T and Nakaminami, H and Uchiya, KI}, title = {Contribution of amino acid substitutions in ParE to quinolone resistance in Haemophilus haemolyticus revealed through a horizontal transfer assay using Haemophilus influenzae.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {78}, number = {5}, pages = {1225-1230}, doi = {10.1093/jac/dkad074}, pmid = {36949027}, issn = {1460-2091}, mesh = {Amino Acid Substitution ; Levofloxacin ; DNA Topoisomerase IV/genetics ; Anti-Bacterial Agents/pharmacology ; Haemophilus influenzae ; Microbial Sensitivity Tests ; Humans ; Drug Resistance, Bacterial/genetics ; Haemophilus ; Child ; DNA Gyrase/genetics ; Agar ; *Quinolones/pharmacology ; }, abstract = {BACKGROUND: In 2019, a high-level quinolone-resistant Haemophilus haemolyticus strain (levofloxacin MIC = 16 mg/L) was isolated from a paediatric patient. In this study, we aimed to determine whether the quinolone resistance of H. haemolyticus could be transferred to Haemophilus influenzae and to identify the mechanism underlying the high-level quinolone resistance of H. haemolyticus.<br><br>METHODS: A horizontal gene transfer assay to H. influenzae was performed using genomic DNA or PCR-amplified quinolone-targeting genes from the high-level quinolone-resistant H. haemolyticus 2019-19 strain. The amino acids responsible for conferring quinolone resistance were identified through site-directed mutagenesis.<br><br>RESULTS: By adding the genomic DNA of H. haemolyticus 2019-19, resistant colonies were obtained on agar plates containing quinolones. Notably, H. influenzae grown on levofloxacin agar showed the same level of resistance as H. haemolyticus. Sequencing analysis showed that gyrA, parC and parE of H. influenzae were replaced by those of H. haemolyticus, suggesting that horizontal transfer occurred between the two strains. When the quinolone-targeting gene fragments were added sequentially, the addition of parE, as well as gyrA and parC, contributed to high-level resistance. In particular, amino acid substitutions at both the 439th and 502nd residues of ParE were associated with high-level resistance.<br><br>CONCLUSIONS: These findings indicate that quinolone resistance can be transferred between species and that amino acid substitutions at the 439th and 502nd residues of ParE, in addition to amino acid substitutions in both GyrA and ParC, contribute to high-level quinolone resistance.}, }
@article {pmid36948313, year = {2023}, author = {Fenibo, EO and Selvarajan, R and Abia, ALK and Matambo, T}, title = {Medium-chain alkane biodegradation and its link to some unifying attributes of alkB genes diversity.}, journal = {The Science of the total environment}, volume = {877}, number = {}, pages = {162951}, doi = {10.1016/j.scitotenv.2023.162951}, pmid = {36948313}, issn = {1879-1026}, mesh = {Animals ; Humans ; *Alkanes/metabolism ; Biodegradation, Environmental ; Ecosystem ; Hydrocarbons/metabolism ; Iron ; Phylogeny ; *Pseudomonas putida/metabolism ; Genes, Bacterial ; }, abstract = {Hydrocarbon footprints in the environment, via biosynthesis, natural seepage, anthropogenic activities and accidents, affect the ecosystem and induce a shift in the healthy biogeochemical equilibrium that drives needed ecological services. In addition, these imbalances cause human diseases and reduce animal and microorganism diversity. Microbial bioremediation, which capitalizes on functional genes, is a sustainable mitigation option for cleaning hydrocarbon-impacted environments. This review focuses on the bacterial alkB functional gene, which codes for a non-heme di‑iron monooxygenase (AlkB) with a di‑iron active site that catalyzes C8-C16 medium-chain alkane metabolism. These enzymes are ubiquitous and share common attributes such as being controlled by global transcriptional regulators, being a component of most super hydrocarbon degraders, and their distributions linked to horizontal gene transfer (HGT) events. The phylogenetic approach used in the HGT detection suggests that AlkB tree topology clusters bacteria functionally and that a preferential gradient dictates gene distribution. The alkB gene also acts as a biomarker for bioremediation, although it is found in pristine environments and absent in some hydrocarbon degraders. For instance, a quantitative molecular method has failed to link alkB copy number to contamination concentration levels. This limitation may be due to AlkB homologues, which have other functions besides n-alkane assimilation. Thus, this review, which focuses on Pseudomonas putida GPo1 alkB, shows that AlkB proteins are diverse but have some unifying trends around hydrocarbon-degrading bacteria; it is erroneous to rely on alkB detection alone as a monitoring parameter for hydrocarbon degradation, alkB gene distribution are preferentially distributed among bacteria, and the plausible explanation for AlkB affiliation to broad-spectrum metabolism of hydrocarbons in super-degraders hitherto reported. Overall, this review provides a broad perspective of the ecology of alkB-carrying bacteria and their directed biodegradation pathways.}, }
@article {pmid36946779, year = {2023}, author = {Johnston, EL and Zavan, L and Bitto, NJ and Petrovski, S and Hill, AF and Kaparakis-Liaskos, M}, title = {Planktonic and Biofilm-Derived Pseudomonas aeruginosa Outer Membrane Vesicles Facilitate Horizontal Gene Transfer of Plasmid DNA.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0517922}, pmid = {36946779}, issn = {2165-0497}, abstract = {Outer membrane vesicles (OMVs) produced by Gram-negative bacteria package various cargo, including DNA that can be transferred to other bacteria or to host cells. OMV-associated DNA has been implicated in mediating horizontal gene transfer (HGT) between bacteria, which includes the dissemination of antibiotic resistance genes within and between bacterial species. Despite the known ability of OMVs to mediate HGT, the mechanisms of DNA packaging into OMVs remain poorly characterized, as does the effect of bacterial growth conditions on the DNA cargo composition of OMVs and their subsequent abilities to mediate HGT. In this study, we examined the DNA content of OMVs produced by the opportunistic pathogen Pseudomonas aeruginosa grown in either planktonic or biofilm conditions. Analysis of planktonic growth-derived OMVs revealed their ability to package and protect plasmid DNA from DNase degradation and to transfer plasmid-encoded antibiotic resistance genes to recipient, antibiotic-sensitive P. aeruginosa bacteria at a greater efficiency than transformation with plasmid alone. Comparisons of planktonic and biofilm-derived P. aeruginosa OMVs demonstrated that biofilm-derived OMVs were smaller but were associated with more plasmid DNA than planktonic-derived OMVs. Additionally, biofilm-derived P. aeruginosa OMVs were more efficient in the transformation of competent P. aeruginosa bacteria, compared to transformations with an equivalent number of planktonic-derived OMVs. The findings of this study highlight the importance of bacterial growth conditions for the packaging of DNA within P. aeruginosa OMVs and their ability to facilitate HGT, thus contributing to the spread of antibiotic resistance genes between P. aeruginosa bacteria. IMPORTANCE Bacterial membrane vesicles (BMVs) mediate interbacterial communication, and their ability to package DNA specifically contributes to biofilm formation, antibiotic resistance, and HGT between bacteria. However, the ability of P. aeruginosa OMVs to mediate HGT has not yet been demonstrated. Here, we reveal that P. aeruginosa planktonic and biofilm-derived OMVs can deliver plasmid-encoded antibiotic resistance to recipient P. aeruginosa. Additionally, we demonstrated that P. aeruginosa biofilm-derived OMVs were associated with more plasmid DNA compared to planktonic-derived OMVs and were more efficient in the transfer of plasmid DNA to recipient bacteria. Overall, this demonstrated the ability of P. aeruginosa OMVs to facilitate the dissemination of antibiotic resistance genes, thereby enabling the survival of susceptible bacteria during antibiotic treatment. Investigating the roles of biofilm-derived BMVs may contribute to furthering our understanding of the role of BMVs in HGT and the spread of antibiotic resistance in the environment.}, }
@article {pmid36945052, year = {2023}, author = {Wang, Y and Zhang, Y and Hu, Y and Liu, L and Liu, SJ and Zhang, T}, title = {Genome-centric metagenomics reveals the host-driven dynamics and ecological role of CPR bacteria in an activated sludge system.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {56}, pmid = {36945052}, issn = {2049-2618}, mesh = {Humans ; *Sewage/microbiology ; *Bacteria/genetics/metabolism ; Metagenomics ; Metagenome/genetics ; Metabolic Networks and Pathways ; Phylogeny ; }, abstract = {BACKGROUND: Candidate phyla radiation (CPR) constitutes highly diverse bacteria with small cell sizes and are likely obligate intracellular symbionts. Given their distribution and complex associations with bacterial hosts, genetic and biological features of CPR bacteria in low-nutrient environments have received increasing attention. However, CPR bacteria in wastewater treatment systems remain poorly understood. We utilized genome-centric metagenomics to answer how CPR communities shift over 11 years and what kind of ecological roles they act in an activated sludge system.<br><br>RESULTS: We found that approximately 9% (135) of the 1,526 non-redundant bacterial and archaeal metagenome-assembled genomes were affiliated with CPR. CPR bacteria were consistently abundant with a relative abundance of up to 7.5% in the studied activated sludge system. The observed striking fluctuations in CPR community compositions and the limited metabolic and biosynthetic capabilities in CPR bacteria collectively revealed the nature that CPR dynamics may be directly determined by the available hosts. Similarity-based network analysis further confirmed the broad bacterial hosts of CPR lineages. The proteome contents of activated sludge-associated CPR had a higher similarity to those of environmental-associated CPR than to those of human-associated ones. Comparative genomic analysis observed significant enrichment of genes for oxygen stress resistance in activated sludge-associated CPR bacteria. Furthermore, genes for carbon cycling and horizontal gene transfer were extensively identified in activated sludge-associated CPR genomes.<br><br>CONCLUSIONS: These findings highlight the presence of specific host interactions among CPR lineages in activated sludge systems. Despite the lack of key metabolic pathways, these small, yet abundant bacteria may have significant involvements in biogeochemical cycling and bacterial evolution in activated sludge systems. Video Abstract.}, }
@article {pmid36944262, year = {2023}, author = {Milner, DS and Galindo, LJ and Irwin, NAT and Richards, TA}, title = {Transporter Proteins as Ecological Assets and Features of Microbial Eukaryotic Pangenomes.}, journal = {Annual review of microbiology}, volume = {77}, number = {}, pages = {45-66}, doi = {10.1146/annurev-micro-032421-115538}, pmid = {36944262}, issn = {1545-3251}, mesh = {*Eukaryota/genetics ; *Eukaryotic Cells ; Membrane Transport Proteins ; Gene Duplication ; Phenotype ; }, abstract = {Here we review two connected themes in evolutionary microbiology: (a) the nature of gene repertoire variation within species groups (pangenomes) and (b) the concept of metabolite transporters as accessory proteins capable of providing niche-defining "bolt-on" phenotypes. We discuss the need for improved sampling and understanding of pangenome variation in eukaryotic microbes. We then review the factors that shape the repertoire of accessory genes within pangenomes. As part of this discussion, we outline how gene duplication is a key factor in both eukaryotic pangenome variation and transporter gene family evolution. We go on to outline how, through functional characterization of transporter-encoding genes, in combination with analyses of how transporter genes are gained and lost from accessory genomes, we can reveal much about the niche range, the ecology, and the evolution of virulence of microbes. We advocate for the coordinated systematic study of eukaryotic pangenomes through genome sequencing and the functional analysis of genes found within the accessory gene repertoire.}, }
@article {pmid36943061, year = {2023}, author = {Nielsen, FD and Skov, MN and Sydenham, TV and Justesen, US}, title = {Development and Clinical Application of a Multilocus Sequence Typing Scheme for Bacteroides fragilis Based on Whole-Genome Sequencing Data.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0511122}, pmid = {36943061}, issn = {2165-0497}, abstract = {Bacteroides fragilis is among the most abundant and pathogenic bacterial species in the gut microbiota and is associated with diarrheal disease in children, inflammatory bowel disease, and the development of colorectal cancer. It is increasingly resistant to potent antimicrobial agents such as carbapenems and metronidazole, making it among the most resistant anaerobic bacteria. These factors combined call for increased monitoring of B. fragilis and its population structure on a worldwide scale. Here, we present a possible solution through the development of a multilocus sequence typing scheme (MLST). The scheme is based on seven core gene fragments: groL (hsp60), rpoB, recA, dnaJ, rprX, prfA, and fusA. These gene fragments possess high discriminatory power while retaining concordance with whole core genome-based phylogenetic analysis. The scheme proved capable of differentiating B. fragilis isolates at the strain level. It offers a standardized method for molecular typing and can be applied to isolates from various sampling backgrounds, such as patient isolates, environmental samples, and strains obtained from food and animal sources. In total, 567 B. fragilis genomes were sequence typed and their isolate data collected. The MLST scheme clearly divided the B. fragilis population into two divisions based on the presence of the cfiA and cepA resistance genes. However, no other specific subpopulations within the analyzed genomes were found to be associated with any specific diseases or geographical location. With this MLST scheme, we hope to provide a powerful tool for the study and monitoring of B. fragilis on an international scale. IMPORTANCE Here, we present the first MLST scheme for Bacteroides fragilis, one of the most abundant pathogenic bacteria in the human gut microbiota. The scheme enables standard classification and monitoring of B. fragilis on a worldwide scale and groups the majority of current isolate data in one place. A more unified approach to the collection and analysis of B. fragilis data could provide crucial insights into how the pathogen operates and develops as a species. Close monitoring of B. fragilis is especially relevant, as it is increasingly resistant to potent antimicrobial agents and engages in horizontal gene transfer with other bacteria. Hopefully, this approach will guide new discoveries into how B. fragilis evolves and interacts with its human host. Additionally, the scheme could potentially be applied to other species of the genus Bacteroides.}, }
@article {pmid36943058, year = {2023}, author = {Rao, YZ and Li, YX and Li, ZW and Qu, YN and Qi, YL and Jiao, JY and Shu, WS and Hua, ZS and Li, WJ}, title = {Metagenomic Discovery of "Candidatus Parvarchaeales"-Related Lineages Sheds Light on Adaptation and Diversification from Neutral-Thermal to Acidic-Mesothermal Environments.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0125222}, pmid = {36943058}, issn = {2379-5077}, mesh = {*Metagenome/genetics ; Phylogeny ; *Biological Evolution ; Adaptation, Physiological/genetics ; Archaea/genetics ; Acids/metabolism ; Amino Acids/genetics ; }, abstract = {"Candidatus Parvarchaeales" microbes, representing a DPANN archaeal group with limited metabolic potential and reliance on hosts for their growth, were initially found in acid mine drainage (AMD). Due to the lack of representatives, however, their ecological roles and adaptation to extreme habitats such as AMD as well as how they diverge across the lineage remain largely unexplored. By applying genome-resolved metagenomics, 28 Parvarchaeales-associated metagenome-assembled genomes (MAGs) representing two orders and five genera were recovered. Among them, we identified three new genera and proposed the names "Candidatus Jingweiarchaeum," "Candidatus Haiyanarchaeum," and "Candidatus Rehaiarchaeum," with the former two belonging to a new order, "Candidatus Jingweiarchaeales." Further analyses of the metabolic potentials revealed substantial niche differentiation between Jingweiarchaeales and Parvarchaeales. Jingweiarchaeales may rely on fermentation, salvage pathways, partial glycolysis, and the pentose phosphate pathway (PPP) for energy conservation reservation, while the metabolic potentials of Parvarchaeales might be more versatile. Comparative genomic analyses suggested that Jingweiarchaeales favor habitats with higher temperatures and that Parvarchaeales are better adapted to acidic environments. We further revealed that the thermal adaptation of these lineages, especially Haiyanarchaeum, might rely on genomic features such as the usage of specific amino acids, genome streamlining, and hyperthermophile featured genes such as rgy. Notably, the adaptation of Parvarchaeales to acidic environments was possibly driven by horizontal gene transfer (HGT). The reconstruction of ancestral states demonstrated that both may have originated from thermal and neutral environments and later spread to mesothermal and acidic environments. These evolutionary processes may also be accompanied by adaptation to oxygen-rich environments via HGT. IMPORTANCE "Candidatus Parvarchaeales" microbes may represent a lineage uniquely distributed in extreme environments such as AMD and hot springs. However, little is known about the strategies and processes of how they adapted to these extreme environments. By the discovery of potential new order-level lineages, "Ca. Jingweiarchaeales," and in-depth comparative genomic analysis, we unveiled the functional differentiation of these lineages. Furthermore, we show that the adaptation of these lineages to high-temperature and acidic environments was driven by different strategies, with the former relying more on genomic characteristics such as genome streamlining and amino acid compositions and the latter relying more on the acquisition of genes associated with acid tolerance. Finally, by the reconstruction of the ancestral states of the optimal growth temperature (OGT) and isoelectric point (pI), we showed the potential evolutionary process of Parvarchaeales-related lineages with regard to the shift from the high-temperature environment of their common ancestors to low-temperature (potentially acidic) environments.}, }
@article {pmid36941487, year = {2023}, author = {Bhakta, S and Bhattacharya, A}, title = {In silico evolutionary and structural analysis of cAMP response proteins (CARPs) from Leishmania major.}, journal = {Archives of microbiology}, volume = {205}, number = {4}, pages = {125}, pmid = {36941487}, issn = {1432-072X}, support = {AU/REG/2019-20/12/008//Adamas University/ ; SRG/2020/000702//Science and Engineering Research Board/ ; }, mesh = {Animals ; *Leishmania major/genetics/metabolism ; Cyclic AMP/metabolism ; Phylogeny ; Signal Transduction/physiology ; *Carps ; }, abstract = {With unidentified chemical triggers and novel-effectors, cAMP signaling is broadly noncanonical in kinetoplastida parasites. Though novel protein kinase A regulatory subunits (PKAR) have been identified earlier, cAMP Response Proteins (CARPs) have been identified as a unique and definite cAMP effector of trypanosomatids. CARP1-CARP4 emerged as critical regulatory components of cAMP signaling pathway in Trypanosoma with evidences that CARP3 can directly interact with a flagellar adenylate cyclase (AC). CARP-mediated regulations, identified so far, reflects the mechanistic diversity of cAMP signaling. Albeit the function of the orthologous is not yet delineated, in kinetoplastids like Leishmania, presence of CARP1, 2 and 4 orthologues suggests existence of conserved effector mechanisms. Targeting CARP orthologues in Leishmania, a comprehensive evolutionary analysis of CARPs have been aimed in this study which revealed phylogenetic relationship, codon adaptation and structural heterogeneity among the orthologues, warranting functional analysis in future to explore their involvement in infectivity.}, }
@article {pmid36941328, year = {2023}, author = {Zumkeller, S and Polsakiewicz, M and Knoop, V}, title = {Rickettsial DNA and a trans-splicing rRNA group I intron in the unorthodox mitogenome of the fern Haplopteris ensiformis.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {296}, pmid = {36941328}, issn = {2399-3642}, mesh = {Introns/genetics ; *Ferns/genetics ; *Genome, Mitochondrial ; Trans-Splicing ; Plants/genetics ; DNA, Mitochondrial/genetics ; }, abstract = {Plant mitochondrial genomes can be complex owing to highly recombinant structures, lack of gene syntenies, heavy RNA editing and invasion of chloroplast, nuclear or even foreign DNA by horizontal gene transfer (HGT). Leptosporangiate ferns remained the last major plant clade without an assembled mitogenome, likely owing to a demanding combination of the above. We here present both organelle genomes now for Haplopteris ensiformis. More than 1,400 events of C-to-U RNA editing and over 500 events of reverse U-to-C edits affect its organelle transcriptomes. The Haplopteris mtDNA is gene-rich, lacking only the ccm gene suite present in ancestral land plant mitogenomes, but is highly unorthodox, indicating extraordinary recombinogenic activity. Although eleven group II introns known in disrupted trans-splicing states in seed plants exist in conventional cis-arrangements, a particularly complex structure is found for the mitochondrial rrnL gene, which is split into two parts needing reassembly on RNA level by a trans-splicing group I intron. Aside from ca. 80 chloroplast DNA inserts that complicated the mitogenome assembly, the Haplopteris mtDNA features as an idiosyncrasy 30 variably degenerated protein coding regions from Rickettiales bacteria indicative of heavy bacterial HGT on top of tRNA genes of chlamydial origin.}, }
@article {pmid36940043, year = {2023}, author = {Chaudhary, S and Kishen, S and Singh, M and Jassal, S and Pathania, R and Bisht, K and Sareen, D}, title = {Phylogeny-guided genome mining of roseocin family lantibiotics to generate improved variants of roseocin.}, journal = {AMB Express}, volume = {13}, number = {1}, pages = {34}, pmid = {36940043}, issn = {2191-0855}, support = {09/135(0773)/2017-EMR-I//Council for Scientific and Industrial Research, New Delhi/ ; CRG/2018/004218//DST-SERB/ ; }, abstract = {Roseocin, the two-peptide lantibiotic from Streptomyces roseosporus, carries extensive intramolecular (methyl)lanthionine bridging in the peptides and exhibits synergistic antibacterial activity against clinically relevant Gram-positive pathogens. Both peptides have a conserved leader but a diverse core region. The biosynthesis of roseocin involves post-translational modification of the two precursor peptides by a single promiscuous lanthipeptide synthetase, RosM, to install an indispensable disulfide bond in the Rosα core along with four and six thioether rings in Rosα and Rosβ cores, respectively. RosM homologs in the phylum actinobacteria were identified here to reveal twelve other members of the roseocin family which diverged into three types of biosynthetic gene clusters (BGCs). Further, the evolutionary rate among the BGC variants and analysis of variability within the core peptide versus leader peptide revealed a phylum-dependent lanthipeptide evolution. Analysis of horizontal gene transfer revealed its role in the generation of core peptide diversity. The naturally occurring diverse congeners of roseocin peptides identified from the mined novel BGCs were carefully aligned to identify the conserved sites and the substitutions in the core peptide region. These selected sites in the Rosα peptide were mutated for permitted substitutions, expressed heterologously in E. coli, and post-translationally modified by RosM in vivo. Despite a limited number of generated variants, two variants, RosαL8F and RosαL8W exhibited significantly improved inhibitory activity in a species-dependent manner compared to the wild-type roseocin. Our study proves that a natural repository of evolved variants of roseocin is present in nature and the key variations can be used to generate improved variants.}, }
@article {pmid36937147, year = {2023}, author = {Cao, H and Liang, S and Zhang, C and Liu, B and Fei, Y}, title = {Molecular Profiling of a Multi-Strain Hypervirulent Klebsiella pneumoniae Infection Within a Single Patient.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {1367-1380}, pmid = {36937147}, issn = {1178-6973}, abstract = {BACKGROUND: The rising prevalence of infections caused by carbapenem-resistant and hypervirulent Klebsiella pneumoniae (CR-hvKP) has outpaced our understanding of their evolutionary diversity. By straining the antimicrobial options and constant horizontal gene transfer of various pathogenic elements, CR-hvKP poses a global health threat.<br><br>METHODS: Six KP isolates (KP1~KP6) from urine, sputum and groin infection secretion of a single patient were characterized phenotypically and genotypically. The antimicrobial susceptibility, carbapenemase production, hypermucoviscosity, serum resistance, virulence factors, MLST and serotypes were profiled. Genomic variations were identified by whole-genome sequencing and the phylogenetic differentiation was analyzed by Enterobacterial repetitive intergenic consensus (ERIC)-PCR.<br><br>RESULTS: All KP strains were multi-drug resistant. Four of them (KP1, KP3, KP5 and KP6) belonged to ST11-K64, with high genetic closeness (relatedness coefficient above 0.96), sharing most resistance and virulence genes. Compared with KP1, the later isolates KP3, KP5 and KP6 acquired bla KPC-1 and lost bla SHV-182 genes. KP2 and KP4 had the same clonal origin of ST35-K16 (relatedness coefficient 0.98), containing almost identical genes for resistance and virulence. They were non-mucoid and carried bla NDM-5 gene.<br><br>CONCLUSION: A co-infection with two types of CR-hvKP affiliated with different clades within a single patient amplified the treatment difficulties. In addition to source control and epidemiological surveillance, investigation of the in-host interactions between CR-hvKP variants may provide valuable treatment solutions.}, }
@article {pmid36933870, year = {2023}, author = {Yang, Q and Zhu, Y and Schwarz, S and Wang, L and Liu, W and Yang, W and Liu, S and Zhang, W}, title = {Integrative and conjugative elements in streptococci can act as vectors for plasmids and translocatable units integrated via IS1216E.}, journal = {International journal of antimicrobial agents}, volume = {61}, number = {5}, pages = {106793}, doi = {10.1016/j.ijantimicag.2023.106793}, pmid = {36933870}, issn = {1872-7913}, mesh = {*Conjugation, Genetic ; Plasmids/genetics ; *Streptococcus/genetics ; Drug Resistance, Microbial ; Gene Transfer, Horizontal ; }, abstract = {Mobile genetic elements (MGEs), such as integrative and conjugative elements (ICEs), plasmids and translocatable units (TUs), are important drivers for the spread of antibiotic resistance. Although ICEs have been reported to support the spread of plasmids among different bacteria, their role in mobilizing resistance plasmids and TUs has not yet been fully explored. In this study, a novel TU bearing optrA, a novel non-conjugative plasmid p5303-cfrD carrying cfr(D) and a new member of the ICESa2603 family, ICESg5301 were identified in streptococci. Polymerase chain reaction (PCR) assays revealed that three different types of cointegrates can be formed by IS1216E-mediated cointegration between the three different MGEs, including ICESg5301::p5303-cfrD::TU, ICESg5301::p5303-cfrD, and ICESg5301::TU. Conjugation assays showed that ICEs carrying p5303-cfrD and/or TU successfully transferred into recipient strains, thereby confirming that ICEs can serve as vectors for other non-conjugative MGEs, such as TUs and p5303-cfrD. As neither the TU nor plasmid p5303-cfrD can spread on their own between different bacteria, their integration into an ICE via IS1216E-mediated cointegrate formation not only increases the plasticity of ICEs, but also furthers the dissemination of plasmids and TUs carrying oxazolidinone resistance genes.}, }
@article {pmid36932546, year = {2023}, author = {Weaver, BP and Haselwandter, CA and Boedicker, JQ}, title = {Stochastic effects in bacterial communication mediated by extracellular vesicles.}, journal = {Physical review. E}, volume = {107}, number = {2-1}, pages = {024409}, doi = {10.1103/PhysRevE.107.024409}, pmid = {36932546}, issn = {2470-0053}, mesh = {*Bacteria ; Quorum Sensing/physiology ; Communication ; *Extracellular Vesicles ; }, abstract = {Quorum sensing (QS) allows bacterial cells to sense changes in local cell density and, hence, to regulate multicellular processes, including biofilm formation, regulation of virulence, and horizontal gene transfer. While, traditionally, QS was thought to involve the exchange of extracellular signal molecules free in solution, recent experiments have shown that for some bacterial systems a substantial fraction of signal molecules are packaged and delivered in extracellular vesicles. How the packaging of signal molecules in extracellular vesicles influences the ability of cells to communicate and coordinate multicellular behaviors remains largely unknown. We present here a stochastic reaction-diffusion model of QS that accounts for the exchange of both freely diffusing and vesicle-associated signal molecules. We find that the delivery of signal molecules via extracellular vesicles amplifies local fluctuations in the signal concentration, which can strongly affect the dynamics and spatial range of bacterial communication. For systems with multiple bacterial colonies, extracellular vesicles provide an alternate pathway for signal transport between colonies, and may be crucial for long-distance signal exchange in environments with strong degradation of free signal molecules.}, }
@article {pmid36931217, year = {2023}, author = {Zhao, Q and Hu, Z and Zhang, J and Wang, Y}, title = {Determination of the fate of antibiotic resistance genes and the response mechanism of plants during enhanced antibiotic degradation in a bioelectrochemical-constructed wetland system.}, journal = {Journal of hazardous materials}, volume = {451}, number = {}, pages = {131207}, doi = {10.1016/j.jhazmat.2023.131207}, pmid = {36931217}, issn = {1873-3336}, mesh = {*Anti-Bacterial Agents/pharmacology/analysis ; *Wastewater ; Waste Disposal, Fluid ; Wetlands ; Genes, Bacterial ; Chloramphenicol/analysis ; Drug Resistance, Microbial/genetics ; }, abstract = {Chloramphenicol (CAP) has a high concentration and detection frequency in aquatic environments due to its insufficient degradation in traditional biological wastewater treatment processes. In this study, bioelectrochemical assistant-constructed wetland systems (BES-CWs) were developed as advanced processes for efficient CAP removal, in which the degradation and transfer of CAP and the fate of antibiotic resistance genes (ARGs) were evaluated. The CAP removal efficiency could reach as high as 90.2%, while the removed CAP can be partially adsorbed and bioaccumulated in plants, significantly affecting plant growth. The vertical gene transfer and horizontal gene transfer increased the abundance of ARGs under high voltage and CAP concentrations. Microbial community analysis showed that CAP pressure and electrical stimulation selected the functional bacteria to increase CAP removal and antibiotic resistance. CAP degradation species carrying ARGs could increase their opposition to the biotoxicity of CAP and maintain system performance. In addition, ARGs are transferred into the plant and upward, which can potentially enter the food chain. This study provides an essential reference for enhancing antibiotic degradation and offers fundamental support for the underlying mechanism and ARG proliferation during antibiotic biodegradation.}, }
@article {pmid36931215, year = {2023}, author = {Lin, D and Zhu, L and Yao, Y and Zhu, L and Wang, M}, title = {The ecological and molecular mechanism underlying effective reduction of antibiotic resistance genes pollution in soil by fermentation broth from fruit and vegetable waste.}, journal = {Journal of hazardous materials}, volume = {451}, number = {}, pages = {131201}, doi = {10.1016/j.jhazmat.2023.131201}, pmid = {36931215}, issn = {1873-3336}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Vegetables ; Soil ; Fermentation ; Fruit ; Genes, Bacterial ; Tetracycline/pharmacology ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Soil Microbiology ; }, abstract = {The strategies to relieve antibiotic resistance genes (ARGs) pollution are urgently needed. Fermentation broth from fruit and vegetable waste (FFVW), an agricultural amendment, exhibits a remarkable capacity to reduce ARG pollution; however, the underlying mechanism of this effect remains unclear. We performed microcosm experiments to reappear the phenomenon of FFVW-driven reduction in ARGs. Moderate-level FFVW reduced gene resistance to sulfonamide (41.2 %), macrolide-lincosamide-streptogramin (MLS) (47.2 %), chloramphenicol (63.2 %), and tetracycline (61.4 %). Binning and network analyses revealed that Actinobacteria comprise the primary hosts of ARGs in arable soil, and FFVW substantially inhibited the growth and metabolic activity of these organisms. Moreover, tetracycline and MLS production was partially/completely inhibited by FFVW, further reducing the transfer frequency by 52.9-86.1 % and 46.6-66.6 % in the intragenic and intergenic mating systems, respectively. Furthermore, the expression of genes related to conjugation pairing and plasmid transfer was downregulated. Thus, FFVW effectively reduces ARG pollution by inhibiting Actinobacteria proliferation, thereby reducing selective pressure and restricting horizontal gene transfer. Our findings highlight the important underlying mechanisms of FFVW involved in ARG reduction, supporting its use in arable soil.}, }
@article {pmid36928121, year = {2023}, author = {Gandini, CL and Garcia, LE and Abbona, CC and Ceriotti, LF and Kushnir, S and Geelen, D and Sanchez-Puerta, MV}, title = {Break-induced replication is the primary recombination pathway in plant somatic hybrid mitochondria: a model for mitochondrial horizontal gene transfer.}, journal = {Journal of experimental botany}, volume = {74}, number = {12}, pages = {3503-3517}, doi = {10.1093/jxb/erad104}, pmid = {36928121}, issn = {1460-2431}, mesh = {*Gene Transfer, Horizontal ; *Mitochondria/genetics ; Nicotiana/genetics ; DNA Repair ; Homologous Recombination ; }, abstract = {Somatic hybrids between distant species offer a remarkable model to study genomic recombination events after mitochondrial fusion. Recently, we described highly chimeric mitogenomes in two somatic hybrids between the Solanaceae Nicotiana tabacum and Hyoscyamus niger resulting from interparental homologous recombination. To better examine the recombination map in somatic hybrid mitochondria, we developed a more sensitive bioinformatic strategy to detect recombination activity based on high-throughput sequencing without assembling the hybrid mitogenome. We generated a new intergeneric somatic hybrid between N. tabacum and Physochlaina orientalis, and re-analyzed the somatic hybrids that we previously generated. We inferred 213 homologous recombination events across repeats of 2.1 kb on average. Most of them (~80%) were asymmetrical, consistent with the break-induced replication pathway. Only rare (2.74%) non-homologous events were detected. Interestingly, independent events frequently occurred in the same regions within and across somatic hybrids, suggesting the existence of recombination hotspots in plant mitogenomes. Break-induced replication is the main pathway of interparental recombination in somatic hybrid mitochondria. Findings of this study are relevant to mitogenome editing assays and to mechanistic aspects of DNA integration following mitochondrial DNA horizontal transfer events.}, }
@article {pmid36927397, year = {2024}, author = {Teklemariam, AD and Al Hindi, R and Qadri, I and Alharbi, MG and Hashem, AM and Alrefaei, AA and Basamad, NA and Haque, S and Alamri, T and Harakeh, S}, title = {Phage cocktails - an emerging approach for the control of bacterial infection with major emphasis on foodborne pathogens.}, journal = {Biotechnology &amp; genetic engineering reviews}, volume = {40}, number = {1}, pages = {36-64}, doi = {10.1080/02648725.2023.2178870}, pmid = {36927397}, issn = {2046-5556}, mesh = {*Phage Therapy/methods ; *Bacteriophages ; Humans ; *Foodborne Diseases/therapy/microbiology/prevention &amp; control ; *Bacterial Infections/therapy ; Bacteria/virology ; }, abstract = {Phage therapy has recently attracted a great deal of attention to counteract the rapid emergence of antibiotic-resistant bacteria. In comparison to monophage therapy, phage cocktails are typically used to treat individual and/or multi-bacterial infections since the bacterial agents are unlikely to become resistant as a result of exposure to multiple phages simultaneously. The bacteriolytic effect of phage cocktails may produce efficient killing effect in comparison to individual phage. However, multiple use of phages (complex cocktails) may lead to undesirable side effects such as dysbiosis, horizontal gene transfer, phage resistance, cross resistance, and/or higher cost of production. Cocktail formulation, therefore, representa compromise between limiting the complexity of the cocktail and achieving substantial bacterial load reduction towards the targeted host organisms. Despite some constraints, the applications of monophage therapy have been well documented in the literature. However, phage cocktails-based approaches and their role for the control of pathogens have not been well investigated. In this review, we discuss the principle of phage cocktail formulations, their optimization strategies, major phage cocktail preparations, and their efficacy in inactivating various food borne bacterial pathogens.}, }
@article {pmid36927158, year = {2023}, author = {Karnkowska, A and Yubuki, N and Maruyama, M and Yamaguchi, A and Kashiyama, Y and Suzaki, T and Keeling, PJ and Hampl, V and Leander, BS}, title = {Euglenozoan kleptoplasty illuminates the early evolution of photoendosymbiosis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {12}, pages = {e2220100120}, pmid = {36927158}, issn = {1091-6490}, mesh = {*Photosynthesis/genetics ; Plastids/genetics/metabolism ; Eukaryota/genetics ; *Chlorophyta/genetics/metabolism ; Transcriptome ; Phylogeny ; Symbiosis/genetics ; }, abstract = {Kleptoplasts (kP) are distinct among photosynthetic organelles in eukaryotes (i.e., plastids) because they are routinely sequestered from prey algal cells and function only temporarily in the new host cell. Therefore, the hosts of kleptoplasts benefit from photosynthesis without constitutive photoendosymbiosis. Here, we report that the euglenozoan Rapaza viridis has only kleptoplasts derived from a specific strain of green alga, Tetraselmis sp., but no canonical plastids like those found in its sister group, the Euglenophyceae. R. viridis showed a dynamic change in the accumulation of cytosolic polysaccharides in response to light-dark cycles, and [13]C isotopic labeling of ambient bicarbonate demonstrated that these polysaccharides originate in situ via photosynthesis; these data indicate that the kleptoplasts of R. viridis are functionally active. We also identified 276 sequences encoding putative plastid-targeting proteins and 35 sequences of presumed kleptoplast transporters in the transcriptome of R. viridis. These genes originated in a wide range of algae other than Tetraselmis sp., the source of the kleptoplasts, suggesting a long history of repeated horizontal gene transfer events from different algal prey cells. Many of the kleptoplast proteins, as well as the protein-targeting system, in R. viridis were shared with members of the Euglenophyceae, providing evidence that the early evolutionary stages in the green alga-derived secondary plastids of euglenophytes also involved kleptoplasty.}, }
@article {pmid36925471, year = {2023}, author = {Cerbino, GN and Traglia, GM and Ayala Nuñez, T and Parmeciano Di Noto, G and Ramírez, MS and Centrón, D and Iriarte, A and Quiroga, C}, title = {Comparative genome analysis of the genus Shewanella unravels the association of key genetic traits with known and potential pathogenic lineages.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1124225}, pmid = {36925471}, issn = {1664-302X}, abstract = {Shewanella spp. are Gram-negative rods widely disseminated in aquatic niches that can also be found in human-associated environments. In recent years, reports of infections caused by these bacteria have increased significantly. Mobilome and resistome analysis of a few species showed that they are versatile; however, comprehensive comparative studies in the genus are lacking. Here, we analyzed the genetic traits of 144 genomes from Shewanella spp. isolates focusing on the mobilome, resistome, and virulome to establish their evolutionary relationship and detect unique features based on their genome content and habitat. Shewanella spp. showed a great diversity of mobile genetic elements (MGEs), most of them associated with monophyletic lineages of clinical isolates. Furthermore, 79/144 genomes encoded at least one antimicrobial resistant gene with their highest occurrence in clinical-related lineages. CRISPR-Cas systems, which confer immunity against MGEs, were found in 41 genomes being I-E and I-F the more frequent ones. Virulome analysis showed that all Shewanella spp. encoded different virulence genes (motility, quorum sensing, biofilm, adherence, etc.) that may confer adaptive advantages for survival against hosts. Our data revealed that key accessory genes are frequently found in two major clinical-related groups, which encompass the opportunistic pathogens Shewanella algae and Shewanella xiamenensis together with several other species. This work highlights the evolutionary nature of Shewanella spp. genomes, capable of acquiring different key genetic traits that contribute to their adaptation to different niches and facilitate the emergence of more resistant and virulent isolates that impact directly on human and animal health.}, }
@article {pmid36922599, year = {2023}, author = {Nyerges, A and Vinke, S and Flynn, R and Owen, SV and Rand, EA and Budnik, B and Keen, E and Narasimhan, K and Marchand, JA and Baas-Thomas, M and Liu, M and Chen, K and Chiappino-Pepe, A and Hu, F and Baym, M and Church, GM}, title = {A swapped genetic code prevents viral infections and gene transfer.}, journal = {Nature}, volume = {615}, number = {7953}, pages = {720-727}, pmid = {36922599}, issn = {1476-4687}, support = {R35 GM133700/GM/NIGMS NIH HHS/United States ; }, mesh = {*Amino Acids/genetics/metabolism ; Codon/genetics ; Ecosystem ; *Escherichia coli/genetics/virology ; *Genetic Code/genetics ; Leucine/genetics/metabolism ; *Protein Biosynthesis/genetics ; RNA, Transfer/genetics/metabolism ; Serine/genetics ; *Virus Diseases/genetics/prevention &amp; control ; *Host Microbial Interactions/genetics ; Organisms, Genetically Modified/genetics ; Genome, Bacterial/genetics ; *Gene Transfer, Horizontal/genetics ; Viral Proteins/genetics/metabolism ; }, abstract = {Engineering the genetic code of an organism has been proposed to provide a firewall from natural ecosystems by preventing viral infections and gene transfer[1-6]. However, numerous viruses and mobile genetic elements encode parts of the translational apparatus[7-9], potentially rendering a genetic-code-based firewall ineffective. Here we show that such mobile transfer RNAs (tRNAs) enable gene transfer and allow viral replication in Escherichia coli despite the genome-wide removal of 3 of the 64 codons and the previously essential cognate tRNA and release factor genes. We then establish a genetic firewall by discovering viral tRNAs that provide exceptionally efficient codon reassignment allowing us to develop cells bearing an amino acid-swapped genetic code that reassigns two of the six serine codons to leucine during translation. This amino acid-swapped genetic code renders cells resistant to viral infections by mistranslating viral proteomes and prevents the escape of synthetic genetic information by engineered reliance on serine codons to produce leucine-requiring proteins. As these cells may have a selective advantage over wild organisms due to virus resistance, we also repurpose a third codon to biocontain this virus-resistant host through dependence on an amino acid not found in nature[10]. Our results may provide the basis for a general strategy to make any organism safely resistant to all natural viruses and prevent genetic information flow into and out of genetically modified organisms.}, }
@article {pmid36915058, year = {2023}, author = {Zumkeller, S and Knoop, V}, title = {Categorizing 161 plant (streptophyte) mitochondrial group II introns into 29 families of related paralogues finds only limited links between intron mobility and intron-borne maturases.}, journal = {BMC ecology and evolution}, volume = {23}, number = {1}, pages = {5}, pmid = {36915058}, issn = {2730-7182}, mesh = {Introns/genetics ; *Evolution, Molecular ; *Mitochondria/genetics ; Plants/genetics ; Cell Nucleus ; }, abstract = {Group II introns are common in the two endosymbiotic organelle genomes of the plant lineage. Chloroplasts harbor 22 positionally conserved group II introns whereas their occurrence in land plant (embryophyte) mitogenomes is highly variable and specific for the seven major clades: liverworts, mosses, hornworts, lycophytes, ferns, gymnosperms and flowering plants. Each plant group features "signature selections" of ca. 20-30 paralogues from a superset of altogether 105 group II introns meantime identified in embryophyte mtDNAs, suggesting massive intron gains and losses along the backbone of plant phylogeny. We report on systematically categorizing plant mitochondrial group II introns into "families", comprising evidently related paralogues at different insertion sites, which may even be more similar than their respective orthologues in phylogenetically distant taxa. Including streptophyte (charophyte) algae extends our sampling to 161 and we sort 104 streptophyte mitochondrial group II introns into 25 core families of related paralogues evidently arising from retrotransposition events. Adding to discoveries of only recently created intron paralogues, hypermobile introns and twintrons, our survey led to further discoveries including previously overlooked "fossil" introns in spacer regions or e.g., in the rps8 pseudogene of lycophytes. Initially excluding intron-borne maturase sequences for family categorization, we added an independent analysis of maturase phylogenies and find a surprising incongruence between intron mobility and the presence of intron-borne maturases. Intriguingly, however, we find that several examples of nuclear splicing factors meantime characterized simultaneously facilitate splicing of independent paralogues now placed into the same intron families. Altogether this suggests that plant group II intron mobility, in contrast to their bacterial counterparts, is not intimately linked to intron-encoded maturases.}, }
@article {pmid36914349, year = {2023}, author = {Wang, D and Fletcher, GC and Gagic, D and On, SLW and Palmer, JS and Flint, SH}, title = {Comparative genome identification of accessory genes associated with strong biofilm formation in Vibrio parahaemolyticus.}, journal = {Food research international (Ottawa, Ont.)}, volume = {166}, number = {}, pages = {112605}, doi = {10.1016/j.foodres.2023.112605}, pmid = {36914349}, issn = {1873-7145}, mesh = {*Vibrio parahaemolyticus/genetics ; Biofilms ; Genomics ; Operon ; Cellulose ; }, abstract = {Vibrio parahaemolyticus biofilms on the seafood processing plant surfaces are a potential source of seafood contamination and subsequent food poisoning. Strains differ in their ability to form biofilm, but little is known about the genetic characteristics responsible for biofilm development. In this study, pangenome and comparative genome analysis of V. parahaemolyticus strains reveals genetic attributes and gene repertoire that contribute to robust biofilm formation. The study identified 136 accessory genes that were exclusively present in strong biofilm forming strains and these were functionally assigned to the Gene Ontology (GO) pathways of cellulose biosynthesis, rhamnose metabolic and catabolic processes, UDP-glucose processes and O antigen biosynthesis (p < 0.05). Strategies of CRISPR-Cas defence and MSHA pilus-led attachment were implicated via Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation. Higher levels of horizontal gene transfer (HGT) were inferred to confer more putatively novel properties on biofilm-forming V. parahaemolyticus. Furthermore, cellulose biosynthesis, a neglected potential virulence factor, was identified as being acquired from within the order Vibrionales. The cellulose synthase operons in V. parahaemolyticus were examined for their prevalence (22/138, 15.94 %) and were found to consist of the genes bcsG, bcsE, bcsQ, bcsA, bcsB, bcsZ, bcsC. This study provides insights into robust biofilm formation of V. parahaemolyticus at the genomic level and facilitates: identification of key attributes for robust biofilm formation, elucidation of biofilm formation mechanisms and development of potential targets for novel control strategies of persistent V. parahaemolyticus.}, }
@article {pmid36913905, year = {2023}, author = {Despotovic, M and de Nies, L and Busi, SB and Wilmes, P}, title = {Reservoirs of antimicrobial resistance in the context of One Health.}, journal = {Current opinion in microbiology}, volume = {73}, number = {}, pages = {102291}, pmid = {36913905}, issn = {1879-0364}, mesh = {Animals ; Humans ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; *One Health ; Bacteria/genetics ; Genes, Bacterial ; }, abstract = {The emergence and spread of antimicrobial resistance (AMR) and resistant bacteria, are a global public health challenge. Through horizontal gene transfer, potential pathogens can acquire antimicrobial resistance genes (ARGs) that can subsequently be spread between human, animal, and environmental reservoirs. To understand the dissemination of ARGs and linked microbial taxa, it is necessary to map the resistome within different microbial reservoirs. By integrating knowledge on ARGs in the different reservoirs, the One Health approach is crucial to our understanding of the complex mechanisms and epidemiology of AMR. Here, we highlight the latest insights into the emergence and spread of AMR from the One Health perspective, providing a baseline of understanding for future scientific investigations into this constantly growing global health threat.}, }
@article {pmid36912846, year = {2023}, author = {Qi, Q and Ghaly, TM and Penesyan, A and Rajabal, V and Stacey, JA and Tetu, SG and Gillings, MR}, title = {Uncovering Bacterial Hosts of Class 1 Integrons in an Urban Coastal Aquatic Environment with a Single-Cell Fusion-Polymerase Chain Reaction Technology.}, journal = {Environmental science &amp; technology}, volume = {57}, number = {12}, pages = {4870-4879}, doi = {10.1021/acs.est.2c09739}, pmid = {36912846}, issn = {1520-5851}, mesh = {Humans ; *Integrons/genetics ; *Drug Resistance, Bacterial/genetics ; Cell Fusion ; Bacteria/genetics ; Polymerase Chain Reaction ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Horizontal gene transfer (HGT) is a key driver of bacterial evolution via transmission of genetic materials across taxa. Class 1 integrons are genetic elements that correlate strongly with anthropogenic pollution and contribute to the spread of antimicrobial resistance (AMR) genes via HGT. Despite their significance to human health, there is a shortage of robust, culture-free surveillance technologies for identifying uncultivated environmental taxa that harbor class 1 integrons. We developed a modified version of epicPCR (emulsion, paired isolation, and concatenation polymerase chain reaction (PCR)) that links class 1 integrons amplified from single bacterial cells to taxonomic markers from the same cells in emulsified aqueous droplets. Using this single-cell genomic approach and Nanopore sequencing, we successfully assigned class 1 integron gene cassette arrays containing mostly AMR genes to their hosts in coastal water samples that were affected by pollution. Our work presents the first application of epicPCR for targeting variable, multigene loci of interest. We also identified the Rhizobacter genus as novel hosts of class 1 integrons. These findings establish epicPCR as a powerful tool for linking taxa to class 1 integrons in environmental bacterial communities and offer the potential to direct mitigation efforts toward hotspots of class 1 integron-mediated dissemination of AMR.}, }
@article {pmid36912090, year = {2023}, author = {Deng, L and Wang, C and Zhang, X and Yang, W and Tang, H and Chen, X and Du, S and Chen, X}, title = {Cell-to-cell natural transformation in Bacillus subtilis facilitates large scale of genomic exchanges and the transfer of long continuous DNA regions.}, journal = {Nucleic acids research}, volume = {51}, number = {8}, pages = {3820-3835}, pmid = {36912090}, issn = {1362-4962}, mesh = {*Bacillus subtilis/genetics ; DNA/genetics ; DNA, Bacterial/genetics ; Genome ; Genomics ; *Transformation, Bacterial ; }, abstract = {Natural transformation is one of the major mechanisms of horizontal gene transfer. Although it is usually studied using purified DNA in the laboratory, recent studies showed that many naturally competent bacteria acquired exogenous DNA from neighboring donor cells. Our previous work indicates that cell-to-cell natural transformation (CTCNT) using two different Bacillus subtilis strains is a highly efficient process; however, the mechanism is unclear. In this study, we further characterized CTCNT and mapped the transferred DNA in the recombinants using whole genome sequencing. We found that a recombinant strain generated by CTCNT received up to 66 transferred DNA segments; the average length of acquired continuous DNA stretches was approximately 27 kb with a maximum length of 347 kb. Moreover, up to 1.54 Mb genomic DNA (37% of the chromosome) was transferred from the donors into one recipient cell. These results suggest that B. subtilis CTCNT facilitates horizontal gene transfer by increasing the transfer of DNA segments and fostering the exchange of large continuous genomic regions. This indicates that the potency of bacterial natural transformation is underestimated using traditional approaches and reveals that DNA donor cells may play an important role in the transformation process in natural environments.}, }
@article {pmid36909625, year = {2023}, author = {Verhoeve, VI and Lehman, SS and Driscoll, TP and Beckmann, JF and Gillespie, JJ}, title = {Metagenome diversity illuminates origins of pathogen effectors.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {36909625}, issn = {2692-8205}, support = {R21 AI126108/AI/NIAID NIH HHS/United States ; R21 AI146773/AI/NIAID NIH HHS/United States ; R21 AI156762/AI/NIAID NIH HHS/United States ; R21 AI166832/AI/NIAID NIH HHS/United States ; }, abstract = {Recent metagenome assembled genome (MAG) analyses have profoundly impacted Rickettsiology systematics. Discovery of basal lineages (Mitibacteraceae and Athabascaceae) with predicted extracellular lifestyles reveals an evolutionary timepoint for the transition to host dependency, which occurred independent of mitochondrial evolution. Notably, these basal rickettsiae carry the Rickettsiales vir homolog (rvh) type IV secretion system (T4SS) and purportedly use rvh to kill congener microbes rather than parasitize host cells as described for derived rickettsial pathogens. MAG analysis also substantially increased diversity for genus Rickettsia and delineated a basal lineage (Tisiphia) that stands to inform on the rise of human pathogens from protist and invertebrate endosymbionts. Herein, we probed Rickettsiales MAG and genomic diversity for the distribution of Rickettsia rvh effectors to ascertain their origins. A sparse distribution of most Rickettsia rvh effectors outside of Rickettsiaceae lineages indicates unique rvh evolution from basal extracellular species and other rickettsial families. Remarkably, nearly every effector was found in multiple divergent forms with variable architectures, illuminating profound roles for gene duplication and recombination in shaping effector repertoires in Rickettsia pathogens. Lateral gene transfer plays a prominent role shaping the rvh effector landscape, as evinced by the discover of many effectors on plasmids and conjugative transposons, as well as pervasive effector gene exchange between Rickettsia and Legionella species. Our study exemplifies how MAGs can provide incredible insight on the origins of pathogen effectors and how their architectural modifications become tailored to eukaryotic host cell biology.}, }
@article {pmid36909515, year = {2023}, author = {Boys, IN and Johnson, AG and Quinlan, M and Kranzusch, PJ and Elde, NC}, title = {Structural homology screens reveal poxvirus-encoded proteins impacting inflammasome-mediated defenses.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {36909515}, issn = {2692-8205}, support = {R01 CA260414/CA/NCI NIH HHS/United States ; R35 GM134936/GM/NIGMS NIH HHS/United States ; }, abstract = {Viruses acquire host genes via horizontal gene transfer and can express them to manipulate host biology during infections. Some viral and host homologs retain sequence identity, but evolutionary divergence can obscure host origins. We used structural modeling to compare vaccinia virus proteins with metazoan proteomes. We identified vaccinia A47L as a homolog of gasdermins, the executioners of pyroptosis. An X-ray crystal structure of A47 confirmed this homology and cell-based assays revealed that A47 inhibits pyroptosis. We also identified vaccinia C1L as the product of a cryptic gene fusion event coupling a Bcl-2 related fold with a pyrin domain. C1 associates with components of the inflammasome, a cytosolic innate immune sensor involved in pyroptosis, yet paradoxically enhances inflammasome activity, suggesting a benefit to poxvirus replication in some circumstances. Our findings demonstrate the potential of structural homology screens to reveal genes that viruses capture from hosts and repurpose to benefit viral fitness.}, }
@article {pmid36901726, year = {2023}, author = {Sonnenberg, CB and Haugen, P}, title = {Bipartite Genomes in Enterobacterales: Independent Origins of Chromids, Elevated Openness and Donors of Horizontally Transferred Genes.}, journal = {International journal of molecular sciences}, volume = {24}, number = {5}, pages = {}, pmid = {36901726}, issn = {1422-0067}, mesh = {*Genome, Bacterial ; Plasmids ; Bacteria/genetics ; *Gammaproteobacteria ; Codon Usage ; Gene Transfer, Horizontal ; }, abstract = {Multipartite bacteria have one chromosome and one or more chromid. Chromids are believed to have properties that enhance genomic flexibility, making them a favored integration site for new genes. However, the mechanism by which chromosomes and chromids jointly contribute to this flexibility is not clear. To shed light on this, we analyzed the openness of chromosomes and chromids of the two bacteria, Vibrio and Pseudoalteromonas, both which belong to the Enterobacterales order of Gammaproteobacteria, and compared the genomic openness with that of monopartite genomes in the same order. We applied pangenome analysis, codon usage analysis and the HGTector software to detect horizontally transferred genes. Our findings suggest that the chromids of Vibrio and Pseudoalteromonas originated from two separate plasmid acquisition events. Bipartite genomes were found to be more open compared to monopartite. We found that the shell and cloud pangene categories drive the openness of bipartite genomes in Vibrio and Pseudoalteromonas. Based on this and our two recent studies, we propose a hypothesis that explains how chromids and the chromosome terminus region contribute to the genomic plasticity of bipartite genomes.}, }
@article {pmid36897935, year = {2023}, author = {Carr, VR and Pissis, SP and Mullany, P and Shoaie, S and Gomez-Cabrero, D and Moyes, DL}, title = {Palidis: fast discovery of novel insertion sequences.}, journal = {Microbial genomics}, volume = {9}, number = {3}, pages = {}, pmid = {36897935}, issn = {2057-5858}, support = {BB/M009513/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/S016899/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Humans ; *DNA Transposable Elements ; *Bacteria/genetics ; Computational Biology ; Genome, Microbial ; Metagenomics ; }, abstract = {The diversity of microbial insertion sequences, crucial mobile genetic elements in generating diversity in microbial genomes, needs to be better represented in current microbial databases. Identification of these sequences in microbiome communities presents some significant problems that have led to their underrepresentation. Here, we present a bioinformatics pipeline called Palidis that recognizes insertion sequences in metagenomic sequence data rapidly by identifying inverted terminal repeat regions from mixed microbial community genomes. Applying Palidis to 264 human metagenomes identifies 879 unique insertion sequences, with 519 being novel and not previously characterized. Querying this catalogue against a large database of isolate genomes reveals evidence of horizontal gene transfer events across bacterial classes. We will continue to apply this tool more widely, building the Insertion Sequence Catalogue, a valuable resource for researchers wishing to query their microbial genomes for insertion sequences.}, }
@article {pmid36897181, year = {2023}, author = {Wackett, LP}, title = {Horizontal gene transfer (HGT) and microbial evolution: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology.}, journal = {Environmental microbiology}, volume = {25}, number = {3}, pages = {772-773}, doi = {10.1111/1462-2920.16053}, pmid = {36897181}, issn = {1462-2920}, mesh = {*Gene Transfer, Horizontal ; *Environmental Microbiology ; }, }
@article {pmid36896589, year = {2023}, author = {Yu, R and Chen, X and Long, L and Jost, M and Zhao, R and Liu, L and Mower, JP and dePamphilis, CW and Wanke, S and Jiao, Y}, title = {De novo Assembly and Comparative Analyses of Mitochondrial Genomes in Piperales.}, journal = {Genome biology and evolution}, volume = {15}, number = {3}, pages = {}, pmid = {36896589}, issn = {1759-6653}, mesh = {*Genome, Mitochondrial ; Biological Evolution ; *Magnoliopsida/genetics ; Introns ; Gene Transfer, Horizontal ; Phylogeny ; }, abstract = {The mitochondrial genome of Liriodendron tulipifera exhibits many ancestral angiosperm features and a remarkably slow evolutionary rate, while mitochondrial genomes of other magnoliids remain yet to be characterized. We assembled nine new mitochondrial genomes, representing all genera of perianth-bearing Piperales, as well as for a member of the sister clade: three complete or nearly complete mitochondrial genomes from Aristolochiaceae and six additional draft assemblies including Thottea, Asaraceae, Lactoridaceae, and Hydnoraceae. For comparative purpose, a complete mitochondrial genome was assembled for Saururus, a member of the perianth-less Piperales. The average number of short repeats (50-99 bp) was much larger in genus Aristolochia than in other angiosperm mitochondrial genomes, and approximately 30% of repeats (<350 bp) were found to have the capacity to mediate recombination. We found mitochondrial genomes in perianth-bearing Piperales comprising conserved repertories of protein-coding genes and rRNAs but variable copy numbers of tRNA genes. We identified several shifts from cis- to trans-splicing of the Group II introns of nad1i728, cox2i373, and nad7i209. Two short regions of the cox1 and atp8 genes were likely derived from independent horizontal gene transfer events in perianth-bearing Piperales. We found biased enrichment of specific substitution types in different lineages of magnoliids and the Aristolochiaceae family showed the highest ratio of A:T > T:A substitutions of all other investigated angiosperm groups. Our study reports the first mitochondrial genomes for Piperales and uses this new information for a better understanding of the evolutionary patterns of magnoliids and angiosperms in general.}, }
@article {pmid36893903, year = {2023}, author = {Khan, AA and Nema, V and Ashraf, MT}, title = {Host-microbiota interactions and oncogenesis: Crosstalk and its implications in etiology.}, journal = {Microbial pathogenesis}, volume = {178}, number = {}, pages = {106063}, doi = {10.1016/j.micpath.2023.106063}, pmid = {36893903}, issn = {1096-1208}, mesh = {Humans ; Carcinogenesis ; *Microbiota/genetics ; *Neoplasms ; Host Microbial Interactions ; }, abstract = {A number of articles have discussed the potential of microbiota in oncogenesis. Several of these have evaluated the modulation of microbiota and its influence on cancer development. Even in recent past, a plethora of studies have gathered in order to understand the difference in microbiota population among different cancer and normal individuals. Although in majority of studies, microbiota mediated oncogenesis has been primarily attributed to the inflammatory mechanisms, there are several other ways through which microbiota can influence oncogenesis. These relatively less discussed aspects including the hormonal modulation through estrobolome and endobolome, production of cyclomodulins, and lateral gene transfer need more attention of scientific community. We prepared this article to discuss the role of microbiota in oncogenesis in order to provide concise information on these relatively less discussed microbiota mediated oncogenesis mechanisms.}, }
@article {pmid36892288, year = {2023}, author = {Große, C and Scherer, J and Schleuder, G and Nies, DH}, title = {Interplay between Two-Component Regulatory Systems Is Involved in Control of Cupriavidus metallidurans Metal Resistance Genes.}, journal = {Journal of bacteriology}, volume = {205}, number = {4}, pages = {e0034322}, pmid = {36892288}, issn = {1098-5530}, mesh = {*Bacterial Proteins/genetics/metabolism ; Metals/metabolism ; Zinc/metabolism ; *Cupriavidus/genetics/metabolism ; }, abstract = {Metal resistance of Cupriavidus metallidurans is based on determinants that were acquired in the past by horizontal gene transfer during evolution. Some of these determinants encode transmembrane metal efflux systems. Expression of most of the respective genes is controlled by two-component regulatory systems composed of a membrane-bound sensor/sensory histidine kinase (HK) and a cytoplasmic, DNA-binding response regulator (RR). Here, we investigated the interplay between the three closely related two-component regulatory systems CzcRS, CzcR2S2, and AgrRS. All three systems regulate the response regulator CzcR, while the RRs AgrR and CzcR2 were not involved in czc regulation. Target promoters were czcNp and czcPp for genes upstream and downstream of the central czc gene region. The two systems together repressed CzcRS-dependent upregulation of czcP-lacZ at low zinc concentrations in the presence of CzcS but activated this signal transmission at higher zinc concentrations. AgrRS and CzcR2S2 interacted to quench CzcRS-mediated expression of czcNp-lacZ and czcPp-lacZ. Together, cross talk between the three two-component regulatory systems enhanced the capabilities of the Czc systems by controlling expression of the additional genes czcN and czcP. IMPORTANCE Bacteria are able to acquire genes encoding resistance to metals and antibiotics by horizontal gene transfer. To bestow an evolutionary advantage on their host cell, new genes must be expressed, and their expression should be regulated so that resistance-mediating proteins are produced only when needed. Newly acquired regulators may interfere with those already present in a host cell. Such an event was studied here in the metal-resistant bacterium Cupriavidus metallidurans. The results demonstrate how regulation by the acquired genes interacts with the host's extant regulatory network. This leads to emergence of a new system level of complexity that optimizes the response of the cell to periplasmic signals.}, }
@article {pmid36892285, year = {2023}, author = {Brown, PJB and Chang, JH and Fuqua, C}, title = {Agrobacterium tumefaciens: a Transformative Agent for Fundamental Insights into Host-Microbe Interactions, Genome Biology, Chemical Signaling, and Cell Biology.}, journal = {Journal of bacteriology}, volume = {205}, number = {4}, pages = {e0000523}, pmid = {36892285}, issn = {1098-5530}, support = {R01 GM120337/GM/NIGMS NIH HHS/United States ; }, mesh = {*Agrobacterium tumefaciens/genetics ; *Host Microbial Interactions ; Plant Tumors/microbiology ; Plant Diseases/microbiology ; Plants/microbiology ; Bacteria ; Biology ; }, abstract = {Agrobacterium tumefaciens incites the formation of readily visible macroscopic structures known as crown galls on plant tissues that it infects. Records from biologists as early as the 17th century noted these unusual plant growths and began examining the basis for their formation. These studies eventually led to isolation of the infectious agent, A. tumefaciens, and decades of study revealed the remarkable mechanisms by which A. tumefaciens causes crown gall through stable horizontal genetic transfer to plants. This fundamental discovery generated a barrage of applications in the genetic manipulation of plants that is still under way. As a consequence of the intense study of A. tumefaciens and its role in plant disease, this pathogen was developed as a model for the study of critical processes that are shared by many bacteria, including host perception during pathogenesis, DNA transfer and toxin secretion, bacterial cell-cell communication, plasmid biology, and more recently, asymmetric cell biology and composite genome coordination and evolution. As such, studies of A. tumefaciens have had an outsized impact on diverse areas within microbiology and plant biology that extend far beyond its remarkable agricultural applications. In this review, we attempt to highlight the colorful history of A. tumefaciens as a study system, as well as current areas that are actively demonstrating its value and utility as a model microorganism.}, }
@article {pmid36892101, year = {2023}, author = {Sun, H and Li, H and Zhang, X and Liu, Y and Chen, H and Zheng, L and Zhai, Y and Zheng, H}, title = {The honeybee gut resistome and its role in antibiotic resistance dissemination.}, journal = {Integrative zoology}, volume = {18}, number = {6}, pages = {1014-1026}, doi = {10.1111/1749-4877.12714}, pmid = {36892101}, issn = {1749-4877}, support = {32000346//National Natural Science Foundation of China Projects/ ; 32170495//National Natural Science Foundation of China Projects/ ; }, mesh = {Animals ; Bees/genetics ; Drug Resistance, Microbial/genetics ; *Bacteria/genetics ; Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome ; }, abstract = {There is now general concern about widespread antibiotic resistance, and growing evidence indicates that gut microbiota is critical in providing antibiotic resistance. Honeybee is an important pollinator; the incidence of antibiotic resistance genes in honeybee gut causes potential risks to not only its own health but also to public and animal health, for its potential disseminator role, thus receiving more attention from the public. Recent analysis results reveal that the gut of honeybee serves as a reservoir of antibiotic resistance genes, probably due to antibiotics application history in beekeeping and horizontal gene transfer from the highly polluted environment. These antibiotic resistance genes accumulate in the honeybee gut and could be transferred to the pathogen, even having the potential to spread during pollination, tending, social interactions, etc. Newly acquired resistance traits may cause fitness reduction in bacteria whereas facilitating adaptive evolution as well. This review outlines the current knowledge about the resistome in honeybee gut and emphasizes its role in antibiotic resistance dissemination.}, }
@article {pmid36889142, year = {2023}, author = {Hussain, M and Etebari, K and Asgari, S}, title = {Analysing inhibition of dengue virus in Wolbachia-infected mosquito cells following the removal of Wolbachia.}, journal = {Virology}, volume = {581}, number = {}, pages = {48-55}, doi = {10.1016/j.virol.2023.02.017}, pmid = {36889142}, issn = {1096-0341}, mesh = {Animals ; *Dengue Virus/physiology ; *Wolbachia/physiology ; Virus Replication ; *RNA Viruses/genetics ; *Aedes ; *Dengue ; }, abstract = {Wolbachia pipientis is known to block replication of positive sense RNA viruses. Previously, we created an Aedes aegypti Aag2 cell line (Aag2.wAlbB) transinfected with the wAlbB strain of Wolbachia and a matching tetracycline-cured Aag2.tet cell line. While dengue virus (DENV) was blocked in Aag2.wAlbB cells, we found significant inhibition of DENV in Aag2.tet cells. RNA-Seq analysis of the cells confirmed removal of Wolbachia and lack of expression of Wolbachia genes that could have been due to lateral gene transfer in Aag2.tet cells. However, we noticed a substantial increase in the abundance of phasi charoen-like virus (PCLV) in Aag2.tet cells. When RNAi was used to reduce the PCLV levels, DENV replication was significantly increased. Further, we found significant changes in the expression of antiviral and proviral genes in Aag2.tet cells. Overall, the results reveal an antagonistic interaction between DENV and PCLV and how PCLV-induced changes could contribute to DENV inhibition.}, }
@article {pmid36889077, year = {2023}, author = {Yang, X and Niu, Y and Yang, Y and Zhou, H and Li, J and Fu, X and Shen, Z and Wang, J and Qiu, Z}, title = {Pheromone effect of estradiol regulates the conjugative transfer of pCF10 carrying antibiotic resistance genes.}, journal = {Journal of hazardous materials}, volume = {451}, number = {}, pages = {131087}, doi = {10.1016/j.jhazmat.2023.131087}, pmid = {36889077}, issn = {1873-3336}, mesh = {*Anti-Bacterial Agents/metabolism ; *Pheromones/pharmacology/genetics/metabolism ; Estradiol/pharmacology/metabolism ; Plasmids/genetics ; Drug Resistance, Microbial/genetics ; Enterococcus faecalis/genetics/metabolism ; Gene Transfer, Horizontal ; }, abstract = {Horizontal gene transfer (HGT) mediated by conjugative plasmids greatly contributes to bacteria evolution and the transmission of antibiotic resistance genes (ARGs). In addition to the selective pressure imposed by extensive antibiotic use, environmental chemical pollutants facilitate the dissemination of antibiotic resistance, consequently posing a serious threat to the ecological environment. Presently, the majority of studies focus on the effects of environmental compounds on R plasmid-mediated conjugation transfer, and pheromone-inducible conjugation has largely been neglected. In this study, we explored the pheromone effect and potential molecular mechanisms of estradiol in promoting the conjugative transfer of pCF10 plasmid in Enterococcus faecalis. Environmentally relevant concentrations of estradiol significantly increased the conjugative transfer of pCF10 with a maximum frequency of 3.2 × 10[-2], up to 3.5-fold change compared to that of control. Exposure to estradiol induced the activation of pheromone signaling cascade by increasing the expression of ccfA. Furthermore, estradiol might directly bind to the pheromone receptor PrgZ and promote pCF10 induction and finally enhance the conjugative transfer of pCF10. These findings cast valuable insights on the roles of estradiol and its homolog in increasing antibiotic resistance and the potential ecological risk.}, }
@article {pmid36881118, year = {2023}, author = {Veremeichik, GN and Bulgakov, DV and Solomatina, TO and Makhazen, DS}, title = {In the interkingdom horizontal gene transfer, the small rolA gene is a big mystery.}, journal = {Applied microbiology and biotechnology}, volume = {107}, number = {7-8}, pages = {2097-2109}, pmid = {36881118}, issn = {1432-0614}, support = {23-24-00215//Russian Science Foundation/ ; }, mesh = {Plants, Genetically Modified ; *Gene Transfer, Horizontal ; DNA ; Genetic Engineering ; Oncogenes ; *Rhizobium/genetics ; }, abstract = {The biological function of the agrobacterial oncogene rolA is very poorly understood compared to other components of the mechanism of horizontal gene transfer during agrobacterial colonization of plants. Research groups around the world have worked on this problem, and available information is reviewed in this review, but other rol oncogenes have been studied much more thoroughly. Having one unexplored element makes it impossible to form a complete picture. However, the limited data suggest that the rolA oncogene and its regulatory apparatus have great potential in plant biotechnology and genetic engineering. Here, we collect and discuss available experimental data about the function and structure of rolA. There is still no clear understanding of the mechanism of RolA and its structure and localization. We believe this is because of the nucleotide structure of a frameshift in the most well-studied rolA gene of the agropine type pRi. In fact, interest in the genes of agrobacteria as natural tools for the phenotypic or biochemical engineering of plants increased. We believe that a detailed understanding of the molecular mechanisms will be forthcoming. KEY POINTS: • Among pRi T-DNA oncogenes, rolA is the least understood in spite of many studies. • Frameshift may be the reason for the failure to elucidate the role of agropine rolA. • Understanding of rolA is promising for the phenotypic and biochemical engineering of plants.}, }
@article {pmid36880348, year = {2023}, author = {Tholl, D and Rebholz, Z and Morozov, AV and O'Maille, PE}, title = {Terpene synthases and pathways in animals: enzymology and structural evolution in the biosynthesis of volatile infochemicals.}, journal = {Natural product reports}, volume = {40}, number = {4}, pages = {766-793}, doi = {10.1039/d2np00076h}, pmid = {36880348}, issn = {1460-4752}, mesh = {Animals ; Phylogeny ; *Alkyl and Aryl Transferases/genetics ; Terpenes/metabolism ; Pheromones ; Mammals ; }, abstract = {Covering: up to the beginning of 2023Many animals release volatile or semi-volatile terpenes as semiochemicals in intra- and inter-specific interactions. Terpenes are important constituents of pheromones and serve as chemical defenses to ward off predators. Despite the occurrence of terpene specialized metabolites from soft corals to mammals, the biosynthetic origin of these compounds has largely remained obscure. An increasing number of animal genome and transcriptome resources is facilitating the identification of enzymes and pathways that allow animals to produce terpenes independent of their food sources or microbial endosymbionts. Substantial evidence has emerged for the presence of terpene biosynthetic pathways such as in the formation of the iridoid sex pheromone nepetalactone in aphids. In addition, terpene synthase (TPS) enzymes have been discovered that are evolutionary unrelated to canonical plant and microbial TPSs and instead resemble precursor enzymes called isoprenyl diphosphate synthases (IDSs) in central terpene metabolism. Structural modifications of substrate binding motifs in canonical IDS proteins presumably facilitated the transition to TPS function at an early state in insect evolution. Other arthropods such as mites appear to have adopted their TPS genes from microbial sources via horizontal gene transfer. A similar scenario likely occurred in soft corals, where TPS families with closer resemblance to microbial TPSs have been discovered recently. Together, these findings will spur the identification of similar or still unknown enzymes in terpene biosynthesis in other lineages of animals. They will also help develop biotechnological applications for animal derived terpenes of pharmaceutical value or advance sustainable agricultural practices in pest management.}, }
@article {pmid36878032, year = {2023}, author = {Yu, X and Zhou, ZC and Shuai, XY and Lin, ZJ and Liu, Z and Zhou, JY and Lin, YH and Zeng, GS and Ge, ZY and Chen, H}, title = {Microplastics exacerbate co-occurrence and horizontal transfer of antibiotic resistance genes.}, journal = {Journal of hazardous materials}, volume = {451}, number = {}, pages = {131130}, doi = {10.1016/j.jhazmat.2023.131130}, pmid = {36878032}, issn = {1873-3336}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Microplastics/toxicity ; *Genes, Bacterial ; Plastics/analysis ; Anti-Bacterial Agents/toxicity ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; }, abstract = {Microplastic pollution is a rising environmental issue worldwide. Microplastics can provide a niche for the microbiome, especially for antibiotic-resistant bacteria, which could increase the transmission of antibiotic resistance genes (ARGs). However, the interactions between microplastics and ARGs are still indistinct in environmental settings. Microplastics were found to be significantly correlated with ARGs (p < 0.001), based on the analysis of samples taken from a chicken farm and its surrounding farmlands. Analysis of chicken feces revealed the highest abundance of microplastics (14.9 items/g) and ARGs (6.24 ×10[8] copies/g), suggesting that chicken farms could be the hotspot for the co-spread of microplastics and ARGs. Conjugative transfer experiments were performed to investigate the effects of microplastic exposure for different concentrations and sizes on the horizontal gene transfer (HGT) of ARGs between bacteria. Results showed that the microplastics significantly enhanced the bacterial conjugative transfer frequency by 1.4-1.7 folds indicating that microplastics could aggravate ARG dissemination in the environment. Potential mechanisms related to the up-regulation of rpoS, ompA, ompC, ompF, trbBp, traF, trfAp, traJ, and down-regulation of korA, korB, and trbA were induced by microplastics. These findings highlighted the co-occurrence of microplastics and ARGs in the agricultural environment and the exacerbation of ARGs' prevalence via rising the HGT derived from microplastics.}, }
@article {pmid36874978, year = {2023}, author = {Fuchsman, CA and Garcia Prieto, D and Hays, MD and Cram, JA}, title = {Associations between picocyanobacterial ecotypes and cyanophage host genes across ocean basins and depth.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e14924}, pmid = {36874978}, issn = {2167-8359}, mesh = {*Ecotype ; Phylogeny ; *Genes, Viral ; Genome, Viral ; Cycadopsida ; }, abstract = {BACKGROUND: Cyanophages, viruses that infect cyanobacteria, are globally abundant in the ocean's euphotic zone and are a potentially important cause of mortality for marine picocyanobacteria. Viral host genes are thought to increase viral fitness by either increasing numbers of genes for synthesizing nucleotides for virus replication, or by mitigating direct stresses imposed by the environment. The encoding of host genes in viral genomes through horizontal gene transfer is a form of evolution that links viruses, hosts, and the environment. We previously examined depth profiles of the proportion of cyanophage containing various host genes in the Eastern Tropical North Pacific Oxygen Deficient Zone (ODZ) and at the subtropical North Atlantic (BATS). However, cyanophage host genes have not been previously examined in environmental depth profiles across the oceans.<br><br>METHODOLOGY: We examined geographical and depth distributions of picocyanobacterial ecotypes, cyanophage, and their viral-host genes across ocean basins including the North Atlantic, Mediterranean Sea, North Pacific, South Pacific, and Eastern Tropical North and South Pacific ODZs using phylogenetic metagenomic read placement. We determined the proportion of myo and podo-cyanophage containing a range of host genes by comparing to cyanophage single copy core gene terminase (terL). With this large dataset (22 stations), network analysis identified statistical links between 12 of the 14 cyanophage host genes examined here with their picocyanobacteria host ecotypes.<br><br>RESULTS: Picyanobacterial ecotypes, and the composition and proportion of cyanophage host genes, shifted dramatically and predictably with depth. For most of the cyanophage host genes examined here, we found that the composition of host ecotypes predicted the proportion of viral host genes harbored by the cyanophage community. Terminase is too conserved to illuminate the myo-cyanophage community structure. Cyanophage cobS was present in almost all myo-cyanophage and did not vary in proportion with depth. We used the composition of cobS phylotypes to track changes in myo-cyanophage composition.<br><br>CONCLUSIONS: Picocyanobacteria ecotypes shift with changes in light, temperature, and oxygen and many common cyanophage host genes shift concomitantly. However, cyanophage phosphate transporter gene pstS appeared to instead vary with ocean basin and was most abundant in low phosphate regions. Abundances of cyanophage host genes related to nutrient acquisition may diverge from host ecotype constraints as the same host can live in varying nutrient concentrations. Myo-cyanophage community in the anoxic ODZ had reduced diversity. By comparison to the oxic ocean, we can see which cyanophage host genes are especially abundant (nirA, nirC, and purS) or not abundant (myo psbA) in ODZs, highlighting both the stability of conditions in the ODZ and the importance of nitrite as an N source to ODZ endemic LLV Prochlorococcus.}, }
@article {pmid36871940, year = {2023}, author = {Yan, K and Wei, M and Li, F and Wu, C and Yi, S and Tian, J and Liu, Y and Lu, H}, title = {Diffusion and enrichment of high-risk antibiotic resistance genes (ARGs) via the transmission chain (mulberry leave, guts and feces of silkworm, and soil) in an ecological restoration area of manganese mining, China: Role of heavy metals.}, journal = {Environmental research}, volume = {225}, number = {}, pages = {115616}, doi = {10.1016/j.envres.2023.115616}, pmid = {36871940}, issn = {1096-0953}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Bombyx/genetics ; Manganese ; Genes, Bacterial ; *Morus/genetics ; Soil ; Escherichia coli ; Drug Resistance, Microbial/genetics ; *Metals, Heavy/toxicity ; Feces ; Mining ; }, abstract = {This study investigated the diffusion and enrichment of antibiotic resistance genes (ARGs) and pathogens via the transmission chain (mulberry leaves - silkworm guts - silkworm feces - soil) near a manganese mine restoration area (RA) and control area (CA, away from RA). Horizontal gene transfer (HGT) of ARGs was testified by an IncP a-type broad host range plasmid RP4 harboring ARGs (tetA) and conjugative genes (e.g., korB, trbA, and trbB) as an indicator. Compared to leaves, the abundances of ARGs and pathogens in feces after silkworms ingested leaves from RA increased by 10.8% and 52.3%, respectively, whereas their abundance in feces from CA dropped by 17.1% and 97.7%, respectively. The predominant ARG types in feces involved the resistances to β-lactam, quinolone, multidrug, peptide, and rifamycin. Therein, several high-risk ARGs (e.g., qnrB, oqxA, and rpoB) carried by pathogens were more enriched in feces. However, HGT mediated by plasmid RP4 in this transmission chain was not a main factor to promote the enrichment of ARGs due to the harsh survival environment of silkworm guts for the plasmid RP4 host E. coli. Notably, Zn, Mn, and As in feces and guts promoted the enrichment of qnrB and oqxA. Worriedly, the abundance of qnrB and oqxA in soil increased by over 4-fold after feces from RA were added into soil for 30 days regardless of feces with or without E. coli RP4. Overall, ARGs and pathogens could diffuse and enrich in environment via the sericulture transmission chain developed at RA, especially some high-risk ARGs carried by pathogens. Thus, greater attentions should be paid to dispel such high-risk ARGs to support benign development of sericulture industry in the safe utilization of some RAs.}, }
@article {pmid36871872, year = {2023}, author = {Henoun Loukili, N and Loquet, A and Perrin, A and Gaillot, O and Bruandet, A and Sendid, B and Zahar, JR and Nseir, S}, title = {Time to intestinal clearance of carbapenemase-producing Enterobacterales in hospital patients: a longitudinal retrospective observational cohort study.}, journal = {The Journal of hospital infection}, volume = {135}, number = {}, pages = {4-10}, doi = {10.1016/j.jhin.2023.01.022}, pmid = {36871872}, issn = {1532-2939}, mesh = {Humans ; Female ; Retrospective Studies ; *Escherichia coli ; beta-Lactamases/genetics ; Bacterial Proteins/genetics ; Hospitals ; *Enterobacteriaceae Infections/epidemiology/drug therapy ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {BACKGROUND: Intestinal clearance of carbapenemase-producing Enterobacterales (CPE-IC) is a cornerstone to discontinue isolation precautions for CPE patients in hospitals. This study aimed to evaluate the time to spontaneous CPE-IC and identify its potential associated risk factors.<br><br>METHODS: This retrospective cohort study was carried out between January 2018 and September 2020 on all patients in a 3200-bed teaching referral hospital with confirmed CPE intestinal carriage. CPE-IC was defined as at least three consecutive CPE-negative rectal swab cultures without a subsequent positive result. A survival analysis was performed to determine the median time to CPE-IC. A multivariate Cox model was implemented to explore the factors associated with CPE-IC.<br><br>RESULTS: A total of 110 patients were positives for CPE, of whom 27 (24.5%) achieved CPE-IC. Median time to CPE-IC was 698 days. Univariate analysis showed that female sex (P=0.046), multiple CPE-species in index cultures (P=0.005), Escherichia coli or Klebsiella spp. (P=0.001 and P=0.028, respectively) were significantly associated with the time to CPE-IC. Multivariate analysis highlighted that identification of E. coli carbapenemase-producing or CPEs harbouring ESBL genes in index culture extended the median time to CPE-IC, respectively (adjusted hazard ratio (aHR)&#xa0;= 0.13 (95% confidence interval: 0.04-0.45]; P=0.001 and aHR&#xa0;= 0.34 (95% confidence interval: 0.12-0.90); P=0.031).<br><br>CONCLUSION: Intestinal decolonization of CPE can take several months to years to occur. Carbapenemase-producing E.&#xa0;coli are likely to play a key role in delaying intestinal decolonization, probably through horizontal gene transfer between species. Therefore, discontinuation of isolation precautions in CPE-patients should be considered with caution.}, }
@article {pmid36867924, year = {2023}, author = {Mirtaleb, MS and Falak, R and Heshmatnia, J and Bakhshandeh, B and Taheri, RA and Soleimanjahi, H and Zolfaghari Emameh, R}, title = {An insight overview on COVID-19 mRNA vaccines: Advantageous, pharmacology, mechanism of action, and prospective considerations.}, journal = {International immunopharmacology}, volume = {117}, number = {}, pages = {109934}, pmid = {36867924}, issn = {1878-1705}, mesh = {Humans ; COVID-19 Vaccines ; *COVID-19/prevention &amp; control ; Pandemics/prevention &amp; control ; Prospective Studies ; SARS-CoV-2 ; RNA, Messenger ; mRNA Vaccines ; *Viral Vaccines ; }, abstract = {The worldwide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has urged scientists to present some novel vaccine platforms during this pandemic to provide a rather prolonged immunity against this respiratory viral infection. In spite of many campaigns formed against the administration of mRNA-based vaccines, those platforms were the most novel types, which helped us meet the global demand by developing protection against COVID-19 and reducing the development of severe forms of this respiratory viral infection. Some societies are worry about the COVID-19 mRNA vaccine administration and the potential risk of genetic integration of inoculated mRNA into the human genome. Although the efficacy and long-term safety of mRNA vaccines have not yet been fully clarified, obviously their application has switched the mortality and morbidity of the COVID-19 pandemic. This study describes the structural features and technologies used in producing of COVID-19 mRNA-based vaccines as the most influential factor in controlling this pandemic and a successful pattern for planning to produce other kind of genetic vaccines against infections or cancers.}, }
@article {pmid36864029, year = {2023}, author = {Lee, K and Raguideau, S and Sirén, K and Asnicar, F and Cumbo, F and Hildebrand, F and Segata, N and Cha, CJ and Quince, C}, title = {Population-level impacts of antibiotic usage on the human gut microbiome.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1191}, pmid = {36864029}, issn = {2041-1723}, support = {BBS/E/F/000PR10355/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/T/000PR9817/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Microbiota ; Metagenome/genetics ; Genome, Human ; }, abstract = {The widespread usage of antimicrobials has driven the evolution of resistance in pathogenic microbes, both increased prevalence of antimicrobial resistance genes (ARGs) and their spread across species by horizontal gene transfer (HGT). However, the impact on the wider community of commensal microbes associated with the human body, the microbiome, is less well understood. Small-scale studies have determined the transient impacts of antibiotic consumption but we conduct an extensive survey of ARGs in 8972 metagenomes to determine the population-level impacts. Focusing on 3096 gut microbiomes from healthy individuals not taking antibiotics we demonstrate highly significant correlations between both the total ARG abundance and diversity and per capita antibiotic usage rates across ten countries spanning three continents. Samples from China were notable outliers. We use a collection of 154,723 human-associated metagenome assembled genomes (MAGs) to link these ARGs to taxa and detect HGT. This reveals that the correlations in ARG abundance are driven by multi-species mobile ARGs shared between pathogens and commensals, within a highly connected central component of the network of MAGs and ARGs. We also observe that individual human gut ARG profiles cluster into two types or resistotypes. The less frequent resistotype has higher overall ARG abundance, is associated with certain classes of resistance, and is linked to species-specific genes in the Proteobacteria on the periphery of the ARG network.}, }
@article {pmid36863279, year = {2023}, author = {Zhang, H and Song, J and Zheng, Z and Li, T and Shi, N and Han, Y and Zhang, L and Yu, Y and Fang, H}, title = {Fungicide exposure accelerated horizontal transfer of antibiotic resistance genes via plasmid-mediated conjugation.}, journal = {Water research}, volume = {233}, number = {}, pages = {119789}, doi = {10.1016/j.watres.2023.119789}, pmid = {36863279}, issn = {1879-2448}, mesh = {*Anti-Bacterial Agents/pharmacology ; Escherichia coli/genetics ; *Fungicides, Industrial ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Plasmids/genetics ; Gene Transfer, Horizontal ; }, abstract = {Co-pollution of soil with pesticide residues and antibiotic resistance genes (ARGs) is increasing due to the substantial usage of pesticides and organic fertilizers in greenhouse-based agricultural production. Non-antibiotic stresses, including those from agricultural fungicides, are potential co-selectors for the horizontal transfer of ARGs, but the underlying mechanism remains unclear. Intragenus and intergenus conjugative transfer systems of the antibiotic resistant plasmid RP4 were established to examine conjugative transfer frequency under stress from four widely used fungicides: triadimefon, chlorothalonil, azoxystrobin, and carbendazim. The mechanisms were elucidated at the cellular and molecular levels using transmission electron microscopy, flow cytometry, RT-qPCR, and RNA-seq techniques. The conjugative transfer frequency of plasmid RP4 between Escherichia coli strains increased with the rising exposure concentrations of chlorothalonil, azoxystrobin, and carbendazim, but was suppressed between E. coli and Pseudomonas putida by a high fungicide concentration (10 µg/mL). Triadimefon did not significantly affect conjugative transfer frequency. Exploration of the underlying mechanisms revealed that: (i) chlorothalonil exposure mainly promoted generation of intracellular reactive oxygen species, stimulated the SOS response, and increased cell membrane permeability, while (ii) azoxystrobin and carbendazim primarily enhanced expression of conjugation-related genes on the plasmid. These findings reveal the fungicide-triggered mechanisms associated with plasmid conjugation and highlight the potential role of non-bactericidal pesticides on the dissemination of ARGs.}, }
@article {pmid36863168, year = {2023}, author = {Horne, T and Orr, VT and Hall, JP}, title = {How do interactions between mobile genetic elements affect horizontal gene transfer?.}, journal = {Current opinion in microbiology}, volume = {73}, number = {}, pages = {102282}, doi = {10.1016/j.mib.2023.102282}, pmid = {36863168}, issn = {1879-0364}, mesh = {*Gene Transfer, Horizontal ; Interspersed Repetitive Sequences ; Bacteria/genetics ; Biological Evolution ; *Microbiota ; }, abstract = {Horizontal gene transfer is central to bacterial adaptation and is facilitated by mobile genetic elements (MGEs). Increasingly, MGEs are being studied as agents with their own interests and adaptations, and the interactions MGEs have with one another are recognised as having a powerful effect on the flow of traits between microbes. Collaborations and conflicts between MGEs are nuanced and can both promote and inhibit the acquisition of new genetic material, shaping the maintenance of newly acquired genes and the dissemination of important adaptive traits through microbiomes. We review recent studies that shed light on this dynamic and oftentimes interlaced interplay, highlighting the importance of genome defence systems in mediating MGE-MGE conflicts, and outlining the consequences for evolutionary change, that resonate from the molecular to microbiome and ecosystem levels.}, }
@article {pmid36863149, year = {2023}, author = {Zhang, Y and Xiang, Y and Xu, R and Huang, J and Deng, J and Zhang, X and Wu, Z and Huang, Z and Yang, Z and Xu, J and Xiong, W and Li, H}, title = {Magnetic biochar promotes the risk of mobile genetic elements propagation in sludge anaerobic digestion.}, journal = {Journal of environmental management}, volume = {335}, number = {}, pages = {117492}, doi = {10.1016/j.jenvman.2023.117492}, pmid = {36863149}, issn = {1095-8630}, mesh = {*Sewage ; *Genes, Bacterial ; Anaerobiosis ; Anti-Bacterial Agents/pharmacology ; Interspersed Repetitive Sequences ; Magnetic Phenomena ; Manure/microbiology ; }, abstract = {Mobile genetic elements (MGEs) mediated horizontal gene transfer is the primary reason for the propagation of antibiotic resistance genes in environment. The behavior of MGEs under magnetic biochar pressure in sludge anaerobic digestion (AD) is still unknown. This study evaluated the effects of different dosage magnetic biochar on the MGEs in AD reactors. The results showed that the biogas yield was highest (106.68 ± 1.16 mL g[-1] VSadded) with adding optimal dosage of magnetic biochar (25 mg g[-1] TSadded), due to it increased the microorganism's abundance involved in hydrolysis and methanogenesis. While, the total absolute abundance of MGEs in the reactors with magnetic biochar addition increased by 11.58%-77.37% compared with the blank reactor. When the dosage of magnetic biochar was 12.5 mg g[-1] TSadded, the relative abundance of most MGEs was the highest. The enrichment effect on ISCR1 was the most significant, and the enrichment rate reached 158.90-214.16%. Only the intI1 abundance was reduced and the removal rates yield 14.38-40.00%, which was inversely proportional to the dosage of magnetic biochar. Co-occurrence network explored that Proteobacteria (35.64%), Firmicutes (19.80%) and Actinobacteriota (15.84%) were the main potential host of MGEs. Magnetic biochar changed MGEs abundance by affecting the potential MGEs-host community structure and abundance. Redundancy analysis and variation partitioning analysis showed that the combined effect of polysaccharides, protein and sCOD exhibited the greatest contribution (accounted for 34.08%) on MGEs variation. These findings demonstrated that magnetic biochar increases the risk of MGEs proliferation in AD system.}, }
@article {pmid36858028, year = {2023}, author = {Martins, SJ and Pasche, J and Silva, HAO and Selten, G and Savastano, N and Abreu, LM and Bais, HP and Garrett, KA and Kraisitudomsook, N and Pieterse, CMJ and Cernava, T}, title = {The Use of Synthetic Microbial Communities to Improve Plant Health.}, journal = {Phytopathology}, volume = {113}, number = {8}, pages = {1369-1379}, doi = {10.1094/PHYTO-01-23-0016-IA}, pmid = {36858028}, issn = {0031-949X}, abstract = {Despite the numerous benefits plants receive from probiotics, maintaining consistent results across applications is still a challenge. Cultivation-independent methods associated with reduced sequencing costs have considerably improved the overall understanding of microbial ecology in the plant environment. As a result, now, it is possible to engineer a consortium of microbes aiming for improved plant health. Such synthetic microbial communities (SynComs) contain carefully chosen microbial species to produce the desired microbiome function. Microbial biofilm formation, production of secondary metabolites, and ability to induce plant resistance are some of the microbial traits to consider when designing SynComs. Plant-associated microbial communities are not assembled randomly. Ecological theories suggest that these communities have a defined phylogenetic organization structured by general community assembly rules. Using machine learning, we can study these rules and target microbial functions that generate desired plant phenotypes. Well-structured assemblages are more likely to lead to a stable SynCom that thrives under environmental stressors as compared with the classical selection of single microbial activities or taxonomy. However, ensuring microbial colonization and long-term plant phenotype stability is still one of the challenges to overcome with SynComs, as the synthetic community may change over time with microbial horizontal gene transfer and retained mutations. Here, we explored the advances made in SynCom research regarding plant health, focusing on bacteria, as they are the most dominant microbial form compared with other members of the microbiome and the most commonly found in SynCom studies.}, }
@article {pmid36853054, year = {2023}, author = {Du, Y and Zou, J and Yin, Z and Chen, T}, title = {Pan-Chromosome and Comparative Analysis of Agrobacterium fabrum Reveal Important Traits Concerning the Genetic Diversity, Evolutionary Dynamics, and Niche Adaptation of the Species.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0292422}, pmid = {36853054}, issn = {2165-0497}, abstract = {Agrobacterium fabrum has been critical for the development of plant genetic engineering and agricultural biotechnology due to its ability to transform eukaryotic cells. However, the gene composition, evolutionary dynamics, and niche adaptation of this species is still unknown. Therefore, we established a comparative genomic analysis based on a pan-chromosome data set to evaluate the genetic diversity of A. fabrum. Here, 25 A. fabrum genomes were selected for analysis by core genome phylogeny combined with the average nucleotide identity (ANI), amino acid identity (AAI), and in silico DNA-DNA hybridization (DDH) values. An open pan-genome of A. fabrum exhibits genetic diversity with variable accessorial genes as evidenced by a consensus pan-genome of 12 representative genomes. The genomic plasticity of A. fabrum is apparent in its putative sequences for mobile genetic elements (MGEs), limited horizontal gene transfer barriers, and potentially horizontally transferred genes. The evolutionary constraints and functional enrichment in the pan-chromosome were measured by the Clusters of Orthologous Groups (COG) categories using eggNOG-mapper software, and the nonsynonymous/synonymous rate ratio (dN/dS) was determined using HYPHY software. Comparative analysis revealed significant differences in the functional enrichment and the degree of purifying selection between the core genome and non-core genome. We demonstrate that the core gene families undergo stronger purifying selection but have a significant bias to contain one or more positively selected sites. Furthermore, although they shared similar genetic diversity, we observed significant differences between chromosome 1 (Chr I) and the chromid in their functional features and evolutionary constraints. We demonstrate that putative genetic elements responsible for plant infection, ecological adaptation, and speciation represent the core genome, highlighting their importance in the adaptation of A. fabrum to plant-related niches. Our pan-chromosome analysis of A. fabrum provides comprehensive insights into the genetic properties, evolutionary patterns, and niche adaptation of the species. IMPORTANCE Agrobacterium spp. live in diverse plant-associated niches such as soil, the rhizosphere, and vegetation, which are challenged by multiple stressors such as diverse energy sources, plant defenses, and microbial competition. They have evolved the ability to utilize diverse resources, escape plant defenses, and defeat competitors. However, the underlying genetic diversity and evolutionary dynamics of Agrobacterium spp. remain unexplored. We examined the phylogeny and pan-genome of A. fabrum to define intraspecies evolutionary relationships. Our results indicate an open pan-genome and numerous MGEs and horizontally transferred genes among A. fabrum genomes, reflecting the flexibility of the chromosomes and the potential for genetic exchange. Furthermore, we observed significant differences in the functional features and evolutionary constraints between the core and accessory genomes and between Chr I and the chromid, respectively.}, }
@article {pmid36851563, year = {2023}, author = {Elois, MA and Silva, RD and Pilati, GVT and Rodríguez-Lázaro, D and Fongaro, G}, title = {Bacteriophages as Biotechnological Tools.}, journal = {Viruses}, volume = {15}, number = {2}, pages = {}, pmid = {36851563}, issn = {1999-4915}, mesh = {*Bacteriophages/genetics ; Prophages ; Lysogeny ; Biofilms ; Biotechnology ; }, abstract = {Bacteriophages are ubiquitous organisms that can be specific to one or multiple strains of hosts, in addition to being the most abundant entities on the planet. It is estimated that they exceed ten times the total number of bacteria. They are classified as temperate, which means that phages can integrate their genome into the host genome, originating a prophage that replicates with the host cell and may confer immunity against infection by the same type of phage; and lytics, those with greater biotechnological interest and are viruses that lyse the host cell at the end of its reproductive cycle. When lysogenic, they are capable of disseminating bacterial antibiotic resistance genes through horizontal gene transfer. When professionally lytic-that is, obligately lytic and not recently descended from a temperate ancestor-they become allies in bacterial control in ecological imbalance scenarios; these viruses have a biofilm-reducing capacity. Phage therapy has also been advocated by the scientific community, given the uniqueness of issues related to the control of microorganisms and biofilm production when compared to other commonly used techniques. The advantages of using bacteriophages appear as a viable and promising alternative. This review will provide updates on the landscape of phage applications for the biocontrol of pathogens in industrial settings and healthcare.}, }
@article {pmid36847532, year = {2023}, author = {Cooke, MB and Herman, C}, title = {Conjugation's Toolkit: the Roles of Nonstructural Proteins in Bacterial Sex.}, journal = {Journal of bacteriology}, volume = {205}, number = {3}, pages = {e0043822}, pmid = {36847532}, issn = {1098-5530}, support = {DP1 AI152073/AI/NIAID NIH HHS/United States ; }, mesh = {Plasmids ; *Type IV Secretion Systems/genetics ; *Conjugation, Genetic ; Gene Transfer, Horizontal ; Bacterial Proteins/genetics/metabolism ; }, abstract = {Bacterial conjugation, a form of horizontal gene transfer, relies on a type 4 secretion system (T4SS) and a set of nonstructural genes that are closely linked. These nonstructural genes aid in the mobile lifestyle of conjugative elements but are not part of the T4SS apparatus for conjugative transfer, such as the membrane pore and relaxosome, or the plasmid maintenance and replication machineries. While these nonstructural genes are not essential for conjugation, they assist in core conjugative functions and mitigate the cellular burden on the host. This review compiles and categorizes known functions of nonstructural genes by the stage of conjugation they modulate: dormancy, transfer, and new host establishment. Themes include establishing a commensalistic relationship with the host, manipulating the host for efficient T4SS assembly and function and assisting in conjugative evasion of recipient cell immune functions. These genes, taken in a broad ecological context, play important roles in ensuring proper propagation of the conjugation system in a natural environment.}, }
@article {pmid36844929, year = {2023}, author = {Nielsen, FD and Møller-Jensen, J and Jørgensen, MG}, title = {Adding context to the pneumococcal core genes using bioinformatic analysis of the intergenic pangenome of Streptococcus pneumoniae.}, journal = {Frontiers in bioinformatics}, volume = {3}, number = {}, pages = {1074212}, pmid = {36844929}, issn = {2673-7647}, abstract = {Introduction: Whole genome sequencing offers great opportunities for linking genotypes to phenotypes aiding in our understanding of human disease and bacterial pathogenicity. However, these analyses often overlook non-coding intergenic regions (IGRs). By disregarding the IGRs, crucial information is lost, as genes have little biological function without expression. Methods/Results: In this study, we present the first complete pangenome of the important human pathogen Streptococcus pneumoniae (pneumococcus), spanning both the genes and IGRs. We show that the pneumococcus species retains a small core genome of IGRs that are present across all isolates. Gene expression is highly dependent on these core IGRs, and often several copies of these core IGRs are found across each genome. Core genes and core IGRs show a clear linkage as 81% of core genes are associated with core IGRs. Additionally, we identify a single IGR within the core genome that is always occupied by one of two highly distinct sequences, scattered across the phylogenetic tree. Discussion: Their distribution indicates that this IGR is transferred between isolates through horizontal regulatory transfer independent of the flanking genes and that each type likely serves different regulatory roles depending on their genetic context.}, }
@article {pmid36841913, year = {2023}, author = {Stockdale, SR and Shkoporov, AN and Khokhlova, EV and Daly, KM and McDonnell, SA and O' Regan, O and Nolan, JA and Sutton, TDS and Clooney, AG and Ryan, FJ and Sheehan, D and Lavelle, A and Draper, LA and Shanahan, F and Ross, RP and Hill, C}, title = {Interpersonal variability of the human gut virome confounds disease signal detection in IBD.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {221}, pmid = {36841913}, issn = {2399-3642}, support = {SFI/12/RC/2273//Science Foundation Ireland (SFI)/ ; 101001684//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; SFI/14/SP APC/B3032//Science Foundation Ireland (SFI)/ ; 220646/Z/20/Z//Wellcome Trust (Wellcome)/ ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; Virome/genetics ; *Gastrointestinal Microbiome/genetics ; *Viruses/genetics ; *Colitis, Ulcerative/genetics/microbiology ; *Inflammatory Bowel Diseases/genetics ; }, abstract = {Viruses are increasingly recognised as important components of the human microbiome, fulfilling numerous ecological roles including bacterial predation, immune stimulation, genetic diversification, horizontal gene transfer, microbial interactions, and augmentation of metabolic functions. However, our current view of the human gut virome is tainted by previous sequencing requirements that necessitated the amplification of starting nucleic acids. In this study, we performed an original longitudinal analysis of 40 healthy control, 19 Crohn's disease, and 20 ulcerative colitis viromes over three time points without an amplification bias, which revealed and highlighted the interpersonal individuality of the human gut virome. In contrast to a 16 S rRNA gene analysis of matched samples, we show that α- and β-diversity metrics of unamplified viromes are not as efficient at discerning controls from patients with inflammatory bowel disease. Additionally, we explored the intrinsic properties of unamplified gut viromes and show there is considerable interpersonal variability in viral taxa, infrequent longitudinal persistence of intrapersonal viruses, and vast fluctuations in the abundance of temporal viruses. Together, these properties of unamplified faecal viromes confound the ability to discern disease associations but significantly advance toward an unbiased and accurate representation of the human gut virome.}, }
@article {pmid36840598, year = {2023}, author = {Densi, A and Iyer, RS and Bhat, PJ}, title = {Synonymous and Nonsynonymous Substitutions in Dictyostelium discoideum Ammonium Transporter amtA Are Necessary for Functional Complementation in Saccharomyces cerevisiae.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0384722}, pmid = {36840598}, issn = {2165-0497}, abstract = {Ammonium transporters are present in all three domains of life. They have undergone extensive horizontal gene transfer (HGT), gene duplication, and functional diversification and therefore offer an excellent paradigm to study protein evolution. We attempted to complement a mep1Δmep2Δmep3Δ strain of Saccharomyces cerevisiae (triple-deletion strain), which otherwise cannot grow on ammonium as a sole nitrogen source at concentrations of <3 mM, with amtA of Dictyostelium discoideum, an orthologue of S. cerevisiae MEP2. We observed that amtA did not complement the triple-deletion strain of S. cerevisiae for growth on low-ammonium medium. We isolated two mutant derivatives of amtA (amtA M1 and amtA M2) from a PCR-generated mutant plasmid library that complemented the triple-deletion strain of S. cerevisiae. amtA M1 bears three nonsynonymous and two synonymous substitutions, which are necessary for its functionality. amtA M2 bears two nonsynonymous substitutions and one synonymous substitution, all of which are necessary for functionality. Interestingly, AmtA M1 transports ammonium but does not confer methylamine toxicity, while AmtA M2 transports ammonium and confers methylamine toxicity, demonstrating functional diversification. Preliminary biochemical analyses indicated that the mutants differ in their conformations as well as their mechanisms of ammonium transport. These intriguing results clearly point out that protein evolution cannot be fathomed by studying nonsynonymous and synonymous substitutions in isolation. The above-described observations have significant implications for various facets of biological processes and are discussed in detail. IMPORTANCE Functional diversification following gene duplication is one of the major driving forces of protein evolution. While the role of nonsynonymous substitutions in the functional diversification of proteins is well recognized, knowledge of the role of synonymous substitutions in protein evolution is in its infancy. Using functional complementation, we isolated two functional alleles of the D. discoideum ammonium transporter gene (amtA), which otherwise does not function in S. cerevisiae as an ammonium transporters. One of them is an ammonium transporter, while the other is an ammonium transporter that also confers methylammonium (ammonium analogue) toxicity, suggesting functional diversification. Surprisingly, both alleles require a combination of synonymous and nonsynonymous substitutions for their functionality. These results bring out a hitherto-unknown pathway of protein evolution and pave the way for not only understanding protein evolution but also interpreting single nucleotide polymorphisms (SNPs).}, }
@article {pmid36840559, year = {2023}, author = {Winter, M and Harms, K and Johnsen, P and Vos, M}, title = {Collection of Annotated Acinetobacter Genome Sequences.}, journal = {Microbiology resource announcements}, volume = {12}, number = {3}, pages = {e0109422}, pmid = {36840559}, issn = {2576-098X}, support = {NE/T008083/1//UKRI | Natural Environment Research Council (NERC)/ ; NE/S007504/1//UKRI | Natural Environment Research Council (NERC)/ ; }, abstract = {The genus Acinetobacter contains environmental species as well as opportunistic pathogens of humans. Several species are competent for natural transformation, an important mechanism of horizontal gene transfer. Here, we present the genome sequences of 19 Acinetobacter strains used in past and upcoming studies of natural transformation.}, }
@article {pmid36838481, year = {2023}, author = {Tsilipounidaki, K and Florou, Z and Skoulakis, A and Fthenakis, GC and Miriagou, V and Petinaki, E}, title = {Diversity of Bacterial Clones and Plasmids of NDM-1 Producing Escherichia coli Clinical Isolates in Central Greece.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, pmid = {36838481}, issn = {2076-2607}, abstract = {The objective of the present study was to genetically characterize ten NDM-1 producing Escherichia coli isolates, recovered from patients in a hospital in Central Greece during the period 2017 to 2021.The isolates were studied by whole genome sequencing to obtain multi-locus sequencing typing (MLST), identification of blaNDM1-environment, resistome and plasmid content. MLST analysis showed the presence of eight sequence types: ST46* (two isolates), ST46, ST744, ST998, ST410, ST224, ST4380, ST683 and ST12 (one isolate each). Apart of the presence of blaNDM-1, the isolates carried a combination of various to β-lactams encoding resistance genes: blaTEM-1B, blaCTX-15, blaOXA-1, blaVIM-1, blaSHV-5, blaOXA-16, blaOXA-10 and blaVEB-1. Additionally, plurality of resistance genes to aminoglycosides, macrolides, rifamycin, phenicols, sulfonamides and tetracycline was detected. The presence of multiple replicons was observed, with predominance of IncFII and IncFIB. Analysis of blaNDM-1 genetic environment of the isolates showed that seven had 100% identity with the pS-3002cz plasmid (Accession Number KJ 958927), two with the pB-3002cz plasmid (Accession Number KJ958926) and one with the pEc19397-131 plasmid (Accession Number MG878866). Τhis latter plasmid was derived by the fusion of two, previously identified, plasmids, pAMPD2 and pLK75 (Accession Numbers CP078058 and KJ440076, respectively). The diversity of clones and plasmids of NDM-1 producing E. coli isolated from patients in Greece indicates a continuous horizontal gene transfer.}, }
@article {pmid36838414, year = {2023}, author = {Zayed, AR and Bitar, DM and Steinert, M and Lück, C and Spröer, C and Brettar, I and Höfle, MG and Bunk, B}, title = {Comparative Genomics of Legionella pneumophila Isolates from the West Bank and Germany Support Molecular Epidemiology of Legionnaires' Disease.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, pmid = {36838414}, issn = {2076-2607}, support = {HO-930/5-1/2//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Legionella pneumophila is an environmental bacterium and clinical pathogen that causes many life-threating outbreaks of an atypical pneumonia called Legionnaires' disease (LD). Studies of this pathogen have focused mainly on Europe and the United States. A shortage in L. pneumophila data is clearly observed for developing countries. To reduce this knowledge gap, L. pneumophila isolates were studied in two widely different geographical areas, i.e., the West Bank and Germany. For this study, we sequenced and compared the whole genome of 38 clinical and environmental isolates of L. pneumophila covering different MLVA-8(12) genotypes in the two areas. Sequencing was conducted using the Illumina HiSeq 2500 platform. In addition, two isolates (A194 and H3) were sequenced using a Pacific Biosciences (PacBio) RSII platform to generate complete reference genomes from each of the geographical areas. Genome sequences from 55 L. pneumophila strains, including 17 reference strains, were aligned with the genome sequence of the closest strain (L. pneumophila strain Alcoy). A whole genome phylogeny based on single nucleotide polymorphisms (SNPs) was created using the ParSNP software v 1.0. The reference genomes obtained for isolates A194 and H3 consisted of circular chromosomes of 3,467,904 bp and 3,691,263 bp, respectively. An average of 36,418 SNPs (min. 8569, max. 70,708 SNPs) against our reference strain L. pneumophila str. Alcoy, and 2367 core-genes were identified among the fifty-five strains. An analysis of the genomic population structure by SNP comparison divided the fifty-five L. pneumophila strains into six branches. Individual isolates in sub-lineages in these branches differed by less than 120 SNPs if they had the same MLVA genotype and were isolated from the same location. A bioinformatics analysis identified the genomic islands (GIs) for horizontal gene transfer and mobile genetic elements, demonstrating that L. pneumophila showed high genome plasticity. Four L. pneumophila isolates (H3, A29, A129 and L10-091) contained well-defined plasmids. On average, only about half of the plasmid genes could be matched to proteins in databases. In silico phage findings suggested that 43 strains contained at least one phage. However, none of them were found to be complete. BLASTp analysis of proteins from the type IV secretion Dot/Icm system showed those proteins highly conserved, with less than 25% structural differences in the new L. pneumophila isolates. Overall, we demonstrated that whole genome sequencing provides a molecular surveillance tool for L. pneumophila at the highest conceivable discriminatory level, i.e., two to eight SNPs were observed for isolates from the same location but several years apart.}, }
@article {pmid36838403, year = {2023}, author = {Hirose, J}, title = {Diversity and Evolution of Integrative and Conjugative Elements Involved in Bacterial Aromatic Compound Degradation and Their Utility in Environmental Remediation.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, pmid = {36838403}, issn = {2076-2607}, abstract = {Integrative and conjugative elements (ICEs) are mobile DNA molecules that can be transferred through excision, conjugation, and integration into chromosomes. They contribute to the horizontal transfer of genomic islands across bacterial species. ICEs carrying genes encoding aromatic compound degradation pathways are of interest because of their contribution to environmental remediation. Recent advances in DNA sequencing technology have increased the number of newly discovered ICEs in bacterial genomes and have enabled comparative analysis of their evolution. The two different families of ICEs carry various aromatic compound degradation pathway genes. ICEclc and its related ICEs contain a number of members with diverse catabolic capabilities. In addition, the Tn4371 family, which includes ICEs that carry the chlorinated biphenyl catabolic pathway, has been identified. It is apparent that they underwent evolution through the acquisition, deletion, or exchange of modules to adapt to an environmental niche. ICEs have the property of both stability and mobility in the chromosome. Perspectives on the use of ICEs in environmental remediation are also discussed.}, }
@article {pmid36838273, year = {2023}, author = {Werner, KA and Feyen, L and Hübner, T and Brüggemann, N and Prost, K and Grohmann, E}, title = {Fate of Horizontal-Gene-Transfer Markers and Beta-Lactamase Genes during Thermophilic Composting of Human Excreta.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, pmid = {36838273}, issn = {2076-2607}, support = {01DG18005//Federal Ministry of Education and Research/ ; 01DG17010//Federal Ministry of Education and Research/ ; 57354010//German Academic Exchange Service/ ; }, abstract = {Thermophilic composting is a suitable treatment for the recycling of organic wastes for agriculture. However, using human excreta as feedstock for composting raises concerns about antibiotic resistances. We analyzed samples from the start and end of a thermophilic composting trial of human excreta, together with green cuttings and straw, with and without biochar. Beta-lactamase genes blaCTX-M, blaIMP, and blaTEM conferring resistance to broad-spectrum beta-lactam antibiotics, as well as horizontal gene transfer marker genes, intI1 and korB, were quantified using qPCR. We found low concentrations of the beta-lactamase genes in all samples, with non-significant mean decreases in blaCTX-M and blaTEM copy numbers and a mean increase in blaIMP copy numbers. The decrease in both intI1 and korB genes from start to end of composting indicated that thermophilic composting can decrease the horizontal spread of resistance genes. Thus, thermophilic composting can be a suitable treatment for the recycling of human excreta.}, }
@article {pmid36835573, year = {2023}, author = {Ngcobo, PE and Nkosi, BVZ and Chen, W and Nelson, DR and Syed, K}, title = {Evolution of Cytochrome P450 Enzymes and Their Redox Partners in Archaea.}, journal = {International journal of molecular sciences}, volume = {24}, number = {4}, pages = {}, pmid = {36835573}, issn = {1422-0067}, support = {C686//Universit of Zululand/ ; MND200527525406//National Research Foundation (NRF), South Africa/ ; }, mesh = {Humans ; *Ferredoxins/metabolism ; *Archaea/metabolism ; Phylogeny ; Oxidation-Reduction ; Cytochrome P-450 Enzyme System/metabolism ; Bacteria/metabolism ; }, abstract = {Cytochrome P450 monooxygenases (CYPs/P450s) and their redox partners, ferredoxins, are ubiquitous in organisms. P450s have been studied in biology for over six decades owing to their distinct catalytic activities, including their role in drug metabolism. Ferredoxins are ancient proteins involved in oxidation-reduction reactions, such as transferring electrons to P450s. The evolution and diversification of P450s in various organisms have received little attention and no information is available for archaea. This study is aimed at addressing this research gap. Genome-wide analysis revealed 1204 P450s belonging to 34 P450 families and 112 P450 subfamilies, where some families and subfamilies are expanded in archaea. We also identified 353 ferredoxins belonging to the four types 2Fe-2S, 3Fe-4S, 7Fe-4S and 2[4Fe-4S] in 40 archaeal species. We found that bacteria and archaea shared the CYP109, CYP147 and CYP197 families, as well as several ferredoxin subtypes, and that these genes are co-present on archaeal plasmids and chromosomes, implying the plasmid-mediated lateral transfer of these genes from bacteria to archaea. The absence of ferredoxins and ferredoxin reductases in the P450 operons suggests that the lateral transfer of these genes is independent. We present different scenarios for the evolution and diversification of P450s and ferredoxins in archaea. Based on the phylogenetic analysis and high affinity to diverged P450s, we propose that archaeal P450s could have diverged from CYP109, CYP147 and CYP197. Based on this study's results, we propose that all archaeal P450s are bacterial in origin and that the original archaea had no P450s.}, }
@article {pmid36833369, year = {2023}, author = {Wittich, RM and Haïdour, A and Aguilar-Romero, I and de la Torre-Zúñiga, J and van Dillewijn, P}, title = {Biodegradation of Microtoxic Phenylpropanoids (Phenylpropanoic Acid and Ibuprofen) by Bacteria and the Relevance for Their Removal from Wastewater Treatment Plants.}, journal = {Genes}, volume = {14}, number = {2}, pages = {}, pmid = {36833369}, issn = {2073-4425}, mesh = {*Ibuprofen/chemistry/metabolism ; Anti-Inflammatory Agents, Non-Steroidal ; Bacteria/metabolism ; Biodegradation, Environmental ; *Water Purification ; }, abstract = {The NSAID ibuprofen (2-(4-isobutylphenyl)propanoic acid) and the structurally related 3-phenylpropanoic acid (3PPA), are widely used pharmaceutical and personal care products (PPCPs) which enter municipal waste streams but whose relatively low rates of elimination by wastewater treatment plants (WWTPs) are leading to the contamination of aquatic resources. Here, we report the isolation of three bacterial strains from a municipal WWTP, which as a consortium are capable of mineralizing ibuprofen. These were identified as the Pseudomonas citronellolis species, termed RW422, RW423 and RW424, in which the first two of these isolates were shown to contain the catabolic ipf operon responsible for the first steps of ibuprofen mineralization. These ipf genes which are associated with plasmids could, experimentally, only be transferred between other Sphingomonadaceae species, such as from the ibuprofen degrading Sphingopyxis granuli RW412 to the dioxins degrading Rhizorhabdus wittichii RW1, generating RW421, whilst a transfer from the P. citronellolis isolates to R. wittichii RW1 was not observed. RW412 and its derivative, RW421, as well as the two-species consortium RW422/RW424, can also mineralize 3PPA. We show that IpfF can convert 3PPA to 3PPA-CoA; however, the growth of RW412 with 3PPA produces a major intermediate that was identified by NMR to be cinnamic acid. This and the identification of other minor products from 3PPA allows us to propose the major pathway used by RW412 to mineralize 3PPA. Altogether, the findings in this study highlight the importance of ipf genes, horizontal gene transfer, and alternative catabolic pathways in the bacterial populations of WWTPs to eliminate ibuprofen and 3PPA.}, }
@article {pmid36833214, year = {2023}, author = {Gosselin, SP and Arsenault, DR and Jennings, CA and Gogarten, JP}, title = {The Evolutionary History of a DNA Methylase Reveals Frequent Horizontal Transfer and Within-Gene Recombination.}, journal = {Genes}, volume = {14}, number = {2}, pages = {}, pmid = {36833214}, issn = {2073-4425}, mesh = {*Evolution, Molecular ; *Inteins/genetics ; Gene Transfer, Horizontal ; Endonucleases/genetics ; DNA ; }, abstract = {Inteins, often referred to as protein introns, are highly mobile genetic elements that invade conserved genes throughout the tree of life. Inteins have been found to invade a wide variety of key genes within actinophages. While in the process of conducting a survey of these inteins in actinophages, we discovered that one protein family of methylases contained a putative intein, and two other unique insertion elements. These methylases are known to occur commonly in phages as orphan methylases (possibly as a form of resistance to restriction-modification systems). We found that the methylase family is not conserved within phage clusters and has a disparate distribution across divergent phage groups. We determined that two of the three insertion elements have a patchy distribution within the methylase protein family. Additionally, we found that the third insertion element is likely a second homing endonuclease, and that all three elements (the intein, the homing endonuclease, and what we refer to as the ShiLan domain) have different insertion sites that are conserved in the methylase gene family. Furthermore, we find strong evidence that both the intein and ShiLan domain are partaking in long-distance horizontal gene transfer events between divergent methylases in disparate phage hosts within the already dispersed methylase distribution. The reticulate evolutionary history of methylases and their insertion elements reveals high rates of gene transfer and within-gene recombination in actinophages.}, }
@article {pmid36833201, year = {2023}, author = {Liu, S and Jiao, J and Tian, CF}, title = {Adaptive Evolution of Rhizobial Symbiosis beyond Horizontal Gene Transfer: From Genome Innovation to Regulation Reconstruction.}, journal = {Genes}, volume = {14}, number = {2}, pages = {}, pmid = {36833201}, issn = {2073-4425}, mesh = {*Rhizobium/genetics ; Symbiosis/genetics ; Gene Transfer, Horizontal ; Ecosystem ; Nitrogen Fixation/genetics ; *Fabaceae/microbiology ; }, abstract = {There are ubiquitous variations in symbiotic performance of different rhizobial strains associated with the same legume host in agricultural practices. This is due to polymorphisms of symbiosis genes and/or largely unexplored variations in integration efficiency of symbiotic function. Here, we reviewed cumulative evidence on integration mechanisms of symbiosis genes. Experimental evolution, in concert with reverse genetic studies based on pangenomics, suggests that gain of the same circuit of key symbiosis genes through horizontal gene transfer is necessary but sometimes insufficient for bacteria to establish an effective symbiosis with legumes. An intact genomic background of the recipient may not support the proper expression or functioning of newly acquired key symbiosis genes. Further adaptive evolution, through genome innovation and reconstruction of regulation networks, may confer the recipient of nascent nodulation and nitrogen fixation ability. Other accessory genes, either co-transferred with key symbiosis genes or stochastically transferred, may provide the recipient with additional adaptability in ever-fluctuating host and soil niches. Successful integrations of these accessory genes with the rewired core network, regarding both symbiotic and edaphic fitness, can optimize symbiotic efficiency in various natural and agricultural ecosystems. This progress also sheds light on the development of elite rhizobial inoculants using synthetic biology procedures.}, }
@article {pmid36830600, year = {2023}, author = {Zhao, B and van Bodegom, PM and Trimbos, KB}, title = {Antibiotic Resistance Genes in Interconnected Surface Waters as Affected by Agricultural Activities.}, journal = {Biomolecules}, volume = {13}, number = {2}, pages = {}, pmid = {36830600}, issn = {2218-273X}, support = {201808310084//China Scholarship Council/ ; }, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; Drug Resistance, Microbial ; Sulfonamides/pharmacology ; }, abstract = {Pastures have become one of the most important sources of antibiotic resistance genes (ARGs) pollution, bringing risks to human health through the environment and the food that is grown there. Another significant source of food production is greenhouse horticulture, which is typically located near pastures. Through waterways, pasture-originated ARGs may transfer to the food in greenhouses. However, how these pasture-originated ARGs spread to nearby waterways and greenhouses has been much less investigated, while this may pose risks to humans through agricultural products. We analyzed 29 ARGs related to the most used antibiotics in livestock in the Netherlands at 16 locations in an agricultural area, representing pastures, greenhouses and lakes. We found that ARGs were prevalent in all surface waters surrounding pastures and greenhouses and showed a similar composition, with sulfonamide ARGs being dominant. This indicates that both pastures and greenhouses cause antibiotic resistance pressures on neighboring waters. However, lower pressures were found in relatively larger and isolated lakes, suggesting that a larger water body or a non-agricultural green buffer zone could help reducing ARG impacts from agricultural areas. We also observed a positive relationship between the concentrations of the class 1 integron (intl1 gene)-used as a proxy for horizontal gene transfer-and ARG concentration and composition. This supports that horizontal gene transfer might play a role in dispersing ARGs through landscapes. In contrast, none of the measured four abiotic factors (phosphate, nitrate, pH and dissolved oxygen) showed any impact on ARG concentrations. ARGs from different classes co-occurred, suggesting simultaneous use of different antibiotics. Our findings help to understand the spatial patterns of ARGs, specifically the impacts of ARGs from pastures and greenhouses on each other and on nearby waterways. In this way, this study guides management aiming at reducing ARGs' risk to human health from agricultural products.}, }
@article {pmid36830312, year = {2023}, author = {Bunduruș, IA and Balta, I and Ștef, L and Ahmadi, M and Peț, I and McCleery, D and Corcionivoschi, N}, title = {Overview of Virulence and Antibiotic Resistance in Campylobacter spp. Livestock Isolates.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {2}, pages = {}, pmid = {36830312}, issn = {2079-6382}, abstract = {Campylobacter remains the most prevalent foodborne pathogen bacterium responsible for causing gastroenteritis worldwide. Specifically, this pathogen colonises a ubiquitous range of environments, from poultry, companion pets and livestock animals to humans. The bacterium is uniquely adaptable to various niches, leading to complicated gastroenteritis and, in some cases, difficult to treat due to elevated resistance to certain antibiotics. This increased resistance is currently detected via genomic, clinical or epidemiological studies, with the results highlighting worrying multi-drug resistant (MDR) profiles in many food and clinical isolates. The Campylobacter genome encodes a rich inventory of virulence factors offering the bacterium the ability to influence host immune defences, survive antimicrobials, form biofilms and ultimately boost its infection-inducing potential. The virulence traits responsible for inducing clinical signs are not sufficiently defined because several populations have ample virulence genes with physiological functions that reflect their pathogenicity differences as well as a complement of antimicrobial resistance (AMR) systems. Therefore, exhaustive knowledge of the virulence factors associated with Campylobacter is crucial for collecting molecular insights into the infectivity processes, which could pave the way for new therapeutical targets to combat and control the infection and mitigate the spread of MDR bacteria. This review provides an overview of the spread and prevalence of genetic determinants associated with virulence and antibiotic resistance from studies performed on livestock animals. In addition, we have investigated the relevant coincidental associations between the prevalence of the genes responsible for pathogenic virulence, horizontal gene transfer (HGT) and transmissibility of highly pathogenic Campylobacter strains.}, }
@article {pmid36830244, year = {2023}, author = {Shi, H and Hu, X and Li, W and Zhang, J and Hu, B and Lou, L}, title = {Soil Component: A Potential Factor Affecting the Occurrence and Spread of Antibiotic Resistance Genes.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {2}, pages = {}, pmid = {36830244}, issn = {2079-6382}, support = {2020YFC1806903//National Key Research and Development Program of China/ ; 41877463//National Natural Science Foundation of China/ ; 22193061//National Natural Science Foundation of China/ ; }, abstract = {In recent years, antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in soil have become research hotspots in the fields of public health and environmental ecosystems, but the effects of soil types and soil components on the occurrence and spread of ARGs still lack systematic sorting and in-depth research. Firstly, investigational information about ARB and ARGs contamination of soil was described. Then, existing laboratory studies about the influence of the soil component on ARGs were summarized in the following aspects: the influence of soil types on the occurrence of ARGs during natural or human activities and the control of exogenously added soil components on ARGs from the macro perspectives, the effects of soil components on the HGT of ARGs in a pure bacterial system from the micro perspectives. Following that, the similarities in pathways by which soil components affect HGT were identified, and the potential mechanisms were discussed from the perspectives of intracellular responses, plasmid activity, quorum sensing, etc. In the future, related research on multi-component systems, multi-omics methods, and microbial communities should be carried out in order to further our understanding of the occurrence and spread of ARGs in soil.}, }
@article {pmid36830238, year = {2023}, author = {Michaelis, C and Grohmann, E}, title = {Horizontal Gene Transfer of Antibiotic Resistance Genes in Biofilms.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {2}, pages = {}, pmid = {36830238}, issn = {2079-6382}, abstract = {Most bacteria attach to biotic or abiotic surfaces and are embedded in a complex matrix which is known as biofilm. Biofilm formation is especially worrisome in clinical settings as it hinders the treatment of infections with antibiotics due to the facilitated acquisition of antibiotic resistance genes (ARGs). Environmental settings are now considered as pivotal for driving biofilm formation, biofilm-mediated antibiotic resistance development and dissemination. Several studies have demonstrated that environmental biofilms can be hotspots for the dissemination of ARGs. These genes can be encoded on mobile genetic elements (MGEs) such as conjugative and mobilizable plasmids or integrative and conjugative elements (ICEs). ARGs can be rapidly transferred through horizontal gene transfer (HGT) which has been shown to occur more frequently in biofilms than in planktonic cultures. Biofilm models are promising tools to mimic natural biofilms to study the dissemination of ARGs via HGT. This review summarizes the state-of-the-art of biofilm studies and the techniques that visualize the three main HGT mechanisms in biofilms: transformation, transduction, and conjugation.}, }
@article {pmid36830192, year = {2023}, author = {Sánchez-Osuna, M and Barbé, J and Erill, I}, title = {Systematic In Silico Assessment of Antimicrobial Resistance Dissemination across the Global Plasmidome.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {2}, pages = {}, pmid = {36830192}, issn = {2079-6382}, abstract = {The emergence of pathogenic strains resistant to multiple antimicrobials is a pressing problem in modern healthcare. Antimicrobial resistance is mediated primarily by dissemination of resistance determinants via horizontal gene transfer. The dissemination of some resistance genes has been well documented, but few studies have analyzed the patterns underpinning the dissemination of antimicrobial resistance genes. Analyzing the %GC content of plasmid-borne antimicrobial resistance genes relative to their host genome %GC content provides a means to efficiently detect and quantify dissemination of antimicrobial resistance genes. In this work we automate %GC content analysis to perform a comprehensive analysis of known antimicrobial resistance genes in publicly available plasmid sequences. We find that the degree to which antimicrobial resistance genes are disseminated depends primarily on the resistance mechanism. Our analysis identifies conjugative plasmids as primary dissemination vectors and indicates that most broadly disseminated genes have spread from single genomic backgrounds. We show that resistance dissemination profiles vary greatly among antimicrobials, oftentimes reflecting stewardship measures. Our findings establish %GC content analysis as a powerful, intuitive and scalable method to monitor the dissemination of resistance determinants using publicly available sequence data.}, }
@article {pmid36829548, year = {2023}, author = {Tang, J and Yao, D and Zhou, H and Wang, M and Daroch, M}, title = {Distinct Molecular Patterns of Two-Component Signal Transduction Systems in Thermophilic Cyanobacteria as Revealed by Genomic Identification.}, journal = {Biology}, volume = {12}, number = {2}, pages = {}, pmid = {36829548}, issn = {2079-7737}, support = {31970092//National Natural Science Foundation of China/ ; 32071480//National Natural Science Foundation of China/ ; 3221101094//National Natural Science Foundation of China/ ; GXWD20201231165807007-20200806170221001//Shenzhen Fundamental Research Program/ ; }, abstract = {Two-component systems (TCSs) play crucial roles in sensing and responding to environmental signals, facilitating the acclimation of cyanobacteria to hostile niches. To date, there is limited information on the TCSs of thermophilic cyanobacteria. Here, genome-based approaches were used to gain insights into the structure and architecture of the TCS in 17 well-described thermophilic cyanobacteria, namely strains from the genus Leptodesmis, Leptolyngbya, Leptothermofonsia, Thermoleptolyngbya, Thermostichus, and Thermosynechococcus. The results revealed a fascinating complexity and diversity of the TCSs. A distinct composition of TCS genes existed among these thermophilic cyanobacteria. A majority of TCS genes were classified as orphan, followed by the paired and complex cluster. A high proportion of histidine kinases (HKs) were predicted to be cytosolic subcellular localizations. Further analyses suggested diversified domain architectures of HK and response regulators (RRs), putatively in association with various functions. Comparative and evolutionary genomic analyses indicated that the horizontal gene transfer, as well as duplications events, might be involved in the evolutionary history of TCS genes in Thermostichus and Thermosynechococcus strains. A comparative analysis between thermophilic and mesophilic cyanobacteria indicated that one HK cluster and one RR cluster were uniquely shared by all the thermophilic cyanobacteria studied, while two HK clusters and one RR cluster were common to all the filamentous thermophilic cyanobacteria. These results suggested that these thermophile-unique clusters may be related to thermal characters and morphology. Collectively, this study shed light on the TCSs of thermophilic cyanobacteria, which may confer the necessary regulatory flexibility; these findings highlight that the genomes of thermophilic cyanobacteria have a broad potential for acclimations to environmental fluctuations.}, }
@article {pmid36827095, year = {2023}, author = {Pardo-De la Hoz, CJ and Magain, N and Piatkowski, B and Cornet, L and Dal Forno, M and Carbone, I and Miadlikowska, J and Lutzoni, F}, title = {Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria.}, journal = {Systematic biology}, volume = {72}, number = {3}, pages = {694-712}, doi = {10.1093/sysbio/syad008}, pmid = {36827095}, issn = {1076-836X}, support = {1929994//National Science Foundation/ ; }, mesh = {Phylogeny ; *Genome ; Biological Evolution ; Prokaryotic Cells ; *Cyanobacteria/genetics ; }, abstract = {Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due to widespread horizontal gene transfers (HGTs). Consequently, representing evolutionary relationships of prokaryotes as bifurcating trees has long been controversial. However, studies reporting conflicts among gene trees derived from phylogenomic data sets have shown that these conflicts can be the result of artifacts or evolutionary processes other than HGT, such as incomplete lineage sorting, low phylogenetic signal, and systematic errors due to substitution model misspecification. Here, we present the results of an extensive exploration of phylogenetic conflicts in the cyanobacterial order Nostocales, for which previous studies have inferred strongly supported conflicting relationships when using different concatenated phylogenomic data sets. We found that most of these conflicts are concentrated in deep clusters of short internodes of the Nostocales phylogeny, where the great majority of individual genes have low resolving power. We then inferred phylogenetic networks to detect HGT events while also accounting for incomplete lineage sorting. Our results indicate that most conflicts among gene trees are likely due to incomplete lineage sorting linked to an ancient rapid radiation, rather than to HGTs. Moreover, the short internodes of this radiation fit the expectations of the anomaly zone, i.e., a region of the tree parameter space where a species tree is discordant with its most likely gene tree. We demonstrated that concatenation of different sets of loci can recover up to 17 distinct and well-supported relationships within the putative anomaly zone of Nostocales, corresponding to the observed conflicts among well-supported trees based on concatenated data sets from previous studies. Our findings highlight the important role of rapid radiations as a potential cause of strongly conflicting phylogenetic relationships when using phylogenomic data sets of bacteria. We propose that polytomies may be the most appropriate phylogenetic representation of these rapid radiations that are part of anomaly zones, especially when all possible genomic markers have been considered to infer these phylogenies. [Anomaly zone; bacteria; horizontal gene transfer; incomplete lineage sorting; Nostocales; phylogenomic conflict; rapid radiation; Rhizonema.].}, }
@article {pmid36824529, year = {2022}, author = {Shippy, TD and Miller, S and Tamayo, B and Hosmani, PS and Flores-Gonzalez, M and Mueller, LA and Hunter, WB and Brown, SJ and D'Elia, T and Saha, S}, title = {Manual curation and phylogenetic analysis of chitinase family genes in the Asian citrus psyllid, Diaphorina citri.}, journal = {GigaByte (Hong Kong, China)}, volume = {2022}, number = {}, pages = {gigabyte46}, pmid = {36824529}, issn = {2709-4715}, support = {P20 GM103418/GM/NIGMS NIH HHS/United States ; }, abstract = {Chitinases are enzymes that digest the polysaccharide polymer chitin. During insect development, breakdown of chitin is an essential step in molting of the exoskeleton. Knockdown of chitinases required for molting is lethal to insects, making chitinase genes an interesting target for RNAi-based pest control methods. The Asian citrus psyllid, Diaphorina citri, carries the bacterium causing Huanglongbing, or citrus greening disease, a devastating citrus disease. We identified and annotated 12 chitinase family genes from D. citri as part of a community effort to create high-quality gene models to aid the design of interdictory molecules for pest control. We categorized the D. citri chitinases according to an established classification scheme and re-evaluated the classification of chitinases in other hemipterans. In addition to chitinases from known groups, we identified a novel class of chitinases present in D. citri and several related hemipterans that appears to be the result of horizontal gene transfer.}, }
@article {pmid36823453, year = {2023}, author = {Webb, EA and Held, NA and Zhao, Y and Graham, ED and Conover, AE and Semones, J and Lee, MD and Feng, Y and Fu, FX and Saito, MA and Hutchins, DA}, title = {Importance of mobile genetic element immunity in numerically abundant Trichodesmium clades.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {15}, pmid = {36823453}, issn = {2730-6151}, support = {1657757//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1851222//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1851222//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1850719//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1850719//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1850719//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 2125191//NSF | Directorate for Biological Sciences (BIO)/ ; }, abstract = {The colony-forming cyanobacteria Trichodesmium spp. are considered one of the most important nitrogen-fixing genera in the warm, low nutrient ocean. Despite this central biogeochemical role, many questions about their evolution, physiology, and trophic interactions remain unanswered. To address these questions, we describe Trichodesmium pangenomic potential via significantly improved genomic assemblies from two isolates and 15 new >50% complete Trichodesmium metagenome-assembled genomes from hand-picked, Trichodesmium colonies spanning the Atlantic Ocean. Phylogenomics identified ~four N2 fixing clades of Trichodesmium across the transect, with T. thiebautii dominating the colony-specific reads. Pangenomic analyses showed that all T. thiebautii MAGs are enriched in COG defense mechanisms and encode a vertically inherited Type III-B Clustered Regularly Interspaced Short Palindromic Repeats and associated protein-based immunity system (CRISPR-Cas). Surprisingly, this CRISPR-Cas system was absent in all T. erythraeum genomes, vertically inherited by T. thiebautii, and correlated with increased signatures of horizontal gene transfer. Additionally, the system was expressed in metaproteomic and transcriptomic datasets and CRISPR spacer sequences with 100% identical hits to field-assembled, putative phage genome fragments were identified. While the currently CO2-limited T. erythraeum is expected to be a 'winner' of anthropogenic climate change, their genomic dearth of known phage resistance mechanisms, compared to T. thiebautii, could put this outcome in question. Thus, the clear demarcation of T. thiebautii maintaining CRISPR-Cas systems, while T. erythraeum does not, identifies Trichodesmium as an ecologically important CRISPR-Cas model system, and highlights the need for more research on phage-Trichodesmium interactions.}, }
@article {pmid36823299, year = {2023}, author = {Baek, MG and Kim, KW and Yi, H}, title = {Subspecies-level genome comparison of Lactobacillus delbrueckii.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {3171}, pmid = {36823299}, issn = {2045-2322}, mesh = {*Lactobacillus delbrueckii/classification/genetics ; *Genome, Bacterial ; Gene Transfer, Horizontal ; Biological Evolution ; }, abstract = {Lactobacillus delbrueckii comprises six subspecies, L. delbrueckii subsp. bulgaricus, L. delbrueckii subsp. lactis, L. delbrueckii subsp. jakobsenii, L. delbrueckii subsp. delbrueckii, L. delbrueckii subsp. sunkii, and L. delbrueckii subsp. indicus. We investigated the evolution of the six subspecies of L. delbrueckii using comparative genomics. While the defining feature of the species was the gene number increment driven by mobile elements and gene fragmentation, the repertoire of subspecies-specific gene gains and losses differed among the six subspecies. The horizontal gene transfer analyses indicated that frequent gene transfers between different subspecies had occurred when the six subspecies first diverged from the common ancestor, but recent gene exchange was confined to a subspecies implying independent evolution of the six subspecies. The subspecies bulgaricus is a homogeneous group that diverged from the other subspecies a long time ago and underwent convergent evolution. The subspecies lactis, jakobsenii, delbrueckii, and sunkii were more closely related to each other than to other subspecies. The four subspecies commonly show increasing genetic variability with increasing genome size. However, the four subspecies were distinguished by specific gene contents. The subspecies indicus forms a branch distant from the other subspecies and shows an independent evolutionary trend. These results could explain the differences in the habitat and nutritional requirements of the subspecies of L. delbrueckii.}, }
@article {pmid36822312, year = {2023}, author = {Sun, L and Tang, D and Tai, X and Wang, J and Long, M and Xian, T and Jia, H and Wu, R and Ma, Y and Jiang, Y}, title = {Effect of composted pig manure, biochar, and their combination on antibiotic resistome dissipation in swine wastewater-treated soil.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {323}, number = {}, pages = {121323}, doi = {10.1016/j.envpol.2023.121323}, pmid = {36822312}, issn = {1873-6424}, mesh = {*Composting ; *Manure ; *Drug Resistance, Bacterial ; Brassica/microbiology ; Interspersed Repetitive Sequences ; Soil Microbiology ; *Agriculture/methods ; *Swine ; Animals ; Soil/chemistry ; }, abstract = {The prevalence of antibiotic resistance genes (ARGs), owing to irrigation using untreated swine wastewater, in vegetable-cultivated soils around swine farms poses severe threats to human health. Furthermore, at the field scale, the remediation of such soils is still challenging. Therefore, here, we performed field-scale experiments involving the cultivation of Brassica pekinensis in a swine wastewater-treated soil amended with composted pig manure, biochar, or their combination. Specifically, the ARG and mobile genetic element (MGE) profiles of bulk soil (BS), rhizosphere soil (RS), and root endophyte (RE) samples were examined using high-throughput quantitative polymerase chain reaction. In total, 117 ARGs and 22 MGEs were detected. Moreover, we observed that soil amendment using composted pig manure, biochar, or their combination decreased the absolute abundance of ARGs in BS and RE after 90 days of treatment. However, the decrease in the abundance of ARGs in RS was not significant. We also observed that the manure and biochar co-application showed a minimal synergistic effect. To clarify this observation, we performed network and Spearman correlation analyses and used structure equation models to explore the correlations among ARGs, MGEs, bacterial composition, and soil properties. The results revealed that the soil amendments reduced the abundances of MGEs and potential ARG-carrying bacteria. Additionally, weakened horizontal gene transfer was responsible for the dissipation of ARGs. Thus, our results indicate that composted manure application, with or without biochar, is a useful strategy for soil nutrient supplementation and alleviating farmland ARG pollution, providing a justification for using an alternative to the common agricultural practice of treating the soil using only untreated swine wastewater. Additionally, our results are important in the context of soil health for sustainable agriculture.}, }
@article {pmid36821031, year = {2023}, author = {Milligan, EG and Calarco, J and Davis, BC and Keenum, IM and Liguori, K and Pruden, A and Harwood, VJ}, title = {A Systematic Review of Culture-Based Methods for Monitoring Antibiotic-Resistant Acinetobacter, Aeromonas, and Pseudomonas as Environmentally Relevant Pathogens in Wastewater and Surface Water.}, journal = {Current environmental health reports}, volume = {10}, number = {2}, pages = {154-171}, pmid = {36821031}, issn = {2196-5412}, mesh = {Humans ; *Wastewater ; Genes, Bacterial ; *Aeromonas/genetics ; Pseudomonas/genetics ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Anti-Bacterial Agents/pharmacology ; }, abstract = {PURPOSE OF REVIEW: Mounting evidence indicates that habitats such as wastewater and environmental waters are pathways for the spread of antibiotic-resistant bacteria (ARB) and mobile antibiotic resistance genes (ARGs). We identified antibiotic-resistant members of the genera Acinetobacter, Aeromonas, and Pseudomonas as key opportunistic pathogens that grow or persist in built (e.g., wastewater) or natural aquatic environments. Effective methods for monitoring these ARB in the environment are needed to understand their influence on dissemination of ARB and ARGs, but standard methods have not been developed. This systematic review considers peer-reviewed papers where the ARB above were cultured from wastewater or surface water, focusing on the accuracy of current methodologies.<br><br>RECENT FINDINGS: Recent studies suggest that many clinically important ARGs were originally acquired from environmental microorganisms. Acinetobacter, Aeromonas, and Pseudomonas species are of interest because their ability to persist and grow in the environment provides opportunities to engage in horizontal gene transfer with other environmental bacteria. Pathogenic strains of these organisms resistant to multiple, clinically relevant drug classes have been identified as an urgent threat. However, culture methods for these bacteria were generally developed for clinical samples and are not well-vetted for environmental samples. The search criteria yielded 60 peer-reviewed articles over the past 20&#xa0;years, which reported a wide variety of methods for isolation, confirmation, and antibiotic resistance assays. Based on a systematic comparison of the reported methods, we suggest a path forward for standardizing methodologies for monitoring antibiotic resistant strains of these bacteria in water environments.}, }
@article {pmid36818863, year = {2023}, author = {Matveeva, T and Аndronov, E and Chen, K}, title = {Editorial: Rhizobiaceae mediated HGT: Facts, mechanisms, and evolutionary consequences.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1149426}, doi = {10.3389/fpls.2023.1149426}, pmid = {36818863}, issn = {1664-462X}, }
@article {pmid36813198, year = {2023}, author = {Huang, Q and Liu, Z and Guo, Y and Li, B and Yang, Z and Liu, X and Ni, J and Li, X and Zhang, X and Zhou, N and Yin, H and Jiang, C and Hao, L}, title = {Coal-source acid mine drainage reduced the soil multidrug-dominated antibiotic resistome but increased the heavy metal(loid) resistome and energy production-related metabolism.}, journal = {The Science of the total environment}, volume = {873}, number = {}, pages = {162330}, doi = {10.1016/j.scitotenv.2023.162330}, pmid = {36813198}, issn = {1879-1026}, mesh = {*Soil ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; *Metals, Heavy ; Coal ; }, abstract = {A recent global scale study found that mining-impacted environments have multi-antibiotic resistance gene (ARG)-dominated resistomes with an abundance similar to urban sewage but much higher than freshwater sediment. These findings raised concern that mining may increase the risk of ARG environmental proliferation. The current study assessed how typical multimetal(loid)-enriched coal-source acid mine drainage (AMD) contamination affects soil resistomes by comparing with background soils unaffected by AMD. Both contaminated and background soils have multidrug-dominated antibiotic resistomes attributed to the acidic environment. AMD-contaminated soils had a lower relative abundance of ARGs (47.45 ± 23.34 ×/Gb) than background soils (85.47 ± 19.71 ×/Gb) but held high-level heavy metal(loid) resistance genes (MRGs, 133.29 ± 29.36 ×/Gb) and transposase- and insertion sequence-dominated mobile genetic elements (MGEs, 188.51 ± 21.81 ×/Gb), which was 56.26 % and 412.12 % higher than background soils, respectively. Procrustes analysis showed that the microbial community and MGEs exerted more influence on driving heavy metal(loid) resistome variation than antibiotic resistome. The microbial community increased energy production-related metabolism to fulfill the increasing energy needs required by acid and heavy metal(loid) resistance. Horizontal gene transfer (HGT) events primarily exchanged energy- and information-related genes to adapt to the harsh AMD environment. These findings provide new insight into the risk of ARG proliferation in mining environments.}, }
@article {pmid36809063, year = {2023}, author = {Li, Y and Li, D and Liang, Y and Cui, J and He, K and He, D and Liu, J and Hu, G and Yuan, L}, title = {Characterization of a Tigecycline-Resistant and blaCTX-M-Bearing Klebsiella pneumoniae Strain from a Peacock in a Chinese Zoo.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {3}, pages = {e0176422}, pmid = {36809063}, issn = {1098-5336}, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; beta-Lactamases/genetics ; Colistin ; Drug Resistance, Multiple, Bacterial/genetics ; *Klebsiella Infections/veterinary/microbiology ; *Klebsiella pneumoniae/drug effects/genetics ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Plasmids/genetics ; Tigecycline/pharmacology ; Animals ; Birds/microbiology ; }, abstract = {In Chinese zoos, there are usually specially designed bird parks, similar to petting zoos, that allow children and adults to interact with diverse birds. However, such behaviors present a risk for the transmission of zoonotic pathogens. Recently, we isolated eight strains of Klebsiella pneumoniae and identified two blaCTX-M-positive strains from 110 birds, including parrots, peacocks, and ostriches, using anal or nasal swabs in a bird park of a zoo in China. There, K. pneumoniae LYS105A was obtained from a diseased peacock with chronic respiratory diseases by a nasal swab, which harbored the blaCTX-M-3 gene and exhibited resistance to amoxicillin, cefotaxime, gentamicin, oxytetracycline, doxycycline, tigecycline, florfenicol, and enrofloxacin. According to an analysis by whole-genome sequencing, K. pneumoniae LYS105A belongs to serotype ST859 (sequence type 859)-K19 (capsular serotype 19) and contains two plasmids, of which pLYS105A-2 can be transferred by electrotransformation and harbors numerous resistance genes such as blaCTX-M-3, aac(6')-Ib-cr5, and qnrB91. The above-mentioned genes are located in a novel mobile composite transposon, Tn7131, which makes horizontal transfer more flexible. Although no known genes were identified in the chromosome, a significant increase in SoxS upregulated the expression levels of phoPQ, acrEF-tolC, and oqxAB, which contributed to strain LYS105A acquiring resistance to tigecycline (MIC = 4 mg/L) and intermediate resistance to colistin (MIC = 2 mg/L). Altogether, our findings show that bird parks in zoos may act as important vehicles for the spread of multidrug-resistant bacteria from birds to humans and vice versa. IMPORTANCE A multidrug-resistant ST859-K19 K. pneumoniae strain, LYS105A, was obtained from a diseased peacock in a Chinese zoo. In addition, multiple resistance genes such as blaCTX-M-3, aac(6')-Ib-cr5, and qnrB91 were located in a novel composite transposon, Tn7131, of a mobile plasmid, implying that most of the resistance genes in strain LYS105A can be moved easily via horizontal gene transfer. Meanwhile, an increase in SoxS can further positively regulate the expression of phoPQ, acrEF-tolC, and oqxAB, which is the key factor for strain LYS105A to develop resistance to tigecycline and colistin. Taken together, these findings enrich our understanding of the horizontal cross-species spread of drug resistance genes, which will help us curb the development of bacterial resistance.}, }
@article {pmid36808308, year = {2023}, author = {Zhu, Y and Wang, T and Zhu, W and Wei, Q}, title = {Influence of class 2 integron integrase concentration on gene cassette insertion and excision in vivo.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {54}, number = {2}, pages = {645-653}, pmid = {36808308}, issn = {1678-4405}, support = {EP-C-15-001/EPA/EPA/United States ; }, mesh = {*Integrons/genetics ; *Integrases/genetics/metabolism ; Mutagenesis, Insertional ; Promoter Regions, Genetic ; Plasmids/genetics ; }, abstract = {Integron can capture and express antimicrobial resistance gene cassettes and plays important roles in horizontal gene transfer. The establishment of a complete in vitro reaction system will help to reveal integron integrase mediated site-specific recombination process and regulation mechanism. As an enzymatic reaction, the concentration of integrase is assumed to have a great influence on the reaction rate. To determine the influence of different concentrations of integrase on the reaction rate and to find the best range of enzyme concentration were essential to optimizing the in vitro reaction system. In this study, plasmids with gradient transcription levels of class 2 integron integrase gene intI2 under different promoters were constructed. Among plasmids pI2W16, pINTI2N, pI2W, and pI2NW, intI2 transcription levels ranged from about 0.61-fold to 49.65-fold of that in pINTI2N. And the frequencies of gene cassette sat2 integration and excision catalyzed by IntI2 were positively correlated with the transcription levels of intI2 within this range. Western blotting results indicated high expression of IntI2 partly existed in the form of an inclusion body. When compared with Pc of class 1 integron, the spacer sequence of PintI2 can increase the strength of PcW but decrease the strength of PcS. In conclusion, the frequencies of gene cassette integration and excision were positively correlated with the concentration of IntI2. intI2 driving by PcW with PintI2 spacer sequence can obtain the optimum IntI2 concentration required to achieve the maximum recombination efficiency in vivo in this study.}, }
@article {pmid36805559, year = {2023}, author = {Huang, Y and Sheth, RU and Zhao, S and Cohen, LA and Dabaghi, K and Moody, T and Sun, Y and Ricaurte, D and Richardson, M and Velez-Cortes, F and Blazejewski, T and Kaufman, A and Ronda, C and Wang, HH}, title = {High-throughput microbial culturomics using automation and machine learning.}, journal = {Nature biotechnology}, volume = {41}, number = {10}, pages = {1424-1433}, pmid = {36805559}, issn = {1546-1696}, support = {R01 AI132403/AI/NIAID NIH HHS/United States ; R01 DK118044/DK/NIDDK NIH HHS/United States ; R21 AI146817/AI/NIAID NIH HHS/United States ; T32 GM007367/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Genomics/methods ; *Microbiota/genetics ; Bacteria ; Automation ; Machine Learning ; }, abstract = {Pure bacterial cultures remain essential for detailed experimental and mechanistic studies in microbiome research, and traditional methods to isolate individual bacteria from complex microbial ecosystems are labor-intensive, difficult-to-scale and lack phenotype-genotype integration. Here we describe an open-source high-throughput robotic strain isolation platform for the rapid generation of isolates on demand. We develop a machine learning approach that leverages colony morphology and genomic data to maximize the diversity of microbes isolated and enable targeted picking of specific genera. Application of this platform on fecal samples from 20 humans yields personalized gut microbiome biobanks totaling 26,997 isolates that represented >80% of all abundant taxa. Spatial analysis on >100,000 visually captured colonies reveals cogrowth patterns between Ruminococcaceae, Bacteroidaceae, Coriobacteriaceae and Bifidobacteriaceae families that suggest important microbial interactions. Comparative analysis of 1,197 high-quality genomes from these biobanks shows interesting intra- and interpersonal strain evolution, selection and horizontal gene transfer. This culturomics framework should empower new research efforts to systematize the collection and quantitative analysis of imaging-based phenotypes with high-resolution genomics data for many emerging microbiome studies.}, }
@article {pmid36805463, year = {2023}, author = {Engin, AB and Engin, ED and Engin, A}, title = {Effects of co-selection of antibiotic-resistance and metal-resistance genes on antibiotic-resistance potency of environmental bacteria and related ecological risk factors.}, journal = {Environmental toxicology and pharmacology}, volume = {98}, number = {}, pages = {104081}, doi = {10.1016/j.etap.2023.104081}, pmid = {36805463}, issn = {1872-7077}, mesh = {*Genes, Bacterial ; Bacteria ; Drug Resistance, Microbial/genetics ; *Metals, Heavy ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The inadequate elimination of micropollutants in wastewater treatment plants (WWTP), cause to increase in the incidence of antibiotic resistant bacterial strains. Growth of microbial pathogens in WWTP is one of the serious public health problems. The widespread and simultaneous emergence of antibiotic resistance genes (ARGs) and heavy metal resistance genes (HMRGs) in the environment with heavy metals create persistent and selective pressure for co-selection of both genes on environmental microorganisms. Co-localization of ARGs and HMRGs on the same horizontal mobile genetic elements (MGEs) allows the spreading of numerous antibiotic-resistant strains of bacteria in aquatic and terrestrial environment. The biofilm formation and colonization potential of environmental bacteria leads to the co-selection of multi-antibiotic resistance and multi-metal tolerance. Horizontal gene transfer (HGT), co-localization of both ARGs and HMRGs on the same MGEs, and the shared resistomes are important bacteria-associated ecological risks factors, which reduce the effectiveness of antibiotics against bacterial infections.}, }
@article {pmid36805209, year = {2023}, author = {Rius, M and Rest, JS and Filloramo, GV and Novák Vanclová, AMG and Archibald, JM and Collier, JL}, title = {Horizontal Gene Transfer and Fusion Spread Carotenogenesis Among Diverse Heterotrophic Protists.}, journal = {Genome biology and evolution}, volume = {15}, number = {3}, pages = {}, pmid = {36805209}, issn = {1759-6653}, mesh = {*Carotenoids ; beta Carotene/genetics ; Gene Transfer, Horizontal ; *Stramenopiles ; Bacteria/genetics ; }, abstract = {Thraustochytrids (phylum: Labyrinthulomycota) are nonphotosynthetic marine protists. Some thraustochytrids have crtIBY, a trifunctional fusion gene encoding a protein capable of β-carotene biosynthesis from geranylgeranyl pyrophosphate. Here we show that crtIBY is essential in, and encodes the sole pathway for, carotenoid biosynthesis in the thraustochytrid Aurantiochytrium limacinum ATCC MYA-1381. We explore the evolutionary origins of CrtIBY and discover that the closest related protein domains are present in a small but diverse group of other heterotrophic protists, including the apusomonad Thecamonas trahens and the dinoflagellates Oxyrrhis marina and Noctiluca scintillans. Each organism within this cluster also contains one or more β-carotene 15-15' oxygenase genes (blh and rpe65), suggesting that the acquisition of β-carotene biosynthesis genes may have been related to the production of retinal. Our findings support a novel origin of eukaryotic (apo)carotenoid biosynthesis by horizontal gene transfer from Actinobacteria, Bacteroidetes, and/or Archaea. This reveals a remarkable case of parallel evolution of eukaryotic (apo)carotenogenesis in divergent protistan lineages by repeated gene transfers.}, }
@article {pmid36798152, year = {2023}, author = {Kosmopoulos, JC and Campbell, DE and Whitaker, RJ and Wilbanks, EG}, title = {Horizontal gene transfer and CRISPR targeting drive phage-bacterial host interactions and coevolution in pink berry marine microbial aggregates.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.02.06.527410}, pmid = {36798152}, issn = {2692-8205}, abstract = {UNLABELLED: Bacteriophages (phages), viruses that infect bacteria, are the most abundant components of microbial communities and play roles in community dynamics and host evolution. The study of phage-host interactions, however, is made difficult by a paucity of model systems from natural environments and known and cultivable phage-host pairs. Here, we investigate phage-host interactions in the "pink berry" consortia, naturally-occurring, low-diversity, macroscopic aggregates of bacteria found in the Sippewissett Salt Marsh (Falmouth, MA, USA). We leverage metagenomic sequence data and a comparative genomics approach to identify eight compete phage genomes, infer their bacterial hosts from host-encoded clustered regularly interspaced short palindromic repeats (CRISPR), and observe the potential evolutionary consequences of these interactions. Seven of the eight phages identified infect the known pink berry symbionts Desulfofustis sp. PB-SRB1, Thiohalocapsa sp. PB-PSB1, and Rhodobacteraceae sp. A2, and belong to entirely novel viral taxa, except for one genome which represents the second member of the Knuthellervirus genus. We further observed increased nucleotide variation over a region of a conserved phage capsid gene that is commonly targeted by host CRISPR systems, suggesting that CRISPRs may drive phage evolution in pink berries. Finally, we identified a predicted phage lysin gene that was horizontally transferred to its bacterial host, potentially via a transposon intermediary, emphasizing the role of phages in bacterial evolution in pink berries. Taken together, our results demonstrate that pink berry consortia contain diverse and variable phages, and provide evidence for phage-host co-evolution via multiple mechanisms in a natural microbial system.<br><br>IMPORTANCE: Phages (viruses that infect bacteria) are important components of all microbial systems, where they drive the turnover of organic matter by lysing host cells, facilitate horizontal gene transfer (HGT), and co-evolve with their bacterial hosts. Bacteria resist phage infection, which is often costly or lethal, through a diversity of mechanisms. One of these mechanisms are CRISPR systems, which encode arrays of phage-derived sequences from past infections to block subsequent infection with related phages. Here, we investigate bacteria and phage populations from a simple marine microbial community known as "pink berries" found in salt marshes of Falmouth, Massachusetts, as a model of phage-host co-evolution. We identify eight novel phages, and characterize a case of putative CRISPR-driven phage evolution and an instance of HGT between phage and host, together suggesting that phages have large evolutionary impacts in a naturally-occuring microbial community.}, }
@article {pmid36795748, year = {2023}, author = {Johnston, CHG and Hope, R and Soulet, AL and Dewailly, M and De Lemos, D and Polard, P}, title = {The RecA-directed recombination pathway of natural transformation initiates at chromosomal replication forks in the pneumococcus.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {8}, pages = {e2213867120}, pmid = {36795748}, issn = {1091-6490}, mesh = {*Streptococcus pneumoniae/genetics/metabolism ; *Rec A Recombinases/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Chromosomes/metabolism ; DNA/metabolism ; DNA, Single-Stranded/genetics/metabolism ; }, abstract = {Homologous recombination (HR) is a crucial mechanism of DNA strand exchange that promotes genetic repair and diversity in all kingdoms of life. Bacterial HR is driven by the universal recombinase RecA, assisted in the early steps by dedicated mediators that promote its polymerization on single-stranded DNA (ssDNA). In bacteria, natural transformation is a prominent HR-driven mechanism of horizontal gene transfer specifically dependent on the conserved DprA recombination mediator. Transformation involves internalization of exogenous DNA as ssDNA, followed by its integration into the chromosome by RecA-directed HR. How DprA-mediated RecA filamentation on transforming ssDNA is spatiotemporally coordinated with other cellular processes remains unknown. Here, we tracked the localization of fluorescent fusions to DprA and RecA in Streptococcus pneumoniae and revealed that both accumulate in an interdependent manner with internalized ssDNA at replication forks. In addition, dynamic RecA filaments were observed emanating from replication forks, even with heterologous transforming DNA, which probably represent chromosomal homology search. In conclusion, this unveiled interaction between HR transformation and replication machineries highlights an unprecedented role for replisomes as landing pads for chromosomal access of tDNA, which would define a pivotal early HR step for its chromosomal integration.}, }
@article {pmid36792883, year = {2023}, author = {Lau, DYL and Aguirre Sánchez, JR and Baker-Austin, C and Martinez-Urtaza, J}, title = {What Whole Genome Sequencing Has Told Us About Pathogenic Vibrios.}, journal = {Advances in experimental medicine and biology}, volume = {1404}, number = {}, pages = {337-352}, pmid = {36792883}, issn = {0065-2598}, mesh = {Humans ; Phylogeny ; *Vibrio cholerae/genetics ; *Vibrio parahaemolyticus/genetics ; *Vibrio vulnificus/genetics ; Whole Genome Sequencing ; }, abstract = {When the first microbial genome sequences were published just 20 years ago, our understanding regarding the microbial world changed dramatically. The genomes of the first pathogenic vibrios sequenced, including Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus revealed a functional and phylogenetic diversity previously unimagined as well as a genome structure indelibly shaped by horizontal gene transfer. The initial glimpses into these organisms also revealed a genomic plasticity that allowed these bacteria to thrive in challenging and varied aquatic and marine environments, but critically also a suite of pathogenicity attributes. In this review we outline how our understanding of vibrios has changed over the last two decades with the advent of genomics and advances in bioinformatic and data analysis techniques, it has become possible to provide a more cohesive understanding regarding these bacteria: how these pathogens have evolved and emerged from environmental sources, their evolutionary routes through time and space, how they interact with other bacteria and the human host, as well as initiate disease. We outline novel approaches to the use of whole genome sequencing for this important group of bacteria and how new sequencing technologies may be applied to study these organisms in future studies.}, }
@article {pmid36792876, year = {2023}, author = {Amaro, C and Carmona-Salido, H}, title = {Vibrio vulnificus, an Underestimated Zoonotic Pathogen.}, journal = {Advances in experimental medicine and biology}, volume = {1404}, number = {}, pages = {175-194}, pmid = {36792876}, issn = {0065-2598}, mesh = {Humans ; Animals ; *Vibrio vulnificus/genetics ; *Vibrio Infections/veterinary/epidemiology ; Aquaculture ; Gene Transfer, Horizontal ; Virulence/genetics ; }, abstract = {V. vulnificus, continues being an underestimated yet lethal zoonotic pathogen. In this chapter, we provide a comprehensive review of numerous aspects of the biology, epidemiology, and virulence mechanisms of this poorly understood pathogen. We will emphasize the widespread role of horizontal gene transfer in V. vulnificus specifically virulence plasmids and draw parallels from aquaculture farms to human health. By placing current findings in the context of climate change, we will also contend that fish farms act as evolutionary drivers that accelerate species evolution and the emergence of new virulent groups. Overall, we suggest that on-farm control measures should be adopted both to protect animals from Vibriosis, and also as a public health measure to prevent the emergence of new zoonotic groups.}, }
@article {pmid36792581, year = {2023}, author = {Filée, J and Becker, HF and Mellottee, L and Eddine, RZ and Li, Z and Yin, W and Lambry, JC and Liebl, U and Myllykallio, H}, title = {Bacterial origins of thymidylate metabolism in Asgard archaea and Eukarya.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {838}, pmid = {36792581}, issn = {2041-1723}, mesh = {*Archaea/metabolism ; *Eukaryota/genetics/metabolism ; Phylogeny ; Thymidylate Synthase/genetics/metabolism ; Bacteria/genetics/metabolism ; Amino Acids/metabolism ; Folic Acid/metabolism ; DNA/metabolism ; }, abstract = {Asgard archaea include the closest known archaeal relatives of eukaryotes. Here, we investigate the evolution and function of Asgard thymidylate synthases and other folate-dependent enzymes required for the biosynthesis of DNA, RNA, amino acids and vitamins, as well as syntrophic amino acid utilization. Phylogenies of Asgard folate-dependent enzymes are consistent with their horizontal transmission from various bacterial groups. We experimentally validate the functionality of thymidylate synthase ThyX of the cultured 'Candidatus Prometheoarchaeum syntrophicum'. The enzyme efficiently uses bacterial-like folates and is inhibited by mycobacterial ThyX inhibitors, even though the majority of experimentally tested archaea are known to use carbon carriers distinct from bacterial folates. Our phylogenetic analyses suggest that the eukaryotic thymidylate synthase, required for de novo DNA synthesis, is not closely related to archaeal enzymes and might have been transferred from bacteria to protoeukaryotes during eukaryogenesis. Altogether, our study suggests that the capacity of eukaryotic cells to duplicate their genetic material is a sum of archaeal (replisome) and bacterial (thymidylate synthase) characteristics. We also propose that recent prevalent lateral gene transfer from bacteria has markedly shaped the metabolism of Asgard archaea.}, }
@article {pmid36792019, year = {2023}, author = {Lekired, A and Cherif-Silini, H and Silini, A and Ben Yahia, H and Ouzari, HI}, title = {Comparative genomics reveals the acquisition of mobile genetic elements by the plant growth-promoting Pantoea eucrina OB49 in polluted environments.}, journal = {Genomics}, volume = {115}, number = {2}, pages = {110579}, doi = {10.1016/j.ygeno.2023.110579}, pmid = {36792019}, issn = {1089-8646}, mesh = {*Metals, Heavy ; *Pantoea/genetics ; Biodegradation, Environmental ; Interspersed Repetitive Sequences ; Genomics ; }, abstract = {Heavy metal-tolerant plant growth-promoting bacteria (PGPB) have gained popularity in bioremediation in recent years. A genome-assisted study of a heavy metal-tolerant PGPB Pantoea eucrina OB49 isolated from the rhizosphere of wheat grown on a heavy metal-contaminated site is presented. Comparative pan-genome analysis indicated that OB49 acquired heavy metal resistance genes through horizontal gene transfer. On contigs S10 and S12, OB49 has two arsRBCH operons that give arsenic resistance. On the S12 contig, an arsRBCH operon was discovered in conjunction with the merRTPCADE operon, which provides mercury resistance. P. eucrina OB49 may be involved in an ecological alternative for heavy metal remediation and growth promotion of wheat grown in metal-polluted soils. Our results suggested the detection of mobile genetic elements that harbour the ars operon and the fluoride resistance genes adjacent to the mer operon.}, }
@article {pmid36791498, year = {2023}, author = {Sharma, A and Gupta, S and Paul, K}, title = {Evolution of codon and amino acid usage in bacterial protein toxins.}, journal = {Biochemical and biophysical research communications}, volume = {651}, number = {}, pages = {47-55}, doi = {10.1016/j.bbrc.2023.02.001}, pmid = {36791498}, issn = {1090-2104}, mesh = {*Bacterial Proteins/genetics/metabolism ; Amino Acids/metabolism ; *Bacterial Toxins/chemistry ; Bacteria/genetics/metabolism ; Codon/genetics ; }, abstract = {Toxin proteins are secreted by most pathogens as an integral part of pathogenic mechanism(s). The toxins act by either damaging the host cell membrane (for example, pore-forming toxins and RTX toxins) or by modulation of important cellular pathways (for example, inhibition of protein translation by ribosome-inactivating proteins). The mechanism of action of these toxins provides the pathogen with strategies for adaptation in the unfavorable host environment. Though, secreted by different pathogenic species, the protein toxins seem to share common features that allow the protein to bind to specific molecules and enter the host cell. Earlier studies have suggested role of several events like horizontal gene transfer and insertion-deletion mutations in evolution of protein toxins. The present study involving 125 bacterial protein toxins secreted by 49 pathogenic bacteria focuses on the role and constraints of the bacterial genome on evolution of codon and amino acid usage in respective bacterial protein toxins. We compare the nucleotide composition, codon and dinucleotide usage trends between different classes of bacterial protein toxins and between individual toxins and the parent bacterial genome expressing the toxin(s).}, }
@article {pmid36790109, year = {2023}, author = {van Rooijen, LE and Tromer, EC and van Hooff, JJE and Kops, GJPL and Snel, B}, title = {Increased Sampling and Intracomplex Homologies Favor Vertical Over Horizontal Inheritance of the Dam1 Complex.}, journal = {Genome biology and evolution}, volume = {15}, number = {3}, pages = {}, pmid = {36790109}, issn = {1759-6653}, mesh = {Humans ; *Kinetochores ; Microtubule-Associated Proteins/genetics ; Phylogeny ; Microtubules ; Cell Division ; Cell Cycle Proteins/genetics ; *Saccharomyces cerevisiae Proteins/genetics ; Chromosomal Proteins, Non-Histone/genetics ; }, abstract = {Kinetochores connect chromosomes to spindle microtubules to ensure their correct segregation during cell division. Kinetochores of human and yeasts are largely homologous, their ability to track depolymerizing microtubules, however, is carried out by the nonhomologous complexes Ska1-C and Dam1-C, respectively. We previously reported the unique anti-correlating phylogenetic profiles of Dam1-C and Ska-C found among a wide variety of eukaryotes. Based on these profiles and the limited presence of Dam1-C, we speculated that horizontal gene transfer could have played a role in the evolutionary history of Dam1-C. Here, we present an expanded analysis of Dam1-C evolution, using additional genome as well as transcriptome sequences and recently published 3D structures. This analysis revealed a wider and more complete presence of Dam1-C in Cryptista, Rhizaria, Ichthyosporea, CRuMs, and Colponemidia. The fungal Dam1-C cryo-EM structure supports earlier hypothesized intracomplex homologies, which enables the reconstruction of rooted and unrooted phylogenies. The rooted tree of concatenated Dam1-C subunits is statistically consistent with the species tree of eukaryotes, suggesting that Dam1-C is ancient, and that the present-day phylogenetic distribution is best explained by multiple, independent losses and no horizontal gene transfer was involved. Furthermore, we investigated the ancient origin of Dam1-C via profile-versus-profile searches. Homology among 8 out of the 10 Dam1-C subunits suggests that the complex largely evolved from a single multimerizing subunit that diversified into a hetero-octameric core via stepwise subunit duplication and subfunctionalization of the subunits before the origin of the last eukaryotic common ancestor.}, }
@article {pmid36788632, year = {2023}, author = {Sezmis, AL and Woods, LC and Peleg, AY and McDonald, MJ}, title = {Horizontal Gene Transfer, Fitness Costs and Mobility Shape the Spread of Antibiotic Resistance Genes into Experimental Populations of Acinetobacter Baylyi.}, journal = {Molecular biology and evolution}, volume = {40}, number = {3}, pages = {}, pmid = {36788632}, issn = {1537-1719}, support = {FT170100441//Australia Research Council Future Fellowship/ ; APP1186140//National Health Medical Research Council/ ; }, mesh = {Acinetobacter ; Plasmids ; Gene Transfer, Horizontal ; Drug Resistance, Microbial ; *Anti-Bacterial Agents ; *Acinetobacter baumannii/genetics ; }, abstract = {Horizontal gene transfer (HGT) is important for microbial evolution, but how evolutionary forces shape the frequencies of horizontally transferred genetic variants in the absence of strong selection remains an open question. In this study, we evolve laboratory populations of Acinetobacter baylyi (ADP1) with HGT from two clinically relevant strains of multidrug-resistant Acinetobacter baumannii (AB5075 and A9844). We find that DNA can cross the species barrier, even without strong selection, and despite substantial DNA sequence divergence between the two species. Our results confirm previous findings that HGT can drive the spread of antibiotic resistance genes (ARGs) without selection for that antibiotic, but not for all of the resistance genes present in the donor genome. We quantify the costs and benefits of horizontally transferred variants and use whole population sequencing to track the spread of ARGs from HGT donors into antibiotic-sensitive recipients. We find that even though most ARGs are taken up by populations of A. baylyi, the long-term fate of an individual gene depends both on its fitness cost and on the type of genetic element that carries the gene. Interestingly, we also found that an integron, but not its host plasmid, is able to spread in A. baylyi populations despite its strong deleterious effect. Altogether, our results show how HGT provides an evolutionary advantage to evolving populations by facilitating the spread of non-selected genetic variation including costly ARGs.}, }
@article {pmid36787297, year = {2023}, author = {Thompson, CMA and Hall, JPJ and Chandra, G and Martins, C and Saalbach, G and Panturat, S and Bird, SM and Ford, S and Little, RH and Piazza, A and Harrison, E and Jackson, RW and Brockhurst, MA and Malone, JG}, title = {Plasmids manipulate bacterial behaviour through translational regulatory crosstalk.}, journal = {PLoS biology}, volume = {21}, number = {2}, pages = {e3001988}, pmid = {36787297}, issn = {1545-7885}, support = {BB/R018154/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/J/000PR9797/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T004363/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R014884/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R014884/2/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T010568/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Proteomics ; Plasmids/genetics ; *Bacteria/genetics ; Conjugation, Genetic/genetics ; Gene Transfer, Horizontal ; Bacterial Proteins/genetics/metabolism ; }, abstract = {Beyond their role in horizontal gene transfer, conjugative plasmids commonly encode homologues of bacterial regulators. Known plasmid regulator homologues have highly targeted effects upon the transcription of specific bacterial traits. Here, we characterise a plasmid translational regulator, RsmQ, capable of taking global regulatory control in Pseudomonas fluorescens and causing a behavioural switch from motile to sessile lifestyle. RsmQ acts as a global regulator, controlling the host proteome through direct interaction with host mRNAs and interference with the host's translational regulatory network. This mRNA interference leads to large-scale proteomic changes in metabolic genes, key regulators, and genes involved in chemotaxis, thus controlling bacterial metabolism and motility. Moreover, comparative analyses found RsmQ to be encoded on a large number of divergent plasmids isolated from multiple bacterial host taxa, suggesting the widespread importance of RsmQ for manipulating bacterial behaviour across clinical, environmental, and agricultural niches. RsmQ is a widespread plasmid global translational regulator primarily evolved for host chromosomal control to manipulate bacterial behaviour and lifestyle.}, }
@article {pmid36786613, year = {2023}, author = {Yang, D and Yang, Y and Qiao, P and Jiang, F and Zhang, X and Zhao, Z and Cai, T and Li, G and Cai, W}, title = {Genomic Island-Encoded Histidine Kinase and Response Regulator Coordinate Mannose Utilization with Virulence in Enterohemorrhagic Escherichia coli.}, journal = {mBio}, volume = {14}, number = {2}, pages = {e0315222}, pmid = {36786613}, issn = {2150-7511}, mesh = {Animals ; Mice ; Humans ; *Enterohemorrhagic Escherichia coli/metabolism ; Virulence/genetics ; Histidine Kinase/genetics/metabolism ; Genomic Islands ; Mannose ; HeLa Cells ; *Escherichia coli Proteins/genetics/metabolism ; Type III Secretion Systems/metabolism ; *Escherichia coli Infections/microbiology ; Gene Expression Regulation, Bacterial ; }, abstract = {Enterohemorrhagic Escherichia coli (EHEC) is a highly adaptive pathogen and has acquired diverse genetic elements, such as genomic islands and prophages, via horizontal gene transfer to promote fitness in vivo. Two-component signaling systems (TCSs) allow bacteria to sense, respond to, and adapt to various environments. This study identified a putative two-component signaling system composed of the histidine kinase EDL5436 (renamed LmvK) and the response regulator EDL5428 (renamed LmvR) in EHEC. lmvK and lmvR along with EDL5429 to EDL5434 (EDL5429-5434) between them constitute the OI167 genomic island and are highly associated with the EHEC pathotype. EDL5429-5434 encode transporters and metabolic enzymes that contribute to growth on mannose and are directly upregulated by LmvK/LmvR in the presence of mannose, as revealed by quantitative PCR (qPCR) and DNase I footprint assays. Moreover, LmvR directly activates the expression of the type III secretion system in response to mannose and promotes the formation of attaching and effacing lesions on HeLa cells. Using human colonoid and mouse infection models, we show that lmvK and lmvR contributed greatly to adherence and microcolony (MC) formation ex vivo and colonization in vivo. Finally, RNA sequencing and chromatin immunoprecipitation coupled with sequencing analyses identified additional direct targets of LmvR, most of which are involved in metabolism. Given that mannose is a mucus-derived sugar that induces virulence and is preferentially used by EHEC during infection, our data revealed a previously unknown mechanism by which EHEC recognizes the host metabolic landscape and regulates virulence expression accordingly. Our findings provide insights into how pathogenic bacteria evolve by acquiring genetic elements horizontally to adapt to host environments. IMPORTANCE The gastrointestinal tract represents a complex and challenging environment for enterohemorrhagic Escherichia coli (EHEC). However, EHEC is a highly adaptable pathogen, requiring only 10 to 100 CFUs to cause infection. This ability was achieved partially by acquiring mobile genetic elements, such as genomic islands, that promote overall fitness. Mannose is an intestinal mucus-derived sugar that stimulates virulence and is preferentially used by EHEC during infection. Here, we characterize the OI167 genomic island of EHEC, which encodes a novel two-component signaling system (TCS) and transporters and metabolic enzymes (EDL5429-5434) involved in mannose utilization. The TCS directly upregulates EDL5429-5434 and genes encoding the type III secretion system in the presence of mannose. Moreover, the TCS contributes greatly to EHEC virulence ex vivo and in vivo. Our data demonstrate an elegant example in which EHEC strains evolve by acquiring genetic elements horizontally to recognize the host metabolic landscape and regulate virulence expression accordingly, leading to successful infections.}, }
@article {pmid36781732, year = {2023}, author = {Suzuki, M and Hashimoto, Y and Hirabayashi, A and Yahara, K and Yoshida, M and Fukano, H and Hoshino, Y and Shibayama, K and Tomita, H}, title = {Genomic Epidemiological Analysis of Antimicrobial-Resistant Bacteria with Nanopore Sequencing.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2632}, number = {}, pages = {227-246}, pmid = {36781732}, issn = {1940-6029}, mesh = {*Nanopore Sequencing ; Bacteria/genetics ; Plasmids/genetics ; Genomics ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {Antimicrobial-resistant (AMR) bacterial infections caused by clinically important bacteria, including ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) and mycobacteria (Mycobacterium tuberculosis and nontuberculous mycobacteria), have become a global public health threat. Their epidemic and pandemic clones often accumulate useful accessory genes in their genomes, such as AMR genes (ARGs) and virulence factor genes (VFGs). This process is facilitated by horizontal gene transfer among microbial communities via mobile genetic elements (MGEs), such as plasmids and phages. Nanopore long-read sequencing allows easy and inexpensive analysis of complex bacterial genome structures, although some aspects of sequencing data calculation and genome analysis methods are not systematically understood. Here we describe the latest and most recommended experimental and bioinformatics methods available for the construction of complete bacterial genomes from nanopore sequencing data and the detection and classification of genotypes of bacterial chromosomes, ARGs, VFGs, plasmids, and other MGEs based on their genomic sequences for genomic epidemiological analysis of AMR bacteria.}, }
@article {pmid36780569, year = {2023}, author = {McKeithen-Mead, SA and Grossman, AD}, title = {Timing of integration into the chromosome is critical for the fitness of an integrative and conjugative element and its bacterial host.}, journal = {PLoS genetics}, volume = {19}, number = {2}, pages = {e1010524}, pmid = {36780569}, issn = {1553-7404}, support = {R01 GM050895/GM/NIGMS NIH HHS/United States ; R35 GM122538/GM/NIGMS NIH HHS/United States ; T32 GM007287/GM/NIGMS NIH HHS/United States ; }, mesh = {DNA, Bacterial/genetics ; *Conjugation, Genetic ; *Gene Transfer, Horizontal ; Chromosomes/metabolism ; Bacteria/genetics ; DNA Transposable Elements ; }, abstract = {Integrative and conjugative elements (ICEs) are major contributors to genome plasticity in bacteria. ICEs reside integrated in the chromosome of a host bacterium and are passively propagated during chromosome replication and cell division. When activated, ICEs excise from the chromosome and may be transferred through the ICE-encoded conjugation machinery into a recipient cell. Integration into the chromosome of the new host generates a stable transconjugant. Although integration into the chromosome of a new host is critical for the stable acquisition of ICEs, few studies have directly investigated the molecular events that occur in recipient cells during generation of a stable transconjugant. We found that integration of ICEBs1, an ICE of Bacillus subtilis, occurred several generations after initial transfer to a new host. Premature integration in new hosts led to cell death and hence decreased fitness of the ICE and transconjugants. Host lethality due to premature integration was caused by rolling circle replication that initiated in the integrated ICEBs1 and extended into the host chromosome, resulting in catastrophic genome instability. Our results demonstrate that the timing of integration of an ICE is linked to cessation of autonomous replication of the ICE, and that perturbing this linkage leads to a decrease in ICE and host fitness due to a loss of viability of transconjugants. Linking integration to cessation of autonomous replication appears to be a conserved regulatory scheme for mobile genetic elements that both replicate and integrate into the chromosome of their host.}, }
@article {pmid36779718, year = {2023}, author = {Kuntová, L and Mašlaňová, I and Obořilová, R and Šimečková, H and Finstrlová, A and Bárdy, P and Šiborová, M and Troianovska, L and Botka, T and Gintar, P and Šedo, O and Farka, Z and Doškař, J and Pantůček, R}, title = {Staphylococcus aureus Prophage-Encoded Protein Causes Abortive Infection and Provides Population Immunity against Kayviruses.}, journal = {mBio}, volume = {14}, number = {2}, pages = {e0249022}, pmid = {36779718}, issn = {2150-7511}, support = {224067/Z/21/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Prophages/genetics ; Staphylococcus aureus/genetics ; Lysogeny ; *Staphylococcal Infections/microbiology ; Staphylococcus ; Staphylococcus Phages/genetics ; Membrane Proteins/genetics ; }, abstract = {Both temperate and obligately lytic phages have crucial roles in the biology of staphylococci. While superinfection exclusion among closely related temperate phages is a well-characterized phenomenon, the interactions between temperate and lytic phages in staphylococci are not understood. Here, we present a resistance mechanism toward lytic phages of the genus Kayvirus, mediated by the membrane-anchored protein designated PdpSau encoded by Staphylococcus aureus prophages, mostly of the Sa2 integrase type. The prophage accessory gene pdpSau is strongly linked to the lytic genes for holin and ami2-type amidase and typically replaces genes for the toxin Panton-Valentine leukocidin (PVL). The predicted PdpSau protein structure shows the presence of a membrane-binding α-helix in its N-terminal part and a cytoplasmic positively charged C terminus. We demonstrated that the mechanism of action of PdpSau does not prevent the infecting kayvirus from adsorbing onto the host cell and delivering its genome into the cell, but phage DNA replication is halted. Changes in the cell membrane polarity and permeability were observed from 10 min after the infection, which led to prophage-activated cell death. Furthermore, we describe a mechanism of overcoming this resistance in a host-range Kayvirus mutant, which was selected on an S. aureus strain harboring prophage 53 encoding PdpSau, and in which a chimeric gene product emerged via adaptive laboratory evolution. This first case of staphylococcal interfamily phage-phage competition is analogous to some other abortive infection defense systems and to systems based on membrane-destructive proteins. IMPORTANCE Prophages play an important role in virulence, pathogenesis, and host preference, as well as in horizontal gene transfer in staphylococci. In contrast, broad-host-range lytic staphylococcal kayviruses lyse most S. aureus strains, and scientists worldwide have come to believe that the use of such phages will be successful for treating and preventing bacterial diseases. The effectiveness of phage therapy is complicated by bacterial resistance, whose mechanisms related to therapeutic staphylococcal phages are not understood in detail. In this work, we describe a resistance mechanism targeting kayviruses that is encoded by a prophage. We conclude that the defense mechanism belongs to a broader group of abortive infections, which is characterized by suicidal behavior of infected cells that are unable to produce phage progeny, thus ensuring the survival of the host population. Since the majority of staphylococcal strains are lysogenic, our findings are relevant for the advancement of phage therapy.}, }
@article {pmid36778249, year = {2023}, author = {Zhou, W and Karan, KR and Gu, W and Klein, HU and Sturm, G and De Jager, PL and Bennett, DA and Hirano, M and Picard, M and Mills, RE}, title = {Somatic nuclear mitochondrial DNA insertions are prevalent in the human brain and accumulate over time in fibroblasts.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {36778249}, issn = {2692-8205}, support = {P30 AG072975/AG/NIA NIH HHS/United States ; U01 AG046152/AG/NIA NIH HHS/United States ; R01 AG066828/AG/NIA NIH HHS/United States ; U01 AG061356/AG/NIA NIH HHS/United States ; R01 AG017917/AG/NIA NIH HHS/United States ; P30 AG010161/AG/NIA NIH HHS/United States ; R21 HG011493/HG/NHGRI NIH HHS/United States ; P30 AG072931/AG/NIA NIH HHS/United States ; R01 AG015819/AG/NIA NIH HHS/United States ; }, abstract = {The transfer of mitochondrial DNA into the nuclear genomes of eukaryotes (Numts) has been linked to lifespan in non-human species [1-3] and recently demonstrated to occur in rare instances from one human generation to the next [4]. Here we investigated numtogenesis dynamics in humans in two ways. First, we quantified Numts in 1,187 post-mortem brain and blood samples from different individuals. Compared to circulating immune cells (n=389), post-mitotic brain tissue (n=798) contained more Numts, consistent with their potential somatic accumulation. Within brain samples we observed a 5.5-fold enrichment of somatic Numt insertions in the dorsolateral prefrontal cortex compared to cerebellum samples, suggesting that brain Numts arose spontaneously during development or across the lifespan. Moreover, more brain Numts was linked to earlier mortality. The brains of individuals with no cognitive impairment who died at younger ages carried approximately 2 more Numts per decade of life lost than those who lived longer. Second, we tested the dynamic transfer of Numts using a repeated-measures WGS design in a human fibroblast model that recapitulates several molecular hallmarks of aging [5]. These longitudinal experiments revealed a gradual accumulation of one Numt every ~13 days. Numtogenesis was independent of large-scale genomic instability and unlikely driven cell clonality. Targeted pharmacological perturbations including chronic glucocorticoid signaling or impairing mitochondrial oxidative phosphorylation (OxPhos) only modestly increased the rate of numtogenesis, whereas patient-derived SURF1-mutant cells exhibiting mtDNA instability accumulated Numts 4.7-fold faster than healthy donors. Combined, our data document spontaneous numtogenesis in human cells and demonstrate an association between brain cortical somatic Numts and human lifespan. These findings open the possibility that mito-nuclear horizontal gene transfer among human post-mitotic tissues produce functionally-relevant human Numts over timescales shorter than previously assumed.}, }
@article {pmid36778052, year = {2022}, author = {Seshadri, R and Roux, S and Huber, KJ and Wu, D and Yu, S and Udwary, D and Call, L and Nayfach, S and Hahnke, RL and Pukall, R and White, JR and Varghese, NJ and Webb, C and Palaniappan, K and Reimer, LC and Sardà, J and Bertsch, J and Mukherjee, S and Reddy, TBK and Hajek, PP and Huntemann, M and Chen, IA and Spunde, A and Clum, A and Shapiro, N and Wu, ZY and Zhao, Z and Zhou, Y and Evtushenko, L and Thijs, S and Stevens, V and Eloe-Fadrosh, EA and Mouncey, NJ and Yoshikuni, Y and Whitman, WB and Klenk, HP and Woyke, T and Göker, M and Kyrpides, NC and Ivanova, NN}, title = {Expanding the genomic encyclopedia of Actinobacteria with 824 isolate reference genomes.}, journal = {Cell genomics}, volume = {2}, number = {12}, pages = {100213}, pmid = {36778052}, issn = {2666-979X}, abstract = {The phylum Actinobacteria includes important human pathogens like Mycobacterium tuberculosis and Corynebacterium diphtheriae and renowned producers of secondary metabolites of commercial interest, yet only a small part of its diversity is represented by sequenced genomes. Here, we present 824 actinobacterial isolate genomes in the context of a phylum-wide analysis of 6,700 genomes including public isolates and metagenome-assembled genomes (MAGs). We estimate that only 30%-50% of projected actinobacterial phylogenetic diversity possesses genomic representation via isolates and MAGs. A comparison of gene functions reveals novel determinants of host-microbe interaction as well as environment-specific adaptations such as potential antimicrobial peptides. We identify plasmids and prophages across isolates and uncover extensive prophage diversity structured mainly by host taxonomy. Analysis of >80,000 biosynthetic gene clusters reveals that horizontal gene transfer and gene loss shape secondary metabolite repertoire across taxa. Our observations illustrate the essential role of and need for high-quality isolate genome sequences.}, }
@article {pmid36772873, year = {2023}, author = {Molina-Santiago, C and Bernal, P}, title = {Nanotube-mediated plasmid transfer as a natural alternative for the improvement of industrially relevant bacteria.}, journal = {Microbial biotechnology}, volume = {16}, number = {4}, pages = {706-708}, pmid = {36772873}, issn = {1751-7915}, mesh = {Plasmids ; DNA, Bacterial ; *Bacteria/genetics ; *Gene Transfer, Horizontal ; Conjugation, Genetic ; }, }
@article {pmid36772829, year = {2023}, author = {Shen, M and Goldlust, K and Daniel, S and Lesterlin, C and Yamaichi, Y}, title = {Recipient UvrD helicase is involved in single- to double-stranded DNA conversion during conjugative plasmid transfer.}, journal = {Nucleic acids research}, volume = {51}, number = {6}, pages = {2790-2799}, pmid = {36772829}, issn = {1362-4962}, mesh = {Conjugation, Genetic/genetics ; DNA ; *DNA Helicases/genetics/metabolism ; DNA, Bacterial/genetics/metabolism ; *DNA, Single-Stranded/genetics ; Escherichia coli/genetics/metabolism ; *Escherichia coli Proteins/genetics ; Gene Transfer, Horizontal/genetics ; Plasmids/genetics ; }, abstract = {Dissemination of antibiotic resistance, a current societal challenge, is often driven by horizontal gene transfer through bacterial conjugation. During conjugative plasmid transfer, single-stranded (ss) DNA is transferred from the donor to the recipient cell. Subsequently, a complete double-stranded (ds) plasmid molecule is generated and plasmid-encoded genes are expressed, allowing successful establishment of the transconjugant cell. Such dynamics of transmission can be modulated by host- or plasmid-encoded factors, either in the donor or in the recipient cell. We applied transposon insertion sequencing to identify host-encoded factors that affect conjugative transfer frequency in Escherichia coli. Disruption of the recipient uvrD gene decreased the acquisition frequency of conjugative plasmids belonging to different incompatibility groups. Results from various UvrD mutants suggested that dsDNA binding activity and interaction with RNA polymerase are dispensable, but ATPase activity is required for successful plasmid establishment of transconjugant cells. Live-cell microscopic imaging showed that the newly transferred ssDNA within a uvrD- recipient often failed to be converted to dsDNA. Our work suggested that in addition to its role in maintaining genome integrity, UvrD is also key for the establishment of horizontally acquired plasmid DNA that drives genome diversity and evolution.}, }
@article {pmid36768888, year = {2023}, author = {Zhang, C and Jiao, C and Sun, X and Li, X}, title = {A MYB Transcription Factor Atlas Provides Insights into the Evolution of Environmental Adaptations in Plants.}, journal = {International journal of molecular sciences}, volume = {24}, number = {3}, pages = {}, pmid = {36768888}, issn = {1422-0067}, support = {32102318//National Natural Science Foundation of China/ ; 2022LFR048//Development Foundation of Zhejiang A &amp; F University/ ; }, mesh = {*Transcription Factors/genetics/metabolism ; Phylogeny ; DNA Copy Number Variations ; Plants/genetics/metabolism ; Genome, Plant ; *Magnoliopsida/genetics ; Plant Proteins/genetics/metabolism ; Gene Expression Regulation, Plant ; Evolution, Molecular ; }, abstract = {The MYB transcription factor superfamily includes key regulators of plant development and responses to environmental changes. The diversity of lifestyles and morphological characteristics exhibited by plants are potentially associated with the genomic dynamics of the MYB superfamily. With the release of the plant genomes, a comprehensive phylogenomic analysis of the MYB superfamily across Viridiplantae is allowed. The present study performed phylogenetic, phylogenomic, syntenic, horizontal gene transfer, and neo/sub-functionalization analysis of the MYB superfamily to explore the evolutionary contributions of MYB members to species diversification, trait formation, and environmental adaptation in 437 different plant species. We identified major changes in copy number variation and genomic context within subclades across lineages. Multiple MYB subclades showed highly conserved copy number patterns and synteny across flowering plants, whereas others were more dynamic and showed lineage-specific patterns. As examples of lineage-specific morphological divergence, we hypothesize that the gain of a MYB orthogroup associated with flower development and environmental responses and an orthogroup associated with auxin and wax biosynthesis in angiosperms were correlated with the emergence of flowering plants, unbiased neo-/sub-functionalization of gene duplicates contributed to environmental adaptation, and species-specific neo-/sub-functionalization contributed to phenotype divergence between species. Transposable element insertion in promoter regions may have facilitated the sub-/neo-functionalization of MYB genes and likely played a tissue-specific role contributing to sub-/neo-functionalization in plant root tissues. This study provides new insights into the evolutionary divergence of the MYB superfamily across major flowering and non-flowering lineages and emphasizes the need for lineage-/tissue-specific characterization to further understand trait variability and environmental adaptation.}, }
@article {pmid36764681, year = {2023}, author = {Van Etten, J and Benites, LF and Stephens, TG and Yoon, HS and Bhattacharya, D}, title = {Algae obscura: The potential of rare species as model systems.}, journal = {Journal of phycology}, volume = {59}, number = {2}, pages = {293-300}, doi = {10.1111/jpy.13321}, pmid = {36764681}, issn = {1529-8817}, mesh = {Phylogeny ; *Biological Evolution ; Plants ; Eukaryota/genetics ; *Rhodophyta/genetics ; Plastids/genetics ; Symbiosis/genetics ; }, abstract = {Model organism research has provided invaluable knowledge about foundational biological principles. However, most of these studies have focused on species that are in high abundance, easy to cultivate in the lab, and represent only a small fraction of extant biodiversity. Here, we present three examples of rare algae with unusual features that we refer to as "algae obscura." The Cyanidiophyceae (Rhodophyta), Glaucophyta, and Paulinella (rhizarian) lineages have all transitioned out of obscurity to become models for fundamental evolutionary research. Insights have been gained into the prevalence and importance of eukaryotic horizontal gene transfer, early Earth microbial community dynamics, primary plastid endosymbiosis, and the origin of Archaeplastida. By reviewing the research that has come from the exploration of these organisms, we demonstrate that underappreciated algae have the potential to help us formulate, refine, and substantiate core hypotheses and that such organisms should be considered when establishing future model systems.}, }
@article {pmid36764395, year = {2023}, author = {Van Dijck, C and Laumen, JGE and de Block, T and Abdellati, S and De Baetselier, I and Tsoumanis, A and Malhotra-Kumar, S and Manoharan-Basil, SS and Kenyon, C and Xavier, BB}, title = {The oropharynx of men using HIV pre-exposure prophylaxis is enriched with antibiotic resistance genes: A cross-sectional observational metagenomic study.}, journal = {The Journal of infection}, volume = {86}, number = {4}, pages = {329-337}, doi = {10.1016/j.jinf.2023.02.006}, pmid = {36764395}, issn = {1532-2742}, mesh = {Male ; Humans ; Homosexuality, Male ; Sexual Behavior ; *Pre-Exposure Prophylaxis ; *HIV Infections/prevention &amp; control/epidemiology ; Anti-Bacterial Agents/pharmacology ; Cross-Sectional Studies ; *Sexual and Gender Minorities ; Oropharynx ; Drug Resistance, Microbial ; Fluoroquinolones ; Macrolides ; }, abstract = {BACKGROUND: Phenotypic studies have found high levels of antimicrobial resistance to cephalosporins, macrolides and fluoroquinolones in commensal Neisseria species in the oropharynx of men who have sex with men (MSM) using HIV pre-exposure prophylaxis (PrEP). These species include Neisseria subflava and Neisseria mucosa. This may represent a risk to pathogens like Neisseria gonorrhoeae which tend to take up antibiotic resistance genes (ARGs) from other bacteria. We aimed to explore to what extent the oropharyngeal resistome of MSM using PrEP differed from the general population.<br><br>METHODS: We collected oropharyngeal swabs from 32 individuals of the general population and from 64 MSM using PrEP. Thirty-two MSM had consumed antibiotics in the previous six months, whereas none of the other participants had. Samples underwent shotgun metagenomic sequencing. Sequencing reads were mapped against MEGARes 2.0 to estimate ARG abundance. ARG abundance was compared between groups by zero-inflated negative binomial regression.<br><br>FINDINGS: ARG abundance was significantly lower in the general population than in MSM (ratio 0.41, 95% CI 0.26-0.65). More specifically, this was the case for fluoroquinolones (0.33, 95% CI 0.15-0.69), macrolides (0.37, 95% CI 0.25-0.56), tetracyclines (0.41, 95% CI 0.25-0.69), and multidrug efflux pumps (0.11, 95% CI 0.03-0.33), but not for beta-lactams (1.38, 95% CI 0.73-2.61). There were no significant differences in ARG abundance between MSM who had used antibiotics and those that had not.<br><br>INTERPRETATION: The resistome of MSM using PrEP is enriched with ARGs, independent of recent antibiotic use. Stewardship campaigns should aim to reduce antibiotic consumption in populations at high risk for STIs.}, }
@article {pmid36762480, year = {2023}, author = {Arbel-Goren, R and McKeithen-Mead, SA and Voglmaier, D and Afremov, I and Teza, G and Grossman, AD and Stavans, J}, title = {Target search by an imported conjugative DNA element for a unique integration site along a bacterial chromosome during horizontal gene transfer.}, journal = {Nucleic acids research}, volume = {51}, number = {7}, pages = {3116-3129}, pmid = {36762480}, issn = {1362-4962}, support = {R35 GM122538/GM/NIGMS NIH HHS/United States ; T32 GM007287/GM/NIGMS NIH HHS/United States ; R01 GM050895/GM/NIGMS NIH HHS/United States ; }, mesh = {*Gene Transfer, Horizontal ; *DNA ; DNA Replication ; Chromosomes, Bacterial/genetics ; Chemical Phenomena ; Conjugation, Genetic ; DNA, Bacterial/genetics ; }, abstract = {Integrative and conjugative elements (ICEs) are mobile genetic elements that can transfer by conjugation to recipient cells. Some ICEs integrate into a unique site in the genome of their hosts. We studied quantitatively the process by which an ICE searches for its unique integration site in the Bacillus subtilis chromosome. We followed the motion of both ICEBs1 and the chromosomal integration site in real time within individual cells. ICEBs1 exhibited a wide spectrum of dynamical behaviors, ranging from rapid sub-diffusive displacements crisscrossing the cell, to kinetically trapped states. The chromosomal integration site moved sub-diffusively and exhibited pronounced dynamical asymmetry between longitudinal and transversal motions, highlighting the role of chromosomal structure and the heterogeneity of the bacterial interior in the search. The successful search for and subsequent recombination into the integration site is a key step in the acquisition of integrating mobile genetic elements. Our findings provide new insights into intracellular transport processes involving large DNA molecules.}, }
@article {pmid36762093, year = {2022}, author = {Li, Z and Shen, J and Wang, F and Wang, M and Shen, J and Li, Y and Zhu, Q and Wu, J}, title = {Impacts of organic materials amendment on the soil antibiotic resistome in subtropical paddy fields.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1075234}, pmid = {36762093}, issn = {1664-302X}, abstract = {The organic material amendment has been proven to change the soil antibiotic resistance genes (ARGs) profile, which may threaten human health through the food chain, but the effects and mechanisms of different organic materials on ARGs in paddy soils are less explored. In this study, a field experiment was set up with the treatments of conventional chemical fertilization (NPK) and common organic material amendment [rice straw (RS), swine manure (SM), and biochar (BC)] to explore the effects and mechanisms. In total, 84 unique ARGs were found across the soil samples with different organic material amendments, and they conferred resistance to the major antibiotic classes. Compared with NPK, SM significantly increased the detected number and relative abundance of ARGs. A higher detected number of ARGs than NPK was observed in BC, whereas BC had a lower relative abundance of ARGs than NPK. Compared with NPK, a detected number decrease was observed in RS, although abundance showed no significant differences. Compared with other treatments, a higher detected number and relative abundance of mobile genetic elements (MGEs) were observed in BC, indicating a higher potential for horizontal gene transfer. There were significantly positive relationships between the relative abundances of total ARGs and MGEs and the bacterial abundance. The network analysis suggested the important role of MGEs and bacterial communities in shaping the ARGs profile. Mantel test and redundancy analysis (RDA) suggested that soil carbon, nitrogen, and C/N were the major chemical drivers of the ARGs profile. The risk of ARGs spreading to the food chain should be considered when applying SM and biochar, which shifted the ARGs and MGEs profiles, respectively. Pre-treatment measures need to be studied to reduce the dissemination of ARGs in paddy fields.}, }
@article {pmid36758922, year = {2023}, author = {Wang, M and Lian, Y and Wang, Y and Zhu, L}, title = {The role and mechanism of quorum sensing on environmental antimicrobial resistance.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {322}, number = {}, pages = {121238}, doi = {10.1016/j.envpol.2023.121238}, pmid = {36758922}, issn = {1873-6424}, mesh = {*Quorum Sensing ; *Anti-Bacterial Agents/toxicity ; Drug Resistance, Bacterial/genetics ; Bacteria/genetics ; Genes, Bacterial ; }, abstract = {As more environmental contaminants emerging, antibiotics and antibiotic resistance genes (ARGs) have caused a substantial increase of antimicrobial resistance (AMR) in environment. Quorum sensing (QS) is a bacterial cell-to-cell communication process that regulates many traits and gene expression, including ARGs and the related genes that contribute to AMR development. Herein, we summarize the role, physiology, and genetic mechanisms of bacterial QS in AMR development in the environment. First, the effect of QS on AMR is introduced. Next, the role of QS in bacterial physiological behaviors that promote AMR development, including membrane permeability, tactic movement, biofilm formation, persister formation, and small colony variants (SCVs), is systematically analyzed. Furthermore, the regulation of QS on the expression of ARGs, generation of reactive oxygen species (ROS), which affects ARGs formation, and horizontal gene transfer (HGT), which accelerates the transmission of ARGs, are discussed to reveal the molecular mechanism for AMR development. This review provides a reference for a better understanding of AMR evolution and novel insights into AMR prevention.}, }
@article {pmid36758429, year = {2023}, author = {Li, X and Lu, H and Yang, K and Zhu, L}, title = {Attenuation of tetracyclines and related resistance genes in soil when exposed to nanoscale zero-valent iron.}, journal = {Journal of hazardous materials}, volume = {448}, number = {}, pages = {130867}, doi = {10.1016/j.jhazmat.2023.130867}, pmid = {36758429}, issn = {1873-3336}, mesh = {Humans ; *Tetracyclines/pharmacology ; Soil ; Iron ; Anti-Bacterial Agents/pharmacology ; Biodegradation, Environmental ; *Environmental Restoration and Remediation ; }, abstract = {Antibiotics pollution in soil poses increasing threats to human health due to stimulated proliferation and transmission of antibiotic resistance genes (ARGs). Nanoscale zero-valent iron (NZVI) is a promising material for the remediation of antibiotics, but how NZVI affects the diversity, abundance, and horizontal gene transfer potentials of ARGs remains unclear. Herein, the biotic and abiotic effects of NZVI at different concentrations on tetracyclines (TCs) and the associated ARGs were investigated. Results showed NZVI could effectively accelerate the degradation of TCs, which increased from 51.38% (without NZVI) to 57.96%- 71.66% (1-10 g NZVI/kg) in 20 days. Biotic degradation contributed to 66.10%- 76.30% of the total TCs removal. NZVI induced TCs biodegradation was probably due to alleviated toxicity of TCs on cells and increased microbial biomass and enzyme activities. Additionally, TCs-related ARGs were attenuated with decreased horizontal gene transfer potentials of intI1 and ISCR1, but opposite effects were observed for non TC-related ARGs, especially during excess exposure to NZVI. This study illustrated the possibility of remediating of antibiotic contaminated soil by NZVI and meanwhile reducing the potential risks of ARGs.}, }
@article {pmid36756971, year = {2024}, author = {Chen, Y and Jia, B and Li, JY and Li, D and He, W}, title = {Characteristics and driving factors of antibiotic resistance genes in aquaculture products from freshwater ponds in China Yangtze River Delta.}, journal = {Environmental technology}, volume = {45}, number = {12}, pages = {2459-2470}, doi = {10.1080/09593330.2023.2176261}, pmid = {36756971}, issn = {1479-487X}, mesh = {Humans ; *Ponds/analysis ; *Genes, Bacterial ; Anti-Bacterial Agents/analysis ; RNA, Ribosomal, 16S ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; China ; Aquaculture ; }, abstract = {Antibiotic resistance genes (ARGs) are widespread in aquaculture and pose a huge threat to aquaculture organisms and human health. In this study, occurrences and relative abundances of ARGs were analysed in the guts of products cultured in freshwater ponds in the Yangtze River Delta region in China. A total of 29 ARGs were found in the gut samples, with detection frequencies ranging from 4.8% to 81%, and the relative abundances (ARGs/16S rRNA) ranging from 10[-7] to 1. In addition, the human dietary intake of ARGs via aquaculture products was assessed, where the daily intake of most ARGs via aquaculture products was higher than those via PM2.5 and drinking water, but lower than that via vegetables. The relative abundances of MGE (IS613, Tp614, tnpA and int1) were significantly correlated with those of multiple ARGs, indicating the horizontal gene transfer (HGT) of ARGs among gut microorganisms. Proteobacteria, Firmicutes and Actinobacteria were the dominated microbial communities found in the guts of aquaculture products. In addition, significant correlations were found between Cyanobacteria and int1, between Nitrospira and tetE, and between sul2 and aadA2, indicating potential same hosts of these genes. In addition, results from co-correlation indicated both HGT (dominated by MGEs) of ARGs and the enrichment of ARGs in bacteria. MGEs, mostly int1, were more effective than bacteria in increasing the ARG abundance. This study could provide a better understanding of the transmission of ARGs in the aquaculture environment and improve the quality of aquaculture products and the ecology.}, }
@article {pmid36753420, year = {2023}, author = {Beamud, B and García-González, N and Gómez-Ortega, M and González-Candelas, F and Domingo-Calap, P and Sanjuan, R}, title = {Genetic determinants of host tropism in Klebsiella phages.}, journal = {Cell reports}, volume = {42}, number = {2}, pages = {112048}, pmid = {36753420}, issn = {2211-1247}, mesh = {Humans ; *Klebsiella/genetics ; *Bacteriophages/genetics ; Viral Tropism ; Klebsiella pneumoniae/genetics ; Genome, Viral ; }, abstract = {Bacteriophages play key roles in bacterial ecology and evolution and are potential antimicrobials. However, the determinants of phage-host specificity remain elusive. Here, we isolate 46 phages to challenge 138 representative clinical isolates of Klebsiella pneumoniae, a widespread opportunistic pathogen. Spot tests show a narrow host range for most phages, with <2% of 6,319 phage-host combinations tested yielding detectable interactions. Bacterial capsule diversity is the main factor restricting phage host range. Consequently, phage-encoded depolymerases are key determinants of host tropism, and depolymerase sequence types are associated with the ability to infect specific capsular types across phage families. However, all phages with a broader host range found do not encode canonical depolymerases, suggesting alternative modes of entry. These findings expand our knowledge of the complex interactions between bacteria and their viruses and point out the feasibility of predicting the first steps of phage infection using bacterial and phage genome sequences.}, }
@article {pmid36752380, year = {2023}, author = {Yuan, L and Lu, H and Li, F and Nielsen, J and Kerkhoven, EJ}, title = {HGTphyloDetect: facilitating the identification and phylogenetic analysis of horizontal gene transfer.}, journal = {Briefings in bioinformatics}, volume = {24}, number = {2}, pages = {}, pmid = {36752380}, issn = {1477-4054}, mesh = {Phylogeny ; *Gene Transfer, Horizontal ; *Genomics ; Genome ; Evolution, Molecular ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT) is an important driver in genome evolution, gain-of-function, and metabolic adaptation to environmental niches. Genome-wide identification of putative HGT events has become increasingly practical, given the rapid growth of genomic data. However, existing HGT analysis toolboxes are not widely used, limited by their inability to perform phylogenetic reconstruction to explore potential donors, and the detection of HGT from both evolutionarily distant and closely related species.<br><br>RESULTS: In this study, we have developed HGTphyloDetect, which is a versatile computational toolbox that combines high-throughput analysis with phylogenetic inference, to facilitate comprehensive investigation of HGT events. Two case studies with Saccharomyces cerevisiae and Candida versatilis demonstrate the ability of HGTphyloDetect to identify horizontally acquired genes with high accuracy. In addition, HGTphyloDetect enables phylogenetic analysis to illustrate a likely path of gene transmission among the evolutionarily distant or closely related species.<br><br>CONCLUSIONS: The HGTphyloDetect computational toolbox is designed for ease of use and can accurately find HGT events with a very low false discovery rate in a high-throughput manner. The HGTphyloDetect toolbox and its related user tutorial are freely available at https://github.com/SysBioChalmers/HGTphyloDetect.}, }
@article {pmid36750723, year = {2023}, author = {Beltran, LC and Cvirkaite-Krupovic, V and Miller, J and Wang, F and Kreutzberger, MAB and Patkowski, JB and Costa, TRD and Schouten, S and Levental, I and Conticello, VP and Egelman, EH and Krupovic, M}, title = {Archaeal DNA-import apparatus is homologous to bacterial conjugation machinery.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {666}, pmid = {36750723}, issn = {2041-1723}, support = {/WT_/Wellcome Trust/United Kingdom ; K99 GM138756/GM/NIGMS NIH HHS/United States ; U24 GM116790/GM/NIGMS NIH HHS/United States ; R35 GM122510/GM/NIGMS NIH HHS/United States ; R00 GM138756/GM/NIGMS NIH HHS/United States ; S10 RR025067/RR/NCRR NIH HHS/United States ; P30 CA044579/CA/NCI NIH HHS/United States ; G20 RR031199/RR/NCRR NIH HHS/United States ; }, mesh = {*Agrobacterium tumefaciens/genetics ; Bacterial Proteins/genetics ; *Conjugation, Genetic ; Cryoelectron Microscopy ; *DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; Plasmids ; *Aeropyrum/genetics ; *Pyrobaculum/genetics ; }, abstract = {Conjugation is a major mechanism of horizontal gene transfer promoting the spread of antibiotic resistance among human pathogens. It involves establishing a junction between a donor and a recipient cell via an extracellular appendage known as the mating pilus. In bacteria, the conjugation machinery is encoded by plasmids or transposons and typically mediates the transfer of cognate mobile genetic elements. Much less is known about conjugation in archaea. Here, we determine atomic structures by cryo-electron microscopy of three conjugative pili, two from hyperthermophilic archaea (Aeropyrum pernix and Pyrobaculum calidifontis) and one encoded by the Ti plasmid of the bacterium Agrobacterium tumefaciens, and show that the archaeal pili are homologous to bacterial mating pili. However, the archaeal conjugation machinery, known as Ced, has been 'domesticated', that is, the genes for the conjugation machinery are encoded on the chromosome rather than on mobile genetic elements, and mediates the transfer of cellular DNA.}, }
@article {pmid36748704, year = {2023}, author = {Anbo, M and Jelsbak, L}, title = {A bittersweet fate: detection of serotype switching in Pseudomonas aeruginosa.}, journal = {Microbial genomics}, volume = {9}, number = {1}, pages = {}, pmid = {36748704}, issn = {2057-5858}, mesh = {Serogroup ; *Pseudomonas aeruginosa ; Drug Resistance, Microbial ; *Gene Transfer, Horizontal ; }, abstract = {High-risk clone types in Pseudomonas aeruginosa are problematic global multidrug-resistant clones. However, apart from their ability to resist antimicrobial treatment, not much is known about what sets these clones apart from the multitude of other clones. In high-risk clone ST111, it has previously been shown that replacement of the native serotype biosynthetic gene cluster (O4) by a different gene cluster (O12) by horizontal gene transfer and recombination may have contributed to the global success of this clone. However, the extent to which isolates undergo this type of serotype switching has not been adequately explored in P. aeruginosa. In the present study, a bioinformatics tool has been developed and utilized to provide a first estimate of serotype switching in groups of multidrug resistant (MDR) clinical isolates. The tool detects serotype switching by analysis of core-genome phylogeny and in silico serotype. Analysis of a national survey of MDR isolates found a prevalence of 3.9 % of serotype-switched isolates in high-risk clone types ST111, ST244 and ST253. A global survey of MDR isolates was additionally analysed, and it was found that 2.3 % of isolates had undergone a serotype switch. To further understand this process, we determined the exact boundaries of the horizontally transferred serotype O12 island. We found that the size of the serotype island correlates with the clone type of the receiving isolate and additionally we found intra-clone type variations in size and boundaries. This suggests multiple serotype switch events. Moreover, we found that the housekeeping gene gyrA is co-transferred with the O12 serotype island, which prompted us to analyse this allele for all serotype O12 isolates. We found that 95 % of ST111 O12 isolates had a resistant gyrA allele and 86 % of all O12 isolates had a resistant gyrA allele. The rates of resistant gyrA alleles in isolates with other prevalent serotypes are all lower. Together, these results show that the transfer and acquisition of serotype O12 in high-risk clone ST111 has happened multiple times and may be facilitated by multiple donors, which clearly suggests a strong selection pressure for this process. However, gyrA-mediated antibiotic resistance may not be the only evolutionary driver.}, }
@article {pmid36748580, year = {2022}, author = {Wietz, M and López-Pérez, M and Sher, D and Biller, SJ and Rodriguez-Valera, F}, title = {Microbe Profile: Alteromonas macleodii - a widespread, fast-responding, 'interactive' marine bacterium.}, journal = {Microbiology (Reading, England)}, volume = {168}, number = {11}, pages = {}, doi = {10.1099/mic.0.001236}, pmid = {36748580}, issn = {1465-2080}, mesh = {*Genome, Bacterial/genetics ; *Alteromonas/genetics/metabolism ; Phenotype ; Adaptation, Physiological ; Phylogeny ; Seawater/microbiology ; }, abstract = {Alteromonas macleodii is a marine heterotrophic bacterium with widespread distribution - from temperate to tropical oceans, and from surface to deep waters. Strains of A. macleodii exhibit considerable genomic and metabolic variability, and can grow rapidly on diverse organic compounds. A. macleodii is a model organism for the study of population genomics, physiological adaptations and microbial interactions, with individual genomes encoding diverse phenotypic traits influenced by recombination and horizontal gene transfer.}, }
@article {pmid36748576, year = {2022}, author = {Kupczok, A and Bailey, ZM and Refardt, D and Wendling, CC}, title = {Co-transfer of functionally interdependent genes contributes to genome mosaicism in lambdoid phages.}, journal = {Microbial genomics}, volume = {8}, number = {11}, pages = {}, pmid = {36748576}, issn = {2057-5858}, mesh = {*Bacteriophages/genetics ; Mosaicism ; Operon ; }, abstract = {Lambdoid (or Lambda-like) phages are a group of related temperate phages that can infect Escherichia coli and other gut bacteria. A key characteristic of these phages is their mosaic genome structure, which served as the basis for the 'modular genome hypothesis'. Accordingly, lambdoid phages evolve by transferring genomic regions, each of which constitutes a functional unit. Nevertheless, it is unknown which genes are preferentially transferred together and what drives such co-transfer events. Here we aim to characterize genome modularity by studying co-transfer of genes among 95 distantly related lambdoid (pro-)phages. Based on gene content, we observed that the genomes cluster into 12 groups, which are characterized by a highly similar gene content within the groups and highly divergent gene content across groups. Highly similar proteins can occur in genomes of different groups, indicating that they have been transferred. About 26 % of homologous protein clusters in the four known operons (i.e. the early left, early right, immunity and late operon) engage in gene transfer, which affects all operons to a similar extent. We identified pairs of genes that are frequently co-transferred and observed that these pairs tend to be near one another on the genome. We find that frequently co-transferred genes are involved in related functions and highlight interesting examples involving structural proteins, the cI repressor and Cro regulator, proteins interacting with DNA, and membrane-interacting proteins. We conclude that epistatic effects, where the functioning of one protein depends on the presence of another, play an important role in the evolution of the modular structure of these genomes.}, }
@article {pmid36748570, year = {2023}, author = {Sengupta, S and Azad, RK}, title = {Leveraging comparative genomics to uncover alien genes in bacterial genomes.}, journal = {Microbial genomics}, volume = {9}, number = {1}, pages = {}, pmid = {36748570}, issn = {2057-5858}, mesh = {*Genome, Bacterial ; *Genomics/methods ; Algorithms ; Biological Evolution ; }, abstract = {A significant challenge in bacterial genomics is to catalogue genes acquired through the evolutionary process of horizontal gene transfer (HGT). Both comparative genomics and sequence composition-based methods have often been invoked to quantify horizontally acquired genes in bacterial genomes. Comparative genomics methods rely on completely sequenced genomes and therefore the confidence in their predictions increases as the databases become more enriched in completely sequenced genomes. Recent developments including in microbial genome sequencing call for reassessment of alien genes based on information-rich resources currently available. We revisited the comparative genomics approach and developed a new algorithm for alien gene detection. Our algorithm compared favourably with the existing comparative genomics-based methods and is capable of detecting both recent and ancient transfers. It can be used as a standalone tool or in concert with other complementary algorithms for comprehensively cataloguing alien genes in bacterial genomes.}, }
@article {pmid36748564, year = {2023}, author = {Colombi, E and Hill, Y and Lines, R and Sullivan, JT and Kohlmeier, MG and Christophersen, CT and Ronson, CW and Terpolilli, JJ and Ramsay, JP}, title = {Population genomics of Australian indigenous Mesorhizobium reveals diverse nonsymbiotic genospecies capable of nitrogen-fixing symbioses following horizontal gene transfer.}, journal = {Microbial genomics}, volume = {9}, number = {1}, pages = {}, pmid = {36748564}, issn = {2057-5858}, mesh = {Gene Transfer, Horizontal ; *Mesorhizobium/genetics ; Symbiosis/genetics ; Metagenomics ; Nitrogen ; Australia ; *Lotus/microbiology ; Soil ; }, abstract = {Mesorhizobia are soil bacteria that establish nitrogen-fixing symbioses with various legumes. Novel symbiotic mesorhizobia frequently evolve following horizontal transfer of symbiosis-gene-carrying integrative and conjugative elements (ICESyms) to indigenous mesorhizobia in soils. Evolved symbionts exhibit a wide range in symbiotic effectiveness, with some fixing nitrogen poorly or not at all. Little is known about the genetic diversity and symbiotic potential of indigenous soil mesorhizobia prior to ICESym acquisition. Here we sequenced genomes of 144 Mesorhizobium spp. strains cultured directly from cultivated and uncultivated Australian soils. Of these, 126 lacked symbiosis genes. The only isolated symbiotic strains were either exotic strains used previously as legume inoculants, or indigenous mesorhizobia that had acquired exotic ICESyms. No native symbiotic strains were identified. Indigenous nonsymbiotic strains formed 22 genospecies with phylogenomic diversity overlapping the diversity of internationally isolated symbiotic Mesorhizobium spp. The genomes of indigenous mesorhizobia exhibited no evidence of prior involvement in nitrogen-fixing symbiosis, yet their core genomes were similar to symbiotic strains and they generally lacked genes for synthesis of biotin, nicotinate and thiamine. Genomes of nonsymbiotic mesorhizobia harboured similar mobile elements to those of symbiotic mesorhizobia, including ICESym-like elements carrying aforementioned vitamin-synthesis genes but lacking symbiosis genes. Diverse indigenous isolates receiving ICESyms through horizontal gene transfer formed effective symbioses with Lotus and Biserrula legumes, indicating most nonsymbiotic mesorhizobia have an innate capacity for nitrogen-fixing symbiosis following ICESym acquisition. Non-fixing ICESym-harbouring strains were isolated sporadically within species alongside effective symbionts, indicating chromosomal lineage does not predict symbiotic potential. Our observations suggest previously observed genomic diversity amongst symbiotic Mesorhizobium spp. represents a fraction of the extant diversity of nonsymbiotic strains. The overlapping phylogeny of symbiotic and nonsymbiotic clades suggests major clades of Mesorhizobium diverged prior to introduction of symbiosis genes and therefore chromosomal genes involved in symbiosis have evolved largely independent of nitrogen-fixing symbiosis.}, }
@article {pmid36748528, year = {2022}, author = {Tamminga, SM and Völpel, SL and Schipper, K and Stehle, T and Pannekoek, Y and van Sorge, NM}, title = {Genetic diversity of Staphylococcus aureus wall teichoic acid glycosyltransferases affects immune recognition.}, journal = {Microbial genomics}, volume = {8}, number = {12}, pages = {}, pmid = {36748528}, issn = {2057-5858}, mesh = {Humans ; *Staphylococcus aureus/genetics/metabolism ; Glycosyltransferases/genetics/chemistry/metabolism ; Teichoic Acids/chemistry/metabolism ; Bacterial Proteins/metabolism ; *Staphylococcal Infections ; Codon, Nonsense/metabolism ; }, abstract = {Staphylococcus aureus is a leading cause of skin and soft tissue infections and systemic infections. Wall teichoic acids (WTAs) are cell wall-anchored glycopolymers that are important for S. aureus nasal colonization, phage-mediated horizontal gene transfer, and antibiotic resistance. WTAs consist of a polymerized ribitol phosphate (RboP) chain that can be glycosylated with N-acetylglucosamine (GlcNAc) by three glycosyltransferases: TarS, TarM, and TarP. TarS and TarP modify WTA with β-linked GlcNAc at the C-4 (β1,4-GlcNAc) and the C-3 position (β1,3-GlcNAc) of the RboP subunit, respectively, whereas TarM modifies WTA with α-linked GlcNAc at the C-4 position (α1,4-GlcNAc). Importantly, these WTA glycosylation patterns impact immune recognition and clearance of S. aureus. Previous studies suggest that tarS is near-universally present within the S. aureus population, whereas a smaller proportion co-contain either tarM or tarP. To gain more insight into the presence and genetic variation of tarS, tarM and tarP in the S. aureus population, we analysed a collection of 25 652 S. aureus genomes within the PubMLST database. Over 99 % of isolates contained tarS. Co-presence of tarS/tarM or tarS/tarP occurred in 37 and 7 % of isolates, respectively, and was associated with specific S. aureus clonal complexes. We also identified 26 isolates (0.1 %) that contained all three glycosyltransferase genes. At sequence level, we identified tar alleles with amino acid substitutions in critical enzymatic residues or with premature stop codons. Several tar variants were expressed in a S. aureus tar-negative strain. Analysis using specific monoclonal antibodies and human langerin showed that WTA glycosylation was severely attenuated or absent. Overall, our data provide a broad overview of the genetic diversity of the three WTA glycosyltransferases in the S. aureus population and the functional consequences for immune recognition.}, }
@article {pmid36748517, year = {2022}, author = {Greig, DR and Bird, MT and Chattaway, MA and Langridge, GC and Waters, EV and Ribeca, P and Jenkins, C and Nair, S}, title = {Characterization of a P1-bacteriophage-like plasmid (phage-plasmid) harbouring bla CTX-M-15 in Salmonella enterica serovar Typhi.}, journal = {Microbial genomics}, volume = {8}, number = {12}, pages = {}, pmid = {36748517}, issn = {2057-5858}, support = {BB/R012504/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10348/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Salmonella typhi/genetics ; *Bacteriophages/genetics ; Bacteriophage P1/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Plasmids/genetics ; beta-Lactamases/genetics ; }, abstract = {Antimicrobial-resistance (AMR) genes can be transferred between microbial cells via horizontal gene transfer (HGT), which involves mobile and integrative elements such as plasmids, bacteriophages, transposons, integrons and pathogenicity islands. Bacteriophages are found in abundance in the microbial world, but their role in virulence and AMR has not fully been elucidated in the Enterobacterales. With short-read sequencing paving the way to systematic high-throughput AMR gene detection, long-read sequencing technologies now enable us to establish how such genes are structurally connected into meaningful genomic units, raising questions about how they might cooperate to achieve their biological function. Here, we describe a novel ~98 kbp circular P1-bacteriophage-like plasmid termed ph681355 isolated from a clinical Salmonella enterica serovar Typhi isolate. It carries bla CTX-M-15, an IncY plasmid replicon (repY gene) and the ISEcP1 mobile element and is, to our knowledge, the first reported P1-bacteriophage-like plasmid (phage-plasmid) in S. enterica Typhi. We compared ph681355 to two previously described phage-plasmids, pSJ46 from S. enterica serovar Indiana and pMCR-1-P3 from Escherichia coli, and found high nucleotide similarity across the backbone. However, we saw low ph681355 backbone similarity to plasmid p60006 associated with the extensively drug-resistant S. enterica Typhi outbreak isolate in Pakistan, providing evidence of an alternative route for bla CTX-M-15 transmission. Our discovery highlights the importance of utilizing long-read sequencing in interrogating bacterial genomic architecture to fully understand AMR mechanisms and their clinical relevance. It also raises questions regarding how widespread bacteriophage-mediated HGT might be, suggesting that the resulting genomic plasticity might be higher than previously thought.}, }
@article {pmid36744899, year = {2023}, author = {Prasad, A and Ene, A and Jablonska, S and Du, J and Wolfe, AJ and Putonti, C}, title = {Comparative Genomic Study of Streptococcus anginosus Reveals Distinct Group of Urinary Strains.}, journal = {mSphere}, volume = {8}, number = {2}, pages = {e0068722}, pmid = {36744899}, issn = {2379-5042}, support = {R25 DK122954/DK/NIDDK NIH HHS/United States ; 5 R25 DK122954-04/NH/NIH HHS/United States ; }, mesh = {Female ; Humans ; *Streptococcus anginosus/genetics ; Streptococcus/genetics ; Genomics ; *Urinary Tract Infections ; Multilocus Sequence Typing ; }, abstract = {Streptococcus anginosus is a prevalent member of the human flora. While it has been found in the microbiota of "healthy" asymptomatic individuals, it has also been associated with genitourinary tract infections and bacteremia. Based upon multilocus sequence analysis, two subspecies and two genomosubspecies have been characterized for the species. We previously conducted whole-genome sequencing of 85 S. anginosus isolates from the urinary tract. Here, we present genomic analysis of this species, including isolates from the urinary tract as well as gut and fecal, vaginal, oral, respiratory, and blood and heart samples. Average nucleotide identity and core genome analysis revealed that these strains form two distinct groups. Group 1 is comprised of the S. anginosus type strain and other previously identified S. anginosus subspecies and genomosubspecies, including isolates from throughout the human body. In contrast, group 2 consists of predominantly urinary streptococci (n = 77; 85.6%). Both of these S. anginosus groups are distinct from other members of the Streptococcus anginosus group (SAG) species S. intermedius and S. constellatus. Genes conserved among all strains of one group but not in any strains in the other group were next identified. Group 1 strains included genes found in S. intermedius and S. constellatus, suggesting that they were lost within the ancestor of the group 2 strains. In contrast, genes unique to the group 2 strains were homologous to more distant streptococci, indicative of acquisition via horizontal gene transfer. These genes are ideal candidates for use as marker genes to distinguish between the two groups in the human microbiota. IMPORTANCE Whole-genome analysis of S. anginosus strains provides greater insight into the diversity of this species than from marker genes alone. Our investigation of 166 publicly available S. anginosus genomes via average nucleotide identity and core genome analysis revealed two phylogenomically distinct groups of this species, with one group almost exclusively consisting of isolates from the urinary tract. In contrast, only 8 urinary strains were identified within the other group, which contained the S. anginosus type strain, as well as all identified subspecies and genomosubspecies. While genomic analysis suggested that this urinary group of S. anginosus is genomically different from the previously characterized S. anginosus subspecies, phenotypic characterization is still needed. Given prior reports of the prevalence of S. anginosus in the urinary tract of both continent and incontinent females, future studies are needed to investigate if the symptom state of the urinary tract is associated with these two different groups.}, }
@article {pmid36744093, year = {2023}, author = {Qi, Q and Rajabal, V and Ghaly, TM and Tetu, SG and Gillings, MR}, title = {Identification of integrons and gene cassette-associated recombination sites in bacteriophage genomes.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1091391}, pmid = {36744093}, issn = {1664-302X}, abstract = {Bacteriophages are versatile mobile genetic elements that play key roles in driving the evolution of their bacterial hosts through horizontal gene transfer. Phages co-evolve with their bacterial hosts and have plastic genomes with extensive mosaicism. In this study, we present bioinformatic and experimental evidence that temperate and virulent (lytic) phages carry integrons, including integron-integrase genes, attC/attI recombination sites and gene cassettes. Integrons are normally found in Bacteria, where they capture, express and re-arrange mobile gene cassettes via integron-integrase activity. We demonstrate experimentally that a panel of attC sites carried in virulent phage can be recognized by the bacterial class 1 integron-integrase (IntI1) and then integrated into the paradigmatic attI1 recombination site using an attC x attI recombination assay. With an increasing number of phage genomes projected to become available, more phage-associated integrons and their components will likely be identified in the future. The discovery of integron components in bacteriophages establishes a new route for lateral transfer of these elements and their cargo genes between bacterial host cells.}, }
@article {pmid36741554, year = {2022}, author = {Lombard, L and van Doorn, R and Groenewald, JZ and Tessema, T and Kuramae, EE and Etolo, DW and Raaijmakers, JM and Crous, PW}, title = {Fusarium diversity associated with the Sorghum-Striga interaction in Ethiopia.}, journal = {Fungal systematics and evolution}, volume = {10}, number = {}, pages = {177-215}, pmid = {36741554}, issn = {2589-3831}, abstract = {Sorghum production is seriously threatened by the root parasitic weeds (RPWs) Striga hermonthica and Striga asiatica in sub-Saharan Africa. Research has shown that Striga control depends on eliminating its seed reserves in soil. Several species of the genus Fusarium (Nectriaceae, Hypocreales), which have been isolated from diseased Striga plants have proven to be highly pathogenic to all developmental stages of these RPWs. In the present study 439 isolates of Fusarium spp. were found associated with soils from Sorghum growing fields, Sorghum rhizosphere, or as endophytes with Sorghum roots and seeds, or as endophytes of Striga stems and seeds. Based on multi-locus phylogenies of combinations of CaM, tef1, rpb1 and rpb2 alignments, and morphological characteristics, 42 species were identified, including three species that are newly described, namely F. extenuatum and F. tangerinum from Sorghum soils, and F. pentaseptatum from seed of Striga hermonthica. Using a previously published AFLP-derived marker that is specific to detect isolates of F. oxysporum f.sp. strigae, an effective soil-borne biocontrol agent against Striga, we also detected the gene in several other Fusarium species. As these isolates were all associated with the Striga/Sorghum pathosystem, the possibility of horizontal gene transfer among these fusaria will be of interest to further investigate in future. Citation: Lombard L, van Doorn R, Groenewald JZ, Tessema T, Kuramae EE, Etolo DW, Raaijmakers JM, Crous PW (2022). Fusarium diversity associated with the Sorghum-Striga interaction in Ethiopia. Fungal Systematics and Evolution 10: 177-215. doi: 10.3114/fuse.2022.10.08.}, }
@article {pmid36740055, year = {2023}, author = {Markowicz, A}, title = {The significance of metallic nanoparticles in the emerging, development and spread of antibiotic resistance.}, journal = {The Science of the total environment}, volume = {871}, number = {}, pages = {162029}, doi = {10.1016/j.scitotenv.2023.162029}, pmid = {36740055}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; *Metal Nanoparticles/toxicity ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; }, abstract = {An ever-increasing number of newly synthesised nanoparticles have a constantly expanding range of applications. The large-scale implementation of nanoparticles will inevitably lead to intentional or accidental contamination of various environments. Since the major benefit of using several metallic nanoparticles is antimicrobial activity, these emerging contaminants may have a potentially hazardous impact on the development and spread of antibiotic resistance - a challenge that threats infection therapy worldwide. Few studies underline that metallic nanoparticles may affect the emergence and evolution of resistance via mutations and horizontal transfer between different bacterial species. Due to the complexity of factors and mechanisms involved in disseminating antibiotic resistance, it is crucial to investigate if metallic nanoparticles play a significant role in this process through co-selection ability and pressure exerted on bacteria. The aim of this review is to summarise the current research on mutations and three main horizontal gene transfer modes facilitated by nanoparticles. Here, the current results in the field are presented, major knowledge gaps and the necessity for more environmentally relevant studies are discussed.}, }
@article {pmid36739179, year = {2023}, author = {Islam, T and Azad, RB and Kasfy, SH and Rahman, AA and Khan, TZ}, title = {Horizontal gene transfer from plant to whitefly.}, journal = {Trends in biotechnology}, volume = {41}, number = {7}, pages = {853-856}, doi = {10.1016/j.tibtech.2023.01.007}, pmid = {36739179}, issn = {1879-3096}, mesh = {Animals ; *Hemiptera/genetics ; Gene Transfer, Horizontal ; }, abstract = {The recent discovery of the horizontal transfer of a toxin-neutralizing gene from plant to whitefly (Bemisia tabaci), a polyphagous insect, sparked a new area of study. In this forum, we discuss some potential biotechnological applications of this newly discovered knowledge in the coevolutionary arms race between plants and whitefly.}, }
@article {pmid36738814, year = {2023}, author = {Bhowmik, P and Bharatham, N and Murakami, S and Ramachandran, V and Datta, S}, title = {Identification of key amino acid residues in OqxB mediated efflux of fluoroquinolones using site-directed mutagenesis.}, journal = {Research in microbiology}, volume = {174}, number = {4}, pages = {104039}, doi = {10.1016/j.resmic.2023.104039}, pmid = {36738814}, issn = {1769-7123}, mesh = {*Fluoroquinolones/pharmacology ; *Amino Acids ; Anti-Bacterial Agents/pharmacology/metabolism ; Nitrofurantoin ; Escherichia coli/genetics/metabolism ; Mutagenesis, Site-Directed ; Drug Resistance, Multiple, Bacterial/genetics ; Microbial Sensitivity Tests ; Bacterial Proteins/metabolism ; }, abstract = {OqxB belongs to the RND (Resistance-Nodulation-Division) efflux pump family, recognized widely as a major contributor towards enhancing antimicrobial resistance. It is known to be predominantly present in all Klebsiella spp. and is attributed for its role in increasing resistance against an array of antibiotics like nitrofurantoin, quinolones, β-lactams and colistin. However, the presence of oqxB encoding this efflux pump is not limited only to Klebsiella spp., but is also found to occur via horizontal gene transfer in other bacterial genera like Escherichia coli, Enterobacter cloacae and Salmonella spp. Recently, we reported the crystal structure of OqxB and its structure-function relationship required for the efflux of fluoroquinolones. Extending these findings further, we characterized the structural architecture of this efflux pump along with identifying some critical amino acids at the substrate binding domain of OqxB. Based on our in silico modelling studies, both hydrophobic residues (F180, L280, L621, F626) and polar residues (R48, E50, E184, R157, R774) were found to be located at this site. The present work reports the importance of these key amino acid residues and the crucial ion-pair interactions at the substrate-binding pocket, thereby establishing their role in OqxB mediated efflux and the resultant resistance development against fluoroquinolones.}, }
@article {pmid36738611, year = {2023}, author = {Zhang, Y and Zhao, Z and Xu, H and Wang, L and Liu, R and Jia, X}, title = {Fate of antibiotic resistance genes and bacteria in a coupled water-processing system with wastewater treatment plants and constructed wetlands in coastal eco-industrial parks.}, journal = {Ecotoxicology and environmental safety}, volume = {252}, number = {}, pages = {114606}, doi = {10.1016/j.ecoenv.2023.114606}, pmid = {36738611}, issn = {1090-2414}, mesh = {*Anti-Bacterial Agents/pharmacology/analysis ; *Waste Disposal, Fluid ; Genes, Bacterial ; Wetlands ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Tetracycline/pharmacology ; Sulfanilamide ; Aminoglycosides/pharmacology ; }, abstract = {In coastal eco-industrial zones, wastewater treatment plants (WWTPs) and constructed wetlands (CWs) can alleviate the challenge of water shortage and the negative effect of sewage discharge, while the problems of antibiotic resistance genes (ARGs) have not attracted enough attention. In this research, the Wafergen SmartChip system was adopted to investigate the ARG profiles in a coupled system combined WWTPs and CWs in a coastal industrial park. Potential risks of antibiotic resistance in chemical industrial wastewater were confirmed due to the higher abundance of target ARGs (> 10[7] copies/mL). General decline with partial enrichment in absolute and relative abundance of ARGs from the WWTPs to CWs revealed the effective removal of ARGs in the coupled system, while the fate of different ARG types varied greatly. Aminoglycoside and sulfonamide ARGs were detected with higher abundance (up to 5.34 ×10[7] and 3.61 ×10[7] copies/mL), especially aac(6')-Ib and sul1. Denitrification, secondary sedimentation, and acid hydrolysis contributed to the removal of aminoglycoside, sulfonamide, β-lactamase, chloramphenicol, and multidrug ARGs. Catalytic ozonation contributed to the removal of tetracycline and MLSB ARGs. Subsurface CWs worked effectively for the removal of sulfonamide, tetracycline, and multidrug ARGs, especially tetX, cphA, tetG, and strB. Close correlations between ARGs and MGEs emphasized the vital roles of anthropogenic pollutants and horizontal gene transfer on the diffusion of ARGs. Actinobacteria, Bacteroidota, and Cyanobacteria were dominant in the CWs, while Proteobacteria, Firmicutes, and Planctomycetota were prevalent in the WWTPs. Redundancy analysis and variance partitioning analysis indicated that transposase and water quality posed greater influences on the distribution of ARGs. Co-occurrence network revealed that potential multiple antibiotic resistant pathogenic bacteria decreased in the CWs. The coupled system has a limited effect on the reduction of ARGs and potential ARG hosts, providing a comprehensive insight into the fate of ARGs in conventional water-processing systems.}, }
@article {pmid37938682, year = {2022}, author = {Orevi, T and Sørensen, SJ and Kashtan, N}, title = {Droplet size and surface hydrophobicity enhance bacterial plasmid transfer rates in microscopic surface wetness.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {72}, pmid = {37938682}, issn = {2730-6151}, support = {#220020475//James S. McDonnell Foundation (McDonnell Foundation)/ ; #1396/19//Israel Science Foundation (ISF)/ ; NNF200C0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; }, abstract = {Conjugal plasmids constitute a major engine for horizontal gene transfer in bacteria, and are key drivers of the spread of antibiotic resistance, virulence, and metabolic functions. Bacteria in terrestrial habitats often inhabit surfaces that are not constantly water-saturated, where microscopic surface wetness (MSW), comprised of thin liquid films and microdroplets, permanently or intermittently occurs. How physical properties of microdroplets, and of the surfaces they reside on, affect plasmid transfer rates is not well understood. Here, building on microscopy-based microdroplet experiments, we examined the relation between droplet properties (size and spread) and plasmid transfer rates at single-cell and individual droplet resolution, using Pseudomonas putida as a model species. We show that transfer rates increase with droplet size, due to higher densities of cells on the surface in larger droplets, resulting from lower ratio between the area of the liquid-solid interface and droplet volumes. We further show that surface hydrophobicity promotes transfer rates via the same mechanism. Our results provide new insights into how physical properties of surfaces and MSW affect plasmid transfer rates, and more generally, microbial interactions mediated by cell-to-cell contact, with important implications for our understanding of the ecology and evolution of bacteria in unsaturated environments.}, }
@article {pmid37938745, year = {2022}, author = {Kujawska, M and Raulo, A and Millar, M and Warren, F and Baltrūnaitė, L and Knowles, SCL and Hall, LJ}, title = {Bifidobacterium castoris strains isolated from wild mice show evidence of frequent host switching and diverse carbohydrate metabolism potential.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {20}, pmid = {37938745}, issn = {2730-6151}, support = {/WT_/Wellcome Trust/United Kingdom ; BBS/E/F/00044409/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {Members of the gut microbiota genus Bifidobacterium are widely distributed human and animal symbionts believed to exert beneficial effects on their hosts. However, in-depth genomic analyses of animal-associated species and strains are somewhat lacking, particularly in wild animal populations. Here, to examine patterns of host specificity and carbohydrate metabolism capacity, we sequenced whole genomes of Bifidobacterium isolated from wild-caught small mammals from two European countries (UK and Lithuania). Members of Bifidobacterium castoris, Bifidobacterium animalis and Bifodobacterium pseudolongum were detected in wild mice (Apodemus sylvaticus, Apodemus agrarius and Apodemus flavicollis), but not voles or shrews. B. castoris constituted the most commonly recovered Bifidobacterium (78% of all isolates), with the majority of strains only detected in a single population, although populations frequently harboured multiple co-circulating strains. Phylogenetic analysis revealed that the mouse-associated B. castoris clades were not specific to a particular location or host species, and their distribution across the host phylogeny was consistent with regular host shifts rather than host-microbe codiversification. Functional analysis, including in vitro growth assays, suggested that mouse-derived B. castoris strains encoded an extensive arsenal of carbohydrate-active enzymes, including putative novel glycosyl hydrolases such as chitosanases, along with genes encoding putative exopolysaccharides, some of which may have been acquired via horizontal gene transfer. Overall, these results provide a rare genome-level analysis of host specificity and genomic capacity among important gut symbionts of wild animals, and reveal that Bifidobacterium has a labile relationship with its host over evolutionary time scales.}, }
@article {pmid37334233, year = {2021}, author = {Liguori, R and Rommel, SH and Bengtsson-Palme, J and Helmreich, B and Wurzbacher, C}, title = {Microbial retention and resistances in stormwater quality improvement devices treating road runoff.}, journal = {FEMS microbes}, volume = {2}, number = {}, pages = {xtab008}, pmid = {37334233}, issn = {2633-6685}, abstract = {Current knowledge about the microbial communities that occur in urban road runoff is scarce. Road runoff of trafficked roads can be heavily polluted and is treated by stormwater quality improvement devices (SQIDs). However, microbes may influence the treatment process of these devices or could lead to stress resistant opportunistic microbial strains. In this study, the microbial community in the influent, effluent and the filter materials used to remove dissolved heavy metals from two different SQIDs were analyzed to determine microbial load, retention, composition, and mobile resistance genes. Although the microbes were replaced by new taxa in the effluent, there was no major retention of microbial genera. Further, the bacterial abundance of the SQIDs effluent was relatively stable over time. The heavy metal content correlated with intl1 and with microbial genera. The filter media itself was enriched with Intl1 gene cassettes, carrying several heavy metal and multidrug resistance genes (e.g. czrA, czcA, silP, mexW and mexI), indicating that this is a hot spot for horizontal gene transfer. Overall, the results shed light on road runoff microbial communities, and pointed to distinct bacterial communities within the SQIDs, which subsequently influence the microbial community and the genes released with the treated water.}, }
@article {pmid37744100, year = {2021}, author = {Stabel, M and Hagemeister, J and Heck, Z and Aliyu, H and Ochsenreither, K}, title = {Characterization and Phylogenetic Analysis of a Novel GH43 β-Xylosidase From Neocallimastix californiae.}, journal = {Frontiers in fungal biology}, volume = {2}, number = {}, pages = {692804}, pmid = {37744100}, issn = {2673-6128}, abstract = {Degradation of lignocellulosic materials to release fermentable mono- and disaccharides is a decisive step toward a sustainable bio-based economy, thereby increasing the demand of robust and highly active lignocellulolytic enzymes. Anaerobic fungi of the phylum Neocallimastigomycota are potent biomass degraders harboring a huge variety of such enzymes. Compared to cellulose, hemicellulose degradation has received much less attention; therefore, the focus of this study has been the enzymatic xylan degradation of anaerobic fungi as these organisms produce some of the most effective known hydrolytic enzymes. We report the heterologous expression of a GH43 xylosidase, Xyl43Nc, and a GH11 endoxylanase, X11Nc, from the anaerobic fungus Neocallimastix californiae in Escherichia coli. The enzymes were identified by screening of the putative proteome. Xyl43Nc was highly active against 4-Nitrophenol-xylopyranosides with a Km of 0.72 mM, a kcat of 29.28 s[-1], a temperature optimum of 32°C and a pH optimum of 6. When combined, Xyl43Nc and X11Nc released xylose from beechwood xylan and arabinoxylan from wheat. Phylogenetic analysis revealed that Xyl43Nc shares common ancestry with enzymes from Spirochaetes and groups separately from Ascomycete sequences in our phylogeny, highlighting the importance of horizontal gene transfer in the evolution of the anaerobic fungi.}, }
@article {pmid37223257, year = {2021}, author = {Liu, J and Soler, N and Gorlas, A and Cvirkaite-Krupovic, V and Krupovic, M and Forterre, P}, title = {Extracellular membrane vesicles and nanotubes in Archaea.}, journal = {microLife}, volume = {2}, number = {}, pages = {uqab007}, pmid = {37223257}, issn = {2633-6693}, abstract = {Membrane-bound extracellular vesicles (EVs) are secreted by cells from all three domains of life and their implication in various biological processes is increasingly recognized. In this review, we summarize the current knowledge on archaeal EVs and nanotubes, and emphasize their biological significance. In archaea, the EVs and nanotubes have been largely studied in representative species from the phyla Crenarchaeota and Euryarchaeota. The archaeal EVs have been linked to several physiological processes such as detoxification, biomineralization and transport of biological molecules, including chromosomal, viral or plasmid DNA, thereby taking part in genome evolution and adaptation through horizontal gene transfer. The biological significance of archaeal nanotubes is yet to be demonstrated, although they could participate in EV biogenesis or exchange of cellular contents. We also discuss the biological mechanisms leading to EV/nanotube biogenesis in Archaea. It has been recently demonstrated that, similar to eukaryotes, EV budding in crenarchaea depends on the ESCRT machinery, whereas the mechanism of EV budding in euryarchaeal lineages, which lack the ESCRT-III homologues, remains unknown.}, }
@article {pmid37223255, year = {2021}, author = {Afonina, I and Tien, B and Nair, Z and Matysik, A and Lam, LN and Veleba, M and Jie, AKJ and Rashid, R and Cazenave-Gassiot, A and Wenk, M and Wai, SN and Kline, KA}, title = {The composition and function of Enterococcus faecalis membrane vesicles.}, journal = {microLife}, volume = {2}, number = {}, pages = {uqab002}, pmid = {37223255}, issn = {2633-6693}, abstract = {Membrane vesicles (MVs) contribute to various biological processes in bacteria, including virulence factor delivery, antimicrobial resistance, host immune evasion and cross-species communication. MVs are frequently released from the surface of both Gram-negative and Gram-positive bacteria during growth. In some Gram-positive bacteria, genes affecting MV biogenesis have been identified, but the mechanism of MV formation is unknown. In Enterococcus faecalis, a causative agent of life-threatening bacteraemia and endocarditis, neither mechanisms of MV formation nor their role in virulence has been examined. Since MVs of many bacterial species are implicated in host-pathogen interactions, biofilm formation, horizontal gene transfer, and virulence factor secretion in other species, we sought to identify, describe and functionally characterize MVs from E. faecalis. Here, we show that E. faecalis releases MVs that possess unique lipid and protein profiles, distinct from the intact cell membrane and are enriched in lipoproteins. MVs of E. faecalis are specifically enriched in unsaturated lipids that might provide membrane flexibility to enable MV formation, providing the first insights into the mechanism of MV formation in this Gram-positive organism.}, }
@article {pmid36732595, year = {2023}, author = {Bhattacharjee, AS and Schulz, F and Woyke, T and Orcutt, BN and Martínez Martínez, J}, title = {Genomics discovery of giant fungal viruses from subsurface oceanic crustal fluids.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {10}, pmid = {36732595}, issn = {2730-6151}, support = {GBMF5334//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; DE-AC02-05CH11231//DOE | Advanced Research Projects Agency - Energy (Advanced Research Projects Agency - Energy - U.S. Department of Energy)/ ; DE-AC02-05CH11231//DOE | Advanced Research Projects Agency - Energy (Advanced Research Projects Agency - Energy - U.S. Department of Energy)/ ; OCE-0939564//National Science Foundation (NSF)/ ; }, abstract = {The oceanic igneous crust is a vast reservoir for microbial life, dominated by diverse and active bacteria, archaea, and fungi. Archaeal and bacterial viruses were previously detected in oceanic crustal fluids at the Juan de Fuca Ridge (JdFR). Here we report the discovery of two eukaryotic Nucleocytoviricota genomes from the same crustal fluids by sorting and sequencing single virions. Both genomes have a tRNA[Tyr] gene with an intron (20 bps) at the canonical position between nucleotide 37 and 38, a common feature in eukaryotic and archaeal tRNA genes with short introns (<100 bps), and fungal genes acquired through horizontal gene transfer (HGT) events. The dominance of Ascomycota fungi as the main eukaryotes in crustal fluids and the evidence for HGT point to these fungi as the putative hosts, making these the first putative fungi-Nucleocytoviricota specific association. Our study suggests active host-viral dynamics for the only eukaryotic group found in the subsurface oceanic crust and raises important questions about the impact of viral infection on the productivity and biogeochemical cycling in this ecosystem.}, }
@article {pmid36727472, year = {2023}, author = {Daveri, A and Benigno, V and van der Meer, JR}, title = {Characterization of an atypical but widespread type IV secretion system for transfer of the integrative and conjugative element (ICEclc) in Pseudomonas putida.}, journal = {Nucleic acids research}, volume = {51}, number = {5}, pages = {2345-2362}, pmid = {36727472}, issn = {1362-4962}, mesh = {*Pseudomonas putida/genetics ; Type IV Secretion Systems/genetics ; Bacterial Proteins/genetics ; Plasmids/genetics ; Conjugation, Genetic/genetics ; Gene Transfer, Horizontal ; }, abstract = {Conjugation of DNA relies on multicomponent protein complexes bridging two bacterial cytoplasmic compartments. Whereas plasmid conjugation systems have been well documented, those of integrative and conjugative elements (ICEs) have remained poorly studied. We characterize here the conjugation system of the ICEclc element in Pseudomonas putida UWC1 that is a model for a widely distributed family of ICEs. By in frame deletion and complementation, we show the importance on ICE transfer of 22 genes in a 20-kb conserved ICE region. Protein comparisons recognized seven homologs to plasmid type IV secretion system components, another six homologs to frequent accessory proteins, and the rest without detectable counterparts. Stationary phase imaging of P. putida ICEclc with in-frame fluorescent protein fusions to predicted type IV components showed transfer-competent cell subpopulations with multiple fluorescent foci, largely overlapping in dual-labeled subcomponents, which is suggestive for multiple conjugation complexes per cell. Cross-dependencies between subcomponents in ICE-type IV secretion system assembly were revealed by quantitative foci image analysis in a variety of ICEclc mutant backgrounds. In conclusion, the ICEclc family presents an evolutionary distinct type IV conjugative system with transfer competent cells specialized in efficient transfer.}, }
@article {pmid36726572, year = {2022}, author = {Calero-Cáceres, W and Rodríguez, K and Medina, A and Medina, J and Ortuño-Gutiérrez, N and Sunyoto, T and Dias, CAG and Bastidas-Caldes, C and Ramírez, MS and Harries, AD}, title = {Genomic insights of mcr-1 harboring Escherichia coli by geographical region and a One-Health perspective.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1032753}, pmid = {36726572}, issn = {1664-302X}, abstract = {The importance of the One Health concept in attempting to deal with the increasing levels of multidrug-resistant bacteria in both human and animal health is a challenge for the scientific community, policymakers, and the industry. The discovery of the plasmid-borne mobile colistin resistance (mcr) in 2015 poses a significant threat because of the ability of these plasmids to move between different bacterial species through horizontal gene transfer. In light of these findings, the World Health Organization (WHO) recommends that countries implement surveillance strategies to detect the presence of plasmid-mediated colistin-resistant microorganisms and take suitable measures to control and prevent their dissemination. Seven years later, ten different variants of the mcr gene (mcr-1 to mcr-10) have been detected worldwide in bacteria isolated from humans, animals, foods, the environment, and farms. However, the possible transmission mechanisms of the mcr gene among isolates from different geographical origins and sources are largely unknown. This article presents an analysis of whole-genome sequences of Escherichia coli that harbor mcr-1 gene from different origins (human, animal, food, or environment) and geographical location, to identify specific patterns related to virulence genes, plasmid content and antibiotic resistance genes, as well as their phylogeny and their distribution with their origin. In general, E. coli isolates that harbor mcr-1 showed a wide plethora of ARGs. Regarding the plasmid content, the highest concentration of plasmids was found in animal samples. In turn, Asia was the continent that led with the largest diversity and occurrence of these plasmids. Finally, about virulence genes, terC, gad, and traT represent the most frequent virulence genes detected. These findings highlight the relevance of analyzing the environmental settings as an integrative part of the surveillance programs to understand the origins and dissemination of antimicrobial resistance.}, }
@article {pmid36726175, year = {2023}, author = {Petersen, C and Sørensen, T and Nielsen, MR and Sondergaard, TE and Sørensen, JL and Fitzpatrick, DA and Frisvad, JC and Nielsen, KL}, title = {Comparative genomic study of the Penicillium genus elucidates a diverse pangenome and 15 lateral gene transfer events.}, journal = {IMA fungus}, volume = {14}, number = {1}, pages = {3}, pmid = {36726175}, issn = {2210-6340}, support = {NNF18OC0034952//Novo Nordisk Fonden/ ; }, abstract = {The Penicillia are known to produce a wide range natural products-some with devastating outcome for the agricultural industry and others with unexploited potential in different applications. However, a large-scale overview of the biosynthetic potential of different species has been lacking. In this study, we sequenced 93 Penicillium isolates and, together with eleven published genomes that hold similar assembly characteristics, we established a species phylogeny as well as defining a Penicillium pangenome. A total of 5612 genes were shared between ≥ 98 isolates corresponding to approximately half of the average number of genes a Penicillium genome holds. We further identified 15 lateral gene transfer events that have occurred in this collection of Penicillium isolates, which might have played an important role, such as niche adaption, in the evolution of these fungi. The comprehensive characterization of the genomic diversity in the Penicillium genus supersedes single-reference genomes, which do not necessarily capture the entire genetic variation.}, }
@article {pmid36724669, year = {2023}, author = {Adenaya, A and Berger, M and Brinkhoff, T and Ribas-Ribas, M and Wurl, O}, title = {Usage of antibiotics in aquaculture and the impact on coastal waters.}, journal = {Marine pollution bulletin}, volume = {188}, number = {}, pages = {114645}, doi = {10.1016/j.marpolbul.2023.114645}, pmid = {36724669}, issn = {1879-3363}, mesh = {Humans ; *Anti-Bacterial Agents/analysis ; Ecosystem ; Aquaculture ; *Environmental Pollutants ; Water ; }, abstract = {For decades, coastal marine ecosystems have been threatened by a wide range of anthropogenic pollutants. Recently, there has been increasing concern about the accumulation and impacts of antibiotic compounds on marine ecosystems. However, information regarding the accumulation of antibiotics and the impacts they may have on microbial communities in coastal water bodies and on human health is sparse in literature. Antibiotics from aquacultures are constantly discharged into marine environments via rivers. Large rivers transport tons of antibiotics every year into coastal waters, e.g., 12 tons of sulfonamide by the river Mekong. Here, we discuss a potential influence of such imported antibiotics on bacterial communities in coastal waters. Potential accumulation of antibiotics in the uppermost surface layer of aquatic ecosystems, the so-called sea surface microlayer (SML), is of interest. Because of the ability of the SML to accumulate anthropogenic pollutants, it may serve as a pool for antibiotics and correspondingly also for resistant organisms. Also, due to its biofilm-like structure, the SML could serve as a hotspot for horizontal gene transfer, speeding up the spread of antibiotic resistant strains to encompassing marine environments. The emergence of antibiotic resistant bacteria is a global threat and scientists projected that it could pave the way for the next pandemic that could ravage the world in the next decades. For this reason, it is time to focus research on understanding and minimizing the impact of antibiotics on the sustainability of coastal waters and on the health of humans who depend on coastal resources for food and recreational purposes. Also, knowledge about antibiotics in the SML is necessary to understand the effects they are likely to have on bacterial abundance, diversity, and metabolic activities in coastal water bodies.}, }
@article {pmid36724283, year = {2023}, author = {Sarma, S and Bhattacharjee, A and Devi, MV and Panyang, PP and Singh, AK}, title = {Long-term adaptation of ParA, RelE/ParE partition system, replication protein and phage proteins encoding low-cost plasmids of Escherichia species isolated from diarrheic children of North East India.}, journal = {Journal of applied microbiology}, volume = {134}, number = {2}, pages = {}, doi = {10.1093/jambio/lxac065}, pmid = {36724283}, issn = {1365-2672}, support = {IF-170007//DST-INSPIRE/ ; OLP-2035//Council of Scientific and Industrial Research/ ; GPP-0329//Department of Science and Technology-SERB/ ; }, mesh = {Humans ; Child ; beta-Lactamases/genetics/metabolism ; Escherichia coli/genetics ; Klebsiella pneumoniae/genetics/metabolism ; Plasmids/genetics ; Klebsiella/metabolism ; India ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; *Bacterial Toxins ; *Escherichia coli Proteins/genetics ; }, abstract = {AIMS: The prevalent distribution of plasmid-mediated β-lactam resistance is the most pressing global problem in enteric diseases. The current work aims to characterize plasmid-carrying β-lactam resistant Enterobacteriaceae isolates from North East India for horizontal gene transfer (HGT) and plasmid adaptation study.<br><br>METHODS AND RESULTS: In vitro transconjugation and transformation showed overall high conjugation frequency (4.11&#xa0;&#xd7;&#xa0;10-1-9.2&#xa0;&#xd7;&#xa0;10-1) and moderate transformation efficiency/&#xb5;g DNA (1.02&#xa0;&#xd7;&#xa0;102 -1&#xa0;&#xd7;&#xa0;103), and the highest conjugation frequency (9.2&#xa0;&#xd7;&#xa0;10-1) and transformation efficiency (1&#xa0;&#xd7;&#xa0;103) for Escherichia species S-10. Intra/intergenus plasmid transformation efficiency was highest for the transformation of Klebsiella pneumoniae S-2 to Shigellaflexneri S-42 (1.3&#xa0;&#xd7;&#xa0;103) and lowest for Escherichia species S-10 to Escherichia fergusonii S-30 (2&#xa0;&#xd7;&#xa0;102). In the plasmid stability test, S-10 was detected with the highest plasmid carrying frequency (83.44%) and insignificant segregational loss rate (0.0004) until the 60th day with low plasmid cost on the host. The above findings were also validated by whole-plasmid sequencing of Escherichia species S-10. The genome was identified with two plasmids constituting multiple phage proteins, relaxosomal protein NikA, replication protein RepA, and the plasmid maintenance proteins (ParA, RelE/ParE), thus assisting stable plasmid maintenance.<br><br>CONCLUSIONS: The results thus indicate that the high conjugation ability and low plasmid fitness cost might lead to horizontal gene transfer of the plasmid to the environment due to their prolonged adaptation in nonselective conditions, intensifying the infection's severity.}, }
@article {pmid36722946, year = {2023}, author = {Carrilero, L and Dunn, SJ and Moran, RA and McNally, A and Brockhurst, MA}, title = {Evolutionary Responses to Acquiring a Multidrug Resistance Plasmid Are Dominated by Metabolic Functions across Diverse Escherichia coli Lineages.}, journal = {mSystems}, volume = {8}, number = {1}, pages = {e0071322}, pmid = {36722946}, issn = {2379-5077}, support = {BB/R006253/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R006261/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /DH_/Department of Health/United Kingdom ; }, mesh = {*Escherichia coli/genetics ; Plasmids/genetics ; *Genome, Bacterial/genetics ; Drug Resistance, Multiple ; Genomics ; }, abstract = {Multidrug resistance (MDR) plasmids drive the spread of antibiotic resistance between bacterial lineages. The immediate impact of MDR plasmid acquisition on fitness and cellular processes varies among bacterial lineages, but how the evolutionary processes enabling the genomic integration of MDR plasmids vary is less well understood, particularly in clinical pathogens. Using diverse Escherichia coli lineages experimentally evolved for ~700 generations, we show that the evolutionary response to gaining the MDR plasmid pLL35 was dominated by chromosomal mutations affecting metabolic and regulatory functions, with both strain-specific and shared mutational targets. The expression of several of these functions, such as anaerobic metabolism, is known to be altered upon acquisition of pLL35. Interactions with resident mobile genetic elements, notably several IS-elements, potentiated parallel mutations, including insertions upstream of hns that were associated with its upregulation and the downregulation of the plasmid-encoded extended-spectrum beta-lactamase gene. Plasmid parallel mutations targeted conjugation-related genes, whose expression was also commonly downregulated in evolved clones. Beyond their role in horizontal gene transfer, plasmids can be an important selective force shaping the evolution of bacterial chromosomes and core cellular functions. IMPORTANCE Plasmids drive the spread of antimicrobial resistance genes between bacterial genomes. However, the evolutionary processes allowing plasmids to be assimilated by diverse bacterial genomes are poorly understood, especially in clinical pathogens. Using experimental evolution with diverse E. coli lineages and a clinical multidrug resistance plasmid, we show that although plasmids drove unique evolutionary paths per lineage, there was a surprising degree of convergence in the functions targeted by mutations across lineages, dominated by metabolic functions. Remarkably, these same metabolic functions show higher evolutionary rates in MDR-lineages in nature and in some cases, like anaerobic metabolism, their expression is directly manipulated by the plasmid. Interactions with other mobile elements resident in the genomes accelerated adaptation by disrupting genes and regulatory sequences that they inserted into. Beyond their role in horizontal gene transfer, plasmids are an important selective force driving the evolution of bacterial genomes and core cellular functions.}, }
@article {pmid36720410, year = {2023}, author = {Zhao, H and Liu, X and Sun, Y and Liu, J and Waigi, MG}, title = {Effects and mechanisms of plant growth regulators on horizontal transfer of antibiotic resistance genes through plasmid-mediated conjugation.}, journal = {Chemosphere}, volume = {318}, number = {}, pages = {137997}, doi = {10.1016/j.chemosphere.2023.137997}, pmid = {36720410}, issn = {1879-1298}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Escherichia coli/genetics ; Plant Growth Regulators/pharmacology ; Drug Resistance, Microbial/genetics ; Bacteria ; Genes, Bacterial ; Plasmids/genetics ; Gene Transfer, Horizontal ; }, abstract = {A vast number of bacteria occur in both soil and plants, with some of them harboring antibiotic resistance genes (ARGs). When bacteria congregate on the interface of soil particles or on plant root surfaces, these ARGs can be transferred between bacteria via conjugation, leading to the formation of antibiotic-resistant pathogens that threaten human health. Plant growth regulators (PGRs) are widely used in agricultural production, promoting plant growth and increasing crop yields. However, until now, little information has been known about the effects of PGRs on the horizontal gene transfer (HGT) of ARGs. In this study, with Escherichia coli DH5α (carrying RP4 plasmid with Tet[R], Amp[R], Kan[R]) as the donor and E. coli HB101 as the recipient, a series of diparental conjugation experiments were conducted to investigate the effects of indoleacetic acid (IAA), ethel (ETH) and gibberellin (GA3) on HGT of ARGs via plasmid-mediated conjugation. Furthermore, the mechanisms involved were also clarified. The results showed that all three PGRs affected the ARG transfer frequency by inducing the intracellular reactive oxygen species (ROS) formation, changing the cell membrane permeability, and regulating the gene transcription of traA, traL, trfAp, trbBp, kilA, and korA in plasmid RP4. In detail, 50-100 mg⋅L[-1] IAA, 20-50 mg⋅L[-1] ETH and 1500-2500 mg⋅L[-1] GA3 all significantly promoted the ARG conjugation. This study indicated that widespread use of PGRs in agricultural production could affect the HGT of ARGs via plasmid-mediated conjugation, and the application of reasonable concentrations of PGRs could reduce the ARG transmission in both soil environments and plants.}, }
@article {pmid36719227, year = {2023}, author = {Cesa-Luna, C and Geudens, N and Girard, L and De Roo, V and Maklad, HR and Martins, JC and Höfte, M and De Mot, R}, title = {Charting the Lipopeptidome of Nonpathogenic Pseudomonas.}, journal = {mSystems}, volume = {8}, number = {1}, pages = {e0098822}, pmid = {36719227}, issn = {2379-5077}, mesh = {*Pseudomonas/genetics ; *Pseudomonas fluorescens/genetics ; Lipopeptides ; Phylogeny ; }, abstract = {A major source of pseudomonad-specialized metabolites is the nonribosomal peptide synthetases (NRPSs) assembling siderophores and lipopeptides. Cyclic lipopeptides (CLPs) of the Mycin and Peptin families are frequently associated with, but not restricted to, phytopathogenic species. We conducted an in silico analysis of the NRPSs encoded by lipopeptide biosynthetic gene clusters in nonpathogenic Pseudomonas genomes, covering 13 chemically diversified families. This global assessment of lipopeptide production capacity revealed it to be confined to the Pseudomonas fluorescens lineage, with most strains synthesizing a single type of CLP. Whereas certain lipopeptide families are specific for a taxonomic subgroup, others are found in distant groups. NRPS activation domain-guided peptide predictions enabled reliable family assignments, including identification of novel members. Focusing on the two most abundant lipopeptide families (Viscosin and Amphisin), a portion of their uncharted diversity was mapped, including characterization of two novel Amphisin family members (nepenthesin and oakridgin). Using NMR fingerprint matching, known Viscosin-family lipopeptides were identified in 15 (type) species spread across different taxonomic groups. A bifurcate genomic organization predominates among Viscosin-family producers and typifies Xantholysin-, Entolysin-, and Poaeamide-family producers but most families feature a single NRPS gene cluster embedded between cognate regulator and transporter genes. The strong correlation observed between NRPS system phylogeny and rpoD-based taxonomic affiliation indicates that much of the structural diversity is linked to speciation, providing few indications of horizontal gene transfer. The grouping of most NRPS systems in four superfamilies based on activation domain homology suggests extensive module dynamics driven by domain deletions, duplications, and exchanges. IMPORTANCE Pseudomonas species are prominent producers of lipopeptides that support proliferation in a multitude of environments and foster varied lifestyles. By genome mining of biosynthetic gene clusters (BGCs) with lipopeptide-specific organization, we mapped the global Pseudomonas lipopeptidome and linked its staggering diversity to taxonomy of the producers, belonging to different groups within the major Pseudomonas fluorescens lineage. Activation domain phylogeny of newly mined lipopeptide synthetases combined with previously characterized enzymes enabled assignment of predicted BGC products to specific lipopeptide families. In addition, novel peptide sequences were detected, showing the value of substrate specificity analysis for prioritization of BGCs for further characterization. NMR fingerprint matching proved an excellent tool to unequivocally identify multiple lipopeptides bioinformatically assigned to the Viscosin family, by far the most abundant one in Pseudomonas and with stereochemistry of all its current members elucidated. In-depth analysis of activation domains provided insight into mechanisms driving lipopeptide structural diversification.}, }
@article {pmid36717488, year = {2023}, author = {Ishibashi, K and Tanaka, Y and Morishita, Y}, title = {Evolutionary Overview of Aquaporin Superfamily.}, journal = {Advances in experimental medicine and biology}, volume = {1398}, number = {}, pages = {81-98}, pmid = {36717488}, issn = {0065-2598}, mesh = {Phylogeny ; *Genome ; *Aquaporins/genetics/chemistry/metabolism ; }, abstract = {Aquaporins (AQPs) are present not only in three domains of life, bacteria, eukaryotes, and archaea, but also in viruses. With the accumulating arrays of AQP superfamily, the evolutional relationship has attracted much attention with multiple publications on "the genome-wide identification and phylogenetic analysis" of AQP superfamily. A pair of NPA boxes forming a pore is highly conserved throughout the evolution and renders key residues for the classification of AQP superfamily into four groups: AQP1-like, AQP3-like, AQP8-like, and AQP11-like. The complexity of AQP family has mostly been achieved in nematodes and subsequent evolution has been directed toward increasing the number of AQPs through whole-genome duplications (WGDs) to extend the tissue specific expression and regulation. The discovery of the intracellular AQP (iAQP: AQP8-like and AQP11-like) and substrate transports by the plasma membrane AQP (pAQP: AQP1-like and AQP3-like) have accelerated the AQP research much more toward the transport of substrates with complex profiles. This evolutionary overview based on a simple classification of AQPs into four subfamilies will provide putative structural, functional, and localization information and insights into the role of AQP as well as clues to understand the complex diversity of AQP superfamily.}, }
@article {pmid36715351, year = {2023}, author = {Liu, H and Huang, W and Yu, Y and Chen, D}, title = {Lightning-Rod Effect on Nanowire Tips Reinforces Electroporation and Electrochemical Oxidation: An Efficient Strategy for Eliminating Intracellular Antibiotic Resistance Genes.}, journal = {ACS nano}, volume = {17}, number = {3}, pages = {3037-3046}, doi = {10.1021/acsnano.2c11811}, pmid = {36715351}, issn = {1936-086X}, mesh = {Angiotensin Receptor Antagonists/pharmacology ; Angiotensin-Converting Enzyme Inhibitors/pharmacology ; Anti-Bacterial Agents/pharmacology ; Disinfection ; *Drinking Water ; Drug Resistance, Microbial/genetics ; Electroporation ; Genes, Bacterial ; *Lightning ; *Nanowires ; *Water Purification/methods ; Oxidation-Reduction ; Intracellular Space/metabolism ; }, abstract = {Conventional oxidative disinfection methods are usually inefficient to eliminate intracellular antibiotic resistance genes (i-ARGs) due to competitive oxidation of cellular components of antibiotic-resistant bacteria (ARB), resulting in the ubiquitous occurrence of ARGs in drinking water systems. Herein, we developed the strategy of coupling electroporation and electrochemical oxidation on a Co3O4-nanowires-modified electrode to destroy the multiresistant Escherichia coli cells and promote subsequent i-ARG (blaTEM-1 and aac(3)-II) degradation. The lightning-rod effect over nanowire tips can form finite regions with a locally enhanced electric field and highly concentrated charge density, in turn facilitating the electroporation for ARB cell damage and electrochemical reactivity for reactive chlorine/oxygen species generation. Characterization of the ARB membrane integrity and morphology revealed that electroporation-induced cell pores were further enlarged by the oxidation of reactive species, resulting in i-ARG removal at lower applied voltages and with 6-9 times lower energy consumption than the conventional electrochemical oxidation approach with a Co3O4-film-modified electrode. The satisfactory application and effective inhibition of horizontal gene transfer in tap water further demonstrated the great potential of our strategy in the control of the ARG dissemination risk in drinking water systems.}, }
@article {pmid36714980, year = {2023}, author = {Cheng, YY and Zhou, Z and Papadopoulos, JM and Zuke, JD and Falbel, TG and Anantharaman, K and Burton, BM and Venturelli, OS}, title = {Efficient plasmid transfer via natural competence in a microbial co-culture.}, journal = {Molecular systems biology}, volume = {19}, number = {3}, pages = {e11406}, pmid = {36714980}, issn = {1744-4292}, support = {R35GM124774//HHS &#xa6; NIH &#xa6; National Institute of General Medical Sciences (NIGMS)/ ; T32 GM007215/GM/NIGMS NIH HHS/United States ; }, mesh = {Coculture Techniques ; Plasmids/genetics ; *DNA ; *Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; }, abstract = {The molecular and ecological factors shaping horizontal gene transfer (HGT) via natural transformation in microbial communities are largely unknown, which is critical for understanding the emergence of antibiotic-resistant pathogens. We investigate key factors shaping HGT in a microbial co-culture by quantifying extracellular DNA release, species growth, and HGT efficiency over time. In the co-culture, plasmid release and HGT efficiency are significantly enhanced than in the respective monocultures. The donor is a key determinant of HGT efficiency as plasmids induce the SOS response, enter a multimerized state, and are released in high concentrations, enabling efficient HGT. However, HGT is reduced in response to high donor lysis rates. HGT is independent of the donor viability state as both live and dead cells transfer the plasmid with high efficiency. In sum, plasmid HGT via natural transformation depends on the interplay of plasmid properties, donor stress responses and lysis rates, and interspecies interactions.}, }
@article {pmid36714722, year = {2022}, author = {Zhu, X and Chen, WJ and Bhatt, K and Zhou, Z and Huang, Y and Zhang, LH and Chen, S and Wang, J}, title = {Innovative microbial disease biocontrol strategies mediated by quorum quenching and their multifaceted applications: A review.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {1063393}, pmid = {36714722}, issn = {1664-462X}, abstract = {With the increasing resistance exhibited by undesirable bacteria to traditional antibiotics, the need to discover alternative (or, at least, supplementary) treatments to combat chemically resistant bacteria is becoming urgent. Quorum sensing (QS) refers to a novel bacterial communication system for monitoring cell density and regulation of a network of gene expression that is mediated by a group of signaling molecules called autoinducers (AIs). QS-regulated multicellular behaviors include biofilm formation, horizontal gene transfer, and antibiotic synthesis, which are demonstrating increasing pathogenicity to plants and aquacultural animals as well as contamination of wastewater treatment devices. To inhibit QS-regulated microbial behaviors, the strategy of quorum quenching (QQ) has been developed. Different quorum quenchers interfere with QS through different mechanisms, such as competitively inhibiting AI perception (e.g., by QS inhibitors) and AI degradation (e.g., by QQ enzymes). In this review, we first introduce different signaling molecules, including diffusible signal factor (DSF) and acyl homoserine lactones (AHLs) for Gram-negative bacteria, AIPs for Gram-positive bacteria, and AI-2 for interspecies communication, thus demonstrating the mode of action of the QS system. We next exemplify the QQ mechanisms of various quorum quenchers, such as chemical QS inhibitors, and the physical/enzymatic degradation of QS signals. We devote special attention to AHL-degrading enzymes, which are categorized in detail according to their diverse catalytic mechanisms and enzymatic properties. In the final part, the applications and advantages of quorum quenchers (especially QQ enzymes and bacteria) are summarized in the context of agricultural/aquacultural pathogen biocontrol, membrane bioreactors for wastewater treatment, and the attenuation of human pathogenic bacteria. Taken together, we present the state-of-the-art in research considering QS and QQ, providing theoretical evidence and support for wider application of this promising environmentally friendly biocontrol strategy.}, }
@article {pmid36712336, year = {2022}, author = {Kuroyanagi, T and Bulasag, AS and Fukushima, K and Ashida, A and Suzuki, T and Tanaka, A and Camagna, M and Sato, I and Chiba, S and Ojika, M and Takemoto, D}, title = {Botrytis cinerea identifies host plants via the recognition of antifungal capsidiol to induce expression of a specific detoxification gene.}, journal = {PNAS nexus}, volume = {1}, number = {5}, pages = {pgac274}, pmid = {36712336}, issn = {2752-6542}, abstract = {The gray mold pathogen Botrytis cinerea has a broad host range, causing disease in >400 plant species, but it is not known how this pathogen evolved this polyxenous nature. Botrytis cinerea can metabolize a wide range of phytoalexins, including the stilbenoid resveratrol in grape, and the sesquiterpenoids capsidiol in tobacco and rishitin in potato and tomato. In this study, we analyzed the metabolism of sesquiterpenoid phytoalexins by B. cinerea. Capsidiol was dehydrogenated to capsenone, which was then further oxidized, while rishitin was directly oxidized to epoxy- or hydroxyrishitins, indicating that B. cinerea has separate mechanisms to detoxify structurally similar sesquiterpenoid phytoalexins. RNA-seq analysis revealed that a distinct set of genes were induced in B. cinerea when treated with capsidiol or rishitin, suggesting that B. cinerea can distinguish structurally similar phytoalexins to activate appropriate detoxification mechanisms. The gene most highly upregulated by capsidiol treatment encoded a dehydrogenase, designated Bccpdh. Heterologous expression of Bccpdh in a capsidiol-sensitive plant symbiotic fungus, Epichloë festucae, resulted in an acquired tolerance of capsidiol and the ability to metabolize capsidiol to capsenone, while B. cinerea Δbccpdh mutants became relatively sensitive to capsidiol. The Δbccpdh mutant showed reduced virulence on the capsidiol producing Nicotiana and Capsicum species but remained fully pathogenic on potato and tomato. Homologs of Bccpdh are found in taxonomically distant Ascomycota fungi but not in related Leotiomycetes species, suggesting that B. cinerea acquired the ancestral Bccpdh by horizontal gene transfer, thereby extending the pathogenic host range of this polyxenous pathogen to capsidiol-producing plant species.}, }
@article {pmid36708845, year = {2023}, author = {Xiao, R and Huang, D and Du, L and Song, B and Yin, L and Chen, Y and Gao, L and Li, R and Huang, H and Zeng, G}, title = {Antibiotic resistance in soil-plant systems: A review of the source, dissemination, influence factors, and potential exposure risks.}, journal = {The Science of the total environment}, volume = {869}, number = {}, pages = {161855}, doi = {10.1016/j.scitotenv.2023.161855}, pmid = {36708845}, issn = {1879-1026}, mesh = {Humans ; *Soil/chemistry ; *Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Soil Microbiology ; }, abstract = {As an emerging environmental contaminant, the widespread of antibiotic resistance has caused a series of environmental issues and human health concerns. A load of antibiotic residues induced by agricultural practices have exerted selective pressure to bacterial communities in the soil-plant system, which facilitated the occurrence and dissemination of antibiotic resistance genes (ARGs) through horizontal gene transfer. As a result, the enrichment of ARGs within crops at harvest under the influence of food ingestion could lead to critical concerns of public health. In this review, the prevalence and dissemination of antibiotic resistance in the soil-plant system are highlighted. Moreover, different underlying mechanisms and detection methods for ARGs transfer between the soil environment and plant compartments are summarized and discussed. On the other hand, a wide range of influencing factors for the transfer and distribution of antibiotic resistance within the soil-plant system are also presented and discussed. In response to exposure of antibiotic residues and resistomes, corresponding hazard identification assessments have been summarized, which could provide beneficial guides of the toxicological tolerance for the general population. Finally, further research priorities for detection and management ARGs spread are also suggested.}, }
@article {pmid36706177, year = {2023}, author = {Melamed, JR and Yerneni, SS and Arral, ML and LoPresti, ST and Chaudhary, N and Sehrawat, A and Muramatsu, H and Alameh, MG and Pardi, N and Weissman, D and Gittes, GK and Whitehead, KA}, title = {Ionizable lipid nanoparticles deliver mRNA to pancreatic β cells via macrophage-mediated gene transfer.}, journal = {Science advances}, volume = {9}, number = {4}, pages = {eade1444}, pmid = {36706177}, issn = {2375-2548}, support = {R01 AI153064/AI/NIAID NIH HHS/United States ; F32 EB029345/EB/NIBIB NIH HHS/United States ; DP2 HD098860/HD/NICHD NIH HHS/United States ; R01 AI124429/AI/NIAID NIH HHS/United States ; U19 AI142596/AI/NIAID NIH HHS/United States ; R01 AI146101/AI/NIAID NIH HHS/United States ; }, mesh = {RNA, Messenger/genetics ; *Insulin-Secreting Cells ; Lipids ; *Nanoparticles ; Macrophages ; }, abstract = {Systemic messenger RNA (mRNA) delivery to organs outside the liver, spleen, and lungs remains challenging. To overcome this issue, we hypothesized that altering nanoparticle chemistry and administration routes may enable mRNA-induced protein expression outside of the reticuloendothelial system. Here, we describe a strategy for delivering mRNA potently and specifically to the pancreas using lipid nanoparticles. Our results show that delivering lipid nanoparticles containing cationic helper lipids by intraperitoneal administration produces robust and specific protein expression in the pancreas. Most resultant protein expression occurred within insulin-producing β cells. Last, we found that pancreatic mRNA delivery was dependent on horizontal gene transfer by peritoneal macrophage exosome secretion, an underappreciated mechanism that influences the delivery of mRNA lipid nanoparticles. We anticipate that this strategy will enable gene therapies for intractable pancreatic diseases such as diabetes and cancer.}, }
@article {pmid36695602, year = {2023}, author = {Anderson, REV and Chalmers, G and Murray, R and Mataseje, L and Pearl, DL and Mulvey, M and Topp, E and Boerlin, P}, title = {Characterization of Escherichia coli and Other Enterobacterales Resistant to Extended-Spectrum Cephalosporins Isolated from Dairy Manure in Ontario, Canada.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {2}, pages = {e0186922}, pmid = {36695602}, issn = {1098-5336}, mesh = {Animals ; Cattle ; Humans ; *Cephalosporins/pharmacology ; Escherichia coli/genetics ; Manure ; Anti-Bacterial Agents/pharmacology ; Ontario ; Multilocus Sequence Typing ; Phylogeny ; beta-Lactamases/genetics ; *Escherichia coli Infections/microbiology ; Plasmids/genetics ; }, abstract = {Extended-spectrum cephalosporins (ESCs) resistance genes, such as blaCTX-M, blaCMY, and blaSHV, have been found regularly in bacteria from livestock. However, information on their distribution in dairy cattle in Canada and on the associated genome sequences of ESC-resistant Enterobacterales is sparse. In this study, the diversity and distribution of ESC-resistant Escherichia coli throughout manure treatments in six farms in Southern Ontario were assessed over a one-year period, and their ESC-resistance plasmids were characterized. The manure samples were enriched using selective media. The resulting isolates were screened via polymerase chain reaction for blaCTX-M, blaCMY, and blaSHV. No E. coli carrying blaSHV were detected. Escherichia coli (n = 248) carrying blaCTX-M or blaCMY underwent whole-genome sequencing using an Illumina MiSeq/NextSeq. These isolates were typed using multilocus sequence typing (MLST) and their resistance gene profiles. A subset of E. coli (n = 28) were sequenced using Oxford Nanopore Technologies. Plasmids were assembled using Unicycler and characterized via the resistance genes pattern, replicon type, plasmid MLST, phylogenetic analysis, and Mauve alignments. The recovery of ESC-resistant Enterobacterales (18 species, 8 genera) was drastically reduced in manure outputs. However, multiple treatment stages were needed to attain a significant reduction. 62 sequence types were identified, with ST10, ST46, ST58, ST155, ST190, ST398, ST685, and ST8761 being detected throughout the treatment pipeline. These STs overlapped with those found on multiple farms. The ESC-resistance determinants included CTX-M-1, -14, -15, -17, -24, -32, -55, and CMY-2. The plasmids carrying blaCTX-M were more diverse than were the plasmids carrying blaCMY. Known "epidemic plasmids" were detected for both blaCTX-M and blaCMY. IMPORTANCE The increase in antimicrobial resistance is of concern for human and animal health, especially when resistance is conferred to extended-spectrum cephalosporins, which are used to treat serious infections in both human and veterinary medicine. Bacteria carrying extended-spectrum cephalosporin resistance genes, including blaCTX-M and blaCMY, are frequently found in dairy manure. Manure treatment influences the loads and diversity of bacteria, including those carrying antimicrobial resistance genes, such as Enterobacterales and Escherichia coli. Any bacteria that survive the treatment process are subsequently applied to the environment. Enterobacterales carrying blaCTX-M or blaCMY can contaminate soil and crops consumed by humans and animals, thereby increasing the potential for antimicrobial resistance genes to integrate into the human gut microflora through horizontal gene transfer. This furthers the dissemination of resistance. Therefore, it is imperative to understand the effects manure treatments have on ESC-resistance in environmentally applied manure.}, }
@article {pmid36692711, year = {2023}, author = {Li, Y and Xiong, L and Yu, H and Xiang, Y and Wei, Y and Zhang, Q and Ji, X}, title = {Biogeochemical sulfur cycling of virus auxiliary metabolic genes involved in Napahai plateau wetland.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {15}, pages = {44430-44438}, pmid = {36692711}, issn = {1614-7499}, support = {32160294//Innovative Research Group Project of the National Natural Science Foundation of China/ ; 31860147//Innovative Research Group Project of the National Natural Science Foundation of China/ ; }, mesh = {*Wetlands ; Phylogeny ; Oxidation-Reduction ; *Microbiota ; Sulfur/metabolism ; }, abstract = {Virus plays important roles in regulating microbial community structure, horizontal gene transfer, and promoting biological evolution, also augmenting host metabolism during infection via the expression of auxiliary metabolic genes (AMGs), and thus affect biogeochemical cycling in the oceans. As the "kidney of the earth," wetlands have rich biodiversity and abundant resources. Based on metagenomic data, 10 AMGs associated with sulfur cycling, i.e., tusA, moaD, dsrE, soxA, soxB, soxC, soxD, soxX, soxY, and soxZ, were analyzed in Napahai plateau wetland. The phylogenetic trees of AMGs involved in sulfur metabolism from different habitats and host origins were constructed. Combined with principal coordinate analysis, it revealed that most AMGs associated with sulfur metabolism clustered separately, indicating the abundance and uniqueness in this region. The sulfur metabolism pathways involved by AMGs were mainly SOX systems, among which sulfur oxidation was associated with moaD and dsrE genes, while sulfur transport was related to tusA genes. It provides an insight into the biogeochemical sulfur cycling in plateau wetlands and lays the foundation for further study on the co-evolution of virus and host.}, }
@article {pmid36692352, year = {2023}, author = {Chen, M and Shao, Y and Luo, J and Yuan, L and Wang, M and Chen, M and Guo, Q}, title = {Penicillin and Cefotaxime Resistance of Quinolone-Resistant Neisseria meningitidis Clonal Complex 4821, Shanghai, China, 1965-2020.}, journal = {Emerging infectious diseases}, volume = {29}, number = {2}, pages = {341-350}, pmid = {36692352}, issn = {1080-6059}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Neisseria meningitidis/genetics ; Penicillins ; *Quinolones/pharmacology ; Cefotaxime/pharmacology ; China/epidemiology ; Neisseria/genetics ; Microbial Sensitivity Tests ; Anti-Bacterial Agents/pharmacology ; Penicillin Resistance/genetics ; }, abstract = {Clonal complex 4821 (CC4821) Neisseria meningitidis, usually resistant to quinolones but susceptible to penicillin and third-generation cephalosporins, is increasing worldwide. To characterize the penicillin-nonsusceptible (Pen[NS]) meningococci, we analyzed 491 meningococci and 724 commensal Neisseria isolates in Shanghai, China, during 1965-2020. The Pen[NS] proportion increased from 0.3% in 1965-1985 to 7.0% in 2005-2014 and to 33.3% in 2015-2020. Of the 26 Pen[NS] meningococci, 11 (42.3%) belonged to the CC4821 cluster; all possessed mutations in penicillin-binding protein 2, mostly from commensal Neisseria. Genetic analyses and transformation identified potential donors of 6 penA alleles. Three Pen[NS] meningococci were resistant to cefotaxime, 2 within the CC4821 cluster. With 96% of the Pen[NS] meningococci beyond the coverage of scheduled vaccination and the cefotaxime-resistant isolates all from toddlers, quinolone-resistant CC4821 has acquired penicillin and cefotaxime resistance closely related to the internationally disseminated ceftriaxone-resistant gonococcal FC428 clone, posing a greater threat especially to young children.}, }
@article {pmid36690118, year = {2023}, author = {Yue, Z and Zhang, J and Ding, C and Wang, Y and Zhou, Z and Yu, X and Zhang, T and Wang, X}, title = {Transfer and distribution of antibiotic resistance genes in the soil-peanut system receiving manure for years.}, journal = {The Science of the total environment}, volume = {869}, number = {}, pages = {161742}, doi = {10.1016/j.scitotenv.2023.161742}, pmid = {36690118}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Soil ; Arachis ; Genes, Bacterial ; Manure/analysis ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Drug Resistance, Microbial/genetics ; }, abstract = {Antibiotic resistance gene (ARG)-contaminated food from manure application is gaining widespread interest, but little is known about the distribution and uptake of ARGs in peanuts that are subjected to manure routinely. In this study, the ARG profile and bacterial community in soil and peanut plants from a 7-year manure-fertilized field were investigated using high-throughput qPCR and 16S rRNA gene sequencing. Manure application increased the abundance of ARGs in soil and peanuts by 59-72 and 4-10 fold, respectively. The abundance of ARGs from high to low was as follows: manure, shell-sphere soil, rhizosphere soil, bulk soil, stems, shells, needles, kernels, and roots. Source-tracker analyses were used to investigate the potential source of ARGs in peanut kernels, which revealed that the ARGs in peanut kernels may be primarily absorbed by the roots from the soil. The horizontal gene transfer (HGT) of ARGs was the primary factor in the spread of ARGs, and Proteobacteria were the primary agents of HGT between different parts of peanut plants. Additionally, norank_Chloroplast from the phylum Cyanobacteria was the most important contributor to the abundance of ARGs in peanut kernels. Overall, our findings fill a gap in our understanding of the distribution patterns of ARGs in peanut plants and the migratory pathways of ARGs from soil to peanut kernels.}, }
@article {pmid36689882, year = {2023}, author = {An, R and Qi, Y and Zhang, XX and Ma, L}, title = {Xenogenetic evolutionary of integrons promotes the environmental pollution of antibiotic resistance genes - Challenges, progress and prospects.}, journal = {Water research}, volume = {231}, number = {}, pages = {119629}, doi = {10.1016/j.watres.2023.119629}, pmid = {36689882}, issn = {1879-2448}, mesh = {Humans ; *Integrons/genetics ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Genes, Bacterial ; Environmental Pollution ; }, abstract = {Environmental pollution of antibiotic resistance genes (ARGs) has been a great public concern. Integrons, as mobile genetic elements, with versatile gene acquisition systems facilitate the horizontal gene transfer (HGT) and pollution disseminations of ARGs. However, little is understood about the characteristics of ARGs mediated by integrons, which hampers our monitoring and control of the mobile antimicrobial resistance risks. To address these issues, we reviewed 3,322 publications concerning detection methods and pipeline, ARG diversity and evolutionary progress, environmental and geographical distribution, bacterial hosts, gene cassettes arrangements, and based on which to identify ARGs with high risk levels mediated by integrons. Diverse ARGs of 516 subtypes attributed to 12 types were capable of being carried by integrons, with 62 core ARG subtypes prevalent in pollution source, natural and human-related environments. Hosts of ARG-carrying integrons reached 271 bacterial species, most frequently carried by opportunistic pathogens Escherichia coli, Pseudomonas aeruginosa and Klebsiella pneumoniae. Moreover, the observed emergence of ARGs together with their multiple arrangements indicated the accumulation of ARGs mediated by integrons, and thus pose increasing HGT risks under modern selective agents. With the concerns of public health, we urgently call for a better monitoring and control of these high-risk ARGs. Our identified Risk Rank I ARGs (aacA7, blaOXA10, catB3, catB8, dfrA5) with high mobility, reviewed key trends and noteworthy advancements, and proposed future directions could be reference and guidance for standard formulation.}, }
@article {pmid36688638, year = {2023}, author = {Bhandari, M and Rathnayake, IU and Huygens, F and Jennison, AV}, title = {Clinical and Environmental Vibrio cholerae Non-O1, Non-O139 Strains from Australia Have Similar Virulence and Antimicrobial Resistance Gene Profiles.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0263122}, pmid = {36688638}, issn = {2165-0497}, mesh = {Humans ; *Cholera/epidemiology/microbiology ; *Vibrio cholerae non-O1/genetics ; Virulence/genetics ; Anti-Bacterial Agents/pharmacology ; Serogroup ; Phylogeny ; Travel ; Genetic Variation ; Drug Resistance, Bacterial/genetics ; }, abstract = {Cholera caused by pathogenic Vibrio cholerae is still considered one of the major health problems in developing countries including those in Asia and Africa. Australia is known to have unique V. cholerae strains in Queensland waterways, resulting in sporadic cholera-like disease being reported in Queensland each year. We conducted virulence and antimicrobial genetic characterization of O1 and non-O1, non-O139 V. cholerae (NOVC) strains (1983 to 2020) from Queensland with clinical significance and compared these to environmental strains that were collected as part of a V. cholerae monitoring project in 2012 of Queensland waterways. In this study, 87 V. cholerae strains were analyzed where O1 (n = 5) and NOVC (n = 54) strains from Queensland and international travel-associated NOVC (n = 2) (61 in total) strains were sequenced, characterized, and compared with seven previously sequenced O1 strains and 18 other publicly available NOVC strains from Australia and overseas to visualize the genetic context among them. Of the 61 strains, three clinical and environmental NOVC serogroup strains had cholera toxin-producing genes, namely, the CTX phage (identified in previous outbreaks) and the complete Vibrio pathogenicity island 1. Phylogenetic analysis based on core genome analysis showed more than 10 distinct clusters and interrelatedness between clinical and environmental V. cholerae strains from Australia. Moreover, 30 (55%) NOVC strains had the cholix toxin gene (chxA) while only 11 (20%) strains had the mshA gene. In addition, 18 (34%) NOVC strains from Australia had the type three secretion system and discrete expression of type six secretion system genes. Interestingly, four NOVC strains from Australia and one NOVC strain from Indonesia had intSXT, a mobile genetic element. Several strains were found to have beta-lactamase (blaCARB-9) and chloramphenicol acetyltransferase (catB9) genes. Our study suggests that Queensland waterways can harbor highly divergent V. cholerae strains and serve as a reservoir for various V. cholerae-associated virulence genes which could be shared among O1 and NOVC V. cholerae strains via mobile genetic elements or horizontal gene transfer. IMPORTANCE Australia has its own V. cholerae strains, both toxigenic and nontoxigenic, that are associated with cholera disease. This study aimed to characterize a collection of clinical and environmental NOVC strains from Australia to understand their virulence and antimicrobial resistance profile and to place strains from Australia in the genetic context of international strains. The findings from this study suggest the toxigenic V. cholerae strains in the Queensland River water system are of public health concern. Therefore, ongoing monitoring and genomic characterization of V. cholerae strains from the Queensland environment are important and would assist public health departments to track the source of cholera infection early and implement prevention strategies for future outbreaks. Understanding the genomics of V. cholerae could also inform the natural ecology and evolution of this bacterium in natural environments.}, }
@article {pmid36685277, year = {2022}, author = {Gomis-Rüth, FX and Stöcker, W}, title = {Structural and evolutionary insights into astacin metallopeptidases.}, journal = {Frontiers in molecular biosciences}, volume = {9}, number = {}, pages = {1080836}, pmid = {36685277}, issn = {2296-889X}, abstract = {The astacins are a family of metallopeptidases (MPs) that has been extensively described from animals. They are multidomain extracellular proteins, which have a conserved core architecture encompassing a signal peptide for secretion, a prodomain or prosegment and a zinc-dependent catalytic domain (CD). This constellation is found in the archetypal name-giving digestive enzyme astacin from the European crayfish Astacus astacus. Astacin catalytic domains span ∼200 residues and consist of two subdomains that flank an extended active-site cleft. They share several structural elements including a long zinc-binding consensus sequence (HEXXHXXGXXH) immediately followed by an EXXRXDRD motif, which features a family-specific glutamate. In addition, a downstream SIMHY-motif encompasses a "Met-turn" methionine and a zinc-binding tyrosine. The overall architecture and some structural features of astacin catalytic domains match those of other more distantly related MPs, which together constitute the metzincin clan of metallopeptidases. We further analysed the structures of PRO-, MAM, TRAF, CUB and EGF-like domains, and described their essential molecular determinants. In addition, we investigated the distribution of astacins across kingdoms and their phylogenetic origin. Through extensive sequence searches we found astacin CDs in > 25,000 sequences down the tree of life from humans beyond Metazoa, including Choanoflagellata, Filasterea and Ichtyosporea. We also found < 400 sequences scattered across non-holozoan eukaryotes including some fungi and one virus, as well as in selected taxa of archaea and bacteria that are pathogens or colonizers of animal hosts, but not in plants. Overall, we propose that astacins originate in the root of Holozoa consistent with Darwinian descent and that the latter genes might be the result of horizontal gene transfer from holozoan donors.}, }
@article {pmid36684780, year = {2022}, author = {Wang, Y and Shahid, MQ}, title = {Genome sequencing and resequencing identified three horizontal gene transfers and uncovered the genetic mechanism on the intraspecies adaptive evolution of Gastrodia elata Blume.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {1035157}, pmid = {36684780}, issn = {1664-462X}, abstract = {Horizontal gene transfer is a rare and useful genetic mechanism in higher plants. Gastrodia elata Blume (GE) (Orchidaceae), well known as traditional medicinal material in East Asia, adopts a heterotrophic lifestyle, thus being considered to be more prone to horizontal gene transfer (HGT). GE is a "polytypic species" that currently comprised of five recognized forms according to the plant morphology. G. elata Blume forma elata (GEE) and G. elata Bl.f.glauca (GEG) are two common forms that naturally grow in different habitats with difference in altitude and latitude. G. elata Bl.f.viridis (GEV) often occurs sporadically in cultivated populations of GEE and GEG. However, the genetic relationships and genetic mechanism underpinned the divergent ecological adaptations of GEE and GEG have not been revealed. Here, we assembled a chromosome-level draft genome of GEE with 1.04 Gb. Among predicted 17,895 protein coding genes, we identified three HGTs. Meanwhile, we resequenced 10 GEE accessions, nine GEG accessions, and 10 GEV accessions, and identified two independent genetic lineages: GEG_pedigree (GEG individuals and GEV individuals collected from GEG populations) and GEE_pedigree (GEE individuals and GEV individuals collected from GEE populations), which strongly support the taxonomic status of GEE and GEG as subspecies, not as different forms. In highly differentiated genomic regions of GEE_pedigree and GEG_pedigree, three chalcone synthase-encoding genes and one Phox/Bem1p (PB1) domain of encoding Auxin (AUX)/Indoleacetic acid (IAA) were identified in selection sweeping genome regions, which suggested that differentiation between GEE_pedigree and GEG_pedigree was promoted by the selection of genes related to photoresponse and growth and development. Overall, this new genome would be helpful for breeding and utilization of GE and the new findings would deepen the understanding about ecological adaptation and evolution of GE.}, }
@article {pmid36680934, year = {2023}, author = {Tang, Y and Shi, Y and Jia, B and Zhang, Y and Wang, Q}, title = {Evolution and function analysis of glycerol kinase GlpK in Pseudomonasaeruginosa.}, journal = {Biochemical and biophysical research communications}, volume = {645}, number = {}, pages = {30-39}, doi = {10.1016/j.bbrc.2022.12.060}, pmid = {36680934}, issn = {1090-2104}, mesh = {Humans ; Glycerol/metabolism ; *Glycerol Kinase/genetics/metabolism ; Phosphorylation ; *Pseudomonas aeruginosa/enzymology/genetics ; Bacterial Proteins/genetics/metabolism ; }, abstract = {Pseudomonas aeruginosa is a Gram-negative bacterium capable of widespread niches, which is also one of the main bacteria that cause patient infection. The metabolic diversity of Pseudomonas aeruginosa is an essential factor in adapting to a variety of environments. Based on the previous studies, adaptive genetic variation in the glycerol kinase GlpK, the glycerol 3-phosphotransferase, contributes to the fitness of bacteria in human bodies, such as Mycobacterium tuberculosis and Escherichia coli. Thus, this study aimed to explore the molecular evolution and function of glpK in P. aeruginosa. Using extensive population genomic data, we have identified the prevalence of two glpK copies in P. aeruginosa that clustered into distinct branches, which were later known as Clade 1 and 2. The evolution analysis revealed that glpK in Clade 1 derived from an ancestral P. aeruginosa species and the other from an ancient horizontal gene transfer event. In addition, we confirmed that the GlpK in Clade 2 still retained glycerol kinase activity but was much weaker than that of GlpK in Clade 1. We demonstrated the importance of the critical amino acid Q70 in GlpK glycerol kinase activity by point mutation. Furthermore, Co-expression network analysis implied that the two glpK copies of P. aeruginosa regulate separate networks and may be a strategy to improve fitness in P. aeruginosa.}, }
@article {pmid36680256, year = {2023}, author = {Pchelin, IM and Tkachev, PV and Azarov, DV and Gorshkov, AN and Drachko, DO and Zlatogursky, VV and Dmitriev, AV and Goncharov, AE}, title = {A Genome of Temperate Enterococcus Bacteriophage Placed in a Space of Pooled Viral Dark Matter Sequences.}, journal = {Viruses}, volume = {15}, number = {1}, pages = {}, pmid = {36680256}, issn = {1999-4915}, mesh = {Humans ; *Bacteriophages ; Enterococcus/genetics ; Genome, Viral ; Sequence Analysis, DNA ; Phylogeny ; Myoviridae/genetics ; }, abstract = {In the human gut, temperate bacteriophages interact with bacteria through predation and horizontal gene transfer. Relying on taxonomic data, metagenomic studies have associated shifts in phage abundance with a number of human diseases. The temperate bacteriophage VEsP-1 with siphovirus morphology was isolated from a sample of river water using Enterococcus faecalis as a host. Starting from the whole genome sequence of VEsP-1, we retrieved related phage genomes in blastp searches of the tail protein and large terminase sequences, and blastn searches of the whole genome sequences, with matches compiled from several different databases, and visualized a part of viral dark matter sequence space. The genome network and phylogenomic analyses resulted in the proposal of a novel genus "Vespunovirus", consisting of temperate, mainly metagenomic phages infecting Enterococcus spp.}, }
@article {pmid36677319, year = {2022}, author = {Shivaramu, S and Tomasch, J and Kopejtka, K and Nupur,  and Saini, MK and Bokhari, SNH and Küpper, H and Koblížek, M}, title = {The Influence of Calcium on the Growth, Morphology and Gene Regulation in Gemmatimonas phototrophica.}, journal = {Microorganisms}, volume = {11}, number = {1}, pages = {}, pmid = {36677319}, issn = {2076-2607}, abstract = {The bacterium Gemmatimonas phototrophica AP64 isolated from a freshwater lake in the western Gobi Desert represents the first phototrophic member of the bacterial phylum Gemmatimonadota. This strain was originally cultured on agar plates because it did not grow in liquid medium. In contrast, the closely related species G. groenlandica TET16 grows both on solid and in liquid media. Here, we show that the growth of G. phototrophica in liquid medium can be induced by supplementing the medium with 20 mg CaCl2 L[-1]. When grown at a lower concentration of calcium (2 mg CaCl2 L[-1]) in the liquid medium, the growth was significantly delayed, cells were elongated and lacked flagella. The elevated requirement for calcium is relatively specific as it can be partially substituted by strontium, but not by magnesium. The transcriptome analysis documented that several groups of genes involved in flagella biosynthesis and transport of transition metals were co-activated after amendment of 20 mg CaCl2 L[-1] to the medium. The presented results document that G. phototrophica requires a higher concentration of calcium for its metabolism and growth compared to other Gemmatimonas species.}, }
@article {pmid36676100, year = {2023}, author = {Lila, ASA and Rajab, AAH and Abdallah, MH and Rizvi, SMD and Moin, A and Khafagy, ES and Tabrez, S and Hegazy, WAH}, title = {Biofilm Lifestyle in Recurrent Urinary Tract Infections.}, journal = {Life (Basel, Switzerland)}, volume = {13}, number = {1}, pages = {}, pmid = {36676100}, issn = {2075-1729}, abstract = {Urinary tract infections (UTIs) represent one of the most common infections that are frequently encountered in health care facilities. One of the main mechanisms used by bacteria that allows them to survive hostile environments is biofilm formation. Biofilms are closed bacterial communities that offer protection and safe hiding, allowing bacteria to evade host defenses and hide from the reach of antibiotics. Inside biofilm communities, bacteria show an increased rate of horizontal gene transfer and exchange of resistance and virulence genes. Additionally, bacterial communication within the biofilm allows them to orchestrate the expression of virulence genes, which further cements the infestation and increases the invasiveness of the infection. These facts stress the necessity of continuously updating our information and understanding of the etiology, pathogenesis, and eradication methods of this growing public health concern. This review seeks to understand the role of biofilm formation in recurrent urinary tact infections by outlining the mechanisms underlying biofilm formation in different uropathogens, in addition to shedding light on some biofilm eradication strategies.}, }
@article {pmid36675876, year = {2022}, author = {Li, Y and Qi, M and Zhang, Q and Xu, Z and Zhang, Y and Gao, Y and Qi, Y and Qiu, L and Wang, M}, title = {Phylogenesis of the Functional 1-Aminocyclopropane-1-Carboxylate Oxidase of Fungi and Plants.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {1}, pages = {}, pmid = {36675876}, issn = {2309-608X}, support = {202102110044//the Science and Technology Department of Henan Province/ ; 222102110302//the Science and Technology Department of Henan Province/ ; 32102455//the National Natural Science Foundation of China/ ; }, abstract = {The 1-aminocyclopropane-1-carboxylic acid (ACC) pathway that synthesizes ethylene is shared in seed plants, fungi and probably other organisms. However, the evolutionary relationship of the key enzyme ACC oxidase (ACO) in the pathway among organisms remains unknown. Herein, we cloned, expressed and characterized five ACOs from the straw mushroom (Volvariella volvacea) and the oyster mushroom (Pleurotus ostreatus): VvACO1-4 and PoACO. The five mushroom ACOs and the previously identified AbACO of the button mushroom contained all three conserved residues that bound to Fe(II) in plant ACOs. They also had variable residues that were conserved and bound to ascorbate and bicarbonate in plant ACOs and harbored only 1-2 of the five conserved ACO motifs in plant ACOs. Particularly, VvACO2 and AbACO had only one ACO motif 2. Additionally, VvACO4 shared 44.23% sequence identity with the cyanobacterium Hapalosiphon putative functional ACO. Phylogenetic analysis showed that the functional ACOs of monocotyledonous and dicotyledonous plants co-occurred in Type I, Type II and Type III, while putative functional gymnosperm ACOs also appeared in Type III. The putative functional bacterial ACO, functional fungi and slime mold ACOs were clustered in ancestral Type IV. These results indicate that ACO motif 2, ACC and Fe(II) are essential for ACO activity. The ACOs of the other organisms may come from the horizontal transfer of fungal ACOs, which were found ordinarily in basidiomycetes. It is mostly the first case for the horizontal gene transfers from fungi to seed plants. The horizontal transfer of ACOs from fungi to plants probably facilitates the fungal-plant symbioses, plant-land colonization and further evolution to form seeds.}, }
@article {pmid36671285, year = {2023}, author = {Canellas, ALB and de Oliveira, BFR and Laport, MS}, title = {Hiding in Plain Sight: Characterization of Aeromonas Species Isolated from a Recreational Estuary Reveals the Carriage and Putative Dissemination of Resistance Genes.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {1}, pages = {}, pmid = {36671285}, issn = {2079-6382}, support = {306395/2020-7//National Council for Scientific and Technological Development/ ; E-26/200.948/2021//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; E-26/211.284/2021//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; 88887.613830/2021-00//Coordena&#xe7;&#xe3;o de Aperfeicoamento de Pessoal de N&#xed;vel Superior/ ; code 001//Coordena&#xe7;&#xe3;o de Aperfeicoamento de Pessoal de N&#xed;vel Superior/ ; E26/211.554/2019//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; }, abstract = {Antimicrobial resistance (AMR) has become one of the greatest challenges worldwide, hampering the treatment of a plethora of infections. Indeed, the AMR crisis poses a threat to the achievement of the United Nations' Sustainable Development Goals and, due to its multisectoral character, a holistic approach is needed to tackle this issue. Thus, the investigation of environments beyond the clinic is of utmost importance. Here, we investigated thirteen strains of antimicrobial-resistant Aeromonas isolated from an urban estuary in Brazil. Most strains carried at least one antimicrobial resistance gene and 11 carried at least one heavy metal resistance gene. Noteworthy, four (30.7%) strains carried the blaKPC gene, coding for a carbapenemase. In particular, the whole-genome sequence of Aeromonas hydrophila strain 34SFC-3 was determined, revealing not only the presence of antimicrobial and heavy metal resistance genes but also a versatile virulome repertoire. Mobile genetic elements, including insertion sequences, transposons, integrative conjugative elements, and an IncQ1 plasmid were also detected. Considering the ubiquity of Aeromonas species, their genetic promiscuity, pathogenicity, and intrinsic features to endure environmental stress, our findings reinforce the concept that A. hydrophila truly is a "Jack of all trades'' that should not be overlooked under the One Health perspective.}, }
@article {pmid36671228, year = {2022}, author = {Selvarajan, R and Obize, C and Sibanda, T and Abia, ALK and Long, H}, title = {Evolution and Emergence of Antibiotic Resistance in Given Ecosystems: Possible Strategies for Addressing the Challenge of Antibiotic Resistance.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {1}, pages = {}, pmid = {36671228}, issn = {2079-6382}, abstract = {Antibiotics were once considered the magic bullet for all human infections. However, their success was short-lived, and today, microorganisms have become resistant to almost all known antimicrobials. The most recent decade of the 20th and the beginning of the 21st century have witnessed the emergence and spread of antibiotic resistance (ABR) in different pathogenic microorganisms worldwide. Therefore, this narrative review examined the history of antibiotics and the ecological roles of antibiotics, and their resistance. The evolution of bacterial antibiotic resistance in different environments, including aquatic and terrestrial ecosystems, and modern tools used for the identification were addressed. Finally, the review addressed the ecotoxicological impact of antibiotic-resistant bacteria and public health concerns and concluded with possible strategies for addressing the ABR challenge. The information provided in this review will enhance our understanding of ABR and its implications for human, animal, and environmental health. Understanding the environmental dimension will also strengthen the need to prevent pollution as the factors influencing ABR in this setting are more than just antibiotics but involve others like heavy metals and biocides, usually not considered when studying ABR.}, }
@article {pmid36669850, year = {2023}, author = {Tonkin-Hill, G and Gladstone, RA and Pöntinen, AK and Arredondo-Alonso, S and Bentley, SD and Corander, J}, title = {Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe.}, journal = {Genome research}, volume = {33}, number = {1}, pages = {129-140}, pmid = {36669850}, issn = {1549-5469}, support = {204016/Z/16/Z//Wellcome Trust/United Kingdom ; 206194//Wellcome Trust/United Kingdom ; }, mesh = {Humans ; Phylogeny ; *Evolution, Molecular ; *Prokaryotic Cells ; Genome, Bacterial ; Gene Transfer, Horizontal ; }, abstract = {Horizontal gene transfer (HGT) plays a critical role in the evolution and diversification of many microbial species. The resulting dynamics of gene gain and loss can have important implications for the development of antibiotic resistance and the design of vaccine and drug interventions. Methods for the analysis of gene presence/absence patterns typically do not account for errors introduced in the automated annotation and clustering of gene sequences. In particular, methods adapted from ecological studies, including the pangenome gene accumulation curve, can be misleading as they may reflect the underlying diversity in the temporal sampling of genomes rather than a difference in the dynamics of HGT. Here, we introduce Panstripe, a method based on generalized linear regression that is robust to population structure, sampling bias, and errors in the predicted presence/absence of genes. We show using simulations that Panstripe can effectively identify differences in the rate and number of genes involved in HGT events, and illustrate its capability by analyzing several diverse bacterial genome data sets representing major human pathogens.}, }
@article {pmid36669792, year = {2023}, author = {Breidenstein, A and Ter Beek, J and Berntsson, RP}, title = {Structural and functional characterization of TraI from pKM101 reveals basis for DNA processing.}, journal = {Life science alliance}, volume = {6}, number = {4}, pages = {}, pmid = {36669792}, issn = {2575-1077}, mesh = {*Escherichia coli Proteins/metabolism ; Type IV Secretion Systems ; Plasmids/genetics ; DNA ; Esterases/genetics ; }, abstract = {Type 4 secretion systems are large and versatile protein machineries that facilitate the spread of antibiotic resistance and other virulence factors via horizontal gene transfer. Conjugative type 4 secretion systems depend on relaxases to process the DNA in preparation for transport. TraI from the well-studied conjugative plasmid pKM101 is one such relaxase. Here, we report the crystal structure of the trans-esterase domain of TraI in complex with its substrate oriT DNA, highlighting the conserved DNA-binding mechanism of conjugative relaxases. In addition, we present an apo structure of the trans-esterase domain of TraI that includes most of the flexible thumb region. This allows us for the first time to visualize the large conformational change of the thumb subdomain upon DNA binding. We also characterize the DNA binding, nicking, and religation activity of the trans-esterase domain, helicase domain, and full-length TraI. Unlike previous indications in the literature, our results reveal that the TraI trans-esterase domain from pKM101 behaves in a conserved manner with its homologs from the R388 and F plasmids.}, }
@article {pmid36669117, year = {2023}, author = {Ishikawa, M and Fujiwara, A and Kosetsu, K and Horiuchi, Y and Kamamoto, N and Umakawa, N and Tamada, Y and Zhang, L and Matsushita, K and Palfalvi, G and Nishiyama, T and Kitasaki, S and Masuda, Y and Shiroza, Y and Kitagawa, M and Nakamura, T and Cui, H and Hiwatashi, Y and Kabeya, Y and Shigenobu, S and Aoyama, T and Kato, K and Murata, T and Fujimoto, K and Benfey, PN and Hasebe, M and Kofuji, R}, title = {GRAS transcription factors regulate cell division planes in moss overriding the default rule.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {4}, pages = {e2210632120}, pmid = {36669117}, issn = {1091-6490}, support = {20H05891 21H02499 and 21K19250//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; No grant number//Howard Hughes Medical Institute (HHMI)/ ; MIRA 1R35GM131725//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R35 GM131725/GM/NIGMS NIH HHS/United States ; 18H04846 20H04892 20H05430&#xa0;and 22H04738//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 20H05415//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 16H06378//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; }, mesh = {*Arabidopsis Proteins/metabolism ; *Arabidopsis/genetics ; Transcription Factors/genetics/metabolism ; Cell Division/genetics ; Plant Roots/metabolism ; Gene Expression Regulation, Plant ; }, abstract = {Plant cells are surrounded by a cell wall and do not migrate, which makes the regulation of cell division orientation crucial for development. Regulatory mechanisms controlling cell division orientation may have contributed to the evolution of body organization in land plants. The GRAS family of transcription factors was transferred horizontally from soil bacteria to an algal common ancestor of land plants. SHORTROOT (SHR) and SCARECROW (SCR) genes in this family regulate formative periclinal cell divisions in the roots of flowering plants, but their roles in nonflowering plants and their evolution have not been studied in relation to body organization. Here, we show that SHR cell autonomously inhibits formative periclinal cell divisions indispensable for leaf vein formation in the moss Physcomitrium patens, and SHR expression is positively and negatively regulated by SCR and the GRAS member LATERAL SUPPRESSOR, respectively. While precursor cells of a leaf vein lacking SHR usually follow the geometry rule of dividing along the division plane with the minimum surface area, SHR overrides this rule and forces cells to divide nonpericlinally. Together, these results imply that these bacterially derived GRAS transcription factors were involved in the establishment of the genetic regulatory networks modulating cell division orientation in the common ancestor of land plants and were later adapted to function in flowering plant and moss lineages for their specific body organizations.}, }
@article {pmid36668832, year = {2022}, author = {Proctor, RH and Hao, G and Kim, HS and Whitaker, BK and Laraba, I and Vaughan, MM and McCormick, SP}, title = {A Novel Trichothecene Toxin Phenotype Associated with Horizontal Gene Transfer and a Change in Gene Function in Fusarium.}, journal = {Toxins}, volume = {15}, number = {1}, pages = {}, pmid = {36668832}, issn = {2072-6651}, mesh = {Phylogeny ; *Fusarium/metabolism ; Gene Transfer, Horizontal ; *Trichothecenes/metabolism ; *Mycotoxins/chemistry ; Phenotype ; }, abstract = {Fusarium trichothecenes are among the mycotoxins of most concern to food and feed safety. Production of these mycotoxins and presence of the trichothecene biosynthetic gene (TRI) cluster have been confirmed in only two multispecies lineages of Fusarium: the Fusarium incarnatum-equiseti (Incarnatum) and F. sambucinum (Sambucinum) species complexes. Here, we identified and characterized a TRI cluster in a species that has not been formally described and is represented by Fusarium sp. NRRL 66739. This fungus is reported to be a member of a third Fusarium lineage: the F. buharicum species complex. Cultures of NRRL 66739 accumulated only two trichothecenes, 7-hydroxyisotrichodermin and 7-hydroxyisotrichodermol. Although these are not novel trichothecenes, the production profile of NRRL 66739 is novel, because in previous reports 7-hydroxyisotrichodermin and 7-hydroxyisotrichodermol were components of mixtures of 6-8 trichothecenes produced by several Fusarium species in Sambucinum. Heterologous expression analysis indicated that the TRI13 gene in NRRL 66739 confers trichothecene 7-hydroxylation. This contrasts the trichothecene 4-hydroxylation function of TRI13 in other Fusarium species. Phylogenetic analyses suggest that NRRL 66739 acquired the TRI cluster via horizontal gene transfer from a close relative of Incarnatum and Sambucinum. These findings provide insights into evolutionary processes that have shaped the distribution of trichothecene production among Fusarium species and the structural diversity of the toxins.}, }
@article {pmid36655280, year = {2023}, author = {Shin, H and Kim, Y and Han, S and Hur, HG}, title = {Resistome Study in Aquatic Environments.}, journal = {Journal of microbiology and biotechnology}, volume = {33}, number = {3}, pages = {277-287}, pmid = {36655280}, issn = {1738-8872}, mesh = {*Genes, Bacterial ; *Anti-Bacterial Agents/pharmacology ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Bacteria/genetics ; }, abstract = {Since the first discovery of antibiotics, introduction of new antibiotics has been coupled with the occurrence of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Rapid dissemination of ARB and ARGs in the aquatic environments has become a global concern. ARB and ARGs have been already disseminated in the aquatic environments via various routes. Main hosts of most of ARGs were found to belong to Gammaproteobacteria class, including clinically important potential pathogens. Transmission of ARGs also occurs by horizontal gene transfer (HGT) mechanisms between bacterial strains in the aquatic environments, resulting in ubiquity of ARGs. Thus, a few of ARGs and MGEs (e.g., strA, sul1, int1) have been suggested as indicators for global comparability of contamination level in the aquatic environments. With ARB and ARGs contamination, the occurrence of critical pathogens has been globally issued due to their widespread in the aquatic environments. Thus, active surveillance systems have been launched worldwide. In this review, we described advancement of methodologies for ARGs detection, and occurrence of ARB and ARGs and their dissemination in the aquatic environments. Even though numerous studies have been conducted for ARB and ARGs, there is still no clear strategy to tackle antibiotic resistance (AR) in the aquatic environments. At least, for consistent surveillance, a strict framework should be established for further research in the aquatic environments.}, }
@article {pmid36653393, year = {2023}, author = {Couturier, A and Virolle, C and Goldlust, K and Berne-Dedieu, A and Reuter, A and Nolivos, S and Yamaichi, Y and Bigot, S and Lesterlin, C}, title = {Real-time visualisation of the intracellular dynamics of conjugative plasmid transfer.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {294}, pmid = {36653393}, issn = {2041-1723}, mesh = {DNA, Bacterial/genetics/metabolism ; *Escherichia coli/genetics/metabolism ; *Conjugation, Genetic ; Plasmids/genetics ; DNA ; DNA, Single-Stranded/genetics ; Gene Transfer, Horizontal ; }, abstract = {Conjugation is a contact-dependent mechanism for the transfer of plasmid DNA between bacterial cells, which contributes to the dissemination of antibiotic resistance. Here, we use live-cell microscopy to visualise the intracellular dynamics of conjugative transfer of F-plasmid in E. coli, in real time. We show that the transfer of plasmid in single-stranded form (ssDNA) and its subsequent conversion into double-stranded DNA (dsDNA) are fast and efficient processes that occur with specific timing and subcellular localisation. Notably, the ssDNA-to-dsDNA conversion determines the timing of plasmid-encoded protein production. The leading region that first enters the recipient cell carries single-stranded promoters that allow the early and transient synthesis of leading proteins immediately upon entry of the ssDNA plasmid. The subsequent conversion into dsDNA turns off leading gene expression, and activates the expression of other plasmid genes under the control of conventional double-stranded promoters. This molecular strategy allows for the timely production of factors sequentially involved in establishing, maintaining and disseminating the plasmid.}, }
@article {pmid36653270, year = {2023}, author = {Murakami, H and Sano, K and Motomura, K and Kuroda, A and Hirota, R}, title = {Assessment of horizontal gene transfer-mediated destabilization of Synechococcus elongatus PCC 7942 biocontainment system.}, journal = {Journal of bioscience and bioengineering}, volume = {135}, number = {3}, pages = {190-195}, doi = {10.1016/j.jbiosc.2022.12.002}, pmid = {36653270}, issn = {1347-4421}, mesh = {*Gene Transfer, Horizontal ; Ecosystem ; *Synechococcus/metabolism ; Phosphates/metabolism ; Bacterial Proteins/genetics/metabolism ; }, abstract = {Biological containment is a biosafety strategy that prevents the dispersal of genetically modified organisms in natural ecosystems. We previously established a biocontainment system that makes bacterial growth dependent on the availability of phosphite (Pt), an ecologically rare form of phosphorus (P), by introducing Pt metabolic pathway genes and disrupting endogenous phosphate and organic phosphate transporter genes. Although this system proved highly effective, horizontal gene transfer (HGT) mediated recovery of a P transporter gene is considered as a potential pathway to abolish the Pt-dependent growth, resulting in escape from the containment. Here, we assessed the risk of HGT driven escape using the Pt-dependent cyanobacterium Synechococcus elongatus PCC 7942. Transformation experiments revealed that the Pt-dependent strain could regain phosphate transporter genes from the S. elongatus PCC 7942 wild-type genome and from the genome of the closely related strain, S. elongatus UTEX 2973. Transformed S. elongatus PCC 7942 became viable in a phosphate-containing medium. Meanwhile, transformation of the Synechocystis sp. PCC 6803 genome or environmental DNA did not yield escape strains, suggesting that only genetic material derived from phylogenetically-close species confer high risk to generate escape. Eliminating a single gene necessary for natural competence from the Pt-dependent strain reduced the escape occurrence rate. These results demonstrate that natural competence could be a potential risk to destabilize Pt-dependence, and therefore inhibiting exogenous DNA uptake would be effective for enhancing the robustness of the gene disruption-dependent biocontainment.}, }
@article {pmid36641904, year = {2023}, author = {Alnahhas, RN and Dunlop, MJ}, title = {Advances in linking single-cell bacterial stress response to population-level survival.}, journal = {Current opinion in biotechnology}, volume = {79}, number = {}, pages = {102885}, pmid = {36641904}, issn = {1879-0429}, support = {R01 AI102922/AI/NIAID NIH HHS/United States ; }, mesh = {*Anti-Bacterial Agents ; *Bacteria/genetics ; Phenotype ; }, abstract = {Stress response mechanisms can allow bacteria to survive a myriad of challenges, including nutrient changes, antibiotic encounters, and antagonistic interactions with other microbes. Expression of these stress response pathways, in addition to other cell features such as growth rate and metabolic state, can be heterogeneous across cells and over time. Collectively, these single-cell-level phenotypes contribute to an overall population-level response to stress. These include diversifying actions, which can be used to enable bet-hedging, and coordinated actions, such as biofilm production, horizontal gene transfer, and cross-feeding. Here, we highlight recent results and emerging technologies focused on both single-cell and population-level responses to stressors, and we draw connections about the combined impact of these effects on survival of bacterial communities.}, }
@article {pmid36639816, year = {2023}, author = {Zhu, J and Yang, F and Du, K and Wei, ZL and Wu, QF and Chen, Y and Li, WF and Li, Q and Zhou, CZ}, title = {Phylogenomics of five Pseudanabaena cyanophages and evolutionary traces of horizontal gene transfer.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {3}, pmid = {36639816}, issn = {2524-6372}, support = {No. 202104i07020004//Key Research and Development Projects of Anhui Province/ ; No. WK2070000195 and WK9100000015//Fundamental Research Funds for the Central Universities/ ; No. U19A2020//National Natural Science Foundation of China/ ; No. 2018YFA0903100//Ministry of Science and Technology of the People's Republic of China/ ; }, abstract = {BACKGROUND: Along with the fast development and urbanization in developing countries, the waterbodies aside the growing cities become heavily polluted and highly eutrophic, thus leading to the seasonal outbreak of cyanobacterial bloom. Systematic isolation and characterization of freshwater cyanophages might provide a biological solution to control the awful blooms. However, genomic sequences and related investigations on the freshwater cyanophages remain very limited to date.<br><br>RESULTS: Following our recently reported five cyanophages Pam1~Pam5 from Lake Chaohu in China, here we isolated another five cyanophages, termed Pan1~Pan5, which infect the cyanobacterium Pseudanabaena sp. Chao 1811. Whole-genome sequencing showed that they all contain a double-stranded DNA genome of 37.2 to 72.0&#xa0;kb in length, with less than half of the putative open reading frames annotated with known functions. Remarkably, the siphophage Pan1 encodes an auxiliary metabolic gene phoH and constitutes, together with the host, a complete queuosine modification pathway. Proteomic analyses revealed that although Pan1~Pan5 are distinct from each other in evolution, Pan1 and Pan3 are somewhat similar to our previously identified cyanophages Pam3 and Pam1 at the genomic level, respectively. Moreover, phylogenetic analyses suggested that Pan1 resembles the &#x3b1;-proteobacterial phage vB_DshS-R5C, revealing direct evidence for phage-mediated horizontal gene transfer between cyanobacteria and &#x3b1;-proteobacteria.<br><br>CONCLUSION: In addition to the previous reports of Pam1~Pam5, the present findings on Pan1~Pan5 largely enrich the library of reference freshwater cyanophages. The abundant genomic information provides a pool to identify novel genes and proteins of unknown function. Moreover, we found for the first time the evolutionary traces in the cyanophage that horizontal gene transfer might occur at the level of not only inter-species, but even inter-phylum. It indicates that the bacteriophage or cyanophage could be developed as a powerful tool for gene manipulation among various species or phyla.}, }
@article {pmid36638983, year = {2023}, author = {Yang, K and Chen, ML and Zhu, D}, title = {Exposure to benzalkonium chloride disinfectants promotes antibiotic resistance in sewage sludge microbiomes.}, journal = {The Science of the total environment}, volume = {867}, number = {}, pages = {161527}, pmid = {36638983}, issn = {1879-1026}, mesh = {Humans ; Sewage/microbiology ; Benzalkonium Compounds/pharmacology ; Genes, Bacterial ; *Disinfectants ; *COVID-19 ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; *Microbiota ; }, abstract = {Disinfectants are routinely used in human environments to control and prevent the transmission of microbial disease, and this is particularly true during the current COVID-19 crisis. However, it remains unclear whether the increased disinfectant loadings to wastewater treatment plants facilitate the dissemination of antibiotic resistance genes (ARGs) in sewage sludge microbiomes. Here, we investigated the impacts of benzalkonium chlorides (BACs), widely used disinfectants, on ARGs profiles and microbial community structures in sewage sludge by using high-throughput quantitative PCR and Illumina sequencing. A total of 147 unique ARGs and 39 mobile genetic elements (MGEs) were detected in all sewage sludge samples. Our results show that exposure to BACs disinfectants at environmentally relevant concentrations significantly promotes both the diversity and absolute abundance of ARGs in sludge microbiomes, indicating the co-selection of ARGs by BACs disinfectants. The enrichment of ARGs abundance varied from 2.15-fold to 3.63-fold compared to controls. In addition, BACs exposure significantly alters bacterial and protistan communities, resulting in dysbiosis of the sludge microbiota. The Mantel test and Procrustes analysis confirm that bacterial communities are significantly correlated with ARGs profiles under BACs treatments. The structural equation model explains 83.8 % of the total ARGs variation and further illustrates that the absolute abundance of MGEs exerts greater impacts on the variation of absolute abundance of ARGs than microbial communities under BACs exposure, suggesting BACs may promote antibiotic resistance by enhancing the horizontal gene transfer of ARGs across sludge microbiomes. Collectively, our results provide new insights into the proliferation of antibiotic resistance through disinfectant usage during the pandemic and highlight the necessity to minimize the environmental release of disinfectants into the non-target environment for combating antibiotic resistance.}, }
@article {pmid36638546, year = {2023}, author = {Gibson, PS and Veening, JW}, title = {Gaps in the wall: understanding cell wall biology to tackle amoxicillin resistance in Streptococcus pneumoniae.}, journal = {Current opinion in microbiology}, volume = {72}, number = {}, pages = {102261}, doi = {10.1016/j.mib.2022.102261}, pmid = {36638546}, issn = {1879-0364}, mesh = {Child ; Humans ; *Amoxicillin/pharmacology ; Streptococcus pneumoniae/genetics ; *Respiratory Tract Infections/microbiology ; Peptidoglycan ; Biology ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Streptococcus pneumoniae is the most common cause of community-acquired pneumonia, and one of the main pathogens responsible for otitis media infections in children. Amoxicillin (AMX) is a broad-spectrum β-lactam antibiotic, used frequently for the treatment of bacterial respiratory tract infections. Here, we discuss the pneumococcal response to AMX, including the mode of action of AMX, the effects on autolysin regulation, and the evolution of resistance through natural transformation. We discuss current knowledge gaps in the synthesis and translocation of peptidoglycan and teichoic acids, major constituents of the pneumococcal cell wall and critical to AMX activity. Furthermore, an outlook of AMX resistance research is presented, including the development of natural competence inhibitors to block evolution via horizontal gene transfer, and the use of high-throughput essentiality screens for the discovery of novel cotherapeutics.}, }
@article {pmid36634159, year = {2024}, author = {Ryan, MP and Carraro, N and Slattery, S and Pembroke, JT}, title = {Integrative Conjugative Elements (ICEs) of the SXT/R391 family drive adaptation and evolution in γ-Proteobacteria.}, journal = {Critical reviews in microbiology}, volume = {50}, number = {1}, pages = {105-126}, doi = {10.1080/1040841X.2022.2161870}, pmid = {36634159}, issn = {1549-7828}, mesh = {*Gammaproteobacteria/genetics ; DNA Transposable Elements ; Conjugation, Genetic ; Anti-Bacterial Agents ; }, abstract = {Integrative Conjugative Elements (ICEs) are mosaics containing functional modules allowing maintenance by site-specific integration and excision into and from the host genome and conjugative transfer to a specific host range. Many ICEs encode a range of adaptive functions that aid bacterial survival and evolution in a range of niches. ICEs from the SXT/R391 family are found in γ-Proteobacteria. Over 100 members have undergone epidemiological and molecular characterization allowing insight into their diversity and function. Comparative analysis of SXT/R391 elements from a wide geographic distribution has revealed conservation of key functions, and the accumulation and evolution of adaptive genes. This evolution is associated with gene acquisition in conserved hotspots and variable regions within the SXT/R391 ICEs catalysed via element-encoded recombinases. The elements can carry IS elements and transposons, and a mutagenic DNA polymerase, PolV, which are associated with their evolution. SXT/R391 ICEs isolated from different niches appear to have retained adaptive functions related to that specific niche; phage resistance determinants in ICEs carried by wastewater bacteria, antibiotic resistance determinants in clinical isolates and metal resistance determinants in bacteria recovered from polluted environments/ocean sediments. Many genes found in the element hotspots are undetermined and have few homologs in the nucleotide databases.}, }
@article {pmid36629415, year = {2023}, author = {Finks, SS and Martiny, JBH}, title = {Plasmid-Encoded Traits Vary across Environments.}, journal = {mBio}, volume = {14}, number = {1}, pages = {e0319122}, pmid = {36629415}, issn = {2150-7511}, mesh = {Humans ; *Ecosystem ; Plasmids/genetics ; *Bacteria/genetics ; Anti-Bacterial Agents ; Gene Transfer, Horizontal ; }, abstract = {Plasmids are key mobile genetic elements in bacterial evolution and ecology as they allow the rapid adaptation of bacteria under selective environmental changes. However, the genetic information associated with plasmids is usually considered separately from information about their environmental origin. To broadly understand what kinds of traits may become mobilized by plasmids in different environments, we analyzed the properties and accessory traits of 9,725 unique plasmid sequences from a publicly available database with known bacterial hosts and isolation sources. Although most plasmid research focuses on resistance traits, such genes made up <1% of the total genetic information carried by plasmids. Similar to traits encoded on the bacterial chromosome, plasmid accessory trait compositions (including general Clusters of Orthologous Genes [COG] functions, resistance genes, and carbon and nitrogen genes) varied across seven broadly defined environment types (human, animal, wastewater, plant, soil, marine, and freshwater). Despite their potential for horizontal gene transfer, plasmid traits strongly varied with their host's taxonomic assignment. However, the trait differences across environments of broad COG categories could not be entirely explained by plasmid host taxonomy, suggesting that environmental selection acts on the plasmid traits themselves. Finally, some plasmid traits and environments (e.g., resistance genes in human-related environments) were more often associated with mobilizable plasmids (those having at least one detected relaxase) than others. Overall, these findings underscore the high level of diversity of traits encoded by plasmids and provide a baseline to investigate the potential of plasmids to serve as reservoirs of adaptive traits for microbial communities. IMPORTANCE Plasmids are well known for their role in the transmission of antibiotic resistance-conferring genes. Beyond human and clinical settings, however, they disseminate many other types of genes, including those that contribute to microbially driven ecosystem processes. In this study, we identified the distribution of traits genetically encoded by plasmids isolated from seven broadly categorized environments. We find that plasmid trait content varied with both bacterial host taxonomy and environment and that, on average, half of the plasmids were potentially mobilizable. As anthropogenic activities impact ecosystems and the climate, investigating and identifying the mechanisms of how microbial communities can adapt will be imperative for predicting the impacts on ecosystem functioning.}, }
@article {pmid36626782, year = {2022}, author = {Sundarraj, S and Sudarmani, DNP and Samuel, P and Sevarkodiyone, SP}, title = {Bioremediation of hexavalent chromium by transformation of Escherichia coli DH5α with chromate reductase (ChrR) genes of Pseudomonas putida isolated from tannery effluent.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxac019}, pmid = {36626782}, issn = {1365-2672}, abstract = {AIMS: Hexavalent chromium (Cr(VI)), a toxic heavy metal, is a serious pollutant from tannery effluent, and its accumulation in soil and water causes severe environmental concerns and increasing public health issues. The present study focuses on the isolation and identification of chromium-reducing bacteria collected from the tannery industry in Dindigul, Tamil Nadu. Chromium-reducing bacteria Pseudomonas putida were identified by 16S rRNA sequencing followed by BLAST search. The plasmid with Cr(VI) reductase gene was isolated from Ps. putida and transferred to Escherichia coli DH5α for further studies.<br><br>METHODS AND RESULTS: The bacterial cultures were kept under controlled conditions for 72&#xa0;h to observe the growth rates and bacterial resistance to chromium. When strains wild-type and transformant E. coli DH5&#x3b1; were grown in chromium-supplemented media, they revealed significant growth, but strains cured type Ps. putida and E. coli DH5&#x3b1; recorded minimum growth. The Cr(VI) reduction employed by transformant E. coli DH5&#x3b1; and wild Ps. putida was 42.52&#xa0;&#xb1;&#xa0;1.48% and 44.46&#xa0;&#xb1;&#xa0;0.55%, respectively. The culture supernatant of the wild Ps. putida and transformant E. coli DH5&#x3b1; showed an increased reduction of Cr(VI) compared with cell extract supernatant and cell debris due to the extracellular activity of chromium reductase being responsible for Cr(VI) reduction. Besides, the chromium reductase gene was confirmed in the isolated Ps. putida and transformant E. coli DH5&#x3b1;.<br><br>CONCLUSIONS: Transformant bacteria could employ an alternative method for heavy metal detoxification in contaminated environments like tannery effluent and mining processes.<br><br>High Cr(VI) concentration resistance and high Cr(VI) reducing the strain's ability make it suitable for bioremediation. These possible horizontal gene transfer events indicated in this study may have enabled transformant E. coli DH5&#x3b1; as a good candidate for reducing the heavy metal pollution.}, }
@article {pmid36623672, year = {2023}, author = {Sazykin, IS and Sazykina, MA}, title = {The role of oxidative stress in genome destabilization and adaptive evolution of bacteria.}, journal = {Gene}, volume = {857}, number = {}, pages = {147170}, doi = {10.1016/j.gene.2023.147170}, pmid = {36623672}, issn = {1879-0038}, mesh = {*Oxidative Stress/genetics ; *Bacteria/genetics ; Mutagenesis ; Genome, Bacterial ; }, abstract = {The review is devoted to bacterial genome destabilization by oxidative stress. The article discusses the main groups of substances causing such stress. Stress regulons involved in destabilization of genetic material and mechanisms enhancing mutagenesis, bacterial genome rearrangements, and horizontal gene transfer, induced by oxidative damage to cell components are also considered. Based on the analysis of publications, it can be claimed that rapid development of new food substrates and ecological niches by microorganisms occurs due to acceleration of genetic changes induced by oxidative stress, mediated by several stress regulons (SOS, RpoS and RpoE) and under selective pressure. The authors conclude that non-lethal oxidative stress is probably-one of the fundamental processes that guide evolution of prokaryotes and a powerful universal trigger for adaptive destabilization of bacterial genome under changing environmental conditions.}, }
@article {pmid36623656, year = {2023}, author = {Wang, C and Jia, Y and Li, J and Wang, Y and Niu, H and Qiu, H and Li, X and Fang, W and Qiu, Z}, title = {Effect of bioaugmentation on tetracyclines influenced chicken manure composting and antibiotics resistance.}, journal = {The Science of the total environment}, volume = {867}, number = {}, pages = {161457}, doi = {10.1016/j.scitotenv.2023.161457}, pmid = {36623656}, issn = {1879-1026}, mesh = {Animals ; *Composting ; Manure ; Chickens ; Tetracyclines ; Genes, Bacterial ; Anti-Bacterial Agents ; }, abstract = {Antibiotic residue in husbandry waste has become a serious concern. In this study, contaminated chicken manure composting was conducted to reveal the bioaugmentation effect on tetracyclines residue and antibiotics resistance genes (ARGs). The bioaugmented composting removed most of the antibiotics in 7 days. Under bioaugmentation, 96.88 % of tetracycline and 92.31 % of oxytetracycline were removed, 6.32 % and 20.93 % higher than the control (P < 0.05). The high-temperature period was the most effective phase for eliminating antibiotics. The treatment showed a long high-temperature period (7 days), while no high-temperature period was in control. After composting, the treatment showed 13.87 % higher TN (26.51 g/kg) and 13.42 % higher NO3[-]-N (2.45 g/kg) than control (23.28 and 2.16 g/kg, respectively) but 12.72 % lower C/N, indicating fast decomposition and less nutrient loss. Exogenous microorganisms from bioaugmentation significantly reshaped the microbial community structure and facilitated the enrichment of genera such as Truepera and Fermentimonas, whose abundance increased by 71.10 % and 75.37 % than the control, respectively. Remarkably, ARGs, including tetC, tetG, and tetW, were enhanced by 198.77 %, 846.77 %, and 62.63 % compared with the control, while the integron gene (intl1) was elevated by 700.26 %, indicating horizontal gene transfer of ARGs. Eventually, bioaugmentation was efficient in regulating microbial metabolism, relieving antibiotic stress, and eliminating antibiotics in composting. However, the ability to remove ARGs should be further investigated. Such an approach should be further considered for treating pollutants-influenced organic waste to eliminate environmental concerns.}, }
@article {pmid36622346, year = {2023}, author = {Nieves, C and Vincent, AT and Zarantonelli, L and Picardeau, M and Veyrier, FJ and Buschiazzo, A}, title = {Horizontal transfer of the rfb cluster in Leptospira is a genetic determinant of serovar identity.}, journal = {Life science alliance}, volume = {6}, number = {2}, pages = {}, pmid = {36622346}, issn = {2575-1077}, mesh = {Humans ; *Leptospira/genetics ; Serogroup ; Lipopolysaccharides ; Phenotype ; }, abstract = {Leptospira bacteria comprise numerous species, several of which cause serious disease to a broad range of hosts including humans. These spirochetes exhibit large intraspecific variation, resulting in complex tabulations of serogroups/serovars that crisscross the species classification. Serovar identity, linked to biological/clinical phenotypes, depends on the structure of surface-exposed LPS. Many LPS biosynthesis-encoding genes reside within the chromosomic rfb gene cluster. However, the genetic basis of intraspecies variability is not fully understood, constraining diagnostics/typing methods to cumbersome serologic procedures. We now show that the gene content of the rfb cluster strongly correlates with Leptospira serovar designation. Whole-genome sequencing of pathogenic L. noguchii, including strains of different serogroups, reveals that the rfb cluster undergoes extensive horizontal gene transfer. The rfb clusters from several Leptospira species disclose a univocal correspondence between gene composition and serovar identity. This work paves the way to genetic typing of Leptospira serovars, and to pinpointing specific genes within the distinct rfb clusters, encoding host-specific virulence traits. Further research shall unveil the molecular mechanism of rfb transfer among Leptospira strains and species.}, }
@article {pmid36622251, year = {2023}, author = {Lindqvist, LL and Jarmusch, SA and Sonnenschein, EC and Strube, ML and Kim, J and Nielsen, MW and Kempen, PJ and Schoof, EM and Zhang, SD and Gram, L}, title = {Tropodithietic Acid, a Multifunctional Antimicrobial, Facilitates Adaption and Colonization of the Producer, Phaeobacter piscinae.}, journal = {mSphere}, volume = {8}, number = {1}, pages = {e0051722}, pmid = {36622251}, issn = {2379-5042}, mesh = {*Type IV Secretion Systems/metabolism ; *Rhodobacteraceae/genetics ; Anti-Bacterial Agents/metabolism ; }, abstract = {In the marine environment, surface-associated bacteria often produce an array of antimicrobial secondary metabolites, which have predominantly been perceived as competition molecules. However, they may also affect other hallmarks of surface-associated living, such as motility and biofilm formation. Here, we investigate the ecological significance of an antibiotic secondary metabolite, tropodithietic acid (TDA), in the producing bacterium, Phaeobacter piscinae S26. We constructed a markerless in-frame deletion mutant deficient in TDA biosynthesis, S26ΔtdaB. Molecular networking demonstrated that other chemical sulfur-containing features, likely related to TDA, were also altered in the secondary metabolome. We found several changes in the physiology of the TDA-deficient mutant, ΔtdaB, compared to the wild type. Growth of the two strains was similar; however, ΔtdaB cells were shorter and more motile. Transcriptome and proteome profiling revealed an increase in gene expression and protein abundance related to a type IV secretion system, and to a prophage, and a gene transfer agent in ΔtdaB. All these systems may contribute to horizontal gene transfer (HGT), which may facilitate adaptation to novel niches. We speculate that once a TDA-producing population has been established in a new niche, the accumulation of TDA acts as a signal of successful colonization, prompting a switch to a sessile lifestyle. This would lead to a decrease in motility and the rate of HGT, while filamentous cells could form the base of a biofilm. In addition, the antibiotic properties of TDA may inhibit invading competing microorganisms. This points to a role of TDA in coordinating colonization and adaptation. IMPORTANCE Despite the broad clinical usage of microbial secondary metabolites with antibiotic activity, little is known about their role in natural microbiomes. Here, we studied the effect of production of the antibiotic tropodithietic acid (TDA) on the producing strain, Phaeobacter piscinae S26, a member of the Roseobacter group. We show that TDA affects several phenotypes of the producing strain, including motility, cell morphology, metal metabolism, and three horizontal gene transfer systems: a prophage, a type IV secretion system, and a gene transfer agent. Together, this indicates that TDA participates in coordinating the colonization process of the producer. TDA is thus an example of a multifunctional secondary metabolite that can mediate complex interactions in microbial communities. This work broadens our understanding of the ecological role that secondary metabolites have in microbial community dynamics.}, }
@article {pmid36620013, year = {2022}, author = {Lieberman, LA}, title = {Outer membrane vesicles: A bacterial-derived vaccination system.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1029146}, pmid = {36620013}, issn = {1664-302X}, abstract = {Outer membrane vesicles (OMVs) are non-living spherical nanostructures that derive from the cell envelope of Gram-negative bacteria. OMVs are important in bacterial pathogenesis, cell-to-cell communication, horizontal gene transfer, quorum sensing, and in maintaining bacterial fitness. These structures can be modified to express antigens of interest using glycoengineering and genetic or chemical modification. The resulting OMVs can be used to immunize individuals against the expressed homo- or heterologous antigens. Additionally, cargo can be loaded into OMVs and they could be used as a drug delivery system. OMVs are inherently immunogenic due to proteins and glycans found on Gram negative bacterial outer membranes. This review focuses on OMV manipulation to increase vesiculation and decrease antigenicity, their utility as vaccines, and novel engineering approaches to extend their application.}, }
@article {pmid36611105, year = {2023}, author = {Aldaihani, R and Heath, LS}, title = {Connecting genomic islands across prokaryotic and phage genomes via protein families.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {344}, pmid = {36611105}, issn = {2045-2322}, mesh = {*Genomic Islands/genetics ; *Bacteriophages/genetics ; Prokaryotic Cells ; Proteins/genetics ; Bacteria/genetics ; Computational Biology/methods ; Gene Transfer, Horizontal ; Genome, Bacterial ; }, abstract = {Prokaryotic genomes evolve via horizontal gene transfer (HGT), mutations, and rearrangements. A noteworthy part of the HGT process is facilitated by genomic islands (GIs). While previous computational biology research has focused on developing tools to detect GIs in prokaryotic genomes, there has been little research investigating GI patterns and biological connections across species. We have pursued the novel idea of connecting GIs across prokaryotic and phage genomes via patterns of protein families. Such patterns are sequences of protein families frequently present in the genomes of multiple species. We combined the large data set from the IslandViewer4 database with protein families from Pfam while implementing a comprehensive strategy to identify patterns making use of HMMER, BLAST, and MUSCLE. we also implemented Python programs that link the analysis into a single pipeline. Research results demonstrated that related GIs often exist in species that are evolutionarily unrelated and in multiple bacterial phyla. Analysis of the discovered patterns led to the identification of biological connections among prokaryotes and phages. These connections suggest broad HGT connections across the bacterial kingdom and its associated phages. The discovered patterns and connections could provide the basis for additional analysis on HGT breadth and the patterns in pathogenic GIs.}, }
@article {pmid36610752, year = {2023}, author = {Botelho, J and Cazares, A and Schulenburg, H}, title = {The ESKAPE mobilome contributes to the spread of antimicrobial resistance and CRISPR-mediated conflict between mobile genetic elements.}, journal = {Nucleic acids research}, volume = {51}, number = {1}, pages = {236-252}, pmid = {36610752}, issn = {1362-4962}, mesh = {Humans ; *Interspersed Repetitive Sequences/genetics ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Plasmids/genetics ; Gene Transfer, Horizontal/genetics ; Prophages/genetics ; }, abstract = {Mobile genetic elements (MGEs) mediate the shuffling of genes among organisms. They contribute to the spread of virulence and antibiotic resistance (AMR) genes in human pathogens, such as the particularly problematic group of ESKAPE pathogens. Here, we performed the first systematic analysis of MGEs, including plasmids, prophages, and integrative and conjugative/mobilizable elements (ICEs/IMEs), across all ESKAPE pathogens. We found that different MGE types are asymmetrically distributed across these pathogens, and that most horizontal gene transfer (HGT) events are restricted by phylum or genus. We show that the MGEs proteome is involved in diverse functional processes and distinguish widespread proteins within the ESKAPE context. Moreover, anti-CRISPRs and AMR genes are overrepresented in the ESKAPE mobilome. Our results also underscore species-specific trends shaping the number of MGEs, AMR, and virulence genes across pairs of conspecific ESKAPE genomes with and without CRISPR-Cas systems. Finally, we observed that CRISPR spacers found on prophages, ICEs/IMEs, and plasmids have different targeting biases: while plasmid and prophage CRISPRs almost exclusively target other plasmids and prophages, respectively, ICEs/IMEs CRISPRs preferentially target prophages. Overall, our study highlights the general importance of the ESKAPE mobilome in contributing to the spread of AMR and mediating conflict among MGEs.}, }
@article {pmid36608829, year = {2023}, author = {Tan, Y and Cao, X and Chen, S and Ao, X and Li, J and Hu, K and Liu, S and Penttinen, P and Yang, Y and Yu, X and Liu, A and Liu, C and Zhao, K and Zou, L}, title = {Antibiotic and heavy metal resistance genes in sewage sludge survive during aerobic composting.}, journal = {The Science of the total environment}, volume = {866}, number = {}, pages = {161386}, doi = {10.1016/j.scitotenv.2023.161386}, pmid = {36608829}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents ; Sewage/microbiology ; Genes, Bacterial ; *Composting ; *Metals, Heavy ; Bacteria/genetics ; Manure ; }, abstract = {Municipal sewage sludge has been generated in increasing amounts with the acceleration of urbanization and economic development. The nutrient rich sewage sludge can be recycled by composting that has a great potential to produce stabilized organic fertilizer and substrate for plant cultivation. However, little is known about the metals, pathogens and antibiotic resistance transfer risks involved in applying the composted sludge in agriculture. We studied changes in and relationships between heavy metal contents, microbial communities, and antibiotic resistance genes (ARGs), heavy metal resistance genes (HMRGs) and mobile genetic elements (MGEs) in aerobic composting of sewage sludge. The contents of most of the analyzed heavy metals were not lower after composting. The bacterial α-diversity was lower, and the community composition was different after composting. Firmicutes were enriched, and Proteobacteria and potential pathogens in the genera Arcobacter and Acinetobacter were depleted in the composted sludge. The differences in bacteria were possibly due to the high temperature phase during the composting which was likely to affect temperature-sensitive bacteria. The number of detected ARGs, HMRGs and MGEs was lower, and the relative abundances of several resistance genes were lower after composting. However, the abundance of seven ARGs and six HMRGs remained on the same level after composting. Co-occurrence analysis of bacterial taxa and the genes suggested that the ARGs may spread via horizontal gene transfer during composting. In summary, even though aerobic composting is effective for managing sewage sludge and to decrease the relative abundance of potential pathogens, ARGs and HMRGs, it might include a potential risk for the dissemination of ARGs in the environment.}, }
@article {pmid36608658, year = {2023}, author = {Utter, DR and Orphan, VJ}, title = {Gifts hidden in shadowy genome islands.}, journal = {Cell}, volume = {186}, number = {1}, pages = {5-7}, doi = {10.1016/j.cell.2022.12.001}, pmid = {36608658}, issn = {1097-4172}, mesh = {Archaea/genetics ; *Bacteria/genetics ; Gene Transfer, Horizontal ; Genome, Bacterial/genetics ; Interspersed Repetitive Sequences ; }, abstract = {Despite being typically perceived as "clonal" organisms, bacteria and archaea possess numerous mechanisms to share and co-opt genetic material from other lineages. Several mechanisms for horizontal gene transfer have been discovered, but the high mosaicity observed in many bacterial genomes outscales that explained by known mechanisms, hinting at yet undiscovered processes. In this issue of Cell, Hackl et al. introduce a new category of mobile genetic elements called tycheposons, providing a novel mechanism that contributes to the prodigious genomic diversity within microbial populations. The discovery and characterization of tycheposons prompts a reevaluation of microbial diversification in complex environments.}, }
@article {pmid36608657, year = {2023}, author = {Hackl, T and Laurenceau, R and Ankenbrand, MJ and Bliem, C and Cariani, Z and Thomas, E and Dooley, KD and Arellano, AA and Hogle, SL and Berube, P and Leventhal, GE and Luo, E and Eppley, JM and Zayed, AA and Beaulaurier, J and Stepanauskas, R and Sullivan, MB and DeLong, EF and Biller, SJ and Chisholm, SW}, title = {Novel integrative elements and genomic plasticity in ocean ecosystems.}, journal = {Cell}, volume = {186}, number = {1}, pages = {47-62.e16}, doi = {10.1016/j.cell.2022.12.006}, pmid = {36608657}, issn = {1097-4172}, mesh = {*Ecosystem ; *Genome, Bacterial/genetics ; Phylogeny ; Oceans and Seas ; Genomics ; }, abstract = {Horizontal gene transfer accelerates microbial evolution. The marine picocyanobacterium Prochlorococcus exhibits high genomic plasticity, yet the underlying mechanisms are elusive. Here, we report a novel family of DNA transposons-"tycheposons"-some of which are viral satellites while others carry cargo, such as nutrient-acquisition genes, which shape the genetic variability in this globally abundant genus. Tycheposons share distinctive mobile-lifecycle-linked hallmark genes, including a deep-branching site-specific tyrosine recombinase. Their excision and integration at tRNA genes appear to drive the remodeling of genomic islands-key reservoirs for flexible genes in bacteria. In a selection experiment, tycheposons harboring a nitrate assimilation cassette were dynamically gained and lost, thereby promoting chromosomal rearrangements and host adaptation. Vesicles and phage particles harvested from seawater are enriched in tycheposons, providing a means for their dispersal in the wild. Similar elements are found in microbes co-occurring with Prochlorococcus, suggesting a common mechanism for microbial diversification in the vast oligotrophic oceans.}, }
@article {pmid36602323, year = {2023}, author = {Regmi, A and Tague, JG and Boas Lichty, KE and Boyd, EF}, title = {A Class IV Adenylate Cyclase, CyaB, Is Required for Capsule Polysaccharide Production and Biofilm Formation in Vibrio parahaemolyticus.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {1}, pages = {e0187422}, pmid = {36602323}, issn = {1098-5336}, mesh = {*Adenylyl Cyclases/genetics/metabolism ; *Vibrio parahaemolyticus/genetics/metabolism ; Escherichia coli/genetics/metabolism ; Phylogeny ; Cyclic AMP/metabolism ; Bacterial Proteins/genetics/metabolism ; Cyclic AMP Receptor Protein/genetics/metabolism ; Biofilms ; Polysaccharides ; }, abstract = {Cyclic AMP (cAMP) receptor protein (CRP), encoded by crp, is a global regulator that is activated by cAMP, a second messenger synthesized by a class I adenylate cyclase (AC-I) encoded by cyaA in Escherichia coli. cAMP-CRP is required for growth on nonpreferred carbon sources and is a global regulator. We constructed in-frame nonpolar deletions of the crp and cyaA homologs in Vibrio parahaemolyticus and found that the Δcrp mutant did not grow in minimal media supplemented with nonpreferred carbon sources, but the ΔcyaA mutant grew similarly to the wild type. Bioinformatics analysis of the V. parahaemolyticus genome identified a 181-amino-acid protein annotated as a class IV adenylate cyclase (AC-IV) named CyaB, a member of the CYTH protein superfamily. AC-IV phylogeny showed that CyaB was present in Gammaproteobacteria and Alphaproteobacteria as well as Planctomycetes and Archaea. Only the bacterial CyaB proteins contained an N-terminal motif, HFxxxxExExK, indicative of adenylyl cyclase activity. Both V. parahaemolyticus cyaA and cyaB genes functionally complemented an E. coli ΔcyaA mutant. The Δcrp and ΔcyaB ΔcyaA mutants showed defects in growth on nonpreferred carbon sources and in swimming and swarming motility, indicating that cAMP-CRP is an activator. The ΔcyaA and ΔcyaB single mutants had no defects in these phenotypes, indicating that AC-IV complements AC-I. Capsule polysaccharide and biofilm production assays showed significant defects in the Δcrp, ΔcyaBΔcyaA, and ΔcyaB mutants, whereas the ΔcyaA strain behaved similarly to the wild type. This is consistent with a role of cAMP-CRP as an activator of these phenotypes and establishes a cellular role for AC-IV in capsule and biofilm formation, which to date has been unestablished. IMPORTANCE Here, we characterized the roles of CRP and CyaA in V. parahaemolyticus, showing that cAMP-CRP is an activator of metabolism, motility, capsule production, and biofilm formation. These results are in contrast to cAMP-CRP in V. cholerae, which represses capsule and biofilm formation. Previously, only an AC-I CyaA had been identified in Vibrio species. Our data showed that an AC-IV CyaB homolog is present in V. parahaemolyticus and is required for optimal growth. The data demonstrated that CyaB is essential for capsule production and biofilm formation, uncovering a physiological role of AC-IV in bacteria. The data showed that the cyaB gene was widespread among Vibrionaceae species and several other Gammaproteobacteria, but in general, its phylogenetic distribution was limited. Our phylogenetic analysis also demonstrated that in some species the cyaB gene was acquired by horizontal gene transfer.}, }
@article {pmid36599855, year = {2023}, author = {Cho, CH and Park, SI and Huang, TY and Lee, Y and Ciniglia, C and Yadavalli, HC and Yang, SW and Bhattacharya, D and Yoon, HS}, title = {Genome-wide signatures of adaptation to extreme environments in red algae.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {10}, pmid = {36599855}, issn = {2041-1723}, mesh = {*Rhodophyta/genetics ; Genome/genetics ; Acclimatization ; *Hot Springs ; *Metals, Heavy ; Phylogeny ; }, abstract = {The high temperature, acidity, and heavy metal-rich environments associated with hot springs have a major impact on biological processes in resident cells. One group of photosynthetic eukaryotes, the Cyanidiophyceae (Rhodophyta), has successfully thrived in hot springs and associated sites worldwide for more than 1 billion years. Here, we analyze chromosome-level assemblies from three representative Cyanidiophyceae species to study environmental adaptation at the genomic level. We find that subtelomeric gene duplication of functional genes and loss of canonical eukaryotic traits played a major role in environmental adaptation, in addition to horizontal gene transfer events. Shared responses to environmental stress exist in Cyanidiales and Galdieriales, however, most of the adaptive genes (e.g., for arsenic detoxification) evolved independently in these lineages. Our results underline the power of local selection to shape eukaryotic genomes that may face vastly different stresses in adjacent, extreme microhabitats.}, }
@article {pmid36598481, year = {2023}, author = {O'Leary, ML and Burbank, LP}, title = {Natural Recombination among Type I Restriction-Modification Systems Creates Diverse Genomic Methylation Patterns among Xylella fastidiosa Strains.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {1}, pages = {e0187322}, pmid = {36598481}, issn = {1098-5336}, mesh = {Crops, Agricultural ; DNA Methylation ; Gene Transfer, Horizontal ; Genomics ; *Plant Diseases/genetics/microbiology ; *Xylella/genetics/pathogenicity ; }, abstract = {Xylella fastidiosa is an important bacterial plant pathogen causing high-consequence diseases in agricultural crops around the world. Although as a species X. fastidiosa can infect many host plants, there is significant variability between strains regarding virulence on specific host plant species and other traits. Natural competence and horizontal gene transfer are believed to occur frequently in X. fastidiosa and likely influence the evolution of this pathogen. However, some X. fastidiosa strains are difficult to manipulate genetically using standard transformation techniques. Several type I restriction-modification (R-M) systems are encoded in the X. fastidiosa genome, which may influence horizontal gene transfer and recombination. Type I R-M systems themselves may undergo recombination, exchanging target recognition domains (TRDs) between specificity subunits (hsdS) to generate novel alleles with new target specificities. In this study, several conserved type I R-M systems were compared across 129 X. fastidiosa genome assemblies representing all known subspecies and 32 sequence types. Forty-four unique TRDs were identified among 50 hsdS alleles, which are arrayed in 31 allele profiles that are generally conserved within a monophyletic cluster of strains. Inactivating mutations were identified in type I R-M systems of specific strains, showing heterogeneity in the complements of functional type I R-M systems across X. fastidiosa. Genomic DNA methylation patterns were characterized in 20 X. fastidiosa strains and associated with type I R-M system allele profiles. Overall, these data suggest hsdS genes recombine among Xylella strains and/or unknown donors, and the resulting TRD reassortment establishes differential epigenetic modifications across Xylella lineages. IMPORTANCE Economic impacts on agricultural production due to X. fastidiosa have been severe in the Americas, Europe, and parts of Asia. Despite a long history of research on this pathogen, certain fundamental questions regarding the biology, pathogenicity, and evolution of X. fastidiosa have still not been answered. Wide-scale whole-genome sequencing has begun to provide more insight into X. fastidiosa genetic diversity and horizontal gene transfer, but the mechanics of genomic recombination in natural settings and the extent to which this directly influences bacterial phenotypes such as plant host range are not well understood. Genome methylation is an important factor in horizontal gene transfer and bacterial recombination that has not been comprehensively studied in X. fastidiosa. This study characterizes methylation associated with type I restriction-modification systems across a wide range of X. fastidiosa strains and lays the groundwork for a better understanding of X. fastidiosa biology and evolution through epigenetics.}, }
@article {pmid36598279, year = {2023}, author = {Xu, C and Rao, J and Xie, Y and Lu, J and Li, Z and Dong, C and Wang, L and Jiang, J and Chen, C and Chen, S}, title = {The DNA Phosphorothioation Restriction-Modification System Influences the Antimicrobial Resistance of Pathogenic Bacteria.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0350922}, pmid = {36598279}, issn = {2165-0497}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Bacteria/genetics ; DNA Restriction-Modification Enzymes/genetics ; DNA ; Gene Transfer, Horizontal ; }, abstract = {Bacterial defense barriers, such as DNA methylation-associated restriction-modification (R-M) and the CRISPR-Cas system, play an important role in bacterial antimicrobial resistance (AMR). Recently, a novel R-M system based on DNA phosphorothioate (PT) modification has been shown to be widespread in the kingdom of Bacteria as well as Archaea. However, the potential role of the PT R-M system in bacterial AMR remains unclear. In this study, we explored the role of PT R-Ms in AMR with a series of common clinical pathogenic bacteria. By analyzing the distribution of AMR genes related to mobile genetic elements (MGEs), it was shown that the presence of PT R-M effectively reduced the distribution of horizontal gene transfer (HGT)-derived AMR genes in the genome, even in the bacteria that did not tend to acquire AMR genes by HGT. In addition, unique gene variation analysis based on pangenome analysis and MGE prediction revealed that the presence of PT R-M could suppress HGT frequency. Thus, this is the first report showing that the PT R-M system has the potential to repress HGT-derived AMR gene acquisition by reducing the HGT frequency. IMPORTANCE In this study, we demonstrated the effect of DNA PT modification-based R-M systems on horizontal gene transfer of AMR genes in pathogenic bacteria. We show that there is no apparent association between the genetic background of the strains harboring PT R-Ms and the number of AMR genes or the kinds of gene families. The strains equipped with PT R-M harbor fewer plasmid-derived, prophage-derived, or integrating mobile genetic element (iMGE)-related AMR genes and have a lower HGT frequency, but the degree of inhibition varies among different bacteria. In addition, compared with Salmonella enterica and Escherichia coli, Klebsiella pneumoniae prefers to acquire MGE-derived AMR genes, and there is no coevolution between PT R-M clusters and bacterial core genes.}, }
@article {pmid36597348, year = {2023}, author = {Lai, CK and Lee, YC and Ke, HM and Lu, MR and Liu, WA and Lee, HH and Liu, YC and Yoshiga, T and Kikuchi, T and Chen, PJ and Tsai, IJ}, title = {The Aphelenchoides genomes reveal substantial horizontal gene transfers in the last common ancestor of free-living and major plant-parasitic nematodes.}, journal = {Molecular ecology resources}, volume = {23}, number = {4}, pages = {905-919}, doi = {10.1111/1755-0998.13752}, pmid = {36597348}, issn = {1755-0998}, support = {AS-CDA-107-L01//Academia Sinica/ ; }, mesh = {Animals ; *Gene Transfer, Horizontal ; *Nematoda/genetics ; Phylogeny ; Plants/genetics/parasitology ; }, abstract = {Aphelenchoides besseyi is a plant-parasitic nematode (PPN) in the family Aphelenchoididae capable of infecting more than 200 plant species. A. besseyi is also a species complex with strains exhibiting varying pathogenicity to plants. We present the genome and annotations of six Aphelenchoides species, four of which belonged to the A. besseyi species complex. Most Aphelenchoides genomes have a size of 44.7-47.4 Mb and are among the smallest in clade IV, with the exception of A. fujianensis, which has a size of 143.8 Mb and is one of the largest. Phylogenomic analysis successfully delimited the species complex into A. oryzae and A. pseudobesseyi and revealed a reduction of transposon elements in the last common ancestor of Aphelenchoides. Synteny analyses between reference genomes indicated that three chromosomes in A. besseyi were derived from fission and fusion events. A systematic identification of horizontal gene transfer (HGT) genes across 27 representative nematodes allowed us to identify two major episodes of acquisition corresponding to the last common ancestor of clade IV or major PPNs, respectively. These genes were mostly lost and differentially retained between clades or strains. Most HGT events were acquired from bacteria, followed by fungi, and also from plants; plant HGT was especially prevalent in Bursaphelenchus mucronatus. Our results comprehensively improve the understanding of HGT in nematodes.}, }
@article {pmid36592614, year = {2023}, author = {Liu, Y and Chen, J and Raj, K and Baerg, L and Nathan, N and Philpott, DJ and Mahadevan, R}, title = {A Universal Strategy to Promote Secretion of G+/G- Bacterial Extracellular Vesicles and Its Application in Host Innate Immune Responses.}, journal = {ACS synthetic biology}, volume = {12}, number = {1}, pages = {319-328}, doi = {10.1021/acssynbio.2c00583}, pmid = {36592614}, issn = {2161-5063}, mesh = {Humans ; *Escherichia coli/genetics ; Anti-Bacterial Agents/pharmacology ; HEK293 Cells ; Gram-Positive Bacteria ; Gram-Negative Bacteria ; Bacteria ; Immunity, Innate ; *Extracellular Vesicles ; }, abstract = {Both Gram-positive and Gram-negative bacteria release nanosized extracellular vesicles called membrane vesicles (MVs, 20-400 nm), which have great potential in various biomedical applications due to their abilities to deliver effector molecules and induce therapeutic responses. To fully utilize bacterial MVs for therapeutic purposes, regulated and enhanced production of MVs would be highly advantageous. In this study, we developed a universal method to enhance MV yields in both G+/G- bacteria through an autonomous controlled peptidoglycan hydrolase (PGase) expression system. A significant increase (9.37-fold) of MV concentration was observed in engineered E. coli Nissle 1917 compared to the wild-type. With the help of this autonomous system, for the first time we experimentally confirmed horizontal gene transfer and nutrient acquisition in a cocultured bacterial consortium. Furthermore, the engineered probiotic E. coli strains with high yield of MVs showed higher activation of the innate immune responses in human embryonic kidney 293T (HEK293T) and human colorectal carcinoma cells (HCT116), thereby demonstrating the great potential of engineering probiotics in immunology and further living therapeutics in humans.}, }
@article {pmid36588930, year = {2022}, author = {Martinez-Vaz, BM and Dodge, AG and Lucero, RM and Stockbridge, RB and Robinson, AA and Tassoulas, LJ and Wackett, LP}, title = {Wastewater bacteria remediating the pharmaceutical metformin: Genomes, plasmids and products.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {10}, number = {}, pages = {1086261}, pmid = {36588930}, issn = {2296-4185}, support = {R35 GM128768/GM/NIGMS NIH HHS/United States ; }, abstract = {Metformin is used globally to treat type II diabetes, has demonstrated anti-ageing and COVID mitigation effects and is a major anthropogenic pollutant to be bioremediated by wastewater treatment plants (WWTPs). Metformin is not adsorbed well by activated carbon and toxic N-chloro derivatives can form in chlorinated water. Most earlier studies on metformin biodegradation have used wastewater consortia and details of the genomes, relevant genes, metabolic products, and potential for horizontal gene transfer are lacking. Here, two metformin-biodegrading bacteria from a WWTP were isolated and their biodegradation characterized. Aminobacter sp. MET metabolized metformin stoichiometrically to guanylurea, an intermediate known to accumulate in some environments including WWTPs. Pseudomonas mendocina MET completely metabolized metformin and utilized all the nitrogen atoms for growth. Pseudomonas mendocina MET also metabolized metformin breakdown products sometimes observed in WWTPs: 1-N-methylbiguanide, biguanide, guanylurea, and guanidine. The genome of each bacterium was obtained. Genes involved in the transport of guanylurea in Aminobacter sp. MET were expressed heterologously and shown to serve as an antiporter to expel the toxic guanidinium compound. A novel guanylurea hydrolase enzyme was identified in Pseudomonas mendocina MET, purified, and characterized. The Aminobacter and Pseudomonas each contained one plasmid of 160 kb and 90 kb, respectively. In total, these studies are significant for the bioremediation of a major pollutant in WWTPs today.}, }
@article {pmid36587809, year = {2023}, author = {Trissi, N and Troczka, BJ and Ozsanlav-Harris, L and Singh, KS and Mallott, M and Aishwarya, V and O'Reilly, A and Bass, C and Wilding, CS}, title = {Differential regulation of the Tor gene homolog drives the red/green pigmentation phenotype in the aphid Myzuspersicae.}, journal = {Insect biochemistry and molecular biology}, volume = {153}, number = {}, pages = {103896}, doi = {10.1016/j.ibmb.2022.103896}, pmid = {36587809}, issn = {1879-0240}, mesh = {Animals ; *Aphids/physiology ; Lycopene/metabolism ; Pigmentation/genetics ; Carotenoids/metabolism ; }, abstract = {In some aphid species, intraspecific variation in body colour is caused by differential carotenoid content: whilst green aphids contain only yellow carotenoids (β-, γ-, and β,γ-carotenes), red aphids additionally possess red carotenoids (torulene and 3,4-didehydrolycopene). Unusually, within animals who typically obtain carotenoids from their diet, ancestral horizontal gene transfer of carotenoid biosynthetic genes from fungi (followed by gene duplication), have imbued aphids with the intrinsic gene repertoire necessary to biosynthesise carotenoids. In the pea aphid, Acyrthosiphon pisum a lycopene (phytoene) desaturase gene (Tor) underpins the red/green phenotype, with this locus present in heterozygous form in red individuals but absent in green aphids, resulting in them being unable to convert lycopene into the red compounds 3,4-didehydrolycopene and torulene. The green peach aphid, Myzus persicae, separated from the pea aphid for ≈45MY also exists as distinct colour variable morphs, with both red and green individuals present. Here, we examined genomic data for both red and green morphs of M. persicae and identified an enlarged (compared to A. pisum) repertoire of 16 carotenoid biosynthetic genes (11 carotenoid desaturases and five carotenoid cyclase/synthase genes). From these, we identify the homolog of A. pisum Tor (here called carotene desaturase 2 or CDE-2) and show through 3D modelling that this homolog can accommodate the torulene precursor lycopene and, through RNA knockdown feeding experiments, demonstrate that disabling CDE-2 expression in red M. persicae clones results in green-coloured offspring. Unlike in A. pisum, we show that functional CDE-2 is present in the genomes of both red and green aphids. However, expression differences between the two colour morphs (350-700 fold CDE-2 overexpression in red clones), potentially driven by variants identified in upstream putative regulatory elements, underpin this phenotype. Thus, whilst aphids have a common origin of their carotenoid biosynthetic pathway, two aphid species separated for over 40MY have evolved very different drivers of intraspecific colour variation.}, }
@article {pmid36586689, year = {2023}, author = {Shi, H and Hu, X and Xu, J and Hu, B and Ma, L and Lou, L}, title = {Conjugation-mediated transfer of antibiotic resistance genes influenced by primary soil components and underlying mechanisms.}, journal = {The Science of the total environment}, volume = {865}, number = {}, pages = {161232}, doi = {10.1016/j.scitotenv.2022.161232}, pmid = {36586689}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Soil ; Bentonite ; Kaolin ; Quartz/pharmacology ; Gene Transfer, Horizontal ; Drug Resistance, Microbial/genetics ; Escherichia coli/genetics ; Genes, Bacterial ; Bacteria/genetics ; Plasmids ; }, abstract = {Soil is the main natural reservoir of antibiotic resistant bacteria and antibiotic resistance genes (ARGs). Their dissemination and proliferation were largely motivated by conjugative transfer, while the influence of soil components on bacterial conjugative transfer and the underlying mechanisms remain poorly understood. In the present study, two Escherichia coli strains were exposed to soil minerals (quartz, kaolinite and montmorillonite) and organic matters (humic acid, biochar and soot) respectively to investigate their impact on ARGs conjugation. The results showed that quartz had no significant effect on conjugation; montmorillonite promoted the growth of the donor, but inhibited the recipient and conjugant; kaolinite and three organic matters significantly promoted the production of conjugant, while biochar promoted and then inhibited it with time prolong. Within the range of bacterial concentration involved in this study, the concentration of conjugant increased with the ratio of the concentration of donor and recipient (RD/R), indicating that the variation of conjugant production was mainly mediated by changing RD/R. Further observation of biochar treatment group showed that the bacterial responses such as cell membrane permeability, cell surface hydrophobicity and biofilm formation ability shifted with the exposure time, which might be a potential factor affecting conjugative transfer. Collectively, our findings suggest that the type and exposure time of soil components jointly affected conjugation, while the change of RD/R and related bacterial responses are the main underlying mechanisms.}, }
@article {pmid36586329, year = {2023}, author = {Nnorom, MA and Saroj, D and Avery, L and Hough, R and Guo, B}, title = {A review of the impact of conductive materials on antibiotic resistance genes during the anaerobic digestion of sewage sludge and animal manure.}, journal = {Journal of hazardous materials}, volume = {446}, number = {}, pages = {130628}, doi = {10.1016/j.jhazmat.2022.130628}, pmid = {36586329}, issn = {1873-3336}, mesh = {Animals ; Humans ; *Sewage/microbiology ; *Genes, Bacterial ; Manure/microbiology ; Anti-Bacterial Agents/pharmacology ; Anaerobiosis ; Drug Resistance, Microbial/genetics ; }, abstract = {The urgent need to reduce the environmental burden of antibiotic resistance genes (ARGs) has become even more apparent as concerted efforts are made globally to tackle the dissemination of antimicrobial resistance. Concerning levels of ARGs abound in sewage sludge and animal manure, and their inadequate attenuation during conventional anaerobic digestion (AD) compromises the safety of the digestate, a nutrient-rich by-product of AD commonly recycled to agricultural land for improvement of soil quality. Exogenous ARGs introduced into the natural environment via the land application of digestate can be transferred from innocuous environmental bacteria to clinically relevant bacteria by horizontal gene transfer (HGT) and may eventually reach humans through food, water, and air. This review, therefore, discusses the prospects of using carbon- and iron-based conductive materials (CMs) as additives to mitigate the proliferation of ARGs during the AD of sewage sludge and animal manure. The review spotlights the core mechanisms underpinning the influence of CMs on the resistome profile, the steps to maximize ARG attenuation using CMs, and the current knowledge gaps. Data and information gathered indicate that CMs can profoundly reduce the abundance of ARGs in the digestate by easing selective pressure on ARGs, altering microbial community structure, and diminishing HGT.}, }
@article {pmid36583227, year = {2023}, author = {Sloan, DB and Warren, JM and Williams, AM and Kuster, SA and Forsythe, ES}, title = {Incompatibility and Interchangeability in Molecular Evolution.}, journal = {Genome biology and evolution}, volume = {15}, number = {1}, pages = {}, pmid = {36583227}, issn = {1759-6653}, support = {R01 GM118046/GM/NIGMS NIH HHS/United States ; T32 GM132057/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {*Hybridization, Genetic ; *Evolution, Molecular ; }, abstract = {There is remarkable variation in the rate at which genetic incompatibilities in molecular interactions accumulate. In some cases, minor changes-even single-nucleotide substitutions-create major incompatibilities when hybridization forces new variants to function in a novel genetic background from an isolated population. In other cases, genes or even entire functional pathways can be horizontally transferred between anciently divergent evolutionary lineages that span the tree of life with little evidence of incompatibilities. In this review, we explore whether there are general principles that can explain why certain genes are prone to incompatibilities while others maintain interchangeability. We summarize evidence pointing to four genetic features that may contribute to greater resistance to functional replacement: (1) function in multisubunit enzyme complexes and protein-protein interactions, (2) sensitivity to changes in gene dosage, (3) rapid rate of sequence evolution, and (4) overall importance to cell viability, which creates sensitivity to small perturbations in molecular function. We discuss the relative levels of support for these different hypotheses and lay out future directions that may help explain the striking contrasts in patterns of incompatibility and interchangeability throughout the history of molecular evolution.}, }
@article {pmid36582150, year = {2024}, author = {Manaia, CM and Aga, DS and Cytryn, E and Gaze, WH and Graham, DW and Guo, J and Leonard, AFC and Li, L and Murray, AK and Nunes, OC and Rodriguez-Mozaz, S and Topp, E and Zhang, T}, title = {The Complex Interplay Between Antibiotic Resistance and Pharmaceutical and Personal Care Products in the Environment.}, journal = {Environmental toxicology and chemistry}, volume = {43}, number = {3}, pages = {637-652}, doi = {10.1002/etc.5555}, pmid = {36582150}, issn = {1552-8618}, support = {MR/P028195/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; *Genes, Bacterial ; Bacteria ; Angiotensin Receptor Antagonists/pharmacology ; Angiotensin-Converting Enzyme Inhibitors/pharmacology ; Drug Resistance, Microbial/genetics ; *Cosmetics ; Pharmaceutical Preparations ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are important environmental contaminants. Nonetheless, what drives the evolution, spread, and transmission of antibiotic resistance dissemination is still poorly understood. The abundance of ARB and ARGs is often elevated in human-impacted areas, especially in environments receiving fecal wastes, or in the presence of complex mixtures of chemical contaminants, such as pharmaceuticals and personal care products. Self-replication, mutation, horizontal gene transfer, and adaptation to different environmental conditions contribute to the persistence and proliferation of ARB in habitats under strong anthropogenic influence. Our review discusses the interplay between chemical contaminants and ARB and their respective genes, specifically in reference to co-occurrence, potential biostimulation, and selective pressure effects, and gives an overview of mitigation by existing man-made and natural barriers. Evidence and strategies to improve the assessment of human health risks due to environmental antibiotic resistance are also discussed. Environ Toxicol Chem 2024;43:637-652. © 2022 SETAC.}, }
@article {pmid36575565, year = {2023}, author = {Chen, H and Tao, S and Li, N and Zhu, Q and Liu, L and Fang, Y and Xu, Y and Liang, W}, title = {Anti-restriction protein ArdA promotes clinical Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae spread and its molecular mechanism.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {78}, number = {2}, pages = {521-530}, doi = {10.1093/jac/dkac423}, pmid = {36575565}, issn = {1460-2091}, mesh = {Humans ; *Klebsiella pneumoniae ; Klebsiella/genetics ; *Klebsiella Infections/microbiology ; Molecular Epidemiology ; Bacterial Proteins/genetics ; beta-Lactamases/genetics/metabolism ; Plasmids ; }, abstract = {BACKGROUND: Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae (KPC-KP) has spread worldwide and has become a major threat to public health. The restriction modification system provides an innate defence of bacteria against plasmids or transposons, while many different types of plasmid encoding the anti-restriction protein ArdA can specifically affect the restriction activity in bacteria.<br><br>OBJECTIVES: To detect the codistribution of ArdA and blaKPC-2 plasmids in KPC-KP and explore the molecular mechanism of ArdA promoting KPC-KP spread.<br><br>METHODS: We collected 65 clinical CRKP isolates from Ningbo, China, and 68 cases of plasmid complete sequences in GenBank to determine the prevalence of ArdA gene on the K. pneumoniae blaKPC-2 plasmid. The anti-restriction function of ArdA in promoting horizontal gene transfer (HGT) was verified by transformation, conjugation and transduction methods, and the pull-down experiment was used to investigate the molecular mechanism of ArdA protein in vitro.<br><br>RESULTS: We found that ArdA was widely distributed in KPC-KP in 100% of cases, which was detected in 0% of drug susceptible K. pneumoniae, and the plasmids containing the ArdA gene in 90% of the 30 cases randomly retrieved from the database. We also verified that ArdA has a good anti-restriction function (P&#x200a;<&#x200a;0.05) through two aspects of HGT (transformation, transduction), and explored the non-occurrence interaction of ArdA and the hsdM subunit protein of EcoKI enzyme from the perspective of protein molecules.<br><br>CONCLUSIONS: These findings suggest that the coexistence advantage of ArdA with the blaKPC-2 plasmids may provide KPC-producing K. pneumoniae with a very efficient evasion of the restriction of type I systems, which not only favours ArdA-containing mobile genetic elements in the same species HGT between bacteria also facilitates HGT between other bacterial species.}, }
@article {pmid36573357, year = {2023}, author = {Bethke, JH and Ma, HR and Tsoi, R and Cheng, L and Xiao, M and You, L}, title = {Vertical and horizontal gene transfer tradeoffs direct plasmid fitness.}, journal = {Molecular systems biology}, volume = {19}, number = {2}, pages = {e11300}, pmid = {36573357}, issn = {1744-4292}, support = {R01 AI125604/AI/NIAID NIH HHS/United States ; R01 GM098642/GM/NIGMS NIH HHS/United States ; R01 EB031869/EB/NIBIB NIH HHS/United States ; }, mesh = {*Gene Transfer, Horizontal ; *Escherichia coli/genetics ; Plasmids/genetics ; Drug Resistance, Microbial ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Plasmid fitness is directed by two orthogonal processes-vertical transfer through cell division and horizontal transfer through conjugation. When considered individually, improvements in either mode of transfer can promote how well a plasmid spreads and persists. Together, however, the metabolic cost of conjugation could create a tradeoff that constrains plasmid evolution. Here, we present evidence for the presence, consequences, and molecular basis of a conjugation-growth tradeoff across 40 plasmids derived from clinical Escherichia coli pathogens. We discover that most plasmids operate below a conjugation efficiency threshold for major growth effects, indicating strong natural selection for vertical transfer. Below this threshold, E. coli demonstrates a remarkable growth tolerance to over four orders of magnitude change in conjugation efficiency. This tolerance fades as nutrients become scarce and horizontal transfer attracts a greater share of host resources. Our results provide insight into evolutionary constraints directing plasmid fitness and strategies to combat the spread of antibiotic resistance.}, }
@article {pmid36572269, year = {2023}, author = {Beltrán de Heredia, I and Garbisu, C and Alkorta, I and Urra, J and González-Gaya, B and Ruiz-Romera, E}, title = {Spatio-seasonal patterns of the impact of wastewater treatment plant effluents on antibiotic resistance in river sediments.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {319}, number = {}, pages = {120883}, doi = {10.1016/j.envpol.2022.120883}, pmid = {36572269}, issn = {1873-6424}, mesh = {*Genes, Bacterial ; Seasons ; *Ecosystem ; Wastewater ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/analysis ; Water ; }, abstract = {There is a growing concern about the risk of antibiotic resistance emergence and dissemination in the environment. Here, we evaluated the spatio-seasonal patterns of the impact of wastewater treatment plant (WWTP) effluents on antibiotic resistance in river sediments. To this purpose, sediment samples were collected in three river basins affected by WWTP effluents in wet (high-water period) and dry (low-water period) hydrological conditions at three locations: (i) upstream the WWTPs; (ii) WWTP effluent discharge points (effluent outfall); and (iii) downstream the WWTPs (500 m downriver from the effluent outfall). The absolute and relative abundances of 9 antibiotic resistance genes (ARGs), 3 mobile genetic element (MGE) genes, and 4 metal resistance genes (MRGs) were quantified in sediment samples, as well as a variety of physicochemical parameters, metal contents, and antibiotic concentrations in both sediment and water samples. In sediments, significantly higher relative abundances of most genes were observed in downstream vs. upstream sampling points. Seasonal changes (higher values in low-water vs. high-water period) were observed for both ARG absolute and relative abundances in sediment samples. Chemical data revealed the contribution of effluents from WWTPs as a source of antibiotic and metal contamination in river ecosystems. The observed positive correlations between ARG and MGE genes relative abundances point out to the role of horizontal gene transfer in antibiotic resistance dissemination. Monitoring plans that take into consideration spatio-temporal patterns must be implemented to properly assess the environmental fate of WWTP-related emerging contaminants in river ecosystems.}, }
@article {pmid36571993, year = {2023}, author = {Su, Z and Wen, D and Gu, AZ and Zheng, Y and Tang, Y and Chen, L}, title = {Industrial effluents boosted antibiotic resistome risk in coastal environments.}, journal = {Environment international}, volume = {171}, number = {}, pages = {107714}, doi = {10.1016/j.envint.2022.107714}, pmid = {36571993}, issn = {1873-6750}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Wastewater ; Bacteria/genetics ; Genes, Bacterial ; Sewage ; }, abstract = {Wastewater treatment plants (WWTPs) have been regarded as an important source of antibiotic resistance genes (ARGs) in environment, but out of municipal domestic WWTPs, few evidences show how environment is affected by industrial WWTPs. Here we chose Hangzhou Bay (HZB), China as our study area, where land-based municipal and industrial WWTPs discharged their effluent into the bay for decades. We adopted high-throughput metagenomic sequencing to examine the antibiotic resistome of the WWTP effluent and coastal sediment samples. And we proposed a conceptual framework for the assessment of antibiotic resistome risk, and a new bioinformatic pipeline for the evaluation of the potential horizontal gene transfer (HGT) frequency. Our results revealed that the diversity and abundance of ARGs in the WWTP's effluent were significantly higher than those in the sediment. Furthermore, the antibiotic resistome in the effluent-receiving area (ERA) showed significant difference from that in HZB. For the first time, we identified that industrial WWTP effluent boosted antibiotic resistome risk in coastal sediment. The crucial evidences included: 1) the proportion of ARGs derived from WWTP activated sludge (WA) was higher (14.3 %) and two high-risky polymyxin resistance genes (mcr-4 and mcr-5) were enriched in the industrial effluent receiving area; 2) the HGT potential was higher between resistant microbiome of the industrial effluent and its ERA sediment; and 3) the highest resistome risk was determined in the industrial effluent, and some biocide resistance genes located on high-risky contigs were related to long-term stress of industrial chemicals. These findings highlight the important effects of industrial activities on the development of environmental antimicrobial resistance.}, }
@article {pmid36571495, year = {2023}, author = {Sun, M and Yuan, S and Xia, R and Ye, M and Balcázar, JL}, title = {Underexplored viral auxiliary metabolic genes in soil: Diversity and eco-evolutionary significance.}, journal = {Environmental microbiology}, volume = {25}, number = {4}, pages = {800-810}, doi = {10.1111/1462-2920.16329}, pmid = {36571495}, issn = {1462-2920}, mesh = {Genes, Viral ; *Bacteriophages/genetics ; Biological Evolution ; Bacteria/metabolism ; *Microbiota/genetics ; Soil ; }, abstract = {Bacterial viruses are the most abundant biological entities in soil ecosystems. Owing to the advent of metagenomics and viromics approaches, an ever-increasing diversity of virus-encoded auxiliary metabolic genes (AMGs) have been identified in soils, including those involved in the transformation of carbon, phosphorus, and sulfur, degradation of organic pollutants, and antibiotic resistance, among other processes. These viral AMGs can alter soil biogeochemical processes and metabolic activities by interfering with bacterial host metabolism. It is recognized that viral AMGs compensate for host bacterial metabolism outputs by encoding accessory functional genes and are favourable for the hosts' adaptation to stressed soil environments. The eco-evolutionary mechanisms behind this fascinating diversity of viral AMGs in soil microbiomes have begun to emerge, such as horizontal gene transfer, lytic-lysogenic conversion, and single-nucleotide polymorphisms. In this mini-review, we summarize recent advances in the diversity and function of virus-encoded AMGs in the soil environment, especially focusing on the evolutionary significance of AMGs involved in virus-host interactions. This mini-review also sheds light on the existing gaps and future perspectives that could have major significance for viral AMGs research in soils.}, }
@article {pmid36568361, year = {2022}, author = {Nayar, G and Terrizzano, I and Seabolt, E and Agarwal, A and Boucher, C and Ruiz, J and Slizovskiy, IB and Kaufman, JH and Noyes, NR}, title = {ggMOB: Elucidation of genomic conjugative features and associated cargo genes across bacterial genera using genus-genus mobilization networks.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {1024577}, pmid = {36568361}, issn = {1664-8021}, abstract = {Horizontal gene transfer mediated by conjugation is considered an important evolutionary mechanism of bacteria. It allows organisms to quickly evolve new phenotypic properties including antimicrobial resistance (AMR) and virulence. The frequency of conjugation-mediated cargo gene exchange has not yet been comprehensively studied within and between bacterial taxa. We developed a frequency-based network of genus-genus conjugation features and candidate cargo genes from whole-genome sequence data of over 180,000 bacterial genomes, representing 1,345 genera. Using our method, which we refer to as ggMOB, we revealed that over half of the bacterial genomes contained one or more known conjugation features that matched exactly to at least one other genome. Moreover, the proportion of genomes containing these conjugation features varied substantially by genus and conjugation feature. These results and the genus-level network structure can be viewed interactively in the ggMOB interface, which allows for user-defined filtering of conjugation features and candidate cargo genes. Using the network data, we observed that the ratio of AMR gene representation in conjugative versus non-conjugative genomes exceeded 5:1, confirming that conjugation is a critical force for AMR spread across genera. Finally, we demonstrated that clustering genomes by conjugation profile sometimes correlated well with classical phylogenetic structuring; but that in some cases the clustering was highly discordant, suggesting that the importance of the accessory genome in driving bacterial evolution may be highly variable across both time and taxonomy. These results can advance scientific understanding of bacterial evolution, and can be used as a starting point for probing genus-genus gene exchange within complex microbial communities that include unculturable bacteria. ggMOB is publicly available under the GNU licence at https://ruiz-hci-lab.github.io/ggMOB/.}, }
@article {pmid36567403, year = {2023}, author = {Feng, R and Duan, L and Shen, S and Cheng, Y and Wang, Y and Wang, W and Yang, S}, title = {Temporal dynamic of antibiotic resistance genes in the Zaohe-Weihe hyporheic zone: driven by oxygen and bacterial community.}, journal = {Ecotoxicology (London, England)}, volume = {32}, number = {1}, pages = {57-72}, doi = {10.1007/s10646-022-02616-5}, pmid = {36567403}, issn = {1573-3017}, mesh = {*Genes, Bacterial ; *Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Sulfanilamide ; }, abstract = {The widespread spread of antibiotic resistance genes (ARGs) in hyporheic zone (HZ) has become an emerging environmental problem due to their potentially harmful nature. In this research, three different oxygen treatment systems were set up to study the effects of oxygen changes on the abundance of ARGs in the HZ. In addition, the effects of temperature and salinity on ARGs were investigated under aerobic and anaerobic systems, respectively. The bacterial community composition of sediment samples and the relationship with ARGs were analyzed. The explanation ratio and causality of the driving factors affecting ARGs were analyzed using variation partitioning analysis (VPA) and structural equation model (SEM). The relative abundance of ARGs and mobile genetic elements (MGEs) in the anaerobic system increased significantly, which was higher than that in the aerobic system and the aerobic-anaerobic interaction system. The experiment of salinity and temperature also further proved this result. There were many bacterial communities that affected tetracycline and sulfonamide ARGs in sediments, and these host bacteria are mainly concentrated in Proteobacteria, Firmicutes and Bacteroidetes. VPA and SEM further revealed that the abundance of ARGs was mainly influenced by changes in bacterial communities and oxygen conditions, and horizontal gene transfer (HGT) of MGEs also had a positive effect on the spread of ARGs. Those findings suggest that complex oxygen conditions in the HZ alter bacterial communities and promote MGEs-mediated horizontal transfer, which together lead to the spread of ARGs. This study has value as a reference for formulating effective strategies to minimize the propagation of ARGs in underground environment.}, }
@article {pmid36563663, year = {2022}, author = {Vatanen, T and Jabbar, KS and Ruohtula, T and Honkanen, J and Avila-Pacheco, J and Siljander, H and Stražar, M and Oikarinen, S and Hyöty, H and Ilonen, J and Mitchell, CM and Yassour, M and Virtanen, SM and Clish, CB and Plichta, DR and Vlamakis, H and Knip, M and Xavier, RJ}, title = {Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism.}, journal = {Cell}, volume = {185}, number = {26}, pages = {4921-4936.e15}, pmid = {36563663}, issn = {1097-4172}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; }, mesh = {Female ; Humans ; Infant ; Pregnancy ; *Gastrointestinal Microbiome/genetics ; *Microbiota/genetics ; Mothers ; Breast Feeding ; Feces ; Interspersed Repetitive Sequences ; }, abstract = {The perinatal period represents a critical window for cognitive and immune system development, promoted by maternal and infant gut microbiomes and their metabolites. Here, we tracked the co-development of microbiomes and metabolomes from late pregnancy to 1 year of age using longitudinal multi-omics data from a cohort of 70 mother-infant dyads. We discovered large-scale mother-to-infant interspecies transfer of mobile genetic elements, frequently involving genes associated with diet-related adaptations. Infant gut metabolomes were less diverse than maternal but featured hundreds of unique metabolites and microbe-metabolite associations not detected in mothers. Metabolomes and serum cytokine signatures of infants who received regular-but not extensively hydrolyzed-formula were distinct from those of exclusively breastfed infants. Taken together, our integrative analysis expands the concept of vertical transmission of the gut microbiome and provides original insights into the development of maternal and infant microbiomes and metabolomes during late pregnancy and early life.}, }
@article {pmid36561977, year = {2022}, author = {González-Villarreal, JA and González-Lozano, KJ and Aréchiga-Carvajal, ET and Morlett-Chávez, JA and Luévanos-Escareño, MP and Balagurusamy, N and Salinas-Santander, MA}, title = {Molecular mechanisms of multidrug resistance in clinically relevant enteropathogenic bacteria (Review).}, journal = {Experimental and therapeutic medicine}, volume = {24}, number = {6}, pages = {753}, pmid = {36561977}, issn = {1792-1015}, abstract = {Multidrug resistant (MDR) enteropathogenic bacteria are a growing problem within the clinical environment due to their acquired tolerance to a wide range of antibiotics, thus causing severe illnesses and a tremendous economic impact in the healthcare sector. Due to its difficult treatment, knowledge and understanding of the molecular mechanisms that confer this resistance are needed. The aim of the present review is to describe the mechanisms of antibiotic resistance from a genomic perspective observed in bacteria, including naturally acquired resistance. The present review also discusses common pharmacological and alternative treatments used in cases of infection caused by MDR bacteria, thus covering necessary information for the development of novel antimicrobials and adjuvant molecules inhibiting bacterial proliferation.}, }
@article {pmid36560776, year = {2022}, author = {Nale, JY and Thanki, AM and Rashid, SJ and Shan, J and Vinner, GK and Dowah, ASA and Cheng, JKJ and Sicheritz-Pontén, T and Clokie, MRJ}, title = {Diversity, Dynamics and Therapeutic Application of Clostridioides difficile Bacteriophages.}, journal = {Viruses}, volume = {14}, number = {12}, pages = {}, pmid = {36560776}, issn = {1999-4915}, support = {RM38G0140/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Humans ; *Bacteriophages/genetics ; *Clostridioides difficile ; Clostridioides ; Prophages/genetics ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {Clostridioides difficile causes antibiotic-induced diarrhoea and pseudomembranous colitis in humans and animals. Current conventional treatment relies solely on antibiotics, but C. difficile infection (CDI) cases remain persistently high with concomitant increased recurrence often due to the emergence of antibiotic-resistant strains. Antibiotics used in treatment also induce gut microbial imbalance; therefore, novel therapeutics with improved target specificity are being investigated. Bacteriophages (phages) kill bacteria with precision, hence are alternative therapeutics for the targeted eradication of the pathogen. Here, we review current progress in C. difficile phage research. We discuss tested strategies of isolating C. difficile phages directly, and via enrichment methods from various sample types and through antibiotic induction to mediate prophage release. We also summarise phenotypic phage data that reveal their morphological, genetic diversity, and various ways they impact their host physiology and pathogenicity during infection and lysogeny. Furthermore, we describe the therapeutic development of phages through efficacy testing in different in vitro, ex vivo and in vivo infection models. We also discuss genetic modification of phages to prevent horizontal gene transfer and improve lysis efficacy and formulation to enhance stability and delivery of the phages. The goal of this review is to provide a more in-depth understanding of C. difficile phages and theoretical and practical knowledge on pre-clinical, therapeutic evaluation of the safety and effectiveness of phage therapy for CDI.}, }
@article {pmid36560636, year = {2022}, author = {Ács, N and Holohan, R and Dunne, LJ and Fernandes, AR and Clooney, AG and Draper, LA and Ross, RP and Hill, C}, title = {Comparing In Vitro Faecal Fermentation Methods as Surrogates for Phage Therapy Application.}, journal = {Viruses}, volume = {14}, number = {12}, pages = {}, pmid = {36560636}, issn = {1999-4915}, mesh = {Humans ; Fermentation ; *Phage Therapy ; Feces ; Gastrointestinal Tract ; *Bacteriophages/genetics ; }, abstract = {The human microbiome and its importance in health and disease have been the subject of numerous research articles. Most microbes reside in the digestive tract, with up to 10[12] cells per gram of faecal material found in the colon. In terms of gene number, it has been estimated that the gut microbiome harbours >100 times more genes than the human genome. Several human intestinal diseases are strongly associated with disruptions in gut microbiome composition. Less studied components of the gut microbiome are the bacterial viruses called bacteriophages that may be present in numbers equal to or greater than the prokaryotes. Their potential to lyse their bacterial hosts, or to act as agents of horizontal gene transfer makes them important research targets. In this study in vitro faecal fermentation systems were developed and compared for their ability to act as surrogates for the human colon. Changes in bacterial and viral composition occurred after introducing a high-titre single phage preparation both with and without a known bacterial host during the 24 h-long fermentation. We also show that during this timeframe 50 mL plastic tubes can provide data similar to that generated in a sophisticated faecal fermenter system. This knowledge can guide us to a better understanding of the short-term impact of bacteriophage transplants on the bacteriomes and viromes of human recipients.}, }
@article {pmid36558750, year = {2022}, author = {de Brito, FAE and de Freitas, APP and Nascimento, MS}, title = {Multidrug-Resistant Biofilms (MDR): Main Mechanisms of Tolerance and Resistance in the Food Supply Chain.}, journal = {Pathogens (Basel, Switzerland)}, volume = {11}, number = {12}, pages = {}, pmid = {36558750}, issn = {2076-0817}, support = {001//Coordena&#xe7;&#xe3;o de Aperfeicoamento de Pessoal de N&#xed;vel Superior/ ; 403925/2021-5//National Council for Scientific and Technological Development/ ; }, abstract = {Biofilms are mono- or multispecies microbial communities enclosed in an extracellular matrix (EPS). They have high potential for dissemination and are difficult to remove. In addition, biofilms formed by multidrug-resistant strains (MDRs) are even more aggravated if we consider antimicrobial resistance (AMR) as an important public health issue. Quorum sensing (QS) and horizontal gene transfer (HGT) are mechanisms that significantly contribute to the recalcitrance (resistance and tolerance) of biofilms, making them more robust and resistant to conventional sanitation methods. These mechanisms coordinate different strategies involved in AMR, such as activation of a quiescent state of the cells, moderate increase in the expression of the efflux pump, decrease in the membrane potential, antimicrobial inactivation, and modification of the antimicrobial target and the architecture of the EPS matrix itself. There are few studies investigating the impact of the use of inhibitors on the mechanisms of recalcitrance and its impact on the microbiome. Therefore, more studies to elucidate the effect and applications of these methods in the food production chain and the possible combination with antimicrobials to establish new strategies to control MDR biofilms are needed.}, }
@article {pmid36555178, year = {2022}, author = {Janczarek, M}, title = {The Ros/MucR Zinc-Finger Protein Family in Bacteria: Structure and Functions.}, journal = {International journal of molecular sciences}, volume = {23}, number = {24}, pages = {}, pmid = {36555178}, issn = {1422-0067}, support = {2018/31/B/NZ9/00663//National Science Center/ ; }, mesh = {Phylogeny ; Amino Acid Sequence ; *Bacterial Proteins/metabolism ; *Zinc Fingers/genetics ; Transcription Factors/genetics ; Bacteria/metabolism ; Zinc/metabolism ; }, abstract = {Ros/MucR is a widespread family of bacterial zinc-finger-containing proteins that integrate multiple functions, such as symbiosis, virulence, transcription regulation, motility, production of surface components, and various other physiological processes in cells. This regulatory protein family is conserved in bacteria and is characterized by its zinc-finger motif, which has been proposed as the ancestral domain from which the eukaryotic C2H2 zinc-finger structure has evolved. The first prokaryotic zinc-finger domain found in the transcription regulator Ros was identified in Agrobacterium tumefaciens. In the past decades, a large body of evidence revealed Ros/MucR as pleiotropic transcriptional regulators that mainly act as repressors through oligomerization and binding to AT-rich target promoters. The N-terminal domain and the zinc-finger-bearing C-terminal region of these regulatory proteins are engaged in oligomerization and DNA binding, respectively. These properties of the Ros/MucR proteins are similar to those of xenogeneic silencers, such as H-NS, MvaT, and Lsr2, which are mainly found in other lineages. In fact, a novel functional model recently proposed for this protein family suggests that they act as H-NS-'like' gene silencers. The prokaryotic zinc-finger domain exhibits interesting structural and functional features that are different from that of its eukaryotic counterpart (a βββα topology), as it folds in a significantly larger zinc-binding globular domain (a βββαα topology). Phylogenetic analysis of Ros/MucR homologs suggests an ancestral origin of this type of protein in α-Proteobacteria. Furthermore, multiple duplications and lateral gene transfer events contributing to the diversity and phyletic distribution of these regulatory proteins were found in bacterial genomes.}, }
@article {pmid36551459, year = {2022}, author = {Lienen, T and Grobbel, M and Tenhagen, BA and Maurischat, S}, title = {Plasmid-Coded Linezolid Resistance in Methicillin-Resistant Staphylococcus aureus from Food and Livestock in Germany.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {12}, pages = {}, pmid = {36551459}, issn = {2079-6382}, support = {1322-769//Federal Institute for Risk Assessment/ ; }, abstract = {Resistance of methicillin-resistant Staphylococcus aureus (MRSA) from food and livestock to last resort antibiotics such as linezolid is highly concerning, since treatment options for infections in humans might be diminished. Known mechanisms of linezolid resistance include point mutations in the 23S rRNA gene and in the ribosomal proteins L3, L4 and L22 as well as an acquisition of the cfr, optrA or poxtA gene. The objective of our study was to characterize antimicrobial resistance (AMR) determinants and phylogenetic relationships among linezolid-resistant (LR-) MRSA from food and livestock. In total, from more than 4000 incoming isolates in the years 2012 to 2021, only two strains from 2015 originating from pig samples exhibited linezolid resistance in the antimicrobial susceptibility testing with MICs of ≥8 mg/L. These LR-MRSA were characterized in detail by whole-genome sequencing and phylogenetic analyses using cgMLST. The LR-MRSA strains showed resistances to ten and eight different antibiotics, respectively. Both strains harbored plasmid-coded cfr genes mediating the linezolid resistance. The cfr genes showed identical sequences in both strains. In addition to the cfr gene, genes for phenicol and clindamycin resistance were detected on the respective plasmids, opening the possibility for a co-selection. The LR-MRSA differed distantly in the phylogenetic analyses and also to other MRSA from pig samples in the year 2015. In conclusion, the occurrence of LR-MRSA in food and livestock seems to be very rare in Germany. However, carriage of plasmids with linezolid resistance determinants could lead to further linezolid-resistant strains by horizontal gene transfer.}, }
@article {pmid36549493, year = {2023}, author = {Abudureheman, M and Ailijiang, N and Mamat, A and Feng, Y and He, C and Pu, M}, title = {Enhanced biodegradation of fluoroquinolones and the changes of bacterial communities and antibiotic-resistant genes under intermittent electrical stimulation.}, journal = {Environmental research}, volume = {219}, number = {}, pages = {115127}, doi = {10.1016/j.envres.2022.115127}, pmid = {36549493}, issn = {1096-0953}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Fluoroquinolones/pharmacology/analysis/metabolism ; Wastewater ; Bacteria/genetics/metabolism ; Electric Stimulation ; Genes, Bacterial ; }, abstract = {In this study, an anaerobic-aerobic coupling system under intermittent electrical stimulation was used to improve the biodegradation of synthetic wastewater containing fluoroquinolones (FQs). The effect of electrical stimulation on FQ removal performance is more pronounced with appropriate voltage and hydraulic retention time. In addition, the combination of anaerobic-anodic and aerobic-cathodic chambers is more conducive to improving the removal efficiency of FQs. Under 0.9 V, the removal efficiencies of ofloxacin, norfloxacin, ciprofloxacin, and enrofloxacin were significantly improved in the anaerobic-anodic and aerobic-cathodic system. The contribution of the anaerobic/aerobic anodic chambers to FQ removal was greater than that of the anaerobic/aerobic cathodic chambers. Electrical stimulation selectively enriched electroactive bacteria related to biodegradation (Desulfovibrio and Terrimonas), antibiotic-resistant bacteria (Atopobium and Neochlamydia), and nitrifying bacteria (SM1A02 and Reyranella). This study indicated the potential effectiveness of intermittent electrical stimulation in treating fluoroquinolone-containing wastewater in a biofilm reactor. However, electrical stimulation led to an increase in mobile genetic elements , induced horizontal gene transfer and enriched resistant bacteria, which accelerated the spread of antibiotic-resistant genes (ARGs) in the system, indicating that the diffusion of ARGs remains a challenge.}, }
@article {pmid36539881, year = {2022}, author = {Kwun, MJ and Ion, AV and Cheng, HC and D'Aeth, JC and Dougan, S and Oggioni, MR and Goulding, DA and Bentley, SD and Croucher, NJ}, title = {Post-vaccine epidemiology of serotype 3 pneumococci identifies transformation inhibition through prophage-driven alteration of a non-coding RNA.}, journal = {Genome medicine}, volume = {14}, number = {1}, pages = {144}, pmid = {36539881}, issn = {1756-994X}, support = {102169/Z/13/Z/WT_/Wellcome Trust/United Kingdom ; MR/T016434/1/MRC_/Medical Research Council/United Kingdom ; BB/N002903/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 206194/WT_/Wellcome Trust/United Kingdom ; 104169/Z/14/A/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MR/R015600/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; *Streptococcus pneumoniae/genetics ; Serogroup ; *Pneumococcal Infections/epidemiology/prevention &amp; control/microbiology ; Prophages/genetics ; Pneumococcal Vaccines ; Vaccines, Conjugate ; RNA, Untranslated/genetics/pharmacology ; }, abstract = {BACKGROUND: The respiratory pathogen Streptococcus pneumoniae (the pneumococcus) is a genetically diverse bacterium associated with over 101 immunologically distinct polysaccharide capsules (serotypes). Polysaccharide conjugate vaccines (PCVs) have successfully eliminated multiple targeted serotypes, yet the mucoid serotype 3 has persisted despite its inclusion in PCV13. This capsule type is predominantly associated with a single globally disseminated strain, GPSC12 (clonal complex 180).<br><br>METHODS: A genomic epidemiology study combined previous surveillance datasets of serotype 3 pneumococci to analyse the population structure, dynamics,&#xa0;and differences in rates of diversification within GPSC12 during the period of PCV introductions. Transcriptomic analyses, whole genome sequencing, mutagenesis, and electron microscopy were used to characterise the phenotypic impact of loci hypothesised to affect this strain's evolution.<br><br>RESULTS: GPSC12 was split into clades by a genomic analysis. Clade I, the most common, rarely underwent transformation, but was typically infected with the prophage &#x3d5;OXC141. Prior to the introduction of PCV13, this clade's composition shifted towards a &#x3d5;OXC141-negative subpopulation in a systematically sampled UK collection. In the post-PCV13 era, more rapidly recombining non-Clade I isolates, also &#x3d5;OXC141-negative, have risen in prevalence. The low in vitro transformation efficiency of a Clade I isolate could not be fully explained by the ~100-fold reduction attributable to the serotype 3 capsule. Accordingly, prophage &#x3d5;OXC141 was found to modify csRNA3, a non-coding RNA that inhibits the induction of transformation. This alteration was identified in ~30% of all pneumococci and was particularly common in the unusually clonal serotype 1 GPSC2 strain. RNA-seq and quantitative reverse transcriptase PCR experiments using a genetically tractable pneumococcus demonstrated the altered csRNA3 was more effective at inhibiting production of the competence-stimulating peptide pheromone. This resulted in a reduction in the induction of competence for transformation.<br><br>CONCLUSION: This interference with the quorum sensing needed to induce competence reduces the risk of the prophage being deleted by homologous recombination. Hence the selfish prophage-driven alteration of a regulatory RNA limits cell-cell communication and horizontal gene transfer, complicating the interpretation of post-vaccine population dynamics.}, }
@article {pmid36537743, year = {2022}, author = {Lisboa, MP and Canal, D and Filgueiras, JPC and Turchetto-Zolet, AC}, title = {Molecular evolution and diversification of phytoene synthase (PSY) gene family.}, journal = {Genetics and molecular biology}, volume = {45}, number = {4}, pages = {e20210411}, pmid = {36537743}, issn = {1415-4757}, abstract = {Phytoene synthase (PSY) is a crucial enzyme required for carotenoid biosynthesis, encoded by a gene family conserved in carotenoid-producing organisms. This gene family is diversified in angiosperms through distinct duplication events. Understanding diversification patterns and the evolutionary history of the PSY gene family is important for explaining carotenogenesis in different plant tissues. This study identified 351 PSY genes in 166 species, including Viridiplantae, brown and red algae, cyanobacteria, fungi, arthropods, and bacteria. All PSY genes displayed conserved intron/exon organization. Fungi and arthropod PSY sequences were grouped with prokaryote PSY, suggesting the occurrence of horizontal gene transfer. Angiosperm PSY is split into five subgroups. One includes the putative ortholog of PSY3 (Subgroup E3) from eudicots, and the other four subgroups include PSY from both monocots and eudicots (subgroups E1, E2, M1, and M2). Expression profile analysis revealed that PSY genes are constitutively expressed across developmental stages and anatomical parts, except for the eudicot PSY3, with root-specific expression. This study elucidates the molecular evolution and diversification of the PSY gene family, furthering our understanding of variations in carotenogenesis.}, }
@article {pmid36536072, year = {2023}, author = {Camargo, AP and de Souza, RSC and Jose, J and Gerhardt, IR and Dante, RA and Mukherjee, S and Huntemann, M and Kyrpides, NC and Carazzolle, MF and Arruda, P}, title = {Plant microbiomes harbor potential to promote nutrient turnover in impoverished substrates of a Brazilian biodiversity hotspot.}, journal = {The ISME journal}, volume = {17}, number = {3}, pages = {354-370}, pmid = {36536072}, issn = {1751-7370}, mesh = {*Ecosystem ; Brazil ; Soil Microbiology ; Biodiversity ; *Microbiota ; Bacteria/genetics/metabolism ; Plants/metabolism ; Soil/chemistry ; Phosphorus/metabolism ; Nitrogen/metabolism ; }, abstract = {The substrates of the Brazilian campos rupestres, a grassland ecosystem, have extremely low concentrations of phosphorus and nitrogen, imposing restrictions to plant growth. Despite that, this ecosystem harbors almost 15% of the Brazilian plant diversity, raising the question of how plants acquire nutrients in such a harsh environment. Here, we set out to uncover the taxonomic profile, the compositional and functional differences and similarities, and the nutrient turnover potential of microbial communities associated with two plant species of the campos rupestres-dominant family Velloziaceae that grow over distinct substrates (soil and rock). Using amplicon sequencing data, we show that, despite the pronounced composition differentiation, the plant-associated soil and rock communities share a core of highly efficient colonizers that tend to be highly abundant and is enriched in 21 bacterial families. Functional investigation of metagenomes and 522 metagenome-assembled genomes revealed that the microorganisms found associated to plant roots are enriched in genes involved in organic compound intake, and phosphorus and nitrogen turnover. We show that potential for phosphorus transport, mineralization, and solubilization are mostly found within bacterial families of the shared microbiome, such as Xanthobacteraceae and Bryobacteraceae. We also detected the full repertoire of nitrogen cycle-related genes and discovered a lineage of Isosphaeraceae that acquired nitrogen-fixing potential via horizontal gene transfer and might be also involved in nitrification via a metabolic handoff association with Binataceae. We highlight that plant-associated microbial populations in the campos rupestres harbor a genetic repertoire with potential to increase nutrient availability and that the microbiomes of biodiversity hotspots can reveal novel mechanisms of nutrient turnover.}, }
@article {pmid36532464, year = {2022}, author = {Li, P and Luo, W and Xiang, TX and Jiang, Y and Liu, P and Wei, DD and Fan, L and Huang, S and Liao, W and Liu, Y and Zhang, W}, title = {Horizontal gene transfer via OMVs co-carrying virulence and antimicrobial-resistant genes is a novel way for the dissemination of carbapenem-resistant hypervirulent Klebsiella pneumoniae.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {945972}, pmid = {36532464}, issn = {1664-302X}, abstract = {INTRODUCTION: The rapidly increased isolation rate of CR-HvKP worldwide has brought great difficulties in controlling clinical infection. Moreover, it has been demonstrated that the transmission of drug-resistant genes among bacteria can be mediated by outer membrane vesicles (OMVs), which is a new way of horizontal gene transfer (HGT). The transmission of virulence genes among bacteria has also been well studied; however, it remains unclear whether virulence and drug-resistant genes can be co-transmitted simultaneously. Co-transmission of virulence and drug-resistant genes is essential for the formation and prevalence of CR-HvKP.<br><br>METHODS: First, we isolated OMVs from CR-HvKP by cushioned-density gradient ultracentrifugation (C-DGUC). TEM and DLS were used to examine the morphology and size of bacterial OMVs. OMV-mediated gene transfer in liquid cultures and the acquisition of the carbapenem gene and virulence gene was confirmed using colony-PCR. Antimicrobial susceptibility testing, mCIM and eCIM were conducted for the resistance of transformant. Serum killing assay, assessment of the anti-biofilm effect and galleria mellonella infection model, mucoviscosity assay, extraction and quantification of capsules were verified the virulence of transformant. Pulsed-field gel electrophoresis (PFGE), S1 nuclease-pulsed-field gel electrophoresis (S1-PFGE), Southern blotting hybridization confirmed the plasmid of transformant.<br><br>RESULTS: Firstly, OMVs were isolated from CR-HvKP NUHL30457 (K2, ST86). TEM and DLS analyses revealed the spherical morphology of the vesicles. Secondly, our study demonstrated that CR-HvKP delivered genetic material, incorporated DNA within the OMVs, and protected it from degradation by extracellular exonucleases. Thirdly, the vesicular lumen DNA was delivered to the recipient cells after determining the presence of virulence and carbapenem-resistant genes in the CR-HvKP OMVs. Importantly, S1-PFGE and Southern hybridization analysis of the 700603 transformant strain showed that the transformant contained both drug-resistant and virulence plasmids.<br><br>DISCUSSION: In the present study, we aimed to clarify the role of CRHvKP-OMVs in transmitting CR-HvKP among K. pneumoniae. Collectively, our findings provided valuable insights into the evolution of CR-HvKP.}, }
@article {pmid36532424, year = {2022}, author = {Pillay, S and Calderón-Franco, D and Urhan, A and Abeel, T}, title = {Metagenomic-based surveillance systems for antibiotic resistance in non-clinical settings.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1066995}, pmid = {36532424}, issn = {1664-302X}, abstract = {The success of antibiotics as a therapeutic agent has led to their ineffectiveness. The continuous use and misuse in clinical and non-clinical areas have led to the emergence and spread of antibiotic-resistant bacteria and its genetic determinants. This is a multi-dimensional problem that has now become a global health crisis. Antibiotic resistance research has primarily focused on the clinical healthcare sectors while overlooking the non-clinical sectors. The increasing antibiotic usage in the environment - including animals, plants, soil, and water - are drivers of antibiotic resistance and function as a transmission route for antibiotic resistant pathogens and is a source for resistance genes. These natural compartments are interconnected with each other and humans, allowing the spread of antibiotic resistance via horizontal gene transfer between commensal and pathogenic bacteria. Identifying and understanding genetic exchange within and between natural compartments can provide insight into the transmission, dissemination, and emergence mechanisms. The development of high-throughput DNA sequencing technologies has made antibiotic resistance research more accessible and feasible. In particular, the combination of metagenomics and powerful bioinformatic tools and platforms have facilitated the identification of microbial communities and has allowed access to genomic data by bypassing the need for isolating and culturing microorganisms. This review aimed to reflect on the different sequencing techniques, metagenomic approaches, and bioinformatics tools and pipelines with their respective advantages and limitations for antibiotic resistance research. These approaches can provide insight into resistance mechanisms, the microbial population, emerging pathogens, resistance genes, and their dissemination. This information can influence policies, develop preventative measures and alleviate the burden caused by antibiotic resistance.}, }
@article {pmid36532220, year = {2022}, author = {Boury, N and Van den Bogaard, MED and Wasendorf, C and Amon, J and Judson, S and Maroushek, SR and Peters, NT}, title = {The Use of a Multimodal Case Study To Illustrate Microbial Genetics, Metabolism, and Evolution: The Emergence of VRSA-1.}, journal = {Journal of microbiology &amp; biology education}, volume = {23}, number = {3}, pages = {}, pmid = {36532220}, issn = {1935-7877}, abstract = {Antibiotic Resistance (ABR) is a global concern and while many students are aware of this issue, many of them are unclear on the mechanisms by which ABR may emerge. The mechanism of horizontal gene transfer is something many students are not familiar with. In this curriculum contribution we present 2 versions of an 'interrupted case study' that is designed as an introduction to horizontal gene transfer for early major students and as a review case for advanced major students in biology and life sciences. The case is based on an authentic patient who developed infections with both methicillin resistant Staphylococcus aureus and vancomycin resistant S. aureus. The interrupted case study is appropriate for small and large groups and engages students while content is introduced in a highly structured way. This type of case study can be done by novice and seasoned instructors and lead to considerable learning gains in both introductory and intermediate microbiology courses.}, }
@article {pmid36528203, year = {2023}, author = {Jaiswal, S and Singh, DK and Shukla, P}, title = {Degradation effectiveness of hexachlorohexane (ϒ-HCH) by bacterial isolate Bacillus cereus SJPS-2, its gene annotation for bioremediation and comparison with Pseudomonas putida KT2440.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {318}, number = {}, pages = {120867}, doi = {10.1016/j.envpol.2022.120867}, pmid = {36528203}, issn = {1873-6424}, mesh = {*Hexachlorocyclohexane/metabolism ; Biodegradation, Environmental ; *Pseudomonas putida/genetics ; Bacillus cereus/genetics ; Molecular Sequence Annotation ; }, abstract = {The contamination of Hexachlorohexane (Lindane) in soil and water has toxic effects due to its persistent nature. In our study, an indigenous HCH (gamma isomer) degrading bacterium viz Bacillus cereus SJPS-2 was isolated from Yamuna river water using enrichment culture method. The growth curve indicated that Bacillus cereus SJPS-2 was able to degrade ϒ-HCH effectively with 80.98% degradation. Further, process was improved by using immobilization using alginate beads which showed enhanced degradation (89.34%). Interestingly, in presence of fructose, the ϒ-HCH degradation was up to 79.24% with exponential growth curve whereas the degradation was only 5.61% in presence of glucose revealing diauxic growth curve. Furthermore, The FTIR results confirmed the potential lindane degradation capability of Bacillus cereus SJPS-2 and the bonds were recorded at wavelengths viz. 2900-2500 cm-[1], 3300-2800 cm-[1] and 785-540 cm-[1]. Similarity, the GC studies also reconfirmed the degradation potential with retention time (RT) of ethyl acetate and lindane was 2.12 and 11.0 respectively. Further, we studied the metabolic pathway involved for lindane utilization in Bacillus cereus using KEGG-KASS and functional gene annotation through Rapid Annotation using Subsystems Technology (RAST) resulted in the annotation of the lin genes (lin A, lin B, lin C, lin X, lin D, lin E) and respective encoding enzymes. The comparative ϒ-HCH degradation potential of B. cereus and P. putida KT2440 was also evaluated. The island viewer showed the different colors on circular genome indicate the coordinates of genomic islands resulted with some common genomic islands (GEIs) between both bacteria indicating the possibility of horizontal gene transfer at contaminated site or natural environment. These genomic islands (GEIs) contribute in the rearrangement genetic material or to evolve bacteria in stress conditions, as a result the metabolic pathways evolve by formation of catabolic genes. This study establishes the potential of Bacillus cereus SJPS-2 for effectual ϒ-HCH degradation.}, }
@article {pmid36527364, year = {2023}, author = {Knoop, V}, title = {C-to-U and U-to-C: RNA editing in plant organelles and beyond.}, journal = {Journal of experimental botany}, volume = {74}, number = {7}, pages = {2273-2294}, doi = {10.1093/jxb/erac488}, pmid = {36527364}, issn = {1460-2431}, mesh = {*RNA Editing ; Uridine/genetics/metabolism ; *Organelles/genetics/metabolism ; Plants/genetics/metabolism ; Chloroplasts/metabolism ; RNA, Plant/genetics/metabolism ; Plant Proteins/metabolism ; }, abstract = {The genomes in the two energy-converting organelles of plant cells, chloroplasts and mitochondria, contain numerous 'errors' that are corrected at the level of RNA transcript copies. The genes encoded in the two endosymbiotic organelles would not function properly if their transcripts were not altered by site-specific cytidine-to-uridine (C-to-U) exchanges and by additional reverse U-to-C exchanges in hornworts, lycophytes, and ferns. These peculiar processes of plant RNA editing, re-establishing genetic information that could alternatively be present at the organelle genome level, has spurred much research over >30 years. Lately new studies have revealed numerous interesting insights, notably on the biochemical machinery identifying specific pyrimidine nucleobases for conversion from C to U and vice versa. Here, I will summarize prominent research findings that lately have contributed to our better understanding of these phenomena introducing an added layer of information processing in plant cells. Some of this recent progress is based on the successful functional expression of plant RNA editing factors in bacteria and mammalian cells. These research approaches have recapitulated natural processes of horizontal gene transfer through which some protist lineages seem to have acquired plant RNA editing factors and adapted them functionally for their own purposes.}, }
@article {pmid36525956, year = {2022}, author = {Liu, HW and Roisné-Hamelin, F and Beckert, B and Li, Y and Myasnikov, A and Gruber, S}, title = {DNA-measuring Wadjet SMC ATPases restrict smaller circular plasmids by DNA cleavage.}, journal = {Molecular cell}, volume = {82}, number = {24}, pages = {4727-4740.e6}, doi = {10.1016/j.molcel.2022.11.015}, pmid = {36525956}, issn = {1097-4164}, mesh = {*Adenosine Triphosphatases/genetics/metabolism ; *DNA Cleavage ; Plasmids/genetics ; Chromosomes/metabolism ; DNA/genetics ; Cell Cycle Proteins/genetics ; Chromosomes, Bacterial/genetics/metabolism ; }, abstract = {Structural maintenance of chromosome (SMC) complexes fold DNA by loop extrusion to support chromosome segregation and genome maintenance. Wadjet systems (JetABCD/MksBEFG/EptABCD) are derivative SMC complexes with roles in bacterial immunity against selfish DNA. Here, we show that JetABCD restricts circular plasmids with an upper size limit of about 100 kb, whereas a linear plasmid evades restriction. Purified JetABCD complexes cleave circular DNA molecules, regardless of the DNA helical topology; cleavage is DNA sequence nonspecific and depends on the SMC ATPase. A cryo-EM structure reveals a distinct JetABC dimer-of-dimers geometry, with the two SMC dimers facing in opposite direction-rather than the same as observed with MukBEF. We hypothesize that JetABCD is a DNA-shape-specific endonuclease and propose the "total extrusion model" for DNA cleavage exclusively when extrusion of an entire plasmid has been completed by a JetABCD complex. Total extrusion cannot be achieved on the larger chromosome, explaining how self-DNA may evade processing.}, }
@article {pmid36525447, year = {2022}, author = {Zou, X and Nguyen, M and Overbeek, J and Cao, B and Davis, JJ}, title = {Classification of bacterial plasmid and chromosome derived sequences using machine learning.}, journal = {PloS one}, volume = {17}, number = {12}, pages = {e0279280}, pmid = {36525447}, issn = {1932-6203}, mesh = {Plasmids/genetics ; *Genome, Bacterial ; *Chromosomes, Bacterial/genetics ; Bacteria/genetics ; Machine Learning ; Nucleotides ; }, abstract = {Plasmids are important genetic elements that facilitate horizonal gene transfer between bacteria and contribute to the spread of virulence and antimicrobial resistance. Most bacterial genome sequences in the public archives exist in draft form with many contigs, making it difficult to determine if a contig is of chromosomal or plasmid origin. Using a training set of contigs comprising 10,584 chromosomes and 10,654 plasmids from the PATRIC database, we evaluated several machine learning models including random forest, logistic regression, XGBoost, and a neural network for their ability to classify chromosomal and plasmid sequences using nucleotide k-mers as features. Based on the methods tested, a neural network model that used nucleotide 6-mers as features that was trained on randomly selected chromosomal and plasmid subsequences 5kb in length achieved the best performance, outperforming existing out-of-the-box methods, with an average accuracy of 89.38% ± 2.16% over a 10-fold cross validation. The model accuracy can be improved to 92.08% by using a voting strategy when classifying holdout sequences. In both plasmids and chromosomes, subsequences encoding functions involved in horizontal gene transfer-including hypothetical proteins, transporters, phage, mobile elements, and CRISPR elements-were most likely to be misclassified by the model. This study provides a straightforward approach for identifying plasmid-encoding sequences in short read assemblies without the need for sequence alignment-based tools.}, }
@article {pmid36523753, year = {2022}, author = {Alam, M and Bano, N and Upadhyay, TK and Binsuwaidan, R and Alshammari, N and Sharangi, AB and Kaushal, RS and Saeed, M}, title = {Enzymatic Activity and Horizontal Gene Transfer of Heavy Metals and Antibiotic Resistant Proteus vulgaris from Hospital Wastewater: An Insight.}, journal = {The Canadian journal of infectious diseases &amp; medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale}, volume = {2022}, number = {}, pages = {3399137}, pmid = {36523753}, issn = {1712-9532}, abstract = {Globally, the issue of microbial resistance to medicines and heavy metals is getting worse. There are few reports or data available for Proteus vulgaris (P. vulgaris), particularly in India. This investigation intends to reveal the bacteria's ability to transmit genes and their level of resistance as well. The wastewater samples were taken from several hospitals in Lucknow City, India, and examined for the presence of Gram-negative bacteria that were resistant to antibiotics and heavy metals. The microbial population count in different hospital wastewaters decreases with increasing concentrations of metal and antibiotics. Among all the examined metals, Ni and Zn had the highest viable counts, whereas Hg, Cd, and Co had the lowest viable counts. Penicillin, ampicillin, and amoxicillin, among the antibiotics, demonstrated higher viable counts, whereas tetracycline and erythromycin exhibited lower viable counts. The MIC values for the P. vulgaris isolates tested ranged from 50 to 16,00 μg/ml for each metal tested. The multiple metal resistance (MMR) index, which ranged from 0.04 to 0.50, showed diverse heavy metal resistance patterns in all P. vulgaris isolates (in the case of 2-7 metals in various combinations). All of the tested isolates had methicillin resistance, whereas the least number of isolates had ofloxacin, gentamycin, or neomycin resistance. The P. vulgaris isolates displayed multidrug resistance patterns (2-12 drugs) in various antibiotic combinations. The MAR indexes were shown to be between (0.02-0.7). From the total isolates, 98%, 84%, and 80% had urease, gelatinase, and amylase activity, whereas 68% and 56% displayed protease and beta-lactamase activity. Plasmids were present in all the selected resistant isolates and varied in size from 42.5 to 57.0 kb and molecular weight from 27.2 to 37.0 MD. The transmission of the antibiotic/metal resistance genes was evaluated between a total of 7 pairs of isolates. A higher transfer frequency (4.4 × 10[-1]) was observed among antibiotics, although a lower transfer frequency (1.0 × 10[-2]) was observed against metals in both the media from the entire site tested. According to exponential decay, the population of hospital wastewater declined in the following order across all sites: Site II > Site IV > Site III > Site I for antibiotics and site IV > site II > site I >site III for metal. Different metal and antibiotic concentrations have varying effects on the population. The metal-tolerant P. vulgaris from hospital wastewater was studied in the current study had multiple distinct patterns of antibiotic resistance. It could provide cutting-edge methods for treating infectious diseases, which are essential for managing and assessing the risks associated with hospital wastewater, especially in the case of P. vulgaris.}, }
@article {pmid36522135, year = {2023}, author = {Dorrell, RG and Kuo, A and Füssy, Z and Richardson, EH and Salamov, A and Zarevski, N and Freyria, NJ and Ibarbalz, FM and Jenkins, J and Pierella Karlusich, JJ and Stecca Steindorff, A and Edgar, RE and Handley, L and Lail, K and Lipzen, A and Lombard, V and McFarlane, J and Nef, C and Novák Vanclová, AM and Peng, Y and Plott, C and Potvin, M and Vieira, FRJ and Barry, K and de Vargas, C and Henrissat, B and Pelletier, E and Schmutz, J and Wincker, P and Dacks, JB and Bowler, C and Grigoriev, IV and Lovejoy, C}, title = {Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae.}, journal = {Life science alliance}, volume = {6}, number = {3}, pages = {}, pmid = {36522135}, issn = {2575-1077}, mesh = {*Gene Transfer, Horizontal/genetics ; *Microalgae/genetics ; Arctic Regions ; Oceans and Seas ; Ice Cover ; Bacteria ; }, abstract = {Microbial communities in the world ocean are affected strongly by oceanic circulation, creating characteristic marine biomes. The high connectivity of most of the ocean makes it difficult to disentangle selective retention of colonizing genotypes (with traits suited to biome specific conditions) from evolutionary selection, which would act on founder genotypes over time. The Arctic Ocean is exceptional with limited exchange with other oceans and ice covered since the last ice age. To test whether Arctic microalgal lineages evolved apart from algae in the global ocean, we sequenced four lineages of microalgae isolated from Arctic waters and sea ice. Here we show convergent evolution and highlight geographically limited HGT as an ecological adaptive force in the form of PFAM complements and horizontal acquisition of key adaptive genes. Notably, ice-binding proteins were acquired and horizontally transferred among Arctic strains. A comparison with Tara Oceans metagenomes and metatranscriptomes confirmed mostly Arctic distributions of these IBPs. The phylogeny of Arctic-specific genes indicated that these events were independent of bacterial-sourced HGTs in Antarctic Southern Ocean microalgae.}, }
@article {pmid36522081, year = {2023}, author = {Fan, X and Su, J and Zhou, S and An, X and Li, H}, title = {Plant cultivar determined bacterial community and potential risk of antibiotic resistance gene spread in the phyllosphere.}, journal = {Journal of environmental sciences (China)}, volume = {127}, number = {}, pages = {508-518}, doi = {10.1016/j.jes.2022.06.006}, pmid = {36522081}, issn = {1001-0742}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Soil/chemistry ; Soil Microbiology ; Plants ; }, abstract = {The global increased antibiotic resistance level in pathogenic microbes has posed a significant threat to human health. Fresh vegetables have been recognized to be an important vehicle of antibiotic resistance genes (ARGs) from environments to human beings. Phyllosphere ARGs have been indicated to be changed with plant species, yet the influence of plant cultivar on the phyllospheric resistome is still unclear. Here, we detected the ARGs and bacterial communities in the phyllosphere of two cultivars of cilantros and their corresponding soils using high-throughput quantitative PCR technique and bacterial 16S rRNA gene-based high-throughput sequencing, respectively. We further identified the potential bacterial pathogens and analyzed the effects of plant cultivar on ARGs, mobile genetic elements (MGEs), microbiome and potential bacterial pathogens. The results showed that the cultivars did not affect the ARG abundance and composition, but significantly shaped the abundance of MGEs and the composition structure of bacteria in the phyllosphere. The relative abundance of potential bacterial pathogens was significantly higher in the phyllosphere than that in soils. Mantel test showed that the ARG patterns were significantly correlated to the patterns of potential bacterial pathogens. Our results suggested that the horizontal gene transfer of ARGs in the phyllosphere might be different between the two cultivars of cilantro and highlighted the higher risk of phyllospheric microorganisms compared with those in soils. These findings extend our knowledge on the vegetable microbiomes, ARGs, and potential pathogens, suggesting more agricultural and hygiene protocols are needed to control the risk of foodborne ARGs.}, }
@article {pmid36522071, year = {2023}, author = {Yan, X and Liu, W and Wen, S and Wang, L and Zhu, L and Wang, J and Kim, YM and Wang, J}, title = {Effect of sulfamethazine on the horizontal transfer of plasmid-mediated antibiotic resistance genes and its mechanism of action.}, journal = {Journal of environmental sciences (China)}, volume = {127}, number = {}, pages = {399-409}, doi = {10.1016/j.jes.2022.06.014}, pmid = {36522071}, issn = {1001-0742}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Sulfamethazine ; Escherichia coli/genetics ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Plasmids/genetics ; RNA, Messenger ; }, abstract = {As a new type of environmental pollutant, antibiotic resistance genes (ARGs) pose a huge challenge to global health. Horizontal gene transfer (HGT) represents an important route for the spread of ARGs. The widespread use of sulfamethazine (SM2) as a broad-spectrum bacteriostatic agent leads to high residual levels in the environment, thereby increasing the spread of ARGs. Therefore, we chose to study the effect of SM2 on the HGT of ARGs mediated by plasmid RP4 from Escherichia coli (E. coli) HB101 to E. coli NK5449 as well as its mechanism of action. The results showed that compared with the control group, SM2 at concentrations of 10 mg/L and 200 mg/L promoted the HGT of ARGs, but transfer frequency decreased at concentrations of 100 mg/L and 500 mg/L. The transfer frequency at 200 mg/L was 3.04 × 10[-5], which was 1.34-fold of the control group. The mechanism of SM2 improving conjugation transfer is via enhancement of the mRNA expression of conjugation genes (trbBP, trfAP) and oxidative stress genes, inhibition of the mRNA expression of vertical transfer genes, up regulation of the outer membrane protein genes (ompC, ompA), promotion of the formation of cell pores, and improvement of the permeability of cell membrane to promote the conjugation transfer of plasmid RP4. The results of this study provide theoretical support for studying the spread of ARGs in the environment.}, }
@article {pmid36518176, year = {2022}, author = {Cangui-Panchi, SP and Ñacato-Toapanta, AL and Enríquez-Martínez, LJ and Reyes, J and Garzon-Chavez, D and Machado, A}, title = {Biofilm-forming microorganisms causing hospital-acquired infections from intravenous catheter: A systematic review.}, journal = {Current research in microbial sciences}, volume = {3}, number = {}, pages = {100175}, pmid = {36518176}, issn = {2666-5174}, abstract = {The high prevalence of nosocomial infections is related to the use of medical insertion devices such as central venous catheters (CVCs). Most of the microorganisms causing nosocomial infections are biofilm producers, this characteristic allows them to adhere to abiotic surfaces and cause initial catheter infections that can lead to bloodstream infections. Our main goal in this systematic review was to evaluate the prevalence of biofilm among CVC-related infections, particularly among Intensive Care Unit (ICU) patients, in the studies applying different in vitro and in vivo methodologies. All studies reporting clinical isolates from patients with catheter-related nosocomial infections and biofilm evaluation published up to 24 June 2022 in the PubMed and Scopus databases were included. Twenty-five studies met the eligibility criteria and were included in this systematic review for analysis. Different methodologies were applied in the assessment of biofilm-forming microorganisms including in vitro assays, catheter-infected in vitro, and in vivo mouse models. The present study showed that between 59 and 100% of clinical isolates were able to form biofilms, and the prevalence rate of biofilm formation varied significantly between studies from different countries and regions. Among the clinical isolates collected in our study set, a wide variety of microorganisms including Gram-positive strains, Gram-negative strains, and Candida albicans were found. Many authors studied resistance mechanisms and genes related to biofilm development and surface adherence properties. In some cases, the studies also evaluated biofilm inhibition assays using various kinds of catheter coatings.}, }
@article {pmid36517909, year = {2022}, author = {Vasco, K and Guevara, N and Mosquera, J and Zapata, S and Zhang, L}, title = {Characterization of the gut microbiome and resistome of Galapagos marine iguanas (Amblyrhynchus cristatus) from uninhabited islands.}, journal = {Animal microbiome}, volume = {4}, number = {1}, pages = {65}, pmid = {36517909}, issn = {2524-4671}, support = {Faculty discretional fund//Michigan State University/ ; POA 2018//Universidad San Francisco de Quito/ ; POA 2018//Galapagos Science Center/ ; }, abstract = {BACKGROUND: Understanding the natural microbiome and resistome of wildlife from remote places is necessary to monitor the human footprint on the environment including antimicrobial use (AU). Marine iguanas are endemic species from the Galapagos Islands where they are highly affected by anthropogenic factors that can alter their microbiota as well as their abundance and diversity of antimicrobial-resistant genes (ARGs). Thus, this study aims to apply culture-independent approaches to characterize the marine iguana's gut metagenomic composition of samples collected from the uninhabited islands Rabida (n = 8) and Fernandina (Cabo Douglas, n = 30; Punta Espinoza, n = 30). Fresh feces from marine iguanas were analyzed through SmartChip RT-PCR, 16S rRNA, and metagenomic next-generation sequencing (mNGS) to identify their microbiome, microbial-metabolic pathways, resistome, mobilome, and virulome.<br><br>RESULTS: The marine iguana's gut microbiome composition was highly conserved despite differences in ecological niches, where 86% of taxa were shared in the three locations. However, site-specific differences were mainly identified in resistome, mobilome, virulorome, and metabolic pathway composition, highlighting the existence of factors that induce microbial adaptations in each location. Functional gut microbiome analyses revealed its role in the biosynthesis and degradation of vitamins, cofactors, proteinogenic amino acids, carbohydrates, nucleosides and nucleotides, fatty acids, lipids, and other compounds necessary for the marine iguanas. The overall bacterial ARG abundance was relatively low (0.006%); nevertheless, the presence of genes encoding resistance to 22 drug classes was identified in the iguana's gut metagenome. ARG-carrying contig and co-occurrence network analyses revealed that commensal bacteria are the main hosts of ARGs. Taxa of public health interest such as Salmonella, Vibrio, and Klebsiella also carried multidrug-resistance genes associated with MGEs which can influence the dissemination of ARGs through horizontal gene transfer.<br><br>CONCLUSION: Marine iguanas depend on the gut microbiome for the biosynthesis and degradation of several compounds through a symbiotic relationship. Niche-specific adaptations were evidenced in the pool of microbial accessory genes (i.e., ARGs, MGEs, and virulence) and metabolic pathways, but not in the microbiome composition. Culture-independent approaches outlined the presence of a diverse resistome composition in the Galapagos marine iguanas from remote islands. The presence of AR pathogens in marine iguanas raises concerns about the dispersion of microbial-resistant threats in pristine areas, highlighting wildlife as sentinel species to identify the impact of AU.}, }
@article {pmid36517527, year = {2023}, author = {Dziuba, MV and Paulus, A and Schramm, L and Awal, RP and Pósfai, M and Monteil, CL and Fouteau, S and Uebe, R and Schüler, D}, title = {Silent gene clusters encode magnetic organelle biosynthesis in a non-magnetotactic phototrophic bacterium.}, journal = {The ISME journal}, volume = {17}, number = {3}, pages = {326-339}, pmid = {36517527}, issn = {1751-7370}, mesh = {*Magnetospirillum/genetics ; *Magnetosomes/genetics ; Bacteria/genetics ; Gram-Negative Bacteria/genetics ; Bacteria, Aerobic/genetics ; Multigene Family ; Magnetic Phenomena ; Bacterial Proteins/genetics ; }, abstract = {Horizontal gene transfer is a powerful source of innovations in prokaryotes that can affect almost any cellular system, including microbial organelles. The formation of magnetosomes, one of the most sophisticated microbial mineral-containing organelles synthesized by magnetotactic bacteria for magnetic navigation in the environment, was also shown to be a horizontally transferrable trait. However, the mechanisms determining the fate of such genes in new hosts are not well understood, since non-adaptive gene acquisitions are typically rapidly lost and become unavailable for observation. This likely explains why gene clusters encoding magnetosome biosynthesis have never been observed in non-magnetotactic bacteria. Here, we report the first discovery of a horizontally inherited dormant gene clusters encoding biosynthesis of magnetosomes in a non-magnetotactic phototrophic bacterium Rhodovastum atsumiense. We show that these clusters were inactivated through transcriptional silencing and antisense RNA regulation, but retain functionality, as several genes were able to complement the orthologous deletions in a remotely related magnetotactic bacterium. The laboratory transfer of foreign magnetosome genes to R. atsumiense was found to endow the strain with magnetosome biosynthesis, but strong negative selection led to rapid loss of this trait upon subcultivation, highlighting the trait instability in this organism. Our results provide insight into the horizontal dissemination of gene clusters encoding complex prokaryotic organelles and illuminate the potential mechanisms of their genomic preservation in a dormant state.}, }
@article {pmid36516783, year = {2022}, author = {Nishimoto, AT and Dao, TH and Jia, Q and Ortiz-Marquez, JC and Echlin, H and Vogel, P and van Opijnen, T and Rosch, JW}, title = {Interspecies recombination, not de novo mutation, maintains virulence after β-lactam resistance acquisition in Streptococcus pneumoniae.}, journal = {Cell reports}, volume = {41}, number = {11}, pages = {111835}, pmid = {36516783}, issn = {2211-1247}, support = {U01 AI124302/AI/NIAID NIH HHS/United States ; }, mesh = {Mice ; Animals ; *Streptococcus pneumoniae/genetics ; Gene Transfer, Horizontal ; *Pneumococcal Infections ; Virulence/genetics ; Microbial Sensitivity Tests ; beta-Lactam Resistance/genetics ; Penicillin-Binding Proteins/genetics/metabolism ; Mutation/genetics ; Bacterial Proteins/metabolism ; Anti-Bacterial Agents/pharmacology/metabolism ; }, abstract = {As opposed to de novo mutation, β-lactam resistance in S. pneumoniae is often conferred via homologous recombination during horizontal gene transfer. We hypothesize that β-lactam resistance in pathogenic streptococci is restricted to naturally competent species via intra-/interspecies recombination due to in vivo fitness trade-offs of de novo penicillin-binding protein (PBP) mutations. We show that de novo mutant populations have abrogated invasive disease capacity and are difficult to evolve in vivo. Conversely, serially transformed recombinant strains efficiently integrate resistant oral streptococcal DNA, gain penicillin resistance and tolerance, and retain virulence in mice. Large-scale changes in pbp2X, pbp2B, and non-PBP-related genes occur in recombinant isolates. Our results indicate that horizontal transfer of β-lactam resistance engenders initially favorable or minimal cost changes in vivo compared with de novo mutation(s), underscoring the importance of recombination in the emergence of β-lactam resistance and suggesting why some pathogenic streptococci lacking innate competence remain universally susceptible.}, }
@article {pmid36515883, year = {2023}, author = {Martins-Silva, P and Dias, CP and Vilar, LC and de Queiroz Silva, S and Rossi, CC and Giambiagi-deMarval, M}, title = {Dispersion and persistence of antimicrobial resistance genes among Staphylococcus spp. and Mammaliicoccus spp. isolated along a swine manure treatment plant.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {12}, pages = {34709-34719}, pmid = {36515883}, issn = {1614-7499}, support = {E-26/010.000172/2016//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; 010.00128/2016//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; 101056/2018//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; 001463/2019//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; 211.554/2019//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; 201.071/2020//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; 200.895/2021//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; 305940/2018-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; FinanceCode 001 (CAPES ProEx//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 23038.002486/2018-26)//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; }, mesh = {Humans ; Swine ; Animals ; *Staphylococcus ; *Anti-Bacterial Agents/pharmacology ; Manure ; Drug Resistance, Bacterial/genetics ; Cefoxitin ; Microbial Sensitivity Tests ; }, abstract = {Staphylococcus spp. and Mammaliicoccus spp. colonize the skin and mucosa of humans and other animals and are responsible for several opportunistic infections. Staphylococci antibiotic resistance may be present in the environment due to the spread of treated and untreated manure from the livestock industry due to antibiotic use to disease control or growth promoter. In this work, we analyzed the species distribution and antimicrobial susceptibility of Staphylococcus and Mammaliicoccus species along different sites of a swine manure treatment plant from Southeastern Brazil. Bacterial colonies were obtained on mannitol salt agar, selected after catalase test and Gram staining, and finally identified by mass spectrometry and sequencing of the tuf gene. According to the results, S.cohnii and S. simulans were the most prevalent species. Antibiotic resistance test revealed that several strains were resistant to multiple drugs, with high levels of chloramphenicol resistance (98%), followed by erythromycin (79%), tetracycline (73%), gentamicin (46%), ciprofloxacin (42%), cefoxitin (18%), sulfamethoxazole + trimethoprim (12%), and linezolid (4%). In addition, gene detection by PCR showed that all strains carried at least 2 resistance genes and one of them carried all 11 genes investigated. Using the GTG5-PCR approach, a high genetic similarity was observed between some strains that were isolated from different points of the treatment plant. Although some were seemingly identical, differences in their resistance phenotype and genotype suggest horizontal gene transfer. The presence of resistant bacteria and resistance genes along the treatment system highlights the potential risk of contamination by people in direct contact with these animals and the soil since the effluent is used as a biofertilizer in the surrounding environment.}, }
@article {pmid36515719, year = {2022}, author = {Almalki, F and Choudhary, M and Azad, RK}, title = {Analysis of multipartite bacterial genomes using alignment free and alignment-based pipelines.}, journal = {Archives of microbiology}, volume = {205}, number = {1}, pages = {25}, pmid = {36515719}, issn = {1432-072X}, mesh = {*Genome, Bacterial ; Genomics ; Biological Evolution ; *Rhodobacter sphaeroides/genetics ; Evolution, Molecular ; Chromosomes, Bacterial/genetics ; }, abstract = {Since the discovery of second chromosome in Rhodobacter sphaeroides 2.4.1 in 1989, multipartite genomes have been reported in over three hundred bacterial species under nine different phyla. This has shattered the unipartite (single chromosome) genome dogma in bacteria. Since then, many questions on various aspects of multipartite genomes in bacteria have been addressed. However, our understanding of how multipartite genomes emerge and evolve is still lacking. Importantly, the knowledge of genetic factors underlying the differences in multipartite and single-chromosome genomes is lacking. In this work, we have performed comparative evolutionary and functional genomics analyses to identify molecular factors that discriminate multipartite from unipartite bacteria, with the goal to decipher taxon-specific factors, and those that are prevalent across the taxa, underlying these traits. We assessed the roles of evolutionary mechanisms, specifically gene gain, in driving the divergence of bacteria with single and multiple chromosomes. In addition, we performed functional genomic analysis to garner support for our findings from comparative evolutionary analysis. We found genes such as those encoding conserved hypothetical proteins in Deinococcus radiodurans R1, and putative phage phi-C31 gp36 major capsid like and hypothetical proteins in Rhodobacter sphaeroides 2.4.1, which are located on accessory chromosomes in these bacteria but were not found in the inferred ancestral sequences, and on the primary chromosomes, as well as were not found in their closest relatives with single chromosome within the same clade. Our study shines a new light on the potential roles of the secondary chromosomes in helping bacteria with multipartite genomes to adapt to specialized environments or growth conditions.}, }
@article {pmid36515529, year = {2023}, author = {Brennan, G and Stoian, AMM and Yu, H and Rahman, MJ and Banerjee, S and Stroup, JN and Park, C and Tazi, L and Rothenburg, S}, title = {Molecular Mechanisms of Poxvirus Evolution.}, journal = {mBio}, volume = {14}, number = {1}, pages = {e0152622}, pmid = {36515529}, issn = {2150-7511}, support = {R01 AI114851/AI/NIAID NIH HHS/United States ; R01 AI146915/AI/NIAID NIH HHS/United States ; R21 AI135257/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Evolution, Molecular ; *Poxviridae/genetics ; Host Specificity ; Gene Duplication ; }, abstract = {Poxviruses are often thought to evolve relatively slowly because they are double-stranded DNA pathogens with proofreading polymerases. However, poxviruses have highly adaptable genomes and can undergo relatively rapid genotypic and phenotypic change, as illustrated by the recent increase in human-to-human transmission of monkeypox virus. Advances in deep sequencing technologies have demonstrated standing nucleotide variation in poxvirus populations, which has been underappreciated. There is also an emerging understanding of the role genomic architectural changes play in shaping poxvirus evolution. These mechanisms include homologous and nonhomologous recombination, gene duplications, gene loss, and the acquisition of new genes through horizontal gene transfer. In this review, we discuss these evolutionary mechanisms and their potential roles for adaption to novel host species and modulating virulence.}, }
@article {pmid36515045, year = {2023}, author = {de Morais Oliveira-Tintino, CD and Muniz, DF and Dos Santos Barbosa, CR and Silva Pereira, RL and Begnini, IM and Rebelo, RA and da Silva, LE and Mireski, SL and Nasato, MC and Lacowicz Krautler, MI and Barros Oliveira, CV and Pereira, PS and Rodrigues Teixeira, AM and Tintino, SR and de Menezes, IRA and Melo Coutinho, HD and da Silva, TG}, title = {NorA, Tet(K), MepA, and MsrA Efflux Pumps in Staphylococcus aureus, their Inhibitors and 1,8-Naphthyridine Sulfonamides.}, journal = {Current pharmaceutical design}, volume = {29}, number = {5}, pages = {323-355}, doi = {10.2174/1381612829666221212101501}, pmid = {36515045}, issn = {1873-4286}, support = {IBPG-1241-4.03/16.//Funda&#xe7;&#xe3;o de Amparo &#xe0; Ci&#xea;ncia e Tecnologia do Estado de Pernambuco/ ; }, mesh = {Humans ; *Staphylococcus aureus ; *Bacterial Proteins/genetics/chemistry ; Sulfonamides/pharmacology ; Bacteria ; Anti-Bacterial Agents/pharmacology ; Sulfanilamide/pharmacology ; Naphthyridines/pharmacology ; Microbial Sensitivity Tests ; }, abstract = {Antibiotic resistance can be characterized, in biochemical terms, as an antibiotic's inability to reach its bacterial target at a concentration that was previously effective. Microbial resistance to different agents can be intrinsic or acquired. Intrinsic resistance occurs due to inherent functional or structural characteristics of the bacteria, such as antibiotic-inactivating enzymes, nonspecific efflux pumps, and permeability barriers. On the other hand, bacteria can acquire resistance mechanisms via horizontal gene transfer in mobile genetic elements such as plasmids. Acquired resistance mechanisms include another category of efflux pumps with more specific substrates, which are plasmid-encoded. Efflux pumps are considered one of the main mechanisms of bacterial resistance to antibiotics and biocides, presenting themselves as integral membrane transporters. They are essential in both bacterial physiology and defense and are responsible for exporting structurally diverse substrates, falling into the following main families: ATP-binding cassette (ABC), multidrug and toxic compound extrusion (MATE), major facilitator superfamily (MFS), small multidrug resistance (SMR) and resistance-nodulation-cell division (RND). The Efflux pumps NorA and Tet(K) of the MFS family, MepA of the MATE family, and MsrA of the ABC family are some examples of specific efflux pumps that act in the extrusion of antibiotics. In this review, we address bacterial efflux pump inhibitors (EPIs), including 1,8-naphthyridine sulfonamide derivatives, given the pre-existing knowledge about the chemical characteristics that favor their biological activity. The modification and emergence of resistance to new EPIs justify further research on this theme, aiming to develop efficient compounds for clinical use.}, }
@article {pmid36512900, year = {2023}, author = {Puxty, RJ and Millard, AD}, title = {Functional ecology of bacteriophages in the environment.}, journal = {Current opinion in microbiology}, volume = {71}, number = {}, pages = {102245}, doi = {10.1016/j.mib.2022.102245}, pmid = {36512900}, issn = {1879-0364}, mesh = {*Bacteriophages/genetics ; Bacteria/genetics ; Ecology ; }, abstract = {Bacteriophages are as ubiquitous as their bacterial hosts and often more abundant. Understanding how bacteriophages control their bacterial host populations requires a number of different approaches. Bacteriophages can control bacterial populations through lysis, drive evolution of bacterial immunity systems through infection, provide a conduit for horizontal gene transfer and alter host metabolism by carriage of auxiliary metabolic genes. Understanding and quantifying how bacteriophages drive these processes, requires both technological developments to take measurements in situ, and laboratory-based studies to understand mechanisms. Technological advances have allowed quantification of the number of infected cells in situ, revealing far-lower levels than expected. Understanding how observations in laboratory conditions relate to what occurs in the environment, and experimental confirmation of the predicted function of phage genes from observations in environmental omics data, remains challenging.}, }
@article {pmid36511859, year = {2022}, author = {Kim, SK and Kim, H and Woo, SG and Kim, TH and Rha, E and Kwon, KK and Lee, H and Lee, SG and Lee, DH}, title = {CRISPRi-based programmable logic inverter cascade for antibiotic-free selection and maintenance of multiple plasmids.}, journal = {Nucleic acids research}, volume = {50}, number = {22}, pages = {13155-13171}, pmid = {36511859}, issn = {1362-4962}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; *Escherichia coli/drug effects/genetics ; Plasmids/genetics ; *Microbiological Techniques/methods ; }, abstract = {Antibiotics have been widely used for plasmid-mediated cell engineering. However, continued use of antibiotics increases the metabolic burden, horizontal gene transfer risks, and biomanufacturing costs. There are limited approaches to maintaining multiple plasmids without antibiotics. Herein, we developed an inverter cascade using CRISPRi by building a plasmid containing a single guide RNA (sgRNA) landing pad (pSLiP); this inhibited host cell growth by repressing an essential cellular gene. Anti-sgRNAs on separate plasmids restored cell growth by blocking the expression of growth-inhibitory sgRNAs in pSLiP. We maintained three plasmids in Escherichia coli with a single antibiotic selective marker. To completely avoid antibiotic use and maintain the CRISPRi-based logic inverter cascade, we created a novel d-glutamate auxotrophic E. coli. This enabled the stable maintenance of the plasmid without antibiotics, enhanced the production of the terpenoid, (-)-α-bisabolol, and generation of an antibiotic-resistance gene-free plasmid. CRISPRi is therefore widely applicable in genetic circuits and may allow for antibiotic-free biomanufacturing.}, }
@article {pmid36511824, year = {2023}, author = {Liu, C and Li, Y and Chen, Y and Chen, XX and Huang, J and Rokas, A and Shen, XX}, title = {How has horizontal gene transfer shaped the evolution of insect genomes?.}, journal = {Environmental microbiology}, volume = {25}, number = {3}, pages = {642-645}, pmid = {36511824}, issn = {1462-2920}, support = {R01 AI153356/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Gene Transfer, Horizontal ; *Evolution, Molecular ; Ecosystem ; Prokaryotic Cells ; Insecta ; Genome, Insect ; Phylogeny ; }, abstract = {As the most diverse group of animals on Earth, insects are key organisms in ecosystems. Horizontal gene transfer (HGT) refers to the transfer of genetic material between species by non-reproductive means. HGT is a major evolutionary force in prokaryotic genome evolution, but its importance in different eukaryotic groups, such as insects, has only recently begun to be understood. Genomic data from hundreds of insect species have enabled the detection of large numbers of HGT events and the elucidation of the functions of some of these foreign genes. Although quantification of the extent of HGT in insects broadens our understanding of its role in insect evolution, the scope of its influence and underlying mechanism(s) of its occurrence remain open questions for the field.}, }
@article {pmid36507660, year = {2023}, author = {Zheng, J and Liang, JL and Jia, P and Feng, SW and Lu, JL and Luo, ZH and Ai, HX and Liao, B and Li, JT and Shu, WS}, title = {Diverse Methylmercury (MeHg) Producers and Degraders Inhabit Acid Mine Drainage Sediments, but Few Taxa Correlate with MeHg Accumulation.}, journal = {mSystems}, volume = {8}, number = {1}, pages = {e0073622}, pmid = {36507660}, issn = {2379-5077}, mesh = {*Methylmercury Compounds/analysis ; Bacteria/genetics ; Phylogeny ; Metagenome ; Firmicutes/genetics ; }, abstract = {Methylmercury (MeHg) is a notorious neurotoxin, and its production and degradation in the environment are mainly driven by microorganisms. A variety of microbial MeHg producers carrying the gene pair hgcAB and degraders carrying the merB gene have been separately reported in recent studies. However, surprisingly little attention has been paid to the simultaneous investigation of the diversities of microbial MeHg producers and degraders in a given habitat, and no studies have been performed to explore to what extent these two contrasting microbial groups correlate with MeHg accumulation in the habitat of interest. Here, we collected 86 acid mine drainage (AMD) sediments from an area spanning approximately 500,000 km[2] in southern China and profiled the sediment-borne putative MeHg producers and degraders using genome-resolved metagenomics. 46 metagenome-assembled genomes (MAGs) containing hgcAB and 93 MAGs containing merB were obtained, including those from various taxa without previously known MeHg-metabolizing microorganisms. These diverse MeHg-metabolizing MAGs were formed largely via multiple independent horizontal gene transfer (HGT) events. The putative MeHg producers from Deltaproteobacteria and Firmicutes as well as MeHg degraders from Acidithiobacillia were closely correlated with MeHg accumulation in the sediments. Furthermore, these three taxa, in combination with two abiotic factors, explained over 60% of the variance in MeHg accumulation. Most of the members of these taxa were characterized by their metabolic potential for nitrogen fixation and copper tolerance. Overall, these findings improve our understanding of the ecology of MeHg-metabolizing microorganisms and likely have implications for the development of management strategies for the reduction of MeHg accumulation in the AMD sediments. IMPORTANCE Microorganisms are the main drivers of MeHg production and degradation in the environment. However, little attention has been paid to the simultaneous investigation of the diversities of microbial MeHg producers and degraders in a given habitat. We used genome-resolved metagenomics to reveal the vast phylogenetic and metabolic diversities of putative MeHg producers and degraders in AMD sediments. Our results show that the diversity of MeHg-metabolizing microorganisms (particularly MeHg degraders) in AMD sediments is much higher than was previously recognized. Via multiple linear regression analysis, we identified both microbial and abiotic factors affecting MeHg accumulation in AMD sediments. Despite their great diversity, only a few taxa of MeHg-metabolizing microorganisms were closely correlated with MeHg accumulation. This work underscores the importance of using genome-resolved metagenomics to survey MeHg-metabolizing microorganisms and provides a framework for the illumination of the microbial basis of MeHg accumulation via the characterization of physicochemical properties, MeHg-metabolizing microorganisms, and the correlations between them.}, }
@article {pmid36507655, year = {2023}, author = {Guan, Y and Ma, L and Wang, Q and Zhao, J and Wang, S and Wu, J and Liu, Y and Sun, H and Huang, J}, title = {Horizontally acquired fungal killer protein genes affect cell development in mosses.}, journal = {The Plant journal : for cell and molecular biology}, volume = {113}, number = {4}, pages = {665-676}, doi = {10.1111/tpj.16060}, pmid = {36507655}, issn = {1365-313X}, mesh = {*Bryophyta/metabolism ; Calcium/metabolism ; Fungal Proteins/genetics ; Fungi/metabolism ; *Bryopsida/genetics ; }, abstract = {The moss Physcomitrium patens is crucial for studying plant development and evolution. Although the P. patens genome includes genes acquired from bacteria, fungi and viruses, the functions and evolutionary significance of these acquired genes remain largely unclear. Killer protein 4 (KP4) is a toxin secreted by the phytopathogenic fungus Ustilago maydis that inhibits the growth of sensitive target strains by blocking their calcium uptake. Here, we show that KP4 genes in mosses were acquired from fungi through at least three independent events of horizontal gene transfer. Two paralogous copies of KP4 (PpKP4-1 and PpKP4-2) exist in P. patens. Knockout mutants ppkp4-1 and ppkp4-2 showed cell death at the protonemal stage, and ppkp4-2 also exhibited defects in tip growth. We provide experimental evidence indicating that PpKP4-1/2 affects P. patens protonemal cell development by mediating cytoplasmic calcium and that KP4 genes are functionally conserved between P. patens and fungi. The present study provides additional insights into the role of horizontal gene transfer in land plant development and evolution.}, }
@article {pmid36506112, year = {2023}, author = {Alvarez-Molina, A and Trigal, E and Prieto, M and López, M and Alvarez-Ordóñez, A}, title = {Assessment of a plasmid conjugation procedure to monitor horizontal transfer of an extended-spectrum β-lactamase resistance gene under food chain scenarios.}, journal = {Current research in food science}, volume = {6}, number = {}, pages = {100405}, pmid = {36506112}, issn = {2665-9271}, abstract = {Plasmids are relevant reservoirs of antimicrobial resistance genes (ARGs) which confer adaptive advantages to their host and can be horizontally transferred. The aims of this study were to develop a conjugation procedure to monitor the horizontal transfer of a 193 kb plasmid containing the extended-spectrum β-lactamase production gene bla CTX-M-14 between two Escherichia coli strains under a range of food chain-related scenarios, including temperature (20-37 °C), pH (5.0-9.0) or the presence of some biocidal agents (benzalkonium chloride, sodium hypochlorite or peracetic acid). The average conjugation rate in LB broth after 18 h at 37 °C was 2.09e-04 and similar rates were observed in a food matrix (cow's milk). The conjugation was reduced at temperatures below 37 °C, at alkaline pH (especially at pH 9.0) or in the presence of benzalkonium chloride. Peracetic acid and sodium hypochlorite slightly increased conjugation rates, which reached 5.59e-04 and 6.77e-03, respectively. The conjugation procedure described can be used to identify risk scenarios leading to an enhanced ARGs transmission via plasmid conjugation, as well as to identify novel intervention strategies impairing plasmid conjugation and tackling antimicrobial resistance.}, }
@article {pmid36503799, year = {2023}, author = {Wang, S and Li, S and Du, D and Abass, OK and Nasir, MS and Yan, W}, title = {Stimulants and donors promote megaplasmid pND6-2 horizontal gene transfer in activated sludge.}, journal = {Journal of environmental sciences (China)}, volume = {126}, number = {}, pages = {742-753}, doi = {10.1016/j.jes.2022.03.011}, pmid = {36503799}, issn = {1001-0742}, mesh = {*Gene Transfer, Horizontal ; *Sewage ; Naphthalenes ; Tetracycline ; Anti-Bacterial Agents ; }, abstract = {The activated sludge process is characterized by high microbial density and diversity, both of which facilitate antibiotic resistance gene transfer. Many studies have suggested that antibiotic and non-antibiotic drugs at sub-inhibitory concentrations are major inducers of conjugative gene transfer. The self-transmissible plasmid pND6-2 is one of the endogenous plasmids harbored in Pseudomonas putida ND6, which can trigger the transfer of another co-occurring naphthalene-degrading plasmid pND6-1. Therefore, to illustrate the potential influence of stimulants on conjugative transfer of pND6-2, we evaluated the effects of four antibiotics (ampicillin, gentamycin, kanamycin, and tetracycline) and naphthalene, on the conjugal transfer efficiency of pND6-2 by filter-mating experiment. Our findings demonstrated that all stimulants within an optimal dose promoted conjugative transfer of pND6-2 from Pseudomonas putida GKND6 to P. putida KT2440, with tetracycline being the most effective (100 µg/L and 10 µg/L), as it enhanced pND6-2-mediated intra-genera transfer by approximately one hundred-fold. Subsequently, seven AS reactors were constructed with the addition of donors and different stimulants to further elucidate the conjugative behavior of pND6-2 in natural environment. The stimulants positively affected the conjugal process of pND6-2, while donors reshaped the host abundance in the sludge. This was likely because stimulant addition enhanced the expression levels of conjugation transfer-related genes. Furthermore, Blastocatella and Chitinimonas were identified as the potential receptors of plasmid pND6-2, which was not affected by donor types. These findings demonstrate the positive role of sub-inhibitory stimulant treatment on pND6-2 conjugal transfer and the function of donors in re-shaping the host spectrum of pND6-2.}, }
@article {pmid36502290, year = {2023}, author = {Kinateder, T and Drexler, L and Straub, K and Merkl, R and Sterner, R}, title = {Experimental and computational analysis of the ancestry of an evolutionary young enzyme from histidine biosynthesis.}, journal = {Protein science : a publication of the Protein Society}, volume = {32}, number = {1}, pages = {e4536}, pmid = {36502290}, issn = {1469-896X}, mesh = {*Histidine/genetics/metabolism ; Phylogeny ; *Phosphoric Monoester Hydrolases/genetics/chemistry/metabolism ; Histidinol-Phosphatase/chemistry ; Escherichia coli/genetics ; }, abstract = {The conservation of fold and chemistry of the enzymes associated with histidine biosynthesis suggests that this pathway evolved prior to the diversification of Bacteria, Archaea, and Eukaryotes. The only exception is the histidinol phosphate phosphatase (HolPase). So far, non-homologous HolPases that possess distinct folds and belong to three different protein superfamilies have been identified in various phylogenetic clades. However, their evolution has remained unknown to date. Here, we analyzed the evolutionary history of the HolPase from γ-Proteobacteria (HisB-N). It has been argued that HisB-N and its closest homologue d-glycero-d-manno-heptose-1,7-bisphosphate 7-phosphatase (GmhB) have emerged from the same promiscuous ancestral phosphatase. GmhB variants catalyze the hydrolysis of the anomeric d-glycero-d-manno-heptose-1,7-bisphosphate (αHBP or βHBP) with a strong preference for one anomer (αGmhB or βGmhB). We found that HisB-N from Escherichia coli shows promiscuous activity for βHBP but not αHBP, while βGmhB from Crassaminicella sp. shows promiscuous activity for HolP. Accordingly, a combined phylogenetic tree of αGmhBs, βGmhBs, and HisB-N sequences revealed that HisB-Ns form a compact subcluster derived from βGmhBs. Ancestral sequence reconstruction and in vitro analysis revealed a promiscuous HolPase activity in the resurrected enzymes prior to functional divergence of the successors. The following increase in catalytic efficiency of the HolP turnover is reflected in the shape and electrostatics of the active site predicted by AlphaFold. An analysis of the phylogenetic tree led to a revised evolutionary model that proposes the horizontal gene transfer of a promiscuous βGmhB from δ- to γ-Proteobacteria where it evolved to the modern HisB-N.}, }
@article {pmid36498841, year = {2022}, author = {Carpanzano, S and Santorsola, M and Nf-Core Community,  and Lescai, F}, title = {hgtseq: A Standard Pipeline to Study Horizontal Gene Transfer.}, journal = {International journal of molecular sciences}, volume = {23}, number = {23}, pages = {}, pmid = {36498841}, issn = {1422-0067}, support = {FRG - Fondo Ricerca &amp; Giovani//University of Pavia/ ; }, mesh = {Animals ; Humans ; *Gene Transfer, Horizontal ; *Evolution, Molecular ; Prokaryotic Cells ; Bacteria/genetics ; Base Sequence ; Phylogeny ; Mammals/genetics ; }, abstract = {Horizontal gene transfer (HGT) is well described in prokaryotes: it plays a crucial role in evolution, and has functional consequences in insects and plants. However, less is known about HGT in humans. Studies have reported bacterial integrations in cancer patients, and microbial sequences have been detected in data from well-known human sequencing projects. Few of the existing tools for investigating HGT are highly automated. Thanks to the adoption of Nextflow for life sciences workflows, and to the standards and best practices curated by communities such as nf-core, fully automated, portable, and scalable pipelines can now be developed. Here we present nf-core/hgtseq to facilitate the analysis of HGT from sequencing data in different organisms. We showcase its performance by analysing six exome datasets from five mammals. Hgtseq can be run seamlessly in any computing environment and accepts data generated by existing exome and whole-genome sequencing projects; this will enable researchers to expand their analyses into this area. Fundamental questions are still open about the mechanisms and the extent or role of horizontal gene transfer: by releasing hgtseq we provide a standardised tool which will enable a systematic investigation of this phenomenon, thus paving the way for a better understanding of HGT.}, }
@article {pmid36495587, year = {2023}, author = {Farghaly, M and Hynes, MF and Nazari, M and Checkley, S and Liljebjelke, K}, title = {Examination of the horizontal gene transfer dynamics of an integrative and conjugative element encoding multidrug resistance in Histophilus somni.}, journal = {Canadian journal of microbiology}, volume = {69}, number = {3}, pages = {123-135}, doi = {10.1139/cjm-2021-0349}, pmid = {36495587}, issn = {1480-3275}, mesh = {*Gene Transfer, Horizontal ; Drug Resistance, Multiple, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; *Pasteurellaceae ; Ciprofloxacin ; Tetracyclines ; Conjugation, Genetic ; }, abstract = {Integrative and conjugative elements (ICEs) are self-transferable mobile genetic elements that play a significant role in disseminating antimicrobial resistance between bacteria via horizontal gene transfer. A recently identified ICE in a clinical isolate of Histophilus somni (ICEHs02) is 72 914 base pairs in length and harbours seven predicted antimicrobial resistance genes conferring resistance to tetracycline (tetR-tet(H)), florfenicol (floR), sulfonamide (Sul2), aminoglycosides (APH(3″)-Ib, APH(6)-Id, APH(3')-Ia), and copper (mco). This study investigated ICEHs02 host range, assessed effects of antimicrobial stressors on transfer frequency, and examined effects of ICEHs02 acquisition on hosts. Conjugation assays examined transfer frequency of ICEHs02 to H. somni and Pasteurella multocida strains. Polymerase chain reaction assays confirmed the presence of a circular intermediate, ICE-associated core genes, and cargo genes in recipient strains. Susceptibility testing examined ICEHs02-associated resistance phenotypes in recipient strains. Tetracycline and ciprofloxacin induction significantly increased the transfer rates of ICEHs02 in vitro. The copy numbers of the circular intermediate of ICEHs02 per chromosome exhibited significant increases of ∼37-fold after tetracycline exposure and ∼4-fold after ciprofloxacin treatment. The acquisition of ICEHs02 reduced the relative fitness of H. somni transconjugants (TG) by 28% (w = 0.72 ± 0.04) and the relative fitness of P. multocida TG was decreased by 15% (w = 0.85 ± 0.01).}, }
@article {pmid36495352, year = {2022}, author = {Kim, J and Cha, IT and Lee, KE and Son, YK and Yu, J and Seol, D}, title = {Characteristics and adaptability of Flavobacterium panici BSSL-CR3 in tidal flat revealed by comparative genomic and enzymatic analysis.}, journal = {Archives of microbiology}, volume = {205}, number = {1}, pages = {22}, pmid = {36495352}, issn = {1432-072X}, support = {NIBR202134204//National Institute of Biological Resources/ ; }, mesh = {*Flavobacterium/genetics ; *Genomics ; Genomic Islands ; Plants ; }, abstract = {Tidal flat microbes play an important ecological role by removing organic pollutants and providing an energy source. However, bacteria isolated from tidal flats and their genomes have been scarcely reported, making it difficult to elucidate which genes and pathways are potentially involved in the above roles. In this study, strain BSSL-CR3, the third reported species among the tidal flat Flavobacterium was analyzed using whole-genome sequencing to investigate its adaptability and functionality in tidal flats. BSSL-CR3 is comprised of a circular chromosome of 5,972,859 bp with a GC content of 33.84%. Genome annotation and API ZYM results showed that BSSL-CR3 has a variety of secondary metabolic gene clusters and enzyme activities including α-galactosidase. BSSL-CR3 had more proteins with a low isoelectric point (pI) than terrestrial Flavobacterium strains, and several genes related to osmotic regulation were found in the genomic island (GI). Comparative genomic analysis with other tidal flat bacteria also revealed that BSSL-CR3 had the largest number of genes encoding Carbohydrate Active EnZymes (CAZymes) which are related to algae degradation. This study will provide insight into the adaptability of BSSL-CR3 to the tidal flats and contribute to facilitating future comparative analysis of bacteria in tidal flats.}, }
@article {pmid36472431, year = {2023}, author = {Brown, P and Kucerova, Z and Gorski, L and Chen, Y and Ivanova, M and Leekitcharoenphon, P and Parsons, C and Niedermeyer, J and Jackson, J and Kathariou, S}, title = {Horizontal Gene Transfer and Loss of Serotype-Specific Genes in Listeria monocytogenes Can Lead to Incorrect Serotype Designations with a Commonly-Employed Molecular Serotyping Scheme.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0274522}, pmid = {36472431}, issn = {2165-0497}, mesh = {Pregnancy ; Female ; Humans ; Aged ; *Listeria monocytogenes/genetics ; Serogroup ; Serotyping ; Gene Transfer, Horizontal ; *Listeriosis ; }, abstract = {Listeria monocytogenes is a Gram-positive, facultative intracellular foodborne pathogen capable of causing severe, invasive illness (listeriosis). Three serotypes, 1/2a, 1/2b, and 4b, are leading contributors to human listeriosis, with 4b including the major hypervirulent clones. The multiplex PCR scheme developed by Doumith and collaborators employs primers targeting specific lineages (e.g., lineage II-specific lmo0737, lineage I-specific LMOf2365_2059) or serotypes (e.g., serotype 4b-specific LMOf2365_1900). The Doumith scheme (DS) is extensively employed for molecular serotyping of L. monocytogenes due to its high accuracy, relative ease, and affordability. However, for certain strains, the DS serotype designations are in conflict with those relying on antibody-based schemes or whole-genome sequence (WGS) analysis. In the current study, all 27 tested serotype 4b strains with sequence type 782 (ST782) within the hypervirulent clonal complex 2 (CC2) were designated 1/2b/3b using the DS. These strains lacked the serotype 4b-specific gene LMOf2365_1900, while retaining LMOf2365_2059, which, together with prs, yields the DS 1/2b/3b profile. Furthermore, 15 serotype 1/2a strains of four STs, mostly from water, were designated 1/2b/3b using the DS. These strains lacked the lmo0737 cassette but harbored genomic islands with LMOf2365_2059, thus yielding the DS 1/2b/3b profile. Lastly, we investigated a novel, dual 1/2a-1/2b profile obtained using the DS with 21 serotype 1/2a strains of four STs harboring both the lmo0737 cassette and genomic islands with LMOf2365_2059. The findings suggest that for certain strains and clones of L. monocytogenes the DS designations should be viewed with caution and complemented with alternative tools, e.g., traditional serotyping or WGS analysis. IMPORTANCE Listeria monocytogenes is a foodborne pathogen responsible for severe illness (listeriosis), especially in pregnant women and their fetuses, immunocompromised individuals, and the elderly. Three serotypes, 1/2a, 1/2b, and 4b, account for most human listeriosis, with certain serotype 4b clonal complexes (CCs) overrepresented in human disease. Serotyping remains extensively employed in Listeria epidemiologic investigations, and a multiplex PCR-based serotyping scheme is widely used. However, the PCR gene targets can be lost or gained via horizontal gene transfer, leading to novel PCR profiles without known serotype designations or to incorrect serotype assignments. Thus, an entire serotype 4b clone of the hypervirulent CC2 would be misidentified as serotype 1/2b, and several strains of serotype 1/2a would be identified as serotype 1/2b. Such challenges are especially common in novel clones from underexplored habitats, e.g., wildlife and surface water. The findings suggest caution in application of molecular serotyping, while highlighting Listeria's diversity and potential for horizontal gene transfer.}, }
@article {pmid36471715, year = {2022}, author = {Wen, Y and Xie, X and Xu, P and Yang, C and Zhu, Z and Zhu, J and Lv, J and Zhang, H and Chen, L and Du, H}, title = {NDM-1 and OXA-48-Like Carbapenemases (OXA-48, OXA-181 and OXA-252) Co-Producing Shewanella xiamenensis from Hospital Wastewater, China.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {6927-6938}, pmid = {36471715}, issn = {1178-6973}, abstract = {BACKGROUND: Shewanella genus, as an important carrier of resistance genes, has the potential to transmit resistance to many antimicrobials in many circumstances, especially in aquatic environment. The aim of the study was to describe the risk of Shewanella xiamenensis in hospital environment through analysis of genomic comparison and resistance status.<br><br>METHODS: Seven S. xiamenensis strains were isolated from hospital wastewater. PCR and Sanger sequencing were carried out for detection of common carbapenemase genes. Antimicrobial susceptibility testing was performed to determine the antimicrobial profile. Whole genome sequencing was applied, and sequences were further used for genomic analysis.<br><br>RESULTS: Seven Shewanella xiamenensis were all positive for bla NDM and bla OXA-48. Antimicrobial susceptibility testing showed all Shewanella xiamenensis were resistant to cefotaxime, ceftazidime, imipenem, meropenem, gentamycin and trimethoprim-sulfamethoxazole. Whole genome sequencing and phylogenetic analysis demonstrated the diversity of Shewanella xiamenensis despite isolating from one wastewater pool.<br><br>CONCLUSION: To the best of our knowledge, this is the first report of detection of three types bla OXA-48-like genes in one hospital in China. And we have detected multi-drug resistant S. xiamenensis from hospital wastewater. This emphasizes that the presence of naturally existing carbapenemases in the environment may be significantly overlooked and that the bla OXA-48-like genes in China may originate through the horizontal gene transfer from S. xiamenensis to Enterobacterales rather than import from other countries.}, }
@article {pmid36462475, year = {2023}, author = {Huang, Y and Wen, X and Li, J and Niu, Q and Tang, A and Li, Q}, title = {Metagenomic insights into role of red mud in regulating fate of compost antibiotic resistance genes mediated by both direct and indirect ways.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {317}, number = {}, pages = {120795}, doi = {10.1016/j.envpol.2022.120795}, pmid = {36462475}, issn = {1873-6424}, mesh = {*Genes, Bacterial ; *Composting ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Manure/microbiology ; }, abstract = {In this study, the amendment of red mud (RM) in dairy manure composting on the fate of antibiotic resistance genes (ARGs) by both direct (bacteria community, mobile genetic elements and quorum sensing) and indirect ways (environmental factors and antibiotics) was analyzed. The results showed that RM reduced the total relative abundances of 10 ARGs and 4 mobile genetic elements (MGEs). And the relative abundances of total ARGs and MGEs decreased by 53.48% and 22.30% in T (with RM added) on day 47 compared with day 0. Meanwhile, the modification of RM significantly increased the abundance of lsrK, pvdQ and ahlD in quorum quenching (QQ) and decreased the abundance of luxS in quorum sensing (QS) (P < 0.05), thereby attenuating the intercellular genes frequency of communication. The microbial community and network analysis showed that 25 potential hosts of ARGs were mainly related to Firmicutes, Proteobacteria and Actinobacteria. Redundancy analysis (RDA) and structural equation model (SEM) further indicated that RM altered microbial community structure by regulating antibiotic content and environmental factors (temperature, pH, moisture content and organic matter content), which then affected horizontal gene transfer (HGT) in ARGs mediated by QS and MGEs. These results provide new insights into the dissemination mechanism and removal of ARGs in composting process.}, }
@article {pmid36458228, year = {2022}, author = {Lal, D and Pandey, H and Lal, R}, title = {Phylogenetic Analyses of Microbial Hydrolytic Dehalogenases Reveal Polyphyletic Origin.}, journal = {Indian journal of microbiology}, volume = {62}, number = {4}, pages = {651-657}, pmid = {36458228}, issn = {0046-8991}, abstract = {UNLABELLED: Hydrolytic dehalogenases form an important class of dehalogenases that include haloacid dehalogenase, haloalkane dehalogenase, haloacetate dehalogenase, and atrazine chlorohydrolase. These enzymes are involved in biodegradation of various environmental pollutants and therefore it is important to understand their phylogeny. In the present study, it was found that the enzymes haloalkane and haloacetate dehalogenases share a common ancestry with enzymes such as carboxyesterase, epoxide hydrolase, and lipases, which can be traced to ancestral α/β hydrolase fold enzyme. Haloacid dehalogenases and atrazine chlorohydrolases have probabaly evolved from ancestral enzymes with phosphatase and deaminases activity, respectively. These findings were supported by the similarities in the secondary structure, key catalytic motifs and placement of catalytic residues. The phylogeny of haloalkane dehalogenases and haloacid dehalogenases differs from 16S rRNA gene phylogeny, suggesting spread through horizontal gene transfer. Hydrolytic dehalogenases are polyphyletic and do not share a common evolutionay history, the functional similarities are due to convergent evolution. The present study also identifies key functional residues, mutating which, can help in generating better enzymes for clean up of the persistent environmental pollutants using enzymatic bioremediation.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-022-01043-8.}, }
@article {pmid36456543, year = {2022}, author = {Gaines, MC and Isupov, MN and Sivabalasarma, S and Haque, RU and McLaren, M and Mollat, CL and Tripp, P and Neuhaus, A and Gold, VAM and Albers, SV and Daum, B}, title = {Electron cryo-microscopy reveals the structure of the archaeal thread filament.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {7411}, pmid = {36456543}, issn = {2041-1723}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Cryoelectron Microscopy ; *Archaea ; *Electrons ; Cytoskeleton ; Software ; }, abstract = {Pili are filamentous surface extensions that play roles in bacterial and archaeal cellular processes such as adhesion, biofilm formation, motility, cell-cell communication, DNA uptake and horizontal gene transfer. The model archaeaon Sulfolobus acidocaldarius assembles three filaments of the type-IV pilus superfamily (archaella, archaeal adhesion pili and UV-inducible pili), as well as a so-far uncharacterised fourth filament, named "thread". Here, we report on the cryo-EM structure of the archaeal thread. The filament is highly glycosylated and consists of subunits of the protein Saci_0406, arranged in a head-to-tail manner. Saci_0406 displays structural similarity, but low sequence homology, to bacterial type-I pilins. Thread subunits are interconnected via donor strand complementation, a feature reminiscent of bacterial chaperone-usher pili. However, despite these similarities in overall architecture, archaeal threads appear to have evolved independently and are likely assembled by a distinct mechanism.}, }
@article {pmid36455559, year = {2022}, author = {Ruan, C and Ramoneda, J and Gogia, G and Wang, G and Johnson, DR}, title = {Fungal hyphae regulate bacterial diversity and plasmid-mediated functional novelty during range expansion.}, journal = {Current biology : CB}, volume = {32}, number = {24}, pages = {5285-5294.e4}, doi = {10.1016/j.cub.2022.11.009}, pmid = {36455559}, issn = {1879-0445}, mesh = {*Hyphae/genetics ; *Bacteria/genetics ; Plasmids/genetics ; }, abstract = {The amount of bacterial diversity present on many surfaces is enormous; however, how these levels of diversity persist in the face of the purifying processes that occur as bacterial communities expand across space (referred to here as range expansion) remains enigmatic. We shed light on this apparent paradox by providing mechanistic evidence for a strong role of fungal hyphae-mediated dispersal on regulating bacterial diversity during range expansion. Using pairs of fluorescently labeled bacterial strains and a hyphae-forming fungal strain that expand together across a nutrient-amended surface, we show that a hyphal network increases the spatial intermixing and extent of range expansion of the bacterial strains. This is true regardless of the type of interaction (competition or resource cross-feeding) imposed between the bacterial strains. We further show that the underlying cause is that flagellar motility drives bacterial dispersal along the hyphal network, which counteracts the purifying effects of ecological drift at the expansion frontier. We finally demonstrate that hyphae-mediated spatial intermixing increases the conjugation-mediated spread of plasmid-encoded antibiotic resistance. In conclusion, fungal hyphae are important regulators of bacterial diversity and promote plasmid-mediated functional novelty during range expansion in an interaction-independent manner.}, }
@article {pmid36455257, year = {2022}, author = {Zhang, X and Yao, MC and Chen, L and Sheng, GP}, title = {Lewis Acid-Base Interaction Triggering Electron Delocalization to Enhance the Photodegradation of Extracellular Antibiotic Resistance Genes Adsorbed on Clay Minerals.}, journal = {Environmental science &amp; technology}, volume = {56}, number = {24}, pages = {17684-17693}, doi = {10.1021/acs.est.2c05785}, pmid = {36455257}, issn = {1520-5851}, mesh = {Clay ; *Kaolin/chemistry ; *Anti-Bacterial Agents ; Lewis Acids ; Electrons ; Photolysis ; Minerals/chemistry ; Drug Resistance, Microbial/genetics ; Adsorption ; }, abstract = {The transformation of extracellular antibiotic resistance genes (eARGs) is largely influenced by their inevitable photodegradation in environments where they tend to be adsorbed by ubiquitous clay minerals instead of being in a free form. However, the photodegradation behaviors and mechanisms of the adsorbed eARGs may be quite different from those of the free form and still remain unclear. Herein, we found that kaolinite, a common 1:1-type clay, markedly enhanced eARG photodegradation and made eARGs undergo direct photodegradation under UVA. The decrease in the transformation efficiency of eARGs caused by photodegradation was also promoted. Spectroscopy methods combined with density functional theory calculations revealed that the Lewis acid-base interaction between P-O in eARGs and Al-OH on kaolinite delocalized electrons of eARGs, thus resulting in increased photon absorption ability of eARGs. This ultimately led to enhanced photodegradation of kaolinite-adsorbed eARGs. Additionally, divalent Ca[2+] could reduce the Lewis acid-base interaction-mediated adsorption of eARGs by kaolinite, thereby weakening the enhanced photodegradation of eARGs caused by electron delocalization. In contrast, the 2:1-type clay montmorillonite without strong Lewis acid sites was unable to delocalize the electrons to enhance the photodegradation of eARGs. This work allowed us to better evaluate eARGs' fate and risk in real aqueous environments.}, }
@article {pmid36451580, year = {2023}, author = {Danneels, B and Blignaut, M and Marti, G and Sieber, S and Vandamme, P and Meyer, M and Carlier, A}, title = {Cyclitol metabolism is a central feature of Burkholderia leaf symbionts.}, journal = {Environmental microbiology}, volume = {25}, number = {2}, pages = {454-472}, doi = {10.1111/1462-2920.16292}, pmid = {36451580}, issn = {1462-2920}, support = {203141/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Cyclitols ; *Burkholderia/genetics ; Symbiosis/genetics ; Endophytes/genetics ; Plants/microbiology ; Plant Leaves/microbiology ; Phylogeny ; }, abstract = {The symbioses between plants of the Rubiaceae and Primulaceae families with Burkholderia bacteria represent unique and intimate plant-bacterial relationships. Many of these interactions have been identified through PCR-dependent typing methods, but there is little information available about their functional and ecological roles. We assembled 17 new endophyte genomes representing endophytes from 13 plant species, including those of two previously unknown associations. Genomes of leaf endophytes belonging to Burkholderia s.l. show extensive signs of genome reduction, albeit to varying degrees. Except for one endophyte, none of the bacterial symbionts could be isolated on standard microbiological media. Despite their taxonomic diversity, all endophyte genomes contained gene clusters linked to the production of specialized metabolites, including genes linked to cyclitol sugar analog metabolism and in one instance non-ribosomal peptide synthesis. These genes and gene clusters are unique within Burkholderia s.l. and are likely horizontally acquired. We propose that the acquisition of secondary metabolite gene clusters through horizontal gene transfer is a prerequisite for the evolution of a stable association between these endophytes and their hosts.}, }
@article {pmid36451084, year = {2022}, author = {Jones, CT and Susko, E and Bielawski, JP}, title = {Evolution of the connectivity and indispensability of a transferable gene: the simplicity hypothesis.}, journal = {BMC ecology and evolution}, volume = {22}, number = {1}, pages = {140}, pmid = {36451084}, issn = {2730-7182}, mesh = {*Gene Transfer, Horizontal ; *RNA ; Referral and Consultation ; }, abstract = {BACKGROUND: The number of interactions between a transferable gene or its protein product and genes or gene products native to its microbial host is referred to as connectivity. Such interactions impact the tendency of the gene to be retained by evolution following horizontal gene transfer (HGT) into a microbial population. The complexity hypothesis posits that the protein product of a transferable gene with lower connectivity is more likely to function in a way that is beneficial to a new microbial host compared to the protein product of a transferable gene with higher connectivity. A gene with lower connectivity is consequently more likely to be fixed in any microbial population it enters by HGT. The more recently proposed simplicity hypothesis posits that the connectivity of a transferable gene might increase over time within any single microbial population due to gene-host coevolution, but that differential rates of colonization of microbial populations by HGT in accordance with differences in connectivity might act to counter this and even reduce connectivity over time, comprising an evolutionary trade-off.<br><br>RESULTS: We present a theoretical model that can be used to predict the conditions under which gene-host coevolution might increase or decrease the connectivity of a transferable gene over time. We show that the opportunity to enter new microbial populations by HGT can cause the connectivity of a transferable gene to evolve toward lower values, particularly in an environment that is unstable with respect to the function of the gene's protein product. We also show that a lack of such opportunity in a stable environment can cause the connectivity of a transferable gene to evolve toward higher values.<br><br>CONCLUSION: Our theoretical model suggests that the connectivity of a transferable gene can change over time toward higher values corresponding to a more sessile state of lower transferability or lower values corresponding to a more itinerant state of higher transferability, depending on the ecological milieu in which the gene exists. We note, however, that a better understanding of gene-host coevolutionary dynamics in natural microbial systems is required before any further conclusions about the veracity of the simplicity hypothesis can be drawn.}, }
@article {pmid36448285, year = {2022}, author = {Hao, C and Dewar, AE and West, SA and Ghoul, M}, title = {Gene transferability and sociality do not correlate with gene connectivity.}, journal = {Proceedings. Biological sciences}, volume = {289}, number = {1987}, pages = {20221819}, pmid = {36448285}, issn = {1471-2954}, support = {834164/ERC_/European Research Council/International ; }, mesh = {*Social Behavior ; *Gene Transfer, Horizontal ; Prokaryotic Cells ; RNA ; }, abstract = {The connectivity of a gene, defined as the number of interactions a gene's product has with other genes' products, is a key characteristic of a gene. In prokaryotes, the complexity hypothesis predicts that genes which undergo more frequent horizontal transfer will be less connected than genes which are only very rarely transferred. We tested the role of horizontal gene transfer, and other potentially important factors, by examining the connectivity of chromosomal and plasmid genes, across 134 diverse prokaryotic species. We found that (i) genes on plasmids were less connected than genes on chromosomes; (ii) connectivity of plasmid genes was not correlated with plasmid mobility; and (iii) the sociality of genes (cooperative or private) was not correlated with gene connectivity.}, }
@article {pmid36447017, year = {2023}, author = {Nieuwenhuis, M and Groeneveld, J and Aanen, DK}, title = {Horizontal transfer of tRNA genes to mitochondrial plasmids facilitates gene loss from fungal mitochondrial DNA.}, journal = {Current genetics}, volume = {69}, number = {1}, pages = {55-65}, pmid = {36447017}, issn = {1432-0983}, support = {86514007//NWO/ ; }, mesh = {*DNA, Mitochondrial/genetics ; DNA, Fungal/genetics ; *Mitochondria/genetics ; Plasmids/genetics ; RNA, Transfer/genetics ; Gene Transfer, Horizontal ; }, abstract = {Fungal and plant mitochondria are known to exchange DNA with retroviral plasmids. Transfer of plasmid DNA to the organellar genome is best known and occurs through wholesale insertion of the plasmid. Less well known is the transfer of organellar DNA to plasmids, in particular tRNA genes. Presently, it is unknown whether fungal plasmids can adopt mitochondrial functions such as tRNA production through horizontal gene transfer. In this paper, we studied the exchange of DNA between fungal linear plasmids and fungal mtDNA, mainly focusing on the basidiomycete family Lyophyllaceae. We report at least six independent transfers of complete tRNA genes to fungal plasmids. Furthermore, we discovered two independent cases of loss of a tRNA gene from a fungal mitochondrial genome following transfer of such a gene to a linear mitochondrial plasmid. We propose that loss of a tRNA gene from mtDNA following its transfer to a plasmid creates a mutualistic dependency of the host mtDNA on the plasmid. We also find that tRNA genes transferred to plasmids encode codons that occur at the lowest frequency in the host mitochondrial genomes, possibly due to a higher number of unused transcripts. We discuss the potential consequences of mtDNA transfer to plasmids for both the host mtDNA and the plasmid.}, }
@article {pmid36446404, year = {2022}, author = {Sengupta, S and Azad, RK}, title = {Reconstructing horizontal gene flow network to understand prokaryotic evolution.}, journal = {Open biology}, volume = {12}, number = {11}, pages = {220169}, pmid = {36446404}, issn = {2046-2441}, mesh = {*Gene Flow ; Phylogeny ; *Prokaryotic Cells ; Gene Regulatory Networks ; Computational Biology ; }, abstract = {Horizontal gene transfer (HGT) is a major source of phenotypic innovation and a mechanism of niche adaptation in prokaryotes. Quantification of HGT is critical to decipher its myriad roles in microbial evolution and adaptation. Advances in genome sequencing and bioinformatics have augmented our ability to understand the microbial world, particularly the direct or indirect influence of HGT on diverse life forms. Methods for detecting HGT can be classified into phylogenetic-based and parametric or composition-based approaches. Here, we exploited the complementary strengths of both the approaches to construct a high confidence horizontal gene flow network. Our network is unique in its ability to detect the transfer of native genes of a genome to genomes from other taxa, thus establishing donor and recipient organisms (taxa), rather than through a post hoc analysis as is the practice with several other approaches. The scale-free horizontal gene flow network presented here provides new insights into modes of transfer for the exchange of genetic information and also illuminates differential gene flow across phyla.}, }
@article {pmid36445094, year = {2022}, author = {Yu, Y and Cheng, W and Chen, X and Guo, Q and Cao, H}, title = {Cyanobacterial Blooms Are Not a Result of Positive Selection by Freshwater Eutrophication.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0319422}, pmid = {36445094}, issn = {2165-0497}, mesh = {Phylogeny ; *Lakes/microbiology ; *Cyanobacteria/genetics ; Harmful Algal Bloom ; Water ; }, abstract = {Long-standing cyanobacterial harmful algal blooms (CyanoHABs) are known to result from synergistic interaction between elevated nutrients and superior ecophysiology of cyanobacteria. However, it remains to be determined whether CyanoHABs are a result of positive selection by eutrophic waters. To address this, we conducted molecular evolutionary analyses on the genomes of 9 bloom-forming cyanobacteria, combined with pangenomics and metatranscriptomics. The results showed no positive selection by water eutrophication. Instead, all homologous genes in the species are under strong purifying selection based on the ratio of divergence at nonsynonymous and synonymous sites (dN/dS) and phylogeny. The dN/dS < 0.85 (median = 0.3) for all homologous genes are similar between the genes in the pathways driving CyanoHABs and housekeeping functions. Phylogenetic support for non-positive selection comes from the mixed clustering of strains: strains of the same species from diverse geographic origins form the same clusters, while strains from the same origins form different clusters. Further support lies in the codon adaptation index (CAI) and single nucleotide polymorphism (SNP). The CAI ranged from 0.42 to 0.9 (mean = 0.75), which indicates high-level codon usage bias; the pathways for CyanoHABs and housekeeping functions showed a similar CAI. Interestingly, CAI was negatively correlated with gene expression in 3 metatranscriptomes. The numbers of SNPs were concentrated around 5 to 50. As the SNP number increases, the gene expression level decreases. These negative correlations agree with the population-level dN/dS and phylogeny in supporting purifying selection in bloom-forming cyanobacteria. In summary, superior ecophysiology appears to be acquired prior to water eutrophication. IMPORTANCE CyanoHABs are global environmental hazards, and their mechanisms of action are being intensively investigated. On an ecological scale, CyanoHABs are consequences of synergistic interactions between biological functions and elevated nutrients in eutrophic waters. On an evolutionary scale, one important question is how bloom-forming cyanobacteria acquire these superior biological functions. There are several possibilities, including adaptive evolution and horizontal gene transfer. Here, we explored the possibility of positive selection. We reasoned that there are two possible periods for cyanobacteria to acquire these functions: before the onset of water eutrophication or during water eutrophication. Either way, there should be molecular signatures in protein sequences for positive selection. Interestingly, we found no positive selection by water eutrophication, but strong purifying selection instead on nearly all the genes, suggesting these superior functions aiding CyanoHABs are acquired prior to water eutrophication.}, }
@article {pmid36443412, year = {2022}, author = {Ekhlas, D and Soro, AB and Leonard, FC and Manzanilla, EG and Burgess, CM}, title = {Examining the impact of zinc on horizontal gene transfer in Enterobacterales.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {20503}, pmid = {36443412}, issn = {2045-2322}, mesh = {Animals ; Humans ; *Gene Transfer, Horizontal ; Zinc/pharmacology ; *Gammaproteobacteria ; Conjugation, Genetic ; Ampicillin ; Escherichia coli/genetics ; }, abstract = {Antimicrobial resistance is one of the main international health concerns for humans, animals, and the environment, and substantial efforts have focused on reducing its development and spread. While there is evidence for correlations between antimicrobial usage and antimicrobial resistance development, specific information on the effect of heavy metal/antimicrobial usage on bacterial conjugation is more limited. The aim of this study was to investigate the effects of zinc and antimicrobials in different concentrations on horizontal gene transfer of an ampicillin resistance gene, using a multi-drug resistant Escherichia coli donor strain and three different Salmonella enterica serovars as recipient strains. Differences in conjugation frequencies for the different Salmonella recipients were observed, independent of the presence of zinc or the antimicrobials. Selective pressure on the recipient strains, in the form of ampicillin, resulted in a decrease in conjugation frequencies, while, the presence of rifampicin resulted in increases. Zinc exposure affected conjugation frequencies of only one of the three recipient strains, thus the effect of zinc on conjugation frequencies seemed to be concentration and strain dependent. Furthermore, differences in growth rates due to plasmid carriage were observed for one of the Salmonella strains.}, }
@article {pmid36442505, year = {2023}, author = {Ares-Arroyo, M and Coluzzi, C and Rocha, EPC}, title = {Origins of transfer establish networks of functional dependencies for plasmid transfer by conjugation.}, journal = {Nucleic acids research}, volume = {51}, number = {7}, pages = {3001-3016}, pmid = {36442505}, issn = {1362-4962}, mesh = {Chromosomes ; *Conjugation, Genetic ; *Gene Transfer, Horizontal ; Plasmids/genetics ; *Escherichia coli/genetics/physiology ; *Staphylococcus aureus/genetics/physiology ; Replication Origin ; }, abstract = {Plasmids can be transferred between cells by conjugation, thereby driving bacterial evolution by horizontal gene transfer. Yet, we ignore the molecular mechanisms of transfer for many plasmids because they lack all protein-coding genes required for conjugation. We solved this conundrum by identifying hundreds of plasmids and chromosomes with conjugative origins of transfer in Escherichia coli and Staphylococcus aureus. These plasmids (pOriT) hijack the relaxases of conjugative or mobilizable elements, but not both. The functional dependencies between pOriT and other plasmids explain their co-occurrence: pOriT are abundant in cells with many plasmids, whereas conjugative plasmids are the most common in the others. We systematically characterized plasmid mobility in relation to conjugation and alternative mechanisms of transfer and can now propose a putative mechanism of transfer for ∼90% of them. In most cases, plasmid mobility seems to involve conjugation. Interestingly, the mechanisms of mobility are important determinants of plasmid-encoded accessory traits, since pOriTs have the highest densities of antimicrobial resistance genes, whereas plasmids lacking putative mechanisms of transfer have the lowest. We illuminate the evolutionary relationships between plasmids and suggest that many pOriT may have arisen by gene deletions in other types of plasmids. These results suggest that most plasmids can be transferred by conjugation.}, }
@article {pmid36439225, year = {2022}, author = {Hosseini-Giv, N and Basas, A and Hicks, C and El-Omar, E and El-Assaad, F and Hosseini-Beheshti, E}, title = {Bacterial extracellular vesicles and their novel therapeutic applications in health and cancer.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {962216}, pmid = {36439225}, issn = {2235-2988}, mesh = {Humans ; Anti-Bacterial Agents/metabolism ; Gram-Negative Bacteria/metabolism ; Gram-Positive Bacteria/metabolism ; *Extracellular Vesicles/metabolism ; *Neoplasms/therapy/metabolism ; }, abstract = {Bacterial cells communicate with host cells and other bacteria through the release of membrane vesicles known as bacterial extracellular vesicles (BEV). BEV are established mediators of intracellular signaling, stress tolerance, horizontal gene transfer, immune stimulation and pathogenicity. Both Gram-positive and Gram-negative bacteria produce extracellular vesicles through different mechanisms based on cell structure. BEV contain and transfer different types of cargo such as nucleic acids, proteins and lipids, which are used to interact with and affect host cells such as cytotoxicity and immunomodulation. The role of these membranous microvesicles in host communication, intra- and inter-species cell interaction and signaling, and contribution to various diseases have been well demonstrated. Due to their structure, these vesicles can be easily engineered to be utilized for clinical application, as shown with its role in vaccine therapy, and could be used as a diagnostic and cancer drug delivery tool in the future. However, like other novel therapeutic approaches, further investigation and standardization is imperative for BEV to become a routine vector or a conventional treatment method.}, }
@article {pmid36437887, year = {2023}, author = {Adyari, B and Hou, L and Zhang, L and Chen, N and Ju, F and Zhu, L and Yu, CP and Hu, A}, title = {Seasonal hydrological dynamics govern lifestyle preference of aquatic antibiotic resistome.}, journal = {Environmental science and ecotechnology}, volume = {13}, number = {}, pages = {100223}, pmid = {36437887}, issn = {2666-4984}, abstract = {Antibiotic resistance genes (ARGs) are a well-known environmental concern. Yet, limited knowledge exists on the fate and transport of ARGs in deep freshwater reservoirs experiencing seasonal hydrological changes, especially in the context of particle-attached (PA) and free-living (FL) lifestyles. Here, the ARG profiles were examined using high-throughput quantitative PCR in PA and FL lifestyles during four seasons representing two hydrological phenomena (vertical mixing and thermal stratification) in the Shuikou Reservoir (SR), Southern China. The results indicated that seasonal hydrological dynamics were critical for influencing the ARGs in PA and FL and the transition of ARGs between the two lifestyles. ARG profiles both in PA and FL were likely to be shaped by horizontal gene transfer. However, they exhibited distinct responses to the physicochemical (e.g., nutrients and dissolved oxygen) changes under seasonal hydrological dynamics. The particle-association niche (PAN) index revealed 94 non-conservative ARGs (i.e., no preferences for PA and FL) and 23 and 16 conservative ARGs preferring PA and FL lifestyles, respectively. A sharp decline in conservative ARGs under stratified hydrologic suggested seasonal influence on the ARGs transition between PA and FL lifestyles. Remarkably, the conservative ARGs (in PA or FL lifestyle) were more closely related to bacterial OTUs in their preferred lifestyle than their counterparts, indicating lifestyle-dependent ARG enrichment. Altogether, these findings enhanced our understanding of the ARG lifestyles and the role of seasonal hydrological changes in governing the ARG transition between the lifestyles in a typical deep freshwater ecosystem.}, }
@article {pmid36436581, year = {2023}, author = {Cuetero-Martínez, Y and Flores-Ramírez, A and De Los Cobos-Vasconcelos, D and Aguirre-Garrido, JF and López-Vidal, Y and Noyola, A}, title = {Removal of bacterial pathogens and antibiotic resistance bacteria by anaerobic sludge digestion with thermal hydrolysis pre-treatment and alkaline stabilization post-treatment.}, journal = {Chemosphere}, volume = {313}, number = {}, pages = {137383}, doi = {10.1016/j.chemosphere.2022.137383}, pmid = {36436581}, issn = {1879-1298}, mesh = {Humans ; *Sewage/microbiology ; Anaerobiosis ; Hydrolysis ; *Angiotensin Receptor Antagonists ; Biosolids ; Angiotensin-Converting Enzyme Inhibitors ; Bacteria ; Salmonella ; Escherichia coli ; Drug Resistance, Microbial ; Digestion ; Bacteria, Anaerobic ; }, abstract = {Primary sludge (PS) is associated with public health and environmental risks, so regulations focus on reducing the pathogenic and heavy metal contents of the treated material (biosolids), intended for soil amendments and land reclamation. The regulations set limits for Escherichia coli (or fecal coliforms), Salmonella spp., helminth eggs and enterovirus. However, the potential risk due to antibiotic resistant bacteria (ARB) and other human potential pathogenic bacteria (HPB) are not considered. In this work, three sludge treatment processes, having in common an anaerobic digestion step, were applied to assess the removal of regulated bacteria (fecal coliforms, Salmonella spp), ARB and HPB. The treatment arrangements, fed with PS from a full-scale wastewater treatment plant were: 1) Mesophilic anaerobic digestion followed by alkaline stabilization post-treatment (MAD-CaO); 2) Thermophilic anaerobic digestion (TAD) and, 3) Pre-treatment (mild thermo-hydrolysis) followed by TAD (PT-TAD). The results address the identification, quantification (colony forming units) and taxonomic characterization of ARB resistant to β-lactams and vancomycin, as well as the taxonomic characterization of HPB by sequencing with PacBio. In addition, quantification based on culture media of fecal coliforms and Salmonella spp. is presented. The capabilities and limitations of microbiological and metataxonomomic analyses based on PacBio sequencing are discussed, emphasizing that they complement each other. Genus Aeromonas, Acinetobacter, Citrobacter, Enterobacter, Escherichia, Klebsiella, Ochrobactrum, Pseudomonas and Raoultella, among others, were found in the PS, which are of clinical or environmental importance, being either HPB, HPB-ARB, or non-pathogenic ARB with the potentiality of horizontal gene transfer. Based on the analysis of fecal coliforms and Salmonella spp., the three processes produced class A (highest) biosolids, suitable for unrestricted agriculture applications. Mild thermo-hydrolisis was effective in decreasing ARB cultivability, but it reappeared after the following TAD. O. intermedium (HPB-ARB) was enriched in MAD and TAD while Laribacter hongkongensis (HPB) did persist after the applied treatments.}, }
@article {pmid36436244, year = {2023}, author = {Sun, W and Qian, X and Wang, X and Gu, J}, title = {Residual enrofloxacin in cattle manure increased persistence and dissemination risk of antibiotic resistance genes during anaerobic digestion.}, journal = {Journal of environmental management}, volume = {326}, number = {Pt B}, pages = {116864}, doi = {10.1016/j.jenvman.2022.116864}, pmid = {36436244}, issn = {1095-8630}, mesh = {Cattle ; Animals ; *Manure/analysis ; *Anti-Bacterial Agents/pharmacology/metabolism ; Enrofloxacin/pharmacology ; Anaerobiosis ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; }, abstract = {Anaerobic digestion is a common approach to dispose and recycle livestock manures, and the agricultural application of anaerobic digestives represents an important pathway of spreading antibiotic resistance genes (ARGs) from livestock manures to soils. Enrofloxacin is a clinically important fluoroquinolone antibiotic with high residual concentrations in livestock manure, and propagation of fluoroquinolone resistance genes poses a huge risk to public health. Compared with other antibiotics, enrofloxacin is relatively durable in anaerobic digestion system. However, its effect on the persistence of ARGs during anaerobic digestion and its mechanism are not clear. In this study, we investigated effects of 0, 4, and 8 mg/L enrofloxacin on the abundance, persistence, and transferring risk of five plasmid-mediated fluroquinolone ARGs and five typic clinically important non-fluoroquinolone ARGs during cattle manure digestion. The responses of integrons and microbial communities to enrofloxacin were assessed to uncover the underlying mechanisms. All the ten detected ARGs were highly persistent in anaerobic digestion, among them seven ARGs increased over 8.2 times after digestion. Network analysis revealed that the potential hosts of ARGs were critical functional taxa during anaerobic digestion, which can explain the high persistence of ARGs. Residual enrofloxacin significantly increased the abundance of aac(6')-ib-cr, sul1, intI1, and intI2 throughout the digestion, but had no impact on the other ARGs, demonstrating its role in facilitating horizontal gene transfer of the plasmid-mediated aac(6')-ib-cr. The influence of enrofloxacin on microbial communities disappeared at the end of digestion, but the ARG profiles remained distinctive between the enrofloxacin treatments and the control, suggesting the high persistence of enrofloxacin induced ARGs. Our results suggested the high persistence of ARGs in anaerobic digestion system, and highlighted the role of residual enrofloxacin in livestock manure in increasing dissemination risk of fluroquinolone resistance genes.}, }
@article {pmid36425127, year = {2022}, author = {Memili, A and Kutchy, N and Braimah, OA and Morenikeji, OB}, title = {Evolutionary conservation of motifs within vanA and vanB of vancomycin-resistant enterococci.}, journal = {Veterinary world}, volume = {15}, number = {10}, pages = {2407-2413}, pmid = {36425127}, issn = {0972-8988}, abstract = {BACKGROUND AND AIM: Global Health is threatened by the rapid emergence of multidrug-resistant bacteria. Antibiotic resistomes rapidly evolve, yet conserved motifs elucidated in our study have the potential for future drug targets for precision medicine. This study aimed to identify conserved genetic sequences and their evolutionary pathways among vancomycin-resistant Enterococcus species such as Enterococcus faecium and Enterococcus faecalis.<br><br>MATERIALS AND METHODS: We retrieved a total of 26 complete amino acid and nucleotide sequences of resistance determinant genes against vancomycin (vanA and vanB), streptomycin (aac-aah), and penicillin (pbp5) from the publicly available genetic sequence database, GenBank. The sequences were comprised of bacteria classified under the genera of Enterococcus, Staphylococcus, Amycolatopsis, Ruminococcus, and Clostridium. Sequences were aligned with Clustal Omega Multiple Sequence Alignment program and Percent Identity Matrices were derived. Phylogenetic analyses to elucidate evolutionary relationships between sequences were conducted with the neighbor-end joining method through the Molecular Evolutionary Genetics Analysis (MEGAX) software, developed by the Institute of Molecular Evolutionary Genetics at Pennsylvania State University. Subsequent network analyses of the resistance gene, vanB, within E. faecium were derived from ScanProsite and InterPro.<br><br>RESULTS: We observed the highest nucleotide sequence similarity of vanA regions within strains of E. faecium (100%) and E. faecalis (100%). Between Enterococcus genera, we continued to observe high sequence conservation for vanA and vanB, up to 99.9% similarity. Phylogenetic tree analyses suggest rapid acquisition of these determinants between strains within vanA and vanB, particularly between strains of Enterococcus genera, which may be indicative of horizontal gene transfer. Within E. faecium, Adenosine 5'-Triphosphate (ATP)-Grasp and D-ala-D-ala ligase (Ddl) were found as conserved domains of vanA and vanB. We additionally found that there is notable sequence conservation, up to 66.67%, between resistomes against vancomycin and streptomycin among E. faecium.<br><br>CONCLUSION: Resistance genes against vancomycin have highly conserved sequences between strains of Enterococcus bacteria. These conserved sequences within vanA and vanB encode for ATP-Grasp and Ddl motifs, which have functional properties for maintaining cell wall integrity. High sequence conservation is also observed among resistance genes against penicillin and streptomycin, which can inform future drug targets for broader spectrum therapies.}, }
@article {pmid36425042, year = {2022}, author = {Andersson, T and Makenga, G and Francis, F and Minja, DTR and Overballe-Petersen, S and Tang, ME and Fuursted, K and Baraka, V and Lood, R}, title = {Enrichment of antibiotic resistance genes within bacteriophage populations in saliva samples from individuals undergoing oral antibiotic treatments.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1049110}, pmid = {36425042}, issn = {1664-302X}, abstract = {Spread of antibiotic resistance is a significant challenge for our modern health care system, and even more so in developing countries with higher prevalence of both infections and resistant bacteria. Faulty usage of antibiotics has been pinpointed as a driving factor in spread of resistant bacteria through selective pressure. However, horizontal gene transfer mediated through bacteriophages may also play an important role in this spread. In a cohort of Tanzanian patients suffering from bacterial infections, we demonstrate significant differences in the oral microbial diversity between infected and non-infected individuals, as well as before and after oral antibiotics treatment. Further, the resistome carried both by bacteria and bacteriophages vary significantly, with bla CTX-M1 resistance genes being mobilized and enriched within phage populations. This may impact how we consider spread of resistance in a biological context, as well in terms of treatment regimes.}, }
@article {pmid36423222, year = {2023}, author = {Balparda, M and Schmitz, J and Duemmel, M and Wuthenow, IC and Schmidt, M and Alseekh, S and Fernie, AR and Lercher, MJ and Maurino, VG}, title = {Viridiplantae-specific GLXI and GLXII isoforms co-evolved and detoxify glucosone in planta.}, journal = {Plant physiology}, volume = {191}, number = {2}, pages = {1214-1233}, pmid = {36423222}, issn = {1532-2548}, mesh = {Magnesium Oxide ; *Lactoylglutathione Lyase/chemistry/genetics/metabolism ; Protein Isoforms/genetics ; *Arabidopsis/genetics/metabolism ; }, abstract = {Reactive carbonyl species (RCS) such as methylglyoxal (MGO) and glyoxal (GO) are highly reactive, unwanted side-products of cellular metabolism maintained at harmless intracellular levels by specific scavenging mechanisms.MGO and GO are metabolized through the glyoxalase (GLX) system, which consists of two enzymes acting in sequence, GLXI and GLXII. While plant genomes encode a number of different GLX isoforms, their specific functions and how they arose during evolution are unclear. Here, we used Arabidopsis (Arabidopsis thaliana) as a model species to investigate the evolutionary history of GLXI and GLXII in plants and whether the GLX system can protect plant cells from the toxicity of RCS other than MGO and GO. We show that plants possess two GLX systems of different evolutionary origins and with distinct structural and functional properties. The first system is shared by all eukaryotes, scavenges MGO and GO, especially during seedling establishment, and features Zn2+-type GLXI proteins with a metal cofactor preference that were present in the last eukaryotic common ancestor. GLXI and GLXII of the second system, featuring Ni2+-type GLXI, were acquired by the last common ancestor of Viridiplantae through horizontal gene transfer from proteobacteria and can together metabolize keto-D-glucose (KDG, glucosone), a glucose-derived RCS, to D-gluconate. When plants displaying loss-of-function of a Viridiplantae-specific GLXI were grown in KDG, D-gluconate levels were reduced to 10%-15% of those in the wild type, while KDG levels showed an increase of 48%-67%. In contrast to bacterial GLXI homologs, which are active as dimers, plant Ni2+-type GLXI proteins contain a domain duplication, are active as monomers, and have a modified second active site. The acquisition and neofunctionalization of a structurally, biochemically, and functionally distinct GLX system indicates that Viridiplantae are under strong selection to detoxify diverse RCS.}, }
@article {pmid36422324, year = {2022}, author = {Khayi, S and Chan, KG and Faure, D}, title = {Patterns of Genomic Variations in the Plant Pathogen Dickeya solani.}, journal = {Microorganisms}, volume = {10}, number = {11}, pages = {}, pmid = {36422324}, issn = {2076-2607}, support = {I2BC-2022//French National Centre for Scientific Research/ ; RMF1252-2021//University of Malaya/ ; }, abstract = {The plant pathogen Dickeya solani causes soft rot and blackleg diseases in several crops including Solanum tuberosum. Unveiling the patterns of its diversity contributes to understanding the emergence and virulence of this pathogen in potato agro-systems. In this study, we analyzed the genome of several D. solani strains exhibiting an atypically high number of genetic variations. Variant calling and phylogenomics support the evidence that the strains RNS10-105-1A, A623S-20A-17 and RNS05.1.2A belong to a divergent sub-group of D. solani for which we proposed RNS05.1.2A as a reference strain. In addition, we showed that the variations (1253 to 1278 snp/indels) in strains RNS13-30-1A, RNS13-31-1A and RNS13-48-1A were caused by a horizontal gene transfer event from a donor belonging to the D. solani RNS05.1.2A subgroup. The overall results highlight the patterns driving the diversification in D. solani species. This work contributes to understanding patterns and causes of diversity in the emerging pathogen D. solani.}, }
@article {pmid36422323, year = {2022}, author = {Belova, SE and Naumoff, DG and Suzina, NE and Kovalenko, VV and Loiko, NG and Sorokin, VV and Dedysh, SN}, title = {Building a Cell House from Cellulose: The Case of the Soil Acidobacterium Acidisarcina polymorpha SBC82[T].}, journal = {Microorganisms}, volume = {10}, number = {11}, pages = {}, pmid = {36422323}, issn = {2076-2607}, support = {122041100029-2//Ministry of Science and Higher Education of Russian Federation/ ; 122040800164-6//Ministry of Science and Higher Education of Russian Federation/ ; 122040400089-6//FIC CP RAS FFZE-2022-0011/ ; }, abstract = {Acidisarcina polymorpha SBC82[T] is a recently described representative of the phylum Acidobacteriota from lichen-covered tundra soil. Cells of this bacterium occur within unusual saccular chambers, with the chamber envelope formed by tightly packed fibrils. These extracellular structures were most pronounced in old cultures of strain SBC82[T] and were organized in cluster-like aggregates. The latter were efficiently destroyed by incubating cell suspensions with cellulase, thus suggesting that they were composed of cellulose. The diffraction pattern obtained for 45-day-old cultures of strain SBC82[T] by using small angle X-ray scattering was similar to those reported earlier for mature wood samples. The genome analysis revealed the presence of a cellulose biosynthesis locus bcs. Cellulose synthase key subunits A and B were encoded by the bcsAB gene whose close homologs are found in genomes of many members of the order Acidobacteriales. More distant homologs of the acidobacterial bcsAB occurred in representatives of the Proteobacteria. A unique feature of bcs locus in strain SBC82[T] was the non-orthologous displacement of the bcsZ gene, which encodes the GH8 family glycosidase with a GH5 family gene. Presumably, these cellulose-made extracellular structures produced by A. polymorpha have a protective function and ensure the survival of this acidobacterium in habitats with harsh environmental conditions.}, }
@article {pmid36422313, year = {2022}, author = {Tavares, RDS and Tacão, M and Ramalheira, E and Ferreira, S and Henriques, I}, title = {Report and Comparative Genomics of an NDM-5-Producing Escherichia coli in a Portuguese Hospital: Complex Class 1 Integrons as Important Players in blaNDM Spread.}, journal = {Microorganisms}, volume = {10}, number = {11}, pages = {}, pmid = {36422313}, issn = {2076-2607}, support = {UIDP/50017/2020+UIDB/50017/2020 + LA/P/0094/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; UIDB/04004/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; SFRH/BD/145147/2019//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; CEECIND/00977/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; }, abstract = {BACKGROUND: New Delhi metallo-beta-lactamase (NDM) has been spreading across the globe, but the causes of its success are poorly understood. We characterized a blaNDM-5-positive Escherichia coli strain from a Portuguese hospital and conducted comparative genomic analyses to understand the role of clonal background and horizontal gene transfer in blaNDM-5 dissemination.<br><br>METHODS: After blaNDM PCR screening and genome sequencing, Ec355340 was subjected to mating, transformation, and plasmid curing assays and MICs determination for several antibiotics. Comparison with data compiled from public databases was performed.<br><br>RESULTS: blaNDM-5 was in a complex integron co-located in a FIB-FII plasmid (pEc355340_NDM-5). The mating assays were unsuccessful, but plasmid transformation into a susceptible host led to resistance to all beta-lactams and to sulfamethoxazole-trimethoprim. The profile of virulence genes (n = 73) was compatible with extraintestinal pathogenesis. An analysis of genomes from public databases suggested that blaNDM-5 has rarely been associated with ST156 strains (such as Ec355340), while is has frequently been found on strains of the ST10 clonal complex. However, ST156 may play a role in the co-spreading of blaNDM and mcr genes. Regardless, comparative genomics confirmed the presence of blaNDM in similar complex integrons in plasmids (48/100 plasmids most similar to pEc355340_NDM-5) and ST156 genomes (20/41 blaNDM-positive genomes).<br><br>CONCLUSIONS: blaNDM-5 and other blaNDM variants were more frequently associated to complex integrons than previously reported and, therefore, these platforms may be important drivers in their dissemination. The identification of blaNDM-5 for the first time in Portugal could be a game-changer in the current Portuguese antibiotic resistance scenario, as this gene encodes a higher-level resistance phenotype, and its spread may be facilitated due to the association with complex integrons.}, }
@article {pmid36421375, year = {2022}, author = {Ding, H and Bi, D and Zhang, S and Han, S and Ye, Y and Yi, R and Yang, J and Liu, B and Wu, L and Zhuo, R and Kan, X}, title = {The Mitogenome of Sedum plumbizincicola (Crassulaceae): Insights into RNA Editing, Lateral Gene Transfer, and Phylogenetic Implications.}, journal = {Biology}, volume = {11}, number = {11}, pages = {}, pmid = {36421375}, issn = {2079-7737}, support = {NEL&amp;MARA-003//the Opening Foundation of National Engineering Laboratory of Soil Pollution Control and Remediation Technologies, and Key Laboratory of Heavy Metal Pollution Prevention &amp; Control, Ministry of Agriculture and Rural Affairs/ ; BK20211078//the Basic Research Program (Natural Science Foundation) of Jiangsu Province/ ; YJS20210136//the Scientific Research Project Foundation of Postgraduate of the Anhui Higher Education Institutions of China/ ; }, abstract = {As the largest family within the order Saxifragales, Crassulaceae contains about 34 genera with 1400 species. Mitochondria play a critical role in cellular energy production. Since the first land plant mitogenome was reported in Arabidopsis, more than 400 mitogenomic sequences have been deposited in a public database. However, no entire mitogenome data have been available for species of Crassulaceae to date. To better understand the evolutionary history of the organelles of Crassulaceae, we sequenced and performed comprehensive analyses on the mitogenome of Sedum plumbizincicola. The master mitogenomic circle is 212,159 bp in length, including 31 protein-coding genes (PCGs), 14 tRNA genes, and 3 rRNA genes. We further identified totally 508 RNA editing sites in PCGs, and demonstrated that the second codon positions of mitochondrial genes are most prone to RNA editing events. Notably, by neutrality plot analyses, we observed that the mitochondrial RNA editing events have large effects on the driving forces of plant evolution. Additionally, 4 MTPTs and 686 NUMTs were detected in the mitochondrial and nuclear genomes of S. plumbizincicola, respectively. Additionally, we conducted further analyses on gene transfer, secondary structures of mitochondrial RNAs, and phylogenetic implications. Therefore, the findings presented here will be helpful for future investigations on plant mitogenomes.}, }
@article {pmid36419429, year = {2022}, author = {Ding, M and Ye, Z and Liu, L and Wang, W and Chen, Q and Zhang, F and Wang, Y and Sjöling, &#xc5; and Martín-Rodríguez, AJ and Hu, R and Chen, W and Zhou, Y}, title = {Subinhibitory antibiotic concentrations promote the horizontal transfer of plasmid-borne resistance genes from Klebsiellae pneumoniae to Escherichia coli.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1017092}, pmid = {36419429}, issn = {1664-302X}, abstract = {Horizontal gene transfer plays an important role in the spread of antibiotic resistance, in which plasmid-mediated conjugation transfer is the most important mechanism. While sub-minimal inhibitory concentrations (sub-MIC) of antibiotics could promote conjugation frequency, the mechanism by which sub-MIC levels of antibiotics affect conjugation frequency is not clear. Here, we used Klebsiella pneumoniae SW1780 carrying the multi-drug resistance plasmid pSW1780-KPC as the donor strain, to investigate the effects of sub-MICs of meropenem (MEM), ciprofloxacin (CIP), cefotaxime (CTX), and amikacin (AK) on conjugational transfer of pSW1780-KPC from SW1780 to Escherichia coli J53. Our results showed that the transfer frequencies increased significantly by treating SW1780 strain with sub-MIC levels of MEM, CIP, CTX and AK. Transfer frequencies at sub-MIC conditions in a Galleria mellonella were significantly higher than in vitro. To investigate gene expression and metabolic effects, RT-qPCR and LC-MS-based metabolome sequencing were performed. Transcript levels of T4SS genes virB1, virB2, virB4, virB8, and conjugation-related genes traB, traK, traE, and traL were significantly upregulated by exposure to sub-MICs of MEM, CIP, CTX, and AK. Metabolome sequencing revealed nine differentially regulated metabolites. Our findings are an early warning for a wide assessment of the roles of sub-MIC levels of antibiotics in the spread of antibiotic resistance.}, }
@article {pmid36418956, year = {2022}, author = {Lu, J and Duan, J and Han, Y and Gou, M and Li, J and Li, Q and Pang, Y}, title = {A novel serum spherical lectin from lamprey reveals a more efficient mechanism of immune initiation and regulation in jawless vertebrates.}, journal = {Cellular &amp; molecular biology letters}, volume = {27}, number = {1}, pages = {102}, pmid = {36418956}, issn = {1689-1392}, mesh = {Animals ; *Lampreys/metabolism ; *Lectins/metabolism ; Phylogeny ; Mannose-Binding Protein-Associated Serine Proteases/genetics/metabolism ; Mannose-Binding Lectins ; Mammals ; }, abstract = {The innate immune system is the body's first line of defense against pathogens and involves antibody and complement system-mediated antigen removal. Immune-response-related complement molecules have been identified in lamprey, and the occurrence of innate immune response via the mannose-binding lectin-associated serine proteases of the lectin cascade has been reported. We have previously shown that lamprey (Lampetra japonica) serum can efficiently and specifically eliminate foreign pathogens. Therefore, we aimed to understand the immune mechanism of lamprey serum in this study. We identified and purified a novel spherical lectin (LSSL) from lamprey serum. LSSL had two structural calcium ions coordinated with conserved amino acids, as determined through cryogenic electron microscopy. LSSL showed high binding capacity with microbial and mammalian glycans and demonstrated agglutination activity against bacteria. Phylogenetic analysis revealed that LSSL was transferred from phage transposons to the lamprey genome via horizontal gene transfer. Furthermore, LSSL was associated with mannose-binding lectin-associated serine protease 1 and promoted the deposition of the C3 fragment on the surface of target cells upon binding. These results led us to conclude that LSSL initiates and regulates agglutination, resulting in exogenous pathogen and tumor cell eradication. Our observations will give a greater understanding of the origin and evolution of the complement system in higher vertebrates and lead to the identification of novel immune molecules and pathways for defense against pathogens and tumor cells.}, }
@article {pmid36417430, year = {2022}, author = {Gozashti, L and Roy, SW and Thornlow, B and Kramer, A and Ares, M and Corbett-Detig, R}, title = {Transposable elements drive intron gain in diverse eukaryotes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {48}, pages = {e2209766119}, pmid = {36417430}, issn = {1091-6490}, support = {R35 GM128932/GM/NIGMS NIH HHS/United States ; R35 GM145266/GM/NIGMS NIH HHS/United States ; T32 HG008345/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Introns/genetics ; *Eukaryota/genetics ; *DNA Transposable Elements/genetics ; Phylogeny ; Eukaryotic Cells ; }, abstract = {There is massive variation in intron numbers across eukaryotic genomes, yet the major drivers of intron content during evolution remain elusive. Rapid intron loss and gain in some lineages contrast with long-term evolutionary stasis in others. Episodic intron gain could be explained by recently discovered specialized transposons called Introners, but so far Introners are only known from a handful of species. Here, we performed a systematic search across 3,325 eukaryotic genomes and identified 27,563 Introner-derived introns in 175 genomes (5.2%). Species with Introners span remarkable phylogenetic diversity, from animals to basal protists, representing lineages whose last common ancestor dates to over 1.7 billion years ago. Aquatic organisms were 6.5 times more likely to contain Introners than terrestrial organisms. Introners exhibit mechanistic diversity but most are consistent with DNA transposition, indicating that Introners have evolved convergently hundreds of times from nonautonomous transposable elements. Transposable elements and aquatic taxa are associated with high rates of horizontal gene transfer, suggesting that this combination of factors may explain the punctuated and biased diversity of species containing Introners. More generally, our data suggest that Introners may explain the episodic nature of intron gain across the eukaryotic tree of life. These results illuminate the major source of ongoing intron creation in eukaryotic genomes.}, }
@article {pmid36416260, year = {2024}, author = {Stanton, IC and Tipper, HJ and Chau, K and Klümper, U and Subirats, J and Murray, AK}, title = {Does Environmental Exposure to Pharmaceutical and Personal Care Product Residues Result in the Selection of Antimicrobial-Resistant Microorganisms, and is this Important in Terms of Human Health Outcomes?.}, journal = {Environmental toxicology and chemistry}, volume = {43}, number = {3}, pages = {623-636}, doi = {10.1002/etc.5498}, pmid = {36416260}, issn = {1552-8618}, support = {MRF_MRF-145-0004-TPG-AVISO/MRF/MRF/United Kingdom ; }, mesh = {Humans ; Environmental Monitoring ; Environmental Exposure ; *Cosmetics/toxicity/analysis ; *Anti-Infective Agents ; Water ; Anti-Bacterial Agents/toxicity/analysis ; Outcome Assessment, Health Care ; Pharmaceutical Preparations ; *Water Pollutants, Chemical/toxicity/analysis ; }, abstract = {The environment plays a critical role in the development, dissemination, and transmission of antimicrobial resistance (AMR). Pharmaceuticals and personal care products (PPCPs) enter the environment through direct application to the environment and through anthropogenic pollution. Although there is a growing body of evidence defining minimal selective concentrations (MSCs) of antibiotics and the role antibiotics play in horizontal gene transfer (HGT), there is limited evidence on the role of non-antibiotic PPCPs. Existing data show associations with the development of resistance or effects on bacterial growth rather than calculating selective endpoints. Research has focused on laboratory-based systems rather than in situ experiments, although PPCP concentrations found throughout wastewater, natural water, and soil environments are often within the range of laboratory-derived MSCs and at concentrations shown to promote HGT. Increased selection and HGT of AMR by PPCPs will result in an increase in total AMR abundance in the environment, increasing the risk of exposure and potential transmission of environmental AMR to humans. There is some evidence to suggest that humans can acquire resistance from environmental settings, with water environments being the most frequently studied. However, because this is currently limited, we recommend that more evidence be gathered to understand the risk the environment plays in regard to human health. In addition, we recommend that future research efforts focus on MSC-based experiments for non-antibiotic PPCPS, particularly in situ, and investigate the effect of PPCP mixtures on AMR. Environ Toxicol Chem 2024;43:623-636. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.}, }
@article {pmid36414122, year = {2023}, author = {Oyanedel, D and Rojas, R and Brokordt, K and Schmitt, P}, title = {Crassostrea gigas oysters from a non-intensive farming area naturally harbor potentially pathogenic vibrio strains.}, journal = {Journal of invertebrate pathology}, volume = {196}, number = {}, pages = {107856}, doi = {10.1016/j.jip.2022.107856}, pmid = {36414122}, issn = {1096-0805}, mesh = {Animals ; *Crassostrea ; *Vibrio ; Virulence ; Virulence Factors ; Aquaculture ; }, abstract = {Farming intensification and climate change are inevitably linked to pathogen emergence in aquaculture. In this context, infectious diseases associated with vibrios span all developmental stages of the Pacific Oyster Crassostrea gigas. Moreover, virulence factors associated with pathogenicity spread among the vibrio community through horizontal gene transfer as part of the natural eco-evolutive dynamic of this group. Therefore, risk factors associated with the emergence of pathogens should be assessed before the appearance of mass mortalities in developing rearing areas. In this context, we characterized the vibrios community associated with oysters cultured in a non-intensive area free of massive mortalities located at Tongoy bay, Chile, through a culture-dependent approach. We taxonomically affiliated our isolates at the species level through the partial sequencing of the heat shock protein 60 gene and estimated their virulence potential through experimental infection of juvenile C. gigas. The vibrio community belonged almost entirely to the Splendidus clade, with Vibrio lentus being the most abundant species. The virulence potential of selected isolates was highly contrasted with oyster survival ranging between 100 and 30 %. Moreover, different vibrio species affected oyster survival at different rates, for instance V. splendidus TO2_12 produced most mortalities just 24 h after injection, while the V. lentus the most virulent strain TO6_11 produced sustained mortalities reaching 30 % of survival at day 4 after injection. Production of enzymes associated with pathogenicity was detected and hemolytic activity was positive for 50 % of the virulent strains and negative for 90 % of non-virulent strains, representing the phenotype that better relates to the virulence status of strains. Overall, results highlight that virulence is a trait present in the absence of disease expression, and therefore the monitoring of potentially pathogenic groups such as vibrios is essential to anticipate and manage oyster disease emergence in both established and under-development rearing areas.}, }
@article {pmid36412071, year = {2023}, author = {Shimpi, GG and Bentlage, B}, title = {Ancient endosymbiont-mediated transmission of a selfish gene provides a model for overcoming barriers to gene transfer into animal mitochondrial genomes.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {45}, number = {2}, pages = {e2200190}, doi = {10.1002/bies.202200190}, pmid = {36412071}, issn = {1521-1878}, mesh = {Animals ; *Genome, Mitochondrial/genetics ; Gene Transfer, Horizontal/genetics ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Repetitive Sequences, Nucleic Acid/genetics ; Phylogeny ; Evolution, Molecular ; }, abstract = {In contrast to bilaterian animals, non-bilaterian mitochondrial genomes contain atypical genes, often attributed to horizontal gene transfer (HGT) as an ad hoc explanation. Although prevalent in plants, HGT into animal mitochondrial genomes is rare, lacking suitable explanatory models for their occurrence. HGT of the mismatch DNA repair gene (mtMutS) from giant viruses to octocoral (soft corals and their kin) mitochondrial genomes provides a model for how barriers to HGT to animal mitochondria may be overcome. A review of the available literature suggests that this HGT was mediated by an alveolate endosymbiont infected with a lysogenic phycodnavirus that enabled insertion of the homing endonuclease containing mtMutS into octocoral mitochondrial genomes. We posit that homing endonuclease domains and similar selfish elements play a crucial role in such inter-domain gene transfers. Understanding the role of selfish genetic elements in HGT has the potential to aid development of tools for manipulating animal mitochondrial DNA.}, }
@article {pmid36410487, year = {2023}, author = {Deng, Y and Jiang, J and Huang, Y and Cheng, C and Lin, Z and Liu, G and Guo, Z and Feng, J}, title = {Hypoxia triggers the proliferation of antibiotic resistance genes in a marine aquaculture system.}, journal = {The Science of the total environment}, volume = {859}, number = {Pt 1}, pages = {160305}, doi = {10.1016/j.scitotenv.2022.160305}, pmid = {36410487}, issn = {1879-1026}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology/analysis ; *Genes, Bacterial ; RNA, Ribosomal, 16S ; Drug Resistance, Microbial/genetics ; Aquaculture ; Hypoxia ; Cell Proliferation ; }, abstract = {The transmission of antibiotic resistance genes (ARGs) affects the safety of aquaculture animals. Dissolved oxygen (DO) can affect the transmission of ARGs, but its mechanism of action in this process is unclear. We conducted laboratory breeding experiment with low and control DO groups. Combined quantitative PCR and 16S rRNA sequencing to study the effect of DO on the spread of ARGs. Hypoxia treatment significantly increased the accumulation of ammonium and nitrite in aquaculture water, and it increased the relative abundances of ARGs and mobile genetic elements (MGEs), especially the ARGs resistant to drugs in the categories of sulfonamide, (flor)/(chlor)/(am)phenicol, and MLSB (macrolide, lincosamide and streptogramin B) and the MGE intI-1(clinic), by 2.39-95.69 % in 28 days relative to the control DO treatment. Though the abundance of ARG carries, especially the Rhodocyclaceae, Caldilineaceae, Cyclobacteriaceae, Saprospiraceae, Enterobacteriaceae, Sphingomonadaceae families, showed higher abundance in low DO groups, relating to the vertical transmission of ARGs. Hypoxia treatment is more likely to promote the horizontal gene transfer (HGT)-related pathways, including ABC transporters, two component system, and quorum sensing, thus to induce the HGT of ARGs. The changed bacterial proliferation also altered the abundance of MGEs, especially intI-1(clinic), which induced HGT of ARGs as well. Additionally, pearson correlation results revealed that the succession of bacterial community function played the strongest role in ARG proliferation, followed by bacterial community structure and MGEs. Our results highlight the importance of suitable DO concentration in controlling the spread of ARGs especially the HGT of ARGs. In the context of global attention to food safety, our results provide important information for ensuring the safety of aquatic products and the sustainable development of aquaculture.}, }
@article {pmid36409903, year = {2022}, author = {Liu, B and Liu, Y and Yang, B and Wang, Q and Liu, X and Qin, J and Zhao, K and Li, F and Feng, X and Li, L and Wu, P and Liu, M and Zhu, S and Feng, L and Wang, L}, title = {Escherichia coli O157:H7 senses microbiota-produced riboflavin to increase its virulence in the gut.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {48}, pages = {e2212436119}, pmid = {36409903}, issn = {1091-6490}, mesh = {Animals ; Humans ; Mice ; *Enterohemorrhagic Escherichia coli/genetics ; *Escherichia coli O157/genetics ; *Microbiota ; Riboflavin ; Virulence/genetics ; Intestines ; }, abstract = {Riboflavin is produced by most commensal bacteria in the human colon, where enterohemorrhagic Escherichia coli (EHEC) colonizes and causes diseases. Sensing environmental signals to site-specifically express the type-III secretion system (T3SS), which injects effectors into host cells leading to intestinal colonization and disease, is key to the pathogenesis of EHEC. Here, we reveal that EHEC O157:H7, a dominant EHEC serotype frequently associated with severe diseases, acquired a previously uncharacterized two-component regulatory system rbfSR, which senses microbiota-produced riboflavin to directly activate the expression of LEE genes encoding the T3SS in the colon. rbfSR is present in O157:H7 and O145:H28 but absent from other EHEC serotypes. The binding site of RbfR through which it regulates LEE gene expression was identified and is conserved in all EHEC serotypes and Citrobacter rodentium, a surrogate for EHEC in mice. Introducing rbfSR into C. rodentium enabled bacteria to sense microbiota-produced riboflavin in the mouse colon to increase the expression of LEE genes, causing increased disease severity in mice. Phylogenic analysis showed that the O55:H7 ancestor of O157:H7 obtained rbfSR which has been kept in O157:H7 since then. Thus, acquiring rbfSR represents an essential step in the evolution of the highly pathogenic O157:H7. The expression of LEE genes and cell attachment ability of other EHEC serotypes in the presence of riboflavin significantly increased when rbfSR was introduced into them, indicating that those serotypes are ready to use RbfSR to increase their pathogenicity. This may present a potential public health issue as horizontal gene transfer is frequent in enteric bacteria.}, }
@article {pmid36407614, year = {2022}, author = {Li, L and Peng, S and Wang, Z and Zhang, T and Li, H and Xiao, Y and Li, J and Liu, Y and Yin, H}, title = {Genome mining reveals abiotic stress resistance genes in plant genomes acquired from microbes via HGT.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {1025122}, pmid = {36407614}, issn = {1664-462X}, abstract = {Colonization by beneficial microbes can enhance plant tolerance to abiotic stresses. However, there are still many unknown fields regarding the beneficial plant-microbe interactions. In this study, we have assessed the amount or impact of horizontal gene transfer (HGT)-derived genes in plants that have potentials to confer abiotic stress resistance. We have identified a total of 235 gene entries in fourteen high-quality plant genomes belonging to phyla Chlorophyta and Streptophyta that confer resistance against a wide range of abiotic pressures acquired from microbes through independent HGTs. These genes encode proteins contributed to toxic metal resistance (e.g., ChrA, CopA, CorA), osmotic and drought stress resistance (e.g., Na[+]/proline symporter, potassium/proton antiporter), acid resistance (e.g., PcxA, ArcA, YhdG), heat and cold stress resistance (e.g., DnaJ, Hsp20, CspA), oxidative stress resistance (e.g., GST, PoxA, glutaredoxin), DNA damage resistance (e.g., Rad25, Rad51, UvrD), and organic pollutant resistance (e.g., CytP450, laccase, CbbY). Phylogenetic analyses have supported the HGT inferences as the plant lineages are all clustering closely with distant microbial lineages. Deep-learning-based protein structure prediction and analyses, in combination with expression assessment based on codon adaption index (CAI) further corroborated the functionality and expressivity of the HGT genes in plant genomes. A case-study applying fold comparison and molecular dynamics (MD) of the HGT-driven CytP450 gave a more detailed illustration on the resemblance and evolutionary linkage between the plant recipient and microbial donor sequences. Together, the microbe-originated HGT genes identified in plant genomes and their participation in abiotic pressures resistance indicate a more profound impact of HGT on the adaptive evolution of plants.}, }
@article {pmid36406448, year = {2022}, author = {Hinnekens, P and Fayad, N and Gillis, A and Mahillon, J}, title = {Conjugation across Bacillus cereus and kin: A review.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1034440}, pmid = {36406448}, issn = {1664-302X}, abstract = {Horizontal gene transfer (HGT) is a major driving force in shaping bacterial communities. Key elements responsible for HGT are conjugation-like events and transmissible plasmids. Conjugative plasmids can promote their own transfer as well as that of co-resident plasmids. Bacillus cereus and relatives harbor a plethora of plasmids, including conjugative plasmids, which are at the heart of the group species differentiation and specification. Since the first report of a conjugation-like event between strains of B. cereus sensu lato (s.l.) 40 years ago, many have studied the potential of plasmid transfer across the group, especially for plasmids encoding major toxins. Over the years, more than 20 plasmids from B. cereus isolates have been reported as conjugative. However, with the increasing number of genomic data available, in silico analyses indicate that more plasmids from B. cereus s.l. genomes present self-transfer potential. B. cereus s.l. bacteria occupy diverse environmental niches, which were mimicked in laboratory conditions to study conjugation-related mechanisms. Laboratory mating conditions remain nonetheless simplistic compared to the complex interactions occurring in natural environments. Given the health, economic and ecological importance of strains of B. cereus s.l., it is of prime importance to consider the impact of conjugation within this bacterial group.}, }
@article {pmid36404338, year = {2022}, author = {Orata, FD and Hussain, NAS and Liang, KYH and Hu, D and Boucher, YF}, title = {Genomes of Vibrio metoecus co-isolated with Vibrio cholerae extend our understanding of differences between these closely related species.}, journal = {Gut pathogens}, volume = {14}, number = {1}, pages = {42}, pmid = {36404338}, issn = {1757-4749}, abstract = {BACKGROUND: Vibrio cholerae, the causative agent of cholera, is a well-studied species, whereas Vibrio metoecus is a recently described close relative that is also associated with human infections. The availability of V. metoecus genomes provides further insight into its genetic differences from V. cholerae. Additionally, both species have been co-isolated from a cholera-free brackish coastal pond and have been suggested to interact with each other by horizontal gene transfer (HGT).<br><br>RESULTS: The genomes of 17 strains from each species were sequenced. All strains share a large core genome (2675 gene families) and very few genes are unique to each species (<&#x2009;3% of the pan-genome of both species). This led to the identification of potential molecular markers-for nitrite reduction, as well as peptidase and rhodanese activities-to further distinguish V. metoecus from V. cholerae. Interspecies HGT events were inferred in 21% of the core genes and 45% of the accessory genes. A directional bias in gene transfer events was found in the core genome, where V. metoecus was a recipient of three times (75%) more genes from V. cholerae than it was a donor (25%).<br><br>CONCLUSION: V. metoecus was misclassified as an atypical variant of V. cholerae due to their resemblance in a majority of biochemical characteristics. More distinguishing phenotypic assays can be developed based on the discovery of potential gene markers to avoid any future misclassifications. Furthermore, differences in relative abundance or seasonality were observed between the species and could contribute to the bias in directionality of HGT.}, }
@article {pmid36400772, year = {2022}, author = {Kim, HJ and Black, M and Edwards, RA and Peillard-Fiorente, F and Panigrahi, R and Klingler, D and Eidelpes, R and Zeindl, R and Peng, S and Su, J and Omar, AR and MacMillan, AM and Kreutz, C and Tollinger, M and Charpentier, X and Attaiech, L and Glover, JNM}, title = {Structural basis for recognition of transcriptional terminator structures by ProQ/FinO domain RNA chaperones.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {7076}, pmid = {36400772}, issn = {2041-1723}, support = {P 32773/FWF_/Austrian Science Fund FWF/Austria ; P 33953/FWF_/Austrian Science Fund FWF/Austria ; P 34370/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*RNA-Binding Proteins/metabolism ; *RNA, Small Untranslated/genetics ; }, abstract = {The ProQ/FinO family of RNA binding proteins mediate sRNA-directed gene regulation throughout gram-negative bacteria. Here, we investigate the structural basis for RNA recognition by ProQ/FinO proteins, through the crystal structure of the ProQ/FinO domain of the Legionella pneumophila DNA uptake regulator, RocC, bound to the transcriptional terminator of its primary partner, the sRNA RocR. The structure reveals specific recognition of the 3' nucleotide of the terminator by a conserved pocket involving a β-turn-α-helix motif, while the hairpin portion of the terminator is recognized by a conserved α-helical N-cap motif. Structure-guided mutagenesis reveals key RNA contact residues that are critical for RocC/RocR to repress the uptake of environmental DNA in L. pneumophila. Structural analysis and RNA binding studies reveal that other ProQ/FinO domains also recognize related transcriptional terminators with different specificities for the length of the 3' ssRNA tail.}, }
@article {pmid36400617, year = {2023}, author = {Zhai, Z and Cui, C and Li, X and Yan, J and Sun, E and Wang, C and Guo, H and Hao, Y}, title = {Prevalence, antimicrobial susceptibility, and antibiotic resistance gene transfer of Bacillus strains isolated from pasteurized milk.}, journal = {Journal of dairy science}, volume = {106}, number = {1}, pages = {75-83}, doi = {10.3168/jds.2022-22199}, pmid = {36400617}, issn = {1525-3198}, mesh = {Animals ; *Milk/microbiology ; Prevalence ; Drug Resistance, Microbial ; *Bacillus/genetics ; Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests/veterinary ; }, abstract = {Pasteurization is carried out in dairy industries to kill harmful bacteria present in raw milk. However, endospore-forming bacteria, such as Bacillus, cannot be completely eliminated by pasteurization. In this study, a total of 114 Bacillus strains were isolated from 133 pasteurized milk samples. Antibiotic susceptibility tests showed that the percentage of Bacillus with intrinsic resistance to ampicillin and penicillin were 80 and 86%, respectively. Meanwhile, some Bacillus isolates had acquired resistance, including trimethoprim-sulfamethoxazole resistance (10 isolates), clindamycin resistance (8 isolates), erythromycin resistance (2 isolates), and tetracycline resistance (1 isolate). To further locate these acquired resistance genes, the plasmids were investigated in these 16 Bacillus strains. The plasmid profile indicated that Bacillus cereus BA008, BA117, and BA119 harbored plasmids, respectively. Subsequently, the Illumina Novaseq PE150 was applied for the genomic and plasmid DNA sequencing. Notably, the gene tetL encoding tetracycline efflux protein was found to be located on plasmid pBC46-TL of B. cereus BA117. In vitro conjugative transfer indicated that pBC46-TL can be transferred into Bacillus invictae BA142, Bacillus safensis BA143, and Bacillus licheniformis BA130. The frequencies were of 1.5 × 10[-7] to 1.7 × 10[-5] transconjugants per donor cells. Therefore, Bacillus strains with acquired antibiotic resistance may represent a potential risk for the spread of antibiotic resistance between Bacillus and other clinical pathogens via horizontal gene transfer.}, }
@article {pmid36386695, year = {2022}, author = {Gerlach, D and Sieber, RN and Larsen, J and Krusche, J and De Castro, C and Baumann, J and Molinaro, A and Peschel, A}, title = {Horizontal transfer and phylogenetic distribution of the immune evasion factor tarP.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {951333}, pmid = {36386695}, issn = {1664-302X}, abstract = {Methicillin-resistant Staphylococcus aureus (MRSA), a major human pathogen, uses the prophage-encoded tarP gene as an important immune evasion factor. TarP glycosylates wall teichoic acid (WTA) polymers, major S. aureus surface antigens, to impair WTA immunogenicity and impede host defence. However, tarP phages appear to be restricted to only a few MRSA clonal lineages, including clonal complexes (CC) 5 and 398, for unknown reasons. We demonstrate here that tarP-encoding prophages can be mobilized to lysogenize other S. aureus strains. However, transfer is largely restricted to closely related clones. Most of the non-transducible clones encode tarM, which generates a WTA glycosylation pattern distinct from that mediated by TarP. However, tarM does not interfere with infection by tarP phages. Clonal complex-specific Type I restriction-modification systems were the major reasons for resistance to tarP phage infection. Nevertheless, tarP phages were found also in unrelated S. aureus clones indicating that tarP has the potential to spread to distant clonal lineages and contribute to the evolution of new MRSA clones.}, }
@article {pmid36386682, year = {2022}, author = {Pan, X and Zhou, Z and Liu, B and Wu, Z}, title = {A novel therapeutic concern: Antibiotic resistance genes in common chronic diseases.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1037389}, pmid = {36386682}, issn = {1664-302X}, abstract = {Infections caused by multidrug-resistant bacteria carrying antibiotic resistance genes pose a severe threat to global public health and human health. In clinical practice, it has been found that human gut microbiota act as a "reservoir" of antibiotic resistance genes (ARGs) since gut microbiota contain a wide variety of ARGs, and that the structure of the gut microbiome is influenced by the profile of the drug resistance genes present. In addition, ARGs can spread within and between species of the gut microbiome in multiple ways. To better understand gut microbiota ARGs and their effects on patients with chronic diseases, this article reviews the generation of ARGs, common vectors that transmit ARGs, the characteristics of gut microbiota ARGs in common chronic diseases, their impact on prognosis, the current state of treatment for ARGs, and what should be addressed in future research.}, }
@article {pmid36386654, year = {2022}, author = {Guzman-Otazo, J and Joffré, E and Agramont, J and Mamani, N and Jutkina, J and Boulund, F and Hu, YOO and Jumilla-Lorenz, D and Farewell, A and Larsson, DGJ and Flach, CF and Iñiguez, V and Sjöling, &#xc5;}, title = {Conjugative transfer of multi-drug resistance IncN plasmids from environmental waterborne bacteria to Escherichia coli.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {997849}, pmid = {36386654}, issn = {1664-302X}, abstract = {Watersheds contaminated with municipal, hospital, and agricultural residues are recognized as reservoirs for bacteria carrying antibiotic resistance genes (ARGs). The objective of this study was to determine the potential of environmental bacterial communities from the highly contaminated La Paz River basin in Bolivia to transfer ARGs to an Escherichia coli lab strain used as the recipient. Additionally, we tested ZnSO4 and CuSO4 at sub-inhibitory concentrations as stressors and analyzed transfer frequencies (TFs), diversity, richness, and acquired resistance profiles. The bacterial communities were collected from surface water in an urban site close to a hospital and near an agricultural area. High transfer potentials of a large set of resistance factors to E. coli were observed at both sites. Whole-genome sequencing revealed that putative plasmids belonging to the incompatibility group N (IncN, IncN2, and IncN3) were predominant among the transconjugants. All IncN variants were verified to be mobile by a second conjugation step. The plasmid backbones were similar to other IncN plasmids isolated worldwide and carried a wide range of ARGs extensively corroborated by phenotypic resistance patterns. Interestingly, all transconjugants also acquired the class 1 integron intl1, which is commonly known as a proxy for anthropogenic pollution. The addition of ZnSO4 and CuSO4 at sub-inhibitory concentrations did not affect the transfer rate. Metal resistance genes were absent from most transconjugants, suggesting a minor role, if any, of metals in the spread of multidrug-resistant plasmids at the investigated sites.}, }
@article {pmid36386652, year = {2022}, author = {de la Higuera, I and Lázaro, E}, title = {Viruses in astrobiology.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1032918}, pmid = {36386652}, issn = {1664-302X}, abstract = {Viruses are the most abundant biological entities on Earth, and yet, they have not received enough consideration in astrobiology. Viruses are also extraordinarily diverse, which is evident in the types of relationships they establish with their host, their strategies to store and replicate their genetic information and the enormous diversity of genes they contain. A viral population, especially if it corresponds to a virus with an RNA genome, can contain an array of sequence variants that greatly exceeds what is present in most cell populations. The fact that viruses always need cellular resources to multiply means that they establish very close interactions with cells. Although in the short term these relationships may appear to be negative for life, it is evident that they can be beneficial in the long term. Viruses are one of the most powerful selective pressures that exist, accelerating the evolution of defense mechanisms in the cellular world. They can also exchange genetic material with the host during the infection process, providing organisms with capacities that favor the colonization of new ecological niches or confer an advantage over competitors, just to cite a few examples. In addition, viruses have a relevant participation in the biogeochemical cycles of our planet, contributing to the recycling of the matter necessary for the maintenance of life. Therefore, although viruses have traditionally been excluded from the tree of life, the structure of this tree is largely the result of the interactions that have been established throughout the intertwined history of the cellular and the viral worlds. We do not know how other possible biospheres outside our planet could be, but it is clear that viruses play an essential role in the terrestrial one. Therefore, they must be taken into account both to improve our understanding of life that we know, and to understand other possible lives that might exist in the cosmos.}, }
@article {pmid36384846, year = {2022}, author = {Wang, YJ and Tang, YJ and Zhang, YP and Zhang, MY and Chu, SS and Qiu, RL}, title = {[Retarding potential of biochar on antibiotic resistance genes in soil and the mechanisms: A review.].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {33}, number = {11}, pages = {3116-3126}, doi = {10.13287/j.1001-9332.202211.014}, pmid = {36384846}, issn = {1001-9332}, mesh = {Humans ; *Soil/chemistry ; Anti-Bacterial Agents/pharmacology ; Soil Microbiology ; Drug Resistance, Microbial/genetics ; *Metals, Heavy/analysis ; Bacteria/genetics ; }, abstract = {Antibiotic resistance genes (ARGs) in soil pose a major challenge to global environment and health. The development of effective technologies to reduce their negative effects has implications for maintaining soil health and human health. Biochar would be a suitable control material due to its characteristics of high carbon content, large surface area, excellent adsorption capacity, and economic advantages. There are three mechanisms underlying its negative effects on the abundance of ARGs: 1) adsorption of certain pollutants (e.g., antibiotics and heavy metals) to reduce the co-selective pressure of ARGs; 2) alteration of microbial composition through altering soil physico-chemical properties, and thereby limiting the ability of bacteria to undergo horizontal transfer of ARGs; 3) direct impairment of horizontal gene transfer by the adsorption of horizontal transfer vectors such as plasmids, transposons, and integrons. However, the negative effect of biochar depends on the source of material, pyrolysis process, and its amount added. Furthermore, field aging of biochar may reduce its ability to block ARGs. Endogenous contaminants of biochar, such as polycyclic aromatic hydrocarbons and heavy metals, may cause the enrichment of specific antibiotic-resistant bacteria in the environment or induce horizontal gene transfer. In further studies, suitable biochar should be selected according to soil environments, and biochar aging control measures should be taken to improve its retarding effect on ARGs.}, }
@article {pmid36384625, year = {2022}, author = {Wang, YJ and Si, YM and Li, YJ}, title = {[Research progress on the application of quorum sensing in the colonization and degradation enhancement of bioaugmentation functional bacteria].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {33}, number = {10}, pages = {2871-2880}, doi = {10.13287/j.1001-9332.202210.031}, pmid = {36384625}, issn = {1001-9332}, mesh = {Quorum Sensing/physiology ; Sewage ; Bacteria/genetics ; *Water Purification ; *Environmental Pollutants/metabolism ; }, abstract = {Due to the impacts of refractory organic pollutants and environment on the water treatment system, the sewage quality can not reach the standard. It is an effective measure to improve the efficiency of wastewater treatment by introducing exogenous engineering strains with relevant functional genes and the ability of horizontal gene transfer. In sewage treatment system, there are bacteria secreting signal molecules with quorum sensing. When population density reaches induction threshold, the bacteria would activate the related genes expression (such as biofilm formation, bioluminescent, antibiotics synthesis and virulence factor expression, etc.) through releasing signaling molecules, and thus trigger the behavior of other groups. Previously, researches about quorum sensing mainly concentrated on signal transduction, microbial social behavior, and medical microbiology. In recent years, stu-dies found that quorum sensing plays an important role in wastewater biological treatment and affects the colonization of the microorganism strain and pollutants degradation. Therefore, the regulation of quorum-sensing behavior is the key factor in the bioaugmentation performance. Here, we review the signaling molecules mechanism, the release of signaling molecules and its influence factors, the colonization of microbial community and the removal of pollutants. We further discussed the research from the perspective of quorum sensing biological process. The aim was to provide new idea for the effective implementation of bioaugmentation technology and the improvement of wastewater treatment efficiency, and to provide a theoretical reference for the in-depth understanding of quorum sensing regulation behavior in the process of bioaugmentation.}, }
@article {pmid36383678, year = {2022}, author = {Ghaly, TM and Tetu, SG and Penesyan, A and Qi, Q and Rajabal, V and Gillings, MR}, title = {Discovery of integrons in Archaea: Platforms for cross-domain gene transfer.}, journal = {Science advances}, volume = {8}, number = {46}, pages = {eabq6376}, pmid = {36383678}, issn = {2375-2548}, abstract = {Horizontal gene transfer between different domains of life is increasingly being recognized as an important evolutionary driver, with the potential to increase the pace of biochemical innovation and environmental adaptation. However, the mechanisms underlying the recruitment of exogenous genes from foreign domains are mostly unknown. Integrons are a family of genetic elements that facilitate this process within Bacteria. However, they have not been reported outside Bacteria, and thus their potential role in cross-domain gene transfer has not been investigated. Here, we discover that integrons are also present in 75 archaeal metagenome-assembled genomes from nine phyla, and are particularly enriched among Asgard archaea. Furthermore, we provide experimental evidence that integrons can facilitate the recruitment of archaeal genes by bacteria. Our findings establish a previously unknown mechanism of cross-domain gene transfer whereby bacteria can incorporate archaeal genes from their surrounding environment via integron activity. These findings have important implications for prokaryotic ecology and evolution.}, }
@article {pmid36381231, year = {2022}, author = {Benites, LF and Stephens, TG and Bhattacharya, D}, title = {Multiple waves of viral invasions in Symbiodiniaceae algal genomes.}, journal = {Virus evolution}, volume = {8}, number = {2}, pages = {veac101}, pmid = {36381231}, issn = {2057-1577}, abstract = {Dinoflagellates from the family Symbiodiniaceae are phototrophic marine protists that engage in symbiosis with diverse hosts. Their large and distinct genomes are characterized by pervasive gene duplication and large-scale retroposition events. However, little is known about the role and scale of horizontal gene transfer (HGT) in the evolution of this algal family. In other dinoflagellates, high levels of HGTs have been observed, linked to major genomic transitions, such as the appearance of a viral-acquired nucleoprotein that originated via HGT from a large DNA algal virus. Previous work showed that Symbiodiniaceae from different hosts are actively infected by viral groups, such as giant DNA viruses and ssRNA viruses, that may play an important role in coral health. Latent viral infections may also occur, whereby viruses could persist in the cytoplasm or integrate into the host genome as a provirus. This hypothesis received experimental support; however, the cellular localization of putative latent viruses and their taxonomic affiliation are still unknown. In addition, despite the finding of viral sequences in some genomes of Symbiodiniaceae, viral origin, taxonomic breadth, and metabolic potential have not been explored. To address these questions, we searched for putative viral-derived proteins in thirteen Symbiodiniaceae genomes. We found fifty-nine candidate viral-derived HGTs that gave rise to twelve phylogenies across ten genomes. We also describe the taxonomic affiliation of these virus-related sequences, their structure, and their genomic context. These results lead us to propose a model to explain the origin and fate of Symbiodiniaceae viral acquisitions.}, }
@article {pmid36377945, year = {2022}, author = {Aytan-Aktug, D and Grigorjev, V and Szarvas, J and Clausen, PTLC and Munk, P and Nguyen, M and Davis, JJ and Aarestrup, FM and Lund, O}, title = {SourceFinder: a Machine-Learning-Based Tool for Identification of Chromosomal, Plasmid, and Bacteriophage Sequences from Assemblies.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0264122}, pmid = {36377945}, issn = {2165-0497}, support = {75N93019C00076/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Genome, Bacterial ; *Bacteriophages/genetics ; Plasmids/genetics ; Chromosomes, Bacterial/genetics ; Machine Learning ; }, abstract = {High-throughput genome sequencing technologies enable the investigation of complex genetic interactions, including the horizontal gene transfer of plasmids and bacteriophages. However, identifying these elements from assembled reads remains challenging due to genome sequence plasticity and the difficulty in assembling complete sequences. In this study, we developed a classifier, using random forest, to identify whether sequences originated from bacterial chromosomes, plasmids, or bacteriophages. The classifier was trained on a diverse collection of 23,211 chromosomal, plasmid, and bacteriophage sequences from hundreds of bacterial species. In order to adapt the classifier to incomplete sequences, each complete sequence was subsampled into 5,000 nucleotide fragments and further subdivided into k-mers. This three-class classifier succeeded in identifying chromosomes, plasmids, and bacteriophages using k-mer distributions of complete and partial genome sequences, including simulated metagenomic scaffolds with minimum performance of 0.939 area under the receiver operating characteristic curve (AUC). This classifier, implemented as SourceFinder, has been made available as an online web service to help the community with predicting the chromosomal, plasmid, and bacteriophage sources of assembled bacterial sequence data (https://cge.food.dtu.dk/services/SourceFinder/). IMPORTANCE Extra-chromosomal genes encoding antimicrobial resistance, metal resistance, and virulence provide selective advantages for bacterial survival under stress conditions and pose serious threats to human and animal health. These accessory genes can impact the composition of microbiomes by providing selective advantages to their hosts. Accurately identifying extra-chromosomal elements in genome sequence data are critical for understanding gene dissemination trajectories and taking preventative measures. Therefore, in this study, we developed a random forest classifier for identifying the source of bacterial chromosomal, plasmid, and bacteriophage sequences.}, }
@article {pmid36375055, year = {2022}, author = {Wu, C and Tang, D and Dai, J and Tang, X and Bao, Y and Ning, J and Zhen, Q and Song, H and St Leger, RJ and Fang, W}, title = {Bioremediation of mercury-polluted soil and water by the plant symbiotic fungus Metarhizium robertsii.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {47}, pages = {e2214513119}, pmid = {36375055}, issn = {1091-6490}, mesh = {Biodegradation, Environmental ; Water ; *Mercury/toxicity ; *Methylmercury Compounds ; Phylogeny ; Ecosystem ; *Metarhizium/genetics ; Soil ; }, abstract = {Fungi are central to every terrestrial and many aquatic ecosystems, but the mechanisms underlying fungal tolerance to mercury, a global pollutant, remain unknown. Here, we show that the plant symbiotic fungus Metarhizium robertsii degrades methylmercury and reduces divalent mercury, decreasing mercury accumulation in plants and greatly increasing their growth in contaminated soils. M. robertsii does this by demethylating methylmercury via a methylmercury demethylase (MMD) and using a mercury ion reductase (MIR) to reduce divalent mercury to volatile elemental mercury. M. robertsii can also remove methylmercury and divalent mercury from fresh and sea water even in the absence of added nutrients. Overexpression of MMD and MIR significantly improved the ability of M. robertsii to bioremediate soil and water contaminated with methylmercury and divalent mercury. MIR homologs, and thereby divalent mercury tolerance, are widespread in fungi. In contrast, MMD homologs were patchily distributed among the few plant associates and soil fungi that were also able to demethylate methylmercury. Phylogenetic analysis suggests that fungi could have acquired methylmercury demethylase genes from bacteria via two independent horizontal gene transfer events. Heterologous expression of MMD in fungi that lack MMD homologs enabled them to demethylate methylmercury. Our work reveals the mechanisms underlying mercury tolerance in fungi, and may provide a cheap and environmentally friendly means of cleaning up mercury pollution.}, }
@article {pmid36374836, year = {2022}, author = {Kurlovs, AH and De Beer, B and Ji, M and Vandenhole, M and De Meyer, T and Feyereisen, R and Clark, RM and Van Leeuwen, T}, title = {Trans-driven variation in expression is common among detoxification genes in the extreme generalist herbivore Tetranychus urticae.}, journal = {PLoS genetics}, volume = {18}, number = {11}, pages = {e1010333}, pmid = {36374836}, issn = {1553-7404}, mesh = {Animals ; *Tetranychidae/genetics ; Herbivory ; Gene Transfer, Horizontal ; Adaptation, Physiological ; Plants ; *Pesticides ; }, abstract = {The extreme adaptation potential of the generalist herbivore Tetranychus urticae (the two-spotted spider mite) to pesticides as well as diverse host plants has been associated with clade-specific gene expansions in known detoxifying enzyme families, and with extensive and rapid transcriptional responses. However, how this broad transcriptional potential is regulated remains largely unknown. Using a parental/F1 design in which four inbred strains were crossed to a common inbred strain, we assessed the genetic basis and inheritance of gene expression variation in T. urticae. Mirroring known phenotypic variation in the progenitor strains of the inbreds, we confirmed that the inbred strains we created were genetically distinct, varied markedly in pesticide resistance, and also captured variation in host plant fitness as is commonly observed in this species. By examining differences in gene expression between parents and allele-specific expression in F1s, we found that variation in RNA abundance was more often explained in trans as compared to cis, with the former associated with dominance in inheritance. Strikingly, in a gene ontology analysis, detoxification genes of the cytochrome P450 monooxygenase (CYP) family, as well as dioxygenases (DOGs) acquired from horizontal gene transfer from fungi, were specifically enriched at the extremes of trans-driven up- and downregulation. In particular, multiple CYPs and DOGs with broad substrate-specificities for pesticides or plant specialized compounds were exceptionally highly upregulated as a result of trans-regulatory variation, or in some cases synergism of cis and trans, in the most multi-pesticide resistant strains. Collectively, our findings highlight the potential importance of trans-driven expression variation in genes associated with xenobiotic metabolism and host plant use for rapid adaptation in T. urticae, and also suggests modular control of these genes, a regulatory architecture that might ameliorate negative pleiotropic effects.}, }
@article {pmid36374047, year = {2022}, author = {Kogay, R and Zhaxybayeva, O}, title = {Selection for Translational Efficiency in Genes Associated with Alphaproteobacterial Gene Transfer Agents.}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0089222}, pmid = {36374047}, issn = {2379-5077}, mesh = {Bacteria ; *Viruses ; DNA ; *Alphaproteobacteria ; }, abstract = {Gene transfer agents (GTAs) are virus-like elements that are encoded by some bacterial and archaeal genomes. The production of GTAs can be induced by carbon depletion and results in host lysis and the release of virus-like particles that contain mostly random fragments of the host DNA. The remaining members of a GTA-producing population act as GTA recipients by producing proteins needed for GTA-mediated DNA acquisition. Here, we detected a codon usage bias toward codons with more readily available tRNAs in the RcGTA-like GTA genes of alphaproteobacterial genomes. Such bias likely improves the translational efficacy during GTA gene expression. While the strength of codon usage bias fluctuates substantially among individual GTA genes and across taxonomic groups, it is especially pronounced in Sphingomonadales, whose members are known to inhabit nutrient-depleted environments. By screening genomes for gene families with trends in codon usage biases similar to those in GTA genes, we found a gene that likely encodes head completion protein in some GTAs where it appeared missing, and 13 genes previously not implicated in the GTA life cycle. The latter genes are involved in various molecular processes, including the homologous recombination and transport of scarce organic matter. Our findings provide insights into the role of selection for translational efficiency in the evolution of GTA genes and outline genes that are potentially involved in the previously hypothesized integration of GTA-delivered DNA into the host genome. IMPORTANCE Horizontal gene transfer (HGT) is a fundamental process that drives evolution of microorganisms. HGT can result in a rapid dissemination of beneficial genes within and among microbial communities and can be achieved via multiple mechanisms. One peculiar HGT mechanism involves viruses "domesticated" by some bacteria and archaea (their hosts). These so-called gene transfer agents (GTAs) are encoded in hosts' genomes, produced under starvation conditions, and cannot propagate themselves as viruses. We show that GTA genes are under selection to improve the efficiency of their translation when the host activates GTA production. The selection is especially pronounced in bacteria that occupy nutrient-depleted environments. Intriguingly, several genes involved in incorporation of DNA into a genome are under similar selection pressure, suggesting that they may facilitate the integration of GTA-delivered DNA into the host genome. Our findings underscore the potential importance of GTAs as a mechanism of HGT under nutrient-limited conditions, which are widespread in microbial habitats.}, }
@article {pmid36371907, year = {2022}, author = {Zhao, CX and Su, XX and Xu, MR and An, XL and Su, JQ}, title = {Uncovering the diversity and contents of gene cassettes in class 1 integrons from the endophytes of raw vegetables.}, journal = {Ecotoxicology and environmental safety}, volume = {247}, number = {}, pages = {114282}, doi = {10.1016/j.ecoenv.2022.114282}, pmid = {36371907}, issn = {1090-2414}, mesh = {Humans ; *Integrons/genetics ; *Endophytes/genetics ; Vegetables/genetics ; Anti-Bacterial Agents/pharmacology ; Integrases/genetics ; }, abstract = {Rapid spread of antibiotic resistance genes (ARGs) in pathogens is threatening human health. Integrons allow bacteria to integrate and express foreign genes, facilitating horizontal transfer of ARGs in environments. Consumption of raw vegetables represents a pathway for human exposure to environmental ARGs. However, few studies have focused on integron-associated ARGs in the endophytes of raw vegetables. Here, based on the approach of qPCR and clone library, we quantified the abundance of integrase genes and analyzed the diversity and contents of resistance gene cassettes in class 1 integrons from the endophytes of six common raw vegetables. The results revealed that integrase genes for class 1 integron were most prevalent compared with class 2 and class 3 integron integrase genes (1-2 order magnitude, P < 0.05). The cucumber endophytes harbored a higher absolute abundance of integrase genes than other vegetables, while the highest bacterial abundance was detected in cabbage and cucumber endophytes. Thirty-two unique resistance gene cassettes were detected, the majority of which were associated with the genes encoding resistance to beta-lactam and aminoglycoside. Antibiotic resistance gene cassettes accounted for 52.5 % of the functionally annotated gene cassettes, and blaTEM-157 and aadA2 were the most frequently detected resistance cassettes. Additionally, carrot endophytes harbored the highest proportion of antibiotic resistance gene cassettes in the class 1 integrons. Collectively, these results provide an in-depth view of acquired resistance genes by integrons in the raw vegetable endophytes and highlight the potential health risk of the transmission of ARGs via the food chain.}, }
@article {pmid36371221, year = {2022}, author = {Uruén, C and García, C and Fraile, L and Tommassen, J and Arenas, J}, title = {How Streptococcus suis escapes antibiotic treatments.}, journal = {Veterinary research}, volume = {53}, number = {1}, pages = {91}, pmid = {36371221}, issn = {1297-9716}, support = {PID2020-114617RB-100//Agencia Estatal de Investigaci&#xf3;n/ ; LMP58_21//Gobierno de Arag&#xf3;n/ ; }, mesh = {Humans ; Swine ; Animals ; *Streptococcus suis/genetics ; *Streptococcal Infections/drug therapy/veterinary ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Macrolides ; *Swine Diseases/drug therapy/prevention &amp; control ; }, abstract = {Streptococcus suis is a zoonotic agent that causes sepsis and meningitis in pigs and humans. S. suis infections are responsible for large economic losses in pig production. The lack of effective vaccines to prevent the disease has promoted the extensive use of antibiotics worldwide. This has been followed by the emergence of resistance against different classes of antibiotics. The rates of resistance to tetracyclines, lincosamides, and macrolides are extremely high, and resistance has spread worldwide. The genetic origin of S. suis resistance is multiple and includes the production of target-modifying and antibiotic-inactivating enzymes and mutations in antibiotic targets. S. suis genomes contain traits of horizontal gene transfer. Many mobile genetic elements carry a variety of genes that confer resistance to antibiotics as well as genes for autonomous DNA transfer and, thus, S. suis can rapidly acquire multiresistance. In addition, S. suis forms microcolonies on host tissues, which are associations of microorganisms that generate tolerance to antibiotics through a variety of mechanisms and favor the exchange of genetic material. Thus, alternatives to currently used antibiotics are highly demanded. A deep understanding of the mechanisms by which S. suis becomes resistant or tolerant to antibiotics may help to develop novel molecules or combinations of antimicrobials to fight these infections. Meanwhile, phage therapy and vaccination are promising alternative strategies, which could alleviate disease pressure and, thereby, antibiotic use.}, }
@article {pmid36370776, year = {2023}, author = {Dinesh, R and Sreena, CP and Sheeja, TE and Charles, S and Srinivasan, V and Sajith, V and Subila, KP and Haritha, P}, title = {Metagenomics indicates abundance of biofilm related genes and horizontal transfer of multidrug resistant genes among bacterial communities in nano zinc oxide polluted soil.}, journal = {The Science of the total environment}, volume = {859}, number = {Pt 1}, pages = {160032}, doi = {10.1016/j.scitotenv.2022.160032}, pmid = {36370776}, issn = {1879-1026}, mesh = {*Zinc Oxide/toxicity ; Soil ; *Nanoparticles ; Biofilms ; *Metal Nanoparticles/toxicity ; Oxides ; }, abstract = {The unsafe and reckless disposal of metal oxide nanoparticles like ZnO (nZnO) into the soil could seriously impact bacterial behavioural responses and functions. Under such stress, biofilm formation is considered to be a robust mechanism for bacterial survival in soil. We examined the response of bacterial metagenomes in soils exposed to varying levels of Zn (50, 200, 500 and 1000 mg kg[-1]) as nano Zn oxide (nZnO) in terms of biofilm genesis and regulation and their co-occurrences with multidrug resistance genes (MDRGs) and mobile genetic elements (MGEs). The size-specific effects of nZnO were verified using its bulk counterpart (bZnO). Both nZnO and bZnO facilitated profusion of biofilm related genes (BGs) especially at higher Zn levels (500 and 1000 mg kg[-1] Zn), though maximum abundance was registered at a comparatively lower level under nZnO. In general, nZnO favoured an enhancement of genes involved in exopolysaccharide biosynthesis and attachment, while bZnO favoured genes related to capsule formation, chemotaxis and biofilm dispersion. Co-occurrence network analysis revealed significant positive correlations between abundances of BGs, MDRGs and MGEs, indicating an enhanced probability for horizontal gene transfer of MDRGs in nZnO polluted soils.}, }
@article {pmid36370236, year = {2022}, author = {Kerber-Diaz, JC and Leos-Ramírez, MA and Flores-Ceron, AA and Ponce-Mendoza, A and Estrada-de Los Santos, P and Ibarra, JA}, title = {Distribution of CRISPR-Cas systems in the Burkholderiaceae family and its biological implications.}, journal = {Archives of microbiology}, volume = {204}, number = {12}, pages = {703}, pmid = {36370236}, issn = {1432-072X}, support = {2022-0660//Secretaria de investigacion y posgrado, IPN/ ; 2022-0679//Secretaria de investigacion y posgrado, IPN/ ; A1-S-25438//Consejo Nacional de Ciencia y Tecnolog&#xed;a,Mexico/ ; }, mesh = {CRISPR-Cas Systems ; *Burkholderiaceae/genetics ; Plasmids ; Computational Biology ; *Bacteriophages/genetics ; Bacteria/genetics ; }, abstract = {CRISPR-Cas systems are composed of repeated sequences separated by non-repeated sequences that are near genes coding for Cas proteins, which are involved in the function of these systems. Their function has been mostly related to "genetic immunity" against foreign genetic material, among other roles. Interest in them increased after their use in genetic manipulation was uncovered and surveys to find and classify them have been done in several bacterial groups. To determine the presence of these genetic elements in the Burkholderiaceae family members, a bioinformatic approach was followed. Attention in this family comes as it is formed by a great diversity of microorganisms that include opportunistic and true pathogens, and symbiotic and saprophytic organisms, among others. Results show that, in contrast to other bacterial groups, only 8.4% of family members harbor complete CRISPR-Cas systems and the rest either do not have one or have remains or sections of one. Analyses of the spacer sequences indicated that most of them have identity to sections of the same genomes they were found, while a few had identities with either plasmids or phages. The genus with the higher proportion of self-directed spacers is Ralstonia, and their possible roles are discussed. Most of the systems (60%) belong to the class I subtype I-E and a few to subtypes I-C (13.3%), I-F (18.3%), II-C (5%), IV-A (1.7%) and V-C (1.7%). To the best of our knowledge, this is the first study to uncover the CRISPR-Cas system for the whole Burkholderiaceae family.}, }
@article {pmid36368125, year = {2022}, author = {Ropars, J and Giraud, T}, title = {Convergence in domesticated fungi used for cheese and dry-cured meat maturation: beneficial traits, genomic mechanisms, and degeneration.}, journal = {Current opinion in microbiology}, volume = {70}, number = {}, pages = {102236}, doi = {10.1016/j.mib.2022.102236}, pmid = {36368125}, issn = {1879-0364}, mesh = {Humans ; *Cheese/microbiology ; Fungi/genetics ; Meat ; Gene Transfer, Horizontal ; Genomics ; }, abstract = {Humans have domesticated genetically distant fungi for similar uses, the fermentation of lipid-rich and sugar-rich food to generate attractive aspects, odor and aroma, and to improve shelf life and product safety. Multiple independent domestication events also occurred within species. We review recent evidence of phenotypic convergence during the domestication of fungi for making cheese (Saccharomyces cerevisiae, Penicillium roqueforti, P. camemberti, and Geotrichum candidum) and for dry-cured meat making (P. nalgiovense and P. salamii). Convergence following adaptation to similar ecological niches involved colony aspect (fluffiness and color), lipolysis, proteolysis, volatile compound production, and competitive ability against food spoilers. We review evidence for convergence in genetic diversity loss in domesticated populations and in the degeneration of unused traits, such as toxin production and sexual reproduction. Phenotypic convergence sometimes occurred by similar mechanisms of genomic adaptation, in particular horizontal gene transfers and loss of genes.}, }
@article {pmid36361992, year = {2022}, author = {Larrea, E and Fernández-Rubio, C and Peña-Guerrero, J and Guruceaga, E and Nguewa, PA}, title = {The BRCT Domain from the Homologue of the Oncogene PES1 in Leishmania major (LmjPES) Promotes Malignancy and Drug Resistance in Mammalian Cells.}, journal = {International journal of molecular sciences}, volume = {23}, number = {21}, pages = {}, pmid = {36361992}, issn = {1422-0067}, support = {PID2020-112713RB-C21//Spanish Ministry of Science and Innovation/ ; LCF/PR/PR13/51080005//Fundaci&#xf3;n La Caixa/ ; 2022//Fundaci&#xf3;n Roviralta/ ; 2022//Ubesol/ ; }, mesh = {Animals ; Humans ; Mice ; Adaptor Proteins, Signal Transducing/metabolism ; CARD Signaling Adaptor Proteins/metabolism ; HEK293 Cells ; *Leishmania major/genetics/metabolism ; Mammals/metabolism ; Oncogenes ; Proteins/metabolism ; *RNA-Binding Proteins/genetics ; Leishmaniasis/complications ; *Drug Resistance, Neoplasm/genetics ; *Carcinogenesis/genetics ; }, abstract = {Around 15% of cancer cases are attributable to infectious agents. Epidemiological studies suggest that an association between leishmaniasis and cancer does exist. Recently, the homologue of PES1 in Leishmania major (LmjPES) was described to be involved in parasite infectivity. Mammalian PES1 protein has been implicated in cellular processes like cell cycle regulation. Its BRCT domain has been identified as a key factor in DNA damage-responsive checkpoints. This work aimed to elucidate the hypothetical oncogenic implication of BRCT domain from LmjPES in host cells. We generated a lentivirus carrying this BRCT domain sequence (lentiBRCT) and a lentivirus expressing the luciferase protein (lentiLuc), as control. Then, HEK293T and NIH/3T3 mammalian cells were infected with these lentiviruses. We observed that the expression of BRCT domain from LmjPES conferred to mammal cells in vitro a greater replication rate and higher survival. In in vivo experiments, we observed faster tumor growth in mice inoculated with lentiBRCT respect to lentiLuc HEK293T infected cells. Moreover, the lentiBRCT infected cells were less sensitive to the genotoxic drugs. Accordingly, gene expression profiling analysis revealed that BRCT domain from LmjPES protein altered the expression of proliferation- (DTX3L, CPA4, BHLHE41, BMP2, DHRS2, S100A1 and PARP9), survival- (BMP2 and CARD9) and chemoresistance-related genes (DPYD, Dok3, DTX3L, PARP9 and DHRS2). Altogether, our results reinforced the idea that in eukaryotes, horizontal gene transfer might be also achieved by parasitism like Leishmania infection driving therefore to some crucial biological changes such as proliferation and drug resistance.}, }
@article {pmid36360308, year = {2022}, author = {Bernelot-Moens, R and Beatty, JT}, title = {DNA Gyrase Inhibitors Increase the Frequency of Bacteriophage-like RcGTA-Mediated Gene Transfer in Rhodobacter capsulatus.}, journal = {Genes}, volume = {13}, number = {11}, pages = {}, pmid = {36360308}, issn = {2073-4425}, mesh = {*Rhodobacter capsulatus/genetics/metabolism ; Topoisomerase II Inhibitors/pharmacology ; Gene Expression Regulation, Bacterial ; *Bacteriophages ; Novobiocin/pharmacology/metabolism ; Ecosystem ; Bacterial Proteins/metabolism ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Rhodobacter capsulatus produces a bacteriophage-like particle called the gene transfer agent (RcGTA) that mediates horizontal gene transfer. RcGTA particles transfer random ~4.5-kb fragments of genomic DNA that integrate into recipient genomes by allelic replacement. This work addresses the effect of sub-inhibitory concentrations of antibiotics on gene transfer by RcGTA. A transduction assay was developed to test the effects of various substances on gene transfer. Using this assay, low concentrations of DNA gyrase inhibitors were found to increase the frequency of gene transfer. Novobiocin was studied in more detail, and it was found that this antibiotic did not influence the production or release of RcGTA but instead appeared to act on the recipient cells. The target of novobiocin in other species has been shown to be the GyrB subunit of DNA gyrase (a heterotetramer of 2GyrA and 2GyrB). R. capsulatus encodes GyrA and GyrB homologues, and a GyrB overexpression plasmid was created and found to confer resistance to novobiocin. The presence of the overexpression plasmid in recipient cells greatly diminished the novobiocin-mediated increase in gene transfer, confirming that this effect is due to the binding of novobiocin by GyrB. The results of this work show that antibiotics affect gene transfer in R. capsulatus and may be relevant to microbial genetic exchange in natural ecosystems.}, }
@article {pmid36360197, year = {2022}, author = {Yushchuk, O and Binda, E and Fedorenko, V and Marinelli, F}, title = {Occurrence of vanHAX and Related Genes beyond the Actinobacteria Phylum.}, journal = {Genes}, volume = {13}, number = {11}, pages = {}, pmid = {36360197}, issn = {2073-4425}, mesh = {*Bacteria ; Anti-Bacterial Agents ; Gene Transfer, Horizontal ; Glycopeptides ; Firmicutes ; *Actinobacteria/genetics ; }, abstract = {Clinically relevant glycopeptide antibiotics remain among the most successful classes of natural antibacterials. This success, however, is endangered by the spread of glycopeptide resistance genes, also known as van genes. Thus, it is important to trace and comprehend possible routes of van gene dissemination. In the current work, we present a comprehensive bioinformatic analysis aimed at mapping the occurrence of van genes beyond the Actinobacteria phylum-the most likely natural reservoir of van genes. We show that two additional classes of Gram-positive bacteria, Erysipelotrichia and Ktedonobacteria, as well as one class of Gram-negative bacteria, Anaerolineae, carry van genes. Additionally, we demonstrate that various new genera belonging to the classes Clostridia and Bacilli also carry van genes. The majority of discovered van loci are co-localized with MGE-related genes of various types. Finally, we propose a phylogeny-based scenario for the spread of van genes, unraveling a network of consequential horizontal gene transfer events linking the phylum Actinobacteria with the five other bacterial classes carrying van genes.}, }
@article {pmid36357451, year = {2022}, author = {Downing, T and Rahm, A}, title = {Bacterial plasmid-associated and chromosomal proteins have fundamentally different properties in protein interaction networks.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {19203}, pmid = {36357451}, issn = {2045-2322}, mesh = {*Protein Interaction Maps/genetics ; Plasmids/genetics ; *Gene Transfer, Horizontal ; Bacteria/genetics ; Bacterial Proteins/genetics ; }, abstract = {Plasmids facilitate horizontal gene transfer, which enables the diversification of pathogens into new anatomical and environmental niches, implying that plasmid-encoded genes can cooperate well with chromosomal genes. We hypothesise that such mobile genes are functionally different to chromosomal ones due to this ability to encode proteins performing non-essential functions like antimicrobial resistance and traverse distinct host cells. The effect of plasmid-driven gene gain on protein-protein interaction network topology is an important question in this area. Moreover, the extent to which these chromosomally- and plasmid-encoded proteins interact with proteins from their own groups compared to the levels with the other group remains unclear. Here, we examined the incidence and protein-protein interactions of all known plasmid-encoded proteins across representative specimens from most bacteria using all available plasmids. We found that plasmid-encoded genes constitute ~ 0.65% of the total number of genes per bacterial sample, and that plasmid genes are preferentially associated with different species but had limited taxonomical power beyond this. Surprisingly, plasmid-encoded proteins had both more protein-protein interactions compared to chromosomal proteins, countering the hypothesis that genes with higher mobility rates should have fewer protein-level interactions. Nonetheless, topological analysis and investigation of the protein-protein interaction networks' connectivity and change in the number of independent components demonstrated that the plasmid-encoded proteins had limited overall impact in > 96% of samples. This paper assembled extensive data on plasmid-encoded proteins, their interactions and associations with diverse bacterial specimens that is available for the community to investigate in more detail.}, }
@article {pmid36356515, year = {2023}, author = {Jin, X and Liu, S and Zhang, Z and Liu, T and Li, N and Liang, Y and Zheng, J and Peng, N}, title = {Enrofloxacin-induced transfer of multiple-antibiotic resistance genes and emergence of novel resistant bacteria in red swamp crayfish guts and pond sediments.}, journal = {Journal of hazardous materials}, volume = {443}, number = {Pt B}, pages = {130261}, doi = {10.1016/j.jhazmat.2022.130261}, pmid = {36356515}, issn = {1873-3336}, mesh = {Animals ; Humans ; *Anti-Bacterial Agents/pharmacology ; Astacoidea/genetics ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Ecosystem ; Enrofloxacin/pharmacology ; Genes, Bacterial ; *Ponds/analysis ; Geologic Sediments ; }, abstract = {Antibiotic resistance genes (ARGs) can be transferred from environmental microbes to human pathogens, thus leading to bacterial infection treatment failures. The aquaculture polluted by over-used antibiotics is considered as a notorious reservoir of ARGs. However, the origin, diachronic changes, and mobility of ARGs under antibiotic exposure in aquaculture systems remain elusive. Our findings showed that enrofloxacin application also increased the relative abundance of various ARGs in addition to quinolone-resistance genes and induced ARG dissemination in crayfish gut and sediment bacteria. Further investigation indicated that the transposase-mediated recombination was the major driver of horizontal gene transfer (HGT) of ARGs under antibiotic stress. Notably, enrofloxacin application also induced the generation of some metagenome-assembled genomes (MAGs) carrying multiple ARGs, which were identified as novel species. Additionally, Enterobacteriaceae constituted a mobile ARG pool in aquaculture. Therefore, aquaculture provides potential wide environmental pathways for generation and spread of antibiotic resistance. Our findings of ARG temporal variations and dissemination pattern in aquaculture with artificial use of antibiotics are critical to the management of antibiotic resistance, which is of great ecosystem and health implications.}, }
@article {pmid36354153, year = {2023}, author = {Wang, H and Li, Y and Zhang, Z and Zhong, B}, title = {Horizontal gene transfer: Driving the evolution and adaptation of plants.}, journal = {Journal of integrative plant biology}, volume = {65}, number = {3}, pages = {613-616}, doi = {10.1111/jipb.13407}, pmid = {36354153}, issn = {1744-7909}, mesh = {Phylogeny ; Gene Transfer, Horizontal ; Plants/genetics ; *Embryophyta/genetics ; *Viridiplantae ; }, abstract = {Horizontal gene transfer greatly contributes to the diversification and long-term evolution of green plants. Recent studies suggest that horizontal gene transfer events drove the evolution and adaptation of charophyte green algae and land plants.}, }
@article {pmid36351400, year = {2022}, author = {Hua, M and Dai, D and Du, P and Chen, N and Duan, A and Yue, J and Jia, H and Rong, C and Li, A and Zeng, H and Chen, C}, title = {A chromosome-encoded T4SS independently contributes to horizontal gene transfer in Enterococcus faecalis.}, journal = {Cell reports}, volume = {41}, number = {6}, pages = {111609}, doi = {10.1016/j.celrep.2022.111609}, pmid = {36351400}, issn = {2211-1247}, mesh = {*Enterococcus faecalis/genetics/metabolism ; *Gene Transfer, Horizontal/genetics ; Plasmids/genetics ; Type IV Secretion Systems/metabolism ; Chromosomes/metabolism ; Bacterial Proteins/genetics/metabolism ; }, abstract = {Bacterial type IV secretion systems (T4SSs) are the specific devices that mediate the dissemination of antibiotic resistant genes via horizontal gene transfer (HGT). Multi-drug-resistant Enterococcus faecalis (E. faecalis) represents a clinical public health threat because of its transferable plasmid with a functional plasmid-encoded (PE)-T4SS. Here, we report a chromosome-encoded (CE)-T4SS that exists in 40% of E. faecalis isolates. Compared with the PE-T4SS, CE-T4SS displays distinct characteristics in protein architecture and is capable of mediating large and genome-wide gene transfer in an imprecise manner. Reciprocal exchange of CE-T4SS- or PE-T4SS-associated origin of transfer (oriT) could disrupt HGT function, indicating that CE-T4SS is an independent system compared with PE-T4SS. Taken together, the CE-T4SS sheds light on the knowledge of HGT in gram-positive bacteria and triggers us to explore more evolutionary mechanisms in E. faecalis.}, }
@article {pmid36350852, year = {2022}, author = {Koutsovoulos, GD and Granjeon Noriot, S and Bailly-Bechet, M and Danchin, EGJ and Rancurel, C}, title = {AvP: A software package for automatic phylogenetic detection of candidate horizontal gene transfers.}, journal = {PLoS computational biology}, volume = {18}, number = {11}, pages = {e1010686}, pmid = {36350852}, issn = {1553-7358}, mesh = {*Gene Transfer, Horizontal/genetics ; Phylogeny ; *Biological Evolution ; Genome ; Software ; Evolution, Molecular ; }, abstract = {Horizontal gene transfer (HGT) is the transfer of genes between species outside the transmission from parent to offspring. Due to their impact on the genome and biology of various species, HGTs have gained broader attention, but high-throughput methods to robustly identify them are lacking. One rapid method to identify HGT candidates is to calculate the difference in similarity between the most similar gene in closely related species and the most similar gene in distantly related species. Although metrics on similarity associated with taxonomic information can rapidly detect putative HGTs, these methods are hampered by false positives that are difficult to track. Furthermore, they do not inform on the evolutionary trajectory and events such as duplications. Hence, phylogenetic analysis is necessary to confirm HGT candidates and provide a more comprehensive view of their origin and evolutionary history. However, phylogenetic reconstruction requires several time-consuming manual steps to retrieve the homologous sequences, produce a multiple alignment, construct the phylogeny and analyze the topology to assess whether it supports the HGT hypothesis. Here, we present AvP which automatically performs all these steps and detects candidate HGTs within a phylogenetic framework.}, }
@article {pmid36350849, year = {2022}, author = {Coyte, KZ and Stevenson, C and Knight, CG and Harrison, E and Hall, JPJ and Brockhurst, MA}, title = {Horizontal gene transfer and ecological interactions jointly control microbiome stability.}, journal = {PLoS biology}, volume = {20}, number = {11}, pages = {e3001847}, pmid = {36350849}, issn = {1545-7885}, mesh = {*Gene Transfer, Horizontal/genetics ; *Microbiota/genetics ; Anti-Bacterial Agents/therapeutic use ; Plasmids/genetics ; }, abstract = {Genes encoding resistance to stressors, such as antibiotics or environmental pollutants, are widespread across microbiomes, often encoded on mobile genetic elements. Yet, despite their prevalence, the impact of resistance genes and their mobility upon the dynamics of microbial communities remains largely unknown. Here we develop eco-evolutionary theory to explore how resistance genes alter the stability of diverse microbiomes in response to stressors. We show that adding resistance genes to a microbiome typically increases its overall stability, particularly for genes on mobile genetic elements with high transfer rates that efficiently spread resistance throughout the community. However, the impact of resistance genes upon the stability of individual taxa varies dramatically depending upon the identity of individual taxa, the mobility of the resistance gene, and the network of ecological interactions within the community. Nonmobile resistance genes can benefit susceptible taxa in cooperative communities yet damage those in competitive communities. Moreover, while the transfer of mobile resistance genes generally increases the stability of previously susceptible recipient taxa to perturbation, it can decrease the stability of the originally resistant donor taxon. We confirmed key theoretical predictions experimentally using competitive soil microcosm communities. Here the stability of a susceptible microbial community to perturbation was increased by adding mobile resistance genes encoded on conjugative plasmids but was decreased when these same genes were encoded on the chromosome. Together, these findings highlight the importance of the interplay between ecological interactions and horizontal gene transfer in driving the eco-evolutionary dynamics of diverse microbiomes.}, }
@article {pmid36350646, year = {2023}, author = {Choi, Y and Ahn, S and Park, M and Lee, S and Cho, S and Kim, H}, title = {HGTree v2.0: a comprehensive database update for horizontal gene transfer (HGT) events detected by the tree-reconciliation method.}, journal = {Nucleic acids research}, volume = {51}, number = {D1}, pages = {D1010-D1018}, pmid = {36350646}, issn = {1362-4962}, mesh = {*Databases, Genetic ; Evolution, Molecular ; *Gene Transfer, Horizontal/genetics ; *Genome, Bacterial/genetics ; Phylogeny ; Prokaryotic Cells ; }, abstract = {HGTree is a database that provides horizontal gene transfer (HGT) event information on 2472 prokaryote genomes using the tree-reconciliation method. HGTree was constructed in 2015, and a large number of prokaryotic genomes have been additionally published since then. To cope with the rapid rise of prokaryotic genome data, we present HGTree v2.0 (http://hgtree2.snu.ac.kr), a newly updated version of our HGT database with much more extensive data, including a total of 20 536 completely sequenced non-redundant prokaryotic genomes, and more reliable HGT information results curated with various steps. As a result, HGTree v2.0 has a set of expanded data results of 6 361 199 putative horizontally transferred genes integrated with additional functional information such as the KEGG pathway, virulence factors and antimicrobial resistance. Furthermore, various visualization tools in the HGTree v2.0 database website provide intuitive biological insights, allowing the users to investigate their genomes of interest.}, }
@article {pmid36350115, year = {2022}, author = {Koppenhöfer, S and Tomasch, J and Lang, AS}, title = {Shared properties of gene transfer agent and core genes revealed by comparative genomics of Alphaproteobacteria.}, journal = {Microbial genomics}, volume = {8}, number = {11}, pages = {}, pmid = {36350115}, issn = {2057-5858}, mesh = {*Alphaproteobacteria/genetics ; Gene Transfer, Horizontal ; *Rhodobacter capsulatus/genetics ; Prophages/genetics ; Genomics ; }, abstract = {Gene transfer agents (GTAs) are phage-like particles that transfer pieces of cellular genomic DNA to other cells. Homologues of the Rhodobacter capsulatus GTA (RcGTA) structural genes are widely distributed in the Alphaproteobacteria and particularly well conserved in the order Rhodobacterales. Possible reasons for their widespread conservation are still being discussed. It has been suggested that these alphaproteobacterial elements originate from a prophage that was present in an ancestral bacterium and subsequently evolved into a GTA that is now widely maintained in extant descendant lineages. Here, we analysed genomic properties that might relate to the conservation of these alphaproteobacterial GTAs. This revealed that the chromosomal locations of the GTA gene clusters are biased. They primarily occur on the leading strand of DNA replication, at large distances from long repetitive elements, and thus are in regions of lower plasticity, and in areas of extreme GC skew, which also accumulate core genes. These extreme GC skew regions arise from the preferential use of codons with an excess of G over C, a distinct phenomenon from the elevated GC content that has previously been found to be associated with GTA genes. The observed properties, along with their high level of conservation, show that GTA genes share multiple features with core genes in the examined lineages of the Alphaproteobacteria.}, }
@article {pmid36346786, year = {2022}, author = {Lang, AS}, title = {Virus-derived gene transfer agents benefit host cells by providing templates for DNA repair.}, journal = {PLoS biology}, volume = {20}, number = {11}, pages = {e3001874}, pmid = {36346786}, issn = {1545-7885}, mesh = {Prophages/genetics ; Gene Transfer, Horizontal ; *Caulobacter crescentus ; *Bacteriophages/genetics ; DNA Repair ; }, abstract = {The potential benefits of producing gene transfer agents (GTAs) have long been speculated. A new study in PLOS Biology shows that DNA transfer by these phage-like elements allows cells with DNA damage to perform DNA repair and survive.}, }
@article {pmid36345550, year = {2022}, author = {Shokrollahi, P and Hasani, A and Aghazadeh, M and Memar, MY and Hasani, A and Zaree, M and Rezaee, MA and Sadeghi, J}, title = {Contribution of Arginine Catabolic Mobile Element and Copper and Mercury Resistance Element in Methicillin-Resistant Staphylococcus aureus: A Vantage Point.}, journal = {The Canadian journal of infectious diseases &amp; medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale}, volume = {2022}, number = {}, pages = {9916255}, pmid = {36345550}, issn = {1712-9532}, abstract = {Different clones of community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) are dominating geographically. One of the significant, hypervirulent, CA-MRSA and a significant health concern clones is USA3000, found worldwide regionally with varying frequencies. The clone harbors several mobile genetic elements (MGEs) including, arginine catabolic mobile element (ACME) and copper and mercury resistance genes (COMER), accomplished by horizontal gene transfer from S. epidermidis. Evidence suggests that ACME and COMER have a more prominent role in enhancing biofilm capacity and ultimately persistent infections. This review highlights the comprehensive view on ACME and COMER structure, their distribution, and the mechanism of action along with pathogenetic features of USA3000 encompassing their role in biofilm formation, adhesion, quorum sensing, resistance to antibiotics, chemotaxis, and nutrient uptake. We also provided an insight into the role of ACME and COMER genes in the survival of bacterium. Our results shed light on the emergence of two independent clones possessing ACME (North American) and COMER (South American) elements which later disseminated to other regions. ACME and COMER both are adjacent to staphylococcal cassette chromosome mec type IV (SCCmec IV). The acquisition of mecA, followed by COMER or ACME has been shown as a significant factor in the rise and fall of MRSA strains and their complex ability to adapt to hostile environments. The presence of ACME increases fitness, thereby allowing bacteria to colonize the skin and mucous membrane while COMER contributes to genetic stability by knocking over the copper-mediated killing in macrophages. Evidence suggests that ACME and COMER have a more prominent role in enhancing biofilm capacity and ultimately persistent infections. Interestingly, ACME strains have been shown to possess the ability to counteract skin acidity, thereby allowing increased skin colonization. A profound understanding of MGEs in S. aureus plays an important role in the prevention of epidemic clones.}, }
@article {pmid36343341, year = {2023}, author = {Wang, R and Xiao, J and Wang, Q and Zhao, W and Liu, X and Liu, Y and Fu, S}, title = {Genomic analysis of a new type VI secretion system in Vibrio parahaemolyticus and its implications for environmental adaptation in shrimp ponds.}, journal = {Canadian journal of microbiology}, volume = {69}, number = {1}, pages = {53-61}, doi = {10.1139/cjm-2022-0096}, pmid = {36343341}, issn = {1480-3275}, mesh = {*Type VI Secretion Systems/genetics ; *Vibrio parahaemolyticus/genetics ; Ponds ; Genomics ; Anti-Bacterial Agents/pharmacology ; *Vibrio cholerae/genetics ; Bacterial Proteins/genetics ; }, abstract = {The type VI secretion system (T6SS) in Vibrio spp. is often used to kill heteroclonal neighbors by direct injection of toxic effectors, but its strategies in aquacultural environments receive limited attention. In this study, we conducted genomic analysis for a T6SS-harboring plasmid in V. parahaemolyticus strain VP157. Coculture assays were further conducted to verify its antibacterial function. The results showed that strain VP157 harbored a 132-kb plasmid, pVP157-1, which consists of two fragments: an 87.8-kb fragment identical to plasmid pTJ114-1 and a 44.2-kb T6SS gene cluster with only 4% DNA identity to T6SS1 in the V. parahaemolyticus reference genome. Gene-by-gene analysis of six genes representing core T6SS components suggested that each gene has distinct evolutionary origins. In vitro experimental evolution revealed that pVP157-1 can excise from the VP157 genome with an excision rate of 4%. A coculture assay suggested that strain VP157 had significantly higher antibacterial activity against Bacillus pumilus and V. cholerae than the strain without pVP157-1(VP157[∆T6SS]). In contrast, a rapid decline was observed for the proportion of VP157[∆] [T6SS] in a mock microbial community, which decreased from 10.7% to 2.1% in 5 days. The results highlighted that the acquisition of T6SS fostered the fitness of V . parahaemolyticus in a complex environment.}, }
@article {pmid36342184, year = {2022}, author = {Tran, F and Gangan, MS and Weaver, BP and Boedicker, JQ}, title = {Membrane-Binding Biomolecules Influence the Rate of Vesicle Exchange between Bacteria.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {23}, pages = {e0134622}, pmid = {36342184}, issn = {1098-5336}, mesh = {*Bacteria/genetics/metabolism ; Gene Transfer, Horizontal ; *Extracellular Vesicles/metabolism ; Membranes ; Eukaryota ; }, abstract = {The exchange of bacterial extracellular vesicles facilitates molecular exchange between cells, including the horizontal transfer of genetic material. Given the implications of such transfer events on cell physiology and adaptation, some bacterial cells have likely evolved mechanisms to regulate vesicle exchange. Past work has identified mechanisms that influence the formation of extracellular vesicles, including the production of small molecules that modulate membrane structure; however, whether these mechanisms also modulate vesicle uptake and have an overall impact on the rate of vesicle exchange is unknown. Here, we show that membrane-binding molecules produced by microbes influence both the formation and uptake of extracellular vesicles and have the overall impact of increasing the vesicle exchange rate within a bacterial coculture. In effect, production of compounds that increase vesicle exchange rates encourage gene exchange between neighboring cells. The ability of several membrane-binding compounds to increase vesicle exchange was demonstrated. Three of these compounds, nisin, colistin, and polymyxin B, are antimicrobial peptides added at sub-inhibitory concentrations. These results suggest that a potential function of exogenous compounds that bind to membranes may be the regulation of vesicle exchange between cells. IMPORTANCE The exchange of bacterial extracellular vesicles is one route of gene transfer between bacteria, although it was unclear if bacteria developed strategies to modulate the rate of gene transfer within vesicles. In eukaryotes, there are many examples of specialized molecules that have evolved to facilitate the production, loading, and uptake of vesicles. Recent work with bacteria has shown that some small molecules influence membrane curvature and induce vesicle formation. Here, we show that similar compounds facilitate vesicle uptake, thereby increasing the overall rate of vesicle exchange within bacterial populations. The addition of membrane-binding compounds, several of them antibiotics at subinhibitory concentrations, to a bacterial coculture increased the rate of horizontal gene transfer via vesicle exchange.}, }
@article {pmid36342139, year = {2022}, author = {Fidopiastis, PM and Childs, C and Esin, JJ and Stellern, J and Darin, A and Lorenzo, A and Mariscal, VT and Lorenz, J and Gopan, V and McAnulty, S and Visick, KL}, title = {Vibrio fischeri Possesses Xds and Dns Nucleases That Differentially Influence Phosphate Scavenging, Aggregation, Competence, and Symbiotic Colonization of Squid.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {22}, pages = {e0163522}, pmid = {36342139}, issn = {1098-5336}, support = {R35 GM130355/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Aliivibrio fischeri/genetics ; *Decapodiformes/microbiology ; Symbiosis ; Phosphates ; Biofilms ; }, abstract = {Cells of Vibrio fischeri colonize the light organ of Euprymna scolopes, providing the squid bioluminescence in exchange for nutrients and protection. The bacteria encounter DNA-rich mucus throughout their transition to a symbiotic lifestyle, leading us to hypothesize a role for nuclease activity in the colonization process. In support of this, we detected abundant extracellular nuclease activity in growing cells of V. fischeri. To discover the gene(s) responsible for this activity, we screened a V. fischeri transposon mutant library for nuclease-deficient strains. Interestingly, only one strain, whose transposon insertion mapped to nuclease gene VF_1451, showed complete loss of nuclease activity in our screens. A database search revealed that VF_1451 is homologous to the nuclease-encoding gene xds in Vibrio cholerae. However, V. fischeri strains lacking xds eventually revealed slight nuclease activity on plates after 72 h. This led us to hypothesize that a second secreted nuclease, identified through a database search as VF_0437, a homolog of V. cholerae dns, might be responsible for the residual nuclease activity. Here, we show that Xds and/or Dns are involved in essential aspects of V. fischeri biology, including natural transformation, aggregation, and phosphate scavenging. Furthermore, strains lacking either nuclease were outcompeted by the wild type for squid colonization. Understanding the specific role of nuclease activity in the squid colonization process represents an intriguing area of future research. IMPORTANCE From soil and water to host-associated secretions such as mucus, environments that bacteria inhabit are awash in DNA. Extracellular DNA (eDNA) is a nutritious resource that microbes dedicate significant energy to exploit. Calcium binds eDNA to promote cell-cell aggregation and horizontal gene transfer. eDNA hydrolysis impacts construction of and dispersal from biofilms. Strategies in which pathogens use nucleases to avoid phagocytosis or disseminate by degrading host secretions are well documented; significantly less is known about nucleases in mutualistic associations. This study describes the role of nucleases in the mutualism between V. fischeri and its squid host, Euprymna scolopes. We find that nuclease activity is an important determinant of colonization in V. fischeri, broadening our understanding of how microbes establish and maintain beneficial associations.}, }
@article {pmid36341518, year = {2023}, author = {Kessler, C and Hou, J and Neo, O and Buckner, MMC}, title = {In situ, in vivo, and in vitro approaches for studying AMR plasmid conjugation in the gut microbiome.}, journal = {FEMS microbiology reviews}, volume = {47}, number = {1}, pages = {}, pmid = {36341518}, issn = {1574-6976}, support = {MR/V009885/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Drug Resistance, Bacterial/genetics ; Plasmids/genetics ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Gene Transfer, Horizontal ; Conjugation, Genetic ; }, abstract = {Antimicrobial resistance (AMR) is a global threat, with evolution and spread of resistance to frontline antibiotics outpacing the development of novel treatments. The spread of AMR is perpetuated by transfer of antimicrobial resistance genes (ARGs) between bacteria, notably those encoded by conjugative plasmids. The human gut microbiome is a known 'melting pot' for plasmid conjugation, with ARG transfer in this environment widely documented. There is a need to better understand the factors affecting the incidence of these transfer events, and to investigate methods of potentially counteracting the spread of ARGs. This review describes the use and potential of three approaches to studying conjugation in the human gut: observation of in situ events in hospitalized patients, modelling of the microbiome in vivo predominantly in rodent models, and the use of in vitro models of various complexities. Each has brought unique insights to our understanding of conjugation in the gut. The use and development of these systems, and combinations thereof, will be pivotal in better understanding the significance, prevalence, and manipulability of horizontal gene transfer in the gut microbiome.}, }
@article {pmid36340844, year = {2022}, author = {Lynch, T and Nandi, T and Jayaprakash, T and Gregson, D and Church, DL}, title = {Genomic analysis of group A Streptococcus isolated during a correctional facility outbreak of MRSA in 2004.}, journal = {Journal of the Association of Medical Microbiology and Infectious Disease Canada = Journal officiel de l'Association pour la microbiologie medicale et l'infectiologie Canada}, volume = {7}, number = {1}, pages = {23-35}, pmid = {36340844}, issn = {2371-0888}, abstract = {BACKGROUND: In 2004-2005, an outbreak of impetigo occurred at a correctional facility during a sentinel outbreak of methicillin- resistant Staphylococcus aureus (MRSA) in Alberta, Canada. Next-generation sequencing (NGS) was used to characterize the group A Streptococcus (GAS) isolates and evaluate whether genomic biomarkers could distinguish between those recovered alone and those co-isolated with S. aureus.<br><br>METHODS: Superficial wound swabs collected from all adults with impetigo during this outbreak were cultured using standard methods. NGS was used to characterize and compare all of the GAS and S. aureus genomes.<br><br>RESULTS: Fifty-three adults were culture positive for GAS, with a subset of specimens also positive for MRSA (n = 5) or methicillin-sensitive S. aureus (n = 3). Seventeen additional MRSA isolates from this facility from the same time frame (no GAS co-isolates) were also included. All 78 bacterial genomes were analyzed for the presence of known virulence factors, plasmids, and antimicrobial resistance (AMR) genes. Among the GAS isolates were 12 emm types, the most common being 41.2 (n = 27; 51%). GAS genomes were phylogenetically compared with local and public datasets of invasive and non-invasive isolates. GAS genomes had diverse profiles for virulence factors, plasmids, and AMR genes. Pangenome analysis did not identify horizontally transferred genes in the co-infection versus single infections.<br><br>CONCLUSIONS: GAS recovered from invasive and non-invasive sources were not genetically distinguishable. Virulence factors, plasmids, and AMR profiles grouped by emm type, and no genetic changes were identified that predict co-infection or horizontal gene transfer between GAS and S. aureus.}, }
@article {pmid36338125, year = {2022}, author = {Yu, W and Li, S and Zhang, G and Xu, HHK and Zhang, K and Bai, Y}, title = {New frontiers of oral sciences: Focus on the source and biomedical application of extracellular vesicles.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {10}, number = {}, pages = {1023700}, pmid = {36338125}, issn = {2296-4185}, abstract = {Extracellular vesicles (EVs) are a class of nanoparticles that are derived from almost any type of cell in the organism tested thus far and are present in all body fluids. With the capacity to transfer "functional cargo and biological information" to regulate local and distant intercellular communication, EVs have developed into an attractive focus of research for various physiological and pathological conditions. The oral cavity is a special organ of the human body. It includes multiple types of tissue, and it is also the beginning of the digestive tract. Moreover, the oral cavity harbors thousands of bacteria. The importance and particularity of oral function indicate that EVs derived from oral cavity are quite complex but promising for further research. This review will discuss the extensive source of EVs in the oral cavity, including both cell sources and cell-independent sources. Besides, accumulating evidence supports extensive biomedical applications of extracellular vesicles in oral tissue regeneration and development, diagnosis and treatment of head and neck tumors, diagnosis and therapy of systemic disease, drug delivery, and horizontal gene transfer (HGT). The immune cell source, odontoblasts and ameloblasts sources, diet source and the application of EVs in tooth development and HGT were reviewed for the first time. In conclusion, we concentrate on the extensive source and potential applications offered by these nanovesicles in oral science.}, }
@article {pmid36338046, year = {2022}, author = {Yang, C and Han, J and Berglund, B and Zou, H and Gu, C and Zhao, L and Meng, C and Zhang, H and Ma, X and Li, X}, title = {Dissemination of bla NDM-5 and mcr-8.1 in carbapenem-resistant Klebsiella pneumoniae and Klebsiella quasipneumoniae in an animal breeding area in Eastern China.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1030490}, pmid = {36338046}, issn = {1664-302X}, abstract = {Animal farms have become one of the most important reservoirs of carbapenem-resistant Klebsiella spp. (CRK) owing to the wide usage of veterinary antibiotics. "One Health"-studies observing animals, the environment, and humans are necessary to understand the dissemination of CRK in animal breeding areas. Based on the concept of "One-Health," 263 samples of animal feces, wastewater, well water, and human feces from 60 livestock and poultry farms in Shandong province, China were screened for CRK. Five carbapenem-resistant Klebsiella pneumoniae (CRKP) and three carbapenem-resistant Klebsiella quasipneumoniae (CRKQ) strains were isolated from animal feces, human feces, and well water. The eight strains were characterized by antimicrobial susceptibility testing, plasmid conjugation assays, whole-genome sequencing, and bioinformatics analysis. All strains carried the carbapenemase-encoding gene bla NDM-5, which was flanked by the same core genetic structure (IS5-bla NDM-5-ble MBL-trpF-dsbD-IS26-ISKox3) and was located on highly related conjugative IncX3 plasmids. The colistin resistance gene mcr-8.1 was carried by three CRKP and located on self-transmissible IncFII(K)/IncFIA(HI1) and IncFII(pKP91)/IncFIA(HI1) plasmids. The genetic context of mcr-8.1 consisted of IS903-orf-mcr-8.1-copR-baeS-dgkA-orf-IS903 in three strains. Single nucleotide polymorphism (SNP) analysis confirmed the clonal spread of CRKP carrying-bla NDM-5 and mcr-8.1 between two human workers in the same chicken farm. Additionally, the SNP analysis showed clonal expansion of CRKP and CRKQ strains from well water in different farms, and the clonal CRKP was clonally related to isolates from animal farms and a wastewater treatment plant collected in other studies in the same province. These findings suggest that CRKP and CRKQ are capable of disseminating via horizontal gene transfer and clonal expansion and may pose a significant threat to public health unless preventative measures are taken.}, }
@article {pmid36338036, year = {2022}, author = {Kraemer, SA and Barbosa da Costa, N and Oliva, A and Huot, Y and Walsh, DA}, title = {A resistome survey across hundreds of freshwater bacterial communities reveals the impacts of veterinary and human antibiotics use.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {995418}, pmid = {36338036}, issn = {1664-302X}, abstract = {Our decreasing ability to fight bacterial infections is a major health concern. It is arising due to the evolution of antimicrobial resistance (AMR) in response to the mis- and overuse of antibiotics in both human and veterinary medicine. Lakes integrate watershed processes and thus may act as receptors and reservoirs of antibiotic resistance genes (ARGs) introduced into the watershed by human activities. The resistome - the diversity of ARGs - under varying anthropogenic watershed pressures has been previously studied either focused on few select genes or few lakes. Here, we link the resistome of ~350 lakes sampled across Canada to human watershed activity, trophic status, as well as point sources of ARG pollution including wastewater treatment plants and hospitals in the watershed. A high percentage of the resistance genes detected was either unimpacted by human activity or highly prevalent in pristine lakes, highlighting the role of AMR in microbial ecology in aquatic systems, as well as a pool of genes available for potential horizontal gene transfer to pathogenic species. Nonetheless, watershed agricultural and pasture area significantly impacted the resistome. Moreover, the number of hospitals and the population density in a watershed, the volume of wastewater entering the lake, as well as the fraction of manure applied in the watershed as fertilizer significantly impacted ARG diversity. Together, these findings indicate that lake resistomes are regularly stocked with resistance genes evolved in the context of both veterinary and human antibiotics use and represent reservoirs of ARGs that require further monitoring.}, }
@article {pmid36335713, year = {2022}, author = {Newson, JP and Gaissmaier, MS and McHugh, SC and Hardt, WD}, title = {Studying antibiotic persistence in vivo using the model organism Salmonella Typhimurium.}, journal = {Current opinion in microbiology}, volume = {70}, number = {}, pages = {102224}, doi = {10.1016/j.mib.2022.102224}, pmid = {36335713}, issn = {1879-0364}, mesh = {Animals ; *Salmonella typhimurium/genetics ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria/genetics ; Gene Transfer, Horizontal ; Virulence ; }, abstract = {Antibiotic persistence permits a subpopulation of susceptible bacteria to survive lethal concentrations of bactericidal antibiotics. This prolongs antibiotic therapy, promotes the evolution of antibiotic-resistant pathogen strains and can select for pathogen virulence within infected hosts. Here, we review the literature exploring antibiotic persistence in vivo, and describe the consequences of recalcitrant subpopulations, with a focus on studies using the model pathogen Salmonella Typhimurium. In vitro studies have established a concise set of features distinguishing true persisters from other forms of bacterial recalcitrance to bactericidal antibiotics. We discuss how animal infection models are useful for exploring these features in vivo, and describe how technical challenges can sometimes prevent the conclusive identification of true antibiotic persistence within infected hosts. We propose using two complementary working definitions for studying antibiotic persistence in vivo: the strict definition for studying the mechanisms of persister formation, and an operative definition for functional studies assessing the links between invasive virulence and persistence as well as the consequences for horizontal gene transfer, or the emergence of antibiotic-resistant mutants. This operative definition will enable further study of how antibiotic persisters arise in vivo, and of how surviving populations contribute to diverse downstream effects such as pathogen transmission, horizontal gene transfer and the evolution of virulence and antibiotic resistance. Ultimately, such studies will help to improve therapeutic control of antibiotic- recalcitrant populations.}, }
@article {pmid36334179, year = {2022}, author = {Tripathi, S and Purchase, D and Govarthanan, M and Chandra, R and Yadav, S}, title = {Regulatory and innovative mechanisms of bacterial quorum sensing-mediated pathogenicity: a review.}, journal = {Environmental monitoring and assessment}, volume = {195}, number = {1}, pages = {75}, pmid = {36334179}, issn = {1573-2959}, support = {YSS/2015/000768//DST(SERB), New Delhi/ ; }, mesh = {Humans ; *Quorum Sensing/physiology ; Virulence ; Environmental Monitoring ; Bacteria ; Biofilms ; Anti-Bacterial Agents/toxicity/metabolism ; *Anti-Infective Agents/metabolism ; }, abstract = {Quorum sensing (QS) is a system of bacteria in which cells communicate with each other; it is linked to cell density in the microbiome. The high-density colony population can provide enough small molecular signals to enable a range of cellular activities, gene expression, pathogenicity, and antibiotic resistance that cause damage to the hosts. QS is the basis of chronic illnesses in human due to microbial sporulation, expression of virulence factors, biofilm formation, secretion of enzymes, or production of membrane vesicles. The transfer of antimicrobial resistance gene (ARG) among antibiotic resistance bacteria is a major public health concern. QS-mediated biofilm is a hub for ARG horizontal gene transfer. To develop innovative approach to prevent microbial pathogenesis, it is essential to understand the role of QS especially in response to environmental stressors such as exposure to antibiotics. This review provides the latest knowledge on the relationship of QS and pathogenicity and explore the novel approach to control QS via quorum quenching (QQ) using QS inhibitors (QSIs) and QQ enzymes. The state-of-the art knowledge on the role of QS and the potential of using QQ will help to overcome the threats of rapidly emerging bacterial pathogenesis.}, }
@article {pmid36332408, year = {2022}, author = {Zhou, M and Cai, Q and Zhang, C and Ouyang, P and Yu, L and Xu, Y}, title = {Antibiotic resistance bacteria and antibiotic resistance genes survived from the extremely acidity posing a risk on intestinal bacteria in an in vitro digestion model by horizontal gene transfer.}, journal = {Ecotoxicology and environmental safety}, volume = {247}, number = {}, pages = {114247}, doi = {10.1016/j.ecoenv.2022.114247}, pmid = {36332408}, issn = {1090-2414}, mesh = {Humans ; *Gene Transfer, Horizontal ; *Angiotensin Receptor Antagonists ; Anti-Bacterial Agents/pharmacology ; Angiotensin-Converting Enzyme Inhibitors ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Digestion ; }, abstract = {Antibiotic resistance bacteria (ARB) and antibiotic resistance genes (ARGs) are emerging contaminants posing risk to human health. To investigate the pathogenic ARBs and the horizontal gene transfer (HGT) via both extracellular ARGs (eARGs) and intracellular ARGs (iARGs), an in vitro digestion simulation system was established to monitoring the ARB and ARGs passing through the artificial digestive tract. The results showed that ARB was mostly affected by the acidity of the gastric fluid with about 99% ARB (total population of 2.45 × 10[9]-2.54 × 10[9]) killed at pH 2.0 and severe damage of bacterial cell membrane. However, more than 80% ARB (total population of 2.71 × 10[9]-3.90 × 10[9]) survived the challenge when the pH of the gastric fluid was 3.0 and above. Most ARB died from the high acidity, but its ARGs, intI1 and 16 S rRNA could be detected. The eARGs (accounting for 0.03-24.56% of total genes) were less than iARGs obviously. The eARGs showed greater HGT potential than that of iARGs, suggesting that transformation occurred more easily than conjugation. The transferring potential followed: tet (100%) > sul (75%) > bla (58%), related to the high correlation of intI1 with tetA and sul2 (p < 0.01). Moreover, gastric juice of pH 1.0 could decrease the transfer frequency of ARGs by 2-3 order of magnitude compared to the control, but still posing potential risks to human health. Under the treatment of digestive fluid, ARGs showed high gene horizontal transfer potential, suggesting that food-borne ARBs pose a great risk of horizontal transfer of ARGs to intestinal bacteria.}, }
@article {pmid36328265, year = {2023}, author = {Li, H and Dechesne, A and He, Z and Jensen, MM and Song, HL and Smets, BF}, title = {Electrochemical disinfection may increase the spread of antibiotic resistance genes by promoting conjugal plasmid transfer.}, journal = {The Science of the total environment}, volume = {858}, number = {Pt 1}, pages = {159846}, doi = {10.1016/j.scitotenv.2022.159846}, pmid = {36328265}, issn = {1879-1026}, mesh = {*Disinfection ; Gene Transfer, Horizontal ; Angiotensin Receptor Antagonists/pharmacology ; Reactive Oxygen Species ; Angiotensin-Converting Enzyme Inhibitors/pharmacology ; Plasmids ; Drug Resistance, Microbial/genetics ; *Pseudomonas putida/genetics ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Current in the milliampere range can be used for electrochemical inactivation of bacteria. Yet, bacteria-including antibiotic resistant bacteria (ARB) may be subjected to sublethal conditions due to imperfect mixing or energy savings measures during electrochemical disinfection. It is not known whether such sublethal current intensities have the potential to stimulate plasmid transfer from ARB. In this study, conjugal transfer of plasmid pKJK5 was investigated between Pseudomonas putida strains under conditions reflecting electrochemical disinfection. Although the abundance of culturable and membrane-intact donor and recipient cells decreased with applied current (0-60 mA), both transconjugant density and transconjugant frequency increased. Both active chlorine and superoxide radicals were generated electrolytically, and ROS generation was induced. In addition, we detected significant over expression of a core oxidative stress defense gene (ahpCF) with current. Expression of selected conjugation related genes (traE, traI, trbJ, and trbL) also significantly correlated with current intensity. ROS accumulation, SOS response and subsequent derepression of conjugation are therefore the plausible consequence of sublethal current exposure. These findings suggest that sublethal intensities of current can enhance conjugal plasmid transfer, and that it is essential that conditions of electrochemical disinfection (applied voltage, current density, time and mixing) are carefully controlled to avoid conjugal ARG transmission.}, }
@article {pmid36327832, year = {2023}, author = {Kothari, A and Kumar, P and Gaurav, A and Kaushal, K and Pandey, A and Yadav, SRM and Jain, N and Omar, BJ}, title = {Association of antibiotics and heavy metal arsenic to horizontal gene transfer from multidrug-resistant clinical strains to antibiotic-sensitive environmental strains.}, journal = {Journal of hazardous materials}, volume = {443}, number = {Pt B}, pages = {130260}, doi = {10.1016/j.jhazmat.2022.130260}, pmid = {36327832}, issn = {1873-3336}, mesh = {Humans ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; *Arsenic/toxicity ; Drug Resistance, Multiple, Bacterial/genetics ; *Metals, Heavy/toxicity ; Plasmids ; Bacteria/genetics ; Water ; }, abstract = {The emergence of multidrug-resistant bacteria is currently posing a significant threat to global public health. By testing for resistance to different antibiotic classes, we discovered that the majority of clinical bacteria are multidrug-resistant. These clinical multidrug-resistant species have antibiotic resistance genes on their plasmids that can be horizontally transferred to various antibiotic susceptible environmental bacterial species, resulting in antibiotic-resistant transconjugates. Furthermore, we discovered that the presence of an optimal concentration of antibiotics or heavy metal (arsenic) facilitates horizontal gene transfer through the formation of transconjugants. Notably, the addition of a conjugation inhibitor (2-hexadecynoic acid, a synthetic fatty acid) completely blocked the formation of antibiotic or arsenic-induced transconjugants. We discovered a high level of arsenic in water from the Shukratal region, Uttarakhand, India, which corresponded to a high serum level of arsenic in clinically infected individuals from the Shukratal region compared to other locations in Uttarakhand. Importantly, bacterial strains isolated from infected people who drink water from the Shukratal region with high arsenic levels were found to be more antibiotic-resistant than strains isolated from other sites. We discovered that bacterial strains isolated from individuals with high serum arsenic levels are significantly more resistant to antibiotics than individuals with low serum arsenic levels within the Shurkratal. This research sheds light on imminent threats to global health in which improper clinical, industrial, and other waste disposal, increased antibiotic concentrations in the environment, and increased human interference can easily transform commensal and pathogenic bacteria found in environmental niches into life-threatening multidrug-resistant superbugs.}, }
@article {pmid36327744, year = {2022}, author = {Carr, M and Leadbeater, BSC}, title = {Re-evaluating Loricate Choanoflagellate Phylogenetics: Molecular Evidence Points to the Paraphyly of Tectiform Species.}, journal = {Protist}, volume = {173}, number = {6}, pages = {125924}, doi = {10.1016/j.protis.2022.125924}, pmid = {36327744}, issn = {1618-0941}, mesh = {*Choanoflagellata/genetics ; Phylogeny ; }, abstract = {Lorica-bearing choanoflagellates belong to the order Acanthoecida, a taxon which has been consistently recovered as monophyletic in molecular phylogenies. Based upon differences in lorica development and morphology, as well as the presence or absence of a motile dispersal stage, species are labelled as either nudiform or tectiform. Whilst Acanthoecida is robustly resolved in molecular phylogenies, the placement of the root of the clade is less certain with two different positions identified in past studies. One recovered root has been placed between the nudiform family Acanthoecidae and the tectiform family Stephanoecidae. An alternative root placement falls within the tectiform species, recovering the monophyletic Acanthoecidae nested within a paraphyletic Stephanoecidae. Presented here is a 14-gene phylogeny, based upon nucleotide and amino acid sequences, which strongly supports tectiform paraphyly. The horizontal transfer of a ribosomal protein gene, from a possible SAR donor, into a subset of acanthoecid species provides further, independent, support for this root placement. Differing patterns of codon usage bias across the choanoflagellates are proposed as the cause of artefactual phylogenetic signals that lead to the recovery of tectiform monophyly.}, }
@article {pmid36327213, year = {2022}, author = {Gozzi, K and Tran, NT and Modell, JW and Le, TBK and Laub, MT}, title = {Prophage-like gene transfer agents promote Caulobacter crescentus survival and DNA repair during stationary phase.}, journal = {PLoS biology}, volume = {20}, number = {11}, pages = {e3001790}, pmid = {36327213}, issn = {1545-7885}, support = {R01 GM082899/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; BBS/E/J/000PR9791/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Prophages/genetics/metabolism ; *Caulobacter crescentus/genetics/metabolism ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial ; DNA Repair/genetics ; Bacterial Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial ; }, abstract = {Gene transfer agents (GTAs) are prophage-like entities found in many bacterial genomes that cannot propagate themselves and instead package approximately 5 to 15 kbp fragments of the host genome that can then be transferred to related recipient cells. Although suggested to facilitate horizontal gene transfer (HGT) in the wild, no clear physiological role for GTAs has been elucidated. Here, we demonstrate that the α-proteobacterium Caulobacter crescentus produces bona fide GTAs. The production of Caulobacter GTAs is tightly regulated by a newly identified transcription factor, RogA, that represses gafYZ, the direct activators of GTA synthesis. Cells lacking rogA or expressing gafYZ produce GTAs harboring approximately 8.3 kbp fragment of the genome that can, after cell lysis, be transferred into recipient cells. Notably, we find that GTAs promote the survival of Caulobacter in stationary phase and following DNA damage by providing recipient cells a template for homologous recombination-based repair. This function may be broadly conserved in other GTA-producing organisms and explain the prevalence of this unusual HGT mechanism.}, }
@article {pmid36326505, year = {2022}, author = {Wilson, A and Molinar, J and Aldrich, J and Chintala, G and Smit, K and Miller, K and Bollivar, DW and Alvey, RM}, title = {Expansion of Known Rhodobacter capsulatus Bacteriophage Diversity with 24 Additional Genomes.}, journal = {Microbiology resource announcements}, volume = {11}, number = {12}, pages = {e0087922}, pmid = {36326505}, issn = {2576-098X}, abstract = {We report the genome sequences of 24 newly discovered bacteriophages that infect Rhodobacter capsulatus, a model for photosynthesis and horizontal gene transfer studies. All have substantial relatedness to previously reported siphovirus bacteriophages. Most are categorized in known clusters (RcB, RcC, RcD, and RcF), with one forming a new cluster, RcG.}, }
@article {pmid36325933, year = {2022}, author = {Corning, PA}, title = {The synergism hypothesis (revisited): a theory whose time has come?.}, journal = {Theoretical biology forum}, volume = {115}, number = {1-2}, pages = {85-97}, doi = {10.19272/202211402006}, pmid = {36325933}, issn = {2282-2593}, mesh = {*Biological Evolution ; Selection, Genetic ; *Heredity ; Hybridization, Genetic ; Gene Transfer, Horizontal ; }, abstract = {A major theoretical issue in evolutionary biology over the past two decades has concerned the rise of complexity over time in the natural world, and a search has been underway for "a Grand Unified Theory" - as biologist Daniel McShea characterized it - that is consistent with Darwin's great vision. As it happens, such a theory already exists. It was first proposed many years ago in The Synergism Hypothesis: A Theory of Progressive Evolution, and it involves an economic (or perhaps bioeconomic) theory of complexity. Simply stated, cooperative interactions of various kinds, however they may occur, can produce novel combined effects - synergies - with functional advantages that may, in turn, become direct causes of natural selection. In other words, the Synergism Hypothesis is a theory about the unique combined effects produced by the relationships between things. I refer to it as Holistic Darwinism; it is entirely con - sistent with natural selection theory, properly understood. Because the Synergism Hypothesis was first proposed during a time when the genecentric, neo-Darwinist paradigm was domi nant in evolutionary biology, it was largely overlooked. But times have changed. Biologist Richard Michod has concluded that "cooperation is now seen as the primary creative force behind ever greater levels of complexity and organization in all of biology." And Martin Nowak has called cooperation "the master architect of evolution." Here I will revisit this theory in the light of the many theoretical developments and research findings in recent years that are supportive of it, including the role of symbiogenesis in evolution, the phenomenon of hybridization, lateral gene transfer in prokaryotes, "developmental plasticity" (evo-devo), epigenetic inheritance, the role of behaviour (and teleonomy) in evolution, and gene-culture coevolution. The Synergism Hypothesis is especially relevant to the evolution of humankind.}, }
@article {pmid36324140, year = {2022}, author = {Slizovskiy, IB and Oliva, M and Settle, JK and Zyskina, LV and Prosperi, M and Boucher, C and Noyes, NR}, title = {Target-enriched long-read sequencing (TELSeq) contextualizes antimicrobial resistance genes in metagenomes.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {185}, pmid = {36324140}, issn = {2049-2618}, support = {R01 AI141810/AI/NIAID NIH HHS/United States ; 1R01AI141810-01/NH/NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Metagenome/genetics ; *Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; Metagenomics/methods ; }, abstract = {BACKGROUND: Metagenomic data can be used to profile high-importance genes within microbiomes. However, current metagenomic workflows produce data that suffer from low sensitivity and an inability to accurately reconstruct partial or full genomes, particularly those in low abundance. These limitations preclude colocalization analysis, i.e., characterizing the genomic context of genes and functions within a metagenomic sample. Genomic context is especially crucial for functions associated with horizontal gene transfer (HGT) via mobile genetic elements (MGEs), for example antimicrobial resistance (AMR). To overcome this current limitation of metagenomics, we present a method for comprehensive and accurate reconstruction of antimicrobial resistance genes (ARGs) and MGEs from metagenomic DNA, termed target-enriched long-read sequencing (TELSeq).<br><br>RESULTS: Using technical replicates of diverse sample types, we compared TELSeq performance to that of non-enriched PacBio and short-read Illumina sequencing. TELSeq achieved much higher&#xa0;ARG&#xa0;recovery (>1,000-fold) and sensitivity than the other methods across diverse metagenomes, revealing an extensive resistome profile comprising many low-abundance ARGs, including some with public health importance. Using the long reads generated by TELSeq, we identified numerous MGEs and cargo genes flanking the low-abundance ARGs, indicating that these ARGs could be transferred across bacterial taxa via HGT.<br><br>CONCLUSIONS: TELSeq can provide a nuanced view of the genomic context of microbial resistomes and thus has wide-ranging applications in public, animal, and human health, as well as environmental surveillance and monitoring of AMR. Thus, this technique represents a fundamental advancement for microbiome research and application. Video abstract.}, }
@article {pmid36322896, year = {2022}, author = {Huang, H and Lin, L and Bu, F and Su, Y and Zheng, X and Chen, Y}, title = {Reductive Stress Boosts the Horizontal Transfer of Plasmid-Borne Antibiotic Resistance Genes: The Neglected Side of the Intracellular Redox Spectrum.}, journal = {Environmental science &amp; technology}, volume = {56}, number = {22}, pages = {15594-15606}, doi = {10.1021/acs.est.2c04276}, pmid = {36322896}, issn = {1520-5851}, mesh = {*Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; Escherichia coli/genetics ; Plasmids/genetics ; Drug Resistance, Microbial/genetics ; *Pseudomonas putida ; Oxidation-Reduction ; Conjugation, Genetic ; }, abstract = {The dissemination of plasmid-borne antibiotic resistance genes (ARGs) among bacteria is becoming a global challenge to the "One Health" concept. During conjugation, the donor/recipient usually encounter diverse stresses induced by the surrounding environment. Previous studies mainly focused on the effects of oxidative stress on plasmid conjugation, but ignored the potential contribution of reductive stress (RS), the other side of the intracellular redox spectrum. Herein, we demonstrated for the first time that RS induced by dithiothreitol could significantly boost the horizontal transfer of plasmid RP4 from Escherichia coli K12 to different recipients (E. coli HB101, Salmonella Typhimurium, and Pseudomonas putida KT2440). Phenotypic and genotypic tests confirmed that RS upregulated genes encoding the transfer apparatus of plasmid RP4, which was attributed to the promoted consumption of intracellular glutamine in the donor rather than the widely reported SOS response. Moreover, RS was verified to benefit ATP supply by activating glycolysis (e.g., GAPDH) and the respiratory chain (e.g., appBC), triggering the deficiency of intracellular free Mg[2+] by promoting its binding, and reducing membrane permeability by stimulating cardiolipin biosynthesis, all of which were beneficial to the functioning of transfer apparatus. Overall, our findings uncovered the neglected risks of RS in ARG spreading and updated the regulatory mechanism of plasmid conjugation.}, }
@article {pmid36314801, year = {2022}, author = {Jiang, W and Zhang, M and Gao, S and Zhu, Q and Qiu, J and Yan, X and Xin, F and Jiang, M and Hong, Q}, title = {Comparative Genomic Analysis of Carbofuran-Degrading Sphingomonads Reveals the Carbofuran Catabolism Mechanism in Sphingobium sp. Strain CFD-1.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {22}, pages = {e0102422}, pmid = {36314801}, issn = {1098-5336}, mesh = {*Carbofuran/metabolism ; *Insecticides/metabolism ; Biodegradation, Environmental ; *Sphingomonadaceae/metabolism ; Genomics ; Phenols/metabolism ; }, abstract = {The worldwide use of the carbamate insecticide carbofuran has caused considerable concern about its environmental fate. Degradation of carbofuran by Sphingobium sp. strain CFD-1 is initiated via the hydrolysis of its ester bond by carbamate hydrolase CehA to form carbofuran phenol. In this study, another carbofuran-degrading strain, Sphingobium sp. CFD-2, was isolated. Subsequently, a cfd gene cluster responsible for the catabolism of carbofuran phenol was predicted by comparing the genomes of strains CFD-1, CFD-2, and Novosphingobium sp. strain KN65.2. The key genes verified to be involved in the catabolism of carbofuran phenol within the cfd cluster include the hydroxylase gene cfdC, epoxide hydrolase gene cfdF, and ring cleavage dioxygenase gene cfdE and are responsible for the successive conversion of carbofuran phenol, resulting in complete ring cleavage. These carbofuran-catabolic genes (cehA and the cfd cluster) are distributed on two plasmids in strain CFD-1 and are highly conserved among the carbofuran-degrading sphingomonad strains. The mobile genetic element IS6100 flanks cehA and the cfd gene cluster, indicating the importance of horizontal gene transfer in the formation of carbofuran degradation gene clusters. The elucidation of the molecular mechanism of carbofuran catabolism provides insights into the evolutionary scenario of the conserved carbofuran catabolic pathway. IMPORTANCE Owing to the extensive use of carbofuran over the past 50 years, bacteria have evolved catabolic pathways to mineralize this insecticide, which plays an important role in eliminating carbofuran residue in the environment. In this study, the cfd gene cluster, responsible for the catabolism of carbofuran phenol, was predicted by comparing sphingomonad genomes. The function of key enzymatic genes in this gene cluster was identified. Furthermore, the carbamate hydrolase gene cehA and the cfd gene cluster are highly conserved in different carbofuran-degrading strains. Additionally, the horizontal gene transfer elements flanking the cfd gene cluster were investigated. These findings help elucidate the molecular mechanism of microbial carbofuran degradation and enhance our understanding of the evolutionary mechanism of the carbofuran catabolic pathway.}, }
@article {pmid36313567, year = {2022}, author = {Cellier, MFM}, title = {Nramp: Deprive and conquer?.}, journal = {Frontiers in cell and developmental biology}, volume = {10}, number = {}, pages = {988866}, pmid = {36313567}, issn = {2296-634X}, abstract = {Solute carriers 11 (Slc11) evolved from bacterial permease (MntH) to eukaryotic antibacterial defense (Nramp) while continuously mediating proton (H[+])-dependent manganese (Mn[2+]) import. Also, Nramp horizontal gene transfer (HGT) toward bacteria led to mntH polyphyly. Prior demonstration that evolutionary rate-shifts distinguishing Slc11 from outgroup carriers dictate catalytic specificity suggested that resolving Slc11 family tree may provide a function-aware phylogenetic framework. Hence, MntH C (MC) subgroups resulted from HGTs of prototype Nramp (pNs) parologs while archetype Nramp (aNs) correlated with phagocytosis. PHI-Blast based taxonomic profiling confirmed MntH B phylogroup is confined to anaerobic bacteria vs. MntH A (MA)'s broad distribution; suggested niche-related spread of MC subgroups; established that MA-variant MH, which carries 'eukaryotic signature' marks, predominates in archaea. Slc11 phylogeny shows MH is sister to Nramp. Site-specific analysis of Slc11 charge network known to interact with the protonmotive force demonstrates sequential rate-shifts that recapitulate Slc11 evolution. 3D mapping of similarly coevolved sites across Slc11 hydrophobic core revealed successive targeting of discrete areas. The data imply that pN HGT could advantage recipient bacteria for H[+]-dependent Mn[2+] acquisition and Alphafold 3D models suggest conformational divergence among MC subgroups. It is proposed that Slc11 originated as a bacterial stress resistance function allowing Mn[2+]-dependent persistence in conditions adverse for growth, and that archaeal MH could contribute to eukaryogenesis as a Mn[2+] sequestering defense perhaps favoring intracellular growth-competent bacteria.}, }
@article {pmid36312970, year = {2022}, author = {Wang, X and Wang, T and Guo, M and Zhang, C and Bo, Z and Wu, Y and Chao, G}, title = {The large plasmid carried class 1 integrons mediated multidrug resistance of foodborne Salmonella Indiana.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {991326}, pmid = {36312970}, issn = {1664-302X}, abstract = {Salmonella enterica serovar Indiana (S. Indiana) has aroused widespread concern as an important zoonotic pathogen. The molecular mechanism of multidrug resistance (MDR) in S. Indiana is not known and should be assessed. We aim to investigate the molecular mechanism of MDR and the importance of large plasmids carried class 1 integrons in the MDR of foodborne S. Indiana. Class 1 integrons in 48 S. Indiana isolates and 200 isolates of 7 other Salmonella serotypes were detected by polymerase chain reaction (PCR). To analyze the antimicrobial resistance genes (ARGs) of two S. Indiana isolates, designated S. Indiana 15 and S. Indiana 222, next-generation sequencing (NGS) was performed, and the resulting sequences were compared with the complete nucleotide sequences of S. Indiana D90 and S. Indiana C629. Comparative functional analysis was conducted between the intI1 (1,014 bp) of S. Indiana 222 and the intI1 (699 bp) of S. Indiana 15. Plasmid conjugation transfer analysis was performed to analyze the horizontal gene transfer of the integrons-related resistance genes with integron-positive and integron-negative Salmonella isolates. 64.58% of S. Indiana isolates carried class 1 integrons, which was significantly higher than that of other Salmonella serotypes (p < 0.001). The NGS results showed that the S. Indiana 15 and S. Indiana 222 isolates carried a large plasmid with a class 1 integron and multiple ARGs, similar to S. Indiana D90 and S. Indiana C629. Two integrases found in S. Indiana isolates belong to class 1 integrases and could integrate resistance genes into specific integration sites of the integrons. The conjugation frequency of intI1 (1,014 bp) was 6.08 × 10[-5], which was significantly higher than that of intI1 (699 bp) (p < 0.01). The large plasmids carrying a class 1 integron and the number of ARGs were strongly correlated (p < 0.001). The conjugation frequency of integron-positive S. Indiana recipient isolates was significantly higher than that of integron-negative recipient isolates (p < 0.05). S. Indiana containing large plasmids carrying a class 1 integron more easily captured resistance genes from other bacteria (S. Enteritidis and S. Derby), which could be an important cause of the emerging pandemic of MDR clones. Graphical abstractS. Indiana containing large plasmids carrying a class 1 integron more easily captured resistance genes from other bacteria (S. Enteritidis and S. Derby), which could be an important cause of the emerging pandemic of MDR clones.}, }
@article {pmid36309447, year = {2023}, author = {Alonso García, E and Benomar, N and Lavilla Lerma, L and de la Fuente Ordoñez, JJ and Knapp, CW and Abriouel, H}, title = {Changes in resistome profile of potential probiotic Lactiplantibacillus pentosus in response to edible oil adaptation.}, journal = {Food microbiology}, volume = {109}, number = {}, pages = {104148}, doi = {10.1016/j.fm.2022.104148}, pmid = {36309447}, issn = {1095-9998}, mesh = {Food Microbiology ; Fermentation ; *Lactobacillus pentosus/metabolism ; *Probiotics/metabolism ; *Olea ; Anti-Bacterial Agents/pharmacology/metabolism ; Oils ; }, abstract = {Despite increasing interest to investigate horizontal gene transfer as a leading cause of antibiotic resistance spread, the resistome is not only influenced by the influx and efflux of genes in different environments. Rather, the expression of existing genes under different stress conditions requires special attention. This study determined whether pre-adapting Lactiplantibacillus pentosus strains, isolated from Aloreña green table olives, to vegetable-based edible oils influence their phenotypic and genotypic responses to antibiotics. This has significant diet, food matrix, gut health, and food safety concerns. Pre-adapting L. pentosus strains to oils significantly changed their susceptibility profile to antibiotics. However, results generally differed among the three strains; although changes in the Minimum Inhibitory Concentration (MIC) of antibiotics occurred, it depended on the L. pentosus strain and the oil used for adaptation. The pre-adaptation of L. pentosus strains with olive, sunflower, argan and linseed oils induced gene expressions (e.g., rpsL, recA and uvrB) in several stress responses. Thus, to analyze this fact in-depth, transcriptional changes were reported in the selected potential probiotic L. pentosus CF2-10 adapted with olive or sunflower, rerouting its metabolic pathways to export toxic molecules through efflux pumps and ABC transporters. Pre-adaptation of some lactobacilli with olive or sunflower oils may represent a novel approach for manufacturing probiotic products with improved stability, functionality and robustness.}, }
@article {pmid36308932, year = {2023}, author = {Ye, C and Zhang, K and Wu, X and Wan, K and Cai, WF and Feng, M and Yu, X}, title = {Uncovering novel disinfection mechanisms of solar light/periodate system: The dominance of singlet oxygen and metabolomic insights.}, journal = {Journal of hazardous materials}, volume = {443}, number = {Pt A}, pages = {130177}, doi = {10.1016/j.jhazmat.2022.130177}, pmid = {36308932}, issn = {1873-3336}, mesh = {Humans ; Disinfection ; Singlet Oxygen ; Escherichia coli ; Pandemics ; *COVID-19 ; *Water Purification ; Water/pharmacology ; }, abstract = {Disinfection plays an essential role in waterborne pathogen control and disease prevention, especially during the COVID-19 pandemic. Catalyst-free solar light/periodate (PI) system has recently presented great potential in water disinfection, whereas the in-depth chemical and microbiological mechanisms for efficient bacterial inactivation remain unclear. Our work delineated firstly the critical role of singlet oxygen, instead of reported hydroxyl radicals and superoxide radicals, in dominating bacterial inactivation by the PI/simulated sunlight (SSL) system. Multi-evidence demonstrated the prominent disinfection performance of this system for Staphylococcus aureus in terms of culturability (> 6 logs CFU), cellular integrity, and metabolic activity. Particularly, the excellent intracellular DNA removal (> 95%) indicated that PI/SSL system may function as a selective disinfection strategy to diminish bacterial culturability without damaging the cell membrane. The PI/SSL system could also effectively inhibit bacterial regrowth for > 5 days and horizontal gene transfer between E. coli genera. Nontargeted metabolomic analysis suggested that PI/SSL system inactivated bacteria by triggering the accumulation of intracellular reactive oxygen species and the depletion of reduced glutathione. Additionally, the PI/SSL system could accomplish simultaneous micropollutant removal and bacterial inactivation, suggesting its versatility in water decontamination. Overall, this study deciphers more comprehensive antibacterial mechanisms of this environmentally friendly disinfection system, facilitating the technical development and application of the selective disinfection strategy in environmental pathogen control.}, }
@article {pmid36308328, year = {2022}, author = {Golparian, D and Jacobsson, S and Sánchez-Busó, L and Bazzo, ML and Lan, PT and Galarza, P and Ohnishi, M and Unemo, M}, title = {GyrB in silico mining in 27 151 global gonococcal genomes from 1928-2021 combined with zoliflodacin in vitro testing of 71 international gonococcal isolates with different GyrB, ParC and ParE substitutions confirms high susceptibility.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {78}, number = {1}, pages = {150-154}, doi = {10.1093/jac/dkac366}, pmid = {36308328}, issn = {1460-2091}, mesh = {Male ; Humans ; Anti-Bacterial Agents/pharmacology ; *Gonorrhea ; DNA Gyrase/genetics ; DNA Topoisomerase IV/genetics ; *Anti-Infective Agents/pharmacology ; Neisseria gonorrhoeae/genetics ; Mutation ; Microbial Sensitivity Tests ; Drug Resistance, Bacterial/genetics ; }, abstract = {OBJECTIVES: Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a global threat and novel treatment alternatives are imperative. Herein, susceptibility to the novel antimicrobial zoliflodacin, currently in a global Phase 3 randomized controlled clinical trial for gonorrhoea treatment, was investigated by screening for zoliflodacin GyrB target mutations in publicly available gonococcal genomes and, where feasible, determination of the associated zoliflodacin MIC.<br><br>METHODS: The European Nucleotide Archive was queried using the search term 'Taxon: 485'. DNA sequences from 27&#x200a;151 gonococcal isolates were analysed and gyrB, gyrA, parC and parE alleles characterized.<br><br>RESULTS: GyrB amino acid alterations were rare (97.0% of isolates had a wild-type GyrB sequence). GyrB V470L (2.7% of isolates) was the most prevalent alteration, followed by S467N (0.12%), N. meningitidis GyrB (0.092%), V470I (0.059%), Q468R/P (0.015%), A466T (0.0074%), L425I&#x200a;+&#x200a;L465I (0.0037%), L465I (0.0037%), G482S (0.0037%) and D429V (0.0037%). Only one isolate (0.0037%) carried a substitution in a resistance-associated GyrB codon (D429V), resulting in a zoliflodacin MIC of 8&#x2005;mg/L. None of the other detected gyrB, gyrA, parC or parE mutations caused a zoliflodacin MIC outside the wild-type MIC distribution.<br><br>CONCLUSIONS: The zoliflodacin target GyrB was highly conserved among 27&#x200a;151 global gonococcal isolates cultured in 1928-2021. The single zoliflodacin-resistant clinical isolate (0.0037%) was cultured from a male patient in Japan in 2000. Evidently, this strain has not clonally expanded nor has the gyrB zoliflodacin-resistance mutation disseminated through horizontal gene transfer to other strains. Phenotypic and genomic surveillance, including gyrB mutations, of zoliflodacin susceptibility are imperative.}, }
@article {pmid36307484, year = {2022}, author = {Tran, HNH and Thu, TNH and Nguyen, PH and Vo, CN and Doan, KV and Nguyen Ngoc Minh, C and Nguyen, NT and Ta, VND and Vu, KA and Hua, TD and Nguyen, TNT and Van, TT and Pham Duc, T and Duong, BL and Nguyen, PM and Hoang, VC and Pham, DT and Thwaites, GE and Hall, LJ and Slade, DJ and Baker, S and Tran, VH and Chung The, H}, title = {Tumour microbiomes and Fusobacterium genomics in Vietnamese colorectal cancer patients.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {87}, pmid = {36307484}, issn = {2055-5008}, support = {BBS/E/F/00044409/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 220876/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 215515/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 100974/C/13/Z/WT_/Wellcome Trust/United Kingdom ; 218726/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Fusobacterium/genetics ; Genomics ; *Microbiota ; *Colorectal Neoplasms/microbiology ; Asian People ; }, abstract = {Perturbations in the gut microbiome have been associated with colorectal cancer (CRC), with the colonic overabundance of Fusobacterium nucleatum shown as the most consistent marker. Despite its significance in the promotion of CRC, genomic studies of Fusobacterium is limited. We enrolled 43 Vietnamese CRC patients and 25 participants with non-cancerous colorectal polyps to study the colonic microbiomes and genomic diversity of Fusobacterium in this population, using a combination of 16S rRNA gene profiling, anaerobic microbiology, and whole genome analysis. Oral bacteria, including F. nucleatum and Leptotrichia, were significantly more abundant in the tumour microbiomes. We obtained 53 Fusobacterium genomes, representing 26 strains, from the saliva, tumour and non-tumour tissues of six CRC patients. Isolates from the gut belonged to diverse F. nucleatum subspecies (nucleatum, animalis, vincentii, polymorphum) and a potential new subspecies of Fusobacterium periodonticum. The Fusobacterium population within each individual was distinct and in some cases diverse, with minimal intra-clonal variation. Phylogenetic analyses showed that within four individuals, tumour-associated Fusobacterium were clonal to those isolated from non-tumour tissues. Genes encoding major virulence factors (Fap2 and RadD) showed evidence of horizontal gene transfer. Our work provides a framework to understand the genomic diversity of Fusobacterium within the CRC patients, which can be exploited for the development of CRC diagnostic and therapeutic options targeting this oncobacterium.}, }
@article {pmid36306437, year = {2023}, author = {Kronmiller, BA and Feau, N and Shen, D and Tabima, JF and Ali, SS and Armitage, AD and Arredondo, F and Bailey, BA and Bollmann, SR and Dale, A and Harrison, RJ and Hrywkiw, K and Kasuga, T and McDougal, R and Nellist, CF and Panda, P and Tripathy, S and Williams, NM and Ye, W and Wang, Y and Hamelin, RC and Grünwald, NJ}, title = {Comparative Genomic Analysis of 31 Phytophthora Genomes Reveals Genome Plasticity and Horizontal Gene Transfer.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {36}, number = {1}, pages = {26-46}, doi = {10.1094/MPMI-06-22-0133-R}, pmid = {36306437}, issn = {0894-0282}, mesh = {*Phytophthora/genetics ; Phylogeny ; Gene Transfer, Horizontal ; Genome ; Genomics ; Plants/genetics ; }, abstract = {Phytophthora species are oomycete plant pathogens that cause great economic and ecological impacts. The Phytophthora genus includes over 180 known species, infecting a wide range of plant hosts, including crops, trees, and ornamentals. We sequenced the genomes of 31 individual Phytophthora species and 24 individual transcriptomes to study genetic relationships across the genus. De novo genome assemblies revealed variation in genome sizes, numbers of predicted genes, and in repetitive element content across the Phytophthora genus. A genus-wide comparison evaluated orthologous groups of genes. Predicted effector gene counts varied across Phytophthora species by effector family, genome size, and plant host range. Predicted numbers of apoplastic effectors increased as the host range of Phytophthora species increased. Predicted numbers of cytoplasmic effectors also increased with host range but leveled off or decreased in Phytophthora species that have enormous host ranges. With extensive sequencing across the Phytophthora genus, we now have the genomic resources to evaluate horizontal gene transfer events across the oomycetes. Using a machine-learning approach to identify horizontally transferred genes with bacterial or fungal origin, we identified 44 candidates over 36 Phytophthora species genomes. Phylogenetic reconstruction indicates that the transfers of most of these 44 candidates happened in parallel to major advances in the evolution of the oomycetes and Phytophthora spp. We conclude that the 31 genomes presented here are essential for investigating genus-wide genomic associations in genus Phytophthora. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.}, }
@article {pmid36303123, year = {2022}, author = {Vaughan, AL and Altermann, E and Glare, TR and Hurst, MRH}, title = {Genome sequence of the entomopathogenic Serratia entomophila isolate 626 and characterisation of the species specific itaconate degradation pathway.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {728}, pmid = {36303123}, issn = {1471-2164}, mesh = {Animals ; *Serratia/genetics ; Virulence/genetics ; Plasmids ; *Coleoptera/genetics ; Larva ; Serratia marcescens/genetics ; }, abstract = {BACKGROUND: Isolates of Serratia entomophila and S. proteamaculans (Yersiniaceae) cause disease specific to the endemic New Zealand pasture pest, Costelytra giveni (Coleoptera: Scarabaeidae). Previous genomic profiling has shown that S. entomophila isolates appear to have conserved genomes and, where present, conserved plasmids. In the absence of C. giveni larvae, S. entomophila prevalence reduces in the soil over time, suggesting that S. entomophila has formed a host-specific relationship with C. giveni. To help define potential genetic mechanisms driving retention of the chronic disease of S. entomophila, the genome of the isolate 626 was sequenced, enabling the identification of unique chromosomal properties, and defining the gain/loss of accessory virulence factors relevant to pathogenicity to C. giveni larvae.<br><br>RESULTS: We report the complete sequence of S. entomophila isolate 626, a causal agent of amber disease in C. giveni larvae. The genome of S. entomophila 626 is 5,046,461&#xa0;bp, with 59.1% G&#x2009;+&#x2009;C content and encoding 4,695 predicted CDS. Comparative analysis with five previously sequenced Serratia species, S. proteamaculans 336X, S. marcescens Db11, S. nematodiphila DH-S01, S. grimesii BXF1, and S. ficaria NBRC 102596, revealed a core of 1,165 genes shared. Further comparisons between S. entomophila 626 and S. proteamaculans 336X revealed fewer predicted phage-like regions and genomic islands in 626, suggesting less horizontally acquired genetic material. Genomic analyses revealed the presence of a four-gene itaconate operon, sharing a similar gene order as the Yersinia pestis ripABC complex. Assessment of a constructed 626::RipC mutant revealed that the operon confer a possible metabolic advantage to S. entomophila in the initial stages of C. giveni infection.<br><br>CONCLUSIONS: Evidence is presented where, relative to S. proteamaculans 336X, S. entomophila 626 encodes fewer genomic islands and phages, alluding to limited horizontal gene transfer in S. entomophila. Bioassay assessments of a S. entomophila-mutant with a targeted mutation of the itaconate degradation region unique to this species, found the mutant to have a reduced capacity to replicate post challenge of the C. giveni larval host, implicating the itaconate operon in establishment within the host.}, }
@article {pmid36301081, year = {2022}, author = {Castro-Gutierrez, V and Fuller, E and Garcillán-Barcia, MP and Helgason, T and Hassard, F and Moir, J}, title = {Dissemination of metaldehyde catabolic pathways is driven by mobile genetic elements in Proteobacteria.}, journal = {Microbial genomics}, volume = {8}, number = {10}, pages = {}, pmid = {36301081}, issn = {2057-5858}, mesh = {*Proteobacteria/genetics ; Gene Transfer, Horizontal ; Plasmids/genetics ; DNA Transposable Elements/genetics ; *Sphingomonadaceae/genetics ; Escherichia coli/genetics ; }, abstract = {Bioremediation of metaldehyde from drinking water using metaldehyde-degrading strains has recently emerged as a promising alternative. Whole-genome sequencing was used to obtain full genomes for metaldehyde degraders Acinetobacter calcoaceticus E1 and Sphingobium CMET-H. For the former, the genetic context of the metaldehyde-degrading genes had not been explored, while for the latter, none of the degrading genes themselves had been identified. In A. calcoaceticus E1, IS91 and IS6-family insertion sequences (ISs) were found surrounding the metaldehyde-degrading gene cluster located in plasmid pAME76. This cluster was located in closely-related plasmids and associated to identical ISs in most metaldehyde-degrading β- and γ-Proteobacteria, indicating horizontal gene transfer (HGT). For Sphingobium CMET-H, sequence analysis suggested a phytanoyl-CoA family oxygenase as a metaldehyde-degrading gene candidate due to its close homology to a previously identified metaldehyde-degrading gene known as mahX. Heterologous gene expression in Escherichia coli alongside degradation tests verified its functional significance and the degrading gene homolog was henceforth called mahS. It was found that mahS is hosted within the conjugative plasmid pSM1 and its genetic context suggested a crossover between the metaldehyde and acetoin degradation pathways. Here, specific replicons and ISs responsible for maintaining and dispersing metaldehyde-degrading genes in α, β and γ-Proteobacteria through HGT were identified and described. In addition, a homologous gene implicated in the first step of metaldehyde utilisation in an α-Proteobacteria was uncovered. Insights into specific steps of this possible degradation pathway are provided.}, }
@article {pmid36298845, year = {2022}, author = {Harrison, RL and Rowley, DL}, title = {The Parapoynx stagnalis Nucleopolyhedrovirus (PastNPV), a Divergent Member of the Alphabaculovirus Group I Clade, Encodes a Homolog of Ran GTPase.}, journal = {Viruses}, volume = {14}, number = {10}, pages = {}, pmid = {36298845}, issn = {1999-4915}, mesh = {Animals ; *Nucleopolyhedroviruses ; Phylogeny ; Genome, Viral ; GTP Phosphohydrolases/genetics ; Open Reading Frames ; *Moths ; Nucleotides ; }, abstract = {We report the analysis of the genome of a novel Alphabaculovirus, Parapoynx stagnalis nucleopolyhedrovirus isolate 473 (PastNPV-473), from cadavers of the rice case bearer, Parapoynx stagnalis Zeller (Lepidoptera: Crambidae), collected in rice fields in Kerala, India. High-throughput sequencing of DNA from PastNPV occlusion bodies and assembly of the data yielded a circular genome-length contig of 114,833 bp with 126 annotated opening reading frames (ORFs) and six homologous regions (hrs). Phylogenetic inference based on baculovirus core gene amino acid sequence alignments indicated that PastNPV is a member of the group I clade of viruses in genus Alphabaculovirus, but different phylogenetic methods yielded different results with respect to the placement of PastNPV and four similarly divergent alphabaculoviruses in the group I clade. Branch lengths and Kimura-2-parameter pairwise nucleotide distances indicated that PastNPV-473 cannot be classified in any of the currently listed species in genus Alphabaculovirus. A unique feature of the PastNPV genome was the presence of an ORF encoding a homolog of Ran GTPase, a regulator of nucleocytoplasmic trafficking. PastNPV appears to have acquired a homolog of Ran relatively recently from a lepidopteran host via horizontal gene transfer.}, }
@article {pmid36298721, year = {2022}, author = {Lal, A and Kil, EJ and Vo, TTB and Wira Sanjaya, IGNP and Qureshi, MA and Nattanong, B and Ali, M and Shuja, MN and Lee, S}, title = {Interspecies Recombination-Led Speciation of a Novel Geminivirus in Pakistan.}, journal = {Viruses}, volume = {14}, number = {10}, pages = {}, pmid = {36298721}, issn = {1999-4915}, mesh = {*Geminiviridae/genetics ; DNA, Viral/genetics ; Phylogeny ; Gene Transfer, Horizontal ; Pakistan ; Plant Diseases ; *Begomovirus ; Sequence Analysis, DNA ; Genome, Viral ; }, abstract = {Recombination between isolates of different virus species has been known to be one of the sources of speciation. Weeds serve as mixing vessels for begomoviruses, infecting a wide range of economically important plants, thereby facilitating recombination. Chenopodium album is an economically important weed spread worldwide. Here, we present the molecular characterization of a novel recombinant begomovirus identified from C. album in Lahore, Pakistan. The complete DNA- A genome of the virus associated with the leaf distortion occurred in the infected C. album plants was cloned and sequenced. DNA sequence analysis showed that the nucleotide sequence of the virus shared 93% identity with those of the rose leaf curl virus and the duranta leaf curl virus. Interestingly, this newly identified virus is composed of open reading frames (ORFs) from different origins. Phylogenetic networks and complementary recombination detection methods revealed extensive recombination among the sequences. The infectious clone of the newly detected virus was found to be fully infectious in C. album and Nicotiana benthamiana as the viral DNA was successfully reconstituted from systemically infected tissues of inoculated plants, thus fulfilling Koch's postulates. Our study reveals a new speciation of an emergent ssDNA plant virus associated with C. album through recombination and therefore, proposed the tentative name 'Chenopodium leaf distortion virus' (CLDV).}, }
@article {pmid36296271, year = {2022}, author = {Navarro, A and Rodea, GE and Castelán-Sánchez, HG and Saucedo-Pastrana, HA and Licona-Moreno, D and Eslava-Campos, C and Tirado-Gómez, LL and Vilchis-Reyes, A and García de la Torre, G and Cruz-Licea, V}, title = {Importance of Microbiome of Fecal Samples Obtained from Adolescents with Different Weight Conditions on Resistance Gene Transfer.}, journal = {Microorganisms}, volume = {10}, number = {10}, pages = {}, pmid = {36296271}, issn = {2076-2607}, abstract = {Antimicrobial resistance (AMR) is a relevant public health problem worldwide, and microbiome bacteria may contribute to the horizontal gene transfer associated with antimicrobial resistance. The microbiome of fecal samples from Mexican adolescents were analyzed and correlated with eating habits, and the presence of AMR genes on bacteria in the microbiome was evaluated. Fecal samples from adolescents were collected and processed to extract genomic DNA. An Illumina HiSeq 1500 system was used to determine resistance genes and the microbiome of adolescents through the amplification of gene resistance and the V3-V4 regions of RNA, respectively. Analysis of the microbiome from fecal samples taken from 18 obese, overweight, and normal-weight adolescents revealed that the Firmicutes was the most frequent phylum, followed by Bacteroidetes, Actinobacteria, Proteobacteria and Verrucomicrobia. The following species were detected as the most frequent in the samples: F. prausnitzii, P. cori, B. adolescentis, E. coli and A. muciniphila. The presence of Bacteroides, Prevotella and Ruminococcus was used to establish the enterotype; enterotype 1 was more common in women and enterotype 2 was more common in men. Twenty-nine AMR genes were found for β-lactamases, fluoroquinolones, aminoglycosides, macrolide, lincosamides, streptogramin (MLS), tetracyclines and sulfonamides. The presence of microorganisms in fecal samples that harbor AMR genes that work against antimicrobials frequently used for the treatment of microbial infections such as b-lactams, macrolides, aminoglycosides, MLS, and tetracyclines is of great concern, as these organisms may be an important reservoir for horizontal AMR gene transfer.}, }
@article {pmid36292780, year = {2022}, author = {Li, M and Chen, Q and Wu, C and Li, Y and Wang, S and Chen, X and Qiu, B and Li, Y and Mao, D and Lin, H and Yu, D and Cao, Y and Huang, Z and Cui, C and Zhong, Z}, title = {A Novel Module Promotes Horizontal Gene Transfer in Azorhizobium caulinodans ORS571.}, journal = {Genes}, volume = {13}, number = {10}, pages = {}, pmid = {36292780}, issn = {2073-4425}, mesh = {*Azorhizobium caulinodans/genetics ; Gene Transfer, Horizontal ; *Sesbania/microbiology ; Integrases/metabolism ; Flavonoids/metabolism ; Soil ; }, abstract = {Azorhizobium caulinodans ORS571 contains an 87.6 kb integrative and conjugative element (ICE[Ac]) that conjugatively transfers symbiosis genes to other rhizobia. Many hypothetical redundant gene fragments (rgfs) are abundant in ICE[Ac], but their potential function in horizontal gene transfer (HGT) is unknown. Molecular biological methods were employed to delete hypothetical rgfs, expecting to acquire a minimal ICE[Ac] and consider non-functional rgfs as editable regions for inserting genes related to new symbiotic functions. We determined the significance of rgf4 in HGT and identified the physiological function of genes designated rihF1a (AZC_3879), rihF1b (AZC_RS26200), and rihR (AZC_3881). In-frame deletion and complementation assays revealed that rihF1a and rihF1b work as a unit (rihF1) that positively affects HGT frequency. The EMSA assay and lacZ-based reporter system showed that the XRE-family protein RihR is not a regulator of rihF1 but promotes the expression of the integrase (intC) that has been reported to be upregulated by the LysR-family protein, AhaR, through sensing host's flavonoid. Overall, a conservative module containing rihF1 and rihR was characterized, eliminating the size of ICE[Ac] by 18.5%. We propose the feasibility of constructing a minimal ICE[Ac] element to facilitate the exchange of new genetic components essential for symbiosis or other metabolic functions between soil bacteria.}, }
@article {pmid36291676, year = {2022}, author = {Mocchetti, E and Morette, L and Mulliert, G and Mathiot, S and Guillot, B and Dehez, F and Chauvat, F and Cassier-Chauvat, C and Brochier-Armanet, C and Didierjean, C and Hecker, A}, title = {Biochemical and Structural Characterization of Chi-Class Glutathione Transferases: A Snapshot on the Glutathione Transferase Encoded by sll0067 Gene in the Cyanobacterium Synechocystis sp. Strain PCC 6803.}, journal = {Biomolecules}, volume = {12}, number = {10}, pages = {}, pmid = {36291676}, issn = {2218-273X}, mesh = {*Glutathione Transferase/metabolism ; *Synechocystis/genetics/metabolism ; Pyruvaldehyde ; Glutathione/metabolism ; Protein Structure, Secondary ; }, abstract = {Glutathione transferases (GSTs) constitute a widespread superfamily of enzymes notably involved in detoxification processes and/or in specialized metabolism. In the cyanobacterium Synechocsytis sp. PCC 6803, SynGSTC1, a chi-class GST (GSTC), is thought to participate in the detoxification process of methylglyoxal, a toxic by-product of cellular metabolism. A comparative genomic analysis showed that GSTCs were present in all orders of cyanobacteria with the exception of the basal order Gloeobacterales. These enzymes were also detected in some marine and freshwater noncyanobacterial bacteria, probably as a result of horizontal gene transfer events. GSTCs were shorter of about 30 residues compared to most cytosolic GSTs and had a well-conserved SRAS motif in the active site ([10]SRAS[13] in SynGSTC1). The crystal structure of SynGSTC1 in complex with glutathione adopted the canonical GST fold with a very open active site because the α4 and α5 helices were exceptionally short. A transferred multipolar electron-density analysis allowed a fine description of the solved structure. Unexpectedly, Ser10 did not have an electrostatic influence on glutathione as usually observed in serinyl-GSTs. The S10A variant was only slightly less efficient than the wild-type and molecular dynamics simulations suggested that S10 was a stabilizer of the protein backbone rather than an anchor site for glutathione.}, }
@article {pmid36289972, year = {2022}, author = {Cherak, Z and Loucif, L and Bendjama, E and Moussi, A and Benbouza, A and Grainat, N and Rolain, JM}, title = {Dissemination of Carbapenemases and MCR-1 Producing Gram-Negative Bacteria in Aquatic Environments in Batna, Algeria.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {10}, pages = {}, pmid = {36289972}, issn = {2079-6382}, abstract = {Antibiotic-resistant-bacteria are being considered as emerging environmental contaminants where the importance of the surrounding environment in their emergence and dissemination has been emphasized. The aim of this study was to screen for the presence and diversity of carbapenem- and colistin-resistant Gram-negative bacteria (GNBs) in different aquatic environments. Water samples were collected in Batna, Algeria. Carbapenem- and colistin-resistant GNBs were selectively isolated and then identified using matrix-assisted laser desorption and ionization time-of-flight mass spectrometry. After phenotypic antibiotic susceptibility testing, the molecular mechanisms of β-lactams and colistin-resistance were investigated by PCR and sequencing. The clonality of mcr-1 positive Escherichia coli was determined by multi-locus sequence typing. We noticed a high level of resistance in both tap water and wastewater. The most commonly found carbapenem-resistance mechanism was the OXA-48 enzyme, but other carbapenemases were also detected. In addition, the mcr-1 gene was detected in 18 E. coli of different sequence types. Our findings highlight the role of aquatic environments in the dissemination of resistant-bacteria, especially considering that water is a connecting medium between different ecological systems and can easily transmit resistant-bacteria and promote horizontal gene transfer. Thus, the development of effective treatment strategies for eliminating antibiotic-resistance is seriously needed.}, }
@article {pmid36289941, year = {2022}, author = {Sekizuka, T and Tanaka, R and Hashino, M and Yatsu, K and Kuroda, M}, title = {Comprehensive Genome and Plasmidome Analysis of Antimicrobial Resistant Bacteria in Wastewater Treatment Plant Effluent of Tokyo.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {10}, pages = {}, pmid = {36289941}, issn = {2079-6382}, support = {JP21fk0108103//Japan Agency for Medical Research and Development/ ; JP22fk0108131//Japan Agency for Medical Research and Development/ ; H30 Shinkogyosei-Ippan-002//a grant for research on emerging and reemerging infectious diseases and immunization from the Ministry of Health, Labour and Welfare/ ; R4 Shinkogyosei-Ippan-002)//a grant for research on emerging and reemerging infectious diseases and immunization from the Ministry of Health, Labour and Welfare/ ; }, abstract = {To characterize environmental antimicrobial resistance (AMR) in urban areas, extended-spectrum β-lactamase- (ESBL)/carbapenemase-producing bacteria (EPB/CPB, respectively) from urban wastewater treatment plant effluents in Tokyo were isolated on CHROMagar ESBL plate. Complete genome sequence analysis, including plasmids, indicated that 126 CTX-M-positive isolates (31%) were identified among the 404 obtained isolates. The CTX-M-9 group was predominant (n = 65, 52%), followed by the CTX-M-1 group (n = 44, 35%). Comparative genome analysis revealed that CTX-M-27-positive E. coli O16:H5-ST131-fimH41 exhibited a stable genome structure and clonal-global dissemination. Plasmidome network analysis revealed that 304 complete plasmid sequences among 85 isolates were grouped into 14 incompatibility (Inc) network communities (Co1 to Co14). Co10 consisted of primarily IncFIA/IncFIB plasmids harboring blaCTX-M in E. coli, whereas Co12 consisted primarily of IncFIA(HI1)/Inc FIB(K) plasmids harboring blaCTX-M, blaKPC, and blaGES in Klebsiella spp. Co11 was markedly located around Co10 and Co12. Co11 exhibited blaCTX-M, blaKPC, and blaNDM, and was mainly detected in E. coli and Klebsiella spp. from human and animal sources, suggesting a mutual role of Co11 in horizontal gene transfer between E. coli and Klebsiella spp. This comprehensive resistome analysis uncovers the mode of relational transfer among bacterial species, highlighting the potential source of AMR burden on public health in urban communities.}, }
@article {pmid36287061, year = {2022}, author = {Li, Y and Shi, X and Zuo, Y and Li, T and Liu, L and Shen, Z and Shen, J and Zhang, R and Wang, S}, title = {Multiplexed Target Enrichment Enables Efficient and In-Depth Analysis of Antimicrobial Resistome in Metagenomes.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0229722}, pmid = {36287061}, issn = {2165-0497}, mesh = {Humans ; *Metagenome ; *Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Sewage ; Metagenomics/methods ; }, abstract = {Antibiotic resistance genes (ARGs) pose a serious threat to public health and ecological security in the 21st century. However, the resistome only accounts for a tiny fraction of metagenomic content, which makes it difficult to investigate low-abundance ARGs in various environmental settings. Thus, a highly sensitive, accurate, and comprehensive method is needed to describe ARG profiles in complex metagenomic samples. In this study, we established a high-throughput sequencing method based on targeted amplification, which could simultaneously detect ARGs (n = 251), mobile genetic element genes (n = 8), and metal resistance genes (n = 19) in metagenomes. The performance of amplicon sequencing was compared with traditional metagenomic shotgun sequencing (MetaSeq). A total of 1421 primer pairs were designed, achieving extremely high coverage of target genes. The amplicon sequencing significantly improved the recovery of target ARGs (~9 × 10[4]-fold), with higher sensitivity and diversity, less cost, and computation burden. Furthermore, targeted enrichment allows deep scanning of single nucleotide polymorphisms (SNPs), and elevated SNPs detection was shown in this study. We further performed this approach for 48 environmental samples (37 feces, 20 soils, and 7 sewage) and 16 clinical samples. All samples tested in this study showed high diversity and recovery of targeted genes. Our results demonstrated that the approach could be applied to various metagenomic samples and served as an efficient tool in the surveillance and evolution assessment of ARGs. Access to the resistome using the enrichment method validated in this study enabled the capture of low-abundance resistomes while being less costly and time-consuming, which can greatly advance our understanding of local and global resistome dynamics. IMPORTANCE ARGs, an increasing global threat to human health, can be transferred into health-related microorganisms in the environment by horizontal gene transfer, posing a serious threat to public health. Advancing profiling methods are needed for monitoring and predicting the potential risks of ARGs in metagenomes. Our study described a customized amplicon sequencing assay that could enable a high-throughput, targeted, in-depth analysis of ARGs and detect a low-abundance portion of resistomes. This method could serve as an efficient tool to assess the variation and evolution of specific ARGs in the clinical and natural environment.}, }
@article {pmid36286524, year = {2022}, author = {Akob, DM and Sutton, JM and Bushman, TJ and Baesman, SM and Klein, E and Shrestha, Y and Andrews, R and Fierst, JL and Kolton, M and Gushgari-Doyle, S and Oremland, RS and Freeman, JL}, title = {Acetylenotrophic and Diazotrophic Bradyrhizobium sp. Strain I71 from TCE-Contaminated Soils.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {22}, pages = {e0121922}, pmid = {36286524}, issn = {1098-5336}, mesh = {*Bradyrhizobium ; *Trichloroethylene/metabolism ; Nitrogen Fixation/genetics ; Soil/chemistry ; Acetylene/metabolism ; Phylogeny ; Symbiosis ; RNA, Ribosomal, 16S/genetics ; Root Nodules, Plant/microbiology ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; }, abstract = {Acetylene (C2H2) is a molecule rarely found in nature, with very few known natural sources, but acetylenotrophic microorganisms can use acetylene as their primary carbon and energy source. As of 2018 there were 15 known strains of aerobic and anaerobic acetylenotrophs; however, we hypothesize there may yet be unrecognized diversity of acetylenotrophs in nature. This study expands the known diversity of acetylenotrophs by isolating the aerobic acetylenotroph, Bradyrhizobium sp. strain I71, from trichloroethylene (TCE)-contaminated soils. Strain I71 is a member of the class Alphaproteobacteria and exhibits acetylenotrophic and diazotrophic activities, the only two enzymatic reactions known to transform acetylene. This unique capability in the isolated strain may increase the genus' economic impact beyond agriculture as acetylenotrophy is closely linked to bioremediation of chlorinated contaminants. Computational analyses indicate that the Bradyrhizobium sp. strain I71 genome contains 522 unique genes compared to close relatives. Moreover, applying a novel hidden Markov model of known acetylene hydratase (AH) enzymes identified a putative AH enzyme. Protein annotation with I-TASSER software predicted the AH from the microbe Syntrophotalea acetylenica as the closest structural and functional analog. Furthermore, the putative AH was flanked by horizontal gene transfer (HGT) elements, like that of AH in anaerobic acetylenotrophs, suggesting an unknown source of acetylene or acetylenic substrate in the environment that is selecting for the presence of AH. IMPORTANCE The isolation of Bradyrhizobium strain I71 expands the distribution of acetylene-consuming microbes to include a group of economically important microorganisms. Members of Bradyrhizobium are well studied for their abilities to improve plant health and increase crop yields by providing bioavailable nitrogen. Additionally, acetylene-consuming microbes have been shown to work in tandem with other microbes to degrade soil contaminants. Based on genome, cultivation, and protein prediction analysis, the ability to consume acetylene is likely not widespread within the genus Bradyrhizobium. These findings suggest that the suite of phenotypic capabilities of strain I71 may be unique and make it a good candidate for further study in several research avenues.}, }
@article {pmid36285389, year = {2023}, author = {Hulin, MT and Rabiey, M and Zeng, Z and Vadillo Dieguez, A and Bellamy, S and Swift, P and Mansfield, JW and Jackson, RW and Harrison, RJ}, title = {Genomic and functional analysis of phage-mediated horizontal gene transfer in Pseudomonas syringae on the plant surface.}, journal = {The New phytologist}, volume = {237}, number = {3}, pages = {959-973}, pmid = {36285389}, issn = {1469-8137}, mesh = {Pseudomonas syringae/genetics ; Gene Transfer, Horizontal ; *Bacteriophages/genetics ; Genomics ; Genome, Bacterial ; *Prunus avium ; Plant Diseases/genetics ; }, abstract = {Many strains of Pseudomonas colonise plant surfaces, including the cherry canker pathogens, Pseudomonas syringae pathovars syringae and morsprunorum. We have examined the genomic diversity of P. syringae in the cherry phyllosphere and focused on the role of prophages in transfer of genes encoding Type 3 secreted effector (T3SE) proteins contributing to the evolution of virulence. Phylogenomic analysis was carried out on epiphytic pseudomonads in the UK orchards. Significant differences in epiphytic populations occurred between regions. Nonpathogenic strains were found to contain reservoirs of T3SE genes. Members of P. syringae phylogroups 4 and 10 were identified for the first time from Prunus. Using bioinformatics, we explored the presence of the gene encoding T3SE HopAR1 within related prophage sequences in diverse P. syringae strains including cherry epiphytes and pathogens. Results indicated that horizontal gene transfer (HGT) of this effector between phylogroups may have involved phage. Prophages containing hopAR1 were demonstrated to excise, circularise and transfer the gene on the leaf surface. The phyllosphere provides a dynamic environment for prophage-mediated gene exchange and the potential for the emergence of new more virulent pathotypes. Our results suggest that genome-based epidemiological surveillance of environmental populations will allow the timely application of control measures to prevent damaging diseases.}, }
@article {pmid36282569, year = {2022}, author = {Cerqueira de Araujo, A and Josse, T and Sibut, V and Urabe, M and Asadullah, A and Barbe, V and Nakai, M and Huguet, E and Periquet, G and Drezen, JM}, title = {Chelonus inanitus bracovirus encodes lineage-specific proteins and truncated immune IκB-like factors.}, journal = {The Journal of general virology}, volume = {103}, number = {10}, pages = {}, doi = {10.1099/jgv.0.001791}, pmid = {36282569}, issn = {1465-2099}, mesh = {Humans ; Animals ; *Polydnaviridae/genetics ; Phylogeny ; *Wasps/genetics ; Viral Proteins/genetics ; Biological Evolution ; }, abstract = {Bracoviruses and ichnoviruses are endogenous viruses of parasitic wasps that produce particles containing virulence genes expressed in host tissues and necessary for parasitism success. In the case of bracoviruses the particles are produced by conserved genes of nudiviral origin integrated permanently in the wasp genome, whereas the virulence genes can strikingly differ depending on the wasp lineage. To date most data obtained on bracoviruses concerned species from the braconid subfamily of Microgastrinae. To gain a broader view on the diversity of virulence genes we sequenced the genome packaged in the particles of Chelonus inanitus bracovirus (CiBV) produced by a wasp belonging to a different subfamily: the Cheloninae. These are egg-larval parasitoids, which means that they oviposit into the host egg and the wasp larvae then develop within the larval stages of the host. We found that most of CiBV virulence genes belong to families that are specific to Cheloninae. As other bracoviruses and ichnoviruses however, CiBV encode v-ank genes encoding truncated versions of the immune cactus/IκB factor, which suggests these proteins might play a key role in host-parasite interactions involving domesticated endogenous viruses. We found that the structures of CiBV V-ANKs are different from those previously reported. Phylogenetic analysis supports the hypothesis that they may originate from a cactus/IκB immune gene from the wasp genome acquired by the bracovirus. However, their evolutionary history is different from that shared by other V-ANKs, whose common origin probably reflects horizontal gene transfer events of virus sequences between braconid and ichneumonid wasps.}, }
@article {pmid36282171, year = {2022}, author = {Koonin, EV and Krupovic, M}, title = {A life LINE for large viruses.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {36282171}, issn = {2050-084X}, mesh = {*Retroelements ; *Poxviridae/genetics ; Vaccinia virus/genetics ; Virus Replication ; }, abstract = {As long suspected, poxviruses capture host genes through a reverse-transcription process now shown to be mediated by retrotransposons.}, }
@article {pmid36280316, year = {2022}, author = {Paul, D and Das, B}, title = {Gut microbiome in the emergence of antibiotic-resistant bacterial pathogens.}, journal = {Progress in molecular biology and translational science}, volume = {192}, number = {1}, pages = {1-31}, doi = {10.1016/bs.pmbts.2022.07.009}, pmid = {36280316}, issn = {1878-0814}, mesh = {Humans ; *Gastrointestinal Microbiome ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Ecosystem ; Bacteria/genetics ; Gene Transfer, Horizontal ; }, abstract = {The human gastrointestinal tract is home to a complex and dynamic community of microorganisms known as gut microbiota, which provide the host with important metabolic, signaling, and immunomodulatory functions. Both the commensal and pathogenic members of the gut microbiome serve as reservoirs of antimicrobial-resistance genes (ARG), which can cause potential health threats to the host and can transfer the ARGs to the susceptible microbes and into the environment. Antimicrobial resistance is becoming a major burden on human health and is widely recognized as a global challenge. The diversity and abundance of ARGs in the gut microbiome are variable and depend on the exposure to healthcare-associated antibiotics, usage of antibiotics in veterinary and agriculture, and the migration of the population. The transfer frequency of the ARGs through horizontal gene transfer (HGT) with the help of mobile genetic elements (MGEs) like plasmids, transposons, or phages is much higher among bacteria living in the GI tract compared to other microbial ecosystems. HGT in gut bacteria is facilitated through multiple gene transfer mechanisms, including transformation, conjugation, transduction, and vesicle fusion. It is the need of the hour to implement strict policies to limit indiscriminate antibiotic usage when needed. Developing rapid diagnostic tests for resistance determination and alternatives to antibiotics like vaccination, probiotics, and bacteriophage therapy should have the highest priority in the research and development sectors. Collective actions for sustainable development against resistant pathogens by promoting endogenous gut microbial growth and diversity through interdisciplinary research and findings are key to overcoming the current antimicrobial resistance crisis.}, }
@article {pmid36279613, year = {2022}, author = {Yang, J and Xiang, J and Xie, Y and Yu, K and Li, J and Wang, H and Li, P and Gin, KY and He, Y}, title = {Removal behavior and key drivers of antibiotic resistance genes in two full-scale leachate treatment plants.}, journal = {Water research}, volume = {226}, number = {}, pages = {119239}, doi = {10.1016/j.watres.2022.119239}, pmid = {36279613}, issn = {1879-2448}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; Ecosystem ; Drug Resistance, Microbial/genetics ; Bioreactors ; Bacteria/genetics ; }, abstract = {Leachate is a critical reservoir of antibiotic resistance genes (ARGs) and its proper treatment is closely related to human health and ecosystem safety. Here, we used high-throughput qPCR to explore the removal behavior of ARGs in two full-scale leachate treatment plants (LTPs) where biological treatment and membrane filtration processes were integrated. A total of 286 ARGs and 55 mobile genetic elements (MGEs) were detected, with aminoglycoside, multidrug and MLSB resistance genes being the most prevalent and abundant. Anaerobic digestion was found to be an important pretreatment process for leachate, while anoxic/aerobic tanks in membrane bioreactor (MBR) acted as incubators for ARGs due to their significant proliferation effect on ARGs. Integrated membrane filtration (UF-NF-RO) excelled in ARGs removal with absolute abundances reduced by 3 to 6 orders of magnitude, from about 10[9] copies/mL in raw leachate to 10[3]-10[5] copies/mL in effluents. Our results also showed that leachate treatment processes significantly altered the composition of ARGs and bacterial communities. Procrustes analysis and network analysis revealed strong associations between microbes and ARGs, with several hub genes and bacterial genera identified. Structural equation models (SEMs) indicated that bacterial composition, MGEs and basic water properties were the key drivers shaping ARGs dynamics in the raw leachate, biological system and filtration system, respectively. Notably, several pathogens (e.g., Klebsiella, Vibrio, Aeromonas) were closely correlated with ARGs in raw leachate and may amplify the dissemination risks of ARGs. Moreover, insertion sequences in biological systems would accelerate the horizontal gene transfer of ARGs. In short, this study provides new insights into the mechanisms of ARGs removal and dissemination behavior in industrial-scale LTPs.}, }
@article {pmid36275512, year = {2022}, author = {Wang, X and Yoo, E and Lee, S and Cho, GT and Lee, GA and Yi, JY and Du, X and Han, S and Hyun, DY and Ro, N and Kim, KM}, title = {Classification of 17 species Aegilops using DNA barcoding and SNPs, reveals gene flow among Aegilops biuncialis, Aegilops juvenalis, and Aegilops columnaris.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {984825}, pmid = {36275512}, issn = {1664-462X}, abstract = {Rapid changes in agricultural environments caused by global warming pose a major challenge to food production and safety. Common wheat (Triticum aestivum) is a hexaploid plant (AABBDD) that shares large numbers of quantitative traits and resistance genes with B and D genomes of Aegilops species, which are responsible for several metabolic functions and biosynthetic processes, particularly in plant adaptation to biotic as well as abiotic stresses. Comparatively, the abundance of the Aegilops gene pool is much higher than that of Triticum. Therefore, we used four universal DNA barcodes for plants (ITS2, matK, rbcL, and psbM-petN) to construct a phylogenetic tree to classify the genus Aegilops. Fourteen species were distinguished among a total of 17 representative species. Aegilops biuncialis, Aegilops juvenalis, and Aegilops umbellulata could not be grouped into any of the clusters in the phylogenetic tree, indicating that these three species could not be distinguished by four DNA barcodes. Therefore, from 2408 SNPs obtained using genotyping by sequencing (GBS), we manually screened 30 SNPs that could be potentially used to classify these three species. The results of gene flow and genetic differentiation index (Fst) showed that the genetic differentiation among the three species was small, and there was bidirectional horizontal gene transfer between the three species, which was consistent with our results that the three species were difficult to classify by DNA barcode.}, }
@article {pmid36271797, year = {2022}, author = {Wisniewska, A and Wons, E and Potrykus, K and Hinrichs, R and Gucwa, K and Graumann, PL and Mruk, I}, title = {Molecular basis for lethal cross-talk between two unrelated bacterial transcription factors - the regulatory protein of a restriction-modification system and the repressor of a defective prophage.}, journal = {Nucleic acids research}, volume = {50}, number = {19}, pages = {10964-10980}, pmid = {36271797}, issn = {1362-4962}, mesh = {*Transcription Factors/genetics/metabolism ; *DNA Restriction-Modification Enzymes/genetics ; Prophages/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Escherichia coli/genetics/metabolism ; Gene Regulatory Networks ; }, abstract = {Bacterial gene expression depends on the efficient functioning of global transcriptional networks, however their interconnectivity and orchestration rely mainly on the action of individual DNA binding proteins called transcription factors (TFs). TFs interact not only with their specific target sites, but also with secondary (off-target) sites, and vary in their promiscuity. It is not clear yet what mechanisms govern the interactions with secondary sites, and how such rewiring affects the overall regulatory network, but this could clearly constrain horizontal gene transfer. Here, we show the molecular mechanism of one such off-target interaction between two unrelated TFs in Escherichia coli: the C regulatory protein of a Type II restriction-modification system, and the RacR repressor of a defective prophage. We reveal that the C protein interferes with RacR repressor expression, resulting in derepression of the toxic YdaT protein. These results also provide novel insights into regulation of the racR-ydaST operon. We mapped the C regulator interaction to a specific off-target site, and also visualized C protein dynamics, revealing intriguing differences in single molecule dynamics in different genetic contexts. Our results demonstrate an apparent example of horizontal gene transfer leading to adventitious TF cross-talk with negative effects on the recipient's viability. More broadly, this study represents an experimentally-accessible model of a regulatory constraint on horizontal gene transfer.}, }
@article {pmid36270189, year = {2023}, author = {Yu, Y and Xie, Z and Yang, J and Yang, R and Li, Y and Zhu, Y and Zhao, Y and Yang, Q and Chen, J and Alwathnani, HA and Feng, R and Rensing, C and Herzberg, M}, title = {Citrobacter portucalensis Sb-2 contains a metalloid resistance determinant transmitted by Citrobacter phage Chris1.}, journal = {Journal of hazardous materials}, volume = {443}, number = {Pt A}, pages = {130184}, doi = {10.1016/j.jhazmat.2022.130184}, pmid = {36270189}, issn = {1873-3336}, mesh = {Antimony/toxicity ; *Arsenites ; *Arsenic ; *Metalloids ; *Bacteriophages/genetics ; Citrobacter/genetics ; }, abstract = {Bacterial adaptation to extreme environments is often mediated by horizontal gene transfer (HGT) via genetic mobile elements. Nevertheless, phage-mediated HGT conferring bacterial arsenic resistance determinants has rarely been investigated. In this study, a highly arsenite and antimonite resistant bacterium, Citrobacter portucalensis strain Sb-2, was isolated, and genome analysis showed that several putative arsenite and antimonite resistance determinants were flanked or embedded in prophages. Furthermore, an active bacteriophage carrying one of the ars clusters (arsRDABC arsR-yraQ/arsP) was obtained and sequenced. These genes encoding putative arsenic resistance determinants were induced by arsenic and antimony as demonstrated by RT-qPCR, and one gene arsP/yraQ of the ars cluster was shown to give resistance to MAs(III) and Rox(III), thereby showing function. Here, we were able to directly show that these phage-mediated arsenic and antimony resistances play a significant role in adapting to As- and Sb-contaminated environments. In addition, we demonstrate that this phage is responsible for conferring arsenic and antimony resistances to C. portucalensis strain Sb-2.}, }
@article {pmid36268794, year = {2022}, author = {McLellan, LK and Anderson, ME and Grossman, AD}, title = {TnSmu1 is a functional integrative and conjugative element in Streptococcus mutans that when expressed causes growth arrest of host bacteria.}, journal = {Molecular microbiology}, volume = {118}, number = {6}, pages = {652-669}, pmid = {36268794}, issn = {1365-2958}, support = {R35 GM122538/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Streptococcus mutans/genetics ; Conjugation, Genetic ; *Dental Caries ; Gene Transfer, Horizontal ; DNA Transposable Elements ; }, abstract = {Integrative and conjugative elements (ICEs) are major drivers of horizontal gene transfer in bacteria. They mediate their own transfer from host cells (donors) to recipients and allow bacteria to acquire new phenotypes, including pathogenic and metabolic capabilities and drug resistances. Streptococcus mutans, a major causative agent of dental caries, contains a putative ICE, TnSmu1, integrated at the 3' end of a leucyl tRNA gene. We found that TnSmu1 is a functional ICE, containing all the genes necessary for ICE function. It excised from the chromosome and excision was stimulated by DNA damage. We identified the DNA junctions generated by excision of TnSmu1, defined the ends of the element, and detected the extrachromosomal circle. We found that TnSmu1 can transfer from S. mutans donors to recipients when co-cultured on solid medium. The presence of TnSmu1 in recipients inhibited successful acquisition of another copy and this inhibition was mediated, at least in part, by the likely transcriptional repressor encoded by the element. Using microscopy to track individual cells, we found that activation of TnSmu1 caused an arrest of cell growth. Our results demonstrate that TnSmu1 is a functional ICE that affects the biology of its host cells.}, }
@article {pmid36267172, year = {2022}, author = {Fernanda, PA and Liu, S and Yuan, T and Ramalingam, B and Lu, J and Sekar, R}, title = {Diversity and abundance of antibiotic resistance genes and their relationship with nutrients and land use of the inflow rivers of Taihu Lake.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1009297}, pmid = {36267172}, issn = {1664-302X}, abstract = {Taihu Lake is the third largest freshwater lake in China and an important source for drinking water, flood protection, aquaculture, agriculture, and other activities. This lake is connected to many principal and small rivers with inflow from west and outflow on the eastern side of the lake and these inflow rivers are believed to significantly contribute to the water pollution of the lake. This study was aimed at assessing the diversity and abundance of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), and their relationship with water quality parameters and land use patterns. Water samples were collected from 10 major inflow rivers and the source water protection area of the Taihu Lake in spring and summer 2019. High-throughput profiling was used to detect and quantify 384 ARGs and MGEs and in addition, 11 water quality parameters were analyzed. The results showed that the number of ARGs/MGEs detected in each inflow river ranged from 105 to 185 in spring and 107 to 180 in summer. The aminoglycoside resistance genes were the most dominant types ARGs detected followed by beta-lactam resistance, multidrug resistance, macrolide-lincosamide-streptogramin B (MLSB) resistance genes, which contributed to 65% of the ARGs. The water quality parameters showed significant correlation with absolute abundance of ARGs. Furthermore, significant correlation between ARGs and MGEs were also observed which demonstrates potential gene transfer among organisms through horizontal gene transfer via MGEs. ARGs showed strong positive correlation with cultivated and industrial lands whereas, negative correlation was observed with river, lake, forest, land for green buffer, and land for port and harbor. The overall results indicate that the inflow rivers of Taihu Lake are polluted by various sources including multiple nutrients and high abundance of ARGs, which needs attention for better management of the inflow rivers of this lake.}, }
@article {pmid36264827, year = {2022}, author = {Zürcher, JF and Robertson, WE and Kappes, T and Petris, G and Elliott, TS and Salmond, GPC and Chin, JW}, title = {Refactored genetic codes enable bidirectional genetic isolation.}, journal = {Science (New York, N.Y.)}, volume = {378}, number = {6619}, pages = {516-523}, pmid = {36264827}, issn = {1095-9203}, support = {MC_U105181009/MRC_/Medical Research Council/United Kingdom ; MC_UP_A024_1008/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Amino Acids/genetics ; *Codon/genetics ; Escherichia coli/genetics ; *Gene Transfer, Horizontal ; *Genetic Code ; Protein Biosynthesis/genetics ; Genome, Bacterial ; *Cell Engineering ; }, abstract = {The near-universal genetic code defines the correspondence between codons in genes and amino acids in proteins. We refactored the structure of the genetic code in Escherichia coli and created orthogonal genetic codes that restrict the escape of synthetic genetic information into natural life. We developed orthogonal and mutually orthogonal horizontal gene transfer systems, which permit the transfer of genetic information between organisms that use the same genetic code but restrict the transfer of genetic information between organisms that use different genetic codes. Moreover, we showed that locking refactored codes into synthetic organisms completely blocks invasion by mobile genetic elements, including viruses, which carry their own translation factors and successfully invade organisms with canonical and compressed genetic codes.}, }
@article {pmid36261788, year = {2022}, author = {Chong, SL and Tan, JL and Ngeow, YF}, title = {The resistomes of Mycobacteroides abscessus complex and their possible acquisition from horizontal gene transfer.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {715}, pmid = {36261788}, issn = {1471-2164}, mesh = {Humans ; *Mycobacterium abscessus/genetics ; Gene Transfer, Horizontal ; Phylogeny ; beta-Lactams ; Anti-Bacterial Agents ; Aminoglycosides ; }, abstract = {BACKGROUND: Mycobacteroides abscessus complex (MABC), an emerging pathogen, causes human infections resistant to multiple antibiotics. In this study, the genome data of 1,581 MABC strains were downloaded from NCBI database for phylogenetic relatedness inference, resistance profile identification and the estimation of evolutionary pressure on resistance genes in silico.<br><br>RESULTS: From genes associated with resistance to 28 antibiotic classes, 395 putative proteins (ARPs) were identified, based on the information in two antibiotic resistance databases (CARD and ARG-ANNOT). The ARPs most frequently identified in MABC were those associated with resistance to multiple antibiotic classes, beta-lactams and aminoglycosides. After excluding ARPs that had undergone recombination, two ARPs were predicted to be under diversifying selection and 202 under purifying selection. This wide occurrence of purifying selection suggested that the diversity of commonly shared ARPs in MABC have been reduced to achieve stability. The unequal distribution of ARPs in members of the MABC could be due to horizontal gene transfer or ARPs pseudogenization events. Most (81.5%) of the ARPs were observed in the accessory genome and 72.2% ARPs were highly homologous to proteins associated with mobile genetic elements such as plasmids, prophages and viruses. On the other hand, with TBLASTN search, only 18 of the ARPs were identified as pseudogenes.<br><br>CONCLUSION: Altogether, our results suggested an important role of horizontal gene transfer in shaping the resistome of MABC.}, }
@article {pmid36261510, year = {2023}, author = {Palomino, A and Gewurz, D and DeVine, L and Zajmi, U and Moralez, J and Abu-Rumman, F and Smith, RP and Lopatkin, AJ}, title = {Metabolic genes on conjugative plasmids are highly prevalent in Escherichia coli and can protect against antibiotic treatment.}, journal = {The ISME journal}, volume = {17}, number = {1}, pages = {151-162}, pmid = {36261510}, issn = {1751-7370}, support = {R15 GM143694/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Escherichia coli/genetics ; Anti-Bacterial Agents/pharmacology ; Plasmids/genetics ; *Escherichia coli Infections/microbiology ; Drug Resistance, Microbial/genetics ; Conjugation, Genetic ; Gene Transfer, Horizontal ; }, abstract = {Conjugative plasmids often encode antibiotic resistance genes that provide selective advantages to their bacterial hosts during antibiotic treatment. Previous studies have predominantly considered these established genes as the primary benefit of antibiotic-mediated plasmid dissemination. However, many genes involved in cellular metabolic processes may also protect against antibiotic treatment and provide selective advantages. Despite the diversity of such metabolic genes and their potential ecological impact, their plasmid-borne prevalence, co-occurrence with canonical antibiotic resistance genes, and phenotypic effects remain widely understudied. To address this gap, we focused on Escherichia coli, which can often act as a pathogen, and is known to spread antibiotic resistance genes via conjugation. We characterized the presence of metabolic genes on 1,775 transferrable plasmids and compared their distribution to that of known antibiotic resistance genes. We found high abundance of genes involved in cellular metabolism and stress response. Several of these genes demonstrated statistically significant associations or disassociations with known antibiotic resistance genes at the strain level, indicating that each gene type may impact the spread of the other across hosts. Indeed, in vitro characterization of 13 statistically relevant metabolic genes confirmed that their phenotypic impact on antibiotic susceptibility was largely consistent with in situ relationships. These results emphasize the ecological importance of metabolic genes on conjugal plasmids, and that selection dynamics of E. coli pathogens arises as a complex consequence of both canonical mechanisms and their interactions with metabolic pathways.}, }
@article {pmid36261416, year = {2022}, author = {Siddique, S and Radakovic, ZS and Hiltl, C and Pellegrin, C and Baum, TJ and Beasley, H and Bent, AF and Chitambo, O and Chopra, D and Danchin, EGJ and Grenier, E and Habash, SS and Hasan, MS and Helder, J and Hewezi, T and Holbein, J and Holterman, M and Janakowski, S and Koutsovoulos, GD and Kranse, OP and Lozano-Torres, JL and Maier, TR and Masonbrink, RE and Mendy, B and Riemer, E and Sobczak, M and Sonawala, U and Sterken, MG and Thorpe, P and van Steenbrugge, JJM and Zahid, N and Grundler, F and Eves-van den Akker, S}, title = {The genome and lifestage-specific transcriptomes of a plant-parasitic nematode and its host reveal susceptibility genes involved in trans-kingdom synthesis of vitamin B5.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {6190}, pmid = {36261416}, issn = {2041-1723}, support = {/WT_/Wellcome Trust/United Kingdom ; BB/N021908/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/S006397/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, mesh = {Animals ; *Parasites ; Pantothenic Acid ; Transcriptome ; *Tylenchida ; *Cysts ; }, abstract = {Plant-parasitic nematodes are a major threat to crop production in all agricultural systems. The scarcity of classical resistance genes highlights a pressing need to find new ways to develop nematode-resistant germplasm. Here, we sequence and assemble a high-quality phased genome of the model cyst nematode Heterodera schachtii to provide a platform for the first system-wide dual analysis of host and parasite gene expression over time, covering all major parasitism stages. Analysis of the hologenome of the plant-nematode infection site identified metabolic pathways that were incomplete in the parasite but complemented by the host. Using a combination of bioinformatic, genetic, and biochemical approaches, we show that a highly atypical completion of vitamin B5 biosynthesis by the parasitic animal, putatively enabled by a horizontal gene transfer from a bacterium, is required for full pathogenicity. Knockout of either plant-encoded or now nematode-encoded steps in the pathway significantly reduces parasitic success. Our experiments establish a reference for cyst nematodes, further our understanding of the evolution of plant-parasitism by nematodes, and show that congruent differential expression of metabolic pathways in the infection hologenome represents a new way to find nematode susceptibility genes. The approach identifies genome-editing-amenable targets for future development of nematode-resistant crops.}, }
@article {pmid36259734, year = {2022}, author = {Zhao, D and Zhang, S and Kumar, S and Zhou, H and Xue, Q and Sun, W and Zhou, J and Xiang, H}, title = {Comparative Genomic Insights into the Evolution of Halobacteria-Associated "Candidatus Nanohaloarchaeota".}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0066922}, pmid = {36259734}, issn = {2379-5077}, mesh = {*Euryarchaeota ; Phylogeny ; Halobacterium ; Archaea ; Genomics ; *Microbiota ; }, abstract = {Members of the phylum "Candidatus Nanohaloarchaeota," a representative lineage within the DPANN superphylum, are characterized by their nanosized cells and symbiotic lifestyle with Halobacteria. However, the development of the symbiosis remains unclear. Here, we propose two novel families, "Candidatus Nanoanaerosalinaceae" and "Candidatus Nanohalalkaliarchaeaceae" in "Ca. Nanohaloarchaeota," represented by five dereplicated metagenome-assembled genomes obtained from hypersaline sediments or related enrichment cultures of soda-saline lakes. Phylogenetic analyses reveal that the two novel families are placed at the root of the family "Candidatus Nanosalinaceae," including the cultivated taxa. The two novel families prefer hypersaline sediments, and the acid shift of predicted proteomes indicates a "salt-in" strategy for hypersaline adaptation. They contain a lower proportion of putative horizontal gene transfers from Halobacteria than "Ca. Nanosalinaceae," suggesting a weaker association with Halobacteria. Functional prediction and historical events reconstruction disclose that they exhibit divergent potentials in carbohydrate and organic acid metabolism and environmental responses. Globally, comparative genomic analyses based on the new families enrich the taxonomic and functional diversity of "Ca. Nanohaloarchaeota" and provide insights into the evolutionary process of "Ca. Nanohaloarchaeota" and their symbiotic relationship with Halobacteria. IMPORTANCE The DPANN superphylum is a group of archaea widely distributed in various habitats. They generally have small cells and have a symbiotic lifestyle with other archaea. The archaeal symbiotic interaction is vital to understanding microbial communities. However, the formation and evolution of the symbiosis between the DPANN lineages and other diverse archaea remain unclear. Based on phylogeny, habitat distribution, hypersaline adaptation, host prediction, functional potentials, and historical events of "Ca. Nanohaloarchaeota," a representative phylum within the DPANN superphylum, we report two novel families representing intermediate stages, and we infer the evolutionary process of "Ca. Nanohaloarchaeota" and their Halobacteria-associated symbiosis. Altogether, this research helps in understanding the evolution of symbiosis in "Ca. Nanohaloarchaeota" and provides a model for the evolution of other DPANN lineages.}, }
@article {pmid36256808, year = {2022}, author = {Eppley, JM and Biller, SJ and Luo, E and Burger, A and DeLong, EF}, title = {Marine viral particles reveal an expansive repertoire of phage-parasitizing mobile elements.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {43}, pages = {e2212722119}, pmid = {36256808}, issn = {1091-6490}, mesh = {*Bacteriophages/genetics ; Seawater/microbiology ; Oceans and Seas ; *Viruses/genetics ; Virion/genetics ; Genome, Viral/genetics ; }, abstract = {Phage satellites are mobile genetic elements that propagate by parasitizing bacteriophage replication. We report here the discovery of abundant and diverse phage satellites that were packaged as concatemeric repeats within naturally occurring bacteriophage particles in seawater. These same phage-parasitizing mobile elements were found integrated in the genomes of dominant co-occurring bacterioplankton species. Like known phage satellites, many marine phage satellites encoded genes for integration, DNA replication, phage interference, and capsid assembly. Many also contained distinctive gene suites indicative of unique virus hijacking, phage immunity, and mobilization mechanisms. Marine phage satellite sequences were widespread in local and global oceanic virioplankton populations, reflecting their ubiquity, abundance, and temporal persistence in marine planktonic communities worldwide. Their gene content and putative life cycles suggest they may impact host-cell phage immunity and defense, lateral gene transfer, bacteriophage-induced cell mortality and cellular host and virus productivity. Given that marine phage satellites cannot be distinguished from bona fide viral particles via commonly used microscopic techniques, their predicted numbers (∼3.2 × 10[26] in the ocean) may influence current estimates of virus densities, production, and virus-induced mortality. In total, the data suggest that marine phage satellites have potential to significantly impact the ecology and evolution of bacteria and their viruses throughout the oceans. We predict that any habitat that harbors bacteriophage will also harbor similar phage satellites, making them a ubiquitous feature of most microbiomes on Earth.}, }
@article {pmid36255244, year = {2022}, author = {Zhu, N and Sun, S and Leng, F and Fan, W and Chen, J and Ma, J and He, H and Yang, G and Wang, Y}, title = {Identification of Key Genes during Ca[2+]-Induced Genetic Transformation in Escherichia coli by Combining Multi-Omics and Gene Knockout Techniques.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {21}, pages = {e0058722}, pmid = {36255244}, issn = {1098-5336}, mesh = {*Escherichia coli/genetics ; Gene Knockout Techniques ; Plasmids ; *Gene Transfer, Horizontal ; Transformation, Genetic ; }, abstract = {The molecular mechanism of the Ca[2+]-mediated formation of competent cells in Escherichia coli remains unclear. In this study, transcriptome and proteomics techniques were used to screen genes in response to Ca[2+] treatment. A total of 333 differentially expressed genes (317 upregulated and 16 downregulated) and 145 differentially expressed proteins (54 upregulated and 91 downregulated) were obtained. These genes and proteins are mainly enriched in cell membrane components, transmembrane transport, and stress response-related functional terms. Fifteen genes with these functions, including yiaW, ygiZ, and osmB, are speculated to play a key role in the cellular response to Ca[2+]. Three single-gene deletion strains were constructed with the Red homologous recombination method to verify its function in genetic transformation. The transformation efficiencies of yiaW, ygiZ, and osmB deletion strains for different-size plasmids were significantly increased. None of the three gene deletion strains changed in size, which is one of the main elements of microscopic morphology, but they exhibited different membrane permeabilities and transformation efficiencies. This study demonstrates that Ca[2+]-mediated competence formation in E. coli is not a simple physicochemical process and may involve the regulation of genes in response to Ca[2+]. This study lays the foundation for further in-depth analyses of the molecular mechanism of Ca[2+]-mediated transformation. IMPORTANCE Using transcriptome and proteome techniques and association analysis, we identified several key genes involved in the formation of Ca[2+]-mediated E. coli DH5α competent cells. We used Red homologous recombination technology to construct three single-gene deletion strains and found that the transformation efficiencies of yiaW, ygiZ, and osmB deletion strains for different-size plasmids were significantly increased. These results proved that the genetic transformation process is not only a physicochemical process but also a reaction process involving multiple genes. These results suggest ways to improve the horizontal gene transfer mechanism of foodborne microorganisms and provide new ideas for ensuring the safety of food preservation and processing.}, }
@article {pmid36252757, year = {2022}, author = {Li, S and Gao, M and Dong, H and Jiang, Y and Liang, W and Jiang, J and Ho, SH and Li, F}, title = {Deciphering the fate of antibiotic resistance genes in norfloxacin wastewater treated by a bio-electro-Fenton system.}, journal = {Bioresource technology}, volume = {364}, number = {}, pages = {128110}, doi = {10.1016/j.biortech.2022.128110}, pmid = {36252757}, issn = {1873-2976}, abstract = {The misuse of antibiotics has increased the prevalence of antibiotic resistance genes (ARGs), considered a class of critical environmental contaminants due to their ubiquitous and persistent nature. Previous studies reported the potentiality of bio-electro-Fenton processes for antibiotic removal and ARGs control. However, the production and fate of ARGs in bio-electro-Fenton processes triggered by microbial fuel cells are rare. In this study, the norfloxacin (NFLX) average residual concentrations within two days were 2.02, 6.07 and 14.84 mg/L, and the average removal efficiency of NFLX was 79.8 %, 69.6 % and 62.9 % at the initial antibiotic concentrations of 10, 20 and 40 mg/L, respectively. The most prevalent resistance gene type in all processes was the fluoroquinolone antibiotic gene. Furthermore, Proteobacteria was the dominant ARG-carrying bacteria. Overall, this study can provide theoretical support for the efficient treatment of high antibiotics-contained wastewater by bio-electro-Fenton systems to better control ARGs from the perspective of ecological security.}, }
@article {pmid36251935, year = {2022}, author = {Lu, J and Yu, Z and Ding, P and Guo, J}, title = {Triclosan Promotes Conjugative Transfer of Antibiotic Resistance Genes to Opportunistic Pathogens in Environmental Microbiome.}, journal = {Environmental science &amp; technology}, volume = {56}, number = {21}, pages = {15108-15119}, doi = {10.1021/acs.est.2c05537}, pmid = {36251935}, issn = {1520-5851}, mesh = {Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Microbiota ; Plasmids ; RNA, Ribosomal, 16S/genetics ; Sewage/microbiology ; *Triclosan/pharmacology ; }, abstract = {Although triclosan, as a widely used antiseptic chemical, is known to promote the transmission of antibiotic resistance to diverse hosts in pure culture, it is still unclear whether and how triclosan could affect the transmission of broad-host-range plasmids among complex microbial communities. Here, bacterial culturing, fluorescence-based cell sorting, and high-throughput 16S rRNA gene amplicon sequencing were combined to investigate contributions of triclosan on the transfer rate and range of an IncP-type plasmid from a proteobacterial donor to an activated sludge microbiome. Our results demonstrate that triclosan significantly enhances the conjugative transfer of the RP4 plasmid among activated sludge communities at environmentally relevant concentrations. High-throughput 16S rRNA gene sequencing on sorted transconjugants demonstrates that triclosan not only promoted the intergenera transfer but also the intragenera transfer of the RP4 plasmid among activated sludge communities. Moreover, triclosan mediated the transfer of the RP4 plasmid to opportunistic human pathogens, for example, Legionella spp. The mechanism of triclosan-mediated conjugative transfer is primarily associated with excessive oxidative stress, followed by increased membrane permeability and provoked SOS response. Our findings offer insights into the impacts of triclosan on the dissemination of antibiotic resistance in the aquatic environmental microbiome.}, }
@article {pmid36246261, year = {2022}, author = {Dela Ahator, S and Liu, Y and Wang, J and Zhang, LH}, title = {The virulence factor regulator and quorum sensing regulate the type I-F CRISPR-Cas mediated horizontal gene transfer in Pseudomonas aeruginosa.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {987656}, pmid = {36246261}, issn = {1664-302X}, abstract = {Pseudomonas aeruginosa is capable of thriving in diverse environments due to its network of regulatory components for effective response to stress factors. The survival of the bacteria is also dependent on the ability to discriminate between the acquisition of beneficial and non-beneficial genetic materials via horizontal gene transfer (HGT). Thus, bacteria have evolved the CRISPR-Cas adaptive immune system for defense against the deleterious effect of phage infection and HGT. By using the transposon mutagenesis approach, we identified the virulence factor regulator (Vfr) as a key regulator of the type I-F CRISPR-Cas system in P. aeruginosa. We showed that Vfr influences the expression of the CRISPR-Cas system through two signaling pathways in response to changes in calcium levels. Under calcium-rich conditions, Vfr indirectly regulates the CRISPR-Cas system via modulation of the AHL-QS gene expression, which could be vital for defense against phage infection at high cell density. When encountering calcium deficiency, however, Vfr can directly regulate the CRISPR-Cas system via a cAMP-dependent pathway. Furthermore, we provide evidence that mutation of vfr reduces the CRISPR-Cas spacer acquisition and interference of HGT. The results from this study add to the regulatory network of factors controlling the CRISPR-Cas system in response to abiotic factors in the environment. The findings may facilitate the design of effective and reliable phage therapies against P. aeruginosa infections, as targeting Vfr could prevent the development of the CRISPR-Cas mediated phage resistance.}, }
@article {pmid36244140, year = {2022}, author = {Liu, J and Bao, Z and Wang, C and Wei, J and Wei, Y and Chen, M}, title = {Understanding of mercury and methylmercury transformation in sludge composting by metagenomic analysis.}, journal = {Water research}, volume = {226}, number = {}, pages = {119204}, doi = {10.1016/j.watres.2022.119204}, pmid = {36244140}, issn = {1879-2448}, mesh = {*Methylmercury Compounds ; *Mercury ; Sewage ; *Composting ; Metagenome ; Bacteria/genetics/metabolism ; Bacteroidetes ; }, abstract = {Municipal sewage especially the produced sewage sludge is a significant source releasing mercury (Hg) to the environment. However, the Hg speciation especially methylmercury (MeHg) transformation in sewage sludge treatment process remains poorly understood. This study investigated the transformation of Hg speciation especially MeHg in sludge composting. The distribution of Hg transformation related gene pairs hgcAB and merAB, and their putative microbial hosts were comprehensively analyzed. Both Hg (from 3.16±0.22 mg/kg to 3.20±0.19 mg/kg) and MeHg content (from 4.77±0.64 ng/g to 4.36±0.37 ng/g) were not obviously changed before and after composting, but about 19.69% of Hg and 27.36% of MeHg were lost according to mass balance calculation. The metagenomic analysis further revealed that anaerobes (Desulfobacterota and Euryarchaeota) were the mainly putative Hg methylators especially carrying high abundance of hgcA gene in the initial periods of composting. Among the 151 reconstructed metagenome-assembled genomes (MAGs), only 4 hgcA gene carriers (Myxococcota, Firmicutes, Cyclobacteriaceae, and Methanothermobacter) and 16 merB gene carriers were identified. But almost all of the MAGs carried hgcB gene and merA gene. The merA gene was widely distributed in genomes, which indicated the widespread functionality of microbes for reducing Hg(II) to Hg(0). The hgcA carrying microbes tends to present the similar metabolic pathways including methanogenesis and sulfur metabolism. Besides, both the irregular distribution of hgcA in various species (including Actinobacteria, Archaea, Bacteroidetes, Desulfobacterota, Euryarchaeota, and Nitrospirae, etc.) and opposite evolution trends between hgcA gene abundance and its host genome abundance can be an indication of horizontal gene transfer or gene deletions of hgcA during composting. Our findings thus revealed that sludge composting is not only a hotspot for Hg speciation transformation, but also a potential hotspot for MeHg transformation.}, }
@article {pmid36243187, year = {2022}, author = {Yun, Y and Su, T and Gui, Z and Tian, X and Chen, Y and Cao, Y and Yang, S and Xie, J and Anwar, N and Li, M and Li, G and Ma, T}, title = {Stress-responses of microbes in oil reservoir under high tetracycline exposure and their environmental risks.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {315}, number = {}, pages = {120355}, doi = {10.1016/j.envpol.2022.120355}, pmid = {36243187}, issn = {1873-6424}, mesh = {*Oil and Gas Fields ; Genes, Bacterial ; RNA, Ribosomal, 16S ; Tetracycline ; Anti-Bacterial Agents/analysis ; *Microbiota ; }, abstract = {As the groundwater ecosystem is connected with surface, antibiotics and antibiotic resistance genes (ARGs) in aquatic environments will gradually infiltrate into the deep environment, posing a potential threat to groundwater ecosystem. However, knowledge on the environmental risk of antibiotics and ARGs in groundwater ecosystem and their ecological process still remains unexplored. In this study, lab-scale oil reservoirs under high tetracycline stress were performed to evaluate the dynamics of microbial communities, ARGs and potential functions by using 16S rRNA gene sequencing and metagenomics analysis. Although the presence of antibiotics remarkably reduced the microbial abundance and diversity in a short term, but remain stable or even increased after a long-term incubation. Antibiotic stress caused a greater diversity and abundance of ARGs, and higher numbers of ARGs-related species with the capacity to transfer ARGs to other microbes through horizontal gene transfer. Thus, a much more frequent associations of microbial community at both node- and network-level and a selective pressure on enrichment of antibiotic resistant bacteria related to "anaerobic n-alkane degradation" and "methylotrophic methanogenesis" were observed. It is important to emphasize that high antibiotic stress could also prevent some microbes related to "Sulfate reduction", "Fe(II) oxidation", "Nitrate reduction", and "Xylene and Toluene degradation". This study provides an insight into the long-term stress-responses of microbial communities and functions in oil reservoir under tetracycline exposure, which may help to elucidate the effect of antibiotic stress on biogeochemical cycling with microbial involvement in groundwater ecosystem.}, }
@article {pmid36228898, year = {2023}, author = {Yuasa, HJ}, title = {Metazoan tryptophan indole-lyase: Are they still active?.}, journal = {Comparative biochemistry and physiology. Part B, Biochemistry &amp; molecular biology}, volume = {263}, number = {}, pages = {110801}, doi = {10.1016/j.cbpb.2022.110801}, pmid = {36228898}, issn = {1879-1107}, abstract = {Tryptophan indole-lyase (TIL), also known as tryptophanase, is a pyridoxal-5'-phosphate dependent bacterial enzyme that catalyzes the reversible hydrolytic cleavage of l-tryptophan (l-Trp) to indole and ammonium pyruvate. TIL is also found in some metazoans, and they may have been acquired by horizontal gene transfer. In this study, two metazoans, Nematostella vectensis (starlet sea anemone) and Bradysia coprophila (fungus gnat) TILs were bacterially expressed and characterized. The kcat values of metazoan TILs were low, < 1/200 of the kcat of Escherichia coli TIL. By contrast, metazoan TILs showed lower Km values than the TILs of common bacteria, indicating that their affinity for l-Trp is higher than that of bacterial TILs. Analysis of a series of chimeric enzymes based on B. coprophila and bacterial TILs revealed that the low Km value of B. coprophila TIL is not accidental due to the substitution of a single residue, but is due to the cooperative effect of multiple residues. This suggests that high affinity for l-Trp was positively selected during the molecular evolution of metazoan TIL. This is the first report that metazoan TILs have low but obvious activity.}, }
@article {pmid36228885, year = {2022}, author = {Al Mamun, AAM and Kissoon, K and Kishida, K and Shropshire, WC and Hanson, B and Christie, PJ}, title = {IncFV plasmid pED208: Sequence analysis and evidence for translocation of maintenance/leading region proteins through diverse type IV secretion systems.}, journal = {Plasmid}, volume = {123-124}, number = {}, pages = {102652}, pmid = {36228885}, issn = {1095-9890}, support = {K01 AI148593/AI/NIAID NIH HHS/United States ; R01 GM048746/GM/NIGMS NIH HHS/United States ; R21 AI159970/AI/NIAID NIH HHS/United States ; R35 GM131892/GM/NIGMS NIH HHS/United States ; }, mesh = {*Type IV Secretion Systems/genetics ; Plasmids/genetics ; *Escherichia coli/genetics ; F Factor ; Sequence Analysis ; Conjugation, Genetic ; Bacterial Proteins/metabolism ; }, abstract = {Two phylogenetically distantly-related IncF plasmids, F and pED208, serve as important models for mechanistic and structural studies of F-like type IV secretion systems (T4SSFs) and F pili. Here, we present the pED208 sequence and compare it to F and pUMNF18, the closest match to pED208 in the NCBI database. As expected, gene content of the three cargo regions varies extensively, although the maintenance/leading regions (MLRs) and transfer (Tra) regions also carry novel genes or motifs with predicted modulatory effects on plasmid stability, dissemination and host range. By use of a Cre recombinase assay for translocation (CRAfT), we recently reported that pED208-carrying donors translocate several products of the MLR (ParA, ParB1, ParB2, SSB, PsiB, PsiA) intercellularly through the T4SSF. Here, we extend these findings by reporting that pED208-carrying donors translocate 10 additional MLR proteins during conjugation. In contrast, two F plasmid-encoded toxin components of toxin-antitoxin (TA) modules, CcdB and SrnB, were not translocated at detectable levels through the T4SSF. Remarkably, most or all of the pED208-encoded MLR proteins and CcdB and SrnB were translocated through heterologous T4SSs encoded by IncN and IncP plasmids pKM101 and RP4, respectively. Together, our sequence analyses underscore the genomic diversity of the F plasmid superfamily, and our experimental data demonstrate the promiscuous nature of conjugation machines for protein translocation. Our findings raise intriguing questions about the nature of T4SS translocation signals and of the biological and evolutionary consequences of conjugative protein transfer.}, }
@article {pmid36227733, year = {2022}, author = {Acar Kirit, H and Bollback, JP and Lagator, M}, title = {The Role of the Environment in Horizontal Gene Transfer.}, journal = {Molecular biology and evolution}, volume = {39}, number = {11}, pages = {}, pmid = {36227733}, issn = {1537-1719}, support = {/WT_/Wellcome Trust/United Kingdom ; 216779/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Gene Transfer, Horizontal ; *Escherichia coli/genetics ; Salmonella typhimurium/genetics ; Bacteria/genetics ; Environment ; }, abstract = {Gene-by-environment interactions play a crucial role in horizontal gene transfer by affecting how the transferred genes alter host fitness. However, how the environment modulates the fitness effect of transferred genes has not been tested systematically in an experimental study. We adapted a high-throughput technique for obtaining very precise estimates of bacterial fitness, in order to measure the fitness effects of 44 orthologs transferred from Salmonella Typhimurium to Escherichia coli in six physiologically relevant environments. We found that the fitness effects of individual genes were highly dependent on the environment, while the distributions of fitness effects across genes were not, with all tested environments resulting in distributions of same shape and spread. Furthermore, the extent to which the fitness effects of a gene varied between environments depended on the average fitness effect of that gene across all environments, with nearly neutral and nearly lethal genes having more consistent fitness effects across all environments compared to deleterious genes. Put together, our results reveal the unpredictable nature of how environmental conditions impact the fitness effects of each individual gene. At the same time, distributions of fitness effects across environments exhibit consistent features, pointing to the generalizability of factors that shape horizontal gene transfer of orthologous genes.}, }
@article {pmid36226968, year = {2022}, author = {Jana, B and Keppel, K and Fridman, CM and Bosis, E and Salomon, D}, title = {Multiple T6SSs, Mobile Auxiliary Modules, and Effectors Revealed in a Systematic Analysis of the Vibrio parahaemolyticus Pan-Genome.}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0072322}, pmid = {36226968}, issn = {2379-5077}, mesh = {Animals ; Humans ; *Type VI Secretion Systems/genetics ; *Vibrio parahaemolyticus/genetics ; Bacterial Proteins/genetics ; Bacteria/metabolism ; Anti-Bacterial Agents/metabolism ; }, abstract = {Type VI secretion systems (T6SSs) play a major role in interbacterial competition and in bacterial interactions with eukaryotic cells. The distribution of T6SSs and the effectors they secrete vary between strains of the same bacterial species. Therefore, a pan-genome investigation is required to better understand the T6SS potential of a bacterial species of interest. Here, we performed a comprehensive, systematic analysis of T6SS gene clusters and auxiliary modules found in the pan-genome of Vibrio parahaemolyticus, an emerging pathogen widespread in marine environments. We identified 4 different T6SS gene clusters within genomes of this species; two systems appear to be ancient and widespread, whereas the other 2 systems are rare and appear to have been more recently acquired via horizontal gene transfer. In addition, we identified diverse T6SS auxiliary modules containing putative effectors with either known or predicted toxin domains. Many auxiliary modules are possibly horizontally shared between V. parahaemolyticus genomes, since they are flanked by DNA mobility genes. We further investigated a DUF4225-containing protein encoded on an Hcp auxiliary module, and we showed that it is an antibacterial T6SS effector that exerts its toxicity in the bacterial periplasm, leading to cell lysis. Computational analyses of DUF4225 revealed a widespread toxin domain associated with various toxin delivery systems. Taken together, our findings reveal a diverse repertoire of T6SSs and auxiliary modules in the V. parahaemolyticus pan-genome, as well as novel T6SS effectors and toxin domains that can play a major role in the interactions of this species with other cells. IMPORTANCE Gram-negative bacteria employ toxin delivery systems to mediate their interactions with neighboring cells. Vibrio parahaemolyticus, an emerging pathogen of humans and marine animals, was shown to deploy antibacterial toxins into competing bacteria via the type VI secretion system (T6SS). Here, we analyzed 1,727 V. parahaemolyticus genomes and revealed the pan-genome T6SS repertoire of this species, including the T6SS gene clusters, horizontally shared auxiliary modules, and toxins. We also identified a role for a previously uncharacterized domain, DUF4225, as a widespread antibacterial toxin associated with diverse toxin delivery systems.}, }
@article {pmid36224268, year = {2023}, author = {Rathmann, I and Förster, M and Yüksel, M and Horst, L and Petrungaro, G and Bollenbach, T and Maier, B}, title = {Distribution of fitness effects of cross-species transformation reveals potential for fast adaptive evolution.}, journal = {The ISME journal}, volume = {17}, number = {1}, pages = {130-139}, pmid = {36224268}, issn = {1751-7370}, mesh = {*Gene Transfer, Horizontal ; *Bacillus subtilis/genetics ; Adaptation, Physiological ; }, abstract = {Bacterial transformation, a common mechanism of horizontal gene transfer, can speed up adaptive evolution. How its costs and benefits depend on the growth environment is poorly understood. Here, we characterize the distributions of fitness effects (DFE) of transformation in different conditions and test whether they predict in which condition transformation is beneficial. To determine the DFEs, we generate hybrid libraries between the recipient Bacillus subtilis and different donor species and measure the selection coefficient of each hybrid strain. In complex medium, the donor Bacillus vallismortis confers larger fitness effects than the more closely related donor Bacillus spizizenii. For both donors, the DFEs show strong effect beneficial transfers, indicating potential for fast adaptive evolution. While some transfers of B. vallismortis DNA show pleiotropic effects, various transfers are beneficial only under a single growth condition, indicating that the recipient can benefit from a variety of donor genes to adapt to varying growth conditions. We scrutinize the predictive value of the DFEs by laboratory evolution under different growth conditions and show that the DFEs correctly predict the condition at which transformation confers a benefit. We conclude that transformation has a strong potential for speeding up adaptation to varying environments by profiting from a gene pool shared between closely related species.}, }
@article {pmid36223775, year = {2022}, author = {Wang, B and Pandey, T and Long, Y and Delgado-Rodriguez, SE and Daugherty, MD and Ma, DK}, title = {Co-opted genes of algal origin protect C. elegans against cyanogenic toxins.}, journal = {Current biology : CB}, volume = {32}, number = {22}, pages = {4941-4948.e3}, pmid = {36223775}, issn = {1879-0445}, support = {P40 OD010440/OD/NIH HHS/United States ; R35 GM133633/GM/NIGMS NIH HHS/United States ; R35 GM139618/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Caenorhabditis elegans/genetics/metabolism ; *Amygdalin/metabolism ; Phylogeny ; *Caenorhabditis elegans Proteins/metabolism ; Cyanides/metabolism ; }, abstract = {Amygdalin is a cyanogenic glycoside enriched in the tissues of many edible plants, including seeds of stone fruits such as cherry (Prunus avium), peach (Prunus persica), and apple (Malus domestica). These plants biosynthesize amygdalin in defense against herbivore animals, as amygdalin generates poisonous cyanide upon plant tissue destruction.[1][,][2][,][3][,][4] Poisonous to many animals, amygdalin-derived cyanide is detoxified by potent enzymes commonly found in bacteria and plants but not most animals.[5] Here we show that the nematode C. elegans can detoxify amygdalin by a genetic pathway comprising cysl-1, egl-9, hif-1, and cysl-2. A screen of a natural product library for hypoxia-independent regulators of HIF-1 identifies amygdalin as a potent activator of cysl-2, a HIF-1 transcriptional target that encodes a cyanide detoxification enzyme in C. elegans. As a cysl-2 paralog similarly essential for amygdalin resistance, cysl-1 encodes a protein homologous to cysteine biosynthetic enzymes in bacteria and plants but functionally co-opted in C. elegans. We identify exclusively HIF-activating egl-9 mutations in a cysl-1 suppressor screen and show that cysl-1 confers amygdalin resistance by regulating HIF-1-dependent cysl-2 transcription to protect against amygdalin toxicity. Phylogenetic analysis indicates that cysl-1 and cysl-2 were likely acquired from green algae through horizontal gene transfer (HGT) and functionally co-opted in protection against amygdalin. Since acquisition, these two genes evolved division of labor in a cellular circuit to detect and detoxify cyanide. Thus, algae-to-nematode HGT and subsequent gene function co-option events may facilitate host survival and adaptation to adverse environmental stresses and biogenic toxins.}, }
@article {pmid36215219, year = {2022}, author = {Ali, A and Imran, M and Sial, S and Khan, A}, title = {Effective antibiotic dosing in the presence of resistant strains.}, journal = {PloS one}, volume = {17}, number = {10}, pages = {e0275762}, pmid = {36215219}, issn = {1932-6203}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Bacteria ; Follow-Up Studies ; Gene Transfer, Horizontal ; Models, Theoretical ; }, abstract = {Mathematical models can be very useful in determining efficient and successful antibiotic dosing regimens. In this study, we consider the problem of determining optimal antibiotic dosing when bacteria resistant to antibiotics are present in addition to susceptible bacteria. We consider two different models of resistance acquisition, both involve the horizontal transfer (HGT) of resistant genes from a resistant to a susceptible strain. Modeling studies on HGT and study of optimal antibiotic dosing protocols in the literature, have been mostly focused on transfer of resistant genes via conjugation, with few studies on HGT via transformation. We propose a deterministic ODE based model of resistance acquisition via transformation, followed by a model that takes into account resistance acquisition through conjugation. Using a numerical optimization algorithm to determine the 'best' antibiotic dosing strategy. To illustrate our optimization method, we first consider optimal dosing when all the bacteria are susceptible to the antibiotic. We then consider the case where resistant strains are present. We note that constant periodic dosing may not always succeed in eradicating the bacteria while an optimal dosing protocol is successful. We determine the optimal dosing strategy in two different scenarios: one where the total bacterial population is to be minimized, and the next where we want to minimize the bacterial population at the end of the dosing period. We observe that the optimal strategy in the first case involves high initial dosing with dose tapering as time goes on, while in the second case, the optimal dosing strategy is to increase the dosing at the beginning of the dose cycles followed by a possible dose tapering. As a follow up study we intend to look at models where 'persistent' bacteria may be present in additional to resistant and susceptible strain and determine the optimal dosing protocols in this case.}, }
@article {pmid36214559, year = {2022}, author = {Matilla, MA and Monson, RE and Murphy, A and Schicketanz, M and Rawlinson, A and Duncan, C and Mata, J and Leeper, F and Salmond, GPC}, title = {Solanimycin: Biosynthesis and Distribution of a New Antifungal Antibiotic Regulated by Two Quorum-Sensing Systems.}, journal = {mBio}, volume = {13}, number = {6}, pages = {e0247222}, pmid = {36214559}, issn = {2150-7511}, support = {BB/N008081/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Humans ; *Antifungal Agents/metabolism ; Phylogeny ; *Bacteria/metabolism ; Enterobacteriaceae/genetics ; Fungi/metabolism ; Anti-Bacterial Agents/metabolism ; }, abstract = {The increasing emergence of drug-resistant fungal infections has necessitated a search for new compounds capable of combating fungal pathogens of plants, animals, and humans. Microorganisms represent the main source of antibiotics with applicability in agriculture and in the clinic, but many aspects of their metabolic potential remain to be explored. This report describes the discovery and characterization of a new antifungal compound, solanimycin, produced by a hybrid polyketide/nonribosomal peptide (PKS/NRPS) system in Dickeya solani, the enterobacterial pathogen of potato. Solanimycin was active against a broad range of plant-pathogenic fungi of global economic concern and the human pathogen Candida albicans. The genomic cluster responsible for solanimycin production was defined and analyzed to identify the corresponding biosynthetic proteins, which include four multimodular PKS/NRPS proteins and several tailoring enzymes. Antifungal production in D. solani was enhanced in response to experimental conditions found in infected potato tubers and high-density fungal cultures. Solanimycin biosynthesis was cell density dependent in D. solani and was controlled by both the ExpIR acyl-homoserine lactone and Vfm quorum-sensing systems of the bacterial phytopathogen. The expression of the solanimycin cluster was also regulated at the post-transcriptional level, with the regulator RsmA playing a major role. The solanimycin biosynthetic cluster was conserved across phylogenetically distant bacterial genera, and multiple pieces of evidence support that the corresponding gene clusters were acquired by horizontal gene transfer. Given its potent broad-range antifungal properties, this study suggests that solanimycin and related molecules may have potential utility for agricultural and clinical exploitation. IMPORTANCE Fungal infections represent a major clinical, agricultural, and food security threat worldwide, which is accentuated due to the difficult treatment of these infections. Microorganisms represent a prolific source of antibiotics, and current data support that this enormous biosynthetic potential has been scarcely explored. To improve the performance in the discovery of novel antimicrobials, there is a need to diversify the isolation niches for new antibiotic-producing microorganisms as well as to scrutinize novel phylogenetic positions. With the identification of the antifungal antibiotic solanimycin in a broad diversity of phytopathogenic Dickeya spp., we provide further support for the potential of plant-associated bacteria for the biosynthesis of novel antimicrobials. The complex regulatory networks involved in solanimycin production reflect the high metabolic cost of bacterial secondary metabolism. This metabolic regulatory control makes many antibiotics cryptic under standard laboratory conditions, and mimicking environmental conditions, as shown here, is a strategy to activate cryptic antibiotic clusters.}, }
@article {pmid36214558, year = {2022}, author = {Suchland, RJ and Carrell, SJ and Ramsey, SA and Hybiske, K and Debrine, AM and Sanchez, J and Celum, C and Rockey, DD}, title = {Genomic Analysis of MSM Rectal Chlamydia trachomatis Isolates Identifies Predicted Tissue-Tropic Lineages Generated by Intraspecies Lateral Gene Transfer-Mediated Evolution.}, journal = {Infection and immunity}, volume = {90}, number = {11}, pages = {e0026522}, pmid = {36214558}, issn = {1098-5522}, support = {R01 AI126785/AI/NIAID NIH HHS/United States ; R03 AI156514/AI/NIAID NIH HHS/United States ; R21 AI144865/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Male ; *Chlamydia Infections/microbiology ; Chlamydia trachomatis/genetics ; Gene Transfer, Horizontal ; Genome-Wide Association Study ; Genomics ; *Homosexuality, Male ; }, abstract = {Chlamydia trachomatis is an obligate intracellular bacterium that causes serious diseases in humans. Rectal infection and disease caused by this pathogen are important yet understudied aspects of C. trachomatis natural history. The University of Washington Chlamydia Repository has a large collection of male-rectal-sourced strains (MSM rectal strains) isolated in Seattle, USA and Lima, Peru. Initial characterization of strains collected over 30 years in both Seattle and Lima led to an association of serovars G and J with male rectal infections. Serovar D, E, and F strains were also collected from MSM patients. Genome sequence analysis of a subset of MSM rectal strains identified a clade of serovar G and J strains that had high overall genomic identity. A genome-wide association study was then used to identify genomic loci that were correlated with tissue tropism in a collection of serovar-matched male rectal and female cervical strains. The polymorphic membrane protein PmpE had the strongest correlation, and amino acid sequence alignments identified a set of PmpE variable regions (VRs) that were correlated with host or tissue tropism. Examination of the positions of VRs by the protein structure-predicting Alphafold2 algorithm demonstrated that the VRs were often present in predicted surface-exposed loops in both PmpE and PmpH protein structure. Collectively, these studies identify possible tropism-predictive loci for MSM rectal C. trachomatis infections and identify predicted surface-exposed variable regions of Pmp proteins that may function in MSM rectal versus cervical tropism differences.}, }
@article {pmid36212863, year = {2022}, author = {Han, B and Ma, L and Yu, Q and Yang, J and Su, W and Hilal, MG and Li, X and Zhang, S and Li, H}, title = {The source, fate and prospect of antibiotic resistance genes in soil: A review.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {976657}, pmid = {36212863}, issn = {1664-302X}, abstract = {Antibiotic resistance genes (ARGs), environmental pollutants of emerging concern, have posed a potential threat to the public health. Soil is one of the huge reservoirs and propagation hotspot of ARGs. To alleviate the potential risk of ARGs, it is necessary to figure out the source and fate of ARGs in the soil. This paper mainly reviewed recent studies on the association of ARGs with the microbiome and the transmission mechanism of ARGs in soil. The compositions and abundance of ARGs can be changed by modulating microbiome, soil physicochemical properties, such as pH and moisture. The relationships of ARGs with antibiotics, heavy metals, polycyclic aromatic hydrocarbons and pesticides were discussed in this review. Among the various factors mentioned above, microbial community structure, mobile genetic elements, pH and heavy metals have a relatively more important impact on ARGs profiles. Moreover, human health could be impacted by soil ARGs through plants and animals. Understanding the dynamic changes of ARGs with influencing factors promotes us to develop strategies for mitigating the occurrence and dissemination of ARGs to reduce health risks.}, }
@article {pmid36212841, year = {2022}, author = {Neira, G and Vergara, E and Holmes, DS}, title = {Genome-guided prediction of acid resistance mechanisms in acidophilic methanotrophs of phylogenetically deep-rooted Verrucomicrobia isolated from geothermal environments.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {900531}, pmid = {36212841}, issn = {1664-302X}, abstract = {Verrucomicrobia are a group of microorganisms that have been proposed to be deeply rooted in the Tree of Life. Some are methanotrophs that oxidize the potent greenhouse gas methane and are thus important in decreasing atmospheric concentrations of the gas, potentially ameliorating climate change. They are widespread in various environments including soil and fresh or marine waters. Recently, a clade of extremely acidophilic Verrucomicrobia, flourishing at pH < 3, were described from high-temperature geothermal ecosystems. This novel group could be of interest for studies about the emergence of life on Earth and to astrobiologists as homologs for possible extraterrestrial life. In this paper, we describe predicted mechanisms for survival of this clade at low pH and suggest its possible evolutionary trajectory from an inferred neutrophilic ancestor. Extreme acidophiles are defined as organisms that thrive in extremely low pH environments (≤ pH 3). Many are polyextremophiles facing high temperatures and high salt as well as low pH. They are important to study for both providing fundamental insights into biological mechanisms of survival and evolution in such extreme environments and for understanding their roles in biotechnological applications such as industrial mineral recovery (bioleaching) and mitigation of acid mine drainage. They are also, potentially, a rich source of novel genes and pathways for the genetic engineering of microbial strains. Acidophiles of the Verrucomicrobia phylum are unique as they are the only known aerobic methanotrophs that can grow optimally under acidic (pH 2-3) and moderately thermophilic conditions (50-60°C). Three moderately thermophilic genera, namely Methylacidiphilum, Methylacidimicrobium, and Ca. Methylacidithermus, have been described in geothermal environments. Most of the investigations of these organisms have focused on their methane oxidizing capabilities (methanotrophy) and use of lanthanides as a protein cofactor, with no extensive study that sheds light on the mechanisms that they use to flourish at extremely low pH. In this paper, we extend the phylogenetic description of this group of acidophiles using whole genome information and we identify several mechanisms, potentially involved in acid resistance, including "first line of defense" mechanisms that impede the entry of protons into the cell. These include the presence of membrane-associated hopanoids, multiple copies of the outer membrane protein (Slp), and inner membrane potassium channels (kup, kdp) that generate a reversed membrane potential repelling the intrusion of protons. Acidophilic Verrucomicrobia also display a wide array of proteins potentially involved in the "second line of defense" where protons that evaded the first line of defense and entered the cell are expelled or neutralized, such as the glutamate decarboxylation (gadAB) and phosphate-uptake systems. An exclusive N-type ATPase F0-F1 was identified only in acidophiles of Verrucomicrobia and is predicted to be a specific adaptation in these organisms. Phylogenetic analyses suggest that many predicted mechanisms are evolutionarily conserved and most likely entered the acidophilic lineage of Verrucomicrobia by vertical descent from a common ancestor. However, it is likely that some defense mechanisms such as gadA and kup entered the acidophilic Verrucomicrobia lineage by horizontal gene transfer.}, }
@article {pmid36212306, year = {2022}, author = {Zhong, Y and Yu, R and Chen, J and Liu, Y and Zhou, R}, title = {Highly active repeat-mediated recombination in the mitogenome of the holoparasitic plant Aeginetia indica.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {988368}, pmid = {36212306}, issn = {1664-462X}, abstract = {Mitogenomes of most flowering plants evolve slowly in sequence, but rapidly in structure. The rearrangements in structure are mainly caused by repeat-mediated recombination. However, patterns of repeat-mediated recombination vary substantially among plants, and to provide a comprehensive picture, characterization of repeat-mediated recombination should extend to more plant species, including parasitic plants with a distinct heterotrophic lifestyle. Here we assembled the mitogenome of the holoparasitic plant Aeginetia indica (Orobanchaceae) using Illumina sequencing reads. The mitogenome was assembled into a circular chromosome of 420,362 bp, 18,734 bp longer than that of another individual of A. indica which was assembled before as a linear molecule. Synteny analysis between the two mitogenomes revealed numerous rearrangements, unique regions of each individual and 0.2% sequence divergence in their syntenic regions. The A. indica mitogenome contains a gene content typical of flowering plants (33 protein-coding, 3 rRNA, and 17 tRNA genes). Repetitive sequences >30 bp in size totals 57,060 bp, representing 13.6% of the mitogenome. We examined recombination mediated by repeats >100 bp in size and found highly active recombination for all the repeats, including a very large repeat of ~16 kb. Recombination between these repeats can form much smaller subgenomic circular chromosomes, which may lead to rapid replication of mitochondrial DNA and thus be advantageous for A. indica with a parasitic lifestyle. In addition, unlike some other parasitic plants, A. indica shows no evidence for horizontal gene transfer of protein-coding genes in its mitogenome.}, }
@article {pmid36206680, year = {2022}, author = {Xu, C and Lu, J and Shen, C and Wang, J and Li, F}, title = {Deciphering the mechanisms shaping the plastisphere antibiotic resistome on riverine microplastics.}, journal = {Water research}, volume = {225}, number = {}, pages = {119192}, doi = {10.1016/j.watres.2022.119192}, pmid = {36206680}, issn = {1879-2448}, mesh = {*Microplastics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Plastics ; Vancomycin ; Polyethylene Terephthalates ; Bacteria/genetics ; *Rifamycins ; Water ; }, abstract = {Microplastics in urban rivers provide bacterial niches and serve as dispersal vectors for antibiotic resistant genes (ARGs) dissemination, which may exacerbate risks in the aquatic systems. However, whether MPs in the river would also selectively enrich ARGs and the underlying mechanisms shaping the resistome on MPs remains largely unknown. In this study, we explored the occurrence of ARGs, bacterial communities, and mobile genetic elements (MGEs) on MPs and in waters from the Huangpu River in China. Microplastics were widely distributed in the river (1.78 ± 0.84 items/L), with overwhelming percentages of polyethylene terephthalate fibers. Although reduced ARG abundances were observed on MPs than in waters, MPs selectively enriched the ARGs resistant to Rifamycin and Vancomycin. A clear variation for ARG profiles was elucidated between water and MPs samples. Network analysis suggested that MPs created a unique niche for the genus Afipia to colonize, potentially contributing to the vertical dissemination of ARGs. Additionally, the co-occurrence between ARGs and MGEs revealed that the MPs favor the propagation of some plasmid-associated ARGs mediated by horizontal gene transfer. The null model-based stochasticity ratio and the neutral community model suggested that the ARG assembly on MPs was dominantly driven by stochastic process. The results further indicated that microbial communities and MGEs played significant roles in shaping ARG profiles and dynamics on MPs. Our findings provided new insights into the ecological processes of antibiotic resistome of the aquatic plastisphere.}, }
@article {pmid36205822, year = {2022}, author = {Deb, S}, title = {Pan-genome evolution and its association with divergence of metabolic functions in Bifidobacterium genus.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {38}, number = {12}, pages = {231}, pmid = {36205822}, issn = {1573-0972}, mesh = {*Bifidobacterium/genetics ; Carbohydrates ; Evolution, Molecular ; *Genome, Bacterial/genetics ; Humans ; Phylogeny ; }, abstract = {Previous studies were mainly focused on genomic evolution and diversity of type species of Bifidobacterium genus due to their health-promoting effect on host. However, those studies were mainly based on species-level taxonomic resolution, adaptation, and characterization of carbohydrate metabolic features of the bifidobacterial species. Here, a comprehensive analysis of the type strain genome unveils the association of pan-genome evolution with the divergence of metabolic function of the Bifidobacterium genus. This study has also demonstrated that horizontal gene transfer, as well as genome expansion and reduction events, leads to the divergence of metabolic functions in Bifidobacterium genus. Furthermore, the genome-based search of probiotic traits among all the available bifidobacterial type strains gives hints on type species, that could confer health benefits to nutrient-deficient individuals. Altogether, the present study provides insight into the developments of genomic evolution, functional divergence, and potential probiotic type species of the Bifidobacterium genus.}, }
@article {pmid36205197, year = {2023}, author = {Gontier, N and Sukhoverkhov, A}, title = {Reticulate evolution underlies synergistic trait formation in human communities.}, journal = {Evolutionary anthropology}, volume = {32}, number = {1}, pages = {26-38}, doi = {10.1002/evan.21962}, pmid = {36205197}, issn = {1520-6505}, support = {DL57/2016/CP1479/CT0066//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, mesh = {Animals ; Humans ; Phenotype ; *Plants/genetics ; }, abstract = {This paper investigates how reticulate evolution contributes to a better understanding of human sociocultural evolution in general, and community formation in particular. Reticulate evolution is evolution as it occurs by means of symbiosis, symbiogenesis, lateral gene transfer, infective heredity, and hybridization. From these mechanisms and processes, we mainly zoom in on symbiosis and we investigate how it underlies the rise of (1) human, plant, animal, and machine interactions typical of agriculture, animal husbandry, farming, and industrialization; (2) diet-microbiome relationships; and (3) host-virome and other pathogen interactions that underlie human health and disease. We demonstrate that reticulate evolution necessitates an understanding of behavioral and cultural evolution at a community level, where reticulate causal processes underlie the rise of synergistic organizational traits.}, }
@article {pmid36203131, year = {2022}, author = {Somee, MR and Amoozegar, MA and Dastgheib, SMM and Shavandi, M and Maman, LG and Bertilsson, S and Mehrshad, M}, title = {Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {690}, pmid = {36203131}, issn = {1471-2164}, mesh = {*Archaea ; Bacteria ; Biodegradation, Environmental ; Carbon/metabolism ; Hydrocarbons/metabolism ; Hydrogen/metabolism ; *Petroleum/metabolism ; Phylogeny ; }, abstract = {BACKGROUND: Hydrocarbons (HCs) are organic compounds composed solely of carbon and hydrogen that are mainly accumulated in oil reservoirs. As the introduction of all classes of hydrocarbons including crude oil and oil products into the environment has increased significantly, oil pollution has become a global ecological problem. However, our perception of pathways for biotic degradation of major HCs and key enzymes in these bioconversion processes has mainly been based on cultured microbes and is biased by uneven taxonomic representation. Here we used Annotree to provide a gene-centric view of the aerobic degradation ability of aliphatic and aromatic HCs in 23,446 genomes from 123 bacterial and 14 archaeal phyla. RESULTS: Apart from the widespread genetic potential for HC degradation in Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes, genomes from an additional 18 bacterial and 3 archaeal phyla also hosted key HC degrading enzymes. Among these, such degradation potential has not been previously reported for representatives in the phyla UBA8248, Tectomicrobia, SAR324, and Eremiobacterota. Genomes containing whole pathways for complete degradation of HCs were only detected in Proteobacteria and Actinobacteriota. Except for several members of Crenarchaeota, Halobacterota, and Nanoarchaeota that have tmoA, ladA, and alkB/M key genes, respectively, representatives of archaeal genomes made a small contribution to HC degradation. None of the screened archaeal genomes coded for complete HC degradation pathways studied here; however, they contribute significantly to peripheral routes of HC degradation with bacteria.<br><br>CONCLUSION: Phylogeny reconstruction showed that the reservoir of key aerobic hydrocarbon-degrading enzymes in Bacteria and Archaea undergoes extensive diversification via gene duplication and horizontal gene transfer. This diversification could potentially enable microbes to rapidly adapt to novel and manufactured HCs that reach the environment.}, }
@article {pmid36202926, year = {2023}, author = {Barnum, TP and Coates, JD}, title = {Chlorine redox chemistry is widespread in microbiology.}, journal = {The ISME journal}, volume = {17}, number = {1}, pages = {70-83}, pmid = {36202926}, issn = {1751-7370}, mesh = {*Chlorates ; *Chlorine/metabolism ; Chlorides/metabolism ; Oxidation-Reduction ; Bacteria/metabolism ; }, abstract = {Chlorine is abundant in cells and biomolecules, yet the biology of chlorine oxidation and reduction is poorly understood. Some bacteria encode the enzyme chlorite dismutase (Cld), which detoxifies chlorite (ClO2[-]) by converting it to chloride (Cl[-]) and molecular oxygen (O2). Cld is highly specific for chlorite and aside from low hydrogen peroxide activity has no known alternative substrate. Here, we reasoned that because chlorite is an intermediate oxidation state of chlorine, Cld can be used as a biomarker for oxidized chlorine species. Cld was abundant in metagenomes from various terrestrial habitats. About 5% of bacterial and archaeal genera contain a microorganism encoding Cld in its genome, and within some genera Cld is highly conserved. Cld has been subjected to extensive horizontal gene transfer. Genes found to have a genetic association with Cld include known genes for responding to reactive chlorine species and uncharacterized genes for transporters, regulatory elements, and putative oxidoreductases that present targets for future research. Cld was repeatedly co-located in genomes with genes for enzymes that can inadvertently reduce perchlorate (ClO4[-]) or chlorate (ClO3[-]), indicating that in situ (per)chlorate reduction does not only occur through specialized anaerobic respiratory metabolisms. The presence of Cld in genomes of obligate aerobes without such enzymes suggested that chlorite, like hypochlorous acid (HOCl), might be formed by oxidative processes within natural habitats. In summary, the comparative genomics of Cld has provided an atlas for a deeper understanding of chlorine oxidation and reduction reactions that are an underrecognized feature of biology.}, }
@article {pmid36200778, year = {2022}, author = {da Silva Barreira, D and Lapaquette, P and Novion Ducassou, J and Couté, Y and Guzzo, J and Rieu, A}, title = {Spontaneous Prophage Induction Contributes to the Production of Membrane Vesicles by the Gram-Positive Bacterium Lacticaseibacillus casei BL23.}, journal = {mBio}, volume = {13}, number = {5}, pages = {e0237522}, pmid = {36200778}, issn = {2150-7511}, mesh = {*Peptidoglycan ; Virus Activation ; *Lacticaseibacillus casei/genetics ; Prophages/genetics ; N-Acetylmuramoyl-L-alanine Amidase ; Anti-Bacterial Agents/pharmacology ; Mitomycins ; beta-Lactams ; }, abstract = {The formation of membrane vesicles (MVs) by Gram-positive bacteria has gained increasing attention over the last decade. Recently, models of vesicle formation have been proposed and involve the digestion of the cell wall by prophage-encoded or stress-induced peptidoglycan (PG) hydrolases and the inhibition of PG synthesis by β-lactam antibiotics. The impact of these mechanisms on vesicle formation is largely dependent on the strain and growth conditions. To date, no information on the production of vesicles by the lactobacilli family has been reported. Here, we aimed to characterize the MVs released by the Gram-positive bacteria Lacticaseibacillus casei BL23 and also investigated the mechanisms involved in vesicle formation. Using electron microscopy, we established that the size of the majority of L. casei BL23 vesicles ranged from 50 to 100 nm. Furthermore, we showed that the vesicles were released consistently throughout the growth of the bacteria in standard culture conditions. The protein composition of the vesicles released in the supernatant was identified and a significant number of prophage proteins was detected. Moreover, using a mutant strain harboring a defective PLE2 prophage, we were able to show that the spontaneous and mitomycin-triggered induction of the prophage PLE2 contribute to the production of MVs by L. casei BL23. Finally, we also demonstrated the influence of prophages on the membrane integrity of bacteria. Overall, our results suggest a key role of the prophage PLE2 in the production of MVs by L. casei BL23 in the absence or presence of genotoxic stress. IMPORTANCE The last few decades have demonstrated that membrane vesicles (MVs) produced by microorganisms can have a wide variety of functions. This diversity places MVs at the crossroads of major research topics in current microbiology such as antibiotic resistance, horizontal gene transfer, cell communication, biofilm development, bacteriophage resistance, and pathogenesis. In particular, vesicles produced by probiotic strains have been shown to play a significant role in their beneficial effects. Thus, the study of vesicle biogenesis is a key element for promoting and improving their release. Overall, our results suggest a key role of spontaneous and mitomycin-triggered prophage induction in MV production by the Gram-positive bacteria Lacticaseibacillus casei BL23. This phenomenon is of great interest as prophage-induced MVs could potentially influence bacterial behavior, stress resistance, and vesicle functions.}, }
@article {pmid36200773, year = {2022}, author = {Sattler, J and Tsvetkov, T and Stelzer, Y and Schäfer, S and Sommer, J and Noster, J and Göttig, S and Hamprecht, A}, title = {Emergence of Tn1999.7, a New Transposon in blaOXA-48-Harboring Plasmids Associated with Increased Plasmid Stability.}, journal = {Antimicrobial agents and chemotherapy}, volume = {66}, number = {11}, pages = {e0078722}, pmid = {36200773}, issn = {1098-6596}, mesh = {*Bacterial Proteins/genetics ; *beta-Lactamases/genetics/metabolism ; *DNA Transposable Elements/genetics ; Europe ; Germany ; *Plasmids/genetics ; Enterobacteriaceae/genetics/pathogenicity ; Genetic Variation ; }, abstract = {OXA-48 is the most common carbapenemase in Enterobacterales in Germany and many other European countries. Depending on the genomic location of blaOXA-48, OXA-48-producing isolates vary in phenotype and intra- and interspecies transferability of blaOXA-48. In most bacterial isolates, blaOXA-48 is located on one of seven variants of Tn1999 (Tn1999.1 to Tn1999.6 and invTn1999.2). Here, a novel Tn1999 variant, Tn1999.7, is described, which was identified in 11 clinical isolates from 2016 to 2020. Tn1999.7 differs from Tn1999.1 by the insertion of the 8,349-bp Tn3 family transposon Tn7442 between the lysR gene and blaOXA-48 open reading frame. Tn7442 carries genes coding for a restriction endonuclease and a DNA methyltransferase as cargo, forming a type III restriction modification system. Tn1999.7 was carried on an ~71-kb IncL plasmid in 9/11 isolates. In one isolate, Tn1999.7 was situated on an ~76-kb plasmid, harboring an additional insertion sequence in the plasmid backbone. In one isolate, the plasmid size is only ~63 kb due to a deletion adjacent to Tn7442 that extends into the plasmid backbone. Mean conjugation rates of the Tn1999.7-harboring plasmids in J53 ranged from 4.47 × 10[-5] to 2.03 × 10[-2], similar to conjugation rates of other pOXA-48-type IncL plasmids. The stability of plasmids with Tn1999.7 was significantly higher than that of a Tn1999.2-harboring plasmid in vitro. This increase in stability could be related to the insertion of a restriction-modification system, which can promote postsegregational killing. The increased plasmid stability associated with Tn1999.7 could contribute to the further spread of OXA-48.}, }
@article {pmid36198712, year = {2022}, author = {Faddetta, T and Vassallo, A and Del Duca, S and Gallo, G and Fani, R and Puglia, AM}, title = {Unravelling the DNA sequences carried by Streptomyces coelicolor membrane vesicles.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {16651}, pmid = {36198712}, issn = {2045-2322}, mesh = {Bacteria/genetics ; Bacterial Proteins/metabolism ; Base Sequence ; Gene Expression Regulation, Bacterial ; Lipids ; *Nucleic Acids/metabolism ; RNA/metabolism ; *Streptomyces coelicolor/genetics/metabolism ; }, abstract = {Membrane vesicles (MVs) are spherical particles with nanoscale dimensions and characterized by the presence of diverse cargos, such as nucleic acids, proteins, lipids, and cellular metabolites. Many examples of (micro)organisms producing MVs are reported in literature. Among them, bacterial MVs are of particular interest because they are now considered as the fourth mechanism of horizontal gene transfer. Streptomyces bacteria are well-known for their ecological roles and ability to synthesize bioactive compounds, with Streptomyces coelicolor being the model organism. It was previously demonstrated that it can produce distinct populations of MVs characterized by different protein and metabolite cargos. In this work we demonstrated for the first time that MVs of S. coelicolor carry both DNA and RNA and that their DNA content represents the entire chromosome of the bacterium. These findings suggest that MV DNA could have a role in the evolution of Streptomyces genomes and that MVs could be exploited in new strain engineering strategies.}, }
@article {pmid36195901, year = {2022}, author = {Kelly, JB and Carlson, DE and Low, JS and Thacker, RW}, title = {Novel trends of genome evolution in highly complex tropical sponge microbiomes.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {164}, pmid = {36195901}, issn = {2049-2618}, mesh = {Bacteria/genetics ; Evolution, Molecular ; *Lipopolysaccharides ; Metagenome/genetics ; Metagenomics ; *Microbiota/genetics ; Phylogeny ; Steroids ; Sterols ; }, abstract = {BACKGROUND: Tropical members of the sponge genus Ircinia possess highly complex microbiomes that perform a broad spectrum of chemical processes that influence host fitness. Despite the pervasive role of microbiomes in Ircinia biology, it is still unknown how they remain in stable association across tropical species. To address this question, we performed a comparative analysis of the microbiomes of 11 Ircinia species using whole-metagenomic shotgun sequencing data to investigate three aspects of bacterial symbiont genomes-the redundancy in metabolic pathways across taxa, the evolution of genes involved in pathogenesis, and the nature of selection acting on genes relevant to secondary metabolism.<br><br>RESULTS: A total of 424 new, high-quality bacterial metagenome-assembled genomes (MAGs) were produced for 10 Caribbean Ircinia species, which were evaluated alongside 113 publicly available MAGs sourced from the Pacific species Ircinia ramosa. Evidence of redundancy was discovered in that the core genes of several primary metabolic pathways could be found in the genomes of multiple bacterial taxa. Across hosts, the metagenomes were depleted in genes relevant to pathogenicity and enriched in eukaryotic-like proteins (ELPs) that likely mimic the hosts' molecular patterning. Finally, clusters of steroid biosynthesis genes (CSGs), which appear to be under purifying selection and undergo horizontal gene transfer, were found to be a defining feature of Ircinia metagenomes.<br><br>CONCLUSIONS: These results illustrate patterns of genome evolution within highly complex microbiomes that illuminate how associations with hosts are maintained. The metabolic redundancy within the microbiomes could help buffer the hosts from changes in the ambient chemical and physical regimes and from fluctuations in the population sizes of the individual microbial strains that make up the microbiome. Additionally, the enrichment of ELPs and depletion of LPS and cellular motility genes provide a model for how alternative strategies to virulence can evolve in microbiomes undergoing mixed-mode transmission that do not ultimately result in higher levels of damage (i.e., pathogenicity) to the host. Our last set of results provides evidence that sterol biosynthesis in Ircinia-associated bacteria is widespread and that these molecules are important for the survival of bacteria in highly complex Ircinia microbiomes. Video Abstract.}, }
@article {pmid36194009, year = {2022}, author = {Cook, D and Flannigan, MD and Candra, BV and Compton, KD and Hare, JM}, title = {The DdrR Coregulator of the Acinetobacter baumannii Mutagenic DNA Damage Response Potentiates UmuDAb Repression of Error-Prone Polymerases.}, journal = {Journal of bacteriology}, volume = {204}, number = {11}, pages = {e0016522}, pmid = {36194009}, issn = {1098-5530}, support = {P20 RR016481/RR/NCRR NIH HHS/United States ; R15 GM085722/GM/NIGMS NIH HHS/United States ; P20 GM103436/GM/NIGMS NIH HHS/United States ; }, mesh = {*Acinetobacter baumannii/genetics/metabolism ; Mutagens ; DNA-Directed DNA Polymerase/genetics/metabolism ; Mutagenesis ; DNA Damage ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics/metabolism ; }, abstract = {Acinetobacter baumannii strain 17978 is an opportunistic pathogen with a unique DNA damage repair response that lacks the LexA repressor but induces ~150 genes after DNA damage. It uses the UmuD homolog UmuDAb and the small protein DdrR, unique to Acinetobacter, to repress multiple horizontally acquired umuDC error-prone polymerase genes through an unknown mechanism. We used reverse transcription-quantitative PCR and immunoblotting to elucidate UmuDAb regulatory requirements and DdrR contributions to the corepression of this specialized regulon. Mutations in the putative UmuDAb helix-turn-helix (HTH) domain could not repress the expression of the UmuDAb/DdrR regulon. A ddrR insertion mutation in these HTH mutant backgrounds produced even greater derepression of the regulon, suggesting that DdrR exerts an additional level of control over this mutagenic response. These ddrR HTH mutant A. baumannii cells overexpressed UmuDAb, cleaving it after treatment with the DNA-damaging agent mitomycin C. This showed that DdrR was not required for UmuDAb self-cleavage and that UmuDAb repression and self-cleavage actions were independent. An uncleavable umuDAb mutant with an A-to-Y change at position 83 (A83Y) could neither induce the UmuDAb/DdrR regulon nor conduct SOS mutagenesis. However, a prophage-encoded umuDrumB operon was still partially induced after DNA damage in this mutant. Surprisingly, that prophage's putative repressor was dispensable for prophage-encoded umuDrumB induction, implying another repressor's involvement. This study revealed that UmuDAb behaves like LexA, requiring an N-terminal HTH motif for repression and C-terminal self-cleavage for gene induction and subsequent SOS mutagenesis, and DdrR cooperates with it to exert an additional level of repressive control on this pathogen's mutagenic response to DNA damage. IMPORTANCE Acinetobacter baumannii is a nosocomial pathogen that acquires antibiotic resistance genes through conjugative transfer and carries out a robust mutagenic DNA damage response. After exposure to conditions typically encountered in health care settings, such as antibiotics, UV light, and desiccation, this species induces error-prone UmuD'2C polymerases. This mutagenic capability increases A. baumannii survival and virulence and is regulated by the UmuDAb/DdrR corepressor system unique to the Acinetobacter genus. Our study has revealed that the DdrR protein provides an additional layer of control in preventing mutagenic polymerase expression by enhancing UmuDAb repression actions. Understanding these repressors could lead to new drug targets, as multidrug resistance in hospital-acquired infections has decreased treatment options, with limited new drugs being developed.}, }
@article {pmid36187977, year = {2022}, author = {Shami, AY and Abulfaraj, AA and Refai, MY and Barqawi, AA and Binothman, N and Tashkandi, MA and Baeissa, HM and Baz, L and Abuauf, HW and Ashy, RA and Jalal, RS}, title = {Abundant antibiotic resistance genes in rhizobiome of the human edible Moringa oleifera medicinal plant.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {990169}, pmid = {36187977}, issn = {1664-302X}, abstract = {Moringa oleifera (or the miracle tree) is a wild plant species widely grown for its seed pods and leaves, and is used in traditional herbal medicine. The metagenomic whole genome shotgun sequencing (mWGS) approach was used to characterize antibiotic resistance genes (ARGs) of the rhizobiomes of this wild plant and surrounding bulk soil microbiomes and to figure out the chance and consequences for highly abundant ARGs, e.g., mtrA, golS, soxR, oleC, novA, kdpE, vanRO, parY, and rbpA, to horizontally transfer to human gut pathogens via mobile genetic elements (MGEs). The results indicated that abundance of these ARGs, except for golS, was higher in rhizosphere of M. oleifera than that in bulk soil microbiome with no signs of emerging new soil ARGs in either soil type. The most highly abundant metabolic processes of the most abundant ARGs were previously detected in members of phyla Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, and Firmicutes. These processes refer to three resistance mechanisms namely antibiotic efflux pump, antibiotic target alteration and antibiotic target protection. Antibiotic efflux mechanism included resistance-nodulation-cell division (RND), ATP-binding cassette (ABC), and major facilitator superfamily (MFS) antibiotics pumps as well as the two-component regulatory kdpDE system. Antibiotic target alteration included glycopeptide resistance gene cluster (vanRO), aminocoumarin resistance parY, and aminocoumarin self-resistance parY. While, antibiotic target protection mechanism included RbpA bacterial RNA polymerase (rpoB)-binding protein. The study supports the claim of the possible horizontal transfer of these ARGs to human gut and emergence of new multidrug resistant clinical isolates. Thus, careful agricultural practices are required especially for plants used in circles of human nutrition industry or in traditional medicine.}, }
@article {pmid36186424, year = {2022}, author = {Walker, AR and Shields, RC}, title = {Investigating CRISPR spacer targets and their impact on genomic diversification of Streptococcus mutans.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {997341}, pmid = {36186424}, issn = {1664-8021}, support = {R03 DE029882/DE/NIDCR NIH HHS/United States ; }, abstract = {CRISPR-Cas is a bacterial immune system that restricts the acquisition of mobile DNA elements. These systems provide immunity against foreign DNA by encoding CRISPR spacers that help target DNA if it re-enters the cell. In this way, CRISPR spacers are a type of molecular tape recorder of foreign DNA encountered by the host microorganism. Here, we extracted ∼8,000 CRISPR spacers from a collection of over three hundred Streptococcus mutans genomes. Phage DNA is a major target of S. mutans spacers. S. mutans strains have also generated immunity against mobile DNA elements such as plasmids and integrative and conjugative elements. There may also be considerable immunity generated against bacterial DNA, although the relative contribution of self-targeting versus bona fide intra- or inter-species targeting needs to be investigated further. While there was clear evidence that these systems have acquired immunity against foreign DNA, there appeared to be minimal impact on horizontal gene transfer (HGT) constraints on a species-level. There was little or no impact on genome size, GC content and 'openness' of the pangenome when comparing between S. mutans strains with low or high CRISPR spacer loads. In summary, while there is evidence of CRISPR spacer acquisition against self and foreign DNA, CRISPR-Cas does not act as a barrier on the expansion of the S. mutans accessory genome.}, }
@article {pmid36186036, year = {2022}, author = {Perez Saura, P and Chabi, M and Corato, A and Cardol, P and Remacle, C}, title = {Cell adaptation of the extremophilic red microalga Galdieria sulphuraria to the availability of carbon sources.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {978246}, pmid = {36186036}, issn = {1664-462X}, abstract = {Global energy demand and fossil fuels impact on climate can be partially managed by an increase in the use of biofuels for transports and industries. Biodiesel production is generally preceded by a transesterification process of the green biomass triacylglycerols that generates large amounts of glycerol as a by-product. In this study, the extremophilic red microalga Galdieria sulphuraria 074W was cultivated in heterotrophy. The microalgal growth parameters and biomass composition were compared when grown on an equivalent molar concentration of carbon of either glucose or glycerol as unique carbon source. The maximal biomass reached in these two conditions was not significantly different (∼2.5 g.L[-1]). Fatty acid profile, protein and storage carbohydrate contents were also statistically similar, irrespectively of the metabolized carbon source. We also observed that the pigment content of G. sulphuraria cells decreased during heterotrophic growth compared to photoautotrophic cultivated cells, and that this diminution was more important in the presence of glucose than glycerol: cells were yellowish in the presence of glucose and green in the presence of glycerol. The pigmentation was restored when glucose was totally consumed in the medium, suggesting that the presence of glucose repressed pigment synthesis. Based on this observation, a transcriptome analysis was performed in order to better understand the mechanisms involved in the loss of color mediated by darkness and by glucose in G. sulphuraria. Three conditions were analyzed: heterotrophy with glycerol or glucose and phototrophy. This allowed us to understand the transcriptional response of cells to light and dark environments both at the nuclear and chloroplast levels, and to show that transcription of gene families, acquired by horizontal gene transfer, such as sugar, amino acid, or acetate transporters, were involved in the response to the availability of different (in)organic sources.}, }
@article {pmid36183960, year = {2022}, author = {Sharma, V and Sood, A and Ray, P and Angrup, A}, title = {Comparative genomics reveals the evolution of antimicrobial resistance in Bacteroides nordii.}, journal = {Microbial pathogenesis}, volume = {173}, number = {Pt A}, pages = {105811}, doi = {10.1016/j.micpath.2022.105811}, pmid = {36183960}, issn = {1096-1208}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial ; Metronidazole ; Drug Resistance, Bacterial/genetics ; Genomics ; *Anti-Infective Agents/pharmacology ; }, abstract = {Bacteroides nordii, is an understudied member of the pathogenic B. fragilis group which comprises several multidrug-resistant (MDR) strains. Thus, it is of great interest to study the genome biology of Bacteroides nordii. However, no detailed study is available that characterized B. nordii at the genetic level and explored its role as a potential pathogen. We isolated an MDR strain viz., B. nordii PGMM4098 from the pus sample and subjected it to whole genome sequencing using Illumina technology. The draft genome was de-novo assembled and annotated, followed by comprehensive comparative genomics analyses using the publicly available genome dataset of B. nordii. The pan-genome analysis revealed the open nature of B. nordii, indicating the continuous accumulation of novel genes in non-core components leading to the emergence of new strains of this species. The thirteen antimicrobial resistance (AMR) genes identified in the genomes of all B. nordii strains were part of the non-core component of the pan-genome. Of these, four AMR genes, nimE, aadS, mef(En2), and ermB/F/G were found to be acquired via the process of horizontal gene transfer (HGT) from anaerobic Bacteroidetes. Importantly, the nimE gene conferring metronidazole resistance was found to be present only in B. nordii PGMM4098, which harbors five other AMR genes encoded in its genome. Of these, nimE (metronidazole resistance), ermB/F/G (macrolide-lincosamide-streptogramin B resistance), and cfxA2/A3 (class A β-lactam resistance) genes were further validated using targeted polymerase chain reaction assay. Notably, these three genes were also found to be under the operation of positive selective pressure suggesting the diversification of these genes, which might lead to the emergence of new MDR strains of B. nordii in the near future. Our study reported and characterized the genome of the first MDR strain of B. nordii and revealed the AMR evolution in this species using a comprehensive comparative genomics approach.}, }
@article {pmid36181826, year = {2023}, author = {Ren, Z and Zhao, Y and Han, S and Li, X}, title = {Regulatory strategies for inhibiting horizontal gene transfer of ARGs in paddy and dryland soil through computer-based methods.}, journal = {The Science of the total environment}, volume = {856}, number = {Pt 1}, pages = {159096}, doi = {10.1016/j.scitotenv.2022.159096}, pmid = {36181826}, issn = {1879-1026}, mesh = {*Soil ; *Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; Escherichia coli/genetics ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Computers ; }, abstract = {Antibiotic resistance genes (ARGs) have been regarded as emerging pollutants due to their potential risk of resistance. Horizontal gene transfer (HGT) is the main pathway for ARGs to lead to environmental threats. Therefore, the inhabitation of ARGs' HGT can effectively inhibit ARGs' potential drug resistance risk within a single strain. In this paper, the characteristics of ARGs' HGT in paddy and dryland soils were identified and regulated by a combination of ARGs' HGT feature identification, transfer mechanism analysis and transfer process regulation. The homology modeling algorithm was used to simulate the construction of the Tn5 plasmid transposase of Escherichia coli (E. coli) for identifying ARGs' HGT characteristics. The GCG (212.617 Å) was thus determined as the target codon. Through integrated computer-based methods, results showed that the most important environmental disturbance factors for the HGT of ARGs in the paddy and dryland soils were rough farmyard manure/sewage irrigation and mining pollution, respectively. Under the disturbance of key environmental factors, the inhibitory effect of HGT of ARGs in paddy and dryland soil was reduced by 35.01 % and 34.74 %, respectively. Results demonstrated that the proposed theoretical mechanism and control strategies could effectively inhibit the HGT of E. coli ARGs in the soil environment.}, }
@article {pmid36181435, year = {2022}, author = {Zhang, X and Huang, Y and Liu, Y and Xu, W and Pan, J and Zheng, X and Du, H and Zhang, C and Lu, Z and Zou, D and Liu, Z and Cai, M and Xiong, J and Zhu, Y and Dong, Z and Jiang, H and Dong, H and Jiang, J and Luo, Z and Huang, L and Li, M}, title = {An Ancient Respiratory System in the Widespread Sedimentary Archaea Thermoprofundales.}, journal = {Molecular biology and evolution}, volume = {39}, number = {10}, pages = {}, pmid = {36181435}, issn = {1537-1719}, mesh = {*Archaea/genetics/metabolism ; *Hydrogenase/chemistry/genetics/metabolism ; Sodium Chloride/metabolism ; Phylogeny ; Respiratory System/metabolism ; Amino Acids/genetics ; Antiporters/genetics/metabolism ; }, abstract = {Thermoprofundales, formerly Marine Benthic Group D (MBG-D), is a ubiquitous archaeal lineage found in sedimentary environments worldwide. However, its taxonomic classification, metabolic pathways, and evolutionary history are largely unexplored because of its uncultivability and limited number of sequenced genomes. In this study, phylogenomic analysis and average amino acid identity values of a collection of 146 Thermoprofundales genomes revealed five Thermoprofundales subgroups (A-E) with distinct habitat preferences. Most of the microorganisms from Subgroups B and D were thermophiles inhabiting hydrothermal vents and hot spring sediments, whereas those from Subgroup E were adapted to surface environments where sunlight is available. H2 production may be featured in Thermoprofundales as evidenced by a gene cluster encoding the ancient membrane-bound hydrogenase (MBH) complex. Interestingly, a unique structure separating the MBH gene cluster into two modular units was observed exclusively in the genomes of Subgroup E, which included a peripheral arm encoding the [NiFe] hydrogenase domain and a membrane arm encoding the Na+/H+ antiporter domain. These two modular structures were confirmed to function independently by detecting the H2-evolving activity in vitro and salt tolerance to 0.2 M NaCl in vivo, respectively. The peripheral arm of Subgroup E resembles the proposed common ancestral respiratory complex of modern respiratory systems, which plays a key role in the early evolution of life. In addition, molecular dating analysis revealed that Thermoprofundales is an early emerging archaeal lineage among the extant MBH-containing microorganisms, indicating new insights into the evolution of this ubiquitous archaea lineage.}, }
@article {pmid36177458, year = {2022}, author = {Choufa, C and Tidjani, AR and Gauthier, A and Harb, M and Lao, J and Leblond-Bourget, N and Vos, M and Leblond, P and Bontemps, C}, title = {Prevalence and mobility of integrative and conjugative elements within a Streptomyces natural population.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {970179}, pmid = {36177458}, issn = {1664-302X}, abstract = {Horizontal Gene Transfer (HGT) is a powerful force generating genomic diversity in bacterial populations. HGT in Streptomyces is in large part driven by conjugation thanks to plasmids, Integrative and Conjugative elements (ICEs) and Actinomycete ICEs (AICEs). To investigate the impact of ICE and AICE conjugation on Streptomyces genome evolution, we used in silico and experimental approaches on a set of 11 very closely related strains isolated from a millimeter scale rhizosphere population. Through bioinformatic searches of canonical conjugation proteins, we showed that AICEs are the most frequent integrative conjugative elements, with the central chromosome region being a hotspot for integrative element insertion. Strains exhibited great variation in AICE composition consistent with frequent HGT and/or gene loss. We found that single insertion sites can be home to different elements in different strains (accretion) and conversely, elements belonging to the same family can be found at different insertion sites. A wide variety of cargo genes was present in the AICEs with the potential to mediate strain-specific adaptation (e.g., DNA metabolism and resistance genes to antibiotic and phages). However, a large proportion of AICE cargo genes showed hallmarks of pseudogenization, consistent with deleterious effects of cargo genes on fitness. Pock assays enabled the direct visualization of conjugal AICE transfer and demonstrated the transfer of AICEs between some, but not all, of the isolates. Multiple AICEs were shown to be able to transfer during a single mating event. Although we did not obtain experimental evidence for transfer of the sole chromosomal ICE in this population, genotoxic stress mediated its excision from the chromosome, suggesting its functionality. Our results indicate that AICE-mediated HGT in Streptomyces populations is highly dynamic, with likely impact on strain fitness and the ability to adapt to environmental change.}, }
@article {pmid36177035, year = {2022}, author = {Martínez-Vicente, P and Poblador, F and Leitner, J and Farré, D and Steinberger, P and Engel, P and Angulo, A}, title = {Discovery of the first PD-1 ligand encoded by a pathogen.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {1007334}, pmid = {36177035}, issn = {1664-3224}, mesh = {*B7-H1 Antigen/metabolism ; DNA ; Ligands ; Membrane Glycoproteins/metabolism ; *Programmed Cell Death 1 Ligand 2 Protein/metabolism ; Programmed Cell Death 1 Receptor/genetics ; Viral Proteins ; }, abstract = {Large double-stranded DNA viruses deploy multiple strategies to subvert host immune defenses. Some of these tactics are mediated by viral gene products acquired by horizontal gene transfer from the corresponding hosts and shaped throughout evolution. The programmed death-1 (PD-1) receptor and its ligands, PD-L1 and PD-L2, play a pivotal role attenuating T-cell responses and regulating immune tolerance. In this study, we report the first functional PD-L1 homolog gene (De2) found in a pathogen. De2, captured by a γ-herpesvirus from its host during co-evolution around 50 million years ago, encodes a cell-surface glycoprotein that interacts with high affinity and stability with host PD-1. We also find that mutations evolved by the viral protein result in a significant loss of its ability to interact in cis with CD80, an interaction that for PD-L1:CD80 has been reported to block PD-1 inhibitory pathways. Furthermore, we demonstrate that the viral protein strongly inhibits T-cell signaling. Our observations suggest that PD-L1 homologs may enable viruses to evade T cell responses, favor their replication, and prevent excessive tissue damage. Altogether, our findings reveal a novel viral immunosuppressive strategy and highlight the importance of the modulation of the PD-1/PD-L1 axis during viral infections.}, }
@article {pmid36175544, year = {2022}, author = {Harris, BJ and Clark, JW and Schrempf, D and Szöllősi, GJ and Donoghue, PCJ and Hetherington, AM and Williams, TA}, title = {Divergent evolutionary trajectories of bryophytes and tracheophytes from a complex common ancestor of land plants.}, journal = {Nature ecology &amp; evolution}, volume = {6}, number = {11}, pages = {1634-1643}, pmid = {36175544}, issn = {2397-334X}, support = {BB/N000919/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T012773/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Biological Evolution ; *Embryophyta/genetics ; Phylogeny ; Plants/genetics ; Fossils ; *Tracheophyta ; }, abstract = {The origin of plants and their colonization of land fundamentally transformed the terrestrial environment. Here we elucidate the basis of this formative episode in Earth history through patterns of lineage, gene and genome evolution. We use new fossil calibrations, a relative clade age calibration (informed by horizontal gene transfer) and new phylogenomic methods for mapping gene family origins. Distinct rooting strategies resolve tracheophytes (vascular plants) and bryophytes (non-vascular plants) as monophyletic sister groups that diverged during the Cambrian, 515-494 million years ago. The embryophyte stem is characterized by a burst of gene innovation, while bryophytes subsequently experienced an equally dramatic episode of reductive genome evolution in which they lost genes associated with the elaboration of vasculature and the stomatal complex. Overall, our analyses reveal that extant tracheophytes and bryophytes are both highly derived from a more complex ancestral land plant. Understanding the origin of land plants requires tracing character evolution across a diversity of modern lineages.}, }
@article {pmid36173309, year = {2022}, author = {Gan, X and Li, M and Xu, J and Yan, S and Wang, W and Li, F}, title = {Emerging of Multidrug-Resistant Cronobacter sakazakii Isolated from Infant Supplementary Food in China.}, journal = {Microbiology spectrum}, volume = {10}, number = {5}, pages = {e0119722}, pmid = {36173309}, issn = {2165-0497}, mesh = {Ampicillin ; Anti-Bacterial Agents/pharmacology ; Chloramphenicol ; *Cronobacter/genetics ; *Cronobacter sakazakii/genetics ; Food Microbiology ; Infant Formula/microbiology ; Sulfamethoxazole ; Tetracycline ; Trimethoprim ; Virulence Factors/genetics ; }, abstract = {Cronobacter is a foodborne pathogen associated with severe infections in restricted populations and particularly with high mortality in neonates and infants. The prevalence and antimicrobial resistance (AMR) phenotype of Cronobacter cultured from powdered infant formula and supplementary food were studied. The virulence factors, AMR genes, and genomic environments of the multidrug-resistant isolates were further studied. A total of 1,055 Cronobacter isolates were recovered from 12,105 samples of powdered infant formula and supplementary food collected from 29 provinces between 2018 and 2019 in China. Among these, 1,048 isolates were from infant supplementary food and 7 were from powdered infant formula. Regarding antimicrobial resistance susceptibility, 11 (1.0%) isolates were resistant and two showed resistance to four antimicrobials (ampicillin [AMP], tetracycline [TET], sulfamethoxazole-trimethoprim [SXT], and chloramphenicol [CHL]), defined as MDR. These two MDR isolates were subsequently identified as Cronobacter sakazakii sequence type 4 (ST4) (C. sakazakii Crono-589) and ST40 (C. sakazakii Crono-684). Both MDR isolates contain 11 types of virulence genes and 7 AMR genes on their genomes. Meanwhile, the IncFIB plasmids of both MDR C. sakazakii isolates also harbored 2 types of virulence genes. Results of the genomic comparative analysis indicated that food-associated C. sakazakii could acquire antimicrobial resistance determinants through horizontal gene transfer (HGT). IMPORTANCE As a foodborne pathogen, Cronobacter can cause serious infections in restricted populations and lead to death or chronic sequelae. Although a number of investigations showed that Cronobacter isolates are susceptible to most antimicrobial agents, MDR Cronobacter isolates, isolated mainly from clinical cases but occasionally from foods, have been reported in recent years. In this study, we successfully identified two MDR Cronobacter sakazakii isolates from infant foods based on nationwide surveillance and genome sequencing in China. Genomic analysis revealed that these two MDR C. sakazakii strains acquired resistance genes from other species via different evolution and transmission routes. It is important to monitor MDR C. sakazakii isolates in infant foods, and appropriate control measures should be taken to reduce the contamination with and transmission of this MDR bacterium.}, }
@article {pmid36161953, year = {2022}, author = {Kirsch, R and Okamura, Y and Haeger, W and Vogel, H and Kunert, G and Pauchet, Y}, title = {Metabolic novelty originating from horizontal gene transfer is essential for leaf beetle survival.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {40}, pages = {e2205857119}, pmid = {36161953}, issn = {1091-6490}, mesh = {Animals ; *Coleoptera/enzymology/genetics ; Gene Knockout Techniques ; *Gene Transfer, Horizontal ; Pectins/metabolism ; Phylogeny ; Plants/chemistry ; *Polygalacturonase/genetics ; }, abstract = {Horizontal gene transfer (HGT) provides an evolutionary shortcut for recipient organisms to gain novel functions. Although reports of HGT in higher eukaryotes are rapidly accumulating, in most cases the evolutionary trajectory, metabolic integration, and ecological relevance of acquired genes remain unclear. Plant cell wall degradation by HGT-derived enzymes is widespread in herbivorous insect lineages. Pectin is an abundant polysaccharide in the walls of growing parts of plants. We investigated the significance of horizontally acquired pectin-digesting polygalacturonases (PGs) of the leaf beetle Phaedon cochleariae. Using a CRISPR/Cas9-guided gene knockout approach, we generated a triple knockout and a quadruple PG-null mutant in order to investigate the enzymatic, biological, and ecological effects. We found that pectin-digestion 1) is exclusively linked to the horizontally acquired PGs from fungi, 2) became fixed in the host genome by gene duplication leading to functional redundancy, 3) compensates for nutrient-poor diet by making the nutritious cell contents more accessible, and 4) facilitates the beetles development and survival. Our analysis highlights the selective advantage PGs provide to herbivorous insects and demonstrate the impact of HGT on the evolutionary success of leaf-feeding beetles, major contributors to species diversity.}, }
@article {pmid36161931, year = {2022}, author = {Choi, J and Schmukler, M and Groisman, EA}, title = {Degradation of gene silencer is essential for expression of foreign genes and bacterial colonization of the mammalian gut.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {40}, pages = {e2210239119}, pmid = {36161931}, issn = {1091-6490}, support = {R01 AI049561/AI/NIAID NIH HHS/United States ; AI49561//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; }, mesh = {Animals ; Bacterial Proteins/genetics/metabolism ; DNA-Binding Proteins/metabolism ; Escherichia coli/genetics/metabolism ; *Escherichia coli Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Gene Silencing ; Mammals/metabolism ; Mice ; *Protease La/genetics/metabolism ; }, abstract = {Horizontal gene transfer drives bacterial evolution. To confer new properties, horizontally acquired genes must overcome gene silencing by nucleoid-associated proteins, such as the heat-stable nucleoid structuring (H-NS) protein. Enteric bacteria possess proteins that displace H-NS from foreign genes, form nonfunctional oligomers with H-NS, and degrade H-NS, raising the question of whether any of these mechanisms play a role in overcoming foreign gene silencing in vivo. To answer this question, we mutagenized the hns gene and identified a variant specifying an H-NS protein that binds foreign DNA and silences expression of the corresponding genes, like wild-type H-NS, but resists degradation by the Lon protease. Critically, Escherichia coli expressing this variant alone fails to produce curli, which are encoded by foreign genes and required for biofilm formation, and fails to colonize the murine gut. Our findings establish that H-NS proteolysis is a general mechanism of derepressing foreign genes and essential for colonization of mammalian hosts.}, }
@article {pmid36161739, year = {2023}, author = {Riley, AB and Grillo, MA and Epstein, B and Tiffin, P and Heath, KD}, title = {Discordant population structure among rhizobium divided genomes and their legume hosts.}, journal = {Molecular ecology}, volume = {32}, number = {10}, pages = {2646-2659}, doi = {10.1111/mec.16704}, pmid = {36161739}, issn = {1365-294X}, mesh = {Genome, Bacterial/genetics ; *Medicago truncatula/genetics/microbiology ; *Rhizobium/genetics ; Sequence Analysis, DNA ; Sinorhizobium meliloti/genetics ; Symbiosis/genetics ; }, abstract = {Symbiosis often occurs between partners with distinct life history characteristics and dispersal mechanisms. Many bacterial symbionts have genomes comprising multiple replicons with distinct rates of evolution and horizontal transmission. Such differences might drive differences in population structure between hosts and symbionts and among the elements of the divided genomes of bacterial symbionts. These differences might, in turn, shape the evolution of symbiotic interactions and bacterial evolution. Here we use whole genome resequencing of a hierarchically structured sample of 191 strains of Sinorhizobium meliloti collected from 21 locations in southern Europe to characterize population structures of this bacterial symbiont, which forms a root nodule symbiosis with the host plant Medicago truncatula. S. meliloti genomes showed high local (within-site) variation and little isolation by distance. This was particularly true for the two symbiosis elements, pSymA and pSymB, which have population structures that are similar to each other, but distinct from both the bacterial chromosome and the host plant. Given limited recombination on the chromosome, compared to the symbiosis elements, distinct population structures may result from differences in effective gene flow. Alternatively, positive or purifying selection, with little recombination, may explain distinct geographical patterns at the chromosome. Discordant population structure between hosts and symbionts indicates that geographically and genetically distinct host populations in different parts of the range might interact with genetically similar symbionts, potentially minimizing local specialization.}, }
@article {pmid36161197, year = {2022}, author = {Amábile-Cuevas, CF}, title = {Phage Therapies: Lessons (Not) Learned from the "Antibiotic Era".}, journal = {PHAGE (New Rochelle, N.Y.)}, volume = {3}, number = {1}, pages = {12-14}, pmid = {36161197}, issn = {2641-6549}, abstract = {The use of phages as therapeutic or prophylactic approaches is gaining increased interest amid the growing menace of antibiotic resistance. Phages, along with other new anti-infective strategies, are certainly welcome as much needed additions to the medicinal arsenal. However, we can easily make with phages the same mistakes we made with antibiotics, which caused the current resistance crisis. The oversimplification of the ecological role of antibiotics, neglecting ancient resistance and the role of horizontal gene transfer; the active search for wide spectrum, and the massive agricultural abuse; and, most importantly, the financial greed behind the development and use of antibiotics; these are all trends that are now visible in phage research. Should we bring phages to the same track that wasted antibiotics, we could be looking at a "postphage era" in our near future.}, }
@article {pmid36160247, year = {2022}, author = {Soliman, AM and Ramadan, H and Yu, L and Hisatsune, J and Sugai, M and Elnahriry, SS and Nariya, H and El-Domany, RA and Shimamoto, T and Jackson, CR and Shimamoto, T}, title = {Complete genome sequences of two Escherichia coli clinical isolates from Egypt carrying mcr-1 on IncP and IncX4 plasmids.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {989045}, pmid = {36160247}, issn = {1664-302X}, abstract = {Colistin is a last-resort antibiotic used in the treatment of multidrug resistant Gram-negative bacteria. However, the activity and efficacy of colistin has been compromised by the worldwide spread of the mobile colistin resistance genes (mcr-1 to mcr-10). In this study, two clinical Escherichia coli strains, named EcCAI51, and EcCAI73, harbored mcr-1, showed multidrug-resistant phenotypes (with colistin MIC = 4 μg/ml), and belonged to phylogroup D: multilocus sequence type 1011 (ST1011) and phylogroup A: ST744, respectively. Findings revealed the existence of mcr-1 gene on two conjugable plasmids, pAMS-51-MCR1 (∼122 kb IncP) and pAMS-73-MCR1 (∼33 kb IncX4), in EcCAI51, and EcCAI73, respectively. The mcr-1-pap2 element was detected in the two plasmids. Additionally, the composite transposon (ISApl1-IS5D-pap2-mcr-1-ISApl1) was identified only in pAMS-51-MCR1 suggesting the potential for horizontal gene transfer. The two strains carried from 16 to 18 different multiple acquired antimicrobial resistance genes (ARGs). Additionally, two different multireplicon virulence plasmids (∼117 kb pAMS-51-Vr and ∼226 kb pAMS-73-Vr) carrying the sit operon, the Salmochelin siderophore iroBCDE operon and other several virulence genes were identified from the two strains. Hierarchical clustering of core genome MLST (HierCC) revealed clustering of EcCAI73, and EcCAI51 with global E. coli lineages at HC levels of 50 (HC50) to 100 (HC100) core genome allelic differences. To the best of our knowledge, this study presented the first complete genomic sequences of mcr-1-carrying IncP and IncX4 plasmids from human clinical E. coli isolates in Egypt. In addition, the study illustrated the mcr-1 broad dissemination in diverse plasmids and dissimilar E. coli clones.}, }
@article {pmid36159637, year = {2022}, author = {Yu, Z and Zhang, Z and Shi, L and Hua, S and Luan, T and Lin, Q and Zheng, Z and Feng, X and Liu, M and Li, X}, title = {In silico characterization of IncX3 plasmids carrying bla OXA-181 in Enterobacterales.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {988236}, pmid = {36159637}, issn = {2235-2988}, mesh = {Anti-Bacterial Agents/pharmacology ; Carbapenems ; *DNA Transposable Elements ; Escherichia coli/genetics/metabolism ; Humans ; Microbial Sensitivity Tests ; Plasmids/genetics ; *Type IV Secretion Systems ; beta-Lactamases/genetics/metabolism ; }, abstract = {Carbapenem-resistant Enterobacterales poses a global urgent antibiotic resistance threat because of its ability to transfer carbapenemase genes to other bacteria via horizontal gene transfer mediated by mobile genetic elements such as plasmids. Oxacillinase-181 (OXA-181) is one of the most common OXA-48-like carbapenemases, and OXA-181-producing Enterobacterales has been reported in many countries worldwide. However, systematic research concerning the overall picture of plasmids harboring bla OXA-181 in Enterobacterales is currently scarce. In this study, we aimed to determine the phylogeny and evolution of bla OXA-181-positive (gene encoding OXA-181) plasmids. To characterize the plasmids harboring bla OXA-181 in Enterobacterales, we identified 81 bla OXA-181-positive plasmids from 35,150 bacterial plasmids downloaded from the NCBI RefSeq database. Our results indicated that diverse plasmid types harbored bla OXA-181 but was predominantly carried by IncX3-type plasmids. We systematically compared the host strains, plasmid types, conjugative transfer regions, and genetic contexts of bla OXA-181 among the 66 bla OXA-181-positive IncX3 plasmids. We found that IncX3 plasmids harboring bla OXA-181 were mostly ColKP3-IncX3 hybrid plasmids with a length of 51 kb each and were mainly distributed in Escherichia coli and Klebsiella pneumoniae. Most of the IncX3 plasmids harboring bla OXA-181 were human origin. Almost all the bla OXA-181-positive IncX3 plasmids were found to carry genes coding for relaxases of the MOBP family and VirB-like type IV secretion system (T4SS) gene clusters, and all the 66 IncX3 plasmids were found to carry the genes encoding type IV coupling proteins (T4CPs) of the VirD4/TraG subfamily. Most IncX3 plasmids harbored both bla OXA-181 and qnrS1 in their genomes, and the two antibiotic resistance genes were found to a composite transposon bracketed by two copies of insertion sequence IS26 in the same orientation. Our findings provide important insights into the phylogeny and evolution of bla OXA-181-positive IncX3 plasmids and further address their role in acquiring and spreading bla OXA-181 genes in Enterobacterales.}, }
@article {pmid36155788, year = {2022}, author = {Gilbert, C and Maumus, F}, title = {Multiple Horizontal Acquisitions of Plant Genes in the Whitefly Bemisia tabaci.}, journal = {Genome biology and evolution}, volume = {14}, number = {10}, pages = {}, pmid = {36155788}, issn = {1759-6653}, mesh = {Animals ; *Hemiptera/genetics ; Genes, Plant ; Gene Transfer, Horizontal ; }, abstract = {The extent to which horizontal gene transfer (HGT) has shaped eukaryote evolution remains an open question. Two recent studies reported four plant-like genes acquired through two HGT events by the whitefly Bemisia tabaci, a major agricultural pest (Lapadula WJ, Mascotti ML, Juri Ayub M. 2020. Whitefly genomes contain ribotoxin coding genes acquired from plants. Sci Rep. 10(1):15503; Xia J, et al. 2021. Whitefly hijacks a plant detoxification gene that neutralizes plant toxins. Cell 184(7):1693-1705 e1617.). Here, we uncovered a total of 49 plant-like genes deriving from at least 24 independent HGT events in the genome of the Middle East Asia Minor 1 (MEAM1) whitefly. Orthologs of these genes are present in three cryptic B. tabaci species, they are phylogenetically nested within plant sequences, they are expressed and have evolved under purifying selection. The predicted functions of these genes suggest that most of them are involved in plant-insect interactions. Thus, substantial plant-to-insect HGT may have facilitated the evolution of B. tabaci toward adaptation to a large host spectrum. Our study shows that eukaryote-to-eukaryote HGT may be relatively common in some lineages and it provides new candidate genes that may be targeted to improve current control strategies against whiteflies.}, }
@article {pmid36155273, year = {2022}, author = {Bhargav, A and Gupta, S and Seth, S and James, S and Fatima, F and Chaurasia, P and Ramachandran, S}, title = {Knowledgebase of potential multifaceted solutions to antimicrobial resistance.}, journal = {Computational biology and chemistry}, volume = {101}, number = {}, pages = {107772}, doi = {10.1016/j.compbiolchem.2022.107772}, pmid = {36155273}, issn = {1476-928X}, mesh = {Humans ; *Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology ; Bacteria ; *Anti-Infective Agents/pharmacology ; Knowledge Bases ; }, abstract = {Antimicrobial resistance (AMR), a top threat to global health, challenges preventive and treatment strategies of infections. AMR strains of microbial pathogens arise through multiple mechanisms. The underlying "antibiotic resistance genes" (ARGs) spread through various species by lateral gene transfer thereby causing global dissemination. Human methods also augment this process through inappropriate use, non-compliance to treatment schedule, and environmental waste. Worldwide significant efforts are being invested to discover novel therapeutic solutions for tackling resistant pathogens. Diverse therapeutic strategies have evolved over recent years. In this work we have developed a comprehensive knowledgebase by collecting alternative antimicrobial therapeutic strategies from literature data. Therapeutic strategies against bacteria, virus, fungus and parasites were extracted from PubMed literature using text mining. We have used a subjective (sentimental) approach for data mining new strategies, resulting in broad coverage of novel entities and subsequently add objective data like entity name (including IUPAC), potency, and safety information. The extracted data was organized in a freely accessible web platform, KOMBAT. The KOMBAT comprises 1104 Chemical compounds, 220 of newly identified antimicrobial peptides, 42 bacteriophages, 242 phytochemicals, 106 nanocomposites, and 94 novel entities for phototherapy. Entities tested and evaluated on AMR pathogens are included. We envision that this database will be useful for developing future therapeutics against AMR pathogens. The database can be accessed through http://kombat.igib.res.in/.}, }
@article {pmid36154280, year = {2022}, author = {Goytia, M and Wadsworth, CB}, title = {Canary in the Coal Mine: How Resistance Surveillance in Commensals Could Help Curb the Spread of AMR in Pathogenic Neisseria.}, journal = {mBio}, volume = {13}, number = {5}, pages = {e0199122}, pmid = {36154280}, issn = {2150-7511}, mesh = {Humans ; Azithromycin/pharmacology ; Drug Resistance, Bacterial/genetics ; Penicillin-Binding Proteins/metabolism ; Neisseria/genetics ; DNA Gyrase ; Neisseria gonorrhoeae ; *Gonorrhea/epidemiology ; Anti-Bacterial Agents/pharmacology/metabolism ; Ciprofloxacin/pharmacology ; *Anti-Infective Agents/metabolism ; beta-Lactams/pharmacology ; Microbial Sensitivity Tests ; }, abstract = {Antimicrobial resistance (AMR) is widespread within Neisseria gonorrhoeae populations. Recent work has highlighted the importance of commensal Neisseria (cN) as a source of AMR for their pathogenic relatives through horizontal gene transfer (HGT) of AMR alleles, such as mosaic penicillin binding protein 2 (penA), multiple transferable efflux pump (mtr), and DNA gyrase subunit A (gyrA) which impact beta-lactam, azithromycin, and ciprofloxacin susceptibility, respectively. However, nonpathogenic commensal species are rarely characterized. Here, we propose that surveillance of the universally carried commensal Neisseria may play the role of the "canary in the coal mine," and reveal circulating known and novel antimicrobial resistance determinants transferable to pathogenic Neisseria. We summarize the current understanding of commensal Neisseria as an AMR reservoir, and call to increase research on commensal Neisseria species, through expanding established gonococcal surveillance programs to include the collection, isolation, antimicrobial resistance phenotyping, and whole-genome sequencing (WGS) of commensal isolates. This will help combat AMR in the pathogenic Neisseria by: (i) determining the contemporary AMR profile of commensal Neisseria, (ii) correlating AMR phenotypes with known and novel genetic determinants, (iii) qualifying and quantifying horizontal gene transfer (HGT) for AMR determinants, and (iv) expanding commensal Neisseria genomic databases, perhaps leading to the identification of new drug and vaccine targets. The proposed modification to established Neisseria collection protocols could transform our ability to address AMR N. gonorrhoeae, while requiring minor modifications to current surveillance practices. IMPORTANCE Contemporary increases in the prevalence of antimicrobial resistance (AMR) in Neisseria gonorrhoeae populations is a direct threat to global public health and the effective treatment of gonorrhea. Substantial effort and financial support are being spent on identifying resistance mechanisms circulating within the gonococcal population. However, these surveys often overlook a known source of resistance for gonococci-the commensal Neisseria. Commensal Neisseria and pathogenic Neisseria frequently share DNA through horizontal gene transfer, which has played a large role in rendering antibiotic therapies ineffective in pathogenic Neisseria populations. Here, we propose the expansion of established gonococcal surveillance programs to integrate a collection, AMR profiling, and genomic sequencing pipeline for commensal species. This proposed expansion will enhance the field's ability to identify resistance in and from nonpathogenic reservoirs and anticipate AMR trends in pathogenic Neisseria.}, }
@article {pmid36149586, year = {2022}, author = {Gonçalves, OS and de Assis, JCS and Santana, MF}, title = {Breaking the ICE: an easy workflow for identifying and analyzing integrative and conjugative elements in bacterial genomes.}, journal = {Functional &amp; integrative genomics}, volume = {22}, number = {6}, pages = {1139-1145}, pmid = {36149586}, issn = {1438-7948}, support = {001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; }, mesh = {Workflow ; *Genome, Bacterial ; *Gene Transfer, Horizontal ; }, }
@article {pmid36145457, year = {2022}, author = {Crestani, C and Seligsohn, D and Forde, TL and Zadoks, RN}, title = {How GBS Got Its Hump: Genomic Analysis of Group B Streptococcus from Camels Identifies Host Restriction as well as Mobile Genetic Elements Shared across Hosts and Pathogens.}, journal = {Pathogens (Basel, Switzerland)}, volume = {11}, number = {9}, pages = {}, pmid = {36145457}, issn = {2076-0817}, support = {BB/R012075/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; VR2015-03583//Swedish Research Council/ ; 00336045//University of Glasgow/ ; }, abstract = {Group B Streptococcus (GBS) literature largely focuses on humans and neonatal disease, but GBS also affects numerous animals, with significant impacts on health and productivity. Spill-over events occur between humans and animals and may be followed by amplification and evolutionary adaptation in the new niche, including changes in the core or accessory genome content. Here, we describe GBS from one-humped camels (Camelus dromedarius), a relatively poorly studied GBS host of increasing importance for food security in arid regions. Genomic analysis shows that virtually all GBS from camels in East Africa belong to a monophyletic clade, sublineage (SL)609. Capsular types IV and VI, including a new variant of type IV, were over-represented compared to other host species. Two genomic islands with signatures of mobile elements contained most camel-associated genes, including genes for metal and carbohydrate utilisation. Lactose fermentation genes were associated with milk isolates, albeit at lower prevalence in camel than bovine GBS. The presence of a phage with high identity to Streptococcus pneumoniae and Streptococcus suis suggests lateral gene transfer between GBS and bacterial species that have not been described in camels. The evolution of camel GBS appears to combine host restriction with the sharing of accessory genome content across pathogen and host species.}, }
@article {pmid36144411, year = {2022}, author = {García-Ríos, E and Guillamón, JM}, title = {Genomic Adaptations of Saccharomyces Genus to Wine Niche.}, journal = {Microorganisms}, volume = {10}, number = {9}, pages = {}, pmid = {36144411}, issn = {2076-2607}, support = {PCIN-2015-143//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2019-108722RB-C31//Fondo Europeo de Desarrollo Regional/ ; }, abstract = {Wine yeast have been exposed to harsh conditions for millennia, which have led to adaptive evolutionary strategies. Thus, wine yeasts from Saccharomyces genus are considered an interesting and highly valuable model to study human-drive domestication processes. The rise of whole-genome sequencing technologies together with new long reads platforms has provided new understanding about the population structure and the evolution of wine yeasts. Population genomics studies have indicated domestication fingerprints in wine yeast, including nucleotide variations, chromosomal rearrangements, horizontal gene transfer or hybridization, among others. These genetic changes contribute to genetically and phenotypically distinct strains. This review will summarize and discuss recent research on evolutionary trajectories of wine yeasts, highlighting the domestication hallmarks identified in this group of yeast.}, }
@article {pmid36144405, year = {2022}, author = {Sowah, RA and Molina, M and Georgacopoulos, O and Snyder, B and Cyterski, M}, title = {Sources and Drivers of ARGs in Urban Streams in Atlanta, Georgia, USA.}, journal = {Microorganisms}, volume = {10}, number = {9}, pages = {}, pmid = {36144405}, issn = {2076-2607}, support = {Corporate Funding//US Environmental Protection Agency/ ; }, abstract = {The spread of antibiotic resistance genes (ARGs) in the aquatic environment is an emerging concern in the interest of protecting public health. Stemming the environmental dissemination of ARGs will require a better understanding of the sources and drivers of ARGs in the water environment. In this study, we used direct measurement of sewage-associated molecular markers, the class 1 integron gene, standard water quality parameters, and watershed characteristics to evaluate the sources and drivers of ARGs in an urban watershed impacted by a gradient of human activities. Quantitative polymerase chain reaction (qPCR) was used to quantify the abundance of the sewage-associated HF183, the E. coli fecal indicator, class 1 integron gene (int1), and the ARGs sulI, sulII, tetW, tetM, ampC, and blaSHV in stream water samples collected from the Proctor Creek watershed in Atlanta, Georgia. Our findings show that ARGs were widely distributed, with detection frequencies of 96% (sulI and sulII), 82% (tetW and tetM), and 49% (ampC and blaSHV). All the ARGs were positively and significantly correlated (r > 0.5) with the HF183 and E. coli markers. Non-linear machine learning models developed using generalized boosting show that more than 70% of the variation in ARG loads in the watershed could be explained by fecal source loading, with other factors such as class 1 integron, which is associated with acquired antibiotic resistance, and environmental factors contributing < 30% to ARG variation. These results suggest that input from fecal sources is a more critical driver of ARG dissemination than environmental stressors or horizontal gene transfer in aquatic environments highly impacted by anthropogenic pollution. Finally, our results provide local watershed managers and stakeholders with information to mitigate the burden of ARGs and fecal bacteria in urban streams.}, }
@article {pmid36142804, year = {2022}, author = {Maslova, O and Mindlin, S and Beletsky, A and Mardanov, A and Petrova, M}, title = {Plasmids as Key Players in Acinetobacter Adaptation.}, journal = {International journal of molecular sciences}, volume = {23}, number = {18}, pages = {}, pmid = {36142804}, issn = {1422-0067}, support = {122040800186-8//Ministry of Scinece and Higher Eduaction/ ; support in the framework of the Kurchatov Genome Center development Program (Agreement 075-15-2019-1664)//Ministry of Science and Higher Education of Russian Federation/ ; }, mesh = {*Acinetobacter/genetics ; *Acinetobacter baumannii/genetics ; Anti-Bacterial Agents ; *Arsenic ; *Metals, Heavy ; Plasmids/genetics ; }, abstract = {This review briefly summarizes the data on the mechanisms of development of the adaptability of Acinetobacters to various living conditions in the environment and in the clinic. A comparative analysis of the genomes of free-living and clinical strains of A. lwoffii, as well as the genomes of A. lwoffii and A. baumannii, has been carried out. It has been shown that plasmids, both large and small, play a key role in the formation of the adaptability of Acinetobacter to their living conditions. In particular, it has been demonstrated that the plasmids of various strains of Acinetobacter differ from each other in their structure and gene composition depending on the lifestyle of their host bacteria. Plasmids of modern strains are enriched with antibiotic-resistant genes, while the content of genes involved in resistance to heavy metals and arsenic is comparable to plasmids from modern and ancient strains. It is concluded that Acinetobacter plasmids may ensure the survival of host bacteria under conditions of various types of environmental and clinical stresses. A brief overview of the main mechanisms of horizontal gene transfer on plasmids inherent in Acinetobacter strains is also given.}, }
@article {pmid36140010, year = {2022}, author = {Riva, V and Patania, G and Riva, F and Vergani, L and Crotti, E and Mapelli, F}, title = {Acinetobacter baylyi Strain BD413 Can Acquire an Antibiotic Resistance Gene by Natural Transformation on Lettuce Phylloplane and Enter the Endosphere.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {9}, pages = {}, pmid = {36140010}, issn = {2079-6382}, support = {2018-0995//Fondazione Cariplo/ ; }, abstract = {Antibiotic resistance spread must be considered in a holistic framework which comprises the agri-food ecosystems, where plants can be considered a bridge connecting water and soil habitats with the human microbiome. However, the study of horizontal gene transfer events within the plant microbiome is still overlooked. Here, the environmental strain Acinetobacter baylyi BD413 was used to study the acquisition of extracellular DNA (exDNA) carrying an antibiotic resistance gene (ARG) on lettuce phylloplane, performing experiments at conditions (i.e., plasmid quantities) mimicking those that can be found in a water reuse scenario. Moreover, we assessed how the presence of a surfactant, a co-formulant widely used in agriculture, affected exDNA entry in bacteria and plant tissues, besides the penetration and survival of bacteria into the leaf endosphere. Natural transformation frequency in planta was comparable to that occurring under optimal conditions (i.e., temperature, nutrient provision, and absence of microbial competitors), representing an entrance pathway of ARGs into an epiphytic bacterium able to penetrate the endosphere of a leafy vegetable. The presence of the surfactant determined a higher presence of culturable transformant cells in the leaf tissues but did not significantly increase exDNA entry in A. baylyi BD413 cells and lettuce leaves. More research on HGT (Horizontal Gene Transfer) mechanisms in planta should be performed to obtain experimental data on produce safety in terms of antibiotic resistance.}, }
@article {pmid36138780, year = {2022}, author = {Chitayat Levi, L and Rippin, I and Ben Tulila, M and Galron, R and Tuller, T}, title = {Modulating Gene Expression within a Microbiome Based on Computational Models.}, journal = {Biology}, volume = {11}, number = {9}, pages = {}, pmid = {36138780}, issn = {2079-7737}, support = {Non//Safra center of bioinformatics at TAU/ ; }, abstract = {Recent research in the field of bioinformatics and molecular biology has revealed the immense complexity and uniqueness of microbiomes, while also showcasing the impact of the symbiosis between a microbiome and its host or environment. A core property influencing this process is horizontal gene transfer between members of the bacterial community used to maintain genetic variation. The essential effect of this mechanism is the exposure of genetic information to a wide array of members of the community, creating an additional "layer" of information in the microbiome named the "plasmidome". From an engineering perspective, introduction of genetic information to an environment must be facilitated into chosen species which will be able to carry out the desired effect instead of competing and inhibiting it. Moreover, this process of information transfer imposes concerns for the biosafety of genetic engineering of microbiomes as exposure of genetic information into unwanted hosts can have unprecedented ecological impacts. Current technologies are usually experimentally developed for a specific host/environment, and only deal with the transformation process itself at best, ignoring the impact of horizontal gene transfer and gene-microbiome interactions that occur over larger periods of time in uncontrolled environments. The goal of this research was to design new microbiome-specific versions of engineered genetic information, providing an additional layer of compatibility to existing engineering techniques. The engineering framework is entirely computational and is agnostic to the selected microbiome or gene by reducing the problem into the following set up: microbiome species can be defined as wanted or unwanted hosts of the modification. Then, every element related to gene expression (e.g., promoters, coding regions, etc.) and regulation is individually examined and engineered by novel algorithms to provide the defined expression preferences. Additionally, the synergistic effect of the combination of engineered gene blocks facilitates robustness to random mutations that might occur over time. This method has been validated using both computational and experimental tools, stemming from the research done in the iGEM 2021 competition, by the TAU group.}, }
@article {pmid36138049, year = {2022}, author = {Zielezinski, A and Loch, JI and Karlowski, WM and Jaskolski, M}, title = {Massive annotation of bacterial L-asparaginases reveals their puzzling distribution and frequent gene transfer events.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {15797}, pmid = {36138049}, issn = {2045-2322}, mesh = {Ammonia ; *Asparaginase/genetics ; *Asparagine/genetics ; Aspartic Acid/genetics ; Bacteria/enzymology ; Bacterial Proteins/genetics ; Gene Transfer, Horizontal ; Phylogeny ; }, abstract = {L-Asparaginases, which convert L-asparagine to L-aspartate and ammonia, come in five types, AI-AV. Some bacterial type AII enzymes are a key element in the treatment of acute lymphoblastic leukemia in children, but new L-asparaginases with better therapeutic properties are urgently needed. Here, we search publicly available bacterial genomes to annotate L-asparaginase proteins belonging to the five known types. We characterize taxonomic, phylogenetic, and genomic patterns of L-asparaginase occurrences pointing to frequent horizontal gene transfer (HGT) events, also occurring multiple times in the same recipient species. We show that the reference AV gene, encoding a protein originally found and structurally studied in Rhizobium etli, was acquired via HGT from Burkholderia. We also describe the sequence variability of the five L-asparaginase types and map the conservation levels on the experimental or predicted structures of the reference enzymes, finding the most conserved residues in the protein core near the active site, and the most variable ones on the protein surface. Additionally, we highlight the most common sequence features of bacterial AII proteins that may aid in selecting therapeutic L-asparaginases. Finally, we point to taxonomic units of bacteria that do not contain recognizable sequences of any of the known L-asparaginase types, implying that those microorganisms most likely contain new, as yet unknown types of L-asparaginases. Such novel enzymes, when properly identified and characterized, could hold promise as antileukemic drugs.}, }
@article {pmid36138004, year = {2022}, author = {Kapteijn, R and Shitut, S and Aschmann, D and Zhang, L and de Beer, M and Daviran, D and Roverts, R and Akiva, A and van Wezel, GP and Kros, A and Claessen, D}, title = {Endocytosis-like DNA uptake by cell wall-deficient bacteria.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {5524}, pmid = {36138004}, issn = {2041-1723}, mesh = {*Bacteria/genetics ; Cell Wall/metabolism ; DNA/metabolism ; DNA, Bacterial/genetics ; *Dextrans ; Endocytosis ; Liposomes ; Nanoparticles ; Sodium Azide ; }, abstract = {Horizontal gene transfer in bacteria is widely believed to occur via conjugation, transduction and transformation. These mechanisms facilitate the passage of DNA across the protective cell wall using sophisticated machinery. Here, we report that cell wall-deficient bacteria can engulf DNA and other extracellular material via an endocytosis-like process. Specifically, we show that L-forms of the filamentous actinomycete Kitasatospora viridifaciens can take up plasmid DNA, polysaccharides (dextran) and 150-nm lipid nanoparticles. The process involves invagination of the cytoplasmic membrane, leading to formation of intracellular vesicles that encapsulate extracellular material. DNA uptake is not affected by deletion of genes homologous to comEC and comEA, which are required for natural transformation in other species. However, uptake is inhibited by sodium azide or incubation at 4 °C, suggesting the process is energy-dependent. The encapsulated materials are released into the cytoplasm upon degradation of the vesicle membrane. Given that cell wall-deficient bacteria are considered a model for early life forms, our work reveals a possible mechanism for primordial cells to acquire food or genetic material before invention of the bacterial cell wall.}, }
@article {pmid36130651, year = {2022}, author = {Balbuena-Alonso, MG and Cortés-Cortés, G and Kim, JW and Lozano-Zarain, P and Camps, M and Del Carmen Rocha-Gracia, R}, title = {Genomic analysis of plasmid content in food isolates of E. coli strongly supports its role as a reservoir for the horizontal transfer of virulence and antibiotic resistance genes.}, journal = {Plasmid}, volume = {123-124}, number = {}, pages = {102650}, pmid = {36130651}, issn = {1095-9890}, support = {R41 AI122740/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Plasmids/genetics ; *Escherichia coli/genetics ; Anti-Bacterial Agents/pharmacology ; Virulence/genetics ; Drug Resistance, Microbial/genetics ; Genomics ; *Escherichia coli Infections ; Gene Transfer, Horizontal ; }, abstract = {The link between E. coli strains contaminating foods and human disease is unclear, with some reports supporting a direct transmission of pathogenic strains via food and others highlighting their role as reservoirs for resistance and virulence genes. Here we take a genomics approach, analyzing a large set of fully-assembled genomic sequences from E. coli available in GenBank. Most of the strains isolated in food are more closely related to each other than to clinical strains, arguing against a frequent direct transmission of pathogenic strains from food to the clinic. We also provide strong evidence of genetic exchanges between food and clinical strains that are facilitated by plasmids. This is based on an overlapped representation of virulence and resistance genes in plasmids isolated from these two sources. We identify clusters of phylogenetically-related plasmids that are largely responsible for the observed overlap and see evidence of specialization, with some food plasmid clusters preferentially transferring virulence factors over resistance genes. Consistent with these observations, food plasmids have a high mobilization potential based on their plasmid taxonomic unit classification and on an analysis of mobilization gene content. We report antibiotic resistance genes of high clinical relevance and their specific incompatibility group associations. Finally, we also report a striking enrichment for adhesins in food plasmids and their association with specific IncF replicon subtypes. The identification of food plasmids with specific markers (Inc and PTU combinations) as mediators of horizontal transfer between food and clinical strains opens new research avenues and should assist with the design of surveillance strategies.}, }
@article {pmid36125448, year = {2023}, author = {Zaman, S and Sledzieski, S and Berger, B and Wu, YC and Bansal, MS}, title = {virDTL: Viral Recombination Analysis Through Phylogenetic Reconciliation and Its Application to Sarbecoviruses and SARS-CoV-2.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {30}, number = {1}, pages = {3-20}, pmid = {36125448}, issn = {1557-8666}, support = {R35 GM141861/GM/NIGMS NIH HHS/United States ; R01 GM081871/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Humans ; SARS-CoV-2/genetics ; *COVID-19/epidemiology/genetics ; Phylogeny ; *Severe acute respiratory syndrome-related coronavirus ; Pandemics ; Gene Transfer, Horizontal/genetics ; *Chiroptera/genetics ; Genome, Viral/genetics ; Evolution, Molecular ; }, abstract = {An accurate understanding of the evolutionary history of rapidly-evolving viruses like SARS-CoV-2, responsible for the COVID-19 pandemic, is crucial to tracking and preventing the spread of emerging pathogens. However, viruses undergo frequent recombination, which makes it difficult to trace their evolutionary history using traditional phylogenetic methods. In this study, we present a phylogenetic workflow, virDTL, for analyzing viral evolution in the presence of recombination. Our approach leverages reconciliation methods developed for inferring horizontal gene transfer in prokaryotes and, compared to existing tools, is uniquely able to identify ancestral recombinations while accounting for several sources of inference uncertainty, including in the construction of a strain tree, estimation and rooting of gene family trees, and reconciliation itself. We apply this workflow to the Sarbecovirus subgenus and demonstrate how a principled analysis of predicted recombination gives insight into the evolution of SARS-CoV-2. In addition to providing confirming evidence for the horseshoe bat as its zoonotic origin, we identify several ancestral recombination events that merit further study.}, }
@article {pmid36125273, year = {2022}, author = {Uppal, S and Metz, JL and Xavier, RKM and Nepal, KK and Xu, D and Wang, G and Kwan, JC}, title = {Uncovering Lasonolide A Biosynthesis Using Genome-Resolved Metagenomics.}, journal = {mBio}, volume = {13}, number = {5}, pages = {e0152422}, pmid = {36125273}, issn = {2150-7511}, support = {R21 CA209189/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; RNA, Ribosomal, 16S/genetics ; Polyketide Synthases/genetics ; Phylogeny ; Symbiosis/genetics ; Acyl Carrier Protein/genetics ; Metagenomics ; *Porifera/microbiology ; Bacteria/genetics ; *Biological Products/pharmacology ; *Antineoplastic Agents ; Acyltransferases/genetics ; }, abstract = {Invertebrates, particularly sponges, have been a dominant source of new marine natural products. For example, lasonolide A (LSA) is a potential anticancer molecule isolated from the marine sponge Forcepia sp., with nanomolar growth inhibitory activity and a unique cytotoxicity profile against the National Cancer Institute 60-cell-line screen. Here, we identified the putative biosynthetic pathway for LSA. Genomic binning of the Forcepia sponge metagenome revealed a Gram-negative bacterium belonging to the phylum Verrucomicrobia as the candidate producer of LSA. Phylogenetic analysis showed that this bacterium, here named "Candidatus Thermopylae lasonolidus," only has 88.78% 16S rRNA identity with the closest relative, Pedosphaera parvula Ellin514, indicating that it represents a new genus. The lasonolide A (las) biosynthetic gene cluster (BGC) was identified as a trans-acyltransferase (AT) polyketide synthase (PKS) pathway. Compared with its host genome, the las BGC exhibits a significantly different GC content and pentanucleotide frequency, suggesting a potential horizontal acquisition of the gene cluster. Furthermore, three copies of the putative las pathway were identified in the candidate producer genome. Differences between the three las repeats were observed, including the presence of three insertions, two single-nucleotide polymorphisms, and the absence of a stand-alone acyl carrier protein in one of the repeats. Even though the verrucomicrobial producer shows signs of genome reduction, its genome size is still fairly large (about 5 Mbp), and, compared to its closest free-living relative, it contains most of the primary metabolic pathways, suggesting that it is in the early stages of reduction. IMPORTANCE While sponges are valuable sources of bioactive natural products, a majority of these compounds are produced in small quantities by uncultured symbionts, hampering the study and clinical development of these unique compounds. Lasonolide A (LSA), isolated from marine sponge Forcepia sp., is a cytotoxic molecule active at nanomolar concentrations, which causes premature chromosome condensation, blebbing, cell contraction, and loss of cell adhesion, indicating a novel mechanism of action and making it a potential anticancer drug lead. However, its limited supply hampers progression to clinical trials. We investigated the microbiome of Forcepia sp. using culture-independent DNA sequencing, identified genes likely responsible for LSA synthesis in an uncultured bacterium, and assembled the symbiont's genome. These insights provide future opportunities for heterologous expression and cultivation efforts that may minimize LSA's supply problem.}, }
@article {pmid36124853, year = {2022}, author = {Tanaka, E and Wajima, T and Nakaminami, H and Uchiya, KI}, title = {Alternative quinolone-resistance pathway caused by simultaneous horizontal gene transfer in Haemophilus influenzae.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {77}, number = {12}, pages = {3270-3274}, doi = {10.1093/jac/dkac312}, pmid = {36124853}, issn = {1460-2091}, mesh = {*Haemophilus influenzae/genetics ; *Quinolones/pharmacology ; DNA Topoisomerase IV/genetics ; DNA Gyrase/genetics ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Mutation ; Fluoroquinolones ; Drug Resistance, Bacterial/genetics ; }, abstract = {BACKGROUND: Quinolone-resistant bacteria are known to emerge via the accumulation of mutations in a stepwise manner. Recent studies reported the emergence of quinolone low-susceptible Haemophilus influenzae ST422 isolates harbouring two relevant mutations, although ST422 isolates harbouring one mutation were never identified.<br><br>OBJECTIVES: To investigate if GyrA and ParC from quinolone low-susceptible isolates can be transferred horizontally and simultaneously to susceptible isolates.<br><br>METHODS: Genomic DNA was extracted from an H. influenzae isolate harbouring amino acid substitutions in both gyrA and parC and mixed with clinical isolates. The emergence of resistant isolates was compared, and WGS analysis was performed.<br><br>RESULTS: By adding the genomic DNA harbouring both mutated gyrA and parC, resistant bacteria exhibiting recombination at gyrA only or both gyrA and parC loci were obtained on nalidixic acid and pipemidic acid plates, and the frequency was found to increase with the amount of DNA. Recombination events in gyrA only and in both gyrA and parC occurred with at least 1 and 1-100&#x2005;ng of DNA, respectively. The genome sequence of a representative strain showed recombination events throughout the genome. The MIC of quinolone for the resulting strains was found to be similar to that of the donor. Although the recombination efficacy was different among the various strains, all strains used in this study obtained multiple genes simultaneously.<br><br>CONCLUSIONS: These findings indicate that H. influenzae can simultaneously obtain more than two mutated genes. This mechanism of horizontal transfer could be an alternative pathway for attaining quinolone resistance.}, }
@article {pmid36123439, year = {2022}, author = {Purtschert-Montenegro, G and Cárcamo-Oyarce, G and Pinto-Carbó, M and Agnoli, K and Bailly, A and Eberl, L}, title = {Pseudomonas putida mediates bacterial killing, biofilm invasion and biocontrol with a type IVB secretion system.}, journal = {Nature microbiology}, volume = {7}, number = {10}, pages = {1547-1557}, pmid = {36123439}, issn = {2058-5276}, support = {169307/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {Biofilms ; *Solanum lycopersicum/microbiology ; *Pseudomonas putida/genetics ; *Ralstonia solanacearum ; Soil ; }, abstract = {Many bacteria utilize contact-dependent killing machineries to eliminate rivals in their environmental niches. Here we show that the plant root colonizer Pseudomonas putida strain IsoF is able to kill a wide range of soil and plant-associated Gram-negative bacteria with the aid of a type IVB secretion system (T4BSS) that delivers a toxic effector into bacterial competitors in a contact-dependent manner. This extends the range of targets of T4BSSs-so far thought to transfer effectors only into eukaryotic cells-to prokaryotes. Bioinformatic and genetic analyses showed that this killing machine is entirely encoded by the kib gene cluster located within a rare genomic island, which was recently acquired by horizontal gene transfer. P. putida IsoF utilizes this secretion system not only as a defensive weapon to kill bacterial competitors but also as an offensive weapon to invade existing biofilms, allowing the strain to persist in its natural environment. Furthermore, we show that strain IsoF can protect tomato plants against the phytopathogen Ralstonia solanacearum in a T4BSS-dependent manner, suggesting that IsoF can be exploited for pest control and sustainable agriculture.}, }
@article {pmid36121484, year = {2022}, author = {Sheikh, BA and Bhat, BA and Mir, MA}, title = {Antimicrobial resistance: new insights and therapeutic implications.}, journal = {Applied microbiology and biotechnology}, volume = {106}, number = {19-20}, pages = {6427-6440}, pmid = {36121484}, issn = {1432-0614}, support = {DST-SERB-Grant No. TAR/001213/2018//Science Engineering and Research Board IN/ ; }, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria ; *Drug Resistance, Bacterial ; Humans ; }, abstract = {Antimicrobial resistance has not been a new phenomenon. Still, the number of resistant organisms, the geographic areas affected by emerging drug resistance, and the magnitude of resistance in a single organism are enormous and mounting. Disease and disease-causing agents formerly thought to be contained by antibiotics are now returning in new forms resistant to existing therapies. Antimicrobial resistance is one of the most severe and complicated health issues globally, driven by interrelated dynamics in humans, animals, and environmental health sectors. Coupled with various epidemiological factors and a limited pipeline for new antimicrobials, all these misappropriations allow the transmission of drug-resistant organisms. The problem is likely to worsen soon. Antimicrobial resistance in general and antibiotic resistance in particular is a shared global problem. Actions taken by any single country can adversely or positively affect the other country. Targeted coordination and prevention strategies are critical in stopping the spread of antibiotic-resistant organisms and hence its overall management. This article has provided in-depth knowledge about various methods that can help mitigate the emergence and spread of antimicrobial resistance globally. KEY POINTS: • Overview of antimicrobial resistance as a global challenge and explain various reasons for its rapid progression. • Brief about the intrinsic and acquired resistance to antimicrobials and development of antibiotic resistance in bacteria. • Systematically organized information is provided on different strategies for tackling antimicrobial resistance for the welfare of human health.}, }
@article {pmid36118580, year = {2022}, author = {Philips, JG and Martin-Avila, E and Robold, AV}, title = {Horizontal gene transfer from genetically modified plants - Regulatory considerations.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {10}, number = {}, pages = {971402}, pmid = {36118580}, issn = {2296-4185}, abstract = {Gene technology regulators receive applications seeking permission for the environmental release of genetically modified (GM) plants, many of which possess beneficial traits such as improved production, enhanced nutrition and resistance to drought, pests and diseases. The regulators must assess the risks to human and animal health and to the environment from releasing these GM plants. One such consideration, of many, is the likelihood and potential consequence of the introduced or modified DNA being transferred to other organisms, including people. While such gene transfer is most likely to occur to sexually compatible relatives (vertical gene transfer), horizontal gene transfer (HGT), which is the acquisition of genetic material that has not been inherited from a parent, is also a possibility considered during these assessments. Advances in HGT detection, aided by next generation sequencing, have demonstrated that HGT occurrence may have been previously underestimated. In this review, we provide updated evidence on the likelihood, factors and the barriers for the introduced or modified DNA in GM plants to be horizontally transferred into a variety of recipients. We present the legislation and frameworks the Australian Gene Technology Regulator adheres to with respect to the consideration of risks posed by HGT. Such a perspective may generally be applicable to regulators in other jurisdictions as well as to commercial and research organisations who develop GM plants.}, }
@article {pmid36116192, year = {2022}, author = {Wang, D and Meng, Y and Meng, F}, title = {Genome-centric metagenomics insights into functional divergence and horizontal gene transfer of denitrifying bacteria in anammox consortia.}, journal = {Water research}, volume = {224}, number = {}, pages = {119062}, doi = {10.1016/j.watres.2022.119062}, pmid = {36116192}, issn = {1879-2448}, mesh = {Amino Acids ; Anaerobic Ammonia Oxidation ; Animals ; Bacteria/metabolism ; *Bioreactors/microbiology ; Biotin/genetics/metabolism ; Carbohydrates ; Denitrification ; *Gene Transfer, Horizontal ; Metagenomics ; Methionine/genetics/metabolism ; Nitrogen/metabolism ; Oxidation-Reduction ; Swine ; Thiamine/metabolism ; Vitamins/metabolism ; }, abstract = {Denitrifying bacteria with high abundances in anammox communities play crucial roles in achieving stable anammox-based systems. Despite the relative constant composition of denitrifying bacteria, their functional diversity remains to be explored in anammox communities. Herein, a total of 77 high-quality metagenome-assembled genomes (MAGs) of denitrifying bacteria were recovered from the anammox community in a full-scale swine wastewater treatment plant. Among these microbes, a total of 26 MAGs were affiliated with the seven dominant denitrifying genera that have total abundances higher than 1%. A meta-analysis of these species suggested that external organics reduced the abundances of genus Ignavibacterium and species MAG.305 of UTPRO2 in anammox communities. Comparative genome analysis revealed functional divergence across different denitrifying bacteria, largely owing to their distinct capabilities for carbohydrate (including endogenous and exogenous) utilization and vitamin (e.g., pantothenate and thiamine) biosynthesis. Serval microbes in this system contained fewer genes encoding biotin, pantothenate and methionine biosynthesis compared with their related species from other habitats. In addition, the genes encoding energy production and conversion (73 genes) and inorganic ion transport (53 genes) putatively transferred from other species to denitrifying bacteria, while these denitrifying bacteria (especially genera UTPRO2 and SCN-69-89) likely donated the genes encoding nutrients (e.g., inorganic ion and amino acid) transporter (64 genes) for other members to utilize new metabolites. Collectively, these findings highlighted the functional divergence of these denitrifying bacteria and speculated that the genetic interactions within anammox communities through horizontal gene transfer may be one of the reasons for their functional divergence.}, }
@article {pmid36114974, year = {2023}, author = {Azhogina, T and Sazykina, M and Konstantinova, E and Khmelevtsova, L and Minkina, T and Antonenko, E and Sushkova, S and Khammami, M and Mandzhieva, S and Sazykin, I}, title = {Bioaccessible PAH influence on distribution of antibiotic resistance genes and soil toxicity of different types of land use.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {5}, pages = {12695-12713}, pmid = {36114974}, issn = {1614-7499}, support = {0852-2020-0029//Ministry of Science and Higher Education of the Russian Federation/ ; }, mesh = {Soil/chemistry ; Anti-Bacterial Agents/pharmacology ; *Soil Pollutants/analysis ; Agriculture ; *Polycyclic Aromatic Hydrocarbons/analysis ; Drug Resistance, Microbial/genetics ; Soil Microbiology ; Genes, Bacterial ; }, abstract = {For a better understanding of the dissemination of antibiotic resistance genes (ARGs) in natural microbial communities, it is necessary to study the factors influencing it. There are not enough studies showing the connection of some pollutants with the dissemination of ARGs and especially few works on the effect of polycyclic aromatic compounds (PAHs) on the spread of resistance in microbiocenosis. In this respect, the aim of the study was to determine the effect of bioaccessible PAHs on soil resistome. The toxicity and the content of bioaccessible PAHs and ARGs were studied in 64 samples of soils of different types of land use in the Rostov Region of Russia. In most soils, a close positive correlation was demonstrated between different ARGs and bioaccessible PAHs with different content of rings in the structure. Six of the seven studied ARGs correlated with the content of 2-, 3-, 4-, 5- or 6-ring PAHs. The greatest number of close correlations was found between the content of PAHs and ARGs in the soils of protected areas, for agricultural purposes, and in soils of hospitals. The diverse composition of microbial communities in these soils might greatly facilitate this process. A close correlation between various toxic effects identified with a battery of whole-cell bacterial biosensors and bioaccessible PAHs of various compositions was established. This correlation showed possible mechanisms of PAHs' influence on microorganisms (DNA damage, oxidative stress, etc.), which led to a significant increase in horizontal gene transfer and spread of some ARGs in soil microbial communities. All this information, taken together, suggests that bioaccessible PAHs can enhance the spread of antibiotic resistance genes.}, }
@article {pmid36114450, year = {2022}, author = {Zhang, C and Lin, Q and Zhang, J and Huang, Z and Nan, P and Li, L and Song, Z and Zhang, W and Yang, J and Wang, Y}, title = {Comparing complete organelle genomes of holoparasitic Christisonia kwangtungensis (Orabanchaceae) with its close relatives: how different are they?.}, journal = {BMC plant biology}, volume = {22}, number = {1}, pages = {444}, pmid = {36114450}, issn = {1471-2229}, mesh = {*Genome, Mitochondrial/genetics ; *Genome, Plastid/genetics ; *Orobanchaceae/genetics ; Plastids/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Orobanchaceae is the only flowering plant family with species from free-living nonparasite, hemi-parasite to holoparasite, making it an ideal system for studying the evolution of parasitism. However, both plastid and mitochondrial genome have been sequenced in only few parasitic species in Orobanchaceae. Therefore, further comparative study is wanted to investigate the impact of holoparasitism on organelle genomes evolution between close relatives. Here, we sequenced organelle genomes and transcriptome of holoparasitic Christisonia kwangtungensis and compared it with its closely related groups to analyze similarities and differences in adaption strategies to the holoparasitic lifestyle.<br><br>RESULTS: The plastid genome of C. kwangtungensis has undergone extensive pseudogenization and gene loss, but its reduction pattern is different from that of Aeginetia indica, the close relative of C. kwangtungensis. Similarly, the gene expression detected in the photosynthetic pathway of these two genera is different. In Orobanchaceae, holoparasites in Buchnereae have more plastid gene loss than Rhinantheae, which reflects their longer history of holoparasitism. Distinct from severe degradation of the plastome, protein-coding genes in the mitochondrial genome of C. kwangtungensis are relatively conserved. Interestingly, besides intracellularly transferred genes which are still retained in its plastid genome, we also found several horizontally transferred genes of plastid origin from diverse donors other than their current hosts in the mitochondrial genome, which probably indicate historical hosts.<br><br>CONCLUSION: Even though C. kwangtungensis and A. indica are closely related and share severe degradation of plastome, they adapt organelle genomes to the parasitic lifestyle in different ways. The difference between their gene loss and gene expression shows they ultimately lost photosynthetic genes but through different pathways. Our study exemplifies how parasites part company after achieving holoparasitism.}, }
@article {pmid36113785, year = {2023}, author = {Wang, L and Yan, X and Zhu, L and Wang, J and Xing, B and Kim, YM and Wang, J}, title = {Spread and driving factors of antibiotic resistance genes in soil-plant system in long-term manured greenhouse under lead (Pb) stress.}, journal = {The Science of the total environment}, volume = {855}, number = {}, pages = {158756}, doi = {10.1016/j.scitotenv.2022.158756}, pmid = {36113785}, issn = {1879-1026}, mesh = {*Manure/microbiology ; *Soil ; Lead ; Anti-Bacterial Agents/pharmacology ; Soil Microbiology ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; }, abstract = {Livestock manure is often used as fertilizer in greenhouses, resulting in simultaneous enrichment of heavy metals and antibiotic resistance genes (ARGs) in soils. The soil-plant system is a non-negligible way to spread ARGs; however, the effects of lead (Pb) on the spread of ARGs and their driving factors in the greenhouse soil-plant system remain unclear. In this present study, the occurrence of ARGs in greenhouse soils and their spread into plants under Pb stress were studied. Overall, Pb promoted the accumulation of ARGs in root endophytes at 10, 50, and 100 mg/kg as well as in soils at 10 and 200 mg/kg, but reduced the total relative abundance of ARGs in leaf endophytes. Particularly, Pb increased the mobile genetic elements (MGEs) relative abundance and endophytic bacterial community diversity in roots, consistent with the change in the total relative abundance of ARGs. Network analysis revealed that bacterial community and MGEs may jointly affect the migration of ARGs in the soil-plant system of greenhouses. Overall, this study extended our knowledge of how Pb can promote the transmission of ARGs to plant roots from greenhouse soils receiving long-term manure applications, which must be considered when assessing the risk of ARGs to public health.}, }
@article {pmid36113173, year = {2022}, author = {Gao, Q and Ma, X and Wang, Z and Chen, H and Luo, Y and Wu, B and Qi, S and Lin, M and Tian, J and Qiao, Y and Grossart, HP and Xu, W and Huang, L}, title = {Seasonal variation, virulence gene and antibiotic resistance of Vibrio in a semi-enclosed bay with mariculture (Dongshan Bay, Southern China).}, journal = {Marine pollution bulletin}, volume = {184}, number = {}, pages = {114112}, doi = {10.1016/j.marpolbul.2022.114112}, pmid = {36113173}, issn = {1879-3363}, mesh = {Virulence/genetics ; Seasons ; Hemolysin Proteins ; Bays ; *Vibrio ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; China/epidemiology ; *Vibrio parahaemolyticus/genetics ; }, abstract = {In this study, the virulence genes, antibiotic resistance of culturable Vibrio and the environmental factors affecting Vibrio abundance were analyzed in four seasons in DongShan Bay with different intensity of aquaculture practice. A total of 253 bacteria isolates were obtained, of which 177 Vibrio strains belonged to 26 species. Annual Vibrio abundance in this region ranged from 20 to 11,600 CFU mL[-1] and the most significant positive correlation occurred with temperature. Detection of 9 different Vibrio virulence genes revealed that most isolates contained atypical virulence genes in addition to the typical ones. In particular, virulence genes of hemolysin such as tdh, trh, and hlyA (6.32 %, 15.52 %, and 11.30 %) showed different degrees of horizontal gene transfer (HGT). In our antibiotic resistance test, the multiple antibiotic resistance (MAR) index of the isolates ranged from 0.01 to 0.03 in different seasons, and three MAR Vibrio strains were detected. Overall, our study sheds new light on the spatial distribution patterns and the occurrence of virulence genes and antibiotics resistance Vibrio isolated from a subtropical bay with intensive aquaculture. Our study provides a suitable microbial quality surveillance in a mariculture impacted coastal environment. It will help to establish effective disease prevention measures in this area and provide useful guidance and support for formulating local antibiotics use policies.}, }
@article {pmid36108440, year = {2022}, author = {Oliveira, V and Polónia, ARM and Cleary, DFR and Huang, YM and de Voogd, NJ and Keller-Costa, T and Costa, R and Gomes, NCM}, title = {Assessing the genomic composition, putative ecological relevance and biotechnological potential of plasmids from sponge bacterial symbionts.}, journal = {Microbiological research}, volume = {265}, number = {}, pages = {127183}, doi = {10.1016/j.micres.2022.127183}, pmid = {36108440}, issn = {1618-0623}, mesh = {Animals ; Bacteria/genetics ; Genomics ; Phylogeny ; Plasmids/genetics ; *Porifera/microbiology ; }, abstract = {Plasmid-mediated transfer of genes can have direct consequences in several biological processes within sponge microbial communities. However, very few studies have attempted genomic and functional characterization of plasmids from marine host-associated microbial communities in general and those of sponges in particular. In the present study, we used an endogenous plasmid isolation method to obtain plasmids from bacterial symbionts of the marine sponges Stylissa carteri and Paratetilla sp. and investigated the genomic composition, putative ecological relevance and biotechnological potential of these plasmids. In total, we isolated and characterized three complete plasmids, three plasmid prophages and one incomplete plasmid. Our results highlight the importance of plasmids to transfer relevant genetic traits putatively involved in microbial symbiont adaptation and host-microbe and microbe-microbe interactions. For example, putative genes involved in bacterial response to chemical stress, competition, metabolic versatility and mediation of bacterial colonization and pathogenicity were detected. Genes coding for enzymes and toxins of biotechnological potential were also detected. Most plasmid prophage coding sequences were, however, hypothetical proteins with unknown functions. Overall, this study highlights the ecological relevance of plasmids in the marine sponge microbiome and provides evidence that plasmids of sponge bacterial symbionts may represent an untapped resource of genes of biotechnological interest.}, }
@article {pmid36107279, year = {2022}, author = {Huber, KT and Moulton, V and Scholz, GE}, title = {Forest-Based Networks.}, journal = {Bulletin of mathematical biology}, volume = {84}, number = {10}, pages = {119}, pmid = {36107279}, issn = {1522-9602}, mesh = {Humans ; Forests ; *Mathematical Concepts ; Models, Biological ; *Models, Genetic ; Phylogeny ; }, abstract = {In evolutionary studies, it is common to use phylogenetic trees to represent the evolutionary history of a set of species. However, in case the transfer of genes or other genetic information between the species or their ancestors has occurred in the past, a tree may not provide a complete picture of their history. In such cases, tree-based phylogenetic networks can provide a useful, more refined representation of the species' evolution. Such a network is essentially a phylogenetic tree with some arcs added between the tree's edges so as to represent reticulate events such as gene transfer, hybridization and recombination. Even so, this model does not permit the direct representation of evolutionary scenarios where reticulate events have taken place between different subfamilies or lineages of species. To represent such scenarios, in this paper we introduce the notion of a forest-based network, that is, a collection of leaf-disjoint phylogenetic trees on a set of species with arcs added between the edges of distinct trees within the collection. Forest-based networks include the recently introduced class of overlaid species forests which can be used to model introgression. As we shall see, even though the definition of forest-based networks is closely related to that of tree-based networks, they lead to new mathematical theory which complements that of tree-based networks. As well as studying the relationship of forest-based networks with other classes of phylogenetic networks, such as tree-child networks and universal tree-based networks, we present some characterizations of some special classes of forest-based networks. We expect that our results will be useful for developing new models and algorithms to understand reticulate evolution, such as introgression and gene transfer between species.}, }
@article {pmid36107214, year = {2022}, author = {Wang, J and Yuan, L and Wu, W and Yan, Y}, title = {Characterization of the phosphotriesterase capable of hydrolyzing aryl-organophosphate flame retardants.}, journal = {Applied microbiology and biotechnology}, volume = {106}, number = {19-20}, pages = {6493-6504}, pmid = {36107214}, issn = {1432-0614}, support = {31540067//National Natural Science Foundation of China/ ; 21876201//National Natural Science Foundation of China/ ; 1610042018005//Basic Research Fund of Chinese Academy of Agricultural Sciences/ ; 1610042018006//Basic Research Fund of Chinese Academy of Agricultural Sciences/ ; }, mesh = {Biphenyl Compounds ; Esters ; *Flame Retardants/metabolism ; Organophosphates/metabolism ; Phosphates ; *Phosphoric Triester Hydrolases/chemistry/genetics/metabolism ; Polymers ; Recombinant Proteins ; Resorcinols ; Sphingomonadaceae ; Transposases ; *Tritolyl Phosphates ; }, abstract = {A related group of phosphotriesters known as organophosphate flame retardants (OPFRs) has become emerging contaminants due to its worldwide use. The lack of an easily hydrolysable bond renders OPFRs inert to the well-known phosphotriesterases capable of hydrolyzing the neurotoxic organophosphates. An OPFRs phosphotriesterase gene stpte was cloned from plasmid pStJH of strain Sphingopyxis terrae subsp. terrae YC-JH3 and was heterologously expressed in Escherichia coli. The recombinant protein St-PTE was purified and analyzed. St-PTE showed the highest catalytic activity at pH 8.5 and 35 °C. The optimal substrate for St-PTE is triphenyl phosphate, with kcat/Km of 5.03 × 10[6] M[-1] s[-1], two orders of magnitude higher than those of tricresyl phosphate (4.17 × 10[4] M[-1] s[-1]), 2-ethylhexyl diphenyl phosphate (2.03 × 10[4] M[-1] s[-1]) and resorcinol bis(diphenyl phosphate) (6.30 × 10[4] M[-1] s[-1]). St-PTE could break the P-O bond of tri-esters and convert aryl-OPFRs into their corresponding di-ester metabolites, including polymers of resorcinol bis(diphenyl phosphate). Mediated by transposase, the gene of OPFRs phosphotriesterase could be transferred horizontally among closely related strains of Sphingomonas, Sphingobium and Sphingopyxis. KEY POINTS: • St-PTE from Sphingopyxis terrae subsp. terrae YC-JH3 could hydrolyze aryl-OPFRs. • Metabolites of RBDPP hydrolyzed by phosphotriesterase were identified. • St-PTE could hydrolyze the P-O cleavage of dimer and trimer of RBDPP. • Phosphotriesterase genes transfer among Sphingomonadaceae mediated by transposase.}, }
@article {pmid36106856, year = {2022}, author = {Bourassa, JS and Jeannotte, G and Lebel-Beaucage, S and Beauregard, PB}, title = {Second-Generation Transfer Mediates Efficient Propagation of ICEBs1 in Biofilms.}, journal = {Journal of bacteriology}, volume = {204}, number = {10}, pages = {e0018122}, pmid = {36106856}, issn = {1098-5530}, support = {2019-PR-253077//FRQ | Fonds de recherche du Qu&#xe9;bec - Nature et technologies (FRQNT)/ ; 271990//FRQ | Fonds de recherche du Qu&#xe9;bec - Nature et technologies (FRQNT)/ ; }, mesh = {*Conjugation, Genetic ; *Bacillus subtilis/genetics ; Gene Transfer, Horizontal ; Biofilms ; Drug Resistance, Microbial ; }, abstract = {Horizontal gene transfer (HGT) by integrative and conjugative elements (ICEs) is an important mechanism in the spread of antibiotic resistance genes. However, little is known about the spatiotemporal dynamic of ICE propagation in bacterial biofilms, which are multicellular structures ubiquitous in natural and clinical environments. We report here that a high level of biofilm matrix production favors ICEBs1 acquisition. Also, using a fluorescently marked ICEBs1, we observed that conjugation appears restricted to clusters of bacteria in a close neighborhood in which a high level of ICEBs1 transfer occurs. These conjugative clusters are heterogeneously distributed in the biofilm, forming close to the air-biofilm interface. Importantly, we established that transconjugant cells are the main contributors to ICEBs1 propagation in biofilms. Our findings provide a novel spatiotemporal understanding of ICEs propagation in biofilms, which should have an important role in our understanding of horizontal gene transfer in relevant settings. IMPORTANCE The transfer of mobile genetic elements between bacteria is the main cause of the spread of antibiotic resistance genes. While biofilms are the predominant bacterial lifestyle both in the environment and in clinical settings, their impact on the propagation of mobile genetic elements is still poorly understood. In this study, we examined the spatiotemporal propagation of the well-characterized ICEBs1. Using the Gram-positive Bacillus subtilis, we observed that the main actors of ICEBs1 propagation in biofilms are the newly formed transconjugants that allow rapid transfer of ICEBs1 to new recipients. Our study provides a better understanding of the spatiotemporal dynamic of conjugative transfer in biofilms.}, }
@article {pmid36106855, year = {2022}, author = {Payot, S}, title = {Key Role of Transconjugants for Dissemination of the Integrative Conjugative Element ICEBs1 in Biofilms.}, journal = {Journal of bacteriology}, volume = {204}, number = {10}, pages = {e0032722}, pmid = {36106855}, issn = {1098-5530}, mesh = {*Conjugation, Genetic ; *Gene Transfer, Horizontal ; Bacillus subtilis/genetics ; Biofilms ; }, abstract = {In this issue of the Journal of Bacteriology, J.-S. Bourassa, G. Jeannotte, S. Lebel-Beaucage, and P. B. Beauregard (J Bacteriol 204:e00181-22, 2022, https://doi.org/10.1128/jb.00181-22) showed that ICEBs1 propagation in Bacillus subtilis biofilm relies almost exclusively on transconjugants. It appears restricted to clusters of bacteria in a close neighborhood of initial donor cells, which are heterogeneously distributed in the biofilm and expand vertically toward the air-liquid interface.}, }
@article {pmid36104761, year = {2022}, author = {Gheorghe-Barbu, I and Barbu, IC and Popa, LI and Pîrcălăbioru, GG and Popa, M and Măruțescu, L and Niță-Lazar, M and Banciu, A and Stoica, C and Gheorghe, &#x218; and Lucaciu, I and Săndulescu, O and Paraschiv, S and Surleac, M and Talapan, D and Muntean, AA and Preda, M and Muntean, MM and Dragomirescu, CC and Popa, MI and Oțelea, D and Chifiriuc, MC}, title = {Temporo-spatial variations in resistance determinants and clonality of Acinetobacter baumannii and Pseudomonas aeruginosa strains from Romanian hospitals and wastewaters.}, journal = {Antimicrobial resistance and infection control}, volume = {11}, number = {1}, pages = {115}, pmid = {36104761}, issn = {2047-2994}, mesh = {*Acinetobacter baumannii ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Hospitals ; Interleukin-1 Receptor-Like 1 Protein ; Microbial Sensitivity Tests ; Pseudomonas aeruginosa/genetics ; Romania/epidemiology ; Wastewater/microbiology ; Wastewater-Based Epidemiological Monitoring ; beta-Lactamases/genetics ; }, abstract = {BACKGROUND: Romania is one of the European countries reporting very high antimicrobial resistance (AMR) rates and consumption of antimicrobials. We aimed to characterize the AMR profiles and clonality of 304 multi-drug resistant (MDR) Acinetobacter baumannii (Ab) and Pseudomonas aeruginosa (Pa) strains isolated during two consecutive years (2018 and 2019) from hospital settings, hospital collecting sewage tanks and the receiving wastewater treatment plants (WWTPs) located in the main geographical regions of Romania.<br><br>METHODS: The strains were isolated on chromogenic media and identified by MALDI-TOF-MS. Antibiotic susceptibility testing and confirmation of ESBL- and CP- producing phenotypes and genotypes were performed. The genetic characterization also included horizontal gene transfer experiments, whole-genome sequencing (WGS), assembling, annotation and characterization.<br><br>RESULTS: Both clinical and aquatic isolates exhibited high MDR rates, especially the Ab strains isolated from nosocomial infections and hospital effluents. The phenotypic resistance profiles and MDR rates have largely varied by sampling point and geographic location. The highest MDR rates in the aquatic isolates were recorded in Gala&#x21b;i WWTP, followed by Bucharest. The Ab strains harbored mostly blaOXA-23, blaOXA-24, blaSHV, blaTEM and blaGES, while Pa strains blaIMP, blaVIM, blaNDM, blaVEB, blaGES and blaTEM, with high variations depending on the geographical zone and the sampling point. The WGS analysis revealed the presence of antibiotic resistance genes (ARGs) to other antibiotic classes, such as aminoglycosides, tetracyclines, sulphonamides, fosfomycin, phenicols, trimethoprim-sulfamethoxazole as well as class 1 integrons. The molecular analyses highlighted: (i) The presence of epidemic clones such as ST2 for Ab and ST233 and ST357 for Pa; (ii) The relatedness between clinical and hospital wastewater strains and (iii) The possible dissemination of clinical Ab belonging to ST2 (also proved in the conjugation assays for blaOXA-23 or blaOXA-72 genes), ST79 and ST492 and of Pa strains belonging to ST357, ST640 and ST621 in the wastewaters.<br><br>CONCLUSION: Our study reveals the presence of CP-producing Ab and Pa in all sampling points and the clonal dissemination of clinical Ab ST2 strains in the wastewaters. The prevalent clones were correlated with the presence of class 1 integrons, suggesting that these isolates could be a significant reservoir of ARGs, being able to persist in the environment.}, }
@article {pmid36100085, year = {2022}, author = {Wang, Q and Olesen, AK and Maccario, L and Madsen, JS}, title = {An easily modifiable conjugative plasmid for studying horizontal gene transfer.}, journal = {Plasmid}, volume = {123-124}, number = {}, pages = {102649}, doi = {10.1016/j.plasmid.2022.102649}, pmid = {36100085}, issn = {1095-9890}, mesh = {*Gene Transfer, Horizontal ; Plasmids/genetics ; *Conjugation, Genetic ; beta-Lactamases/genetics ; Anti-Bacterial Agents ; }, abstract = {Horizontal gene transfer is an important mechanism in bacterial evolution and can occur at striking frequencies when mediated by mobile genetic elements. Conjugative plasmids are mobile genetic elements that are main drivers of horizontal transfer and a major facilitator in the spread of antibiotic resistance genes. However, conjugative plasmid models that readily can be genetically modified with the aim to study horizontal transfer are not currently available. The aim of this study was to develop a conjugative plasmid model where the insertion of gene cassettes such as reporter genes (e.g., fluorescent proteins) or antibiotic resistance genes would be efficient and convenient. Here, we introduced a single attTn7 site into the conjugative broad-host-range IncP-1 plasmid pKJK5 in a non-disruptive manner. Furthermore, a version with lower transfer rate and a non-conjugative version of pKJK5-attTn7 were also constructed. The advantage of having the attTn7 sites is that genes of interest can be introduced in a single step with very high success rate using the Tn7 transposition system. In addition, larger genetic fragments can be inserted. To illustrate the efficacy of the constructed pKJK5 plasmids, they were complemented with sfGFP (a gene encoding superfolder green fluorescent protein) in addition to seven different β-lactamase genes representing the four known classes of β-lactamases.}, }
@article {pmid36098534, year = {2022}, author = {Sherlock, D and Fogg, PCM}, title = {Loss of the Rhodobacter capsulatus Serine Acetyl Transferase Gene, cysE1, Impairs Gene Transfer by Gene Transfer Agents and Biofilm Phenotypes.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {19}, pages = {e0094422}, pmid = {36098534}, issn = {1098-5336}, support = {/WT_/Wellcome Trust/United Kingdom ; 109363/Z/15/A/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Biofilms ; Cysteine/metabolism ; DNA/metabolism ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Phenotype ; *Rhodobacter capsulatus/genetics ; Serine ; Serine O-Acetyltransferase/genetics/metabolism ; }, abstract = {Biofilms are widespread in the environment, where they allow bacterial species to survive adverse conditions. Cells in biofilms are densely packed, and this proximity is likely to increase the frequency of horizontal gene transfer. Gene transfer agents (GTAs) are domesticated viruses with the potential to spread any gene between bacteria. GTA production is normally restricted to a small subpopulation of bacteria, and regulation of GTA loci is highly coordinated, but the environmental conditions that favor GTA production are poorly understood. Here, we identified a serine acetyltransferase gene, cysE1, in Rhodobacter capsulatus that is required for optimal receipt of GTA DNA, accumulation of extracellular polysaccharide, and biofilm formation. The cysE1 gene is directly downstream of the core Rhodobacter-like GTA (RcGTA) structural gene cluster and upregulated in an RcGTA overproducer strain, although it is expressed on a separate transcript. The data we present suggest that GTA production and biofilm are coregulated, which could have important implications for the study of rapid bacterial evolution and understanding the full impact of GTAs in the environment. IMPORTANCE Direct exchange of genes between bacteria leads to rapid evolution and is the major factor underlying the spread of antibiotic resistance. Gene transfer agents (GTAs) are an unusual but understudied mechanism for genetic exchange that are capable of transferring any gene from one bacterium to another, and therefore, GTAs are likely to be important factors in genome plasticity in the environment. Despite the potential impact of GTAs, our knowledge of their regulation is incomplete. In this paper, we present evidence that elements of the cysteine biosynthesis pathway are involved in coregulation of various phenotypes required for optimal biofilm formation by Rhodobacter capsulatus and successful infection by the archetypal RcGTA. Establishing the regulatory mechanisms controlling GTA-mediated gene transfer is a key stepping stone to allow a full understanding of their role in the environment and wider impact.}, }
@article {pmid36096030, year = {2022}, author = {Shi, X and Xia, Y and Wei, W and Ni, BJ}, title = {Accelerated spread of antibiotic resistance genes (ARGs) induced by non-antibiotic conditions: Roles and mechanisms.}, journal = {Water research}, volume = {224}, number = {}, pages = {119060}, doi = {10.1016/j.watres.2022.119060}, pmid = {36096030}, issn = {1879-2448}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; Microplastics ; Plastics ; }, abstract = {The global spread of antibiotic resistance genes (ARGs) has wreaked havoc with the treatment efficiency of antibiotics and, ultimately, anti-microbial chemotherapy, and has been conventionally attributed to the abuse and misuse of antibiotics. However, the ancient ARGs have alterative functions in bacterial physiology and thus they could be co-regulated by non-antibiotic conditions. Recent research has demonstrated that many non-antibiotic chemicals such as microplastics, metallic nanoparticles and non-antibiotic drugs, as well as some non-antibiotic conditions, can accelerate the dissemination of ARGs. These results suggested that the role of antibiotics might have been previously overestimated whereas the effects of non-antibiotic conditions were possibly ignored. Thus, in an attempt to fully understand the fate and behavior of ARGs in the eco-system, it is urgent to critically highlight the role and mechanisms of non-antibiotic chemicals and related environmental factors in the spread of ARGs. To this end, this timely review assessed the evolution of ARGs, especially its function alteration, summarized the non-antibiotic chemicals promoting the spread of ARGs, evaluated the non-antibiotic conditions related to ARG dissemination and analyzed the molecular mechanisms related to spread of ARGs induced by the non-antibiotic factors. Finally, this review then provided several critical perspectives for future research.}, }
@article {pmid36090102, year = {2022}, author = {Zhao, H and Wang, J and Peng, Y and Cai, X and Liu, Y and Huang, W and Huang, H and Nie, Y}, title = {Genomic insights from Paraclostridium bifermentans HD0315_2: General features and pathogenic potential.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {928153}, pmid = {36090102}, issn = {1664-302X}, abstract = {BACKGROUND: Paraclostridium bifermentans is the most diverse distributed species of Paraclostridium and can cause fatal human infections under rare conditions. However, its pathogenic mechanisms and adaptation ability behind infections remain unclear. Herein, we reported the complete genome sequence of P. bifermentans HD0315_2 isolated from the feces of a patient with Crohn's disease. Then, we performed genomic analyses to understand its pathogenic mechanisms and adaptation ability.<br><br>RESULTS: The de novo assembly revealed that the HD0315_2 strain carried a circular chromosome of 3.27 Mb and six circular plasmids (19.41 to 139.50 kb). The phylogenomic analysis assigned the HD0315_2 strain as P. bifermentans and reclassified some previously non-P. bifermentans strains into this clade. The general genomic features showed that this species harbored a flexible genomic pool characterized by variable genome length and multiple plasmids. Then, the HD0315_2 strain was predicted as a human pathogen with high probability, and Listeria LIPI-1 virulence proteins were identified on its genome. Besides, abundant antibiotics/metal/stress resistant genes, such as asrABCH, cat, mccF, macB, entS, albA, bcrA, and tetB, were carried by either the genome or the plasmids. Furthermore, we proposed that transposase-directed horizontal gene transfer was responsible for the distribution of multiple copies of the hin gene in the plasmids.<br><br>CONCLUSION: The flexible genomic pool of P. bifermentans encodes abundant functions for antimicrobial or oxidative stress resistance, helping it successfully inhabit and adapt to diverse environments. Moreover, P. bifermentans HD0315_2 might infect hosts via a Listeria LIPI-1-like cycle, with the help of a plasmid expressing the Hin DNA invertase to evade host immune responses.}, }
@article {pmid36089145, year = {2022}, author = {Hembach, N and Bierbaum, G and Schreiber, C and Schwartz, T}, title = {Facultative pathogenic bacteria and antibiotic resistance genes in swine livestock manure and clinical wastewater: A molecular biology comparison.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {313}, number = {}, pages = {120128}, doi = {10.1016/j.envpol.2022.120128}, pmid = {36089145}, issn = {1873-6424}, mesh = {Animals ; Anti-Bacterial Agents/analysis/pharmacology ; Bacteria ; Drug Resistance, Microbial/genetics ; Escherichia coli ; *Escherichia coli Proteins/genetics ; Genes, Bacterial ; Humans ; Livestock ; *Manure/analysis ; Molecular Biology ; Soil ; Soil Microbiology ; Swine ; Wastewater/analysis ; }, abstract = {Manure contains vast amounts of biological contaminants of veterinary origin. Only few studies analyse clinically critical resistance genes against reserve antibiotics in manure. In general, resistances against these high priority antibiotics involve a high potential health risk. Therefore, their spread in the soil as well as the aquatic environment has to be prevented. Manures of 29 different swine livestock were analysed. Abundances of facultative pathogenic bacteria including representatives of the clinically critical ESKAPE-pathogens (P. aeruginosa, K. pneumoniae, A. baumannii, E. faecium) and E. coli were investigated via qPCR. Antibiotic resistance genes against commonly used veterinary antibiotics (ermB, tetM, sul1) as well as various resistance genes against important (mecA, vanA) and reserve antibiotics (blaNDM, blaKPC3, mcr-1), which are identified by the WHO, were also obtained by qPCR analysis. The manures of all swine livestock contained facultative pathogenic bacteria and commonly known resistance genes against antibiotics used in veterinary therapies, but more important also a significant amount of clinically critical resistance genes against reserve antibiotics for human medicine. To illustrate the impact the occurrence of these clinically critical resistance genes, comparative measurements were taken of the total wastewater of a large tertiary care hospital (n = 8). Both manure as well as raw hospital wastewaters were contaminated with significant abundances of gene markers for facultative pathogens and with critical resistance genes of reserve antibiotics associated with genetic mobile elements for horizontal gene transfer. Hence, both compartments bear an exceptional potential risk for the dissemination of facultative pathogens and critical antibiotic resistance genes.}, }
@article {pmid36085101, year = {2022}, author = {Prasad, A and Chirom, O and Prasad, M}, title = {Horizontal gene transfer and the evolution of land plants.}, journal = {Trends in plant science}, volume = {27}, number = {12}, pages = {1203-1205}, doi = {10.1016/j.tplants.2022.08.020}, pmid = {36085101}, issn = {1878-4372}, mesh = {*Gene Transfer, Horizontal/genetics ; Evolution, Molecular ; *Embryophyta/genetics ; Phylogeny ; }, abstract = {Horizontal gene transfer (HGT) is the transfer of genetic material between organisms. It has been known for some time that HGT in eukaryotes is not a rare phenomenon. A recent study by Ma et al. has shown that HGT has played a crucial role in shaping the evolution of land plants.}, }
@article {pmid36084857, year = {2022}, author = {Ribeiro, IDA and Bach, E and Passaglia, LMP}, title = {Alternative nitrogenase of Paenibacillus sonchi genomovar Riograndensis: An insight in the origin of Fe-nitrogenase in the Paenibacillaceae family.}, journal = {Molecular phylogenetics and evolution}, volume = {177}, number = {}, pages = {107624}, doi = {10.1016/j.ympev.2022.107624}, pmid = {36084857}, issn = {1095-9513}, mesh = {Nitrogen Fixation/genetics ; *Nitrogenase/genetics/metabolism ; *Paenibacillus/genetics/metabolism ; Phylogeny ; }, abstract = {Paenibacillus sonchi genomovar Riograndensis is a nitrogen-fixing bacteria isolated from wheat that displays diverse plant growth-promoting abilities. Beyond conventional Mo-nitrogenase, this organism also harbors an alternative Fe-nitrogenase, whose many aspects related to regulation, physiology, and evolution remain to be elucidated. In this work, the origins of this alternative system were investigated, exploring the distribution and diversification of nitrogenases in the Panibacillaceae family. Our analysis showed that diazotrophs represent 17% of Paenibacillaceae genomes, of these, only 14.4% (2.5% of all Paenibacillaceae genomes) also contained Fe or V- nitrogenases. Diverse nif-like sequences were also described, occurring mainly in genomes that also harbor the alternative systems. The analysis of genomes containing Fe-nitrogenase showed a conserved cluster of nifEN anfHDGK across three genera: Gorillibacterium, Fontibacillus, and Paenibacillus. A phylogeny of anfHDGK separated the Fe-nitrogenases into three main groups. Our analysis suggested that Fe-nitrogenase was acquired by the ancestral lineage of Fontibacillus, Gorillibacterium, and Paenibacillus genera via horizontal gene transfer (HGT), and further events of transfer and gene loss marked the evolution of this alternative nitrogenase in these groups. The species phylogeny of N-fixing Paenibacillaceae separated the diazotrophs into five clades, one of these containing all occurrences of strains harboring alternative nitrogenases in the Paenibacillus genus. The pangenome of this clade is open and composed of more than 96% of accessory genes. Diverse functional categories were enriched in the flexible genome, including functions related to replication and repair. The latter involved diverse genes related to HGT, suggesting that such events may have an important role in the evolution of diazotrophic Paenibacillus. This study provided an insight into the organization, distribution, and evolution of alternative nitrogenase genes in Paenibacillaceae, considering different genomic aspects.}, }
@article {pmid36084285, year = {2022}, author = {Cunliffe, TG and Parker, AL and Jaramillo, A}, title = {Pseudotyping Bacteriophage P2 Tail Fibers to Extend the Host Range for Biomedical Applications.}, journal = {ACS synthetic biology}, volume = {11}, number = {10}, pages = {3207-3215}, pmid = {36084285}, issn = {2161-5063}, support = {BB/M017982/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 520464/MRC_/Medical Research Council/United Kingdom ; 515374/MRC_/Medical Research Council/United Kingdom ; BB/P020615/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Host Specificity ; *Bacteriophage P2 ; Lipopolysaccharides ; Proteome ; *Bacteriophages/genetics ; Anti-Bacterial Agents ; }, abstract = {Bacteriophages (phages) represent powerful potential treatments against antibiotic-resistant bacterial infections. Antibiotic-resistant bacteria represent a significant threat to global health, with an estimated 70% of infection-causing bacteria being resistant to one or more antibiotics. Developing novel antibiotics against the limited number of cellular targets is expensive and time-consuming, and bacteria can rapidly develop resistance. While bacterial resistance to phage can evolve, bacterial resistance to phage does not appear to spread through lateral gene transfer, and phage may similarly adapt through mutation to recover infectivity. Phages have been identified for all known bacteria, allowing the strain-selective killing of pathogenic bacteria. Here, we re-engineered the Escherichia coli phage P2 to alter its tropism toward pathogenic bacteria. Chimeric tail fibers formed between P2 and S16 genes were designed and generated through two approaches: homology- and literature-based. By presenting chimeric P2:S16 fibers on the P2 particle, our data suggests that the resultant phages were effectively detargeted from the native P2 cellular target, lipopolysaccharide, and were instead able to infect via the proteinaceous receptor, OmpC, the natural S16 receptor. Our work provides evidence that pseudotyping P2 is feasible and can be used to extend the host range of P2 to alternative receptors. Extension of this work could produce alternative chimeric tail fibers to target pathogenic bacterial threats. Our engineering of P2 allows adsorption through a heterologous outer-membrane protein without culturing in its native host, thus providing a potential means of engineering designer phages against pathogenic bacteria from knowledge of their surface proteome.}, }
@article {pmid36083451, year = {2022}, author = {Bansal, MS}, title = {Deciphering Microbial Gene Family Evolution Using Duplication-Transfer-Loss Reconciliation and RANGER-DTL.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2569}, number = {}, pages = {233-252}, pmid = {36083451}, issn = {1940-6029}, mesh = {Algorithms ; *Evolution, Molecular ; *Gene Duplication ; Gene Transfer, Horizontal ; Genes, Microbial ; Models, Genetic ; Phylogeny ; }, abstract = {Phylogenetic reconciliation has emerged as a principled, highly effective technique for investigating the origin, spread, and evolutionary history of microbial gene families. Proper application of phylogenetic reconciliation requires a clear understanding of potential pitfalls and sources of error, and knowledge of the most effective reconciliation-based tools and protocols to use to maximize accuracy. In this book chapter, we provide a brief overview of Duplication-Transfer-Loss (DTL) reconciliation, the standard reconciliation model used to study microbial gene families and provide a step-by-step computational protocol to maximize the accuracy of DTL reconciliation and minimize false-positive evolutionary inferences.}, }
@article {pmid36083447, year = {2022}, author = {Zhu, Q and Mirarab, S}, title = {Assembling a Reference Phylogenomic Tree of Bacteria and Archaea by Summarizing Many Gene Phylogenies.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2569}, number = {}, pages = {137-165}, pmid = {36083447}, issn = {1940-6029}, mesh = {*Archaea/genetics ; *Bacteria/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Phylogeny ; Software ; }, abstract = {Phylogenomics is the inference of phylogenetic trees based on multiple marker genes sampled in the genomes of interest. An important challenge in phylogenomics is the potential incongruence among the evolutionary histories of individual genes, which can be widespread in microorganisms due to the prevalence of horizontal gene transfer. This protocol introduces the procedures for building a phylogenetic tree of a large number of microbial genomes using a broad sampling of marker genes that are representative of whole-genome evolution. The protocol highlights the use of a gene tree summary method, which can effectively reconstruct the species tree while accounting for the topological conflicts among individual gene trees. The pipeline described in this protocol is scalable to tens of thousands of genomes while retaining high accuracy. We discussed multiple software tools, libraries, and scripts to enable convenient adoption of the protocol. The protocol is suitable for microbiology and microbiome studies based on public genomes and metagenomic data.}, }
@article {pmid36083444, year = {2022}, author = {Davín, AA and Schrempf, D and Williams, TA and Hugenholtz, P and Szöllősi, GJ}, title = {Relative Time Inference Using Lateral Gene Transfers.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2569}, number = {}, pages = {75-94}, pmid = {36083444}, issn = {1940-6029}, mesh = {*Biological Evolution ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome ; Phylogeny ; }, abstract = {Many organisms are able to incorporate exogenous DNA into their genomes. This process, called lateral gene transfer (LGT), has the potential to benefit the recipient organism by providing useful coding sequences, such as antibiotic resistance genes or enzymes which expand the organism's metabolic niche. For evolutionary biologists, LGTs have often been considered a nuisance because they complicate the reconstruction of the underlying species tree that many analyses aim to recover. However, LGT events between distinct organisms harbor information on the relative divergence time of the donor and recipient lineages. As a result transfers provide a novel and as yet mostly unexplored source of information to determine the order of divergence of clades, with the potential for absolute dating if linked to the fossil record.}, }
@article {pmid36083443, year = {2022}, author = {Fournier, GP and Parsons, CW and Cutts, EM and Tamre, E}, title = {Standard Candles for Dating Microbial Lineages.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2569}, number = {}, pages = {41-74}, pmid = {36083443}, issn = {1940-6029}, mesh = {Animals ; Bayes Theorem ; *Biological Evolution ; Eukaryotic Cells ; Evolution, Molecular ; *Fossils ; Phylogeny ; Plants/genetics ; }, abstract = {Molecular clock analyses are challenging for microbial phylogenies, due to a lack of fossil calibrations that can reliably provide absolute time constraints. An alternative source of temporal constraints for microbial groups is provided by the inheritance of proteins that are specific for the utilization of eukaryote-derived substrates, which have often been dispersed across the Tree of Life via horizontal gene transfer. In particular, animal, algal, and plant-derived substrates are often produced by groups with more precisely known divergence times, providing an older-bound on their availability within microbial environments. Therefore, these ages can serve as "standard candles" for dating microbial groups across the Tree of Life, expanding the reach of informative molecular clock investigations. Here, we formally develop the concept of substrate standard candles and describe how they can be propagated and applied using both microbial species trees and individual gene family phylogenies. We also provide detailed evaluations of several candidate standard candles and discuss their suitability in light of their often complex evolutionary and metabolic histories.}, }
@article {pmid36075475, year = {2022}, author = {Cui, Y and Gao, J and Guo, Y and Li, Z and Wang, Z and Zhao, Y}, title = {Unraveling the impact and mechanism of antipyretic paracetamol on intergenera conjugative plasmid transfer.}, journal = {Environmental research}, volume = {215}, number = {Pt 1}, pages = {114263}, doi = {10.1016/j.envres.2022.114263}, pmid = {36075475}, issn = {1096-0953}, mesh = {Acetaminophen/pharmacology ; *Analgesics, Non-Narcotic ; Anti-Bacterial Agents ; *Antipyretics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Plasmids/genetics ; Reactive Oxygen Species ; }, abstract = {Antimicrobial resistance has been considered as a great threat to biosecurity and human health. And the transmission of antibiotic resistance genes (ARGs) by conjugated plasmid is a key factor in the prevalence of antimicrobial resistance. Paracetamol (PRC), one of nonopioid analgesics, is an extensively used antipyretic and mild analgesic worldwide available for numerous prescriptions. It was unclear whether PRC could promote the spread of ARGs. Here, it was demonstrated that PRC promoted intergenera conjugative plasmid transfer in an established conjugation model. Both donor and recipient strains treated by PRC emerged the variations of reactive oxygen species (ROS), SOS response and cell membrane permeability. Correspondingly, transcriptome analysis revealed that the gene expression involved in cell membrane permeability and SOS response was up-regulated significantly after PRC exposure. More directly, PRC also increased the expressions of conjugation related genes of trbG and trbP in donor. This study proved for the first time that PRC could enhance the intergenera conjugative plasmid transfer. Collectively, these findings manifested the potential threat associated with the existence of non-antibiotic substance PRC, which could provide an important insight into antimicrobial resistance spread.}, }
@article {pmid36073816, year = {2022}, author = {Castellani, LG and Luchetti, A and Nilsson, JF and Pérez-Giménez, J and Struck, B and Schlüter, A and Pühler, A and Niehaus, K and Romero, D and Pistorio, M and Torres Tejerizo, G}, title = {RcgA and RcgR, Two Novel Proteins Involved in the Conjugative Transfer of Rhizobial Plasmids.}, journal = {mBio}, volume = {13}, number = {5}, pages = {e0194922}, pmid = {36073816}, issn = {2150-7511}, support = {H23 IP000678/IP/NCIRD CDC HHS/United States ; }, mesh = {*Conjugation, Genetic ; Plasmids/genetics ; *Quorum Sensing ; Bacteria/genetics ; Nitrogen ; DNA ; Gene Transfer, Horizontal ; }, abstract = {Rhizobia are Gram-negative bacteria that are able to establish a nitrogen-fixing symbiotic interaction with leguminous plants. Rhizobia genomes usually harbor several plasmids which can be transferred to other organisms by conjugation. Two main mechanisms of the regulation of rhizobial plasmid transfer have been described: quorum sensing (QS) and the rctA/rctB system. Nevertheless, new genes and molecules that modulate conjugative transfer have recently been described, demonstrating that new actors can tightly regulate the process. In this work, by means of bioinformatics tools and molecular biology approaches, two hypothetical genes are identified as playing key roles in conjugative transfer. These genes are located between conjugative genes of plasmid pRfaLPU83a from Rhizobium favelukesii LPU83, a plasmid that shows a conjugative transfer behavior depending on the genomic background. One of the two mentioned genes, rcgA, is essential for conjugation, while the other, rcgR, acts as an inhibitor of the process. In addition to introducing this new regulatory system, we show evidence of the functions of these genes in different genomic backgrounds and confirm that homologous proteins from non-closely related organisms have the same functions. These findings set up the basis for a new regulatory circuit of the conjugative transfer of plasmids. IMPORTANCE Extrachromosomal DNA elements, such as plasmids, allow for the adaptation of bacteria to new environments by conferring new determinants. Via conjugation, plasmids can be transferred between members of the same bacterial species, different species, or even to organisms belonging to a different kingdom. Knowledge about the regulatory systems of plasmid conjugative transfer is key in understanding the dynamics of their dissemination in the environment. As the increasing availability of genomes raises the number of predicted proteins with unknown functions, deeper experimental procedures help to elucidate the roles of these determinants. In this work, two uncharacterized proteins that constitute a new regulatory circuit with a key role in the conjugative transfer of rhizobial plasmids were discovered.}, }
@article {pmid36072670, year = {2022}, author = {Chen, K and Zhuang, Y and Wang, L and Li, H and Lei, T and Li, M and Gao, M and Wei, J and Dang, H and Raza, A and Yang, Q and Sharif, Y and Yang, H and Zhang, C and Zou, H and Zhuang, W}, title = {Comprehensive genome sequence analysis of the devastating tobacco bacterial phytopathogen Ralstonia solanacearum strain FJ1003.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {966092}, pmid = {36072670}, issn = {1664-8021}, abstract = {Due to its high genetic diversity and broad host range, Ralstonia solanacearum, the causative phytopathogen of the bacterial wilt (BW) disease, is considered a "species complex". The R. solanacearum strain FJ1003 belonged to phylotype I, and was isolated from the Fuzhou City in Fujian Province of China. The pathogen show host specificity and infects tobacco, especially in the tropical and subtropical regions. To elucidate the pathogenic mechanisms of FJ1003 infecting tobacco, a complete genome sequencing of FJ1003 using single-molecule real-time (SMRT) sequencing technology was performed. The full genome size of FJ1003 was 5.90 Mb (GC%, 67%), containing the chromosome (3.7 Mb), megaplasmid (2.0 Mb), and small plasmid (0.2 Mb). A total of 5133 coding genes (3446 and 1687 genes for chromosome and megaplasmid, respectively) were predicted. A comparative genomic analysis with other strains having the same and different hosts showed that the FJ1003 strain had 90 specific genes, possibly related to the host range of R. solanacearum. Horizontal gene transfer (HGT) was widespread in the genome. A type Ⅲ effector protein (Rs_T3E_Hyp14) was present on both the prophage and genetic island (GI), suggesting that this gene might have been acquired from other bacteria via HGT. The Rs_T3E_Hyp14 was proved to be a virulence factor in the pathogenic process of R. solanacearum through gene knockout strategy, which affects the pathogenicity and colonization ability of R. solanacearum in the host. Therefore, this study will improve our understanding of the virulence of R. solanacearum and provide a theoretical basis for tobacco disease resistance breeding.}, }
@article {pmid36069678, year = {2022}, author = {Rahman, MJ and Haller, SL and Stoian, AMM and Li, J and Brennan, G and Rothenburg, S}, title = {LINE-1 retrotransposons facilitate horizontal gene transfer into poxviruses.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {36069678}, issn = {2050-084X}, support = {R01 AI146915/AI/NIAID NIH HHS/United States ; }, mesh = {Gene Transfer, Horizontal ; Phylogeny ; *Poxviridae/genetics ; Retroelements/genetics ; Vaccinia virus/genetics ; }, abstract = {There is ample phylogenetic evidence that many critical virus functions, like immune evasion, evolved by the acquisition of genes from their hosts through horizontal gene transfer (HGT). However, the lack of an experimental system has prevented a mechanistic understanding of this process. We developed a model to elucidate the mechanisms of HGT into vaccinia virus, the prototypic poxvirus. All identified gene capture events showed signatures of long interspersed nuclear element-1 (LINE-1)-mediated retrotransposition, including spliced-out introns, polyadenylated tails, and target site duplications. In one case, the acquired gene integrated together with a polyadenylated host U2 small nuclear RNA. Integrations occurred across the genome, in some cases knocking out essential viral genes. These essential gene knockouts were rescued through a process of complementation by the parent virus followed by nonhomologous recombination during serial passaging to generate a single, replication-competent virus. This work links multiple evolutionary mechanisms into one adaptive cascade and identifies host retrotransposons as major drivers for virus evolution.}, }
@article {pmid36069526, year = {2022}, author = {Fixsen, SM and Cone, KR and Goldstein, SA and Sasani, TA and Quinlan, AR and Rothenburg, S and Elde, NC}, title = {Poxviruses capture host genes by LINE-1 retrotransposition.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {36069526}, issn = {2050-084X}, support = {R01 AI146915/AI/NIAID NIH HHS/United States ; R35 GM134936/GM/NIGMS NIH HHS/United States ; T32 AI055434/AI/NIAID NIH HHS/United States ; T32 GM007464/GM/NIGMS NIH HHS/United States ; }, mesh = {Evolution, Molecular ; Gene Transfer, Horizontal ; Phylogeny ; *Poxviridae/genetics ; RNA, Messenger ; *Viruses/genetics ; Retroelements ; }, abstract = {Horizontal gene transfer (HGT) provides a major source of genetic variation. Many viruses, including poxviruses, encode genes with crucial functions directly gained by gene transfer from hosts. The mechanism of transfer to poxvirus genomes is unknown. Using genome analysis and experimental screens of infected cells, we discovered a central role for Long Interspersed Nuclear Element-1 retrotransposition in HGT to virus genomes. The process recapitulates processed pseudogene generation, but with host messenger RNA directed into virus genomes. Intriguingly, hallmark features of retrotransposition appear to favor virus adaption through rapid duplication of captured host genes on arrival. Our study reveals a previously unrecognized conduit of genetic traffic with fundamental implications for the evolution of many virus classes and their hosts.}, }
@article {pmid36067042, year = {2022}, author = {Laforest, M and Martin, S and Soufiane, B and Bisaillon, K and Maheux, L and Fortin, S and James, T and Miville, D and Marcoux, A and Simard, MJ}, title = {Distribution and genetic characterization of bird rape mustard (Brassica rapa) populations and analysis of glyphosate resistance introgression.}, journal = {Pest management science}, volume = {78}, number = {12}, pages = {5471-5478}, doi = {10.1002/ps.7170}, pmid = {36067042}, issn = {1526-4998}, support = {//Agriculture and Agri-Food Canada/ ; }, mesh = {Animals ; *Brassica rapa ; Mustard Plant ; Plants, Genetically Modified/genetics ; *Brassica napus ; Hybridization, Genetic ; Plant Weeds/genetics ; Birds/genetics ; Glyphosate ; }, abstract = {BACKGROUND: The introgression of a transgene conferring glyphosate resistance from Brassica napus (rapeseed, canola) to Brassica rapa weeds (bird rape) was documented at a single location in 2007. In 2015, several cases of glyphosate resistant mustard were reported by growers in areas where rapeseed was seldom grown.<br><br>RESULTS: Survey result indicated glyphosate resistant bird rape mustard is present in areas where glyphosate tolerant corn and soybean are often grown in rotation. Genetic analyses reveal that hybridization followed by introgression and progressive loss of chromosome is the likely mechanism for the horizontal gene transfer (HGT) of glyphosate resistance.<br><br>CONCLUSION: Introgression of the glyphosate-resistance conferring transgene in the populations studied appears to have occurred several times, consistent with the ease for B. rapa to form hybrids with B. napus. The introduction of a transgene into a crop should therefore take into account the weediness of the species that share a common genome and their ability to form hybrids. We provide here such an example between B. napus and B. rapa, and potentially between B. napus and Raphanistrum raphanistrum. &#xa9; 2022 Her Majesty the Queen in Right of Canada. Pest Management Science &#xa9; 2022 Society of Chemical Industry. Reproduced with the permission of the Minister of Agriculture and Agri-Food Canada.}, }
@article {pmid36063716, year = {2023}, author = {Tang, T and Chen, Y and Du, Y and Yao, B and Liu, M}, title = {Effects of functional modules and bacterial clusters response on transmission performance of antibiotic resistance genes under antibiotic stress during anaerobic digestion of livestock wastewater.}, journal = {Journal of hazardous materials}, volume = {441}, number = {}, pages = {129870}, doi = {10.1016/j.jhazmat.2022.129870}, pmid = {36063716}, issn = {1873-3336}, mesh = {Anaerobiosis ; Animals ; *Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Livestock ; *Oxytetracycline/pharmacology ; Reactive Oxygen Species/pharmacology ; Sulfamethoxazole ; Type IV Secretion Systems ; Wastewater/analysis ; }, abstract = {The formation and transmission of antibiotic resistance genes (ARGs) have attracted increasing attention. It is unclear whether the internal mechanisms by which antibiotics affect horizontal gene transfer (HGT) of ARGs during anaerobic digestion (AD) were influenced by dose and type. We investigated the effects of two major antibiotics (oxytetracycline, OTC, and sulfamethoxazole, SMX) on ARGs during AD according to antibiotic concentration in livestock wastewater influent. The low-dose antibiotic (0.5 mg/L) increased ROS and SOS responses, promoting the formation of ARGs. Meanwhile, low-dose antibiotics could also promote the spread of ARGs by promoting pili, communication responses, and the type IV secretion system (T4SS). However, different types and doses of antibiotics would lead to changes in the above functional modules and then affect the enrichment of ARGs. With the increasing dose of SMX, the advantages of pili and communication responses would gradually change. In the OTC system, low-dose has the strongest promoting ability in both pili and communication responses. Similarly, an increase in the dose of SMX would change T4SS from facilitation to inhibition, while OTC completely inhibits T4SS. Microbial and network analysis also revealed that low-dose antibiotics were more favorable for the growth of host bacteria.}, }
@article {pmid36060751, year = {2022}, author = {Shen, L and Qiu, T and Guo, Y and Gao, M and Gao, H and Zhao, G and Wang, X}, title = {Enhancing control of multidrug-resistant plasmid and its host community with a prolonged thermophilic phase during composting.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {989085}, pmid = {36060751}, issn = {1664-302X}, abstract = {The plasmid-mediated horizontal transfer of antibiotic resistance genes (ARGs) among bacteria facilitates the evolution and dissemination of antibiotic resistance. Broad-host-range plasmids can be transferred to different bacterial hosts in soil, plant rhizospheres, and wastewater treatment plants. Although composting is an effective way to convert organic waste into fertilizer and reduce some ARGs, few studies have focused on its effects on the spread of ARG-carrying plasmids and their bacterial host communities during composting. In this study, a fluorescently labeled Pseudomonas putida (P. putida) harboring a broad-host-range plasmid RP4 carrying three ARGs was inoculated into a raw material microcosm and composted with different durations of the thermophilic phase. The fate of the donor and RP4 in composting was investigated. The prolonged thermophilic composting removed 95.1% of dsRed and 98.0% of gfp, and it inhibited the rebound of P. putida and RP4 during the maturation phase. The spread potential of RP4 decreased from 10[-4] to 10[-6] transconjugants per recipient after composting. In addition, we sorted and analyzed the composition of RP4 recipient bacteria using fluorescence-activated cell sorting combined with 16S rRNA gene amplicon sequencing. The recipient bacteria of RP4 belonged to eight phyla, and Firmicutes, accounting for 75.3%-90.1%, was the dominant phylum in the transconjugants. The diversity and richness of the RP4 recipient community were significantly reduced by prolonged thermophilic periods. Overall, these findings provide new insights for assessing the contribution of composting in mitigating the dissemination of plasmid-mediated ARGs, and the prolonged thermophilic phase of composting can limit the transfer of multidrug-resistant plasmids.}, }
@article {pmid36060733, year = {2022}, author = {Yadav, G and Singh, R}, title = {In silico analysis reveals the co-existence of CRISPR-Cas type I-F1 and type I-F2 systems and its association with restricted phage invasion in Acinetobacter baumannii.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {909886}, pmid = {36060733}, issn = {1664-302X}, abstract = {INTRODUCTION: Acinetobacter baumannii, an opportunistic pathogen, rapidly acquires antibiotic resistance, thus compelling researchers to develop alternative treatments at utmost priority. Phage-based therapies are of appreciable benefit; however, CRISPR-Cas systems are a major constraint in this approach. Hence for effective implementation and a promising future of phage-based therapies, a multifaceted understanding of the CRISPR-Cas systems is necessary.<br><br>METHODS: This study investigated 4,977 RefSeq genomes of A. baumannii from the NCBI database to comprehend the distribution and association of CRISPR-Cas systems with genomic determinants.<br><br>RESULTS: Approximately 13.84% (n = 689/4,977) isolates were found to carry the CRSIPR-Cas system, and a small fraction of isolates, 1.49% (n = 74/4,977), exhibited degenerated CRISPR-Cas systems. Of these CRISPR-Cas positive (+) isolates, 67.48% (465/689) isolates harbored type I-F1, 28.59% (197/689) had type I-F2, and 3.7% (26/689) had co-existence of both type I-F1 and type I-F2 systems. Co-existing type I-F1 and type I-F2 systems are located distantly (&#x223c;1.733 Mb). We found a strong association of CRISPR-Cas systems within STs for type I-F1 and type I-F2, whereas the type I-F1 + F2 was not confined to any particular ST. Isolates with type I-F1 + F2 exhibited a significantly high number of mean spacers (n = 164.58 &#xb1; 46.41) per isolate as compared to isolates with type I-F2 (n = 82.87 &#xb1; 36.14) and type I-F1 (n = 54.51 &#xb1; 26.27) with majority targeting the phages. Isolates with type I-F1 (p < 0.0001) and type I-F2 (p < 0.0115) displayed significantly larger genome sizes than type I-F1 + F2. A significantly reduced number of integrated phages in isolates with co-existence of type I-F1 + F2 compared with other counterparts was observed (p = 0.0041). In addition, the isolates carrying type I-F1 + F2 did not exhibit reduced resistance and virulence genes compared to CRISPR-Cas(-) and CRISPR-Cas (+) type I-F1 and type I-F2, except for bap, abaI, and abaR.<br><br>CONCLUSION: Our observation suggests that the co-existence of type I-F1 and F2 is more effective in constraining the horizontal gene transfer and phage invasion in A. baumannii than the isolates exhibiting only type I-F1 and only type I-F2 systems.}, }
@article {pmid36059613, year = {2022}, author = {Alshaker, H and Hunter, E and Salter, M and Ramadass, A and Westra, W and Winkler, M and Green, J and Akoulitchev, A and Pchejetski, D}, title = {Monocytes acquire prostate cancer specific chromatin conformations upon indirect co-culture with prostate cancer cells.}, journal = {Frontiers in oncology}, volume = {12}, number = {}, pages = {990842}, pmid = {36059613}, issn = {2234-943X}, abstract = {BACKGROUND: Three-dimensional chromosome loop conformations are powerful regulators of gene expression. These chromosome conformations can be detected both in tumour and in circulating cells and have significant disease biomarker potential. We have recently detected specific chromosome conformations in circulating cells of patients with prostate cancer (PCa) which were similar to ones found in their primary tumours, however, the possibility of horizontal transfer of chromosome conformations was not studied previously.<br><br>METHODS: Human monocytes (U937) were co-cultured in Boyden chambers through 0.4 uM membrane with or without PC-3 human PCa cells or their conditioned media and a custom DNA microarray for 900,000 chromosomal loops covering all coding loci and non-coding RNA genes was performed on each part of the co-culture system.<br><br>RESULTS: We have detected 684 PC-3 cell-specific chromosome conformations across the whole genome that were absent in na&#xef;ve monocytes but appeared in monocytes co-cultured with PC-3 cells or with PC-3-conditioned media. Comparing PC3-specific conformations to the ones we have previously detected in systemic circulation of high-risk PCa patients revealed 9 positive loops present in both settings.<br><br>CONCLUSIONS: Our results demonstrate for the first time a proof of concept for horizontal transfer of chromosome conformations without direct cell-cell contact. This carries high clinical relevance as we have previously observed chromatin conformations in circulating cells of patients with melanoma and PCa similar to ones in their primary tumours. These changes can be used as highly specific biomarkers for diagnosis and prognosis. Further studies are required to elucidate the specific mechanism of chromosome conformations transfer and its clinical significance in particular diseases.}, }
@article {pmid36054646, year = {2022}, author = {Ding, P and Lu, J and Wang, Y and Schembri, MA and Guo, J}, title = {Antidepressants promote the spread of antibiotic resistance via horizontally conjugative gene transfer.}, journal = {Environmental microbiology}, volume = {24}, number = {11}, pages = {5261-5276}, pmid = {36054646}, issn = {1462-2920}, mesh = {Humans ; *Proteomics ; *Depressive Disorder, Major/genetics ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Plasmids/genetics ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Antidepressive Agents/pharmacology ; Genes, Bacterial ; }, abstract = {Antibiotic resistance is a global concern threatening public health. Horizontal gene transfer (HGT) between bacterial species contributes greatly to the dissemination of antibiotic resistance. Conjugation is one of the major HGT pathways responsible for the spread of antibiotic resistance genes (ARGs). Antidepressant drugs are commonly prescribed antipsychotics for major depressive disorders and are frequently detected in aquatic environments. However, little is known about how antidepressants stress bacteria and whether such effect can promote conjugation. Here, we report that commonly prescribed antidepressants, sertraline, duloxetine, fluoxetine, and bupropion, can promote the conjugative transfer of plasmid-borne multidrug resistance genes carried by environmentally and clinically relevant plasmids. Noteworthy, the transfer of plasmids across bacterial genera is significantly enhanced by antidepressants at clinically relevant concentrations. We also reveal the underlying mechanisms of enhanced conjugative transfer by employing flow cytometric analysis, genome-wide RNA sequencing and proteomic analysis. Antidepressants induce the production of reactive oxygen species and the SOS response, increase cell membrane permeability, and upregulate the expression of conjugation relevant genes. Given the contribution of HGT in the dissemination of ARGs, our findings highlight the importance of prudent prescription of antidepressants and to the potential connection between antidepressants and increasing antibiotic resistance.}, }
@article {pmid36051753, year = {2022}, author = {Chen, CY and Fuqua, C and Jackson, CR and Kadlec, K and Top, EM}, title = {Editorial: Plasmid transfer-mechanisms, ecology, evolution and applications.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {993628}, pmid = {36051753}, issn = {1664-302X}, }
@article {pmid36050562, year = {2022}, author = {Hao, H and Shi, B and Zhang, J and Dai, A and Li, W and Chen, H and Ji, W and Gong, C and Zhang, C and Li, J and Chen, L and Yao, B and Hu, P and Yang, H and Brosius, J and Lai, S and Shi, Q and Deng, C}, title = {The vertebrate- and testis- specific transmembrane protein C11ORF94 plays a critical role in sperm-oocyte membrane binding.}, journal = {Molecular biomedicine}, volume = {3}, number = {1}, pages = {27}, pmid = {36050562}, issn = {2662-8651}, support = {32170498//National Natural Science Foundation of China/ ; 31970388//National Natural Science Foundation of China/ ; 32000587//National Natural Science Foundation of China/ ; 2021YFF0702000//Key Technologies Research and Development Program/ ; 2018YFD0900602//Key Technologies Research and Development Program/ ; ZYJC21050//1.3+.5 project for disciplines of excellence, West China Hospital, Sichuan University/ ; 2022YFH0116//Science and Technology Department of Sichuan Province/ ; }, abstract = {Sperm-oocyte membrane fusion is necessary for mammalian fertilization. The factors that determine the fusion of sperm with oocytes are largely unknown. So far, spermatozoon factor IZUMO1 and the IZUMO1 counter-receptor JUNO on the oocyte membrane has been identified as a protein requiring fusion. Some sperm membrane proteins such as FIMP, SPACA6 and TEME95, have been proved not to directly regulate fusion, but their knockout will affect the fusion process of sperm and oocytes. Here, we identified a novel gene C11orf94 encoding a testicular-specific small transmembrane protein that emerges in vertebrates likely acquired via horizontal gene transfer from bacteria and plays an indispensable role in sperm-oocyte binding. We demonstrated that the deletion of C11orf94 dramatically decreased male fertility in mice. Sperm from C11orf94-deficient mice could pass through the zona pellucida, but failed to bind to the oocyte membrane, thus accumulating in the perivitelline space. In consistence, when the sperm of C11orf94-deficient mice were microinjected into the oocyte cytoplasm, fertilized oocytes were obtained and developed normally to blastocysts. Proteomics analysis revealed that C11orf94 influenced the expression of multiple gene products known to be indispensable for sperm-oocyte binding and fusion, including IZUMO1, EQTN and CRISP1. Thus, our study indicated that C11ORF94 is a vertebrate- and testis-specific small transmembrane protein that plays a critical role in sperm binding to the oolemma.}, }
@article {pmid36050493, year = {2022}, author = {Wang, T and Weiss, A and Aqeel, A and Wu, F and Lopatkin, AJ and David, LA and You, L}, title = {Horizontal gene transfer enables programmable gene stability in synthetic microbiota.}, journal = {Nature chemical biology}, volume = {18}, number = {11}, pages = {1245-1252}, pmid = {36050493}, issn = {1552-4469}, support = {R01 AI125604/AI/NIAID NIH HHS/United States ; R01 DK116187/DK/NIDDK NIH HHS/United States ; R01 EB031869/EB/NIBIB NIH HHS/United States ; }, mesh = {*Gene Transfer, Horizontal ; *Microbiota/genetics ; Plasmids/genetics ; }, abstract = {The functions of many microbial communities exhibit remarkable stability despite fluctuations in the compositions of these communities. To date, a mechanistic understanding of this function-composition decoupling is lacking. Statistical mechanisms have been commonly hypothesized to explain such decoupling. Here, we proposed that dynamic mechanisms, mediated by horizontal gene transfer (HGT), also enable the independence of functions from the compositions of microbial communities. We combined theoretical analysis with numerical simulations to illustrate that HGT rates can determine the stability of gene abundance in microbial communities. We further validated these predictions using engineered microbial consortia of different complexities transferring one or more than a dozen clinically isolated plasmids, as well as through the reanalysis of data from the literature. Our results demonstrate a generalizable strategy to program the gene stability of microbial communities.}, }
@article {pmid36046020, year = {2022}, author = {Jans, C and Wambui, J and Stevens, MJA and Tasara, T}, title = {Comparative genomics of dairy-associated Staphylococcus aureus from selected sub-Saharan African regions reveals milk as reservoir for human-and animal-derived strains and identifies a putative animal-related clade with presumptive novel siderophore.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {923080}, pmid = {36046020}, issn = {1664-302X}, abstract = {Staphylococcus aureus infection is considered to be a neglected tropical disease with huge impact on human and animal health alike. Dairy production in sub-Saharan Africa (SSA) relies heavily on various animals such as cows, goats, and camels, depending on the region. S. aureus causes mastitis and exhibits high prevalence in raw milk. The population structure including genotypic and phenotypic traits of dairy S. aureus in relation to animal and human isolates is, however, unknown for SSA. In this work, 20 S. aureus dairy isolates from East and West Africa were selected for comparative genomics and phenotypic analysis. Comparing their population structure revealed a large diversity of different origins suggesting milk to be a reservoir for human and animal strains alike. Furthermore, a novel putative siderophore was detected in multiple strains in a distinct animal-clade with strains of global origin. This putative siderophore shares a high genetic identity with that from Streptococcus equi suggesting possible horizontal gene transfer. These findings combined with the virulence genes harbored by these dairy-derived strains such as pvl, human evasion factor scn, various enterotoxin, leucocidin and antibiotic resistance genes, stresses the need for an integrative One Health approach to tackle the problem of S. aureus infections in animals and humans in sub-Saharan Africa.}, }
@article {pmid36042984, year = {2022}, author = {Rios-Miguel, AB and Smith, GJ and Cremers, G and van Alen, T and Jetten, MSM and Op den Camp, HJM and Welte, CU}, title = {Microbial paracetamol degradation involves a high diversity of novel amidase enzyme candidates.}, journal = {Water research X}, volume = {16}, number = {}, pages = {100152}, pmid = {36042984}, issn = {2589-9147}, abstract = {Pharmaceuticals are relatively new to nature and often not completely removed in wastewater treatment plants (WWTPs). Consequently, these micropollutants end up in water bodies all around the world posing a great environmental risk. One exception to this recalcitrant conversion is paracetamol, whose full degradation has been linked to several microorganisms. However, the genes and corresponding proteins involved in microbial paracetamol degradation are still elusive. In order to improve our knowledge of the microbial paracetamol degradation pathway, we inoculated a bioreactor with sludge of a hospital WWTP (Pharmafilter, Delft, NL) and fed it with paracetamol as the sole carbon source. Paracetamol was fully degraded without any lag phase and the enriched microbial community was investigated by metagenomic and metatranscriptomic analyses, which demonstrated that the microbial community was very diverse. Dilution and plating on paracetamol-amended agar plates yielded two Pseudomonas sp. isolates: a fast-growing Pseudomonas sp. that degraded 200 mg/L of paracetamol in approximately 10 h while excreting 4-aminophenol, and a slow-growing Pseudomonas sp. that degraded paracetamol without obvious intermediates in more than 90 days. Each Pseudomonas sp. contained a different highly-expressed amidase (31% identity to each other). These amidase genes were not detected in the bioreactor metagenome suggesting that other as-yet uncharacterized amidases may be responsible for the first biodegradation step of paracetamol. Uncharacterized deaminase genes and genes encoding dioxygenase enzymes involved in the catabolism of aromatic compounds and amino acids were the most likely candidates responsible for the degradation of paracetamol intermediates based on their high expression levels in the bioreactor metagenome and the Pseudomonas spp. genomes. Furthermore, cross-feeding between different community members might have occurred to efficiently degrade paracetamol and its intermediates in the bioreactor. This study increases our knowledge about the ongoing microbial evolution towards biodegradation of pharmaceuticals and points to a large diversity of (amidase) enzymes that are likely involved in paracetamol metabolism in WWTPs.}, }
@article {pmid36040324, year = {2022}, author = {Coral-Medina, A and Fenton, DA and Varela, J and Baranov, PV and Camarasa, C and Morrissey, JP}, title = {The evolution and role of the periplasmic asparaginase Asp3 in yeast.}, journal = {FEMS yeast research}, volume = {22}, number = {1}, pages = {}, pmid = {36040324}, issn = {1567-1364}, mesh = {*Asparaginase/genetics/metabolism ; Asparagine ; Fermentation ; Nitrogen/metabolism ; *Saccharomyces cerevisiae/metabolism ; }, abstract = {The study of nitrogen assimilation in yeast is of interest from genetic, evolutionary, and biotechnological perspectives. Over the course of evolution, yeasts have developed sophisticated control mechanisms to regulate nitrogen metabolism, with domesticated lineages sometimes displaying particular specialisation. The focus of this study was on assimilation of asparagine, which is a significant nutritional source for some alcoholic fermentations. We were particularly interested in ASP3, which encodes a periplasmic asparaginase and that was proposed to have been acquired relatively recently in S. cerevisiae by horizontal gene transfer. We examined 1680 S. cerevisiae genome assemblies to evaluate the distribution and evolutionary trajectory of ASP3. Our findings suggest an alternative hypothesis that ASP3 is an ancient Saccharomyces gene that has generally been lost over the course of evolution but has been retained in certain fermentative environments. As asparagine is the major nitrogen source in apple juice, we explored whether the presence of ASP3 would confer a growth advantage. Interestingly, we found that although ASP3 enhances growth when asparagine is the sole nitrogen source, the same effect is not seen in apple juice. These data indicate that growth in pure culture may not reflect the original selective environment for ASP3+ strains and highlight the role that complex regulation may play in optimising nitrogen assimilation in yeasts.}, }
@article {pmid36037921, year = {2022}, author = {Nava, AR and Daneshian, L and Sarma, H}, title = {Antibiotic resistant genes in the environment-exploring surveillance methods and sustainable remediation strategies of antibiotics and ARGs.}, journal = {Environmental research}, volume = {215}, number = {Pt 1}, pages = {114212}, doi = {10.1016/j.envres.2022.114212}, pmid = {36037921}, issn = {1096-0953}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Genes, Bacterial ; Humans ; Wastewater/analysis ; *Water Pollutants, Chemical ; }, abstract = {Antibiotic Resistant Genes (ARGs) are an emerging environmental health threat due to the potential change in the human microbiome and selection for the emergence of antibiotic resistant bacteria. The rise of antibiotic resistant bacteria has caused a global health burden. The WHO (world health organization) predicts a rise in deaths due to antibiotic resistant infections. Since bacteria can acquire ARGs through horizontal transmission, it is important to assess the dissemination of antibioticresistant genes from anthropogenic sources. There are several sources of antibiotics, antibiotic resistant bacteria and genes in the environment. These include wastewater treatment plants, landfill leachate, agricultural, animal industrial sources and estuaries. The use of antibiotics is a worldwide practice that has resulted in the evolution of resistance to antibiotics. Our review provides a more comprehensive look into multiple sources of ARG's and antibiotics rather than one. Moreover, we focus on effective surveillance methods of ARGs and antibiotics and sustainable abiotic and biotic remediation strategies for removal and reduction of antibiotics and ARGs from both terrestrial and aquatic environments. Further, we consider the impact on public health as this problem cannot be addressed without a global transdisciplinary effort.}, }
@article {pmid36036580, year = {2022}, author = {Jiang, C and Zhang, T and Li, Q and Jiang, H and Mao, X}, title = {A Novel Carrageenan Metabolic Pathway in Flavobacterium algicola.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {18}, pages = {e0110022}, pmid = {36036580}, issn = {1098-5336}, mesh = {Carrageenan/metabolism ; Flavobacterium/genetics/metabolism ; *Galactose ; Galactosidases/metabolism ; *Glycoside Hydrolases/genetics/metabolism ; Metabolic Networks and Pathways/genetics ; Polysaccharides ; }, abstract = {Carbohydrate-active enzymes are important components of the polysaccharide metabolism system in marine bacteria. Carrageenase is indispensable for forming carrageenan catalytic pathways. Here, two GH16_13 carrageenases showed likely hydrolysis activities toward different types of carrageenans (e.g., κ-, hybrid β/κ, hybrid α/ι, and hybrid λ), which indicates that a novel pathway is present in the marine bacterium Flavobacterium algicola to use κ-carrageenan (KC), ι-carrageenan (IC), and λ-carrageenan (LC). A comparative study described the different features with another reported pathway based on the specific carrageenans (κ, ι, and λ) and expanded the carrageenan metabolic versatility in F. algicola. A further comparative genomic analysis of carrageenan-degrading bacteria indicated different distributions of carrageenan metabolism-related genes in marine bacteria. The crucial core genes encoding the GH127 α-3,6-anhydro-d-galactosidase (ADAG) and 3,6-anhydro-d-galactose (d-AHG)-utilized cluster have been conserved during evolution. This analysis further revealed the horizontal gene transfer (HGT) phenomenon of the carrageenan polysaccharide utilization loci (CarPUL) from Bacteroidetes to other bacterial phyla, as well as the versatility of carrageenan catalytic activities in marine bacteria through different metabolic pathways. IMPORTANCE Based on the premise that the specific carrageenan-based pathway involved in carrageenan use by Flavobacterium algicola has been identified, another pathway was further analyzed, and it involved two GH16_13 carrageenases. Among all the characterized carrageenases, the members of GH16_13 accounted for only a small portion. Here, the functional analysis of two GH16_13 carrageenases suggested their hydrolysis effects on different types of carrageenans (e.g., κ, hybrid β/κ, hybrid α/ι-, and hybrid λ-), which led to the identification of another pathway. Further exploration enabled us to elucidate the novel pathway that metabolizes KC and IC in F. algicola successfully. The coexistence of these two pathways may provide improved survivability by F. algicola in the marine environment.}, }
@article {pmid36028018, year = {2022}, author = {Li, W and Zhang, WG and Zhang, MS and Lei, ZF and Li, PF and Ma, Y and Gao, Y}, title = {Environmentally relevant concentrations of mercury facilitate the horizontal transfer of plasmid-mediated antibiotic resistance genes.}, journal = {The Science of the total environment}, volume = {852}, number = {}, pages = {158272}, doi = {10.1016/j.scitotenv.2022.158272}, pmid = {36028018}, issn = {1879-1026}, mesh = {Conjugation, Genetic ; Anti-Bacterial Agents/pharmacology ; Escherichia coli/genetics ; Genes, Bacterial ; *Mercury/toxicity ; Antioxidants ; Reactive Oxygen Species ; Drug Resistance, Microbial/genetics ; Plasmids ; *Escherichia coli K12 ; Glutathione ; Malondialdehyde ; Gene Transfer, Horizontal ; }, abstract = {Abundant antibiotic resistance genes (ARGs) are typically found in mercury (Hg)-contaminated aquatic environments. This phenomenon is partly attributed to the co-resistance, cross-resistance, and shared regulatory responses to Hg and antibiotics. However, it remains unclear whether and how Hg influences the conjugative transfer of ARGs mediated by mobilizable plasmids. In the present study, we found that Hg[2+] at the environmentally relevant concentrations (0.001-0.5 mg L[-1]) facilitated the conjugative transfer of ARGs through the mobilizable plasmid RP4 from the donor Escherichia coli HB101 to the recipient E. coli K12. Exposure to Hg[2+] significantly increases the formation of reactive oxygen species, malondialdehyde production, antioxidant enzyme activities, and cell membrane permeability, while decreasing the concentration of glutathione. Scanning electron microscopy and transmission electron microscopy showed that the cell membrane suffered from oxidative damage, which is beneficial for conjugative transfer. The expression of global regulatory genes (korA, korB, and trbA) negatively regulating conjugative transfer was restrained by Hg[2+], while promoting the expression of positive regulatory genes involved in the mating pair formation system (trbBp and traF) and the DNA transfer and replication systems (trfAp and traJ). Although a high Hg[2+] concentration (1.0 mg L[-1]) suppressed ARGs conjugative transfer, our results suggest that Hg[2+] facilitates the dissemination of ARGs in aquatic environments at environmentally relevant concentrations. This study improves our understanding of ARGs dissemination in Hg-contaminated aquatic environments.}, }
@article {pmid36026509, year = {2022}, author = {Li, Z and Li, Y and Xue, AZ and Dang, V and Holmes, VR and Johnston, JS and Barrick, JE and Moran, NA}, title = {The Genomic Basis of Evolutionary Novelties in a Leafhopper.}, journal = {Molecular biology and evolution}, volume = {39}, number = {9}, pages = {}, pmid = {36026509}, issn = {1537-1719}, mesh = {Animals ; Biological Evolution ; Genomics ; *Hemiptera/genetics ; Proteomics ; Symbiosis/genetics ; }, abstract = {Evolutionary innovations generate phenotypic and species diversity. Elucidating the genomic processes underlying such innovations is central to understanding biodiversity. In this study, we addressed the genomic basis of evolutionary novelties in the glassy-winged sharpshooter (Homalodisca vitripennis, GWSS), an agricultural pest. Prominent evolutionary innovations in leafhoppers include brochosomes, proteinaceous structures that are excreted and used to coat the body, and obligate symbiotic associations with two bacterial types that reside within cytoplasm of distinctive cell types. Using PacBio long-read sequencing and Dovetail Omni-C technology, we generated a chromosome-level genome assembly for the GWSS and then validated the assembly using flow cytometry and karyotyping. Additional transcriptomic and proteomic data were used to identify novel genes that underlie brochosome production. We found that brochosome-associated genes include novel gene families that have diversified through tandem duplications. We also identified the locations of genes involved in interactions with bacterial symbionts. Ancestors of the GWSS acquired bacterial genes through horizontal gene transfer (HGT), and these genes appear to contribute to symbiont support. Using a phylogenomics approach, we inferred HGT sources and timing. We found that some HGT events date to the common ancestor of the hemipteran suborder Auchenorrhyncha, representing some of the oldest known examples of HGT in animals. Overall, we show that evolutionary novelties in leafhoppers are generated by the combination of acquiring novel genes, produced both de novo and through tandem duplication, acquiring new symbiotic associations that enable use of novel diets and niches, and recruiting foreign genes to support symbionts and enhance herbivory.}, }
@article {pmid36015378, year = {2022}, author = {Guo, X and Wang, M and Kang, H and Zhou, Y and Han, F}, title = {Distribution, Polymorphism and Function Characteristics of the GST-Encoding Fhb7 in Triticeae.}, journal = {Plants (Basel, Switzerland)}, volume = {11}, number = {16}, pages = {}, pmid = {36015378}, issn = {2223-7747}, support = {2016YFD0102001//National Key Research and Development Program of China/ ; }, abstract = {Encoding a glutathione S-transferase (GST) and conferring resistance to Fusarium head blight (FHB), Fhb7 was successfully isolated from the newly assembled Thinopyrum elongatum genome by researchers, with blasting searches revealing that Thinopyrum gained Fhb7 through horizontal gene transfer from an endophytic Epichloë species. On the contrary, our molecular evidence reveals that the homologs of Fhb7 are distributed commonly in Triticeae. Other than Thinopyrum, the Fhb7 homologs were also detected in four other genera, Elymus, Leymus, Roegneria and Pseudoroegneria, respectively. Sequence comparisons revealed that the protein sequences were at least 94% identical across all of the Fhb7 homologs in Triticeae plants, which in turn suggested that the horizontal gene transfer of the Fhb7 might have occurred before Triticeae differentiation instead of Thinopyrum. The multiple Fhb7 homologs detected in some Triticeae accessions and wheat-Thinopyrum derivatives might be attributed to the alloploid nature and gene duplication during evolution. In addition, we discovered that some wheat-Thinopyrum derivatives carrying the Fhb7 homologs had a completely different reaction to Fusarium head blight, which made us question the ability of the GST-encoding Fhb7 to resist FHB.}, }
@article {pmid36014979, year = {2022}, author = {Dewing, C and Van der Nest, MA and Santana, QC and Proctor, RH and Wingfield, BD and Steenkamp, ET and De Vos, L}, title = {Characterization of Host-Specific Genes from Pine- and Grass-Associated Species of the Fusarium fujikuroi Species Complex.}, journal = {Pathogens (Basel, Switzerland)}, volume = {11}, number = {8}, pages = {}, pmid = {36014979}, issn = {2076-0817}, support = {SARChI grant number 98353//Brenda Wingfield/ ; }, abstract = {The Fusarium fujikuroi species complex (FFSC) includes socioeconomically important pathogens that cause disease for numerous crops and synthesize a variety of secondary metabolites that can contaminate feedstocks and food. Here, we used comparative genomics to elucidate processes underlying the ability of pine-associated and grass-associated FFSC species to colonize tissues of their respective plant hosts. We characterized the identity, possible functions, evolutionary origins, and chromosomal positions of the host-range-associated genes encoded by the two groups of fungi. The 72 and 47 genes identified as unique to the respective genome groups were potentially involved in diverse processes, ranging from transcription, regulation, and substrate transport through to virulence/pathogenicity. Most genes arose early during the evolution of Fusarium/FFSC and were only subsequently retained in some lineages, while some had origins outside Fusarium. Although differences in the densities of these genes were especially noticeable on the conditionally dispensable chromosome of F. temperatum (representing the grass-associates) and F. circinatum (representing the pine-associates), the host-range-associated genes tended to be located towards the subtelomeric regions of chromosomes. Taken together, these results demonstrate that multiple mechanisms drive the emergence of genes in the grass- and pine-associated FFSC taxa examined. It also highlighted the diversity of the molecular processes potentially underlying niche-specificity in these and other Fusarium species.}, }
@article {pmid36014080, year = {2022}, author = {Chen, Y and Shah, S and Dougan, KE and van Oppen, MJH and Bhattacharya, D and Chan, CX}, title = {Improved Cladocopium goreaui Genome Assembly Reveals Features of a Facultative Coral Symbiont and the Complex Evolutionary History of Dinoflagellate Genes.}, journal = {Microorganisms}, volume = {10}, number = {8}, pages = {}, pmid = {36014080}, issn = {2076-2607}, support = {DP150101875//Australian Research Council/ ; DP190102474//Australian Research Council/ ; FL180100036//Australian Research Council/ ; Research Training Program//University of Queensland/ ; }, abstract = {Dinoflagellates of the family Symbiodiniaceae are crucial photosymbionts in corals and other marine organisms. Of these, Cladocopium goreaui is one of the most dominant symbiont species in the Indo-Pacific. Here, we present an improved genome assembly of C. goreaui combining new long-read sequence data with previously generated short-read data. Incorporating new full-length transcripts to guide gene prediction, the C. goreaui genome (1.2 Gb) exhibits a high extent of completeness (82.4% based on BUSCO protein recovery) and better resolution of repetitive sequence regions; 45,322 gene models were predicted, and 327 putative, topologically associated domains of the chromosomes were identified. Comparison with other Symbiodiniaceae genomes revealed a prevalence of repeats and duplicated genes in C. goreaui, and lineage-specific genes indicating functional innovation. Incorporating 2,841,408 protein sequences from 96 taxonomically diverse eukaryotes and representative prokaryotes in a phylogenomic approach, we assessed the evolutionary history of C. goreaui genes. Of the 5246 phylogenetic trees inferred from homologous protein sets containing two or more phyla, 35-36% have putatively originated via horizontal gene transfer (HGT), predominantly (19-23%) via an ancestral Archaeplastida lineage implicated in the endosymbiotic origin of plastids: 10-11% are of green algal origin, including genes encoding photosynthetic functions. Our results demonstrate the utility of long-read sequence data in resolving structural features of a dinoflagellate genome, and highlight how genetic transfer has shaped genome evolution of a facultative symbiont, and more broadly of dinoflagellates.}, }
@article {pmid36013391, year = {2022}, author = {Gibert, M and Jiménez, CJ and Comas, J and Zechner, EL and Madrid, C and Balsalobre, C}, title = {In Situ Monitoring and Quantitative Determination of R27 Plasmid Conjugation.}, journal = {Life (Basel, Switzerland)}, volume = {12}, number = {8}, pages = {}, pmid = {36013391}, issn = {2075-1729}, support = {PGC2018-096958-B-I00//Spanish Ministry of Science, Innovation and Universities/ ; 2017SGR499//Government of Catalonia/ ; }, abstract = {Horizontal gene transfer (HGT) by plasmid conjugation is a major driving force in the spread of antibiotic resistance among Enterobacteriaceae. Most of the conjugation studies are based on calculation of conjugation ratios (number of transconjugants/number of donors) after viable counting of transconjugant and donor cells. The development of robust, fast and reliable techniques for in situ monitoring and quantification of conjugation ratios might accelerate progress in understanding the impact of this cellular process in the HGT. The IncHI1 plasmids, involved in multiresistance phenotypes of relevant pathogens such as Salmonella and E. coli, are distinguished by the thermosensitivity of their conjugative transfer. Conjugation mediated by IncHI1 plasmids is more efficient at temperatures lower than 30 °C, suggesting that the transfer process takes place during the environmental transit of the bacteria. In this report, we described a methodology to monitor in situ the conjugation process during agar surface matings of the IncHI1 plasmid R27 and its derepressed derivative drR27 at different temperatures. A three-color-labeling strategy was used to visualize the spatial distribution of transconjugants within the heterogeneous environment by epifluorescence and confocal microscopy. Moreover, the fluorescent labelling was also used to quantify conjugation frequencies in liquid media by flow cytometry.}, }
@article {pmid36012061, year = {2022}, author = {Zhang, K and Li, K and Liu, Z and Li, Q and Li, W and Chen, Q and Xia, Y and Hu, F and Yang, F}, title = {The Sources and Potential Hosts Identification of Antibiotic Resistance Genes in the Yellow River, Revealed by Metagenomic Analysis.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {16}, pages = {}, pmid = {36012061}, issn = {1660-4601}, mesh = {*Anti-Bacterial Agents/analysis/pharmacology ; China ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Humans ; Metagenomics/methods ; *Rivers/microbiology ; }, abstract = {The fate of antibiotic resistance genes (ARGs) has been revealed in various environmental media in recent years. Namely, the emergence of genes that resist colistin and carbapenems has attracted wide attention. However, the pollution condition of ARGs and sources in the Yellow River is still little understood, despite the river being the second longest in China. The present study determined the levels of ARG pollution in the Henan section of the Yellow River and evaluated the role of the aquaculture industry in the spread of ARGs. As revealed by the results, a total of 9 types of ARGs were detected in the sediments of the Yellow River, and the total ARG content in the Yellow River ranges from 7.27 to 245.45 RPKM. Sul1 and sul2 are the dominant ARGs, and the huge usage of sulfonamides, horizontal gene transfer, and wide bacteria host contribute to the prevalence of these two genes. The results of Spearman correlation analysis indicate that the breeding industry has little influence on ARGs in the Yellow River. Network analysis reveals that the opportunistic pathogen Pseudomonas is the potential host of sul1, tetG, and ANT(3'')-IIa, which can pose a risk to human health.}, }
@article {pmid36011312, year = {2022}, author = {Le, NG and van Ulsen, P and van Spanning, R and Brouwer, A and van Straalen, NM and Roelofs, D}, title = {A Functional Carbohydrate Degrading Enzyme Potentially Acquired by Horizontal Gene Transfer in the Genome of the Soil Invertebrate Folsomia candida.}, journal = {Genes}, volume = {13}, number = {8}, pages = {}, pmid = {36011312}, issn = {2073-4425}, mesh = {Animals ; *Arthropods/genetics ; Bacteria/genetics ; Carbohydrates ; Escherichia coli/genetics ; Eukaryota ; *Gene Transfer, Horizontal ; Insecta ; Protein Sorting Signals/genetics ; Soil ; }, abstract = {Horizontal gene transfer (HGT) is defined as the acquisition by an organism of hereditary material from a phylogenetically unrelated organism. This process is mostly observed among bacteria and archaea, and considered less likely between microbes and multicellular eukaryotes. However, recent studies provide compelling evidence of the evolutionary importance of HGT in eukaryotes, driving functional innovation. Here, we study an HGT event in Folsomia candida (Collembola, Hexapoda) of a carbohydrate-active enzyme homologous to glycosyl hydrase group 43 (GH43). The gene encodes an N-terminal signal peptide, targeting the product for excretion, which suggests that it contributes to the diversity of digestive capacities of the detritivore host. The predicted α-L-arabinofuranosidase shows high similarity to genes in two other Collembola, an insect and a tardigrade. The gene was cloned and expressed in Escherichia coli using a cell-free protein expression system. The expressed protein showed activity against p-nitrophenyl-α-L-arabinofuranoside. Our work provides evidence for functional activity of an HGT gene in a soil-living detritivore, most likely from a bacterial donor, with genuine eukaryotic properties, such as a signal peptide. Co-evolution of metazoan GH43 genes with the Panarthropoda phylogeny suggests the HGT event took place early in the evolution of this ecdysozoan lineage.}, }
@article {pmid36009992, year = {2022}, author = {Palm, M and Fransson, A and Hultén, J and Búcaro Stenman, K and Allouche, A and Chiang, OE and Constandse, ML and van Dijk, KJ and Icli, S and Klimesova, B and Korhonen, E and Martínez-Crespo, G and Meggers, D and Naydenova, M and Polychronopoulou, MA and Schuntermann, DB and Unal, H and Wasylkowska, A and Farewell, A}, title = {The Effect of Heavy Metals on Conjugation Efficiency of an F-Plasmid in Escherichia coli.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {8}, pages = {}, pmid = {36009992}, issn = {2079-6382}, support = {N/A//Centre for Antibiotic Resistance Research/ ; }, abstract = {Conjugation, the process by which conjugative plasmids are transferred between bacteria, is regarded as a major contributor to the spread of antibiotic resistance, in both environmental and clinical settings. Heavy metals are known to co-select for antibiotic resistance, but the impact of the presence of these metals on conjugation itself is not clear. Here, we systematically investigate the impact that five heavy metals (arsenic, cadmium, copper, manganese, and zinc) have on the transfer of an IncF conjugative plasmid in Escherichia coli. Our results show that two of the metals, cadmium and manganese, have no significant impact, while arsenic and zinc both reduce conjugation efficiency by approximately 2-fold. Copper showed the largest impact, with an almost 100-fold decrease in conjugation efficiency. This was not mediated by any change in transcription from the major Py promoter responsible for transcription of the conjugation machinery genes. Further, we show that in order to have this severe impact on the transfer of the plasmid, copper sulfate needs to be present during the mating process, and we suggest explanations for this.}, }
@article {pmid36009937, year = {2022}, author = {Zhai, W and Tian, Y and Shao, D and Zhang, M and Li, J and Song, H and Sun, C and Wang, Y and Liu, D and Zhang, Y}, title = {Fecal Carriage of Escherichia coli Harboring the tet(X4)-IncX1 Plasmid from a Tertiary Class-A Hospital in Beijing, China.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {8}, pages = {}, pmid = {36009937}, issn = {2079-6382}, support = {31930110//National Natural Science Foundation of China/ ; 81991535//National Natural Science Foundation of China/ ; 32002340//National Natural Science Foundation of China/ ; }, abstract = {The emergence of the mobile tigecycline-resistance gene, tet(X4), poses a significant threat to public health. To investigate the prevalence and genetic characteristics of the tet(X4)-positive Escherichia coli in humans, 1101 human stool samples were collected from a tertiary class-A hospital in Beijing, China, in 2019. Eight E. coli isolates that were positive for tet(X4) were identified from clinical departments of oncology (n = 3), hepatology (n = 2), nephrology (n = 1), urology (n = 1), and general surgery (n = 1). They exhibited resistance to multiple antibiotics, including tigecycline, but remained susceptible to meropenem and polymyxin B. A phylogenetic analysis revealed that the clonal spread of four tet(X4)-positive E. coli from different periods of time or departments existed in this hospital, and three isolates were phylogenetically close to the tet(X4)-positive E. coli from animals and the environment. All tet(X4)-positive E. coli isolates contained the IncX1-plasmid replicon. Three isolates successfully transferred their tigecycline resistance to the recipient strain, C600, demonstrating that the plasmid-mediated horizontal gene transfer constitutes another critical mechanism for transmitting tet(X4). Notably, all tet(X4)-bearing plasmids identified in this study had a high similarity to several plasmids recovered from animal-derived strains. Our findings revealed the importance of both the clonal spread and horizontal gene transfer in the spread of tet(X4) within human clinics and between different sources.}, }
@article {pmid36007892, year = {2022}, author = {Shi, WT and Zhang, B and Li, ML and Liu, KH and Jiao, J and Tian, CF}, title = {The convergent xenogeneic silencer MucR predisposes α-proteobacteria to integrate AT-rich symbiosis genes.}, journal = {Nucleic acids research}, volume = {50}, number = {15}, pages = {8580-8598}, pmid = {36007892}, issn = {1362-4962}, mesh = {*Alphaproteobacteria/genetics ; Bacterial Proteins/metabolism ; DNA ; Escherichia coli/genetics/metabolism ; *Gene Expression Regulation, Bacterial ; Symbiosis ; }, abstract = {Bacterial adaptation is largely shaped by horizontal gene transfer, xenogeneic silencing mediated by lineage-specific DNA bridgers (H-NS, Lsr2, MvaT and Rok), and various anti-silencing mechanisms. No xenogeneic silencing DNA bridger is known for α-proteobacteria, from which mitochondria evolved. By investigating α-proteobacterium Sinorhizobium fredii, a facultative legume microsymbiont, here we report the conserved zinc-finger bearing MucR as a novel xenogeneic silencing DNA bridger. Self-association mediated by its N-terminal domain (NTD) is required for DNA-MucR-DNA bridging complex formation, maximizing MucR stability, transcriptional silencing, and efficient symbiosis in legume nodules. Essential roles of NTD, CTD (C-terminal DNA-binding domain), or full-length MucR in symbiosis can be replaced by non-homologous NTD, CTD, or full-length protein of H-NS from γ-proteobacterium Escherichia coli, while NTD rather than CTD of Lsr2 from Gram-positive Mycobacterium tuberculosis can replace the corresponding domain of MucR in symbiosis. Chromatin immunoprecipitation sequencing reveals similar recruitment profiles of H-NS, MucR and various functional chimeric xenogeneic silencers across the multipartite genome of S. fredii, i.e. preferring AT-rich genomic islands and symbiosis plasmid with key symbiosis genes as shared targets. Collectively, the convergently evolved DNA bridger MucR predisposed α-proteobacteria to integrate AT-rich foreign DNA including symbiosis genes, horizontal transfer of which is strongly selected in nature.}, }
@article {pmid36003770, year = {2022}, author = {Valcz, G and Újvári, B and Buzás, EI and Krenács, T and Spisák, S and Kittel, &#xc1; and Tulassay, Z and Igaz, P and Takács, I and Molnár, B}, title = {Small extracellular vesicle DNA-mediated horizontal gene transfer as a driving force for tumor evolution: Facts and riddles.}, journal = {Frontiers in oncology}, volume = {12}, number = {}, pages = {945376}, pmid = {36003770}, issn = {2234-943X}, abstract = {The basis of the conventional gene-centric view on tumor evolution is that vertically inherited mutations largely define the properties of tumor cells. In recent years, however, accumulating evidence shows that both the tumor cells and their microenvironment may acquire external, non-vertically inherited genetic properties via horizontal gene transfer (HGT), particularly through small extracellular vesicles (sEVs). Many phases of sEV-mediated HGT have been described, such as DNA packaging into small vesicles, their release, uptake by recipient cells, and incorporation of sEV-DNA into the recipient genome to modify the phenotype and properties of cells. Recent techniques in sEV separation, genome sequencing and editing, as well as the identification of new secretion mechanisms, shed light on a number of additional details of this phenomenon. Here, we discuss the key features of this form of gene transfer and make an attempt to draw relevant conclusions on the contribution of HGT to tumor evolution.}, }
@article {pmid36002568, year = {2022}, author = {Ocaña-Pallarès, E and Williams, TA and López-Escardó, D and Arroyo, AS and Pathmanathan, JS and Bapteste, E and Tikhonenkov, DV and Keeling, PJ and Szöllősi, GJ and Ruiz-Trillo, I}, title = {Divergent genomic trajectories predate the origin of animals and fungi.}, journal = {Nature}, volume = {609}, number = {7928}, pages = {747-753}, pmid = {36002568}, issn = {1476-4687}, support = {616960/ERC_/European Research Council/International ; 714774/ERC_/European Research Council/International ; 615274/ERC_/European Research Council/International ; }, mesh = {Animals ; *Evolution, Molecular ; *Fungi/genetics ; Gene Transfer, Horizontal ; Genes ; *Genome/genetics ; Genome, Fungal/genetics ; *Genomics ; Metabolism/genetics ; *Phylogeny ; }, abstract = {Animals and fungi have radically distinct morphologies, yet both evolved within the same eukaryotic supergroup: Opisthokonta[1,2]. Here we reconstructed the trajectory of genetic changes that accompanied the origin of Metazoa and Fungi since the divergence of Opisthokonta with a dataset that includes four novel genomes from crucial positions in the Opisthokonta phylogeny. We show that animals arose only after the accumulation of genes functionally important for their multicellularity, a tendency that began in the pre-metazoan ancestors and later accelerated in the metazoan root. By contrast, the pre-fungal ancestors experienced net losses of most functional categories, including those gained in the path to Metazoa. On a broad-scale functional level, fungal genomes contain a higher proportion of metabolic genes and diverged less from the last common ancestor of Opisthokonta than did the gene repertoires of Metazoa. Metazoa and Fungi also show differences regarding gene gain mechanisms. Gene fusions are more prevalent in Metazoa, whereas a larger fraction of gene gains were detected as horizontal gene transfers in Fungi and protists, in agreement with the long-standing idea that transfers would be less relevant in Metazoa due to germline isolation[3-5]. Together, our results indicate that animals and fungi evolved under two contrasting trajectories of genetic change that predated the origin of both groups. The gradual establishment of two clearly differentiated genomic contexts thus set the stage for the emergence of Metazoa and Fungi.}, }
@article {pmid36000914, year = {2022}, author = {Xu, J and Mei, C and Zhi, Y and Liang, ZX and Zhang, X and Wang, HJ}, title = {Comparative Genomics Analysis and Outer Membrane Vesicle-Mediated Horizontal Antibiotic-Resistance Gene Transfer in Avibacterium paragallinarum.}, journal = {Microbiology spectrum}, volume = {10}, number = {5}, pages = {e0137922}, pmid = {36000914}, issn = {2165-0497}, mesh = {Animals ; Chickens/microbiology ; *Poultry Diseases/microbiology ; *Haemophilus Infections/microbiology/veterinary ; *Haemophilus paragallinarum/genetics ; Gram-Negative Bacteria ; Drug Resistance, Microbial ; Tetracycline ; Anti-Bacterial Agents/pharmacology ; Chloramphenicol ; Erythromycin ; Streptomycin ; Genomics ; Deoxyribonucleases ; }, abstract = {Avibacterium paragallinarum is the etiological agent of infectious coryza, an acute respiratory disease of chickens that is globally distributed and causes serious economic losses for chicken production. A. paragallinarum is a Gram-negative bacterium that releases outer membrane vesicles (OMVs). In this study, a comparative genomic analysis of A. paragallinarum isolate P4chr1 and its OMVs was carried out, and the ability to transfer antibiotic resistance genes (ARGs) via the OMVs was studied. Sequencing and data analyses demonstrated that the genomic size of A. paragallinarum P4chr1 was approximately 2.77 Mb with a 25 kb tolerance island that covered six types of antibiotics and 11 ARGs. The genomic size of its OMVs was approximately 2.69 Mb, covering 97% of the genomic length and almost all the gene sequences of P4chr1. Purified and DNase-treated A. paragallinarum P4chr1 OMVs were cocultured with the antibiotic-sensitive A. paragallinarum Modesto strain on an antibiotic (chloramphenicol, erythromycin, tetracycline, or streptomycin)-containing plate, and the corresponding ARGs were detected in the colonies grown on the plates. However, using an antimicrobial susceptibility test, we found that ARGs delivered by OMVs were not persistent but only appeared transiently on the antibiotic-containing plates. Antibiotic resistance and ARGs were lost by the second bacterial passage. IMPORTANCE The functions and roles of OMVs on ARG and virulent gene transfer and dissemination have been reported in numerous Gram-negative bacteria. However, the role of OMVs in mediating antibiotic resistance in A. paragallinarum has not been reported. This study is the first report to compare the genomic characteristics of OMVs with its parent A. paragallinarum strain and to study A. paragallinarum ARG transfer via OMVs. This work has provided useful data for further studies focusing on nonplasmid ARG transfer mediated by A. paragallinarum OMVs.}, }
@article {pmid35994648, year = {2022}, author = {Colnaghi, M and Lane, N and Pomiankowski, A}, title = {Repeat sequences limit the effectiveness of lateral gene transfer and favored the evolution of meiotic sex in early eukaryotes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {35}, pages = {e2205041119}, pmid = {35994648}, issn = {1091-6490}, support = {BB/V003542/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/S003681/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, mesh = {Computer Simulation ; *DNA Repeat Expansion/genetics ; *Eukaryota/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal/genetics ; Genome/genetics ; *Meiosis/genetics ; Mutation ; Mutation Accumulation ; Phylogeny ; Prokaryotic Cells ; }, abstract = {The transition from prokaryotic lateral gene transfer to eukaryotic meiotic sex is poorly understood. Phylogenetic evidence suggests that it was tightly linked to eukaryogenesis, which involved an unprecedented rise in both genome size and the density of genetic repeats. Expansion of genome size raised the severity of Muller's ratchet, while limiting the effectiveness of lateral gene transfer (LGT) at purging deleterious mutations. In principle, an increase in recombination length combined with higher rates of LGT could solve this problem. Here, we show using a computational model that this solution fails in the presence of genetic repeats prevalent in early eukaryotes. The model demonstrates that dispersed repeat sequences allow ectopic recombination, which leads to the loss of genetic information and curtails the capacity of LGT to prevent mutation accumulation. Increasing recombination length in the presence of repeat sequences exacerbates the problem. Mutational decay can only be resisted with homology along extended sequences of DNA. We conclude that the transition to homologous pairing along linear chromosomes was a key innovation in meiotic sex, which was instrumental in the expansion of eukaryotic genomes and morphological complexity.}, }
@article {pmid35992716, year = {2022}, author = {Zhang, Y and Guo, Y and Qiu, T and Gao, M and Wang, X}, title = {Bacteriophages: Underestimated vehicles of antibiotic resistance genes in the soil.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {936267}, pmid = {35992716}, issn = {1664-302X}, abstract = {Bacteriophages (phages), the most abundant biological entities on Earth, have a significant effect on the composition and dynamics of microbial communities, biogeochemical cycles of global ecosystems, and bacterial evolution. A variety of antibiotic resistance genes (ARGs) have been identified in phage genomes in different soil samples. Phages can mediate the transfer of ARGs between bacteria via transduction. Recent studies have suggested that anthropogenic activities promote phage-mediated horizontal gene transfer events. Therefore, the role of phages in the dissemination of ARGs, which are a potential threat to human health, may be underestimated. However, the contribution of phages to the transfer of ARGs is still poorly understood. Considering the growing and wide concerns of antibiotic resistance, phages should be considered a research focus in the mobile resistome. This review aimed to provide an overview of phages as vehicles of ARGs in soil. Here, we summarized the current knowledge on the diversity and abundance of ARGs in soilborne phages and analyzed the contribution of phages to the horizontal transfer of ARGs. Finally, research deficiencies and future perspectives were discussed. This study provides a reference for preventing and controlling ARG pollution in agricultural systems.}, }
@article {pmid35991959, year = {2022}, author = {,  and More, S and Bampidis, V and Benford, D and Bragard, C and Halldorsson, T and Hernández-Jerez, A and Bennekou, SH and Koutsoumanis, K and Lambré, C and Machera, K and Mullins, E and Nielsen, SS and Schlatter, J and Schrenk, D and Turck, D and Younes, M and Herman, L and Pelaez, C and van Loveren, H and Vlak, J and Revez, J and Aguilera, J and Schoonjans, R and Cocconcelli, PS}, title = {Evaluation of existing guidelines for their adequacy for the food and feed risk assessment of microorganisms obtained through synthetic biology.}, journal = {EFSA journal. European Food Safety Authority}, volume = {20}, number = {8}, pages = {e07479}, pmid = {35991959}, issn = {1831-4732}, abstract = {EFSA was asked by the European Commission to evaluate synthetic biology (SynBio) developments for agri-food use in the near future and to determine whether or not they are expected to constitute potential new hazards/risks. Moreover, EFSA was requested to evaluate the adequacy of existing guidelines for risk assessment of SynBio and if updated guidance is needed. The scope of this Opinion covers food and feed risk assessment, the variety of microorganisms that can be used in the food/feed chain and the whole spectrum of techniques used in SynBio. This Opinion complements a previously adopted Opinion with the evaluation of existing guidelines for the microbial characterisation and environmental risk assessment of microorganisms obtained through SynBio. The present Opinion confirms that microbial SynBio applications for food and feed use, with the exception of xenobionts, could be ready in the European Union in the next decade. New hazards were identified related to the use or production of unusual and/or new-to-nature components. Fifteen cases were selected for evaluating the adequacy of existing guidelines. These were generally adequate for assessing the product, the production process, nutritional and toxicological safety, allergenicity, exposure and post-market monitoring. The comparative approach and a safety assessment per se could be applied depending on the degree of familiarity of the SynBio organism/product with the non-genetically modified counterparts. Updated guidance is recommended for: (i) bacteriophages, protists/microalgae, (ii) exposure to plant protection products and biostimulants, (iii) xenobionts and (iv) feed additives for insects as target species. Development of risk assessment tools is recommended for assessing nutritional value of biomasses, influence of microorganisms on the gut microbiome and the gut function, allergenic potential of new-to-nature proteins, impact of horizontal gene transfer and potential risks of living cell intake. A further development towards a strain-driven risk assessment approach is recommended.}, }
@article {pmid35989606, year = {2022}, author = {Haudiquet, M and de Sousa, JM and Touchon, M and Rocha, EPC}, title = {Selfish, promiscuous and sometimes useful: how mobile genetic elements drive horizontal gene transfer in microbial populations.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {377}, number = {1861}, pages = {20210234}, pmid = {35989606}, issn = {1471-2970}, mesh = {Biological Evolution ; *Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences ; }, abstract = {Horizontal gene transfer (HGT) drives microbial adaptation but is often under the control of mobile genetic elements (MGEs) whose interests are not necessarily aligned with those of their hosts. In general, transfer is costly to the donor cell while potentially beneficial to the recipients. The diversity and plasticity of cell-MGEs interactions, and those among MGEs, result in complex evolutionary processes where the source, or even the existence of selection for maintaining a function in the genome, is often unclear. For example, MGE-driven HGT depends on cell envelope structures and defense systems, but many of these are transferred by MGEs themselves. MGEs can spur periods of intense gene transfer by increasing their own rates of horizontal transmission upon communicating, eavesdropping, or sensing the environment and the host physiology. This may result in high-frequency transfer of host genes unrelated to the MGE. Here, we review how MGEs drive HGT and how their transfer mechanisms, selective pressures and genomic traits affect gene flow, and therefore adaptation, in microbial populations. The encoding of many adaptive niche-defining microbial traits in MGEs means that intragenomic conflicts and alliances between cells and their MGEs are key to microbial functional diversification. This article is part of a discussion meeting issue 'Genomic population structures of microbial pathogens'.}, }
@article {pmid35989605, year = {2022}, author = {Huisman, JS and Vaughan, TG and Egli, A and Tschudin-Sutter, S and Stadler, T and Bonhoeffer, S}, title = {The effect of sequencing and assembly on the inference of horizontal gene transfer on chromosomal and plasmid phylogenies.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {377}, number = {1861}, pages = {20210245}, pmid = {35989605}, issn = {1471-2970}, mesh = {Animals ; Anti-Bacterial Agents ; Escherichia coli/genetics ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; Phylogeny ; Plasmids/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {The spread of antibiotic resistance genes on plasmids is a threat to human and animal health. Phylogenies of bacteria and their plasmids contain clues regarding the frequency of plasmid transfer events, as well as the co-evolution of plasmids and their hosts. However, whole genome sequencing data from diverse ecological or clinical bacterial samples are rarely used to study plasmid phylogenies and resistance gene transfer. This is partially due to the difficulty of extracting plasmids from short-read sequencing data. Here, we use both short- and long-read sequencing data of 24 clinical extended-spectrum [Formula: see text]-lactamase (ESBL)-producing Escherichia coli to estimate chromosomal and plasmid phylogenies. We compare the impact of different sequencing and assembly methodologies on these phylogenies and on the inference of horizontal gene transfer. We find that chromosomal phylogenies can be estimated robustly with all methods, whereas plasmid phylogenies have more variable topology and branch lengths across the methods used. Specifically, hybrid methods that use long reads to resolve short-read assemblies (HybridSPAdes and Unicycler) perform better than those that started from long reads during assembly graph generation (Canu). By contrast, the inference of plasmid and antibiotic resistance gene transfer using a parsimony-based criterion is mostly robust to the choice of sequencing and assembly method. This article is part of a discussion meeting issue 'Genomic population structures of microbial pathogens'.}, }
@article {pmid35986092, year = {2022}, author = {Kikuchi, Y and Matsui, H and Asami, Y and Kuwae, A and Inahashi, Y and Hanaki, H and Abe, A}, title = {Landscape of blaNDM genes in Enterobacteriaceae.}, journal = {The Journal of antibiotics}, volume = {75}, number = {10}, pages = {559-566}, pmid = {35986092}, issn = {1881-1469}, support = {JP20nk0101552//Japan Agency for Medical Research and Development (AMED)/ ; JP22nk0101587//Japan Agency for Medical Research and Development (AMED)/ ; }, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; *Enterobacteriaceae/genetics ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Plasmids/genetics ; *beta-Lactamases/genetics/metabolism ; }, abstract = {The blaNDM-1 gene encodes a carbapenemase, New Delhi metallo-β-lactamase (NDM-1), and the ability to produce NDM-1 is spread among Enterobacteriaceae via horizontal gene transfer of plasmids. It has been widely accepted that blaNDM-1 is regulated by a hybrid promoter (PISAba125) consisting of a -10 box from the original blaNDM-1 and a -35 box from ISAba125. However, the conservation of this promoter and the vertical transmission of blaNDM genes by chromosomal integration have not been comprehensively analyzed. We retrieved the region containing the ORF of blaNDM-1 (>95% translated protein identity) and a region 120 bp upstream of the blaNDM-1 start codon from the complete sequence data of Enterobacteriaceae plasmids (n = 10,914) and chromosomes (n = 4908) deposited in GenBank, and the 310 extracted blaNDM genes were analyzed by an in-silico approach. The results showed that most blaNDM genes (99.0%) utilized the promoter, PISAba125. Interestingly, two blaNDM-1 genes from the genus Citrobacter utilized the ISCR1-derived outward-oriented promoters POUT (PISCR1). Furthermore, the insertion of ISAba125 and ISCR1 occurred upstream of the CCATATTT sequence, which is located upstream of the -10 box. We also confirmed that most of the blaNDM genes were disseminated by horizontal gene transfer of the plasmid, but 10 cases of the blaNDM genes were integrated into the chromosome via mobile genetic elements such as IS26, IS150, ISCR1, ICE, and Tn7-like elements. Thus, plasmid-mediated transmission of the PISAba125-blaNDM genes is predominant in Enterobacteriaceae. However, the spread of blaNDM genes with new promoters and vertical dissemination via chromosomal integrations may pose additional serious clinical problems.}, }
@article {pmid35985927, year = {2022}, author = {Marcilla, A and Sánchez-López, CM}, title = {Extracellular vesicles as a horizontal gene transfer mechanism in Leishmania.}, journal = {Trends in parasitology}, volume = {38}, number = {10}, pages = {823-825}, doi = {10.1016/j.pt.2022.08.004}, pmid = {35985927}, issn = {1471-5007}, mesh = {Animals ; Drug Resistance ; *Extracellular Vesicles ; Gene Transfer, Horizontal ; *Leishmania/genetics ; *Parasites ; }, abstract = {Douanne et al. recently reported horizontal gene transfer (HGT) mediated by extracellular vesicles (EVs) in Leishmania; this constitutes the first report of this phenomenon in parasites. They showed that EVs facilitate the transmission of drug-resistance genes and increased cell fitness in stressful environments, indicating potential clinical application of these findings.}, }
@article {pmid35985290, year = {2022}, author = {Fillol-Salom, A and Rostøl, JT and Ojiogu, AD and Chen, J and Douce, G and Humphrey, S and Penadés, JR}, title = {Bacteriophages benefit from mobilizing pathogenicity islands encoding immune systems against competitors.}, journal = {Cell}, volume = {185}, number = {17}, pages = {3248-3262.e20}, doi = {10.1016/j.cell.2022.07.014}, pmid = {35985290}, issn = {1097-4172}, support = {MR/V000772/1/MRC_/Medical Research Council/United Kingdom ; BB/V002376/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/M003876/1/MRC_/Medical Research Council/United Kingdom ; MR/S00940X/2/MRC_/Medical Research Council/United Kingdom ; 201531/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; BB/N002873/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/S00940X/1/MRC_/Medical Research Council/United Kingdom ; BB/S003835/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteria/genetics ; *Bacteriophages/genetics ; Gene Transfer, Horizontal ; *Genomic Islands ; Immune System ; Plasmids ; }, abstract = {Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display high genetic mobility. How this variability and mobility occurs remains largely unknown. Here, we demonstrate that a widespread family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms, which can be disseminated intra- and inter-generically by helper phages. These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer. Our results demonstrate that phages can mobilize PICI-encoded immunity systems to use them against other mobile genetic elements, which compete with the phages for the same bacterial hosts. Therefore, despite the cost, mobilization of PICIs may be beneficial for phages, PICIs, and bacteria in nature. Our results suggest that PICIs are important players controlling horizontal gene transfer and that PICIs and phages establish mutualistic interactions that drive bacterial ecology and evolution.}, }
@article {pmid35985212, year = {2022}, author = {Peng, S and Zhang, H and Song, D and Chen, H and Lin, X and Wang, Y and Ji, L}, title = {Distribution of antibiotic, heavy metals and antibiotic resistance genes in livestock and poultry feces from different scale of farms in Ningxia, China.}, journal = {Journal of hazardous materials}, volume = {440}, number = {}, pages = {129719}, doi = {10.1016/j.jhazmat.2022.129719}, pmid = {35985212}, issn = {1873-3336}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Cattle ; Chickens/genetics ; *Chlortetracycline ; Doxycycline ; Drug Resistance, Microbial/genetics ; *Environmental Pollutants ; Farms ; Feces ; Genes, Bacterial ; Livestock ; Manure ; *Metals, Heavy/toxicity ; Poultry/genetics ; Sheep/genetics ; Swine ; }, abstract = {With the rapid development of livestock and poultry breeding industries, pollution problems caused by the discharge of animal feces have become increasingly severe. Nevertheless, there are limited investigations about nutrients and pollutants in animal feces from different scale of farms, especially in Northwest China. Here we investigated nutrients content, 19 antibiotics, 7 heavy metals, 329 antibiotic resistance genes (ARGs) and 35 mobile genetic elements (MGEs) in six main livestock and poultry feces collected from 5 coastal regions of Ningxia. Pig and chicken feces exhibited higher levels of nutrients content, but antibiotics, heavy metals, ARGs and MGEs were also more abundant than those in cattle and sheep feces. Chlortetracycline hydrochloride and doxycycline hyclate were the most commonly used antibiotic, which detected with the highest rate and concentrations, especially in broiler, layer and pig feces. Strong positive correlations were found among different ARGs or between ARGs and MGEs, indicated the risk of horizontal gene transfer of ARGs. Residual antibiotic and heavy metals significantly affect the abundance of ARGs. Feeding mode and the scales of the animal farms served little effect on the distribution of the pollutants (including residual antibiotics, heavy metals, MGEs and ARGs), which were significantly different among animal types. Use of antibiotics and heavy metals should be strictly regulated, especially in chicken and pig farms, in order to control contaminants and reduce potential risks to the environment.}, }
@article {pmid35983328, year = {2022}, author = {Qian, C and Ma, J and Liang, J and Zhang, L and Liang, X}, title = {Comprehensive deciphering prophages in genus Acetobacter on the ecology, genomic features, toxin-antitoxin system, and linkage with CRISPR-Cas system.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {951030}, pmid = {35983328}, issn = {1664-302X}, abstract = {Acetobacter is the predominant microbe in vinegar production, particularly in those natural fermentations that are achieved by complex microbial communities. Co-evolution of prophages with Acetobacter, including integration, release, and dissemination, heavily affects the genome stability and production performance of industrial strains. However, little has been discussed yet about prophages in Acetobacter. Here, prophage prediction analysis using 148 available genomes from 34 Acetobacter species was carried out. In addition, the type II toxin-antitoxin systems (TAs) and CRISPR-Cas systems encoded by prophages or the chromosome were analyzed. Totally, 12,000 prophage fragments were found, of which 350 putatively active prophages were identified in 86.5% of the selected genomes. Most of the active prophages (83.4%) belonged to the order Caudovirales dominated by the families Siphoviridae and Myroviridae prophages (71.4%). Notably, Acetobacter strains survived in complex environments that frequently carried multiple prophages compared with that in restricted habits. Acetobacter prophages showed high genome diversity and horizontal gene transfer across different bacterial species by genomic feature characterization, average nucleotide identity (ANI), and gene structure visualization analyses. About 31.14% of prophages carry type II TAS, suggesting its important role in addiction, bacterial defense, and growth-associated bioprocesses to prophages and hosts. Intriguingly, the genes coding for Cse1, Cse2, Cse3, Cse4, and Cas5e involved in type I-E and Csy4 involved in type I-F CRISPR arrays were firstly found in two prophages. Type II-C CRISPR-Cas system existed only in Acetobacter aceti, while the other Acetobacter species harbored the intact or eroded type I CRISPR-Cas systems. Totally, the results of this study provide fundamental clues for future studies on the role of prophages in the cell physiology and environmental behavior of Acetobacter.}, }
@article {pmid35980276, year = {2024}, author = {Zhang, C and Saad, Z and Zhang, S and Chen, B and He, X and Liu, S}, title = {Effects of voltage and tetracycline on horizontal transfer of ARGs in microbial electrolysis cells.}, journal = {Environmental technology}, volume = {45}, number = {3}, pages = {559-568}, doi = {10.1080/09593330.2022.2114860}, pmid = {35980276}, issn = {1479-487X}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Escherichia coli/genetics ; Angiotensin Receptor Antagonists/pharmacology ; Genes, Bacterial ; Angiotensin-Converting Enzyme Inhibitors/pharmacology ; Drug Resistance, Microbial/genetics ; Tetracycline/pharmacology ; Bacteria ; Electrolysis ; Plasmids ; }, abstract = {The abuse of antibiotics leads to the production of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Microbial electrolysis cells (MECs) have been widely applicated in the field of degrading antibiotics. ARGs were increased via horizontal transfer in single and two-chamber MECs. As one of the critical parameters in MECs, voltage has a particular impact on the ARGs transfer via horizontal transfer. However, there have been few studies of ARGs transfer under the exposure of antibiotics and voltage in MECs. In this study, five concentrations of tetracycline (0, 1, 5, 10, 20 mg/L) were selected to explore the conjugative transfer frequency of plasmid-encoded the ARGs from the donor (E. coli RP4) to receptor (E. coli HB101) in MECs, two voltages (1.5 and 2.0 V) were used to explore the conjugative transfer frequency of ARGs in MECs, then, the transfer of ARGs in MECs under the co-effect of tetracycline and voltage was explored. The results showed that the conjugative transfer frequency of ARGs was significantly increased with the increase of tetracycline concentration and voltage, respectively (p < 0.05). Under the pressure of tetracycline and voltage, the conjugative transfer frequency of ARGs is significantly enhanced with the co-effect of tetracycline and voltage (p < 0.05). The oxidative response induced by electrical stimulation promotes the overproduction of reactive oxygen species and the enhancement of cell membrane permeability of donor and recipient bacteria in MECs. These findings provide insights for studying the spread of ARGs in MECs.}, }
@article {pmid35979495, year = {2022}, author = {Uzun, M and Koziaeva, V and Dziuba, M and Leão, P and Krutkina, M and Grouzdev, D}, title = {Detection of interphylum transfers of the magnetosome gene cluster in magnetotactic bacteria.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {945734}, pmid = {35979495}, issn = {1664-302X}, abstract = {Magnetosome synthesis in magnetotactic bacteria (MTB) is regarded as a very ancient evolutionary process that dates back to deep-branching phyla. Magnetotactic bacteria belonging to one of such phyla, Nitrospirota, contain the classical genes for the magnetosome synthesis (e.g., mam, mms) and man genes, which were considered to be specific for this group. However, the recent discovery of man genes in MTB from the Thermodesulfobacteriota phylum has raised several questions about the inheritance of these genes in MTB. In this work, three new man genes containing MTB genomes affiliated with Nitrospirota and Thermodesulfobacteriota, were obtained. By applying reconciliation with these and the previously published MTB genomes, we demonstrate that the last common ancestor of all Nitrospirota was most likely not magnetotactic as assumed previously. Instead, our findings suggest that the genes for magnetosome synthesis were transmitted to the phylum Nitrospirota by horizontal gene transfer (HGT), which is the first case of the interphylum transfer of magnetosome genes detected to date. Furthermore, we provide evidence for the HGT of magnetosome genes from the Magnetobacteriaceae to the Dissulfurispiraceae family within Nitrospirota. Thus, our results imply a more significant role of HGT in the MTB evolution than deemed before and challenge the hypothesis of the ancient origin of magnetosome synthesis.}, }
@article {pmid35977641, year = {2022}, author = {Neethu, CS and Saravanakumar, C and Purvaja, R and Robin, RS and Ramesh, R}, title = {Arsenic resistance and horizontal gene transfer are associated with carbon and nitrogen enrichment in bacteria.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {311}, number = {}, pages = {119937}, doi = {10.1016/j.envpol.2022.119937}, pmid = {35977641}, issn = {1873-6424}, mesh = {*Arsenic/pharmacology ; *Betaproteobacteria ; Carbon ; Escherichia coli ; *Gammaproteobacteria/genetics ; Gene Transfer, Horizontal ; Nitrogen/pharmacology ; Phylogeny ; }, abstract = {Coastal waters are confluences receiving large amounts of point and non-point sources of pollution. An attempt was made to explore microbial community interactions in response to carbon, nitrogen and metal pollution. Additionally, experiments were designed to analyze the influence of these factors on horizontal gene transfer (HGT). Shift in bacterial diversity dynamics by arsenic stress and nutrient addition in coastal waters was explored by metagenomics of microcosm setups. Phylogenetic analysis revealed equal distribution of Gammaproteobacteria (29%) and Betaproteobacteria (28%) in control microcosm. This proportional diversity from control switched to unique distribution of Gammaproteobacteria (44.5%)> Flavobacteria (17.7%)> Bacteriodia (11.92%)> Betaproteobacteria (11.52%) in microcosm supplemented with carbon, nitrogen and metal (C + N + M). Among metal-stressed systems, alpha diversity analysis indicated highest diversity of genera in C + N + M followed by N + M > C+M> metal alone. Arsenic and ampicillin sensitive E. coli XL1 blue and environmental strains (Vibrio tubiashii W85 and E. coli W101) were tested for efficiency of uptake of plasmid (P) pUCminusMCS (arsB[R]amp[R]) under varying stress conditions. Transformation experiments revealed that combined effect of carbon, nitrogen and metal on horizontal gene transfer (HGT) was significantly higher (p < 0.01) than individual factors. The effect of carbon on HGT was proved to be superior to nitrogen under metal stressed conditions. Presence of arsenic in experimental setups (P + M, P + N + M and P + C + M) enhanced the HGT compared to non-metal counterparts supplemented with carbon or nitrogen. Arsenic resistant bacterial isolates (n = 200) were tested for the ability to utilize various carbon and nitrogen substrates and distinct positive correlation (p < 0.001) was found between arsenic resistance and utilization of urea and nitrate. However, evident positive correlation was not found between carbon sources and arsenic resistance. Our findings suggest that carbon and nitrogen pollution in aquatic habitats under arsenic stress determine the microbial community dynamics and critically influence uptake of genetic material from the surrounding environment.}, }
@article {pmid35977623, year = {2022}, author = {Qiu, D and Ke, M and Zhang, Q and Zhang, F and Lu, T and Sun, L and Qian, H}, title = {Response of microbial antibiotic resistance to pesticides: An emerging health threat.}, journal = {The Science of the total environment}, volume = {850}, number = {}, pages = {158057}, doi = {10.1016/j.scitotenv.2022.158057}, pmid = {35977623}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents/metabolism/toxicity ; Bacteria/metabolism ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; *Pesticides/metabolism/toxicity ; }, abstract = {The spread of microbial antibiotic resistance has seriously threatened public health globally. Non-antibiotic stressors have significantly contributed to the evolution of bacterial antibiotic resistance. Although numerous studies have been conducted on the potential risk of pesticide pollution for bacterial antibiotic resistance, a systematic review of these concerns is still lacking. In the present study, we elaborate the mechanism underlying the effects of pesticides on bacterial antibiotic resistance acquisition as well as the propagation of antimicrobial resistance. Pesticide stress enhanced the acquisition of antibiotic resistance in bacteria via various mechanisms, including the activation of efflux pumps, inhibition of outer membrane pores for resistance to antibiotics, and gene mutation induction. Horizontal gene transfer is a major mechanism whereby pesticides influence the transmission of antibiotic resistance genes (ARGs) in bacteria. Pesticides promoted the conjugation transfer of ARGs by increasing cell membrane permeability and increased the proportion of bacterial mobile gene elements, which facilitate the spread of ARGs. This review can improve our understanding regarding the pesticide-induced generation and spread of ARGs and antibiotic resistant bacteria. Moreover, it can be applied to reduce the ecological risks of ARGs in the future.}, }
@article {pmid35974915, year = {2022}, author = {Hemamalini, N and Shanmugam, SA and Kathirvelpandian, A and Deepak, A and Kaliyamurthi, V and Suresh, E and Ezhilmathi, S}, title = {Prevalence, Antimicrobial Susceptibility and Resistance Gene Detection in Bacteria Isolated from Goldfish and Tiger Barb from Ornamental Fish Farms of Tamil Nadu.}, journal = {Indian journal of microbiology}, volume = {62}, number = {3}, pages = {441-446}, pmid = {35974915}, issn = {0046-8991}, abstract = {UNLABELLED: This study aims to determine the antimicrobial resistance (AMR) pattern in freshwater ornamental cyprinids, such as Goldfish and Tiger barb. Molecular characterization of bacterial isolates confirmed the presence of 7 bacterial isolates in Goldfish and 6 in Tiger barb. Antimicrobial susceptibility test using 36 antibiotics revealed a higher resistance pattern for bacitracin, rifampicin, trimethoprim, cefalexin, ampicillin, amoxicillin, nalidixic acid and nitrofurantoin. Sulphafurazole, norfloxacin and ciprofloxacin were effective against all the bacterial isolates derived from Goldfish and Tiger barb. Most bacterial isolates exhibited > 0.2 multi-drug resistance index (MDR), indicating the severity of antibiotic use in the culture system. The finding of the present study suggests that ornamental fish may act as the reservoir of MDR bacteria and dissemination of resistance genes to clinical and human commensal bacteria through horizontal gene transfer.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-022-01023-y.}, }
@article {pmid35970720, year = {2022}, author = {González-Villalobos, E and Balcázar, JL}, title = {Does phage-mediated horizontal gene transfer represent an environmental risk?.}, journal = {Trends in microbiology}, volume = {30}, number = {11}, pages = {1022-1024}, doi = {10.1016/j.tim.2022.07.011}, pmid = {35970720}, issn = {1878-4380}, mesh = {Anti-Bacterial Agents ; *Bacteriophages/genetics ; *Gene Transfer, Horizontal ; }, abstract = {A growing number of recent studies suggest that the contribution of phages to antibiotic resistance should not be underestimated. Here we describe their implications for public and environmental health, with a special emphasis on the mechanisms underlying phage-mediated horizontal gene transfer.}, }
@article {pmid35967855, year = {2022}, author = {Chen, H and Tao, S and Li, N and Wang, F and Wang, L and Tang, Y and Liang, W}, title = {Functional comparison of anti-restriction and anti-methylation activities of ArdA, KlcA, and KlcAHS from Klebsiella pneumoniae.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {916547}, pmid = {35967855}, issn = {2235-2988}, mesh = {*Gene Transfer, Horizontal ; *Klebsiella pneumoniae/genetics ; Plasmids/genetics ; Protein Processing, Post-Translational ; }, abstract = {Anti-restriction proteins are typically encoded by plasmids, conjugative transposons, or phages to improve their chances of entering a new bacterial host with a type I DNA restriction and modification (RM) system. The invading DNA is normally destroyed by the RM system. The anti-restriction proteins ArdA, KlcA, and their homologues are usually encoded on plasmid of carbapenemase-resistant Klebsiella pneumoniae. We found that the plasmid sequence and restriction proteins affected horizontal gene transfer, and confirmed the anti-restriction and anti-methylation activities of ArdA and KlcA during transformation and transduction. Among the three anti-restriction proteins, ArdA shows stronger anti-restriction and anti-methylation effects, and KlcAHS was weaker. KlcA shows anti-methylation only during transformation. Understanding the molecular mechanism underlying the clinical dissemination of K. pneumoniae and other clinically resistant strains from the perspective of restrictive and anti-restrictive systems will provide basic theoretical support for the prevention and control of multidrug-resistant bacteria, and new strategies for delaying or even controlling the clinical dissemination of resistant strains in the future.}, }
@article {pmid35966708, year = {2022}, author = {Entfellner, E and Li, R and Jiang, Y and Ru, J and Blom, J and Deng, L and Kurmayer, R}, title = {Toxic/Bioactive Peptide Synthesis Genes Rearranged by Insertion Sequence Elements Among the Bloom-Forming Cyanobacteria Planktothrix.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {901762}, pmid = {35966708}, issn = {1664-302X}, support = {P 24070/FWF_/Austrian Science Fund FWF/Austria ; P 32193/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {It has been generally hypothesized that mobile elements can induce genomic rearrangements and influence the distribution and functionality of toxic/bioactive peptide synthesis pathways in microbes. In this study, we performed in depth genomic analysis by completing the genomes of 13 phylogenetically diverse strains of the bloom-forming freshwater cyanobacteria Planktothrix spp. to investigate the role of insertion sequence (IS) elements in seven pathways. Chromosome size varied from 4.7-4.8 Mbp (phylogenetic Lineage 1 of P. agardhii/P. rubescens thriving in shallow waterbodies) to 5.4-5.6 Mbp (Lineage 2 of P. agardhii/P. rubescens thriving in deeper physically stratified lakes and reservoirs) and 6.3-6.6 Mbp (Lineage 3, P. pseudagardhii/P. tepida including planktic and benthic ecotypes). Although the variation in chromosome size was positively related to the proportion of IS elements (1.1-3.7% on chromosome), quantitatively, IS elements and other paralogs only had a minor share in chromosome size variation. Thus, the major part of genomic variation must have resulted from gene loss processes (ancestor of Lineages 1 and 2) and horizontal gene transfer (HGT). Six of seven peptide synthesis gene clusters were found located on the chromosome and occurred already in the ancestor of P. agardhii/P. rubescens, and became partly lost during evolution of Lineage 1. In general, no increased IS element frequency in the vicinity of peptide synthesis gene clusters was observed. We found a higher proportion of IS elements in ten breaking regions related to chromosomal rearrangements and a tendency for colocalization of toxic/bioactive peptide synthesis gene clusters on the chromosome.}, }
@article {pmid35963060, year = {2022}, author = {Hou, L and Li, J and Wang, H and Chen, Q and Su, JQ and Gad, M and Ahmed, W and Yu, CP and Hu, A}, title = {Storm promotes the dissemination of antibiotic resistome in an urban lagoon through enhancing bio-interactions.}, journal = {Environment international}, volume = {168}, number = {}, pages = {107457}, doi = {10.1016/j.envint.2022.107457}, pmid = {35963060}, issn = {1873-6750}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Bacteria/genetics ; Water ; }, abstract = {Antibiotic-resistance genes (ARGs) and resistant bacteria (ARB) are abundant in stormwater that could cause serious infections, posing a potential threat to public health. However, there is no inference about how stormwater contributes to ARG profiles as well as the dynamic interplay between ARGs and bacteria via vertical gene transfer (VGT) or horizontal gene transfer (HGT) in urban water ecosystems. In this study, the distribution of ARGs, their host communities, and the source and community assembly process of ARGs were investigated in Yundang Lagoon (China) via high-throughput quantitative PCR, 16S rRNA gene amplicon sequencing, and application of SourceTracker before, after and recovering from an extreme precipitation event (132.1 mm). The abundance of ARGs and mobile genetic elements (MGEs) was the highest one day after precipitation and then decreased 2 days after precipitation and so on. Based on SourceTracker and NMDS analysis, the ARG and bacterial communities in lagoon surface water from one day after precipitation were mainly contributed by the wastewater treatment plant (WWTP) influent and effluent. However, the contribution of WWTP to ARG communities was minor 11 days after the precipitation, suggesting that the storm promoted the ARG levels by introducing the input of ARGs, MGEs, and ARB from point and non-point sources, such as sewer overflow and land-applied manure. Based on a novel microbial network analysis framework, the contribution of positive biological interactions between ARGs and MGEs or bacteria was the highest one day after precipitation, indicating a promoted VGT and HGT for ARG dissemination. The microbial networks deconstructed 11 days after precipitation, suggesting the stormwater practices (e.g., tide gate opening, diversion channels, and pumping) alleviated the spread of ARGs. These results advanced our understanding of the distribution and transport of ARGs associated with their source in urban stormwater runoff.}, }
@article {pmid35962419, year = {2022}, author = {de Assis, JCS and Gonçalves, OS and Fernandes, AS and de Queiroz, MV and Bazzolli, DMS and Santana, MF}, title = {Genomic analysis reveals the role of integrative and conjugative elements in plant pathogenic bacteria.}, journal = {Mobile DNA}, volume = {13}, number = {1}, pages = {19}, pmid = {35962419}, issn = {1759-8753}, support = {001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; }, abstract = {BACKGROUND: ICEs are mobile genetic elements found integrated into bacterial chromosomes that can excise and be transferred to a new cell. They play an important role in horizontal gene transmission and carry accessory genes that may provide interesting phenotypes for the bacteria. Here, we seek to research the presence and the role of ICEs in 300 genomes of phytopathogenic bacteria with the greatest scientific and economic impact.<br><br>RESULTS: Seventy-eight ICEs (45 distinct elements) were identified and characterized in chromosomes of Agrobacterium tumefaciens, Dickeya dadantii, and D. solani, Pectobacterium carotovorum and P. atrosepticum, Pseudomonas syringae, Ralstonia solanacearum Species Complex, and Xanthomonas campestris. Intriguingly, the co-occurrence of four ICEs was observed in some P. syringae strains. Moreover, we identified 31 novel elements, carrying 396 accessory genes with potential influence on virulence and fitness, such as genes coding for functions related to T3SS, cell wall degradation and resistance to heavy metals. We also present the analysis of previously reported data on the expression of cargo genes related to the virulence of P. atrosepticum ICEs, which evidences the role of these genes in the infection process of tobacco plants.<br><br>CONCLUSIONS: Altogether, this paper has highlighted the potential of ICEs to affect the pathogenicity and lifestyle of these phytopathogens and direct the spread of significant putative virulence genes in phytopathogenic bacteria.}, }
@article {pmid35953866, year = {2022}, author = {Wang, Y and Yu, Z and Ding, P and Lu, J and Klümper, U and Murray, AK and Gaze, WH and Guo, J}, title = {Non-antibiotic pharmaceuticals promote conjugative plasmid transfer at a community-wide level.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {124}, pmid = {35953866}, issn = {2049-2618}, mesh = {*Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; *Gene Transfer, Horizontal ; Pharmaceutical Preparations ; Plasmids/genetics ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT) plays a critical role in the spread of antibiotic resistance and the evolutionary shaping of bacterial communities. Conjugation is the most well characterized pathway for the spread of antibiotic resistance, compared to transformation and transduction. While antibiotics have been found to induce HGT, it remains unknown whether non-antibiotic pharmaceuticals can facilitate conjugation at a microbial community-wide level.<br><br>RESULTS: In this study, we demonstrate that several commonly consumed non-antibiotic pharmaceuticals (including carbamazepine, ibuprofen, naproxen and propranolol), at environmentally relevant concentrations (0.5&#xa0;mg/L), can promote the conjugative transfer of IncP1-&#x3b1; plasmid-borne antibiotic resistance across entire microbial communities. The over-generation of reactive oxygen species in response to these non-antibiotic pharmaceuticals may contribute to the enhanced conjugation ratios. Cell sorting and 16S rRNA gene amplicon sequencing analyses indicated that non-antibiotic pharmaceuticals modulate transconjugant microbial communities at both phylum and genus levels. Moreover, microbial uptake ability of the IncP1-&#x3b1; plasmid was also upregulated under non-antibiotic pharmaceutical exposure. Several opportunistic pathogens, such as Acinetobacter and Legionella, were more likely to acquire the plasmid conferring multidrug resistance.<br><br>CONCLUSIONS: Considering the high possibility of co-occurrence of pathogenic bacteria, conjugative IncP1-&#x3b1; plasmids and non-antibiotic pharmaceuticals in various environments (e.g., activated sludge systems), our findings illustrate the potential risk associated with increased dissemination of antibiotic resistance promoted by non-antibiotic pharmaceuticals in complex environmental settings. Video abstract.}, }
@article {pmid35949392, year = {2022}, author = {Chase, EE and Desnues, C and Blanc, G}, title = {Integrated viral elements suggest the dual lifestyle of Tetraselmis spp. Polinton-like viruses.}, journal = {Virus evolution}, volume = {8}, number = {2}, pages = {veac068}, pmid = {35949392}, issn = {2057-1577}, abstract = {In this study, we aimed at exploring horizontal gene transfer between viruses and Chlorodendraceae green algae (Chlorophyta) using available genomic and transcriptomic sequences for twenty algal strains. We identified a significant number of genes sharing a higher sequence similarity with viral homologues, thus signalling their possible involvement in horizontal gene transfers with viruses. Further characterization showed that many of these genes were clustered in DNA regions of several tens to hundreds of kilobases in size, originally belonging to viruses related to known Tetraselmis spp. viruses (TetV and TsV). In contrast, the remaining candidate HGT genes were randomly dispersed in the algal genomes, were more frequently transcribed, and belonged to large multigene families. The presence of homologues in Viridiplantae suggested that the latter were more likely of algal rather than viral origin. We found a remarkable diversity in polinton-like virus (PLV) elements inserted in Tetraselmis genomes, all of which were most similar to the Tetraselmis striata virus (TsV). The genes of PLV elements are transcriptionally inactive with the notable exception of the homologue of the TVSG_00024 gene of TsV whose function is unknown. We suggest that this gene may be involved in a sentinel process to trigger virus reactivation and excision in response to an environmental stimulus. Altogether, these results provide evidence that TsV-related viruses have a dual lifestyle, alternating between a free viral phase (i.e. virion) and a phase integrated into host genomes.}, }
@article {pmid35947951, year = {2022}, author = {Sherlock, D and Fogg, PCM}, title = {The archetypal gene transfer agent RcGTA is regulated via direct interaction with the enigmatic RNA polymerase omega subunit.}, journal = {Cell reports}, volume = {40}, number = {6}, pages = {111183}, pmid = {35947951}, issn = {2211-1247}, support = {/WT_/Wellcome Trust/United Kingdom ; 109363/Z/15/A/WT_/Wellcome Trust/United Kingdom ; BB/V016288/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Alphaproteobacteria ; Bacterial Proteins/genetics/metabolism ; DNA/metabolism ; DNA-Directed RNA Polymerases/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; *Rhodobacter capsulatus/genetics/metabolism ; }, abstract = {Gene transfer agents (GTAs) are small virus-like particles that indiscriminately package and transfer any DNA present in their host cell, with clear implications for bacterial evolution. The first transcriptional regulator that directly controls GTA expression, GafA, was recently discovered, but its mechanism of action has remained elusive. Here, we demonstrate that GafA controls GTA gene expression via direct interaction with the RNA polymerase omega subunit (Rpo-ω) and also positively autoregulates its own expression by an Rpo-ω-independent mechanism. We show that GafA is a modular protein with distinct DNA and protein binding domains. The functional domains we observe in Rhodobacter GafA also correspond to two-gene operons in Hyphomicrobiales pathogens. These data allow us to produce the most complete regulatory model for a GTA and point toward an atypical mechanism for RNA polymerase recruitment and specific transcriptional activation in the Alphaproteobacteria.}, }
@article {pmid35947446, year = {2022}, author = {Swarthout, JM and Chan, EMG and Garcia, D and Nadimpalli, ML and Pickering, AJ}, title = {Human Colonization with Antibiotic-Resistant Bacteria from Nonoccupational Exposure to Domesticated Animals in Low- and Middle-Income Countries: A Critical Review.}, journal = {Environmental science &amp; technology}, volume = {56}, number = {21}, pages = {14875-14890}, doi = {10.1021/acs.est.2c01494}, pmid = {35947446}, issn = {1520-5851}, mesh = {Animals ; Humans ; *Developing Countries ; *Animals, Domestic/genetics ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Bacteria/genetics ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; }, abstract = {Data on community-acquired antibiotic-resistant bacterial infections are particularly sparse in low- and middle-income countries (LMICs). Limited surveillance and oversight of antibiotic use in food-producing animals, inadequate access to safe drinking water, and insufficient sanitation and hygiene infrastructure in LMICs could exacerbate the risk of zoonotic antibiotic resistance transmission. This critical review compiles evidence of zoonotic exchange of antibiotic-resistant bacteria (ARB) or antibiotic resistance genes (ARGs) within households and backyard farms in LMICs, as well as assesses transmission mechanisms, risk factors, and environmental transmission pathways. Overall, substantial evidence exists for exchange of antibiotic resistance between domesticated animals and in-contact humans. Whole bacteria transmission and horizontal gene transfer between humans and animals were demonstrated within and between households and backyard farms. Further, we identified water, soil, and animal food products as environmental transmission pathways for exchange of ARB and ARGs between animals and humans, although directionality of transmission is poorly understood. Herein we propose study designs, methods, and topical considerations for priority incorporation into future One Health research to inform effective interventions and policies to disrupt zoonotic antibiotic resistance exchange in low-income communities.}, }
@article {pmid35946347, year = {2022}, author = {Chen, MY and Teng, WK and Zhao, L and Han, BP and Song, LR and Shu, WS}, title = {Phylogenomics Uncovers Evolutionary Trajectory of Nitrogen Fixation in Cyanobacteria.}, journal = {Molecular biology and evolution}, volume = {39}, number = {9}, pages = {}, pmid = {35946347}, issn = {1537-1719}, mesh = {*Cyanobacteria/genetics ; Gene Transfer, Horizontal ; Nitrogen/metabolism ; *Nitrogen Fixation/genetics ; Photosynthesis/genetics ; Phylogeny ; }, abstract = {Biological nitrogen fixation (BNF) by cyanobacteria is of significant importance for the Earth's biogeochemical nitrogen cycle but is restricted to a few genera that do not form monophyletic group. To explore the evolutionary trajectory of BNF and investigate the driving forces of its evolution, we analyze 650 cyanobacterial genomes and compile the database of diazotrophic cyanobacteria based on the presence of nitrogen fixation gene clusters (NFGCs). We report that 266 of 650 examined genomes are NFGC-carrying members, and these potentially diazotrophic cyanobacteria are unevenly distributed across the phylogeny of Cyanobacteria, that multiple independent losses shaped the scattered distribution. Among the diazotrophic cyanobacteria, two types of NFGC exist, with one being ancestral and abundant, which have descended from diazotrophic ancestors, and the other being anaerobe-like and sparse, possibly being acquired from anaerobic microbes through horizontal gene transfer. Interestingly, we illustrate that the origin of BNF in Cyanobacteria coincide with two major evolutionary events. One is the origin of multicellularity of cyanobacteria, and the other is concurrent genetic innovations with massive gene gains and expansions, implicating their key roles in triggering the evolutionary transition from nondiazotrophic to diazotrophic cyanobacteria. Additionally, we reveal that genes involved in accelerating respiratory electron transport (coxABC), anoxygenic photosynthetic electron transport (sqr), as well as anaerobic metabolisms (pfor, hemN, nrdG, adhE) are enriched in diazotrophic cyanobacteria, representing adaptive genetic signatures that underpin the diazotrophic lifestyle. Collectively, our study suggests that multicellularity, together with concurrent genetic adaptations contribute to the evolution of diazotrophic cyanobacteria.}, }
@article {pmid35944516, year = {2023}, author = {Goldman, AD and Kaçar, B}, title = {Very early evolution from the perspective of microbial ecology.}, journal = {Environmental microbiology}, volume = {25}, number = {1}, pages = {5-10}, doi = {10.1111/1462-2920.16144}, pmid = {35944516}, issn = {1462-2920}, mesh = {*Evolution, Molecular ; Genome ; Ecology ; Gene Transfer, Horizontal ; *Microbiota ; Phylogeny ; Biological Evolution ; }, abstract = {The universal ancestor at the root of the species tree of life depicts a population of organisms with a surprising degree of complexity, posessing genomes and translation systems much like that of microbial life today. As the first life forms were most likely to have been simple replicators, considerable evolutionary change must have taken place prior to the last universal common ancestor. It is often assumed that the lack of earlier branches on the tree of life is due to a prevalence of random horizontal gene transfer that obscured the delineations between lineages and hindered their divergence. Therefore, principles of microbial evolution and ecology may give us some insight into these early stages in the history of life. Here, we synthesize the current understanding of organismal and genome evolution from the perspective of microbial ecology and apply these evolutionary principles to the earliest stages of life on Earth. We focus especially on broad evolutionary modes pertaining to horizontal gene transfer, pangenome structure, and microbial mat communities.}, }
@article {pmid35944241, year = {2022}, author = {Wu, Y and Yan, H and Zhu, X and Liu, C and Chu, C and Zhu, X and Chen, B}, title = {Biochar Effectively Inhibits the Horizontal Transfer of Antibiotic Resistance Genes via Restraining the Energy Supply for Conjugative Plasmid Transfer.}, journal = {Environmental science &amp; technology}, volume = {56}, number = {17}, pages = {12573-12583}, doi = {10.1021/acs.est.2c02701}, pmid = {35944241}, issn = {1520-5851}, mesh = {Adenosine Triphosphate/pharmacology ; *Anti-Bacterial Agents/pharmacology ; Charcoal ; Drug Resistance, Microbial/genetics ; *Escherichia coli/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Plasmids/genetics ; }, abstract = {Horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) through plasmid-mediated conjugation poses a major threat to global public health. Biochar, a widely used environmental remediation material, has remarkable impacts on the fate of ARGs. However, although biochar was reported being able to inhibit the HGT of ARGs via conjugation and transformation, little is known about the intracellular process that mediates the inhibition effects. On the other hand, as typical natural organic matter, fulvic acid is a common environmental influencer, and how it interferes with the effect of biochar on the HGT of ARGs is unknown. Therefore, this study investigated the effects on the conjugative transfer of ARGs between Escherichia coli MG1655 and E. coli HB101 carrying plasmid RP4, with biochars pyrolyzed at three temperatures and with the corresponding biochars coating with fulvic acid. Results showed that biochar with higher pyrolyzed temperature had a more substantial inhibitory effect on the conjugative transfer of the RP4 plasmid. The inhibitory effect of biochar was mainly attributed to (i) down-regulation of plasmid transfer gene expression, including the formation of conjugative transfer channel and plasmid replication, due to restrained adenosine triphosphate (ATP) energy supply and (ii) decreased cell membrane permeability. Conversely, the fulvic acid coating diminished this inhibition effect of biochar, mainly by providing more ATP and strengthening intracellular reactive oxygen species (ROS) defense. Our findings shed light on the intracellular process that mediates the effects of biochar on the conjugative transfer of ARGs, which would provide support for using biochar to reduce the spread of ARGs.}, }
@article {pmid35942309, year = {2022}, author = {Tao, S and Chen, H and Li, N and Liang, W}, title = {The Application of the CRISPR-Cas System in Antibiotic Resistance.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {4155-4168}, pmid = {35942309}, issn = {1178-6973}, abstract = {The emergence and global epidemic of antimicrobial resistance (AMR) poses a serious threat to global public health in recent years. AMR genes are shared between bacterial pathogens mainly via horizontal gene transfer (HGT) on mobile genetic elements (MGEs), thereby accelerating the spread of antimicrobial resistance (AMR) and increasing the burden of drug resistance. There is an urgent need to develop new strategies to control bacterial infections and the spread of antimicrobial resistance. The clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) are an RNA-guided adaptive immune system in prokaryotes that recognizes and defends against invasive genetic elements such as phages and plasmids. Because of its specifically target and cleave DNA sequences encoding antibiotic resistance genes, CRISPR/Cas system has been developed into a new gene-editing tool for the prevention and control of bacterial drug resistance. CRISPR-Cas plays a potentially important role in controlling horizontal gene transfer and limiting the spread of antibiotic resistance. In this review, we will introduce the structure and working mechanism of CRISPR-Cas systems, followed by delivery strategies, and then focus on the relationship between antimicrobial resistance and CRISPR-Cas. Moreover, the challenges and prospects of this research field are discussed, thereby providing a reference for the prevention and control of the spread of antibiotic resistance.}, }
@article {pmid35942087, year = {2022}, author = {Gao, C and Liang, Y and Jiang, Y and Paez-Espino, D and Han, M and Gu, C and Wang, M and Yang, Y and Liu, F and Yang, Q and Gong, Z and Zhang, X and Luo, Z and He, H and Guo, C and Shao, H and Zhou, C and Shi, Y and Xin, Y and Xing, J and Tang, X and Qin, Q and Zhang, YZ and He, J and Jiao, N and McMinn, A and Tian, J and Suttle, CA and Wang, M}, title = {Virioplankton assemblages from challenger deep, the deepest place in the oceans.}, journal = {iScience}, volume = {25}, number = {8}, pages = {104680}, pmid = {35942087}, issn = {2589-0042}, abstract = {Hadal ocean biosphere, that is, the deepest part of the world's oceans, harbors a unique microbial community, suggesting a potential uncovered co-occurring virioplankton assemblage. Herein, we reveal the unique virioplankton assemblages of the Challenger Deep, comprising 95,813 non-redundant viral contigs from the surface to the hadal zone. Almost all of the dominant viral contigs in the hadal zone were unclassified, potentially related to Alteromonadales and Oceanospirillales. 2,586 viral auxiliary metabolic genes from 132 different KEGG orthologous groups were mainly related to the carbon, nitrogen, sulfur, and arsenic metabolism. Lysogenic viral production and integrase genes were augmented in the hadal zone, suggesting the prevalence of viral lysogenic life strategy. Abundant rve genes in the hadal zone, which function as transposase in the caudoviruses, further suggest the prevalence of viral-mediated horizontal gene transfer. This study provides fundamental insights into the virioplankton assemblages of the hadal zone, reinforcing the necessity of incorporating virioplankton into the hadal biogeochemical cycles.}, }
@article {pmid35941147, year = {2022}, author = {Stone, J and Edgar, JO and Gould, JA and Telling, J}, title = {Tectonically-driven oxidant production in the hot biosphere.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {4529}, pmid = {35941147}, issn = {2041-1723}, mesh = {Biological Evolution ; Earth, Planet ; *Hydrogen Peroxide ; *Oxidants ; Oxygen ; Photosynthesis/physiology ; }, abstract = {Genomic reconstructions of the common ancestor to all life have identified genes involved in H2O2 and O2 cycling. Commonly dismissed as an artefact of lateral gene transfer after oxygenic photosynthesis evolved, an alternative is a geological source of H2O2 and O2 on the early Earth. Here, we show that under oxygen-free conditions high concentrations of H2O2 can be released from defects on crushed silicate rocks when water is added and heated to temperatures close to boiling point, but little is released at temperatures <80 °C. This temperature window overlaps the growth ranges of evolutionary ancient heat-loving and oxygen-respiring Bacteria and Archaea near the root of the Universal Tree of Life. We propose that the thermal activation of mineral surface defects during geological fault movements and associated stresses in the Earth's crust was a source of oxidants that helped drive the (bio)geochemistry of hot fractures where life first evolved.}, }
@article {pmid35940152, year = {2022}, author = {Zhou, Q and Zhang, J and Zhang, M and Wang, X and Zhang, D and Pan, X}, title = {Persistent versus transient, and conventional plastic versus biodegradable plastic? -Two key questions about microplastic-water exchange of antibiotic resistance genes.}, journal = {Water research}, volume = {222}, number = {}, pages = {118899}, doi = {10.1016/j.watres.2022.118899}, pmid = {35940152}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents/pharmacology ; *Biodegradable Plastics/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Humans ; Microplastics ; *Plastics ; Water/pharmacology ; }, abstract = {The ubiquitous microplastics (MPs) in water environment play an important role in the dissemination of antibiotic resistance genes (ARGs) due to their exchange between floating MPs and receiving waters. However, whether the ARG exchange is persistent or transient and what are the differences in ARG exchange between conventional plastics and biodegradable plastics are the two key issues to be addressed. In this study, biodegradable PBAT and non-biodegradable PET MPs were chosen to explore the MP-water ARG exchange after the MPs floated to the receiving waters. The results demonstrated that the active exchange of ARGs between MPs and receiving waters occurred, which, however, were transient for most of ARGs. The relative abundance of ARGs both on the MPs and in the waters rapidly decreased to the initial or lower levels within 4 weeks. Approximately 25-50% (ARG subtype number ratio) of studied ARG subtypes were introduced into the receiving waters by MPs, and 35-65% of studied ARG subtypes went through fluctuation in terms of abundance on MPs and in the receiving water. ARGs tended to converge between MPs and the receiving waters with time. Furthermore, the ARG exchange between MPs and waters facilitated horizontal gene transfer (HGT). IntI1 and tnpA05 played the crucial roles in HGT, which was indicated by their correlated change with most ARGs; in contrast, tnpA04 showed the obvious lagging responses. The biodegradable MP of PBAT generally accumulated higher levels of most ARGs including multidrug resistant genes than the non-biodegradable MP of PET. The transient exchange of most ARGs between MPs and water implies that the on-off hitchhiking of ARGs on MPs in aquatic environment may not exert significant influence on ARG transmission. However, compared with the conventional plastics, the biodegradable MPs might pose much higher ARG dissemination risks due to the higher enrichment of ARGs particularly with people's ever-increasingly usage. Enough attention must be paid to this emerging issue.}, }
@article {pmid35938813, year = {2022}, author = {Wang, Y and Yang, J and Sun, X and Li, M and Zhang, P and Zhu, Z and Jiao, H and Guo, T and Li, G}, title = {CRISPR-Cas in Acinetobacter baumannii Contributes to Antibiotic Susceptibility by Targeting Endogenous AbaI.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0082922}, pmid = {35938813}, issn = {2165-0497}, mesh = {*Acinetobacter baumannii/genetics/metabolism ; Anti-Bacterial Agents/pharmacology ; Bacteria/metabolism ; Bacterial Proteins/genetics/metabolism ; Biofilms ; *CRISPR-Associated Proteins/genetics/metabolism ; CRISPR-Cas Systems ; Drug Resistance, Multiple, Bacterial/genetics ; Humans ; Reactive Oxygen Species/metabolism ; }, abstract = {Acinetobacter baumannii is a well-known human opportunistic pathogen in nosocomial infections, and the emergence of multidrug-resistant Acinetobacter baumannii has become a complex problem for clinical anti-infective treatments. The ways this organism obtains multidrug resistance phenotype include horizontal gene transfer and other mechanisms, such as altered targets, decreased permeability, increased enzyme production, overexpression of efflux pumps, metabolic changes, and biofilm formation. A CRISPR-Cas system generally consists of a CRISPR array and one or more operons of cas genes, which can restrict horizontal gene transfer in bacteria. Nevertheless, it is unclear how CRISPR-Cas systems regulate antibiotic resistance in Acinetobacter baumannii. Thus, we sought to assess how CRISPR-Cas affects biofilm formation, membrane permeability, efflux pump, reactive oxygen species, and quorum sensing to clarify further the mechanism of CRISPR-Cas regulation of Acinetobacter baumannii antibiotic resistance. In the clinical isolate AB43, which has a complete I-Fb CRISPR-Cas system, we discovered that the Cas3 nuclease of this type I-F CRISPR-Cas system regulates Acinetobacter baumannii quorum sensing and has a unique function in changing drug resistance. As a result of quorum sensing, synthase abaI is reduced, allowing efflux pumps to decrease, biofilm formation to become weaker, reactive oxygen species to generate, and drug resistance to decrease in response to CRISPR-Cas activity. These observations suggest that the CRISPR-Cas system targeting endogenous abaI may boost bacterial antibiotic sensitivity. IMPORTANCE CRISPR-Cas systems are vital for genome editing, bacterial virulence, and antibiotic resistance. How CRISPR-Cas systems regulate antibiotic resistance in Acinetobacter baumannii is almost wholly unknown. In this study, we reveal that the quorum sensing regulator abaI mRNA was a primary target of the I-Fb CRISPR-Cas system and the cleavage activity of Cas3 was the most critical factor in regulating abaI mRNA degradation. These results advance our understanding of how CRISPR-Cas systems inhibit drug resistance. However, the mechanism of endogenous targeting of abaI by CRISPR-Cas needs to be further explored.}, }
@article {pmid35938729, year = {2022}, author = {Du, S and Zhang, Y and Shen, JP and Hu, HW and Zhang, J and Shu, C and He, JZ}, title = {Alteration of Manure Antibiotic Resistance Genes via Soil Fauna Is Associated with the Intestinal Microbiome.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0052922}, pmid = {35938729}, issn = {2379-5077}, mesh = {Animals ; Humans ; *Gastrointestinal Microbiome/genetics ; Soil ; Manure/analysis ; Anti-Bacterial Agents/analysis ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Larva/genetics ; }, abstract = {Livestock wastes contain high levels of antibiotic resistance genes (ARGs) and a variety of human-related pathogens. Bioconversion of livestock manure using larvae of the beetle Protaetia brevitarsis is an effective technique for waste reduction and value creation; however, the fate of manure ARGs during gut passage and interaction with the gut microbiome of P. brevitarsis remains unclear. To investigate this, we fed P. brevitarsis with dry chicken manure for 6 days and measured bacterial community dynamics and ARG abundance and diversity along the P. brevitarsis gut tract using high-throughput quantitative PCR and metagenomics approaches. The diversity of ARGs was significantly lower in larval midgut, hindgut, and frass than in raw chicken manure, and around 80% of pathogenicity-related genes (PRGs) exhibited reduced abundance. Network analysis demonstrated that Bacteroidetes and Firmicutes were the key bacterial phyla associated with ARG reduction. Metagenomic analysis further indicated that ARGs, mobile genetic elements (MGEs), and PRGs were simultaneously attenuated in the hindgut, implicating a decreased likelihood for horizontal gene transfer (HGT) of ARGs among bacteria and pathogens during manure bioconversion. Our findings demonstrated that the attenuation of ARGs is strongly associated with the variation of the gut microbiome of P. brevitarsis, providing insights into mechanisms of risk mitigation of ARG dissemination during manure bioconversion. IMPORTANCE Saprophagous fauna like the oriental edible beetle (P. brevitarsis) plays a fundamental role in converting organic wastes into biofertilizer. Accumulating evidence has shown that soil fauna can reduce the abundance of ARGs, although the underlying mechanism of ARG reduction is still unclear. In our previous research, we found a large reduction of ARGs in vegetable roots and leaves from frass compared with raw manure, providing a promising biofertilizer for soil-vegetable systems. Therefore, in this study, temporal dynamic changes in the microbiomes of the donor (chicken manure) and host (P. brevitarsis) were investigated, and we found a close association between the gut microbiome and the alteration of ARGs. These results shed new light on how the insect gut microbiome can mitigate manure-borne ARGs and provide insights into the bioconversion process via a typical member of the saprophagous fauna, P. brevitarsis.}, }
@article {pmid35934149, year = {2022}, author = {Di Pippo, F and Crognale, S and Levantesi, C and Vitanza, L and Sighicelli, M and Pietrelli, L and Di Vito, S and Amalfitano, S and Rossetti, S}, title = {Plastisphere in lake waters: Microbial diversity, biofilm structure, and potential implications for freshwater ecosystems.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {310}, number = {}, pages = {119876}, doi = {10.1016/j.envpol.2022.119876}, pmid = {35934149}, issn = {1873-6424}, mesh = {Biofilms ; Eukaryota ; Lakes ; *Microbiota ; *Plastics ; Spectroscopy, Fourier Transform Infrared ; Water ; }, abstract = {Once dispersed in water, microplastic (MP) particles are rapidly colonised by aquatic microbes, which can adhere and grow onto solid surfaces in the form of biofilms. This study provides new insights on microbial diversity and biofilm structure of plastisphere in lake waters. By combining Fourier Confocal Laser Scanning Microscopy (CLSM), Transform Infrared Spectroscopy (FT-IR) and high-throughput DNA sequencing, we investigated the microbial colonization patterns on floating MPs and, for the first time, the occurrence of eukaryotic core members and their possible relations with biofilm-forming bacterial taxa within the plastisphere of four different lakes. Through PCR-based methods (qPCR, LAMP-PCR), we also evaluated the role of lake plastisphere as long-term dispersal vectors of potentially harmful organisms (including pathogens) and antibiotic resistance genes (ARGs) in freshwater ecosystems. Consistent variation patterns of the microbial community composition occurred between water and among the plastisphere samples of the different lakes. The eukaryotic core microbiome was mainly composed by typical freshwater biofilm colonizers, such as diatoms (Pennales, Bacillariophyceaea) and green algae (Chlorophyceae), which interact with eukaryotic and prokaryotic microbes of different trophic levels. Results also showed that MPs are suitable vectors of biofilm-forming opportunistic pathogens and a hotspot for horizontal gene transfer, likely facilitating antibiotic resistance spread in the environments.}, }
@article {pmid35925827, year = {2023}, author = {Kwak, Y and Argandona, JA and Degnan, PH and Hansen, AK}, title = {Chromosomal-level assembly of Bactericera cockerelli reveals rampant gene family expansions impacting genome structure, function and insect-microbe-plant-interactions.}, journal = {Molecular ecology resources}, volume = {23}, number = {1}, pages = {233-252}, pmid = {35925827}, issn = {1755-0998}, support = {//National Institute of Food and Agriculture (NIFA)/ ; //University of California, Riverside (UCR)/ ; 2019-70016-29066//United States Department of Agriculture (USDA)/ ; }, mesh = {Animals ; *Hemiptera/genetics ; Symbiosis/genetics ; Genome ; Bacteria/genetics ; Chromosomes ; }, abstract = {Lineage specific expansions and gene duplications are some of the most important sources of evolutionary novelty in eukaryotes. Although not as prevalent in eukaryotes compared to bacteria, horizontal gene transfer events can also result in key adaptations for insects, especially for those involved in insect-microbe interactions. In this study we assemble the first chromosomal assembly of the psyllid Bactericera cockerelli and reveal that the B. cockerelli genome has experienced significantly more gene expansion events compared to other Hemipteran representatives with fully sequenced genomes. We also reveal that B. cockerelli's genome is the largest psyllid genome (567 Mb) sequenced to date and is ~15% larger than the other two psyllid species genomes sequenced (Pachypsylla venusta and Diaphorina citri). Structurally, B. cockerelli appears to have an additional chromosome compared to the distantly related psyllid species P. venusta due to a previous chromosomal fission or fusion event. The increase in genome size and dynamic nature of the B. cockerelli genome may largely be contributed to the widespread expansion of type I and II repeat elements that are rampant across all of B. cockerelli's. chromosomes. These repeat elements are distributed near equally in both euchromatic and heterochromatic regions. Furthermore, significant gene family expansions and gene duplications were uncovered for genes that are expected to be important in its adaptation to insect-plant and microbe interactions, which include transcription factors, proteases, odorant receptors, and horizontally transferred genes that are involved in the nutritional symbioses with their long-term nutritional endosymbiont Carsonella.}, }
@article {pmid35919999, year = {2022}, author = {Malaka De Silva, P and Stenhouse, GE and Blackwell, GA and Bengtsson, RJ and Jenkins, C and Hall, JPJ and Baker, KS}, title = {A tale of two plasmids: contributions of plasmid associated phenotypes to epidemiological success among Shigella.}, journal = {Proceedings. Biological sciences}, volume = {289}, number = {1980}, pages = {20220581}, pmid = {35919999}, issn = {1471-2954}, support = {BB/V009184/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 106690/A/14/Z/WT_/Wellcome Trust/United Kingdom ; MR/N013840/1/MRC_/Medical Research Council/United Kingdom ; MR/R020787/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Phenotype ; Plasmids ; *Shigella/genetics ; }, abstract = {Dissemination of antimicrobial resistance (AMR) genes by horizontal gene transfer (HGT) mediated through plasmids is a major global concern. Genomic epidemiology studies have shown varying success of different AMR plasmids during outbreaks, but the underlying reasons for these differences are unclear. Here, we investigated two Shigella plasmids (pKSR100 and pAPR100) that circulated in the same transmission network but had starkly contrasting epidemiological outcomes to identify plasmid features that may have contributed to the differences. We used plasmid comparative genomics to reveal divergence between the two plasmids in genes encoding AMR, SOS response alleviation and conjugation. Experimental analyses revealed that these genomic differences corresponded with reduced conjugation efficiencies for the epidemiologically successful pKSR100, but more extensive AMR, reduced fitness costs, and a reduced SOS response in the presence of antimicrobials, compared with the less successful pAPR100. The discrepant phenotypes between the two plasmids are consistent with the hypothesis that plasmid-associated phenotypes contribute to determining the epidemiological outcome of AMR HGT and suggest that phenotypes relevant in responding to antimicrobial pressure and fitness impact may be more important than those around conjugation in this setting. Plasmid phenotypes could thus be valuable tools in conjunction with genomic epidemiology for predicting AMR dissemination.}, }
@article {pmid35917316, year = {2022}, author = {Nonaka, L and Masuda, M and Yano, H}, title = {Atypical integrative element with strand-biased circularization activity assists interspecies antimicrobial resistance gene transfer from Vibrio alfacsensis.}, journal = {PloS one}, volume = {17}, number = {8}, pages = {e0271627}, pmid = {35917316}, issn = {1932-6203}, mesh = {*Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; Drug Resistance, Bacterial/genetics ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Plasmids/genetics ; *Vibrio/genetics ; }, abstract = {The exchange of antimicrobial resistance (AMR) genes between aquaculture and terrestrial microbial populations has emerged as a serious public health concern. However, the nature of the mobile genetic elements in marine bacteria is poorly documented. To gain insight into the genetic mechanisms underlying AMR gene transfer from marine bacteria, we mated a multidrug-resistant Vibrio alfacsensis strain with an Escherichia coli strain, and then determined the complete genome sequences of the donor and the transconjugant strains. Sequence analysis revealed a conjugative multidrug resistance plasmid in the donor strain, which was integrated into the chromosome of the recipient. The plasmid backbone in the transconjugant chromosome was flanked by two copies of a 7.1 kb unclassifiable integrative element harboring a β-lactamase gene. The 7.1 kb element and the previously reported element Tn6283 share four coding sequences, two of which encode the catalytic R-H-R-Y motif of tyrosine recombinases. Polymerase chain reaction and sequencing experiments revealed that these elements generate a circular copy of one specific strand without leaving an empty site on the donor molecule, in contrast to the movement of integron gene cassettes or ICE/IMEs discovered to date. These elements are termed SEs (strand-biased circularizing integrative elements): SE-6945 (the 7.1 kb element) and SE-6283 (Tn6283). The copy number and location of SE-6945 in the chromosome affected the antibiotic resistance levels of the transconjugants. SEs were identified in the genomes of other Vibrio species. Overall, these results suggest that SEs are involved in the spread of AMR genes among marine bacteria.}, }
@article {pmid35916503, year = {2022}, author = {Singh, A and Bansal, K and Kumar, S and Patil, PB}, title = {Deep Population Genomics Reveals Systematic and Parallel Evolution at a Lipopolysaccharide Biosynthetic Locus in Xanthomonas Pathogens That Infect Rice and Sugarcane.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {16}, pages = {e0055022}, pmid = {35916503}, issn = {1098-5336}, mesh = {Genome, Bacterial ; Lipopolysaccharides ; Metagenomics ; *Oryza/microbiology ; Plant Diseases/microbiology ; *Saccharum/genetics ; *Xanthomonas/genetics ; }, abstract = {The advent of high-throughput sequencing and population genomics has enabled researchers to investigate selection pressure at hypervariable genomic loci encoding pathogen-associated molecular pattern (PAMP) molecules like lipopolysaccharide (LPS). Xanthomonas is a model and a major group of phytopathogenic bacteria that infect hosts in tissue-specific manner. Our in-depth population-based genomic investigation revealed the emergence of major lineages in two Xanthomonas pathogens that infect xylem of rice and sugarcane is associated with the acquisition and later large-scale replacement by distinct type of LPS cassettes. In the population of the rice xylem pathogen, Xanthomonas oryzae pv. oryzae (Xoo) and sugarcane pathogens Xanthomonas sacchari (Xsac) and Xanthomonas vasicola (Xvv), the BXO8 type of LPS cassette is replaced by a BXO1 type of cassette in Xoo and by Xvv type LPS cassette in Xsac and Xvv. These findings suggest a wave of parallel evolution at an LPS locus mediated by horizontal gene transfer (HGT) events during its adaptation and emergence. Aside from xylem pathogens, two closely related lineages of Xoo that infect parenchyma of rice and Leersia hexandra grass have acquired an LPS cassette from Xanthomonas pathogens that infect parenchyma of citrus, walnut, and strawberries, indicating yet another instance of parallel evolution mediated by HGT at an LPS locus. Our targeted and megapopulation-based genome dynamic studies revealed the acquisition and dominance of specific types of LPS cassettes in adaptation and success of a major group of phytopathogenic bacteria. IMPORTANCE Lipopolysaccharide (LPS) is a major microbe associated molecular pattern and hence a major immunomodulator. As a major and outer member component, it is expected that LPS is a frontline defense mechanism to deal with different host responses. Limited studies have indicated that LPS loci are also highly variable at strain and species level in plant-pathogenic bacteria, suggesting strong selection pressure from plants and associated niches. The advent of high-throughput genomics has led to the availability of a large set of genomic resources at taxonomic and population levels. This provides an exciting and important opportunity to carryout megascale targeted and population-based comparative genomic/association studies at important loci like those encoding LPS biosynthesis to understand their role in the evolution of the host, tissue specificity, and also predominant lineages. Such studies will also fill major gap in understanding host and tissue specificity in pathogenic bacteria. Our pioneering study uses the Xanthomonas group of phytopathogens that are known for their characteristic host and tissue specificity. The present deep phylogenomics of diverse Xanthomonas species and its members revealed lineage association and dominance of distinct types of LPS in accordance with their origin, host, tissue specificity, and evolutionary success.}, }
@article {pmid35916502, year = {2022}, author = {Liang, J and Liu, J and Wang, X and Sun, H and Zhang, Y and Ju, F and Thompson, F and Zhang, XH}, title = {Genomic Analysis Reveals Adaptation of Vibrio campbellii to the Hadal Ocean.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {16}, pages = {e0057522}, pmid = {35916502}, issn = {1098-5336}, mesh = {Genomics ; Oceans and Seas ; Phylogeny ; *Vibrio/genetics ; Water ; }, abstract = {The genus Vibrio is characterized by high metabolic flexibility and genome plasticity and is widely distributed in the ocean from euphotic layers to deep-sea environments. The relationship between genome features and environmental adaptation strategies of Vibrio has been extensively investigated in coastal environments, yet very little is known about their survival strategies in oligotrophic deep-sea. In this study, we compared genomes of five Vibrio campbellii strains isolated from the Mariana and Yap Trenches at different water depths, including two epipelagic strains and three hadopelagic strains, to identify genomic characteristics that facilitate survival in the deep sea. Genome streamlining is found in pelagic strains, such as smaller genome sizes, lower G+C contents, and higher gene densities, which might be caused by long-term residence in an oligotrophic environment. Phylogenetic results showed that these five Vibrio strains are clustered into two clades according to their collection depth. Indeed, hadopelagic isolates harbor more genes involved in amino acid metabolism and transport, cell wall/membrane/envelope biogenesis, and inorganic ion transport and metabolism through comparative genomics analysis. Specific macrolide export gene and more tellurite resistance genes present in hadopelagic strains by the annotation of antibiotic and metal resistance genes. In addition, several genes related to substrate degradation are enriched in hadopelagic strains, such as chitinase genes, neopullulanase genes, and biopolymer transporter genes. In contrast, epipelagic strains are unique in their capacity for assimilatory nitrate reduction. The genomic characteristics investigated here provide insights into how Vibrio adapts to the deep-sea environment through genomic evolution. IMPORTANCE With the development of deep-sea sampling technology, an increasing number of deep-sea Vibrio strains have been isolated, but the adaptation mechanism of these eutrophic Vibrio strains to the deep-sea environment is unclear. Here, our results show that the genome of pelagic Vibrio is streamlined to adapt to a long-term oligotrophic environment. Through a phylogenomic analysis, we find that genomic changes in marine Vibrio campbellii strains are related to water depth. Our data suggest that an increase in genes related to antibiotic resistance, degradation of macromolecular and refractory substrates, and utilization of rare ions is related to the adaptation of V. campbellii strains to adapt to hadal environments, and most of the increased genes were acquired by horizontal gene transfer. These findings may deepen our understanding of adaptation strategies of marine bacteria to the extreme environment in hadal zones.}, }
@article {pmid35913911, year = {2022}, author = {Ward, LM and Shih, PM}, title = {Phototrophy and carbon fixation in Chlorobi postdate the rise of oxygen.}, journal = {PloS one}, volume = {17}, number = {8}, pages = {e0270187}, pmid = {35913911}, issn = {1932-6203}, mesh = {Carbon Cycle ; *Chlorobi/genetics ; Iron/metabolism ; Oxygen/metabolism ; Photosynthesis ; Phototrophic Processes ; Phylogeny ; }, abstract = {While most productivity on the surface of the Earth today is fueled by oxygenic photosynthesis, for much of Earth history it is thought that anoxygenic photosynthesis-using compounds like ferrous iron or sulfide as electron donors-drove most global carbon fixation. Anoxygenic photosynthesis is still performed by diverse bacteria in niche environments today. Of these, the Chlorobi (formerly green sulfur bacteria) are often interpreted as being particularly ancient and are frequently proposed to have fueled the biosphere during late Archean and early Paleoproterozoic time before the rise of oxygenic photosynthesis. Here, we perform comparative genomic, phylogenetic, and molecular clock analyses to determine the antiquity of the Chlorobi and their characteristic phenotypes. We show that contrary to common assumptions, the Chlorobi clade is relatively young, with anoxygenic phototrophy, carbon fixation via the rTCA pathway, and iron oxidation all significantly postdating the rise of oxygen ~2.3 billion years ago. The Chlorobi therefore could not have fueled the Archean biosphere, but instead represent a relatively young radiation of organisms which likely acquired the capacity for anoxygenic photosynthesis and other traits via horizontal gene transfer sometime after the evolution of oxygenic Cyanobacteria.}, }
@article {pmid35909963, year = {2022}, author = {Soontrapa, P and Jitmuang, A and Ruenchit, P and Tiewcharoen, S and Sarasombath, PT and Rattanabannakit, C}, title = {The First Molecular Genotyping of Naegleria fowleri Causing Primary Amebic Meningoencephalitis in Thailand With Epidemiology and Clinical Case Reviews.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {931546}, pmid = {35909963}, issn = {2235-2988}, mesh = {*Central Nervous System Protozoal Infections/epidemiology ; Genotype ; Humans ; *Naegleria fowleri/genetics ; Phylogeny ; RNA, Ribosomal, 16S ; Retrospective Studies ; Thailand/epidemiology ; }, abstract = {Primary amebic meningoencephalitis (PAM) is a rare and fatal central nervous system infection caused by Naegleria fowleri, a free-living amoeba found in the environment. To date, eight pathogenic N. fowleri genotypes have been reported worldwide. We aimed to explore the genotypes of N. fowleri that cause primary amebic meningoencephalitis in Thailand. In 2021, the 17th PAM case was reported, and a retrospective literature search of PAM cases in Thailand from 1982 through April 2021 was performed. Phylogenetic and genotyping analyses of the two mitochondrial (12S rRNA and 16S rRNA) and nuclear (ITS1 and 5.8s rRNA) genes of N. fowleri were performed on four available clinical isolates. Based on the mitochondrial and nuclear genes, N. fowleri genotype T3 was found to cause PAM in three out of four cases. However, disagreement between the genotype based on the mitochondrial and nuclear genes was found in one of the PAM cases, in which the 12S rRNA locus suggested the causative genotype as T1, while the ITS1 implied genotype T4. The discrepancy between the mitochondrial and nuclear genome was previously observed, which suggests the possible horizontal gene transfer among N. fowleri species. Based on the ITS1 gene, two N. fowleri genotypes, T3 and T4, were found to be the genotypes causing PAM in this study. In addition, N. fowleri genotype T2 was previously reported in a traveler who was infected in Thailand. Thus, at least three genotypes (T2, T3, and T4) of N. fowleri are found to be associated with PAM in Thailand.}, }
@article {pmid35909620, year = {2022}, author = {Kasagaki, S and Hashimoto, M and Maeda, S}, title = {Subminimal inhibitory concentrations of ampicillin and mechanical stimuli cooperatively promote cell-to-cell plasmid transformation in Escherichia coli.}, journal = {Current research in microbial sciences}, volume = {3}, number = {}, pages = {100130}, pmid = {35909620}, issn = {2666-5174}, abstract = {Horizontal gene transfer (HGT) is a bacterial evolution tool for improved survival. Although several environmental stimuli induce or promote HGT, the diversity and complexity of the environmental factors have not been sufficiently elucidated. In this study, we showed that the biofilm culture of Escherichia coli at the air-solid interface in the presence of a subminimal inhibitory concentration (sub-MIC) of ampicillin (∼0.5-4 µg/mL) and subsequent mechanical stimulation (rolling small glass balls, ø = 5-8 mm) cooperatively promoted horizontal plasmid transfer without the usual competence-inducing conditions. Either of the two treatments promoted plasmid transfer at a lower frequency than when the treatments were combined. The effect of several parameters on the two treatments was tested and then optimized, achieving a high frequency of plasmid transfer (up to 10[-6] per cell) under optimal conditions. Plasmid transfer was DNase-sensitive for both treatments, demonstrating its mechanism of transformation. Plasmid transfer occurred using various E. coli strains, plasmids, ball materials, shaking conditions, and even the mechanical stimulation of brushing the biofilm with a toothbrush, indicating the conditional flexibility of this phenomenon. This is the first demonstration of the promoting effect of the combination of a sub-MIC antibiotic and mechanical stimulation on horizontal plasmid transfer between E. coli cells via transformation. Regarding environmental bacterial physiology, the aggregations or biofilms of bacterial cells may encounter both sub-MIC antibiotics and mechanical stimuli in some specific environments, therefore, this type of HGT could also occur naturally.}, }
@article {pmid35909010, year = {2022}, author = {Macquet, J and Mounichetty, S and Raffaele, S}, title = {Genetic co-option into plant-filamentous pathogen interactions.}, journal = {Trends in plant science}, volume = {27}, number = {11}, pages = {1144-1158}, doi = {10.1016/j.tplants.2022.06.011}, pmid = {35909010}, issn = {1878-4372}, mesh = {Biological Evolution ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Host-Pathogen Interactions/genetics ; *Plant Diseases/genetics ; *Plants/genetics/metabolism ; Virulence/genetics ; }, abstract = {Plants are engaged in a coevolutionary arms race with their pathogens that drives rapid diversification and specialization of genes involved in resistance and virulence. However, some major innovations in plant-pathogen interactions, such as molecular decoys, trans-kingdom RNA interference, two-speed genomes, and receptor networks, evolved through the expansion of the functional landscape of genes. This is a typical outcome of genetic co-option, the evolutionary process by which available genes are recruited into new biological functions. Co-option into plant-pathogen interactions emerges generally from (i) cis-regulatory variation, (ii) horizontal gene transfer (HGT), (iii) mutations altering molecular promiscuity, and (iv) rewiring of gene networks and protein complexes. Understanding these molecular mechanisms is key for the functional and predictive biology of plant-pathogen interactions.}, }
@article {pmid35906926, year = {2022}, author = {Leducq, JB and Sneddon, D and Santos, M and Condrain-Morel, D and Bourret, G and Martinez-Gomez, NC and Lee, JA and Foster, JA and Stolyar, S and Shapiro, BJ and Kembel, SW and Sullivan, JM and Marx, CJ}, title = {Comprehensive Phylogenomics of Methylobacterium Reveals Four Evolutionary Distinct Groups and Underappreciated Phyllosphere Diversity.}, journal = {Genome biology and evolution}, volume = {14}, number = {8}, pages = {}, pmid = {35906926}, issn = {1759-6653}, mesh = {Ecosystem ; *Methylobacterium ; Phylogeny ; Plant Leaves ; Plants/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Methylobacterium is a group of methylotrophic microbes associated with soil, fresh water, and particularly the phyllosphere, the aerial part of plants that has been well studied in terms of physiology but whose evolutionary history and taxonomy are unclear. Recent work has suggested that Methylobacterium is much more diverse than thought previously, questioning its status as an ecologically and phylogenetically coherent taxonomic genus. However, taxonomic and evolutionary studies of Methylobacterium have mostly been restricted to model species, often isolated from habitats other than the phyllosphere and have yet to utilize comprehensive phylogenomic methods to examine gene trees, gene content, or synteny. By analyzing 189 Methylobacterium genomes from a wide range of habitats, including the phyllosphere, we inferred a robust phylogenetic tree while explicitly accounting for the impact of horizontal gene transfer (HGT). We showed that Methylobacterium contains four evolutionarily distinct groups of bacteria (namely A, B, C, D), characterized by different genome size, GC content, gene content, and genome architecture, revealing the dynamic nature of Methylobacterium genomes. In addition to recovering 59 described species, we identified 45 candidate species, mostly phyllosphere-associated, stressing the significance of plants as a reservoir of Methylobacterium diversity. We inferred an ancient transition from a free-living lifestyle to association with plant roots in Methylobacteriaceae ancestor, followed by phyllosphere association of three of the major groups (A, B, D), whose early branching in Methylobacterium history has been heavily obscured by HGT. Together, our work lays the foundations for a thorough redefinition of Methylobacterium taxonomy, beginning with the abandonment of Methylorubrum.}, }
@article {pmid35904761, year = {2023}, author = {Liu, C and Kenney, T and Beiko, RG and Gu, H}, title = {The Community Coevolution Model with Application to the Study of Evolutionary Relationships between Genes Based on Phylogenetic Profiles.}, journal = {Systematic biology}, volume = {72}, number = {3}, pages = {559-574}, pmid = {35904761}, issn = {1076-836X}, support = {RGPIN/4945-2014//Natural Sciences and Engineering Research Council of Canada/ ; //Genome Canada/ ; //Research Nova Scotia/ ; }, mesh = {Phylogeny ; *Biological Evolution ; *Proteins ; Phenotype ; Genome, Bacterial ; }, abstract = {Organismal traits can evolve in a coordinated way, with correlated patterns of gains and losses reflecting important evolutionary associations. Discovering these associations can reveal important information about the functional and ecological linkages among traits. Phylogenetic profiles treat individual genes as traits distributed across sets of genomes and can provide a fine-grained view of the genetic underpinnings of evolutionary processes in a set of genomes. Phylogenetic profiling has been used to identify genes that are functionally linked and to identify common patterns of lateral gene transfer in microorganisms. However, comparative analysis of phylogenetic profiles and other trait distributions should take into account the phylogenetic relationships among the organisms under consideration. Here, we propose the Community Coevolution Model (CCM), a new coevolutionary model to analyze the evolutionary associations among traits, with a focus on phylogenetic profiles. In the CCM, traits are considered to evolve as a community with interactions, and the transition rate for each trait depends on the current states of other traits. Surpassing other comparative methods for pairwise trait analysis, CCM has the additional advantage of being able to examine multiple traits as a community to reveal more dependency relationships. We also develop a simulation procedure to generate phylogenetic profiles with correlated evolutionary patterns that can be used as benchmark data for evaluation purposes. A simulation study demonstrates that CCM is more accurate than other methods including the Jaccard Index and three tree-aware methods. The parameterization of CCM makes the interpretation of the relations between genes more direct, which leads to Darwin's scenario being identified easily based on the estimated parameters. We show that CCM is more efficient and fits real data better than other methods resulting in higher likelihood scores with fewer parameters. An examination of 3786 phylogenetic profiles across a set of 659 bacterial genomes highlights linkages between genes with common functions, including many patterns that would not have been identified under a nonphylogenetic model of common distribution. We also applied the CCM to 44 proteins in the well-studied Mitochondrial Respiratory Complex I and recovered associations that mapped well onto the structural associations that exist in the complex. [Coevolution; evolutionary rates; gene network; graphical models; phylogenetic profiles; phylogeny.].}, }
@article {pmid35900180, year = {2023}, author = {Galindo, LJ and Torruella, G and López-García, P and Ciobanu, M and Gutiérrez-Preciado, A and Karpov, SA and Moreira, D}, title = {Phylogenomics Supports the Monophyly of Aphelids and Fungi and Identifies New Molecular Synapomorphies.}, journal = {Systematic biology}, volume = {72}, number = {3}, pages = {505-515}, doi = {10.1093/sysbio/syac054}, pmid = {35900180}, issn = {1076-836X}, support = {/ERC_/European Research Council/International ; }, mesh = {Phylogeny ; *Eukaryota ; Fungi/genetics ; *Microsporidia/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {The supergroup Holomycota, composed of Fungi and several related lineages of unicellular organisms (Nucleariida, Rozellida, Microsporidia, and Aphelida), represents one of the major branches in the phylogeny of eukaryotes. Nevertheless, except for the well-established position of Nucleariida as the first holomycotan branch to diverge, the relationships among the other lineages have so far remained unresolved largely owing to the lack of molecular data for some groups. This was notably the case aphelids, a poorly known group of endobiotic phagotrophic protists that feed on algae with cellulose walls. The first molecular phylogenies including aphelids supported their sister relationship with Rozellida and Microsporidia which, collectively, formed a new group called Opisthosporidia (the "Opisthosporidia hypothesis"). However, recent phylogenomic analyses including massive sequence data from two aphelid genera, Paraphelidium and Amoeboaphelidium, suggested that the aphelids are sister to fungi (the "Aphelida $+$ Fungi hypothesis"). Should this position be confirmed, aphelids would be key to understanding the early evolution of Holomycota and the origin of Fungi. Here, we carry out phylogenomic analyses with an expanded taxonomic sampling for aphelids after sequencing the transcriptomes of two species of the genus Aphelidium (Aphelidium insulamus and Aphelidium tribonematis) in order to test these competing hypotheses. Our new phylogenomic analyses including species from the three known aphelid genera strongly rejected the Opisthosporidia hypothesis. Furthermore, comparative genomic analyses further supported the Aphelida $+$ Fungi hypothesis via the identification of 19 orthologous genes exclusively shared by these two lineages. Seven of them originated from ancient horizontal gene transfer events predating the aphelid-fungal split and the remaining 12 likely evolved de novo, constituting additional molecular synapomorphies for this clade. Ancestral trait reconstruction based on our well-resolved phylogeny of Holomycota suggests that the progenitor of both fungi and rozellids, was aphelid-like, having an amoeboflagellate state and likely preying endobiotically on cellulose-containing, cell-walled organisms. Two lineages, which we propose to call Phytophagea and Opisthophagea, evolved from this ancestor. Phytophagea, grouping aphelids and classical fungi, mainly specialized in endobiotic predation of algal cells. Fungi emerged from this lineage after losing phagotrophy in favor of osmotrophy. Opisthophagea, grouping rozellids and Microsporidia, became parasites, mostly of chitin-containing hosts. This lineage entered a progressive reductive process that resulted in a unique lifestyle, especially in the highly derived Microsporidia. [Aphelida, fungi, Holomycota, horizontal gene transfer, phylogenomics, synapomorphy.].}, }
@article {pmid35900091, year = {2022}, author = {Hansen, AK and Sanchez, AN and Kwak, Y}, title = {Divergent Host-Microbe Interaction and Pathogenesis Proteins Detected in Recently Identified Liberibacter Species.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0209122}, pmid = {35900091}, issn = {2165-0497}, mesh = {Fimbriae, Bacterial ; Host Microbial Interactions ; *Liberibacter ; Plant Diseases/microbiology ; Plants ; *Rhizobiaceae/genetics ; Sequence Analysis, DNA ; }, abstract = {Candidatus (Ca.) Liberibacter taxa are economically important bacterial plant pathogens that are not culturable; however, genome-enabled insights can help us develop a deeper understanding of their host-microbe interactions and evolution. The draft genome of a recently identified Liberibacter taxa, Ca. Liberibacter capsica, was curated and annotated here with a total draft genome size of 1.1 MB with 1,036 proteins, which is comparable to other Liberibacter species with complete genomes. A total of 459 orthologous clusters were identified among Ca. L. capsica, Ca. L. asiaticus, Ca. L. psyllaurous, Ca. L. americanus, Ca. L. africanus, and L. crescens, and these genes within these clusters consisted of housekeeping and environmental response functions. We estimated the rates of molecular evolution for each of the 443 one-to-one ortholog clusters and found that all Ca. L. capsica orthologous pairs were under purifying selection when the synonymous substitutions per synonymous site (dS) were not saturated. These results suggest that these genes are largely maintaining their conserved functions. We also identified the most divergent single-copy orthologous proteins in Ca. L. capsica by analyzing the ortholog pairs that represented the highest nonsynonymous substitutions per nonsynonymous site (dN) values for each pairwise comparison. From these analyses, we found that 21 proteins which are known to be involved in pathogenesis and host-microbe interactions, including the Tad pilus complex, were consistently divergent between Ca. L. capsica and the majority of other Liberibacter species. These results further our understanding of the evolutionary genetics of Ca. L. capsica and, more broadly, the evolution of Liberibacter. IMPORTANCE "Candidatus" (Ca.) Liberibacter taxa are economically important plant pathogens vectored by insects; however, these host-dependent bacterial taxa are extremely difficult to study because they are unculturable. Recently, we identified a new Ca. Liberibacter lineage (Ca. Liberibacter capsica) from a rare insect metagenomic sample. In this current study, we report that the draft genome of Ca. Liberibacter capsica is similar in genome size and protein content compared to the other Ca. Liberibacter taxa. We provide evidence that many of their shared genes, which encode housekeeping and environmental response functions, are evolving under purifying selection, suggesting that these genes are maintaining similar functions. Our study also identifies 21 proteins that are rapidly evolving amino acid changes in Ca. Liberibacter capsica compared to the majority of other Liberibacter taxa. Many of these proteins represent key genes involved in Liberibacter-host interactions and pathogenesis and are valuable candidate genes for future studies.}, }
@article {pmid35900090, year = {2022}, author = {Li, X and Zhang, J and Yang, C and Li, J and Wang, J and Huang, W and Zeng, L and Liang, X and Long, W and Zhang, X}, title = {Increased Expression and Amplification of blaKPC-2 Contributes to Resistance to Ceftazidime/Avibactam in a Sequence Type 11 Carbapenem-Resistant Klebsiella pneumoniae Strain.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0095522}, pmid = {35900090}, issn = {2165-0497}, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Azabicyclo Compounds ; Bacterial Proteins/genetics/metabolism ; Carbapenems/pharmacology/therapeutic use ; *Ceftazidime/pharmacology/therapeutic use ; Humans ; *Klebsiella Infections/drug therapy ; Klebsiella pneumoniae/genetics ; Microbial Sensitivity Tests ; beta-Lactamases/genetics ; }, abstract = {Ceftazidime/avibactam (CAZ/AVI) is regarded as an effective alternative antibiotic for the clinical treatment of Klebsiella pneumoniae carbapenemase (KPC)-producing isolates. As resistance has been reported in some strains, it is critical to understand the key mechanisms contributing to the acquired resistance to CAZ/AVI. From January 2018 to April 2020, 127 KPC-producing carbapenem-resistant Klebsiella pneumoniae strains (CRKPs) were isolated at a university hospital in Chongqing, China, and 25 strains showed reduced susceptibility to CAZ/AVI. All reduced-susceptibility CRKPs were deficient in Ompk35 and Ompk36 porins, and 24 strains had a premature termination at amino acid position 63 in Ompk35 and 134 to 135 glycine and aspartic acid (GD) insertion in OmpK36, while the blaKPC-2 expression level showed no significant difference compared to that of strain BAA-1705. Four reduced-susceptibility strains evolved resistance under selective pressure of CAZ/AVI with the blaKPC-2 expression level increased, and two of these strains had mutations in the Ω-loop. The study found a strain of CRKP55 with changes in the resistance phenotype during conjugation, evolving from reduced sensitivity to high-level resistance to CAZ/AVI. Through plasmid sequencing and reverse transcription-quantitative PCR, it was speculated that insertion sequence (IS)26-mediated blaKPC-2 gene amplification caused the MIC value change in the conjugant JKP55. Our findings illustrated the potential of CAZ/AVI resistance under antibiotic stress and demonstrated that IS26 may mediate blaKPC-2 replication transposition, leading to high-level resistance during horizontal gene transfer. Investigation of CAZ/AVI resistance mechanisms may offer a unique opportunity to study the horizontal evolutionary trajectories of K. pneumoniae high-risk clones. IMPORTANCE Klebsiella pneumoniae carbapenemase (KPC) production is the most common mechanism of K. pneumoniae resistance to carbapenems in China. Currently, CAZ/AVI is considered a potential alternative therapeutic option for infections caused by these isolates. However, there have been increasing reports of resistant or reduced-sensitivity strains since the approval of this agent. In this study, resistance to CAZ/AVI was induced under drug-selective pressure and was caused by blaKPC-2 overexpression and/or substitutions in the Ω-loop of KPC. Additionally, it was demonstrated that a conjugative plasmid carrying blaKPC-2 could transfer horizontally between species, and perhaps, IS26-derived tandem amplification of blaKPC-2 during this period led to high-level resistance to CAZ/AVI. Our research suggests that IS26-mediated resistance evolution may have important implications in guiding clinical antibiotic use.}, }
@article {pmid35899254, year = {2022}, author = {Zhang, L and Fu, Y and Zhang, L and Xu, Q and Yang, Y and He, J and Leptihn, S and Loh, B and Moran, RA and van Schaik, W and Toleman, MA and Chen, Q and Liu, L and Yu, Y and Hua, X}, title = {Co-evolutionary adaptations of Acinetobacter baumannii and a clinical carbapenemase-encoding plasmid during carbapenem exposure.}, journal = {Evolutionary applications}, volume = {15}, number = {7}, pages = {1045-1061}, pmid = {35899254}, issn = {1752-4571}, support = {MR/S013660/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {OXA-23 is the predominant carbapenemase in carbapenem-resistant Acinetobacter baumannii. The co-evolutionary dynamics of A. baumannii and OXA-23-encoding plasmids are poorly understood. Here, we transformed A. baumannii ATCC 17978 with pAZJ221, a bla OXA-23-containing plasmid from clinical A. baumannii isolate A221, and subjected the transformant to experimental evolution in the presence of a sub-inhibitory concentration of imipenem for nearly 400 generations. We used population sequencing to track genetic changes at six time points and evaluated phenotypic changes. Increased fitness of evolving populations, temporary duplication of bla OXA-23 in pAZJ221, interfering allele dynamics, and chromosomal locus-level parallelism were observed. To characterize genotype-to-phenotype associations, we focused on six mutations in parallel targets predicted to affect small RNAs and a cyclic dimeric (3' → 5') GMP-metabolizing protein. Six isogenic mutants with or without pAZJ221 were engineered to test for the effects of these mutations on fitness costs and plasmid kinetics, and the evolved plasmid containing two copies of bla OXA-23 was transferred to ancestral ATCC 17978. Five of the six mutations contributed to improved fitness in the presence of pAZJ221 under imipenem pressure, and all but one of them impaired plasmid conjugation ability. The duplication of bla OXA-23 increased host fitness under carbapenem pressure but imposed a burden on the host in antibiotic-free media relative to the ancestral pAZJ221. Overall, our study provides a framework for the co-evolution of A. baumannii and a clinical bla OXA-23-containing plasmid in the presence of imipenem, involving early bla OXA-23 duplication followed by chromosomal adaptations that improved the fitness of plasmid-carrying cells.}, }
@article {pmid35898691, year = {2022}, author = {Tao, S and Chen, H and Li, N and Wang, T and Liang, W}, title = {The Spread of Antibiotic Resistance Genes In Vivo Model.}, journal = {The Canadian journal of infectious diseases &amp; medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale}, volume = {2022}, number = {}, pages = {3348695}, pmid = {35898691}, issn = {1712-9532}, abstract = {Infections caused by antibiotic-resistant bacteria are a major public health threat. The emergence and spread of antibiotic resistance genes (ARGs) in the environment or clinical setting pose a serious threat to human and animal health worldwide. Horizontal gene transfer (HGT) of ARGs is one of the main reasons for the dissemination of antibiotic resistance in vitro and in vivo environments. There is a consensus on the role of mobile genetic elements (MGEs) in the spread of bacterial resistance. Most drug resistance genes are located on plasmids, and the spread of drug resistance genes among microorganisms through plasmid-mediated conjugation transfer is the most common and effective way for the spread of multidrug resistance. Experimental studies of the processes driving the spread of antibiotic resistance have focused on simple in vitro model systems, but the current in vitro protocols might not correctly reflect the HGT of antibiotic resistance genes in realistic conditions. This calls for better models of how resistance genes transfer and disseminate in vivo. The in vivo model can better mimic the situation that occurs in patients, helping study the situation in more detail. This is crucial to develop innovative strategies to curtail the spread of antibiotic resistance genes in the future. This review aims to give an overview of the mechanisms of the spread of antibiotic resistance genes and then demonstrate the spread of antibiotic resistance genes in the in vivo model. Finally, we discuss the challenges in controlling the spread of antibiotic resistance genes and their potential solutions.}, }
@article {pmid35897639, year = {2022}, author = {Lipszyc, A and Szuplewska, M and Bartosik, D}, title = {How Do Transposable Elements Activate Expression of Transcriptionally Silent Antibiotic Resistance Genes?.}, journal = {International journal of molecular sciences}, volume = {23}, number = {15}, pages = {}, pmid = {35897639}, issn = {1422-0067}, mesh = {*Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; *DNA Transposable Elements/genetics ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Integrons ; }, abstract = {The rapidly emerging phenomenon of antibiotic resistance threatens to substantially reduce the efficacy of available antibacterial therapies. Dissemination of resistance, even between phylogenetically distant bacterial species, is mediated mainly by mobile genetic elements, considered to be natural vectors of horizontal gene transfer. Transposable elements (TEs) play a major role in this process-due to their highly recombinogenic nature they can mobilize adjacent genes and can introduce them into the pool of mobile DNA. Studies investigating this phenomenon usually focus on the genetic load of transposons and the molecular basis of their mobility. However, genes introduced into evolutionarily distant hosts are not necessarily expressed. As a result, bacterial genomes contain a reservoir of transcriptionally silent genetic information that can be activated by various transposon-related recombination events. The TEs themselves along with processes associated with their transposition can introduce promoters into random genomic locations. Thus, similarly to integrons, they have the potential to convert dormant genes into fully functional antibiotic resistance determinants. In this review, we describe the genetic basis of such events and by extension the mechanisms promoting the emergence of new drug-resistant bacterial strains.}, }
@article {pmid35896060, year = {2022}, author = {Macedo, G and Olesen, AK and Maccario, L and Hernandez Leal, L and V D Maas, P and Heederik, D and Mevius, D and Sørensen, SJ and Schmitt, H}, title = {Horizontal Gene Transfer of an IncP1 Plasmid to Soil Bacterial Community Introduced by Escherichia coli through Manure Amendment in Soil Microcosms.}, journal = {Environmental science &amp; technology}, volume = {56}, number = {16}, pages = {11398-11408}, pmid = {35896060}, issn = {1520-5851}, mesh = {Anti-Bacterial Agents ; Bacteria/genetics ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; *Manure/microbiology ; Plasmids/genetics ; RNA, Ribosomal, 16S/genetics ; *Soil ; Soil Microbiology ; }, abstract = {The quantification and identification of new plasmid-acquiring bacteria in representative mating conditions is critical to characterize the risk of horizontal gene transfer in the environment. This study aimed to quantify conjugation events resulting from manure application to soils and identify the transconjugants resulting from these events. Conjugation was quantified at multiple time points by plating and flow cytometry, and the transconjugants were recovered by fluorescence-activated cell sorting and identified by 16S rRNA sequencing. Overall, transconjugants were only observed within the first 4 days after manure application and at values close to the detection limits of this experimental system (1.00-2.49 log CFU/g of manured soil, ranging between 10[-5] and 10[-4] transconjugants-to-donor ratios). In the pool of recovered transconjugants, we found amplicon sequence variants (ASVs) of genera whose origin was traced to soils (Bacillus and Nocardioides) and manure (Comamonas and Rahnella). This work showed that gene transfer from fecal to soil bacteria occurred despite the less-than-optimal conditions faced by manure bacteria when transferred to soils, but these events were rare, mainly happened shortly after manure application, and the plasmid did not colonize the soil community. This study provides important information to determine the risks of AMR spread via manure application.}, }
@article {pmid35895240, year = {2022}, author = {Hossain, M and Ibne Momen, AM and Rahman, A and Biswas, J and Yasmin, M and Nessa, J and Ahsan, CR}, title = {Draft-genome analysis provides insights into the virulence properties and genome plasticity of Vibrio fluvialis organisms isolated from shrimp farms and Turag river in Bangladesh.}, journal = {Archives of microbiology}, volume = {204}, number = {8}, pages = {527}, pmid = {35895240}, issn = {1432-072X}, mesh = {Aquaculture ; Bangladesh ; Rivers ; Seafood ; *Vibrio/genetics ; *Vibrio cholerae ; Virulence/genetics ; }, abstract = {Vibrio fluvialis is an opportunistic waterborne and seafood-borne enteric pathogen capable of causing severe diarrhea leading to death. This pathogen is endemic to Bangladesh, a country which is a major producer of cultured shrimp and wild-caught prawns. In this study, we carried out whole-genome sequencing of three V. fluvialis organisms isolated from shrimp farm and river sediment showing strong pathogenic characteristics in vivo and in vitro and compared their genomes against other V. fluvialis and related pathogenic species to glean insights into their potential as pathogens. Numerous virulence-associated genes including hemolysins, cytolysins, three separate Type IV pili, Types II and VI secretion systems, biofilm, and the V. cholerae pathogenesis regulating gene, toxR, were identified. Moreover, we found strain S-10 to have the propensity to acquire antibiotic resistance genes through horizontal gene transfer. These findings indicate that shrimp farms and rivers could be potential sources of V. fluvialis organisms which are an infection threat of public health concern.}, }
@article {pmid35890320, year = {2022}, author = {Chen, Q and Dharmaraj, T and Cai, PC and Burgener, EB and Haddock, NL and Spakowitz, AJ and Bollyky, PL}, title = {Bacteriophage and Bacterial Susceptibility, Resistance, and Tolerance to Antibiotics.}, journal = {Pharmaceutics}, volume = {14}, number = {7}, pages = {}, pmid = {35890320}, issn = {1999-4923}, support = {K24 AI166718/AI/NIAID NIH HHS/United States ; R01 HL148184/HL/NHLBI NIH HHS/United States ; T32 GM139791/GM/NIGMS NIH HHS/United States ; T32 HL129970/HL/NHLBI NIH HHS/United States ; }, abstract = {Bacteriophages, viruses that infect and replicate within bacteria, impact bacterial responses to antibiotics in complex ways. Recent studies using lytic bacteriophages to treat bacterial infections (phage therapy) demonstrate that phages can promote susceptibility to chemical antibiotics and that phage/antibiotic synergy is possible. However, both lytic and lysogenic bacteriophages can contribute to antimicrobial resistance. In particular, some phages mediate the horizontal transfer of antibiotic resistance genes between bacteria via transduction and other mechanisms. In addition, chronic infection filamentous phages can promote antimicrobial tolerance, the ability of bacteria to persist in the face of antibiotics. In particular, filamentous phages serve as structural elements in bacterial biofilms and prevent the penetration of antibiotics. Over time, these contributions to antibiotic tolerance favor the selection of resistance clones. Here, we review recent insights into bacteriophage contributions to antibiotic susceptibility, resistance, and tolerance. We discuss the mechanisms involved in these effects and address their impact on bacterial fitness.}, }
@article {pmid35889177, year = {2022}, author = {Florent, P and Cauchie, HM and Herold, M and Jacquet, S and Ogorzaly, L}, title = {Soil pH, Calcium Content and Bacteria as Major Factors Responsible for the Distribution of the Known Fraction of the DNA Bacteriophage Populations in Soils of Luxembourg.}, journal = {Microorganisms}, volume = {10}, number = {7}, pages = {}, pmid = {35889177}, issn = {2076-2607}, support = {PRIDE15/10623093//Fonds National de la Recherche/ ; }, abstract = {Bacteriophages participate in soil life by influencing bacterial community structure and function, biogeochemical cycling and horizontal gene transfer. Despite their great abundance, diversity, and importance in microbial processes, they remain little explored in environmental studies. The influence of abiotic factors on the persistence of bacteriophages is now recognized; however, it has been mainly studied under experimental conditions. This study aimed to determine whether the abiotic factors well-known to influence bacteriophage persistence also control the natural distribution of the known DNA bacteriophage populations. To this end, soil from eight study sites including forests and grasslands located in the Attert River basin (Grand Duchy of Luxembourg) were sampled, covering different soil and land cover characteristics. Shotgun metagenomics, reference-based bioinformatics and statistical analyses allowed characterising the diversity of known DNA bacteriophage and bacterial communities. After combining soil properties with the identified DNA bacteriophage populations, our in-situ study highlighted the influence of pH and calcium cations on the diversity of the known fraction of the soil DNA bacteriophages. More interestingly, significant relationships were established between bacteriophage and bacterial populations. This study provides new insights into the importance of abiotic and biotic factors in the distribution of DNA bacteriophages and the natural ecology of terrestrial bacteriophages.}, }
@article {pmid35889093, year = {2022}, author = {Yamamoto, H and Uesaka, K and Tsuzuki, Y and Yamakawa, H and Itoh, S and Fujita, Y}, title = {Comparative Genomic Analysis of the Marine Cyanobacterium Acaryochloris marina MBIC10699 Reveals the Impact of Phycobiliprotein Reacquisition and the Diversity of Acaryochloris Plasmids.}, journal = {Microorganisms}, volume = {10}, number = {7}, pages = {}, pmid = {35889093}, issn = {2076-2607}, support = {19K21143//Japan Society for the Promotion of Science/ ; 17K07440//Japan Society for the Promotion of Science/ ; 20K06684//Japan Society for the Promotion of Science/ ; 16H04754//Japan Society for the Promotion of Science/ ; 18K19173//Japan Society for the Promotion of Science/ ; 20H03196//Japan Society for the Promotion of Science/ ; 20K06542//Japan Society for the Promotion of Science/ ; JPMJPF2102//Japan Science and Technology Agency/ ; }, abstract = {Acaryochloris is a marine cyanobacterium that synthesizes chlorophyll d, a unique chlorophyll that absorbs far-red lights. Acaryochloris is also characterized by the loss of phycobiliprotein (PBP), a photosynthetic antenna specific to cyanobacteria; however, only the type-strain A. marina MBIC11017 retains PBP, suggesting that PBP-related genes were reacquired through horizontal gene transfer (HGT). Acaryochloris is thought to have adapted to various environments through its huge genome size and the genes acquired through HGT; however, genomic information on Acaryochloris is limited. In this study, we report the complete genome sequence of A. marina MBIC10699, which was isolated from the same area of ocean as A. marina MBIC11017 as a PBP-less strain. The genome of A.marina MBIC10699 consists of a 6.4 Mb chromosome and four large plasmids totaling about 7.6 Mb, and the phylogenic analysis shows that A.marina MBIC10699 is the most closely related to A. marina MBIC11017 among the Acaryochloris species reported so far. Compared with A. marina MBIC11017, the chromosomal genes are highly conserved between them, while the genes encoded in the plasmids are significantly diverse. Comparing these genomes provides clues as to how the genes for PBPs were reacquired and what changes occurred in the genes for photosystems during evolution.}, }
@article {pmid35889069, year = {2022}, author = {Bukhari, SAR and Irfan, M and Ahmad, I and Chen, L}, title = {Comparative Genomics and Pan-Genome Driven Prediction of a Reduced Genome of Akkermansia muciniphila.}, journal = {Microorganisms}, volume = {10}, number = {7}, pages = {}, pmid = {35889069}, issn = {2076-2607}, support = {RGP.02-87-43//King Khalid University/ ; 31572150//National Natural Science Foundation of China/ ; }, abstract = {Akkermanisia muciniphila imparts important health benefits and is considered a next-generation probiotic. It is imperative to understand the genomic diversity and metabolic potential of the species for safer applications as probiotics. As it resides with both health-promoting and pathogenic bacteria, understanding the evolutionary patterns are crucial, but this area remains largely unexplored. Moreover, pan-genome has previously been established based on only a limited number of strains and without careful strain selection. The pan-genomics have become very important for understanding species diversity and evolution. In the current study, a systematic approach was used to find a refined pan-genome profile of A. muciniphila by excluding too-diverse strains based on average nucleotide identity-based species demarcation. The strains were divided into four phylogroups using a variety of clustering techniques. Horizontal gene transfer and recombination patterns were also elucidated. Evolutionary patterns revealed that different phylogroups were expanding differently. Furthermore, a comparative evaluation of the metabolic potential of the pan-genome and its subsections was performed. Lastly, the study combines functional annotation, persistent genome, and essential genes to devise an approach to determine a minimal genome that can systematically remove unwanted genes, including virulent factors. The selection of one strain to be used as a chassis for the prediction of a reduced genome was very carefully performed by analyzing several genomic parameters, including the number of unique genes and the resistance and pathogenic potential of the strains. The strategy could be applied to other microbes, including human-associated microbiota, towards a common goal of predicting a minimal or a reduced genome.}, }
@article {pmid35889010, year = {2022}, author = {Levi, G and Lurie-Weinberger, M and Keren-Paz, A and Andremont, AO and Schwartz, D and Carmeli, Y}, title = {Unraveling the Diversity of Co-Colonization by CPE.}, journal = {Microorganisms}, volume = {10}, number = {7}, pages = {}, pmid = {35889010}, issn = {2076-2607}, abstract = {Antibiotic-resistant bacteria, and more specifically, carbapenem-producing Enterobacterales (CPE) strains, are increasing worldwide. Despite their growing prevalence, in most high-income countries, the detection of CPE is still considered a low-frequency event. Sporadically, patients co-colonized with distinct CPE strains and/or different carbapenemase enzymes are detected. In this paper, we present three cases that illustrate the underlying mechanisms of co-colonization, focusing on horizontal gene transfer (HGT) and patient-to-patient transmission. We also demonstrate the diversity of CPE species and discuss the potential consequences of co-colonization.}, }
@article {pmid35884226, year = {2022}, author = {Costa, M and Meirinhos, C and Cunha, E and Gomes, D and Pereira, M and Dias, R and Tavares, L and Oliveira, M}, title = {Nisin Mutant Prevention Concentration and the Role of Subinhibitory Concentrations on Resistance Development by Diabetic Foot Staphylococci.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {7}, pages = {}, pmid = {35884226}, issn = {2079-6382}, support = {PTDC/SAUINF/28466/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; }, abstract = {The most prevalent microorganism in diabetic foot infections (DFI) is Staphylococcus aureus, an important multidrug-resistant pathogen. The antimicrobial peptide nisin is a promising compound for DFI treatment, being effective against S. aureus. However, to avoid the selection of resistant mutants, correct drug therapeutic doses must be established, being also important to understand if nisin subinhibitory concentrations (subMIC) can potentiate resistant genes transfer between clinical isolates or mutations in genes associated with nisin resistance. The mutant selection window (MSW) of nisin was determined for 23 DFI S. aureus isolates; a protocol aiming to prompt vanA horizontal transfer between enterococci to clinical S. aureus was performed; and nisin subMIC effect on resistance evolution was assessed through whole-genome sequencing (WGS) applied to isolates subjected to a MEGA-plate assay. MSW ranged from 5-360 μg/mL for two isolates, from 5-540 μg/mL for three isolates, and from 5-720 μg/mL for one isolate. In the presence of nisin subMIC values, no transconjugants were obtained, indicating that nisin does not seem to promote vanA transfer. Finally, WGS analysis showed that incubation in the presence of nisin subMIC did not promote the occurrence of significant mutations in genes related to nisin resistance, supporting nisin application to DFI treatment.}, }
@article {pmid35884138, year = {2022}, author = {Thacharodi, A and Lamont, IL}, title = {Aminoglycoside-Modifying Enzymes Are Sufficient to Make Pseudomonas aeruginosa Clinically Resistant to Key Antibiotics.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {7}, pages = {}, pmid = {35884138}, issn = {2079-6382}, abstract = {Aminoglycosides are widely used to treat infections of Pseudomonas aeruginosa. Genes encoding aminoglycoside-modifying enzymes (AMEs), acquired by horizontal gene transfer, are commonly associated with aminoglycoside resistance, but their effects have not been quantified. The aim of this research was to determine the extent to which AMEs increase the antibiotic tolerance of P. aeruginosa. Bioinformatics analysis identified AME-encoding genes in 48 out of 619 clinical isolates of P. aeruginosa, with ant(2')-Ia and aac(6')-Ib3, which are associated with tobramcyin and gentamicin resistance, being the most common. These genes and aph(3')-VIa (amikacin resistance) were deleted from antibiotic-resistant strains. Antibiotic minimum inhibitory concentrations (MICs) were reduced by up to 64-fold, making the mutated bacteria antibiotic-sensitive in several cases. Introduction of the same genes into four antibiotic-susceptible P. aeruginosa strains increased the MIC by up to 128-fold, making the bacteria antibiotic-resistant in all cases. The cloned genes also increased the MIC in mutants lacking the MexXY-OprM efflux pump, which is an important contributor to aminoglycoside resistance, demonstrating that AMEs and this efflux pump act independently in determining levels of aminoglycoside tolerance. Quantification of the effects of AMEs on antibiotic susceptibility demonstrates the large effect that these enzymes have on antibiotic resistance.}, }
@article {pmid35882476, year = {2022}, author = {Deekshit, VK and Srikumar, S}, title = {'To be, or not to be'-The dilemma of 'silent' antimicrobial resistance genes in bacteria.}, journal = {Journal of applied microbiology}, volume = {133}, number = {5}, pages = {2902-2914}, doi = {10.1111/jam.15738}, pmid = {35882476}, issn = {1365-2672}, support = {G00003366//Start-Up Grant/ ; }, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology/metabolism ; Drug Resistance, Bacterial/genetics ; Bacteria/metabolism ; Gene Transfer, Horizontal ; *Bacterial Infections/drug therapy ; }, abstract = {Antimicrobial resistance is a serious threat to public health that dramatically undermines our ability to treat bacterial infections. Microorganisms exhibit resistance to different drug classes by acquiring resistance determinants through multiple mechanisms including horizontal gene transfer. The presence of drug resistance genotypes is mostly associated with corresponding phenotypic resistance against the particular antibiotic. However, bacterial communities harbouring silent antimicrobial resistance genes-genes whose presence is not associated with a corresponding resistant phenotype do exist. Under suitable conditions, the expression pattern of such genes often revert and regain resistance and could potentially lead to therapeutic failure. We often miss the presence of silent genes, since the current experimental paradigms are focused on resistant strains. Therefore, the knowledge on the prevalence, importance and mechanism of silent antibiotic resistance genes in bacterial pathogens are very limited. Silent genes, therefore, provide an additional level of complexity in the war against drug-resistant bacteria, reminding us that not only phenotypically resistant strains but also susceptible strains should be carefully investigated. In this review, we discuss the presence of silent antimicrobial resistance genes in bacteria, their relevance and their importance in public health.}, }
@article {pmid35879957, year = {2022}, author = {Nakazato, G and Bello-Toledo, HM and Zhang, A and Stehling, EG}, title = {Editorial: Molecular Characterization of Clinically Important Gram-Negative Bacteria Recovered From the Environment: Antimicrobial Resistance, Virulence and Epidemiology.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {962840}, doi = {10.3389/fmicb.2022.962840}, pmid = {35879957}, issn = {1664-302X}, }
@article {pmid35879588, year = {2023}, author = {Rahman, Z and Dandekar, MP}, title = {Implication of Paraprobiotics in Age-Associated Gut Dysbiosis and Neurodegenerative Diseases.}, journal = {Neuromolecular medicine}, volume = {25}, number = {1}, pages = {14-26}, pmid = {35879588}, issn = {1559-1174}, mesh = {Aged ; Humans ; *Neurodegenerative Diseases/therapy ; Dysbiosis/therapy ; *Probiotics/therapeutic use ; Prebiotics ; *Gastrointestinal Microbiome ; }, abstract = {Neurodegenerative diseases, including Alzheimer's and Parkinson's disease, are major age-related concerns in elderly people. Since no drug fully addresses the progression of neurodegenerative diseases, advance treatment strategies are urgently needed. Several studies have noted the senescence of immune system and the perturbation of gut microbiota in the aged population. In recent years, the role of gut microbiota has been increasingly studied in the manifestation of age-related CNS disorders. In this context, prebiotics, probiotics, and paraprobiotics are reported to improve the behavioural and neurobiological abnormalities in elderly patients. As live microbiota, prescribed in the form of probiotics, shows some adverse effects like sepsis, translocation, and horizontal gene transfer, paraprobiotics could be a possible alternative strategy in designing microbiome-based therapeutics. This review describes the health-beneficial effects of paraprobiotics in age-associated neurodegenerative diseases.}, }
@article {pmid35877768, year = {2022}, author = {Gibson, PS and Bexkens, E and Zuber, S and Cowley, LA and Veening, JW}, title = {The acquisition of clinically relevant amoxicillin resistance in Streptococcus pneumoniae requires ordered horizontal gene transfer of four loci.}, journal = {PLoS pathogens}, volume = {18}, number = {7}, pages = {e1010727}, pmid = {35877768}, issn = {1553-7374}, mesh = {*Amoxicillin/metabolism/pharmacology ; Anti-Bacterial Agents/metabolism/pharmacology ; Bacterial Proteins/genetics/metabolism ; Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; Penicillin Resistance/genetics ; Penicillin-Binding Proteins/genetics ; *Streptococcus pneumoniae/metabolism ; }, abstract = {Understanding how antimicrobial resistance spreads is critical for optimal application of new treatments. In the naturally competent human pathogen Streptococcus pneumoniae, resistance to β-lactam antibiotics is mediated by recombination events in genes encoding the target proteins, resulting in reduced drug binding affinity. However, for the front-line antibiotic amoxicillin, the exact mechanism of resistance still needs to be elucidated. Through successive rounds of transformation with genomic DNA from a clinically resistant isolate, we followed amoxicillin resistance development. Using whole genome sequencing, we showed that multiple recombination events occurred at different loci during one round of transformation. We found examples of non-contiguous recombination, and demonstrated that this could occur either through multiple D-loop formation from one donor DNA molecule, or by the integration of multiple DNA fragments. We also show that the final minimum inhibitory concentration (MIC) differs depending on recipient genome, explained by differences in the extent of recombination at key loci. Finally, through back transformations of mutant alleles and fluorescently labelled penicillin (bocillin-FL) binding assays, we confirm that pbp1a, pbp2b, pbp2x, and murM are the main resistance determinants for amoxicillin resistance, and that the order of allele uptake is important for successful resistance evolution. We conclude that recombination events are complex, and that this complexity contributes to the highly diverse genotypes of amoxicillin-resistant pneumococcal isolates.}, }
@article {pmid35876510, year = {2022}, author = {Nusrin, S and Asad, A and Hayat, S and Islam, B and Begum, R and Nabila, FH and Islam, Z}, title = {Multiple Mechanisms Confer Resistance to Azithromycin in Shigella in Bangladesh: a Comprehensive Whole Genome-Based Approach.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0074122}, pmid = {35876510}, issn = {2165-0497}, support = {K43 TW011447/TW/FIC NIH HHS/United States ; D43 TW010540/TW/FIC NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Azithromycin/pharmacology ; Bangladesh ; Drug Resistance, Bacterial/genetics ; *Dysentery, Bacillary/drug therapy ; Humans ; Macrolides/pharmacology ; Microbial Sensitivity Tests ; *Shigella/genetics ; }, abstract = {Shigella is the second leading cause of diarrheal deaths worldwide. Azithromycin (AZM) is a potential treatment option for Shigella infection; however, the recent emergence of AZM resistance in Shigella threatens the current treatment strategy. Therefore, we conducted a comprehensive whole genome-based approach to identify the mechanism(s) of AZM resistance in Shigella. We performed antimicrobial susceptibility tests, polymerase chain reaction (PCR), Sanger (amplicon) sequencing, and whole genome-based bioinformatics approaches to conduct the study. Fifty-seven (38%) of the Shigella isolates examined were AZM resistant; Shigella sonnei exhibited the highest rate of resistance against AZM (80%). PCR amplification for 15 macrolide resistance genes (MRGs) followed by whole-genome analysis of 13 representative Shigella isolates identified two AZM-modifying genes, mph(A) (in all Shigella isolates resistant to AZM) and mph(E) (in 2 AZM-resistant Shigella isolates), as well as one 23S rRNA-methylating gene, erm(B) (41% of AZM-resistant Shigella isolates) and one efflux pump mediator gene, msr(E) [in the same two Shigella isolates that harbored the mph(E) gene]. This is the first report of msr(E) and mph(E) genes in Shigella. Moreover, we found that an IncFII-type plasmid predominates and can possess all four MRGs. We also detected two plasmid-borne resistance gene clusters: IS26-mph(A)-mrx(A)-mph(R)(A)-IS6100, which is linked to global dissemination of MRGs, and mph(E)-msr(E)-IS482-IS6, which is reported for the first time in Shigella. In conclusion, this study demonstrates that MRGs in association with pathogenic IS6 family insertion sequences generate resistance gene clusters that propagate through horizontal gene transfer (HGT) in Shigella. IMPORTANCE Shigella can frequently transform into a superbug due to uncontrolled and rogue administration of antibiotics and the emergence of HGT of antimicrobial resistance factors. The advent of AZM resistance in Shigella has become a serious concern in the treatment of shigellosis. However, there is an obvious scarcity of clinical data and research on genetic mechanisms that induce AZM resistance in Shigella, particularly in low- and middle-income countries. Therefore, this study is an approach to raise the alarm for the next lifeline. We show that two key MRGs [mph(A) and erm(B)] and the newly identified MRGs [mph(E) and msr(E)], with their origination in plasmid-borne pathogenic islands, are fundamental mechanisms of AZM resistance in Shigella in Bangladesh. Overall, this study predicts an abrupt decrease in the effectiveness of AZM against Shigella in the very near future and suggests prompt focus on seeking a more effective treatment alternative to AZM for shigellosis.}, }
@article {pmid35876475, year = {2022}, author = {Yong, M and Chen, Y and Oo, G and Chang, KC and Chu, WHW and Teo, J and Venkatachalam, I and Thevasagayam, NM and Sridatta, PSR and Koh, V and Marcoleta, AE and Chen, H and Nagarajan, N and Kalisvar, M and Ng, OT and Gan, YH}, title = {Dominant Carbapenemase-Encoding Plasmids in Clinical Enterobacterales Isolates and Hypervirulent Klebsiella pneumoniae, Singapore.}, journal = {Emerging infectious diseases}, volume = {28}, number = {8}, pages = {1578-1588}, pmid = {35876475}, issn = {1080-6059}, mesh = {Anti-Bacterial Agents ; Bacterial Proteins/genetics ; Humans ; *Klebsiella Infections/epidemiology/microbiology ; *Klebsiella pneumoniae ; Plasmids/genetics ; Singapore/epidemiology ; beta-Lactamases/genetics ; }, abstract = {Dissemination of carbapenemase-encoding plasmids by horizontal gene transfer in multidrug-resistant bacteria is the major driver of rising carbapenem-resistance, but the conjugative mechanics and evolution of clinically relevant plasmids are not yet clear. We performed whole-genome sequencing on 1,215 clinical Enterobacterales isolates collected in Singapore during 2010-2015. We identified 1,126 carbapenemase-encoding plasmids and discovered pKPC2 is becoming the dominant plasmid in Singapore, overtaking an earlier dominant plasmid, pNDM1. pKPC2 frequently conjugates with many Enterobacterales species, including hypervirulent Klebsiella pneumoniae, and maintains stability in vitro without selection pressure and minimal adaptive sequence changes. Furthermore, capsule and decreasing taxonomic relatedness between donor and recipient pairs are greater conjugation barriers for pNDM1 than pKPC2. The low fitness costs pKPC2 exerts in Enterobacterales species indicate previously undetected carriage selection in other ecological settings. The ease of conjugation and stability of pKPC2 in hypervirulent K. pneumoniae could fuel spread into the community.}, }
@article {pmid35870604, year = {2022}, author = {Darphorn, TS and Brul, S and Ter Kuile, BH}, title = {Genetic editing of multi-resistance plasmids in Escherichia coli isolated from meat during transfer.}, journal = {Plasmid}, volume = {122}, number = {}, pages = {102640}, doi = {10.1016/j.plasmid.2022.102640}, pmid = {35870604}, issn = {1095-9890}, mesh = {Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; *Escherichia coli/genetics ; *Escherichia coli Infections ; Gene Transfer, Horizontal ; Humans ; Meat ; Plasmids/genetics ; }, abstract = {Resistance plasmids mediate the rapid spread of antimicrobial resistance, which poses a threat to veterinary and human healthcare. This study addresses the question whether resistance plasmids from Escherichia coli isolated from foodstuffs always transfer unchanged to recipient E. coli cells, or that genetic editing can occur. Strains containing between one and five different plasmids were co-incubated with a standard recipient strain. Plasmids isolated from transconjugant strains were sequenced using short and long read technologies and compared to the original plasmids from the donor strains. After one hour of co-incubation only a single plasmid was transferred from donor to recipient strains. If the donor possessed several plasmids, longer co-incubation resulted in multiple plasmids being transferred. Transferred plasmids showed mutations, mostly in mobile genetic elements, in the conjugative transfer gene pilV and in genes involved in plasmid maintenance. In one transconjugant, a resistance cluster encoding tetracycline resistance was acquired by the IncI1 plasmid from the IncX1 plasmid that was also present in the donor strain, but that was not transferred. A single plasmid transferred twelve times back and forth between E. coli strains resulted in a fully conserved plasmid with no mutations, apart from repetitive rearrangements of pilV from and back to its original conformation in the donor strain. The overall outcome suggests that some genetic mutations and rearrangements can occur during plasmid transfer. The possibility of such mutations should be taken into consideration in epidemiological research aimed at attribution of resistance to specific sources.}, }
@article {pmid35865929, year = {2022}, author = {Li, Y and Wang, Y and Liu, J}, title = {Genomic Insights Into the Interspecific Diversity and Evolution of Mobiluncus, a Pathogen Associated With Bacterial Vaginosis.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {939406}, pmid = {35865929}, issn = {1664-302X}, abstract = {Bacterial vaginosis (BV) is a common vaginal infection and has been associated with increased risk for a wide array of health issues. BV is linked with a variety of heterogeneous pathogenic anaerobic bacteria, among which Mobiluncus is strongly associated with BV diagnosis. However, their genetic features, pathogenicity, interspecific diversity, and evolutionary characters have not been illustrated at genomic level. The current study performed phylogenomic and comparative genomic analyses of Mobiluncus. Phylogenomic analyses revealed remarkable phylogenetic distinctions among different species. Compared with M. curtisii, M. mulieris had a larger genome and pangenome size with more insertion sequences but less CRISPR-Cas systems. In addition, these two species were diverse in profile of virulence factors, but harbored similar antibiotic resistance genes. Statistically different functional genome profiles between strains from the two species were determined, as well as correlations of some functional genes/pathways with putative pathogenicity. We also showed that high levels of horizontal gene transfer might be an important strategy for species diversification and pathogenicity. Collectively, this study provides the first genome sequence level description of Mobiluncus, and may shed light on its virulence/pathogenicity, functional diversification, and evolutionary dynamics. Our study could facilitate the further investigations of this important pathogen, and might improve the future treatment of BV.}, }
@article {pmid35862819, year = {2022}, author = {Nies, F and Springstein, BL and Hanke, DM and Dagan, T}, title = {Natural Competence in the Filamentous, Heterocystous Cyanobacterium Chlorogloeopsis fritschii PCC 6912.}, journal = {mSphere}, volume = {7}, number = {4}, pages = {e0099721}, pmid = {35862819}, issn = {2379-5042}, mesh = {*Cyanobacteria/genetics/metabolism ; Gene Transfer, Horizontal ; Photosynthesis ; }, abstract = {Lateral gene transfer plays an important role in the evolution of genetic diversity in prokaryotes. DNA transfer via natural transformation depends on the ability of recipient cells to actively transport DNA from the environment into the cytoplasm, termed natural competence, which relies on the presence of type IV pili and other competence proteins. Natural competence has been described in cyanobacteria for several organisms, including unicellular and filamentous species. However, natural competence in cyanobacteria that differentiate specialized cells for N2-fixation (heterocysts) and form branching or multiseriate cell filaments (termed subsection V) remains unknown. Here, we show that genes essential for natural competence are conserved in subsection V cyanobacteria. Furthermore, using the replicating plasmid pRL25C, we experimentally demonstrate natural competence in a subsection V organism: Chlorogloeopsis fritschii PCC 6912. Our results suggest that natural competence is a common trait in cyanobacteria forming complex cell filament morphologies. IMPORTANCE Cyanobacteria are crucial players in the global biogeochemical cycles, where they contribute to CO2- and N2-fixation. Their main ecological significance is the primary biomass production owing to oxygenic photosynthesis. Cyanobacteria are a diverse phylum, in which the most complex species differentiate specialized cell types and form true-branching or multiseriate cell filament structures (termed subsection V cyanobacteria). These bacteria are considered a peak in the evolution of prokaryotic multicellularity. Among others, species in that group inhabit fresh and marine water habitats, soil, and extreme habitats such as thermal springs. Here, we show that the core genes required for natural competence are frequent in subsection V cyanobacteria and demonstrate for the first time natural transformation in a member of subsection V. The prevalence of natural competence has implications for the role of DNA acquisition in the genome evolution of cyanobacteria. Furthermore, the presence of mechanisms for natural transformation opens up new possibilities for the genetic modification of subsection V cyanobacteria.}, }
@article {pmid35862683, year = {2022}, author = {Baseggio, L and Rudenko, O and Engelstädter, J and Barnes, AC}, title = {The Evolution of a Specialized, Highly Virulent Fish Pathogen through Gene Loss and Acquisition of Host-Specific Survival Mechanisms.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {14}, pages = {e0022222}, pmid = {35862683}, issn = {1098-5336}, mesh = {Animals ; *Fish Diseases/microbiology ; Fishes/microbiology ; *Gram-Negative Bacterial Infections/microbiology ; Photobacterium/metabolism ; Phylogeny ; }, abstract = {Photobacterium damselae comprises two subspecies, P. damselae subsp. damselae and P. damselae subsp. piscicida, that contrast remarkably despite their taxonomic relationship. The former is opportunistic and free-living but can cause disease in compromised individuals from a broad diversity of taxa, while the latter is a highly specialized, primary fish pathogen. Here, we employ new closed curated genome assemblies from Australia to estimate the global phylogenetic structure of the species P. damselae. We identify genes responsible for the shift from an opportunist to a host-adapted fish pathogen, potentially via an arthropod vector as fish-to-fish transmission was not achieved in repeated cohabitation challenges despite high virulence for Seriola lalandi. Acquisition of ShdA adhesin and of thiol peroxidase may have allowed the environmental, generalist ancestor to colonize zooplankton and to occasionally enter in fish host sentinel cells. As dependence on the host has increased, P. damselae has lost nonessential genes, such as those related to nitrite and sulfite reduction, urea degradation, a type 6 secretion system (T6SS) and several toxin-antitoxin (TA) systems. Similar to the evolution of Yersinia pestis, the loss of urease may be the crucial event that allowed the pathogen to stably colonize zooplankton vectors. Acquisition of host-specific genes, such as those required to form a sialic acid capsule, was likely necessary for the emergent P. damselae subsp. piscicida to become a highly specialized, facultative intracellular fish pathogen. Processes that have shaped P. damselae subsp. piscicida from subsp. damselae are similar to those underlying evolution of Yersinia pestis from Y. pseudotuberculosis. IMPORTANCE Photobacterium damselae subsp. damselae is a ubiquitous marine bacterium and opportunistic pathogen of compromised hosts of diverse taxa. In contrast, its sister subspecies P. damselae subsp. piscicida (Pdp) is highly virulent in fish. Pdp has evolved from a single subclade of Pdd through gene loss and acquisition. We show that fish-to-fish transmission does not occur in repeated infection models in the primary host, Seriola lalandi, and present genomic evidence for vector-borne transmission, potentially via zooplankton. The broad genomic changes from generalist Pdd to specialist Pdp parallel those of the environmental opportunist Yersinia pseudotuberculosis to vector-borne plague bacterium Y. pestis and demonstrate that evolutionary processes in bacterial pathogens are universal between the terrestrial and marine biosphere.}, }
@article {pmid35861439, year = {2022}, author = {Zangishei, Z and Annacondia, ML and Gundlach, H and Didriksen, A and Bruckmüller, J and Salari, H and Krause, K and Martinez, G}, title = {Parasitic plant small RNA analyses unveil parasite-specific signatures of microRNA retention, loss, and gain.}, journal = {Plant physiology}, volume = {190}, number = {2}, pages = {1242-1259}, pmid = {35861439}, issn = {1532-2548}, mesh = {Animals ; *Cuscuta/genetics ; *MicroRNAs/genetics ; *Orobanche/genetics ; *Parasites ; RNA, Plant/genetics ; }, abstract = {Parasitism is a successful life strategy that has evolved independently in several families of vascular plants. The genera Cuscuta and Orobanche represent examples of the two profoundly different groups of parasites: one parasitizing host shoots and the other infecting host roots. In this study, we sequenced and described the overall repertoire of small RNAs from Cuscuta campestris and Orobanche aegyptiaca. We showed that C. campestris contains a number of novel microRNAs (miRNAs) in addition to a conspicuous retention of miRNAs that are typically lacking in other Solanales, while several typically conserved miRNAs seem to have become obsolete in the parasite. One new miRNA appears to be derived from a horizontal gene transfer event. The exploratory analysis of the miRNA population (exploratory due to the absence of a full genomic sequence for reference) from the root parasitic O. aegyptiaca also revealed a loss of a number of miRNAs compared to photosynthetic species from the same order. In summary, our study shows partly similar evolutionary signatures in the RNA silencing machinery in both parasites. Our data bear proof for the dynamism of this regulatory mechanism in parasitic plants.}, }
@article {pmid35858561, year = {2022}, author = {Douanne, N and Dong, G and Amin, A and Bernardo, L and Blanchette, M and Langlais, D and Olivier, M and Fernandez-Prada, C}, title = {Leishmania parasites exchange drug-resistance genes through extracellular vesicles.}, journal = {Cell reports}, volume = {40}, number = {3}, pages = {111121}, doi = {10.1016/j.celrep.2022.111121}, pmid = {35858561}, issn = {2211-1247}, support = {173450//CIHR/Canada ; 168959//CIHR/Canada ; }, mesh = {Animals ; Drug Resistance/genetics ; Eukaryota ; *Extracellular Vesicles/metabolism ; *Leishmania/genetics/metabolism ; *Parasites ; }, abstract = {Leishmania are eukaryotic parasites that have retained the ability to produce extracellular vesicles (EVs) through evolution. To date, it has been unclear if different DNA entities could be associated with Leishmania EVs and whether these could constitute a mechanism of horizontal gene transfer (HGT). Herein, we investigate the DNA content of EVs derived from drug-resistant parasites, as well as the EVs' potential to act as shuttles for DNA transfer. Next-generation sequencing and PCR assays confirm the enrichment of amplicons carrying drug-resistance genes associated with EVs. Transfer assays of drug-resistant EVs highlight a significant impact on the phenotype of recipient parasites induced by the expression of the transferred DNA. Recipient parasites display an enhanced growth and better control of oxidative stress. We provide evidence that eukaryotic EVs function as efficient mediators in HGT, thereby facilitating the transmission of drug-resistance genes and increasing the fitness of cells when encountering stressful environments.}, }
@article {pmid35856561, year = {2022}, author = {Munke, A and Kimura, K and Tomaru, Y and Wang, H and Yoshida, K and Mito, S and Hongo, Y and Okamoto, K}, title = {Primordial Capsid and Spooled ssDNA Genome Structures Unravel Ancestral Events of Eukaryotic Viruses.}, journal = {mBio}, volume = {13}, number = {4}, pages = {e0015622}, pmid = {35856561}, issn = {2150-7511}, mesh = {*Capsid/metabolism ; Capsid Proteins/genetics/metabolism ; Cryoelectron Microscopy ; DNA Viruses/genetics ; DNA, Single-Stranded/genetics ; Ecosystem ; Eukaryota/genetics ; Genome, Viral ; Phylogeny ; *Viruses/genetics ; }, abstract = {Marine algae viruses are important for controlling microorganism communities in the marine ecosystem and played fundamental roles during the early events of viral evolution. Here, we have focused on one major group of marine algae viruses, the single-stranded DNA (ssDNA) viruses from the Bacilladnaviridae family. We present the capsid structure of the bacilladnavirus Chaetoceros tenuissimus DNA virus type II (CtenDNAV-II), determined at 2.4-Å resolution. A structure-based phylogenetic analysis supported the previous theory that bacilladnaviruses have acquired their capsid protein via horizontal gene transfer from a ssRNA virus. The capsid protein contains the widespread virus jelly-roll fold but has additional unique features; a third β-sheet and a long C-terminal tail. Furthermore, a low-resolution reconstruction of the CtenDNAV-II genome revealed a partially spooled structure, an arrangement previously only described for dsRNA and dsDNA viruses. Together, these results exemplify the importance of genetic recombination for the emergence and evolution of ssDNA viruses and provide important insights into the underlying mechanisms that dictate genome organization. IMPORTANCE Single-stranded DNA (ssDNA) viruses are an extremely widespread group of viruses that infect diverse hosts from all three domains of life, consequently having great economic, medical, and ecological importance. In particular, bacilladnaviruses are highly abundant in marine sediments and greatly influence the dynamic appearance and disappearance of certain algae species. Despite the importance of ssDNA viruses and the last couple of years' advancements in cryo-electron microscopy, structural information on the genomes of ssDNA viruses remains limited. This paper describes two important achievements: (i) the first atomic structure of a bacilladnavirus capsid, which revealed that the capsid protein gene presumably was acquired from a ssRNA virus in early evolutionary events; and (ii) the structural organization of a ssDNA genome, which retains a spooled arrangement that previously only been observed for double-stranded viruses.}, }
@article {pmid35854227, year = {2022}, author = {Athanasouli, M and Rödelsperger, C}, title = {Analysis of repeat elements in the Pristionchus pacificus genome reveals an ancient invasion by horizontally transferred transposons.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {523}, pmid = {35854227}, issn = {1471-2164}, mesh = {Animals ; *DNA Transposable Elements/genetics ; Gene Transfer, Horizontal ; Genomics ; Retroelements/genetics ; *Rhabditida/genetics ; }, abstract = {BACKGROUND: Repetitive sequences and mobile elements make up considerable fractions of individual genomes. While transposition events can be detrimental for organismal fitness, repetitive sequences form an enormous reservoir for molecular innovation. In this study, we aim to add repetitive elements to the annotation of the Pristionchus pacificus genome and assess their impact on novel gene formation.<br><br>RESULTS: Different computational approaches define up to 24% of the P. pacificus genome as repetitive sequences. While retroelements are more frequently found at the chromosome arms, DNA transposons are distributed more evenly. We found multiple DNA transposons, as well as LTR and LINE elements with abundant evidence of expression as single-exon transcripts. When testing whether transposons disproportionately contribute towards new gene formation, we found that roughly 10-20% of genes across all age classes overlap transposable elements with the strongest trend being an enrichment of low complexity regions among the oldest genes. Finally, we characterized a horizontal gene transfer of Zisupton elements into diplogastrid nematodes. These DNA transposons invaded nematodes from eukaryotic donor species and experienced a recent burst of activity in the P. pacificus lineage.<br><br>CONCLUSIONS: The comprehensive annotation of repetitive elements in the P. pacificus genome builds a resource for future functional genomic analyses as well as for more detailed investigations of molecular innovations.}, }
@article {pmid35853593, year = {2022}, author = {Lu, T and Zhang, J and Su, T and Liang, X and Wei, Y and He, T}, title = {Coupled mechanism of enhanced and inhibitory effects of nanoscale zero-valent iron on methane production and antibiotic resistance genes in anaerobic digestion of swine manure.}, journal = {Bioresource technology}, volume = {360}, number = {}, pages = {127635}, doi = {10.1016/j.biortech.2022.127635}, pmid = {35853593}, issn = {1873-2976}, mesh = {Anaerobiosis ; Animals ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Iron/pharmacology ; *Manure ; Methane ; Swine ; }, abstract = {In this study, the turning point for nanoscale zero-valent iron's (NZVI) promotion and inhibition effects of methane production coupled with the reduction of antibiotic resistance genes (ARGs) was investigated. Adding 150 mmol/L NZVI increased methane production by maximum of 23.8 %, which was due to the chemical reaction producing H2 and enhancement of direct interspecies electron transfer (DIET) by NZVI. NZVI350 dramatically repressed methane generation by 48.0 %, which might be associated with the large quantity of reactive oxygen species (ROS) and excessive H2 inhibiting the functioning of microorganisms. The fate of ARGs was significantly related to daily methane production, indicating that the more methane production finally generated, the less the abundance of ARGs at last left. The reduction of ARGs was enhanced by maximum of 61.0 %, which was attributed to the inhibition of vertical gene transfer (VGT) and horizontal gene transfer (HGT) caused by steric hindrance associated with NZVI corrosion.}, }
@article {pmid35853453, year = {2022}, author = {Li, Y and Liu, Z and Liu, C and Shi, Z and Pang, L and Chen, C and Chen, Y and Pan, R and Zhou, W and Chen, XX and Rokas, A and Huang, J and Shen, XX}, title = {HGT is widespread in insects and contributes to male courtship in lepidopterans.}, journal = {Cell}, volume = {185}, number = {16}, pages = {2975-2987.e10}, pmid = {35853453}, issn = {1097-4172}, support = {R01 AI153356/AI/NIAID NIH HHS/United States ; R56 AI146096/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Butterflies/genetics ; Courtship ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Male ; Phylogeny ; }, abstract = {Horizontal gene transfer (HGT) is an important evolutionary force shaping prokaryotic and eukaryotic genomes. HGT-acquired genes have been sporadically reported in insects, a lineage containing >50% of animals. We systematically examined HGT in 218 high-quality genomes of diverse insects and found that they acquired 1,410 genes exhibiting diverse functions, including many not previously reported, via 741 distinct transfers from non-metazoan donors. Lepidopterans had the highest average number of HGT-acquired genes. HGT-acquired genes containing introns exhibited substantially higher expression levels than genes lacking introns, suggesting that intron gains were likely involved in HGT adaptation. Lastly, we used the CRISPR-Cas9 system to edit the prevalent unreported gene LOC105383139, which was transferred into the last common ancestor of moths and butterflies. In diamondback moths, males lacking LOC105383139 courted females significantly less. We conclude that HGT has been a major contributor to insect adaptation.}, }
@article {pmid35853206, year = {2022}, author = {Chowdhury, NN and Hicks, E and Wiesner, MR}, title = {Investigating and Modeling the Regulation of Extracellular Antibiotic Resistance Gene Bioavailability by Naturally Occurring Nanoparticles.}, journal = {Environmental science &amp; technology}, volume = {56}, number = {21}, pages = {15044-15053}, pmid = {35853206}, issn = {1520-5851}, support = {T32 ES021432/ES/NIEHS NIH HHS/United States ; }, mesh = {*Anti-Bacterial Agents/pharmacology ; Biological Availability ; Drug Resistance, Microbial/genetics ; Bacteria ; *Nanoparticles ; Deoxyribonuclease I ; }, abstract = {Extracellular antibiotic resistance genes (eARGs) are widespread in the environment and can genetically transform bacteria. This work examined the role of environmentally relevant nanoparticles (NPs) in regulating eARG bioavailability. eARGs extracted from antibiotic-resistant B. subtilis were incubated with nonresistant recipient B. subtilis cells. In the mixture, particle type (either humic acid coated nanoparticles (HASNPs) or their micron-sized counterpart (HASPs)), DNase I concentration, and eARG type were systematically varied. Transformants were counted on selective media. Particles decreased bacterial growth and eARG bioavailability in systems without nuclease. When DNase I was present (≥5 μg/mL), particles increased transformation via chromosomal (but not plasmid-borne) eARGs. HASNPs increased transformation more than HASPs, indicating that the smaller nanoparticle with greater surface area per volume is more effective in increasing eARG bioavailability. These results were also modeled via particle aggregation theory, which represented eARG-bacteria interactions as transport leading to collision, followed by attachment. Using attachment efficiency as a fitting factor, the model predicted transformant concentrations within 35% of experimental data. These results confirm the ability of NPs to increase eARG bioavailability and suggest that particle aggregation theory may be a simplified and suitable framework to broadly predict eARG uptake.}, }
@article {pmid35849537, year = {2022}, author = {Dimitriu, T}, title = {Evolution of horizontal transmission in antimicrobial resistance plasmids.}, journal = {Microbiology (Reading, England)}, volume = {168}, number = {7}, pages = {}, doi = {10.1099/mic.0.001214}, pmid = {35849537}, issn = {1465-2080}, mesh = {*Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Bacterial/genetics ; *Gene Transfer, Horizontal ; Plasmids/genetics ; }, abstract = {Mobile genetic elements (MGEs) are one of the main vectors for the spread of antimicrobial resistance (AMR) across bacteria, due to their ability to move horizontally between bacterial lineages. Horizontal transmission of AMR can increase AMR prevalence at multiple scales, from increasing the prevalence of infections by resistant bacteria to pathogen epidemics and worldwide spread of AMR across species. Among MGEs, conjugative plasmids are the main contributors to the spread of AMR. This review discusses the selective pressures acting on MGEs and their hosts to promote or limit the horizontal transmission of MGEs, the mechanisms by which transmission rates can evolve, and their implications for limiting the spread of AMR, with a focus on AMR plasmids.}, }
@article {pmid35849532, year = {2022}, author = {Zaayman, M and Wheatley, RM}, title = {Fitness costs of CRISPR-Cas systems in bacteria.}, journal = {Microbiology (Reading, England)}, volume = {168}, number = {7}, pages = {}, doi = {10.1099/mic.0.001209}, pmid = {35849532}, issn = {1465-2080}, mesh = {*Bacteria/genetics ; *CRISPR-Cas Systems ; Genome, Bacterial/genetics ; }, abstract = {CRISPR-Cas systems provide bacteria with both specificity and adaptability in defence against invading genetic elements. From a theoretical perspective, CRISPR-Cas systems confer many benefits. However, they are observed at an unexpectedly low prevalence across the bacterial domain. While these defence systems can be gained horizontally, fitness costs may lead to selection against their carriage. Understanding the source of CRISPR-related fitness costs will help us to understand the evolutionary dynamics of CRISPR-Cas systems and their role in shaping bacterial genome evolution. Here, we review our current understanding of the potential fitness costs associated with CRISPR-Cas systems. In addition to potentially restricting the acquisition of genetic material that could confer fitness benefits, we explore five alternative biological factors that from a theoretical perspective may influence the fitness costs associated with CRISPR-Cas system carriage: (1) the repertoire of defence mechanisms a bacterium has available to it, (2) the potential for a metabolic burden, (3) larger-scale population and environmental factors, (4) the phenomenon of self-targeting spacers, and (5) alternative non-defence roles for CRISPR-Cas.}, }
@article {pmid35849337, year = {2022}, author = {Laroussi, H and Aoudache, Y and Robert, E and Libante, V and Thiriet, L and Mias-Lucquin, D and Douzi, B and Roussel, Y and Chauvot de Beauchêne, I and Soler, N and Leblond-Bourget, N}, title = {Exploration of DNA processing features unravels novel properties of ICE conjugation in Gram-positive bacteria.}, journal = {Nucleic acids research}, volume = {50}, number = {14}, pages = {8127-8142}, pmid = {35849337}, issn = {1362-4962}, mesh = {*Bacterial Proteins/genetics/metabolism ; Binding Sites ; *Conjugation, Genetic ; *DNA Nucleotidyltransferases/genetics/metabolism ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; *Gram-Positive Bacteria/genetics ; *Interspersed Repetitive Sequences ; Plasmids/genetics ; }, abstract = {Integrative and conjugative elements (ICEs) are important drivers of horizontal gene transfer in prokaryotes. They are responsible for antimicrobial resistance spread, a major current health concern. ICEs are initially processed by relaxases that recognize the binding site of oriT sequence and nick at a conserved nic site. The ICESt3/Tn916/ICEBs1 superfamily, which is widespread among Firmicutes, encodes uncanonical relaxases belonging to a recently identified family called MOBT. This family is related to the rolling circle replication initiators of the Rep_trans family. The nic site of these MOBT relaxases is conserved but their DNA binding site is still unknown. Here, we identified the bind site of RelSt3, the MOBT relaxase from ICESt3. Unexpectedly, we found this bind site distantly located from the nic site. We revealed that the binding of the RelSt3 N-terminal HTH domain is required for efficient nicking activity. We also deciphered the role of RelSt3 in the initial and final stages of DNA processing during conjugation. Especially, we demonstrated a strand transfer activity, and the formation of covalent DNA-relaxase intermediate for a MOBT relaxase.}, }
@article {pmid35847067, year = {2022}, author = {Ott, LC and Mellata, M}, title = {Models for Gut-Mediated Horizontal Gene Transfer by Bacterial Plasmid Conjugation.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {891548}, pmid = {35847067}, issn = {1664-302X}, abstract = {The emergence of new antimicrobial resistant and virulent bacterial strains may pose a threat to human and animal health. Bacterial plasmid conjugation is a significant contributor to rapid microbial evolutions that results in the emergence and spread of antimicrobial resistance (AR). The gut of animals is believed to be a potent reservoir for the spread of AR and virulence genes through the horizontal exchange of mobile genetic elements such as plasmids. The study of the plasmid transfer process in the complex gut environment is limited due to the confounding factors that affect colonization, persistence, and plasmid conjugation. Furthermore, study of plasmid transfer in the gut of humans is limited to observational studies, leading to the need to identify alternate models that provide insight into the factors regulating conjugation in the gut. This review discusses key studies on the current models for in silico, in vitro, and in vivo modeling of bacterial conjugation, and their ability to reflect the gut of animals. We particularly emphasize the use of computational and in vitro models that may approximate aspects of the gut, as well as animal models that represent in vivo conditions to a greater extent. Directions on future research studies in the field are provided.}, }
@article {pmid35841879, year = {2022}, author = {Gonçalves, P and Gonçalves, C}, title = {Horizontal gene transfer in yeasts.}, journal = {Current opinion in genetics &amp; development}, volume = {76}, number = {}, pages = {101950}, doi = {10.1016/j.gde.2022.101950}, pmid = {35841879}, issn = {1879-0380}, mesh = {*Bacteria/genetics ; *Gene Transfer, Horizontal/genetics ; Phylogeny ; }, abstract = {Horizontal gene transfer (HGT), defined as the exchange of genetic material other than from parent to progeny, is very common in bacteria and appears to constitute the most important mechanism contributing to enlarge a species gene pool. However, in eukaryotes, HGT is certainly much less common and some early insufficiently consubstantiated cases involving bacterial donors led some to consider that it was unlikely to occur in eukaryotes outside the host/endosymbiont relationship. More recently, plenty of reports of interdomain HGT have seen the light based on the strictest criteria, many concerning filamentous fungi and yeasts. Here, we attempt to summarize the most prominent instances of HGT reported in yeasts as well as what we have been able to learn so far concerning frequency and distribution, mechanisms, barriers, function of horizontally acquired genes, and the role of HGT in domestication.}, }
@article {pmid35841790, year = {2022}, author = {Ji, H and Cai, Y and Wang, Z and Li, G and An, T}, title = {Sub-lethal photocatalysis promotes horizontal transfer of antibiotic resistance genes by conjugation and transformability.}, journal = {Water research}, volume = {221}, number = {}, pages = {118808}, doi = {10.1016/j.watres.2022.118808}, pmid = {35841790}, issn = {1879-2448}, mesh = {*Angiotensin Receptor Antagonists/pharmacology ; Angiotensin-Converting Enzyme Inhibitors/pharmacology ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Water ; }, abstract = {The spread of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in water is increasingly becoming a worldwide problem due to frequent recent major public health events. Herein, the horizontal ARG transfer mechanisms were studied under sub-lethal photocatalysis. The results show that ARGs had at most a 3- to 6-fold increase in the conjugative transfer frequency when only donor bacteria were induced with sub-lethal photocatalysis, while the frequency exhibited a trend toward inhibition when only the recipient bacteria were induced. However, when the donor or recipient bacteria were induced beforehand for a specific time, the frequency increased by a maximum of 10- to 22-fold. Moreover, the horizontal transfer frequency and its mechanism were related to the oxidative stress systems, ATP systems and the expression of related genes. Furthermore, the transformability of extracellular plasmids of the ARB and the contribution in horizontal transfer were also studied. Results show that the transformation frequency accounted for up to 50% of the total number of transconjugants, indicating that transformation might be a primary mode of horizontal ARG transfer by ARB in water. All of the above results demonstrate that sub-lethal photocatalysis will increase the frequency of horizontal gene transfer of ARGs through both conjugative transfer and the transformation pathway, which increases the risk of ARB in aquatic environments.}, }
@article {pmid35841431, year = {2022}, author = {Mitra, A and Acharya, K and Bhattacharya, A}, title = {Evolutionary analysis of globin domains from kinetoplastids.}, journal = {Archives of microbiology}, volume = {204}, number = {8}, pages = {493}, pmid = {35841431}, issn = {1432-072X}, support = {SRG/2020/000702//Science and Engineering Research Board/ ; }, mesh = {Amino Acid Sequence ; Codon ; *Gene Transfer, Horizontal ; *Globins/chemistry/genetics/metabolism ; Heme/chemistry/metabolism ; Phylogeny ; }, abstract = {Globin (Gb) domains function in sensing gaseous ligands like oxygen and nitric oxide. In recent years, Gb domain containing heme binding adenylate cyclases (OsAC or GbAC) emerged as significant modulator of Leishmania response to hypoxia and oxidative stress. During progression of life cycle stages, kinetoplastids experience altered condition in insect vectors or other hosts. Moreover, marked diversity in life style has been accounted among kinetoplastids. Distribution and abundance of Gb-domains vary between different groups of kinetoplastids. While in bodonoids, Gbs are not combined with any other functional domains, in trypanosomatids it is either fused with adenylate cyclase (AC) or oxidoreductase (OxR) domains. In salivarian trypanosomatids and Leishmania (Viannia) subtypes, no gene product featuring Gbs can be identified. In this context, evolution of Gb-domains in kinetoplastids was explored. GbOxR derived Gbs clustered with bacterial flavohemoglobins (fHb) including one fHb from Advenella, an endosymbiont of monoxeneous trypanosomatids. Codon adaptation and other evolutionary analysis suggested that OsAC (LmjF.28.0090), the solitary Gb-domain featuring gene product in Leishmania, was acquired via possible horizontal gene transfer. Substantial functional divergence was estimated between orthologues of genes encoding GbAC or GbOxR; an observation also reflected in structural alignment and heme-binding residue predictions. Orthologue-paralogue and synteny analysis indicated genomic reduction in GbOxR and GbAC loci for dixeneous trypanosomatids.}, }
@article {pmid35833268, year = {2022}, author = {Chouhan, B and Tak, N and Bissa, G and Adhikari, D and Barik, SK and Sprent, JI and James, EK and Jha, S and Gehlot, HS}, title = {Evolution of novel strains of Ensifer nodulating the invasive legume Leucaena leucocephala (Lam.) de Wit in different climatic regions of India through lateral gene transfer.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {9}, pages = {}, doi = {10.1093/femsec/fiac086}, pmid = {35833268}, issn = {1574-6941}, mesh = {DNA, Bacterial ; *Fabaceae ; Gene Transfer, Horizontal ; *Mesorhizobium ; Phylogeny ; RNA, Ribosomal, 16S ; *Rhizobiaceae ; *Rhizobium ; Root Nodules, Plant ; Soil ; Symbiosis ; }, abstract = {More than 200 root-nodule bacterial strains were isolated from Leucaena leucocephala growing at 42 sampling sites across 12 states and three union territories of India. Genetic diversity was observed among 114 strains from various climatic zones; based on recA, these were identified as strains of Ensifer, Mesorhizobium, Rhizobium, and Bradyrhizobium. In multilocus sequence analysis (MLSA) strains clustered into several novel clades and lineages. Ensifer were predominant nodulating genotype isolated from majority of alkaline soils, while Mesorhizobium and Rhizobium strains were isolated from a limited sampling in North-Eastern states with acidic soils. Positive nodulation assays of selected Ensifer representing different genetic combinations of housekeeping and sym genes suggested their broad host range within the closely related mimosoid genera Vachellia, Senegalia, Mimosa, and Prosopis. Leucaena selected diverse strains of Ensifer and Mesorhizobium as symbionts depending on available soil pH, climatic, and other edaphic conditions in India. Lateral gene transfer seems to play a major role in genetic diversification of Ensifer exhibited in terms of Old World vs. Neotropical genetic make-up and mixed populations at several sites. Although Neotropical Ensifer strains were most symbiotically effective on Leucaena, the native Ensifer are promiscuous and particularly well-adapted to a wide range of sampling sites with varied climates and edaphic factors.}, }
@article {pmid35817106, year = {2022}, author = {Zhai, H and Guo, Y and Zhang, L and Miao, Y and Wang, J}, title = {Presence of bromide and iodide promotes the horizontal transfer of antibiotic resistance genes during chlorination: A preliminary study.}, journal = {The Science of the total environment}, volume = {846}, number = {}, pages = {157250}, doi = {10.1016/j.scitotenv.2022.157250}, pmid = {35817106}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents/pharmacology ; Bromides ; Bromine ; Chlorine ; Drug Resistance, Microbial/genetics ; Escherichia coli/genetics ; *Escherichia coli K12 ; Gene Transfer, Horizontal ; Genes, Bacterial ; Halogenation ; Humans ; Iodides ; *Iodine ; Oxidants ; Plasmids ; }, abstract = {Chlorination was reported to have a great potential to increase horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs), which poses a great threat to global human health. Bromide (Br[-]) and iodide (I[-]) ions are widely spread ions in water and wastewater. In chlorination, Br[-] and I[-] can be oxidized to active bromine and iodine species. The influence of the co-existing different halogen oxidants (chlorine + bromine or iodine species) on HGT of ARGs were rarely investigated. In this study, the conjugative transfer of ARGs between a donor strain E. coli K12 and a recipient strain E. coli HB101 was investigated in chlorination without/with the presence of Br[-] or I[-]. Immediately after the addition of sodium hypochlorite, 53-88 % of the dosed chlorine was rapidly consumed, 10 %-42 % fast transformed into organic combined chloramines, and only low levels of free chlorine (0.02-0.8 mg/L as Cl2) left in the diluted cultural medium. Conjugative transfer mediated by the RP4 plasmid was not significantly enhanced in chlorination without the presence of Br[-] or I[-]. With the presence of Br[-] (0.5-5.0 mg/L) or I[-] (0.05-0.5 mg/L) in chlorination, the co-existing free halogen oxidants and their organic combined ones up-regulated the mRNA expression of the oxidative stress-regulatory gene (rpoS), outer membrane protein gene (ompC), and conjugation-relevant genes (trbBp and trfAp), and caused more damage to cell entirety. As a result, the co-existing reactive halogen oxidants enhanced the HGT of ARGs probably via conjugative transfer and transformation. This study showed that the presence of Br[-] and I[-] of common levels in aquatic environment promoted HGT of ARGs in chlorination, thus accelerating the transmission and prevalence of ARGs.}, }
@article {pmid35815847, year = {2023}, author = {Tanwar, N and Arya, SS and Rookes, JE and Cahill, DM and Lenka, SK and Bansal, KC}, title = {Prospects of chloroplast metabolic engineering for developing nutrient-dense food crops.}, journal = {Critical reviews in biotechnology}, volume = {43}, number = {7}, pages = {1001-1018}, doi = {10.1080/07388551.2022.2092717}, pmid = {35815847}, issn = {1549-7801}, abstract = {Addressing nutritional deficiencies in food crops through biofortification is a sustainable approach to tackling malnutrition. Biofortification is continuously being attempted through conventional breeding as well as through various plant biotechnological interventions, ranging from molecular breeding to genetic engineering and genome editing for enriching crops with various health-promoting metabolites. Genetic engineering is used for the rational incorporation of desired nutritional traits in food crops and predominantly operates through nuclear and chloroplast genome engineering. In the recent past, chloroplast engineering has been deployed as a strategic tool to develop model plants with enhanced nutritional traits due to the various advantages it offers over nuclear genome engineering. However, this approach needs to be extended for the nutritional enhancement of major food crops. Further, this platform could be combined with strategies, such as synthetic biology, chloroplast editing, nanoparticle-mediated rapid chloroplast transformation, and horizontal gene transfer through grafting for targeting endogenous metabolic pathways for overproducing native nutraceuticals, production of biopharmaceuticals, and biosynthesis of designer nutritional compounds. This review focuses on exploring various features of chloroplast genome engineering for nutritional enhancement of food crops by enhancing the levels of existing metabolites, restoring the metabolites lost during crop domestication, and introducing novel metabolites and phytonutrients needed for a healthy daily diet.}, }
@article {pmid35814695, year = {2022}, author = {Belloso Daza, MV and Milani, G and Cortimiglia, C and Pietta, E and Bassi, D and Cocconcelli, PS}, title = {Genomic Insights of Enterococcus faecium UC7251, a Multi-Drug Resistant Strain From Ready-to-Eat Food, Highlight the Risk of Antimicrobial Resistance in the Food Chain.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {894241}, pmid = {35814695}, issn = {1664-302X}, abstract = {The presence of multi-drug resistant (MDR) bacteria in ready-to-eat foods comprises a threat for public health due to their ability to acquire and transfer antibiotic-resistant determinants that could settle in the microbiome of the human digestive tract. In this study, Enterococcus faecium UC7251 isolated from a fermented dry sausage was characterized phenotypically and genotypically to hold resistance to multiple antibiotics including aminoglycosides, macrolides, β-lactams, and tetracyclines. We further investigated this strain following a hybrid sequencing and assembly approach (short and long reads) and determined the presence of various mobile genetic elements (MGEs) responsible of horizontal gene transfer (HGT). On the chromosome of UC7251, we found one integrative and conjugative element (ICE) and a conjugative transposon Tn916-carrying tetracycline resistance. UC7251 carries two plasmids: one small plasmid harboring a rolling circle replication and one MDR megaplasmid. The latter was identified as mobilizable and containing a putative integrative and conjugative element-like region, prophage sequences, insertion sequences, heavy-metal resistance genes, and several antimicrobial resistance (AMR) genes, confirming the phenotypic resistance characteristics. The transmissibility potential of AMR markers was observed through mating experiments, where Tn916-carried tetracycline resistance was transferred at intra- and inter-species levels. This work highlights the significance of constant monitoring of products of animal origin, especially RTE foodstuffs, to stimulate the development of novel strategies in the race for constraining the spread of antibiotic resistance.}, }
@article {pmid35811376, year = {2022}, author = {Villain, P and Catchpole, R and Forterre, P and Oberto, J and da Cunha, V and Basta, T}, title = {Expanded Dataset Reveals the Emergence and Evolution of DNA Gyrase in Archaea.}, journal = {Molecular biology and evolution}, volume = {39}, number = {8}, pages = {}, pmid = {35811376}, issn = {1537-1719}, mesh = {*Archaea/genetics/metabolism ; Bacteria/genetics ; *DNA Gyrase/genetics ; DNA Topoisomerases, Type I/genetics ; Gene Transfer, Horizontal ; }, abstract = {DNA gyrase is a type II topoisomerase with the unique capacity to introduce negative supercoiling in DNA. In bacteria, DNA gyrase has an essential role in the homeostatic regulation of supercoiling. While ubiquitous in bacteria, DNA gyrase was previously reported to have a patchy distribution in Archaea but its emergent function and evolutionary history in this domain of life remains elusive. In this study, we used phylogenomic approaches and an up-to date sequence dataset to establish global and archaea-specific phylogenies of DNA gyrases. The most parsimonious evolutionary scenario infers that DNA gyrase was introduced into the lineage leading to Euryarchaeal group II via a single horizontal gene transfer from a bacterial donor which we identified as an ancestor of Gracilicutes and/or Terrabacteria. The archaea-focused trees indicate that DNA gyrase spread from Euryarchaeal group II to some DPANN and Asgard lineages via rare horizontal gene transfers. The analysis of successful recent transfers suggests a requirement for syntropic or symbiotic/parasitic relationship between donor and recipient organisms. We further show that the ubiquitous archaeal Topoisomerase VI may have co-evolved with DNA gyrase to allow the division of labor in the management of topological constraints. Collectively, our study reveals the evolutionary history of DNA gyrase in Archaea and provides testable hypotheses to understand the prerequisites for successful establishment of DNA gyrase in a naive archaeon and the associated adaptations in the management of topological constraints.}, }
@article {pmid35801640, year = {2022}, author = {Brahim Belhaouari, D and Pires De Souza, GA and Lamb, DC and Kelly, SL and Goldstone, JV and Stegeman, JJ and Colson, P and La Scola, B and Aherfi, S}, title = {Metabolic arsenal of giant viruses: Host hijack or self-use?.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {35801640}, issn = {2050-084X}, support = {P01 ES021923/ES/NIEHS NIH HHS/United States ; }, mesh = {*Amoeba ; DNA Viruses/genetics ; Genome, Viral ; *Giant Viruses/genetics ; Phylogeny ; *Viruses/genetics ; }, abstract = {Viruses generally are defined as lacking the fundamental properties of living organisms in that they do not harbor an energy metabolism system or protein synthesis machinery. However, the discovery of giant viruses of amoeba has fundamentally challenged this view because of their exceptional genome properties, particle sizes and encoding of the enzyme machinery for some steps of protein synthesis. Although giant viruses are not able to replicate autonomously and still require a host for their multiplication, numerous metabolic genes involved in energy production have been recently detected in giant virus genomes from many environments. These findings have further blurred the boundaries that separate viruses and living organisms. Herein, we summarize information concerning genes and proteins involved in cellular metabolic pathways and their orthologues that have, surprisingly, been discovered in giant viruses. The remarkable diversity of metabolic genes described in giant viruses include genes encoding enzymes involved in glycolysis, gluconeogenesis, tricarboxylic acid cycle, photosynthesis, and β-oxidation. These viral genes are thought to have been acquired from diverse biological sources through lateral gene transfer early in the evolution of Nucleo-Cytoplasmic Large DNA Viruses, or in some cases more recently. It was assumed that viruses are capable of hijacking host metabolic networks. But the giant virus auxiliary metabolic genes also may represent another form of host metabolism manipulation, by expanding the catalytic capabilities of the host cells especially in harsh environments, providing the infected host cells with a selective evolutionary advantage compared to non-infected cells and hence favoring the viral replication. However, the mechanism of these genes' functionality remains unclear to date.}, }
@article {pmid35799218, year = {2022}, author = {Hassler, HB and Probert, B and Moore, C and Lawson, E and Jackson, RW and Russell, BT and Richards, VP}, title = {Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {104}, pmid = {35799218}, issn = {2049-2618}, mesh = {Bacteria/genetics ; Genes, rRNA ; Humans ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The 16S rRNA gene is used extensively in bacterial phylogenetics, in species delineation, and now widely in microbiome studies. However, the gene suffers from intragenomic heterogeneity, and reports of recombination and an unreliable phylogenetic signal are accumulating. Here, we compare core gene phylogenies to phylogenies constructed using core gene concatenations to estimate the strength of signal for the 16S rRNA gene, its hypervariable regions, and all core genes at the intra- and inter-genus levels. Specifically, we perform four intra-genus analyses (Clostridium, n = 65; Legionella, n = 47; Staphylococcus, n = 36; and Campylobacter, n = 17) and one inter-genus analysis [41 core genera of the human gut microbiome (31 families, 17 orders, and 12 classes), n = 82].<br><br>RESULTS: At both taxonomic levels, the 16S rRNA gene was recombinant and subject to horizontal gene transfer. At the intra-genus level, the gene showed one of the lowest levels of concordance with the core genome phylogeny (50.7% average). Concordance for hypervariable regions was lower still, with entropy masking providing little to no benefit. A major factor influencing concordance was SNP count, which showed a positive logarithmic association. Using this relationship, we determined that 690&#x2009;&#xb1;&#x2009;110 SNPs were required for 80% concordance (average 16S rRNA gene SNP count was 254). We also found a wide range in 16S-23S-5S rRNA operon copy number among genomes (1-27). At the inter-genus level, concordance for the whole 16S rRNA gene was markedly higher (73.8% - 10th out of 49 loci); however, the most concordant hypervariable regions (V4, V3-V4, and V1-V2) ranked in the third quartile (62.5 to 60.0%).<br><br>CONCLUSIONS: Ramifications of a poor phylogenetic performance for the 16S rRNA gene are far reaching. For example, in addition to incorrect species/strain delineation and phylogenetic inference, it has the potential to confound community diversity metrics if phylogenetic information is incorporated - for example,&#xa0;with popular approaches such as Faith's phylogenetic diversity and UniFrac. Our results highlight the problematic nature of these approaches and their use (along with entropy masking) is discouraged. Lastly, the wide range in 16S rRNA gene copy number among genomes also has a strong potential to confound diversity metrics. Video Abstract.}, }
@article {pmid35798684, year = {2022}, author = {Tahiri, N and Veriga, A and Koshkarov, A and Morozov, B}, title = {Invariant transformers of Robinson and Foulds distance matrices for Convolutional Neural Network.}, journal = {Journal of bioinformatics and computational biology}, volume = {20}, number = {4}, pages = {2250012}, doi = {10.1142/S0219720022500123}, pmid = {35798684}, issn = {1757-6334}, mesh = {*Algorithms ; Gene Transfer, Horizontal ; *Neural Networks, Computer ; Phylogeny ; Software ; }, abstract = {The evolutionary histories of genes are susceptible of differing greatly from each other which could be explained by evolutionary variations in horizontal gene transfers or biological recombinations. A phylogenetic tree would therefore represent the evolutionary history of each gene, which may present different patterns from the species tree that defines the main evolutionary patterns. In addition, phylogenetic trees of closely related species should be merged, thus minimizing the topological conflicts they present and obtaining consensus trees (in the case of homogeneous data) or supertrees (in the case of heterogeneous data). The traditional approaches are consensus tree inference (if the set of trees contains the same set of species) or supertrees (if the set of trees contains different, but overlapping sets of species). Consensus trees and supertrees are constructed to produce unique trees. However, these methods lose precision with respect to different evolutionary variability. Other approaches have been implemented to preserve this variability using the [Formula: see text]-means algorithm or the [Formula: see text]-medoids algorithm. Using a new method, we determine all possible consensus trees and supertrees that best represent the most significant evolutionary models in a set of phylogenetic trees, thereby increasing the precision of the results and decreasing the time required. Results: This paper presents in detail a new method for predicting the number of clusters in a Robinson and Foulds (RF) distance matrix using a convolutional neural network (CNN). We developed a new CNN approach (called CNNTrees) for multiple tree classification. This new strategy returns a number of clusters of the input phylogenetic trees for different-size sets of trees, which makes the new approach more stable and more robust. The paper provides an in-depth analysis of the relevant, but very difficult, problem of constructing alternative supertrees using phylogenies with different but overlapping sets of taxa. This new model will play an important role in the inference of Trees of Life (ToL). Availability and implementation: CNNTrees is available through a web server at https://tahirinadia.github.io/. The source code, data and information about installation procedures are also available at https://github.com/TahiriNadia/CNNTrees. Supplementary information: Supplementary data are available on GitHub platform. The evolutionary history of species is not unique, but is specific to sets of genes. Indeed, each gene has its own evolutionary history that differs considerably from one gene to another. For example, some individual genes or operons may be affected by specific horizontal gene transfer and recombination events. Thus, the evolutionary history of each gene must be represented by its own phylogenetic tree, which may exhibit different evolutionary patterns than the species tree that accounts for the major vertical descent patterns. The result of traditional consensus tree or supertree inference methods is a single consensus tree or supertree. In this paper, we present in detail a new method for predicting the number of clusters in a Robinson and Foulds (RF) distance matrix using a convolutional neural network (CNN). We developed a new CNN approach (CNNTrees) to construct multiple tree classification. This new strategy returns a number of clusters in the order of the input trees, which allows this new approach to be more stable and also more robust.}, }
@article {pmid35798255, year = {2022}, author = {Sengeruan, LP and van Zwetselaar, M and Kumburu, H and Aarestrup, FM and Kreppel, K and Sauli, E and Sonda, T}, title = {Plasmid characterization in bacterial isolates of public health relevance in a tertiary healthcare facility in Kilimanjaro region, Tanzania.}, journal = {Journal of global antimicrobial resistance}, volume = {30}, number = {}, pages = {384-389}, doi = {10.1016/j.jgar.2022.06.030}, pmid = {35798255}, issn = {2213-7173}, mesh = {Escherichia coli/genetics ; *Klebsiella pneumoniae/genetics ; Plasmids/genetics ; *Public Health ; Tanzania/epidemiology ; Tertiary Healthcare ; }, abstract = {OBJECTIVES: Plasmids are infectious double stranded DNA molecules that are found within bacteria. Horizontal gene transfer promotes successful spread of different types of plasmids within or among bacteria species, making their detection an important task for guiding clinical treatment. We used whole genome sequenced data to determine the prevalence of plasmid replicon types in clinical bacterial isolates, the presence of resistance and virulence genes in plasmid replicon types, and the relationship between resistance and virulence genes within each plasmid replicon.<br><br>METHODS: All bacterial sequences were de novo assembled using Unicycler before extraction of plasmids. Assembly graphs were submitted to Gplas+plasflow for plasmid contigs prediction. The predicted plasmid contigs were validated using PlasmidFinder.<br><br>RESULTS: A total of 159 (56.2%) out of 283 bacterial isolates were found to carry plasmid replicons, with Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus being the most prevalent plasmid carriers. A total of 26 (86.7%) multiple-replicon types were found to carry both resistance and virulence genes compared to 4 (13.3%) single plasmid replicons. No statistically significant correlation was found between the number of antibiotic resistance and virulence genes in multiple-replicon types (r&#xa0;=&#xa0;- 0.14, P > 0.05).<br><br>CONCLUSION: Our findings show a relatively high proportion of plasmid replicon-carrying isolates suggesting selection pressure due to antibiotic use in the hospital. Co-occurrence of antibiotic resistance and virulence genes in clinical isolates is a public health problem warranting attention.}, }
@article {pmid35796971, year = {2022}, author = {Palatini, U and Pischedda, E and Bonizzoni, M}, title = {Computational Methods for the Discovery and Annotation of Viral Integrations.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2509}, number = {}, pages = {293-313}, pmid = {35796971}, issn = {1940-6029}, mesh = {DNA Viruses/genetics ; *RNA Viruses/genetics ; RNA, Small Interfering/genetics ; Virus Integration ; *Viruses/genetics ; }, abstract = {The transfer of genetic material between viruses and eukaryotic cells is pervasive. Somatic integrations of DNA viruses and retroviruses have been linked to persistent viral infection and genotoxic effects. Integrations into germline cells, referred to as Endogenous Viral Elements (EVEs), can be co-opted for host functions. Besides DNA viruses and retroviruses, EVEs can also derive from nonretroviral RNA viruses, which have often been observed in piRNA clusters. Here, we describe a bioinformatic framework to annotate EVEs in a genome assembly, study their widespread occurrence and polymorphism and identify sample-specific viral integrations using whole genome sequencing data.}, }
@article {pmid35790381, year = {2022}, author = {Stadnichuk, IN and Tropin, IV}, title = {Cyanidiales as Polyextreme Eukaryotes.}, journal = {Biochemistry. Biokhimiia}, volume = {87}, number = {5}, pages = {472-487}, doi = {10.1134/S000629792205008X}, pmid = {35790381}, issn = {1608-3040}, mesh = {Archaea/genetics ; Biological Evolution ; *Eukaryota/genetics ; *Gene Transfer, Horizontal ; Phylogeny ; }, abstract = {Cyanidiales were named enigmatic microalgae due to their unique polyextreme properties, considered for a very long time unattainable for eukaryotes. Cyanidiales mainly inhabit hot sulfuric springs with high acidity (pH 0-4), temperatures up to 56°C, and ability to survive in the presence of dissolved heavy metals. Owing to the minimal for eukaryotes genome size, Cyanidiales have become one of the most important research objects in plant cell physiology, biochemistry, molecular biology, phylogenomics, and evolutionary biology. They play an important role in studying many aspects of oxygenic photosynthesis and chloroplasts origin. The ability to survive in stressful habitats and the corresponding metabolic pathways were acquired by Cyanidiales from archaea and bacteria via horizontal gene transfer (HGT). Thus, the possibility of gene transfer from prokaryotes to eukaryotes was discovered, which was a new step in understanding of the origin of eukaryotic cell.}, }
@article {pmid35789842, year = {2022}, author = {Job, V and Gomez-Valero, L and Renier, A and Rusniok, C and Bouillot, S and Chenal-Francisque, V and Gueguen, E and Adrait, A and Robert-Genthon, M and Jeannot, K and Panchev, P and Elsen, S and Fauvarque, MO and Couté, Y and Buchrieser, C and Attrée, I}, title = {Genomic erosion and horizontal gene transfer shape functional differences of the ExlA toxin in Pseudomonas spp.}, journal = {iScience}, volume = {25}, number = {7}, pages = {104596}, pmid = {35789842}, issn = {2589-0042}, abstract = {Two-partner secretion (TPS) is widespread in the bacterial world. The pore-forming TPS toxin ExlA of Pseudomonas aeruginosa is conserved in pathogenic and environmental Pseudomonas. While P. chlororaphis and P. entomophila displayed ExlA-dependent killing, P. putida did not cause damage to eukaryotic cells. ExlA proteins interacted with epithelial cell membranes; however, only ExlA [Pch] induced the cleavage of the adhesive molecule E-cadherin. ExlA proteins participated in insecticidal activity toward the larvae of Galleria mellonella and the fly Drosophila melanogaster. Evolutionary analyses demonstrated that the differences in the C-terminal domains are partly due to horizontal movements of the operon within the genus Pseudomonas. Reconstruction of the evolutionary history revealed the complex horizontal acquisitions. Together, our results provide evidence that conserved TPS toxins in environmental Pseudomonas play a role in bacteria-insect interactions and discrete differences in CTDs may determine their specificity and mode of action toward eukaryotic cells.}, }
@article {pmid35781905, year = {2022}, author = {Wu, D and Hu, Y and Akashi, S and Nojiri, H and Guo, L and Ye, CY and Zhu, QH and Okada, K and Fan, L}, title = {Lateral transfers lead to the birth of momilactone biosynthetic gene clusters in grass.}, journal = {The Plant journal : for cell and molecular biology}, volume = {111}, number = {5}, pages = {1354-1367}, pmid = {35781905}, issn = {1365-313X}, mesh = {*Diterpenes/metabolism ; *Echinochloa/genetics/metabolism ; Multigene Family ; *Oryza/metabolism ; Plants/metabolism ; Poaceae/genetics/metabolism ; }, abstract = {Momilactone A, an important plant labdane-related diterpenoid, functions as a phytoalexin against pathogens and an allelochemical against neighboring plants. The genes involved in the biosynthesis of momilactone A are found in clusters, i.e., momilactone A biosynthetic gene clusters (MABGCs), in the rice and barnyardgrass genomes. In addition, we know little about the origin and evolution of MABGCs. Here, we integrated results from comprehensive phylogeny and comparative genomic analyses of the core genes of MABGC-like clusters and MABGCs in 40 monocot plant genomes, providing convincing evidence for the birth and evolution of MABGCs in grass species. The MABGCs found in the PACMAD clade of the core grass lineage (including Panicoideae and Chloridoideae) originated from a MABGC-like cluster in Triticeae (BOP clade) via lateral gene transfer (LGT) and followed by recruitment of MAS1/2 and CYP76L1 genes. The MABGCs in Oryzoideae originated from PACMAD through another LGT event and lost CYP76L1 afterwards. The Oryza MABGC and another Oryza diterpenoid cluster c2BGC are two distinct clusters, with the latter originating from gene duplication and relocation within Oryzoideae. Further comparison of the expression patterns of the MABGC genes between rice and barnyardgrass in response to pathogen infection and allelopathy provides novel insights into the functional innovation of MABGCs in plants. Our results demonstrate LGT-mediated origination of MABGCs in grass and shed lights into the evolutionary innovation and optimization of plant biosynthetic pathways.}, }
@article {pmid35780898, year = {2022}, author = {Zhang, J and Lu, T and Xin, Y and Wei, Y}, title = {Ferric chloride further simplified the horizontal gene transfer network of antibiotic resistance genes in anaerobic digestion.}, journal = {The Science of the total environment}, volume = {844}, number = {}, pages = {157054}, doi = {10.1016/j.scitotenv.2022.157054}, pmid = {35780898}, issn = {1879-1026}, mesh = {Anaerobiosis ; Animals ; *Anti-Bacterial Agents/pharmacology ; Chlorides ; Drug Resistance, Microbial/genetics ; Ferric Compounds ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Manure ; Swine ; }, abstract = {The role of ferric chloride (FC) on the reduction of antibiotic resistance genes (ARGs) in anaerobic digestion (AD) system was investigated from the perspective of vertical (VGT) and horizontal gene transfer (HGT) network through the high-throughput qPCR (HT-qPCR). Although FC showed limited impacts on methane production in AD of swine manure, the tetracycline and MLSB resistance genes were specifically reduced at the end, where tetQ of antibiotic target protection and ermF of antibiotic target alteration contributed the most to the reduction. Both VGT and HGT network were divided into three modules, and the complexity of HGT network was largely reduced along with AD, where the HGT connection was reduced from 683 (Module III) to 172 (Module I), and FC addition could further reduce the relative abundance of ARG hosts in Module I. The contribution of VGT and HGT to the changes of ARGs in AD was further deciphered, and although the VGT reflected by the changes of microbial community contributed the most to the dynamics of ARGs (68.0 %), the HGT contribution could further be reduced by the FC addition. This study provided a new perspective on the fate of ARGs response to the FC addition in the AD system.}, }
@article {pmid35779456, year = {2022}, author = {Ye, C and Feng, M and Chen, Y and Zhang, Y and Chen, Q and Yu, X}, title = {Dormancy induced by oxidative damage during disinfection facilitates conjugation of ARGs through enhancing efflux and oxidative stress: A lagging response.}, journal = {Water research}, volume = {221}, number = {}, pages = {118798}, doi = {10.1016/j.watres.2022.118798}, pmid = {35779456}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; *Chlorine/pharmacology ; *Disinfection/methods ; Gene Transfer, Horizontal ; Genes, Bacterial ; Oxidative Stress ; Water/pharmacology ; }, abstract = {Disinfection is known to greatly alter bacterial characteristics in water, and high horizontal gene transfer (HGT) frequency occurs in eutrophic conditions. Interestingly, these two seemingly irrelevant phenomena were closely linked by a lagging response of the increased conjugation frequency probably via daily water disinfection in this study. Three disinfection methods (UV, chlorine, and UV/chlorine) were selected to investigate the increased frequency of conjugation of ARGs during the stage of continuing culture after disinfection. The results showed that the conjugative transfer frequency was inhibited for all disinfection treatments after 24 h of co-incubation. Unexpectedly, after 3-7 days of co-cultivation, the HGT frequencies were increased by 2.71-5.61-fold and 5.46-13.96-fold in chlorine (30 min) and UV/chlorine (1 min) groups compared to the control, but not in UV-irradiated groups. A neglected lagging response was found for the first time, i.e., oxidative disinfection-induced dormancy promotes conjugative transfer of ARGs. Furthermore, mechanistic insights were gained from (1) membrane permeability, (2) conjugation-regulated system, (3) efflux pump system, and (4) oxidative stress system, suggesting the critical role of enhancing efflux and oxidative stress in the propagation of ARGs. Finally, the known instantaneous effect of oxidation disinfection was compared to address the controversial debate in this research field, proposing that the dormancy level of donor bacteria is the key to evaluating whether it can promote the HGT process. This study has important environmental implications for elucidating the transmission of ARGs after oxidation disinfection.}, }
@article {pmid35770172, year = {2022}, author = {Venhorst, J and van der Vossen, JMBM and Agamennone, V}, title = {Battling Enteropathogenic Clostridia: Phage Therapy for Clostridioides difficile and Clostridium perfringens.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {891790}, pmid = {35770172}, issn = {1664-302X}, abstract = {The pathogenic Clostridioides difficile and Clostridium perfringens are responsible for many health care-associated infections as well as systemic and enteric diseases. Therefore, they represent a major health threat to both humans and animals. Concerns regarding increasing antibiotic resistance (related to C. difficile and C. perfringens) have caused a surge in the pursual of novel strategies that effectively combat pathogenic infections, including those caused by both pathogenic species. The ban on antibiotic growth promoters in the poultry industry has added to the urgency of finding novel antimicrobial therapeutics for C. perfringens. These efforts have resulted in various therapeutics, of which bacteriophages (in short, phages) show much promise, as evidenced by the Eliava Phage Therapy Center in Tbilisi, Georgia (https://eptc.ge/). Bacteriophages are a type of virus that infect bacteria. In this review, the (clinical) impact of clostridium infections in intestinal diseases is recapitulated, followed by an analysis of the current knowledge and applicability of bacteriophages and phage-derived endolysins in this disease indication. Limitations of phage and phage endolysin therapy were identified and require considerations. These include phage stability in the gastrointestinal tract, influence on gut microbiota structure/function, phage resistance development, limited host range for specific pathogenic strains, phage involvement in horizontal gene transfer, and-for phage endolysins-endolysin resistance, -safety, and -immunogenicity. Methods to optimize features of these therapeutic modalities, such as mutagenesis and fusion proteins, are also addressed. The future success of phage and endolysin therapies require reliable clinical trial data for phage(-derived) products. Meanwhile, additional research efforts are essential to expand the potential of exploiting phages and their endolysins for mitigating the severe diseases caused by C. difficile and C. perfringens.}, }
@article {pmid35769590, year = {2022}, author = {Xia, ZQ and Wei, ZY and Shen, H and Shu, JP and Wang, T and Gu, YF and Jaisi, A and Yan, YH}, title = {Lycophyte transcriptomes reveal two whole-genome duplications in Lycopodiaceae: Insights into the polyploidization of Phlegmariurus.}, journal = {Plant diversity}, volume = {44}, number = {3}, pages = {262-270}, pmid = {35769590}, issn = {2468-2659}, abstract = {Lycophytes are an ancient clade of the non-flowering vascular plants with chromosome numbers that vary from tens to hundreds. They are an excellent study system for examining whole-genome duplications (WGDs), or polyploidization, in spore-dispersed vascular plants. However, a lack of genome sequence data limits the reliable detection of very ancient WGDs, small-scale duplications (SSDs), and recent WGDs. Here, we integrated phylogenomic analysis and the distribution of synonymous substitutions per synonymous sites (Ks) of the transcriptomes of 13 species of lycophytes to identify, locate, and date multiple WGDs in the lycophyte family Lycopodiaceae. Additionally, we examined the genus Phlegmariurus for signs of genetic discordance, which can provide valuable insight into the underlying causes of such conflict (e.g., hybridization, incomplete lineage sorting, or horizontal gene transfer).We found strong evidence that two WGD events occurred along the phylogenetic backbone of Lycopodiaceae, with one occurring in the common ancestor of extant Phlegmariurus (Lycopodiaceae) approximately 22-23 million years ago (Mya) and the other occurring in the common ancestor of Lycopodiaceae around 206-214 Mya. Interestingly, we found significant genetic discordance in the genus Phlegmariurus, indicating that the genus has a complex evolutionary history. This study provides molecular evidence for multiple WGDs in Lycopodiaceae and offers phylogenetic clues to the evolutionary history of Lycopodiaceae.}, }
@article {pmid35769291, year = {2022}, author = {Kim, JI and Jo, BY and Park, MG and Yoo, YD and Shin, W and Archibald, JM}, title = {Evolutionary Dynamics and Lateral Gene Transfer in Raphidophyceae Plastid Genomes.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {896138}, pmid = {35769291}, issn = {1664-462X}, abstract = {The Raphidophyceae is an ecologically important eukaryotic lineage of primary producers and predators that inhabit marine and freshwater environments worldwide. These organisms are of great evolutionary interest because their plastids are the product of eukaryote-eukaryote endosymbiosis. To obtain deeper insight into the evolutionary history of raphidophycean plastids, we sequenced and analyzed the plastid genomes of three freshwater and three marine species. Our comparison of these genomes, together with the previously reported plastid genome of Heterosigma akashiwo, revealed unexpected variability in genome structure. Unlike the genomes of other analyzed species, the plastid genome of Gonyostomum semen was found to contain only a single rRNA operon, presumably due to the loss of genes from the inverted repeat (IR) region found in most plastid genomes. In contrast, the marine species Fibrocapsa japonica contains the largest IR region and overall plastid genome for any raphidophyte examined thus far, mainly due to the presence of four large gene-poor regions and foreign DNA. Two plastid genes, tyrC in F. japonica and He. akashiwo and serC in F. japonica, appear to have arisen via lateral gene transfer (LGT) from diatoms, and several raphidophyte open reading frames are demonstrably homologous to sequences in diatom plasmids and plastid genomes. A group II intron in the F. japonica psbB gene also appears to be derived by LGT. Our results provide important insights into the evolutionary history of raphidophyte plastid genomes via LGT from the plastids and plasmid DNAs of diatoms.}, }
@article {pmid35765180, year = {2022}, author = {Pandey, SD and Biswas, I}, title = {Clp ATPases differentially affect natural competence development in Streptococcus mutans.}, journal = {MicrobiologyOpen}, volume = {11}, number = {3}, pages = {e1288}, pmid = {35765180}, issn = {2045-8827}, support = {R01 GM128241/GM/NIGMS NIH HHS/United States ; }, mesh = {*Adenosine Triphosphatases/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Endopeptidases/genetics ; Gene Expression Regulation, Bacterial ; *Streptococcus mutans ; }, abstract = {In naturally competent bacteria, DNA transformation through horizontal gene transfer is an evolutionary mechanism to receive extracellular DNA. Bacteria need to maintain a state of competence to accept foreign DNA, and this is an energy-driven phenomenon that is tightly controlled. In Streptococcus, competence development is a complex process that is not fully understood. In this study, we used Streptococcus mutans, an oral bacterium, to determine how cell density affects competence development. We found that in S. mutans the transformation efficiency is maximum when the transforming DNA was added at low cell density and incubated for 2.5 h before selecting for transformants. We also found that S. mutans cells remain competent until the mid-logarithmic phase, after which the competence decreases drastically. Surprisingly, we observed that individual components of Clp proteolytic complexes differentially regulate competence. If the transformation is carried out at the early growth phase, both ClpP protease and ClpX ATPase are needed for competence. In contrast, we found that both ClpC and ClpE negatively affect competence. We also found that if the transformation is carried out at the mid-logarithmic growth phase ClpX is still required for competence, but ClpP negatively affects competence. While the exact reason for this differential effect of ClpP and ClpX on transformation is currently unknown, we found that both ClpC and ClpE have a negative effect on transformation, which was not reported before.}, }
@article {pmid35764672, year = {2022}, author = {Jenkins, HL and Graham, R and Porter, JS and Vieira, LM and de Almeida, ACS and Hall, A and O'Dea, A and Coppard, SE and Waeschenbach, A}, title = {Unprecedented frequency of mitochondrial introns in colonial bilaterians.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {10889}, pmid = {35764672}, issn = {2045-2322}, mesh = {Animals ; *Gene Transfer, Horizontal ; Introns/genetics ; *Mitochondria/genetics ; Phylogeny ; RNA-Directed DNA Polymerase/genetics ; }, abstract = {Animal mitogenomes are typically devoid of introns. Here, we report the largest number of mitochondrial introns ever recorded from bilaterian animals. Mitochondrial introns were identified for the first time from the phylum Bryozoa. They were found in four species from three families (Order Cheilostomatida). A total of eight introns were found in the complete mitogenome of Exechonella vieirai, and five, 17 and 18 introns were found in the partial mitogenomes of Parantropora penelope, Discoporella cookae and Cupuladria biporosa, respectively. Intron-encoded protein domains reverse transcriptase and intron maturase (RVT-IM) were identified in all species. Introns in E. vieirai and P. penelope had conserved Group II intron ribozyme domains V and VI. Conserved domains were lacking from introns in D. cookae and C. biporosa, preventing their further categorization. Putative origins of metazoan introns were explored in a phylogenetic context, using an up-to-date alignment of mitochondrial RVT-IM domains. Results confirmed previous findings of multiple origins of annelid, placozoan and sponge RVT-IM domains and provided evidence for common intron donor sources across metazoan phyla. Our results corroborate growing evidence that some metazoans with regenerative abilities (i.e. placozoans, sponges, annelids and bryozoans) are susceptible to intron integration, most likely via horizontal gene transfer.}, }
@article {pmid35763818, year = {2022}, author = {Shin, NR and Doucet, D and Pauchet, Y}, title = {Duplication of horizontally acquired GH5_2 enzymes played a central role in the evolution of longhorned beetles.}, journal = {Molecular biology and evolution}, volume = {39}, number = {6}, pages = {}, pmid = {35763818}, issn = {1537-1719}, abstract = {The rise of functional diversity through gene duplication contributed to the adaption of organisms to various environments. Here we investigate the evolution of putative cellulases of the subfamily 2 of glycoside hydrolase family 5 (GH5_2) in the Cerambycidae (longhorned beetles), a megadiverse assemblage of mostly xylophagous beetles. Cerambycidae originally acquired GH5_2 from a bacterial donor through horizontal gene transfer (HGT), and extant species harbor multiple copies that arose from gene duplication. We ask how these digestive enzymes contributed to the ability of these beetles to feed on wood. We analyzed 113 GH5_2, including the functional characterization of 52 of them, derived from 25 species covering most subfamilies of Cerambycidae. Ancestral gene duplications led to five well-defined groups with distinct substrate specificity, allowing these beetles to break down, in addition to cellulose, polysaccharides that are abundant in plant cell walls (PCWs), namely, xyloglucan, xylan, and mannans. Resurrecting the ancestral enzyme originally acquired by HGT, we show it was a cellulase that was able to break down glucomannan and xylan. Finally, recent gene duplications further expanded the catalytic repertoire of cerambycid GH5_2, giving rise to enzymes that favor transglycosylation over hydrolysis. We suggest that HGT and gene duplication, which shaped the evolution of GH5_2, played a central role in the ability of cerambycid beetles to use a PCW-rich diet and may have contributed to their successful radiation.}, }
@article {pmid35763548, year = {2022}, author = {Sulser, S and Vucicevic, A and Bellini, V and Moritz, R and Delavat, F and Sentchilo, V and Carraro, N and van der Meer, JR}, title = {A bistable prokaryotic differentiation system underlying development of conjugative transfer competence.}, journal = {PLoS genetics}, volume = {18}, number = {6}, pages = {e1010286}, pmid = {35763548}, issn = {1553-7404}, mesh = {*Conjugation, Genetic/genetics ; *Gene Transfer, Horizontal/genetics ; Prokaryotic Cells ; Promoter Regions, Genetic ; Pseudomonas/genetics ; }, abstract = {The mechanisms and impact of horizontal gene transfer processes to distribute gene functions with potential adaptive benefit among prokaryotes have been well documented. In contrast, little is known about the life-style of mobile elements mediating horizontal gene transfer, whereas this is the ultimate determinant for their transfer fitness. Here, we investigate the life-style of an integrative and conjugative element (ICE) within the genus Pseudomonas that is a model for a widespread family transmitting genes for xenobiotic compound metabolism and antibiotic resistances. Previous work showed bimodal ICE activation, but by using single cell time-lapse microscopy coupled to combinations of chromosomally integrated single copy ICE promoter-driven fluorescence reporters, RNA sequencing and mutant analysis, we now describe the complete regulon leading to the arisal of differentiated dedicated transfer competent cells. The regulon encompasses at least three regulatory nodes and five (possibly six) further conserved gene clusters on the ICE that all become expressed under stationary phase conditions. Time-lapse microscopy indicated expression of two regulatory nodes (i.e., bisR and alpA-bisDC) to precede that of the other clusters. Notably, expression of all clusters except of bisR was confined to the same cell subpopulation, and was dependent on the same key ICE regulatory factors. The ICE thus only transfers from a small fraction of cells in a population, with an estimated proportion of between 1.7-4%, which express various components of a dedicated transfer competence program imposed by the ICE, and form the centerpiece of ICE conjugation. The components mediating transfer competence are widely conserved, underscoring their selected fitness for efficient transfer of this class of mobile elements.}, }
@article {pmid35762208, year = {2022}, author = {Matuszewska, M and Murray, GGR and Ba, X and Wood, R and Holmes, MA and Weinert, LA}, title = {Stable antibiotic resistance and rapid human adaptation in livestock-associated MRSA.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {35762208}, issn = {2050-084X}, support = {/WT_/Wellcome Trust/United Kingdom ; /MRC_/Medical Research Council/United Kingdom ; 109385/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; BB/L018934/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial ; Humans ; Livestock/microbiology ; *Methicillin-Resistant Staphylococcus aureus/genetics ; *Staphylococcal Infections/microbiology ; }, abstract = {Mobile genetic elements (MGEs) are agents of horizontal gene transfer in bacteria, but can also be vertically inherited by daughter cells. Establishing the dynamics that led to contemporary patterns of MGEs in bacterial genomes is central to predicting the emergence and evolution of novel and resistant pathogens. Methicillin-resistant Staphylococcus aureus (MRSA) clonal-complex (CC) 398 is the dominant MRSA in European livestock and a growing cause of human infections. Previous studies have identified three categories of MGEs whose presence or absence distinguishes livestock-associated CC398 from a closely related and less antibiotic-resistant human-associated population. Here, we fully characterise the evolutionary dynamics of these MGEs using a collection of 1180 CC398 genomes, sampled from livestock and humans, over 27 years. We find that the emergence of livestock-associated CC398 coincided with the acquisition of a Tn916 transposon carrying a tetracycline resistance gene, which has been stably inherited for 57 years. This was followed by the acquisition of a type V SCCmec that carries methicillin, tetracycline, and heavy metal resistance genes, which has been maintained for 35 years, with occasional truncations and replacements with type IV SCCmec. In contrast, a class of prophages that carry a human immune evasion gene cluster and that are largely absent from livestock-associated CC398 have been repeatedly gained and lost in both human- and livestock-associated CC398. These contrasting dynamics mean that when livestock-associated MRSA is transmitted to humans, adaptation to the human host outpaces loss of antibiotic resistance. In addition, the stable inheritance of resistance-associated MGEs suggests that the impact of ongoing reductions in antibiotic and zinc oxide use in European farms on livestock-associated MRSA will be slow to be realised.}, }
@article {pmid35760883, year = {2022}, author = {Wang, P and Zhao, Y and Wang, W and Lin, S and Tang, K and Liu, T and Wood, TK and Wang, X}, title = {Mobile genetic elements used by competing coral microbial populations increase genomic plasticity.}, journal = {The ISME journal}, volume = {16}, number = {9}, pages = {2220-2229}, pmid = {35760883}, issn = {1751-7370}, mesh = {Animals ; *Anthozoa/genetics ; Conjugation, Genetic ; DNA Transposable Elements ; Gene Transfer, Horizontal ; Genomic Islands ; Genomics ; *Pseudoalteromonas/genetics ; *Vibrio/genetics ; }, abstract = {Intraspecies diversification and niche adaptation by members of the Vibrio genus, one of the most diverse bacterial genera, is thought to be driven by horizontal gene transfer. However, the intrinsic driving force of Vibrio species diversification is much less explored. Here, by studying two dominant and competing cohabitants of the gastric cavity of corals, we found that a phenotype influencing island (named VPII) in Vibrio alginolyticus was eliminated upon coculturing with Pseudoalteromonas. The loss of VPII reduced the biofilm formation and phage resistance, but activated motility, which may allow V. alginolyticus to expand to other niches. Mechanistically, we discovered that the excision of this island is mediated by the cooperation of two unrelated mobile genetic elements harbored in Pseudoalteromonas spp., an integrative and conjugative element (ICE) and a mobilizable genomic island (MGI). More importantly, these mobile genetic elements are widespread in cohabitating Gram-negative bacteria. Altogether, we discovered a new strategy by which the mobilome is employed by competitors to increase the genomic plasticity of rivals.}, }
@article {pmid35757882, year = {2022}, author = {de Lorenzo, V}, title = {Environmental Galenics: large-scale fortification of extant microbiomes with engineered bioremediation agents.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {377}, number = {1857}, pages = {20210395}, pmid = {35757882}, issn = {1471-2970}, mesh = {Biodegradation, Environmental ; Biotechnology ; Gene Transfer, Horizontal ; *Microbiota ; *Synthetic Biology/methods ; }, abstract = {Contemporary synthetic biology-based biotechnologies are generating tools and strategies for reprogramming genomes for specific purposes, including improvement and/or creation of microbial processes for tackling climate change. While such activities typically work well at a laboratory or bioreactor scale, the challenge of their extensive delivery to multiple spatio-temporal dimensions has hardly been tackled thus far. This state of affairs creates a research niche for what could be called Environmental Galenics (EG), i.e. the science and technology of releasing designed biological agents into deteriorated ecosystems for the sake of their safe and effective recovery. Such endeavour asks not just for an optimal performance of the biological activity at stake, but also the material form and formulation of the agents, their propagation and their interplay with the physico-chemical scenario where they are expected to perform. EG also encompasses adopting available physical carriers of microorganisms and channels of horizontal gene transfer as potential paths for spreading beneficial activities through environmental microbiomes. While some of these propositions may sound unsettling to anti-genetically modified organisms sensitivities, they may also fall under the tag of TINA (there is no alternative) technologies in the cases where a mere reduction of emissions will not help the revitalization of irreversibly lost ecosystems. This article is part of the theme issue 'Ecological complexity and the biosphere: the next 30 years'.}, }
@article {pmid35745530, year = {2022}, author = {Jungkhun, N and Gomes de Farias, AR and Watcharachaiyakup, J and Kositcharoenkul, N and Ham, JH and Patarapuwadol, S}, title = {Phylogenetic Characterization and Genome Sequence Analysis of Burkholderia glumae Strains Isolated in Thailand as the Causal Agent of Rice Bacterial Panicle Blight.}, journal = {Pathogens (Basel, Switzerland)}, volume = {11}, number = {6}, pages = {}, pmid = {35745530}, issn = {2076-0817}, support = {1015305//National Institute of Food and Agriculture (NIFA) - USDA/ ; }, abstract = {Burkholderia glumae is one of the most critical rice-pathogenic bacteria, and it causes bacterial panicle blight (BPB) in rice plants. In 2017, BPB symptoms were observed from rice fields in Chiang Rai, Northern Thailand. Sixty-one isolates obtained from the symptomatic panicles of rice were initially identified as B. glumae by polymerase chain reaction (PCR) using species-specific primers. Among them, six selected strains isolated from the susceptible japonica rice cultivar DOA2 were characterized in terms of morpho-physiology, pathology, phylogenetics, and genomics. Our genome sequence analysis of the six selected strains revealed the presence of multiple prophages, which may reflect the high level of diversity in this bacterial species through dynamic horizontal gene transfer processes, including phage infection. This notion was supported by the results of phylogenetic and phylogenomic analyses, which showed the formation of several subgroups not related to the years of isolation or the geographical origins. This study reports the isolation of B. glumae as the causal pathogen of BPB disease in japonica rice in Thailand and provides genomic resources to better understand the biology and diversity of this plant pathogenic bacterium. Further studies with a vast collection of B. glumae strains from various rice-growing regions around the world are needed to elucidate the evolution, variability, and lifestyle of the pathogen.}, }
@article {pmid35741357, year = {2022}, author = {Merkevičienė, L and Butrimaitė-Ambrozevičienė, &#x10c; and Paškevičius, G and Pikūnienė, A and Virgailis, M and Dailidavičienė, J and Daukšienė, A and Šiugždinienė, R and Ruzauskas, M}, title = {Serological Variety and Antimicrobial Resistance in Salmonella Isolated from Reptiles.}, journal = {Biology}, volume = {11}, number = {6}, pages = {}, pmid = {35741357}, issn = {2079-7737}, abstract = {Salmonella enterica is one of the best adapted bacterial pathogens causing infections in a wide variety of vertebrate species. The aim of this study was to investigate the prevalence of Salmonella in different reptile species and to evaluate their serological variety and patterns of antimicrobial resistance. In total, 97 samples from 25 wild and domesticated reptile species were investigated in Lithuania. Serological variety, as well as phenotypical and genotypical resistance to antimicrobials, were investigated. Fifty isolates of Salmonella were obtained from the ninety-seven tested samples (51.5%; 95% CI 41.2−61.2). A significantly higher prevalence of Salmonella was detected in domesticated individuals (61.3%; 95% CI 50.0−71.5) compared with wild ones (18.2%; 95% CI 7.3−38.5). All isolates belonged to a single species, Salmonella enterica. Results demonstrated that reptiles carry a large variety of Salmonella serovars. Thirty-four isolates (68%) of Salmonella were resistant to at least one antimicrobial drug. The most frequent resistance of the isolates was to streptomycin (26%), cefoxitin, gentamicin, tetracycline and chloramphenicol (16%). Genes encoding resistance to tetracyclines, aminoglycosides, sulphonamides and trimethoprim were detected. No integrons that are associated with horizontal gene transfer were found. Data obtained provided knowledge about the adaptation of Salmonella in reptiles. Healthy individuals, irrespective of their origin, often carry Salmonella, including multi-resistant strains. Due to its large serological diversity, zoonotic potential and antimicrobial resistance, Salmonella in reptiles poses a risk to other animals and humans.}, }
@article {pmid35738252, year = {2022}, author = {George, EE and Tashyreva, D and Kwong, WK and Okamoto, N and Horák, A and Husnik, F and Lukeš, J and Keeling, PJ}, title = {Gene Transfer Agents in Bacterial Endosymbionts of Microbial Eukaryotes.}, journal = {Genome biology and evolution}, volume = {14}, number = {7}, pages = {}, pmid = {35738252}, issn = {1759-6653}, mesh = {Bacteria/genetics ; *Eukaryota/genetics ; Gene Transfer, Horizontal ; Phylogeny ; Symbiosis/genetics ; *Viruses ; }, abstract = {Gene transfer agents (GTAs) are virus-like structures that package and transfer prokaryotic DNA from donor to recipient prokaryotic cells. Here, we describe widespread GTA gene clusters in the highly reduced genomes of bacterial endosymbionts from microbial eukaryotes (protists). Homologs of the GTA capsid and portal complexes were initially found to be present in several highly reduced alphaproteobacterial endosymbionts of diplonemid protists (Rickettsiales and Rhodospirillales). Evidence of GTA expression was found in polyA-enriched metatranscriptomes of the diplonemid hosts and their endosymbionts, but due to biases in the polyA-enrichment methods, levels of GTA expression could not be determined. Examining the genomes of closely related bacteria revealed that the pattern of retained GTA head/capsid complexes with missing tail components was common across Rickettsiales and Holosporaceae (Rhodospirillales), all obligate symbionts with a wide variety of eukaryotic hosts. A dN/dS analysis of Rickettsiales and Holosporaceae symbionts revealed that purifying selection is likely the main driver of GTA evolution in symbionts, suggesting they remain functional, but the ecological function of GTAs in bacterial symbionts is unknown. In particular, it is unclear how increasing horizontal gene transfer in small, largely clonal endosymbiont populations can explain GTA retention, and, therefore, the structures may have been repurposed in endosymbionts for host interactions. Either way, their widespread retention and conservation in endosymbionts of diverse eukaryotes suggests an important role in symbiosis.}, }
@article {pmid35736713, year = {2022}, author = {Velasco-Amo, MP and Arias-Giraldo, LF and Olivares-García, C and Denancé, N and Jacques, MA and Landa, BB}, title = {Use of traC Gene to Type the Incidence and Distribution of pXFAS_5235 Plasmid-Bearing Strains of Xylella fastidiosa subsp. fastidiosa ST1 in Spain.}, journal = {Plants (Basel, Switzerland)}, volume = {11}, number = {12}, pages = {}, pmid = {35736713}, issn = {2223-7747}, support = {XF-ACTORS 727987//Horizon 2020 Framework Research Programme/ ; E-RTA2017-00004-C06-02//AEI-INIA Spain and the Spanish Olive Oil Interprofessional/ ; }, abstract = {Xylella fastidiosa (Xf) is a phytopathogenic bacterium with a repertoire of self-replicating genetic elements, including plasmids, pathogenicity islands, and prophages. These elements provide potential avenues for horizontal gene transfer both within and between species and have the ability to confer new virulence traits, including the ability to colonize new host plants. However, they can also serve as a 'footprint' to type plasmid-bearing strains. Genome sequencing of several strains of Xf subsp. fastidiosa sequence type (ST) 1 from Mallorca Island, Spain, revealed the presence of a 38 kb plasmid (pXFAS_5235). In this study, we developed a PCR-based typing approach using primers targeting the traC gene to determine the presence of pXFAS_5235 plasmid or other plasmids carrying this gene in a world-wide collection of 65 strains X. fastidiosa from different subspecies and STs or in 226 plant samples naturally infected by the bacterium obtained from the different outbreaks of Xf in Spain. The traC gene was amplified only in the plant samples obtained from Mallorca Island infected by Xf subsp. fastidiosa ST1 and from all Spanish strains belonging to this ST. Maximum-likelihood phylogenetic tree of traC revealed a close relatedness among Spanish and Californian strains carrying similar plasmids. Our results confirm previous studies, which suggested that a single introduction event of Xf subsp. fastidiosa ST1 occurred in the Balearic Islands. Further studies on the presence and role of plasmids in Xf strains belonging to the same or different subspecies and STs can provide important information in studies of epidemiology, ecology, and evolution of this plant pathogen.}, }
@article {pmid35731940, year = {2022}, author = {Romero Picazo, D and Werner, A and Dagan, T and Kupczok, A}, title = {Pangenome Evolution in Environmentally Transmitted Symbionts of Deep-Sea Mussels Is Governed by Vertical Inheritance.}, journal = {Genome biology and evolution}, volume = {14}, number = {7}, pages = {}, pmid = {35731940}, issn = {1759-6653}, mesh = {Animals ; Bacteria/genetics ; Gene Transfer, Horizontal ; Genome, Bacterial ; Methane ; *Mytilidae/genetics/microbiology ; Phylogeny ; Sulfur ; Symbiosis/genetics ; }, abstract = {Microbial pangenomes vary across species; their size and structure are determined by genetic diversity within the population and by gene loss and horizontal gene transfer (HGT). Many bacteria are associated with eukaryotic hosts where the host colonization dynamics may impact bacterial genome evolution. Host-associated lifestyle has been recognized as a barrier to HGT in parentally transmitted bacteria. However, pangenome evolution of environmentally acquired symbionts remains understudied, often due to limitations in symbiont cultivation. Using high-resolution metagenomics, here we study pangenome evolution of two co-occurring endosymbionts inhabiting Bathymodiolus brooksi mussels from a single cold seep. The symbionts, sulfur-oxidizing (SOX) and methane-oxidizing (MOX) gamma-proteobacteria, are environmentally acquired at an early developmental stage and individual mussels may harbor multiple strains of each symbiont species. We found differences in the accessory gene content of both symbionts across individual mussels, which are reflected by differences in symbiont strain composition. Compared with core genes, accessory genes are enriched in genome plasticity functions. We found no evidence for recent HGT between both symbionts. A comparison between the symbiont pangenomes revealed that the MOX population is less diverged and contains fewer accessory genes, supporting that the MOX association with B. brooksi is more recent in comparison to that of SOX. Our results show that the pangenomes of both symbionts evolved mainly by vertical inheritance. We conclude that genome evolution of environmentally transmitted symbionts that associate with individual hosts over their lifetime is affected by a narrow symbiosis where the frequency of HGT is constrained.}, }
@article {pmid35731825, year = {2022}, author = {Cote-L'Heureux, A and Maurer-Alcalá, XX and Katz, LA}, title = {Old genes in new places: A taxon-rich analysis of interdomain lateral gene transfer events.}, journal = {PLoS genetics}, volume = {18}, number = {6}, pages = {e1010239}, pmid = {35731825}, issn = {1553-7404}, support = {R15 HG010409/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Eukaryota/genetics ; Eukaryotic Cells ; *Evolution, Molecular ; *Gene Transfer, Horizontal/genetics ; Phylogeny ; Prokaryotic Cells ; }, abstract = {Vertical inheritance is foundational to Darwinian evolution, but fails to explain major innovations such as the rapid spread of antibiotic resistance among bacteria and the origin of photosynthesis in eukaryotes. While lateral gene transfer (LGT) is recognized as an evolutionary force in prokaryotes, the role of LGT in eukaryotic evolution is less clear. With the exception of the transfer of genes from organelles to the nucleus, a process termed endosymbiotic gene transfer (EGT), the extent of interdomain transfer from prokaryotes to eukaryotes is highly debated. A common critique of studies of interdomain LGT is the reliance on the topology of single-gene trees that attempt to estimate more than one billion years of evolution. We take a more conservative approach by identifying cases in which a single clade of eukaryotes is found in an otherwise prokaryotic gene tree (i.e. exclusive presence). Starting with a taxon-rich dataset of over 13,600 gene families and passing data through several rounds of curation, we identify and categorize the function of 306 interdomain LGT events into diverse eukaryotes, including 189 putative EGTs, 52 LGTs into Opisthokonta (i.e. animals, fungi and their microbial relatives), and 42 LGTs nearly exclusive to anaerobic eukaryotes. To assess differential gene loss as an explanation for exclusive presence, we compare branch lengths within each LGT tree to a set of vertically-inherited genes subsampled to mimic gene loss (i.e. with the same taxonomic sampling) and consistently find shorter relative distance between eukaryotes and prokaryotes in LGT trees, a pattern inconsistent with gene loss. Our methods provide a framework for future studies of interdomain LGT and move the field closer to an understanding of how best to model the evolutionary history of eukaryotes.}, }
@article {pmid35731345, year = {2022}, author = {Da Silva, WM and Larzabal, M and Aburjaile, FF and Riviere, N and Martorelli, L and Bono, J and Amadio, A and Cataldi, A}, title = {Whole-genome sequencing analysis of Shiga toxin-producing Escherichia coli O22:H8 isolated from cattle prediction pathogenesis and colonization factors and position in STEC universe phylogeny.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {60}, number = {7}, pages = {689-704}, pmid = {35731345}, issn = {1976-3794}, mesh = {Animals ; Cattle ; *Escherichia coli Infections/microbiology/veterinary ; *Escherichia coli Proteins/genetics ; Phylogeny ; Shiga Toxin/genetics ; *Shiga-Toxigenic Escherichia coli/genetics ; Virulence Factors/genetics/metabolism ; }, abstract = {Shiga toxin-producing Escherichia coli (STEC) is a foodborne pathogen capable of causing illness in humans. In a previous study, our group showed that a STEC isolate belonging to O22:H8 serotype (strain 154) can interfere with STEC O157:H7 colonization both in vitro and in vivo. Using whole-genome sequencing and genomic comparative, we predicted a subset of genes acquired by O22:H8 strain 154 through horizontal gene transfer that might be responsible for the phenotype previously described by our group. Among them were identified genes related to the pathogenesis of non-LEE (locus of enterocyte effacement) STEC, specific metabolic processes, antibiotic resistance and genes encoding for the T6SS-1 that is related to inter-bacterial competition. In addition, we showed that this strain carries stx1c and stx2dact, a mucus-inducible variant. The results obtained in this study provide insights into STEC genomic plasticity and the importance of genomic islands in the adaptation and pathogenesis of this pathogen.}, }
@article {pmid35729152, year = {2022}, author = {Li, XT and Huang, ZS and Tang, YQ and Lin, CQ and Wang, CM}, title = {[Generation mechanism and control methods of antibiotic and heavy metal resistance genes in poultry waste: A review].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {33}, number = {6}, pages = {1719-1728}, doi = {10.13287/j.1001-9332.202210.029}, pmid = {35729152}, issn = {1001-9332}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Bacteria ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Metals, Heavy ; Poultry/genetics ; }, abstract = {As antibiotics and heavy metals are often mixed in animal feed, their excretion through animal feces would cause bacteria to produce antibiotic resistance genes and heavy metal resistance genes. The pollution of antibiotics resistance gene and heavy metal resistance gene has become a major threat to human health and ecological environment. From the perspective of bacterial evolution, we proposed the importance of bacterial long-term evolution experiments about antibiotics and heavy metals. There is a complex co-selection resistance between antibiotic resistance genes and heavy metal resistance genes, which interact with each other and collectively determine the environmental behavior of bacteria. Horizontal transfer of resistance gene increases its variability in the environment. Mobile genetic elements play an important role in horizontal transfer of resistance gene. As for resistance gene pollution control, advanced oxidation technology has a good resistance gene removal effect. The UV/TiO2 oxidation technology can reduce the abundance of antibiotic resistance genes of 4.7-5.8 log, with an efficiency of >99.99%. Other control strategies, such as the use of Macleaya cordata extract and the combination of bacteriophage and antibiotics, are also of significance for controlling resistance genes.}, }
@article {pmid35728321, year = {2022}, author = {Song, L and Jiang, G and Wang, C and Ma, J and Chen, H}, title = {Effects of antibiotics consumption on the behavior of airborne antibiotic resistance genes in chicken farms.}, journal = {Journal of hazardous materials}, volume = {437}, number = {}, pages = {129288}, doi = {10.1016/j.jhazmat.2022.129288}, pmid = {35728321}, issn = {1873-3336}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; *Chickens/genetics ; Drug Resistance, Microbial/genetics ; Farms ; Genes, Bacterial ; }, abstract = {The antibiotics and antibiotic resistance genes (ARGs) have caused pollution of livestock farm environments. There are limited investigations about airborne ARGs and what role the antibiotics play remains largely unclear. The dynamics of various antibiotics were compared between feces samples from chicken fed a diet with and without antibiotics. In contrast to the farm with no antibiotics drugs, the hazard quotients (HQs) of OTC (24.8-205.4) and CTC (18.0-317.0) are particularly high in the farm with in-feed antibiotics drugs. The high ecological risks of antibiotics in chicken feces with in-feed antibiotic drugs were 100 % as determined. We quantified mobile genetic elements (MGEs) and ARGs and investigated bacterial communities in feces and air samples. The concentration of airborne ARG/MGE subtypes with in-feed antibiotic drugs is about two orders of magnitude higher than those without drugs. This study reveals that the indoor air of chicken farms is a reservoir of ARGs in the environment. Continuous feeding of antibiotics can change the intestinal microbial community structure of the chicken. The possibility of horizontal gene transfer of ARGs in air and feces samples might be increased by in-feed antibiotic drugs. The enrichment of ARGs in the chicken farm can be reduced by minimizing antibiotic use.}, }
@article {pmid35719354, year = {2022}, author = {Lindemann, PC and Mylvaganam, H and Oppegaard, O and Anthonisen, IL and Zecic, N and Skaare, D}, title = {Case Report: Whole-Genome Sequencing of Serially Collected Haemophilus influenzae From a Patient With Common Variable Immunodeficiency Reveals Within-Host Evolution of Resistance to Trimethoprim-Sulfamethoxazole and Azithromycin After Prolonged Treatment With These Antibiotics.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {896823}, pmid = {35719354}, issn = {2235-2988}, mesh = {Anti-Bacterial Agents/metabolism/pharmacology/therapeutic use ; Azithromycin/pharmacology/therapeutic use ; *Common Variable Immunodeficiency ; Dihydropteroate Synthase/genetics/metabolism ; *Haemophilus Infections/drug therapy/microbiology ; Haemophilus influenzae ; Humans ; Microbial Sensitivity Tests ; Trimethoprim, Sulfamethoxazole Drug Combination/pharmacology/therapeutic use ; }, abstract = {We report within-host evolution of antibiotic resistance to trimethoprim-sulfamethoxazole and azithromycin in a nontypeable Haemophilus influenzae strain from a patient with common variable immunodeficiency (CVID), who received repeated or prolonged treatment with these antibiotics for recurrent respiratory tract infections. Whole-genome sequencing of three longitudinally collected sputum isolates during the period April 2016 to January 2018 revealed persistence of a strain of sequence type 2386. Reduced susceptibility to trimethoprim-sulfamethoxazole in the first two isolates was associated with mutations in genes encoding dihydrofolate reductase (folA) and its promotor region, dihydropteroate synthase (folP), and thymidylate synthase (thyA), while subsequent substitution of a single amino acid in dihydropteroate synthase (G225A) rendered high-level resistance in the third isolate from 2018. Azithromycin co-resistance in this isolate was associated with amino acid substitutions in 50S ribosomal proteins L4 (W59R) and L22 (G91D), possibly aided by a substitution in AcrB (A604E) of the AcrAB efflux pump. All three isolates were resistant to aminopenicillins and cefotaxime due to TEM-1B beta-lactamase and identical alterations in penicillin-binding protein 3. Further resistance development to trimethoprim-sulfamethoxazole and azithromycin resulted in a multidrug-resistant phenotype. Evolution of multidrug resistance due to horizontal gene transfer and/or spontaneous mutations, along with selection of resistant subpopulations is a particular risk in CVID and other patients requiring repeated and prolonged antibiotic treatment or prophylaxis. Such challenging situations call for careful antibiotic stewardship together with supportive and supplementary treatment. We describe the clinical and microbiological course of events in this case report and address the challenges encountered.}, }
@article {pmid35714926, year = {2022}, author = {Aslan, E and Arslanyolu, M}, title = {Discovery of deoxyribonuclease II-like proteins in bacteria.}, journal = {Molecular phylogenetics and evolution}, volume = {174}, number = {}, pages = {107554}, doi = {10.1016/j.ympev.2022.107554}, pmid = {35714926}, issn = {1095-9513}, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics ; *Endodeoxyribonucleases/chemistry/genetics/metabolism ; *Eukaryota/genetics ; Phylogeny ; Sequence Alignment ; }, abstract = {Deoxyribonuclease II (DNase II) is one of the earliest enzymes discovered in the history of biochemistry. Its role in apoptosis and development has been documented with great detail in eukaryotes. Prior in silico analyses showed its complete absence in bacterial genomes, with the exception of single bacterial genus: Burkholderia. It is therefore considered to be a eukaryotic enzyme. Here we show that the presence of DNase II is not limited to Burkholderia, as we find over one hundred DNase II-like sequences spanning 90 bacteria species belonging to 54 different genera and seven phyla. The majority of the significant hits (85%) come from Bacteroidetes and Proteobacteria phyla. Sequence analyses reveal that bacterial DNase II-like proteins possess a signature catalytic motif of eukaryotic DNase II. In phylogenetic analyses, we find that bacterial DNase II-like proteins are divided into two distinct clades. Our structural analyses reveal high levels of similarity between experimentally determined crystal structures of recombinant Burkholderia thailandensis DNase II and candidate bacterial DNase II-like proteins. We also biochemically show that Chromobacterium violaceum cell lysate possesses acidic DNase II-like activities. Collectively, our results indicate that DNase II has deeper evolutionary roots than previously thought. We argue that either some prokaryotic lineages have undergone losses of DNase II genes, resulting in rare conservation, or some lineages have acquired DNase II genes from eukaryotes through lateral gene transfer. We also discuss the possible involvement of DNase II as a part of an anti-phage defense system in bacteria.}, }
@article {pmid35714537, year = {2022}, author = {Schmidt, SBI and Rodríguez-Rojas, A and Rolff, J and Schreiber, F}, title = {Biocides used as material preservatives modify rates of de novo mutation and horizontal gene transfer in bacteria.}, journal = {Journal of hazardous materials}, volume = {437}, number = {}, pages = {129280}, doi = {10.1016/j.jhazmat.2022.129280}, pmid = {35714537}, issn = {1873-3336}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacillus subtilis ; *Disinfectants/pharmacology ; Drug Resistance, Bacterial/genetics ; Escherichia coli/genetics ; *Gene Transfer, Horizontal ; Mutation ; Permethrin ; }, abstract = {Antimicrobial resistance (AMR) is a global health problem with the environment being an important compartment for the evolution and transmission of AMR. Previous studies showed that de-novo mutagenesis and horizontal gene transfer (HGT) by conjugation or transformation - important processes underlying resistance evolution and spread - are affected by antibiotics, metals and pesticides. However, natural microbial communities are also frequently exposed to biocides used as material preservatives, but it is unknown if these substances induce mutagenesis and HGT. Here, we show that active substances used in material preservatives can increase rates of mutation and conjugation in a species- and substance-dependent manner, while rates of transformation are not increased. The bisbiguanide chlorhexidine digluconate, the quaternary ammonium compound didecyldimethylammonium chloride, the metal copper, the pyrethroid-insecticide permethrin, and the azole-fungicide propiconazole increase mutation rates in Escherichia coli, whereas no increases were identified for Bacillus subtilis and Acinetobacter baylyi. Benzalkonium chloride, chlorhexidine and permethrin increased conjugation in E. coli. Moreover, our results show a connection between the RpoS-mediated general stress and the RecA-linked SOS response with increased rates of mutation and conjugation, but not for all biocides. Taken together, our data show the importance of assessing the contribution of material preservatives on AMR evolution and spread.}, }
@article {pmid35709577, year = {2022}, author = {Akram, F and Haq, IU and Shah, FI and Aqeel, A and Ahmed, Z and Mir, AS and Qureshi, SS and Raja, SI}, title = {Genus Thermotoga: A valuable home of multifunctional glycoside hydrolases (GHs) for industrial sustainability.}, journal = {Bioorganic chemistry}, volume = {127}, number = {}, pages = {105942}, doi = {10.1016/j.bioorg.2022.105942}, pmid = {35709577}, issn = {1090-2120}, mesh = {*Bacteria/genetics ; *Glycoside Hydrolases/genetics ; Thermotoga ; }, abstract = {Nature is a dexterous and prolific chemist for cataloging a number of hostile niches that are the ideal residence of various thermophiles. Apart from having other species, these subsurface environments are considered a throne of bacterial genus Thermotoga. The genome sequence of Thermotogales encodes complex and incongruent clusters of glycoside hydrolases (GHs), which are superior to their mesophilic counterparts and play a prominent role in various applications due to their extreme intrinsic stability. They have a tremendous capacity to use a wide variety of simple and multifaceted carbohydrates through GHs, formulate fermentative hydrogen and bioethanol at extraordinary yield, and catalyze high-temperature reactions for various biotechnological applications. Nevertheless, no stringent rules exist for the thermo-stabilization of biocatalysts present in the genus Thermotoga. These enzymes endure immense attraction in fundamental aspects of how these polypeptides attain and stabilize their distinctive three-dimensional (3D) structures to accomplish their physiological roles. Moreover, numerous genome sequences from Thermotoga species have revealed a significant fraction of genes most closely related to those of archaeal species, thus firming a staunch belief of lateral gene transfer mechanism. However, the question of its magnitude is still in its infancy. In addition to GHs, this genus is a paragon of encapsulins which carry pharmacological and industrial significance in the field of life sciences. This review highlights an intricate balance between the genomic organizations, factors inducing the thermostability, and pharmacological and industrial applications of GHs isolated from genus Thermotoga.}, }
@article {pmid35709500, year = {2022}, author = {Pepperell, CS}, title = {Evolution of Tuberculosis Pathogenesis.}, journal = {Annual review of microbiology}, volume = {76}, number = {}, pages = {661-680}, doi = {10.1146/annurev-micro-121321-093031}, pmid = {35709500}, issn = {1545-3251}, support = {R01 AI113287/AI/NIAID NIH HHS/United States ; }, mesh = {Evolution, Molecular ; Gene Transfer, Horizontal ; Humans ; *Mycobacterium tuberculosis/genetics ; *Tuberculosis/microbiology ; Virulence/genetics ; Virulence Factors/genetics ; }, abstract = {Mycobacterium tuberculosis is a globally distributed, lethal pathogen of humans. The virulence armamentarium of M. tuberculosis appears to have been developed on a scaffold of antiphagocytic defenses found among diverse, mostly free-living species of Mycobacterium. Pathoadaptation was further aided by the modularity, flexibility, and interactivity characterizing mycobacterial effectors and their regulators. During emergence of M. tuberculosis, novel genetic material was acquired, created, and integrated with existing tools. The major mutational mechanisms underlying these adaptations are discussed in this review, with examples. During its evolution, M. tuberculosis lost the ability and/or opportunity to engage in lateral gene transfer, but despite this it has retained the adaptability that characterizes mycobacteria. M. tuberculosis exemplifies the evolutionary genomic mechanisms underlying adoption of the pathogenic niche, and studies of its evolution have uncovered a rich array of discoveries about how new pathogens are made.}, }
@article {pmid35709325, year = {2023}, author = {Kotsaridis, K and Tsakiri, D and Sarris, PF}, title = {Understanding enemy's weapons to an effective prevention: common virulence effects across microbial phytopathogens kingdoms.}, journal = {Critical reviews in microbiology}, volume = {49}, number = {4}, pages = {528-542}, doi = {10.1080/1040841X.2022.2083939}, pmid = {35709325}, issn = {1549-7828}, mesh = {Virulence ; *Plants ; *Plant Diseases/prevention &amp; control ; Host-Pathogen Interactions ; }, abstract = {Plant-pathogens interaction is an ongoing confrontation leading to the emergence of new diseases. The majority of the invading microorganisms inject effector proteins into the host cell, to bypass the sophisticated defense system of the host. However, the effectors could also have other specialized functions, which can disrupt various biological pathways of the host cell. Pathogens can enrich their effectors arsenal to increase infection success or expand their host range. This usually is accomplished by the horizontal gene transfer. Nowadays, the development of specialized software that can predict proteins structure, has changed the experimental designing in effectors' function research. Different effectors of distinct plant pathogens tend to fold alike and have the same function and focussed structural studies on microbial effectors can help to uncover their catalytic/functional activities, while the structural similarity can enable cataloguing the great number of pathogens' effectors. In this review, we collectively present phytopathogens' effectors with known enzymatic functions and proteins structure, originated from all the kingdoms of microbial plant pathogens. Presentation of their common domains and motifs is also included. We believe that the in-depth understanding of the enemy's weapons will help the development of new strategies to prevent newly emerging or re-emerging plant pathogens.}, }
@article {pmid35706928, year = {2022}, author = {Chen, H and Mai, H and Lopes, B and Wen, F and Patil, S}, title = {Novel Pseudomonas aeruginosa Strains Co-Harbouring bla NDM-1 Metallo β-Lactamase and mcr-1 Isolated from Immunocompromised Paediatric Patients.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {2929-2936}, pmid = {35706928}, issn = {1178-6973}, abstract = {BACKGROUND: The rising resistance to carbapenems in Gram-negative bacteria worldwide poses a major clinical and public health risk. This study aimed to characterise carbapenem- and colistin-resistance genes, bla NDM-1 and mcr-1 located on IncX4 plasmid in MDR Pseudomonas aeruginosa, isolated from paediatric patients undergoing chemotherapy as a result of leukaemia.<br><br>METHODS: In this study, six carbapenem-resistant strains of P. aeruginosa were isolated from two paediatric patients under chemotherapy treatment (1.8 years old female and 2.1 years male) from the Shenzhen Hospital, China, in the year 2019. Isolates were screened for conventional antibiotics such as tobramycin, cefepime, imipenem, and ciprofloxacin in additional colistin by using the broth dilution method. Furthermore, resistance determinants: mcr-1, bla NDM-1, bla KPC-1, and bla GES were screened using PCR and sequencing followed by multi-locus sequence typing. The horizontal gene transfer and location of mcr-1 and bla NDM-1 were determined by a liquid mating assay. In addition, Incompatibility type (Inc), PCR-based replicon type, and subgroup (MOB) of plasmid were studied.<br><br>RESULTS: The screening for conventional antibiotics isolates showed 100% resistance to all the tested antibiotics except tobramycin. All isolates harboured carbapenemase encoding bla NDM-1, of which three also had mcr-1 located on a single IncX4 transferable plasmid. MLST typing revealed that four strains had a novel (new) STs type, while two belonged to ST1966.<br><br>CONCLUSION: This study identified for the first time colistin- and carbapenem-resistant MDR P. aeruginosa in paediatric patients with leukaemia in Shenzhen, China. It highlights the need for continuous surveillance in high-risk clones of MDR P. aeruginosa. Prudent use of antibiotics based on local antimicrobial susceptibility and clinical characteristics can help in reducing mortality in immunocompromised patients.}, }
@article {pmid35706021, year = {2022}, author = {Wu, B and Hao, W and Cox, MP}, title = {Reconstruction of gene innovation associated with major evolutionary transitions in the kingdom Fungi.}, journal = {BMC biology}, volume = {20}, number = {1}, pages = {144}, pmid = {35706021}, issn = {1741-7007}, mesh = {Animals ; *Evolution, Molecular ; *Fungi/genetics ; Gene Transfer, Horizontal ; Phylogeny ; Plants/genetics ; }, abstract = {BACKGROUND: Fungi exhibit astonishing diversity with multiple major phenotypic transitions over the kingdom's evolutionary history. As part of this process, fungi developed hyphae, adapted to land environments (terrestrialization), and innovated their sexual structures. These changes also helped fungi establish ecological relationships with other organisms (animals and plants), but the genomic basis of these changes remains largely unknown.<br><br>RESULTS: By systematically analyzing 304 genomes from all major fungal groups, together with a broad range of eukaryotic outgroups, we have identified 188 novel orthogroups associated with major changes during the evolution of fungi. Functional annotations suggest that many of these orthogroups were involved in the formation of key trait innovations in extant fungi and are functionally connected. These innovations include components for cell wall formation, functioning of the spindle pole body, polarisome formation, hyphal growth, and mating group signaling. Innovation of mitochondria-localized proteins occurred widely during fungal transitions, indicating their previously unrecognized importance. We also find that prokaryote-derived horizontal gene transfer provided a small source of evolutionary novelty with such genes involved in key metabolic pathways.<br><br>CONCLUSIONS: The overall picture is one of a relatively small number of novel genes appearing at major evolutionary transitions in the phylogeny of fungi, with most arising de novo and horizontal gene transfer providing only a small additional source of evolutionary novelty. Our findings contribute to an increasingly detailed portrait of the gene families that define fungal phyla and underpin core features of extant fungi.}, }
@article {pmid35705132, year = {2022}, author = {Hoang, HTT and Higashi, A and Yamaguchi, T and Kawahara, R and Calvopina, M and Bastidas-Caldés, A and Yamamoto, M and Yamamoto, Y}, title = {Fusion plasmid carrying the colistin resistance gene mcr of Escherichia coli isolated from healthy residents.}, journal = {Journal of global antimicrobial resistance}, volume = {30}, number = {}, pages = {152-154}, doi = {10.1016/j.jgar.2022.06.007}, pmid = {35705132}, issn = {2213-7173}, mesh = {Colistin/pharmacology ; Drug Resistance, Bacterial/genetics ; Escherichia coli ; *Escherichia coli Infections/microbiology ; *Escherichia coli Proteins/genetics ; Humans ; Plasmids/genetics ; }, abstract = {OBJECTIVES: The extensive spread of colistin resistance represents an enormous concern to infectious disease treatment, because colistin is one of the few effective antibiotics against multidrug-resistant bacterial infections, including carbapenem-resistant bacteria. This dissemination can be caused by plasmid transfer containing the colistin resistance gene mcr. Therefore, the plasmid host range affects horizontal gene transfer. This study reports a fusion plasmid of different incompatibility types, which could easily expand the plasmid host range, allowing widespread mcr prevalence in the microbial community.<br><br>METHODS: Genome sequences of colistin-resistant Escherichia coli isolates from stool specimens of healthy human residents in Ecuador were determined using the DNBSEQ and MinION platforms. Hybrid genome assembly was performed using Unicycler, and the genomes were annotated using DFAST. Genome analysis was performed using the Geneious Prime software.<br><br>RESULTS: Two colistin-resistant E. coli strains isolated separately from different residents presented mcr-carrying plasmids with fused different incompatibility types, IncFIA, IncHIIA, and IncHIIB. The phylogenies of these host bacteria were different. The sizes of the mcr-carrying fusion plasmids pLR-06 and pLR-50 with the full Tn6330 mcr-transposon were 260 Kbp and 198 Kbp, respectively. Both fusion plasmids possessed other resistance genes, including tet(B), tet(M), blaTEM-1b, sul3, cmlA1, aadA1, aadA2, fosA3, and dfrA12.<br><br>CONCLUSION: This is the first report of a fusion plasmid comprising different incompatibility types with mcr from colistin-resistant E. coli strains isolated from community residents. The mcr fusion plasmid may play a crucial role in achieving horizontal mcr transmission and the evolution of the multidrug resistance plasmid among hosts.}, }
@article {pmid35703039, year = {2022}, author = {Kurushima, J and Tomita, H}, title = {Advances of genetic engineering in streptococci and enterococci.}, journal = {Microbiology and immunology}, volume = {66}, number = {9}, pages = {411-417}, doi = {10.1111/1348-0421.13015}, pmid = {35703039}, issn = {1348-0421}, support = {//The Naito Foundation/ ; 22K07052//Japan Society for Promotion of Science (JSPS) KAKENHI/ ; 22K07067//Japan Society for Promotion of Science (JSPS) KAKENHI/ ; 21KA1004//Japanese Ministry of Health, Labor and Welfare (Research Program on ensuring Food Safety)/ ; JP22fk0108604h0902//Japan Agency for Medical Research and Development (AMED)/ ; JP22wm0225008h0203//Japan Agency for Medical Research and Development (AMED)/ ; //Ohyama Health Foundation Inc./ ; //GSK Japan research grant/ ; }, mesh = {CRISPR-Cas Systems ; *Enterococcus/genetics ; *Gene Editing/methods ; Genetic Engineering/methods ; Streptococcus/genetics ; }, abstract = {In the post-genome era, reverse genetic engineering is an indispensable methodology for experimental molecular biology to provide a deeper understanding of the principal relationship between genomic features and biological phenotypes. Technically, genetic engineering is carried out through allele replacement of a target genomic locus with a designed nucleotide sequence, so called site-directed mutagenesis. To artificially manipulate allele replacement through homologous recombination, researchers have improved various methodologies that are optimized to the bacterial species of interest. Here, we review widely used genetic engineering technologies, particularly for streptococci and enterococci, and recent advances that enable more effective and flexible manipulation. The development of genetic engineering has been promoted by synthetic biology approaches based on basic biological knowledge of horizontal gene transfer systems, such as natural conjugative transfer, natural transformation, and the CRISPR/Cas system. Therefore, this review also describes basic insights into molecular biology that underlie improvements in genetic engineering technology.}, }
@article {pmid35701521, year = {2022}, author = {Tekle, YI and Wang, F and Tran, H and Hayes, TD and Ryan, JF}, title = {The draft genome of Cochliopodium minus reveals a complete meiosis toolkit and provides insight into the evolution of sexual mechanisms in Amoebozoa.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {9841}, pmid = {35701521}, issn = {2045-2322}, support = {R15 GM116103/GM/NIGMS NIH HHS/United States ; 1R15GM116103-02/NH/NIH HHS/United States ; }, mesh = {*Amoeba/genetics ; *Amoebozoa/genetics ; Evolution, Molecular ; Genome/genetics ; Genomics ; Meiosis/genetics ; Phylogeny ; }, abstract = {To date, genomic analyses in amoebozoans have been mostly limited to model organisms or medically important lineages. Consequently, the vast diversity of Amoebozoa genomes remain unexplored. A draft genome of Cochliopodium minus, an amoeba characterized by extensive cellular and nuclear fusions, is presented. C. minus has been a subject of recent investigation for its unusual sexual behavior. Cochliopodium's sexual activity occurs during vegetative stage making it an ideal model for studying sexual development, which is sorely lacking in the group. Here we generate a C. minus draft genome assembly. From this genome, we detect a substantial number of lateral gene transfer (LGT) instances from bacteria (15%), archaea (0.9%) and viruses (0.7%) the majority of which are detected in our transcriptome data. We identify the complete meiosis toolkit genes in the C. minus genome, as well as the absence of several key genes involved in plasmogamy and karyogamy. Comparative genomics of amoebozoans reveals variation in sexual mechanism exist in the group. Similar to complex eukaryotes, C. minus (some amoebae) possesses Tyrosine kinases and duplicate copies of SPO11. We report a first example of alternative splicing in a key meiosis gene and draw important insights on molecular mechanism of sex in C. minus using genomic and transcriptomic data.}, }
@article {pmid35700229, year = {2022}, author = {Lin, Q and Banerjee, A and Stefanović, S}, title = {Mitochondrial phylogenomics of Cuscuta (Convolvulaceae) reveals a potentially functional horizontal gene transfer from the host.}, journal = {Genome biology and evolution}, volume = {14}, number = {6}, pages = {}, pmid = {35700229}, issn = {1759-6653}, abstract = {Horizontal gene transfers (HGTs) from host or other organisms have been reported in mitochondrial genomes of parasitic plants. Genes transferred in this fashion have usually been found non-functional. Several examples of HGT from the mitochondrial genome of parasitic Cuscuta (Convolvulaceae) to its hosts have been reported, but not vice versa. Here we used 31 protein-coding mitochondrial genes to infer the phylogeny of Cuscuta, and compared it with previous nuclear and plastid phylogenetic estimates. We also investigated the presence of HGTs within these lineages. Unlike in plastid genomes, we did not find extensive gene loss in their mitochondrial counterparts. Our results reveal the first example of organellar HGT from host to Cuscuta. Mitochondrial atp1 genes of South African subgenus Pachystigma were inferred to be transferred from Lamiales, with high support. Moreover, the horizontally transferred atp1 gene has functionally replaced the native, vertically transmitted copy, has an intact open reading frame, and is under strong purifying selection, all of which suggests that this xenolog remains functional. The mitochondrial phylogeny of Cuscuta is generally consistent with previous plastid and nuclear phylogenies, except for the misplacement of Pachystigma when atp1 is included. This incongruence may be caused by the HGT mentioned above. No example of HGT was found within mitochondrial genes of three other, independently evolved parasitic lineages we sampled: Cassytha/Laurales, Krameria/Zygophyllales, and Lennooideae/Boraginales.}, }
@article {pmid35699339, year = {2022}, author = {Ahator, SD and Sagar, S and Zhu, M and Wang, J and Zhang, LH}, title = {Nutrient Availability and Phage Exposure Alter the Quorum-Sensing and CRISPR-Cas-Controlled Population Dynamics of Pseudomonas aeruginosa.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0009222}, pmid = {35699339}, issn = {2379-5077}, mesh = {Quorum Sensing/genetics ; Pseudomonas aeruginosa/genetics ; *Bacteriophages/genetics ; CRISPR-Cas Systems/genetics ; Acyl-Butyrolactones/pharmacology ; *Anti-Infective Agents/pharmacology ; }, abstract = {Quorum sensing (QS) coordinates bacterial communication and cooperation essential for virulence and dominance in polymicrobial settings. QS also regulates the CRISPR-Cas system for targeted defense against parasitic genomes from phages and horizontal gene transfer. Although the QS and CRISPR-Cas systems are vital for bacterial survival, they undergo frequent selection in response to biotic and abiotic factors. Using the opportunistic Pseudomonas aeruginosa with well-established QS and CRISPR-Cas systems, we show how the social interactions between the acyl-homoserine lactone (AHL)-QS signal-blind mutants (ΔlasRrhlR) and the CRISPR-Cas mutants are affected by phage exposure and nutrient availability. We demonstrate that media conditions and phage exposure alter the resistance and relative fitness of ΔlasRrhlR and CRISPR-Cas mutants while tipping the fitness advantage in favor of the QS signal-blind mutants under nutrient-limiting conditions. We also show that the AHL signal-blind mutants are less selected by phages under QS-inducing conditions than the CRISPR-Cas mutants, whereas the mixed population of the CRISPR-Cas and AHL signal-blind mutants reduce phage infectivity, which can improve survival during phage exposure. Our data reveal that phage exposure and nutrient availability reshape the population dynamics between the ΔlasRrhlR QS mutants and CRISPR-Cas mutants, with key indications for cooperation and conflict between the strains. IMPORTANCE The increase in antimicrobial resistance has created the need for alternative interventions such as phage therapy. However, as previously observed with antimicrobial resistance, phage therapy will not be effective if bacteria evolve resistance and persist in the presence of the phages. The QS is commonly known as an arsenal for bacteria communication, virulence, and regulation of the phage defense mechanism, the CRISPR-Cas system. The QS and CRISPR-Cas systems are widespread in bacteria. However, they are known to evolve rapidly under the influence of biotic and abiotic factors in the bacterial environment, resulting in alteration in bacterial genotypes, which enhance phage resistance and fitness. We believe that adequate knowledge of the influence of environmental factors on the bacterial community lifestyle and phage defense mechanisms driven by the QS and CRISPR-Cas system is necessary for developing effective phage therapy.}, }
@article {pmid35697144, year = {2022}, author = {Carson, J and Ledda, A and Ferretti, L and Keeling, M and Didelot, X}, title = {The bounded coalescent model: Conditioning a genealogy on a minimum root date.}, journal = {Journal of theoretical biology}, volume = {548}, number = {}, pages = {111186}, doi = {10.1016/j.jtbi.2022.111186}, pmid = {35697144}, issn = {1095-8541}, mesh = {*Algorithms ; Computer Simulation ; Genetics, Population ; Humans ; *Models, Genetic ; Phylogeny ; Probability ; }, abstract = {The coalescent model represents how individuals sampled from a population may have originated from a last common ancestor. The bounded coalescent model is obtained by conditioning the coalescent model such that the last common ancestor must have existed after a certain date. This conditioned model arises in a variety of applications, such as speciation, horizontal gene transfer or transmission analysis, and yet the bounded coalescent model has not been previously analysed in detail. Here we describe a new algorithm to simulate from this model directly, without resorting to rejection sampling. We show that this direct simulation algorithm is more computationally efficient than the rejection sampling approach. We also show how to calculate the probability of the last common ancestor occurring after a given date, which is required to compute the probability density of realisations under the bounded coalescent model. Our results are applicable in both the isochronous (when all samples have the same date) and heterochronous (where samples can have different dates) settings. We explore the effect of setting a bound on the date of the last common ancestor, and show that it affects a number of properties of the resulting phylogenies. All our methods are implemented in a new R package called BoundedCoalescent which is freely available online.}, }
@article {pmid35695507, year = {2022}, author = {Mustapha, MM and Srinivasa, VR and Griffith, MP and Cho, ST and Evans, DR and Waggle, K and Ezeonwuka, C and Snyder, DJ and Marsh, JW and Harrison, LH and Cooper, VS and Van Tyne, D}, title = {Genomic Diversity of Hospital-Acquired Infections Revealed through Prospective Whole-Genome Sequencing-Based Surveillance.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0138421}, pmid = {35695507}, issn = {2379-5077}, support = {U01 AI124302/AI/NIAID NIH HHS/United States ; KL2 TR001856/TR/NCATS NIH HHS/United States ; R21Al109459//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01 AI127472/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Genome, Bacterial/genetics ; *Genomics ; Whole Genome Sequencing ; Anti-Bacterial Agents ; Hospitals ; }, abstract = {Healthcare-associated infections (HAIs) cause mortality, morbidity, and waste of health care resources. HAIs are also an important driver of antimicrobial resistance, which is increasing around the world. Beginning in November 2016, we instituted an initiative to detect outbreaks of HAIs using prospective whole-genome sequencing-based surveillance of bacterial pathogens collected from hospitalized patients. Here, we describe the diversity of bacteria sampled from hospitalized patients at a single center, as revealed through systematic analysis of bacterial isolate genomes. We sequenced the genomes of 3,004 bacterial isolates from hospitalized patients collected over a 25-month period. We identified bacteria belonging to 97 distinct species, which were distributed among 14 groups of related species. Within these groups, isolates could be distinguished from one another by both average nucleotide identity (ANI) and principal-component analysis of accessory genes (PCA-A). Core genome genetic distances and rates of evolution varied among species, which has practical implications for defining shared ancestry during outbreaks and for our broader understanding of the origins of bacterial strains and species. Finally, antimicrobial resistance genes and putative mobile genetic elements were frequently observed, and our systematic analysis revealed patterns of occurrence across the different species sampled from our hospital. Overall, this study shows how understanding the population structure of diverse pathogens circulating in a single health care setting can improve the discriminatory power of genomic epidemiology studies and can help define the processes leading to strain and species differentiation. IMPORTANCE Hospitalized patients are at increased risk of becoming infected with antibiotic-resistant organisms. We used whole-genome sequencing to survey and compare over 3,000 clinical bacterial isolates collected from hospitalized patients at a large medical center over a 2-year period. We identified nearly 100 different bacterial species, which we divided into 14 different groups of related species. When we examined how genetic relatedness differed between species, we found that different species were likely evolving at different rates within our hospital. This is significant because the identification of bacterial outbreaks in the hospital currently relies on genetic similarity cutoffs, which are often applied uniformly across organisms. Finally, we found that antibiotic resistance genes and mobile genetic elements were abundant and were shared among the bacterial isolates we sampled. Overall, this study provides an in-depth view of the genomic diversity and evolutionary processes of bacteria sampled from hospitalized patients, as well as genetic similarity estimates that can inform hospital outbreak detection and prevention efforts.}, }
@article {pmid35695430, year = {2022}, author = {Fansler, RT and Zhu, W}, title = {Mind the Gap: Bridging the Divide from Sequencing Data to Empiric Phenotypes in the Human Gut Microbiota.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0020722}, pmid = {35695430}, issn = {2379-5077}, support = {R01 DK134692/DK/NIDDK NIH HHS/United States ; R35 GM147470/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Bacteria/genetics ; Polysaccharides ; *Microbiota ; Genomics ; }, abstract = {The gut microbiome exerts a powerful influence on human health and disease. Elucidating the underlying mechanisms of the microbiota's influence is hindered by the immense complexity of the gut microbial community and the glycans they forage. Despite a wealth of genomic and metagenomic sequencing information, there remains a lack of informative phenotypic measurements. Pudlo NA, Urs K, Crawford R, Pirani A, et al. (mSystems 7: e00947-21, 2022, https://doi.org/10.1128/msystems.00947-21) decode this complexity by introducing a scalable assay to measure specific carbohydrate utilization in the dominant microbiota phylum Bacteroidetes. The results reveal a mosaic structure of glycan utilization, both genetic and functional, underpinning niche construction in the human gastrointestinal tract. This Commentary highlights the significance of their findings in connection to the field's growing appreciation for competition, cooperation, and horizontal gene transfer in shaping the highly complex microbial community.}, }
@article {pmid35694630, year = {2022}, author = {Lee, G and Yoo, K}, title = {A review of the emergence of antibiotic resistance in bioaerosols and its monitoring methods.}, journal = {Re/views in environmental science and bio/technology}, volume = {21}, number = {3}, pages = {799-827}, pmid = {35694630}, issn = {1572-9826}, abstract = {Despite significant public health concerns regarding infectious diseases in air environments, potentially harmful microbiological indicators, such as antibiotic resistance genes (ARGs) in bioaerosols, have not received significant attention. Traditionally, bioaerosol studies have focused on the characterization of microbial communities; however, a more serious problem has recently arisen due to the presence of ARGs in bioaerosols, leading to an increased prevalence of horizontal gene transfer (HGT). This constitutes a process by which bacteria transfer genes to other environmental media and consequently cause infectious disease. Antibiotic resistance in water and soil environments has been extensively investigated in the past few years by applying advanced molecular and biotechnological methods. However, ARGs in bioaerosols have not received much attention. In addition, ARG and HGT profiling in air environments is greatly limited in field studies due to the absence of suitable methodological approaches. Therefore, this study comprehensively describes recent findings from published studies and some of the appropriate molecular and biotechnological methods for monitoring antibiotic resistance in bioaerosols. In addition, this review discusses the main knowledge gaps regarding current methodological issues and future research directions.}, }
@article {pmid35684209, year = {2022}, author = {Palomba, E and Chiaiese, P and Termolino, P and Paparo, R and Filippone, E and Mazzoleni, S and Chiusano, ML}, title = {Effects of Extracellular Self- and Nonself-DNA on the Freshwater Microalga Chlamydomonas reinhardtii and on the Marine Microalga Nannochloropsis gaditana.}, journal = {Plants (Basel, Switzerland)}, volume = {11}, number = {11}, pages = {}, pmid = {35684209}, issn = {2223-7747}, abstract = {The role of extracellular DNA (exDNA) in soil and aquatic environments was mainly discussed in terms of source of mineral nutrients and of genetic material for horizontal gene transfer. Recently, the self-exDNA (conspecific) has been shown to have an inhibitory effect on the growth of that organism, while the same was not evident for nonself-exDNA (non conspecific). The inhibitory effect of self-exDNA was proposed as a universal phenomenon, although evidence is mainly reported for terrestrial species. The current study showed the inhibitory effect of self-exDNA also on photosynthetic aquatic microorganisms. We showed that self-exDNA inhibits the growth of the microalgae Chlamydomonas reinhardtii and Nannochloropsis gaditana, a freshwater and a marine species, respectively. In addition, the study also revealed the phenotypic effects post self-exDNA treatments. Indeed, Chlamydomonas showed the formation of peculiar heteromorphic aggregates of palmelloid cells embedded in an extracellular matrix, favored by the presence of DNA in the environment, that is not revealed after exposure to nonself-exDNA. The differential effect of self and nonself-exDNA on both microalgae, accompanied by the inhibitory growth effect of self-exDNA are the first pieces of evidence provided for species from aquatic environments.}, }
@article {pmid35682936, year = {2022}, author = {Shikov, AE and Malovichko, YV and Nizhnikov, AA and Antonets, KS}, title = {Current Methods for Recombination Detection in Bacteria.}, journal = {International journal of molecular sciences}, volume = {23}, number = {11}, pages = {}, pmid = {35682936}, issn = {1422-0067}, support = {20-76-10044//Russian Science Foundation/ ; }, mesh = {Bacteria/genetics ; Computational Biology/methods ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Homologous Recombination ; Phylogeny ; }, abstract = {The role of genetic exchanges, i.e., homologous recombination (HR) and horizontal gene transfer (HGT), in bacteria cannot be overestimated for it is a pivotal mechanism leading to their evolution and adaptation, thus, tracking the signs of recombination and HGT events is importance both for fundamental and applied science. To date, dozens of bioinformatics tools for revealing recombination signals are available, however, their pros and cons as well as the spectra of solvable tasks have not yet been systematically reviewed. Moreover, there are two major groups of software. One aims to infer evidence of HR, while the other only deals with horizontal gene transfer (HGT). However, despite seemingly different goals, all the methods use similar algorithmic approaches, and the processes are interconnected in terms of genomic evolution influencing each other. In this review, we propose a classification of novel instruments for both HR and HGT detection based on the genomic consequences of recombination. In this context, we summarize available methodologies paying particular attention to the type of traceable events for which a certain program has been designed.}, }
@article {pmid35679514, year = {2022}, author = {Wang, Z and Wen, Z and Jiang, M and Xia, F and Wang, M and Zhuge, X and Dai, J}, title = {Dissemination of virulence and resistance genes among Klebsiella pneumoniae via outer membrane vesicle: An important plasmid transfer mechanism to promote the emergence of carbapenem-resistant hypervirulent Klebsiella pneumoniae.}, journal = {Transboundary and emerging diseases}, volume = {69}, number = {5}, pages = {e2661-e2676}, doi = {10.1111/tbed.14615}, pmid = {35679514}, issn = {1865-1682}, support = {31872479//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Carbapenem-Resistant Enterobacteriaceae ; Carbapenems/pharmacology ; Escherichia coli/genetics ; Humans ; *Klebsiella Infections/microbiology/veterinary ; Klebsiella pneumoniae/genetics ; Plasmids/genetics ; Virulence/genetics ; beta-Lactamases ; }, abstract = {Klebsiella pneumoniae is well-known opportunistic enterobacteria involved in complex clinical infections in humans and animals. The domestic animals might be a source of the multidrug-resistant virulent K. pneumoniae to humans. K. pneumoniae infections in domestic animals are considered as an emergent global concern. The horizontal gene transfer plays essential roles in bacterial genome evolution by spread of virulence and resistance determinants. However, the virulence genes can be transferred horizontally via K. pneumoniae-derived outer membrane vesicles (OMVs) remains to be unreported. In this study, we performed complete genome sequencing of two K. pneumoniae HvK2115 and CRK3022 with hypervirulent or carbapenem-resistant traits. OMVs from K. pneumoniae HvK2115 and CRK3022 were purified and observed. The carriage of virulence or resistance genes in K. pneumoniae OMVs was identified. The influence of OMVs on the horizontal transfer of virulence-related or drug-resistant plasmids among K. pneumoniae strains was evaluated thoroughly. The plasmid transfer to recipient bacteria through OMVs was identified by polymerase chain reaction, pulsed field gel electrophoresis and Southern blot. This study revealed that OMVs could mediate the intraspecific and interspecific horizontal transfer of the virulence plasmid phvK2115. OMVs could simultaneously transfer two resistance plasmids into K. pneumoniae and Escherichia coli recipient strains. OMVs-mediated horizontal transfer of virulence plasmid phvK2115 could significantly enhance the pathogenicity of human carbapenem-resistant K. pneumoniae CRK3022. The CRK3022 acquired the virulence plasmid phvK2115 could become a CR-hvKp strain. It was critically important that OMVs-mediated horizontal transfer of phvK2115 lead to the coexistence of virulence and carbapenem-resistance genes in K. pneumoniae, resulting in the emerging of carbapenem-resistant hypervirulent K. pneumoniae.}, }
@article {pmid35678538, year = {2022}, author = {Robison, T and Nelson, JM and Hauser, DA and Lewis, LA and Li, FW}, title = {Dynamic plastid and mitochondrial genomes in Chaetopeltidales (Chlorophyceae) and characterization of a new chlorophyte taxon.}, journal = {American journal of botany}, volume = {109}, number = {6}, pages = {939-951}, doi = {10.1002/ajb2.16015}, pmid = {35678538}, issn = {1537-2197}, mesh = {*Chlorophyceae ; Chloroplasts ; Evolution, Molecular ; *Genome, Chloroplast/genetics ; *Genome, Mitochondrial/genetics ; *Genome, Plastid ; Introns ; Phylogeny ; }, abstract = {PREMISE: Chaetopeltidales is a poorly characterized order in the Chlorophyceae, with only two plastid and no mitochondrial genomes published. Here we describe a new taxon in Chaetopeltidales, Gormaniella terricola gen. et sp. nov. and characterize both of its organellar genomes.<br><br>METHODS: Gormaniella terricola was inadvertently isolated from a surface-sterilized hornwort thallus. Light microscopy was used to characterize its vegetative morphology. Organellar genomes were assembled, annotated, and analyzed using a variety of software packages.<br><br>RESULTS: The mitochondrial genome (66,927&#x2009;bp) represents the first complete mitochondrial genome published for Chaetopeltidales. The chloroplast genome, measuring 428,981&#x2009;bp, is one of the largest plastid genomes published to date and shares this large size and an incredible number of short, dispersed repeats with the other sequenced chloroplast genomes in Chaetopeltidales. Despite these shared features, the chloroplast genomes of Chaetopeltidales appear to be highly rearranged when compared to one another, with numerous inversions, translocations, and duplications, suggesting a particularly dynamic chloroplast genome. Both the chloroplast and mitochondrial genomes of G. terricola contain a number of mobile group I and group II introns, which appear to have invaded separately. Three of the introns within the mitochondrial genome encode homing endonucleases that are phylogenetically nested within those found in fungi, rather than algae, suggesting a possible case of horizontal gene transfer.<br><br>CONCLUSIONS: These results help to shed light on a poorly understood group of algae and their unusual organellar genomes, raising additional questions about the unique patterns of genome evolution within Chaetopeltidales.}, }
@article {pmid35676049, year = {2022}, author = {Wulandari, D and Tittabutr, P and Songwattana, P and Piromyou, P and Teamtisong, K and Boonkerd, N and Boonchuen, P and Teaumroong, N}, title = {Symbiosis Contribution of Non-nodulating Bradyrhizobium cosmicum S23321 after Transferal of the Symbiotic Plasmid pDOA9.}, journal = {Microbes and environments}, volume = {37}, number = {2}, pages = {}, pmid = {35676049}, issn = {1347-4405}, mesh = {*Bradyrhizobium/genetics ; *Fabaceae/microbiology ; Phylogeny ; Plant Root Nodulation/genetics ; Plasmids/genetics ; Root Nodules, Plant/microbiology ; Symbiosis/genetics ; }, abstract = {The symbiotic properties of rhizobial bacteria are driven by the horizontal gene transfer of symbiotic genes, which are located in symbiosis islands or on plasmids. The symbiotic megaplasmid pDOA9 of Bradyrhizobium sp. DOA9, carrying the nod, nif, fix, and type three secretion system (T3SS) genes, has been conjugatively transferred to different Bradyrhizobium strains. In the present study, non-nodulating B. cosmicum S23321, which shows a close phylogenetic relationship with Bradyrhizobium sp. DOA9, but lacks symbiotic properties, was used to carry pDOA9 (annotated as chimeric S2:pDOA9). The results obtained showed that pDOA9 conferred symbiotic properties on S23321; however, nodulation phenotypes varied among the DOA9, chimeric ORS278:pDOA9, and S2:pDOA9 strains even though they all carried symbiotic pDOA9 plasmid. S23321 appeared to gain symbiotic nodulation from pDOA9 by processing nodulation genes and broadening the host range. The present results also showed the successful formation of active nodules in Arachis hypogaea (Dalbergoid) and Vigna radiata (Millitoid) by chimeric S2:pDOA9, while Crotalaria juncea (Genistoid) and Macroptilium atropurpureum (Millitoid) formed nodule-like structures. The formation of nodules and nodule-like structures occurred in a nod factor-dependent manner because the nod factor-lacking strain (S2:pDOA9ΩnodB) completely abolished nodulation in all legumes tested. Moreover, T3SS carried by S2:pDOA9 exerted negative effects on symbiosis with Crotalaria juncea, which was consistent with the results obtained on DOA9. T3SS exhibited symbiotic compatibility with V. radiata when nodulated by S23321. These outcomes implied that pDOA9 underwent changes during legume evolution that broadened host specificity and the compatibility of nodulation in a manner that was dependent on the chromosomal background of the recipient as well as legume host restrictions.}, }
@article {pmid35675326, year = {2022}, author = {Yin, Y and Ogilvie, HA and Nakhleh, L}, title = {Annotation-free delineation of prokaryotic homology groups.}, journal = {PLoS computational biology}, volume = {18}, number = {6}, pages = {e1010216}, pmid = {35675326}, issn = {1553-7358}, mesh = {Gene Transfer, Horizontal ; *Genome, Bacterial/genetics ; Phylogeny ; *Prokaryotic Cells ; Sequence Alignment ; }, abstract = {Phylogenomic studies of prokaryotic taxa often assume conserved marker genes are homologous across their length. However, processes such as horizontal gene transfer or gene duplication and loss may disrupt this homology by recombining only parts of genes, causing gene fission or fusion. We show using simulation that it is necessary to delineate homology groups in a set of bacterial genomes without relying on gene annotations to define the boundaries of homologous regions. To solve this problem, we have developed a graph-based algorithm to partition a set of bacterial genomes into Maximal Homologous Groups of sequences (MHGs) where each MHG is a maximal set of maximum-length sequences which are homologous across the entire sequence alignment. We applied our algorithm to a dataset of 19 Enterobacteriaceae species and found that MHGs cover much greater proportions of genomes than markers and, relatedly, are less biased in terms of the functions of the genes they cover. We zoomed in on the correlation between each individual marker and their overlapping MHGs, and show that few phylogenetic splits supported by the markers are supported by the MHGs while many marker-supported splits are contradicted by the MHGs. A comparison of the species tree inferred from marker genes with the species tree inferred from MHGs suggests that the increased bias and lack of genome coverage by markers causes incorrect inferences as to the overall relationship between bacterial taxa.}, }
@article {pmid35672875, year = {2022}, author = {Sagrillo, C and Changey, F and Bellanger, X}, title = {Bacteriophages vehiculate a high amount of antibiotic resistance determinants of bacterial origin in the Orne River ecosystem.}, journal = {Environmental microbiology}, volume = {24}, number = {9}, pages = {4317-4328}, doi = {10.1111/1462-2920.16083}, pmid = {35672875}, issn = {1462-2920}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; *Bacteriophages/genetics ; DNA, Bacterial ; Drug Resistance, Microbial/genetics ; Ecosystem ; Genes, Bacterial ; RNA, Ribosomal, 16S/genetics ; *Rivers/microbiology ; Water ; }, abstract = {Aquatic environments are important dissemination routes of antibiotic resistance genes (ARGs) from and to pathogenic bacteria. Nevertheless, in these complex matrices, identifying and characterizing the driving microbial actors and ARG dissemination mechanisms they are involved in remain difficult. We here explored the distribution/compartmentalization of a panel of ARGs and mobile genetic elements (MGEs) in bacteria and bacteriophages collected in the water, suspended material and surface sediments from the Orne River ecosystem (France). By using a new bacteriophage DNA extraction method, we showed that, when packaging bacterial DNA, bacteriophages rather encapsidate both ARGs and MGEs than 16S rRNA genes, i.e. chromosomal fragments. We also show that the bacteria and bacteriophage capsid contents in ARGs/MGEs were similarly influenced by seasonality but that the distribution of ARGs/MGEs between the river physical compartments (water vs. suspended mater vs. sediment) is more impacted when these markers were carried by bacteria. These demonstrations will likely modify our understanding of the formation and fate of transducing viral particles in the environment. Consequently, they will also likely modify our estimations of the relative frequencies of the different horizontal gene transfer mechanisms in disseminating antibiotic resistance by reinforcing the roles played by environmental bacteriophages and transduction.}, }
@article {pmid35671755, year = {2022}, author = {Tvedte, ES and Gasser, M and Zhao, X and Tallon, LJ and Sadzewicz, L and Bromley, RE and Chung, M and Mattick, J and Sparklin, BC and Dunning Hotopp, JC}, title = {Accumulation of endosymbiont genomes in an insect autosome followed by endosymbiont replacement.}, journal = {Current biology : CB}, volume = {32}, number = {12}, pages = {2786-2795.e5}, pmid = {35671755}, issn = {1879-0445}, support = {R01 CA206188/CA/NCI NIH HHS/United States ; U19 AI110820/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Chromosomes ; Drosophila/genetics/microbiology ; Gene Transfer, Horizontal ; Genome ; Symbiosis/genetics ; *Wolbachia/genetics ; }, abstract = {Eukaryotic genomes can acquire bacterial DNA via lateral gene transfer (LGT).[1] A prominent source of LGT is Wolbachia,[2] a widespread endosymbiont of arthropods and nematodes that is transmitted maternally through female germline cells.[3,4] The DNA transfer from the Wolbachia endosymbiont wAna to Drosophila ananassae is extensive[5-7] and has been localized to chromosome 4, contributing to chromosome expansion in this lineage.[6] As has happened frequently with claims of bacteria-to-eukaryote LGT, the contribution of wAna transfers to the expanded size of D. ananassae chromosome 4 has been specifically contested[8] owing to an assembly where Wolbachia sequences were classified as contaminants and removed.[9] Here, long-read sequencing with DNA from a Wolbachia-cured line enabled assembly of 4.9 Mbp of nuclear Wolbachia transfers (nuwts) in D. ananassae and a 24-kbp nuclear mitochondrial transfer. The nuwts are <8,000 years old in at least two locations in chromosome 4 with at least one whole-genome integration followed by rapid extensive duplication of most of the genome with regions that have up to 10 copies. The genes in nuwts are accumulating small indels and mobile element insertions. Among the highly duplicated genes are cifA and cifB, two genes associated with Wolbachia-mediated Drosophila cytoplasmic incompatibility. The wAna strain that was the source of nuwts was subsequently replaced by a different wAna endosymbiont. Direct RNA Nanopore sequencing of Wolbachia-cured lines identified nuwt transcripts, including spliced transcripts, but functionality, if any, remains elusive.}, }
@article {pmid35667126, year = {2022}, author = {Gophna, U and Altman-Price, N}, title = {Horizontal Gene Transfer in Archaea-From Mechanisms to Genome Evolution.}, journal = {Annual review of microbiology}, volume = {76}, number = {}, pages = {481-502}, doi = {10.1146/annurev-micro-040820-124627}, pmid = {35667126}, issn = {1545-3251}, mesh = {*Archaea/genetics ; Bacteria/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Phylogeny ; }, abstract = {Archaea remains the least-studied and least-characterized domain of life despite its significance not just to the ecology of our planet but also to the evolution of eukaryotes. It is therefore unsurprising that research into horizontal gene transfer (HGT) in archaea has lagged behind that of bacteria. Indeed, several archaeal lineages may owe their very existence to large-scale HGT events, and thus understanding both the molecular mechanisms and the evolutionary impact of HGT in archaea is highly important. Furthermore, some mechanisms of gene exchange, such as plasmids that transmit themselves via membrane vesicles and the formation of cytoplasmic bridges that allows transfer of both chromosomal and plasmid DNA, may be archaea-specific. This review summarizes what we know about HGT in archaea, and the barriers that restrict it, highlighting exciting recent discoveries and pointing out opportunities for future research.}, }
@article {pmid35665806, year = {2022}, author = {Ewald, JM and Schnoor, JL and Mattes, TE}, title = {Combined read- and assembly-based metagenomics to reconstruct a Dehalococcoides mccartyi genome from PCB-contaminated sediments and evaluate functional differences among organohalide-respiring consortia in the presence of different halogenated contaminants.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {7}, pages = {}, pmid = {35665806}, issn = {1574-6941}, support = {P42 ES013661/ES/NIEHS NIH HHS/United States ; R01 ES032671/ES/NIEHS NIH HHS/United States ; }, mesh = {Biodegradation, Environmental ; *Chloroflexi/chemistry/genetics ; Dehalococcoides ; Halogenation ; Phylogeny ; *Polychlorinated Biphenyls ; }, abstract = {Microbial communities that support respiration of halogenated organic contaminants by Dehalococcoides sp. facilitate full-scale bioremediation of chlorinated ethenes and demonstrate the potential to aid in bioremediation of halogenated aromatics like polychlorinated biphenyls (PCBs). However, it remains unclear if Dehalococcoides-containing microbial community dynamics observed in sediment-free systems quantitatively resemble that of sediment environments. To evaluate that possibility we assembled, annotated, and analyzed a Dehalococcoides sp. metagenome-assembled genome (MAG) from PCB-contaminated sediments. Phylogenetic analysis of reductive dehalogenase gene (rdhA) sequences within the MAG revealed that pcbA1 and pcbA4/5-like rdhA were absent, while several candidate PCB dehalogenase genes and potentially novel rdhA sequences were identified. Using a compositional comparative metagenomics approach, we quantified Dehalococcoides-containing microbial community structure shifts in response to halogenated organics and the presence of sediments. Functional level analysis revealed significantly greater abundances of genes associated with cobamide remodeling and horizontal gene transfer in tetrachloroethene-fed cultures as compared to halogenated aromatic-exposed consortia with or without sediments, despite little evidence of statistically significant differences in microbial community taxonomic structure. Our findings support the use of a generalizable comparative metagenomics workflow to evaluate Dehalococcoides-containing consortia in sediments and sediment-free environments to eludicate functions and microbial interactions that facilitate bioremediation of halogenated organic contaminants.}, }
@article {pmid35663853, year = {2022}, author = {Rodrigues, G and Souza Santos, L and Franco, OL}, title = {Antimicrobial Peptides Controlling Resistant Bacteria in Animal Production.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {874153}, pmid = {35663853}, issn = {1664-302X}, abstract = {In the last few decades, antimicrobial resistance (AMR) has been a worldwide concern. The excessive use of antibiotics affects animal and human health. In the last few years, livestock production has used antibiotics as food supplementation. This massive use can be considered a principal factor in the accelerated development of genetic modifications in bacteria. These modifications are responsible for AMR and can be widespread to pathogenic and commensal bacteria. In addition, these antibiotic residues can be dispersed by water and sewer water systems, the contamination of soil and, water and plants, in addition, can be stocked in tissues such as muscle, milk, eggs, fat, and others. These residues can be spread to humans by the consumption of water or contaminated food. In addition, studies have demonstrated that antimicrobial resistance may be developed by vertical and horizontal gene transfer, producing a risk to public health. Hence, the World Health Organization in 2000 forbid the use of antibiotics for feed supplementation in livestock. In this context, to obtain safe food production, one of the potential substitutes for traditional antibiotics is the use of antimicrobial peptides (AMPs). In general, AMPs present anti-infective activity, and in some cases immune response. A limited number of AMP-based drugs are now available for use in animals and humans. This use is still not widespread due to a few problems like in-vivo effectiveness, stability, and high cost of production. This review will elucidate the different AMPs applications in animal diets, in an effort to generate safe food and control AMR.}, }
@article {pmid35663734, year = {2022}, author = {Ejileugha, C}, title = {Biochar can mitigate co-selection and control antibiotic resistant genes (ARGs) in compost and soil.}, journal = {Heliyon}, volume = {8}, number = {5}, pages = {e09543}, pmid = {35663734}, issn = {2405-8440}, abstract = {Heavy metals (HMs) contamination raises the expression of antibiotic resistance (AR) in bacteria through co-selection. Biochar application in composting improves the effectiveness of composting and the quality of compost. This improvement includes the elimination and reduction of antibiotic resistant genes (ARGs). The use of biochar in contaminated soils reduces the bioaccessibility and bioavailability of the contaminants hence reducing the biological and environmental toxicity. This decrease in contaminant bioavailability reduces contaminants induced co-selection pressure. Conditions which favour reduction in HMs bioavailable fraction (BF) appear to favour reduction in ARGs in compost and soil. Biochar can prevent horizontal gene transfer (HGT) and can eliminate ARGs carried by mobile genetic elements (MGEs). This effect reduces maintenance and propagation of ARGs. Firmicutes, Proteobacteria, and Actinobacteria are the major bacteria phyla identified to be responsible for dissipation, maintenance, and propagation of ARGs. Biochar application rate at 2-10% is the best for the elimination of ARGs. This review provides insight into the usefulness of biochar in the prevention of co-selection and reduction of AR, including challenges of biochar application and future research prospects.}, }
@article {pmid35659286, year = {2022}, author = {Yamamoto, Y and Higashi, A and Ikawa, K and Hoang, HTT and Yamaguchi, T and Kawahara, R and Noguchi, H and Nguyen, TN and Khong, DT and Tran, HT}, title = {Horizontal transfer of a plasmid possessing mcr-1 marked with a single nucleotide mutation between Escherichia coli isolates from community residents.}, journal = {BMC research notes}, volume = {15}, number = {1}, pages = {196}, pmid = {35659286}, issn = {1756-0500}, support = {20H00561//The Japan Society for the Promotion of Science/ ; 012RP2021//Research Organization of Information and Systems/ ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Colistin ; Drug Resistance, Bacterial/genetics ; Escherichia coli ; *Escherichia coli Infections/microbiology ; *Escherichia coli Proteins/genetics ; Humans ; Microbial Sensitivity Tests ; Mutation ; Nucleotides ; Plasmids/genetics ; }, abstract = {OBJECTIVES: The widespread dissemination of phenotypic colistin-resistant (COR) bacteria in the community threatens public health. The horizontal gene transfer of the mobile colistin resistance gene via plasmids is thought to be one of the main mechanisms for dissemination. However, genotypic evidence to prove this in community settings is limited. This study used genome analysis to demonstrate the direct horizontal colistin resistance gene transfer via plasmids in isolates from the community.<br><br>RESULTS: A total of 19 isolates of COR Escherichia coli from stool specimens of 23 residents from seven households in the Vietnamese community were assessed in this study. The whole-genome sequence data of isolates were acquired using a combination of DNBSEQ short-reads and Nanopore long-read sequencing. Analysis of genomic data was performed using online tools such as Geneious. Analysis of the genomic information of COR E. coli isolates revealed that the isolates from two residents of different households had a similar IncP1 plasmid possessing mcr-1.1, marked with a single nucleotide mutation at the same position. The study provided direct evidence to prove that mcr was horizontally transmitted among bacteria in community residents.}, }
@article {pmid35658860, year = {2022}, author = {Njiru, C and Xue, W and De Rouck, S and Alba, JM and Kant, MR and Chruszcz, M and Vanholme, B and Dermauw, W and Wybouw, N and Van Leeuwen, T}, title = {Intradiol ring cleavage dioxygenases from herbivorous spider mites as a new detoxification enzyme family in animals.}, journal = {BMC biology}, volume = {20}, number = {1}, pages = {131}, pmid = {35658860}, issn = {1741-7007}, mesh = {Animals ; *Dioxygenases/genetics ; Herbivory ; *Solanum lycopersicum/genetics ; Phylogeny ; Plants ; *Tetranychidae/genetics ; }, abstract = {BACKGROUND: Generalist herbivores such as the two-spotted spider mite Tetranychus urticae thrive on a wide variety of plants and can rapidly adapt to novel hosts. What traits enable polyphagous herbivores to cope with the diversity of secondary metabolites in their variable plant diet is unclear. Genome sequencing of T. urticae revealed the presence of 17 genes that code for secreted proteins with strong homology to "intradiol ring cleavage dioxygenases (DOGs)" from bacteria and fungi, and phylogenetic analyses show that they have been acquired by horizontal gene transfer from fungi. In bacteria and fungi, DOGs have been well characterized and cleave aromatic rings in catecholic compounds between adjacent hydroxyl groups. Such compounds are found in high amounts in solanaceous plants like tomato, where they protect against herbivory. To better understand the role of this gene family in spider mites, we used a multi-disciplinary approach to functionally characterize the various T. urticae DOG genes.<br><br>RESULTS: We confirmed that DOG genes were present in the T. urticae genome and performed a phylogenetic reconstruction using transcriptomic and genomic data to advance our understanding of the evolutionary history of spider mite DOG genes. We found that DOG expression differed between mites from different plant hosts and was induced in response to jasmonic acid defense signaling. In consonance with a presumed role in detoxification, expression was localized in the mite's gut region. Silencing selected DOGs expression by dsRNA injection reduced the mites' survival rate on tomato, further supporting a role in mitigating the plant defense response. Recombinant purified DOGs displayed a broad substrate promiscuity, cleaving a surprisingly wide array of aromatic plant metabolites, greatly exceeding the metabolic capacity of previously characterized microbial DOGs.<br><br>CONCLUSION: Our findings suggest that the laterally acquired spider mite DOGs function as detoxification enzymes in the gut, disarming plant metabolites before they reach toxic levels. We provide experimental evidence to support the hypothesis that this proliferated gene family in T. urticae is causally linked to its ability to feed on an extremely wide range of host plants.}, }
@article {pmid35654895, year = {2022}, author = {Björk, JR and Dasari, MR and Roche, K and Grieneisen, L and Gould, TJ and Grenier, JC and Yotova, V and Gottel, N and Jansen, D and Gesquiere, LR and Gordon, JB and Learn, NH and Wango, TL and Mututua, RS and Kinyua Warutere, J and Siodi, L and Mukherjee, S and Barreiro, LB and Alberts, SC and Gilbert, JA and Tung, J and Blekhman, R and Archie, EA}, title = {Synchrony and idiosyncrasy in the gut microbiome of wild baboons.}, journal = {Nature ecology &amp; evolution}, volume = {6}, number = {7}, pages = {955-964}, pmid = {35654895}, issn = {2397-334X}, support = {P2C HD065563/HD/NICHD NIH HHS/United States ; R01 HD088558/HD/NICHD NIH HHS/United States ; R35 GM128716/GM/NIGMS NIH HHS/United States ; P01 AG031719/AG/NIA NIH HHS/United States ; R01 AG053330/AG/NIA NIH HHS/United States ; R21 AG049936/AG/NIA NIH HHS/United States ; R01 AG034513/AG/NIA NIH HHS/United States ; P30 AG024361/AG/NIA NIH HHS/United States ; R01 AG071684/AG/NIA NIH HHS/United States ; R03 AG045459/AG/NIA NIH HHS/United States ; R21 AG055777/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics ; Diet ; *Gastrointestinal Microbiome/genetics ; Humans ; *Microbiota ; Papio ; }, abstract = {Human gut microbial dynamics are highly individualized, making it challenging to link microbiota to health and to design universal microbiome therapies. This individuality is typically attributed to variation in host genetics, diets, environments and medications but it could also emerge from fundamental ecological forces that shape microbiota more generally. Here, we leverage extensive gut microbial time series from wild baboons-hosts who experience little interindividual dietary and environmental heterogeneity-to test whether gut microbial dynamics are synchronized across hosts or largely idiosyncratic. Despite their shared lifestyles, baboon microbiota were only weakly synchronized. The strongest synchrony occurred among baboons living in the same social group, probably because group members range over the same habitat and simultaneously encounter the same sources of food and water. However, this synchrony was modest compared to each host's personalized dynamics. In support, host-specific factors, especially host identity, explained, on average, more than three times the deviance in longitudinal dynamics compared to factors shared with social group members and ten times the deviance of factors shared across the host population. These results contribute to mounting evidence that highly idiosyncratic gut microbiomes are not an artefact of modern human environments and that synchronizing forces in the gut microbiome (for example, shared environments, diets and microbial dispersal) are not strong enough to overwhelm key drivers of microbiome personalization, such as host genetics, priority effects, horizontal gene transfer and functional redundancy.}, }
@article {pmid35653470, year = {2022}, author = {Zheng, W and Zhao, S and Yin, Y and Zhang, H and Needham, DM and Evans, ED and Dai, CL and Lu, PJ and Alm, EJ and Weitz, DA}, title = {High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome.}, journal = {Science (New York, N.Y.)}, volume = {376}, number = {6597}, pages = {eabm1483}, doi = {10.1126/science.abm1483}, pmid = {35653470}, issn = {1095-9203}, support = {P01 HL120839/HL/NHLBI NIH HHS/United States ; R21 AI125990/AI/NIAID NIH HHS/United States ; R21 AI128623/AI/NIAID NIH HHS/United States ; R01 AI153156/AI/NIAID NIH HHS/United States ; }, mesh = {*Bacteria/genetics ; Bacteriophages/genetics ; Bacteroides/genetics/virology ; DNA, Bacterial/genetics ; *Gastrointestinal Microbiome/genetics ; Gene Transfer, Horizontal ; Genome, Bacterial ; Genomics/methods ; High-Throughput Nucleotide Sequencing ; Humans ; *Microbial Interactions ; Single-Cell Analysis/methods ; }, abstract = {Characterizing complex microbial communities with single-cell resolution has been a long-standing goal of microbiology. We present Microbe-seq, a high-throughput method that yields the genomes of individual microbes from complex microbial communities. We encapsulate individual microbes in droplets with microfluidics and liberate their DNA, which we then amplify, tag with droplet-specific barcodes, and sequence. We explore the human gut microbiome, sequencing more than 20,000 microbial single-amplified genomes (SAGs) from a single human donor and coassembling genomes of almost 100 bacterial species, including several with multiple subspecies strains. We use these genomes to probe microbial interactions, reconstructing the horizontal gene transfer (HGT) network and observing HGT between 92 species pairs; we also identify a significant in vivo host-phage association between crAssphage and one strain of Bacteroides vulgatus. Microbe-seq contributes high-throughput culture-free capabilities to investigate genomic blueprints of complex microbial communities with single-microbe resolution.}, }
@article {pmid35653335, year = {2022}, author = {Alikhan, NF and Moreno, LZ and Castellanos, LR and Chattaway, MA and McLauchlin, J and Lodge, M and O'Grady, J and Zamudio, R and Doughty, E and Petrovska, L and Cunha, MPV and Knöbl, T and Moreno, AM and Mather, AE}, title = {Dynamics of Salmonella enterica and antimicrobial resistance in the Brazilian poultry industry and global impacts on public health.}, journal = {PLoS genetics}, volume = {18}, number = {6}, pages = {e1010174}, pmid = {35653335}, issn = {1553-7404}, support = {MR/R000948/1/MRC_/Medical Research Council/United Kingdom ; BB/R022682/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/S018913/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/CCG1860/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Brazil/epidemiology ; Chickens ; Drug Resistance, Bacterial/genetics ; Poultry ; Public Health ; Salmonella ; *Salmonella enterica/genetics ; Sulfonamides ; Tetracyclines ; beta-Lactams ; }, abstract = {Non-typhoidal Salmonella enterica is a common cause of diarrhoeal disease; in humans, consumption of contaminated poultry meat is believed to be a major source. Brazil is the world's largest exporter of chicken meat globally, and previous studies have indicated the introduction of Salmonella serovars through imported food products from Brazil. Here we provide an in-depth genomic characterisation and evolutionary analysis to investigate the most prevalent serovars and antimicrobial resistance (AMR) in Brazilian chickens and assess the impact to public health of products contaminated with S. enterica imported into the United Kingdom from Brazil. To do so, we examine 183 Salmonella genomes from chickens in Brazil and 357 genomes from humans, domestic poultry and imported Brazilian poultry products isolated in the United Kingdom. S. enterica serovars Heidelberg and Minnesota were the most prevalent serovars in Brazil and in meat products imported from Brazil into the UK. We extended our analysis to include 1,259 publicly available Salmonella Heidelberg and Salmonella Minnesota genomes for context. The Brazil genomes form clades distinct from global isolates, with temporal analysis suggesting emergence of these Salmonella Heidelberg and Salmonella Minnesota clades in the early 2000s, around the time of the 2003 introduction of the Enteritidis vaccine in Brazilian poultry. Analysis showed genomes within the Salmonella Heidelberg and Salmonella Minnesota clades shared resistance to sulphonamides, tetracyclines and beta-lactams conferred by sul2, tetA and blaCMY-2 genes, not widely observed in other co-circulating serovars despite similar selection pressures. The sul2 and tetA genes were concomitantly carried on IncC plasmids, whereas blaCMY-2 was either co-located with the sul2 and tetA genes on IncC plasmids or independently on IncI1 plasmids. Long-term surveillance data collected in the UK showed no increase in the incidence of Salmonella Heidelberg or Salmonella Minnesota in human cases of clinical disease in the UK following the increase of these two serovars in Brazilian poultry. In addition, almost all of the small number of UK-derived genomes which cluster with the Brazilian poultry-derived sequences could either be attributed to human cases with a recent history of foreign travel or were from imported Brazilian food products. These findings indicate that even should Salmonella from imported Brazilian poultry products reach UK consumers, they are very unlikely to be causing disease. No evidence of the Brazilian strains of Salmonella Heidelberg or Salmonella Minnesota were observed in UK domestic chickens. These findings suggest that introduction of the Salmonella Enteritidis vaccine, in addition to increasing antimicrobial use, could have resulted in replacement of salmonellae in Brazilian poultry flocks with serovars that are more drug resistant, but less associated with disease in humans in the UK. The plasmids conferring resistance to beta-lactams, sulphonamides and tetracyclines likely conferred a competitive advantage to the Salmonella Minnesota and Salmonella Heidelberg serovars in this setting of high antimicrobial use, but the apparent lack of transfer to other serovars present in the same setting suggests barriers to horizontal gene transfer that could be exploited in intervention strategies to reduce AMR. The insights obtained reinforce the importance of One Health genomic surveillance.}, }
@article {pmid35652645, year = {2022}, author = {Shao, Y and Chen, M and Luo, J and Li, D and Yuan, L and Yang, X and Wang, M and Chen, M and Guo, Q}, title = {Serogroup Y Clonal Complex 23 Meningococcus in China Acquiring Penicillin Resistance from Commensal Neisseria lactamica Species.}, journal = {Antimicrobial agents and chemotherapy}, volume = {66}, number = {6}, pages = {e0238321}, pmid = {35652645}, issn = {1098-6596}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {China/epidemiology ; Humans ; *Meningococcal Infections ; *Neisseria lactamica/genetics ; *Neisseria meningitidis/genetics ; Neisseria meningitidis, Serogroup Y ; Penicillin Resistance/genetics ; Serogroup ; }, abstract = {Invasive meningococcal disease (IMD) due to serogroup Y Neisseria meningitidis (NmY) is rare in China; recently, an invasive NmY isolate, Nm512, was discovered in Shanghai with decreased susceptibility to penicillin (Pen[NS]). Here, we investigated the epidemiology of NmY isolates in Shanghai and explored the potential commensal Neisseria lactamica donor of the Pen[NS] NmY isolate. A total of 491 N. meningitidis and 724 commensal Neisseria spp. isolates were collected. Eleven NmY isolates were discovered from IMD (n = 1) and carriers (n = 10), including two Pen[NS] isolates with five-key-mutation-harboring (F504L-A510V-I515V-H541N-I566V) penA genes. Five of the eight ST-175 complex (CC175) isolates had a genotype [Y:P1.5-1,2-2:F5-8:ST-175(CC175)] identical to that of the predominant invasive clone found in South Africa. Only one invasive NmY CC23 isolate (Nm512) was discovered; this isolate carried a novel Pen[NS]penA832 allele, which was identified in commensal N. lactamica isolates locally. Recombination analysis and transformation of the penA allele highlighted that N. meningitidis Nm512 may acquire resistance from its commensal donor; this was supported by the similar distribution of transformation-required DNA uptake sequence variants and the highly cognate receptor ComP between N. meningitidis and N. lactamica. In 2,309 NmY CC23 genomes from the PubMLST database, isolates with key-mutation-harboring penA genes comprised 12% and have been increasing since the 1990s, accompanied by recruitment of the blaROB-1 and/or quinolone resistance allele. Moreover, penA22 was predominant among genomes without key mutations in penA. These results strongly suggest that Nm512 is a descendant of the penA22-harboring CC23 isolate from Europe and acquired its penicillin resistance locally from commensal N. lactamica species by natural transformation.}, }
@article {pmid35652640, year = {2022}, author = {Morogovsky, A and Handelman, M and Abou Kandil, A and Shadkchan, Y and Osherov, N}, title = {Horizontal Gene Transfer of Triazole Resistance in Aspergillus fumigatus.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0111222}, pmid = {35652640}, issn = {2165-0497}, mesh = {Antifungal Agents/pharmacology ; *Aspergillus fumigatus/genetics ; Drug Resistance, Fungal/genetics ; Fungal Proteins/genetics ; Fungi ; Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; *Triazoles/pharmacology ; Voriconazole ; }, abstract = {Aspergillus fumigatus is the primary mold pathogen in humans. It can cause a wide range of diseases in humans, with high mortality rates in immunocompromised patients. The first-line treatments for invasive A. fumigatus infections are the triazole antifungals that inhibit Cyp51 lanosterol demethylase activity, blocking ergosterol biosynthesis. However, triazole-resistant strains of A. fumigatus are increasingly encountered, leading to increased mortality. The most common triazole resistance mechanisms in A. fumigatus are alterations in the cyp51A gene or promoter. We tested the hypothesis that A. fumigatus can acquire triazole resistance by horizontal gene transfer (HGT) of resistance-conferring gene cyp51A. HGT has not been experimentally analyzed in filamentous fungi. Therefore, we developed an HGT assay containing donor A. fumigatus strains carrying resistance-conferring mutated cyp51A, either in its chromosomal locus or in a self-replicating plasmid, and recipient strains that were hygromycin resistant and triazole sensitive. Donor and recipient A. fumigatus strains were cocultured and transferred to selective conditions, and the recipient strain tested for transferred triazole resistance. We found that chromosomal transfer of triazole resistance required selection under both voriconazole and hygromycin, resulting in diploid formation. Notably, plasmid-mediated transfer was also activated by voriconazole or hypoxic stress alone, suggesting a possible route to HGT of antifungal resistance in A. fumigatus, both in the environment and during host infection. This study provides, for the first time, preliminary experimental evidence for HGT mediating antifungal resistance in a pathogenic fungus. IMPORTANCE It is well known that bacteria can transfer antibiotic resistance from one strain to another by horizontal gene transfer (HGT), leading to the current worldwide crisis of rapidly emerging antibiotic-resistant bacteria. However, in fungi, HGT events have only been indirectly documented by whole-genome sequencing. This study directly examined fungal HGT of antibiotic resistance in a laboratory setting. We show that HGT of antifungal triazole resistance occurs in the important human fungal pathogen Aspergillus fumigatus. Importantly, we show a plasmid-mediated transfer of triazole resistance occurs under conditions likely to prevail in the environment and in infected patients. This study provides an experimental foundation for future work identifying the drivers and mechanistic underpinnings of HGT in fungi.}, }
@article {pmid35650553, year = {2022}, author = {Pan, L and Luo, Y and Wang, J and Li, X and Tang, B and Yang, H and Hou, X and Liu, F and Zou, X}, title = {Evolution and functional diversification of catalase genes in the green lineage.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {411}, pmid = {35650553}, issn = {1471-2164}, mesh = {Catalase/genetics ; *Chlorophyta/genetics ; *Embryophyta/genetics ; Evolution, Molecular ; Genes, Plant ; Phylogeny ; Plants/genetics ; }, abstract = {BACKGROUND: Catalases (CATs) break down hydrogen peroxide into water and oxygen to prevent cellular oxidative damage, and play key roles in the development, biotic and abiotic stresses of plants. However, the evolutionary relationships of the plant CAT gene family have not been systematically reported.<br><br>RESULTS: Here, we conducted genome-wide comparative, phylogenetic, and structural analyses of CAT orthologs from 29 out of 31 representative green lineage species to characterize the evolution and functional diversity of CATs. We found that CAT genes in land plants were derived from core chlorophytes and detected a lineage-specific loss of CAT genes in Fabaceae, suggesting that the CAT genes in this group possess divergent functions. All CAT genes were split into three major groups (group &#x3b1;, &#x3b2;1, and &#x3b2;2) based on the phylogeny. CAT genes were transferred from bacteria to core chlorophytes and charophytes by lateral gene transfer, and this led to the independent evolution of two types of CAT genes: &#x3b1; and &#x3b2; types. Ten common motifs were detected in both &#x3b1; and &#x3b2; groups, and &#x3b2; CAT genes had five unique motifs, respectively. The findings of our study are inconsistent with two previous hypotheses proposing that (i) new CAT genes are acquired through intron loss and that (ii) the Cys-343 residue is highly conserved in plants. We found that new CAT genes in most higher plants were produced through intron acquisition and that the Cys-343 residue was only present in monocots, Brassicaceae and Pp_CatX7 in P. patens, which indicates the functional specificity of the CATs in these three lineages. Finally, our finding that CAT genes show high overall sequence identity but that individual CAT genes showed developmental stage and organ-specific expression patterns suggests that CAT genes have functionally diverged independently.<br><br>CONCLUSIONS: Overall, our analyses of the CAT gene family provide new insights into their evolution and functional diversification in green lineage species.}, }
@article {pmid35649163, year = {2023}, author = {Sundaramoorthy, NS and Shankaran, P and Gopalan, V and Nagarajan, S}, title = {New tools to mitigate drug resistance in Enterobacteriaceae - Escherichia coli and Klebsiella pneumoniae.}, journal = {Critical reviews in microbiology}, volume = {49}, number = {4}, pages = {435-454}, doi = {10.1080/1040841X.2022.2080525}, pmid = {35649163}, issn = {1549-7828}, mesh = {*Enterobacteriaceae ; *Escherichia coli/genetics ; Klebsiella pneumoniae/genetics ; Colistin/pharmacology/therapeutic use ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacterial Proteins/genetics ; beta-Lactamases/genetics ; Plasmids ; Monobactams/pharmacology ; Drug Resistance ; Microbial Sensitivity Tests ; Drug Resistance, Bacterial/genetics ; }, abstract = {Treatment to common bacterial infections are becoming ineffective of late, owing to the emergence and dissemination of antibiotic resistance globally. Escherichia coli and Klebsiella pneumoniae are the most notorious microorganisms and are among the critical priority pathogens listed by WHO in 2017. These pathogens are the predominant cause of sepsis, urinary tract infections (UTIs), pneumonia, meningitis and pyogenic liver abscess. Concern arises due to the resistance of bacteria to most of the beta lactam antibiotics like penicillin, cephalosporin, monobactams and carbapenems, even to the last resort antibiotics like colistin. Preventing influx by modulation of porins, extruding the antibiotics by overexpression of efflux pumps, mutations of drug targets/receptors, biofilm formation, altering the drug molecules and rendering them ineffective are few resistance mechanisms that are adapted by Enterobacteriaeceae upon exposure to antibiotics. The situation is exacerbated due to the process of horizontal gene transfer (HGT), wherein the genes encoding resistance mechanisms are transferred to the neighbouring bacteria through plasmids/phages/uptake of free DNA. Carbapenemases, other beta lactamases and mcr genes coding for colistin resistance are widely disseminated leading to limited/no therapeutic options against those infections. Development of new antibiotics can be viewed as a possible solution but it involves major investment, time and labour despite which, the bacteria can easily adapt to the new antibiotic and evolve resistance in a relatively short time. Targeting the resistance mechanisms can be one feasible alternative to tackle these multidrug resistant (MDR) pathogens. Removal of plasmid (plasmid curing) causing resistance, use of bacteriophages and bacteriotherapy can be other potential approaches to combat infections caused by MDR E. coli and K. pneumoniae. The present review discusses the efficacies of these therapies in mitigating these infections, which can be potentially used as an adjuvant therapy along with existing antibiotics.}, }
@article {pmid35647734, year = {2023}, author = {Wang, R and Wu, J and Jiang, N and Lin, H and An, F and Wu, C and Yue, X and Shi, H and Wu, R}, title = {Recent developments in horizontal gene transfer with the adaptive innovation of fermented foods.}, journal = {Critical reviews in food science and nutrition}, volume = {63}, number = {5}, pages = {569-584}, doi = {10.1080/10408398.2022.2081127}, pmid = {35647734}, issn = {1549-7852}, mesh = {*Gene Transfer, Horizontal ; Bacteria/genetics ; Food ; *Fermented Foods ; }, abstract = {Horizontal gene transfer (HGT) has contributed significantly to the adaptability of bacteria, yeast and mold in fermented foods, whose evidence has been found in several fermented foods. Although not every HGT has biological significance, it plays an important role in improving the quality of fermented foods. In this review, how HGT facilitated microbial domestication and adaptive evolution in fermented foods was discussed. HGT can assist in the industrial innovation of fermented foods, and this adaptive evolution strategy can improve the quality of fermented foods. Additionally, the mechanism underlying HGT in fermented foods were analyzed. Furthermore, the critical bottlenecks involved in optimizing HGT during the production of fermented foods and strategies for optimizing HGT were proposed. Finally, the prospect of HGT for promoting the industrial innovation of fermented foods was highlighted. The comprehensive report on HGT in fermented foods provides a new trend for domesticating preferable starters for food fermentation, thus optimizing the quality and improving the industrial production of fermented foods.}, }
@article {pmid35646736, year = {2022}, author = {Laborda, P and Sanz-García, F and Ochoa-Sánchez, LE and Gil-Gil, T and Hernando-Amado, S and Martínez, JL}, title = {Wildlife and Antibiotic Resistance.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {873989}, pmid = {35646736}, issn = {2235-2988}, mesh = {Animals ; *Animals, Wild ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria ; Drug Resistance, Microbial ; *Microbiota ; Rats ; }, abstract = {Antibiotic resistance is a major human health problem. While health care facilities are main contributors to the emergence, evolution and spread of antibiotic resistance, other ecosystems are involved in such dissemination. Wastewater, farm animals and pets have been considered important contributors to the development of antibiotic resistance. Herein, we review the impact of wildlife in such problem. Current evidence supports that the presence of antibiotic resistance genes and/or antibiotic resistant bacteria in wild animals is a sign of anthropic pollution more than of selection of resistance. However, once antibiotic resistance is present in the wild, wildlife can contribute to its transmission across different ecosystems. Further, the finding that antibiotic resistance genes, currently causing problems at hospitals, might spread through horizontal gene transfer among the bacteria present in the microbiomes of ubiquitous animals as cockroaches, fleas or rats, supports the possibility that these organisms might be bioreactors for the horizontal transfer of antibiotic resistance genes among human pathogens. The contribution of wildlife in the spread of antibiotic resistance among different hosts and ecosystems occurs at two levels. Firstly, in the case of non-migrating animals, the transfer will take place locally; a One Health problem. Paradigmatic examples are the above mentioned animals that cohabit with humans and can be reservoirs and vehicles for antibiotic resistance dissemination. Secondly, migrating animals, such as gulls, fishes or turtles may participate in the dissemination of antibiotic resistance across different geographic areas, even between different continents, which constitutes a Global Health issue.}, }
@article {pmid35643394, year = {2022}, author = {Moradi, J and Fathollahi, M and Halimi, S and Alvandi, A and Abiri, R and Vaziri, S and Rezaei, A}, title = {Characterization of the resistome in Lactobacillus genomic sequences from the human gut.}, journal = {Journal of global antimicrobial resistance}, volume = {30}, number = {}, pages = {451-458}, doi = {10.1016/j.jgar.2022.05.014}, pmid = {35643394}, issn = {2213-7173}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria ; Drug Resistance, Microbial/genetics ; *Gene Transfer, Horizontal ; Genomics ; Humans ; *Lactobacillus ; }, abstract = {OBJECTIVES: The gut is a complex environment inhabited by a wide range of bacterial species. Lactobacillus species constitute a significant proportion of this environment and, due to their mobile genetic elements such as plasmids and transposons, are more likely to acquire and transfer antibiotic resistance genes through horizontal gene transfer (HGT).<br><br>METHODS: The current study obtained and analysed 321 genome assemblies to determine the prevalence of intrinsic and acquired antibiotic resistance genes (ARGs) among Lactobacillus species colonizing the human gastrointestinal tract.<br><br>RESULTS: A total of four high-frequency resistance genes were identified, including dfra42 (42%), poxtA (17.4%), lmrB (12%), and BJP-1 (7.7%); aside from dfra42, which is an intrinsic resistance gene, the other genes are acquired resistance genes. PoxtA was found in several different species, mainly in L. paracasei, whereas BJP-1 and lmrB were found in only one species, L. rhamnosus. IS5-like elements family transposase flanked 11% and 8% of detected lmrB and BJP-1, respectively, while a variety of insertion sequences surrounded 22% of identified poxtA. Furthermore, to the best of our knowledge, this is the first report of BJP-1 in lactobacilli that would suggest it has transferred from soil microbiota to humans.<br><br>CONCLUSION: According to the 'One Health' perspective, early detection of a new reservoir would control the global spread of the antibiotic-resistant bacterial species among the three environments, which include humans, the environment, and animals. Finally, the study's findings may then highlight the possibility of lactobacilli acquiring or transmitting resistance to other species within or outside the human intestine.}, }
@article {pmid35639760, year = {2022}, author = {Coluzzi, C and Garcillán-Barcia, MP and de la Cruz, F and Rocha, EPC}, title = {Evolution of Plasmid Mobility: Origin and Fate of Conjugative and Nonconjugative Plasmids.}, journal = {Molecular biology and evolution}, volume = {39}, number = {6}, pages = {}, pmid = {35639760}, issn = {1537-1719}, mesh = {Bacteria/genetics/metabolism ; *Conjugation, Genetic ; *DNA Transposable Elements/genetics ; Gene Transfer, Horizontal ; Plasmids/genetics ; Prokaryotic Cells ; }, abstract = {Conjugation drives the horizontal transfer of adaptive traits across prokaryotes. One-fourth of the plasmids encode the functions necessary to conjugate autonomously, the others being eventually mobilizable by conjugation. To understand the evolution of plasmid mobility, we studied plasmid size, gene repertoires, and conjugation-related genes. Plasmid gene repertoires were found to vary rapidly in relation to the evolutionary rate of relaxases, for example, most pairs of plasmids with 95% identical relaxases have fewer than 50% of homologs. Among 249 recent transitions of mobility type, we observed a clear excess of plasmids losing the capacity to conjugate. These transitions are associated with even greater changes in gene repertoires, possibly mediated by transposable elements, including pseudogenization of the conjugation locus, exchange of replicases reducing the problem of incompatibility, and extensive loss of other genes. At the microevolutionary scale of plasmid taxonomy, transitions of mobility type sometimes result in the creation of novel taxonomic units. Interestingly, most transitions from conjugative to mobilizable plasmids seem to be lost in the long term. This suggests a source-sink dynamic, where conjugative plasmids generate nonconjugative plasmids that tend to be poorly adapted and are frequently lost. Still, in some cases, these relaxases seem to have evolved to become efficient at plasmid mobilization in trans, possibly by hijacking multiple conjugative systems. This resulted in specialized relaxases of mobilizable plasmids. In conclusion, the evolution of plasmid mobility is frequent, shapes the patterns of gene flow in bacteria, the dynamics of gene repertoires, and the ecology of plasmids.}, }
@article {pmid35639596, year = {2022}, author = {Weisberg, AJ and Sachs, JL and Chang, JH}, title = {Dynamic Interactions Between Mega Symbiosis ICEs and Bacterial Chromosomes Maintain Genome Architecture.}, journal = {Genome biology and evolution}, volume = {14}, number = {6}, pages = {}, pmid = {35639596}, issn = {1759-6653}, mesh = {Chromosomes, Bacterial/genetics ; *Conjugation, Genetic ; DNA Transposable Elements ; Gene Transfer, Horizontal ; Genome, Bacterial ; *Symbiosis/genetics ; }, abstract = {Acquisition of mobile genetic elements can confer novel traits to bacteria. Some integrative and conjugative elements confer upon members of Bradyrhizobium the capacity to fix nitrogen in symbiosis with legumes. These so-called symbiosis integrative conjugative elements (symICEs) can be extremely large and vary as monopartite and polypartite configurations within chromosomes of related strains. These features are predicted to impose fitness costs and have defied explanation. Here, we show that chromosome architecture is largely conserved despite diversity in genome composition, variations in locations of attachment sites recognized by integrases of symICEs, and differences in large-scale chromosomal changes that occur upon integration. Conversely, many simulated nonnative chromosome-symICE combinations are predicted to result in lethal deletions or disruptions to architecture. Findings suggest that there is compatibility between chromosomes and symICEs. We hypothesize that the size and structural flexibility of symICEs are important for generating combinations that maintain chromosome architecture across a genus of nitrogen-fixing bacteria with diverse and dynamic genomes.}, }
@article {pmid35637228, year = {2022}, author = {So, WL and Nong, W and Xie, Y and Baril, T and Ma, HY and Qu, Z and Haimovitz, J and Swale, T and Gaitan-Espitia, JD and Lau, KF and Tobe, SS and Bendena, WG and Kai, ZP and Hayward, A and Hui, JHL}, title = {Myriapod genomes reveal ancestral horizontal gene transfer and hormonal gene loss in millipedes.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {3010}, pmid = {35637228}, issn = {2041-1723}, support = {BB/N020146/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M009122/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *Arthropods/genetics ; Chilopoda ; *Gene Transfer, Horizontal ; Genome/genetics ; Phylogeny ; }, abstract = {Animals display a fascinating diversity of body plans. Correspondingly, genomic analyses have revealed dynamic evolution of gene gains and losses among animal lineages. Here we sequence six new myriapod genomes (three millipedes, three centipedes) at key phylogenetic positions within this major but understudied arthropod lineage. We combine these with existing genomic resources to conduct a comparative analysis across all available myriapod genomes. We find that millipedes generally have considerably smaller genomes than centipedes, with the repeatome being a major contributor to genome size, driven by independent large gains of transposons in three centipede species. In contrast to millipedes, centipedes gained a large number of gene families after the subphyla diverged, with gains contributing to sensory and locomotory adaptations that facilitated their ecological shift to predation. We identify distinct horizontal gene transfer (HGT) events from bacteria to millipedes and centipedes, with no identifiable HGTs shared among all myriapods. Loss of juvenile hormone O-methyltransferase, a key enzyme in catalysing sesquiterpenoid hormone production in arthropods, was also revealed in all millipede lineages. Our findings suggest that the rapid evolution of distinct genomic pathways in centipede and millipede lineages following their divergence from the myriapod ancestor, was shaped by differing ecological pressures.}, }
@article {pmid35635697, year = {2022}, author = {Goldlust, K and Couturier, A and Terradot, L and Lesterlin, C}, title = {Live-Cell Visualization of DNA Transfer and Pilus Dynamics During Bacterial Conjugation.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2476}, number = {}, pages = {63-74}, pmid = {35635697}, issn = {1940-6029}, mesh = {*Conjugation, Genetic ; DNA ; *Fimbriae, Bacterial/genetics ; Gene Transfer, Horizontal ; Plasmids/genetics ; }, abstract = {Bacterial genomes are highly plastic and evolve rapidly by acquiring new genetic information through horizontal gene transfer mechanisms. Capturing DNA transfer by conjugation between bacterial cells in real time is relevant to address bacterial genomes' dynamic architecture comprehensively. Here, we describe a method allowing the direct visualization of bacterial conjugation in live cells, including the fluorescent labeling of the conjugative pilus and the monitoring of plasmid DNA transfer from donor to recipient cells.}, }
@article {pmid35632801, year = {2022}, author = {Visnapuu, A and Van der Gucht, M and Wagemans, J and Lavigne, R}, title = {Deconstructing the Phage-Bacterial Biofilm Interaction as a Basis to Establish New Antibiofilm Strategies.}, journal = {Viruses}, volume = {14}, number = {5}, pages = {}, pmid = {35632801}, issn = {1999-4915}, support = {819800/ERC_/European Research Council/International ; }, mesh = {Bacteria/genetics ; *Bacteriophages/genetics ; Biofilms ; }, abstract = {The bacterial biofilm constitutes a complex environment that endows the bacterial community within with an ability to cope with biotic and abiotic stresses. Considering the interaction with bacterial viruses, these biofilms contain intrinsic defense mechanisms that protect against phage predation; these mechanisms are driven by physical, structural, and metabolic properties or governed by environment-induced mutations and bacterial diversity. In this regard, horizontal gene transfer can also be a driver of biofilm diversity and some (pro)phages can function as temporary allies in biofilm development. Conversely, as bacterial predators, phages have developed counter mechanisms to overcome the biofilm barrier. We highlight how these natural systems have previously inspired new antibiofilm design strategies, e.g., by utilizing exopolysaccharide degrading enzymes and peptidoglycan hydrolases. Next, we propose new potential approaches including phage-encoded DNases to target extracellular DNA, as well as phage-mediated inhibitors of cellular communication; these examples illustrate the relevance and importance of research aiming to elucidate novel antibiofilm mechanisms contained within the vast set of unknown ORFs from phages.}, }
@article {pmid35631122, year = {2022}, author = {Crosby, FL and Eskeland, S and Bø-Granquist, EG and Munderloh, UG and Price, LD and Al-Khedery, B and Stuen, S and Barbet, AF}, title = {Comparative Whole Genome Analysis of an Anaplasma phagocytophilum Strain Isolated from Norwegian Sheep.}, journal = {Pathogens (Basel, Switzerland)}, volume = {11}, number = {5}, pages = {}, pmid = {35631122}, issn = {2076-0817}, support = {R01 AI042792/AI/NIAID NIH HHS/United States ; 244173/E50//Norwegian research funding for agriculture and the food industry (Matfondavtalen)/ ; }, abstract = {Anaplasma phagocytophilum is a Gram-negative obligate intracellular tick-borne alphaproteobacteria (family Anaplasmatacea, order Rickettsiales) with a worldwide distribution. In Norway, tick borne fever (TBF), caused by A. phagocytophilum, presents a major challenge in sheep farming. Despite the abundance of its tick vector, Ixodes ricinus, and A. phagocytophilum infections in wild and domestic animals, reports of infections in humans are low compared with cases in the U.S. Although A. phagocytophilum is genetically diverse and complex infections (co-infection and superinfection) in ruminants and other animals are common, the underlying genetic basis of intra-species interactions and host-specificity remains unexplored. Here, we performed whole genome comparative analysis of a newly cultured Norwegian A. phagocytophilum isolate from sheep (ApSheep_NorV1) with 27 other A. phagocytophilum genome sequences derived from human and animal infections worldwide. Although the compared strains are syntenic, there is remarkable genetic diversity between different genomic loci including the pfam01617 superfamily that encodes the major, neutralization-sensitive, surface antigen Msp2/p44. Blast comparisons between the msp2/p44 pseudogene repertoires from all the strains showed high divergence between U. S. and European strains and even between two Norwegian strains. Based on these comparisons, we concluded that in ruminants, complex infections can be attributed to infection with strains that differ in their msp2/p44 repertoires, which has important implications for pathogen evolution and vaccine development. We also present evidence for integration of rickettsial DNA into the genome of ISE6 tick cells.}, }
@article {pmid35630353, year = {2022}, author = {Shimizu, T and Aritoshi, T and Beatty, JT and Masuda, T}, title = {Persulfide-Responsive Transcription Factor SqrR Regulates Gene Transfer and Biofilm Formation via the Metabolic Modulation of Cyclic di-GMP in Rhodobacter capsulatus.}, journal = {Microorganisms}, volume = {10}, number = {5}, pages = {}, pmid = {35630353}, issn = {2076-2607}, support = {JP18H03941//Japan Society for the Promotion of Science/ ; JP19H03241//Japan Society for the Promotion of Science/ ; JP20K06681//Japan Society for the Promotion of Science/ ; JP21K15038//Japan Society for the Promotion of Science/ ; JP21H05271//Japan Society for the Promotion of Science/ ; 20B004//Kurita Water and Environment Foundation/ ; 21K001//Kurita Water and Environment Foundation/ ; G-2019-2-010//Institute for Fermentation/ ; RGPIN 2018-03898//Natural Sciences and Engineering Research Council/ ; }, abstract = {Bacterial phage-like particles (gene transfer agents-GTAs) are widely employed as a crucial genetic vector in horizontal gene transfer. GTA-mediated gene transfer is induced in response to various stresses; however, regulatory mechanisms are poorly understood. We found that the persulfide-responsive transcription factor SqrR may repress the expression of several GTA-related genes in the photosynthetic bacterium Rhodobacter capsulatus. Here, we show that the sqrR deletion mutant (ΔsqrR) produces higher amounts of intra- and extracellular GTA and gene transfer activity than the wild type (WT). The transcript levels of GTA-related genes are also increased in ΔsqrR. In spite of the presumption that GTA-related genes are regulated in response to sulfide by SqrR, treatment with sulfide did not alter the transcript levels of these genes in the WT strain. Surprisingly, hydrogen peroxide increased the transcript levels of GTA-related genes in the WT, and this alteration was abolished in the ΔsqrR strain. Moreover, the absence of SqrR changed the intracellular cyclic dimeric GMP (c-di-GMP) levels, and the amount of c-di-GMP was correlated with GTA activity and biofilm formation. These results suggest that SqrR is related to the repression of GTA production and the activation of biofilm formation via control of the intracellular c-di-GMP levels.}, }
@article {pmid35628478, year = {2022}, author = {Martin, JF and Alvarez-Alvarez, R and Liras, P}, title = {Penicillin-Binding Proteins, β-Lactamases, and β-Lactamase Inhibitors in β-Lactam-Producing Actinobacteria: Self-Resistance Mechanisms.}, journal = {International journal of molecular sciences}, volume = {23}, number = {10}, pages = {}, pmid = {35628478}, issn = {1422-0067}, mesh = {*Actinobacteria/genetics/metabolism ; Anti-Bacterial Agents/pharmacology ; Cephalosporins/pharmacology ; Cephamycins/pharmacology ; Clavulanic Acid/pharmacology ; *Penicillin-Binding Proteins/metabolism ; Penicillins/pharmacology ; *beta-Lactamase Inhibitors/pharmacology ; *beta-Lactamases/metabolism ; beta-Lactams/pharmacology ; }, abstract = {The human society faces a serious problem due to the widespread resistance to antibiotics in clinical practice. Most antibiotic biosynthesis gene clusters in actinobacteria contain genes for intrinsic self-resistance to the produced antibiotics, and it has been proposed that the antibiotic resistance genes in pathogenic bacteria originated in antibiotic-producing microorganisms. The model actinobacteria Streptomyces clavuligerus produces the β-lactam antibiotic cephamycin C, a class A β-lactamase, and the β lactamases inhibitor clavulanic acid, all of which are encoded in a gene supercluster; in addition, it synthesizes the β-lactamase inhibitory protein BLIP. The secreted clavulanic acid has a synergistic effect with the cephamycin produced by the same strain in the fight against competing microorganisms in its natural habitat. High levels of resistance to cephamycin/cephalosporin in actinobacteria are due to the presence (in their β-lactam clusters) of genes encoding PBPs which bind penicillins but not cephalosporins. We have revised the previously reported cephamycin C and clavulanic acid gene clusters and, in addition, we have searched for novel β-lactam gene clusters in protein databases. Notably, in S. clavuligerus and Nocardia lactamdurans, the β-lactamases are retained in the cell wall and do not affect the intracellular formation of isopenicillin N/penicillin N. The activity of the β-lactamase in S. clavuligerus may be modulated by the β-lactamase inhibitory protein BLIP at the cell-wall level. Analysis of the β-lactam cluster in actinobacteria suggests that these clusters have been moved by horizontal gene transfer between different actinobacteria and have culminated in S. clavuligerus with the organization of an elaborated set of genes designed for fine tuning of antibiotic resistance and cell wall remodeling for the survival of this Streptomyces species. This article is focused specifically on the enigmatic connection between β-lactam biosynthesis and β-lactam resistance mechanisms in the producer actinobacteria.}, }
@article {pmid35604129, year = {2022}, author = {de Korne-Elenbaas, J and Bruisten, SM and van Dam, AP and Maiden, MCJ and Harrison, OB}, title = {The Neisseria gonorrhoeae Accessory Genome and Its Association with the Core Genome and Antimicrobial Resistance.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0265421}, pmid = {35604129}, issn = {2165-0497}, support = {/WT_/Wellcome Trust/United Kingdom ; 218205/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; 214374/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; *Gonorrhea ; Humans ; Microbial Sensitivity Tests ; *Neisseria gonorrhoeae/genetics ; }, abstract = {The bacterial accessory genome provides the genetic flexibility needed to facilitate environment and host adaptation. In Neisseria gonorrhoeae, known accessory elements include plasmids which can transfer and mediate antimicrobial resistance (AMR); however, chromosomal accessory genes could also play a role in AMR. Here, the gonococcal accessory genome was characterized using gene-by-gene approaches and its association with the core genome and AMR were assessed. The gonococcal accessory gene pool consisted of 247 genes, which were mainly genes located on large mobile genetic elements, phage associated genes, or genes encoding putative secretion systems. Accessory elements showed similar synteny across genomes, indicating either a predisposition for particular genomic locations or ancestral inheritance that are conserved during strain expansion. Significant associations were found between the prevalence of accessory elements and core genome multi-locus sequence types (cgMLST), consistent with a structured gonococcal population despite frequent horizontal gene transfer (HGT). Increased prevalence of putative DNA exchange regulators was significantly associated with AMR, which included a putative secretion system, methyltransferases and a toxin-antitoxin system. Although frequent HGT results in high genetic diversity in the gonococcus, we found that this is mediated by a small gene pool. In fact, a highly organized genome composition was identified with a strong association between the accessory and core genome. Increased prevalence of DNA exchange regulators in antimicrobial resistant isolates suggests that genetic material exchange plays a role in the development or maintenance of AMR. These findings enhance our understanding of gonococcal genome architecture and have important implications for gonococcal population biology. IMPORTANCE The emergence of antimicrobial resistance (AMR) against third generation cephalosporins in Neisseria gonorrhoeae is a major public health concern, as these are antibiotics of last resort for the effective treatment of gonorrhea. Although the resistance mechanisms against this class of antibiotics have not been entirely resolved, resistance against other classes of antibiotics, such as tetracyclines, is known to be mediated through plasmids, which are known gonococcal extra-chromosomal accessory elements. A complete assessment of the chromosomal accessory genome content and its role in AMR has not yet been undertaken. Here, we comprehensively characterize the gonococcal accessory genome to better understand genome architecture as well as the evolution and mechanisms of AMR in this species.}, }
@article {pmid35604118, year = {2022}, author = {Cornet, L and Cleenwerck, I and Praet, J and Leonard, RR and Vereecken, NJ and Michez, D and Smagghe, G and Baurain, D and Vandamme, P}, title = {Phylogenomic Analyses of Snodgrassella Isolates from Honeybees and Bumblebees Reveal Taxonomic and Functional Diversity.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0150021}, pmid = {35604118}, issn = {2379-5077}, mesh = {Animals ; Bees ; Phylogeny ; *Neisseriaceae/genetics ; *Microbiota ; }, abstract = {Snodgrassella is a genus of Betaproteobacteria that lives in the gut of honeybees (Apis spp.) and bumblebees (Bombus spp). It is part of a conserved microbiome that is composed of a few core phylotypes and is essential for bee health and metabolism. Phylogenomic analyses using whole-genome sequences of 75 Snodgrassella strains from 4 species of honeybees and 14 species of bumblebees showed that these strains formed a monophyletic lineage within the Neisseriaceae family, that Snodgrassella isolates from Asian honeybees diverged early from the other species in their evolution, that isolates from honeybees and bumblebees were well separated, and that this genus consists of at least seven species. We propose to formally name two new Snodgrassella species that were isolated from bumblebees: i.e., Snodgrassella gandavensis sp. nov. and Snodgrassella communis sp. nov. Possible evolutionary scenarios for 107 species- or group-specific genes revealed very limited evidence for horizontal gene transfer. Functional analyses revealed the importance of small proteins, defense mechanisms, amino acid transport and metabolism, inorganic ion transport and metabolism and carbohydrate transport and metabolism among these 107 specific genes. IMPORTANCE The microbiome of honeybees (Apis spp.) and bumblebees (Bombus spp.) is highly conserved and represented by few phylotypes. This simplicity in taxon composition makes the bee's microbiome an emergent model organism for the study of gut microbial communities. Since the description of the Snodgrassella genus, which was isolated from the gut of honeybees and bumblebees in 2013, a single species (i.e., Snodgrassella alvi), has been named. Here, we demonstrate that this genus is actually composed of at least seven species, two of which (Snodgrassella gandavensis sp. nov. and Snodgrassella communis sp. nov.) are formally described and named in the present publication. We also report the presence of 107 genes specific to Snodgrassella species, showing notably the importance of small proteins and defense mechanisms in this genus.}, }
@article {pmid35603365, year = {2022}, author = {Jamieson-Lane, AD and Blasius, B}, title = {The gossip paradox: Why do bacteria share genes?.}, journal = {Mathematical biosciences and engineering : MBE}, volume = {19}, number = {6}, pages = {5482-5508}, doi = {10.3934/mbe.2022257}, pmid = {35603365}, issn = {1551-0018}, mesh = {*Bacteria/genetics ; Drug Resistance, Microbial ; *Gene Transfer, Horizontal ; Phenotype ; Plasmids/genetics ; }, abstract = {Bacteria, in contrast to eukaryotic cells, contain two types of genes: chromosomal genes that are fixed to the cell, and plasmids, smaller loops of DNA capable of being passed from one cell to another. The sharing of plasmid genes between individual bacteria and between bacterial lineages has contributed vastly to bacterial evolution, allowing specialized traits to 'jump ship' between one lineage or species and the next. The benefits of this generosity from the point of view of both recipient cell and plasmid are generally understood: plasmids receive new hosts and ride out selective sweeps across the population, recipient cells gain new traits (such as antibiotic resistance). Explaining this behavior from the point of view of donor cells is substantially more difficult. Donor cells pay a fitness cost in order to share plasmids, and run the risk of sharing advantageous genes with their competition and rendering their own lineage redundant, while seemingly receiving no benefit in return. Using both compartment based models and agent based simulations we demonstrate that 'secretive' genes which restrict horizontal gene transfer are favored over a wide range of models and parameter values, even when sharing carries no direct cost. 'Generous' chromosomal genes which are more permissive of plasmid transfer are found to have neutral fitness at best, and are generally disfavored by selection. Our findings lead to a peculiar paradox: given the obvious benefits of keeping secrets, why do bacteria share information so freely?}, }
@article {pmid35602040, year = {2022}, author = {Geng, R and Cheng, L and Cao, C and Liu, Z and Liu, D and Xiao, Z and Wu, X and Huang, Z and Feng, Q and Luo, C and Chen, Z and Zhang, Z and Jiang, C and Ren, M and Yang, A}, title = {Comprehensive Analysis Reveals the Genetic and Pathogenic Diversity of Ralstonia solanacearum Species Complex and Benefits Its Taxonomic Classification.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {854792}, pmid = {35602040}, issn = {1664-302X}, abstract = {Ralstonia solanacearum species complex (RSSC) is a diverse group of plant pathogens that attack a wide range of hosts and cause devastating losses worldwide. In this study, we conducted a comprehensive analysis of 131 RSSC strains to detect their genetic diversity, pathogenicity, and evolution dynamics. Average nucleotide identity analysis was performed to explore the genomic relatedness among these strains, and finally obtained an open pangenome with 32,961 gene families. To better understand the diverse evolution and pathogenicity, we also conducted a series of analyses of virulence factors (VFs) and horizontal gene transfer (HGT) in the pangenome and at the single genome level. The distribution of VFs and mobile genetic elements (MGEs) showed significant differences among different groups and strains, which were consistent with the new nomenclatures of the RSSC with three distinct species. Further functional analysis showed that most HGT events conferred from Burkholderiales and played a great role in shaping the genomic plasticity and genetic diversity of RSSC genomes. Our work provides insights into the genetic polymorphism, evolution dynamics, and pathogenetic variety of RSSC and provides strong supports for the new taxonomic classification, as well as abundant resources for studying host specificity and pathogen emergence.}, }
@article {pmid35599327, year = {2022}, author = {Zhu, X and Ji, L and Cheng, M and Wei, H and Wang, Z and Ning, K}, title = {Sustainability of the rice-crayfish co-culture aquaculture model: microbiome profiles based on multi-kingdom analyses.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {27}, pmid = {35599327}, issn = {2524-6372}, abstract = {While the rice-crayfish culture (RCFP) model, an important aquaculture model in Asia, is generally considered a sustainable model, its sustainability in terms of microbial community profiles has not been evaluated. In this study, multi-kingdom analyses of microbiome profiles (i.e., bacteria, archaea, viruses, and eukaryotes) were performed using environmental (i.e., water and sediment) and animal gut (i.e., crayfish and crab gut) microbial samples from the RCFP and other aquaculture models, including the crab-crayfish co-culture, crayfish culture, and crab culture models, to evaluate the sustainability of the RCFP systematically. Results showed that RCFP samples are enriched with a distinct set of microbes, including Shewanella, Ferroplasma, Leishmania, and Siphoviridae, when compared with other aquaculture models. Additionally, most microbes in the RCFP samples, especially microbes from different kingdoms, were densely and positively connected, which indicates their robustness against environmental stress. Whereas microbes in different aquaculture models demonstrated moderate levels of horizontal gene transfer (HGT) across kingdoms, the RCFP showed relatively lower frequencies of HGT events, especially those involving antibiotic resistance genes. Finally, environmental factors, including pH, oxidation-reduction potential, temperature, and total nitrogen, contributed profoundly to shaping the microbial communities in these aquaculture models. Interestingly, compared with other models, the microbial communities of the RCFP model were less influenced by these environmental factors, which suggests that microbes in the latter have stronger ability to resist environmental stress. The findings collectively reflect the unique multi-kingdom microbial patterns of the RCFP model and suggest that this model is a sustainable model from the perspective of microbiome profiles.}, }
@article {pmid35597186, year = {2022}, author = {Chakraborty, J and Roy, RP and Chatterjee, R and Chaudhuri, P}, title = {Performance assessment of genomic island prediction tools with an improved version of Design-Island.}, journal = {Computational biology and chemistry}, volume = {98}, number = {}, pages = {107698}, doi = {10.1016/j.compbiolchem.2022.107698}, pmid = {35597186}, issn = {1476-928X}, mesh = {Algorithms ; Bacteria/genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial ; *Genomic Islands/genetics ; }, abstract = {Genomic Islands (GIs) play an important role in the evolution and adaptation of prokaryotes. The origin and extent of ecological diversity of prokaryotes can be analyzed by comparing GIs across closely or distantly related prokaryotes. Understanding the importance of GI and to study the bacterial evolution, several GI prediction tools have been generated. An unsupervised method, Design-Island, was developed to identify GIs using Monte-Carlo statistical test on randomly selected segments of a chromosome. Here, in the present study Design-Island was modified with the incorporation of majority voting, multiple hypothesis testing correction. The performance of the modified version, Design-Island-II was tested and compared with the existing GI prediction tools. The performance assessment and benchmarking of the GI prediction tools require experimentally validated dataset, which is lacking. So, different datasets, generated or taken from literature were utilized to compare the sensitivity (SN), specificity (SP), precision (PPV) and accuracy (AC) of Design-Island-II. It showed substantial enhancement in term of SN, SP, PPV and AC, and significantly reduced the computation time of the algorithm. The performance of Design-Island-II has also been compared with several GI prediction tools using curated dataset of putative horizontally transferred genes. Design-Island-II showed the highest sensitivity and F1 score, comparable specificity, precision and accuracy in comparison to the other available methods. IslandViewer4 and Islander outperformed all the available methods in terms of AC and PPV respectively. Our study suggested Design-Island-II, IslandViewer4 and GIHunter among the top performing GI prediction tools considering both sensitivity and specificity of the methods.}, }
@article {pmid35593155, year = {2023}, author = {Richard, D and Roumagnac, P and Pruvost, O and Lefeuvre, P}, title = {A network approach to decipher the dynamics of Lysobacteraceae plasmid gene sharing.}, journal = {Molecular ecology}, volume = {32}, number = {10}, pages = {2660-2673}, doi = {10.1111/mec.16536}, pmid = {35593155}, issn = {1365-294X}, mesh = {Animals ; Humans ; *Gene Transfer, Horizontal ; Plasmids/genetics ; *Genome, Bacterial/genetics ; Anti-Bacterial Agents ; Bacteria/genetics ; }, abstract = {Plasmids provide an efficient vehicle for gene sharing among bacterial populations, playing a key role in bacterial evolution. Network approaches are particularly suitable to represent multipartite relationships and are useful tools to characterize plasmid-mediated gene sharing events. The bacterial family Lysobacteraceae includes plant commensal, plant pathogenic and opportunistic human pathogens for which plasmid-mediated adaptation has been reported. We searched for homologues of plasmid gene sequences from this family in the entire diversity of available bacterial genome sequences and built a network of plasmid gene sharing from the results. While plasmid genes are openly shared between the bacteria of the family Lysobacteraceae, taxonomy strongly defined the boundaries of these exchanges, which only barely reached other families. Most inferred plasmid gene sharing events involved a few genes only, and evidence of full plasmid transfers were restricted to taxonomically closely related taxa. We detected multiple plasmid-chromosome gene transfers, including the known sharing of a heavy metal resistance transposon. In the network, bacterial lifestyles shaped substructures of isolates colonizing specific ecological niches and harbouring specific types of resistance genes. Genes associated with pathogenicity or antibiotic and metal resistance were among those that most importantly structured the network, highlighting the imprints of human-mediated selective pressure on pathogenic populations. A massive sequencing effort on environmental Lysobacteraceae is therefore required to refine our understanding of how this reservoir fuels the emergence and the spread of genes among this family and its potential impact on plant, animal and human health.}, }
@article {pmid35592653, year = {2022}, author = {Verhoeve, VI and Fauntleroy, TD and Risteen, RG and Driscoll, TP and Gillespie, JJ}, title = {Cryptic Genes for Interbacterial Antagonism Distinguish Rickettsia Species Infecting Blacklegged Ticks From Other Rickettsia Pathogens.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {880813}, pmid = {35592653}, issn = {2235-2988}, support = {R21 AI146773/AI/NIAID NIH HHS/United States ; R21 AI156762/AI/NIAID NIH HHS/United States ; R21 AI166832/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Antidotes ; Humans ; *Ixodes/microbiology ; Mammals ; Phylogeny ; *Rickettsia/genetics ; Symbiosis ; }, abstract = {BACKGROUND: The genus Rickettsia (Alphaproteobacteria: Rickettsiales) encompasses numerous obligate intracellular species with predominantly ciliate and arthropod hosts. Notable species are pathogens transmitted to mammals by blood-feeding arthropods. Mammalian pathogenicity evolved from basal, non-pathogenic host-associations; however, some non-pathogens are closely related to pathogens. One such species, Rickettsia buchneri, is prevalent in the blacklegged tick, Ixodes scapularis. While I. scapularis transmits several pathogens to humans, it does not transmit Rickettsia pathogens. We hypothesize that R. buchneri established a mutualism with I. scapularis, blocking tick superinfection with Rickettsia pathogens.<br><br>METHODS: To improve estimates for assessing R. buchneri infection frequency in blacklegged tick populations, we used comparative genomics to identify an R. buchneri gene (REIS_1424) not present in other Rickettsia species present throughout the I. scapularis geographic range. Bioinformatic and phylogenomics approaches were employed to propose a function for the hypothetical protein (263 aa) encoded by REIS_1424.<br><br>RESULTS: REIS_1424 has few analogs in other Rickettsiales genomes and greatest similarity to non-Proteobacteria proteins. This cohort of proteins varies greatly in size and domain composition, possessing characteristics of Recombination hotspot (Rhs) and contact dependent growth inhibition (CDI) toxins, with similarity limited to proximal C-termini (~145 aa). This domain was named CDI-like/Rhs-like C-terminal toxin (CRCT). As such proteins are often found as toxin-antidote (TA) modules, we interrogated REIS_1423 (151 aa) as a putative antidote. Indeed, REIS_1423 is similar to proteins encoded upstream of CRCT domain-containing proteins. Accordingly, we named these proteins CDI-like/Rhs-like C-terminal toxin antidotes (CRCA). R. buchneri expressed both REIS_1423 and REIS_1424 in tick cell culture, and PCR assays showed specificity for R. buchneri over other rickettsiae and utility for positive detection in three tick populations. Finally, phylogenomics analyses uncovered divergent CRCT/CRCA modules in varying states of conservation; however, only R. buchneri and related Tamurae/Ixodes Group rickettsiae carry complete TA modules.<br><br>CONCLUSION: We hypothesize that Rickettsia CRCT/CRCA modules circulate in the Rickettsia mobile gene pool, arming rickettsiae for battle over arthropod colonization. While its functional significance remains to be tested, R. buchneri CRCT/CRCA serves as a marker to positively identify infection and begin deciphering the role this endosymbiont plays in the biology of the blacklegged tick.}, }
@article {pmid35592433, year = {2022}, author = {Oh, MW and Lella, M and Kuo, SH and Tal-Gan, Y and Lau, GW}, title = {Pharmacological Evaluation of Synthetic Dominant-Negative Peptides Derived from the Competence-Stimulating Peptide of Streptococcus pneumoniae.}, journal = {ACS pharmacology &amp; translational science}, volume = {5}, number = {5}, pages = {299-305}, pmid = {35592433}, issn = {2575-9108}, support = {R01 HL142626/HL/NHLBI NIH HHS/United States ; }, abstract = {The competence regulon of Streptococcus pneumoniae (pneumococcus) is a quorum-sensing circuitry that regulates the ability of this pathogen to acquire antibiotic resistance or perform serotype switching, leading to vaccine-escape serotypes, via horizontal gene transfer, as well as initiate virulence. Induction of the competence regulon is centered on binding of the competence-stimulating peptide (CSP) to its cognate receptor, ComD. We have recently synthesized multiple dominant-negative peptide analogs capable of inhibiting competence induction and virulence in S. pneumoniae. However, the pharmacodynamics and safety profiles of these peptide drug leads have not been characterized. Therefore, in this study, we compared the biostability of cyanine-7.5-labeled wild-type CSPs versus dominant-negative peptide analogs (dnCSPs) spatiotemporally by using an IVIS Spectrum in vivo imaging system. Moreover, in vitro cytotoxicity and in vivo toxicity were evaluated. We conclude that our best peptide analog, CSP1-E1A-cyc(Dap6E10), is an attractive therapeutic agent against pneumococcal infection with superior safety and pharmacokinetics profiles.}, }
@article {pmid35590416, year = {2022}, author = {Wawerka, M and Dąbkowski, D and Rutecka, N and Mykowiecka, A and Górecki, P}, title = {Embedding gene trees into phylogenetic networks by conflict resolution algorithms.}, journal = {Algorithms for molecular biology : AMB}, volume = {17}, number = {1}, pages = {11}, pmid = {35590416}, issn = {1748-7188}, support = {2019/33/B/ST6/00737//Narodowe Centrum Nauki/ ; }, abstract = {BACKGROUND: Phylogenetic networks are mathematical models of evolutionary processes involving reticulate events such as hybridization, recombination, or horizontal gene transfer. One of the crucial notions in phylogenetic network modelling is displayed tree, which is obtained from a network by removing a set of reticulation edges. Displayed trees may represent an evolutionary history of a gene family if the evolution is shaped by reticulation events.<br><br>RESULTS: We address the problem of inferring an optimal tree displayed by a network, given a gene tree G and a tree-child network N, under the deep coalescence and duplication costs. We propose an O(mn)-time dynamic programming algorithm (DP) to compute a lower bound of the optimal displayed tree cost, where m and n are the sizes of G and N, respectively. In addition, our algorithm can verify whether the solution is exact. Moreover, it provides a set of reticulation edges corresponding to the obtained cost. If the cost is exact, the set induces an optimal displayed tree. Otherwise, the set contains pairs of conflicting edges, i.e., edges sharing a reticulation node. Next, we show a conflict resolution algorithm that requires [Formula: see text] invocations of DP in the worst case, where r is the number of reticulations. We propose a similar [Formula: see text]-time algorithm for level-k tree-child networks and a branch and bound solution to compute lower and upper bounds of optimal costs. We also extend the algorithms to a broader class of phylogenetic networks. Based on simulated data, the average runtime is [Formula: see text] under the deep-coalescence cost and [Formula: see text] under the duplication cost.<br><br>CONCLUSIONS: Despite exponential complexity in the worst case, our algorithms perform significantly well on empirical and simulated datasets, due to the strategy of resolving internal dissimilarities between gene trees and networks. Therefore, the algorithms are efficient alternatives to enumeration strategies commonly proposed in the literature and enable analyses of complex networks with dozens of reticulations.}, }
@article {pmid35588244, year = {2022}, author = {Gluck-Thaler, E and Ralston, T and Konkel, Z and Ocampos, CG and Ganeshan, VD and Dorrance, AE and Niblack, TL and Wood, CW and Slot, JC and Lopez-Nicora, HD and Vogan, AA}, title = {Giant Starship Elements Mobilize Accessory Genes in Fungal Genomes.}, journal = {Molecular biology and evolution}, volume = {39}, number = {5}, pages = {}, pmid = {35588244}, issn = {1537-1719}, mesh = {DNA Transposable Elements ; Eukaryotic Cells ; *Genome, Fungal ; Humans ; *Virulence Factors ; }, abstract = {Accessory genes are variably present among members of a species and are a reservoir of adaptive functions. In bacteria, differences in gene distributions among individuals largely result from mobile elements that acquire and disperse accessory genes as cargo. In contrast, the impact of cargo-carrying elements on eukaryotic evolution remains largely unknown. Here, we show that variation in genome content within multiple fungal species is facilitated by Starships, a newly discovered group of massive mobile elements that are 110 kb long on average, share conserved components, and carry diverse arrays of accessory genes. We identified hundreds of Starship-like regions across every major class of filamentous Ascomycetes, including 28 distinct Starships that range from 27 to 393 kb and last shared a common ancestor ca. 400 Ma. Using new long-read assemblies of the plant pathogen Macrophomina phaseolina, we characterize four additional Starships whose activities contribute to standing variation in genome structure and content. One of these elements, Voyager, inserts into 5S rDNA and contains a candidate virulence factor whose increasing copy number has contrasting associations with pathogenic and saprophytic growth, suggesting Voyager's activity underlies an ecological trade-off. We propose that Starships are eukaryotic analogs of bacterial integrative and conjugative elements based on parallels between their conserved components and may therefore represent the first dedicated agents of active gene transfer in eukaryotes. Our results suggest that Starships have shaped the content and structure of fungal genomes for millions of years and reveal a new concerted route for evolution throughout an entire eukaryotic phylum.}, }
@article {pmid35587542, year = {2022}, author = {Bolten, S and Harrand, AS and Skeens, J and Wiedmann, M}, title = {Nonsynonymous Mutations in fepR Are Associated with Adaptation of Listeria monocytogenes and Other Listeria spp. to Low Concentrations of Benzalkonium Chloride but Do Not Increase Survival of L. monocytogenes and Other Listeria spp. after Exposure to Benzalkonium Chloride Concentrations Recommended for Use in Food Processing Environments.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {11}, pages = {e0048622}, pmid = {35587542}, issn = {1098-5336}, mesh = {Benzalkonium Compounds/pharmacology ; Drug Resistance, Bacterial/genetics ; Food Handling ; Food Microbiology ; *Listeria/genetics ; *Listeria monocytogenes/genetics ; Mutation ; Quaternary Ammonium Compounds ; }, abstract = {Selection for Listeria monocytogenes strains that are tolerant to quaternary ammonium compounds (such as benzalkonium chloride [BC]) is a concern across the food industry, including in fresh produce processing environments. This study evaluated the ability of 67 strains of produce-associated L. monocytogenes and other Listeria spp. ("parent strains") to show enhanced BC tolerance after serial passaging in increasing BC concentrations and to maintain this tolerance after substreaking in the absence of BC. After serial passaging in BC, 62/67 "BC passaged cultures" showed higher MICs (4 to 20 mg/L) than parent strains (2 to 6 mg/L). After the substreaking of two isolates from BC passaged cultures for each parent strain, 105/134 "adapted isolates" maintained MICs (4 to 6 mg/L) higher than parent strain MICs. These results suggested that adapted isolates acquired heritable adaptations that confer BC tolerance. Whole-genome sequencing and Sanger sequencing of fepR, a local repressor of the MATE family efflux pump FepA, identified nonsynonymous fepR mutations in 48/67 adapted isolates. The mean inactivation of adapted isolates after exposure to use-level concentrations of BC (300 mg/L) was 4.48 log, which was not significantly different from inactivation observed in parent strains. Serial passaging of cocultures of L. monocytogenes strains containing bcrABC or qacH did not yield adapted isolates that showed enhanced BC tolerance in comparison to that of monocultures. These results suggest that horizontal gene transfer either did not occur or did not yield isolates with enhanced BC tolerance. Overall, this study provides new insights into selection of BC tolerance among L. monocytogenes and other Listeria spp. IMPORTANCE Listeria monocytogenes tolerance to quaternary ammonium compounds has been raised as a concern with regard to L. monocytogenes persistence in food processing environments, including in fresh produce packing and processing environments. Persistence of L. monocytogenes can increase the risk of product contamination, food recalls, and foodborne illness outbreaks. Our study shows that strains of L. monocytogenes and other Listeria spp. can acquire heritable adaptations that confer enhanced tolerance to low concentrations of benzalkonium chloride, but these adaptations do not increase survival of L. monocytogenes and other Listeria spp. when exposed to concentrations of benzalkonium chloride used for food contact surface sanitation (300 mg/L). Overall, these findings suggest that the emergence of benzalkonium chloride-tolerant Listeria strains in food processing environments is of limited concern, as even strains adapted to gain higher MICs in vitro maintain full sensitivity to the concentrations of benzalkonium chloride used for food contact surface sanitation.}, }
@article {pmid35587447, year = {2022}, author = {Bonis, BM and Hunter, RC}, title = {JMM Profile: Achromobacter xylosoxidans: the cloak-and-dagger opportunist.}, journal = {Journal of medical microbiology}, volume = {71}, number = {5}, pages = {}, doi = {10.1099/jmm.0.001505}, pmid = {35587447}, issn = {1473-5644}, mesh = {*Achromobacter denitrificans/genetics ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Cystic Fibrosis/complications ; *Gram-Negative Bacterial Infections/drug therapy ; Humans ; Phylogeny ; }, abstract = {Achromobacter xylosoxidans is associated with resilient nosocomial infections, with bacteraemia, pneumonia and chronic cystic fibrosis lung infection being the most common clinical presentations. Innate multi-drug resistance and a suite of virulence factors select for A. xylosoxidans infection during long-term antibiotic therapy, contributing to its persistence, treatment recalcitrance, association with poor clinical outcomes and emergence as a problematic pathogen. Horizontal gene transfer and maintenance of large genomes underpin the resilience and cosmopolitan lifestyle of A. xylosoxidans, and complicate its phylogenetic characterization.}, }
@article {pmid35586069, year = {2022}, author = {Goyal, A}, title = {Horizontal gene transfer drives the evolution of dependencies in bacteria.}, journal = {iScience}, volume = {25}, number = {5}, pages = {104312}, pmid = {35586069}, issn = {2589-0042}, abstract = {Many naturally occurring bacteria lead a lifestyle of metabolic dependency for crucial resources. We do not understand what factors drive bacteria toward this lifestyle and how. Here, we systematically show the crucial role of horizontal gene transfer (HGT) in dependency evolution in bacteria. Across 835 bacterial species, we map gene gain-loss dynamics on a deep evolutionary tree and assess the impact of HGT and gene loss on metabolic networks. Our analyses suggest that HGT-enabled gene gains can affect which genes are later lost. HGT typically adds new catabolic routes to bacterial metabolic networks, leading to new metabolic interactions between bacteria. We also find that gaining new routes can promote the loss of ancestral routes ("coupled gains and losses", CGLs). Phylogenetic patterns indicate that both dependencies-mediated by CGLs and those purely by gene loss-are equally likely. Our results highlight HGT as an important driver of metabolic dependency evolution in bacteria.}, }
@article {pmid35585492, year = {2022}, author = {Ghimire, N and Kim, B and Lee, CM and Oh, TJ}, title = {Comparative genome analysis among Variovorax species and genome guided aromatic compound degradation analysis emphasizing 4-hydroxybenzoate degradation in Variovorax sp. PAMC26660.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {375}, pmid = {35585492}, issn = {1471-2164}, support = {PM21030//the Ministry of Oceans and Fisheries, Korea/ ; }, mesh = {Carbon ; *Parabens ; Phylogeny ; *Xenobiotics ; }, abstract = {BACKGROUND: While the genus Variovorax is known for its aromatic compound metabolism, no detailed study of the peripheral and central pathways of aromatic compound degradation has yet been reported. Variovorax sp. PAMC26660 is a lichen-associated bacterium isolated from Antarctica. The work presents the genome-based elucidation of peripheral and central catabolic pathways of aromatic compound degradation genes in Variovorax sp. PAMC26660. Additionally, the accessory, core and unique genes were identified among Variovorax species using the pan genome analysis tool. A detailed analysis of the genes related to xenobiotic metabolism revealed the potential roles of Variovorax sp. PAMC26660 and other species in bioremediation.<br><br>RESULTS: TYGS analysis, dDDH, phylogenetic placement and average nucleotide identity (ANI) analysis identified the strain as Variovorax sp. Cell morphology was assessed using scanning electron microscopy (SEM). On analysis of the core, accessory, and unique genes, xenobiotic metabolism accounted only for the accessory and unique genes. On detailed analysis&#xa0;of the aromatic compound catabolic genes, peripheral pathway related to 4-hydroxybenzoate (4-HB) degradation was found among all species while phenylacetate and tyrosine degradation pathways were present in most of the species including PAMC26660. Likewise, central catabolic pathways, like protocatechuate, gentisate, homogentisate, and phenylacetyl-CoA, were also present. The peripheral pathway for 4-HB degradation was functionally tested using PAMC26660, which resulted in the growth using it as a sole source of carbon.<br><br>CONCLUSIONS: Computational tools for genome and pan genome analysis are important to understand the behavior of an organism. Xenobiotic metabolism-related genes, that only account for the accessory and unique genes infer evolution through events like lateral gene transfer, mutation and gene rearrangement. 4-HB, an aromatic compound present among lichen species is utilized by lichen-associated Variovorax sp. PAMC26660 as the sole source of carbon. The strain holds genes and pathways for its utilization. Overall, this study outlines the importance of Variovorax in bioremediation and presents the genomic information of the species.}, }
@article {pmid35584135, year = {2022}, author = {Bean, EL and Herman, C and Anderson, ME and Grossman, AD}, title = {Biology and engineering of integrative and conjugative elements: Construction and analyses of hybrid ICEs reveal element functions that affect species-specific efficiencies.}, journal = {PLoS genetics}, volume = {18}, number = {5}, pages = {e1009998}, pmid = {35584135}, issn = {1553-7404}, support = {R35 GM122538/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacillus subtilis/genetics ; Biology ; *Conjugation, Genetic/genetics ; DNA ; DNA Transposable Elements/genetics ; DNA, Bacterial/genetics ; *Gene Transfer, Horizontal/genetics ; }, abstract = {Integrative and conjugative elements (ICEs) are mobile genetic elements that reside in a bacterial host chromosome and are prominent drivers of bacterial evolution. They are also powerful tools for genetic analyses and engineering. Transfer of an ICE to a new host involves many steps, including excision from the chromosome, DNA processing and replication, transfer across the envelope of the donor and recipient, processing of the DNA, and eventual integration into the chromosome of the new host (now a stable transconjugant). Interactions between an ICE and its host throughout the life cycle likely influence the efficiencies of acquisition by new hosts. Here, we investigated how different functional modules of two ICEs, Tn916 and ICEBs1, affect the transfer efficiencies into different host bacteria. We constructed hybrid elements that utilize the high-efficiency regulatory and excision modules of ICEBs1 and the conjugation genes of Tn916. These elements produced more transconjugants than Tn916, likely due to an increase in the number of cells expressing element genes and a corresponding increase in excision. We also found that several Tn916 and ICEBs1 components can substitute for one another. Using B. subtilis donors and three Enterococcus species as recipients, we found that different hybrid elements were more readily acquired by some species than others, demonstrating species-specific interactions in steps of the ICE life cycle. This work demonstrates that hybrid elements utilizing the efficient regulatory functions of ICEBs1 can be built to enable efficient transfer into and engineering of a variety of other species.}, }
@article {pmid35581398, year = {2022}, author = {Morgado, S and Vicente, AC}, title = {Diversity and distribution of Type VI Secretion System gene clusters in bacterial plasmids.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {8249}, pmid = {35581398}, issn = {2045-2322}, mesh = {Bacterial Proteins/metabolism ; Bacterial Secretion Systems ; Multigene Family ; Plasmids/genetics ; Proteobacteria/genetics ; *Type VI Secretion Systems/genetics/metabolism ; }, abstract = {Type VI Secretion System (T6SS) is a nanomolecular apparatus that allows the delivery of effector molecules through the cell envelope of a donor bacterium to prokaryotic and/or eukaryotic cells, playing a role in the bacterial competition, virulence, and host interaction. T6SS is patchily distributed in bacterial genomes, suggesting an association with horizontal gene transfer (HGT). In fact, T6SS gene loci are eventually found within genomic islands (GIs), and there are some reports in plasmids and integrative and conjugative elements (ICEs). The impact that T6SS may have on bacteria fitness and the lack of evidence on its spread mechanism led us to question whether plasmids could represent a key mechanism in the spread of T6SS in bacteria. Therefore, we performed an in-silico analysis to reveal the association between T6SS and plasmids. T6SS was mined on 30,660 plasmids from NCBI based on the presence of at least six T6SS core proteins. T6SS was identified in 330 plasmids, all belonging to the same type (T6SS[i]), mainly in Proteobacteria (328/330), particularly in Rhizobium and Ralstonia. Interestingly, most genomes carrying T6SS-harboring plasmids did not encode T6SS in their chromosomes, and, in general, chromosomal and plasmid T6SSs did not form separate clades.}, }
@article {pmid35580352, year = {2022}, author = {Davies, PL}, title = {Reflections on antifreeze proteins and their evolution.}, journal = {Biochemistry and cell biology = Biochimie et biologie cellulaire}, volume = {}, number = {}, pages = {}, doi = {10.1139/bcb-2022-0029}, pmid = {35580352}, issn = {1208-6002}, abstract = {The discovery of radically different antifreeze proteins (AFPs) in fishes during the 1970s and 1980s suggested that these proteins had recently and independently evolved to protect teleosts from freezing in icy seawater. Early forays into the isolation and characterization of AFP genes in these fish showed they were massively amplified, often in long tandem repeats. The work of many labs in the 1980s onward led to the discovery and characterization of AFPs in other kingdoms, such as insects, plants, and many different microorganisms. The distinct ice-binding property that these ice-binding proteins (IBPs) share has facilitated their purification through adsorption to ice, and the ability to produce recombinant versions of IBPs has enabled their structural characterization and the mapping of their ice-binding sites (IBSs) using site-directed mutagenesis. One hypothesis for their ice affinity is that the IBS organizes surface waters into an ice-like pattern that freezes the protein onto ice. With access now to a rapidly expanding database of genomic sequences, it has been possible to trace the origins of some fish AFPs through the process of gene duplication and divergence, and to even show the horizontal transfer of an AFP gene from one species to another.}, }
@article {pmid35579343, year = {2022}, author = {Tahiri, N and Fichet, B and Makarenkov, V}, title = {Building alternative consensus trees and supertrees using k-means and Robinson and Foulds distance.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {13}, pages = {3367-3376}, doi = {10.1093/bioinformatics/btac326}, pmid = {35579343}, issn = {1367-4811}, support = {//Natural Sciences and Engineering Research Council of Canada/ ; //Fonds de Recherche sur la Sant&#xe9; of Qu&#xe9;bec and Fonds de Recherche sur la Nature et Technologies of Qu&#xe9;bec/ ; }, mesh = {Phylogeny ; Consensus ; *Software ; Cluster Analysis ; *Algorithms ; }, abstract = {MOTIVATION: Each gene has its own evolutionary history which can substantially differ from evolutionary histories of other genes. For example, some individual genes or operons can be affected by specific horizontal gene transfer or recombination events. Thus, the evolutionary history of each gene should be represented by its own phylogenetic tree which may display different evolutionary patterns from the species tree that accounts for the main patterns of vertical descent. However, the output of traditional consensus tree or supertree inference methods is a unique consensus tree or supertree.<br><br>RESULTS: We present a new efficient method for inferring multiple alternative consensus trees and supertrees to best represent the most important evolutionary patterns of a given set of gene phylogenies. We show how an adapted version of the popular k-means clustering algorithm, based on some remarkable properties of the Robinson and Foulds distance, can be used to partition a given set of trees into one (for homogeneous data) or multiple (for heterogeneous data) cluster(s) of trees. Moreover, we adapt the popular Cali&#x144;ski-Harabasz, Silhouette, Ball and Hall, and Gap cluster validity indices to tree clustering with k-means. Special attention is given to the relevant but very challenging problem of inferring alternative supertrees. The use of the Euclidean property of the objective function of the method makes it faster than the existing tree clustering techniques, and thus better suited for analyzing large evolutionary datasets.<br><br>Our KMeansSuperTreeClustering program along with its C++ source code is available at: https://github.com/TahiriNadia/KMeansSuperTreeClustering.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid35577916, year = {2022}, author = {Rahman, MH and Mahbub, KR and Espinoza-Vergara, G and Ritchie, A and Hoque, MM and Noorian, P and Cole, L and McDougald, D and Labbate, M}, title = {Protozoal food vacuoles enhance transformation in Vibrio cholerae through SOS-regulated DNA integration.}, journal = {The ISME journal}, volume = {16}, number = {8}, pages = {1993-2001}, pmid = {35577916}, issn = {1751-7370}, mesh = {Bacteria/genetics ; Chitin ; DNA ; Escherichia coli/genetics ; Phagosomes ; Vacuoles ; *Vibrio cholerae/genetics ; }, abstract = {Vibrio cholerae, the bacterial pathogen responsible for the diarrheal disease cholera, resides in the aquatic environment between outbreaks. For bacteria, genetic variation by lateral gene transfer (LGT) is important for survival and adaptation. In the aquatic environment, V. cholerae is predominantly found in biofilms associated with chitinous organisms or with chitin "rain". Chitin induces competency in V. cholerae, which can lead to LGT. In the environment, V. cholerae is also subjected to predation pressure by protist. Here we investigated whether protozoal predation affected LGT using the integron as a model. Integrons facilitate the integration of mobile DNA (gene cassettes) into the bacterial chromosome. We report that protozoal predation enhances transformation of a gene cassette by as much as 405-fold. We show that oxidative radicals produced in the protozoal phagosome induces the universal SOS response, which in turn upregulates the integron-integrase, the recombinase that facilitates cassette integration. Additionally, we show that during predation, V. cholerae requires the type VI secretion system to acquire the gene cassette from Escherichia coli. These results show that protozoal predation enhances LGT thus producing genetic variants that may have increased capacity to survive grazing. Additionally, the conditions in the food vacuole may make it a "hot spot" for LGT by accumulating diverse bacteria and inducing the SOS response helping drive genetic diversification and evolution.}, }
@article {pmid35576144, year = {2022}, author = {Dordet-Frisoni, E and Vandecasteele, C and Contarin, R and Sagné, E and Baranowski, E and Klopp, C and Nouvel, LX and Citti, C}, title = {Impacts of Mycoplasma agalactiae restriction-modification systems on pan-epigenome dynamics and genome plasticity.}, journal = {Microbial genomics}, volume = {8}, number = {5}, pages = {}, pmid = {35576144}, issn = {2057-5858}, mesh = {*DNA Restriction-Modification Enzymes/genetics ; Epigenome ; Gene Transfer, Horizontal ; Genome, Bacterial ; *Mycoplasma agalactiae/genetics ; }, abstract = {DNA methylations play an important role in the biology of bacteria. Often associated with restriction modification (RM) systems, they are important drivers of bacterial evolution interfering in horizontal gene transfer events by providing a defence against foreign DNA invasion or by favouring genetic transfer through production of recombinogenic DNA ends. Little is known regarding the methylome of the Mycoplasma genus, which encompasses several pathogenic species with small genomes. Here, genome-wide detection of DNA methylations was conducted using single molecule real-time (SMRT) and bisulphite sequencing in several strains of Mycoplasma agalactiae, an important ruminant pathogen and a model organism. Combined with whole-genome analysis, this allowed the identification of 19 methylated motifs associated with three orphan methyltransferases (MTases) and eight RM systems. All systems had a homolog in at least one phylogenetically distinct Mycoplasma spp. Our study also revealed that several superimposed genetic events may participate in the M. agalactiae dynamic epigenomic landscape. These included (i) DNA shuffling and frameshift mutations that affect the MTase and restriction endonuclease content of a clonal population and (ii) gene duplication, erosion, and horizontal transfer that modulate MTase and RM repertoires of the species. Some of these systems were experimentally shown to play a major role in mycoplasma conjugative, horizontal DNA transfer. While the versatility of DNA methylation may contribute to regulating essential biological functions at cell and population levels, RM systems may be key in mycoplasma genome evolution and adaptation by controlling horizontal gene transfers.}, }
@article {pmid35575901, year = {2022}, author = {Forni, D and Cagliani, R and Molteni, C and Arrigoni, F and Mozzi, A and Clerici, M and De Gioia, L and Sironi, M}, title = {Homology-based classification of accessory proteins in coronavirus genomes uncovers extremely dynamic evolution of gene content.}, journal = {Molecular ecology}, volume = {31}, number = {13}, pages = {3672-3692}, pmid = {35575901}, issn = {1365-294X}, mesh = {Amino Acid Sequence ; *Coronavirus/chemistry/genetics ; Evolution, Molecular ; Genome, Viral/genetics ; Open Reading Frames/genetics ; }, abstract = {Coronaviruses (CoVs) have complex genomes that encode a fixed array of structural and nonstructural components, as well as a variety of accessory proteins that differ even among closely related viruses. Accessory proteins often play a role in the suppression of immune responses and may represent virulence factors. Despite their relevance for CoV phenotypic variability, information on accessory proteins is fragmentary. We applied a systematic approach based on homology detection to create a comprehensive catalogue of accessory proteins encoded by CoVs. Our analyses grouped accessory proteins into 379 orthogroups and 12 super-groups. No orthogroup was shared by the four CoV genera and very few were present in all or most viruses in the same genus, reflecting the dynamic evolution of CoV genomes. We observed differences in the distribution of accessory proteins in CoV genera. Alphacoronaviruses harboured the largest diversity of accessory open reading frames (ORFs), deltacoronaviruses the smallest. However, the average number of accessory proteins per genome was highest in betacoronaviruses. Analysis of the evolutionary history of some orthogroups indicated that the different CoV genera adopted similar evolutionary strategies. Thus, alphacoronaviruses and betacoronaviruses acquired phosphodiesterases and spike-like accessory proteins independently, whereas horizontal gene transfer from reoviruses endowed betacoronaviruses and deltacoronaviruses with fusion-associated small transmembrane (FAST) proteins. Finally, analysis of accessory ORFs in annotated CoV genomes indicated ambiguity in their naming. This complicates cross-communication among researchers and hinders automated searches of large data sets (e.g., PubMed, GenBank). We suggest that orthogroup membership is used together with a naming system to provide information on protein function.}, }
@article {pmid35575816, year = {2022}, author = {Estrada, A and Suárez-Díaz, E and Becerra, A}, title = {Reconstructing the Last Common Ancestor: Epistemological and Empirical Challenges.}, journal = {Acta biotheoretica}, volume = {70}, number = {2}, pages = {15}, pmid = {35575816}, issn = {1572-8358}, support = {460604//consejo nacional de ciencia y tecnolog&#xed;a/ ; }, mesh = {Animals ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Phylogeny ; }, abstract = {Reconstructing the genetic traits of the Last Common Ancestor (LCA) and the Tree of Life (TOL) are two examples of the reaches of contemporary molecular phylogenetics. Nevertheless, the whole enterprise has led to paradoxical results. The presence of Lateral Gene Transfer poses epistemic and empirical challenges to meet these goals; the discussion around this subject has been enriched by arguments from philosophers and historians of science. At the same time, a few but influential research groups have aimed to reconstruct the LCA with rich-in-detail hypotheses and high-resolution gene catalogs and metabolic traits. We argue that LGT poses insurmountable challenges for detailed and rich in details reconstructions and propose, instead, a middle-ground position with the reconstruction of a slim LCA based on traits under strong pressures of Negative Natural Selection, and for the need of consilience with evidence from organismal biology and geochemistry. We defend a cautionary perspective that goes beyond the statistical analysis of gene similarities and assumes the broader consequences of evolving empirical data and epistemic pluralism in the reconstruction of early life.}, }
@article {pmid35574173, year = {2022}, author = {Edwards, O and Jander, G and Ochman, H and Schuurink, R and Singh, KB}, title = {Insects Co-opt Host Genes to Overcome Plant Defences.}, journal = {Faculty reviews}, volume = {11}, number = {}, pages = {10}, pmid = {35574173}, issn = {2732-432X}, abstract = {Insect pests of plants, such as whiteflies, cause immense economic damage both through direct feeding and by transmitting viruses. In a major breakthrough, a paper by Xia et al.[1] shows that some whiteflies have co-opted a gene from their plant host that has helped them neutralize a key component of the plant's defense. Plants produce a range of toxins as part of their defense against insect predation, and Xia et al. [1] show that, through a horizontal gene transfer (HGT) event from plant to insect, some whiteflies have acquired a gene whose original function was to protect the plants themselves from such damaging toxins through chemical modification that converts them to less harmful forms. Targeting of this gene in whiteflies using RNAi technology provided effective resistance in this ground-breaking study, which should lead others interested in crop protection to explore genes that have been transferred from plants to insects.}, }
@article {pmid35562911, year = {2022}, author = {Du, Y and Jin, Y and Li, B and Yue, J and Yin, Z}, title = {Comparative Genomic Analysis of Vibrio cincinnatiensis Provides Insights into Genetic Diversity, Evolutionary Dynamics, and Pathogenic Traits of the Species.}, journal = {International journal of molecular sciences}, volume = {23}, number = {9}, pages = {}, pmid = {35562911}, issn = {1422-0067}, support = {ZR2021QC208//Shandong Provincial Natural Science Foundation/ ; 010/721000//Scientific Research Foundation of Shandong Agricultural University/ ; 2018ZX10101-003-001-008//the National Science and Technology Major Project of Infectious Diseases/ ; }, mesh = {Gene Transfer, Horizontal ; Genetic Variation ; *Genome, Bacterial ; Genomics/methods ; Phylogeny ; *Vibrio/genetics ; }, abstract = {Vibrio cincinnatiensis is a poorly understood pathogenic Vibrio species, and the underlying mechanisms of its genetic diversity, genomic plasticity, evolutionary dynamics, and pathogenicity have not yet been comprehensively investigated. Here, a comparative genomic analysis of V. cincinnatiensis was constructed. The open pan-genome with a flexible gene repertoire exhibited genetic diversity. The genomic plasticity and stability were characterized by the determinations of diverse mobile genetic elements (MGEs) and barriers to horizontal gene transfer (HGT), respectively. Evolutionary divergences were exhibited by the difference in functional enrichment and selective pressure between the different components of the pan-genome. The evolution on the Chr I and Chr II core genomes was mainly driven by purifying selection. Predicted essential genes in V. cincinnatiensis were mainly found in the core gene families on Chr I and were subject to stronger evolutionary constraints. We identified diverse virulence-related elements, including the gene clusters involved in encoding flagella, secretion systems, several pili, and scattered virulence genes. Our results indicated the pathogenic potential of V. cincinnatiensis and highlighted that HGT events from other Vibrio species promoted pathogenicity. This pan-genome study provides comprehensive insights into this poorly understood species from the genomic perspective.}, }
@article {pmid35561860, year = {2022}, author = {Arbita, AA and Paul, NA and Cox, J and Zhao, J}, title = {Amino acid sequence of two new milk-clotting proteases from the macroalga Gracilaria edulis.}, journal = {International journal of biological macromolecules}, volume = {211}, number = {}, pages = {499-505}, doi = {10.1016/j.ijbiomac.2022.05.038}, pmid = {35561860}, issn = {1879-0003}, mesh = {Amino Acid Sequence ; Animals ; Chromatography, Liquid ; Electrophoresis, Polyacrylamide Gel ; *Gracilaria/chemistry ; Milk/chemistry ; *Seaweed/chemistry ; Serine Proteases/chemistry/genetics ; Tandem Mass Spectrometry ; }, abstract = {This study is aimed at identifying and characterising the proteases we previously extracted from the red seaweed Gracilaria edulis with the potential as milk-clotting enzymes. The protease extract was first analysed by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) and zymography. Two protease bands with a molecular weight of 44 and 108 kDa were identified, and analysed using in-gel digestion and liquid chromatography-tandem mass spectrometry/mass spectrometry (LC-MS/MS). Eight peptides from the LC-MS/MS analysis matched those in existing protein databases but they were not related to any protease of the genera Gracilaria and Hydropuntia. Further analysis revealed that more than 80% of the peptide sequence of the algal proteases matched with those from members of the bacteria kingdom, including Gallaecimonas and Alteromonas. Among these, twelve matching homolog proteases were identified as metalloprotease and serine protease. The results indicated that the algal proteases have a close relationship with both algae and bacteria, and suggest that the proteases might have resulted from past bacterial colonisation of the algae and subsequent horizontal gene transfer between bacteria and algae.}, }
@article {pmid35560986, year = {2022}, author = {Ullah, R and Zhu, B and Kakar, KU and Nawaz, Z and Mushtaq, M and Durrani, TS and Islam, ZU and Nawaz, F}, title = {Micro-synteny conservation analysis revealed the evolutionary history of bacterial biphenyl degradation pathway.}, journal = {Environmental microbiology reports}, volume = {14}, number = {4}, pages = {494-505}, doi = {10.1111/1758-2229.13081}, pmid = {35560986}, issn = {1758-2229}, mesh = {Biodegradation, Environmental ; Biphenyl Compounds ; Genes, Bacterial ; Phylogeny ; *Polychlorinated Biphenyls/metabolism ; Synteny ; }, abstract = {Phenolic compounds have been enlisted by the United States Environmental Protection Agency (USEPA) and the European Union (EU) as pollutants of priority concern. The biphenyl degradation pathway plays an essential role in prokaryote polychlorinated biphenyls degradation. Our understanding of prokaryotic pathways and their evolution has dramatically increased in recent years with the advancements in prokaryotic genome sequencing and analysis tools. In this work, we applied bioinformatics tools to study the evolution of the biphenyl degradation pathway focusing on the phylogeny and initiation of four representative species (Burkholderia xenovorans LB400, Polaromonas naphthalenivorans CJ2, Pseudomonas putida F1 and Rhodococcus jostii RHA1). These species contained partial or full concatenated genes from bph gene cluster (i.e. bphRbphA1A2A3A4BCKHJID). The aim was to establish this pathway's origin and development mode in the prokaryotic world. Genomic screening revealed that many bacterial species possess genes for the biphenyl degradation pathway. However, the micro-synteny conservation analysis indicated that massive gene recruitment events might have occurred during the evolution of the biphenyl degradation pathway. Combining with the phylogenetic positions, this work points to the evolutionary process of acquiring the biphenyl degradation pathway by different fragments through horizontal gene transfer in these bacterial groups. This study reports the first-ever evidence of the birth of this pathway in the represented species.}, }
@article {pmid35560066, year = {2022}, author = {Xu, Y and Wang, H and Sahu, SK and Li, L and Liang, H and Günther, G and Wong, GK and Melkonian, B and Melkonian, M and Liu, H and Wang, S}, title = {Chromosome-level genome of Pedinomonas minor (Chlorophyta) unveils adaptations to abiotic stress in a rapidly fluctuating environment.}, journal = {The New phytologist}, volume = {235}, number = {4}, pages = {1409-1425}, doi = {10.1111/nph.18220}, pmid = {35560066}, issn = {1469-8137}, mesh = {*Chlorophyta/metabolism ; Chromosomes ; *DNA Transposable Elements/genetics ; Phylogeny ; Stress, Physiological/genetics ; }, abstract = {The Pedinophyceae (Viridiplantae) comprise a class of small uniflagellate algae with a pivotal position in the phylogeny of the Chlorophyta as the sister group of the 'core chlorophytes'. We present a chromosome-level genome assembly of the freshwater type species of the class, Pedinomonas minor. We sequenced the genome using Pacbio, Illumina and Hi-C technologies, performed comparative analyses of genome and gene family evolution, and analyzed the transcriptome under various abiotic stresses. Although the genome is relatively small (55 Mb), it shares many traits with core chlorophytes including number of introns and protein-coding genes, messenger RNA (mRNA) lengths, and abundance of transposable elements. Pedinomonas minor is only bounded by the plasma membrane, thriving in temporary habitats that frequently dry out. Gene family innovations and expansions and transcriptomic responses to abiotic stresses have shed light on adaptations of P. minor to its fluctuating environment. Horizontal gene transfers from bacteria and fungi have possibly contributed to the evolution of some of these traits. We identified a putative endogenization site of a nucleocytoplasmic large DNA virus and hypothesized that endogenous viral elements donated foreign genes to the host genome, their spread enhanced by transposable elements, located at gene boundaries in several of the expanded gene families.}, }
@article {pmid35549857, year = {2022}, author = {Majumdar, R and Karthikeyan, H and Senthilnathan, V and Sugumar, S}, title = {Review on Stenotrophomonas maltophilia: An Emerging Multidrug- resistant Opportunistic Pathogen.}, journal = {Recent patents on biotechnology}, volume = {16}, number = {4}, pages = {329-354}, doi = {10.2174/1872208316666220512121205}, pmid = {35549857}, issn = {2212-4012}, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Drug Resistance, Multiple, Bacterial ; *Gram-Negative Bacterial Infections/drug therapy/microbiology ; Humans ; Microbial Sensitivity Tests ; Opportunistic Infections/microbiology ; Patents as Topic ; *Stenotrophomonas maltophilia/drug effects/genetics ; Virulence Factors/genetics/therapeutic use ; beta-Lactamases/genetics/therapeutic use ; }, abstract = {Stenotrophomonas maltophilia is an opportunistic pathogen that results in nosocomial infections in immunocompromised individuals. These bacteria colonize on the surface of medical devices and therapeutic equipment like urinary catheters, endoscopes, and ventilators, causing respiratory and urinary tract infections. The low outer membrane permeability of multidrug-resistance efflux systems and the two chromosomally encoded β- lactamases present in S. maltophilia are challenging for arsenal control. The cell-associated and extracellular virulence factors in S. maltophilia are involved in colonization and biofilm formation on the host surfaces. The spread of antibiotic-resistant genes in the pathogenic S. maltophilia attributes to bacterial resistance against a wide range of antibiotics, including penicillin, quinolones, and carbapenems. So far, tetracycline derivatives, fluoroquinolones, and trimethoprim-sulfamethoxazole (TMP-SMX) are considered promising antibiotics against S. maltophilia. Due to the adaptive nature of the intrinsically resistant mechanism towards the number of antibiotics and its ability to acquire new resistance via mutation and horizontal gene transfer, it is quite tricky for medicinal contribution against S. maltophilia. The current review summarizes the literary data on pathogenicity, quorum sensing, biofilm formation, virulence factors, and antibiotic resistance of S. maltophilia.}, }
@article {pmid35542181, year = {2022}, author = {Zarlenga, D and Thompson, P and Mitreva, M and Rosa, BA and Hoberg, E}, title = {Horizontal gene transfer provides insights into the deep evolutionary history and biology of Trichinella.}, journal = {Food and waterborne parasitology}, volume = {27}, number = {}, pages = {e00155}, pmid = {35542181}, issn = {2405-6766}, support = {R01 AI159450/AI/NIAID NIH HHS/United States ; }, abstract = {Evolution involves temporal changes in the characteristics of a species that are subsequently propagated or rejected through natural selection. In the case of parasites, host switching also plays a prominent role in the evolutionary process. These changes are rooted in genetic variation and gene flow where genes may be deleted, mutated (sequence), duplicated, rearranged and/or translocated and then transmitted through vertical gene transfer. However, the introduction of new genes is not driven only by Mendelian inheritance and mutation but also by the introduction of DNA from outside a lineage in the form of horizontal gene transfer between donor and recipient organisms. Once introduced and integrated into the biology of the recipient, vertical inheritance then perpetuates the newly acquired genetic factor, where further functionality may involve co-option of what has become a pre-existing physiological capacity. Upon sequencing the Trichinella spiralis (Clade I) genome, a cyanate hydratase (cyanase) gene was identified that is common among bacteria, fungi, and plants, but rarely observed among other eukaryotes. The sequence of the Trichinella cyanase gene clusters with those derived from the Kingdom Plantae in contrast to the genes found in some Clade III and IV nematodes that cluster with cyanases of bacterial origin. Phylogenetic analyses suggest that the Trichinella cyanase was acquired during the Devonian period and independently from those of other nematodes. These data may help inform us of the deep evolutionary history and ecological connectivity of early ancestors within the lineage of contemporary Trichinella. Further, in many extant organisms, cyanate detoxification has been largely superseded by energy requirements for metabolism. Thus, deciphering the function of Trichinella cyanase may provide new avenues for treatment and control.}, }
@article {pmid35538580, year = {2022}, author = {Guédon, G and Lao, J and Payot, S and Lacroix, T and Chiapello, H and Leblond-Bourget, N}, title = {FirmiData: a set of 40 genomes of Firmicutes with a curated annotation of ICEs and IMEs.}, journal = {BMC research notes}, volume = {15}, number = {1}, pages = {157}, pmid = {35538580}, issn = {1756-0500}, mesh = {Chromosomes ; *Conjugation, Genetic ; DNA Transposable Elements ; *Firmicutes ; Gene Transfer, Horizontal ; Genome, Bacterial/genetics ; }, abstract = {OBJECTIVES: 'Integrative and Conjugative Elements' (ICEs) and 'Integrative and Mobilizable Elements' (IMEs) are two classes of mobile genetic elements that are complex to detect and delineate. Therefore, they are yet poorly annotated in bacterial genomes. FirmiData provides to the scientific community of microbiologists and bioinformaticians a reference resource of annotated ICEs and of IMEs from Firmicutes. It illustrates their prevalence and their diversity but also gives information on their organization. FirmiData was designed to assist the scientific community in identifying and annotating these elements by using the sequences of these ICEs and IMEs for the identification of related elements in other genomes of Firmicutes. Therefore, Firmidata meets the needs of the scientific community.<br><br>DATA DESCRIPTION: Firmidata provides a manually curated annotation of 98 ICEs and 148 IMEs identified in 40 chromosomes of Firmicutes. The delineation at the nucleotide level of almost all of these elements allows for the characterization of the genes they carry.}, }
@article {pmid35537575, year = {2022}, author = {Zheng, W and Li, Y and Tang, W and Wei, M and Li, Y and Shi, P and Jiang, L and Zhu, H and Yu, X and Chen, G and Wang, J and Zhang, J and Zhang, X}, title = {Whole genome analysis of a novel adenovirus discovered from Oriolus chinesis.}, journal = {Virus research}, volume = {317}, number = {}, pages = {198799}, doi = {10.1016/j.virusres.2022.198799}, pmid = {35537575}, issn = {1872-7492}, mesh = {Adenoviridae/genetics ; *Adenoviridae Infections ; Animals ; *Aviadenovirus/genetics ; Genome, Viral ; *Passeriformes/genetics ; Phylogeny ; }, abstract = {We present the first complete genome sequence of an aviadenovirus Oriolus adenovirus (OrAdV) sequenced from the cloaca of a Oriolus chinensis (a passerine bird widely distributed in Asia), which was collected from an island off the east coast of China. Thirty-one protein coding genes were predicted in this 40425-bp-long genome. OrAdV genome is highly divergent and has only 57% average protein identity compared with other aviadenovirus genomes. Comparative genomic analysis indicates that this passerine virus is a new species of aviadenovirus. One unique thymidylate kinase gene was discovered in OrAdV genome. This gene is absent in other adenovirus genomes and usually reported to occur in herpesvirus. Protein sequence alignment against all known proteins indicates that this gene may be originated from ancient horizontal gene transfer event between virus and parasitic eukaryote like protozoan. This new aviadenovirus genome enriches the genomic information of adenovirus and suggests that there is a large unknown space of adenovirus world.}, }
@article {pmid35537514, year = {2022}, author = {Sun, R and He, L and Li, T and Dai, Z and Sun, S and Ren, L and Liang, YQ and Zhang, Y and Li, C}, title = {Impact of the surrounding environment on antibiotic resistance genes carried by microplastics in mangroves.}, journal = {The Science of the total environment}, volume = {837}, number = {}, pages = {155771}, doi = {10.1016/j.scitotenv.2022.155771}, pmid = {35537514}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Microplastics ; *Plastics ; Polyethylene ; Polypropylenes ; }, abstract = {The pollution of antibiotic resistance genes (ARGs) carried by microplastics (MPs) is a growing concern. Mangroves are located at the intersection of land and sea and are seriously affected by MP pollution. However, few studies have systematic research evaluating the transmission risk of ARGs carried by MPs in mangroves. We conducted in situ experiments by burying five different MPs (polypropylene, high-density polyethylene, polystyrene, polyethylene glycol terephthalate, and polycaprolactone particles) in mangroves with different surrounding environments. A total of 10 genes in the MPs of mangroves were detected using quantitative real-time polymerase chain reactions, including eight ARGs and two mobile genetic elements (MGEs). The abundance of ARGs in Guanhai park mangroves in living areas (GH) was higher than that of Gaoqiao mangroves in protected areas (GQ) and Beiyue dike mangroves in aquaculture pond areas (BY). Pathogenic bacteria, such as Acinetobacter, Bacillus, and Vibrio were found on the MP surfaces of the mangroves. The number of ARGs carried by multiple drug-resistant bacteria in the GH mangroves was greater than that in the GQ and BY mangroves. Moreover, the ARGs carried by MPs in GH mangroves had the highest potential transmission risk by horizontal gene transfer. Sociometric and environmental factors were the main drivers shaping the distribution characteristics of ARGs and MGEs. Polypropylene and high-density polyethylene particles are preferred substrates for obtaining diffuse ARGs. This study investigated the drivers of ARGs in the MPs of mangroves and provided essential guidance on the use and handling of plastics.}, }
@article {pmid35536747, year = {2022}, author = {Gotoh, Y and Atsuta, Y and Taniguchi, T and Nishida, R and Nakamura, K and Ogura, Y and Misawa, N and Hayashi, T}, title = {Helicobacter cinaedi is a human-adapted lineage in the Helicobacter cinaedi/canicola/'magdeburgensis' complex.}, journal = {Microbial genomics}, volume = {8}, number = {5}, pages = {}, pmid = {35536747}, issn = {2057-5858}, mesh = {Animals ; *Bacteremia ; Cricetinae ; Dogs ; *Helicobacter/genetics ; *Helicobacter Infections ; Humans ; Rats ; }, abstract = {Helicobacter cinaedi is an enterohepatic Helicobacter that causes bacteremia and other diseases in humans. While H. cinaedi-like strains are isolated from animals, including dog isolates belonging to a recently proposed H. canicola, little is known about the genetic differences between H. cinaedi and these animal isolates. Here, we sequenced 43 H. cinaedi- or H. canicola-like strains isolated from humans, hamsters, rats and dogs and collected 81 genome sequences of H. cinaedi, H. canicola and other enterohepatic Helicobacter strains from public databases. Genomic comparison of these strains identified four distinct clades (clades I-IV) in H. cinaedi/canicola/'magderbugensis' (HCCM) complex. Among these, clade I corresponds to H. cinaedi sensu stricto and represents a human-adapted lineage in the complex. We identified several genomic features unique to clade I. They include the accumulation of antimicrobial resistance-related mutations that reflects the human association of clade I and the larger genome size and the presence of a CRISPR-Cas system and multiple toxin-antitoxin and restriction-modification systems, both of which indicate the contribution of horizontal gene transfer to the evolution of clade I. In addition, nearly all clade I strains but only a few strains belonging to one minor clade contained a highly variable genomic region encoding a type VI secretion system (T6SS), which could play important roles in gut colonization by killing competitors or inhibiting their growth. We also developed a method to systematically search for H. cinaedi sequences in large metagenome data sets based on the results of genome comparison. Using this method, we successfully identified multiple HCCM complex-containing human faecal metagenome samples and obtained the sequence information covering almost the entire genome of each strain. Importantly, all were clade I strains, supporting our conclusion that H. cinaedi sensu stricto is a human-adapted lineage in the HCCM complex.}, }
@article {pmid35536007, year = {2022}, author = {Mo, R and Liu, Y and Chen, Y and Mao, Y and Gao, B}, title = {Evolutionary Principles of Bacterial Signaling Capacity and Complexity.}, journal = {mBio}, volume = {13}, number = {3}, pages = {e0076422}, pmid = {35536007}, issn = {2150-7511}, mesh = {Adaptation, Physiological ; Bacteria/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; *Cyclic GMP/metabolism ; Gene Expression Regulation, Bacterial ; Histidine Kinase/genetics/metabolism ; *Signal Transduction ; }, abstract = {Microbes rely on signal transduction systems to sense and respond to environmental changes for survival and reproduction. It is generally known that niche adaptation plays an important role in shaping the signaling repertoire. However, the evolution of bacterial signaling capacity lacks systematic studies with a temporal direction. In particular, it is unclear how complexity evolved from simplicity or vice versa for signaling networks. Here, we examine the evolutionary processes of major signal transduction systems in Campylobacterota (formerly Epsilonproteobacteria), a phylum with sufficient evolutionary depth and ecological diversity. We discovered that chemosensory system increases complexity by horizontal gene transfer (HGT) of entire chemosensory classes, and different chemosensory classes rarely mix their components. Two-component system gains complexity by atypical histidine kinases fused with receiver domain to achieve multistep or branched signal transduction process. The presence and complexity of c-di-GMP-mediated system is related to the size of signaling network, and c-di-GMP pathways are easy to rewire, since enzymes and effectors can be linked without direct protein-protein interaction. Overall, signaling capacity and complexity rise and drop together in Campylobacterota, determined by sensory demand, genetic resources, and coevolution within the genomic context. These findings reflect plausible evolutionary principles for other cellular networks and genome evolution of the Bacteria domain. IMPORTANCE Bacteria are capable of sensing and responding to environmental changes by several signal transduction systems with different mechanisms. Much attention is paid to model organisms with complex signaling networks to understand their composition and function, but how a complicated network evolved from a simple one or vice versa lacks systematic studies. Here, we tracked the evolutionary process of each signaling system in a bacterial phylum with robust "eco-evo" framework and summarized the general principles of signaling network evolution. Our findings bridge the gaps in bacterial signaling capacity from highly sophisticated to extremely streamlined, shedding light on rational design of genetic circuitry. This study may serve as a paradigm to examine the complex construction of other cellular networks and genome evolution.}, }
@article {pmid35535514, year = {2022}, author = {Xiong, Q and Wan, AT and Liu, X and Fung, CS and Xiao, X and Malainual, N and Hou, J and Wang, L and Wang, M and Yang, KY and Cui, Y and Leung, EL and Nong, W and Shin, SK and Au, SW and Jeong, KY and Chew, FT and Hui, JH and Leung, TF and Tungtrongchitr, A and Zhong, N and Liu, Z and Tsui, SK}, title = {Comparative Genomics Reveals Insights into the Divergent Evolution of Astigmatic Mites and Household Pest Adaptations.}, journal = {Molecular biology and evolution}, volume = {39}, number = {5}, pages = {}, pmid = {35535514}, issn = {1537-1719}, mesh = {*Adaptation, Physiological/genetics ; Genome ; *Genomics ; Humans ; Uridine Diphosphate ; }, abstract = {Highly diversified astigmatic mites comprise many medically important human household pests such as house dust mites causing ∼1-2% of all allergic diseases globally; however, their evolutionary origin and diverse lifestyles including reversible parasitism have not been illustrated at the genomic level, which hampers allergy prevention and our exploration of these household pests. Using six high-quality assembled and annotated genomes, this study not only refuted the monophyly of mites and ticks, but also thoroughly explored the divergence of Acariformes and the diversification of astigmatic mites. In monophyletic Acariformes, Prostigmata known as notorious plant pests first evolved, and then rapidly evolving Astigmata diverged from soil oribatid mites. Within astigmatic mites, a wide range of gene families rapidly expanded via tandem gene duplications, including ionotropic glutamate receptors, triacylglycerol lipases, serine proteases and UDP glucuronosyltransferases. Gene diversification after tandem duplications provides many genetic resources for adaptation to sensing environmental signals, digestion, and detoxification in rapidly changing household environments. Many gene decay events only occurred in the skin-burrowing parasitic mite Sarcoptes scabiei. Throughout the evolution of Acariformes, massive horizontal gene transfer events occurred in gene families such as UDP glucuronosyltransferases and several important fungal cell wall lytic enzymes, which enable detoxification and digestive functions and provide perfect drug targets for pest control. This comparative study sheds light on the divergent evolution and quick adaptation to human household environments of astigmatic mites and provides insights into the genetic adaptations and even control of human household pests.}, }
@article {pmid35534719, year = {2022}, author = {Kralemann, LEM and de Pater, S and Shen, H and Kloet, SL and van Schendel, R and Hooykaas, PJJ and Tijsterman, M}, title = {Distinct mechanisms for genomic attachment of the 5' and 3' ends of Agrobacterium T-DNA in plants.}, journal = {Nature plants}, volume = {8}, number = {5}, pages = {526-534}, pmid = {35534719}, issn = {2055-0278}, mesh = {*Agrobacterium tumefaciens/genetics ; *Arabidopsis/genetics/metabolism ; Bacterial Proteins/genetics ; DNA End-Joining Repair ; DNA, Bacterial/genetics/metabolism ; Genomics ; Plants/genetics ; }, abstract = {Agrobacterium tumefaciens, a pathogenic bacterium capable of transforming plants through horizontal gene transfer, is nowadays the preferred vector for plant genetic engineering. The vehicle for transfer is the T-strand, a single-stranded DNA molecule bound by the bacterial protein VirD2, which guides the T-DNA into the plant's nucleus where it integrates. How VirD2 is removed from T-DNA, and which mechanism acts to attach the liberated end to the plant genome is currently unknown. Here, using newly developed technology that yields hundreds of T-DNA integrations in somatic tissue of Arabidopsis thaliana, we uncover two redundant mechanisms for the genomic capture of the T-DNA 5' end. Different from capture of the 3' end of the T-DNA, which is the exclusive action of polymerase theta-mediated end joining (TMEJ), 5' attachment is accomplished either by TMEJ or by canonical non-homologous end joining (cNHEJ). We further find that TMEJ needs MRE11, whereas cNHEJ requires TDP2 to remove the 5' end-blocking protein VirD2. As a consequence, T-DNA integration is severely impaired in plants deficient for both MRE11 and TDP2 (or other cNHEJ factors). In support of MRE11 and cNHEJ specifically acting on the 5' end, we demonstrate rescue of the integration defect of double-deficient plants by using T-DNAs that are capable of forming telomeres upon 3' capture. Our study provides a mechanistic model for how Agrobacterium exploits the plant's own DNA repair machineries to transform it.}, }
@article {pmid35533945, year = {2022}, author = {Ribeiro, GM and Lahr, DJG}, title = {A comparative study indicates vertical inheritance and horizontal gene transfer of arsenic resistance-related genes in eukaryotes.}, journal = {Molecular phylogenetics and evolution}, volume = {173}, number = {}, pages = {107479}, doi = {10.1016/j.ympev.2022.107479}, pmid = {35533945}, issn = {1095-9513}, mesh = {*Arsenic ; Bacteria/genetics/metabolism ; Eukaryota/genetics/metabolism ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Phylogeny ; }, abstract = {Arsenic is a ubiquitous element in the environment, a source of constant evolutionary pressure on organisms. The arsenic resistance machinery is thoroughly described for bacteria. Highly resistant lineages are also common in eukaryotes, but evolutionary knowledge is much more limited. While the origin of the resistance machinery in eukaryotes is loosely attributed to horizontal gene transfer (HGT) from bacteria, only a handful of eukaryotes were deeply studied. Here we investigate the origin and evolution of the core genes in arsenic resistance in eukaryotes using a broad phylogenetic framework. We hypothesize that, as arsenic pressure is constant throughout Earth's history, resistance mechanisms are probably ancestral to eukaryotes. We identified homologs for each of the arsenic resistance genes in eukaryotes and traced their possible origin using phylogenetic reconstruction. We reveal that: i. an important component of the arsenic-resistant machinery originated before the last eukaryotic common ancestor; ii. later events of gene duplication and HGT generated new homologs that, in many cases, replaced ancestral ones. Even though HGT has an important contribution to the expansion of arsenic metabolism in eukaryotes, we propose the hypothesis of ancestral origin and differential retention of arsenic resistance mechanisms in the group. Key-words: Environmental adaptation; resistance to toxic metalloids; detoxification; comparative genomics; functional phylogenomics.}, }
@article {pmid35533275, year = {2022}, author = {Luo, H and Hallen-Adams, HE and Lüli, Y and Sgambelluri, RM and Li, X and Smith, M and Yang, ZL and Martin, FM}, title = {Genes and evolutionary fates of the amanitin biosynthesis pathway in poisonous mushrooms.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {20}, pages = {e2201113119}, pmid = {35533275}, issn = {1091-6490}, mesh = {Amanita/genetics ; *Amanitins/genetics ; Biological Evolution ; Biosynthetic Pathways/genetics ; Gene Transfer, Horizontal ; *Toxins, Biological ; }, abstract = {The deadly toxin α-amanitin is a bicyclic octapeptide biosynthesized on ribosomes. A phylogenetically disjunct group of mushrooms in Agaricales (Amanita, Lepiota, and Galerina) synthesizes α-amanitin. This distribution of the toxin biosynthetic pathway is possibly related to the horizontal transfer of metabolic gene clusters among taxonomically unrelated mushrooms with overlapping habitats. Here, our work confirms that two biosynthetic genes, P450-29 and FMO1, are oxygenases important for amanitin biosynthesis. Phylogenetic and genetic analyses of these genes strongly support their origin through horizontal transfer, as is the case for the previously characterized biosynthetic genes MSDIN and POPB. Our analysis of multiple genomes showed that the evolution of the α-amanitin biosynthetic pathways in the poisonous agarics in the Amanita, Lepiota, and Galerina clades entailed distinct evolutionary pathways including gene family expansion, biosynthetic genes, and genomic rearrangements. Unrelated poisonous fungi produce the same deadly amanitin toxins using variations of the same pathway. Furthermore, the evolution of the amanitin biosynthetic pathway(s) in Amanita species generates a much wider range of toxic cyclic peptides. The results reported here expand our understanding of the genetics, diversity, and evolution of the toxin biosynthetic pathway in fungi.}, }
@article {pmid35531659, year = {2022}, author = {Friães, A and Mamede, R and Ferreira, M and Melo-Cristino, J and Ramirez, M}, title = {Annotated Whole-Genome Multilocus Sequence Typing Schema for Scalable High-Resolution Typing of Streptococcus pyogenes.}, journal = {Journal of clinical microbiology}, volume = {60}, number = {6}, pages = {e0031522}, pmid = {35531659}, issn = {1098-660X}, support = {LISBOA-01-0145-FEDER-016417//MEC | Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia (FCT)/ ; 2020.08493.BD//MEC | Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia (FCT)/ ; }, mesh = {Disease Outbreaks ; Electrophoresis, Gel, Pulsed-Field ; Genome, Bacterial/genetics ; *Genome-Wide Association Study ; Humans ; Multilocus Sequence Typing/methods ; *Streptococcus pyogenes/genetics ; }, abstract = {Streptococcus pyogenes is a major human pathogen with high genetic diversity, largely created by recombination and horizontal gene transfer, making it difficult to use single nucleotide polymorphism (SNP)-based genome-wide analyses for surveillance. Using a gene-by-gene approach on 208 complete genomes of S. pyogenes, a novel whole-genome multilocus sequence typing (wgMLST) schema was developed, comprising 3,044 target loci. The schema was used for core-genome MLST (cgMLST) analyses of previously published data sets and 265 newly sequenced draft genomes with other molecular and phenotypic typing data. Clustering based on cgMLST data supported the genetic heterogeneity of many emm types and correlated poorly with pulsed-field gel electrophoresis macrorestriction profiling, superantigen gene profiling, and MLST sequence type, highlighting the limitations of older typing methods. While 763 loci were present in all isolates of a data set representative of S. pyogenes genetic diversity, the proposed schema allows scalable cgMLST analysis, which can include more loci for an increased resolution when typing closely related isolates. The cgMLST and PopPUNK clusters were broadly consistent in this diverse population. The cgMLST analyses presented results comparable to those of SNP-based methods in the identification of two recently emerged sublineages of emm1 and emm89 and the clarification of the genetic relatedness among isolates recovered in outbreak contexts. The schema was thoroughly annotated and made publicly available on the chewie-NS online platform (https://chewbbaca.online/species/1/schemas/1), providing a framework for high-resolution typing and analyzing the genetic variability of loci of particular biological interest.}, }
@article {pmid35524279, year = {2022}, author = {Hwengwere, K and Paramel Nair, H and Hughes, KA and Peck, LS and Clark, MS and Walker, CA}, title = {Antimicrobial resistance in Antarctica: is it still a pristine environment?.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {71}, pmid = {35524279}, issn = {2049-2618}, mesh = {Animals ; Animals, Wild ; Antarctic Regions ; *Anti-Bacterial Agents/pharmacology ; Bacteria ; Birds ; *Drug Resistance, Bacterial ; }, abstract = {Although the rapid spread of antimicrobial resistance (AMR), particularly in relation to clinical settings, is causing concern in many regions of the globe, remote, extreme environments, such as Antarctica, are thought to be relatively free from the negative impact of human activities. In fact, Antarctica is often perceived as the last pristine continent on Earth. Such remote regions, which are assumed to have very low levels of AMR due to limited human activity, represent potential model environments to understand the mechanisms and interactions underpinning the early stages of evolution, de novo development, acquisition and transmission of AMR. Antarctica, with its defined zones of human colonisation (centred around scientific research stations) and large populations of migratory birds and animals, also has great potential with regard to mapping and understanding the spread of early-stage zoonotic interactions. However, to date, studies of AMR in Antarctica are limited. Here, we survey the current literature focussing on the following: i) Dissection of human-introduced AMR versus naturally occurring AMR, based on the premise that multiple drug resistance and resistance to synthetic antibiotics not yet found in nature are the results of human contamination ii) The potential role of endemic wildlife in AMR spread There is clear evidence for greater concentrations of AMR around research stations, and although data show reverse zoonosis of the characteristic human gut bacteria to endemic wildlife, AMR within birds and seals appears to be very low, albeit on limited samplings. Furthermore, areas where there is little, to no, human activity still appear to be free from anthropogenically introduced AMR. However, a comprehensive assessment of AMR levels in Antarctica is virtually impossible on current data due to the wide variation in reporting standards and methodologies used and poor geographical coverage. Thus, future studies should engage directly with policymakers to promote the implementation of continent-wide AMR reporting standards. The development of such standards alongside a centralised reporting system would provide baseline data to feedback directly into wastewater treatment policies for the Antarctic Treaty Area to help preserve this relatively pristine environment. Video Abstract.}, }
@article {pmid35518360, year = {2022}, author = {Gan, R and Zhou, F and Si, Y and Yang, H and Chen, C and Ren, C and Wu, J and Zhang, F}, title = {DBSCAN-SWA: An Integrated Tool for Rapid Prophage Detection and Annotation.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {885048}, pmid = {35518360}, issn = {1664-8021}, abstract = {As an intracellular form of a bacteriophage in the bacterial host genome, a prophage usually integrates into bacterial DNA with high specificity and contributes to horizontal gene transfer (HGT). With the exponentially increasing number of microbial sequences uncovered in genomic or metagenomics studies, there is a massive demand for a tool that is capable of fast and accurate identification of prophages. Here, we introduce DBSCAN-SWA, a command line software tool developed to predict prophage regions in bacterial genomes. DBSCAN-SWA runs faster than any previous tools. Importantly, it has great detection power based on analysis using 184 manually curated prophages, with a recall of 85% compared with Phage_Finder (63%), VirSorter (74%), and PHASTER (82%) for (Multi-) FASTA sequences. Moreover, DBSCAN-SWA outperforms the existing standalone prophage prediction tools for high-throughput sequencing data based on the analysis of 19,989 contigs of 400 bacterial genomes collected from Human Microbiome Project (HMP) project. DBSCAN-SWA also provides user-friendly result visualizations including a circular prophage viewer and interactive DataTables. DBSCAN-SWA is implemented in Python3 and is available under an open source GPLv2 license from https://github.com/HIT-ImmunologyLab/DBSCAN-SWA/.}, }
@article {pmid35516430, year = {2022}, author = {Boase, K and González, C and Vergara, E and Neira, G and Holmes, D and Watkin, E}, title = {Prediction and Inferred Evolution of Acid Tolerance Genes in the Biotechnologically Important Acidihalobacter Genus.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {848410}, pmid = {35516430}, issn = {1664-302X}, abstract = {Acidihalobacter is a genus of acidophilic, gram-negative bacteria known for its ability to oxidize pyrite minerals in the presence of elevated chloride ions, a capability rare in other iron-sulfur oxidizing acidophiles. Previous research involving Acidihalobacter spp. has focused on their applicability in saline biomining operations and their genetic arsenal that allows them to cope with chloride, metal and oxidative stress. However, an understanding of the molecular adaptations that enable Acidihalobacter spp. to thrive under both acid and chloride stress is needed to provide a more comprehensive understanding of how this genus can thrive in such extreme biomining conditions. Currently, four genomes of the Acidihalobacter genus have been sequenced: Acidihalobacter prosperus DSM 5130[T], Acidihalobacter yilgarnensis DSM 105917[T], Acidihalobacter aeolianus DSM 14174[T], and Acidihalobacter ferrooxydans DSM 14175[T]. Phylogenetic analysis shows that the Acidihalobacter genus roots to the Chromatiales class consisting of mostly halophilic microorganisms. In this study, we aim to advance our knowledge of the genetic repertoire of the Acidihalobacter genus that has enabled it to cope with acidic stress. We provide evidence of gene gain events that are hypothesized to help the Acidihalobacter genus cope with acid stress. Potential acid tolerance mechanisms that were found in the Acidihalobacter genomes include multiple potassium transporters, chloride/proton antiporters, glutamate decarboxylase system, arginine decarboxylase system, urease system, slp genes, squalene synthesis, and hopanoid synthesis. Some of these genes are hypothesized to have entered the Acidihalobacter via vertical decent from an inferred non-acidophilic ancestor, however, horizontal gene transfer (HGT) from other acidophilic lineages is probably responsible for the introduction of many acid resistance genes.}, }
@article {pmid35512279, year = {2022}, author = {Huang, H and Feng, G and Wang, M and Liu, C and Wu, Y and Dong, L and Feng, L and Zheng, X and Chen, Y}, title = {Nitric Oxide: A Neglected Driver for the Conjugative Transfer of Antibiotic Resistance Genes among Wastewater Microbiota.}, journal = {Environmental science &amp; technology}, volume = {56}, number = {10}, pages = {6466-6478}, doi = {10.1021/acs.est.2c01889}, pmid = {35512279}, issn = {1520-5851}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; *Escherichia coli/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Microbiota ; Nitric Oxide ; Plasmids ; Wastewater ; }, abstract = {The dissemination of plasmid-borne antibiotic resistance genes (ARGs) in wastewater is becoming an urgent concern. Previous studies mainly focused on the effects of coexisting contaminants on plasmid conjugation, but ignored the potential contribution of some byproducts inevitably released from wastewater treatment processes. Herein, we demonstrate for the first time that nitric oxide (NO), an intermediate of the wastewater nitrogen cycle, can significantly boost the conjugative transfer of plasmid RP4 from Escherichia coli K12 to different recipients (E. coli HB101, Salmonella typhimurium, and wastewater microbiota). Phenotypic and genotypic tests confirmed that NO-induced promotion was not attributed to the SOS response, a well-recognized driver for horizontal gene transfer. Instead, NO exposure increased the outer membrane permeability of both the donor and recipient by inhibiting the expression of key genes involved in lipopolysaccharide biosynthesis (such as waaJ), thereby lowering the membrane barrier for conjugation. On the other hand, NO exposure not only resulted in the accumulation of intracellular tryptophan but also triggered the deficiency of intracellular methionine, both of which were validated to play key roles in regulating the global regulatory genes (korA, korB, and trbA) of plasmid RP4, activating its encoding transfer apparatus (represented by trfAp and trbBp). Overall, our findings highlighted the risks of NO in spreading ARGs among wastewater microbiota and updated the regulation mechanism of plasmid conjugation.}, }
@article {pmid35510788, year = {2022}, author = {White, H and Vos, M and Sheppard, SK and Pascoe, B and Raymond, B}, title = {Signatures of selection in core and accessory genomes indicate different ecological drivers of diversification among Bacillus cereus clades.}, journal = {Molecular ecology}, volume = {31}, number = {13}, pages = {3584-3597}, pmid = {35510788}, issn = {1365-294X}, support = {BB/M009122/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Bacillus cereus/genetics ; Gene Transfer, Horizontal/genetics ; *Genome, Bacterial/genetics ; Phenotype ; Phylogeny ; }, abstract = {Bacterial clades are often ecologically distinct, despite extensive horizontal gene transfer (HGT). How selection works on different parts of bacterial pan-genomes to drive and maintain the emergence of clades is unclear. Focusing on the three largest clades in the diverse and well-studied Bacillus cereus sensu lato group, we identified clade-specific core genes (present in all clade members) and then used clade-specific allelic diversity to identify genes under purifying and diversifying selection. Clade-specific accessory genes (present in a subset of strains within a clade) were characterized as being under selection using presence/absence in specific clades. Gene ontology analyses of genes under selection revealed that different gene functions were enriched in different clades. Furthermore, some gene functions were enriched only amongst clade-specific core or accessory genomes. Genes under purifying selection were often clade-specific, while genes under diversifying selection showed signs of frequent HGT. These patterns are consistent with different selection pressures acting on both the core and the accessory genomes of different clades and can lead to ecological divergence in both cases. Examining variation in allelic diversity allows us to uncover genes under clade-specific selection, allowing ready identification of strains and their ecological niche.}, }
@article {pmid35504157, year = {2022}, author = {Hegarty, B and Dai, Z and Raskin, L and Pinto, A and Wigginton, K and Duhaime, M}, title = {A snapshot of the global drinking water virome: Diversity and metabolic potential vary with residual disinfectant use.}, journal = {Water research}, volume = {218}, number = {}, pages = {118484}, doi = {10.1016/j.watres.2022.118484}, pmid = {35504157}, issn = {1879-2448}, mesh = {Bacteria/genetics ; Chlorine ; *Disinfectants/pharmacology ; *Drinking Water ; Metagenomics ; Virome ; *Viruses/genetics ; *Water Purification ; }, abstract = {Viruses are important drivers of microbial community ecology and evolution, influencing microbial mortality, metabolism, and horizontal gene transfer. However, the effects of viruses remain largely unknown in many environments, including in drinking water systems. Drinking water metagenomic studies have offered a whole community perspective of bacterial impacts on water quality, but have not yet considered the influences of viruses. In this study, we address this gap by mining viral DNA sequences from publicly available drinking water metagenomes from distribution systems in six countries around the world. These datasets provide a snapshot of the taxonomic diversity and metabolic potential of the global drinking water virome; and provide an opportunity to investigate the effects of geography, climate, and drinking water treatment practices on viral diversity. Both environmental conditions and differences in sample processing were found to influence the viral composition. Using free chlorine as the residual disinfectant was associated with clear differences in viral taxonomic diversity and metabolic potential, with significantly fewer viral populations and less even viral community structures than observed in distribution systems without residual disinfectant. Additionally, drinking water viruses carry antibiotic resistance genes (ARGs), as well as genes to survive oxidative stress and nitrogen limitation. Through this study, we have demonstrated that viral communities are diverse across drinking water systems and vary with the use of residual disinfectant. Our findings offer directions for future research to develop a more robust understanding of how virus-bacteria interactions in drinking water distribution systems affect water quality.}, }
@article {pmid35504055, year = {2022}, author = {Bottery, MJ}, title = {Ecological dynamics of plasmid transfer and persistence in microbial communities.}, journal = {Current opinion in microbiology}, volume = {68}, number = {}, pages = {102152}, pmid = {35504055}, issn = {1879-0364}, support = {221663/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacteria/genetics ; Conjugation, Genetic ; *Gene Transfer, Horizontal ; *Microbiota ; Plasmids/genetics ; }, abstract = {Plasmids are a major driver of horizontal gene transfer in prokaryotes, allowing the sharing of ecologically important accessory traits between distantly related bacterial taxa. Within microbial communities, interspecies transfer of conjugative plasmids can rapidly drive the generation genomic innovation and diversification. Recent studies are starting to shed light on how the microbial community context, that is, the bacterial diversity together with interspecies interactions that occur within a community, can alter the dynamics of conjugative plasmid transfer and persistence. Here, I summarise the latest research exploring how community ecology can both facilitate and impose barriers to the spread of conjugative plasmids within complex microbial communities. Ultimately, the fate of plasmids within communities is unlikely to be determined by any one individual host, rather it will depend on the interacting factors imposed by the community in which it is embedded.}, }
@article {pmid35503986, year = {2022}, author = {Hu, X and Waigi, MG and Yang, B and Gao, Y}, title = {Impact of Plastic Particles on the Horizontal Transfer of Antibiotic Resistance Genes to Bacterium: Dependent on Particle Sizes and Antibiotic Resistance Gene Vector Replication Capacities.}, journal = {Environmental science &amp; technology}, volume = {56}, number = {21}, pages = {14948-14959}, doi = {10.1021/acs.est.2c00745}, pmid = {35503986}, issn = {1520-5851}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Escherichia coli/genetics ; Genes, Bacterial ; Particle Size ; Plastics/pharmacology ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Plasmids/genetics ; Bacteria/genetics ; }, abstract = {Plastic particles impact the propagation of antibiotic resistance genes (ARGs) in environmental media, and their perturbation on the horizontal gene transfer (HGT) of ARGs is recognized as a critical influencing mechanism. However, studies concerning the influence and influencing mechanisms of plastic particles on the HGT of ARGs were limited, particularly for the effect of particle sizes and ARG vector-associated mechanisms. This study explored the impact of polystyrene (PS) particles with sizes of 75, 90, 100, 1000, and 10000 nm on the HGT (via transformation) of ARGs mediated by pUC19, pSTV29, and pBR322 plasmids into Escherichia coli cells. PS particles with sizes ≤100 nm impacted the transformation of ARGs, but large particles (1000 and 10000 nm) showed no obvious effects. Effects of PS particles on the transfer of three plasmids were vastly distinct. For pUC19 with high replication capacities, the transfer was monotonously promoted. However, for pSTV29 and pBR322 with low replication capacities, suppressing effects were observed. This was attributed to two competing mechanisms. The enhancing mechanism was that the direct interaction of PS particles with membrane lipids and the indirect effect associated with bacterial oxidative stress response induced pore formation on the cell membrane and increased membrane permeability, thus enhancing plasmid entrance. The inhibiting mechanism was that PS particles interfered with plasmid replication inside E. coli, thus decreasing the bacterial tranformation. This study deepened our understanding of the environmental dissemination of ARGs in plastic contamination.}, }
@article {pmid35503141, year = {2022}, author = {Kong, S and Pons, JC and Kubatko, L and Wicke, K}, title = {Classes of explicit phylogenetic networks and their biological and mathematical significance.}, journal = {Journal of mathematical biology}, volume = {84}, number = {6}, pages = {47}, pmid = {35503141}, issn = {1432-1416}, mesh = {Algorithms ; Biological Evolution ; *Gene Transfer, Horizontal ; *Hybridization, Genetic ; Models, Genetic ; Phylogeny ; }, abstract = {The evolutionary relationships among organisms have traditionally been represented using rooted phylogenetic trees. However, due to reticulate processes such as hybridization or lateral gene transfer, evolution cannot always be adequately represented by a phylogenetic tree, and rooted phylogenetic networks that describe such complex processes have been introduced as a generalization of rooted phylogenetic trees. In fact, estimating rooted phylogenetic networks from genomic sequence data and analyzing their structural properties is one of the most important tasks in contemporary phylogenetics. Over the last two decades, several subclasses of rooted phylogenetic networks (characterized by certain structural constraints) have been introduced in the literature, either to model specific biological phenomena or to enable tractable mathematical and computational analyses. In the present manuscript, we provide a thorough review of these network classes, as well as provide a biological interpretation of the structural constraints underlying these networks where possible. In addition, we discuss how imposing structural constraints on the network topology can be used to address the scalability and identifiability challenges faced in the estimation of phylogenetic networks from empirical data.}, }
@article {pmid35495730, year = {2022}, author = {Nagar, S and Talwar, C and Motelica-Heino, M and Richnow, HH and Shakarad, M and Lal, R and Negi, RK}, title = {Microbial Ecology of Sulfur Biogeochemical Cycling at a Mesothermal Hot Spring Atop Northern Himalayas, India.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {848010}, pmid = {35495730}, issn = {1664-302X}, abstract = {Sulfur related prokaryotes residing in hot spring present good opportunity for exploring the limitless possibilities of integral ecosystem processes. Metagenomic analysis further expands the phylogenetic breadth of these extraordinary sulfur (S) metabolizing microorganisms as well as their complex metabolic networks and syntrophic interactions in environmental biosystems. Through this study, we explored and expanded the microbial genetic repertoire with focus on S cycling genes through metagenomic analysis of S contaminated hot spring, located at the Northern Himalayas. The analysis revealed rich diversity of microbial consortia with established roles in S cycling such as Pseudomonas, Thioalkalivibrio, Desulfovibrio, and Desulfobulbaceae (Proteobacteria). The major gene families inferred to be abundant across microbial mat, sediment, and water were assigned to Proteobacteria as reflected from the reads per kilobase (RPKs) categorized into translation and ribosomal structure and biogenesis. An analysis of sequence similarity showed conserved pattern of both dsrAB genes (n = 178) retrieved from all metagenomes while other S disproportionation proteins were diverged due to different structural and chemical substrates. The diversity of S oxidizing bacteria (SOB) and sulfate reducing bacteria (SRB) with conserved (r)dsrAB suggests for it to be an important adaptation for microbial fitness at this site. Here, (i) the oxidative and reductive dsr evolutionary time-scale phylogeny proved that the earliest (but not the first) dsrAB proteins belong to anaerobic Thiobacillus with other (rdsr) oxidizers, also we confirm that (ii) SRBs belongs to δ-Proteobacteria occurring independent lateral gene transfer (LGT) of dsr genes to different and few novel lineages. Further, the structural prediction of unassigned DsrAB proteins confirmed their relatedness with species of Desulfovibrio (TM score = 0.86, 0.98, 0.96) and Archaeoglobus fulgidus (TM score = 0.97, 0.98). We proposed that the genetic repertoire might provide the basis of studying time-scale evolution and horizontal gene transfer of these genes in biogeochemical S cycling.}, }
@article {pmid35491833, year = {2022}, author = {Kirchberger, PC and Martinez, ZA and Ochman, H}, title = {Organizing the Global Diversity of Microviruses.}, journal = {mBio}, volume = {13}, number = {3}, pages = {e0058822}, pmid = {35491833}, issn = {2150-7511}, support = {R35 GM118038/GM/NIGMS NIH HHS/United States ; }, mesh = {*Bacteriophages/genetics ; DNA, Single-Stranded ; Genome, Viral ; Humans ; Metagenome ; *Microviridae/genetics ; Microvirus/genetics ; Phylogeny ; }, abstract = {Microviruses encompass an astonishing array of small, single-stranded DNA phages that, due to the surge in metagenomic surveys, are now known to be prevalent in most environments. Current taxonomy concedes the considerable diversity within this lineage to a single family (the Microviridae), which has rendered it difficult to adequately and accurately assess the amount of variation that actually exists within this group. We amassed and curated the largest collection of microviral genomes to date and, through a combination of protein-sharing networks and phylogenetic analysis, discovered at least three meaningful taxonomic levels between the current ranks of family and genus. When considering more than 13,000 microviral genomes from recognized lineages and as-yet-unclassified microviruses in metagenomic samples, microviral diversity is better understood by elevating microviruses to the level of an order that consists of three suborders and at least 19 putative families, each with their respective subfamilies. These revisions enable fine-scale assessment of microviral dynamics: for example, in the human gut, there are considerable differences in the abundances of microviral families both between urban and rural populations and in individuals over time. In addition, our analysis of genome contents and gene exchange shows that microviral families carry no recognizable accessory metabolic genes and rarely, if ever, engage in horizontal gene transfer across microviral families or with their bacterial hosts. These insights bring microviral taxonomy in line with current developments in the taxonomy of other phages and increase the understanding of microvirus biology. IMPORTANCE Microviruses are the most abundant single-stranded DNA phages on the planet and an important component of the human gut virome. And yet, productive research into their biology is hampered by the inadequacies of current taxonomic ordering: microviruses are lumped into a single family and treated as a monolithic group, thereby obscuring the extent of their diversity and resulting in little comparative research. Our investigations into the diversity of microviruses define numerous groups, most lacking any isolated representatives, and point toward high-value targets for future research. To expedite microvirus discovery and comparison, we developed a pipeline that enables the fast and facile sorting of novel microvirus genomes into well-defined taxonomic groups. These improvements provide new insights into the biology of microviruses and emphasize fundamental differences between these miniature phages and their large, double-stranded DNA phage competitors.}, }
@article {pmid35491831, year = {2022}, author = {Fang, GY and Chai, LJ and Zhong, XZ and Lu, ZM and Zhang, XJ and Wu, LH and Wang, ST and Shen, CH and Shi, JS and Xu, ZH}, title = {Comparative Genomics Unveils the Habitat Adaptation and Metabolic Profiles of Clostridium in an Artificial Ecosystem for Liquor Production.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0029722}, pmid = {35491831}, issn = {2379-5077}, mesh = {*Alcoholic Beverages/analysis ; Bacteria/genetics ; Clostridium/genetics ; Ethanol/metabolism ; *Microbiota/genetics ; Genomics ; Metabolome ; }, abstract = {Clostridium inhabiting pit mud (PM) is one of the important bacterial populations for synthesizing flavor compounds of Chinese strong-flavor baijiu. The long-term cereal fermentation with sorghum as the main raw material creates an environment rich in starch, ethanol, and organic acids (mainly lactic acid). However, the genetic factors underpinning Clostridium's adaptation to PM remain poorly understood. Here, we performed comparative genomic analysis between 30 pit mud-associated (PMA) and 100 non-pit mud-associated (NPMA) Clostridium strains. Comparison analysis of the enrichment of KEGG pathways between PMA and NPMA Clostridium strains showed two-component system, flagellar assembly, and bacterial chemotaxis pathways related to environmental adaptation were enriched in PMA strains. The number of genes encoding alcohol dehydrogenase and l-lactate dehydrogenase in PMA Clostridium strains was significantly higher than that in NPMA, which is helpful for them to adapt to the ethanol- and lactic acid-rich environment. The analysis of carbohydrate-active enzymes demonstrated that glycoside hydrolases (GHs) was the most abundant family in all Clostridium strains, and genes encoding GH4 and GH13, involved in starch and sucrose metabolism, were enriched in PMA Clostridium. Horizontal gene transfer analysis revealed that multiple genes encoding the enzymes involved in carbohydrate and amino acid metabolism were transferred from Bacillus to Clostridium in pit mud. Most of the PMA Clostridium strains had good potential for butyric acid synthesis from ethanol, lactic acid, and starch. Collectively, this study furthers our understanding of the habitat adaptation and metabolic potential of PMA Clostridium strains. IMPORTANCE Pit mud is a typical artificial ecosystem for Chinese liquor production. Clostridium inhabiting pit mud plays essential roles in the flavor formation of strong-flavor baijiu. The relative abundance of Clostridium increased with pit mud quality, further influencing the quality of baijiu. So far, the ecological adaptation of Clostridium to a pit mud-associated lifestyle is largely unknown. Here, comparative genomic analysis of pit mud-associated (PMA) and non-pit mud-associated (NPMA) Clostridium strains was performed. We found genes related to the metabolism of starch, ethanol, and lactic acid were enriched in PMA Clostridium strains, which facilitated their adaptation to the unique brewing environment. In addition, horizontal gene transfer contributed to the adaptation of Clostridium to pit mud. Our findings provide genetic insights on PMA Clostridium strains' ecological adaptation and metabolic characteristics.}, }
@article {pmid35491001, year = {2022}, author = {Yan, M and Zhu, C and Song, T and Li, B and Su, S and Li, H}, title = {Impact of different manure-derived dissolved organic matters on the fate of arsenic-antibiotic in co-contaminated paddy soils.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {306}, number = {}, pages = {119376}, doi = {10.1016/j.envpol.2022.119376}, pmid = {35491001}, issn = {1873-6424}, mesh = {Animals ; Anti-Bacterial Agents ; *Arsenic ; Bacteria ; Dissolved Organic Matter ; Genes, Bacterial ; *Manure ; Soil ; Soil Microbiology ; Swine ; }, abstract = {Manure application increases the transfer risk of antibiotic resistance to farmland. Especially, its impact remains unclear when it occurs in arsenic (As)-contaminated paddy soils, which is considered as a global environmental problem. In this work, we investigated the fate of antibiotic resistance genes (ARGs) in As-antibiotic co-contaminated paddy soils under the application of manure from different sources (pig manure, cow dung, and chicken manure). Differences in the aliphatic carbon and electron-donating capacities of these dissolved organic matters (DOM) regulated the transformation of iron and As by both biotic and abiotic processes. The regulation by pig manure was stronger than that by cow dung and chicken manure. DOM regulation increased the abundance of As-related functional genes (arsC, arrA, aioA, and arsM) in the soil and accelerated the transformation of As speciation, the highest proportion of As(III) being 45%-61%. Meanwhile, the continuous selection pressure provided by the highly toxic As(III) increased the risk of ARGs and mobile genetic elements (MGEs) via horizontal gene transfer. As-resistant bacteria, including Bacillus, Geobacter, and Desulfitobacterium, were finally considered as potential host bacteria for ARGs and MGEs. In summary, this study clarified the synergistic mechanism of As-antibiotic on the fate of ARGs in co-contaminated paddy soils, and provided practical guidance for the proper application of organic fertilizers.}, }
@article {pmid35490629, year = {2022}, author = {Lamberte, LE and van Schaik, W}, title = {Antibiotic resistance in the commensal human gut microbiota.}, journal = {Current opinion in microbiology}, volume = {68}, number = {}, pages = {102150}, doi = {10.1016/j.mib.2022.102150}, pmid = {35490629}, issn = {1879-0364}, support = {BB/S017941/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Bacterial/genetics ; *Gastrointestinal Microbiome/genetics ; Gene Transfer, Horizontal ; Humans ; Symbiosis ; }, abstract = {Antibiotic-resistant infections are a major threat to global public health and there is an urgent need to develop new drugs and interventions to treat and prevent infections caused by antibiotic-resistant bacteria. The human gut microbiota harbours both commensals and opportunistic pathogens which can acquire resistance to antibiotics through mutation and horizontal gene transfer. The powerful combination of modern high-throughput DNA sequencing and microbiological culture methods is providing novel insights into the mechanisms of antibiotic resistance among, up to recently poorly studied, commensal bacteria in the gut. Interventions to minimise the abundance of antibiotic-resistant commensals and opportunistic pathogens include faecal microbiota transplantation and the use of live biotherapeutics, but the efficacy of these treatments remains elusive.}, }
@article {pmid35490406, year = {2022}, author = {Harden, MM and Anderson, ME and Grossman, AD}, title = {A CRISPR interference screen reveals a role for cell wall teichoic acids in conjugation in Bacillus subtilis.}, journal = {Molecular microbiology}, volume = {117}, number = {6}, pages = {1366-1383}, pmid = {35490406}, issn = {1365-2958}, support = {R01 GM050895/GM/NIGMS NIH HHS/United States ; R35 GM122538/GM/NIGMS NIH HHS/United States ; T32 GM007287/GM/NIGMS NIH HHS/United States ; }, mesh = {*Bacillus subtilis/genetics ; Cell Wall ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; *Conjugation, Genetic ; Gene Transfer, Horizontal ; Teichoic Acids ; }, abstract = {Conjugative elements are widespread in bacteria and include plasmids and integrative and conjugative elements (ICEs). They transfer from donor to recipient cells via an element-encoded type IV secretion system. These elements interact with and utilize host functions for their lifecycles. We sought to identify essential host genes involved in the lifecycle of the integrative and conjugative element ICEBs1 of Bacillus subtilis. We constructed a library of strains for inducible knockdown of essential B. subtilis genes using CRISPR interference. Each strain expressed one guide RNA in ICEBs1. We induced partial interference of essential genes and identified those that caused an acute defect in acquisition of ICEBs1 by recipient cells. This screen revealed that reducing expression of genes needed for synthesis of cell wall teichoic acids caused a decrease in conjugation. Using three different ways to reduce their synthesis, we found that wall teichoic acids were necessary in both donors and recipients for efficient conjugative transfer of ICEBs1. Further, we found that depletion of wall teichoic acids caused cells involved in ICEBs1 conjugation to die, most likely from damage to the cell envelope. Our results indicate that wall teichoic acids help protect against envelope stress caused by active conjugation machines.}, }
@article {pmid35489476, year = {2022}, author = {Li, D and Gao, J and Dai, H and Wang, Z and Zhao, Y and Cui, Y}, title = {Higher spreading risk of antibacterial biocide and heavy metal resistance genes than antibiotic resistance genes in aerobic granular sludge.}, journal = {Environmental research}, volume = {212}, number = {Pt C}, pages = {113356}, doi = {10.1016/j.envres.2022.113356}, pmid = {35489476}, issn = {1096-0953}, mesh = {Anti-Bacterial Agents/pharmacology ; *Disinfectants ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; *Metals, Heavy ; Sewage ; }, abstract = {Metagenomic approach was applied to simultaneously reveal the antibiotic resistance genes (ARGs) and antibacterial biocide &amp; metal resistance genes (BMRGs), and the corresponding microbial hosts with high mobility during aerobic granular sludge (AGS) formation process. The results showed that the relative abundance of BMRGs was 88-123 times that of ARGs. AGS process was easier to enrich BMRGs, leading to a greater risk of drug resistance caused by BMRGs than that by ARGs. The enrichments of ARGs and BMRGs in AGS were closely related to several enhanced microbial metabolisms (i.e., cell motility, transposase and ATP-binding cassette transporters) and their corresponding regulatory genes. Several enhanced KEGG Orthologs (KO) functions, such as K01995, K01996, K01997 and K02002, might cause a positive impact on the spread of ARGs and BMRGs, and the main contributors were the largely enriched glycogens accumulating organisms. The first dominant ARGs (adeF) was carried by lots of microbial hosts, which might be enriched and propagated mainly through horizontal gene transfer. Candidatus Competibacter denitrificans simultaneously harbored ARG (cmx) and Cu related RGs (corR). Many enriched bacteria contained simultaneously multiple BMRGs (copR and corR) and mobile genetic elements (integrons and plasmids), granting them high mobility capabilities and contributing to the spread of BMRGs. This study might provide deeper understandings of the proliferation and mobility of ARGs and BMRGs, importantly, highlighted the status of BMRGs, which laid the foundation for the controlling widespread of resistance genes in AGS.}, }
@article {pmid35483672, year = {2022}, author = {Malmstrom, CM and Martin, MD and Gagnevin, L}, title = {Exploring the Emergence and Evolution of Plant Pathogenic Microbes Using Historical and Paleontological Sources.}, journal = {Annual review of phytopathology}, volume = {60}, number = {}, pages = {187-209}, doi = {10.1146/annurev-phyto-021021-041830}, pmid = {35483672}, issn = {1545-2107}, mesh = {Animals ; Archaea ; Bacteria ; *Fungi ; Humans ; *Microbiota ; Plants ; }, abstract = {Biotechnological advances now permit broad exploration of past microbial communities preserved in diverse substrates. Despite biomolecular degradation, high-throughput sequencing of preserved materials can yield invaluable genomic and metagenomic data from the past. This line of research has expanded from its initial human- and animal-centric foci to include plant-associated microbes (viruses, archaea, bacteria, fungi, and oomycetes), for which historical, archaeological, and paleontological data illuminate past epidemics and evolutionary history. Genetic mechanisms underlying the acquisition of microbial pathogenicity, including hybridization, polyploidization, and horizontal gene transfer, can now be reconstructed, as can gene-for-gene coevolution with plant hosts. Epidemiological parameters, such as geographic origin and range expansion, can also be assessed. Building on published case studies with individual phytomicrobial taxa, the stage is now set for broader, community-wide studies of preserved plant microbiomes to strengthen mechanistic understanding of microbial interactions and plant disease emergence.}, }
@article {pmid35483268, year = {2022}, author = {Wei, Z and Shen, W and Feng, K and Feng, Y and He, Z and Li, Y and Jiang, C and Liu, S and Zhu, YG and Deng, Y}, title = {Organic fertilizer potentiates the transfer of typical antibiotic resistance gene among special bacterial species.}, journal = {Journal of hazardous materials}, volume = {435}, number = {}, pages = {128985}, doi = {10.1016/j.jhazmat.2022.128985}, pmid = {35483268}, issn = {1873-3336}, mesh = {Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; *Fertilizers/analysis ; Genes, Bacterial ; *Manure/microbiology ; RNA, Ribosomal, 16S/genetics ; Soil ; Soil Microbiology ; }, abstract = {The propagation of antibiotic resistance genes (ARGs) in environments has evoked many attentions, however, how to identify their host pathogenic bacteria in situ remains a great challenge. Here we explored the bacterial host distribution and dissemination of a typical ARG, sul1 gene, in agricultural soils through the simultaneous detection of sul1 and its host 16S rRNA gene by emulsion paired isolation and concatenation PCR (epicPCR). Compared to chemical fertilizer, organic fertilizer (chicken manure) led to a higher prevalence of sul1 gene in the soil, and dominant bacterial hosts of sul1 gene were classified into Proteobacteria and Bacteroidetes phyla. Additionally, significant higher diversity of antibiotic resistance bacteria (ARB), higher rate of horizontal gene transfer (HGT), higher rate of mobile genetic elements (MGE) and higher proportion of pathogens were all observed in the treatment of organic fertilizer. This study alerts potential health risks of manure applications in agricultural soils.}, }
@article {pmid35477739, year = {2022}, author = {Dranenko, NO and Tutukina, MN and Gelfand, MS and Kondrashov, FA and Bochkareva, OO}, title = {Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {6868}, pmid = {35477739}, issn = {2045-2322}, support = {I 5127/FWF_/Austrian Science Fund FWF/Austria ; I5127-B/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Cattle ; Chromosomes/metabolism ; Escherichia coli/genetics/metabolism ; *Shigella ; *Ubiquitin/genetics ; Ubiquitin-Protein Ligases/metabolism ; }, abstract = {Until recently, Shigella and enteroinvasive Escherichia coli were thought to be primate-restricted pathogens. The base of their pathogenicity is the type 3 secretion system (T3SS) encoded by the pINV virulence plasmid, which facilitates host cell invasion and subsequent proliferation. A large family of T3SS effectors, E3 ubiquitin-ligases encoded by the ipaH genes, have a key role in the Shigella pathogenicity through the modulation of cellular ubiquitination that degrades host proteins. However, recent genomic studies identified ipaH genes in the genomes of Escherichia marmotae, a potential marmot pathogen, and an E. coli extracted from fecal samples of bovine calves, suggesting that non-human hosts may also be infected by these strains, potentially pathogenic to humans. We performed a comparative genomic study of the functional repertoires in the ipaH gene family in Shigella and enteroinvasive Escherichia from human and predicted non-human hosts. We found that fewer than half of Shigella genomes had a complete set of ipaH genes, with frequent gene losses and duplications that were not consistent with the species tree and nomenclature. Non-human host IpaH proteins had a diverse set of substrate-binding domains and, in contrast to the Shigella proteins, two variants of the NEL C-terminal domain. Inconsistencies between strains phylogeny and composition of effectors indicate horizontal gene transfer between E. coli adapted to different hosts. These results provide a framework for understanding of ipaH-mediated host-pathogens interactions and suggest a need for a genomic study of fecal samples from diseased animals.}, }
@article {pmid35474424, year = {2022}, author = {Lu, J and Zhang, H and Pan, L and Guan, W and Lou, Y}, title = {Environmentally relevant concentrations of triclosan exposure promote the horizontal transfer of antibiotic resistance genes mediated by Edwardsiella piscicida.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {43}, pages = {64622-64632}, pmid = {35474424}, issn = {1614-7499}, support = {QTJ19019//Wenzhou Medical University/ ; 81772229//National Natural Science Foundation of China/ ; 82072310//National Natural Science Foundation of China/ ; 2018ZX10201001-009//National Major Science and Technology Projects of China/ ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Edwardsiella ; Gene Transfer, Horizontal ; Genes, Bacterial ; Plasmids ; Reactive Oxygen Species ; *Triclosan/pharmacology ; }, abstract = {Aquaculture pathogen and antibiotic resistance genes (ARGs) co-occur in the aquatic environment. Accumulated evidence suggests that aquaculture pathogens can facilitate the horizontal transfer of plasmid-mediated ARGs. However, the role of Edwardsiella piscicida (E. piscicida) in ARG dissemination is still not fully understood. In addition, the potential impact of triclosan (TCS) on the spread of ARGs mediated by E. piscicida is still unknown, so a mating model system was established to investigate the transfer process of ARGs. The results showed that E. piscicida disseminated ARGs on RP4 by horizontal gene transfer (HGT). Furthermore, TCS exposure promoted this process. The conjugative transfer frequencies were enhanced approximately 1.2-1.4-fold by TCS at concentrations from 2 to 20 μg/L, when compared with the control. TCS promoted the HGT of ARGs by stimulating reactive oxygen species (ROS) production, increasing cell membrane permeability, and altering expressions of conjugative transfer-associated genes. Together, the results suggested that aquaculture pathogens spread ARGs and that the emerging contaminant TCS enhanced the transfer of ARGs between bacteria.}, }
@article {pmid35472311, year = {2022}, author = {Naumann, C and Heisters, M and Brandt, W and Janitza, P and Alfs, C and Tang, N and Toto Nienguesso, A and Ziegler, J and Imre, R and Mechtler, K and Dagdas, Y and Hoehenwarter, W and Sawers, G and Quint, M and Abel, S}, title = {Bacterial-type ferroxidase tunes iron-dependent phosphate sensing during Arabidopsis root development.}, journal = {Current biology : CB}, volume = {32}, number = {10}, pages = {2189-2205.e6}, pmid = {35472311}, issn = {1879-0445}, mesh = {*Arabidopsis/metabolism ; *Arabidopsis Proteins/metabolism ; Bacteria/metabolism ; Ceruloplasmin/genetics/metabolism ; Gene Expression Regulation, Plant ; Iron/metabolism ; Phosphates/metabolism ; Plant Roots ; }, abstract = {Access to inorganic phosphate (Pi), a principal intermediate of energy and nucleotide metabolism, profoundly affects cellular activities and plant performance. In most soils, antagonistic Pi-metal interactions restrict Pi bioavailability, which guides local root development to maximize Pi interception. Growing root tips scout the essential but immobile mineral nutrient; however, the mechanisms monitoring external Pi status are unknown. Here, we show that Arabidopsis LOW PHOSPHATE ROOT 1 (LPR1), one key determinant of Fe-dependent Pi sensing in root meristems, encodes a novel ferroxidase of high substrate specificity and affinity (apparent KM ∼ 2 μM Fe[2+]). LPR1 typifies an ancient, Fe-oxidizing multicopper protein family that evolved early upon bacterial land colonization. The ancestor of streptophyte algae and embryophytes (land plants) acquired LPR1-type ferroxidase from soil bacteria via horizontal gene transfer, a hypothesis supported by phylogenomics, homology modeling, and biochemistry. Our molecular and kinetic data on LPR1 regulation indicate that Pi-dependent Fe substrate availability determines LPR1 activity and function. Guided by the metabolic lifestyle of extant sister bacterial genera, we propose that Arabidopsis LPR1 monitors subtle concentration differentials of external Fe availability as a Pi-dependent cue to adjust root meristem maintenance via Fe redox signaling and cell wall modification. We further hypothesize that the acquisition of bacterial LPR1-type ferroxidase by embryophyte progenitors facilitated the evolution of local Pi sensing and acquisition during plant terrestrialization.}, }
@article {pmid35471580, year = {2022}, author = {Dowson, AJ and Lloyd, AJ and Cuming, AC and Roper, DI and Frigerio, L and Dowson, CG}, title = {Plant peptidoglycan precursor biosynthesis: Conservation between moss chloroplasts and Gram-negative bacteria.}, journal = {Plant physiology}, volume = {190}, number = {1}, pages = {165-179}, pmid = {35471580}, issn = {1532-2548}, support = {MR/N002679/1/MRC_/Medical Research Council/United Kingdom ; MR/S014934/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Bacteria/metabolism ; *Cell Wall/metabolism ; Chloroplasts/metabolism ; Gram-Negative Bacteria/metabolism ; Ligases/metabolism ; Lysine/metabolism ; *Peptidoglycan/chemistry/genetics/metabolism ; Uridine Diphosphate/metabolism ; }, abstract = {Accumulating evidence suggests that peptidoglycan, consistent with a bacterial cell wall, is synthesized around the chloroplasts of many photosynthetic eukaryotes, from glaucophyte algae to early-diverging land plants including pteridophyte ferns, but the biosynthetic pathway has not been demonstrated. Here, we employed mass spectrometry and enzymology in a two-fold approach to characterize the synthesis of peptidoglycan in chloroplasts of the moss Physcomitrium (Physcomitrella) patens. To drive the accumulation of peptidoglycan pathway intermediates, P. patens was cultured with the antibiotics fosfomycin, D-cycloserine, and carbenicillin, which inhibit key peptidoglycan pathway proteins in bacteria. Mass spectrometry of the trichloroacetic acid-extracted moss metabolome revealed elevated levels of five of the predicted intermediates from uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) through the uridine diphosphate N-acetylmuramic acid (UDP-MurNAc)-D,L-diaminopimelate (DAP)-pentapeptide. Most Gram-negative bacteria, including cyanobacteria, incorporate meso-diaminopimelic acid (D,L-DAP) into the third residue of the stem peptide of peptidoglycan, as opposed to L-lysine, typical of most Gram-positive bacteria. To establish the specificity of D,L-DAP incorporation into the P. patens precursors, we analyzed the recombinant protein UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase (MurE) from both P. patens and the cyanobacterium Anabaena sp. (Nostoc sp. strain PCC 7120). Both ligases incorporated D,L-DAP in almost complete preference to L-Lys, consistent with the mass spectrophotometric data, with catalytic efficiencies similar to previously documented Gram-negative bacterial MurE ligases. We discuss how these data accord with the conservation of active site residues common to DL-DAP-incorporating bacterial MurE ligases and of the probability of a horizontal gene transfer event within the plant peptidoglycan pathway.}, }
@article {pmid35470617, year = {2022}, author = {Wang, C and Liu, Z and Tang, B and Yang, H and Sun, D}, title = {[Prevention and control of antimicrobial resistance using CRISPR-Cas system: a review].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {38}, number = {4}, pages = {1432-1445}, doi = {10.13345/j.cjb.210348}, pmid = {35470617}, issn = {1872-2075}, mesh = {Anti-Bacterial Agents ; *Bacteriophages/genetics ; *CRISPR-Cas Systems ; Drug Resistance, Bacterial/genetics ; Plasmids/genetics ; }, abstract = {Bacterial multi-drug resistance (MDR) is a global challenge in the fields of medicine and health, agriculture and fishery, ecology and environment. The cross-region spread of antibiotic resistance genes (ARGs) among different species is one of the main cause of bacterial MDR. However, there is no effective strategies for addressing the intensifying bacterial MDR. The CRISPR-Cas system, consisting of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR associated proteins, can targetedly degrade exogenous nucleic acids, thus exhibiting high application potential in preventing and controlling bacterial MDR caused by ARGs. This review briefly introduced the working mechanism of CRISPR-Cas systems, followed by discussing recent advances in reducing ARGs by CRISPR-Cas systems delivered through mediators (e.g. plasmids, bacteriophages and nanoparticle). Moreover, the trends of this research field were envisioned, providing a new perspective on preventing and controlling MDR.}, }
@article {pmid35470043, year = {2022}, author = {Brown, DW and Kim, HS and McGovern, AE and Probyn, CE and Proctor, RH}, title = {Genus-wide analysis of Fusarium polyketide synthases reveals broad chemical potential.}, journal = {Fungal genetics and biology : FG &amp; B}, volume = {160}, number = {}, pages = {103696}, doi = {10.1016/j.fgb.2022.103696}, pmid = {35470043}, issn = {1096-0937}, mesh = {Animals ; *Biological Products/metabolism ; *Fusarium ; Phylogeny ; Polyketide Synthases/genetics/metabolism ; *Polyketides/metabolism ; }, abstract = {The genus Fusarium includes pathogens of global concern to animal and plant health. Natural products (NPs) synthesized by Fusarium can contribute to pathogenesis or competitiveness of the fungus in the environment and to animal diseases, including cancer and neural tube defects. Polyketide synthases (PKSs) are a family of large, multi-domain enzymes that are required for synthesis of most fungal NPs. To gain insight into the NP potential of Fusarium, we retrieved 2974 PKS gene sequences from the genomes of 206 Fusarium species. Phylogenetic analysis resolved these PKSs, along with 118 previously described PKSs from other fungi, into 123 clades. Based on results from previous studies, we propose that PKSs in the same clade generally synthesize the same polyketide, which is structurally distinct from polyketides synthesized by PKSs in other clades. We predict that the 123 clades potentially produce 113 structurally distinct families of polyketide-derived NPs because some NPs (e.g., zearalenone) require two PKSs for their synthesis. Collectively, the clades include PKSs required for synthesis of six NPs whose production has not previously been reported in Fusarium, including two NPs with significant pharmaceutical interest: chaetoviridin and a statin. Our results highlight the NP diversity of Fusarium and the potential of the genus to produce metabolites with medical and other applications.}, }
@article {pmid35468809, year = {2022}, author = {He, L and Huang, X and Zhang, G and Yuan, L and Shen, E and Zhang, L and Zhang, XH and Zhang, T and Tao, L and Ju, F}, title = {Distinctive signatures of pathogenic and antibiotic resistant potentials in the hadal microbiome.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {19}, pmid = {35468809}, issn = {2524-6372}, support = {2018YFE0110500//national key research and development program of china/ ; 51908467//national natural science foundation of china/ ; 31970129//national natural science foundation of china/ ; 31800128//national natural science foundation of china/ ; LR20C010001//natural science foundation of zhejiang province/ ; }, abstract = {BACKGROUND: Hadal zone of the deep-sea trenches accommodates microbial life under extreme energy limitations and environmental conditions, such as low temperature, high pressure, and low organic matter down to 11,000 m below sea level. However, microbial pathogenicity, resistance, and adaptation therein remain unknown. Here we used culture-independent metagenomic approaches to explore the virulence and antibiotic resistance in the hadal microbiota of the Mariana Trench.<br><br>RESULTS: The results indicate that the 10,898&#xa0;m Challenger Deep bottom sediment harbored prosperous microbiota with contrasting signatures of virulence factors and antibiotic resistance, compared with the neighboring but shallower 6038&#xa0;m steep wall site and the more nearshore 5856&#xa0;m Pacific basin site. Virulence genes including several famous large translocating virulence genes (e.g., botulinum neurotoxins, tetanus neurotoxin, and Clostridium difficile toxins) were uniquely detected in the trench bottom. However, the shallower and more nearshore site sediment had a higher abundance and richer diversity of known antibiotic resistance genes (ARGs), especially for those clinically relevant ones (e.g., fosX, sul1, and TEM-family extended-spectrum beta-lactamases), revealing resistance selection under anthropogenic stresses. Further analysis of mobilome (i.e., the collection of mobile genetic elements, MGEs) suggests horizontal gene transfer mediated by phage and integrase as the major mechanism for the evolution of Mariana Trench sediment bacteria. Notably, contig-level co-occurring and taxonomic analysis shows emerging evidence for substantial co-selection of virulence genes and ARGs in taxonomically diverse bacteria in the hadal sediment, especially for the Challenger Deep bottom where mobilized ARGs and virulence genes are favorably enriched in largely unexplored bacteria.<br><br>CONCLUSIONS: This study reports the landscape of virulence factors, antibiotic resistome, and mobilome in the sediment and seawater microbiota residing hadal environment of the deepest ocean bottom on earth. Our work unravels the contrasting and unique features of virulence genes, ARGs, and MGEs in the Mariana Trench bottom, providing new insights into the eco-environmental and biological processes underlying microbial pathogenicity, resistance, and adaptative evolution in the hadal environment.}, }
@article {pmid35467500, year = {2022}, author = {Unni, R and Pintor, KL and Diepold, A and Unterweger, D}, title = {Presence and absence of type VI secretion systems in bacteria.}, journal = {Microbiology (Reading, England)}, volume = {168}, number = {4}, pages = {}, doi = {10.1099/mic.0.001151}, pmid = {35467500}, issn = {1465-2080}, mesh = {Bacteria/genetics ; Bacterial Proteins/genetics ; Gram-Negative Bacteria/genetics ; *Type VI Secretion Systems/genetics ; }, abstract = {The type VI secretion system (T6SS) is a molecular puncturing device that enables Gram-negative bacteria to kill competitors, manipulate host cells and take up nutrients. Who would want to miss such superpowers? Indeed, many studies show how widespread the secretion apparatus is among microbes. However, it is becoming evident that, on multiple taxonomic levels, from phyla to species and strains, some bacteria lack a T6SS. Here, we review who does and does not have a type VI secretion apparatus and speculate on the dynamic process of gaining and losing the secretion system to better understand its spread and distribution across the microbial world.}, }
@article {pmid35464980, year = {2022}, author = {Custer, GF and Bresciani, L and Dini-Andreote, F}, title = {Ecological and Evolutionary Implications of Microbial Dispersal.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {855859}, pmid = {35464980}, issn = {1664-302X}, abstract = {Dispersal is simply defined as the movement of species across space and time. Despite this terse definition, dispersal is an essential process with direct ecological and evolutionary implications that modulate community assembly and turnover. Seminal ecological studies have shown that environmental context (e.g., local edaphic properties, resident community), dispersal timing and frequency, and species traits, collectively account for patterns of species distribution resulting in either their persistence or unsuccessful establishment within local communities. Despite the key importance of this process, relatively little is known about how dispersal operates in microbiomes across divergent systems and community types. Here, we discuss parallels of macro- and micro-organismal ecology with a focus on idiosyncrasies that may lead to novel mechanisms by which dispersal affects the structure and function of microbiomes. Within the context of ecological implications, we revise the importance of short- and long-distance microbial dispersal through active and passive mechanisms, species traits, and community coalescence, and how these align with recent advances in metacommunity theory. Conversely, we enumerate how microbial dispersal can affect diversification rates of species by promoting gene influxes within local communities and/or shifting genes and allele frequencies via migration or de novo changes (e.g., horizontal gene transfer). Finally, we synthesize how observed microbial assemblages are the dynamic outcome of both successful and unsuccessful dispersal events of taxa and discuss these concepts in line with the literature, thus enabling a richer appreciation of this process in microbiome research.}, }
@article {pmid35462594, year = {2022}, author = {Bin Umair, M and Akusa, FN and Kashif, H and Seerat-E-Fatima,  and Butt, F and Azhar, M and Munir, I and Ahmed, M and Khalil, W and Sharyar, H and Rafique, S and Shahid, M and Afzal, S}, title = {Viruses as tools in gene therapy, vaccine development, and cancer treatment.}, journal = {Archives of virology}, volume = {167}, number = {6}, pages = {1387-1404}, pmid = {35462594}, issn = {1432-8798}, mesh = {Adenoviridae/genetics ; Genetic Therapy/methods ; Genetic Vectors/genetics ; *Herpesviridae/genetics ; Humans ; *Neoplasms/genetics/therapy ; Vaccine Development ; *Viral Vaccines ; }, abstract = {Using viruses to our advantage has been a huge leap for humanity. Their ability to mediate horizontal gene transfer has made them useful tools for gene therapy, vaccine development, and cancer treatment. Adenoviruses, adeno-associated viruses, retroviruses, lentiviruses, alphaviruses, and herpesviruses are a few of the most common candidates for use as therapeutic agents or efficient gene delivery systems. Efforts are being made to improve and perfect viral-vector-based therapies to overcome potential or reported drawbacks. Some preclinical trials of viral vector vaccines have yielded positive results, indicating their potential as prophylactic or therapeutic vaccine candidates. Utilization of the oncolytic activity of viruses is the future of cancer therapy, as patients will then be free from the harmful effects of chemo- or radiotherapy. This review discusses in vitro and in vivo studies showing the brilliant therapeutic potential of viruses.}, }
@article {pmid35460285, year = {2022}, author = {Bartha, L and Mandáková, T and Kovařík, A and Bulzu, PA and Rodde, N and Mahelka, V and Lysak, MA and Fustier, MA and Šafář, J and Cápal, P and Keresztes, L and Banciu, HL}, title = {Intact ribosomal DNA arrays of Potentilla origin detected in Erythronium nucleus suggest recent eudicot-to-monocot horizontal transfer.}, journal = {The New phytologist}, volume = {235}, number = {3}, pages = {1246-1259}, doi = {10.1111/nph.18171}, pmid = {35460285}, issn = {1469-8137}, mesh = {DNA, Ribosomal/genetics ; DNA, Ribosomal Spacer/genetics ; In Situ Hybridization, Fluorescence ; *Liliaceae ; Phylogeny ; *Potentilla/genetics ; }, abstract = {During our initial phylogenetic study of the monocot genus Erythronium (Liliaceae), we observed peculiar eudicot-type internal transcribed spacer (ITS) sequences in a dataset derived from genomic DNA of Erythronium dens-canis. This raised the possibility of horizontal transfer of a eudicot alien ribosomal DNA (rDNA) into the Erythronium genome. In this work we aimed to support this hypothesis by carrying out genomic, molecular, and cytogenetic analyses. Genome skimming coupled by PacBio HiFi sequencing of a bacterial artificial chromosome clone derived from flow-sorted nuclei was used to characterise the alien 45S rDNA. Integration of alien rDNA in the recipient genome was further proved by Southern blotting and fluorescence in situ hybridization using specific probes. Alien rDNA, nested among Potentilla species in phylogenetic analysis, likely entered the Erythronium lineage in the common ancestor of E. dens-canis and E. caucasicum. Transferred eudicot-type rDNA preserved its tandemly arrayed feature on a single chromosome and was found to be transcribed in the monocot host, albeit much less efficiently than the native counterpart. This study adds a new example to the rarely documented nuclear-to-nuclear jumps of DNA between eudicots and monocots while holding the scientific community continually in suspense about the mode of DNA transfer.}, }
@article {pmid35459792, year = {2022}, author = {Wilbanks, EG and Doré, H and Ashby, MH and Heiner, C and Roberts, RJ and Eisen, JA}, title = {Metagenomic methylation patterns resolve bacterial genomes of unusual size and structural complexity.}, journal = {The ISME journal}, volume = {16}, number = {8}, pages = {1921-1931}, pmid = {35459792}, issn = {1751-7370}, mesh = {Bacteria/genetics ; Genome, Bacterial ; *Metagenome ; *Metagenomics ; Methylation ; }, abstract = {The plasticity of bacterial and archaeal genomes makes examining their ecological and evolutionary dynamics both exciting and challenging. The same mechanisms that enable rapid genomic change and adaptation confound current approaches for recovering complete genomes from metagenomes. Here, we use strain-specific patterns of DNA methylation to resolve complex bacterial genomes from long-read metagenomic data of a marine microbial consortium, the "pink berries" of the Sippewissett Marsh (USA). Unique combinations of restriction-modification (RM) systems encoded by the bacteria produced distinctive methylation profiles that were used to accurately bin and classify metagenomic sequences. Using this approach, we finished the largest and most complex circularized bacterial genome ever recovered from a metagenome (7.9 Mb with >600 transposons), the finished genome of Thiohalocapsa sp. PB-PSB1 the dominant bacteria in the consortia. From genomes binned by methylation patterns, we identified instances of horizontal gene transfer between sulfur-cycling symbionts (Thiohalocapsa sp. PB-PSB1 and Desulfofustis sp. PB-SRB1), phage infection, and strain-level structural variation. We also linked the methylation patterns of each metagenome-assembled genome with encoded DNA methyltransferases and discovered new RM defense systems, including novel associations of RM systems with RNase toxins.}, }
@article {pmid35456156, year = {2022}, author = {Li, C and Wen, R and Mu, R and Chen, X and Ma, P and Gu, K and Huang, Z and Ju, Z and Lei, C and Tang, Y and Wang, H}, title = {Outer Membrane Vesicles of Avian PathogenicEscherichia coli Mediate the Horizontal Transmission of blaCTX-M-55.}, journal = {Pathogens (Basel, Switzerland)}, volume = {11}, number = {4}, pages = {}, pmid = {35456156}, issn = {2076-0817}, support = {U21A20257//National Natural Science Foundation of China/ ; CARS-40-K14//National System for Layer Production Technology/ ; 2020NZZJ001//Sichuan Science and Technology Program/ ; 2020SCUNL206//Fundamental Research Funds for the Central Universities/ ; }, abstract = {The CTX-M-55 type extended-spectrum β-lactamase (ESBL) producing Enterobacteriaceae is increasing in prevalence worldwide without the transmission mechanism being fully clarified, which threatens public and livestock health. Outer membrane vesicles (OMVs) have been shown to mediate the gene horizontal transmission in some species. However, whether blaCTX-M-55 can be transmitted horizontally through OMVs in avian pathogenic Escherichia coli (APEC) has not been reported yet. To test this hypothesis, an ESBL-producing APEC was isolated and whole-genome sequencing (WGS) was performed to analyze the location of blaCTX-M-55. Ultracentrifugation and size exclusion chromatography was used to isolate and purify OMVs, and the transfer experiment of blaCTX-M-55 via OMVs was performed finally. Our results showed that the blaCTX-M-55 was located on an IncI2 plasmid. The number and diameter of OMVs secreted by ESBL-producing APEC treated with different antibiotics were significantly varied. The transfer experiment showed that the OMVs could mediate the horizontal transfer of blaCTX-M-55, and the frequency of gene transfer ranged from 10[-5] to 10[-6] CFU/mL with the highest frequency observed in the Enrofloxacin treatment group. These findings contribute to a better understanding of the antibiotics in promoting and disseminating resistance in the poultry industry and support the restrictions on the use of antibiotics in the poultry industry.}, }
@article {pmid35453263, year = {2022}, author = {Vassallo, A and Kett, S and Purchase, D and Marvasi, M}, title = {The Bacterial Urban Resistome: Recent Advances.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {4}, pages = {}, pmid = {35453263}, issn = {2079-6382}, abstract = {Cities that are densely populated are reservoirs of antibiotic resistant genes (ARGs). The overall presence of all resistance genes in a specific environment is defined as a resistome. Spatial proximity of surfaces and different hygienic conditions leads to the transfer of antibiotic resistant bacteria (ARB) within urban environments. Built environments, public transportation, green spaces, and citizens' behaviors all support persistence and transfer of antimicrobial resistances (AMR). Various unique aspects of urban settings that promote spread and resilience of ARGs/ARB are discussed: (i) the role of hospitals and recreational parks as reservoirs; (ii) private and public transportation as carriers of ARGs/ARB; (iii) the role of built environments as a hub for horizontal gene transfer even though they support lower microbial biodiversity than outdoor environments; (iv) the need to employ ecological and evolutionary concepts, such as modeling the fate of a specific ARG/ARB, to gain enhanced health risk assessments. Our understanding and our ability to control the rise of AMR in an urban setting is linked to our knowledge of the network connecting urban reservoirs and the environment.}, }
@article {pmid35453238, year = {2022}, author = {Andrés-Lasheras, S and Jelinski, M and Zaheer, R and McAllister, TA}, title = {Bovine Respiratory Disease: Conventional to Culture-Independent Approaches to Studying Antimicrobial Resistance in North America.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {4}, pages = {}, pmid = {35453238}, issn = {2079-6382}, support = {ANH 30.17//Beef Cattle Research Council/ ; 001//Genomics Research and Development Initiative/ ; 001//University of Calgary One Health Consortium, Major Innovation Fund, Government of Alberta/ ; }, abstract = {Numerous antimicrobial resistance (AMR) surveillance studies have been conducted in North American feedlot cattle to investigate the major bacterial pathogens of the bovine respiratory disease (BRD) complex, specifically: Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mycoplasma bovis. While most bacterial isolates recovered from healthy cattle are susceptible to a repertoire of antimicrobials, multidrug resistance is common in isolates recovered from cattle suffering from BRD. Integrative and conjugative elements (ICE) have gained increasing notoriety in BRD-Pasteurellaceae as they appear to play a key role in the concentration and dissemination of antimicrobial resistant genes. Likewise, low macrolide susceptibility has been described in feedlot isolates of M. bovis. Horizontal gene transfer has also been implicated in the spread of AMR within mycoplasmas, and in-vitro experiments have shown that exposure to antimicrobials can generate high levels of resistance in mycoplasmas via a single conjugative event. Consequently, antimicrobial use (AMU) could be accelerating AMR horizontal transfer within all members of the bacterial BRD complex. While metagenomics has been applied to the study of AMR in the microbiota of the respiratory tract, the potential role of the respiratory tract microbiome as an AMR reservoir remains uncertain. Current and prospective molecular tools to survey and characterize AMR need to be adapted as point-of-care technologies to enhance prudent AMU in the beef industry.}, }
@article {pmid35447310, year = {2022}, author = {Neffe, L and Abendroth, L and Bautsch, W and Häussler, S and Tomasch, J}, title = {High plasmidome diversity of extended-spectrum beta-lactam-resistant Escherichia coli isolates collected during one year in one community hospital.}, journal = {Genomics}, volume = {114}, number = {3}, pages = {110368}, doi = {10.1016/j.ygeno.2022.110368}, pmid = {35447310}, issn = {1089-8646}, mesh = {Humans ; *Escherichia coli/genetics ; beta-Lactams ; *Escherichia coli Infections ; Hospitals, Community ; beta-Lactamases/genetics ; Anti-Bacterial Agents/pharmacology ; Plasmids/genetics ; }, abstract = {Plasmid-encoded antibiotic resistance encompasses many classes of currently used antibiotics. In globally distributed Escherichia coli lineages plasmids, which spread via horizontal gene transfer, are responsible for the dissemination of genes encoding extended-spectrum β-lactamases (ESBL). In this study, we combined 2nd and 3rd generation sequencing techniques to reconstruct the plasmidome of overall 97 clinical ESBL-E. coli isolates. Our results highlight the enormous plasmid diversity in respect to size, replicon-type and genetic content. Furthermore, we emphasize the diverse plasmid distribution patterns among the clinical isolates and the high intra- and extracellular mobility potential of resistance conferring genes. While the majority of resistance conferring genes were located on large plasmids of known replicon type, small cryptic plasmids seem to be underestimated resistance gene vectors. Our results contribute to a better understanding of the dissemination of resistance-conferring genes through horizontal gene transfer as well as clonal spread.}, }
@article {pmid35441582, year = {2022}, author = {Oruganti, RK and Katam, K and Show, PL and Gadhamshetty, V and Upadhyayula, VKK and Bhattacharyya, D}, title = {A comprehensive review on the use of algal-bacterial systems for wastewater treatment with emphasis on nutrient and micropollutant removal.}, journal = {Bioengineered}, volume = {13}, number = {4}, pages = {10412-10453}, pmid = {35441582}, issn = {2165-5987}, mesh = {Bacteria/genetics/metabolism ; Biomass ; *Microalgae/metabolism ; Nutrients ; Waste Disposal, Fluid/methods ; Wastewater/chemistry ; *Water Purification ; }, abstract = {The scarcity of water resources and environmental pollution have highlighted the need for sustainable wastewater treatment. Existing conventional treatment systems are energy-intensive and not always able to meet stringent disposal standards. Recently, algal-bacterial systems have emerged as environmentally friendly sustainable processes for wastewater treatment and resource recovery. The algal-bacterial systems work on the principle of the symbiotic relationship between algae and bacteria. This paper comprehensively discusses the most recent studies on algal-bacterial systems for wastewater treatment, factors affecting the treatment, and aspects of resource recovery from the biomass. The algal-bacterial interaction includes cell-to-cell communication, substrate exchange, and horizontal gene transfer. The quorum sensing (QS) molecules and their effects on algal-bacterial interactions are briefly discussed. The effect of the factors such as pH, temperature, C/N/P ratio, light intensity, and external aeration on the algal-bacterial systems have been discussed. An overview of the modeling aspects of algal-bacterial systems has been provided. The algal-bacterial systems have the potential for removing micropollutants because of the diverse possible interactions between algae-bacteria. The removal mechanisms of micropollutants - sorption, biodegradation, and photodegradation, have been reviewed. The harvesting methods and resource recovery aspects have been presented. The major challenges associated with algal-bacterial systems for real scale implementation and future perspectives have been discussed. Integrating wastewater treatment with the algal biorefinery concept reduces the overall waste component in a wastewater treatment system by converting the biomass into a useful product, resulting in a sustainable system that contributes to the circular bioeconomy.}, }
@article {pmid35437346, year = {2022}, author = {Kaewnirat, K and Chuaychob, S and Chukamnerd, A and Pomwised, R and Surachat, K and Phoo, MTP and Phaothong, C and Sakunrang, C and Jeenkeawpiam, K and Hortiwakul, T and Charernmak, B and Chusri, S}, title = {In vitro Synergistic Activities of Fosfomycin in Combination with Other Antimicrobial Agents Against Carbapenem-Resistant Escherichia coli Harboring bla NDM-1 on the IncN2 Plasmid and a Study of the Genomic Characteristics of These Pathogens.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {1777-1791}, pmid = {35437346}, issn = {1178-6973}, abstract = {PURPOSE: The spread of New Delhi metallo-β-lactamase (NDM) encoded by the bla NDM gene has been a global health crisis for many years. Most of bla NDM-harboring bacteria commonly carry various antimicrobial resistance (AMR) genes on their chromosomes or plasmids, leading to limited treatment options. Thus, we aimed to evaluate the synergistic effects of fosfomycin in combination with other antimicrobial agents against bla NDM-harboring carbapenem-resistant Escherichia coli (CREC) and to characterize the whole-genome and plasmid sequences of these pathogens.<br><br>METHODS: Thirty-eight CREC isolates were collected from patients in the Medicine Ward, Songklanagarind Hospital, Thailand. The activity of fosfomycin in combination with other antimicrobial agents against CREC isolates harboring bla NDM on the plasmid was evaluated using the checkerboard method. In this method, the serial dilutions of two antibiotics were mixed with the cultured CREC, the mixtures were incubated, and FICI was calculated to interpret the synergistic activity of the combination. The whole-genome and particular plasmids of these pathogens were sequenced using next-generation sequencing. Sequence analysis, especially on antimicrobial resistance (AMR) genes, mobile-genetic elements (MGEs), and virulence genes was performed using many bioinformatics tools.<br><br>RESULTS: Of the E. coli 38 isolates, only 3 isolates contained the bla NDM-1 gene, which is located on the IncN2 plasmid. The combinations of fosfomycin with aminoglycosides, colistin, tigecycline, sitafloxacin, and ciprofloxacin were synergies against bla NDM-1-harboring CREC isolates. Genomic analysis revealed that these isolates harbored many &#x3b2;-lactam resistance genes and other AMR genes that may confer resistance to aminoglycoside, fluoroquinolone, rifampicin, trimethoprim, sulfonamide, tetracycline, and macrolide. Also, various MGEs, especially the bla NDM-1-bearing IncN2 plasmid, were present in these isolates.<br><br>CONCLUSION: Our study demonstrated some synergistic effects of antimicrobial combination against CREC isolates harboring bla NDM-1 on the IncN2 plasmid. Also, our data on the whole-genome and plasmid sequences might be beneficial in the control of the spread of bla NDM-1-harboring CREC isolates. The linkages between bla NDM-1-carrying plasmid, patient information, and time of collection will be elucidated to track the horizontal gene transfer in the future.}, }
@article {pmid35437096, year = {2022}, author = {Hua, Y and Wang, J and Huang, M and Huang, Y and Zhang, R and Bu, F and Yang, B and Chen, J and Lin, X and Hu, X and Zheng, L and Wang, Q}, title = {Outer membrane vesicles-transmitted virulence genes mediate the emergence of new antimicrobial-resistant hypervirulent Klebsiella pneumoniae.}, journal = {Emerging microbes &amp; infections}, volume = {11}, number = {1}, pages = {1281-1292}, pmid = {35437096}, issn = {2222-1751}, mesh = {Anti-Bacterial Agents ; Humans ; *Klebsiella Infections/microbiology ; *Klebsiella pneumoniae ; Virulence/genetics ; Virulence Factors/genetics ; }, abstract = {Hypervirulent Klebsiella pneumoniae (hvKp) is a notorious clinical pathogen that is more likely to cause severe primary and metastatic abscesses. The dissemination of antimicrobial-resistant hvKp isolates has been reported worldwide, posing a great challenge and severe clinical threat. However, the mechanisms of antimicrobial-resistant hvKp isolates prevalent worldwide are not well precise. Outer membrane vesicles (OMVs) secreted from gram-negative bacteria are an important vehicle for delivering effector molecules inter- and intra-species. To explore whether OMVs as the vector of virulence genes horizontal transfer among Klebsiella pneumoniae and to explain the potential mechanism for the development of antimicrobial-resistant hvKp isolates, we isolated OMVs from hvKp and classical Klebsiella pneumoniae (cKp) by sequential differential centrifugation, respectively. Then, the characteristics and contents of hvKp-OMVs and cKp-OMVs were analyzed. These hvKp-OMVs contain virulence genes, which could be transferred from hvKp horizontally to extended-spectrum beta lactamase (ESBL)-producing cKp, leading to the production of antimicrobial-resistant hypervirulent transformants. Further experiments confirmed the transformants exhibited antimicrobial resistance and hypervirulent phenotypes in vitro and in vivo. In short, this work demonstrated that hvKp-OMVs facilitated virulence genes transfer, allowing an increase in the virulence level of ESBL-producing cKp and providing a new mechanism for the emergence of antimicrobial-resistant hvKp isolates.}, }
@article {pmid35437001, year = {2022}, author = {Liu, Y and Wang, S and Li, L and Yang, T and Dong, S and Wei, T and Wu, S and Liu, Y and Gong, Y and Feng, X and Ma, J and Chang, G and Huang, J and Yang, Y and Wang, H and Liu, M and Xu, Y and Liang, H and Yu, J and Cai, Y and Zhang, Z and Fan, Y and Mu, W and Sahu, SK and Liu, S and Lang, X and Yang, L and Li, N and Habib, S and Yang, Y and Lindstrom, AJ and Liang, P and Goffinet, B and Zaman, S and Wegrzyn, JL and Li, D and Liu, J and Cui, J and Sonnenschein, EC and Wang, X and Ruan, J and Xue, JY and Shao, ZQ and Song, C and Fan, G and Li, Z and Zhang, L and Liu, J and Liu, ZJ and Jiao, Y and Wang, XQ and Wu, H and Wang, E and Lisby, M and Yang, H and Wang, J and Liu, X and Xu, X and Li, N and Soltis, PS and Van de Peer, Y and Soltis, DE and Gong, X and Liu, H and Zhang, S}, title = {The Cycas genome and the early evolution of seed plants.}, journal = {Nature plants}, volume = {8}, number = {4}, pages = {389-401}, pmid = {35437001}, issn = {2055-0278}, mesh = {Cycadopsida/genetics ; *Cycas/genetics ; Genes, Plant ; Ginkgo biloba/genetics ; Phylogeny ; Seeds/genetics ; }, abstract = {Cycads represent one of the most ancient lineages of living seed plants. Identifying genomic features uniquely shared by cycads and other extant seed plants, but not non-seed-producing plants, may shed light on the origin of key innovations, as well as the early diversification of seed plants. Here, we report the 10.5-Gb reference genome of Cycas panzhihuaensis, complemented by the transcriptomes of 339 cycad species. Nuclear and plastid phylogenomic analyses strongly suggest that cycads and Ginkgo form a clade sister to all other living gymnosperms, in contrast to mitochondrial data, which place cycads alone in this position. We found evidence for an ancient whole-genome duplication in the common ancestor of extant gymnosperms. The Cycas genome contains four homologues of the fitD gene family that were likely acquired via horizontal gene transfer from fungi, and these genes confer herbivore resistance in cycads. The male-specific region of the Y chromosome of C. panzhihuaensis contains a MADS-box transcription factor expressed exclusively in male cones that is similar to a system reported in Ginkgo, suggesting that a sex determination mechanism controlled by MADS-box genes may have originated in the common ancestor of cycads and Ginkgo. The C. panzhihuaensis genome provides an important new resource of broad utility for biologists.}, }
@article {pmid35434837, year = {2022}, author = {Kishida, K and Bosserman, RE and Harb, L and Khara, P and Song, L and Hu, B and Zeng, L and Christie, PJ}, title = {Contributions of F-specific subunits to the F plasmid-encoded type IV secretion system and F pilus.}, journal = {Molecular microbiology}, volume = {117}, number = {5}, pages = {1275-1290}, pmid = {35434837}, issn = {1365-2958}, support = {R21 AI142378/AI/NIAID NIH HHS/United States ; R35 GM138301/GM/NIGMS NIH HHS/United States ; R21 AI156846/AI/NIAID NIH HHS/United States ; R35 GM131892/GM/NIGMS NIH HHS/United States ; R01 GM048746/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/metabolism ; Conjugation, Genetic ; Escherichia coli/genetics ; *Escherichia coli Proteins/metabolism ; *F Factor ; Fimbriae, Bacterial/genetics/metabolism ; Plasmids/genetics ; Type IV Secretion Systems/genetics/metabolism ; }, abstract = {F plasmids circulate widely among the Enterobacteriaceae through encoded type IV secretion systems (T4SSF s). Assembly of T4SSF s and associated F pili requires 10 VirB/VirD4-like Tra subunits and eight or more F-specific subunits. Recently, we presented evidence using in situ cryoelectron tomography (cryoET) that T4SSF s undergo structural transitions when activated for pilus production, and that assembled pili are deposited onto alternative basal platforms at the cell surface. Here, we deleted eight conserved F-specific genes from the MOBF12C plasmid pED208 and quantitated effects on plasmid transfer, pilus production by fluorescence microscopy, and elaboration of T4SSF structures by in situ cryoET. Mutant phenotypes supported the assignment of F-specific subunits into three functional Classes: (i) TraF, TraH, and TraW are required for all T4SSF -associated activities, (ii) TraU, TraN, and TrbC are nonessential but contribute significantly to distinct T4SSF functions, and (iii) TrbB is essential for F pilus production but not for plasmid transfer. Equivalent mutations in a phylogenetically distantly related MOB12A F plasmid conferred similar phenotypes and generally supported these Class assignments. We present a new structure-driven model in which F-specific subunits contribute to distinct steps of T4SSF assembly or activation to regulate DNA transfer and F pilus dynamics and deposition onto alternative platforms.}, }
@article {pmid35433121, year = {2022}, author = {Li, Q and Zhou, Y and Lu, R and Zheng, P and Wang, Y}, title = {Phylogeny, distribution and potential metabolism of candidate bacterial phylum KSB1.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13241}, pmid = {35433121}, issn = {2167-8359}, mesh = {Phylogeny ; Oxidation-Reduction ; *Bacteria/genetics ; *Metagenome/genetics ; Hydrocarbons/metabolism ; }, abstract = {Candidate phylum KSB1 is composed of uncultured bacteria and has been reported across various environments. However, the phylogeny and metabolic potential of KSB1 have not been studied comprehensively. In this study, phylogenomic analysis of KSB1 genomes from public databases and eleven metagenome-assembled genomes (MAGs) from marine and hydrothermal sediments revealed that those genomes were clustered into four clades. Isolation source and relative abundance of KSB1 genomes showed that clade I was particularly abundant in bioreactor sludge. Genes related to dissimilatory reduction of nitrate to ammonia (DNRA), the last step of denitrification converting nitrous oxide to nitrogen and assimilatory sulfur reduction were observed in the expanded genomes of clade I, which may due to horizontal gene transfer that frequently occurred in bioreactor. Annotation and metabolic reconstruction of clades II and IV showed flagellum assembly and chemotaxis genes in the genomes, which may indicate that exploration and sensing for nutrients and chemical gradients are critical for the two clades in deep-sea and hydrothermal sediment. Metabolic potentials of fatty acids and short-chain hydrocarbons utilization were predicted in clades I and IV of KSB1. Collectively, phylogenomic and metabolic analyses of KSB1 clades provide insight into their anaerobic heterotrophic lifestyle and differentiation in potential ecological roles.}, }
@article {pmid35432284, year = {2022}, author = {Algarni, S and Ricke, SC and Foley, SL and Han, J}, title = {The Dynamics of the Antimicrobial Resistance Mobilome of Salmonella enterica and Related Enteric Bacteria.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {859854}, pmid = {35432284}, issn = {1664-302X}, abstract = {The foodborne pathogen Salmonella enterica is considered a global public health risk. Salmonella enterica isolates can develop resistance to several antimicrobial drugs due to the rapid spread of antimicrobial resistance (AMR) genes, thus increasing the impact on hospitalization and treatment costs, as well as the healthcare system. Mobile genetic elements (MGEs) play key roles in the dissemination of AMR genes in S. enterica isolates. Multiple phenotypic and molecular techniques have been utilized to better understand the biology and epidemiology of plasmids including DNA sequence analyses, whole genome sequencing (WGS), incompatibility typing, and conjugation studies of plasmids from S. enterica and related species. Focusing on the dynamics of AMR genes is critical for identification and verification of emerging multidrug resistance. The aim of this review is to highlight the updated knowledge of AMR genes in the mobilome of Salmonella and related enteric bacteria. The mobilome is a term defined as all MGEs, including plasmids, transposons, insertion sequences (ISs), gene cassettes, integrons, and resistance islands, that contribute to the potential spread of genes in an organism, including S. enterica isolates and related species, which are the focus of this review.}, }
@article {pmid35432273, year = {2022}, author = {de Block, T and González, N and Abdellati, S and Laumen, JGE and Van Dijck, C and De Baetselier, I and Van den Bossche, D and Manoharan-Basil, SS and Kenyon, C}, title = {Successful Intra- but Not Inter-species Recombination of msr(D) in Neisseria subflava.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {855482}, pmid = {35432273}, issn = {1664-302X}, abstract = {Resistance acquisition via natural transformation is a common process in the Neisseria genus. Transformation has played an important role in the emergence of resistance to many antimicrobials in Neisseria gonorrhoeae and Neisseria meningitidis. In a previous study, we found that currently circulating isolates of Neisseria subflava had acquired an msr(D) gene that has been found to result in macrolide resistance in other bacteria but never found in Neisseria species before. To determine if this resistance mechanism is transferable among Neisseria species, we assessed if we could transform the msr(D) gene into other commensal and pathogenic Neisseria under low dose azithromycin pressure. Intraspecies recombination in commensal N. subflava was confirmed with PCR and resulted in high-level macrolide resistance. Whole-genome sequencing of these transformed strains identified the complete uptake of the msr(D) integration fragment. Sequence analysis showed that a large fragment of DNA (5 and 12 kb) was transferred through a single horizontal gene transfer event. Furthermore, uptake of the msr(D) gene had no apparent fitness cost. Interspecies transformation of msr(D) from N. subflava to N. gonorrhoeae was, however, not successful.}, }
@article {pmid35432262, year = {2022}, author = {Werner, KA and Schneider, D and Poehlein, A and Diederich, N and Feyen, L and Axtmann, K and Hübner, T and Brüggemann, N and Prost, K and Daniel, R and Grohmann, E}, title = {Metagenomic Insights Into the Changes of Antibiotic Resistance and Pathogenicity Factor Pools Upon Thermophilic Composting of Human Excreta.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {826071}, pmid = {35432262}, issn = {1664-302X}, abstract = {In times of climate change, practicing a form of sustainable, climate-resilient and productive agriculture is of primordial importance. Compost could be one form of sustainable fertilizer, which is increasing humus, water holding capacity, and nutrient contents of soils. It could thereby strengthen agriculture toward the adverse effects of climate change, especially when additionally combined with biochar. To get access to sufficient amounts of suitable materials for composting, resources, which are currently treated as waste, such as human excreta, could be a promising option. However, the safety of the produced compost regarding human pathogens, pharmaceuticals (like antibiotics) and related resistance genes must be considered. In this context, we have investigated the effect of 140- and 154-days of thermophilic composting on the hygienization of human excreta and saw dust from dry toilets together with straw and green cuttings with and without addition of biochar. Compost samples were taken at the beginning and end of the composting process and metagenomic analysis was conducted to assess the fate of antibiotic resistance genes (ARGs) and pathogenicity factors of the microbial community over composting. Potential ARGs conferring resistance to major classes of antibiotics, such as beta-lactam antibiotics, vancomycin, the MLSB group, aminoglycosides, tetracyclines and quinolones were detected in all samples. However, relative abundance of ARGs decreased from the beginning to the end of composting. This trend was also found for genes encoding type III, type IV, and type VI secretion systems, that are involved in pathogenicity, protein effector transport into eukaryotic cells and horizontal gene transfer between bacteria, respectively. The results suggest that the occurrence of potentially pathogenic microorganisms harboring ARGs declines during thermophilic composting. Nevertheless, ARG levels did not decline below the detection limit of quantitative PCR (qPCR). Thresholds for the usage of compost regarding acceptable resistance gene levels are yet to be evaluated and defined.}, }
@article {pmid35430877, year = {2022}, author = {Xu, S and Wei, M and Li, G and Li, Z and Che, Y and Han, L and Jia, W and Li, F and Li, D and Li, Z}, title = {Comprehensive Analysis of the Nocardia cyriacigeorgica Complex Reveals Five Species-Level Clades with Different Evolutionary and Pathogenicity Characteristics.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0140621}, pmid = {35430877}, issn = {2379-5077}, mesh = {Humans ; Virulence/genetics ; Phylogeny ; *Nocardia/genetics ; Virulence Factors/genetics ; }, abstract = {Nocardia cyriacigeorgica is a common etiological agent of nocardiosis that has increasingly been implicated in serious pulmonary infections, especially in immunocompromised individuals. However, the evolution, diversity, and pathogenesis of N. cyriacigeorgica have remained unclear. Here, we performed a comparative genomic analysis using 91 N. cyriacigeorgica strains, 45 of which were newly sequenced in this study. Phylogenetic and average nucleotide identity (ANI) analyses revealed that N. cyriacigeorgica contained five species-level clades (8.6 to 14.6% interclade genetic divergence), namely, the N. cyriacigeorgica complex (NCC). Further pan-genome analysis revealed extensive differences among the five clades in nine functional categories, such as energy production, lipid metabolism, secondary metabolites, and signal transduction mechanisms. All 2,935 single-copy core genes undergoing purifying selection were highly conserved across NCC. However, clades D and E exhibited reduced selective constraints, compared to clades A to C. Horizontal gene transfer (HGT) and mobile genetic elements contributed to genomic plasticity, and clades A and B had experienced a higher level of HGT events than other clades. A total of 129 virulence factors were ubiquitous across NCC, such as the mce operon, hemolysin, and type VII secretion system (T7SS). However, different distributions of three toxin-coding genes and two new types of mce operons were detected, which might contribute to pathogenicity differences among the members of the NCC. Overall, our study provides comprehensive insights into the evolution, genetic diversity, and pathogenicity of NCC, facilitating the prevention of infections. IMPORTANCE Nocardia species are opportunistic bacterial pathogens that can affect all organ systems, primarily the skin, lungs, and brain. N. cyriacigeorgica is the most prevalent species within the genus, exhibits clinical significance, and can cause severe infections when disseminated throughout the body. However, the evolution, diversity, and pathogenicity of N. cyriacigeorgica remain unclear. Here, we have conducted a comparative genomic analysis of 91 N. cyriacigeorgica strains and revealed that N. cyriacigeorgica is not a single species but is composed of five closely related species. In addition, we discovered that these five species differ in many ways, involving selection pressure, horizontal gene transfer, functional capacity, pathogenicity, and antibiotic resistance. Overall, our work provides important clues in dissecting the evolution, genetic diversity, and pathogenicity of NCC, thereby advancing prevention measures against these infections.}, }
@article {pmid35429822, year = {2022}, author = {Wang, T and Li, J and Jing, H and Qin, S}, title = {Picocyanobacterial Synechococcus in marine ecosystem: Insights from genetic diversity, global distribution, and potential function.}, journal = {Marine environmental research}, volume = {177}, number = {}, pages = {105622}, doi = {10.1016/j.marenvres.2022.105622}, pmid = {35429822}, issn = {1879-0291}, mesh = {Ecosystem ; Genetic Variation ; Phylogeny ; Seawater/microbiology ; *Synechococcus/genetics ; }, abstract = {Marine Synechococcus, a main group of picocyanobacteria, has been ubiquitously observed across the global oceans. Synechococcus exhibits high phylogenetical and phenotypical diversity, and horizontal gene transfer makes its genetic evolution much more intricate. With the development of measurement technologies and analysis methods, the genomic information and niche partition of each Synechococcus lineage tend to be precisely described, but the global analysis is still lacking. Therefore, it is necessary to summarize existing studies and integrate published data to gain a comprehensive understanding of Synechococcus on genetic variation, niche division, and potential functions. In this review, the maximum likelihood trees are constructed based on existing sequence data, including both phylogenetic and pigmentary gene markers. The global distribution characteristics of abundance, lineages, and pigment types are concluded through pooled analysis of more than 700 samples obtained from approximately 50 scientific research cruises. The potential functions of Synechococcus are explored in element cycles and biological interactions. Future work on Synechococcus is suggested to focus on not only elucidating the nature of Synechococcus biodiversity but also demonstrating its interactions with the ecosystem by combining bioinformatics and macroscopic isotope-labeled environmental parameters.}, }
@article {pmid35426933, year = {2022}, author = {Briand, S and Dessimoz, C and El-Mabrouk, N and Nevers, Y}, title = {A Linear Time Solution to the Labeled Robinson-Foulds Distance Problem.}, journal = {Systematic biology}, volume = {71}, number = {6}, pages = {1391-1403}, pmid = {35426933}, issn = {1076-836X}, support = {183723/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {*Algorithms ; *Gene Transfer, Horizontal ; Phylogeny ; }, abstract = {A large variety of pairwise measures of similarity or dissimilarity have been developed for comparing phylogenetic trees, for example, species trees or gene trees. Due to its intuitive definition in terms of tree clades and bipartitions and its computational efficiency, the Robinson-Foulds (RF) distance is the most widely used for trees with unweighted edges and labels restricted to leaves (representing the genetic elements being compared). However, in the case of gene trees, an important information revealing the nature of the homologous relation between gene pairs (orthologs, paralogs, and xenologs) is the type of event associated to each internal node of the tree, typically speciations or duplications, but other types of events may also be considered, such as horizontal gene transfers. This labeling of internal nodes is usually inferred from a gene tree/species tree reconciliation method. Here, we address the problem of comparing such event-labeled trees. The problem differs from the classical problem of comparing uniformly labeled trees (all labels belonging to the same alphabet) that may be done using the Tree Edit Distance (TED) mainly due to the fact that, in our case, two different alphabets are considered for the leaves and internal nodes of the tree, and leaves are not affected by edit operations. We propose an extension of the RF distance to event-labeled trees, based on edit operations comparable to those considered for TED: node insertion, node deletion, and label substitution. We show that this new Labeled Robinson-Foulds (LRF) distance can be computed in linear time, in addition of maintaining other desirable properties: being a metric, reducing to RF for trees with no labels on internal nodes and maintaining an intuitive interpretation. The algorithm for computing the LRF distance enables novel analyses on event-label trees such as reconciled gene trees. Here, we use it to study the impact of taxon sampling on labeled gene tree inference and conclude that denser taxon sampling yields trees with better topology but worse labeling. [Algorithms; combinatorics; gene trees; phylogenetics; Robinson-Foulds; tree distance.].}, }
@article {pmid35425613, year = {2022}, author = {Borodovich, T and Shkoporov, AN and Ross, RP and Hill, C}, title = {Phage-mediated horizontal gene transfer and its implications for the human gut microbiome.}, journal = {Gastroenterology report}, volume = {10}, number = {}, pages = {goac012}, pmid = {35425613}, issn = {2052-0034}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {Horizontal gene transfer (HGT) in the microbiome has profound consequences for human health and disease. The spread of antibiotic resistance genes, virulence, and pathogenicity determinants predominantly occurs by way of HGT. Evidence exists of extensive horizontal transfer in the human gut microbiome. Phage transduction is a type of HGT event in which a bacteriophage transfers non-viral DNA from one bacterial host cell to another. The abundance of tailed bacteriophages in the human gut suggests that transduction could act as a significant mode of HGT in the gut microbiome. Here we review in detail the known mechanisms of phage-mediated HGT, namely specialized and generalized transduction, lateral transduction, gene-transfer agents, and molecular piracy, as well as methods used to detect phage-mediated HGT, and discuss its potential implications for the human gut microbiome.}, }
@article {pmid35422843, year = {2022}, author = {Peng, F and Engel, U and Aliyu, H and Rudat, J}, title = {Origin and Evolution of Enzymes with MIO Prosthetic Group: Microbial Coevolution After the Mass Extinction Event.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {851738}, pmid = {35422843}, issn = {1664-8021}, abstract = {After major mass extinction events, ancient plants and terrestrial vertebrates were faced with various challenges, especially ultraviolet (UV) light. These stresses probably resulted in changes in the biosynthetic pathways, which employed the MIO (3,5-dihydro-5-methylidene-4H-imidazole-4-one)-dependent enzymes (ammonia-lyase and aminomutase), leading to enhanced accumulation of metabolites for defense against UV radiation, pathogens, and microorganisms. Up to now, the origin and evolution of genes from this superfamily have not been extensively studied. In this report, we perform an analysis of the phylogenetic relations between the members of the aromatic amino acid MIO-dependent enzymes (AAM), which demonstrate that they most probably have a common evolutionary origin from ancient bacteria. In early soil environments, numerous bacterial species with tyrosine ammonia-lyase genes (TAL; EC 4.3.1.23) developed tyrosine aminomutase (TAM; EC 5.4.3.6) activity as a side reaction for competing with their neighbors in the community. These genes also evolved into other TAL-like enzymes, such as histidine ammonia-lyase (HAL, EC 4.3.1.3) and phenylalanine ammonia-lyase (PAL; EC 4.3.1.24), in different bacterial species for metabolite production and accumulation for adaptation to adverse terrestrial environmental conditions. On the other hand, the existence of phenylalanine aminomutase (PAM; EC 5.4.3.10) and phenylalanine/tyrosine ammonia-lyase (PTAL; EC 4.3.1.25) strongly indicates the horizontal gene transfer (HGT) between bacteria, fungi, and plants in symbiotic association after acquiring the PAL gene from their ancestor.}, }
@article {pmid35418239, year = {2022}, author = {Orazi, G and Collins, AJ and Whitaker, RJ}, title = {Prediction of Prophages and Their Host Ranges in Pathogenic and Commensal Neisseria Species.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0008322}, pmid = {35418239}, issn = {2379-5077}, mesh = {Humans ; Prophages/genetics ; Neisseria/genetics ; Host Specificity/genetics ; *Bacteriophages/genetics ; Genomics ; Neisseria gonorrhoeae ; *Neisseria meningitidis ; }, abstract = {The genus Neisseria includes two pathogenic species, N. gonorrhoeae and N. meningitidis, and numerous commensal species. Neisseria species frequently exchange DNA with one another, primarily via transformation and homologous recombination and via multiple types of mobile genetic elements (MGEs). Few Neisseria bacteriophages (phages) have been identified, and their impact on bacterial physiology is poorly understood. Furthermore, little is known about the range of species that Neisseria phages can infect. In this study, we used three virus prediction tools to scan 248 genomes of 21 different Neisseria species and identified 1,302 unique predicted prophages. Using comparative genomics, we found that many predictions are dissimilar from prophages and other MGEs previously described to infect Neisseria species. We also identified similar predicted prophages in genomes of different Neisseria species. Additionally, we examined CRISPR-Cas targeting of each Neisseria genome and predicted prophage. While CRISPR targeting of chromosomal DNA appears to be common among several Neisseria species, we found that 20% of the prophages we predicted are targeted significantly more than the rest of the bacterial genome in which they were identified (i.e., backbone). Furthermore, many predicted prophages are targeted by CRISPR spacers encoded by other species. We then used these results to infer additional host species of known Neisseria prophages and predictions that are highly targeted relative to the backbone. Together, our results suggest that we have identified novel Neisseria prophages, several of which may infect multiple Neisseria species. These findings have important implications for understanding horizontal gene transfer between members of this genus. IMPORTANCE Drug-resistant Neisseria gonorrhoeae is a major threat to human health. Commensal Neisseria species are thought to serve as reservoirs of antibiotic resistance and virulence genes for the pathogenic species N. gonorrhoeae and N. meningitidis. Therefore, it is important to understand both the diversity of mobile genetic elements (MGEs) that can mediate horizontal gene transfer within this genus and the breadth of species these MGEs can infect. In particular, few bacteriophages (phages) are known to infect Neisseria species. In this study, we identified a large number of candidate phages integrated in the genomes of commensal and pathogenic Neisseria species, many of which appear to be novel phages. Importantly, we discovered extensive interspecies targeting of predicted phages by Neisseria CRISPR-Cas systems, which may reflect their movement between different species. Uncovering the diversity and host range of phages is essential for understanding how they influence the evolution of their microbial hosts.}, }
@article {pmid35417559, year = {2022}, author = {Kambayashi, C and Kakehashi, R and Sato, Y and Mizuno, H and Tanabe, H and Rakotoarison, A and Künzel, S and Furuno, N and Ohshima, K and Kumazawa, Y and Nagy, ZT and Mori, A and Allison, A and Donnellan, SC and Ota, H and Hoso, M and Yanagida, T and Sato, H and Vences, M and Kurabayashi, A}, title = {Geography-Dependent Horizontal Gene Transfer from Vertebrate Predators to Their Prey.}, journal = {Molecular biology and evolution}, volume = {39}, number = {4}, pages = {}, pmid = {35417559}, issn = {1537-1719}, mesh = {Animals ; Cattle ; *Gene Transfer, Horizontal ; Geography ; *Parasites/genetics ; Phylogeny ; Predatory Behavior ; Retroelements ; Vertebrates/genetics ; }, abstract = {Horizontal transfer (HT) of genes between multicellular animals, once thought to be extremely rare, is being more commonly detected, but its global geographic trend and transfer mechanism have not been investigated. We discovered a unique HT pattern of Bovine-B (BovB) LINE retrotransposons in vertebrates, with a bizarre transfer direction from predators (snakes) to their prey (frogs). At least 54 instances of BovB HT were detected, which we estimate to have occurred across time between 85 and 1.3 Ma. Using comprehensive transcontinental sampling, our study demonstrates that BovB HT is highly prevalent in one geographical region, Madagascar, suggesting important regional differences in the occurrence of HTs. We discovered parasite vectors that may plausibly transmit BovB and found that the proportion of BovB-positive parasites is also high in Madagascar where BovB thus might be physically transported by parasites to diverse vertebrates, potentially including humans. Remarkably, in two frog lineages, BovB HT occurred after migration from a non-HT area (Africa) to the HT hotspot (Madagascar). These results provide a novel perspective on how the prevalence of parasites influences the occurrence of HT in a region, similar to pathogens and their vectors in some endemic diseases.}, }
@article {pmid35416714, year = {2022}, author = {Gu, X and Lu, X and Lin, S and Shi, X and Shen, Y and Lu, Q and Yang, Y and Yang, J and Cai, J and Fu, C and Lou, Y and Zheng, M}, title = {A Comparative Genomic Approach to Determine the Virulence Factors and Horizontal Gene Transfer Events of Clinical Acanthamoeba Isolates.}, journal = {Microbiology spectrum}, volume = {10}, number = {2}, pages = {e0002522}, pmid = {35416714}, issn = {2165-0497}, mesh = {*Acanthamoeba/genetics/microbiology ; *Gene Transfer, Horizontal ; Genomics ; Humans ; Phylogeny ; Pseudomonas ; Virulence Factors/genetics ; }, abstract = {Acanthamoeba species are among the most ubiquitous protists that are widespread in soil and water and act as both a replicative niche and vectors for dispersal. They are the most important human intracellular pathogens, causing Acanthamoeba keratitis (AK) and severely damaging the human cornea. The sympatric lifestyle within the host and amoeba-resisting microorganisms (ARMs) promotes horizontal gene transfer (HGT). However, the genomic diversity of only A. castellanii and A. polyphaga has been widely studied, and the pathogenic mechanisms remain unknown. Thus, we examined 7 clinically pathogenic strains by comparative genomic, phylogenetic, and rhizome gene mosaicism analyses to explore amoeba-symbiont interactions that possibly contribute to pathogenesis. Genetic characterization and phylogenetic analysis showed differences in functional characteristics between the "open" state of T3 and T4 isolates, which may contribute to the differences in virulence and pathogenicity. Through comparative genomic analysis, we identified potential genes related to virulence, such as metalloprotease, laminin-binding protein, and HSP, that were specific to the genus Acanthamoeba. Then, analysis of putative sequence trafficking between Acanthamoeba and Pandoraviruses or Acanthamoeba castellanii medusaviruses provided the best hits with viral genes; among bacteria, Pseudomonas had the most significant numbers. The most parsimonious evolutionary scenarios were between Acanthamoeba and endosymbionts; nevertheless, in most cases, the scenarios are more complex. In addition, the differences in exchanged genes were limited to the same family. In brief, this study provided extensive data to suggest the existence of HGT between Acanthamoeba and ARMs, explaining the occurrence of diseases and challenging Darwin's concept of eukaryotic evolution. IMPORTANCEAcanthamoeba has the ability to cause serious blinding keratitis. Although the prevalence of this phenomenon has increased in recent years, our knowledge of the underlying opportunistic pathogenic mechanism maybe remains incomplete. In this study, we highlighted the importance of Pseudomonas in the pathogenesis pathway using comprehensive a whole genomics approach of clinical isolates. The horizontal gene transfer events help to explain how endosymbionts contribute Acanthamoeba to act as an opportunistic pathogen. Our study opens up several potential avenues for future research on the differences in pathogenicity and interactions among clinical strains.}, }
@article {pmid35416680, year = {2022}, author = {Oladeinde, A and Abdo, Z and Zwirzitz, B and Woyda, R and Lakin, SM and Press, MO and Cox, NA and Thomas, JC and Looft, T and Rothrock, MJ and Zock, G and Plumblee Lawrence, J and Cudnik, D and Ritz, C and Aggrey, SE and Liachko, I and Grove, JR and Wiersma, C}, title = {Litter Commensal Bacteria Can Limit the Horizontal Gene Transfer of Antimicrobial Resistance to Salmonella in Chickens.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {9}, pages = {e0251721}, pmid = {35416680}, issn = {1098-5336}, support = {R44 AI150008/AI/NIAID NIH HHS/United States ; R44 AI162570/AI/NIAID NIH HHS/United States ; T32 GM132057/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Chickens/microbiology ; Drug Resistance, Bacterial/genetics ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; RNA, Ribosomal, 16S ; Salmonella/genetics ; *Salmonella enterica/genetics ; }, abstract = {Fostering a "balanced" gut microbiome through the administration of beneficial microbes that can competitively exclude pathogens has gained a lot of attention and use in human and animal medicine. However, little is known about how microbes affect the horizontal gene transfer of antimicrobial resistance (AMR). To shed more light on this question, we challenged neonatal broiler chicks raised on reused broiler chicken litter-a complex environment made up of decomposing pine shavings, feces, uric acid, feathers, and feed-with Salmonella enterica serovar Heidelberg (S. Heidelberg), a model pathogen. Neonatal chicks challenged with S. Heidelberg and raised on reused litter were more resistant to S. Heidelberg cecal colonization than chicks grown on fresh litter. Furthermore, chicks grown on reused litter were at a lower risk of colonization with S. Heidelberg strains that encoded AMR on IncI1 plasmids. We used 16S rRNA gene sequencing and shotgun metagenomics to show that the major difference between chicks grown on fresh litter and those grown on reused litter was the microbiome harbored in the litter and ceca. The microbiome of reused litter samples was more uniform and enriched in functional pathways related to the biosynthesis of organic and antimicrobial molecules than that in fresh litter samples. We found that Escherichia coli was the main reservoir of plasmids encoding AMR and that the IncI1 plasmid was maintained at a significantly lower copy per cell in reused litter compared to fresh litter. These findings support the notion that commensal bacteria play an integral role in the horizontal transfer of plasmids encoding AMR to pathogens like Salmonella. IMPORTANCE Antimicrobial resistance spread is a worldwide health challenge, stemming in large part from the ability of microorganisms to share their genetic material through horizontal gene transfer. To address this issue, many countries and international organizations have adopted a One Health approach to curtail the proliferation of antimicrobial-resistant bacteria. This includes the removal and reduction of antibiotics used in food animal production and the development of alternatives to antibiotics. However, there is still a significant knowledge gap in our understanding of how resistance spreads in the absence of antibiotic selection and the role commensal bacteria play in reducing antibiotic resistance transfer. In this study, we show that commensal bacteria play a key role in reducing the horizontal gene transfer of antibiotic resistance to Salmonella, provide the identity of the bacterial species that potentially perform this function in broiler chickens, and also postulate the mechanism involved.}, }
@article {pmid35414589, year = {2022}, author = {Shalon, N and Relman, DA and Yaffe, E}, title = {Precise genotyping of circular mobile elements from metagenomic data uncovers human-associated plasmids with recent common ancestors.}, journal = {Genome research}, volume = {32}, number = {5}, pages = {986-1003}, pmid = {35414589}, issn = {1549-5469}, support = {R01 AI147023/AI/NIAID NIH HHS/United States ; }, mesh = {Genotype ; Humans ; *Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; Plasmids/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Mobile genetic elements with circular genomes play a key role in the evolution of microbial communities. Their circular genomes correspond to circular walks in metagenome graphs, and yet, assemblies derived from natural microbial communities produce graphs riddled with spurious cycles, complicating the accurate reconstruction of circular genomes. We present DomCycle, an algorithm that reconstructs likely circular genomes based on the identification of so-called "dominant" graph cycles. In the implementation, we leverage paired reads to bridge assembly gaps and scrutinize cycles through a nucleotide-level analysis, making the approach robust to misassembly artifacts. We validated the approach using simulated and real sequencing data. Application of DomCycle to 32 publicly available DNA shotgun sequence data sets from diverse natural environments led to the reconstruction of hundreds of circular mobile genomes. Clustering revealed 20 highly prevalent and cryptic plasmids that have clonal population structures with recent common ancestors. This method facilitates the study of microbial communities that evolve through horizontal gene transfer.}, }
@article {pmid35413299, year = {2022}, author = {Li, W and Zhang, G}, title = {Detection and various environmental factors of antibiotic resistance gene horizontal transfer.}, journal = {Environmental research}, volume = {212}, number = {Pt B}, pages = {113267}, doi = {10.1016/j.envres.2022.113267}, pmid = {35413299}, issn = {1096-0953}, mesh = {*Angiotensin Receptor Antagonists/pharmacology ; *Angiotensin-Converting Enzyme Inhibitors/pharmacology ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Water ; }, abstract = {Bacterial antibiotic resistance in water environments is becoming increasingly severe, and new antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) have also attracted the attention of researchers. The horizontal transfer of ARGs in water environments is considered one of the main sources of bacterial resistance in the natural environment. Horizontal gene transfer (HGT) mainly includes conjugation, natural transformation, and transduction, and conjugation has been investigated most. Several studies have shown that there are a large number of environmental factors that might affect the horizontal transfer of ARGs in water environments, such as nanomaterials, various oxidants, and light; however, there is still a lack of systematic and comprehensive reviews on the detection and the effects of the influence factors of on ARG horizontal transfer. Therefore, this study introduced three HGT modes, analysed the advantages and disadvantages of current methods for monitoring HGT, and then summarized the influence and mechanism of various factors on ARG horizontal transfer, and the possible reasons for the different effects caused by similar factors were mainly critically discussed. Finally, existing research deficiencies and future research directions of ARG horizontal transfer in water environments were discussed.}, }
@article {pmid35412609, year = {2022}, author = {Gomez-Simmonds, A and Annavajhala, MK and Tang, N and Rozenberg, FD and Ahmad, M and Park, H and Lopatkin, AJ and Uhlemann, AC}, title = {Population structure of blaKPC-harbouring IncN plasmids at a New York City medical centre and evidence for multi-species horizontal transmission.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {77}, number = {7}, pages = {1873-1882}, pmid = {35412609}, issn = {1460-2091}, support = {R15 GM143694/GM/NIGMS NIH HHS/United States ; //National Institute of Allergy and Infectious Diseases/ ; R01 AI116939/AI/NIAID NIH HHS/United States ; K23 AI137316/AI/NIAID NIH HHS/United States ; 2040697//National Sciences Foundation/ ; }, mesh = {Bacterial Proteins/genetics ; Carbapenems/pharmacology ; *Gene Transfer, Horizontal ; Humans ; *Klebsiella Infections/epidemiology/microbiology ; Klebsiella pneumoniae ; Multilocus Sequence Typing ; New York City ; Phylogeny ; Plasmids/genetics ; beta-Lactamases/genetics/metabolism ; }, abstract = {BACKGROUND: Carbapenem-resistant Enterobacterales (CRE) are highly concerning MDR pathogens. Horizontal transfer of broad-host-range IncN plasmids may contribute to the dissemination of the Klebsiella pneumoniae carbapenemase (KPC), spreading carbapenem resistance among unrelated bacteria. However, the population structure and genetic diversity of IncN plasmids has not been fully elucidated.<br><br>OBJECTIVES: We reconstructed blaKPC-harbouring IncN plasmid genomes to characterize shared gene content, structural variability, and putative horizontal transfer within and across patients and diverse bacterial clones.<br><br>METHODS: We performed short- and long-read sequencing and hybrid assembly on 45 CRE isolates with blaKPC-harbouring IncN plasmids. Eight serial isolates from two patients were included to assess intra-patient plasmid dynamics. Comparative genomic analysis was performed to assess structural and sequence similarity across plasmids. Within IncN sublineages defined by plasmid MLST and kmer-based clustering, phylogenetic analysis was used to identify closely related plasmids.<br><br>RESULTS: Comparative analysis of IncN plasmid genomes revealed substantial heterogeneity including large rearrangements in serial patient plasmids and differences in structure and content across plasmid clusters. Within plasmid sublineages, core genome content and resistance gene regions were largely conserved. Closely related plasmids (&#x2264;1 SNP) were found in highly diverse isolates, including ten pST6 plasmids found in eight bacterial clones from three different species.<br><br>CONCLUSIONS: Genomic analysis of blaKPC-harbouring IncN plasmids revealed the presence of several distinct sublineages as well as substantial host diversity within plasmid clusters suggestive of frequent mobilization. This study reveals complex plasmid dynamics within a single plasmid family, highlighting the challenge of tracking plasmid-mediated transmission of blaKPC in clinical settings.}, }
@article {pmid35412593, year = {2023}, author = {Farzana, R and Jones, LS and Rahman, MA and Sands, K and van Tonder, AJ and Portal, E and Criollo, JM and Parkhill, J and Guest, MF and Watkins, WJ and Pervin, M and Boostrom, I and Hassan, B and Mathias, J and Kalam, MA and Walsh, TR}, title = {Genomic Insights Into the Mechanism of Carbapenem Resistance Dissemination in Enterobacterales From a Tertiary Public Heath Setting in South Asia.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {76}, number = {1}, pages = {119-133}, pmid = {35412593}, issn = {1537-6591}, mesh = {Humans ; *Enterobacteriaceae Infections/drug therapy/epidemiology/microbiology ; Asia, Southern ; *Carbapenem-Resistant Enterobacteriaceae/genetics ; beta-Lactamases/genetics ; Microbial Sensitivity Tests ; Bangladesh ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Carbapenems/pharmacology/therapeutic use ; Escherichia coli/genetics ; Klebsiella pneumoniae/genetics ; Genomics ; }, abstract = {SUMMARY: 10.6% patients were CRE positive. Only 27% patients were prescribed at least 1 antibiotic to which infecting pathogen was susceptible. Burn and ICU admission and antibiotics exposures facilitate CRE acquisition. Escherichia coli ST167 was the dominant CRE clone.<br><br>BACKGROUND: Given the high prevalence of multidrug resistance (MDR) across South Asian (SA) hospitals, we documented the epidemiology of carbapenem-resistant Enterobacterales (CRE) infections at Dhaka Medical College Hospital between October 2016 and September 2017.<br><br>METHODS: We enrolled patients and collected epidemiology and outcome data. All Enterobacterales were characterized phenotypically and by whole-genome sequencing. Risk assessment for the patients with CRE was performed compared with patients with carbapenem-susceptible Enterobacterales (CSE).<br><br>RESULTS: 10.6% of all 1831 patients with a clinical specimen collected had CRE. In-hospital 30-day mortality was significantly higher with CRE [50/180 (27.8%)] than CSE [42/312 (13.5%)] (P = .001); however, for bloodstream infections, this was nonsignificant. Of 643 Enterobacterales isolated, 210 were CRE; blaNDM was present in 180 isolates, blaOXA-232 in 26, blaOXA-181 in 24, and blaKPC-2 in 5. Despite this, ceftriaxone was the most commonly prescribed empirical antibiotic and only 27% of patients were prescribed at least 1 antibiotic to which their infecting pathogen was susceptible. Significant risk factors for CRE isolation included burns unit and intensive care unit admission, and prior exposure to levofloxacin, amikacin, clindamycin, and meropenem. Escherichia coli ST167 was the dominant CRE clone. Clustering suggested clonal transmission of Klebsiella pneumoniae ST15 and the MDR hypervirulent clone, ST23. The major trajectories involved in horizontal gene transfer were IncFII and IncX3, IS26, and Tn3.<br><br>CONCLUSIONS: This is the largest study from an SA public hospital combining outcome, microbiology, and genomics. The findings indicate the urgent implementation of targeted diagnostics, appropriate antibiotic use, and infection-control interventions in SA public institutions.}, }
@article {pmid35411114, year = {2022}, author = {Cubillos-Ruiz, A and Alcantar, MA and Donghia, NM and Cárdenas, P and Avila-Pacheco, J and Collins, JJ}, title = {An engineered live biotherapeutic for the prevention of antibiotic-induced dysbiosis.}, journal = {Nature biomedical engineering}, volume = {6}, number = {7}, pages = {910-921}, pmid = {35411114}, issn = {2157-846X}, mesh = {Ampicillin/pharmacology ; Animals ; Anti-Bacterial Agents/pharmacology ; *Clostridioides difficile ; *Dysbiosis/chemically induced/drug therapy/prevention &amp; control ; Mice ; beta-Lactamases/metabolism ; }, abstract = {Antibiotic-induced alterations in the gut microbiota are implicated in many metabolic and inflammatory diseases, increase the risk of secondary infections and contribute to the emergence of antimicrobial resistance. Here we report the design and in vivo performance of an engineered strain of Lactococcus lactis that altruistically degrades the widely used broad-spectrum antibiotics β-lactams (which disrupt commensal bacteria in the gut) through the secretion and extracellular assembly of a heterodimeric β-lactamase. The engineered β-lactamase-expression system does not confer β-lactam resistance to the producer cell, and is encoded via a genetically unlinked two-gene biosynthesis strategy that is not susceptible to dissemination by horizontal gene transfer. In a mouse model of parenteral ampicillin treatment, oral supplementation with the engineered live biotherapeutic minimized gut dysbiosis without affecting the ampicillin concentration in serum, precluded the enrichment of antimicrobial resistance genes in the gut microbiome and prevented the loss of colonization resistance against Clostridioides difficile. Engineered live biotherapeutics that safely degrade antibiotics in the gut may represent a suitable strategy for the prevention of dysbiosis and its associated pathologies.}, }
@article {pmid35410999, year = {2022}, author = {Bakkeren, E and Gül, E and Huisman, JS and Steiger, Y and Rocker, A and Hardt, WD and Diard, M}, title = {Impact of horizontal gene transfer on emergence and stability of cooperative virulence in Salmonella Typhimurium.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {1939}, pmid = {35410999}, issn = {2041-1723}, mesh = {Bacterial Proteins/metabolism ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Humans ; Inflammation ; *Salmonella typhimurium/metabolism ; Transcription Factors/metabolism ; Virulence/genetics ; }, abstract = {Intestinal inflammation fuels the transmission of Salmonella Typhimurium (S.Tm). However, a substantial fitness cost is associated with virulence expression. Mutations inactivating transcriptional virulence regulators generate attenuated variants profiting from inflammation without enduring virulence cost. Such variants interfere with the transmission of fully virulent clones. Horizontal transfer of functional regulatory genes (HGT) into attenuated variants could nevertheless favor virulence evolution. To address this hypothesis, we cloned hilD, coding for the master regulator of virulence, into a conjugative plasmid that is highly transferrable during intestinal colonization. The resulting mobile hilD allele allows virulence to emerge from avirulent populations, and to be restored in attenuated mutants competing against virulent clones within-host. However, mutations inactivating the mobile hilD allele quickly arise. The stability of virulence mediated by HGT is strongly limited by its cost, which depends on the hilD expression level, and by the timing of transmission. We conclude that robust evolution of costly virulence expression requires additional selective forces such as narrow population bottlenecks during transmission.}, }
@article {pmid35410010, year = {2022}, author = {Laghari, AA and Liu, L and Kalhoro, DH and Chen, H and Wang, C}, title = {Mechanism for Reducing the Horizontal Transfer Risk of the Airborne Antibiotic-Resistant Genes of Escherichia coli Species through Microwave or UV Irradiation.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {7}, pages = {}, pmid = {35410010}, issn = {1660-4601}, mesh = {Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; *Anti-Bacterial Agents/pharmacology ; *Escherichia coli/genetics/radiation effects ; Genes, Bacterial ; Microwaves ; }, abstract = {Antibiotic-resistant bacteria (ARBs) and antibiotic-resistant genes (ARGs) as new types of contaminants are discharged into the environment, increasing the risk of horizontal gene transfer (HGT). However, few researchers have examined the impacts of airborne ARB deactivation on HGT risk. The deactivation of airborne Escherichia coli 10667 (carrying sul genes) and the emission and removal of ARGs were mainly investigated in this study. Moreover, the potential mechanisms of HGT and transfer frequencies under microwave (MW) and ultraviolet (UV) irradiation were investigated using the nonresistant E. coli GMCC 13373 and E. coli DH5α with plasmid RP4 as the recipient and donor, respectively. E. coli CICC 10667 and E. coli DH5α with RP4 plasmid achieve log inactivation values as high as 5.5-log and 5.0-log, respectively, which were quite different from the antibiotic-sensitive strain E. coli CGMCC 13373 (3.4-log) subjected to MW irradiation. For UV disinfection, E. coli DH5α with the RP4 plasmid was reduced at 4.4-log, E. coli CGMCC 13373 was reduced at 2.3-log, and E. coli CICC 10667 was inactivated at 2.1-log. The removal rates of ARGs and HGT frequencies under MW irradiation were compared with those under UV irradiation. The ARGs removal efficiency (85.5%) obtained by MW was higher than that obtained by UV (48.2%). Consequently, the HGT frequency (0.008) of airborne ARGs released to the recipient (forward transfer) decreased and was lower than that under UV irradiation (0.014). Moreover, the plasmid RP4 was transferred from the donor to the surviving damaged E. coli 10667 as cell permeability (reverse transfer) was increased at a high HGT frequency (0.003) by MW, which was close to the value by UV (0.002). Additionally, sul1 and sul2 genes were confirmed to be more resistant to MW than the sul3 gene. These findings reveal the mechanism of HGT between damaged E. coli 10667 and surrounding environmental microbes. Microwave is a promising technology for disinfecting airborne microbes and preventing the spread of antibiotic resistance.}, }
@article {pmid35405387, year = {2022}, author = {Dong, N and Yang, X and Chan, EW and Zhang, R and Chen, S}, title = {Klebsiella species: Taxonomy, hypervirulence and multidrug resistance.}, journal = {EBioMedicine}, volume = {79}, number = {}, pages = {103998}, pmid = {35405387}, issn = {2352-3964}, mesh = {*Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; *Drug Resistance, Multiple, Bacterial ; *Klebsiella/classification/drug effects ; Klebsiella pneumoniae ; Plasmids ; }, abstract = {Members of the genus Klebsiella have rapidly evolved within the past decade, generating organisms that simultaneously exhibit both multidrug resistance and hypervirulence (MDR-hv) phenotypes; such organisms are associated with severe hospital- and community-acquired infections. Carbapenem-resistant infections with unknown optimal treatment regime were of particular concern among the MDR-hv Klebsiella strains. Recent studies have revealed the molecular features and the mobile resistance elements they harbour, allowing identification of genetic loci responsible for transmission, stable inheritance, and expression of mobile resistance or virulence-encoding elements that confer the new phenotypic characteristics of MDR-hv Klebsiella spp. Here, we provide a comprehensive review on the taxonomic position, species composition and different phylotypes of Klebsiella spp., describing the diversity and worldwide distribution of the MDR-hv clones, the genetic mutation and horizontal gene transfer events that drive the evolution of such clones, and the potential impact of MDR-hv infections on human health.}, }
@article {pmid35402511, year = {2022}, author = {Benler, S and Koonin, EV}, title = {Recruitment of Mobile Genetic Elements for Diverse Cellular Functions in Prokaryotes.}, journal = {Frontiers in molecular biosciences}, volume = {9}, number = {}, pages = {821197}, pmid = {35402511}, issn = {2296-889X}, abstract = {Prokaryotic genomes are replete with mobile genetic elements (MGE) that span a continuum of replication autonomy. On numerous occasions during microbial evolution, diverse MGE lose their autonomy altogether but, rather than being quickly purged from the host genome, assume a new function that benefits the host, rendering the immobilized MGE subject to purifying selection, and resulting in its vertical inheritance. This mini-review highlights the diversity of the repurposed (exapted) MGE as well as the plethora of cellular functions that they perform. The principal contribution of the exaptation of MGE and their components is to the prokaryotic functional systems involved in biological conflicts, and in particular, defense against viruses and other MGE. This evolutionary entanglement between MGE and defense systems appears to stem both from mechanistic similarities and from similar evolutionary predicaments whereby both MGEs and defense systems tend to incur fitness costs to the hosts and thereby evolve mechanisms for survival including horizontal mobility, causing host addiction, and exaptation for functions beneficial to the host. The examples discussed demonstrate that the identity of an MGE, overall mobility and relationship with the host cell (mutualistic, symbiotic, commensal, or parasitic) are all factors that affect exaptation.}, }
@article {pmid35402433, year = {2022}, author = {Roy, S and Chowdhury, G and Mukhopadhyay, AK and Dutta, S and Basu, S}, title = {Convergence of Biofilm Formation and Antibiotic Resistance in Acinetobacter baumannii Infection.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {793615}, pmid = {35402433}, issn = {2296-858X}, abstract = {Acinetobacter baumannii (A. baumannii) is a leading cause of nosocomial infections as this pathogen has certain attributes that facilitate the subversion of natural defenses of the human body. A. baumannii acquires antibiotic resistance determinants easily and can thrive on both biotic and abiotic surfaces. Different resistance mechanisms or determinants, both transmissible and non-transmissible, have aided in this victory over antibiotics. In addition, the propensity to form biofilms (communities of organism attached to a surface) allows the organism to persist in hospitals on various medical surfaces (cardiac valves, artificial joints, catheters, endotracheal tubes, and ventilators) and also evade antibiotics simply by shielding the bacteria and increasing its ability to acquire foreign genetic material through lateral gene transfer. The biofilm formation rate in A. baumannii is higher than in other species. Recent research has shown how A. baumannii biofilm-forming capacity exerts its effect on resistance phenotypes, development of resistome, and dissemination of resistance genes within biofilms by conjugation or transformation, thereby making biofilm a hotspot for genetic exchange. Various genes control the formation of A. baumannii biofilms and a beneficial relationship between biofilm formation and "antimicrobial resistance" (AMR) exists in the organism. This review discusses these various attributes of the organism that act independently or synergistically to cause hospital infections. Evolution of AMR in A. baumannii, resistance mechanisms including both transmissible (hydrolyzing enzymes) and non-transmissible (efflux pumps and chromosomal mutations) are presented. Intrinsic factors [biofilm-associated protein, outer membrane protein A, chaperon-usher pilus, iron uptake mechanism, poly-β-(1, 6)-N-acetyl glucosamine, BfmS/BfmR two-component system, PER-1, quorum sensing] involved in biofilm production, extrinsic factors (surface property, growth temperature, growth medium) associated with the process, the impact of biofilms on high antimicrobial tolerance and regulation of the process, gene transfer within the biofilm, are elaborated. The infections associated with colonization of A. baumannii on medical devices are discussed. Each important device-related infection is dealt with and both adult and pediatric studies are separately mentioned. Furthermore, the strategies of preventing A. baumannii biofilms with antibiotic combinations, quorum sensing quenchers, natural products, efflux pump inhibitors, antimicrobial peptides, nanoparticles, and phage therapy are enumerated.}, }
@article {pmid35395365, year = {2022}, author = {Hu, T and Zhen, L and Gu, J and Wang, X and Sun, W and Song, Z and Xie, J and An, L and Luo, B and Qian, X}, title = {Clarifying the beneficial effects of plant growth-promoting rhizobacteria for reducing abundances of antibiotic resistance genes during swine manure composting.}, journal = {Bioresource technology}, volume = {353}, number = {}, pages = {127117}, doi = {10.1016/j.biortech.2022.127117}, pmid = {35395365}, issn = {1873-2976}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Composting ; Drug Resistance, Microbial/genetics ; Genes, Bacterial/genetics ; Manure/microbiology ; Swine ; }, abstract = {This study investigated the effects on antibiotic resistance genes (ARGs) and the related mechanisms of different plant growth-promoting rhizobacteria (PGPR) inoculation strategies during composting: no inoculation (CK), inoculation in initial phase (T1), inoculation in cooling phase (T2), and inoculation in both initial and cooling phases (T3). After composting, the total relative abundances (RAs) of ARGs decreased by 0.26 and 0.03 logs under T3 and T2, respectively, but increased by 0.05 and 0.22 logs under T1 and CK. The abundances of eight ARGs were lowest under T3, including some high risk ARGs with clinical importance. Bioavailable Cu significantly affected the readily removed ARGs, and PGPR inoculation decreased the bioavailability of Cu. T3 reduced the abundances of potential pathogen hosts, inhibited horizontal gene transfer by reducing the RAs of mobile gene elements (0.48 logs), and downregulated the expression of genes related to ARG propagation, thereby decreasing the ecological risk of ARGs.}, }
@article {pmid35393155, year = {2022}, author = {Fronk, DC and Sachs, JL}, title = {Symbiotic organs: the nexus of host-microbe evolution.}, journal = {Trends in ecology &amp; evolution}, volume = {37}, number = {7}, pages = {599-610}, doi = {10.1016/j.tree.2022.02.014}, pmid = {35393155}, issn = {1872-8383}, mesh = {Animals ; *Plants/genetics ; *Symbiosis/genetics ; }, abstract = {Diverse plants and animals have evolved specialized structures to filter and house beneficial microbes. These symbiotic organs form crucial points of exchange between host and symbiont, are often shaped by both partners, and exhibit features that facilitate a suite of microbial services. While symbiotic organs exhibit varied function, morphology, and developmental plasticity, they share core features linked to the evolutionary maintenance of beneficial symbiosis. Moreover, these organs can have a significant role in altering the demographic forces that shape microbial genomes, driving population bottlenecks and horizontal gene transfer (HGT). To advance our understanding of these 'joint phenotypes' across varied systems, future research must consider the emergent forces that can shape symbiotic organs, including fitness feedbacks and conflicts between interacting genomes.}, }
@article {pmid35389819, year = {2022}, author = {Sharma, P and Singh, SP and Iqbal, HMN and Parra-Saldivar, R and Varjani, S and Tong, YW}, title = {Genetic modifications associated with sustainability aspects for sustainable developments.}, journal = {Bioengineered}, volume = {13}, number = {4}, pages = {9508-9520}, pmid = {35389819}, issn = {2165-5987}, mesh = {Agriculture ; Biotechnology ; *Crops, Agricultural/genetics ; Genetic Engineering ; Humans ; Plants, Genetically Modified/genetics ; *Sustainable Development ; }, abstract = {Sustainable development serves as the foundation for a range of international and national policymaking. Traditional breeding methods have been used to modify plant genomes and production. Genetic engineering is the practice of assisting agricultural systems in adapting to rapidly changing global growth by hastening the breeding of new varieties. On the other hand, the development of genetic engineering has enabled more precise control over the genomic alterations made in recent decades. Genetic changes from one species can now be introduced into a completely unrelated species, increasing agricultural output or making certain elements easier to manufacture. Harvest plants and soil microorganisms are just a few of the more well-known genetically modified creatures. Researchers assess current studies and illustrate the possibility of genetically modified organisms (GMOs) from the perspectives of various stakeholders. GMOs increase yields, reduce costs, and reduce agriculture's terrestrial and ecological footprint. Modern technology benefits innovators, farmers, and consumers alike. Agricultural biotechnology has numerous applications, each with its own set of potential consequences. This will be able to reach its full potential if more people have access to technology and excessive regulation is avoided. This paper covers the regulations for genetically modified crops (GMCs) as well as the economic implications. It also includes sections on biodiversity and environmental impact, as well as GMCs applications. This recounts biotechnological interventions for long-term sustainability in the field of GMCs, as well as the challenges and opportunities in this field of research.Abbreviations: GMCs-Genetically modified crops; GMOs- Genetically modified organisms; GE- Genetic engineering; Bt- Bacillus thuringiensisNIH- National Institutes of Health; FDA- Food and Drug Administration; HGT- Horizontal gene transfer; GM- Genetically modified; rDNA- Ribosomal deoxyribonucleic acid; USDA- United States Department of Agriculture; NIH- National Institutes of Health.}, }
@article {pmid35389232, year = {2022}, author = {Chen, Y and Wang, X and Liao, ME and Song, Y and Zhang, YY and Cui, J}, title = {Evolution and Genetic Diversity of the Retroviral Envelope in Anamniotes.}, journal = {Journal of virology}, volume = {96}, number = {8}, pages = {e0207221}, pmid = {35389232}, issn = {1098-5514}, mesh = {Animals ; *Endogenous Retroviruses/classification/genetics ; *Evolution, Molecular ; *Gene Products, env/genetics ; *Genetic Variation ; Phylogeny ; Vertebrates/genetics ; }, abstract = {Retroviruses are widely distributed in all vertebrates, as are their endogenous forms, endogenous retroviruses (ERV), which serve as "fossil" evidence to trace the ancient origins and history of virus-host interactions over millions of years. The retroviral envelope (Env) plays a significant role in host range determination, but major information on their genetic diversification and evolution in anamniotes is lacking. Here, by incorporating multiple-round in silico similarity search and phylogenomic analysis, more than 30,000 copies of ERV lineages with gamma-type Env (GTE), covalently associated Env, were discovered by searching against all fish and amphibian genomes and transcriptomic assemblies, but no beta-type Env (BTE), noncovalently associated Env, was found. Furthermore, a nine-type classification system of anamniote GTE was proposed by combining phylogenetic and domain/motif analyses. The elastic genomic organization and overall phylogenetic incongruence between anamniotic Env and its neighboring polymerase (Pol) implied that early retroviral diversification in anamniotic vertebrates was facilitated by frequent recombination. At last, host cellular opioid growth factor receptor (OGFr) gene capturing by anamniotic ERVs with GTE was reported for the first time. Overall, our findings overturn traditional Pol genotyping and reveal a complex evolutionary history of anamniotic retroviruses inferred by Env evolution. IMPORTANCE Although the retroviral envelope (Env) protein in amniotes has been well studied, its evolutionary history in anamniotic vertebrates is ambiguous. By analyzing more than 30,000 copies of ERV lineages with gamma-type Env (GTE) in anamniotes, several important evolutionary features were identified. First, GTE was found to be widely distributed among different amphibians and fish. Second, nine types of GTE were discovered and defined, revealing their great genetic diversity. Third, the incongruence between the Env and Pol phylogenies suggested that frequent recombination shaped the early evolution of anamniote retroviruses. Fourth, an ancient horizontal gene transfer event was discovered from anamniotes to ERVs with GTE. These findings reveal a complex evolution pattern for retroviral Env in anamniotes.}, }
@article {pmid35388483, year = {2022}, author = {Burch, TR and Firnstahl, AD and Spencer, SK and Larson, RA and Borchardt, MA}, title = {Fate and seasonality of antimicrobial resistance genes during full-scale anaerobic digestion of cattle manure across seven livestock production facilities.}, journal = {Journal of environmental quality}, volume = {51}, number = {3}, pages = {352-363}, doi = {10.1002/jeq2.20350}, pmid = {35388483}, issn = {1537-2537}, mesh = {Anaerobiosis ; Animals ; *Anti-Bacterial Agents/pharmacology ; Cattle ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Livestock/genetics ; *Manure ; }, abstract = {Anaerobic digestion has been suggested as an intervention to attenuate antibiotic resistance genes (ARGs) in livestock manure but supporting data have typically been collected at laboratory scale. Few studies have quantified ARG fate during full-scale digestion of livestock manure. We sampled untreated manure and digestate from seven full-scale mesophilic dairy manure digesters to assess ARG fate through each system. Samples were collected biweekly from December through August (i.e., winter, spring, and summer; n = 235 total) and analyzed by quantitative polymerase chain reaction for intI1, erm(B), sul1, tet(A), and tet(W). Concentrations of intI1, sul1, and tet(A) decreased during anaerobic digestion, but their removal was less extensive than expected based on previous laboratory studies. Removal for intI1 during anaerobic digestion equaled 0.28 ± 0.03 log10 units (mean ± SE), equivalent to only 48% removal and notable given intI1's role in horizontal gene transfer and multiple resistance. Furthermore, tet(W) concentrations were unchanged during anaerobic digestion (p > 0.05), and erm(B) concentrations increased by 0.52 ± 0.03 log10 units (3.3-fold), which is important given erythromycin's status as a critically important antibiotic for human medicine. Seasonal log10 changes in intI1, sul1, and tet(A) concentrations were ≥50% of corresponding log10 removals by anaerobic digestion, and variation in ARG and intI1 concentrations among digesters was quantitatively comparable to anaerobic digestion effects. These results suggest that mesophilic anaerobic digestion may be limited as an intervention for ARGs in livestock manure and emphasize the need for multiple farm-level interventions to attenuate antibiotic resistance.}, }
@article {pmid35388218, year = {2022}, author = {Jaskólska, M and Adams, DW and Blokesch, M}, title = {Two defence systems eliminate plasmids from seventh pandemic Vibrio cholerae.}, journal = {Nature}, volume = {604}, number = {7905}, pages = {323-329}, pmid = {35388218}, issn = {1476-4687}, support = {724630/ERC_/European Research Council/International ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {*Cholera/epidemiology/microbiology ; Genomic Islands/genetics ; Humans ; Pandemics ; Plasmids/genetics ; *Vibrio cholerae/genetics ; }, abstract = {Horizontal gene transfer can trigger rapid shifts in bacterial evolution. Driven by a variety of mobile genetic elements-in particular bacteriophages and plasmids-the ability to share genes within and across species underpins the exceptional adaptability of bacteria. Nevertheless, invasive mobile genetic elements can also present grave risks to the host; bacteria have therefore evolved a vast array of defences against these elements[1]. Here we identify two plasmid defence systems conserved in the Vibrio cholerae El Tor strains responsible for the ongoing seventh cholera pandemic[2-4]. These systems, termed DdmABC and DdmDE, are encoded on two major pathogenicity islands that are a hallmark of current pandemic strains. We show that the modules cooperate to rapidly eliminate small multicopy plasmids by degradation. Moreover, the DdmABC system is widespread and can defend against bacteriophage infection by triggering cell suicide (abortive infection, or Abi). Notably, we go on to show that, through an Abi-like mechanism, DdmABC increases the burden of large low-copy-number conjugative plasmids, including a broad-host IncC multidrug resistance plasmid, which creates a fitness disadvantage that counterselects against plasmid-carrying cells. Our results answer the long-standing question of why plasmids, although abundant in environmental strains, are rare in pandemic strains; have implications for understanding the dissemination of antibiotic resistance plasmids; and provide insights into how the interplay between two defence systems has shaped the evolution of the most successful lineage of pandemic V. cholerae.}, }
@article {pmid35388097, year = {2022}, author = {Slow, S and Anderson, T and Murdoch, DR and Bloomfield, S and Winter, D and Biggs, PJ}, title = {Extensive epigenetic modification with large-scale chromosomal and plasmid recombination characterise the Legionella longbeachae serogroup 1 genome.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {5810}, pmid = {35388097}, issn = {2045-2322}, mesh = {Chromosomes ; Epigenesis, Genetic ; Humans ; *Legionella/genetics ; *Legionella longbeachae/genetics ; *Legionella pneumophila/genetics ; *Legionnaires' Disease/microbiology ; Plasmids/genetics ; Recombination, Genetic ; Serogroup ; }, abstract = {Legionella longbeachae is an environmental bacterium that is the most clinically significant Legionella species in New Zealand (NZ), causing around two-thirds of all notified cases of Legionnaires' disease. Here we report the sequencing and analysis of the geo-temporal genetic diversity of 54 L. longbeachae serogroup 1 (sg1) clinical isolates, derived from cases from around NZ over a 22-year period, including one complete genome and its associated methylome. The 54 sg1 isolates belonged to two main clades that last shared a common ancestor between 95 BCE and 1694 CE. There was diversity at the genome-structural level, with large-scale arrangements occurring in some regions of the chromosome and evidence of extensive chromosomal and plasmid recombination. This includes the presence of plasmids derived from recombination and horizontal gene transfer between various Legionella species, indicating there has been both intra- and inter-species gene flow. However, because similar plasmids were found among isolates within each clade, plasmid recombination events may pre-empt the emergence of new L. longbeachae strains. Our complete NZ reference genome consisted of a 4.1 Mb chromosome and a 108 kb plasmid. The genome was highly methylated with two known epigenetic modifications, m[4]C and m[6]A, occurring in particular sequence motifs within the genome.}, }
@article {pmid35384690, year = {2022}, author = {Weise, K and Winter, L and Fischer, E and Kneis, D and de la Cruz Barron, M and Kunze, S and Berendonk, TU and Jungmann, D and Klümper, U}, title = {Multiwalled Carbon Nanotubes Promote Bacterial Conjugative Plasmid Transfer.}, journal = {Microbiology spectrum}, volume = {10}, number = {2}, pages = {e0041022}, pmid = {35384690}, issn = {2165-0497}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Escherichia coli/genetics ; Humans ; *Nanotubes, Carbon ; Plasmids/genetics ; Plastics/pharmacology ; }, abstract = {Multiwalled carbon nanotubes (MWCNTs) regularly enter aquatic environments due to their ubiquity in consumer products and engineering applications. However, the effects of MWCNT pollution on the environmental microbiome are poorly understood. Here, we evaluated whether these carbon nanoparticles can elevate the spread of antimicrobial resistance by promoting bacterial plasmid transfer, which has previously been observed for copper nanomaterials with antimicrobial properties as well as for microplastics. Through a combination of experimental liquid mating assays between Pseudomonas putida donor and recipient strains with plasmid pKJK5::gfpmut3b and mathematical modeling, we here demonstrate that the presence of MWCNTs leads to increased plasmid transfer rates in a concentration-dependent manner. The percentage of transconjugants per recipient significantly increased from 0.21 ± 0.04% in absence to 0.41 ± 0.09% at 10 mg L[-1] MWCNTs. Similar trends were observed when using an Escherichia coli donor hosting plasmid pB10. The identified mechanism underlying the observed dynamics was the agglomeration of MWCNTs. A significantly increased number of particles with >6 μm diameter was detected in the presence of MWCNTs, which can in turn provide novel surfaces for bacterial interactions between donor and recipient cells after colonization. Fluorescence microscopy confirmed that MWCNT agglomerates were indeed covered in biofilms that contained donor bacteria as well as elevated numbers of green fluorescent transconjugant cells containing the plasmid. Consequently, MWCNTs provide bacteria with novel surfaces for intense cell-to-cell interactions in biofilms and can promote bacterial plasmid transfer, hence potentially elevating the spread of antimicrobial resistance. IMPORTANCE In recent decades, the use of carbon nanoparticles, especially multiwalled carbon nanotubes (MWCNTs), in a variety of products and engineering applications has been growing exponentially. As a result, MWCNT pollution into environmental compartments has been increasing. We here demonstrate that the exposure to MWCNTs can affect bacterial plasmid transfer rates in aquatic environments, an important process connected to the spread of antimicrobial resistance genes in microbial communities. This is mechanistically explained by the ability of MWCNTs to form bigger agglomerates, hence providing novel surfaces for bacterial interactions. Consequently, increasing pollution with MWCNTs has the potential to elevate the ongoing spread of antimicrobial resistance, a major threat to human health in the 21st century.}, }
@article {pmid35383231, year = {2022}, author = {Bueris, V and Sellera, FP and Fuga, B and Sano, E and Carvalho, MPN and Couto, SCF and Moura, Q and Lincopan, N}, title = {Convergence of virulence and resistance in international clones of WHO critical priority enterobacterales isolated from Marine Bivalves.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {5707}, pmid = {35383231}, issn = {2045-2322}, support = {OPP1193112/GATES/Bill &amp; Melinda Gates Foundation/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Bivalvia ; Clone Cells ; Drug Resistance, Multiple, Bacterial/genetics ; *Escherichia coli ; Microbial Sensitivity Tests ; Virulence/genetics ; World Health Organization ; beta-Lactamases/genetics ; }, abstract = {The global spread of critical-priority antimicrobial-resistant Enterobacterales by food is a public health problem. Wild-caught seafood are broadly consumed worldwide, but exposure to land-based pollution can favor their contamination by clinically relevant antimicrobial-resistant bacteria. As part of the Grand Challenges Explorations: New Approaches to Characterize the Global Burden of Antimicrobial Resistance Program, we performed genomic surveillance and cell culture-based virulence investigation of WHO critical priority Enterobacterales isolated from marine bivalves collected in the Atlantic Coast of South America. Broad-spectrum cephalosporin-resistant Klebsiella pneumoniae and Escherichia coli isolates were recovered from eight distinct geographical locations. These strains harbored blaCTX-M-type or blaCMY-type genes. Most of the surveyed genomes confirmed the convergence of wide virulome and resistome (i.e., antimicrobials, heavy metals, biocides, and pesticides resistance). We identified strains belonging to the international high-risk clones K. pneumoniae ST307 and E. coli ST131 carrying important virulence genes, whereas in vitro experiments confirmed the high virulence potential of these strains. Thermolabile and thermostable toxins were identified in some strains, and all of them were biofilm producers. These data point to an alarming presence of resistance and virulence genes in marine environments, which may favor horizontal gene transfer and the spread of these traits to other bacterial species.}, }
@article {pmid35382558, year = {2022}, author = {Aytan-Aktug, D and Clausen, PTLC and Szarvas, J and Munk, P and Otani, S and Nguyen, M and Davis, JJ and Lund, O and Aarestrup, FM}, title = {PlasmidHostFinder: Prediction of Plasmid Hosts Using Random Forest.}, journal = {mSystems}, volume = {7}, number = {2}, pages = {e0118021}, pmid = {35382558}, issn = {2379-5077}, support = {75N93019C00076/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Random Forest ; Plasmids ; Bacteria/genetics ; Genomics ; *Anti-Infective Agents ; }, abstract = {Plasmids play a major role facilitating the spread of antimicrobial resistance between bacteria. Understanding the host range and dissemination trajectories of plasmids is critical for surveillance and prevention of antimicrobial resistance. Identification of plasmid host ranges could be improved using automated pattern detection methods compared to homology-based methods due to the diversity and genetic plasticity of plasmids. In this study, we developed a method for predicting the host range of plasmids using machine learning-specifically, random forests. We trained the models with 8,519 plasmids from 359 different bacterial species per taxonomic level; the models achieved Matthews correlation coefficients of 0.662 and 0.867 at the species and order levels, respectively. Our results suggest that despite the diverse nature and genetic plasticity of plasmids, our random forest model can accurately distinguish between plasmid hosts. This tool is available online through the Center for Genomic Epidemiology (https://cge.cbs.dtu.dk/services/PlasmidHostFinder/). IMPORTANCE Antimicrobial resistance is a global health threat to humans and animals, causing high mortality and morbidity while effectively ending decades of success in fighting against bacterial infections. Plasmids confer extra genetic capabilities to the host organisms through accessory genes that can encode antimicrobial resistance and virulence. In addition to lateral inheritance, plasmids can be transferred horizontally between bacterial taxa. Therefore, detection of the host range of plasmids is crucial for understanding and predicting the dissemination trajectories of extrachromosomal genes and bacterial evolution as well as taking effective countermeasures against antimicrobial resistance.}, }
@article {pmid35380451, year = {2022}, author = {Ota, Y and Prah, I and Nukui, Y and Koike, R and Saito, R}, title = {blaKPC-2-Encoding IncP-6 Plasmids in Citrobacter freundii and Klebsiella variicola Strains from Hospital Sewage in Japan.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {8}, pages = {e0001922}, pmid = {35380451}, issn = {1098-5336}, mesh = {Anti-Bacterial Agents ; Carbapenems ; *Citrobacter freundii/genetics ; Hospitals ; Japan ; Klebsiella ; Plasmids/genetics ; *Sewage ; Water ; }, abstract = {Klebsiella pneumoniae carbapenemase (KPC) producers are an emerging threat to global health, and the hospital water environment is considered an important reservoir of these life-threatening bacteria. We characterized plasmids of KPC-2-producing Citrobacter freundii and Klebsiella variicola isolates recovered from hospital sewage in Japan. Antimicrobial susceptibility testing, whole-genome sequencing analysis, bacterial conjugation, and transformation experiments were performed for both KPC-2 producers. The blaKPC-2 gene was located on the Tn3 transposon-related region from an IncP-6 replicon plasmid that could not be transferred via conjugation. Compared to the blaKPC-2-encoding plasmid of the C. freundii isolate, alignment analysis of plasmids with blaKPC-2 showed that the blaKPC-2-encoding plasmid of the K. variicola isolate was a novel IncP-6/IncF-like hybrid plasmid containing a 75,218-bp insertion sequence composed of IncF-like plasmid conjugative transfer proteins. Carbapenem-resistant transformants harboring blaKPC-2 were obtained for both isolates. However, no IncF-like insertion region was found in the K. variicola donor plasmid of the transformant, suggesting that this IncF-like region is not readily functional for plasmid conjugative transfer and is maintained depending on the host cells. The findings on the KPC-2 producers and novel genetic content emphasize the key role of hospital sewage as a potential reservoir of pathogens and its linked dissemination of blaKPC-2 through the hospital water environment. Our results indicate that continuous monitoring for environmental emergence of antimicrobial-resistant bacteria might be needed to control the spread of these infectious bacteria. Moreover, it will help elucidate both the evolution and transmission pathways of these bacteria harboring antimicrobial resistance. IMPORTANCE Antimicrobial resistance is a significant problem for global health, and the hospital environment has been recognized as a reservoir of antimicrobial resistance. Here, we provide insight into the genomic features of blaKPC-2-harboring isolates of Citrobacter freundii and Klebsiella variicola obtained from hospital sewage in Japan. The findings of carbapenem-resistant bacteria containing this novel genetic context emphasize that hospital sewage could act as a potential reservoir of pathogens and cause the subsequent spread of blaKPC-2 via horizontal gene transfer in the hospital water environment. This indicates that serial monitoring for environmental bacteria possessing antimicrobial resistance may help us control the spread of infection and also lead to elucidating the evolution and transmission pathways of these bacteria.}, }
@article {pmid35380107, year = {2022}, author = {Gupta, D and Shalvarjian, KE and Nayak, DD}, title = {An Archaea-specific c-type cytochrome maturation machinery is crucial for methanogenesis in Methanosarcina acetivorans.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {35380107}, issn = {2050-084X}, mesh = {*Archaea/metabolism ; Cytochromes/metabolism ; Electron Transport/genetics ; Methane/metabolism ; *Methanosarcina/genetics ; }, abstract = {c-Type cytochromes (cyt c) are proteins that undergo post-translational modification to covalently bind heme, which allows them to facilitate redox reactions in electron transport chains across all domains of life. Genomic evidence suggests that cyt c are involved in electron transfer processes among the Archaea, especially in members that produce or consume the potent greenhouse gas methane. However, neither the maturation machinery for cyt c in Archaea nor their role in methane metabolism has ever been functionally characterized. Here, we have used CRISPR-Cas9 genome editing tools to map a distinct pathway for cyt c biogenesis in the model methanogenic archaeon Methanosarcina acetivorans, and have also identified substrate-specific functional roles for cyt c during methanogenesis. Although the cyt c maturation machinery from M. acetivorans is universally conserved in the Archaea, our evolutionary analyses indicate that different clades of Archaea acquired this machinery through multiple independent horizontal gene transfer events from different groups of Bacteria. Overall, we demonstrate the convergent evolution of a novel Archaea-specific cyt c maturation machinery and its physiological role during methanogenesis, a process which contributes substantially to global methane emissions.}, }
@article {pmid35379360, year = {2022}, author = {Salamzade, R and Manson, AL and Walker, BJ and Brennan-Krohn, T and Worby, CJ and Ma, P and He, LL and Shea, TP and Qu, J and Chapman, SB and Howe, W and Young, SK and Wurster, JI and Delaney, ML and Kanjilal, S and Onderdonk, AB and Bittencourt, CE and Gussin, GM and Kim, D and Peterson, EM and Ferraro, MJ and Hooper, DC and Shenoy, ES and Cuomo, CA and Cosimi, LA and Huang, SS and Kirby, JE and Pierce, VM and Bhattacharyya, RP and Earl, AM}, title = {Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance.}, journal = {Genome medicine}, volume = {14}, number = {1}, pages = {37}, pmid = {35379360}, issn = {1756-994X}, support = {1K08AI132716/NH/NIH HHS/United States ; T32 AI007061/AI/NIAID NIH HHS/United States ; T32 HD055148/HD/NICHD NIH HHS/United States ; K08 AI132716/AI/NIAID NIH HHS/United States ; T32HD055148/NH/NIH HHS/United States ; T32AI007061/NH/NIH HHS/United States ; U19 AI110818/AI/NIAID NIH HHS/United States ; U19AI110818/NH/NIH HHS/United States ; R33AI119114/NH/NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; *Carbapenems/pharmacology ; *Gene Transfer, Horizontal ; Humans ; Plasmids/genetics ; Prospective Studies ; }, abstract = {BACKGROUND: Carbapenem-resistant Enterobacterales (CRE) are an urgent global health threat. Inferring the dynamics of local CRE dissemination is currently limited by our inability to confidently trace the spread of resistance determinants to unrelated bacterial hosts. Whole-genome sequence comparison is useful for identifying CRE clonal transmission and outbreaks, but high-frequency horizontal gene transfer (HGT) of carbapenem resistance genes and subsequent genome rearrangement complicate tracing the local persistence and mobilization of these genes across organisms.<br><br>METHODS: To overcome this limitation, we developed a new approach to identify recent HGT of large, near-identical plasmid segments across species boundaries, which also allowed us to overcome technical challenges with genome assembly. We applied this to complete and near-complete genome assemblies to examine the local spread of CRE in a systematic, prospective collection of all CRE, as well as time- and species-matched carbapenem-susceptible Enterobacterales, isolated from patients from four US hospitals over nearly 5 years.<br><br>RESULTS: Our CRE collection comprised a diverse range of species, lineages, and carbapenem resistance mechanisms, many of which were encoded on a variety of promiscuous plasmid types. We found and quantified rearrangement, persistence, and repeated transfer of plasmid segments, including those harboring carbapenemases, between organisms over multiple years. Some plasmid segments were found to be strongly associated with specific locales, thus representing geographic signatures that make it possible to trace recent and localized HGT events. Functional analysis of these signatures revealed genes commonly found in plasmids of nosocomial pathogens, such as functions required for plasmid retention and spread, as well survival against a variety of antibiotic and antiseptics common to the hospital environment.<br><br>CONCLUSIONS: Collectively, the framework we developed provides a clearer, high-resolution picture of the epidemiology of antibiotic resistance importation, spread, and persistence in patients and healthcare networks.}, }
@article {pmid35372505, year = {2022}, author = {Beyer, HM and Iwaï, H}, title = {Structural Basis for the Propagation of Homing Endonuclease-Associated Inteins.}, journal = {Frontiers in molecular biosciences}, volume = {9}, number = {}, pages = {855511}, pmid = {35372505}, issn = {2296-889X}, abstract = {Inteins catalyze their removal from a host protein through protein splicing. Inteins that contain an additional site-specific endonuclease domain display genetic mobility via a process termed "homing" and thereby act as selfish DNA elements. We elucidated the crystal structures of two archaeal inteins associated with an active or inactive homing endonuclease domain. This analysis illustrated structural diversity in the accessory domains (ACDs) associated with the homing endonuclease domain. To augment homing endonucleases with highly specific DNA cleaving activity using the intein scaffold, we engineered the ACDs and characterized their homing site recognition. Protein engineering of the ACDs in the inteins illuminated a possible strategy for how inteins could avoid their extinction but spread via the acquisition of a diverse accessory domain.}, }
@article {pmid35369513, year = {2022}, author = {Manoharan-Basil, SS and González, N and Laumen, JGE and Kenyon, C}, title = {Horizontal Gene Transfer of Fluoroquinolone Resistance-Conferring Genes From Commensal Neisseria to Neisseria gonorrhoeae: A Global Phylogenetic Analysis of 20,047 Isolates.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {793612}, pmid = {35369513}, issn = {1664-302X}, abstract = {Antimicrobial resistance in Neisseria gonorrhoeae is an important global health concern. The genetically related commensal Neisseria act as a reservoir of resistance genes, and horizontal gene transfer (HGT) has been shown to play an important role in the genesis of resistance to cephalosporins and macrolides in N. gonorrhoeae. In this study, we evaluated if there was evidence of HGT in the genes gyrA/gyrB and parC/parE responsible for fluoroquinolone resistance. Even though the role of gyrB and parE in quinolone resistance is unclear, the subunits gyrB and parE were included as zoliflodacin, a promising new drug to treat N. gonorrhoeae targets the gyrB subunit. We analyzed a collection of 20,047 isolates; 18,800 N. gonorrhoeae, 1,238 commensal Neisseria spp., and nine Neisseria meningitidis. Comparative genomic analyses identified HGT events in genes, gyrA, gyrB, parC, and parE. Recombination events were predicted in N. gonorrhoeae and Neisseria commensals. Neisseria lactamica, Neisseria macacae, and Neisseria mucosa were identified as likely progenitors of the HGT events in gyrA, gyrB, and parE, respectively.}, }
@article {pmid35369504, year = {2022}, author = {Wong, A and Matijasic, BB and Ibana, JA and Lim, RLH}, title = {Editorial: Antimicrobial Resistance Along the Food Chain: Are We What We Eat?.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {881882}, pmid = {35369504}, issn = {1664-302X}, }
@article {pmid35366350, year = {2022}, author = {Murugesan, AC and Varughese, HS}, title = {Analysis of CRISPR-Cas system and antimicrobial resistance in Staphylococcus coagulans isolates.}, journal = {Letters in applied microbiology}, volume = {75}, number = {1}, pages = {126-134}, doi = {10.1111/lam.13713}, pmid = {35366350}, issn = {1472-765X}, support = {EMR/2016/006141//Department of Science and Technology-Science and Engineering Research Board, Government of India/ ; }, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; *CRISPR-Cas Systems ; Dogs ; Drug Resistance, Bacterial ; Staphylococcus ; }, abstract = {CRISPR-Cas system contributes adaptive immunity to protect the bacterial and archaeal genome against invading mobile genetic elements. In this study, an attempt was made to characterize the CRISPR-Cas system in Staphylococcus coagulans, the second most prevalent coagulase positive staphylococci causing skin infections in dogs. Out of 45 S. coagulans isolates, 42/45 (93·33%) strains contained CRISPR-Cas system and 45 confirmed CRISPR system was identified in 42 S. coagulans isolates. The length of CRISPR loci ranged from 167 to 2477 bp, and the number of spacers in each CRISPR was varied from two spacers to as high as 37 numbers. Direct repeat (DR) sequences were between 30 and 37, but most (35/45) of the DRs contained 36 sequences. The predominant S. coagulans strains 29/45 did not possess any antimicrobial resistant genes (ARG); 26/29 strains contained Type IIC CRISPR-Cas system. Three isolates from Antarctica seals neither contain CRISPR-Cas system nor ARG. Only 15/45 S. coagulans strains (33·33%) harboured at least one ARG and 13/15 of them were having mecA gene. All the methicillin susceptible S. coagulans isolates contained Type IIC CRISPR-Cas system. In contrast, many (10/13) S. coagulans isolates which were methicillin resistant had Type IIIA CRISPR-Cas system, and this Type IIIA CRISPR-Cas system was present within the SCCmec mobile genetic element. Hence, this study suggests that Type II CRISPR-Cas in S. coagulans isolates might have played a possible role in preventing acquisition of plasmid/phage invasion and Type IIIA CRISPR-Cas system may have an insignificant role in the prevention of horizontal gene transfer of antimicrobial resistance genes in S. coagulans species.}, }
@article {pmid35366344, year = {2022}, author = {Russell, JN and Yost, CK}, title = {Metagenomic and metatranscriptomic analyses reveal that biobed systems can enrich for antibiotic resistance and genetic mobility genes.}, journal = {Letters in applied microbiology}, volume = {75}, number = {1}, pages = {145-151}, doi = {10.1111/lam.13714}, pmid = {35366344}, issn = {1472-765X}, support = {//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Biodegradation, Environmental ; Drug Resistance, Microbial ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Pesticides/analysis/metabolism ; }, abstract = {Antibiotic resistance gene pollution in the environment has been identified as a potential contributor to the global issue of antibiotic resistance prevalence, creating a need to identify and characterize environmental reservoirs for antibiotic resistance genes. Because many polluted environments have been shown to contain elevated levels of antibiotic resistance genes, agriculturally based pesticide bioremediation systems called 'biobeds' could serve as environmental reservoirs for antibiotic resistance genes, although this has never been extensively explored. Metagenomic and metatranscriptomic analyses of an on-farm biobed system sampled before and after a season of pesticide use demonstrated that in situ pesticide applications applied to biobeds can enrich for multidrug, sulphonamide, aminoglycoside and beta-lactam resistance genes. Additionally, this study demonstrated an enrichment for genes associated with gene mobilization, such as genes involved in horizontal gene transfer and plasmid mobility, as well as transposons and integrases.}, }
@article {pmid35359176, year = {2022}, author = {Ceriotti, LF and Gatica-Soria, L and Sanchez-Puerta, MV}, title = {Cytonuclear coevolution in a holoparasitic plant with highly disparate organellar genomes.}, journal = {Plant molecular biology}, volume = {109}, number = {6}, pages = {673-688}, pmid = {35359176}, issn = {1573-5028}, support = {PICT-2017-0691//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; 06/A724//Universidad Nacional de Cuyo/ ; }, mesh = {*Balanophoraceae/genetics ; Cell Nucleus/genetics ; Chloroplast Proteins/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Plant/genetics ; Phylogeny ; Plants/genetics ; *Plastids/genetics ; }, abstract = {Contrasting substitution rates in the organellar genomes of Lophophytum agree with the DNA repair, replication, and recombination gene content. Plastid and nuclear genes whose products form multisubunit complexes co-evolve. The organellar genomes of the holoparasitic plant Lophophytum (Balanophoraceae) show disparate evolution. In the plastid, the genome has been severely reduced and presents a > 85% AT content, while in the mitochondria most protein-coding genes have been replaced by homologs acquired by horizontal gene transfer (HGT) from their hosts (Fabaceae). Both genomes carry genes whose products form multisubunit complexes with those of nuclear genes, creating a possible hotspot of cytonuclear coevolution. In this study, we assessed the evolutionary rates of plastid, mitochondrial and nuclear genes, and their impact on cytonuclear evolution of genes involved in multisubunit complexes related to lipid biosynthesis and proteolysis in the plastid and those in charge of the oxidative phosphorylation in the mitochondria. Genes from the plastid and the mitochondria (both native and foreign) of Lophophytum showed extremely high and ordinary substitution rates, respectively. These results agree with the biased loss of plastid-targeted proteins involved in angiosperm organellar repair, replication, and recombination machinery. Consistent with the high rate of evolution of plastid genes, nuclear-encoded subunits of plastid complexes showed disproportionate increases in non-synonymous substitution rates, while those of the mitochondrial complexes did not show different rates than the control (i.e. non-organellar nuclear genes). Moreover, the increases in the nuclear-encoded subunits of plastid complexes were positively correlated with the level of physical interaction they possess with the plastid-encoded ones. Overall, these results suggest that a structurally-mediated compensatory factor may be driving plastid-nuclear coevolution in Lophophytum, and that mito-nuclear coevolution was not altered by HGT.}, }
@article {pmid35358636, year = {2022}, author = {Liu, L and Yu, X and Wu, D and Su, J}, title = {Antibiotic resistance gene profile in aerobic granular reactor under antibiotic stress: Can eukaryotic microalgae act as inhibiting factor?.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {304}, number = {}, pages = {119221}, doi = {10.1016/j.envpol.2022.119221}, pmid = {35358636}, issn = {1873-6424}, mesh = {Anti-Bacterial Agents/toxicity ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Eukaryota ; Genes, Bacterial ; *Microalgae/genetics ; Phylogeny ; *Scenedesmus ; Sewage/microbiology ; Tetracycline ; }, abstract = {Antibiotic resistance gene (ARG) pollution is critical environmental problem, and horizontal gene transfer acts as a driving evolutionary force. In theory, due to the phylogenetic distance between eukaryotes and prokaryotes, eukaryotic microalgae can be a natural barrier that plays a negative role in ARG transfer among the symbiotic bacteria to decrease ARG abundance in sludge during wastewater treatment. However, this hypothesis is far from proven and needs to be tested experimentally, so this study investigated the influence of eukaryote microalgae (Scenedesmus) on the ARG profile of symbiotic bacteria based on aerobic granular reactor. The results indicated that Scenedesmus symbiosis could affect ARG diversity of bacteria, and the detected numbers of ARG in aerobic granular sludge (AG) group and algae-bacteria granular consortia (AAG) group were 45-53 and 44-47, respectively. In terms of relative abundance, after target microalgae symbiosis, the total abundance of ARGs significantly decreased from 1.17 × 10°, 2.69 × 10° and 1.36 × 10[-1] to 6.53 × 10[-1], 9.64 × 10[-1] and 1.04 × 10[-1] in the systems with the addition of streptomycin, azithromycin and vancomycin, respectively (P < 0.05), yet there was no significant difference between AG and AAG under the stress of ampicillin, sulfamethazine and tetracycline (P > 0.05). Redundancy analysis showed that the eukaryotic microalgae were significant factor explaining the change in ARG relative abundance (P < 0.05), which contributed 15.3% of ARG variation. Furthermore, the results show that, except for the tetracycline treatment system, the total relative abundances of MGEs in the AAG under the stress of the other five antibiotics were 3.54 × 10[-2]-7.13 × 10[-1], which were all significantly lower than those in the AG (8.38 × 10[-2]-1.59 × 10°). There was a more significant positive correlation relationship between ARGs and mobile genetic elements (MGEs) than that between ARGs and dominated bacteria.}, }
@article {pmid35358556, year = {2022}, author = {Wang, PH and Chen, YL and Wu, TY and Wu, YW and Wang, TY and Shih, CJ and Wei, ST and Lai, YL and Liu, CX and Chiang, YR}, title = {Omics and mechanistic insights into di-(2-ethylhexyl) phthalate degradation in the O2-fluctuating estuarine sediments.}, journal = {Chemosphere}, volume = {299}, number = {}, pages = {134406}, doi = {10.1016/j.chemosphere.2022.134406}, pmid = {35358556}, issn = {1879-1298}, mesh = {Biodegradation, Environmental ; *Diethylhexyl Phthalate/metabolism ; *Phthalic Acids/metabolism ; Thauera ; }, abstract = {Di-(2-ethylhexyl) phthalate (DEHP) represents the most used phthalate plasticizer with an annual production above the millions of tons worldwide. Due to its inadequate disposal, outstanding chemical stability, and extremely low solubility (3 mg/L), endocrine-disrupting DEHP often accumulates in urban estuarine sediments at concentrations above the predicted no-effect concentration (20-100 mg/kg). Our previous study suggested that microbial DEHP degradation in estuarine sediments proceeds synergistically where DEHP side-chain hydrolysis to form phthalic acid represents a bottleneck. Here, we resolved this bottleneck and deconstructed the microbial synergy in O2-fluctuating estuarine sediments. Metagenomic analysis and RNA sequencing suggested that orthologous genes encoding extracellular DEHP hydrolase NCU65476 in Acidovorax sp. strain 210-6 are often flanked by the co-expressed composite transposon and are widespread in aquatic environments worldwide. Therefore, we developed a turbidity-based microplate assay to characterize NCU65476. The optimized assay conditions (with 1 mM Ca[2+] and pH 6.0) increased the DEHP hydrolysis rate by a factor of 10. Next, we isolated phthalic acid-degrading Hydrogenophaga spp. and Thauera chlorobenzoica from Guandu estuarine sediment to study the effect of O2(aq) on their metabolic synergy with strain 210-6. The results of co-culture experiments suggested that after DEHP side-chain hydrolysis by strain 210-6, phthalic acid can be degraded by Hydrogenophaga sp. when O2(aq) is above 1 mg/L or degraded by Thauera chlorobenzoica anaerobically. Altogether, our data demonstrates that DEHP could be degraded synergistically in estuarine sediments via divergent pathways responding to O2 availability. The optimized conditions for NCU65476 could facilitate the practice of DEHP bioremediation in estuarine sediments.}, }
@article {pmid35357213, year = {2022}, author = {Shropshire, WC and Dinh, AQ and Earley, M and Komarow, L and Panesso, D and Rydell, K and Gómez-Villegas, SI and Miao, H and Hill, C and Chen, L and Patel, R and Fries, BC and Abbo, L and Cober, E and Revolinski, S and Luterbach, CL and Chambers, H and Fowler, VG and Bonomo, RA and Shelburne, SA and Kreiswirth, BN and van Duin, D and Hanson, BM and Arias, CA}, title = {Accessory Genomes Drive Independent Spread of Carbapenem-Resistant Klebsiella pneumoniae Clonal Groups 258 and 307 in Houston, TX.}, journal = {mBio}, volume = {13}, number = {2}, pages = {e0049722}, pmid = {35357213}, issn = {2150-7511}, support = {P01 AI152999/AI/NIAID NIH HHS/United States ; R21 AI143229/AI/NIAID NIH HHS/United States ; I01 BX003741/BX/BLRD VA/United States ; R01 AI143910/AI/NIAID NIH HHS/United States ; K24 AI121296/AI/NIAID NIH HHS/United States ; K01 AI148593/AI/NIAID NIH HHS/United States ; R01 AI148342/AI/NIAID NIH HHS/United States ; R01 AI134637/AI/NIAID NIH HHS/United States ; UM1 AI104681/AI/NIAID NIH HHS/United States ; }, mesh = {*Carbapenem-Resistant Enterobacteriaceae/genetics ; Carbapenems/pharmacology ; Humans ; *Klebsiella Infections/epidemiology ; Klebsiella pneumoniae ; Prospective Studies ; }, abstract = {Carbapenem-resistant Klebsiella pneumoniae (CRKp) is an urgent public health threat. Worldwide dissemination of CRKp has been largely attributed to clonal group (CG) 258. However, recent evidence indicates the global emergence of a CRKp CG307 lineage. Houston, TX, is the first large city in the United States with detected cocirculation of both CRKp CG307 and CG258. We sought to characterize the genomic and clinical factors contributing to the parallel endemic spread of CG258 and CG307. CRKp isolates were collected as part of the prospective, Consortium on Resistance against Carbapenems in Klebsiella and other Enterobacterales 2 (CRACKLE-2) study. Hybrid short-read and long-read genome assemblies were generated from 119 CRKp isolates (95 originated from Houston hospitals). A comprehensive characterization of phylogenies, gene transfer, and plasmid content with pan-genome analysis was performed on all CRKp isolates. Plasmid mating experiments were performed with CG307 and CG258 isolates of interest. Dissection of the accessory genomes suggested independent evolution and limited horizontal gene transfer between CG307 and CG258 lineages. CG307 contained a diverse repertoire of mobile genetic elements, which were shared with other non-CG258 K. pneumoniae isolates. Three unique clades of Houston CG307 isolates clustered distinctly from other global CG307 isolates, indicating potential selective adaptation of particular CG307 lineages to their respective geographical niches. CG307 strains were often isolated from the urine of hospitalized patients, likely serving as important reservoirs for genes encoding carbapenemases and extended-spectrum β-lactamases. Our findings suggest parallel cocirculation of high-risk lineages with potentially divergent evolution. IMPORTANCE The prevalence of carbapenem-resistant Klebsiella pneumoniae (CRKp) infections in nosocomial settings remains a public health challenge. High-risk clones such as clonal group 258 (CG258) are particularly concerning due to their association with blaKPC carriage, which can severely complicate antimicrobial treatments. There is a recent emergence of clonal group 307 (CG307) worldwide with little understanding of how this successful clone has been able to adapt while cocirculating with CG258. We provide the first evidence of potentially divergent evolution between CG258 and CG307 with limited sharing of adaptive genes. Houston, TX, is home to the largest medical center in the world, with a large influx of domestic and international patients. Thus, our unique geographical setting, where two pandemic strains of CRKp are circulating, provides an indication of how differential accessory genome content can drive stable, endemic populations of CRKp. Pan-genomic analyses such as these can reveal unique signatures of successful CRKp dissemination, such as the CG307-associated plasmid (pCG307_HTX), and provide invaluable insights into the surveillance of local carbapenem-resistant Enterobacterales (CRE) epidemiology.}, }
@article {pmid35356516, year = {2022}, author = {De Miccolis Angelini, RM and Landi, L and Raguseo, C and Pollastro, S and Faretra, F and Romanazzi, G}, title = {Tracking of Diversity and Evolution in the Brown Rot Fungi Monilinia fructicola, Monilinia fructigena, and Monilinia laxa.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {854852}, pmid = {35356516}, issn = {1664-302X}, abstract = {Monilinia species are among the most devastating fungi worldwide as they cause brown rot and blossom blight on fruit trees. To understand the molecular bases of their pathogenic lifestyles, we compared the newly assembled genomes of single strains of Monilinia fructicola, M. fructigena and M. laxa, with those of Botrytis cinerea and Sclerotinia sclerotiorum, as the closest species within Sclerotiniaceae. Phylogenomic analysis of orthologous proteins and syntenic investigation suggest that M. laxa is closer to M. fructigena than M. fructicola, and is closest to the other investigated Sclerotiniaceae species. This indicates that M. laxa was the earliest result of the speciation process. Distinct evolutionary profiles were observed for transposable elements (TEs). M. fructicola and M. laxa showed older bursts of TE insertions, which were affected (mainly in M. fructicola) by repeat-induced point (RIP) mutation gene silencing mechanisms. These suggested frequent occurrence of the sexual process in M. fructicola. More recent TE expansion linked with low RIP action was observed in M. fructigena, with very little in S. sclerotiorum and B. cinerea. The detection of active non-syntenic TEs is indicative of horizontal gene transfer and has resulted in alterations in specific gene functions. Analysis of candidate effectors, biosynthetic gene clusters for secondary metabolites and carbohydrate-active enzymes, indicated that Monilinia genus has multiple virulence mechanisms to infect host plants, including toxins, cell-death elicitor, putative virulence factors and cell-wall-degrading enzymes. Some species-specific pathogenic factors might explain differences in terms of host plant and organ preferences between M. fructigena and the other two Monilinia species.}, }
@article {pmid35355876, year = {2022}, author = {Sevillya, G}, title = {Relation between two evolutionary clocks reveal new insights in bacterial evolution.}, journal = {Access microbiology}, volume = {4}, number = {2}, pages = {000265}, pmid = {35355876}, issn = {2516-8290}, abstract = {New insights in evolution are available thanks to next-generation sequencing technologies in recent years. However, due to the network of complex relations between species, caused by the intensive horizontal gene transfer (HGT) between different bacterial species, it is difficult to discover bacterial evolution. This difficulty leads to new research in the field of phylogeny, including the gene-based phylogeny, in contrast to sequence-based phylogeny. In previous articles, we presented evolutionary insights of Synteny Index (SI) study on a large biological dataset. We showed that the SI approach naturally clusters 1133 species into 39 cliques of closely related species. In addition, we presented a model that enables calculation of the number of translocation events between genomes based on their SI distance. Here, these two studies are combined together and lead to new insights. A principal result is the relation between two evolutionary clocks: the well-known sequence-based clock influenced by point mutations, and SI distance clock influenced by translocation events. A surprising linear relation between these two evolutionary clocks rising for closely related species across all genus. In other words, these two different clocks are ticking at the same rate inside the genus level. Conversely, a phase-transition manner discovered between these two clocks across non-closely related species. This may suggest a new genus definition based on an analytic approach, since the phase-transition occurs where each gene, on average, undergoes one translocation event. In addition, rare cases of HGT among highly conserved genes can be detected as outliers from the phase-transition pattern.}, }
@article {pmid35354279, year = {2022}, author = {Gonçalves, C and Marques, M and Gonçalves, P}, title = {Contrasting Strategies for Sucrose Utilization in a Floral Yeast Clade.}, journal = {mSphere}, volume = {7}, number = {2}, pages = {e0003522}, pmid = {35354279}, issn = {2379-5042}, mesh = {Glucose/metabolism ; Glucosides/metabolism ; Humans ; Maltose/metabolism ; *Saccharomyces cerevisiae/genetics/metabolism ; *Saccharomycetales/genetics ; Sucrose/metabolism ; }, abstract = {Yeast species in the Wickerhamiella and Starmerella genera (W/S clade) thrive in the sugar-rich floral niche. We have previously shown that species belonging to this clade harbor an unparalleled number of genes of bacterial origin, among which is the SUC2 gene, encoding a sucrose-hydrolyzing enzyme. In this study, we used complementary in silico and experimental approaches to examine sucrose utilization in a broader cohort of species representing extant diversity in the W/S clade. Distinct strategies and modes of sucrose assimilation were unveiled, involving either extracellular sucrose hydrolysis through secreted bacterial Suc2 or intracellular assimilation using broad-substrate-range α-glucoside/H[+] symporters and α-glucosidases. The intracellular pathway is encoded in two types of gene clusters reminiscent of the MAL clusters in Saccharomyces cerevisiae, where they are involved in maltose utilization. The genes composing each of the two types of MAL clusters found in the W/S clade have disparate evolutionary histories, suggesting that they formed de novo. Both transporters and glucosidases were shown to be functional and additionally involved in the metabolization of other disaccharides, such as maltose and melezitose. In one Wickerhamiella species lacking the α-glucoside transporter, maltose assimilation is accomplished extracellularly, an attribute which has been rarely observed in fungi. Sucrose assimilation in Wickerhamiella generally escaped both glucose repression and the need for an activator and is thus essentially constitutive, which is consistent with the abundance of both glucose and sucrose in the floral niche. The notable plasticity associated with disaccharide utilization in the W/S clade is discussed in the context of ecological implications and energy metabolism. IMPORTANCE Microbes usually have flexible metabolic capabilities and are able to use different compounds to meet their needs. The yeasts belonging to the Wickerhamiella and Starmerella genera (forming the so-called W/S clade) are usually found in flowers or insects that visit flowers and are known for having acquired many genes from bacteria by a process called horizontal gene transfer. One such gene, dubbed SUC2, is used to assimilate sucrose, which is one of the most abundant sugars in floral nectar. Here, we show that different lineages within the W/S clade used different solutions for sucrose utilization that dispensed SUC2 and differed in their energy requirements, in their capacity to scavenge small amounts of sucrose from the environment, and in the potential for sharing this resource with other microbial species. We posit that this plasticity is possibly dictated by adaptation to the specific requirements of each species.}, }
@article {pmid35351585, year = {2022}, author = {Jaramillo, AVC and Cory, MB and Li, A and Kohli, RM and Wuest, WM}, title = {Exploration of inhibitors of the bacterial LexA repressor-protease.}, journal = {Bioorganic &amp; medicinal chemistry letters}, volume = {65}, number = {}, pages = {128702}, pmid = {35351585}, issn = {1464-3405}, support = {R01 GM127593/GM/NIGMS NIH HHS/United States ; R01 GM129325/GM/NIGMS NIH HHS/United States ; R35 GM119426/GM/NIGMS NIH HHS/United States ; F31 AI152459/AI/NIAID NIH HHS/United States ; T32 AI141393/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/metabolism ; Bacterial Proteins/metabolism ; Gene Expression Regulation, Bacterial ; *Peptide Hydrolases ; *SOS Response, Genetics ; Serine Endopeptidases/metabolism ; }, abstract = {Resistant and tolerant bacterial infections lead to billions in healthcare costs and cause hundreds of thousands of deaths each year. The bulk of current antibiotic research efforts focus on molecules which, although novel, are not immune from acquired resistance and seldomly affect tolerant populations. The bacterial SOS response has been implicated in several resistance and tolerance mechanisms, making it an attractive antibiotic target. Using small molecule inhibitors targeting a key step in the deployment of the SOS response, our approach focused on preventing the deployment of mechanisms such as biofilm formation, horizontal gene transfer, and error-prone DNA repair. Herein we report the synthesis and testing of analogs of a triazole-containing tricyclic inhibitor of LexA proteolysis, the key event in the SOS response. Our results hint that our inhibitor's may function by adopting a β-hairpin conformation, reminiscent of the native cleavage loop of LexA.}, }
@article {pmid35349073, year = {2022}, author = {Das, S and Bombaywala, S and Srivastava, S and Kapley, A and Dhodapkar, R and Dafale, NA}, title = {Genome plasticity as a paradigm of antibiotic resistance spread in ESKAPE pathogens.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {27}, pages = {40507-40519}, pmid = {35349073}, issn = {1614-7499}, mesh = {*Acinetobacter baumannii ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Drug Resistance, Microbial/genetics ; *Enterococcus faecium/genetics ; Gene Transfer, Horizontal ; Klebsiella pneumoniae ; }, abstract = {The major reason behind the spread of antibiotic resistance genes (ARGs) is persistent selective pressure in the environment encountered by bacteria. Genome plasticity plays a crucial role in dissemination of antibiotic resistance among bacterial pathogens. Mobile genetic elements harboring ARGs are reported to dodge bacterial immune system and mediate horizontal gene transfer (HGT) under selective pressure. Residual antibiotic pollutants develop selective pressures that force the bacteria to lose their defense mechanisms (CRISPR-cas) and acquire resistance. The present study targets the ESKAPE organisms (namely, Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.) causing various nosocomial infections and emerging multidrug-resistant species. The role of CRISPR-cas systems in inhibition of HGT in prokaryotes and its loss due to presence of various stressors in the environment is also focused in the study. IncF and IncH plasmids were identified in all strains of E. faecalis and K. pneumoniae, carrying Beta-lactam and fluoroquinolone resistance genes, whereas sal3, phiCTX, and SEN34 prophages harbored aminoglycoside resistance genes (aadA, aac). Various MGEs present in selected environmental niches that aid the bacterial genome plasticity and transfer of ARGs contributing to its spread are also identified.}, }
@article {pmid35348893, year = {2022}, author = {Li, W and Chen, S and Liu, Y and Wang, L and Jiang, J and Zhao, S and Fang, W and Chen, F and Guan, Z}, title = {Long-distance transport RNAs between rootstocks and scions and graft hybridization.}, journal = {Planta}, volume = {255}, number = {5}, pages = {96}, pmid = {35348893}, issn = {1432-2048}, support = {32030098//Key Programme/ ; }, mesh = {*Hybridization, Genetic ; *Phloem/genetics ; Plants/genetics ; RNA, Messenger/genetics ; RNA, Small Interfering ; }, abstract = {The present review addresses the advances of the identification methods, functions, and transportation mechanism of long-distance transport RNAs between rootstock and scion. In addition, we highlight the cognitive processes and potential mechanisms of graft hybridization. Phloem, the main transport channel of higher plants, plays an important role in the growth and development of plants. Numerous studies have identified a large number of RNAs, including mRNAs, miRNAs, siRNAs, and lncRNAs, in the plant phloem. They can not only be transported to long distances across the grafting junction in the phloem, but also act as signal molecules to regulate the growth, development, and stress resistance of remote cells or tissues, resulting in changes in the traits of rootstocks and scions. Many mobile RNAs have been discovered, but their detection methods, functions, and long-distance transport mechanisms remain to be elucidated. In addition, grafting hybridization, a phenomenon that has been questioned before, and which has an important role in selecting for superior traits, is gradually being recognized with the emergence of new evidence and the prevalence of horizontal gene transfer between parasitic plants. In this review, we outline the species, functions, identification methods, and potential mechanisms of long-distance transport RNAs between rootstocks and scions after grafting. In addition, we summarize the process of recognition and the potential mechanisms of graft hybridization. This study aimed to emphasize the role of grafting in the study of long-distance signals and selection for superior traits and to provide ideas and clues for further research on long-distance transport RNAs and graft hybridization.}, }
@article {pmid35347261, year = {2022}, author = {Yao, Y and Maddamsetti, R and Weiss, A and Ha, Y and Wang, T and Wang, S and You, L}, title = {Intra- and interpopulation transposition of mobile genetic elements driven by antibiotic selection.}, journal = {Nature ecology &amp; evolution}, volume = {6}, number = {5}, pages = {555-564}, pmid = {35347261}, issn = {2397-334X}, support = {R01 AI125604/AI/NIAID NIH HHS/United States ; R01 GM110494/GM/NIGMS NIH HHS/United States ; }, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; *Gene Transfer, Horizontal ; Interspersed Repetitive Sequences ; Plasmids/genetics ; }, abstract = {The spread of genes encoding antibiotic resistance is often mediated by horizontal gene transfer (HGT). Many of these genes are associated with transposons, a type of mobile genetic element that can translocate between the chromosome and plasmids. It is widely accepted that the translocation of antibiotic resistance genes onto plasmids potentiates their spread by HGT. However, it is unclear how this process is modulated by environmental factors, especially antibiotic treatment. To address this issue, we asked whether antibiotic exposure would select for the transposition of resistance genes from chromosomes onto plasmids and, if so, whether antibiotic concentration could tune the distribution of resistance genes between chromosomes and plasmids. We addressed these questions by analysing the transposition dynamics of synthetic and natural transposons that encode resistance to different antibiotics. We found that stronger antibiotic selection leads to a higher fraction of cells carrying the resistance on plasmids because the increased copy number of resistance genes on multicopy plasmids leads to higher expression of those genes and thus higher cell survival when facing antibiotic selection. Once they have transposed to plasmids, antibiotic resistance genes are primed for rapid spread by HGT. Our results provide quantitative evidence for a mechanism by which antibiotic selection accelerates the spread of antibiotic resistance in microbial communities.}, }
@article {pmid35347213, year = {2022}, author = {Nagy, S&#xc1; and Tóth, AG and Papp, M and Kaplan, S and Solymosi, N}, title = {Antimicrobial resistance determinants in silage.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {5243}, pmid = {35347213}, issn = {2045-2322}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Cattle ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Silage ; }, abstract = {Animal products may play a role in developing and spreading antimicrobial resistance in several ways. On the one hand, residues of antibiotics not adequately used in animal farming can enter the human body via food. However, resistant bacteria may also be present in animal products, which can transfer the antimicrobial resistance genes (ARG) to the bacteria in the consumer's body by horizontal gene transfer. As previous studies have shown that fermented foods have a meaningful ARG content, it is indicated that such genes may also be present in silage used as mass feed in the cattle sector. In our study, we aspired to answer what ARGs occur in silage and what mobility characteristics they have? For this purpose, we have analyzed bioinformatically 52 freely available deep sequenced silage samples from shotgun metagenome next-generation sequencing. A total of 16 perfect matched ARGs occurred 54 times in the samples. More than half of these ARGs are mobile because they can be linked to integrative mobile genetic elements, prophages or plasmids. Our results point to a neglected but substantial ARG source in the food chain.}, }
@article {pmid35347179, year = {2022}, author = {Caliandro, R and de Diego, I and Gomis-Rüth, FX}, title = {Crystal structure report of the ImmR transcriptional regulator DNA-binding domain of the Bacillus subtilis ICEBs1 transposon.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {5258}, pmid = {35347179}, issn = {2045-2322}, mesh = {*Bacillus subtilis/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; *Conjugation, Genetic ; DNA/metabolism ; Gene Transfer, Horizontal ; Humans ; }, abstract = {Bacillus subtilis is a commensal member of the human oral and gut microbiomes, which can become infectious to immunocompromised patients. It possesses a conjugative transposon, ICEBs1, which includes > 20 genes and can be passed by horizontal gene transfer to other bacteria, including pathogenic Bacillus anthracis and Listeria monocytogenes. ICEBs1 is regulated by the ImmR/ImmA tandem, which are a transcriptional repressor that constitutively blocks transcription and a metallopeptidase that acts as anti-repressor and inactivates ImmR by proteolytic cleavage. We here report the production and purification of 127-residue ImmR from ICEBs1 and the crystal structure of its DNA-binding domain. It features a five-helix bundle centred on a helix-turn-helix motif potentially binding the major grove of double-stranded target DNA. ImmR shows structural and mechanistic similarity with the B. subtilis SinR repressor, which is engaged in sporulation inhibition.}, }
@article {pmid35346363, year = {2022}, author = {Ghanam, J and Chetty, VK and Barthel, L and Reinhardt, D and Hoyer, PF and Thakur, BK}, title = {DNA in extracellular vesicles: from evolution to its current application in health and disease.}, journal = {Cell &amp; bioscience}, volume = {12}, number = {1}, pages = {37}, pmid = {35346363}, issn = {2045-3701}, support = {DKS 2018.17//Deutsche Kinderkrebsstiftung/ ; DFG D/106-21742//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Extracellular vesicle (EV) secretion is a highly conserved evolutionary trait in all organisms in the three domains of life. The packaging and release of EVs appears to be a bulk-flow process which takes place mainly under extreme conditions. EVs participate in horizontal gene transfer, which supports the survival of prokaryotic and eukaryotic microbes. In higher eukaryotes, almost all cells secrete a heterogeneous population of EVs loaded with various biomolecules. EV secretion is typically higher in cancer microenvironments, promoting tumor progression and metastasis. EVs are now recognized as additional mediators of autocrine and paracrine communication in health and disease. In this context, proteins and RNAs have been studied the most, but extracellular vesicle DNA (EV-DNA) has started to gain in importance in the last few years. In this review, we summarize new findings related to the loading mechanism(s), localization, and post-shedding function of EV-DNA. We also discuss the feasibility of using EV-DNA as a biomarker when performing a liquid biopsy, at the same time emphasizing the lack of data from clinical trials in this regard. Finally, we outline the potential of EV-DNA uptake and its interaction with the host genome as a promising tool for understanding the mechanisms of cancer evolution.}, }
@article {pmid35346038, year = {2022}, author = {Queffelec, J and Postma, A and Allison, JD and Slippers, B}, title = {Remnants of horizontal transfers of Wolbachia genes in a Wolbachia-free woodwasp.}, journal = {BMC ecology and evolution}, volume = {22}, number = {1}, pages = {36}, pmid = {35346038}, issn = {2730-7182}, mesh = {Animals ; *Nematoda ; *Pinus ; *Wasps/genetics ; *Wolbachia/genetics ; }, abstract = {BACKGROUND: Wolbachia is a bacterial endosymbiont of many arthropod and nematode species. Due to its capacity to alter host biology, Wolbachia plays an important role in arthropod and nematode ecology and evolution. Sirex noctilio is a woodwasp causing economic loss in pine plantations of the Southern Hemisphere. An investigation into the genome of this wasp revealed the presence of Wolbachia sequences. Due to the potential impact of Wolbachia on the populations of this wasp, as well as its potential use as a biological control agent against invasive insects, this discovery warranted investigation.<br><br>RESULTS: In this study we first investigated the presence of Wolbachia in S. noctilio and demonstrated that South African populations of the wasp are unlikely to be infected. We then screened the full genome of S. noctilio and found 12 Wolbachia pseudogenes. Most of these genes constitute building blocks of various transposable elements originating from the Wolbachia genome. Finally, we demonstrate that these genes are distributed in all South African populations of the wasp.<br><br>CONCLUSIONS: Our results provide evidence that S. noctilio might be compatible with a Wolbachia infection and that the bacteria could potentially be used in the future to regulate invasive populations of the wasp. Understanding the mechanisms that led to a loss of Wolbachia infection in S. noctilio could indicate which host species or host population should be sampled to find a Wolbachia strain that could be used as a biological control against S. noctilio.}, }
@article {pmid35344558, year = {2022}, author = {Ibarra-Chávez, R and Brady, A and Chen, J and Penadés, JR and Haag, AF}, title = {Phage-inducible chromosomal islands promote genetic variability by blocking phage reproduction and protecting transductants from phage lysis.}, journal = {PLoS genetics}, volume = {18}, number = {3}, pages = {e1010146}, pmid = {35344558}, issn = {1553-7404}, support = {MR/S00940X/1/MRC_/Medical Research Council/United Kingdom ; MR/V000772/1/MRC_/Medical Research Council/United Kingdom ; BB/V002376/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/M003876/1/MRC_/Medical Research Council/United Kingdom ; MR/S00940X/2/MRC_/Medical Research Council/United Kingdom ; BB/N002873/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 201531/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; BB/S003835/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteria/genetics ; *Bacteriophages/genetics ; Gene Transfer, Horizontal/genetics ; Genomic Islands/genetics ; Reproduction ; }, abstract = {Phage-inducible chromosomal islands (PICIs) are a widespread family of highly mobile genetic elements that disseminate virulence and toxin genes among bacterial populations. Since their life cycle involves induction by helper phages, they are important players in phage evolution and ecology. PICIs can interfere with the lifecycle of their helper phages at different stages resulting frequently in reduced phage production after infection of a PICI-containing strain. Since phage defense systems have been recently shown to be beneficial for the acquisition of exogenous DNA via horizontal gene transfer, we hypothesized that PICIs could provide a similar benefit to their hosts and tested the impact of PICIs in recipient strains on host cell viability, phage propagation and transfer of genetic material. Here we report an important role for PICIs in bacterial evolution by promoting the survival of phage-mediated transductants of chromosomal or plasmid DNA. The presence of PICIs generates favorable conditions for population diversification and the inheritance of genetic material being transferred, such as antibiotic resistance and virulence genes. Our results show that by interfering with phage reproduction, PICIs can protect the bacterial population from phage attack, increasing the overall survival of the bacterial population as well as the transduced cells. Moreover, our results also demonstrate that PICIs reduce the frequency of lysogenization after temperate phage infection, creating a more genetically diverse bacterial population with increased bet-hedging opportunities to adapt to new niches. In summary, our results identify a new role for the PICIs and highlight them as important drivers of bacterial evolution.}, }
@article {pmid35344092, year = {2022}, author = {Cardona, GI and Escobar, MC and Acosta-González, A and Marín, P and Marqués, S}, title = {Highly mercury-resistant strains from different Colombian Amazon ecosystems affected by artisanal gold mining activities.}, journal = {Applied microbiology and biotechnology}, volume = {106}, number = {7}, pages = {2775-2793}, pmid = {35344092}, issn = {1432-0614}, mesh = {Bacteria/genetics ; Colombia ; Ecosystem ; Gold ; Humans ; *Mercury/analysis ; Mining ; Soil ; }, abstract = {Two sites of the Colombian Amazon region with different levels of human intervention and mercury pollution were selected for the collection of samples of river and lake water, sediments, and associated forest soils. The Tarapacá region, affected mainly by barrage mining, showed low mercury concentrations, whilst in the Taraira region, affected by underground mining, there were several points with high mercury pollution levels. A collection of 72 bacterial and 10 yeast strains with different levels of mercury resistance was isolated and characterized. Most of the highly resistant bacterial strains (MIC > 40 mg L[-1] HgCl2) were isolated from soil and sediment samples and belonged to either Pseudomonas (60%) or Bacillus (20%). Most of highly resistant bacterial strains were positive for the presence of the merA gene, suggesting an active mercury resistance mechanism. This was confirmed in the two most resistant strains, Pseudomonas sp. TP30 and Burkholderia contaminans TR100 (MIC = 64 and 71 mg L[-1] HgCl2, respectively), which in the presence of increasing mercury concentrations expressed the merA gene at increasing levels, concomitant with a significant mercury reduction activity. Analysis of the MerA sequences present in the different isolates suggested a high gene conservation within the taxonomic groups but also several horizontal gene transfer events between taxonomically distant genera. We also observed a positive correspondence between the presence of the merA gene and the number of antibiotics to which the strains were resistant to. The most resistant strains are good candidates for future applications in the bioremediation of mercury-contaminated sites in the Amazon.Key points• Amazon sediments affected by underground gold mining have higher Hg levels.• Highly Hg-resistant isolates belonged to Pseudomonas and Bacillus genera.• TR100 and TP30 strains showed remediation potential to be used in the Amazon region.}, }
@article {pmid35343787, year = {2022}, author = {Boumasmoud, M and Dengler Haunreiter, V and Schweizer, TA and Meyer, L and Chakrakodi, B and Schreiber, PW and Seidl, K and Kühnert, D and Kouyos, RD and Zinkernagel, AS}, title = {Genomic Surveillance of Vancomycin-Resistant Enterococcus faecium Reveals Spread of a Linear Plasmid Conferring a Nutrient Utilization Advantage.}, journal = {mBio}, volume = {13}, number = {2}, pages = {e0377121}, pmid = {35343787}, issn = {2150-7511}, support = {Precision Medicine for Bacterial Infections//UZH, Clinical Research Priority Program/ ; 31003A_176252/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {*Enterococcus faecium/genetics ; Genomics ; *Gram-Positive Bacterial Infections/microbiology ; Humans ; Nutrients ; Plasmids/genetics ; Vancomycin/pharmacology ; *Vancomycin-Resistant Enterococci/genetics ; }, abstract = {Healthcare-associated outbreaks of vancomycin-resistant Enterococcus faecium (VREfm) are a worldwide problem with increasing prevalence. The genomic plasticity of this hospital-adapted pathogen contributes to its efficient spread despite infection control measures. Here, we aimed to identify the genomic and phenotypic determinants of health care-associated transmission of VREfm. We assessed the VREfm transmission networks at the tertiary-care University Hospital of Zurich (USZ) between October 2014 and February 2018 and investigated microevolutionary dynamics of this pathogen. We performed whole-genome sequencing for the 69 VREfm isolates collected during this time frame and assessed the population structure and variability of the vancomycin resistance transposon. Phylogenomic analysis allowed us to reconstruct transmission networks and to unveil external or wider transmission networks undetectable by routine surveillance. Notably, it unveiled a persistent clone, sampled 31 times over a 29-month period. Exploring the evolutionary dynamics of this clone and characterizing the phenotypic consequences revealed the spread of a variant with decreased daptomycin susceptibility and the acquired ability to utilize N-acetyl-galactosamine (GalNAc), one of the primary constituents of the human gut mucins. This nutrient utilization advantage was conferred by a novel plasmid, termed pELF_USZ, which exhibited a linear topology. This plasmid, which was harbored by two distinct clones, was transferable by conjugation. Overall, this work highlights the potential of combining epidemiological, functional genomic, and evolutionary perspectives to unveil adaptation strategies of VREfm. IMPORTANCE Sequencing microbial pathogens causing outbreaks has become a common practice to characterize transmission networks. In addition to the signal provided by vertical evolution, bacterial genomes harbor mobile genetic elements shared horizontally between clones. While macroevolutionary studies have revealed an important role of plasmids and genes encoding carbohydrate utilization systems in the adaptation of Enterococcus faecium to the hospital environment, mechanisms of dissemination and the specific function of many of these genetic determinants remain to be elucidated. Here, we characterize a plasmid providing a nutrient utilization advantage and show evidence for its clonal and horizontal spread at a local scale. Further studies integrating epidemiological, functional genomics, and evolutionary perspectives will be critical to identify changes shaping the success of this pathogen.}, }
@article {pmid35343419, year = {2022}, author = {Singh, NS and Singhal, N and Kumar, M and Virdi, JS}, title = {Public health implications of plasmid-mediated quinolone and aminoglycoside resistance genes in Escherichia coli inhabiting a major anthropogenic river of India.}, journal = {Epidemiology and infection}, volume = {150}, number = {}, pages = {1-21}, pmid = {35343419}, issn = {1469-4409}, abstract = {Presence of antimicrobial resistance (AMR) genes in Escherichia coli inhabiting anthropogenic rivers is an important public health concern because plasmid-mediated AMR genes can easily spread to other pathogens by horizontal gene transfer. Besides β-lactams, quinolones and aminoglycosides are the major antibiotics against E. coli. In the present study, we have investigated the presence of plasmid-mediated quinolone resistance (PMQR) and aminoglycoside resistance genes in E. coli isolated from a major river of northern India. Our results revealed that majority of the strains were phenotypically susceptible for fluoroquinolones and some aminoglycosides like amikacin, netilmicin, tobramycin and gentamicin. However, 16.39% of the strains were resistant for streptomycin, 8.19% for kanamycin and 3.30% for gentamicin. Of the various PMQR genes investigated, only qnrS1 was present in 24.59% of the strains along with ISEcl2. Aminoglycoside-resistance genes like strA-strB were found to be present in 16.39%, aphA1 in 8.19% and aacC2 in only 3.30% of the strains. Though, no co-relation was observed between phenotypic resistance for fluorquinolones and presence of PMQR genes, phenotypic resistance for streptomycin, kanamycin and gentamicin exactly co-related with the presence of the genes strA-strB, aphA1 and aacC2, respectively. Moreover, all the AMR genes discerned in aquatic E. coli were found to be situated on conjugative plasmids and, thus easily transferrable. Our study accentuates the importance of routine surveillance of urban rivers to curtail the spread of AMR genes in aquatic pathogens.}, }
@article {pmid35339358, year = {2023}, author = {Van Etten, J and Cho, CH and Yoon, HS and Bhattacharya, D}, title = {Extremophilic red algae as models for understanding adaptation to hostile environments and the evolution of eukaryotic life on the early earth.}, journal = {Seminars in cell &amp; developmental biology}, volume = {134}, number = {}, pages = {4-13}, doi = {10.1016/j.semcdb.2022.03.007}, pmid = {35339358}, issn = {1096-3634}, mesh = {Humans ; Eukaryota ; *Extremophiles/genetics ; *Rhodophyta/genetics ; Genome ; Soil ; Phylogeny ; }, abstract = {Extremophiles have always garnered great interest because of their exotic lifestyles and ability to thrive at the physical limits of life. In hot springs environments, the Cyanidiophyceae red algae are the only photosynthetic eukaryotes able to live under extremely low pH (0-5) and relatively high temperature (35ºC to 63ºC). These extremophiles live as biofilms in the springs, inhabit acid soils near the hot springs, and form endolithic populations in the surrounding rocks. Cyanidiophyceae represent a remarkable source of knowledge about the evolution of extremophilic lifestyles and their genomes encode specialized enzymes that have applied uses. Here we review the evolutionary origin, taxonomy, genome biology, industrial applications, and use of Cyanidiophyceae as genetic models. Currently, Cyanidiophyceae comprise a single order (Cyanidiales), three families, four genera, and nine species, including the well-known Cyanidioschyzon merolae and Galdieria sulphuraria. These algae have small, gene-rich genomes that are analogous to those of prokaryotes they live and compete with. There are few spliceosomal introns and evidence exists for horizontal gene transfer as a driver of local adaptation to gain access to external fixed carbon and to extrude toxic metals. Cyanidiophyceae offer a variety of commercial opportunities such as phytoremediation to detoxify contaminated soils or waters and exploitation of their mixotrophic lifestyles to support the efficient production of bioproducts such as phycocyanin and floridosides. In terms of exobiology, Cyanidiophyceae are an ideal model system for understanding the evolutionary effects of foreign gene acquisition and the interactions between different organisms inhabiting the same harsh environment on the early Earth. Finally, we describe ongoing research with C. merolae genetics and summarize the unique insights they offer to the understanding of algal biology and evolution.}, }
@article {pmid35338964, year = {2022}, author = {Wang, H and Gong, S and Li, X and Chong, Y and Ge, Q and Wang, J and Zhang, Y and Liu, Y and Jiao, X}, title = {SDS coated Fe3O4@MoS2 with NIR-enhanced photothermal-photodynamic therapy and antibiotic resistance gene dissemination inhibition functions.}, journal = {Colloids and surfaces. B, Biointerfaces}, volume = {214}, number = {}, pages = {112457}, doi = {10.1016/j.colsurfb.2022.112457}, pmid = {35338964}, issn = {1873-4367}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial ; Escherichia coli/genetics ; *Methicillin-Resistant Staphylococcus aureus ; Molybdenum/pharmacology ; *Nanocomposites ; *Photochemotherapy ; }, abstract = {Infection caused by antibiotic-resistant bacteria is serious threat for public health, and calls for novel antibacterial agents with versatile functions. In particular, nanomaterial is one of promising candidates to fight the increasing antibiotic resistance crisis. Here, we synthesized distinct Fe3O4@MoS2@SDS nanocomposites by ultrasonication assisted SDS coating on the Fe3O4@MoS2. Photothermal investigation indicated that the Fe3O4@MoS2@SDS showed excellent and stable photothermal performance and could be a NIR-induced photothermal reagent. It also displayed superior disinfection ability of Escherichia coli (E. coli), Methicillin-resistant Staphylococcus aureus (MRSA), and Pseudomonas aeruginosa (P. aeruginosa) and in vivo wound healing ability with the help of NIR irradiation. According to the results of electron paramagnetic resonance (EPR) and radical capture tests, plenty of superoxide, hydroxyl radicals, singlet oxygen and living cell reactive oxygen species can be observed under NIR irradiation. Besides, the synergistic effect Fe3O4@MoS2@SDS and NIR irradiation eradicated almost all the biofilms of MRSA, so this kind of function enhanced the disinfection ability of Fe3O4@MoS2@SDS under NIR irradiation. Furthermore, its inhibition effect on antibiotic resistance gene dissemination was also investigated. As expected, the Fe3O4@MoS2@SDS could efficiently and broadly block the horizontal transfer of antibiotic resistance genes which mediated by conjugative plasmids, and its blocking effect was better than that we have reported Fe3O4@MoS2. Overall, our findings revealed that the Fe3O4@MoS2@SDS could be a potential candidate for photothermal-photodynamic therapy and antibiotic resistance gene dissemination inhibition.}, }
@article {pmid35337880, year = {2022}, author = {Junaid, M and Siddiqui, JA and Sadaf, M and Liu, S and Wang, J}, title = {Enrichment and dissemination of bacterial pathogens by microplastics in the aquatic environment.}, journal = {The Science of the total environment}, volume = {830}, number = {}, pages = {154720}, doi = {10.1016/j.scitotenv.2022.154720}, pmid = {35337880}, issn = {1879-1026}, mesh = {Bacteria/genetics ; Ecosystem ; Humans ; *Microplastics/toxicity ; Plastics/toxicity ; Wastewater ; *Water Pollutants, Chemical/analysis/toxicity ; }, abstract = {Microplastic pollution and associated impacts in the aquatic environment are spreading at an alarming rate worldwide. Plastic waste is increasing in the environment, and microplastics (MPs) are becoming a growing issue because they serve as vectors for pathogen transmission. This is the first comprehensive review that specifically addresses MPs as a source and vector of pathogenic bacteria, mainly associated with genera Vibrio, Pseudomonas, Acinetobacter, and so on, which are discovered to be more abundant on the aquatic plastisphere than that in the surrounding wastewater, freshwater, and marine water ecosystems. The horizontal gene transfer, chemotaxis, and co-selection and cross-selection could be the potential mechanism involved in the enrichment and dissemination of bacterial pathogens through the aquatic plastisphere. Further, bacterial pathogens through aquatic plastisphere can cause various ecological and human health impacts such as disrupted food chain, oxidative stress, tissue damages, disease transmission, microbial dysbiosis, metabolic disorders, among others. Last but not least, future research directions are also described to find answers to the challenging questions about bacterial pathogens in the aquatic plastisphere to ensure the integrity and safety of ecological and human health.}, }
@article {pmid35336183, year = {2022}, author = {Van Wonterghem, L and De Chiara, M and Liti, G and Warringer, J and Farewell, A and Verstraeten, N and Michiels, J}, title = {Genome-Wide Association Study Reveals Host Factors Affecting Conjugation in Escherichia coli.}, journal = {Microorganisms}, volume = {10}, number = {3}, pages = {}, pmid = {35336183}, issn = {2076-2607}, support = {JPIAMR_2016_P006//TransPred/ ; C16/17/006//KU Leuven Research Council/ ; G0B0420N//Research Foundation Flanders/ ; }, abstract = {The emergence and dissemination of antibiotic resistance threaten the treatment of common bacterial infections. Resistance genes are often encoded on conjugative elements, which can be horizontally transferred to diverse bacteria. In order to delay conjugative transfer of resistance genes, more information is needed on the genetic determinants promoting conjugation. Here, we focus on which bacterial host factors in the donor assist transfer of conjugative plasmids. We introduced the broad-host-range plasmid pKJK10 into a diverse collection of 113 Escherichia coli strains and measured by flow cytometry how effectively each strain transfers its plasmid to a fixed E. coli recipient. Differences in conjugation efficiency of up to 2.7 and 3.8 orders of magnitude were observed after mating for 24 h and 48 h, respectively. These differences were linked to the underlying donor strain genetic variants in genome-wide association studies, thereby identifying candidate genes involved in conjugation. We confirmed the role of fliF, fliK, kefB and ucpA in the donor ability of conjugative elements by validating defects in the conjugation efficiency of the corresponding lab strain single-gene deletion mutants. Based on the known cellular functions of these genes, we suggest that the motility and the energy supply, the intracellular pH or salinity of the donor affect the efficiency of plasmid transfer. Overall, this work advances the search for targets for the development of conjugation inhibitors, which can be administered alongside antibiotics to more effectively treat bacterial infections.}, }
@article {pmid35336144, year = {2022}, author = {Miller, SR and Abresch, HE and Baroch, JJ and Fishman Miller, CK and Garber, AI and Oman, AR and Ulrich, NJ}, title = {Genomic and Functional Variation of the Chlorophyll d-Producing Cyanobacterium Acaryochloris marina.}, journal = {Microorganisms}, volume = {10}, number = {3}, pages = {}, pmid = {35336144}, issn = {2076-2607}, support = {NNA15BB04A/NASA/NASA/United States ; }, abstract = {The Chlorophyll d-producing cyanobacterium Acaryochloris marina is widely distributed in marine environments enriched in far-red light, but our understanding of its genomic and functional diversity is limited. Here, we take an integrative approach to investigate A. marina diversity for 37 strains, which includes twelve newly isolated strains from previously unsampled locations in Europe and the Pacific Northwest of North America. A genome-wide phylogeny revealed both that closely related A. marina have migrated within geographic regions and that distantly related A. marina lineages can co-occur. The distribution of traits mapped onto the phylogeny provided evidence of a dynamic evolutionary history of gene gain and loss during A. marina diversification. Ancestral genes that were differentially retained or lost by strains include plasmid-encoded sodium-transporting ATPase and bidirectional NiFe-hydrogenase genes that may be involved in salt tolerance and redox balance under fermentative conditions, respectively. The acquisition of genes by horizontal transfer has also played an important role in the evolution of new functions, such as nitrogen fixation. Together, our results resolve examples in which genome content and ecotypic variation for nutrient metabolism and environmental tolerance have diversified during the evolutionary history of this unusual photosynthetic bacterium.}, }
@article {pmid35334272, year = {2022}, author = {Liu, Y and Gao, J and Wang, Y and Duan, W and Zhang, Y and Zhang, H and Zhao, M}, title = {Synergistic effect of sulfidated nanoscale zerovalent iron in donor and recipient bacterial inactivation and gene conjugative transfer inhibition.}, journal = {Journal of hazardous materials}, volume = {432}, number = {}, pages = {128722}, doi = {10.1016/j.jhazmat.2022.128722}, pmid = {35334272}, issn = {1873-3336}, mesh = {*Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Iron/pharmacology ; }, abstract = {Antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) are widespread in urban wastewater treatment plants (UWTPs). In this research, a horizontal transfer model of recipient (Pseudomonas. HLS-6) and donor (Escherichia coli DH5α carries RP4 plasmid) was constructed to explore the effect of sulfidated nanoscale zerovalent iron (S-nZVI) on the efficiency of plasmid-mediated horizontal transfer. When the S/Fe was 0.1, the inactivation efficiency of 1120 mg/L S-nZVI on the donor and recipient bacteria were 2.36 ± 0.03 log and 3.50 ± 0.17 log after 30 min, respectively (initial ARB concentration ≈ 5 ×10[7] CFU/mL). Effects of treatment time, S/Fe molar ratio, S-nZVI dosage and initial bacterial concentration were systemically studied. S-nZVI treatment could increase the extracellular alkaline phosphatase and malondialdehyde content of the ARB, cause oxidative stress in the bacteria, destroy the cell structure and damage the intracellular DNA. This study provided evidence and insights into possible underlying mechanisms for reducing conjugative transfer, such as hindering cell membrane repair, inducing the overproduction of reactive oxygen species, inhibiting the SOS response, reducing the expression of ARGs and related transfer genes. S-nZVI could inhibit the gene conjugative transfer while inactivating the ARB. The findings provided an alternative method for controlling antibiotic resistance.}, }
@article {pmid35333546, year = {2022}, author = {Lara, YJ and McCann, A and Malherbe, C and François, C and Demoulin, CF and Sforna, MC and Eppe, G and De Pauw, E and Wilmotte, A and Jacques, P and Javaux, EJ}, title = {Characterization of the Halochromic Gloeocapsin Pigment, a Cyanobacterial Biosignature for Paleobiology and Astrobiology.}, journal = {Astrobiology}, volume = {22}, number = {6}, pages = {735-754}, doi = {10.1089/ast.2021.0061}, pmid = {35333546}, issn = {1557-8070}, mesh = {*Cyanobacteria/chemistry ; *Exobiology ; Pigments, Biological ; Spectroscopy, Fourier Transform Infrared ; Tandem Mass Spectrometry ; }, abstract = {Ultraviolet (UV)-screening compounds represent a substantial asset for the survival of cyanobacteria in extreme environments exposed to high doses of UV radiations on modern and early Earth. Among these molecules, the halochromic pigment gloeocapsin remains poorly characterized and studied. In this study, we identified a gloeocapsin-producing cultivable cyanobacteria: the strain Phormidesmis nigrescens ULC007. We succeeded to extract, to partially purify, and to compare the dark blue pigment from both the ULC007 culture and an environmental Gloeocapsa alpina dominated sample. FT-IR and Raman spectra of G. alpina and P. nigrescens ULC007 pigment extracts strongly suggested a common backbone structure. The high-pressure liquid chromatography-UV-MS/MS analysis of the ULC007 pigment extract allowed to narrow down the molecular formula of gloeocapsin to potentially five candidates within three classes of halochromic molecules: anthraquinone derivatives, coumarin derivatives, and flavonoids. With the discovery of gloeocapsin in P. nigrescens, the production of this pigment is now established for three lineages of cyanobacteria (including G. alpina, P. nigrescens, and Solentia paulocellulare) that belong to three distinct orders (Chroococcales, Pleurocapsales, Synechoccocales), inhabiting very diverse environments. This suggests that gloeocapsin production was a trait of their common ancestor or was acquired by lateral gene transfer. This work represents an important step toward the elucidation of the structure of this enigmatic pigment and its biosynthesis, and it potentially provides a new biosignature for ancient cyanobacteria. It also gives a glimpse on the evolution of UV protection strategies, which are relevant for early phototrophic life on Earth and possibly beyond.}, }
@article {pmid35333321, year = {2022}, author = {Morgado, S and Vicente, AC}, title = {Conjugative transfer of naturally occurring plasmid in Mycolicibacterium sp.}, journal = {FEMS microbiology letters}, volume = {369}, number = {1}, pages = {}, doi = {10.1093/femsle/fnac035}, pmid = {35333321}, issn = {1574-6968}, mesh = {Bacteria/genetics ; *Conjugation, Genetic ; Gene Transfer, Horizontal ; *Mycobacteriaceae/genetics ; Plasmids/genetics ; }, abstract = {Conjugation is considered the main horizontal gene transfer mechanism in bacterial adaptation and evolution. In the Mycobacteriaceae family, Mycolicibacterium smegmatis has been used as the model organism for the conjugative transfer of hybrid plasmids. However, the natural conjugation process in any bacteria would involve the transfer of naturally occurring plasmids. Currently, there is a gap in this regard about this abundant environmental genus of Mycobacteriaceae. Here, we performed conjugation experiments between wild Mycolicibacterium sp. strains involving naturally occurring plasmids, and interestingly, evidence of conjugative transfer was obtained. Thus, it is likely that conjugation occurs in Mycolicibacterium in the natural environment, representing a source of diversification and evolution in this genus of bacteria.}, }
@article {pmid35332832, year = {2022}, author = {Crits-Christoph, A and Hallowell, HA and Koutouvalis, K and Suez, J}, title = {Good microbes, bad genes? The dissemination of antimicrobial resistance in the human microbiome.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2055944}, pmid = {35332832}, issn = {1949-0984}, support = {DP5 OD029603/OD/NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Bacterial/genetics ; *Gastrointestinal Microbiome/genetics ; Genes, Bacterial ; Humans ; Metagenomics ; *Microbiota/genetics ; }, abstract = {A global rise in antimicrobial resistance among pathogenic bacteria has proved to be a major public health threat, with the rate of multidrug-resistant bacterial infections increasing over time. The gut microbiome has been studied as a reservoir of antibiotic resistance genes (ARGs) that can be transferred to bacterial pathogens via horizontal gene transfer (HGT) of conjugative plasmids and mobile genetic elements (the gut resistome). Advances in metagenomic sequencing have facilitated the identification of resistome modulators, including live microbial therapeutics such as probiotics and fecal microbiome transplantation that can either expand or reduce the abundances of ARG-carrying bacteria in the gut. While many different gut microbes encode for ARGs, they are not uniformly distributed across, or transmitted by, various members of the microbiome, and not all are of equal clinical relevance. Both experimental and theoretical approaches in microbial ecology have been applied to understand differing frequencies of ARG horizontal transfer between commensal microbes as well as between commensals and pathogens. In this commentary, we assess the evidence for the role of commensal gut microbes in encoding antimicrobial resistance genes, the degree to which they are shared both with other commensals and with pathogens, and the host and environmental factors that can impact resistome dynamics. We further discuss novel sequencing-based approaches for identifying ARGs and predicting future transfer events of clinically relevant ARGs from commensals to pathogens.}, }
@article {pmid35330209, year = {2022}, author = {Park, SH and Kyndt, JA and Brown, JK}, title = {Comparison of Auxenochlorella protothecoides and Chlorella spp. Chloroplast Genomes: Evidence for Endosymbiosis and Horizontal Virus-like Gene Transfer.}, journal = {Life (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, pmid = {35330209}, issn = {2075-1729}, support = {DE-EE0003046//United States Department of Energy/ ; DE-EE0006269//United States Department of Energy/ ; }, abstract = {Resequencing of the chloroplast genome (cpDNA) of Auxenochlorella protothecoides UTEX 25 was completed (GenBank Accession no. KC631634.1), revealing a genome size of 84,576 base pairs and 30.8% GC content, consistent with features reported for the previously sequenced A. protothecoides 0710, (GenBank Accession no. KC843975). The A. protothecoides UTEX 25 cpDNA encoded 78 predicted open reading frames, 32 tRNAs, and 4 rRNAs, making it smaller and more compact than the cpDNA genome of C. variabilis (124,579 bp) and C. vulgaris (150,613 bp). By comparison, the compact genome size of A. protothecoides was attributable primarily to a lower intergenic sequence content. The cpDNA coding regions of all known Chlorella species were found to be organized in conserved colinear blocks, with some rearrangements. The Auxenochlorella and Chlorella species genome structure and composition were similar, and of particular interest were genes influencing photosynthetic efficiency, i.e., chlorophyll synthesis and photosystem subunit I and II genes, consistent with other biofuel species of interest. Phylogenetic analysis revealed that Prototheca cutis is the closest known A. protothecoides relative, followed by members of the genus Chlorella. The cpDNA of A. protothecoides encodes 37 genes that are highly homologous to representative cyanobacteria species, including rrn16, rrn23, and psbA, corroborating a well-recognized symbiosis. Several putative coding regions were identified that shared high nucleotide sequence identity with virus-like sequences, suggestive of horizontal gene transfer. Despite these predictions, no corresponding transcripts were obtained by RT-PCR amplification, indicating they are unlikely to be expressed in the extant lineage.}, }
@article {pmid35328480, year = {2022}, author = {Chambon, L and Gillet, FX and Chieb, M and Cobessi, D and Pfannschmidt, T and Blanvillain, R}, title = {PAP8/pTAC6 Is Part of a Nuclear Protein Complex and Displays RNA Recognition Motifs of Viral Origin.}, journal = {International journal of molecular sciences}, volume = {23}, number = {6}, pages = {}, pmid = {35328480}, issn = {1422-0067}, support = {ANR-17-CE11-0031-02//Agence Nationale de la Recherche/ ; }, mesh = {*Arabidopsis/genetics/metabolism ; *Arabidopsis Proteins/genetics/metabolism ; Chloroplasts/metabolism ; DNA-Directed RNA Polymerases/genetics/metabolism ; Gene Expression Regulation, Plant ; Mutation ; Nuclear Proteins/genetics ; Plastids/metabolism ; RNA Recognition Motif ; }, abstract = {Chloroplast biogenesis depends on a complex transcriptional program involving coordinated expression of plastid and nuclear genes. In particular, photosynthesis-associated plastid genes are expressed by the plastid-encoded polymerase (PEP) that undergoes a structural rearrangement during chloroplast formation. The prokaryotic-type core enzyme is rebuilt into a larger complex by the addition of nuclear-encoded PEP-associated proteins (PAP1 to PAP12). Among the PAPs, some have been detected in the nucleus (PAP5 and PAP8), where they could serve a nuclear function required for efficient chloroplast biogenesis. Here, we detected PAP8 in a large nuclear subcomplex that may include other subunits of the plastid-encoded RNA polymerase. We have made use of PAP8 recombinant proteins in Arabidopsis thaliana to decouple its nucleus- and chloroplast-associated functions and found hypomorphic mutants pointing at essential amino acids. While the origin of the PAP8 gene remained elusive, we have found in its sequence a micro-homologous domain located within a large structural homology with a rhinoviral RNA-dependent RNA polymerase, highlighting potential RNA recognition motifs in PAP8. PAP8 in vitro RNA binding activity suggests that this domain is functional. Hence, we propose that the acquisition of PAPs may have occurred during evolution by different routes, including lateral gene transfer.}, }
@article {pmid35327291, year = {2022}, author = {Xu, W and Shen, P and Li, R and Liu, B and Yang, L}, title = {Development of an Event-Specific Droplet Digital PCR Assay for Quantification and Evaluation of the Transgene DNAs in Trace Samples of GM PRNP-Knockout Goat.}, journal = {Foods (Basel, Switzerland)}, volume = {11}, number = {6}, pages = {}, pmid = {35327291}, issn = {2304-8158}, support = {2016ZX08012-005//The Chinese National Transgenic Plant Special Funds/ ; No number//the Program for Professor of Special Appointment (Eastern Scholar) at Shanghai Institutions of Higher Learning/ ; }, abstract = {The prion protein (PRNP) gene encoding prion protein is considered a prerequisite for the occurrence of scrapie disease, and knockout of the PRNP gene in transgenic goat is one effective approach to avoid scrapie. This study aims to establish an event-specific droplet digital polymerase chain reaction (ddPCR) assay to detect and quantify the content of genetically modified (GM) PRNP-knockout goat event KoP1. The developed ddPCR assay presents high specificity, sensitivity, accuracy, precision and wide dynamic range. The limits of detection and quantification were as low as 1.44 and 7.2 haploid genome equivalent (HGE) per reaction, respectively. Furthermore, this assay was successfully applied in quantifying the goat KoP1 GM content in milk, feces and living environmental soil samples. We believe that the developed ddPCR assay has the potential to be used in the evaluation of horizontal gene transfer and the practical risk assessment of GM goat event KoP1 and its derivatives.}, }
@article {pmid35326376, year = {2022}, author = {Richard, E and Darracq, B and Loot, C and Mazel, D}, title = {Unbridled Integrons: A Matter of Host Factors.}, journal = {Cells}, volume = {11}, number = {6}, pages = {}, pmid = {35326376}, issn = {2073-4409}, support = {EQU202103012569//Fondation pour la Recherche M&#xe9;dicale/ ; ANR-17-CE13-0010-01//Agence Nationale de la Recherche/ ; ANR-10-LABX-62- IBEID//Agence Nationale de la Recherche/ ; UMR-3525//French National Centre for Scientific Research/ ; 024313//Institut Pasteur/ ; }, mesh = {Bacteria/genetics ; Drug Resistance, Microbial ; *Gene Transfer, Horizontal ; Integrases/genetics ; *Integrons/genetics ; }, abstract = {Integrons are powerful recombination systems found in bacteria, which act as platforms capable of capturing, stockpiling, excising and reordering mobile elements called cassettes. These dynamic genetic machineries confer a very high potential of adaptation to their host and have quickly found themselves at the forefront of antibiotic resistance, allowing for the quick emergence of multi-resistant phenotypes in a wide range of bacterial species. Part of the success of the integron is explained by its ability to integrate various environmental and biological signals in order to allow the host to respond to these optimally. In this review, we highlight the substantial interconnectivity that exists between integrons and their hosts and its importance to face changing environments. We list the factors influencing the expression of the cassettes, the expression of the integrase, and the various recombination reactions catalyzed by the integrase. The combination of all these host factors allows for a very tight regulation of the system at the cost of a limited ability to spread by horizontal gene transfer and function in remotely related hosts. Hence, we underline the important consequences these factors have on the evolution of integrons. Indeed, we propose that sedentary chromosomal integrons that were less connected or connected via more universal factors are those that have been more successful upon mobilization in mobile genetic structures, in contrast to those that were connected to species-specific host factors. Thus, the level of specificity of the involved host factors network may have been decisive for the transition from chromosomal integrons to the mobile integrons, which are now widespread. As such, integrons represent a perfect example of the conflicting relationship between the ability to control a biological system and its potential for transferability.}, }
@article {pmid35323968, year = {2022}, author = {Khedkar, S and Smyshlyaev, G and Letunic, I and Maistrenko, OM and Coelho, LP and Orakov, A and Forslund, SK and Hildebrand, F and Luetge, M and Schmidt, TSB and Barabas, O and Bork, P}, title = {Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes.}, journal = {Nucleic acids research}, volume = {50}, number = {6}, pages = {3155-3168}, pmid = {35323968}, issn = {1362-4962}, support = {BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Bacteria/genetics ; *Bacteriophages/genetics ; DNA Transposable Elements/genetics ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Phylogeny ; Recombinases/genetics ; }, abstract = {Prokaryotic Mobile Genetic Elements (MGEs) such as transposons, integrons, phages and plasmids, play important roles in prokaryotic evolution and in the dispersal of cargo functions like antibiotic resistance. However, each of these MGE types is usually annotated and analysed individually, hampering a global understanding of phylogenetic and environmental patterns of MGE dispersal. We thus developed a computational framework that captures diverse MGE types, their cargos and MGE-mediated horizontal transfer events, using recombinases as ubiquitous MGE marker genes and pangenome information for MGE boundary estimation. Applied to ∼84k genomes with habitat annotation, we mapped 2.8 million MGE-specific recombinases to six operational MGE types, which together contain on average 13% of all the genes in a genome. Transposable elements (TEs) dominated across all taxa (∼1.7 million occurrences), outnumbering phages and phage-like elements (<0.4 million). We recorded numerous MGE-mediated horizontal transfer events across diverse phyla and habitats involving all MGE types, disentangled and quantified the extent of hitchhiking of TEs (17%) and integrons (63%) with other MGE categories, and established TEs as dominant carriers of antibiotic resistance genes. We integrated all these findings into a resource (proMGE.embl.de), which should facilitate future studies on the large mobile part of genomes and its horizontal dispersal.}, }
@article {pmid35323025, year = {2022}, author = {Kittredge, HA and Dougherty, KM and Evans, SE}, title = {Dead but Not Forgotten: How Extracellular DNA, Moisture, and Space Modulate the Horizontal Transfer of Extracellular Antibiotic Resistance Genes in Soil.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {7}, pages = {e0228021}, pmid = {35323025}, issn = {1098-5336}, mesh = {*Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; DNA ; Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; Humans ; Soil ; Soil Microbiology ; Wastewater ; }, abstract = {Antibiotic-resistant bacteria and the spread of antibiotic resistance genes (ARGs) pose a serious risk to human and veterinary health. While many studies focus on the movement of live antibiotic-resistant bacteria to the environment, it is unclear whether extracellular ARGs (eARGs) from dead cells can transfer to live bacteria to facilitate the evolution of antibiotic resistance in nature. Here, we use eARGs from dead, antibiotic-resistant Pseudomonas stutzeri cells to track the movement of eARGs to live P. stutzeri cells via natural transformation, a mechanism of horizontal gene transfer involving the genomic integration of eARGs. In sterile, antibiotic-free agricultural soil, we manipulated the eARG concentration, soil moisture, and proximity to eARGs. We found that transformation occurred in soils inoculated with just 0.25 μg of eDNA g[-1] soil, indicating that even low concentrations of soil eDNA can facilitate transformation (previous estimates suggested ∼2 to 40 μg eDNA g[-1] soil). When eDNA was increased to 5 μg g[-1] soil, there was a 5-fold increase in the number of antibiotic-resistant P. stutzeri cells. We found that eARGs were transformed under soil moistures typical of terrestrial systems (5 to 30% gravimetric water content) but inhibited at very high soil moistures (>30%). Overall, this work demonstrates that dead bacteria and their eARGs are an overlooked path to antibiotic resistance. More generally, the spread of eARGs in antibiotic-free soil suggests that transformation allows genetic variants to establish in the absence of antibiotic selection and that the soil environment plays a critical role in regulating transformation. IMPORTANCE Bacterial death can release eARGs into the environment. Agricultural soils can contain upwards of 10[9] ARGs g[-1] soil, which may facilitate the movement of eARGs from dead to live bacteria through a mechanism of horizontal gene transfer called natural transformation. Here, we track the spread of eARGs from dead, antibiotic-resistant Pseudomonas stutzeri cells to live antibiotic-susceptible P. stutzeri cells in sterile agricultural soil. Transformation increased with the abundance of eARGs and occurred in soils ranging from 5 to 40% gravimetric soil moisture but was lowest in wet soils (>30%). Transformants appeared in soil after 24 h and persisted for up to 15 days even when eDNA concentrations were only a fraction of those found in field soils. Overall, our results show that natural transformation allows eARGs to spread and persist in antibiotic-free soils and that the biological activity of eDNA after bacterial death makes environmental eARGs a public health concern.}, }
@article {pmid35321661, year = {2022}, author = {Ueda, K and Kawahara, K and Kimoto, N and Yamaguchi, Y and Yamada, K and Oki, H and Yoshida, T and Matsuda, S and Matsumoto, Y and Motooka, D and Kawatsu, K and Iida, T and Nakamura, S and Ohkubo, T and Yonogi, S}, title = {Analysis of the complete genome sequences of Clostridium perfringens strains harbouring the binary enterotoxin BEC gene and comparative genomics of pCP13-like family plasmids.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {226}, pmid = {35321661}, issn = {1471-2164}, mesh = {*Clostridium perfringens/genetics ; *Enterotoxins/genetics ; Genome, Bacterial ; Genomics ; Phylogeny ; Plasmids/genetics ; }, abstract = {BACKGROUND: BEC-producing Clostridium perfringens is a causative agent of foodborne gastroenteritis. It was first reported in 2014, and since then, several isolates have been identified in Japan and the United Kingdom. The novel binary ADP-ribosylating toxin BEC, which consists of two components (BECa and BECb), is encoded on a plasmid that is similar to pCP13 and harbours a conjugation locus, called Pcp, encoding homologous proteins of the type 4 secretion system. Despite the high in vitro conjugation frequency of pCP13, its dissemination and that of related plasmids, including bec-harbouring plasmids, in the natural environment have not been characterised. This lack of knowledge has limited our understanding of the genomic epidemiology of bec-harbouring C. perfringens strains.<br><br>RESULTS: In this study, we determined the complete genome sequences of five bec-harbouring C. perfringens strains isolated from 2009 to 2019. Each isolate contains a&#x2009;~&#x2009;3.36 Mbp chromosome and 1-3 plasmids of either the pCW3-like family, pCP13-like family, or an unknown family, and the bec-encoding region in all five isolates was located on a&#x2009;~&#x2009;54 kbp pCP13-like plasmid. Phylogenetic and SNP analyses of these complete genome sequences and the 211 assembled C. perfringens genomes in GenBank showed that although these bec-harbouring strains were split into two phylogenetic clades, the sequences of the bec-encoding plasmids were nearly identical (>99.81%), with a significantly smaller SNP accumulation rate than that of their chromosomes. Given that the Pcp locus is conserved in these pCP13-like plasmids, we propose a mechanism in which the plasmids were disseminated by horizontal gene transfer. Data mining showed that strains carrying pCP13-like family plasmids were unexpectedly common (58/216 strains) and widely disseminated among the various C. perfringens clades. Although these plasmids possess a conserved Pcp locus, their 'accessory regions' can accommodate a wide variety of genes, including virulence-associated genes, such as becA/becB and cbp2. These results suggest that this family of plasmids can integrate various foreign genes and is transmissible among C. perfringens strains.<br><br>CONCLUSION: This study demonstrates the potential significance of pCP13-like plasmids, including bec-encoding plasmids, for the characterisation and monitoring of the dissemination of pathogenic C. perfringens strains.}, }
@article {pmid35321311, year = {2022}, author = {Marti, H and Suchland, RJ and Rockey, DD}, title = {The Impact of Lateral Gene Transfer in Chlamydia.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {861899}, pmid = {35321311}, issn = {2235-2988}, mesh = {Animals ; *Chlamydia/genetics ; Chlamydia trachomatis/genetics ; *Gene Transfer, Horizontal ; Tetracycline Resistance/genetics ; }, abstract = {Lateral gene transfer (LGT) facilitates many processes in bacterial ecology and pathogenesis, especially regarding pathogen evolution and the spread of antibiotic resistance across species. The obligate intracellular chlamydiae, which cause a range of diseases in humans and animals, were historically thought to be highly deficient in this process. However, research over the past few decades has demonstrated that this was not the case. The first reports of homologous recombination in the Chlamydiaceae family were published in the early 1990s. Later, the advent of whole-genome sequencing uncovered clear evidence for LGT in the evolution of the Chlamydiaceae, although the acquisition of tetracycline resistance in Chlamydia (C.) suis is the only recent instance of interphylum LGT. In contrast, genome and in vitro studies have shown that intraspecies DNA exchange occurs frequently and can even cross species barriers between closely related chlamydiae, such as between C. trachomatis, C. muridarum, and C. suis. Additionally, whole-genome analysis led to the identification of various DNA repair and recombination systems in C. trachomatis, but the exact machinery of DNA uptake and homologous recombination in the chlamydiae has yet to be fully elucidated. Here, we reviewed the current state of knowledge concerning LGT in Chlamydia by focusing on the effect of homologous recombination on the chlamydial genome, the recombination machinery, and its potential as a genetic tool for Chlamydia.}, }
@article {pmid35321080, year = {2022}, author = {Tawfick, MM and Elshamy, AA and Mohamed, KT and El Menofy, NG}, title = {Gut Commensal Escherichia coli, a High-Risk Reservoir of Transferable Plasmid-Mediated Antimicrobial Resistance Traits.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {1077-1091}, pmid = {35321080}, issn = {1178-6973}, abstract = {BACKGROUND: Escherichia coli (E. coli), the main human gut microorganism, is one of the evolved superbugs because of acquiring antimicrobial resistance (AMR) determinants via horizontal gene transfer (HGT).<br><br>PURPOSE: This study aimed to screen isolates of gut commensal E. coli from healthy adult individuals for antimicrobial susceptibility and plasmid-mediated AMR encoding genes.<br><br>METHODS: Gut commensal E. coli bacteria were isolated from fecal samples that were taken from healthy adult individuals and investigated phenotypically for their antimicrobial susceptibility against diverse classes of antimicrobials using the Kirby Bauer disc method. PCR-based molecular assays were carried out to detect diverse plasmid-carried AMR encoding genes and virulence genes of different E. coli pathotypes (eaeA, stx, ipaH, est, elt, aggR and pCVD432). The examined AMR genes were &#x3b2;-lactam resistance encoding genes (bla CTX-M1, bla TEM, bla CMY-2), tetracycline resistance encoding genes (tetA, tetB), sulfonamides resistance encoding genes (sul1, sulII), aminoglycoside resistance encoding genes (aac(3)-II, aac(6')-Ib-cr) and quinolones resistance encoding genes (qnrA, qnrB, qnrS).<br><br>RESULTS: PCR results revealed the absence of pathotypes genes in 56 isolates that were considered gut commensal isolates. E. coli isolates showed high resistance rates against tested antimicrobial agents belonging to both &#x3b2;-lactams and sulfonamides (42/56, 75%) followed by quinolones (35/56, 62.5%), tetracyclines (31/56, 55.4%), while the lowest resistance rate was to aminoglycosides (24/56, 42.9%). Antimicrobial susceptibility profiles revealed that 64.3% of isolates were multidrug-resistant (MDR). High prevalence frequencies of plasmid-carried AMR genes were detected including bla TEM (64%) sulI (60.7%), qnrA (51.8%), aac(3)-II (37.5%), and tetA (46.4%). All isolates harbored more than one gene with the most frequent genetic profile among isolates was bla TEM-bla CTX-M1-like-qnrA-qnrB-tetA-sulI.<br><br>CONCLUSION: Results are significant in the evaluation of plasmid-carried AMR genes in the human gut commensal E. coli, suggesting a potential human health risk and the necessity of strict regulation of the use of antibiotics in Egypt. Commensal E. coli bacteria may constitute a potential reservoir of AMR genes that can be transferred to other bacterial species.}, }
@article {pmid35318523, year = {2022}, author = {Zhang, S and Wang, S and Fang, Z and Lang, BF and Zhang, YJ}, title = {Characterization of the mitogenome of Gongronella sp. w5 reveals substantial variation in Mucoromycota.}, journal = {Applied microbiology and biotechnology}, volume = {106}, number = {7}, pages = {2587-2601}, pmid = {35318523}, issn = {1432-0614}, support = {31872162//National Natural Science Foundation of China/ ; }, mesh = {Gene Order ; Genes, Mitochondrial ; *Genome, Mitochondrial ; *Mucorales ; Phylogeny ; }, abstract = {Gongronella is a genus of fungi in Mucorales (Mucoromycota). Some of its members have important biotechnological applications, but until now, not a single mitogenome has been characterized in Gongronella. Here, we present the complete mitogenome assembly of Gongronella sp. w5, a soil isolate known to interact with plants and several fungi. Its 36,593-bp circular mitogenome encodes the large and small subunit rRNAs, 14 standard mitochondrial proteins, 24 tRNAs, three free-standing ORF proteins, and the RNA subunit of RNase P (rnpB). These genes arrange in an order novel to known fungal mitogenomes. Three group I introns are present in the cob, cox1, and nad5 genes, respectively, and they are probably acquired by horizontal gene transfer. Phylogenetic analysis based on mitochondrion-encoded proteins supports the grouping of Gongronella sp. w5 with Absidia glauca, forming the Cunninghamellaceae clade within Mucoromycota. Gongronella and most other Mucoromycota species are predicted to use the standard genetic code in mitochondrial translation, rather than code 4 assigned by GenBank. A comparison among seven publicly available mitogenomes in Mucoromycota reveals the presence of the same 14 typical protein-coding genes plus rnpB, yet substantial variation in mitogenome size, intron number, gene order, and orientation. In this comparison, the uniqueness of Gongronella is evident from similarly large differences to its closest phylogenetic neighbor, A. glauca. This study promotes our understanding of fungal evolution in Mucoromycota. KEY POINTS: • This study reports the first mitogenome in Gongronella, which presents a novel gene order. • Different Mucoromycota mitogenomes show substantial variation of gene organizations. • Most Mucoromycota species use the standard genetic code to translate mitochondrial genes.}, }
@article {pmid35314402, year = {2022}, author = {Abdoulaye, AH and Jia, J and Abbas, A and Hai, D and Cheng, J and Fu, Y and Lin, Y and Jiang, D and Xie, J}, title = {Fusarivirus accessory helicases present an evolutionary link for viruses infecting plants and fungi.}, journal = {Virologica Sinica}, volume = {37}, number = {3}, pages = {427-436}, pmid = {35314402}, issn = {1995-820X}, mesh = {*Fungal Viruses/genetics ; Genome, Viral ; Open Reading Frames ; Phylogeny ; Plants ; *RNA Viruses/genetics ; RNA, Viral/genetics ; RNA-Dependent RNA Polymerase/genetics ; Rhizoctonia/genetics ; }, abstract = {A significant number of mycoviruses have been identified that are related to plant viruses, but their evolutionary relationships are largely unexplored. A fusarivirus, Rhizoctonia solani fusarivirus 4 (RsFV4), was identified in phytopathogenic fungus Rhizoctonia solani (R. solani) strain XY74 co-infected by an alphaendornavirus. RsFV4 had a genome of 10,833 nt (excluding the poly-A tail), and consisted of four non-overlapping open reading frames (ORFs). ORF1 encodes an 825 aa protein containing a conserved helicase domain (Hel1). ORF3 encodes 1550 aa protein with two conserved domains, namely an RNA-dependent RNA polymerase (RdRp) and another helicase (Hel2). The ORF2 and ORF4 likely encode two hypothetical proteins (520 and 542 aa) with unknown functions. The phylogenetic analysis based on Hel2 and RdRp suggest that RsFV4 was positioned within the fusarivirus group, but formed an independent branch with three previously reported fusariviruses of R. solani. Notably, the Hel1 and its relatives were phylogenetically closer to helicases of potyviruses and hypoviruses than fusariviruses, suggesting fusarivirus Hel1 formed an evolutionary link between these three virus groups. This finding provides evidence of the occurrence of a horizontal gene transfer or recombination event between mycoviruses and plant viruses or between mycoviruses. Our findings are likely to enhance the understanding of virus evolution and diversity.}, }
@article {pmid35311576, year = {2022}, author = {Leclerc, QJ and Wildfire, J and Gupta, A and Lindsay, JA and Knight, GM}, title = {Growth-Dependent Predation and Generalized Transduction of Antimicrobial Resistance by Bacteriophage.}, journal = {mSystems}, volume = {7}, number = {2}, pages = {e0013522}, pmid = {35311576}, issn = {2379-5077}, support = {MR/P014658/1//Medical Research Council/United Kingdom ; MR/P028322/1//Medical Research Council/United Kingdom ; MR/N013638/1//UKRI | Medical Research Council (MRC)/ ; }, mesh = {Animals ; *Bacteriophages ; Anti-Bacterial Agents/pharmacology ; *Methicillin-Resistant Staphylococcus aureus ; Predatory Behavior ; Drug Resistance, Bacterial ; }, abstract = {Bacteriophage (phage) are both predators and evolutionary drivers for bacteria, notably contributing to the spread of antimicrobial resistance (AMR) genes by generalized transduction. Our current understanding of this complex relationship is limited. We used an interdisciplinary approach to quantify how these interacting dynamics can lead to the evolution of multidrug-resistant bacteria. We cocultured two strains of methicillin-resistant Staphylococcus aureus, each harboring a different antibiotic resistance gene, with generalized transducing phage. After a growth phase of 8 h, bacteria and phage surprisingly coexisted at a stable equilibrium in our culture, the level of which was dependent on the starting concentration of phage. We detected double-resistant bacteria as early as 7 h, indicating that transduction of AMR genes had occurred. We developed multiple mathematical models of the bacteria and phage relationship and found that phage-bacteria dynamics were best captured by a model in which phage burst size decreases as the bacteria population reaches stationary phase and where phage predation is frequency-dependent. We estimated that one in every 10[8] new phage generated was a transducing phage carrying an AMR gene and that double-resistant bacteria were always predominantly generated by transduction rather than by growth. Our results suggest a shift in how we understand and model phage-bacteria dynamics. Although rates of generalized transduction could be interpreted as too rare to be significant, they are sufficient in our system to consistently lead to the evolution of multidrug-resistant bacteria. Currently, the potential of phage to contribute to the growing burden of AMR is likely underestimated. IMPORTANCE Bacteriophage (phage), viruses that can infect and kill bacteria, are being investigated through phage therapy as a potential solution to the threat of antimicrobial resistance (AMR). In reality, however, phage are also natural drivers of bacterial evolution by transduction when they accidentally carry nonphage DNA between bacteria. Using laboratory work and mathematical models, we show that transduction leads to evolution of multidrug-resistant bacteria in less than 8 h and that phage production decreases when bacterial growth decreases, allowing bacteria and phage to coexist at stable equilibria. The joint dynamics of phage predation and transduction lead to complex interactions with bacteria, which must be clarified to prevent phage from contributing to the spread of AMR.}, }
@article {pmid35311569, year = {2022}, author = {Tuttle, MJ and May, FS and Basso, JTR and Gann, ER and Xu, J and Buchan, A}, title = {Plasmid-Mediated Stabilization of Prophages.}, journal = {mSphere}, volume = {7}, number = {2}, pages = {e0093021}, pmid = {35311569}, issn = {2379-5042}, mesh = {*Bacteriophages/genetics ; Ecosystem ; Plasmids/genetics ; Prophages/genetics ; *Rhodobacteraceae/genetics ; }, abstract = {Mobile genetic elements (MGEs) drive bacterial evolution, alter gene availability within microbial communities, and facilitate adaptation to ecological niches. In natural systems, bacteria simultaneously possess or encounter multiple MGEs, yet their combined influences on microbial communities are poorly understood. Here, we investigate interactions among MGEs in the marine bacterium Sulfitobacter pontiacus. Two related strains, CB-D and CB-A, each harbor a single prophage. These prophages share high sequence identity with one another and an integration site within the host genome, yet these strains exhibit differences in "spontaneous" prophage induction (SPI) and consequent fitness. To better understand mechanisms underlying variation in SPI between these lysogens, we closed their genomes, which revealed that in addition to harboring different prophage genotypes, CB-A lacks two of the four large, low-copy-number plasmids possessed by CB-D. To assess the relative roles of plasmid content versus prophage genotype on host physiology, a panel of derivative strains varying in MGE content were generated. Characterization of these derivatives revealed a robust link between plasmid content and SPI, regardless of prophage genotype. Strains possessing all four plasmids had undetectable phage in cell-free lysates, while strains lacking either one plasmid (pSpoCB-1) or a combination of two plasmids (pSpoCB-2 and pSpoCB-4) produced high (>10[5] PFU/mL) phage titers. Homologous plasmid sequences were identified in related bacteria, and plasmid and phage genes were found to be widespread in Tara Oceans metagenomic data sets. This suggests that plasmid-dependent stabilization of prophages may be commonplace throughout the oceans. IMPORTANCE The consequences of prophage induction on the physiology of microbial populations are varied and include enhanced biofilm formation, conferral of virulence, and increased opportunity for horizontal gene transfer. These traits lead to competitive advantages for lysogenized bacteria and influence bacterial lifestyles in a variety of niches. However, biological controls of "spontaneous" prophage induction, the initiation of phage replication and phage-mediated cell lysis without an overt stressor, are not well understood. In this study, we observed a novel interaction between plasmids and prophages in the marine bacterium Sulfitobacter pontiacus. We found that loss of one or more distinct plasmids-which we show carry genes ubiquitous in the world's oceans-resulted in a marked increase in prophage induction within lysogenized strains. These results demonstrate cross talk between different mobile genetic elements and have implications for our understanding of the lysogenic-lytic switches of prophages found not only in marine environments, but throughout all ecosystems.}, }
@article {pmid35311568, year = {2022}, author = {Große, C and Grau, J and Große, I and Nies, DH}, title = {Importance of RpoD- and Non-RpoD-Dependent Expression of Horizontally Acquired Genes in Cupriavidus metallidurans.}, journal = {Microbiology spectrum}, volume = {10}, number = {2}, pages = {e0012122}, pmid = {35311568}, issn = {2165-0497}, mesh = {Bacterial Proteins/genetics/metabolism ; *Cupriavidus/genetics/metabolism ; Hydrogen/metabolism ; Metals/metabolism ; *Sigma Factor/metabolism ; }, abstract = {The genome of the metal-resistant, hydrogen-oxidizing bacterium Cupriavidus metallidurans contains a large number of horizontally acquired plasmids and genomic islands that were integrated into its chromosome or chromid. For the C. metallidurans CH34 wild-type strain growing under nonchallenging conditions, 5,763 transcriptional starting sequences (TSSs) were determined. Using a custom-built motif discovery software based on hidden Markov models, patterns upstream of the TSSs were identified. The pattern TTGACA, -35.6 ± 1.6 bp upstream of the TSSs, in combination with a TATAAT sequence 15.8 ± 1.4 bp upstream occurred frequently, especially upstream of the TSSs for 48 housekeeping genes, and these were assigned to promoters used by RNA polymerase containing the main housekeeping sigma factor RpoD. From patterns upstream of the housekeeping genes, a score for RpoD-dependent promoters in C. metallidurans was derived and applied to all 5,763 TSSs. Among these, 2,572 TSSs could be associated with RpoD with high probability, 373 with low probability, and 2,818 with no probability. In a detailed analysis of horizontally acquired genes involved in metal resistance and not involved in this process, the TSSs responsible for the expression of these genes under nonchallenging conditions were assigned to RpoD- or non-RpoD-dependent promoters. RpoD-dependent promoters occurred frequently in horizontally acquired metal resistance and other determinants, which should allow their initial expression in a new host. However, other sigma factors and sense/antisense effects also contribute-maybe to mold in subsequent adaptation steps the assimilated gene into the regulatory network of the cell. IMPORTANCE In their natural environment, bacteria are constantly acquiring genes by horizontal gene transfer. To be of any benefit, these genes should be expressed. We show here that the main housekeeping sigma factor RpoD plays an important role in the expression of horizontally acquired genes in the metal-resistant hydrogen-oxidizing bacterium C. metallidurans. By conservation of the RpoD recognition consensus sequence, a newly arriving gene has a high probability to be expressed in the new host cell. In addition to integrons and genes travelling together with that for their sigma factor, conservation of the RpoD consensus sequence may be an important contributor to the overall evolutionary success of horizontal gene transfer in bacteria. Using C. metallidurans as an example, this publication sheds some light on the fate and function of horizontally acquired genes in bacteria.}, }
@article {pmid35311538, year = {2022}, author = {Donner, L and Staley, ZR and Petali, J and Sangster, J and Li, X and Mathews, W and Snow, D and Howe, A and Soupir, M and Bartelt-Hunt, S}, title = {The Human Health Implications of Antibiotic Resistance in Environmental Isolates from Two Nebraska Watersheds.}, journal = {Microbiology spectrum}, volume = {10}, number = {2}, pages = {e0208221}, pmid = {35311538}, issn = {2165-0497}, support = {P20 GM103427/GM/NIGMS NIH HHS/United States ; P30 CA036727/CA/NCI NIH HHS/United States ; P30 GM110768/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Bacterial/genetics ; *Genes, Bacterial/genetics ; Humans ; Nebraska ; *Wastewater ; Water ; }, abstract = {One Health field-based approaches are needed to connect the occurrence of antibiotics present in the environment with the presence of antibiotic resistance genes (ARGs) in Gram-negative bacteria that confer resistance to antibiotics important in for both veterinary and human health. Water samples from two Nebraska watersheds influenced by wastewater effluent and agricultural runoff were tested for the presence of antibiotics used in veterinary and human medicine. The water samples were also cultured to identify the bacteria present. Of those bacteria isolated, the Gram-negative rods capable of causing human infections had antimicrobial susceptibility testing and whole-genome sequencing (WGS) performed to identify ARGs present. Of the 211 bacterial isolates identified, 37 belonged to pathogenic genera known to cause human infections. Genes conferring resistance to beta-lactams, aminoglycosides, fosfomycins, and quinolones were the most frequently detected ARGs associated with horizontal gene transfer (HGT) in the watersheds. WGS also suggest recent HGT events involving ARGs transferred between watershed isolates and bacteria of human and animal origins. The results of this study demonstrate the linkage of antibiotics and bacterial ARGs present in the environment with potential human and/or veterinary health impacts. IMPORTANCE One health is a transdisciplinary approach to achieve optimal health for humans, animals, plants and their shared environment, recognizing the interconnected nature of health in these domains. Field based research is needed to connect the occurrence of antibiotics used in veterinary medicine and human health with the presence of antibiotic resistance genes (ARGs). In this study, the presence of antibiotics, bacteria and ARGs was determined in two watersheds in Nebraska, one with agricultural inputs and the other with both agricultural and wastewater inputs. The results presented in this study provide evidence of transfer of highly mobile ARG between environment, clinical, and animal-associated bacteria.}, }
@article {pmid35306411, year = {2022}, author = {Xin, K and Chen, X and Zhang, Z and Zhang, Z and Pang, H and Yang, J and Jiang, H and Lu, J}, title = {Trace antibiotics increase the risk of antibiotic resistance genes transmission by regulating the biofilm extracellular polymeric substances and microbial community in the sewer.}, journal = {Journal of hazardous materials}, volume = {432}, number = {}, pages = {128634}, doi = {10.1016/j.jhazmat.2022.128634}, pmid = {35306411}, issn = {1873-3336}, mesh = {Anti-Bacterial Agents/pharmacology ; Biofilms ; Drug Resistance, Microbial/genetics ; *Extracellular Polymeric Substance Matrix ; Genes, Bacterial ; *Microbiota ; Sulfamethoxazole ; Tetracycline/pharmacology ; Wastewater ; }, abstract = {Sewer is considered a potential hotspot for antibiotic resistance, but the occurrence and proliferation of antibiotic resistance genes (ARGs) under trace antibiotics exposure have received little attention. This work evaluated the effects of tetracycline (TC) and sulfamethoxazole (SMX) individually and in combination in the sewer system and revealed the related mechanisms of ARG proliferation. The relative abundance of tetA and sul1 increased the most under TC and SMX stress, respectively, whereas sul1 increased the most under combined stress. Intl1 was abundant in both the liquid phase and the biofilm, and redundancy analysis confirmed that horizontal gene transfer was the main reason for the proliferation of ARGs. The increase in extracellular polymeric substances (EPS) secretion and the enhancement of the main hydrophobic functional groups facilitated the accumulation of biofilms, which promoted the proliferation of ARGs in biofilms. The relative abundance of most ARGs in the liquid phase was significantly correlated with EPS, protein and tryptophan-like substances. Furthermore, the microbial community structure and diversity affected the proliferation and spread of ARGs in the sewer. These findings contribute to our further understanding of the proliferation and development of ARGs in the sewer and lay the foundation for the front-end control of ARGs.}, }
@article {pmid35301310, year = {2022}, author = {Forster, SC and Liu, J and Kumar, N and Gulliver, EL and Gould, JA and Escobar-Zepeda, A and Mkandawire, T and Pike, LJ and Shao, Y and Stares, MD and Browne, HP and Neville, BA and Lawley, TD}, title = {Strain-level characterization of broad host range mobile genetic elements transferring antibiotic resistance from the human microbiome.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {1445}, pmid = {35301310}, issn = {2041-1723}, support = {/WT_/Wellcome Trust/United Kingdom ; 206194/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Host Specificity/genetics ; Humans ; Interspersed Repetitive Sequences/genetics ; *Microbiota/genetics ; }, abstract = {Mobile genetic elements (MGEs) carrying antibiotic resistance genes (ARGs) disseminate ARGs when they mobilise into new bacterial hosts. The nature of such horizontal gene transfer (HGT) events between human gut commensals and pathogens remain poorly characterised. Here, we compare 1354 cultured commensal strains (540 species) to 45,403 pathogen strains (12 species) and find 64,188 MGE-mediated ARG transfer events between the two groups using established methods. Among the 5931 MGEs, we find 15 broad host range elements predicted to have crossed different bacterial phyla while also occurring in animal and environmental microbiomes. We experimentally demonstrate that predicted broad host range MGEs can mobilise from commensals Dorea longicatena and Hungatella hathewayi to pathogen Klebsiella oxytoca, crossing phyla simultaneously. Our work establishes the MGE-mediated ARG dissemination network between human gut commensals and pathogens and highlights broad host range MGEs as targets for future ARG dissemination management.}, }
@article {pmid35300489, year = {2022}, author = {Huang, CT and Cho, ST and Lin, YC and Tan, CM and Chiu, YC and Yang, JY and Kuo, CH}, title = {Comparative Genome Analysis of 'Candidatus Phytoplasma luffae' Reveals the Influential Roles of Potential Mobile Units in Phytoplasma Evolution.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {773608}, pmid = {35300489}, issn = {1664-302X}, abstract = {Phytoplasmas are insect-transmitted plant pathogens that cause substantial losses in agriculture. In addition to economic impact, phytoplasmas induce distinct disease symptoms in infected plants, thus attracting attention for research on molecular plant-microbe interactions and plant developmental processes. Due to the difficulty of establishing an axenic culture of these bacteria, culture-independent genome characterization is a crucial tool for phytoplasma research. However, phytoplasma genomes have strong nucleotide composition biases and are repetitive, which make it challenging to produce complete assemblies. In this study, we utilized Illumina and Oxford Nanopore sequencing technologies to obtain the complete genome sequence of 'Candidatus Phytoplasma luffae' strain NCHU2019 that is associated with witches' broom disease of loofah (Luffa aegyptiaca) in Taiwan. The fully assembled circular chromosome is 769 kb in size and is the first representative genome sequence of group 16SrVIII phytoplasmas. Comparative analysis with other phytoplasmas revealed that NCHU2019 has a remarkably repetitive genome, possessing a pair of 75 kb repeats and at least 13 potential mobile units (PMUs) that account for ∼25% of its chromosome. This level of genome repetitiveness is exceptional for bacteria, particularly among obligate pathogens with reduced genomes. Our genus-level analysis of PMUs demonstrated that these phytoplasma-specific mobile genetic elements can be classified into three major types that differ in gene organization and phylogenetic distribution. Notably, PMU abundance explains nearly 80% of the variance in phytoplasma genome sizes, a finding that provides a quantitative estimate for the importance of PMUs in phytoplasma genome variability. Finally, our investigation found that in addition to horizontal gene transfer, PMUs also contribute to intra-genomic duplications of effector genes, which may provide redundancy for subfunctionalization or neofunctionalization. Taken together, this work improves the taxon sampling for phytoplasma genome research and provides novel information regarding the roles of mobile genetic elements in phytoplasma evolution.}, }
@article {pmid35300477, year = {2022}, author = {Bongrand, C and Koch, E and Mende, D and Romano, A and Lawhorn, S and McFall-Ngai, M and DeLong, EF and Ruby, EG}, title = {Evidence of Genomic Diversification in a Natural Symbiotic Population Within Its Host.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {854355}, pmid = {35300477}, issn = {1664-302X}, support = {R01 GM135254/GM/NIGMS NIH HHS/United States ; R01 OD011024/OD/NIH HHS/United States ; R37 AI050661/AI/NIAID NIH HHS/United States ; }, abstract = {Planktonic cells of the luminous marine bacterium Vibrio fischeri establish themselves in the light-emitting organ of each generation of newly hatched Euprymna scolopes bobtail squid. A symbiont population is maintained within the 6 separated crypts of the organ for the ∼9-month life of the host. In the wild, the initial colonization step is typically accomplished by a handful of planktonic V. fischeri cells, leading to a species-specific, but often multi-strain, symbiont population. Within a few hours, the inoculating cells proliferate within the organ's individual crypts, after which there is evidently no supernumerary colonization. Nevertheless, every day at dawn, the majority of the symbionts is expelled, and the regrowth of the remaining ∼5% of cells provides a daily opportunity for the population to evolve and diverge, thereby increasing its genomic diversity. To begin to understand the extent of this diversification, we characterized the light-organ population of an adult animal. First, we used 16S sequencing to determine that species in the V. fischeri clade were essentially the only ones detectable within a field-caught E. scolopes. Efforts to colonize the host with a minor species that appeared to be identified, V. litoralis, revealed that, although some cells could be imaged within the organ, they were <0.1% of the typical V. fischeri population, and did not persist. Next, we determined the genome sequences of seventy-two isolates from one side of the organ. While all these isolates were associated with one of three clusters of V. fischeri strains, there was considerable genomic diversity within this natural symbiotic population. Comparative analyses revealed a significant difference in both the number and the presence/absence of genes within each cluster; in contrast, there was little accumulation of single-nucleotide polymorphisms. These data suggest that, in nature, the light organ is colonized by a small number of V. fischeri strains that can undergo significant genetic diversification, including by horizontal-gene transfer, over the course of ∼1500 generations of growth in the organ. When the resulting population of symbionts is expelled into seawater, its genomic mix provides the genetic basis for selection during the subsequent environmental dispersal, and transmission to the next host.}, }
@article {pmid35298339, year = {2022}, author = {Nguyen, ANT and Woods, LC and Gorrell, R and Ramanan, S and Kwok, T and McDonald, MJ}, title = {Recombination resolves the cost of horizontal gene transfer in experimental populations of Helicobacter pylori.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {12}, pages = {e2119010119}, pmid = {35298339}, issn = {1091-6490}, mesh = {*Gene Transfer, Horizontal/genetics ; *Helicobacter pylori/genetics ; }, abstract = {Horizontal gene transfer (HGT) is important for microbial evolution, yet we know little about the fitness effects and dynamics of horizontally transferred genetic variants. In this study, we evolve laboratory populations of Helicobacter pylori, which take up DNA from their environment by natural transformation, and measure the fitness effects of thousands of transferred genetic variants. We find that natural transformation increases the rate of adaptation but comes at the cost of significant genetic load. We show that this cost is circumvented by recombination, which increases the efficiency of selection by decoupling deleterious and beneficial genetic variants. Our results show that adaptation with HGT, pervasive in natural microbial populations, is shaped by a combination of selection, recombination, and genetic drift not accounted for in existing models of evolution.}, }
@article {pmid35297758, year = {2022}, author = {Sharma, P and Johnson, MA and Mazloom, R and Allen, C and Heath, LS and Lowe-Power, TM and Vinatzer, BA}, title = {Meta-analysis of the Ralstonia solanacearum species complex (RSSC) based on comparative evolutionary genomics and reverse ecology.}, journal = {Microbial genomics}, volume = {8}, number = {3}, pages = {}, pmid = {35297758}, issn = {2057-5858}, mesh = {Biological Evolution ; Genome, Bacterial ; Genomics ; *Ralstonia solanacearum/genetics ; }, abstract = {Ralstonia solanacearum species complex (RSSC) strains are bacteria that colonize plant xylem tissue and cause vascular wilt diseases. However, individual strains vary in host range, optimal disease temperatures and physiological traits. To increase our understanding of the evolution, diversity and biology of the RSSC, we performed a meta-analysis of 100 representative RSSC genomes. These 100 RSSC genomes contain 4940 genes on average, and a pangenome analysis found that there are 3262 genes in the core genome (~60 % of the mean RSSC genome) with 13 128 genes in the extensive flexible genome. A core genome phylogenetic tree and a whole-genome similarity matrix aligned with the previously named species (R. solanacearum , R. pseudosolanacearum , R. syzygii) and phylotypes (I–IV). These analyses also highlighted a third unrecognized sub-clade of phylotype II. Additionally, we identified differences between phylotypes with respect to gene content and recombination rate, and we delineated population clusters based on the extent of horizontal gene transfer. Multiple analyses indicate that phylotype II is the most diverse phylotype, and it may thus represent the ancestral group of the RSSC. We also used our genome-based framework to test whether the RSSC sequence variant (sequevar) taxonomy is a robust method to define within-species relationships of strains. The sequevar taxonomy is based on alignments of a single conserved gene (egl). Although sequevars in phylotype II describe monophyletic groups, the sequevar system breaks down in the highly recombinogenic phylotype I, which highlights the need for an improved, cost-effective method for genotyping strains in phylotype I. Finally, we enabled quick and precise genome-based identification of newly sequenced RSSC strains by assigning Life Identification Numbers (LINs) to the 100 strains and by circumscribing the RSSC and its sub-groups in the LINbase Web service.}, }
@article {pmid35297726, year = {2022}, author = {Goff, KL and Hug, LA}, title = {Environmental Potential for Microbial 1,4-Dioxane Degradation Is Sparse despite Mobile Elements Playing a Role in Trait Distribution.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {7}, pages = {e0209121}, pmid = {35297726}, issn = {1098-5336}, mesh = {Bacteria ; Biodegradation, Environmental ; Dioxanes/metabolism ; *Groundwater ; Phylogeny ; *Water Pollutants, Chemical/metabolism ; }, abstract = {1,4-Dioxane (dioxane) is an emerging contaminant of concern for which bioremediation is seen as a promising solution. To date, eight distinct gene families have been implicated in dioxane degradation, though only dioxane monooxygenase (DXMO) from Pseudonocardia dioxanivorans is routinely used as a biomarker in environmental surveys. In order to assess the functional and taxonomic diversity of bacteria capable of dioxane degradation, we collated existing, poorly-organized information on known biodegraders to create a curated suite of biomarkers with confidence levels for assessing 1,4-dioxane degradation potential. The characterized enzyme systems for dioxane degradation are frequently found on mobile elements, and we identified that many of the curated biomarkers are associated with other hallmarks of genomic rearrangements, indicating lateral gene transfer plays a role in dissemination of this trait. This is contrasted by the extremely limited phylogenetic distribution of known dioxane degraders, where all representatives belong to four classes within three bacterial phyla. Based on the curated set of expanded biomarkers, a search of more than 11,000 publicly available metagenomes identified a sparse and taxonomically limited distribution of potential dioxane degradation proteins. Our work provides an important and necessary structure to the current knowledge base for dioxane degradation and clarifies the potential for natural attenuation of dioxane across different environments. It further highlights a disconnect between the apparent mobility of these gene families and their limited distributions, indicating dioxane degradation may be difficult to integrate into a microorganism's metabolism. IMPORTANCE New regulatory limits for 1,4-dioxane in groundwater have been proposed or adopted in many countries, including the United States and Canada, generating a direct need for remediation options as well as better tools for assessing the fate of dioxane in an environment. A comprehensive suite of biomarkers associated with dioxane degradation was identified and then leveraged to examine the global potential for dioxane degradation in natural and engineered environments. We identified consistent differences in the dioxane-degrading gene families associated with terrestrial, aquatic, and wetland environments, indicating reliance on a single biomarker for assessing natural attenuation of dioxane is likely to miss key players. Most environments do not currently host the capacity for dioxane degradation-the sparse distribution of dioxane degradation potential highlights the need for bioaugmentation approaches over biostimulation of naturally occurring microbial communities.}, }
@article {pmid35297678, year = {2022}, author = {Clark, RR and Lapierre, P and Lasek-Nesselquist, E and Gray, TA and Derbyshire, KM}, title = {A Polymorphic Gene within the Mycobacterium smegmatis esx1 Locus Determines Mycobacterial Self-Identity and Conjugal Compatibility.}, journal = {mBio}, volume = {13}, number = {2}, pages = {e0021322}, pmid = {35297678}, issn = {2150-7511}, support = {R21 AI135173/AI/NIAID NIH HHS/United States ; AI135173-02//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; MCB 1614178//National Science Foundation (NSF)/ ; }, mesh = {Conjugation, Genetic ; DNA/metabolism ; Genome-Wide Association Study ; *Mycobacterium/genetics ; *Mycobacterium smegmatis/genetics/metabolism ; }, abstract = {Mycobacteria mediate horizontal gene transfer (HGT) by a process called distributive conjugal transfer (DCT) that is mechanistically distinct from oriT-mediated plasmid transfer. The transfer of multiple, independent donor chromosome segments generates transconjugants with genomes that are mosaic blends of their parents. Previously, we had characterized contact-dependent conjugation between two independent isolates of Mycobacterium smegmatis. Here, we expand our analyses to include five independent isolates of M. smegmatis and establish that DCT is both active and prevalent among natural isolates of M. smegmatis. Two of these five strains were recipients but exhibited distinct conjugal compatibilities with donor strains, suggesting an ability to distinguish between potential donor partners. We determined that a single gene, Msmeg0070, was responsible for conferring mating compatibility using a combination of comparative DNA sequence analysis, bacterial genome-wide association studies (GWAS), and targeted mutagenesis. Msmeg0070 maps within the esx1 secretion locus, and we establish that it confers mycobacterial self-identity with parallels to kin recognition. Similar to other kin model systems, orthologs of Msmeg0070 are highly polymorphic. The identification of a kin recognition system in M. smegmatis reinforces the concept that communication between cells is an important checkpoint prior to DCT commitment and implies that there are likely to be other, unanticipated forms of social behaviors in mycobacteria. IMPORTANCE Conjugation, unlike other forms of HGT, requires direct interaction between two viable bacteria, which must be capable of distinguishing between mating types to allow successful DNA transfer from donor to recipient. We show that the conjugal compatibility of Mycobacterium smegmatis isolates is determined by a single, polymorphic gene located within the conserved esx1 secretion locus. This gene confers self-identity; the expression of identical Msmeg0070 proteins in both donor-recipient partners prevents DNA transfer. The presence of this polymorphic locus in many environmental mycobacteria suggests that kin identification is important in promoting beneficial gene flow between nonkin mycobacteria. Cell-cell communication, mediated by kin recognition and ESX secretion, is a key checkpoint in mycobacterial conjugation and likely plays a more global role in mycobacterial biology.}, }
@article {pmid35297657, year = {2022}, author = {Du, P and Liu, C and Fan, S and Baker, S and Guo, J}, title = {The Role of Plasmid and Resistance Gene Acquisition in the Emergence of ST23 Multi-Drug Resistant, Hypervirulent Klebsiella pneumoniae.}, journal = {Microbiology spectrum}, volume = {10}, number = {2}, pages = {e0192921}, pmid = {35297657}, issn = {2165-0497}, mesh = {Anti-Bacterial Agents/pharmacology ; *Klebsiella Infections/epidemiology ; *Klebsiella pneumoniae/genetics ; Plasmids/genetics ; Serogroup ; Virulence/genetics ; }, abstract = {Multidrug-resistant (MDR) hypervirulent Klebsiella pneumoniae (hvKp) sequence type (ST) 23 (MDR-ST23-hvKp) is emerging in China. Despite its increasing importance, this pathogen has not yet been subject to detailed genomic interrogation. We identified 28 ST23 Kp isolated from three hospitals in China. The organisms were subjected to antimicrobial susceptibility testing and whole-genome sequencing (WGS). These novel genomic sequences were analyzed in combination with 218 publicly available genome sequences. We performed molecular serotyping and subtyping, assessed the composition of virulence-associated and antimicrobial resistance (AMR) genes, and determined mobile elements associated with horizontal gene transfer. Two MDR-ST23-hvKp were sequenced by long-read sequencing. The genetic characteristics of MDR and non-MDR isolates were compared. Among the 28 novel ST23 isolates, all were hvKp and 2/28 (7.1%) were MDR-hvKp. From the collection of 246 genomes, KL1 was the predominant serotype (224/246; 91.1%) and the siderophore combination of YbST46-CbST29-AbST1-SmST2 was dominant (101/246; 41.1%); 34/246 (13.8%) organisms belonged to MDR-ST23-hvKp. IncF and IncR plasmid replicons were significantly more prevalent in the MDR group (P < 0.05) than in the non-MDR group. IS26 was commonly involved in AMR acquisition. We observed that the acquisition of AMR genes within the ST23-hvKp was not associated with a loss of virulence genes. A 28-bp fusion site was highly conserved with two copies of the virulence-associated plasmid in ST23-hvKp, and we harbored by some of the IncFII plasmids of MDR-ST23-hvKp. Our data suggest that MDR-ST23-hvKp has undergone multiple independent genetic acquisition and recombination events within different sublineages. Notably, the acquisition of IncFII plasmids and/or IS26 contributed to the horizontal transfer of AMR genes within ST23-hvKp. Genomic surveillance is essential for further tracking of kMDR-ST23-hvKp. IMPORTANCE Hypervirulent Klebsiella pneumoniae (hvKp) has become the dominant pathotype in hospitals recently. The sequence type (ST) 23 hvKp, which are more commonly associated with the community-acquired infections previously, may have the capacity to acquire multidrug-resistant (MDR) phenotypes creating a new "superbug" (MDR-hvKp) in hospital. In the present study, we studied the associations of MDR and hypervirulence among ST23 K. pneumoniae from our strain collection and publicly accessible genome data. By comparative analysis of the carriage of resistance genes, virulence genes plasmid replicon types, and plasmid sequences, we found that IncFII plasmids were significantly more prevalent in MDR isolates and IS26 were commonly involved in resistance gene acquisition. We also discovered new MDR plasmids. These results provided an overview landscape of the genetic elements associated with MDR-ST23-hvKp based on currently accessible genome data and calling for further genomic surveillance and well-designed control studies of MDR-ST23-hvKp.}, }
@article {pmid35293798, year = {2022}, author = {Allard, N and Neil, K and Grenier, F and Rodrigue, S}, title = {The Type IV Pilus of Plasmid TP114 Displays Adhesins Conferring Conjugation Specificity and Is Important for DNA Transfer in the Mouse Gut Microbiota.}, journal = {Microbiology spectrum}, volume = {10}, number = {2}, pages = {e0230321}, pmid = {35293798}, issn = {2165-0497}, support = {159817//CIHR/Canada ; }, mesh = {Adhesins, Bacterial/genetics ; Animals ; Bacteria/genetics ; Conjugation, Genetic ; DNA ; Escherichia coli/genetics ; Fimbriae, Bacterial/genetics ; *Gastrointestinal Microbiome/genetics ; Gene Transfer, Horizontal ; Mice ; Plasmids/genetics ; }, abstract = {Type IV pili (T4P) are common bacterial surface appendages involved in different biological processes such as adherence, motility, competence, pathogenesis, and conjugation. In this work, we describe the T4P of TP114, an IncI2 enterobacterial conjugative plasmid recently shown to disseminate at high rates in the mouse intestinal tract. This pilus is composed of the major PilS and minor PilV pilins that are both important for conjugation in broth and in the gut microbiota but not on a solid support. The PilV-coding sequence is part of a shufflon and can bear different C-terminal domains. The shufflon is a multiple DNA inversion system containing many DNA cassettes flanked by recombination sites that are recognized by a shufflon-specific tyrosine recombinase (shufflase) promoting the recombination between DNA segments. The different PilV variants act as adhesins that can modify the affinity for different recipient bacteria. Eight PilV variants were identified in TP114, including one that has not been described in other shufflons. All PilV variants allowed conjugative transfer with different recipient Escherichia coli strains. We conclude that the T4P carried by TP114 plays a major role in mating pair stabilization in broth as well as in the gut microbiota and that the shufflon acts as a biological switch modifying the conjugative host range specificity. IMPORTANCE Conjugative plasmids are involved in horizontal gene transfer in the gut microbiota, which constitutes an important antibiotic resistance gene reservoir. However, the molecular mechanisms used by conjugative plasmids to select recipient bacteria and transfer at high rates in the mouse gut microbiota remain poorly characterized. We studied the type IV pilus carried by TP114 and demonstrated that the minor pilin PilV acts as an adhesin that can efficiently select target cells for conjugative transfer. Moreover, the pilV gene can be rapidly modified by a shufflon, hence modulating the nature of the recipient bacteria during conjugation. Our study highlights the role of mating pair stabilization for conjugation in broth as well as in the gut microbiome and explains how the host spectrum of a plasmid can be expanded simply by remodeling the PilV adhesin.}, }
@article {pmid35291951, year = {2022}, author = {Roux, E and Nicolas, A and Valence, F and Siekaniec, G and Chuat, V and Nicolas, J and Le Loir, Y and Guédon, E}, title = {The genomic basis of the Streptococcus thermophilus health-promoting properties.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {210}, pmid = {35291951}, issn = {1471-2164}, mesh = {*Genomics ; Humans ; Lactose/metabolism ; Phenotype ; *Streptococcus thermophilus/genetics/metabolism ; }, abstract = {BACKGROUND: Streptococcus thermophilus is a Gram-positive bacterium widely used as starter in the dairy industry as well as in many traditional fermented products. In addition to its technological importance, it has also gained interest in recent years as beneficial bacterium due to human health-promoting functionalities. The objective of this study was to inventory the main health-promoting properties of S. thermophilus and to study their intra-species diversity at the genomic and genetic level within a collection of representative strains.<br><br>RESULTS: In this study various health-related functions were analyzed at the genome level from 79 genome sequences of strains isolated over a long time period from diverse products and different geographic locations. While some functions are widely conserved among isolates (e.g., degradation of lactose, folate production) suggesting their central physiological and ecological role for the species, others including the tagatose-6-phosphate pathway involved in the catabolism of galactose, and the production of bioactive peptides and gamma-aminobutyric acid are strain-specific. Most of these strain-specific health-promoting properties seems to have been acquired via horizontal gene transfer events. The genetic basis for the phenotypic diversity between strains for some health related traits have also been investigated. For instance, substitutions in the galK promoter region correlate with the ability of some strains to catabolize galactose via the Leloir pathway. Finally, the low occurrence in S. thermophilus genomes of genes coding for biogenic amine production and antibiotic resistance is also a contributing factor to its safety status.<br><br>CONCLUSIONS: The natural intra-species diversity of S. thermophilus, therefore, represents an interesting source for innovation in the field of fermented products enriched for healthy components that can be exploited to improve human health. A better knowledge of the health-promoting properties and their genomic and genetic diversity within the species may facilitate the selection and application of strains for specific biotechnological and human health-promoting purpose. Moreover, by pointing out that a substantial part of its functional potential still defies us, our work opens the way to uncover additional health-related functions through the intra-species diversity exploration of S. thermophilus by comparative genomics approaches.}, }
@article {pmid35290758, year = {2022}, author = {van der Putten, BCL and Huijsmans, NAH and Mende, DR and Schultsz, C}, title = {Benchmarking the topological accuracy of bacterial phylogenomic workflows using in silico evolution.}, journal = {Microbial genomics}, volume = {8}, number = {3}, pages = {}, pmid = {35290758}, issn = {2057-5858}, support = {MR/R002762/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Algorithms ; *Genome ; Phylogeny ; Workflow ; }, abstract = {Phylogenetic analyses are widely used in microbiological research, for example to trace the progression of bacterial outbreaks based on whole-genome sequencing data. In practice, multiple analysis steps such as de novo assembly, alignment and phylogenetic inference are combined to form phylogenetic workflows. Comprehensive benchmarking of the accuracy of complete phylogenetic workflows is lacking. To benchmark different phylogenetic workflows, we simulated bacterial evolution under a wide range of evolutionary models, varying the relative rates of substitution, insertion, deletion, gene duplication, gene loss and lateral gene transfer events. The generated datasets corresponded to a genetic diversity usually observed within bacterial species (≥95 % average nucleotide identity). We replicated each simulation three times to assess replicability. In total, we benchmarked 19 distinct phylogenetic workflows using 8 different simulated datasets. We found that recently developed k-mer alignment methods such as kSNP and ska achieve similar accuracy as reference mapping. The high accuracy of k-mer alignment methods can be explained by the large fractions of genomes these methods can align, relative to other approaches. We also found that the choice of de novo assembly algorithm influences the accuracy of phylogenetic reconstruction, with workflows employing SPAdes or skesa outperforming those employing Velvet. Finally, we found that the results of phylogenetic benchmarking are highly variable between replicates. We conclude that for phylogenomic reconstruction, k-mer alignment methods are relevant alternatives to reference mapping at the species level, especially in the absence of suitable reference genomes. We show de novo genome assembly accuracy to be an underappreciated parameter required for accurate phylogenomic reconstruction.}, }
@article {pmid35286518, year = {2022}, author = {Mohanraj, RS and Mandal, J}, title = {Azithromycin can induce SOS response and horizontal gene transfer of SXT element in Vibrio cholerae.}, journal = {Molecular biology reports}, volume = {49}, number = {6}, pages = {4737-4748}, pmid = {35286518}, issn = {1573-4978}, support = {27(0336)/18/EMR-II//Council&#xa0;of&#xa0;Scientific and Industrial Research, India/ ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Azithromycin/pharmacology ; Ciprofloxacin/pharmacology ; DNA Transposable Elements ; Gene Transfer, Horizontal/genetics ; SOS Response, Genetics/genetics ; Tetracyclines ; *Vibrio cholerae/genetics ; }, abstract = {BACKGROUND: The emergence and spread of drug resistance in Vibrio cholerae are mainly attributed to horizontal gene transfer of mobile genetic elements, especially the SXT (sulfamethoxazole and trimethoprim) element, an integrative conjugative element carrying multiple drug resistance genes. SOS (save our souls) bacterial stress response in Vibrio cholerae plays a pivotal role in inducing the SXT element transfer and induction of the CTX prophage, carrying the important virulence factor cholera toxin encoded by the ctxAB gene.<br><br>METHODS: This study investigated whether the subinhibitory concentration of antibiotics like ciprofloxacin, tetracycline, and azithromycin induce SOS response by detecting the expression of recA and lexA, the key genes of SOS response by reverse transcriptase real time PCR (RT-qPCR). We also studied the transfer of SXT element in response to these three antibiotics by bacterial conjugation. Transfer of SXT elements was confirmed by detecting the SXT element-specific conserved genes.<br><br>RESULTS: The results of the real-time PCR showed that all three antibiotics induced SOS response with more robust induction by tetracycline and azithromycin relative to ciprofloxacin. We observed a higher frequency of transfer of SXT elements in cultures exposed to these antibiotics and the control mitomycin C compared to unexposed cultures.<br><br>CONCLUSION: Our study indicates that antibiotics including azithromycin, ciprofloxacin, and tetracycline activate SOS response in Vibrio cholerae and demonstrates a robust mechanism for wide dissemination of drug resistance.}, }
@article {pmid35286398, year = {2022}, author = {Birkholz, N and Jackson, SA and Fagerlund, RD and Fineran, PC}, title = {A mobile restriction-modification system provides phage defence and resolves an epigenetic conflict with an antagonistic endonuclease.}, journal = {Nucleic acids research}, volume = {50}, number = {6}, pages = {3348-3361}, pmid = {35286398}, issn = {1362-4962}, mesh = {*Bacteriophages/genetics/metabolism ; DNA Methylation/genetics ; DNA Restriction Enzymes/genetics/metabolism ; *DNA Restriction-Modification Enzymes/genetics/metabolism ; Endonucleases/metabolism ; Epigenesis, Genetic ; Gene Expression Regulation, Bacterial ; }, abstract = {Epigenetic DNA methylation plays an important role in bacteria by influencing gene expression and allowing discrimination between self-DNA and intruders such as phages and plasmids. Restriction-modification (RM) systems use a methyltransferase (MTase) to modify a specific sequence motif, thus protecting host DNA from cleavage by a cognate restriction endonuclease (REase) while leaving invading DNA vulnerable. Other REases occur solitarily and cleave methylated DNA. REases and RM systems are frequently mobile, influencing horizontal gene transfer by altering the compatibility of the host for foreign DNA uptake. However, whether mobile defence systems affect pre-existing host defences remains obscure. Here, we reveal an epigenetic conflict between an RM system (PcaRCI) and a methylation-dependent REase (PcaRCII) in the plant pathogen Pectobacterium carotovorum RC5297. The PcaRCI RM system provides potent protection against unmethylated plasmids and phages, but its methylation motif is targeted by the methylation-dependent PcaRCII. This potentially lethal co-existence is enabled through epigenetic silencing of the PcaRCII-encoding gene via promoter methylation by the PcaRCI MTase. Comparative genome analyses suggest that the PcaRCII-encoding gene was already present and was silenced upon establishment of the PcaRCI system. These findings provide a striking example for selfishness of RM systems and intracellular competition between different defences.}, }
@article {pmid35286209, year = {2022}, author = {Haj Hammadeh, H and Serrano, A and Wernet, V and Stomberg, N and Hellmeier, D and Weichert, M and Brandt, U and Sieg, B and Kanofsky, K and Hehl, R and Fischer, R and Fleißner, A}, title = {A dialogue-like cell communication mechanism is conserved in filamentous ascomycete fungi and mediates interspecies interactions.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {12}, pages = {e2112518119}, pmid = {35286209}, issn = {1091-6490}, mesh = {*Ascomycota/genetics/metabolism ; Cell Communication ; Fungal Proteins/genetics/metabolism ; *Fungi/genetics/metabolism ; Gene Transfer, Horizontal ; Signal Transduction ; }, abstract = {In many filamentous fungi, germinating spores cooperate by fusing into supracellular structures, which develop into the mycelial colony. In the model fungus Neurospora crassa, this social behavior is mediated by an intriguing mode of communication, in which two fusing cells take turns in signal sending and receiving. Here we show that this dialogue-like cell communication mechanism is highly conserved in distantly related fungal species and mediates interspecies interactions. In mixed populations, cells of N. crassa and the phytopathogenic gray mold Botrytis cinerea coordinate their behavior over a spatial distance and establish physical contact. Subsequent cell–cell fusion is, however, restricted to germlings of the same species, indicating that species specificity of germling fusion has evolved not on the level of the signal/receptor but at subsequent levels of the fusion process. In B. cinerea, fusion and infectious growth are mutually exclusive cellular programs. Remarkably, the presence of N. crassa can reprogram this behavior and induce fusion of the gray mold on plant surfaces, potentially weakening its pathogenic potential. In a third fungal species, the nematode-trapping fungus Arthrobotrys flagrans, the conserved signaling mechanism mediates vegetative fusion within mycelial colonies but has also been repurposed for the formation of nematode-catching traps. In summary, this study identified the cell dialogue mechanism as a conserved complex trait and revealed that even distantly related fungi possess a common molecular language, which promotes cellular contact formation across species borders.}, }
@article {pmid35285243, year = {2022}, author = {Li, B and Li, X and Wang, B and Yan, T}, title = {A Metagenomic Approach for Characterizing Antibiotic Resistance Genes in Specific Bacterial Populations: Demonstration with Escherichia coli in Cattle Manure.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {7}, pages = {e0255421}, pmid = {35285243}, issn = {1098-5336}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Cattle ; Drug Resistance, Microbial/genetics ; Escherichia coli/genetics ; *Genes, Bacterial ; *Manure/microbiology ; }, abstract = {The high diversity of bacterial antibiotic resistance genes (ARGs) and the different health risks due to their association with different bacterial hosts require environmental ARG risk assessment to have capabilities of both high throughput and host differentiation. Current whole genome sequencing of cultivated isolates is low in throughput, while direct metagenomic next generation sequencing (mNGS) of environmental samples is nonselective with respect to bacterial hosts. This study introduced a population metagenomic approach that combines isolate library construction and mNGS of the population metagenomic DNA, which enables studying ARGs and their association with mobile genetic elements (MGEs) in a specific bacterial population. The population metagenomic approach was demonstrated with the E. coli population in cattle manure, which detected the co-location of multiple ARGs on the same MGEs and their correspondence to the prevalence of resistance phenotypes of the E. coli isolates. When compared with direct mNGS of the cattle manure samples, the E. coli population metagenomes exhibited a significantly different resistome and an overall higher relative abundance of ARGs and horizontal gene transfer risks. IMPORTANCE Bacterial antibiotic resistance genes in the environment are ubiquitous and can pose different levels of human health risks due to their bacterial host association and subsequent mobility. This study introduced a population metagenomic approach to study ARGs and their mobility in specific bacterial populations through a combination of selective cultivation followed by next generation sequencing and bioinformatic analysis of the combined metagenome of isolates. The utility of this approach was demonstrated with the E. coli population in cattle manure samples, which showed that ARGs detected in the E. coli population corresponded to the observed resistance phenotypes, co-location of multiple ARGs on the same mobile genetic elements.}, }
@article {pmid35283838, year = {2022}, author = {Herbert, A and Hancock, CN and Cox, B and Schnabel, G and Moreno, D and Carvalho, R and Jones, J and Paret, M and Geng, X and Wang, H}, title = {Oxytetracycline and Streptomycin Resistance Genes in Xanthomonas arboricola pv. pruni, the Causal Agent of Bacterial Spot in Peach.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {821808}, pmid = {35283838}, issn = {1664-302X}, support = {P20 GM139769/GM/NIGMS NIH HHS/United States ; }, abstract = {Xanthomonas arboricola pv. pruni (Xap) causes bacterial spot, a major worldwide disease of Prunus species. Very few chemical management options are available for this disease and frequent applications of oxytetracycline (OTC) in the United States peach orchards have raised concerns about resistance development. During 2017-2020, 430 Xap strains were collected from ten peach orchards in South Carolina. Seven OTC-resistant (OTC [R]) Xap strains were found in 2017 and 2020 from four orchards about 20-270 km apart. Interestingly, the seven strains were also resistant to streptomycin (STR). Six strains grew on media amended with ≤100 μg/mL OTC, while one strain, R1, grew on ≤250 μg/mL OTC. Genome sequence analysis of four representative OTC [R] strains revealed a 14-20 kb plasmid carrying tetC, tetR, and strAB in each strain. These three genes were transferable to Xanthomonas perforans via conjugation, and they were PCR confirmed in all seven OTC [R] Xap strains. When tetC and tetR were cloned and expressed together in a sensitive strain, the transconjugants showed resistance to ≤100 μg/mL OTC. When tetC was cloned and expressed alone in a sensitive strain, the transconjugants showed resistance to ≤250 μg/mL OTC. TetC and tetR expression was inducible by OTC in all six wild-type strains resistant to ≤100 μg/mL OTC. However, in the R1 strain resistant to ≤250 μg/mL OTC, tetR was not expressed, possibly due to the presence of Tn3 in the tetR gene, and in this case tetC was constitutively expressed. These data suggest that tetC confers OTC resistance in Xap strains, and tetR regulates the level of OTC resistance conferred by tetC. To our knowledge, this is the first report of OTC resistance in plant pathogenic xanthomonads.}, }
@article {pmid35283813, year = {2022}, author = {Kraus-Römer, S and Wielert, I and Rathmann, I and Grossbach, J and Maier, B}, title = {External Stresses Affect Gonococcal Type 4 Pilus Dynamics.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {839711}, pmid = {35283813}, issn = {1664-302X}, abstract = {Bacterial type 4 pili (T4P) are extracellular polymers that serve both as adhesins and molecular motors. Functionally, they are involved in adhesion, colony formation, twitching motility, and horizontal gene transfer. T4P of the human pathogen Neisseria gonorrhoeae have been shown to enhance survivability under treatment with antibiotics or hydrogen peroxide. However, little is known about the effect of external stresses on T4P production and motor properties. Here, we address this question by directly visualizing gonococcal T4P dynamics. We show that in the absence of stress gonococci produce T4P at a remarkably high rate of ∼200 T4P min[-1]. T4P retraction succeeds elongation without detectable time delay. Treatment with azithromycin or ceftriaxone reduces the T4P production rate. RNA sequencing results suggest that reduced piliation is caused by combined downregulation of the complexes required for T4P extrusion from the cell envelope and cellular energy depletion. Various other stresses including inhibitors of cell wall synthesis and DNA replication, as well as hydrogen peroxide and lactic acid, inhibit T4P production. Moreover, hydrogen peroxide and acidic pH strongly affect pilus length and motor function. In summary, we show that gonococcal T4P are highly dynamic and diverse external stresses reduce piliation despite the protective effect of T4P against some of these stresses.}, }
@article {pmid35279076, year = {2022}, author = {Garber, AI and Armbruster, CR and Lee, SE and Cooper, VS and Bomberger, JM and McAllister, SM}, title = {SprayNPray: user-friendly taxonomic profiling of genome and metagenome contigs.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {202}, pmid = {35279076}, issn = {1471-2164}, support = {CFF BOMBER18G0/NH/NIH HHS/United States ; U01AI124302/NH/NIH HHS/United States ; UL1 TR000005/TR/NCATS NIH HHS/United States ; T32HL129949/NH/NIH HHS/United States ; R33HL137077/NH/NIH HHS/United States ; CFF RDP BOMBER19R0/NH/NIH HHS/United States ; R01HL12377/NH/NIH HHS/United States ; }, mesh = {Bacteria/genetics ; *Metagenome ; Metagenomics ; *Microbiota/genetics ; Software ; }, abstract = {BACKGROUND: Shotgun sequencing of cultured microbial isolates/individual eukaryotes (whole-genome sequencing) and microbial communities (metagenomics) has become commonplace in biology. Very often, sequenced samples encompass organisms spanning multiple domains of life, necessitating increasingly elaborate software for accurate taxonomic classification of assembled sequences.<br><br>RESULTS: While many software tools for taxonomic classification exist, SprayNPray offers a quick and user-friendly, semi-automated approach, allowing users to separate contigs by taxonomy (and other metrics) of interest. Easy installation, usage, and intuitive output, which is amenable to visual inspection and/or further computational parsing, will reduce barriers for biologists beginning to analyze genomes and metagenomes. This approach can be used for broad-level overviews, preliminary analyses, or as a supplement to other taxonomic classification or binning software. SprayNPray profiles contigs using multiple metrics, including closest homologs from a user-specified reference database, gene density, read coverage, GC content, tetranucleotide frequency, and codon-usage bias.<br><br>CONCLUSIONS: The output from this software is designed to allow users to spot-check metagenome-assembled genomes, identify, and remove contigs from putative contaminants in isolate assemblies, identify bacteria in eukaryotic assemblies (and vice-versa), and identify possible horizontal gene transfer events.}, }
@article {pmid35278945, year = {2022}, author = {Zha, Y and Li, Z and Zhong, Z and Ruan, Y and Sun, L and Zuo, F and Li, L and Hou, S}, title = {Size-dependent enhancement on conjugative transfer of antibiotic resistance genes by micro/nanoplastics.}, journal = {Journal of hazardous materials}, volume = {431}, number = {}, pages = {128561}, doi = {10.1016/j.jhazmat.2022.128561}, pmid = {35278945}, issn = {1873-3336}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Escherichia coli/genetics ; *Escherichia coli K12 ; Gene Transfer, Horizontal ; Genes, Bacterial ; Microplastics ; Plasmids/genetics ; Reactive Oxygen Species ; }, abstract = {Recently micro/nanoplastics (MNPs) have raised intensive concerns due to their possible enhancement effect on the dissemination of antibiotic genes. Unfortunately, data is still lacking to verify the effect. In the study, the influence of polystyrene MNPs on the conjugative gene transfer was studied by using E. coli DH5ɑ with RP4 plasmid as the donor bacteria and E. coli K12 MG1655 as the recipient bacteria. We found that influence of MNPs on gene transfer was size-dependent. Small MNPs (10 nm in radius) caused an increase and then a decrease in gene transfer efficiency with their concentration increasing. Moderate-sized MNPs (50 nm in radius) caused an increase in gene transfer efficiency. Large MNPs (500 nm in radius) had almost no influence on gene transfer. The gene transfer could be further enhanced by optimizing mating time and mating ratio. Scavenging reactive oxygen species (ROS) production did not affect the cell membrane permeability, indicating that the increase in cell membrane permeability was not related to ROS production. The mechanism of the enhanced gene transfer efficiency was attributed to a combined effect of the increased ROS production and the increased cell membrane permeability, which ultimately regulated the expression of corresponding genes.}, }
@article {pmid35278942, year = {2022}, author = {Wu, S and Ren, P and Wu, Y and Liu, J and Huang, Q and Cai, P}, title = {Effects of hematite on the dissemination of antibiotic resistance in pathogens and underlying mechanisms.}, journal = {Journal of hazardous materials}, volume = {431}, number = {}, pages = {128537}, doi = {10.1016/j.jhazmat.2022.128537}, pmid = {35278942}, issn = {1873-3336}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Ferric Compounds ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Plasmids/genetics ; }, abstract = {The dissemination of antibiotic resistance genes (ARGs) in pathogens is becoming a pervasive global health threat, to which the importance of the environment attracts more and more attention. However, how natural minerals affect ARGs transfer in pathogens is still unclear. In this study, the concentration and size effects of hematite on the ARGs conjugative transfer to a common zoonotic pathogen Escherichia coli O157:H7 and underlying mechanisms were explored. Results revealed that bulk hematite reduced the conjugation of resistant plasmids by inhibiting cell growth at any concentration (1-100 mg/L), different from nano-hematite. Low concentrations of nano-hematite (≤ 25 mg/L) induced significant increases in conjugative transfer frequency of 1.83-4.49 folds, while its high concentrations (50 and 100 mg/L) showed no impact, compared with the control group. This low-concentration effect was likely attributed to the increased intracellular ROS level, the reduced intercellular repulsion by increasing the extracellular polymeric substances production and cell surface hydrophobicity, the formation of transfer channels and the increased membrane permeability evidenced by significant changes in gene expression level, and the increased proton motive force by increasing the transmembrane potential of recipients. These findings shed light on potential health risks caused by nano minerals-mediated ARGs dissemination in pathogens in the environment.}, }
@article {pmid35276007, year = {2022}, author = {Grébert, T and Garczarek, L and Daubin, V and Humily, F and Marie, D and Ratin, M and Devailly, A and Farrant, GK and Mary, I and Mella-Flores, D and Tanguy, G and Labadie, K and Wincker, P and Kehoe, DM and Partensky, F}, title = {Diversity and Evolution of Pigment Types in Marine Synechococcus Cyanobacteria.}, journal = {Genome biology and evolution}, volume = {14}, number = {4}, pages = {}, pmid = {35276007}, issn = {1759-6653}, mesh = {Ecosystem ; Phycobiliproteins/genetics ; Phycobilisomes/genetics ; Phylogeny ; *Synechococcus/genetics ; }, abstract = {Synechococcus cyanobacteria are ubiquitous and abundant in the marine environment and contribute to an estimated 16% of the ocean net primary productivity. Their light-harvesting complexes, called phycobilisomes (PBS), are composed of a conserved allophycocyanin core, from which radiates six to eight rods with variable phycobiliprotein and chromophore content. This variability allows Synechococcus cells to optimally exploit the wide variety of spectral niches existing in marine ecosystems. Seven distinct pigment types or subtypes have been identified so far in this taxon based on the phycobiliprotein composition and/or the proportion of the different chromophores in PBS rods. Most genes involved in their biosynthesis and regulation are located in a dedicated genomic region called the PBS rod region. Here, we examine the variability of gene content and organization of this genomic region in a large set of sequenced isolates and natural populations of Synechococcus representative of all known pigment types. All regions start with a tRNA-PheGAA and some possess mobile elements for DNA integration and site-specific recombination, suggesting that their genomic variability relies in part on a "tycheposon"-like mechanism. Comparison of the phylogenies obtained for PBS and core genes revealed that the evolutionary history of PBS rod genes differs from the core genome and is characterized by the co-existence of different alleles and frequent allelic exchange. We propose a scenario for the evolution of the different pigment types and highlight the importance of incomplete lineage sorting in maintaining a wide diversity of pigment types in different Synechococcus lineages despite multiple speciation events.}, }
@article {pmid35271855, year = {2022}, author = {Huisman, JS and Benz, F and Duxbury, SJN and de Visser, JAGM and Hall, AR and Fischer, EAJ and Bonhoeffer, S}, title = {Estimating plasmid conjugation rates: A new computational tool and a critical comparison of methods.}, journal = {Plasmid}, volume = {121}, number = {}, pages = {102627}, doi = {10.1016/j.plasmid.2022.102627}, pmid = {35271855}, issn = {1095-9890}, mesh = {Anti-Bacterial Agents ; *Bacteria/genetics ; *Conjugation, Genetic ; Gene Transfer, Horizontal ; Plasmids/genetics ; }, abstract = {Plasmids are important vectors for the spread of genes among diverse populations of bacteria. However, there is no standard method to determine the rate at which they spread horizontally via conjugation. Here, we compare commonly used methods on simulated and experimental data, and show that the resulting conjugation rate estimates often depend strongly on the time of measurement, the initial population densities, or the initial ratio of donor to recipient populations. Differences in growth rate, e.g. induced by sub-lethal antibiotic concentrations or temperature, can also significantly bias conjugation rate estimates. We derive a new 'end-point' measure to estimate conjugation rates, which extends the well-known Simonsen method to include the effects of differences in population growth and conjugation rates from donors and transconjugants. We further derive analytical expressions for the parameter range in which these approximations remain valid. We present an easy to use R package and web interface which implement both new and previously existing methods to estimate conjugation rates. The result is a set of tools and guidelines for accurate and comparable measurement of plasmid conjugation rates.}, }
@article {pmid35271656, year = {2022}, author = {Dwiyanto, J and Hor, JW and Reidpath, D and Su, TT and Lee, SWH and Ayub, Q and Mustapha, FB and Lee, SM and Foo, SC and Chong, CW and Rahman, S}, title = {Pan-genome and resistome analysis of extended-spectrum ß-lactamase-producing Escherichia coli: A multi-setting epidemiological surveillance study from Malaysia.}, journal = {PloS one}, volume = {17}, number = {3}, pages = {e0265142}, pmid = {35271656}, issn = {1932-6203}, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; *Escherichia coli/genetics ; *Escherichia coli Infections/drug therapy/epidemiology ; Humans ; Malaysia/epidemiology ; Microbial Sensitivity Tests ; Plasmids/genetics ; Virulence Factors ; beta-Lactamases/genetics ; }, abstract = {OBJECTIVES: This study profiled the prevalence of extended-spectrum ß-lactamase-producing Escherichia coli (ESBL-EC) in the community and compared their resistome and genomic profiles with isolates from clinical patients through whole-genome sequencing.<br><br>METHODS: Fecal samples from 233 community dwellers from Segamat, a town in southern Malaysia, were obtained between May through August 2018. Putative ESBL strains were screened and tested using antibiotic susceptibility tests. Additionally, eight clinical ESBL-EC were obtained from a hospital in the same district between June through October 2020. Whole-genome sequencing was then conducted on selected ESBL-EC from both settings (n = 40) for pan-genome comparison, cluster analysis, and resistome profiling.<br><br>RESULTS: A mean ESBL-EC carriage rate of 17.82% (95% CI: 10.48%- 24.11%) was observed in the community and was consistent across demographic factors. Whole-genome sequences of the ESBL-EC (n = 40) enabled the detection of multiple plasmid replicon groups (n = 28), resistance genes (n = 34) and virulence factors (n = 335), with no significant difference in the number of genes carried between the community and clinical isolates (plasmid replicon groups, p = 0.13; resistance genes, p = 0.47; virulence factors, p = 0.94). Virulence gene marker analysis detected the presence of extraintestinal pathogenic E. coli (ExPEC), uropathogenic E. coli (UPEC), and enteroaggregative E. coli (EAEC) in both the community and clinical isolates. Multiple blaCTX-M variants were observed, dominated by blaCTX-M-27 (n = 12), blaCTX-M-65 (n = 10), and blaCTX-M-15 (n = 9). The clinical and community isolates did not cluster together based on the pan-genome comparison, suggesting isolates from the two settings were clonally unrelated. However, cluster analysis based on carried plasmids, resistance genes and phenotypic susceptibility profiles identified four distinct clusters, with similar patterns between the community and clinical isolates.<br><br>CONCLUSION: ESBL-EC from the clinical and community settings shared similar resistome profiles, suggesting the frequent exchange of genetic materials through horizontal gene transfer.}, }
@article {pmid35266867, year = {2022}, author = {Hinkel, LA and Willsey, GG and Lenahan, SM and Eckstrom, K and Schutz, KC and Wargo, MJ}, title = {Creatine utilization as a sole nitrogen source in Pseudomonas putida KT2440 is transcriptionally regulated by CahR.}, journal = {Microbiology (Reading, England)}, volume = {168}, number = {3}, pages = {}, pmid = {35266867}, issn = {1465-2080}, support = {R21 AI137453/AI/NIAID NIH HHS/United States ; T32 AI055402/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/metabolism ; Creatine/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Nitrogen/metabolism ; Phylogeny ; Promoter Regions, Genetic ; *Pseudomonas putida/genetics/metabolism ; }, abstract = {Glutamine amidotransferase-1 domain-containing AraC-family transcriptional regulators (GATRs) are present in the genomes of many bacteria, including all Pseudomonas species. The involvement of several characterized GATRs in amine-containing compound metabolism has been determined, but the full scope of GATR ligands and regulatory networks are still unknown. Here, we characterize Pseudomonas putida's detection of the animal-derived amine compound creatine, a compound particularly enriched in muscle and ciliated cells by a creatine-specific GATR, PP_3665, here named CahR (Creatine amidohydrolase Regulator). cahR is necessary for transcription of the gene encoding creatinase (PP_3667/creA) in the presence of creatine and is critical for P. putida's ability to utilize creatine as a sole source of nitrogen. The CahR/creatine regulon is small, and an electrophoretic mobility shift assay demonstrates strong and specific CahR binding only at the creA promoter, supporting the conclusion that much of the regulon is dependent on downstream metabolites. Phylogenetic analysis of creA orthologues associated with cahR orthologues highlights a strain distribution and organization supporting probable horizontal gene transfer, particularly evident within the genus Acinetobacter. This study identifies and characterizes the GATR that transcriptionally controls P. putida's metabolism of creatine, broadening the scope of known GATR ligands and suggesting GATR diversification during evolution of metabolism for aliphatic nitrogen compounds.}, }
@article {pmid35258077, year = {2022}, author = {Chakraborty, J and Chatterjee, R}, title = {Comparative genomics analysis of statistically significant genomic islands of Helicobacter pylori strains for better understanding the disease prognosis.}, journal = {Bioscience reports}, volume = {42}, number = {3}, pages = {}, pmid = {35258077}, issn = {1573-4935}, mesh = {Bacterial Proteins/genetics/metabolism ; Genomic Islands/genetics ; Genomics ; *Helicobacter Infections/genetics/microbiology/pathology ; *Helicobacter pylori/genetics ; Humans ; Virulence Factors/genetics ; }, abstract = {Bacterial virulence factors are often located in their genomic islands (GIs). Helicobacter pylori, a highly diverse organism is reported to be associated with several gastrointestinal diseases like, gastritis, gastric cancer (GC), peptic ulcer, duodenal ulcer (DU) etc. A novel similarity score (Sm)-based comparative analysis with GIs of 50 H. pylori strains revealed clear idea of the various factors which promote disease progression. Two putative pathogenic GIs in some of the H. pylori strains were identified. One GI, having a putative labile enterotoxin and other dynamin-like proteins (DLPs), is predicted to increase the release of toxin by membrane vesicular formation. Another island contains a virulence-associated protein D (vapD) which is a component of a type-II toxin-antitoxin system (TAs), leads to enhance the severity of the H. pylori infection. Besides the well-known virulence factors like Cytotoxin-associated gene A (CagA) and vacA, several GIs have been identified which showed to have direct or indirect impact on H. pylori clinical outcomes. One such GI, containing lipopolysaccharide (LPS) biosynthesis genes was revealed to be directly connected with disease development by inhibiting the immune response. Another collagenase-containing GI worsens ulcers by slowing down the healing process. GI consisted of fliD operon was found to be connected to flagellar assembly and biofilm production. By residing in biofilms, bacteria can avoid antibiotic therapy, resulting in chronic infection. Along with well-studied CagA and vacuolating toxin A (vacA) virulent genes, it is equally important to study these identified virulence factors for better understanding H. pylori-induced disease prognosis.}, }
@article {pmid35257370, year = {2022}, author = {Sanders, WB}, title = {The photoaerogens: algae and plants reunited conceptually.}, journal = {American journal of botany}, volume = {109}, number = {3}, pages = {363-365}, doi = {10.1002/ajb2.1828}, pmid = {35257370}, issn = {1537-2197}, mesh = {Biological Evolution ; *Gene Transfer, Horizontal ; Photosynthesis ; Phylogeny ; *Plants ; Plastids ; Symbiosis ; }, }
@article {pmid35254902, year = {2022}, author = {Acker, M and Hogle, SL and Berube, PM and Hackl, T and Coe, A and Stepanauskas, R and Chisholm, SW and Repeta, DJ}, title = {Phosphonate production by marine microbes: Exploring new sources and potential function.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {11}, pages = {e2113386119}, pmid = {35254902}, issn = {1091-6490}, mesh = {Aquatic Organisms/genetics/*metabolism ; Bacteria/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genes, Bacterial ; Models, Biological ; Organophosphonates/*metabolism ; Prochlorococcus/genetics/metabolism ; Quantitative Trait, Heritable ; Seawater/microbiology ; }, abstract = {SignificancePhosphonates are a class of phosphorus metabolites characterized by a highly stable C-P bond. Phosphonates accumulate to high concentrations in seawater, fuel a large fraction of marine methane production, and serve as a source of phosphorus to microbes inhabiting nutrient-limited regions of the oligotrophic ocean. Here, we show that 15% of all bacterioplankton in the surface ocean have genes phosphonate synthesis and that most belong to the abundant groups Prochlorococcus and SAR11. Genomic and chemical evidence suggests that phosphonates are incorporated into cell-surface phosphonoglycoproteins that may act to mitigate cell mortality by grazing and viral lysis. These results underscore the large global biogeochemical impact of relatively rare but highly expressed traits in numerically abundant groups of marine bacteria.}, }
@article {pmid35254236, year = {2022}, author = {Tomasch, J and Ringel, V and Wang, H and Freese, HM and Bartling, P and Brinkmann, H and Vollmers, J and Jarek, M and Wagner-Döbler, I and Petersen, J}, title = {Fatal affairs - conjugational transfer of a dinoflagellate-killing plasmid between marine Rhodobacterales.}, journal = {Microbial genomics}, volume = {8}, number = {3}, pages = {}, pmid = {35254236}, issn = {2057-5858}, mesh = {*Dinoflagellida/genetics ; Plasmids/genetics ; Replicon ; Rhodobacteraceae ; *Roseobacter/genetics ; }, abstract = {The roseobacter group of marine bacteria is characterized by a mosaic distribution of ecologically important phenotypes. These are often encoded on mobile extrachromosomal replicons. So far, conjugation had only been experimentally proven between the two model organisms Phaeobacter inhibens and Dinoroseobacter shibae. Here, we show that two large natural RepABC-type plasmids from D. shibae can be transferred into representatives of all known major Rhodobacterales lineages. Complete genome sequencing of the newly established Phaeobacter inhibens transconjugants confirmed their genomic integrity. The conjugated plasmids were stably maintained as single copy number replicons in the genuine as well as the new host. Co-cultivation of Phaeobacter inhibens and the transconjugants with the dinoflagellate Prorocentrum minimum demonstrated that Phaeobacter inhibens is a probiotic strain that improves the yield and stability of the dinoflagellate culture. The transconjugant carrying the 191 kb plasmid, but not the 126 kb sister plasmid, killed the dinoflagellate in co-culture.}, }
@article {pmid35248462, year = {2022}, author = {Balasubramanian, D and López-Pérez, M and Grant, TA and Ogbunugafor, CB and Almagro-Moreno, S}, title = {Molecular mechanisms and drivers of pathogen emergence.}, journal = {Trends in microbiology}, volume = {30}, number = {9}, pages = {898-911}, doi = {10.1016/j.tim.2022.02.003}, pmid = {35248462}, issn = {1878-4380}, mesh = {*Bacteria/genetics ; }, abstract = {Pathogen emergence (PE) is a complex phenomenon with major public health implications. Over the past decades, numerous underlying mechanisms facilitating the emergence of pathogenic bacteria have been elucidated. In this review, we highlight the diverse molecular and environmental drivers associated with PE, with an emphasis on the interplay of canonical gene transfer mechanisms and the increasingly appreciated role of genetic variations, providing a more coherent picture of this process. Given the interactive and multifactorial nature of PE, we contend that the development of approaches that embrace the integration of these factors is indispensable in order to truly comprehend this complex phenomenon and develop strategies to mitigate this threat.}, }
@article {pmid35247986, year = {2022}, author = {Dufault-Thompson, K and Hall, B and Jiang, X}, title = {Taxonomic distribution and evolutionary analysis of the equol biosynthesis gene cluster.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {182}, pmid = {35247986}, issn = {1471-2164}, mesh = {*Actinobacteria/genetics ; Equol/metabolism ; Humans ; *Isoflavones/metabolism ; Multigene Family ; Phylogeny ; }, abstract = {BACKGROUND: Equol, an isoflavonoid metabolite with possible health benefits in humans, is known to be produced by some human gut bacteria. While the genes encoding the equol production pathway have been characterized in a few bacterial strains, a systematic analysis of the equol production pathway is currently lacking.<br><br>RESULTS: This study presents an analysis of the taxonomic distribution and evolutionary history of the gene cluster encoding the equol production pathway. A survey for equol gene clusters within the Genome Taxonomy Database bacterial genomes and human gut metagenomes resulted in the identification of a highly conserved gene cluster found in nine bacterial species from the Eggerthellaceae family. The identified gene clusters from human gut metagenomes revealed potential variations in the equol gene cluster organization and gene content within the equol-producing Eggerthellaceae clades. Subsequent analysis showed that in addition to the four genes directly involved in equol production, multiple other genes were consistently found in the equol gene clusters. These genes were predicted to encode a putative electron transport complex and hydrogenase maturase system, suggesting potential roles for them in the equol production pathway. Analysis of the gene clusters and a phylogenetic reconstruction of a putative NAD kinase gene provided evidence of the recent transfer of the equol gene cluster from a basal Eggerthellaceae species to Slackia_A equolifaciens, Enteroscipio sp000270285, and Lactococcus garvieae 20-92.<br><br>CONCLUSIONS: This analysis demonstrates that the highly conserved equol gene cluster is taxonomically restricted to the Eggerthellaceae family of bacteria and provides evidence of the role of horizontal gene transfer in the evolutionary history of these genes. These results provide a foundation for future studies of equol production in the human gut and future efforts related to bioengineering and the use of equol-producing bacteria as probiotics.}, }
@article {pmid35247696, year = {2022}, author = {Zhang, K and Wang, T and Chen, J and Guo, J and Luo, H and Chen, W and Mo, Y and Wei, Z and Huang, X}, title = {The reduction and fate of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in microbial fuel cell (MFC) during treatment of livestock wastewater.}, journal = {Journal of contaminant hydrology}, volume = {247}, number = {}, pages = {103981}, doi = {10.1016/j.jconhyd.2022.103981}, pmid = {35247696}, issn = {1873-6009}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Bioelectric Energy Sources ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Interspersed Repetitive Sequences ; Livestock/genetics ; RNA, Ribosomal, 16S ; Sulfonamides ; Tetracycline ; *Wastewater ; }, abstract = {The fate and removal efficiency of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in livestock wastewater by microbial fuel cell (MFC) was evaluated by High-throughput quantitative PCR. The results showed that 137 ARGs and 9 MGEs were detected in untreated livestock wastewater. The ARG number of macrolide-lincosamide-streptogramin group B (MLSB), tetracycline and sulfonamide were relatively higher. Throughout the treatment process, the number and abundance of ARGs and MGEs significantly decreased. The relative abundance of tetracycline, sulfonamide and chloramphenicol resistance genes showed the most obvious decreasing trend, and the relative abundance of MGEs decreased by 75% (from 0.012 copies/16S rRNA copies to 0.003 copies/16S rRNA copies). However, the absolute abundance of beta-lactamase resistance genes slightly increased. The operation process of MFC produces selective pressure on microorganisms, and Actinobacteria were predominant and had the ability to decompose antibiotics. The COD removal rate and TN removal rate of livestock wastewater were 67.81% and 62.09%, and the maximum power density and coulomb efficiency (CE) reached 11.49% and 38.40% respectively. This study demonstrated that although the removal of COD and TN by MFC was limited, MFC was quite effective in reducing the risk of antibiotic toxicity and horizontal gene transfer.}, }
@article {pmid35247556, year = {2022}, author = {Damtie, MM and Lee, J and Shin, J and Shin, SG and Son, H and Wang, J and Kim, YM}, title = {Identification of factors affecting removal of antibiotic resistance genes in full-scale anaerobic digesters treating organic solid wastes.}, journal = {Bioresource technology}, volume = {351}, number = {}, pages = {126929}, doi = {10.1016/j.biortech.2022.126929}, pmid = {35247556}, issn = {1873-2976}, mesh = {Anaerobiosis ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Food ; *Refuse Disposal ; Sewage ; *Solid Waste ; }, abstract = {Efficiencies of removing antibiotic resistance genes (ARGs) and intI1 were explored using eight full-scale anaerobic digesters. The digesters demonstrated different characteristics on the basis of substrate types (food waste, manure or sludge); configuration (single or two-stage); temperature (psychrophilic, mesophilic or thermophilic); hydraulic retention time (HRT) (9.7-44 days); and operation mode (continuous stirred tank reactor or plug flow reactor). Digesters' configuration or operating parameters showed a greater effect on abundance of ARGs than the type of input substrate. Redundancy analysis (RDA) accounted for 85.2% of the total variances and digesters with the same configuration and operational conditions showed similar performance for removal of ARGs. The highest efficiencies of removing ARGs (99.99%) were observed in two-stage thermophilic digesters with relatively long HRTs (32 days). The lowest removal efficiency (97.93%) was observed in single-stage mesophilic with relatively short HRTs (9.7 days), likely due to vertical and horizontal gene transfer.}, }
@article {pmid35244541, year = {2022}, author = {D'Angelo, F and Fernández-Fueyo, E and Garcia, PS and Shomar, H and Pelosse, M and Manuel, RR and Büke, F and Liu, S and van den Broek, N and Duraffourg, N and de Ram, C and Pabst, M and Bouveret, E and Gribaldo, S and Py, B and Ollagnier de Choudens, S and Barras, F and Bokinsky, G}, title = {Cellular assays identify barriers impeding iron-sulfur enzyme activity in a non-native prokaryotic host.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {35244541}, issn = {2050-084X}, mesh = {Escherichia coli/genetics/metabolism ; *Escherichia coli Proteins/metabolism ; Iron/metabolism ; *Iron-Sulfur Proteins/genetics/metabolism ; Phylogeny ; Sulfur/metabolism ; }, abstract = {Iron-sulfur (Fe-S) clusters are ancient and ubiquitous protein cofactors and play irreplaceable roles in many metabolic and regulatory processes. Fe-S clusters are built and distributed to Fe-S enzymes by dedicated protein networks. The core components of these networks are widely conserved and highly versatile. However, Fe-S proteins and enzymes are often inactive outside their native host species. We sought to systematically investigate the compatibility of Fe-S networks with non-native Fe-S enzymes. By using collections of Fe-S enzyme orthologs representative of the entire range of prokaryotic diversity, we uncovered a striking correlation between phylogenetic distance and probability of functional expression. Moreover, coexpression of a heterologous Fe-S biogenesis pathway increases the phylogenetic range of orthologs that can be supported by the foreign host. We also find that Fe-S enzymes that require specific electron carrier proteins are rarely functionally expressed unless their taxon-specific reducing partners are identified and co-expressed. We demonstrate how these principles can be applied to improve the activity of a radical S-adenosyl methionine(rSAM) enzyme from a Streptomyces antibiotic biosynthesis pathway in Escherichia coli. Our results clarify how oxygen sensitivity and incompatibilities with foreign Fe-S and electron transfer networks each impede heterologous activity. In particular, identifying compatible electron transfer proteins and heterologous Fe-S biogenesis pathways may prove essential for engineering functional Fe-S enzyme-dependent pathways.}, }
@article {pmid35242113, year = {2021}, author = {González-Rosales, C and Vergara, E and Dopson, M and Valdés, JH and Holmes, DS}, title = {Integrative Genomics Sheds Light on Evolutionary Forces Shaping the Acidithiobacillia Class Acidophilic Lifestyle.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {822229}, pmid = {35242113}, issn = {1664-302X}, abstract = {Extreme acidophiles thrive in environments rich in protons (pH values <3) and often high levels of dissolved heavy metals. They are distributed across the three domains of the Tree of Life including members of the Proteobacteria. The Acidithiobacillia class is formed by the neutrophilic genus Thermithiobacillus along with the extremely acidophilic genera Fervidacidithiobacillus, Igneacidithiobacillus, Ambacidithiobacillus, and Acidithiobacillus. Phylogenomic reconstruction revealed a division in the Acidithiobacillia class correlating with the different pH optima that suggested that the acidophilic genera evolved from an ancestral neutrophile within the Acidithiobacillia. Genes and mechanisms denominated as "first line of defense" were key to explaining the Acidithiobacillia acidophilic lifestyle including preventing proton influx that allows the cell to maintain a near-neutral cytoplasmic pH and differ from the neutrophilic Acidithiobacillia ancestors that lacked these systems. Additional differences between the neutrophilic and acidophilic Acidithiobacillia included the higher number of gene copies in the acidophilic genera coding for "second line of defense" systems that neutralize and/or expel protons from cell. Gain of genes such as hopanoid biosynthesis involved in membrane stabilization at low pH and the functional redundancy for generating an internal positive membrane potential revealed the transition from neutrophilic properties to a new acidophilic lifestyle by shaping the Acidithiobacillaceae genomic structure. The presence of a pool of accessory genes with functional redundancy provides the opportunity to "hedge bet" in rapidly changing acidic environments. Although a core of mechanisms for acid resistance was inherited vertically from an inferred neutrophilic ancestor, the majority of mechanisms, especially those potentially involved in resistance to extremely low pH, were obtained from other extreme acidophiles by horizontal gene transfer (HGT) events.}, }
@article {pmid35241653, year = {2022}, author = {Forrest, D and Warman, EA and Erkelens, AM and Dame, RT and Grainger, DC}, title = {Xenogeneic silencing strategies in bacteria are dictated by RNA polymerase promiscuity.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {1149}, pmid = {35241653}, issn = {2041-1723}, support = {/WT_/Wellcome Trust/United Kingdom ; 212193/Z/18/Z//Wellcome Trust (Wellcome)/ ; }, mesh = {Bacillus subtilis/genetics/metabolism ; *Bacterial Proteins/genetics/metabolism ; DNA ; DNA-Directed RNA Polymerases/genetics/metabolism ; *Escherichia coli/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Transcription, Genetic ; }, abstract = {Horizontal gene transfer facilitates dissemination of favourable traits among bacteria. However, foreign DNA can also reduce host fitness: incoming sequences with a higher AT content than the host genome can misdirect transcription. Xenogeneic silencing proteins counteract this by modulating RNA polymerase binding. In this work, we compare xenogeneic silencing strategies of two distantly related model organisms: Escherichia coli and Bacillus subtilis. In E. coli, silencing is mediated by the H-NS protein that binds extensively across horizontally acquired genes. This prevents spurious non-coding transcription, mostly intragenic in origin. By contrast, binding of the B. subtilis Rok protein is more targeted and mostly silences expression of functional mRNAs. The difference reflects contrasting transcriptional promiscuity in E. coli and B. subtilis, largely attributable to housekeeping RNA polymerase σ factors. Thus, whilst RNA polymerase specificity is key to the xenogeneic silencing strategy of B. subtilis, transcriptional promiscuity must be overcome to silence horizontally acquired DNA in E. coli.}, }
@article {pmid35240335, year = {2022}, author = {Wertheim, B}, title = {Adaptations and counter-adaptations in Drosophila host-parasitoid interactions: advances in the molecular mechanisms.}, journal = {Current opinion in insect science}, volume = {51}, number = {}, pages = {100896}, doi = {10.1016/j.cois.2022.100896}, pmid = {35240335}, issn = {2214-5753}, mesh = {Acclimatization ; Animals ; *Drosophila ; *Host-Parasite Interactions ; Larva ; Phenotype ; }, abstract = {Both hosts and parasitoids evolved a diverse array of traits and strategies for their antagonistic interactions, affecting their chances of encounter, attack and survival after parasitoid attack. This review summarizes the recent progress that has been made in elucidating the molecular mechanisms of these adaptations and counter-adaptations in various Drosophila host-parasitoid interactions. For the hosts, it focuses on the neurobiological and genetic control of strategies in Drosophila adults and larvae of avoidance or escape behaviours upon sensing the parasitoids, and the immunological defences involving diverse classes of haemocytes. For the parasitoids, it highlights their behavioural strategies in host finding, as well as the rich variety of venom components that evolved and were partially acquired through horizontal gene transfer. Recent studies revealed the mechanisms by which these venom components manipulate their parasitized hosts in exhibiting escape behaviour to avoid superparasitism, and their counter-strategies to evade or obstruct the hosts' immunological defences.}, }
@article {pmid35240255, year = {2022}, author = {Yang, R and Zhang, B and Xu, Y and Zhang, G and Liu, Y and Zhang, D and Zhang, W and Chen, T and Liu, G}, title = {Genomic insights revealed the environmental adaptability of Planococcus halotolerans Y50 isolated from petroleum-contaminated soil on the Qinghai-Tibet Plateau.}, journal = {Gene}, volume = {823}, number = {}, pages = {146368}, doi = {10.1016/j.gene.2022.146368}, pmid = {35240255}, issn = {1879-0038}, mesh = {Base Composition ; Biodegradation, Environmental ; Genome Size ; *Genome, Bacterial ; Petroleum/analysis/*microbiology ; Phylogeny ; Planococcaceae/classification/genetics/isolation &amp; purification/*physiology ; Soil Microbiology ; Tibet ; Whole Genome Sequencing ; }, abstract = {The Tibetan Plateau niche provides unprecedented opportunities to find microbes that are functional and commercial significance. The present study investigated the physiological and genomic characteristics of Planococcus halotolerans Y50 that was isolated from a petroleum-contaminated soil sample from the Qinghai-Tibet Plateau, and it displayed psychrotolerant, antiradiation, and oil-degraded characteristics. Whole genome sequencing indicated that strain Y50 has a 3.52 Mb genome and 44.7% G + C content, and it possesses 3377 CDSs. The presence of a wide range of UV damage repair genes uvrX and uvsE, DNA repair genes radA and recN, superoxide dismutase, peroxiredoxin and dioxygenase genes provided the genomic basis for the adaptation of the plateau environment polluted by petroleum. Related experiments also verified that the Y50 strain could degrade n-alkanes from C11-C23, and approximately 30% of the total petroleum at 25 °C within 7 days. Meanwhile, strain Y50 could withstand 5 × 10[3] J/m[2] UVC and 10 KGy gamma ray radiation, and it had strong antioxidant and high radical scavengers for superoxide anion, hydroxyl radical and DPPH. In addition, pan-genome analysis and horizontal gene transfers revealed that strains with different niches have obtained various genes through horizontal gene transfer in the process of evolution, and the more similar their geographical locations, the more similar their members are genetically and ecologically. In conclusion, P. halotolerans Y50 possesses high potential of applications in the bioremediation of alpine hydrocarbons contaminated environment.}, }
@article {pmid35240043, year = {2022}, author = {Pudlo, NA and Pereira, GV and Parnami, J and Cid, M and Markert, S and Tingley, JP and Unfried, F and Ali, A and Varghese, NJ and Kim, KS and Campbell, A and Urs, K and Xiao, Y and Adams, R and Martin, D and Bolam, DN and Becher, D and Eloe-Fadrosh, EA and Schmidt, TM and Abbott, DW and Schweder, T and Hehemann, JH and Martens, EC}, title = {Diverse events have transferred genes for edible seaweed digestion from marine to human gut bacteria.}, journal = {Cell host &amp; microbe}, volume = {30}, number = {3}, pages = {314-328.e11}, pmid = {35240043}, issn = {1934-6069}, support = {R01 DK118024/DK/NIDDK NIH HHS/United States ; R01 DK125445/DK/NIDDK NIH HHS/United States ; R01 GM099513/GM/NIGMS NIH HHS/United States ; R03 DK096023/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteria/genetics/metabolism ; Bacteroides/metabolism ; Digestion ; *Gastrointestinal Microbiome/genetics ; Humans ; Polysaccharides/metabolism ; *Seaweed/metabolism ; }, abstract = {Humans harbor numerous species of colonic bacteria that digest fiber polysaccharides in commonly consumed terrestrial plants. More recently in history, regional populations have consumed edible macroalgae seaweeds containing unique polysaccharides. It remains unclear how extensively gut bacteria have adapted to digest these nutrients. Here, we show that the ability of gut bacteria to digest seaweed polysaccharides is more pervasive than previously appreciated. Enrichment-cultured Bacteroides harbor previously discovered genes for seaweed degradation, which have mobilized into several members of this genus. Additionally, other examples of marine bacteria-derived genes, and their mobile DNA elements, are involved in gut microbial degradation of seaweed polysaccharides, including genes in gut-resident Firmicutes. Collectively, these results uncover multiple separate events that have mobilized the genes encoding seaweed-degrading-enzymes into gut bacteria. This work further underscores the metabolic plasticity of the human gut microbiome and global exchange of genes in the context of dietary selective pressures.}, }
@article {pmid35235827, year = {2022}, author = {Ma, J and Wang, S and Zhu, X and Sun, G and Chang, G and Li, L and Hu, X and Zhang, S and Zhou, Y and Song, CP and Huang, J}, title = {Major episodes of horizontal gene transfer drove the evolution of land plants.}, journal = {Molecular plant}, volume = {15}, number = {5}, pages = {857-871}, doi = {10.1016/j.molp.2022.02.001}, pmid = {35235827}, issn = {1752-9867}, mesh = {Animals ; *Embryophyta/genetics ; *Gene Transfer, Horizontal/genetics ; Seeds ; }, abstract = {How horizontal gene transfer (HGT) has contributed to the evolution of animals and plants remains a major puzzle. Despite recent progress, defining the overall scale and pattern of HGT events in land plants has been largely elusive. In this study, we performed systematic analyses for acquired genes in different plant groups and throughout land plant evolution. We found that relatively recent HGT events occurred in charophytes and all major land plant groups, but their frequency declined rapidly in seed plants. Two major episodes of HGT events occurred in land plant evolution, corresponding to the early evolution of streptophytes and the origin of land plants, respectively. Importantly, a vast majority of the genes acquired in the two episodes have been retained in descendant groups, affecting numerous activities and processes of land plants. We analyzed some of the acquired genes involved in stress responses, ion and metabolite transport, growth and development, and specialized metabolism, and further assessed the cumulative effects of HGT in land plants.}, }
@article {pmid35234510, year = {2022}, author = {Liu, Y and Yang, F and Wang, S and Chi, W and Ding, L and Liu, T and Zhu, F and Ji, D and Zhou, J and Fang, Y and Zhang, J and Xiang, P and Zhang, Y and Zhao, H}, title = {HopE and HopD Porin-Mediated Drug Influx Contributes to Intrinsic Antimicrobial Susceptibility and Inhibits Streptomycin Resistance Acquisition by Natural Transformation in Helicobacter pylori.}, journal = {Microbiology spectrum}, volume = {10}, number = {2}, pages = {e0198721}, pmid = {35234510}, issn = {2165-0497}, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; *Anti-Infective Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; *Helicobacter Infections ; *Helicobacter pylori/genetics ; Humans ; Microbial Sensitivity Tests ; Porins/genetics/pharmacology ; Streptomycin/pharmacology ; }, abstract = {Helicobacter pylori is a human pathogen competent for natural transformation. Intrinsic and acquired antibiotic resistance contribute to the survival and multiplication of H. pylori under antibiotics. While drug-resistance dissemination by natural transformation (NT)-mediated horizontal gene transfer remains poorly understood in H. pylori. The purpose of the study was to investigate the role of H. pylori porins (HopA, HopB, HopC, HopD, and HopE) in the intrinsic antibiotic resistance and to preliminarily reveal the potential effect of HopE and HopD porins in streptomycin resistance acquisition after NT in the presence of antibiotics. Using traditional antibiotic susceptibility tests and growth curve analysis, we found the MIC values of metronidazole, clarithromycin, levofloxacin, tetracycline, rifampin, and streptomycin in mutants lacking HopE and/or HopD were significantly elevated compare to those in wild-type strain. The quantitative analysis of the tetramethyl rhodamine isothiocyanate (TRITC)-labeled streptomycin accumulation at the single-cell level showed reduced streptomycin intracellular fluorescence in ΔhopE and ΔhopD mutant cells. Furthermore, in the presence of translation-inhibiting antibiotic streptomycin, the resistance acquisition frequency was decreased in the wild-type strain, which could be reversed by mutants lacking HopE and HopD that restored relatively high resistance acquisition frequencies. By transforming a pUC19-rpsLmut-sfgfp linear plasmid carrying a streptomycin conferring mutation, we observed that the impaired ability of rpsLmut synthesis in the wild-type strain was restored in the ΔhopE and ΔhopD mutant transformants. Our study revealed that in the presence of streptomycin, resistance acquisition at least partially relied on the deletion of the hopE and hopD genes, because their loss reduced streptomycin concentration in the cell and thus restored the expression of the resistance-conferring gene, which was inhibited by streptomycin in wild-type strain. The loss of HopE and HopD influx activity may also preserve resistance acquisition by transformation in the presence of antibiotics with other modes of action. IMPORTANCE Helicobacter pylori is constitutively competent for natural transformation (NT) and possesses an efficient system for homologous recombination, which could be utilized to study the NT-mediated horizontal gene transfer induced antibiotic resistance acquisition. Bacterial porins have drawn renewed attention because of their crucial role in antibiotic susceptibility. From the perspective of porin-mediated influx in H. pylori, our study preliminarily revealed the important role of HopE and HopD porins not only in preserving the intrinsic susceptibility to specific antibiotic but also in evading acquired antibiotic resistance by NT in the presence of translation-inhibiting antimicrobial. Therefore, the loss of HopE or HopD porin in H. pylori genomes, combined with the large number of secreted or cell-free genetic elements carrying mutations conferring antibiotic resistance, may raise the possibility that this mechanism plays a potential role in the propagation of antibiotic resistance within H. pylori communities.}, }
@article {pmid35230931, year = {2022}, author = {Hilbi, H and Buchrieser, C}, title = {Microbe Profile: Legionella pneumophila - a copycat eukaryote.}, journal = {Microbiology (Reading, England)}, volume = {168}, number = {3}, pages = {}, doi = {10.1099/mic.0.001142}, pmid = {35230931}, issn = {1465-2080}, mesh = {Bacterial Proteins/genetics/metabolism ; Eukaryota ; Gene Transfer, Horizontal ; Humans ; *Legionella pneumophila/genetics/metabolism ; }, abstract = {Legionella pneumophila is an environmental bacterium that parasitizes aquatic protozoa and uses the same processes to infect humans. The facultative intracellular pathogen causes a life-threatening pneumonia with possible systemic complications. The co-evolution with protozoa is reflected in an armoury of bacterial effectors, and many of these type IV-secreted proteins have likely been acquired by interdomain horizontal gene transfer (HGT) from hosts. The unique features of L. pneumophila are the largest bacterial effector repertoire known to date, subversion of virtually all eukaryotic signalling pathways and acquisition of eukaryotic enzyme activities used to manipulate the host cell to the pathogen's advantage.}, }
@article {pmid35230132, year = {2022}, author = {Yin, Z and Liu, X and Qian, C and Sun, L and Pang, S and Liu, J and Li, W and Huang, W and Cui, S and Zhang, C and Song, W and Wang, D and Xie, Z}, title = {Pan-Genome Analysis of Delftia tsuruhatensis Reveals Important Traits Concerning the Genetic Diversity, Pathogenicity, and Biotechnological Properties of the Species.}, journal = {Microbiology spectrum}, volume = {10}, number = {2}, pages = {e0207221}, pmid = {35230132}, issn = {2165-0497}, mesh = {*Anti-Infective Agents ; Delftia ; Genetic Variation ; *Genome, Bacterial ; Humans ; Phosphate Transport Proteins/genetics ; Phylogeny ; Virulence/genetics ; Virulence Factors/genetics ; }, abstract = {Delftia tsuruhatensis strains have long been known to promote plant growth and biological control. Recently, it has become an emerging opportunistic pathogen in humans. However, the genomic characteristics of the genetic diversity, pathogenicity, and biotechnological properties have not yet been comprehensively investigated. Here, a comparative pan-genome analysis was constructed. The open pan-genome with a large and flexible gene repertoire exhibited a high degree of genetic diversity. The purifying selection was the main force to drive pan-genome evolution. Significant differences were observed in the evolutionary relationship, functional enrichment, and degree of selective pressure between the different components of the pan-genome. A high degree of genetic plasticity was characterized by the determinations of diverse mobile genetic elements (MGEs), massive genomic rearrangement, and horizontal genes. Horizontal gene transfer (HGT) plays an important role in the genetic diversity of this bacterium and the formation of genomic traits. Our results revealed the occurrence of diverse virulence-related elements associated with macromolecular secretion systems, virulence factors associated with multiple nosocomial infections, and antimicrobial resistance, indicating the pathogenic potential. Lateral flagellum, T1SS, T2SS, T6SS, Tad pilus, type IV pilus, and a part of virulence-related genes exhibited general properties, whereas polar flagellum, T4SS, a part of virulence-related genes, and resistance genes presented heterogeneous properties. The pan-genome also harbors abundant genetic traits related to secondary metabolism, carbohydrate active enzymes (CAZymes), and phosphate transporter, indicating rhizosphere adaptation, plant growth promotion, and great potential uses in agriculture and biological control. This study provides comprehensive insights into this uncommon species from the genomic perspective. IMPORTANCE D. tsuruhatensis is considered a plant growth-promoting rhizobacterium (PGPR), an organic pollutant degradation strain, and an emerging opportunistic pathogen to the human. However, the genetic diversity, the evolutionary dynamics, and the genetic basis of these remarkable traits are still little known. We constructed a pan-genome analysis for D. tsuruhatensis and revealed extensive genetic diversity and genetic plasticity exhibited by open pan-genome, diverse mobile genetic elements (MGEs), genomic rearrangement, and horizontal genes. Our results highlight that horizontal gene transfer (HGT) and purifying selection are important forces in D. tsuruhatensis genetic evolution. The abundant virulence-related elements associated with macromolecular secretion systems, virulence factors, and antimicrobial resistance could contribute to the pathogenicity of this bacterium. Therefore, clinical microbiologists need to be aware of D. tsuruhatensis as an opportunistic pathogen. The genetic profiles of secondary metabolism, carbohydrate active enzymes (CAZymes), and phosphate transporter could provide insight into the genetic armory of potential applications for agriculture and biological control of D. tsuruhatensis in general.}, }
@article {pmid35230128, year = {2022}, author = {Xiao, X and Zeng, F and Li, R and Liu, Y and Wang, Z}, title = {Subinhibitory Concentration of Colistin Promotes the Conjugation Frequencies of Mcr-1- and blaNDM-5-Positive Plasmids.}, journal = {Microbiology spectrum}, volume = {10}, number = {2}, pages = {e0216021}, pmid = {35230128}, issn = {2165-0497}, mesh = {Anti-Bacterial Agents/pharmacology ; Colistin/pharmacology ; Drug Resistance, Bacterial/genetics ; Escherichia coli/genetics ; *Escherichia coli Infections/microbiology ; *Escherichia coli Proteins/genetics ; Humans ; Microbial Sensitivity Tests ; Plasmids/genetics ; }, abstract = {Horizontal gene transfer (HGT) plays a significant role in the spread of antibiotic resistance genes (ARGs). Most reported compounds promote HGT by increasing the cell membrane permeability. Colistin has been reported to increase the cell membrane permeability when exhibiting its antibacterial effect. Therefore, this study aimed to investigate the potential role of colistin in facilitating the dissemination of ARGs via plasmid conjugation by establishing an in vitro mating model. Three strains Escherichia coli (E. coli) DH5α, E. coli L65, and E. coli LD67-1 carrying plasmid RP4-7, blaNDM-5 positive IncX3 plasmid, and mcr-1 positive IncI2 plasmid, respectively, were regarded as the donor strains and E. coli J53 as the recipient strain. Exposure to subinhibitory concentrations of colistin (1/4, 1/8, 1/16 MIC) significantly stimulated the conjugation frequency of RP-4 plasmid, wide-type IncI2 and IncX3 plasmid. Scanning electron microscopy revealed the shrunken cell membrane after colistin treatment, whereas propidium iodide dye and 1-N-Phenylnaphthylamine fluorescent probe showed the increased cell membrane permeability. Additionally, the expression level of the outer membrane proteins (ompF and ompC) was increased. These results indicate a break in the membrane barrier. The expression of the mating pair formation gene (trbBp) was promoted and the expression of the global regulatory genes (korA, trbA), which downregulates trbBp expression, was inhibited. Thus, the production of the mating pairing machine could be elevated after colistin exposure. These findings aid in understanding the hidden risks of colistin on the spread of antimicrobial resistance. IMPORTANCE Antimicrobial resistance (AMR) dissemination is a growing global threat. As a last-resort treatment against multidrug-resistant and extensively drug-resistant Gram-negative bacteria, colistin has been used for prophylactic and therapeutic purposes in veterinary medicine. Previous studies have reported the presence of colistin residues in the intestinal tract and feces. The role of colistin in facilitating the conjugation frequency of mcr-1- and blaNDM-5-positive plasmids was confirmed in this study along with elucidating its potential mechanisms. This study raises awareness of the potential AMR dissemination roles induced by colistin in environmental settings.}, }
@article {pmid35229649, year = {2022}, author = {Yin, Z and Wang, X and Hu, Y and Zhang, J and Li, H and Cui, Y and Zhao, D and Dong, X and Zhang, X and Liu, K and Du, B and Ding, Y and Wang, C}, title = {Metabacillus dongyingensis sp. nov. Is Represented by the Plant Growth-Promoting Bacterium BY2G20 Isolated from Saline-Alkaline Soil and Enhances the Growth of Zea mays L. under Salt Stress.}, journal = {mSystems}, volume = {7}, number = {2}, pages = {e0142621}, pmid = {35229649}, issn = {2379-5077}, mesh = {*Zea mays ; *Soil/chemistry ; Ecosystem ; Phylogeny ; Bacteria/genetics ; Salt Stress ; }, abstract = {A novel plant growth-promoting rhizobacterium (PGPR), which was designated strain BY2G20, was isolated from saline-alkaline soil in Dongying, China. Strain BY2G20 can grow at a NaCl range from 0 to 7% and a pH range from 7 to 9 and can prevent the growth of the phytopathogen Ralstonia solanacearum. Based on its phenotypic and genomic characteristics and phylogenetic analysis, strain BY2G20 represents a novel species of the genus Metabacillus, for which the name Metabacillus dongyingensis sp. nov. is proposed. Comparative genomic analysis of strain BY2G20 with its closely related species exhibited a high level of evolutionary plasticity derived by horizontal gene transfer, which facilitated adaptative evolution. Different evolutionary constraints have operated on the diverse functions of BY2G20, with the gene adapted to saline-alkaline ecosystems experiencing functional constraints. We determined the genetic properties of saline-alkaline tolerance and plant growth promotion, such as cation-proton antiporters, cation transporters, osmoprotectant synthesis and transport, H[+]-transporting F1F0-ATPase, indole-3-acetic acid production, and secondary metabolite synthesis. We also evaluated the effects of strain BY2G20 on the growth of Zea mays L. (maize) under salt stress. The physiological parameters of maize such as plant height, stem diameter, dry biomass, and fresh biomass were significantly higher after inoculating strain BY2G20 under salt stress, indicating that inoculation with BY2G20 enhanced the growth of maize in saline areas. This study demonstrates that M. dongyingensis sp. nov. BY2G20 is a potential candidate for organic agriculture biofertilizers in saline-alkaline areas. IMPORTANCE Plant growth and yield are adversely affected by soil salinity. PGPRs can promote plant growth and enhance plant tolerance to salt stress. In this study, a saline-alkaline tolerant PGPR strain BY2G20 was isolated from the rhizosphere of Ulmus pumila in Dongying, China. Strain BY2G20 represents a novel species within the genus Metabacillus based on phenotypic, genomic, and phylogenetic analysis. Genomic components have undergone different functional constraints, and the disparity in the evolutionary rate may be associated with the adaptation to a specific niche. Genomic analysis revealed numerous adaptive features of strain BY2G20 to a saline-alkaline environment and rhizosphere, especially genes related to salt tolerance, pH adaptability, and plant growth promotion. Our work also exhibited that inoculation of strain BY2G20 enhanced the growth of maize under salt stress. This study demonstrates that PGPRs play an important role in stimulating salt tolerance in plants and can be used as biofertilizers to enhance the growth of crops in saline-alkaline areas.}, }
@article {pmid35229647, year = {2022}, author = {Liu, M and Nie, H and Luo, X and Yang, S and Chen, H and Cai, P}, title = {A Polysaccharide Biosynthesis Locus in Vibrio parahaemolyticus Important for Biofilm Formation Has Homologs Widely Distributed in Aquatic Bacteria Mainly from Gammaproteobacteria.}, journal = {mSystems}, volume = {7}, number = {2}, pages = {e0122621}, pmid = {35229647}, issn = {2379-5077}, mesh = {*Vibrio parahaemolyticus/genetics ; *Gammaproteobacteria ; Biofilms ; Quorum Sensing ; }, abstract = {Vibrio parahaemolyticus is a seafood-borne pathogen that poses a great threat to public health worldwide. It is found in either a planktonic cell or a biofilm form in the natural environment. The cps locus has been the only extensively studied polysaccharide biosynthesis gene cluster involved in biofilm formation for this bacterium. In this study, we found that an additional polysaccharide biosynthesis locus, scv, is also necessary for biofilm maturation. The scv locus is composed of two operons, and a loss of their expression leads to a defective biofilm phenotype. The transcription of the scv locus is under the control of a sigma 54-dependent response regulator, ScvE. In contrast, the quorum-sensing regulator AphA stimulates the expression of the cps locus and the scvABCD operon found in the scv locus. Bioinformatic analyses demonstrated that scv loci are divergent and widely distributed among 28 genera, including 26 belonging to the Gammaproteobacteria and 2 within the Alphaproteobacteria. We also determined that all scv locus-positive species are water-dwelling. Some strains of Aeromonas, Aliivibrio salmonicida, Pseudomonas anguilliseptica, Vibrio breoganii, and Vibrio scophthalmi probably acquired scv loci through insertion sequences and/or integrase-mediated horizontal gene transfer. Gene duplication and fusion were also detected in some scv homologs. Together, our results suggest that the genome of V. parahaemolyticus harbors two distinct polysaccharide biosynthesis loci, which may play a role in fine-tuning biofilm development, and that scv loci likely evolved by horizontal gene transfer, gene loss, gene duplication, and fragment fusion. IMPORTANCE Polysaccharides are the major component of biofilms, which provide survival advantages for bacteria in aquatic environments. The seafood-borne pathogen V. parahaemolyticus possesses a functionally uncharacterized polysaccharide biosynthesis locus, scv. We demonstrated that the scv locus is important for biofilm maturation and that scv expression is positively regulated by ScvE. Strains from 148 aquatic bacterial species possess scv homolog loci. These bacterial species belong to 28 genera, most of which belong to the Gammaproteobacteria class. The evolution and diversification of scv loci are likely driven by horizontal gene transfer, gene loss, gene duplication, and fragment fusion. Our results provide new insights into the function and evolution of this widespread polysaccharide biosynthesis locus.}, }
@article {pmid35228526, year = {2022}, author = {Rodriguez, F and Yushenova, IA and DiCorpo, D and Arkhipova, IR}, title = {Bacterial N4-methylcytosine as an epigenetic mark in eukaryotic DNA.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {1072}, pmid = {35228526}, issn = {2041-1723}, support = {R01 GM111917/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/genetics/metabolism ; Chromatin ; DNA/metabolism ; DNA Methylation ; Epigenesis, Genetic ; *Eukaryota/genetics/metabolism ; *Histones/genetics/metabolism ; }, abstract = {DNA modifications are used to regulate gene expression and defend against invading genetic elements. In eukaryotes, modifications predominantly involve C5-methylcytosine (5mC) and occasionally N6-methyladenine (6mA), while bacteria frequently use N4-methylcytosine (4mC) in addition to 5mC and 6mA. Here we report that 4mC can serve as an epigenetic mark in eukaryotes. Bdelloid rotifers, tiny freshwater invertebrates with transposon-poor genomes rich in foreign genes, lack canonical eukaryotic C5-methyltransferases for 5mC addition, but encode an amino-methyltransferase, N4CMT, captured from bacteria >60 Mya. N4CMT deposits 4mC at active transposons and certain tandem repeats, and fusion to a chromodomain shapes its "histone-read-DNA-write" architecture recognizing silent chromatin marks. Furthermore, amplification of SETDB1 H3K9me3 histone methyltransferases yields variants preferentially binding 4mC-DNA, suggesting "DNA-read-histone-write" partnership to maintain chromatin-based silencing. Our results show how non-native DNA methyl groups can reshape epigenetic systems to silence transposons and demonstrate the potential of horizontal gene transfer to drive regulatory innovation in eukaryotes.}, }
@article {pmid35226812, year = {2022}, author = {Fletcher, K and Shin, OH and Clark, KJ and Feng, C and Putman, AI and Correll, JC and Klosterman, SJ and Van Deynze, A and Michelmore, RW}, title = {Ancestral Chromosomes for Family Peronosporaceae Inferred from a Telomere-to-Telomere Genome Assembly of Peronospora effusa.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {35}, number = {6}, pages = {450-463}, doi = {10.1094/MPMI-09-21-0227-R}, pmid = {35226812}, issn = {0894-0282}, mesh = {*Oomycetes/genetics ; *Peronospora/genetics ; Plant Diseases/microbiology ; Spinacia oleracea ; Telomere/genetics ; }, abstract = {Downy mildew disease of spinach, caused by the oomycete Peronospora effusa, causes major losses to spinach production. In this study, the 17 chromosomes of P. effusa were assembled telomere-to-telomere, using Pacific Biosciences high-fidelity reads. Of these, 16 chromosomes are complete and gapless; chromosome 15 contains one gap bridging the nucleolus organizer region. This is the first telomere-to-telomere genome assembly for an oomycete. Putative centromeric regions were identified on all chromosomes. This new assembly enables a reevaluation of the genomic composition of Peronospora spp.; the assembly was almost double the size and contained more repeat sequences than previously reported for any Peronospora species. Genome fragments consistently underrepresented in six previously reported assemblies of P. effusa typically encoded repeats. Some genes annotated as encoding effectors were organized into multigene clusters on several chromosomes. Putative effectors were annotated on 16 of the 17 chromosomes. The intergenic distances between annotated genes were consistent with compartmentalization of the genome into gene-dense and gene-sparse regions. Genes encoding putative effectors were enriched in gene-sparse regions. The near-gapless assembly revealed apparent horizontal gene transfer from Ascomycete fungi. Gene order was highly conserved between P. effusa and the genetically oriented assembly of the oomycete Bremia lactucae; high levels of synteny were also detected with Phytophthora sojae. Extensive synteny between phylogenetically distant species suggests that many other oomycete species may have similar chromosome organization. Therefore, this assembly provides the foundation for genomic analyses of diverse oomycetes.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.}, }
@article {pmid35222299, year = {2021}, author = {Wentz, TG and Tremblay, BJM and Bradshaw, M and Doxey, AC and Sharma, SK and Sauer, JD and Pellett, S}, title = {Endogenous CRISPR-Cas Systems in Group I Clostridium botulinum and Clostridium sporogenes Do Not Directly Target the Botulinum Neurotoxin Gene Cluster.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {787726}, pmid = {35222299}, issn = {1664-302X}, support = {R01 AI137070/AI/NIAID NIH HHS/United States ; R01 AI139306/AI/NIAID NIH HHS/United States ; R21 AI144060/AI/NIAID NIH HHS/United States ; }, abstract = {Most strains of proteolytic group I Clostridium botulinum (G1 C. botulinum) and some strains of Clostridium sporogenes possess genes encoding botulinum neurotoxin (BoNT), a potent neuroparalytic agent. Within G1 C. botulinum, conserved bont gene clusters of three major toxin serotypes (bont/A/B/F) can be found on conjugative plasmids and/or within chromosomal pathogenicity islands. CRISPR-Cas systems enable site-specific targeting of previously encountered mobile genetic elements (MGE) such as plasmids and bacteriophage through the creation of a spacer library complementary to protospacers within the MGEs. To examine whether endogenous CRISPR-Cas systems restrict the transfer of bont gene clusters across strains we conducted a bioinformatic analysis profiling endogenous CRISPR-Cas systems from 241 G1 C. botulinum and C. sporogenes strains. Approximately 6,200 CRISPR spacers were identified across the strains and Type I-B, III-A/B/D cas genes and CRISPR array features were identified in 83% of the strains. Mapping the predicted spacers against the masked strain and RefSeq plasmid dataset identified 56,000 spacer-protospacer matches. While spacers mapped heavily to targets within bont(+) plasmids, no protospacers were identified within the bont gene clusters. These results indicate the toxin is not a direct target of CRISPR-Cas but the plasmids predominantly responsible for its mobilization are. Finally, while the presence of a CRISPR-Cas system did not reliably indicate the presence or absence of a bont gene cluster, comparative genomics across strains indicates they often occupy the same hypervariable loci common to both species, potentially suggesting similar mechanisms are involved in the acquisition and curation of both genomic features.}, }
@article {pmid35221573, year = {2022}, author = {Tariq, M and Jameel, F and Ijaz, U and Abdullah, M and Rashid, K}, title = {Biofertilizer microorganisms accompanying pathogenic attributes: a potential threat.}, journal = {Physiology and molecular biology of plants : an international journal of functional plant biology}, volume = {28}, number = {1}, pages = {77-90}, pmid = {35221573}, issn = {0971-5894}, abstract = {Application of biofertilizers containing living or dormant plant growth promoting bacterial cells is considered to be an ecofriendly alternative of chemical fertilizers for improved crop production. Biofertilizers opened myriad doors towards sustainable agriculture as they effectively reduce heavy use of chemical fertilizers and pesticides by keeping soils profuse in micro and macronutrients, regulating plant hormones and restraining infections caused by the pests present in soil without inflicting environmental damage. Generally, pathogenicity and biosafety testing of potential plant growth promoting bacteria (PGPB) are not performed, and the bacteria are reported to be beneficial solely on testing plant growth promoting characteristics. Unfortunately, some rhizosphere and endophytic PGPB are reported to be involved in various diseases. Such PGPB can also spread virulence and multidrug resistance genes carried by them through horizontal gene transfer to other bacteria in the environment. Therefore, deployment of such microbial populations in open fields could lead to disastrous side effects on human health and environment. Careless declaration of bacteria as PGPB is more pronounced in research publications. Here, we present a comprehensive report of declared PGPB which are reported to be pathogenic in other studies. This review also suggests the employment of some additional safety assessment protocols before reporting a bacteria as beneficial and product development.}, }
@article {pmid35219813, year = {2022}, author = {Xia, L and Cheng, C and Zhao, X and He, X and Yu, X and Li, J and Wang, Y and Chen, J}, title = {Characterization of the mitochondrial genome of Cucumis hystrix and comparison with other cucurbit crops.}, journal = {Gene}, volume = {823}, number = {}, pages = {146342}, doi = {10.1016/j.gene.2022.146342}, pmid = {35219813}, issn = {1879-0038}, mesh = {Crops, Agricultural/genetics ; Cucumis/*genetics ; Cucurbitaceae/classification/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome Size ; *Genome, Mitochondrial ; Genomics ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {The mitochondria ofCucumis genus contain several intriguing features such as paternal inheritance and three-ring genome structure. However, the evolutionary relationships of mitochondria inCucumisremain elusive. Here, we assembled the mitochondrial genome ofC. hystrixand performed a comparative genomic analysis with other crops inthe Cucurbitaceae. The mitochondrial genome ofC. hystrixhas three circular-mapping chromosomes of lengths 1,113,461 bp, 110,683 bp, and 92,288 bp, which contain 73 genes including 38 protein-coding genes, 31tRNAgenes, and 4rRNAgenes. Repeat sequences, RNA editing, and horizontal gene transfer events were identified. The results of phylogenetic analyses, collinearity and gene clusters revealed thatC. hystrixis closer toC. sativus than to C. melo. Meanwhile, wedemonstrated mitochondrial paternal inheritance inC. hystrixbymolecular markers. In comparison with other cucurbitcrops, wefound amarker foridentification of germplasm resources ofCucumis. Collectively, our findings provide a tool to help clarify the paternal lineage within that genus in the evolution of Cucumis.}, }
@article {pmid35208854, year = {2022}, author = {Tsalgatidou, PC and Thomloudi, EE and Baira, E and Papadimitriou, K and Skagia, A and Venieraki, A and Katinakis, P}, title = {Integrated Genomic and Metabolomic Analysis Illuminates Key Secreted Metabolites Produced by the Novel Endophyte Bacillus halotolerans Cal.l.30 Involved in Diverse Biological Control Activities.}, journal = {Microorganisms}, volume = {10}, number = {2}, pages = {}, pmid = {35208854}, issn = {2076-2607}, abstract = {The endophytic strain Cal.l.30, isolated from the medicinal plant Calendula officinalis, was selected among seven Bacillus strains with plant growth promoting activity and strong biological potential against the postharvest fungal pathogen Botrytis cinerea. Treatment by inoculating Cal.l.30 bacterial cell culture or cell free supernatant on harvested grapes and cherry tomato fruits, significantly reduced gray mold disease severity index and disease incidence. Based on 16S rRNA sequence analysis and whole genome phylogeny, Cal.l.30 was identified as Bacillus halotolerans. Genome mining revealed that B. halotolerans Cal.l.30 is endowed with a diverse arsenal of secondary metabolite biosynthetic gene clusters (SM-BGCs) responsible for metabolite production with antimicrobial properties. A sub-set of the identified SM-BGCs (mojavensin A, 'bacillunoic acid') appears to be the result of recent horizontal gene transfer events. Its genome was also mined for CAZymes associated with antifungal activity. Further UHPLC-HRMS analysis indicated that Cal.l.30 synthesizes and secretes secondary metabolites with antimicrobial activity, including the lipopeptides, fengycin, surfactin and mojavensin A, bacillaene isoforms, L-dihydroanticapsin and bacillibactin. Other compounds with known antimicrobial activity were also detected, such as azelaic acid, 15- hydroxypentadecanoid acid and 2-hydroxyphenylacetic acid. The genomic and metabolomic features of the B. halotolerans Cal.l.30 provided new perspectives on the exploitation of novel Bacillus sp. as a biocontrol agent.}, }
@article {pmid35208682, year = {2022}, author = {Li, IC and Yu, GY and Huang, JF and Chen, ZW and Chou, CH}, title = {Comparison of Reference-Based Assembly and De Novo Assembly for Bacterial Plasmid Reconstruction and AMR Gene Localization in Salmonella enterica Serovar Schwarzengrund Isolates.}, journal = {Microorganisms}, volume = {10}, number = {2}, pages = {}, pmid = {35208682}, issn = {2076-2607}, abstract = {It is well established that plasmids carrying multiple antimicrobial resistance (AMR) genes can be easily transferred among bacterial isolates by horizontal gene transfer. Previous studies have shown that a combination of short- and long-read approaches is effective in reconstructing accurate plasmids. However, high-quality Illumina short reads mapped onto the long reads in the context of an AMR hybrid monitoring strategy have not yet been explored. Hence, this study aimed to improve the reconstruction of plasmids, including the localization of AMR genes, using the above-described parameters on whole-genome sequencing (WGS) results. To the best of our knowledge, this study is the first to use S1 nuclease pulsed-field gel electrophoresis (S1-PFGE) to confirm the number and sizes of plasmids detected by in silico-based predictions in Salmonella strains. Our results showed that de novo assembly did not detect the number of bacterial plasmids more accurately than reference-based assembly did. As this new hybrid mapping strategy surpassed de novo assembly in bacterial reconstruction, it was further used to identify the presence and genomic location of AMR genes among three Salmonella enterica serovar Schwarzengrund isolates. The AMR genes identified in the bacterial chromosome among the three Salmonella enterica serovar Schwarzengrund isolates included: AAC(3)-IV, AAC(6')-Iy, aadA2, APH(4)-Ia, cmlA1, golS, mdsA, mdsB, mdsC, mdtK, qacH, sdiA, sul2, sul3, and TEM-1 genes. Moreover, the presence of TEM-1, AAC(3)-IV, aadA2, APH(4)-Ia, cmlA1, dfrA12, floR, sul1, sul3, and tet(A) genes found within three IncFIB plasmids and one IncX1 plasmid highlight their possible transmission into the environment, which is a public health risk. In conclusion, the generated data using this new hybrid mapping strategy will contribute to the improvement of AMR monitoring and support the risk assessment of AMR dissemination.}, }
@article {pmid35208668, year = {2022}, author = {Silva-Andrade, C and Martin, AJ and Garrido, D}, title = {Comparative Genomics of Clostridium baratii Reveals Strain-Level Diversity in Toxin Abundance.}, journal = {Microorganisms}, volume = {10}, number = {2}, pages = {}, pmid = {35208668}, issn = {2076-2607}, support = {21191605//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; EQM190070//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; 1190074//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; 1181089//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; }, abstract = {Clostridium baratii strains are rare opportunistic pathogens associated with botulism intoxication. They have been isolated from foods, soil and be carried asymptomatically or cause botulism outbreaks. Is not taxonomically related to Clostridium botulinum, but some strains are equipped with BoNT/F7 cluster. Despite their relationship with diseases, our knowledge regarding the genomic features and phylogenetic characteristics is limited. We analyzed the pangenome of C. baratii to understand the diversity and genomic features of this species. We compared existing genomes in public databases, metagenomes, and one newly sequenced strain isolated from an asymptomatic subject. The pangenome was open, indicating it comprises genetically diverse organisms. The core genome contained 28.49% of the total genes of the pangenome. Profiling virulence factors confirmed the presence of phospholipase C in some strains, a toxin capable of disrupting eukaryotic cell membranes. Furthermore, the genomic analysis indicated significant horizontal gene transfer (HGT) events as defined by the presence of prophage genomes. Seven strains were equipped with BoNT/F7 cluster. The active site was conserved in all strains, identifying a missing 7-aa region upstream of the active site in C. baratii genomes. This analysis could be important to advance our knowledge regarding opportunistic clostridia and better understand their contribution to disease.}, }
@article {pmid35207574, year = {2022}, author = {Smith, D and Palacios-Pérez, M and Jheeta, S}, title = {The Enclosed Intestinal Microbiome: Semiochemical Signals from the Precambrian and Their Disruption by Heavy Metal Pollution.}, journal = {Life (Basel, Switzerland)}, volume = {12}, number = {2}, pages = {}, pmid = {35207574}, issn = {2075-1729}, abstract = {It is increasingly likely that many non-communicable diseases of humans and associated animals are due to the degradation of their intestinal microbiomes, a situation often referred to as dysbiosis. An analysis of the resultant diseases offers an opportunity to probe the function of these microbial partners of multicellular animals. In our view, it now seems likely that vertebrate animals and their microbiomes have coevolved throughout the Ediacaran-Cambrian transition and beyond, operating by semiochemical messaging between the multicellular host and its microbial community guest. A consideration of the overall role of the mutualistic intestinal microbiome as an enclosed bioreactor throws up a variety of challenging concepts. In particular: the significance of the microbiome with respect to the immune system suggests that microeukaryotes could act as microbial sentinel cells; the ubiquity of bacteriophage viruses implies the rapid turnover of microbial composition by a viral-shunt mechanism; and high microbial diversity is needed to ensure that horizontal gene transfer allows valuable genetic functions to be expressed. We have previously postulated that microbes of sufficient diversity must be transferred from mother to infant by seemingly accidental contamination during the process of natural birth. We termed this maternal microbial inheritance and suggested that it operates alongside parental genetic inheritance to modify gene expression. In this way, the adjustment of the neonate immune system by the microbiome may represent one of the ways in which the genome of a vertebrate animal interacts with its microbial environment. The absence of such critical functions in the neonate may help to explain the observation of persistent immune-system problems in affected adults. Equally, granted that the survival of the guest microbiome depends on the viability of its host, one function of microbiome-generated semiochemicals could be to facilitate the movement of food through the digestive tract, effectively partitioning nutrition between host and guest. In the event of famine, downregulation of microbial growth and therefore of semiochemical production would allow all available food to be consumed by the host. Although it is often thought that non-communicable diseases, such as type 2 diabetes, are caused by consumption of food containing insufficient dietary fibre, our hypothesis suggests that poor-quality food is not the prime cause but that the tendency for disease follows the degradation of the intestinal microbiome, when fat build-up occurs because the relevant semiochemicals can no longer be produced. It is the purpose of this paper to highlight the possibility that the origins of the microbiome lie in the Precambrian and that the disconnection of body and microbiome gives rise to non-communicable disease through the loss of semiochemical signalling. We further surmise that this disconnect has been largely brought about by heavy metal poisoning, potentially illuminating a facet of the exposome, the sum total of environmental insults that influence the expression of the genetic inheritance of an animal.}, }
@article {pmid35205950, year = {2022}, author = {Sonnabend, R and Seiler, L and Gressler, M}, title = {Regulation of the Leucine Metabolism in Mortierella alpina.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {8}, number = {2}, pages = {}, pmid = {35205950}, issn = {2309-608X}, abstract = {The oleaginous fungus Mortierella alpina is a safe source of polyunsaturated fatty acids (PUFA) in industrial food and feed production. Besides PUFA production, pharmaceutically relevant surface-active and antimicrobial oligopeptides were isolated from this basal fungus. Both production of fatty acids and oligopeptides rely on the biosynthesis and high turnover of branched-chain-amino acids (BCAA), especially l-leucine. However, the regulation of BCAA biosynthesis in basal fungi is largely unknown. Here, we report on the regulation of the leucine, isoleucine, and valine metabolism in M. alpina. In contrast to higher fungi, the biosynthetic genes for BCAA are hardly transcriptionally regulated, as shown by qRT-PCR analysis, which suggests a constant production of BCAAs. However, the enzymes of the leucine metabolism are tightly metabolically regulated. Three enzymes of the leucine metabolism were heterologously produced in Escherichia coli, one of which is inhibited by allosteric feedback loops: The key regulator is the α-isopropylmalate synthase LeuA1, which is strongly disabled by l-leucine, α-ketoisocaproate, and propionyl-CoA, the precursor of the odd-chain fatty acid catabolism. Its gene is not related to homologs from higher fungi, but it has been inherited from a phototrophic ancestor by horizontal gene transfer.}, }
@article {pmid35205274, year = {2022}, author = {Bai, FY and Han, DY and Duan, SF and Wang, QM}, title = {The Ecology and Evolution of the Baker's Yeast Saccharomyces cerevisiae.}, journal = {Genes}, volume = {13}, number = {2}, pages = {}, pmid = {35205274}, issn = {2073-4425}, mesh = {DNA Copy Number Variations ; Ecology ; Genetics, Population ; *Genome, Fungal ; *Saccharomyces cerevisiae/genetics ; }, abstract = {The baker's yeast Saccharomyces cerevisiae has become a powerful model in ecology and evolutionary biology. A global effort on field survey and population genetics and genomics of S. cerevisiae in past decades has shown that the yeast distributes ubiquitously in nature with clearly structured populations. The global genetic diversity of S. cerevisiae is mainly contributed by strains from Far East Asia, and the ancient basal lineages of the species have been found only in China, supporting an 'out-of-China' origin hypothesis. The wild and domesticated populations are clearly separated in phylogeny and exhibit hallmark differences in sexuality, heterozygosity, gene copy number variation (CNV), horizontal gene transfer (HGT) and introgression events, and maltose utilization ability. The domesticated strains from different niches generally form distinct lineages and harbor lineage-specific CNVs, HGTs and introgressions, which contribute to their adaptations to specific fermentation environments. However, whether the domesticated lineages originated from a single, or multiple domestication events is still hotly debated and the mechanism causing the diversification of the wild lineages remains to be illuminated. Further worldwide investigations on both wild and domesticated S. cerevisiae, especially in Africa and West Asia, will be helpful for a better understanding of the natural and domestication histories and evolution of S. cerevisiae.}, }
@article {pmid35205080, year = {2022}, author = {Liu, C and Cao, J and Zhang, H and Yin, J}, title = {Evolutionary History of RNA Modifications at N6-Adenosine Originating from the R-M System in Eukaryotes and Prokaryotes.}, journal = {Biology}, volume = {11}, number = {2}, pages = {}, pmid = {35205080}, issn = {2079-7737}, support = {20ZR1463600//Natural Science Foundation of Shanghai/ ; GWV-10.2-YQ31//Shanghai Municipal Health Commission/ ; 201908310036//China Scholarship Council/ ; 81702030//National Natural Science Foundation of China/ ; }, abstract = {Methylation at the N6-position of adenosine (N6mA) on mRNA (m[6]A) is one of the most widespread, highly selective and dynamically regulated RNA modifications and plays an important role in transcription and translation. In the present study, a comprehensive analysis of phylogenetic relationships, conserved domain sequence characteristics and protein structure comparisons were employed to explore the distribution of RNA N6mA modification (m[6]A, m[6,6]A, m[6]Am, m[6, 6]Am and m[6]t[6]A)-associated proteins (writers, readers and erasers) in three kingdoms of life and reveal the evolutionary history of these modifications. These findings further confirmed that the restriction-modification (R-M) system is the origin of DNA and RNA N6mA modifications. Among them, the existing mRNA m[6]A modification system derived from the last eukaryotic common ancestor (LECA) is the evolutionary product of elements from the last universal common ancestor (LUCA) or driven by horizontal gene transfer (HGT) from bacterial elements. The subsequent massive gene gains and losses contribute to the development of unique and diverse functions in distinct species. Particularly, RNA methyltransferases (MTases) as the writer responsible for adding N6mA marks on mRNA and ncRNAs may have evolved from class α and β prokaryotic "orphan" MTases originating from the R-M system. The reader, YTH proteins that specifically recognize the m[6]A deposit, may be acquired by LECA from an individual prokaryotic YTH-domain protein that evolved from N-terminals of an R-M system endonuclease. The eraser, which emerged from the ALKB family (ALKBH5 and FTO) in eukaryotes, may be driven by independent HTG from bacterial ALKB proteins. The evolutionary history of RNA N6mA modifications was inferred in the present study, which will deepen our understanding of these modifications in different species.}, }
@article {pmid35205019, year = {2022}, author = {Lienen, T and Schnitt, A and Hammerl, JA and Maurischat, S and Tenhagen, BA}, title = {Mammaliicoccus spp. from German Dairy Farms Exhibit a Wide Range of Antimicrobial Resistance Genes and Non-Wildtype Phenotypes to Several Antibiotic Classes.}, journal = {Biology}, volume = {11}, number = {2}, pages = {}, pmid = {35205019}, issn = {2079-7737}, support = {01KI1727C//Federal Ministry of Education and Research/ ; 1322-769//German Federal Institute for Risk Assessment/ ; }, abstract = {Mammaliicocci might play a major role in antimicrobial resistance (AMR) gene transmission between organisms of the family Staphylococcaceae, such as the potentially pathogenic species Staphylococcus aureus. The interest of this study was to analyze AMR profiles of mammaliicocci from German dairy farms to evaluate the AMR transmission potential. In total, 65 mammaliicocci isolates from 17 dairy farms with a history of MRSA detection were analyzed for AMR genotypes and phenotypes using whole genome sequencing and antimicrobial susceptibility testing against 19 antibiotics. The various genotypic and phenotypic AMR profiles of mammaliicocci from German dairy farms indicated the simultaneous occurrence of several different strains on the farms. The isolates exhibited a non-wildtype phenotype to penicillin (58/64), cefoxitin (25/64), chloramphenicol (26/64), ciprofloxacin (25/64), clindamycin (49/64), erythromycin (17/64), fusidic acid (61/64), gentamicin (8/64), kanamycin (9/64), linezolid (1/64), mupirocin (4/64), rifampicin (1/64), sulfamethoxazol (1/64), streptomycin (20/64), quinupristin/dalfopristin (26/64), tetracycline (37/64), tiamulin (59/64), and trimethoprim (30/64). Corresponding AMR genes against several antimicrobial classes were detected. Linezolid resistance was associated with the cfr gene in the respective isolate. However, discrepancies between genotypic prediction and phenotypic resistance profiles, such as for fusidic acid and tiamulin, were also observed. In conclusion, mammaliicocci from dairy farms may carry a broad variety of antimicrobial resistance genes and exhibit non-wildtype phenotypes to several antimicrobial classes; therefore, they may represent an important source for horizontal gene transfer of AMR genes to pathogenic Staphylococcaceae.}, }
@article {pmid35203843, year = {2022}, author = {Zebrowska, J and Witkowska, M and Struck, A and Laszuk, PE and Raczuk, E and Ponikowska, M and Skowron, PM and Zylicz-Stachula, A}, title = {Antimicrobial Potential of the Genera Geobacillus and Parageobacillus, as Well as Endolysins Biosynthesized by Their Bacteriophages.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {2}, pages = {}, pmid = {35203843}, issn = {2079-6382}, support = {TECHMATSTRATEG2/410747/11/NCBR/2019//The National Center for Research and Development/ ; }, abstract = {In the recent decades, antibiotic resistance has emerged and spread rapidly among clinically relevant pathogens. The natural ability of bacteria to transmit resistance determinants through horizontal gene transfer poses constant challenges to drug development. Natural molecules produced by soil microorganisms continue to be a key source of new antimicrobial agents. In this context, bacteria from the Geobacillus and Parageobacillus genera deserve special attention. Although there is commercial and industrial interest in these microorganisms, the full range of antibacterial compounds biosynthesized by the Geobacillus and Parageobacillus species remains largely unexplored. The aim of this review is to present the strong antimicrobial potential of these bacteria and endolysins produced by their bacteriophages.}, }
@article {pmid35198129, year = {2022}, author = {Crespo, I and Bernardo, N and Cuppari, A and Calisto, BM and Val-Calvo, J and Miguel-Arribas, A and Meijer, WJJ and Carpena, X and Gil-Ortiz, F and Malfois, M and Boer, DR}, title = {Structural and biochemical characterization of the relaxosome auxiliary proteins encoded on the Bacillus subtilis plasmid pLS20.}, journal = {Computational and structural biotechnology journal}, volume = {20}, number = {}, pages = {757-765}, pmid = {35198129}, issn = {2001-0370}, abstract = {Bacterial conjugation is an important route for horizontal gene transfer. The initial step in this process involves a macromolecular protein-DNA complex called the relaxosome, which in plasmids consists of the origin of transfer (oriT) and several proteins that prepare the transfer. The relaxosome protein named relaxase introduces a nick in one of the strands of the oriT to initiate the process. Additional relaxosome proteins can exist. Recently, several relaxosome proteins encoded on the Bacillus subtilis plasmid pLS20 were identified, including the relaxase, named RelpLS20, and two auxiliary DNA-binding factors, named Aux1pLS20 and Aux2pLS20. Here, we extend this characterization in order to define their function. We present the low-resolution SAXS envelope of the Aux1pLS20 and the atomic X-ray structure of the C-terminal domain of Aux2pLS20. We also study the interactions between the auxiliary proteins and the full-length RelpLS20, as well as its separate domains. The results show that the quaternary structure of the auxiliary protein Aux1pLS20 involves a tetramer, as previously determined. The crystal structure of the C-terminal domain of Aux2pLS20 shows that it forms a tetramer and suggests that it is an analog of TraMpF of plasmid F. This is the first evidence of the existence of a TraMpF analog in gram positive conjugative systems, although, unlike other TraMpF analogs, Aux2pLS20 does not interact with the relaxase. Aux1pLS20 interacts with the C-terminal domain, but not the N-terminal domain, of the relaxase RelpLS20. Thus, the pLS20 relaxosome exhibits some unique features despite the apparent similarity to some well-studied G- conjugation systems.}, }
@article {pmid35196218, year = {2022}, author = {Francés-Cuesta, C and Ansari, I and Fernández-Garayzábal, JF and Gibello, A and González-Candelas, F}, title = {Comparative genomics and evolutionary analysis of Lactococcus garvieae isolated from human endocarditis.}, journal = {Microbial genomics}, volume = {8}, number = {2}, pages = {}, pmid = {35196218}, issn = {2057-5858}, mesh = {Animals ; Biological Evolution ; *Endocarditis ; Genomics/methods ; Humans ; *Lactococcus/genetics ; Mammals ; }, abstract = {Lactococcus garvieae is a well-known pathogen of fish, but is rarely involved in infections in humans and other mammals. In humans, the main clinical manifestation of L. garvieae infections is endocarditis usually related to the ingestion of contaminated food, such as undercooked fish and shellfish. This study presents the first complete genomic sequence of a clinical L. garvieae strain isolated from a patient with endocarditis and its comparative analysis with other genomes. This human isolate contains a circular chromosome of 2 099 060 bp and one plasmid of 50 557 bp. In comparison with other fully sequenced L. garvieae strains, the chromosomal DNA of L. garvieae Lg-Granada carries a low proportion of insertion sequence elements and a higher number of putative prophages. Our results show that, in general, L. garvieae is a highly recombinogenic species with an open pangenome in which almost 30 % of its genome has undergone horizontal transfers. Within the genus Lactococcus, L. lactis is the main donor of genetic components to L. garvieae but, taking Lg-Granada as a representative, this bacterium tends to import more genes from Bacilli taxa than from other Lactococcus species.}, }
@article {pmid35196217, year = {2022}, author = {Donà, V and Ramette, A and Perreten, V}, title = {Comparative genomics of 26 complete circular genomes of 18 different serotypes of Actinobacillus pleuropneumoniae.}, journal = {Microbial genomics}, volume = {8}, number = {2}, pages = {}, pmid = {35196217}, issn = {2057-5858}, mesh = {*Actinobacillus pleuropneumoniae/genetics ; Animals ; Genomics/methods ; Lipopolysaccharides ; Multilocus Sequence Typing ; Serogroup ; Swine ; }, abstract = {Actinobacillus pleuropneumoniae is a Gram-negative, rod-shaped bacterium of the family Pasteurellaceae causing pig pleuropneumonia associated with great economic losses worldwide. Nineteen serotypes with distinctive lipopolysaccharide (LPS) and capsular (CPS) compositions have been described so far, yet complete circular genomes are publicly available only for the reference strains of serotypes 1, 4 and 5b, and for field strains of serotypes 1, 3, 7 and 8. We aimed to complete this picture by sequencing the reference strains of 17 different serotypes with the MinION sequencer (Oxford Nanopore Technologies, ONT) and on an Illumina HiSeq (Illumina) platform. We also included two field isolates of serotypes 2 and 3 that were PacBio- and MinION-sequenced, respectively. Genome assemblies were performed following two different strategies, i.e. PacBio- or ONT-only de novo assemblies polished with Illumina reads or a hybrid assembly by directly combining ONT and Illumina reads. Both methods proved successful in obtaining accurate circular genomes with comparable qualities. blast-based genome comparisons and core-genome phylogeny based on core genes, SNP typing and multi-locus sequence typing (cgMLST) of the 26 circular genomes indicated well-conserved genomes across the 18 different serotypes, differing mainly in phage insertions, and CPS, LPS and RTX-toxin clusters, which, consistently, encode serotype-specific antigens. We also identified small antibiotic resistance plasmids, and complete subtype I-F and subtype II-C CRISPR-Cas systems. Of note, highly similar clusters encoding all those serotype-specific traits were also found in other pathogenic and commensal Actinobacillus species. Taken together with the presence of transposable elements surrounding these loci, we speculate a dynamic intra- and interspecies exchange of such virulence-related factors by horizontal gene transfer. In conclusion, our comprehensive genomics analysis provides useful information for diagnostic test and vaccine development, but also for whole-genome-based epidemiological studies, as well as for the surveillance of the evolution of antibiotic resistance and virulence genes in A. pleuropneumoniae.}, }
@article {pmid35194656, year = {2022}, author = {Nag, A and Mehra, S}, title = {Involvement of the SCO3366 efflux pump from S. coelicolor in rifampicin resistance and its regulation by a TetR regulator.}, journal = {Applied microbiology and biotechnology}, volume = {106}, number = {5-6}, pages = {2175-2190}, pmid = {35194656}, issn = {1432-0614}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/metabolism ; Chloramphenicol ; Ciprofloxacin/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Membrane Transport Proteins/genetics ; *Rifampin/pharmacology ; *Streptomyces coelicolor/genetics/metabolism ; }, abstract = {Overexpression of efflux pumps represents a key mechanism of resistance in bacteria. Soil bacteria such as Streptomyces harbour a vast array of efflux genes that are transcriptionally silent under laboratory conditions. However, dissemination of many of these genes into clinical pathogens via horizontal gene transfer results in conferring resistance to multiple drugs. In this study, we have identified the role of a MFS transporter, SCO3366 from Streptomyces coelicolor, in governing multidrug resistance. Overexpression and knockout studies revealed that SCO3366 provides resistance to several structurally unrelated drugs including ciprofloxacin, chloramphenicol, rifampicin and EtBr, with rifampicin being the major substrate. Beyond multidrug resistance, SCO3366 was efficient in providing tolerance towards oxidative stress. A combinatorial mechanism of increased oxidative stress tolerance decreased intracellular drug levels and decreased permeability act synergistically to provide resistance towards rifampicin. Shedding light on the regulation of SCO3366, we find the pump to be directly regulated by the TetR regulator SCO3367 in a negative manner and the repression was found to be relieved in presence of different compounds recognized as substrates of SCO3366. KEY POINTS: • First reported rifampicin efflux pump in Streptomyces coelicolor • Resistance to rifampicin is the result of a synergistic action of increased efflux with increased oxidative stress tolerance and decreased permeability, which can potentially arise in clinically relevant bacteria • SCO3366-SCO3367 to be a novel system that operates to protect the bacteria under varied environmental stress conditions.}, }
@article {pmid35192531, year = {2022}, author = {Elbir, H and Almathen, F and Almuhasen, FM}, title = {Genomic differences among strains of Corynebacterium cystitidis isolated from uterus of camels.}, journal = {Journal of infection in developing countries}, volume = {16}, number = {1}, pages = {134-146}, doi = {10.3855/jidc.15023}, pmid = {35192531}, issn = {1972-2680}, mesh = {Animals ; *Camelus ; Cattle ; *Corynebacterium/genetics ; Female ; Genomics ; Phylogeny ; Uterus ; }, abstract = {INTRODUCTION: Members of the Corynebacterium cystitidis species are usually isolated from kidney and urine of cow having pyelonephritis. Nevertheless, we have isolated Corynebacterium cystitidis for the first time from uterus of camels, extending the type of mammalian host for this species. Furthermore, it remains unknown whether there are significant genetic variations between strains isolated from different host species and anatomic sites. In this perspective, we investigated the genomic diversity of Corynebacterium cystitidis species, whose pan genome remain unexplored to date.<br><br>METHODOLOGY: Thus, we sequenced and compared the genomes of five Corynebacterium cystitidis of camel origin and a public genome of cow associated Corynebacterium cystitidis.<br><br>RESULTS: Results revealed open pan genome of 4,038 gene clusters and horizontal gene transfer played a role in the extensive genetic diversity. Further, we found an obvious distinction between cow and camel associated C. cystitidis via phylogenomic analysis and by average nucleotide identity value of 95% between the two distant lineages and > 99% within camel associated C. cystitidis strains. Moreover, our data supports the hypothesis that the gene repertoire of cow associated Corynebacterium cystitidis developed so as to become more adaptable to the urine milieu. These genetic potentials are specifically evident for genes required for benzoate breakdown, iron transport, citrate and alanine utilization.<br><br>CONCLUSIONS: Our findings confirm the differentiation of strains into camel lineage and cow lineage. These different niches, comprising the uterus of camel and urinary tract of cow probably played a role in shaping the gene repertoire of strains.}, }
@article {pmid35191377, year = {2022}, author = {Mourkas, E and Yahara, K and Bayliss, SC and Calland, JK and Johansson, H and Mageiros, L and Muñoz-Ramirez, ZY and Futcher, G and Méric, G and Hitchings, MD and Sandoval-Motta, S and Torres, J and Jolley, KA and Maiden, MCJ and Ellström, P and Waldenström, J and Pascoe, B and Sheppard, SK}, title = {Host ecology regulates interspecies recombination in bacteria of the genus Campylobacter.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {35191377}, issn = {2050-084X}, support = {MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; MR/V001213/2/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MR/M501608/1/MRC_/Medical Research Council/United Kingdom ; 088786/C/09/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Anti-Infective Agents ; Bacteria/genetics ; Biological Evolution ; *Campylobacter/genetics ; Gene Transfer, Horizontal ; Phylogeny ; }, abstract = {Horizontal gene transfer (HGT) can allow traits that have evolved in one bacterial species to transfer to another. This has potential to rapidly promote new adaptive trajectories such as zoonotic transfer or antimicrobial resistance. However, for this to occur requires gaps to align in barriers to recombination within a given time frame. Chief among these barriers is the physical separation of species with distinct ecologies in separate niches. Within the genus Campylobacter, there are species with divergent ecologies, from rarely isolated single-host specialists to multihost generalist species that are among the most common global causes of human bacterial gastroenteritis. Here, by characterizing these contrasting ecologies, we can quantify HGT among sympatric and allopatric species in natural populations. Analyzing recipient and donor population ancestry among genomes from 30 Campylobacter species, we show that cohabitation in the same host can lead to a six-fold increase in HGT between species. This accounts for up to 30% of all SNPs within a given species and identifies highly recombinogenic genes with functions including host adaptation and antimicrobial resistance. As described in some animal and plant species, ecological factors are a major evolutionary force for speciation in bacteria and changes to the host landscape can promote partial convergence of distinct species through HGT.}, }
@article {pmid35183733, year = {2022}, author = {Villarroel, CA and González-González, A and Alvarez-Baca, JK and Villarreal, P and Ballesteros, GI and Figueroa, CC and Cubillos, FA and Ramírez, CC}, title = {Genome sequencing of a predominant clonal lineage of the grain aphid Sitobion avenae.}, journal = {Insect biochemistry and molecular biology}, volume = {143}, number = {}, pages = {103742}, doi = {10.1016/j.ibmb.2022.103742}, pmid = {35183733}, issn = {1879-0240}, mesh = {Animals ; *Aphids/genetics ; Base Sequence ; Genome ; Genotype ; *Insecticides ; }, abstract = {The English grain aphid, Sitobion avenae, is a cosmopolitan pest that feeds on cereals, provoking substantial yield losses by injuring plant tissue and by vectoring plant viruses. Here we report a highly complete, de novo draft genome of the grain aphid using long-read sequencing. We generated an assembly of 2740 contigs with a N50 of 450 kb. We compared this draft genome with that of other aphid species, inspecting gene family evolution, genome-wide positive selection, and searched for horizontal gene transfer events. In addition, we described a recent copy number variant expansion of gene families involving aconitase, ABC transporter, and esterase genes that could be associated with resistance to insecticides and plant chemical defenses. This S. avenae genome obtained from a predominant invasive genotype can provide a framework for studying the spatial-temporal success of these clonal lineages in invaded agroecosystems.}, }
@article {pmid35181506, year = {2022}, author = {Patané, JSL and Moreira, LM and de Melo Teixeira, M and Martins, J and Setubal, JC and Varani, AM}, title = {New insights into plant natriuretic peptide evolution: From the lysogenic conversion in Xanthomonas to the lateral transfer to the whitefly Bemisia tabaci.}, journal = {Gene}, volume = {821}, number = {}, pages = {146326}, doi = {10.1016/j.gene.2022.146326}, pmid = {35181506}, issn = {1879-0038}, mesh = {Animals ; Bacterial Proteins/genetics ; Citrus/*genetics ; Evolution, Molecular ; *Gene Duplication ; Gene Transfer, Horizontal ; Hemiptera/*genetics ; Insect Proteins/genetics ; Molecular Docking Simulation ; Multigene Family ; Natriuretic Peptides/*genetics ; Phylogeny ; Plant Proteins/genetics ; Xanthomonas/*genetics ; }, abstract = {Plant natriuretic peptide-like (PNP) are signaling molecules related to adaptive responses to stress. The Arabidopsis thaliana PNP (AtPNP-A) is capable of modulating catalase 2 (CAT2) and rubisco activase (RCA) activity in some circumstances. Interestingly, many plant-pathogens co-opted PNP-like molecules to their benefit. For instance, the citrus pathogen Xanthomonas citri carries a PNP-like (XacPNP) that can mimic and regulate plant homeostasis, and many phytopathogenic fungi carry effectors (e.g., Ave1 and AvrLm6) that are indeed PNP-like homologs. This work investigates the PNP-like evolution across the tree of life, revealing many parallel gains and duplications in plant and fungi kingdoms. All PNP-like proteins in the final dataset are structurally similar, containing the AtPNP-A active domains modulating CAT2 activity and RCA interaction. Comparative genomics evinced that XacPNP is a lysogenic conversion factor associated with a Myoviridae-like prophage identified in many Xanthomonas species. Surprisingly, a PNP-like homolog was identified in Bemisia tabaci, an important agricultural pest, being to date the second example of lateral gene transfer (LGT) from plant to the whitefly. Moreover, the Bemisia PNP-like homolog can also be considered a potential new effector of this phloem-feeding insect. Noteworthy, the whiteflies infest many plants carrying PNP-like copies and interact with some of their bacterial and fungal pathogens, strongly suggesting complex recipient/donor traits of PNP by LGT and bringing new insights into the evolution of host-pathogen arms race across the tree of life.}, }
@article {pmid35181368, year = {2022}, author = {Man, Y and Li, W and Wang, J and Tam, NF and Tai, Y and Tao, R and Yang, Y}, title = {Plants inhibit the relative abundance of sulfonamide resistance genes and class 1 integron by influencing bacterial community in rhizosphere of constructed wetlands.}, journal = {The Science of the total environment}, volume = {824}, number = {}, pages = {153977}, doi = {10.1016/j.scitotenv.2022.153977}, pmid = {35181368}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents ; Bacteria ; *Cyperus ; Genes, Bacterial ; Integrons ; Rhizosphere ; Sulfanilamide ; Sulfonamides ; Waste Disposal, Fluid ; Wastewater/analysis ; *Wetlands ; }, abstract = {Antibiotic resistance genes (ARGs) commonly detected in wastewater can potentially lead to a health crisis. Constructed wetlands (CWs) remove ARGs and sulfonamides (SAs) from wastewater, but the importance of plants in the process is seldom reported. We compared the effect of three wetland plant species (Cyperus alternifolius, Juncus effuses, and Cyperus papyrus), sample distance from the root, and SA presence on the environmental abundance of class 1 integron (intI1) and SA resistance genes (sul) using specially designed CW rhizoboxes. Quantitative polymerase chain reaction revealed that the relative abundance of the target genes in planted CWs, especially in C. alternifolius planted CWs, was significantly lower than that in unplanted CWs (P < 0.05). The substrate in the rhizosphere or near-/moderate-rhizosphere (closest to the root) showed the lowest average relative abundance of the target genes, while the bulk substrate (without the root) showed the highest abundance of these genes, irrespective of the planted species. Further, the influence of plants was more evident after 8 weeks of wastewater treatment. The trend was the same in SA-treated and untreated groups, although the relative abundance of the target genes was significantly higher in the former (P < 0.05). The weaker correlation between the intI1 and sul genes in the rhizosphere and near-/moderate-rhizosphere in comparison to the bulk substrate in the SA group suggested that the risk of horizontal gene transfer was probably higher in the bulk substrate and unplanted CW. A partial least-squares path model revealed that dissolved organic carbon and oxygen content significantly influenced SA concentration, microbial community, and intI1 genes, and then shaping the sul genes together. Finally, redundancy analysis suggested that abundance of sul genes was influenced by bacteria enriched in the bulk substrate and unplanted CWs. The findings provide new insights into the importance for controlling risk of ARGs by wetland plants.}, }
@article {pmid35179459, year = {2022}, author = {Park, S and Jung, D and O'Brien, B and Ruffini, J and Dussault, F and Dube-Duquette, A and Demontier, &#xc9; and Lucier, JF and Malouin, F and Dufour, S and Ronholm, J}, title = {Comparative genomic analysis of Staphylococcus aureus isolates associated with either bovine intramammary infections or human infections demonstrates the importance of restriction-modification systems in host adaptation.}, journal = {Microbial genomics}, volume = {8}, number = {2}, pages = {}, pmid = {35179459}, issn = {2057-5858}, mesh = {Animals ; Cattle ; DNA Restriction-Modification Enzymes ; Female ; Genomics ; Host Adaptation ; Humans ; *Mastitis, Bovine/microbiology ; *Staphylococcal Infections/microbiology ; Staphylococcus aureus ; }, abstract = {Staphylococcus aureus is a major etiological agent of clinical and subclinical bovine mastitis. The versatile and adaptative evolutionary strategies of this bacterium have challenged mastitis control and prevention globally, and the high incidence of S. aureus mastitis increases concerns about antimicrobial resistance (AMR) and zoonosis. This study aims to describe the evolutionary relationship between bovine intramammary infection (IMI)-associated S. aureus and human pathogenic S. aureus and further elucidate the specific genetic composition that leads to the emergence of successful bovine IMI-associated S. aureus lineages. We performed a phylogenomic analysis of 187 S. aureus isolates that originated from either dairy cattle or humans. Our results revealed that bovine IMI-associated S. aureus isolates showed distinct clades compared to human-originated S. aureus isolates. From a pan-genome analysis, 2070 core genes were identified. Host-specific genes and clonal complex (CC)-specific genes were also identified in bovine S. aureus isolates, mostly located in mobile genetic elements (MGEs). Additionally, the genome sequences of three apparent human-adapted isolates (two from CC97 and one from CC8), isolated from bovine mastitis samples, may provide an snapshot of the genomic characteristics in early host spillover events. Virulence and AMR genes were not conserved among bovine IMI-associated S. aureus isolates. Restriction-modification (R-M) genes in bovine IMI-associated S. aureus demonstrated that the Type I R-M system was lineage-specific and Type II R-M system was sequence type (ST)-specific. The distribution of exclusive, virulence, and AMR genes were closely correlated with the presence of R-M systems in S. aureus, suggesting that R-M systems may contribute to shaping clonal diversification by providing a genetic barrier to the horizontal gene transfer (HGT). Our findings indicate that the CC or ST lineage-specific R-M systems may limit genetic exchange between bovine-adapted S. aureus isolates from different lineages.}, }
@article {pmid35175529, year = {2022}, author = {Zhao, XL and Qi, Z and Huang, H and Tu, J and Song, XJ and Qi, KZ and Shao, Y}, title = {Coexistence of antibiotic resistance genes, fecal bacteria, and potential pathogens in anthropogenically impacted water.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {31}, pages = {46977-46990}, pmid = {35175529}, issn = {1614-7499}, support = {GXXT-2019-035//University Synergy Innovation Program of Anhui Province/ ; 1604a0702033//Integration and Demonstration of Quality and Safety Control Technology for Green Ecological Livestock and Poultry Products Industry Chain/ ; }, mesh = {*Anti-Bacterial Agents/pharmacology ; Bacteria ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; RNA, Ribosomal, 16S ; *Wastewater ; Water ; }, abstract = {Microbial indicators are often used to monitor microbial safety of aquatic environments. However, information regarding the correlation between microbial indicators and ecotoxicological factors such as potential pathogens and antibiotic resistance genes (ARGs) in anthropogenically impacted waters remains highly limited. Here, we investigated the bacterial community composition, potential pathogens, ARGs diversity, ARG hosts, and horizontal gene transfer (HGT) potential in urban river and wastewater samples from Chaohu Lake Basin using 16S rRNA and metagenomic sequencing. The composition of the microbial community and potential pathogens differed significantly in wastewater and river water samples, and the total relative abundance of fecal indicator bacteria was positively correlated with the total relative abundance of potential pathogens (p < 0.001 and Pearson's r = 0.758). Network analysis indicated that partial ARG subtypes such as dfrE, sul2, and PmrE were significantly correlated with indicator bacteria (p < 0.05 and Pearson's r > 0.6). Notably, Klebsiella was the indicator bacteria significantly correlated with 4 potential pathogens and 14 ARG subtypes. ARGs coexisting with mobile gene elements were mainly found in Thauera, Pseudomonas, Escherichia, and Acinetobacter. Next-generation sequencing (NGS) can be used to conduct preliminary surveys of environmental samples to access potential health risks, thereby facilitating water resources management.}, }
@article {pmid35173698, year = {2022}, author = {Wang, G and Li, Y and Liu, J and Chen, B and Su, H and Liang, J and Huang, W and Yu, K}, title = {Comparative Genomics Reveal the Animal-Associated Features of the Acanthopleuribacteraceae Bacteria, and Description of Sulfidibacter corallicola gen. nov., sp., nov.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {778535}, pmid = {35173698}, issn = {1664-302X}, abstract = {Members of the phylum Acidobacteria are ubiquitous in various environments. Soil acidobacteria have been reported to present a variety of strategies for their success in terrestrial environments. However, owing to lack of pure culture, information on animal-associated acidobacteria are limited, except for those obtained from 16S rRNA genes. To date, only two acidobacteria have been isolated from animals, namely strain M133[T] obtained from coral Porites lutea and Acanthopleuribacter pedis KCTC 12899[T] isolated from chiton. Genomics and physiological characteristics of strain M133[T] and A. pedis KCTC 12899[T] were compared with 19 other isolates (one strain from each genus) in the phylum Acidobacteria. The results revealed that strain M133[T] represents a new species in a new genus in the family Acanthopleuribacteraceae. To date, these two Acanthopleuribacteraceae isolates have the largest genomes (10.85-11.79 Mb) in the phylum Acidobacteria. Horizontal gene transfer and gene duplication influenced the structure and plasticity of these large genomes. Dissimilatory nitrate reduction and abundant secondary metabolite biosynthetic gene clusters (including eicosapentaenoic acid de novo biosynthesis) are two distinct features of the Acanthopleuribacteraceae bacteria in the phylum Acidobacteria. The absence of glycoside hydrolases involved in plant polysaccharide degradation and presence of animal disease-related peptidases indicate that these bacteria have evolved to adapt to the animal hosts. In addition to low- and high-affinity respiratory oxygen reductases, enzymes for nitrate to nitrogen, and sulfhydrogenase were also detected in strain M133[T], suggesting the capacity and flexibility to grow in aerobic and anaerobic environments. This study highlighted the differences in genome structure, carbohydrate and protein utilization, respiration, and secondary metabolism between animal-associated acidobacteria and other acidobacteria, especially the soil acidobacteria, displaying flexibility and versatility of the animal-associated acidobacteria in environmental adaption.}, }
@article {pmid35172831, year = {2022}, author = {Lin, Y and Li, P and Zhang, Y and Akhter, D and Pan, R and Fu, Z and Huang, M and Li, X and Feng, Y}, title = {Unprecedented organelle genomic variations in morning glories reveal independent evolutionary scenarios of parasitic plants and the diversification of plant mitochondrial complexes.}, journal = {BMC biology}, volume = {20}, number = {1}, pages = {49}, pmid = {35172831}, issn = {1741-7007}, mesh = {*Cuscuta/genetics ; Evolution, Molecular ; *Genome, Mitochondrial ; Phylogeny ; Plants/genetics ; Plastids/genetics ; }, abstract = {BACKGROUND: The morning glories (Convolvulaceae) are distributed worldwide and produce economically important crops, medicinal herbs, and ornamentals. Members of this family are diverse in morphological characteristics and trophic modes, including the leafless parasitic Cuscuta (dodders). Organelle genomes were generally used for studying plant phylogeny and genomic variations. Notably, plastomes in parasitic plants always show non-canonical features, such as reduced size and accelerated rates. However, few organelle genomes of this group have been sequenced, hindering our understanding of their evolution, and dodder mitogenome in particular.<br><br>RESULTS: We assembled 22 new mitogenomes and 12 new plastomes in Convolvulaceae. Alongside previously known ones, we totally analyzed organelle genomes of 23 species in the family. Our sampling includes 16 leafy autotrophic species and 7 leafless parasitic dodders, covering 8 of the 12 tribes. Both the plastid and mitochondrial genomes of these plants have encountered variations that were rarely observed in other angiosperms. All of the plastomes possessed atypical IR boundaries. Besides the gene and IR losses in dodders, some leafy species also showed gene and intron losses, duplications, structural variations, and insertions of foreign DNAs. The phylogeny reconstructed by plastid protein coding sequences confirmed the previous relationship of the tribes. However, the monophyly of 'Merremieae' and the sister group of Cuscuta remained uncertain. The mitogenome was significantly inflated in Cuscuta japonica, which has exceeded over 800 kb and integrated massive DNAs from other species. In other dodders, mitogenomes were maintained in small size, revealing divergent evolutionary strategies. Mutations unique to plants were detected in the mitochondrial gene ccmFc, which has broken into three fragments through gene fission and splicing shift. The unusual changes likely initially happened to the common ancestor of the family and were caused by a foreign insertion from rosids followed by double-strand breaks and imprecise DNA repairs. The coding regions of ccmFc expanded at both sides after the fission, which may have altered the protein structure.<br><br>CONCLUSIONS: Our family-scale analyses uncovered unusual scenarios for both organelle genomes in Convolvulaceae, especially in parasitic plants. The data provided valuable genetic resources for studying the evolution of Convolvulaceae and plant parasitism.}, }
@article {pmid35172602, year = {2022}, author = {Keter, MT and El Halfawy, NM and El-Naggar, MY}, title = {Incidence of virulence determinants and antibiotic resistance in lactic acid bacteria isolated from food products.}, journal = {Future microbiology}, volume = {17}, number = {}, pages = {325-337}, doi = {10.2217/fmb-2021-0053}, pmid = {35172602}, issn = {1746-0921}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; Humans ; Incidence ; *Lactobacillales/genetics ; Microbial Sensitivity Tests ; Virulence/genetics ; Virulence Factors/genetics ; }, abstract = {Background: Lactic acid bacteria (LAB) confer beneficial health effects in humans. However, the safety of these bacteria and their potential to spread resistance in the environment must be evaluated. Materials &amp; methods: Fifty-three LAB were isolated from different food samples and assessed for the prevalence of virulence determinants and antibiotic resistance profile. Results: Multiple resistance was reported for Lactobacillus brevis MIM04, having revealed phenotypic resistance to vancomycin (MIC >128 μg/ml), ampicillin, cefotaxime, oxacillin and gentamicin. Virulence traits (cylA, gelE, esp and agg) were detected using specific primers. Enterococcus faecium CHE32, Lactobacillus plantarum CHE37 and E. faecium MLK68 lack virulence genes, possess antimicrobial activity and survive in low pH and bile salt conditions. Conclusion: Isolated LAB revealed probiotic properties.}, }
@article {pmid35171032, year = {2022}, author = {Barceló, IM and Torrens, G and Escobar-Salom, M and Jordana-Lluch, E and Capó-Bauzá, MM and Ramón-Pallín, C and García-Cuaresma, D and Fraile-Ribot, PA and Mulet, X and Oliver, A and Juan, C}, title = {Impact of Peptidoglycan Recycling Blockade and Expression of Horizontally Acquired β-Lactamases on Pseudomonas aeruginosa Virulence.}, journal = {Microbiology spectrum}, volume = {10}, number = {1}, pages = {e0201921}, pmid = {35171032}, issn = {2165-0497}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Cell Wall/metabolism ; Cephalosporinase ; Gene Transfer, Horizontal ; Membrane Transport Proteins ; Microbial Sensitivity Tests ; Moths ; Peptidoglycan/*drug effects/*metabolism ; Pseudomonas Infections/drug therapy ; Pseudomonas aeruginosa/drug effects/*genetics/*metabolism ; Virulence/drug effects ; beta-Lactam Resistance/drug effects/genetics ; beta-Lactamases/*genetics/*metabolism ; }, abstract = {In the current scenario of antibiotic resistance magnification, new weapons against top nosocomial pathogens like Pseudomonas aeruginosa are urgently needed. The interplay between β-lactam resistance and virulence is considered a promising source of targets to be attacked by antivirulence therapies, and in this regard, we previously showed that a peptidoglycan recycling blockade dramatically attenuated the pathogenic power of P. aeruginosa strains hyperproducing the chromosomal β-lactamase AmpC. Here, we sought to ascertain whether this observation could be applicable to other β-lactamases. To do so, P. aeruginosa wild-type or peptidoglycan recycling-defective strains (ΔampG and ΔnagZ) harboring different cloned β-lactamases (transferable GES, VIM, and OXA types) were used to assess their virulence in Galleria mellonella larvae by determining 50% lethal doses (LD50s). A mild yet significant LD50 increase was observed after peptidoglycan recycling disruption per se, whereas the expression of class A and B enzymes did not impact virulence. While the production of the narrow-spectrum class D OXA-2 entailed a slight attenuation, its extended-spectrum derivatives OXA-226 (W159R [bearing a change of W to R at position 159]), OXA-161 (N148D), and principally, OXA-539 (D149 duplication) were associated with outstanding virulence impairments, especially in recycling-defective backgrounds (with some LD50s being >1,000-fold that of the wild type). Although their exact molecular bases remain to be deciphered, these results suggest that mutations affecting the catalytic center and, therefore, the hydrolytic spectrum of OXA-2-derived enzymes also drastically impact the pathogenic power of P. aeruginosa. This work provides new and relevant knowledge to the complex topic of the interplay between the production of β-lactamases and virulence that could be useful to build future therapeutic strategies against P. aeruginosa. IMPORTANCE Pseudomonas aeruginosa is one of the leading nosocomial pathogens whose growing resistance makes the development of therapeutic options extremely urgent. The resistance-virulence interplay has classically aroused researchers' interest as a source of therapeutic targets. In this regard, we describe a wide array of virulence attenuations associated with different transferable β-lactamases, among which the production of OXA-2-derived extended-spectrum β-lactamases stood out as a dramatic handicap for pathogenesis, likely as a side effect of mutations causing the expansion of their hydrolytic spectrums. Moreover, our results confirm the validity of disturbing peptidoglycan recycling as a weapon to attenuate P. aeruginosa virulence in class C and D β-lactamase production backgrounds. In the current scenario of dissemination of horizontally acquired β-lactamases, this work brings out new data on the complex interplay between the production of specific enzymes and virulence attenuation that, if complemented with the characterization of the underlying mechanisms, will likely be exploitable to develop future virulence-targeting antipseudomonal strategies.}, }
@article {pmid35170999, year = {2022}, author = {Kralova, S and Davidova-Gerzova, L and Valcek, A and Bezdicek, M and Rychlik, I and Rezacova, V and Cizek, A}, title = {Paraphocaeicola brunensis gen. nov., sp. nov., Carrying Two Variants of nimB Resistance Gene from Bacteroides fragilis, and Caecibacteroides pullorum gen. nov., sp. nov., Two Novel Genera Isolated from Chicken Caeca.}, journal = {Microbiology spectrum}, volume = {10}, number = {1}, pages = {e0195421}, pmid = {35170999}, issn = {2165-0497}, mesh = {Animals ; Anti-Bacterial Agents ; Bacterial Proteins/*genetics ; Bacterial Typing Techniques ; Bacteroidaceae/classification/drug effects/*genetics/isolation &amp; purification ; Bacteroides fragilis/classification/drug effects/*genetics/isolation &amp; purification ; Cecum/microbiology ; Chickens/*microbiology ; Drug Resistance, Bacterial/*genetics ; Drug Resistance, Microbial ; *Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {Three difficult-to-cultivate, strictly anaerobic strains, AN20[T], AN421[T], and AN502, were analyzed within a project studying possible probiotics for newly hatched chickens. Phylogenetic analyses showed that strains AN20[T], AN421[T], and AN502 formed two well-separated phylogenetic lineages in all phylogenetic and phylogenomic trees comprising members of the family Bacteroidaceae. Comparison to reference genomes of type species Bacteroides fragilis NCTC 9343[T], Phocaeicola abscessus CCUG 55929[T], and Capsularis zoogleoformans ATCC 33285[T] showed low relatedness based on the calculated genome-to-genome distance and orthologous average nucleotide identity. Analysis of fatty acid profiles showed iso-C15:0, anteiso-C15:0, C16:0, C18:1ω9c, and iso-C17:0 3OH as the major fatty acids for all three strains and additionally C16:0 3OH for AN421[T] and AN502. A specific combination of respiratory quinones different from related taxa was found in analyzed strains, MK-5 plus MK-11 in strain AN20[T] and MK-5 plus MK-10 in strains AN421[T] and AN502. Strains AN421[T] and AN502 harbor complete CRISPR loci with CRISPR array, type II-C, accompanied by a set of cas genes (cas9, cas1, and cas2) in close proximity. Interestingly, strain AN20[T] was found to harbor two copies of nimB gene with >95% similarity to nimB of B. fragilis, suggesting a horizontal gene transfer between these taxa. In summary, three isolates characterized in this study represent two novel species, which we proposed to be classified in two novel genera of the family Bacteroidaceae, for which the names Paraphocaeicola brunensis sp. nov. (AN20[T] = CCM 9041[T] = DSM 111154[T]) and Caecibacteroides pullorum sp. nov. (AN421[T]= CCM 9040[T] = DSM 111155[T]) are proposed. IMPORTANCE This study represents follow-up research on three difficult-to-cultivate anaerobic isolates originally isolated within a project focused on strains that are able to stably colonize newly hatched chickens, thus representing possible probiotics. This project is exceptional in that it successfully isolates several miscellaneous strains that required modified and richly supplemented anaerobic media, as information on many gut-colonizing bacteria is based predominantly on metagenomic studies. Superior colonization of newly hatched chickens by Bacteroides spp., Phocaeicola spp., or related taxa can be considered of importance for development of future probiotics. Although different experiments can also be performed with provisionally characterized isolates, precise taxonomical definition is necessary for subsequent broad communication. The aim of this study is therefore to thoroughly characterize these isolates that represent novel genera and precisely determine their taxonomic position among related taxa to facilitate further research and communication involving these strains.}, }
@article {pmid35170998, year = {2022}, author = {Yang, Y and Kuang, X and Han, RJ and Zhai, YJ and He, DD and Zhao, JF and Liu, JH and Hu, GZ}, title = {Characterization of a Novel Linezolid Resistance Gene optrA and Bacitracin Resistance Locus-Carrying Multiple Antibiotic Resistant Integrative and Conjugative Element ICESsu1112S in Streptococccus Suis.}, journal = {Microbiology spectrum}, volume = {10}, number = {1}, pages = {e0196321}, pmid = {35170998}, issn = {2165-0497}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacitracin/*pharmacology ; China ; Conjugation, Genetic ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Linezolid/*pharmacology ; Streptococcal Infections ; Streptococcus suis/*drug effects/*genetics/isolation &amp; purification ; Swine ; }, abstract = {Streptococcus suis strain 1112S was isolated from a diseased pig in a feedlot from Henan, China, in 2019. The isolate harbored a linezolid resistance gene optrA. WGS data revealed that the optrA gene was associated with a single copy ETAf ISS1S, in tandem with erm(B) and tet(O), located in a novel 72,587 bp integrative and conjugative element (ICE). Notably, this novel element, designated ICESsu1112S, also carried a novel bacitracin resistance locus. ICESsu1112S could be excised from chromosome and transferred to the recipient strain S. suis P1/7 with a frequency of 5.9 × 10[-6] transconjugants per donor cell. This study provided the first description of the coexistence of optrA and a novel bacitracin locus on a multiple antibiotic resistant ICE and highlighted that ICE were major vehicle and contribute to the potential transfer of clinically relevant antibiotic resistance genes. IMPORTANCE Antimicrobial resistance (AMR) caused by the imprudent use of antimicrobials has become a global problem, which poses a serious threat to treatment of S. suis infection in pigs and humans. Importantly, AMR genes can horizontally spread among commensal organisms and pathogenic microbiota, thereby accelerating the dissemination of AMR determinants. These transfers are mainly mediated by mobile genetic elements, including ICEs. In S. suis, ICEs are the major vehicles that contribute to the natural transfers of AMR genes among different bacterial pathogens. However, ICEs that carry optrA and bacitracin resistance locus are rarely investigated in S. suis isolates. Here, we investigated a S. suis isolate carrying an optrA and a novel bacitracin resistance locus, which were co-located on a novel multiple antibiotic resistant ICESsu1112S. Our study suggests that more research is needed to access the real significance of ICEs that horizontally spread clinical important resistance genes.}, }
@article {pmid35170993, year = {2022}, author = {Xiong, M and Chen, L and Zhao, J and Xiao, X and Zhou, J and Fang, F and Li, X and Pan, Y and Li, Y}, title = {Genomic Analysis of the Unusual Staphylococcus aureus ST630 Isolates Harboring WTA Glycosyltransferase Genes tarM and tagN.}, journal = {Microbiology spectrum}, volume = {10}, number = {1}, pages = {e0150121}, pmid = {35170993}, issn = {2165-0497}, mesh = {Bacterial Proteins/*genetics/metabolism ; Cell Wall/genetics/metabolism ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomics ; Glycosyltransferases/*genetics/metabolism ; Multigene Family ; Phylogeny ; Staphylococcus aureus/classification/*enzymology/genetics ; Teichoic Acids/*metabolism ; }, abstract = {Staphylococcus aureus (S. aureus) can cause a broad spectrum of diseases ranging from skin infections to life-threatening diseases in both community and hospital settings. The surface-exposed wall teichoic acid (WTA) has a strong impact on host interaction, pathogenicity, horizontal gene transfer, and biofilm formation in S. aureus. The unusual S. aureus ST630 strains containing both ribitol-phosphate (RboP) WTA glycosyltransferase gene tarM and glycerol-phosphate (GroP) WTA glycosyltransferase gene tagN have been found recently. Native PAGE analysis showed that the WTA of tagN, tarM-encoding ST630 strains migrated slower than that of non-tagN-encoding ST630 strains, indicating the differences in WTA structure. Some mobile genetic elements (MGEs) such as the unique GroP-WTA biosynthetic gene cluster (SaGroWI), SCCmec element, and prophages that probably originated from the CoNS were identified in tagN, tarM-encoding ST630 strains. The SaGroWI element was first defined in S. aureus ST395 strain, which was refractory to exchange MGEs with typical RboP-WTA expressing S. aureus but could undergo horizontal gene transfer events with other species and genera via the specific bacteriophage Φ187. Overall, our data indicated that this rare ST630 was prone to acquire DNA from CoNS and might serve as a novel hub for the exchange of MGEs between CoNS and S. aureus. IMPORTANCE The structure of wall-anchored glycopolymers wall teichoic acid (WTA) produced by most Gram-positive bacteria is highly variable. While most dominant Staphylococcus aureus lineages produce poly-ribitol-phosphate (RboP) WTA, the tagN, tarM-encoding ST630 lineage probably has a poly-glycerol-phosphate (GroP) WTA backbone like coagulase-negative staphylococci (CoNS). There is growing evidence that staphylococcal horizontal gene transfer depends largely on transducing helper phages via WTA as the receptor. The structural difference of WTA greatly affects the transfer of mobile genetic elements among various bacteria. With the growing advances in sequencing and analysis technologies, genetic analysis has revolutionized research activities in the field of the important pathogen S. aureus. Here, we analyzed the molecular characteristics of ST630 and found an evolutionary link between ST630 and CoNS. Elucidating the genetic information of ST630 lineage will contribute to understanding the emergence and diversification of new pathogenic strains in S. aureus.}, }
@article {pmid35170725, year = {2022}, author = {Martyn, JE and Gomez-Valero, L and Buchrieser, C}, title = {The evolution and role of eukaryotic-like domains in environmental intracellular bacteria: the battle with a eukaryotic cell.}, journal = {FEMS microbiology reviews}, volume = {46}, number = {4}, pages = {}, doi = {10.1093/femsre/fuac012}, pmid = {35170725}, issn = {1574-6976}, mesh = {Animals ; Bacteria/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; *Eukaryota/metabolism ; Eukaryotic Cells/metabolism ; Host-Pathogen Interactions ; *Legionella/genetics/metabolism ; }, abstract = {Intracellular pathogens that are able to thrive in different environments, such as Legionella spp. that preferentially live in protozoa in aquatic environments or environmental Chlamydiae that replicate either within protozoa or a range of animals, possess a plethora of cellular biology tools to influence their eukaryotic host. The host manipulation tools that evolved in the interaction with protozoa confer these bacteria the capacity to also infect phylogenetically distinct eukaryotic cells, such as macrophages, and thus they can also be human pathogens. To manipulate the host cell, bacteria use protein secretion systems and molecular effectors. Although these molecular effectors are encoded in bacteria, they are expressed and function in a eukaryotic context often mimicking or inhibiting eukaryotic proteins. Indeed, many of these effectors have eukaryotic-like domains. In this review, we propose that the main pathways that environmental intracellular bacteria need to subvert in order to establish the host eukaryotic cell as a replication niche are chromatin remodelling, ubiquitination signalling and modulation of protein-protein interactions via tandem repeat domains. We then provide mechanistic insight into how these proteins might have evolved. Finally, we highlight that in environmental intracellular bacteria the number of eukaryotic-like domains and proteins is considerably higher than in intracellular bacteria specialized to an isolated niche, such as obligate intracellular human pathogens. As mimics of eukaryotic proteins are critical components of host-pathogen interactions, this distribution of eukaryotic-like domains suggests that the environment has selected them.}, }
@article {pmid35169846, year = {2022}, author = {Tricou, T and Tannier, E and de Vienne, DM}, title = {Ghost Lineages Highly Influence the Interpretation of Introgression Tests.}, journal = {Systematic biology}, volume = {71}, number = {5}, pages = {1147-1158}, pmid = {35169846}, issn = {1076-836X}, mesh = {Biological Evolution ; *Gene Flow/genetics ; Gene Transfer, Horizontal ; *Hybridization, Genetic ; Phylogeny ; }, abstract = {Most species are extinct, those that are not are often unknown. Sequenced and sampled species are often a minority of known ones. Past evolutionary events involving horizontal gene flow, such as horizontal gene transfer, hybridization, introgression, and admixture, are therefore likely to involve "ghosts," that is extinct, unknown, or unsampled lineages. The existence of these ghost lineages is widely acknowledged, but their possible impact on the detection of gene flow and on the identification of the species involved is largely overlooked. It is generally considered as a possible source of error that, with reasonable approximation, can be ignored. We explore the possible influence of absent species on an evolutionary study by quantifying the effect of ghost lineages on introgression as detected by the popular D-statistic method. We show from simulated data that under certain frequently encountered conditions, the donors and recipients of horizontal gene flow can be wrongly identified if ghost lineages are not taken into account. In particular, having a distant outgroup, which is usually recommended, leads to an increase in the error probability and to false interpretations in most cases. We conclude that introgression from ghost lineages should be systematically considered as an alternative possible, even probable, scenario. [ABBA-BABA; D-statistic; gene flow; ghost lineage; introgression; simulation.].}, }
@article {pmid35168548, year = {2022}, author = {García-Martín, AB and Roder, T and Schmitt, S and Zeeh, F and Bruggmann, R and Perreten, V}, title = {Whole-genome analyses reveal a novel prophage and cgSNPs-derived sublineages of Brachyspira hyodysenteriae ST196.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {131}, pmid = {35168548}, issn = {1471-2164}, support = {1.16.04//Swiss Federal Food Safety and Veterinary Office (SFVO)/ ; 1.19.05//Swiss Federal Food Safety and Veterinary Office (SFVO)/ ; 1.16.04//Swiss Federal Food Safety and Veterinary Office (SFVO)/ ; 1.16.04//Swiss Federal Food Safety and Veterinary Office (SFVO)/ ; }, mesh = {Animals ; Anti-Bacterial Agents ; *Brachyspira ; *Brachyspira hyodysenteriae/genetics ; *Gram-Negative Bacterial Infections ; Macrolides ; Prophages/genetics ; Swine ; *Swine Diseases ; }, abstract = {BACKGROUND: Brachyspira (B.) hyodysenteriae is a fastidious anaerobe spirochete that can cause swine dysentery, a severe mucohaemorragic colitis that affects pig production and animal welfare worldwide. In Switzerland, the population of B. hyodysenteriae is characterized by the predominance of macrolide-lincosamide-resistant B. hyodysenteriae isolates of sequence type (ST) ST196, prompting us to obtain deeper insights into the genomic structure and variability of ST196 using pangenome and whole genome variant analyses.<br><br>RESULTS: The draft genome of 14 B. hyodysenteriae isolates of ST196, sampled during a 7-year period from geographically distant pig herds, was obtained by whole-genome sequencing (WGS) and compared to the complete genome of the B. hyodysenteriae isolate Bh743-7 of ST196 used as reference. Variability results revealed the existence of 30 to 52 single nucleotide polymorphisms (SNPs), resulting in eight sublineages of ST196. The pangenome analysis led to the identification of a novel prophage, pphBhCH20, of the Siphoviridae family in a single isolate of ST196, which suggests that horizontal gene transfer events may drive changes in genomic structure.<br><br>CONCLUSIONS: This study contributes to the catalogue of publicly available genomes and provides relevant bioinformatic tools and information for further comparative genomic analyses for B. hyodysenteriae. It reveals that Swiss B. hyodysenteriae isolates of the same ST may have evolved independently over time by point mutations and acquisition of larger genetic elements. In line with this, the third type of mobile genetic element described so far in B. hyodysenteriae, the novel prophage pphBhCH20, has been identified in a single isolate of B. hyodysenteriae of ST196.}, }
@article {pmid35167690, year = {2022}, author = {Carruthers, T and Sun, M and Baker, WJ and Smith, SA and de Vos, JM and Eiserhardt, WL}, title = {The Implications of Incongruence between Gene Tree and Species Tree Topologies for Divergence Time Estimation.}, journal = {Systematic biology}, volume = {71}, number = {5}, pages = {1124-1146}, pmid = {35167690}, issn = {1076-836X}, mesh = {Computer Simulation ; *Fossils ; Hybridization, Genetic ; *Models, Genetic ; Phylogeny ; }, abstract = {Phylogenetic analyses are increasingly being performed with data sets that incorporate hundreds of loci. Due to incomplete lineage sorting, hybridization, and horizontal gene transfer, the gene trees for these loci may often have topologies that differ from each other and from the species tree. The effect of these topological incongruences on divergence time estimation has not been fully investigated. Using a series of simulation experiments and empirical analyses, we demonstrate that when topological incongruence between gene trees and the species tree is not accounted for, the temporal duration of branches in regions of the species tree that are affected by incongruence is underestimated, whilst the duration of other branches is considerably overestimated. This effect becomes more pronounced with higher levels of topological incongruence. We show that this pattern results from the erroneous estimation of the number of substitutions along branches in the species tree, although the effect is modulated by the assumptions inherent to divergence time estimation, such as those relating to the fossil record or among-branch-substitution-rate variation. By only analyzing loci with gene trees that are topologically congruent with the species tree, or only taking into account the branches from each gene tree that are topologically congruent with the species tree, we demonstrate that the effects of topological incongruence can be ameliorated. Nonetheless, even when topologically congruent gene trees or topologically congruent branches are selected, error in divergence time estimates remains. This stems from temporal incongruences between divergence times in species trees and divergence times in gene trees, and more importantly, the difficulty of incorporating necessary assumptions for divergence time estimation. [Divergence time estimation; gene trees; species tree; topological incongruence.].}, }
@article {pmid35167684, year = {2022}, author = {Heo, G and Kong, H and Kim, N and Lee, S and Sul, S and Jeong, DW and Lee, JH}, title = {Antibiotic susceptibility of Bacillus velezensis.}, journal = {FEMS microbiology letters}, volume = {369}, number = {1}, pages = {}, doi = {10.1093/femsle/fnac017}, pmid = {35167684}, issn = {1574-6968}, mesh = {Anti-Bacterial Agents/pharmacology ; *Bacillus/genetics ; *Clindamycin ; Drug Resistance, Bacterial/genetics ; Humans ; Streptomycin ; Tetracycline/pharmacology ; }, abstract = {We evaluated the antibiotic minimum inhibitory concentrations (MICs) of 123 Bacillus velezensis strains predominantly isolated from fermented soybean foods from Korea. When the 2018 European Food Safety Authority breakpoint values for Bacillus spp. were applied, all the strains were sensitive to chloramphenicol, clindamycin, erythromycin, gentamicin, kanamycin, tetracycline and vancomycin, and eight strains (6.5%) were resistant to streptomycin. The population distribution in MIC tests with streptomycin was continuous and the profile was clearly different from that expected for acquired antibiotic resistance. As of 25 October 2021, there were 181 complete published genomes of B. velezensis strains; 175 (96.7%) and 136 (75.2%) of these strains, respectively, possess potential tetracycline and streptomycin resistance genes tetL and ant(6) in the chromosome. In Bacillus licheniformis, SpeG confers resistance to clindamycin and there is an 'speG' gene annotated in the genomes of 180 B. velezensis strains; however, the gene products exhibit ≤26.6% amino acid identity with that from B. licheniformis DSM 13T. All the potential antibiotic resistance genes in the 181 B. velezensis strains were intrinsic, and traits of lateral gene transfer were not found. In this context, B. velezensis may not present a high risk in terms of antibiotic resistance in food fermentation or human use.}, }
@article {pmid35163016, year = {2022}, author = {Akimova, E and Gassner, FJ and Greil, R and Zaborsky, N and Geisberger, R}, title = {Detecting Bacterial-Human Lateral Gene Transfer in Chronic Lymphocytic Leukemia.}, journal = {International journal of molecular sciences}, volume = {23}, number = {3}, pages = {}, pmid = {35163016}, issn = {1422-0067}, support = {P 32762/FWF_/Austrian Science Fund FWF/Austria ; P32762-B//FWF Austrian Science Fund/ ; }, mesh = {Bacteria/*genetics/growth &amp; development ; Case-Control Studies ; *Chromosome Aberrations ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genome, Human ; Humans ; Leukemia, Lymphocytic, Chronic, B-Cell/genetics/microbiology/*pathology ; *Microbiota ; }, abstract = {Chronic lymphocytic leukemia (CLL) is a very common and mostly incurable B-cell malignancy. Recent studies revealed high interpatient mutational heterogeneity and worsened therapy response and survival of patients with complex genomic aberrations. In line with this, a better understanding of the underlying mechanisms of specific genetic aberrations would reveal new prognostic factors and possible therapeutic targets. It is known that chromosomal rearrangements including DNA insertions often play a role during carcinogenesis. Recently it was reported that bacteria (microbiome)-human lateral gene transfer occurs in somatic cells and is enriched in cancer samples. To further investigate this mechanism in CLL, we analyzed paired-end RNA sequencing data of 45 CLL patients and 9 healthy donors, in which we particularly searched for bacterial DNA integrations into the human somatic genome. Applying the Burrows-Wheeler aligner (BWA) first on a human genome and then on bacterial genome references, we differentiated between sequencing reads mapping to the human genome, to the microbiome or to bacterial integrations into the human genome. Our results indicate that CLL samples featured bacterial DNA integrations more frequently (approx. two-fold) compared to normal samples, which corroborates the latest findings in other cancer entities. Moreover, we determined common integration sites and recurrent integrated bacterial transcripts. Finally, we investigated the contribution of bacterial integrations to oncogenesis and disease progression.}, }
@article {pmid35157704, year = {2022}, author = {Johnson, CM and Harden, MM and Grossman, AD}, title = {Interactions between mobile genetic elements: An anti-phage gene in an integrative and conjugative element protects host cells from predation by a temperate bacteriophage.}, journal = {PLoS genetics}, volume = {18}, number = {2}, pages = {e1010065}, pmid = {35157704}, issn = {1553-7404}, support = {R01 GM050895/GM/NIGMS NIH HHS/United States ; R35 GM122538/GM/NIGMS NIH HHS/United States ; T32 GM007287/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Bacteriophages/genetics ; *Conjugation, Genetic/genetics ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal/genetics ; Interspersed Repetitive Sequences/genetics ; Predatory Behavior ; }, abstract = {Most bacterial genomes contain horizontally acquired and transmissible mobile genetic elements, including temperate bacteriophages and integrative and conjugative elements. Little is known about how these elements interact and co-evolved as parts of their host genomes. In many cases, it is not known what advantages, if any, these elements provide to their bacterial hosts. Most strains of Bacillus subtilis contain the temperate phage SPß and the integrative and conjugative element ICEBs1. Here we show that the presence of ICEBs1 in cells protects populations of B. subtilis from predation by SPß, likely providing selective pressure for the maintenance of ICEBs1 in B. subtilis. A single gene in ICEBs1 (yddK, now called spbK for SPß killing) was both necessary and sufficient for this protection. spbK inhibited production of SPß, during both activation of a lysogen and following de novo infection. We found that expression spbK, together with the SPß gene yonE constitutes an abortive infection system that leads to cell death. spbK encodes a TIR (Toll-interleukin-1 receptor)-domain protein with similarity to some plant antiviral proteins and animal innate immune signaling proteins. We postulate that many uncharacterized cargo genes in ICEs may confer selective advantage to cells by protecting against other mobile elements.}, }
@article {pmid35154192, year = {2021}, author = {Xiong, Y and Yu, Q and Xiong, Y and Zhao, J and Lei, X and Liu, L and Liu, W and Peng, Y and Zhang, J and Li, D and Bai, S and Ma, X}, title = {The Complete Mitogenome of Elymus sibiricus and Insights Into Its Evolutionary Pattern Based on Simple Repeat Sequences of Seed Plant Mitogenomes.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {802321}, pmid = {35154192}, issn = {1664-462X}, abstract = {The most intriguing characteristics of plant mitochondrial genomes (mitogenomes) include their high variation in both sequence and structure, the extensive horizontal gene transfer (HGT), and the important role they play in hypoxic adaptation. However, the investigation of the mechanisms of hypoxic adaptation and HGT in plant mitochondria remains challenging due to the limited number of sequenced mitogenomes and non-coding nature of the transferred DNA. In this study, the mitogenome of Elymus sibiricus (Gramineae, Triticeae), a perennial grass species native to the Qinghai-Tibet plateau (QTP), was de novo assembled and compared with the mitogenomes of eight Gramineae species. The unique haplotype composition and higher TE content compared to three other Triticeae species may be attributed to the long-term high-altitude plateau adaptability of E. sibiricus. We aimed to discover the connection between mitogenome simple sequence repeats (SSRs) (mt-SSRs) and HGT. Therefore, we predicted and annotated the mt-SSRs of E. sibiricus along with the sequencing of 87 seed plants. The clustering result based on all of the predicted compound mitogenome SSRs (mt-c-SSRs) revealed an expected synteny within systematic taxa and also inter-taxa. The mt-c-SSRs were annotated to 11 genes, among which "(ATA)3agtcaagtcaag (AAT)3" occurred in the nad5 gene of 8 species. The above-mentioned results further confirmed the HGT of mitogenomes sequences even among distant species from the aspect of mt-c-SSRs. Two genes, nad4 and nad7, possessed a vast number of SSRs in their intron regions across the seed plant mitogenomes. Furthermore, five pairs of SSRs developed from the mitogenome of E. sibiricus could be considered as potential markers to distinguish between the species E. sibiricus and its related sympatric species E. nutans.}, }
@article {pmid35150038, year = {2022}, author = {Deb, S and Gokulan, CG and Nathawat, R and Patel, HK and Sonti, RV}, title = {Suppression of XopQ-XopX-induced immune responses of rice by the type III effector XopG.}, journal = {Molecular plant pathology}, volume = {23}, number = {5}, pages = {634-648}, pmid = {35150038}, issn = {1364-3703}, mesh = {Bacterial Proteins/metabolism ; Immunity ; Mutation/genetics ; *Oryza/metabolism ; Plant Diseases/microbiology ; Virulence/genetics ; *Xanthomonas ; }, abstract = {Effectors that suppress effector-triggered immunity (ETI) are an essential part of the arms race in the co-evolution of bacterial pathogens and their host plants. Xanthomonas oryzae pv. oryzae uses multiple type III secretion system (T3SS) secreted effectors such as XopU, XopV, XopP, XopG, and AvrBs2 to suppress rice immune responses that are induced by the interaction of two other effectors, XopQ and XopX. Here we show that each of these five suppressors can interact individually with both XopQ and XopX. One of the suppressors, XopG, is a predicted metallopeptidase that appears to have been introduced into X. oryzae pv. oryzae by horizontal gene transfer. XopQ and XopX interact with each other in the nucleus while interaction with XopG sequesters them in the cytoplasm. The XopG E76A and XopG E85A mutants are defective in interaction with XopQ and XopX, and are also defective in suppression of XopQ-XopX-mediated immune responses. Both mutations individually affect the virulence-promoting ability of XopG. These results indicate that XopG is important for X. oryzae pv. oryzae virulence and provide insights into the mechanisms by which this protein suppresses ETI in rice.}, }
@article {pmid35146465, year = {2022}, author = {van Hal, SJ and Willems, RJL and Gouliouris, T and Ballard, SA and Coque, TM and Hammerum, AM and Hegstad, K and Pinholt, M and Howden, BP and Malhotra-Kumar, S and Werner, G and Yanagihara, K and Earl, AM and Raven, KE and Corander, J and Bowden, R and , }, title = {The interplay between community and hospital Enterococcus faecium clones within health-care settings: a genomic analysis.}, journal = {The Lancet. Microbe}, volume = {3}, number = {2}, pages = {e133-e141}, pmid = {35146465}, issn = {2666-5247}, support = {U19 AI110818/AI/NIAID NIH HHS/United States ; HHSN272200900018C/AI/NIAID NIH HHS/United States ; 203141/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Clone Cells ; *Enterococcus faecium/genetics ; Genome, Bacterial/genetics ; Genomics ; Hospitals ; Humans ; Phylogeny ; }, abstract = {BACKGROUND: The genomic relationships among Enterococcus faecium isolates are the subject of ongoing research that seeks to clarify the origins of observed lineages and the extent of horizontal gene transfer between them, and to robustly identify links between genotypes and phenotypes. E faecium is considered to form distinct groups-A and B-corresponding to isolates derived from patients who were hospitalised (A) and isolates from humans in the community (B). The additional separation of A into the so-called clades A1 and A2 remains an area of uncertainty. We aimed to investigate the relationships between A1 and non-A1 groups and explore the potential role of non-A1 isolates in shaping the population structure of hospital E faecium.<br><br>METHODS: We collected short-read sequence data from invited groups that had previously published E faecium genome data. This hospital-based isolate collection could be separated into three groups (or clades, A1, A2, and B) by augmenting the study genomes with published sequences derived from human samples representing the previously defined genomic clusters. We performed phylogenetic analyses, by constructing maximum-likelihood phylogenetic trees, and identified historical recombination events. We assessed the pan-genome, did resistome analysis, and examined the genomic data to identify mobile genetic elements. Each genome underwent chromosome painting by use of ChromoPainter within FineSTRUCTURE software to assess ancestry and identify hybrid groups. We further assessed highly admixed regions to infer recombination directionality.<br><br>FINDINGS: We assembled a collection of 1095 hospital E faecium sequences from 34 countries, further augmented by 33 published sequences. 997 (88%) of 1128 genomes clustered as A1, 92 (8%) as A2, and 39 (4%) as B. We showed that A1 probably emerged as a clone from within A2 and that, because of ongoing gene flow, hospital isolates currently identified as A2 represent a genetic continuum between A1 and community E faecium. This interchange of genetic material between isolates from different groups results in the emergence of hybrid genomes between clusters. Of the 1128 genomes, 49 (4%) hybrid genomes were identified: 33 previously labelled as A2 and 16 previously labelled as A1. These interactions were fuelled by a directional pattern of recombination mediated by mobile genetic elements. By contrast, the contribution of B group genetic material to A1 was limited to a few small regions of the genome and appeared to be driven by genomic sweep events.<br><br>INTERPRETATION: A2 and B isolates coming into the hospital form an important reservoir for ongoing A1 adaptation, suggesting that effective long-term control of the effect of E faecium could benefit from strategies to reduce these genomic interactions, such as a focus on reducing the acquisition of hospital A1 strains by patients entering the hospital.<br><br>FUNDING: Wellcome Trust.}, }
@article {pmid35145997, year = {2021}, author = {Chen, R and Zhao, L and Gan, R and Feng, Z and Cui, C and Xie, X and Hao, F and Zhang, Z and Wang, L and Ran, T and Wang, W and Zhang, S and Li, Y and Zhang, W and Pang, M and Xiong, Q and Shao, G}, title = {Evidence for the Rapid and Divergent Evolution of Mycoplasmas: Structural and Phylogenetic Analysis of Enolases.}, journal = {Frontiers in molecular biosciences}, volume = {8}, number = {}, pages = {811106}, pmid = {35145997}, issn = {2296-889X}, abstract = {Mycoplasmas are a group of prokaryotes without cell walls that have evolved through several rounds of degenerative evolution. With a low cell DNA G + C content and definitively long genetic lineages, mycoplasmas are thought to be in a state of rapid evolution. However, little associated evidence has been provided. Enolase is a key enzyme in glycolysis that is widely found in all species from the three domains, and it is evolutionarily conserved. In our previous studies, enolase acted as a virulence factor and participated in cell-surface adhesion in Mycoplasma hyopneumoniae. Furthermore, unique loop regions were first found in the crystal structure of Mhp Eno. Here, enolase structures from Mycoplasma pneumoniae and Mycoplasma bovis were determined. An extra helix 7 is specific and conservatively found in almost all mycoplasma enolases, as confirmed by crystal structures and sequence alignment. Particular motifs for helix 7, which is composed of F-K/G-K-L/F-K-X-A-I, have been proposed and could be regarded as molecular markers. To our surprise, the genetic distances between any two mycoplasma enolases were obviously longer than those between the two corresponding species themselves, indicating divergent evolution of mycoplasma enolases, whereas no horizontal gene transfer was detected in mycoplasma enolase genens. Furthermore, different evolutionary patterns were adopted by different loop regions of mycoplasma enolase. Enolases from different Mycoplasma species also showed different affinities for PLG and fibronectin. Our results indicate the rapid and divergent evolution of mycoplasma enolase and mycoplasmas. This study will also aid understanding the independent evolution of Mycoplasma species after separation from their common ancestor.}, }
@article {pmid35143804, year = {2022}, author = {Narsing Rao, MP and Luo, ZH and Dong, ZY and Li, Q and Liu, BB and Guo, SX and Nie, GX and Li, WJ}, title = {Metagenomic analysis further extends the role of Chloroflexi in fundamental biogeochemical cycles.}, journal = {Environmental research}, volume = {209}, number = {}, pages = {112888}, doi = {10.1016/j.envres.2022.112888}, pmid = {35143804}, issn = {1096-0953}, mesh = {*Chloroflexi/genetics/metabolism ; Metabolic Networks and Pathways ; Metagenome ; Metagenomics ; Phylogeny ; }, abstract = {Chloroflexi members are ubiquitous and have been extensively studied; however, the evolution and metabolic pathways of Chloroflexi members have long been debated. In the present study, the evolution and the metabolic potentials of 17 newly obtained Chloroflexi metagenome-assembled genomes (MAGs) were evaluated using genome and horizontal gene transfer (HGT) analysis. Taxonomic analysis suggests that the MAGs of the present study might be novel. One MAG encodes genes for anoxygenic phototrophy. The HGT analysis suggest that genes responsible for anoxygenic phototrophy in the MAG might have been transferred from Proteobacteria/Chlorobi. The evolution of anaerobic photosynthesis, which has long been questioned, has now been shown to be the result of HGT events. An incomplete Wood-Ljungdahl pathway (with missing genes metF, acsE, fdh, and acsA) was reported in Dehalococcoidetes members. In the present study, MAGs that were not the Dehalococcoidetes members encode genes acsA, acsB, metF and acsE. The genes responsible for sulfate reduction (sat, cysC and sir), dissimilatory sulfite reductase (dsrA and dsrB), and aerobic and anaerobic carbon monoxide oxidation (coxSML and cooSF) were detected in the present study MAGs. The present study expands our knowledge of the possible metabolic potentials of the phylum Chloroflexi and clarifies the evolution of anaerobic photosynthesis.}, }
@article {pmid35143795, year = {2022}, author = {Yang, P and Hao, S and Han, M and Xu, J and Yu, S and Chen, C and Zhang, H and Ning, K}, title = {Analysis of antibiotic resistance genes reveals their important roles in influencing the community structure of ocean microbiome.}, journal = {The Science of the total environment}, volume = {823}, number = {}, pages = {153731}, doi = {10.1016/j.scitotenv.2022.153731}, pmid = {35143795}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Microbiota ; Oceans and Seas ; }, abstract = {Antibiotic resistance gene (ARG) content is a well-established driver of microbial abundance and diversity in an environment. By reanalyzing 132 metagenomic datasets from the Tara Oceans project, we aim to unveil the associations between environmental factors, the ocean microbial community structure and ARG contents. We first investigated the structural patterns of microbial communities including both prokaryotes such as bacteria and eukaryotes such as protists. Additionally, several ARG-dominant horizontal gene transfer events between Protist and Prokaryote have been identified, indicating the potential roles of ARG in shaping the ocean microbial communities. For a deeper insight into the role of ARGs in ocean microbial communities on a global scale, we identified 1926 unique types of ARGs and discovered that the ARGs are more abundant and diverse in the mesopelagic zone than other water layers, potentially caused by limited resources. Finally, we found that ARG-enriched genera were often more abundant compared to their ARG-less neighbors in the same environment (e.g. coastal oceans). A deeper understanding of the ARG-microbiome relationships could help in the conservation of the oceanic ecosystem.}, }
@article {pmid35138674, year = {2022}, author = {Saraiva, MMS and Silva, NMV and Ferreira, VA and Moreira Filho, ALB and Givisiez, PEN and Freitas Neto, OC and Berchieri Júnior, A and Gebreyes, WA and de Oliveira, CJB}, title = {Residual concentrations of antimicrobial growth promoters in poultry litter favour plasmid conjugation among Escherichia coli.}, journal = {Letters in applied microbiology}, volume = {74}, number = {5}, pages = {831-838}, doi = {10.1111/lam.13671}, pmid = {35138674}, issn = {1472-765X}, support = {2018/03189-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2018/21301-2//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 313678/2020-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; //Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents/pharmacology ; Cellulose/pharmacology ; Conjugation, Genetic ; Escherichia coli/genetics ; *Escherichia coli Infections/microbiology ; Lincomycin/pharmacology ; Monensin ; Plasmids/genetics ; Poultry/microbiology ; *Saccharum ; Virginiamycin/pharmacology ; }, abstract = {Considering that plasmid conjugation is a major driver for the dissemination of antimicrobial resistance in bacteria, this study aimed to investigate the effects of residual concentrations of antimicrobial growth promoters (AGPs) in poultry litter on the frequencies of IncFII-FIB plasmid conjugation among Escherichia coli organisms. A 2 × 5 factorial trial was performed in vitro, using two types of litter materials (sugarcane bagasse and wood shavings) and five treatments of litter: non-treated (CON), herbal alkaloid sanguinarine (SANG), AGPs monensin (MON), lincomycin (LCM) and virginiamycin (VIR). E. coli H2332 and E. coli J62 were used as donor and recipient strains, respectively. The presence of residues of monensin, lincomycin and virginiamycin increased the frequency of plasmid conjugation among E. coli in both types of litter materials. On the contrary, sanguinarine significantly reduced the frequency of conjugation among E. coli in sugarcane bagasse litter. The conjugation frequencies were significantly higher in wood shavings compared with sugarcane bagasse only in the presence of AGPs. Considering that the presence of AGPs in the litter can increase the conjugation of IncFII-FIB plasmids carrying antimicrobial resistance genes, the real impact of this phenomenon on the dissemination of antimicrobial resistant bacteria in the poultry production chain must be investigated.}, }
@article {pmid35138195, year = {2022}, author = {Lasarte-Monterrubio, C and Guijarro-Sánchez, P and Bellés, A and Vázquez-Ucha, JC and Arca-Suárez, J and Fernández-Lozano, C and Bou, G and Beceiro, A and , }, title = {Carbapenem Resistance in Acinetobacter nosocomialis and Acinetobacter junii Conferred by Acquisition of blaOXA-24/40 and Genetic Characterization of the Transmission Mechanism between Acinetobacter Genomic Species.}, journal = {Microbiology spectrum}, volume = {10}, number = {1}, pages = {e0273421}, pmid = {35138195}, issn = {2165-0497}, mesh = {Acinetobacter/*drug effects/enzymology/*genetics ; Acinetobacter Infections/*microbiology ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics/metabolism ; Carbapenems/*pharmacology ; Drug Resistance, Bacterial ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Genomics ; Humans ; Microbial Sensitivity Tests ; Plasmids/genetics/metabolism ; beta-Lactamases/genetics/metabolism ; }, abstract = {Carbapenem resistance is increasing among Gram-negative bacteria, including the genus Acinetobacter. This study aimed to characterize, for the first time, the development of carbapenem resistance in clinical isolates of Acinetobacter junii and Acinetobacter nosocomialis conferred by the acquisition of a plasmid-borne blaOXA-24/40 gene and also to characterize the dissemination of this gene between species of Acinetobacter. Carbapenem-resistant A. nosocomialis HUAV-AN66 and A. junii HUAV-AJ77 strains were isolated in the Arnau de Vilanova Hospital (Spain). The genomes were sequenced, and in silico analysis were performed to characterize the genetic environment and the OXA-24/40 transmission mechanism. Antibiotic MICs were determined, and horizontal transfer assays were conducted to evaluate interspecies transmission of OXA-24/40. Carbapenems MICs obtained were ≥64 mg/L for HUAV-AN66 and HUAV-AJ77. Genome analysis revealed the presence in both strains of a new plasmid, designated pHUAV/OXA-24/40, harboring the carbapenem-resistance gene blaOXA-24/40 and flanked by sequences XerC/XerD. pHUAV/OXA-24/40 was successfully transferred from A. nosocomialis and A. junii to a carbapenem-susceptible A. baumannii strain, thus conferring carbapenem resistance. A second plasmid (pHUAV/AMG-R) was identified in both clinical isolates for the successful horizontal transfer of pHUAV/OXA-24/40. blaOXA-24/40-carrying plasmids of the GR12 group and showing high identity with pHUAV/OXA-24/40 were identified in at least 8 Acinetobacter species. In conclusion the carbapenemase OXA-24/40 is described for the first time in A. nosocomialis and A. junii. In both isolates the blaOXA-24/40 gene was located in the GR12 pHUAV/OXA-24/40 plasmid. GR12 plasmids are implicated in the dissemination and spread of carbapenem resistance among Acinetobacter species. IMPORTANCE Acinetobacter baumannii is one of the most relevant pathogens in terms of antibiotic resistance. The main resistance mechanisms are the carbapenem-hydrolyzing class D β-lactamases (CHDLs), especially OXA-23 and OXA-24/40. In addition to A. baumannii, there are other species within the genus Acinetobacter, which in general exhibit much lower resistance rates. In this work we characterize for the first time two clinical isolates of Acinetobacter nosocomialis and Acinetobacter junii, isolated in the same hospital, carrying the carbapenemase OXA-24/40 and displaying high resistance rates to carbapenems. By means of bioinformatics analysis we have also been able to characterize the mechanism by which this carbapenemase is horizontally transferred interspecies of Acinetobacter spp. The dissemination of carbapenemase OXA-24/40 between non-baumannii Acinetobacter species is concerning since it prevents the use of most β-lactam antibiotics in the fight against these resistant isolates.}, }
@article {pmid35138167, year = {2022}, author = {Bowring, JZ and Su, Y and Alsaadi, A and Svenningsen, SL and Parkhill, J and Ingmer, H}, title = {Screening for Highly Transduced Genes in Staphylococcus aureus Revealed Both Lateral and Specialized Transduction.}, journal = {Microbiology spectrum}, volume = {10}, number = {1}, pages = {e0242321}, pmid = {35138167}, issn = {2165-0497}, support = {/WT_/Wellcome Trust/United Kingdom ; WT098051/WT_/Wellcome Trust/United Kingdom ; }, mesh = {DNA, Bacterial/genetics/metabolism ; Gene Transfer, Horizontal ; Interspersed Repetitive Sequences ; Staphylococcus Phages/*genetics/physiology ; Staphylococcus aureus/*genetics/metabolism/*virology ; *Transduction, Genetic ; }, abstract = {Bacteriophage-mediated transduction of bacterial DNA is a major route of horizontal gene transfer in the human pathogen, Staphylococcus aureus. Transduction involves the packaging of bacterial DNA by viruses and enables the transmission of virulence and resistance genes between cells. To learn more about transduction in S. aureus, we searched a transposon mutant library for genes and mutations that enhanced transfer mediated by the temperate phage, ϕ11. Using a novel screening strategy, we performed multiple rounds of transduction of transposon mutant pools selecting for an antibiotic resistance marker within the transposon element. When determining the locations of transferred mutations, we found that the screen had selected for just 1 or 2 transposon mutant(s) within each pool of 96 mutants. Subsequent analysis showed that the position of the transposon, rather than the inactivation of bacterial genes, was responsible for the phenotype. Interestingly, from multiple rounds, we identified a pattern of transduction that encompassed mobile genetic elements as well as chromosomal regions both upstream and downstream of the phage integration site. The latter was confirmed by DNA sequencing of purified phage lysates. Importantly, transduction frequencies were lower for phage lysates obtained by phage infection rather than induction. Our results confirmed previous reports of lateral transduction of bacterial DNA downstream of the integrated phage but also indicated a novel form of specialized transduction of DNA upstream of the phage. These findings illustrated the complexity of transduction processes and increased our understanding of the mechanisms by which phages transfer bacterial DNA. IMPORTANCE Horizontal transfer of DNA between bacterial cells contributes to the spread of virulence and antibiotic resistance genes in human pathogens. For Staphylococcus aureus, bacterial viruses play a major role in facilitating the horizontal transfer. These viruses, termed bacteriophages, can transfer bacterial DNA between cells by a process known as transduction, which despite its importance is only poorly characterized. Here, we employed a transposon mutant library to investigate transduction in S. aureus. We showed that the genomic location of bacterial DNA relative to where bacteriophages integrated into that bacterial genome affected how frequently that DNA was transduced. Based on serial transduction of transposon mutant pools and direct sequencing of bacterial DNA in bacteriophage particles, we demonstrated both lateral and specialized transduction. The use of mutant libraries to investigate the genomic patterns of bacterial DNA transferred between cells could help us understand how horizontal transfer influences virulence and resistance development.}, }
@article {pmid35137542, year = {2022}, author = {Dolan, SK and Matilla, MA}, title = {Tools of the trade: plasmid repositories and standardized plasmid manipulation for molecular and synthetic biology.}, journal = {Microbial biotechnology}, volume = {15}, number = {5}, pages = {1318-1320}, pmid = {35137542}, issn = {1751-7915}, mesh = {Bacteria/genetics ; *Gene Transfer, Horizontal ; Plasmids/genetics ; Reproducibility of Results ; *Synthetic Biology ; }, abstract = {Plasmids are extrachromosomal genetic elements capable of autonomous replication within a host cell. They play a key role in bacterial ecology and evolution, facilitating the mobilization of accessory genes by horizontal gene transfer. Crucially, plasmids also serve as valuable tools in modern molecular biology. Here, we highlight recent articles aimed at implementing standardized plasmid assembly techniques and plasmid repositories to promote open science as well as to improve experimental reproducibility across laboratories. Research focused on assisting these fundamental aims is a further step towards improving standardization in molecular and synthetic biology.}, }
@article {pmid35134550, year = {2022}, author = {Both, A and Kruse, F and Mirwald, N and Franke, G and Christner, M and Huang, J and Hansen, JL and Kröger, N and Berneking, L and Lellek, H and Aepfelbacher, M and Rohde, H}, title = {Population dynamics in colonizing vancomycin-resistant Enterococcus faecium isolated from immunosuppressed patients.}, journal = {Journal of global antimicrobial resistance}, volume = {28}, number = {}, pages = {267-273}, doi = {10.1016/j.jgar.2022.01.027}, pmid = {35134550}, issn = {2213-7173}, mesh = {*Enterococcus faecium/genetics ; Humans ; Multilocus Sequence Typing ; Population Dynamics ; Vancomycin ; *Vancomycin-Resistant Enterococci/genetics ; }, abstract = {OBJECTIVES: Vancomycin-resistant Enterococcus faecium and Enterococcus faecalis (VRE) are a common cause of healthcare-associated infections. Whole genome sequencing-based typing methods yield the highest discriminatory power for outbreak surveillance in the hospital. We analysed the clonal composition of enteric VRE populations of at-risk patients over several weeks to characterise VRE population diversity and dynamics.<br><br>METHODS: Five bone marrow transplant recipients (three colonised with vanA-positive isolates, two colonised with vanB-positive isolates) contributed three rectal swabs over a course of several weeks. Fourteen VRE colonies per swab were analysed by core genome multi locus sequence typing (cgMLST) and typing of the van-element.<br><br>RESULTS: VRE populations were clonally diverse in three of five patients, and population composition changed dynamically over the time of observation. Besides new acquisition of VRE isolates, shared van-elements localised on nearly identical plasmids between clonally different isolates indicate horizontal gene transfer as a mechanism behind VRE population diversity within single patients.<br><br>CONCLUSION: Outbreak detection relies on typing of isolates, usually by analysing one isolate per patient. We here show that this approach is insufficient for outbreak surveillance of VRE in highly vulnerable patients, as it does not take into account VRE population heterogeneity and horizontal gene transfer of the resistance element.}, }
@article {pmid35134226, year = {2022}, author = {Colgan, TJ and Arce, AN and Gill, RJ and Ramos Rodrigues, A and Kanteh, A and Duncan, EJ and Li, L and Chittka, L and Wurm, Y}, title = {Genomic Signatures of Recent Adaptation in a Wild Bumblebee.}, journal = {Molecular biology and evolution}, volume = {39}, number = {2}, pages = {}, pmid = {35134226}, issn = {1537-1719}, support = {BB/K004204/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T015683/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bees/genetics ; *Ecosystem ; *Genomics ; }, abstract = {Environmental changes threaten insect pollinators, creating risks for agriculture and ecosystem stability. Despite their importance, we know little about how wild insects respond to environmental pressures. To understand the genomic bases of adaptation in an ecologically important pollinator, we analyzed genomes of Bombus terrestris bumblebees collected across Great Britain. We reveal extensive genetic diversity within this population, and strong signatures of recent adaptation throughout the genome affecting key processes including neurobiology and wing development. We also discover unusual features of the genome, including a region containing 53 genes that lacks genetic diversity in many bee species, and a horizontal gene transfer from a Wolbachia bacteria. Overall, the genetic diversity we observe and how it is distributed throughout the genome and the population should support the resilience of this important pollinator species to ongoing and future selective pressures. Applying our approach to more species should help understand how they can differ in their adaptive potential, and to develop conservation strategies for those most at risk.}, }
@article {pmid35130720, year = {2021}, author = {Liu, KH and Zhang, B and Yang, BS and Shi, WT and Li, YF and Wang, Y and Zhang, P and Jiao, J and Tian, CF}, title = {Rhizobiales-Specific RirA Represses a Naturally "Synthetic" Foreign Siderophore Gene Cluster To Maintain Sinorhizobium-Legume Mutualism.}, journal = {mBio}, volume = {13}, number = {1}, pages = {e0290021}, pmid = {35130720}, issn = {2150-7511}, mesh = {Siderophores/metabolism ; *Fabaceae/microbiology ; *Sinorhizobium/metabolism ; Symbiosis/genetics ; Anti-Bacterial Agents ; Bacterial Proteins/metabolism ; Gram-Negative Bacteria/metabolism ; Gram-Positive Bacteria/metabolism ; Iron/metabolism ; Bacteria/metabolism ; Membrane Transport Proteins ; Vegetables ; *Rhizobium/metabolism ; }, abstract = {Iron homeostasis is strictly regulated in cellular organisms. The Rhizobiales order enriched with symbiotic and pathogenic bacteria has evolved a lineage-specific regulator, RirA, responding to iron fluctuations. However, the regulatory role of RirA in bacterium-host interactions remains largely unknown. Here, we report that RirA is essential for mutualistic interactions of Sinorhizobium fredii with its legume hosts by repressing a gene cluster directing biosynthesis and transport of petrobactin siderophore. Genes encoding an inner membrane ABC transporter (fat) and the biosynthetic machinery (asb) of petrobactin siderophore are sporadically distributed in Gram-positive and Gram-negative bacteria. An outer membrane siderophore receptor gene (fprA) was naturally assembled with asb and fat, forming a long polycistron in S. fredii. An indigenous regulation cascade harboring an inner membrane protease (RseP), a sigma factor (FecI), and its anti-sigma protein (FecR) were involved in direct activation of the fprA-asb-fat polycistron. Operons harboring fecI and fprA-asb-fat, and those encoding the indigenous TonB-ExbB-ExbD complex delivering energy to the outer membrane transport activity, were directly repressed by RirA under iron-replete conditions. The rirA deletion led to upregulation of these operons and iron overload in nodules, impaired intracellular persistence, and symbiotic nitrogen fixation of rhizobia. Mutualistic defects of the rirA mutant can be rescued by blocking activities of this naturally "synthetic" circuit for siderophore biosynthesis and transport. These findings not only are significant for understanding iron homeostasis of mutualistic interactions but also provide insights into assembly and integration of foreign machineries for biosynthesis and transport of siderophores, horizontal transfer of which is selected in microbiota. IMPORTANCE Iron is a public good explored by both eukaryotes and prokaryotes. The abundant ferric form is insoluble under neutral and basic pH conditions, and many bacteria secrete siderophores forming soluble ferric siderophore complexes, which can be then taken up by specific receptors and transporters. Siderophore biosynthesis and uptake machineries can be horizontally transferred among bacteria in nature. Despite increasing attention on the importance of siderophores in host-microbiota interactions, the regulatory integration process of transferred siderophore biosynthesis and transport genes is poorly understood in an evolutionary context. By focusing on the mutualistic rhizobium-legume symbiosis, here, we report how a naturally synthetic foreign siderophore gene cluster was integrated with the rhizobial indigenous regulation cascade, which is essential for maintaining mutualistic interactions.}, }
@article {pmid35126321, year = {2021}, author = {Hu, Y and Zheng, J and Zhang, J}, title = {Natural Transformation in Acinetobacter baumannii W068: A Genetic Analysis Reveals the Involvements of the CRP, XcpV, XcpW, TsaP, and TonB2.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {738034}, pmid = {35126321}, issn = {1664-302X}, abstract = {Acinetobacter baumannii is a serious threat to public health, and there is increasing attention to the development of antibiotic resistance in this bacterium. Natural transformation is a major horizontal gene transfer mechanism that can lead to antibiotic resistance. To better understand the mechanism of natural transformation in A. baumannii, we selected a clinical isolate that was transformable but had no visible extracellular type IV pili (T4P) filaments and then examined the effects of multiple single-gene knockouts on natural plasmid transformation. Among 33 candidate genes, 28 knockout mutants had severely or completely impaired transformability. Some of these genes had established roles in T4P biogenesis; DNA transfer across the outer membrane, periplasm, or inner membrane; and protection of intracellular single-stranded DNA (ssDNA). Other genes had no previously reported roles in natural transformation of A. baumannii, including competence activator cAMP receptor protein (CRP), a periplasmic protein that may function in T4P assembly (TonB2), a T4P secretin-associated protein (TsaP), and two type II secretion system (T2SS) minor pseudopilus assembly prime complex competent proteins (XcpV and XcpW). The deletion of the T2SS assembly platform protein X had no effect on transformation, and the minor pseudopilins were capable of initiating major pilin assembly. Thus, we speculate that XcpV and XcpW may function in DNA uptake with major pilin assembly, a non-T2SS-dependent mechanism and that a competence pseudopilus similar to T4P constituted the central part of the DNA uptake complex. These results may help guide future research on the alarming increase of antibiotic resistance in this pathogen.}, }
@article {pmid35122749, year = {2022}, author = {Wang, Y and Taylor, SL and Choo, JM and Papanicolas, LE and Keating, R and Hindmarsh, K and Thomson, RM and Morgan, L and Rogers, GB and Burr, LD}, title = {Carriage and Transmission of Macrolide Resistance Genes in Patients With Chronic Respiratory Conditions and Their Close Contacts.}, journal = {Chest}, volume = {162}, number = {1}, pages = {56-65}, doi = {10.1016/j.chest.2022.01.045}, pmid = {35122749}, issn = {1931-3543}, mesh = {*Anti-Bacterial Agents ; Drug Resistance, Bacterial/genetics ; Humans ; *Macrolides/pharmacology/therapeutic use ; Oropharynx ; }, abstract = {BACKGROUND: Long-term macrolide therapy has been shown to provide benefit to those with a range of chronic respiratory conditions. However, concerns remain about the impact of macrolide exposure on the carriage and abundance of antibiotic resistance genes within the oropharynx. The potential for onward transmission of resistance from macrolide recipients to their close contacts also is poorly understood.<br><br>RESEARCH QUESTION: Does long-term macrolide use impact carriage of resistance within the oropharyngeal microbiota in people with chronic respiratory conditions and risk of onward transmission to their close contacts?<br><br>STUDY DESIGN AND METHODS: Oropharyngeal swabs were collected from 93 individuals with chronic respiratory conditions, 53 of whom were receiving long-term macrolide therapy. An oropharyngeal swab also was collected from a close cohabiting contact of each patient. Detection and abundance of 10 macrolide-associated resistance genes with the potential to disseminate via horizontal gene transfer were assessed by quantitative polymerase chain reaction analysis.<br><br>RESULTS: Detection of resistance genes in macrolide recipients was comparable with that in nonrecipients. However, the normalized gene abundance of erm(B) was significantly higher in the macrolide recipient group (P&#xa0;= .045). Among the close contacts, no between-group differences in resistance gene detection or abundance were identified. Within-group analysis showed that the detection of erm(F) and mef in macrolide recipients, but not nonrecipients, was associated significantly with detection in close contacts (P&#xa0;= .003 and P&#xa0;= .004, respectively). However, between-group analysis showed that treatment group did not predict cocarriage between patients and their close contacts (P > .05 for each gene).<br><br>INTERPRETATION: Although levels of erm(B) were higher in those receiving long-term macrolide therapy and evidence of gene cocarriage with close contacts was found, no evidence was found that macrolide use increased the onward transmission risk to their close contacts. This study therefore addresses concerns that long-term macrolide therapy could promote the dissemination of transmissible macrolide resistance.}, }
@article {pmid35120643, year = {2022}, author = {Hie, BL and Yang, KK and Kim, PS}, title = {Evolutionary velocity with protein language models predicts evolutionary dynamics of diverse proteins.}, journal = {Cell systems}, volume = {13}, number = {4}, pages = {274-285.e6}, doi = {10.1016/j.cels.2022.01.003}, pmid = {35120643}, issn = {2405-4720}, mesh = {Amino Acid Sequence ; *Evolution, Molecular ; *Language ; Mutation/genetics ; Proteins/genetics ; }, abstract = {The degree to which evolution is predictable is a fundamental question in biology. Previous attempts to predict the evolution of protein sequences have been limited to specific proteins and to small changes, such as single-residue mutations. Here, we demonstrate that by using a protein language model to predict the local evolution within protein families, we recover a dynamic "vector field" of protein evolution that we call evolutionary velocity (evo-velocity). Evo-velocity generalizes to evolution over vastly different timescales, from viral proteins evolving over years to eukaryotic proteins evolving over geologic eons, and can predict the evolutionary dynamics of proteins that were not used to develop the original model. Evo-velocity also yields new evolutionary insights by predicting strategies of viral-host immune escape, resolving conflicting theories on the evolution of serpins, and revealing a key role of horizontal gene transfer in the evolution of eukaryotic glycolysis.}, }
@article {pmid35118168, year = {2022}, author = {Tumuluri, VS and Saikrishnan, K}, title = {Heterologous Expression and High Degree Purification of the Restriction Endonuclease SauUSI.}, journal = {Bio-protocol}, volume = {12}, number = {1}, pages = {e4275}, pmid = {35118168}, issn = {2331-8325}, abstract = {Mechanisms that target and destroy foreign nucleic acids are major barriers to horizontal gene transfer (HGT) in prokaryotes. Amongst them, restriction-modification (R-M) systems are found in ≥75% of the sequenced genomes in Bacteria and Archaea. Due to their high target sequence specificity and potent nucleolytic activity, R-M systems are used as a paradigm to elucidate the mechanisms of DNA binding and cleavage. Since these enzymes modulate HGT, they are one of the machineries implicated in the ability of a bacterium to gain antibiotic resistance. This protocol provides a detailed purification strategy for the Type IV restriction endonuclease SauUSI from Staphylococcus aureus. This protocol eventually leads to ≥95% purity of protein which can then be used for crystallographic and biochemical purposes. Graphic abstract: Workflow for purification of SauUSI.}, }
@article {pmid35113779, year = {2022}, author = {Butler, J and Kelly, SD and Muddiman, KJ and Besinis, A and Upton, M}, title = {Hospital sink traps as a potential source of the emerging multidrug-resistant pathogen Cupriavidus pauculus: characterization and draft genome sequence of strain MF1.}, journal = {Journal of medical microbiology}, volume = {71}, number = {2}, pages = {}, pmid = {35113779}, issn = {1473-5644}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Cupriavidus/drug effects/genetics ; Drug Resistance, Multiple, Bacterial ; Equipment Contamination ; *Genome, Bacterial ; Hospitals ; Humans ; Moths ; *Water Supply ; }, abstract = {Introduction. Cupriavidus pauculus is historically found in soil and water but has more recently been reported to cause human infection and death. Hospital sink traps can serve as a niche for bacterial persistence and a platform for horizontal gene transfer, with evidence of dissemination of pathogens in hospital plumbing systems driving nosocomial infection.Gap Statement. This paper presents the first C. pauculus strain isolated from a hospital sink trap. There are only six genome assemblies available on NCBI for C. pauculus; two of these are PacBio/Illumina hybrids. This paper presents the first ONT/Illumina hybrid assembly, with five contigs. The other assemblies available consist of 37, 38, 111 and 227 contigs. This paper also presents data on biofilm formation and lethal dose in Galleria mellonella; there is little published information describing these aspects of virulence.Aim. The aims were to identify the isolate found in a hospital sink trap, characterize its genome, and assess whether it could pose a risk to human health.Methodology. The genome was sequenced, and a hybrid assembly of short and long reads produced. Antimicrobial susceptibility was determined by the broth microdilution method. Virulence was assessed by measuring in vitro biofilm formation compared to Pseudomonas aeruginosa and in vivo lethality in Galleria mellonella larvae.Results. The isolate was confirmed to be a strain of C. pauculus, with a 6.8 Mb genome consisting of 6468 coding sequences and an overall G+C content of 63.9 mol%. The genome was found to contain 12 antibiotic resistance genes, 8 virulence factor genes and 33 metal resistance genes. The isolate can be categorized as resistant to meropenem, amoxicillin, amikacin, gentamicin and colistin, but susceptible to cefotaxime, cefepime, imipenem and ciprofloxacin. Clear biofilm formation was seen in all conditions over 72 h and exceeded that of P. aeruginosa when measured at 37 °C in R2A broth. Lethality in G. mellonella larvae over 48 h was relatively low.Conclusion. The appearance of a multidrug-resistant strain of C. pauculus in a known pathogen reservoir within a clinical setting should be considered concerning. Further work should be completed to compare biofilm formation and in vivo virulence between clinical and environmental strains, to determine how easily environmental strains may establish human infection. Infection control teams and clinicians should be aware of the emerging nature of this pathogen and further work is needed to minimize the impact of contaminated hospital plumbing systems on patient outcomes.}, }
@article {pmid35112737, year = {2022}, author = {Kejnovsky, E and Jedlicka, P}, title = {Nucleic acids movement and its relation to genome dynamics of repetitive DNA: Is cellular and intercellular movement of DNA and RNA molecules related to the evolutionary dynamic genome components?: Is cellular and intercellular movement of DNA and RNA molecules related to the evolutionary dynamic genome components?.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {44}, number = {4}, pages = {e2100242}, doi = {10.1002/bies.202100242}, pmid = {35112737}, issn = {1521-1878}, mesh = {DNA Transposable Elements ; Eukaryota/genetics ; Evolution, Molecular ; Genomics/methods ; *Nucleic Acids ; RNA/genetics ; }, abstract = {There is growing evidence of evolutionary genome plasticity. The evolution of repetitive DNA elements, the major components of most eukaryotic genomes, involves the amplification of various classes of mobile genetic elements, the expansion of satellite DNA, the transfer of fragments or entire organellar genomes and may have connections with viruses. In addition to various repetitive DNA elements, a plethora of large and small RNAs migrate within and between cells during individual development as well as during evolution and contribute to changes of genome structure and function. Such migration of DNA and RNA molecules often results in horizontal gene transfer, thus shaping the whole genomic network of interconnected species. Here, we propose that a high evolutionary dynamism of repetitive genome components is often related to the migration/movement of DNA or RNA molecules. We speculate that the cytoplasm is probably an ideal compartment for such evolutionary experiments.}, }
@article {pmid35111143, year = {2021}, author = {Reyes-Umana, V and Kretschmer, J and Coates, JD}, title = {Isolation of a Dissimilatory Iodate-Reducing Aromatoleum sp. From a Freshwater Creek in the San Francisco Bay Area.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {804181}, pmid = {35111143}, issn = {1664-302X}, abstract = {Recent reports of dissimilatory iodate-reducing microorganisms (DIRM) have arisen from studies of bacteria in marine environments. These studies described the physiology and distribution of DIRM while also demonstrating their presence in iodine-rich marine environments. We posited that despite lower iodine concentrations, terrestrial and freshwater ecosystems should also harbor DIRM. We established numerous enrichments from coastal and freshwater environments that actively remove amended iodate. We describe the physiology and genome of a new DIRM isolate, Aromatoleum toluclasticum sp. TC-10, emerging from a freshwater creek microcosm. Like other DIRM, A. toluclasticum sp. TC-10 couples acetate oxidation to iodate reduction with a concomitant increase in the OD600. Our results indicate that A. toluclasticum sp. TC-10 performs dissimilatory iodate reduction (DIR) using the recently described iodate reductase (Idr). We provide further evidence of horizontal gene transfer of the idr genes by demonstrating the lack of Idr in the closely related (99.93% 16S rDNA sequence identity) A. toluclasticum sp. MF63 and describe the heterogeneity of the accessory proteins associated with the iodate reduction island (IRI). These observations provide additional evidence that DIR is a horizontally acquired metabolism with broad environmental distribution beyond exclusively marine environments.}, }
@article {pmid35110408, year = {2022}, author = {Steele, TS and Brunson, JK and Maeno, Y and Terada, R and Allen, AE and Yotsu-Yamashita, M and Chekan, JR and Moore, BS}, title = {Domoic acid biosynthesis in the red alga Chondria armata suggests a complex evolutionary history for toxin production.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {6}, pages = {}, pmid = {35110408}, issn = {1091-6490}, support = {F31 ES030613/ES/NIEHS NIH HHS/United States ; }, mesh = {Biological Evolution ; Biosynthetic Pathways/genetics ; Diatoms/genetics/metabolism ; Dimethylallyltranstransferase/*genetics/*metabolism ; Harmful Algal Bloom/physiology ; Kainic Acid/*analogs &amp; derivatives/metabolism ; Multigene Family/genetics ; Neurotoxins/genetics/*metabolism ; Phylogeny ; Rhodophyta/*metabolism ; Shellfish Poisoning/metabolism ; }, abstract = {Domoic acid (DA), the causative agent of amnesic shellfish poisoning, is produced by select organisms within two distantly related algal clades: planktonic diatoms and red macroalgae. The biosynthetic pathway to isodomoic acid A was recently solved in the harmful algal bloom-forming diatom Pseudonitzschia multiseries, establishing the genetic basis for the global production of this potent neurotoxin. Herein, we sequenced the 507-Mb genome of Chondria armata, the red macroalgal seaweed from which DA was first isolated in the 1950s, identifying several copies of the red algal DA (rad) biosynthetic gene cluster. The rad genes are organized similarly to the diatom DA biosynthesis cluster in terms of gene synteny, including a cytochrome P450 (CYP450) enzyme critical to DA production that is notably absent in red algae that produce the simpler kainoid neurochemical, kainic acid. The biochemical characterization of the N-prenyltransferase (RadA) and kainoid synthase (RadC) enzymes support a slightly altered DA biosynthetic model in C. armata via the congener isodomoic acid B, with RadC behaving more like the homologous diatom enzyme despite higher amino acid similarity to red algal kainic acid synthesis enzymes. A phylogenetic analysis of the rad genes suggests unique origins for the red macroalgal and diatom genes in their respective hosts, with native eukaryotic CYP450 neofunctionalization combining with the horizontal gene transfer of N-prenyltransferases and kainoid synthases to establish DA production within the algal lineages.}, }
@article {pmid35107338, year = {2022}, author = {Stephens, ME and Benjamino, J and Graf, J and Gage, DJ}, title = {Simultaneous Single-Cell Genome and Transcriptome Sequencing of Termite Hindgut Protists Reveals Metabolic and Evolutionary Traits of Their Endosymbionts.}, journal = {mSphere}, volume = {7}, number = {1}, pages = {e0002122}, pmid = {35107338}, issn = {2379-5042}, mesh = {Animals ; Bacteria ; Carbon/metabolism ; Eukaryota/genetics ; *Isoptera/microbiology ; Phylogeny ; Symbiosis/genetics ; Transcriptome ; }, abstract = {Some of the protist species which colonize the hindguts of wood-feeding Reticulitermes termites are associated with endosymbiotic bacteria belonging to the genus Endomicrobium. In this study, we focused on the endosymbionts of three protist species from Reticulitermes flavipes, as follows: Pyrsonympha vertens, Trichonympha agilis, and Dinenympha species II. Since these protist hosts represented members of different taxa which colonize separate niches within the hindguts of their termite hosts, we investigated if these differences translated to differential gene content and expression in their endosymbionts. Following assembly and comparative genome and transcriptome analyses, we discovered that these endosymbionts differed with respect to some possible niche-specific traits, such as carbon metabolism. Our analyses suggest that species-specific genes related to carbon metabolism were acquired by horizontal gene transfer (HGT) and may have come from taxa which are common in the termite hind gut. In addition, our analyses suggested that these endosymbionts contain and express genes related to natural transformation (competence) and recombination. Taken together, the presence of genes acquired by HGT and a putative competence pathway suggest that these endosymbionts are not cut off from gene flow and that competence may be a mechanism by which members of Endomicrobium can acquire new traits. IMPORTANCE The composition and structure of wood, which contains cellulose, hemicellulose, and lignin, prevent most organisms from using this common food source. Termites are a rare exception among animals, and they rely on a complex microbiota housed in their hindguts to use wood as a source of food. The lower termite, Reticulitermes flavipes, houses a variety of protists and prokaryotes that are the key players in the disassembly of lignocellulose. Here, we describe the genomes and the gene expression profiles of five Endomicrobium endosymbionts living inside three different protist species from R. flavipes. Data from these genomes suggest that these Endomicrobium species have different mechanisms for using carbon. In addition, they harbor genes that may be used to import DNA from their environment. This process of DNA uptake may contribute to the high levels of horizontal gene transfer noted previously in Endomicrobium species.}, }
@article {pmid35107332, year = {2022}, author = {Peng, M and Wang, D and Lui, LM and Nielsen, T and Tian, R and Kempher, ML and Tao, X and Pan, C and Chakraborty, R and Deutschbauer, AM and Thorgersen, MP and Adams, MWW and Fields, MW and Hazen, TC and Arkin, AP and Zhou, A and Zhou, J}, title = {Genomic Features and Pervasive Negative Selection in Rhodanobacter Strains Isolated from Nitrate and Heavy Metal Contaminated Aquifer.}, journal = {Microbiology spectrum}, volume = {10}, number = {1}, pages = {e0259121}, pmid = {35107332}, issn = {2165-0497}, mesh = {Base Composition ; Gammaproteobacteria/classification/*genetics/*isolation &amp; purification/metabolism ; Gene Transfer, Horizontal ; Genome Size ; Genome, Bacterial ; Genomic Islands ; Genomics ; Groundwater/microbiology ; Metals, Heavy/analysis/metabolism ; Nitrates/*analysis/metabolism ; Phylogeny ; Water Pollutants, Chemical/*analysis/metabolism ; }, abstract = {Rhodanobacter species dominate in the Oak Ridge Reservation (ORR) subsurface environments contaminated with acids, nitrate, metal radionuclides, and other heavy metals. To uncover the genomic features underlying adaptations to these mixed-waste environments and to guide genetic tool development, we sequenced the whole genomes of eight Rhodanobacter strains isolated from the ORR site. The genome sizes ranged from 3.9 to 4.2 Mb harboring 3,695 to 4,035 protein-coding genes and GC contents approximately 67%. Seven strains were classified as R. denitrificans and one strain, FW510-R12, as R. thiooxydans based on full length 16S rRNA sequences. According to gene annotation, the top two Cluster of Orthologous Groups (COGs) with high pan-genome expansion rates (Pan/Core gene ratio) were "replication, recombination and repair" and "defense mechanisms." The denitrifying genes had high DNA homologies except the predicted protein structure variances in NosZ. In contrast, heavy metal resistance genes were diverse with between 7 to 34% of them were located in genomic islands, and these results suggested origins from horizontal gene transfer. Analysis of the methylation patterns in four strains revealed the unique 5mC methylation motifs. Most orthologs (78%) had ratios of nonsynonymous to synonymous substitutions (dN/dS) less than one when compared to the type strain 2APBS1, suggesting the prevalence of negative selection. Overall, the results provide evidence for the important roles of horizontal gene transfer and negative selection in genomic adaptation at the contaminated field site. The complex restriction-modification system genes and the unique methylation motifs in Rhodanobacter strains suggest the potential recalcitrance to genetic manipulation. IMPORTANCE Despite the dominance of Rhodanobacter species in the subsurface of the contaminated Oak Ridge Reservation (ORR) site, very little is known about the mechanisms underlying their adaptions to the various stressors present at ORR. Recently, multiple Rhodanobacter strains have been isolated from the ORR groundwater samples from several wells with varying geochemical properties. Using Illumina, PacBio, and Oxford Nanopore sequencing platforms, we obtained the whole genome sequences of eight Rhodanobacter strains. Comparison of the whole genomes demonstrated the genetic diversity, and analysis of the long nanopore reads revealed the heterogeneity of methylation patterns in strains isolated from the same well. Although all strains contained a complete set of denitrifying genes, the predicted tertiary structures of NosZ differed. The sequence comparison results demonstrate the important roles of horizontal gene transfer and negative selection in adaptation. In addition, these strains may be recalcitrant to genetic manipulation due to the complex restriction-modification systems and methylations.}, }
@article {pmid35102526, year = {2022}, author = {Choi, E and Huh, A and Oh, C and Oh, JI and Kang, HY and Hwang, J}, title = {Functional characterization of HigBA toxin-antitoxin system in an Arctic bacterium, Bosea sp. PAMC 26642.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {60}, number = {2}, pages = {192-206}, pmid = {35102526}, issn = {1976-3794}, mesh = {Antitoxins/genetics/*metabolism ; Arctic Regions ; Bacterial Proteins/genetics/metabolism ; Bacterial Toxins/genetics/*metabolism ; Bradyrhizobiaceae/*genetics ; Escherichia coli/genetics/*growth &amp; development/*metabolism ; Gene Expression Regulation, Bacterial ; Genomic Islands ; Multigene Family ; RNA, Messenger/metabolism ; *Toxin-Antitoxin Systems ; }, abstract = {Toxin-antitoxin (TA) systems are growth-controlling genetic elements consisting of an intracellular toxin protein and its cognate antitoxin. TA systems have been spread among microbial genomes through horizontal gene transfer and are now prevalent in most bacterial and archaeal genomes. Under normal growth conditions, antitoxins tightly counteract the activity of the toxins. Upon stresses, antitoxins are inactivated, releasing activated toxins, which induce growth arrest or cell death. In this study, among nine functional TA modules in Bosea sp. PAMC 26642 living in Arctic lichen, we investigated the functionality of BoHigBA2. BohigBA2 is located close to a genomic island and adjacent to flagellar gene clusters. The expression of BohigB2 induced the inhibition of E. coli growth at 37°C, which was more manifest at 18°C, and this growth defect was reversed when BohigA2 was co-expressed, suggesting that this BoHigBA2 module might be an active TA module in Bosea sp. PAMC 26642. Live/dead staining and viable count analyses revealed that the BoHigB2 toxin had a bactericidal effect, causing cell death. Furthermore, we demonstrated that BoHigB2 possessed mRNA-specific ribonuclease activity on various mRNAs and cleaved only mRNAs being translated, which might impede overall translation and consequently lead to cell death. Our study provides the insight to understand the cold adaptation of Bosea sp. PAMC 26642 living in the Arctic.}, }
@article {pmid35100457, year = {2022}, author = {Timmons, CM and Shazib, SUA and Katz, LA}, title = {Epigenetic influences of mobile genetic elements on ciliate genome architecture and evolution.}, journal = {The Journal of eukaryotic microbiology}, volume = {69}, number = {5}, pages = {e12891}, pmid = {35100457}, issn = {1550-7408}, support = {DEB-1541511//National Science Foundation/ ; DEB-1651908//National Science Foundation/ ; R15 HG010409/HG/NHGRI NIH HHS/United States ; OCE-1924570//National Science Foundation/ ; }, mesh = {*Ciliophora/genetics ; DNA Transposable Elements/genetics ; Epigenesis, Genetic ; Evolution, Molecular ; Genome ; Humans ; Interspersed Repetitive Sequences ; }, abstract = {Mobile genetic elements (MGEs) are transient genetic material that can move either within a single organism's genome or between individuals or species. While historically considered "junk" DNA (i.e., deleterious or at best neutral), more recent studies reveal the potential adaptive advantages MGEs provide in lineages across the tree of life. Ciliates, a group of single-celled microbial eukaryotes characterized by nuclear dimorphism, exemplify how epigenetic influences from MGEs shape genome architecture and patterns of molecular evolution. Ciliate nuclear dimorphism may have evolved as a response to transposon invasion and ciliates have since co-opted transposons to carry out programmed DNA deletion. Another example of the effect of MGEs is in providing mechanisms for lateral gene transfer (LGT) from bacteria, which introduces genetic diversity and, in several cases, may drive ecological specialization in ciliates. As a third example, the integration of viral DNA, likely through transduction, provides new genetic materials and can change the way host cells defend themselves against other viral pathogens. We argue that the acquisition of MGEs through non-Mendelian patterns of inheritance, coupled with their effects on ciliate genome architecture and persistence throughout evolutionary history, exemplify how the transmission of mobile elements should be considered a mechanism of transgenerational epigenetic inheritance.}, }
@article {pmid35087906, year = {2022}, author = {Liu, J and Gu, X and Li, H}, title = {Assembly of 97 Novel Bacterial Genomes in the Microbial Community Affiliated with Polyvinyl Alcohol in Soil of Northern China.}, journal = {BioMed research international}, volume = {2022}, number = {}, pages = {2229147}, pmid = {35087906}, issn = {2314-6141}, mesh = {Bacteria ; China ; Genome, Bacterial/genetics ; *Microbiota/genetics ; Oxidoreductases/metabolism ; Phylogeny ; Polyvinyl Alcohol ; RNA, Ribosomal, 16S/genetics ; *Soil ; Soil Microbiology ; }, abstract = {BACKGROUND: Undeveloped ecosystems belong to rich source of microbial population, of which resources remain unearthed. A kind of polymeric compound system with high polyvinyl alcohol (PVA) content has been reported and named Taisui. Marker gene amplification showed that Taisui harbored little-explored microbial communities.<br><br>AIM: To address this issue, our study attempted to recover draft genomes and functional potential from microbial communities in Taisui using the metagenomic approach. Material and Methods. Taisui communities provided 97 novel bacterial genomes from 13 bacterial phyla, including bacteria candidate phylum. Two novel genus-level lineages were recovered from Planctomycetes and Chloroflexi. Based on the draft genomes, we expanded the number of taxa with potential productions of PKS and NRPS in phyla including Candidatus Dadabacteria, Chloroflexi, and Planctomycetes.<br><br>RESULTS: A rich diversity of PVA dehydrogenase genes from 4 phyla, involving Proteobacteria, Acidobacteria, Acitinobacteria, and Planctomycetes, were identified. The phylogenetic tree of PVA dehydrogenase showed the possibility of horizontal gene transfer between microbes.<br><br>CONCLUSION: Our study underscores the substantial microbial diversity and PVA degradation potential in the previously unexplored Taisui system.}, }
@article {pmid35087053, year = {2022}, author = {Yassine, I and Lefèvre, S and Hansen, EE and Ruckly, C and Carle, I and Lejay-Collin, M and Fabre, L and Rafei, R and Clermont, D and de la Gandara, MP and Dabboussi, F and Thomson, NR and Weill, FX}, title = {Population structure analysis and laboratory monitoring of Shigella by core-genome multilocus sequence typing.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {551}, pmid = {35087053}, issn = {2041-1723}, support = {/WT_/Wellcome Trust/United Kingdom ; 206194/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Disease Outbreaks ; Escherichia coli ; *Genome, Bacterial ; Genotype ; Humans ; Molecular Epidemiology ; Multigene Family ; Multilocus Sequence Typing/*methods ; Phylogeny ; Shigella/*classification/*genetics/*isolation &amp; purification ; Whole Genome Sequencing ; }, abstract = {The laboratory surveillance of bacillary dysentery is based on a standardised Shigella typing scheme that classifies Shigella strains into four serogroups and more than 50 serotypes on the basis of biochemical tests and lipopolysaccharide O-antigen serotyping. Real-time genomic surveillance of Shigella infections has been implemented in several countries, but without the use of a standardised typing scheme. Here, we study over 4000 reference strains and clinical isolates of Shigella, covering all serotypes, with both the current serotyping scheme and the standardised EnteroBase core-genome multilocus sequence typing scheme (cgMLST). The Shigella genomes are grouped into eight phylogenetically distinct clusters, within the E. coli species. The cgMLST hierarchical clustering (HC) analysis at different levels of resolution (HC2000 to HC400) recognises the natural population structure of Shigella. By contrast, the serotyping scheme is affected by horizontal gene transfer, leading to a conflation of genetically unrelated Shigella strains and a separation of genetically related strains. The use of this cgMLST scheme will facilitate the transition from traditional phenotypic typing to routine whole-genome sequencing for the laboratory surveillance of Shigella infections.}, }
@article {pmid35085844, year = {2022}, author = {Zhang, C and Zhao, X and Wang, C and Hakizimana, I and Crittenden, JC and Laghari, AA}, title = {Electrochemical flow-through disinfection reduces antibiotic resistance genes and horizontal transfer risk across bacterial species.}, journal = {Water research}, volume = {212}, number = {}, pages = {118090}, doi = {10.1016/j.watres.2022.118090}, pmid = {35085844}, issn = {1879-2448}, mesh = {Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; *Disinfection ; Drug Resistance, Microbial/genetics ; *Escherichia coli/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Ultraviolet Rays ; Wastewater ; }, abstract = {Antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs), as emerging pollutants, are released into environment, increasing the risk of horizontal gene transfer (HGT). However, a limited number of studies quantified the effects of ARB disinfection on the HGT risk. This study investigated the inactivation of E. coli 10667 (sul) and the release and removal of ARGs using an electrochemical flow-through reactor (EFTR). Furthermore, the transfer frequencies and potential mechanisms of HGT after disinfection were explored using non-resistant E. coli GMCC 13373 as the recipient and E. coli DH5α carrying plasmid RP4 as the donor. A threshold of current density (0.25 mA/cm[2]) was observed to destroy cells and release intracellular ARGs (iARGs) to increase extracellular ARGs (eARGs) concentration. The further increase in the current density to 1 mA/cm[2] resulted in the decline of eARGs concentration due to the higher degradation rate of eARGs than the release rate of iARGs. The performance of ARGs degradation and HGT frequency by EFTR were compared with those of conventional disinfection processes, including chlorination and ultraviolet radiation (UV). A higher ARGs degradation (83.46%) was observed by EFTR compared with that under chlorination (10.23%) and UV (27.07%). Accordingly, EFTR reduced the HGT frequency (0.69) of released ARGs into the recipient (Forward transfer), and the value was lower than that by chlorination (2.69) and UV (1.73). Meanwhile, the surviving injured E. coli 10667 (sul) with increased cell permeability was transferred by plasmid RP4 from the donor (Reverse transfer) with a higher frequency of 0.33 by EFTR compared with that under chlorination (0.26) and UV (0.16). In addition, the sul3 gene was the least resistant to EFTR than sul1 and sul2 gene. These findings provide important insights into the mechanism of HGT between the injured E. coli 10667 (sul) and environmental bacteria. EFTR is a promising disinfection technology for preventing the spread of antibiotic resistance.}, }
@article {pmid35085657, year = {2022}, author = {Baek, JH and Kim, KH and Lee, Y and Jeong, SE and Jin, HM and Jia, B and Jeon, CO}, title = {Elucidating the biodegradation pathway and catabolic genes of benzophenone-3 in Rhodococcus sp. S2-17.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {299}, number = {}, pages = {118890}, doi = {10.1016/j.envpol.2022.118890}, pmid = {35085657}, issn = {1873-6424}, mesh = {Benzophenones/metabolism ; Biodegradation, Environmental ; Cytochrome P-450 Enzyme System/metabolism ; *Rhodococcus/genetics/metabolism ; }, abstract = {A new bacterium, Rhodococcus sp. S2-17, which could completely degrade an emerging organic pollutant, benzophenone-3 (BP-3), was isolated from contaminated sediment through an enrichment procedure, and its BP-3 catabolic pathway and genes were identified through metabolic intermediate and transcriptomic analyses and biochemical and genetic studies. Metabolic intermediate analysis suggested that strain S2-17 may degrade BP-3 using a catabolic pathway progressing via the intermediates BP-1, 2,4,5-trihydroxy-benzophenone, 3-hydroxy-4-benzoyl-2,4-hexadienedioic acid, 4-benzoyl-3-oxoadipic acid, 3-oxoadipic acid, and benzoic acid. A putative BP-3 catabolic gene cluster including cytochrome P450, flavin-dependent oxidoreductase, hydroxyquinol 1,2-dioxygenase, maleylacetate reductase, and α/β hydrolase genes was identified through genomic and transcriptomic analyses. Genes encoding the cytochrome P450 complex that demethylates BP-3 to BP-1 were functionally verified through protein expression, and the functions of the other genes were also verified through knockout mutant construction and intermediate analysis. This study suggested that strain S2-17 might have acquired the ability to catabolize BP-3 by recruiting the cytochrome P450 complex and α/β hydrolase, which hydrolyzes 4-benzoyl-3-oxoadipic acid to benzoic acid and 3-oxoadipic acid, genes, providing insights into the recruitment of genes of for the catabolism of emerging organic pollutants.}, }
@article {pmid35084524, year = {2022}, author = {La, SR and Ndhlovu, A and Durand, PM}, title = {The Ancient Origins of Death Domains Support the 'Original Sin' Hypothesis for the Evolution of Programmed Cell Death.}, journal = {Journal of molecular evolution}, volume = {90}, number = {1}, pages = {95-113}, pmid = {35084524}, issn = {1432-1432}, mesh = {Apoptosis ; *Archaea/genetics/metabolism ; Bacteria/genetics/metabolism ; Caspases/genetics/metabolism ; Death Domain ; Evolution, Molecular ; *Genome, Archaeal/genetics ; Peptide Hydrolases/genetics/metabolism ; Phylogeny ; }, abstract = {The discovery of caspase homologs in bacteria highlighted the relationship between programmed cell death (PCD) evolution and eukaryogenesis. However, the origin of PCD genes in prokaryotes themselves (bacteria and archaea) is poorly understood and a source of controversy. Whether archaea also contain C14 peptidase enzymes and other death domains is largely unknown because of a historical dearth of genomic data. Archaeal genomic databases have grown significantly in the last decade, which allowed us to perform a detailed comparative study of the evolutionary histories of PCD-related death domains in major archaeal phyla, including the deepest branching phyla of Candidatus Aenigmarchaeota, Candidatus Woesearchaeota, and Euryarchaeota. We identified death domains associated with executioners of PCD, like the caspase homologs of the C14 peptidase family, in 321 archaea sequences. Of these, 15.58% were metacaspase type I orthologues and 84.42% were orthocaspases. Maximum likelihood phylogenetic analyses revealed a scattered distribution of orthocaspases and metacaspases in deep-branching bacteria and archaea. The tree topology was incongruent with the prokaryote 16S phylogeny suggesting a common ancestry of PCD genes in prokaryotes and subsequent massive horizontal gene transfer coinciding with the divergence of archaea and bacteria. Previous arguments for the origin of PCD were philosophical in nature with two popular propositions being the "addiction" and 'original sin' hypotheses. Our data support the 'original sin' hypothesis, which argues for a pleiotropic origin of the PCD toolkit with pro-life and pro-death functions tracing back to the emergence of cellular life-the Last Universal Common Ancestor State.}, }
@article {pmid35084301, year = {2022}, author = {Lund, D and Kieffer, N and Parras-Moltó, M and Ebmeyer, S and Berglund, F and Johnning, A and Larsson, DGJ and Kristiansson, E}, title = {Large-scale characterization of the macrolide resistome reveals high diversity and several new pathogen-associated genes.}, journal = {Microbial genomics}, volume = {8}, number = {1}, pages = {}, pmid = {35084301}, issn = {2057-5858}, mesh = {Azithromycin/pharmacology ; Bacteria/drug effects/genetics/*growth &amp; development ; Bacterial Proteins/genetics ; Computational Biology/*methods ; *Drug Resistance, Bacterial ; Erythromycin/pharmacology ; Escherichia coli/drug effects/genetics/growth &amp; development ; Evolution, Molecular ; Macrolides/*pharmacology ; Markov Chains ; Metagenomics ; Methyltransferases/*genetics ; Microbial Sensitivity Tests ; Multigene Family ; Phosphotransferases/*genetics ; Phylogeny ; }, abstract = {Macrolides are broad-spectrum antibiotics used to treat a range of infections. Resistance to macrolides is often conferred by mobile resistance genes encoding Erm methyltransferases or Mph phosphotransferases. New erm and mph genes keep being discovered in clinical settings but their origins remain unknown, as is the type of macrolide resistance genes that will appear in the future. In this study, we used optimized hidden Markov models to characterize the macrolide resistome. Over 16 terabases of genomic and metagenomic data, representing a large taxonomic diversity (11 030 species) and diverse environments (1944 metagenomic samples), were searched for the presence of erm and mph genes. From this data, we predicted 28 340 macrolide resistance genes encoding 2892 unique protein sequences, which were clustered into 663 gene families (<70 % amino acid identity), of which 619 (94 %) were previously uncharacterized. This included six new resistance gene families, which were located on mobile genetic elements in pathogens. The function of ten predicted new resistance genes were experimentally validated in Escherichia coli using a growth assay. Among the ten tested genes, seven conferred increased resistance to erythromycin, with five genes additionally conferring increased resistance to azithromycin, showing that our models can be used to predict new functional resistance genes. Our analysis also showed that macrolide resistance genes have diverse origins and have transferred horizontally over large phylogenetic distances into human pathogens. This study expands the known macrolide resistome more than ten-fold, provides insights into its evolution, and demonstrates how computational screening can identify new resistance genes before they become a significant clinical problem.}, }
@article {pmid35078531, year = {2022}, author = {Che, Y and Xu, X and Yang, Y and Břinda, K and Hanage, W and Yang, C and Zhang, T}, title = {High-resolution genomic surveillance elucidates a multilayered hierarchical transfer of resistance between WWTP- and human/animal-associated bacteria.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {16}, pmid = {35078531}, issn = {2049-2618}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; *Genomics ; Humans ; Plasmids/genetics ; *Water Purification ; }, abstract = {BACKGROUND: Our interconnected world and the ability of bacteria to quickly swap antibiotic resistance genes (ARGs) make it particularly important to establish the epidemiological links of multidrug resistance (MDR) transfer between wastewater treatment plant (WWTP)- and human/animal-associated bacteria, under the One Health framework. However, evidence of ARGs exchange and potential factors that contribute to this transfer remain limited.<br><br>RESULTS: Here, by combining culture-based population genomics and genetic comparisons with publicly available datasets, we reconstructed the complete genomes of 82 multidrug-resistant isolates from WWTPs and found that most WWTP-associated isolates were genetically distinct from their closest human/animal-associated relatives currently available in the public database. Even in the minority of lineages that were closely related, WWTP-associated isolates were characterized by quite different plasmid compositions. We identified a high diversity of circular plasmids (264 in total, of which 141 were potentially novel), which served as the main source of resistance, and showed potential horizontal transfer of ARG-bearing plasmids between WWTP- and humans/animal-associated bacteria. Notably, the potentially transferred ARGs and virulence factors (VFs) with different genetic backgrounds were closely associated with flanking insertion sequences (ISs), suggesting the importance of synergy between plasmids and ISs in mediating a multilayered hierarchical transfer of MDR and potentiating the emergence of MDR-hypervirulent clones.<br><br>CONCLUSION: Our findings advance the current efforts to establish potential epidemiological links of MDR transmission between WWTP- and human/animal-associated bacteria. Plasmids play an important role in mediating the transfer of ARGs and the IS-associated ARGs that are carried by conjugative plasmids should be prioritized to tackle the spread of resistance. Video Abstract.}, }
@article {pmid35075990, year = {2022}, author = {Hernández-González, IL and Mateo-Estrada, V and Castillo-Ramirez, S}, title = {The promiscuous and highly mobile resistome of Acinetobacter baumannii.}, journal = {Microbial genomics}, volume = {8}, number = {1}, pages = {}, pmid = {35075990}, issn = {2057-5858}, mesh = {Acinetobacter baumannii/*classification/drug effects/genetics ; Bacterial Proteins/*genetics ; Computational Biology/*methods ; Databases, Genetic ; *Drug Resistance, Multiple, Bacterial ; Gene Flow ; Gene Transfer, Horizontal ; Phylogeny ; Whole Genome Sequencing ; }, abstract = {Antimicrobial resistance (AR) is a major global threat to public health. Understanding the population dynamics of AR is critical to restrain and control this issue. However, no study has provided a global picture of the whole resistome of Acinetobacter baumannii, a very important nosocomial pathogen. Here we analyse 1450+ genomes (covering >40 countries and >4 decades) to infer the global population dynamics of the resistome of this species. We show that gene flow and horizontal transfer have driven the dissemination of AR genes in A. baumannii. We found considerable variation in AR gene content across lineages. Although the individual AR gene histories have been affected by recombination, the AR gene content has been shaped by the phylogeny. Furthermore, many AR genes have been transferred to other well-known pathogens, such as Pseudomonas aeruginosa or Klebsiella pneumoniae. Despite using this massive data set, we were not able to sample the whole diversity of AR genes, which suggests that this species has an open resistome. Our results highlight the high mobilization risk of AR genes between important pathogens. On a broader perspective, this study gives a framework for an emerging perspective (resistome-centric) on the genomic epidemiology (and surveillance) of bacterial pathogens.}, }
@article {pmid35075883, year = {2022}, author = {Han, L and Lou, Q and Qiao, M and Liu, MT and Zhong, JY and Ding, HJ}, title = {[Pollution Characteristics and Driving Factors of Antibiotic Resistance Genes in Dexing Copper Mine].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {43}, number = {2}, pages = {1089-1096}, doi = {10.13227/j.hjkx.202105243}, pmid = {35075883}, issn = {0250-3301}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Copper/toxicity ; Drug Resistance, Microbial/genetics ; Genes, Bacterial/genetics ; Soil ; }, abstract = {Environmental antibiotic resistance genes (ARGs) are a type of emerging pollutant that has been widely concerning. However, investigations into the contamination of ARGs in mining areas have been scarce. Here, the types, abundances, and influencing factors of ARGs and mobile genetic elements (MGEs) were investigated in soil/sediment of the Dexing copper mine area in June 2019 by using high-throughput quantitative polymerase chain reaction (HT-qPCR). Furthermore, the influence of heavy metals and MGEs factors on ARGs was studied using the multivariate statistical analysis method. The results showed that there were a variety of ARGs in the Dexing copper mining area, and the maximum detected number of ARGs was 70. At the relative abundance level, the relative abundance of individual sites reached 0.085. In the Dexing copper mine, multidrug, MLSB, β-lactamases, tetracycline, and aminoglycoside resistance genes were the dominant ARG classes based on their numbers. The efflux pump was the most dominant resistance mechanism, followed by antibiotic deactivation and cellular protection. There was a significant positive correlation between the abundance of ARGs and MGEs (P<0.05), and TnpA04 and Inti1 were the most important MEGs in Dexing copper mine samples, indicating that horizontal gene transfer might be an important mechanism for the spread of environmental ARGs. The results of Pearson correlation analysis and RDA analysis showed that the content of Cu was significantly positively correlated with the detected numbers and abundance of ARGs (P<0.05), suggesting that the high content of Cu in the Dexing copper mining area might be an important driving factor for the formation of ARGs.}, }
@article {pmid35074363, year = {2022}, author = {Fu, S and Wang, Q and Wang, R and Zhang, Y and Lan, R and He, F and Yang, Q}, title = {Horizontal transfer of antibiotic resistance genes within the bacterial communities in aquacultural environment.}, journal = {The Science of the total environment}, volume = {820}, number = {}, pages = {153286}, doi = {10.1016/j.scitotenv.2022.153286}, pmid = {35074363}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/pharmacology ; Aquaculture ; *Drug Resistance, Bacterial/genetics ; Enterobacter/genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Providencia/genetics ; RNA, Ribosomal, 16S ; Shewanella/genetics ; *Vibrio parahaemolyticus/genetics ; }, abstract = {Very little is known about how microbiome interactions shape the horizontal transfer of antibiotic resistance genes in aquacultural environment. To this end, we first conducted 16S rRNA gene amplicon sequencing to monitor the dynamics of bacterial community compositions in one shrimp farm from 2019 to 2020. Next, co-occurrence analysis was then conducted to reveal the interactions network between Vibrio spp. and other species. Subsequently, 21 V. parahaemolyticus isolates and 15 related bacterial species were selected for whole-genome sequencing (WGS). The 16S rDNA amplicon sequencing results identified a remarkable increase of Vibrio and Providencia in September-2019 and a significant rise of Enterobacter and Shewanella in Septtember-2020. Co-occurrence analysis revealed that Vibrio spp. positively interacted with the above species, leading to the sequencing of their isolates to further understand the sharing of the resistant genomic islands (GIs). Subsequent pan-genomic analysis of V. parahaemolyticus genomes identified 278 horizontally transferred genes in 10 GIs, most of which were associated with antibiotic resistance, virulence, and fitness of metabolism. Most of the GIs have also been identified in Providencia, and Enterobacter, suggesting that exchange of genetic traits might occur in V. parahaemolyticus and other cooperative species in a specific niche. No genetic exchange was found between the species with negative relationships. The knowledge generated from this study would greatly improve our capacity to predict and mitigate the emergence of new resistant population and provide practical guidance on the microbial management during the aquacultural activities.}, }
@article {pmid35073754, year = {2022}, author = {Godeux, AS and Svedholm, E and Barreto, S and Potron, A and Venner, S and Charpentier, X and Laaberki, MH}, title = {Interbacterial Transfer of Carbapenem Resistance and Large Antibiotic Resistance Islands by Natural Transformation in Pathogenic Acinetobacter.}, journal = {mBio}, volume = {13}, number = {1}, pages = {e0263121}, pmid = {35073754}, issn = {2150-7511}, support = {ANR-11-LABX-0048//Agence Nationale de la Recherche (ANR)/ ; ANR-11-IDEX-0007//Agence Nationale de la Recherche (ANR)/ ; PhD funding VetAgro Sup//VetAgro Sup (VetAgro-Sup)/ ; }, mesh = {*Acinetobacter Infections/microbiology ; *Acinetobacter baumannii ; Animals ; Anti-Bacterial Agents/pharmacology ; Carbapenems/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Microbial Sensitivity Tests ; }, abstract = {Acinetobacter baumannii infection poses a major health threat, with recurrent treatment failure due to antibiotic resistance, notably to carbapenems. While genomic analyses of clinical strains indicate that homologous recombination plays a major role in the acquisition of antibiotic resistance genes, the underlying mechanisms of horizontal gene transfer often remain speculative. Our understanding of the acquisition of antibiotic resistance is hampered by the lack of experimental systems able to reproduce genomic observations. We here report the detection of recombination events occurring spontaneously in mixed bacterial populations and which can result in the acquisition of resistance to carbapenems. We show that natural transformation is the main driver of intrastrain but also interstrain recombination events between A. baumannii clinical isolates and pathogenic species of Acinetobacter. We observed that interbacterial natural transformation in mixed populations is more efficient at promoting the acquisition of large resistance islands (AbaR4 and AbaR1) than when the same bacteria are supplied with large amounts of purified genomic DNA. Importantly, analysis of the genomes of the recombinant progeny revealed large recombination tracts (from 13 to 123 kb) similar to those observed in the genomes of clinical isolates. Moreover, we highlight that transforming DNA availability is a key determinant of the rate of recombinants and results from both spontaneous release and interbacterial predatory behavior. In the light of our results, natural transformation should be considered a leading mechanism of genome recombination and horizontal gene transfer of antibiotic resistance genes in Acinetobacter baumannii. IMPORTANCE Acinetobacter baumannii is a multidrug-resistant pathogen responsible for difficult-to-treat hospital-acquired infections. Understanding the mechanisms leading to the emergence of the multidrug resistance in this pathogen today is crucial. Horizontal gene transfer is assumed to largely contribute to this multidrug resistance. However, in A. baumannii, the mechanisms leading to genome recombination and the horizontal transfer of resistance genes are poorly understood. We describe experimental evidence that natural transformation, a horizontal gene transfer mechanism recently highlighted in A. baumannii, allows the highly efficient interbacterial transfer of genetic elements carrying resistance to last-line antibiotic carbapenems. Importantly, we demonstrated that natural transformation, occurring in mixed populations of Acinetobacter, enables the transfer of large resistance island-mobilizing multiple-resistance genes.}, }
@article {pmid35068397, year = {2022}, author = {Jalili, M and Ansari, N and Pourhossein, B and Fazeli, M and Jalilian, FA}, title = {An Overview of Antiviral Properties of Bacteriophages with Emphasis on the Treatment of COVID-19 Infection.}, journal = {Infectious disorders drug targets}, volume = {22}, number = {6}, pages = {e240122200472}, doi = {10.2174/1871526522666220124110547}, pmid = {35068397}, issn = {2212-3989}, mesh = {Antiviral Agents ; Bacteria ; *Bacteriophages ; *COVID-19 ; Humans ; *Phage Therapy ; }, abstract = {Bacteriophages or phages are the most abundant organisms in the biosphere. Scientists considered phages an appropriate tool for understanding molecular biology, horizontal gene transfer vectors, stimulants of bacterial evolution, a source of diagnostic and genetic tools, and new therapeutic agents. Therefore, studying the biology of phages and their interactions with their hosts is crucial to gaining a deeper knowledge of biological systems. Numerous studies confirmed that bacteriophages are a genetic tool with high potential for treating infectious diseases, including bacterial, fungal, and viral infections. Therefore, phages may be used as an appropriate therapeutic target against some viruses, such as COVID-19 infection. In this study, we describe the role of phages in modulating the host immune system, the production of specific antibodies against the COVID-19 virus by the host immune system, and the minimization of damage caused by the COVID-19 virus to the host. Also, the present study expresses our understanding of the prospect of phage therapy as an adjunctive therapy.}, }
@article {pmid35064802, year = {2022}, author = {Xu, Y and Yang, L and Wang, Y and Zhu, Z and Yan, J and Qin, S and Chen, L}, title = {Prophage-encoded gene VpaChn25_0734 amplifies ecological persistence of Vibrio parahaemolyticus CHN25.}, journal = {Current genetics}, volume = {68}, number = {2}, pages = {267-287}, pmid = {35064802}, issn = {1432-0983}, support = {31671946//National Natural Science Foundation of China/ ; 17050502200//Science and Technology Commission of Shanghai Municipality/ ; }, mesh = {Caco-2 Cells ; Gene Expression Profiling ; Humans ; Prophages/genetics ; *Vibrio parahaemolyticus/genetics/metabolism ; Virulence ; }, abstract = {Vibrio parahaemolyticus is a waterborne pathogen that can cause acute gastroenteritis, wound infection, and septicemia in humans. The molecular basis of its pathogenicity is not yet fully understood. Phages are found most abundantly in aquatic environments and play a critical role in horizontal gene transfer. Nevertheless, current literature on biological roles of prophage-encoded genes remaining in V. parahaemolyticus is rare. In this study, we characterized one such gene VpaChn25_0734 (543-bp) in V. parahaemolyticus CHN25 genome. A deletion mutant ΔVpaChn25_0734 (543-bp) was obtained by homologous recombination, and a revertant ΔVpaChn25_0734-com (543-bp) was also constructed. The ΔVpaChn25_0734 (543-bp) mutant was defective in growth and swimming mobility particularly at lower temperatures and/or pH 7.0-8.5. Cell surface hydrophobicity and biofilm formation were significantly decreased in the ΔVpaChn25_0734 (543-bp) mutant (p < 0.05). Based on the in vitro Caco-2 cell model, the deletion of VpaChn25_0734 (543-bp) gene significantly reduced the cytotoxicity of V. parahaemolyticus CHN25 to human intestinal epithelial cells (p < 0.05). Comparative secretomic and transcriptomic analyses revealed a slightly increased extracellular proteins, and thirteen significantly changed metabolic pathways in the ΔVpaChn25_0734 (543-bp) mutant, showing down-regulated carbon source transport and utilization, biofilm formation, and type II secretion system (p < 0.05), consistent with the observed defective phenotypes. Taken, the prophage-encoded gene VpaChn25_0734 (543-bp) enhanced V. parahaemolyticus CHN25 fitness for survival in the environment and the host. The results in this study facilitate better understanding of pathogenesis and genome evolution of V. parahaemolyticus, the leading sea foodborne pathogen worldwide.}, }
@article {pmid35063120, year = {2022}, author = {Urquhart, AS and Chong, NF and Yang, Y and Idnurm, A}, title = {A large transposable element mediates metal resistance in the fungus Paecilomyces variotii.}, journal = {Current biology : CB}, volume = {32}, number = {5}, pages = {937-950.e5}, doi = {10.1016/j.cub.2021.12.048}, pmid = {35063120}, issn = {1879-0445}, mesh = {Byssochlamys ; *Cadmium/toxicity ; Copper/toxicity ; *DNA Transposable Elements/genetics ; Zinc ; }, abstract = {The horizontal transfer of large gene clusters by mobile elements is a key driver of prokaryotic adaptation in response to environmental stresses. Eukaryotic microbes face similar stresses; however, a parallel role for mobile elements has not been established. A stress faced by many microorganisms is toxic metal ions in their environment. In fungi, identified mechanisms for protection against metals generally rely on genes that are dispersed within an organism's genome. Here, we discover a large (∼85 kb) region that confers tolerance to five metal/metalloid ions (arsenate, cadmium, copper, lead, and zinc) in the genomes of some, but not all, strains of a fungus, Paecilomyces variotii. We name this region HEPHAESTUS (Hφ) and present evidence that it is mobile within the P. variotii genome with features characteristic of a transposable element. HEPHAESTUS contains the greatest complement of host-beneficial genes carried by a transposable element in eukaryotes, suggesting that eukaryotic transposable elements might play a role analogous to bacteria in the horizontal transfer of large regions of host-beneficial DNA. Genes within HEPHAESTUS responsible for individual metal tolerances include those encoding a P-type ATPase transporter-PcaA-required for cadmium and lead tolerance, a transporter-ZrcA-providing tolerance to zinc, and a multicopper oxidase-McoA-conferring tolerance to copper. In addition, a subregion of Hφ confers tolerance to arsenate. The genome sequences of other fungi in the Eurotiales contain further examples of HEPHAESTUS, suggesting that it is responsible for independently assembling tolerance to a diverse array of ions, including chromium, mercury, and sodium.}, }
@article {pmid35061668, year = {2022}, author = {Stubenrauch, CJ and Bamert, RS and Wang, J and Lithgow, T}, title = {A noncanonical chaperone interacts with drug efflux pumps during their assembly into bacterial outer membranes.}, journal = {PLoS biology}, volume = {20}, number = {1}, pages = {e3001523}, pmid = {35061668}, issn = {1545-7885}, mesh = {Bacterial Outer Membrane/physiology ; Bacterial Outer Membrane Proteins/*metabolism ; Biological Transport ; Drug Resistance, Bacterial/physiology ; Escherichia coli/*physiology ; Escherichia coli Proteins ; Membrane Transport Proteins ; *Molecular Chaperones ; Phylogeny ; }, abstract = {Bacteria have membrane-spanning efflux pumps to secrete toxic compounds ranging from heavy metal ions to organic chemicals, including antibiotic drugs. The overall architecture of these efflux pumps is highly conserved: with an inner membrane energy-transducing subunit coupled via an adaptor protein to an outer membrane conduit subunit that enables toxic compounds to be expelled into the environment. Here, we map the distribution of efflux pumps across bacterial lineages to show these proteins are more widespread than previously recognised. Complex phylogenetics support the concept that gene cassettes encoding the subunits for these pumps are commonly acquired by horizontal gene transfer. Using TolC as a model protein, we demonstrate that assembly of conduit subunits into the outer membrane uses the chaperone TAM to physically organise the membrane-embedded staves of the conduit subunit of the efflux pump. The characteristics of this assembly pathway have impact for the acquisition of efflux pumps across bacterial species and for the development of new antimicrobial compounds that inhibit efflux pump function.}, }
@article {pmid35061176, year = {2022}, author = {Guo, ZB and Sun, WL and Zuo, XJ and Song, HL and Ling, H and Zhang, S}, title = {Increase of antibiotic resistance genes via horizontal transfer in single- and two-chamber microbial electrolysis cells.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {24}, pages = {36216-36224}, pmid = {35061176}, issn = {1614-7499}, support = {BK20200816//natural science foundation of jiangsu province/ ; 52070101//national natural science foundation of china/ ; 20KJB610009//key university science research project of jiangsu province/ ; 1421071801005//project of jiangsu specially-appointed professor/ ; 41873016//National Natural Science Foundation of China/ ; }, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Electrolysis ; Gene Transfer, Horizontal ; *Genes, Bacterial ; }, abstract = {Microbial electrolysis cells (MECs) have been applied for antibiotic degradation but simultaneously induced antibiotic resistance genes (ARGs), thus representing a risk to disseminate antibiotic resistance. However, few studies were on the potential and risk of ARGs transmission in the MECs. This work assessed conjugative transfer of ARGs under three tested conditions (voltages, cell concentration, and donor/recipient ratio) in both single- and two-chamber MECs. The results indicated that voltages (> 0.9 V) facilitated the horizontal frequency of ARGs in the single-chamber MECs and anode chamber of two-chamber MECs. The donor cell number (donor/recipient ratio was 2:1) increased the transfer frequency of ARGs. Furthermore, voltages ranged from 0.9 to 2.5 V increased reactive oxygen species (ROS) production and cell membrane permeability in MECs. These findings offer new insights into the roles of ARG transfer under different applied voltages in the MECs, which should not be ignored for horizontal transfer of antibiotic resistance.}, }
@article {pmid35060074, year = {2022}, author = {Zhang, X and Liu, Z and Xu, W and Pan, J and Huang, Y and Cai, M and Luo, Z and Li, M}, title = {Genomic insights into versatile lifestyle of three new bacterial candidate phyla.}, journal = {Science China. Life sciences}, volume = {65}, number = {8}, pages = {1547-1562}, pmid = {35060074}, issn = {1869-1889}, mesh = {*Bacteria ; Genome, Bacterial/genetics ; Genomics ; *Metagenome ; Phylogeny ; Sulfates/metabolism ; }, abstract = {Metagenomic explorations of the Earth's biosphere enable the discovery of previously unknown bacterial lineages of phylogenetic and ecological significance. Here, we retrieved 11 metagenomic-assembled genomes (MAGs) affiliated to three new monophyletic bacterial lineages from the seawater of the Yap Trench. Phylogenomic analysis revealed that each lineage is a new bacterial candidate phylum, subsequently named Candidatus Qinglongiota, Candidatus Heilongiota, and Candidatus Canglongiota. Metabolic reconstruction of genomes from the three phyla suggested that they adopt a versatile lifestyle, with the potential to utilize various types of sugars, proteins, and/or short-chain fatty acids through anaerobic pathways. This was further confirmed by a global distribution map of the three phyla, indicating a preference for oxygen-limited or particle-attached niches, such as anoxic sedimentary environments. Of note, Candidatus Canglongiota genomes harbor genes for the complete Wood- Ljungdahl pathway and sulfate reduction that are similar to those identified in some sulfate-reducing bacteria. Evolutionary analysis indicated that gene gain and loss events, and horizontal gene transfer (HGT) play important roles in shaping the genomic and metabolic features of the three new phyla. This study presents the genomic insight into the ecology, metabolism, and evolution of three new phyla, which broadens the phylum-level diversity within the domain Bacteria.}, }
@article {pmid35058893, year = {2021}, author = {Luo, A and Wang, F and Sun, D and Liu, X and Xin, B}, title = {Formation, Development, and Cross-Species Interactions in Biofilms.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {757327}, pmid = {35058893}, issn = {1664-302X}, abstract = {Biofilms, which are essential vectors of bacterial survival, protect microbes from antibiotics and host immune attack and are one of the leading causes that maintain drug-resistant chronic infections. In nature, compared with monomicrobial biofilms, polymicrobial biofilms composed of multispecies bacteria predominate, which means that it is significant to explore the interactions between microorganisms from different kingdoms, species, and strains. Cross-microbial interactions exist during biofilm development, either synergistically or antagonistically. Although research into cross-species biofilms remains at an early stage, in this review, the important mechanisms that are involved in biofilm formation are delineated. Then, recent studies that investigated cross-species cooperation or synergy, competition or antagonism in biofilms, and various components that mediate those interactions will be elaborated. To determine approaches that minimize the harmful effects of biofilms, it is important to understand the interactions between microbial species. The knowledge gained from these investigations has the potential to guide studies into microbial sociality in natural settings and to help in the design of new medicines and therapies to treat bacterial infections.}, }
@article {pmid35058576, year = {2022}, author = {Guo, BB and Wu, JP and Chen, JW and Zhang, H and Li, JJ}, title = {Effects of Chinese medicine herbal residues on antibiotic resistance genes and the bacterial community in chicken manure composting.}, journal = {The Journal of antibiotics}, volume = {75}, number = {3}, pages = {164-171}, pmid = {35058576}, issn = {1881-1469}, mesh = {Animals ; Anti-Bacterial Agents/*adverse effects ; Bacteria/genetics ; Chickens ; Composting/*methods ; Drug Resistance, Microbial/*drug effects/*genetics ; Drugs, Chinese Herbal/*pharmacology ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/*drug effects/genetics ; Livestock/microbiology ; Manure/*microbiology ; Medicine, Chinese Traditional/methods ; Microbiota/*drug effects/genetics ; }, abstract = {The use of livestock manure is an important way for antibiotic resistance genes (ARGs) to enter the environment, and composting is an effective method for removing ARGs from livestock manure. In this study, different volume ratios of Chinese medicinal herbal residues (CMHRs) were added to laboratory-scale chicken manure composting to evaluate their effects, if any, on the behavior of ARGs, mobile genetic elements (MGEs), and the bacterial community. At the end of the composting period, the composition of the microbial community changed. Firmicutes decreased and Bacteroidetes increased. The most striking effect was that the relative abundance of the 21 ARGs and 5 MGEs detected decreased by varying degrees in the different treatments (except for sulI and intI1). The removal rate of the ARGs increased with the increased addition of CMHRs. The correlations between transferase genes (tnpA and tnpA-02) and ARGs were significant (p < 0.05); therefore, transposons play an important role in the horizontal gene transfer of ARGs in chicken manure. The results imply that CMHRs would be an effective bulking agent for the removal of ARGs from chicken manure composting.}, }
@article {pmid35058462, year = {2022}, author = {Liu, M and Liu, J and Liu, G and Wang, H and Wang, X and Deng, Z and He, Y and Ou, HY}, title = {ICEO, a biological ontology for representing and analyzing bacterial integrative and conjugative elements.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {11}, pmid = {35058462}, issn = {2052-4463}, support = {32070572//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Biological Ontologies ; *Conjugation, Genetic ; *DNA Transposable Elements ; *Gene Transfer, Horizontal ; Klebsiella pneumoniae ; }, abstract = {Bacterial integrative and conjugative elements (ICEs) are highly modular mobile genetic elements critical to the horizontal transfer of antibiotic resistance and virulence factor genes. To better understand and analyze the ongoing increase of ICEs, we developed an Integrative and Conjugative Element Ontology (ICEO) to represent the gene components, functional modules, and other information of experimentally verified ICEs. ICEO is aligned with the upper-level Basic Formal Ontology and reuses existing reliable ontologies. There are 31,081 terms, including 26,814 classes from 14 ontologies and 4128 ICEO-specific classes, representing the information of 271 known experimentally verified ICEs from 235 bacterial strains in ICEO currently and 311 predicted ICEs of 272 completely sequenced Klebsiella pneumoniae strains. Three ICEO use cases were illustrated to investigate complex joins of ICEs and their harboring antibiotic resistance or virulence factor genes by using SPARQL or DL query. ICEO has been approved as an Open Biomedical Ontology library ontology. It may be dedicated to facilitating systematical ICE knowledge representation, integration, and computer-assisted queries.}, }
@article {pmid35056600, year = {2022}, author = {Mujakić, I and Piwosz, K and Koblížek, M}, title = {Phylum Gemmatimonadota and Its Role in the Environment.}, journal = {Microorganisms}, volume = {10}, number = {1}, pages = {}, pmid = {35056600}, issn = {2076-2607}, support = {19-28778X//Czech Science Foundation/ ; }, abstract = {Bacteria are an important part of every ecosystem that they inhabit on Earth. Environmental microbiologists usually focus on a few dominant bacterial groups, neglecting less abundant ones, which collectively make up most of the microbial diversity. One of such less-studied phyla is Gemmatimonadota. Currently, the phylum contains only six cultured species. However, data from culture-independent studies indicate that members of Gemmatimonadota are common in diverse habitats. They are abundant in soils, where they seem to be frequently associated with plants and the rhizosphere. Moreover, Gemmatimonadota were found in aquatic environments, such as freshwaters, wastewater treatment plants, biofilms, and sediments. An important discovery was the identification of purple bacterial reaction centers and anoxygenic photosynthesis in this phylum, genes for which were likely acquired via horizontal gene transfer. So far, the capacity for anoxygenic photosynthesis has been described for two cultured species: Gemmatimonas phototrophica and Gemmatimonas groenlandica. Moreover, analyses of metagenome-assembled genomes indicate that it is also common in uncultured lineages of Gemmatimonadota. This review summarizes the current knowledge about this understudied bacterial phylum with an emphasis on its environmental distribution.}, }
@article {pmid35055035, year = {2022}, author = {Ilinsky, Y and Demenkova, M and Bykov, R and Bugrov, A}, title = {Narrow Genetic Diversity of Wolbachia Symbionts in Acrididae Grasshopper Hosts (Insecta, Orthoptera).}, journal = {International journal of molecular sciences}, volume = {23}, number = {2}, pages = {}, pmid = {35055035}, issn = {1422-0067}, support = {19-04-00983//Russian Foundation for Basic Research/ ; 121031800061-7//Ministry of Science and Higher Education (Russian Federation)/ ; }, mesh = {Animals ; Gene Transfer, Horizontal ; *Genetic Variation ; Grasshoppers/*microbiology ; Insecta/microbiology ; Multilocus Sequence Typing ; Phylogeny ; Symbiosis ; Wolbachia/*classification/*genetics ; }, abstract = {Bacteria of the Wolbachia genus are maternally inherited symbionts of Nematoda and numerous Arthropoda hosts. There are approximately 20 lineages of Wolbachia, which are called supergroups, and they are designated alphabetically. Wolbachia strains of the supergroups A and B are predominant in arthropods, especially in insects, and supergroup F seems to rank third. Host taxa have been studied very unevenly for Wolbachia symbionts, and here, we turn to one of largely unexplored insect families: Acrididae. On the basis of five genes subject to multilocus sequence typing, we investigated the incidence and genetic diversity of Wolbachia in 41 species belonging three subfamilies (Gomphocerinae, Oedipodinae, and Podisminae) collected in Turkey, Kazakhstan, Tajikistan, Russia, and Japan, making 501 specimens in total. Our results revealed a high incidence and very narrow genetic diversity of Wolbachia. Although only the strains belonging to supergroups A and B are commonly present in present, the Acrididae hosts here proved to be infected with supergroups B and F without A-supergroup variants. The only trace of an A-supergroup lineage was noted in one case of an inter-supergroup recombinant haplotype, where the ftsZ gene came from supergroup A, and the others from supergroup B. Variation in the Wolbachia haplotypes in Acrididae hosts within supergroups B and F was extremely low. A comprehensive genetic analysis of Wolbachia diversity confirmed specific features of the Wolbachia allelic set in Acrididae hosts. This result can help to elucidate the crucial issue of Wolbachia biology: the route(s) and mechanism(s) of Wolbachia horizontal transmission.}, }
@article {pmid35052991, year = {2022}, author = {Hazra, M and Durso, LM}, title = {Performance Efficiency of Conventional Treatment Plants and Constructed Wetlands towards Reduction of Antibiotic Resistance.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {1}, pages = {}, pmid = {35052991}, issn = {2079-6382}, support = {National Program 212 base funding//United States Department of Agriculture/ ; }, abstract = {Domestic and industrial wastewater discharges harbor rich bacterial communities, including both pathogenic and commensal organisms that are antibiotic-resistant (AR). AR pathogens pose a potential threat to human and animal health. In wastewater treatment plants (WWTP), bacteria encounter environments suitable for horizontal gene transfer, providing an opportunity for bacterial cells to acquire new antibiotic-resistant genes. With many entry points to environmental components, especially water and soil, WWTPs are considered a critical control point for antibiotic resistance. The primary and secondary units of conventional WWTPs are not designed for the reduction of resistant microbes. Constructed wetlands (CWs) are viable wastewater treatment options with the potential for mitigating AR bacteria, their genes, pathogens, and general pollutants. Encouraging performance for the removal of AR (2-4 logs) has highlighted the applicability of CW on fields. Their low cost of construction, operation and maintenance makes them well suited for applications across the globe, especially in developing and low-income countries. The present review highlights a better understanding of the performance efficiency of conventional treatment plants and CWs for the elimination/reduction of AR from wastewater. They are viable alternatives that can be used for secondary/tertiary treatment or effluent polishing in combination with WWTP or in a decentralized manner.}, }
@article {pmid35052959, year = {2022}, author = {Martín, JF and Liras, P}, title = {Comparative Molecular Mechanisms of Biosynthesis of Naringenin and Related Chalcones in Actinobacteria and Plants: Relevance for the Obtention of Potent Bioactive Metabolites.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {1}, pages = {}, pmid = {35052959}, issn = {2079-6382}, abstract = {Naringenin and its glycosylated derivative naringin are flavonoids that are synthesized by the phenylpropanoid pathway in plants. We found that naringenin is also formed by the actinobacterium Streptomyces clavuligerus, a well-known microorganism used to industrially produce clavulanic acid. The production of naringenin in S. clavuligerus involves a chalcone synthase that uses p-coumaric as a starter unit and a P450 monoxygenase, encoded by two adjacent genes (ncs-ncyP). The p-coumaric acid starter unit is formed by a tyrosine ammonia lyase encoded by an unlinked, tal, gene. Deletion and complementation studies demonstrate that these three genes are required for biosynthesis of naringenin in S. clavuligerus. Other actinobacteria chalcone synthases use caffeic acid, ferulic acid, sinapic acid or benzoic acid as starter units in the formation of different antibiotics and antitumor agents. The biosynthesis of naringenin is restricted to a few Streptomycess species and the encoding gene cluster is present also in some Saccharotrix and Kitasatospora species. Phylogenetic comparison of S. clavuligerus naringenin chalcone synthase with homologous proteins of other actinobacteria reveal that this protein is closely related to chalcone synthases that use malonyl-CoA as a starter unit for the formation of red-brown pigment. The function of the core enzymes in the pathway, such as the chalcone synthase and the tyrosine ammonia lyase, is conserved in plants and actinobacteria. However, S. clavuligerus use a P450 monooxygenase proposed to complete the cyclization step of the naringenin chalcone, whereas this reaction in plants is performed by a chalcone isomerase. Comparison of the plant and S. clavuligerus chalcone synthases indicates that they have not been transmitted between these organisms by a recent horizontal gene transfer phenomenon. We provide a comprehensive view of the molecular genetics and biochemistry of chalcone synthases and their impact on the development of antibacterial and antitumor compounds. These advances allow new bioactive compounds to be obtained using combinatorial strategies. In addition, processes of heterologous expression and bioconversion for the production of naringenin and naringenin-derived compounds in yeasts are described.}, }
@article {pmid35052563, year = {2021}, author = {Neira, G and Vergara, E and Cortez, D and Holmes, DS}, title = {A Large-Scale Multiple Genome Comparison of Acidophilic Archaea (pH ≤ 5.0) Extends Our Understanding of Oxidative Stress Responses in Polyextreme Environments.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {11}, number = {1}, pages = {}, pmid = {35052563}, issn = {2076-3921}, support = {1181717//Fondecyt/ ; FB210008//Centro Ciencia &amp; Vida, Financiamiento Basal para Centros Cient&#xed;ficos y Tecnol&#xf3;gicos de Excelencia de ANID/ ; }, abstract = {Acidophilic archaea thrive in anaerobic and aerobic low pH environments (pH < 5) rich in dissolved heavy metals that exacerbate stress caused by the production of reactive oxygen species (ROS) such as hydrogen peroxide (H2O2), hydroxyl radical (·OH) and superoxide (O2[-]). ROS react with lipids, proteins and nucleic acids causing oxidative stress and damage that can lead to cell death. Herein, genes and mechanisms potentially involved in ROS mitigation are predicted in over 200 genomes of acidophilic archaea with sequenced genomes. These organisms are often be subjected to simultaneous multiple stresses such as high temperature, high salinity, low pH and high heavy metal loads. Some of the topics addressed include: (1) the phylogenomic distribution of these genes and what this can tell us about the evolution of these mechanisms in acidophilic archaea; (2) key differences in genes and mechanisms used by acidophilic versus non-acidophilic archaea and between acidophilic archaea and acidophilic bacteria and (3) how comparative genomic analysis predicts novel genes or pathways involved in oxidative stress responses in archaea and likely horizontal gene transfer (HGT) events.}, }
@article {pmid35052550, year = {2021}, author = {Chmelová, &#x13d; and Bianchi, C and Albanaz, ATS and Režnarová, J and Wheeler, R and Kostygov, AY and Kraeva, N and Yurchenko, V}, title = {Comparative Analysis of Three Trypanosomatid Catalases of Different Origin.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {11}, number = {1}, pages = {}, pmid = {35052550}, issn = {2076-3921}, support = {21-09283S//Czech Science Foundation/ ; CZ.02.1.01/16_019/0000759//European Regional Development Fund/ ; 211075/Z/18/Z//Well-come Trust/ ; }, abstract = {Most trypanosomatid flagellates do not have catalase. In the evolution of this group, the gene encoding catalase has been independently acquired at least three times from three different bacterial groups. Here, we demonstrate that the catalase of Vickermania was obtained by horizontal gene transfer from Gammaproteobacteria, extending the list of known bacterial sources of this gene. Comparative biochemical analyses revealed that the enzymes of V. ingenoplastis, Leptomonas pyrrhocoris, and Blastocrithidia sp., representing the three independent catalase-bearing trypanosomatid lineages, have similar properties, except for the unique cyanide resistance in the catalase of the latter species.}, }
@article {pmid35047995, year = {2021}, author = {Serrage, HJ and Jepson, MA and Rostami, N and Jakubovics, NS and Nobbs, AH}, title = {Understanding the Matrix: The Role of Extracellular DNA in Oral Biofilms.}, journal = {Frontiers in oral health}, volume = {2}, number = {}, pages = {640129}, pmid = {35047995}, issn = {2673-4842}, abstract = {Dental plaque is the key etiological agent in caries formation and the development of the prevalent chronic oral inflammatory disease, periodontitis. The dental plaque biofilm comprises a diverse range of microbial species encased within a rich extracellular matrix, of which extracellular DNA (eDNA) has been identified as an important component. The molecular mechanisms of eDNA release and the structure of eDNA have yet to be fully characterized. Nonetheless, key functions that have been proposed for eDNA include maintaining biofilm structural integrity, initiating adhesion to dental surfaces, acting as a nutrient source, and facilitating horizontal gene transfer. Thus, eDNA is a potential therapeutic target for the management of oral disease-associated biofilm. This review aims to summarize advances in the understanding of the mechanisms of eDNA release from oral microorganisms and in the methods of eDNA detection and quantification within oral biofilms.}, }
@article {pmid35045829, year = {2022}, author = {Šuto, S and Bedenić, B and Likić, S and Kibel, S and Anušić, M and Tičić, V and Zarfel, G and Grisold, A and Barišić, I and Vraneš, J}, title = {Diffusion of OXA-48 carbapenemase among urinary isolates of Klebsiella pneumoniae in non-hospitalized elderly patients.}, journal = {BMC microbiology}, volume = {22}, number = {1}, pages = {30}, pmid = {35045829}, issn = {1471-2180}, mesh = {Aged ; Aged, 80 and over ; Anti-Bacterial Agents/pharmacology ; Croatia/epidemiology ; Drug Resistance, Multiple, Bacterial ; Female ; Hospitalization ; Humans ; Klebsiella Infections/*epidemiology/*urine ; Klebsiella pneumoniae/drug effects/*enzymology ; Male ; Microbial Sensitivity Tests ; Middle Aged ; Multilocus Sequence Typing ; beta-Lactamases/genetics/*metabolism ; }, abstract = {BACKGROUND: Recently, a dramatic increase of Klebsiella pneumoniae positive for OXA-48 β-lactamases was observed first in the hospital setting and later in the long-term care facilities (LTCFs) and community in the Zagreb County, particularly, in urinary isolates. The aim of the study was to analyse the epidemiology and the mechanisms of antibiotic resistance of OXA-48 carbapenemase producing K. pneumoniae strains isolated from urine of non-hospitalized elderly patients.<br><br>RESULTS: The isolates were classified into two groups: one originated from the LTCFs and the other from the community. Extended-spectrum &#x3b2;-lactamases (ESBLs) were detected by double disk-synergy (DDST) and combined disk tests in 55% of the isolates (51/92). The ESBL-positive isolates exhibited resistance to expanded-spectrum cephalosporins (ESC) and in majority of cases to gentamicin. LTCFs isolates showed a significantly lower rate of additional ESBLs and consequential resistance to ESC and a lower gentamicin resistance rate compared to the community isolates, similarly to hospital isolates in Zagreb, pointing out to the possible transmission from hospitals.ESBL production was associated with group 1 of CTX-M or SHV-12 &#x3b2;-lactamases. Ertapenem resistance was transferable from only 12 isolates. blaOXA-48 genes were carried by IncL plasmid in 42 isolates. In addition IncFII and IncFIB were identified in 18 and 2 isolates, respectively. Two new sequence types were reported: ST4870 and ST4781.<br><br>CONCLUSIONS: This study showed eruptive and extensive diffusion of OXA-48 carbapenemase to LTCFs and community population in Zagreb County, particularly affecting patients with UTIs and urinary catheters. On the basis of susceptibility testing, &#x3b2;-lactamase production, conjugation experiments, MLST and plasmid characterization it can be concluded that there was horizontal gene transfer between unrelated isolates, responsible for epidemic spread of OXA-48 carbapenemase in the LTCFs and the community The rapid spread of OXA-48 producing K. pneumoniae points out to the shortcomings in the infection control measures.}, }
@article {pmid35044532, year = {2022}, author = {Wani, AK and Akhtar, N and Sher, F and Navarrete, AA and Américo-Pinheiro, JHP}, title = {Microbial adaptation to different environmental conditions: molecular perspective of evolved genetic and cellular systems.}, journal = {Archives of microbiology}, volume = {204}, number = {2}, pages = {144}, pmid = {35044532}, issn = {1432-072X}, mesh = {Acclimatization ; *Adaptation, Physiological/genetics ; Cold Temperature ; *Ecosystem ; Gene Transfer, Horizontal ; }, abstract = {Microorganisms are ubiquitous on Earth and can inhabit almost every environment. In a complex heterogeneous environment or in face of ecological disturbance, the microbes adjust to fluctuating environmental conditions through a cascade of cellular and molecular systems. Their habitats differ from cold microcosms of Antarctica to the geothermal volcanic areas, terrestrial to marine, highly alkaline zones to the extremely acidic areas and freshwater to brackish water sources. The diverse ecological microbial niches are attributed to the versatile, adaptable nature under fluctuating temperature, nutrient availability and pH of the microorganisms. These organisms have developed a series of mechanisms to face the environmental changes and thereby keep their role in mediate important ecosystem functions. The underlying mechanisms of adaptable microbial nature are thoroughly investigated at the cellular, genetic and molecular levels. The adaptation is mediated by a spectrum of processes like natural selection, genetic recombination, horizontal gene transfer, DNA damage repair and pleiotropy-like events. This review paper provides the fundamentals insight into the microbial adaptability besides highlighting the molecular network of microbial adaptation under different environmental conditions.}, }
@article {pmid35044219, year = {2022}, author = {Tansirichaiya, S and Goodman, RN and Guo, X and Bulgasim, I and Samuelsen, &#xd8; and Al-Haroni, M and Roberts, AP}, title = {Intracellular Transposition and Capture of Mobile Genetic Elements following Intercellular Conjugation of Multidrug Resistance Conjugative Plasmids from Clinical Enterobacteriaceae Isolates.}, journal = {Microbiology spectrum}, volume = {10}, number = {1}, pages = {e0214021}, pmid = {35044219}, issn = {2165-0497}, support = {MR/S004793/1/MRC_/Medical Research Council/United Kingdom ; MR/N013514/1/MRC_/Medical Research Council/United Kingdom ; NIHR200632/DH_/Department of Health/United Kingdom ; }, mesh = {Anti-Bacterial Agents/pharmacology ; *Conjugation, Genetic ; *DNA Transposable Elements ; *Drug Resistance, Multiple, Bacterial ; Enterobacteriaceae/drug effects/*genetics/metabolism ; Enterobacteriaceae Infections/*microbiology ; Escherichia coli/drug effects/genetics/metabolism ; Gene Transfer, Horizontal ; Humans ; Klebsiella pneumoniae/drug effects/genetics/metabolism ; Plasmids/*genetics/metabolism ; }, abstract = {Mobile genetic elements (MGEs) are often associated with antimicrobial resistance genes (ARGs). They are responsible for intracellular transposition between different replicons and intercellular conjugation and are therefore important agents of ARG dissemination. Detection and characterization of functional MGEs, especially in clinical isolates, would increase our understanding of the underlying pathways of transposition and recombination and allow us to determine interventional strategies to interrupt this process. Entrapment vectors can be used to capture active MGEs, as they contain a positive selection genetic system conferring a selectable phenotype upon the insertion of an MGE within certain regions of that system. Previously, we developed the pBACpAK entrapment vector that results in a tetracycline-resistant phenotype when MGEs translocate and disrupt the cI repressor gene. We have previously used pBACpAK to capture MGEs in clinical Escherichia coli isolates following transformation with pBACpAK. In this study, we aimed to extend the utilization of pBACpAK to other bacterial taxa. We utilized an MGE-free recipient E. coli strain containing pBACpAK to capture MGEs on conjugative, ARG-containing plasmids following conjugation from clinical Enterobacteriaceae donors. Following the conjugative transfer of multiple conjugative plasmids and screening for tetracycline resistance in these transconjugants, we captured several insertion sequence (IS) elements and novel transposons (Tn7350 and Tn7351) and detected the de novo formation of novel putative composite transposons where the pBACpAK-located tet(A) is flanked by ISKpn25 from the transferred conjugative plasmid, as well as the ISKpn14-mediated integration of an entire 119-kb, blaNDM-1-containing conjugative plasmid from Klebsiella pneumoniae. IMPORTANCE By analyzing transposition activity within our MGE-free recipient, we can gain insights into the interaction and evolution of multidrug resistance-conferring MGEs following conjugation, including the movement of multiple ISs, the formation of composite transposons, and cointegration and/or recombination between different replicons in the same cell. This combination of recipient and entrapment vector will allow fine-scale experimental studies of factors affecting intracellular transposition and MGE formation in and from ARG-encoding MGEs from multiple species of clinically relevant Enterobacteriaceae.}, }
@article {pmid35041498, year = {2022}, author = {Foster, HR and Lin, X and Srikant, S and Cueny, RR and Falbel, TG and Keck, JL and Gaudet, R and Burton, BM}, title = {Natural Transformation Protein ComFA Exhibits Single-Stranded DNA Translocase Activity.}, journal = {Journal of bacteriology}, volume = {204}, number = {3}, pages = {e0051821}, pmid = {35041498}, issn = {1098-5530}, support = {R01-GM120996/NH/NIH HHS/United States ; R01 GM121865/GM/NIGMS NIH HHS/United States ; International Research Scholar/HHMI/Howard Hughes Medical Institute/United States ; R01-GM121865/NH/NIH HHS/United States ; R01 GM120996/GM/NIGMS NIH HHS/United States ; }, mesh = {*Adenosine Triphosphatases/genetics/metabolism ; Adenosine Triphosphate/metabolism ; DEAD-box RNA Helicases/metabolism ; DNA ; DNA Helicases/metabolism ; *DNA, Single-Stranded/genetics ; }, abstract = {Natural transformation is one of the major mechanisms of horizontal gene transfer in bacterial populations and has been demonstrated in numerous species of bacteria. Despite the prevalence of natural transformation, much of the molecular mechanism remains unexplored. One major outstanding question is how the cell powers DNA import, which is rapid and highly processive. ComFA is one of a few proteins required for natural transformation in Gram-positive bacteria. Its structural resemblance to the DEAD box helicase family has led to a long-held hypothesis that ComFA acts as a motor to help drive DNA import into the cytosol. Here, we explored the helicase and translocase activity of ComFA to address this hypothesis. We followed the DNA-dependent ATPase activity of ComFA and, combined with mathematical modeling, demonstrated that ComFA likely translocates on single-stranded DNA from 5' to 3'. However, this translocase activity does not lead to DNA unwinding under the conditions we tested. Further, we analyzed the ATPase cycle of ComFA and found that ATP hydrolysis stimulates the release of DNA, providing a potential mechanism for translocation. These findings help define the molecular contribution of ComFA to natural transformation and support the conclusion that ComFA plays a key role in powering DNA uptake. IMPORTANCE Competence, or the ability of bacteria to take up and incorporate foreign DNA in a process called natural transformation, is common in the bacterial kingdom. Research in several bacterial species suggests that long, contiguous stretches of DNA are imported into cells in a processive manner, but how bacteria power transformation remains unclear. Our finding that ComFA, a DEAD box helicase required for competence in Gram-positive bacteria, translocates on single-stranded DNA from 5' to 3', supports the long-held hypothesis that ComFA may be the motor powering DNA transport during natural transformation. Moreover, ComFA may be a previously unidentified type of DEAD box helicase-one with the capability of extended translocation on single-stranded DNA.}, }
@article {pmid35040700, year = {2022}, author = {Moller, AG and Petit, RA and Read, TD}, title = {Species-Scale Genomic Analysis of Staphylococcus aureus Genes Influencing Phage Host Range and Their Relationships to Virulence and Antibiotic Resistance Genes.}, journal = {mSystems}, volume = {7}, number = {1}, pages = {e0108321}, pmid = {35040700}, issn = {2379-5077}, support = {R21 AI138079/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Staphylococcus aureus/genetics ; *Bacteriophages ; Virulence ; Host Specificity ; Anti-Bacterial Agents ; *Superinfection ; Genomics ; *Staphylococcal Infections/microbiology ; Drug Resistance, Microbial ; }, abstract = {Phage therapy has been proposed as a possible alternative treatment for infections caused by the ubiquitous bacterial pathogen Staphylococcus aureus. However, successful therapy requires understanding the genetic basis of host range-the subset of strains in a species that could be killed by a particular phage. We searched diverse sets of S. aureus public genome sequences against a database of genes suggested from prior studies to influence host range to look for patterns of variation across the species. We found that genes encoding biosynthesis of molecules that were targets of S. aureus phage adsorption to the outer surface of the cell were the most conserved in the pangenome. Putative phage resistance genes that were core components of the pangenome genes had similar nucleotide diversity, ratio of nonsynonymous to synonymous substitutions, and functionality (measured by delta-bitscore) to other core genes. However, phage resistance genes that were not part of the core genome were significantly less consistent with the core genome phylogeny than all noncore genes in this set, suggesting more frequent movement between strains by horizontal gene transfer. Only superinfection immunity genes encoded by temperate phages inserted in the genome correlated with experimentally determined temperate phage resistance. Taken together, these results suggested that, while phage adsorption genes are heavily conserved in the S. aureus species, HGT may play a significant role in strain-specific evolution of host range patterns. IMPORTANCE Staphylococcus aureus is a widespread, hospital- and community-acquired pathogen that is commonly antibiotic resistant. It causes diverse diseases affecting both the skin and internal organs. Its ubiquity, antibiotic resistance, and disease burden make new therapies urgent, such as phage therapy, in which viruses specific to infecting bacteria clear infection. S. aureus phage host range not only determines whether phage therapy will be successful by killing bacteria but also horizontal gene transfer through transduction of host genetic material by phages. In this work, we comprehensively reviewed existing literature to build a list of S. aureus phage resistance genes and searched our database of almost 43,000 S. aureus genomes for these genes to understand their patterns of evolution, finding that prophages' superinfection immunity correlates best with phage resistance and HGT. These findings improved our understanding of the relationship between known phage resistance genes and phage host range in the species.}, }
@article {pmid35031426, year = {2022}, author = {Gatica-Soria, LM and Ceriotti, LF and Garcia, LE and Virginia Sanchez-Puerta, M}, title = {Native and foreign mitochondrial and nuclear encoded proteins conform the OXPHOS complexes of a holoparasitic plant.}, journal = {Gene}, volume = {817}, number = {}, pages = {146176}, doi = {10.1016/j.gene.2021.146176}, pmid = {35031426}, issn = {1879-0038}, mesh = {Balanophoraceae/*genetics/physiology ; Cell Nucleus/genetics ; Cytochromes c/genetics ; Evolution, Molecular ; Fabaceae/parasitology ; *Gene Transfer, Horizontal ; *Genes, Mitochondrial ; Oxidative Phosphorylation ; Phylogeny ; Plant Proteins/*genetics ; RNA, Plant ; RNA-Seq ; }, abstract = {The intimate contact between the holoparasitic plant Lophophytum mirabile (Balanophoraceae) and its host plant (Fabaceae) facilitates the exchange of genetic information, increasing the frequency of horizontal gene transfer (HGT). Lophophytum stands out because it acquired a large number of mitochondrial genes (greater than 20) from its legume host that replaced the majority of the native homologs. These foreign genes code for proteins that form multisubunit enzyme complexes, such as those in the oxidative phosphorylation system (OXPHOS) and cytochrome c maturation (ccm) system, together with dozens of nuclear-encoded subunits. However, the existence and the origin of the nuclear subunits that form the major part of the OXPHOS and ccm system in Lophophytum remain unknown. It was proposed that nuclear-encoding genes whose products interact with foreign mitochondrial proteins are also foreign, minimizing the incompatibilities that could arise in the assembly and functioning of these multiprotein complexes. We identified a nearly complete set of OXPHOS and ccm system subunits evolving under selective constraints in the transcriptome of Lophophytum, indicating that OXPHOS is functional and resembles that of free-living angiosperms. Maximum Likelihood phylogenetic analyses revealed a single case of HGT in the nuclear genes, which results in mosaic OXPHOS and ccm system in Lophophytum. These observations raise new questions about the evolution and physiology of this parasitic plant. A putative case of cooperation between two foreign (one mitochondrial and one nuclear) genes is presented.}, }
@article {pmid35030982, year = {2022}, author = {Tan, R and Jin, M and Shao, Y and Yin, J and Li, H and Chen, T and Shi, D and Zhou, S and Li, J and Yang, D}, title = {High-sugar, high-fat, and high-protein diets promote antibiotic resistance gene spreading in the mouse intestinal microbiota.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2022442}, pmid = {35030982}, issn = {1949-0984}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/*drug effects/*genetics/metabolism ; Bacterial Proteins/metabolism ; Dietary Fats/adverse effects/analysis/*metabolism ; Dietary Proteins/adverse effects/analysis/*metabolism ; Dietary Sugars/adverse effects/analysis/*metabolism ; *Drug Resistance, Bacterial ; *Gastrointestinal Microbiome ; Gene Amplification ; Gene Transfer, Horizontal ; Humans ; Male ; Mice ; Mice, Inbred BALB C ; }, abstract = {Diet can not only provide nutrition for intestinal microbiota, it can also remodel them. However, is unclear whether and how diet affects the spread of antibiotic resistance genes (ARGs) in the intestinal microbiota. Therefore, we employed selected high-sugar, high-fat, high-protein, and normal diets to explore the effect. The results showed that high-sugar, high-fat, and high-protein diets promoted the amplification and transfer of exogenous ARGs among intestinal microbiota, and up-regulated the expression of trfAp and trbBp while significantly altered the intestinal microbiota and its metabolites. Inflammation-related products were strongly correlated with the spread of ARGs, suggesting the intestinal microenvironment after diet remodeling might be conducive to the spreading of ARGs. This may be attributed to changes in bacterial membrane permeability, the SOS response, and bacterial composition and diversity caused by diet-induced inflammation. In addition, acceptor bacteria (zygotes) screened by flow cytometry were mostly Proteobacteria, Firmicutes and Actinobacteria, and most were derived from dominant intestinal bacteria remodeled by diet, indicating that the transfer of ARGs was closely linked to diet, and had some selectivity. Metagenomic results showed that the gut resistance genome could be affected not only by diet, but by exogenous antibiotic resistant bacteria (ARB). Many ARG markers coincided with bacterial markers in diet groups. Therefore, dominant bacteria in different diets are important hosts of ARGs in specific dietary environments, but the many pathogenic bacteria present may cause serious harm to human health.}, }
@article {pmid35026464, year = {2022}, author = {Silva, CP and Oliveira, CJB and Leite, EL and Cibulski, SP and Fernandes, M and Vasconcelos, PC and Dias, LM and Silva, NMVD and Garino Júnior, F and Fernandes, ACC}, title = {CTX-M-15-producing Klebsiella pneumoniae ST273 associated with nasal infection in a domestic cat.}, journal = {Journal of global antimicrobial resistance}, volume = {28}, number = {}, pages = {203-205}, doi = {10.1016/j.jgar.2022.01.004}, pmid = {35026464}, issn = {2213-7173}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Cats ; Drug Resistance, Multiple, Bacterial/genetics ; *Klebsiella Infections/drug therapy/veterinary ; *Klebsiella pneumoniae ; Male ; Multilocus Sequence Typing ; beta-Lactamases/genetics ; }, abstract = {OBJECTIVES: The aim of this study was to investigate the genetic context of expanded-spectrum β-lactam resistance in a Klebsiella pneumoniae strain causing a hard-to-treat nasal infection in a domestic cat.<br><br>METHODS: A K. pneumoniae isolate was recovered from a 4-year-old male cat hospitalised in a veterinary hospital in Para&#xed;ba, Northeastern Brazil. Following phenotypic confirmation of multidrug resistance by the disk diffusion method, the genome was sequenced using an Illumina MiSeq system. Multilocus sequence typing (MLST) and structural features related to antimicrobial resistance were determined by downstream bioinformatics analyses.<br><br>RESULTS: The strain was confirmed as sequence type 273 (ST273) K. pneumoniae harbouring a variety of genes conferring antimicrobial resistance to phenicols tetracyclines, aminoglycosides, &#x3b2;-lactams, fosfomycin, sulfonamides and quinolones. Two plasmids were identified. Plasmid p114PB_I co-harboured a set of plasmid-borne resistance genes [blaCTX-M-15, blaTEM-1, qnrS1, tetD, tetR, sul2, aph(6)-Id, aph(3'') and cat2]. Notably, the multiresistance region was characterised as a chimeric plasmid structure sharing high sequence homology with several plasmids from Enterobacteriaceae. The second plasmid (p114PB_II) was characterised as a plasmid present in many genomes belonging to K. pneumoniae.<br><br>CONCLUSION: The genetic context of the plasmid sequences harboured by a veterinary pathogenic K. pneumoniae isolate reveals the high complexity of horizontal gene transfer mechanisms in the acquisition of antimicrobial resistance genes. The emergence, dissemination and evolution of antimicrobial resistance must be investigated from a One Health perspective.}, }
@article {pmid35025885, year = {2022}, author = {Rocha, EPC and Bikard, D}, title = {Microbial defenses against mobile genetic elements and viruses: Who defends whom from what?.}, journal = {PLoS biology}, volume = {20}, number = {1}, pages = {e3001514}, pmid = {35025885}, issn = {1545-7885}, mesh = {Archaea/*genetics/physiology ; Bacteria/*genetics ; Bacterial Physiological Phenomena ; Bacteriophages ; Gene Transfer, Horizontal ; Interspersed Repetitive Sequences/*genetics ; Prophages ; }, abstract = {Prokaryotes have numerous mobile genetic elements (MGEs) that mediate horizontal gene transfer (HGT) between cells. These elements can be costly, even deadly, and cells use numerous defense systems to filter, control, or inactivate them. Recent studies have shown that prophages, conjugative elements, their parasites (phage satellites and mobilizable elements), and other poorly described MGEs encode defense systems homologous to those of bacteria. These constitute a significant fraction of the repertoire of cellular defense genes. As components of MGEs, these defense systems have presumably evolved to provide them, not the cell, adaptive functions. While the interests of the host and MGEs are aligned when they face a common threat such as an infection by a virulent phage, defensive functions carried by MGEs might also play more selfish roles to fend off other antagonistic MGEs or to ensure their maintenance in the cell. MGEs are eventually lost from the surviving host genomes by mutational processes and their defense systems can be co-opted when they provide an advantage to the cell. The abundance of defense systems in MGEs thus sheds new light on the role, effect, and fate of the so-called "cellular defense systems," whereby they are not only merely microbial defensive weapons in a 2-partner arms race, but also tools of intragenomic conflict between multiple genetic elements with divergent interests that shape cell fate and gene flow at the population level.}, }
@article {pmid35024089, year = {2022}, author = {Wang, Y and Dong, J and Wang, J and Chi, W and Zhou, W and Tian, Q and Hong, Y and Zhou, X and Ye, H and Tian, X and Hu, R and Wong, A}, title = {Assessing the drug resistance profiles of oral probiotic lozenges.}, journal = {Journal of oral microbiology}, volume = {14}, number = {1}, pages = {2019992}, pmid = {35024089}, issn = {2000-2297}, abstract = {BACKGROUND: Probiotic lozenges have been developed to harvest the benefits of probiotics for oral health, but their long-term consumption may encourage the transfer of resistance genes from probiotics to commensals, and eventually to disease-causing bacteria.<br><br>AIM: To screen commercial probiotic lozenges for resistance to antibiotics, characterize the resistance determinants, and examine their transferability in vitro.<br><br>RESULTS: Probiotics of all lozenges were resistant to glycopeptide, sulfonamide, and penicillin antibiotics, while some were resistant to aminoglycosides and cephalosporins. High minimum inhibitory concentrations (MICs) were detected for streptomycin (>128&#xa0;&#xb5;g/mL) and chloramphenicol (> 512&#xa0;&#xb5;g/mL) for all probiotics but only one was resistant to piperacillin (MIC&#xa0;=&#xa0;32&#xa0;&#xb5;g/mL). PCR analysis detected erythromycin (erm(T), ermB or mefA) and fluoroquinolone (parC or gyr(A)) resistance genes in some lozenges although there were no resistant phenotypes. The dfrD, cat-TC, vatE, aadE, vanX, and aph(3")-III or ant(2")-I genes conferring resistance to trimethoprim, chloramphenicol, quinupristin/dalfopristin, vancomycin, and streptomycin, respectively, were detected in resistant probiotics. The rifampicin resistance gene rpoB was also present. We found no conjugal transfer of streptomycin resistance genes in our co-incubation experiments.<br><br>CONCLUSION: Our study represents the first antibiotic resistance profiling of probiotics from oral lozenges, thus highlighting the health risk especially in the prevailing threat of drug resistance globally.}, }
@article {pmid35022403, year = {2022}, author = {Bornemann, TLV and Adam, PS and Turzynski, V and Schreiber, U and Figueroa-Gonzalez, PA and Rahlff, J and Köster, D and Schmidt, TC and Schunk, R and Krauthausen, B and Probst, AJ}, title = {Genetic diversity in terrestrial subsurface ecosystems impacted by geological degassing.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {284}, pmid = {35022403}, issn = {2041-1723}, mesh = {Archaea/genetics ; Bacteria/genetics ; *Ecosystem ; *Genetic Variation ; *Geology ; *Metagenomics ; Phylogeny ; Prokaryotic Cells ; Soil Microbiology ; Water Microbiology ; }, abstract = {Earth's mantle releases 38.7 ± 2.9 Tg/yr CO2 along with other reduced and oxidized gases to the atmosphere shaping microbial metabolism at volcanic sites across the globe, yet little is known about its impact on microbial life under non-thermal conditions. Here, we perform comparative metagenomics coupled to geochemical measurements of deep subsurface fluids from a cold-water geyser driven by mantle degassing. Key organisms belonging to uncultivated Candidatus Altiarchaeum show a global biogeographic pattern and site-specific adaptations shaped by gene loss and inter-kingdom horizontal gene transfer. Comparison of the geyser community to 16 other publicly available deep subsurface sites demonstrate a conservation of chemolithoautotrophic metabolism across sites. In silico replication measures suggest a linear relationship of bacterial replication with ecosystems depth with the exception of impacted sites, which show near surface characteristics. Our results suggest that subsurface ecosystems affected by geological degassing are hotspots for microbial life in the deep biosphere.}, }
@article {pmid35022241, year = {2022}, author = {Sakai, HD and Nur, N and Kato, S and Yuki, M and Shimizu, M and Itoh, T and Ohkuma, M and Suwanto, A and Kurosawa, N}, title = {Insight into the symbiotic lifestyle of DPANN archaea revealed by cultivation and genome analyses.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {3}, pages = {}, pmid = {35022241}, issn = {1091-6490}, mesh = {Archaea/classification/cytology/*genetics/*physiology ; Coculture Techniques ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Archaeal ; Genomics ; Nanoarchaeota ; Phylogeny ; Symbiosis/*genetics/*physiology ; }, abstract = {Decades of culture-independent analyses have resulted in proposals of many tentative archaeal phyla with no cultivable representative. Members of DPANN (an acronym of the names of the first included phyla Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanohaloarchaeota, and Nanoarchaeota), an archaeal superphylum composed of at least 10 of these tentative phyla, are generally considered obligate symbionts dependent on other microorganisms. While many draft/complete genome sequences of DPANN archaea are available and their biological functions have been considerably predicted, only a few examples of their successful laboratory cultivation have been reported, limiting our knowledge of their symbiotic lifestyles. Here, we investigated physiology, morphology, and host specificity of an archaeon of the phylum "Candidatus Micrarchaeota" (ARM-1) belonging to the DPANN superphylum by cultivation. We constructed a stable coculture system composed of ARM-1 and its original host Metallosphaera sp. AS-7 belonging to the order Sulfolobales Further host-switching experiments confirmed that ARM-1 grew on five different archaeal species from three genera-Metallosphaera, Acidianus, and Saccharolobus-originating from geologically distinct hot, acidic environments. The results suggested the existence of DPANN archaea that can grow by relying on a range of hosts. Genomic analyses showed inferred metabolic capabilities, common/unique genetic contents of ARM-1 among cultivated micrarchaeal representatives, and the possibility of horizontal gene transfer between ARM-1 and members of the order Sulfolobales Our report sheds light on the symbiotic lifestyles of DPANN archaea and will contribute to the elucidation of their biological/ecological functions.}, }
@article {pmid35022048, year = {2022}, author = {Chou, L and Lin, YC and Haryono, M and Santos, MNM and Cho, ST and Weisberg, AJ and Wu, CF and Chang, JH and Lai, EM and Kuo, CH}, title = {Modular evolution of secretion systems and virulence plasmids in a bacterial species complex.}, journal = {BMC biology}, volume = {20}, number = {1}, pages = {16}, pmid = {35022048}, issn = {1741-7007}, mesh = {*Bacteria/genetics ; *Bacterial Proteins/genetics/metabolism ; Bacterial Secretion Systems/genetics ; Phylogeny ; Plasmids/genetics ; Virulence ; }, abstract = {BACKGROUND: Many named species as defined in current bacterial taxonomy correspond to species complexes. Uncertainties regarding the organization of their genetic diversity challenge research efforts. We utilized the Agrobacterium tumefaciens species complex (a.k.a. Agrobacterium biovar 1), a taxon known for its phytopathogenicity and applications in transformation, as a study system and devised strategies for investigating genome diversity and evolution of species complexes.<br><br>RESULTS: We utilized 35 genome assemblies, including 14 newly generated ones, to achieve a phylogenetically balanced sampling of A. tumefaciens. Our genomic analysis suggested that the 10 genomospecies described previously are distinct biological species and supported a quantitative guideline for species delineation. Furthermore, our inference of gene content and core-genome phylogeny allowed for investigations of genes critical in fitness and ecology. For the type VI secretion system (T6SS) involved in interbacterial competition and thought to be conserved, we detected multiple losses and one horizontal gene transfer. For the tumor-inducing plasmids (pTi) and pTi-encoded type IV secretion system (T4SS) that are essential for agrobacterial phytopathogenicity, we uncovered novel diversity and hypothesized their involvement in shaping this species complex. Intriguingly, for both T6SS and T4SS, genes encoding structural components are highly conserved, whereas extensive diversity exists for genes encoding effectors and other proteins.<br><br>CONCLUSIONS: We demonstrate that the combination of a phylogeny-guided sampling scheme and an emphasis on high-quality assemblies provides a cost-effective approach for robust analysis in evolutionary genomics. We show that the T6SS VgrG proteins involved in specific effector binding and delivery can be classified into distinct types based on domain organization. The co-occurrence patterns of VgrG-associated domains and the neighboring genes that encode different chaperones/effectors can be used to infer possible interacting partners. Similarly, the associations between plant host preference and the pTi type among these strains can be used to infer phenotype-genotype correspondence. Our strategies for multi-level investigations at scales that range from whole genomes to intragenic domains and phylogenetic depths from between- to within-species are applicable to other bacteria. Furthermore, modularity observed in the molecular evolution of genes and domains is useful for inferring functional constraints and informing experimental works.}, }
@article {pmid35021210, year = {2022}, author = {Morel, B and Schade, P and Lutteropp, S and Williams, TA and Szöllősi, GJ and Stamatakis, A}, title = {SpeciesRax: A Tool for Maximum Likelihood Species Tree Inference from Gene Family Trees under Duplication, Transfer, and Loss.}, journal = {Molecular biology and evolution}, volume = {39}, number = {2}, pages = {}, pmid = {35021210}, issn = {1537-1719}, mesh = {*Algorithms ; *Gene Duplication ; Models, Genetic ; Pedigree ; Phylogeny ; }, abstract = {Species tree inference from gene family trees is becoming increasingly popular because it can account for discordance between the species tree and the corresponding gene family trees. In particular, methods that can account for multiple-copy gene families exhibit potential to leverage paralogy as informative signal. At present, there does not exist any widely adopted inference method for this purpose. Here, we present SpeciesRax, the first maximum likelihood method that can infer a rooted species tree from a set of gene family trees and can account for gene duplication, loss, and transfer events. By explicitly modeling events by which gene trees can depart from the species tree, SpeciesRax leverages the phylogenetic rooting signal in gene trees. SpeciesRax infers species tree branch lengths in units of expected substitutions per site and branch support values via paralogy-aware quartets extracted from the gene family trees. Using both empirical and simulated data sets we show that SpeciesRax is at least as accurate as the best competing methods while being one order of magnitude faster on large data sets at the same time. We used SpeciesRax to infer a biologically plausible rooted phylogeny of the vertebrates comprising 188 species from 31,612 gene families in 1 h using 40 cores. SpeciesRax is available under GNU GPL at https://github.com/BenoitMorel/GeneRax and on BioConda.}, }
@article {pmid35019771, year = {2022}, author = {Li, Y and Huang, Y}, title = {Distribution and Evolutionary History of Sialic Acid Catabolism in the Phylum Actinobacteria.}, journal = {Microbiology spectrum}, volume = {10}, number = {1}, pages = {e0238021}, pmid = {35019771}, issn = {2165-0497}, mesh = {Actinobacteria/classification/*genetics/isolation &amp; purification/*metabolism ; Animals ; Bacterial Proteins/genetics/metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; Multigene Family ; N-Acetylneuraminic Acid/*metabolism ; Phylogeny ; }, abstract = {Sialic acids are present in humans and other metazoans, playing essential roles in physiological and pathological processes. Commensal and pathogenic bacteria have evolved the capacity to utilize sialic acids as nutrient and energy sources. However, in some actinobacteria, sialic acid catabolism (SAC) is associated with free-living populations. To unravel the distribution and evolutionary history of SAC in the phylum Actinobacteria, we analyzed the presence and diversity of the putative SAC gene cluster (nan) in 7,180 high-quality, nonredundant actinobacterial genomes that covered 1,969 species. The results showed that ∼13% of actinobacterial species had the potential to utilize sialic acids, with 45 species capable of anhydro-SAC, all except two of them through the canonical pathway. These species belonged to 20 orders and 81 genera, with ∼36% of them from four genera, Actinomyces, Bifidobacterium, Corynebacterium, and Streptomyces. Moreover, ∼40% of the nan-positive species are free living. Phylogenetic analysis of the key nan genes, nanA, nanK, and nanE, revealed a strong signal of horizontal gene transfer (HGT), accompanied with vertical inheritance and gene loss. This evolutionary pattern led to high diversity and differential distribution of nan among actinobacterial taxa and might cause the cluster to spread to some free-living species while losing in some host-associated species. The evolution of SAC in actinobacteria probably represents the evolution of certain kinds of noncore bacterial functions for environmental adaptation and lifestyle switch, in which HGT plays a dominant role. IMPORTANCE Sialic acids play essential roles in the physiology of humans and other metazoan animals, and microbial sialic acid catabolism (SAC) is one of the processes critical for pathogenesis. To date, microbial SAC is studied mainly in commensals and pathogens, while its distribution in free-living microbes and evolutionary pathway remain largely unexplored. Here, by examining all actinobacterial genomes available, we demonstrate that putative SAC is present in a small proportion of actinobacterial species, of which, however, ∼40% are free-living species. We also reveal remarkable difference in the distribution of SAC among actinobacterial taxa and high diversity of the putative SAC gene clusters. HGT plays a significant role in the evolution of SAC, accompanied with vertical inheritance and gene loss. Our results provide a comprehensive and systematic picture of the distribution and evolutionary history of SAC in actinobacteria, expanding the current knowledge on bacterial adaptation and diversification.}, }
@article {pmid35019703, year = {2022}, author = {Yu, R and Xu, Y and Schwarz, S and Shang, Y and Yuan, X and Zhang, Y and Li, D and Du, XD}, title = {erm(T)-Mediated Macrolide-Lincosamide Resistance in Streptococcus suis.}, journal = {Microbiology spectrum}, volume = {10}, number = {1}, pages = {e0165721}, pmid = {35019703}, issn = {2165-0497}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics/*metabolism ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Humans ; Lincosamides/*pharmacology ; Macrolides/*pharmacology ; Microbial Sensitivity Tests ; Staphylococcus aureus/genetics ; Streptococcal Infections/microbiology ; Streptococcus pneumoniae/genetics ; Streptococcus suis/drug effects/genetics/*metabolism ; }, abstract = {To investigate the presence and location of erm(T) in clinical Streptococcus suis isolates and explore the transmission ability and fitness cost of erm(T)-carrying mobile genetic elements among S. suis isolates, MICs were determined by broth microdilution. The presence of erm(T) in S. suis was detected by PCR. The genetic environment of erm(T) in S. suis was explored by whole-genome sequencing (WGS) analysis. Intraspecies and interspecies transmission were examined by electrotransformation. The fitness cost associated with the carriage of an erm(T)-harboring plasmid or an integrative and conjugative element (ICE) was examined by competition experiments. Of 237 nonduplicate strains, erm(T) was detected in 2 S. suis strains (SC262-ST954 and SC117-ST1314), with its location on a 5,125-bp plasmid in S. suis SC262 and on a 64,013-bp ICESsuSC117 in S. suis SC117, respectively. Both the erm(T)-carrying plasmid pSC262 and the ICESsuSC117 were transmissible by transformation. Plasmid pSC262 can replicate and express macrolide-lincosamide resistance in heterologous hosts, including S. aureus and S. pneumoniae. Both the erm(T)-carrying plasmid and the ICE posed a fitness cost to the host S. suis isolate. To the best of our knowledge, this is the first report of the macrolide-lincosamide-streptogramin B resistance gene erm(T) in S. suis. Its location on a plasmid or an ICE will aid in its transmission. The low detection rate of erm(T) gene among the S. suis population might be due to the fitness cost of the erm(T)-carrying plasmid and ICE. IMPORTANCE Macrolide and lincosamide resistance due to the presence of erm(T) have posed a challenge for the treatment of Gram-positive pathogens. Although the low detection rate of erm(T) gene among the S. suis population due to the fitness cost of the erm(T)-carrying plasmid and ICE, the presence of erm(T) in S. suis and its potential transmission to other Gram-positive pathogens will be of important significance.}, }
@article {pmid35018289, year = {2021}, author = {Mola, I and Onibokun, A and Oranusi, S}, title = {Prevalence of multi-drug resistant bacteria associated with foods and drinks in Nigeria (2015-2020): A systematic review.}, journal = {Italian journal of food safety}, volume = {10}, number = {4}, pages = {9417}, pmid = {35018289}, issn = {2239-7132}, abstract = {Foods are essential vehicles in human exposure to antibiotic resistant bacteria which serve as reservoirs for resistance genes and a rising food safety concern. Antimicrobial resistance, including multidrug resistance (MDR), is an increasing problem globally and poses a serious concern to human health. This study was designed to synthesize data regarding the prevalence of MDR bacteria associated with foods and drinks sold within Nigeria in order to contribute to the existing findings in this area. A comprehensive literature search on the prevalence of multi-drug resistant bacteria associated with foods and drinks in Nigeria from 2015 to 2020 was conducted using three databases; PubMed, Science Direct and Scopus. After screening and selection, 26 out of 82 articles were used for the qualitative data synthesis. Of the total of one thousand three hundred and twenty-six MDR bacteria reportedly isolated in all twenty-six articles, the highest prevalence (660) was observed in drinks, including water, while the lowest (20) was observed in the article which combined results for both protein and vegetable-based foods. Escherichia sp. had the most frequency of occurrence, appearing as MDR bacteria in ten out of the twenty-six articles. Salmonella sp. appeared as MDR in seven out of the twenty-six articles included in this study, in all seven articles where it was reported, it had the highest percentage (85.4%) prevalence as MDR bacteria. Public health personnel need to ensure critical control during the production and handling of foods and drinks, as well as create more awareness on proper hygienic practices to combat the spread of MDR bacteria becoming a growing food safety issue (Zurfluh et al., 2019; Mesbah et al., 2017; Campos et al., 2019). Foods can be contaminated by different means, including exposure to irrigation water, manure, feces or soil with pathogenic bacteria. Foods can also become contaminated as they are harvested, handled after harvest or during processing if food safety standards are not correctly applied (Meshbah et al., 2017). Food-borne diseases caused by resistant organisms are one of the most important public health problems as they contribute to the risk of development of antibiotic resistance in the food production chain (Hehempour-Baltork et al., 2019). Apart from pathogenic bacteria causing foodborne diseases, foods that are raw or not processed following standard procedures can introduce several antibiotic-resistant bacteria (ARB) to consumers (Gekemidis et al., 2018). Antibiotic resistance, though harbored in non-pathogenic bacteria, can potentially be spread through horizontal gene transfer to other species including opportunistic pathogens that are present in the environment or after consumption of ARB-contaminated foods. When ARB-contaminated foods are consumed, the spread of antibiotic resistant genes may affect the gut microbiome thereby contributing to the pool of antibiotic-resistance genes (ARG) in the human gut (Gekemidis et al, 2018). MDR bacteria have been defined as bacteria that are resistant to at least one antimicrobial agent present in three or more antimicrobial classes (Sweeny et al., 2018). There has been an increase in drug resistance in pathogens isolated from food for human consumption with species of Escherichia coli and Salmonella enterica being considered among the most important pathogens due to their ability to effect zoonotic transfer of resistant genes (Canton et al., 2018; Maneilla-Becerra et al., 2019). However, other pathogens, such as Vibrio spp., some species of Aeromonas, spores of Clostridium botulinum type F, and Campylobacter, have been linked to food-borne diseases in humans who have consumed seafood or other animal foods (Maneilla-Becerra et al., 2019). Some other resistant bacteria associated with foods include Staphylococcus aureus, Listeria spp., and Shigella spp. (Maneilla-Becerra et al., 2019) This study was therefore designed to synthesize data (2015-2020) regarding the prevalence of MDR bacteria associated with foods and drinks sold within Nigeria in order to contribute to the existing findings in this area.}, }
@article {pmid35016024, year = {2022}, author = {Cáliz, J and Subirats, J and Triadó-Margarit, X and Borrego, CM and Casamayor, EO}, title = {Global dispersal and potential sources of antibiotic resistance genes in atmospheric remote depositions.}, journal = {Environment international}, volume = {160}, number = {}, pages = {107077}, doi = {10.1016/j.envint.2022.107077}, pmid = {35016024}, issn = {1873-6750}, mesh = {*Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Antibiotic resistance has become a major Global Health concern and a better understanding on the global spread mechanisms of antibiotic resistant bacteria (ARB) and intercontinental ARB exchange is needed. We measured atmospheric depositions of antibiotic resistance genes (ARGs) by quantitative (q)PCR in rain/snow collected fortnightly along 4 y. at a remote high mountain LTER (Long-Term Ecological Research) site located above the atmospheric boundary layer (free troposphere). Bacterial composition was characterized by 16S rRNA gene sequencing, and air mass provenances were determined by modelled back trajectories and rain/snow chemical composition. We hypothesize that the free troposphere may act as permanent reservoir and vector for ARB and ARGs global dispersal. We aimed to i) determine whether ARGs are long-range intercontinental and persistently dispersed through aerosols, ii) assess ARGs long-term atmospheric deposition dynamics in a remote high mountain area, and iii) unveil potential diffuse ARGs pollution sources. We showed that the ARGs sul1 (resistance to sulfonamides), tetO (resistance to tetracyclines), and intI1 (a proxy for horizontal gene transfer and anthropogenic pollution) were long-range and persistently dispersed in free troposphere aerosols. Major depositions of tetracyclines resistance matched with intensification of African dust outbreaks. Potential ARB mostly traced their origin back into agricultural soils. Our study unveils that air masses pathways are shaping ARGs intercontinental dispersal and global spread of antibiotic resistances, with potential predictability for interannual variability and remote deposition rates. Because climate regulates aerosolization and long-range air masses movement patterns, we call for a more careful evaluation of the connections between land use, climate change and ARB long-range intercontinental dispersal.}, }
@article {pmid35014098, year = {2022}, author = {Olesen, AK and Pinilla-Redondo, R and Hansen, MF and Russel, J and Dechesne, A and Smets, BF and Madsen, JS and Nesme, J and Sørensen, SJ}, title = {IncHI1A plasmids potentially facilitate horizontal flow of antibiotic resistance genes to pathogens in microbial communities of urban residential sewage.}, journal = {Molecular ecology}, volume = {31}, number = {5}, pages = {1595-1608}, doi = {10.1111/mec.16346}, pmid = {35014098}, issn = {1365-294X}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal/genetics ; *Microbiota ; Plasmids/genetics ; *Sewage/microbiology ; }, abstract = {Horizontal gene transfer via plasmids is important for the dissemination of antibiotic resistance genes among medically relevant pathogens. Specifically, the transfer of IncHI1A plasmids is believed to facilitate the spread of antibiotic resistance genes, such as carbapenemases, within the clinically important family Enterobacteriaceae. The microbial community of urban wastewater treatment plants has been shown to be highly permissive towards conjugal transfer of IncP1 plasmids. Here, we tracked the transfer of the P1 plasmid pB10 and the clinically relevant HI1A plasmid R27 in the microbial communities present in urban residential sewage entering full-scale wastewater treatment plants. We found that both plasmids readily transferred to these communities and that strains in the sewage were able to further disseminate them. Furthermore, R27 has a broad potential host range, but a low host divergence. Interestingly, although the majority of R27 transfer events were to members of Enterobacteriaceae, we found a subset of transfer events to other families, even other phyla. This indicates that HI1A plasmids facilitate horizontal gene transfer both within Enterobacteriaceae, but also across families of, in particular, Gammaproteobacteria, such as Moraxellaceae, Pseudomonadaceae and Shewanellaceae. pB10 displayed a similar potential host range to R27. In contrast to R27, pB10 had a high host divergence. By culture enrichment of the transconjugant communities, we show that sewage strains of Enterobacteriaceae and Aeromonadaceae can stably maintain R27 and pB10, respectively. Our results suggest that dissemination in the urban residual water system of HI1A plasmids may result in an accelerated acquisition of antibiotic resistance genes among pathogens.}, }
@article {pmid35012680, year = {2022}, author = {Shen, Z and Tang, CM and Liu, GY}, title = {Towards a better understanding of antimicrobial resistance dissemination: what can be learnt from studying model conjugative plasmids?.}, journal = {Military Medical Research}, volume = {9}, number = {1}, pages = {3}, pmid = {35012680}, issn = {2054-9369}, support = {102908/Z/13/Z/WT_/Wellcome Trust/United Kingdom ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Anti-Bacterial Agents/pharmacology ; *Conjugation, Genetic/genetics ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal/genetics ; Humans ; Plasmids/genetics ; }, abstract = {Bacteria can evolve rapidly by acquiring new traits such as virulence, metabolic properties, and most importantly, antimicrobial resistance, through horizontal gene transfer (HGT). Multidrug resistance in bacteria, especially in Gram-negative organisms, has become a global public health threat often through the spread of mobile genetic elements. Conjugation represents a major form of HGT and involves the transfer of DNA from a donor bacterium to a recipient by direct contact. Conjugative plasmids, a major vehicle for the dissemination of antimicrobial resistance, are selfish elements capable of mediating their own transmission through conjugation. To spread to and survive in a new bacterial host, conjugative plasmids have evolved mechanisms to circumvent both host defense systems and compete with co-resident plasmids. Such mechanisms have mostly been studied in model plasmids such as the F plasmid, rather than in conjugative plasmids that confer antimicrobial resistance (AMR) in important human pathogens. A better understanding of these mechanisms is crucial for predicting the flow of antimicrobial resistance-conferring conjugative plasmids among bacterial populations and guiding the rational design of strategies to halt the spread of antimicrobial resistance. Here, we review mechanisms employed by conjugative plasmids that promote their transmission and establishment in Gram-negative bacteria, by following the life cycle of conjugative plasmids.}, }
@article {pmid35012352, year = {2022}, author = {Lanois-Nouri, A and Pantel, L and Fu, J and Houard, J and Ogier, JC and Polikanov, YS and Racine, E and Wang, H and Gaudriault, S and Givaudan, A and Gualtieri, M}, title = {The Odilorhabdin Antibiotic Biosynthetic Cluster and Acetyltransferase Self-Resistance Locus Are Niche and Species Specific.}, journal = {mBio}, volume = {13}, number = {1}, pages = {e0282621}, pmid = {35012352}, issn = {2150-7511}, mesh = {Animals ; Humans ; Phylogeny ; Acetyltransferases/genetics ; Chromatography, Liquid ; Tandem Mass Spectrometry ; Bacteria/metabolism ; *Nematoda/microbiology ; *Xenorhabdus/genetics ; *Anti-Infective Agents/metabolism ; Anti-Bacterial Agents/metabolism ; }, abstract = {Antibiotic resistance is an increasing threat to human health. A direct link has been established between antimicrobial self-resistance determinants of antibiotic producers, environmental bacteria, and clinical pathogens. Natural odilorhabdins (ODLs) constitute a new family of 10-mer linear cationic peptide antibiotics inhibiting bacterial translation by binding to the 30S subunit of the ribosome. These bioactive secondary metabolites are produced by entomopathogenic bacterial symbiont Xenorhabdus (Morganellaceae), vectored by the soil-dwelling nematodes. ODL-producing Xenorhabdus nematophila symbionts have mechanisms of self-protection. In this study, we cloned the 44.5-kb odl biosynthetic gene cluster (odl-BGC) of the symbiont by recombineering and showed that the N-acetyltransferase-encoding gene, oatA, is responsible for ODL resistance. In vitro acetylation and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses showed that OatA targeted the side chain amino group of ODL rare amino acids, leading to a loss of translation inhibition and antibacterial properties. Functional, genomic, and phylogenetic analyses of oatA revealed an exclusive cis-link to the odilorhabdin BGC, found only in X. nematophila and a specific phylogenetic clade of Photorhabdus. This work highlights the coevolution of antibiotic production and self-resistance as ancient features of this unique tripartite complex of host-vector-symbiont interactions without odl-BGC dissemination by lateral gene transfer. IMPORTANCE Odilorhabdins (ODLs) constitute a novel antibiotic family with promising properties for treating problematic multidrug-resistant Gram-negative bacterial infections. ODLs are 10-mer linear cationic peptides inhibiting bacterial translation by binding to the small subunit of the ribosome. These natural peptides are produced by Xenorhabdus nematophila, a bacterial symbiont of entomopathogenic nematodes well known to produce large amounts of specialized secondary metabolites. Like other antimicrobial producers, ODL-producing Xenorhabdus nematophila has mechanisms of self-protection. In this study, we cloned the ODL-biosynthetic gene cluster of the symbiont by recombineering and showed that the N-acetyltransferase-encoding gene, oatA, is responsible for ODL resistance. In vitro acetylation and LC-MS/MS analyses showed that OatA targeted the side chain amino group of ODL rare amino acids, leading to a loss of translation inhibition and antibacterial properties. Functional, genomic, and phylogenetic analyses of oatA revealed the coevolution of antibiotic production and self-resistance as ancient feature of this particular niche in soil invertebrates without resistance dissemination.}, }
@article {pmid35012344, year = {2022}, author = {Gómez-Garzón, C and Barrick, JE and Payne, SM}, title = {Disentangling the Evolutionary History of Feo, the Major Ferrous Iron Transport System in Bacteria.}, journal = {mBio}, volume = {13}, number = {1}, pages = {e0351221}, pmid = {35012344}, issn = {2150-7511}, support = {R01 AI091957/AI/NIAID NIH HHS/United States ; }, mesh = {*Bacterial Proteins/metabolism ; *Nucleoside-Triphosphatase/metabolism ; Bacteria/metabolism ; Membrane Transport Proteins/metabolism ; Iron/metabolism ; }, abstract = {Iron acquisition is essential for almost all living organisms. In certain environments, ferrous iron is the most prevalent form of this element. Feo is the most widespread system for ferrous iron uptake in bacteria and is critical for virulence in some species. The canonical architecture of Feo consists of a large transmembrane nucleoside triphosphatase (NTPase) protein, FeoB, and two accessory cytoplasmic proteins, FeoA and FeoC. The role of the latter components and the mechanism by which Feo orchestrates iron transport are unclear. In this study, we conducted a comparative analysis of Feo protein sequences to gain insight into the evolutionary history of this transporter. We identified instances of how horizontal gene transfer contributed to the evolution of Feo. Also, we found that FeoC, while absent in most lineages, is largely present in the Gammaproteobacteria group, although its sequence is poorly conserved. We propose that FeoC, which may couple FeoB NTPase activity with pore opening, was an ancestral element that has been dispensed with through mutations in FeoA and FeoB in some lineages. We provide experimental evidence supporting this hypothesis by isolating and characterizing FeoC-independent mutants of the Vibrio cholerae Feo system. Also, we confirmed that the closely related species Shewanella oneidensis does not require FeoC; thus, Vibrio FeoC sequences may resemble transitional forms on an evolutionary pathway toward FeoC-independent transporters. Finally, by combining data from our bioinformatic analyses with this experimental evidence, we propose an evolutionary model for the Feo system in bacteria. IMPORTANCE Feo, a ferrous iron transport system composed of three proteins (FeoA, -B, and -C), is the most prevalent bacterial iron transporter. It plays an important role in iron acquisition in low-oxygen environments and some host-pathogen interactions. The large transmembrane protein FeoB provides the channel for the transport of iron into the bacterial cell, but the functions of the two small, required accessory proteins FeoA and FeoC are not well understood. Analysis of the evolution of this transporter shows that FeoC is poorly conserved and has been lost from many bacterial lineages. Experimental evidence indicates that FeoC may have different functions in different species that retain this protein, and the loss of FeoC is promoted by mutations in FeoA or by the fusion of FeoA and FeoB.}, }
@article {pmid35010733, year = {2022}, author = {Cepec, E and Trček, J}, title = {Antimicrobial Resistance of Acetobacter and Komagataeibacter Species Originating from Vinegars.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {1}, pages = {}, pmid = {35010733}, issn = {1660-4601}, mesh = {Acetic Acid ; *Acetobacter ; Anti-Bacterial Agents/pharmacology ; Bacteria ; Drug Resistance, Bacterial/genetics ; Humans ; Microbial Sensitivity Tests ; }, abstract = {Consumers' preference towards healthy and novel foods dictates the production of organic unfiltered bottled vinegar that still contains acetic acid bacteria. After ingesting vinegar, the bacteria come into close contact with the human microbiota, creating the possibility of horizontal gene transfer, including genetic determinants for antibiotic resistance. Due to the global spread of antimicrobial resistance (AMR), we analyzed the AMR of Acetobacter and Komagataeibacter species originating mainly from vinegars. Six antibiotics from different structural groups and mechanisms of action were selected for testing. The AMR was assessed with the disk diffusion method using various growth media. Although the number of resistant strains differed among the growth media, 97.4%, 74.4%, 56.4%, and 33.3% of strains were resistant to trimethoprim, erythromycin, ciprofloxacin, and chloramphenicol, respectively, on all three media. Moreover, 17.9% and 53.8% of all strains were resistant to four and three antibiotics of different antimicrobial classes, respectively. We then looked for antimicrobial resistance genes in the genome sequences of the reference strains. The most common genetic determinant potentially involved in AMR encodes an efflux pump. Since these genes pass through the gastrointestinal tract and may be transferred to human microbiota, further experiments are needed to analyze the probability of this scenario in more detail.}, }
@article {pmid35008986, year = {2022}, author = {Wu, Y and Luo, D and Fang, L and Zhou, Q and Liu, W and Liu, Z}, title = {Bidirectional lncRNA Transfer between Cuscuta Parasites and Their Host Plant.}, journal = {International journal of molecular sciences}, volume = {23}, number = {1}, pages = {}, pmid = {35008986}, issn = {1422-0067}, support = {32071862//National Natural Science Foundation of China/ ; 31722055//National Natural Science Foundation of China/ ; 19ZD2NA002//Major science and Technology Project of Gansu Province/ ; }, mesh = {Animals ; Computational Biology/methods ; Cuscuta/*genetics/*parasitology ; Gene Expression Profiling ; Gene Ontology ; *Gene Transfer, Horizontal ; High-Throughput Nucleotide Sequencing ; *Host-Parasite Interactions ; Parasites/genetics ; RNA Interference ; *RNA, Long Noncoding ; Glycine max/genetics/parasitology ; Transcriptome ; }, abstract = {Dodder species (Cuscuta spp.) are holoparasites that have extensive material exchange with their host plants through vascular connections. Recent studies on cross-species transfer have provided breakthrough insights, but little is known about the interaction mechanisms of the inter-plant mobile substances in parasitic systems. We sequenced the transcriptomes of dodder growing on soybean hosts to characterize the long non-coding RNA (lncRNA) transfer between the two species, and found that lncRNAs can move in high numbers (365 dodder lncRNAs and 14 soybean lncRNAs) in a bidirectional manner. Reverse transcription-polymerase chain reaction further confirmed that individual lncRNAs were trafficked in the dodder-soybean parasitic system. To reveal the potential functions of mobile transcripts, the Gene Ontology terms of mobile lncRNA target genes were predicted, and mobile dodder target genes were found to be mainly enriched in "metabolic process", "catalytic activity", "signaling", and "response to stimulus" categories, whereas mobile soybean target genes were enriched in organelle-related categories, indicating that specific mobile lncRNAs may be important in regulating dodder parasitism. Our findings reveal that lncRNAs are transferred between dodder and its host soybean plants, which may act as critical regulators to coordinate the host-dodder interaction at the whole parasitic level.}, }
@article {pmid35007603, year = {2022}, author = {An, XL and Abass, OK and Zhao, CX and Xu, MR and Pan, T and Pu, Q and Liao, H and Li, H and Zhu, YG and Su, JQ}, title = {Nanopore sequencing analysis of integron gene cassettes in sewages and soils.}, journal = {The Science of the total environment}, volume = {817}, number = {}, pages = {152766}, doi = {10.1016/j.scitotenv.2021.152766}, pmid = {35007603}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Integrons/genetics ; *Nanopore Sequencing ; Sewage ; Soil ; }, abstract = {Integrons are genetic elements that can facilitate rapid spread of antibiotic resistance by insertion and removal of genes. However, knowledge about the diversity and distribution of gene cassettes embedded in class 1 integron is still limited. In this study, we sequenced integron gene cassettes using nanopore sequencing and quantified antibiotic resistance genes (ARGs) and integrase genes in the manured soils and sewages of a bioreactor. The results showed that class 1 integron integrase genes were the most abundant in soils and sewages compared with class 2 and class 3 integrase genes. Long-term manure application exacerbated the enrichment of total ARGs, integrase genes and antibiotic resistance-associated gene cassettes, while antibiotics and heavy metals showed no impact on the overall resistome profile. Sewage treatment could efficiently remove the absolute abundance of integrase genes (~3 orders of magnitude, copies/L) and antibiotic resistance gene cassettes. The resistance gene cassettes mainly carried the ARGs conferring resistance to aminoglycoside and beta-lactams in soils and sewages, some of which were persistent during the sewage treatment. This study underlined that soil and sewage were potential reservoirs for integron-mediated ARGs transfer, indicating that anthropogenic activity played a vital role in the prevalence and diversity of resistance gene cassettes in integrons.}, }
@article {pmid35003274, year = {2021}, author = {Stasiak, M and Maćkiw, E and Kowalska, J and Kucharek, K and Postupolski, J}, title = {Silent Genes: Antimicrobial Resistance and Antibiotic Production.}, journal = {Polish journal of microbiology}, volume = {70}, number = {4}, pages = {421-429}, pmid = {35003274}, issn = {2544-4646}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; }, abstract = {Silent genes are DNA sequences that are generally not expressed or expressed at a very low level. These genes become active as a result of mutation, recombination, or insertion. Silent genes can also be activated in laboratory conditions using pleiotropic, targeted genome-wide, or biosynthetic gene cluster approaches. Like every other gene, silent genes can spread through horizontal gene transfer. Most studies have focused on strains with phenotypic resistance, which is the most common subject. However, to fully understand the mechanism behind the spreading of antibiotic resistance, it is reasonable to study the whole resistome, including silent genes.}, }
@article {pmid35003006, year = {2021}, author = {Cortés-Albayay, C and Sangal, V and Klenk, HP and Nouioui, I}, title = {Comparative Genomic Study of Vinyl Chloride Cluster and Description of Novel Species, Mycolicibacterium vinylchloridicum sp. nov.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {767895}, pmid = {35003006}, issn = {1664-302X}, abstract = {Advanced physicochemical and chemical absorption methods for chlorinated ethenes are feasible but incur high costs and leave traces of pollutants on the site. Biodegradation of such pollutants by anaerobic or aerobic bacteria is emerging as a potential alternative. Several mycobacteria including Mycolicibacterium aurum L1, Mycolicibacterium chubuense NBB4, Mycolicibacterium rhodesiae JS60, Mycolicibacterium rhodesiae NBB3 and Mycolicibacterium smegmatis JS623 have previously been described as assimilators of vinyl chloride (VC). In this study, we compared nucleotide sequence of VC cluster and performed a taxogenomic evaluation of these mycobacterial species. The results showed that the complete VC cluster was acquired by horizontal gene transfer and not intrinsic to the genus Mycobacterium sensu lato. These results also revealed the presence of an additional xcbF1 gene that seems to be involved in Coenzyme M biosynthesis, which is ultimately used in the VC degradation pathway. Furthermore, we suggest for the first time that S/N-Oxide reductase encoding gene was involved in the dissociation of the SsuABC transporters from the organosulfur, which play a crucial role in the Coenzyme M biosynthesis. Based on genomic data, M. aurum L1, M. chubuense NBB4, M. rhodesiae JS60, M. rhodesiae NBB3 and M. smegmatis JS623 were misclassified and form a novel species within the genus Mycobacterium sensu lato. Mycolicibacterium aurum L1[T] (CECT 8761[T] = DSM 6695[T]) was the subject of polyphasic taxonomic studies and showed ANI and dDDH values of 84.7 and 28.5% with its close phylogenetic neighbour, M. sphagni ATCC 33027[T]. Phenotypic, chemotaxonomic and genomic data considering strain L1[T] (CECT 8761[T] = DSM 6695[T]) as a type strain of novel species with the proposed name, Mycolicibacterium vinylchloridicum sp. nov.}, }
@article {pmid34998773, year = {2022}, author = {Li, D and Gao, J and Dai, H and Wang, Z and Cui, Y and Zhao, Y and Zhou, Z}, title = {Triclosan enriched resistance genes more easily than copper in the presence of environmental tetracycline in aerobic granular sludge system.}, journal = {The Science of the total environment}, volume = {815}, number = {}, pages = {152871}, doi = {10.1016/j.scitotenv.2021.152871}, pmid = {34998773}, issn = {1879-1026}, mesh = {Copper/toxicity ; RNA, Ribosomal, 16S ; *Sewage ; Tetracycline ; *Triclosan/toxicity ; Wastewater ; }, abstract = {Triclosan (TCS) and copper (Cu[2+]) were exposed to aerobic granular sludge (AGS) system treating wastewater containing environmental tetracycline, respectively, to explore the different biochemical responses, more importantly, the fates of resistance genes (RGs) in AGS system. The results showed that TCS and Cu[2+] could significantly inhibit the N and P removal in AGS system by reducing several key functional genes, including amoA gene of ammonia-oxidizing bacteria, Nitrospira and phosphorus accumulating organisms 16S rRNA genes. TCS caused higher degree of RGs' enrichment than Cu[2+], which made the average total relative abundance of RGs of 1.38 ± 0.73 and 0.78 ± 0.24 in TCS and Cu system, respectively. Cu[2+] could induce a wider range of horizontal gene transfer than TCS, leading to the detections of more potential hosts harboring RGs in Cu system. Cu system seemed to have stronger repair, immunity and defense ability than TCS system, which enabled it to have sufficient ability to trigger protection mechanism to realize self-protection, eventually the RGs also were controlled. Integron (intI1 and intI3) and plasmids (trb-C and IncQ) might cooperate with microorganisms and water quality parameters to enhance the enrichment of RGs in TCS system, however this interaction among various environmental factors was not obvious in Cu system, which might be responsible for the lower abundance of RGs. The increasing levels of TCS and Cu[2+] in wastewater should be paid more attentions during the treatment of wastewater containing environmental tetracycline by AGS system. Especially for TCS, it had the ability to enrich RGs more easily than Cu[2+], which should be prevented from entering wastewater treatment plants as far as possible, to avoid more serious proliferation and dissemination of various RGs.}, }
@article {pmid34996446, year = {2022}, author = {Kim, D and Lee, J and Cho, CH and Kim, EJ and Bhattacharya, D and Yoon, HS}, title = {Group II intron and repeat-rich red algal mitochondrial genomes demonstrate the dynamic recent history of autocatalytic RNAs.}, journal = {BMC biology}, volume = {20}, number = {1}, pages = {2}, pmid = {34996446}, issn = {1741-7007}, support = {80NSSC19K0462/ImNASA/Intramural NASA/United States ; }, mesh = {Evolution, Molecular ; *Genome, Mitochondrial ; Humans ; Introns/genetics ; Phylogeny ; Plastids/genetics ; *Rhodophyta/genetics ; }, abstract = {BACKGROUND: Group II introns are mobile genetic elements that can insert at specific target sequences, however, their origins are often challenging to reconstruct because of rapid sequence decay following invasion and spread into different sites. To advance understanding of group II intron spread, we studied the intron-rich mitochondrial genome (mitogenome) in the unicellular red alga, Porphyridium.<br><br>RESULTS: Analysis of mitogenomes in three closely related species in this genus revealed they were 3-6-fold larger in size (56-132 kbp) than in other red algae, that have genomes of size 21-43 kbp. This discrepancy is explained by two factors, group II intron invasion and expansion of repeated sequences in large intergenic regions. Phylogenetic analysis demonstrates that many mitogenome group II intron families are specific to Porphyridium, whereas others are closely related to sequences in fungi and in the red alga-derived plastids of stramenopiles. Network analysis of intron-encoded proteins (IEPs) shows a clear link between plastid and mitochondrial IEPs in distantly related species, with both groups associated with prokaryotic sequences.<br><br>CONCLUSION: Our analysis of group II introns in Porphyridium mitogenomes demonstrates the dynamic nature of group II intron evolution, strongly supports the lateral movement of group II introns among diverse eukaryotes, and reveals their ability to proliferate, once integrated in mitochondrial DNA.}, }
@article {pmid34993479, year = {2022}, author = {Hashimoto, Y and Hisatsune, J and Suzuki, M and Kurushima, J and Nomura, T and Hirakawa, H and Kojima, N and Ono, Y and Hasegawa, Y and Tanimoto, K and Sugai, M and Tomita, H}, title = {Elucidation of host diversity of the VanD-carrying genomic islands in enterococci and anaerobes.}, journal = {JAC-antimicrobial resistance}, volume = {4}, number = {1}, pages = {dlab189}, pmid = {34993479}, issn = {2632-1823}, abstract = {BACKGROUND: VanD is a rare type of vancomycin resistance worldwide. However, the host diversity of the vanD gene cluster and the structural similarity of their genomic islands are not well understood.<br><br>METHODS: Three VanD-type Enterococcus faecium strains (AA620, AA622 and AA624) isolated from a Japanese patient who underwent vancomycin treatment in 2017 were analysed. This study utilized WGS analysis to characterize the three VanD-type E. faecium strains and describes the diversity of hosts possessing VanD-carrying genomic islands.<br><br>RESULTS: The three isolates exhibited variable MICs of vancomycin. In the relatively vancomycin-resistant AA620, mutations were identified in vanSD and ddl. The strains AA622 and AA624 had intact ddl and harboured two vanD gene clusters. qRT-PCR results revealed the ddl mutation to be a factor affecting the high vancomycin resistance range of AA620. WGS data showed the 155 kb and 185 kb genomic islands harbouring the vanD gene cluster inserted in the coding region of the lysS gene, located in the chromosome in AA620 and AA622/624, respectively. Comparing the VanD-carrying genomic islands to available sequences of other enterococci and enteric anaerobes revealed how the genomic islands of these organisms isolated worldwide shared similar core genes and backbones. These anaerobes belonged to various genera within the order Eubacteriales. The phylogenetic cluster of the genomic island core genome alignment did not correlate with the host-species lineage, indicating horizontal gene transfer in the gut microbiota.<br><br>CONCLUSIONS: By horizontal gene transfer, various bacteria forming the gut microbiota maintain VanD-carrying genomic islands.}, }
@article {pmid34992589, year = {2021}, author = {Fayad, N and Koné, KM and Gillis, A and Mahillon, J}, title = {Bacillus cytotoxicus Genomics: Chromosomal Diversity and Plasmidome Versatility.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {789929}, pmid = {34992589}, issn = {1664-302X}, abstract = {Bacillus cytotoxicus is the thermotolerant representative of the Bacillus cereus group. This group, also known as B. cereus sensu lato, comprises both beneficial and pathogenic members and includes psychrotolerant and thermotolerant species. Bacillus cytotoxicus was originally recovered from a fatal outbreak in France in 1998. This species forms a remote cluster from the B. cereus group members and reliably contains the cytk-1 gene, coding for a cytotoxic variant of cytotoxin K. Although this species was originally thought to be homogenous, intra-species diversity has been recently described with four clades, six random amplified polymorphic DNA (RAPD) patterns, and 11 plasmids profiles. This study aimed to get new insights into the genomic diversity of B. cytotoxicus and to decipher the underlying chromosomal and plasmidial variations among six representative isolates through whole genome sequencing (WGS). Among the six sequenced strains, four fitted the previously described genomic clades A and D, while the remaining two constituted new distinct branches. As for the plasmid content of these strains, three large plasmids were putatively conjugative and three small ones potentially mobilizable, harboring coding genes for putative leaderless bacteriocins. Mobile genetic elements, such as prophages, Insertion Sequences (IS), and Bacillus cereus repeats (bcr) greatly contributed to the B. cytotoxicus diversity. As for IS elements and bcr, IS3 and bcr1 were the most abundant elements and, along with the group II intron B.c.I8, were found in all analyzed B. cytotoxicus strains. When compared to other B. cytotoxicus strains, the type-strain NVH 391-98 displayed a relatively low number of IS. Our results shed new light on the contribution of mobile genetic elements to the genome plasticity of B. cytotoxicus and their potential role in horizontal gene transfer.}, }
@article {pmid34992389, year = {2021}, author = {Doub, JB}, title = {Risk of Bacteriophage Therapeutics to Transfer Genetic Material and Contain Contaminants Beyond Endotoxins with Clinically Relevant Mitigation Strategies.}, journal = {Infection and drug resistance}, volume = {14}, number = {}, pages = {5629-5637}, pmid = {34992389}, issn = {1178-6973}, abstract = {Bacteriophage therapy is a promising adjuvant therapeutic in the treatment of multidrug-resistant infections and chronic biofilm infections. However, there is limited knowledge about how to best utilize these agents in vivo, leading to a wide range of treatment protocols. Moreover, while bacteriophages are similar to antibiotics in their antimicrobial effects, these are active viruses and are very different from conventional antibiotics. One main difference that clinicians should be cognizant about is the potential ability of these therapeutics to horizontally transfer genetic material, and the clinical ramifications of such events. In addition, while bacteriophage therapeutics are readily tested for sterility and endotoxins, clinicians should also be aware of other contaminants, such as exotoxins, pathogenicity islands and prophages, that can contaminate bacteriophage therapeutics, and their clinical ramifications. While the perception may be that these are only theoretical issues, regulatory agencies are starting to recommend their evaluation when using bacteriophage therapy and subsequently these topics are discussed herein, as are ways to test for and mitigate the adverse effects of these issues.}, }
@article {pmid34990722, year = {2022}, author = {Wang, B and Peng, Q and Wang, R and Yu, S and Li, Q and Huang, C}, title = {Efficient Microcystis removal and sulfonamide-resistance gene propagation mitigation by constructed wetlands and functional genes analysis.}, journal = {Chemosphere}, volume = {292}, number = {}, pages = {133481}, doi = {10.1016/j.chemosphere.2021.133481}, pmid = {34990722}, issn = {1879-1298}, mesh = {*Microcystis/genetics ; Sulfanilamide ; Waste Disposal, Fluid ; Wastewater/analysis ; *Water Purification ; Wetlands ; }, abstract = {Increasingly prevalent Microcystis blooms and the propagation of the associated resistance genes represent global environmental problems. Constructed wetlands (CWs) are a cost-effective technology used for wastewater treatment. In this study, the herb Alisma orientale and three industrial byproducts, namely, blast furnace slag, biochar, and sawdust, were selected to construct mini-CW units. Their potential to remediate toxic Microcystis and their influences on the behaviors of antibiotic-resistant genes (ARGs, sul1, sul2, and intl1) were analyzed. Approximately 98.46% of Microcystis cells were removed by the sawdust-based CW in just 2 d, wherein <0.37 μg/L residual microcystin (MC)-LR was detected, with a removal efficiency of >96.47%, which is potentially caused by the higher relative abundance of MC-degrading gene mlrA on the substrate. Lower target ARG accumulations in the sawdust-based CW may be attributed to the lower intl1 relative abundance and microbial function mobile element content, which could influence horizontal gene transfer. In three sequential batches for the treatment of eutrophic lake water, six sawdust-based CW units were assembled into CW microcosms. The efficiency of removal of Microcystis and MC-LR by planted CW microcosms ranged between 92.00% and 95.88% and between 86.48% and 94.82%, respectively; this was significantly (P < 0.05) higher than that by unplanted ones. Less accumulation of target ARGs was also observed in planted CWs. Planting considerably improved nitrogen removal, possibly owing to the enrichment of genes involved in the KEGG nitrogen metabolism pathway in the substrate through metagenomic analysis.}, }
@article {pmid34990667, year = {2022}, author = {Li, W and Li, Y and Zheng, N and Ge, C and Yao, H}, title = {Occurrence and distribution of antibiotics and antibiotic resistance genes in the guts of shrimp from different coastal areas of China.}, journal = {The Science of the total environment}, volume = {815}, number = {}, pages = {152756}, doi = {10.1016/j.scitotenv.2021.152756}, pmid = {34990667}, issn = {1879-1026}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Aquaculture ; China ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Humans ; *Penaeidae ; }, abstract = {With the continuous increase in shrimp (Litopenaeus vannamei) aquaculture production, the widespread use of antibiotics as a means of preventing and treating diseases has adversely affected the environment, animal health and symbiotic microorganisms in gut environments. At the same time, antibiotic resistance genes (ARGs) are widespread in aquaculture and pose a great threat to aquatic organisms and humans. Therefore, in the present study, the occurrence and distribution of 17 antibiotics, ARGs and mobile genetic elements (MGEs) were detected in the guts of shrimp collected from 12 coastal regions of China. The results showed that sulfadiazine, ciprofloxacin and norfloxacin were detectable in the guts of L. vannamei at all sampling sites. Sul1, sul2, floR and intI-1 were also detected in the guts of L. vannamei at all sampling sites. The total relative abundances of ARGs and MGEs were significantly positively correlated according to Pearson correlation analysis. Sulfonamide resistance genes (sul1 and sul2) were significantly positively correlated with intI-1. These results indicated that MGEs could increase the risk of horizontal gene transfer of ARGs in a gut environment. MGEs are the most important factors promoting the spread of ARGs. Correlation analysis showed that sulfadiazine was significantly positively correlated with sul1 and sul2 and that fluoroquinolone antibiotics were significantly positively correlated with floR, indicating that antibiotics could induce the production of ARGs. Network analysis indicated that Iamia and Alkaliphilus species may harbor the most antibiotic resistance genes, and these bacteria were closely related to the proliferation and spread of ARGs in a gut environment. Antibiotic use and the spread of ARGs in mariculture systems may have negative effects on shrimp and human health. The use of antibiotics should be strictly regulated to control contaminants in mariculture systems, including pathogens and ARGs, thereby reducing potential risks to human health.}, }
@article {pmid34990042, year = {2022}, author = {Conwell, M and Dooley, JSG and Naughton, PJ}, title = {Enterococcal biofilm-A nidus for antibiotic resistance transfer?.}, journal = {Journal of applied microbiology}, volume = {132}, number = {5}, pages = {3444-3460}, pmid = {34990042}, issn = {1365-2672}, support = {//Department for the Economy/ ; }, mesh = {Anti-Bacterial Agents/pharmacology ; *Biofilms ; Drug Resistance, Multiple, Bacterial/genetics ; *Enterococcus/genetics ; Gene Transfer, Horizontal ; }, abstract = {Enterococci, which are on the WHO list of priority pathogens, are commonly encountered in hospital acquired infection and are becoming increasing significant due to the development of strains resistant to multiple antibiotics. Enterococci are also important microorganisms in the environment, and their presence is frequently used as an indicator of faecal pollution. Their success is related to their ability to survive within a broad range of habitats and the ease by which they acquire mobile genetic elements, including plasmids, from other bacteria. The enterococci are frequently present within a bacterial biofilm, which provides stability and protection to the bacterial population along with an opportunity for a variety of bacterial interactions. Enterococci can accept extrachromosomal DNA both from within its own species and from other bacterial species, and this is enhanced by the proximity of the donor and recipient strains. It is this exchange of genetic material that makes the role of biofilms such an important aspect of the success of enterococci. There remain many questions regarding the most suitable model systems to study enterococci in biofilms and regarding the transfer of genetic material including antibiotic resistance in these biofilms. This review focuses on some important aspects of biofilm in the context of horizontal gene transfer (HGT) in enterococci.}, }
@article {pmid34986571, year = {2022}, author = {He, K and Xue, B and Yang, X and Wang, S and Li, C and Zhang, X and Zhao, C and Wang, X and Qiu, Z and Shen, Z and Wang, J}, title = {Low-concentration of trichloromethane and dichloroacetonitrile promote the plasmid-mediated horizontal transfer of antibiotic resistance genes.}, journal = {Journal of hazardous materials}, volume = {425}, number = {}, pages = {128030}, doi = {10.1016/j.jhazmat.2021.128030}, pmid = {34986571}, issn = {1873-3336}, mesh = {Acetonitriles ; *Anti-Bacterial Agents/pharmacology ; *Chloroform ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Plasmids/genetics ; }, abstract = {Disinfection by-products (DBPs) are one of the unintended consequences of water disinfection that are commonly detected in various water environments. Although DBPs are known to induce antimicrobial resistance via stimulation of chromosomal mutations, it remains unclear whether low-concentration of DBPs could stimulate the conjugative transfer of antibiotic resistance genes (ARGs). The present study aimed to investigate the effect of two typical DBPs, namely trichloromethane (TCM) and dichloroacetonitrile (DCAN), on the conjugative transfer of RP4 plasmid in Escherichia coli genera. The results of the study demonstrated that exposure to low concentrations of TCM and DCAN significantly stimulated conjugative transfer of ARGs, wherein application of 25 μg/L of TCM and 10 μg/L of DCAN resulted in maximum fold change of ~5.5- and ~6.0-fold, respectively, at 16 h of exposure. Further, assessment of underlying mechanisms revealed the involvement of intracellular reactive oxygen species generation, SOS response, increase in cell membrane permeability, upregulation of expression of genes and proteins related to pilus generation, ATP synthesis, and RP4 gene expression. Our findings provided a better understanding of the hidden biological effects and the ecological risks of DBPs in the water environment, especially concerning their effect on the spread of antibiotic resistance.}, }
@article {pmid34986320, year = {2022}, author = {Hüttener, M and Hergueta, J and Bernabeu, M and Prieto, A and Aznar, S and Merino, S and Tomás, J and Juárez, A}, title = {Roles of Proteins Containing Immunoglobulin-Like Domains in the Conjugation of Bacterial Plasmids.}, journal = {mSphere}, volume = {7}, number = {1}, pages = {e0097821}, pmid = {34986320}, issn = {2379-5042}, mesh = {*Anti-Infective Agents ; Bacteria/genetics ; *Conjugation, Genetic ; Gene Transfer, Horizontal ; Immunoglobulin Domains ; Plasmids/genetics ; }, abstract = {Horizontal transfer of bacterial plasmids generates genetic variability and contributes to the dissemination of the genes that enable bacterial cells to develop antimicrobial resistance (AMR). Several aspects of the conjugative process have long been known, namely, those related to the proteins that participate in the establishment of cell-to-cell contact and to the enzymatic processes associated with the processing of plasmid DNA and its transfer to the recipient cell. In this work, we describe the roles of newly identified proteins that influence the conjugation of several plasmids. Genes encoding high-molecular-weight bacterial proteins that contain one or several immunoglobulin-like domains (Big) are located in the transfer regions of several plasmids that usually harbor AMR determinants. These Big proteins are exported to the external medium and target two extracellular organelles: the flagella and conjugative pili. The plasmid gene-encoded Big proteins facilitate conjugation by reducing cell motility and facilitating cell-to-cell contact by binding both to the flagella and to the conjugative pilus. They use the same export machinery as that used by the conjugative pilus components. In the examples characterized in this paper, these proteins influence conjugation at environmental temperatures (i.e., 25°C). This suggests that they may play relevant roles in the dissemination of plasmids in natural environments. Taking into account that they interact with outer surface organelles, they could be targeted to control the dissemination of different bacterial plasmids carrying AMR determinants. IMPORTANCE Transmission of a plasmid from one bacterial cell to another, in several instances, underlies the dissemination of antimicrobial resistance (AMR) genes. The process requires well-characterized enzymatic machinery that facilitates cell-to-cell contact and the transfer of the plasmid. Our paper identifies novel plasmid gene-encoded high-molecular-weight proteins that contain an immunoglobulin-like domain and are required for plasmid transmission. They are encoded by genes on different groups of plasmids. These proteins are exported outside the cell. They bind to extracellular cell appendages such as the flagella and conjugative pili. Expression of these proteins reduces cell motility and increases the ability of the bacterial cells to transfer the plasmid. These proteins could be targeted with specific antibodies to combat infections caused by AMR microorganisms that harbor these plasmids.}, }
@article {pmid34978575, year = {2022}, author = {Han, Z and Sieriebriennikov, B and Susoy, V and Lo, WS and Igreja, C and Dong, C and Berasategui, A and Witte, H and Sommer, RJ}, title = {Horizontally Acquired Cellulases Assist the Expansion of Dietary Range in Pristionchus Nematodes.}, journal = {Molecular biology and evolution}, volume = {39}, number = {2}, pages = {}, pmid = {34978575}, issn = {1537-1719}, mesh = {Animals ; *Cellulases/genetics ; Escherichia coli K12 ; *Gene Transfer, Horizontal ; Phylogeny ; *Rhabditida/enzymology/genetics ; }, abstract = {Horizontal gene transfer (HGT) enables the acquisition of novel traits via non-Mendelian inheritance of genetic material. HGT plays a prominent role in the evolution of prokaryotes, whereas in animals, HGT is rare and its functional significance is often uncertain. Here, we investigate horizontally acquired cellulase genes in the free-living nematode model organism Pristionchus pacificus. We show that these cellulase genes 1) are likely of eukaryotic origin, 2) are expressed, 3) have protein products that are secreted and functional, and 4) result in endo-cellulase activity. Using CRISPR/Cas9, we generated an octuple cellulase mutant, which lacks all eight cellulase genes and cellulase activity altogether. Nonetheless, this cellulase-null mutant is viable and therefore allows a detailed analysis of a gene family that was horizontally acquired. We show that the octuple cellulase mutant has associated fitness costs with reduced fecundity and slower developmental speed. Furthermore, by using various Escherichia coli K-12 strains as a model for cellulosic biofilms, we demonstrate that cellulases facilitate the procurement of nutrients from bacterial biofilms. Together, our analysis of cellulases in Pristionchus provides comprehensive evidence from biochemistry, genetics, and phylogeny, which supports the integration of horizontally acquired genes into the complex life history strategy of this soil nematode.}, }
@article {pmid34975778, year = {2021}, author = {Zhang, P and Dong, X and Zhou, K and Zhu, T and Liang, J and Shi, W and Gao, M and Feng, C and Li, Q and Zhang, X and Ren, P and Lu, J and Lin, X and Li, K and Zhu, M and Bao, Q and Zhang, H}, title = {Characterization of a Novel Chromosome-Encoded AmpC β-Lactamase Gene, bla PRC-1, in an Isolate of a Newly Classified Pseudomonas Species, Pseudomonas wenzhouensis A20, From Animal Farm Sewage.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {732932}, pmid = {34975778}, issn = {1664-302X}, abstract = {In this work, we characterized a novel chromosome-encoded AmpC β-lactamase gene, bla PRC-1, in an isolate of a newly classified Pseudomonas species designated Pseudomonas wenzhouensis A20, which was isolated from sewage discharged from an animal farm in Wenzhou, China. Susceptibility testing, molecular cloning, and enzyme kinetic parameter analysis were performed to determine the function and enzymatic properties of the β-lactamase. Sequencing and comparative genomic analysis were conducted to clarify the phylogenetic relationship and genetic context of the bla PRC-1 gene. PRC-1 is a 379-amino acid AmpC β-lactamase with a molecular weight of 41.48 kDa and a predicted pI of 6.44, sharing the highest amino acid identity (57.7%) with the functionally characterized AmpC β-lactamase PDC-211 (ARX71249). bla PRC-1 confers resistance to many β-lactam antibiotics, including penicillins (penicillin G, amoxicillin, and amoxicillin-clavulanic acid) and cephalosporins (cefazolin, ceftriaxone, and cefotaxime). The kinetic properties of PRC-1 were compatible with those of a typical class C β-lactamase showing hydrolytic activities against β-lactam antibiotics, and the hydrolytic activity was strongly inhibited by avibactam. The genetic context of bla PRC-1 was relatively conserved, and no mobile genetic element was predicted in its surrounding region. Identification of a novel β-lactamase gene in an unusual environmental bacterium reveals that there might be numerous unknown resistance mechanisms in bacterial populations, which may pose potential risks to human health due to universal horizontal gene transfer between microorganisms. It is therefore of great value to carry out extensive research on the mechanism of antibiotic resistance.}, }
@article {pmid34972821, year = {2022}, author = {Irwin, NAT and Pittis, AA and Richards, TA and Keeling, PJ}, title = {Systematic evaluation of horizontal gene transfer between eukaryotes and viruses.}, journal = {Nature microbiology}, volume = {7}, number = {2}, pages = {327-336}, pmid = {34972821}, issn = {2058-5276}, mesh = {Eukaryota/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Host Microbial Interactions ; Phylogeny ; Viruses/*genetics ; }, abstract = {Gene exchange between viruses and their hosts acts as a key facilitator of horizontal gene transfer and is hypothesized to be a major driver of evolutionary change. Our understanding of this process comes primarily from bacteria and phage co-evolution, but the mode and functional importance of gene transfers between eukaryotes and their viruses remain anecdotal. Here we systematically characterized viral-eukaryotic gene exchange across eukaryotic and viral diversity, identifying thousands of transfers and revealing their frequency, taxonomic distribution and projected functions. Eukaryote-derived viral genes, abundant in the Nucleocytoviricota, highlighted common strategies for viral host-manipulation, including metabolic reprogramming, proteolytic degradation and extracellular modification. Furthermore, viral-derived eukaryotic genes implicate genetic exchange in the early evolution and diversification of eukaryotes, particularly through viral-derived glycosyltransferases, which have impacted structures as diverse as algal cell walls, trypanosome mitochondria and animal tissues. These findings illuminate the nature of viral-eukaryotic gene exchange and its impact on the evolution of viruses and their eukaryotic hosts.}, }
@article {pmid34969463, year = {2022}, author = {Li, X and Wen, C and Liu, C and Lu, S and Xu, Z and Yang, Q and Chen, Z and Liao, H and Zhou, S}, title = {Herbicide promotes the conjugative transfer of multi-resistance genes by facilitating cellular contact and plasmid transfer.}, journal = {Journal of environmental sciences (China)}, volume = {115}, number = {}, pages = {363-373}, doi = {10.1016/j.jes.2021.08.006}, pmid = {34969463}, issn = {1001-0742}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial ; Extracellular Polymeric Substance Matrix ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Herbicides/toxicity ; Plasmids/genetics ; }, abstract = {The global dissemination of antibiotic resistance genes (ARGs), especially via plasmid-mediated horizontal transfer, is becoming a pervasive health threat. While our previous study found that herbicides can accelerate the horizontal gene transfer (HGT) of ARGs in soil bacteria, the underlying mechanisms by which herbicides promote the HGT of ARGs across and within bacterial genera are still unclear. Here, the underlying mechanism associated with herbicide-promoted HGT was analyzed by detecting intracellular reactive oxygen species (ROS) production, extracellular polymeric substance composition, cell membrane integrity and proton motive force combined with genome-wide RNA sequencing. Exposure to herbicides induced a series of the above bacterial responses to promote HGT except for the ROS response, including compact cell-to-cell contact by enhancing pilus-encoded gene expression and decreasing cell surface charge, increasing cell membrane permeability, and enhancing the proton motive force, providing additional power for DNA uptake. This study provides a mechanistic understanding of the risk of bacterial resistance spread promoted by herbicides, which elucidates a new perspective on nonantibiotic agrochemical acceleration of the HGT of ARGs.}, }
@article {pmid34969351, year = {2022}, author = {Leung, KY and Wang, Q and Zheng, X and Zhuang, M and Yang, Z and Shao, S and Achmon, Y and Siame, BA}, title = {Versatile lifestyles of Edwardsiella: Free-living, pathogen, and core bacterium of the aquatic resistome.}, journal = {Virulence}, volume = {13}, number = {1}, pages = {5-18}, pmid = {34969351}, issn = {2150-5608}, mesh = {Animals ; Bacterial Proteins/genetics/metabolism ; *Edwardsiella/genetics ; *Enterobacteriaceae Infections/microbiology/veterinary ; *Fish Diseases/microbiology ; Virulence/genetics ; }, abstract = {Edwardsiella species in aquatic environments exist either as individual planktonic cells or in communal biofilms. These organisms encounter multiple stresses, include changes in salinity, pH, temperature, and nutrients. Pathogenic species such as E. piscicida, can multiply within the fish hosts. Additionally, Edwardsiella species (E. tarda), can carry antibiotic resistance genes (ARGs) on chromosomes and/or plasmids, that can be transmitted to the microbiome via horizontal gene transfer. E. tarda serves as a core in the aquatic resistome. Edwardsiela uses molecular switches (RpoS and EsrB) to control gene expression for survival in different environments. We speculate that free-living Edwardsiella can transition to host-living and vice versa, using similar molecular switches. Understanding such transitions can help us understand how other similar aquatic bacteria switch from free-living to become pathogens. This knowledge can be used to devise ways to slow down the spread of ARGs and prevent disease outbreaks in aquaculture and clinical settings.}, }
@article {pmid34965489, year = {2022}, author = {Cho, KH and Wolny, J and Kase, JA and Unno, T and Pachepsky, Y}, title = {Interactions of E. coli with algae and aquatic vegetation in natural waters.}, journal = {Water research}, volume = {209}, number = {}, pages = {117952}, doi = {10.1016/j.watres.2021.117952}, pmid = {34965489}, issn = {1879-2448}, abstract = {Both algae and bacteria are essential inhabitants of surface waters. Their presence is of ecological significance and sometimes of public health concern triggering various control actions. Interactions of microalgae, macroalgae, submerged aquatic vegetation, and bacteria appear to be important phenomena necessitating a deeper understanding by those involved in research and management of microbial water quality. Given the long-standing reliance on Escherichia coli as an indicator of the potential presence of pathogens in natural waters, understanding its biology in aquatic systems is necessary. The major effects of algae and aquatic vegetation on E. coli growth and survival, including changes in the nutrient supply, modification of water properties and constituents, impact on sunlight radiation penetration, survival as related to substrate attachment, algal mediation of secondary habitats, and survival inhibition due to the release of toxic substances and antibiotics, are discussed in this review. An examination of horizontal gene transfer and antibiotic resistance potential, strain-specific interactions, effects on the microbial, microalgae, and grazer community structure, and hydrodynamic controls is given. Outlooks due to existing and expected consequences of climate change and advances in observation technologies via high-resolution satellite imaging, unmanned aerial vehicles (drones), and mathematical modeling are additionally covered. The multiplicity of interactions among bacteria, algae, and aquatic vegetation as well as multifaceted impacts of these interactions, create a wide spectrum of research opportunities and technology developments.}, }
@article {pmid34965410, year = {2021}, author = {Frye, KA and Piamthai, V and Hsiao, A and Degnan, PH}, title = {Mobilization of vitamin B12 transporters alters competitive dynamics in a human gut microbe.}, journal = {Cell reports}, volume = {37}, number = {13}, pages = {110164}, pmid = {34965410}, issn = {2211-1247}, support = {R01 AI157106/AI/NIAID NIH HHS/United States ; R35 GM124724/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacterial Proteins/genetics/*metabolism ; Bacteroidetes/growth &amp; development/*metabolism ; Corrinoids/*metabolism ; Female ; *Gastrointestinal Microbiome ; Humans ; *Interspersed Repetitive Sequences ; Male ; Membrane Transport Proteins/*metabolism ; Mice ; Mice, Inbred C57BL ; Vitamin B 12/*metabolism ; Vitamin B Complex/metabolism ; }, abstract = {The functional and genomic diversity of the human gut microbiome is shaped by horizontal transfer of mobile genetic elements (MGEs). Characterized MGEs can encode genes beneficial for their host's self-defense (e.g., antibiotic resistance) or ability to compete for essential or limited resources (e.g., vitamins). Vitamin B12 and related compounds (corrinoids) are critical nutrients that enable colonization by members of the common gut microbe phylum, the Bacteroidetes. Herein, we identify a distinct class of MGEs in the Bacteroidetes responsible for the mobilization and exchange of the genes required for transport of corrinoids, a group of cyclic tetrapyrrole cofactors including vitamin B12 (btuGBFCD). This class includes two distinct groups of conjugative transposons (CTns) and one group of phage. Conjugative transfer and vitamin B12 transport activity of two of the CTns were confirmed in vitro and in vivo, demonstrating the important role MGEs play in distribution of corrinoid transporters in the Bacteroidetes.}, }
@article {pmid34964291, year = {2021}, author = {Larsen, JS and Miller, M and Oakley, AJ and Dixon, NE and Lewis, PJ}, title = {Multiple classes and isoforms of the RNA polymerase recycling motor protein HelD.}, journal = {MicrobiologyOpen}, volume = {10}, number = {6}, pages = {e1251}, pmid = {34964291}, issn = {2045-8827}, mesh = {Bacteria/*chemistry/classification/genetics ; Bacterial Proteins/*chemistry/*classification/genetics/metabolism ; DNA Helicases/chemistry/classification/genetics/metabolism ; DNA-Directed RNA Polymerases/metabolism ; Gene Transfer, Horizontal ; Models, Molecular ; Phylogeny ; Protein Domains ; Protein Isoforms/chemistry/classification/genetics/metabolism ; Transcription Factors/*chemistry/*classification/genetics/metabolism ; Transcription, Genetic ; }, abstract = {Efficient control of transcription is essential in all organisms. In bacteria, where DNA replication and transcription occur simultaneously, the replication machinery is at risk of colliding with highly abundant transcription complexes. This can be exacerbated by the fact that transcription complexes pause frequently. When pauses are long-lasting, the stalled complexes must be removed to prevent collisions with either another transcription complex or the replication machinery. HelD is a protein that represents a new class of ATP-dependent motor proteins distantly related to helicases. It was first identified in the model Gram-positive bacterium Bacillus subtilis and is involved in removing and recycling stalled transcription complexes. To date, two classes of HelD have been identified: one in the low G+C and the other in the high G+C Gram-positive bacteria. In this work, we have undertaken the first comprehensive investigation of the phylogenetic diversity of HelD proteins. We show that genes in certain bacterial classes have been inherited by horizontal gene transfer, many organisms contain multiple expressed isoforms of HelD, some of which are associated with antibiotic resistance, and that there is a third class of HelD protein found in Gram-negative bacteria. In summary, HelD proteins represent an important new class of transcription factors associated with genome maintenance and antibiotic resistance that are conserved across the Eubacterial kingdom.}, }
@article {pmid34963542, year = {2022}, author = {Chen, J and Yang, Y and Jiang, X and Ke, Y and He, T and Xie, S}, title = {Metagenomic insights into the profile of antibiotic resistomes in sediments of aquaculture wastewater treatment system.}, journal = {Journal of environmental sciences (China)}, volume = {113}, number = {}, pages = {345-355}, doi = {10.1016/j.jes.2021.06.026}, pmid = {34963542}, issn = {1001-0742}, mesh = {Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; *Anti-Bacterial Agents/pharmacology ; Aquaculture ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Water Purification ; }, abstract = {To meet the rapidly growing global demand for aquaculture products, large amounts of antibiotics were used in aquaculture, which might accelerate the evolution of antibiotic-resistant bacteria (ARB) and the propagation of antibiotic genes (ARGs). In our research, we revealed the ARGs profiles, their co-occurrence with mobile genetic elements (MGEs), and potential hosts in sediments of a crab pond wastewater purification system based on metagenomic analysis. The residual antibiotic seems to increase the propagation of ARGs in the crab pond, but there was no clear relationship between a given antibiotic type and the corresponding resistance genes. The effect of aquaculture on sediment was not as profound as that of other anthropogentic activities, but increased the relative abundance of sulfonamide resistance gene. A higher abundance of MGEs, especially plasmid, increased the potential ARGs dissemination risk in crab and purification ponds. Multidrug and sulfonamide resistance genes had greater potential to transfer because they were more frequently carried by MGEs. The horizontal gene transfer was likely to occur among a variety of microorganisms, and various ARGs hosts including Pseudomonas, Acinetobacter, Escherichia, and Klebsiella were identified. Bacterial community influenced the composition of ARG hosts, and Proteobacteria was the predominant hosts. Overall, our study provides novel insights into the environmental risk of ARGs in sediments of aquaculture wastewater treatment system.}, }
@article {pmid34960610, year = {2021}, author = {Li, N and Zeng, Y and Hu, B and Zhu, T and Svenningsen, SL and Middelboe, M and Tan, D}, title = {Interactions between the Prophage 919TP and Its Vibrio cholerae Host: Implications of gmd Mutation for Phage Resistance, Cell Auto-Aggregation, and Motility.}, journal = {Viruses}, volume = {13}, number = {12}, pages = {}, pmid = {34960610}, issn = {1999-4915}, mesh = {Bacterial Proteins/genetics ; Cholera/*microbiology ; Host Microbial Interactions ; Host Specificity ; Lysogeny ; O Antigens/*genetics ; Prophages/*metabolism ; *Vibrio cholerae O1/metabolism/virology ; Virus Activation ; }, abstract = {Prophage 919TP is widely distributed among Vibrio cholera and is induced to produce free φ919TP phage particles. However, the interactions between prophage φ919TP, the induced phage particle, and its host remain unknown. In particular, phage resistance mechanisms and potential fitness trade-offs, resulting from phage resistance, are unresolved. In this study, we examined a prophage 919TP-deleted variant of V. cholerae and its interaction with a modified lytic variant of the induced prophage (φ919TP cI[-]). Specifically, the phage-resistant mutant was isolated by challenging a prophage-deleted variant with lytic phage φ919TP cI[-]. Further, the comparative genomic analysis of wild-type and φ919TP cI[-]-resistant mutant predicted that phage φ919TP cI[-] selects for phage-resistant mutants harboring a mutation in key steps of lipopolysaccharide (LPS) O-antigen biosynthesis, causing a single-base-pair deletion in gene gmd. Our study showed that the gmd-mediated O-antigen defect can cause pleiotropic phenotypes, e.g., cell autoaggregation and reduced swarming motility, emphasizing the role of phage-driven diversification in V. cholerae. The developed approach assists in the identification of genetic determinants of host specificity and is used to explore the molecular mechanism underlying phage-host interactions. Our findings contribute to the understanding of prophage-facilitated horizontal gene transfer and emphasize the potential for developing new strategies to optimize the use of phages in bacterial pathogen control.}, }
@article {pmid34959593, year = {2021}, author = {Glen, KA and Lamont, IL}, title = {β-lactam Resistance in Pseudomonas aeruginosa: Current Status, Future Prospects.}, journal = {Pathogens (Basel, Switzerland)}, volume = {10}, number = {12}, pages = {}, pmid = {34959593}, issn = {2076-0817}, support = {17/372 and 20/812//Health Research Council of New Zealand/ ; }, abstract = {Pseudomonas aeruginosa is a major opportunistic pathogen, causing a wide range of acute and chronic infections. β-lactam antibiotics including penicillins, carbapenems, monobactams, and cephalosporins play a key role in the treatment of P. aeruginosa infections. However, a significant number of isolates of these bacteria are resistant to β-lactams, complicating treatment of infections and leading to worse outcomes for patients. In this review, we summarize studies demonstrating the health and economic impacts associated with β-lactam-resistant P. aeruginosa. We then describe how β-lactams bind to and inhibit P. aeruginosa penicillin-binding proteins that are required for synthesis and remodelling of peptidoglycan. Resistance to β-lactams is multifactorial and can involve changes to a key target protein, penicillin-binding protein 3, that is essential for cell division; reduced uptake or increased efflux of β-lactams; degradation of β-lactam antibiotics by increased expression or altered substrate specificity of an AmpC β-lactamase, or by the acquisition of β-lactamases through horizontal gene transfer; and changes to biofilm formation and metabolism. The current understanding of these mechanisms is discussed. Lastly, important knowledge gaps are identified, and possible strategies for enhancing the effectiveness of β-lactam antibiotics in treating P. aeruginosa infections are considered.}, }
@article {pmid34955225, year = {2022}, author = {Dong, Y and Wu, S and Fan, H and Li, X and Li, Y and Xu, S and Bai, Z and Zhuang, X}, title = {Ecological selection of bacterial taxa with larger genome sizes in response to polycyclic aromatic hydrocarbons stress.}, journal = {Journal of environmental sciences (China)}, volume = {112}, number = {}, pages = {82-93}, doi = {10.1016/j.jes.2021.04.027}, pmid = {34955225}, issn = {1001-0742}, mesh = {*Bacteria/classification/metabolism ; Biodegradation, Environmental ; *Genome Size ; *Polycyclic Aromatic Hydrocarbons/analysis/metabolism ; Soil Microbiology ; *Soil Pollutants/analysis/metabolism ; }, abstract = {Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous priority pollutants that cause great damage to the natural environment and health. Average genome size in a community is critical for shedding light on microbiome's functional response to pollution stress within an environment. Here, microcosms under different concentrations were performed to evaluate the selection of PAHs stress on the average genome size in a community. We found the distinct communities of significantly larger genome size with the increase of PAHs concentration gradients in soils, and consistent trends were discovered in soils at different latitudes. The abundance of Proteobacteria and Deinococcus-Thermus with relatively larger genomes increased along with PAHs stress and well adapted to polluted environments. In contrast, the abundance of Patescibacteria with a highly streamlined and smaller genome decreased, implying complex interactions between environmental selection and functional fitness resulted in bacteria with larger genomes becoming more abundant. Moreover, we confirmed the increased capacity for horizontal transfer of degrading genes between communities by showing an increased connection number per node positively related to the nidA gene along the concentration gradients in the co-occurrence network. Our findings suggest PAHs tend to select bacterial taxa with larger genome sizes, with significant consequences for community stability and potential biodegradation strategies.}, }
@article {pmid34955195, year = {2022}, author = {Deng, B and Li, W and Lu, H and Zhu, L}, title = {Film mulching reduces antibiotic resistance genes in the phyllosphere of lettuce.}, journal = {Journal of environmental sciences (China)}, volume = {112}, number = {}, pages = {121-128}, doi = {10.1016/j.jes.2021.04.032}, pmid = {34955195}, issn = {1001-0742}, mesh = {*Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Lactuca ; Soil ; Soil Microbiology ; }, abstract = {Phyllosphere is an important reservoir of antibiotic resistance genes (ARGs), but the transfer mechanism of ARGs from soil and air to phyllosphere remains unclear. This study demonstrated that soil-air-phyllosphere was the dominant ARG transfer pathway, and blocking it by film mulching can reduce typical phyllosphere ARGs in lettuce by 80.7% - 98.7% (89.5% on average). To further eliminate phyllosphere ARGs in lettuce grown with film mulching, the internal soil-endosphere-phyllosphere transfer pathway deserves more attention. We analyzed the ARG hosts and the resistome in lettuce rhizosphere and phyllosphere with film mulching via hybrid Illumina-Nanopore sequencing. Pseudomonas sp. 7SR1 was more abundant than other ARG hosts, accounting for 1.0% and 47.1% of the total bacteria in rhizosphere and phyllosphere, respectively. The species has flagella that can promote mobility and can excrete extracellular polymeric substances and/or surfactant-like microbial products, which benefits its colonization in the phyllosphere. Impeding the migration of Pseudomonas sp. 7SR1 via the soil-endosphere-phyllosphere pathway would be effective to further reduce ARGs in phyllosphere. Multidrug resistant genes were predominant in phyllosphere (40.3% of the total), and 87.6% of the phyllosphere ARGs were located on chromosomes, indicating relatively low horizontal gene transfer (HGT) potentials. This study provides insights into the transfer mechanism, hosts, and control strategies of phyllosphere ARGs in typical plants.}, }
@article {pmid34954103, year = {2022}, author = {Cordeiro-Moura, JR and Kraychete, GB and Longo, LGA and Corrêa, LL and da Silva, NMV and Campana, EH and Oliveira, CJB and Picão, RC}, title = {Description and comparative genomic analysis of a mcr-1-carrying Escherichia coli ST683/CC155 recovered from touristic coastal water in Northeastern Brazil.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {97}, number = {}, pages = {105196}, doi = {10.1016/j.meegid.2021.105196}, pmid = {34954103}, issn = {1567-7257}, mesh = {Brazil ; Colistin/pharmacology ; *Drug Resistance, Bacterial ; Escherichia coli/genetics/*isolation &amp; purification ; Escherichia coli Proteins/*genetics ; *Genome, Bacterial ; Genomics ; Microbial Sensitivity Tests ; Phylogeny ; Seawater/microbiology ; }, abstract = {Polymyxin resistance is an emerging health issue aggravated by mcr dissemination among Enterobacterales recovered from various sources. Commensal Escherichia coli plays a key role in the spread of antimicrobial resistance in community settings and is likely to spread silently. It may transfer resistance genes to pathogenic bacteria in the gastrointestinal tract and the environment, and may cause difficult-to-treat infections, especially in immunocompromised patients. Unraveling actors disseminating resistance to last-resort antimicrobials might support the future development of control measures. Here we report the occurrence of a commensal ST683/CC155 colistin-resistant mcr-1.1-harboring E. coli (JP24) obtained from touristic coastal water. JP24's genome was sequenced and comparatively analyzed with other genomes from ST683/CC155 isolated worldwide and with mcr-carrying isolates recovered from various sources in Brazil. Besides mcr-1, JP24 carried blaCTX-M-8, tet(A), tet(34), dfrA12, sul2, sul3, aph(3')-Ia, aph(3')-IIa, aadA1, aadA2, cmlA1, Inu(G), mef(B) and mdf(a). mcr-1 and blaCTX-M-8 were transferable by IncX4 and IncI1/Iγ plasmids, respectively. Tree-based phylogeny of the ST683/CC155 isolates core genome revealed two larger clades. E. coli JP24 was grouped into a subclade together with an isolate from Thailand (ERR4221036), both carrying mcr-1. The core genome-based tree of the isolates carrying mcr-1 from Brazil revealed proximity with E. coli ECEST9 recovered from a mangrove also located in Northeastern Brazil. Accessory genome-based tree clustered most environmental isolates apart from the clinical ones and remained JP24 closer to ECEST9. High sequence conservation was observed between mcr-1-harboring plasmids detected in different species and reservoirs in Brazil and other countries. In addition to recreational coastal waters being potential sources for community exposure to antimicrobial-resistant bacteria, our findings reinforce a more prominent role of horizontal gene transfer, other than clonal expansion, in mcr dissemination in the community.}, }
@article {pmid34952454, year = {2022}, author = {Zhang, Q and Liu, Y and Zhang, C and Zhou, D}, title = {Easily biodegradable substrates are crucial for enhancing antibiotic risk reduction: Low-carbon discharging policies need to be more specified.}, journal = {Water research}, volume = {210}, number = {}, pages = {117972}, doi = {10.1016/j.watres.2021.117972}, pmid = {34952454}, issn = {1879-2448}, mesh = {*Anti-Bacterial Agents ; Carbon ; Genes, Bacterial ; Humans ; Policy ; Risk Reduction Behavior ; *Wastewater ; }, abstract = {Governments have formulated stricter wastewater treatment plant (WWTP) discharge standards to address water pollution; however, with the cost of aggravating the refractory of the discharges. These policies are not in line with the classic co-metabolism theory; thus, we evaluated the effects of an easily biodegradable substrate on the removal efficiency of antibiotics and antibiotic resistance genes (ARGs) in the receiving water. In this study, reactor with 8 d of hydraulic retention time (HRT) was constructed to simulate a receiving river, and several antibiotics (0.30 mg/L each) were continuously discharged to the reactor (tetracycline, ciprofloxacin, amoxicillin, chloramphenicol, and sulfamethoxazole). Sodium acetate (NaAc) was used as a representative easily biodegradable substrate, and treatment protocols with and without a co-substrate were compared. The attenuation of the antibiotics in the simulated river and the production and dissemination of ARGs were analyzed. The results showed that 50 mg/L NaAc activated non-specific enzymes (a log2-fold change of 3.1-8.8 compared with 0 mg/L NaAc). The removal rate of the antibiotics was increased by 4-32%, and the toxicity of the downstream water was reduced by 35%. The upregulation of antioxidant enzymes caused the intracellular reactive oxygen species (ROSs) decreased by up to 47%, inhibiting horizontal gene transfer and reducing mobile genetic element-mediated ARGs (mARGs) by 18-56%. Furthermore, NaAc also increased the alpha diversity of the microbial community by 5-15% (Shannon-Wiener Index) and reduced the abundance of human bacterial pathogens by 22-36%. In summary, easily biodegradable substrates in the receiving water are crucial for reducing antibiotic risk.}, }
@article {pmid34951622, year = {2022}, author = {Ebmeyer, S and Coertze, RD and Berglund, F and Kristiansson, E and Larsson, DGJ}, title = {GEnView: a gene-centric, phylogeny-based comparative genomics pipeline for bacterial genomes and plasmids.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {6}, pages = {1727-1728}, pmid = {34951622}, issn = {1367-4811}, support = {2018-05771//Swedish Research Council VR/ ; 2018-00787//Swedish Research Council for Environment, Agriculture and Spatial Planning (FORMAS)/ ; }, mesh = {Phylogeny ; *Genomics ; *Software ; Genome, Bacterial ; Plasmids/genetics ; }, abstract = {SUMMARY: Comparing genomic loci of a given bacterial gene across strains and species can provide insights into their evolution, including information on e.g. acquired mobility, the degree of conservation between different taxa or indications of horizontal gene transfer events. While thousands of bacterial genomes are available to date, there is no software that facilitates comparisons of individual gene loci for a large number of genomes. GEnView (Genetic Environment View) is a Python-based pipeline for the comparative analysis of gene-loci in a large number of bacterial genomes, providing users with automated, taxon-selective access to the >800.000 genomes and plasmids currently available in the NCBI Assembly and RefSeq databases, and is able to process local genomes that are not deposited at NCBI, enabling searches for genomic sequences and to analyze their genetic environments through the interactive visualization and extensive metadata files created by GEnView.<br><br>GEnView is implemented in Python 3. Instructions for download and usage can be found at https://github.com/EbmeyerSt/GEnView under GLP3.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid34951405, year = {2021}, author = {Buysse, M and Floriano, AM and Gottlieb, Y and Nardi, T and Comandatore, F and Olivieri, E and Giannetto, A and Palomar, AM and Makepeace, BL and Bazzocchi, C and Cafiso, A and Sassera, D and Duron, O}, title = {A dual endosymbiosis supports nutritional adaptation to hematophagy in the invasive tick Hyalomma marginatum.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {34951405}, issn = {2050-084X}, mesh = {Animals ; Francisella/genetics/*metabolism ; Gene Transfer, Horizontal ; Ixodidae/*microbiology/physiology ; Rickettsiales/genetics/*metabolism ; Symbiosis/physiology ; Vitamin B Complex/biosynthesis ; }, abstract = {Many animals are dependent on microbial partners that provide essential nutrients lacking from their diet. Ticks, whose diet consists exclusively on vertebrate blood, rely on maternally inherited bacterial symbionts to supply B vitamins. While previously studied tick species consistently harbor a single lineage of those nutritional symbionts, we evidence here that the invasive tick Hyalomma marginatum harbors a unique dual-partner nutritional system between an ancestral symbiont, Francisella, and a more recently acquired symbiont, Midichloria. Using metagenomics, we show that Francisella exhibits extensive genome erosion that endangers the nutritional symbiotic interactions. Its genome includes folate and riboflavin biosynthesis pathways but deprived functional biotin biosynthesis on account of massive pseudogenization. Co-symbiosis compensates this deficiency since the Midichloria genome encompasses an intact biotin operon, which was primarily acquired via lateral gene transfer from unrelated intracellular bacteria commonly infecting arthropods. Thus, in H. marginatum, a mosaic of co-evolved symbionts incorporating gene combinations of distant phylogenetic origins emerged to prevent the collapse of an ancestral nutritional symbiosis. Such dual endosymbiosis was never reported in other blood feeders but was recently documented in agricultural pests feeding on plant sap, suggesting that it may be a key mechanism for advanced adaptation of arthropods to specialized diets.}, }
@article {pmid34948225, year = {2021}, author = {Maruyama, H and Nambu, T and Mashimo, C and Okinaga, T and Takeyasu, K}, title = {Single-Molecule/Cell Analyses Reveal Principles of Genome-Folding Mechanisms in the Three Domains of Life.}, journal = {International journal of molecular sciences}, volume = {22}, number = {24}, pages = {}, pmid = {34948225}, issn = {1422-0067}, support = {17K15254//Japan Society for the Promotion of Science/ ; }, mesh = {*Bacteria/genetics/metabolism ; Eukaryota/genetics/metabolism ; *Euryarchaeota/genetics/metabolism ; *Evolution, Molecular ; *Genome ; }, abstract = {Comparative structural/molecular biology by single-molecule analyses combined with single-cell dissection, mass spectroscopy, and biochemical reconstitution have been powerful tools for elucidating the mechanisms underlying genome DNA folding. All genomes in the three domains of life undergo stepwise folding from DNA to 30-40 nm fibers. Major protein players are histone (Eukarya and Archaea), Alba (Archaea), and HU (Bacteria) for fundamental structural units of the genome. In Euryarchaeota, a major archaeal phylum, either histone or HTa (the bacterial HU homolog) were found to wrap DNA. This finding divides archaea into two groups: those that use DNA-wrapping as the fundamental step in genome folding and those that do not. Archaeal transcription factor-like protein TrmBL2 has been suggested to be involved in genome folding and repression of horizontally acquired genes, similar to bacterial H-NS protein. Evolutionarily divergent SMC proteins contribute to the establishment of higher-order structures. Recent results are presented, including the use of Hi-C technology to reveal that archaeal SMC proteins are involved in higher-order genome folding, and the use of single-molecule tracking to reveal the detailed functions of bacterial and eukaryotic SMC proteins. Here, we highlight the similarities and differences in the DNA-folding mechanisms in the three domains of life.}, }
@article {pmid34946064, year = {2021}, author = {Hirose, J and Watanabe, T and Futagami, T and Fujihara, H and Kimura, N and Suenaga, H and Goto, M and Suyama, A and Furukawa, K}, title = {A New ICEclc Subfamily Integrative and Conjugative Element Responsible for Horizontal Transfer of Biphenyl and Salicylic Acid Catabolic Pathway in the PCB-Degrading Strain Pseudomonas stutzeri KF716.}, journal = {Microorganisms}, volume = {9}, number = {12}, pages = {}, pmid = {34946064}, issn = {2076-2607}, abstract = {Integrative and conjugative elements (ICEs) are chromosomally integrated self-transmissible mobile genetic elements. Although some ICEs are known to carry genes for the degradation of aromatic compounds, information on their genetic features is limited. We identified a new member of the ICEclc family carrying biphenyl catabolic bph genes and salicylic acid catabolic sal genes from the PCB-degrading strain Pseudomonas stutzeri KF716. The 117-kb ICEbph-salKF716 contains common core regions exhibiting homology with those of degradative ICEclc from P. knackmussii B13 and ICEXTD from Azoarcus sp. CIB. A comparison of the gene loci collected from the public database revealed that several putative ICEs from P. putida B6-2, P, alcaliphila JAB1, P. stutzeri AN10, and P. stutzeri 2A20 had highly conserved core regions with those of ICEbph-salKF716, along with the variable region that encodes the catabolic genes for biphenyl, naphthalene, toluene, or phenol. These data indicate that this type of ICE subfamily is ubiquitously distributed within aromatic compound-degrading bacteria. ICEbph-salKF716 was transferred from P. stutzeri KF716 to P. aeruginosa PAO1 via a circular extrachromosomal intermediate form. In this study, we describe the structure and genetic features of ICEbph-salKF716 compared to other catabolic ICEs.}, }
@article {pmid34943744, year = {2021}, author = {Wang, C and Zeng, Y and Wei, M and Cui, L and Song, Y and Zhang, G and Li, Y and Feng, J}, title = {Streptococcus sputorum, a Novel Member of Streptococcus with Multidrug Resistance, Exhibits Cytotoxicity.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {10}, number = {12}, pages = {}, pmid = {34943744}, issn = {2079-6382}, support = {31872632//National Natural Science Foundation of China/ ; 31861133001//National Natural Science Foundation of China/ ; 31870134//National Natural Science Foundation of China/ ; 109282-001//IDRC Grant/ ; }, abstract = {We describe the genomic and phenotypic characteristics of a novel member of Streptococcus with multidrug resistance (MDR) isolated from hospital samples. Strains SP218 and SP219 were identified as a novel Streptococcus, S. sputorum, using whole-genome sequencing and biochemical tests. Average nucleotide identity values of strains SP218 and SP219 with S. pseudopneumoniae IS7493 and S. pneumoniae ST556 were 94.3% and 93.3%, respectively. Genome-to-genome distance values of strains SP218 and SP219 with S. pseudopneumoniae IS7493 and S. pneumoniae ST556 were 56.70% (54-59.5%) and 56.40% (52.8-59.9%), respectively. The biochemical test results distinguished these strains from S. pseudopneumoniae and S. pneumoniae, particularly hydrolysis of equine urate and utilization of ribose to produce acid. These isolates were resistant to six major classes of antibiotics, which correlated with horizontal gene transfer and mutation. Notably, strain SP219 exhibited cytotoxicity against human lung epithelial cell line A549. Our results indicate the pathogenic potential of S. sputorum, and provide valuable insights into mitis group of streptococci.}, }
@article {pmid34943651, year = {2021}, author = {Yamamoto, A and Tanaka, S and Ohishi, K}, title = {Quantitative Evaluation of Nucleic Acid Degradability of Copper Alloy Surfaces and Its Correlation to Antibacterial Activity.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {10}, number = {12}, pages = {}, pmid = {34943651}, issn = {2079-6382}, abstract = {Copper (Cu) and its alloys have bactericidal activity known as "contact killing" with degradation of nucleic acids inside the bacteria, which is beneficial to inhibit horizontal gene transfer (HGF). In order to understand the nucleic acid degradability of Cu and its alloy surfaces, we developed a new in vitro method to quantitatively evaluate it by a swab method under a "dry" condition and compared it with that of commercially available antibacterial materials such as antibacterial stainless steel, pure silver, and antibacterial resins. As a result, only Cu and its alloys showed continuous degradation of nucleic acids for up to 6 h of contact time. The nucleic acid degradability levels of the Cu alloys and other antibacterial materials correlate to their antibacterial activities evaluated by a film method referring to JIS Z 2801:2012 for Gram-negative (Escherichia coli) and Gram-positive (Staphylococcus aureus) bacteria. Nucleic acid degradation by copper (I) and (II) chlorides was confirmed at the ranges over 10 mM and 1-20 mM, respectively, suggesting that the copper ion release may be responsible for the degradation of the nucleic acids on Cu and its alloy surfaces. In conclusion, the higher Cu content in the alloys gave higher nucleic acid degradability and higher antibacterial activities.}, }
@article {pmid34937181, year = {2021}, author = {Fu, J and Zhong, C and Zhou, Y and Lu, M and Zong, G and Zhang, P and Cheng, M and Cao, G}, title = {The Integrative and Conjugative Element ICECspPOL2 Contributes to the Outbreak of Multi-Antibiotic-Resistant Bacteria for Chryseobacterium Spp. and Elizabethkingia Spp.}, journal = {Microbiology spectrum}, volume = {9}, number = {3}, pages = {e0200521}, pmid = {34937181}, issn = {2165-0497}, mesh = {Anti-Bacterial Agents/*pharmacology ; Chryseobacterium/classification/*drug effects/*genetics/isolation &amp; purification ; Conjugation, Genetic ; *Drug Resistance, Multiple, Bacterial ; Flavobacteriaceae/classification/*drug effects/*genetics/isolation &amp; purification ; Flavobacteriaceae Infections/*microbiology ; Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; Phylogeny ; Wastewater/microbiology ; }, abstract = {Antibiotic resistance genes (ARGs) and horizontal transfer of ARGs among bacterial species in the environment can have serious clinical implications as such transfers can lead to disease outbreaks from multidrug-resistant (MDR) bacteria. Infections due to antibiotic-resistant Chryseobacterium and Elizabethkingia in intensive care units have been increasing in recent years. In this study, the multi-antibiotic-resistant strain Chryseobacterium sp. POL2 was isolated from the wastewater of a livestock farm. Whole-genome sequencing and annotation revealed that the POL2 genome encodes dozens of ARGs. The integrative and conjugative element (ICE) ICECspPOL2, which encodes ARGs associated with four types of antibiotics, including carbapenem, was identified in the POL2 genome, and phylogenetic affiliation analysis suggested that ICECspPOL2 evolved from related ICEEas of Elizabethkingia spp. Conjugation assays verified that ICECspPOL2 can horizontally transfer to Elizabethkingia species, suggesting that ICECspPOL2 contributes to the dissemination of multiple ARGs among Chryseobacterium spp. and Elizabethkingia spp. Because Elizabethkingia spp. is associated with clinically significant infections and high mortality, there would be challenges to clinical treatment if these bacteria acquire ICECspPOL2 with its multiple ARGs, especially the carbapenem resistance gene. Therefore, the results of this study support the need for monitoring the dissemination of this type of ICE in Chryseobacterium and Elizabethkingia strains to prevent further outbreaks of MDR bacteria. IMPORTANCE Infections with multiple antibiotic-resistant Chryseobacterium and Elizabethkingia in intensive care units have been increasing in recent years. In this study, the mobile integrative and conjugative element ICECspPOL2, which was associated with the transmission of a carbapenem resistance gene, was identified in the genome of the multi-antibiotic-resistant strain Chryseobacterium sp. POL2. ICECspPOL2 is closely related to the ICEEas from Elizabethkingia species, and ICECspPOL2 can horizontally transfer to Elizabethkingia species with the tRNA-Glu-TTC gene as the insertion site. Because Elizabethkingia species are associated with clinically significant infections and high mortality, the ability of ICECspPOL2 to transfer carbapenem resistance from environmental strains of Chryseobacterium to Elizabethkingia is of clinical concern.}, }
@article {pmid34935428, year = {2021}, author = {Zhang, RM and Sun, J and Sun, RY and Wang, MG and Cui, CY and Fang, LX and Liao, MN and Lu, XQ and Liu, YX and Liao, XP and Liu, YH}, title = {Source Tracking and Global Distribution of the Tigecycline Non-Susceptible tet(X).}, journal = {Microbiology spectrum}, volume = {9}, number = {3}, pages = {e0116421}, pmid = {34935428}, issn = {2165-0497}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/*genetics/metabolism ; Bacteroidaceae/drug effects/*genetics/metabolism ; DNA Transposable Elements ; Drug Resistance, Bacterial ; Escherichia coli/drug effects/*genetics/metabolism ; Flavobacteriaceae/drug effects/*genetics/metabolism ; Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; Plasmids/genetics/metabolism ; Riemerella/drug effects/*genetics/metabolism ; Tigecycline/*pharmacology ; }, abstract = {The emergence of tet(X) genes has compromised the clinical use of the last-line antibiotic tigecycline. We identified 322 (1.21%) tet(X) positive samples from 12,829 human microbiome samples distributed in four continents (Asia, Europe, North America, and South America) using retrospective data from worldwide. These tet(X) genes were dominated by tet(X2)-like orthologs but we also identified 12 samples carrying novel tet(X) genes, designed tet(X45), tet(X46), and tet(X47), were resistant to tigecycline. The metagenomic analysis indicated these tet(X) genes distributed in anaerobes dominated by Bacteroidaceae (78.89%) of human-gut origin. Two mobile elements ISBf11 and IS4351 were most likely to promote the transmission of these tet(X2)-like orthologs between Bacteroidaceae and Riemerella anatipestifer. tet(X2)-like orthologs was also developed during transmission by mutation to high-level tigecycline resistant genes tet(X45), tet(X46), and tet(X47). Further tracing these tet(X) in single bacterial isolate from public repository indicated tet(X) genes were present as early as 1960s in R. anatipestifer that was the primary tet(X) carrier at early stage (before 2000). The tet(X2) and non-tet(X2) orthologs were primarily distributed in humans and food animals respectively, and non-tet(X2) were dominated by tet(X3) and tet(X4). Genomic comparison indicated these tet(X) genes were likely to be generated during tet(X) transmission between Flavobacteriaceae and E. coli/Acinetobacter spp., and ISCR2 played a key role in the transmission. These results suggest R. anatipestifer was the potential ancestral source of tet(X). In addition, Bacteroidaceae of human-gut origin was an important hidden reservoir and mutational incubator for the mobile tet(X) genes that enabled spread to facultative anaerobes and aerobes. IMPORTANCE The emergence of the tigecycline resistance gene tet(X) has posed a severe threat to public health. However, reports of its origin and distribution in human remain rare. Here, we explore the origin and distribution of tet(X) from large-scale metagenomic data of human-gut origin and public repository. This study revealed the emergency of tet(X) gene in 1960s, which has refreshed a previous standpoint that the earliest presence of tet(X) was in 1980s. The metagenomic analysis from data mining covered the unculturable bacteria, which has overcome the traditional bacteria isolating and purificating technologies, and the analysis indicated that the Bacteroidaceae of human-gut origin was an important hidden reservoir for tet(X) that enabled spread to facultative anaerobes and aerobes. The continuous monitoring of mobile tigecycline resistance determinants from both culturable and unculturable microorganisms is imperative for understanding and tackling the dissemination of tet(X) genes in both the health care and agricultural sectors.}, }
@article {pmid34933456, year = {2021}, author = {Smith, TE and Lee, M and Person, MD and Hesek, D and Mobashery, S and Moran, NA}, title = {Horizontal-Acquisition of a Promiscuous Peptidoglycan-Recycling Enzyme Enables Aphids To Influence Symbiont Cell Wall Metabolism.}, journal = {mBio}, volume = {12}, number = {6}, pages = {e0263621}, pmid = {34933456}, issn = {2150-7511}, support = {R35 GM131685/GM/NIGMS NIH HHS/United States ; F32 GM126706/GM/NIGMS NIH HHS/United States ; R35 GM131738/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Aphids/*enzymology/genetics/microbiology/physiology ; Bacterial Proteins/*genetics/metabolism ; Buchnera/*enzymology/genetics/metabolism ; Cell Wall/genetics/*metabolism ; *Gene Transfer, Horizontal ; Insect Proteins/*genetics/metabolism ; N-Acetylmuramoyl-L-alanine Amidase/*genetics/metabolism ; Peptidoglycan/*biosynthesis ; Symbiosis ; }, abstract = {During evolution, enzymes can undergo shifts in preferred substrates or in catalytic activities. An intriguing question is how enzyme function changes following horizontal gene transfer, especially for bacterial genes that have moved to animal genomes. Some insects have acquired genes that encode enzymes for the biosynthesis of bacterial cell wall components and that appear to function to support or control their obligate endosymbiotic bacteria. In aphids, the bacterial endosymbiont Buchnera aphidicola provides essential amino acids for aphid hosts but lacks most genes for remodeling of the bacterial cell wall. The aphid genome has acquired seven genes with putative functions in cell wall metabolism that are primarily expressed in the aphid cells harboring Buchnera. In analyses of aphid homogenates, we detected peptidoglycan (PGN) muropeptides indicative of the reactions of PGN hydrolases encoded by horizontally acquired aphid genes but not by Buchnera genes. We produced one such host enzyme, ApLdcA, and characterized its activity with both cell wall derived and synthetic PGN. Both ApLdcA and the homologous enzyme in Escherichia coli, which functions as an l,d-carboxypeptidase in the cytoplasmic PGN recycling pathway, exhibit turnover of PGN substrates containing stem pentapeptides and cross-linkages via l,d-endopeptidase activity, consistent with a potential role in cell wall remodeling. Our results suggest that ApLdcA derives its functions from the promiscuous activities of an ancestral LdcA enzyme, whose acquisition by the aphid genome may have enabled hosts to influence Buchnera cell wall metabolism as a means to control symbiont growth and division. IMPORTANCE Most enzymes are capable of performing biologically irrelevant side reactions. During evolution, promiscuous enzyme activities may acquire new biological roles, especially after horizontal gene transfer to new organisms. Pea aphids harbor obligate bacterial symbionts called Buchnera and encode horizontally acquired bacterial genes with putative roles in cell wall metabolism. Though Buchnera lacks cell wall endopeptidase genes, we found evidence of endopeptidase activity among peptidoglycan muropeptides purified from aphids. We characterized a multifunctional, aphid-encoded enzyme, ApLdcA, which displays l,d-endopeptidase activities considered promiscuous for the Escherichia coli homolog, for which these activities do not contribute to its native role in peptidoglycan recycling. These results exemplify the roles of enzyme promiscuity and horizontal gene transfer in enzyme evolution and demonstrate how aphids influence symbiont cell wall metabolism.}, }
@article {pmid34930424, year = {2021}, author = {Kelly, S}, title = {The economics of organellar gene loss and endosymbiotic gene transfer.}, journal = {Genome biology}, volume = {22}, number = {1}, pages = {345}, pmid = {34930424}, issn = {1474-760X}, mesh = {Arabidopsis/genetics ; Bacteria/*genetics ; Cell Nucleus ; Chloroplasts ; Gene Transfer, Horizontal ; *Genome, Chloroplast ; *Genome, Mitochondrial ; Genome, Plant ; Host Microbial Interactions/genetics ; Mitochondria/genetics ; Proteomics ; Symbiosis/*genetics ; }, abstract = {BACKGROUND: The endosymbiosis of the bacterial progenitors of the mitochondrion and the chloroplast are landmark events in the evolution of life on Earth. While both organelles have retained substantial proteomic and biochemical complexity, this complexity is not reflected in the content of their genomes. Instead, the organellar genomes encode fewer than 5% of the genes found in living relatives of their ancestors. While many of the 95% of missing organellar genes have been discarded, others have been transferred to the host nuclear genome through a process known as endosymbiotic gene transfer.<br><br>RESULTS: Here, we demonstrate that the difference in the per-cell copy number of the organellar and nuclear genomes presents an energetic incentive to the cell to either delete organellar&#xa0;genes or transfer them to the nuclear genome. We show that, for the majority of transferred organellar&#xa0;genes, the energy saved by nuclear transfer exceeds the costs incurred from importing the encoded protein into the organelle where it can provide its function. Finally, we show that the net energy saved by endosymbiotic gene transfer can constitute an appreciable proportion of total cellular energy budgets and is therefore sufficient to impart a selectable advantage to the cell.<br><br>CONCLUSION: Thus, reduced cellular cost and improved energy efficiency likely played a role in the reductive evolution of mitochondrial and chloroplast genomes and the transfer of organellar genes to the nuclear genome.}, }
@article {pmid34928389, year = {2022}, author = {Arhab, Y and Miścicka, A and Pestova, TV and Hellen, CUT}, title = {Horizontal gene transfer as a mechanism for the promiscuous acquisition of distinct classes of IRES by avian caliciviruses.}, journal = {Nucleic acids research}, volume = {50}, number = {2}, pages = {1052-1068}, pmid = {34928389}, issn = {1362-4962}, support = {R01 AI123406/AI/NIAID NIH HHS/United States ; R35 GM122602/GM/NIGMS NIH HHS/United States ; R01 AI123406/NH/NIH HHS/United States ; }, mesh = {Caliciviridae/*genetics ; Gene Transfer, Horizontal ; *Internal Ribosome Entry Sites ; Nucleic Acid Conformation ; Protein Biosynthesis ; RNA, Viral/*metabolism ; Ribosomes/*metabolism ; }, abstract = {In contrast to members of Picornaviridae which have long 5'-untranslated regions (5'UTRs) containing internal ribosomal entry sites (IRESs) that form five distinct classes, members of Caliciviridae typically have short 5'UTRs and initiation of translation on them is mediated by interaction of the viral 5'-terminal genome-linked protein (VPg) with subunits of eIF4F rather than by an IRES. The recent description of calicivirus genomes with 500-900nt long 5'UTRs was therefore unexpected and prompted us to examine them in detail. Sequence analysis and structural modelling of the atypically long 5'UTRs of Caliciviridae sp. isolate yc-13 and six other caliciviruses suggested that they contain picornavirus-like type 2 IRESs, whereas ruddy turnstone calicivirus (RTCV) and Caliciviridae sp. isolate hwf182cal1 calicivirus contain type 4 and type 5 IRESs, respectively. The suggestion that initiation on RTCV mRNA occurs by the type 4 IRES mechanism was confirmed experimentally using in vitro reconstitution. The high sequence identity between identified calicivirus IRESs and specific picornavirus IRESs suggests a common evolutionary origin. These calicivirus IRESs occur in a single phylogenetic branch of Caliciviridae and were likely acquired by horizontal gene transfer.}, }
@article {pmid34923900, year = {2022}, author = {Cohen, H and Adani, B and Cohen, E and Piscon, B and Azriel, S and Desai, P and Bähre, H and McClelland, M and Rahav, G and Gal-Mor, O}, title = {The ancestral stringent response potentiator, DksA has been adapted throughout Salmonella evolution to orchestrate the expression of metabolic, motility, and virulence pathways.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {1997294}, pmid = {34923900}, issn = {1949-0984}, support = {R01 AI054959/AI/NIAID NIH HHS/United States ; R01 AI136520/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/*genetics/*metabolism ; Citric Acid Cycle ; Escherichia coli/genetics/metabolism ; Escherichia coli Proteins/classification/genetics/metabolism ; *Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Glycolysis ; Humans ; Pyrimidines/biosynthesis ; Regulon ; Salmonella/cytology/*genetics/*metabolism/pathogenicity ; Salmonella Infections/microbiology ; Salmonella typhimurium/cytology/*genetics/metabolism/pathogenicity ; Virulence ; Virulence Factors/*genetics/*metabolism ; }, abstract = {DksA is a conserved RNA polymerase-binding protein known to play a key role in the stringent response of proteobacteria species, including many gastrointestinal pathogens. Here, we used RNA-sequencing of Escherichia coli, Salmonella bongori and Salmonella enterica serovar Typhimurium, together with phenotypic comparison to study changes in the DksA regulon, during Salmonella evolution. Comparative RNA-sequencing showed that under non-starved conditions, DksA controls the expression of 25%, 15%, and 20% of the E. coli, S. bongori, and S. enterica genes, respectively, indicating that DksA is a pleiotropic regulator, expanding its role beyond the canonical stringent response. We demonstrate that DksA is required for the growth of these three enteric bacteria species in minimal medium and controls the expression of the TCA cycle, glycolysis, pyrimidine biosynthesis, and quorum sensing. Interestingly, at multiple steps during Salmonella evolution, the type I fimbriae and various virulence genes encoded within SPIs 1, 2, 4, 5, and 11 have been transcriptionally integrated under the ancestral DksA regulon. Consequently, we show that DksA is necessary for host cells invasion by S. Typhimurium and S. bongori and for intracellular survival of S. Typhimurium in bone marrow-derived macrophages (BMDM). Moreover, we demonstrate regulatory inversion of the conserved motility-chemotaxis regulon by DksA, which acts as a negative regulator in E. coli, but activates this pathway in S. bongori and S. enterica. Overall, this study demonstrates the regulatory assimilation of multiple horizontally acquired virulence genes under the DksA regulon and provides new insights into the evolution of virulence genes regulation in Salmonella spp.}, }
@article {pmid34923019, year = {2022}, author = {Chen, X and Wang, J and Pan, C and Feng, L and Guo, Q and Chen, S and Xie, S}, title = {Metagenomic analysis reveals the response of microbial community in river sediment to accidental antimony contamination.}, journal = {The Science of the total environment}, volume = {813}, number = {}, pages = {152484}, doi = {10.1016/j.scitotenv.2021.152484}, pmid = {34923019}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents ; Antimony/analysis/toxicity ; Genes, Bacterial ; Humans ; Metagenomics ; *Metals, Heavy ; *Microbiota ; Rivers ; }, abstract = {The mining of deposits containing metals like antimony (Sb) causes serious environmental issues that threaten human health and ecological systems. However, information on the effect of Sb on freshwater sediment microorganisms and the mechanism of microbial Sb resistance is still very limited. This was the first attempt to explore microbial communities in river sediments impacted by accidental Sb spill. Metagenomic analysis revealed the high relative abundance of Proteobacteria and Actinobacteria in all the studied river sediments, showing their advantage in resistance to Sb pollution. Under Sb stress, microbial functions related to DNA repair and ion transport were enhanced. Increase in heavy metal resistance genes (HMRGs), particularly Sb transport-related arsB gene, was observed at Sb spill-impacted sites. HMRGs were significantly correlated with ARGs and MGEs, and the abundant MGEs at Sb spill-impacted sites might contribute to the increase in HMRGs and ARGs via horizontal gene transfer. Deinococcus, Sphingopyxis and Paracoccus were identified as potential tolerant genera under Sb pressure and might be related to the transmission of HMRGs and ARGs. This study can add new insights towards the effect of accidental metal spill on sediment microbial community.}, }
@article {pmid34915016, year = {2022}, author = {Kang, M and Yang, J and Kim, S and Park, J and Kim, M and Park, W}, title = {Occurrence of antibiotic resistance genes and multidrug-resistant bacteria during wastewater treatment processes.}, journal = {The Science of the total environment}, volume = {811}, number = {}, pages = {152331}, doi = {10.1016/j.scitotenv.2021.152331}, pmid = {34915016}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Genes, Bacterial ; Wastewater ; *Water Purification ; }, abstract = {Wastewater treatment plants (WWTPs) constantly receive a wide variety of contaminants, including pharmaceuticals, and are potential reservoirs of antibiotic resistance genes (ARGs). This favors the development of multidrug-resistant bacteria (MRB) through horizontal gene transfer. Samples from five different WWTP processes were collected in September 2020 and January 2021 to monitor ARG resistomes and culturable MRB in the presence of eight different antibiotics. Nanopore-based ARG abundance and bacterial community analyses suggested that ARG accumulation favors the generation of MRB. Activated and mixed sludges tended to have lower bacterial diversity and ARG abundance because of selective forces that favored the growth of specific microorganisms during aeration processes. Escherichia strains enriched in WWTPs (up to 71%) were dominant in all the samples, whereas Cloacamonas species were highly abundant only in anaerobically digested sludge samples (60%-79%). Two ARG types [sulfonamide resistance genes (sul1) and aminoglycoside resistance genes (aadA1, aadA13, and aadA2)] were prevalent in all the processes. The total counts of culturable MRB, such as Niabella, Enterococcus, Bacillus, and Chryseobacterium species, gradually increased during aerobic WWTP processes. Genomic analyses of all MRB isolated from the samples revealed that the resistome of Enterococcus species harbored the highest number of ARGs (7-18 ARGs), commonly encoding ant(6)-la, lnu(B), erm(B), and tet(S/M). On the other hand, Niablella strains possibly had intrinsic resistant phenotypes without ARGs. All MRB possessed ARGs originating from the same mobile genetic elements, suggesting that WWTPs are hotspots for the migration of ARGs and emergence of MRB.}, }
@article {pmid34912309, year = {2021}, author = {Aktar, S and Okamoto, Y and Ueno, S and Tahara, YO and Imaizumi, M and Shintani, M and Miyata, M and Futamata, H and Nojiri, H and Tashiro, Y}, title = {Incorporation of Plasmid DNA Into Bacterial Membrane Vesicles by Peptidoglycan Defects in Escherichia coli.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {747606}, pmid = {34912309}, issn = {1664-302X}, abstract = {Membrane vesicles (MVs) are released by various prokaryotes and play a role in the delivery of various cell-cell interaction factors. Recent studies have determined that these vesicles are capable of functioning as mediators of horizontal gene transfer. Outer membrane vesicles (OMVs) are a type of MV that is released by Gram-negative bacteria and primarily composed of outer membrane and periplasm components; however, it remains largely unknown why DNA is contained within OMVs. Our study aimed to understand the mechanism by which DNA that is localized in the cytoplasm is incorporated into OMVs in Gram-negative bacteria. We compared DNA associated with OMVs using Escherichia coli BW25113 cells harboring the non-conjugative, non-mobilized, and high-copy plasmid pUC19 and its hypervesiculating mutants that included ΔnlpI, ΔrseA, and ΔtolA. Plasmid copy per vesicle was increased in OMVs derived from ΔnlpI, in which peptidoglycan (PG) breakdown and synthesis are altered. When supplemented with 1% glycine to inhibit PG synthesis, both OMV formation and plasmid copy per vesicle were increased in the wild type. The bacterial membrane condition test indicated that membrane permeability was increased in the presence of glycine at the late exponential phase, in which cell lysis did not occur. Additionally, quick-freeze deep-etch and replica electron microscopy observations revealed that outer-inner membrane vesicles (O-IMVs) are formed in the presence of glycine. Thus, two proposed routes for DNA incorporation into OMVs under PG-damaged conditions are suggested. These routes include DNA leakage due to increased membrane permeation and O-IMV formation. Additionally, our findings contribute to a greater understanding of the vesicle-mediated horizontal gene transfer that occurs in nature and the utilization of MVs for DNA cargo.}, }
@article {pmid34910578, year = {2022}, author = {Große, C and Kohl, TA and Niemann, S and Herzberg, M and Nies, DH}, title = {Loss of Mobile Genomic Islands in Metal-Resistant, Hydrogen-Oxidizing Cupriavidus metallidurans.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {4}, pages = {e0204821}, pmid = {34910578}, issn = {1098-5336}, mesh = {Bacterial Proteins/genetics/metabolism ; *Cupriavidus/genetics/metabolism ; Gene Expression Regulation, Bacterial ; *Genomic Islands ; Hydrogen/metabolism ; Oxidation-Reduction ; }, abstract = {The genome of the metal-resistant, hydrogen-oxidizing bacterium Cupriavidus metallidurans strain CH34 contains horizontally acquired plasmids and genomic islands. Metal-resistance determinants on the two plasmids may exert genetic dominance over other related determinants. To investigate whether these recessive determinants can be activated in the absence of the dominant ones, the transcriptome of the highly zinc-sensitive deletion mutant Δe4 (ΔcadA ΔzntA ΔdmeF ΔfieF) of the plasmid-free parent AE104 was characterized using gene arrays. As a consequence of some unexpected results, close examination by PCR and genomic resequencing of strains CH34, AE104, Δe4, and others revealed that the genomic islands CMGI2, 3, 4, D, and E, but no other islands or recessive determinants, were deleted in some of these strains. Provided that wild-type CH34 was kept under alternating zinc and nickel selection pressure, no comparable deletions occurred. All current data suggest that genes were actually deleted and were not, as surmised previously, silenced in the respective strain. As a consequence, a cured database was compiled from the newly generated and previously published gene array data. An analysis of data from this database indicated that some genes of recessive, no longer needed determinants were nevertheless expressed and upregulated. Their products may interact with those of the dominant determinants to mediate a mosaic phenotype. The ability to contribute to such a mosaic phenotype may prevent deletion of the recessive determinant. The data suggest that the bacterium actively modifies its genome to deal with metal stress and at the same time ensures metal homeostasis. IMPORTANCE In their natural environment, bacteria continually acquire genes by horizontal gene transfer, and newly acquired determinants may become dominant over related ones already present in the host genome. When a bacterium is taken into laboratory culture, it is isolated from the horizontal gene transfer network. It can no longer gain genes but instead may lose them. This phenomenon was indeed observed in Cupriavidus metallidurans for the loss key metal resistance determinants when no selection pressure was kept continuously. However, some recessive metal resistance determinants were maintained in the genome. It is proposed that they might contribute some accessory genes to related dominant resistance determinants, for instance periplasmic metal-binding proteins or two-component regulatory systems. Alternatively, they may remain in the genome only because their DNA serves as a scaffold for the nucleoid. Using C. metallidurans as an example, this study sheds light on the fate and function of horizontally acquired genes in bacteria.}, }
@article {pmid34910574, year = {2021}, author = {Mey, AR and Gómez-Garzón, C and Payne, SM}, title = {Iron Transport and Metabolism in Escherichia, Shigella, and Salmonella.}, journal = {EcoSal Plus}, volume = {9}, number = {2}, pages = {eESP00342020}, pmid = {34910574}, issn = {2324-6200}, support = {R01 AI016935/AI/NIAID NIH HHS/United States ; R01 AI091957/AI/NIAID NIH HHS/United States ; R37 AI016935/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/metabolism ; Escherichia ; *Gene Expression Regulation, Bacterial ; Iron/metabolism ; Salmonella/genetics/metabolism ; *Shigella/genetics ; }, abstract = {Iron is an essential element for Escherichia, Salmonella, and Shigella species. The acquisition of sufficient amounts of iron is difficult in many environments, including the intestinal tract, where these bacteria usually reside. Members of these genera have multiple iron transport systems to transport both ferrous and ferric iron. These include transporters for free ferrous iron, ferric iron associated with chelators, and heme. The numbers and types of transport systems in any species reflect the diversity of niches that it can inhabit. Many of the iron transport genes are found on mobile genetic elements or pathogenicity islands, and there is evidence of the spread of the genes among different species and pathotypes. This is notable among the pathogenic members of the genera in which iron transport systems acquired by horizontal gene transfer allow the bacteria to overcome host innate defenses that act to restrict the availability of iron to the pathogen. The need for iron is balanced by the need to avoid iron overload since excess iron is toxic to the cell. Genes for iron transport and metabolism are tightly regulated and respond to environmental cues, including iron availability, oxygen, and temperature. Master regulators, the iron sensor Fur and the Fur-regulated small RNA (sRNA) RyhB, coordinate the expression of iron transport and cellular metabolism genes in response to the availability of iron.}, }
@article {pmid34903061, year = {2021}, author = {Gill, JL and Hedge, J and Wilson, DJ and MacLean, RC}, title = {Evolutionary Processes Driving the Rise and Fall of Staphylococcus aureus ST239, a Dominant Hybrid Pathogen.}, journal = {mBio}, volume = {12}, number = {6}, pages = {e0216821}, pmid = {34903061}, issn = {2150-7511}, support = {/WT_/Wellcome Trust/United Kingdom ; 106918/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; BB/M011224/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 101237/Z/13/B/WT_/Wellcome Trust/United Kingdom ; 203141/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics/metabolism ; *Evolution, Molecular ; Genome, Bacterial ; Humans ; Phylogeny ; *Recombination, Genetic ; Staphylococcal Infections/*microbiology ; Staphylococcus aureus/drug effects/*genetics/pathogenicity/physiology ; Virulence ; }, abstract = {Selection plays a key role in the spread of antibiotic resistance, but the evolutionary drivers of clinically important resistant strains remain poorly understood. Here, we use genomic analyses and competition experiments to study Staphylococcus aureus ST239, a prominent MRSA strain that is thought to have been formed by large-scale recombination between ST8 and ST30. Genomic analyses allowed us to refine the hybrid model for the origin of ST239 and to date the origin of ST239 to 1920 to 1945, which predates the clinical introduction of methicillin in 1959. Although purifying selection has dominated the evolution of ST239, parallel evolution has occurred in genes involved in antibiotic resistance and virulence, suggesting that ST239 has evolved toward an increasingly pathogenic lifestyle. Crucially, ST239 isolates have low competitive fitness relative to both ST8 and ST30 isolates, supporting the idea that fitness costs have driven the demise of this once-dominant pathogen strain. IMPORTANCE The rise of antibiotic resistance in most pathogenic bacteria has been driven by the spread of a small number of epidemically successful resistant strains. However, the processes that drive the rise and fall of these "superbugs" remain poorly understood. In our study, we investigated Staphylococcus aureus ST239, an important MRSA strain that has been a leading cause of serious hospital-acquired infections. We show here that ST239 was formed by the exchange of a very large fragment of DNA carrying resistance genes between strains of S. aureus sometime before 1945. The introduction of the antibiotic methicillin in 1959 provided a key advantage for Methicillin-Resistant Staphylococcus aureus (MRSA) strains. Interestingly, we found that ST239 has low competitive ability compared to other strains of S. aureus, and this evolutionary hindrance may explain why the prevalence of ST239 has declined precipitously at a global scale.}, }
@article {pmid34902517, year = {2022}, author = {Karbalaie, K and Kiani-Esfahani, A and Rasouli, K and Hossein Nasr-Esfahani, M}, title = {Stem cells from human exfoliated deciduous teeth (SHED) have mitochondrial transfer ability in stromal-derived inducing activity (SDIA) co-culture system.}, journal = {Neuroscience letters}, volume = {769}, number = {}, pages = {136392}, doi = {10.1016/j.neulet.2021.136392}, pmid = {34902517}, issn = {1872-7972}, mesh = {Calcium/metabolism ; *Cell Communication ; Cell Line ; Cell Membrane Structures/*metabolism ; Coculture Techniques/methods ; Extracellular Matrix/metabolism ; Gap Junctions/metabolism ; Humans ; Induced Pluripotent Stem Cells/*metabolism/physiology ; Mitochondria/metabolism/*physiology ; Nanotubes ; Tooth, Deciduous/cytology ; }, abstract = {Stem cells from human exfoliated deciduous teeth (SHED) have stromal-derived inducing activity (SDIA): which means these stromal cells induce neural differentiation where they are used as a substratum for embryonic stem cell (ESCs) culture. Recent studies show that mitochondria or mitochondrial products, as paracrine factors, can be released and transferred from one cell to another. With this information, we were curious to know whether in the SDIA co-culture system, SHED release or donate their mitochondria to ESCs. For this purpose, before co-culture, SHED s' mitochondria and ESCs s' cell membranes were separately labeled with specific fluorescent probes. After co-culture, SHED s' mitochondria were tracked by fluorescent microscope and flow cytometry analysis. Co-culture also performed in the presence of inhibitors that block probable transfer pathways suchlike tunneling nanotubes, gap junctions or vesicles. Results showed that mitochondrial transfer takes place from SHED to ESCs. This transfer partly occurs by tunneling nanotubes and not through gap junctions or vesicles; also was not dependent on intracellular calcium level. This kind of horizontal gene transfer may open a new prospect for further research on probable role of mitochondria on fate choice and neural induction processes.}, }
@article {pmid34896514, year = {2022}, author = {Yang, B and Wang, Z and Jia, Y and Fang, D and Li, R and Liu, Y}, title = {Paclitaxel and its derivative facilitate the transmission of plasmid-mediated antibiotic resistance genes through conjugative transfer.}, journal = {The Science of the total environment}, volume = {810}, number = {}, pages = {152245}, doi = {10.1016/j.scitotenv.2021.152245}, pmid = {34896514}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Paclitaxel ; Plasmids/genetics ; }, abstract = {The rapid dissemination of antibiotic resistance by horizontal gene transfer (HGT) renders the global resistance crisis more tense and urgent as few effective antimicrobials are available to combat multidrug-resistant (MDR) pathogens at present. Conjugation is one of the most dominant and representative pathways of HGT. Antibiotic residue in environment is recognized as an important accelerator for conjugal transfer, whereas the roles of non-antibiotic pharmaceuticals in this process are not fully understood. Here we found that environmentally relevant concentrations of paclitaxel as well as its derivative docetaxel, two commonly used anticancer drugs, remarkably facilitated the conjugative transfer of resistance plasmids carrying multiple antibiotic resistance genes (ARGs). The underlying mechanisms accounting for the enhanced conjugation were investigated by detecting the activity of RpoS regulon, membrane permeability, SOS response and gene expression of conjugative transfer systems. Our results showed that paclitaxel induced a series of cellular responses, including up-regulation of rpoS expression, activated SOS response, increased cell membrane permeability, enhanced plasmid replication and mating pilus formation. Collectively, our data provide new insight on the roles of paclitaxel and its derivative in promoting the conjugal transfer of ARGs, highlighting the importance of good antimicrobial stewardship.}, }
@article {pmid34896510, year = {2022}, author = {Zhou, L and Xu, P and Gong, J and Huang, S and Chen, W and Fu, B and Zhao, Z and Huang, X}, title = {Metagenomic profiles of the resistome in subtropical estuaries: Co-occurrence patterns, indicative genes, and driving factors.}, journal = {The Science of the total environment}, volume = {810}, number = {}, pages = {152263}, doi = {10.1016/j.scitotenv.2021.152263}, pmid = {34896510}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Ecosystem ; *Estuaries ; Genes, Bacterial ; *Metagenomics ; }, abstract = {Estuaries are resistome hotspots owing to resistome accumulation and propagation at these locations from surrounding rivers, yet the large-scale biogeographic pattern of resistome, especially biocide and metal resistance genes (BMRGs) and its driving mechanisms in estuarine waters remains to be elucidated. Here, a metagenomics-based approach was firstly used to investigate resistome and mobilome profiles in waters from 30 subtropical estuaries, South China. The Pearl River estuaries had a higher diversity and abundance of antibiotic resistance genes (ARGs), BMRGs, and mobile genetic elements (MGEs) when compared with estuaries from east and west regions. Genes resistant to multiple antibiotics, metals, and biocides were the most abundant gene types in the resistome. The abundance of MGEs (e.g., intI1, IS91, and tnpA) was highly associated with the total abundance of resistance genes, suggesting their utility as potential indicators for quantitative estimations of the resistome contamination. Further, MGEs contributed more than bacterial communities in shaping the resistome in subtropical estuaries. Physicochemical factors (e.g., pH) regulated MGE composition and stochastic assembly, which mediated the co-selection of ARGs and BMRGs via horizontal gene transfer. Our findings have important implications and provide a reference on the management of ARGs and BMRGs in subtropical estuarine ecosystems.}, }
@article {pmid34896335, year = {2022}, author = {Álvarez, VE and Massó, MG and D'amico González, G and Gambino, AS and Knecht, CA and Prack Mc Cormick, B and Leguina, C and Piekar, M and Poklepovich, T and Campos, J and Arduino, S and Centrón, D and Quiroga, MP}, title = {Emergence of colistin resistance in Klebsiella pneumoniae ST15 disseminating blaKPC-2 in a novel genetic platform.}, journal = {Journal of global antimicrobial resistance}, volume = {29}, number = {}, pages = {537-539}, doi = {10.1016/j.jgar.2021.12.001}, pmid = {34896335}, issn = {2213-7173}, mesh = {Anti-Bacterial Agents/metabolism/pharmacology ; *Carbapenem-Resistant Enterobacteriaceae/genetics ; Colistin/pharmacology ; Humans ; *Klebsiella Infections/epidemiology ; Klebsiella pneumoniae ; Multilocus Sequence Typing ; Phylogeny ; beta-Lactamases/genetics/metabolism ; }, abstract = {OBJECTIVES: Isolation of colistin- and carbapenem-resistant Klebsiella pneumoniae (CCR-Kp) is increasing in hospital settings worldwide, which is related to increased morbidity, mortality and healthcare costs. The aim of this work was to perform whole-genome sequencing (WGS), genomic and phylogenetic analysis, and conjugation assays of an extensively drug-resistant (XDR) CCR-Kp isolate from Argentina.<br><br>METHODS: WGS of strain KpS26 isolated from a bloodstream infection was performed using Illumina MiSeq-I, and de novo assembly was achieved using SPAdes v.3.11. A maximum likelihood tree was created using MEGA7 based on core genome single nucleotide polymorphisms from whole-genome alignment of K. pneumoniae isolates identified in silico as sequence type 15 (ST15). The resistome, plasmids and integrons were analysed using ResFinder, AMRFinderPlus, ISfinder, plasmidSPAdes, PlasmidFinder and IntegronFinder. Standard conjugation was performed.<br><br>RESULTS: KpS26 belonged to ST15, which is less common than ST258, ST25 and ST11 that are globally reported as responsible for CCR-Kp outbreaks. Fourteen transferable antimicrobial resistance genes (ARGs), including blaKPC-2 in a novel genetic platform transferable by conjugation, were detected contributing to the XDR phenotype. The amino acid substitution T157P in the protein encoded by the pmrB gene of KpS26, previously reported as being responsible for resistance to colistin in K. pneumoniae lineages globally disseminated, was also identified in this strain.<br><br>CONCLUSION: The XDR CCR-Kp isolate analysed here shows that ST15 is also disseminating blaKPC-2 in Argentina alongside other ARGs, evidencing that KPC epidemiology continues to be shaped by intricate and assorted ways of lateral gene transfer.}, }
@article {pmid34895114, year = {2021}, author = {Janssen, R and Liu, P}, title = {Comparing the topology of phylogenetic network generators.}, journal = {Journal of bioinformatics and computational biology}, volume = {19}, number = {6}, pages = {2140012}, doi = {10.1142/S0219720021400126}, pmid = {34895114}, issn = {1757-6334}, mesh = {Algorithms ; Bayes Theorem ; *Biological Evolution ; *Gene Transfer, Horizontal ; Models, Genetic ; Phylogeny ; }, abstract = {Phylogenetic networks represent evolutionary history of species and can record natural reticulate evolutionary processes such as horizontal gene transfer and gene recombination. This makes phylogenetic networks a more comprehensive representation of evolutionary history compared to phylogenetic trees. Stochastic processes for generating random trees or networks are important tools in evolutionary analysis, especially in phylogeny reconstruction where they can be utilized for validation or serve as priors for Bayesian methods. However, as more network generators are developed, there is a lack of discussion or comparison for different generators. To bridge this gap, we compare a set of phylogenetic network generators by profiling topological summary statistics of the generated networks over the number of reticulations and comparing the topological profiles.}, }
@article {pmid34895113, year = {2022}, author = {Chen, ZZ and Deng, F and Wang, L}, title = {Identifying duplications and lateral gene transfers simultaneously and rapidly.}, journal = {Journal of bioinformatics and computational biology}, volume = {20}, number = {1}, pages = {2150033}, doi = {10.1142/S0219720021500335}, pmid = {34895113}, issn = {1757-6334}, mesh = {Algorithms ; *Evolution, Molecular ; Gene Duplication ; *Gene Transfer, Horizontal ; Phylogeny ; }, abstract = {This paper deals with the problem of enumerating all minimum-cost LCA-reconciliations involving gene duplications and lateral gene transfers (LGTs) for a given species tree [Formula: see text] and a given gene tree [Formula: see text]. Previously, [Tofigh A, Hallett M, Lagergren J, Simultaneous identification of duplications and lateral gene transfers, IEEE/ACM Trans Comput Biol Bioinf 517-535, 2011.] gave a fixed-parameter algorithm for this problem that runs in [Formula: see text] time, where [Formula: see text] is the number of vertices in [Formula: see text], [Formula: see text] is the number of vertices in [Formula: see text], and [Formula: see text] is the minimum cost of an LCA-reconciliation between [Formula: see text] and [Formula: see text]. In this paper, by refining their algorithm, we obtain a new one for the same problem that finds and outputs the solutions in a compact form within [Formula: see text] time. In the most interesting case where [Formula: see text], our algorithm is [Formula: see text] times faster.}, }
@article {pmid34894259, year = {2022}, author = {Liu, G and Thomsen, LE and Olsen, JE}, title = {Antimicrobial-induced horizontal transfer of antimicrobial resistance genes in bacteria: a mini-review.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {77}, number = {3}, pages = {556-567}, doi = {10.1093/jac/dkab450}, pmid = {34894259}, issn = {1460-2091}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; }, abstract = {The emergence and spread of antimicrobial resistance (AMR) among pathogenic bacteria constitute an accelerating crisis for public health. The selective pressures caused by increased use and misuse of antimicrobials in medicine and livestock production have accelerated the overall selection of resistant bacteria. In addition, horizontal gene transfer (HGT) plays an important role in the spread of resistance genes, for example mobilizing reservoirs of AMR from commensal bacteria into pathogenic ones. Antimicrobials, besides antibacterial function, also result in undesirable effects in the microbial populations, including the stimulation of HGT. The main aim of this narrative review was to present an overview of the current knowledge of the impact of antimicrobials on HGT in bacteria, including the effects of transformation, transduction and conjugation, as well as other less well-studied mechanisms of HGT. It is widely accepted that conjugation plays a major role in the spread of AMR in bacteria, and the focus of this review is therefore mainly on the evidence provided that antimicrobial treatment affects this process. Other mechanisms of HGT have so far been deemed less important in this respect; however, recent discoveries suggest their role may be larger than previously thought, and the review provides an update on the rather limited knowledge currently available regarding the impact of antimicrobial treatment on these processes as well. A conclusion from the review is that there is an urgent need to investigate the mechanisms of antimicrobial-induced HGT, since this will be critical for developing new strategies to combat the spread of AMR.}, }
@article {pmid34887843, year = {2021}, author = {Mafiz, A and He, Y and Zhang, W and Zhang, Y}, title = {Soil Bacteria in Urban Community Gardens Have the Potential to Disseminate Antimicrobial Resistance Through Horizontal Gene Transfer.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {771707}, pmid = {34887843}, issn = {1664-302X}, support = {U19 FD005322/FD/FDA HHS/United States ; }, abstract = {Fifteen soil and 45 vegetable samples from Detroit community gardens were analyzed for potential antimicrobial resistance contamination. Soil bacteria were isolated and tested by antimicrobial susceptibility profiling, horizontal gene transfer, and whole-genome sequencing. High-throughput 16S rRNA sequencing analysis was conducted on collected soil samples to determine the total bacterial composition. Of 226 bacterial isolates recovered, 54 were from soil and 172 from vegetables. A high minimal inhibitory concentration (MIC) was defined as the MIC greater than or equal to the resistance breakpoint of Escherichia coli for Gram-negative bacteria or Staphylococcus aureus for Gram-positive bacteria. The high MIC was observed in 63.4 and 69.8% of Gram-negative isolates from soil and vegetables, respectively, against amoxicillin/clavulanic acid, as well as 97.5 and 82.7% against ampicillin, 97.6 and 90.7% against ceftriaxone, 85.4 and 81.3% against cefoxitin, 65.8 and 70.5% against chloramphenicol, and 80.5 and 59.7% against ciprofloxacin. All Gram-positive bacteria showed a high MIC to gentamicin, kanamycin, and penicillin. Forty of 57 isolates carrying tetM (70.2%) successfully transferred tetracycline resistance to a susceptible recipient via conjugation. Whole-genome sequencing analysis identified a wide array of antimicrobial resistance genes (ARGs), including those encoding AdeIJK, Mex, and SmeDEF efflux pumps, suggesting a high potential of the isolates to become antimicrobial resistant, despite some inconsistency between the gene profile and the resistance phenotype. In conclusion, soil bacteria in urban community gardens can serve as a reservoir of antimicrobial resistance with the potential to transfer to clinically important pathogens, resulting in food safety and public health concerns.}, }
@article {pmid34882531, year = {2021}, author = {Laskey, A and Devenish, J and Kang, M and Savic, M and Chmara, J and Dan, H and Lin, M and Robertson, J and Bessonov, K and Gurnik, S and Liu, K and Nash, JHE and Topp, E and Guan, J}, title = {Mobility of β-lactam resistance under ampicillin treatment in gut microbiota suffering from pre-disturbance.}, journal = {Microbial genomics}, volume = {7}, number = {12}, pages = {}, pmid = {34882531}, issn = {2057-5858}, mesh = {Ampicillin/*administration &amp; dosage/pharmacology ; Animals ; Antibiotic Prophylaxis ; Disease Models, Animal ; Escherichia coli/drug effects/*genetics/pathogenicity ; Feces/microbiology ; Female ; Gene Transfer, Horizontal ; Gram-Negative Bacterial Infections/*drug therapy/microbiology ; Mice ; Proof of Concept Study ; RNA, Ribosomal, 16S/genetics ; Salmonella Infections ; Salmonella enterica/drug effects/*genetics/pathogenicity ; Streptomycin/*administration &amp; dosage/pharmacology ; Whole Genome Sequencing ; *beta-Lactam Resistance ; beta-Lactamases/*genetics ; }, abstract = {Ingestion of food- or waterborne antibiotic-resistant bacteria may lead to dissemination of antibiotic resistance genes (ARGs) in the gut microbiota. The gut microbiota often suffers from various disturbances. It is not clear whether and how disturbed microbiota may affect ARG mobility under antibiotic treatments. For proof of concept, in the presence or absence of streptomycin pre-treatment, mice were inoculated orally with a β-lactam-susceptible Salmonella enterica serovar Heidelberg clinical isolate (recipient) and a β-lactam resistant Escherichia coli O80:H26 isolate (donor) carrying a blaCMY-2 gene on an IncI2 plasmid. Immediately following inoculation, mice were treated with or without ampicillin in drinking water for 7 days. Faeces were sampled, donor, recipient and transconjugant were enumerated, blaCMY-2 abundance was determined by quantitative PCR, faecal microbial community composition was determined by 16S rRNA amplicon sequencing and cecal samples were observed histologically for evidence of inflammation. In faeces of mice that received streptomycin pre-treatment, the donor abundance remained high, and the abundance of S. Heidelberg transconjugant and the relative abundance of Enterobacteriaceae increased significantly during the ampicillin treatment. Co-blooming of the donor, transconjugant and commensal Enterobacteriaceae in the inflamed intestine promoted significantly (P<0.05) higher and possibly wider dissemination of the blaCMY-2 gene in the gut microbiota of mice that received the combination of streptomycin pre-treatment and ampicillin treatment (Str-Amp) compared to the other mice. Following cessation of the ampicillin treatment, faecal shedding of S. Heidelberg transconjugant persisted much longer from mice in the Str-Amp group compared to the other mice. In addition, only mice in the Str-Amp group shed a commensal E. coli O2:H6 transconjugant, which carries three copies of the blaCMY-2 gene, one on the IncI2 plasmid and two on the chromosome. The findings highlight the significance of pre-existing gut microbiota for ARG dissemination and persistence during and following antibiotic treatments of infectious diseases.}, }
@article {pmid34878842, year = {2021}, author = {Xu, JJ and Zhang, XF and Jiang, Y and Fan, H and Li, JX and Li, CY and Zhao, Q and Yang, L and Hu, YH and Martin, C and Chen, XY}, title = {A unique flavoenzyme operates in ubiquinone biosynthesis in photosynthesis-related eukaryotes.}, journal = {Science advances}, volume = {7}, number = {50}, pages = {eabl3594}, pmid = {34878842}, issn = {2375-2548}, support = {BBS/E/J/000PR9790/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {Coenzyme Q (CoQ) is an electron transporter in the mitochondrial respiratory chain, yet the biosynthetic pathway in eukaryotes remains only partially resolved. C6-hydroxylation completes the benzoquinone ring full substitution, a hallmark of CoQ. Here, we show that plants use a unique flavin-dependent monooxygenase (CoqF), instead of di-iron enzyme (Coq7) operating in animals and fungi, as a C6-hydroxylase. CoqF evolved early in eukaryotes and became widely distributed in photosynthetic and related organisms ranging from plants, algae, apicomplexans, and euglenids. Independent alternative gene losses in different groups and lateral gene transfer have ramified CoqF across the eukaryotic tree with predominance in green lineages. The exclusive presence of CoqF in Streptophyta hints at an association of the flavoenzyme with photoautotrophy in terrestrial environments. CoqF provides a phylogenetic marker distinguishing eukaryotes and represents a previously unknown target for drug design against parasitic protists.}, }
@article {pmid34878814, year = {2022}, author = {Dunon, V and Holmsgaard, PN and Dealtry, S and Lavigne, R and Sørensen, SJ and Smalla, K and Top, EM and Springael, D}, title = {Long-Range PCR Reveals the Genetic Cargo of IncP-1 Plasmids in the Complex Microbial Community of an On-Farm Biopurification System Treating Pesticide-Contaminated Wastewater.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {3}, pages = {e0164821}, pmid = {34878814}, issn = {1098-5336}, mesh = {DNA, Bacterial/genetics ; Farms ; *Microbiota ; *Pesticides/metabolism ; Plasmids/genetics ; Polymerase Chain Reaction ; Wastewater/microbiology ; }, abstract = {Promiscuous plasmids like IncP-1 plasmids play an important role in the bacterial adaptation to pollution by acquiring and distributing xenobiotic catabolic genes. However, most information comes from isolates and the role of plasmids in governing community-wide bacterial adaptation to xenobiotics and other adaptive forces is not fully understood. Current information on the contribution of IncP-1 plasmids in community adaptation is limited because methods are lacking that directly isolate and identify the plasmid borne adaptive functions in whole-community DNA. In this study, we optimized long-range PCR to directly access and identify the cargo carried by IncP-1 plasmids in environmental DNA. The DNA between the IncP-1 backbone genes trbP and traC, a main insertion site of adaptive trait determinants, is amplified and its content analyzed by high-throughput sequencing. The method was applied to DNA of an on-farm biopurification system (BPS), treating pesticide contaminated wastewater, to examine whether horizontal gene exchange of catabolic functions by IncP-1 plasmids is a main driver of community adaptation in BPS. The cargo recovered from BPS community DNA encoded catabolic but also resistance traits and various other (un)known functions. Unexpectedly, genes with catabolic traits composed only a minor fraction of the cargo, indicating that the IncP-1 region between trbP and traC is not a major contributor to catabolic adaptation of the BPS microbiome. Instead, it contains a functionally diverse set of genes which either may assist biodegradation functions, be remnants of random gene recruitment, or confer other crucial functions for proliferation in the BPS environment. IMPORTANCE This study presents a long-range PCR for direct and cultivation-independent access to the identity of the cargo of a major insertion hot spot of adaptive genes in IncP-1 plasmids and hence a new mobilome tool for understanding the role of IncP-1 plasmids in complex communities. The method was applied to DNA of an on-farm biopurification system (BPS) treating pesticide-contaminated wastewater, aiming at new insights on whether horizontal exchange of catabolic functions by IncP-1 plasmids is a main driver of community adaptation in BPS. Unexpectedly, catabolic functions represented a small fraction of the cargo genes while multiple other gene functions were recovered. These results show that the cargo of the target insertion hot spot in IncP-1 plasmids in a community, not necessarily relates to the main obvious selective trait imposed on that community. Instead, these functions might contribute to adaptation to unknown selective forces or represent remnants of random gene recruitment.}, }
@article {pmid34878299, year = {2022}, author = {Garcillán-Barcia, MP and Pluta, R and Lorenzo-Díaz, F and Bravo, A and Espinosa, M}, title = {The Facts and Family Secrets of Plasmids That Replicate via the Rolling-Circle Mechanism.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {86}, number = {1}, pages = {e0022220}, pmid = {34878299}, issn = {1098-5557}, mesh = {Bacterial Proteins/genetics/metabolism ; *DNA ; *DNA Replication/genetics ; DNA, Bacterial/genetics ; Plasmids/genetics ; }, abstract = {Plasmids are self-replicative DNA elements that are transferred between bacteria. Plasmids encode not only antibiotic resistance genes but also adaptive genes that allow their hosts to colonize new niches. Plasmid transfer is achieved by conjugation (or mobilization), phage-mediated transduction, and natural transformation. Thousands of plasmids use the rolling-circle mechanism for their propagation (RCR plasmids). They are ubiquitous, have a high copy number, exhibit a broad host range, and often can be mobilized among bacterial species. Based upon the replicon, RCR plasmids have been grouped into several families, the best known of them being pC194 and pUB110 (Rep_1 family), pMV158 and pE194 (Rep_2 family), and pT181 and pC221 (Rep_trans family). Genetic traits of RCR plasmids are analyzed concerning (i) replication mediated by a DNA-relaxing initiator protein and its interactions with the cognate DNA origin, (ii) lagging-strand origins of replication, (iii) antibiotic resistance genes, (iv) mobilization functions, (v) replication control, performed by proteins and/or antisense RNAs, and (vi) the participating host-encoded functions. The mobilization functions include a relaxase initiator of transfer (Mob), an origin of transfer, and one or two small auxiliary proteins. There is a family of relaxases, the MOBV family represented by plasmid pMV158, which has been revisited and updated. Family secrets, like a putative open reading frame of unknown function, are reported. We conclude that basic research on RCR plasmids is of importance, and our perspectives contemplate the concept of One Earth because we should incorporate bacteria into our daily life by diminishing their virulence and, at the same time, respecting their genetic diversity.}, }
@article {pmid34876337, year = {2022}, author = {Wang, Q and Smith, SM and Huang, J}, title = {Origins of strigolactone and karrikin signaling in plants.}, journal = {Trends in plant science}, volume = {27}, number = {5}, pages = {450-459}, doi = {10.1016/j.tplants.2021.11.009}, pmid = {34876337}, issn = {1878-4372}, mesh = {*Arabidopsis Proteins/metabolism ; Furans ; Heterocyclic Compounds, 3-Ring ; Lactones/metabolism ; Phylogeny ; *Plant Growth Regulators/metabolism ; Pyrans ; Signal Transduction/genetics ; }, abstract = {Strigolactones (SLs) and karrikins (KARs) are butenolides that influence multiple aspects of plant growth and development. D14 and KAI2 are members of the α/β-fold hydrolase superfamily and act as receptors of SLs and KARs, as well as of unidentified endogenous KAI2-ligands (KLs). Phylogenetic analyses suggest that plant KAI2 was derived from bacterial RsbQ via horizontal gene transfer (HGT) before the emergence of streptophytes. The D14/KAI2 and RsbQ proteins share conserved tertiary structures and functional features. In this opinion article, we suggest that the acquisition of RsbQ by plant cells was fundamental to the formation of butenolide sensing systems. Recruitment of additional signal transduction components and gene duplication subsequently led to versatile butenolide signaling systems throughout land plants.}, }
@article {pmid34874897, year = {2021}, author = {O'Malley, K and McNamara, P and McDonald, W}, title = {Antibiotic resistance genes in an urban stream before and after a state fair.}, journal = {Journal of water and health}, volume = {19}, number = {6}, pages = {885-894}, doi = {10.2166/wh.2021.151}, pmid = {34874897}, issn = {1477-8920}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; *Genes, Bacterial/genetics ; RNA, Ribosomal, 16S ; Wastewater/analysis ; }, abstract = {The global spread of antibiotic resistance genes (ARGs) concomitant with a decrease in antibiotic effectiveness is a major public health issue. While research has demonstrated the impact of various urban sources, such as wastewater treatment plant (WWTP) effluent, stormwater runoff, and industrial discharge on ARG abundance in receiving waters, the impact of short-term gatherings such as state fairs is not comprehensively understood. The objective of this research was to explore the impact of a 2-week Wisconsin State Fair gathering - over 1.1 million visitors and 7,100 farm animals - on the abundance of the ARG blaTEM, the integrase of the class 1 integron (intI1), a marker for horizontal gene transfer, and the 16S rRNA gene, a marker for total biomass, in an urban stream receiving runoff from the state fair. Stream samples downstream of the state fair were taken before and after the event and quantified via a droplet digital polymerase chain reaction. The absolute abundance of all genes was significantly higher (p<0.05) following the event. This research showcases the prevalence and persistence of ARG contamination in an urban stream before and after a state fair gathering, suggesting that short-term events can be a significant source of ARGs into the environment.}, }
@article {pmid34874249, year = {2021}, author = {Bohr, LL and Youngblom, MA and Eldholm, V and Pepperell, CS}, title = {Genome reorganization during emergence of host-associated Mycobacterium abscessus.}, journal = {Microbial genomics}, volume = {7}, number = {12}, pages = {}, pmid = {34874249}, issn = {2057-5858}, support = {R01 AI113287/AI/NIAID NIH HHS/United States ; T32 AI055396/AI/NIAID NIH HHS/United States ; }, mesh = {Adaptation, Physiological ; Australia ; Chromosomes, Bacterial/*genetics ; Databases, Genetic ; Denmark ; Gene Transfer, Horizontal ; High-Throughput Nucleotide Sequencing ; Humans ; Mycobacterium Infections, Nontuberculous/*microbiology ; Mycobacterium abscessus/*classification/genetics/isolation &amp; purification ; Netherlands ; Norway ; Phylogeny ; Phylogeography ; Plasmids/*genetics ; Prophages/*genetics ; Recombination, Genetic ; United Kingdom ; Whole Genome Sequencing/*methods ; }, abstract = {Mycobacterium abscessus is a rapid growing, free-living species of bacterium that also causes lung infections in humans. Human infections are usually acquired from the environment; however, dominant circulating clones (DCCs) have emerged recently in both M. abscessus subsp. massiliense and subsp. abscessus that appear to be transmitted among humans and are now globally distributed. These recently emerged clones are potentially informative about the ecological and evolutionary mechanisms of pathogen emergence and host adaptation. The geographical distribution of DCCs has been reported, but the genomic processes underlying their transition from environmental bacterium to human pathogen are not well characterized. To address this knowledge gap, we delineated the structure of M. abscessus subspecies abscessus and massiliense using genomic data from 200 clinical isolates of M. abscessus from seven geographical regions. We identified differences in overall patterns of lateral gene transfer (LGT) and barriers to LGT between subspecies and between environmental and host-adapted bacteria. We further characterized genome reorganization that accompanied bacterial host adaptation, inferring selection pressures acting at both genic and intergenic loci. We found that both subspecies encode an expansive pangenome with many genes at rare frequencies. Recombination appears more frequent in M. abscessus subsp. massiliense than in subsp. abscessus, consistent with prior reports. We found evidence suggesting that phage are exchanged between subspecies, despite genetic barriers evident elsewhere throughout the genome. Patterns of LGT differed according to niche, with less LGT observed among host-adapted DCCs versus environmental bacteria. We also found evidence suggesting that DCCs are under distinct selection pressures at both genic and intergenic sites. Our results indicate that host adaptation of M. abscessus was accompanied by major changes in genome evolution, including shifts in the apparent frequency of LGT and impacts of selection. Differences were evident among the DCCs as well, which varied in the degree of gene content remodelling, suggesting they were placed differently along the evolutionary trajectory toward host adaptation. These results provide insight into the evolutionary forces that reshape bacterial genomes as they emerge into the pathogenic niche.}, }
@article {pmid34873717, year = {2022}, author = {Hartmann, FE}, title = {Using structural variants to understand the ecological and evolutionary dynamics of fungal plant pathogens.}, journal = {The New phytologist}, volume = {234}, number = {1}, pages = {43-49}, doi = {10.1111/nph.17907}, pmid = {34873717}, issn = {1469-8137}, mesh = {Adaptation, Physiological ; *Biological Evolution ; Fungi/genetics ; *Genomics ; Phenotype ; }, abstract = {Deletions, duplications, insertions, inversions and translocations are commonly referred to as structural variants (SVs). Fungal plant pathogens have compact genomes, facilitating the generation of accurate maps of SVs for these species in recent studies. Structural variants have been found to constitute a significant proportion of the standing genetic variation in fungal plant pathogen populations, potentially leading to the generation of accessory genes, regions or chromosomes enriched in pathogenicity factors. Structural variants are involved in the rapid adaptation and ecological traits of pathogens, including host specialization and mating. Long-read sequencing techniques coupled with theoretical and experimental approaches have considerable potential for elucidating the phenotypic effects of SVs and deciphering the evolutionary and genomic mechanisms underlying the formation of SVs in fungal plant pathogens.}, }
@article {pmid34872631, year = {2021}, author = {Bakkeren, E and Herter, JA and Huisman, JS and Steiger, Y and Gül, E and Newson, JPM and Brachmann, AO and Piel, J and Regoes, R and Bonhoeffer, S and Diard, M and Hardt, WD}, title = {Pathogen invasion-dependent tissue reservoirs and plasmid-encoded antibiotic degradation boost plasmid spread in the gut.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {34872631}, issn = {2050-084X}, mesh = {Animals ; Conjugation, Genetic ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Mice ; Mice, 129 Strain ; Plasmids/*genetics/physiology ; Salmonella Infections/drug therapy/microbiology ; Salmonella typhimurium/drug effects/*genetics/metabolism ; beta-Lactams/metabolism/pharmacology ; }, abstract = {Many plasmids encode antibiotic resistance genes. Through conjugation, plasmids can be rapidly disseminated. Previous work identified gut luminal donor/recipient blooms and tissue-lodged plasmid-bearing persister cells of the enteric pathogen Salmonella enterica serovar Typhimurium (S.Tm) that survive antibiotic therapy in host tissues, as factors promoting plasmid dissemination among Enterobacteriaceae. However, the buildup of tissue reservoirs and their contribution to plasmid spread await experimental demonstration. Here, we asked if re-seeding-plasmid acquisition-invasion cycles by S.Tm could serve to diversify tissue-lodged plasmid reservoirs, and thereby promote plasmid spread. Starting with intraperitoneal mouse infections, we demonstrate that S.Tm cells re-seeding the gut lumen initiate clonal expansion. Extended spectrum beta-lactamase (ESBL) plasmid-encoded gut luminal antibiotic degradation by donors can foster recipient survival under beta-lactam antibiotic treatment, enhancing transconjugant formation upon re-seeding. S.Tm transconjugants can subsequently re-enter host tissues introducing the new plasmid into the tissue-lodged reservoir. Population dynamics analyses pinpoint recipient migration into the gut lumen as rate-limiting for plasmid transfer dynamics in our model. Priority effects may be a limiting factor for reservoir formation in host tissues. Overall, our proof-of-principle data indicates that luminal antibiotic degradation and shuttling between the gut lumen and tissue-resident reservoirs can promote the accumulation and spread of plasmids within a host over time.}, }
@article {pmid34872347, year = {2021}, author = {Benler, S and Faure, G and Altae-Tran, H and Shmakov, S and Zheng, F and Koonin, E}, title = {Cargo Genes of Tn7-Like Transposons Comprise an Enormous Diversity of Defense Systems, Mobile Genetic Elements, and Antibiotic Resistance Genes.}, journal = {mBio}, volume = {12}, number = {6}, pages = {e0293821}, pmid = {34872347}, issn = {2150-7511}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/*drug effects/*genetics ; Bacterial Proteins/*genetics/metabolism ; *DNA Transposable Elements ; *Drug Resistance, Bacterial ; Phylogeny ; Recombination, Genetic ; }, abstract = {Transposition is a major mechanism of horizontal gene mobility in prokaryotes. However, exploration of the genes mobilized by transposons (cargo) is hampered by the difficulty in delineating integrated transposons from their surrounding genetic context. Here, we present a computational approach that allowed us to identify the boundaries of 6,549 Tn7-like transposons. We found that 96% of these transposons carry at least one cargo gene. Delineation of distinct communities in a gene-sharing network demonstrates how transposons function as a conduit of genes between phylogenetically distant hosts. Comparative analysis of the cargo genes reveals significant enrichment of mobile genetic elements (MGEs) nested within Tn7-like transposons, such as insertion sequences and toxin-antitoxin modules, and of genes involved in recombination, anti-MGE defense, and antibiotic resistance. More unexpectedly, cargo also includes genes encoding central carbon metabolism enzymes. Twenty-two Tn7-like transposons carry both an anti-MGE defense system and antibiotic resistance genes, illustrating how bacteria can overcome these combined pressures upon acquisition of a single transposon. This work substantially expands the distribution of Tn7-like transposons, defines their evolutionary relationships, and provides a large-scale functional classification of prokaryotic genes mobilized by transposition. IMPORTANCE Transposons are major vehicles of horizontal gene transfer that, in addition to genes directly involved in transposition, carry cargo genes. However, characterization of these genes is hampered by the difficulty of identification of transposon boundaries. We developed a computational approach for detecting transposon ends and applied it to perform a comprehensive census of the cargo genes of Tn7-like transposons, a large class of bacterial mobile genetic elements (MGE), many of which employ a unique, CRISPR-mediated mechanism of site-specific transposition. The cargo genes encompass a striking diversity of MGE, defense, and antibiotic resistance systems. Unexpectedly, we also identified cargo genes encoding metabolic enzymes. Thus, Tn7-like transposons mobilize a vast repertoire of genes that can have multiple effects on the host bacteria.}, }
@article {pmid34867877, year = {2021}, author = {Hammerl, JA and Göllner, C and Jäckel, C and Swidan, F and Gutmann, H and Strauch, E}, title = {The Acquisition of the scr Gene Cluster Encoding Sucrose Metabolization Enzymes Enables Strains of Vibrio parahaemolyticus and Vibrio vulnificus to Utilize Sucrose as Carbon Source.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {754464}, pmid = {34867877}, issn = {1664-302X}, abstract = {Most strains of Vibrio parahaemolyticus are unable to utilize sucrose as carbon source, though few exceptions exist. We investigated a sucrose-positive V. parahaemolyticus strain by whole-genome sequencing (WGS) and confirmed the presences of a genomic island containing sucrose utilization genes. A 4.7 kb DNA cluster consisting of three genes: scrA encoding a sucrose uptake protein, scrK encoding a fructokinase, and scrB coding for a sucrose-6-phosphate hydrolase, was PCR amplified and inserted into the Vibrio/Escherichia coli shuttle vector pVv3. Two recombinant plasmids, only differing in the orientation of the insert with respect to the pVv3-lacZα-fragment, conferred the E. coli K12 transformants the ability to utilize sucrose. The introduction of the two plasmids into sucrose-negative V. parahaemolyticus and V. vulnificus strains also results in a change of the sucrose utilization phenotype from negative to positive. By performing a multiplex PCR targeting scrA, scrK, and scrB, 43 scr-positive V. parahaemolyticus isolates from our collection of retail strains were detected and confirmed to be able to use sucrose as carbon source. Strains unable to utilize the disaccharide were negative by PCR for the scr genes. For in-depth characterization, 17 sucrose-positive V. parahaemolyticus were subjected to WGS. A genomic island with a nucleotide identity of >95% containing scrA, scrB, scrK and three additional coding sequences (CDS) were identified in all strains. The additional genes were predicted as a gene coding for a transcriptional regulator (scrR), a porin encoding gene and a CDS of unknown function. Sequence comparison indicated that the genomic island was located in the same region of the chromosome II in all analyzed V. parahaemolyticus strains. Structural comparison of the genomes with sequences of the sucrose utilizing species V. alginolyticus revealed the same genomic island, which indicates a possible distribution of this genetic structure by horizontal gene transfer. The comparison of all genome sequences based on SNP differences reveals that the presence of sucrose utilizing genes is found in genetically diverse V. parahaemolyticus strains and is not restricted to a subset of closely related strains.}, }
@article {pmid34867865, year = {2021}, author = {Lages, MA and Lemos, ML and Balado, M}, title = {The Temperature-Dependent Expression of the High-Pathogenicity Island Encoding Piscibactin in Vibrionaceae Results From the Combined Effect of the AraC-Like Transcriptional Activator PbtA and Regulatory Factors From the Recipient Genome.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {748147}, pmid = {34867865}, issn = {1664-302X}, abstract = {The high-pathogenicity island irp-HPI is widespread among Vibrionaceae encoding the piscibactin siderophore system. The expression of piscibactin genes in the fish pathogen Vibrio anguillarum is favored by low temperatures. However, information about the regulatory mechanism behind irp-HPI gene expression is scarce. In this work, in-frame deletion mutants of V. anguillarum defective in the putative regulators AraC1 and AraC2, encoded by irp-HPI, and in the global regulators H-NS and ToxRS, were constructed and their effect on irp-HPI gene expression was analyzed at 15 and 25°C. The results proved that only AraC1 (renamed as PbtA) is required for the expression of piscibactin biosynthesis and transport genes. PbtA inactivation led to an inability to grow under iron restriction, a loss of the outer membrane piscibactin transporter FrpA, and a significant decrease in virulence for fish. Inactivation of the global repressor H-NS, which is involved in silencing of horizontally acquired genes, also resulted in a lower transcriptional activity of the frpA promoter. Deletion of toxR-S, however, did not have a relevant effect on the expression of the irp-HPI genes. Therefore, while irp-HPI would not be part of the ToxR regulon, H-NS must exert an indirect effect on piscibactin gene expression. Thus, the temperature-dependent expression of the piscibactin-encoding pathogenicity island described in V. anguillarum is the result of the combined effect of the AraC-like transcriptional activator PbtA, harbored in the island, and other not yet defined regulator(s) encoded by the genome. Furthermore, different expression patterns were detected within different irp-HPI evolutionary lineages, which supports a long-term evolution of the irp-HPI genomic island within Vibrionaceae. The mechanism that modulates piscibactin gene expression could also be involved in global regulation of virulence factors in response to temperature changes.}, }
@article {pmid34855011, year = {2021}, author = {Mouftah, SF and Pál, T and Higgins, PG and Ghazawi, A and Idaghdour, Y and Alqahtani, M and Omrani, AS and Rizvi, TA and Sonnevend, &#xc1;}, title = {Diversity of carbapenem-resistant Klebsiella pneumoniae ST14 and emergence of a subgroup with KL64 capsular locus in the Arabian Peninsula.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, pmid = {34855011}, issn = {1435-4373}, support = {UPAR-31M235//United Arab Emirates University/ ; Kisp&#xe1;l Gyula Grant 300852//&#xc1;ltal&#xe1;nos Orvostudom&#xe1;nyi Kar, P&#xe9;csi Tudom&#xe1;nyegyetem/ ; }, abstract = {To understand the reasons of successful spread of carbapenem-resistant Klebsiella pneumoniae ST14 (CRKP-ST14) in countries of the Arabian Peninsula, the resistome, capsular locus, carbapenemase carrying plasmid types, and core genome of isolates from the region were compared to global isolates. Thirty-nine CRKP-ST14 strains isolated from 13 hospitals in the United Arab Emirates, Bahrain, and Saudi Arabia were selected for whole genome sequencing on Illumina MiSeq platform based on the variety of carbapenemase genes carried and plasmids bearing these genes. Their resistome, capsular locus, and core genome MLST were compared to 173 CRKP-ST14 genomes available in public databases. The selected 39 CRKP-ST14 produced either NDM-1, OXA-48, OXA-162, OXA-232, KPC-2, or co-produced NDM-1 and an OXA-48-like carbapenemase. cgMLST revealed three clusters: 16 isolates from five UAE cities (C1), 11 isolates from three UAE cities and Bahrain (C2), and 5 isolates from Saudi Arabia (C3), respectively, and seven singletons. Resistance gene profile, carbapenemase genes, and their plasmid types were variable in both C1 and C2 clusters. The majority of CRKP-ST14 had KL2, but members of the C2 cluster and two further singletons possessed KL64 capsular locus. Based on cgMLST comparison of regional and global isolates, CRKP-ST14 with KL64 from four continents formed a distinct cluster, suggesting a recent emergence and spread of this variant. Our findings confirmed clonal transmission coupled with likely horizontal gene transfer in carbapenem-resistant Klebsiella pneumoniae ST14. Dissemination of this genetically flexible, highly resistant clone warrants further monitoring.}, }
@article {pmid34851165, year = {2021}, author = {Nodari, CS and Fuchs, SA and Xanthopoulou, K and Cayô, R and Seifert, H and Gales, AC and Dilthey, A and Higgins, PG}, title = {pmrCAB Recombination Events among Colistin-Susceptible and -Resistant Acinetobacter baumannii Clinical Isolates Belonging to International Clone 7.}, journal = {mSphere}, volume = {6}, number = {6}, pages = {e0074621}, pmid = {34851165}, issn = {2379-5042}, mesh = {Acinetobacter Infections/drug therapy/microbiology ; Acinetobacter baumannii/drug effects/*genetics ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/*genetics ; Brazil ; Clone Cells/metabolism ; Colistin/*pharmacology ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; Microbial Sensitivity Tests ; Mutation ; }, abstract = {Acinetobacter baumannii is a successful nosocomial pathogen due to its genomic plasticity. Homologous recombination allows genetic exchange and allelic variation among different clonal lineages and is one of the mechanisms associated with horizontal gene transfer (HGT) of resistance determinants. The main mechanism of colistin resistance in A. baumannii is mediated through mutations in the pmrCAB operon. Here, we describe two A. baumannii clinical isolates belonging to International Clone 7 (IC7) that have undergone recombination in the pmrCAB operon and evaluate the contribution of mobile genetic elements (MGE) to this phenomenon. Isolates 67569 and 72554 were colistin susceptible and resistant, respectively, and were submitted for short- and long-read genome sequencing using Illumina MiSeq and MinION platforms. Hybrid assemblies were built with Unicycler, and the assembled genomes were compared to reference genomes using NUCmer, Cortex, and SplitsTree. Genomes were annotated using Prokka, and MGEs were identified with ISfinder and repeat match. Both isolates presented a 21.5-kb recombining region encompassing pmrCAB. In isolate 67659, this region originated from IC5, while in isolate 72554 multiple recombination events might have happened, with the 5-kb recombining region encompassing pmrCAB associated with an isolate representing IC4. We could not identify MGEs involved in the mobilization of pmrCAB in these isolates. In summary, A. baumannii belonging to IC7 can present additional sequence divergence due to homologous recombination across clonal lineages. Such variation does not seem to be driven by antibiotic pressure but could contribute to HGT mediating colistin resistance. IMPORTANCE Colistin resistance rates among Acinetobacter baumannii clinical isolates have increased over the last 20 years. Despite reports of the spread of plasmid-mediated colistin resistance among Enterobacterales, the presence of mcr-type genes in Acinetobacter spp. remains rare, and reduced colistin susceptibility is mainly associated with the acquisition of nonsynonymous mutations in pmrCAB. We have recently demonstrated that distinct pmrCAB sequences are associated with different A. baumannii International Clones (IC). In this study, we identified the presence of homologous recombination as an additional cause of genetic variation in this operon, which, to the best of our knowledge, was not mediated by mobile genetic elements. Even though this phenomenon was observed in both colistin-susceptible and -resistant isolates, it has the potential to contribute to the spread of resistance-conferring alleles, leading to reduced susceptibility to this last-resort antimicrobial agent.}, }
@article {pmid34848115, year = {2022}, author = {Brockhurst, MA and Harrison, E}, title = {Ecological and evolutionary solutions to the plasmid paradox.}, journal = {Trends in microbiology}, volume = {30}, number = {6}, pages = {534-543}, doi = {10.1016/j.tim.2021.11.001}, pmid = {34848115}, issn = {1878-4380}, support = {BB/R006253/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R014884/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteria/genetics ; *Biological Evolution ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Plasmids/genetics ; }, abstract = {The 'plasmid paradox' arises because, although plasmids are common features of bacterial genomes, theoretically they should not exist: rates of conjugation were believed insufficient to allow plasmids to persist by infectious transmission, whereas the costs of plasmid maintenance meant that plasmids should be purged by negative selection regardless of whether they encoded beneficial accessory traits because these traits should eventually be captured by the chromosome, enabling the loss of the redundant plasmid. In the decade since the plasmid paradox was described, new data and theory show that a range of ecological and evolutionary mechanisms operate in bacterial populations and communities to explain the widespread distribution and stable maintenance of plasmids. We conclude, therefore, that multiple solutions to the plasmid paradox are now well understood. The current challenge for the field, however, is to better understand how these solutions operate in natural bacterial communities to explain and predict the distribution of plasmids and the dynamics of the horizontal gene transfer that they mediate in bacterial (pan)genomes.}, }
@article {pmid34846836, year = {2021}, author = {Wang, DB and Cui, MM and Li, M and Zhang, XE}, title = {Biosensors for the Detection of Bacillus anthracis.}, journal = {Accounts of chemical research}, volume = {54}, number = {24}, pages = {4451-4461}, doi = {10.1021/acs.accounts.1c00407}, pmid = {34846836}, issn = {1520-4898}, mesh = {Animals ; *Bacillus anthracis ; *Biosensing Techniques ; Gold ; Humans ; *Metal Nanoparticles ; Quartz Crystal Microbalance Techniques ; }, abstract = {Bacillus anthracis, present in two forms of vegetative cells and spores, is a pathogen that infects humans through contact with infected animals or contaminated animal products and is also maliciously used in terrorist acts. Therefore, a rapid and sensitive test for B. anthracis is necessary but challenging. The challenge comes from the following aspects: an accurate distinction of B. anthracis from other Bacillus species due to their high genomic similarity and the horizontal gene transfer between Bacillus members; direct detection of the B. anthracis spores without damaging them for component extraction to avoid the risk of spore atomization; and the rapid detections of B. anthracis in complex samples, such as soil and suspicious powders, without sample pretreatments and expensive large-scale equipment. Although culturing B. anthracis from samples is the conventional method for the detection of B. anthracis, it is time-consuming and the detection results would not be easy to interpret because many Bacillus species share similar phenotypic features such as a lack of motility and hemolysis, resistance to gamma phages, and so on. Intensive and extensive effort has been expended to develop reliable detection technologies, among which biosensors exhibit comprehensive advantages in terms of sensitivity, specificity, and portability. Here, we briefly review the research progress, providing highlights of the latest achievements and our own practice and experience. The contents can be summarized in three aspects: the discovery of detection targets, including genes, toxins, and other components; the creation of molecular recognition elements, such as monoclonal antibodies, single-chain antibody fragments, specific peptides, and aptamers; and the design and construction of biosensing systems by the integration of appropriate molecular recognition elements and transducer devices. These sensor devices have their own characteristics and different principles. For example, the surface plasmon resonance biosensor and quartz crystal microbalance biosensor are very sensitive, while the multiplex PCR-on-a-chip can detect multitargets. Biosensors for direct spore detection are highly recommended because they are not only fast but also avoid contamination from aerosol-containing spores. The introduction of nanotechnology has significantly improved the performance of biosensors. Superparamagnetic nanoparticles and phage-displayed gold nanoparticle ligand peptides have made the results of spore detection visible to the naked eye. Because of space constraints, many advanced biosensors for B. anthracis are not described in detail but are cited as references. Although biosensors provide a variety of options for various application scenarios, the challenges have not been fully addressed, which leaves room for the development of more advanced and practical B. anthracis detection means.}, }
@article {pmid34846275, year = {2022}, author = {Tang, Y and Li, G and Shen, P and Zhang, Y and Jiang, X}, title = {Replicative transposition contributes to the evolution and dissemination of KPC-2-producing plasmid in Enterobacterales.}, journal = {Emerging microbes &amp; infections}, volume = {11}, number = {1}, pages = {113-122}, pmid = {34846275}, issn = {2222-1751}, mesh = {Carbapenem-Resistant Enterobacteriaceae/drug effects/*genetics/isolation &amp; purification ; Carbapenems/pharmacology ; DNA Replication ; *DNA Transposable Elements ; DNA, Bacterial/genetics ; Disease Outbreaks ; Drug Resistance, Multiple, Bacterial/genetics ; Enterobacteriaceae Infections/epidemiology/*microbiology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Humans ; Klebsiella Infections/epidemiology/microbiology ; Klebsiella pneumoniae/drug effects/genetics/isolation &amp; purification ; Molecular Epidemiology ; Multilocus Sequence Typing ; *Plasmids ; beta-Lactamases/biosynthesis/*genetics ; }, abstract = {ABSTRACTKlebsiella pneumoniae carbapenemase (KPC)-producing Enterobacterales are prevalent worldwide and pose an alarming threat to public health. The incidence and transmission of blaKPC-2 gene via horizontal gene transfer (e.g. transposition) have been well documented. However, the dynamics of transposon structure bearing blaKPC-2 and their exact effects on the evolution and dissemination of blaKPC-2 gene are not well characterized. Here, we collected all 161 carbapenem-resistant Enterobacterales (CRE) isolates during the early stage of CRE pandemic. We observed that the prevalence of KPC-2-producing Enterobacterales was mediated by multiple species and sequence types (STs), and that blaKPC-2 gene was located on three diverse variants of Tn1721 in multi-drug resistance (MDR) region of plasmid. Notably, the outbreak of KPC-2-producing plasmid is correlated with the dynamics of transposon structure. Furthermore, we experimentally demonstrated that replicative transposition of Tn1721 and IS26 promotes horizontal transfer of blaKPC-2 and the evolution of KPC-2-producing plasmid. The Tn1721 variants appearing concurrently with the peak of an epidemic (A2- and B-type) showed higher transposition frequencies and a certain superior ability to propagation. Overall, our work suggests replicative transposition contributes to the evolution and transmission of KPC-2-producing plasmid and highlights its important role in the inter- and intra-species dissemination of blaKPC-2 gene in Enterobacterales.}, }
@article {pmid34845206, year = {2021}, author = {Göller, PC and Elsener, T and Lorgé, D and Radulovic, N and Bernardi, V and Naumann, A and Amri, N and Khatchatourova, E and Coutinho, FH and Loessner, MJ and Gómez-Sanz, E}, title = {Multi-species host range of staphylococcal phages isolated from wastewater.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {6965}, pmid = {34845206}, issn = {2041-1723}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Ecosystem ; Gene Transfer, Horizontal ; *Genome, Viral ; *Host Specificity ; Microbial Consortia/genetics ; Microbial Sensitivity Tests ; Phylogeny ; Staphylococcus/classification/drug effects/*genetics/virology ; Staphylococcus Phages/classification/*genetics/isolation &amp; purification ; *Wastewater/microbiology/virology ; Water Microbiology ; }, abstract = {The host range of bacteriophages defines their impact on bacterial communities and genome diversity. Here, we characterize 94 novel staphylococcal phages from wastewater and establish their host range on a diversified panel of 117 staphylococci from 29 species. Using this high-resolution phage-bacteria interaction matrix, we unveil a multi-species host range as a dominant trait of the isolated staphylococcal phages. Phage genome sequencing shows this pattern to prevail irrespective of taxonomy. Network analysis between phage-infected bacteria reveals that hosts from multiple species, ecosystems, and drug-resistance phenotypes share numerous phages. Lastly, we show that phages throughout this network can package foreign genetic material enclosing an antibiotic resistance marker at various frequencies. Our findings indicate a weak host specialism of the tested phages, and therefore their potential to promote horizontal gene transfer in this environment.}, }
@article {pmid34844806, year = {2022}, author = {Yuan, Q and Sun, R and Yu, P and Cheng, Y and Wu, W and Bao, J and Alvarez, PJJ}, title = {UV-aging of microplastics increases proximal ARG donor-recipient adsorption and leaching of chemicals that synergistically enhance antibiotic resistance propagation.}, journal = {Journal of hazardous materials}, volume = {427}, number = {}, pages = {127895}, doi = {10.1016/j.jhazmat.2021.127895}, pmid = {34844806}, issn = {1873-3336}, mesh = {Adsorption ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Escherichia coli/genetics ; *Microplastics ; *Plastics ; }, abstract = {Despite growing attention to environmental pollution by microplastics (MP), the effects of MP aging on bacterial horizontal gene transfer (HGT) have not been systematically investigated. Here, we used UV-aged polystyrene microplastics (PS-MPs) to investigate how aging affects antibiotic resistance genes (ARGs) transfer efficiency from various ARG vectors to recipient bacteria. The adsorption capacity of MP20 (20-day UV-aged PS-MPs) towards E. coli (harboring plasmid-borne blaTEM-1), plasmid pET29 (harboring blaNDM-1) and phage lambda (carrying the aphA1 ARG) increased by 6.6-, 5.2- and 8.3-fold, respectively, relative to pristine PS-MPs (MP0), due to increased specific surface area and affinity for these ARG vectors. Moreover, MP20 released more organic compounds (TOC 1.6 mg/g-MP20, versus 0.2 mg/g-MP0 in 4 h) -possibly depolymerization byproducts (verified by GC-MS), which induced intracellular ROS generation, increased cell permeability and upregulated HGT associated genes. Accordingly, MP20 enhanced ARG transfer frequency from E. coli, plasmid pET29 and phage lambda (relative to MP0) by 1.3-, 4.7- and 3.5-fold, respectively. The Bliss independence model infers that higher bacterial adsorption and exposure to chemicals released during MP aging synergistically enhanced ARG transfer. This underscores the need to assess the significance of this overlooked phenomenon to the environmental dissemination of antibiotic resistance and other HGT processes.}, }
@article {pmid34844427, year = {2021}, author = {Pinilla-Redondo, R and Olesen, AK and Russel, J and de Vries, LE and Christensen, LD and Musovic, S and Nesme, J and Sørensen, SJ}, title = {Broad Dissemination of Plasmids across Groundwater-Fed Rapid Sand Filter Microbiomes.}, journal = {mBio}, volume = {12}, number = {6}, pages = {e0306821}, pmid = {34844427}, issn = {2150-7511}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; Filtration ; *Gene Transfer, Horizontal ; Groundwater/*microbiology ; Humans ; *Microbiota ; Phylogeny ; Plasmids/*genetics ; Silicon Dioxide/chemistry ; }, abstract = {Biological rapid sand filtration is a commonly employed method for the removal of organic and inorganic impurities in water which relies on the degradative properties of microorganisms for the removal of diverse contaminants, but their bioremediation capabilities vary greatly across waterworks. Bioaugmentation efforts with degradation-proficient bacteria have proven difficult due to the inability of the exogenous microbes to stably colonize the sand filters. Plasmids are extrachromosomal DNA elements that can often transfer between bacteria and facilitate the flow of genetic information across microbiomes, yet their ability to spread within rapid sand filters has remained unknown. Here, we examine the permissiveness of rapid sand filter communities toward four environmentally transmissible plasmids, RP4, RSF1010, pKJK5, and TOL (pWWO), using a dual-fluorescence bioreporter platform combined with fluorescence-activated cell sorting (FACS) and 16S rRNA gene amplicon sequencing. Our results reveal that plasmids can transfer at high frequencies and across distantly related taxa from rapid sand filter communities, emphasizing their potential suitability for introducing bioremediation determinants in the microbiomes of underperforming water purification plants. IMPORTANCE The supply of clean water for human consumption is being challenged by the appearance of anthropogenic pollutants in groundwater ecosystems. Because many plasmids can transfer horizontally between members of bacterial communities, they comprise promising vectors for the dissemination of pollutant-degrading genetic determinants within water purification plants. However, their ability to spread within groundwater-fed rapid sand filters has not been explored. Here, we investigate the transfer dynamics of four transmissible plasmids across rapid sand filter communities originating from three different waterworks in Denmark. Our results revealed a significant ability of natural plasmids to transfer at high frequencies and across distantly related taxa in the absence of plasmid selection, indicating their potential suitability as vectors for the spread of bioremediation determinants in water purification plants. Future work is required to assess the biotechnological applicability and long-term maintenance of exogenous plasmids within sand filter communities.}, }
@article {pmid34843593, year = {2021}, author = {Bao, XY and Yan, JY and Yao, YL and Wang, YB and Visendi, P and Seal, S and Luan, JB}, title = {Lysine provisioning by horizontally acquired genes promotes mutual dependence between whitefly and two intracellular symbionts.}, journal = {PLoS pathogens}, volume = {17}, number = {11}, pages = {e1010120}, pmid = {34843593}, issn = {1553-7374}, mesh = {Animals ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Halomonadaceae/*physiology ; Hemiptera/genetics/growth &amp; development/*microbiology ; Lysine/genetics/*metabolism ; Rickettsia/*physiology ; *Symbiosis ; }, abstract = {Horizontal gene transfer is widespread in insects bearing intracellular symbionts. Horizontally transferred genes (HTGs) are presumably involved in amino acid synthesis in sternorrhynchan insects. However, their role in insect-symbiont interactions remains largely unknown. We found symbionts Portiera, Hamiltonella and Rickettsia possess most genes involved in lysine synthesis in the whitefly Bemisia tabaci MEAM1 although their genomes are reduced. Hamiltonella maintains a nearly complete lysine synthesis pathway. In contrast, Portiera and Rickettsia require the complementation of whitefly HTGs for lysine synthesis and have lysE, encoding a lysine exporter. Furthermore, each horizontally transferred lysine gene of ten B. tabaci cryptic species shares an evolutionary origin. We demonstrated that Hamiltonella did not alter the titers of Portiera and Rickettsia or lysine gene expression of Portiera, Rickettsia and whiteflies. Hamiltonella also did not impact on lysine levels or protein localization in bacteriocytes harboring Portiera and ovaries infected with Rickettsia. Complementation with whitefly lysine synthesis HTGs rescued E. coli lysine gene knockout mutants. Silencing whitefly lysA in whiteflies harboring Hamiltonella reduced lysine levels, adult fecundity and titers of Portiera and Rickettsia without influencing the expression of Hamiltonella lysA. Furthermore, silencing whitefly lysA in whiteflies lacking Hamiltonella reduced lysine levels, adult fecundity and titers of Portiera and Rickettsia in ovarioles. Therefore, we, for the first time, demonstrated an essential amino acid lysine synthesized through HTGs is important for whitefly reproduction and fitness of both obligate and facultative symbionts, and it illustrates the mutual dependence between whitefly and its two symbionts. Collectively, this study reveals that acquisition of horizontally transferred lysine genes contributes to coadaptation and coevolution between B. tabaci and its symbionts.}, }
@article {pmid34841315, year = {2021}, author = {van Leeuwen, HC and Roelofs, D and Corver, J and Hensbergen, P}, title = {Phylogenetic analysis of the bacterial Pro-Pro-endopeptidase domain reveals a diverse family including secreted and membrane anchored proteins.}, journal = {Current research in microbial sciences}, volume = {2}, number = {}, pages = {100024}, pmid = {34841315}, issn = {2666-5174}, abstract = {Pro-Pro-endopeptidases (PPEP, EC 3.4.24.89) are secreted, zinc metalloproteases that have the unusual capacity to cleave a peptide bond between two prolines, a bond that is generally less sensitive to proteolytic cleavage. Two well studied members of the family are PPEP-1 and PPEP-2, produced by Clostridioides difficile, a human pathogen, and Paenibacillus alvei, a bee secondary invader, respectively. Both proteases seem to be involved in mediating bacterial adhesion by cleaving cell surface anchor proteins on the bacterium itself. By using basic alignment and phylogenetic profiling analysis, this work shows that the complete family of proteins that contain a PPEP domain includes proteins from more than 130 species spread over 9 genera. These analyses also suggest that the PPEP domain spread through horizontal gene transfer events between species within the Firmicutes' classes Bacilli and Clostridia. Bacterial species containing PPEP homologs are found in diverse habitats, varying from human pathogens and gut microbiota to free-living bacteria, which were isolated from various environments, including extreme conditions such as hot springs, desert soil and salt lakes. The phylogenetic tree reveals the relationships between family members and suggests that smaller subgroups could share cleavage specificity, substrates and functional similarity. Except for PPEP-1 and PPEP-2, no cleavage specificity, specific physiological target, or function has been assigned for any of the other PPEP-family members. Some PPEP proteins have acquired additional domains that recognize and bind noncovalently to various elements of the bacterial peptidoglycan cell-wall, anchoring these PPEPs. Secreted or anchored to the cell-wall surface PPEP proteins seem to perform various functions.}, }
@article {pmid34839714, year = {2022}, author = {Pursey, E and Dimitriu, T and Paganelli, FL and Westra, ER and van Houte, S}, title = {CRISPR-Cas is associated with fewer antibiotic resistance genes in bacterial pathogens.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {377}, number = {1842}, pages = {20200464}, pmid = {34839714}, issn = {1471-2970}, support = {BB/S017674/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R010781/10/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; *CRISPR-Cas Systems ; Drug Resistance, Microbial ; Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; }, abstract = {The acquisition of antibiotic resistance (ABR) genes via horizontal gene transfer (HGT) is a key driver of the rise in multidrug resistance amongst bacterial pathogens. Bacterial defence systems per definition restrict the influx of foreign genetic material, and may therefore limit the acquisition of ABR. CRISPR-Cas adaptive immune systems are one of the most prevalent defences in bacteria, found in roughly half of bacterial genomes, but it has remained unclear if and how much they contribute to restricting the spread of ABR. We analysed approximately 40 000 whole genomes comprising the full RefSeq dataset for 11 species of clinically important genera of human pathogens, including Enterococcus, Staphylococcus, Acinetobacter and Pseudomonas. We modelled the association between CRISPR-Cas and indicators of HGT, and found that pathogens with a CRISPR-Cas system were less likely to carry ABR genes than those lacking this defence system. Analysis of the mobile genetic elements (MGEs) targeted by CRISPR-Cas supports a model where this host defence system blocks important vectors of ABR. These results suggest a potential 'immunocompromised' state for multidrug-resistant strains that may be exploited in tailored interventions that rely on MGEs, such as phages or phagemids, to treat infections caused by bacterial pathogens. This article is part of the theme issue 'The secret lives of microbial mobile genetic elements'.}, }
@article {pmid34839713, year = {2022}, author = {Moura de Sousa, JA and Rocha, EPC}, title = {To catch a hijacker: abundance, evolution and genetic diversity of P4-like bacteriophage satellites.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {377}, number = {1842}, pages = {20200475}, pmid = {34839713}, issn = {1471-2970}, mesh = {*Bacteriophages/genetics ; Evolution, Molecular ; Genetic Variation ; Genome, Viral ; Host Specificity ; Phylogeny ; }, abstract = {Bacteriophages (phages) are bacterial parasites that can themselves be parasitized by phage satellites. The molecular mechanisms used by satellites to hijack phages are sometimes understood in great detail, but the origins, abundance, distribution and composition of these elements are poorly known. Here, we show that P4-like elements are present in more than 30% of the genomes of Enterobacterales, and in almost half of those of Escherichia coli, sometimes in multiple distinct copies. We identified over 1000 P4-like elements with very conserved genetic organization of the core genome and a few hotspots with highly variable genes. These elements are never found in plasmids and have very little homology to known phages, suggesting an independent evolutionary origin. Instead, they are scattered across chromosomes, possibly because their integrases are often exchanged with other elements. The rooted phylogenies of hijacking functions are correlated and suggest longstanding coevolution. They also reveal broad host ranges in P4-like elements, as almost identical elements can be found in distinct bacterial genera. Our results show that P4-like phage satellites constitute a very distinct, widespread and ancient family of mobile genetic elements. They pave the way for studying the molecular evolution of antagonistic interactions between phages and their satellites. This article is part of the theme issue 'The secret lives of microbial mobile genetic elements'.}, }
@article {pmid34839712, year = {2022}, author = {Rodríguez-Beltrán, J and León-Sampedro, R and Ramiro-Martínez, P and de la Vega, C and Baquero, F and Levin, BR and San Millán, &#xc1;}, title = {Translational demand is not a major source of plasmid-associated fitness costs.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {377}, number = {1842}, pages = {20200463}, pmid = {34839712}, issn = {1471-2970}, mesh = {*Bacteria/genetics ; Drug Resistance, Microbial ; *Gene Transfer, Horizontal ; Plasmids/genetics ; }, abstract = {Plasmids are key drivers of bacterial evolution because they are crucial agents for the horizontal transfer of adaptive traits, such as antibiotic resistance. Most plasmids entail a metabolic burden that reduces the fitness of their host if there is no selection for plasmid-encoded genes. It has been hypothesized that the translational demand imposed by plasmid-encoded genes is a major mechanism driving the fitness cost of plasmids. Plasmid-encoded genes typically present a different codon usage from host chromosomal genes. As a consequence, the translation of plasmid-encoded genes might sequestrate ribosomes on plasmid transcripts, overwhelming the translation machinery of the cell. However, the pervasiveness and origins of the translation-derived costs of plasmids are yet to be assessed. Here, we systematically altered translation efficiency in the host cell to disentangle the fitness effects produced by six natural antibiotic resistance plasmids. We show that limiting translation efficiency either by reducing the number of available ribosomes or their processivity does not increase plasmid costs. Overall, our results suggest that ribosomal paucity is not a major contributor to plasmid fitness costs. This article is part of the theme issue 'The secret lives of microbial mobile genetic elements'.}, }
@article {pmid34839711, year = {2022}, author = {Smith, BA and Dougherty, K and Clark, M and Baltrus, DA}, title = {Experimental evolution of the megaplasmid pMPPla107 in Pseudomonas stutzeri enables identification of genes contributing to sensitivity to an inhibitory agent.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {377}, number = {1842}, pages = {20200474}, pmid = {34839711}, issn = {1471-2970}, mesh = {Gene Transfer, Horizontal ; Plasmids/genetics ; *Pseudomonas stutzeri/genetics ; Pseudomonas syringae/genetics ; Sequence Analysis, DNA ; }, abstract = {Horizontally transferred elements, such as plasmids, can burden host cells with various metabolic and fitness costs and may lead to other potentially detrimental phenotypic effects. Acquisition of the Pseudomonas syringae megaplasmid pMPPla107 by various Pseudomonads causes sensitivity to a growth-inhibiting substance that is produced in cultures by Pseudomonads during growth under standard laboratory conditions. After approximately 500 generations of laboratory passage of Pseudomonas stutzeri populations containing pMPPla107, strains from two out of six independent passage lines displayed resistance to this inhibitory agent. Resistance was transferable and is, therefore, associated with mutations occurring on pMPPla107. Resequencing experiments demonstrated that resistance is likely due to a large deletion on the megaplasmid in one line, and to a nonsynonymous change in an uncharacterized megaplasmid locus in the other strain. We further used allele exchange experiments to confirm that resistance is due to this single amino acid change in a previously uncharacterized megaplasmid protein, which we name SkaA. These results provide further evidence that costs and phenotypic changes associated with horizontal gene transfer can be compensated through single mutational events and emphasize the power of experimental evolution and resequencing to better understand the genetic basis of evolved phenotypes. This article is part of the theme issue 'The secret lives of microbial mobile genetic elements'.}, }
@article {pmid34839710, year = {2022}, author = {Ghaly, TM and Gillings, MR}, title = {New perspectives on mobile genetic elements: a paradigm shift for managing the antibiotic resistance crisis.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {377}, number = {1842}, pages = {20200462}, pmid = {34839710}, issn = {1471-2970}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Humans ; *Interspersed Repetitive Sequences ; }, abstract = {Mobile genetic elements (MGEs) are primary facilitators in the global spread of antibiotic resistance. Here, we present novel ecological and evolutionary perspectives to understand and manage these elements: as selfish entities that exhibit biological individuality, as pollutants that replicate and as invasive species that thrive under human impact. Importantly, each viewpoint suggests new means to control their activity and spread. When seen as biological individuals, MGEs can be regarded as therapeutic targets in their own right. We highlight promising conjugation-inhibiting compounds that could be administered alongside antibiotic treatment. Viewed as pollutants, sewage treatment methods could be modified to efficiently remove antimicrobials and the resistance genes that they select. Finally, by recognizing the invasive characteristics of MGEs, we might apply strategies developed for the management of invasive species. These include environmental restoration to reduce antimicrobial selection, early detection to help inform appropriate antibiotic usage, and biocontrol strategies that target MGEs, constituting precision antimicrobials. These actions, which embody the One Health approach, target different characteristics of MGEs that are pertinent at the cellular, community, landscape and global levels. The strategies could act on multiple fronts and, together, might provide a more fruitful means to combat the global resistance crisis. This article is part of the theme issue 'The secret lives of microbial mobile genetic elements'.}, }
@article {pmid34839708, year = {2022}, author = {Billane, K and Harrison, E and Cameron, D and Brockhurst, MA}, title = {Why do plasmids manipulate the expression of bacterial phenotypes?.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {377}, number = {1842}, pages = {20200461}, pmid = {34839708}, issn = {1471-2970}, mesh = {Adaptation, Physiological ; *Bacteria/genetics ; *Conjugation, Genetic ; Gene Transfer, Horizontal ; Phenotype ; Plasmids/genetics ; }, abstract = {Conjugative plasmids play an important role in bacterial evolution by transferring niche-adaptive traits between lineages, thus driving adaptation and genome diversification. It is increasingly clear, however, that in addition to this evolutionary role, plasmids also manipulate the expression of a broad range of bacterial phenotypes. In this review, we argue that the effects that plasmids have on the expression of bacterial phenotypes may often represent plasmid adaptations, rather than mere deleterious side effects. We begin by summarizing findings from untargeted omics analyses, which give a picture of the global effects of plasmid acquisition on host cells. Thereafter, because many plasmids are capable of both vertical and horizontal transmission, we distinguish plasmid-mediated phenotypic effects into two main classes based upon their potential fitness benefit to plasmids: (i) those that promote the competitiveness of the host cell in a given niche and thereby increase plasmid vertical transmission, and (ii) those that promote plasmid conjugation and thereby increase plasmid horizontal transmission. Far from being mere vehicles for gene exchange, we propose that plasmids often act as sophisticated genetic parasites capable of manipulating their bacterial hosts for their own benefit. This article is part of the theme issue 'The secret lives of microbial mobile genetic elements'.}, }
@article {pmid34839707, year = {2022}, author = {Hall, JPJ and Botelho, J and Cazares, A and Baltrus, DA}, title = {What makes a megaplasmid?.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {377}, number = {1842}, pages = {20200472}, pmid = {34839707}, issn = {1471-2970}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Plasmids/genetics ; }, abstract = {Naturally occurring plasmids come in different sizes. The smallest are less than a kilobase of DNA, while the largest can be over three orders of magnitude larger. Historically, research has tended to focus on smaller plasmids that are usually easier to isolate, manipulate and sequence, but with improved genome assemblies made possible by long-read sequencing, there is increased appreciation that very large plasmids-known as megaplasmids-are widespread, diverse, complex, and often encode key traits in the biology of their host microorganisms. Why are megaplasmids so big? What other features come with large plasmid size that could affect bacterial ecology and evolution? Are megaplasmids 'just' big plasmids, or do they have distinct characteristics? In this perspective, we reflect on the distribution, diversity, biology, and gene content of megaplasmids, providing an overview to these large, yet often overlooked, mobile genetic elements. This article is part of the theme issue 'The secret lives of microbial mobile genetic elements'.}, }
@article {pmid34839705, year = {2022}, author = {Wardell, GE and Hynes, MF and Young, PJ and Harrison, E}, title = {Why are rhizobial symbiosis genes mobile?.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {377}, number = {1842}, pages = {20200471}, pmid = {34839705}, issn = {1471-2970}, mesh = {*Fabaceae/microbiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Rhizobium/genetics ; Symbiosis ; }, abstract = {Rhizobia are one of the most important and best studied groups of bacterial symbionts. They are defined by their ability to establish nitrogen-fixing intracellular infections within plant hosts. One surprising feature of this symbiosis is that the bacterial genes required for this complex trait are not fixed within the chromosome, but are encoded on mobile genetic elements (MGEs), namely plasmids or integrative and conjugative elements. Evidence suggests that many of these elements are actively mobilizing within rhizobial populations, suggesting that regular symbiosis gene transfer is part of the ecology of rhizobial symbionts. At first glance, this is counterintuitive. The symbiosis trait is highly complex, multipartite and tightly coevolved with the legume hosts, while transfer of genes can be costly and disrupt coadaptation between the chromosome and the symbiosis genes. However, horizontal gene transfer is a process driven not only by the interests of the host bacterium, but also, and perhaps predominantly, by the interests of the MGEs that facilitate it. Thus understanding the role of horizontal gene transfer in the rhizobium-legume symbiosis requires a 'mobile genetic element's-eye view' on the ecology and evolution of this important symbiosis. This article is part of the theme issue 'The secret lives of microbial mobile genetic elements'.}, }
@article {pmid34839704, year = {2022}, author = {Igler, C and Schwyter, L and Gehrig, D and Wendling, CC}, title = {Conjugative plasmid transfer is limited by prophages but can be overcome by high conjugation rates.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {377}, number = {1842}, pages = {20200470}, pmid = {34839704}, issn = {1471-2970}, mesh = {*Conjugation, Genetic ; Drug Resistance, Microbial ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Plasmids/genetics ; *Prophages/genetics ; }, abstract = {Antibiotic resistance spread via plasmids is a serious threat to successfully fight infections and makes understanding plasmid transfer in nature crucial to prevent the rise of antibiotic resistance. Studies addressing the dynamics of plasmid conjugation have yet neglected one omnipresent factor: prophages (viruses integrated into bacterial genomes), whose activation can kill host and surrounding bacterial cells. To investigate the impact of prophages on conjugation, we combined experiments and mathematical modelling. Using Escherichia coli, prophage λ and the multidrug-resistant plasmid RP4 we find that prophages can substantially limit the spread of conjugative plasmids. This inhibitory effect was strongly dependent on environmental conditions and bacterial genetic background. Our empirically parameterized model reproduced experimental dynamics of cells acquiring either the prophage or the plasmid well but could only reproduce the number of cells acquiring both elements by assuming complex interactions between conjugative plasmids and prophages in sequential infections. Varying phage and plasmid infection parameters over empirically realistic ranges revealed that plasmids can overcome the negative impact of prophages through high conjugation rates. Overall, the presence of prophages introduces an additional death rate for plasmid carriers, the magnitude of which is determined in non-trivial ways by the environment, the phage and the plasmid. This article is part of the theme issue 'The secret lives of microbial mobile genetic elements'.}, }
@article {pmid34839702, year = {2022}, author = {Wang, Y and Batra, A and Schulenburg, H and Dagan, T}, title = {Gene sharing among plasmids and chromosomes reveals barriers for antibiotic resistance gene transfer.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {377}, number = {1842}, pages = {20200467}, pmid = {34839702}, issn = {1471-2970}, mesh = {*Anti-Bacterial Agents/pharmacology ; Chromosomes ; Drug Resistance, Microbial/genetics ; *Gene Transfer, Horizontal ; Phylogeny ; Plasmids/genetics ; }, abstract = {The emergence of antibiotic resistant bacteria is a major threat to modern medicine. Rapid adaptation to antibiotics is often mediated by the acquisition of plasmids carrying antibiotic resistance (ABR) genes. Nonetheless, the determinants of plasmid-mediated ABR gene transfer remain debated. Here, we show that the propensity of ABR gene transfer via plasmids is higher for accessory chromosomal ABR genes in comparison with core chromosomal ABR genes, regardless of the resistance mechanism. Analysing the pattern of ABR gene occurrence in the genomes of 2635 Enterobacteriaceae isolates, we find that 33% of the 416 ABR genes are shared between chromosomes and plasmids. Phylogenetic reconstruction of ABR genes occurring on both plasmids and chromosomes supports their evolution by lateral gene transfer. Furthermore, accessory ABR genes (encoded in less than 10% of the chromosomes) occur more abundantly in plasmids in comparison with core ABR genes (encoded in greater than or equal to 90% of the chromosomes). The pattern of ABR gene occurrence in plasmids and chromosomes is similar to that in the total Escherichia genome. Our results thus indicate that the previously recognized barriers for gene acquisition by lateral gene transfer apply also to ABR genes. We propose that the functional complexity of the underlying ABR mechanism is an important determinant of ABR gene transferability. This article is part of the theme issue 'The secret lives of microbial mobile genetic elements'.}, }
@article {pmid34839701, year = {2022}, author = {Igler, C and Huisman, JS and Siedentop, B and Bonhoeffer, S and Lehtinen, S}, title = {Plasmid co-infection: linking biological mechanisms to ecological and evolutionary dynamics.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {377}, number = {1842}, pages = {20200478}, pmid = {34839701}, issn = {1471-2970}, mesh = {Bacteria/genetics ; *Coinfection ; Gene Transfer, Horizontal ; Humans ; Plasmids/genetics ; }, abstract = {As infectious agents of bacteria and vehicles of horizontal gene transfer, plasmids play a key role in bacterial ecology and evolution. Plasmid dynamics are shaped not only by plasmid-host interactions but also by ecological interactions between plasmid variants. These interactions are complex: plasmids can co-infect the same cell and the consequences for the co-resident plasmid can be either beneficial or detrimental. Many of the biological processes that govern plasmid co-infection-from systems that exclude infection by other plasmids to interactions in the regulation of plasmid copy number-are well characterized at a mechanistic level. Modelling plays a central role in translating such mechanistic insights into predictions about plasmid dynamics and the impact of these dynamics on bacterial evolution. Theoretical work in evolutionary epidemiology has shown that formulating models of co-infection is not trivial, as some modelling choices can introduce unintended ecological assumptions. Here, we review how the biological processes that govern co-infection can be represented in a mathematical model, discuss potential modelling pitfalls, and analyse this model to provide general insights into how co-infection impacts ecological and evolutionary outcomes. In particular, we demonstrate how beneficial and detrimental effects of co-infection give rise to frequency-dependent selection on plasmid variants. This article is part of the theme issue 'The secret lives of microbial mobile genetic elements'.}, }
@article {pmid34839699, year = {2022}, author = {van Dijk, B and Bertels, F and Stolk, L and Takeuchi, N and Rainey, PB}, title = {Transposable elements promote the evolution of genome streamlining.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {377}, number = {1842}, pages = {20200477}, pmid = {34839699}, issn = {1471-2970}, mesh = {*DNA Transposable Elements ; Eukaryota/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Prokaryotic Cells ; }, abstract = {Eukaryotes and prokaryotes have distinct genome architectures, with marked differences in genome size, the ratio of coding/non-coding DNA, and the abundance of transposable elements (TEs). As TEs replicate independently of their hosts, the proliferation of TEs is thought to have driven genome expansion in eukaryotes. However, prokaryotes also have TEs in intergenic spaces, so why do prokaryotes have small, streamlined genomes? Using an in silico model describing the genomes of single-celled asexual organisms that coevolve with TEs, we show that TEs acquired from the environment by horizontal gene transfer can promote the evolution of genome streamlining. The process depends on local interactions and is underpinned by rock-paper-scissors dynamics in which populations of cells with streamlined genomes beat TEs, which beat non-streamlined genomes, which beat streamlined genomes, in continuous and repeating cycles. Streamlining is maladaptive to individual cells, but improves lineage viability by hindering the proliferation of TEs. Streamlining does not evolve in sexually reproducing populations because recombination partially frees TEs from the deleterious effects they cause. This article is part of the theme issue 'The secret lives of microbial mobile genetic elements'.}, }
@article {pmid34838594, year = {2022}, author = {Alderson, MR and Arkwright, PD and Bai, X and Black, S and Borrow, R and Caugant, DA and Dinleyici, EC and Harrison, LH and Lucidarme, J and McNamara, LA and Meiring, S and Sáfadi, MAP and Shao, Z and Stephens, DS and Taha, MK and Vazquez, J and Zhu, B and Collaborators, G}, title = {Surveillance and control of meningococcal disease in the COVID-19 era: A Global Meningococcal Initiative review.}, journal = {The Journal of infection}, volume = {84}, number = {3}, pages = {289-296}, pmid = {34838594}, issn = {1532-2742}, mesh = {*COVID-19/prevention &amp; control ; Communicable Disease Control ; Humans ; *Meningococcal Infections/epidemiology/microbiology/prevention &amp; control ; *Meningococcal Vaccines/therapeutic use ; *Neisseria meningitidis/genetics ; SARS-CoV-2 ; Serogroup ; }, abstract = {This review article incorporates information from the 4th Global Meningococcal Initiative summit meeting. Since the introduction of stringent COVID-19 infection control and lockdown measures globally in 2020, there has been an impact on IMD prevalence, surveillance, and vaccination compliance. Incidence rates and associated mortality fell across various regions during 2020. A reduction in vaccine uptake during 2020 remains a concern globally. In addition, several Neisseria meningitidis clonal complexes, particularly CC4821 and CC11, continue to exhibit resistance to antibiotics, with resistance to ciprofloxacin or beta-lactams mainly linked to modifications of gyrA or penA alleles, respectively. Beta-lactamase acquisition was also reported through horizontal gene transfer (blaROB-1) involving other bacterial species. Despite the challenges over the past year, progress has also been made on meningococcal vaccine development, with several pentavalent (serogroups ABCWY and ACWYX) vaccines currently being studied in late-stage clinical trial programmes.}, }
@article {pmid34835338, year = {2021}, author = {Ghaly, TM and Gillings, MR and Penesyan, A and Qi, Q and Rajabal, V and Tetu, SG}, title = {The Natural History of Integrons.}, journal = {Microorganisms}, volume = {9}, number = {11}, pages = {}, pmid = {34835338}, issn = {2076-2607}, abstract = {Integrons were first identified because of their central role in assembling and disseminating antibiotic resistance genes in commensal and pathogenic bacteria. However, these clinically relevant integrons represent only a small proportion of integron diversity. Integrons are now known to be ancient genetic elements that are hotspots for genomic diversity, helping to generate adaptive phenotypes. This perspective examines the diversity, functions, and activities of integrons within both natural and clinical environments. We show how the fundamental properties of integrons exquisitely pre-adapted them to respond to the selection pressures imposed by the human use of antimicrobial compounds. We then follow the extraordinary increase in abundance of one class of integrons (class 1) that has resulted from its acquisition by multiple mobile genetic elements, and subsequent colonisation of diverse bacterial species, and a wide range of animal hosts. Consequently, this class of integrons has become a significant pollutant in its own right, to the extent that it can now be detected in most ecosystems. As human activities continue to drive environmental instability, integrons will likely continue to play key roles in bacterial adaptation in both natural and clinical settings. Understanding the ecological and evolutionary dynamics of integrons can help us predict and shape these outcomes that have direct relevance to human and ecosystem health.}, }
@article {pmid34834933, year = {2021}, author = {Turzynski, V and Monsees, I and Moraru, C and Probst, AJ}, title = {Imaging Techniques for Detecting Prokaryotic Viruses in Environmental Samples.}, journal = {Viruses}, volume = {13}, number = {11}, pages = {}, pmid = {34834933}, issn = {1999-4915}, mesh = {Genome, Viral ; Metagenomics ; Microscopy/*methods ; Microscopy, Electron/*methods ; Virome ; Viruses/classification/*genetics/isolation &amp; purification/ultrastructure ; }, abstract = {Viruses are the most abundant biological entities on Earth with an estimate of 10[31] viral particles across all ecosystems. Prokaryotic viruses-bacteriophages and archaeal viruses-influence global biogeochemical cycles by shaping microbial communities through predation, through the effect of horizontal gene transfer on the host genome evolution, and through manipulating the host cellular metabolism. Imaging techniques have played an important role in understanding the biology and lifestyle of prokaryotic viruses. Specifically, structure-resolving microscopy methods, for example, transmission electron microscopy, are commonly used for understanding viral morphology, ultrastructure, and host interaction. These methods have been applied mostly to cultivated phage-host pairs. However, recent advances in environmental genomics have demonstrated that the majority of viruses remain uncultivated, and thus microscopically uncharacterized. Although light- and structure-resolving microscopy of viruses from environmental samples is possible, quite often the link between the visualization and the genomic information of uncultivated prokaryotic viruses is missing. In this minireview, we summarize the current state of the art of imaging techniques available for characterizing viruses in environmental samples and discuss potential links between viral imaging and environmental genomics for shedding light on the morphology of uncultivated viruses and their lifestyles in Earth's ecosystems.}, }
@article {pmid34829250, year = {2021}, author = {Becerra-Rodríguez, C and Taghouti, G and Portier, P and Dequin, S and Casal, M and Paiva, S and Galeote, V}, title = {Yeast Plasma Membrane Fungal Oligopeptide Transporters Display Distinct Substrate Preferences despite Their High Sequence Identity.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {7}, number = {11}, pages = {}, pmid = {34829250}, issn = {2309-608X}, support = {764927//European Union's Horizon 2020 Research and Innovation Program/ ; }, abstract = {Fungal Oligopeptide Transporters (Fot) Fot1, Fot2 and Fot3 have been found in Saccharomyces cerevisiae wine strains, but not in strains from other environments. In the S. cerevisiae wine strain EC1118, Fot1 and Fot2 are responsible for a broader range of oligopeptide utilization in comparison with strains not containing any Fot. This leads to better fermentation efficiency and an increased production of desirable organoleptic compounds in wine. Despite the benefits associated with Fot activity in S. cerevisiae within the wine environment, little is known about this family of transporters in yeast. The presence of Fot1, Fot2 and Fot3 in S. cerevisiae wine strains is due to horizontal gene transfer from the yeast Torulaspora microellipsoides, which harbors Fot2Tm, FotX and FotY proteins. Sequence analyses revealed that Fot family members have a high sequence identity in these yeast species. In this work, we aimed to further characterize the different Fot family members in terms of subcellular localization, gene expression in enological fermentation and substrate specificity. Using CRISPR/Cas9, we constructed S. cerevisiae wine strains containing each different Fot as the sole oligopeptide transporter to analyze their oligopeptide preferences by phenotype microarrays. The results of oligopeptide consumption show that Fot counterparts have different di-/tripeptide specificities, suggesting that punctual sequence divergence between FOT genes can be crucial for substrate recognition, binding and transport activity. FOT gene expression levels in different S. cerevisiae wine strains during enological fermentation, together with predicted binding motifs for transcriptional regulators in nitrogen metabolism, indicate that these transporters may be under the control of the Nitrogen Catabolite Repression (NCR) system. Finally, we demonstrated that Fot1 is located in the yeast plasma membrane. This work contributes to a better understanding of this family of oligopeptide transporters, which have demonstrated a key role in the utilization of oligopeptides by S. cerevisiae in enological fermentation.}, }
@article {pmid34829248, year = {2021}, author = {Kawachi, T and Inuki, Y and Ogata, Y}, title = {Gcorn fungi: A Web Tool for Detecting Biases between Gene Evolution and Speciation in Fungi.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {7}, number = {11}, pages = {}, pmid = {34829248}, issn = {2309-608X}, abstract = {(1) Background: Fungi contain several millions of species, and the diversification of fungal genes has been achieved by speciation, gene duplication, and horizontal gene transfer. Although several databases provide information on orthologous and paralogous events, these databases show no information on biases between gene mutation and speciation. Here, we designed the Gcorn fungi database to better understand such biases. (2) Methods: Amino acid sequences of fungal genes in 249 species, which contain 2,345,743 sequences, were used for this database. Homologous genes were grouped at various thresholds of the homology index, which was based on the percentages of gene mutations. By grouping genes that showed highly similar homology indices to each other, we showed functional and evolutionary traits in the phylogenetic tree depicted for the gene of interest. (3) Results: Gcorn fungi provides well-summarized information on the evolution of a gene lineage and on the biases between gene evolution and speciation, which are quantitatively identified by the Robinson-Foulds metric. The database helps users visualize these traits using various depictions. (4) Conclusions: Gcorn fungi is an open access database that provides a variety of information with which to understand gene function and evolution.}, }
@article {pmid34827225, year = {2021}, author = {Tóth, AG and Csabai, I and Judge, MF and Maróti, G and Becsei, &#xc1; and Spisák, S and Solymosi, N}, title = {Mobile Antimicrobial Resistance Genes in Probiotics.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {10}, number = {11}, pages = {}, pmid = {34827225}, issn = {2079-6382}, support = {TKP 2020-4.1.1.-TKP2020//ITM Hungary/ ; 874735 (VEO)//Horizon 2020 Framework Programme/ ; Lend&#xfc;let-Programme (LP2020-5/2020)//Hungarian Academy of Sciences/ ; }, abstract = {Even though people worldwide tend to consume probiotic products for their beneficial health effects on a daily basis, recently, concerns were outlined regarding the uptake and potential intestinal colonisation of the bacteria that they carry. These bacteria are capable of executing horizontal gene transfer (HGT) which facilitates the movement of various genes, including antimicrobial resistance genes (ARGs), among the donor and recipient bacterial populations. Within our study, 47 shotgun sequencing datasets deriving from various probiotic samples (isolated strains and metagenomes) were bioinformatically analysed. We detected more than 70 ARGs, out of which rpoB mutants conferring resistance to rifampicin, tet(W/N/W) and potentially extended-spectrum beta-lactamase (ESBL) coding TEM-116 were the most common. Numerous ARGs were associated with integrated mobile genetic elements, plasmids or phages promoting the HGT. Our findings raise clinical and public health concerns as the consumption of probiotic products may lead to the transfer of ARGs to human gut bacteria.}, }
@article {pmid34818756, year = {2022}, author = {Du, S and Ge, AH and Liang, ZH and Xiang, JF and Xiao, JL and Zhang, Y and Liu, YR and Zhang, LM and Shen, JP}, title = {Fumigation practice combined with organic fertilizer increase antibiotic resistance in watermelon rhizosphere soil.}, journal = {The Science of the total environment}, volume = {805}, number = {}, pages = {150426}, doi = {10.1016/j.scitotenv.2021.150426}, pmid = {34818756}, issn = {1879-1026}, mesh = {*Citrullus ; Drug Resistance, Microbial ; Fertilizers ; Fumigation ; Genes, Bacterial ; Rhizosphere ; *Soil ; Soil Microbiology ; }, abstract = {Chemical fumigants and organic fertilizer are commonly used in facility agriculture to control soil-borne diseases and promote soil health. However, there is a lack of evidence for the effect of non-antibiotic fumigants on the distribution of antibiotic resistance genes (ARGs) in plant rhizosphere soils. Here, the response of a wide spectrum of ARGs and mobile genetic elements (MGEs) to dazomet fumigation practice in the rhizosphere soil of watermelon was investigated along its branching, flowering and fruiting growth stages in plastic shelters using high-throughput quantitative PCR approach. Our results indicated that soil fumigation combined with organic fertilizer application significantly increased the relative abundance of ARGs and MGEs in the rhizosphere soil of watermelon plant. The positive correlations between the relative abundance of ARGs and MGEs suggested that soil fumigation might increase the horizontal gene transfer (HGT) potential of ARGs. This result was further confirmed by the enhanced associations between ARG and MGE subtypes in the networks of fumigation treatments. Moreover, bipartite associations between ARGs/MGEs and microbial communities (bacteria and fungi) revealed a higher percentage of linkage between MGEs and microbial taxa in the fumigated soils. Structural equation model analysis further suggested that the increases in antibiotic resistance after fumigation and organic fertilizer application were mainly driven by MGEs and fungal community. Together, our results provide vital evidence that dazomet fumigation process combined with organic fertilizer in plastic shelters has the great potential to promote ARGs' dissemination in the rhizosphere, and raise cautions of the acquired resistance by soil-borne fungal pathogen and the potential spreading of ARGs along soil-plant continuum.}, }
@article {pmid34818109, year = {2022}, author = {Martínez de la Escalera, G and Segura, AM and Kruk, C and Ghattas, B and Cohan, FM and Iriarte, A and Piccini, C}, title = {Genotyping and Multivariate Regression Trees Reveal Ecological Diversification within the Microcystis aeruginosa Complex along a Wide Environmental Gradient.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {3}, pages = {e0147521}, pmid = {34818109}, issn = {1098-5336}, mesh = {Biodiversity ; Fresh Water/microbiology ; Genotype ; Harmful Algal Bloom ; Microcystins ; *Microcystis/genetics ; }, abstract = {Addressing the ecological and evolutionary processes underlying biodiversity patterns is essential to identify the mechanisms shaping community structure and function. In bacteria, the formation of new ecologically distinct populations (ecotypes) is proposed as one of the main drivers of diversification. New ecotypes arise when mutations in key functional genes or acquisition of new metabolic pathways by horizontal gene transfer allow the population to exploit new resources, permitting their coexistence with the parental population. We previously reported the presence of microcystin-producing organisms of the Microcystis aeruginosa complex (toxic MAC) through an 800-km environmental gradient ranging from freshwater to estuarine-marine waters in South America. We hypothesize that the success of toxic MAC in such a gradient is due to the existence of very closely related populations that are ecologically distinct (ecotypes), each specialized to a specific arrangement of environmental variables. Here, we analyzed toxic MAC genetic diversity through quantitative PCR (qPCR) and high-resolution melting analysis (HRMA) of a functional gene (mcyJ, microcystin synthetase cluster). We explored the variability of the mcyJ gene along the environmental gradient by multivariate classification and regression trees (mCART). Six groups of mcyJ genotypes were distinguished and associated with different combinations of water temperature, conductivity, and turbidity. We propose that each mcyJ variant associated with a defined environmental condition is an ecotype (or species) whose relative abundances vary according to their fitness in the local environment. This mechanism would explain the success of toxic MAC in such a wide array of environmental conditions. IMPORTANCE Organisms of the Microcystis aeruginosa complex form harmful algal blooms (HABs) in nutrient-rich water bodies worldwide. MAC HABs are difficult to manage owing to the production of potent toxins (microcystins) that resist water treatment. In addition, the role of microcystins in the ecology of MAC organisms is still elusive, meaning that the environmental conditions driving the toxicity of the bloom are not clear. Furthermore, the lack of coherence between morphology-based and genomic-based species classification makes it difficult to draw sound conclusions about when and where each member species of the MAC will dominate the bloom. Here, we propose that the diversification process and success of toxic MAC in a wide range of water bodies involves the generation of ecotypes, each specialized in a particular niche, whose relative abundance varies according to its fitness in the local environment. This knowledge can improve the generation of accurate prediction models of MAC growth and toxicity, helping to prevent human and animal intoxication.}, }
@article {pmid34817285, year = {2021}, author = {Xiao, Y and Jiang, R and Wu, X and Zhong, Q and Li, Y and Wang, H}, title = {Comparative Genomic Analysis of Stenotrophomonas maltophilia Strain W18 Reveals Its Adaptative Genomic Features for Degrading Polycyclic Aromatic Hydrocarbons.}, journal = {Microbiology spectrum}, volume = {9}, number = {3}, pages = {e0142021}, pmid = {34817285}, issn = {2165-0497}, mesh = {Adaptation, Physiological/genetics ; Alcohol Dehydrogenase/genetics ; *Biodegradation, Environmental ; Environmental Pollutants/metabolism ; Genome, Bacterial/*genetics ; Genomics ; Phylogeny ; Polycyclic Aromatic Hydrocarbons/*metabolism ; Stenotrophomonas maltophilia/*genetics/*metabolism ; }, abstract = {Polycyclic aromatic hydrocarbons (PAHs) are hazardous pollutants that are ubiquitous in the environment. Numerous bacteria have evolved to have degrading genes or pathways to degrade PAHs. Stenotrophomonas maltophilia strain W18 was found to be able to degrade PAHs. Including 43 other complete genome sequences of S. maltophilia strains, we performed a comparative genomic analysis of 44 S. maltophilia strains by running OrthoFinder. A KEGG pathway enrichment analysis of environmental and clinical isolates of S. maltophilia revealed that environmental isolates tended to enhance gene functions such as "energy metabolism," "amino acid metabolism," "xenobiotic biodegradation and metabolism," and "folding, sorting, and degradation." The pangenome of the 44 S. maltophilia strains was open, while the core genome was estimated to reach a steady plateau. Based on gene annotations, we inferred that most of the degradation potential came from the core genome of S. maltophilia, while character genes and accessory genes also contributed to the degradation ability of S. maltophilia W18. The genes expression level of core genes, character genes and accessory genes were proved by RT-qPCR experiment, and accessory genes encoding alcohol dehydrogenase were upregulated most compared with genes with similar functions. We performed a credible comparative genomic analysis of S. maltophilia strains. S. maltophilia W18 was set as a model PAH-degrading bacterium of this species in this study, which would provide guidance for understanding and predicting the degradation mechanisms of other PAH-degrading S. maltophilia strains lacking complete genome data or waiting to be determined. IMPORTANCE This study provided the latest comparative genomic analysis on Stenotrophomonas maltophilia strains and focused on analyzing their genomic features that allow them to adapt to natural environments. In this study, we set S. maltophilia W18 as a typical PAH-degrading strain of this species. By discussing the genomic adaptative features of degrading PAH, we can predict genomic adaptative features of other S. maltophilia PAH-degrading strains since the core function of this species is stable. The gene functions of how S. maltophilia environmental isolates are enhanced for adaptation to various natural environments compared with clinical isolates have been revealed. Combined with a pangenome analysis and RT-qPCR results, we have proved that core genes, character genes, and accessory genes are all involved in PAH degradation. Accessory genes encoding alcohol dehydrogenase were upregulated most compared with core and character genes with similar functions, which suggests that PAH metabolization potential might be enhanced by horizontal gene transfer.}, }
@article {pmid34815098, year = {2022}, author = {Lee, IPA and Eldakar, OT and Gogarten, JP and Andam, CP}, title = {Bacterial cooperation through horizontal gene transfer.}, journal = {Trends in ecology &amp; evolution}, volume = {37}, number = {3}, pages = {223-232}, doi = {10.1016/j.tree.2021.11.006}, pmid = {34815098}, issn = {1872-8383}, mesh = {*Bacteria/genetics ; *Gene Transfer, Horizontal ; Humans ; }, abstract = {Cooperation exists across all scales of biological organization, from genetic elements to complex human societies. Bacteria cooperate by secreting molecules that benefit all individuals in the population (i.e., public goods). Genes associated with cooperation can spread among strains through horizontal gene transfer (HGT). We discuss recent findings on how HGT mediated by mobile genetic elements promotes bacterial cooperation, how cooperation in turn can facilitate more frequent HGT, and how the act of HGT itself may be considered as a form of cooperation. We propose that HGT is an important enforcement mechanism in bacterial populations, thus creating a positive feedback loop that further maintains cooperation. To enforce cooperation, HGT serves as a homogenizing force by transferring the cooperative trait, effectively eliminating cheaters.}, }
@article {pmid34813930, year = {2022}, author = {Jia, Y and Yang, B and Shi, J and Fang, D and Wang, Z and Liu, Y}, title = {Melatonin prevents conjugative transfer of plasmid-mediated antibiotic resistance genes by disrupting proton motive force.}, journal = {Pharmacological research}, volume = {175}, number = {}, pages = {105978}, doi = {10.1016/j.phrs.2021.105978}, pmid = {34813930}, issn = {1096-1186}, mesh = {Adenosine Triphosphate/metabolism ; Ampicillin ; Animals ; Anti-Bacterial Agents ; Cell Membrane Permeability/drug effects ; Chloramphenicol ; Drug Resistance, Microbial/*genetics ; Escherichia coli/drug effects/genetics/growth &amp; development/metabolism ; Escherichia coli Infections ; Escherichia coli Proteins/genetics ; Female ; Genes, Bacterial ; Melatonin/*pharmacology ; Mice, Inbred ICR ; Plasmids ; Proton-Motive Force/*drug effects ; Reactive Oxygen Species/metabolism ; Mice ; }, abstract = {The widespread dissemination of antibiotic resistance genes (ARGs) is a serious problem and constitutes a threat for public health. Plasmid-mediated conjugative transfer of ARGs is recognized as one of the most important pathways accounting for this global crisis. Inhibiting the conjugative transfer of resistant gene-bearing plasmids provides a feasible strategy to prevent the spread of antibiotic resistance. Here we found that melatonin, a neurohormone secreted from pineal gland, substantially inhibited the horizontal transfer of RP4-7 plasmid in a dose-dependent manner. Furthermore, melatonin could also suppress the conjugal frequency of different types of clinical plasmids that carrying colistin resistance gene mcr-1 rather than blaNDM or tet(X) genes. Next, we investigated the mechanisms underlying the inhibitory effect of melatonin on conjugation. As a result, we showed that the addition of melatonin markedly reduced bacterial membrane permeability and inhibited the oxidative stress. In line with these observations, the conjugative transfer-related genes were regulated accordingly. Most importantly, we uncovered that melatonin disrupted bacterial proton motive force (PMF), which is an essential bacterial energy metabolism substance and is important for conjugative process. Collectively, these results provide implications that some non-antibiotics such as melatonin are effective inhibitors of transmission of ARGs and raise a promising strategy to confront the increasing resistant infections.}, }
@article {pmid34813845, year = {2022}, author = {Kaur, K and Reddy, S and Barathe, P and Oak, U and Shriram, V and Kharat, SS and Govarthanan, M and Kumar, V}, title = {Microplastic-associated pathogens and antimicrobial resistance in environment.}, journal = {Chemosphere}, volume = {291}, number = {Pt 2}, pages = {133005}, doi = {10.1016/j.chemosphere.2021.133005}, pmid = {34813845}, issn = {1879-1298}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents ; Drug Resistance, Bacterial ; Ecosystem ; Humans ; *Microplastics ; Plastics ; }, abstract = {The ubiquitous use of microplastics and their release into the environment especially the water bodies by anthropogenic/industrial activities are the major resources for microplastic contamination. The widespread and often injudicious use of antimicrobial drugs or antibiotics in various sectors including human health and hygiene, agriculture, animal husbandry and food industries are leading to the release of antibiotics into the wastewater/sewage and other water bodies, particularly in urban setups and thus leads to the antimicrobial resistance (AMR) in the microbes. Microplastics are emerging as the hubs as well as effective carriers of these microbial pathogens beside their AMR-genes (ARGs) in marine, freshwater, sewage/wastewater, and urban river ecosystems. These drug resistant bacteria interact with microplastics forming synthetic plastispheres, the ideal niche for biofilm formations which in turn facilitates the transfer of ARGs via horizontal gene transfer and further escalates the occurrence and levels of AMR. Microplastic-associated AMR is an emerging threat for human health and healthcare besides being a challenge for the research community for effective management/address of this menace. In this review, we encompass the increasing prevalence of microplastics in environment, emphasizing mainly on water environments, how they act as centers and vectors of microbial pathogens with their associated bacterial assemblage compositions and ultimately lead to AMR. It further discusses the mechanistic insights on how microplastics act as hosts of biofilms (creating the plastisphere). We have also presented the modern toolbox used for microplastic-biofilm analyses. A review on potential strategies for addressing microplastic-associated AMR is given with recent success stories, challenges and future prospects.}, }
@article {pmid34809942, year = {2022}, author = {Pswarayi, F and Qiao, N and Gaur, G and Gänzle, M}, title = {Antimicrobial plant secondary metabolites, MDR transporters and antimicrobial resistance in cereal-associated lactobacilli: is there a connection?.}, journal = {Food microbiology}, volume = {102}, number = {}, pages = {103917}, doi = {10.1016/j.fm.2021.103917}, pmid = {34809942}, issn = {1095-9998}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/*genetics ; *Edible Grain/metabolism/microbiology ; Fermented Beverages/microbiology ; Genes, Bacterial ; *Genes, MDR ; *Lactobacillus/drug effects/genetics ; Secondary Metabolism ; Zimbabwe ; }, abstract = {Cereal-associated lactobacilli resist antimicrobial plant secondary metabolites. This study aimed to identify multi-drug-resistance (MDR) transporters in isolates from mahewu, a Zimbabwean fermented cereal beverage, and to determine whether these MDR-transporters relate to resistance against phenolic compounds and antibiotics. Comparative genomic analyses indicated that all seven mahewu isolates harbored multiple MATE and MFS MDR proteins. Strains of Lactiplantibacillus plantarum and Limosilactobacillus fermentum encoded for the same gene, termed mahewu phenolics resistance gene mprA, with more than 99% nucleotide identity, suggesting horizontal gene transfer. Strains of Lp. plantarum were more resistant than strains of Lm. fermentum to phenolic acids, other antimicrobials and antibiotics but the origins of strains were not related to resistance. The resistance of several strains exceeded EFSA thresholds for several antibiotics. Analysis of gene expression in one strain each of Lp. plantarum and Lm. fermentum revealed that at least one MDR gene in each strain was over-expressed during growth in wheat, sorghum and millet relative to growth in MRS5 broth. In addition, both strains over-expressed a phenolic acid reductase. The results suggest that diverse lactobacilli in mahewu share MDR transporters acquired by lateral gene transfer, and that these transporters mediate resistance to secondary plant metabolites and antibiotics.}, }
@article {pmid34809466, year = {2021}, author = {Chase, AB and Sweeney, D and Muskat, MN and Guillén-Matus, DG and Jensen, PR}, title = {Vertical Inheritance Facilitates Interspecies Diversification in Biosynthetic Gene Clusters and Specialized Metabolites.}, journal = {mBio}, volume = {12}, number = {6}, pages = {e0270021}, pmid = {34809466}, issn = {2150-7511}, support = {R01 GM085770/GM/NIGMS NIH HHS/United States ; T32 GM067550/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/metabolism ; Biosynthetic Pathways ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Micromonosporaceae/classification/*genetics/*metabolism ; *Multigene Family ; Phylogeny ; Recombination, Genetic ; Secondary Metabolism ; }, abstract = {While specialized metabolites are thought to mediate ecological interactions, the evolutionary processes driving chemical diversification, particularly among closely related lineages, remain poorly understood. Here, we examine the evolutionary dynamics governing the distribution of natural product biosynthetic gene clusters (BGCs) among 118 strains representing all nine currently named species of the marine actinobacterial genus Salinispora. While much attention has been given to the role of horizontal gene transfer (HGT) in structuring BGC distributions, we find that vertical descent facilitates interspecies BGC diversification over evolutionary timescales. Moreover, we identified a distinct phylogenetic signal among Salinispora species at both the BGC and metabolite level, indicating that specialized metabolism represents a conserved phylogenetic trait. Using a combination of genomic analyses and liquid chromatography-high-resolution tandem mass spectrometry (LC-MS/MS) targeting nine experimentally characterized BGCs and their small molecule products, we identified gene gain/loss events, constrained interspecies recombination, and other evolutionary processes associated with vertical inheritance as major contributors to BGC diversification. These evolutionary dynamics had direct consequences for the compounds produced, as exemplified by species-level differences in salinosporamide production. Together, our results support the concept that specialized metabolites, and their cognate BGCs, can represent phylogenetically conserved functional traits with chemical diversification proceeding in species-specific patterns over evolutionary time frames. IMPORTANCE Microbial natural products are traditionally exploited for their pharmaceutical potential, yet our understanding of the evolutionary processes driving BGC evolution and compound diversification remain poorly developed. While HGT is recognized as an integral driver of BGC distributions, we find that the effects of vertical inheritance on BGC diversification had direct implications for species-level specialized metabolite production. As such, understanding the degree of genetic variation that corresponds to species delineations can enhance natural product discovery efforts. Resolving the evolutionary relationships between closely related strains and specialized metabolism can also facilitate our understanding of the ecological roles of small molecules in structuring the environmental distribution of microbes.}, }
@article {pmid34804105, year = {2021}, author = {Ramos-González, PL and Pons, T and Chabi-Jesus, C and Arena, GD and Freitas-Astua, J}, title = {Poorly Conserved P15 Proteins of Cileviruses Retain Elements of Common Ancestry and Putative Functionality: A Theoretical Assessment on the Evolution of Cilevirus Genomes.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {771983}, pmid = {34804105}, issn = {1664-462X}, abstract = {The genus Cilevirus groups enveloped single-stranded (+) RNA virus members of the family Kitaviridae, order Martellivirales. Proteins P15, scarcely conserved polypeptides encoded by cileviruses, have no apparent homologs in public databases. Accordingly, the open reading frames (ORFs) p15, located at the 5'-end of the viral RNA2 molecules, are considered orphan genes (ORFans). In this study, we have delved into ORFs p15 and the relatively poorly understood biochemical properties of the proteins P15 to posit their importance for viruses across the genus and theorize on their origin. We detected that the ORFs p15 are under purifying selection and that, in some viral strains, the use of synonymous codons is biased, which might be a sign of adaptation to their plant hosts. Despite the high amino acid sequence divergence, proteins P15 show the conserved motif [FY]-L-x(3)-[FL]-H-x-x-[LIV]-S-C-x-C-x(2)-C-x-G-x-C, which occurs exclusively in members of this protein family. Proteins P15 also show a common predicted 3D structure that resembles the helical scaffold of the protein ORF49 encoded by radinoviruses and the phosphoprotein C-terminal domain of mononegavirids. Based on the 3D structural similarities of P15, we suggest elements of common ancestry, conserved functionality, and relevant amino acid residues. We conclude by postulating a plausible evolutionary trajectory of ORFans p15 and the 5'-end of the RNA2 of cileviruses considering both protein fold superpositions and comparative genomic analyses with the closest kitaviruses, negeviruses, nege/kita-like viruses, and unrelated viruses that share the ecological niches of cileviruses.}, }
@article {pmid34803938, year = {2021}, author = {Popin, RV and Alvarenga, DO and Castelo-Branco, R and Fewer, DP and Sivonen, K}, title = {Mining of Cyanobacterial Genomes Indicates Natural Product Biosynthetic Gene Clusters Located in Conjugative Plasmids.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {684565}, pmid = {34803938}, issn = {1664-302X}, abstract = {Microbial natural products are compounds with unique chemical structures and diverse biological activities. Cyanobacteria commonly possess a wide range of biosynthetic gene clusters (BGCs) to produce natural products. Although natural product BGCs have been found in almost all cyanobacterial genomes, little attention has been given in cyanobacterial research to the partitioning of these biosynthetic pathways in chromosomes and plasmids. Cyanobacterial plasmids are believed to disperse several natural product BGCs, such as toxins, by plasmids through horizontal gene transfer. Therefore, plasmids may confer the ability to produce toxins and may play a role in the evolution of diverse natural product BGCs from cyanobacteria. Here, we performed an analysis of the distribution of natural product BGCs in 185 genomes and mapped the presence of genes involved in the conjugation in plasmids. The 185 analyzed genomes revealed 1817 natural products BGCs. Individual genomes contained 1-42 biosynthetic pathways (mean 8), 95% of which were present in chromosomes and the remaining 5% in plasmids. Of the 424 analyzed cyanobacterial plasmids, 12% contained homologs of genes involved in conjugation and natural product biosynthetic pathways. Among the biosynthetic pathways in plasmids, manual curation identified those to produce aeruginosin, anabaenopeptin, ambiguine, cryptophycin, hassallidin, geosmin, and microcystin. These compounds are known toxins, protease inhibitors, odorous compounds, antimicrobials, and antitumorals. The present study provides in silico evidence using genome mining that plasmids may be involved in the distribution of natural product BGCs in cyanobacteria. Consequently, cyanobacterial plasmids have importance in the context of biotechnology, water management, and public health risk assessment. Future research should explore in vivo conjugation and the end products of natural product BGCs in plasmids via chemical analyses.}, }
@article {pmid34803935, year = {2021}, author = {Hernández-Beltrán, JCR and San Millán, A and Fuentes-Hernández, A and Peña-Miller, R}, title = {Mathematical Models of Plasmid Population Dynamics.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {606396}, pmid = {34803935}, issn = {1664-302X}, abstract = {With plasmid-mediated antibiotic resistance thriving and threatening to become a serious public health problem, it is paramount to increase our understanding of the forces that enable the spread and maintenance of drug resistance genes encoded in mobile genetic elements. The relevance of plasmids as vehicles for the dissemination of antibiotic resistance genes, in addition to the extensive use of plasmid-derived vectors for biotechnological and industrial purposes, has promoted the in-depth study of the molecular mechanisms controlling multiple aspects of a plasmids' life cycle. This body of experimental work has been paralleled by the development of a wealth of mathematical models aimed at understanding the interplay between transmission, replication, and segregation, as well as their consequences in the ecological and evolutionary dynamics of plasmid-bearing bacterial populations. In this review, we discuss theoretical models of plasmid dynamics that span from the molecular mechanisms of plasmid partition and copy-number control occurring at a cellular level, to their consequences in the population dynamics of complex microbial communities. We conclude by discussing future directions for this exciting research topic.}, }
@article {pmid34801721, year = {2022}, author = {Yin, Z and Zhou, X and Kang, J and Pei, F and Du, R and Ye, Z and Ding, H and Ping, W and Ge, J}, title = {Intraspecific and interspecific quorum sensing of bacterial community affects the fate of antibiotic resistance genes during chicken manure composting under penicillin G stress.}, journal = {Bioresource technology}, volume = {347}, number = {}, pages = {126372}, doi = {10.1016/j.biortech.2021.126372}, pmid = {34801721}, issn = {1873-2976}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Chickens ; *Composting ; Drug Resistance, Microbial ; Genes, Bacterial ; Manure ; Penicillin G ; Quorum Sensing ; }, abstract = {In this study, the effects of penicillin G (PENG) on the fate of bacterial communities and β-lactamase antibiotic resistance genes (ARGs) during chicken manure composting were assessed, to illustrate the roles of PENG in ARGs behavior. The results showed that the total absolute abundances of 9 ARGs and 4 mobile genetic elements (MGEs) was significantly increased by PENG (P < 0.05). Dozens of potential hosts for ARGs were predominantly affiliated with Firmicutes, Proteobacteria, and Actinobacteria. Meanwhile, the higher concentration of PENG significantly increased the abundance of luxI and luxS in quorum sensing (QS) (P < 0.05), which enhanced the frequency of inter/intraspecific gene "communication." Redundancy analysis and structural equation modeling further revealed that QS had a strong regulatory role in horizontal gene transfer of ARGs mediated via MGEs. These results provide new insight into the mechanism of ARGs propagation in aerobic composting modified by PENG.}, }
@article {pmid34799177, year = {2022}, author = {Guo, A and Zhou, Q and Bao, Y and Qian, F and Zhou, X}, title = {Prochloraz alone or in combination with nano-CuO promotes the conjugative transfer of antibiotic resistance genes between Escherichia coli in pure water.}, journal = {Journal of hazardous materials}, volume = {424}, number = {Pt D}, pages = {127761}, doi = {10.1016/j.jhazmat.2021.127761}, pmid = {34799177}, issn = {1873-3336}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; *Escherichia coli/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Imidazoles ; Plasmids/genetics ; Water ; }, abstract = {Conjugative plasmid transfer is a major contributor to the spread of antibiotic resistance genes (ARGs). However, the role of conventional fungicides on conjugative plasmid transfer has been neglected. Based on the condition that the increasing use of the combination of nano- and conventional fungicides will lead to combined contamination, the effects of a conventional fungicide prochloraz alone or in combination with nano-CuO on the conjugation of plasmid RP4 between Escherichia coli in phosphate-buffered saline were investigated in this study. The results demonstrated that 50 µg/L prochloraz alone significantly increased the conjugative transfer by 1.82 folds. The combination of 100 µg/L nano-CuO and prochloraz at 5, 50, and 500 µg/L significantly increased the conjugation by 2.56, 3.61, and 2.13 folds, respectively. The promotion of conjugative transfer of ARGs mediated by fungicides is mainly attributed to (i) the increased cell membrane permeability, (ii) the increased cell adhesion via enhancing the synthesis of polysaccharides in extracellular polymeric substances, and (iii) the up-regulation of the genes relevant to conjugation, oxidative stress, SOS response, outer membrane, polysaccharide export, intercellular adhesion, and ATP synthesis. Our findings provide evidence for the contribution of fungicides to ARGs transfer, which is significant to control the risk of ARGs dissemination.}, }
@article {pmid34793465, year = {2021}, author = {Rapala, J and Miller, B and Garcia, M and Dolan, M and Bockman, M and Hansson, M and Russell, DA and Garlena, RA and Cresawn, SG and Westbye, AB and Beatty, JT and Alvey, RM and Bollivar, DW}, title = {Genomic diversity of bacteriophages infecting Rhodobacter capsulatus and their relatedness to its gene transfer agent RcGTA.}, journal = {PloS one}, volume = {16}, number = {11}, pages = {e0255262}, pmid = {34793465}, issn = {1932-6203}, mesh = {Bacterial Proteins/*genetics ; Bacteriophages/*genetics ; *Gene Expression Regulation, Bacterial ; Gene Transfer Techniques ; *Genetic Variation ; Rhodobacter capsulatus/*virology ; }, abstract = {The diversity of bacteriophages is likely unparalleled in the biome due to the immense variety of hosts and the multitude of viruses that infect them. Recent efforts have led to description at the genomic level of numerous bacteriophages that infect the Actinobacteria, but relatively little is known about those infecting other prokaryotic phyla, such as the purple non-sulfur photosynthetic α-proteobacterium Rhodobacter capsulatus. This species is a common inhabitant of freshwater ecosystems and has been an important model system for the study of photosynthesis. Additionally, it is notable for its utilization of a unique form of horizontal gene transfer via a bacteriophage-like element known as the gene transfer agent (RcGTA). Only three bacteriophages of R. capsulatus had been sequenced prior to this report. Isolation and characterization at the genomic level of 26 new bacteriophages infecting this host advances the understanding of bacteriophage diversity and the origins of RcGTA. These newly discovered isolates can be grouped along with three that were previously sequenced to form six clusters with four remaining as single representatives. These bacteriophages share genes with RcGTA that seem to be related to host recognition. One isolate was found to cause lysis of a marine bacterium when exposed to high-titer lysate. Although some clusters are more highly represented in the sequenced genomes, it is evident that many more bacteriophage types that infect R. capsulatus are likely to be found in the future.}, }
@article {pmid34789573, year = {2021}, author = {Chlebek, JL and Denise, R and Craig, L and Dalia, AB}, title = {Motor-independent retraction of type IV pili is governed by an inherent property of the pilus filament.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {47}, pages = {}, pmid = {34789573}, issn = {1091-6490}, support = {R35 GM128674/GM/NIGMS NIH HHS/United States ; }, mesh = {Acinetobacter ; Adenosine Triphosphatases ; Fimbriae Proteins/*chemistry/*genetics ; Fimbriae, Bacterial/*chemistry/*genetics ; Type II Secretion Systems ; Vibrio cholerae ; Virulence ; }, abstract = {Type IV pili (T4P) are dynamic surface appendages that promote virulence, biofilm formation, horizontal gene transfer, and motility in diverse bacterial species. Pilus dynamic activity is best characterized in T4P that use distinct ATPase motors for pilus extension and retraction. Many T4P systems, however, lack a dedicated retraction motor, and the mechanism underlying this motor-independent retraction remains a mystery. Using the Vibrio cholerae competence pilus as a model system, we identify mutations in the major pilin gene that enhance motor-independent retraction. These mutants likely diminish pilin-pilin interactions within the filament to produce less-stable pili. One mutation adds a bulky residue to α1C, a universally conserved feature of T4P. We found that inserting a bulky residue into α1C of the retraction motor-dependent Acinetobacter baylyi competence T4P enhances motor-independent retraction. Conversely, removing bulky residues from α1C of the retraction motor-independent, V. cholerae toxin-coregulated T4P stabilizes the filament and diminishes pilus retraction. Furthermore, alignment of pilins from the broader type IV filament (T4F) family indicated that retraction motor-independent T4P, gram-positive Com pili, and type II secretion systems generally encode larger residues within α1C oriented toward the pilus core compared to retraction motor-dependent T4P. Together, our data demonstrate that motor-independent retraction relies, in part, on the inherent instability of the pilus filament, which may be a conserved feature of diverse T4Fs. This provides evidence for a long-standing yet previously untested model in which pili retract in the absence of a motor by spontaneous depolymerization.}, }
@article {pmid34788805, year = {2021}, author = {Heß, S and Kneis, D and Virta, M and Hiltunen, T}, title = {The spread of the plasmid RP4 in a synthetic bacterial community is dependent on the particular donor strain.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {12}, pages = {}, doi = {10.1093/femsec/fiab147}, pmid = {34788805}, issn = {1574-6941}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Conjugation, Genetic ; Drug Resistance, Microbial ; *Escherichia coli/genetics ; *Gene Transfer, Horizontal ; Plasmids/genetics ; }, abstract = {The rapid spread of antibiotic resistance challenges modern medicine. So far, mechanistic and quantitative knowledge concerning the spread of resistance genes mainly relies on laboratory experiments with simplified setups, e.g. two strain communities. Thus, the transferability of the obtained process rates might be limited. To investigate the role of a diverse community concerning the dissemination of the multidrug resistance plasmid RP4, an Escherichia coli harboring RP4 invaded a microbial community consisting of 21 species. Changes in the community composition as well as plasmid uptake by community members were monitored for 22 days. Special focus was laid on the question of whether the observed changes were dependent on the actual invading donor isolate and the ambient antibiotic concentration. In our microcosm experiment, the community composition was primarily influenced by the given environmental variables and only secondarily by the particular invader E. coli. The establishment of resistance within the community, however, was directly dependent on the donor identity. The extent to which ambient conditions influence the spread of RP4 depended on the E. coli donor strain. These results emphasize that even within one species there are great differences in the ability to conquer an ecological niche and to spread antibiotic resistance.}, }
@article {pmid34788437, year = {2022}, author = {Schmidt, JW and Murray, SA and Dickey, AM and Wheeler, TL and Harhay, DM and Arthur, TM}, title = {Twenty-Four-Month Longitudinal Study Suggests Little to No Horizontal Gene Transfer In Situ between Third-Generation Cephalosporin-Resistant Salmonella and Third-Generation Cephalosporin-Resistant Escherichia coli in a Beef Cattle Feedyard.}, journal = {Journal of food protection}, volume = {85}, number = {2}, pages = {323-335}, doi = {10.4315/JFP-21-371}, pmid = {34788437}, issn = {1944-9097}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Cattle ; Cephalosporins/pharmacology ; *Escherichia coli ; Gene Transfer, Horizontal ; Longitudinal Studies ; *Salmonella enterica/genetics ; }, abstract = {ABSTRACT: Third-generation cephalosporins (3GCs) are preferred treatments for serious human Salmonella enterica infections. Beef cattle are suspected to contribute to human 3GC-resistant Salmonella infections. Commensal 3GC-resistant Escherichia coli are thought to act as reservoirs of 3GC resistance because these strains are isolated more frequently than are 3GC-resistant Salmonella strains at beef cattle feedyards. During each of 24 consecutive months, four samples of pen surface material were obtained from five pens (N = 480) at a Nebraska feedyard to determine to the contribution of 3GC-resistant E. coli to the occurrence of 3GC-resistant Salmonella. Illumina whole genome sequencing was performed, and susceptibility to 14 antimicrobial agents was determined for 121 3GC-susceptible Salmonella, 121 3GC-resistant Salmonella, and 203 3GC-resistant E. coli isolates. 3GC-susceptible Salmonella isolates were predominantly from serotypes Muenchen (70.2%) and Montevideo clade 1 (23.1%). 3GC-resistant Salmonella isolates were predominantly from serotypes Montevideo clade 2 (84.3%). One bla gene type (blaCMY-2) and the IncC plasmid replicon were present in 100 and 97.5% of the 3GC-resistant Salmonella, respectively. Eleven bla gene types were detected in the 3GC-resistant E. coli, which were distributed across 42 multilocus sequence types. The blaCMY-2 gene and IncC plasmid replicon were present in 37.9 and 9.9% of the 3GC-resistant E. coli, respectively. These results suggest that 3GC resistance in Salmonella was primarily due the persistence of Salmonella Montevideo clade 2 with very minimal or no contribution from 3GC-resistant E. coli via horizontal gene transfer and that 3GC-resistant E. coli may not be a useful indicator for 3GC-resistant Salmonella in beef cattle production environments.}, }
@article {pmid34786676, year = {2022}, author = {Pandey, RS and Azad, RK}, title = {A Protocol for Horizontally Acquired Metabolic Gene Detection in Algae.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2396}, number = {}, pages = {61-69}, pmid = {34786676}, issn = {1940-6029}, mesh = {*Gene Transfer, Horizontal ; Genomics ; Phylogeny ; Prokaryotic Cells ; }, abstract = {Horizontal gene transfer (HGT) or lateral gene transfer (LGT), the exchange of genetic materials among organisms by means of other than parent-to-offspring (vertical) inheritance, plays a major role in prokaryotic genome evolution, facilitating adaptation of prokaryotes to changes in the environment. Phylogenetic methods have been frequently invoked to catalog horizontally acquired genes; however, these methods are often constrained by the paucity of sequenced genomes of close relatives (and even distant relatives) for a robust analysis and reliable inference. In this chapter, we describe a HGT quantification protocol that exploits the complementary strengths of the integrative segmentation and clustering method and the comparative genomics approach to identify foreign genes. Users can use this pipeline in combination with phylogenetic tree reconstruction to identify foreign genes that are supported by multiple lines of evidence, that is, atypical composition, atypical distribution in close relatives, and aberrant phylogenetic pattern.}, }
@article {pmid34784078, year = {2021}, author = {Nagy, I and Szabó, M and Hegyi, A and Kiss, J}, title = {Salmonella Genomic Island 1 requires a self-encoded small RNA for mobilization.}, journal = {Molecular microbiology}, volume = {116}, number = {6}, pages = {1533-1551}, pmid = {34784078}, issn = {1365-2958}, mesh = {Bacterial Proteins/genetics/metabolism ; Conjugation, Genetic ; Drug Resistance, Multiple, Bacterial ; *Gene Transfer, Horizontal ; *Genomic Islands ; Plasmids/genetics/metabolism ; RNA, Bacterial/*genetics/metabolism ; Salmonella/*genetics/metabolism ; }, abstract = {The SGI1-family elements that are specifically mobilized by the IncA- and IncC-family plasmids are important vehicles of antibiotic resistance among enteric bacteria. Although SGI1 exploits many plasmid-derived conjugation and regulatory functions, the basic mobilization module of the island is unrelated to that of IncC plasmids. This module contains the oriT and encodes the mobilization proteins MpsA and MpsB, which belong to the tyrosine recombinases and not to relaxases. Here we report an additional, essential transfer factor of SGI1. This is a small RNA deriving from the 3'-end of a primary RNA that can also serve as mRNA of ORF S022. The functional domain of this sRNA named sgm-sRNA is encoded between the mpsA gene and the oriT of SGI1. Terminator-like sequence near the promoter of the primary transcript possibly has a regulatory function in controlling the amount of full-length primary RNA, which is converted to the active sgm-sRNA through consecutive maturation steps influenced by the 5'-end of the primary RNA. The mobilization module of SGI1 seems unique due to its atypical relaxase and the newly identified sgm-sRNA, which is required for the horizontal transfer of the island but appears to act differently from classical regulatory sRNAs.}, }
@article {pmid34779763, year = {2021}, author = {Algora-Gallardo, L and Schniete, JK and Mark, DR and Hunter, IS and Herron, PR}, title = {Bilateral symmetry of linear streptomycete chromosomes.}, journal = {Microbial genomics}, volume = {7}, number = {11}, pages = {}, pmid = {34779763}, issn = {2057-5858}, support = {BB/M018792/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteria/genetics ; *Chromosomes, Bacterial/genetics ; Plasmids/genetics ; *Replicon/genetics ; }, abstract = {Here, we characterize an uncommon set of telomeres from Streptomyces rimosus ATCC 10970, the parental strain of a lineage of one of the earliest-discovered antibiotic producers. Following the closure of its genome sequence, we compared unusual telomeres from this organism with the other five classes of replicon ends found amongst streptomycetes. Closed replicons of streptomycete chromosomes were organized with respect to their phylogeny and physical orientation, which demonstrated that different telomeres were not associated with particular clades and are likely shared amongst different strains by plasmid-driven horizontal gene transfer. Furthermore, we identified a ~50 kb origin island with conserved synteny that is located at the core of all streptomycete chromosomes and forms an axis around which symmetrical chromosome inversions can take place. Despite this chromosomal bilateral symmetry, a bias in parS sites to the right of oriC is maintained across the family Streptomycetaceae and suggests that the formation of ParB/parS nucleoprotein complexes on the right replichore is a conserved feature in streptomycetes. Consequently, our studies reveal novel features of linear bacterial replicons that, through their manipulation, may lead to improvements in growth and productivity of this important industrial group of bacteria.}, }
@article {pmid34775173, year = {2022}, author = {Smits, WK and Roseboom, AM and Corver, J}, title = {Plasmids of Clostridioides difficile.}, journal = {Current opinion in microbiology}, volume = {65}, number = {}, pages = {87-94}, doi = {10.1016/j.mib.2021.10.016}, pmid = {34775173}, issn = {1879-0364}, mesh = {Clostridioides ; *Clostridioides difficile/genetics ; *Clostridium Infections ; Humans ; Plasmids/genetics ; }, abstract = {Plasmids are ubiquitous in the bacterial world. In many microorganisms, plasmids have been implicated in important aspects of bacterial physiology and contribute to horizontal gene transfer. In contrast, knowledge on plasmids of the enteropathogen Clostridioides difficile is limited, and there appears to be no phenotypic consequence to carriage of many of the identified plasmids. Emerging evidence suggests, however, that plasmids are common in C. difficile and may encode functions relevant to pathogenesis, such as antimicrobial resistance and toxin production. Here, we review our current knowledge about the abundance, functions and clinical relevance of plasmids in C. difficile.}, }
@article {pmid34774958, year = {2022}, author = {Guo, Y and Gao, J and Cui, Y and Wang, Z and Li, Z and Duan, W and Wang, Y and Wu, Z}, title = {Chloroxylenol at environmental concentrations can promote conjugative transfer of antibiotic resistance genes by multiple mechanisms.}, journal = {The Science of the total environment}, volume = {816}, number = {}, pages = {151599}, doi = {10.1016/j.scitotenv.2021.151599}, pmid = {34774958}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/toxicity ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Xylenes ; }, abstract = {The intergeneric conjugative transfer of antibiotic resistance genes (ARGs) is recognized as an important way to the dissemination of antibiotic resistance. However, it is unknown whether the extensive use of chloroxylenol (para-chloro-meta-xylenol, PCMX) in many pharmaceutical personal care products will lead to the spread of ARGs. In this study, the abilities and mechanisms of PCMX to accelerate the intergeneric conjugative transfer were investigated. Results showed that exposure of bacteria to environmental concentrations of PCMX (0.20-1.00 mg/L) can significantly stimulate the increase of conjugative transfer by 8.45-9.51 fold. The phenotypic experiments and genome-wide RNA sequencing revealed that 0.02-5.00 mg/L PCMX exposure could increase the content of alkaline phosphatase and malondialdehyde, which are characteristic products of cell wall and membrane damage. In addition, PCMX could lead to excessive production of reactive oxygen species (ROS) by 1.26-2.00 times, the superoxide dismutase and catalase produced by bacteria in response to oxidative stress were not enough to neutralize the damage of ROS, thus promoting the conjugative transfer. Gene Ontology enrichment analysis indicated that cell membrane permeability, pili, some chemical compounds transport and energy metabolism affected conjugative transfer. This study deepened the understanding of PCMX in promoting propagation of ARGs, and provided new perspectives for use and treatment of personal care products.}, }
@article {pmid34774508, year = {2022}, author = {Cui, H and Smith, AL}, title = {Impact of engineered nanoparticles on the fate of antibiotic resistance genes in wastewater and receiving environments: A comprehensive review.}, journal = {Environmental research}, volume = {204}, number = {Pt D}, pages = {112373}, doi = {10.1016/j.envres.2021.112373}, pmid = {34774508}, issn = {1096-0953}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Nanoparticles ; *Wastewater ; }, abstract = {Nanoparticles (NPs) and antibiotic resistance elements are ubiquitous in wastewater and consequently, in receiving environments. Sub-lethal levels of engineered NPs potentially result in a selective pressure on antibiotic resistance gene (ARG) propagation in wastewater treatment plants. Conversely, emergent NPs are being designed to naturally attenuate ARGs based on special physical and electrochemical properties, which could alleviate dissemination of ARGs to the environment. The complex interactions between NPs and antibiotic resistance elements have heightened interest in elucidating the potential positive and negative implications. This review focuses on the properties of NPs and ARGs and how their interactions could increase or decrease antibiotic resistance at wastewater treatment plants and in receiving environments. Further, the potential for sub-lethal level NPs to facilitate horizontal gene transfer of ARGs and increase mutagenesis rates, which adds a layer of complexity to combatting antibiotic resistance associated with wastewater management, is discussed. Notably, the literature revealed that sub-lethal exposure of engineered NPs may facilitate conjugative transfer of ARGs by increasing cell membrane permeability. The enhanced permeability is a result of direct damage via NP attachment and indirect damage by generating reactive oxygen species (ROS) and causing genetic changes relevant to conjugation. Finally, current knowledge gaps and future research directions (e.g., deciphering the fate of NPs in the environment and examining the long-term cytotoxicity of NPs) are identified for this emerging field.}, }
@article {pmid34773620, year = {2022}, author = {Cuartas, R and Coque, TM and de la Cruz, F and Garcillán-Barcia, MP}, title = {PLASmid TAXonomic PCR (PlasTax-PCR), a Multiplex Relaxase MOB Typing to Assort Plasmids into Taxonomic Units.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2392}, number = {}, pages = {127-142}, pmid = {34773620}, issn = {1940-6029}, mesh = {Bacterial Proteins/genetics ; Conjugation, Genetic ; DNA Primers ; Drug Resistance, Microbial ; Enterobacteriaceae/genetics ; Gene Transfer, Horizontal ; Plasmids/*genetics ; Polymerase Chain Reaction ; }, abstract = {Plasmids transmissible by conjugation are responsible for disseminating antibiotic-resistance genes, making plasmid detection relevant for pathogen tracking. We describe the use of a multiplex PCR method for the experimental identification of specific plasmid taxonomic units (PTUs) of transmissible plasmids. The PCR primers were designed to target conserved segments of the relaxase MOB gene of PTUs encoding adaptive traits for enterobacteria (antimicrobial resistance, virulence, and metabolism). In this way, PlasTax-PCR detects the presence of these plasmids and allows their direct assignation to a PTU.}, }
@article {pmid34773098, year = {2022}, author = {Arnold, BJ and Huang, IT and Hanage, WP}, title = {Horizontal gene transfer and adaptive evolution in bacteria.}, journal = {Nature reviews. Microbiology}, volume = {20}, number = {4}, pages = {206-218}, pmid = {34773098}, issn = {1740-1534}, mesh = {*Bacteria/genetics ; Computational Biology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Bacterial/genetics ; Genomics ; Phylogeny ; }, abstract = {Horizontal gene transfer (HGT) is arguably the most conspicuous feature of bacterial evolution. Evidence for HGT is found in most bacterial genomes. Although HGT can considerably alter bacterial genomes, not all transfer events may be biologically significant and may instead represent the outcome of an incessant evolutionary process that only occasionally has a beneficial purpose. When adaptive transfers occur, HGT and positive selection may result in specific, detectable signatures in genomes, such as gene-specific sweeps or increased transfer rates for genes that are ecologically relevant. In this Review, we first discuss the various mechanisms whereby HGT occurs, how the genetic signatures shape patterns of genomic variation and the distinct bioinformatic algorithms developed to detect these patterns. We then discuss the evolutionary theory behind HGT and positive selection in bacteria, and discuss the approaches developed over the past decade to detect transferred DNA that may be involved in adaptation to new environments.}, }
@article {pmid34772334, year = {2021}, author = {Anderson, BM and Krause, K and Petersen, G}, title = {Mitochondrial genomes of two parasitic Cuscuta species lack clear evidence of horizontal gene transfer and retain unusually fragmented ccmFC genes.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {816}, pmid = {34772334}, issn = {1471-2164}, support = {16-TF-KK//Troms&#xf8; Research Foundation/ ; }, mesh = {*Cuscuta/genetics ; Gene Transfer, Horizontal ; Genes, Mitochondrial ; *Genome, Mitochondrial/genetics ; Phylogeny ; }, abstract = {BACKGROUND: The intimate association between parasitic plants and their hosts favours the exchange of genetic material, potentially leading to horizontal gene transfer (HGT) between plants. With the recent publication of several parasitic plant nuclear genomes, there has been considerable focus on such non-sexual exchange of genes. To enhance the picture on HGT events in a widely distributed parasitic genus, Cuscuta (dodders), we assembled and analyzed the organellar genomes of two recently sequenced species, C. australis and C. campestris, making this the first account of complete mitochondrial genomes (mitogenomes) for this genus.<br><br>RESULTS: The mitogenomes are 265,696 and 275,898&#x2009;bp in length and contain a typical set of mitochondrial genes, with 10 missing or pseudogenized genes often lost from angiosperm mitogenomes. Each mitogenome also possesses a structurally unusual ccmFC gene, which exhibits splitting of one exon and a shift to trans-splicing of its intron. Based on phylogenetic analysis of mitochondrial genes from across angiosperms and similarity-based searches, there is little to no indication of HGT into the Cuscuta mitogenomes. A few candidate regions for plastome-to-mitogenome transfer were identified, with one suggestive of possible HGT.<br><br>CONCLUSIONS: The lack of HGT is surprising given examples from the nuclear genomes, and may be due in part to the relatively small size of the Cuscuta mitogenomes, limiting the capacity to integrate foreign sequences.}, }
@article {pmid34769480, year = {2021}, author = {Abade Dos Santos, FA and Carvalho, CL and Parra, F and Dalton, KP and Peleteiro, MC and Duarte, MD}, title = {A Quadruplex qPCR for Detection and Differentiation of Classic and Natural Recombinant Myxoma Virus Strains of Leporids.}, journal = {International journal of molecular sciences}, volume = {22}, number = {21}, pages = {}, pmid = {34769480}, issn = {1422-0067}, support = {SFRH/BD/137067/2018//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDP/CVT/00276/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; AGL2017-83395-R//Spanish Ministerio de Ciencia Innovaci&#xf3;n y Universidades, cofinanced by FEDER/ ; }, mesh = {Animals ; Animals, Wild ; Diagnosis, Differential ; Gene Transfer, Horizontal/genetics ; Lagomorpha/*virology ; Molecular Typing/methods/veterinary ; *Myxoma virus/classification/genetics ; Myxomatosis, Infectious/*diagnosis/virology ; Rabbits ; Real-Time Polymerase Chain Reaction/*methods/veterinary ; Reproducibility of Results ; Sensitivity and Specificity ; Spain ; }, abstract = {A natural recombinant myxoma virus (referred to as ha-MYXV or MYXV-Tol08/18) emerged in the Iberian hare (Lepus granatensis) and the European rabbit (Oryctolagus cuniculus) in late 2018 and mid-2020, respectively. This new virus is genetically distinct from classic myxoma virus (MYXV) strains that caused myxomatosis in rabbits until then, by acquiring an additional 2.8 Kbp insert within the m009L gene that disrupted it into ORFs m009L-a and m009L-b. To distinguish ha-MYXV from classic MYXV strains, we developed a robust qPCR multiplex technique that combines the amplification of the m000.5L/R duplicated gene, conserved in all myxoma virus strains including ha-MYXV, with the amplification of two other genes targeted by the real-time PCR systems designed during this study, specific either for classic MYXV or ha-MYXV strains. The first system targets the boundaries between ORFs m009L-a and m009L-b, only contiguous in classic strains, while the second amplifies a fragment within gene m060L, only present in recombinant MYXV strains. All amplification reactions were validated and normalized by a fourth PCR system directed to a housekeeping gene (18S rRNA) conserved in eukaryotic organisms, including hares and rabbits. The multiplex PCR (mPCR) technique described here was optimized for Taqman[®] and Evagreen[®] systems allowing the detection of as few as nine copies of viral DNA in the sample with an efficiency > 93%. This real-time multiplex is the first fast method available for the differential diagnosis between classic and recombinant MYXV strains, also allowing the detection of co-infections. The system proves to be an essential and effective tool for monitoring the geographical spread of ha-MYXV in the hare and wild rabbit populations, supporting the management of both species in the field.}, }
@article {pmid34768762, year = {2021}, author = {Kim, E and Shin, SW and Kwak, HS and Cha, MH and Yang, SM and Gwak, YS and Woo, GJ and Kim, HY}, title = {Prevalence and Characteristics of Phenicol-Oxazolidinone Resistance Genes in Enterococcus Faecalis and Enterococcus Faecium Isolated from Food-Producing Animals and Meat in Korea.}, journal = {International journal of molecular sciences}, volume = {22}, number = {21}, pages = {}, pmid = {34768762}, issn = {1422-0067}, mesh = {Animals ; Anti-Infective Agents/*pharmacology ; Cattle/microbiology ; Chloramphenicol/*pharmacology ; Computational Biology ; Drug Resistance, Multiple, Bacterial/*genetics ; Enterococcus faecalis/drug effects/*genetics/isolation &amp; purification ; Enterococcus faecium/drug effects/*genetics/isolation &amp; purification ; Food Analysis ; Gene Transfer, Horizontal ; Genes, Bacterial/drug effects ; Genome, Bacterial ; Meat/*microbiology ; Multilocus Sequence Typing ; Oxazolidinones/*pharmacology ; Plasmids ; Republic of Korea ; Swine/microbiology ; Whole Genome Sequencing ; }, abstract = {The use of phenicol antibiotics in animals has increased. In recent years, it has been reported that the transferable gene mediates phenicol-oxazolidinone resistance. This study analyzed the prevalence and characteristics of phenicol-oxazolidinone resistance genes in Enterococcus faecalis and Enterococcus faecium isolated from food-producing animals and meat in Korea in 2018. Furthermore, for the first time, we reported the genome sequence of E. faecalis strain, which possesses the phenicol-oxazolidinone resistance gene on both the chromosome and plasmid. Among the 327 isolates, optrA, poxtA, and fexA genes were found in 15 (4.6%), 8 (2.5%), and 17 isolates (5.2%), respectively. Twenty E. faecalis strains carrying resistance genes belonged to eight sequence types (STs), and transferability was found in 17 isolates. The genome sequences revealed that resistant genes were present in the chromosome or plasmid, or both. In strains EFS17 and EFS108, optrA was located downstream of the ermA and ant(9)-1 genes. The strains EFS36 and EFS108 harboring poxtA-encoding plasmid cocarried fexA and cfr(D). These islands also contained IS1216E or the transposon Tn554, enabling the horizontal transfer of the phenicol-oxazolidinone resistance with other antimicrobial-resistant genes. Our results suggest that it is necessary to promote the prudent use of antibiotics through continuous monitoring and reevaluation.}, }
@article {pmid34768089, year = {2021}, author = {Watkins, A}, title = {Multi-model approaches to phylogenetics: Implications for idealization.}, journal = {Studies in history and philosophy of science}, volume = {90}, number = {}, pages = {285-297}, doi = {10.1016/j.shpsa.2021.10.006}, pmid = {34768089}, issn = {0039-3681}, mesh = {*Gene Transfer, Horizontal ; *Hybridization, Genetic ; Models, Genetic ; Phylogeny ; }, abstract = {Phylogenetic models traditionally represent the history of life as having a strictly-branching tree structure. However, it is becoming increasingly clear that the history of life is often not strictly-branching; lateral gene transfer, endosymbiosis, and hybridization, for example, can all produce lateral branching events. There is thus motivation to allow phylogenetic models to have a reticulate structure. One proposal involves the reconciliation of genealogical discordance. Briefly, this method uses patterns of disagreement - discordance - between trees of different genes to add lateral branching events to phylogenetic trees of taxa, and to estimate the most likely cause of these events. I use this practice to argue for: (1) a need for expanded accounts of multiple-models idealization, (2) a distinction between automatic and manual de-idealization, and (3) recognition that idealization may serve the meso-level aims of science in a different way than hitherto acknowledged.}, }
@article {pmid34767888, year = {2022}, author = {Wang, L and Yuan, L and Li, ZH and Zhang, X and Leung, KMY and Sheng, GP}, title = {Extracellular polymeric substances (EPS) associated extracellular antibiotic resistance genes in activated sludge along the AAO process: Distribution and microbial secretors.}, journal = {The Science of the total environment}, volume = {816}, number = {}, pages = {151575}, doi = {10.1016/j.scitotenv.2021.151575}, pmid = {34767888}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; *Extracellular Polymeric Substance Matrix ; Genes, Bacterial ; *Sewage ; Wastewater ; }, abstract = {Wastewater treatment plants (WWTPs) are important sources of antibiotic resistance genes (ARGs). Increasing attention has been paid to extracellular ARGs in cell-free form due to their horizontal gene transfer via transformation. However, the fate of the adsorbed form of extracellular ARGs that exist in extracellular polymeric substances (EPS) of activated sludge in WWTP remains largely unknown. Herein, seven EPS-associated ARGs along the anaerobic-anoxic-aerobic (AAO) process were quantified using quantitative polymerase chain reaction. Results show that the absolute abundances of EPS-associated ARGs were 0.69-4.52 logs higher than those of cell-free ARGs. There was no significant difference in the abundances of EPS-associated ARGs along the AAO process. Among these target genes, the abundances of EPS-associated sul genes were higher than those of EPS-associated tet and bla genes. Proteobacteria and Bacteroidetes were identified as the major secretors of EPS-associated ARGs, and they may play an important role in the proliferation of extracellular ARGs. Moreover, the transformation efficiencies of EPS-associated ARGs were 3.55-4.65 logs higher than those of cell-free ARGs, indicating that EPS-associated ARGs have higher environmental risks. These findings have advanced our understanding of EPS-associated ARGs and are useful for the control and risk assessment of ARGs in WWTPs.}, }
@article {pmid34757168, year = {2022}, author = {Avontuur, JR and Palmer, M and Beukes, CW and Chan, WY and Tasiya, T and van Zyl, E and Coetzee, MPA and Stepkowski, T and Venter, SN and Steenkamp, ET}, title = {Bradyrhizobium altum sp. nov., Bradyrhizobium oropedii sp. nov. and Bradyrhizobium acaciae sp. nov. from South Africa show locally restricted and pantropical nodA phylogeographic patterns.}, journal = {Molecular phylogenetics and evolution}, volume = {167}, number = {}, pages = {107338}, doi = {10.1016/j.ympev.2021.107338}, pmid = {34757168}, issn = {1095-9513}, mesh = {*Bradyrhizobium ; DNA, Bacterial/genetics ; *Fabaceae/genetics/microbiology ; Nitrogen Fixation ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Root Nodules, Plant/microbiology ; Sequence Analysis, DNA ; South Africa ; Symbiosis/genetics ; }, abstract = {Africa is known for its rich legume diversity with a significant number of endemic species originating in South Africa. Many of these legumes associate with rhizobial symbionts of the genus Bradyrhizobium, of which most represent new species. Yet, none of the Bradyrhizobium species from South Africa have been described. In this study, phylogenetic analysis of 16S rRNA gene sequences of fourteen strains isolated in southern Africa from root nodules of diverse legumes (i.e., from the tribes Crotalarieae, Acacieae, Genisteae, Phaseoleae and Cassieae) revealed that they belong to the Bradyrhizobium elkanii supergroup. The taxonomic position and possible novelty of these strains were further interrogated using genealogical concordance of five housekeeping genes (atpD, dnaK, glnII, gyrB and rpoB). These phylogenies consistently recovered four monophyletic groups and one singleton within Bradyrhizobium. Of these groups, two were conspecific with Bradyrhizobium brasilense UFLA 03-321[T] and Bradyrhizobium ivorense CI-1B[T], while the remaining three represented novel taxa. Their existence was further supported with genome data, as well as metabolic and physiological traits. Analysis of nodA gene sequences further showed that the evolution of these bacteria likely involved adapting to local legume hosts and environmental conditions through the acquisition, via horizontal gene transfer, of optimal symbiotic loci. We accordingly propose the following names Bradyrhizobium acaciae sp. nov. 10BB[T] (SARCC 730[T] = LMG 31409[T]), Bradyrhizobium oropedii sp. nov. Pear76[T] (SARCC 731[T] = LMG 31408[T]), and Bradyrhizobium altum sp. nov. Pear77[T] (SARCC 754[T] = LMG 31407[T]) to accommodate three novel species, all of which are symbionts of legumes in South Africa.}, }
@article {pmid34756069, year = {2021}, author = {Suarez, SA and Martiny, AC}, title = {Gene Amplification Uncovers Large Previously Unrecognized Cryptic Antibiotic Resistance Potential in E. coli.}, journal = {Microbiology spectrum}, volume = {9}, number = {3}, pages = {e0028921}, pmid = {34756069}, issn = {2165-0497}, mesh = {Anti-Bacterial Agents/*pharmacology ; *Drug Resistance, Bacterial ; Escherichia coli/classification/drug effects/*genetics/isolation &amp; purification ; Escherichia coli Proteins/genetics ; *Gene Amplification ; Gene Transfer, Horizontal ; Genome, Bacterial ; Phylogeny ; }, abstract = {The activation of unrecognized antibiotic resistance genes in the bacterial cell can give rise to antibiotic resistance without the need for major mutations or horizontal gene transfer. We hypothesize that bacteria harbor an extensive array of diverse cryptic genes that can be activated in response to antibiotics via adaptive resistance. To test this hypothesis, we developed a plasmid assay to randomly manipulate gene copy numbers in Escherichia coli cells and identify genes that conferred resistance when amplified. We then tested for cryptic resistance to 18 antibiotics and identified genes conferring resistance. E. coli could become resistant to 50% of the antibiotics tested, including chloramphenicol, d-cycloserine, polymyxin B, and 6 beta-lactam antibiotics, following this manipulation. Known antibiotic resistance genes comprised 13% of the total identified genes, where 87% were unclassified (cryptic) antibiotic resistance genes. These unclassified genes encoded cell membrane proteins, stress response/DNA repair proteins, transporters, and miscellaneous or hypothetical proteins. Stress response/DNA repair genes have a broad antibiotic resistance potential, as this gene class, in aggregate, conferred cryptic resistance to nearly all resistance-positive antibiotics. We found that antibiotics that are hydrophilic, those that are amphipathic, and those that inhibit the cytoplasmic membrane or cell wall biosynthesis were more likely to induce cryptic resistance in E. coli. This study reveals a diversity of cryptic genes that confer an antibiotic resistance phenotype when present in high copy number. Thus, our assay can identify potential novel resistance genes while also describing which antibiotics are prone to induce cryptic antibiotic resistance in E. coli. IMPORTANCE Predicting where new antibiotic resistance genes will rise is a challenge and is especially important when new antibiotics are developed. Adaptive resistance allows sensitive bacterial cells to become transiently resistant to antibiotics. This provides an opportune time for cells to develop more efficient resistance mechanisms, such as tolerance and permanent resistance to higher antibiotic concentrations. The biochemical diversity harbored within bacterial genomes may lead to the presence of genes that could confer resistance when timely activated. Therefore, it is crucial to understand adaptive resistance to identify potential resistance genes and prolong antibiotics. Here, we investigate cryptic resistance, an adaptive resistance mechanism, and identify unknown (cryptic) antibiotic resistance genes that confer resistance when amplified in a laboratory strain of E. coli. We also pinpoint antibiotic characteristics that are likely to induce cryptic resistance. This study may help detect novel antibiotic resistance genes and provide the foundation to help develop more effective antibiotics.}, }
@article {pmid34755863, year = {2021}, author = {Villain, P and da Cunha, V and Villain, E and Forterre, P and Oberto, J and Catchpole, R and Basta, T}, title = {The hyperthermophilic archaeon Thermococcus kodakarensis is resistant to pervasive negative supercoiling activity of DNA gyrase.}, journal = {Nucleic acids research}, volume = {49}, number = {21}, pages = {12332-12347}, pmid = {34755863}, issn = {1362-4962}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics/metabolism ; Base Sequence ; Biocatalysis ; Ciprofloxacin/pharmacology ; DNA Gyrase/*genetics/metabolism ; DNA, Archaeal/*genetics/metabolism ; DNA, Superhelical/*genetics/metabolism ; Gene Expression Regulation, Archaeal/drug effects ; Gene Expression Regulation, Enzymologic ; *Hot Temperature ; Microscopy, Confocal ; Plasmids/genetics/metabolism ; Sequence Homology, Nucleic Acid ; Thermococcus/drug effects/*genetics/metabolism ; Thermotoga maritima/enzymology/genetics ; }, abstract = {In all cells, DNA topoisomerases dynamically regulate DNA supercoiling allowing essential DNA processes such as transcription and replication to occur. How this complex system emerged in the course of evolution is poorly understood. Intriguingly, a single horizontal gene transfer event led to the successful establishment of bacterial gyrase in Archaea, but its emergent function remains a mystery. To better understand the challenges associated with the establishment of pervasive negative supercoiling activity, we expressed the gyrase of the bacterium Thermotoga maritima in a naïve archaeon Thermococcus kodakarensis which naturally has positively supercoiled DNA. We found that the gyrase was catalytically active in T. kodakarensis leading to strong negative supercoiling of plasmid DNA which was stably maintained over at least eighty generations. An increased sensitivity of gyrase-expressing T. kodakarensis to ciprofloxacin suggested that gyrase also modulated chromosomal topology. Accordingly, global transcriptome analyses revealed large scale gene expression deregulation and identified a subset of genes responding to the negative supercoiling activity of gyrase. Surprisingly, the artificially introduced dominant negative supercoiling activity did not have a measurable effect on T. kodakarensis growth rate. Our data suggest that gyrase can become established in Thermococcales archaea without critically interfering with DNA transaction processes.}, }
@article {pmid34753206, year = {2022}, author = {Ragheb, SM and Govinden, U and Osei Sekyere, J}, title = {Genetic support of carbapenemases: a One Health systematic review and meta-analysis of current trends in Africa.}, journal = {Annals of the New York Academy of Sciences}, volume = {1509}, number = {1}, pages = {50-73}, doi = {10.1111/nyas.14703}, pmid = {34753206}, issn = {1749-6632}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacterial Proteins/genetics ; Carbapenems/pharmacology/therapeutic use ; Humans ; *One Health ; Plasmids/genetics ; beta-Lactamases/genetics ; }, abstract = {Antimicrobial resistance (AMR) is a public health threat globally. Carbapenems are β-lactam antibiotics used as last-resort agents for treating antibiotic-resistant infections. Mobile genetic elements (MGEs) play an important role in the dissemination and expression of antimicrobial resistance genes (ARGs), including the mobilization of ARGs within and between species. The presence of MGEs around carbapenem-hydrolyzing enzymes, called carbapenemases, in bacterial isolates in Africa is concerning. The association between MGEs and carbapenemases is described herein. Specific plasmid replicons, integrons, transposons, and insertion sequences were found flanking specific and different carbapenemases across the same and different clones and species isolated from humans, animals, and the environment. Notably, similar genetic contexts have been reported in non-African countries, supporting the importance of MGEs in driving the intra- and interclonal and species transmission of carbapenemases in Africa and globally. Technical and budgetary limitations remain challenges for epidemiological analysis of carbapenemases in Africa, as studies undertaken with whole-genome sequencing remained relatively few. Characterization of MGEs in antibiotic-resistant infections can deepen our understanding of carbapenemase epidemiology and facilitate the control of AMR in Africa. Investment in genomic epidemiology will facilitate faster clinical interventions and containment of outbreaks.}, }
@article {pmid34751223, year = {2021}, author = {Wang, Y and Mao, T and Li, Y and Xiao, W and Liang, X and Duan, G and Yang, H}, title = {Characterization of 67 Confirmed Clustered Regularly Interspaced Short Palindromic Repeats Loci in 52 Strains of Staphylococci.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {736565}, pmid = {34751223}, issn = {1664-302X}, abstract = {Staphylococcus aureus (S. aureus), which is one of the most important species of Staphylococci, poses a great threat to public health. Clustered regularly interspaced short palindromic repeats (CRISPR) and their CRISPR-associated proteins (Cas) are an adaptive immune platform to combat foreign mobile genetic elements (MGEs) such as plasmids and phages. The aim of this study is to describe the distribution and structure of CRISPR-Cas system in S. aureus, and to explore the relationship between CRISPR and horizontal gene transfer (HGT). Here, we analyzed 67 confirmed CRISPR loci and 15 companion Cas proteins in 52 strains of Staphylococci with bioinformatics methods. Comparing with the orphan CRISPR loci in Staphylococci, the strains harboring complete CRISPR-Cas systems contained multiple CRISPR loci, direct repeat sequences (DR) forming stable RNA secondary structures with lower minimum free energy (MFE), and variable spacers with detectable protospacers. In S. aureus, unlike the orphan CRISPRs away from Staphylococcal cassette chromosome mec (SCCmec), the complete CRISPR-Cas systems were in J1 region of SCCmec. In addition, we found a conserved motif 5'-TTCTCGT-3' that may protect their downstream sequences from DNA interference. In general, orphan CRISPR locus in S. aureus differed greatly from the structural characteristics of the CRISPR-Cas system. Collectively, our results provided new insight into the diversity and characterization of the CRISPR-Cas system in S. aureus.}, }
@article {pmid34750532, year = {2021}, author = {Dewar, AE and Thomas, JL and Scott, TW and Wild, G and Griffin, AS and West, SA and Ghoul, M}, title = {Plasmids do not consistently stabilize cooperation across bacteria but may promote broad pathogen host-range.}, journal = {Nature ecology &amp; evolution}, volume = {5}, number = {12}, pages = {1624-1636}, pmid = {34750532}, issn = {2397-334X}, support = {834164/ERC_/European Research Council/International ; BB/M011224/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Bacteria/genetics ; *Gene Transfer, Horizontal ; Host Specificity ; Plasmids/genetics ; }, abstract = {Horizontal gene transfer via plasmids could favour cooperation in bacteria, because transfer of a cooperative gene turns non-cooperative cheats into cooperators. This hypothesis has received support from theoretical, genomic and experimental analyses. By contrast, we show here, with a comparative analysis across 51 diverse species, that genes for extracellular proteins, which are likely to act as cooperative 'public goods', were not more likely to be carried on either: (1) plasmids compared to chromosomes; or (2) plasmids that transfer at higher rates. Our results were supported by theoretical modelling which showed that, while horizontal gene transfer can help cooperative genes initially invade a population, it has less influence on the longer-term maintenance of cooperation. Instead, we found that genes for extracellular proteins were more likely to be on plasmids when they coded for pathogenic virulence traits, in pathogenic bacteria with a broad host-range.}, }
@article {pmid34750368, year = {2021}, author = {Humphrey, S and Fillol-Salom, A and Quiles-Puchalt, N and Ibarra-Chávez, R and Haag, AF and Chen, J and Penadés, JR}, title = {Bacterial chromosomal mobility via lateral transduction exceeds that of classical mobile genetic elements.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {6509}, pmid = {34750368}, issn = {2041-1723}, support = {MR/M003876/1/MRC_/Medical Research Council/United Kingdom ; BB/V002376/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 201531/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; MR/S00940X/2/MRC_/Medical Research Council/United Kingdom ; BB/N002873/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MR/S00940X/1/MRC_/Medical Research Council/United Kingdom ; MR/V000772/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Bacterial Proteins/*genetics/metabolism ; Chromosomes, Bacterial/*genetics/metabolism ; Gene Transfer, Horizontal/genetics/physiology ; Salmonella enterica/*genetics/metabolism ; Staphylococcus aureus/*genetics/metabolism ; Transduction, Genetic ; }, abstract = {It is commonly assumed that the horizontal transfer of most bacterial chromosomal genes is limited, in contrast to the frequent transfer observed for typical mobile genetic elements. However, this view has been recently challenged by the discovery of lateral transduction in Staphylococcus aureus, where temperate phages can drive the transfer of large chromosomal regions at extremely high frequencies. Here, we analyse previously published as well as new datasets to compare horizontal gene transfer rates mediated by different mechanisms in S. aureus and Salmonella enterica. We find that the horizontal transfer of core chromosomal genes via lateral transduction can be more efficient than the transfer of classical mobile genetic elements via conjugation or generalized transduction. These results raise questions about our definition of mobile genetic elements, and the potential roles played by lateral transduction in bacterial evolution.}, }
@article {pmid34749181, year = {2022}, author = {Lu, Y and Meng, X and Wang, J and Yorgan Dieketseng, M and Xiao, Y and Yan, S and Chen, Y and Zhou, L and Zheng, G}, title = {Bioleaching rather than chemical conditioning using Fe[III]/CaO or polyacrylamide mitigates antibiotic resistance in sludge composting via pre-removing antibiotic resistance genes and limiting horizontal gene transfer.}, journal = {Waste management (New York, N.Y.)}, volume = {137}, number = {}, pages = {89-99}, doi = {10.1016/j.wasman.2021.10.029}, pmid = {34749181}, issn = {1879-2456}, mesh = {Acrylic Resins ; Anti-Bacterial Agents/pharmacology ; *Composting ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Sewage ; }, abstract = {Conditioning can drastically improve the dewaterability of sewage sludge and is widely practiced in most wastewater treatment plants (WWTPs). Sludge conditioning was also reported as a crucial step in sludge treatment to attenuate antibiotic resistance, but it remains unclear whether the attenuated antibiotic resistance by conditioning treatments would guarantee low abundance of antibiotic resistance genes (ARGs) in the compost products of municipal sewage sludge. Herein, the impacts of three conditioning treatments, including bioleaching and chemical conditioning using Fe[III]/CaO or polyacrylamide (PAM), on the abundances of 20 ARGs and 4 mobile genetic elements (MGEs) during conventional aerobic composting of dewatered sludge were investigated. It was found that the absolute and relative abundances of total ARGs in compost product of bioleached sludge accounted for only 13.8%-28.8% of that in compost products of un-conditioned, Fe[III]/CaO-conditioned, or PAM-conditioned sludges. Besides, bioleaching conditioning resulted in the lowest abundances of ARG subtypes and ARG-associated bacteria in the sludge compost product. The shift of ARG profiles in the bioleached sludge composting can be mainly ascribed to the ARG-associated bacteria, while the MGEs drove the ARG profiles during conventional composting of un-conditioned sludge and the two chemically conditioned sludge. Thus, bioleaching conditioning is superior to the chemical conditioning using Fe[III]/CaO or PAM in mitigating antibiotic resistance in sludge compost products, which was contributed by the pre-removal of ARGs prior to composting treatment and the potential limitation of ARGs transfer during conventional composting.}, }
@article {pmid34748609, year = {2021}, author = {Vieira, P and Myers, RY and Pellegrin, C and Wram, C and Hesse, C and Maier, TR and Shao, J and Koutsovoulos, GD and Zasada, I and Matsumoto, T and Danchin, EGJ and Baum, TJ and Eves-van den Akker, S and Nemchinov, LG}, title = {Targeted transcriptomics reveals signatures of large-scale independent origins and concerted regulation of effector genes in Radopholus similis.}, journal = {PLoS pathogens}, volume = {17}, number = {11}, pages = {e1010036}, pmid = {34748609}, issn = {1553-7374}, support = {BB/R011311/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/N021908/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/S006397/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *Gene Expression Regulation ; Helminth Proteins/genetics/*metabolism ; Phylogeny ; Plant Diseases/*parasitology ; Nicotiana/growth &amp; development/*parasitology ; *Transcriptome ; Tylenchida/*physiology ; }, abstract = {The burrowing nematode, Radopholus similis, is an economically important plant-parasitic nematode that inflicts damage and yield loss to a wide range of crops. This migratory endoparasite is widely distributed in warmer regions and causes extensive destruction to the root systems of important food crops (e.g., citrus, banana). Despite the economic importance of this nematode, little is known about the repertoire of effectors owned by this species. Here we combined spatially and temporally resolved next-generation sequencing datasets of R. similis to select a list of candidates for the identification of effector genes for this species. We confirmed spatial expression of transcripts of 30 new candidate effectors within the esophageal glands of R. similis by in situ hybridization, revealing a large number of pioneer genes specific to this nematode. We identify a gland promoter motif specifically associated with the subventral glands (named Rs-SUG box), a putative hallmark of spatial and concerted regulation of these effectors. Nematode transcriptome analyses confirmed the expression of these effectors during the interaction with the host, with a large number of pioneer genes being especially abundant. Our data revealed that R. similis holds a diverse and emergent repertoire of effectors, which has been shaped by various evolutionary events, including neofunctionalization, horizontal gene transfer, and possibly by de novo gene birth. In addition, we also report the first GH62 gene so far discovered for any metazoan and putatively acquired by lateral gene transfer from a bacterial donor. Considering the economic damage caused by R. similis, this information provides valuable data to elucidate the mode of parasitism of this nematode.}, }
@article {pmid34747462, year = {2022}, author = {Kanesaka, I and Ohno, A and Katsuse, AK and Takahashi, H and Kobayashi, I}, title = {The emergence of the ceftriaxone-resistant Neisseria gonorrhoeae FC428 clone by transfer of resistance from an oral Neisseria subflava reservoir of resistance.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {77}, number = {2}, pages = {364-373}, doi = {10.1093/jac/dkab390}, pmid = {34747462}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/pharmacology ; Ceftriaxone/pharmacology ; Clone Cells ; Drug Resistance, Bacterial/*genetics ; *Gene Transfer, Horizontal ; Gonorrhea/drug therapy/microbiology ; Humans ; Microbial Sensitivity Tests ; Neisseria/*genetics ; *Neisseria gonorrhoeae/drug effects/genetics ; }, abstract = {BACKGROUND: The ceftriaxone-resistant Neisseria gonorrhoeae FC428 clone was first discovered in Japan in 2015.<br><br>OBJECTIVES: We investigated the possibility of horizontal gene transfer from Neisseria subflava harbouring the mosaic-like PBP-2 in the emergence of the FC428 clone. We also analysed whether there were fitness costs associated with the sustained international dissemination of the clone.<br><br>METHODS: Sequencing of the penA gene in ceftriaxone-resistant N. subflava strains was performed. For transformation experiments between donor N. subflava and ciprofloxacin-resistant wild-type penA N. gonorrhoeae recipient, the full-length PCR amplification product of the penA gene, including DUS regions, was used as the donor DNA. Biological fitness of the transformants was measured by growth competition assays. The impact of QRDR and mtrR mutations, which have been reported as compensatory mutations, on fitness was also assessed.<br><br>RESULTS: The penA mosaic allele of the FC428 clone showed 100%, 91.8%, and 89.8% homology, respectively, with penA genes of three ceftriaxone-resistant N. subflava strains, No. 30, No. 9 and No. 14. Results were consistent with homologous recombination with the donated penA mosaic allele. In co-cultures with the parent strain, transformants showed comparable growth indicating that a gyrA mutation compensates for the fitness cost of mosaic penA alleles.<br><br>CONCLUSIONS: Our findings support the hypothesis that the FC428 clone was generated by transformation of the mosaic penA allele from oropharyngeal N. subflava to N. gonorrhoeae. Furthermore, it suggests that mutations in the gyrA QRDR region compensate for fitness costs and contribute to the continued transmission of the FC428 clone.}, }
@article {pmid34741016, year = {2021}, author = {Sato, Y and Jang, S and Takeshita, K and Itoh, H and Koike, H and Tago, K and Hayatsu, M and Hori, T and Kikuchi, Y}, title = {Insecticide resistance by a host-symbiont reciprocal detoxification.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {6432}, pmid = {34741016}, issn = {2041-1723}, mesh = {Animals ; Burkholderia/drug effects/genetics ; Heteroptera/drug effects/genetics ; Insecticide Resistance ; Insecticides/*pharmacology ; Organophosphorus Compounds/pharmacology ; Symbiosis/drug effects/genetics ; }, abstract = {Insecticide resistance is one of the most serious problems in contemporary agriculture and public health. Although recent studies revealed that insect gut symbionts contribute to resistance, the symbiont-mediated detoxification process remains unclear. Here we report the in vivo detoxification process of an organophosphorus insecticide, fenitrothion, in the bean bug Riptortus pedestris. Using transcriptomics and reverse genetics, we reveal that gut symbiotic bacteria degrade this insecticide through a horizontally acquired insecticide-degrading enzyme into the non-insecticidal but bactericidal compound 3-methyl-4-nitrophenol, which is subsequently excreted by the host insect. This integrated "host-symbiont reciprocal detoxification relay" enables the simultaneous maintenance of symbiosis and efficient insecticide degradation. We also find that the symbiont-mediated detoxification process is analogous to the insect genome-encoded fenitrothion detoxification system present in other insects. Our findings highlight the capacity of symbiosis, combined with horizontal gene transfer in the environment, as a powerful strategy for an insect to instantly eliminate a toxic chemical compound, which could play a critical role in the human-pest arms race.}, }
@article {pmid34740368, year = {2021}, author = {Santoro, F and Fox, V and Romeo, A and Lazzeri, E and Pozzi, G and Iannelli, F}, title = {Chromosomal integration of Tn5253 occurs downstream of a conserved 11-bp sequence of the rbgA gene in Streptococcus pneumoniae and in all the other known hosts of this integrative conjugative element (ICE).}, journal = {Mobile DNA}, volume = {12}, number = {1}, pages = {25}, pmid = {34740368}, issn = {1759-8753}, support = {20177J5Y3P//Ministero dell'Istruzione, dell'Universit&#xe0; e della Ricerca/ ; }, abstract = {BACKGROUND: Tn5253, a composite Integrative Conjugative Element (ICE) of Streptococcus pneumoniae carrying tet(M) and cat resistance determinants, was found to (i) integrate at specific 83-bp integration site (attB), (ii) produce circular forms joined by a 84-bp sequence (attTn), and (iii) restore the chromosomal integration site. The purpose of this study is to functionally characterize the attB in S. pneumoniae strains with different genetic backgrounds and in other bacterial species, and to investigate the presence of Tn5253 attB site into bacterial genomes.<br><br>RESULTS: Analysis of representative Tn5253-carryng transconjugants obtained in S. pneumoniae strains with different genetic backgrounds and in other bacterial species, namely Streptococcus agalactiae, Streptococcus gordonii, Streptococcus pyogenes, and Enterococcus faecalis showed that: (i) Tn5253 integrates in rbgA of S. pneumoniae and in orthologous rbgA genes of other bacterial species, (ii) integration occurs always downstream of a 11-bp sequence conserved among streptococcal and enterococcal hosts, (iii) length of the attB site corresponds to length of the duplication after Tn5253 integration, (iv) attB duplication restores rbgA CDS, (v) Tn5253 produced circular forms containing the attTn site at a concentration ranging between 2.0&#x2009;&#xd7;&#x2009;10[-5] to 1.2&#x2009;&#xd7;&#x2009;10[-2] copies per chromosome depending on bacterial species and strain, (vi) reconstitution of attB sites occurred at 3.7&#x2009;&#xd7;&#x2009;10[-5] to 1.7&#x2009;&#xd7;&#x2009;10[-2] copies per chromosome. A database search of complete microbial genomes using Tn5253 attB as a probe showed that (i) thirteen attB variants were present in the 85 complete pneumococcal genomes, (ii) in 75 pneumococcal genomes (88.3&#x2009;%), the attB site was 83 or 84 nucleotides in length, while in 10 (11.7&#x2009;%) it was 41 nucleotides, (iii) in other 19 bacterial species attB was located in orthologous rbgA genes and its size ranged between 17 and 84 nucleotides, (iv) the 11-bp sequence, which correspond to the last 11 nucleotides of attB sites, is conserved among the different bacterial species and can be considered the core of the Tn5253 integration site.<br><br>CONCLUSIONS: A functional characterization of the Tn5253 attB integration site combined with genome analysis contributed to elucidating the potential of Tn5253 horizontal gene transfer among different bacterial species.}, }
@article {pmid34740157, year = {2022}, author = {Chen, HY and Li, XK and Meng, L and Liu, G and Ma, X and Piao, C and Wang, K}, title = {The fate and behavior mechanism of antibiotic resistance genes and microbial communities in anaerobic reactors treating oxytetracycline manufacturing wastewater.}, journal = {Journal of hazardous materials}, volume = {424}, number = {Pt C}, pages = {127352}, doi = {10.1016/j.jhazmat.2021.127352}, pmid = {34740157}, issn = {1873-3336}, mesh = {Anaerobiosis ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Microbiota ; *Oxytetracycline ; Sewage ; Wastewater ; }, abstract = {In this study, two parallel-operated expanded granular sludge bed (EGSB) reactors, one used to treat oxytetracycline (OTC) manufacturing wastewater with gradual increase of OTC concentration as experimental reactor and the other fed with the same wastewater without OTC as control reactor, were operated to investigate the behavior of antibiotics resistance genes (ARGs) and mobile genetic elements (MGEs) and their possible relationships with bacterial community among influent, sludge and effluent environments. Though the average absolute abundance of ARGs slightly decreased (0.26 - log), the ARGs' relative abundance normalized to 16S-rRNA gene copy numbers showed a significant upward trend in effluent (2 multiples - increase) and the absolute and relative abundances both extremely increased in anaerobic sludge, indicating that anaerobic treatment process cannot reduce ARGs efficiently, inversely can increase the risk of ARGs through the proliferation of antibiotics resistance bacteria (ARB) under the suppression of OTC. MGEs, bacterial communities and OTC concentration mainly impacted the ARGs profiles, which contributed 88.4% to the variation of ARGs. The differences and correlations of hosts in influent, effluent and sludge were further confirmed by network analysis. Overall, this study enhanced the understanding of the prevalence and transfer of ARGs in OTC production effluents during anaerobic treatment.}, }
@article {pmid34738268, year = {2021}, author = {Dimond, ZE and Suchland, RJ and Baid, S and LaBrie, SD and Soules, KR and Stanley, J and Carrell, S and Kwong, F and Wang, Y and Rockey, DD and Hybiske, K and Hefty, PS}, title = {Inter-species lateral gene transfer focused on the Chlamydia plasticity zone identifies loci associated with immediate cytotoxicity and inclusion stability.}, journal = {Molecular microbiology}, volume = {116}, number = {6}, pages = {1433-1448}, pmid = {34738268}, issn = {1365-2958}, support = {P20 GM103638/GM/NIGMS NIH HHS/United States ; P20 GM113117/GM/NIGMS NIH HHS/United States ; R01 AI126785/AI/NIAID NIH HHS/United States ; T32 GM008545/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacterial Proteins/genetics/metabolism ; Chlamydia Infections/*microbiology ; Chlamydia muridarum/*genetics/metabolism ; Chlamydia trachomatis/*genetics/metabolism ; Female ; *Gene Transfer, Horizontal ; Genetic Variation ; Humans ; Mice, Inbred C57BL ; Mice ; }, abstract = {Chlamydia muridarum actively grows in murine mucosae and is a representative model of human chlamydial genital tract disease. In contrast, C. trachomatis infections in mice are limited and rarely cause disease. The factors that contribute to these differences in host adaptation and specificity remain elusive. Overall genomic similarity leads to challenges in the understanding of these significant differences in tropism. A region of major genetic divergence termed the plasticity zone (PZ) has been hypothesized to contribute to the host specificity. To evaluate this hypothesis, lateral gene transfer was used to generate multiple hetero-genomic strains that are predominately C. trachomatis but have replaced regions of the PZ with those from C. muridarum. In vitro analysis of these chimeras revealed C. trachomatis-like growth as well as poor mouse infection capabilities. Growth-independent cytotoxicity phenotypes have been ascribed to three large putative cytotoxins (LCT) encoded in the C. muridarum PZ. However, analysis of PZ chimeras supported that gene products other than the LCTs are responsible for cytopathic and cytotoxic phenotypes. Growth analysis of associated chimeras also led to the discovery of an inclusion protein, CTL0402 (CT147), and homolog TC0424, which was critical for the integrity of the inclusion and preventing apoptosis.}, }
@article {pmid34737280, year = {2021}, author = {Jian, H and Xu, G and Yi, Y and Hao, Y and Wang, Y and Xiong, L and Wang, S and Liu, S and Meng, C and Wang, J and Zhang, Y and Chen, C and Feng, X and Luo, H and Zhang, H and Zhang, X and Wang, L and Wang, Z and Deng, Z and Xiao, X}, title = {The origin and impeded dissemination of the DNA phosphorothioation system in prokaryotes.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {6382}, pmid = {34737280}, issn = {2041-1723}, mesh = {DNA/*metabolism ; Phylogeny ; Shewanella/genetics ; Transcriptome/genetics ; }, abstract = {Phosphorothioate (PT) modification by the dnd gene cluster is the first identified DNA backbone modification and constitute an epigenetic system with multiple functions, including antioxidant ability, restriction modification, and virus resistance. Despite these advantages for hosting dnd systems, they are surprisingly distributed sporadically among contemporary prokaryotic genomes. To address this ecological paradox, we systematically investigate the occurrence and phylogeny of dnd systems, and they are suggested to have originated in ancient Cyanobacteria after the Great Oxygenation Event. Interestingly, the occurrence of dnd systems and prophages is significantly negatively correlated. Further, we experimentally confirm that PT modification activates the filamentous phage SW1 by altering the binding affinity of repressor and the transcription level of its encoding gene. Competition assays, concurrent epigenomic and transcriptomic sequencing subsequently show that PT modification affects the expression of a variety of metabolic genes, which reduces the competitive fitness of the marine bacterium Shewanella piezotolerans WP3. Our findings strongly suggest that a series of negative effects on microorganisms caused by dnd systems limit horizontal gene transfer, thus leading to their sporadic distribution. Overall, our study reveals putative evolutionary scenario of the dnd system and provides novel insights into the physiological and ecological influences of PT modification.}, }
@article {pmid34737135, year = {2022}, author = {Yue, Z and Zhang, J and Zhou, Z and Ding, C and Zhang, T and Wan, L and Wang, X}, title = {Antibiotic degradation dominates the removal of antibiotic resistance genes during composting.}, journal = {Bioresource technology}, volume = {344}, number = {Pt B}, pages = {126229}, doi = {10.1016/j.biortech.2021.126229}, pmid = {34737135}, issn = {1873-2976}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Composting ; Drug Resistance, Microbial/genetics ; Genes, Bacterial/genetics ; Manure ; Swine ; }, abstract = {To identify the key hosts involved in horizontal gene transfer (HGT) and vertical gene transfer (VGT) of antibiotic resistance genes (ARGs) and to determine the extent to and ways in which environmental properties contribute to ARG removal, the changes in ARG profile and key hosts during biogas residue and pig manure composting were investigated using metagenomic sequencing coupled with network analysis. Composting significantly reduced the abundances of ARGs other than bacA. Seventy and 41 hosts from Firmicutes, Actinobacteria, Proteobacteria and Bacteroidetes were associated with HGT and VGT, respectively. The key environmental properties were determined using structural equation modelling. Antibiotics directly affected HGT and determined ARG removal. Temperature indirectly affected HGT, mainly by influencing the degradation of antibiotics. BacA was associated only with hosts involved in VGT, which may lead to its low removal rate. These findings specify the priority and pathway of antibiotics and temperature affecting ARG profile.}, }
@article {pmid34735552, year = {2021}, author = {Bhukya, KK and Bhukya, B}, title = {Unraveling the probiotic efficiency of bacterium Pediococcus pentosaceus OBK05 isolated from buttermilk: An in vitro study for cholesterol assimilation potential and antibiotic resistance status.}, journal = {PloS one}, volume = {16}, number = {11}, pages = {e0259702}, pmid = {34735552}, issn = {1932-6203}, mesh = {Buttermilk/*microbiology ; Cholesterol/*metabolism ; Drug Resistance, Microbial ; Humans ; Pediococcus pentosaceus/drug effects/*metabolism ; Probiotics/*metabolism ; Tomography, Optical Coherence ; }, abstract = {The present study describes the probiotic potential and functional properties of the lactic acid bacterium Pediococcus pentosaceus OBK05 isolated from buttermilk. The isolate OBK05 was assessed for its probiotic properties. The isolate showed notable tolerance to pH 2.0 and 3.0 (8.44, 8.35 log CFU/mL), oxbile of 0.5% at 2 and 4 h of incubation (6.97, 6.35 log CFU/mL) and higher aggregation (auto-aggregation, adhesion to hydrocarbons) than the referral strain, Lactobacillus acidophilus MTCC 10307. The adhesion efficiency to HT-29 cells was found to be maximum, corresponding to 93.5% and 97% at 1 and 2 h incubation, respectively. In addition, the isolate OBK05 showed antagonistic solid activity against bacterial pathogens like Pseudomonas aeruginosa MTCC 424 and Bacillus subtilis MTCC 1133. The phenotypic antibiotic resistance of the isolate was examined before and after curing plasmids. Among the known five structural genes responsible for different antibiotic resistance, four genes indicating antibiotic resistance to kanamycin-Aph (3´´)-III, streptomycin-strA, vancomycin-vanA and ciprofloxacin-gyrA were detected by PCR amplification of genomic DNA. Further, the horizontal gene transfer from OBK05 isolate to pathogens was not found for these antibiotic resistance markers when filter and food mating were carried out as no transconjugants developed on media plates containing respective antibiotics. This indicates that the intrinsic resistance is harbored on chromosomal genes, and hence it is nontransferable to other microbes. In addition, strain OBK05 exhibited good DPPH scavenging activity of 56 to 77% and liberated free amino acid from conjugated bile acid. The strain OBK05 demonstrated a strong ability to reduce cholesterol at 12 h (17%), 24 h (27%) and 48 h (67%) of incubation.}, }
@article {pmid34730826, year = {2022}, author = {Chen, H and Chu, JS and Chen, J and Luo, Q and Wang, H and Lu, R and Zhu, Z and Yuan, G and Yi, X and Mao, Y and Lu, C and Wang, Z and Gu, D and Jin, Z and Zhang, C and Weng, Z and Li, S and Yan, X and Yang, R}, title = {Insights into the Ancient Adaptation to Intertidal Environments by Red Algae Based on a Genomic and Multiomics Investigation of Neoporphyra haitanensis.}, journal = {Molecular biology and evolution}, volume = {39}, number = {1}, pages = {}, pmid = {34730826}, issn = {1537-1719}, mesh = {Acclimatization/genetics ; Adaptation, Physiological/genetics ; Ecosystem ; *Proteomics ; *Rhodophyta/genetics ; }, abstract = {Colonization of land from marine environments was a major transition for biological life on Earth, and intertidal adaptation was a key evolutionary event in the transition from marine- to land-based lifestyles. Multicellular intertidal red algae exhibit the earliest, systematic, and successful adaptation to intertidal environments, with Porphyra sensu lato (Bangiales, Rhodophyta) being a typical example. Here, a chromosome-level 49.67 Mb genome for Neoporphyra haitanensis comprising 9,496 gene loci is described based on metagenome-Hi-C-assisted whole-genome assembly, which allowed the isolation of epiphytic bacterial genome sequences from a seaweed genome for the first time. The compact, function-rich N. haitanensis genome revealed that ancestral lineages of red algae share common horizontal gene transfer events and close relationships with epiphytic bacterial populations. Specifically, the ancestor of N. haitanensis obtained unique lipoxygenase family genes from bacteria for complex chemical defense, carbonic anhydrases for survival in shell-borne conchocelis lifestyle stages, and numerous genes involved in stress tolerance. Combined proteomic, transcriptomic, and metabolomic analyses revealed complex regulation of rapid responses to intertidal dehydration/rehydration cycling within N. haitanensis. These adaptations include rapid regulation of its photosynthetic system, a readily available capacity to utilize ribosomal stores, increased methylation activity to rapidly synthesize proteins, and a strong anti-oxidation system to dissipate excess redox energy upon exposure to air. These novel insights into the unique adaptations of red algae to intertidal lifestyles inform our understanding of adaptations to intertidal ecosystems and the unique evolutionary steps required for intertidal colonization by biological life.}, }
@article {pmid34730808, year = {2022}, author = {Cummings, TFM and Gori, K and Sanchez-Pulido, L and Gavriilidis, G and Moi, D and Wilson, AR and Murchison, E and Dessimoz, C and Ponting, CP and Christophorou, MA}, title = {Citrullination Was Introduced into Animals by Horizontal Gene Transfer from Cyanobacteria.}, journal = {Molecular biology and evolution}, volume = {39}, number = {2}, pages = {}, pmid = {34730808}, issn = {1537-1719}, support = {/WT_/Wellcome Trust/United Kingdom ; MC_UU_00007/15/MRC_/Medical Research Council/United Kingdom ; MC_UU_12008/1/MRC_/Medical Research Council/United Kingdom ; 105642/A/14/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Citrullination ; Conserved Sequence ; *Cyanobacteria/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Phylogeny ; }, abstract = {Protein posttranslational modifications add great sophistication to biological systems. Citrullination, a key regulatory mechanism in human physiology and pathophysiology, is enigmatic from an evolutionary perspective. Although the citrullinating enzymes peptidylarginine deiminases (PADIs) are ubiquitous across vertebrates, they are absent from yeast, worms, and flies. Based on this distribution PADIs were proposed to have been horizontally transferred, but this has been contested. Here, we map the evolutionary trajectory of PADIs into the animal lineage. We present strong phylogenetic support for a clade encompassing animal and cyanobacterial PADIs that excludes fungal and other bacterial homologs. The animal and cyanobacterial PADI proteins share functionally relevant primary and tertiary synapomorphic sequences that are distinct from a second PADI type present in fungi and actinobacteria. Molecular clock calculations and sequence divergence analyses using the fossil record estimate the last common ancestor of the cyanobacterial and animal PADIs to be less than 1 billion years old. Additionally, under an assumption of vertical descent, PADI sequence change during this evolutionary time frame is anachronistically low, even when compared with products of likely endosymbiont gene transfer, mitochondrial proteins, and some of the most highly conserved sequences in life. The consilience of evidence indicates that PADIs were introduced from cyanobacteria into animals by horizontal gene transfer (HGT). The ancestral cyanobacterial PADI is enzymatically active and can citrullinate eukaryotic proteins, suggesting that the PADI HGT event introduced a new catalytic capability into the regulatory repertoire of animals. This study reveals the unusual evolution of a pleiotropic protein modification.}, }
@article {pmid34730375, year = {2021}, author = {Sugita, K and Aoki, K and Komori, K and Nagasawa, T and Ishii, Y and Iwata, S and Tateda, K}, title = {Molecular Analysis of blaKPC-2-Harboring Plasmids: Tn4401a Interplasmid Transposition and Tn4401a-Carrying ColRNAI Plasmid Mobilization from Klebsiella pneumoniae to Citrobacter europaeus and Morganella morganii in a Single Patient.}, journal = {mSphere}, volume = {6}, number = {6}, pages = {e0085021}, pmid = {34730375}, issn = {2379-5042}, mesh = {Bacterial Proteins/*genetics ; Citrobacter/enzymology/*genetics/isolation &amp; purification ; Enterobacteriaceae Infections/microbiology ; *Gene Transfer, Horizontal ; Humans ; Klebsiella Infections/microbiology ; Klebsiella pneumoniae/enzymology/*genetics/isolation &amp; purification ; Microbial Sensitivity Tests ; Morganella morganii/enzymology/*genetics/isolation &amp; purification ; Plasmids ; Whole Genome Sequencing ; beta-Lactamases/*genetics ; }, abstract = {The spread of Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacterales is a public health concern. KPC-encoding blaKPC is predominantly spread by strains of a particular phylogenetic lineage, clonal group 258, but can also be spread by horizontal transfer of blaKPC-carrying plasmids. Here, we report the transfer of a blaKPC-2-harboring plasmid via mobilization from K. pneumoniae to Citrobacter freundii complex and Morganella morganii strains in a single patient. We performed draft whole-genome sequencing to analyze 20 carbapenemase-producing Enterobacterales strains (15 of K. pneumoniae, two of C. freundii complex, and three of M. morganii) and all K. pneumoniae strains using MiSeq and/or MinION isolated from a patient who was hospitalized in New York and Montreal before returning to Japan. All strains harbored blaKPC-2-containing Tn4401a. The 15 K. pneumoniae strains each belonged to sequence type 258 and harbored a Tn4401a-carrying multireplicon-type plasmid, IncN and IncR (IncN+R). Three of these K. pneumoniae strains also possessed a Tn4401a-carrying ColRNAI plasmid, suggesting that Tn4401a underwent interplasmid transposition. Of these three ColRNAI plasmids, two and one were identical to plasmids harbored by two Citrobacter europaeus and three M. morganii strains, respectively. The Tn4401a-carrying ColRNAI plasmids were each 23,753 bp long and incapable of conjugal transfer via their own genes alone, but they mobilized during the conjugal transfer of Tn4401a-carrying IncN+R plasmids in K. pneumoniae. Interplasmid transposition of Tn4401a from an IncN+R plasmid to a ColRNAI plasmid in K. pneumoniae and mobilization of Tn4401a-carrying ColRNAI plasmids contributed to the acquisition of blaKPC-2 in C. europaeus and M. morganii. IMPORTANCE Plasmid transfer plays an important role in the interspecies spread of carbapenemase genes, including the Klebsiella pneumoniae carbapenemase (KPC)-coding gene, blaKPC. We conducted whole-genome sequencing (WGS) analysis and transmission experiments to analyze blaKPC-2-carrying mobile genetic elements (MGEs) between the blaKPC-2-harboring K. pneumoniae, Citrobacter europaeus, and Morganella morganii strains isolated from a single patient. blaKPC-2 was contained within an MGE, Tn4401a. WGS of blaKPC-2-carrying K. pneumoniae, C. europaeus, and M. morganii strains isolated from one patient revealed that Tn4401a-carrying ColRNAI plasmids were generated by plasmid-to-plasmid transfer of Tn4401a from a multireplicon-type IncN and IncR (IncN+R) plasmid in K. pneumoniae strains. Tn4401a-carrying ColRNAI plasmids were incapable of conjugal transfer in C. europaeus and M. morganii but mobilized from K. pneumoniae to a recipient Escherichia coli strain during the conjugal transfer of Tn4401a-carrying IncN+R plasmid. Therefore, Tn4401a-carrying ColRNAI plasmids contributed to the acquisition of blaKPC-2 in C. europaeus and M. morganii.}, }
@article {pmid34729475, year = {2021}, author = {Val-Calvo, J and Miguel-Arribas, A and Abia, D and Wu, LJ and Meijer, WJJ}, title = {pLS20 is the archetype of a new family of conjugative plasmids harboured by Bacillus species.}, journal = {NAR genomics and bioinformatics}, volume = {3}, number = {4}, pages = {lqab096}, pmid = {34729475}, issn = {2631-9268}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {Conjugation plays important roles in genome plasticity, adaptation and evolution but is also the major horizontal gene-transfer route responsible for spreading toxin, virulence and antibiotic resistance genes. A better understanding of the conjugation process is required for developing drugs and strategies to impede the conjugation-mediated spread of these genes. So far, only a limited number of conjugative elements have been studied. For most of them, it is not known whether they represent a group of conjugative elements, nor about their distribution patterns. Here we show that pLS20 from the Gram-positive bacterium Bacillus subtilis is the prototype conjugative plasmid of a family of at least 35 members that can be divided into four clades, and which are harboured by different Bacillus species found in different global locations and environmental niches. Analyses of their phylogenetic relationship and their conjugation operons have expanded our understanding of a family of conjugative plasmids of Gram-positive origin.}, }
@article {pmid34719836, year = {2021}, author = {Wang, X and Yu, D and Chen, G and Liu, C and Xu, A and Tang, Z}, title = {Effects of interactions between quorum sensing and quorum quenching on microbial aggregation characteristics in wastewater treatment: A review.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {93}, number = {12}, pages = {2883-2902}, doi = {10.1002/wer.1657}, pmid = {34719836}, issn = {1554-7531}, support = {2020T130033//China Postdoctoral Science Foundation/ ; 51978348//National Natural Science Foundation of China/ ; 2019GSF110014//Shandong Key Research and Development Program/ ; }, mesh = {Acyl-Butyrolactones ; Bacterial Physiological Phenomena ; *Quorum Sensing ; Sewage ; *Wastewater ; }, abstract = {Due to the increasingly urgent demand for effective wastewater denitrification and dephosphorization systems, there is a need to improve the performance of existing biological treatment technologies. As a bacteria-level communication mechanism, quorum sensing (QS) synchronizes gene expression in a density-dependent manner and regulates bacterial physiological behavior. On this basis, the QS-based bacterial communication mechanism and environmental factors affecting QS are discussed. This paper reviews the influence of QS on sludge granulation, biofilm formation, emerging contaminants (ECs) removal, and horizontal gene transfer in sewage treatment system. Furthermore, the QS inhibition strategies are compared. Based on the coexistence and balance of QQ and QS in the long-term operation system, QQ, as an effective tool to regulate the growth density of microorganisms, provides a promising exogenous regulation strategy for residual sludge reduction and biofilm pollution control. This paper reviews the potential of improving wastewater treatment efficiency based on QS theory and points out the feasibility and prospect of exogenous regulation strategy. PRACTITIONER POINTS: The mechanism of bacterial communication based on QS and the environmental factors affecting QS were discussed. The application of QS and QQ in improving the sludge performance of biological treatment systems was described. The significance of QS and QQ coexistence in sewage treatment process was described.}, }
@article {pmid34718760, year = {2022}, author = {Fuentes, D and Molina, M and Chorostecki, U and Capella-Gutiérrez, S and Marcet-Houben, M and Gabaldón, T}, title = {PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies.}, journal = {Nucleic acids research}, volume = {50}, number = {D1}, pages = {D1062-D1068}, pmid = {34718760}, issn = {1362-4962}, mesh = {Animals ; *Databases, Genetic ; *Evolution, Molecular ; Genome/*genetics ; Humans ; Knowledge Bases ; Molecular Sequence Annotation ; Phylogeny ; Plants/genetics ; Proteome/genetics ; *Software ; }, abstract = {PhylomeDB is a unique knowledge base providing public access to minable and browsable catalogues of pre-computed genome-wide collections of annotated sequences, alignments and phylogenies (i.e. phylomes) of homologous genes, as well as to their corresponding phylogeny-based orthology and paralogy relationships. In addition, PhylomeDB trees and alignments can be downloaded for further processing to detect and date gene duplication events, infer past events of inter-species hybridization and horizontal gene transfer, as well as to uncover footprints of selection, introgression, gene conversion, or other relevant evolutionary processes in the genes and organisms of interest. Here, we describe the latest evolution of PhylomeDB (version 5). This new version includes a newly implemented web interface and several new functionalities such as optimized searching procedures, the possibility to create user-defined phylome collections, and a fully redesigned data structure. This release also represents a significant core data expansion, with the database providing access to 534 phylomes, comprising over 8 million trees, and homology relationships for genes in over 6000 species. This makes PhylomeDB the largest and most comprehensive public repository of gene phylogenies. PhylomeDB is available at http://www.phylomedb.org.}, }
@article {pmid36311810, year = {2021}, author = {Zhao, X and Fu, X and Yin, C and Lu, F}, title = {Wheat speciation and adaptation: perspectives from reticulate evolution.}, journal = {aBIOTECH}, volume = {2}, number = {4}, pages = {386-402}, pmid = {36311810}, issn = {2662-1738}, abstract = {Reticulate evolution through the interchanging of genetic components across organisms can impact significantly on the fitness and adaptation of species. Bread wheat (Triticum aestivum subsp. aestivum) is one of the most important crops in the world. Allopolyploid speciation, frequent hybridization, extensive introgression, and occasional horizontal gene transfer (HGT) have been shaping a typical paradigm of reticulate evolution in bread wheat and its wild relatives, which is likely to have a substantial influence on phenotypic traits and environmental adaptability of bread wheat. In this review, we outlined the evolutionary history of bread wheat and its wild relatives with a highlight on the interspecific hybridization events, demonstrating the reticulate relationship between species/subspecies in the genera Triticum and Aegilops. Furthermore, we discussed the genetic mechanisms and evolutionary significance underlying the introgression of bread wheat and its wild relatives. An in-depth understanding of the evolutionary process of Triticum species should be beneficial to future genetic study and breeding of bread wheat.}, }
@article {pmid34814374, year = {2013}, author = {Hoffmann, M and Monday, SR and McCarthy, PJ and Lopez, JV and Fischer, M and Brown, EW}, title = {Genetic and phylogenetic evidence for horizontal gene transfer among ecologically disparate groups of marine Vibrio.}, journal = {Cladistics : the international journal of the Willi Hennig Society}, volume = {29}, number = {1}, pages = {46-64}, doi = {10.1111/j.1096-0031.2012.00416.x}, pmid = {34814374}, issn = {1096-0031}, abstract = {Vibrio represents a diverse bacterial genus found in different niches of the marine environment, including numerous genera of marine sponges (phylum Porifera), inhabiting different depths and regions of benthic seas, that are potentially important in driving adaptive change among Vibrio spp. Using 16S rRNA gene sequencing, a previous study showed that sponge-derived (SD) vibrios clustered with their mainstream counterparts present in shallow, coastal ecosystems, suggesting a genetic relatedness between these populations. Sequences from the topA, ftsZ, mreB, rpoD, rctB and toxR genes were used to investigate the degree of relatedness existing between these two separate populations by examining their phylogenetic and genetic disparity. Phylogenies were constructed from the concatenated sequences of the six housekeeping genes using maximum-parsimony, maximum-likelihood and neighbour-joining algorithms. Genetic recombination was evaluated using the incongruence length difference test, Split decomposition and measuring overall compatibility of sites. This combined technical approach provided evidence that SD Vibrio strains are largely genetically homologous to their shallow-water counterparts. Moreover, the analyses conducted support the existence of extensive horizontal gene transfer between these two groups, supporting the idea of a single panmictic population structure among vibrios from two seemingly distinct, marine environments.}, }
@article {pmid34875790, year = {2011}, author = {Kurt Lienau, E and DeSalle, R and Allard, M and Brown, EW and Swofford, D and Rosenfeld, JA and Sarkar, IN and Planet, PJ}, title = {The mega-matrix tree of life: using genome-scale horizontal gene transfer and sequence evolution data as information about the vertical history of life.}, journal = {Cladistics : the international journal of the Willi Hennig Society}, volume = {27}, number = {4}, pages = {417-427}, doi = {10.1111/j.1096-0031.2010.00337.x}, pmid = {34875790}, issn = {1096-0031}, abstract = {Because horizontal gene transfer can confound the recovery of the largely prokaryotic tree of life (ToL), most genome-based techniques seek to eliminate horizontal signal from ToL analyses, commonly by sieving out incongruent genes and data. This approach greatly limits the number of gene families analysed to a subset thought to be representative of vertical evolutionary history. However, formalized tests have not been performed to determine whether combining the massive amounts of information available in fully sequenced genomes can recover a reasonable ToL. Consequently, we used empirically defined gene homology definitions from a previous study that delineate xenologous gene families (gene families derived from a common transfer event) to generate a massively concatenated, combined-data ToL matrix derived from 323 404 translated open reading frames arranged into 12 381 gene homologue groups coded as amino acid data and 63 336, 64 105, 65 153, 66 922 and 67 109 gene homologue groups coded as gene presence/absence data for 166 fully sequenced genomes. This whole-genome gene presence/absence and amino acid sequence ToL data matrix is composed of 4867 184 characters (a combined data-type mega-matrix). Phylogenetic analysis of this mega-matrix yielded a fully resolved ToL that classifies all three commonly accepted domains of life as monophyletic and groups most taxa in traditionally recognized locations with high support. Most importantly, these results corroborate the existence of a common evolutionary history for these taxa present in both data types that is evident only when these data are analysed in combination. © The Willi Hennig Society 2010.}, }
@article {pmid34875761, year = {2010}, author = {Lienau, EK and DeSalle, R}, title = {Is the microbial tree of life verificationist?.}, journal = {Cladistics : the international journal of the Willi Hennig Society}, volume = {26}, number = {2}, pages = {195-201}, doi = {10.1111/j.1096-0031.2009.00288.x}, pmid = {34875761}, issn = {1096-0031}, abstract = {The field of microbial phylogenetics has questioned the feasibility of using a tree-like structure to the describe microbial evolution. This debate centres on two main points. First, because microorganisms are able to transfer genes from one to another in zero generations (horizontal gene transfer, or HGT), the use of molecular characters to perform phylogenetic analyses will yield an erroneous topology and HGT clearly makes the evolution of microorganisms non tree-like. Second, the use of concatenated gene sequences in a total evidence approach to phylogenetic systematics is a verificationist endeavour, the aim of which is to bolster support. However, the goal of the total evidence approach to phylogenetic research is based in the idea of increasing explanatory power over background knowledge through test and corroboration, rather than to bolster support for nodes in a tree. In this context, the testing of phylogenetic data is a falsificationist endeavour that includes the possibility of not rejecting the null hypothesis that there is no tree-like structure in molecular phylogenetic data. We discuss several tests that aim to test rigorously the hypothesis that a tree of life exists for microorganisms. We also discuss the philosophical ramifications of background knowledge and corroboration in microbial studies that need to be considered when suggesting that HGT confounds the tree of life. © The Willi Hennig Society 2009.}, }
@article {pmid36151642, year = {2009}, author = {Berdjeb, L and Jacquet, S}, title = {[The viriosphere: which importance in the functioning and evolution of aquatic ecosystems (part II)?].}, journal = {Virologie (Montrouge, France)}, volume = {13}, number = {4}, pages = {189-199}, doi = {10.1684/13-4.2011.15352}, pmid = {36151642}, issn = {1267-8694}, abstract = {Besides the lethal effect of viruses on the microbial community (typically the bacteria and the phytoplankton), the viral activity can affect significantly not only the structure of this community but also the cycling of carbon and other nutrients within aquatic ecosystems. Due to their activities, viruses could maintain the prokaryotic community diversity by lysing the most dominant populations then allowing the development of the minor groups. Also, viruses constitute the major driver of horizontal gene transfer between bacterial species or genus and therefore they could be the principal actor in the diversification of microbial communities. The viral lysis which induces the transformation of the biomass into dissolved organic matter pool could stimulate the microbial respiration and reduce the transfer of carbon to higher trophic levels as well as the sedimentation of organic particles towards the bottom. At last, aquatic viruses may generate an important interest for applied issues, typically the phagotherapy for aquaculture, even if an important effort remains to be done in the comprehension of the real efficiency of this therapy and the possible underlying resistance phenomena.}, }
@article {pmid34718689, year = {2022}, author = {Mungan, MD and Blin, K and Ziemert, N}, title = {ARTS-DB: a database for antibiotic resistant targets.}, journal = {Nucleic acids research}, volume = {50}, number = {D1}, pages = {D736-D740}, pmid = {34718689}, issn = {1362-4962}, mesh = {Anti-Bacterial Agents ; Bacteria/drug effects/genetics ; Biosynthetic Pathways/drug effects/genetics ; *Databases, Factual ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial ; Metagenome/*genetics ; *Software ; }, abstract = {As a result of the continuous evolution of drug resistant bacteria, new antibiotics are urgently needed. Encoded by biosynthetic gene clusters (BGCs), antibiotic compounds are mostly produced by bacteria. With the exponential increase in the number of publicly available, sequenced genomes and the advancements of BGC prediction tools, genome mining algorithms have uncovered millions of uncharacterized BGCs for further evaluation. Since compound identification and characterization remain bottlenecks, a major challenge is prioritizing promising BGCs. Recently, researchers adopted self-resistance based strategies allowing them to predict the biological activities of natural products encoded by uncharacterized BGCs. Since 2017, the Antibiotic Resistant Target Seeker (ARTS) facilitated this so-called target-directed genome mining (TDGM) approach for the prioritization of BGCs encoding potentially novel antibiotics. Here, we present the ARTS database, available at https://arts-db.ziemertlab.com/. The ARTS database provides pre-computed ARTS results for >70,000 genomes and metagenome assembled genomes in total. Advanced search queries allow users to rapidly explore the fundamental criteria of TDGM such as BGC proximity, duplication and horizontal gene transfers of essential housekeeping genes. Furthermore, the ARTS database provides results interconnected throughout the bacterial kingdom as well as links to known databases in natural product research.}, }
@article {pmid34718420, year = {2022}, author = {Cattaneo, G and Ferraro Petrillo, U and Giancarlo, R and Palini, F and Romualdi, C}, title = {The power of word-frequency-based alignment-free functions: a comprehensive large-scale experimental analysis.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {4}, pages = {925-932}, doi = {10.1093/bioinformatics/btab747}, pmid = {34718420}, issn = {1367-4811}, support = {//INdAM - GNCS Project 2019/ ; //MIUR-PRIN project 'Multicriteria Data Structures/ ; IG21837//Italian Association of Cancer Research (AIRC)/ ; }, mesh = {*Algorithms ; *Software ; Sequence Analysis ; Genomics ; }, abstract = {MOTIVATION: Alignment-free (AF) distance/similarity functions are a key tool for sequence analysis. Experimental studies on real datasets abound and, to some extent, there are also studies regarding their control of false positive rate (Type I error). However, assessment of their power, i.e. their ability to identify true similarity, has been limited to some members of the D2 family. The corresponding experimental studies have concentrated on short sequences, a scenario no longer adequate for current applications, where sequence lengths may vary considerably. Such a State of the Art is methodologically problematic, since information regarding a key feature such as power is either missing or limited.<br><br>RESULTS: By concentrating on a representative set of word-frequency-based AF functions, we perform the first coherent and uniform evaluation of the power, involving also Type I error for completeness. Two alternative models of important genomic features (CIS Regulatory Modules and Horizontal Gene Transfer), a wide range of sequence lengths from a few thousand to millions, and different values of k have been used. As a result, we provide a characterization of those AF functions that is novel and informative. Indeed, we identify weak and strong points of each function considered, which may be used as a guide to choose one for analysis tasks. Remarkably, of the 15 functions that we have considered, only four stand out, with small differences between small and short sequence length scenarios. Finally, to encourage the use of our methodology for validation of future AF functions, the Big Data platform supporting it is public.<br><br>The software is available at: https://github.com/pipp8/power_statistics.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid34718024, year = {2022}, author = {Zhang, S and Sun, WL and Song, HL and Zhang, T and Yin, M and Wang, Q and Zuo, X}, title = {Effects of voltage on the emergence and spread of antibiotic resistance genes in microbial electrolysis cells: From mutation to horizontal gene transfer.}, journal = {Chemosphere}, volume = {291}, number = {Pt 1}, pages = {132703}, doi = {10.1016/j.chemosphere.2021.132703}, pmid = {34718024}, issn = {1879-1298}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial ; Electrolysis ; Escherichia coli ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Mutation ; }, abstract = {Microbial electrolysis cells (MECs) are widely considered as promising alternatives for degrading antibiotics. As one of the major operating parameters in MECs, voltage might affect the spread of antibiotic resistance genes (ARGs) given it can affect the physiological characteristics of bacteria. However, little is known about the impacts of voltage on the acceleration of bacterial mutation and the promotion of ARG dissemination via horizontal transfer in MECs. In this study, two voltages (0.9 V and 1.5 V) were applied to identify if electrical stimulation could increase bacterial mutation frequency. Three voltages (0.9 V, 1.5 V, and 2.5 V) were used to evaluate the conjugative transfer frequency of plasmid-encoded the ARGs from the donor (E. coli K-12) to the recipient (E. coli HB101) in MECs. After repeating subculture in MECs for 10 days, the mutation frequency of E. coli K-12 was promoted, consequently, the generated mutants became more resistant against tetracycline. When the voltage was higher than 0.9 V, conjugative ARG transfer frequency was significantly increased in the anode chamber (p < 0.05). The over-production of reactive oxygen species (ROS) (voltage >0.9 V) and cell membrane permeability (voltage >1.5 V) were significantly enhanced under electrical stimulations (p < 0.05). Genome-wide RNA sequencing indicated that the expressions of genes related to oxidative stress and cell membrane were upregulated with exposure to electrical stimulation. Electrical stimulations induced oxidative reactions, which triggered ROS over-production, SOS response, and enhancement of cell membrane permeability for both donor and recipient in the MECs. These findings provide insights into the potential role of voltage in the generation and spread of ARGs in MECs.}, }
@article {pmid34714534, year = {2021}, author = {Ramesh, C and Bessho-Uehara, M}, title = {Acquisition of bioluminescent trait by non-luminous organisms from luminous organisms through various origins.}, journal = {Photochemical &amp; photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology}, volume = {20}, number = {11}, pages = {1547-1562}, pmid = {34714534}, issn = {1474-9092}, support = {SERB/N-PDF/2016/ 000354//Science and Engineering Research Board/ ; DST/IF120230/2012/280//Department of Science and Technology, Ministry of Science and Technology/ ; }, mesh = {Animals ; Fishes ; Luciferases ; *Luciferins ; *Luminescence ; Luminescent Measurements ; Phenotype ; }, abstract = {Bioluminescence is a natural light emitting phenomenon that occurs due to a chemical reaction between luciferin and luciferase. It is primarily an innate and inherited trait in most terrestrial luminous organisms. However, most luminous organisms produce light in the ocean by acquiring luminous symbionts, luciferin (substrate), and/or luciferase (enzyme) through various transmission pathways. For instance, coelenterazine, a well-known luciferin, is obtained by cnidarians, crustaceans, and deep-sea fish through multi-level dietary linkages from coelenterazine producers such as ctenophores, decapods, and copepods. In contrast, some non-luminous Vibrio bacteria became bioluminescent by obtaining lux genes from luminous Vibrio species by horizontal gene transfer. Various examples detailed in this review show how non-luminescent organisms became luminescent by acquiring symbionts, dietary luciferins and luciferases, and genes. This review highlights three modes (symbiosis, ingestion, and horizontal gene transfer) that allow organisms lacking genes for autonomous bioluminescent systems to obtain the ability to produce light. In addition to bioluminescence, this manuscript discusses the acquisition of other traits such as pigments, fluorescence, toxins, and others, to infer the potential processes of acquisition.}, }
@article {pmid34713606, year = {2021}, author = {Antelo, V and Giménez, M and Azziz, G and Valdespino-Castillo, P and Falcón, LI and Ruberto, LAM and Mac Cormack, WP and Mazel, D and Batista, S}, title = {Metagenomic strategies identify diverse integron-integrase and antibiotic resistance genes in the Antarctic environment.}, journal = {MicrobiologyOpen}, volume = {10}, number = {5}, pages = {e1219}, pmid = {34713606}, issn = {2045-8827}, mesh = {Antarctic Regions ; Bacteria/*genetics ; Computational Biology/methods ; Drug Resistance, Microbial/*genetics ; *Genes, Bacterial ; High-Throughput Nucleotide Sequencing ; Integrases/*genetics ; Integrons/*genetics ; *Metagenome ; Metagenomics/methods ; Phylogeny ; Soil Microbiology ; }, abstract = {The objective of this study is to identify and analyze integrons and antibiotic resistance genes (ARGs) in samples collected from diverse sites in terrestrial Antarctica. Integrons were studied using two independent methods. One involved the construction and analysis of intI gene amplicon libraries. In addition, we sequenced 17 metagenomes of microbial mats and soil by high-throughput sequencing and analyzed these data using the IntegronFinder program. As expected, the metagenomic analysis allowed for the identification of novel predicted intI integrases and gene cassettes (GCs), which mostly encode unknown functions. However, some intI genes are similar to sequences previously identified by amplicon library analysis in soil samples collected from non-Antarctic sites. ARGs were analyzed in the metagenomes using ABRIcate with CARD database and verified if these genes could be classified as GCs by IntegronFinder. We identified 53 ARGs in 15 metagenomes, but only four were classified as GCs, one in MTG12 metagenome (Continental Antarctica), encoding an aminoglycoside-modifying enzyme (AAC(6´)acetyltransferase) and the other three in CS1 metagenome (Maritime Antarctica). One of these genes encodes a class D β-lactamase (blaOXA-205) and the other two are located in the same contig. One is part of a gene encoding the first 76 amino acids of aminoglycoside adenyltransferase (aadA6), and the other is a qacG2 gene.}, }
@article {pmid34711526, year = {2021}, author = {Aljowaie, RM and Abdel Gawwad, MR and Al Farraj, DA and H, JK and Rajendran, P}, title = {In-vitro antimicrobial susceptibility pattern of lipopeptide against drug resistant Vibrio species.}, journal = {Journal of infection and public health}, volume = {14}, number = {12}, pages = {1887-1892}, doi = {10.1016/j.jiph.2021.10.015}, pmid = {34711526}, issn = {1876-035X}, mesh = {Animals ; *Anti-Infective Agents ; Humans ; Lipopeptides/pharmacology ; Microbial Sensitivity Tests ; *Pharmaceutical Preparations ; *Vibrio ; }, abstract = {BACKGROUND: The unrestricted application of antibiotics increased antimicrobial resistance in bacteria through horizontal gene transfer of resistant genes from the pathogenic sources and the evolution of multi-drug resistance organisms. The application of antibiotics caused severe risk to human health because animals may transmit diseases to humans. Hence, the search of novel antimicrobial agents from microbial sources is an urgent need.<br><br>METHODS: A lipopeptide producing stain SU05 was isolated from the pond water by serial dilution method. The lipopeptide yield was improved after optimization method and the yield was analyzed using High Performance Liquid chromatography. The influence of wheat bran (0.5%-2.5%) and rice bran (0.5%-2.5%), pH (5.5-8.5), temperature (25-40 &#xb0;C) were screened to improve the production of lipopeptides by stain SU05 in submerged fermentation. Antibacterial activity of crude lipopeptide was tested against Vibrio anguillarum, Vibrio harveyi, Vibrio vulnificus, Vibrio salmonicida, Vibrio septicus, Vibrio fischeri, and Vibrio splendidus. The influence of lipopeptide on enzymes and antimicrobial property was analyzed.<br><br>RESULTS: Lipopeptide production was improved after nutrient supplements and optimization of physical factors. Lipopeptide showed potent activity against multi-drug resistant bacterial strains such as, V. anguillarum, V. harveyi, V. vulnificus, V. salmonicida, V. septicus, V. fischeri, and V. splendidus. Lipopeptide shows stability on various enzymes and this clearly revealed that the purified lipopeptide was highly stable in the presence of proteolytic enzymes. The findings suggest that lipopeptide SU05 characterized from the bacteria can survive at acidic environment in the intestine, and could be used to formulate fish feed.<br><br>CONCLUSIONS: The finding showed that the characterized lipopepties synthesized by B. amyloliquefaciens SU05 had a broad spectrum antibiotic potential against multidrug resistant Vibriosis causing bacterial pathogens. They were highly stable at broad temperature and pH ranges. These results demonstrated stability of lipopeptide at extreme conditions. The stability and activity of lipopeptide at extreme climatic condition is also useful for the application in pharmaceutical and food processing industries.}, }
@article {pmid34710742, year = {2021}, author = {Winter, M and Buckling, A and Harms, K and Johnsen, PJ and Vos, M}, title = {Antimicrobial resistance acquisition via natural transformation: context is everything.}, journal = {Current opinion in microbiology}, volume = {64}, number = {}, pages = {133-138}, doi = {10.1016/j.mib.2021.09.009}, pmid = {34710742}, issn = {1879-0364}, mesh = {*Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Humans ; }, abstract = {Natural transformation is a process where bacterial cells actively take up free DNA from the environment and recombine it into their genome or reconvert it into extra-chromosomal genetic elements. Although this mechanism is known to mediate the uptake of antibiotic resistance determinants in a range of human pathogens, its importance in the spread of antimicrobial resistance is not always appreciated. This review highlights the context in which transformation takes place: in diverse microbiomes, in interaction with other forms of horizontal gene transfer and in increasingly polluted environments. This examination of the abiotic and biotic drivers of transformation reveals that it could be more important in the dissemination of resistance genes than is often recognised.}, }
@article {pmid34710434, year = {2022}, author = {Arthur, R and Nicholson, A}, title = {Selection principles for Gaia.}, journal = {Journal of theoretical biology}, volume = {533}, number = {}, pages = {110940}, doi = {10.1016/j.jtbi.2021.110940}, pmid = {34710434}, issn = {1095-8541}, mesh = {*Earth, Planet ; Entropy ; }, abstract = {The Gaia hypothesis considers the life-environment coupled system as a single entity that acts to regulate and maintain habitable conditions on Earth. In this paper we discuss three mechanisms which could potentially lead to Gaia: Selection by Survival, Sequential Selection and Entropic Hierarchy. We use the Tangled Nature Model of co-evolution as a common framework for investigating all three, using an extended version of the standard model to elaborate on Gaia as an example of an entropic hierarchy. This idea, which combines sequential selection together with a reservoir of diversity that acts as a 'memory', implies a tendency towards growth and increasing resilience of the Gaian system over time. We then discuss how Gaian memory could be realised in practice via the microbial seed bank, climate refugia and lateral gene transfer and conclude by discussing testable implications of an entropic hierarchy for the study of Earth history and the search for life in the universe. This paper adds to the existing taxonomy of Gaia hypotheses to suggest an "Entropic Gaia" where we argue that increasing biomass, complexity and enhanced habitability over time is a statistically likely feature of a co-evolving system.}, }
@article {pmid34707579, year = {2021}, author = {Uluseker, C and Kaster, KM and Thorsen, K and Basiry, D and Shobana, S and Jain, M and Kumar, G and Kommedal, R and Pala-Ozkok, I}, title = {A Review on Occurrence and Spread of Antibiotic Resistance in Wastewaters and in Wastewater Treatment Plants: Mechanisms and Perspectives.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {717809}, pmid = {34707579}, issn = {1664-302X}, abstract = {This paper reviews current knowledge on sources, spread and removal mechanisms of antibiotic resistance genes (ARGs) in microbial communities of wastewaters, treatment plants and downstream recipients. Antibiotic is the most important tool to cure bacterial infections in humans and animals. The over- and misuse of antibiotics have played a major role in the development, spread, and prevalence of antibiotic resistance (AR) in the microbiomes of humans and animals, and microbial ecosystems worldwide. AR can be transferred and spread amongst bacteria via intra- and interspecies horizontal gene transfer (HGT). Wastewater treatment plants (WWTPs) receive wastewater containing an enormous variety of pollutants, including antibiotics, and chemicals from different sources. They contain large and diverse communities of microorganisms and provide a favorable environment for the spread and reproduction of AR. Existing WWTPs are not designed to remove micropollutants, antibiotic resistant bacteria (ARB) and ARGs, which therefore remain present in the effluent. Studies have shown that raw and treated wastewaters carry a higher amount of ARB in comparison to surface water, and such reports have led to further studies on more advanced treatment processes. This review summarizes what is known about AR removal efficiencies of different wastewater treatment methods, and it shows the variations among different methods. Results vary, but the trend is that conventional activated sludge treatment, with aerobic and/or anaerobic reactors alone or in series, followed by advanced post treatment methods like UV, ozonation, and oxidation removes considerably more ARGs and ARB than activated sludge treatment alone. In addition to AR levels in treated wastewater, it examines AR levels in biosolids, settled by-product from wastewater treatment, and discusses AR removal efficiency of different biosolids treatment procedures. Finally, it puts forward key-points and suggestions for dealing with and preventing further increase of AR in WWTPs and other aquatic environments, together with a discussion on the use of mathematical models to quantify and simulate the spread of ARGs in WWTPs. Mathematical models already play a role in the analysis and development of WWTPs, but they do not consider AR and challenges remain before models can be used to reliably study the dynamics and reduction of AR in such systems.}, }
@article {pmid34704920, year = {2021}, author = {Mullally, CA and Mikucki, A and Wise, MJ and Kahler, CM}, title = {Modelling evolutionary pathways for commensalism and hypervirulence in Neisseria meningitidis.}, journal = {Microbial genomics}, volume = {7}, number = {10}, pages = {}, pmid = {34704920}, issn = {2057-5858}, mesh = {Bacterial Proteins/*genetics ; Evolution, Molecular ; Frameshift Mutation ; Gene Transfer, Horizontal ; Genome, Bacterial ; Genomic Islands ; Humans ; Loss of Function Mutation ; Meningococcal Infections/*microbiology ; Nasopharynx/microbiology ; Neisseria meningitidis/genetics/*pathogenicity ; Symbiosis ; Virulence ; Whole Genome Sequencing/*methods ; }, abstract = {Neisseria meningitidis, the meningococcus, resides exclusively in humans and causes invasive meningococcal disease (IMD). The population of N. meningitidis is structured into stable clonal complexes by limited horizontal recombination in this naturally transformable species. N. meningitidis is an opportunistic pathogen, with some clonal complexes, such as cc53, effectively acting as commensal colonizers, while other genetic lineages, such as cc11, are rarely colonizers but are over-represented in IMD and are termed hypervirulent. This study examined theoretical evolutionary pathways for pathogenic and commensal lineages by examining the prevalence of horizontally acquired genomic islands (GIs) and loss-of-function (LOF) mutations. Using a collection of 4850 genomes from the BIGSdb database, we identified 82 GIs in the pan-genome of 11 lineages (10 hypervirulent and one commensal lineage). A new computational tool, Phaser, was used to identify frameshift mutations, which were examined for statistically significant association with genetic lineage. Phaser identified a total of 144 frameshift loci of which 105 were shown to have a statistically significant non-random distribution in phase status. The 82 GIs, but not the LOF loci, were associated with genetic lineage and invasiveness using the disease carriage ratio metric. These observations have been integrated into a new model that infers the early events of the evolution of the human adapted meningococcus. These pathways are enriched for GIs that are involved in modulating attachment to the host, growth rate, iron uptake and toxin expression which are proposed to increase competition within the meningococcal population for the limited environmental niche of the human nasopharynx. We surmise that competition for the host mucosal surface with the nasopharyngeal microbiome has led to the selection of isolates with traits that enable access to cell types (non-phagocytic and phagocytic) in the submucosal tissues leading to an increased risk for IMD.}, }
@article {pmid34703675, year = {2021}, author = {Yu, R and Sun, C and Liu, Y and Zhou, R}, title = {Shifts from cis-to trans-splicing of five mitochondrial introns in Tolypanthus maclurei.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e12260}, pmid = {34703675}, issn = {2167-8359}, abstract = {Shifts from cis-to trans-splicing of mitochondrial introns tend to correlate with relative genome rearrangement rates during vascular plant evolution, as is particularly apparent in some lineages of gymnosperms. However, although many angiosperms have also relatively high mitogenomic rearrangement rates, very few cis-to trans-splicing shifts except for five trans-spliced introns shared in seed plants have been reported. In this study, we sequenced and characterized the mitogenome of Tolypanthus maclurei, a hemiparasitic plant from the family Loranthaceae (Santalales). The mitogenome was assembled into a circular chromosome of 256,961 bp long, relatively small compared with its relatives from Santalales. It possessed a gene content of typical angiosperm mitogenomes, including 33 protein-coding genes, three rRNA genes and ten tRNA genes. Plastid-derived DNA fragments took up 9.1% of the mitogenome. The mitogenome contained one group I intron (cox1i729) and 23 group II introns. We found shifts from cis-to trans-splicing of five additional introns in its mitogenome, of which two are specific in T. maclurei. Moreover, atp1 is a chimeric gene and phylogenetic analysis indicated that a 356 bp region near the 3' end of atp1 of T. maclurei was acquired from Lamiales via horizontal gene transfer. Our results suggest that shifts to trans-splicing of mitochondrial introns may not be uncommon among angiosperms.}, }
@article {pmid34699617, year = {2022}, author = {Shoguchi, E}, title = {Gene clusters for biosynthesis of mycosporine-like amino acids in dinoflagellate nuclear genomes: Possible recent horizontal gene transfer between species of Symbiodiniaceae (Dinophyceae).}, journal = {Journal of phycology}, volume = {58}, number = {1}, pages = {1-11}, pmid = {34699617}, issn = {1529-8817}, mesh = {*Amino Acids/biosynthesis ; Animals ; *Anthozoa/genetics ; Coral Reefs ; *Dinoflagellida/genetics ; Gene Transfer, Horizontal ; Multigene Family ; Phylogeny ; Symbiosis ; }, abstract = {Global warming increases the temperature of the ocean surface, which can disrupt dinoflagellate-coral symbioses and result in coral bleaching. Photosynthetic dinoflagellates of the family Symbiodiniaceae include bleaching-tolerant and bleaching-sensitive coral symbionts. Therefore, understanding the molecular mechanisms for changing symbiont diversity is potentially useful to assist recovery of coral holobionts (corals and their associated microbes, including multiple species of Symbiodiniaceae), although sexual reproduction has not been observed in the Symbiodiniaceae. Recent molecular phylogenetic analyses estimate that the Symbiodiniaceae appeared 160 million years ago and diversified into 15 groups, five genera of which now have available draft genomes (i.e., Symbiodinium, Durusdinium, Breviolum, Fugacium, and Cladocopium). Comparative genomic analyses have suggested that crown groups have fewer gene families than early-diverging groups, although many genes that were probably acquired via gene duplications and horizontal gene transfers (HGTs) have been found in each decoded genome. Because UV stress is likely a contributor to coral bleaching, and because the highly conserved gene cluster for mycosporine-like amino acid (MAA) biosynthesis has been found in thermal-tolerant symbiont genomes, I reviewed genomic features of the Symbiodiniaceae, focusing on possible acquisition of a biosynthetic gene cluster for MAAs, which absorb UV radiation. On the basis of highly conserved noncoding sequences, I hypothesized that HGTs have occurred among members of the Symbiodiniaceae and have contributed to the diversification of Symbiodiniaceae-host relationships. Finally, I proposed that bleaching tolerance may be strengthened by multiple MAAs from both symbiotic dinoflagellates and corals.}, }
@article {pmid34699529, year = {2021}, author = {Orlando, M and Buchholz, PCF and Lotti, M and Pleiss, J}, title = {The GH19 Engineering Database: Sequence diversity, substrate scope, and evolution in glycoside hydrolase family 19.}, journal = {PloS one}, volume = {16}, number = {10}, pages = {e0256817}, pmid = {34699529}, issn = {1932-6203}, mesh = {Animals ; Bacterial Proteins/chemistry/genetics/metabolism ; Catalytic Domain ; Chitinases/chemistry/*genetics/metabolism ; Databases, Protein ; Endopeptidases/chemistry/*genetics/metabolism ; Evolution, Molecular ; Fungi/chemistry/genetics/metabolism ; Humans ; Models, Molecular ; Phylogeny ; Plant Proteins/chemistry/genetics/metabolism ; Protein Conformation ; Substrate Specificity ; }, abstract = {The glycoside hydrolase 19 (GH19) is a bifunctional family of chitinases and endolysins, which have been studied for the control of plant fungal pests, the recycle of chitin biomass, and the treatment of multi-drug resistant bacteria. The GH19 domain-containing sequences (22,461) were divided into a chitinase and an endolysin subfamily by analyzing sequence networks, guided by taxonomy and the substrate specificity of characterized enzymes. The chitinase subfamily was split into seventeen groups, thus extending the previous classification. The endolysin subfamily is more diverse and consists of thirty-four groups. Despite their sequence diversity, twenty-six residues are conserved in chitinases and endolysins, which can be distinguished by two specific sequence patterns at six and four positions, respectively. Their location outside the catalytic cleft suggests a possible mechanism for substrate specificity that goes beyond the direct interaction with the substrate. The evolution of the GH19 catalytic domain was investigated by large-scale phylogeny. The inferred evolutionary history and putative horizontal gene transfer events differ from previous works. While no clear patterns were detected in endolysins, chitinases varied in sequence length by up to four loop insertions, causing at least eight distinct presence/absence loop combinations. The annotated GH19 sequences and structures are accessible via the GH19 Engineering Database (GH19ED, https://gh19ed.biocatnet.de). The GH19ED has been developed to support the prediction of substrate specificity and the search for novel GH19 enzymes from neglected taxonomic groups or in regions of the sequence space where few sequences have been described yet.}, }
@article {pmid34699256, year = {2022}, author = {Bearson, SMD}, title = {Salmonella in Swine: Prevalence, Multidrug Resistance, and Vaccination Strategies.}, journal = {Annual review of animal biosciences}, volume = {10}, number = {}, pages = {373-393}, doi = {10.1146/annurev-animal-013120-043304}, pmid = {34699256}, issn = {2165-8110}, mesh = {Animals ; Anti-Bacterial Agents ; *Drug Resistance, Multiple, Bacterial/genetics ; Prevalence ; *Salmonella/genetics ; Swine ; United States ; Vaccination/veterinary ; }, abstract = {An estimated 1.3 million Salmonella infections and 420 deaths occur annually in the United States, with an estimated economic burden of $3.7 billion. More than 50% of US swine operations test positive for Salmonella according to the National Animal Health Monitoring System, and 20% of Salmonella from swine are multidrug resistant (resistant to ≥3 antimicrobial classes) as reported by the National Antimicrobial Resistance Monitoring System. This review on Salmonella in swine addresses the current status of these topics by discussing antimicrobial resistance and metal tolerance in Salmonella and the contribution of horizontal gene transfer. A major challenge in controlling Salmonella is that Salmonella is a foodborne pathogen in humans but is often a commensal in food animals and thereby establishes an asymptomatic reservoir state in such animals, including swine. As food animal production systems continue to expand and antimicrobial usage becomes more limited, the need for Salmonella interventions has intensified. A promising mitigation strategy is vaccination against Salmonella in swine to limit animal, environmental, and food contamination.}, }
@article {pmid34699171, year = {2021}, author = {Schoen, ME and Jahne, MA and Garland, J and Ramirez, L and Lopatkin, AJ and Hamilton, KA}, title = {Quantitative Microbial Risk Assessment of Antimicrobial Resistant and Susceptible Staphylococcus aureus in Reclaimed Wastewaters.}, journal = {Environmental science &amp; technology}, volume = {55}, number = {22}, pages = {15246-15255}, pmid = {34699171}, issn = {1520-5851}, support = {EPA999999/ImEPA/Intramural EPA/United States ; }, mesh = {Anti-Bacterial Agents ; *Communicable Diseases/drug therapy ; Humans ; Risk Assessment ; *Staphylococcus aureus ; Wastewater ; }, abstract = {The annual risks of colonization, skin infection, bloodstream infection (BSI), and disease burden from exposures to antibiotic-resistant and susceptible Staphylococcus aureus (S. aureus) were estimated using quantitative microbial risk assessment (QMRA). We estimated the probability of nasal colonization after immersion in wastewater (WW) or greywater (GW) treated across a range of treatment alternatives and subsequent infection. Horizontal gene transfer was incorporated into the treatment model but had little effect on the predicted risk. The cumulative annual probability of infection (resulting from self-inoculation) was most sensitive to the treatment log10 reduction value (LRV), S. aureus concentration, and the newly calculated morbidity ratios and was below the health benchmark of 10[-4] infections per person per year (ppy) given a treatment LRV of roughly 3.0. The predicted annual disability-adjusted life years (DALYs), which were dominated by BSI, were below the health benchmark of 10[-6] DALYs ppy for resistant and susceptible S. aureus, given LRVs of 4.5 and 3.5, respectively. Thus, the estimated infection risks and disease burdens resulting from nasal colonization are below the relevant health benchmarks for risk-based, nonpotable, or potable reuse systems but possibly above for immersion in minimally treated GW or WW. Strain-specific data to characterize dose-response and concentration in WW are needed to substantiate the QMRA.}, }
@article {pmid34698119, year = {2021}, author = {Nzuza, N and Padayachee, T and Chen, W and Gront, D and Nelson, DR and Syed, K}, title = {Diversification of Ferredoxins across Living Organisms.}, journal = {Current issues in molecular biology}, volume = {43}, number = {3}, pages = {1374-1390}, pmid = {34698119}, issn = {1467-3045}, support = {114159//National Research Foundation, South Africa/ ; C686//University of Zululand/ ; 2018/29/B/ST6/01989//Polish National Science Centre (NCN)/ ; }, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; Computational Biology/methods ; Databases, Genetic ; Eukaryota/classification/genetics ; Evolution, Molecular ; Ferredoxins/*chemistry/classification/*genetics ; *Genetic Variation ; Phylogeny ; Species Specificity ; }, abstract = {Ferredoxins, iron-sulfur (Fe-S) cluster proteins, play a key role in oxidoreduction reactions. To date, evolutionary analysis of these proteins across the domains of life have been confined to observing the abundance of Fe-S cluster types (2Fe-2S, 3Fe-4S, 4Fe-4S, 7Fe-8S (3Fe-4s and 4Fe-4S) and 2[4Fe-4S]) and the diversity of ferredoxins within these cluster types was not studied. To address this research gap, here we propose a subtype classification and nomenclature for ferredoxins based on the characteristic spacing between the cysteine amino acids of the Fe-S binding motif as a subtype signature to assess the diversity of ferredoxins across the living organisms. To test this hypothesis, comparative analysis of ferredoxins between bacterial groups, Alphaproteobacteria and Firmicutes and ferredoxins collected from species of different domains of life that are reported in the literature has been carried out. Ferredoxins were found to be highly diverse within their types. Large numbers of alphaproteobacterial species ferredoxin subtypes were found in Firmicutes species and the same ferredoxin subtypes across the species of Bacteria, Archaea, and Eukarya, suggesting shared common ancestral origin of ferredoxins between Archaea and Bacteria and lateral gene transfer of ferredoxins from prokaryotes (Archaea/Bacteria) to eukaryotes. This study opened new vistas for further analysis of diversity of ferredoxins in living organisms.}, }
@article {pmid34697892, year = {2021}, author = {Merges, D and Dal Grande, F and Greve, C and Otte, J and Schmitt, I}, title = {Virus diversity in metagenomes of a lichen symbiosis (Umbilicaria phaea): complete viral genomes, putative hosts and elevational distributions.}, journal = {Environmental microbiology}, volume = {23}, number = {11}, pages = {6637-6650}, doi = {10.1111/1462-2920.15802}, pmid = {34697892}, issn = {1462-2920}, mesh = {*Ascomycota/genetics ; *Bacteriophages/genetics ; Genome, Viral/genetics ; *Lichens/genetics/microbiology ; Metagenome ; Phylogeny ; Symbiosis ; }, abstract = {Viruses can play critical roles in symbioses by initiating horizontal gene transfer, affecting host phenotypes, or expanding their host's ecological niche. However, knowledge of viral diversity and distribution in symbiotic organisms remains elusive. Here we use deep-sequenced metagenomic DNA (PacBio Sequel II; two individuals), paired with a population genomics approach (Pool-seq; 11 populations, 550 individuals) to understand viral distributions in the lichen Umbilicaria phaea. We assess (i) viral diversity in lichen thalli, (ii) putative viral hosts (fungi, algae, bacteria) and (iii) viral distributions along two replicated elevation gradients. We identified five novel viruses, showing 28%-40% amino acid identity to known viruses. They tentatively belong to the families Caulimoviridae, Myoviridae, Podoviridae and Siphoviridae. Our analysis suggests that the Caulimovirus is associated with green algal photobionts (Trebouxia) of the lichen, and the remaining viruses with bacterial hosts. We did not detect viral sequences in the mycobiont. Caulimovirus abundance decreased with increasing elevation, a pattern reflected by a specific algal lineage hosting this virus. Bacteriophages showed population-specific patterns. Our work provides the first comprehensive insights into viruses associated with a lichen holobiont and suggests an interplay of viral hosts and environment in structuring viral distributions.}, }
@article {pmid34691012, year = {2021}, author = {Ferreira, JL and Coleman, I and Addison, ML and Zachs, T and Quigley, BL and Wuichet, K and Beeby, M}, title = {Corrigendum: The "Jack-of-all-Trades" Flagellum From Salmonella and E. coli Was Horizontally Acquired From an Ancestral β-Proteobacterium.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {773675}, doi = {10.3389/fmicb.2021.773675}, pmid = {34691012}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2021.643180.].}, }
@article {pmid34690978, year = {2021}, author = {Pazhani, GP and Chowdhury, G and Ramamurthy, T}, title = {Adaptations of Vibrio parahaemolyticus to Stress During Environmental Survival, Host Colonization, and Infection.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {737299}, pmid = {34690978}, issn = {1664-302X}, abstract = {Vibrio parahaemolyticus (Vp) is an aquatic Gram-negative bacterium that may infect humans and cause gastroenteritis and wound infections. The first pandemic of Vp associated infection was caused by the serovar O3:K6 and epidemics caused by the other serovars are increasingly reported. The two major virulence factors, thermostable direct hemolysin (TDH) and/or TDH-related hemolysin (TRH), are associated with hemolysis and cytotoxicity. Vp strains lacking tdh and/or trh are avirulent and able to colonize in the human gut and cause infection using other unknown factors. This pathogen is well adapted to survive in the environment and human host using several genetic mechanisms. The presence of prophages in Vp contributes to the emergence of pathogenic strains from the marine environment. Vp has two putative type-III and type-VI secretion systems (T3SS and T6SS, respectively) located on both the chromosomes. T3SS play a crucial role during the infection process by causing cytotoxicity and enterotoxicity. T6SS contribute to adhesion, virulence associated with interbacterial competition in the gut milieu. Due to differential expression, type III secretion system 2 (encoded on chromosome-2, T3SS2) and other genes are activated and transcribed by interaction with bile salts within the host. Chromosome-1 encoded T6SS1 has been predominantly identified in clinical isolates. Acquisition of genomic islands by horizontal gene transfer provides enhanced tolerance of Vp toward several antibiotics and heavy metals. Vp consists of evolutionarily conserved targets of GTPases and kinases. Expression of these genes is responsible for the survival of Vp in the host and biochemical changes during its survival. Advanced genomic analysis has revealed that various genes are encoded in Vp pathogenicity island that control and expression of virulence in the host. In the environment, the biofilm gene expression has been positively correlated to tolerance toward aerobic, anaerobic, and micro-aerobic conditions. The genetic similarity analysis of toxin/antitoxin systems of Escherichia coli with VP genome has shown a function that could induce a viable non-culturable state by preventing cell division. A better interpretation of the Vp virulence and other mechanisms that support its environmental fitness are important for diagnosis, treatment, prevention and spread of infections. This review identifies some of the common regulatory pathways of Vp in response to different stresses that influence its survival, gut colonization and virulence.}, }
@article {pmid34690959, year = {2021}, author = {Shafranskaya, D and Chori, A and Korobeynikov, A}, title = {Graph-Based Approaches Significantly Improve the Recovery of Antibiotic Resistance Genes From Complex Metagenomic Datasets.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {714836}, pmid = {34690959}, issn = {1664-302X}, abstract = {The lack of control over the usage of antibiotics leads to propagation of the microbial strains that are resistant to many antimicrobial substances. This situation is an emerging threat to public health and therefore the development of approaches to infer the presence of resistant strains is a topic of high importance. The resistome construction of an isolate microbial species could be considered a solved task with many state-of-the-art tools available. However, when it comes to the analysis of the resistome of a microbial community (metagenome), then there exist many challenges that influence the accuracy and precision of the predictions. For example, the prediction sensitivity of the existing tools suffer from the fragmented metagenomic assemblies due to interspecies repeats: usually it is impossible to recover conservative parts of antibiotic resistance genes that belong to different species that occur due to e.g., horizontal gene transfer or residing on a plasmid. The recent advances in development of new graph-based methods open a way to recover gene sequences of interest directly from the assembly graph without relying on cumbersome and incomplete metagenomic assembly. We present GraphAMR-a novel computational pipeline for recovery and identification of antibiotic resistance genes from fragmented metagenomic assemblies. The pipeline involves the alignment of profile hidden Markov models of target genes directly to the assembly graph of a metagenome with further dereplication and annotation of the results using state-of-the art tools. We show significant improvement of the quality of the results obtained (both in terms of accuracy and completeness) as compared to the analysis of an output of ordinary metagenomic assembly as well as different read mapping approaches. The pipeline is freely available from https://github.com/ablab/graphamr.}, }
@article {pmid34683477, year = {2021}, author = {Boya, BR and Kumar, P and Lee, JH and Lee, J}, title = {Diversity of the Tryptophanase Gene and Its Evolutionary Implications in Living Organisms.}, journal = {Microorganisms}, volume = {9}, number = {10}, pages = {}, pmid = {34683477}, issn = {2076-2607}, abstract = {Tryptophanase encoded by the gene tnaA is a pyridoxal phosphate-dependent enzyme that catalyses the conversion of tryptophan to indole, which is commonly used as an intra- and interspecies signalling molecule, particularly by microbes. However, the production of indole is rare in eukaryotic organisms. A nucleotide and protein database search revealed tnaA is commonly reported in various Gram-negative bacteria, but that only a few Gram-positive bacteria and archaea possess the gene. The presence of tnaA in eukaryotes, particularly protozoans and marine organisms, demonstrates the importance of this gene in the animal kingdom. Here, we document the distribution of tnaA and its acquisition and expansion among different taxonomic groups, many of which are usually categorized as non-indole producers. This study provides an opportunity to understand the intriguing role played by tnaA, and its distribution among various types of organisms.}, }
@article {pmid34683343, year = {2021}, author = {Beyi, AF and Brito-Goulart, D and Hawbecker, T and Slagel, C and Ruddell, B and Hassall, A and Dewell, R and Dewell, G and Sahin, O and Zhang, Q and Plummer, PJ}, title = {Danofloxacin Treatment Alters the Diversity and Resistome Profile of Gut Microbiota in Calves.}, journal = {Microorganisms}, volume = {9}, number = {10}, pages = {}, pmid = {34683343}, issn = {2076-2607}, abstract = {Fluoroquinolones, such as danofloxacin, are used to control bovine respiratory disease complex in beef cattle; however, little is known about their effects on gut microbiota and resistome. The objectives were to evaluate the effect of subcutaneously administered danofloxacin on gut microbiota and resistome, and the composition of Campylobacter in calves. Twenty calves were injected with a single dose of danofloxacin, and ten calves were kept as a control. The effects of danofloxacin on microbiota and the resistome were assessed using 16S rRNA sequencing, quantitative real-time PCR, and metagenomic Hi-C ProxiMeta. Alpha and beta diversities were significantly different (p < 0.05) between pre-and post-treatment samples, and the compositions of several bacterial taxa shifted. The patterns of association between the compositions of Campylobacter and other genera were affected by danofloxacin. Antimicrobial resistance genes (ARGs) conferring resistance to five antibiotics were identified with their respective reservoirs. Following the treatment, some ARGs (e.g., ant9, tet40, tetW) increased in frequencies and host ranges, suggesting initiation of horizontal gene transfer, and new ARGs (aac6, ermF, tetL, tetX) were detected in the post-treatment samples. In conclusion, danofloxacin induced alterations of gut microbiota and selection and enrichment of resistance genes even against antibiotics that are unrelated to danofloxacin.}, }
@article {pmid34680871, year = {2021}, author = {Amirsoleimani, A and Brion, G and Francois, P}, title = {Co-Carriage of Metal and Antibiotic Resistance Genes in Sewage Associated Staphylococci.}, journal = {Genes}, volume = {12}, number = {10}, pages = {}, pmid = {34680871}, issn = {2073-4425}, mesh = {Anti-Bacterial Agents/adverse effects/therapeutic use ; Bacterial Proteins/*genetics ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial/genetics ; Humans ; Membrane Proteins/*genetics ; Metals/adverse effects/therapeutic use ; Plasmids/genetics ; Sewage/microbiology ; Staphylococcal Infections/drug therapy/*genetics/microbiology ; Staphylococcus/drug effects/genetics ; Staphylococcus aureus/*genetics/pathogenicity ; Whole Genome Sequencing ; }, abstract = {Controlling spread of resistance genes from wastewater to aquatic systems requires more knowledge on how resistance genes are acquired and transmitted. Whole genomic sequences from sewage-associated staphylococcus isolates (20 S. aureus, 2 Staphylococcus warneri, and 2 Staphylococcus delphini) were analyzed for the presence of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs). Plasmid sequences were identified in each isolate to investigate co-carriage of ARGs and MRGs within. BLASTN analysis showed that 67% of the isolates carried more than one ARG. The carriage of multiple plasmids was observed more in CC5 than CC8 S. aureus strains. Plasmid exchange was observed in all staphylococcus species except the two S. delphini isolates that carried multiple MRGs, no ARGs, and no plasmids. 85% of S. aureus isolates carried the blaZ gene, 76% co-carried blaZ with cadD and cadX, with 62% of these isolates carrying blaZ, cadD, and cadX on the same plasmid. The co-carriage of ARGs and MRGs in S. warneri isolates, and carriage of MRGs in S. delphini, without plasmids suggests non-conjugative transmission routes for gene acquisition. More studies are required that focus on the transduction and transformation routes of transmission to prevent interspecies exchange of ARGs and MRGs in sewage-associated systems.}, }
@article {pmid34680816, year = {2021}, author = {Juraschek, K and Käsbohrer, A and Malorny, B and Schwarz, S and Meemken, D and Hammerl, JA}, title = {Dissection of Highly Prevalent qnrS1-Carrying IncX Plasmid Types in Commensal Escherichia coli from German Food and Livestock.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {10}, number = {10}, pages = {}, pmid = {34680816}, issn = {2079-6382}, support = {773830//Horizon 2020 - ARDIG/ ; 43-001//German Federal Institute for Risk Assessment/ ; }, abstract = {Plasmids are mobile genetic elements, contributing to the spread of resistance determinants by horizontal gene transfer. Plasmid-mediated quinolone resistances (PMQRs) are important determinants able to decrease the antimicrobial susceptibility of bacteria against fluoroquinolones and quinolones. The PMQR gene qnrS1, especially, is broadly present in the livestock and food sector. Thus, it is of interest to understand the characteristics of plasmids able to carry and disseminate this determinant and therewith contribute to the resistance development against this class of high-priority, critically important antimicrobials. Therefore, we investigated all commensal Escherichia (E.) coli isolates, with reduced susceptibility to quinolones, recovered during the annual zoonosis monitoring 2017 in the pork and beef production chain in Germany (n = 2799). Through short-read whole-genome sequencing and bioinformatics analysis, the composition of the plasmids and factors involved in their occurrence were determined. We analysed the presence and structures of predominant plasmids carrying the PMQR qnrS1. This gene was most frequently located on IncX plasmids. Although the E. coli harbouring these IncX plasmids were highly diverse in their sequence types as well as their phenotypic resistance profiles, the IncX plasmids-carrying the qnrS1 gene were rather conserved. Thus, we only detected three distinct IncX plasmids carrying qnrS1 in the investigated isolates. The IncX plasmids were assigned either to IncX1 or to IncX3. All qnrS1-carrying IncX plasmids further harboured a β-lactamase gene (bla). In addition, all investigated IncX plasmids were transmissible. Overall, we found highly heterogenic E. coli harbouring conserved IncX plasmids as vehicles for the most prevalent qnr gene qnrS1. These IncX plasmids may play an important role in the dissemination of those two resistance determinants and their presence, transfer and co-selection properties require a deeper understanding for a thorough risk assessment.}, }
@article {pmid34678229, year = {2022}, author = {Alderliesten, JB and Zwart, MP and de Visser, JAGM and Stegeman, A and Fischer, EAJ}, title = {Second compartment widens plasmid invasion conditions: Two-compartment pair-formation model of conjugation in the gut.}, journal = {Journal of theoretical biology}, volume = {533}, number = {}, pages = {110937}, doi = {10.1016/j.jtbi.2021.110937}, pmid = {34678229}, issn = {1095-8541}, mesh = {Animals ; Bacteria ; *Conjugation, Genetic ; Drug Resistance, Microbial ; *Gene Transfer, Horizontal ; Humans ; Plasmids/genetics ; }, abstract = {Understanding under which conditions conjugative plasmids encoding antibiotic resistance can invade bacterial communities in the gut is of particular interest to combat the spread of antibiotic resistance within and between animals and humans. We extended a one-compartment model of conjugation to a two-compartment model, to analyse how differences in plasmid dynamics in the gut lumen and at the gut wall affect the invasion of plasmids. We compared scenarios with one and two compartments, different migration rates between the lumen and wall compartments, and different population dynamics. We focused on the effect of attachment and detachment rates on plasmid dynamics, explicitly describing pair formation followed by plasmid transfer in the pairs. The parameter space allowing plasmid invasion in the one-compartment model is affected by plasmid costs and intrinsic conjugation rates of the transconjugant, but not by these characteristics of the donor. The parameter space allowing plasmid invasion in the two-compartment model is affected by attachment and detachment rates in the lumen and wall compartment, and by the bacterial density at the wall. The one- and two-compartment models predict the same parameter space for plasmid invasion if the conditions in both compartments are equal to the conditions in the one-compartment model. In contrast, the addition of the wall compartment widens the parameter space allowing invasion compared with the one-compartment model, if the density at the wall is higher than in the lumen, or if the attachment rate at the wall is high and the detachment rate at the wall is low. We also compared the pair-formation models with bulk-conjugation models that describe conjugation by instantaneous transfer of the plasmid at contact between cells, without explicitly describing pair formation. Our results show that pair-formation and bulk-conjugation models predict the same parameter space for plasmid invasion. From our simulations, we conclude that conditions at the gut wall should be taken into account to describe plasmid dynamics in the gut and that transconjugant characteristics rather than donor characteristics should be used to parameterize the models.}, }
@article {pmid34678056, year = {2021}, author = {Zhou, H and Beltrán, JF and Brito, IL}, title = {Functions predict horizontal gene transfer and the emergence of antibiotic resistance.}, journal = {Science advances}, volume = {7}, number = {43}, pages = {eabj5056}, pmid = {34678056}, issn = {2375-2548}, support = {DP2 HL141007/HL/NHLBI NIH HHS/United States ; }, abstract = {Phylogenetic distance, shared ecology, and genomic constraints are often cited as key drivers governing horizontal gene transfer (HGT), although their relative contributions are unclear. Here, we apply machine learning algorithms to a curated set of diverse bacterial genomes to tease apart the importance of specific functional traits on recent HGT events. We find that functional content accurately predicts the HGT network [area under the receiver operating characteristic curve (AUROC) = 0.983], and performance improves further (AUROC = 0.990) for transfers involving antibiotic resistance genes (ARGs), highlighting the importance of HGT machinery, niche-specific, and metabolic functions. We find that high-probability not-yet detected ARG transfer events are almost exclusive to human-associated bacteria. Our approach is robust at predicting the HGT networks of pathogens, including Acinetobacter baumannii and Escherichia coli, as well as within localized environments, such as an individual’s gut microbiome.}, }
@article {pmid34676984, year = {2021}, author = {Lu, H and Li, F and Yuan, L and Domenzain, I and Yu, R and Wang, H and Li, G and Chen, Y and Ji, B and Kerkhoven, EJ and Nielsen, J}, title = {Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection.}, journal = {Molecular systems biology}, volume = {17}, number = {10}, pages = {e10427}, pmid = {34676984}, issn = {1744-4292}, mesh = {Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; Genome ; *Metabolic Networks and Pathways/genetics ; *Saccharomyces cerevisiae/genetics ; }, abstract = {Yeasts are known to have versatile metabolic traits, while how these metabolic traits have evolved has not been elucidated systematically. We performed integrative evolution analysis to investigate how genomic evolution determines trait generation by reconstructing genome-scale metabolic models (GEMs) for 332 yeasts. These GEMs could comprehensively characterize trait diversity and predict enzyme functionality, thereby signifying that sequence-level evolution has shaped reaction networks towards new metabolic functions. Strikingly, using GEMs, we can mechanistically map different evolutionary events, e.g. horizontal gene transfer and gene duplication, onto relevant subpathways to explain metabolic plasticity. This demonstrates that gene family expansion and enzyme promiscuity are prominent mechanisms for metabolic trait gains, while GEM simulations reveal that additional factors, such as gene loss from distant pathways, contribute to trait losses. Furthermore, our analysis could pinpoint to specific genes and pathways that have been under positive selection and relevant for the formulation of complex metabolic traits, i.e. thermotolerance and the Crabtree effect. Our findings illustrate how multidimensional evolution in both metabolic network structure and individual enzymes drives phenotypic variations.}, }
@article {pmid34673769, year = {2021}, author = {Hill, V and Akarsu, H and Barbarroja, RS and Cippà, VL and Kuhnert, P and Heller, M and Falquet, L and Heller, M and Stoffel, MH and Labroussaa, F and Jores, J}, title = {Minimalistic mycoplasmas harbor different functional toxin-antitoxin systems.}, journal = {PLoS genetics}, volume = {17}, number = {10}, pages = {e1009365}, pmid = {34673769}, issn = {1553-7404}, mesh = {Animals ; Bacteria/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Goats/microbiology ; Mycoplasma/*genetics/*metabolism ; Phylogeny ; Proteomics/methods ; Toxin-Antitoxin Systems/*genetics ; Transcriptome/genetics ; }, abstract = {Mycoplasmas are minute bacteria controlled by very small genomes ranging from 0.6 to 1.4 Mbp. They encompass several important medical and veterinary pathogens that are often associated with a wide range of chronic diseases. The long persistence of mycoplasma cells in their hosts can exacerbate the spread of antimicrobial resistance observed for many species. However, the nature of the virulence factors driving this phenomenon in mycoplasmas is still unclear. Toxin-antitoxin systems (TA systems) are genetic elements widespread in many bacteria that were historically associated with bacterial persistence. Their presence on mycoplasma genomes has never been carefully assessed, especially for pathogenic species. Here we investigated three candidate TA systems in M. mycoides subsp. capri encoding a (i) novel AAA-ATPase/subtilisin-like serine protease module, (ii) a putative AbiEii/AbiEi pair and (iii) a putative Fic/RelB pair. We sequence analyzed fourteen genomes of M. mycoides subsp. capri and confirmed the presence of at least one TA module in each of them. Interestingly, horizontal gene transfer signatures were also found in several genomic loci containing TA systems for several mycoplasma species. Transcriptomic and proteomic data confirmed differential expression profiles of these TA systems during mycoplasma growth in vitro. While the use of heterologous expression systems based on E. coli and B. subtilis showed clear limitations, the functionality and neutralization capacities of all three candidate TA systems were successfully confirmed using M. capricolum subsp. capricolum as a host. Additionally, M. capricolum subsp. capricolum was used to confirm the presence of functional TA system homologs in mycoplasmas of the Hominis and Pneumoniae phylogenetic groups. Finally, we showed that several of these M. mycoides subsp. capri toxins tested in this study, and particularly the subtilisin-like serine protease, could be used to establish a kill switch in mycoplasmas for industrial applications.}, }
@article {pmid34673373, year = {2021}, author = {Shao, S and Li, C and Zhao, L and Zhang, Y and Yin, K and Wang, Q}, title = {Interplay between ferric uptake regulator Fur and horizontally acquired virulence regulator EsrB coordinates virulence gene expression in Edwardsiella piscicida.}, journal = {Microbiological research}, volume = {253}, number = {}, pages = {126892}, doi = {10.1016/j.micres.2021.126892}, pmid = {34673373}, issn = {1618-0623}, mesh = {*Bacterial Proteins/genetics/metabolism ; *Edwardsiella/genetics/pathogenicity ; *Gene Expression Regulation, Bacterial/genetics ; Gene Transfer, Horizontal ; *Repressor Proteins/genetics/metabolism ; *Virulence/genetics ; }, abstract = {Edwardsiella piscicida mediates hemorrhagic septicemia and is a leading pathogen of fish. E. piscicida invades and colonizes macrophages using type III and VI secretion systems (T3/T6SS) that are controlled by a two-component system (TCS) EsrA-EsrB. Iron acquisition is essential for E. piscicida pathogenesis and coordination between iron and TCS signaling in modulating bacterial virulence is not well understood. Here, we show that iron uptake systems are co-regulated by ferric uptake regulator (Fur) in E. piscicida. Fur bound to 98 genes that harbored conserved Fur-box to globally control the expression of ∼755 genes, including those encoding iron uptake systems, T3/T6SS, and Icc, cAMP phosphodiesterase that represses biofilm formation. Additionally, Fur, in complex with iron, bound to the esrB promoter to repress expression and ultimately attenuated virulence. Conversely, EsrB activated the expression of T3/T6SS and iron uptake systems to mitigate a shortage of intracellular iron during iron scarcity. Furthermore, EsrB directly bound to and activated the fur promoter, leading to Fur-ferrous ion-dependent esrB repression in the presence of iron. Finally, Fur-EsrB interplay was essential for bacterial fitness during in vivo infection and survival in seawater environments. Collectively, we highlight the mechanisms that underlie the reciprocal regulatory networks of iron homeostasis and virulence systems in E. piscicida.}, }
@article {pmid34672103, year = {2021}, author = {Karthikeyan, S and Hatt, JK and Kim, M and Spain, JC and Huettel, M and Kostka, JE and Konstantinidis, KT}, title = {A novel, divergent alkane monooxygenase (alkB) clade involved in crude oil biodegradation.}, journal = {Environmental microbiology reports}, volume = {13}, number = {6}, pages = {830-840}, doi = {10.1111/1758-2229.13018}, pmid = {34672103}, issn = {1758-2229}, mesh = {Alkanes/metabolism ; *Biodegradation, Environmental ; *Cyanobacteria/enzymology ; *Cytochrome P-450 CYP4A/genetics/metabolism ; Ecosystem ; *Petroleum/metabolism ; Phylogeny ; }, abstract = {Alkanes are ubiquitous in marine ecosystems and originate from diverse sources ranging from natural oil seeps to anthropogenic inputs and biogenic production by cyanobacteria. Enzymes that degrade cyanobacterial alkanes (typically C15-C17 compounds) such as the alkane monooxygenase (AlkB) are widespread, but it remains unclear whether or not AlkB variants exist that specialize in degradation of crude oil from natural or accidental spills, a much more complex mixture of long-chain hydrocarbons. In the present study, large-scale analysis of available metagenomic and genomic data from the Gulf of Mexico (GoM) oil spill revealed a novel, divergent AlkB clade recovered from genomes with no cultured representatives that was dramatically increased in abundance in crude-oil impacted ecosystems. In contrast, the AlkB clades associated with biotransformation of cyanobacterial alkanes belonged to 'canonical' or hydrocarbonoclastic clades, and based on metatranscriptomics data and compared to the novel clade, were much more weakly expressed during crude oil biodegradation in laboratory mesocosms. The absence of this divergent AlkB clade in metagenomes of uncontaminated samples from the global ocean survey but not from the GoM as well as its frequent horizontal gene transfer indicated a priming effect of the Gulf for crude oil biodegradation likely driven by natural oil seeps.}, }
@article {pmid34671336, year = {2021}, author = {Carranza, G and Menguiano, T and Valenzuela-Gómez, F and García-Cazorla, Y and Cabezón, E and Arechaga, I}, title = {Monitoring Bacterial Conjugation by Optical Microscopy.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {750200}, pmid = {34671336}, issn = {1664-302X}, abstract = {Bacterial conjugation is the main mechanism for horizontal gene transfer, conferring plasticity to the genome repertoire. This process is also the major instrument for the dissemination of antibiotic resistance genes. Hence, gathering primary information of the mechanism underlying this genetic transaction is of a capital interest. By using fluorescent protein fusions to the ATPases that power conjugation, we have been able to track the localization of these proteins in the presence and absence of recipient cells. Moreover, we have found that more than one copy of the conjugative plasmid is transferred during mating. Altogether, these findings provide new insights into the mechanism of such an important gene transfer device.}, }
@article {pmid34671327, year = {2021}, author = {Bajić, D and Rebolleda-Gómez, M and Muñoz, MM and Sánchez, &#xc1;}, title = {The Macroevolutionary Consequences of Niche Construction in Microbial Metabolism.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {718082}, pmid = {34671327}, issn = {1664-302X}, abstract = {Microorganisms display a stunning metabolic diversity. Understanding the origin of this diversity requires understanding how macroevolutionary processes such as innovation and diversification play out in the microbial world. Metabolic networks, which govern microbial resource use, can evolve through different mechanisms, e.g., horizontal gene transfer or de novo evolution of enzymes and pathways. This process is governed by a combination of environmental factors, selective pressures, and the constraints imposed by the genetic architecture of metabolic networks. In addition, many independent results hint that the process of niche construction, by which organisms actively modify their own and each other's niches and selective pressures, could play a major role in microbial innovation and diversification. Yet, the general principles by which niche construction shapes microbial macroevolutionary patterns remain largely unexplored. Here, we discuss several new hypotheses and directions, and suggest metabolic modeling methods that could allow us to explore large-scale empirical genotype-phenotype-(G-P)-environment spaces in order to study the macroevolutionary effects of niche construction. We hope that this short piece will further stimulate a systematic and quantitative characterization of macroevolutionary patterns and processes in microbial metabolism.}, }
@article {pmid34669423, year = {2022}, author = {García-Galán, A and Baranowski, E and Hygonenq, MC and Walch, M and Croville, G and Citti, C and De la Fe, C and Nouvel, LX}, title = {Genome Mosaicism in Field Strains of Mycoplasma bovis as Footprints of In-Host Horizontal Chromosomal Transfer.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {1}, pages = {e0166121}, pmid = {34669423}, issn = {1098-5336}, support = {AGL2016-76568-R//Spanish Ministry of Economy and Competitiveness (Spanish Government) co-financed by FEDER funds/ ; BES-2017-080186//State Subprogram Training of the State Program for the Promotion of Talent and its Employability/ ; //INRAE/ ; BQR Nanopore//ENVT/ ; }, mesh = {Animals ; Cattle ; Gene Transfer, Horizontal ; Mosaicism ; *Mycoplasma bovis/genetics ; Phylogeny ; *Tenericutes ; }, abstract = {Horizontal gene transfer was long thought to be marginal in Mollicutes, but the capacity of some of these wall-less bacteria to exchange large chromosomal regions has been recently documented. Mycoplasma chromosomal transfer (MCT) is an unconventional mechanism that relies on the presence of a functional integrative conjugative element (ICE) in at least one partner and involves the horizontal acquisition of small and large chromosomal fragments from any part of the donor genome, which results in progenies composed of an infinite variety of mosaic genomes. The present study focuses on Mycoplasma bovis, an important pathogen of cattle responsible for major economic losses worldwide. By combining phylogenetic tree reconstructions and detailed comparative genome analyses of 36 isolates collected in Spain (2016 to 2018), we confirmed the mosaic nature of 16 field isolates and mapped chromosomal transfers exchanged between their hypothetical ancestors. This study provides evidence that MCT can take place in the field, most likely during coinfections by multiple strains. Because mobile genetic elements (MGEs) are classical contributors of genome plasticity, the presence of phages, insertion sequences (ISs), and ICEs was also investigated. Data revealed that these elements are widespread within the M. bovis species and evidenced classical horizontal transfer of phages and ICEs in addition to MCT. These events contribute to wide-genome diversity and reorganization within this species and may have a tremendous impact on diagnostic and disease control. IMPORTANCE Mycoplasma bovis is a major pathogen of cattle that has significant detrimental effects on economics and animal welfare in cattle rearing worldwide. Understanding the evolution and the adaptative potential of pathogenic mycoplasma species in the natural host is essential to combating them. In this study, we documented the occurrence of mycoplasma chromosomal transfer, an atypical mechanism of horizontal gene transfer, in field isolates of M. bovis that provide new insights into the evolution of this pathogenic species in their natural host. Although these events are expected to occur at low frequency, their impact is accountable for genome-wide variety and reorganization within M. bovis species, which may compromise both diagnostic and disease control.}, }
@article {pmid34668756, year = {2021}, author = {Ott, LC and Engelken, M and Scott, SM and McNeill, EM and Mellata, M}, title = {Drosophila Model for Gut-Mediated Horizontal Transfer of Narrow- and Broad-Host-Range Plasmids.}, journal = {mSphere}, volume = {6}, number = {5}, pages = {e0069821}, pmid = {34668756}, issn = {2379-5042}, mesh = {Animals ; Bacteria/genetics/isolation &amp; purification ; Drosophila melanogaster/*microbiology ; Drug Resistance, Multiple, Bacterial/*genetics ; Female ; Gastrointestinal Microbiome/*genetics ; Gene Transfer, Horizontal/*genetics ; Host Specificity ; Male ; Plasmids/*genetics ; Sex Characteristics ; Virulence ; }, abstract = {Horizontal gene transfer (HGT) is a driving force of microbial evolution. The gut of animals acts as a potent reservoir for the lateral transfer of virulence, fitness, and antimicrobial resistance genes through plasmids. Reduced-complexity models for the examination of host-microbe interactions involved in plasmid transfer are greatly desired. Thus, this study identifies the use of Drosophila melanogaster as a model organism for the conjugation of plasmids of various incompatibility groups in the gut. Enterobacteriaceae conjugation pairs were identified in vitro and used for oral inoculation of the Drosophila gut. Flies were enumerated for the donor, recipient, and transconjugant populations. Each donor-recipient pair was observed to persist in fly guts for the duration of the experiment. Gut concentrations of the donors and recipients were significantly different between male and female flies, with females generally demonstrating increased concentrations. Furthermore, host genetics significantly altered the concentrations of donors and recipients. However, transconjugant concentrations were not affected by host sex or genetics and were detected only in the IncPε and IncI1 plasmid groups. This study demonstrates Drosophila melanogaster as a model for gut-mediated plasmid transfer. IMPORTANCE Microbial evolution in the gut of animals due to horizontal gene transfer (HGT) is of significant interest for microbial evolution as well as within the context of human and animal health. Microbial populations evolve within the host, and factors from the bacteria and host interact to regulate this evolution. However, little is currently known about how host and bacterial factors regulate plasmid-mediated HGT in the gut. This study demonstrates the use of Drosophila and the roles of sexual dimorphism as well as plasmid incompatibility groups in HGT in the gut.}, }
@article {pmid34668737, year = {2021}, author = {Shimada, S and Nakai, R and Aoki, K and Kudoh, S and Imura, S and Shimoeda, N and Ohno, G and Watanabe, K and Miyazaki, Y and Ishii, Y and Tateda, K}, title = {Characterization of the First Cultured Psychrotolerant Representative of Legionella from Antarctica Reveals Its Unique Genome Structure.}, journal = {Microbiology spectrum}, volume = {9}, number = {2}, pages = {e0042421}, pmid = {34668737}, issn = {2165-0497}, mesh = {Antarctic Regions ; Bacterial Typing Techniques ; Cold Temperature ; DNA, Bacterial/genetics ; Fatty Acids/metabolism ; *Genome, Bacterial ; Genomics ; Interspersed Repetitive Sequences ; Lakes/chemistry/*microbiology ; Legionella/classification/*genetics/*isolation &amp; purification/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Culture-independent analysis shows that Legionella spp. inhabit a wide range of low-temperature environments, but to date, no psychrotolerant or psychrophilic strains have been reported. Here, we characterized the first cultivated psychrotolerant representative, designated strain TUM19329[T], isolated from an Antarctic lake using a polyphasic approach and comparative genomic analysis. A genome-wide phylogenetic tree indicated that this strain was phylogenetically separate at the species level. Strain TUM19329[T] shared common physiological traits (e.g., Gram-negative, limited growth on buffered charcoal-yeast extract α-ketoglutarate [BCYEα] agar with l-cysteine requirements) with its relatives, but it also showed psychrotolerant growth properties (e.g., growth at 4°C to 25°C). Moreover, this strain altered its own cellular fatty acid composition to accumulate unsaturated fatty acid at a lower temperature, which may help maintain the cell membrane fluidity. Through comparative genomic analysis, we found that this strain possessed massive mobile genetic elements compared with other species, amounting to up to 17% of the total genes. The majority of the elements were the result of the spread of only a few insertion sequences (ISs), which were spread throughout the genome by a "copy-and-paste" mechanism. Furthermore, we found metabolic genes, such as fatty acid synthesis-related genes, acquired by horizontal gene transfer (HGT). The expansion of ISs and HGT events may play a major role in shaping the phenotype and physiology of this strain. On the basis of the features presented here, we propose a new species-Legionella antarctica sp. nov.-represented by strain TUM19329[T] (= GTC 22699[T] = NCTC 14581[T]). IMPORTANCE This study characterized a unique cultivated representative of the genus Legionella isolated from an Antarctic lake. This psychrotolerant strain had some common properties of known Legionella species but also displayed other characteristics, such as plasticity in fatty acid composition and an enrichment of mobile genes in the genome. These remarkable properties, as well as other factors, may contribute to cold hardiness, and this first cultivated cold-tolerant strain of the genus Legionella may serve as a model bacterium for further studies. It is worth noting that environmentally derived 16S rRNA gene phylotypes closely related to the strain characterized here have been detected from diverse environments outside Antarctica, suggesting a wide distribution of psychrotolerant Legionella bacteria. Our culture- and genome-based findings may accelerate the ongoing studies of the behavior and pathogenicity of Legionella spp., which have been monitored for many years in the context of public health.}, }
@article {pmid34668564, year = {2022}, author = {Szöllõsi, GJ and Höhna, S and Williams, TA and Schrempf, D and Daubin, V and Boussau, B}, title = {Relative Time Constraints Improve Molecular Dating.}, journal = {Systematic biology}, volume = {71}, number = {4}, pages = {797-809}, pmid = {34668564}, issn = {1076-836X}, support = {/ERC_/European Research Council/International ; }, mesh = {Bayes Theorem ; Evolution, Molecular ; *Fossils ; *Gene Transfer, Horizontal ; Phylogeny ; Symbiosis ; }, abstract = {Dating the tree of life is central to understanding the evolution of life on Earth. Molecular clocks calibrated with fossils represent the state of the art for inferring the ages of major groups. Yet, other information on the timing of species diversification can be used to date the tree of life. For example, horizontal gene transfer events and ancient coevolutionary interactions such as (endo)symbioses occur between contemporaneous species and thus can imply temporal relationships between two nodes in a phylogeny. Temporal constraints from these alternative sources can be particularly helpful when the geological record is sparse, for example, for microorganisms, which represent the majority of extant and extinct biodiversity. Here, we present a new method to combine fossil calibrations and relative age constraints to estimate chronograms. We provide an implementation of relative age constraints in RevBayes that can be combined in a modular manner with the wide range of molecular dating methods available in the software. We use both realistic simulations and empirical datasets of 40 Cyanobacteria and 62 Archaea to evaluate our method. We show that the combination of relative age constraints with fossil calibrations significantly improves the estimation of node ages. [Archaea, Bayesian analysis, cyanobacteria, dating, endosymbiosis, lateral gene transfer, MCMC, molecular clock, phylogenetic dating, relaxed molecular clock, revbayes, tree of life.].}, }
@article {pmid34665261, year = {2021}, author = {Douglas, GM and Shapiro, BJ}, title = {Genic Selection Within Prokaryotic Pangenomes.}, journal = {Genome biology and evolution}, volume = {13}, number = {11}, pages = {}, pmid = {34665261}, issn = {1759-6653}, mesh = {*Evolution, Molecular ; *Prokaryotic Cells ; Selection, Genetic ; }, abstract = {Understanding the evolutionary forces shaping prokaryotic pangenome structure is a major goal of microbial evolution research. Recent work has highlighted that a substantial proportion of accessory genes appear to confer niche-specific adaptations. This work has primarily focused on selection acting at the level of individual cells. Herein, we discuss a lower level of selection that also contributes to pangenome variation: genic selection. This refers to cases where genetic elements, rather than individual cells, are the entities under selection. The clearest examples of this form of selection are selfish mobile genetic elements, which are those that have either a neutral or a deleterious effect on host fitness. We review the major classes of these and other mobile elements and discuss the characteristic features of such elements that could be under genic selection. We also discuss how genetic elements that are beneficial to hosts can also be under genic selection, a scenario that may be more prevalent but not widely appreciated, because disentangling the effects of selection at different levels (i.e., organisms vs. genes) is challenging. Nonetheless, an appreciation for the potential action and implications of genic selection is important to better understand the evolution of prokaryotic pangenomes.}, }
@article {pmid34665012, year = {2021}, author = {Keen, EC and Choi, J and Wallace, MA and Azar, M and Mejia-Chew, CR and Mehta, SB and Bailey, TC and Caverly, LJ and Burnham, CD and Dantas, G}, title = {Comparative Genomics of Mycobacterium avium Complex Reveals Signatures of Environment-Specific Adaptation and Community Acquisition.}, journal = {mSystems}, volume = {6}, number = {5}, pages = {e0119421}, pmid = {34665012}, issn = {2379-5077}, support = {CAVERL17A0//Cystic Fibrosis Foundation (CFF)/ ; R01 OH011578/OH/NIOSH CDC HHS/United States ; DGE-1143945//National Science Foundation (NSF)/ ; K23 HL136934/HL/NHLBI NIH HHS/United States ; K23HL136934//HHS | National Institutes of Health (NIH)/ ; R01 AI123394/AI/NIAID NIH HHS/United States ; U01 AI123394/AI/NIAID NIH HHS/United States ; }, abstract = {Nontuberculous mycobacteria, including those in the Mycobacterium avium complex (MAC), constitute an increasingly urgent threat to global public health. Ubiquitous in soil and water worldwide, MAC members cause a diverse array of infections in humans and animals that are often multidrug resistant, intractable, and deadly. MAC lung disease is of particular concern and is now more prevalent than tuberculosis in many countries, including the United States. Although the clinical importance of these microorganisms continues to expand, our understanding of their genomic diversity is limited, hampering basic and translational studies alike. Here, we leveraged a unique collection of genomes to characterize MAC population structure, gene content, and within-host strain dynamics in unprecedented detail. We found that different MAC species encode distinct suites of biomedically relevant genes, including antibiotic resistance genes and virulence factors, which may influence their distinct clinical manifestations. We observed that M. avium isolates from different sources-human pulmonary infections, human disseminated infections, animals, and natural environments-are readily distinguished by their core and accessory genomes, by their patterns of horizontal gene transfer, and by numerous specific genes, including virulence factors. We identified highly similar MAC strains from distinct patients within and across two geographically distinct clinical cohorts, providing important insights into the reservoirs which seed community acquisition. We also discovered a novel MAC genomospecies in one of these cohorts. Collectively, our results provide key genomic context for these emerging pathogens and will facilitate future exploration of MAC ecology, evolution, and pathogenesis. IMPORTANCE Members of the Mycobacterium avium complex (MAC), a group of mycobacteria encompassing M. avium and its closest relatives, are omnipresent in natural environments and emerging pathogens of humans and animals. MAC infections are difficult to treat, sometimes fatal, and increasingly common. Here, we used comparative genomics to illuminate key aspects of MAC biology. We found that different MAC species and M. avium isolates from different sources encode distinct suites of clinically relevant genes, including those for virulence and antibiotic resistance. We identified highly similar MAC strains in patients from different states and decades, suggesting community acquisition from dispersed and stable reservoirs, and we discovered a novel MAC species. Our work provides valuable insight into the genomic features underlying these versatile pathogens.}, }
@article {pmid34662426, year = {2022}, author = {Hill, T and Unckless, RL and Perlmutter, JI}, title = {Positive Selection and Horizontal Gene Transfer in the Genome of a Male-Killing Wolbachia.}, journal = {Molecular biology and evolution}, volume = {39}, number = {1}, pages = {}, pmid = {34662426}, issn = {1537-1719}, support = {P20 GM103418/GM/NIGMS NIH HHS/United States ; P20 GM103638/GM/NIGMS NIH HHS/United States ; R00 GM114714/GM/NIGMS NIH HHS/United States ; R01 AI139154/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Drosophila/genetics/microbiology ; Drosophila melanogaster/genetics ; Gene Transfer, Horizontal ; Genome ; Male ; *Wolbachia/genetics ; }, abstract = {Wolbachia are a genus of widespread bacterial endosymbionts in which some strains can hijack or manipulate arthropod host reproduction. Male killing is one such manipulation in which these maternally transmitted bacteria benefit surviving daughters in part by removing competition with the sons for scarce resources. Despite previous findings of interesting genome features of microbial sex ratio distorters, the population genomics of male-killers remain largely uncharacterized. Here, we uncover several unique features of the genome and population genomics of four Arizonan populations of a male-killing Wolbachia strain, wInn, that infects mushroom-feeding Drosophila innubila. We first compared the wInn genome with other closely related Wolbachia genomes of Drosophila hosts in terms of genome content and confirm that the wInn genome is largely similar in overall gene content to the wMel strain infecting D. melanogaster. However, it also contains many unique genes and repetitive genetic elements that indicate lateral gene transfers between wInn and non-Drosophila eukaryotes. We also find that, in line with literature precedent, genes in the Wolbachia prophage and Octomom regions are under positive selection. Of all the genes under positive selection, many also show evidence of recent horizontal transfer among Wolbachia symbiont genomes. These dynamics of selection and horizontal gene transfer across the genomes of several Wolbachia strains and diverse host species may be important underlying factors in Wolbachia's success as a male-killer of divergent host species.}, }
@article {pmid34662403, year = {2022}, author = {Inoue, J}, title = {ORTHOSCOPE*: A Phylogenetic Pipeline to Infer Gene Histories from Genome-Wide Data.}, journal = {Molecular biology and evolution}, volume = {39}, number = {1}, pages = {}, pmid = {34662403}, issn = {1537-1719}, mesh = {Animals ; Evolution, Molecular ; *Gene Duplication ; Gene Transfer, Horizontal ; *Genome ; Phylogeny ; }, abstract = {Comparative genome-scale analyses of protein-coding gene sequences are employed to examine evidence for whole-genome duplication and horizontal gene transfer. For this purpose, an orthogroup should be delineated to infer evolutionary history regarding each gene, and results of all orthogroup analyses need to be integrated to infer a genome-scale history. An orthogroup is a set of genes descended from a single gene in the last common ancestor of all species under consideration. However, such analyses confront several problems: 1) Analytical pipelines to infer all gene histories with methods comparing species and gene trees are not fully developed, and 2) without detailed analyses within orthogroups, evolutionary events of paralogous genes in the same orthogroup cannot be distinguished for genome-wide integration of results derived from multiple orthogroup analyses. Here I present an analytical pipeline, ORTHOSCOPE* (star), to infer evolutionary histories of animal/plant genes from genome-scale data. ORTHOSCOPE* estimates a tree for a specified gene, detects speciation/gene duplication events that occurred at nodes belonging to only one lineage leading to a species of interest, and then integrates results derived from gene trees estimated for all query genes in genome-wide data. Thus, ORTHOSCOPE* can be used to detect species nodes just after whole-genome duplications as a first step of comparative genomic analyses. Moreover, by examining the presence or absence of genes belonging to species lineages with dense taxon sampling available from the ORTHOSCOPE web version, ORTHOSCOPE* can detect genes lost in specific lineages and horizontal gene transfers. This pipeline is available at https://github.com/jun-inoue/ORTHOSCOPE_STAR.}, }
@article {pmid34661518, year = {2021}, author = {Dieckmann, AL and Riedel, T and Bunk, B and Spröer, C and Overmann, J and Groß, U and Bader, O and Bohne, W and Morgenstern, B and Hosseini, M and Zautner, AE}, title = {Genome and Methylome analysis of a phylogenetic novel Campylobacter coli cluster with C. jejuni introgression.}, journal = {Microbial genomics}, volume = {7}, number = {10}, pages = {}, pmid = {34661518}, issn = {2057-5858}, mesh = {Bacterial Typing Techniques ; Campylobacter Infections/microbiology ; Campylobacter coli/*genetics ; Campylobacter jejuni/*genetics ; Chromosomes, Bacterial/genetics ; DNA, Bacterial/genetics ; *Epigenome ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomics ; Multilocus Sequence Typing ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The intriguing recent discovery of Campylobacter coli strains, especially of clade 1, that (i) possess mosaic C. coli/C. jejuni alleles, (ii) demonstrate mixed multilocus sequence types (MLSTs) and (iii) have undergone genome-wide introgression has led to the speculation that these two species may be involved in an accelerated rate of horizontal gene transfer that is progressively leading to the merging of both species in a process coined 'despeciation'. In an MLST-based neighbour-joining tree of a number of C. coli and C. jejuni isolates of different clades, three prominent Campylobacter isolates formed a seemingly separate cluster besides the previously described C. coli and C. jejuni clades. In the light of the suspected, ongoing genetic introgression between the C. coli and C. jejuni species, this cluster of Campylobacter isolates is proposed to present one of the hybrid clonal complexes in the despeciation process of the genus. Specific DNA methylation as well as restriction modification systems are known to be involved in selective uptake of external DNA and their role in such genetic introgression remains to be further investigated. In this study, the phylogeny and DNA methylation of these putative C. coli/C. jejuni hybrid strains were explored, their genomic mosaic structure caused by C. jejuni introgression was demonstrated and basic phenotypic assays were used to characterize these isolates. The genomes of the three hybrid Campylobacter strains were sequenced using PacBio SMRT sequencing, followed by methylome analysis by Restriction-Modification Finder and genome analysis by Parsnp, Smash++ and blast. Additionally, the strains were phenotypically characterized with respect to growth behaviour, motility, eukaryotic cell invasion and adhesion, autoagglutination, biofilm formation, and water survival ability. Our analyses show that the three hybrid Campylobacter strains are clade 1 C. coli strains, which have acquired between 8.1 and 9.1 % of their genome from C. jejuni. The C. jejuni genomic segments acquired are distributed over the entire genome and do not form a coherent cluster. Most of the genes originating from C. jejuni are involved in chemotaxis and motility, membrane transport, cell signalling, or the resistance to toxic compounds such as bile acids. Interspecies gene transfer from C. jejuni has contributed 8.1-9.1% to the genome of three C. coli isolates and initiated the despeciation between C. jejuni and C. coli. Based on their functional annotation, the genes originating from C. jejuni enable the adaptation of the three strains to an intra-intestinal habitat. The transfer of a fused type II restriction-modification system that recognizes the CAYNNNNNCTC/GAGNNNNNRTG motif seems to be the key for the recombination of the C. jejuni genetic material with C. coli genomes.}, }
@article {pmid34655856, year = {2021}, author = {Makkaew, P and Kongprajug, A and Chyerochana, N and Sresung, M and Precha, N and Mongkolsuk, S and Sirikanchana, K}, title = {Persisting antibiotic resistance gene pollution and its association with human sewage sources in tropical marine beach waters.}, journal = {International journal of hygiene and environmental health}, volume = {238}, number = {}, pages = {113859}, doi = {10.1016/j.ijheh.2021.113859}, pmid = {34655856}, issn = {1618-131X}, mesh = {Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; *Ecosystem ; Genes, Bacterial ; Humans ; *Sewage ; }, abstract = {Antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are pollutants of worldwide concern that threaten human health and ecosystems. Anthropogenic activities and wastewater could be ARB and ARG pollution sources; however, research on ARG abundance and microbial source tracking (MST) of contamination in tropical marine waters is limited. This study examined spatiotemporal variations of six ARGs (blaNDM, blaTEM, blaVIM, mcr-1, sul1, and tetQ) against the widely used antibiotic groups and a class 1 integron-integrase gene (intI1) at two Thai tropical recreational beaches (n = 41). Correlations between ARGs and sewage-specific MST markers (i.e., crAssphage and human polyomaviruses [HPyVs]) and fecal indicator bacteria (i.e., total coliforms, fecal coliforms, and enterococci) were also investigated. BlaTEM, intI1, sul1, and tetQ were ubiquitous at both beaches (85.4-100% detection rate); intI1 was the most abundant (3-6 orders in log10 copies/100 mL), followed by blaTEM (2-4 orders), sul1 (2-3 orders), and tetQ (2-4 orders). BlaNDM was found in 7.3% (up to 4 orders), and no mcr-1 was detected. Interestingly, blaVIM was prevalent at one beach (2-5 orders; n = 17), but found in only one sample at the other (4 orders). Temporal, but not spatial, differences were noticed; blaTEM was at higher levels in the wet season. IntI1 correlated with sul1 and tetQ (Spearman's rho = 0.47-0.97), suggesting potential horizontal gene transfer. CrAssphage, but not HPyVs, correlated with intI1, sul1, and tetQ (Spearman's rho = 0.50-0.74). Higher numbers of ARGs tended to co-occur in samples with higher crAssphage concentrations, implying sewage contribution to the marine water, with a persisting ARG background. This study provides insight into the ARG pollution status of tropical coastal waters and suggests crAssphage as a proxy for ARG pollution, which could facilitate effective management policies to minimize ARG dissemination in marine environments.}, }
@article {pmid34653589, year = {2022}, author = {Tripathi, S and Chandra, R and Purchase, D and Bilal, M and Mythili, R and Yadav, S}, title = {Quorum sensing - a promising tool for degradation of industrial waste containing persistent organic pollutants.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {292}, number = {Pt B}, pages = {118342}, doi = {10.1016/j.envpol.2021.118342}, pmid = {34653589}, issn = {1873-6424}, mesh = {Biofilms ; *Industrial Waste ; Persistent Organic Pollutants ; *Quorum Sensing ; Sewage ; }, abstract = {Restoring an environment contaminated with persistent organic pollutants (POPs) is highly challenging. Biodegradation by biofilm-forming bacteria through quorum sensing (QS) is a promising treatment process to remove these pollutants and promotes eco-restoration. QS plays an important role in biofilm formation, solubilization, and biotransformation of pollutants. QS is a density-based communication between microbial cells via signalling molecules, which coordinates specific characters and helps bacteria to acclimatize against stress conditions. Genetic diversification of a biofilm offers excellent opportunities for horizontal gene transfer, improves resistance against stress, and provides a suitable environment for the metabolism of POPs. To develop this technology in industrial scale, it is important to understand the fundamentals and ubiquitous nature of QS bacteria and appreciate the role of QS in the degradation of POPs. Currently, there are knowledge gaps regarding the environmental niche, abundance, and population of QS bacteria in wastewater treatment systems. This review aims to present up-to-date and state-of-the-art information on the roles of QS and QS-mediated strategies in industrial waste treatment including biological treatments (such as activated sludge), highlighting their potentials using examples from the pulp and paper mill industry, hydrocarbon remediation and phytoremediation. The information will help to provide a throughout understanding of the potential of QS to degrade POPs and advance the use of this technology. Current knowledge of QS strategies is limited to laboratory studies, full-scale applications remain challenging and more research is need to explore QS gene expression and test in full-scale reactors for wastewater treatment.}, }
@article {pmid34651331, year = {2021}, author = {Jian, Z and Zeng, L and Xu, T and Sun, S and Yan, S and Yang, L and Huang, Y and Jia, J and Dou, T}, title = {Antibiotic resistance genes in bacteria: Occurrence, spread, and control.}, journal = {Journal of basic microbiology}, volume = {61}, number = {12}, pages = {1049-1070}, doi = {10.1002/jobm.202100201}, pmid = {34651331}, issn = {1521-4028}, support = {2019HC011//Provincial Innovation Team of Livestock and Poultry Healthy Breeding and Quality Safety of Yunnan Agricultural University/ ; 202005AF150039//Yunnan Province Qiu Shengxiang Expert Workstation/ ; }, mesh = {*Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; *Bacterial Infections ; Drug Resistance, Microbial ; Genes, Bacterial ; Humans ; }, abstract = {The production and use of antibiotics are becoming increasingly common worldwide, and the problem of antibiotic resistance is increasing alarmingly. Drug-resistant infections threaten human life and health and impose a heavy burden on the global economy. The origin and molecular basis of bacterial resistance is the presence of antibiotic resistance genes (ARGs). Investigations on ARGs mostly focus on the environments in which antibiotics are frequently used, such as hospitals and farms. This literature review summarizes the current knowledge of the occurrence of antibiotic-resistant bacteria in nonclinical environments, such as air, aircraft wastewater, migratory bird feces, and sea areas in-depth, which have rarely been involved in previous studies. Furthermore, the mechanism of action of plasmid and phage during horizontal gene transfer was analyzed, and the transmission mechanism of ARGs was summarized. This review highlights the new mechanisms that enhance antibiotic resistance and the evolutionary background of multidrug resistance; in addition, some promising points for controlling or reducing the occurrence and spread of antimicrobial resistance are also proposed.}, }
@article {pmid34646305, year = {2021}, author = {Zeng, Q and Xie, J and Li, Y and Gao, T and Zhang, X and Wang, Q}, title = {Comprehensive Genomic Analysis of the Endophytic Bacillus altitudinis Strain GLB197, a Potential Biocontrol Agent of Grape Downy Mildew.}, journal = {Frontiers in genetics}, volume = {12}, number = {}, pages = {729603}, pmid = {34646305}, issn = {1664-8021}, abstract = {Bacillus has been extensively studied for agricultural application as a biocontrol agent. B. altitudinis GLB197, an endophytic bacterium isolated from grape leaves, exhibits distinctive inhibition to grape downy mildew based on unknown mechanisms. To determine the genetic traits involved in the mechanism of biocontrol and host-interaction traits, the genome sequence of GLB197 was obtained and further analyzed. The genome of B. altitudinis GLB197 consisted of one plasmid and a 3,733,835-bp circular chromosome with 41.56% G + C content, containing 3,770 protein-coding genes. Phylogenetic analysis of 17 Bacillus strains using the concatenated 1,226 single-copy core genes divided into different clusters was conducted. In addition, average nucleotide identity (ANI) values indicate that the current taxonomy of some B. pumilus group strains is incorrect. Comparative analysis of B. altitudinis GLB197 proteins with other B. altitudinis strains identified 3,157 core genes. Furthermore, we found that the pan-genome of B. altitudinis is open. The genome of B. altitudinis GLB197 contains one nonribosomal peptide synthetase (NRPS) gene cluster which was annotated as lichenysin. Interestingly, the cluster in B. altitudinis has two more genes than other Bacillus strains (lgrD and lgrB). The two genes were probably obtained via horizontal gene transfer (HGT) during the evolutionary process from Brevibacillus. Taken together, these observations enable the future application of B. altitudinis GLB197 as a biocontrol agent for control of grape downy mildew and promote our understanding of the beneficial interactions between B. altitudinis GLB197 and plants.}, }
@article {pmid34646252, year = {2021}, author = {Guernier-Cambert, V and Trachsel, J and Maki, J and Qi, J and Sylte, MJ and Hanafy, Z and Kathariou, S and Looft, T}, title = {Natural Horizontal Gene Transfer of Antimicrobial Resistance Genes in Campylobacter spp. From Turkeys and Swine.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {732969}, pmid = {34646252}, issn = {1664-302X}, abstract = {Antibiotic-resistant Campylobacter constitutes a serious threat to public health. The clonal expansion of resistant strains and/or the horizontal spread of resistance genes to other strains and species can hinder the clinical effectiveness of antibiotics to treat severe campylobacteriosis. Still, gaps exist in our understanding of the risks of acquisition and spread of antibiotic resistance in Campylobacter. While the in vitro transfer of antimicrobial resistance genes between Campylobacter species via natural transformation has been extensively demonstrated, experimental studies have favored the use of naked DNA to obtain transformants. In this study, we used experimental designs closer to real-world conditions to evaluate the possible transfer of antimicrobial resistance genes between Campylobacter strains of the same or different species (Campylobacter coli or Campylobacter jejuni) and originating from different animal hosts (swine or turkeys). This was evaluated in vitro through co-culture experiments and in vivo with dual-strain inoculation of turkeys, followed by whole genome sequencing of parental and newly emerged strains. In vitro, we observed four independent horizontal gene transfer events leading to the acquisition of resistance to beta-lactams (blaOXA), aminoglycosides [aph(2'')-If and rpsL] and tetracycline [tet(O)]. Observed events involved the displacement of resistance-associated genes by a mutated version, or the acquisition of genomic islands harboring a resistance determinant by homologous recombination; we did not detect the transfer of resistance-carrying plasmids even though they were present in some strains. In vivo, we recovered a newly emerged strain with dual-resistance pattern and identified the replacement of an existing non-functional tet(O) by a functional tet(O) in the recipient strain. Whole genome comparisons allowed characterization of the events involved in the horizontal spread of resistance genes between Campylobacter following in vitro co-culture and in vivo dual inoculation. Our study also highlights the potential for antimicrobial resistance transfer across Campylobacter species originating from turkeys and swine, which may have implications for farms hosting both species in close proximity.}, }
@article {pmid34645520, year = {2021}, author = {Cobo-Díaz, JF and Alvarez-Molina, A and Alexa, EA and Walsh, CJ and Mencía-Ares, O and Puente-Gómez, P and Likotrafiti, E and Fernández-Gómez, P and Prieto, B and Crispie, F and Ruiz, L and González-Raurich, M and López, M and Prieto, M and Cotter, P and Alvarez-Ordóñez, A}, title = {Microbial colonization and resistome dynamics in food processing environments of a newly opened pork cutting industry during 1.5 years of activity.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {204}, pmid = {34645520}, issn = {2049-2618}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Food Handling ; Genes, Bacterial ; *Pork Meat ; *Red Meat ; Swine ; }, abstract = {BACKGROUND: The microorganisms that inhabit food processing environments (FPE) can strongly influence the associated food quality and safety. In particular, the possibility that FPE may act as a reservoir of antibiotic-resistant microorganisms, and a hotspot for the transmission of antibiotic resistance genes (ARGs) is a concern in meat processing plants. Here, we monitor microbial succession and resistome dynamics relating to FPE through a detailed analysis of a newly opened pork cutting plant over 1.5 years of activity.<br><br>RESULTS: We identified a relatively restricted principal microbiota dominated by Pseudomonas during the first 2 months, while a higher taxonomic diversity, an increased representation of other taxa (e.g., Acinetobacter, Psychrobacter), and a certain degree of microbiome specialization on different surfaces was recorded later on. An increase in total abundance, alpha diversity, and &#x3b2;-dispersion of ARGs, which were predominantly assigned to Acinetobacter and associated with resistance to certain antimicrobials frequently used on pig farms of the region, was detected over time. Moreover, a sharp increase in the occurrence of extended-spectrum &#x3b2;-lactamase-producing Enterobacteriaceae and vancomycin-resistant Enterococcaceae was observed when cutting activities started. ARGs associated with resistance to &#x3b2;-lactams, tetracyclines, aminoglycosides, and sulphonamides frequently co-occurred, and mobile genetic elements (i.e., plasmids, integrons) and lateral gene transfer events were mainly detected at the later sampling times in drains.<br><br>CONCLUSIONS: The observations made suggest that pig carcasses were a source of resistant bacteria that then colonized FPE and that drains, together with some food-contact surfaces, such as equipment and table surfaces, represented a reservoir for the spread of ARGs in the meat processing facility. Video Abstract.}, }
@article {pmid34644303, year = {2021}, author = {Hall, JPJ and Wright, RCT and Harrison, E and Muddiman, KJ and Wood, AJ and Paterson, S and Brockhurst, MA}, title = {Plasmid fitness costs are caused by specific genetic conflicts enabling resolution by compensatory mutation.}, journal = {PLoS biology}, volume = {19}, number = {10}, pages = {e3001225}, pmid = {34644303}, issn = {1545-7885}, support = {/WT_/Wellcome Trust/United Kingdom ; 204822/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Chromosomes, Bacterial/genetics ; Conjugation, Genetic ; Evolution, Molecular ; Gene Expression Regulation, Bacterial ; *Genetic Fitness ; Models, Biological ; Mutation/*genetics ; Plasmids/*genetics ; Pseudomonas fluorescens/genetics ; Transcription, Genetic ; Up-Regulation/genetics ; }, abstract = {Plasmids play an important role in bacterial genome evolution by transferring genes between lineages. Fitness costs associated with plasmid carriage are expected to be a barrier to gene exchange, but the causes of plasmid fitness costs are poorly understood. Single compensatory mutations are often sufficient to completely ameliorate plasmid fitness costs, suggesting that such costs are caused by specific genetic conflicts rather than generic properties of plasmids, such as their size, metabolic burden, or gene expression level. By combining the results of experimental evolution with genetics and transcriptomics, we show here that fitness costs of 2 divergent large plasmids in Pseudomonas fluorescens are caused by inducing maladaptive expression of a chromosomal tailocin toxin operon. Mutations in single genes unrelated to the toxin operon, and located on either the chromosome or the plasmid, ameliorated the disruption associated with plasmid carriage. We identify one of these compensatory loci, the chromosomal gene PFLU4242, as the key mediator of the fitness costs of both plasmids, with the other compensatory loci either reducing expression of this gene or mitigating its deleterious effects by up-regulating a putative plasmid-borne ParAB operon. The chromosomal mobile genetic element Tn6291, which uses plasmids for transmission, remained up-regulated even in compensated strains, suggesting that mobile genetic elements communicate through pathways independent of general physiological disruption. Plasmid fitness costs caused by specific genetic conflicts are unlikely to act as a long-term barrier to horizontal gene transfer (HGT) due to their propensity for amelioration by single compensatory mutations, helping to explain why plasmids are so common in bacterial genomes.}, }
@article {pmid34643711, year = {2021}, author = {Dangla-Pélissier, G and Roux, N and Schmidt, V and Chambonnier, G and Ba, M and Sebban-Kreuzer, C and de Bentzmann, S and Giraud, C and Bordi, C}, title = {The horizontal transfer of Pseudomonas aeruginosa PA14 ICE PAPI-1 is controlled by a transcriptional triad between TprA, NdpA2 and MvaT.}, journal = {Nucleic acids research}, volume = {49}, number = {19}, pages = {10956-10974}, pmid = {34643711}, issn = {1362-4962}, mesh = {Bacterial Proteins/*genetics/metabolism ; Biofilms/growth &amp; development ; Chromosomes, Bacterial ; Conjugation, Genetic ; DNA Transposable Elements ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; *Genomic Islands ; Pseudomonas aeruginosa/*genetics/metabolism/pathogenicity ; Regulon ; Trans-Activators/*genetics/metabolism ; Transcription, Genetic ; Virulence Factors/*genetics/metabolism ; }, abstract = {Pseudomonas aeruginosa is a major cause of nosocomial infections, particularly in immunocompromised patients or in individuals with cystic fibrosis. Genome sequences reveal that most P. aeruginosa strains contain a significant number of accessory genes gathered in genomic islands. Those genes are essential for P. aeruginosa to invade new ecological niches with high levels of antibiotic usage, like hospitals, or to survive during host infection by providing pathogenicity determinants. P. aeruginosa pathogenicity island 1 (PAPI-1), one of the largest genomic islands, encodes several putative virulence factors, including toxins, biofilm genes and antibiotic-resistance traits. The integrative and conjugative element (ICE) PAPI-1 is horizontally transferable by conjugation via a specialized GI-T4SS, but the mechanism regulating this transfer is currently unknown. Here, we show that this GI-T4SS conjugative machinery is directly induced by TprA, a regulator encoded within PAPI-1. Our data indicate that the nucleotide associated protein NdpA2 acts in synergy with TprA, removing a repressive mechanism exerted by MvaT. In addition, using a transcriptomic approach, we unravelled the regulon controlled by Ndpa2/TprA and showed that they act as major regulators on the genes belonging to PAPI-1. Moreover, TprA and NdpA2 trigger an atypical biofilm structure and enhance ICE PAPI-1 transfer.}, }
@article {pmid34641955, year = {2021}, author = {Arikawa, K and Ide, K and Kogawa, M and Saeki, T and Yoda, T and Endoh, T and Matsuhashi, A and Takeyama, H and Hosokawa, M}, title = {Recovery of strain-resolved genomes from human microbiome through an integration framework of single-cell genomics and metagenomics.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {202}, pmid = {34641955}, issn = {2049-2618}, mesh = {Genome, Microbial ; Humans ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; Phylogeny ; }, abstract = {BACKGROUND: Obtaining high-quality (HQ) reference genomes from microbial communities is crucial for understanding the phylogeny and function of uncultured microbes in complex microbial ecosystems. Despite improvements in bioinformatic approaches to generate curated metagenome-assembled genomes (MAGs), existing metagenome binners obtain population consensus genomes but they are nowhere comparable to genomes sequenced from isolates in terms of strain level resolution. Here, we present a framework for the integration of single-cell genomics and metagenomics, referred to as single-cell (sc) metagenomics, to reconstruct strain-resolved genomes from microbial communities at once.<br><br>RESULTS: Our sc-metagenomics integration framework, termed SMAGLinker, uses single-cell amplified genomes (SAGs) generated using microfluidic technology as binning guides and integrates them with metagenome-assembled genomes (MAGs) to recover improved draft genomes. We compared sc-metagenomics with the metagenomics-alone approach using conventional metagenome binners. The sc-metagenomics approach showed precise contig binning and higher recovery rates (>97%) of rRNA and plasmids than conventional metagenomics in genome reconstruction from the cell mock community. In human microbiota samples, sc-metagenomics recovered the largest number of genomes with a total of 103 gut microbial genomes (21 HQ, with 65 showing >90% completeness) and 45 skin microbial genomes (10 HQ, with 40 showing >90% completeness), respectively. Conventional metagenomics recovered one Staphylococcus hominis genome, whereas sc-metagenomics recovered two S. hominis genomes from identical skin microbiota sample. Single-cell sequencing revealed that these S. hominis genomes were derived from two distinct strains harboring specifically different plasmids. We found that all conventional S. hominis MAGs had a substantial lack or excess of genome sequences and contamination from other Staphylococcus species (S. epidermidis).<br><br>CONCLUSIONS: SMAGLinker enabled us to obtain strain-resolved genomes in the mock community and human microbiota samples by assigning metagenomic sequences correctly and covering both highly conserved genes such as rRNA genes and unique extrachromosomal elements, including plasmids. SMAGLinker will provide HQ genomes that are difficult to obtain using metagenomics alone and will facilitate the understanding of microbial ecosystems by elucidating detailed metabolic pathways and horizontal gene transfer networks. SMAGLinker is available at https://github.com/kojiari/smaglinker . Video abstract.}, }
@article {pmid34638784, year = {2021}, author = {Park, M and Sarkhosh, A and Tsolova, V and El-Sharkawy, I}, title = {Horizontal Transfer of LTR Retrotransposons Contributes to the Genome Diversity of Vitis.}, journal = {International journal of molecular sciences}, volume = {22}, number = {19}, pages = {}, pmid = {34638784}, issn = {1422-0067}, support = {2019-38821-29150//United States Department of Agriculture/ ; }, mesh = {*Gene Transfer, Horizontal ; *Genetic Variation ; *Genome, Plant ; *Retroelements ; Vitis/*genetics ; }, abstract = {While horizontally transferred transposable elements (TEs) have been reported in several groups of plants, their importance for genome evolution remains poorly understood. To understand how horizontally transferred TEs contribute to plant genome evolution, we investigated the composition and activity of horizontally transferred TEs in the genomes of four Vitis species. A total of 35 horizontal transfer (HT) events were identified between the four Vitis species and 21 other plant species belonging to 14 different families. We determined the donor and recipient species for 28 of these HTs, with the Vitis species being recipients of 15 of them. As a result of HTs, 8-10 LTR retrotransposon clusters were newly formed in the genomes of the four Vitis species. The activities of the horizontally acquired LTR retrotransposons differed among Vitis species, showing that the consequences of HTs vary during the diversification of the recipient lineage. Our study provides the first evidence that the HT of TEs contributes to the diversification of plant genomes by generating additional TE subfamilies and causing their differential proliferation in host genomes.}, }
@article {pmid34638661, year = {2021}, author = {Chmielowska, C and Korsak, D and Chapkauskaitse, E and Decewicz, P and Lasek, R and Szuplewska, M and Bartosik, D}, title = {Plasmidome of Listeria spp.-The repA-Family Business.}, journal = {International journal of molecular sciences}, volume = {22}, number = {19}, pages = {}, pmid = {34638661}, issn = {1422-0067}, support = {UMO-2016/21/B/NZ8/00383//National Science Centre, Poland/ ; }, mesh = {DNA Transposable Elements/genetics ; Firmicutes/genetics ; Genes, Bacterial/*genetics ; Genome, Bacterial/genetics ; Listeria/*genetics ; Plasmids/*genetics ; Replicon/genetics ; }, abstract = {Bacteria of the genus Listeria (phylum Firmicutes) include both human and animal pathogens, as well as saprophytic strains. A common component of Listeria spp. genomes are plasmids, i.e., extrachromosomal replicons that contribute to gene flux in bacteria. This study provides an in-depth insight into the structure, diversity and evolution of plasmids occurring in Listeria strains inhabiting various environments under different anthropogenic pressures. Apart from the components of the conserved plasmid backbone (providing replication, stable maintenance and conjugational transfer functions), these replicons contain numerous adaptive genes possibly involved in: (i) resistance to antibiotics, heavy metals, metalloids and sanitizers, and (ii) responses to heat, oxidative, acid and high salinity stressors. Their genomes are also enriched by numerous transposable elements, which have influenced the plasmid architecture. The plasmidome of Listeria is dominated by a group of related replicons encoding the RepA replication initiation protein. Detailed comparative analyses provide valuable data on the level of conservation of these replicons and their role in shaping the structure of the Listeria pangenome, as well as their relationship to plasmids of other genera of Firmicutes, which demonstrates the range and direction of flow of genetic information in this important group of bacteria.}, }
@article {pmid34638137, year = {2022}, author = {Nikolaidis, M and Markoulatos, P and Van de Peer, Y and Oliver, SG and Amoutzias, GD}, title = {The Neighborhood of the Spike Gene Is a Hotspot for Modular Intertypic Homologous and Nonhomologous Recombination in Coronavirus Genomes.}, journal = {Molecular biology and evolution}, volume = {39}, number = {1}, pages = {}, pmid = {34638137}, issn = {1537-1719}, mesh = {Coronavirus/*genetics ; *Genome, Viral ; Open Reading Frames ; Phylogeny ; *Recombination, Genetic ; Spike Glycoprotein, Coronavirus/*genetics ; }, abstract = {Coronaviruses (CoVs) have very large RNA viral genomes with a distinct genomic architecture of core and accessory open reading frames (ORFs). It is of utmost importance to understand their patterns and limits of homologous and nonhomologous recombination, because such events may affect the emergence of novel CoV strains, alter their host range, infection rate, tissue tropism pathogenicity, and their ability to escape vaccination programs. Intratypic recombination among closely related CoVs of the same subgenus has often been reported; however, the patterns and limits of genomic exchange between more distantly related CoV lineages (intertypic recombination) need further investigation. Here, we report computational/evolutionary analyses that clearly demonstrate a substantial ability for CoVs of different subgenera to recombine. Furthermore, we show that CoVs can obtain-through nonhomologous recombination-accessory ORFs from core ORFs, exchange accessory ORFs with different CoV genera, with other viruses (i.e., toroviruses, influenza C/D, reoviruses, rotaviruses, astroviruses) and even with hosts. Intriguingly, most of these radical events result from double crossovers surrounding the Spike ORF, thus highlighting both the instability and mobile nature of this genomic region. Although many such events have often occurred during the evolution of various CoVs, the genomic architecture of the relatively young SARS-CoV/SARS-CoV-2 lineage so far appears to be stable.}, }
@article {pmid34638028, year = {2021}, author = {Miles, JA and Egan, JL and Fowler, JA and Machattou, P and Millard, AD and Perry, CJ and Scanlan, DJ and Taylor, PC}, title = {The evolutionary origins of peroxynitrite signalling.}, journal = {Biochemical and biophysical research communications}, volume = {580}, number = {}, pages = {107-112}, doi = {10.1016/j.bbrc.2021.09.071}, pmid = {34638028}, issn = {1090-2104}, mesh = {Animals ; Bacterial Proteins/genetics/metabolism ; Cyanobacteria/genetics/metabolism ; Evolution, Molecular ; Humans ; NADPH Oxidase 5/genetics/metabolism ; Nitric Oxide/genetics/metabolism ; Nitric Oxide Synthase Type III/genetics/metabolism ; Peroxynitrous Acid/genetics/*metabolism ; Phylogeny ; *Signal Transduction ; Superoxides/metabolism ; }, abstract = {Peroxynitrite is a reactive intermediate formed in vivo through uncatalysed reaction of superoxide and nitric oxide radicals. Despite significant interest in detecting peroxynitrite in vivo and understanding its production, little attention has been given to the evolutionary origins of peroxynitrite signalling. Herein we focus on two enzymes that are key to the biosynthesis of superoxide and nitric oxide, NADPH oxidase 5 (NOX5) and endothelial nitric oxide synthase (eNOS), respectively. Multiple sequence alignments of both enzymes including homologues from all domains of life, coupled with a phylogenetic analysis of NOX5, suggest eNOS and NOX5 are present in animals as the result of horizontal gene transfer from ancestral cyanobacteria to ancestral eukaryotes. Therefore, biochemical studies from other laboratories on a NOX5 homologue in Cylindrospermum stagnale and an eNOS homologue in Synechococcus sp. PCC 7335 are likely to be of relevance to human NOX5 and eNOS and to the production of superoxide, nitric oxide and peroxynitrite in humans.}, }
@article {pmid34627113, year = {2022}, author = {Jiang, Q and Feng, M and Ye, C and Yu, X}, title = {Effects and relevant mechanisms of non-antibiotic factors on the horizontal transfer of antibiotic resistance genes in water environments: A review.}, journal = {The Science of the total environment}, volume = {806}, number = {Pt 3}, pages = {150568}, doi = {10.1016/j.scitotenv.2021.150568}, pmid = {34627113}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; }, abstract = {Antibiotic resistance has created obstacles in the treatment of infectious diseases with antibiotics. The horizontal transfer of antibiotic resistance genes (ARGs) can exacerbate the dissemination of antibiotic resistance in water environments. In addition to antibiotic selective pressure, multiple non-antibiotic factors can affect the horizontal transfer of ARGs. Herein, we seek to comprehensively review the effects and relevant mechanisms of non-antibiotic factors on the horizontal transfer of ARGs in water environments, especially contaminants from human activities and water treatment processes. Four pathways have been identified to accomplish horizontal gene transfer (HGT), i.e., conjugation, transformation, transduction, and vesiduction. Changes in conjugative frequencies by non-antibiotic factors are mainly related to their concentrations, which conform to hormesis. Relevant mechanisms involve the alteration in cell membrane permeability, reactive oxygen species, SOS response, pilus, and mRNA expression of relevant genes. Transformation induced by extracellular DNA may be more vulnerable to non-antibiotic factors than other pathways. Except bacteriophage infection, the effects of non-antibiotic factors on transduction exhibit many similarities with that of conjugation. Given the secretion of membrane vesicles stimulated by non-antibiotic factors, their effects on vesiduction can be inferred. Furthermore, contaminants from human activities at sub-inhibitory or environmentally relevant concentrations usually promote HGT, resulting in further dissemination of antibiotic resistance. The horizontal transfer of ARGs is difficult to be inhibited by individual water treatment processes (e.g., chlorination, UV treatment, and photocatalysis) unless they attain sufficient intensity. Accordingly, the synergistic application containing two or more water treatment processes is recommended. Overall, we believe this review can elucidate the significance for risk assessments of contaminants from human activities and provide insights into the development of environment-friendly and cost-efficient water treatment processes to inhibit the horizontal transfer of ARGs.}, }
@article {pmid34626704, year = {2022}, author = {Cheng, Y and Lu, J and Fu, S and Wang, S and Senehi, N and Yuan, Q}, title = {Enhanced propagation of intracellular and extracellular antibiotic resistance genes in municipal wastewater by microplastics.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {292}, number = {Pt A}, pages = {118284}, doi = {10.1016/j.envpol.2021.118284}, pmid = {34626704}, issn = {1873-6424}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Microplastics ; Plastics ; *Wastewater ; }, abstract = {Microplastics (MPs) are an emerging global concern as they are abundant in the environment and can act as vectors of various contaminants. However, whether and how MPs can be vectors of antibiotic resistance genes (ARGs), especially extracellular ARGs (eARGs), remains far from explicit. This study addresses the adsorption of both intracellular ARGs (iARGs) and eARGs by four types of MPs in municipal wastewater, and then explores the potential horizontal gene transfer of iARGs and eARGs exposed to MPs. Results indicate that though MPs significantly adsorbed both iARGs and eARGs, eARGs were adsorbed with a significantly higher fold enrichment (2.0-5.0 log versus 2.0-3.3 log) and rate (0.0056 min[-1] versus 0.0037 min[-1]) than iARGs. While all four types of MPs adsorbed ARGs, polypropylene MPs showed the highest adsorption capacity for ARGs. Background constituents such as humic acid and antibiotics significantly inhibited adsorption of iARGs, but not eARGs on MPs. The presence of sodium chloride didn't significantly affect adsorption of iARGs or eARGs. The adsorption of ARGs was well explained by the extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) interaction energy profile. Higher eARG adsorption was attributed to a lower energy barrier between MPs and eARGs than that between MPs and iARGs. Exposure to MPs enhanced horizontal gene transfer of both iARGs and eARGs by 1.5 and 2.0 times, respectively. The improved contact potential between donors and recipients, as well as the increased cell permeability of recipients induced the improved horizontal gene transfer by MPs. This study underscores the need to address ARG propagation through adsorption to MPs.}, }
@article {pmid34626646, year = {2021}, author = {Latimer, S and Keene, SA and Stutts, LR and Berger, A and Bernert, AC and Soubeyrand, E and Wright, J and Clarke, CF and Block, AK and Colquhoun, TA and Elowsky, C and Christensen, A and Wilson, MA and Basset, GJ}, title = {A dedicated flavin-dependent monooxygenase catalyzes the hydroxylation of demethoxyubiquinone into ubiquinone (coenzyme Q) in Arabidopsis.}, journal = {The Journal of biological chemistry}, volume = {297}, number = {5}, pages = {101283}, pmid = {34626646}, issn = {1083-351X}, support = {R01 GM139978/GM/NIGMS NIH HHS/United States ; RF1 AG061566/AG/NIA NIH HHS/United States ; }, mesh = {*Arabidopsis/enzymology/genetics ; *Arabidopsis Proteins/genetics/metabolism ; *Mitochondria/enzymology/genetics ; *Mixed Function Oxygenases/genetics/metabolism ; *Phylogeny ; *Ubiquinone/genetics/metabolism ; }, abstract = {Ubiquinone (Coenzyme Q) is a vital respiratory cofactor and liposoluble antioxidant. In plants, it is not known how the C-6 hydroxylation of demethoxyubiquinone, the penultimate step in ubiquinone biosynthesis, is catalyzed. The combination of cross-species gene network modeling along with mining of embryo-defective mutant databases of Arabidopsis thaliana identified the embryo lethal locus EMB2421 (At1g24340) as a top candidate for the missing plant demethoxyubiquinone hydroxylase. In marked contrast with prototypical eukaryotic demethoxyubiquinone hydroxylases, the catalytic mechanism of which depends on a carboxylate-bridged di-iron domain, At1g24340 is homologous to FAD-dependent oxidoreductases that instead use NAD(P)H as an electron donor. Complementation assays in Saccharomyces cerevisiae and Escherichia coli demonstrated that At1g24340 encodes a functional demethoxyubiquinone hydroxylase and that the enzyme displays strict specificity for the C-6 position of the benzoquinone ring. Laser-scanning confocal microscopy also showed that GFP-tagged At1g24340 is targeted to mitochondria. Silencing of At1g24340 resulted in 40 to 74% decrease in ubiquinone content and de novo ubiquinone biosynthesis. Consistent with the role of At1g24340 as a benzenoid ring modification enzyme, this metabolic blockage could not be bypassed by supplementation with 4-hydroxybenzoate, the immediate precursor of ubiquinone's ring. Unlike in yeast, in Arabidopsis overexpression of demethoxyubiquinone hydroxylase did not boost ubiquinone content. Phylogenetic reconstructions indicated that plant demethoxyubiquinone hydroxylase is most closely related to prokaryotic monooxygenases that act on halogenated aromatics and likely descends from an event of horizontal gene transfer between a green alga and a bacterium.}, }
@article {pmid34621260, year = {2021}, author = {Wang, J and Luo, Y and Gu, Y and Wei, HL}, title = {Characterization of the SPI-1 Type III Secretion System in Pseudomonas fluorescens 2P24.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {749037}, pmid = {34621260}, issn = {1664-302X}, abstract = {Pseudomonas fluorescens 2P24 is a plant growth-promoting rhizobacterium (PGPR) isolated from wheat take-all decline soil. Genomic analysis of strain 2P24 revealed the presence of a complete SPI-1 type III secretion system (T3SS) gene cluster on the chromosome with an organization and orientation similar to the SPI-1 T3SS gene clusters of Salmonella enterica and P. kilonensis F113. Phylogenetic analysis revealed that the SPI-1 T3SS gene cluster of strain 2P24 might be obtained from Salmonella and Shigella by horizontal gene transfer. Two transcriptional regulator homologs of HilA and InvF were found from the SPI-1 T3SS gene cluster of strain 2P24. HilA regulated the expression of the structural genes positively, such as invG, sipB, sipD, prgI, and prgK. Prediction of transcriptional binding sites and RNA-seq analysis revealed 14 genes were up-regulated by InvF in strain 2P24. Exploring potential roles of SPI-1 T3SS revealed that it was not associated with motility. However, 2P24ΔinvF reduced resistance against Fusarium graminearum significantly. 2P24ΔhilA enhanced formation of biofilm significantly at 48 h. All three mutants 2P24ΔhilA, 2P24ΔinvF, and 2P24ΔinvE-C reduced the chemotactic responses to glucose significantly. Finally, the determination of SPI-1 mutants to trigger innate immunity in Nicotiana benthamiana showed that 2P24ΔinvE-C reduced the ability to induce the production of reactive oxygen species compared with the wild type strain 2P24.}, }
@article {pmid34616401, year = {2021}, author = {Collins, SM and Brown, AC}, title = {Bacterial Outer Membrane Vesicles as Antibiotic Delivery Vehicles.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {733064}, pmid = {34616401}, issn = {1664-3224}, mesh = {Animals ; Anti-Bacterial Agents/*administration &amp; dosage/metabolism ; Bacterial Outer Membrane/*metabolism ; *Drug Carriers ; Drug Compounding ; Extracellular Vesicles/genetics/*metabolism ; Gram-Negative Aerobic Bacteria/genetics/*metabolism ; Humans ; }, abstract = {Bacterial outer membrane vesicles (OMVs) are nanometer-scale, spherical vehicles released by Gram-negative bacteria into their surroundings throughout growth. These OMVs have been demonstrated to play key roles in pathogenesis by delivering certain biomolecules to host cells, including toxins and other virulence factors. In addition, this biomolecular delivery function enables OMVs to facilitate intra-bacterial communication processes, such as quorum sensing and horizontal gene transfer. The unique ability of OMVs to deliver large biomolecules across the complex Gram-negative cell envelope has inspired the use of OMVs as antibiotic delivery vehicles to overcome transport limitations. In this review, we describe the advantages, applications, and biotechnological challenges of using OMVs as antibiotic delivery vehicles, studying both natural and engineered antibiotic applications of OMVs. We argue that OMVs hold great promise as antibiotic delivery vehicles, an urgently needed application to combat the growing threat of antibiotic resistance.}, }
@article {pmid34615350, year = {2021}, author = {Ren, CY and Wu, EL and Hartmann, EM and Zhao, HP}, title = {Biological Mitigation of Antibiotic Resistance Gene Dissemination by Antioxidant-Producing Microorganisms in Activated Sludge Systems.}, journal = {Environmental science &amp; technology}, volume = {55}, number = {23}, pages = {15831-15842}, pmid = {34615350}, issn = {1520-5851}, support = {T32 AI095207/AI/NIAID NIH HHS/United States ; U19 AI135964/AI/NIAID NIH HHS/United States ; }, mesh = {*Anti-Bacterial Agents/pharmacology ; Antioxidants ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Sewage ; }, abstract = {Antibiotic resistance is the principal mechanism of an evergrowing bacterial threat. Antibiotic residues in the environment are a major contributor to the spread of antibiotic resistance genes (ARGs). Subinhibitory concentrations of antibiotics cause bacteria to produce reactive oxygen species (ROS), which can lead to mutagenesis and horizontal gene transfer (HGT) of ARGs; however, little is known about the mitigation of ARG dissemination through ROS removal by antioxidants. In this study, we examine how antioxidant-producing microorganisms inoculated in replicate activated sludge systems can biologically mitigate the dissemination of ARGs. Through quantitative polymerase chain reaction (qPCR), we showed that antioxidant-producing microorganisms could decrease the persistence of the RP4 plasmid and alleviate enrichment of ARGs (sul1) and class 1 integrons (intl1). Metagenomic sequencing identified the most diverse resistome and the most mutated Escherichia coli ARGs in the reactor that contained antibiotics but no antioxidant-producing microorganisms, suggesting that antioxidant-producing microorganisms mitigated ARG enrichment and mutation. Host classification revealed that antioxidant-producing microorganisms decreased the diversity of ARG hosts by shaping the microbial community through competition and functional pathway changes. Conjugative experiments demonstrated that conjugative transfer of ARGs could be mitigated by coculture with antioxidant-producing microorganisms. Overall, this is a novel study that shows how ARG enrichment and HGT can be mitigated through bioaugmentation with antioxidant-producing microorganisms.}, }
@article {pmid34612694, year = {2021}, author = {Pan, Y and Zhang, T and Yu, L and Zong, Z and Zhao, S and Li, R and Wang, Q and Yuan, L and Hu, G and He, D}, title = {IS1294 Reorganizes Plasmids in a Multidrug-Resistant Escherichia coli Strain.}, journal = {Microbiology spectrum}, volume = {9}, number = {2}, pages = {e0050321}, pmid = {34612694}, issn = {2165-0497}, mesh = {Anti-Bacterial Agents/*pharmacology ; Conjugation, Genetic ; *DNA Transposable Elements ; Drug Resistance, Multiple, Bacterial ; Escherichia coli/drug effects/*genetics/metabolism ; Escherichia coli Infections/microbiology ; Escherichia coli Proteins/genetics/metabolism ; Humans ; Microbial Sensitivity Tests ; Plasmids/*genetics/metabolism ; }, abstract = {The aims of this study were to elucidate the role of IS1294 in plasmid reorganization and to analyze biological characteristics of cointegrates derived from different daughter plasmids. The genetic profiles of plasmids in Escherichia coli strain C21 and its transconjugants were characterized by conjugation, S1 nuclease pulsed-field gel electrophoresis (S1-PFGE), Southern hybridization, whole-genome sequencing (WGS) analysis, and PCR. The traits of cointegrates were characterized by conjugation and stability assays. blaCTX-M-55-bearing IncI2 pC21-1 and nonresistant IncI1 pC21-3, as conjugative helper plasmids, were fused with nonconjugative rmtB-bearing IncN-X1 pC21-2, generating cointegrates pC21-F1 and pC21-F2. Similarly, pC21-1 and pC21-3 were fused with nonconjugative IncF33:A-:B- pHB37-2 from another E. coli strain to generate cointegrates pC21-F3 and pC21-F4 under experimental conditions. Four cointegrates were further conjugated into the E. coli strain J53 recipient at high conjugation frequencies, ranging from 2.8 × 10[-3] to 3.2 × 10[-2]. The formation of pC21-F1 and pC21-F4 was the result of host- and IS1294-mediated reactions and occurred at high fusion frequencies of 9.9 × 10[-4] and 2.1 × 10[-4], respectively. Knockout of RecA resulted in a 100-fold decrease in the frequency of plasmid reorganization. The phenomenon of cointegrate pC21-F2 and its daughter plasmids coexisting in transconjugants was detected for the first time in plasmid stability experiments. IS26-orf-oqxAB was excised from cointegrate pC21-F2 through a circular intermediate at a very low frequency, which was experimentally observed. To the best of our knowledge, this is the first report of IS1294-mediated fusion between plasmids with different replicons. This study provides insight into the formation and evolution of cointegrate plasmids under different drug selection pressures, which can promote the dissemination of MDR plasmids. IMPORTANCE The increasing resistance to β-lactams and aminoglycoside antibiotics, mainly due to extended-spectrum β-lactamases (ESBLs) and 16S rRNA methylase genes, is becoming a serious problem in Gram-negative bacteria. Plasmids, as the vehicles for resistance gene capture and horizontal gene transfer, serve a key role in terms of antibiotic resistance emergence and transmission. IS26, present in many antibiotic-resistant plasmids from Gram-negative bacteria, plays a critical role in the spread, clustering, and reorganization of resistance determinant-encoding plasmids and in plasmid reorganization through replicative transposition mechanisms and homologous recombination. However, the role of IS1294, present in many MDR plasmids, in the formation of cointegrates remains unclear. Here, we investigated experimentally the intermolecular recombination of IS1294, which occurred with high frequencies and led to the formation of conjugative MDR cointegrates and facilitated the cotransfer of blaCTX-M-55 and rmtB, and we further uncovered the significance of IS1294 in the formation of cointegrates and the common features of IS1294-driven cointegration of plasmids.}, }
@article {pmid34607101, year = {2022}, author = {Jiang, M and Song, S and Liu, H and Dai, X and Wang, P}, title = {Responses of methane production, microbial community and antibiotic resistance genes to the mixing ratio of gentamicin mycelial residues and wheat straw in anaerobic co-digestion process.}, journal = {The Science of the total environment}, volume = {806}, number = {Pt 2}, pages = {150488}, doi = {10.1016/j.scitotenv.2021.150488}, pmid = {34607101}, issn = {1879-1026}, mesh = {Anaerobiosis ; Anti-Bacterial Agents ; Bioreactors ; Digestion ; Drug Resistance, Microbial/genetics ; Gentamicins ; Methane ; *Microbiota ; *Triticum ; }, abstract = {Anaerobic co-digestion (AcoD) of gentamicin mycelial residues (GMRs), a kind of nitrogen-rich biowaste, and wheat straw (WS) is an attractive technology for the recycling of GMRs. However, the effects of the co-substrate ratio on methane production, system stability and antimicrobial resistance during co-digestion remain unclear. Thus, this study aimed to fill in the blanks through AcoD of GMRs and WS with different mixing ratios (1:0, 2:1, 1:1, 1:2, 0:1, VS basis) via batch tests. Results showed that AcoD facilitated methane production than mono anaerobic digestion and reduced the accumulation of the toxic substances, such as ammonia nitrogen and humic-like substances. The maximum methane production was obtained at the reactors with the mixing ratio of 1:1 and 1:2 (R-1:1 and R-1:2), which matched with the relative abundance of key enzymes related to methanogenesis predicted by PICRUSt. Microbial community analysis indicated that Methanosaeta was the most dominant methanogen in the AcoD reactors. The highest relative abundance of Methanosaeta (45.1%) was obtained at R-1:1 due to the appropriate AcoD conditions, thus, providing greater possibilities for high stability of AcoD system. Additionally, AcoD of the GMRs and WS under the mixing ratio of 1:1 and 1:2 did not prompt the increase of antibiotic resistance genes (ARGs). Not only that, the likelihood of horizontal gene transfer declined in R-1:1 due to the weaker connection and transport between host and recipient bacteria. Findings of this study suggested that the suitable mixing ratio of GMRs and WS contributes to methane production and system stability, and reduces the dissemination risks of ARGs.}, }
@article {pmid34605762, year = {2021}, author = {Colombi, E and Perry, BJ and Sullivan, JT and Bekuma, AA and Terpolilli, JJ and Ronson, CW and Ramsay, JP}, title = {Comparative analysis of integrative and conjugative mobile genetic elements in the genus Mesorhizobium.}, journal = {Microbial genomics}, volume = {7}, number = {10}, pages = {}, pmid = {34605762}, issn = {2057-5858}, mesh = {Bacterial Proteins/genetics ; Conjugation, Genetic ; DNA Transposable Elements ; Evolution, Molecular ; Fabaceae ; Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences ; Mesorhizobium/*genetics ; Nitrogen Fixation ; Plasmids ; Quorum Sensing ; Recombination, Genetic ; Symbiosis/genetics ; }, abstract = {Members of the Mesorhizobium genus are soil bacteria that often form nitrogen-fixing symbioses with legumes. Most characterised Mesorhizobium spp. genomes are ~8 Mb in size and harbour extensive pangenomes including large integrative and conjugative elements (ICEs) carrying genes required for symbiosis (ICESyms). Here, we document and compare the conjugative mobilome of 41 complete Mesorhizobium genomes. We delineated 56 ICEs and 24 integrative and mobilizable elements (IMEs) collectively occupying 16 distinct integration sites, along with 24 plasmids. We also demonstrated horizontal transfer of the largest (853,775 bp) documented ICE, the tripartite ICEMspSym[AA22]. The conjugation systems of all identified ICEs and several plasmids were related to those of the paradigm ICESym ICEMlSym[R7A], with each carrying conserved genes for conjugative pilus formation (trb), excision (rdfS), DNA transfer (rlxS) and regulation (fseA). ICESyms have likely evolved from a common ancestor, despite occupying a variety of distinct integration sites and specifying symbiosis with diverse legumes. We found extensive evidence for recombination between ICEs and particularly ICESyms, which all uniquely lack the conjugation entry-exclusion factor gene trbK. Frequent duplication, replacement and pseudogenization of genes for quorum-sensing-mediated activation and antiactivation of ICE transfer suggests ICE transfer regulation is constantly evolving. Pangenome-wide association analysis of the ICE identified genes potentially involved in symbiosis, rhizosphere colonisation and/or adaptation to distinct legume hosts. In summary, the Mesorhizobium genus has accumulated a large and dynamic pangenome that evolves through ongoing horizontal gene transfer of large conjugative elements related to ICEMlSym[R7A].}, }
@article {pmid34601581, year = {2022}, author = {Zabelkin, A and Yakovleva, Y and Bochkareva, O and Alexeev, N}, title = {PaReBrick: PArallel REarrangements and BReaks identification toolkit.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {2}, pages = {357-363}, pmid = {34601581}, issn = {1367-4811}, support = {//National Center for Cognitive Research of ITMO University and JetBrains Research/ ; 754411//European Union's Horizon 2020 Research and Innovation Programme under the Marie Sk&#x142;odowska-Curie/ ; }, mesh = {Phylogeny ; Synteny ; *Genome, Bacterial ; *Antigenic Variation ; Software ; }, abstract = {MOTIVATION: High plasticity of bacterial genomes is provided by numerous mechanisms including horizontal gene transfer and recombination via numerous flanking repeats. Genome rearrangements such as inversions, deletions, insertions and duplications may independently occur in different strains, providing parallel adaptation or phenotypic diversity. Specifically, such rearrangements might be responsible for virulence, antibiotic resistance and antigenic variation. However, identification of such events requires laborious manual inspection and verification of phyletic pattern consistency.<br><br>RESULTS: Here, we define the term 'parallel rearrangements' as events that occur independently in phylogenetically distant bacterial strains and present a formalization of the problem of parallel rearrangements calling. We implement an algorithmic solution for the identification of parallel rearrangements in bacterial populations as a tool PaReBrick. The tool takes a collection of strains represented as a sequence of oriented synteny blocks and a phylogenetic tree as input data. It identifies rearrangements, tests them for consistency with a tree, and sorts the events by their parallelism score. The tool provides diagrams of the neighbors for each block of interest, allowing the detection of horizontally transferred blocks or their extra copies and the inversions in which copied blocks are involved. We demonstrated PaReBrick's efficiency and accuracy and showed its potential to detect genome rearrangements responsible for pathogenicity and adaptation in bacterial genomes.<br><br>PaReBrick is written in Python and is available on GitHub: https://github.com/ctlab/parallel-rearrangements.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid34599337, year = {2021}, author = {Tria, FDK and Martin, WF}, title = {Gene Duplications Are At Least 50 Times Less Frequent than Gene Transfers in Prokaryotic Genomes.}, journal = {Genome biology and evolution}, volume = {13}, number = {10}, pages = {}, pmid = {34599337}, issn = {1759-6653}, support = {101018894/ERC_/European Research Council/International ; }, mesh = {*Evolution, Molecular ; *Gene Duplication ; Gene Transfer, Horizontal ; Phylogeny ; Prokaryotic Cells ; }, abstract = {The contribution of gene duplications to the evolution of eukaryotic genomes is well studied. By contrast, studies of gene duplications in prokaryotes are scarce and generally limited to a handful of genes or careful analysis of a few prokaryotic lineages. Systematic broad-scale studies of prokaryotic genomes that sample available data are lacking, leaving gaps in our understanding of the contribution of gene duplications as a source of genetic novelty in the prokaryotic world. Here, we report conservative and robust estimates for the frequency of recent gene duplications within prokaryotic genomes relative to recent lateral gene transfer (LGT), as mechanisms to generate multiple copies of related sequences in the same genome. We obtain our estimates by focusing on evolutionarily recent events among 5,655 prokaryotic genomes, thereby avoiding vagaries of deep phylogenetic inference and confounding effects of ancient events and differential loss. We find that recent, genome-specific gene duplications are at least 50 times less frequent and probably 100 times less frequent than recent, genome-specific, gene acquisitions via LGT. The frequency of gene duplications varies across lineages and functional categories. The findings improve our understanding of genome evolution in prokaryotes and have far-reaching implications for evolutionary models that entail LGT to gene duplications ratio as a parameter.}, }
@article {pmid34598063, year = {2022}, author = {Li, X and Rensing, C and Vestergaard, G and Arumugam, M and Nesme, J and Gupta, S and Brejnrod, AD and Sørensen, SJ}, title = {Metagenomic evidence for co-occurrence of antibiotic, biocide and metal resistance genes in pigs.}, journal = {Environment international}, volume = {158}, number = {}, pages = {106899}, doi = {10.1016/j.envint.2021.106899}, pmid = {34598063}, issn = {1873-6750}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Disinfectants ; Genes, Bacterial ; Metagenome ; *Metals, Heavy/toxicity ; Phylogeny ; Swine ; }, abstract = {Antibiotic-resistant pathogens constitute an escalating public health concern. Hence a better understanding of the underlying processes responsible for this expansion is urgently needed. Co-selection of heavy metal/biocide and antibiotic resistance genes (ARGs) has been suggested as one potential mechanism promoting the proliferation of antimicrobial resistance (AMR). This paper aims to elucidate this interplay and exploit differences in antibiotic usage to infer patterns of co-selection by the non-antibiotic factors metals and biocides in the context of pig farming. We examined 278 gut metagenomes from pigs with continuous antibiotic exposure, only at weaning and at no exposure. Metals as growth promoters and biocides as disinfectants are currently used with little restrictions in stock farming. The pigs under continuous antibiotic exposure displayed the highest co-occurrence of ARGs and other genetic elements while the pigs under limited use of antibiotics still showed abundant co-occurrences. Pathogens belonging to Enterobacteriaceae displayed increased co-occurrence phenomena, suggesting that this maintenance is not a random selection process from a mobilized pool but pertains to specific phylogenetic clades. These results suggest that metals and biocides displayed strong selective pressures on ARGs exerted by intensive farming, regardless of the current use of antibiotics.}, }
@article {pmid34597934, year = {2022}, author = {Liu, X and Wang, H and Li, L and Deng, C and Chen, Y and Ding, H and Yu, Z}, title = {Do microplastic biofilms promote the evolution and co-selection of antibiotic and metal resistance genes and their associations with bacterial communities under antibiotic and metal pressures?.}, journal = {Journal of hazardous materials}, volume = {424}, number = {Pt A}, pages = {127285}, doi = {10.1016/j.jhazmat.2021.127285}, pmid = {34597934}, issn = {1873-3336}, mesh = {*Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Biofilms ; Genes, Bacterial ; *Microplastics ; Plastics ; }, abstract = {Microplastic (MP) biofilms with heterogeneous bacterial compositions and structure have become a hotspot of antibiotic resistance genes (ARGs) in aquatic environments. The evolutionary features of ARGs and their related factors including class 1 integron (intI1), metal resistance genes (MRGs), and bacterial communities in MP biofilms under exogenous pressures and how they compared with natural substrates (NS) are unclear. The individual and combined pressures of sulfamethoxazole, tetracycline, and zinc were used to drive the dynamic evolution of ARGs, intI1, MRGs, and bacterial communities in the MP and NS biofilms. The exogenous pressures from the combined selection of sulfamethoxazole, tetracycline, and zinc and their increasing concentrations both significantly enhanced the abundances of ARGs on the MP compared to the NS. Meanwhile, the selective pressures resulted in obvious dissimilarities between the MP and NS bacterial communities. The core bacterial taxa and the co-occurrence patterns of ARGs and bacterial genera in the biofilms of MP and NS were obviously different, and more potential ARG host bacteria selectively colonized the MP. Metal pressure also enhanced the enrichment of ARGs in the MP biofilms by promoting the spread of intI1 via the co-selection mechanism.}, }
@article {pmid34597927, year = {2022}, author = {Wang, G and Liu, H and Gong, P and Wang, J and Dai, X and Wang, P}, title = {Insight into the evolution of antibiotic resistance genes and microbial community during spiramycin fermentation residue composting process after thermally activated peroxydisulfate pretreatment.}, journal = {Journal of hazardous materials}, volume = {424}, number = {Pt A}, pages = {127287}, doi = {10.1016/j.jhazmat.2021.127287}, pmid = {34597927}, issn = {1873-3336}, mesh = {Anti-Bacterial Agents/pharmacology ; *Composting ; Drug Resistance, Microbial/genetics ; Fermentation ; Genes, Bacterial ; Manure ; *Microbiota ; *Spiramycin ; }, abstract = {Previous research has been demonstrated that the residual unextracted antibiotics in spiramycin fermentation residue (SFR) could be efficiently removed by thermally activated peroxodisulfate (TAP) pretreatment, indicating the improvement of biodegradability. This study aimed to investigate the effect of TAP pretreatment on the succession of bacterial community and fate of antibiotic resistance genes (ARGs) during SFR composting. Results indicated that TAP pretreatment increased the composting temperature and promoted the decomposition of organic matters. Furthermore, TAP pretreatment could increase bacterial alpha diversity and significantly reduce the relative abundance of ARGs (1.13-1.75 times) and mobile genetic elements (MGEs) (1.13-1.32 times) after composting. The compost of pretreated SFR by TAP could reduce the enrichment of ARGs and MGEs in the bacterial community, especially the rRNA methylase genes of ermB (4-142-folds). Redundancy analysis showed that Actinobacteria, Bacteroidetes, Proteobacteria and horizontal gene transfer mediated by MGEs (intI1) was positively related to the changes in ARGs (accounted for 97.4%). Network analysis showed that Firmicutes was the main bacterial hosts of ARGs and MGEs. These findings demonstrated that TAP pretreatment combined composting was a promising strategy for SFR safe treatment and disposal that could reduce the proliferation and transfer of ARGs.}, }
@article {pmid34596377, year = {2021}, author = {Chen, ML and An, XL and Liao, H and Yang, K and Su, JQ and Zhu, YG}, title = {Viral Community and Virus-Associated Antibiotic Resistance Genes in Soils Amended with Organic Fertilizers.}, journal = {Environmental science &amp; technology}, volume = {55}, number = {20}, pages = {13881-13890}, doi = {10.1021/acs.est.1c03847}, pmid = {34596377}, issn = {1520-5851}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; *Fertilizers/analysis ; Genes, Bacterial ; Humans ; Manure ; *Soil ; Soil Microbiology ; }, abstract = {Antibiotic resistance is a global health concern. Long-term organic fertilization can influence the antibiotic resistome of agricultural soils, posing potential risks to human health. However, little is known about the contribution of viruses to the dissemination of antibiotic resistance genes (ARGs) in this context. Here, we profiled the viral communities and virus-associated ARGs in a long-term (over 10 years) organic fertilized field by viral metagenomic analysis. A total of 61,520 viral populations (viral operational taxonomic units, vOTUs) were retrieved, of which 21,308 were assigned at the family level. The viral community structures were significantly correlated with the bacterial community structures (P < 0.001) and the dosage of applied sewage sludge (r[2] = 0.782). A total of 16 unique ARGs were detected in soil viromes, and the number of virus-associated ARG subtypes was higher in sewage sludge treatments (except for 1 SS) than others. The network analysis showed that the application of the organic fertilizer increased the bacteria-virus interactions, suggesting that the chances of ARG exchange between viruses and their hosts may increase. Overall, our results provide a novel understanding about virus-associated ARGs and factors affecting the profile of viral community in fertilized soil.}, }
@article {pmid34583585, year = {2021}, author = {Fournier, GP and Moore, KR and Rangel, LT and Payette, JG and Momper, L and Bosak, T}, title = {The Archean origin of oxygenic photosynthesis and extant cyanobacterial lineages.}, journal = {Proceedings. Biological sciences}, volume = {288}, number = {1959}, pages = {20210675}, pmid = {34583585}, issn = {1471-2954}, mesh = {Biological Evolution ; *Cyanobacteria/genetics ; Fossils ; *Oxygen ; Photosynthesis ; Phylogeny ; }, abstract = {The record of the coevolution of oxygenic phototrophs and the environment is preserved in three forms: genomes of modern organisms, diverse geochemical signals of surface oxidation and diagnostic Proterozoic microfossils. When calibrated by fossils, genomic data form the basis of molecular clock analyses. However, different interpretations of the geochemical record, fossil calibrations and evolutionary models produce a wide range of age estimates that are often conflicting. Here, we show that multiple interpretations of the cyanobacterial fossil record are consistent with an Archean origin of crown-group Cyanobacteria. We further show that incorporating relative dating information from horizontal gene transfers greatly improves the precision of these age estimates, by both providing a novel empirical criterion for selecting evolutionary models, and increasing the stringency of sampling of posterior age estimates. Independent of any geochemical evidence or hypotheses, these results support oxygenic photosynthesis evolving at least several hundred million years before the Great Oxygenation Event (GOE), a rapid diversification of major cyanobacterial lineages around the time of the GOE, and a post-Cryogenian origin of extant marine picocyanobacterial diversity.}, }
@article {pmid34582709, year = {2021}, author = {Bokor, E and Flipphi, M and Kocsubé, S and Ámon, J and Vágvölgyi, C and Scazzocchio, C and Hamari, Z}, title = {Genome organization and evolution of a eukaryotic nicotinate co-inducible pathway.}, journal = {Open biology}, volume = {11}, number = {9}, pages = {210099}, pmid = {34582709}, issn = {2046-2441}, mesh = {Aspergillus nidulans/drug effects/*metabolism ; Eukaryota/*metabolism ; *Evolution, Molecular ; Fungal Proteins/genetics/*metabolism ; Gene Duplication ; Gene Expression Regulation, Fungal/*drug effects ; Multigene Family ; Niacin/*pharmacology ; *Phylogeny ; }, abstract = {In Aspergillus nidulans a regulon including 11 hxn genes (hxnS, T, R, P, Y, Z, X, W, V, M and N) is inducible by a nicotinate metabolic derivative, repressible by ammonium and under stringent control of the nitrogen-state-sensitive GATA factor AreA and the specific transcription factor HxnR. This is the first report in a eukaryote of the genomic organization of a possibly complete pathway of nicotinate utilization. In A. nidulans the regulon is organized in three distinct clusters, this organization is variable in the Ascomycota. In some Pezizomycotina species all 11 genes map in a single cluster; in others they map in two clusters. This variable organization sheds light on cluster evolution. Instances of gene duplication followed by or simultaneous with integration in the cluster, partial or total cluster loss, and horizontal gene transfer of several genes (including an example of whole cluster re-acquisition in Aspergillus of section Flavi) were detected, together with the incorporation in some clusters of genes not found in the A. nidulans co-regulated regulon, which underlie both the plasticity and the reticulate character of metabolic cluster evolution. This study provides a comprehensive phylogeny of six members of the cluster across representatives of all Ascomycota classes.}, }
@article {pmid34581604, year = {2021}, author = {Callaghan, MM and Klimowicz, AK and Shockey, AC and Kane, J and Pepperell, CS and Dillard, JP}, title = {Transcriptional and Translational Responsiveness of the Neisseria gonorrhoeae Type IV Secretion System to Conditions of Host Infections.}, journal = {Infection and immunity}, volume = {89}, number = {12}, pages = {e0051921}, pmid = {34581604}, issn = {1098-5522}, support = {R01 AI047958/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Adhesion ; Bacterial Proteins/genetics/metabolism ; Copper/metabolism ; *Gene Expression Regulation, Bacterial ; Gonorrhea/metabolism/*microbiology ; *Host-Pathogen Interactions ; Humans ; Iron/metabolism ; Neisseria gonorrhoeae/*physiology ; *Type IV Secretion Systems ; Zinc/metabolism ; }, abstract = {The type IV secretion system of Neisseria gonorrhoeae translocates single-stranded DNA into the extracellular space, facilitating horizontal gene transfer and initiating biofilm formation. Expression of this system has been observed to be low under laboratory conditions, and multiple levels of regulation have been identified. We used a translational fusion of lacZ to traD, the gene for the type IV secretion system coupling protein, to screen for increased type IV secretion system expression. We identified several physiologically relevant conditions, including surface adherence, decreased manganese or iron, and increased zinc or copper, which increase gonococcal type IV secretion system protein levels through transcriptional and/or translational mechanisms. These metal treatments are reminiscent of the conditions in the macrophage phagosome. The ferric uptake regulator, Fur, was found to repress traD transcript levels but to also have a second role, acting to allow TraD protein levels to increase only in the absence of iron. To better understand type IV secretion system regulation during infection, we examined transcriptomic data from active urethral infection samples from five men. The data demonstrated differential expression of 20 of 21 type IV secretion system genes during infection, indicating upregulation of genes necessary for DNA secretion during host infection.}, }
@article {pmid34581597, year = {2021}, author = {Oladeinde, A and Abdo, Z and Press, MO and Cook, K and Cox, NA and Zwirzitz, B and Woyda, R and Lakin, SM and Thomas, JC and Looft, T and Cosby, DE and Hinton, A and Guard, J and Line, E and Rothrock, MJ and Berrang, ME and Herrington, K and Zock, G and Plumblee Lawrence, J and Cudnik, D and House, S and Ingram, K and Lariscy, L and Wagner, M and Aggrey, SE and Chai, L and Ritz, C}, title = {Erratum for Oladeinde et al., "Horizontal Gene Transfer Is the Main Driver of Antimicrobial Resistance in Broiler Chicks Infected with Salmonella enterica Serovar Heidelberg".}, journal = {mSystems}, volume = {6}, number = {5}, pages = {e0114721}, doi = {10.1128/mSystems.01147-21}, pmid = {34581597}, issn = {2379-5077}, }
@article {pmid34581139, year = {2021}, author = {Lü, XL and Zhao, YP and Lin, QH and Peng, XL and Yin, YF and Jiang, XJ}, title = {[Analysis of the Traits of Nitrogen Metabolism Pathways for Several Forest Soils in Eastern China].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {42}, number = {10}, pages = {4951-4958}, doi = {10.13227/j.hjkx.202101250}, pmid = {34581139}, issn = {0250-3301}, mesh = {Archaea ; China ; Forests ; *Microbiota/genetics ; Nitrification ; Nitrogen ; Oxidation-Reduction ; *Soil ; Soil Microbiology ; }, abstract = {Nitrogen metabolism pathways mediated by microorganisms play an important role in maintaining the structure and functional stability of soil ecosystems. Clarifying the relationships between microbial communities and nitrogen metabolism pathways can expand our understanding of nitrogen metabolism pathways at a microscopic level. However, the horizontal gene transfer of microorganisms means that taxonomy-based methods cannot be easily applied. A growing number of studies have shown that functional traits affect community construction and ecosystem functions. Using methods based on functional traits to study soil microbial communities can, therefore, better characterize nitrogen metabolism pathways. Here, five typical forest soils in China, namely black soil(Harbin, Heilongjiang), dark-brown earth(Changbaishan, Jilin), yellow-brown earth(Wuhan, Hubei), red earth(Fuzhou, Fujian), and humid-thermo ferralitic soil(Ledong, Hainan), were selected to study the traits of nitrogen metabolism pathways using metagenomic technology combined with the trait-based methods. The studied nitrogen metabolism pathways were ammonia assimilation, nitrate dissimilatory reduction, nitrate assimilatory reduction, denitrification, nitrification, nitrogen fixation, and anaerobic ammonia oxidation. The results showed that bacteria dominated the metagenomic library, accounting for 98.02% of all the sequences. Across all domains, the most common pathway was ammonia assimilation. For example, an average of 2830 ammonia assimilation pathway genes were detected for every million annotated bacterial sequences. In comparison, nitrogen fixation and anaerobic ammonia oxidation were the least detected pathways, accounting for 28.3 and 10.7 per million sequences, respectively. Different microorganisms can participate in a same nitrogen metabolism pathway, and the community structure of different soils was variable. The five typical forest soils in China show the same microbial nitrogen metabolism pathway traits; however, the community structure of the microorganisms mediating these processes was found to vary.}, }
@article {pmid34581117, year = {2021}, author = {Zhang, K and Xin, R and Li, KJ and Wang, Q and Wang, YN and Xu, ZH and Cui, XC and Wei, W}, title = {[Seasonal Variation and Influencing Factor Analysis of Antibiotic Resistance Genes in Water Supply Reservoirs of Central China].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {42}, number = {10}, pages = {4753-4760}, doi = {10.13227/j.hjkx.202102127}, pmid = {34581117}, issn = {0250-3301}, mesh = {*Anti-Bacterial Agents/analysis ; China ; Drug Resistance, Microbial/genetics ; Environmental Monitoring ; Factor Analysis, Statistical ; *Genes, Bacterial/genetics ; Seasons ; Water Supply ; }, abstract = {This study quantified an integron gene intI1 and 19 antibiotic resistance genes(ARGs) to identify the ARGs pollution characteristics in 11 drinking water reservoirs of central China. The results indicated that the ARGs abundance did not change significantly over time in the studied reservoir waterbodies. Tetracycline, sulfonamide, and β-lactam ARGs were dominant. The high abundance and detection rate of two sulfonamide ARGs(sul1 and sul2) suggested that they were the predominant ARGs. No polymyxin resistance genes(mcr-1) were detected, which indicated that the antibiotic restriction policy of China has achieved positive outcomes. Compared with that in other environmental media, the ARGs abundance in the reservoir environment was low. The correlation analysis showed relevance between the water quality indicators and the ARGs, which suggested that the water quality indexes can be used as ARGs pollution indicators in the reservoir environment. The abundance and detection rate of carbapenem ARGs were low owing to their dosage restriction and high degradability. Tetracycline ARGs were closely related to the other resistance gene types, which might have been due to horizontal gene transfer. Although the overall correlation between intI1 and ARGs was modest, it might be the main reason for the spread of several individual ARGs in the reservoir environment.}, }
@article {pmid34579777, year = {2021}, author = {Pérez-Carrascal, OM and Tromas, N and Terrat, Y and Moreno, E and Giani, A and Corrêa Braga Marques, L and Fortin, N and Shapiro, BJ}, title = {Single-colony sequencing reveals microbe-by-microbiome phylosymbiosis between the cyanobacterium Microcystis and its associated bacteria.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {194}, pmid = {34579777}, issn = {2049-2618}, mesh = {*Cyanobacteria ; Lakes ; *Microbiota/genetics ; *Microcystis/genetics ; Phylogeny ; }, abstract = {BACKGROUND: Cyanobacteria from the genus Microcystis can form large mucilaginous colonies with attached heterotrophic bacteria-their microbiome. However, the nature of the relationship between Microcystis and its microbiome remains unclear. Is it a long-term, evolutionarily stable association? Which partners benefit? Here we report the genomic diversity of 109 individual Microcystis colonies-including cyanobacteria and associated bacterial genomes-isolated in situ and without culture from Lake Champlain, Canada and Pampulha Reservoir, Brazil.<br><br>RESULTS: We identified 14 distinct Microcystis genotypes from Canada, of which only two have been previously reported, and four genotypes specific to Brazil. Microcystis genetic diversity was much greater between than within colonies, consistent with colony growth by clonal expansion rather than aggregation of Microcystis cells. We also identified 72 bacterial species in the microbiome. Each Microcystis genotype had a distinct microbiome composition, and more closely related genotypes had more similar microbiomes. This pattern of phylosymbiosis could be explained by co-phylogeny in only two out of the nine most prevalent associated bacterial genera, Roseomonas and Rhodobacter. These phylogenetically associated genera could enrich the metabolic repertoire of Microcystis, for example by encoding the biosynthesis of complementary carotenoid molecules. In contrast, other colony-associated bacteria showed weaker signals of co-phylogeny, but stronger evidence of horizontal gene transfer with Microcystis. These observations suggest that acquired genes are more likely to be retained in both partners (Microcystis and members of its microbiome) when they are loosely associated, whereas one gene copy is sufficient when the association is physically tight and evolutionarily long-lasting.<br><br>CONCLUSIONS: We have introduced a method for culture-free isolation of single colonies from nature followed by metagenomic sequencing, which could be applied to other types of microbes. Together, our results expand the known genetic diversity of both Microcystis and its microbiome in natural settings, and support their long-term, specific, and potentially beneficial associations. Video Abstract.}, }
@article {pmid34579567, year = {2021}, author = {Martínez, MMB and Bonomo, RA and Vila, AJ and Maffía, PC and González, LJ}, title = {On the Offensive: the Role of Outer Membrane Vesicles in the Successful Dissemination of New Delhi Metallo-β-lactamase (NDM-1).}, journal = {mBio}, volume = {12}, number = {5}, pages = {e0183621}, pmid = {34579567}, issn = {2150-7511}, support = {R01 AI100560/AI/NIAID NIH HHS/United States ; R01 AI072219/AI/NIAID NIH HHS/United States ; R01 AI063517/AI/NIAID NIH HHS/United States ; I01 BX001974/BX/BLRD VA/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacterial Outer Membrane ; Bacterial Proteins ; Carbapenems ; Drug Resistance, Multiple, Bacterial ; Escherichia coli/*drug effects/*enzymology/genetics ; Escherichia coli Proteins ; Gene Transfer, Horizontal ; Humans ; Meropenem ; Microbial Sensitivity Tests ; Moths ; Pseudomonas aeruginosa/drug effects ; beta-Lactamases/genetics/*metabolism ; }, abstract = {The emergence and worldwide dissemination of carbapenemase-producing Gram-negative bacteria are a major public health threat. Metallo-β-lactamases (MBLs) represent the largest family of carbapenemases. Regrettably, these resistance determinants are spreading worldwide. Among them, the New Delhi metallo-β-lactamase (NDM-1) is experiencing the fastest and largest geographical spread. NDM-1 β-lactamase is anchored to the bacterial outer membrane, while most MBLs are soluble, periplasmic enzymes. This unique cellular localization favors the selective secretion of active NDM-1 into outer membrane vesicles (OMVs). Here, we advance the idea that NDM-containing vesicles serve as vehicles for the local dissemination of NDM-1. We show that OMVs with NDM-1 can protect a carbapenem-susceptible strain of Escherichia coli upon treatment with meropenem in a Galleria mellonella infection model. Survival curves of G. mellonella revealed that vesicle encapsulation enhances the action of NDM-1, prolonging and favoring bacterial protection against meropenem inside the larva hemolymph. We also demonstrate that E. coli cells expressing NDM-1 protect a susceptible Pseudomonas aeruginosa strain within the larvae in the presence of meropenem. By using E. coli variants engineered to secrete variable amounts of NDM-1, we demonstrate that the protective effect correlates with the amount of NDM-1 secreted into vesicles. We conclude that secretion of NDM-1 into OMVs contributes to the survival of otherwise susceptible nearby bacteria at infection sites. These results disclose that OMVs play a role in the establishment of bacterial communities, in addition to traditional horizontal gene transfer mechanisms. IMPORTANCE Resistance to carbapenems, last-resort antibiotics, is spreading worldwide, raising great concern. NDM-1 is one of the most potent and widely disseminated carbapenem-hydrolyzing enzymes spread among many bacteria and is secreted to the extracellular medium within outer membrane vesicles. We show that vesicles carrying NDM-1 can protect carbapenem-susceptible strains of E. coli and P. aeruginosa upon treatment with meropenem in a live infection model. These vesicles act as nanoparticles that encapsulate and transport NDM-1, prolonging and favoring its action against meropenem inside a living organism. Secretion of NDM-1 into vesicles contributes to the survival of otherwise susceptible nearby bacteria at infection sites. We propose that vesicles play a role in the establishment of bacterial communities and the dissemination of antibiotic resistance, in addition to traditional horizontal gene transfer mechanisms.}, }
@article {pmid34578230, year = {2021}, author = {Ramli, SR and Bunk, B and Spröer, C and Geffers, R and Jarek, M and Bhuju, S and Goris, M and Mustakim, S and Pessler, F}, title = {Complete Genome Sequencing of Leptospira interrogans Isolates from Malaysia Reveals Massive Genome Rearrangement but High Conservation of Virulence-Associated Genes.}, journal = {Pathogens (Basel, Switzerland)}, volume = {10}, number = {9}, pages = {}, pmid = {34578230}, issn = {2076-0817}, support = {KKM510-4/4/3/3Jld.4(85)//Ministry of Health, Malaysia/ ; }, abstract = {The ability of Leptospirae to persist in environments and animal hosts but to cause clinically highly variable disease in humans has made leptospirosis the most common zoonotic disease. Considering the paucity of data on variation in complete genomes of human pathogenic Leptospirae, we have used a combination of Single Molecule Real-Time (SMRT) and Illumina sequencing to obtain complete genome sequences of six human clinical L. interrogans isolates from Malaysia. All six contained the larger (4.28-4.56 Mb) and smaller (0.34-0.395 Mb) chromosome typical of human pathogenic Leptospirae and 0-7 plasmids. Only 24% of the plasmid sequences could be matched to databases. We identified a chromosomal core genome of 3318 coding sequences and strain-specific accessory genomes of 49-179 coding sequences. These sequences enabled detailed genomic strain typing (Genome BLAST Distance Phylogeny, DNA-DNA hybridization, and multi locus sequence typing) and phylogenetic classification (whole-genome SNP genotyping). Even though there was some shared synteny and collinearity across the six genomes, there was evidence of major genome rearrangement, likely driven by horizontal gene transfer and homologous recombination. Mobile genetic elements were identified in all strains in highly varying numbers, including in the rfb locus, which defines serogroups and contributes to immune escape and pathogenesis. On the other hand, there was high conservation of virulence-associated genes including those relating to sialic acid, alginate, and lipid A biosynthesis. These findings suggest (i) that the antigenic variation, adaption to various host environments, and broad spectrum of virulence of L. interrogans are in part due to a high degree of genomic plasticity and (ii) that human pathogenic strains maintain a core set of genes required for virulence.}, }
@article {pmid34578208, year = {2021}, author = {Rumpf, C and Lange, J and Schwartbeck, B and Kahl, BC}, title = {Staphylococcus aureus and Cystic Fibrosis-A Close Relationship. What Can We Learn from Sequencing Studies?.}, journal = {Pathogens (Basel, Switzerland)}, volume = {10}, number = {9}, pages = {}, pmid = {34578208}, issn = {2076-0817}, abstract = {Staphylococcus aureus is next to Pseudomonas aeruginosa the most isolated pathogen from the airways of cystic fibrosis (CF) patients, who are often infected by a dominant S. aureus clone for extended periods. To be able to persist, the pathogen has to adapt to the hostile niche of the airways to counteract host defence, antibiotic therapy and the competition with coinfecting pathogens. S. aureus is equipped with many virulence factors including adhesins, toxins that are localized on the chromosome, on plasmids or are phage-related. S. aureus is especially versatile and adaptation and evolution of the pathogen occurs by the acquisition of new genes by horizontal gene transfer (HGT), changes in nucleotides (single nucleotide variations, SNVs) that can cause a selective advantage for the bacteria and become fixed in subpopulations. Methicillin-resistant S. aureus are a special threat to CF patients due to the more severe lung disease occurring in infected patients. Today, with decreasing costs for sequencing, more and more studies using S. aureus isolates cultured from CF patients are being published, which use whole genome sequencing (WGS), multilocus sequence typing (MLST) or spa-sequence typing (spa-typing) to follow the population dynamics of S. aureus, elucidate the underlying mechanisms of phenotypic variants, newly acquired resistance or adaptation to the host response in this particular niche. In the first part of this review, an introduction to the genetic make-up and the pathogenesis of S. aureus with respect to CF is provided. The second part presents an overview of recent studies and their findings using genotypic methods such as single or multilocus sequencing and whole genome sequencing, which identify factors contributing to the adaptation of S. aureus and its evolution in the airways of individuals with CF.}, }
@article {pmid34576822, year = {2021}, author = {Irrgang, A and Zhao, G and Juraschek, K and Kaesbohrer, A and Hammerl, JA}, title = {Characterization of E. coli Isolates Producing Extended Spectrum Beta-Lactamase SHV-Variants from the Food Chain in Germany.}, journal = {Microorganisms}, volume = {9}, number = {9}, pages = {}, pmid = {34576822}, issn = {2076-2607}, support = {43-001//Bundesinstitut f&#xfc;r Risikobewertung/ ; 773830//Horizon 2020/ ; }, abstract = {Resistance of bacteria to 3[rd] generation cephalosporins mediated by beta-lactamases (ESBL, pAmpC) is a public health concern. In this study, 1517 phenotypically cephalosporin-resistant E. coli were screened for the presence of blaSHV genes. Respective genes were detected in 161 isolates. Majority (91%) were obtained from poultry production and meat. The SHV-12 beta-lactamase was the predominant variant (n = 155), while the remaining isolates exhibited SHV-2 (n = 4) or SHV-2a (n = 2). A subset of the isolates (n = 51) was further characterized by PCR, PFGE, or whole-genome sequencing and bioinformatics analysis. The SHV-12-producing isolates showed low phylogenetic relationships, and dissemination of the blaSHV-12 genes seemed to be mainly driven by horizontal gene transfer. In most of the isolates, blaSHV-12 was located on transferable IncX3 (~43 kb) or IncI1 (~100 kb) plasmids. On IncX3, blaSHV-12 was part of a Tn6 composite transposon located next to a Tn3 transposon, which harbored the fluoroquinolone resistance gene qnrS1. On IncI1 plasmids, blaSHV-12 was located on an incomplete class 1 integron as part of a Tn21 transposon. In conclusion, SHV-12 is widely distributed in German poultry production and spreads via horizontal gene transfer. Consumers are at risk by handling raw poultry meat and should take care in appropriate kitchen hygiene.}, }
@article {pmid34576815, year = {2021}, author = {Poyntner, C and Kutzner, A and Margesin, R}, title = {Biodegradation Potential and Putative Catabolic Genes of Culturable Bacteria from an Alpine Deciduous Forest Site.}, journal = {Microorganisms}, volume = {9}, number = {9}, pages = {}, pmid = {34576815}, issn = {2076-2607}, abstract = {Microbiota from Alpine forest soils are key players in carbon cycling, which can be greatly affected by climate change. The aim of this study was to evaluate the degradation potential of culturable bacterial strains isolated from an alpine deciduous forest site. Fifty-five strains were studied with regard to their phylogenetic position, growth temperature range and degradation potential for organic compounds (microtiter scale screening for lignin sulfonic acid, catechol, phenol, bisphenol A) at low (5 °C) and moderate (20 °C) temperature. Additionally, the presence of putative catabolic genes (catechol-1,2-dioxygenase, multicomponent phenol hydroxylase, protocatechuate-3,4-dioxygenase) involved in the degradation of these organic compounds was determined through PCR. The results show the importance of the Proteobacteria phylum as its representatives did show good capabilities for biodegradation and good growth at -5 °C. Overall, 82% of strains were able to use at least one of the tested organic compounds as their sole carbon source. The presence of putative catabolic genes could be shown over a broad range of strains and in relation to their degradation abilities. Subsequently performed gene sequencing indicated horizontal gene transfer for catechol-1,2-dioxygenase and protocatechuate-3,4-dioxygenase. The results show the great benefit of combining molecular and culture-based techniques.}, }
@article {pmid34575109, year = {2021}, author = {Urbaniak, C and Grams, T and Mason, CE and Venkateswaran, K}, title = {Simulated Microgravity Promotes Horizontal Gene Transfer of Antimicrobial Resistance Genes between Bacterial Genera in the Absence of Antibiotic Selective Pressure.}, journal = {Life (Basel, Switzerland)}, volume = {11}, number = {9}, pages = {}, pmid = {34575109}, issn = {2075-1729}, support = {80NSSC21K0320//NASA Space Biology/ ; }, abstract = {Bacteria are able to adapt and survive in harsh and changing environments through many mechanisms, with one of them being horizontal gene transfer (HGT). This process is one of the leading culprits in the spread of antimicrobial resistance (AMR) within bacterial communities and could pose a significant health threat to astronauts if they fell ill, especially on long-duration space missions. In order to better understand the degree of HGT activity that could occur in space, biosafety level-2, donor and recipient bacteria were co-cultured under simulated microgravity (SMG) on Earth with concomitant 1G controls. Two AMR genes, blaOXA-500 and ISAba1, from the donor Acinetobacter pittii, were tracked in four recipient strains of Staphylococcus aureus (which did not harbor those genes) using polymerase chain reaction. All four S. aureus strains that were co-cultured with A. pittii under SMG had a significantly higher number of isolates that were now blaOXA-500- and ISAba1-positive compared to growth at 1G. The acquisition of these genes by the recipient induced a phenotypic change, as these isolates were now resistant to oxacillin, which they were previously susceptible to. This is a novel study, presenting, for the first time, increased HGT activity under SMG and the potential impact of the space environment in promoting increased gene dissemination within bacterial communities.}, }
@article {pmid34573289, year = {2021}, author = {Torasso Kasem, EJ and Angelov, A and Werner, E and Lichev, A and Vanderhaeghen, S and Liebl, W}, title = {Identification of New Chromosomal Loci Involved in com Genes Expression and Natural Transformation in the Actinobacterial Model Organism Micrococcus luteus.}, journal = {Genes}, volume = {12}, number = {9}, pages = {}, pmid = {34573289}, issn = {2073-4425}, mesh = {Chromosomes, Bacterial/genetics ; DNA, Bacterial/genetics ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genetic Loci ; Micrococcus luteus/*genetics ; Mutagenesis ; Promoter Regions, Genetic ; *Transformation, Bacterial ; }, abstract = {Historically, Micrococcus luteus was one of the first organisms used to study natural transformation, one of the main routes of horizontal gene transfer among prokaryotes. However, little is known about the molecular basis of competence development in M. luteus or any other representative of the phylum of high-GC Gram-positive bacteria (Actinobacteria), while this means of genetic exchange has been studied in great detail in Gram-negative and low-GC Gram-positive bacteria (Firmicutes). In order to identify new genetic elements involved in regulation of the comEA-comEC competence operon in M. luteus, we conducted random chemical mutagenesis of a reporter strain expressing lacZ under the control of the comEA-comEC promoter, followed by the screening of dysregulated mutants. Mutants with (i) upregulated com promoter under competence-repressing conditions and (ii) mutants with a repressed com promoter under competence-inducing conditions were isolated. After genotype and phenotype screening, the genomes of several mutant strains were sequenced. A selection of putative com-influencing mutations was reinserted into the genome of the M. luteus reporter strain as markerless single-nucleotide mutations to confirm their effect on com gene expression. This strategy revealed mutations affecting com gene expression at genetic loci different from previously known genes involved in natural transformation. Several of these mutations decreased transformation frequencies by several orders of magnitude, thus indicating significant roles in competence development or DNA acquisition in M. luteus. Among the identified loci, there was a new locus containing genes with similarity to genes of the tad clusters of M. luteus and other bacteria.}, }
@article {pmid34572615, year = {2021}, author = {Harshaw, NS and Stella, NA and Lehner, KM and Romanowski, EG and Kowalski, RP and Shanks, RMQ}, title = {Antibiotics Used in Empiric Treatment of Ocular Infections Trigger the Bacterial Rcs Stress Response System Independent of Antibiotic Susceptibility.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {10}, number = {9}, pages = {}, pmid = {34572615}, issn = {2079-6382}, support = {P30 EY008098/EY/NEI NIH HHS/United States ; R01EY027331/EY/NEI NIH HHS/United States ; P30EY08098/EY/NEI NIH HHS/United States ; unrestricted//Research to Prevent Blindness/ ; }, abstract = {The Rcs phosphorelay is a bacterial stress response system that responds to envelope stresses and in turn controls several virulence-associated pathways, including capsule, flagella, and toxin biosynthesis, of numerous bacterial species. The Rcs system also affects antibiotic tolerance, biofilm formation, and horizontal gene transfer. The Rcs system of the ocular bacterial pathogen Serratia marcescens was recently demonstrated to influence ocular pathogenesis in a rabbit model of keratitis, with Rcs-defective mutants causing greater pathology and Rcs-activated strains demonstrating reduced inflammation. The Rcs system is activated by a variety of insults, including β-lactam antibiotics and polymyxin B. In this study, we developed three luminescence-based transcriptional reporters for Rcs system activity and used them to test whether antibiotics used for empiric treatment of ocular infections influence Rcs system activity in a keratitis isolate of S. marcescens. These included antibiotics to which the bacteria were susceptible and resistant. Results indicate that cefazolin, ceftazidime, polymyxin B, and vancomycin activate the Rcs system to varying degrees in an RcsB-dependent manner, whereas ciprofloxacin and tobramycin activated the promoter fusions, but in an Rcs-independent manner. Although minimum inhibitory concentration (MIC) analysis demonstrated resistance of the test bacteria to polymyxin B and vancomycin, the Rcs system was activated by sub-inhibitory concentrations of these antibiotics. Together, these data indicate that a bacterial stress system that influences numerous pathogenic phenotypes and drug-tolerance is influenced by different classes of antibiotics despite the susceptibility status of the bacterium.}, }
@article {pmid34571766, year = {2021}, author = {Elshamy, AA and Saleh, SE and Alshahrani, MY and Aboshanab, KM and Aboulwafa, MM and Hassouna, NA}, title = {OXA-48 Carbapenemase-Encoding Transferable Plasmids of Klebsiella pneumoniae Recovered from Egyptian Patients Suffering from Complicated Urinary Tract Infections.}, journal = {Biology}, volume = {10}, number = {9}, pages = {}, pmid = {34571766}, issn = {2079-7737}, abstract = {Gram-negative bacteria are common causes of urinary tract infections (UTIs). Such pathogens can acquire genes encoding multiple mechanisms of antimicrobial resistance, including carbapenem resistance. The aim of this study was to detect the carbapenemase-producing ability of some Gram-negative bacterial isolates from urine specimens of patients suffering from complicated UTIs at two vital tertiary care hospitals in Cairo, Egypt; to determine the prevalence of carbapenemase genes among plasmid-bearing isolates; and explore the possibility of horizontal gene transfer to other bacterial species. The collected isolates were subjected to antimicrobial susceptibility testing, phenotypic analysis of carbapenemase production, and molecular detection of plasmid-borne carbapenemase genes, then the extracted plasmids were transformed into competent E. coli DH5α. A total of 256 Gram-negative bacterial clinical isolates were collected, 65 (25.4%) isolates showed carbapenem resistance of which 36 (55.4%) were carbapenemase-producers, and of these 31 (47.7%) harbored plasmids. The extracted plasmids were used as templates for PCR amplification of blaKPC, blaNDM, blaVIM, blaOXA-48, and blaIMP carbapenemase genes. The blaOXA-48 gene was detected in 24 (77.4%) of the tested isolates while blaVIM gene was detected in 8 (25.8%), both blaKPC and blaNDM genes were co-present in 1 (3.2%) isolate. Plasmids carrying the blaOXA-48 gene from 4 K. pneumoniae clinical isolates were successfully transformed into competent E. coli DH5α. The transformants were carbapenemase-producers and acquired resistance to some of the tested antimicrobial agents as compared to untransformed E. coli DH5α. The study concluded that the rate of carbapenem resistance among Gram-negative bacterial uropathogens in Cairo, Egypt is relatively high and can be transferred horizontally to other bacterial host(s).}, }
@article {pmid34571748, year = {2021}, author = {Rakitin, AL and Ermakova, AY and Beletsky, AV and Petrova, M and Mardanov, AV and Ravin, NV}, title = {Genome Analysis of Acinetobacter lwoffii Strains Isolated from Permafrost Soils Aged from 15 Thousand to 1.8 Million Years Revealed Their Close Relationships with Present-Day Environmental and Clinical Isolates.}, journal = {Biology}, volume = {10}, number = {9}, pages = {}, pmid = {34571748}, issn = {2079-7737}, support = {075-15-2020-907//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {Microbial life can be supported at subzero temperatures in permafrost up to several million years old. Genome analysis of strains isolated from permafrost provides a unique opportunity to study microorganisms that have not previously come into contact with the human population. Acinetobacter lwoffii is a typical soil bacterium that has been increasingly reported as hospital pathogens associated with bacteremia. In order to identify the specific genetic characteristics of ancient permafrost-conserved strains of A. lwoffii and their differences from present-day clinical isolates, we carried out a genome-wide analysis of five strains of A. lwoffii isolated from permafrost aged from 15 thousand to 1.8 million years. Surprisingly, we did not identify chromosomal genetic determinants that distinguish permafrost strains from clinical A. lwoffii isolates and strains from other natural habitats. Phylogenetic analysis based on whole genome sequences showed that permafrost strains do not form a separate cluster and some of them are most closely related to clinical isolates. The genomes of clinical and permafrost strains contain similar mobile elements and prophages, which indicates an intense horizontal transfer of genetic material. Comparison of plasmids of modern and permafrost strains showed that plasmids from the modern strains are enriched with antibiotic resistance genes, while the content of genes for resistance to heavy metals and arsenic is nearly the same. The thawing of permafrost caused by global warming could release new potentially pathogenic strains of Acinetobacter.}, }
@article {pmid34566918, year = {2021}, author = {Huang, L and Liu, M and Ammanath, AV and Zhu, D and Jia, R and Chen, S and Zhao, X and Yang, Q and Wu, Y and Zhang, S and Huang, J and Ou, X and Mao, S and Gao, Q and Sun, D and Tian, B and Götz, F and Wang, M and Cheng, A}, title = {Identification of the Natural Transformation Genes in Riemerella anatipestifer by Random Transposon Mutagenesis.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {712198}, pmid = {34566918}, issn = {1664-302X}, abstract = {In our previous study, it was shown that Riemerella anatipestifer, a Gram-negative bacterium, is naturally competent, but the genes involved in the process of natural transformation remain largely unknown. In this study, a random transposon mutant library was constructed using the R. anatipestifer ATCC11845 strain to screen for the genes involved in natural transformation. Among the 3000 insertion mutants, nine mutants had completely lost the ability of natural transformation, and 14 mutants showed a significant decrease in natural transformation frequency. We found that the genes RA0C_RS04920, RA0C_RS04915, RA0C_RS02645, RA0C_RS04895, RA0C_RS05130, RA0C_RS05105, RA0C_RS09020, and RA0C_RS04870 are essential for the occurrence of natural transformation in R. anatipestifer ATCC11845. In particular, RA0C_RS04895, RA0C_RS05130, RA0C_RS05105, and RA0C_RS04870 were putatively annotated as ComEC, DprA, ComF, and RecA proteins, respectively, in the NCBI database. However, RA0C_RS02645, RA0C_RS04920, RA0C_RS04915, and RA0C_RS09020 were annotated as proteins with unknown function, with no homology to any well-characterized natural transformation machinery proteins. The homologs of these proteins are mainly distributed in the members of Flavobacteriaceae. Taken together, our results suggest that R. anatipestifer encodes a unique natural transformation machinery.}, }
@article {pmid34565363, year = {2021}, author = {Wang, Y and Baumdicker, F and Schweiger, P and Kuenzel, S and Staubach, F}, title = {Horizontal gene transfer-mediated bacterial strain variation affects host fitness in Drosophila.}, journal = {BMC biology}, volume = {19}, number = {1}, pages = {187}, pmid = {34565363}, issn = {1741-7007}, mesh = {Animals ; Bacteria/genetics ; *Drosophila melanogaster/genetics ; *Gene Transfer, Horizontal ; Genome-Wide Association Study ; Thiamine ; }, abstract = {BACKGROUND: How microbes affect host fitness and environmental adaptation has become a fundamental research question in evolutionary biology. To better understand the role of microbial genomic variation for host fitness, we tested for associations of bacterial genomic variation and Drosophila melanogaster offspring number in a microbial Genome Wide Association Study (GWAS).<br><br>RESULTS: We performed a microbial GWAS, leveraging strain variation in the genus Gluconobacter, a genus of bacteria that are commonly associated with Drosophila under natural conditions. We pinpoint the thiamine biosynthesis pathway (TBP) as contributing to differences in fitness conferred to the fly host. While an effect of thiamine on fly development has been described, we show that strain variation in TBP between bacterial isolates from wild-caught D. melanogaster contributes to variation in offspring production by the host. By tracing the evolutionary history of TBP genes in Gluconobacter, we find that TBP genes were most likely lost and reacquired by horizontal gene transfer (HGT).<br><br>CONCLUSION: Our study emphasizes the importance of strain variation and highlights that HGT can add to microbiome flexibility and potentially to host adaptation.}, }
@article {pmid34564305, year = {2021}, author = {Iannelli, F and Santoro, F and Fox, V and Pozzi, G}, title = {A Mating Procedure for Genetic Transfer of Integrative and Conjugative Elements (ICEs) of Streptococci and Enterococci.}, journal = {Methods and protocols}, volume = {4}, number = {3}, pages = {}, pmid = {34564305}, issn = {2409-9279}, support = {20177J5Y3P//Italian Ministry of Education, University and Research (MIUR-Italy)/ ; }, abstract = {DNA sequencing of whole bacterial genomes has revealed that the entire set of mobile genes (mobilome) represents as much as 25% of the bacterial genome. Despite the huge availability of sequence data, the functional analysis of the mobile genetic elements (MGEs) is rarely reported. Therefore, established laboratory protocols are needed to investigate the biology of this important part of the bacterial genome. Conjugation is a mechanism of horizontal gene transfer which allows the exchange of MGEs among strains of the same or different bacterial species. In streptococci and enterococci, integrative and conjugative elements (ICEs) represent a large part of the mobilome. Here, we describe an efficient and easy-to-perform plate mating protocol for in vitro conjugative transfer of ICEs in streptococci (Streptococcus pneumoniae, Streptococcus agalactiae, Streptococcus gordonii, Streptococcus pyogenes), Enterococcus faecalis, and Bacillus subtilis. Conjugative transfer is carried out on solid media and selection of transconjugants is performed with a multilayer plating. This protocol allows the transfer of large genetic elements with a size up to 81 kb, and a transfer frequency up to 6.7 × 10[-3] transconjugants/donor cells.}, }
@article {pmid34563930, year = {2021}, author = {Zhao, Q and Guo, W and Luo, H and Xing, C and Wang, H and Liu, B and Si, Q and Ren, N}, title = {Deciphering the transfers of antibiotic resistance genes under antibiotic exposure conditions: Driven by functional modules and bacterial community.}, journal = {Water research}, volume = {205}, number = {}, pages = {117672}, doi = {10.1016/j.watres.2021.117672}, pmid = {34563930}, issn = {1879-2448}, mesh = {*Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; Sewage ; }, abstract = {Antibiotics can exert selective pressures on sludge as well as affect the emergence and spread of antibiotic resistance genes (ARGs). However, the underlying mechanisms of ARGs transfers are still controversial and not fully understood in sludge system. In present study, two anaerobic sequence batch reactors (ASBR) were constructed to investigate the development of ARGs exposed to two sulfonamide antibiotics (SMs, sulfadiazine SDZ and sulfamethoxazole SMX) with increasing concentrations. The abundance of corresponding ARGs and total ARGs obviously increased with presence of SMs. Functional analyses indicated that oxidative stress response, signal transduction and type IV secretion systems were triggered by SMs, which would promote ARGs transfers. Network analysis revealed 18 genera were possible hosts of ARGs, and their abundances increased with SMs. Partial least-squares path modeling suggested functional modules directly influenced mobile genetic elements (MGEs) as well as the ARGs might be driven by both functional modules and bacteria community, while bacteria community composition played a more key role. Sludge with refractory antibiotics (SDZ) may stimulate the relevant functions and shift the microbial composition to a greater extent, causing more ARGs to emerge and spread. The mechanisms of ARGs transfers are revealed from the perspective of functional modules and bacterial community in sludge system for the first time, and it could provide beneficial directions, such as oxidative stress reduction, cellular communication control, bacterial composition directional regulation, for ARGs spread controlling in the future.}, }
@article {pmid34559608, year = {2021}, author = {Sheppard, RJ and Barraclough, TG and Jansen, VAA}, title = {The Evolution of Plasmid Transfer Rate in Bacteria and Its Effect on Plasmid Persistence.}, journal = {The American naturalist}, volume = {198}, number = {4}, pages = {473-488}, doi = {10.1086/716063}, pmid = {34559608}, issn = {1537-5323}, support = {BB/M011178/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Adaptation, Physiological ; *Bacteria/genetics ; Drug Resistance, Microbial ; *Gene Transfer, Horizontal ; Humans ; Plasmids/genetics ; }, abstract = {AbstractPlasmids are extrachromosomal segments of DNA that can transfer genes between bacterial cells. Many plasmid genes benefit bacteria but cause harm to human health by granting antibiotic resistance to pathogens. Transfer rate is a key parameter for predicting plasmid dynamics, but observed rates are highly variable, and the effects of selective forces on their evolution are unclear. We apply evolutionary analysis to plasmid conjugation models to investigate selective pressures affecting plasmid transfer rate, emphasizing host versus plasmid control, the costs of plasmid transfer, and the role of recipient cells. Our analyses show that plasmid-determined transfer rates can be predicted with three parameters (host growth rate, plasmid loss rate, and the cost of plasmid transfer on growth) under some conditions. We also show that low-frequency genetic variation in transfer rate can accumulate, facilitating rapid adaptation to changing conditions. Furthermore, reduced transfer rates due to host control have limited effects on plasmid prevalence until low enough to prevent plasmid persistence. These results provide a framework to predict plasmid transfer rate evolution in different environments and demonstrate the limited impact of host mechanisms to control the costs incurred when plasmids are present.}, }
@article {pmid34559044, year = {2021}, author = {Matlock, W and Lipworth, S and Constantinides, B and Peto, TEA and Walker, AS and Crook, D and Hopkins, S and Shaw, LP and Stoesser, N}, title = {Flanker: a tool for comparative genomics of gene flanking regions.}, journal = {Microbial genomics}, volume = {7}, number = {9}, pages = {}, pmid = {34559044}, issn = {2057-5858}, support = {203141/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; 220422/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; MR/T001151/1/MRC_/Medical Research Council/United Kingdom ; NIHR200915/DH_/Department of Health/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MRF_MRF-145-0004-TPG-AVISO/MRF/MRF/United Kingdom ; }, mesh = {Bacterial Proteins/genetics ; Computational Biology ; *Gene Transfer, Horizontal ; *Genomics ; Interspersed Repetitive Sequences ; Klebsiella Infections/microbiology ; Klebsiella pneumoniae/*genetics ; Plasmids ; beta-Lactamases/*genetics ; }, abstract = {Analysing the flanking sequences surrounding genes of interest is often highly relevant to understanding the role of mobile genetic elements (MGEs) in horizontal gene transfer, particular for antimicrobial-resistance genes. Here, we present Flanker, a Python package that performs alignment-free clustering of gene flanking sequences in a consistent format, allowing investigation of MGEs without prior knowledge of their structure. These clusters, known as 'flank patterns' (FPs), are based on Mash distances, allowing for easy comparison of similarity across sequences. Additionally, Flanker can be flexibly parameterized to fine-tune outputs by characterizing upstream and downstream regions separately, and investigating variable lengths of flanking sequence. We apply Flanker to two recent datasets describing plasmid-associated carriage of important carbapenemase genes (blaOXA-48 and blaKPC-2/3) and show that it successfully identifies distinct clusters of FPs, including both known and previously uncharacterized structural variants. For example, Flanker identified four Tn4401 profiles that could not be sufficiently characterized using TETyper or MobileElementFinder, demonstrating the utility of Flanker for flanking-gene characterization. Similarly, using a large (n=226) European isolate dataset, we confirm findings from a previous smaller study demonstrating association between Tn1999.2 and blaOXA-48 upregulation and demonstrate 17 FPs (compared to the 5 previously identified). More generally, the demonstration in this study that FPs are associated with geographical regions and antibiotic-susceptibility phenotypes suggests that they may be useful as epidemiological markers. Flanker is freely available under an MIT license at https://github.com/wtmatlock/flanker.}, }
@article {pmid34559043, year = {2021}, author = {Horesh, G and Taylor-Brown, A and McGimpsey, S and Lassalle, F and Corander, J and Heinz, E and Thomson, NR}, title = {Different evolutionary trends form the twilight zone of the bacterial pan-genome.}, journal = {Microbial genomics}, volume = {7}, number = {9}, pages = {}, pmid = {34559043}, issn = {2057-5858}, support = {/WT_/Wellcome Trust/United Kingdom ; 217303/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacteria/*genetics ; Escherichia coli/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomics ; Multigene Family ; Phylogeny ; }, abstract = {The pan-genome is defined as the combined set of all genes in the gene pool of a species. Pan-genome analyses have been very useful in helping to understand different evolutionary dynamics of bacterial species: an open pan-genome often indicates a free-living lifestyle with metabolic versatility, while closed pan-genomes are linked to host-restricted, ecologically specialized bacteria. A detailed understanding of the species pan-genome has also been instrumental in tracking the phylodynamics of emerging drug resistance mechanisms and drug-resistant pathogens. However, current approaches to analyse a species' pan-genome do not take the species population structure into account, nor do they account for the uneven sampling of different lineages, as is commonplace due to over-sampling of clinically relevant representatives. Here we present the application of a population structure-aware approach for classifying genes in a pan-genome based on within-species distribution. We demonstrate our approach on a collection of 7500 Escherichia coli genomes, one of the most-studied bacterial species and used as a model for an open pan-genome. We reveal clearly distinct groups of genes, clustered by different underlying evolutionary dynamics, and provide a more biologically informed and accurate description of the species' pan-genome.}, }
@article {pmid34557177, year = {2021}, author = {Huang, CJ and Wu, TL and Zheng, PX and Ou, JY and Ni, HF and Lin, YC}, title = {Comparative Genomic Analysis Uncovered Evolution of Pathogenicity Factors, Horizontal Gene Transfer Events, and Heavy Metal Resistance Traits in Citrus Canker Bacterium Xanthomonas citri subsp. citri.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {731711}, pmid = {34557177}, issn = {1664-302X}, abstract = {Background: Worldwide citrus production is severely threatened by Asiatic citrus canker which is caused by the proteobacterium Xanthomonas citri subsp. citri. Foliar sprays of copper-based bactericides are frequently used to control plant bacterial diseases. Despite the sequencing of many X. citri strains, the genome diversity and distribution of genes responsible for metal resistance in X. citri subsp. citri strains from orchards with different management practices in Taiwan are not well understood. Results: The genomes of three X. citri subsp. citri strains including one copper-resistant strain collected from farms with different management regimes in Taiwan were sequenced by Illumina and Nanopore sequencing and assembled into complete circular chromosomes and plasmids. CRISPR spoligotyping and phylogenomic analysis indicated that the three strains were located in the same phylogenetic lineages and shared ∼3,000 core-genes with published X. citri subsp. citri strains. These strains differed mainly in the CRISPR repeats and pathogenicity-related plasmid-borne transcription activator-like effector (TALE)-encoding pthA genes. The copper-resistant strain has a unique, large copper resistance plasmid due to an unusual ∼40 kbp inverted repeat. Each repeat contains a complete set of the gene cluster responsible for copper and heavy metal resistance. Conversely, the copper sensitive strains carry no metal resistance genes in the plasmid. Through comparative analysis, the origin and evolution of the metal resistance clusters was resolved. Conclusion: Chromosomes remained constant among three strains collected in Taiwan, but plasmids likely played an important role in maintaining pathogenicity and developing bacterial fitness in the field. The evolution of pathogenicity factors and horizontal gene transfer events were observed in the three strains. These data suggest that agricultural management practices could be a potential trigger for the evolution of citrus canker pathogens. The decrease in the number of CRISPR repeats and pthA genes might be the result of adaptation to a less stressful environment. The metal resistance genes in the copper resistant X. citri strain likely originated from the Mauritian strain not the local copper-resistant X. euvesicatoria strain. This study highlights the importance of plasmids as 'vehicles' for exchanging genetic elements between plant pathogenic bacteria and contributing to bacterial adaptation to the environment.}, }
@article {pmid34556764, year = {2021}, author = {Naorem, RS and Goswami, G and Gyorgy, S and Fekete, C}, title = {Comparative analysis of prophages carried by human and animal-associated Staphylococcus aureus strains spreading across the European regions.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {18994}, pmid = {34556764}, issn = {2045-2322}, mesh = {Animals ; Europe ; Gene Transfer, Horizontal ; Genome, Bacterial ; Genomic Islands ; Host Microbial Interactions/genetics ; Humans ; Phylogeny ; Prophages/*genetics ; Species Specificity ; Staphylococcal Infections/*microbiology/transmission ; Staphylococcus aureus/*pathogenicity/virology ; Virulence Factors/genetics ; Zoonoses/*microbiology/transmission ; }, abstract = {Staphylococcus aureus is a major human and animal pathogen although the animal-associated S. aureus can be a potential risk of human zoonoses. Acquisition of phage-related genomic islands determines the S. aureus species diversity. This study characterized and compared the genome architecture, distribution nature, and evolutionary relationship of 65 complete prophages carried by human and animal-associated S. aureus strains spreading across the European regions. The analyzed prophage genomes showed mosaic architecture with extensive variation in genome size. The phylogenetic analyses generated seven clades in which prophages of the animal-associated S. aureus scattered in all the clades. The S. aureus strains with the same SCCmec type, and clonal complex favored the harboring of similar prophage sequences and suggested that the frequency of phage-mediated horizontal gene transfer is higher between them. The presence of various virulence factors in prophages of animal-associated S. aureus suggested that these prophages could have more pathogenic potential than prophages of human-associated S. aureus. This study showed that the S. aureus phages are dispersed among the several S. aureus serotypes and around the European regions. Further, understanding the phage functional genomics is necessary for the phage-host interactions and could be used for tracing the S. aureus strains transmission.}, }
@article {pmid34552144, year = {2021}, author = {Reis, AC and Cunha, MV}, title = {Genome-wide estimation of recombination, mutation and positive selection enlightens diversification drivers of Mycobacterium bovis.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {18789}, pmid = {34552144}, issn = {2045-2322}, mesh = {Chromosome Mapping ; Genetic Variation/*genetics ; Genome, Bacterial/*genetics ; Mutation/*genetics ; Mycobacterium bovis/*genetics ; Recombination, Genetic/*genetics ; Selection, Genetic/genetics ; Whole Genome Sequencing ; }, abstract = {Genome sequencing has reinvigorated the infectious disease research field, shedding light on disease epidemiology, pathogenesis, host-pathogen interactions and also evolutionary processes exerted upon pathogens. Mycobacterium tuberculosis complex (MTBC), enclosing M. bovis as one of its animal-adapted members causing tuberculosis (TB) in terrestrial mammals, is a paradigmatic model of bacterial evolution. As other MTBC members, M. bovis is postulated as a strictly clonal, slowly evolving pathogen, with apparently no signs of recombination or horizontal gene transfer. In this work, we applied comparative genomics to a whole genome sequence (WGS) dataset composed by 70 M. bovis from different lineages (European and African) to gain insights into the evolutionary forces that shape genetic diversification in M. bovis. Three distinct approaches were used to estimate signs of recombination. Globally, a small number of recombinant events was identified and confirmed by two independent methods with solid support. Still, recombination reveals a weaker effect on M. bovis diversity compared with mutation (overall r/m = 0.037). The differential r/m average values obtained across the clonal complexes of M. bovis in our dataset are consistent with the general notion that the extent of recombination may vary widely among lineages assigned to the same taxonomical species. Based on this work, recombination in M. bovis cannot be excluded and should thus be a topic of further effort in future comparative genomics studies for which WGS of large datasets from different epidemiological scenarios across the world is crucial. A smaller M. bovis dataset (n = 42) from a multi-host TB endemic scenario was then subjected to additional analyses, with the identification of more than 1,800 sites wherein at least one strain showed a single nucleotide polymorphism (SNP). The majority (87.1%) was located in coding regions, with the global ratio of non-synonymous upon synonymous alterations (dN/dS) exceeding 1.5, suggesting that positive selection is an important evolutionary force exerted upon M. bovis. A higher percentage of SNPs was detected in genes enriched into "lipid metabolism", "cell wall and cell processes" and "intermediary metabolism and respiration" functional categories, revealing their underlying importance in M. bovis biology and evolution. A closer look on genes prone to horizontal gene transfer in the MTBC ancestor and included in the 3R (DNA repair, replication and recombination) system revealed a global average negative value for Taijima's D neutrality test, suggesting that past selective sweeps and population expansion after a recent bottleneck remain as major evolutionary drivers of the obligatory pathogen M. bovis in its struggle with the host.}, }
@article {pmid34550067, year = {2021}, author = {Kalizang'oma, A and Chaguza, C and Gori, A and Davison, C and Beleza, S and Antonio, M and Beall, B and Goldblatt, D and Kwambana-Adams, B and Bentley, SD and Heyderman, RS}, title = {Streptococcus pneumoniae serotypes that frequently colonise the human nasopharynx are common recipients of penicillin-binding protein gene fragments from Streptococcus mitis.}, journal = {Microbial genomics}, volume = {7}, number = {9}, pages = {}, pmid = {34550067}, issn = {2057-5858}, support = {/WT_/Wellcome Trust/United Kingdom ; 16/136/46/DH_/Department of Health/United Kingdom ; OPP1034556/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacterial Proteins/genetics ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Microbial Sensitivity Tests ; Nasopharynx/*microbiology ; Penicillin-Binding Proteins/*genetics ; Penicillins ; Phylogeny ; Pneumococcal Infections/microbiology ; Pneumococcal Vaccines ; *Serogroup ; Streptococcus/classification/genetics ; Streptococcus mitis/*genetics ; Streptococcus oralis ; Streptococcus pneumoniae/*classification/*genetics ; Whole Genome Sequencing ; beta-Lactam Resistance ; }, abstract = {Streptococcus pneumoniae is an important global pathogen that causes bacterial pneumonia, sepsis and meningitis. Beta-lactam antibiotics are the first-line treatment for pneumococcal disease, however, their effectiveness is hampered by beta-lactam resistance facilitated by horizontal genetic transfer (HGT) with closely related species. Although interspecies HGT is known to occur among the species of the genus Streptococcus, the rates and effects of HGT between Streptococcus pneumoniae and its close relatives involving the penicillin binding protein (pbp) genes remain poorly understood. Here we applied the fastGEAR tool to investigate interspecies HGT in pbp genes using a global collection of whole-genome sequences of Streptococcus mitis, Streptococcus oralis and S. pneumoniae. With these data, we established that pneumococcal serotypes 6A, 13, 14, 16F, 19A, 19F, 23F and 35B were the highest-ranking serotypes with acquired pbp fragments. S. mitis was a more frequent pneumococcal donor of pbp fragments and a source of higher pbp nucleotide diversity when compared with S. oralis. Pneumococci that acquired pbp fragments were associated with a higher minimum inhibitory concentration (MIC) for penicillin compared with pneumococci without acquired fragments. Together these data indicate that S. mitis contributes to reduced β-lactam susceptibility among commonly carried pneumococcal serotypes that are associated with long carriage duration and high recombination frequencies. As pneumococcal vaccine programmes mature, placing increasing pressure on the pneumococcal population structure, it will be important to monitor the influence of antimicrobial resistance HGT from commensal streptococci such as S. mitis.}, }
@article {pmid34548559, year = {2021}, author = {Mozzicafreddo, M and Pucciarelli, S and Swart, EC and Piersanti, A and Emmerich, C and Migliorelli, G and Ballarini, P and Miceli, C}, title = {The macronuclear genome of the Antarctic psychrophilic marine ciliate Euplotes focardii reveals new insights on molecular cold adaptation.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {18782}, pmid = {34548559}, issn = {2045-2322}, mesh = {*Adaptation, Physiological ; Antarctic Regions ; *Cold Temperature ; Euplotes/genetics/*physiology ; *Genome ; }, abstract = {The macronuclear (MAC) genomes of ciliates belonging to the genus Euplotes species are comprised of numerous small DNA molecules, nanochromosomes, each typically encoding a single gene. These genomes are responsible for all gene expression during vegetative cell growth. Here, we report the analysis of the MAC genome from the Antarctic psychrophile Euplotes focardii. Nanochromosomes containing bacterial sequences were not found, suggesting that phenomena of horizontal gene transfer did not occur recently, even though this ciliate species has a substantial associated bacterial consortium. As in other euplotid species, E. focardii MAC genes are characterized by a high frequency of translational frameshifting. Furthermore, in order to characterize differences that may be consequent to cold adaptation and defense to oxidative stress, the main constraints of the Antarctic marine microorganisms, we compared E. focardii MAC genome with those available from mesophilic Euplotes species. We focussed mainly on the comparison of tubulin, antioxidant enzymes and heat shock protein (HSP) 70 families, molecules which possess peculiar characteristic correlated with cold adaptation in E. focardii. We found that α-tubulin genes and those encoding SODs and CATs antioxidant enzymes are more numerous than in the mesophilic Euplotes species. Furthermore, the phylogenetic trees showed that these molecules are divergent in the Antarctic species. In contrast, there are fewer hsp70 genes in E. focardii compared to mesophilic Euplotes and these genes do not respond to thermal stress but only to oxidative stress. Our results suggest that molecular adaptation to cold and oxidative stress in the Antarctic environment may not only be due to particular amino acid substitutions but also due to duplication and divergence of paralogous genes.}, }
@article {pmid34546072, year = {2021}, author = {Flores Ramos, S and Brugger, SD and Escapa, IF and Skeete, CA and Cotton, SL and Eslami, SM and Gao, W and Bomar, L and Tran, TH and Jones, DS and Minot, S and Roberts, RJ and Johnston, CD and Lemon, KP}, title = {Genomic Stability and Genetic Defense Systems in Dolosigranulum pigrum, a Candidate Beneficial Bacterium from the Human Microbiome.}, journal = {mSystems}, volume = {6}, number = {5}, pages = {e0042521}, pmid = {34546072}, issn = {2379-5077}, support = {R01 DE027850/DE/NIDCR NIH HHS/United States ; R01 GM117174/GM/NIGMS NIH HHS/United States ; Stimulus Pilot Grant//The Forsyth Institute/ ; P3SMP3_155315//Swiss National Science Foundation and Swiss Foundation for Grants in Biology and Medicine/ ; R01 DE027850/DE/NIDCR NIH HHS/United States ; R01 GM117174/GM/NIGMS NIH HHS/United States ; 16B065//Novartis Stiftung&#xa0;f&#xfc;r&#xa0;Medizinisch-Biologische Forschung (Novartis Foundation for Medical-Biological Research)/ ; 1449/M//Promedica Stiftung/ ; }, abstract = {Dolosigranulum pigrum is positively associated with indicators of health in multiple epidemiological studies of human nasal microbiota. Knowledge of the basic biology of D. pigrum is a prerequisite for evaluating its potential for future therapeutic use; however, such data are very limited. To gain insight into D. pigrum's chromosomal structure, pangenome, and genomic stability, we compared the genomes of 28 D. pigrum strains that were collected across 20 years. Phylogenomic analysis showed closely related strains circulating over this period and closure of 19 genomes revealed highly conserved chromosomal synteny. Gene clusters involved in the mobilome and in defense against mobile genetic elements (MGEs) were enriched in the accessory genome versus the core genome. A systematic analysis for MGEs identified the first candidate D. pigrum prophage and insertion sequence. A systematic analysis for genetic elements that limit the spread of MGEs, including restriction modification (RM), CRISPR-Cas, and deity-named defense systems, revealed strain-level diversity in host defense systems that localized to specific genomic sites, including one RM system hot spot. Analysis of CRISPR spacers pointed to a wealth of MGEs against which D. pigrum defends itself. These results reveal a role for horizontal gene transfer and mobile genetic elements in strain diversification while highlighting that in D. pigrum this occurs within the context of a highly stable chromosomal organization protected by a variety of defense mechanisms. IMPORTANCE Dolosigranulum pigrum is a candidate beneficial bacterium with potential for future therapeutic use. This is based on its positive associations with characteristics of health in multiple studies of human nasal microbiota across the span of human life. For example, high levels of D. pigrum nasal colonization in adults predicts the absence of Staphylococcus aureus nasal colonization. Also, D. pigrum nasal colonization in young children is associated with healthy control groups in studies of middle ear infections. Our analysis of 28 genomes revealed a remarkable stability of D. pigrum strains colonizing people in the United States across a 20-year span. We subsequently identified factors that can influence this stability, including genomic stability, phage predators, the role of MGEs in strain-level variation, and defenses against MGEs. Finally, these D. pigrum strains also lacked predicted virulence factors. Overall, these findings add additional support to the potential for D. pigrum as a therapeutic bacterium.}, }
@article {pmid34544379, year = {2021}, author = {Zhang, W and Liang, Y and Zheng, K and Gu, C and Liu, Y and Wang, Z and Zhang, X and Shao, H and Jiang, Y and Guo, C and He, H and Wang, H and Sung, YY and Mok, WJ and Zhang, Y and McMinn, A and Wang, M}, title = {Characterization and genomic analysis of the first Oceanospirillum phage, vB_OliS_GJ44, representing a novel siphoviral cluster.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {675}, pmid = {34544379}, issn = {1471-2164}, mesh = {*Bacteriophages/genetics ; DNA, Viral/genetics ; Genome, Viral ; Genomics ; Phylogeny ; *Siphoviridae/genetics ; }, abstract = {BACKGROUND: Marine bacteriophages play key roles in the community structure of microorganisms, biogeochemical cycles, and the mediation of genetic diversity through horizontal gene transfer. Recently, traditional isolation methods, complemented by high-throughput sequencing metagenomics technology, have greatly increased our understanding of the diversity of bacteriophages. Oceanospirillum, within the order Oceanospirillales, are important symbiotic marine bacteria associated with hydrocarbon degradation and algal blooms, especially in polar regions. However, until now there has been no isolate of an Oceanospirillum bacteriophage, and so details of their metagenome has remained unknown.<br><br>RESULTS: Here, we reported the first Oceanospirillum phage, vB_OliS_GJ44, which was assembled into a 33,786&#x2009;bp linear dsDNA genome, which includes abundant tail-related and recombinant proteins. The recombinant module was highly adapted to the host, according to the tetranucleotides correlations. Genomic and morphological analyses identified vB_OliS_GJ44 as a siphovirus, however, due to the distant evolutionary relationship with any other known siphovirus, it is proposed that this virus could be classified as the type phage of a new Oceanospirivirus genus within the Siphoviridae family. vB_OliS_GJ44 showed synteny with six uncultured phages, which supports its representation in uncultured environmental viral contigs from metagenomics. Homologs of several vB_OliS_GJ44 genes have mostly been found in marine metagenomes, suggesting the prevalence of this phage genus in the oceans.<br><br>CONCLUSIONS: These results describe the first Oceanospirillum phage, vB_OliS_GJ44, that represents a novel viral cluster and exhibits interesting genetic features related to phage-host interactions and evolution. Thus, we propose a new viral genus Oceanospirivirus within the Siphoviridae family to reconcile this cluster, with vB_OliS_GJ44 as a representative member.}, }
@article {pmid34542714, year = {2021}, author = {Averhoff, B and Kirchner, L and Pfefferle, K and Yaman, D}, title = {Natural transformation in Gram-negative bacteria thriving in extreme environments: from genes and genomes to proteins, structures and regulation.}, journal = {Extremophiles : life under extreme conditions}, volume = {25}, number = {5-6}, pages = {425-436}, pmid = {34542714}, issn = {1433-4909}, support = {AV 9/6-2//Deutsche Forschungsgemeinschaft/ ; FOR 2251//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Acinetobacter/genetics ; Extreme Environments ; Gene Transfer, Horizontal ; Thermus thermophilus ; }, abstract = {Extremophilic prokaryotes live under harsh environmental conditions which require far-reaching cellular adaptations. The acquisition of novel genetic information via natural transformation plays an important role in bacterial adaptation. This mode of DNA transfer permits the transfer of genetic information between microorganisms of distant evolutionary lineages and even between members of different domains. This phenomenon, known as horizontal gene transfer (HGT), significantly contributes to genome plasticity over evolutionary history and is a driving force for the spread of fitness-enhancing functions including virulence genes and antibiotic resistances. In particular, HGT has played an important role for adaptation of bacteria to extreme environments. Here, we present a survey of the natural transformation systems in bacteria that live under extreme conditions: the thermophile Thermus thermophilus and two desiccation-resistant members of the genus Acinetobacter such as Acinetobacter baylyi and Acinetobacter baumannii. The latter is an opportunistic pathogen and has become a world-wide threat in health-care institutions. We highlight conserved and unique features of the DNA transporter in Thermus and Acinetobacter and present tentative models of both systems. The structure and function of both DNA transporter are described and the mechanism of DNA uptake is discussed.}, }
@article {pmid34538504, year = {2022}, author = {Harrison, MC and LaBella, AL and Hittinger, CT and Rokas, A}, title = {The evolution of the GALactose utilization pathway in budding yeasts.}, journal = {Trends in genetics : TIG}, volume = {38}, number = {1}, pages = {97-106}, pmid = {34538504}, issn = {0168-9525}, support = {R56 AI146096/AI/NIAID NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Galactose/genetics/metabolism ; Genes, Fungal ; Humans ; Multigene Family ; Saccharomyces cerevisiae/genetics/metabolism ; *Saccharomycetales/genetics/metabolism ; }, abstract = {The Leloir galactose utilization or GAL pathway of budding yeasts, including that of the baker's yeast Saccharomyces cerevisiae and the opportunistic human pathogen Candida albicans, breaks down the sugar galactose for energy and biomass production. The GAL pathway has long served as a model system for understanding how eukaryotic metabolic pathways, including their modes of regulation, evolve. More recently, the physical linkage of the structural genes GAL1, GAL7, and GAL10 in diverse budding yeast genomes has been used as a model for understanding the evolution of gene clustering. In this review, we summarize exciting recent work on three different aspects of this iconic pathway's evolution: gene cluster organization, GAL gene regulation, and the population genetics of the GAL pathway.}, }
@article {pmid34537705, year = {2022}, author = {Wu, Y and Wen, Q and Chen, Z and Fu, Q and Bao, H}, title = {Response of antibiotic resistance to the co-exposure of sulfamethoxazole and copper during swine manure composting.}, journal = {The Science of the total environment}, volume = {805}, number = {}, pages = {150086}, doi = {10.1016/j.scitotenv.2021.150086}, pmid = {34537705}, issn = {1879-1026}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Composting ; Copper/toxicity ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Manure ; *Metals, Heavy ; Sulfamethoxazole/pharmacology ; Swine ; }, abstract = {Heavy metals driven co-selection of antibiotic resistance in soil and water bodies has been widely concerned, but the response of antibiotic resistance to co-existence of antibiotics and heavy metals in composting system is still unknown. Commonly used sulfamethoxazole and copper were individually and jointly added into four reactors to explore their effects on antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), heavy metal resistance genes (MRGs) and bacterial community structure. The abundance of total ARGs and MGEs were notably decreased by 68.64%-84.95% and 91.27-97.38%, respectively, after the composting. Individual addition of sulfamethoxazole, individual addition of copper, simultaneously addition of sulfamethoxazole and copper increased the abundance of ARGs and MGEs throughout the composting period. Co-exposure of sulfamethoxazole and copper elevated the total abundance of ARGs by 1.17-1.51 times by the end of the composting compared to individual addition of sulfamethoxazole or copper. Network analysis indicated that the shifts in potential host bacteria determined the ARGs variation. Additionally, MGEs and MRGs had significant effects on ARGs, revealing that horizontal gene transfer and heavy metals induced co-resistance could promote ARGs dissemination.}, }
@article {pmid34536995, year = {2021}, author = {Hong, Z and Liao, X and Ye, Y and Zhang, N and Yang, Z and Zhu, W and Gao, W and Sharbrough, J and Tembrock, LR and Xu, D and Wu, Z}, title = {A complete mitochondrial genome for fragrant Chinese rosewood (Dalbergia odorifera, Fabaceae) with comparative analyses of genome structure and intergenomic sequence transfers.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {672}, pmid = {34536995}, issn = {1471-2164}, mesh = {China ; Chloroplasts ; *Dalbergia/genetics ; *Fabaceae/genetics ; *Genome, Chloroplast ; *Genome, Mitochondrial ; Phylogeny ; Plant Breeding ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Dalbergia odorifera is an economically and culturally important species in the Fabaceae because of the high-quality lumber and traditional Chinese medicines made from this plant, however, overexploitation has increased the scarcity of D. odorifera. Given the rarity and the multiple uses of this species, it is important to expand the genomic resources for utilizing in applications such as tracking illegal logging, determining effective population size of wild stands, delineating pedigrees in marker assisted breeding programs, and resolving gene networks in functional genomics studies. Even the nuclear and chloroplast genomes have been published for D. odorifera, the complete mitochondrial genome has not been assembled or assessed for sequence transfer to other genomic compartments until now. Such work is essential in understanding structural and functional genome evolution in a lineage (Fabaceae) with frequent intergenomic sequence transfers.<br><br>RESULTS: We integrated Illumina short-reads and PacBio CLR long-reads to assemble and annotate the complete mitochondrial genome of D. odorifera. The mitochondrial genome was organized as&#xa0;a single circular structure&#xa0;of&#xa0;435 Kb in length containing 33 protein coding genes, 4 rRNA and 17 tRNA genes. Nearly 4.0% (17,386&#x2009;bp) of the genome was annotated as repetitive DNA. From the sequence transfer analysis, it was found that 114 Kb of DNA originating from the mitochondrial genome has been transferred to the nuclear genome, with most of the transfer events having taken place relatively recently. The high frequency of sequence transfers from the mitochondria to the nuclear genome was similar to that of sequence transfer from the chloroplast to the nuclear genome.<br><br>CONCLUSION: For the first-time, the complete mitochondrial genome of D. odorifera was assembled in this study, which will provide a baseline resource in understanding genomic evolution in the highly specious Fabaceae. In particular, the assessment of intergenomic sequence transfer suggests that transfers have been common and recent indicating a possible role in environmental adaptation as has been found in other lineages. The high turnover rate of genomic colinearly and large differences in mitochondrial genome size found in the comparative analyses herein providing evidence for the rapid evolution of mitochondrial genome structure compared to chloroplasts in Faboideae. While phylogenetic analyses using functional genes indicate that mitochondrial genes are very slowly evolving compared to chloroplast genes.}, }
@article {pmid34534940, year = {2021}, author = {Xie, J and Gu, J and Wang, X and Hu, T and Sun, W and Lei, L and Zhang, R and Guo, H}, title = {Insights into the beneficial effects of woody peat for reducing abundances of antibiotic resistance genes during composting.}, journal = {Bioresource technology}, volume = {342}, number = {}, pages = {125903}, doi = {10.1016/j.biortech.2021.125903}, pmid = {34534940}, issn = {1873-2976}, mesh = {Anti-Bacterial Agents/pharmacology ; *Composting ; Drug Resistance, Microbial/genetics ; Genes, Bacterial/genetics ; Humans ; Soil ; }, abstract = {Antibiotic resistance genes (ARGs) in manure endangered human health, while heavy metals in manure will pose selective pressure on ARGs. This study explored the effects on ARGs of adding woody peat during composting at different ratios (0 (CK), 5% (T1), and 15% (T2)). After composting, the relative abundances of 8/11 ARGs were 6.97-38.09% and 10.73-54.31% lower in T1 and T2, respectively, than CK. The bioavailable Cu content was 1.40% and 18.40% lower in T1 and T2, respectively, than CK. Network analysis showed that ARGs, mobile genetic elements (MGEs), and metal resistance genes possessed common potential host bacteria, such as Streptococcus, Dietzia, and Corynebacterium_1. Environmental factors, especially bioavailable Cu, and MGEs accounted for 80.75% of the changes in the abundances of ARGs. In conclusion, 15% Woody peat is beneficial to decrease the bioavailable Cu content and weaken horizontal gene transfer for controlling the spread of ARGs during composting.}, }
@article {pmid34530277, year = {2022}, author = {Fang, J and Jin, L and Meng, Q and Shan, S and Wang, D and Lin, D}, title = {Biochar effectively inhibits the horizontal transfer of antibiotic resistance genes via transformation.}, journal = {Journal of hazardous materials}, volume = {423}, number = {Pt B}, pages = {127150}, doi = {10.1016/j.jhazmat.2021.127150}, pmid = {34530277}, issn = {1873-3336}, mesh = {*Anti-Bacterial Agents/pharmacology ; Charcoal ; Drug Resistance, Microbial/genetics ; *Escherichia coli/genetics ; Genes, Bacterial ; Humans ; Plasmids/genetics ; }, abstract = {The rapid spread of antibiotic resistance genes (ARGs) has posed a risk to human health. Here, the effects of biochar (BC) on the horizontal transfer of ARG-carrying plasmids to Escherichia coli via transformation were systematically investigated. BC could significantly inhibit the transformation of ARGs and the inhibition degree increased with pyrolysis temperature. Rice straw-derived BC showed a stronger inhibitory effect on the transformation of ARGs than that of peanut shell-derived BC from the same pyrolysis temperature. The inhibitory effect of BC from low pyrolysis temperature (300 ℃) was mainly caused by BC dissolutions, while it was mainly attributed to BC solids for high pyrolysis temperature (700 ℃) BC. BC dissolutions could induce intramolecular condensation and even agglomeration of plasmids, hindering their transformation into competent bacteria. The cell membrane permeability was slightly decreased in BC dissolutions, which might also contribute to the inhibitory effect. Plasmid can be adsorbed by BC solids and the adsorption increased with BC pyrolysis temperature. Meanwhile, BC-adsorbed plasmid could hardly be transformed into E. coli. BC solids could also deactivate E. coli and thereby inhibit their uptake of ARGs. These findings provide a way using BC to limit the spread of ARGs in the environment.}, }
@article {pmid34530104, year = {2021}, author = {Passarelli-Araujo, H and Jacobs, SH and Franco, GR and Venancio, TM}, title = {Phylogenetic analysis and population structure of Pseudomonas alloputida.}, journal = {Genomics}, volume = {113}, number = {6}, pages = {3762-3773}, doi = {10.1016/j.ygeno.2021.09.008}, pmid = {34530104}, issn = {1089-8646}, mesh = {*Gene Transfer, Horizontal ; Humans ; Phylogeny ; Plasmids ; *Pseudomonas/genetics ; }, abstract = {The Pseudomonas putida group comprises strains with biotechnological and clinical relevance. P. alloputida was proposed as a new species and highlighted the misclassification of P. putida. Nevertheless, the population structure of P. alloputida remained unexplored. We retrieved 11,025 Pseudomonas genomes and used P. alloputida Kh7[T] to delineate the species. The P. alloputida population structure comprises at least 7 clonal complexes (CCs). Clinical isolates are mainly found in CC4 and acquired resistance genes are present at low frequency in plasmids. Virulence profiles support the potential of CC7 members to outcompete other plant or human pathogens through a type VI secretion system. Finally, we found that horizontal gene transfer had an important role in shaping the ability of P. alloputida to bioremediate aromatic compounds such as toluene. Our results provide the grounds to understand P. alloputida genetic diversity and its potential for biotechnological applications.}, }
@article {pmid34525757, year = {2022}, author = {Wang, G and Zhu, J and Xing, Y and Yin, Y and Li, Y and Li, Q and Chen, R}, title = {When dewatered swine manure-derived biochar meets swine wastewater in anaerobic digestion: A win-win scenario towards highly efficient energy recovery and antibiotic resistance genes attenuation for swine manure management.}, journal = {The Science of the total environment}, volume = {803}, number = {}, pages = {150126}, doi = {10.1016/j.scitotenv.2021.150126}, pmid = {34525757}, issn = {1879-1026}, mesh = {Anaerobiosis ; Animals ; Anti-Bacterial Agents/pharmacology ; Charcoal ; Drug Resistance, Microbial/genetics ; *Manure ; Swine ; *Wastewater ; }, abstract = {This work explored the feasibility of dewatered swine manure-derived biochar (DSMB) as an additive to facilitate anaerobic digestion (AD) of swine wastewater for energy recovery and antibiotic resistance genes (ARG) attenuation enhancements. With 20 g/L DSMB assistance, the methanogenic lag time of swine wastewater was shortened by 17.4-21.1%, and the maximum CH4 production rate increased from 40.8 mL/d to 48.3-50.5 mL/d, among which DSMB prepared under 300 °C exhibited a better performance than that prepared under 500 °C and 700 °C. Integrated analysis of DSMB electrochemical properties, microbial electron transfer system activity, and microbial community succession revealed the potential of DSMB-300 to act as redox-active electron transfer mediators between syntrophic microbes to accelerate syntrophic methanogenesis via potential direct interspecies electron transfer. Meanwhile, DSMB preparation by pyrolysis dramatically reduced ARG abundance by almost 4 logs. Adding DSMB into AD not only strengthened the attenuation efficiency of ARG in the original swine wastewater, but also effectively controlled the potential risk of horizontal gene transfer by mitigating 74.8% of the mobile gene elements abundance. Accordingly, we proposed a win-win scenario for bio-waste management in swine farms, highlighting the more advanced energy recovery and ARG attenuation compared to the current status.}, }
@article {pmid34524452, year = {2022}, author = {Yang, B and Zhang, Z and Yang, CQ and Wang, Y and Orr, MC and Wang, H and Zhang, AB}, title = {Identification of Species by Combining Molecular and Morphological Data Using Convolutional Neural Networks.}, journal = {Systematic biology}, volume = {71}, number = {3}, pages = {690-705}, doi = {10.1093/sysbio/syab076}, pmid = {34524452}, issn = {1076-836X}, mesh = {Animals ; Biodiversity ; *Butterflies/genetics ; DNA/genetics ; DNA Barcoding, Taxonomic/methods ; Neural Networks, Computer ; Phylogeny ; }, abstract = {Integrative taxonomy is central to modern taxonomy and systematic biology, including behavior, niche preference, distribution, morphological analysis, and DNA barcoding. However, decades of use demonstrate that these methods can face challenges when used in isolation, for instance, potential misidentifications due to phenotypic plasticity for morphological methods, and incorrect identifications because of introgression, incomplete lineage sorting, and horizontal gene transfer for DNA barcoding. Although researchers have advocated the use of integrative taxonomy, few detailed algorithms have been proposed. Here, we develop a convolutional neural network method (morphology-molecule network [MMNet]) that integrates morphological and molecular data for species identification. The newly proposed method (MMNet) worked better than four currently available alternative methods when tested with 10 independent data sets representing varying genetic diversity from different taxa. High accuracies were achieved for all groups, including beetles (98.1% of 123 species), butterflies (98.8% of 24 species), fishes (96.3% of 214 species), and moths (96.4% of 150 total species). Further, MMNet demonstrated a high degree of accuracy ($>$98%) in four data sets including closely related species from the same genus. The average accuracy of two modest subgenomic (single nucleotide polymorphism) data sets, comprising eight putative subspecies respectively, is 90%. Additional tests show that the success rate of species identification under this method most strongly depends on the amount of training data, and is robust to sequence length and image size. Analyses on the contribution of different data types (image vs. gene) indicate that both morphological and genetic data are important to the model, and that genetic data contribute slightly more. The approaches developed here serve as a foundation for the future integration of multimodal information for integrative taxonomy, such as image, audio, video, 3D scanning, and biosensor data, to characterize organisms more comprehensively as a basis for improved investigation, monitoring, and conservation of biodiversity. [Convolutional neural network; deep learning; integrative taxonomy; single nucleotide polymorphism; species identification.].}, }
@article {pmid34518655, year = {2021}, author = {Haag, AF and Podkowik, M and Ibarra-Chávez, R and Gallego Del Sol, F and Ram, G and Chen, J and Marina, A and Novick, RP and Penadés, JR}, title = {A regulatory cascade controls Staphylococcus aureus pathogenicity island activation.}, journal = {Nature microbiology}, volume = {6}, number = {10}, pages = {1300-1308}, pmid = {34518655}, issn = {2058-5276}, support = {MR/S00940X/1/MRC_/Medical Research Council/United Kingdom ; MR/V000772/1/MRC_/Medical Research Council/United Kingdom ; R01 AI139613/AI/NIAID NIH HHS/United States ; BB/S003835/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 201531/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; BB/N002873/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 201531/WT_/Wellcome Trust/United Kingdom ; MR/M003876/1/MRC_/Medical Research Council/United Kingdom ; MR/S00940X/2/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacterial Proteins/genetics/metabolism ; DNA Replication ; DNA, Bacterial/genetics/metabolism ; Gene Transfer, Horizontal ; Genomic Islands/*genetics ; Staphylococcus Phages/physiology ; Staphylococcus aureus/*genetics/pathogenicity/virology ; Transcriptional Activation ; }, abstract = {Staphylococcal pathogenicity islands (SaPIs) are a family of closely related mobile chromosomal islands that encode and disseminate the superantigen toxins, toxic shock syndrome toxin 1 and superantigen enterotoxin B (SEB). They are regulated by master repressors, which are counteracted by helper phage-encoded proteins, thereby inducing their excision, replication, packaging and intercell transfer. SaPIs are major components of the staphylococcal mobilome, occupying five chromosomal att sites, with many strains harbouring two or more. As regulatory interactions between co-resident SaPIs could have profound effects on the spread of superantigen pathobiology, we initiated the current study to search for such interactions. Using classical genetics, we found that, with one exception, their regulatory systems do not cross-react. The exception was SaPI3, which was originally considered defective because it could not be mobilized by any known helper phage. We show here that SaPI3 has an atypical regulatory module and is induced not by a phage but by many other SaPIs, including SaPI2, SaPIbov1 and SaPIn1, each encoding a conserved protein, Sis, which counteracts the SaPI3 repressor, generating an intracellular regulatory cascade: the co-resident SaPI, when conventionally induced by a helper phage, expresses its sis gene which, in turn, induces SaPI3, enabling it to spread. Using bioinformatics analysis, we have identified more than 30 closely related coancestral SEB-encoding SaPI3 relatives occupying the same att site and controlled by a conserved regulatory module, immA-immR-str'. This module is functionally analogous but unrelated to the typical SaPI regulatory module, stl-str. As SaPIs are phage satellites, SaPI3 and its relatives are SaPI satellites.}, }
@article {pmid34518546, year = {2021}, author = {Bharatham, N and Bhowmik, P and Aoki, M and Okada, U and Sharma, S and Yamashita, E and Shanbhag, AP and Rajagopal, S and Thomas, T and Sarma, M and Narjari, R and Nagaraj, S and Ramachandran, V and Katagihallimath, N and Datta, S and Murakami, S}, title = {Structure and function relationship of OqxB efflux pump from Klebsiella pneumoniae.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {5400}, pmid = {34518546}, issn = {2041-1723}, support = {R01 AI136803/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/chemistry/*genetics/metabolism ; Binding Sites/genetics ; Crystallography, X-Ray ; Drug Resistance, Multiple, Bacterial/*genetics ; Klebsiella pneumoniae/*genetics/metabolism ; Membrane Transport Proteins/chemistry/*genetics/metabolism ; Microbial Sensitivity Tests ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Protein Binding ; Protein Conformation ; Protein Multimerization ; Structure-Activity Relationship ; }, abstract = {OqxB is an RND (Resistance-Nodulation-Division) efflux pump that has emerged as a factor contributing to the antibiotic resistance in Klebsiella pneumoniae. OqxB underwent horizontal gene transfer and is now seen in other Gram-negative bacterial pathogens including Escherichia coli, Enterobacter cloacae and Salmonella spp., further disseminating multi-drug resistance. In this study, we describe crystal structure of OqxB with n-dodecyl-β-D-maltoside (DDM) molecules bound in its substrate-binding pocket, at 1.85 Å resolution. We utilize this structure in computational studies to predict the key amino acids contributing to the efflux of fluoroquinolones by OqxB, distinct from analogous residues in related transporters AcrB and MexB. Finally, our complementation assays with mutated OqxB and minimum inhibitory concentration (MIC) experiments with clinical isolates of E. coli provide further evidence that the predicted structural features are indeed involved in ciprofloxacin efflux.}, }
@article {pmid34511070, year = {2021}, author = {Pal, S and Sharma, G and Subramanian, S}, title = {Complete genome sequence and identification of polyunsaturated fatty acid biosynthesis genes of the myxobacterium Minicystis rosea DSM 24000[T].}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {655}, pmid = {34511070}, issn = {1471-2164}, mesh = {Fatty Acids, Unsaturated ; Genome, Bacterial ; Multigene Family ; *Myxococcales/genetics ; Phylogeny ; }, abstract = {BACKGROUND: Myxobacteria harbor numerous biosynthetic gene clusters that can produce a diverse range of secondary metabolites. Minicystis rosea DSM 24000[T] is a soil-dwelling myxobacterium belonging to the suborderSorangiineae and family Polyangiaceae and is known to produce various secondary metabolites as well as polyunsaturated fatty acids (PUFAs). Here, we use whole-genome sequencing to explore the diversity of biosynthetic gene clusters in M. rosea.<br><br>RESULTS: Using PacBio sequencing technology, we assembled the 16.04 Mbp complete genome of M. rosea DSM 24000[T], the largest bacterial genome sequenced to date. About 44% of its coding potential represents paralogous genes predominantly associated with signal transduction, transcriptional regulation, and protein folding. These genes are involved in various essential functions such as cellular organization, diverse niche adaptation, and bacterial cooperation, and enable social behavior like gliding motility, sporulation, and predation, typical of myxobacteria. A profusion of eukaryotic-like kinases (353) and an elevated ratio of phosphatases (8.2/1) in M. rosea as compared to other myxobacteria suggest gene duplication as one of the primary modes of genome expansion. About 7.7% of the genes are involved in the biosynthesis of a diverse array of secondary metabolites such as polyketides, terpenes, and bacteriocins. Phylogeny of the genes involved in PUFA biosynthesis (pfa) together with the conserved synteny of the complete pfa gene cluster suggests acquisition via horizontal gene transfer from Actinobacteria.<br><br>CONCLUSION: Overall, this study describes the complete genome sequence of M. rosea, comparative genomic analysis to explore the putative reasons for its large genome size, and explores the secondary metabolite potential, including the biosynthesis of polyunsaturated fatty acids.}, }
@article {pmid34506557, year = {2021}, author = {Watanabe, Y and Spangenberg, GC and Shinozuka, H}, title = {Fungus-originated glucanase and monooxygenase genes in creeping bent grass (Agrostis stolonifera L.).}, journal = {PloS one}, volume = {16}, number = {9}, pages = {e0257173}, pmid = {34506557}, issn = {1932-6203}, mesh = {Agrostis/*enzymology/*genetics ; Amino Acid Sequence ; Cellulases/chemistry/*genetics/metabolism ; Fungi/*enzymology ; Gene Expression Regulation, Plant ; Gene Transfer, Horizontal ; *Genes, Plant ; Mixed Function Oxygenases/chemistry/*genetics/metabolism ; Phylogeny ; }, abstract = {Recent studies have revealed presence of fungus-originated genes in genomes of cool-season grasses, suggesting occurrence of multiple ancestral gene transfer events between the two distant lineages. The current article describes identification of glucanase-like and monooxygenase-like genes from creeping bent grass, as lateral gene transfer candidates. An in silico analysis suggested presence of the glucanase-like gene in Agrostis, Deyeuxia, and Polypogon genera, but not in other species belonging to the clade 1 of the Poeae tribe. Similarly, the monooxygenase-like gene was confined to Agrostis and Deyeuxia genera. A consistent result was obtained from PCR-based screening. The glucanase-like gene was revealed to be ubiquitously expressed in young seedlings of creeping bent grass. Although expression of the monooxygenase-like gene was suggested in plant tissues, the levels were considerably lower than those of the glucanase-like gene. A phylogenetic analysis revealed close relationships of the two genes between the corresponding genes in fungal endophyte species of the Epichloë genus, suggesting that the genes originated from the Epichloë lineage.}, }
@article {pmid34505571, year = {2021}, author = {Xavier, BB and Coppens, J and De Koster, S and Rajakani, SG and Van Goethem, S and Mzougui, S and Anantharajah, A and Lammens, C and Loens, K and Glupczynski, Y and Goossens, H and Matheeussen, V}, title = {Novel vancomycin resistance gene cluster in Enterococcus faecium ST1486, Belgium, June 2021.}, journal = {Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin}, volume = {26}, number = {36}, pages = {}, pmid = {34505571}, issn = {1560-7917}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Belgium ; *Enterococcus faecium/genetics ; Humans ; Multigene Family ; Vancomycin Resistance/genetics ; }, abstract = {We identified a novel van gene cluster in a clinical Enterococcus faecium isolate with vancomycin minimum inhibitory concentration (MIC) of 4 µg/mL. The ligase gene, vanP, was part of a van operon cluster of 4,589 bp on a putative novel integrative conjugative element located in a ca 98 kb genomic region presumed to be acquired by horizontal gene transfer from Clostridiumscidens and Roseburia sp. 499. Screening for van genes in E. faecium strains with borderline susceptibility to vancomycin is important.}, }
@article {pmid34503524, year = {2021}, author = {Boutanaev, AM and Nemchinov, LG}, title = {Genome-wide identification of endogenous viral sequences in alfalfa (Medicago sativa L.).}, journal = {Virology journal}, volume = {18}, number = {1}, pages = {185}, pmid = {34503524}, issn = {1743-422X}, mesh = {Caulimoviridae/*genetics ; Caulimovirus/*genetics ; Genome, Plant ; *Medicago sativa/genetics/virology ; }, abstract = {Endogenous viral elements (EVEs) have been for the most part described in animals and to a less extent in plants. The endogenization was proposed to contribute toward evolution of living organisms via horizontal gene transfer of novel genetic material and resultant genetic diversity. During the last two decades, several full-length and fragmented EVEs of pararetroviral and non-retroviral nature have been identified in different plant genomes, both monocots and eudicots. Prior to this work, no EVEs have been reported in alfalfa (Medicago sativa L.), the most cultivated forage legume in the world. In this study, taking advantage of the most recent developments in the field of alfalfa research, we have assessed alfalfa genome on the presence of viral-related sequences. Our analysis revealed segmented EVEs resembling two dsDNA reverse-transcribing virus species: Soybean chlorotic mottle virus (family Caulimoviridae, genus Soymovirus) and Figwort mosaic virus (family Caulimoviridae, genus Caulimovirus). The EVEs appear to be stable constituents of the host genome and in that capacity could potentially acquire functional roles in alfalfa's development and response to environmental stresses.}, }
@article {pmid34503305, year = {2021}, author = {Hass, R and von der Ohe, J and Dittmar, T}, title = {Hybrid Formation and Fusion of Cancer Cells In Vitro and In Vivo.}, journal = {Cancers}, volume = {13}, number = {17}, pages = {}, pmid = {34503305}, issn = {2072-6694}, abstract = {The generation of cancer hybrid cells by intra-tumoral cell fusion opens new avenues for tumor plasticity to develop cancer stem cells with altered properties, to escape from immune surveillance, to change metastatic behavior, and to broaden drug responsiveness/resistance. Genomic instability and chromosomal rearrangements in bi- or multinucleated aneuploid cancer hybrid cells contribute to these new functions. However, the significance of cell fusion in tumorigenesis is controversial with respect to the low frequency of cancer cell fusion events and a clonal advantage of surviving cancer hybrid cells following a post-hybrid selection process. This review highlights alternative processes of cancer hybrid cell development such as entosis, emperipolesis, cannibalism, therapy-induced polyploidization/endoreduplication, horizontal or lateral gene transfer, and focusses on the predominant mechanisms of cell fusion. Based upon new properties of cancer hybrid cells the arising clinical consequences of the subsequent tumor heterogeneity after cancer cell fusion represent a major therapeutic challenge.}, }
@article {pmid34502136, year = {2021}, author = {Darphorn, TS and Hu, Y and Koenders-van Sintanneland, BB and Brul, S and Ter Kuile, BH}, title = {Multiplication of ampC upon Exposure to a Beta-Lactam Antibiotic Results in a Transferable Transposon in Escherichia coli.}, journal = {International journal of molecular sciences}, volume = {22}, number = {17}, pages = {}, pmid = {34502136}, issn = {1422-0067}, mesh = {Amoxicillin/toxicity ; Anti-Bacterial Agents/toxicity ; *DNA Transposable Elements ; Escherichia coli ; Escherichia coli Proteins/*genetics ; Gene Transfer, Horizontal ; *beta-Lactam Resistance ; beta-Lactamases/*genetics ; }, abstract = {Plasmids play a crucial role in spreading antimicrobial resistance genes. Plasmids have many ways to incorporate various genes. By inducing amoxicillin resistance in Escherichia coli, followed by horizontal gene transfer experiments and sequencing, we show that the chromosomal beta-lactamase gene ampC is multiplied and results in an 8-13 kb contig. This contig is comparable to a transposon, showing similarities to variable regions found in environmental plasmids, and can be transferred between E. coli cells. As in eight out of nine replicate strains an almost completely identical transposon was isolated, we conclude that this process is under strict control by the cell. The single transposon that differed was shortened at both ends, but otherwise identical. The outcome of this study indicates that as a result of exposure to beta-lactam antibiotics, E. coli can form a transposon containing ampC that can subsequently be integrated into plasmids or genomes. This observation offers an explanation for the large diversity of genes in plasmids found in nature and proposes mechanisms by which the dynamics of plasmids are maintained.}, }
@article {pmid34500344, year = {2021}, author = {Lei, CW and Chen, X and Liu, SY and Li, TY and Chen, Y and Wang, HN}, title = {Clonal spread and horizontal transfer mediate dissemination of phenicol-oxazolidinone-tetracycline resistance gene poxtA in enterococci isolates from a swine farm in China.}, journal = {Veterinary microbiology}, volume = {262}, number = {}, pages = {109219}, doi = {10.1016/j.vetmic.2021.109219}, pmid = {34500344}, issn = {1873-2542}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; China ; Drug Resistance, Bacterial/genetics ; *Enterococcaceae/drug effects/genetics ; Enterococcus faecalis/drug effects/genetics ; *Enterococcus faecium/drug effects/genetics ; Farms ; *Gene Transfer, Horizontal/genetics ; *Gram-Positive Bacterial Infections/epidemiology/microbiology/veterinary ; Microbial Sensitivity Tests/veterinary ; *Oxazolidinones/pharmacology ; Swine ; *Swine Diseases/epidemiology ; *Tetracycline Resistance/genetics ; }, abstract = {The emergence of the phenicol-oxazolidinone-tetracycline resistance gene poxtA becomes a significant challenge for public health, since it confers a decreased susceptibility not only to the last resort drug linezolid, but also to florfenicol and doxycycline widely used in veterinary medicine. To determine the dissemination mechanism of poxtA in enterococci isolates from different healthy pigs in the swine farm, a total of 178 florfenicol-resistant enterococci isolates were collected from 400 fresh faecal swabs in a swine farm in China. The poxtA gene was detected in 11 (6.18 %) enterococci isolates, including 8 E. faecium, 2 E. hirae and 1 E. casseliflavus isolates. Whole genome sequencing indicated that the eight poxtA-harbouring E. faecium strains belonged to four different sequence types, including ST156 and three new STs, ST1818, ST1819 and ST1820. Five out of the 11 poxtA-positive enterococci isolates also harboured optrA gene. Moreover, E. casseliflavus strain DY31 co-harboured poxtA, optrA and cfr. Seven different poxtA-harbouring plasmids were obtained through Nanopore combined with Illumina sequencing. The poxtA-harbouring plasmids exhibited high genetic variation, six out of which belonged to rep2 plasmid of Inc18 family. The poxtA gene was flanked by IS1216E in the left and/or right ends.The optrA and cfr genes were located on different plasmids, respectively, but those genes could be co-transferred with poxtA gene into the recipient E. faecalis strain by electrotransformation. Our study highlights that both clonal spread and horizontal transfer mediated by Inc18 plasmid and IS1216E promote the dissemination of poxtA in enterococci isolates from different healthy pigs in the swine farm.}, }
@article {pmid34498042, year = {2021}, author = {Smith, JT and Andam, CP}, title = {Extensive Horizontal Gene Transfer within and between Species of Coagulase-Negative Staphylococcus.}, journal = {Genome biology and evolution}, volume = {13}, number = {9}, pages = {}, pmid = {34498042}, issn = {1759-6653}, support = {R35 GM142924/GM/NIGMS NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents ; *Coagulase/genetics/metabolism ; Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; Phylogeny ; *Staphylococcal Infections/microbiology ; Staphylococcus/genetics ; }, abstract = {Members of the gram-positive bacterial genus Staphylococcus have historically been classified into coagulase-positive Staphylococcus (CoPS) and coagulase-negative Staphylococcus (CoNS) based on the diagnostic presentation of the coagulase protein. Previous studies have noted the importance of horizontal gene transfer (HGT) and recombination in the more well-known CoPS species Staphylococcus aureus, yet little is known of the contributions of these processes in CoNS evolution. In this study, we aimed to elucidate the phylogenetic relationships, genomic characteristics, and frequencies of HGT in CoNS, which are now being recognized as major opportunistic pathogens of humans. We compiled a data set of 1,876 publicly available named CoNS genomes. These can be delineated into 55 species based on allele differences in 462 core genes and variation in accessory gene content. CoNS species are a reservoir of transferrable genes associated with resistance to diverse classes of antimicrobials. We also identified nine types of the mobile genetic element SCCmec, which carries the methicillin resistance determinant mecA. Other frequently transferred genes included those associated with resistance to heavy metals, surface-associated proteins related to virulence and biofilm formation, type VII secretion system, iron capture, recombination, and metabolic enzymes. The highest frequencies of receipt and donation of recombined DNA fragments were observed in Staphylococcus capitis, Staphylococcus caprae, Staphylococcus hominis, Staphylococcus haemolyticus, and members of the Saprophyticus species group. The variable rates of recombination and biases in transfer partners imply that certain CoNS species function as hubs of gene flow and major reservoir of genetic diversity for the entire genus.}, }
@article {pmid34494951, year = {2021}, author = {Kottara, A and Carrilero, L and Harrison, E and Hall, JPJ and Brockhurst, MA}, title = {The dilution effect limits plasmid horizontal transmission in multispecies bacterial communities.}, journal = {Microbiology (Reading, England)}, volume = {167}, number = {9}, pages = {}, pmid = {34494951}, issn = {1465-2080}, support = {BB/R006253/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R018154/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Bacteria/genetics ; Conjugation, Genetic ; *Gene Transfer, Horizontal ; Plasmids/genetics ; }, abstract = {By transferring ecologically important traits between species, plasmids drive genomic divergence and evolutionary innovation in their bacterial hosts. Bacterial communities are often diverse and contain multiple coexisting plasmids, but the dynamics of plasmids in multi-species communities are poorly understood. Here, we show, using experimental multi-species communities containing two plasmids, that bacterial diversity limits the horizontal transmission of plasmids due to the 'dilution effect'; this is an epidemiological phenomenon whereby living alongside less proficient host species reduces the expected infection risk for a focal host species. In addition, plasmid horizontal transmission was also affected by plasmid diversity, such that the rate of plasmid conjugation was reduced from co-infected host cells carrying both plasmids. In diverse microbial communities, plasmid spread may be limited by the dilution effect and plasmid-plasmid interactions, reducing the rate of horizontal transmission.}, }
@article {pmid34494862, year = {2021}, author = {Yang, X and Liu, X and Yang, C and Chan, EW and Zhang, R and Chen, S}, title = {A Conjugative IncI1 Plasmid Carrying erm(B) and blaCTX-M-104 That Mediates Resistance to Azithromycin and Cephalosporins.}, journal = {Microbiology spectrum}, volume = {9}, number = {2}, pages = {e0028621}, pmid = {34494862}, issn = {2165-0497}, mesh = {Anti-Bacterial Agents/pharmacology ; Azithromycin/*pharmacology ; Cefotaxime/*pharmacology ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/genetics ; Gene Transfer, Horizontal/genetics ; Humans ; Klebsiella Infections/drug therapy ; Klebsiella pneumoniae/*drug effects/*genetics/isolation &amp; purification ; Methyltransferases/genetics ; Microbial Sensitivity Tests ; Plasmids/*genetics ; Salmonella/genetics ; beta-Lactamases/genetics ; }, abstract = {In this study, an IncI1 plasmid encoding resistance to both cefotaxime and azithromycin was recovered from a clinical Klebsiella pneumoniae strain. The azithromycin resistance was confirmed to be mediated by the erm(B) gene. This plasmid could be readily conjugated to strains of Escherichia coli and Salmonella, promoting rapid dissemination of azithromycin- and ceftriaxone-resistance-encoding elements among Gram-negative bacterial pathogens. Transmission of this plasmid in Salmonella is of particular concern, since it could mediate expression of phenotypic resistance to azithromycin and ceftriaxone, which are the current choices for treatment of Salmonella infections. Our findings suggest a need to monitor the efficiency and pattern of transmission of this plasmid among key Gram-negative bacterial pathogens. IMPORTANCE Since the approval by the FDA of azithromycin for treatment of Salmonella infections, efforts have been made to monitor the development of resistance to azithromycin in these organisms. In this study, we report an IncI1 plasmid from a clinical K. pneumoniae strain that encodes resistance to both cefotaxime and azithromycin. This plasmid could be readily conjugated to strains of Escherichia coli and Salmonella, promoting rapid dissemination of azithromycin- and ceftriaxone-resistance-encoding elements among Gram-negative bacterial pathogens. Furthermore, data from this study confirmed for the first time the role of the erm(B) gene in mediating resistance to azithromycin in various bacterial species, particularly Salmonella.}, }
@article {pmid34492813, year = {2021}, author = {Li, ZH and Yuan, L and Geng, YK and Li, N and Sheng, GP}, title = {Evaluating the effect of gradient applied voltages on antibiotic resistance genes proliferation and biogas production in anaerobic electrochemical membrane bioreactor.}, journal = {Journal of hazardous materials}, volume = {416}, number = {}, pages = {125865}, doi = {10.1016/j.jhazmat.2021.125865}, pmid = {34492813}, issn = {1873-3336}, mesh = {Anaerobiosis ; *Anti-Bacterial Agents/pharmacology ; *Biofuels ; Bioreactors ; Cell Proliferation ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; }, abstract = {Anaerobic biological treatment technologies are one of the major hotspots of antibiotic resistance genes (ARGs). Previous studies have applied the electrochemical process to improve biogas production, however, it was challenged that high voltages might promote membrane permeability and reactive oxygen species overproduction to promote ARGs proliferation. Herein, the biogas production and ARGs proliferation in an anaerobic electrochemical membrane bioreactor (AnEMBR) were investigated at the gradient voltages of 0-0.9 V. Results show the reactor performances (average CH4 production and current generation) were distinctly improved with the increase of applied voltage, and reached the optimum at 0.9 V. However, long-term application (>30 day) of 0.9 V deteriorated the reactor performances. Meanwhile, the relative abundances of most target ARGs in the supernatant and effluent of AnEMBR at 0.9 V increased by 0.68-1.55 and 0.42-1.26 logs compared to those before applying voltage, respectively. After disconnecting the circuit, these ARGs abundances all decreased to the original level. Significant correlations between intlI and ARGs (e.g., tetA, tetQ, sulI, and sulII) were observed, indicating horizontal gene transfer may contribute to the increased ARGs. Moreover, the shift of microbial communities caused by the applied voltage enriched potential ARGs-hosts (e.g., Tolumonas), contributing to the proliferation of ARGs.}, }
@article {pmid34492012, year = {2021}, author = {Leonardi, SS and Li, FJ and Chee, MS and Yason, JA and Tay, HY and Chen, JY and Koh, EY and He, CY and Tan, KS}, title = {Characterisation of novel functionality within the Blastocystis tryptophanase gene.}, journal = {PLoS neglected tropical diseases}, volume = {15}, number = {9}, pages = {e0009730}, pmid = {34492012}, issn = {1935-2735}, mesh = {Amino Acid Sequence ; Bacteria/classification/enzymology/genetics ; Bacterial Proteins/chemistry/genetics/metabolism ; Blastocystis/*enzymology/genetics/metabolism ; Gene Transfer, Horizontal ; Humans ; Indoles/metabolism ; Kinetics ; Phylogeny ; Protozoan Proteins/chemistry/genetics/*metabolism ; Sequence Alignment ; Tryptophan/metabolism ; Tryptophanase/chemistry/genetics/*metabolism ; }, abstract = {In recent years, the human gut microbiome has been recognised to play a pivotal role in the health of the host. Intestinal homeostasis relies on this intricate and complex relationship between the gut microbiota and the human host. While much effort and attention has been placed on the characterization of the organisms that inhabit the gut microbiome, the complex molecular cross-talk between the microbiota could also exert an effect on gastrointestinal conditions. Blastocystis is a single-cell eukaryotic parasite of emerging interest, as its beneficial or pathogenic role in the microbiota has been a subject of contention even to-date. In this study, we assessed the function of the Blastocystis tryptophanase gene (BhTnaA), which was acquired by horizontal gene transfer and likely to be of bacterial origin within Blastocystis. Bioinformatic analysis and phylogenetic reconstruction revealed distinct divergence of BhTnaA versus known bacterial homologs. Despite sharing high homology with the E. coli tryptophanase gene, we show that Blastocystis does not readily convert tryptophan into indole. Instead, BhTnaA preferentially catalyzes the conversion of indole to tryptophan. We also show a direct link between E. coli and Blastocystis tryptophan metabolism: In the presence of E. coli, Blastocystis ST7 is less able to metabolise indole to tryptophan. This study examines the potential for functional variation in horizontally-acquired genes relative to their canonical counterparts, and identifies Blastocystis as a possible producer of tryptophan within the gut.}, }
@article {pmid34489883, year = {2021}, author = {Agarwal, G and Choudhary, D and Stice, SP and Myers, BK and Gitaitis, RD and Venter, SN and Kvitko, BH and Dutta, B}, title = {Pan-Genome-Wide Analysis of Pantoea ananatis Identified Genes Linked to Pathogenicity in Onion.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {684756}, pmid = {34489883}, issn = {1664-302X}, abstract = {Pantoea ananatis, a gram negative and facultative anaerobic bacterium is a member of a Pantoea spp. complex that causes center rot of onion, which significantly affects onion yield and quality. This pathogen does not have typical virulence factors like type II or type III secretion systems but appears to require a biosynthetic gene-cluster, HiVir/PASVIL (located chromosomally comprised of 14 genes), for a phosphonate secondary metabolite, and the 'alt' gene cluster (located in plasmid and comprised of 11 genes) that aids in bacterial colonization in onion bulbs by imparting tolerance to thiosulfinates. We conducted a deep pan-genome-wide association study (pan-GWAS) to predict additional genes associated with pathogenicity in P. ananatis using a panel of diverse strains (n = 81). We utilized a red-onion scale necrosis assay as an indicator of pathogenicity. Based on this assay, we differentiated pathogenic (n = 51)- vs. non-pathogenic (n = 30)-strains phenotypically. Pan-genome analysis revealed a large core genome of 3,153 genes and a flexible accessory genome. Pan-GWAS using the presence and absence variants (PAVs) predicted 42 genes, including 14 from the previously identified HiVir/PASVIL cluster associated with pathogenicity, and 28 novel genes that were not previously associated with pathogenicity in onion. Of the 28 novel genes identified, eight have annotated functions of site-specific tyrosine kinase, N-acetylmuramoyl-L-alanine amidase, conjugal transfer, and HTH-type transcriptional regulator. The remaining 20 genes are currently hypothetical. Further, a core-genome SNPs-based phylogeny and horizontal gene transfer (HGT) studies were also conducted to assess the extent of lateral gene transfer among diverse P. ananatis strains. Phylogenetic analysis based on PAVs and whole genome multi locus sequence typing (wgMLST) rather than core-genome SNPs distinguished red-scale necrosis inducing (pathogenic) strains from non-scale necrosis inducing (non-pathogenic) strains of P. ananatis. A total of 1182 HGT events including the HiVir/PASVIL and alt cluster genes were identified. These events could be regarded as a major contributing factor to the diversification, niche-adaptation and potential acquisition of pathogenicity/virulence genes in P. ananatis.}, }
@article {pmid34489599, year = {2021}, author = {Amorim, MJB and Gansemans, Y and Gomes, SIL and Van Nieuwerburgh, F and Scott-Fordsmand, JJ}, title = {Annelid genomes: Enchytraeus crypticus, a soil model for the innate (and primed) immune system.}, journal = {Lab animal}, volume = {50}, number = {10}, pages = {285-294}, pmid = {34489599}, issn = {1548-4475}, mesh = {Animals ; *COVID-19 ; Humans ; Immune System ; *Oligochaeta/genetics ; SARS-CoV-2 ; Soil ; }, abstract = {Enchytraeids (Annelida) are soil invertebrates with worldwide distribution that have served as ecotoxicology models for over 20 years. We present the first high-quality reference genome of Enchytraeus crypticus, assembled from a combination of Pacific Bioscience single-molecule real-time and Illumina sequencing platforms as a 525.2 Mbp genome (910 gapless scaffolds and 18,452 genes). We highlight isopenicillin, acquired by horizontal gene transfer and conferring antibiotic function. Significant gene family expansions associated with regeneration (long interspersed nuclear elements), the innate immune system (tripartite motif-containing protein) and response to stress (cytochrome P450) were identified. The ACE (Angiotensin-converting enzyme) - a homolog of ACE2, which is involved in the coronavirus SARS-CoV-2 cell entry - is also present in E. crypticus. There is an obvious potential of using E. crypticus as a model to study interactions between regeneration, the innate immune system and aging-dependent decline.}, }
@article {pmid34484154, year = {2021}, author = {Deng, A and Sun, Z and Wang, T and Cui, D and Li, L and Liu, S and Huang, F and Wen, T}, title = {Simultaneous Multiplex Genome Engineering via Accelerated Natural Transformation in Bacillus subtilis.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {714449}, pmid = {34484154}, issn = {1664-302X}, abstract = {Multiplex engineering at the scale of whole genomes has become increasingly important for synthetic biology and biotechnology applications. Although several methods have been reported for engineering microbe genomes, their use is limited by their complex procedures using multi-cycle transformations. Natural transformation, involving in species evolution by horizontal gene transfer in many organisms, indicates its potential as a genetic tool. Here, we aimed to develop simultaneous multiplex genome engineering (SMGE) for the simple, rapid, and efficient design of bacterial genomes via one-step of natural transformation in Bacillus subtilis. The transformed DNA, competency factors, and recombinases were adapted to improved co-editing frequencies above 27-fold. Single to octuplet variants with genetic diversity were simultaneously generated using all-in-one vectors harboring multi-gene cassettes. To demonstrate its potential application, the tyrosine biosynthesis pathway was further optimized for producing commercially important resveratrol by high-throughput screening of variant pool in B. subtilis. SMGE represents an accelerated evolution platform that generates diverse multiplex mutations for large-scale genetic engineering and synthetic biology in B. subtilis.}, }
@article {pmid34482446, year = {2021}, author = {Gross, E and van Iersel, L and Janssen, R and Jones, M and Long, C and Murakami, Y}, title = {Distinguishing level-1 phylogenetic networks on the basis of data generated by Markov processes.}, journal = {Journal of mathematical biology}, volume = {83}, number = {3}, pages = {32}, pmid = {34482446}, issn = {1432-1416}, mesh = {Algorithms ; *Evolution, Molecular ; Hybridization, Genetic ; Markov Chains ; *Models, Genetic ; Phylogeny ; }, abstract = {Phylogenetic networks can represent evolutionary events that cannot be described by phylogenetic trees. These networks are able to incorporate reticulate evolutionary events such as hybridization, introgression, and lateral gene transfer. Recently, network-based Markov models of DNA sequence evolution have been introduced along with model-based methods for reconstructing phylogenetic networks. For these methods to be consistent, the network parameter needs to be identifiable from data generated under the model. Here, we show that the semi-directed network parameter of a triangle-free, level-1 network model with any fixed number of reticulation vertices is generically identifiable under the Jukes-Cantor, Kimura 2-parameter, or Kimura 3-parameter constraints.}, }
@article {pmid34482079, year = {2022}, author = {Liu, Y and Gao, J and Wang, Y and Duan, W and Liu, J and Zhang, Y and Zhang, H and Zhao, M}, title = {The removal of antibiotic resistant bacteria and genes and inhibition of the horizontal gene transfer by contrastive research on sulfidated nanoscale zerovalent iron activating peroxymonosulfate or peroxydisulfate.}, journal = {Journal of hazardous materials}, volume = {423}, number = {Pt A}, pages = {126866}, doi = {10.1016/j.jhazmat.2021.126866}, pmid = {34482079}, issn = {1873-3336}, mesh = {*Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Anti-Bacterial Agents/pharmacology ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; *Iron ; Peroxides ; }, abstract = {Antibiotic resistant bacteria (ARB) and the antibiotic resistance genes (ARGs) dissemination via plasmid-mediated conjugation have attracted considerable attentions. In this research, sulfidated nanoscale zerovalent iron (S-nZVI)/peroxymonosulfate (PMS) and S-nZVI/peroxydisulfate (PDS) process were investigated to inactivate ARB (Escherichia coli DH5α with RP4 plasmid, Pseudomonas. HLS-6 contains sul1 and intI1 on genome DNA sequence). S-nZVI/PMS system showed higher efficiency than S-nZVI/PDS on ARB inactivation. Thus, the optimal condition 28 mg/L S-nZVI coupled with 153.7 mg/L (0.5 mM) PMS was applied to remove both intracellular ARGs (iARGs) and ARB. The oxidative damage of ARB cell was systemically studied by cell viability, intracellular Mg[2+] levels, the changes of extracellular and internal structure, integrity of cell walls and membranes and enzymatic activities. S-nZVI/PMS effectively inactivated ARB (~7.32 log) within 15 min. These effects were greatly higher than those achieved individually. Moreover, removal efficiencies of iARGs sul1, intI1 and tetA were 1.52, 1.79 and 1.56 log, respectively. These results revealed that S-nZVI and PMS have a synergistic effect against ARB and iARGs. The regrowth assays illustrated that the ARB were effectively inactivated. By verifying the inhibitory impacts of S-nZVI/PMS treatment on conjugation transfer, this work highlights a promising alternative technique for inhibiting the horizontal gene transfer.}, }
@article {pmid34479645, year = {2021}, author = {Zhou, K and Xu, Y and Zhang, R and Qian, PY}, title = {Arms race in a cell: genomic, transcriptomic, and proteomic insights into intracellular phage-bacteria interplay in deep-sea snail holobionts.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {182}, pmid = {34479645}, issn = {2049-2618}, mesh = {Animals ; Bacteria/genetics ; *Bacteriophages/genetics ; Genomics ; Proteomics ; Snails ; Transcriptome/genetics ; }, abstract = {BACKGROUND: Deep-sea animals in hydrothermal vents often form endosymbioses with chemosynthetic bacteria. Endosymbionts serve essential biochemical and ecological functions, but the prokaryotic viruses (phages) that determine their fate are unknown.<br><br>RESULTS: We conducted metagenomic analysis of a deep-sea vent snail. We assembled four genome bins for Caudovirales phages that had developed dual endosymbiosis with sulphur-oxidising bacteria (SOB) and methane-oxidising bacteria (MOB). Clustered regularly interspaced short palindromic repeat (CRISPR) spacer mapping, genome comparison, and transcriptomic profiling revealed that phages Bin1, Bin2, and Bin4 infected SOB and MOB. The observation of prophages in the snail endosymbionts and expression of the phage integrase gene suggested the presence of lysogenic infection, and the expression of phage structural protein and lysozyme genes indicated active lytic infection. Furthermore, SOB and MOB appear to employ adaptive CRISPR-Cas systems to target phage DNA. Additional expressed defence systems, such as innate restriction-modification systems and dormancy-inducing toxin-antitoxin systems, may co-function and form multiple lines for anti-viral defence. To counter host defence, phages Bin1, Bin2, and Bin3 appear to have evolved anti-restriction mechanisms and expressed methyltransferase genes that potentially counterbalance host restriction activity. In addition, the high-level expression of the auxiliary metabolic genes narGH, which encode nitrate reductase subunits, may promote ATP production, thereby benefiting phage DNA packaging for replication.<br><br>CONCLUSIONS: This study provides new insights into phage-bacteria interplay in intracellular environments of a deep-sea vent snail. Video Abstract.}, }
@article {pmid34479643, year = {2021}, author = {Lipworth, S and Vihta, KD and Chau, K and Barker, L and George, S and Kavanagh, J and Davies, T and Vaughan, A and Andersson, M and Jeffery, K and Oakley, S and Morgan, M and Hopkins, S and Peto, TEA and Crook, DW and Walker, AS and Stoesser, N}, title = {Ten-year longitudinal molecular epidemiology study of Escherichia coli and Klebsiella species bloodstream infections in Oxfordshire, UK.}, journal = {Genome medicine}, volume = {13}, number = {1}, pages = {144}, pmid = {34479643}, issn = {1756-994X}, support = {MR/T001151/1/MRC_/Medical Research Council/United Kingdom ; NIHR200915/DH_/Department of Health/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 203141/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; MRF_MRF-145-0004-TPG-AVISO/MRF/MRF/United Kingdom ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteremia/epidemiology ; Drug Resistance, Multiple, Bacterial ; Escherichia coli/*genetics ; Escherichia coli Infections/*epidemiology ; Humans ; Incidence ; Klebsiella/*genetics ; Klebsiella Infections/*epidemiology ; Klebsiella pneumoniae/genetics ; Longitudinal Studies ; *Molecular Epidemiology ; Plasmids ; Sepsis/*epidemiology/microbiology ; United Kingdom/epidemiology ; Virulence/genetics ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: The incidence of Gram-negative bloodstream infections (BSIs), predominantly caused by Escherichia coli and Klebsiella species, continues to increase; however, the causes of this are unclear and effective interventions are therefore hard to design.<br><br>METHODS: In this study, we sequenced 3468 unselected isolates over a decade in Oxfordshire (UK) and linked this data to routinely collected electronic healthcare records and mandatory surveillance reports. We annotated genomes for clinically relevant genes, contrasting the distribution of these within and between species, and compared incidence trends over time using stacked negative binomial regression.<br><br>RESULTS: We demonstrate that the observed increases in E. coli incidence were not driven by the success of one or more sequence types (STs); instead, four STs continue to dominate a stable population structure, with no evidence of adaptation to hospital/community settings. Conversely in Klebsiella spp., most infections are caused by sporadic STs with the exception of a local drug-resistant outbreak strain (ST490). Virulence elements are highly structured by ST in E. coli but not Klebsiella spp. where they occur in a diverse spectrum of STs and equally across healthcare and community settings. Most clinically hypervirulent (i.e. community-onset) Klebsiella BSIs have no known acquired virulence loci. Finally, we demonstrate a diverse but largely genus-restricted mobilome with close associations between antimicrobial resistance (AMR) genes and insertion sequences but not typically specific plasmid replicon types, consistent with the dissemination of AMR genes being highly contingent on smaller mobile genetic elements (MGEs).<br><br>CONCLUSIONS: Our large genomic study highlights distinct differences in the molecular epidemiology of E. coli and Klebsiella BSIs and suggests that no single specific pathogen genetic factors (e.g. AMR/virulence genes/sequence type) are likely contributing to the increasing incidence of BSI overall, that association with AMR genes in E. coli is a contributor to the increasing number of E. coli BSIs, and that more attention should be given to AMR gene associations with non-plasmid MGEs to try and understand horizontal gene transfer networks.}, }
@article {pmid34478440, year = {2021}, author = {Rabier, CE and Berry, V and Stoltz, M and Santos, JD and Wang, W and Glaszmann, JC and Pardi, F and Scornavacca, C}, title = {On the inference of complex phylogenetic networks by Markov Chain Monte-Carlo.}, journal = {PLoS computational biology}, volume = {17}, number = {9}, pages = {e1008380}, pmid = {34478440}, issn = {1553-7358}, mesh = {Algorithms ; Bayes Theorem ; Computational Biology/methods ; Evolution, Molecular ; Genes, Plant ; Likelihood Functions ; *Markov Chains ; *Monte Carlo Method ; Oryza/classification/genetics ; *Phylogeny ; }, abstract = {For various species, high quality sequences and complete genomes are nowadays available for many individuals. This makes data analysis challenging, as methods need not only to be accurate, but also time efficient given the tremendous amount of data to process. In this article, we introduce an efficient method to infer the evolutionary history of individuals under the multispecies coalescent model in networks (MSNC). Phylogenetic networks are an extension of phylogenetic trees that can contain reticulate nodes, which allow to model complex biological events such as horizontal gene transfer, hybridization and introgression. We present a novel way to compute the likelihood of biallelic markers sampled along genomes whose evolution involved such events. This likelihood computation is at the heart of a Bayesian network inference method called SnappNet, as it extends the Snapp method inferring evolutionary trees under the multispecies coalescent model, to networks. SnappNet is available as a package of the well-known beast 2 software. Recently, the MCMC_BiMarkers method, implemented in PhyloNet, also extended Snapp to networks. Both methods take biallelic markers as input, rely on the same model of evolution and sample networks in a Bayesian framework, though using different methods for computing priors. However, SnappNet relies on algorithms that are exponentially more time-efficient on non-trivial networks. Using simulations, we compare performances of SnappNet and MCMC_BiMarkers. We show that both methods enjoy similar abilities to recover simple networks, but SnappNet is more accurate than MCMC_BiMarkers on more complex network scenarios. Also, on complex networks, SnappNet is found to be extremely faster than MCMC_BiMarkers in terms of time required for the likelihood computation. We finally illustrate SnappNet performances on a rice data set. SnappNet infers a scenario that is consistent with previous results and provides additional understanding of rice evolution.}, }
@article {pmid34470945, year = {2021}, author = {Ward, LM and Li-Hau, F and Kakegawa, T and McGlynn, SE}, title = {Complex History of Aerobic Respiration and Phototrophy in the Chloroflexota Class Anaerolineae Revealed by High-Quality Draft Genome of Ca. Roseilinea mizusawaensis AA3_104.}, journal = {Microbes and environments}, volume = {36}, number = {3}, pages = {}, pmid = {34470945}, issn = {1347-4405}, mesh = {Base Sequence ; Chloroflexi/classification/*genetics/isolation &amp; purification/*metabolism ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Molecular Sequence Data ; Phototrophic Processes ; Phylogeny ; }, abstract = {Roseilinea is a novel lineage of Chloroflexota known only from incomplete metagenome-assembled genomes (MAGs) and preliminary enrichments. Roseilinea is notable for appearing capable of anoxygenic photoheterotrophy despite being only distantly related to well-known phototrophs in the Chloroflexia class such as Chloroflexus and Roseiflexus. Here, we present a high-quality MAG of a member of Roseilinea, improving our understanding of the metabolic capacity and phylogeny of this genus, and resolving the multiple instances of horizontal gene transfer that have led to its metabolic potential. These data allow us to propose a candidate family for these organisms, Roseilineaceae, within the Anaerolineae class.}, }
@article {pmid34468747, year = {2021}, author = {Zou, Y and Bozhkov, PV}, title = {Chlamydomonas proteases: classification, phylogeny, and molecular mechanisms.}, journal = {Journal of experimental botany}, volume = {72}, number = {22}, pages = {7680-7693}, pmid = {34468747}, issn = {1460-2431}, mesh = {*Arabidopsis ; *Chlamydomonas/genetics ; *Chlamydomonas reinhardtii ; Peptide Hydrolases/genetics ; Phylogeny ; }, abstract = {Proteases can regulate myriad biochemical pathways by digesting or processing target proteins. While up to 3% of eukaryotic genes encode proteases, only a tiny fraction of proteases are mechanistically understood. Furthermore, most of the current knowledge about proteases is derived from studies of a few model organisms, including Arabidopsis thaliana in the case of plants. Proteases in other plant model systems are largely unexplored territory, limiting our mechanistic comprehension of post-translational regulation in plants and hampering integrated understanding of how proteolysis evolved. We argue that the unicellular green alga Chlamydomonas reinhardtii has a number of technical and biological advantages for systematic studies of proteases, including reduced complexity of many protease families and ease of cell phenotyping. With this end in view, we share a genome-wide inventory of proteolytic enzymes in Chlamydomonas, compare the protease degradomes of Chlamydomonas and Arabidopsis, and consider the phylogenetic relatedness of Chlamydomonas proteases to major taxonomic groups. Finally, we summarize the current knowledge of the biochemical regulation and physiological roles of proteases in this algal model. We anticipate that our survey will promote and streamline future research on Chlamydomonas proteases, generating new insights into proteolytic mechanisms and the evolution of digestive and limited proteolysis.}, }
@article {pmid34468734, year = {2021}, author = {Takenaka, S and Kawashima, T and Arita, M}, title = {A sugar utilization phenotype contributes to the formation of genetic exchange communities in lactic acid bacteria.}, journal = {FEMS microbiology letters}, volume = {368}, number = {17}, pages = {}, pmid = {34468734}, issn = {1574-6968}, mesh = {*Gene Transfer, Horizontal ; *Lactobacillaceae/genetics ; *Lactobacillales/genetics ; Phenotype ; Sugars/metabolism ; }, abstract = {In prokaryotes, a major contributor to genomic evolution is the exchange of genes via horizontal gene transfer (HGT). Areas with a high density of HGT networks are defined as genetic exchange communities (GECs). Although some phenotypes associated with specific ecological niches are linked to GECs, little is known about the phenotypic influences on HGT in bacterial groups within a taxonomic family. Thanks to the published genome sequences and phenotype data of lactic acid bacteria (LAB), it is now possible to obtain more detailed information about the phenotypes that affect GECs. Here, we have investigated the relationship between HGT and internal and external environmental factors for 178 strains from 24 genera in the Lactobacillaceae family. We found a significant correlation between strains with high utilization of sugars and HGT bias. The result suggests that the phenotype of the utilization of a variety of sugars is key to the construction of GECs in this family. This feature is consistent with the fact that the Lactobacillaceae family contributes to the production of a wide variety of fermented foods by sharing niches such as those in vegetables, dairy products and brewing-related environments. This result provides the first evidence that phenotypes associated with ecological niches contribute to form GECs in the LAB family.}, }
@article {pmid34468190, year = {2021}, author = {Liu, X and Li, R and Dong, N and Ye, L and Chan, EW and Chen, S}, title = {Complete Genetic Analysis of Plasmids Carried by Two Nonclonal blaNDM-5- and mcr-1-Bearing Escherichia coli Strains: Insight into Plasmid Transmission among Foodborne Bacteria.}, journal = {Microbiology spectrum}, volume = {9}, number = {2}, pages = {e0021721}, pmid = {34468190}, issn = {2165-0497}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Carbapenems/pharmacology ; Chickens/microbiology ; Colistin/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Escherichia coli/*drug effects/*genetics ; Escherichia coli Infections/microbiology ; Escherichia coli Proteins/*genetics ; Foodborne Diseases/*microbiology ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/genetics ; Humans ; Meat/microbiology ; Microbial Sensitivity Tests ; Plasmids/*genetics ; Whole Genome Sequencing ; beta-Lactamases/*genetics ; }, abstract = {Our objective was to characterize the genetic features of plasmids harbored by two genetically related, MCR-1 and NDM-5-producing Escherichia coli strains recovered from a chicken meat sample. The genetic profiles of all plasmids harbored by the two test strains, namely, 1106 and 1107, were determined by whole-genome sequencing, S1-pulsed-field gel electrophoresis (PFGE), Southern hybridization, and bioinformatics analysis. The transferability of plasmids harbored by the two strains was assessed by filter mating assay. Strains 1106 and 1107 were resistant to almost all the antibiotics, including colistin and fosfomycin, but remained susceptible to amikacin and tigecycline. The plasmids of p1107-NDM-5 and p1106-NDM-5 both contain a class I integron which lacks the ISAba125 element. The backbone of p1106-IncFII exhibited a high degree of similarity with that of p1106-NDM-5 and p1107-NDM-5, implying that events of plasmid fusion and resolution were involved in the formation of the two plasmids. The plasmids p1106-IncHI2MCR and p1107-IncHI2MCR belong to an IncHI2 replicon type, with three copies of ISApl1 being observed in p1106-IncHI2MCR, implying that the mcr-1 gene was transferable among bacteria that reside in the same food matrix. In this study, p1106-IncFIB, p1107-99K, p1107-111K, and p1107-118K were all found to be phage-like plasmids, with p1106-IncFIB and p1107-118K containing several virulence genes, including iroBCDEN, iucABCD, sitABCD, hlyF, and iss. Surprisingly, resistance genes such as aph(3')-Ia, sul3, and aac(3')-IId could also be found in p1107-118K, but resistance genes were not detected in other phage-like plasmids. In conclusion, enhanced surveillance is required to monitor and control the dissemination of various resistance determinants among foodborne pathogens. IMPORTANCE Carbapenem and colistin are last-resort antibiotics used to treat serious clinical infections caused by multidrug-resistant (MDR) bacterial pathogens. Plasmids encoding resistance to carbapenems and colistin have been reported in clinical pathogens in recent years, and yet few studies reported cocarriage of mcr and blaNDM genes in Escherichia coli strains of food origin. How plasmids encoding these two important resistance determinants are being evolved and transmitted in bacterial pathogens is not well understood. In this study, we investigated the genetic features of plasmids harbored by two nonclonal, mcr-1- and blaNDM-5-bearing E. coli strains (1106 and 1107) recovered from a fresh chicken meat sample to understand and provide evidence of the level and dynamics of MDR plasmid transmission. Our data confirmed that active plasmid fusion and resolution events were involved in the formation of plasmids that harbor multiple resistance genes, which provide insights into the further control of plasmid evolution in bacterial pathogens.}, }
@article {pmid34468183, year = {2021}, author = {Fujita-Yamaguchi, Y and Muramatsu, H and Tapia, A and Bagramyan, K and Desai, M and Takehana, Y and Igarashi, M and Yamaguchi, Y and Kalkum, M}, title = {Proteolytic Processing, Maturation, and Unique Synteny of the Streptomyces Hemagglutinin SHA.}, journal = {Microbiology spectrum}, volume = {9}, number = {2}, pages = {e0076621}, pmid = {34468183}, issn = {2165-0497}, mesh = {Binding Sites ; Chromatography, Liquid ; Hemagglutinins/genetics/*metabolism ; Humans ; Lectins/metabolism ; Polysaccharides ; RNA, Ribosomal, 16S ; Receptors, Cell Surface ; Rhamnose/genetics/metabolism ; Streptomyces/genetics/*metabolism ; *Synteny ; Tandem Mass Spectrometry ; }, abstract = {SHA is an l-rhamnose- and d-galactose-binding lectin that agglutinates human group B erythrocytes and was first purified almost 50 years ago. Although the original SHA-producing Streptomyces strain was lost, the primary structure of SHA was more recently solved by mass spectrometry of the archived protein, which matched it to a similar sequence in the Streptomyces lavendulae genome. Using genomic and protein biochemical analyses, this study aimed to identify SHA-secreting Streptomyces strains to further investigate the expression and binding activities of these putative proteins. Of 67 strains genetically related to S. lavendulae, 17 secreted pro-SHAs in culture. Seven SHA homologues were purified to homogeneity and then subjected to liquid chromatography-high-resolution multistage mass spectrometry (LC-MS/MS) and hemagglutination (HA) assays. Processing of pro-SHAs occurred during and after purification, indicating that associated proteases converted pro-SHAs into mature SHAs with molecular masses and HA activities similar to that of the archived SHA. Previously, the SHA monomer was shown to have two carbohydrate binding sites. The present study, however, found no HA activity in pro-SHAs, suggesting that pro-SHAs have only one binding site. Genetically, the SHA gene resides in conserved syntenic regions. The published genomes of 1,234 Streptomyces strains were analyzed, revealing 18 strains with SHA genes, 16 of which localized to a unique syntenic region. The SHA syntenic region consists of ∼17 open reading frames (ORFs) and is specific to S. lavendulae-related strains. Notably, a lipoprotein gene excludes SHA from the synteny in some strains, suggesting that horizontal gene transfer events during the course of evolution shaped the distribution of SHA genes. IMPORTANCE Lectins are extremely useful molecules for the study of glycans and carbohydrates. Here, we show that homologous genes encoding the l-rhamnose- and d-galactose-binding lectins, SHAs, are present in multiple bacterial strains, genetically related to Streptomyces lavendulae. SHA genes are expressed as precursor pro-SHA proteins that are truncated and mature into fully active lectins with two carbohydrate binding sites, which exhibit hemagglutination activity for type B red blood cells. The SHA gene is located within a conserved syntenic region, hinting at specific but yet-to-be-discovered biological roles of this carbohydrate-binding protein for its soil-dwelling microbial producer.}, }
@article {pmid34465899, year = {2022}, author = {Yu, Z and Wang, Y and Henderson, IR and Guo, J}, title = {Artificial sweeteners stimulate horizontal transfer of extracellular antibiotic resistance genes through natural transformation.}, journal = {The ISME journal}, volume = {16}, number = {2}, pages = {543-554}, pmid = {34465899}, issn = {1751-7370}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial ; Gene Transfer, Horizontal ; Mice ; Plasmids ; *Sweetening Agents/pharmacology ; }, abstract = {Antimicrobial resistance has emerged as a global threat to human health. Natural transformation is an important pathway for horizontal gene transfer, which facilitates the dissemination of antibiotic resistance genes (ARGs) among bacteria. Although it is suspected that artificial sweeteners could exert antimicrobial effects, little is known whether artificial sweeteners would also affect horizontal transfer of ARGs via transformation. Here we demonstrate that four commonly used artificial sweeteners (saccharin, sucralose, aspartame, and acesulfame potassium) promote transfer of ARGs via natural transformation in Acinetobacter baylyi ADP1, a model organism for studying competence and transformation. Such phenomenon was also found in a Gram-positive human pathogen Bacillus subtilis and mice faecal microbiome. We reveal that exposure to these sweeteners increases cell envelope permeability and results in an upregulation of genes encoding DNA uptake and translocation (Com) machinery. In addition, we find that artificial sweeteners induce an increase in plasmid persistence in transformants. We propose a mathematical model established to predict the long-term effects on transformation dynamics under exposure to these sweeteners. Collectively, our findings offer insights into natural transformation promoted by artificial sweeteners and highlight the need to evaluate these environmental contaminants for their antibiotic-like side effects.}, }
@article {pmid34461887, year = {2021}, author = {Yuan, D and Li, S and Shang, Z and Wan, M and Lin, Y and Zhang, Y and Feng, Y and Xu, L and Xiao, L}, title = {Genus-level evolutionary relationships of FAR proteins reflect the diversity of lifestyles of free-living and parasitic nematodes.}, journal = {BMC biology}, volume = {19}, number = {1}, pages = {178}, pmid = {34461887}, issn = {1741-7007}, mesh = {Animals ; Cattle ; Genomics ; Humans ; Life Style ; Mice ; *Nematoda/genetics ; Phylogeny ; Plants ; }, abstract = {BACKGROUND: Nematodes are a widespread and diverse group comprising free-living and parasitic species, some of which have major detrimental effects on crops, animals, and human health. Genomic comparisons of nematodes may help reveal the genetic bases for the evolution of parasitic lifestyles. Fatty acid and retinol-binding proteins (FARs) are thought to be unique to nematodes and play essential roles in their development, reproduction, infection, and possibly parasitism through promoting the uptake, transport, and distribution of lipid and retinol. However, the evolution of FAR family proteins across the phylum Nematoda remains elusive.<br><br>RESULTS: We report here the evolutionary relationship of the FAR gene family across nematodes. No FAR was found in Trichocephalida species and Romanomermis culicivorax from Clade I, and FAR could be found in species from Clades III, IV, and V. FAR proteins are conserved in Clade III species and separated into three clusters. Tandem duplications and high divergence events lead to variable richness and low homology of FARs in Steinernema of Clade IVa, Strongyloides of Clade IVb, and intestinal parasitic nematodes from Clades Vc and Ve. Moreover, different richness and sequence variations of FARs in pine wood, root-knot, stem, and cyst nematodes might be determined by reproduction mode or parasitism. However, murine lungworm Angiostrongylus and bovine lungworm Dictyocaulus viviparus from Clade Vd have only 3-4 orthologs of FAR. RNA-seq data showed that far genes, especially far-1 and far-2, were highly expressed in most nematodes. Angiostrongylus cantonensis FAR-1 and FAR-3 have low sequence homology and distinct ligand-binding properties, leading to differences in the cavity volume of proteins. These data indicate that FAR proteins diverged early and experienced low selective pressure to form genus-level diversity. The far genes are present in endophyte or root-colonized bacteria of Streptomyces, Kitasatospora sp., Bacillus subtilis, and Lysobacter, suggesting that bacterial far genes might be derived from plant-parasitic nematodes by horizontal gene transfer.<br><br>CONCLUSIONS: Data from these comparative analyses have provided insights into genus-level diversity of FAR proteins in the phylum Nematoda. FAR diversification provides a glimpse into the complicated evolution history across free-living and parasitic nematodes.}, }
@article {pmid34461310, year = {2021}, author = {Rohatgi, A and Gupta, P}, title = {Natural and synthetic plant compounds as anti-biofilm agents against Escherichia coli O157:H7 biofilm.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {95}, number = {}, pages = {105055}, doi = {10.1016/j.meegid.2021.105055}, pmid = {34461310}, issn = {1567-7257}, mesh = {Anti-Bacterial Agents/chemistry/*pharmacology ; Biofilms/*drug effects ; Escherichia coli Infections/*drug therapy ; Escherichia coli O157/*drug effects/physiology ; Humans ; Phytochemicals/chemistry/*pharmacology ; }, abstract = {Escherichia coli is a common gram-negative bacterium found in the gut and intestinal tract of warm-blooded animals including humans. An evolved seropathotype E. coli O157:H7 (STEC) came into existence in 1982, since then it has been evolved as a stronger and more robust drug-resistant pathotype of E. coli. This drug resistance is due to horizontal gene transfer, natural gene evolution for survival, and most of the cases due to the ability of STEC to switch to the biofilm growth mode from planktonic lifestyle. During the growth in biofilm mode, Escherichia coli O157:H7 opts more robust ability to grow in adverse environments i.e., in presence of antibiotics and other antimicrobial chemicals. Due to the biofilm matrix, the microbial community acquires drug resistance. This makes the treatment of diseases caused by E. coli O157:H7 a complex challenge. To address the illnesses caused by this biofilm-forming pathogen, there are several possible strategies such as antibiotic therapies, synthetic antimicrobial chemicals, adjunct therapy of synergistic effect of multiple drugs, and more importantly plant originated compounds as a new anti-biofilm candidate. The present review summarizes various phytochemicals and their derivatives reported in the last decade mostly to eliminate the biofilm of STEC. The review will progressively reveal the antibiofilm mechanism of the phytochemicals against STEC and to be a potential candidate for the development of the future antibacterial drugs to STEC induced infections.}, }
@article {pmid34452802, year = {2021}, author = {Watson, AK and Lopez, P and Bapteste, E}, title = {Retracing lineage history: time to emphasize genetic turnover.}, journal = {Trends in microbiology}, volume = {29}, number = {11}, pages = {957-958}, doi = {10.1016/j.tim.2021.08.001}, pmid = {34452802}, issn = {1878-4380}, mesh = {*Evolution, Molecular ; *Gene Transfer, Horizontal ; Models, Genetic ; Phylogeny ; }, }
@article {pmid34450656, year = {2021}, author = {Verster, KI and Tarnopol, RL and Akalu, SM and Whiteman, NK}, title = {Horizontal Transfer of Microbial Toxin Genes to Gall Midge Genomes.}, journal = {Genome biology and evolution}, volume = {13}, number = {9}, pages = {}, pmid = {34450656}, issn = {1759-6653}, support = {R35 GM119816/GM/NIGMS NIH HHS/United States ; T32 GM132022/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Aphids/genetics ; *Diptera/genetics ; Gene Transfer, Horizontal ; Genome ; Phylogeny ; }, abstract = {A growing body of evidence has underscored the role of horizontal gene transfer (HGT) in animal evolution. Previously, we discovered the horizontal transfer of the gene encoding the eukaryotic genotoxin cytolethal distending toxin B (cdtB) from the pea aphid Acyrthosiphon pisum secondary endosymbiont (APSE) phages to drosophilid and aphid nuclear genomes. Here, we report cdtB in the nuclear genome of the gall-forming "swede midge" Contarinia nasturtii (Diptera: Cecidomyiidae) via HGT. We searched all available gall midge genome sequences for evidence of APSE-to-insect HGT events and found five toxin genes (aip56, cdtB, lysozyme, rhs, and sltxB) transferred horizontally to cecidomyiid nuclear genomes. Surprisingly, phylogenetic analyses of HGT candidates indicated APSE phages were often not the ancestral donor lineage of the toxin gene to cecidomyiids. We used a phylogenetic signal statistic to test a transfer-by-proximity hypothesis for animal HGT, which suggested that microbe-to-insect HGT was more likely between taxa that share environments than those from different environments. Many of the toxins we found in midge genomes target eukaryotic cells, and catalytic residues important for toxin function are conserved in insect copies. This class of horizontally transferred, eukaryotic cell-targeting genes is potentially important in insect adaptation.}, }
@article {pmid34449343, year = {2022}, author = {Li, Z and Gao, J and Guo, Y and Cui, Y and Wang, Y and Duan, W and Wu, Z}, title = {Enhancement of antibiotic resistance dissemination by artificial sweetener acesulfame potassium: Insights from cell membrane, enzyme, energy supply and transcriptomics.}, journal = {Journal of hazardous materials}, volume = {422}, number = {}, pages = {126942}, doi = {10.1016/j.jhazmat.2021.126942}, pmid = {34449343}, issn = {1873-3336}, mesh = {*Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Animals ; Anti-Bacterial Agents/toxicity ; Cell Membrane ; Drug Resistance, Microbial ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Sweetening Agents/toxicity ; Thiazines ; Transcriptome ; }, abstract = {The abuse of antibiotics on animals could induce the development of antibiotic resistant genes (ARGs) and antibiotic resistant bacteria (ARB), and acesulfame potassium (ACE) is the widely used artificial sweetener in animal feed. Generally speaking, ACE and ARB often coexist in livestock wastewater, however, the impact of the co-occurrence of ACE and ARB on the transmission of ARGs is still unknown. In this study, the effects of ACE on vertical gene transfer (VGT) and horizontal gene transfer (HGT) were both evaluated. For VGT, ACE may hinder the spread of sul gene in Pseudomonas HLS-6 by blocking ARB growth. As for HGT (from Escherichia coli DH5α to Pseudomonas HLS-6), environmentally relevant ACE concentration could facilitate the conjugative transfer. The underlying mechanisms of HGT were characterized by enhanced cell membrane permeability, reactive oxygen species overproduction, SOS response, energy supply, which were all further verified by the changes in transcription levels of related genes. Interestingly, intracellular Mg[2+] in donor strain was found for the first time as an indicator for the conjugation occurrence in ACE treated mating system. This study may provide new insights into the role of ACE on ARGs proliferation and highlight its potential environmental impacts.}, }
@article {pmid34445438, year = {2021}, author = {Dell'Annunziata, F and Dell'Aversana, C and Doti, N and Donadio, G and Dal Piaz, F and Izzo, V and De Filippis, A and Galdiero, M and Altucci, L and Boccia, G and Galdiero, M and Folliero, V and Franci, G}, title = {Outer Membrane Vesicles Derived from Klebsiella pneumoniae Are a Driving Force for Horizontal Gene Transfer.}, journal = {International journal of molecular sciences}, volume = {22}, number = {16}, pages = {}, pmid = {34445438}, issn = {1422-0067}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins ; Cytoplasmic Vesicles/*genetics ; Drug Resistance, Bacterial ; Gene Dosage ; *Gene Transfer, Horizontal ; Klebsiella pneumoniae/classification/drug effects/*genetics ; Phylogeny ; Plasmids/*genetics ; }, abstract = {Gram-negative bacteria release Outer Membrane Vesicles (OMVs) into the extracellular environment. Recent studies recognized these vesicles as vectors to horizontal gene transfer; however, the parameters that mediate OMVs transfer within bacterial communities remain unclear. The present study highlights for the first time the transfer of plasmids containing resistance genes via OMVs derived from Klebsiella pneumoniae (K. pneumoniae). This mechanism confers DNA protection, it is plasmid copy number dependent with a ratio of 3.6 times among high copy number plasmid (pGR) versus low copy number plasmid (PRM), and the transformation efficiency was 3.6 times greater. Therefore, the DNA amount in the vesicular lumen and the efficacy of horizontal gene transfer was strictly dependent on the identity of the plasmid. Moreover, the role of K. pneumoniae-OMVs in interspecies transfer was described. The transfer ability was not related to the phylogenetic characteristics between the donor and the recipient species. K. pneumoniae-OMVs transferred plasmid to Escherichia coli, Salmonella enterica, Pseudomonas aeruginosa and Burkholderia cepacia. These findings address the pivotal role of K. pneumoniae-OMVs as vectors for antimicrobial resistance genes spread, contributing to the development of antibiotic resistance in the microbial communities.}, }
@article {pmid34442843, year = {2021}, author = {Dechêne-Tempier, M and Marois-Créhan, C and Libante, V and Jouy, E and Leblond-Bourget, N and Payot, S}, title = {Update on the Mechanisms of Antibiotic Resistance and the Mobile Resistome in the Emerging Zoonotic Pathogen Streptococcus suis.}, journal = {Microorganisms}, volume = {9}, number = {8}, pages = {}, pmid = {34442843}, issn = {2076-2607}, abstract = {Streptococcus suis is a zoonotic pathogen causing important economic losses in swine production. The most commonly used antibiotics in swine industry are tetracyclines, beta-lactams, and macrolides. Resistance to these antibiotics has already been observed worldwide (reaching high rates for macrolides and tetracyclines) as well as resistance to aminoglycosides, fluoroquinolones, amphenicols, and glycopeptides. Most of the resistance mechanisms are encoded by antibiotic resistance genes, and a large part are carried by mobile genetic elements (MGEs) that can be transferred through horizontal gene transfer. This review provides an update of the resistance genes, their combination in multidrug isolates, and their localization on MGEs in S. suis. It also includes an overview of the contribution of biofilm to antimicrobial resistance in this bacterial species. The identification of resistance genes and study of their localization in S. suis as well as the environmental factors that can modulate their dissemination appear essential in order to decipher the role of this bacterium as a reservoir of antibiotic genes for other species.}, }
@article {pmid34442840, year = {2021}, author = {Agarwal, G and Gitaitis, RD and Dutta, B}, title = {Pan-Genome of Novel Pantoea stewartii subsp. indologenes Reveals Genes Involved in Onion Pathogenicity and Evidence of Lateral Gene Transfer.}, journal = {Microorganisms}, volume = {9}, number = {8}, pages = {}, pmid = {34442840}, issn = {2076-2607}, support = {AWD00009682//Specialty Crop Block Grant/ ; }, abstract = {Pantoea stewartii subsp. indologenes (Psi) is a causative agent of leafspot on foxtail millet and pearl millet; however, novel strains were recently identified that are pathogenic on onions. Our recent host range evaluation study identified two pathovars; P. stewartii subsp. indologenes pv. cepacicola pv. nov. and P. stewartii subsp. indologenes pv. setariae pv. nov. that are pathogenic on onions and millets or on millets only, respectively. In the current study, we developed a pan-genome using the whole genome sequencing of newly identified/classified Psi strains from both pathovars [pv. cepacicola (n = 4) and pv. setariae (n = 13)]. The full spectrum of the pan-genome contained 7030 genes. Among these, 3546 (present in genomes of all 17 strains) were the core genes that were a subset of 3682 soft-core genes (present in ≥16 strains). The accessory genome included 1308 shell genes and 2040 cloud genes (present in ≤2 strains). The pan-genome showed a clear linear progression with >6000 genes, suggesting that the pan-genome of Psi is open. Comparative phylogenetic analysis showed differences in phylogenetic clustering of Pantoea spp. using PAVs/wgMLST approach in comparison with core genome SNPs-based phylogeny. Further, we conducted a horizontal gene transfer (HGT) study using Psi strains from both pathovars along with strains from other Pantoea species, namely, P. stewartii subsp. stewartii LMG 2715[T], P. ananatis LMG 2665[T], P. agglomerans LMG L15, and P. allii LMG 24248[T]. A total of 317 HGT events among four Pantoea species were identified with most gene transfer events occurring between Psi pv. cepacicola and Psi pv. setariae. Pan-GWAS analysis predicted a total of 154 genes, including seven gene-clusters, which were associated with the pathogenicity phenotype (necrosis on seedling) on onions. One of the gene-clusters contained 11 genes with known functions and was found to be chromosomally located.}, }
@article {pmid34442741, year = {2021}, author = {Koirala, A and Brözel, VS}, title = {Phylogeny of Nitrogenase Structural and Assembly Components Reveals New Insights into the Origin and Distribution of Nitrogen Fixation across Bacteria and Archaea.}, journal = {Microorganisms}, volume = {9}, number = {8}, pages = {}, pmid = {34442741}, issn = {2076-2607}, abstract = {The phylogeny of nitrogenase has only been analyzed using the structural proteins NifHDK. As nifHDKENB has been established as the minimum number of genes necessary for in silico prediction of diazotrophy, we present an updated phylogeny of diazotrophs using both structural (NifHDK) and cofactor assembly proteins (NifENB). Annotated Nif sequences were obtained from InterPro from 963 culture-derived genomes. Nif sequences were aligned individually and concatenated to form one NifHDKENB sequence. Phylogenies obtained using PhyML, FastTree, RapidNJ, and ASTRAL from individuals and concatenated protein sequences were compared and analyzed. All six genes were found across the Actinobacteria, Aquificae, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Deferribacteres, Firmicutes, Fusobacteria, Nitrospira, Proteobacteria, PVC group, and Spirochaetes, as well as the Euryarchaeota. The phylogenies of individual Nif proteins were very similar to the overall NifHDKENB phylogeny, indicating the assembly proteins have evolved together. Our higher resolution database upheld the three cluster phylogeny, but revealed undocumented horizontal gene transfers across phyla. Only 48% of the 325 genera containing all six nif genes are currently supported by biochemical evidence of diazotrophy. In addition, this work provides reference for any inter-phyla comparison of Nif sequences and a quality database of Nif proteins that can be used for identifying new Nif sequences.}, }
@article {pmid34440397, year = {2021}, author = {Wanner, NM and Faulk, C}, title = {Suggested Absence of Horizontal Transfer of Retrotransposons between Humans and Domestic Mammal Species.}, journal = {Genes}, volume = {12}, number = {8}, pages = {}, pmid = {34440397}, issn = {2073-4425}, mesh = {Animals ; *Gene Transfer, Horizontal ; Humans ; Mammals/*genetics ; *Retroelements ; }, abstract = {Transposable element sequences are usually vertically inherited but have also spread across taxa via horizontal transfer. Previous investigations of ancient horizontal transfer of transposons have compared consensus sequences, but this method resists detection of recent single or low copy number transfer events. The relationship between humans and domesticated animals represents an opportunity for potential horizontal transfer due to the consistent shared proximity and exposure to parasitic insects, which have been identified as plausible transfer vectors. The relatively short period of extended human-animal contact (tens of thousands of years or less) makes horizontal transfer of transposons between them unlikely. However, the availability of high-quality reference genomes allows individual element comparisons to detect low copy number events. Using pairwise all-versus-all megablast searches of the complete suite of retrotransposons of thirteen domestic animals against human, we searched a total of 27,949,823 individual TEs. Based on manual comparisons of stringently filtered BLAST search results for evidence of vertical inheritance, no plausible instances of HTT were identified. These results indicate that significant recent HTT between humans and domesticated animals has not occurred despite the close proximity, either due to the short timescale, inhospitable recipient genomes, a failure of vector activity, or other factors.}, }
@article {pmid34438978, year = {2021}, author = {Remus-Emsermann, MNP and Aicher, D and Pelludat, C and Gisler, P and Drissner, D}, title = {Conjugation Dynamics of Self-Transmissible and Mobilisable Plasmids into E. coli O157:H7 on Arabidopsis thaliana Rosettes.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {10}, number = {8}, pages = {}, pmid = {34438978}, issn = {2079-6382}, support = {407240_167068//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; }, abstract = {Many antibiotic resistance genes present in human pathogenic bacteria are believed to originate from environmental bacteria. Conjugation of antibiotic resistance conferring plasmids is considered to be one of the major reasons for the increasing prevalence of antibiotic resistances. A hotspot for plasmid-based horizontal gene transfer is the phyllosphere, i.e., the surfaces of aboveground plant parts. Bacteria in the phyllosphere might serve as intermediate hosts with transfer capability to human pathogenic bacteria. In this study, the exchange of mobilisable and self-transmissible plasmids via conjugation was evaluated. The conjugation from the laboratory strain Escherichia coli S17-1, the model phyllosphere coloniser Pantoea eucalypti 299R, and the model pathogen E. coli O157:H7 to the recipient strain E. coli O157:H7::MRE103 (EcO157:H7red) in the phyllosphere of Arabidopsis thaliana was determined. The results suggest that short-term occurrence of a competent donor is sufficient to fix plasmids in a recipient population of E. coli O157:H7red. The spread of self-transmissible plasmids was limited after initial steep increases of transconjugants that contributed up to 10% of the total recipient population. The here-presented data of plasmid transfer will be important for future modelling approaches to estimate environmental spread of antibiotic resistance in agricultural production environments.}, }
@article {pmid34438974, year = {2021}, author = {Velázquez-Suárez, C and Cebrián, R and Gasca-Capote, C and Sorlózano-Puerto, A and Gutiérrez-Fernández, J and Martínez-Bueno, M and Maqueda, M and Valdivia, E}, title = {Antimicrobial Activity of the Circular Bacteriocin AS-48 against Clinical Multidrug-Resistant Staphylococcus aureus.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {10}, number = {8}, pages = {}, pmid = {34438974}, issn = {2079-6382}, support = {SAF2013-48971-C2-1-R//Ministerio de Econom&#xed;a y Competitividad/ ; }, abstract = {The treatment and hospital-spread-control of methicillin-resistant Staphylococcus aureus (MRSA) is an important challenge since these bacteria are involved in a considerable number of nosocomial infections that are difficult to treat and produce prolonged hospitalization, thus also increasing the risk of death. In fact, MRSA strains are frequently resistant to all β-lactam antibiotics, and co-resistances with other drugs such as macrolides, aminoglycosides, and lincosamides are usually reported, limiting the therapeutical options. To this must be added that the ability of these bacteria to form biofilms on hospital surfaces and devices confer high antibiotic resistance and favors horizontal gene transfer of genetic-resistant mobile elements, the spreading of infections, and relapses. Here, we genotypically and phenotypically characterized 100 clinically isolated S. aureus for their resistance to 18 antibiotics (33% of them were OXA resistant MRSA) and ability to form biofilms. From them, we selected 48 strains on the basis on genotype group, antimicrobial-resistance profile, and existing OXA resistance to be assayed against bacteriocin AS-48. The results showed that AS-48 was active against all strains, regardless of their clinical source, genotype, antimicrobial resistance profile, or biofilm formation capacity, and this activity was enhanced in the presence of the antimicrobial peptide lysozyme. Finally, we explored the effect of AS-48 on formed S. aureus biofilms, observing a reduction in S. aureus S-33 viability. Changes in the matrix structure of the biofilms as well as in the cell division process were observed with scanning electron microscopy in both S-33 and S-48 S. aureus strains.}, }
@article {pmid34437546, year = {2021}, author = {Xu, S and Li, Z and Huang, Y and Han, L and Che, Y and Hou, X and Li, D and Fan, S and Li, Z}, title = {Whole genome sequencing reveals the genomic diversity, taxonomic classification, and evolutionary relationships of the genus Nocardia.}, journal = {PLoS neglected tropical diseases}, volume = {15}, number = {8}, pages = {e0009665}, pmid = {34437546}, issn = {1935-2735}, mesh = {Chromosome Mapping ; Classification/*methods ; *Genome, Bacterial ; Humans ; Nocardia/*classification/*genetics ; Phylogeny ; Whole Genome Sequencing ; }, abstract = {Nocardia is a complex and diverse genus of aerobic actinomycetes that cause complex clinical presentations, which are difficult to diagnose due to being misunderstood. To date, the genetic diversity, evolution, and taxonomic structure of the genus Nocardia are still unclear. In this study, we investigated the pan-genome of 86 Nocardia type strains to clarify their genetic diversity. Our study revealed an open pan-genome for Nocardia containing 265,836 gene families, with about 99.7% of the pan-genome being variable. Horizontal gene transfer appears to have been an important evolutionary driver of genetic diversity shaping the Nocardia genome and may have caused historical taxonomic confusion from other taxa (primarily Rhodococcus, Skermania, Aldersonia, and Mycobacterium). Based on single-copy gene families, we established a high-accuracy phylogenomic approach for Nocardia using 229 genome sequences. Furthermore, we found 28 potentially new species and reclassified 16 strains. Finally, by comparing the topology between a phylogenomic tree and 384 phylogenetic trees (from 384 single-copy genes from the core genome), we identified a novel locus for inferring the phylogeny of this genus. The dapb1 gene, which encodes dipeptidyl aminopeptidase BI, was far superior to commonly used markers for Nocardia and yielded a topology almost identical to that of genome-based phylogeny. In conclusion, the present study provides insights into the genetic diversity, contributes a robust framework for the taxonomic classification, and elucidates the evolutionary relationships of Nocardia. This framework should facilitate the development of rapid tests for the species identification of highly variable species and has given new insight into the behavior of this genus.}, }
@article {pmid34435947, year = {2021}, author = {Petitjean, M and Condamine, B and Burdet, C and Denamur, E and Ruppé, E}, title = {Phylum barrier and Escherichia coli intra-species phylogeny drive the acquisition of antibiotic-resistance genes.}, journal = {Microbial genomics}, volume = {7}, number = {8}, pages = {}, pmid = {34435947}, issn = {2057-5858}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Base Composition ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/*classification/drug effects/*genetics ; Escherichia coli Infections ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Phylogeny ; Shigella/genetics ; }, abstract = {Escherichia coli is a ubiquitous bacterium that has been widely exposed to antibiotics over the last 70 years. It has adapted by acquiring different antibiotic-resistance genes (ARGs), the census of which we aim to characterize here. To do so, we analysed 70 301 E. coli genomes obtained from the EnteroBase database and detected 1 027 651 ARGs using the AMRFinder, Mustard and ResfinderFG ARG databases. We observed a strong phylogroup and clonal lineage specific distribution of some ARGs, supporting the argument for epistasis between ARGs and the strain genetic background. However, each phylogroup had ARGs conferring a similar antibiotic class resistance pattern, indicating phenotypic adaptive convergence. The G+C content or the type of ARG was not associated with the frequency of the ARG in the database. In addition, we identified ARGs from anaerobic, non-Proteobacteria bacteria in four genomes of E. coli, supporting the hypothesis that the transfer between anaerobic bacteria and E. coli can spontaneously occur but remains exceptional. In conclusion, we showed that phylum barrier and intra-species phylogenetic history are major drivers of the acquisition of a resistome in E. coli.}, }
@article {pmid34433898, year = {2022}, author = {Li, C and Zhu, L and Wang, D and Wei, Z and Hao, X and Wang, Z and Li, T and Zhang, L and Lu, Z and Long, M and Wang, Y and Wei, G and Shen, X}, title = {T6SS secretes an LPS-binding effector to recruit OMVs for exploitative competition and horizontal gene transfer.}, journal = {The ISME journal}, volume = {16}, number = {2}, pages = {500-510}, pmid = {34433898}, issn = {1751-7370}, mesh = {Bacterial Outer Membrane Proteins/genetics/metabolism ; *Gene Transfer, Horizontal ; *Lipopolysaccharides ; Signal Transduction ; }, abstract = {Outer membrane vesicles (OMVs) can function as nanoscale vectors that mediate bacterial interactions in microbial communities. How bacteria recognize and recruit OMVs inter-specifically remains largely unknown, thus limiting our understanding of the complex physiological and ecological roles of OMVs. Here, we report a ligand-receptor interaction-based OMV recruitment mechanism, consisting of a type VI secretion system (T6SS)-secreted lipopolysaccharide (LPS)-binding effector TeoL and the outer membrane receptors CubA and CstR. We demonstrated that Cupriavidus necator T6SS1 secretes TeoL to preferentially associate with OMVs in the extracellular milieu through interactions with LPS, one of the most abundant components of OMVs. TeoL associated with OMVs can further bind outer membrane receptors CubA and CstR, which tethers OMVs to the recipient cells and allows cargo to be delivered. The LPS-mediated mechanism enables bacterial cells to recruit OMVs derived from different species, and confers advantages to bacterial cells in iron acquisition, interbacterial competition, and horizontal gene transfer (HGT). Moreover, our findings provide multiple new perspectives on T6SS functionality in the context of bacterial competition and HGT, through the recruitment of OMVs.}, }
@article {pmid34428503, year = {2021}, author = {Beukers, AG and John, MA and Davis, R and Lee, A and van Hal, SJ}, title = {Hospital outbreak of New Delhi metallo-β-lactamase type-1 (NDM-1) in Salmonella enterica with inter-species plasmid transmission.}, journal = {The Journal of hospital infection}, volume = {117}, number = {}, pages = {23-27}, doi = {10.1016/j.jhin.2021.08.014}, pmid = {34428503}, issn = {1532-2939}, mesh = {Anti-Bacterial Agents/pharmacology ; Disease Outbreaks ; Hospitals ; Humans ; *Klebsiella Infections/epidemiology ; Klebsiella pneumoniae/genetics ; Microbial Sensitivity Tests ; Plasmids/genetics ; *Salmonella enterica/genetics ; beta-Lactamases/genetics ; }, abstract = {New Delhi metallo-β-lactamase (NDM) gene confers high-level resistance to an array of β-lactams including carbapenems. Short- and long-read sequencing was used to investigate outbreaks of NDM-positive Enterobacterales including a potential horizontal gene transfer (HGT) event of an NDM-positive plasmid between Salmonella enterica and Klebsiella pneumoniae. Genomic analysis demonstrated a high degree of similarity between NDM-carrying plasmids from patient 1 in K. pneumoniae and patient 2 with S. enterica, K. pneumoniae and Klebsiella oxytoca, confirming an inter-species HGT event. The utility of whole-genome sequencing was demonstrated for in-hospital outbreaks, previously undetected using traditional infection-control surveillance.}, }
@article {pmid34428260, year = {2021}, author = {Mu, F and Li, B and Cheng, S and Jia, J and Jiang, D and Fu, Y and Cheng, J and Lin, Y and Chen, T and Xie, J}, title = {Nine viruses from eight lineages exhibiting new evolutionary modes that co-infect a hypovirulent phytopathogenic fungus.}, journal = {PLoS pathogens}, volume = {17}, number = {8}, pages = {e1009823}, pmid = {34428260}, issn = {1553-7374}, mesh = {Ascomycota/*virology ; *Biological Evolution ; Brassica napus/*virology ; *Cell Lineage ; Fungal Viruses/*classification/genetics/growth &amp; development ; Genome, Viral ; Phylogeny ; Plant Diseases/*virology ; Plant Leaves/*virology ; RNA, Viral ; }, abstract = {Mycoviruses are an important component of the virosphere, but our current knowledge of their genome organization diversity and evolution remains rudimentary. In this study, the mycovirus composition in a hypovirulent strain of Sclerotinia sclerotiorum was molecularly characterized. Nine mycoviruses were identified and assigned into eight potential families. Of them, six were close relatives of known mycoviruses, while the other three had unique genome organizations and evolutionary positions. A deltaflexivirus with a tripartite genome has evolved via arrangement and horizontal gene transfer events, which could be an evolutionary connection from unsegmented to segmented RNA viruses. Two mycoviruses had acquired a second helicase gene by two different evolutionary mechanisms. A rhabdovirus representing an independent viral evolutionary branch was the first to be confirmed to occur naturally in fungi. The major hypovirulence-associated factor, an endornavirus, was finally corroborated. Our study expands the diversity of mycoviruses and potential virocontrol agents, and also provides new insights into virus evolutionary modes including virus genome segmentation.}, }
@article {pmid34427525, year = {2021}, author = {Oladeinde, A and Abdo, Z and Press, MO and Cook, K and Cox, NA and Zwirzitz, B and Woyda, R and Lakin, SM and Thomas, JC and Looft, T and Cosby, DE and Hinton, A and Guard, J and Line, E and Rothrock, MJ and Berrang, ME and Herrington, K and Zock, G and Plumblee Lawrence, J and Cudnik, D and House, S and Ingram, K and Lariscy, L and Wagner, M and Aggrey, SE and Chai, L and Ritz, C}, title = {Horizontal Gene Transfer Is the Main Driver of Antimicrobial Resistance in Broiler Chicks Infected with Salmonella enterica Serovar Heidelberg.}, journal = {mSystems}, volume = {6}, number = {4}, pages = {e0072921}, pmid = {34427525}, issn = {2379-5077}, support = {R44 AI150008/AI/NIAID NIH HHS/United States ; T32 GM132057/GM/NIGMS NIH HHS/United States ; P41 RR006009/RR/NCRR NIH HHS/United States ; }, abstract = {The overuse and misuse of antibiotics in clinical settings and in food production have been linked to the increased prevalence and spread of antimicrobial resistance (AR). Consequently, public health and consumer concerns have resulted in a remarkable reduction in antibiotics used for food animal production. However, there are no data on the effectiveness of antibiotic removal in reducing AR shared through horizontal gene transfer (HGT). In this study, we used neonatal broiler chicks and Salmonella enterica serovar Heidelberg, a model food pathogen, to test if chicks raised antibiotic free harbor transferable AR. We challenged chicks with an antibiotic-susceptible S. Heidelberg strain using various routes of inoculation and determined if S. Heidelberg isolates recovered carried plasmids conferring AR. We used antimicrobial susceptibility testing and whole-genome sequencing (WGS) to show that chicks grown without antibiotics harbored an antimicrobial resistant S. Heidelberg population at 14 days after challenge and chicks challenged orally acquired AR at a higher rate than chicks inoculated via the cloaca. Using 16S rRNA gene sequencing, we found that S. Heidelberg infection perturbed the microbiota of broiler chicks, and we used metagenomics and WGS to confirm that a commensal Escherichia coli population was the main reservoir of an IncI1 plasmid acquired by S. Heidelberg. The carriage of this IncI1 plasmid posed no fitness cost to S. Heidelberg but increased its fitness when exposed to acidic pH in vitro. These results suggest that HGT of plasmids carrying AR shaped the evolution of S. Heidelberg and that antibiotic use reduction alone is insufficient to limit antibiotic resistance transfer from commensal bacteria to Salmonella enterica. IMPORTANCE The reported increase in antibiotic-resistant bacteria in humans has resulted in a major shift away from antibiotic use in food animal production. This shift has been driven by the assumption that removing antibiotics will select for antibiotic susceptible bacterial taxa, which in turn will allow the currently available antibiotic arsenal to be more effective. This change in practice has highlighted new questions that need to be answered to assess the effectiveness of antibiotic removal in reducing the spread of antibiotic resistance bacteria. This research demonstrates that antibiotic-susceptible Salmonella enterica serovar Heidelberg strains can acquire multidrug resistance from commensal bacteria present in the gut of neonatal broiler chicks, even in the absence of antibiotic selection. We demonstrate that exposure to acidic pH drove the horizontal transfer of antimicrobial resistance plasmids and suggest that simply removing antibiotics from food animal production might not be sufficient to limit the spread of antimicrobial resistance.}, }
@article {pmid34425705, year = {2021}, author = {Palencia-Gándara, C and Getino, M and Moyano, G and Redondo, S and Fernández-López, R and González-Zorn, B and de la Cruz, F}, title = {Conjugation Inhibitors Effectively Prevent Plasmid Transmission in Natural Environments.}, journal = {mBio}, volume = {12}, number = {4}, pages = {e0127721}, pmid = {34425705}, issn = {2150-7511}, mesh = {Alkynes/administration &amp; dosage ; Animal Feed ; Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/*genetics ; Escherichia coli/drug effects/*genetics ; Fatty Acids, Unsaturated/administration &amp; dosage ; Gastrointestinal Microbiome/drug effects/*genetics ; Gene Transfer Techniques ; Gene Transfer, Horizontal ; Mice ; Mice, Inbred C57BL ; Plasmids/*genetics ; Rivers/microbiology ; }, abstract = {Plasmid conjugation is a major route for the spread of antibiotic resistance genes. Inhibiting conjugation has been proposed as a feasible strategy to stop or delay the propagation of antibiotic resistance genes. Several compounds have been shown to be conjugation inhibitors in vitro, specifically targeting the plasmid horizontal transfer machinery. However, the in vivo efficiency and the applicability of these compounds to clinical and environmental settings remained untested. Here we show that the synthetic fatty acid 2-hexadecynoic acid (2-HDA), when used as a fish food supplement, lowers the conjugation frequency of model plasmids up to 10-fold in controlled water microcosms. When added to the food for mice, 2-HDA diminished the conjugation efficiency 50-fold in controlled plasmid transfer assays carried out in the mouse gut. These results demonstrate the in vivo efficiency of conjugation inhibitors, paving the way for their potential application in clinical and environmental settings. IMPORTANCE The spread of antibiotic resistance is considered one of the major threats for global health in the immediate future. A key reason for the speed at which antibiotic resistance spread is the ability of bacteria to share genes with each other. Antibiotic resistance genes harbored in plasmids can be easily transferred to commensal and pathogenic bacteria through a process known as bacterial conjugation. Blocking conjugation is thus a potentially useful strategy to curtail the propagation of antibiotic resistance. Conjugation inhibitors (COINS) are a series of compounds that block conjugation in vitro. Here we show that COINS efficiently block plasmid transmission in two controlled natural environments, water microcosms and the mouse gut. These observations indicate that COIN therapy can be used to prevent the spread of antibiotic resistance.}, }
@article {pmid34424033, year = {2021}, author = {Kalafatis, M and Slauch, JM}, title = {Long-Distance Effects of H-NS Binding in the Control of hilD Expression in the Salmonella SPI1 Locus.}, journal = {Journal of bacteriology}, volume = {203}, number = {21}, pages = {e0030821}, pmid = {34424033}, issn = {1098-5530}, support = {R01 GM120182/GM/NIGMS NIH HHS/United States ; GM120182/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/*metabolism ; Biological Evolution ; DNA-Binding Proteins/genetics/*metabolism ; Gene Deletion ; Gene Expression Regulation, Bacterial/*physiology ; Gene Silencing ; Protein Binding ; Salmonella/genetics/*metabolism ; Transcription Factors/genetics/*metabolism ; }, abstract = {Salmonella enterica serovar Typhimurium utilizes a type three secretion system (T3SS) carried on the Salmonella pathogenicity island 1 (SPI1) to invade intestinal epithelial cells and induce inflammatory diarrhea. HilA activates expression of the T3SS structural genes. Expression of hyper invasion locus A (hilA) is controlled by the transcription factors HilD, HilC, and RtsA, which act in a complex feed-forward regulatory loop. The nucleoid-associated protein H-NS is a xenogeneic silencer that has a major effect on SPI1 expression. In this work, we use genetic techniques to show that disruptions of the chromosomal region surrounding hilD have a cis effect on H-NS-mediated repression of the hilD promoter; this effect occurs asymmetrically over ∼4 kb spanning the prgH-hilD intergenic region. CAT cassettes inserted at various positions in this region are also silenced in relation to the proximity to the hilD promoter. We identify a putative H-NS nucleation site, and its mutation results in derepression of the locus. Furthermore, we genetically show that HilD abrogates H-NS-mediated silencing to activate the hilD promoter. In contrast, H-NS-mediated repression of the hilA promoter, downstream of hilD, is through its control of HilD, which directly activates hilA transcription. Likewise, activation of the prgH promoter, although in a region silenced by H-NS, is strictly dependent on HilA. In summary, we propose a model in which H-NS nucleates within the hilD promoter region to polymerize and exert its repressive effect. Thus, H-NS-mediated repression of SPI1 is primarily through the control of hilD expression, with HilD capable of overcoming H-NS to autoactivate. IMPORTANCE Members of the foodborne pathogen Salmonella rely on a type III secretion system to invade intestinal epithelial cells and initiate infection. This system was acquired through horizontal gene transfer, essentially creating the Salmonella genus. Expression of this critical virulence factor is controlled by a complex regulatory network. The nucleoid protein H-NS is a global repressor of horizontally acquired genomic loci. Here, we identify the critical site of H-NS regulation in this system and show that alterations to the DNA over a surprisingly large region affect this regulation, providing important information regarding the mechanism of H-NS action.}, }
@article {pmid34416685, year = {2022}, author = {Qiu, X and Zhou, G and Wang, H}, title = {Nanoscale zero-valent iron inhibits the horizontal gene transfer of antibiotic resistance genes in chicken manure compost.}, journal = {Journal of hazardous materials}, volume = {422}, number = {}, pages = {126883}, doi = {10.1016/j.jhazmat.2021.126883}, pmid = {34416685}, issn = {1873-3336}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Chickens ; *Composting ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Iron ; Manure ; }, abstract = {Livestock manure has been identified as a significant hotspot for antibiotic resistance genes (ARGs). However, the impact of nanoscale zero-valent iron (nZVI) on the fate of ARGs during livestock manure composting remains poorly understood. Here, we investigated the evolution of ARGs in chicken manure compost exposed to 100 and 600 mg kg[-1] nZVI. The results showed that nZVI addition reduced the concentration of some antibiotics such as doxycycline and sulfamethoxazole. Furthermore, nZVI addition decreased the abundances of most ARGs at the end of composting, but nZVI dosage did not have any significant effect. The abundances of the dominant ARGs (sul1 and sul2) were significantly correlated to the class 1 integron-integrase gene (intI1). A network analysis revealed that the genera Bacteroides, Bacillus, Corynebacterium, Thiopseudomonas and Pseudomonas were the main potential hosts for multiple ARGs, and the decreased abundance of these bacteria contributed to the removal of ARGs. Structural equation models demonstrated that the reduction in intI1 played a predominant role in ARG removal. The nZVI also had direct effects on the intI1 abundance. These findings suggest that the addition of nZVI is a promising strategy to minimize ARG release in chicken manure compost.}, }
@article {pmid34415164, year = {2021}, author = {Wei, Z and Feng, K and Wang, Z and Zhang, Y and Yang, M and Zhu, YG and Virta, MPJ and Deng, Y}, title = {High-Throughput Single-Cell Technology Reveals the Contribution of Horizontal Gene Transfer to Typical Antibiotic Resistance Gene Dissemination in Wastewater Treatment Plants.}, journal = {Environmental science &amp; technology}, volume = {55}, number = {17}, pages = {11824-11834}, doi = {10.1021/acs.est.1c01250}, pmid = {34415164}, issn = {1520-5851}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; *Gene Transfer, Horizontal ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Technology ; *Water Purification ; }, abstract = {The spread of antibiotic resistance genes (ARGs) has gained much attention worldwide, while the contribution of vertical gene transfer (VGT) and horizontal gene transfer (HGT) is still elusive. Here, we improved an emerging high-throughput single-cell-based technology, emulsion, paired isolation, and concatenation polymerase chain reaction (epicPCR), by lengthening the sequence of ARG in the fused ARG-16S rRNA fragments to cover the variance of both ARG and its hosts. The improved epicPCR was applied to track the hosts of a widely detected ARG, sul1 gene, in five urban wastewater treatment plants (UWTPs) during two seasons. The sul1 host bacteria were highly diverse and mostly classified as Proteobacteria and Bacteroidetes. Clear seasonal divergence of α-diversity and interaction networks were present in the host community. The consensus phylogenetic trees of the sul1 gene and their host demonstrated incorrespondence on the whole and regularity on abundant groups, suggesting the important role of both HGT and VGT, respectively. The relative importance of these two ways was further measured; HGT (54%) generally played an equal or even more important role as VGT (46%) in UWTPs. The application of the improved epicPCR technology provides a feasible approach to quantify the relative contributions of VGT and HGT in environmental dissemination of ARGs.}, }
@article {pmid34413842, year = {2021}, author = {Chen, Z and Shen, M and Mao, C and Wang, C and Yuan, P and Wang, T and Sun, D}, title = {A Type I Restriction Modification System Influences Genomic Evolution Driven by Horizontal Gene Transfer in Paenibacillus polymyxa.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {709571}, pmid = {34413842}, issn = {1664-302X}, abstract = {Considered a "Generally Recognized As Safe" (GRAS) bacterium, the plant growth-promoting rhizobacterium Paenibacillus polymyxa has been widely applied in agriculture and animal husbandry. It also produces valuable compounds that are used in medicine and industry. Our previous work showed the presence of restriction modification (RM) system in P. polymyxa ATCC 842. Here, we further analyzed its genome and methylome by using SMRT sequencing, which revealed the presence of a larger number of genes, as well as a plasmid documented as a genomic region in a previous report. A number of mobile genetic elements (MGEs), including 78 insertion sequences, six genomic islands, and six prophages, were identified in the genome. A putative lysozyme-encoding gene from prophage P6 was shown to express lysin which caused cell lysis. Analysis of the methylome and genome uncovered a pair of reverse-complementary DNA methylation motifs which were widespread in the genome, as well as genes potentially encoding their cognate type I restriction-modification system PpoAI. Further genetic analysis confirmed the function of PpoAI as a RM system in modifying and restricting DNA. The average frequency of the DNA methylation motifs in MGEs was lower than that in the genome, implicating a role of PpoAI in restricting MGEs during genomic evolution of P. polymyxa. Finally, comparative analysis of R, M, and S subunits of PpoAI showed that homologs of the PpoAI system were widely distributed in species belonging to other classes of Firmicute, implicating a role of the ancestor of PpoAI in the genomic evolution of species beyond Paenibacillus.}, }
@article {pmid34408267, year = {2022}, author = {Mao, X and Chen, J and van Oosterhout, C and Zhang, H and Liu, G and Zhuang, Y and Mock, T}, title = {Diversity, prevalence, and expression of cyanase genes (cynS) in planktonic marine microorganisms.}, journal = {The ISME journal}, volume = {16}, number = {2}, pages = {602-605}, pmid = {34408267}, issn = {1751-7370}, mesh = {*Carbon-Nitrogen Lyases/genetics ; Phylogeny ; *Plankton/metabolism ; Prevalence ; }, abstract = {Cyanate is utilized by many microbes as an organic nitrogen source. The key enzyme for cyanate metabolism is cyanase, converting cyanate to ammonium and carbon dioxide. Although the cyanase gene cynS has been identified in many species, the diversity, prevalence, and expression of cynS in marine microbial communities remains poorly understood. Here, based on the full-length cDNA sequence of a dinoflagellate cynS and 260 homologs across the tree of life, we extend the conserved nature of cyanases by the identification of additional ultra-conserved residues as part of the modeled holoenzyme structure. Our phylogenetic analysis showed that horizontal gene transfer of cynS appears to be more prominent than previously reported for bacteria, archaea, chlorophytes, and metazoans. Quantitative analyses of marine planktonic metagenomes revealed that cynS is as prevalent as ureC (urease subunit alpha), suggesting that cyanate plays an important role in nitrogen metabolism of marine microbes. Highly abundant cynS transcripts from phytoplankton and nitrite-oxidizing bacteria identified in global ocean metatranscriptomes indicate that cyanases potentially occupy a key position in the marine nitrogen cycle by facilitating photosynthetic assimilation of organic N and its remineralisation to NO3 by the activity of nitrifying bacteria.}, }
@article {pmid34402879, year = {2021}, author = {Muthye, V and Lavrov, DV}, title = {Multiple Losses of MSH1, Gain of mtMutS, and Other Changes in the MutS Family of DNA Repair Proteins in Animals.}, journal = {Genome biology and evolution}, volume = {13}, number = {9}, pages = {}, pmid = {34402879}, issn = {1759-6653}, mesh = {Animals ; DNA Repair ; DNA-Binding Proteins/genetics/metabolism ; Fungal Proteins/genetics ; MutS DNA Mismatch-Binding Protein/genetics/metabolism ; Saccharomyces cerevisiae/genetics ; *Saccharomyces cerevisiae Proteins/genetics ; }, abstract = {MutS is a key component of the mismatch repair (MMR) pathway. Members of the MutS protein family are present in prokaryotes, eukaryotes, and viruses. Six MutS homologs (MSH1-6) have been identified in yeast, of which three function in nuclear MMR, while MSH1 functions in mitochondrial DNA repair. MSH proteins are believed to be well conserved in animals, except for MSH1-which is thought to be lost. Two intriguing exceptions to this general picture have been found, both in the class Anthozoa within the phylum Cnidaria. First, an ortholog of the yeast-MSH1 was reported in one hexacoral species. Second, a MutS homolog (mtMutS) has been found in the mitochondrial genome of all octocorals. To understand the origin and potential functional implications of these exceptions, we investigated the evolution of the MutS family both in Cnidaria and in animals in general. Our study confirmed the acquisition of octocoral mtMutS by horizontal gene transfer from a giant virus. Surprisingly, we identified MSH1 in all hexacorals and several sponges and placozoans. By contrast, MSH1 orthologs were lacking in other cnidarians, ctenophores, and bilaterian animals. Furthermore, while we identified MSH2 and MSH6 in nearly all animals, MSH4, MSH5, and, especially, MSH3 were missing in multiple species. Overall, our analysis revealed a dynamic evolution of the MutS family in animals, with multiple losses of MSH1, MSH3, some losses of MSH4 and MSH5, and a gain of the octocoral mtMutS. We propose that octocoral mtMutS functionally replaced MSH1 that was present in the common ancestor of Anthozoa.}, }
@article {pmid34399518, year = {2021}, author = {Qin, X and Wang, H and Miao, C and Yang, X and Zhang, Y and Feng, J and Forsythe, SJ and Man, C and Jiang, Y}, title = {Comparative genomics reveals environmental adaptation differences between Cronobacter species.}, journal = {Food research international (Ottawa, Ont.)}, volume = {147}, number = {}, pages = {110541}, doi = {10.1016/j.foodres.2021.110541}, pmid = {34399518}, issn = {1873-7145}, mesh = {*Cronobacter/genetics ; Genome, Bacterial/genetics ; Genomics ; Species Specificity ; Virulence ; }, abstract = {The genus Cronobacter is an opportunistic food-borne pathogen which is able to adapt to diverse environments and shows considerable genetic diversity. Genomic analysis can be used to reveal the variation across the genus with respect to virulence, drug resistance and factors involved in horizontal gene transfer mechanisms, such as integrons, conjugative plasmids, and recombinases. In this study, whole-genome comparative analysis of 27 Cronobacter genomes (12 existing and 15 newly assembled genomes) was performed. A total of 110,010 protein-coding genes were grouped into 11,262 clusters, including 2637 core genes, 4814 strain-specific genes and 3811 dispensable genes. Clusters of Orthologous Groups (COG) analysis indicated that 97.35% of the core genes were for substrate transport and metabolism, and the antibiotic resistance genetic determinants were classified into 136 antibiotic resistance ontologies (AROs). A total of 80 genomic islands (GIs) were identified which contained several type VI secretion system gene clusters, and these were likely to have been acquired by horizontal gene transfer. This study has generated a comprehensive characterization of the genus Cronobacter, leading to a better understanding of the mechanisms and ecological functions among the genome features, speciation, and environmental adaptation strategies.}, }
@article {pmid34399028, year = {2022}, author = {Ding, BY and Xie, XC and Shang, F and Smagghe, G and Niu, JZ and Wang, JJ}, title = {Characterization of carotenoid biosynthetic pathway genes in the pea aphid (Acyrthosiphon pisum) revealed by heterologous complementation and RNA interference assays.}, journal = {Insect science}, volume = {29}, number = {3}, pages = {645-656}, doi = {10.1111/1744-7917.12958}, pmid = {34399028}, issn = {1744-7917}, mesh = {Animals ; *Aphids/genetics ; *Biosynthetic Pathways/genetics ; Carotenoids ; Pisum sativum ; RNA Interference ; }, abstract = {Carotenoids are involved in many essential physiological functions and are produced from geranylgeranyl pyrophosphate through synthase, desaturase, and cyclase activities. In the pea aphid (Acyrthosiphon pisum), the duplication of carotenoid biosynthetic genes, including carotenoid synthases/cyclases (ApCscA-C) and desaturases (ApCdeA-D), through horizontal gene transfer from fungi has been detected, and ApCdeB has known dehydrogenation functions. However, whether other genes contribute to aphid carotenoid biosynthesis, and its specific regulatory pathway, remains unclear. In the current study, functional analyses of seven genes were performed using heterologous complementation and RNA interference assays. The bifunctional enzymes ApCscA-C were responsible for the synthase of phytoene, and ApCscC may also have a cyclase activity. ApCdeA, ApCdeC, and ApCdeD had diverse dehydrogenation functions. ApCdeA catalyzed the enzymatic conversion of phytoene to neurosporene (three-step product), ApCdeC catalyzed the enzymatic conversion of phytoene to ζ-carotene (two-step product), and ApCdeD catalyzed the enzymatic conversion of phytoene to lycopene (four-step product). Silencing of ApCscs reduced the expression levels of ApCdes, and silencing these carotenoid biosynthetic genes reduced the α-, β-, and γ-carotene levels, as well as the total carotenoid level. The results suggest that these genes were activated and led to carotenoid biosynthesis in the pea aphid.}, }
@article {pmid34398506, year = {2021}, author = {Haverkamp, THA and Lossouarn, J and Zhaxybayeva, O and Lyu, J and Bienvenu, N and Geslin, C and Nesbø, CL}, title = {Newly identified proviruses in Thermotogota suggest that viruses are the vehicles on the highways of interphylum gene sharing.}, journal = {Environmental microbiology}, volume = {23}, number = {11}, pages = {7105-7120}, doi = {10.1111/1462-2920.15723}, pmid = {34398506}, issn = {1462-2920}, mesh = {Bacteria/genetics ; Phylogeny ; *Proviruses/genetics ; Virion/genetics ; *Viruses/genetics ; }, abstract = {Phylogenomic analyses of bacteria from the phylum Thermotogota have shown extensive lateral gene transfer with distantly related organisms, particularly with Firmicutes. One likely mechanism of such DNA transfer is viruses. However, to date, only three temperate viruses have been characterized in this phylum, all infecting bacteria from the Marinitoga genus. Here we report 17 proviruses integrated into genomes of bacteria belonging to eight Thermotogota genera and induce viral particle production from one of the proviruses. All except an incomplete provirus from Mesotoga fall into two groups based on sequence similarity, gene synteny and taxonomic classification. Proviruses of Group 1 are found in the genera Geotoga, Kosmotoga, Marinitoga, Thermosipho and Mesoaciditoga and are similar to the previously characterized Marinitoga viruses, while proviruses from Group 2 are distantly related to the Group 1 proviruses, have different genome organization and are found in Petrotoga and Defluviitoga. Genes carried by both groups are closely related to Firmicutes and Firmicutes (pro)viruses in phylogenetic analyses. Moreover, one of the groups show evidence of recent gene exchange and may be capable of infecting cells from both phyla. We hypothesize that viruses are responsible for a large portion of the observed gene flow between Firmicutes and Thermotogota.}, }
@article {pmid34392041, year = {2021}, author = {Zhang, B and Qin, S and Guan, X and Jiang, K and Jiang, M and Liu, F}, title = {Distribution of Antibiotic Resistance Genes in Karst River and Its Ecological Risk.}, journal = {Water research}, volume = {203}, number = {}, pages = {117507}, doi = {10.1016/j.watres.2021.117507}, pmid = {34392041}, issn = {1879-2448}, mesh = {*Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Humans ; *Rivers ; }, abstract = {In recent years, karst water has been polluted by emerging pollutants such as antibiotics. In this study, the bacterial communities and antibiotic resistance genes (ARGs) in antibiotics contaminated karst river was studied in summer and winter. The concentration of antibiotics in winter karst river is higher than that in summer, and there are significant differences in structure of bacterial community and ARGs between karst river water samples. Aminoglycoside, beta-lactamase and multidrug are the main types of ARGs, and transposons play an important role in the spread of ARGs. The horizontal gene transfer (HGT) of ARGs between bacteria mediated by mobile genetic elements (MGEs) would cause the spread of ARGs and bring potential ecological risks. In addition, we found that the risk of antibiotic resistant pathogenic bacteria (ARPB) in winter was possibly higher than that in summer. It was suggested that the discharge of antibiotics, water amount and seasonal occurrence time of human intestinal diseases affect the risks caused by antibiotics contaminants. This study helps us to understand the transmission mechanism of ARGs and their potential seasonal ecological risks in complex karst water systems.}, }
@article {pmid34390574, year = {2021}, author = {Rangel, LT and Soucy, SM and Setubal, JC and Gogarten, JP and Fournier, GP}, title = {An Efficient, Nonphylogenetic Method for Detecting Genes Sharing Evolutionary Signals in Phylogenomic Data Sets.}, journal = {Genome biology and evolution}, volume = {13}, number = {9}, pages = {}, pmid = {34390574}, issn = {1759-6653}, support = {P20 GM130454/GM/NIGMS NIH HHS/United States ; }, mesh = {Archaea/genetics ; *Evolution, Molecular ; *Genome, Archaeal ; Phylogeny ; Sequence Alignment ; }, abstract = {Assessing the compatibility between gene family phylogenies is a crucial and often computationally demanding step in many phylogenomic analyses. Here, we describe the Evolutionary Similarity Index (IES), a means to assess shared evolution between gene families using a weighted orthogonal distance regression model applied to sequence distances. The utilization of pairwise distance matrices circumvents comparisons between gene tree topologies, which are inherently uncertain and sensitive to evolutionary model choice, phylogenetic reconstruction artifacts, and other sources of error. Furthermore, IES enables the many-to-many pairing of multiple copies between similarly evolving gene families. This is done by selecting non-overlapping pairs of copies, one from each assessed family, and yielding the least sum of squared residuals. Analyses of simulated gene family data sets show that IES's accuracy is on par with popular tree-based methods while also less susceptible to noise introduced by sequence alignment and evolutionary model fitting. Applying IES to an empirical data set of 1,322 genes from 42 archaeal genomes identified eight major clusters of gene families with compatible evolutionary trends. The most cohesive cluster consisted of 62 genes with compatible evolutionary signal, which occur as both single-copy and multiple homologs per genome; phylogenetic analysis of concatenated alignments from this cluster produced a tree closely matching previously published species trees for Archaea. Four other clusters are mainly composed of accessory genes with limited distribution among Archaea and enriched toward specific metabolic functions. Pairwise evolutionary distances obtained from these accessory gene clusters suggest patterns of interphyla horizontal gene transfer. An IES implementation is available at https://github.com/lthiberiol/evolSimIndex.}, }
@article {pmid34387371, year = {2021}, author = {Rizk, S and Henke, P and Santana-Molina, C and Martens, G and Gnädig, M and Nguyen, NA and Devos, DP and Neumann-Schaal, M and Saenz, JP}, title = {Functional diversity of isoprenoid lipids in Methylobacterium extorquens PA1.}, journal = {Molecular microbiology}, volume = {116}, number = {4}, pages = {1064-1078}, doi = {10.1111/mmi.14794}, pmid = {34387371}, issn = {1365-2958}, mesh = {Bacterial Outer Membrane/*metabolism ; Biosynthetic Pathways ; Carotenoids/*metabolism ; Gene Knockdown Techniques ; Geranylgeranyl-Diphosphate Geranylgeranyltransferase/*genetics/metabolism ; Methylobacterium extorquens/*genetics/growth &amp; development/*metabolism ; Oxidative Stress ; Oxidoreductases/*genetics/metabolism ; Phylogeny ; Planctomycetes/genetics ; Sequence Deletion ; Squalene/analogs &amp; derivatives/*metabolism ; }, abstract = {Hopanoids and carotenoids are two of the major isoprenoid-derived lipid classes in prokaryotes that have been proposed to have similar membrane ordering properties as sterols. Methylobacterium extorquens contains hopanoids and carotenoids in their outer membrane, making them an ideal system to investigate the role of isoprenoid lipids in surface membrane function and cellular fitness. By genetically knocking out hpnE and crtB we disrupted the production of squalene and phytoene in M. extorquens PA1, which are the presumed precursors for hopanoids and carotenoids respectively. Deletion of hpnE revealed that carotenoid biosynthesis utilizes squalene as a precursor resulting in pigmentation with a C30 backbone, rather than the previously predicted canonical C40 phytoene-derived pathway. Phylogenetic analysis suggested that M. extorquens may have acquired the C30 pathway through lateral gene transfer from Planctomycetes. Surprisingly, disruption of carotenoid synthesis did not generate any major growth or membrane biophysical phenotypes, but slightly increased sensitivity to oxidative stress. We further demonstrated that hopanoids but not carotenoids are essential for growth at higher temperatures, membrane permeability and tolerance of low divalent cation concentrations. These observations show that hopanoids and carotenoids serve diverse roles in the outer membrane of M. extorquens PA1.}, }
@article {pmid34381435, year = {2021}, author = {Moser, AI and Kuenzli, E and Campos-Madueno, EI and Büdel, T and Rattanavong, S and Vongsouvath, M and Hatz, C and Endimiani, A}, title = {Antimicrobial-Resistant Escherichia coli Strains and Their Plasmids in People, Poultry, and Chicken Meat in Laos.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {708182}, pmid = {34381435}, issn = {1664-302X}, abstract = {Antimicrobial resistant (AMR) Enterobacterales are widely distributed among the healthy population of the Indochinese peninsula, including Laos. However, the local reservoir of these pathogens are currently not known and possible sources such as agricultural settings and food have rarely been analyzed. In this work, we investigated the extended-spectrum cephalosporin- (ESC-) and colistin-resistant Escherichia coli strains (CST-R-Ec) isolated from the gut of local people, feces of poultry, and from chicken meat (60 samples each group) in Laos. Whole-genome sequencing (WGS) analysis based on both short- and long-read sequencing approaches were implemented. The following prevalence of ESC-R-Ec and CST-R-Ec were recorded, respectively: local people (70 and 15%), poultry (20 and 23.3%), and chicken meat (21.7 and 13.3%). Core-genome analysis, coupled with sequence type (ST)/core-genome ST (cgST) definitions, indicated that no common AMR-Ec clones were spreading among the different settings. ESC-R-Ec mostly possessed bla CTX-M-15 and bla CTX-M-55 associated to ISEcp1 or IS26. The majority of CST-R-Ec carried mcr-1 on IncX4, IncI2, IncP1, and IncHI1 plasmids similar or identical to those described worldwide; strains with chromosomal mcr-1 or possessing plasmid-mediated mcr-3 were also found. These results indicate a high prevalence of AMR-Ec in the local population, poultry, and chicken meat. While we did not observe the same clones among the three settings, most of the bla CTX-Ms and mcr-1/-3 were associated with mobile-genetic elements, indicating that horizontal gene transfer may play an important role in the dissemination of AMR-Ec in Laos. More studies should be planned to better understand the extent and dynamics of this phenomenon.}, }
@article {pmid34379789, year = {2021}, author = {Santamaría-Gómez, J and Rubio, M&#xc1; and López-Igual, R and Romero-Losada, AB and Delgado-Chaves, FM and Bru-Martínez, R and Romero-Campero, FJ and Herrero, A and Ibba, M and Ochoa de Alda, JAG and Luque, I}, title = {Role of a cryptic tRNA gene operon in survival under translational stress.}, journal = {Nucleic acids research}, volume = {49}, number = {15}, pages = {8757-8776}, pmid = {34379789}, issn = {1362-4962}, mesh = {Anabaena/genetics ; Anti-Bacterial Agents/pharmacology ; Gene Expression Regulation, Bacterial ; *Genes, Bacterial ; Genome, Bacterial ; Microbial Viability/genetics ; *Operon ; *Protein Biosynthesis ; RNA, Transfer/*genetics/metabolism ; Regulatory Sequences, Nucleic Acid ; Stress, Physiological/*genetics ; }, abstract = {As compared to eukaryotes, bacteria have a reduced tRNA gene set encoding between 30 and 220 tRNAs. Although in most bacterial phyla tRNA genes are dispersed in the genome, many species from distinct phyla also show genes forming arrays. Here, we show that two types of arrays with distinct evolutionary origins exist. This work focuses on long tRNA gene arrays (L-arrays) that encompass up to 43 genes, which disseminate by horizontal gene transfer and contribute supernumerary tRNA genes to the host. Although in the few cases previously studied these arrays were reported to be poorly transcribed, here we show that the L-array of the model cyanobacterium Anabaena sp. PCC 7120, encoding 23 functional tRNAs, is largely induced upon impairment of the translation machinery. The cellular response to this challenge involves a global reprogramming of the transcriptome in two phases. tRNAs encoded in the array are induced in the second phase of the response, directly contributing to cell survival. Results presented here show that in some bacteria the tRNA gene set may be partitioned between a housekeeping subset, which constantly sustains translation, and an inducible subset that is generally silent but can provide functionality under particular conditions.}, }
@article {pmid34379636, year = {2021}, author = {Acharya, S and Dahal, A and Bhattarai, HK}, title = {Evolution and origin of sliding clamp in bacteria, archaea and eukarya.}, journal = {PloS one}, volume = {16}, number = {8}, pages = {e0241093}, pmid = {34379636}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Archaea/*genetics ; Bacteria/*genetics ; DNA/genetics ; DNA Replication/genetics ; DNA-Directed DNA Polymerase/genetics ; Eukaryota/*genetics ; Evolution, Molecular ; Firmicutes/genetics ; Phylogeny ; Proliferating Cell Nuclear Antigen/genetics ; Pyrococcus furiosus/genetics ; }, abstract = {The replication of DNA is an essential process in all domains of life. A protein often involved in replication is the sliding clamp. The sliding clamp encircles the DNA and helps replicative polymerase stay attached to the replication machinery increasing the processivity of the polymerase. In eukaryotes and archaea, the sliding clamp is called the Proliferating Cell Nuclear Antigen (PCNA) and consists of two domains. This PCNA forms a trimer encircling the DNA as a hexamer. In bacteria, the structure of the sliding clamp is highly conserved, but the protein itself, called beta clamp, contains three domains, which dimerize to form a hexamer. The bulk of literature touts a conservation of the structure of the sliding clamp, but fails to recognize the conservation of protein sequence among sliding clamps. In this paper, we have used PSI blast to the second iteration in NCBI to show a statistically significant sequence homology between Pyrococcus furiosus PCNA and Kallipyga gabonensis beta clamp. The last two domains of beta clamp align with the two domains of PCNA. This homology data demonstrates that PCNA and beta clamp arose from a common ancestor. In this paper, we have further used beta clamp and PCNA sequences from diverse bacteria, archaea and eukarya to build maximum likelihood phylogenetic tree. Most, but not all, species in different domains of life harbor one sliding clamp from vertical inheritance. Some of these species that have two or more sliding clamps have acquired them from gene duplication or horizontal gene transfer events.}, }
@article {pmid34378988, year = {2021}, author = {He, J and Sun, L and Zhang, L and Leptihn, S and Yu, Y and Hua, X}, title = {A Novel SXT/R391 Integrative and Conjugative Element Carries Two Copies of the blaNDM-1 Gene in Proteus mirabilis.}, journal = {mSphere}, volume = {6}, number = {4}, pages = {e0058821}, pmid = {34378988}, issn = {2379-5042}, mesh = {Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic/*genetics ; DNA Transposable Elements ; Drug Resistance, Multiple, Bacterial/genetics ; Escherichia coli/genetics ; Gene Transfer Techniques ; Proteus mirabilis/drug effects/*enzymology/*genetics ; beta-Lactamases/*genetics ; }, abstract = {The rapid spread of the blaNDM-1 gene is a major public health concern. Here, we describe the multidrug-resistant Proteus mirabilis strain XH1653, which contains a novel SXT/R391 integrative and conjugative element (ICE), harboring two tandem copies of blaNDM-1 and 21 other resistance genes. XH1653 was resistant to all antibiotics tested, apart from aztreonam. Whole-genome data revealed that two copies of blaNDM-1 embedded in the ISCR1 element are located in HS4 of the novel ICE, which we named ICEPmiChnXH1653. A circular intermediate of ICEPmiChnXH1653 was detected by PCR, and conjugation experiments showed that the ICE can be transferred to the Escherichia coli strain EC600 with frequencies of 1.5 × 10[-7]. In the recipient strain, the ICE exhibited a higher excision frequency and extrachromosomal copy number than the ICE in the donor strain. We also observed that the presence of ICEPmiChnXH1653 has a negative impact on bacterial fitness and leads to changes in the transcriptome of the host. In vitro evolution experiments under nonselective conditions showed that the two tandem copies of the ISCR1 element and the ISVsa3 element can be lost during repeated laboratory passage. This is the first report of a novel SXT/R391 ICE carrying two tandem copies of blaNDM-1, which also illustrates the role that ICEs may play as platforms for the accumulation and transmission of antibiotic resistance genes. IMPORTANCE The occurrence of carbapenemase-producing Proteus mirabilis, especially those strains producing NDM-1 and its variants, is a major public health concern worldwide. The integrative conjugative element (ICE) plays an important role in horizontal acquisition of resistance genes. In this study, we characterized a novel SXT/R391 ICE from a clinical P. mirabilis isolate that we named ICEPmiChnXH1653, which contains two tandem copies of the carbapenemase gene blaNDM-1. We performed an integrative approach to gain insights into different aspects of ICEPmiChnXH1653 evolution and biology and observed that ICEPmiChnXH1653 obtained the carbapenemase gene blaNDM-1 by ISCR1-mediated homologous recombination. Our study reveals that the transmission of blaNDM-1 by ISCR1 elements or ICEs may be an important contributor to the carbapenem resistance development across species, which could improve our understanding of horizontal gene transfer in clinical environments.}, }
@article {pmid34375245, year = {2021}, author = {Mishra, S and Klümper, U and Voolaid, V and Berendonk, TU and Kneis, D}, title = {Simultaneous estimation of parameters governing the vertical and horizontal transfer of antibiotic resistance genes.}, journal = {The Science of the total environment}, volume = {798}, number = {}, pages = {149174}, doi = {10.1016/j.scitotenv.2021.149174}, pmid = {34375245}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/pharmacology ; Bayes Theorem ; *Conjugation, Genetic ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Plasmids/genetics ; }, abstract = {The accelerated spread of antibiotic resistance genes (ARG) in the environment occurs mainly through plasmid transfer facilitated via bacterial conjugation. To predict and efficiently counteract the problems associated with ARG transmission, it is important to estimate conjugation rates under different experimental conditions. The classical models typically used to estimate parameters for mating experiments, while pragmatic in calculating growth and plasmid transfer, often ignore processes such as the reduction in growth due to plasmid bearing costs and are non-inclusive of environmental influences like temperature effects. Here, we present a process-based numerical model taking into account the fitness cost associated with plasmid carriage and temperature dependencies in vertical and horizontal gene transfer processes. Observations from liquid culture conjugation experiments using Escherichia coli and the plasmid pB10 were used to validate our proposed model. We present a comparison between the parameters estimated using the existing and the proposed model. Uncertainties in the estimated parameters were quantified using classical and advanced Bayesian methods. For our mating experiments, we found that at temperatures between 20 and 37 °C, the plasmid bearing costs reduced the growth rates by > 35%. The temperature dependency model of conjugation showed a good fit (mean absolute percentage error < 10%) independent of the bacteria and the plasmid under study. The proposed model simultaneously estimates growth and plasmid transfer rate constants for all three strains (donor, recipient, and transconjugant). Simultaneous estimation of growth and conjugation parameters is particularly useful to estimate the spread of ARG when one of the mating partners inhibits the growth of the other, which is common in multi-species mating or when the incurred plasmid costs are situation dependent (e.g., increased plasmid cost in a mating environment) as observed in this study.}, }
@article {pmid34373516, year = {2021}, author = {Gilbert, C and Tengs, T}, title = {No species-level losses of s2m suggests critical role in replication of SARS-related coronaviruses.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {16145}, pmid = {34373516}, issn = {2045-2322}, support = {ANR-18-CE02-0021-01 TranspHorizon//Agence Nationale de la Recherche/ ; }, mesh = {Animals ; Base Sequence ; COVID-19/virology ; Coronaviridae/classification/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Humans ; Interspersed Repetitive Sequences/*genetics ; Phylogeny ; RNA, Viral/*genetics ; SARS-CoV-2/*genetics/physiology ; Sequence Homology, Nucleic Acid ; Species Specificity ; Virus Replication/*genetics ; }, abstract = {The genetic element s2m has been acquired through horizontal transfer by many distantly related viruses, including the SARS-related coronaviruses. Here we show that s2m is evolutionarily conserved in these viruses. Though several lineages of severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) devoid of the element can be found, these variants seem to have been short lived, indicating that they were less evolutionary fit than their s2m-containing counterparts. On a species-level, however, there do not appear to be any losses and this pattern strongly suggests that the s2m element is essential to virus replication in SARS-CoV-2 and related viruses. Further experiments are needed to elucidate the function of s2m.}, }
@article {pmid34370561, year = {2021}, author = {Johnson, CN and Sheriff, EK and Duerkop, BA and Chatterjee, A}, title = {Let Me Upgrade You: Impact of Mobile Genetic Elements on Enterococcal Adaptation and Evolution.}, journal = {Journal of bacteriology}, volume = {203}, number = {21}, pages = {e0017721}, pmid = {34370561}, issn = {1098-5530}, support = {F31 AI157050/AI/NIAID NIH HHS/United States ; R01 AI141479/AI/NIAID NIH HHS/United States ; T32 AI052066/AI/NIAID NIH HHS/United States ; R01AI141479/AI/NIAID NIH HHS/United States ; }, mesh = {Biological Evolution ; CRISPR-Cas Systems ; Enterococcus faecalis/*genetics ; Enterococcus faecium/*genetics ; Interspersed Repetitive Sequences/*genetics ; }, abstract = {Enterococci are Gram-positive bacteria that have evolved to thrive as both commensals and pathogens, largely due to their accumulation of mobile genetic elements via horizontal gene transfer (HGT). Common agents of HGT include plasmids, transposable elements, and temperate bacteriophages. These vehicles of HGT have facilitated the evolution of the enterococci, specifically Enterococcus faecalis and Enterococcus faecium, into multidrug-resistant hospital-acquired pathogens. On the other hand, commensal strains of Enterococcus harbor CRISPR-Cas systems that prevent the acquisition of foreign DNA, restricting the accumulation of mobile genetic elements. In this review, we discuss enterococcal mobile genetic elements by highlighting their contributions to bacterial fitness, examine the impact of CRISPR-Cas on their acquisition, and identify key areas of research that can improve our understanding of enterococcal evolution and ecology.}, }
@article {pmid34364990, year = {2022}, author = {Yano, D and Suzuki, T}, title = {Phosphagen kinases from five groups of eukaryotic protists (Choanomonada, Alveolate, Stramenopiles, Haptophyta, and Cryptophyta): Diverse enzyme activities and phylogenetic relationship with metazoan enzymes.}, journal = {Comparative biochemistry and physiology. Part B, Biochemistry &amp; molecular biology}, volume = {257}, number = {}, pages = {110663}, doi = {10.1016/j.cbpb.2021.110663}, pmid = {34364990}, issn = {1879-1107}, mesh = {Animals ; Cryptophyta ; Evolution, Molecular ; *Haptophyta ; Phylogeny ; *Stramenopiles/genetics ; }, abstract = {Among 28 groups of eukaryotes, apart from Metazoa, phosphagen kinase (PKs) is distributed in only a few protist groups, including the Choanomonada with the closest affinity to metazoans. To clarify the origin of metazoan PKs, we performed a database search and focused on 11 sequences of PK homologs from five groups of protists: the Choanomonada, Alveolata, Haptophyta, Stramenopiles, and Cryptophyta. The recombinant enzymes were prepared to determine their substrate specificity. Emiliania (Haptophyta), Anophryoides, Pseudocohnilembus, Vitrella and Chromera (Alveolata), and Monosiga (Choanomonada) all contained a gene for arginine kinase (AK). In contrast, Aphanomyces, Albugo and Ectocarpus (Stramenopiles), and Guillardia (Cryptophyta) possessed a gene for taurocyamine kinase (TK). The Guillardia TK enzyme exhibited rather strong substrate inhibition toward taurocyamine, which was analyzed using the most likely kinetic model. This was the first report of substrate inhibition in a TK. Together with the research results from other groups, the AK, TK, or creatine kinase (CK) activities have been observed sporadically in at least six groups of protists. However, it is not clear the three enzyme activities were emerged early in the evolution and divergence of protist groups, or some of enzyme activities were introduced to the protists by horizontal gene transfer. In addition, we found that seven protist enzymes examined in this study possess a myristoylation signaling sequence at the N-terminus. The amino-acid sequence around the guanidine-specificity region and the key residue at 89[th] position of the protist AK and CK were homologous to those of the metazoan enzymes, but those for protist TKs were different indicating that the latter evolved independently.}, }
@article {pmid34364793, year = {2021}, author = {Prasad, A and Chirom, O and Prasad, M}, title = {Insect herbivores benefit from horizontal gene transfer.}, journal = {Trends in plant science}, volume = {26}, number = {11}, pages = {1096-1097}, doi = {10.1016/j.tplants.2021.07.012}, pmid = {34364793}, issn = {1878-4372}, mesh = {Animals ; *Gene Transfer, Horizontal ; *Herbivory ; Insecta ; Phylogeny ; }, abstract = {Evidence suggests that horizontal gene transfer (HGT) is relatively common in eukaryotes, contrary to what was previously believed. For example, insects that feed on complex sugars and neutralize, degrade, and sequester toxic secondary metabolites have recently been shown to benefit by acquiring genes through HGT.}, }
@article {pmid34363756, year = {2021}, author = {Moore, RS and Kaletsky, R and Lesnik, C and Cota, V and Blackman, E and Parsons, LR and Gitai, Z and Murphy, CT}, title = {The role of the Cer1 transposon in horizontal transfer of transgenerational memory.}, journal = {Cell}, volume = {184}, number = {18}, pages = {4697-4712.e18}, pmid = {34363756}, issn = {1097-4172}, support = {DP1 AI124669/AI/NIAID NIH HHS/United States ; DP1 GM119167/GM/NIGMS NIH HHS/United States ; T32 GM007388/GM/NIGMS NIH HHS/United States ; AWD1005048/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Avoidance Learning ; Behavior, Animal ; Caenorhabditis elegans/genetics/physiology ; DNA Transposable Elements/*genetics ; Extracellular Vesicles/metabolism ; Gene Expression Regulation ; Gene Transfer, Horizontal/*genetics ; Genome ; Germ Cells/metabolism ; Inheritance Patterns/*genetics ; Memory/*physiology ; RNA/metabolism ; RNA Interference ; Virion/metabolism ; }, abstract = {Animals face both external and internal dangers: pathogens threaten from the environment, and unstable genomic elements threaten from within. C. elegans protects itself from pathogens by "reading" bacterial small RNAs, using this information to both induce avoidance and transmit memories for four generations. Here, we found that memories can be transferred from either lysed animals or from conditioned media to naive animals via Cer1 retrotransposon-encoded virus-like particles. Moreover, Cer1 functions internally at the step of transmission of information from the germline to neurons and is required for learned avoidance. The presence of the Cer1 retrotransposon in wild C. elegans strains correlates with the ability to learn and inherit small-RNA-induced pathogen avoidance. Together, these results suggest that C. elegans has co-opted a potentially dangerous retrotransposon to instead protect itself and its progeny from a common pathogen through its inter-tissue signaling ability, hijacking this genomic element for its own adaptive immunity benefit.}, }
@article {pmid34361875, year = {2021}, author = {Del Duca, S and Riccardi, C and Vassallo, A and Fontana, G and Castronovo, LM and Chioccioli, S and Fani, R}, title = {The Histidine Biosynthetic Genes in the Superphylum Bacteroidota-Rhodothermota-Balneolota-Chlorobiota: Insights into the Evolution of Gene Structure and Organization.}, journal = {Microorganisms}, volume = {9}, number = {7}, pages = {}, pmid = {34361875}, issn = {2076-2607}, abstract = {One of the most studied metabolic routes is the biosynthesis of histidine, especially in enterobacteria where a single compact operon composed of eight adjacent genes encodes the complete set of biosynthetic enzymes. It is still not clear how his genes were organized in the genome of the last universal common ancestor community. The aim of this work was to analyze the structure, organization, phylogenetic distribution, and degree of horizontal gene transfer (HGT) of his genes in the Bacteroidota-Rhodothermota-Balneolota-Chlorobiota superphylum, a group of phylogenetically close bacteria with different surviving strategies. The analysis of the large variety of his gene structures and organizations revealed different scenarios with genes organized in more or less compact-heterogeneous or homogeneous-operons, in suboperons, or in regulons. The organization of his genes in the extant members of the superphylum suggests that in the common ancestor of this group, genes were scattered throughout the chromosome and that different forces have driven the assembly of his genes in compact operons. Gene fusion events and/or paralog formation, HGT of single genes or entire operons between strains of the same or different taxonomic groups, and other molecular rearrangements shaped the his gene structure in this superphylum.}, }
@article {pmid34360567, year = {2021}, author = {Flórez, AB and Vázquez, L and Rodríguez, J and Mayo, B}, title = {Directed Recovery and Molecular Characterization of Antibiotic Resistance Plasmids from Cheese Bacteria.}, journal = {International journal of molecular sciences}, volume = {22}, number = {15}, pages = {}, pmid = {34360567}, issn = {1422-0067}, support = {Ref. PID2019-110549RB-I00/AEI/10.13039/501100011033)//Spanish Ministry of Economy and Competitiveness/ ; Ref. IDI/2018/000114//Asturias Principality, Spain/ ; BP19-098//Severo Ochoa Program from Asturias Principality (Ph.D. grant)/ ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Cheese/*microbiology ; *Drug Resistance, Microbial ; Erythromycin/*pharmacology ; Lactobacillales/drug effects/*growth &amp; development/isolation &amp; purification ; Plasmids/*genetics ; }, abstract = {Resistance to antimicrobials is a growing problem of worldwide concern. Plasmids are thought to be major drivers of antibiotic resistance spread. The present work reports a simple way to recover replicative plasmids conferring antibiotic resistance from the bacteria in cheese. Purified plasmid DNA from colonies grown in the presence of tetracycline and erythromycin was introduced into plasmid-free strains of Lactococcus lactis, Lactiplantibacillus plantarum and Lacticaseibacillus casei. Following antibiotic selection, the plasmids from resistant transformants were isolated, analyzed by restriction enzyme digestion, and sequenced. Seven patterns were obtained for the tetracycline-resistant colonies, five from L. lactis, and one each from the lactobacilli strains, as well as a single digestion profile for the erythromycin-resistant transformants obtained in L. lactis. Sequence analysis respectively identified tet(S) and ermB in the tetracycline- and erythromycin-resistance plasmids from L. lactis. No dedicated resistance genes were detected in plasmids conferring tetracycline resistance to L. casei and L. plantarum. The present results highlight the usefulness of the proposed methodology for isolating functional plasmids that confer antibiotic resistance to LAB species, widen our knowledge of antibiotic resistance in the bacteria that inhabit cheese, and emphasize the leading role of plasmids in the spread of resistance genes via the food chain.}, }
@article {pmid34358059, year = {2021}, author = {Bonifácio, M and Mateus, C and Alves, AR and Maldonado, E and Duarte, AP and Domingues, F and Oleastro, M and Ferreira, S}, title = {Natural Transformation as a Mechanism of Horizontal Gene Transfer in Aliarcobacter butzleri.}, journal = {Pathogens (Basel, Switzerland)}, volume = {10}, number = {7}, pages = {}, pmid = {34358059}, issn = {2076-0817}, support = {UIDB / 00709/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; CENTRO-01-0145-FEDER-000019 - C4 - Centro de Compet&#xea;ncias em Cloud Computing//European Regional Development Fund/ ; UI/BD/151023/2021//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, abstract = {Aliarcobacter butzleri is an emergent enteropathogen, showing high genetic diversity, which likely contributes to its adaptive capacity to different environments. Whether natural transformation can be a mechanism that generates genetic diversity in A. butzleri is still unknown. In the present study, we aimed to establish if A. butzleri is naturally competent for transformation and to investigate the factors influencing this process. Two different transformation procedures were tested using exogenous and isogenic DNA containing antibiotic resistance markers, and different external conditions influencing the process were evaluated. The highest number of transformable A. butzleri strains were obtained with the agar transformation method when compared to the biphasic system (65% versus 47%). A. butzleri was able to uptake isogenic chromosomal DNA at different growth phases, and the competence state was maintained from the exponential to the stationary phases. Overall, the optimal conditions for transformation with the biphasic system were the use of 1 μg of isogenic DNA and incubation at 30 °C under a microaerobic atmosphere, resulting in a transformation frequency ~8 × 10[-6] transformants/CFU. We also observed that A. butzleri favored the transformation with the genetic material of its own strain/species, with the DNA incorporation process occurring promptly after the addition of genomic material. In addition, we observed that A. butzleri strains could exchange genetic material in co-culture assays. The presence of homologs of well-known genes involved in the competence in the A. butzleri genome corroborates the natural competence of this species. In conclusion, our results show that A. butzleri is a naturally transformable species, suggesting that horizontal gene transfer mediated by natural transformation is one of the processes contributing to its genetic diversity. In addition, natural transformation can be used as a tool for genetic studies of this species.}, }
@article {pmid34356763, year = {2021}, author = {Schneider, YK}, title = {Bacterial Natural Product Drug Discovery for New Antibiotics: Strategies for Tackling the Problem of Antibiotic Resistance by Efficient Bioprospecting.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {10}, number = {7}, pages = {}, pmid = {34356763}, issn = {2079-6382}, support = {GA 721421 H2020-MSCA-ITN-2016//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; }, abstract = {The problem of antibiotic resistance has become a challenge for our public health and society; it has allowed infectious diseases to re-emerge as a risk to human health. New antibiotics that are introduced to the market face the rise of resistant pathogens after a certain period of use. The relatively fast development of resistance against some antibiotics seems to be closely linked to their microbial origin and function in nature. Antibiotics in clinical use are merely products of microorganisms or derivatives of microbial products. The evolution of these antimicrobial compounds has progressed with the evolution of the respective resistance mechanisms in microbes for billions of years. Thus, antimicrobial resistance genes are present within the environment and can be taken up by pathogens through horizontal gene transfer. Natural products from bacteria are an important source of leads for drug development, and microbial natural products have contributed the most antibiotics in current clinical use. Bioprospecting for new antibiotics is a labor-intensive task as obstacles such as redetection of known compounds and low compound yields consume significant resources. The number of bacterial isolates one can theoretically investigate for new secondary metabolites is, on the other hand, immense. Therefore, the available capacity for biodiscovery should be focused on the most promising sources for chemical novelty and bioactivity, employing the appropriate scientific tools. This can be done by first looking into under- or unexplored environments for bacterial isolates and by focusing on the promising candidates to reduce the number of subjects.}, }
@article {pmid34356760, year = {2021}, author = {Kalová, A and Gelbíčová, T and Overballe-Petersen, S and Litrup, E and Karpíšková, R}, title = {Characterisation of Colistin -Resistant Enterobacterales and Acinetobacter Strains Carrying mcr Genes from Asian Aquaculture Products.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {10}, number = {7}, pages = {}, pmid = {34356760}, issn = {2079-6382}, support = {NV 18-09-00254//Ministerstvo Zdravotnictv&#xed; Cesk&#xe9; Republiky/ ; }, abstract = {Aquaculture systems are widely recognised as hotspots for horizontal gene transfer, and the need for screening for bacteria carrying antimicrobial resistance genes in aquaculture systems is becoming more important. In this study, we characterised seventeen bacterial strains (Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, and A. nosocomialis) resistant to colistin originating from retailed aquaculture products imported from Vietnam to the Czech Republic. The mcr-1.1 gene was found located on plasmid types IncHI2, IncI2, and IncX4, as well as on the rarely described plasmid types IncFIB-FIC and IncFIB(K), phage-like plasmid p0111, and on the chromosome of E. coli. One E. coli strain carried the mcr-3.5 gene on IncFII(pCoo) plasmid in addition to the mcr-1.1 gene located on IncHI2 plasmid. K. pneumoniae was found to carry the mcr-1.1 and mcr-8.2 genes on IncFIA(HI1) plasmid. The mcr-4.3 gene was found on similar untypeable plasmids of A. baumannii and A. nosocomialis strains, pointing to the possible interspecies transfer of plasmids carrying the mcr-4 gene. Our results highlight that some aquaculture products of Asian origin can represent an important source of variable plasmids carrying mcr genes. The results showed an involvement of phages in the incorporation of the mcr-1 gene into plasmids or the chromosome in E. coli strains from aquaculture. The detection of E. coli with the mcr-1 gene in the chromosome points to the risks associated with the stabilisation of the mcr genes in the bacterial chromosome.}, }
@article {pmid34356729, year = {2021}, author = {Gargano, V and Sciortino, S and Gambino, D and Costa, A and Agozzino, V and Reale, S and Alduina, R and Vicari, D}, title = {Antibiotic Susceptibility Profile and Tetracycline Resistance Genes Detection in Salmonella spp. Strains Isolated from Animals and Food.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {10}, number = {7}, pages = {}, pmid = {34356729}, issn = {2079-6382}, abstract = {Salmonella spp. is among the leading causes of foodborne infections in humans and a large number of animals. Salmonella spp. is a pathogen involved in the dissemination of antimicrobial resistance because it can accumulate antibiotic resistance genes (ARGs). In this study, the antibiotic resistance profile to 15 antibiotics, belonging to six different classes, of 60 strains of Salmonella spp. collected from pets, farm animals, wildlife, and food in Sicily (Italy) was investigated by the Kirby-Bauer method. Given that almost 33.3% of the Salmonella spp. strains were resistant to tetracycline, Real-Time PCR analysis was applied on all the 60 strains to detect the presence of eight selected tet resistance genes. Besides, the presence of the int1 gene, related to the horizontal gene transfer among bacteria, was also investigated in all the strains by Real-Time PCR analysis. Our data showed that 56% of the isolated strains harbored one or more tet resistance genes and that these strains were most frequently isolated from animals living in close contact with humans. Concerning int1, 17 strains (28.3%) harbored this genetic element and eight of these simultaneously contained tet genes. The results of this study highlight the importance of using a molecular approach to detect resistance genetic determinants, whose spread can increase the diffusion of multidrug-resistant strains. Besides, the study of zoonotic bacteria such as Salmonella spp. which significantly contribute to ARGs dissemination should always follow a One Health approach that considers the health of humans, animals, and the environment to be closely related.}, }
@article {pmid34352499, year = {2021}, author = {Gu, Y and Lü, Z and Cao, C and Sheng, H and Li, W and Cui, S and Li, R and Lü, X and Yang, B}, title = {Cunning plasmid fusion mediates antibiotic resistance genes represented by ESBLs encoding genes transfer in foodborne Salmonella.}, journal = {International journal of food microbiology}, volume = {355}, number = {}, pages = {109336}, doi = {10.1016/j.ijfoodmicro.2021.109336}, pmid = {34352499}, issn = {1879-3460}, mesh = {Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal/genetics ; *Plasmids/genetics ; *Salmonella/drug effects/genetics ; }, abstract = {Foodborne disease caused by antibiotic resistant Salmonella is quite difficult to deal with. In order to further explore the antibiotic resistance associated with gene transfer among foodborne Salmonella, several wild-type Salmonella strains were used as donors and recipients, respectively, to investigate how extended spectrum β-lactamases (ESBLs) encoding genes co-transfer with transposable elements to transmit antibiotic resistance. Antibiotic susceptibility was determined by agar dilution method, the transposase encoding gene was detected via PCR combined with DNA sequencing, S1 nuclease and pulsed field gel electrophoresis (S1-PFGE), and southern-blot. Illumina HiSeq 4000 platform and Nanopore MinION long-read sequencing technology were used to determine the antibiotic resistance encoding genes (ARGs) and their surrounding gene environment. The results indicated that the conjugation frequency was from ×10[-4] to ×10[-5] per recipient cell. A 185,608-bp-long DNA fragment and two short backbone protein encoding regions in pG19 in the donor fused with part genes in pS3 in the recipient during conjugation, the size of this fusion plasmid is as same as that of pG19. Cefoxitin resistance of the transconjugant was mediated by a tnpA21-related blaDHA-1 transfer. Resistance of Salmonella to ceftriaxone, cefoperazone and ceftiofur was mediated by a tnpU1548 related blaTEM-1B and blaCTX-M-3 transfer. The study indicated that transposase synergy and plasmid selective fusion act as important roles for foodborne Salmonella gathering ARGs. The consistent size of the plasmid before and after fusion suggested the invisibility and complexity of bacterial conjugation without DNA sequencing, the fact reminded us that the rampant transmission of antibiotic-resistance encoding genes would pose tremendous threat to food safety.}, }
@article {pmid34349732, year = {2021}, author = {Pallares-Vega, R and Macedo, G and Brouwer, MSM and Hernandez Leal, L and van der Maas, P and van Loosdrecht, MCM and Weissbrodt, DG and Heederik, D and Mevius, D and Schmitt, H}, title = {Temperature and Nutrient Limitations Decrease Transfer of Conjugative IncP-1 Plasmid pKJK5 to Wild Escherichia coli Strains.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {656250}, pmid = {34349732}, issn = {1664-302X}, abstract = {Plasmid-mediated dissemination of antibiotic resistance among fecal Enterobacteriaceae in natural ecosystems may contribute to the persistence of antibiotic resistance genes in anthropogenically impacted environments. Plasmid transfer frequencies measured under laboratory conditions might lead to overestimation of plasmid transfer potential in natural ecosystems. This study assessed differences in the conjugative transfer of an IncP-1 (pKJK5) plasmid to three natural Escherichia coli strains carrying extended-spectrum beta-lactamases, by filter mating. Matings were performed under optimal laboratory conditions (rich LB medium and 37°C) and environmentally relevant temperatures (25, 15 and 9°C) or nutrient regimes mimicking environmental conditions and limitations (synthetic wastewater and soil extract). Under optimal nutrient conditions and temperature, two recipients yielded high transfer frequencies (5 × 10[-1]) while the conjugation frequency of the third strain was 1000-fold lower. Decreasing mating temperatures to psychrophilic ranges led to lower transfer frequencies, albeit all three strains conjugated under all the tested temperatures. Low nutritive media caused significant decreases in transconjugants (-3 logs for synthetic wastewater; -6 logs for soil extract), where only one of the strains was able to produce detectable transconjugants. Collectively, this study highlights that despite less-than-optimal conditions, fecal organisms may transfer plasmids in the environment, but the transfer of pKJK5 between microorganisms is limited mainly by low nutrient conditions.}, }
@article {pmid34347343, year = {2022}, author = {Phale, PS and Mohapatra, B and Malhotra, H and Shah, BA}, title = {Eco-physiological portrait of a novel Pseudomonas sp. CSV86: an ideal host/candidate for metabolic engineering and bioremediation.}, journal = {Environmental microbiology}, volume = {24}, number = {6}, pages = {2797-2816}, doi = {10.1111/1462-2920.15694}, pmid = {34347343}, issn = {1462-2920}, mesh = {Biodegradation, Environmental ; Metabolic Engineering ; Naphthalenes/metabolism ; *Pseudomonas/genetics/metabolism ; *Pseudomonas putida/genetics ; }, abstract = {Pseudomonas sp. CSV86, an Indian soil isolate, degrades wide range of aromatic compounds like naphthalene, benzoate and phenylpropanoids, amongst others. Isolate displays the unique and novel property of preferential utilization of aromatics over glucose and co-metabolizes them with organic acids. Interestingly, as compared to other Pseudomonads, strain CSV86 harbours only high-affinity glucokinase pathway (and absence of low-affinity oxidative route) for glucose metabolism. Such lack of gluconate loop might be responsible for the novel phenotype of preferential utilization of aromatics. The genome analysis and comparative functional mining indicated a large genome (6.79 Mb) with significant enrichment of regulators, transporters as well as presence of various secondary metabolite production clusters, suggesting its eco-physiological and metabolic versatility. Strain harbours various integrative conjugative elements (ICEs) and genomic islands, probably acquired through horizontal gene transfer events, leading to genome mosaicity and plasticity. Naphthalene degradation genes are arranged as regulonic clusters and found to be part of ICECSV86nah . Various eco-physiological properties and absence of major pathogenicity and virulence factors (risk group-1) in CSV86 suggest it to be an ideal candidate for bioremediation. Further, strain can serve as an ideal chassis for metabolic engineering to degrade various xenobiotics preferentially over simple carbon sources for efficient remediation.}, }
@article {pmid34346702, year = {2021}, author = {Plaza, N and Urrutia, IM and Garcia, K and Waldor, MK and Blondel, CJ}, title = {Identification of a Family of Vibrio Type III Secretion System Effectors That Contain a Conserved Serine/Threonine Kinase Domain.}, journal = {mSphere}, volume = {6}, number = {4}, pages = {e0059921}, pmid = {34346702}, issn = {2379-5042}, support = {R01 AI042347/AI/NIAID NIH HHS/United States ; 55008749//Howard Hughes Medical Institute (HHMI)/ ; }, mesh = {Bacterial Proteins/chemistry/*genetics/metabolism ; Caco-2 Cells ; Computational Biology ; Gene Expression Regulation, Bacterial ; Humans ; Interleukin-8/immunology ; Multigene Family ; Protein Serine-Threonine Kinases/*genetics ; Protein Transport ; Serine/metabolism ; Type III Secretion Systems/*genetics/metabolism ; Vibrio parahaemolyticus/*enzymology/*genetics/metabolism/pathogenicity ; }, abstract = {Vibrio parahaemolyticus is a marine Gram-negative bacterium that is a leading cause of seafood-borne gastroenteritis. Pandemic strains of V. parahaemolyticus rely on a specialized protein secretion machinery known as the type III secretion system 2 (T3SS2) to cause disease. The T3SS2 mediates the delivery of effector proteins into the cytosol of infected cells, where they subvert multiple cellular pathways. Here, we identify a new T3SS2 effector protein encoded by VPA1328 (VP_RS21530) in V. parahaemolyticus RIMD2210633. Bioinformatic analysis revealed that VPA1328 is part of a larger family of uncharacterized T3SS effector proteins with homology to the VopG effector protein in Vibrio cholerae AM-19226. These VopG-like proteins are found in many but not all T3SS2 gene clusters and are distributed among diverse Vibrio species, including V. parahaemolyticus, V. cholerae, V. mimicus, and V. diabolicus and also in Shewanella baltica. Structure-based prediction analyses uncovered the presence of a conserved C-terminal kinase domain in VopG orthologs, similar to the serine/threonine kinase domain found in the NleH family of T3SS effector proteins. However, in contrast to NleH effector proteins, in tissue culture-based infections, VopG did not impede host cell death or suppress interleukin 8 (IL-8) secretion, suggesting a yet undefined role for VopG during V. parahaemolyticus infection. Collectively, our work reveals that VopG effector proteins, a new family of likely serine/threonine kinases, is widely distributed in the T3SS2 effector armamentarium among marine bacteria. IMPORTANCE Vibrio parahaemolyticus is the leading bacterial cause of seafood-borne gastroenteritis worldwide. The pathogen relies on a type III secretion system to deliver a variety of effector proteins into the cytosol of infected cells to subvert cellular function. In this study, we identified a novel Vibrio parahaemolyticus effector protein that is similar to the VopG effector of Vibrio cholerae. VopG-like effectors were found in diverse Vibrio species and contain a conserved serine/threonine kinase domain that bears similarity to the kinase domain in the enterohemorrhagic Escherichia coli (EHEC) and Shigella NleH effectors that manipulate host cell survival pathways and host immune responses. Together our findings identify a new family of Vibrio effector proteins and highlight the role of horizontal gene transfer events among marine bacteria in shaping T3SS gene clusters.}, }
@article {pmid34342537, year = {2021}, author = {Pearcy, N and Hu, Y and Baker, M and Maciel-Guerra, A and Xue, N and Wang, W and Kaler, J and Peng, Z and Li, F and Dottorini, T}, title = {Genome-Scale Metabolic Models and Machine Learning Reveal Genetic Determinants of Antibiotic Resistance in Escherichia coli and Unravel the Underlying Metabolic Adaptation Mechanisms.}, journal = {mSystems}, volume = {6}, number = {4}, pages = {e0091320}, pmid = {34342537}, issn = {2379-5077}, support = {//Global Challenges Research Fund (GCRF)/ ; 2018YFE0101500//Ministry of Science and Technology of the People's Republic of China (MOST)/ ; 104986//UK Research and Innovation (UKRI)/ ; }, abstract = {Antimicrobial resistance (AMR) is becoming one of the largest threats to public health worldwide, with the opportunistic pathogen Escherichia coli playing a major role in the AMR global health crisis. Unravelling the complex interplay between drug resistance and metabolic rewiring is key to understand the ability of bacteria to adapt to new treatments and to the development of new effective solutions to combat resistant infections. We developed a computational pipeline that combines machine learning with genome-scale metabolic models (GSMs) to elucidate the systemic relationships between genetic determinants of resistance and metabolism beyond annotated drug resistance genes. Our approach was used to identify genetic determinants of 12 AMR profiles for the opportunistic pathogenic bacterium E. coli. Then, to interpret the large number of identified genetic determinants, we applied a constraint-based approach using the GSM to predict the effects of genetic changes on growth, metabolite yields, and reaction fluxes. Our computational platform leads to multiple results. First, our approach corroborates 225 known AMR-conferring genes, 35 of which are known for the specific antibiotic. Second, integration with the GSM predicted 20 top-ranked genetic determinants (including accA, metK, fabD, fabG, murG, lptG, mraY, folP, and glmM) essential for growth, while a further 17 top-ranked genetic determinants linked AMR to auxotrophic behavior. Third, clusters of AMR-conferring genes affecting similar metabolic processes are revealed, which strongly suggested that metabolic adaptations in cell wall, energy, iron and nucleotide metabolism are associated with AMR. The computational solution can be used to study other human and animal pathogens. IMPORTANCE Escherichia coli is a major public health concern given its increasing level of antibiotic resistance worldwide and extraordinary capacity to acquire and spread resistance via horizontal gene transfer with surrounding species and via mutations in its existing genome. E. coli also exhibits a large amount of metabolic pathway redundancy, which promotes resistance via metabolic adaptability. In this study, we developed a computational approach that integrates machine learning with metabolic modeling to understand the correlation between AMR and metabolic adaptation mechanisms in this model bacterium. Using our approach, we identified AMR genetic determinants associated with cell wall modifications for increased permeability, virulence factor manipulation of host immunity, reduction of oxidative stress toxicity, and changes to energy metabolism. Unravelling the complex interplay between antibiotic resistance and metabolic rewiring may open new opportunities to understand the ability of E. coli, and potentially of other human and animal pathogens, to adapt to new treatments.}, }
@article {pmid34340549, year = {2021}, author = {Mullins, AJ and Webster, G and Kim, HJ and Zhao, J and Petrova, YD and Ramming, CE and Jenner, M and Murray, JAH and Connor, TR and Hertweck, C and Challis, GL and Mahenthiralingam, E}, title = {Discovery of the Pseudomonas Polyyne Protegencin by a Phylogeny-Guided Study of Polyyne Biosynthetic Gene Cluster Diversity.}, journal = {mBio}, volume = {12}, number = {4}, pages = {e0071521}, pmid = {34340549}, issn = {2150-7511}, support = {BB/M009122/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; BB/S007652/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/K002341/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012121/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/S008020/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Biosynthetic Pathways/*genetics ; Evolution, Molecular ; Genome, Bacterial ; Genomics ; *Multigene Family ; *Phylogeny ; Polyynes/*classification/*metabolism ; Pseudomonas/*genetics/*metabolism ; }, abstract = {Natural products that possess alkyne or polyyne moieties have been isolated from a variety of biological sources and possess a broad a range of bioactivities. In bacteria, the basic biosynthesis of polyynes is known, but their biosynthetic gene cluster (BGC) distribution and evolutionary relationship to alkyne biosynthesis have not been addressed. Through comprehensive genomic and phylogenetic analyses, the distribution of alkyne biosynthesis gene cassettes throughout bacteria was explored, revealing evidence of multiple horizontal gene transfer events. After investigation of the evolutionary connection between alkyne and polyyne biosynthesis, a monophyletic clade was identified that possessed a conserved seven-gene cassette for polyyne biosynthesis that built upon the conserved three-gene cassette for alkyne biosynthesis. Further diversity mapping of the conserved polyyne gene cassette revealed a phylogenetic subclade for an uncharacterized polyyne BGC present in several Pseudomonas species, designated pgn. Pathway mutagenesis and high-resolution analytical chemistry showed the Pseudomonas protegens pgn BGC directed the biosynthesis of a novel polyyne, protegencin. Exploration of the biosynthetic logic behind polyyne production, through BGC mutagenesis and analytical chemistry, highlighted the essentiality of a triad of desaturase proteins and a thioesterase in both the P. protegens pgn and Trinickia caryophylli (formerly Burkholderia caryophylli) caryoynencin pathways. We have unified and expanded knowledge of polyyne diversity and uniquely demonstrated that alkyne and polyyne biosynthetic gene clusters are evolutionarily related and widely distributed within bacteria. The systematic mapping of conserved biosynthetic genes across the available bacterial genomic diversity proved to be a fruitful method for discovering new natural products and better understanding polyyne biosynthesis. IMPORTANCE Natural products bearing alkyne (triple carbon bond) or polyyne (multiple alternating single and triple carbon bonds) moieties exhibit a broad range of important biological activities. Polyyne metabolites have been implicated in important ecological roles such as cepacin mediating biological control of plant pathogens and caryoynencin protecting Lagriinae beetle eggs against pathogenic fungi. After further phylogenetic exploration of polyyne diversity, we identified a novel gene cluster in Pseudomonas bacteria with known biological control abilities and proved it was responsible for synthesizing a new polyyne metabolite, protegencin. The evolutionary analysis of polyyne pathways showed that multiple biosynthetic genes were conserved, and using mutagenesis, their essentiality was demonstrated. Our research provides a foundation for the future modification of polyyne metabolites and has identified a novel polyyne, protegencin, with potential bioactive roles of ecological and agricultural importance.}, }
@article {pmid34339990, year = {2022}, author = {Zhang, S and Lu, J and Wang, Y and Verstraete, W and Yuan, Z and Guo, J}, title = {Insights of metallic nanoparticles and ions in accelerating the bacterial uptake of antibiotic resistance genes.}, journal = {Journal of hazardous materials}, volume = {421}, number = {}, pages = {126728}, doi = {10.1016/j.jhazmat.2021.126728}, pmid = {34339990}, issn = {1873-3336}, mesh = {Acinetobacter/genetics ; Anti-Bacterial Agents ; *Drug Resistance, Microbial/genetics ; Humans ; *Ions/toxicity ; *Metal Nanoparticles/toxicity ; }, abstract = {The increasing release of nanomaterials has attracted significant concerns for human and environmental health. Similarly, the dissemination of antimicrobial resistance (AMR) is a global health crisis affecting approximately 700,000 people a year. However, a knowledge gap persists between the spread of AMR and nanomaterials. This study aims to fill this gap by investigating whether and how nanomaterials could directly facilitate the dissemination of AMR through horizontal gene transfer. Our results show that commonly-used nanoparticles (NPs) (Ag, CuO and ZnO NPs) and their ion forms (Ag[+], Cu[2+] and Zn[2+]) at realistic concentrations within aquatic environments can significantly promote the transformation of extracellular antibiotic resistance genes in Acinetobacter baylyi ADP1 by a factor of 11.0-folds, which is comparable to the effects of antibiotics. The enhanced transformation by Ag NPs/Ag[+] and CuO NPs/Cu[2+] was primarily associated with the overproduction of reactive oxygen species and cell membrane damage. ZnO NPs/Zn[2+] might increase the natural transformation rate by stimulating the stress response and ATP synthesis. All tested NPs/ions resulted in upregulating the competence and SOS response-associated genes. These findings highlight a new concern that nanomaterials can speed up the spread of AMR, which should not be ignored when assessing the holistic risk of nanomaterials.}, }
@article {pmid34332528, year = {2021}, author = {Redondo-Salvo, S and Bartomeus-Peñalver, R and Vielva, L and Tagg, KA and Webb, HE and Fernández-López, R and de la Cruz, F}, title = {COPLA, a taxonomic classifier of plasmids.}, journal = {BMC bioinformatics}, volume = {22}, number = {1}, pages = {390}, pmid = {34332528}, issn = {1471-2105}, support = {BFU2017-86378-P//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; DI-17-09164//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; 200-2019-06679/CC/CDC HHS/United States ; }, mesh = {Drug Resistance, Microbial ; *Gene Transfer, Horizontal ; *Genomics ; Plasmids/genetics ; Virulence Factors ; }, abstract = {BACKGROUND: Plasmids are mobile genetic elements, key in the dissemination of antibiotic resistance, virulence determinants and other adaptive traits in bacteria. Obtaining a robust method for plasmid classification is necessary to better understand the genetics and epidemiology of many pathogens. Until now, plasmid classification systems focused on specific traits, which limited their precision and universality. The definition of plasmid taxonomic units (PTUs), based on average nucleotide identity metrics, allows the generation of a universal plasmid classification scheme, applicable to all bacterial taxa. Here we present COPLA, a software able to assign plasmids to known and novel PTUs, based on their genomic sequence.<br><br>RESULTS: We implemented an automated pipeline able to assign a given plasmid DNA sequence to its cognate PTU, and assessed its performance using a sample of 1000 unclassified plasmids. Overall, 41% of the samples could be assigned to a previously defined PTU, a number that reached 63% in well-known taxa such as the Enterobacterales order. The remaining plasmids represent novel PTUs, indicating that a large fraction of plasmid backbones is still uncharacterized.<br><br>CONCLUSIONS: COPLA is a bioinformatic tool for universal, species-independent, plasmid classification. Offered both as an automatable pipeline and an open web service, COPLA will help bacterial geneticists and clinical microbiologists to quickly classify plasmids.}, }
@article {pmid34327906, year = {2021}, author = {Bai, Z and Wang, W and Ji, X and Xiao, Y and Zhang, S and Wang, Z and Li, H and Dong, Q}, title = {[Application of CRISPR in evolution analysis, detecting and typing, virulence and antibiotic resistance regulation in food-borne pathogens].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {37}, number = {7}, pages = {2414-2424}, doi = {10.13345/j.cjb.200539}, pmid = {34327906}, issn = {1872-2075}, mesh = {Bacteria/genetics ; *Bacteriophages/genetics ; CRISPR-Cas Systems/genetics ; *Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Drug Resistance, Microbial/genetics ; Virulence/genetics ; }, abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR) and its associated protein gene system can limit the horizontal gene transfer, thereby effectively preventing the invasion of foreign gene elements such as bacteriophages. CRISPR arrays of different bacteria are diverse. Based on the differences in the CRISPR system, this review summarizes the application of CRISPR in food-borne pathogen evolution analysis, detection and typing, virulence and antibiotic resistance in recent years. We also address bacterial detection typing method developed based on the characteristics of CRISPR arrays and the association of CRISPR with virulence and drug resistance of food-borne pathogens. The shortcomings of CRISPR in evolution, detection and typing, virulence and resistance applications are analyzed. In addition, we suggest standardizing CRISPR typing methods, improving and expanding the CRISPR database of pathogenic bacteria, and further exploring the co-evolution relationship between phages and bacteria, to provide references for further exploration of CRISPR functions.}, }
@article {pmid34326267, year = {2021}, author = {Dimitriu, T and Matthews, AC and Buckling, A}, title = {Increased copy number couples the evolution of plasmid horizontal transmission and plasmid-encoded antibiotic resistance.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {31}, pages = {}, pmid = {34326267}, issn = {1091-6490}, mesh = {Anti-Bacterial Agents/*pharmacology ; Computational Biology ; *DNA Copy Number Variations ; Directed Molecular Evolution ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/*drug effects/genetics ; Gene Transfer, Horizontal ; Plasmids/*genetics ; }, abstract = {Conjugative plasmids are mobile elements that spread horizontally between bacterial hosts and often confer adaptive phenotypes, including antimicrobial resistance (AMR). Theory suggests that opportunities for horizontal transmission favor plasmids with higher transfer rates, whereas selection for plasmid carriage favors less-mobile plasmids. However, little is known about the mechanisms leading to variation in transmission rates in natural plasmids or the resultant effects on their bacterial host. We investigated the evolution of AMR plasmids confronted with different immigration rates of susceptible hosts. Plasmid RP4 did not evolve in response to the manipulations, but plasmid R1 rapidly evolved up to 1,000-fold increased transfer rates in the presence of susceptible hosts. Most evolved plasmids also conferred on their hosts the ability to grow at high concentrations of antibiotics. This was because plasmids evolved greater copy numbers as a function of mutations in the copA gene controlling plasmid replication, causing both higher transfer rates and AMR. Reciprocally, plasmids with increased conjugation rates also evolved when selecting for high levels of AMR, despite the absence of susceptible hosts. Such correlated selection between plasmid transfer and AMR could increase the spread of AMR within populations and communities.}, }
@article {pmid34326235, year = {2021}, author = {Gasmi, L and Sieminska, E and Okuno, S and Ohta, R and Coutu, C and Vatanparast, M and Harris, S and Baldwin, D and Hegedus, DD and Theilmann, DA and Kida, A and Kawabata, M and Sagawa, S and Takatsuka, J and Tateishi, K and Watanabe, K and Inoue, MN and Kunimi, Y and Kim, Y and Erlandson, MA and Herrero, S and Nakai, M}, title = {Horizontally transmitted parasitoid killing factor shapes insect defense to parasitoids.}, journal = {Science (New York, N.Y.)}, volume = {373}, number = {6554}, pages = {535-541}, doi = {10.1126/science.abb6396}, pmid = {34326235}, issn = {1095-9203}, mesh = {Animals ; Apoptosis ; Biological Evolution ; Entomopoxvirinae/*physiology ; Gene Transfer, Horizontal ; Genome, Insect ; Host-Parasite Interactions ; Insect Proteins/chemistry/genetics/metabolism/*toxicity ; Insect Viruses/physiology ; Larva/genetics/parasitology/virology ; Lepidoptera/genetics/metabolism/*parasitology/*virology ; Nucleopolyhedroviruses/physiology ; Spodoptera/genetics/metabolism/parasitology/virology ; Viral Proteins/chemistry/genetics/metabolism/*toxicity ; Wasps/growth &amp; development/*physiology ; }, abstract = {Interkingdom competition occurs between hymenopteran parasitoids and insect viruses sharing the same insect hosts. It has been assumed that parasitoid larvae die with the death of the infected host or as result of competition for host resources. Here we describe a gene family, parasitoid killing factor (pkf), that encodes proteins toxic to parasitoids of the Microgastrinae group and determines parasitism success. Pkfs are found in several entomopathogenic DNA virus families and in some lepidopteran genomes. We provide evidence of equivalent and specific toxicity against endoparasites for PKFs found in entomopoxvirus, ascovirus, baculovirus, and Lepidoptera through a mechanism that elicits apoptosis in the cells of susceptible parasitoids. This highlights the evolutionary arms race between parasitoids, viruses, and their insect hosts.}, }
@article {pmid34325101, year = {2021}, author = {Liu, S and Wang, P and Wang, C and Wang, X and Chen, J}, title = {Anthropogenic disturbances on antibiotic resistome along the Yarlung Tsangpo River on the Tibetan Plateau: Ecological dissemination mechanisms of antibiotic resistance genes to bacterial pathogens.}, journal = {Water research}, volume = {202}, number = {}, pages = {117447}, doi = {10.1016/j.watres.2021.117447}, pmid = {34325101}, issn = {1879-2448}, mesh = {*Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Genes, Bacterial/genetics ; Humans ; *Rivers ; Tibet ; }, abstract = {Human activities can accelerate the antibiotic resistome prevalence and pose threats to ecological safety and public health globally. However, antibiotic resistance gene (ARG) mobility and dissemination into bacterial pathogens under anthropogenic disturbances are still poorly understood. Here, we used a metagenomic approach to profile the biogeography of ARGs and pathogenic antibiotic resistant bacteria (PARB) under anthropogenic disturbances along the Yarlung Tsangpo River. Results showed the ARGs was dominated by bacA gene along the Yarlung Tsangpo River on the Tibetan Plateau. The ARG composition was differently impacted by rapid urbanization and dam construction, which urbanization could promote ARGs resistant to sulfonamide and tetracycline, whereas dam construction could elevate the resistance to chloramphenicol and aminoglycoside. Land use pattern was identified as a critical factor influencing ARG composition under anthropogenic disturbances, as it could directly reflect the land degradation level and indicate the inputs of ARG-selective chemicals of different human activities. Moreover, despite of the lack of variation in ARG relative abundance, PARB were highly promoted by anthropogenic activities, indicating increasing ARG dissemination to pathogen. We found that human-impacted environments harbored high proportion of mobile genetic elements (MGEs), and the MGE carrying ARGs also increased under anthropogenic disturbances in the pathogenic hosts, which confirmed that anthropogenic activities could promote ARG horizontal gene transfer. Furthermore, anthropogenic activities could influence PARB assembly processes. Basically, stochastic processes dominated PARB assembly along the river, and with increasing level of anthropogenic activities, these processes shifted from undominated stochastic processes to dispersal limitation. In summary, this study provides useful strategies in watershed resistome management and reduction of ARG dissemination to pathogens, which should consider the mode and intensity of human activity and its potential influence on horizontal gene transfer and assembly processes.}, }
@article {pmid34324713, year = {2021}, author = {Sandmann, G}, title = {Diversity and origin of carotenoid biosynthesis: its history of coevolution towards plant photosynthesis.}, journal = {The New phytologist}, volume = {232}, number = {2}, pages = {479-493}, doi = {10.1111/nph.17655}, pmid = {34324713}, issn = {1469-8137}, mesh = {Carotenoids/metabolism ; *Chlorophyta/metabolism ; *Cyanobacteria/genetics/metabolism ; Photosynthesis ; Plastids/metabolism ; }, abstract = {The development of photosynthesis was a highlight in the progression of bacteria. In addition to the photosystems with their structural proteins, the photosynthesis apparatus consists of different cofactors including essential carotenoids. Thus, the evolution of the carotenoid pathways in relation to the functionality of the resulting structures in photosynthesis is the focus of this review. Analysis of carotenoid pathway genes indicates early evolutionary roots in prokaryotes. The pathway complexity leading to a multitude of structures is a result of gene acquisition, including their functional modifications, emergence of novel genes and gene exchange between species. Along with the progression of photosynthesis, carotenoid pathways coevolved with photosynthesis according to their advancing functionality. Cyanobacteria, with their oxygenic photosynthesis, became a landmark for evolutionary events including carotenogenesis. Concurrent with endosymbiosis, the cyanobacterial carotenoid pathways were inherited into algal plastids. In the lineage leading to Chlorophyta and plants, carotenoids evolved to their prominent role in protection and regulation of light energy input as constituents of a highly efficient light-harvesting complex.}, }
@article {pmid34319225, year = {2021}, author = {Tarracchini, C and Milani, C and Lugli, GA and Mancabelli, L and Fontana, F and Alessandri, G and Longhi, G and Anzalone, R and Viappiani, A and Turroni, F and van Sinderen, D and Ventura, M}, title = {Phylogenomic disentangling of the Bifidobacterium longum subsp. infantis taxon.}, journal = {Microbial genomics}, volume = {7}, number = {7}, pages = {}, pmid = {34319225}, issn = {2057-5858}, mesh = {Adaptation, Physiological/*genetics ; Animals ; Bifidobacterium longum/*classification/*genetics/isolation &amp; purification ; Breast Feeding ; Gastrointestinal Microbiome/*genetics ; Genome, Bacterial/*genetics ; Humans ; Milk, Human/microbiology ; Oligosaccharides/metabolism ; Phylogeny ; Species Specificity ; Whole Genome Sequencing ; }, abstract = {Members of the Bifidobacterium longum species have been shown to possess adaptive abilities to allow colonization of different mammalian hosts, including humans, primates and domesticated mammalian species, such as dogs, horses, cattle and pigs. To date, three subspecies have formally been recognized to belong to this bifidobacterial taxon, i.e. B. longum subsp. longum, B. longum subsp. infantis and B. longum subsp. suis. Although B. longum subsp. longum is widely distributed in the human gut irrespective of host age, B. longum subsp. infantis appears to play a significant role as a prominent member of the gut microbiota of breast-fed infants. Nevertheless, despite the considerable scientific relevance of these taxa and the vast body of genomic data now available, an accurate dissection of the genetic features that comprehensively characterize the B. longum species and its subspecies is still missing. In the current study, we employed 261 publicly available B. longum genome sequences, combined with those of 11 new isolates, to investigate genomic diversity of this taxon through comparative genomic and phylogenomic approaches. These analyses allowed us to highlight a remarkable intra-species genetic and physiological diversity. Notably, characterization of the genome content of members of B. longum subsp. infantis subspecies suggested that this taxon may have acquired genetic features for increased competitiveness in the gut environment of suckling hosts. Furthermore, specific B. longum subsp. infantis genomic features appear to be responsible for enhanced horizontal gene transfer (HGT) occurrences, underpinning an intriguing dedication toward acquisition of foreign DNA by HGT events.}, }
@article {pmid34319152, year = {2021}, author = {Muller, H and Chebbi, MA and Bouzar, C and Périquet, G and Fortuna, T and Calatayud, PA and Le Ru, B and Obonyo, J and Kaiser, L and Drezen, JM and Huguet, E and Gilbert, C}, title = {Genome-Wide Patterns of Bracovirus Chromosomal Integration into Multiple Host Tissues during Parasitism.}, journal = {Journal of virology}, volume = {95}, number = {22}, pages = {e0068421}, pmid = {34319152}, issn = {1098-5514}, support = {ANR-15-CE32-0011-01//Agence Nationale de la Recherche (ANR)/ ; ANR-17- CE32-0015-02//Agence Nationale de la Recherche (ANR)/ ; }, mesh = {Animals ; *DNA, Viral ; Gene Transfer, Horizontal ; *Genome, Viral ; Host-Parasite Interactions/*genetics ; Polydnaviridae/*genetics ; Wasps/*virology ; }, abstract = {Bracoviruses are domesticated viruses found in parasitic wasp genomes. They are composed of genes of nudiviral origin that are involved in particle production and proviral segments containing virulence genes that are necessary for parasitism success. During particle production, proviral segments are amplified and individually packaged as DNA circles in nucleocapsids. These particles are injected by parasitic wasps into host larvae together with their eggs. Bracovirus circles of two wasp species were reported to undergo chromosomal integration in parasitized host hemocytes, through a conserved sequence named the host integration motif (HIM). Here, we used bulk Illumina sequencing to survey integrations of Cotesia typhae bracovirus circles in the DNA of its host, the maize corn borer (Sesamia nonagrioides), 7 days after parasitism. First, assembly and annotation of a high-quality genome for C. typhae enabled us to characterize 27 proviral segments clustered in proviral loci. Using these data, we characterized large numbers of chromosomal integrations (from 12 to 85 events per host haploid genome) for all 16 bracovirus circles containing a HIM. Integrations were found in four S. nonagrioides tissues and in the body of a caterpillar in which parasitism had failed. The 12 remaining circles do not integrate but are maintained at high levels in host tissues. Surprisingly, we found that HIM-mediated chromosomal integration in the wasp germ line has occurred accidentally at least six times during evolution. Overall, our study furthers our understanding of wasp-host genome interactions and supports HIM-mediated chromosomal integration as a possible mechanism of horizontal transfer from wasps to their hosts. IMPORTANCE Bracoviruses are endogenous domesticated viruses of parasitoid wasps that are injected together with wasp eggs into wasp host larvae during parasitism. Several studies have shown that some DNA circles packaged into bracovirus particles become integrated into host somatic genomes during parasitism, but the phenomenon has never been studied using nontargeted approaches. Here, we use bulk Illumina sequencing to systematically characterize and quantify bracovirus circle integrations that occur in four tissues of the Mediterranean corn borer (Sesamia nonagrioides) during parasitism by the Cotesia typhae wasp. Our analysis reveals that all circles containing a HIM integrate at substantial levels (from 12 to 85 integrations per host cell, in total) in all tissues, while other circles do not integrate. In addition to shedding new light on wasp-bracovirus-host interactions, our study supports HIM-mediated chromosomal integration of bracovirus as a possible source of wasp-to-host horizontal transfer, with long-term evolutionary consequences.}, }
@article {pmid34314594, year = {2021}, author = {Anton, BP and Roberts, RJ}, title = {Beyond Restriction Modification: Epigenomic Roles of DNA Methylation in Prokaryotes.}, journal = {Annual review of microbiology}, volume = {75}, number = {}, pages = {129-149}, doi = {10.1146/annurev-micro-040521-035040}, pmid = {34314594}, issn = {1545-3251}, mesh = {*DNA Methylation ; DNA Restriction-Modification Enzymes/genetics/metabolism ; *Epigenomics ; Methyltransferases/genetics/metabolism ; Prokaryotic Cells/metabolism ; }, abstract = {The amount of bacterial and archaeal genome sequence and methylome data has greatly increased over the last decade, enabling new insights into the functional roles of DNA methylation in these organisms. Methyltransferases (MTases), the enzymes responsible for DNA methylation, are exchanged between prokaryotes through horizontal gene transfer and can function either as part of restriction-modification systems or in apparent isolation as single (orphan) genes. The patterns of DNA methylation they confer on the host chromosome can have significant effects on gene expression, DNA replication, and other cellular processes. Some processes require very stable patterns of methylation, resulting in conservation of persistent MTases in a particular lineage. Other processes require patterns that are more dynamic yet more predictable than what is afforded by horizontal gene transfer and gene loss, resulting in phase-variable or recombination-driven MTase alleles. In this review, we discuss what is currently known about the functions of DNA methylation in prokaryotes in light of these evolutionary patterns.}, }
@article {pmid34313464, year = {2021}, author = {Li, YX and Rao, YZ and Qi, YL and Qu, YN and Chen, YT and Jiao, JY and Shu, WS and Jiang, H and Hedlund, BP and Hua, ZS and Li, WJ}, title = {Deciphering Symbiotic Interactions of "Candidatus Aenigmarchaeota" with Inferred Horizontal Gene Transfers and Co-occurrence Networks.}, journal = {mSystems}, volume = {6}, number = {4}, pages = {e0060621}, pmid = {34313464}, issn = {2379-5077}, support = {91951205//National Natural Science Foundation of China (NSFC)/ ; 91751206//National Natural Science Foundation of China (NSFC)/ ; }, abstract = {"Candidatus Aenigmarchaeota" ("Ca. Aenigmarchaeota") represents one of the earliest proposed evolutionary branches within the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) superphylum. However, their ecological roles and potential host-symbiont interactions are still poorly understood. Here, eight metagenome-assembled genomes (MAGs) were reconstructed from hot spring ecosystems, and further in-depth comparative and evolutionary genomic analyses were conducted on these MAGs and other genomes downloaded from public databases. Although with limited metabolic capacities, we reported that "Ca. Aenigmarchaeota" in thermal environments harbor more genes related to carbohydrate metabolism than "Ca. Aenigmarchaeota" in nonthermal environments. Evolutionary analyses suggested that members from the Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota (TACK) superphylum and Euryarchaeota contribute substantially to the niche expansion of "Ca. Aenigmarchaeota" via horizontal gene transfer (HGT), especially genes related to virus defense and stress responses. Based on co-occurrence network results and recent genetic exchanges among community members, we conjectured that "Ca. Aenigmarchaeota" may be symbionts associated with one MAG affiliated with the genus Pyrobaculum, though host specificity might be wide and variable across different "Ca. Aenigmarchaeota" organisms. This study provides significant insight into possible DPANN-host interactions and ecological roles of "Ca. Aenigmarchaeota." IMPORTANCE Recent advances in sequencing technology promoted the blowout discovery of super tiny microbes in the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) superphylum. However, the unculturable properties of the majority of microbes impeded our investigation of their behavior and symbiotic lifestyle in the corresponding community. By integrating horizontal gene transfer (HGT) detection and co-occurrence network analysis on "Candidatus Aenigmarchaeota" ("Ca. Aenigmarchaeota"), we made one of the first attempts to infer their putative interaction partners and further decipher the potential functional and genetic interactions between the symbionts. We revealed that HGTs contributed by members from the Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota (TACK) superphylum and Euryarchaeota conferred "Ca. Aenigmarchaeota" with the ability to survive under different environmental stresses, such as virus infection, high temperature, and oxidative stress. This study demonstrates that the interaction partners might be inferable by applying informatics analyses on metagenomic sequencing data.}, }
@article {pmid34312432, year = {2021}, author = {Shelomi, M and Danchin, EGJ and Heckel, D and Wipfler, B and Bradler, S and Zhou, X and Pauchet, Y}, title = {Author Correction: Horizontal Gene Transfer of Pectinases from Bacteria Preceded the Diversification of Stick and Leaf Insects.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {15515}, doi = {10.1038/s41598-021-94743-y}, pmid = {34312432}, issn = {2045-2322}, }
@article {pmid34309264, year = {2021}, author = {Zhou, SY and Zhu, YG and Huang, FY}, title = {[Microplastic-Induced Alterations to Antibiotic Resistance Genes in Seawater].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {42}, number = {8}, pages = {3785-3790}, doi = {10.13227/j.hjkx.202101009}, pmid = {34309264}, issn = {0250-3301}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial/genetics ; *Microplastics ; *Plastics ; RNA, Ribosomal, 16S ; Seawater ; }, abstract = {The increasing and combined pollution of microplastics (MPs) and antibiotic resistance genes (ARGs) in aquatic environments is a great ecological and health concern. However, MP-induced alterations to ARGs in seawater is poorly understood, impeding risk assessment of plastics. We profiled the diversity and abundance of ARGs and mobile genetic elements (MGEs) in seawater after the addition of three different MPs (PE, PVC, and PVA) and 49-day aerated incubation.A total of 20, 35, 42, and 64 ARGs were detected in BLK, PE, PVC, and PVA, with 2, 4, 2, and 3 MGEs, respectively. The absolute abundance of ARGs in the seawater aerated with MPs ranged from 4.01×10[6] copies ·L[-1] to 1.05×10[8] copies ·L[-1]. Additionally, the variety and richness of ARGs and MGEs in PVA were significantly higher than in the original seawater, or the seawater aerated with the other two MPs. This indicates that PVA, which is water soluble, could induce more diverse and abundant ARGs in seawater. Significant correlations among ARGs, MGEs, and 16S rRNA genes were observed, implying that the occurrence of MGEs in seawater may accelerate the transmission of ARGs through horizontal gene transfer, and bacterial microorganisms could directly affect the propagation and dissemination of ARGs.}, }
@article {pmid34305992, year = {2021}, author = {Zou, K and Liu, X and Hu, Q and Zhang, D and Fu, S and Zhang, S and Huang, H and Lei, F and Zhang, G and Miao, B and Meng, D and Jiang, L and Liu, H and Yin, H and Liang, Y}, title = {Root Endophytes and Ginkgo biloba Are Likely to Share and Compensate Secondary Metabolic Processes, and Potentially Exchange Genetic Information by LTR-RTs.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {704985}, pmid = {34305992}, issn = {1664-462X}, abstract = {Ginkgo biloba is a pharmaceutical resource for terpenes and flavonoids. However, few insights discussed endophytes' role in Ginkgo, and whether genetic exchange happens between Ginkgo and endophytes remains unclear. Herein, functional gene profiles and repetitive sequences were analyzed to focus on these issues. A total of 25 endophyte strains were isolated from the Ginkgo root and distributed in 16 genera of 6 phyla. Significant morphological diversities lead to the diversity in the COG functional classification. KEGG mapping revealed that endophytic bacteria and fungi potentially synthesize chalcone, while endophytic fungi might also promote flavonoid derivatization. Both bacteria and fungi may facilitate the lignin synthesis. Aspergillus sp. Gbtc_1 exhibited the feasibility of regulating alcohols to lignans. Although Ginkgo and the endophytes have not observed the critical levopimaradiene synthase in ginkgolides synthesis, the upstream pathways of terpenoid precursors are likely intact. The MVK genes in Ginkgo may have alternative non-homologous copies or be compensated by endophytes in long-term symbiosis. Cellulomonas sp. Gbtc_1 became the only bacteria to harbor both MEP and MVA pathways. Endophytes may perform the mutual transformation of IPP and DMAPP in the root. Ginkgo and bacteria may lead to the synthesis and derivatization of the carotenoid pathway. The isoquinoline alkaloid biosynthesis seemed lost in the Ginkgo root community, but L-dopa is more probably converted into dopamine as an essential signal-transduction substance. So, endophytes may participate in the secondary metabolism of the Ginkgo in a shared or complementary manner. Moreover, a few endophytic sequences predicted as Ty3/Gypsy and Ty1/Copia superfamilies exhibited extremely high similarity to those of Ginkgo. CDSs in such endophytic LTR-RT sequences were also highly homologous to one Ginkgo CDS. Therefore, LTR-RTs may be a rare unit flowing between the Ginkgo host and endophytes to exchange genetic information. Collectively, this research effectively expanded the insight on the symbiotic relationship between the Ginkgo host and the endophytes in the root.}, }
@article {pmid34305823, year = {2021}, author = {Malhotra, H and Kaur, S and Phale, PS}, title = {Conserved Metabolic and Evolutionary Themes in Microbial Degradation of Carbamate Pesticides.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {648868}, pmid = {34305823}, issn = {1664-302X}, abstract = {Carbamate pesticides are widely used as insecticides, nematicides, acaricides, herbicides and fungicides in the agriculture, food and public health sector. However, only a minor fraction of the applied quantity reaches the target organisms. The majority of it persists in the environment, impacting the non-target biota, leading to ecological disturbance. The toxicity of these compounds to biota is mediated through cholinergic and non-cholinergic routes, thereby making their clean-up cardinal. Microbes, specifically bacteria, have adapted to the presence of these compounds by evolving degradation pathways and thus play a major role in their removal from the biosphere. Over the past few decades, various genetic, metabolic and biochemical analyses exploring carbamate degradation in bacteria have revealed certain conserved themes in metabolic pathways like the enzymatic hydrolysis of the carbamate ester or amide linkage, funnelling of aryl carbamates into respective dihydroxy aromatic intermediates, C1 metabolism and nitrogen assimilation. Further, genomic and functional analyses have provided insights on mechanisms like horizontal gene transfer and enzyme promiscuity, which drive the evolution of degradation phenotype. Compartmentalisation of metabolic pathway enzymes serves as an additional strategy that further aids in optimising the degradation efficiency. This review highlights and discusses the conclusions drawn from various analyses over the past few decades; and provides a comprehensive view of the environmental fate, toxicity, metabolic routes, related genes and enzymes as well as evolutionary mechanisms associated with the degradation of widely employed carbamate pesticides. Additionally, various strategies like application of consortia for efficient degradation, metabolic engineering and adaptive laboratory evolution, which aid in improvising remediation efficiency and overcoming the challenges associated with in situ bioremediation are discussed.}, }
@article {pmid34302348, year = {2021}, author = {Dong, X and Zhang, C and Li, W and Weng, S and Song, W and Li, J and Wang, Y}, title = {Functional diversity of microbial communities in inactive seafloor sulfide deposits.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {8}, pages = {}, doi = {10.1093/femsec/fiab108}, pmid = {34302348}, issn = {1574-6941}, mesh = {Bacteria/genetics ; *Hydrothermal Vents ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfides ; }, abstract = {The seafloor sulfide structures of inactive vents are known to host abundant and diverse microorganisms potentially supported by mineralogy of sulfides. However, little is known about the diversity and distribution of microbial functions. Here, we used genome-resolved metagenomics to predict microbial metabolic functions and the contribution of horizontal gene transfer to the functionality of microorganisms inhabiting several hydrothermally inactive seafloor deposits among globally distributed deep-sea vent fields. Despite of geographically distant vent fields, similar microbial community patterns were observed with the dominance of Gammaproteobacteria, Bacteroidota and previously overlooked Candidatus Patescibacteria. Metabolically flexible Gammaproteobacteria are major potential primary producers utilizing mainly sulfur, iron and hydrogen as electron donors coupled with oxygen and nitrate respiration for chemolithoautotrophic growth. In addition to heterotrophic microorganisms like free-living Bacteroidota, Ca. Patescibacteria potentially perform fermentative recycling of organic carbon. Finally, we provided evidence that many functional genes that are central to energy metabolism have been laterally transferred among members within the community and largely within the same class. Taken together, these findings shed light on microbial ecology and evolution in inactive seafloor sulfide deposits after the cessation of hydrothermal activities.}, }
@article {pmid34299060, year = {2021}, author = {Dahale, SK and Ghosh, D and Ingole, KD and Chugani, A and Kim, SH and Bhattacharjee, S}, title = {HopA1 Effector from Pseudomonas syringae pv syringae Strain 61 Affects NMD Processes and Elicits Effector-Triggered Immunity.}, journal = {International journal of molecular sciences}, volume = {22}, number = {14}, pages = {}, pmid = {34299060}, issn = {1422-0067}, support = {BT/RLF/Re-entry/09/2012//Department of Biotechnology, Ministry of Science and Technology, India/ ; BT/PR23666/AGIII/-3/1039/2018//Department of Biotechnology, Ministry of Science and Technology, India/ ; 138//SGRF Project Grant/ ; }, mesh = {Arabidopsis/genetics/*immunology/metabolism/microbiology ; Bacterial Proteins/genetics/*metabolism ; *Host-Pathogen Interactions ; *Nonsense Mediated mRNA Decay ; Plant Diseases/genetics/*immunology/microbiology ; *Plant Immunity ; Pseudomonas syringae/*physiology ; Virulence ; }, abstract = {Pseudomonas syringae-secreted HopA1 effectors are important determinants in host range expansion and increased pathogenicity. Their recent acquisitions via horizontal gene transfer in several non-pathogenic Pseudomonas strains worldwide have caused alarming increase in their virulence capabilities. In Arabidopsis thaliana, RESISTANCE TO PSEUDOMONAS SYRINGAE 6 (RPS6) gene confers effector-triggered immunity (ETI) against HopA1pss derived from P. syringae pv. syringae strain 61. Surprisingly, a closely related HopA1pst from the tomato pathovar evades immune detection. These responsive differences in planta between the two HopA1s represents a unique system to study pathogen adaptation skills and host-jumps. However, molecular understanding of HopA1's contribution to overall virulence remain undeciphered. Here, we show that immune-suppressive functions of HopA1pst are more potent than HopA1pss. In the resistance-compromised ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1) null-mutant, transcriptomic changes associated with HopA1pss-elicited ETI are still induced and carry resemblance to PAMP-triggered immunity (PTI) signatures. Enrichment of HopA1pss interactome identifies proteins with regulatory roles in post-transcriptional and translational processes. With our demonstration here that both HopA1 suppress reporter-gene translations in vitro imply that the above effector-associations with plant target carry inhibitory consequences. Overall, with our results here we unravel possible virulence role(s) of HopA1 in suppressing PTI and provide newer insights into its detection in resistant plants.}, }
@article {pmid34297209, year = {2021}, author = {Richards, A and Kubatko, L}, title = {Bayesian-Weighted Triplet and Quartet Methods for Species Tree Inference.}, journal = {Bulletin of mathematical biology}, volume = {83}, number = {9}, pages = {93}, pmid = {34297209}, issn = {1522-9602}, mesh = {Bayes Theorem ; Computer Simulation ; *Genetic Speciation ; *Mathematical Concepts ; Models, Genetic ; Phylogeny ; }, abstract = {Inference of the evolutionary histories of species, commonly represented by a species tree, is complicated by the divergent evolutionary history of different parts of the genome. Different loci on the genome can have different histories from the underlying species tree (and each other) due to processes such as incomplete lineage sorting (ILS), gene duplication and loss, and horizontal gene transfer. The multispecies coalescent is a commonly used model for performing inference on species and gene trees in the presence of ILS. This paper introduces Lily-T and Lily-Q, two new methods for species tree inference under the multispecies coalescent. We then compare them to two frequently used methods, SVDQuartets and ASTRAL, using simulated and empirical data. Both methods generally showed improvement over SVDQuartets, and Lily-Q was superior to Lily-T for most simulation settings. The comparison to ASTRAL was more mixed-Lily-Q tended to be better than ASTRAL when the length of recombination-free loci was short, when the coalescent population parameter [Formula: see text] was small, or when the internal branch lengths were longer.}, }
@article {pmid34295903, year = {2021}, author = {Herrera-Úbeda, C and Garcia-Fernàndez, J}, title = {New Genes Born-In or Invading Vertebrate Genomes.}, journal = {Frontiers in cell and developmental biology}, volume = {9}, number = {}, pages = {713918}, pmid = {34295903}, issn = {2296-634X}, abstract = {Which is the origin of genes is a fundamental question in Biology, indeed a question older than the discovery of genes itself. For more than a century, it was uneven to think in origins other than duplication and divergence from a previous gene. In recent years, however, the intersection of genetics, embryonic development, and bioinformatics, has brought to light that de novo generation from non-genic DNA, horizontal gene transfer and, noticeably, virus and transposon invasions, have shaped current genomes, by integrating those newcomers into old gene networks, helping to shape morphological and physiological innovations. We here summarized some of the recent research in the field, mostly in the vertebrate lineage with a focus on protein-coding novelties, showing that the placenta, the adaptative immune system, or the highly developed neocortex, among other innovations, are linked to de novo gene creation or domestication of virus and transposons. We provocatively suggest that the high tolerance to virus infections by bats may also be related to previous virus and transposon invasions in the bat lineage.}, }
@article {pmid34295840, year = {2021}, author = {Whittard, E and Redfern, J and Xia, G and Millard, A and Ragupathy, R and Malic, S and Enright, MC}, title = {Phenotypic and Genotypic Characterization of Novel Polyvalent Bacteriophages With Potent In Vitro Activity Against an International Collection of Genetically Diverse Staphylococcus aureus.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {698909}, pmid = {34295840}, issn = {2235-2988}, mesh = {*Bacteriophages/genetics ; Genotype ; Humans ; *Methicillin-Resistant Staphylococcus aureus/genetics ; *Staphylococcal Infections ; Staphylococcus ; Staphylococcus Phages/genetics ; Staphylococcus aureus/genetics ; }, abstract = {Phage therapy recently passed a key milestone with success of the first regulated clinical trial using systemic administration. In this single-arm non-comparative safety study, phages were administered intravenously to patients with invasive Staphylococcus aureus infections with no adverse reactions reported. Here, we examined features of 78 lytic S. aureus phages, most of which were propagated using a S. carnosus host modified to be broadly susceptible to staphylococcal phage infection. Use of this host eliminates the threat of contamination with staphylococcal prophage - the main vector of S. aureus horizontal gene transfer. We determined the host range of these phages against an international collection of 185 S. aureus isolates with 56 different multilocus sequence types that included multiple representatives of all epidemic MRSA and MSSA clonal complexes. Forty of our 78 phages were able to infect > 90% of study isolates, 15 were able to infect > 95%, and two could infect all 184 clinical isolates, but not a phage-resistant mutant generated in a previous study. We selected the 10 phages with the widest host range for in vitro characterization by planktonic culture time-kill analysis against four isolates:- modified S. carnosus strain TM300H, methicillin-sensitive isolates D329 and 15981, and MRSA isolate 252. Six of these 10 phages were able to rapidly kill, reducing cell numbers of at least three isolates. The four best-performing phages, in this assay, were further shown to be highly effective in reducing 48 h biofilms on polystyrene formed by eight ST22 and eight ST36 MRSA isolates. Genomes of 22 of the widest host-range phages showed they belonged to the Twortvirinae subfamily of the order Caudovirales in three main groups corresponding to Silviavirus, and two distinct groups of Kayvirus. These genomes assembled as single-linear dsDNAs with an average length of 140 kb and a GC content of c. 30%. Phages that could infect > 96% of S. aureus isolates were found in all three groups, and these have great potential as therapeutic candidates if, in future studies, they can be formulated to maximize their efficacy and eliminate emergence of phage resistance by using appropriate combinations.}, }
@article {pmid34295324, year = {2021}, author = {Kamal, SM and Simpson, DJ and Wang, Z and Gänzle, M and Römling, U}, title = {Horizontal Transmission of Stress Resistance Genes Shape the Ecology of Beta- and Gamma-Proteobacteria.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {696522}, pmid = {34295324}, issn = {1664-302X}, abstract = {The transmissible locus of stress tolerance (tLST) is found mainly in beta- and gamma-Proteobacteria and confers tolerance to elevated temperature, pressure, and chlorine. This genomic island, previously referred to as transmissible locus of protein quality control or locus of heat resistance likely originates from an environmental bacterium thriving in extreme habitats, but has been widely transmitted by lateral gene transfer. Although highly conserved, the gene content on the island is subject to evolution and gene products such as small heat shock proteins are present in several functionally distinct sequence variants. A number of these genes are xenologs of core genome genes with the gene products to widen the substrate spectrum and to be highly (complementary) expressed thus their functionality to become dominant over core genome genes. In this review, we will present current knowledge of the function of core tLST genes and discuss current knowledge on selection and counter-selection processes that favor maintenance of the tLST island, with frequent acquisition of gene products involved in cyclic di-GMP signaling, in different habitats from the environment to animals and plants, processed animal and plant products, man-made environments, and subsequently humans.}, }
@article {pmid34294116, year = {2021}, author = {Herman, EK and Greninger, A and van der Giezen, M and Ginger, ML and Ramirez-Macias, I and Miller, HC and Morgan, MJ and Tsaousis, AD and Velle, K and Vargová, R and Záhonová, K and Najle, SR and MacIntyre, G and Muller, N and Wittwer, M and Zysset-Burri, DC and Eliáš, M and Slamovits, CH and Weirauch, MT and Fritz-Laylin, L and Marciano-Cabral, F and Puzon, GJ and Walsh, T and Chiu, C and Dacks, JB}, title = {Genomics and transcriptomics yields a system-level view of the biology of the pathogen Naegleria fowleri.}, journal = {BMC biology}, volume = {19}, number = {1}, pages = {142}, pmid = {34294116}, issn = {1741-7007}, mesh = {Animals ; Disease Models, Animal ; Genomics ; Mice ; *Naegleria fowleri/genetics ; Transcriptome ; Trogocytosis ; }, abstract = {BACKGROUND: The opportunistic pathogen Naegleria fowleri establishes infection in the human brain, killing almost invariably within 2 weeks. The amoeba performs piece-meal ingestion, or trogocytosis, of brain material causing direct tissue damage and massive inflammation. The cellular basis distinguishing N. fowleri from other Naegleria species, which are all non-pathogenic, is not known. Yet, with the geographic range of N. fowleri advancing, potentially due to climate change, understanding how this pathogen invades and kills is both important and timely.<br><br>RESULTS: Here, we report an -omics approach to understanding N. fowleri biology and infection at the system level. We sequenced two new strains of N. fowleri and performed a transcriptomic analysis of low- versus high-pathogenicity N. fowleri cultured in a mouse infection model. Comparative analysis provides an in-depth assessment of encoded protein complement between strains, finding high conservation. Molecular evolutionary analyses of multiple diverse cellular systems demonstrate that the N. fowleri genome encodes a similarly complete cellular repertoire to that found in free-living N. gruberi. From transcriptomics, neither stress responses nor traits conferred from lateral gene transfer are suggested as critical for pathogenicity. By contrast, cellular systems such as proteases, lysosomal machinery, and motility, together with metabolic reprogramming and novel N. fowleri proteins, are all implicated in facilitating pathogenicity within the host. Upregulation in mouse-passaged N. fowleri of genes associated with glutamate metabolism and ammonia transport suggests adaptation to available carbon sources in the central nervous system.<br><br>CONCLUSIONS: In-depth analysis of Naegleria genomes and transcriptomes provides a model of cellular systems involved in opportunistic pathogenicity, uncovering new angles to understanding the biology of a rare but highly fatal pathogen.}, }
@article {pmid34294041, year = {2021}, author = {Andrade, BGN and Goris, T and Afli, H and Coutinho, FH and Dávila, AMR and Cuadrat, RRC}, title = {Putative mobilized colistin resistance genes in the human gut microbiome.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {220}, pmid = {34294041}, issn = {1471-2180}, mesh = {Colistin/*pharmacology ; Computational Biology ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Genetic Variation ; Humans ; Microbiota/*drug effects/*genetics ; }, abstract = {BACKGROUND: The high incidence of bacterial genes that confer resistance to last-resort antibiotics, such as colistin, caused by mobilized colistin resistance (mcr) genes, poses an unprecedented threat to human health. Understanding the spread, evolution, and distribution of such genes among human populations will help in the development of strategies to diminish their occurrence. To tackle this problem, we investigated the distribution and prevalence of potential mcr genes in the human gut microbiome using a set of bioinformatics tools to screen the Unified Human Gastrointestinal Genome (UHGG) collection for the presence, synteny and phylogeny of putative mcr genes, and co-located antibiotic resistance genes.<br><br>RESULTS: A total of 2079 antibiotic resistance genes (ARGs) were classified as mcr genes in 2046 metagenome assembled genomes (MAGs), distributed across 1596 individuals from 41 countries, of which 215 were identified in plasmidial contigs. The genera that presented the largest number of mcr-like genes were Suterella and Parasuterella. Other potential pathogens carrying mcr genes belonged to the genus Vibrio, Escherichia and Campylobacter. Finally, we identified a total of 22,746 ARGs belonging to 21 different classes in the same 2046 MAGs, suggesting multi-resistance potential in the corresponding bacterial strains, increasing the concern of ARGs impact in the clinical settings.<br><br>CONCLUSION: This study uncovers the diversity of mcr-like genes in the human gut microbiome. We demonstrated the cosmopolitan distribution of these genes in individuals worldwide and the co-presence of other antibiotic resistance genes, including Extended-spectrum Beta-Lactamases (ESBL). Also, we described mcr-like genes fused to a PAP2-like domain in S. wadsworthensis. These novel sequences increase our knowledge about the diversity and evolution of mcr-like genes. Future research should focus on activity, genetic mobility and a potential colistin resistance in the corresponding strains to experimentally validate those findings.}, }
@article {pmid34291089, year = {2021}, author = {Huang, S and Zhao, J and Li, W and Wang, P and Xue, Z and Zhu, G}, title = {Biochemical and Phylogenetic Characterization of a Novel NADP[+]-Specific Isocitrate Dehydrogenase From the Marine Microalga Phaeodactylum tricornutum.}, journal = {Frontiers in molecular biosciences}, volume = {8}, number = {}, pages = {702083}, pmid = {34291089}, issn = {2296-889X}, abstract = {Isocitrate dehydrogenase (IDH) family of proteins is classified into three subfamilies, namely, types I, II, and III. Although IDHs are widely distributed in bacteria, archaea, and eukaryotes, all type III IDHs reported to date are found only in prokaryotes. Herein, a novel type III IDH subfamily member from the marine microalga Phaeodactylum tricornutum (PtIDH2) was overexpressed, purified, and characterized in detail for the first time. Relatively few eukaryotic genomes encode this type of IDH and PtIDH2 shares the highest homology with marine bacterial monomeric IDHs, suggesting that PtIDH2 originated through a horizontal gene transfer event between a marine alga and a bacterium. Size-exclusion chromatography revealed that the native PtIDH2 is a homotetramer (∼320 kDa) in solution, comprising four monomeric IDH-like subunits (80 kDa each). Enzymatic characterization showed that PtIDH2 is a bivalent metal ion-dependent enzyme and Mn[2+] is the optimal activator. The recombinant PtIDH2 protein exhibited maximal activity at 35°C and pH 8.0 in the presence of Mn[2+]. Heat-inactivation analysis revealed that PtIDH2 is a cold-adapted enzyme. Kinetic analysis demonstrated that PtIDH2 is a completely NADP[+]-specific IDH with no detectable NAD[+]-associated catalytic activity. The three putative key NADP[+]-binding residues (His604, Arg615, and Arg664) in PtIDH2 were also evaluated by site-directed mutagenesis. The H[604]L/R[615]D/R[664]S triple mutant showed a 3.25-fold preference for NAD[+] over NADP[+], implying that the coenzyme specificity of PtIDH2 can be converted from NADP[+] to NAD[+] through rational engineering approaches. Additionally, the roles of the conserved residues Ala718 and Leu742 in the thermostability of PtIDH2 were also explored by site-directed mutagenesis. We found that the L[742]F mutant displayed higher thermostability than wild-type PtIDH2. This study expands the phylogeny of the IDH family and provides new insights into the evolution of IDHs.}, }
@article {pmid34290692, year = {2021}, author = {Liu, L and Schubert, DM and Könneke, M and Berg, IA}, title = {(S)-3-Hydroxybutyryl-CoA Dehydrogenase From the Autotrophic 3-Hydroxypropionate/4-Hydroxybutyrate Cycle in Nitrosopumilus maritimus.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {712030}, pmid = {34290692}, issn = {1664-302X}, abstract = {Ammonia-oxidizing archaea of the phylum Thaumarchaeota are among the most abundant organisms that exert primary control of oceanic and soil nitrification and are responsible for a large part of dark ocean primary production. They assimilate inorganic carbon via an energetically efficient version of the 3-hydroxypropionate/4-hydroxybutyrate cycle. In this cycle, acetyl-CoA is carboxylated to succinyl-CoA, which is then converted to two acetyl-CoA molecules with 4-hydroxybutyrate as the key intermediate. This conversion includes the (S)-3-hydroxybutyryl-CoA dehydrogenase reaction. Here, we heterologously produced the protein Nmar_1028 catalyzing this reaction in thaumarchaeon Nitrosopumilus maritimus, characterized it biochemically and performed its phylogenetic analysis. This NAD-dependent dehydrogenase is highly active with its substrate, (S)-3-hydroxybutyryl-CoA, and its low K m value suggests that the protein is adapted to the functioning in the 3-hydroxypropionate/4-hydroxybutyrate cycle. Nmar_1028 is homologous to the dehydrogenase domain of crotonyl-CoA hydratase/(S)-3-hydroxybutyryl-CoA dehydrogenase that is present in many Archaea. Apparently, the loss of the dehydratase domain of the fusion protein in the course of evolution was accompanied by lateral gene transfer of 3-hydroxypropionyl-CoA dehydratase/crotonyl-CoA hydratase from Bacteria. Although (S)-3-hydroxybutyryl-CoA dehydrogenase studied here is neither unique nor characteristic for the HP/HB cycle, Nmar_1028 appears to be the only (S)-3-hydroxybutyryl-CoA dehydrogenase in N. maritimus and is thus essential for the functioning of the 3-hydroxypropionate/4-hydroxybutyrate cycle and for the biology of this important marine archaeon.}, }
@article {pmid34287047, year = {2021}, author = {Korn, AM and Hillhouse, AE and Sun, L and Gill, JJ}, title = {Comparative Genomics of Three Novel Jumbo Bacteriophages Infecting Staphylococcus aureus.}, journal = {Journal of virology}, volume = {95}, number = {19}, pages = {e0239120}, pmid = {34287047}, issn = {1098-5514}, support = {16-143//National Pork Board (NPBF)/ ; 19-051//National Pork Board (NPBF)/ ; R21 AI113508/AI/NIAID NIH HHS/United States ; AI121689//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R33 AI121689/AI/NIAID NIH HHS/United States ; 17-108//National Pork Board (NPBF)/ ; //Texas AgriLife Research/ ; R21 AI121689/AI/NIAID NIH HHS/United States ; DBI-1565146//National Science Foundation (NSF)/ ; }, mesh = {Animals ; DNA, Viral/genetics ; DNA-Directed RNA Polymerases/genetics ; *Genome, Viral ; Genomics ; Introns ; Myoviridae/*genetics/isolation &amp; purification/physiology/ultrastructure ; Sequence Analysis, DNA ; Staphylococcus Phages/*genetics/isolation &amp; purification/physiology/ultrastructure ; Staphylococcus aureus/*virology ; Swine ; Transduction, Genetic ; Viral Proteins/genetics ; }, abstract = {The majority of previously described Staphylococcus aureus bacteriophages belong to three major groups, namely, P68-like podophages, Twort-like or K-like myophages, and a more diverse group of temperate siphophages. Here, we present the following three novel S. aureus "jumbo" phages: MarsHill, Madawaska, and Machias. These phages were isolated from swine production environments in the United States and represent a novel clade of S. aureus myophage. The average genome size for these phages is ∼269 kb with each genome encoding ∼263 predicted protein-coding genes. Phage genome organization and content are similar to those of known jumbo phages of Bacillus sp., including AR9 and vB_BpuM-BpSp. All three phages possess genes encoding complete virion and nonvirion RNA polymerases, multiple homing endonucleases, and a retron-like reverse transcriptase. Like AR9, all of these phages are presumed to have uracil-substituted DNA which interferes with DNA sequencing. These phages are also able to transduce host plasmids, which is significant as these phages were found circulating in swine production environments and can also infect human S. aureus isolates. IMPORTANCE This study describes the comparative genomics of the following three novel S. aureus jumbo phages: MarsHill, Madawaska, and Machias. These three S. aureus myophages represent an emerging class of S. aureus phage. These genomes contain abundant introns which show a pattern consistent with repeated acquisition rather than vertical inheritance, suggesting intron acquisition and loss are active processes in the evolution of these phages. These phages have presumably hypermodified DNA which inhibits sequencing by several different common platforms. Therefore, these phages also represent potential genomic diversity that has been missed due to the limitations of standard sequencing techniques. In particular, such hypermodified genomes may be missed by metagenomic studies due to their resistance to standard sequencing techniques. Phage MarsHill was found to be able to transduce host DNA at levels comparable to that found for other transducing S. aureus phages, making it a potential vector for horizontal gene transfer in the environment.}, }
@article {pmid34284223, year = {2022}, author = {Shin, J and Choi, S and Park, CM and Wang, J and Kim, YM}, title = {Reduction of antibiotic resistome in influent of a wastewater treatment plant (WWTP) via a chemically enhanced primary treatment (CEPT) process.}, journal = {Chemosphere}, volume = {286}, number = {Pt 1}, pages = {131569}, doi = {10.1016/j.chemosphere.2021.131569}, pmid = {34284223}, issn = {1879-1298}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Wastewater/analysis ; *Water Purification ; }, abstract = {Chemically enhanced primary treatment (CEPT) has been considered for maximizing wastewater energy recovery by enhancing the carbon captured through the primary treatment. However, evaluating the potential of CEPT as a primary treatment process for removing antibiotic resistance genes (ARGs) in the influent from a wastewater treatment plant (WWTP) has seldom been investigated. In this study, CEPT was conducted to assess simultaneous reduction of 13 major targeted ARGs and common pollutants in wastewater compared with primary sedimentation alone (non-CEPT). CEPT processes using three types of coagulants (PACl, FeCl3 and alum) effectively reduced absolute abundance of ARGs and intI1 in the influent from municipal WWTP. Average log-removal of absolute abundance of ARGs was achieved up to 1.77 ± 0.41 along with 90% turbidity reduction compared to non-CEPT. Through the simultaneous reduction of ARGs and intI1 genes during a CEPT process, ARGs proliferation may be limited directly through reduction of antibiotic resistant bacteria or indirectly through decreasing the possibility of horizontal gene transfer by intI1 removal. Reduction of ARGs and intI1 was improved by increasing coagulants' doses: abundances of residual ARGs under optimal dose conditions were similar, regardless of the different characteristics of coagulant types. The strongly positive correlation between reduction of turbidity/total phosphorus (T-P) and ARGs was explored, identifying that turbidity or T-P might be suitable indicators linked with variations in the abundance of ARGs during CEPT. As a result, CEPT may prove promising in efforts to control ARGs flowing into a WWTP.}, }
@article {pmid34282939, year = {2021}, author = {Qi, YL and Evans, PN and Li, YX and Rao, YZ and Qu, YN and Tan, S and Jiao, JY and Chen, YT and Hedlund, BP and Shu, WS and Hua, ZS and Li, WJ}, title = {Comparative Genomics Reveals Thermal Adaptation and a High Metabolic Diversity in "Candidatus Bathyarchaeia".}, journal = {mSystems}, volume = {6}, number = {4}, pages = {e0025221}, pmid = {34282939}, issn = {2379-5077}, support = {91951205//National Natural Science Foundation of China (NSFC)/ ; 32061143043//National Natural Science Foundation of China (NSFC)/ ; 2016A030312003//Natural Science Foundation of Guangdong Province (Guangdong Natural Science Foundation)/ ; }, abstract = {"Candidatus Bathyarchaeia" is a phylogenetically diverse and widely distributed lineage often in high abundance in anoxic submarine sediments; however, their evolution and ecological roles in terrestrial geothermal habitats are poorly understood. In the present study, 35 Ca. Bathyarchaeia metagenome-assembled genomes (MAGs) were recovered from hot spring sediments in Tibet and Yunnan, China. Phylogenetic analysis revealed all MAGs of Ca. Bathyarchaeia can be classified into 7 orders and 15 families. Among them, 4 families have been first discovered in the present study, significantly expanding the known diversity of Ca. Bathyarchaeia. Comparative genomics demonstrated Ca. Bathyarchaeia MAGs from thermal habitats to encode a large variety of genes related to carbohydrate degradation, which are likely a metabolic adaptation of these organisms to a lifestyle at high temperatures. At least two families are potential methanogens/alkanotrophs, indicating a potential for the catalysis of short-chain hydrocarbons. Three MAGs from Family-7.3 are identified as alkanotrophs due to the detection of an Mcr complex. Family-2 contains the largest number of genes relevant to alkyl-CoM transformation, indicating the potential for methylotrophic methanogenesis, although their evolutionary history suggests the ancestor of Ca. Bathyarchaeia was unable to metabolize alkanes. Subsequent lineages have acquired the ability via horizontal gene transfer. Overall, our study significantly expands our knowledge and understanding of the metabolic capabilities, habitat adaptations, and evolution of Ca. Bathyarchaeia in thermal environments. IMPORTANCE Ca. Bathyarchaeia MAGs from terrestrial hot spring habitats are poorly revealed, though they have been studied extensively in marine ecosystems. In this study, we uncovered the metabolic capabilities and ecological role of Ca. Bathyarchaeia in hot springs and give a comprehensive comparative analysis between thermal and nonthermal habitats to reveal the thermal adaptability of Ca. Bathyarchaeia. Also, we attempt to determine the evolutionary history of methane/alkane metabolism in Ca. Bathyarchaeia, since it appears to be the first archaea beyond Euryarchaeota which contains the mcrABG genes. The reclassification of Ca. Bathyarchaeia and significant genomic differences among different lineages largely expand our knowledge on these cosmopolitan archaea, which will be beneficial in guiding the future studies.}, }
@article {pmid34282723, year = {2021}, author = {Diebold, PJ and New, FN and Hovan, M and Satlin, MJ and Brito, IL}, title = {Linking plasmid-based beta-lactamases to their bacterial hosts using single-cell fusion PCR.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {34282723}, issn = {2050-084X}, support = {DP2 HL141007/HL/NHLBI NIH HHS/United States ; K23 AI114994/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Cell Fusion/*methods ; Chickens/microbiology ; Clostridiales/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Feces/microbiology ; Gene Transfer, Horizontal ; Humans ; Klebsiella pneumoniae/genetics ; Microbiota/genetics ; Plasmids/*genetics ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S ; beta-Lactamases/*genetics/metabolism ; }, abstract = {The horizonal transfer of plasmid-encoded genes allows bacteria to adapt to constantly shifting environmental pressures, bestowing functional advantages to their bacterial hosts such as antibiotic resistance, metal resistance, virulence factors, and polysaccharide utilization. However, common molecular methods such as short- and long-read sequencing of microbiomes cannot associate extrachromosomal plasmids with the genome of the host bacterium. Alternative methods to link plasmids to host bacteria are either laborious, expensive, or prone to contamination. Here we present the One-step Isolation and Lysis PCR (OIL-PCR) method, which molecularly links plasmid-encoded genes with the bacterial 16S rRNA gene via fusion PCR performed within an emulsion. After validating this method, we apply it to identify the bacterial hosts of three clinically relevant beta-lactamases within the gut microbiomes of neutropenic patients, as they are particularly vulnerable multidrug-resistant infections. We successfully detect the known association of a multi-drug resistant plasmid with Klebsiella pneumoniae, as well as the novel associations of two low-abundance genera, Romboutsia and Agathobacter. Further investigation with OIL-PCR confirmed that our detection of Romboutsia is due to its physical association with Klebsiella as opposed to directly harboring the beta-lactamase genes. Here we put forth a robust, accessible, and high-throughput platform for sensitively surveying the bacterial hosts of mobile genes, as well as detecting physical bacterial associations such as those occurring within biofilms and complex microbial communities.}, }
@article {pmid34280721, year = {2021}, author = {Fan, H and Wu, S and Dong, W and Li, X and Dong, Y and Wang, S and Zhu, YG and Zhuang, X}, title = {Characterization of tetracycline-resistant microbiome in soil-plant systems by combination of H2[18]O-based DNA-Stable isotope probing and metagenomics.}, journal = {Journal of hazardous materials}, volume = {420}, number = {}, pages = {126440}, doi = {10.1016/j.jhazmat.2021.126440}, pmid = {34280721}, issn = {1873-3336}, mesh = {Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Anti-Bacterial Agents ; DNA ; Genes, Bacterial ; Isotopes ; Manure/analysis ; Metagenomics ; *Microbiota/genetics ; *Soil ; Soil Microbiology ; Tetracycline ; }, abstract = {The emergence and spread of antibiotic resistance have been considered as a global health threat. However, effective methods to identify antibiotic-resistant bacteria (ARB) in complex microbial community are lacking, and the potential transmission pathways of ARB and antibiotic resistance genes (ARGs) in the soil-plant system remain scarce. Here in this study, tetracycline was chosen as the target antibiotic due to its globally wide usage and clinical significance. DNA-based stable isotope probing with H2[18]O was applied to identify the tetracycline-resistant bacteria from soil-plant systems. Eighteen-year organic fertilization significantly changed the composition of the tetracycline-resistant microbiome in the soil-wheat system and resulted in a higher relative abundance of ARGs in the wheat endophyte. Rhizosphere harboring the most diverse ARGs and mobile genetic elements was identified as a hot spot for horizontal gene transfer and an important bridge between bulk soil and wheat endophyte. Micrococcaceae and Sphingomonadaceae carrying ARGs associated with abundant mobile genetic elements, were identified as the core bacterial taxa in long-term manure-amended and untreated soil-wheat systems, respectively. This method contributes to a more precise track of ARB in the environment, and our work depicts the high potential of ARG transfer in the rhizosphere mediated by the core species.}, }
@article {pmid34279672, year = {2021}, author = {Zhang, Z and Zhang, X}, title = {Evolution of Subfamily I.1 Lipases in Pseudomonas aeruginosa.}, journal = {Current microbiology}, volume = {78}, number = {9}, pages = {3494-3504}, pmid = {34279672}, issn = {1432-0991}, mesh = {Bacterial Proteins/genetics ; Gene Transfer, Horizontal ; Genomic Islands ; Humans ; *Lipase/genetics/metabolism ; *Pseudomonas aeruginosa/genetics/metabolism ; Virulence ; }, abstract = {The gram-negative Pseudomonas aeruginosa is an opportunistic human pathogen that contains two different types of strains: the "classical" and the "outlier". In the "classical" strain, its bacterial subfamily I.1 lipases, such as LipA and LipC in P. aeruginosa PAO1, play critical roles in its pathogenicity. However, less is known about the subfamily I.1 lipases in the "outlier" strain, nor the evolution paths of those lipases in both types of P. aeruginosa strains. Our genome-scale investigation on I.1 lipases across different bacterial strains demonstrates the presence of one LipA-like and one new type of I.1 lipase (LipC2) in those "outlier" strains. The related genomic islands analyses further suggest that the LipC counterpart gene in the "outlier" strain was lost by gene truncation. In addition, the evolutionary analyses also indicates the horizontal LipC2 gene transfer from other gammaproteobacterial species, as well as the horizontal LipA gene transfer between two different phyla, both suggesting that the gene transfer of bacterial I.1 lipases might occur in different taxonomical levels. Our results not only provide an evidence to understand the pathogenicity among different P. aeruginosa strains, but add to the knowledge of I.1 lipase evolution in bacteria.}, }
@article {pmid34278591, year = {2021}, author = {Wang, T and Weiss, A and Ha, Y and You, L}, title = {Predicting plasmid persistence in microbial communities by coarse-grained modeling.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {43}, number = {9}, pages = {e2100084}, pmid = {34278591}, issn = {1521-1878}, support = {R01 AI125604/AI/NIAID NIH HHS/United States ; R01 EB031869/EB/NIBIB NIH HHS/United States ; }, mesh = {*Gene Transfer, Horizontal ; *Microbiota ; Plasmids/genetics ; }, abstract = {Plasmids are a major type of mobile genetic elements (MGEs) that mediate horizontal gene transfer. The stable maintenance of plasmids plays a critical role in the functions and survival for microbial populations. However, predicting and controlling plasmid persistence and abundance in complex microbial communities remain challenging. Computationally, this challenge arises from the combinatorial explosion associated with the conventional modeling framework. Recently, a plasmid-centric framework (PCF) has been developed to overcome this computational bottleneck. This framework enables the derivation of a simple metric, the persistence potential, to predict plasmid persistence and abundance. Here, we discuss how PCF can be extended to account for plasmid interactions. We also discuss how such model-guided predictions of plasmid fates can benefit from the development of new experimental tools and data-driven computational methods.}, }
@article {pmid34276619, year = {2021}, author = {Lopez-Chavarrias, V and Ugarte-Ruiz, M and Barcena, C and Olarra, A and Garcia, M and Saez, JL and de Frutos, C and Serrano, T and Perez, I and Moreno, MA and Dominguez, L and Alvarez, J}, title = {Monitoring of Antimicrobial Resistance to Aminoglycosides and Macrolides in Campylobacter coli and Campylobacter jejuni From Healthy Livestock in Spain (2002-2018).}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {689262}, pmid = {34276619}, issn = {1664-302X}, abstract = {Antimicrobial resistance (AMR) in Campylobacter spp. (Campylobacter coli and Campylobacter jejuni) is a concern due to its importance in public health, particularly when it involves aminoglycosides and macrolides, drugs of choice for treatment of human cases. Co-resistance to these two antimicrobial classes involves transfer of genetic elements and/or acquisition of mutations in different genetic loci, which can in turn spread through vertical or horizontal gene transfer (HGT) phenomena, with each route having different potential implications. This study aimed at evaluating the association between the presence of phenotypic resistance to these two antimicrobial classes in C. coli and C. jejuni recovered from livestock at slaughterhouses in Spain (as part of the AMR surveillance program), and at assessing the genetic heterogeneity between resistant and susceptible isolates by analysing the "short variable region" (SVR) of the flaA gene. Over the 2002-2018 period, antimicrobial susceptibility test results from 10,965 Campylobacter isolates retrieved from fecal samples of broilers, turkeys, pigs and cattle were collected to compare the proportion of resistant isolates and the Minimum Inhibitory Concentrations (MICs) against six antimicrobials including gentamicin (GEN), streptomycin (STR), and erythromycin (ERY). AMR-associated genes were determined for a group of 51 isolates subjected to whole genome sequencing, and the flaA SVR of a subset of 168 isolates from all hosts with different resistotypes was used to build a Neighbor-Joining-based phylogenetic tree and assess the existence of groups by means of "relative synonymous codon usage" (RSCU) analysis. The proportion of antimicrobial resistant isolates to both, aminoglycosides and macrolides, varied widely for C. coli (7-91%) and less for C. jejuni (all hosts 0-11%). Across hosts, these proportions were 7-56% in poultry, 12-82% in cattle, and 22-91% in pigs for C. coli and 0-8% in poultry and 1-11% in cattle for C. jejuni. Comparison of the MIC distributions revealed significant host-specific differences only for ERY in C. jejuni (p = 0.032). A significant association in the simultaneous presentation of AMR to both antimicrobial classes was observed across hosts/bacterial species. The flaA gene analysis showed clustering of isolates sharing resistotype and to a lesser degree bacterial species and host. Several resistance markers associated with resistance to aminoglycosides and macrolides were found among the sequenced isolates. The consistent association between the simultaneous presentation of AMR to aminoglycosides and macrolides in all hosts could be due to the persistence of strains and/or resistance mechanisms in Campylobacter populations in livestock over time. Further studies based on whole genome sequencing are needed to assess the epidemiological links between hosts and bacterial strains.}, }
@article {pmid34276616, year = {2021}, author = {Bhattacharjee, S and Kharwar, S and Mishra, AK}, title = {Insights Into the Phylogenetic Distribution, Diversity, Structural Attributes, and Substrate Specificity of Putative Cyanobacterial Orthocaspases.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {682306}, pmid = {34276616}, issn = {1664-302X}, abstract = {The functionality of caspase homologs in prokaryotic cell execution has been perceived, yet the dimensions of their metabolic pertinence are still cryptic. Here, a detailed in silico study on putative cyanobacterial caspase homologs, termed orthocaspases, in a sequenced genome of 132 strains was performed. We observed that 473 putative orthocaspases were distributed among 62% cyanobacterial strains subsumed within all the taxonomical orders. However, high diversity among these orthocaspases was also evident as the conventional histidine-cysteine (HC) dyad was present only in 72.03% of orthocaspases (wild-type), whereas the rest 28.18% were pseudo-variants having substituted the catalytic dyad. Besides, the presence of various accessory functional domains with Peptidase C14 probably suggested the multifunctionality of the orthocaspases. Moreover, the early origin and emergence of wild-type orthocaspases were conferred by their presence in Gloeobacter; however, the complex phylogeny displayed by these caspase-homologs perhaps suggested horizontal a gene transfer for their acquisition. However, morpho-physiological advancements and larger genome size favored the acquisition of orthocaspases. Moreover, the conserved caspase hemoglobinase fold not only in the wild-type but also in the pseudo-orthocaspases in Nostoc sp. PCC 7120 ascertained the least effect of catalytic motifs in the protein tertiary structure. Further, the 100-ns molecular dynamic simulation and molecular mechanics/generalized born surface area exhibited stable binding of arginylarginine dipeptide with wild-type orthocaspase of Nostoc sp. PCC 7120, displaying arginine-P1 specificity of wild-type orthocaspases. This study deciphered the distribution, diversity, domain architecture, structure, and basic substrate specificity of putative cyanobacterial orthocaspases, which may aid in functional investigations in the future.}, }
@article {pmid34276582, year = {2021}, author = {Dutta, D and Kaushik, A and Kumar, D and Bag, S}, title = {Foodborne Pathogenic Vibrios: Antimicrobial Resistance.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {638331}, pmid = {34276582}, issn = {1664-302X}, abstract = {Foodborne illness caused by pathogenic Vibrios is generally associated with the consumption of raw or undercooked seafood. Fish and other seafood can be contaminated with Vibrio species, natural inhabitants of the marine, estuarine, and freshwater environment. Pathogenic Vibrios of major public health concerns are Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus. Common symptoms of foodborne Vibrio infection include watery diarrhea, stomach cramping, nausea, vomiting, fever, and chills. Administration of oral or intravenous rehydration salts solution is the mainstay for the management of cholera, and antibiotics are also used to shorten the duration of diarrhea and to limit further transmission of the disease. Currently, doxycycline, azithromycin, or ciprofloxacin are commonly used for V. cholerae, and doxycycline or quinolone are administered for V. parahaemolyticus, whereas doxycycline and a third-generation cephalosporin are recommended for V. vulnificus as initial treatment regimen. The emergence of antimicrobial resistance (AMR) in Vibrios is increasingly common across the globe and a decrease in the effectiveness of commonly available antibiotics poses a global threat to public health. Recent progress in comparative genomic studies suggests that the genomes of the drug-resistant Vibrios harbor mobile genetic elements like plasmids, integrating conjugative elements, superintegron, transposable elements, and insertion sequences, which are the major carriers of genetic determinants encoding antimicrobial resistance. These mobile genetic elements are highly dynamic and could potentially propagate to other bacteria through horizontal gene transfer (HGT). To combat the serious threat of rising AMR, it is crucial to develop strategies for robust surveillance, use of new/novel pharmaceuticals, and prevention of antibiotic misuse.}, }
@article {pmid34273886, year = {2021}, author = {Feng, G and Huang, H and Chen, Y}, title = {Effects of emerging pollutants on the occurrence and transfer of antibiotic resistance genes: A review.}, journal = {Journal of hazardous materials}, volume = {420}, number = {}, pages = {126602}, doi = {10.1016/j.jhazmat.2021.126602}, pmid = {34273886}, issn = {1873-3336}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; *Environmental Pollutants ; Genes, Bacterial ; *Microbiota ; Plastics ; }, abstract = {The emergence and spread of antibiotic resistance genes (ARGs) have become major concerns for both public health and environmental ecosystems. Emerging pollutants (EPs) that accumulate in environmental compartments also pose a potential risk for the enrichment of ARGs in indigenous microorganisms. This paper presents a comprehensive review of the effects and intrinsic mechanisms of EPs, including microplastics, engineered nanomaterials, disinfection byproducts, pharmaceuticals, and personal care products, on the occurrence and dissemination of ARGs. State-of-the-art methods for identifying culture-independent ARG-host interactions and monitoring horizontal gene transfer (HGT) processes in real-time are first reviewed. The contributions of EPs to the abundance and diversity of ARGs are then summarized. Finally, we discussed the underlying mechanisms related to the regulation of HGT, increased mutagenesis, and the evolution of microbial communities. Further details of three HGT (i.e., conjugation, transformation, and transduction) frequency patterns in response to various EPs are also examined. This review contemplates and reassesses the risks of ARG evolution posed by the manufacture and application of EPs.}, }
@article {pmid34272861, year = {2021}, author = {Brancaccio, M and Tangherlini, M and Danovaro, R and Castellano, I}, title = {Metabolic Adaptations to Marine Environments: Molecular Diversity and Evolution of Ovothiol Biosynthesis in Bacteria.}, journal = {Genome biology and evolution}, volume = {13}, number = {9}, pages = {}, pmid = {34272861}, issn = {1759-6653}, mesh = {Aquatic Organisms ; *Bacteria/genetics/metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Methylhistidines/chemistry/metabolism ; }, abstract = {Ovothiols are sulfur-containing amino acids synthesized by marine invertebrates, protozoans, and bacteria. They act as pleiotropic molecules in signaling and protection against oxidative stress. The discovery of ovothiol biosynthetic enzymes, sulfoxide synthase OvoA and β-lyase OvoB, paves the way for a systematic investigation of ovothiol distribution and molecular diversification in nature. In this work, we conducted genomic and metagenomics data mining to investigate the distribution and diversification of ovothiol biosynthetic enzymes in Bacteria. We identified the bacteria endowed with this secondary metabolic pathway, described their taxonomy, habitat and biotic interactions in order to provide insight into their adaptation to specific environments. We report that OvoA and OvoB are mostly encountered in marine aerobic Proteobacteria, some of them establishing symbiotic or parasitic relationships with other organisms. We identified a horizontal gene transfer event of OvoB from Bacteroidetes living in symbiosis with Hydrozoa. Our search within the Ocean Gene Atlas revealed the occurrence of ovothiol biosynthetic genes in Proteobacteria living in a wide range of pelagic and highly oxygenated environments. Finally, we tracked the evolutionary history of ovothiol biosynthesis from marine bacteria to unicellular eukaryotes and metazoans. Our analysis provides new conceptual elements to unravel the evolutionary and ecological significance of ovothiol biosynthesis.}, }
@article {pmid34271377, year = {2021}, author = {Zheng, H and Feng, N and Yang, T and Shi, M and Wang, X and Zhang, Q and Zhao, J and Li, F and Sun, K and Xing, B}, title = {Individual and combined applications of biochar and pyroligneous acid mitigate dissemination of antibiotic resistance genes in agricultural soil.}, journal = {The Science of the total environment}, volume = {796}, number = {}, pages = {148962}, doi = {10.1016/j.scitotenv.2021.148962}, pmid = {34271377}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/pharmacology ; Charcoal ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Humans ; Manure ; *Soil ; Soil Microbiology ; Terpenes ; }, abstract = {Remediation of agricultural soils polluted with antibiotic resistance genes (ARGs) is important for protecting food safety and human health. However, the feasibility of co-application of biochar and pyroligneous acid, two multifunctional soil amendments, for mitigating dissemination of soil ARGs is unknown. Thus, a woody biochar (BC450) and its by-product, pyroligneous acid (PA450) simultaneously produced at 450 °C from blended wood wastes, were used to compare their individual and combined effects on soil ARG abundance using a 65-day pot experiment planted with leafy vegetable Brassica chinensis L. The individual and combined applications of PA450 and BC450 significantly reduced the absolute abundance of ARGs by 65.7-81.4% and 47.5-72.9% in the corresponding rhizosphere and bulk soil. However, the co-application showed little synergistic effect, probably due to the counteractive effect of BC450 on the PA450-mitigated soil ARG proliferation, resulted from the promoted soil bacterial growth and/or adsorption of antimicrobial components of PA450 by BC450. The decreased abundances of mobile genetic element intI1 and Tn916/1545 in the PA450 treatments demonstrated the potential of PA450 for weakening horizontal gene transfer (HGT). Furthermore, weakened HGT by individual PA450, lowered availability of heavy metals by individual BC450, and different bacterial community (e.g., reduced ARGs bacterial host) together with improved soil properties from co-application of PA450 and BC450 all contributed to the reduced ARG level. This study highlighted the feasibility of co-applications of biochar and pyroligneous acid amendment for mitigating soil ARG pollution. These findings provide important information for developing eco-friendly technologies using biochar and pyroligneous acid in remediating ARG-contaminated soils.}, }
@article {pmid34271348, year = {2021}, author = {Manoharan, RK and Srinivasan, S and Shanmugam, G and Ahn, YH}, title = {Shotgun metagenomic analysis reveals the prevalence of antibiotic resistance genes and mobile genetic elements in full scale hospital wastewater treatment plants.}, journal = {Journal of environmental management}, volume = {296}, number = {}, pages = {113270}, doi = {10.1016/j.jenvman.2021.113270}, pmid = {34271348}, issn = {1095-8630}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Bacteroidetes ; Drug Resistance, Microbial/genetics ; Flavobacteriaceae ; Genes, Bacterial ; Hospitals ; Humans ; Interspersed Repetitive Sequences ; Metagenome ; Prevalence ; RNA, Ribosomal, 16S ; Sewage ; *Wastewater ; *Water Purification ; }, abstract = {Wastewater treatment plants are considered as hotspots of emerging antimicrobial genes and mobile genetic elements. We used a shotgun metagenomic approach to examine the wide-spectrum profiles of ARGs (antibiotic resistance genes) and MGEs (mobile genetic elements) in activated sludge samples from two different hospital trains at the wastewater treatment plants (WWTPs) in Daegu, South Korea. The influent activated sludge and effluent of two trains (six samples in total) at WWTPs receiving domestic sewage wastewater (SWW) and hospital wastewater (HWW) samples collected at multiple periods were subjected to high throughput 16S rRNA metagenome sequencing for microbial community diversity. Cloacibacterium caeni and Lewinella nigricans were predominant in SWW effluents, while Bacillus subtilis and Staphylococcus epidermidis were predominant in HWW effluents based on the Miseq platform. Totally, 20,011 reads and 28,545 metagenomic sequence reads were assigned to 25 known ARG types in the SWW2 and HWW5 samples, respectively. The higher abundance of ARGs, including multidrug resistance (>53%, MDR), macrolide-lincosamide-streptogramin (>9%, MLS), beta-lactam (>3.3%), bacitracin (>4.4%), and tetracycline (>3.4%), confirmed the use of these antibiotics in human medicine. In total, 190 subtypes belonging to 23 antibiotic classes were detected in both SWW2 and HWW5 samples. RpoB2, MacB, and multidrug (MDR) ABC transporter shared the maximum matched genes in both activated sludge samples. The high abundance of MGEs, such as a gene transfer agent (GTA) (four times higher), transposable elements (1.6 times higher), plasmid related functions (3.8 times higher), and phages (two times higher) in HWW5 than in SWW2, revealed a risk of horizontal gene transfer in HWW. Domestic wastewater from hospital patients also influenced the abundance of ARGs and MGEs in the activated sludge process.}, }
@article {pmid34259624, year = {2021}, author = {D'Aeth, JC and van der Linden, MP and McGee, L and de Lencastre, H and Turner, P and Song, JH and Lo, SW and Gladstone, RA and Sá-Leão, R and Ko, KS and Hanage, WP and Breiman, RF and Beall, B and Bentley, SD and Croucher, NJ and , }, title = {The role of interspecies recombination in the evolution of antibiotic-resistant pneumococci.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {34259624}, issn = {2050-084X}, support = {R01 AI106786/AI/NIAID NIH HHS/United States ; 102169/Z/13/Z/WT_/Wellcome Trust/United Kingdom ; MR/T016434/1/MRC_/Medical Research Council/United Kingdom ; 106698/WT_/Wellcome Trust/United Kingdom ; 206194/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MR/R015600/1/MRC_/Medical Research Council/United Kingdom ; 098051/WT_/Wellcome Trust/United Kingdom ; 104169/Z/14/A/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; DNA Transposable Elements ; Drug Resistance, Bacterial/*drug effects/*genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Germany ; Humans ; Macrolides/pharmacology ; Phylogeny ; Pneumococcal Vaccines ; Serogroup ; Serotyping ; Streptococcus pneumoniae/drug effects/genetics ; }, abstract = {Multidrug-resistant Streptococcus pneumoniae emerge through the modification of core genome loci by interspecies homologous recombinations, and acquisition of gene cassettes. Both occurred in the otherwise contrasting histories of the antibiotic-resistant S. pneumoniae lineages PMEN3 and PMEN9. A single PMEN3 clade spread globally, evading vaccine-induced immunity through frequent serotype switching, whereas locally circulating PMEN9 clades independently gained resistance. Both lineages repeatedly integrated Tn916-type and Tn1207.1-type elements, conferring tetracycline and macrolide resistance, respectively, through homologous recombination importing sequences originating in other species. A species-wide dataset found over 100 instances of such interspecific acquisitions of resistance cassettes and flanking homologous arms. Phylodynamic analysis of the most commonly sampled Tn1207.1-type insertion in PMEN9, originating from a commensal and disrupting a competence gene, suggested its expansion across Germany was driven by a high ratio of macrolide-to-β-lactam consumption. Hence, selection from antibiotic consumption was sufficient for these atypically large recombinations to overcome species boundaries across the pneumococcal chromosome.}, }
@article {pmid34255978, year = {2021}, author = {Hara, Y and Shibahara, R and Kondo, K and Abe, W and Kunieda, T}, title = {Parallel evolution of trehalose production machinery in anhydrobiotic animals via recurrent gene loss and horizontal transfer.}, journal = {Open biology}, volume = {11}, number = {7}, pages = {200413}, pmid = {34255978}, issn = {2046-2441}, mesh = {Animals ; *Biological Evolution ; Evolution, Molecular ; Gene Expression Profiling ; *Gene Transfer, Horizontal ; Glucosyltransferases/genetics/metabolism ; Phosphoric Monoester Hydrolases/genetics/metabolism ; Phylogeny ; Trehalose/*biosynthesis ; Whole Genome Sequencing ; }, abstract = {Trehalose is a versatile non-reducing sugar. In some animal groups possessing its intrinsic production machinery, it is used as a potent protectant against environmental stresses, as well as blood sugar. However, the trehalose biosynthesis genes remain unidentified in the large majority of metazoan phyla, including vertebrates. To uncover the evolutionary history of trehalose production machinery in metazoans, we scrutinized the available genome resources and identified bifunctional trehalose-6-phosphate synthase-trehalose-6-phosphate phosphatase (TPS-TPP) genes in various taxa. The scan included our newly sequenced genome assembly of a desiccation-tolerant tardigrade Paramacrobiotus sp. TYO, revealing that this species retains TPS-TPP genes activated upon desiccation. Phylogenetic analyses identified a monophyletic group of the many of the metazoan TPS-TPP genes, namely 'pan-metazoan' genes, that were acquired in the early ancestors of metazoans. Furthermore, coordination of our results with the previous horizontal gene transfer studies illuminated that the two tardigrade lineages, nematodes and bdelloid rotifers, all of which include desiccation-tolerant species, independently acquired the TPS-TPP homologues via horizontal transfer accompanied with loss of the 'pan-metazoan' genes. Our results indicate that the parallel evolution of trehalose synthesis via recurrent loss and horizontal transfer of the biosynthesis genes resulted in the acquisition and/or augmentation of anhydrobiotic lives in animals.}, }
@article {pmid34254817, year = {2021}, author = {Li, L and Liu, Z and Zhou, Z and Zhang, M and Meng, D and Liu, X and Huang, Y and Li, X and Jiang, Z and Zhong, S and Drewniak, L and Yang, Z and Li, Q and Liu, Y and Nan, X and Jiang, B and Jiang, C and Yin, H}, title = {Comparative Genomics Provides Insights into the Genetic Diversity and Evolution of the DPANN Superphylum.}, journal = {mSystems}, volume = {6}, number = {4}, pages = {e0060221}, pmid = {34254817}, issn = {2379-5077}, support = {91851206//National Natural Science Foundation of China (NSFC)/ ; 41877345//National Natural Science Foundation of China (NSFC)/ ; }, abstract = {DPANN is known as highly diverse, globally widespread, and mostly ectosymbiotic archaeal superphylum. However, this group of archaea was overlooked for a long time, and there were limited in-depth studies reported. In this investigation, 41 metagenome-assembled genomes (MAGs) belonging to the DPANN superphylum were recovered (18 MAGs had average nucleotide identity [ANI] values of <95% and a percentage of conserved proteins [POCP] of >50%, while 14 MAGs showed a POCP of <50%), which were analyzed comparatively with 515 other published DPANN genomes. Mismatches to known 16S rRNA gene primers were identified among 16S rRNA genes of DPANN archaea. Numbers of gene families lost (mostly related to energy and amino acid metabolism) were over three times greater than those gained in the evolution of DPANN archaea. Lateral gene transfer (LGT; ∼45.5% was cross-domain) had facilitated niche adaption of the DPANN archaea, ensuring a delicate equilibrium of streamlined genomes with efficient niche-adaptive strategies. For instance, LGT-derived cytochrome bd ubiquinol oxidase and arginine deiminase in the genomes of "Candidatus Micrarchaeota" could help them better adapt to aerobic acidic mine drainage habitats. In addition, most DPANN archaea acquired enzymes for biosynthesis of extracellular polymeric substances (EPS) and transketolase/transaldolase for the pentose phosphate pathway from Bacteria. IMPORTANCE The domain Archaea is a key research model for gaining insights into the origin and evolution of life, as well as the relevant biogeochemical processes. The discovery of nanosized DPANN archaea has overthrown many aspects of microbiology. However, the DPANN superphylum still contains a vast genetic novelty and diversity that need to be explored. Comprehensively comparative genomic analysis on the DPANN superphylum was performed in this study, with an attempt to illuminate its metabolic potential, ecological distribution and evolutionary history. Many interphylum differences within the DPANN superphylum were found. For example, Altiarchaeota had the biggest genome among DPANN phyla, possessing many pathways missing in other phyla, such as formaldehyde assimilation and the Wood-Ljungdahl pathway. In addition, LGT acted as an important force to provide DPANN archaeal genetic flexibility that permitted the occupation of diverse niches. This study has advanced our understanding of the diversity and genome evolution of archaea.}, }
@article {pmid34253055, year = {2021}, author = {Jaffe, AL and Thomas, AD and He, C and Keren, R and Valentin-Alvarado, LE and Munk, P and Bouma-Gregson, K and Farag, IF and Amano, Y and Sachdeva, R and West, PT and Banfield, JF}, title = {Patterns of Gene Content and Co-occurrence Constrain the Evolutionary Path toward Animal Association in Candidate Phyla Radiation Bacteria.}, journal = {mBio}, volume = {12}, number = {4}, pages = {e0052121}, pmid = {34253055}, issn = {2150-7511}, mesh = {Animals ; Bacteria/*classification/*genetics ; Ecosystem ; *Evolution, Molecular ; Genome, Bacterial ; Genomics ; *Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Candidate Phyla Radiation (CPR) bacteria are small, likely episymbiotic organisms found across Earth's ecosystems. Despite their prevalence, the distribution of CPR lineages across habitats and the genomic signatures of transitions among these habitats remain unclear. Here, we expand the genome inventory for Absconditabacteria (SR1), Gracilibacteria, and Saccharibacteria (TM7), CPR bacteria known to occur in both animal-associated and environmental microbiomes, and investigate variation in gene content with habitat of origin. By overlaying phylogeny with habitat information, we show that bacteria from these three lineages have undergone multiple transitions from environmental habitats into animal microbiomes. Based on co-occurrence analyses of hundreds of metagenomes, we extend the prior suggestion that certain Saccharibacteria have broad bacterial host ranges and constrain possible host relationships for Absconditabacteria and Gracilibacteria. Full-proteome analyses show that animal-associated Saccharibacteria have smaller gene repertoires than their environmental counterparts and are enriched in numerous protein families, including those likely functioning in amino acid metabolism, phage defense, and detoxification of peroxide. In contrast, some freshwater Saccharibacteria encode a putative rhodopsin. For protein families exhibiting the clearest patterns of differential habitat distribution, we compared protein and species phylogenies to estimate the incidence of lateral gene transfer and genomic loss occurring over the species tree. These analyses suggest that habitat transitions were likely not accompanied by large transfer or loss events but rather were associated with continuous proteome remodeling. Thus, we speculate that CPR habitat transitions were driven largely by availability of suitable host taxa and were reinforced by acquisition and loss of some capacities. IMPORTANCE Studying the genetic differences between related microorganisms from different environment types can indicate factors associated with their movement among habitats. This is particularly interesting for bacteria from the Candidate Phyla Radiation because their minimal metabolic capabilities require associations with microbial hosts. We found that shifts of Absconditabacteria, Gracilibacteria, and Saccharibacteria between environmental ecosystems and mammalian mouths/guts probably did not involve major episodes of gene gain and loss; rather, gradual genomic change likely followed habitat migration. The results inform our understanding of how little-known microorganisms establish in the human microbiota where they may ultimately impact health.}, }
@article {pmid34252921, year = {2021}, author = {Anselmetti, Y and El-Mabrouk, N and Lafond, M and Ouangraoua, A}, title = {Gene tree and species tree reconciliation with endosymbiotic gene transfer.}, journal = {Bioinformatics (Oxford, England)}, volume = {37}, number = {Suppl_1}, pages = {i120-i132}, pmid = {34252921}, issn = {1367-4811}, support = {//Natural Sciences and Engineering Research Council of Canada/ ; //Fonds de recherche Nature et Technologie, Qu&#xe9;bec/ ; }, mesh = {Algorithms ; *Evolution, Molecular ; Gene Duplication ; *Gene Transfer, Horizontal ; Genome ; Phylogeny ; Symbiosis/genetics ; }, abstract = {MOTIVATION: It is largely established that all extant mitochondria originated from a unique endosymbiotic event integrating an α-proteobacterial genome into an eukaryotic cell. Subsequently, eukaryote evolution has been marked by episodes of gene transfer, mainly from the mitochondria to the nucleus, resulting in a significant reduction of the mitochondrial genome, eventually completely disappearing in some lineages. However, in other lineages such as in land plants, a high variability in gene repertoire distribution, including genes encoded in both the nuclear and mitochondrial genome, is an indication of an ongoing process of Endosymbiotic Gene Transfer (EGT). Understanding how both nuclear and mitochondrial genomes have been shaped by gene loss, duplication and transfer is expected to shed light on a number of open questions regarding the evolution of eukaryotes, including rooting of the eukaryotic tree.<br><br>RESULTS: We address the problem of inferring the evolution of a gene family through duplication, loss and EGT events, the latter considered as a special case of horizontal gene transfer occurring between the mitochondrial and nuclear genomes of the same species (in one direction or the other). We consider both EGT events resulting in maintaining (EGTcopy) or removing (EGTcut) the gene copy in the source genome. We present a linear-time algorithm for computing the DLE (Duplication, Loss and EGT) distance, as well as an optimal reconciled tree, for the unitary cost, and a dynamic programming algorithm allowing to output all optimal reconciliations for an arbitrary cost of operations. We illustrate the application of our EndoRex software and analyze different costs settings parameters on a plant dataset and discuss the resulting reconciled trees.<br><br>EndoRex implementation and supporting data are available on the GitHub repository via https://github.com/AEVO-lab/EndoRex.}, }
@article {pmid34252150, year = {2021}, author = {Liu, Q and Zhang, S and Mei, S and Zhou, Y and Wang, J and Han, GZ and Chen, L and Zhou, C and Cao, M}, title = {Viromics unveils extraordinary genetic diversity of the family Closteroviridae in wild citrus.}, journal = {PLoS pathogens}, volume = {17}, number = {7}, pages = {e1009751}, pmid = {34252150}, issn = {1553-7374}, mesh = {Citrus/*virology ; Closteroviridae/*genetics ; Plant Diseases/*virology ; }, abstract = {Our knowledge of citrus viruses is largely skewed toward virus pathology in cultivated orchards. Little is known about the virus diversity in wild citrus species. Here, we used a metatranscriptomics approach to characterize the virus diversity in a wild citrus habitat within the proposed center of the origin of citrus plants. We discovered a total of 44 virus isolates that could be classified into species Citrus tristeza virus and putative species citrus associated ampelovirus 1, citrus associated ampelovirus 2, and citrus virus B within the family Closteroviridae, providing important information to explore the factors facilitating outbreaks of citrus viruses and the evolutionary history of the family Closteroviridae. We found that frequent horizontal gene transfer, gene duplication, and alteration of expression strategy have shaped the genome complexity and diversification of the family Closteroviridae. Recombination frequently occurred among distinct Closteroviridae members, thereby facilitating the evolution of Closteroviridae. Given the potential emergence of similar wild-citrus-originated novel viruses as pathogens, the need for surveillance of their pathogenic and epidemiological characteristics is of utmost priority for global citrus production.}, }
@article {pmid34252089, year = {2021}, author = {Wein, T and Wang, Y and Barz, M and Stücker, FT and Hammerschmidt, K and Dagan, T}, title = {Essential gene acquisition destabilizes plasmid inheritance.}, journal = {PLoS genetics}, volume = {17}, number = {7}, pages = {e1009656}, pmid = {34252089}, issn = {1553-7404}, mesh = {Biological Evolution ; Chromosomes/genetics ; Escherichia coli/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genes, Essential/*genetics/physiology ; Genomics/methods ; Plasmids/*genetics/metabolism ; }, abstract = {Extra-chromosomal genetic elements are important drivers of evolutionary transformations and ecological adaptations in prokaryotes with their evolutionary success often depending on their 'utility' to the host. Examples are plasmids encoding antibiotic resistance genes, which are known to proliferate in the presence of antibiotics. Plasmids carrying an essential host function are recognized as permanent residents in their host. Essential plasmids have been reported in several taxa where they often encode essential metabolic functions; nonetheless, their evolution remains poorly understood. Here we show that essential genes are rarely encoded on plasmids; evolving essential plasmids in Escherichia coli we further find that acquisition of an essential chromosomal gene by a plasmid can lead to plasmid extinction. A comparative genomics analysis of Escherichia isolates reveals few plasmid-encoded essential genes, yet these are often integrated into plasmid-related functions; an example is the GroEL/GroES chaperonin. Experimental evolution of a chaperonin-encoding plasmid shows that the acquisition of an essential gene reduces plasmid fitness regardless of the stability of plasmid inheritance. Our results suggest that essential plasmid emergence leads to a dose effect caused by gene redundancy. The detrimental effect of essential gene acquisition on plasmid inheritance constitutes a barrier for plasmid-mediated lateral gene transfer and supplies a mechanistic understanding for the rarity of essential genes in extra-chromosomal genetic elements.}, }
@article {pmid34242992, year = {2021}, author = {Yoshida, S and Kee, YJ}, title = {Large-scale sequencing paves the way for genomic and genetic analyses in parasitic plants.}, journal = {Current opinion in biotechnology}, volume = {70}, number = {}, pages = {248-254}, doi = {10.1016/j.copbio.2021.06.011}, pmid = {34242992}, issn = {1879-0429}, mesh = {Biological Evolution ; Gene Transfer, Horizontal ; *Genomics ; *Plants/genetics ; Symbiosis ; }, abstract = {Parasitic plants pose a serious agricultural threat, but are also precious resources for valuable metabolites. The heterotrophic nature of these plants has resulted in the development of several morphological and physiological features that are of evolutionary significance. Recent advances in large-scale sequencing technology have provided insights into the evolutionary and molecular mechanisms of plant parasitism. Genome sequencing has revealed gene losses and horizontal gene transfers in parasitic plants. Mobile signals traveling between the parasite and host may have contributed to the increased fitness of parasitic life styles. Transcriptome analyses implicate shared processes among various parasitic species and the establishment of functional analysis is beginning to reveal molecular mechanisms during host and parasite interactions.}, }
@article {pmid34232736, year = {2021}, author = {Bornier, F and Zas, E and Potheret, D and Laaberki, MH and Coupat-Goutaland, B and Charpentier, X}, title = {Environmental Free-Living Amoebae Can Predate on Diverse Antibiotic-Resistant Human Pathogens.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {18}, pages = {e0074721}, pmid = {34232736}, issn = {1098-5336}, mesh = {Amoeba/*physiology ; Anti-Bacterial Agents ; Bacteria/*growth &amp; development ; Carbapenems ; Composting ; Drug Resistance, Bacterial ; Drug Resistance, Multiple, Bacterial ; Humans ; *Microbial Interactions ; Soil Microbiology ; }, abstract = {Here, we sought to test the resistance of human pathogens to unaltered environmental free-living amoebae. Amoebae are ubiquitous eukaryotic microorganisms and important predators of bacteria. Environmental amoebae have also been proposed to serve as both potential reservoirs and training grounds for human pathogens. However, studies addressing their relationships with human pathogens often rely on a few domesticated amoebae that have been selected to feed on rich medium, thereby possibly overestimating the resistance of pathogens to these predatory phagocytes. From an open-air composting site, we recovered over 100 diverse amoebae that were able to feed on Acinetobacter baumannii and Klebsiella pneumoniae. In a standardized and quantitative assay for predation, the isolated amoebae showed a broad predation spectrum, killing clinical isolates of A. baumannii, K. pneumoniae, Pseudomonas aeruginosa, and Staphylococcus aureus. Interestingly, A. baumannii, which was previously reported to resist predation by laboratory strains of Acanthamoeba, was efficiently consumed by closely related environmental amoebae. The isolated amoebae were capable of feeding on highly virulent carbapenem-resistant or methicillin-resistant clinical isolates. In conclusion, the natural environment is a rich source of amoebae with broad-spectrum bactericidal activities, including against antibiotic-resistant isolates. IMPORTANCE Free-living amoebae have been proposed to play an important role in hosting and disseminating various human pathogens. The resistance of human pathogens to predation by amoebae is often derived from in vitro experiments using model amoebae. Here, we sought to isolate environmental amoebae and to test their predation on diverse human pathogens, with results that challenge conclusions based on model amoebae. We found that the natural environment is a rich source of diverse amoebae with broad-spectrum predatory activities against human pathogens, including highly virulent and antibiotic-resistant clinical isolates.}, }
@article {pmid34232406, year = {2022}, author = {Wang, X and Xiao, W and Li, L and Jing, M and Sun, M and Chang, Y and Qu, Y and Jiang, Y and Xu, Q}, title = {Analysis of the molecular characteristics of a blaKPC-2-harbouring untypeable plasmid in Serratia marcescens.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {25}, number = {2}, pages = {237-244}, pmid = {34232406}, issn = {1618-1905}, mesh = {Anti-Bacterial Agents/pharmacology ; Carbapenems/pharmacology ; *Cross Infection ; Gene Transfer, Horizontal ; Humans ; Klebsiella pneumoniae/genetics ; Microbial Sensitivity Tests ; Plasmids/genetics ; *Serratia marcescens/genetics ; beta-Lactamases/genetics ; }, abstract = {INTRODUCTION: Serratia marcescens has attracted increasing attention worldwide as a neglected opportunistic pathogen of public health concern, especially due to its antimicrobial resistance features, which usually cause nosocomial infections in immunocompromised or critically ill patients.<br><br>METHODS: In our study, four carbapenem-resistant Serratia marcescens (CRSM) clinical isolates were characterized in our hospital from February 2018 to May 2018. The conjugation experiment confirmed the transferability of the carbapenem resistance gene. The types of carbapenem resistance genes were detected by PCR. The homology of the strains was analysed by pulsed field gel electrophoresis (PFGE). The characteristics of the plasmid and environment of carbapenem resistance genes were analysed after whole genome sequencing was performed. Then, we compared the amino acid sequence of the replication initiation protein and constructed a dendrogram by the neighbour-joining method.<br><br>RESULTS: All four isolates showed carbapenem resistance conferred by a blaKPC-2-harbouring plasmid. They had exactly the same bands confirmed by PFGE and were defined as the homologous strains. The blaKPC-2 genes in all of the isolates were located in a 42,742 bp plasmid, which was located in the core region of antibiotic resistance and was composed of Tn3 family transposons, recombinant enzyme genes, ISKpn6 and ISKpn27. The core region of antibiotic resistance formed a 'Tn3-ISKpn6-blaKPC-ISKpn27-Tn3' structure, which was an independent region as a movable element belonging to transposon Tn6296 and its derivatives. The plasmid had a similar skeleton to incX6 plasmids and a similar amino acid sequence to the replication initiation protein. The plasmid was defined as an untypeable blaKPC-2-harbouring plasmid named the 'IncX6-like' plasmid.<br><br>CONCLUSION: The four CRSM isolates were mainly clonally disseminated with a blaKPC-2-harbouring plasmid in our hospital. The pKPC-2-HENAN1602 plasmid (CP047392) in our study was first reported in Serratia marcescens, which belongs to an untypeable group named the 'IncX6-like' plasmid. The carbapenem-resistant gene structure surrounding blaKPC-2 as a sole accessory module can be acquired by horizontal gene transfer and might lead to serious nosocomial infection.}, }
@article {pmid34232073, year = {2021}, author = {Kondo, K and Kawano, M and Sugai, M}, title = {Distribution of Antimicrobial Resistance and Virulence Genes within the Prophage-Associated Regions in Nosocomial Pathogens.}, journal = {mSphere}, volume = {6}, number = {4}, pages = {e0045221}, pmid = {34232073}, issn = {2379-5042}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/*drug effects/*genetics/pathogenicity ; Cross Infection/*microbiology ; Drug Resistance, Bacterial/*genetics ; Enterobacter cloacae/drug effects/genetics/pathogenicity ; Escherichia coli/drug effects/pathogenicity ; Genome, Bacterial ; Humans ; Klebsiella pneumoniae/drug effects/genetics/pathogenicity ; Prophages/*genetics ; Virulence/drug effects ; Virulence Factors/*genetics ; }, abstract = {Prophages are often involved in host survival strategies and contribute toward increasing the genetic diversity of the host genome. Prophages also drive horizontal propagation of various genes as vehicles. However, there are few retrospective studies contributing to the propagation of antimicrobial resistance (AMR) and virulence factor (VF) genes by prophage. We extracted the complete genome sequences of seven pathogens, including ESKAPE bacteria and Escherichia coli from a public database, and examined the distribution of both the AMR and VF genes in prophage-like regions. We found that the ratios of AMR and VF genes greatly varied among the seven species. More than 70% of Enterobacter cloacae strains had VF genes, but only 1.2% of Klebsiella pneumoniae strains had VF genes from prophages. AMR and VF genes are unlikely to exist together in the same prophage region except in E. coli and Staphylococcus aureus, and the distribution patterns of prophage types containing AMR genes are distinct from those of VF gene-carrying prophage types. AMR genes in the prophage were located near transposase and/or integrase. The prophage containing class 1 integrase possessed a significantly greater number of AMR genes than did prophages with no class 1 integrase. The results of this study present a comprehensive picture of AMR and VF genes present within, or close to, prophage-like elements and different prophage patterns between AMR- or VF-encoding prophage-like elements. IMPORTANCE Although we believe phages play an important role in horizontal gene transfer in exchanging genetic material, we do not know the distribution of the antimicrobial resistance (AMR) and/or virulence factor (VF) genes in prophages. We collected different prophage elements from the complete genome sequences of seven species-Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter cloacae, and Escherichia coli-and characterized the distribution of antimicrobial resistance and virulence genes located in the prophage region. While virulence genes in prophage were species specific, antimicrobial resistance genes in prophages were highly conserved in various species. An integron structure was detected within specific prophage regions such as P1-like prophage element. Maximum of 10 antimicrobial resistance genes were found in a single prophage region, suggesting that prophages act as a reservoir for antimicrobial resistance genes. The results of this study show the different characteristic structures between AMR- or VF-encoding prophages.}, }
@article {pmid34228713, year = {2021}, author = {Santos-López, A and Rodríguez-Beltrán, J and San Millán, &#xc1;}, title = {The bacterial capsule is a gatekeeper for mobile DNA.}, journal = {PLoS biology}, volume = {19}, number = {7}, pages = {e3001308}, pmid = {34228713}, issn = {1545-7885}, mesh = {Bacteria/genetics ; *Bacterial Capsules ; *Gene Transfer, Horizontal ; }, abstract = {The horizontal transfer of mobile DNA is one of the signature moves of bacterial evolution, but the specific rules that govern this transfer remain elusive. In this PLOS Biology issue, Haudiquet and colleagues revealed that the interactions between mobile genetic elements and the bacterial capsule shape the horizontal flow of DNA in an important bacterial pathogen.}, }
@article {pmid34228700, year = {2021}, author = {Haudiquet, M and Buffet, A and Rendueles, O and Rocha, EPC}, title = {Interplay between the cell envelope and mobile genetic elements shapes gene flow in populations of the nosocomial pathogen Klebsiella pneumoniae.}, journal = {PLoS biology}, volume = {19}, number = {7}, pages = {e3001276}, pmid = {34228700}, issn = {1545-7885}, mesh = {Bacterial Capsules/*metabolism ; Biosynthetic Pathways ; Conjugation, Genetic ; Gene Flow ; Genome, Bacterial ; *Interspersed Repetitive Sequences ; Klebsiella pneumoniae/genetics/*metabolism ; Recombination, Genetic ; }, abstract = {Mobile genetic elements (MGEs) drive genetic transfers between bacteria using mechanisms that require a physical interaction with the cellular envelope. In the high-priority multidrug-resistant nosocomial pathogens (ESKAPE), the first point of contact between the cell and virions or conjugative pili is the capsule. While the capsule can be a barrier to MGEs, it also evolves rapidly by horizontal gene transfer (HGT). Here, we aim at understanding this apparent contradiction by studying the covariation between the repertoire of capsule genes and MGEs in approximately 4,000 genomes of Klebsiella pneumoniae (Kpn). We show that capsules drive phage-mediated gene flow between closely related serotypes. Such serotype-specific phage predation also explains the frequent inactivation of capsule genes, observed in more than 3% of the genomes. Inactivation is strongly epistatic, recapitulating the capsule biosynthetic pathway. We show that conjugative plasmids are acquired at higher rates in natural isolates lacking a functional capsular locus and confirmed experimentally this result in capsule mutants. This suggests that capsule inactivation by phage pressure facilitates its subsequent reacquisition by conjugation. Accordingly, capsule reacquisition leaves long recombination tracts around the capsular locus. The loss and regain process rewires gene flow toward other lineages whenever it leads to serotype swaps. Such changes happen preferentially between chemically related serotypes, hinting that the fitness of serotype-swapped strains depends on the host genetic background. These results enlighten the bases of trade-offs between the evolution of virulence and multidrug resistance and caution that some alternatives to antibiotics by selecting for capsule inactivation may facilitate the acquisition of antibiotic resistance genes (ARGs).}, }
@article {pmid34224899, year = {2021}, author = {Floridia-Yapur, N and Rusman, F and Diosque, P and Tomasini, N}, title = {Genome data vs MLST for exploring intraspecific evolutionary history in bacteria: Much is not always better.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {93}, number = {}, pages = {104990}, doi = {10.1016/j.meegid.2021.104990}, pmid = {34224899}, issn = {1567-7257}, mesh = {Bacteria/*genetics ; *Evolution, Molecular ; *Genome, Bacterial ; Genomics/*methods ; Multilocus Sequence Typing/*methods ; }, abstract = {Genome-based phylogeny has been proposed to be more accurate than phylogeny based in a few genes as MLST-based phylogeny. However, much is not always better. Here we analyzed 368 complete genomes corresponding to 9 bacterial species in order to address intraspecific phylogeny. The studied species were: Burkholderia pseudomallei, Campylobacter jejuni, Chlamydia trachomatis, Helicobacter pylori, Klebsiella pneumoniae, Listeria monocytogenes, Salmonella enterica, Staphylococcus aureus and Streptococcus pyogenes. The intra-specific phylogenies were inferred using the complete genome sequences of different strains of these species and their MLST schemes. A supermatrix approach was used to infer maximum likelihood phylogenies in both cases. The phylogenetic incongruence between the supermatrix-based genome or MLST tree and individual trees (constructed from genome fragments or MLST genes, respectively) was analyzed. In supermatrix-based trees for genomes, most branches showed a high branch support; however, a high number of branches also showed high percentage of topologically incongruent individual trees. Interestingly, genome and MLST trees showed similar levels of incongruence in the phylogeny for each bacteria specie. Both genome and MLST approaches showed that C. trachomatis and S. aureus have a tree-like evolutionary history (low levels of internal incongruence). Instead, B. pseudomallei and S. pyogenes show high levels of incongruence (network-like evolutionary story) probably caused by HGT (horizontal gene transfer). Concluding, our analysis showed that: high branch supports obtained in genome phylogenies could be an artifact probably caused by data size; MLST is valid to address intraspecific phylogenetic structure; and, each species has its own evolutionary history, which could be affected by HGT to different extents.}, }
@article {pmid34222390, year = {2021}, author = {Jaiswal, S and Jagannadham, J and Kumari, J and Iquebal, MA and Gurjar, AKS and Nayan, V and Angadi, UB and Kumar, S and Kumar, R and Datta, TK and Rai, A and Kumar, D}, title = {Genome Wide Prediction, Mapping and Development of Genomic Resources of Mastitis Associated Genes in Water Buffalo.}, journal = {Frontiers in veterinary science}, volume = {8}, number = {}, pages = {593871}, pmid = {34222390}, issn = {2297-1769}, abstract = {Water buffalo (Bubalus bubalis) are an important animal resource that contributes milk, meat, leather, dairy products, and power for plowing and transport. However, mastitis, a bacterial disease affecting milk production and reproduction efficiency, is most prevalent in populations having intensive selection for higher milk yield, especially where the inbreeding level is also high. Climate change and poor hygiene management practices further complicate the issue. The management of this disease faces major challenges, like antibiotic resistance, maximum residue level, horizontal gene transfer, and limited success in resistance breeding. Bovine mastitis genome wide association studies have had limited success due to breed differences, sample sizes, and minor allele frequency, lowering the power to detect the diseases associated with SNPs. In this work, we focused on the application of targeted gene panels (TGPs) in screening for candidate gene association analysis, and how this approach overcomes the limitation of genome wide association studies. This work will facilitate the targeted sequencing of buffalo genomic regions with high depth coverage required to mine the extremely rare variants potentially associated with buffalo mastitis. Although the whole genome assembly of water buffalo is available, neither mastitis genes are predicted nor TGP in the form of web-genomic resources are available for future variant mining and association studies. Out of the 129 mastitis associated genes of cattle, 101 were completely mapped on the buffalo genome to make TGP. This further helped in identifying rare variants in water buffalo. Eighty-five genes were validated in the buffalo gene expression atlas, with the RNA-Seq data of 50 tissues. The functions of 97 genes were predicted, revealing 225 pathways. The mastitis proteins were used for protein-protein interaction network analysis to obtain additional cross-talking proteins. A total of 1,306 SNPs and 152 indels were identified from 101 genes. Water Buffalo-MSTdb was developed with 3-tier architecture to retrieve mastitis associated genes having genomic coordinates with chromosomal details for TGP sequencing for mining of minor alleles for further association studies. Lastly, a web-genomic resource was made available to mine variants of targeted gene panels in buffalo for mastitis resistance breeding in an endeavor to ensure improved productivity and the reproductive efficiency of water buffalo.}, }
@article {pmid34218334, year = {2021}, author = {Schaller, D and Lafond, M and Stadler, PF and Wieseke, N and Hellmuth, M}, title = {Indirect identification of horizontal gene transfer.}, journal = {Journal of mathematical biology}, volume = {83}, number = {1}, pages = {10}, pmid = {34218334}, issn = {1432-1416}, mesh = {*Algorithms ; *Gene Transfer, Horizontal ; Phylogeny ; }, abstract = {Several implicit methods to infer horizontal gene transfer (HGT) focus on pairs of genes that have diverged only after the divergence of the two species in which the genes reside. This situation defines the edge set of a graph, the later-divergence-time (LDT) graph, whose vertices correspond to genes colored by their species. We investigate these graphs in the setting of relaxed scenarios, i.e., evolutionary scenarios that encompass all commonly used variants of duplication-transfer-loss scenarios in the literature. We characterize LDT graphs as a subclass of properly vertex-colored cographs, and provide a polynomial-time recognition algorithm as well as an algorithm to construct a relaxed scenario that explains a given LDT. An edge in an LDT graph implies that the two corresponding genes are separated by at least one HGT event. The converse is not true, however. We show that the complete xenology relation is described by an rs-Fitch graph, i.e., a complete multipartite graph satisfying constraints on the vertex coloring. This class of vertex-colored graphs is also recognizable in polynomial time. We finally address the question "how much information about all HGT events is contained in LDT graphs" with the help of simulations of evolutionary scenarios with a wide range of duplication, loss, and HGT events. In particular, we show that a simple greedy graph editing scheme can be used to efficiently detect HGT events that are implicitly contained in LDT graphs.}, }
@article {pmid34217898, year = {2021}, author = {Villasante, A and Godier-Furnemont, A and Hernandez-Barranco, A and Coq, JL and Boskovic, J and Peinado, H and Mora, J and Samitier, J and Vunjak-Novakovic, G}, title = {Horizontal transfer of the stemness-related markers EZH2 and GLI1 by neuroblastoma-derived extracellular vesicles in stromal cells.}, journal = {Translational research : the journal of laboratory and clinical medicine}, volume = {237}, number = {}, pages = {82-97}, pmid = {34217898}, issn = {1878-1810}, support = {UG3 EB025765/EB/NIBIB NIH HHS/United States ; P41 EB027062/EB/NIBIB NIH HHS/United States ; P41 EB002520/EB/NIBIB NIH HHS/United States ; R01 CA249799/CA/NCI NIH HHS/United States ; UH3 EB025765/EB/NIBIB NIH HHS/United States ; }, mesh = {Biomarkers ; Cell Differentiation ; Cell Line, Tumor ; Enhancer of Zeste Homolog 2 Protein/genetics/*metabolism ; Extracellular Vesicles ; *Gene Transfer, Horizontal ; Humans ; Mesenchymal Stem Cells ; Microscopy, Electron, Scanning ; Neuroblastoma/*metabolism ; RNA, Messenger/genetics/metabolism ; Stromal Cells ; Tissue Engineering ; Zinc Finger Protein GLI1/genetics/*metabolism ; }, abstract = {Neuroblastoma (NB) is the most common extracranial pediatric solid cancer originating from undifferentiated neural crest cells. NB cells express EZH2 and GLI1 genes that are known to maintain the undifferentiated phenotype of cancer stem cells (CSC) in NB. Recent studies suggest that tumor-derived extracellular vesicles (EVs) can regulate the transformation of surrounding cells into CSC by transferring tumor-specific molecules they contain. However, the horizontal transfer of EVs molecules in NB remains largely unknown. We report the analysis of NB-derived EVs in bioengineered models of NB that are based on a collagen 1/hyaluronic acid scaffold designed to mimic the native tumor niche. Using these models, we observed an enrichment of GLI1 and EZH2 mRNAs in NB-derived EVs. As a consequence of the uptake of NB-derived EVs, the host cells increased the expression levels of GLI1 and EZH2. These results suggest the alteration of the expression profile of stromal cells through an EV-based mechanism, and point the GLI1 and EZH2 mRNAs in the EV cargo as diagnostic biomarkers in NB.}, }
@article {pmid34216634, year = {2021}, author = {Roberts, MG and Burgess, S and Toombs-Ruane, LJ and Benschop, J and Marshall, JC and French, NP}, title = {Combining mutation and horizontal gene transfer in a within-host model of antibiotic resistance.}, journal = {Mathematical biosciences}, volume = {339}, number = {}, pages = {108656}, doi = {10.1016/j.mbs.2021.108656}, pmid = {34216634}, issn = {1879-3134}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Bacteria/drug effects/genetics ; *Drug Resistance, Bacterial/genetics ; *Gene Transfer, Horizontal/genetics ; *Host Microbial Interactions/genetics ; Humans ; *Models, Biological ; *Mutation/genetics ; Plasmids/genetics ; }, abstract = {Antibiotics are used extensively to control infections in humans and animals, usually by injection or a course of oral tablets. There are several methods by which bacteria can develop antimicrobial resistance (AMR), including mutation during DNA replication and plasmid mediated horizontal gene transfer (HGT). We present a model for the development of AMR within a single host animal. We derive criteria for a resistant mutant strain to replace the existing wild-type bacteria, and for co-existence of the wild-type and mutant. Where resistance develops through HGT via conjugation we derive criteria for the resistant strain to be excluded or co-exist with the wild-type. Our results are presented as bifurcation diagrams with thresholds determined by the relative fitness of the bacteria strains, expressed in terms of reproduction numbers. The results show that it is possible that applying and then relaxing antibiotic control may lead to the bacterial load returning to pre-control levels, but with an altered structure with regard to the variants that comprise the population. Removing antimicrobial selection pressure will not necessarily reduce AMR and, at a population level, other approaches to infection prevention and control are required, particularly when AMR is driven by both mutation and mobile genetic elements.}, }
@article {pmid34215856, year = {2022}, author = {Marzocchi, U and Thorup, C and Dam, AS and Schramm, A and Risgaard-Petersen, N}, title = {Dissimilatory nitrate reduction by a freshwater cable bacterium.}, journal = {The ISME journal}, volume = {16}, number = {1}, pages = {50-57}, pmid = {34215856}, issn = {1751-7370}, mesh = {*Ammonium Compounds/metabolism ; Bacteria/genetics/metabolism ; Denitrification ; Fresh Water ; *Nitrates/metabolism ; Oxidation-Reduction ; Phylogeny ; }, abstract = {Cable bacteria (CB) are filamentous Desulfobulbaceae that split the energy-conserving reaction of sulfide oxidation into two half reactions occurring in distinct cells. CB can use nitrate, but the reduction pathway is unknown, making it difficult to assess their direct impact on the N-cycle. Here we show that the freshwater cable bacterium Ca. Electronema sp. GS performs dissimilatory nitrate reduction to ammonium (DNRA). [15]NO3[-]-amended sediment with Ca. Electronema sp. GS showed higher rates of DNRA and nitrite production than sediment without Ca. Electronema sp. GS. Electron flux from sulfide oxidation, inferred from electric potential (EP) measurements, matched the electron flux needed to drive CB-mediated nitrate reduction to nitrite and ammonium. Ca. Electronema sp. GS expressed a complete nap operon for periplasmic nitrate reduction to nitrite, and a putative octaheme cytochrome c (pOCC), whose involvement in nitrite reduction to ammonium remains to be verified. Phylogenetic analysis suggests that the capacity for DNRA was acquired in multiple events through horizontal gene transfer from different organisms, before CB split into different salinity niches. The architecture of the nitrate reduction system suggests absence of energy conservation through oxidative phosphorylation, indicating that CB primarily conserve energy through the half reaction of sulfide oxidation.}, }
@article {pmid34212633, year = {2021}, author = {Chen, ML and An, XL and Yang, K and Zhu, YG}, title = {[Soil phage and their mediation on the horizontal transfer of antibiotic resistance genes: A review].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {32}, number = {6}, pages = {2267-2274}, doi = {10.13287/j.1001-9332.202106.031}, pmid = {34212633}, issn = {1001-9332}, mesh = {Anti-Bacterial Agents/pharmacology ; *Bacteriophages/genetics ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Humans ; Soil ; Soil Microbiology ; }, abstract = {The spread of antibiotic resistance in soil is a global threat to public health and food safety, challenging the prevention and treatment of human infectious disease. The horizontal transfer of ARGs mediated by bacteriophages (phages) is an important pathway for the spread of antibiotic resistance genes (ARGs). However, the knowledge on the contribution of phages to ARGs transmission in soil is elusive. Here, we reviewed the distribution characteristics of phages in soil and its driving factors. We summarized the main methods for purification and enrichment of soil phage, reviewed recent achievements in the mechanism of phage-mediated horizontal transfer of ARGs in soil and proposed some outstanding questions. This review would contribute to understanding the important ecological role of phages in driving the horizontal transfer of ARGs, and provide a basis for developing management strategies to mitigate ARGs pollution.}, }
@article {pmid34205995, year = {2021}, author = {Dell'Annunziata, F and Folliero, V and Giugliano, R and De Filippis, A and Santarcangelo, C and Izzo, V and Daglia, M and Galdiero, M and Arciola, CR and Franci, G}, title = {Gene Transfer Potential of Outer Membrane Vesicles of Gram-Negative Bacteria.}, journal = {International journal of molecular sciences}, volume = {22}, number = {11}, pages = {}, pmid = {34205995}, issn = {1422-0067}, mesh = {Bacteria/genetics/pathogenicity ; Bacterial Outer Membrane/*metabolism ; Bacterial Outer Membrane Proteins/*genetics ; *Gene Transfer Techniques ; Gene Transfer, Horizontal/*genetics ; Humans ; Virulence Factors/genetics/metabolism ; }, abstract = {The increasing spread of multidrug-resistant pathogenic bacteria is one of the major threats to public health worldwide. Bacteria can acquire antibiotic resistance and virulence genes through horizontal gene transfer (HGT). A novel horizontal gene transfer mechanism mediated by outer membrane vesicles (OMVs) has been recently identified. OMVs are rounded nanostructures released during their growth by Gram-negative bacteria. Biologically active toxins and virulence factors are often entrapped within these vesicles that behave as molecular carriers. Recently, OMVs have been reported to contain DNA molecules, but little is known about the vesicle packaging, release, and transfer mechanisms. The present review highlights the role of OMVs in HGT processes in Gram-negative bacteria.}, }
@article {pmid34202175, year = {2021}, author = {Drane, K and Huerlimann, R and Power, M and Whelan, A and Ariel, E and Sheehan, M and Kinobe, R}, title = {Testudines as Sentinels for Monitoring the Dissemination of Antibiotic Resistance in Marine Environments: An Integrative Review.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {10}, number = {7}, pages = {}, pmid = {34202175}, issn = {2079-6382}, support = {2256.95982.2331//The Townsville City Council, Queensland Australia/ ; }, abstract = {Dissemination of antibiotic resistance (AR) in marine environments is a global concern with a propensity to affect public health and many ecosystems worldwide. We evaluated the use of sea turtles as sentinel species for monitoring AR in marine environments. In this field, antibiotic-resistant bacteria have been commonly identified by using standard culture and sensitivity tests, leading to an overrepresentation of specific, culturable bacterial classes in the available literature. AR was detected against all major antibiotic classes, but the highest cumulative global frequency of resistance in all represented geographical sites was against the beta-lactam class by a two-fold difference compared to all other antibiotics. Wastewater facilities and turtle rehabilitation centres were associated with higher incidences of multidrug-resistant bacteria (MDRB) accounting for an average of 58% and 49% of resistant isolates, respectively. Furthermore, a relatively similar prevalence of MDRB was seen in all studied locations. These data suggest that anthropogenically driven selection pressures for the development of AR in sea turtles and marine environments are relatively similar worldwide. There is a need, however, to establish direct demonstrable associations between AR in sea turtles in their respective marine environments with wastewater facilities and other anthropogenic activities worldwide.}, }
@article {pmid34200260, year = {2021}, author = {Choi, KS and Park, S}, title = {Complete Plastid and Mitochondrial Genomes of Aeginetia indica Reveal Intracellular Gene Transfer (IGT), Horizontal Gene Transfer (HGT), and Cytoplasmic Male Sterility (CMS).}, journal = {International journal of molecular sciences}, volume = {22}, number = {11}, pages = {}, pmid = {34200260}, issn = {1422-0067}, support = {NRF-2020R1I1A1A01072442//National Research Foundation of Korea/ ; }, mesh = {Cytoplasm/*genetics/metabolism ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Mitochondrial ; *Genome, Plastid ; Orobanchaceae/*genetics ; Phylogeny ; *Plant Infertility ; Plant Proteins/*genetics ; }, abstract = {Orobanchaceae have become a model group for studies on the evolution of parasitic flowering plants, and Aeginetia indica, a holoparasitic plant, is a member of this family. In this study, we assembled the complete chloroplast and mitochondrial genomes of A. indica. The chloroplast and mitochondrial genomes were 56,381 bp and 401,628 bp long, respectively. The chloroplast genome of A. indica shows massive plastid genes and the loss of one IR (inverted repeat). A comparison of the A. indica chloroplast genome sequence with that of a previous study demonstrated that the two chloroplast genomes encode a similar number of proteins (except atpH) but differ greatly in length. The A. indica mitochondrial genome has 53 genes, including 35 protein-coding genes (34 native mitochondrial genes and one chloroplast gene), 15 tRNA (11 native mitochondrial genes and four chloroplast genes) genes, and three rRNA genes. Evidence for intracellular gene transfer (IGT) and horizontal gene transfer (HGT) was obtained for plastid and mitochondrial genomes. ψndhB and ψcemA in the A. indica mitogenome were transferred from the plastid genome of A. indica. The atpH gene in the plastid of A. indica was transferred from another plastid angiosperm plastid and the atpI gene in mitogenome A. indica was transferred from a host plant like Miscanthus siensis. Cox2 (orf43) encodes proteins containing a membrane domain, making ORF (Open Reading Frame) the most likely candidate gene for CMS development in A. indica.}, }
@article {pmid34198813, year = {2021}, author = {Miguela-Villoldo, P and Moreno, MA and Rebollada-Merino, A and Rodríguez-Bertos, A and Hernández, M and Rodríguez-Lázaro, D and Gallardo, A and Quesada, A and Goyache, J and Domínguez, L and Ugarte-Ruiz, M}, title = {Colistin Selection of the Mcr-1 Gene in Broiler Chicken Intestinal Microbiota.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {10}, number = {6}, pages = {}, pmid = {34198813}, issn = {2079-6382}, support = {AGL2016-74882-C3//Ministerio de Econom&#xed;a, Industria y Competitividad, Gobierno de Espa&#xf1;a/ ; S2013/ABI-2747//Comunidad Aut&#xf3;noma de Madrid/ ; BES-2017-080264//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; PEJ-2017-TL/BIO- 7114//European Social Fund and Youth Employment Initiative/ ; IB16073//Junta de Extremadura/ ; GR15075//European Regional Development Fund/ ; }, abstract = {Colistin has a long story of safe use in animals for the treatment and prevention of certain bacterial diseases. Nevertheless, the first description of the mcr-1 gene showed that colistin resistance can spread by horizontal gene transfer and changed the landscape. This study aimed to assess the effect of colistin administration on the dispersion of resistance in the microbiota of day-old broiler chicks and how the presence of mcr-1 genes influences the spread of colistin resistance determinants. In this study, 100 one-day-old chicks were divided into four groups of 25 animals (G1, G2, G3, and G4). Animals from G3/G4 were challenged with mcr-1-carrying Salmonella (day 7), while colistin (600 mg/L) was administered daily to G2/G4 animals through drinking water (from day 8 to day 15). Two quantitative PCR assays were performed to compare the amount of Salmonella and mcr-1 that were present in the caecal samples. We observed that levels of mcr-1 were higher in G3/G4 animals, especially G4, due to the spread of mcr-1-carrying Salmonella. On day 21, Salmonella levels decreased in G4, reaching similar values as those for G3, but mcr-1 levels remained significantly higher, suggesting that colistin may accelerate the spreading process when mcr-1-carrying bacteria reach the gut.}, }
@article {pmid34197607, year = {2021}, author = {Shinohara, N and Nishitani, K}, title = {Cryogenian Origin and Subsequent Diversification of the Plant Cell-Wall Enzyme XTH Family.}, journal = {Plant &amp; cell physiology}, volume = {62}, number = {12}, pages = {1874-1889}, pmid = {34197607}, issn = {1471-9053}, support = {17H03691//Japan Society for the Promotion of Science/ ; 18H05489//Japan Society for the Promotion of Science/ ; 24114005//Japan Society for the Promotion of Science/ ; }, mesh = {Cell Wall/*enzymology ; Embryophyta/*enzymology ; *Evolution, Molecular ; Glycosyltransferases/genetics/metabolism ; *Multigene Family ; Plant Proteins/*genetics/metabolism ; }, abstract = {All land plants encode large multigene families of xyloglucan endotransglucosylase/hydrolases (XTHs), plant-specific enzymes that cleave and reconnect plant cell-wall polysaccharides. Despite the ubiquity of these enzymes, considerable uncertainty remains regarding the evolutionary history of the XTH family. Phylogenomic and comparative analyses in this study traced the non-plant origins of the XTH family to Alphaproteobacteria ExoKs, bacterial enzymes involved in loosening biofilms, rather than Firmicutes licheninases, plant biomass digesting enzymes, as previously supposed. The relevant horizontal gene transfer (HGT) event was mapped to the divergence of non-swimming charophycean algae in the Cryogenian geological period. This HGT event was the likely origin of charophycean EG16-2s, which are putative intermediates between ExoKs and XTHs. Another HGT event in the Cryogenian may have led from EG16-2s or ExoKs to fungal Congo Red Hypersensitive proteins (CRHs) to fungal CRHs, enzymes that cleave and reconnect chitin and glucans in fungal cell walls. This successive transfer of enzyme-encoding genes may have supported the adaptation of plants and fungi to the ancient icy environment by facilitating their sessile lifestyles. Furthermore, several protein evolutionary steps, including coevolution of substrate-interacting residues and putative intra-family gene fusion, occurred in the land plant lineage and drove diversification of the XTH family. At least some of those events correlated with the evolutionary gain of broader substrate specificities, which may have underpinned the expansion of the XTH family by enhancing duplicated gene survival. Together, this study highlights the Precambrian evolution of life and the mode of multigene family expansion in the evolutionary history of the XTH family.}, }
@article {pmid34192695, year = {2022}, author = {Butiuc-Keul, A and Farkas, A and Carpa, R and Iordache, D}, title = {CRISPR-Cas System: The Powerful Modulator of Accessory Genomes in Prokaryotes.}, journal = {Microbial physiology}, volume = {32}, number = {1-2}, pages = {2-17}, doi = {10.1159/000516643}, pmid = {34192695}, issn = {2673-1673}, mesh = {Archaea/genetics ; Bacteria/genetics ; *COVID-19/genetics ; *CRISPR-Cas Systems/genetics ; Humans ; SARS-CoV-2/genetics ; }, abstract = {Being frequently exposed to foreign nucleic acids, bacteria and archaea have developed an ingenious adaptive defense system, called CRISPR-Cas. The system is composed of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) array, together with CRISPR (cas)-associated genes. This system consists of a complex machinery that integrates fragments of foreign nucleic acids from viruses and mobile genetic elements (MGEs), into CRISPR arrays. The inserted segments (spacers) are transcribed and then used by cas proteins as guide RNAs for recognition and inactivation of the targets. Different types and families of CRISPR-Cas systems consist of distinct adaptation and effector modules with evolutionary trajectories, partially independent. The origin of the effector modules and the mechanism of spacer integration/deletion is far less clear. A review of the most recent data regarding the structure, ecology, and evolution of CRISPR-Cas systems and their role in the modulation of accessory genomes in prokaryotes is proposed in this article. The CRISPR-Cas system's impact on the physiology and ecology of prokaryotes, modulation of horizontal gene transfer events, is also discussed here. This system gained popularity after it was proposed as a tool for plant and animal embryo editing, in cancer therapy, as antimicrobial against pathogenic bacteria, and even for combating the novel coronavirus - SARS-CoV-2; thus, the newest and promising applications are reviewed as well.}, }
@article {pmid34192603, year = {2021}, author = {Matveeva, T and Otten, L}, title = {Opine biosynthesis in naturally transgenic plants: Genes and products.}, journal = {Phytochemistry}, volume = {189}, number = {}, pages = {112813}, doi = {10.1016/j.phytochem.2021.112813}, pmid = {34192603}, issn = {1873-3700}, mesh = {*Amino Acids ; *Plant Tumors ; Plants, Genetically Modified/genetics ; Nicotiana ; }, abstract = {The plant pathogen Agrobacterium transfers DNA into plant cells by a specific transfer mechanism. Expression of this transferred DNA or T-DNA leads to crown gall tumors or abnormal, hairy roots and the synthesis of specific compounds, called opines. Opines are produced from common plant metabolites like sugars, amino acids and α-keto acids, which are combined into different low molecular weight structures by T-DNA-encoded opine synthase enzymes. Opines can be converted back by Agrobacterium into the original metabolites and used for agrobacterial growth. Recently it has been discovered that about 7% of Angiosperms carry T-DNA-like sequences. These result from ancient Agrobacterium transformation events, followed by spontaneous regeneration of transformed cells into natural genetically transformed organisms (nGMOs). Nearly all nGMOs identified up to date carry opine synthesis genes, several of these are intact and potentially encode opine synthesis. So far, only tobacco and cuscuta have been demonstrated to contain opines. Whereas opines from crown gall and hairy root tissues have been studied for over 60 years, those from the nGMOs remain to be explored.}, }
@article {pmid34187559, year = {2021}, author = {Snyman, Y and Whitelaw, AC and Barnes, JM and Maloba, MRB and Newton-Foot, M}, title = {Characterisation of mobile colistin resistance genes (mcr-3 and mcr-5) in river and storm water in regions of the Western Cape of South Africa.}, journal = {Antimicrobial resistance and infection control}, volume = {10}, number = {1}, pages = {96}, pmid = {34187559}, issn = {2047-2994}, mesh = {Anti-Bacterial Agents/pharmacology ; Colistin/*pharmacology ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; *Gram-Negative Bacteria/drug effects/genetics ; Microbial Sensitivity Tests ; Rivers/*microbiology ; South Africa ; Water Microbiology ; }, abstract = {BACKGROUND: Colistin is regarded as a last-resort antimicrobial against multi-drug resistant Gram-negative bacteria (GNB), therefore the dissemination of colistin resistance in the environment is of great concern. Horizontal transfer of mobile colistin resistance (mcr) genes to potential pathogens poses a serious problem. This study aimed to describe the presence of colistin resistant GNB and mcr genes in river and storm water in regions of the Western Cape.<br><br>METHODS: Water samples were collected from three rivers during May 2019 and January 2020 and two storm water samples were collected in November 2019. Colistin resistant GNB were cultured on MacConkey agar containing colistin and identified by MALDI-TOF. Colistin resistance was confirmed using broth microdilution (BMD). mcr-1-5 genes were detected by PCR performed directly on the water samples and on the colistin resistant isolates. mcr functionality was assessed by BMD after cloning the mcr genes into pET-48b(+) and expression in SHuffle T7 E. coli.<br><br>RESULTS: mcr-5.1 and various mcr-3 gene variants were detected in the Plankenburg-, Eerste- and Berg rivers and in storm water from Muizenberg, and only mcr-5.1 was detected in storm water from Fish Hoek. Colistin resistant GNB were isolated from all of the water sources. Aeromonas spp. were the most common colistin resistant organisms detected in the water sources; 25% (6/24) of colistin resistant Aeromonas spp. isolated from the Berg river contained novel mcr-3 variants; mcr-3.33 (n&#x2009;=&#x2009;1), mcr-3.34 (n&#x2009;=&#x2009;1) mcr-3.35 (n&#x2009;=&#x2009;1) mcr-3.36 (n&#x2009;=&#x2009;2) and mcr-3.37 (n&#x2009;=&#x2009;1), which were confirmed to confer colistin resistance.<br><br>CONCLUSIONS: The mcr-5.1 and mcr-3 colistin resistance gene variants were present in widely dispersed water sources in regions of the Western Cape. The mcr genes were only detected in water sampled downstream of and alongside communities, suggesting that their presence is driven by human influence/contamination. This is the first documentation of mcr-3 and mcr-5 gene variants in any setting in South Africa. Spill-over of these genes to communities could result in horizontal gene transfer to pathogenic bacteria, exacerbating the challenge of controlling multidrug resistant GNB infections.}, }
@article {pmid34184913, year = {2021}, author = {Kothari, A and Roux, S and Zhang, H and Prieto, A and Soneja, D and Chandonia, JM and Spencer, S and Wu, X and Altenburg, S and Fields, MW and Deutschbauer, AM and Arkin, AP and Alm, EJ and Chakraborty, R and Mukhopadhyay, A}, title = {Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance.}, journal = {mSystems}, volume = {6}, number = {3}, pages = {e0053721}, pmid = {34184913}, issn = {2379-5077}, support = {P30 CA014051/CA/NCI NIH HHS/United States ; }, abstract = {Viruses are ubiquitous microbiome components, shaping ecosystems via strain-specific predation, horizontal gene transfer and redistribution of nutrients through host lysis. Viral impacts are important in groundwater ecosystems, where microbes drive many nutrient fluxes and metabolic processes; however, little is known about the diversity of viruses in these environments. We analyzed four groundwater plasmidomes (the entire plasmid content of an environment) and identified 200 viral sequences, which clustered into 41 genus-level viral clusters (approximately equivalent to viral genera) including 9 known and 32 putative new genera. We used publicly available bacterial whole-genome sequences (WGS) and WGS from 261 bacterial isolates from this groundwater environment to identify potential viral hosts. We linked 76 of the 200 viral sequences to a range of bacterial phyla, the majority associated with Proteobacteria, followed by Firmicutes, Bacteroidetes, and Actinobacteria. The publicly available WGS enabled mapping bacterial hosts to several viral sequences. The WGS of groundwater isolates increased the depth of host prediction by allowing host identification at the strain level. The latter included 4 viruses that were almost entirely (>99% query coverage, >99% identity) identified as integrated in the genomes of Pseudomonas, Acidovorax, and Castellaniella strains, resulting in high-confidence host assignments. Lastly, 21 of these viruses carried putative auxiliary metabolite genes for metal and antibiotic resistance, which might drive their infection cycles and/or provide selective advantage to infected hosts. Exploring the groundwater virome provides a necessary foundation for integration of viruses into ecosystem models where they are key players in microbial adaption to environmental stress. IMPORTANCE To our knowledge, this is the first study to identify the bacteriophage distribution in a groundwater ecosystem shedding light on their prevalence and distribution across metal-contaminated and background sites. Our study is uniquely based on selective sequencing of solely the extrachromosomal elements of a microbiome followed by analysis for viral signatures, thus establishing a more focused approach for phage identifications. Using this method, we detected several novel phage genera along with those previously established. Our approach of using the whole-genome sequences of hundreds of bacterial isolates from the same site enabled us to make host assignments with high confidence, several at strain levels. Certain phage genes suggest that they provide an environment-specific selective advantage to their bacterial hosts. Our study lays the foundation for future research on directed phage isolations using specific bacterial host strains to further characterize groundwater phages, their life cycles, and their effects on groundwater microbiome and biogeochemistry.}, }
@article {pmid34183814, year = {2021}, author = {Jones, EC and Uphoff, S}, title = {Single-molecule imaging of LexA degradation in Escherichia coli elucidates regulatory mechanisms and heterogeneity of the SOS response.}, journal = {Nature microbiology}, volume = {6}, number = {8}, pages = {981-990}, pmid = {34183814}, issn = {2058-5276}, support = {/WT_/Wellcome Trust/United Kingdom ; 206159/WT_/Wellcome Trust/United Kingdom ; 206159/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacterial Proteins/chemistry/genetics/*metabolism ; Escherichia coli/chemistry/genetics/growth &amp; development/*metabolism ; Gene Expression Regulation, Bacterial ; Proteolysis ; *SOS Response, Genetics ; Serine Endopeptidases/chemistry/genetics/*metabolism ; Single Molecule Imaging ; }, abstract = {The bacterial SOS response represents a paradigm of gene networks controlled by a master transcriptional regulator. Self-cleavage of the SOS repressor LexA induces a wide range of cell functions that are critical for survival and adaptation when bacteria experience stress conditions[1] including DNA repair[2], mutagenesis[3,4], horizontal gene transfer[5-7], filamentous growth and the induction of bacterial toxins[8-12], toxin-antitoxin systems[13], virulence factors[6,14] and prophages[15-17]. SOS induction is also implicated in biofilm formation and antibiotic persistence[11,18-20]. Considering the fitness burden of these functions, it is surprising that the expression of LexA-regulated genes is highly variable across cells[10,21-23] and that cell subpopulations induce the SOS response spontaneously even in the absence of stress exposure[9,11,12,16,24,25]. Whether this reflects a population survival strategy or a regulatory inaccuracy is unclear, as are the mechanisms underlying SOS heterogeneity. Here, we developed a single-molecule imaging approach based on a HaloTag fusion to directly monitor LexA in live Escherichia coli cells, demonstrating the existence of three main states of LexA: DNA-bound stationary molecules, free LexA and degraded LexA species. These analyses elucidate the mechanisms by which DNA binding and degradation of LexA regulate the SOS response in vivo. We show that self-cleavage of LexA occurs frequently throughout the population during unperturbed growth, rather than being restricted to a subpopulation of cells. This causes substantial cell-to-cell variation in LexA abundances. LexA variability underlies SOS gene-expression heterogeneity and triggers spontaneous SOS pulses, which enhance bacterial survival in anticipation of stress.}, }
@article {pmid34182338, year = {2021}, author = {Cheng, X and Xu, J and Smith, G and Nirmalakhandan, N and Zhang, Y}, title = {Metagenomic profiling of antibiotic resistance and virulence removal: Activated sludge vs. algal wastewater treatment system.}, journal = {Journal of environmental management}, volume = {295}, number = {}, pages = {113129}, pmid = {34182338}, issn = {1095-8630}, support = {SC2 GM130432/GM/NIGMS NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Sewage ; Virulence ; Wastewater ; *Water Purification ; }, abstract = {Conventional activated sludge-based (CAS) wastewater treatment plants are known to be a source of antibiotic resistance genes (ARGs) and virulence genes (VGs). As an alternative, a single-step mixotrophic algal wastewater treatment (A-WWT) system is proposed here to effectively reduce ARGs and VGs in the final effluent while meeting all the discharge standards. In this study, we applied the metagenomic profiling approach to compare the A-WWT system against the CAS system in terms of removal efficacy of ARG and VGs. A total of 111 ARG and 93 VG subtypes belonging to 10 antibiotic resistant classes and 19 virulence classes were detected in this study. Although the CAS system reduced the relative abundance of most classes of ARGs (7 of 10) and VGs (11 of 19), 3 ARG classes and 7 VG classes had increased abundances. On the other hand, the A-WWT system reduced the relative abundance of all classes of ARGs and VGs, and effectively eliminated most subtypes of ARGs and VGs. In the CAS system, the bacterial genera carrying ARGs and VGs was expanded, and the diversity index was increased greatly, suggesting the occurrence of horizontal gene transfer (HGT). In contrast, the A-WWT system narrowed down the potential host range and decreased their diversity substantially. Results of this study highlight the potential risk of ARGs and VGs in CAS system and demonstrate the feasibility of the algal-based system in removing ARGs and VGs.}, }
@article {pmid34180594, year = {2021}, author = {Kunhikannan, S and Thomas, CJ and Franks, AE and Mahadevaiah, S and Kumar, S and Petrovski, S}, title = {Environmental hotspots for antibiotic resistance genes.}, journal = {MicrobiologyOpen}, volume = {10}, number = {3}, pages = {e1197}, pmid = {34180594}, issn = {2045-8827}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/classification/*drug effects/genetics/metabolism ; Bacterial Proteins/*genetics/metabolism ; *Drug Resistance, Multiple, Bacterial ; *Environmental Microbiology ; Gene Transfer, Horizontal ; }, abstract = {Bacterial resistance toward broad-spectrum antibiotics has become a major concern in recent years. The threat posed by the infectious bacteria and the pace with which resistance determinants are transmitted needs to be deciphered. Soil and water contain unique and diverse microbial communities as well as pools of naturally occurring antibiotics resistant genes. Overuse of antibiotics along with poor sanitary practices expose these indigenous microbial communities to antibiotic resistance genes from other bacteria and accelerate the process of acquisition and dissemination. Clinical settings, where most antibiotics are prescribed, are hypothesized to serve as a major hotspot. The predisposition of the surrounding environments to a pool of antibiotic-resistant bacteria facilitates rapid antibiotic resistance among the indigenous microbiota in the soil, water, and clinical environments via horizontal gene transfer. This provides favorable conditions for the development of more multidrug-resistant pathogens. Limitations in detecting gene transfer mechanisms have likely left us underestimating the role played by the surrounding environmental hotspots in the emergence of multidrug-resistant bacteria. This review aims to identify the major drivers responsible for the spread of antibiotic resistance and hotspots responsible for the acquisition of antibiotic resistance genes.}, }
@article {pmid34177869, year = {2021}, author = {Manoharan-Basil, SS and Laumen, JGE and Van Dijck, C and De Block, T and De Baetselier, I and Kenyon, C}, title = {Evidence of Horizontal Gene Transfer of 50S Ribosomal Genes rplB, rplD, and rplY in Neisseria gonorrhoeae.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {683901}, pmid = {34177869}, issn = {1664-302X}, abstract = {Horizontal gene transfer (HGT) in the penA and multidrug efflux pump genes has been shown to play a key role in the genesis of antimicrobial resistance in Neisseria gonorrhoeae. In this study, we evaluated if there was evidence of HGT in the genes coding for the ribosomal proteins in the Neisseria genus. We did this in a collection of 11,659 isolates of Neisseria, including N. gonorrhoeae and commensal Neisseria species (N. cinerea, N. elongata, N. flavescens, N. mucosa, N. polysaccharea, and N. subflava). Comparative genomic analyses identified HGT events in three genes: rplB, rplD, and rplY coding for ribosomal proteins L2, L4 and L25, respectively. Recombination events were predicted in N. gonorrhoeae and N. cinerea, N. subflava, and N. lactamica were identified as likely progenitors. In total, 2,337, 2,355, and 1,127 isolates possessed L2, L4, and L25 HGT events. Strong associations were found between HGT in L2/L4 and the C2597T 23S rRNA mutation that confers reduced susceptibility to macrolides. Whilst previous studies have found evidence of HGT of entire genes coding for ribosomal proteins in other bacterial species, this is the first study to find evidence of HGT-mediated chimerization of ribosomal proteins.}, }
@article {pmid34175779, year = {2021}, author = {Chen, P and Guo, X and Li, S and Li, F}, title = {A review of the bioelectrochemical system as an emerging versatile technology for reduction of antibiotic resistance genes.}, journal = {Environment international}, volume = {156}, number = {}, pages = {106689}, doi = {10.1016/j.envint.2021.106689}, pmid = {34175779}, issn = {1873-6750}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; Humans ; Sewage ; Technology ; Wastewater ; }, abstract = {Antibiotic contamination and the resulting resistance genes have attracted worldwide attention because of the extensive overuse and abuse of antibiotics, which seriously affects the environment as well as human health. Bioelectrochemical system (BES), a potential avenue to be explored, can alleviate antibiotic pollution and reduce antibiotic resistance genes (ARGs). This review mainly focuses on analyzing the possible reasons for the good performance of ARG reduction by BESs and potential ways to improve its performance on the basis of revealing the generation and transmission of ARGs in BES. This system reduces ARGs through two pathways: (1) the contribution of BES to the low selection pressure of ARGs caused by the efficient removal of antibiotics, and (2) inhibition of ARG transmission caused by low sludge yield. To promote the reduction of ARGs, incorporating additives, improving the removal rate of antibiotics by adjusting the environmental conditions, and controlling the microbial community in BES are proposed. Furthermore, this review also provides an overview of bioelectrochemical coupling systems including the BES coupled with the Fenton system, BES coupled with constructed wetland, and BES coupled with photocatalysis, which demonstrates that this method is applicable in different situations and conditions and provides inspiration to improve these systems to control ARGs. Finally, the challenges and outlooks are addressed, which is constructive for the development of technologies for antibiotic and ARG contamination remediation and blocking risk migration.}, }
@article {pmid34173011, year = {2021}, author = {Tang, S}, title = {The Origin(s) of Cell(s): Pre-Darwinian Evolution from FUCAs to LUCA : To Carl Woese (1928-2012), for his Conceptual Breakthrough of Cellular Evolution.}, journal = {Journal of molecular evolution}, volume = {89}, number = {7}, pages = {427-447}, pmid = {34173011}, issn = {1432-1432}, abstract = {The coming of the Last Universal Cellular Ancestor (LUCA) was the singular watershed event in the making of the biotic world. If the coming of LUCA marked the crossing of the "Darwinian Threshold", then pre-LUCA evolution must have been Pre-Darwinian and at least partly non-Darwinian. But how did Pre-Darwinian evolution before LUCA actually operate? I broaden our understanding of the central mechanism of biological evolution (i.e., variation-selection-inheritance) and then extend this broadened understanding to its natural starting point: the origin(s) of the First Universal Cellular Ancestors (FUCAs) before LUCA. My hypothesis centers upon vesicles' making-and-remaking as variation and competition as selection. More specifically, I argue that vesicles' acquisition and merger, via breaking-and-repacking, proto-endocytosis, proto-endosymbiosis, and other similar processes had been a central force of both variation and selection in the pre-Darwinian epoch. These new perspectives shed important new light upon the origin of FUCAs and their subsequent evolution into LUCA.}, }
@article {pmid34172345, year = {2022}, author = {Patangia, DV and Ryan, CA and Dempsey, E and Stanton, C and Ross, RP}, title = {Vertical transfer of antibiotics and antibiotic resistant strains across the mother/baby axis.}, journal = {Trends in microbiology}, volume = {30}, number = {1}, pages = {47-56}, doi = {10.1016/j.tim.2021.05.006}, pmid = {34172345}, issn = {1878-4380}, mesh = {*Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Multiple, Bacterial ; Female ; Gene Transfer, Horizontal ; Humans ; Infant ; Infant, Newborn ; *Mothers ; }, abstract = {Antibiotic resistance is a health and socioeconomic crisis recognized as a serious threat affecting humans worldwide. Overuse of antibiotics enhances the spread of multidrug-resistant bacteria, causing drug-resistant infections which can be difficult to treat. This resistance, mostly of the acquired type, is thus a major clinical issue. Acquired resistance can occur by horizontal transfer of genes between bacteria (community settings), by vertical transmission that can occur between mother and her offspring at birth and during lactation, or spontaneously due to antibiotic exposure. While there have been multiple studies about the horizontal transfer of antibiotic-resistance genes, not many studies have been conducted to study their vertical transmission. Vertical transmission is of importance as the early bacterial colonization of infants has an impact on their health and immune programming throughout life. This review discusses some possible mechanisms of mother-to-infant transmission of antibiotics and antibiotic-resistant strains and addresses the knowledge gaps for further studies.}, }
@article {pmid34169647, year = {2021}, author = {Schneider, L and Guo, YK and Birch, D and Sarkies, P}, title = {Network-based visualisation reveals new insights into transposable element diversity.}, journal = {Molecular systems biology}, volume = {17}, number = {6}, pages = {e9600}, pmid = {34169647}, issn = {1744-4292}, support = {MC_UP_1102/13/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*DNA Transposable Elements/genetics ; *Evolution, Molecular ; Phylogeny ; RNA, Small Interfering ; }, abstract = {Transposable elements (TEs) are widespread across eukaryotic genomes, yet their content varies widely between different species. Factors shaping the diversity of TEs are poorly understood. Understanding the evolution of TEs is difficult because their sequences diversify rapidly and TEs are often transferred through non-conventional means such as horizontal gene transfer. We developed a method to track TE evolution using network analysis to visualise TE sequence and TE content across different genomes. We illustrate our method by first using a monopartite network to study the sequence evolution of Tc1/mariner elements across focal species. We identify a connection between two subfamilies associated with convergent acquisition of a domain from a protein-coding gene. Second, we use a bipartite network to study how TE content across species is shaped by epigenetic silencing mechanisms. We show that the presence of Piwi-interacting RNAs is associated with differences in network topology after controlling for phylogenetic effects. Together, our method demonstrates how a network-based approach can identify hitherto unknown properties of TE evolution across species.}, }
@article {pmid34165421, year = {2021}, author = {Callens, M and Scornavacca, C and Bedhomme, S}, title = {Evolutionary responses to codon usage of horizontally transferred genes in Pseudomonas aeruginosa: gene retention, amelioration and compensatory evolution.}, journal = {Microbial genomics}, volume = {7}, number = {6}, pages = {}, pmid = {34165421}, issn = {2057-5858}, support = {682819/ERC_/European Research Council/International ; }, mesh = {Codon ; *Codon Usage ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Genome, Bacterial ; Phylogeny ; Pseudomonas aeruginosa/*genetics ; RNA, Transfer/genetics ; }, abstract = {Prokaryote genome evolution is characterized by the frequent gain of genes through horizontal gene transfer (HGT). For a gene, being horizontally transferred can represent a strong change in its genomic and physiological context. If the codon usage of a transferred gene deviates from that of the receiving organism, the fitness benefits it provides can be reduced due to a mismatch with the expression machinery. Consequently, transferred genes with a deviating codon usage can be selected against or elicit evolutionary responses that enhance their integration, such as gene amelioration and compensatory evolution. Within bacterial species, the extent and relative importance of these different mechanisms has never been considered altogether. In this study, a phylogeny-based method was used to investigate the occurrence of these different evolutionary responses in Pseudomonas aeruginosa. Selection on codon usage of genes acquired through HGT was observed over evolutionary time, with the overall codon usage converging towards that of the core genome. Gene amelioration, through the accumulation of synonymous mutations after HGT, did not seem to systematically affect transferred genes. This pattern therefore seemed to be mainly driven by selective retention of transferred genes with an initial codon usage similar to that of the core genes. Additionally, variation in the copy number of tRNA genes was often associated with the acquisition of genes for which the observed variation could enhance their expression. This provides evidence that compensatory evolution might be an important mechanism for the integration of horizontally transferred genes.}, }
@article {pmid34157404, year = {2021}, author = {Moor, J and Aebi, S and Rickli, S and Mostacci, N and Overesch, G and Oppliger, A and Hilty, M}, title = {Dynamics of extended-spectrum cephalosporin-resistant Escherichia coli in pig farms: A longitudinal study.}, journal = {International journal of antimicrobial agents}, volume = {58}, number = {3}, pages = {106382}, doi = {10.1016/j.ijantimicag.2021.106382}, pmid = {34157404}, issn = {1872-7913}, mesh = {Adult ; Aged ; Aged, 80 and over ; Animals ; Anti-Bacterial Agents/*therapeutic use ; Cephalosporin Resistance/*drug effects ; Cephalosporins/*therapeutic use ; Escherichia coli/*drug effects/*genetics ; Escherichia coli Infections/*drug therapy/epidemiology/*veterinary ; Farmers/statistics &amp; numerical data ; Farms/statistics &amp; numerical data ; Feces/*microbiology ; Female ; Genome-Wide Association Study ; Humans ; Longitudinal Studies ; Male ; Middle Aged ; Occupational Exposure/statistics &amp; numerical data ; Prevalence ; Swine ; Switzerland/epidemiology ; }, abstract = {OBJECTIVES: Point prevalence estimates of extended-spectrum cephalosporin-resistant Escherichia coli (ESC-R-Ec) are important surveillance measures but may not uncover the ESC-R-Ec dynamics within pig farms. A longitudinal study was therefore performed by sampling individual pigs, pig farmers and the environment.<br><br>METHODS: On average, 30 (range 10-46) piglets of 31 Swiss farms were sampled during the suckling, weaning and fattening stages (n= 2437 samples). In addition, stool from pig farmers and environmental samples were obtained and metadata collected by questionnaires. ESC-R-Ec was identified by routine culture, and clonal relationships and resistance genes were derived from whole genome sequencing data.<br><br>RESULTS: Working on pig farms was not associated with an increased prevalence of ESC-R-Ec in humans. ESC-R-Ec prevalence significantly decreased from 6.2% to 3.9% and 1.8% for the suckling, weaned and fattening pigs, respectively (P < 0.001). Within the 57 ESC-R-positive suckling piglets, persisting carriage was detected in 25 animals at two consecutive time points and one animal at three consecutive time points. Clonal spread (n=7 farms, 22.6%) and horizontal gene transfer (n=1 farm, 3%) within pigs but not between humans and animals was detected. Liquid manure (n=10 samples, 16.7%) was identified as the major environmental reservoir of ESC-R-Ec in the pig farm environment.<br><br>CONCLUSIONS: Pig farming practices like all-in-all-out systems, but not antimicrobial usage, were associated with reduced risk of ESC-R-Ec at the farm level. As carriage duration is normally short within the individual pigs, the risk of recolonisation and clonal spread of ESC-R-Ec might be reduced by applying appropriate decontamination strategies.}, }
@article {pmid34157135, year = {2021}, author = {Wang, Q and Wang, Y and Wang, J and Gong, Z and Han, GZ}, title = {Plants acquired a major retrotransposon horizontally from fungi during the conquest of land.}, journal = {The New phytologist}, volume = {232}, number = {1}, pages = {11-16}, doi = {10.1111/nph.17568}, pmid = {34157135}, issn = {1469-8137}, mesh = {Fungi/genetics ; Gene Transfer, Horizontal ; Phylogeny ; *Plants/genetics ; *Retroelements/genetics ; }, }
@article {pmid34156293, year = {2021}, author = {Thomas, E and Anderson, RE and Li, V and Rogan, LJ and Huber, JA}, title = {Diverse Viruses in Deep-Sea Hydrothermal Vent Fluids Have Restricted Dispersal across Ocean Basins.}, journal = {mSystems}, volume = {6}, number = {3}, pages = {e0006821}, pmid = {34156293}, issn = {2379-5077}, support = {GBMF3297//Gordon and Betty Moore Foundation (GBMF)/ ; 80NSSC18K1076/ImNASA/Intramural NASA/United States ; Postdoctoral Fellowship//NASA | NASA Astrobiology Institute (NAI)/ ; CDEBI//National Science Foundation (NSF)/ ; 80NSSC18K1076/NASA/NASA/United States ; NNX-327 09AB75G//National Aeronautics and Space Administration (NASA)/ ; Deep Carbon Observatory//Alfred P. Sloan Foundation (The Alfred P. Sloan Foundation)/ ; }, abstract = {In the ocean, viruses impact microbial mortality, regulate biogeochemical cycling, and alter the metabolic potential of microbial lineages. At deep-sea hydrothermal vents, abundant viruses infect a wide range of hosts among the archaea and bacteria that inhabit these dynamic habitats. However, little is known about viral diversity, host range, and biogeography across different vent ecosystems, which has important implications for how viruses manipulate microbial function and evolution. Here, we examined viral diversity, viral and host distribution, and virus-host interactions in microbial metagenomes generated from venting fluids from several vent sites within three different geochemically and geographically distinct hydrothermal systems: Piccard and Von Damm vent fields at the Mid-Cayman Rise in the Caribbean Sea, and at several vent sites within Axial Seamount in the Pacific Ocean. Analysis of viral sequences and clustered regularly interspaced short palindromic repeat (CRISPR) spacers revealed highly diverse viral assemblages and evidence of active infection. Network analysis revealed that viral host range was relatively narrow, with very few viruses infecting multiple microbial lineages. Viruses were largely endemic to individual vent sites, indicating restricted dispersal, and in some cases, viral assemblages persisted over time. Thus, we show that hydrothermal vent fluids are home to novel, diverse viral assemblages that are highly localized to specific regions and taxa. IMPORTANCE Viruses play important roles in manipulating microbial communities and their evolution in the ocean, yet not much is known about viruses in deep-sea hydrothermal vents. However, viral ecology and evolution are of particular interest in hydrothermal vent habitats because of their unique nature: previous studies have indicated that most viruses in hydrothermal vents are temperate rather than lytic, and it has been established that rates of horizontal gene transfer (HGT) are particularly high among thermophilic vent microbes, and viruses are common vectors for HGT. If viruses have broad host range or are widespread across vent sites, they have increased potential to act as gene-sharing "highways" between vent sites. By examining viral diversity, distribution, and infection networks across disparate vent sites, this study provides the opportunity to better characterize and constrain the viral impact on hydrothermal vent microbial communities. We show that viruses in hydrothermal vents are diverse and apparently active, but most have restricted host range and are not widely distributed among vent sites. Thus, the impacts of viral infection are likely to be highly localized and constrained to specific taxa in these habitats.}, }
@article {pmid34156261, year = {2021}, author = {Wachter, J and Martens, C and Barbian, K and Rego, ROM and Rosa, P}, title = {Epigenomic Landscape of Lyme Disease Spirochetes Reveals Novel Motifs.}, journal = {mBio}, volume = {12}, number = {3}, pages = {e0128821}, pmid = {34156261}, issn = {2150-7511}, mesh = {Animals ; Borrelia burgdorferi/classification/*genetics ; DNA, Bacterial/genetics ; *Epigenomics ; Humans ; Lyme Disease/*microbiology ; Methylation ; *Nucleotide Motifs ; Plasmids/*genetics/metabolism ; *Sequence Analysis, DNA ; }, abstract = {Borrelia burgdorferi, the etiological agent of Lyme disease, persists in nature through an enzootic cycle consisting of a vertebrate host and an Ixodes tick vector. The sequence motifs modified by two well-characterized restriction/modification (R/M) loci of B. burgdorferi type strain B31 were recently described, but the methylation profiles of other Lyme disease Borrelia bacteria have not been characterized. Here, the methylomes of B. burgdorferi type strain B31 and 7 clonal derivatives, along with B. burgdorferi N40, B. burgdorferi 297, B. burgdorferi CA-11, B. afzelii PKo, B. afzelii BO23, and B. garinii PBr, were defined through PacBio single-molecule real-time (SMRT) sequencing. This analysis revealed 9 novel sequence motifs methylated by the plasmid-encoded restriction/modification enzymes of these Borrelia strains. Furthermore, while a previous analysis of B. burgdorferi B31 revealed an epigenetic impact of methylation on the global transcriptome, the current data contradict those findings; our analyses of wild-type B. burgdorferi B31 revealed no consistent differences in gene expression among isogenic derivatives lacking one or more restriction/modification enzymes. IMPORTANCE The principal causative agent of Lyme disease in humans in the United States is Borrelia burgdorferi, while B. burgdorferi, B. afzelii, and B. garinii, collectively members of the Borrelia burgdorferi sensu lato species complex, cause Lyme disease in Europe and Asia. Two plasmid-encoded restriction/modification systems have been shown to limit the genetic transformation of B. burgdorferi type strain B31 with foreign DNA, but little is known about the restriction/modification systems of other Lyme disease Borrelia bacteria. This paper describes the methylation motifs present on genomic DNAs of multiple B. burgdorferi, B. afzelii, and B. garinii strains. Contrary to a previous report, we did not find evidence for an epigenetic impact on gene expression by methylation. Knowledge of the motifs recognized and methylated by the restriction/modification enzymes of Lyme disease Borrelia will facilitate molecular genetic investigations of these important human pathogens. Additionally, the similar motifs methylated by orthologous restriction/modification systems of Lyme disease Borrelia bacteria and the presence of these motifs within recombinogenic loci suggest a biological role for these ubiquitous restriction/modification systems in horizontal gene transfer.}, }
@article {pmid34155223, year = {2021}, author = {Gharbi, R and Khanna, V and Frigui, W and Mhenni, B and Brosch, R and Mardassi, H}, title = {Phenotypic and genomic hallmarks of a novel, potentially pathogenic rapidly growing Mycobacterium species related to the Mycobacterium fortuitum complex.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {13011}, pmid = {34155223}, issn = {2045-2322}, mesh = {Computational Biology/methods ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genomics/methods ; Humans ; Molecular Sequence Annotation ; Mycobacterium Infections, Nontuberculous/*microbiology ; Mycobacterium fortuitum/*genetics/*growth &amp; development/pathogenicity ; *Phenotype ; Phylogeny ; Virulence Factors/genetics ; }, abstract = {Previously, we have identified a putative novel rapidly growing Mycobacterium species, referred to as TNTM28, recovered from the sputum of an apparently immunocompetent young man with an underlying pulmonary disease. Here we provide a thorough characterization of TNTM28 genome sequence, which consists of one chromosome of 5,526,191 bp with a 67.3% G + C content, and a total of 5193 predicted coding sequences. Phylogenomic analyses revealed a deep-rooting relationship to the Mycobacterium fortuitum complex, thus suggesting a new taxonomic entity. TNTM28 was predicted to be a human pathogen with a probability of 0.804, reflecting the identification of several virulence factors, including export systems (Sec, Tat, and ESX), a nearly complete set of Mce proteins, toxin-antitoxins systems, and an extended range of other genes involved in intramacrophage replication and persistence (hspX, ahpC, sodA, sodC, katG, mgtC, ClpR, virS, etc.), some of which had likely been acquired through horizontal gene transfer. Such an arsenal of potential virulence factors, along with an almost intact ESX-1 locus, might have significantly contributed to TNTM28 pathogenicity, as witnessed by its ability to replicate efficiently in macrophages. Overall, the identification of this new species as a potential human pathogen will help to broaden our understanding of mycobacterial pathogenesis.}, }
@article {pmid34155212, year = {2021}, author = {Sutter, M and Melnicki, MR and Schulz, F and Woyke, T and Kerfeld, CA}, title = {A catalog of the diversity and ubiquity of bacterial microcompartments.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {3809}, pmid = {34155212}, issn = {2041-1723}, support = {R01 AI114975/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/classification/cytology/*genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Cell Compartmentation ; Gene Transfer, Horizontal ; Genetic Loci ; Genetic Variation ; Organelles/classification/*genetics/metabolism ; Phylogeny ; }, abstract = {Bacterial microcompartments (BMCs) are organelles that segregate segments of metabolic pathways which are incompatible with surrounding metabolism. BMCs consist of a selectively permeable shell, composed of three types of structurally conserved proteins, together with sequestered enzymes that vary among functionally distinct BMCs. Genes encoding shell proteins are typically clustered with those for the encapsulated enzymes. Here, we report that the number of identifiable BMC loci has increased twenty-fold since the last comprehensive census of 2014, and the number of distinct BMC types has doubled. The new BMC types expand the range of compartmentalized catalysis and suggest that there is more BMC biochemistry yet to be discovered. Our comprehensive catalog of BMCs provides a framework for their identification, correlation with bacterial niche adaptation, experimental characterization, and development of BMC-based nanoarchitectures for biomedical and bioengineering applications.}, }
@article {pmid34154411, year = {2021}, author = {Bharathwaj, M and Webb, CT and Vadlamani, G and Stubenrauch, CJ and Palmer, T and Lithgow, T}, title = {The Carbapenemase BKC-1 from Klebsiella pneumoniae Is Adapted for Translocation by Both the Tat and Sec Translocons.}, journal = {mBio}, volume = {12}, number = {3}, pages = {e0130221}, pmid = {34154411}, issn = {2150-7511}, support = {MR/S009213/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics/*metabolism ; Biological Transport ; Escherichia coli/genetics ; Gene Products, tat/*genetics ; Humans ; Klebsiella Infections/microbiology ; Klebsiella pneumoniae/drug effects/enzymology/*genetics ; Microbial Sensitivity Tests ; Periplasm/metabolism ; SEC Translocation Channels/*genetics ; beta-Lactamases/*genetics/*metabolism ; beta-Lactams/pharmacology ; }, abstract = {The cell envelope of Gram-negative bacteria consists of two membranes surrounding the periplasm and peptidoglycan layer. β-Lactam antibiotics target the periplasmic penicillin-binding proteins that synthesize peptidoglycan, resulting in cell death. The primary means by which bacterial species resist the effects of β-lactam drugs is to populate the periplasmic space with β-lactamases. Resistance to β-lactam drugs is spread by lateral transfer of genes encoding β-lactamases from one species of bacteria to another. However, the resistance phenotype depends in turn on these "alien" protein sequences being recognized and exported across the cytoplasmic membrane by either the Sec or Tat protein translocation machinery of the new bacterial host. Here, we examine BKC-1, a carbapenemase from an unknown bacterial source that has been identified in a single clinical isolate of Klebsiella pneumoniae. BKC-1 was shown to be located in the periplasm, and functional in both K. pneumoniae and Escherichia coli. Sequence analysis revealed the presence of an unusual signal peptide with a twin arginine motif and a duplicated hydrophobic region. Biochemical assays showed this signal peptide directs BKC-1 for translocation by both Sec and Tat translocons. This is one of the few descriptions of a periplasmic protein that is functionally translocated by both export pathways in the same organism, and we suggest it represents a snapshot of evolution for a β-lactamase adapting to functionality in a new host. IMPORTANCE Bacteria can readily acquire plasmids via lateral gene transfer (LGT). These plasmids can carry genes for virulence and antimicrobial resistance (AMR). Of growing concern are LGT events that spread β-lactamases, particularly carbapenemases, and it is important to understand what limits this spread. This study provides insight into the sequence features of BKC-1 that exemplify the limitations on the successful biogenesis of β-lactamases, which is one factor limiting the spread of AMR phenotypes by LGT. With a very simple evolutionary adaptation, BKC-1 could become a more effective carbapenemase, underscoring the need to understand the evolution, adaptability, and functional assessment of newly reported β-lactamases rapidly and thoroughly.}, }
@article {pmid34154398, year = {2021}, author = {Perli, T and Vos, AM and Bouwknegt, J and Dekker, WJC and Wiersma, SJ and Mooiman, C and Ortiz-Merino, RA and Daran, JM and Pronk, JT}, title = {Identification of Oxygen-Independent Pathways for Pyridine Nucleotide and Coenzyme A Synthesis in Anaerobic Fungi by Expression of Candidate Genes in Yeast.}, journal = {mBio}, volume = {12}, number = {3}, pages = {e0096721}, pmid = {34154398}, issn = {2150-7511}, mesh = {Anaerobiosis ; Coenzyme A/*biosynthesis ; Fungi/genetics/*metabolism ; *Metabolic Networks and Pathways/genetics/physiology ; Neocallimastix/genetics ; Nucleotides/*metabolism ; Oxygen/*metabolism ; Piromyces/genetics ; Proteome ; Pyridines/*metabolism ; Saccharomyces cerevisiae/*genetics/metabolism ; }, abstract = {Neocallimastigomycetes are unique examples of strictly anaerobic eukaryotes. This study investigates how these anaerobic fungi bypass reactions involved in synthesis of pyridine nucleotide cofactors and coenzyme A that, in canonical fungal pathways, require molecular oxygen. Analysis of Neocallimastigomycetes proteomes identified a candidate l-aspartate-decarboxylase (AdcA) and l-aspartate oxidase (NadB) and quinolinate synthase (NadA), constituting putative oxygen-independent bypasses for coenzyme A synthesis and pyridine nucleotide cofactor synthesis. The corresponding gene sequences indicated acquisition by ancient horizontal gene transfer (HGT) events involving bacterial donors. To test whether these enzymes suffice to bypass corresponding oxygen-requiring reactions, they were introduced into fms1Δ and bna2Δ Saccharomyces cerevisiae strains. Expression of nadA and nadB from Piromyces finnis and adcA from Neocallimastix californiae conferred cofactor prototrophy under aerobic and anaerobic conditions. This study simulates how HGT can drive eukaryotic adaptation to anaerobiosis and provides a basis for elimination of auxotrophic requirements in anaerobic industrial applications of yeasts and fungi. IMPORTANCE NAD (NAD[+]) and coenzyme A (CoA) are central metabolic cofactors whose canonical biosynthesis pathways in fungi require oxygen. Anaerobic gut fungi of the Neocallimastigomycota phylum are unique eukaryotic organisms that adapted to anoxic environments. Analysis of Neocallimastigomycota genomes revealed that these fungi might have developed oxygen-independent biosynthetic pathways for NAD[+] and CoA biosynthesis, likely acquired through horizontal gene transfer (HGT) from prokaryotic donors. We confirmed functionality of these putative pathways under anaerobic conditions by heterologous expression in the yeast Saccharomyces cerevisiae. This approach, combined with sequence comparison, offers experimental insight on whether HGT events were required and/or sufficient for acquiring new traits. Moreover, our results demonstrate an engineering strategy for enabling S. cerevisiae to grow anaerobically in the absence of the precursor molecules pantothenate and nicotinate, thereby contributing to alleviate oxygen requirements and to move closer to prototrophic anaerobic growth of this industrially relevant yeast.}, }
@article {pmid34153824, year = {2021}, author = {Chen, Z and Liu, WS and Zhong, X and Zheng, M and Fei, YH and He, H and Ding, K and Chao, Y and Tang, YT and Wang, S and Qiu, R}, title = {Genome- and community-level interaction insights into the ecological role of archaea in rare earth element mine drainage in South China.}, journal = {Water research}, volume = {201}, number = {}, pages = {117331}, doi = {10.1016/j.watres.2021.117331}, pmid = {34153824}, issn = {1879-2448}, mesh = {*Archaea/genetics ; China ; Genome, Archaeal ; Metagenome ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {Microbial communities play crucial roles in mine drainage generation and remediation. Despite the wide distribution of archaea in the mine ecosystem, their diversity and ecological roles remain less understood than bacteria. Here, we retrieved 56 archaeal metagenome-assembled genomes from a river impacted by rare earth element (REE) mining activities in South China. Genomic analysis showed that archaea represented four distinct lineages, including phyla of Thaumarchaeota, Micrarchaeota, Nanoarchaeota and Thermoplasmata. These archaea represented a considerable fraction (up to 40%) of the total prokaryote community, which might contribute to nitrogen and sulfur cycling in the REE mine drainage. Reconstructed metabolic potential among diverse archaea taxa revealed that archaea were involved in the network of ammonia oxidation, denitrification, sulfate redox reaction, and required substrates supplied by other community members. As the dominant driver of ammonia oxidation, Thaumarchaeota might provide substrates to support the survival of two nano-sized archaea belonging to Micrarchaeota and Nanoarchaeota. Despite the absence of biosynthesis pathways for amino acids and nucleotides, the potential capacity for nitrite reduction (nirD) was observed in Micrarchaeota, indicating that these nano-sized archaea encompassed diverse metabolisms. Moreover, Thermoplasmata, as keystone taxa in community, might be the main genetic donor for the other three archaeal phyla, transferring many environmental resistance related genes (e.g., V/A-type ATPase and Vitamin B12-transporting ATPase). The genetic interactions within archaeal community through horizontal gene transfer might be the key to the formation of archaeal resistance and functional partitioning. This study provides putative metabolic and genetic insights into the diverse archaea taxa from community-level perspectives, and highlights the ecological roles of archaea in REE contaminated aquatic environment.}, }
@article {pmid34151148, year = {2021}, author = {Nachimuthu, R and Kannan, VR and Bozdogan, B and Krishnakumar, V and S, KP and Manohar, P}, title = {CTX-M-type ESBL-mediated resistance to third-generation cephalosporins and conjugative transfer of resistance in Gram-negative bacteria isolated from hospitals in Tamil Nadu, India.}, journal = {Access microbiology}, volume = {3}, number = {3}, pages = {000142}, pmid = {34151148}, issn = {2516-8290}, abstract = {Clinical pathogens, especially Gram-negative bacteria developing resistance to third-generation cephalosporins, are making clinical outcomes more complicated and serious. This study was undertaken to evaluate the distribution of CTX-M-type extended-spectrum β-lactamases (ESBLs) in Tamil Nadu, India. For this study, clinical samples were collected from five different hospitals located in Tamil Nadu and the ESBL-producing Gram-negative isolates were characterized. MIC was performed using cefotaxime and ceftazidime. The bla ESBL-producing genes were screened using multiplex PCR for the genes, CTX-M group-1, -2, -8, -9, -26. The conjugation studies were performed using Escherichia coli AB1157 as a recipient for the isolates harbouring plasmid-borne resistance following broth-mating experiment. In total, 1500 samples were collected and 599 Gram-negative bacteria were isolated that included E. coli (n=233), Klebsiella pneumoniae (n=182), Pseudomonas aeruginosa (n=79), Citrobacter spp. (n=30), Proteus mirabilis (n=28), Salmonella spp. (n=21), Acinetobacter baumannii (n=12), Serratia spp. (n=6), Shigella spp. (n=4), Morganella morganii (n=3) and Providencia spp. (n=1). MIC results showed that 358 isolates were resistant to cefotaxime and ceftazidime. Further, ESBL gene-amplification results showed that 19 isolates had CTX-M group-1 gene including E. coli (n=16), K. pneumoniae (n=2) and P. aeruginosa (n=1) whereas one M. morganii isolate had CTX-M group-9, which was plasmid-borne. Through conjugation studies, 12/20 isolates were found to be involved in the transformation of its plasmid-borne resistance gene. Our study highlighted the importance of horizontal gene transfer in the dissemination of plasmid-borne bla CTX-M-type resistance genes among the clinical isolates.}, }
@article {pmid34149648, year = {2021}, author = {Mores, CR and Montelongo, C and Putonti, C and Wolfe, AJ and Abouelfetouh, A}, title = {Investigation of Plasmids Among Clinical Staphylococcus aureus and Staphylococcus haemolyticus Isolates From Egypt.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {659116}, pmid = {34149648}, issn = {1664-302X}, support = {R01 DK104718/DK/NIDDK NIH HHS/United States ; }, abstract = {Staphylococci can cause a wide array of infections that can be life threatening. These infections become more deadly when the isolates are antibiotic resistant and thus harder to treat. Many resistance determinants are plasmid-mediated; however, staphylococcal plasmids have not yet been fully characterized. In particular, plasmids and their contributions to antibiotic resistance have not been investigated within the Arab states, where antibiotic use is not universally regulated. Here, we characterized the putative plasmid content among 56 Staphylococcus aureus and 10 Staphylococcus haemolyticus clinical isolates from Alexandria, Egypt. Putative plasmid sequences were detected in over half of our collection. In total, we identified 72 putative plasmid sequences in 27 S. aureus and 1 S. haemolyticus isolates. While these isolates typically carried one or two plasmids, we identified one isolate-S. aureus AA53-with 11 putative plasmids. The plasmid sequences most frequently encoded a Rep_1, RepL, or PriCT_1 type replication protein. As expected, antibiotic resistance genes were widespread among the identified plasmid sequences. Related plasmids were identified amongst our clinical isolates; homologous plasmids present in multiple isolates clustered into 11 groups based upon sequence similarity. Plasmids from the same cluster often shared antibiotic resistance genes, including blaZ, which is associated with β-lactam resistance. Our analyses suggest that plasmids are a key factor in the pathology and epidemiology of S. aureus in Egypt. A better characterization of plasmids and the role they contribute to the success of Staphylococci as pathogens will guide the design of effective control strategies to limit their spread.}, }
@article {pmid34149643, year = {2021}, author = {Mayers, CG and Harrington, TC and Wai, A and Hausner, G}, title = {Recent and Ongoing Horizontal Transfer of Mitochondrial Introns Between Two Fungal Tree Pathogens.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {656609}, pmid = {34149643}, issn = {1664-302X}, abstract = {Two recently introduced fungal plant pathogens (Ceratocystis lukuohia and Ceratocystis huliohia) are responsible for Rapid 'ōhi'a Death (ROD) in Hawai'i. Despite being sexually incompatible, the two pathogens often co-occur in diseased 'ōhi'a sapwood, where genetic interaction is possible. We sequenced and annotated 33 mitochondrial genomes of the two pathogens and related species, and investigated 35 total Ceratocystis mitogenomes. Ten mtDNA regions [one group I intron, seven group II introns, and two autonomous homing endonuclease (HE) genes] were heterogeneously present in C. lukuohia mitogenomes, which were otherwise identical. Molecular surveys with specific primers showed that the 10 regions had uneven geographic distribution amongst populations of C. lukuohia. Conversely, identical orthologs of each region were present in every studied isolate of C. huliohia regardless of geographical origin. Close relatives of C. lukuohia lacked or, rarely, had few and dissimilar orthologs of the 10 regions, whereas most relatives of C. huliohia had identical or nearly identical orthologs. Each region included or worked in tandem with HE genes or reverse transcriptase/maturases that could facilitate interspecific horizontal transfers from intron-minus to intron-plus alleles. These results suggest that the 10 regions originated in C. huliohia and are actively moving to populations of C. lukuohia, perhaps through transient cytoplasmic contact of hyphal tips (anastomosis) in the wound surface of 'ōhi'a trees. Such contact would allow for the transfer of mitochondria followed by mitochondrial fusion or cytoplasmic exchange of intron intermediaries, which suggests that further genomic interaction may also exist between the two pathogens.}, }
@article {pmid34147655, year = {2021}, author = {Choi, IS and Wojciechowski, MF and Ruhlman, TA and Jansen, RK}, title = {In and out: Evolution of viral sequences in the mitochondrial genomes of legumes (Fabaceae).}, journal = {Molecular phylogenetics and evolution}, volume = {163}, number = {}, pages = {107236}, doi = {10.1016/j.ympev.2021.107236}, pmid = {34147655}, issn = {1095-9513}, mesh = {Evolution, Molecular ; *Fabaceae/genetics ; *Genome, Mitochondrial ; Introns/genetics ; Phylogeny ; }, abstract = {Plant specific mitoviruses in the 'genus' Mitovirus (Narnaviridae) and their integrated sequences (non-retroviral endogenous RNA viral elements or NERVEs) have been recently identified in various plant lineages. However, the sparse phylogenetic coverage of complete plant mitochondrial genome (mitogenome) sequences and the non-conserved nature of mitochondrial intergenic regions have hindered comparative studies on mitovirus NERVEs in plants. In this study, 10 new mitogenomes were sequenced from legumes (Fabaceae). Based on comparative genomic analysis of 27 total mitogenomes, we identified mitovirus NERVEs and transposable elements across the family. All legume mitogenomes included NERVEs and total NERVE length varied from ca. 2 kb in the papilionoid Trifolium to 35 kb in the mimosoid Acacia. Most of the NERVE integration sites were in highly variable intergenic regions, however, some were positioned in six cis-spliced mitochondrial introns. In the Acacia mitogenome, there were L1-like transposon sequences including an almost full-length copy with target site duplications (TSDs). The integration sites of NERVEs in four introns showed evidence of L1-like retrotransposition events. Phylogenetic analysis revealed that there were multiple instances of precise deletion of NERVEs between TSDs. This study provides clear evidence that a L1-like retrotransposition mechanism has a long history of contributing to the integration of viral RNA into plant mitogenomes while microhomology-mediated deletion can restore the integration site.}, }
@article {pmid34147570, year = {2021}, author = {Lulamba, TE and Green, E and Serepa-Dlamini, MH}, title = {Genome assembly and annotation of Photorhabdus heterorhabditis strain ETL reveals genetic features involved in pathogenicity with its associated entomopathogenic nematode and anti-host effectors with biocontrol potential applications.}, journal = {Gene}, volume = {795}, number = {}, pages = {145780}, doi = {10.1016/j.gene.2021.145780}, pmid = {34147570}, issn = {1879-0038}, mesh = {Animals ; Base Sequence ; Biological Control Agents ; *Genes, Bacterial ; *Genome, Bacterial ; Host-Pathogen Interactions ; Molecular Sequence Annotation ; Photorhabdus/classification/*genetics/*pathogenicity ; Phylogeny ; Strongyloidea/*microbiology ; Virulence/genetics ; }, abstract = {The genome sequences of entomopathogenic nematode (EPN) bacteria and their functional analyses can lead to the genetic engineering of the bacteria for use as biocontrol agents. The bacterial symbiont Photorhabdus heterorhabditis strain ETL isolated from an insect pathogenic nematode, Heterorhabditis zealandica strain ETL, collected in the northernmost region of South Africa was studied to reveal information that can be useful in the design of improvement strategies for both effective and liquid production method of EPN-based pesticides. The strain ETL genome was found closely related to the type strain genome of P. australis DSM 17,609 (~60 to 99.9% CDSs similarity), but closely related to the not yet genome-sequenced type strain, P. heterorhabditis. It has a genome size of 4,866,148 bp and G + C content of 42.4% similar to other Photorhabdus. It contains 4,351 protein coding genes (CDSs) of which, at least 84% are shared with the de facto type strain P. luminescens subsp. laumondii TTO1, and has 318 unknown CDSs and the genome has a higher degree of plasticity allowing it to adapt to different environmental conditions, and to be virulent against various insects; observed through genes acquired through horizontal gene transfer mechanisms, clustered regularly interspaced short palindromic repeats, non-determined polyketide- and non-ribosomal peptide- synthase gene clusters, and many genes associated with uncharacterized proteins; which also justify the strain ETL's genes differences (quantity and quality) compared to P. luminescens subsp. laumondii TTO1. The protein coding sequences contained genes with both bio-engineering and EPNs mass production importance, of which numerous are uncharacterized.}, }
@article {pmid34141272, year = {2021}, author = {Zhao, C and Miao, S and Yin, Y and Zhu, Y and Nabity, P and Bansal, R and Liu, C}, title = {Tripartite parasitic and symbiotic interactions as a possible mechanism of horizontal gene transfer.}, journal = {Ecology and evolution}, volume = {11}, number = {11}, pages = {7018-7028}, pmid = {34141272}, issn = {2045-7758}, abstract = {Herbivory is a highly sophisticated feeding behavior that requires abilities of plant defense suppression, phytochemical detoxification, and plant macromolecule digestion. For plant-sucking insects, salivary glands (SGs) play important roles in herbivory by secreting and injecting proteins into plant tissues to facilitate feeding. Little is known on how insects evolved secretory SG proteins for such specialized functions. Here, we investigated the composition and evolution of secretory SG proteins in the brown marmorated stink bug (Halyomorpha halys) and identified a group of secretory SG phospholipase C (PLC) genes with highest sequence similarity to the bacterial homologs. Further analyses demonstrated that they were most closely related to PLCs of Xenorhabdus, a genus of Gammaproteobacteria living in symbiosis with insect-parasitizing nematodes. These suggested that H. halys might acquire these PLCs from Xenorhabdus through the mechanism of horizontal gene transfer (HGT), likely mediated by a nematode during its parasitizing an insect host. We also showed that the original HGT event was followed by gene duplication and expansion, leading to functional diversification of the bacterial-origin PLC genes in H. halys. Thus, this study suggested that an herbivore might enhance adaptation through gaining genes from an endosymbiont of its parasite in the tripartite parasitic and symbiotic interactions.}, }
@article {pmid34136276, year = {2021}, author = {Lehtinen, S and Huisman, JS and Bonhoeffer, S}, title = {Evolutionary mechanisms that determine which bacterial genes are carried on plasmids.}, journal = {Evolution letters}, volume = {5}, number = {3}, pages = {290-301}, pmid = {34136276}, issn = {2056-3744}, abstract = {The evolutionary pressures that determine the location (chromosomal or plasmid-borne) of bacterial genes are not fully understood. We investigate these pressures through mathematical modeling in the context of antibiotic resistance, which is often found on plasmids. Our central finding is that gene location is under positive frequency-dependent selection: the higher the frequency of one form of resistance compared to the other, the higher its relative fitness. This can keep moderately beneficial genes on plasmids, despite occasional plasmid loss. For these genes, positive frequency dependence leads to a priority effect: whichever form is acquired first-through either mutation or horizontal gene transfer-has time to increase in frequency and thus becomes difficult to displace. Higher rates of horizontal transfer of plasmid-borne than chromosomal genes therefore predict moderately beneficial genes will be found on plasmids. Gene flow between plasmid and chromosome allows chromosomal forms to arise, but positive frequency-dependent selection prevents these from establishing. Further modeling shows that this effect is particularly pronounced when genes are shared across a large number of species, suggesting that antibiotic resistance genes are often found on plasmids because they are moderately beneficial across many species. We also revisit previous theoretical work-relating to the role of local adaptation in explaining gene location and to plasmid persistence-in light of our findings.}, }
@article {pmid34134257, year = {2021}, author = {Argyriadis, JA and He, YH and Jejjala, V and Minic, D}, title = {Dynamics of genetic code evolution: The emergence of universality.}, journal = {Physical review. E}, volume = {103}, number = {5-1}, pages = {052409}, doi = {10.1103/PhysRevE.103.052409}, pmid = {34134257}, issn = {2470-0053}, abstract = {We study the dynamics of genetic code evolution. The model of Vetsigian et al. [Proc. Natl. Acad. Sci. USA 103, 10696 (2006)PNASA60027-842410.1073/pnas.0603780103] and Vetsigian [Collective evolution of biological and physical systems, Ph.D. thesis, 2005] uses the mechanism of horizontal gene transfer to demonstrate convergence of the genetic code to a near universal solution. We reproduce and analyze the algorithm as a dynamical system. All the parameters used in the model are varied to assess their impact on convergence and optimality score. We show that by allowing specific parameters to vary with time, the solution exhibits attractor dynamics. Finally, we study automorphisms of the genetic code arising due to this model. We use this to examine the scaling of the solutions to re-examine universality and find that there is a direct link to mutation rate.}, }
@article {pmid34132784, year = {2021}, author = {N'Guessan, A and Brito, IL and Serohijos, AWR and Shapiro, BJ}, title = {Mobile Gene Sequence Evolution within Individual Human Gut Microbiomes Is Better Explained by Gene-Specific Than Host-Specific Selective Pressures.}, journal = {Genome biology and evolution}, volume = {13}, number = {8}, pages = {}, pmid = {34132784}, issn = {1759-6653}, mesh = {Evolution, Molecular ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; }, abstract = {Pangenomes-the cumulative set of genes encoded by a population or species-arise from the interplay of horizontal gene transfer, drift, and selection. The balance of these forces in shaping pangenomes has been debated, and studies to date focused on ancient evolutionary time scales have suggested that pangenomes generally confer niche adaptation to their bacterial hosts. To shed light on pangenome evolution on shorter evolutionary time scales, we inferred the selective pressures acting on mobile genes within individual human microbiomes from 176 Fiji islanders. We mapped metagenomic sequence reads to a set of known mobile genes to identify single nucleotide variants (SNVs) and calculated population genetic metrics to infer deviations from a neutral evolutionary model. We found that mobile gene sequence evolution varied more by gene family than by human social attributes, such as household or village. Patterns of mobile gene sequence evolution could be qualitatively recapitulated with a simple evolutionary simulation without the need to invoke the adaptive value of mobile genes to either bacterial or human hosts. These results stand in contrast with the apparent adaptive value of pangenomes over longer evolutionary time scales. In general, the most highly mobile genes (i.e., those present in more distinct bacterial host genomes) tend to have higher metagenomic read coverage and an excess of low-frequency SNVs, consistent with their rapid spread across multiple bacterial species in the gut. However, a subset of mobile genes-including those involved in defense mechanisms and secondary metabolism-showed a contrasting signature of intermediate-frequency SNVs, indicating species-specific selective pressures or negative frequency-dependent selection on these genes. Together, our evolutionary models and population genetic data show that gene-specific selective pressures predominate over human or bacterial host-specific pressures during the relatively short time scales of a human lifetime.}, }
@article {pmid34128785, year = {2021}, author = {Wami, H and Wallenstein, A and Sauer, D and Stoll, M and von Bünau, R and Oswald, E and Müller, R and Dobrindt, U}, title = {Insights into evolution and coexistence of the colibactin- and yersiniabactin secondary metabolite determinants in enterobacterial populations.}, journal = {Microbial genomics}, volume = {7}, number = {6}, pages = {}, pmid = {34128785}, issn = {2057-5858}, mesh = {Citrobacter/genetics/metabolism ; Enterobacteriaceae/*genetics/*metabolism ; Escherichia coli/genetics/metabolism ; Escherichia coli Proteins/genetics ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Humans ; Klebsiella/genetics/metabolism ; Mutagens/metabolism ; Peptides/*metabolism ; Phenols/*metabolism ; Polyketides/*metabolism ; *Secondary Metabolism/genetics/physiology ; Thiazoles/*metabolism ; }, abstract = {The bacterial genotoxin colibactin interferes with the eukaryotic cell cycle by causing dsDNA breaks. It has been linked to bacterially induced colorectal cancer in humans. Colibactin is encoded by a 54 kb genomic region in Enterobacteriaceae. The colibactin genes commonly co-occur with the yersiniabactin biosynthetic determinant. Investigating the prevalence and sequence diversity of the colibactin determinant and its linkage to the yersiniabactin operon in prokaryotic genomes, we discovered mainly species-specific lineages of the colibactin determinant and classified three main structural settings of the colibactin-yersiniabactin genomic region in Enterobacteriaceae. The colibactin gene cluster has a similar but not identical evolutionary track to that of the yersiniabactin operon. Both determinants could have been acquired on several occasions and/or exchanged independently between enterobacteria by horizontal gene transfer. Integrative and conjugative elements play(ed) a central role in the evolution and structural diversity of the colibactin-yersiniabactin genomic region. Addition of an activating and regulating module (clbAR) to the biosynthesis and transport module (clbB-S) represents the most recent step in the evolution of the colibactin determinant. In a first attempt to correlate colibactin expression with individual lineages of colibactin determinants and different bacterial genetic backgrounds, we compared colibactin expression of selected enterobacterial isolates in vitro. Colibactin production in the tested Klebsiella species and Citrobacter koseri strains was more homogeneous and generally higher than that in most of the Escherichia coli isolates studied. Our results improve the understanding of the diversity of colibactin determinants and its expression level, and may contribute to risk assessment of colibactin-producing enterobacteria.}, }
@article {pmid34126763, year = {2021}, author = {Hahn, J and DeSantis, M and Dubnau, D}, title = {Mechanisms of Transforming DNA Uptake to the Periplasm of Bacillus subtilis.}, journal = {mBio}, volume = {12}, number = {3}, pages = {e0106121}, pmid = {34126763}, issn = {2150-7511}, support = {R01 GM057720/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacillus subtilis/*genetics/*metabolism ; Biological Transport ; Cell Membrane/metabolism ; DNA, Bacterial/genetics/*metabolism ; Membrane Proteins/metabolism ; Periplasm/*metabolism ; *Transformation, Bacterial ; }, abstract = {We demonstrate here that the acquisition of DNase resistance by transforming DNA, often assumed to indicate transport to the cytoplasm, reflects uptake to the periplasm, requiring a reevaluation of conclusions about the roles of several proteins in transformation. The new evidence suggests that the transformation pilus is needed for DNA binding to the cell surface near the cell poles and for the initiation of uptake. The cellular distribution of the membrane-anchored ComEA of Bacillus subtilis does not dramatically change during DNA uptake as does the unanchored ComEA of Vibrio and Neisseria. Instead, our evidence suggests that ComEA stabilizes the attachment of transforming DNA at localized regions in the periplasm and then mediates uptake, probably by a Brownian ratchet mechanism. Following that, the DNA is transferred to periplasmic portions of the channel protein ComEC, which plays a previously unsuspected role in uptake to the periplasm. We show that the transformation endonuclease NucA also facilitates uptake to the periplasm and that the previously demonstrated role of ComFA in the acquisition of DNase resistance derives from the instability of ComGA when ComFA is deleted. These results prompt a new understanding of the early stages of DNA uptake for transformation. IMPORTANCE Transformation is a widely distributed mechanism of bacterial horizontal gene transfer that plays a role in the spread of antibiotic resistance and virulence genes and more generally in evolution. Although transformation was discovered nearly a century ago and most, if not all the proteins required have been identified in several bacterial species, much remains poorly understood about the molecular mechanism of DNA uptake. This study uses epifluorescence microscopy to investigate the passage of labeled DNA into the compartment between the cell wall and the cell membrane of Bacillus subtilis, a necessary early step in transformation. The roles of individual proteins in this process are identified, and their modes of action are clarified.}, }
@article {pmid34126328, year = {2021}, author = {Simbine, MG and Jaiswal, SK and Dakora, FD}, title = {Diverse symbiovars nodulating cowpea (Vigna unguiculata L. Walp.) in highly adaptable agro-ecological zones in Mozambique.}, journal = {Systematic and applied microbiology}, volume = {44}, number = {4}, pages = {126220}, doi = {10.1016/j.syapm.2021.126220}, pmid = {34126328}, issn = {1618-0984}, mesh = {DNA, Bacterial/genetics ; Genes, Bacterial ; Mozambique ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhizobiaceae/*classification/isolation &amp; purification ; Root Nodules, Plant/microbiology ; Sequence Analysis, DNA ; Soil Microbiology ; Symbiosis ; *Vigna/microbiology ; }, abstract = {The presence of effective microsymbionts in the soil and their compatibility with the host plant are the key determinants to the N2 fixation process. In Sub-Saharan Africa, nitrogen fixation in locally adapted cowpea and the distribution of their symbiovars are not well understood. The Aim of the study was to assess the distribution and symbiotic phylogenetic position of cowpea microsymbionts. Root nodules were sampled from various cowpea genotypes planted in Agro-Ecological Zone 7 and 8 (AEZ 7 and AEZ 8). Root-nodule bacteria were isolated and their molecular characterization was conducted. Physicochemical properties of soil were recorded. Enterobacterial Repetitive Intergenic Consensus (ERIC) distribution patterns in rhizobial genomes resulted in genetically diverse rhizobial population in Northern Mozambique. Principal component analysis showed that location-specific soil environment determined the presence of particular microsymbionts. Based on 16S rRNA and symbiotic gene analysis many diverse symbiovars were found in Mozambican soils. With few discrepancies, the results further confirmed the coevolution of the nifH, nodD, nodC and nodY/K genes, which was indicative of natural events such as vertical/horizontal gene transfer. The results suggested that ecological and phylogenetic studies of the microsymbionts are necessary to better reflect symbiovar identification and the ecological adaptation of the cowpea-nodulating rhizobial community.}, }
@article {pmid34122386, year = {2021}, author = {Hussain, NAS and Kirchberger, PC and Case, RJ and Boucher, YF}, title = {Modular Molecular Weaponry Plays a Key Role in Competition Within an Environmental Vibrio cholerae Population.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {671092}, pmid = {34122386}, issn = {1664-302X}, abstract = {The type VI secretion system (T6SS) operons of Vibrio cholerae contain extraordinarily diverse arrays of toxic effector and cognate immunity genes, which are thought to play an important role in the environmental lifestyle and adaptation of this human pathogen. Through the T6SS, proteinaceous "spears" tipped with antibacterial effectors are injected into adjacent cells, killing those not possessing immunity proteins to these effectors. Here, we investigate the T6SS-mediated dynamics of bacterial competition within a single environmental population of V. cholerae. We show that numerous members of a North American V. cholerae population possess strain-specific repertoires of cytotoxic T6SS effector and immunity genes. Using pairwise competition assays, we demonstrate that the vast majority of T6SS-mediated duels end in stalemates between strains with different T6SS repertoires. However, horizontally acquired effector and immunity genes can significantly alter the outcome of these competitions. Frequently observed horizontal gene transfer events can both increase or reduce competition between distantly related strains by homogenizing or diversifying the T6SS repertoire. Our results also suggest temperature-dependent outcomes in T6SS competition, with environmental isolates faring better against a pathogenic strain under native conditions than under those resembling a host-associated environment. Taken altogether, these interactions produce density-dependent fitness effects and a constant T6SS-mediated arms race in individual V. cholerae populations, which could ultimately preserve intraspecies diversity. Since T6SSs are widespread, we expect within-population diversity in T6SS repertoires and the resulting competitive dynamics to be a common theme in bacterial species harboring this machinery.}, }
@article {pmid34121661, year = {2021}, author = {Sheinman, M and Arkhipova, K and Arndt, PF and Dutilh, BE and Hermsen, R and Massip, F}, title = {Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {34121661}, issn = {2050-084X}, mesh = {Archaea/classification/genetics ; *Bacteria/classification/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome, Archaeal/genetics ; Genome, Bacterial/*genetics ; Genomics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Horizontal gene transfer (HGT) is an essential force in microbial evolution. Despite detailed studies on a variety of systems, a global picture of HGT in the microbial world is still missing. Here, we exploit that HGT creates long identical DNA sequences in the genomes of distant species, which can be found efficiently using alignment-free methods. Our pairwise analysis of 93,481 bacterial genomes identified 138,273 HGT events. We developed a model to explain their statistical properties as well as estimate the transfer rate between pairs of taxa. This reveals that long-distance HGT is frequent: our results indicate that HGT between species from different phyla has occurred in at least 8% of the species. Finally, our results confirm that the function of sequences strongly impacts their transfer rate, which varies by more than three orders of magnitude between different functional categories. Overall, we provide a comprehensive view of HGT, illuminating a fundamental process driving bacterial evolution.}, }
@article {pmid34120381, year = {2021}, author = {Linsky, M and Segal, G}, title = {A horizontally acquired Legionella genomic island encoding a LuxR type regulator and effector proteins displays variation in gene content and regulation.}, journal = {Molecular microbiology}, volume = {116}, number = {3}, pages = {766-782}, doi = {10.1111/mmi.14770}, pmid = {34120381}, issn = {1365-2958}, mesh = {Bacterial Proteins/*genetics/*metabolism ; Factor For Inversion Stimulation Protein/genetics/metabolism ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genome, Bacterial ; *Genomic Islands ; Humans ; Legionella pneumophila/*genetics/*metabolism ; Legionnaires' Disease/microbiology ; Regulatory Sequences, Nucleic Acid ; Repressor Proteins/genetics/metabolism ; Trans-Activators/genetics/metabolism ; }, abstract = {The intracellular pathogen Legionella pneumophila translocates >300 effector proteins into host cells, many of which are regulated at the transcriptional level. Here, we describe a novel L. pneumophila genomic island, which undergoes horizontal gene transfer within the Legionella genus. This island encodes two Icm/Dot effectors: LegK3 and a previously uncharacterized effector which we named CegK3, as well as a LuxR type regulator, which we named RegK3. Analysis of this island in different Legionella species revealed a conserved regulatory element located upstream to the effector-encoding genes in the island. Further analyses, including gene expression analysis, mutagenesis of the RegK3 regulatory element, controlled expression studies, and gel-mobility shift assays, all demonstrate that RegK3 directly activates the expression levels of legK3 and cegK3 effector-encoding genes. Additionally, the expression of all the components of the island is silenced by the Fis repressors. Comparison of expression profiles of these three genes among different Legionella species revealed variability in the activation levels mediated by RegK3, which were positively correlated with the Fis-mediated repression. Furthermore, LegK3 and CegK3 effectors moderately inhibit yeast growth, and importantly, they have a strong synergistic inhibitory effect on yeast growth, suggesting these two effectors are not only co-regulated but also might function together.}, }
@article {pmid34114802, year = {2021}, author = {Xu, H and Chen, Z and Huang, R and Cui, Y and Li, Q and Zhao, Y and Wang, X and Mao, D and Luo, Y and Ren, H}, title = {Antibiotic Resistance Gene-Carrying Plasmid Spreads into the Plant Endophytic Bacteria using Soil Bacteria as Carriers.}, journal = {Environmental science &amp; technology}, volume = {55}, number = {15}, pages = {10462-10470}, doi = {10.1021/acs.est.1c01615}, pmid = {34114802}, issn = {1520-5851}, mesh = {Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial ; *Escherichia coli/genetics ; Genes, Bacterial ; Plasmids/genetics ; *Soil ; }, abstract = {Applications of animal manure and treated wastewater could enrich antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in the plant microbiome. However, the mechanistic studies of the transmission of ARB and ARGs from the environment to plant endophytic bacteria were few. Herein, a genetically engineered fluorescent Escherichia coli harboring a conjugative RP4 plasmid that carries three ARGs was used to trace its spread into Arabidopsis thaliana interior in a tetracycline-amended hydroponic system in the absence or presence of a simulated soil bacterial community. Confocal microscope observation demonstrated that E. coli was internalized into plant tissues and the carried RP4 plasmid was transferred into plant endophytic bacteria. More importantly, we observed that soil bacteria inhibited the internalization of E. coli but substantially promoted RP4 plasmid spread into the plant microbiome. The altered RP4-carrying bacterial community composition in the plant microbiome and the increased core-shared RP4-carrying bacteria number between plant interior and exterior in the presence of soil bacteria collectively confirmed that soil bacteria, especially Proteobacteria, might capture RP4 from E. coli and then translocate into plant microbiome, resulting in the increased RP4 plasmid spread in the plant endophytes. Overall, our findings provided important insights into the dissemination of ARB and ARGs from the environment to the plant microbiome.}, }
@article {pmid34106752, year = {2021}, author = {Lassinantti, L and Camacho, MI and Erickson, RJB and Willett, JLE and De Lay, NR and Ter Beek, J and Dunny, GM and Christie, PJ and Berntsson, RP}, title = {Enterococcal PrgU Provides Additional Regulation of Pheromone-Inducible Conjugative Plasmids.}, journal = {mSphere}, volume = {6}, number = {3}, pages = {e0026421}, pmid = {34106752}, issn = {2379-5042}, support = {R35 GM118079/GM/NIGMS NIH HHS/United States ; R35 GM131892/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Proteins/*genetics ; DNA, Bacterial/genetics ; Enterococcus faecalis/*genetics ; *Gene Expression Regulation, Bacterial ; Operon ; Pheromones/genetics/*metabolism ; Plasmids/*genetics ; Type IV Secretion Systems/genetics/metabolism ; }, abstract = {Efficient horizontal gene transfer of the conjugative plasmid pCF10 from Enterococcus faecalis depends on the expression of its type 4 secretion system (T4SS) genes, controlled by the PQ promoter. Transcription from the PQ promoter is tightly regulated, partially to limit cell toxicity caused by overproduction of PrgB, a T4SS adhesin. PrgU plays an important role in regulating this toxicity by decreasing PrgB levels. PrgU has an RNA-binding fold, prompting us to test whether PrgU exerts its regulatory control through binding of prgQ transcripts. We used a combination of in vivo methods to quantify PrgU effects on prgQ transcripts at both single-cell and population levels. PrgU function requires a specific RNA sequence within an intergenic region (IGR) about 400 bp downstream of PQ. PrgU interaction with the IGR reduces levels of downstream transcripts. Single-cell expression analysis showed that cells expressing prgU decreased transcript levels more rapidly than isogenic prgU-minus cells. PrgU bound RNA in vitro without sequence specificity, suggesting that PrgU requires a specific RNA structure or one or more host factors for selective binding in vivo. PrgU binding to its IGR target might recruit RNase(s) for targeted degradation of downstream transcripts or reduce elongation of nascent transcripts beyond the IGR. IMPORTANCE Bacteria utilize type 4 secretion systems (T4SS) to efficiently transfer DNA between donor and recipient cells, thereby spreading genes encoding antibiotic resistance as well as various virulence factors. Regulation of expression of the T4SS proteins and surface adhesins in Gram-positive bacteria is crucial, as some of these are highly toxic to the cell. The significance of our research lies in identifying the novel mechanism by which PrgU performs its delicate fine-tuning of the expression levels. As prgU orthologs are present in various conjugative plasmids and transposons, our results are likely relevant to understanding of diverse clinically important transfer systems.}, }
@article {pmid34103505, year = {2021}, author = {Stefanic, P and Belcijan, K and Kraigher, B and Kostanjšek, R and Nesme, J and Madsen, JS and Kovac, J and Sørensen, SJ and Vos, M and Mandic-Mulec, I}, title = {Kin discrimination promotes horizontal gene transfer between unrelated strains in Bacillus subtilis.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {3457}, pmid = {34103505}, issn = {2041-1723}, mesh = {Adaptation, Physiological ; Bacillus subtilis/*genetics ; Cell Membrane/metabolism ; DNA, Bacterial/genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Mutation/genetics ; Nucleotides/genetics ; Recombination, Genetic/genetics ; Stress, Physiological ; Transformation, Genetic ; Up-Regulation ; }, abstract = {Bacillus subtilis is a soil bacterium that is competent for natural transformation. Genetically distinct B. subtilis swarms form a boundary upon encounter, resulting in killing of one of the strains. This process is mediated by a fast-evolving kin discrimination (KD) system consisting of cellular attack and defence mechanisms. Here, we show that these swarm antagonisms promote transformation-mediated horizontal gene transfer between strains of low relatedness. Gene transfer between interacting non-kin strains is largely unidirectional, from killed cells of the donor strain to surviving cells of the recipient strain. It is associated with activation of a stress response mediated by sigma factor SigW in the donor cells, and induction of competence in the recipient strain. More closely related strains, which in theory would experience more efficient recombination due to increased sequence homology, do not upregulate transformation upon encounter. This result indicates that social interactions can override mechanistic barriers to horizontal gene transfer. We hypothesize that KD-mediated competence in response to the encounter of distinct neighbouring strains could maximize the probability of efficient incorporation of novel alleles and genes that have proved to function in a genomically and ecologically similar context.}, }
@article {pmid34100915, year = {2021}, author = {Sbaraini, N and Junges, &#xc2; and de Oliveira, ES and Webster, A and Vainstein, MH and Staats, CC and Schrank, A}, title = {The deletion of chiMaD1, a horizontally acquired chitinase of Metarhizium anisopliae, led to higher virulence towards the cattle tick (Rhipicephalus microplus).}, journal = {FEMS microbiology letters}, volume = {368}, number = {12}, pages = {}, doi = {10.1093/femsle/fnab066}, pmid = {34100915}, issn = {1574-6968}, mesh = {Animals ; Chitin/metabolism ; Chitinases/*genetics/metabolism ; Fungal Proteins/*genetics/metabolism ; Gene Deletion ; Gene Transfer, Horizontal ; Host-Pathogen Interactions ; Larva/microbiology ; Metarhizium/classification/enzymology/genetics/*pathogenicity ; Pest Control, Biological ; Phylogeny ; Rhipicephalus/*microbiology ; Tenebrio/microbiology ; Virulence ; }, abstract = {The first line of the Arthropods defense against infections is the hard-structured exoskeleton, a physical barrier, usually rich in insoluble chitin. For entomopathogenic fungi that actively penetrate the host body, an arsenal of hydrolytic enzymes (as chitinases and N-acetylglucosaminidases), that break down chitin, is essential. Notably, twenty-one putative chitinase genes have been identified in the genome of Metarhizium anisopliae, a generalist entomopathogenic fungus. As a multigenic family, with enzymes that, presumably, perform redundant functions, the main goal is to understand the singularity of each one of such genes and to discover their precise role in the fungal life cycle. Specially chitinases that can act as virulence determinants are of interest since these enzymes can lead to more efficient biocontrol agents. Here we explored a horizontally acquired chitinase from M. anisopliae, named chiMaD1. The deletion of this gene did not lead to phenotypic alterations or diminished supernatant's chitinolytic activity. Surprisingly, chiMaD1 deletion enhanced M. anisopliae virulence to the cattle tick (Rhipicephalus microplus) larvae and engorged females, while did not alter the virulence to the mealworm larvae (Tenebrio molitor). These results add up to recent reports of deleted genes that enhanced entomopathogenic virulence, showing the complexity of host-pathogen interactions.}, }
@article {pmid34100640, year = {2021}, author = {Sutradhar, I and Ching, C and Desai, D and Suprenant, M and Briars, E and Heins, Z and Khalil, AS and Zaman, MH}, title = {Computational Model To Quantify the Growth of Antibiotic-Resistant Bacteria in Wastewater.}, journal = {mSystems}, volume = {6}, number = {3}, pages = {e0036021}, pmid = {34100640}, issn = {2379-5077}, support = {DP2 AI131083/AI/NIAID NIH HHS/United States ; T32 EB006359/EB/NIBIB NIH HHS/United States ; 1DP2AI131083//HHS | National Institutes of Health (NIH)/ ; }, abstract = {Although wastewater and sewage systems are known to be significant reservoirs of antibiotic-resistant bacterial populations and periodic outbreaks of drug-resistant infection, there is little quantitative understanding of the drivers behind resistant population growth in these settings. In order to fill this gap in quantitative understanding of the development of antibiotic-resistant infections in wastewater, we have developed a mathematical model synthesizing many known drivers of antibiotic resistance in these settings to help predict the growth of resistant populations in different environmental scenarios. A number of these drivers of drug-resistant infection outbreak, including antibiotic residue concentration, antibiotic interaction, chromosomal mutation, and horizontal gene transfer, have not previously been integrated into a single computational model. We validated the outputs of the model with quantitative studies conducted on the eVOLVER continuous culture platform. Our integrated model shows that low levels of antibiotic residues present in wastewater can lead to increased development of resistant populations and that the dominant mechanism of resistance acquisition in these populations is horizontal gene transfer rather than acquisition of chromosomal mutations. Additionally, we found that synergistic antibiotics at low concentrations lead to increased resistant population growth. These findings, consistent with recent experimental and field studies, provide new quantitative knowledge on the evolution of antibiotic-resistant bacterial reservoirs, and the model developed herein can be adapted for use as a prediction tool in public health policy making, particularly in low-income settings where water sanitation issues remain widespread and disease outbreaks continue to undermine public health efforts. IMPORTANCE The rate at which antimicrobial resistance (AMR) has developed and spread throughout the world has increased in recent years, and according to the Review on Antimicrobial Resistance in 2014, it is suggested that the current rate will lead to AMR-related deaths of several million people by 2050 (Review on Antimicrobial Resistance, Tackling a Crisis for the Health and Wealth of Nations, 2014). One major reservoir of resistant bacterial populations that has been linked to outbreaks of drug-resistant bacterial infections but is not well understood is in wastewater settings, where antibiotic pollution is often present. Using ordinary differential equations incorporating several known drivers of resistance in wastewater, we find that interactions between antibiotic residues and horizontal gene transfer significantly affect the growth of resistant bacterial reservoirs.}, }
@article {pmid34098510, year = {2021}, author = {Moralez, J and Szenkiel, K and Hamilton, K and Pruden, A and Lopatkin, AJ}, title = {Quantitative analysis of horizontal gene transfer in complex systems.}, journal = {Current opinion in microbiology}, volume = {62}, number = {}, pages = {103-109}, doi = {10.1016/j.mib.2021.05.001}, pmid = {34098510}, issn = {1879-0364}, mesh = {*Bacteria/genetics ; *Gene Transfer, Horizontal ; Phenotype ; }, abstract = {Horizontal gene transfer (HGT) plays a significant role in rapidly propagating diverse traits throughout bacterial populations, thereby accelerating natural evolution and leading to complex community structures. Critical gene transfer rates underlying these occurrences dictate the efficiency and speed of gene spread; these rates are often highly specific to HGT mechanism and environmental context, and have historically been challenging to reliably quantify. In this review, we examine recent works that leverage rigorous quantitative methods to precisely measure these rates in a variety of settings beginning with in vitro studies and advancing to in situ measurements; we emphasize contexts where quantification across multiple scales of complexity has led to fundamental biological insights. Finally, we highlight the applications of these measurements and suggest potential methodological advances to improve our understanding.}, }
@article {pmid34097683, year = {2021}, author = {Melkina, OE and Zavilgelsky, GB}, title = {[N-Domain of ArdA Antirestriction Proteins Inhibits the Repression Activity of the Histone-Like H-NS Protein].}, journal = {Molekuliarnaia biologiia}, volume = {55}, number = {3}, pages = {491-499}, doi = {10.31857/S0026898421030125}, pmid = {34097683}, issn = {0026-8984}, mesh = {Bacterial Proteins/genetics ; DNA Restriction Enzymes ; *Escherichia coli Proteins/genetics/metabolism ; *Histones/genetics ; Pseudomonas ; Viral Proteins/metabolism ; }, abstract = {DNA mimicking ArdA anti-restriction proteins specifically inhibit restriction (endonuclease) activity of the type I restriction-modification (RM) system. An ArdA monomer is comprised of three α-β domains (the N-domain, Central domain, and C-domain), each with a different fold. Here we describe an alignment of the amino acid (a.a.) sequences of the ArdA with a conserved 20-a.a. motif in the N domain. The N domains of ArdA proteins of the Gram-positive bacteria Arthrobacter sp. and Bifidobacterium longum, and the Gram-negative bacteria Pseudomonas plecoglossicida are capable of inhibiting the repressive activity of the H-NS global silencer protein in Escherichia coli cells. The presence of the H-NS inhibiting N domain in the ArdA structure enables horizontal gene transfer by mobile elements, including conjugative plasmids and transposons. Specifically, it aids in overcoming intercellular restriction barriers, allowing faster adaption to the genome context of the recipient bacterium.}, }
@article {pmid34097340, year = {2021}, author = {Tokuda, G}, title = {Origin of symbiotic gut spirochetes as key players in the nutrition of termites.}, journal = {Environmental microbiology}, volume = {23}, number = {8}, pages = {4092-4097}, doi = {10.1111/1462-2920.15625}, pmid = {34097340}, issn = {1462-2920}, mesh = {Animals ; Humans ; *Isoptera ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Spirochaetales/genetics ; Symbiosis ; }, abstract = {Termites harbour symbiotic spirochetes in their hindguts, which have long been considered treponemes, although they represent separate lines of descent from known species of Treponema. 'Termite gut treponemes' have a mutualistic relationship with the host termites with their physiological properties including CO2 -reductive acetogenesis, from which the resulting acetate fulfils most of the respiratory requirement of the host. Song and co-workers showed that a spirochetal isolate (strain RmG30) from a Madeira cockroach represents the earliest branching lineage of extremely diverse termite (Treponema) cluster I and was a simple homolactic fermenter, suggesting that CO2 -reductive acetogenesis exhibited by some members of termite cluster I originated via horizontal gene transfer. Phylogenomic and 16S rRNA sequence-based phylogenetic analyses indicated a deeply-branched sister clade containing termite cluster I was distinguishable as a family-level lineage. In this context, a new family, 'Termitinemataceae' has been proposed for this clade. Strain RmG30 has been designated as the type strain of Breznakiella homolactica gen. nov. sp. nov. named after John A. Breznak, an American microbiologist distinguished in termite gut microbiology. The study has posed important questions for the future, including the actual roles of the termite spirochetes in each termite lineage and the evolutionary process of their physiological properties.}, }
@article {pmid34093458, year = {2021}, author = {Zoolkefli, FIRM and Moriguchi, K and Cho, Y and Kiyokawa, K and Yamamoto, S and Suzuki, K}, title = {Isolation and Analysis of Donor Chromosomal Genes Whose Deficiency Is Responsible for Accelerating Bacterial and Trans-Kingdom Conjugations by IncP1 T4SS Machinery.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {620535}, pmid = {34093458}, issn = {1664-302X}, abstract = {Conjugal transfer is a major driving force of genetic exchange in eubacteria, and the system in IncP1-type broad-host-range plasmids transfers DNA even to eukaryotes and archaea in a process known as trans-kingdom conjugation (TKC). Although conjugation factors encoded on plasmids have been extensively analyzed, those on the donor chromosome have not. To identify the potential conjugation factor(s), a genome-wide survey on a comprehensive collection of Escherichia coli gene knockout mutants (Keio collection) as donors to Saccharomyces cerevisiae recipients was performed using a conjugal transfer system mediated by the type IV secretion system (T4SS) of the IncP1α plasmid. Out of 3,884 mutants, three mutants (ΔfrmR, ΔsufA, and ΔiscA) were isolated, which showed an increase by one order of magnitude in both E. coli-E. coli and E. coli-yeast conjugations without an increase in the mRNA accumulation level for the conjugation related genes examined. The double-knockout mutants for these genes (ΔfrmRΔsufA and ΔiscAΔfrmR) did not show synergistic effects on the conjugation efficiency, suggesting that these factors affect a common step in the conjugation machinery. The three mutants demonstrated increased conjugation efficiency in IncP1β-type but not in IncN- and IncW-type broad-host-range plasmid transfers, and the homologous gene knockout mutants against the three genes in Agrobacterium tumefaciens also showed increased TKC efficiency. These results suggest the existence of a specific regulatory system in IncP1 plasmids that enables the control of conjugation efficiency in different hosts, which could be utilized for the development of donor strains as gene introduction tools into bacteria, eukaryotes, and archaea.}, }
@article {pmid34089784, year = {2021}, author = {Assis, RAB and Varani, AM and Sagawa, CHD and Patané, JSL and Setubal, JC and Uceda-Campos, G and da Silva, AM and Zaini, PA and Almeida, NF and Moreira, LM and Dandekar, AM}, title = {A comparative genomic analysis of Xanthomonas arboricola pv. juglandis strains reveal hallmarks of mobile genetic elements in the adaptation and accelerated evolution of virulence.}, journal = {Genomics}, volume = {113}, number = {4}, pages = {2513-2525}, doi = {10.1016/j.ygeno.2021.06.003}, pmid = {34089784}, issn = {1089-8646}, mesh = {DNA Transposable Elements ; *Ecosystem ; *Genomics ; Phylogeny ; Virulence/genetics ; Xanthomonas ; }, abstract = {Xanthomonas arboricola pv. juglandis (Xaj) is the most significant aboveground walnut bacterial pathogen. Disease management uses copper-based pesticides which induce pathogen resistance. We examined the genetic repertoire associated with adaptation and virulence evolution in Xaj. Comparative genomics of 32 Xaj strains reveal the possible acquisition and propagation of virulence factors via insertion sequences (IS). Fine-scale annotation revealed a Tn3 transposon (TnXaj417) encoding copper resistance genes acquired by horizontal gene transfer and associated with adaptation and tolerance to metal-based pesticides commonly used to manage pathogens in orchard ecosystems. Phylogenomic analysis reveals IS involvement in acquisition and diversification of type III effector proteins ranging from two to eight in non-pathogenic strains, 16 to 20 in pathogenic strains, besides six other putative effectors with a reduced identity degree found mostly among pathogenic strains. Yersiniabactin, xopK, xopAI, and antibiotic resistance genes are also located near ISs or inside genomic islands and structures resembling composite transposons.}, }
@article {pmid34089783, year = {2021}, author = {Wang, R and Chen, D and Wang, F and Fan, X and Fan, C and Tang, T and Li, P and Yang, M and Zhao, Y and Qi, K}, title = {An insight into the exploration of proliferation of antibiotic resistance genes in high-fat diet induced obesity mice.}, journal = {Genomics}, volume = {113}, number = {4}, pages = {2503-2512}, doi = {10.1016/j.ygeno.2021.05.041}, pmid = {34089783}, issn = {1089-8646}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Cell Proliferation ; Diet, High-Fat/adverse effects ; Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; Mice ; Obesity/genetics ; }, abstract = {Using mice as an animal model, we first demonstrated the significant proliferation of ARGs and the change of mobile genetic elements (MGEs) in high-fat diet induced obesity (DIO) mice, which the ermB and tnpA-03 genes mostly increased, illuminating that DIO could enrich the abundance of ARGs. Additionally, Lactobacillus sharply increased in the DIO mice and might contribute to the proliferation of ARGs and dramatical change of MGEs in the HFD groups. Finally, procrustes analysis showed the explanatory variables of the MGEs, the metabolites, and the microbial communities for the ARGs accounted for 94.3%, 53.4%, and 68.1%, respectively, and implying that MGEs might be the most direct factor affecting ARGs, and microbiota could be the main driver of the proliferation of ARGs in the DIO mice.}, }
@article {pmid34089318, year = {2021}, author = {Vrzoňová, R and Tóth, R and Siváková, B and Moťovská, A and Gaplovská-Kyselá, K and Baráth, P and Tomáška, &#x13d; and Gácser, A and Gabaldón, T and Nosek, J and Neboháčová, M}, title = {OCT1 - a yeast mitochondrial thiolase involved in the 3-oxoadipate pathway.}, journal = {FEMS yeast research}, volume = {21}, number = {5}, pages = {}, doi = {10.1093/femsyr/foab034}, pmid = {34089318}, issn = {1567-1364}, mesh = {Acetyl-CoA C-Acetyltransferase/genetics ; Acetyl-CoA C-Acyltransferase/genetics ; Animals ; Chromatography, Liquid ; Mitochondria ; Phylogeny ; *Saccharomyces cerevisiae/genetics ; *Tandem Mass Spectrometry ; }, abstract = {The 3-oxoacyl-CoA thiolases catalyze the last step of the fatty acid β-oxidation pathway. In yeasts and plants, this pathway takes place exclusively in peroxisomes, whereas in animals it occurs in both peroxisomes and mitochondria. In contrast to baker's yeast Saccharomyces cerevisiae, yeast species from the Debaryomycetaceae family also encode a thiolase with predicted mitochondrial localization. These yeasts are able to utilize a range of hydroxyaromatic compounds via the 3-oxoadipate pathway the last step of which is catalyzed by 3-oxoadipyl-CoA thiolase and presumably occurs in mitochondria. In this work, we studied Oct1p, an ortholog of this enzyme from Candida parapsilosis. We found that the cells grown on a 3-oxoadipate pathway substrate exhibit increased levels of the OCT1 mRNA. Deletion of both OCT1 alleles impairs the growth of C. parapsilosis cells on 3-oxoadipate pathway substrates and this defect can be rescued by expression of the OCT1 gene from a plasmid vector. Subcellular localization experiments and LC-MS/MS analysis of enriched organellar fraction-proteins confirmed the presence of Oct1p in mitochondria. Phylogenetic profiling of Oct1p revealed an intricate evolutionary pattern indicating multiple horizontal gene transfers among different fungal groups.}, }
@article {pmid34088059, year = {2021}, author = {Huang, Q and Chen, J and Zhu, J and Hao, X and Dao, G and Chen, W and Cai, P and Huang, Q}, title = {Divergent bacterial transformation exerted by soil minerals.}, journal = {The Science of the total environment}, volume = {784}, number = {}, pages = {147173}, doi = {10.1016/j.scitotenv.2021.147173}, pmid = {34088059}, issn = {1879-1026}, mesh = {Adsorption ; Bentonite ; Kaolin ; Minerals ; *Soil ; *Transformation, Bacterial ; }, abstract = {As one of the horizontal gene transfer processes, transformation provides bacteria flexible adaptation to changing environmental conditions. Soil minerals have been shown to inhibit bacterial transformation efficiency due to their high adsorption affinity for DNA molecules. However, the intrinsic mechanisms in regulating genetic transformation by soil components remain elusive. Little is known whether bacterial exposure to minerals may influence competence development which is regarded as a prerequisite of bacterial transformation. In this study, we examined the effects of kaolinite, montmorillonite, and goethite on the transformation of B. subtilis via chemical adsorption, Live-Dead staining, β-galactosidase assay, and qPCR. Results showed that kaolinite and montmorillonite reduced the transformability of B. subtilis by strong adsorption of CSF (competence-stimulating factor), a signaling molecule of cell competence, and the down-regulated transcriptional genes resulting from suppressed competence development. Conversely, goethite depressed bacterial transformation only at low mineral content by DNA adsorption. The striking membrane damage on B. subtilis in presence of high content of goethite yielded a marked increase of bacterial transformation. This finding subverted our previous view regarding the impact of soil minerals on bacterial transformation. Three mechanisms were thus proposed governing bacterial transformation in mineral systems: adsorption of CSF, gene expression and membrane damage. This work has advanced our understanding on the genetic transformation of bacteria as influenced by minerals in a wide range of soils and associated environments.}, }
@article {pmid34079572, year = {2021}, author = {Krak, K and Caklová, P and Kopecký, D and Blattner, FR and Mahelka, V}, title = {Horizontally Acquired nrDNAs Persist in Low Amounts in Host Hordeum Genomes and Evolve Independently of Native nrDNA.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {672879}, pmid = {34079572}, issn = {1664-462X}, abstract = {Nuclear ribosomal DNA (nrDNA) has displayed extraordinary dynamics during the evolution of plant species. However, the patterns and evolutionary significance of nrDNA array expansion or contraction are still relatively unknown. Moreover, only little is known of the fate of minority nrDNA copies acquired between species via horizontal transfer. The barley genus Hordeum (Poaceae) represents a good model for such a study, as species of section Stenostachys acquired nrDNA via horizontal transfer from at least five different panicoid genera, causing long-term co-existence of native (Hordeum-like) and non-native (panicoid) nrDNAs. Using quantitative PCR, we investigated copy number variation (CNV) of nrDNA in the diploid representatives of the genus Hordeum. We estimated the copy number of the foreign, as well as of the native ITS types (ribotypes), and followed the pattern of their CNV in relation to the genus' phylogeny, species' genomes size and the number of nrDNA loci. For the native ribotype, we encountered an almost 19-fold variation in the mean copy number among the taxa analysed, ranging from 1689 copies (per 2C content) in H. patagonicum subsp. mustersii to 31342 copies in H. murinum subsp. glaucum. The copy numbers did not correlate with any of the genus' phylogeny, the species' genome size or the number of nrDNA loci. The CNV was high within the recognised groups (up to 13.2 × in the American I-genome species) as well as between accessions of the same species (up to 4×). Foreign ribotypes represent only a small fraction of the total number of nrDNA copies. Their copy numbers ranged from single units to tens and rarely hundreds of copies. They amounted, on average, to between 0.1% (Setaria ribotype) and 1.9% (Euclasta ribotype) of total nrDNA. None of the foreign ribotypes showed significant differences with respect to phylogenetic groups recognised within the sect. Stenostachys. Overall, no correlation was found between copy numbers of native and foreign nrDNAs suggesting the sequestration and independent evolution of native and non-native nrDNA arrays. Therefore, foreign nrDNA in Hordeum likely poses a dead-end by-product of horizontal gene transfer events.}, }
@article {pmid34078279, year = {2021}, author = {Assaf, R and Xia, F and Stevens, R}, title = {Identifying genomic islands with deep neural networks.}, journal = {BMC genomics}, volume = {22}, number = {Suppl 3}, pages = {281}, pmid = {34078279}, issn = {1471-2164}, support = {HHSN272201400027C/AI/NIAID NIH HHS/United States ; }, mesh = {Eukaryota/genetics ; Gene Transfer, Horizontal ; *Genomic Islands ; Genomics ; *Neural Networks, Computer ; }, abstract = {BACKGROUND: Horizontal gene transfer is the main source of adaptability for bacteria, through which genes are obtained from different sources including bacteria, archaea, viruses, and eukaryotes. This process promotes the rapid spread of genetic information across lineages, typically in the form of clusters of genes referred to as genomic islands (GIs). Different types of GIs exist, and are often classified by the content of their cargo genes or their means of integration and mobility. While various computational methods have been devised to detect different types of GIs, no single method is capable of detecting all types.<br><br>RESULTS: We propose a method, which we call Shutter Island, that uses a deep learning model (Inception V3, widely used in computer vision) to detect genomic islands. The intrinsic value of deep learning methods lies in their ability to generalize. Via a technique called transfer learning, the model is pre-trained on a large generic dataset and then re-trained on images that we generate to represent genomic fragments. We demonstrate that this image-based approach generalizes better than the existing tools.<br><br>CONCLUSIONS: We used a deep neural network and an image-based approach to detect the most out of the correct GI predictions made by other tools, in addition to making novel GI predictions. The fact that the deep neural network was re-trained on only a limited number of GI datasets and then successfully generalized indicates that this approach could be applied to other problems in the field where data is still lacking or hard to curate.}, }
@article {pmid34076710, year = {2021}, author = {Ojha, AK and Shah, NP and Mishra, V}, title = {Conjugal Transfer of Antibiotic Resistances in Lactobacillus spp.}, journal = {Current microbiology}, volume = {78}, number = {8}, pages = {2839-2849}, pmid = {34076710}, issn = {1432-0991}, mesh = {Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial ; Food Microbiology ; Gene Transfer, Horizontal ; Humans ; *Lactobacillus/genetics ; }, abstract = {Lactic acid bacteria (LAB) are a heterogeneous group of bacteria which are Gram-positive, facultative anaerobes and non-motile, non-spore forming, with varied shapes from cocci to coccobacilli and bacilli. Lactobacillus is the largest and most widely used bacterial species amongst LAB in fermented foods and beverages. The genus is a common member of human gut microbiome. Several species are known to provide benefits to the human gut via synergistic interactions with the gut microbiome and their ability to survive the gut environment. This ability to confer positive health effects provide them a status of generally recognized as safe (GRAS) microorganisms. Due to their various beneficial characteristics, other factors such as their resistance acquisition were overlooked. Overuse of antibiotics has made certain bacteria develop resistance against these drugs. Antibiotic resistance was found to be acquired mainly through conjugation which is a type of lateral gene transfer. Several in vitro methods of conjugation have been discussed previously depending on their success to transfer resistance. In this review, we have addressed methods that are employed to study the transfer of resistance genes using the conjugation phenomenon in lactobacilli.}, }
@article {pmid34073520, year = {2021}, author = {Pepi, M and Focardi, S}, title = {Antibiotic-Resistant Bacteria in Aquaculture and Climate Change: A Challenge for Health in the Mediterranean Area.}, journal = {International journal of environmental research and public health}, volume = {18}, number = {11}, pages = {}, pmid = {34073520}, issn = {1660-4601}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Aquaculture ; Bacteria/genetics ; Climate Change ; *Drug Resistance, Bacterial ; Humans ; Mediterranean Sea ; }, abstract = {Aquaculture is the productive activity that will play a crucial role in the challenges of the millennium, such as the need for proteins that support humans and the respect for the environment. Aquaculture is an important economic activity in the Mediterranean basin. A great impact is presented, however, by aquaculture practices as they involve the use of antibiotics for treatment and prophylaxis. As a consequence of the use of antibiotics in aquaculture, antibiotic resistance is induced in the surrounding bacteria in the column water, sediment, and fish-associated bacterial strains. Through horizontal gene transfer, bacteria can diffuse antibiotic-resistance genes and mobile resistance genes further spreading genetic determinants. Once triggered, antibiotic resistance easily spreads among aquatic microbial communities and, from there, can reach human pathogenic bacteria, making vain the use of antibiotics for human health. Climate change claims a significant role in this context, as rising temperatures can affect cell physiology in bacteria in the same way as antibiotics, causing antibiotic resistance to begin with. The Mediterranean Sea represents a 'hot spot' in terms of climate change and aspects of antibiotic resistance in aquaculture in this area can be significantly amplified, thus increasing threats to human health. Practices must be adopted to counteract negative impacts on human health, with a reduction in the use of antibiotics as a pivotal point. In the meantime, it is necessary to act against climate change by reducing anthropogenic impacts, for example by reducing CO2 emissions into the atmosphere. The One Health type approach, which involves the intervention of different skills, such as veterinary, ecology, and medicine in compliance with the principles of sustainability, is necessary and strongly recommended to face these important challenges for human and animal health, and for environmental safety in the Mediterranean area.}, }
@article {pmid34071987, year = {2021}, author = {Sato, N}, title = {Are Cyanobacteria an Ancestor of Chloroplasts or Just One of the Gene Donors for Plants and Algae?.}, journal = {Genes}, volume = {12}, number = {6}, pages = {}, pmid = {34071987}, issn = {2073-4425}, mesh = {Chlorophyta/*genetics ; Chloroplasts/*genetics ; Cyanobacteria/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Peptidoglycan/genetics ; }, abstract = {Chloroplasts of plants and algae are currently believed to originate from a cyanobacterial endosymbiont, mainly based on the shared proteins involved in the oxygenic photosynthesis and gene expression system. The phylogenetic relationship between the chloroplast and cyanobacterial genomes was important evidence for the notion that chloroplasts originated from cyanobacterial endosymbiosis. However, studies in the post-genomic era revealed that various substances (glycolipids, peptidoglycan, etc.) shared by cyanobacteria and chloroplasts are synthesized by different pathways or phylogenetically unrelated enzymes. Membranes and genomes are essential components of a cell (or an organelle), but the origins of these turned out to be different. Besides, phylogenetic trees of chloroplast-encoded genes suggest an alternative possibility that chloroplast genes could be acquired from at least three different lineages of cyanobacteria. We have to seriously examine that the chloroplast genome might be chimeric due to various independent gene flows from cyanobacteria. Chloroplast formation could be more complex than a single event of cyanobacterial endosymbiosis. I present the "host-directed chloroplast formation" hypothesis, in which the eukaryotic host cell that had acquired glycolipid synthesis genes as an adaptation to phosphate limitation facilitated chloroplast formation by providing glycolipid-based membranes (pre-adaptation). The origins of the membranes and the genome could be different, and the origin of the genome could be complex.}, }
@article {pmid34071771, year = {2021}, author = {Skandalis, N and Maeusli, M and Papafotis, D and Miller, S and Lee, B and Theologidis, I and Luna, B}, title = {Environmental Spread of Antibiotic Resistance.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {10}, number = {6}, pages = {}, pmid = {34071771}, issn = {2079-6382}, support = {R01 AI139052/AI/NIAID NIH HHS/United States ; R01AI139052//National Institute of Allergy and Infectious Diseases/ ; }, abstract = {Antibiotic resistance represents a global health concern. Soil, water, livestock and plant foods are directly or indirectly exposed to antibiotics due to their agricultural use or contamination. This selective pressure has acted synergistically to bacterial competition in nature to breed antibiotic-resistant (AR) bacteria. Research over the past few decades has focused on the emergence of AR pathogens in food products that can cause disease outbreaks and the spread of antibiotic resistance genes (ARGs), but One Health approaches have lately expanded the focus to include commensal bacteria as ARG donors. Despite the attempts of national and international authorities of developed and developing countries to reduce the over-prescription of antibiotics to humans and the use of antibiotics as livestock growth promoters, the selective flow of antibiotic resistance transmission from the environment to the clinic (and vice-versa) is increasing. This review focuses on the mechanisms of ARG transmission and the hotspots of antibiotic contamination resulting in the subsequent emergence of ARGs. It follows the transmission of ARGs from farm to plant and animal food products and provides examples of the impact of ARG flow to clinical settings. Understudied and emerging antibiotic resistance selection determinants, such as heavy metal and biocide contamination, are also discussed here.}, }
@article {pmid34071539, year = {2021}, author = {Dobrindt, U and Wami, HT and Schmidt-Wieland, T and Bertsch, D and Oberdorfer, K and Hof, H}, title = {Compared with Cotrimoxazole Nitroxoline Seems to Be a Better Option for the Treatment and Prophylaxis of Urinary Tract Infections Caused by Multidrug-Resistant Uropathogens: An In Vitro Study.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {10}, number = {6}, pages = {}, pmid = {34071539}, issn = {2079-6382}, support = {PhD scholarship//Pharma-Zentrale GmbH/ ; }, abstract = {The resistance of uropathogens to various antibiotics is increasing, but nitroxoline remains active in vitro against some relevant multidrug resistant uropathogenic bacteria. E. coli strains, which are among the most common uropathogens, are unanimously susceptible. Thus, nitroxoline is an option for the therapy of urinary tract infections caused by multiresistant bacteria. Since nitroxoline is active against bacteria in biofilms, it will also be effective in patients with indwelling catheters or foreign bodies in the urinary tract. Cotrimoxazole, on the other hand, which, in principle, can also act on bacteria in biofilms, is frequently inactive against multiresistant uropathogens. Based on phenotypic resistance data from a large number of urine isolates, structural characterisation of an MDR plasmid of a recent ST131 uropathogenic E. coli isolate, and publicly available genomic data of resistant enterobacteria, we show that nitroxoline could be used instead of cotrimoxazole for intervention against MDR uropathogens. Particularly in uropathogenic E. coli, but also in other enterobacterial uropathogens, the frequent parallel resistance to different antibiotics due to the accumulation of multiple antibiotic resistance determinants on mobile genetic elements argues for greater consideration of nitroxoline in the treatment of uncomplicated urinary tract infections.}, }
@article {pmid34071379, year = {2021}, author = {Ku, YS and Wang, Z and Duan, S and Lam, HM}, title = {Rhizospheric Communication through Mobile Genetic Element Transfers for the Regulation of Microbe-Plant Interactions.}, journal = {Biology}, volume = {10}, number = {6}, pages = {}, pmid = {34071379}, issn = {2079-7737}, support = {Area of Excellence Scheme (AoE/M-403/16)//Hong Kong Research Grants Council/ ; To Hon-Ming Lam//Lo Kwee-Seong Biomedical Research Fund/ ; }, abstract = {The transfer of mobile genetic elements (MGEs) has been known as a strategy adopted by organisms for survival and adaptation to the environment. The rhizosphere, where microbes and plants coexist, is a hotspot of MGE transfers. In this review, we discuss the classic mechanisms as well as novel mechanisms of MGE transfers in the rhizosphere. Both intra-kingdom and cross-kingdom MGE transfers will be addressed. MGE transfers could be ancient events which drove evolution or recurrent events which regulate adaptations. Recent findings on MGE transfers between plant and its interacting microbes suggest gene regulations brought forth by such transfers for symbiosis or defense mechanisms. In the natural environment, factors such as temperature and soil composition constantly influence the interactions among different parties in the rhizosphere. In this review, we will also address the effects of various environmental factors on MGE transfers in the rhizosphere. Besides environmental factors, plant root exudates also play a role in the regulation of MGE transfer among microbes in the rhizosphere. The potential use of microbes and plants for bioremediation will be discussed.}, }
@article {pmid34068033, year = {2021}, author = {Nowak, KP and Sobolewska-Ruta, A and Jagiełło, A and Bierczyńska-Krzysik, A and Kierył, P and Wawrzyniak, P}, title = {Molecular and Functional Characterization of MobK Protein-A Novel-Type Relaxase Involved in Mobilization for Conjugational Transfer of Klebsiella pneumoniae Plasmid pIGRK.}, journal = {International journal of molecular sciences}, volume = {22}, number = {10}, pages = {}, pmid = {34068033}, issn = {1422-0067}, mesh = {Bacterial Proteins/genetics/*metabolism ; Base Sequence ; *Conjugation, Genetic ; DNA, Bacterial/*genetics ; Endodeoxyribonucleases/genetics/*metabolism ; Klebsiella pneumoniae/*enzymology/genetics/growth &amp; development ; Plasmids/*genetics/metabolism ; *Recombination, Genetic ; }, abstract = {Conjugation, besides transformation and transduction, is one of the main mechanisms of horizontal transmission of genetic information among bacteria. Conjugational transfer, due to its essential role in shaping bacterial genomes and spreading of antibiotics resistance genes, has been widely studied for more than 70 years. However, new and intriguing facts concerning the molecular basis of this process are still being revealed. Most recently, a novel family of conjugative relaxases (Mob proteins) was distinguished. The characteristic feature of these proteins is that they are not related to any of Mobs described so far. Instead of this, they share significant similarity to tyrosine recombinases. In this study MobK-a tyrosine recombinase-like Mob protein, encoded by pIGRK cryptic plasmid from the Klebsiella pneumoniae clinical strain, was characterized. This study revealed that MobK is a site-specific nuclease and its relaxase activity is dependent on both a conserved catalytic tyrosine residue (Y[179]) that is characteristic of tyrosine recombinases and the presence of Mg[2+] divalent cations. The pIGRK minimal origin of transfer sequence (oriT) was also characterized. This is one of the first reports presenting tyrosine recombinase-like conjugative relaxase protein. It also demonstrates that MobK is a convenient model for studying this new protein family.}, }
@article {pmid34063382, year = {2021}, author = {Paruch, L and Paruch, AM and Iordache, TV and Olaru, AG and Sarbu, A}, title = {Mitigating Antibiotic Resistance Genes in Wastewater by Sequential Treatment with Novel Nanomaterials.}, journal = {Polymers}, volume = {13}, number = {10}, pages = {}, pmid = {34063382}, issn = {2073-4360}, support = {311882//Norges Forskningsr&#xe5;d/ ; 109 BIOSHELL//ERA-NET BlueBio/ ; }, abstract = {Wastewater (WW) has been widely recognized as the major sink of a variety of emerging pathogens (EPs), antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs), which may disseminate and impact wider environments. Improving and maximizing WW treatment efficiency to remove these microbial hazards is fundamentally imperative. Despite a variety of physical, biological and chemical treatment technologies, the efficiency of ARG removal is still far from satisfactory. Within our recently accomplished M-ERA.NET project, novel functionalized nanomaterials, i.e., molecularly imprinted polymer (MIP) films and quaternary ammonium salt (QAS) modified kaolin microparticles, were developed and demonstrated to have significant EP removal effectiveness on both Gram-positive bacteria (GPB) and Gram-negative bacteria (GNB) from WW. As a continuation of this project, we took the further step of exploring their ARG mitigation potential. Strikingly, by applying MIP and QAS functionalized kaolin microparticles in tandem, the ARGs prevalent in wastewater treatment plants (WWTPs), e.g., blaCTXM, ermB and qnrS, can be drastically reduced by 2.7, 3.9 and 4.9 log (copies/100 mL), respectively, whereas sul1, tetO and mecA can be eliminated below their detection limits. In terms of class I integron-integrase I (intI1), a mobile genetic element (MGE) for horizontal gene transfer (HGT), 4.3 log (copies/100 mL) reduction was achieved. Overall, the novel nanomaterials exhibit outstanding performance on attenuating ARGs in WW, being superior to their control references. This finding provides additional merit to the application of developed nanomaterials for WW purification towards ARG elimination, in addition to the proven bactericidal effect.}, }
@article {pmid34061182, year = {2021}, author = {Starko, S and Bringloe, TT and Gomez, MS and Darby, H and Graham, SW and Martone, PT}, title = {Genomic Rearrangements and Sequence Evolution across Brown Algal Organelles.}, journal = {Genome biology and evolution}, volume = {13}, number = {7}, pages = {}, pmid = {34061182}, issn = {1759-6653}, mesh = {Evolution, Molecular ; *Genome, Mitochondrial ; *Genome, Plastid ; Genomics ; Introns ; *Phaeophyceae/genetics ; Phylogeny ; Plastids/genetics ; }, abstract = {Organellar genomes serve as useful models for genome evolution and contain some of the most widely used phylogenetic markers, but they are poorly characterized in many lineages. Here, we report 20 novel mitochondrial genomes and 16 novel plastid genomes from the brown algae. We focused our efforts on the orders Chordales and Laminariales but also provide the first plastid genomes (plastomes) from Desmarestiales and Sphacelariales, the first mitochondrial genome (mitome) from Ralfsiales and a nearly complete mitome from Sphacelariales. We then compared gene content, sequence evolution rates, shifts in genome structural arrangements, and intron distributions across lineages. We confirm that gene content is largely conserved in both organellar genomes across the brown algal tree of life, with few cases of gene gain or loss. We further show that substitution rates are generally lower in plastid than mitochondrial genes, but plastomes are more variable in gene arrangement, as mitomes tend to be colinear even among distantly related lineages (with exceptions). Patterns of intron distribution across organellar genomes are complex. In particular, the mitomes of several laminarialean species possess group II introns that have T7-like ORFs, found previously only in mitochondrial genomes of Pylaiella spp. (Ectocarpales). The distribution of these mitochondrial introns is inconsistent with vertical transmission and likely reflects invasion by horizontal gene transfer between lineages. In the most extreme case, the mitome of Hedophyllum nigripes is ∼40% larger than the mitomes of close relatives because of these introns. Our results provide substantial insight into organellar evolution across the brown algae.}, }
@article {pmid34058749, year = {2021}, author = {Ibtehaz, N and Ahmed, I and Ahmed, MS and Rahman, MS and Azad, RK and Bayzid, MS}, title = {SSG-LUGIA: Single Sequence based Genome Level Unsupervised Genomic Island Prediction Algorithm.}, journal = {Briefings in bioinformatics}, volume = {22}, number = {6}, pages = {}, doi = {10.1093/bib/bbab116}, pmid = {34058749}, issn = {1477-4054}, mesh = {*Algorithms ; Bacteria/*genetics ; *Computational Biology ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genomic Islands ; }, abstract = {BACKGROUND: Genomic Islands (GIs) are clusters of genes that are mobilized through horizontal gene transfer. GIs play a pivotal role in bacterial evolution as a mechanism of diversification and adaptation to different niches. Therefore, identification and characterization of GIs in bacterial genomes is important for understanding bacterial evolution. However, quantifying GIs is inherently difficult, and the existing methods suffer from low prediction accuracy and precision-recall trade-off. Moreover, several of them are supervised in nature, and thus, their applications to newly sequenced genomes are riddled with their dependency on the functional annotation of existing genomes.<br><br>RESULTS: We present SSG-LUGIA, a completely automated and unsupervised approach for identifying GIs and horizontally transferred genes. SSG-LUGIA is a novel method based on unsupervised anomaly detection technique, accompanied by further refinement using cues from signal processing literature. SSG-LUGIA leverages the atypical compositional biases of the alien genes to localize GIs in prokaryotic genomes. SSG-LUGIA was assessed on a large benchmark dataset `IslandPick' and on a set of 15 well-studied genomes in the literature and followed by a thorough analysis on the well-understood Salmonella typhi CT18 genome. Furthermore, the efficacy of SSG-LUGIA in identifying horizontally transferred genes was evaluated on two additional bacterial genomes, namely, those of Corynebacterium diphtheria NCTC13129 and Pseudomonas aeruginosa LESB58. SSG-LUGIA was examined on draft genomes and was demonstrated to be efficient as an ensemble method.<br><br>CONCLUSIONS: Our results indicate that SSG-LUGIA achieved superior performance in comparison to frequently used existing methods. Importantly, it yielded a better trade-off between precision and recall than the existing methods. Its nondependency on the functional annotation of genomes makes it suitable for analyzing newly sequenced, yet uncharacterized genomes. Thus, our study is a significant advance in identification of GIs and horizontally transferred genes. SSG-LUGIA is available as an open source software at https://nibtehaz.github.io/SSG-LUGIA/.}, }
@article {pmid34058579, year = {2021}, author = {Zahedi, S and Gros, M and Balcazar, JL and Petrovic, M and Pijuan, M}, title = {Assessing the occurrence of pharmaceuticals and antibiotic resistance genes during the anaerobic treatment of slaughterhouse wastewater at different temperatures.}, journal = {The Science of the total environment}, volume = {789}, number = {}, pages = {147910}, doi = {10.1016/j.scitotenv.2021.147910}, pmid = {34058579}, issn = {1879-1026}, mesh = {Abattoirs ; Anaerobiosis ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Pharmaceutical Preparations ; Temperature ; Wastewater ; }, abstract = {This study investigates the effect of psychrophilic, mesophilic and thermophilic temperatures on the anaerobic treatment of slaughterhouse wastewater, in terms of biogas production, occurrence of 30 pharmaceutical compounds of veterinary use, 4 antibiotic resistance genes (ARGs) which provide resistance to tetracyclines (tetW), fluoroquinolones (qnrS), macrolide-lincosamide-streptogramin (ermB) and sulfonamides (sul1) antibiotics, as well as class I integron-integrase gene (intI1), related to horizontal gene transfer. The highest methane yield was obtained at a mesophilic temperature (35 °C) (323 mL CH4/g TCOD) followed by the yield obtained at thermophilic temperature (53 °C) (242 mL CH4/g TCOD). Regarding pharmaceuticals, chlortetracycline, oxytetracycline, tilmicosin, and lincomycin were the most abundant in the slaughterhouse wastewater, being detected predominantly in the solid phase (with median concentrations >200 μg/kg dry weight). On the other hand, ciprofloxacin, ofloxacin, norfloxacin, lincomycin and ibuprofen were the most predominant in the anaerobic digestate regardless of the treatment temperature. Psychrophilic temperatures (21 °C) exhibited moderate to low pharmaceuticals removal, while a large fraction of them were removed at a thermophilic temperature reaching 70-90% removals for tetracycline, macrolides and one sulfonamide (sulfapyridine). The highest relative abundance of the quantified ARGs was found at 53 °C, suggesting that thermophilic temperatures normally associated with better removals of pathogens do not necessarily show better removals of antibiotic resistance genes.}, }
@article {pmid34058515, year = {2021}, author = {Jockusch, EL and Fisher, CR}, title = {Something old, something new, something borrowed, something red: the origin of ecologically relevant novelties in Hemiptera.}, journal = {Current opinion in genetics &amp; development}, volume = {69}, number = {}, pages = {154-162}, doi = {10.1016/j.gde.2021.04.003}, pmid = {34058515}, issn = {1879-0380}, mesh = {Animals ; *Evolution, Molecular ; Gene Duplication/genetics ; Gene Expression Regulation/genetics ; Gene Transfer, Horizontal/*genetics ; *Genetic Variation ; Hemiptera/genetics/growth &amp; development ; Insecta/genetics ; Phenotype ; Transcriptome/*genetics ; }, abstract = {Comparative transcriptomics, applied in an evolutionary context, has transformed the possibilities for studying phenotypic evolution in non-model taxa. We review recent discoveries about the development of novel, ecologically relevant phenotypes in hemipteran insects. These discoveries highlight the diverse genomic substrates of novelty: 'something old', when novelty results from changes in the regulation of existing genes or gene duplication; 'something new', wherein lineage-restricted genes contribute to the evolution of new phenotypes; and 'something borrowed', showcasing contributions of horizontal gene transfer to the evolution of novelty, including carotenoid synthesis (resulting in 'something red'). These findings show the power and flexibility of comparative transcriptomic approaches for expanding beyond the 'toolkit' model for the evolution of development. We conclude by raising questions about the relationship between new genes and new traits and outlining a research framework for answering them in Hemiptera.}, }
@article {pmid34055389, year = {2021}, author = {Abdoulaye, AH and Hai, D and Tang, Q and Jiang, D and Fu, Y and Cheng, J and Lin, Y and Li, B and Kotta-Loizou, I and Xie, J}, title = {Two distant helicases in one mycovirus: evidence of horizontal gene transfer between mycoviruses, coronaviruses and other nidoviruses.}, journal = {Virus evolution}, volume = {7}, number = {1}, pages = {veab043}, pmid = {34055389}, issn = {2057-1577}, abstract = {Nidovirales, which accommodates viruses with the largest RNA genomes, includes the notorious coronaviruses; however, the evolutionary route for nidoviruses is not well understood. We have characterized a positive-sense (+) single-stranded (ss) RNA mycovirus, Rhizoctonia solani hypovirus 2 (RsHV2), from the phytopathogenic fungus Rhizoctonia solani. RsHV2 has the largest RNA genome size of 22,219 nucleotides, excluding the poly(A) tail, in all known mycoviruses, and contains two open reading frames (ORF1 and ORF2). ORF1 encodes a protein of 2,009 amino acid (aa) that includes a conserved helicase domain belonging to helicase superfamily I (SFI). In contrast, ORF2 encodes a polyprotein of 4459 aa containing the hallmark genes of hypoviruses. The latter includes a helicase belonging to SFII. Following phylogenetic analysis, the ORF1-encoded helicase (Hel1) unexpectedly clustered in an independent evolutionary branch together with nidovirus helicases, including coronaviruses, and bacteria helicases. Thus, Hel1 presence indicates the occurrence of horizontal gene transfer between viruses and bacteria. These findings also suggest that RsHV2 is most likely a recombinant arising between hypoviruses and nidoviruses.}, }
@article {pmid34054769, year = {2021}, author = {Karlsson, PA and Tano, E and Jernberg, C and Hickman, RA and Guy, L and Järhult, JD and Wang, H}, title = {Molecular Characterization of Multidrug-Resistant Yersinia enterocolitica From Foodborne Outbreaks in Sweden.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {664665}, pmid = {34054769}, issn = {1664-302X}, abstract = {The foodborne pathogen Yersinia enterocolitica causes gastrointestinal infections worldwide. In the spring of 2019, the Swedish Public Health Agency and Statens Serum Institut in Denmark independently identified an outbreak caused by Yersinia enterocolitica 4/O:3 that after sequence comparison turned out to be a cross-border outbreak. A trace-back investigation suggested shipments of fresh prewashed spinach from Italy as a common source for the outbreak. Here, we determined the genome sequences of five Y. enterocolitica clinical isolates during the Swedish outbreak using a combination of Illumina HiSeq short-read and Nanopore Technologies' MinION long-read whole-genome sequencing. WGS results showed that all clinical strains have a fully assembled chromosome of approximately 4.6 Mbp in size and a 72-kbp virulence plasmid; one of the strains was carrying an additional 5.7-kbp plasmid, pYE-tet. All strains showed a high pathogen probability score (87.5%) with associated genes for virulence, all of which are closely related to an earlier clinical strain Y11 from Germany. In addition, we identified a chromosomally encoded multidrug-resistance cassette carrying resistance genes against chloramphenicol (catA1), streptomycin (aadA1), sulfonamides (sul1), and a mercury resistance module. This chromosomally encoded Tn2670 transposon has previously been reported associated with IncFII plasmids in Enterobacteriaceae: a Shigella flexneri clinical isolate from Japan in 1950s, a Klebsiella pneumoniae outbreak from Australia in 1997, and Salmonella enterica serovar Typhimurium. Interestingly, we identified an additional 5.7-kbp plasmid with tetB (encoding an ABC transporter), Rep, and its own ORI and ORIt sites, sharing high homology with small tetB-Rep plasmids from Pasteurellaceae. This is the first time that Tn2670 and Pasteurellaceae plasmids have been reported in Y. enterocolitica. Taken together, our study showed that the Swedish Y. enterocolitica outbreak strains acquired multi-antibiotic and metal-resistance genes through horizontal gene transfer, suggesting a potential reservoir of intraspecies dissemination of multidrug-resistance genes among foodborne pathogens. This study also highlights the concern of food-chain contamination of prewashed vegetables as a perpetual hazard against public health.}, }
@article {pmid34054758, year = {2021}, author = {Sommer, J and Gerbracht, KM and Krause, FF and Wild, F and Tietgen, M and Riedel-Christ, S and Sattler, J and Hamprecht, A and Kempf, VAJ and Göttig, S}, title = {OXA-484, an OXA-48-Type Carbapenem-Hydrolyzing Class D β-Lactamase From Escherichia coli.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {660094}, pmid = {34054758}, issn = {1664-302X}, abstract = {OXA-48-like carbapenemases are among the most frequent carbapenemases in Gram-negative Enterobacterales worldwide with the highest prevalence in the Middle East, North Africa and Europe. Here, we investigated the so far uncharacterized carbapenemase OXA-484 from a clinical E. coli isolate belonging to the high-risk clone ST410 regarding antibiotic resistance pattern, horizontal gene transfer (HGT) and genetic support. OXA-484 differs by the amino acid substitution 214G compared to the most closely related variants OXA-181 (214R) and OXA-232 (214S). The bla OXA - 484 was carried on a self-transmissible 51.5 kb IncX3 plasmid (pOXA-484) showing high sequence similarity with plasmids harboring bla OXA - 181. Intraspecies and intergenus HGT of pOXA-484 to different recipients occurred at low frequencies of 1.4 × 10[-7] to 2.1 × 10[-6]. OXA-484 increased MICs of temocillin and carbapenems similar to OXA-232 and OXA-244, but lower compared with OXA-48 and OXA-181. Hence, OXA-484 combines properties of OXA-181-like plasmid support and transferability as well as β-lactamase activity of OXA-232.}, }
@article {pmid34054753, year = {2021}, author = {Danevčič, T and Dragoš, A and Spacapan, M and Stefanic, P and Dogsa, I and Mandic-Mulec, I}, title = {Surfactin Facilitates Horizontal Gene Transfer in Bacillus subtilis.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {657407}, pmid = {34054753}, issn = {1664-302X}, abstract = {Genetic competence for the uptake and integration of extracellular DNA is a key process in horizontal gene transfer (HGT), one of the most powerful forces driving the evolution of bacteria. In several species, development of genetic competence is coupled with cell lysis. Using Bacillus subtilis as a model bacterium, we studied the role of surfactin, a powerful biosurfactant and antimicrobial lipopeptide, in genetic transformation. We showed that surfactin itself promotes cell lysis and DNA release, thereby promoting HGT. These results, therefore, provide evidence for a fundamental mechanism involved in HGT and significantly increase our understanding of the spreading of antibiotic resistance genes and diversification of microbial communities in the environment.}, }
@article {pmid34051611, year = {2021}, author = {Rahimlou, S and Bahram, M and Tedersoo, L}, title = {Phylogenomics reveals the evolution of root nodulating alpha- and beta-Proteobacteria (rhizobia).}, journal = {Microbiological research}, volume = {250}, number = {}, pages = {126788}, doi = {10.1016/j.micres.2021.126788}, pmid = {34051611}, issn = {1618-0623}, mesh = {Alphaproteobacteria/*genetics ; Betaproteobacteria/*genetics ; Ecosystem ; Fabaceae/microbiology ; Gene Transfer, Horizontal ; Mimosa/microbiology ; Nitrogen Fixation ; *Phylogeny ; Plant Root Nodulation/*genetics ; Rhizobium/classification/*genetics ; Symbiosis/*genetics ; }, abstract = {The symbiosis between legumes and nodulating Proteobacteria (so-called rhizobia) contributes greatly to nitrogen fixation in terrestrial ecosystems. Root nodulating Proteobacteria produce nodulation (Nod) factors during the initiation of rhizobial nodule organogenesis on the roots of legumes. Here, we screened the Nod factor production capacity of the previously reported nodule inducing Proteobacteria genera using their genome sequences and assessed the evolutionary history of symbiosis based on phylogenomics. Our analysis revealed 12 genera as potentially Nod factor producing taxa exclusively from alpha- and beta-Proteobacteria. Based on molecular clock analysis, we estimate that rhizobial nitrogen-fixing symbiosis appeared for the first time about 51 Mya (Eocene epoch) in Rhizobiaceae, and it was laterally transferred to multiple symbiotic taxa in alpha- and beta-Proteobacteria. Coevolutionary tests conducted for measuring the phylogenetic congruence between hosts and symbionts revealed only weak topological similarity between legumes and their bacterial symbionts. We conclude that frequent lateral transfer of symbiotic genes, facultative symbiotic nature of rhizobia, differential evolutionary processes of chromosome versus plasmids, and complex multispecies coevolutionary processes have shaped the rhizobia-host associations.}, }
@article {pmid34048565, year = {2021}, author = {Vit, C and Richard, E and Fournes, F and Whiteway, C and Eyer, X and Lapaillerie, D and Parissi, V and Mazel, D and Loot, C}, title = {Cassette recruitment in the chromosomal Integron of Vibrio cholerae.}, journal = {Nucleic acids research}, volume = {49}, number = {10}, pages = {5654-5670}, pmid = {34048565}, issn = {1362-4962}, mesh = {Chromosomes/genetics/*metabolism ; Escherichia coli/metabolism ; Gene Expression Regulation, Bacterial/genetics ; Gene Transfer, Horizontal/*genetics ; Integrases/genetics/*metabolism ; Integrons/*genetics ; Rec A Recombinases/genetics/metabolism ; Recombination, Genetic/genetics ; Vibrio cholerae/genetics/*metabolism ; }, abstract = {Integrons confer a rapid adaptation capability to bacteria. Integron integrases are able to capture and shuffle novel functions embedded in cassettes. Here, we investigated cassette recruitment in the Vibrio cholerae chromosomal integron during horizontal transfer. We demonstrated that the endogenous integrase expression is sufficiently triggered, after SOS response induction mediated by the entry of cassettes during conjugation and natural transformation, to mediate significant cassette insertions. These insertions preferentially occur at the attIA site, despite the presence of about 180 attC sites in the integron array. Thanks to the presence of a promoter in the attIA site vicinity, all these newly inserted cassettes are expressed and prone to selection. We also showed that the RecA protein is critical for cassette recruitment in the V. cholerae chromosomal integron but not in mobile integrons. Moreover, unlike the mobile integron integrases, that of V. cholerae is not active in other bacteria. Mobile integrons might have evolved from the chromosomal ones by overcoming host factors, explaining their large dissemination in bacteria and their role in antibioresistance expansion.}, }
@article {pmid34046775, year = {2021}, author = {Varner, PM and Gunsch, CK}, title = {Properties affecting transfer and expression of degradative plasmids for the purpose of bioremediation.}, journal = {Biodegradation}, volume = {32}, number = {4}, pages = {361-375}, pmid = {34046775}, issn = {1572-9729}, support = {P42 ES010356/ES/NIEHS NIH HHS/United States ; DGE-1644868//National Science Foundation/ ; }, mesh = {Bacteria/genetics ; Biodegradation, Environmental ; *Conjugation, Genetic ; *Gene Transfer, Horizontal ; Plasmids/genetics ; }, abstract = {Plasmids, circular DNA that exist and replicate outside of the host chromosome, have been important in the spread of non-essential genes as well as the rapid evolution of prokaryotes. Recent advances in environmental engineering have aimed to utilize the mobility of plasmids carrying degradative genes to disseminate them into the environment for cost-effective and environmentally friendly remediation of harmful contaminants. Here, we review the knowledge surrounding plasmid transfer and the conditions needed for successful transfer and expression of degradative plasmids. Both abiotic and biotic factors have a great impact on the success of degradative plasmid transfer and expression of the degradative genes of interest. Properties such as ecological growth strategies of bacteria may also contribute to plasmid transfer and may be an important consideration for bioremediation applications. Finally, the methods for detection of conjugation events have greatly improved and the application of these tools can help improve our understanding of conjugation in complex communities. However, it remains clear that more methods for in situ detection of plasmid transfer are needed to help detangle the complexities of conjugation in natural environments to better promote a framework for precision bioremediation.}, }
@article {pmid34035362, year = {2021}, author = {Maeda, H and Kami, D and Maeda, R and Shikuma, A and Gojo, S}, title = {Generation of somatic mitochondrial DNA-replaced cells for mitochondrial dysfunction treatment.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {10897}, pmid = {34035362}, issn = {2045-2322}, mesh = {Cells, Cultured ; DNA, Mitochondrial/*genetics ; Fibroblasts/*cytology ; Gene Transfer, Horizontal ; Humans ; Maternal Inheritance ; Mitochondrial Diseases/*genetics/therapy ; *Mutation ; Pinocytosis ; Time-Lapse Imaging ; }, abstract = {Mitochondrial diseases currently have no cure regardless of whether the cause is a nuclear or mitochondrial genome mutation. Mitochondrial dysfunction notably affects a wide range of disorders in aged individuals, including neurodegenerative diseases, cancers, and even senescence. Here, we present a procedure to generate mitochondrial DNA-replaced somatic cells with a combination of a temporal reduction in endogenous mitochondrial DNA and coincubation with exogeneous isolated mitochondria. Heteroplasmy in mitochondrial disease patient-derived fibroblasts in which the mutant genotype was dominant over the wild-type genotype was reversed. Mitochondrial disease patient-derived fibroblasts regained respiratory function and showed lifespan extension. Mitochondrial membranous components were utilized as a vehicle to deliver the genetic materials into endogenous mitochondria-like horizontal genetic transfer in prokaryotes. Mitochondrial DNA-replaced cells could be a resource for transplantation to treat maternal inherited mitochondrial diseases.}, }
@article {pmid34034667, year = {2021}, author = {Bertazzoni, S and Jones, DAB and Phan, HT and Tan, KC and Hane, JK}, title = {Chromosome-level genome assembly and manually-curated proteome of model necrotroph Parastagonospora nodorum Sn15 reveals a genome-wide trove of candidate effector homologs, and redundancy of virulence-related functions within an accessory chromosome.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {382}, pmid = {34034667}, issn = {1471-2164}, support = {CUR00023//Grains Research And Development Corporation/ ; y95//Pawsey Supercomputing Centre and National Computational Infrastructure/ ; }, mesh = {Ascomycota ; Australia ; Chromosomes ; *Plant Diseases/genetics ; *Proteome ; Virulence/genetics ; }, abstract = {BACKGROUND: The fungus Parastagonospora nodorum causes septoria nodorum blotch (SNB) of wheat (Triticum aestivum) and is a model species for necrotrophic plant pathogens. The genome assembly of reference isolate Sn15 was first reported in 2007. P. nodorum infection is promoted by its production of proteinaceous necrotrophic effectors, three of which are characterised - ToxA, Tox1 and Tox3.<br><br>RESULTS: A chromosome-scale genome assembly of P. nodorum Australian reference isolate Sn15, which combined long read sequencing, optical mapping and manual curation, produced 23 chromosomes with 21 chromosomes possessing both telomeres. New transcriptome data were combined with fungal-specific gene prediction techniques and manual curation to produce a high-quality predicted gene annotation dataset, which comprises 13,869 high confidence genes, and an additional 2534 lower confidence genes retained to assist pathogenicity effector discovery. Comparison to a panel of 31 internationally-sourced isolates identified multiple hotspots within the Sn15 genome for mutation or presence-absence variation, which was used to enhance subsequent effector prediction. Effector prediction resulted in 257 candidates, of which 98 higher-ranked candidates were selected for in-depth analysis and revealed a wealth of functions related to pathogenicity. Additionally, 11 out of the 98 candidates also exhibited orthology conservation patterns that suggested lateral gene transfer with other cereal-pathogenic fungal species. Analysis of the pan-genome indicated the smallest chromosome of 0.4 Mbp length to be an accessory chromosome (AC23). AC23 was notably absent from an avirulent isolate and is predominated by mutation hotspots with an increase in non-synonymous mutations relative to other chromosomes. Surprisingly, AC23 was deficient in effector candidates, but contained several predicted genes with redundant pathogenicity-related functions.<br><br>CONCLUSIONS: We present an updated series of genomic resources for P. nodorum Sn15 - an important reference isolate and model necrotroph - with a comprehensive survey of its predicted pathogenicity content.}, }
@article {pmid34030967, year = {2021}, author = {Yang, Y}, title = {Emerging Patterns of Microbial Functional Traits.}, journal = {Trends in microbiology}, volume = {29}, number = {10}, pages = {874-882}, doi = {10.1016/j.tim.2021.04.004}, pmid = {34030967}, issn = {1878-4380}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; Bacterial Physiological Phenomena ; *Biodiversity ; Ecosystem ; Environment ; Phenotype ; }, abstract = {Functional traits are measurable characteristics that affect an organism's fitness under certain environmental conditions. The use of functional traits in microbial ecology holds great promise for improving our ability to develop biogeochemical models and predict ecosystem responses to global changes. Notably, functional traits could be decoupled from taxonomic relatedness, owing to horizontal gene transfer among microorganisms and adaptive evolution. In recent years, our knowledge about microbial functional traits has been substantially enhanced, thereby revealing the multitude of ecological processes in driving community assembly and dynamics. Here, I summarize the emerging patterns of how microbial functional traits respond to changing environments, which considerably differ from better-studied microbial taxonomy. I use niche and neutral theories to explain microbial functional traits. Finally, I highlight future challenges to analyze, elucidate, and utilize functional traits in microbial ecology.}, }
@article {pmid34022346, year = {2021}, author = {Kohli, S and Gulati, P and Narang, A and Maini, J and Shamsudheen, KV and Pandey, R and Scaria, V and Sivasubbu, S and Brahmachari, V}, title = {Genome and transcriptome analysis of the mealybug Maconellicoccus hirsutus: Correlation with its unique phenotypes.}, journal = {Genomics}, volume = {113}, number = {4}, pages = {2483-2494}, doi = {10.1016/j.ygeno.2021.05.014}, pmid = {34022346}, issn = {1089-8646}, mesh = {Animals ; Female ; Gene Expression Profiling ; Genome ; *Hemiptera/genetics ; Male ; Phenotype ; Symbiosis ; Transcriptome ; }, abstract = {Mealybugs are aggressive pests with world-wide distribution and are suitable for the study of different phenomena like genomic imprinting and epigenetics. Genomic approaches facilitate these studies in absence of robust genetics in this system. We sequenced, de novo assembled, annotated Maconellicoccus hirsutus genome. We carried out comparative genomics it with four mealybug and eight other insect species, to identify expanded, specific and contracted gene classes that relate to pesticide and desiccation resistance. We identified horizontally transferred genes adding to the mutualism between the mealybug and its endosymbionts. Male and female transcriptome analysis indicates differential expression of metabolic pathway genes correlating with their physiology and the genes for sexual dimorphism. The significantly lower expression of endosymbiont genes in males relates to the depletion of endosymbionts in males during development.}, }
@article {pmid34018688, year = {2021}, author = {Braga, LPP and Coutinho, FH and Amgarten, DE and Kot, W and Hansen, L and Setubal, JC and Philippot, L}, title = {Novel virocell metabolic potential revealed in agricultural soils by virus-enriched soil metagenome analysis.}, journal = {Environmental microbiology reports}, volume = {13}, number = {3}, pages = {348-354}, doi = {10.1111/1758-2229.12939}, pmid = {34018688}, issn = {1758-2229}, mesh = {Ecosystem ; *Metagenome ; Rhizosphere ; Soil ; *Viruses/genetics ; }, abstract = {Viruses are now recognized as important players in microbial dynamics and biogeochemical cycles in the oceans. Yet, compared with aquatic ecosystems, virus discovery in terrestrial ecosystems has been challenging partly due to the inherent complexity of soils. To expand our understanding of soil viruses and their putative contributions to soil microbial processes, we analysed metagenomes of community-level virus-enriched suspensions by tangential flow filtration obtained from two French agricultural soils. We found viral sequences representing a total of 239 viral operational taxonomic units that corresponded to 29.5% of the mapping reads in the metagenomic datasets. The analysis of their genomic sequences revealed novel virocell metabolic potential with implications to virus-host interactions, carbon cycling, plant-beneficial functions in the rhizosphere, horizontal gene transfer and other relevant microbial strategies applied to survive in soils.}, }
@article {pmid34018328, year = {2021}, author = {Smyshlyaev, G and Bateman, A and Barabas, O}, title = {Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes.}, journal = {Molecular systems biology}, volume = {17}, number = {5}, pages = {e9880}, pmid = {34018328}, issn = {1744-4292}, mesh = {Archaea/enzymology/*genetics ; Bacteria/enzymology/*genetics ; Drug Resistance, Microbial ; Evolution, Molecular ; Fungi/enzymology/*genetics ; Interspersed Repetitive Sequences ; Molecular Sequence Annotation ; Recombinases/*metabolism ; Sequence Analysis, Protein/*methods ; Systems Biology ; }, abstract = {Mobile genetic elements (MGEs) sequester and mobilize antibiotic resistance genes across bacterial genomes. Efficient and reliable identification of such elements is necessary to follow resistance spreading. However, automated tools for MGE identification are missing. Tyrosine recombinase (YR) proteins drive MGE mobilization and could provide markers for MGE detection, but they constitute a diverse family also involved in housekeeping functions. Here, we conducted a comprehensive survey of YRs from bacterial, archaeal, and phage genomes and developed a sequence-based classification system that dissects the characteristics of MGE-borne YRs. We revealed that MGE-related YRs evolved from non-mobile YRs by acquisition of a regulatory arm-binding domain that is essential for their mobility function. Based on these results, we further identified numerous unknown MGEs. This work provides a resource for comparative analysis and functional annotation of YRs and aids the development of computational tools for MGE annotation. Additionally, we reveal how YRs adapted to drive gene transfer across species and provide a tool to better characterize antibiotic resistance dissemination.}, }
@article {pmid34011288, year = {2021}, author = {Pinto, G and Sampaio, M and Dias, O and Almeida, C and Azeredo, J and Oliveira, H}, title = {Insights into the genome architecture and evolution of Shiga toxin encoding bacteriophages of Escherichia coli.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {366}, pmid = {34011288}, issn = {1471-2164}, support = {UIDB/04469/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PhageSTEC PTDC/CVT-CVT/29628/2017 [POCI-01-0145-FEDER-029628]//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; SFRH/BD/117365/2016//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, mesh = {*Bacteriophages/genetics ; Lysogeny/genetics ; Shiga Toxin/genetics ; Shiga Toxin 2/genetics ; *Shiga-Toxigenic Escherichia coli/genetics ; }, abstract = {BACKGROUND: A total of 179 Shiga toxin-producing Escherichia coli (STEC) complete genomes were analyzed in terms of serotypes, prophage coding regions, and stx gene variants and their distribution. We further examined the genetic diversity of Stx-converting phage genomes (Stx phages), focusing on the lysis-lysogeny decision and lytic cassettes.<br><br>RESULTS: We show that most STEC isolates belong to non-O157 serotypes (73&#x2009;%), regardless the sources and geographical regions. While the majority of STEC genomes contain a single stx gene (61&#x2009;%), strains containing two (35&#x2009;%), three (3&#x2009;%) and four (1&#x2009;%) stx genes were also found, being stx2 the most prevalent gene variant. Their location is exclusively found in intact prophage regions, indicating that they are phage-borne. We further demonstrate that Stx phages can be grouped into four clusters (A, B, C and D), three subclusters (A1, A2 and A3) and one singleton, based on their shared gene content. This cluster distribution is in good agreement with their predicted virion morphologies. Stx phage genomes are highly diverse with a vast number of 1,838 gene phamilies (phams) of related sequences (of which 677 are orphams i.e. unique genes) and, although having high mosaicism, they are generally organized into three major transcripts. While the mechanisms that guide lysis-lysogeny decision are complex, there is a strong selective pressure to maintain the stx genes location close to the lytic cassette composed of predicted SAR-endolysin and pin-holin lytic proteins. The evolution of STEC Stx phages seems to be strongly related to acquiring genetic material, probably from horizontal gene transfer events.<br><br>CONCLUSIONS: This work provides novel insights on the genetic structure of Stx phages, showing a high genetic diversity throughout the genomes, where the various lysis-lysogeny regulatory systems are in contrast with an uncommon, but conserved, lytic system always adjacent to stx genes.}, }
@article {pmid34009736, year = {2021}, author = {Choi, O and Lee, Y and Park, J and Kang, B and Chun, HJ and Kim, MC and Kim, J}, title = {A novel toxoflavin-quenching regulation in bacteria and its application to resistance cultivars.}, journal = {Microbial biotechnology}, volume = {14}, number = {4}, pages = {1657-1670}, pmid = {34009736}, issn = {1751-7915}, support = {2015R1A6A1A03031413//National Research Foundation of Korea/ ; }, mesh = {*Burkholderia/genetics ; Ecosystem ; Gene Expression Regulation, Bacterial ; *Oryza ; Pyrimidinones ; Quorum Sensing ; Sphingomonas ; Triazines ; }, abstract = {The toxoflavin (Txn), broad host range phytotoxin produced by a variety of bacteria, including Burkholderia glumae, is a key pathogenicity factor of B. glumae in rice and field crops. Two bacteria exhibiting Txn-degrading activity were isolated from healthy rice seeds and identified as Sphingomonas adhaesiva and Agrobacterium sp. respectively. The genes stdR and stdA, encoding proteins responsible for Txn degradation of both bacterial isolates, were identical, indicating that horizontal gene transfer occurred between microbial communities in the same ecosystem. We identified a novel Txn-quenching regulation of bacteria, demonstrating that the LysR-type transcriptional regulator (LTTR) StdR induces the expression of the stdA, which encodes a Txn-degrading enzyme, in the presence of Txn as a coinducer. Here we show that the bacterial StdR[Txn] -quenching regulatory system mimics the ToxR[Txn] -mediated biosynthetic regulation of B. glumae. Substrate specificity investigations revealed that Txn is the only coinducer of StdR and that StdA has a high degree of specificity for Txn. Rice plants expressing StdA showed Txn resistance. Collectively, bacteria mimic the mechanism of Txn biosynthesis regulation, employ it in the development of a Txn-quenching regulatory system and share it with neighbouring bacteria for survival in rice environments full of Txn.}, }
@article {pmid34009306, year = {2021}, author = {Brenner, AE and Muñoz-Leal, S and Sachan, M and Labruna, MB and Raghavan, R}, title = {Coxiella burnetii and Related Tick Endosymbionts Evolved from Pathogenic Ancestors.}, journal = {Genome biology and evolution}, volume = {13}, number = {7}, pages = {}, pmid = {34009306}, issn = {1759-6653}, support = {R03 AI123464/AI/NIAID NIH HHS/United States ; R03 AI133023/AI/NIAID NIH HHS/United States ; R15 AI126385/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Argasidae/microbiology ; Coxiella/genetics ; *Coxiella burnetii/genetics ; Symbiosis ; *Ticks ; }, abstract = {Both symbiotic and pathogenic bacteria in the family Coxiellaceae cause morbidity and mortality in humans and animals. For instance, Coxiella-like endosymbionts (CLEs) improve the reproductive success of ticks-a major disease vector, while Coxiella burnetii causes human Q fever, and uncharacterized coxiellae infect both animals and humans. To better understand the evolution of pathogenesis and symbiosis in this group of intracellular bacteria, we sequenced the genome of a CLE present in the soft tick Ornithodoros amblus (CLEOA) and compared it to the genomes of other bacteria in the order Legionellales. Our analyses confirmed that CLEOA is more closely related to C. burnetii, the human pathogen, than to CLEs in hard ticks, and showed that most clades of CLEs contain both endosymbionts and pathogens, indicating that several CLE lineages have evolved independently from pathogenic Coxiella. We also determined that the last common ancestorof CLEOA and C. burnetii was equipped to infect macrophages and that even though horizontal gene transfer (HGT) contributed significantly to the evolution of C. burnetii, most acquisition events occurred primarily in ancestors predating the CLEOA-C. burnetii divergence. These discoveries clarify the evolution of C. burnetii, which previously was assumed to have emerged when an avirulent tick endosymbiont recently gained virulence factors via HGT. Finally, we identified several metabolic pathways, including heme biosynthesis, that are likely critical to the intracellular growth of the human pathogen but not the tick symbiont, and show that the use of heme analog is a promising approach to controlling C. burnetii infections.}, }
@article {pmid34006663, year = {2021}, author = {Madacki, J and Orgeur, M and Mas Fiol, G and Frigui, W and Ma, L and Brosch, R}, title = {ESX-1-Independent Horizontal Gene Transfer by Mycobacterium tuberculosis Complex Strains.}, journal = {mBio}, volume = {12}, number = {3}, pages = {}, pmid = {34006663}, issn = {2150-7511}, mesh = {Antigens, Bacterial/*genetics ; Bacterial Proteins/*genetics ; Chromosomes/genetics ; Conjugation, Genetic ; DNA/*genetics ; *Evolution, Molecular ; *Gene Transfer Techniques ; Genome, Bacterial ; Mycobacterium tuberculosis/*genetics ; }, abstract = {Current models of horizontal gene transfer (HGT) in mycobacteria are based on "distributive conjugal transfer" (DCT), an HGT type described in the fast-growing, saprophytic model organism Mycobacterium smegmatis, which creates genome mosaicism in resulting strains and depends on an ESX-1 type VII secretion system. In contrast, only few data on interstrain DNA transfer are available for tuberculosis-causing mycobacteria, for which chromosomal DNA transfer between two Mycobacterium canettii strains was reported, a process which, however, was not observed for Mycobacterium tuberculosis strains. Here, we have studied a wide range of human- and animal-adapted members of the Mycobacterium tuberculosis complex (MTBC) using an optimized filter-based mating assay together with three selected strains of M. canettii that acted as DNA recipients. Unlike in previous approaches, we obtained a high yield of thousands of recombinants containing transferred chromosomal DNA fragments from various MTBC donor strains, as confirmed by whole-genome sequence analysis of 38 randomly selected clones. While the genome organizations of the obtained recombinants showed mosaicisms of donor DNA fragments randomly integrated into a recipient genome backbone, reminiscent of those described as being the result of ESX-1-mediated DCT in M. smegmatis, we observed similar transfer efficiencies when ESX-1-deficient donor and/or recipient mutants were used, arguing that in tubercle bacilli, HGT is an ESX-1-independent process. These findings provide new insights into the genetic events driving the pathoevolution of M. tuberculosis and radically change our perception of HGT in mycobacteria, particularly for those species that show recombinogenic population structures despite the natural absence of ESX-1 secretion systems.IMPORTANCE Data on the bacterial sex-mediated impact on mycobacterial evolution are limited. Hence, our results presented here are of importance as they clearly demonstrate the capacity of a wide range of human- and animal-adapted Mycobacterium tuberculosis complex (MTBC) strains to transfer chromosomal DNA to selected strains of Mycobacteriumcanettii Most interestingly, we found that interstrain DNA transfer among tubercle bacilli was not dependent on a functional ESX-1 type VII secretion system, as ESX-1 deletion mutants of potential donor and/or recipient strains yielded numbers of recombinants similar to those of their respective parental strains. These results argue that HGT in tubercle bacilli is organized in a way different from that of the most widely studied Mycobacterium smegmatis model, a finding that is also relevant beyond tubercle bacilli, given that many mycobacteria, like, for example, Mycobacterium avium or Mycobacterium abscessus, are naturally devoid of an ESX-1 secretion system but show recombinogenic, mosaic-like genomic population structures.}, }
@article {pmid34003286, year = {2021}, author = {Duan, B and Ding, P and Navarre, WW and Liu, J and Xia, B}, title = {Xenogeneic Silencing and Bacterial Genome Evolution: Mechanisms for DNA Recognition Imply Multifaceted Roles of Xenogeneic Silencers.}, journal = {Molecular biology and evolution}, volume = {38}, number = {10}, pages = {4135-4148}, pmid = {34003286}, issn = {1537-1719}, support = {PJT-156261//CIHR/Canada ; }, mesh = {*Bacterial Proteins/genetics ; DNA ; DNA, Bacterial ; *DNA-Binding Proteins/genetics ; Gene Silencing ; Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; }, abstract = {Horizontal gene transfer (HGT) is a major driving force for bacterial evolution. To avoid the deleterious effects due to the unregulated expression of newly acquired foreign genes, bacteria have evolved specific proteins named xenogeneic silencers to recognize foreign DNA sequences and suppress their transcription. As there is considerable diversity in genomic base compositions among bacteria, how xenogeneic silencers distinguish self- from nonself DNA in different bacteria remains poorly understood. This review summarizes the progress in studying the DNA binding preferences and the underlying molecular mechanisms of known xenogeneic silencer families, represented by H-NS of Escherichia coli, Lsr2 of Mycobacterium, MvaT of Pseudomonas, and Rok of Bacillus. Comparative analyses of the published data indicate that the differences in DNA recognition mechanisms enable these xenogeneic silencers to have clear characteristics in DNA sequence preferences, which are further correlated with different host genomic features. These correlations provide insights into the mechanisms of how these xenogeneic silencers selectively target foreign DNA in different genomic backgrounds. Furthermore, it is revealed that the genomic AT contents of bacterial species with the same xenogeneic silencer family proteins are distributed in a limited range and are generally lower than those species without any known xenogeneic silencers in the same phylum/class/genus, indicating that xenogeneic silencers have multifaceted roles on bacterial genome evolution. In addition to regulating horizontal gene transfer, xenogeneic silencers also act as a selective force against the GC to AT mutational bias found in bacterial genomes and help the host genomic AT contents maintained at relatively low levels.}, }
@article {pmid34000699, year = {2021}, author = {Hou, L and Wang, H and Chen, Q and Su, JQ and Gad, M and Li, J and Mulla, SI and Yu, CP and Hu, A}, title = {Fecal pollution mediates the dominance of stochastic assembly of antibiotic resistome in an urban lagoon (Yundang lagoon), China.}, journal = {Journal of hazardous materials}, volume = {417}, number = {}, pages = {126083}, doi = {10.1016/j.jhazmat.2021.126083}, pmid = {34000699}, issn = {1873-3336}, mesh = {*Anti-Bacterial Agents/pharmacology ; China ; Drug Resistance, Microbial/genetics ; Environmental Pollution ; *Genes, Bacterial ; }, abstract = {Sewage and fecal pollution cause antibiotic resistance genes (ARGs) pollution in urban lagoons. Seasonality also affects ARG dynamics. However, knowledge of factors controlling ARG community assembly across seasons is still limited. Here, we revealed the seasonal variation of ARGs and depict the underlying assembly processes and drivers via high-throughput quantitative PCR in an urban lagoon, China. A higher richness and abundance of ARGs were observed in summer and winter compared to spring and fall (Kruskal-Wallis test, P < 0.05). Both ARG and prokaryotic communities were mainly governed by stochastic processes, however, these processes drove ARGs and prokaryotes differently across seasons. Stochastic processes played a more dominant role in shaping ARG communities in summer (average stochasticity: 83%) and winter (75%), resulting in a stable antibiotic resistome. However, no such seasonal pattern of stochastic processes was determined for prokaryotes, indicating a decoupling of the assembly process of ARGs and prokaryotes. Moreover, fecal microorganisms (e.g., Bacteroidetes and Faecalibacterium) mediated the stochastic processes of ARG profiles, via enhancement of prokaryotic biomass and mobile genetic element abundances. The tnpA-07 transposase was the key for the horizontal gene transfer. These findings will enhance our understanding of how fecal pollution shapes ARG community assembly in urban lagoons.}, }
@article {pmid34000537, year = {2021}, author = {Yang, Y and Zhang, AN and Che, Y and Liu, L and Deng, Y and Zhang, T}, title = {Underrepresented high diversity of class 1 integrons in the environment uncovered by PacBio sequencing using a new primer.}, journal = {The Science of the total environment}, volume = {787}, number = {}, pages = {147611}, doi = {10.1016/j.scitotenv.2021.147611}, pmid = {34000537}, issn = {1879-1026}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Integrons/genetics ; Sewage ; Swine ; *Wastewater ; }, abstract = {Class 1 integrons (CL1s) are one of the major contributors to the horizontal transfer of antibiotic resistance genes (ARGs). However, our knowledge of CL1 in the environment is still very limited due to the limitations of the current PCR primers and the sequencing methods adopted. This study developed a new primer coupled with PacBio sequencing to investigate the underrepresented diversity of CL1s in a mixed environmental sample (i.e. activated sludge from wastewater treatment plant and pig feces from animal farm). The new primer successfully uncovered 20 extra ARGs subtypes and 57% (422/739) more unique integron array structures than the previous primers. Compared to the whole genome database, CL1s revealed in the environment in this study were of much greater diversity, having 93% (900/967) novel array structures. Antibiotic resistance is the predominant function (78.3% genes) carried by CL1, and a vast majority (98.6% genes) of them confer resistance to aminoglycoside, beta-lactam, trimethoprim, or chloramphenicol. Additionally, 78.5% unique CL1 arrays carried more than one ARGs, and 25.9% of them carried ARGs of clinical relevance with high transferability potential posing threat to the general public. Our results indicated the importance of CL1s in the spread of ARGs. Overall, combining PacBio sequencing with the new primer designed in this study largely broadened our knowledge of CL1s in the environment and their significance in the environmental proliferation of ARGs.}, }
@article {pmid33999798, year = {2021}, author = {Aslani, S and Kiaei, S and Afgar, A and Morones-Ramírez, JR and Aratboni, HA and Faridi, A and Rivera-Mackintosh, LR and Kalantar-Neyestanaki, D}, title = {Determination of incompatibility group plasmids and copy number of the bla NDM-1 gene in carbapenem-resistant Klebsiella pneumoniae strains recovered from different hospitals in Kerman, Iran.}, journal = {Journal of medical microbiology}, volume = {70}, number = {5}, pages = {}, doi = {10.1099/jmm.0.001361}, pmid = {33999798}, issn = {1473-5644}, mesh = {Anti-Bacterial Agents/*pharmacology ; Carbapenems/*pharmacology ; *Gene Dosage ; Humans ; Iran ; Klebsiella Infections/*microbiology ; Klebsiella pneumoniae/classification/*drug effects/*genetics ; Molecular Typing ; *Plasmids ; Random Amplified Polymorphic DNA Technique ; Replicon ; beta-Lactam Resistance ; beta-Lactamases/*genetics ; }, abstract = {Introduction. New Delhi metallo-β-lactamase (NDM)-producing Klebsiella pneumoniae has become a serious global health concern.Hypothesis/Gap Statement. Due to the high genetic diversity among NDM-positive K. pneumoniae, we need further surveillance and studies to better understand the relationships between them. In addition, the coexistence of several plasmid replicon types in NDM-positive K. pneumoniae may affect the copy number of bla NDM, the MIC level to antibiotics, as well as increasing the chance of horizontal gene transfer.Aim. The aim of this study was to determine incompatible plasmid groups and copy numbers of bla NDM, and to investigate the genetic relationship of 37 NDM-positive K. pneumoniae in Kerman, Iran.Methodology. The bla NDM-1 gene was detected and confirmed by PCR-sequencing. The plasmid replicon types were determined by PCR-based replicon typing (PBRT) and the copy number of bla NDM-1 was determined by quantitaive real time-PCR (qPCR). Random amplified polymorphic DNA (RAPD)-PCR typing was used to detect genetic relationships between the strains.Results. In this study, 10 different replicon types, including Frep [n=25 (67.5 %)], FIIAs [n=11 (29.7 %)], FIA [n=5 (13.5 %)], FIB [n=3 (8.1 %)], I1-Iγ [n=2 (5.4 %)], L/M [n=7 (18.9 %)], A/C [n=7 (18.9 %)], Y [n=3 (8.1 %)], P [n=1 (2.7 %)] and FIC [n=1 (2.7 %)] were reported. The copy numbers of the bla NDM-1 gene varied from 30.00 to 5.0×10[6] and no statistically significant correlation was observed between a rise of the MIC to imipenem and the copy numbers of bla NDM-1 (P>0.05). According to RAPD typing results, 35 strains were divided into five clusters, while two strains were non-typeable.Conclusion. The spread of NDM-1-producing K. pneumoniae strains that carry several plasmid replicon types increases the chance of horizontal transfer of antibiotic resistance genes in hospital settings. In this study, 10 different replicon types were identified. We could not find any relationship between the increase of MIC levels to imipenem and the copy numbers of bla NDM-1. Therefore, due to the identification of different replicon types in this study, the type and genetic characteristics of bla NDM-1-carrying plasmids, and other factors such as antibiotic selective pressure, probably affect the copy number of bla NDM-1 and change the MIC level to imipenem.}, }
@article {pmid33998119, year = {2021}, author = {Song, Y and Hervé, V and Radek, R and Pfeiffer, F and Zheng, H and Brune, A}, title = {Characterization and phylogenomic analysis of Breznakiella homolactica gen. nov. sp. nov. indicate that termite gut treponemes evolved from non-acetogenic spirochetes in cockroaches.}, journal = {Environmental microbiology}, volume = {23}, number = {8}, pages = {4228-4245}, doi = {10.1111/1462-2920.15600}, pmid = {33998119}, issn = {1462-2920}, mesh = {Animals ; *Cockroaches ; DNA, Bacterial ; *Isoptera ; Phylogeny ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; Spirochaetales ; Treponema/genetics ; }, abstract = {Spirochetes of the genus Treponema are surprisingly abundant in termite guts, where they play an important role in reductive acetogenesis. Although they occur in all termites investigated, their evolutionary origin is obscure. Here, we isolated the first representative of 'termite gut treponemes' from cockroaches, the closest relatives of termites. Phylogenomic analysis revealed that Breznakiella homolactica gen. nov. sp. nov. represents the most basal lineage of the highly diverse 'termite cluster I', a deep-branching sister group of Treponemataceae (fam. 'Termitinemataceae') that was present already in the cockroach ancestor of termites and subsequently coevolved with its host. Breznakiella homolactica is obligately anaerobic and catalyses the homolactic fermentation of both hexoses and pentoses. Resting cells produced acetate in the presence of oxygen. Genome analysis revealed the presence of pyruvate oxidase and catalase, and a cryptic potential for the formation of acetate, ethanol, formate, CO2 and H2 - the fermentation products of termite gut isolates. Genes encoding key enzymes of reductive acetogenesis, however, are absent, confirming the hypothesis that the ancestral metabolism of the cluster was fermentative, and that the capacity for acetogenesis from H2 plus CO2 - the most intriguing property among termite gut treponemes - was acquired by lateral gene transfer.}, }
@article {pmid33997299, year = {2021}, author = {Skilton, RJ and O'Neill, C and Thomson, NR and Lampe, DJ and Clarke, IN}, title = {Progress towards an inducible, replication-proficient transposon delivery vector for Chlamydia trachomatis.}, journal = {Wellcome open research}, volume = {6}, number = {}, pages = {82}, pmid = {33997299}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {Background Genetic systems have been developed for Chlamydia but the extremely low transformation frequency remains a significant bottleneck. Our goal is to develop a self-replicating transposon delivery vector for C. trachomatis which can be expanded prior to transposase induction. Methods We made E. coli/ C. trachomatis shuttle vectors bearing the Himar1 C9 transposase under control of the tet promoter and a novel rearrangement of the Himar1 transposon with the β-lactamase gene. Activity of the transposase was monitored by immunoblot and by DNA sequencing. Results We constructed pSW2-mCh-C9, a C. trachomatis plasmid designed to act as a self-replicating vector carrying both the Himar1 C9 transposase under tet promoter control and its transposon. However, we were unable to recover this plasmid in C. trachomatis following multiple attempts at transformation. Therefore, we assembled two new deletion plasmids pSW2-mCh-C9-ΔTpon carrying only the Himar1 C9 transposase (under tet promoter control) and a sister vector (same sequence backbone) pSW2-mCh-C9-ΔTpase carrying its cognate transposon. We demonstrated that the biological components that make up both pSW2-mCh-C9-ΔTpon and pSW2-mCh-C9-ΔTpase are active in E. coli. Both these plasmids could be independently recovered in C. trachomatis. We attempted to perform lateral gene transfer by transformation and mixed infection with C. trachomatis strains bearing pSW2-mCh-C9-ΔTpon and pSW2-RSGFP-Tpon (a green fluorescent version of pSW2-mCh-C9-ΔTpase). Despite success in achieving mixed infections, it was not possible to recover progeny bearing both versions of these plasmids. Conclusions We have designed a self-replicating plasmid vector pSW2-mCh-C9 for C. trachomatis carrying the Himar1 C9 transposase under tet promoter control. Whilst this can be transformed into E. coli it cannot be recovered in C. trachomatis. Based on selected deletions and phenotypic analyses we conclude that low level expression from the tet inducible promoter is responsible for premature transposition and hence plasmid loss early on in the transformation process.}, }
@article {pmid33994861, year = {2021}, author = {Li, Y and Li, X and Hao, Y and Liu, Y and Dong, Z and Li, K}, title = {Biological and Physiochemical Methods of Biofilm Adhesion Resistance Control of Medical-Context Surface.}, journal = {International journal of biological sciences}, volume = {17}, number = {7}, pages = {1769-1781}, pmid = {33994861}, issn = {1449-2288}, mesh = {Bacteria/genetics/*growth &amp; development ; Bacterial Adhesion/*genetics ; Bacterial Proteins/*genetics ; *Biofilms ; Humans ; Quorum Sensing/*genetics ; }, abstract = {The formation of biofilms on medical-context surfaces gives the EPS embedded bacterial community protection and additional advantages that planktonic cells would not have such as increased antibiotic resistance and horizontal gene transfer. Bacterial cells tend to attach to a conditioning layer after overcoming possible electrical barriers and go through two phases of attachments: reversible and irreversible. In the first, bacterial attachment to the surface is reversible and occurs quickly whilst the latter is permanent and takes place over a longer period of time. Upon reaching a certain density in the bacterial community, quorum sensing causes phenotypical changes leading to a loss in motility and the production of EPS. This position paper seeks to address the problem of bacterial adhesion and biofilm formation for the medical surfaces by comparing inhabiting physicochemical interactions and biological mechanisms. Several physiochemical methodologies (e.g. ultrasonication, alternating magnetic field and chemical surface coating) and utilizing biological mechanisms (e.g. quorum quenching and EPS degrading enzymes) were suggested. The possible strategical applications of each category were suggested and evaluated to a balanced position to possibly eliminate the adhesion and formation of biofilms on medical-context surfaces.}, }
@article {pmid33990913, year = {2021}, author = {Li, Z and Song, Q and Wang, M and Ren, J and Liu, S and Zhao, S}, title = {Comparative genomics analysis of Pediococcus acidilactici species.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {59}, number = {6}, pages = {573-583}, pmid = {33990913}, issn = {1976-3794}, mesh = {Anti-Bacterial Agents/biosynthesis ; Bacteriocins/biosynthesis ; *Genome, Bacterial ; Genomics ; Pediococcus acidilactici/classification/*genetics/metabolism ; }, abstract = {Pediococcus acidilactici is a reliable bacteriocin producer and a promising probiotic species with wide application in the food and health industry. However, the underlying genetic features of this species have not been analyzed. In this study, we performed a comprehensive comparative genomic analysis of 41 P. acidilactici strains from various ecological niches. The bacteriocin production of 41 strains were predicted and three kinds of bacteriocin encoding genes were identified in 11 P. acidilactici strains, namely pediocin PA-1, enterolysin A, and colicin-B. Moreover, whole-genome analysis showed a high genetic diversity within the population, mainly related to a large proportion of variable genomes, mobile elements, and hypothetical genes obtained through horizontal gene transfer. In addition, comparative genomics also facilitated the genetic explanation of the adaptation for host environment, which specify the protection mechanism against the invasion of foreign DNA (i.e. CRISPR/Cas locus), as well as carbohydrate fermentation. The 41 strains of P. acidilactici can metabolize a variety of carbon sources, which enhances the adaptability of this species and survival in different environments. This study evaluated the antibacterial ability, genome evolution, and ecological flexibility of P. acidilactici from the perspective of genetics and provides strong supporting evidence for its industrial development and application.}, }
@article {pmid33990706, year = {2021}, author = {Tao, J and Wang, S and Liao, T and Luo, H}, title = {Evolutionary origin and ecological implication of a unique nif island in free-living Bradyrhizobium lineages.}, journal = {The ISME journal}, volume = {15}, number = {11}, pages = {3195-3206}, pmid = {33990706}, issn = {1751-7370}, mesh = {*Bradyrhizobium/genetics ; DNA, Bacterial ; *Fabaceae ; Nitrogen Fixation ; Phylogeny ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {The alphaproteobacterial genus Bradyrhizobium has been best known as N2-fixing members that nodulate legumes, supported by the nif and nod gene clusters. Recent environmental surveys show that Bradyrhizobium represents one of the most abundant free-living bacterial lineages in the world's soils. However, our understanding of Bradyrhizobium comes largely from symbiotic members, biasing the current knowledge of their ecology and evolution. Here, we report the genomes of 88 Bradyrhizobium strains derived from diverse soil samples, including both nif-carrying and non-nif-carrying free-living (nod free) members. Phylogenomic analyses of these and 252 publicly available Bradyrhizobium genomes indicate that nif-carrying free-living members independently evolved from symbiotic ancestors (carrying both nif and nod) multiple times. Intriguingly, the nif phylogeny shows that the vast majority of nif-carrying free-living members comprise an independent cluster, indicating that horizontal gene transfer promotes nif expansion among the free-living Bradyrhizobium. Comparative genomics analysis identifies that the nif genes found in free-living Bradyrhizobium are located on a unique genomic island of ~50 kb equipped with genes potentially involved in coping with oxygen tension. We further analyze amplicon sequencing data to show that Bradyrhizobium members presumably carrying this nif island are widespread in a variety of environments. Given the dominance of Bradyrhizobium in world's soils, our findings have implications for global nitrogen cycles and agricultural research.}, }
@article {pmid33990313, year = {2021}, author = {Ma, L and Konkel, ME and Lu, X}, title = {Antimicrobial Resistance Gene Transfer from Campylobacter jejuni in Mono- and Dual-Species Biofilms.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {15}, pages = {e0065921}, pmid = {33990313}, issn = {1098-5336}, mesh = {*Biofilms ; Campylobacter jejuni/*genetics/physiology ; DNA, Bacterial ; Drug Resistance, Bacterial/*genetics ; *Gene Transfer, Horizontal ; }, abstract = {Horizontal gene transfer (HGT) is a driving force for the dissemination of antimicrobial resistance (AMR) genes among Campylobacter jejuni organisms, a leading cause of foodborne gastroenteritis worldwide. Although HGT is well documented for C. jejuni planktonic cells, the role of C. jejuni biofilms in AMR spread that likely occurs in the environment is poorly understood. Here, we developed a cocultivation model to investigate the HGT of chromosomally encoded AMR genes between two C. jejuni F38011 AMR mutants in biofilms. Compared to planktonic cells, C. jejuni biofilms significantly promoted HGT (P < 0.05), resulting in an increase of HGT frequencies by up to 17.5-fold. Dynamic study revealed that HGT in biofilms increased at the early stage (i.e., from 24 h to 48 h) and remained stable during 48 to 72 h. Biofilms continuously released the HGT mutants into supernatant culture, indicating spontaneous dissemination of AMR to broader niches. DNase I treatment confirmed the role of natural transformation in genetic exchange. HGT was not associated with biofilm biomass, cell density, or bacterial metabolic activity, whereas the presence of extracellular DNA was negatively correlated with the altered HGT frequencies. HGT in biofilms also had a strain-to-strain variation. A synergistic HGT effect was observed between C. jejuni with different genomic backgrounds (i.e., C. jejuni NCTC 11168 chloramphenicol-resistant strain and F38011 kanamycin-resistant strain). C. jejuni performed HGT at the frequency of 10[-7] in Escherichia coli-C. jejuni biofilms, while HGT was not detectable in Salmonella enterica-C. jejuni biofilms. IMPORTANCE Antimicrobial-resistant C. jejuni has been listed as a high priority of public health concern worldwide. To tackle the rapid evolution of AMR in C. jejuni, it is of great importance to understand the extent and characteristics of HGT in C. jejuni biofilms, which serve as the main survival strategy of this microbe in the farm-to-table continuum. In this study, we demonstrated that biofilms significantly enhanced HGT compared to the planktonic state (P < 0.05). Biofilm cultivation time and extracellular DNA (eDNA) amount were related to varied HGT frequencies. C. jejuni could spread AMR genes in both monospecies and dual-species biofilms, mimicking the survival mode of C. jejuni in food chains. These findings indicated that the risk and extent of AMR transmission among C. jejuni organisms have been underestimated, as previous HGT studies mainly focused on the planktonic state. Future AMR controlling measures can target biofilms and their main component eDNA.}, }
@article {pmid33989454, year = {2021}, author = {Sutherland, KM and Ward, LM and Colombero, CR and Johnston, DT}, title = {Inter-domain horizontal gene transfer of nickel-binding superoxide dismutase.}, journal = {Geobiology}, volume = {19}, number = {5}, pages = {450-459}, doi = {10.1111/gbi.12448}, pmid = {33989454}, issn = {1472-4669}, mesh = {Amino Acid Sequence ; Archaea/*genetics ; Bacteria/*genetics ; *Gene Transfer, Horizontal ; *Nickel ; Phylogeny ; *Superoxide Dismutase/genetics/metabolism ; }, abstract = {The ability of aerobic microorganisms to regulate internal and external concentrations of the reactive oxygen species (ROS) superoxide directly influences the health and viability of cells. Superoxide dismutases (SODs) are the primary regulatory enzymes that are used by microorganisms to degrade superoxide. SOD is not one, but three separate, non-homologous enzymes that perform the same function. Thus, the evolutionary history of genes encoding for different SOD enzymes is one of convergent evolution, which reflects environmental selection brought about by an oxygenated atmosphere, changes in metal availability, and opportunistic horizontal gene transfer (HGT). In this study, we examine the phylogenetic history of the protein sequence encoding for the nickel-binding metalloform of the SOD enzyme (SodN). The genomic potential to produce SodN is widespread among bacteria, including Actinobacteriota (Actinobacteria), Chloroflexota (Chloroflexi), Cyanobacteria, Proteobacteria, Patescibacteria, and others. The gene is also present in many archaea, with Thermoplasmatota and Nanoarchaeota representing the vast majority of archaeal sodN diversity. A comparison of organismal and SodN protein phylogenetic trees reveals several instances of HGT, including multiple inter-domain transfers of the sodN gene from the bacterial domain to the archaeal domain. Nearly half of the archaeal members with sodN live in the photic zone of the marine water column. The sodN gene is widespread and characterized by apparent vertical gene transfer in some sediment- or soil-associated lineages within the Actinobacteriota and Chloroflexota phyla, suggesting the ancestral sodN likely originated in one of these clades before expanding its taxonomic and biogeographic distribution to additional microbial groups in the surface ocean in response to decreasing iron availability. In addition to decreasing iron quotas, nickel-binding SOD has the added benefit of withstanding high reactant and product ROS concentrations without damaging the enzyme, making it particularly well suited for the modern surface ocean.}, }
@article {pmid33984352, year = {2021}, author = {Blath, J and Tóbiás, A}, title = {The interplay of dormancy and transfer in bacterial populations: Invasion, fixation and coexistence regimes.}, journal = {Theoretical population biology}, volume = {139}, number = {}, pages = {18-49}, doi = {10.1016/j.tpb.2021.05.001}, pmid = {33984352}, issn = {1096-0325}, mesh = {*Bacteria ; *Gene Transfer, Horizontal ; Humans ; Models, Biological ; Phenotype ; Population Dynamics ; Probability ; }, abstract = {In this paper we investigate the interplay between two fundamental mechanisms of microbial population dynamics and evolution, namely dormancy and horizontal gene transfer. The corresponding traits come in many guises and are ubiquitous in microbial communities, affecting their dynamics in important ways. Recently, they have each moved (separately) into the focus of stochastic individual-based modelling (Billiard et al. 2016, 2018; Champagnat, Méléard and Tran, 2021; Blath and Tóbiás 2020). Here, we investigate their combined effects in a unified model. Indeed, we consider the (idealized) scenario of two sub-populations, respectively carrying 'trait 1' and 'trait 2', where trait 1 individuals are able to switch (under competitive pressure) into a dormant state, and trait 2 individuals are able to execute horizontal gene transfer, which in our case means that they can turn trait 1 individuals into trait 2 ones, at a rate depending on the density of individuals. In the large-population limit, we examine the fate of (i) a single trait 2 individual (called 'mutant') arriving in a trait 1 resident population living in equilibrium, and (ii) a trait 1 individual ('mutant') arriving in a trait 2 resident population. We analyse the invasion dynamics in all cases where the resident population is individually fit and the behaviour of the mutant population is initially non-critical. This leads to the identification of parameter regimes for the invasion and fixation of the new trait, stable coexistence of the two traits, and 'founder control' (where the initial resident always dominates, irrespective of its trait). One of our key findings is that horizontal transfer can lead to stable coexistence even if trait 2 is unfit on its own. In the case of founder control, the limiting dynamical system also exhibits a coexistence equilibrium, which, however, is unstable, and with overwhelming probability none of the mutant sub-populations is able to invade. In all cases, we observe the classical (up to three) phases of invasion dynamics à la Champagnat (2006).}, }
@article {pmid33980677, year = {2021}, author = {Fišarová, L and Botka, T and Du, X and Mašlaňová, I and Bárdy, P and Pantůček, R and Benešík, M and Roudnický, P and Winstel, V and Larsen, J and Rosenstein, R and Peschel, A and Doškař, J}, title = {Staphylococcus epidermidis Phages Transduce Antimicrobial Resistance Plasmids and Mobilize Chromosomal Islands.}, journal = {mSphere}, volume = {6}, number = {3}, pages = {}, pmid = {33980677}, issn = {2379-5042}, mesh = {Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Bacterial/*genetics ; Genomic Islands/*genetics ; Humans ; Plasmids/*genetics ; Staphylococcal Infections/microbiology ; Staphylococcus Phages/classification/drug effects/*genetics ; Staphylococcus epidermidis/*drug effects/*virology ; *Transduction, Genetic ; Virulence ; }, abstract = {Staphylococcus epidermidis is a leading opportunistic pathogen causing nosocomial infections that is notable for its ability to form a biofilm and for its high rates of antibiotic resistance. It serves as a reservoir of multiple antimicrobial resistance genes that spread among the staphylococcal population by horizontal gene transfer such as transduction. While phage-mediated transduction is well studied in Staphylococcus aureus, S. epidermidis transducing phages have not been described in detail yet. Here, we report the characteristics of four phages, 27, 48, 456, and 459, previously used for S. epidermidis phage typing, and the newly isolated phage E72, from a clinical S. epidermidis strain. The phages, classified in the family Siphoviridae and genus Phietavirus, exhibited an S. epidermidis-specific host range, and together they infected 49% of the 35 strains tested. A whole-genome comparison revealed evolutionary relatedness to transducing S. aureus phietaviruses. In accordance with this, all the tested phages were capable of transduction with high frequencies up to 10[-4] among S. epidermidis strains from different clonal complexes. Plasmids with sizes from 4 to 19 kb encoding resistance to streptomycin, tetracycline, and chloramphenicol were transferred. We provide here the first evidence of a phage-inducible chromosomal island transfer in S. epidermidis Similarly to S. aureus pathogenicity islands, the transfer was accompanied by phage capsid remodeling; however, the interfering protein encoded by the island was distinct. Our findings underline the role of S. epidermidis temperate phages in the evolution of S. epidermidis strains by horizontal gene transfer, which can also be utilized for S. epidermidis genetic studies.IMPORTANCE Multidrug-resistant strains of S. epidermidis emerge in both nosocomial and livestock environments as the most important pathogens among coagulase-negative staphylococcal species. The study of transduction by phages is essential to understanding how virulence and antimicrobial resistance genes spread in originally commensal bacterial populations. In this work, we provide a detailed description of transducing S. epidermidis phages. The high transduction frequencies of antimicrobial resistance plasmids and the first evidence of chromosomal island transfer emphasize the decisive role of S. epidermidis phages in attaining a higher pathogenic potential of host strains. To date, such importance has been attributed only to S. aureus phages, not to those of coagulase-negative staphylococci. This study also proved that the described transducing bacteriophages represent valuable genetic modification tools in S. epidermidis strains where other methods for gene transfer fail.}, }
@article {pmid33977463, year = {2021}, author = {Blanco-Nistal, MM and Fernández-Fernández, JA}, title = {Antibiotics Therapy in the Multi-Resistant Patient.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2296}, number = {}, pages = {423-439}, pmid = {33977463}, issn = {1940-6029}, mesh = {Anti-Bacterial Agents/*therapeutic use ; Bacteria/drug effects ; Drug Resistance, Multiple, Bacterial/*drug effects ; Humans ; Microbial Sensitivity Tests/methods ; }, abstract = {Antibiotic resistance is not only a European or American problem: it is a global crisis. The emergence of resistance to multiple antimicrobial agents has become a major threat to public health. The main objective of the institution's antimicrobial policy is to adapt the effective treatment to each patient, with a minimum of complications, avoid adverse reactions, control the development and spread of strains of resistant microorganisms as well as reduce hospital costs whenever possible. World Health Organization published a global list of priority pathogens of antibiotic-resistant bacteria to help prioritize research and development of new and effective antibiotic treatments. We must take into account the risk factors related to multiresistance, as well as factors that favor horizontal and vertical transmission. The need to prioritize implementation of these global strategies is complex and involves a lot of effort and valuable time; this point favors the rapid development resistance.}, }
@article {pmid33976161, year = {2021}, author = {Alonso-Del Valle, A and León-Sampedro, R and Rodríguez-Beltrán, J and DelaFuente, J and Hernández-García, M and Ruiz-Garbajosa, P and Cantón, R and Peña-Miller, R and San Millán, A}, title = {Variability of plasmid fitness effects contributes to plasmid persistence in bacterial communities.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {2653}, pmid = {33976161}, issn = {2041-1723}, support = {/WT_/Wellcome Trust/United Kingdom ; 203141/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Algorithms ; Anti-Bacterial Agents/pharmacology ; Bacteria/classification/*genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Enterobacteriaceae/classification/genetics ; Gastrointestinal Microbiome/genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; *Genetic Variation ; Genome, Bacterial/*genetics ; Humans ; Microbiota/genetics ; Phylogeny ; Plasmids/*genetics ; Species Specificity ; }, abstract = {Plasmid persistence in bacterial populations is strongly influenced by the fitness effects associated with plasmid carriage. However, plasmid fitness effects in wild-type bacterial hosts remain largely unexplored. In this study, we determined the fitness effects of the major antibiotic resistance plasmid pOXA-48_K8 in wild-type, ecologically compatible enterobacterial isolates from the human gut microbiota. Our results show that although pOXA-48_K8 produced an overall reduction in bacterial fitness, it produced small effects in most bacterial hosts, and even beneficial effects in several isolates. Moreover, genomic results showed a link between pOXA-48_K8 fitness effects and bacterial phylogeny, helping to explain plasmid epidemiology. Incorporating our fitness results into a simple population dynamics model revealed a new set of conditions for plasmid stability in bacterial communities, with plasmid persistence increasing with bacterial diversity and becoming less dependent on conjugation. These results help to explain the high prevalence of plasmids in the greatly diverse natural microbial communities.}, }
@article {pmid33975933, year = {2021}, author = {Carrilero, L and Kottara, A and Guymer, D and Harrison, E and Hall, JPJ and Brockhurst, MA}, title = {Positive Selection Inhibits Plasmid Coexistence in Bacterial Genomes.}, journal = {mBio}, volume = {12}, number = {3}, pages = {}, pmid = {33975933}, issn = {2150-7511}, support = {BB/R006253/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Adaptation, Physiological/genetics ; Bacteria/*genetics ; *Genetic Fitness ; *Genome, Bacterial ; Phenotype ; Plasmids/*genetics ; *Selection, Genetic ; }, abstract = {Plasmids play an important role in bacterial evolution by transferring niche-adaptive functional genes between lineages, thus driving genomic diversification. Bacterial genomes commonly contain multiple, coexisting plasmid replicons, which could fuel adaptation by increasing the range of gene functions available to selection and allowing their recombination. However, plasmid coexistence is difficult to explain because the acquisition of plasmids typically incurs high fitness costs for the host cell. Here, we show that plasmid coexistence was stably maintained without positive selection for plasmid-borne gene functions and was associated with compensatory evolution to reduce fitness costs. In contrast, with positive selection, plasmid coexistence was unstable despite compensatory evolution. Positive selection discriminated between differential fitness benefits of functionally redundant plasmid replicons, retaining only the more beneficial plasmid. These data suggest that while the efficiency of negative selection against plasmid fitness costs declines over time due to compensatory evolution, positive selection to maximize plasmid-derived fitness benefits remains efficient. Our findings help to explain the forces structuring bacterial genomes: coexistence of multiple plasmids in a genome is likely to require either rare positive selection in nature or nonredundancy of accessory gene functions among the coexisting plasmids.IMPORTANCE Bacterial genomes often contain multiple coexisting plasmids that provide important functions like antibiotic resistance. Using lab experiments, we show that such plasmid coexistence within a genome is stable only in environments where the function they encode is useless but is unstable if the function is useful and beneficial for bacterial fitness. Where competing plasmids perform the same useful function, only the most beneficial plasmid is kept by the cell, a process that is similar to competitive exclusion in ecological communities. This process helps explain how bacterial genomes are structured: bacterial genomes expand in size by acquiring multiple plasmids when selection is relaxed but subsequently contract during periods of strong selection for the useful plasmid-encoded function.}, }
@article {pmid33974066, year = {2021}, author = {Blanquart, S and Groussin, M and Le Roy, A and Szöllosi, GJ and Girard, E and Franzetti, B and Gouy, M and Madern, D}, title = {Resurrection of Ancestral Malate Dehydrogenases Reveals the Evolutionary History of Halobacterial Proteins: Deciphering Gene Trajectories and Changes in Biochemical Properties.}, journal = {Molecular biology and evolution}, volume = {38}, number = {9}, pages = {3754-3774}, pmid = {33974066}, issn = {1537-1719}, mesh = {*Euryarchaeota ; Halobacterium ; Malates ; Phylogeny ; Proteomics ; }, abstract = {Extreme halophilic Archaea thrive in high salt, where, through proteomic adaptation, they cope with the strong osmolarity and extreme ionic conditions of their environment. In spite of wide fundamental interest, however, studies providing insights into this adaptation are scarce, because of practical difficulties inherent to the purification and characterization of halophilic enzymes. In this work, we describe the evolutionary history of malate dehydrogenases (MalDH) within Halobacteria (a class of the Euryarchaeota phylum). We resurrected nine ancestors along the inferred halobacterial MalDH phylogeny, including the Last Common Ancestral MalDH of Halobacteria (LCAHa) and compared their biochemical properties with those of five modern halobacterial MalDHs. We monitored the stability of these various MalDHs, their oligomeric states and enzymatic properties, as a function of concentration for different salts in the solvent. We found that a variety of evolutionary processes, such as amino acid replacement, gene duplication, loss of MalDH gene and replacement owing to horizontal transfer resulted in significant differences in solubility, stability and catalytic properties between these enzymes in the three Halobacteriales, Haloferacales, and Natrialbales orders since the LCAHa MalDH. We also showed how a stability trade-off might favor the emergence of new properties during adaptation to diverse environmental conditions. Altogether, our results suggest a new view of halophilic protein adaptation in Archaea.}, }
@article {pmid33971069, year = {2021}, author = {Tamilmaran, N and Sankaranarayanan, R and Selvakumar A S, P and Munavar, MH}, title = {Horizontal transfer of domains in ssrA gene among Enterobacteriaceae.}, journal = {Genes to cells : devoted to molecular &amp; cellular mechanisms}, volume = {26}, number = {7}, pages = {541-550}, doi = {10.1111/gtc.12869}, pmid = {33971069}, issn = {1365-2443}, mesh = {Enterobacteriaceae/*genetics ; *Gene Transfer, Horizontal ; Nucleotide Motifs ; RNA, Transfer/genetics ; Recombination, Genetic ; }, abstract = {The tmRNA (transfer messenger RNA), encoded by ssrA gene, is involved in rescuing of stalled ribosomes by a process called trans-translation. Additionally, regions of the ssrA gene (coding for tmRNA) were reported to serve as integration sites for various bacteriophages. Though variations in ssrA genes were reported, their functional relevance is less studied. In this study, we investigated the horizontal gene transfer (HGT) of ssrA among the members of Enterobacteriaceae. This was done by predicting recombination signals in ssrA gene (belonging to Enterobacteriaceae) using RDP5 (Recombination Detection Program 5). Our results revealed 7 recombination signals in ssrA gene belonging to different species. We further showed that the recombination signals were more in the domains present in the 3' end than 5' end of tmRNA. Of note, the mRNA region was reported in many recombination signals. Further, members belonging to genera Yersinia, Erwinia, Dickeya and Enterobacter were highly represented in the recombination signals. Sequence analysis revealed the presence of integration sites for different class of bacteriophages in ssrA gene. The locations of phage recognition sites are comparable with recombination signals. Taken together, our results revealed a diverse nature of HGT and recombination which possibly due to transduction mediated by phages.}, }
@article {pmid33967971, year = {2021}, author = {Law, A and Solano, O and Brown, CJ and Hunter, SS and Fagnan, M and Top, EM and Stalder, T}, title = {Biosolids as a Source of Antibiotic Resistance Plasmids for Commensal and Pathogenic Bacteria.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {606409}, pmid = {33967971}, issn = {1664-302X}, support = {P20 GM103408/GM/NIGMS NIH HHS/United States ; P30 GM103324/GM/NIGMS NIH HHS/United States ; }, abstract = {Antibiotic resistance (AR) is a threat to modern medicine, and plasmids are driving the global spread of AR by horizontal gene transfer across microbiomes and environments. Determining the mobile resistome responsible for this spread of AR among environments is essential in our efforts to attenuate the current crisis. Biosolids are a wastewater treatment plant (WWTP) byproduct used globally as fertilizer in agriculture. Here, we investigated the mobile resistome of biosolids that are used as fertilizer. This was done by capturing resistance plasmids that can transfer to human pathogens and commensal bacteria. We used a higher-throughput version of the exogenous plasmid isolation approach by mixing several ESKAPE pathogens and a commensal Escherichia coli with biosolids and screening for newly acquired resistance to about 10 antibiotics in these strains. Six unique resistance plasmids transferred to Salmonella typhimurium, Klebsiella aerogenes, and E. coli. All the plasmids were self-transferable and carried 3-6 antibiotic resistance genes (ARG) conferring resistance to 2-4 antibiotic classes. These plasmids-borne resistance genes were further embedded in genetic elements promoting intracellular recombination (i.e., transposons or class 1 integrons). The plasmids belonged to the broad-host-range plasmid (BHR) groups IncP-1 or PromA. Several of them were persistent in their new hosts when grown in the absence of antibiotics, suggesting that the newly acquired drug resistance traits would be sustained over time. This study highlights the role of BHRs in the spread of ARG between environmental bacteria and human pathogens and commensals, where they may persist. The work further emphasizes biosolids as potential vehicles of highly mobile plasmid-borne antibiotic resistance genes.}, }
@article {pmid33965817, year = {2021}, author = {V M Starling, MC and Mendonça Neto, RP and Pires, GFF and Vilela, PB and Amorim, CC}, title = {Combat of antimicrobial resistance in municipal wastewater treatment plant effluent via solar advanced oxidation processes: Achievements and perspectives.}, journal = {The Science of the total environment}, volume = {786}, number = {}, pages = {147448}, doi = {10.1016/j.scitotenv.2021.147448}, pmid = {33965817}, issn = {1879-1026}, mesh = {Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; Hydrogen Peroxide ; Wastewater ; *Water Purification ; }, abstract = {This review aims to gather main achievements and limitations associated to the application of solar photocatalytic processes with regard to the removal of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) from municipal wastewater treatment plant effluent (MWWTPE). Solar photocatalytic processes were chosen considering the context of developing tropical countries. Among these processes, solar photo-Fenton has been proved effective for the elimination of ARB from MWWTPE at neutral pH in bench and pilot scale and also under continuous flow. Yet, ARG removal varies as according to the gene. Irradiation intensity and matrix composition play a key role on treatment efficiency for this purpose. The use of sulfate radical in modified solar photo-Fenton is still incipient for ARB and ARG removal. Also, investigations related to ARB resistance profile and horizontal gene transfer rates after solar photo-Fenton treatment must be further analyzed. Regarding solar heterogeneous photocatalysis, TiO2 and TiO2-composites applied in suspension are the most commonly investigated for the removal of ARB and ARGs. Irradiation intensity, temperature and catalyst dosage affect treatment efficiency. However, most studies were performed in synthetic solutions using reduced sample volumes. Extended exposition times and addition of H2O2 to the system (solar/TiO2/H2O2) are required to prevent bacteria regrowth and ensure ARG abatement. In addition, enhancement of TiO2 with graphene or (semi)metals improved ARB elimination. Differences concerning irradiation intensity, matrix composition, catalyst dosage, and model ARB and ARGs used in studies analyzed in this review hinder the comparison of photocatalysts synthesized by various research groups. Finally, future research should aim at evaluating the efficiency of solar photocatalytic processes in real matrices originated from sewage treatment systems applied in developing countries; determining indicators of antimicrobial resistance in MWWTPE; and investigating ARB mutation rate as well as the removal of cell-free ARGs present in suspension in MWWTPE.}, }
@article {pmid33964159, year = {2021}, author = {Park, M and Christin, PA and Bennetzen, JL}, title = {Sample Sequence Analysis Uncovers Recurrent Horizontal Transfers of Transposable Elements among Grasses.}, journal = {Molecular biology and evolution}, volume = {38}, number = {9}, pages = {3664-3675}, pmid = {33964159}, issn = {1537-1719}, mesh = {*DNA Transposable Elements/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Oryza/genetics ; Poaceae/genetics ; Sequence Analysis ; }, abstract = {Limited genome resources are a bottleneck in the study of horizontal transfer (HT) of DNA in plants. To solve this issue, we tested the usefulness of low-depth sequencing data generated from 19 previously uncharacterized panicoid grasses for HT investigation. We initially searched for horizontally transferred LTR-retrotransposons by comparing the 19 sample sequences to 115 angiosperm genome sequences. Frequent HTs of LTR-retrotransposons were identified solely between panicoids and rice (Oryza sativa). We consequently focused on additional Oryza species and conducted a nontargeted investigation of HT involving the panicoid genus Echinochloa, which showed the most HTs in the first set of analyses. The comparison of nine Echinochloa samples and ten Oryza species identified recurrent HTs of diverse transposable element (TE) types at different points in Oryza history, but no confirmed cases of HT for sequences other than TEs. One case of HT was observed from one Echinochloa species into one Oryza species with overlapping geographic distributions. Variation among species and data sets highlights difficulties in identifying all HT, but our investigations showed that sample sequence analyses can reveal the importance of HT for the diversification of the TE repertoire of plants.}, }
@article {pmid33962978, year = {2021}, author = {Zou, B and Huang, Y and Zhang, PP and Ding, XM and Op den Camp, HJM and Quan, ZX}, title = {Horizontal Gene Transfer of Genes Encoding Copper-Containing Membrane-Bound Monooxygenase (CuMMO) and Soluble Di-iron Monooxygenase (SDIMO) in Ethane- and Propane-Oxidizing Rhodococcus Bacteria.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {14}, pages = {e0022721}, pmid = {33962978}, issn = {1098-5336}, mesh = {Bacterial Proteins/*genetics ; Ethane/metabolism ; Gene Transfer, Horizontal ; Genes, Bacterial ; Mixed Function Oxygenases/*genetics ; Oxidation-Reduction ; Plasmids ; Propane/metabolism ; Rhodococcus/*genetics/metabolism ; }, abstract = {The families of copper-containing membrane-bound monooxygenases (CuMMOs) and soluble di-iron monooxygenases (SDIMOs) are involved not only in methane oxidation but also in short-chain alkane oxidation. Here, we describe Rhodococcus sp. strain ZPP, a bacterium able to grow with ethane or propane as the sole carbon and energy source, and report on the horizontal gene transfer (HGT) of actinobacterial hydrocarbon monooxygenases (HMOs) of the CuMMO family and the sMMO (soluble methane monooxygenase)-like SDIMO in the genus Rhodococcus. The key function of HMO in strain ZPP for propane oxidation was verified by allylthiourea inhibition. The HMO genes (designated hmoCAB) and those encoding sMMO-like SDIMO (designated smoXYB1C1Z) are located on a linear megaplasmid (pRZP1) of strain ZPP. Comparative genomic analysis of similar plasmids indicated the mobility of these plasmids within the genus Rhodococcus. The plasmid pRZP1 in strain ZPP could be conjugatively transferred to a recipient Rhodococcus erythropolis strain in a mating experiment and showed similar ethane- and propane-consuming activities. Finally, our findings demonstrate that the horizontal transfer of plasmid-based CuMMO and SDIMO genes confers the ability to use ethane and propane on the recipient. IMPORTANCE CuMMOs and SDIMOs initiate the aerobic oxidation of alkanes in bacteria. Here, the supposition that horizontally transferred plasmid-based CuMMO and SDIMO genes confer on the recipient similar abilities to use ethane and propane was proposed and confirmed in Rhodococcus. This study is a living example of HGT of CuMMOs and SDIMOs and outlines the plasmid-borne properties responsible for gaseous alkane degradation. Our results indicate that plasmids can support the rapid evolution of enzyme-mediated biogeochemical processes.}, }
@article {pmid33961980, year = {2021}, author = {Buzzanca, D and Botta, C and Ferrocino, I and Alessandria, V and Houf, K and Rantsiou, K}, title = {Functional pangenome analysis reveals high virulence plasticity of Aliarcobacter butzleri and affinity to human mucus.}, journal = {Genomics}, volume = {113}, number = {4}, pages = {2065-2076}, doi = {10.1016/j.ygeno.2021.05.001}, pmid = {33961980}, issn = {1089-8646}, mesh = {Animals ; *Arcobacter/genetics ; Genome, Bacterial ; Genomics ; Humans ; Mucus ; Phylogeny ; Swine ; Virulence/genetics ; Virulence Factors/genetics ; }, abstract = {Aliarcobacter butzleri is an emerging pathogen that may cause enteritis in humans, however, the incidence of disease caused by this member of the Campylobacteriaceae family is still underestimated. Furthermore, little is known about the precise virulence mechanism and behavior during infection. Therefore, in the present study, through complementary use of comparative genomics and physiological tests on human gut models, we sought to elucidate the genetic background of a set of 32 A. butzleri strains of diverse origin and to explore the correlation with the ability to colonize and invade human intestinal cells in vitro. The simulated infection of human intestinal models showed a higher colonization rate in presence of mucus-producing cells. For some strains, human mucus significantly improved the resistance to physical removal from the in vitro mucosa, while short time-frame growth was even observed. Pangenome analysis highlighted a hypervariable accessory genome, not strictly correlated to the isolation source. Likewise, the strain phylogeny was unrelated to their shared origin, despite a certain degree of segregation was observed among strains isolated from different segments of the intestinal tract of pigs. The putative virulence genes detected in all strains were mostly encompassed in the accessory fraction of the pangenome. The LPS biosynthesis and in particular the chain glycosylation of the O-antigen is harbored in a region of high plasticity of the pangenome, which would indicate frequent horizontal gene transfer phenomena, as well as the involvement of this hypervariable structure in the adaptive behavior and sympatric evolution of A. butzleri. Results of the present study deepen the current knowledge on A. butzleri pangenome by extending the pool of genes regarded as virulence markers and provide bases to develop new diagnostic approaches for the detection of those strains with a higher virulence potential.}, }
@article {pmid33959112, year = {2021}, author = {Hickman, RA and Leangapichart, T and Lunha, K and Jiwakanon, J and Angkititrakul, S and Magnusson, U and Sunde, M and Järhult, JD}, title = {Exploring the Antibiotic Resistance Burden in Livestock, Livestock Handlers and Their Non-Livestock Handling Contacts: A One Health Perspective.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {651461}, pmid = {33959112}, issn = {1664-302X}, abstract = {Antibiotics are freqeuently used in the livestock sector in low- and middle-income countries for treatment, prophylaxis, and growth promotion. However, there is limited information into the zoonotic prevalence and dissemination patterns of antimicrobial resistance (AMR) within these environments. In this study we used pig farming in Thailand as a model to explore AMR; 156 pig farms were included, comprising of small-sized (<50 sows) and medium-sized (≥100 sows) farms, where bacterial isolates were selectively cultured from animal rectal and human fecal samples. Bacterial isolates were subjected to antimicrobial susceptibility testing (AST), and whole-genome sequencing. Our results indicate extensive zoonotic sharing of antibiotic resistance genes (ARGs) by horizontal gene transfer. Resistance to multiple antibiotics was observed with higher prevalence in medium-scale farms. Zoonotic transmission of colistin resistance in small-scale farms had a dissemination gradient from pigs to handlers to non-livestock contacts. We highly recommend reducing the antimicrobial use in animals' feeds and medications, especially the last resort drug colistin.}, }
@article {pmid33959107, year = {2021}, author = {Steczkiewicz, K and Prestel, E and Bidnenko, E and Szczepankowska, AK}, title = {Expanding Diversity of Firmicutes Single-Strand Annealing Proteins: A Putative Role of Bacteriophage-Host Arms Race.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {644622}, pmid = {33959107}, issn = {1664-302X}, abstract = {Bacteriophage-encoded single strand annealing proteins (SSAPs) are recombinases which can substitute the classical, bacterial RecA and manage the DNA metabolism at different steps of phage propagation. SSAPs have been shown to efficiently promote recombination between short and rather divergent DNA sequences and were exploited for in vivo genetic engineering mainly in Gram-negative bacteria. In opposition to the conserved and almost universal bacterial RecA protein, SSAPs display great sequence diversity. The importance for SSAPs in phage biology and phage-bacteria evolution is underlined by their role as key players in events of horizontal gene transfer (HGT). All of the above provoke a constant interest for the identification and study of new phage recombinase proteins in vivo, in vitro as well as in silico. Despite this, a huge body of putative ssap genes escapes conventional classification, as they are not properly annotated. In this work, we performed a wide-scale identification, classification and analysis of SSAPs encoded by the Firmicutes bacteria and their phages. By using sequence similarity network and gene context analyses, we created a new high quality dataset of phage-related SSAPs, substantially increasing the number of annotated SSAPs. We classified the identified SSAPs into seven distinct families, namely RecA, Gp2.5, RecT/Redβ, Erf, Rad52/22, Sak3, and Sak4, organized into three superfamilies. Analysis of the relationships between the revealed protein clusters led us to recognize Sak3-like proteins as a new distinct SSAP family. Our analysis showed an irregular phylogenetic distribution of ssap genes among different bacterial phyla and specific phages, which can be explained by the high rates of ssap HGT. We propose that the evolution of phage recombinases could be tightly linked to the dissemination of bacterial phage-resistance mechanisms (e.g., abortive infection and CRISPR/Cas systems) targeting ssap genes and be a part of the constant phage-bacteria arms race.}, }
@article {pmid33958766, year = {2021}, author = {Warman, EA and Forrest, D and Guest, T and Haycocks, JJRJ and Wade, JT and Grainger, DC}, title = {Widespread divergent transcription from bacterial and archaeal promoters is a consequence of DNA-sequence symmetry.}, journal = {Nature microbiology}, volume = {6}, number = {6}, pages = {746-756}, pmid = {33958766}, issn = {2058-5276}, support = {/WT_/Wellcome Trust/United Kingdom ; 212193/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Archaea/*genetics ; Base Sequence ; DNA, Archaeal/*genetics ; DNA, Bacterial/*genetics ; Escherichia coli/*genetics ; Gene Transfer, Horizontal ; *Promoter Regions, Genetic ; *Transcription Initiation Site ; }, abstract = {Transcription initiates at promoters, DNA regions recognized by a DNA-dependent RNA polymerase. We previously identified horizontally acquired Escherichia coli promoters from which the direction of transcription was unclear. In the present study, we show that more than half of these promoters are bidirectional and drive divergent transcription. Using genome-scale approaches, we demonstrate that 19% of all transcription start sites detected in E. coli are associated with a bidirectional promoter. Bidirectional promoters are similarly common in diverse bacteria and archaea, and have inherent symmetry: specific bases required for transcription initiation are reciprocally co-located on opposite DNA strands. Bidirectional promoters enable co-regulation of divergent genes and are enriched in both intergenic and horizontally acquired regions. Divergent transcription is conserved among bacteria, archaea and eukaryotes, but the underlying mechanisms for bidirectionality are different.}, }
@article {pmid33958449, year = {2021}, author = {Coleman, GA and Davín, AA and Mahendrarajah, TA and Szánthó, LL and Spang, A and Hugenholtz, P and Szöllősi, GJ and Williams, TA}, title = {A rooted phylogeny resolves early bacterial evolution.}, journal = {Science (New York, N.Y.)}, volume = {372}, number = {6542}, pages = {}, doi = {10.1126/science.abe0511}, pmid = {33958449}, issn = {1095-9203}, mesh = {Archaea/classification/genetics ; Bacteria/*classification/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial ; *Phylogeny ; }, abstract = {A rooted bacterial tree is necessary to understand early evolution, but the position of the root is contested. Here, we model the evolution of 11,272 gene families to identify the root, extent of horizontal gene transfer (HGT), and the nature of the last bacterial common ancestor (LBCA). Our analyses root the tree between the major clades Terrabacteria and Gracilicutes and suggest that LBCA was a free-living flagellated, rod-shaped double-membraned organism. Contrary to recent proposals, our analyses reject a basal placement of the Candidate Phyla Radiation, which instead branches sister to Chloroflexota within Terrabacteria. While most gene families (92%) have evidence of HGT, overall, two-thirds of gene transmissions have been vertical, suggesting that a rooted tree provides a meaningful frame of reference for interpreting bacterial evolution.}, }
@article {pmid33953361, year = {2021}, author = {Jiao, JY and Fu, L and Hua, ZS and Liu, L and Salam, N and Liu, PF and Lv, AP and Wu, G and Xian, WD and Zhu, Q and Zhou, EM and Fang, BZ and Oren, A and Hedlund, BP and Jiang, HC and Knight, R and Cheng, L and Li, WJ}, title = {Insight into the function and evolution of the Wood-Ljungdahl pathway in Actinobacteria.}, journal = {The ISME journal}, volume = {15}, number = {10}, pages = {3005-3018}, pmid = {33953361}, issn = {1751-7370}, mesh = {*Actinobacteria/genetics ; *Aldehyde Oxidoreductases ; Carbon Monoxide ; Multienzyme Complexes ; }, abstract = {Carbon fixation by chemoautotrophic microbes such as homoacetogens had a major impact on the transition from the inorganic to the organic world. Recent reports have shown the presence of genes for key enzymes associated with the Wood-Ljungdahl pathway (WLP) in the phylum Actinobacteria, which adds to the diversity of potential autotrophs. Here, we compiled 42 actinobacterial metagenome-assembled genomes (MAGs) from new and existing metagenomic datasets and propose three novel classes, Ca. Aquicultoria, Ca. Geothermincolia and Ca. Humimicrobiia. Most members of these classes contain genes coding for acetogenesis through the WLP, as well as a variety of hydrogenases (NiFe groups 1a and 3b-3d; FeFe group C; NiFe group 4-related hydrogenases). We show that the three classes acquired the hydrogenases independently, yet the carbon monoxide dehydrogenase/acetyl-CoA synthase complex (CODH/ACS) was apparently present in their last common ancestor and was inherited vertically. Furthermore, the Actinobacteria likely donated genes for CODH/ACS to multiple lineages within Nitrospirae, Deltaproteobacteria (Desulfobacterota), and Thermodesulfobacteria through multiple horizontal gene transfer events. Finally, we show the apparent growth of Ca. Geothermincolia and H2-dependent acetate production in hot spring enrichment cultures with or without the methanogenesis inhibitor 2-bromoethanesulfonate, which is consistent with the proposed homoacetogenic metabolism.}, }
@article {pmid33946769, year = {2021}, author = {Oborník, M}, title = {Enigmatic Evolutionary History of Porphobilinogen Deaminase in Eukaryotic Phototrophs.}, journal = {Biology}, volume = {10}, number = {5}, pages = {}, pmid = {33946769}, issn = {2079-7737}, support = {21-03224S//Czech Science Foundation/ ; CZ.02.1.01/0.0/0.0/16_019/0000759//European Regional Development Fund/ ; }, abstract = {In most eukaryotic phototrophs, the entire heme synthesis is localized to the plastid, and enzymes of cyanobacterial origin dominate the pathway. Despite that, porphobilinogen deaminase (PBGD), the enzyme responsible for the synthesis of hydroxymethybilane in the plastid, shows phylogenetic affiliation to α-proteobacteria, the supposed ancestor of mitochondria. Surprisingly, no PBGD of such origin is found in the heme pathway of the supposed partners of the primary plastid endosymbiosis, a primarily heterotrophic eukaryote, and a cyanobacterium. It appears that α-proteobacterial PBGD is absent from glaucophytes but is present in rhodophytes, chlorophytes, plants, and most algae with complex plastids. This may suggest that in eukaryotic phototrophs, except for glaucophytes, either the gene from the mitochondrial ancestor was retained while the cyanobacterial and eukaryotic pseudoparalogs were lost in evolution, or the gene was acquired by non-endosymbiotic gene transfer from an unspecified α-proteobacterium and functionally replaced its cyanobacterial and eukaryotic counterparts.}, }
@article {pmid33941397, year = {2021}, author = {Méteignier, LV and Papon, N and Courdavault, V}, title = {Plant to Insect Horizontal Gene Transfer: Empowering Whiteflies.}, journal = {Trends in genetics : TIG}, volume = {37}, number = {8}, pages = {688-690}, doi = {10.1016/j.tig.2021.04.007}, pmid = {33941397}, issn = {0168-9525}, mesh = {Animals ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Hemiptera/*genetics ; Insecta/genetics ; Phylogeny ; Plants/*genetics ; }, abstract = {Horizontal gene transfer (HGT) is a well-documented evolutionary driving phenomenon in prokaryotes and eukaryotes, but its impact on the plant kingdom has remained elusive. A recent study provides compelling evidences, which support the idea that a plant-derived gene allows for the detoxification of plant defense metabolites in a polyphagous arthropod herbivore.}, }
@article {pmid33940320, year = {2021}, author = {Park, JC and Kim, DH and Kim, MS and Hagiwara, A and Lee, JS}, title = {The genome of the euryhaline rotifer Brachionus paranguensis: Potential use in molecular ecotoxicology.}, journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics}, volume = {39}, number = {}, pages = {100836}, doi = {10.1016/j.cbd.2021.100836}, pmid = {33940320}, issn = {1878-0407}, mesh = {Animals ; *Ecotoxicology ; *Gene Expression Regulation ; *Genome, Helminth ; Helminth Proteins/genetics/*metabolism ; *Metagenomics ; Phylogeny ; Rotifera/*genetics ; Species Specificity ; Water Pollutants, Chemical/*toxicity ; }, abstract = {Brachionus spp. rotifers have been proposed as model organisms for ecotoxicological studies. We analyzed the whole-genome sequence of B. paranguensis through NextDenovo, resulting in a total length of 106.2 Mb and 71 contigs. The N50 and the GC content were 4.13 Mb and 28%, respectively. A total of 18,501 genes were predicted within the genome of B. paranguensis. Prominent detoxification-related gene families of phase I and II detoxifications have been investigated. In parallel with other Brachionus rotifers, high gene expansion was observed in CYP clan 3 and GST sigma class in B. paranguensis. Moreover, species-specific expansion of sulfotransferase (SULTs) and gain of UDP-glucuronosyltransferases (UGTs) through horizontal gene transfer has been specifically found within B. plicatilis complex. This whole-genome analysis of B. paranguensis provides a basis for molecular ecotoxicological studies and provides useful information for comparative studies of the evolution of detoxification mechanisms in Brachionus spp.}, }
@article {pmid33939761, year = {2021}, author = {Johnson, WL and Sohn, MB and Taffner, S and Chatterjee, P and Dunman, PM and Pecora, N and Wozniak, RAF}, title = {Genomics of Staphylococcus aureus ocular isolates.}, journal = {PloS one}, volume = {16}, number = {5}, pages = {e0250975}, pmid = {33939761}, issn = {1932-6203}, support = {R01 AI134685/AI/NIAID NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Child ; Child, Preschool ; Eye/*microbiology ; Female ; Genes, Bacterial/genetics ; Genomics/methods ; Genotype ; Humans ; Infant ; Infant, Newborn ; Male ; Microbial Sensitivity Tests ; Middle Aged ; Staphylococcal Infections/*microbiology ; Staphylococcus aureus/*genetics/*isolation &amp; purification ; Virulence/genetics ; Virulence Factors/genetics ; Whole Genome Sequencing/methods ; Young Adult ; }, abstract = {Staphylococcus aureus is a major cause of ocular infections, often resulting in devastating vision loss. Despite the significant morbidity associated with these infections, little is yet known regarding the specific strain types that may have a predilection for ocular tissues nor the set of virulence factors that drive its pathogenicity in this specific biological niche. Whole genome sequencing (WGS) can provide valuable insight in this regard by providing a prospective, comprehensive assessment of the strain types and virulence factors driving disease among specific subsets of clinical isolates. As such, a set of 163-member S. aureus ocular clinical strains were sequenced and assessed for both common strain types (multilocus sequence type (MLST), spa, agr) associated with ocular infections as well as the presence/absence of 235 known virulence factors in a high throughput manner. This ocular strain set was then directly compared to a fully sequenced 116-member non-ocular S. aureus strain set curated from NCBI in order to identify key differences between ocular and non-ocular S. aureus isolates. The most common sequence types found among ocular S. aureus isolates were ST5, ST8 and ST30, generally reflecting circulating non-ocular pathogenic S. aureus strains. However, importantly, ocular isolates were found to be significantly enriched for a set of enterotoxins, suggesting a potential role for this class of virulence factors in promoting ocular disease. Further genomic analysis revealed that these enterotoxins are located on mobile pathogenicity islands, thus horizontal gene transfer may promote the acquisition of enterotoxins, potentially amplifying S. aureus virulence in ocular tissues.}, }
@article {pmid33932652, year = {2021}, author = {Chen, J and Wang, T and Zhang, K and Luo, H and Chen, W and Mo, Y and Wei, Z}, title = {The fate of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) from livestock wastewater (dominated by quinolone antibiotics) treated by microbial fuel cell (MFC).}, journal = {Ecotoxicology and environmental safety}, volume = {218}, number = {}, pages = {112267}, doi = {10.1016/j.ecoenv.2021.112267}, pmid = {33932652}, issn = {1090-2414}, abstract = {The removal characteristics of antibiotic resistance genes and mobile genetic elements from livestock wastewater (dominated by quinolone antibiotics) treated with MFC were evaluated by High-throughput quantitative (HT-qPCR). The results showed that 144 ARGs and 8 MEGs were detected in the livestock wastewater. After MFC treatment, the number of AGRs decreased as a whole, and the relative abundance of macrolide-lincosamide-streptogramin group B (MLSB) and aminoglycosider decreased by 62.7% and 92.9%, respectively. MGEs decreased by 57.3% and multidrug genes decreased by 90%. After MFC treatment, the absolute abundance of tetracycline in raw sewage decreased by two orders of magnitude from 5.8 × 10[5] copies L[-1] to 5.1.× 10[3] copies L[-1]. However, MFC was less efficient in the removal of vancomycin and beta-lactamase genes. It was also found that chloramphenicol resistance genes slightly increased. Illumina sequencing showed that Syntrophobacterales and Synergistales were predominant in MFCs. Desulfovibrio was resistant to high concentration of moxifloxacin hydrochloride. The removal efficiency of MFC for moxifloxacin hydrochloride at a concentration of 5 mg L[-1] was 86.55%. The maximum power density and coulomb efficiency were 109.3 mV·cm[-3] and 41.97%, respectively. With the increase of antibiotic concentration, the sewage treatment efficiency and electrical performance were inhibited. This study shows that untreated livestock wastewater had a great risk of gene horizontal transfer. Although MFC had limited treatment capacity for high-concentration quinolone wastewater, it is an effective method to reduce ARGs and the risk of horizontal gene transfer.}, }
@article {pmid33931422, year = {2021}, author = {Tran, TT and Scott, A and Tien, YC and Murray, R and Boerlin, P and Pearl, DL and Liu, K and Robertson, J and Nash, JHE and Topp, E}, title = {On-Farm Anaerobic Digestion of Dairy Manure Reduces the Abundance of Antibiotic Resistance-Associated Gene Targets and the Potential for Plasmid Transfer.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {14}, pages = {e0298020}, pmid = {33931422}, issn = {1098-5336}, support = {155232//Canadian Institute of Health Research/ ; }, mesh = {Anaerobiosis ; Animals ; Bacteria/genetics ; Cattle ; DNA, Bacterial/genetics ; Drug Resistance, Microbial/*genetics ; Farms ; Female ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genotype ; *Manure/microbiology ; Phenotype ; Plasmids ; }, abstract = {The present study investigated the impact of on-farm anaerobic digestion on the abundance of enteric bacteria, antibiotic resistance-associated gene targets, and the horizontal transfer potential of extended-spectrum β-lactamase (ESBL) genes. Samples of raw and digested manure were obtained from six commercial dairy farms in Ontario, Canada. Digestion significantly abated populations of viable coliforms in all six farms. Conjugative transfer of plasmids carrying β-lactamase genes from manure bacteria enriched overnight with buffered peptone containing 4 mg/liter cefotaxime into a β-lactam-sensitive green fluorescent protein (GFP)-labeled Escherichia coli recipient strain was evaluated in patch matings. Digestion significantly decreased the frequency of the horizontal transfer of ESBL genes. Twenty-five transconjugants were sequenced, revealing six distinct plasmids, ranging in size from 40 to 180 kb. A variety of ESBL genes were identified: blaCTX-M-1, blaCTX-M-14, blaCTX-M-15, blaCTX-M-27, blaCTX-M-55, and blaPER-1. blaCTX-M-15 was the most prevalent ESBL gene detected on plasmids harbored by transconjugants. Various mobile genetic elements were found located proximal to resistance genes. Ten gene targets, including sul1, str(A), str(B), erm(B), erm(F), intI1, aadA, incW, blaPSE, and blaOXA-20, were quantified by quantitative PCR on a subset of 18 raw and 18 digested samples. Most targets were significantly more abundant in raw manure; however, erm(B) and erm(F) targets were more abundant in digested samples. Overall, on-farm digestion of dairy manure abated coliform bacteria, a number of antibiotic resistance-associated gene targets, and the potential for in vitro conjugation of plasmids conferring resistance to extended-spectrum β-lactams and other classes of antibiotics into E. coli CV601. IMPORTANCE Using livestock manure for fertilization can entrain antibiotic-resistant bacteria into soil. Manure on some dairy farms is anaerobically digested before being land applied. Recommending the widespread implementation of the practice should be founded on understanding the impact of this treatment on various endpoints of human health concern. Although lab-scale anaerobic treatments have shown potential for reducing the abundance of antibiotic resistance genes, there are very few data from commercial farms. Anaerobic digestion of manure on six dairy farms efficiently abated coliform bacteria, E. coli, and a majority of antibiotic resistance-associated gene targets. In addition, the conjugation potential of plasmids carrying ESBL genes into introduced E. coli strain CV601 was reduced. Overall, anaerobic digestion abated coliform bacteria, the genes that they carry, and the potential for ESBL-carrying plasmid transfer.}, }
@article {pmid33931418, year = {2021}, author = {Gomes, SC and Ferreira, MR and Tavares, AF and Silva, IN and Becker, JD and Moreira, LM}, title = {A Histone-Like Nucleoid Structuring Protein Regulates Several Virulence Traits in Burkholderia multivorans.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {14}, pages = {e0036921}, pmid = {33931418}, issn = {1098-5336}, mesh = {Bacterial Adhesion ; Bacterial Proteins/*genetics ; Burkholderia/*genetics/*pathogenicity/physiology ; Cell Aggregation ; Cell Line ; Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Genome, Bacterial ; Histones ; Humans ; Hydrophobic and Hydrophilic Interactions ; Phenotype ; Polysaccharides, Bacterial/biosynthesis ; Virulence/*genetics ; }, abstract = {Burkholderia cepacia complex bacteria comprise opportunistic pathogens causing chronic respiratory infections in cystic fibrosis (CF) patients. These microorganisms produce an exopolysaccharide named cepacian, which is considered a virulence determinant. To find genes implicated in the regulation of cepacian biosynthesis, we characterized an evolved nonmucoid variant (17616nmv) derived from the ancestor, Burkholderia multivorans ATCC 17616, after prolonged stationary phase. Lack of cepacian biosynthesis was correlated with downregulation of the expression of bce genes implicated in its biosynthesis. Furthermore, genome sequencing of the variant identified the transposition of the mobile element IS406 upstream of the coding sequence of an hns-like gene (Bmul_0158) encoding a histone-like nucleoid structuring (H-NS) protein, a known global transcriptional repressor. This insertion sequence (IS) element upregulated the expression of Bmul_0158 by 4-fold. Transcriptome analysis identified the global effects of this mutation on gene expression, with major changes in genes implicated in motility, pilus synthesis, type VI secretion, and chromosome-associated functions. Concomitant with these differences, the nonmucoid variant displays reduced adherence to a CF lung bronchial cell line and reduced surface hydrophobicity and forms smaller cellular aggregates but has an increase in swimming and swarming motilities. Finally, analysis of the GC content of the upstream region of differentially expressed genes led to the identification of various genomic regions, possibly acquired by horizontal gene transfer, which were transcriptionally repressed by the increased expression of the Bmul_0158 gene in the 17616nmv strain. Taken together, the results revealed a significant role for this H-NS protein in the regulation of B. multivorans persistence- and virulence-associated genes. IMPORTANCE Members of the histone-like nucleoid structuring (H-NS) family of proteins, present in many bacteria, are important global regulators of gene expression. Many of the regulated genes were acquired horizontally and include pathogenicity islands and prophages, among others. Additionally, H-NS can play a structural role by bridging and compacting DNA, fulfilling a crucial role in cell physiology. Several virulence phenotypes have been frequently identified in several bacteria as dependent on H-NS activity. Here, we describe an H-NS-like protein of the opportunistic pathogen Burkholderia multivorans, a species commonly infecting the respiratory tract of cystic fibrosis patients. Our results indicate that this protein is involved in regulating virulence traits such as exopolysaccharide biosynthesis, adhesion to biotic surfaces, cellular aggregation, and motility. Furthermore, this H-NS-like protein is one out of eight orthologs present in the B. multivorans ATCC 17616 genome, posing relevant questions to be investigated on how these proteins coordinate the expression of virulence traits.}, }
@article {pmid33930136, year = {2021}, author = {Zilber-Rosenberg, I and Rosenberg, E}, title = {Microbial-driven genetic variation in holobionts.}, journal = {FEMS microbiology reviews}, volume = {45}, number = {6}, pages = {}, doi = {10.1093/femsre/fuab022}, pmid = {33930136}, issn = {1574-6976}, mesh = {Animals ; Biological Evolution ; Gene Transfer, Horizontal ; Genetic Variation/genetics ; Humans ; *Microbiota/genetics ; *Symbiosis/genetics ; }, abstract = {Genetic variation in holobionts (host and microbiome), occurring in both host and microbiome genomes, can be observed from two perspectives: observable variations and processes that bring about the variation. Observable includes the enormous genetic diversity of prokaryotes, which gave rise to eukaryotes. Holobionts then evolved a rich microbiome with a stable core containing essential genes, less so common taxa and a more diverse non-core, enabling considerable genetic variation. Thus, the human gut microbiome, for example, contains 1000 times more unique genes than are present in the human genome. Microbial-driven genetic variation processes in holobionts include: (1) acquisition of novel microbes from the environment, (2) amplification/reduction of certain microbes in the microbiome, (3) horizontal gene transfer between microbes and between microbes and host and (4) mutation, which plays a role in optimizing interactions between microbiota and between microbiota and host. We suggest that invertebrates and plants, where microbes can live intracellularly, have a greater chance of genetic exchange between microbiota and host, a greater chance of vertical transmission and a greater effect of microbiome on evolution than vertebrates. However, even in vertebrates the microbiome can aid in environmental fluctuations by amplification/reduction and by acquisition of novel microorganisms.}, }
@article {pmid33926925, year = {2021}, author = {Bryant, JM and Brown, KP and Burbaud, S and Everall, I and Belardinelli, JM and Rodriguez-Rincon, D and Grogono, DM and Peterson, CM and Verma, D and Evans, IE and Ruis, C and Weimann, A and Arora, D and Malhotra, S and Bannerman, B and Passemar, C and Templeton, K and MacGregor, G and Jiwa, K and Fisher, AJ and Blundell, TL and Ordway, DJ and Jackson, M and Parkhill, J and Floto, RA}, title = {Stepwise pathogenic evolution of Mycobacterium abscessus.}, journal = {Science (New York, N.Y.)}, volume = {372}, number = {6541}, pages = {}, pmid = {33926925}, issn = {1095-9203}, support = {/WT_/Wellcome Trust/United Kingdom ; 098051/WT_/Wellcome Trust/United Kingdom ; 107032/WT_/Wellcome Trust/United Kingdom ; 110224/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Communicable Diseases, Emerging/*microbiology/transmission ; Datasets as Topic ; Epigenesis, Genetic ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Fitness ; Genome, Bacterial ; Humans ; Lung/*microbiology ; Mutation ; Mycobacterium Infections, Nontuberculous/*microbiology/transmission ; Mycobacterium abscessus/*genetics/*pathogenicity ; Pneumonia, Bacterial/*microbiology/transmission ; Virulence/genetics ; }, abstract = {Although almost all mycobacterial species are saprophytic environmental organisms, a few, such as Mycobacterium tuberculosis, have evolved to cause transmissible human infection. By analyzing the recent emergence and spread of the environmental organism M. abscessus through the global cystic fibrosis population, we have defined key, generalizable steps involved in the pathogenic evolution of mycobacteria. We show that epigenetic modifiers, acquired through horizontal gene transfer, cause saltational increases in the pathogenic potential of specific environmental clones. Allopatric parallel evolution during chronic lung infection then promotes rapid increases in virulence through mutations in a discrete gene network; these mutations enhance growth within macrophages but impair fomite survival. As a consequence, we observe constrained pathogenic evolution while person-to-person transmission remains indirect, but postulate accelerated pathogenic adaptation once direct transmission is possible, as observed for M. tuberculosis Our findings indicate how key interventions, such as early treatment and cross-infection control, might restrict the spread of existing mycobacterial pathogens and prevent new, emergent ones.}, }
@article {pmid33925677, year = {2021}, author = {Kern-Zdanowicz, I}, title = {pCTX-M3-Structure, Function, and Evolution of a Multi-Resistance Conjugative Plasmid of a Broad Recipient Range.}, journal = {International journal of molecular sciences}, volume = {22}, number = {9}, pages = {}, pmid = {33925677}, issn = {1422-0067}, support = {N N401 534640//Narodowe Centrum Nauki/ ; }, mesh = {Bacterial Proteins/genetics ; Conjugation, Genetic ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/*genetics ; Enterobacteriaceae/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Host Specificity/genetics ; Plasmids/*genetics ; beta-Lactamases/genetics ; }, abstract = {pCTX-M3 is the archetypic member of the IncM incompatibility group of conjugative plasmids (recently referred to as IncM2). It is responsible for the worldwide dissemination of numerous antibiotic resistance genes, including those coding for extended-spectrum β-lactamases and conferring resistance to aminoglycosides. The IncM plasmids acquired during evolution diverse mobile genetic elements found in one or two multiple resistance regions, MRR(s), grouping antibiotic resistance genes as well as mobile genetic elements or their remnants. The IncM plasmids can be found in bacteria inhabiting various environments. The information on the structure and biology of pCTX-M3 is integrated in this review. It focuses on the functional modules of pCTX-M3 responsible for its replication, stable maintenance, and conjugative transfer, indicating that the host range of the pCTX-M3 replicon is limited to representatives of the family Enterobacteriaceae (Enterobacterales ord. nov.), while the range of recipients of its conjugation system is wide, comprising Alpha-, Beta-, and Gammaproteobacteria, and also Firmicutes.}, }
@article {pmid33924031, year = {2021}, author = {Chernysheva, N and Bystritskaya, E and Likhatskaya, G and Nedashkovskaya, O and Isaeva, M}, title = {Genome-Wide Analysis of PL7 Alginate Lyases in the Genus Zobellia.}, journal = {Molecules (Basel, Switzerland)}, volume = {26}, number = {8}, pages = {}, pmid = {33924031}, issn = {1420-3049}, mesh = {Alginates/chemistry ; Flavobacteriaceae/classification/*enzymology/genetics ; Genome, Bacterial/*genetics ; *Genomics ; Polysaccharide-Lyases/*genetics ; Substrate Specificity ; }, abstract = {We carried out a detailed investigation of PL7 alginate lyases across the Zobellia genus. The main findings were obtained using the methods of comparative genomics and spatial structure modeling, as well as a phylogenomic approach. Initially, in order to elucidate the alginolytic potential of Zobellia, we calculated the content of polysaccharide lyase (PL) genes in each genome. The genus-specific PLs were PL1, PL6, PL7 (the most abundant), PL14, PL17, and PL40. We revealed that PL7 belongs to subfamilies 3, 5, and 6. They may be involved in local and horizontal gene transfer and gene duplication processes. Most likely, an individual evolution of PL7 genes promotes the genetic variability of the Alginate Utilization System across Zobellia. Apparently, the PL7 alginate lyases may acquire a sub-functionalization due to diversification between in-paralogs.}, }
@article {pmid33923461, year = {2021}, author = {Claisse, O and Chaïb, A and Jaomanjaka, F and Philippe, C and Barchi, Y and Lucas, PM and Le Marrec, C}, title = {Distribution of Prophages in the Oenococcus oeni Species.}, journal = {Microorganisms}, volume = {9}, number = {4}, pages = {}, pmid = {33923461}, issn = {2076-2607}, support = {ANR-20-CE20-0008-1//ANR/ ; }, abstract = {Oenococcus oeni is the most exploited lactic acid bacterium in the wine industry and drives the malolactic fermentation of wines. Although prophage-like sequences have been identified in the species, many are not characterized, and a global view of their integration and distribution amongst strains is currently lacking. In this work, we analyzed the complete genomes of 231 strains for the occurrence of prophages, and analyzed their size and positions of insertion. Our data show the limited variation in the number of prophages in O. oeni genomes, and that six sites of insertion within the bacterial genome are being used for site-specific recombination. Prophage diversity patterns varied significantly for different host lineages, and environmental niches. Overall, the findings highlight the pervasive presence of prophages in the O. oeni species, their role as a major source of within-species bacterial diversity and drivers of horizontal gene transfer. Our data also have implications for enhanced understanding of the prophage recombination events which occurred during evolution of O. oeni, as well as the potential of prophages in influencing the fitness of these bacteria in their distinct niches.}, }
@article {pmid33923118, year = {2021}, author = {Filip, E and Skuza, L}, title = {Horizontal Gene Transfer Involving Chloroplasts.}, journal = {International journal of molecular sciences}, volume = {22}, number = {9}, pages = {}, pmid = {33923118}, issn = {1422-0067}, mesh = {Cell Nucleus/*genetics ; Chloroplasts/*genetics ; Endophytes/genetics ; *Gene Transfer, Horizontal ; Genome ; Mitochondria/*genetics ; Plants/genetics ; Plastids/genetics ; }, abstract = {Horizontal gene transfer (HGT)- is defined as the acquisition of genetic material from another organism. However, recent findings indicate a possible role of HGT in the acquisition of traits with adaptive significance, suggesting that HGT is an important driving force in the evolution of eukaryotes as well as prokaryotes. It has been noted that, in eukaryotes, HGT is more prevalent than originally thought. Mitochondria and chloroplasts lost a large number of genes after their respective endosymbiotic events occurred. Even after this major content loss, organelle genomes still continue to lose their own genes. Many of these are subsequently acquired by intracellular gene transfer from the original plastid. The aim of our review was to elucidate the role of chloroplasts in the transfer of genes. This review also explores gene transfer involving mitochondrial and nuclear genomes, though recent studies indicate that chloroplast genomes are far more active in HGT as compared to these other two DNA-containing cellular compartments.}, }
@article {pmid33922426, year = {2021}, author = {Kumar, B and Kaur, C and Pareek, A and Sopory, SK and Singla-Pareek, SL}, title = {Tracing the Evolution of Plant Glyoxalase III Enzymes for Structural and Functional Divergence.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {10}, number = {5}, pages = {}, pmid = {33922426}, issn = {2076-3921}, abstract = {Glyoxalase pathway is the primary route for metabolism of methylglyoxal (MG), a toxic ubiquitous metabolite that affects redox homeostasis. It neutralizes MG using Glyoxalase I and Glyoxalase II (GLYI and GLYII) enzymes in the presence of reduced glutathione. In addition, there also exists a shorter route for the MG detoxification in the form of Glyoxalase III (GLYIII) enzymes, which can convert MG into D-lactate in a single-step without involving glutathione. GLYIII proteins in different systems demonstrate diverse functional capacities and play a vital role in oxidative stress response. To gain insight into their evolutionary patterns, here we studied the evolution of GLYIII enzymes across prokaryotes and eukaryotes, with special emphasis on plants. GLYIII proteins are characterized by the presence of DJ-1_PfpI domains thereby, belonging to the DJ-1_PfpI protein superfamily. Our analysis delineated evolution of double DJ-1_PfpI domains in plant GLYIII. Based on sequence and structural characteristics, plant GLYIII enzymes could be categorized into three different clusters, which followed different evolutionary trajectories. Importantly, GLYIII proteins from monocots and dicots group separately in each cluster and the each of the two domains of these proteins also cluster differentially. Overall, our findings suggested that GLYIII proteins have undergone significant evolutionary changes in plants, which is likely to confer diversity and flexibility in their functions.}, }
@article {pmid33921057, year = {2021}, author = {Seike, T and Narazaki, Y and Kaneko, Y and Shimizu, H and Matsuda, F}, title = {Random Transfer of Ogataea polymorpha Genes into Saccharomyces cerevisiae Reveals a Complex Background of Heat Tolerance.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {7}, number = {4}, pages = {}, pmid = {33921057}, issn = {2309-608X}, support = {18K04851//Grants-in-Aid for Scientific Research (C)/ ; }, abstract = {Horizontal gene transfer, a process through which an organism acquires genes from other organisms, is a rare evolutionary event in yeasts. Artificial random gene transfer can emerge as a valuable tool in yeast bioengineering to investigate the background of complex phenotypes, such as heat tolerance. In this study, a cDNA library was constructed from the mRNA of a methylotrophic yeast, Ogataea polymorpha, and then introduced into Saccharomyces cerevisiae. Ogataea polymorpha was selected because it is one of the most heat-tolerant species among yeasts. Screening of S. cerevisiae populations expressing O. polymorpha genes at high temperatures identified 59 O. polymorpha genes that contribute to heat tolerance. Gene enrichment analysis indicated that certain S. cerevisiae functions, including protein synthesis, were highly temperature-sensitive. Additionally, the results confirmed that heat tolerance in yeast is a complex phenotype dependent on multiple quantitative loci. Random gene transfer would be a useful tool for future bioengineering studies on yeasts.}, }
@article {pmid33920032, year = {2021}, author = {Watanabe, T and Horiike, T}, title = {The Evolution of Molybdenum Dependent Nitrogenase in Cyanobacteria.}, journal = {Biology}, volume = {10}, number = {4}, pages = {}, pmid = {33920032}, issn = {2079-7737}, abstract = {Nitrogen fixation plays a crucial role in the nitrogen cycle by helping to convert nitrogen into a form usable by other organisms. Bacteria capable of fixing nitrogen are found in six phyla including Cyanobacteria. Molybdenum dependent nitrogenase (nif) genes are thought to share a single origin as they have homologs in various phyla. However, diazotrophic bacteria have a mosaic distribution within the cyanobacterial lineage. Therefore, the aim of this study was to determine the cause of this mosaic distribution. We identified nif gene operon structures in the genomes of 85 of the 179 cyanobacterial strains for which whole genome sequences were available. Four nif operons were conserved in each diazotroph Cyanobacterium, although there were some gene translocations and insertions. Phylogenetic inference of these genes did not reveal horizontal gene transfer from outside the phylum Cyanobacteria. These results support the hypothesis that the mosaic distribution of diazotrophic bacteria in the cyanobacterial lineage is the result of the independent loss of nif genes inherited from common cyanobacterial ancestors in each lineage.}, }
@article {pmid33918930, year = {2021}, author = {Conwell, M and Dooley, JSG and Naughton, PJ}, title = {A Novel Biofilm Model System to Visualise Conjugal Transfer of Vancomycin Resistance by Environmental Enterococci.}, journal = {Microorganisms}, volume = {9}, number = {4}, pages = {}, pmid = {33918930}, issn = {2076-2607}, support = {001//Department of Employment and Learning Northern Ireland/ ; }, abstract = {Enterococci and biofilm-associated infections are a growing problem worldwide, given the rise in antibiotic resistance in environmental and clinical settings. The increasing incidence of antibiotic resistance and its propagation potential within enterococcal biofilm is a concern. This requires a deeper understanding of how enterococcal biofilm develops, and how antibiotic resistance transfer takes place in these biofilms. Enterococcal biofilm assays, incorporating the study of antibiotic resistance transfer, require a system which can accommodate non-destructive, real-time experimentation. We adapted a Gene Frame[®] combined with fluorescence microscopy as a novel non-destructive platform to study the conjugal transfer of vancomycin resistance in an established enterococcal biofilm.A multi-purpose fluorescent in situ hybridisation (FISH) probe, in a novel application, allowed the identification of low copy number mobile elements in the biofilm. Furthermore, a Hoechst stain and ENU 1470 FISH probe identified Enterococcus faecium transconjugants by excluding Enterococcus faecalis MF06036 donors. Biofilm created with a rifampicin resistant E. faecalis (MW01105[Rif]) recipient had a transfer efficiency of 2.01 × 10[-3]; double that of the biofilm primarily created by the donor (E. faecalis MF06036). Conjugation in the mixed enterococcal biofilm was triple the efficiency of donor biofilm. Double antibiotic treatment plus lysozyme combined with live/dead imaging provided fluorescent micrographs identifying de novo enterococcal vancomycin resistant transconjugants inside the biofilm. This is a model system for the further study of antibiotic resistance transfer events in enterococci. Biofilms promote the survival of enterococci and reduce the effectiveness of drug treatment in clinical settings, hence giving enterococci an advantage. Enterococci growing in biofilms exchange traits by means of horizontal gene transfer, but currently available models make study difficult. This work goes some way to providing a non-destructive, molecular imaging-based model system for the detection of antibiotic resistance gene transfer in enterococci.}, }
@article {pmid33918911, year = {2021}, author = {Aminov, R}, title = {Acquisition and Spread of Antimicrobial Resistance: A tet(X) Case Study.}, journal = {International journal of molecular sciences}, volume = {22}, number = {8}, pages = {}, pmid = {33918911}, issn = {1422-0067}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria/classification/*drug effects/*genetics ; Bacterial Infections/drug therapy/microbiology ; Bacterial Proteins/genetics/metabolism ; Drug Resistance, Bacterial/*drug effects ; Drug Resistance, Multiple, Bacterial/drug effects ; Gene Transfer, Horizontal ; Humans ; Light-Harvesting Protein Complexes/genetics/metabolism ; Mixed Function Oxygenases/*genetics/metabolism ; Mutation ; Plasmids/genetics ; }, abstract = {Understanding the mechanisms leading to the rise and dissemination of antimicrobial resistance (AMR) is crucially important for the preservation of power of antimicrobials and controlling infectious diseases. Measures to monitor and detect AMR, however, have been significantly delayed and introduced much later after the beginning of industrial production and consumption of antimicrobials. However, monitoring and detection of AMR is largely focused on bacterial pathogens, thus missing multiple key events which take place before the emergence and spread of AMR among the pathogens. In this regard, careful analysis of AMR development towards recently introduced antimicrobials may serve as a valuable example for the better understanding of mechanisms driving AMR evolution. Here, the example of evolution of tet(X), which confers resistance to the next-generation tetracyclines, is summarised and discussed. Initial mechanisms of resistance to these antimicrobials among pathogens were mostly via chromosomal mutations leading to the overexpression of efflux pumps. High-level resistance was achieved only after the acquisition of flavin-dependent monooxygenase-encoding genes from the environmental microbiota. These genes confer resistance to all tetracyclines, including the next-generation tetracyclines, and thus were termed tet(X). ISCR2 and IS26, as well as a variety of conjugative and mobilizable plasmids of different incompatibility groups, played an essential role in the acquisition of tet(X) genes from natural reservoirs and in further dissemination among bacterial commensals and pathogens. This process, which took place within the last decade, demonstrates how rapidly AMR evolution may progress, taking away some drugs of last resort from our arsenal.}, }
@article {pmid33918392, year = {2021}, author = {Abaramak, G and Porras-Domínguez, JR and Janse van Rensburg, HC and Lescrinier, E and Toksoy Öner, E and Kırtel, O and Van den Ende, W}, title = {Functional and Molecular Characterization of the Halomicrobium sp. IBSBa Inulosucrase.}, journal = {Microorganisms}, volume = {9}, number = {4}, pages = {}, pmid = {33918392}, issn = {2076-2607}, abstract = {Fructans are fructose-based (poly)saccharides with inulin and levan being the best-known ones. Thanks to their health-related benefits, inulin-type fructans have been under the focus of scientific and industrial communities, though mostly represented by plant-based inulins, and rarely by microbial ones. Recently, it was discovered that some extremely halophilic Archaea are also able to synthesize fructans. Here, we describe the first in-depth functional and molecular characterization of an Archaeal inulosucrase from Halomicrobium sp. IBSBa (HmcIsc). The HmcIsc enzyme was recombinantly expressed and purified in Escherichia coli and shown to synthesize inulin as proven by nuclear magnetic resonance (NMR) analysis. In accordance with the halophilic lifestyle of its native host, the enzyme showed maximum activity at very high NaCl concentrations (3.5 M), with specific adaptations for that purpose. Phylogenetic analyses suggested that Archaeal inulosucrases have been acquired from halophilic bacilli through horizontal gene transfer, with a HX(H/F)T motif evolving further into a HXHT motif, together with a unique D residue creating the onset of a specific alternative acceptor binding groove. This work uncovers a novel area in fructan research, highlighting unexplored aspects of life in hypersaline habitats, and raising questions about the general physiological relevance of inulosucrases and their products in nature.}, }
@article {pmid33916668, year = {2021}, author = {Willms, IM and Grote, M and Kocatürk, M and Singhoff, L and Kraft, AA and Bolz, SH and Nacke, H}, title = {Novel Soil-Derived Beta-Lactam, Chloramphenicol, Fosfomycin and Trimethoprim Resistance Genes Revealed by Functional Metagenomics.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {10}, number = {4}, pages = {}, pmid = {33916668}, issn = {2079-6382}, support = {NA 848/2-1//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Antibiotic resistance genes (ARGs) in soil are considered to represent one of the largest environmental resistomes on our planet. As these genes can potentially be disseminated among microorganisms via horizontal gene transfer (HGT) and in some cases are acquired by clinical pathogens, knowledge about their diversity, mobility and encoded resistance spectra gained increasing public attention. This knowledge offers opportunities with respect to improved risk prediction and development of strategies to tackle antibiotic resistance, and might help to direct the design of novel antibiotics, before further resistances reach hospital settings or the animal sector. Here, metagenomic libraries, which comprise genes of cultivated microorganisms, but, importantly, also those carried by the uncultured microbial majority, were screened for novel ARGs from forest and grassland soils. We detected three new beta-lactam, a so far unknown chloramphenicol, a novel fosfomycin, as well as three previously undiscovered trimethoprim resistance genes. These ARGs were derived from phylogenetically diverse soil bacteria and predicted to encode antibiotic inactivation, antibiotic efflux, or alternative variants of target enzymes. Moreover, deduced gene products show a minimum identity of ~21% to reference database entries and confer high-level resistance. This highlights the vast potential of functional metagenomics for the discovery of novel ARGs from soil ecosystems.}, }
@article {pmid33916499, year = {2021}, author = {Kim, HT and Kim, JS}, title = {Structural Mutations in the Organellar Genomes of Valeriana sambucifolia f. dageletiana (Nakai. ex Maekawa) Hara Show Dynamic Gene Transfer.}, journal = {International journal of molecular sciences}, volume = {22}, number = {7}, pages = {}, pmid = {33916499}, issn = {1422-0067}, support = {2020R1I1A2053517//National Research Foundation of Korea/ ; }, mesh = {*Gene Transfer, Horizontal ; *Genome, Chloroplast ; *Genome, Mitochondrial ; Mutation ; *Phylogeny ; Valerian/*genetics ; }, abstract = {Valeriana sambucifolia f. dageletiana (Nakai. ex Maekawa) Hara is a broad-leaved valerian endemic to Ulleung Island, a noted hot spot of endemism in Korea. However, despite its widespread pharmacological use, this plant remains comparatively understudied. Plant cells generally contain two types of organellar genomes (the plastome and the mitogenome) that have undergone independent evolution, which accordingly can provide valuable information for elucidating the phylogenetic relationships and evolutionary histories of terrestrial plants. Moreover, the extensive mega-data available for plant genomes, particularly those of plastomes, can enable researchers to gain an in-depth understanding of the transfer of genes between different types of genomes. In this study, we analyzed two organellar genomes (the 155,179 bp plastome and the 1,187,459 bp mitogenome) of V. sambucifolia f. dageletiana and detected extensive changes throughout the plastome sequence, including rapid structural mutations associated with inverted repeat (IR) contraction and genetic variation. We also described features characterizing the first reported mitogenome sequence obtained for a plant in the order Dipsacales and confirmed frequent gene transfer in this mitogenome. We identified eight non-plastome-originated regions (NPRs) distributed within the plastome of this endemic plant, for six of which there were no corresponding sequences in the current nucleotide sequence databases. Indeed, one of these unidentified NPRs unexpectedly showed certain similarities to sequences from bony fish. Although this is ostensibly difficult to explain, we suggest that this surprising association may conceivably reflect the occurrence of gene transfer from a bony fish to the plastome of an ancestor of V. sambucifolia f. dageletiana mediated by either fungi or bacteria.}, }
@article {pmid33914852, year = {2021}, author = {Nakamura, K and Ogura, Y and Gotoh, Y and Hayashi, T}, title = {Prophages integrating into prophages: A mechanism to accumulate type III secretion effector genes and duplicate Shiga toxin-encoding prophages in Escherichia coli.}, journal = {PLoS pathogens}, volume = {17}, number = {4}, pages = {e1009073}, pmid = {33914852}, issn = {1553-7374}, mesh = {Bacteriophages/genetics ; Escherichia coli/metabolism ; Escherichia coli Infections/*microbiology ; Gene Transfer, Horizontal/*genetics/immunology ; Prophages/*genetics/pathogenicity ; Shiga Toxin/*genetics ; Shiga Toxin 2/genetics/*pharmacology ; Virulence/immunology ; Virulence Factors/genetics ; }, abstract = {Bacteriophages (or phages) play major roles in the evolution of bacterial pathogens via horizontal gene transfer. Multiple phages are often integrated in a host chromosome as prophages, not only carrying various novel virulence-related genetic determinants into host bacteria but also providing various possibilities for prophage-prophage interactions in bacterial cells. In particular, Escherichia coli strains such as Shiga toxin (Stx)-producing E. coli (STEC) and enteropathogenic E. coli (EPEC) strains have acquired more than 10 prophages (up to 21 prophages), many of which encode type III secretion system (T3SS) effector gene clusters. In these strains, some prophages are present at a single locus in tandem, which is usually interpreted as the integration of phages that use the same attachment (att) sequence. Here, we present phages integrating into T3SS effector gene cluster-associated loci in prophages, which are widely distributed in STEC and EPEC. Some of the phages integrated into prophages are Stx-encoding phages (Stx phages) and have induced the duplication of Stx phages in a single cell. The identified attB sequences in prophage genomes are apparently derived from host chromosomes. In addition, two or three different attB sequences are present in some prophages, which results in the generation of prophage clusters in various complex configurations. These phages integrating into prophages represent a medically and biologically important type of inter-phage interaction that promotes the accumulation of T3SS effector genes in STEC and EPEC, the duplication of Stx phages in STEC, and the conversion of EPEC to STEC and that may be distributed in other types of E. coli strains as well as other prophage-rich bacterial species.}, }
@article {pmid33911286, year = {2021}, author = {Liu, Y and Makarova, KS and Huang, WC and Wolf, YI and Nikolskaya, AN and Zhang, X and Cai, M and Zhang, CJ and Xu, W and Luo, Z and Cheng, L and Koonin, EV and Li, M}, title = {Expanded diversity of Asgard archaea and their relationships with eukaryotes.}, journal = {Nature}, volume = {593}, number = {7860}, pages = {553-557}, pmid = {33911286}, issn = {1476-4687}, support = {ZIA LM000073/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Archaea/*classification ; Biological Evolution ; Eukaryota ; *Genome, Archaeal ; Metagenomics ; *Phylogeny ; }, abstract = {Asgard is a recently discovered superphylum of archaea that appears to include the closest archaeal relatives of eukaryotes[1-5]. Debate continues as to whether the archaeal ancestor of eukaryotes belongs within the Asgard superphylum or whether this ancestor is a sister group to all other archaea (that is, a two-domain versus a three-domain tree of life)[6-8]. Here we present a comparative analysis of 162 complete or nearly complete genomes of Asgard archaea, including 75 metagenome-assembled genomes that-to our knowledge-have not previously been reported. Our results substantially expand the phylogenetic diversity of Asgard and lead us to propose six additional phyla that include a deep branch that we have provisionally named Wukongarchaeota. Our phylogenomic analysis does not resolve unequivocally the evolutionary relationship between eukaryotes and Asgard archaea, but instead-depending on the choice of species and conserved genes used to build the phylogeny-supports either the origin of eukaryotes from within Asgard (as a sister group to the expanded Heimdallarchaeota-Wukongarchaeota branch) or a deeper branch for the eukaryote ancestor within archaea. Our comprehensive protein domain analysis using the 162 Asgard genomes results in a major expansion of the set of eukaryotic signature proteins. The Asgard eukaryotic signature proteins show variable phyletic distributions and domain architectures, which is suggestive of dynamic evolution through horizontal gene transfer, gene loss, gene duplication and domain shuffling. The phylogenomics of the Asgard archaea points to the accumulation of the components of the mobile archaeal 'eukaryome' in the archaeal ancestor of eukaryotes (within or outside Asgard) through extensive horizontal gene transfer.}, }
@article {pmid33911080, year = {2021}, author = {Moreira, D and Zivanovic, Y and López-Archilla, AI and Iniesto, M and López-García, P}, title = {Reductive evolution and unique predatory mode in the CPR bacterium Vampirococcus lugosii.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {2454}, pmid = {33911080}, issn = {2041-1723}, mesh = {Bacteria/*classification/*genetics/metabolism ; Bacterial Physiological Phenomena/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Symbiosis/*genetics ; }, abstract = {The Candidate Phyla Radiation (CPR) constitutes a large group of mostly uncultured bacterial lineages with small cell sizes and limited biosynthetic capabilities. They are thought to be symbionts of other organisms, but the nature of this symbiosis has been ascertained only for cultured Saccharibacteria, which are epibiotic parasites of other bacteria. Here, we study the biology and the genome of Vampirococcus lugosii, which becomes the first described species of Vampirococcus, a genus of epibiotic bacteria morphologically identified decades ago. Vampirococcus belongs to the CPR phylum Absconditabacteria. It feeds on anoxygenic photosynthetic gammaproteobacteria, fully absorbing their cytoplasmic content. The cells divide epibiotically, forming multicellular stalks whose apical cells can reach new hosts. The genome is small (1.3 Mbp) and highly reduced in biosynthetic metabolism genes, but is enriched in genes possibly related to a fibrous cell surface likely involved in interactions with the host. Gene loss has been continuous during the evolution of Absconditabacteria, and generally most CPR bacteria, but this has been compensated by gene acquisition by horizontal gene transfer and de novo evolution. Our findings support parasitism as a widespread lifestyle of CPR bacteria, which probably contribute to the control of bacterial populations in diverse ecosystems.}, }
@article {pmid33903726, year = {2021}, author = {Liu, J and Cvirkaite-Krupovic, V and Commere, PH and Yang, Y and Zhou, F and Forterre, P and Shen, Y and Krupovic, M}, title = {Archaeal extracellular vesicles are produced in an ESCRT-dependent manner and promote gene transfer and nutrient cycling in extreme environments.}, journal = {The ISME journal}, volume = {15}, number = {10}, pages = {2892-2905}, pmid = {33903726}, issn = {1751-7370}, mesh = {*Archaea/genetics ; Endosomal Sorting Complexes Required for Transport/genetics ; *Extracellular Vesicles ; Extreme Environments ; Nutrients ; }, abstract = {Membrane-bound extracellular vesicles (EVs), secreted by cells from all three domains of life, transport various molecules and act as agents of intercellular communication in diverse environments. Here we demonstrate that EVs produced by a hyperthermophilic and acidophilic archaeon Sulfolobus islandicus carry not only a diverse proteome, enriched in membrane proteins, but also chromosomal and plasmid DNA, and can transfer this DNA to recipient cells. Furthermore, we show that EVs can support the heterotrophic growth of Sulfolobus in minimal medium, implicating EVs in carbon and nitrogen fluxes in extreme environments. Finally, our results indicate that, similar to eukaryotes, production of EVs in S. islandicus depends on the archaeal ESCRT machinery. We find that all components of the ESCRT apparatus are encapsidated into EVs. Using synchronized S. islandicus cultures, we show that EV production is linked to cell division and appears to be triggered by increased expression of ESCRT proteins during this cell cycle phase. Using a CRISPR-based knockdown system, we show that archaeal ESCRT-III and AAA+ ATPase Vps4 are required for EV production, whereas archaea-specific component CdvA appears to be dispensable. In particular, the active EV production appears to coincide with the expression patterns of ESCRT-III-1 and ESCRT-III-2, rather than ESCRT-III, suggesting a prime role of these proteins in EV budding. Collectively, our results suggest that ESCRT-mediated EV biogenesis has deep evolutionary roots, likely predating the divergence of eukaryotes and archaea, and that EVs play an important role in horizontal gene transfer and nutrient cycling in extreme environments.}, }
@article {pmid33902812, year = {2021}, author = {Maeda, T and Takahashi, S and Yoshida, T and Shimamura, S and Takaki, Y and Nagai, Y and Toyoda, A and Suzuki, Y and Arimoto, A and Ishii, H and Satoh, N and Nishiyama, T and Hasebe, M and Maruyama, T and Minagawa, J and Obokata, J and Shigenobu, S}, title = {Chloroplast acquisition without the gene transfer in kleptoplastic sea slugs, Plakobranchus ocellatus.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {33902812}, issn = {2050-084X}, support = {25128713//Japan Society for the Promotion of Science/ ; 22128001//Japan Society for the Promotion of Science/ ; 16H06553//Japan Society for the Promotion of Science/ ; 221S0002//Japan Society for the Promotion of Science/ ; 17H06388//Japan Society for the Promotion of Science/ ; }, mesh = {Animals ; Cell Nucleus/genetics/physiology ; Chlorophyta/genetics/*physiology ; Chloroplasts/*physiology ; Gastropoda/*genetics ; *Gene Transfer, Horizontal ; Phylogeny ; Symbiosis/*genetics ; }, abstract = {Some sea slugs sequester chloroplasts from algal food in their intestinal cells and photosynthesize for months. This phenomenon, kleptoplasty, poses a question of how the chloroplast retains its activity without the algal nucleus. There have been debates on the horizontal transfer of algal genes to the animal nucleus. To settle the arguments, this study reported the genome of a kleptoplastic sea slug, Plakobranchus ocellatus, and found no evidence of photosynthetic genes encoded on the nucleus. Nevertheless, it was confirmed that light illumination prolongs the life of mollusk under starvation. These data presented a paradigm that a complex adaptive trait, as typified by photosynthesis, can be transferred between eukaryotic kingdoms by a unique organelle transmission without nuclear gene transfer. Our phylogenomic analysis showed that genes for proteolysis and immunity undergo gene expansion and are up-regulated in chloroplast-enriched tissue, suggesting that these molluskan genes are involved in the phenotype acquisition without horizontal gene transfer.}, }
@article {pmid33902735, year = {2020}, author = {Ward, LM and Lingappa, UF and Grotzinger, JP and Fischer, WW}, title = {Microbial mats in the Turks and Caicos Islands reveal diversity and evolution of phototrophy in the Chloroflexota order Aggregatilineales.}, journal = {Environmental microbiome}, volume = {15}, number = {1}, pages = {9}, pmid = {33902735}, issn = {2524-6372}, support = {1833247//National Science Foundation/ ; Not applicable//Agouron Institute/ ; Not applicable//Simons Foundation/ ; }, abstract = {Genome-resolved metagenomic sequencing approaches have led to a substantial increase in the recognized diversity of microorganisms; this included the discovery of novel metabolic pathways in previously recognized clades, and has enabled a more accurate determination of the extant distribution of key metabolisms and how they evolved over Earth history. Here, we present metagenome-assembled genomes of members of the Chloroflexota (formerly Chloroflexi or Green Nonsulfur Bacteria) order Aggregatilineales (formerly SBR1031 or Thermofonsia) discovered from sequencing of thick and expansive microbial mats present in an intertidal lagoon on Little Ambergris Cay in the Turks and Caicos Islands. These taxa included multiple new lineages of Type 2 reaction center-containing phototrophs that were not closely related to previously described phototrophic Chloroflexota-revealing a rich and intricate history of horizontal gene transfer and the evolution of phototrophy and other core metabolic pathways within this widespread phylum.}, }
@article {pmid33901575, year = {2021}, author = {Jia, SL and Chi, Z and Chen, L and Liu, GL and Hu, Z and Chi, ZM}, title = {Molecular evolution and regulation of DHN melanin-related gene clusters are closely related to adaptation of different melanin-producing fungi.}, journal = {Genomics}, volume = {113}, number = {4}, pages = {1962-1975}, doi = {10.1016/j.ygeno.2021.04.034}, pmid = {33901575}, issn = {1089-8646}, mesh = {Evolution, Molecular ; Fungi/genetics ; Gene Transfer, Horizontal ; *Melanins/genetics ; *Multigene Family ; }, abstract = {Many genes responsible for melanin biosynthesis in fungi were physically linked together. The PKS gene clusters in most of the melanin-producing fungi were regulated by the Cmr1. It was found that a close rearrangement of the PKS gene clusters had evolved in most of the melanin-producing fungi and various functions of melanin in them were beneficial to their adaptation to the changing environments. The melanin-producing fungi had undergone at least five large-scale differentiations, making their PKS gene clusters be quickly evolved and the fungi be adapted to different harsh environments. The recent gene losses and expansion were remarkably frequent in the PKS gene clusters, leading to their rapid evolution and adaptation of their hosts to different environments. The PKS gene and the CMR1 gene in them were subject to a strong co-evolution, but the horizontal gene transfer events might have occurred in the genome-duplicated species, Aspergillus and Penicillium.}, }
@article {pmid33900494, year = {2021}, author = {Domínguez, A}, title = {Interrogating the 5'UTR tandem repeats of retrotransposon roo of Drosophila about horizontal transfer.}, journal = {Genetica}, volume = {149}, number = {3}, pages = {171-177}, pmid = {33900494}, issn = {1573-6857}, mesh = {*5' Untranslated Regions ; Animals ; Drosophila melanogaster ; Evolution, Molecular ; Gene Duplication ; *Gene Transfer, Horizontal ; Retroelements/*genetics ; Tandem Repeat Sequences ; }, abstract = {Horizontal transfer in Drosophila has been inferred for several families of transposable elements. Specifically, the retroelement roo has been suggested to have been horizontally transferred between the species D. melanogaster, D. simulans, D. sechellia and D. yakuba. The inferences were based on the observation that divergence between transposable elements in different species was lower than the divergence found in typical nuclear genes and in the incongruence of phylogenies of the species and their TEs. Here, we address the question of the possible horizontal transfer of roo between species of the Drosophila genus by studying the presence absence of a duplication of 99 bp in the 5'UTR of the transposon, as well as comparing the sequences of the paralogous and orthologous duplicated repeats within and between species. First, the repeats were only found in five species of the melanogaster subgroup. Second, the date of occurrence of the duplication event originating the repeats was posterior to the split of the subgroup. The duplication date suggests an origin previous to the split of D. simulans and D. sechellia and close to the divergence of D. melanogaster from the D. simulans complex. These data point to horizontal transfer to the afrotropical species D. yakuba and D. erecta from one of the cosmopolitan species D. melanogaster or D. simulans. We propose that the parasitoid wasp Leptopilina could have been the vector of horizontal transfer after the observation that a sequence of 845 bp with high homology to a fragment of roo was isolated from this wasp.}, }
@article {pmid33899656, year = {2021}, author = {Mitchell, S and Bull, M and Muscatello, G and Chapman, B and Coleman, NV}, title = {The equine hindgut as a reservoir of mobile genetic elements and antimicrobial resistance genes.}, journal = {Critical reviews in microbiology}, volume = {47}, number = {5}, pages = {543-561}, doi = {10.1080/1040841X.2021.1907301}, pmid = {33899656}, issn = {1549-7828}, mesh = {Animal Feed ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics ; Dietary Supplements ; Drug Resistance, Bacterial/*genetics ; *Gastrointestinal Microbiome ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Horses/*microbiology ; *Interspersed Repetitive Sequences ; Intestine, Large/*microbiology ; Plasmids ; Soil ; }, abstract = {Antibiotic resistance in bacterial pathogens is a growing problem for both human and veterinary medicine. Mobile genetic elements (MGEs) such as plasmids, transposons, and integrons enable the spread of antibiotic resistance genes (ARGs) among bacteria, and the overuse of antibiotics drives this process by providing the selection pressure for resistance genes to establish and persist in bacterial populations. Because bacteria, MGEs, and resistance genes can readily spread between different ecological compartments (e.g. soil, plants, animals, humans, wastewater), a "One Health" approach is needed to combat this problem. The equine hindgut is an understudied but potentially significant reservoir of ARGs and MGEs, since horses have close contact with humans, their manure is used in agriculture, they have a dense microbiome of both bacteria and fungi, and many antimicrobials used for equine treatment are also used in human medicine. Here, we collate information to date about resistance genes, plasmids, and class 1 integrons from equine-derived bacteria, we discuss why the equine hindgut deserves increased attention as a potential reservoir of ARGs, and we suggest ways to minimize the selection for ARGs in horses, in order to prevent their spread to the wider community.}, }
@article {pmid33893312, year = {2021}, author = {Ellabaan, MMH and Munck, C and Porse, A and Imamovic, L and Sommer, MOA}, title = {Forecasting the dissemination of antibiotic resistance genes across bacterial genomes.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {2435}, pmid = {33893312}, issn = {2041-1723}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/*genetics ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/*genetics ; Genome, Bacterial/*genetics ; Phylogeny ; Species Specificity ; }, abstract = {Antibiotic resistance spreads among bacteria through horizontal transfer of antibiotic resistance genes (ARGs). Here, we set out to determine predictive features of ARG transfer among bacterial clades. We use a statistical framework to identify putative horizontally transferred ARGs and the groups of bacteria that disseminate them. We identify 152 gene exchange networks containing 22,963 bacterial genomes. Analysis of ARG-surrounding sequences identify genes encoding putative mobilisation elements such as transposases and integrases that may be involved in gene transfer between genomes. Certain ARGs appear to be frequently mobilised by different mobile genetic elements. We characterise the phylogenetic reach of these mobilisation elements to predict the potential future dissemination of known ARGs. Using a separate database with 472,798 genomes from Streptococcaceae, Staphylococcaceae and Enterobacteriaceae, we confirm 34 of 94 predicted mobilisations. We explore transfer barriers beyond mobilisation and show experimentally that physiological constraints of the host can explain why specific genes are largely confined to Gram-negative bacteria although their mobile elements support dissemination to Gram-positive bacteria. Our approach may potentially enable better risk assessment of future resistance gene dissemination.}, }
@article {pmid33893118, year = {2021}, author = {Lin, YC and Chen, EH and Chen, RP and Dunny, GM and Hu, WS and Lee, KT}, title = {Probiotic Bacillus Affects Enterococcus faecalis Antibiotic Resistance Transfer by Interfering with Pheromone Signaling Cascades.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {13}, pages = {e0044221}, pmid = {33893118}, issn = {1098-5336}, mesh = {*Bacillus/genetics/metabolism ; Bacterial Proteins/metabolism ; Drug Resistance, Bacterial/*genetics ; Enterococcus faecalis/*genetics/metabolism ; Fermentation ; Gene Transfer, Horizontal ; Oligopeptides/genetics ; Peptide Hydrolases/metabolism ; Pheromones/genetics/metabolism ; Plasmids ; Probiotics/*pharmacology ; Signal Transduction ; Bacillus subtilis ; }, abstract = {Enterococcus faecalis, a member of the commensal flora in the human gastrointestinal tract, has become a threatening nosocomial pathogen because it has developed resistance to many known antibiotics. More concerningly, resistance gene-carrying E. faecalis cells may transfer antibiotic resistance to resistance-free E. faecalis cells through their unique quorum sensing-mediated plasmid transfer system. Therefore, we investigated the role of probiotic bacteria in the transfer frequency of the antibiotic resistance plasmid pCF10 in E. faecalis populations to mitigate the spread of antibiotic resistance. Bacillus subtilis subsp. natto is a probiotic strain isolated from Japanese fermented soybean foods, and its culture fluid potently inhibited pCF10 transfer by suppressing peptide pheromone activity from chromosomally encoded CF10 (cCF10) without inhibiting E. faecalis growth. The inhibitory effect was attributed to at least one 30- to 50-kDa extracellular protease present in B. subtilis subsp. natto. Nattokinase of B. subtilis subsp. natto was involved in the inhibition of pCF10 transfer and cleaved cCF10 (LVTLVFV) into LVTL plus VFV fragments. Moreover, the cleavage product LVTL (L peptide) interfered with the conjugative transfer of pCF10. In addition to cCF10, faecalis-cAM373 and gordonii-cAM373, which are mating inducers of vancomycin-resistant E. faecalis, were also cleaved by nattokinase, indicating that B. subtilis subsp. natto can likely interfere with vancomycin resistance transfer in E. faecalis. Our work shows the feasibility of applying fermentation products of B. subtilis subsp. natto and L peptide to mitigate E. faecalis antibiotic resistance transfer. IMPORTANCE Enterococcus faecalis is considered a leading cause of hospital-acquired infections. Treatment of these infections has become a major challenge for clinicians because some E. faecalis strains are resistant to multiple clinically used antibiotics. Moreover, antibiotic resistance genes can undergo efficient intra- and interspecies transfer via E. faecalis peptide pheromone-mediated plasmid transfer systems. Therefore, this study provided the first experimental demonstration that probiotics are a feasible approach for interfering with conjugative plasmid transfer between E. faecalis strains to stop the transfer of antibiotic resistance. We found that the extracellular protease(s) of Bacillus subtilis subsp. natto cleaved peptide pheromones without affecting the growth of E. faecalis, thereby reducing the frequency of conjugative plasmid transfer. In addition, a specific cleaved pheromone fragment interfered with conjugative plasmid transfer. These findings provide a potential probiotic-based method for interfering with the transfer of antibiotic resistance between E. faecalis strains.}, }
@article {pmid33891610, year = {2021}, author = {Davis, EW and Okrent, RA and Manning, VA and Trippe, KM}, title = {Unexpected distribution of the 4-formylaminooxyvinylglycine (FVG) biosynthetic pathway in Pseudomonas and beyond.}, journal = {PloS one}, volume = {16}, number = {4}, pages = {e0247348}, pmid = {33891610}, issn = {1932-6203}, mesh = {Anti-Bacterial Agents/metabolism ; *Biosynthetic Pathways ; Genes, Bacterial ; Glycine/*analogs &amp; derivatives/genetics/metabolism ; Herbicides/metabolism ; Humans ; Multigene Family ; Phylogeny ; Pseudomonas/genetics/*metabolism ; Pseudomonas Infections/microbiology ; }, abstract = {The biological herbicide and antibiotic 4-formylaminooxyvinylglycine (FVG) was originally isolated from several rhizosphere-associated strains of Pseudomonas fluorescens. Biosynthesis of FVG is dependent on the gvg biosynthetic gene cluster in P. fluorescens. In this investigation, we used comparative genomics to identify strains with the genetic potential to produce FVG due to presence of a gvg gene cluster. These strains primarily belong to two groups of Pseudomonas, P. fluorescens and P. syringae, however, a few strains with the gvg cluster were found outside of Pseudomonas. Mass spectrometry confirmed that all tested strains of the P. fluorescens species group produced FVG. However, P. syringae strains did not produce FVG under standard conditions. Several lines of evidence regarding the transmission of the gvg cluster including a robust phylogenetic analysis suggest that it was introduced multiple times through horizontal gene transfer within the Pseudomonas lineage as well as in select lineages of Thiomonas, Burkholderia and Pantoea. Together, these data broaden our understanding of the evolution and diversity of FVG biosynthesis. In the course of this investigation, additional gene clusters containing only a subset of the genes required to produce FVG were identified in a broad range of bacteria, including many non-pseudomonads.}, }
@article {pmid33891594, year = {2021}, author = {Milner, DS and Wideman, JG and Stairs, CW and Dunn, CD and Richards, TA}, title = {A functional bacteria-derived restriction modification system in the mitochondrion of a heterotrophic protist.}, journal = {PLoS biology}, volume = {19}, number = {4}, pages = {e3001126}, pmid = {33891594}, issn = {1545-7885}, mesh = {Bacteria/*genetics ; Base Sequence ; DNA Restriction-Modification Enzymes/*genetics ; DNA, Mitochondrial/analysis/genetics ; Escherichia coli/genetics ; Eukaryota/classification/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Mitochondrial/genetics ; Mitochondria/*genetics ; Organisms, Genetically Modified ; Phylogeny ; Repetitive Sequences, Nucleic Acid/genetics ; Saccharomyces cerevisiae/genetics ; Sequence Analysis, DNA ; }, abstract = {The overarching trend in mitochondrial genome evolution is functional streamlining coupled with gene loss. Therefore, gene acquisition by mitochondria is considered to be exceedingly rare. Selfish elements in the form of self-splicing introns occur in many organellar genomes, but the wider diversity of selfish elements, and how they persist in the DNA of organelles, has not been explored. In the mitochondrial genome of a marine heterotrophic katablepharid protist, we identify a functional type II restriction modification (RM) system originating from a horizontal gene transfer (HGT) event involving bacteria related to flavobacteria. This RM system consists of an HpaII-like endonuclease and a cognate cytosine methyltransferase (CM). We demonstrate that these proteins are functional by heterologous expression in both bacterial and eukaryotic cells. These results suggest that a mitochondrion-encoded RM system can function as a toxin-antitoxin selfish element, and that such elements could be co-opted by eukaryotic genomes to drive biased organellar inheritance.}, }
@article {pmid33887801, year = {2021}, author = {Hibdige, SGS and Raimondeau, P and Christin, PA and Dunning, LT}, title = {Widespread lateral gene transfer among grasses.}, journal = {The New phytologist}, volume = {230}, number = {6}, pages = {2474-2486}, doi = {10.1111/nph.17328}, pmid = {33887801}, issn = {1469-8137}, mesh = {Evolution, Molecular ; *Gene Transfer, Horizontal ; Phylogeny ; *Poaceae/genetics ; Prokaryotic Cells ; }, abstract = {Lateral gene transfer (LGT) occurs in a broad range of prokaryotes and eukaryotes, occasionally promoting adaptation. LGT of functional nuclear genes has been reported among some plants, but systematic studies are needed to assess the frequency and facilitators of LGT. We scanned the genomes of a diverse set of 17 grass species that span more than 50 Ma of divergence and include major crops to identify grass-to-grass protein-coding LGT. We identified LGTs in 13 species, with significant variation in the amount each received. Rhizomatous species acquired statistically more genes, probably because this growth habit boosts opportunities for transfer into the germline. In addition, the amount of LGT increases with phylogenetic relatedness, which might reflect genomic compatibility among close relatives facilitating successful transfers. However, genetic exchanges among highly divergent species indicates that transfers can occur across almost the entire family. Overall, we showed that LGT is a widespread phenomenon in grasses that has moved functional genes across the grass family into domesticated and wild species alike. Successful LGTs appear to increase with both opportunity and compatibility.}, }
@article {pmid33886019, year = {2021}, author = {Qiao, W and Wang, L and Luo, Y and Miao, J}, title = {Outer membrane vesicles mediated horizontal transfer of an aerobic denitrification gene between Escherichia coli.}, journal = {Biodegradation}, volume = {32}, number = {4}, pages = {435-448}, pmid = {33886019}, issn = {1572-9729}, support = {BK20201388//Natural Science Foundation of Jiangsu Province/ ; BE2018015//the Industry Prospect and Common Key Technologies in Jiangsu Province/ ; }, mesh = {Biodegradation, Environmental ; *Denitrification ; *Escherichia coli/genetics ; Plasmids/genetics ; }, abstract = {Bacterial genetic material can be horizontally transferred between microorganisms via outer membrane vesicles (OMVs) released by bacteria. Up to now, the application of vesicle-mediated horizontal transfer of "degrading genes" in environmental remediation has not been reported. In this study, the nirS gene from an aerobic denitrification bacterium, Pseudomonas stutzeri, was enclosed in a pET28a plasmid, transformed into Escherichia coli (E. coli) DH5α and expressed in E. coli BL21. The E. coli DH5α released OMVs containing the recombination plasmid pET28a-nirS-EGFP. When compared with the free pET28a-nirS-EGFP plasmid's inability to transform, nirS in OMVs could be transferred into E. coli BL21 with the transformation frequency of 2.76 × 10[6] CFU/g when the dosage of OMVs was 200 µg under natural conditions, and nirS could express successfully in recipient bacteria. Furthermore, the recipient bacteria that received OMVs containing pET28a-nirS-EGFP could produce 18.16 U/mL activity of nitrite reductase.}, }
@article {pmid33885815, year = {2021}, author = {Bruger, EL and Chubiz, LM and Rojas Echenique, JI and Renshaw, CJ and Espericueta, NV and Draghi, JA and Marx, CJ}, title = {Genetic Context Significantly Influences the Maintenance and Evolution of Degenerate Pathways.}, journal = {Genome biology and evolution}, volume = {13}, number = {6}, pages = {}, pmid = {33885815}, issn = {1759-6653}, support = {R01 GM078209/GM/NIGMS NIH HHS/United States ; }, mesh = {Epistasis, Genetic ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Glutathione/metabolism ; Metabolic Networks and Pathways/*genetics ; Methylobacteriaceae ; Plasmids ; }, abstract = {Understanding the evolution of novel physiological traits is highly relevant for expanding the characterization and manipulation of biological systems. Acquisition of new traits can be achieved through horizontal gene transfer (HGT). Here, we investigate drivers that promote or deter the maintenance of HGT-driven degeneracy, occurring when processes accomplish identical functions through nonidentical components. Subsequent evolution can optimize newly acquired functions; for example, beneficial alleles identified in an engineered Methylorubrum extorquens strain allowed it to utilize a "Foreign" formaldehyde oxidation pathway substituted for its Native pathway for methylotrophic growth. We examined the fitness consequences of interactions between these alleles when they were combined with the Native pathway or both (Dual) pathways. Unlike the Foreign pathway context where they evolved, these alleles were often neutral or deleterious when moved into these alternative genetic backgrounds. However, there were instances where combinations of multiple alleles resulted in higher fitness outcomes than individual allelic substitutions could provide. Importantly, the genetic context accompanying these allelic substitutions significantly altered the fitness landscape, shifting local fitness peaks and restricting the set of accessible evolutionary trajectories. These findings highlight how genetic context can negatively impact the probability of maintaining native and HGT-introduced functions together, making it difficult for degeneracy to evolve. However, in cases where the cost of maintaining degeneracy was mitigated by adding evolved alleles impacting the function of these pathways, we observed rare opportunities for pathway coevolution to occur. Together, our results highlight the importance of genetic context and resulting epistasis in retaining or losing HGT-acquired degenerate functions.}, }
@article {pmid33883832, year = {2020}, author = {Webale, MK and Guyah, B and Wanjala, C and Nyanga, PL and Webale, SK and Abonyo, C and Kitungulu, N and Kiboi, N and Bowen, N}, title = {Phenotypic and Genotypic Antibiotic Resistant diarrheagenic Escherichia coli pathotypes isolated from Children with Diarrhea in Nairobi City, Kenya.}, journal = {Ethiopian journal of health sciences}, volume = {30}, number = {6}, pages = {881-890}, pmid = {33883832}, issn = {2413-7170}, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Child ; Cross-Sectional Studies ; Diarrhea/drug therapy/epidemiology ; *Escherichia coli/genetics ; *Escherichia coli Infections/drug therapy/epidemiology ; Humans ; Kenya/epidemiology ; Microbial Sensitivity Tests ; }, abstract = {BACKGROUND: The marked genome plasticity of diarrheagenic Escherichia coli promotes emergence of pathotypes displaying unique phenotypic and genotypic resistance. This study examined phenotypic and genotypic antibiotic resistant diarrheagenic Escherichia coli pathotypes among children in Nairobi City, Kenya.<br><br>METHODS: In a cross-sectional study, diarrheagenic Escherichia coli pathotypes were isolated from stool samples and their phenotypic and genotypic resistance against eight antimicrobial agents assayed.<br><br>RESULTS: Diarrheagenic Escherichia coli was detected in 136(36.4%) children. Most of diarrheagenic Escherichia coli that were resistant to ampicillin, ceftriaxone, streptomycin, gentamycin, ciprofloxacin, chloramphenicol, erythromycin and tetracycline, harbored citm, bla CMY, aadA1, aac(3)-IV, qnr, catA, ere(A) and tet(A) corresponding resistant genes.<br><br>CONCLUSION: Antimicrobial-resistant genes are highly prevalent among phenotypic resistant ETEC pathotypes indicating a possibility of horizontal gene transfer in spreading antibiotic resistant genes among E. coli pathotypes.}, }
@article {pmid33881506, year = {2021}, author = {Bikash, B and Vilja, S and Mitchell, L and Keith, Y and Mikael, I and Mikko, MK and Jarmo, N}, title = {Differential regulation of undecylprodigiosin biosynthesis in the yeast-scavenging Streptomyces strain MBK6.}, journal = {FEMS microbiology letters}, volume = {368}, number = {8}, pages = {}, pmid = {33881506}, issn = {1574-6968}, mesh = {Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Molecular Structure ; Pigments, Biological/*biosynthesis ; Prodigiosin/*analogs &amp; derivatives/biosynthesis ; Promoter Regions, Genetic ; Saccharomyces cerevisiae ; Secondary Metabolism ; Streptomyces/genetics/*metabolism ; }, abstract = {Streptomyces are efficient chemists with a capacity to generate diverse and potent chemical scaffolds. The secondary metabolism of these soil-dwelling prokaryotes is stimulated upon interaction with other microbes in their complex ecosystem. We observed such an interaction when a Streptomyces isolate was cultivated in a media supplemented with dead yeast cells. Whole-genome analysis revealed that Streptomyces sp. MBK6 harbors the red cluster that is cryptic under normal environmental conditions. An interactive culture of MBK6 with dead yeast triggered the production of the red pigments metacycloprodigiosin and undecylprodigiosin. Streptomyces sp. MBK6 scavenges dead-yeast cells and preferentially grows in aggregates of sequestered yeasts within its mycelial network. We identified that the activation depends on the cluster-situated regulator, mbkZ, which may act as a cross-regulator. Cloning of this master regulator mbkZ in S. coelicolor with a constitutive promoter and promoter-deprived conditions generated different production levels of the red pigments. These surprising results were further validated by DNA-protein binding assays. The presence of the red cluster in Streptomyces sp. MBK6 provides a vivid example of horizontal gene transfer of an entire metabolic pathway followed by differential adaptation to a new environment through mutations in the receiver domain of the key regulatory protein MbkZ.}, }
@article {pmid33878498, year = {2021}, author = {Tan, Z and Chen, J and Liu, Y and Chen, L and Xu, Y and Zou, Y and Li, Y and Gong, B}, title = {The survival and removal mechanism of Sphingobacterium changzhouense TC931 under tetracycline stress and its' ecological safety after application.}, journal = {Bioresource technology}, volume = {333}, number = {}, pages = {125067}, doi = {10.1016/j.biortech.2021.125067}, pmid = {33878498}, issn = {1873-2976}, mesh = {Anti-Bacterial Agents ; Biodegradation, Environmental ; *Sphingobacterium/genetics ; *Tetracycline/analysis ; }, abstract = {Sphingobacterium changzhouense TC931 was isolated as a novel TC (tetracycline) removal bacterium through adsorption on extracellular polymerase substances (EPS) and cellular surface and biodegradation. TC biodegradation efficiency by strain TC931 was affected by solution initial pH and carbon source. Polysaccharides and hydrocarbons in EPS and cellular surface were responsible for TC biosorption. Eight possible biodegradation products were identified and the biodegradation pathway was proposed. Strain TC931 was rich in antibiotic resistance genes, and tetX-TC931 and antibiotics resistance genome island (GI) may be acquired via horizontal gene transfer in early evolutionary history. The GI was incomplete and may stable in strain TC931, but it could develop into an intact and transferability GI with help of other mobile genetic elements. This work offers a theoretical basis for understanding the survival and biodegradation mechanisms of S. changzhouense TC931 under TC stress, and offers an ecological safety assessment for its application in environmental bioremediation.}, }
@article {pmid33878316, year = {2021}, author = {Chen, Z and Yao, L and Sun, F and Zhu, Y and Li, N and Shen, D and Wang, M}, title = {Antibiotic resistance genes are enriched with prolonged age of refuse in small and medium-sized landfill systems.}, journal = {Environmental research}, volume = {197}, number = {}, pages = {111194}, doi = {10.1016/j.envres.2021.111194}, pmid = {33878316}, issn = {1096-0953}, mesh = {*Anti-Bacterial Agents/toxicity ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Metals, Heavy/analysis ; Solid Waste/analysis ; Waste Disposal Facilities ; }, abstract = {Landfills are sites for the disposal of waste over decades. The dynamics of contaminants during landfill treatment influence the functions and environmental risks of the landfill systems, but the patterns of these dynamics are not fully characterized, especially for antibiotic resistant genes (ARGs), an emerging contaminant of global concern. Here, seventeen typical ARG subtypes were quantitatively investigated in refuse samples from small and medium-sized landfills with ages of <3 years, ~5 years, and 8-10 years. The abundance of ARGs, including tetM, tetX, blaPER, emrB, sul1 and sul2, increased significantly (p < 0.05), approaching 8- to 304-fold on average, from refuse of < 3years to that of 8-10 years, while there was no obvious change (p > 0.05) in abundance for other ARGs, including tetQ, tetW, ampC, blaCTX-M, blaSHV, emrA, mefA, qnrD, qnrS, and mexF. Accordingly, resistance to tetracyclines, macrolides, and sulfonamides increased with landfill age, while resistance to β-lactams and quinolones remained unchanged. The increase in ARG abundance with increasing refuse age was probably related with the increased horizontal gene transfer (HGT) (indicated by the increased abundance of mobile gene elements) and the enhanced co-selective pressure (suggested by the increased contents of heavy metals). These results indicated a potential risk from ARG enrichment with an increase in refuse age in small and medium-sized landfills, which should be managed to ensure landfill safety.}, }
@article {pmid33877574, year = {2021}, author = {Kim, M and Park, J and Kang, M and Yang, J and Park, W}, title = {Gain and loss of antibiotic resistant genes in multidrug resistant bacteria: One Health perspective.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {59}, number = {6}, pages = {535-545}, pmid = {33877574}, issn = {1976-3794}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics/metabolism ; Bacterial Infections/drug therapy/microbiology ; Bacterial Proteins/*genetics/metabolism ; *Drug Resistance, Multiple, Bacterial ; Humans ; One Health ; }, abstract = {The emergence of multidrug resistance (MDR) has become a global health threat due to the increasing unnecessary use of antibiotics. Multidrug resistant bacteria occur mainly by accumulating resistance genes on mobile genetic elements (MGEs), made possible by horizontal gene transfer (HGT). Humans and animal guts along with natural and engineered environments such as wastewater treatment plants and manured soils have proven to be the major reservoirs and hotspots of spreading antibiotic resistance genes (ARGs). As those environments support the dissemination of MGEs through the complex interactions that take place at the human-animal-environment interfaces, a growing One Health challenge is for multiple sectors to communicate and work together to prevent the emergence and spread of MDR bacteria. However, maintenance of ARGs in a bacterial chromosome and/or plasmids in the environments might place energy burdens on bacterial fitness in the absence of antibiotics, and those unnecessary ARGs could eventually be lost. This review highlights and summarizes the current investigations into the gain and loss of ARG genes in MDR bacteria among human-animal-environment interfaces. We also suggest alternative treatments such as combinatory therapies or sequential use of different classes of antibiotics/adjuvants, treatment with enzyme-inhibitors, and phage therapy with antibiotics to solve the MDR problem from the perspective of One Health issues.}, }
@article {pmid33877415, year = {2021}, author = {Luo, X and Lin, J and Yan, J and Kuang, X and Su, H and Lin, W and Luo, L}, title = {Characterization of DinJ-YafQ toxin-antitoxin module in Tetragenococcus halophilus: activity, interplay, and evolution.}, journal = {Applied microbiology and biotechnology}, volume = {105}, number = {9}, pages = {3659-3672}, pmid = {33877415}, issn = {1432-0614}, support = {31771962//National Natural Science Foundation of China/ ; 31271924//National Natural Science Foundation of China/ ; }, mesh = {*Antitoxins ; *Bacterial Toxins/genetics ; Enterococcaceae ; Escherichia coli/genetics ; *Escherichia coli Proteins ; }, abstract = {Tetragenococcus halophilus is a moderately halophilic lactic acid bacterium widely used in high-salt food fermentation because of its coping ability under various stress conditions. Bacterial toxin-antitoxin (TA) modules are widely distributed and play important roles in stress response, but those specific for genus Tetragenococcus have never been explored. Here, a bona fide TA module named DinJ1-YafQ1[tha] was characterized in T. halophilus. The toxin protein YafQ1[tha] acts as a ribonuclease, and its overexpression severely inhibits Escherichia coli growth. These toxic effects can be eliminated by introducing DinJ1[tha], indicating that YafQ1[tha] activity is blocked by the formed DinJ1-YafQ1[tha] complex. In vivo and in vitro assays showed that DinJ1[tha] alone or DinJ1-YafQ1[tha] complex can repress the transcription of dinJ1-yafQ1[tha] operon by binding directly to the promoter sequence. In addition, dinJ1-yafQ1[tha] is involved in plasmid maintenance and stress response, and its transcriptional level is regulated by various stresses. These findings reveal the possible roles of DinJ1-YafQ1[tha] system in the stress adaptation processes of T. halophilus during fermentation. A single antitoxin DinJ2[tha] without a cognate toxin protein was also found. Its sequence shows low similarity to that of DinJ1[tha], indicating that this antitoxin may have evolved from a different ancestor. Moreover, DinJ2[tha] can cross-interact with noncognate toxin YafQ1[tha] and cross-regulate with dinJ1-yafQ1[tha] operon. In summary, DinJ-YafQ[tha] characterization may be helpful in investigating the key roles of TA systems in T. halophilus and serves as a foundation for further research. KEY POINTS: • dinJ1-yafQ1[tha] is the first functional TA module characterized in T. halophilus and upregulated significantly upon osmotic and acidic stress. • DinJ2[tha] can exhibit physical and transcriptional interplay with DinJ1-YafQ1[tha]. • dinJ2[tha] may be acquired from bacteria in distant affiliation and inserted into the T. halophilus genome through horizontal gene transfer.}, }
@article {pmid33875666, year = {2021}, author = {van Gestel, J and Bareia, T and Tenennbaum, B and Dal Co, A and Guler, P and Aframian, N and Puyesky, S and Grinberg, I and D'Souza, GG and Erez, Z and Ackermann, M and Eldar, A}, title = {Short-range quorum sensing controls horizontal gene transfer at micron scale in bacterial communities.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {2324}, pmid = {33875666}, issn = {2041-1723}, mesh = {Bacillus subtilis/genetics/metabolism ; Bacteria/cytology/*genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Conjugation, Genetic/*genetics ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal/*genetics ; Microscopy, Fluorescence/methods ; Quorum Sensing/*genetics ; Signal Transduction/genetics ; }, abstract = {In bacterial communities, cells often communicate by the release and detection of small diffusible molecules, a process termed quorum-sensing. Signal molecules are thought to broadly diffuse in space; however, they often regulate traits such as conjugative transfer that strictly depend on the local community composition. This raises the question how nearby cells within the community can be detected. Here, we compare the range of communication of different quorum-sensing systems. While some systems support long-range communication, we show that others support a form of highly localized communication. In these systems, signal molecules propagate no more than a few microns away from signaling cells, due to the irreversible uptake of the signal molecules from the environment. This enables cells to accurately detect micron scale changes in the community composition. Several mobile genetic elements, including conjugative elements and phages, employ short-range communication to assess the fraction of susceptible host cells in their vicinity and adaptively trigger horizontal gene transfer in response. Our results underscore the complex spatial biology of bacteria, which can communicate and interact at widely different spatial scales.}, }
@article {pmid33874906, year = {2021}, author = {Chen, K and Wang, L and Chen, H and Zhang, C and Wang, S and Chu, P and Li, S and Fu, H and Sun, T and Liu, M and Yang, Q and Zou, H and Zhuang, W}, title = {Complete genome sequence analysis of the peanut pathogen Ralstonia solanacearum strain Rs-P.362200.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {118}, pmid = {33874906}, issn = {1471-2180}, mesh = {Arachis/microbiology ; Base Composition/genetics ; Genome, Bacterial/*genetics ; Genomic Islands/genetics ; Phylogeny ; Ralstonia solanacearum/chemistry/classification/*genetics ; }, abstract = {BACKGROUND: Bacterial wilt caused by Ralstonia solanacearum species complex is an important soil-borne disease worldwide that affects more than 450 plant species, including peanut, leading to great yield and quality losses. However, there are no effective measures to control bacterial wilt. The reason is the lack of research on the pathogenic mechanism of bacterial wilt.<br><br>RESULTS: Here, we report the complete genome of a toxic Ralstonia solanacearum species complex strain, Rs-P.362200, a peanut pathogen, with a total genome size of 5.86&#x2009;Mb, encoding 5056 genes and the average G&#x2009;+&#x2009;C content of 67%. Among the coding genes, 75 type III effector proteins and 12 pseudogenes were predicted. Phylogenetic analysis of 41 strains including Rs-P.362200 shows that genetic distance mainly depended on geographic origins then phylotypes and host species, which associated with the complexity of the strain. The distribution and numbers of effectors and other virulence factors changed among different strains. Comparative genomic analysis showed that 29 families of 113 genes were unique to this strain compared with the other four pathogenic strains. Through the analysis of specific genes, two homologous genes (gene ID: 2_657 and 3_83), encoding virulence protein (such as RipP1) may be associated with the host range of the Rs-P.362200 strain. It was found that the bacteria contained 30 pathogenicity islands and 6 prophages containing 378 genes, 7 effectors and 363 genes, 8 effectors, respectively, which may be related to the mechanism of horizontal gene transfer and pathogenicity evaluation. Although the hosts of HA4-1 and Rs-P.362200 strains are the same, they have specific genes to their own genomes. The number of genomic islands and prophages in HA4-1 genome is more than that in Rs-P.36220, indicating a rapid change of the bacterial wilt pathogens.<br><br>CONCLUSION: The complete genome sequence analysis of peanut bacterial wilt pathogen enhanced the information of R. solanacearum genome. This research lays a theoretical foundation for future research on the interaction between Ralstonia solanacearum and peanut.}, }
@article {pmid33868258, year = {2021}, author = {Pinaud, S and Tetreau, G and Poteaux, P and Galinier, R and Chaparro, C and Lassalle, D and Portet, A and Simphor, E and Gourbal, B and Duval, D}, title = {New Insights Into Biomphalysin Gene Family Diversification in the Vector Snail Biomphalaria glabrata.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {635131}, pmid = {33868258}, issn = {1664-3224}, mesh = {Animals ; Biomphalaria/*genetics/metabolism/parasitology ; *Disease Vectors ; *Evolution, Molecular ; Gene Duplication ; Genetic Variation ; Host-Parasite Interactions ; *Multigene Family ; Phylogeny ; Pore Forming Cytotoxic Proteins/*genetics/metabolism ; Schistosoma mansoni/*pathogenicity ; Species Specificity ; }, abstract = {Aerolysins initially characterized as virulence factors in bacteria are increasingly found in massive genome and transcriptome sequencing data from metazoans. Horizontal gene transfer has been demonstrated as the main way of aerolysin-related toxins acquisition in metazoans. However, only few studies have focused on their potential biological functions in such organisms. Herein, we present an extensive characterization of a multigene family encoding aerolysins - named biomphalysin - in Biomphalaria glabrata snail, the intermediate host of the trematode Schistosoma mansoni. Our results highlight that duplication and domestication of an acquired bacterial toxin gene in the snail genome result in the acquisition of a novel and diversified toxin family. Twenty-three biomphalysin genes were identified. All are expressed and exhibited a tissue-specific expression pattern. An in silico structural analysis was performed to highlight the central role played by two distinct domains i) a large lobe involved in the lytic function of these snail toxins which constrained their evolution and ii) a small lobe which is structurally variable between biomphalysin toxins and that matched to various functional domains involved in moiety recognition of targets cells. A functional approach suggests that the repertoire of biomphalysins that bind to pathogens, depends on the type of pathogen encountered. These results underline a neo-and sub-functionalization of the biomphalysin toxins, which have the potential to increase the range of effectors in the snail's immune arsenal.}, }
@article {pmid33867342, year = {2020}, author = {Javed, S and Mirani, ZA and Pirzada, ZA}, title = {Study of class 1 integrons and plasmid profile among multiple drug resistant uropathogenic Escherichia coli.}, journal = {Pakistan journal of pharmaceutical sciences}, volume = {33}, number = {6}, pages = {2643-2649}, pmid = {33867342}, issn = {1011-601X}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/drug effects/*genetics ; Escherichia coli Infections/microbiology ; Humans ; Integrons/*genetics ; Microbial Sensitivity Tests ; Plasmids/*genetics ; Urinary Tract Infections/microbiology ; Uropathogenic Escherichia coli/*drug effects/*genetics ; }, abstract = {The emergence of multidrug resistance in uropathogenic Escherichia coli (UPEC) is associated with the presence of drug resistant plasmids and integrons which facilitate horizontal gene transfer which impose serious challenges in patients with urinary tract infections (UTIs). The proposed research study is designed to determine emerging antibiotic resistance trends and the presence of plasmids and class 1 integron in UPEC. A total 74 strains of urinary pathogens were procured among them 50 UPEC isolates were selected and their antibiotic resistance pattern was performed by CLSI guidelines. Plasmid DNA of UPEC strains was extracted by kit method and profiling was done using gel electrophoresis. Class 1 integron genes intI1, sul1 and qacEΔ1 were detected by multiplex PCR in UPEC. Among gram negative urinary isolates, 50 (68%) isolates were E. coli, while the rest were Klebsiella, Pseudomonas, Enterobacter etc. All the tested UPEC were totally resistant to quinolones while sensitive to fosfomycin, imipenem and colistin antibiotics. Majority of multidrug resistant UPEC showed common resistant phenotype of fluoroquinolones, cephalosporins, sulfamethoxazole/trimethoprim and aminoglycosides. Out of the 50 UPEC isolates 46 (92%) were multi-drug resistant having one to three plasmids of more than 1kb and 41 (82%) possessed class 1 integron genes. Over all association between antibiotic resistance and presence of class 1 integron genes showed statistically significant results (p<0.05). Our results also depict a strong correlation between multidrug resistance and presence of class 1 integron in UPEC isolates (p<0.05). The presence of multiple plasmid bands in MDR E. coli strains and high prevalence of class 1 integrons indicate the role of plasmids and integrons in the horizontal transmission of antibiotic resistance genes in UPEC.}, }
@article {pmid33866168, year = {2021}, author = {Nguyen, AQ and Vu, HP and Nguyen, LN and Wang, Q and Djordjevic, SP and Donner, E and Yin, H and Nghiem, LD}, title = {Monitoring antibiotic resistance genes in wastewater treatment: Current strategies and future challenges.}, journal = {The Science of the total environment}, volume = {783}, number = {}, pages = {146964}, doi = {10.1016/j.scitotenv.2021.146964}, pmid = {33866168}, issn = {1879-1026}, mesh = {Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Animals ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; Humans ; *Wastewater ; }, abstract = {Antimicrobial resistance (AMR) is a growing threat to human and animal health. Progress in molecular biology has revealed new and significant challenges for AMR mitigation given the immense diversity of antibiotic resistance genes (ARGs), the complexity of ARG transfer, and the broad range of omnipresent factors contributing to AMR. Municipal, hospital and abattoir wastewater are collected and treated in wastewater treatment plants (WWTPs), where the presence of diverse selection pressures together with a highly concentrated consortium of pathogenic/commensal microbes create favourable conditions for the transfer of ARGs and proliferation of antibiotic resistant bacteria (ARB). The rapid emergence of antibiotic resistant pathogens of clinical and veterinary significance over the past 80 years has re-defined the role of WWTPs as a focal point in the fight against AMR. By reviewing the occurrence of ARGs in wastewater and sludge and the current technologies used to quantify ARGs and identify ARB, this paper provides a research roadmap to address existing challenges in AMR control via wastewater treatment. Wastewater treatment is a double-edged sword that can act as either a pathway for AMR spread or as a barrier to reduce the environmental release of anthropogenic AMR. State of the art ARB identification technologies, such as metagenomic sequencing and fluorescence-activated cell sorting, have enriched ARG/ARB databases, unveiled keystone species in AMR networks, and improved the resolution of AMR dissemination models. Data and information provided in this review highlight significant knowledge gaps. These include inconsistencies in ARG reporting units, lack of ARG/ARB monitoring surrogates, lack of a standardised protocol for determining ARG removal via wastewater treatments, and the inability to support appropriate risk assessment. This is due to a lack of standard monitoring targets and agreed threshold values, and paucity of information on the ARG-pathogen host relationship and risk management. These research gaps need to be addressed and research findings need to be transformed into practical guidance for WWTP operators to enable effective progress towards mitigating the evolution and spread of AMR.}, }
@article {pmid33866091, year = {2021}, author = {Shen, C and Ma, F and Deng, S and Zhong, LL and El-Sayed Ahmed, MAE and Zhang, G and Yan, B and Dai, M and Yang, F and Xia, Y and Tian, GB}, title = {Prevalence, genomic characteristics, and transmission dynamics of mcr-1-positive Salmonella enterica Typhimurium from patients with infectious diarrhea.}, journal = {International journal of medical microbiology : IJMM}, volume = {311}, number = {4}, pages = {151501}, doi = {10.1016/j.ijmm.2021.151501}, pmid = {33866091}, issn = {1618-0607}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; China/epidemiology ; Diarrhea/epidemiology ; Genomics ; Humans ; Plasmids/genetics ; Prevalence ; *Salmonella typhimurium/genetics ; Swine ; }, abstract = {BACKGROUND: Previous studies reported the prevalence of mcr-1 among clinical infected Salmonella isolates in China. However, the transmission dynamics of mcr-1 in different ecological niches were not well investigated. Our objective is to exhibit the transmission dynamics of mcr-1 in Salmonella.<br><br>METHODS: 598 Salmonella isolates were recovered from ten hospitals; besides 936 pig faces and 167 pork samples were collected from January 2015 to December 2017 in Guangzhou, China. PCR and sequencing were used to identify mcr-1-positive Salmonella. Antimicrobial susceptibility testing was performed with 16 antimicrobials. Conjugation, S1-PFGE, and Southern blot were used to determine the transferability and location of mcr-1. Whole-genome sequencing was used to investigate pangenome, phylogeny, plasmid, and transposon.<br><br>RESULTS: Eleven mcr-1-positive Salmonella isolates were identified from patients with infectious diarrhea. Five pig fecal samples and three pork samples contained mcr-1-positive Salmonella isolates. All isolates were multi-drug resistant. The mcr-1 genes were located on &#x223c;210-250 kb IncHI2-pST3 plasmids, and 12 mcr-1 genes were transferable. All isolates were assigned to ST34 or its genetically closed STs. The distribution of the core-genome network was significantly correlated with source distributions. The accessory genes-based network demonstrated that the diverse clonal complexes could share highly similar accessory genomes.<br><br>CONCLUSIONS: The prevalence of mcr-1-positive Salmonella among different sources was low. Clonal transmission could not be the main reason for the expansion of mcr-1-positive Salmonella, but be attributed to the horizontal transfer of IncHI2-pST3 plasmid. Continuous surveillance on Salmonella should be performed to investigate the response of colistin banning in food-producing animals by mcr-1-positive Salmonella populations.}, }
@article {pmid33865960, year = {2021}, author = {Hage, H and Rosso, MN and Tarrago, L}, title = {Distribution of methionine sulfoxide reductases in fungi and conservation of the free-methionine-R-sulfoxide reductase in multicellular eukaryotes.}, journal = {Free radical biology &amp; medicine}, volume = {169}, number = {}, pages = {187-215}, doi = {10.1016/j.freeradbiomed.2021.04.013}, pmid = {33865960}, issn = {1873-4596}, mesh = {*Eukaryota/metabolism ; Fungi/genetics ; Methionine/metabolism ; *Methionine Sulfoxide Reductases/genetics/metabolism ; Oxidation-Reduction ; Phylogeny ; }, abstract = {Methionine, either as a free amino acid or included in proteins, can be oxidized into methionine sulfoxide (MetO), which exists as R and S diastereomers. Almost all characterized organisms possess thiol-oxidoreductases named methionine sulfoxide reductase (Msr) enzymes to reduce MetO back to Met. MsrA and MsrB reduce the S and R diastereomers of MetO, respectively, with strict stereospecificity and are found in almost all organisms. Another type of thiol-oxidoreductase, the free-methionine-R-sulfoxide reductase (fRMsr), identified so far in prokaryotes and a few unicellular eukaryotes, reduces the R MetO diastereomer of the free amino acid. Moreover, some bacteria possess molybdenum-containing enzymes that reduce MetO, either in the free or protein-bound forms. All these Msrs play important roles in the protection of organisms against oxidative stress. Fungi are heterotrophic eukaryotes that colonize all niches on Earth and play fundamental functions, in organic matter recycling, as symbionts, or as pathogens of numerous organisms. However, our knowledge on fungal Msrs is still limited. Here, we performed a survey of msr genes in almost 700 genomes across the fungal kingdom. We show that most fungi possess one gene coding for each type of methionine sulfoxide reductase: MsrA, MsrB, and fRMsr. However, several fungi living in anaerobic environments or as obligate intracellular parasites were devoid of msr genes. Sequence inspection and phylogenetic analyses allowed us to identify non-canonical sequences with potentially novel enzymatic properties. Finaly, we identified several ocurences of msr horizontal gene transfer from bacteria to fungi.}, }
@article {pmid33865444, year = {2021}, author = {Van Vlierberghe, M and Philippe, H and Baurain, D}, title = {Broadly sampled orthologous groups of eukaryotic proteins for the phylogenetic study of plastid-bearing lineages.}, journal = {BMC research notes}, volume = {14}, number = {1}, pages = {143}, pmid = {33865444}, issn = {1756-0500}, support = {"Cr&#xe9;dit de d&#xe9;marrage 2012" SFRD-12/04//Universit&#xe9; de Li&#xe8;ge (BE)/ ; "Cr&#xe9;dit de recherche 2014" CDR J.0080.15//Fonds De La Recherche Scientifique - FNRS/ ; }, mesh = {Eukaryota/*genetics ; Evolution, Molecular ; Genome ; *Phylogeny ; Plants ; Plastids/*genetics ; }, abstract = {OBJECTIVES: Identifying orthology relationships among sequences is essential to understand evolution, diversity of life and ancestry among organisms. To build alignments of orthologous sequences, phylogenomic pipelines often start with all-vs-all similarity searches, followed by a clustering step. For the protein clusters (orthogroups) to be as accurate as possible, proteomes of good quality are needed. Here, our objective is to assemble a data set especially suited for the phylogenomic study of algae and formerly photosynthetic eukaryotes, which implies the proper integration of organellar data, to enable distinguishing between several copies of one gene (paralogs), taking into account their cellular compartment, if necessary.<br><br>DATA DESCRIPTION: We submitted 73 top-quality and taxonomically diverse proteomes to OrthoFinder. We obtained 47,266 orthogroups and identified 11,775 orthogroups with at least two algae. Whenever possible, sequences were functionally annotated with eggNOG and tagged after their genomic and target compartment(s). Then we aligned and computed phylogenetic trees for the orthogroups with IQ-TREE. Finally, these trees were further processed by identifying and pruning the subtrees exclusively composed of plastid-bearing organisms to yield a set of 31,784 clans suitable for studying photosynthetic organism genome evolution.}, }
@article {pmid33864959, year = {2021}, author = {Song, L and Wang, C and Jiang, G and Ma, J and Li, Y and Chen, H and Guo, J}, title = {Bioaerosol is an important transmission route of antibiotic resistance genes in pig farms.}, journal = {Environment international}, volume = {154}, number = {}, pages = {106559}, doi = {10.1016/j.envint.2021.106559}, pmid = {33864959}, issn = {1873-6750}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial ; Farms ; *Genes, Bacterial ; Swine ; }, abstract = {Although pig farms are hotspots of antibiotic resistance due to intensive use of antibiotics, little is known about the abundance, diversity and transmission of airborne antibiotic resistance genes (ARGs). This study reports that bioaerosol is an important spread route of ARGs in pig farms. ARGs, mobile genetic elements (MGEs), and bacterial communities were investigated in both air and feces samples during winter and summer. The average concentration of airborne ARGs and MGEs during winter is higher than that during summer when using the ventilation system. The tetM is identified as the predominant airborne ARG with abundance of 6.3 ± 1.2 log copies/m[3]. Clostridium and Streptococcus are two dominant bacteria and several opportunistic pathogens are detected in air samples. High temperature is favorable for more diverse bacterial communities, but relative humidity has negative effects. The wind speed promotes the spread of airborne ARGs. The network analysis results show the average fecal contribution to airborne bacteria is 19.9% and 59.4% during summer and winter, respectively. Horizontal gene transfer plays an important role in the dissemination of airborne ARGs during winter (77.8% possibility), while a lower possibility of 12.0% in summer.}, }
@article {pmid33862079, year = {2021}, author = {Wang, X and Zhang, M and Loh, B and Leptihn, S and Ahmed, T and Li, B}, title = {A novel NRPS cluster, acquired by horizontal gene transfer from algae, regulates siderophore iron metabolism in Burkholderia seminalis R456.}, journal = {International journal of biological macromolecules}, volume = {182}, number = {}, pages = {838-848}, doi = {10.1016/j.ijbiomac.2021.04.051}, pmid = {33862079}, issn = {1879-0003}, mesh = {Bacterial Proteins/*genetics/metabolism ; Burkholderia/*genetics/metabolism ; Chlorophyta/genetics ; Cyanobacteria/genetics ; *Gene Transfer, Horizontal ; Iron/*metabolism ; Peptide Synthases/*genetics/metabolism ; Phenols/metabolism ; Plant Proteins/genetics/metabolism ; Siderophores/*metabolism ; Thiazoles/metabolism ; }, abstract = {In an environment with limited iron levels, sufficiently high intracellular iron concentrations are critical for bacterial survival. When iron levels are low, many bacteria including those of the Burkholderia cepacia group secrete chemically diverse siderophores to capture Fe[3+]. The synthesis of the two main siderophores, ornibactin and pyochelin, is regulated in an iron concentration dependent manner via the regulator protein Fur. In this study, we identified a novel Nonribosomal Peptide Synthetase (NRPS) cluster in strain R456 of Burkholderia seminalis, a member of the B. cepacia group. We show that the NRPS cluster not only allows the production of a so-far undescribed siderophore, but is also required for ornibactin and pyochelin production as it is a crucial component in the signaling pathway targeting the global iron regulating effector Fur which regulates siderophore production. Furthermore, the NRPS cluster is also involved in cell motility and biofilm formation, both of which are directly dependent on iron concentration in various bacteria. Interestingly, our data suggests that this newly discovered NRPS cluster which regulates siderophore iron metabolism in bacteria was obtained by horizontal gene transfer from algae.}, }
@article {pmid33859630, year = {2021}, author = {Ferreira, JL and Coleman, I and Addison, ML and Zachs, T and Quigley, BL and Wuichet, K and Beeby, M}, title = {The "Jack-of-all-Trades" Flagellum From Salmonella and E. coli Was Horizontally Acquired From an Ancestral β-Proteobacterium.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {643180}, pmid = {33859630}, issn = {1664-302X}, support = {//Wellcome Trust/United Kingdom ; MR/P019374/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {The γ-proteobacteria are a group of diverse bacteria including pathogenic Escherichia, Salmonella, Vibrio, and Pseudomonas species. The majority swim in liquids with polar, sodium-driven flagella and swarm on surfaces with lateral, non-chemotactic flagella. Notable exceptions are the enteric Enterobacteriaceae such as Salmonella and E. coli. Many of the well-studied Enterobacteriaceae are gut bacteria that both swim and swarm with the same proton-driven peritrichous flagella. How different flagella evolved in closely related lineages, however, has remained unclear. Here, we describe our phylogenetic finding that Enterobacteriaceae flagella are not native polar or lateral γ-proteobacterial flagella but were horizontally acquired from an ancestral β-proteobacterium. Using electron cryo-tomography and subtomogram averaging, we confirmed that Enterobacteriaceae flagellar motors resemble contemporary β-proteobacterial motors and are distinct to the polar and lateral motors of other γ-proteobacteria. Structural comparisons support a model in which γ-proteobacterial motors have specialized, suggesting that acquisition of a β-proteobacterial flagellum may have been beneficial as a general-purpose motor suitable for adjusting to diverse conditions. This acquisition may have played a role in the development of the enteric lifestyle.}, }
@article {pmid33858100, year = {2021}, author = {Wang, J and Gu, J and Wang, X and Song, Z and Dai, X and Guo, H and Yu, J and Zhao, W and Lei, L}, title = {Enhanced removal of antibiotic resistance genes and mobile genetic elements during swine manure composting inoculated with mature compost.}, journal = {Journal of hazardous materials}, volume = {411}, number = {}, pages = {125135}, doi = {10.1016/j.jhazmat.2021.125135}, pmid = {33858100}, issn = {1873-3336}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Composting ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Interspersed Repetitive Sequences/genetics ; Manure ; Swine ; }, abstract = {Livestock manure is a major source of antibiotic resistance genes (ARGs) that enter the environment. This study assessed the effects of inoculation with mature compost (MC) on the fates of ARGs and the bacterial community during swine manure composting. The results showed that MC prolonged the thermophilic period and promoted the decomposition of organic matter, which was due to the rapid growth and reproduction of thermophilic bacteria (Bacillus, Thermobifida, and Thermobacillus). MC significantly reduced the relative abundances of ARGs (1.02 logs) and mobile genetic elements (MGEs) (1.70 logs) after composting, especially sulfanilamide resistance genes. The total ARGs removal rate was 1.11 times higher in MC than the control. Redundancy analysis and structural equation modeling showed that horizontal gene transfer mediated by MGEs (ISCR1 and intI1) was the main direct factor related to the changes in ARGs during composting, whereas the C/N ratio and pH were the two most important indirect factors. Network analysis showed that members of Firmicutes comprising Romboutsia, Clostridisensu_stricto_1, and Terrisporobacter were the main bacterial hosts of ARGs and MGEs. MC reduced the risk of ARGs transmission by decreasing the abundances of bacterial hosts. Thus, MC is a promising strategy for reducing the proliferation risk of ARGs.}, }
@article {pmid33853933, year = {2021}, author = {Álvarez-Narváez, S and Huber, L and Giguère, S and Hart, KA and Berghaus, RD and Sanchez, S and Cohen, ND}, title = {Epidemiology and Molecular Basis of Multidrug Resistance in Rhodococcus equi.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {85}, number = {2}, pages = {}, pmid = {33853933}, issn = {1098-5557}, mesh = {Actinomycetales Infections/*drug therapy/*epidemiology ; Animals ; Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Multiple/*drug effects ; Humans ; Rhodococcus equi/*drug effects ; Soil ; }, abstract = {The development and spread of antimicrobial resistance are major concerns for human and animal health. The effects of the overuse of antimicrobials in domestic animals on the dissemination of resistant microbes to humans and the environment are of concern worldwide. Rhodococcus equi is an ideal model to illustrate the spread of antimicrobial resistance at the animal-human-environment interface because it is a natural soil saprophyte that is an intracellular zoonotic pathogen that produces severe bronchopneumonia in many animal species and humans. Globally, R. equi is most often recognized as causing severe pneumonia in foals that results in animal suffering and increased production costs for the many horse-breeding farms where the disease occurs. Because highly effective preventive measures for R. equi are lacking, thoracic ultrasonographic screening and antimicrobial chemotherapy of subclinically affected foals have been used for controlling this disease during the last 20 years. The resultant increase in antimicrobial use attributable to this "screen-and-treat" approach at farms where the disease is endemic has likely driven the emergence of multidrug-resistant (MDR) R. equi in foals and their environment. This review summarizes the factors that contributed to the development and spread of MDR R. equi, the molecular epidemiology of the emergence of MDR R. equi, the repercussions of MDR R. equi for veterinary and human medicine, and measures that might mitigate antimicrobial resistance at horse-breeding farms, such as alternative treatments to traditional antibiotics. Knowledge of the emergence and spread of MDR R. equi is of broad importance for understanding how antimicrobial use in domestic animals can impact the health of animals, their environment, and human beings.}, }
@article {pmid33852872, year = {2021}, author = {Danneels, B and Viruel, J and Mcgrath, K and Janssens, SB and Wales, N and Wilkin, P and Carlier, A}, title = {Patterns of transmission and horizontal gene transfer in the Dioscorea sansibarensis leaf symbiosis revealed by whole-genome sequencing.}, journal = {Current biology : CB}, volume = {31}, number = {12}, pages = {2666-2673.e4}, doi = {10.1016/j.cub.2021.03.049}, pmid = {33852872}, issn = {1879-0445}, mesh = {*Dioscorea/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial ; Phylogeny ; Plant Leaves ; *Symbiosis ; }, abstract = {Leaves of the wild yam species Dioscorea sansibarensis display prominent forerunner or "drip" tips filled with extracellular bacteria of the species Orrella dioscoreae.[1] This species of yam is native to Madagascar and tropical Africa and reproduces mainly asexually through aerial bulbils and underground tubers, which also contain a small population of O. dioscoreae.[2][,][3] Despite apparent vertical transmission, the genome of O. dioscoreae does not show any of the hallmarks of genome erosion often found in hereditary symbionts (e.g., small genome size and accumulation of pseudogenes).[4-6] We investigated here the range and distribution of leaf symbiosis between D. sansibarensis and O. dioscoreae using preserved leaf samples from herbarium collections that were originally collected from various locations in Africa. We recovered DNA from the extracellular symbiont in all samples, showing that the symbiosis is widespread throughout continental Africa and Madagascar. Despite the degraded nature of this DNA, we constructed 17 symbiont genomes using de novo methods without relying on a reference. Phylogenetic and genomic analyses revealed that horizontal transmission of symbionts and horizontal gene transfer have shaped the evolution of the symbiont. These mechanisms could help explain lack of signs of reductive genome evolution despite an obligate host-associated lifestyle. Furthermore, phylogenetic analysis of D. sansibarensis based on plastid genomes revealed a strong geographical clustering of samples and provided evidence that the symbiosis originated at least 13 mya, earlier than previously estimated.[3].}, }
@article {pmid33848900, year = {2021}, author = {Chen, B and Han, J and Dai, H and Jia, P}, title = {Biocide-tolerance and antibiotic-resistance in community environments and risk of direct transfers to humans: Unintended consequences of community-wide surface disinfecting during COVID-19?.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {283}, number = {}, pages = {117074}, pmid = {33848900}, issn = {1873-6424}, mesh = {Anti-Bacterial Agents/pharmacology ; *COVID-19 ; *Disinfectants/toxicity ; Drug Resistance, Microbial ; Humans ; Microbial Sensitivity Tests ; SARS-CoV-2 ; }, abstract = {During the current pandemic, chemical disinfectants are ubiquitously and routinely used in community environments, especially on common touch surfaces in public settings, as a means of controlling the virus spread. An underappreciated risk in current regulatory guidelines and scholarly discussions, however, is that the persisting input of chemical disinfectants can exacerbate the growth of biocide-tolerant and antibiotic-resistant bacteria on those surfaces and allow their direct transfers to humans. For COVID-19, the most commonly used disinfecting agents are quaternary ammonium compounds, hydrogen peroxide, sodium hypochlorite, and ethanol, which account for two-thirds of the active ingredients in current EPA-approved disinfectant products for the novel coronavirus. Tolerance to each of these compounds, which can be either intrinsic or acquired, has been observed on various bacterial pathogens. Of those, mutations and horizontal gene transfer, upregulation of efflux pumps, membrane alteration, and biofilm formation are the common mechanisms conferring biocide tolerance in bacteria. Further, the linkage between disinfectant use and antibiotic resistance was suggested in laboratory and real-life settings. Evidence showed that substantial bacterial transfers to hands could effectuate from short contacts with surrounding surfaces and further from fingers to lips. While current literature on disinfectant-induced antimicrobial resistance predominantly focuses on municipal wastes and the natural environments, in reality the community and public settings are most severely impacted by intensive and regular chemical disinfecting during COVID-19 and, due to their proximity to humans, biocide-tolerant and antibiotic-resistant bacteria emerged in these environments may pose risks of direct transfers to humans, particularly in densely populated urban communities. Here we highlight these risk factors by reviewing the most pertinent and up-to-date evidence, and provide several feasible strategies to mitigate these risks in the scenario of a prolonging pandemic.}, }
@article {pmid33848480, year = {2021}, author = {Blais, C and Archibald, JM}, title = {The past, present and future of the tree of life.}, journal = {Current biology : CB}, volume = {31}, number = {7}, pages = {R314-R321}, doi = {10.1016/j.cub.2021.02.052}, pmid = {33848480}, issn = {1879-0445}, mesh = {Animals ; Gene Transfer, Horizontal/genetics ; Genomics/*trends ; *Phylogeny ; Prokaryotic Cells/metabolism ; }, abstract = {The advent of comparative genomics in the late 1990s led to the discovery of extensive lateral gene transfer in prokaryotes. The resulting debate over whether life as a whole is best represented as a tree or a network has since given way to a general consensus in which trees and networks co-exist rather than stand in opposition. Embracing this consensus allows us to move beyond the question of which is true or false. The future of the tree of life debate lies in asking what trees and networks can, and should, do for science.}, }
@article {pmid33848429, year = {2021}, author = {Maeda, HA and Fernie, AR}, title = {Evolutionary History of Plant Metabolism.}, journal = {Annual review of plant biology}, volume = {72}, number = {}, pages = {185-216}, doi = {10.1146/annurev-arplant-080620-031054}, pmid = {33848429}, issn = {1545-2123}, mesh = {Eukaryota ; Evolution, Molecular ; Gene Duplication ; *Gene Transfer, Horizontal ; Metabolic Networks and Pathways ; Phylogeny ; *Plants ; }, abstract = {Tremendous chemical diversity is the hallmark of plants and is supported by highly complex biochemical machinery. Plant metabolic enzymes originated and were transferred from eukaryotic and prokaryotic ancestors and further diversified by the unprecedented rates of gene duplication and functionalization experienced in land plants. Unlike microbes, which have frequent horizontal gene transfer events and multiple inputs of energy and organic carbon, land plants predominantly rely on organic carbon generated from CO2 and have experienced very few, if any, gene transfers during their recent evolutionary history. As such, plant metabolic networks have evolved in a stepwise manner and on existing networks under various evolutionary constraints. This review aims to take a broader view of plant metabolic evolution and lay a framework to further explore evolutionary mechanisms of the complex metabolic network. Understanding the underlying metabolic and genetic constraints is also an empirical prerequisite for rational engineering and redesigning of plant metabolic pathways.}, }
@article {pmid33846600, year = {2021}, author = {Brito, IL}, title = {Examining horizontal gene transfer in microbial communities.}, journal = {Nature reviews. Microbiology}, volume = {19}, number = {7}, pages = {442-453}, pmid = {33846600}, issn = {1740-1534}, support = {DP2 HL141007/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics ; Bacterial Physiological Phenomena ; *Gene Transfer, Horizontal ; Humans ; *Microbiota ; Polymerase Chain Reaction/methods ; Selection, Genetic ; }, abstract = {Bacteria acquire novel DNA through horizontal gene transfer (HGT), a process that enables an organism to rapidly adapt to changing environmental conditions, provides a competitive edge and potentially alters its relationship with its host. Although the HGT process is routinely exploited in laboratories, there is a surprising disconnect between what we know from laboratory experiments and what we know from natural environments, such as the human gut microbiome. Owing to a suite of newly available computational algorithms and experimental approaches, we have a broader understanding of the genes that are being transferred and are starting to understand the ecology of HGT in natural microbial communities. This Review focuses on these new technologies, the questions they can address and their limitations. As these methods are applied more broadly, we are beginning to recognize the full extent of HGT possible within a microbiome and the punctuated dynamics of HGT, specifically in response to external stimuli. Furthermore, we are better characterizing the complex selective pressures on mobile genetic elements and the mechanisms by which they interact with the bacterial host genome.}, }
@article {pmid33845910, year = {2021}, author = {Restrepo, L and Domínguez-Borbor, C and Bajaña, L and Betancourt, I and Rodríguez, J and Bayot, B and Reyes, A}, title = {Microbial community characterization of shrimp survivors to AHPND challenge test treated with an effective shrimp probiotic (Vibrio diabolicus).}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {88}, pmid = {33845910}, issn = {2049-2618}, mesh = {Animals ; Humans ; *Microbiota ; Necrosis ; *Penaeidae ; Phylogeny ; *Probiotics ; RNA, Ribosomal, 16S/genetics ; Survivors ; Vibrio ; *Vibrio parahaemolyticus/genetics ; }, abstract = {BACKGROUND: Acute hepatopancreatic necrosis disease (AHPND) is an important shrimp bacterial disease caused by some Vibrio species. The severity of the impact of this disease on aquaculture worldwide has made it necessary to develop alternatives to prophylactic antibiotics use, such as the application of probiotics. To assess the potential to use probiotics in order to limit the detrimental effects of AHNPD, we evaluated the effect of the ILI strain, a Vibrio sp. bacterium and efficient shrimp probiotic, using metabarcoding (16S rRNA gene) on the gastrointestinal microbiota of shrimp after being challenged with AHPND-causing V. parahaemolyticus.<br><br>RESULTS: We showed how the gastrointestinal microbiome of shrimp varied between healthy and infected organisms. Nevertheless, a challenge of working with AHPND-causing Vibrio pathogens and Vibrio-related bacteria as probiotics is the potential risk of the probiotic strain becoming pathogenic. Consequently, we evaluated whether ILI strain can acquire the plasmid pV-AHPND via horizontal transfer and further cause the disease in shrimp. Conjugation assays were performed resulting in a high frequency (70%) of colonies harboring the pv-AHPND. However, no shrimp mortality was observed when transconjugant colonies of the ILI strain were used in a challenge test using healthy shrimp. We sequenced the genome of the ILI strain and performed comparative genomics analyses using AHPND and non-AHPND Vibrio isolates. Using available phylogenetic and phylogenomics analyses, we reclassified the ILI strain as Vibrio diabolicus. In summary, this work represents an effort to study the role that probiotics play in the normal gastrointestinal shrimp microbiome and in AHPND-infected shrimp, showing that the ILI probiotic was able to control pathogenic bacterial populations in the host's gastrointestinal tract and stimulate the shrimp's survival. The identification of probiotic bacterial species that are effective in the host's colonization is important to promote animal health and prevent disease.<br><br>CONCLUSIONS: This study describes probiotic bacteria capable of controlling pathogenic populations of bacteria in the shrimp gastrointestinal tract. Our work provides new insights into the complex dynamics between shrimp and the changes in the microbiota. It also addresses the practical application of probiotics to solve problems with pathogens that cause high mortality-rate in shrimp farming around the world. Video Abstract.}, }
@article {pmid33844336, year = {2021}, author = {Zhao, D and Yao, Z and Zhang, J and Zhang, R and Mou, Z and Zhang, X and Li, Z and Feng, X and Chen, S and Reiter, RJ}, title = {Melatonin synthesis genes N-acetylserotonin methyltransferases evolved into caffeic acid O-methyltransferases and both assisted in plant terrestrialization.}, journal = {Journal of pineal research}, volume = {71}, number = {3}, pages = {e12737}, doi = {10.1111/jpi.12737}, pmid = {33844336}, issn = {1600-079X}, support = {32060043//National Natural Science Foundation of China/ ; 31960082//National Natural Science Foundation of China/ ; 81560622//National Natural Science Foundation of China/ ; }, mesh = {*Acetylserotonin O-Methyltransferase/genetics ; Ecosystem ; *Melatonin ; Methyltransferases/genetics ; Phylogeny ; Serotonin/analogs &amp; derivatives ; }, abstract = {Terrestrialization is one of the most momentous events in the history of plant life, which leads to the subsequent evolution of plant diversity. The transition species, in this process, had to acquire a range of adaptive mechanisms to cope with the harsh features of terrestrial environments compared to that of aquatic habitat. As an ancient antioxidant, a leading regulator of ROS signaling or homeostasis, and a presumed plant master regulator, melatonin likely assisted plants transition to land and their adaption to terrestrial ecosystems. N-acetylserotonin methyltransferases (ASMT) and caffeic acid O-methyltransferases (COMT), both in the O-methyltransferase (OMT) family, catalyze the core O-methylation reaction in melatonin biosynthesis. How these two enzymes with close relevance evolved in plant evolutionary history and whether they participated in plant terrestrialization remains unknown. Using combined phylogenetic evidence and protein structure analysis, it is revealed that COMT likely evolved from ASMT by gene duplication and subsequent divergence. Newly emergent COMT gained a significantly higher ASMT activity to produce greater amounts of melatonin for immobile plants to acclimate to the stressful land environments after evolving from the more environmentally-stable aquatic conditions. The COMT genes possess more conserved substrate-binding sites at the amino acid level and more open protein conformation compared to ASMT, and getting a new function to catalyze the lignin biosynthesis. This development directly contributed to the dominance of vascular plants among the Earth's flora and prompted plant colonization of land. Thus, ASMT, together with its descendant COMT, might play key roles in plant transition to land. The current study provides new insights into plant terrestrialization with gene duplication contributing to this process along with well-known horizontal gene transfer.}, }
@article {pmid33837440, year = {2021}, author = {Ou, L and Long, J and Teng, Y and Yang, H and Xi, Y and Duan, G and Chen, S}, title = {Diversity of the type I-U CRISPR-Cas system in Bifidobacterium.}, journal = {Archives of microbiology}, volume = {203}, number = {6}, pages = {3235-3243}, pmid = {33837440}, issn = {1432-072X}, support = {2018ZX10301407//National Science and Technology Specific Projects/ ; Grant No. 81573205//National Natural Science Foundation of China/ ; Grant No. 20A330004//Key Scientific Research Project of Colleges and Universities in Henan Province&#xa0;/ ; }, mesh = {*Bifidobacterium/genetics ; *CRISPR-Cas Systems/genetics ; Gene Transfer, Horizontal ; *Genetic Variation ; Humans ; Multilocus Sequence Typing ; }, abstract = {The CRISPR-Cas system is widely distributed in prokaryotes and plays an important role in the adaptive immunity of bacteria and archaea. Bifidobacterium is an important component of the intestinal flora of humans and animals, and some species of this bacterium can be employed as food additives. However, the Bifidobacterium CRISPR-Cas system has not been fully elucidated to date. In this study, the genomes of 110 strains of Bifidobacterium were employed to research the diversity of the type I-U system. The 110 strains were divided into five groups according to the genes adjacent to the CRISPR locus, including group A, B, C, D and E. Strains in the intergroup had unique species classifications and MLST types. An evolutionary tree was constructed based on the conserved cas4/cas1 fusion gene. The results showed that group A had a different evolutionary branch compared with the other groups and had a relatively low spacer number. Notably, group B, C and E had exhibited ABC transporter regulators in the genes adjacent to the CRISPR locus. ABC transporters play important roles in the exocytosis of many antibiotics and are involved in horizontal gene transfer. This mechanism may have promoted the evolution of Bifidobacterium and the horizontal gene transfer of the type I-U system, which may have promoted the generation of system diversity. In summary, our results help to elucidate the role of the type I-U system in the evolution of Bifidobacterium.}, }
@article {pmid33837077, year = {2021}, author = {Shaw, LP and Chau, KK and Kavanagh, J and AbuOun, M and Stubberfield, E and Gweon, HS and Barker, L and Rodger, G and Bowes, MJ and Hubbard, ATM and Pickford, H and Swann, J and Gilson, D and Smith, RP and Hoosdally, SJ and Sebra, R and Brett, H and Peto, TEA and Bailey, MJ and Crook, DW and Read, DS and Anjum, MF and Walker, AS and Stoesser, N and , }, title = {Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae.}, journal = {Science advances}, volume = {7}, number = {15}, pages = {}, pmid = {33837077}, issn = {2375-2548}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {Escherichia coli and other Enterobacteriaceae are diverse species with "open" pangenomes, where genes move intra- and interspecies via horizontal gene transfer. However, most analyses focus on clinical isolates. The pangenome dynamics of natural populations remain understudied, despite their suggested role as reservoirs for antimicrobial resistance (AMR) genes. Here, we analyze near-complete genomes for 827 Enterobacteriaceae (553 Escherichia and 274 non-Escherichia spp.) with 2292 circularized plasmids in total, collected from 19 locations (livestock farms and wastewater treatment works in the United Kingdom) within a 30-km radius at three time points over a year. We find different dynamics for chromosomal and plasmid-borne genes. Plasmids have a higher burden of AMR genes and insertion sequences, and AMR-gene-carrying plasmids show evidence of being under stronger selective pressure. Environmental niche and local geography both play a role in shaping plasmid dynamics. Our results highlight the importance of local strategies for controlling the spread of AMR.}, }
@article {pmid33836654, year = {2021}, author = {Wozniak, A and Figueroa, C and Moya-Flores, F and Guggiana, P and Castillo, C and Rivas, L and Munita, JM and García, PC}, title = {A multispecies outbreak of carbapenem-resistant bacteria harboring the blaKPC gene in a non-classical transposon element.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {107}, pmid = {33836654}, issn = {1471-2180}, support = {Laboratory of Microbiology//Red Salud UC-CHRISTUS/ ; Escuela de Medicina//Pontificia Universidad Cat&#xf3;lica de Chile/ ; Antimicrobial Resistance Surveillance Program//SENTRY/ ; }, mesh = {Bacteria/*drug effects/*genetics ; Bacterial Infections/epidemiology/microbiology ; Carbapenem-Resistant Enterobacteriaceae/*genetics ; Carbapenems/*pharmacology ; DNA Transposable Elements/*genetics ; Disease Outbreaks ; *Gene Transfer, Horizontal ; Humans ; Pseudomonas aeruginosa/genetics ; beta-Lactamases/*genetics ; }, abstract = {BACKGROUND: Klebsiella pneumoniae is the most frequent KPC-producing bacteria. The blaKPC gene is frequently embedded in Tn4401 transposon, and less frequently in non-Tn4401 elements (NTEKPC) variants I-III. The first case of KPC in the UC-CHRISTUS Clinical Hospital was detected in Pseudomonas aeruginosa. Soon after this event, KPC was detected in 2 additional Pseudomonas aeruginosa, 3 Escherichia coli, 3 Enterobacter cloacae, 3 Klebsiella pneumoniae, and 1 Citrobacter freundii, isolated from 6 different patients. We aimed to elucidate the possible mechanisms of genetic transfer and dissemination of the blaKPC gene among isolates of this multispecies outbreak. A molecular epidemiology analysis of the above mentioned clinical isolates (n = 13) through Multi-Locus Sequence Typing, plasmid analysis, Pulsed-Field Gel-Electrophoresis, and Whole-genome sequencing (WGS) was performed.<br><br>RESULTS: High-risk sequence types were found: K. pneumoniae ST11, P. aeruginosa ST654, and E. cloacae ST114. All enterobacterial isolates were not clonal except for 3 E. coli isolated from the same patient. WGS analysis in 6 enterobacterial isolates showed that 4 of them had blaKPC embedded in a novel variant of NTEKPC designated NTEKPC-IIe. Upstream of blaKPC gene there was a 570 pb truncated blaTEM-1 gene followed by an insertion sequence that was 84% similar to ISEc63, a 4473&#x2009;bp element of the Tn3 family. Downstream the blaKPC gene there was a truncated ISKpn6 gene, and the inverted repeat right sequence of Tn4401. The ISec63-like element together with the blaKPC gene plus Tn4401 remnants were inserted in the Tra operon involved in conjugative transfer of the plasmid. This NTE was carried in a broad host-range IncN plasmid. P. aeruginosa isolates carried blaKPC gene embedded in a typical Tn4401b transposon in a different plasmid, suggesting that there was no plasmid transfer between Enterobacteriaceae and P. aeruginosa as initially hypothesized.<br><br>CONCLUSIONS: Most enterobacterial isolates had blaKPC embedded in the same NTEKPC-IIe element, suggesting that this multispecies KPC outbreak was due to horizontal gene transfer rather than clonal spread. This poses a greater challenge to infection control measures often directed against containment of clonal spread.}, }
@article {pmid33835340, year = {2021}, author = {Pereira, AR and Paranhos, AGO and de Aquino, SF and Silva, SQ}, title = {Distribution of genetic elements associated with antibiotic resistance in treated and untreated animal husbandry waste and wastewater.}, journal = {Environmental science and pollution research international}, volume = {28}, number = {21}, pages = {26380-26403}, pmid = {33835340}, issn = {1614-7499}, support = {001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 423101/2018-8//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 2510001557612017-21//Funda&#xe7;&#xe3;o Nacional da Sa&#xfa;de/ ; }, mesh = {Animal Husbandry ; Animals ; Anti-Bacterial Agents/pharmacology ; Cattle ; Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; Manure ; Swine ; *Wastewater ; }, abstract = {Animal breeding for meat production based on swine, cattle, poultry, and aquaculture is an activity that generates several impacts on the environment, among them the spread of antibiotic resistance. There is a worldwide concern related to the massive use of antibiotics, which causes selective pressure on the microbial community, triggering bacteria that contain "antibiotic resistance genes." According to the survey here presented, antibiotic resistance-related genes such as tetracyclines (tet), erythromycin (erm), and sulfonamides (sul), as well as the genetic mobile element interferon (int), are the most reported genetic elements in qualitative and quantitative studies of swine, cattle, poultry, and aquaculture manure/wastewater. It has been observed that biological treatments based on waste composting and anaerobic digestion are effective in ARG removal, particularly for tet, bla, erm, and qnr (quinolone) genes. On the other hand, sul and intI genes were more persistent in such treatments. Tertiary treatments, such advanced oxidative processes, are suitable strategies to improve ARG reduction. In general temperature, hydraulic retention time, and penetration of sunlight are the main operational parameters for ARG reduction in treatments applied to animal waste, and therefore attention should be addressed to optimize their efficacy regarding ARG removal. Despite being reduced, the presence of ARG in treated effluents and in biosolids indicates that there is a potential risk of antibiotic resistance spread in nature, especially through the release of treated livestock waste into the environment.}, }
@article {pmid33834549, year = {2021}, author = {Dudeja, SS and Suneja-Madan, P and Paul, M and Maheswari, R and Kothe, E}, title = {Bacterial endophytes: Molecular interactions with their hosts.}, journal = {Journal of basic microbiology}, volume = {61}, number = {6}, pages = {475-505}, doi = {10.1002/jobm.202000657}, pmid = {33834549}, issn = {1521-4028}, mesh = {Bacteria/genetics/growth &amp; development/metabolism ; *Bacterial Physiological Phenomena ; Computational Biology ; Endophytes/genetics/growth &amp; development/metabolism/*physiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Host Microbial Interactions/*genetics ; Plant Development/genetics ; Plant Growth Regulators/metabolism ; Plants/metabolism/*microbiology ; }, abstract = {Plant growth promotion has been found associated with plants on the surface (epiphytic), inside (endophytic), or close to the plant roots (rhizospheric). Endophytic bacteria mainly have been researched for their beneficial activities in terms of nutrient availability, plant growth hormones, and control of soil-borne and systemic pathogens. Molecular communications leading to these interactions between plants and endophytic bacteria are now being unrevealed using multidisciplinary approaches with advanced techniques such as metagenomics, metaproteomics, metatranscriptomics, metaproteogenomic, microRNAs, microarray, chips as well as the comparison of complete genome sequences. More than 400 genes in both the genomes of host plant and bacterial endophyte are up- or downregulated for the establishment of endophytism and plant growth-promoting activity. The involvement of more than 20 genes for endophytism, about 50 genes for direct plant growth promotion, about 25 genes for biocontrol activity, and about 10 genes for mitigation of different stresses has been identified in various bacterial endophytes. This review summarizes the progress that has been made in recent years by these modern techniques and approaches.}, }
@article {pmid33833746, year = {2021}, author = {Shin, H and Kim, Y and Han, D and Hur, HG}, title = {Emergence of High Level Carbapenem and Extensively Drug Resistant Escherichia coli ST746 Producing NDM-5 in Influent of Wastewater Treatment Plant, Seoul, South Korea.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {645411}, pmid = {33833746}, issn = {1664-302X}, abstract = {High level carbapenem and extensively drug resistant (XDR) Escherichia coli strain N7, which produces a variant of New Delhi metallo-β-lactamase (NDM-5), was isolated from the influent of the Jungnang wastewater treatment plant located on Han River, Seoul, South Korea. Phenotypic and genotypic resistances to carbapenem were tested using agar and broth dilution methods, and polymerase chain reaction. Whole-genome sequencing was performed to characterize the genetic structure of strain N7. E. coli strain N7, which harbors the bla NDM-5 gene, showed high level of carbapenem resistance at concentrations of doripenem (512 mg/L) and meropenem (256 mg/L), and XDR to 15 antibiotics. Based on the genomic sequence analysis, two plasmids, a hybrid IncHI2/N-type and an IncX3 type, were present. The former contains a cluster (bla NDM-5-ble MBL -trpF-dsbD) bracketed by multi-insertional sequences, IS3000, ISAba125, IS5, and IS26. The latter carries the following resistance genes: bla CTX-14, aac(3)-IV, aadA1, aadA2, aph(3')-Ia, aph(4)-Ia, sul1, sul2, sul3, dfrA12, fosA3, oqxA, oqxB, mph(A), and floR, and cmlA1. The chromosome, contig3, and contig5 also carry bla CTX-64 and mdf(A), tet(A), and erm(B), tet(M) and aadA22, respectively. Strain N7 also harbors virulence factors such as fimH, flu, ecpABCDE, sfmA, hlyE, and gadA. This study demonstrates the emergence of high level carbapenem resistant XDR E. coli strain N7 containing bla NDM-5 in aquatic environment, Seoul, South Korea. Due to the presence of mobile genetic elements, this strain could horizontally transfer resistance genes, including bla NDM-5 to environmental bacteria. Thus, it is necessary to conduct continuous surveillance for carbapenem resistance in various aquatic environments.}, }
@article {pmid33833743, year = {2021}, author = {Borin, S and Sosio, M and Vezzulli, L and Viti, C}, title = {Editorial: XXXIII SIMGBM Congress 2019 - Environmental and Industrial Microbiology.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {640033}, doi = {10.3389/fmicb.2021.640033}, pmid = {33833743}, issn = {1664-302X}, }
@article {pmid33833414, year = {2021}, author = {Lopez, JG and Donia, MS and Wingreen, NS}, title = {Modeling the ecology of parasitic plasmids.}, journal = {The ISME journal}, volume = {15}, number = {10}, pages = {2843-2852}, pmid = {33833414}, issn = {1751-7370}, mesh = {Animals ; Drug Resistance, Microbial ; Gene Transfer, Horizontal ; *Parasites ; Plasmids/genetics ; }, abstract = {Plasmids are autonomous genetic elements that can be exchanged between microorganisms via horizontal gene transfer (HGT). Despite the central role they play in antibiotic resistance and modern biotechnology, our understanding of plasmids' natural ecology is limited. Recent experiments have shown that plasmids can spread even when they are a burden to the cell, suggesting that natural plasmids may exist as parasites. Here, we use mathematical modeling to explore the ecology of such parasitic plasmids. We first develop models of single plasmids and find that a plasmid's population dynamics and optimal infection strategy are strongly determined by the plasmid's HGT mechanism. We then analyze models of co-infecting plasmids and show that parasitic plasmids are prone to a "tragedy of the commons" in which runaway plasmid invasion severely reduces host fitness. We propose that this tragedy of the commons is averted by selection between competing populations and demonstrate this effect in a metapopulation model. We derive predicted distributions of unique plasmid types in genomes-comparison to the distribution of plasmids in a collection of 17,725 genomes supports a model of parasitic plasmids with positive plasmid-plasmid interactions that ameliorate plasmid fitness costs or promote the invasion of new plasmids.}, }
@article {pmid33833409, year = {2021}, author = {Li, Y and Zhou, Y and Jing, W and Xu, S and Jin, Y and Xu, Y and Wang, H}, title = {Horizontally acquired cysteine synthase genes undergo functional divergence in lepidopteran herbivores.}, journal = {Heredity}, volume = {127}, number = {1}, pages = {21-34}, pmid = {33833409}, issn = {1365-2540}, mesh = {Animals ; *Cysteine Synthase ; Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; Herbivory ; *Lepidoptera/genetics ; Phylogeny ; }, abstract = {Horizontal gene transfer (HGT) plays an important role in evolutionary processes as organisms adapt to their environments, and now cases of gene duplication after HGT in eukaryotes are emerging at an increasing rate. However, the fate and roles of the duplicated genes over time in eukaryotes remain unclear. Here we conducted a comprehensive analysis of the evolution of cysteine synthase (CYS) in lepidopteran insects. Our results indicate that HGT-derived CYS genes are widespread and have undergone duplication following horizontal transfer in many lepidopteran insects. Moreover, lepidopteran CYS proteins not only have β-cyanoalanine synthase activity but also possess cysteine synthase activity that is involved in sulfur amino acid biosynthesis. Duplicated CYS genes show marked divergence in gene expression patterns and enzymatic properties, suggesting that they probably have undergone subfunctionalization and/or neofunctionalization in Lepidoptera. The gene transfer of CYS genes and subsequent duplication appears to have facilitated the adaptation of lepidopteran insects to different diets and promoted their ecological diversification. Overall, this study provides valuable insights into the ecological and evolutionary contributions of CYS in lepidopteran insects.}, }
@article {pmid33829001, year = {2021}, author = {Marincola, G and Jaschkowitz, G and Kieninger, AK and Wencker, FDR and Feßler, AT and Schwarz, S and Ziebuhr, W}, title = {Plasmid-Chromosome Crosstalk in Staphylococcus aureus: A Horizontally Acquired Transcription Regulator Controls Polysaccharide Intercellular Adhesin-Mediated Biofilm Formation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {660702}, pmid = {33829001}, issn = {2235-2988}, mesh = {Animals ; Bacterial Proteins/genetics ; Biofilms ; Cattle ; Chromosomes/metabolism ; Gene Expression Regulation, Bacterial ; *Methicillin-Resistant Staphylococcus aureus ; Plasmids ; Polysaccharides, Bacterial ; *Staphylococcal Infections ; Staphylococcus aureus/genetics ; Staphylococcus epidermidis/genetics ; }, abstract = {Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) of clonal complex CC398 typically carry various antimicrobial resistance genes, many of them located on plasmids. In the bovine LA-MRSA isolate Rd11, we previously identified plasmid pAFS11 in which resistance genes are co-localized with a novel ica-like gene cluster, harboring genes required for polysaccharide intercellular adhesin (PIA)-mediated biofilm formation. The ica genes on pAFS11 were acquired in addition to a pre-existing ica locus on the S. aureus Rd11 chromosomal DNA. Both loci consist of an icaADBC operon and icaR, encoding a corresponding icaADBC repressor. Despite carrying two biofilm gene copies, strain Rd11 did not produce PIA and transformation of pAFS11 into another S. aureus strain even slightly diminished PIA-mediated biofilm formation. By focusing on the molecular background of the biofilm-negative phenotype of pAFS11-carrying S. aureus, we identified the pAFS11-borne ica locus copy as functionally fully active. However, transcription of both plasmid- and core genome-derived icaADBC operons were efficiently suppressed involving IcaR. Surprisingly, although being different on the amino acid sequence level, the two IcaR repressor proteins are mutually replaceable and are able to interact with the icaA promoter region of the other copy. We speculate that this regulatory crosstalk causes the biofilm-negative phenotype in S. aureus Rd11. The data shed light on an unexpected regulatory interplay between pre-existing and newly acquired DNA traits in S. aureus. This also raises interesting general questions regarding functional consequences of gene transfer events and their putative implications for the adaptation and evolution of bacterial pathogens.}, }
@article {pmid33828299, year = {2021}, author = {Mo, CY and Mathai, J and Rostøl, JT and Varble, A and Banh, DV and Marraffini, LA}, title = {Type III-A CRISPR immunity promotes mutagenesis of staphylococci.}, journal = {Nature}, volume = {592}, number = {7855}, pages = {611-615}, pmid = {33828299}, issn = {1476-4687}, support = {DP1 GM128184/GM/NIGMS NIH HHS/United States ; F30 AI157535/AI/NIAID NIH HHS/United States ; F32 GM128271/GM/NIGMS NIH HHS/United States ; T32 GM007739/GM/NIGMS NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteriophages/classification/physiology ; CRISPR-Associated Proteins/metabolism ; CRISPR-Cas Systems/*genetics/*immunology ; DNA, Single-Stranded/genetics/metabolism ; Deoxyribonucleases/metabolism ; Drug Resistance, Microbial/drug effects ; *Mutagenesis ; *Mutation ; SOS Response, Genetics/drug effects ; Staphylococcus/drug effects/*genetics/immunology/virology ; Staphylococcus aureus/drug effects/genetics/virology ; Staphylococcus epidermidis/drug effects/genetics/virology ; Time Factors ; }, abstract = {Horizontal gene transfer and mutation are the two major drivers of microbial evolution that enable bacteria to adapt to fluctuating environmental stressors[1]. Clustered, regularly interspaced, short palindromic repeats (CRISPR) systems use RNA-guided nucleases to direct sequence-specific destruction of the genomes of mobile genetic elements that mediate horizontal gene transfer, such as conjugative plasmids[2] and bacteriophages[3], thus limiting the extent to which bacteria can evolve by this mechanism. A subset of CRISPR systems also exhibit non-specific degradation of DNA[4,5]; however, whether and how this feature affects the host has not yet been examined. Here we show that the non-specific DNase activity of the staphylococcal type III-A CRISPR-Cas system increases mutations in the host and accelerates the generation of antibiotic resistance in Staphylococcus aureus and Staphylococcus epidermidis. These mutations require the induction of the SOS response to DNA damage and display a distinct pattern. Our results demonstrate that by differentially affecting both mechanisms that generate genetic diversity, type III-A CRISPR systems can modulate the evolution of the bacterial host.}, }
@article {pmid33826062, year = {2021}, author = {Otten, L}, title = {T-DNA regions from 350 Agrobacterium genomes: maps and phylogeny.}, journal = {Plant molecular biology}, volume = {106}, number = {3}, pages = {239-258}, pmid = {33826062}, issn = {1573-5028}, mesh = {Agrobacterium/classification/*genetics ; DNA, Bacterial/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Phylogeny ; Plasmids/*genetics ; Whole Genome Sequencing ; }, abstract = {Analysis of 350 Agrobacterium wgs sequences reveals complex evolutionary history of T-DNA regions Virulent Agrobacterium strains transfer one or more plasmid DNA fragments to plant cells during a well-characterized transformation process. The transferred DNA sequences (T-DNA regions) are delimited by 25 nucleotide long conserved border sequences. Until recently, relatively few T-DNA regions were known. However, due to increased whole genome sequencing efforts, about 400 Agrobacterium sequences have now become available, 350 of which contain T-DNA regions. Detailed analysis identified 92 different T-DNA regions and several new T-DNA genes. T-DNA regions can be divided into three groups. I. Typical Agrobacterium rhizogenes T-DNA regions with rol genes. II. A large group of T-DNA regions with iaa and ipt genes, which can be further subdivided into seven subgroups. III. A small group of unusual T-DNA regions. The evolutionary relation between the T-DNA regions could not be completely elucidated, because of the lack of evolutionary intermediates. Several clusters of highly related structures suggest that evolution of T-DNA regions proceeds by slow, progressive evolution of gene sequences, accompanied by rapid changes in overall structure, due to recombination between T-DNA regions of different origins, and insertion of bacterial insertion sequences (IS). Divergence values for T-DNA genes suggest that they were recruited at different times in evolution. An attempt was made to link T-DNA region evolution to plasmid evolution. The present study provides a solid basis for further studies on T-DNA region diversity and evolution.}, }
@article {pmid33816561, year = {2021}, author = {Meijer, WJJ and Boer, DR and Ares, S and Alfonso, C and Rojo, F and Luque-Ortega, JR and Wu, LJ}, title = {Multiple Layered Control of the Conjugation Process of the Bacillus subtilis Plasmid pLS20.}, journal = {Frontiers in molecular biosciences}, volume = {8}, number = {}, pages = {648468}, pmid = {33816561}, issn = {2296-889X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {Bacterial conjugation is the main horizontal gene transfer route responsible for the spread of antibiotic resistance, virulence and toxin genes. During conjugation, DNA is transferred from a donor to a recipient cell via a sophisticated channel connecting the two cells. Conjugation not only affects many different aspects of the plasmid and the host, ranging from the properties of the membrane and the cell surface of the donor, to other developmental processes such as competence, it probably also poses a burden on the donor cell due to the expression of the large number of genes involved in the conjugation process. Therefore, expression of the conjugation genes must be strictly controlled. Over the past decade, the regulation of the conjugation genes present on the conjugative Bacillus subtilis plasmid pLS20 has been studied using a variety of methods including genetic, biochemical, biophysical and structural approaches. This review focuses on the interplay between RcopLS20, RappLS20 and Phr*pLS20, the proteins that control the activity of the main conjugation promoter P c located upstream of the conjugation operon. Proper expression of the conjugation genes requires the following two fundamental elements. First, conjugation is repressed by default and an intercellular quorum-signaling system is used to sense conditions favorable for conjugation. Second, different layers of regulation act together to repress the P c promoter in a strict manner but allowing rapid activation. During conjugation, ssDNA is exported from the cell by a membrane-embedded DNA translocation machine. Another membrane-embedded DNA translocation machine imports ssDNA in competent cells. Evidences are reviewed indicating that conjugation and competence are probably mutually exclusive processes. Some of the questions that remain unanswered are discussed.}, }
@article {pmid33812918, year = {2021}, author = {Mikhailovsky, GE and Gordon, R}, title = {LUCA to LECA, the Lucacene: A model for the gigayear delay from the first prokaryote to eukaryogenesis.}, journal = {Bio Systems}, volume = {205}, number = {}, pages = {104415}, doi = {10.1016/j.biosystems.2021.104415}, pmid = {33812918}, issn = {1872-8324}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Biological Evolution ; Computer Simulation ; Eukaryota/*genetics ; *Gene Transfer, Horizontal ; *Models, Biological ; Mutation ; *Systems Biology ; Time Factors ; }, abstract = {It is puzzling why life on Earth consisted of prokaryotes for up to 2.5 ± 0.5 billion years (Gy) before the appearance of the first eukaryotes. This period, from LUCA (Last Universal Common Ancestor) to LECA (Last Eucaryotic Common Ancestor), we have named the Lucacene, to suggest all prokaryotic descendants of LUCA before the appearance of LECA. Here we present a simple model based on horizontal gene transfer (HGT). It is the process of HGT from Bacteria to Archaea and its reverse that we wish to simulate and estimate its duration until eukaryogenesis. Rough quantitation of its parameters shows that the model may explain the long duration of the Lucacene.}, }
@article {pmid33811263, year = {2021}, author = {Biswas, R and Halder, U and Kabiraj, A and Mondal, A and Bandopadhyay, R}, title = {Overview on the role of heavy metals tolerance on developing antibiotic resistance in both Gram-negative and Gram-positive bacteria.}, journal = {Archives of microbiology}, volume = {203}, number = {6}, pages = {2761-2770}, pmid = {33811263}, issn = {1432-072X}, mesh = {Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Multiple, Bacterial/drug effects ; Gram-Negative Bacteria/*drug effects ; Gram-Positive Bacteria/*drug effects ; Humans ; Metals, Heavy/metabolism/*toxicity ; }, abstract = {Environmental health is a critical concern, continuously contaminated by physical and biological components (viz., anthropogenic activity), which adversely affect on biodiversity, ecosystems and human health. Nonetheless, environmental pollution has great impact on microbial communities, especially bacteria, which try to evolve in changing environment. For instance, during the course of adaptation, bacteria easily become resistance to antibiotics and heavy metals. Antibiotic resistance genes are now one of the most vital pollutants, provided as a source of frequent horizontal gene transfer. In this review, the environmental cause of multidrug resistance (MDR) that was supposed to be driven by either heavy metals or combination of environmental factors was essentially reviewed, especially focussed on the correlation between accumulation of heavy metals and development of MDR by bacteria. This kind of correlation was seemed to be non-significant, i.e. paradoxical. Gram-positive bacteria accumulating much of toxic heavy metal (i.e. highly stress tolerance) were unlikely to become MDR, whereas Gram-negative bacteria that often avoid accumulation of toxic heavy metal by efflux pump systems were come out to be more prone to MDR. So far, other than antibiotic contaminant, no such available data strongly support the direct influence of heavy metals in bacterial evolution of MDR; combinations of factors may drive the evolution of antibiotic resistance. Therefore, Gram-positive bacteria are most likely to be an efficient member in treatment of industrial waste water, especially in the removal of heavy metals, perhaps inducing the less chance of antibiotic resistance pollution in the environment.}, }
@article {pmid33806962, year = {2021}, author = {de Block, T and Laumen, JGE and Van Dijck, C and Abdellati, S and De Baetselier, I and Manoharan-Basil, SS and Van den Bossche, D and Kenyon, C}, title = {WGS of Commensal Neisseria Reveals Acquisition of a New Ribosomal Protection Protein (MsrD) as a Possible Explanation for High Level Azithromycin Resistance in Belgium.}, journal = {Pathogens (Basel, Switzerland)}, volume = {10}, number = {3}, pages = {}, pmid = {33806962}, issn = {2076-0817}, abstract = {In this study, we characterized all oropharyngeal and anorectal isolates of Neisseria spp. in a cohort of men who have sex with men. This resulted in a panel of pathogenic Neisseria (N. gonorrhoeae [n = 5] and N. meningitidis [n = 5]) and nonpathogenic Neisseria (N. subflava [n = 11], N. mucosa [n = 3] and N. oralis [n = 2]). A high proportion of strains in this panel were resistant to azithromycin (18/26) and ceftriaxone (3/26). Whole genome sequencing (WGS) of these strains identified numerous mutations that are known to confer reduced susceptibility to azithromycin and ceftriaxone in N. gonorrhoeae. The presence or absence of these known mutations did not explain the high level resistance to azithromycin (>256 mg/L) in the nonpathogenic isolates (8/16). After screening for antimicrobial resistance (AMR) genes, we found a ribosomal protection protein, Msr(D), in these highly azithromycin resistant nonpathogenic strains. The complete integration site originated from Streptococcus pneumoniae and is associated with high level resistance to azithromycin in many other bacterial species. This novel AMR resistance mechanism to azithromycin in nonpathogenic Neisseria could be a public health concern if it were to be transmitted to pathogenic Neisseria. This study demonstrates the utility of WGS-based surveillance of nonpathogenic Neisseria.}, }
@article {pmid33805330, year = {2021}, author = {Pierobon, P}, title = {An Interesting Molecule: γ-Aminobutyric Acid. What Can We Learn from Hydra Polyps?.}, journal = {Brain sciences}, volume = {11}, number = {4}, pages = {}, pmid = {33805330}, issn = {2076-3425}, abstract = {Neuronal excitability is controlled primarily by γ-aminobutyric acid (GABA) in the central and peripheral nervous systems of vertebrate as well as invertebrate organisms. Besides its recognized neurotransmitter functions, GABA also plays a fundamental role in neurogenesis and synaptogenesis during embryonic development. In addition, GABAergic mechanisms are also involved in disorders of various peripheral tissues, ranging from diabetes to hypothyroidism to inflammatory responses. The discovery of the molecule and the history of its biosynthetic pathways in vertebrate and invertebrate phyla are summarized here. The occurrence and distribution of GABA, GABA-synthesizing enzymes, and receptors to GABA in the freshwater polyp Hydra vulgaris (Cnidaria: Hydrozoa), endowed with an early evolved nervous system, are discussed in relation to possible interactions with the microbiota, a stable component of Hydra polyps; their contribution to the evolution of nervous systems through microbe-neuronal interactions is proposed.}, }
@article {pmid33803896, year = {2021}, author = {Chatragadda, R and Dufossé, L}, title = {Ecological and Biotechnological Aspects of Pigmented Microbes: A Way Forward in Development of Food and Pharmaceutical Grade Pigments.}, journal = {Microorganisms}, volume = {9}, number = {3}, pages = {}, pmid = {33803896}, issn = {2076-2607}, support = {COLA-BUNALA//CSIR -NIO, India/ ; COLORMAR//Conseil R&#xe9;gional de La R&#xe9;union/ ; }, abstract = {Microbial pigments play multiple roles in the ecosystem construction, survival, and fitness of all kinds of organisms. Considerably, microbial (bacteria, fungi, yeast, and microalgae) pigments offer a wide array of food, drug, colorants, dyes, and imaging applications. In contrast to the natural pigments from microbes, synthetic colorants are widely used due to high production, high intensity, and low cost. Nevertheless, natural pigments are gaining more demand over synthetic pigments as synthetic pigments have demonstrated side effects on human health. Therefore, research on microbial pigments needs to be extended, explored, and exploited to find potential industrial applications. In this review, the evolutionary aspects, the spatial significance of important pigments, biomedical applications, research gaps, and future perspectives are detailed briefly. The pathogenic nature of some pigmented bacteria is also detailed for awareness and safe handling. In addition, pigments from macro-organisms are also discussed in some sections for comparison with microbes.}, }
@article {pmid33803068, year = {2021}, author = {Viñes, J and Cuscó, A and Napp, S and Alvarez, J and Saez-Llorente, JL and Rosàs-Rodoreda, M and Francino, O and Migura-Garcia, L}, title = {Transmission of Similar Mcr-1 Carrying Plasmids among Different Escherichia coli Lineages Isolated from Livestock and the Farmer.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {10}, number = {3}, pages = {}, pmid = {33803068}, issn = {2079-6382}, support = {RTI2018-095586-B-C22//Ministerio de Econom&#xed;a y Competitividad (Gobierno de Espa&#xf1;a)/ ; CERCA program//Generalitat de Catalunya/ ; 2017DI037//Generalitat de Catalunya Industrial Doctorate Program/ ; }, abstract = {Colistin use has mostly been stopped in human medicine, due to its toxicity. However, nowadays, it still is used as a last-resort antibiotic to treat hospital infections caused by multi-drug resistant Enterobacteriaceae. On the contrary, colistin has been used in veterinary medicine until recently. In this study, 210 fecal samples from pigs (n = 57), calves (n = 152), and the farmer (n = 1) were collected from a farm where E. coli harboring mcr-1-mcr-3 was previously detected. Samples were plated, and mcr-genes presence was confirmed by multiplex-PCR. Hybrid sequencing which determined the presence and location of mcr-1, other antibiotic resistance genes, and virulence factors. Eighteen colistin resistant isolates (13 from calves, four from pigs, and one from the farmer) contained mcr-1 associated with plasmids (IncX4, IncI2, and IncHI2), except for two that yielded mcr-1 in the chromosome. Similar plasmids were distributed in different E. coli lineages. Transmission of mcr-1 to the farmer most likely occurred by horizontal gene transfer from E. coli of calf origin, since plasmids were highly similar (99% coverage, 99.97% identity). Moreover, 33 virulence factors, including stx2 for Shiga toxin E. coli (STEC) were detected, highlighting the role of livestock as a reservoir of pathotypes with zoonotic potential.}, }
@article {pmid33802904, year = {2021}, author = {Parsons, C and Brown, P and Kathariou, S}, title = {Use of Bacteriophage Amended with CRISPR-Cas Systems to Combat Antimicrobial Resistance in the Bacterial Foodborne Pathogen Listeria monocytogenes.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {10}, number = {3}, pages = {}, pmid = {33802904}, issn = {2079-6382}, support = {2019-67017-29581//National Institute of Food and Agriculture/ ; }, abstract = {Listeria monocytogenes is a bacterial foodborne pathogen and the causative agent of the disease listeriosis, which though uncommon can result in severe symptoms such as meningitis, septicemia, stillbirths, and abortions and has a high case fatality rate. This pathogen can infect humans and other animals, resulting in massive health and economic impacts in the United States and globally. Listeriosis is treated with antimicrobials, typically a combination of a beta-lactam and an aminoglycoside, and L. monocytogenes has remained largely susceptible to the drugs of choice. However, there are several reports of antimicrobial resistance (AMR) in both L. monocytogenes and other Listeria species. Given the dire health outcomes associated with listeriosis, the prospect of antimicrobial-resistant L. monocytogenes is highly problematic for human and animal health. Developing effective tools for the control and elimination of L. monocytogenes, including strains with antimicrobial resistance, is of the utmost importance to prevent further dissemination of AMR in this pathogen. One tool that has shown great promise in combating antibiotic-resistant pathogens is the use of bacteriophages (phages), which are natural bacterial predators and horizontal gene transfer agents. Although native phages can be effective at killing antibiotic-resistant pathogens, limited host ranges and evolved resistance to phages can compromise their use in the efforts to mitigate the global AMR challenge. However, recent advances can allow the use of CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) to selectively target pathogens and their AMR determinants. Employment of CRISPR-Cas systems for phage amendment can overcome previous limitations in using phages as biocontrol and allow for the effective control of L. monocytogenes and its AMR determinants.}, }
@article {pmid33802850, year = {2021}, author = {Mirghasemi, N and Fanelli, E and Jamali, S and Sohani, MM and De Luca, F}, title = {Molecular Characterization of Three B-1,4-Endoglucanase Genes in Pratylenchus loosi and Functional Analysis of Pl-eng-2 Gene.}, journal = {Plants (Basel, Switzerland)}, volume = {10}, number = {3}, pages = {}, pmid = {33802850}, issn = {2223-7747}, abstract = {Pratylenchus loosi is an important root-lesion nematode that causes damage to tea plantations in Iran and all over the world. The present study reports on the characterization and evolution of three ß-1,4-endoglucanase genes: Pl-eng-2, Pl-eng-3 and Pl-eng-4. The gene structure of Pl-eng-2 was fully determined with the predicted signal peptide and devoid of the linker domain and carbohydrate-binding domain, while Pl-eng-3 and Pl-eng-4 were only partially sequenced. The transcription of Pl-eng-2 was localized in the secretory esophageal glands of all life stages, but it was upregulated in male and female stages. The exon/intron structures of Pl-eng-2, Pl-eng-3 and Pl-eng-4 confirmed that they resulted from gene duplication followed by sequence and gene structure diversification with loss of the linker domain and carbohydrate-binding domain during evolution. A phylogenetic analysis further confirmed that nematode endoglucanases resulted from the horizontal gene transfer of a bacterial gene, as Pl-eng-3 showed sister relationships with the CelB cellulase of Bacillus subtilis. Silencing Pl-eng-2 by in vitro RNA interference produced a 60% decrease of the transcript level. The reproductive ability of silenced P. loosi showed a 35% reduction of eggs and larval stages compared to untreated nematodes, suggesting that this gene is involved in the early steps of invasion.}, }
@article {pmid33798824, year = {2021}, author = {Pu, Q and Fan, XT and Sun, AQ and Pan, T and Li, H and Bo Lassen, S and An, XL and Su, JQ}, title = {Co-effect of cadmium and iron oxide nanoparticles on plasmid-mediated conjugative transfer of antibiotic resistance genes.}, journal = {Environment international}, volume = {152}, number = {}, pages = {106453}, doi = {10.1016/j.envint.2021.106453}, pmid = {33798824}, issn = {1873-6750}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Cadmium/toxicity ; Conjugation, Genetic ; Drug Resistance, Microbial/*genetics ; *Genes, Bacterial ; Magnetic Iron Oxide Nanoparticles ; Plasmids/*genetics ; }, abstract = {Conjunctive transfer of antibiotic resistance genes (ARGs) among bacteria driven by plasmids facilitated the evolution and spread of antibiotic resistance. Heavy metal exposure accelerated the plasmid-mediated conjunctive transfer of ARGs. Nanomaterials are well-known adsorbents for heavy metals removal, with the capability of combatting resistant bacteria/facilitating conjunctive transfer of ARGs. However, co-effect of heavy metals and nanomaterials on plasmid-mediated conjunctive transfer of ARGs was still unknown. In this study, we investigated the effect of the simultaneous exposure of Cd[2+] and nano Fe2O3 on conjugative transfer of plasmid RP4 from Pseudomonas putida KT2442 to water microbial community. The permeability of bacterial cell membranes, antioxidant enzyme activities and conjugation gene expression were also investigated. The results suggested that the combination of Cd[2+] and high concentration nano Fe2O3 (10 mg/L and 100 mg/L) significantly increased conjugative transfer frequencies of RP4 plasmid (p < 0.05). The most transconjugants were detected in the treatment of co-exposure to Cd[2+] and nano Fe2O3, the majority of which were identified to be human pathogens. The mechanisms of the exacerbated conjugative transfer of ARGs were involved in the enhancement of cell membrane permeability, antioxidant enzyme activities, and mRNA expression levels of the conjugation genes by the co-effect of Cd[2+] and nano Fe2O3. This study confirmed that the simultaneous exposure to Cd[2+]and nano Fe2O3 exerted a synergetic co-effect on plasmid-mediated conjunctive transfer of ARGs, emphasizing that the co-effect of nanomaterials and heavy metals should be prudently evaluated when combating antibiotic resistance.}, }
@article {pmid33798437, year = {2021}, author = {Whiteman, NK and Tarnopol, RL}, title = {Whiteflies weaponize a plant defense via horizontal gene transfer.}, journal = {Cell}, volume = {184}, number = {7}, pages = {1657-1658}, doi = {10.1016/j.cell.2021.03.017}, pmid = {33798437}, issn = {1097-4172}, mesh = {Animals ; Gene Transfer, Horizontal ; *Hemiptera ; Plants/genetics ; }, abstract = {Co-opting enemy weapons is a proven strategy in warfare. The war of nature is no different. In this issue of Cell, Xia and colleagues show how a major crop pest stole a plant phenolic glucoside malonyltransferase gene, allowing neutralization of a large class of plant defense compounds.}, }
@article {pmid33794144, year = {2021}, author = {Groussin, M and Poyet, M and Sistiaga, A and Kearney, SM and Moniz, K and Noel, M and Hooker, J and Gibbons, SM and Segurel, L and Froment, A and Mohamed, RS and Fezeu, A and Juimo, VA and Lafosse, S and Tabe, FE and Girard, C and Iqaluk, D and Nguyen, LTT and Shapiro, BJ and Lehtimäki, J and Ruokolainen, L and Kettunen, PP and Vatanen, T and Sigwazi, S and Mabulla, A and Domínguez-Rodrigo, M and Nartey, YA and Agyei-Nkansah, A and Duah, A and Awuku, YA and Valles, KA and Asibey, SO and Afihene, MY and Roberts, LR and Plymoth, A and Onyekwere, CA and Summons, RE and Xavier, RJ and Alm, EJ}, title = {Elevated rates of horizontal gene transfer in the industrialized human microbiome.}, journal = {Cell}, volume = {184}, number = {8}, pages = {2053-2067.e18}, doi = {10.1016/j.cell.2021.02.052}, pmid = {33794144}, issn = {1097-4172}, support = {TL1 TR002380/TR/NCATS NIH HHS/United States ; UL1 TR002377/TR/NCATS NIH HHS/United States ; }, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; DNA, Bacterial/chemistry/isolation &amp; purification/metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; Phylogeny ; Rural Population ; Sequence Analysis, DNA ; Urban Population ; Whole Genome Sequencing ; }, abstract = {Industrialization has impacted the human gut ecosystem, resulting in altered microbiome composition and diversity. Whether bacterial genomes may also adapt to the industrialization of their host populations remains largely unexplored. Here, we investigate the extent to which the rates and targets of horizontal gene transfer (HGT) vary across thousands of bacterial strains from 15 human populations spanning a range of industrialization. We show that HGTs have accumulated in the microbiome over recent host generations and that HGT occurs at high frequency within individuals. Comparison across human populations reveals that industrialized lifestyles are associated with higher HGT rates and that the functions of HGTs are related to the level of host industrialization. Our results suggest that gut bacteria continuously acquire new functionality based on host lifestyle and that high rates of HGT may be a recent development in human history linked to industrialization.}, }
@article {pmid33791281, year = {2021}, author = {Mohapatra, B and Phale, PS}, title = {Microbial Degradation of Naphthalene and Substituted Naphthalenes: Metabolic Diversity and Genomic Insight for Bioremediation.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {9}, number = {}, pages = {602445}, pmid = {33791281}, issn = {2296-4185}, abstract = {Low molecular weight polycyclic aromatic hydrocarbons (PAHs) like naphthalene and substituted naphthalenes (methylnaphthalene, naphthoic acids, 1-naphthyl N-methylcarbamate, etc.) are used in various industries and exhibit genotoxic, mutagenic, and/or carcinogenic effects on living organisms. These synthetic organic compounds (SOCs) or xenobiotics are considered as priority pollutants that pose a critical environmental and public health concern worldwide. The extent of anthropogenic activities like emissions from coal gasification, petroleum refining, motor vehicle exhaust, and agricultural applications determine the concentration, fate, and transport of these ubiquitous and recalcitrant compounds. Besides physicochemical methods for cleanup/removal, a green and eco-friendly technology like bioremediation, using microbes with the ability to degrade SOCs completely or convert to non-toxic by-products, has been a safe, cost-effective, and promising alternative. Various bacterial species from soil flora belonging to Proteobacteria (Pseudomonas, Pseudoxanthomonas, Comamonas, Burkholderia, and Novosphingobium), Firmicutes (Bacillus and Paenibacillus), and Actinobacteria (Rhodococcus and Arthrobacter) displayed the ability to degrade various SOCs. Metabolic studies, genomic and metagenomics analyses have aided our understanding of the catabolic complexity and diversity present in these simple life forms which can be further applied for efficient biodegradation. The prolonged persistence of PAHs has led to the evolution of new degradative phenotypes through horizontal gene transfer using genetic elements like plasmids, transposons, phages, genomic islands, and integrative conjugative elements. Systems biology and genetic engineering of either specific isolates or mock community (consortia) might achieve complete, rapid, and efficient bioremediation of these PAHs through synergistic actions. In this review, we highlight various metabolic routes and diversity, genetic makeup and diversity, and cellular responses/adaptations by naphthalene and substituted naphthalene-degrading bacteria. This will provide insights into the ecological aspects of field application and strain optimization for efficient bioremediation.}, }
@article {pmid33789776, year = {2021}, author = {Mehta, N and Baghela, A}, title = {Quorum sensing-mediated inter-specific conidial anastomosis tube fusion between Colletotrichum gloeosporioides and C. siamense.}, journal = {IMA fungus}, volume = {12}, number = {1}, pages = {7}, pmid = {33789776}, issn = {2210-6340}, support = {CRG/2018/001786//Science and Engineering Research Board/ ; }, abstract = {Many plant pathogenic filamentous fungi undergo fusion of conidia through conidial anastomosis tubes (CATs), which is believed to facilitate horizontal gene transfer between species. We discovered a remarkable inter-specific CAT fusion between two important plant fungal pathogens Colletotrichum gloeosporioides and C. siamense. In an invitro assay, under no selection pressure, the inter-specific CAT fusion was preferred with higher frequency (25% ± 5%) than intra-specific CAT fusion (11% ± 3.6%). Different stages of CAT fusion viz. CAT induction, homing, and fusion were observed during this inter-specific CAT fusion. The CAT fusion was found to be higher in absence of nutrients and under physiological stresses. This CAT fusion involved a quorum sensing phenomenon, wherein the CAT induction was dependent on conidial density and the putative quorum sensing molecule was extractable in chloroform. Movement of nuclei, mitochondria, and lipid droplets were observed during the CAT fusion. Post CAT fusion, the resulting conidia gave rise to putative heterokaryotic progenies with variable colony characteristics as compared to their parental strains. Few heterokaryons showed variable AFLP banding pattern compared to their parental strains, thereby suggesting a possible genetic exchange between the two species through CAT fusion. The heterokaryotic progenies exhibited varied fitness under different stress conditions. Our study illustrated a possible role of inter-specific CAT fusion in generation of genetic and phenotypic diversity in these fungal pathogens.}, }
@article {pmid33785063, year = {2021}, author = {Yahara, K and Ma, KC and Mortimer, TD and Shimuta, K and Nakayama, SI and Hirabayashi, A and Suzuki, M and Jinnai, M and Ohya, H and Kuroki, T and Watanabe, Y and Yasuda, M and Deguchi, T and Eldholm, V and Harrison, OB and Maiden, MCJ and Grad, YH and Ohnishi, M}, title = {Emergence and evolution of antimicrobial resistance genes and mutations in Neisseria gonorrhoeae.}, journal = {Genome medicine}, volume = {13}, number = {1}, pages = {51}, pmid = {33785063}, issn = {1756-994X}, support = {F32 AI145157/AI/NIAID NIH HHS/United States ; }, mesh = {Alleles ; Base Sequence ; *Biological Evolution ; Drug Resistance, Bacterial/drug effects/*genetics ; Fluoroquinolones/pharmacology ; Genome, Bacterial ; Microbial Sensitivity Tests ; Mutation/*genetics ; Neisseria gonorrhoeae/drug effects/*genetics ; Phylogeny ; Polymorphism, Genetic ; }, abstract = {BACKGROUND: Antimicrobial resistance in Neisseria gonorrhoeae is a global health concern. Strains from two internationally circulating sequence types, ST-7363 and ST-1901, have acquired resistance to third-generation cephalosporins, mainly due to mosaic penA alleles. These two STs were first detected in Japan; however, the timeline, mechanism, and process of emergence and spread of these mosaic penA alleles to other countries remain unknown.<br><br>METHODS: We studied the evolution of penA alleles by obtaining the complete genomes from three Japanese ST-1901 clinical isolates harboring mosaic penA allele 34 (penA-34) dating from 2005 and generating a phylogenetic representation of 1075 strains sampled from 35 countries. We also sequenced the genomes of 103 Japanese ST-7363&#x2009;N. gonorrhoeae isolates from 1996 to 2005 and reconstructed a phylogeny including 88 previously sequenced genomes.<br><br>RESULTS: Based on an estimate of the time-of-emergence of ST-1901 (harboring mosaic penA-34) and ST-7363 (harboring mosaic penA-10), and >&#x2009;300 additional genome sequences of Japanese strains representing multiple STs isolated in 1996-2015, we suggest that penA-34 in ST-1901 was generated from penA-10 via recombination with another Neisseria species, followed by recombination with a gonococcal strain harboring wildtype penA-1. Following the acquisition of penA-10 in ST-7363, a dominant sub-lineage rapidly acquired fluoroquinolone resistance mutations at GyrA 95 and ParC 87-88, by independent mutations rather than horizontal gene transfer. Data in the literature suggest that the emergence of these resistance determinants may reflect selection from the standard treatment regimens in Japan at that time.<br><br>CONCLUSIONS: Our findings highlight how antibiotic use and recombination across and within Neisseria species intersect in driving the emergence and spread of drug-resistant gonorrhea.}, }
@article {pmid33782584, year = {2021}, author = {León-Sampedro, R and DelaFuente, J and Díaz-Agero, C and Crellen, T and Musicha, P and Rodríguez-Beltrán, J and de la Vega, C and Hernández-García, M and ,  and López-Fresneña, N and Ruiz-Garbajosa, P and Cantón, R and Cooper, BS and San Millán, &#xc1;}, title = {Pervasive transmission of a carbapenem resistance plasmid in the gut microbiota of hospitalized patients.}, journal = {Nature microbiology}, volume = {6}, number = {5}, pages = {606-616}, pmid = {33782584}, issn = {2058-5276}, support = {MR/K006924/1/MRC_/Medical Research Council/United Kingdom ; 203141/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; 757440/ERC_/European Research Council/International ; /WT_/Wellcome Trust/United Kingdom ; MR/R004536/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/drug effects/*genetics/isolation &amp; purification ; Bacterial Proteins/genetics/metabolism ; Carbapenems/*pharmacology ; Drug Resistance, Bacterial ; Enterobacteriaceae/drug effects/*genetics/isolation &amp; purification/metabolism ; Enterobacteriaceae Infections/*microbiology/therapy ; Female ; *Gastrointestinal Microbiome ; *Gene Transfer, Horizontal ; Hospitalization ; Hospitals, University ; Humans ; Male ; Microbial Sensitivity Tests ; Phylogeny ; Plasmids/*genetics/metabolism ; beta-Lactamases/genetics/metabolism ; }, abstract = {Infections caused by carbapenemase-producing enterobacteria (CPE) are a major concern in clinical settings worldwide. Two fundamentally different processes shape the epidemiology of CPE in hospitals: the dissemination of CPE clones from patient to patient (between-patient transfer), and the transfer of carbapenemase-encoding plasmids between enterobacteria in the gut microbiota of individual patients (within-patient transfer). The relative contribution of each process to the overall dissemination of carbapenem resistance in hospitals remains poorly understood. Here, we used mechanistic models combining epidemiological data from more than 9,000 patients with whole genome sequence information from 250 enterobacteria clones to characterize the dissemination routes of a pOXA-48-like carbapenemase-encoding plasmid in a hospital setting over a 2-yr period. Our results revealed frequent between-patient transmission of high-risk pOXA-48-carrying clones, mostly of Klebsiella pneumoniae and sporadically Escherichia coli. The results also identified pOXA-48 dissemination hotspots within the hospital, such as specific wards and individual rooms within wards. Using high-resolution plasmid sequence analysis, we uncovered the pervasive within-patient transfer of pOXA-48, suggesting that horizontal plasmid transfer occurs in the gut of virtually every colonized patient. The complex and multifaceted epidemiological scenario exposed by this study provides insights for the development of intervention strategies to control the in-hospital spread of CPE.}, }
@article {pmid33779498, year = {2021}, author = {Kang, K and Imamovic, L and Misiakou, MA and Bornakke Sørensen, M and Heshiki, Y and Ni, Y and Zheng, T and Li, J and Ellabaan, MMH and Colomer-Lluch, M and Rode, AA and Bytzer, P and Panagiotou, G and Sommer, MOA}, title = {Expansion and persistence of antibiotic-specific resistance genes following antibiotic treatment.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1-19}, pmid = {33779498}, issn = {1949-0984}, mesh = {Adolescent ; Adult ; Aged ; Anti-Bacterial Agents/*therapeutic use ; Bacteria/virology ; Bacteriophages/drug effects ; Biological Warfare ; Cohort Studies ; *Drug Resistance, Microbial ; Feces/*microbiology/*virology ; Gastrointestinal Microbiome/*drug effects ; Gene Transfer, Horizontal/drug effects ; Humans ; Metagenome/drug effects ; Microbiota/*drug effects ; Middle Aged ; Plasmids/drug effects ; Transcriptome/drug effects ; Virome/drug effects ; Young Adult ; }, abstract = {Oral antibiotics are commonly prescribed to non-hospitalized adults. However, antibiotic-induced changes in the human gut microbiome are often investigated in cohorts with preexisting health conditions and/or concomitant medication, leaving the effects of antibiotics not completely understood. We used a combination of omic approaches to comprehensively assess the effects of antibiotics on the gut microbiota and particularly the gut resistome of a small cohort of healthy adults. We observed that 3 to 19 species per individual proliferated during antibiotic treatment and Gram-negative species expanded significantly in relative abundance. While the overall relative abundance of antibiotic resistance gene homologs did not significantly change, antibiotic-specific gene homologs with presumed resistance toward the administered antibiotics were common in proliferating species and significantly increased in relative abundance. Virome sequencing and plasmid analysis showed an expansion of antibiotic-specific resistance gene homologs even 3 months after antibiotic administration, while paired-end read analysis suggested their dissemination among different species. These results suggest that antibiotic treatment can lead to a persistent expansion of antibiotic resistance genes in the human gut microbiota and provide further data in support of good antibiotic stewardship.Abbreviation: ARG - Antibiotic resistance gene homolog; AsRG - Antibiotic-specific resistance gene homolog; AZY - Azithromycin; CFX - Cefuroxime; CIP - Ciprofloxacin; DOX - Doxycycline; FDR - False discovery rate; GRiD - Growth rate index value; HGT - Horizontal gene transfer; NMDS - Non-metric multidimensional scaling; qPCR - Quantitative polymerase chain reaction; RPM - Reads per million mapped reads; TA - Transcriptional activity; TE - Transposable element; TPM - Transcripts per million mapped reads.}, }
@article {pmid33777835, year = {2021}, author = {Tran, T and Checkley, S and Caffrey, N and Mainali, C and Gow, S and Agunos, A and Liljebjelke, K}, title = {Genetic Characterization of AmpC and Extended-Spectrum Beta-Lactamase Phenotypes in Escherichia coli and Salmonella From Alberta Broiler Chickens.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {622195}, pmid = {33777835}, issn = {2235-2988}, mesh = {Alberta ; Animals ; Anti-Bacterial Agents/pharmacology ; Chickens ; *Escherichia coli/genetics ; *Escherichia coli Infections ; Phenotype ; Plasmids/genetics ; Salmonella/genetics ; beta-Lactamases/genetics ; }, abstract = {Horizontal gene transfer is an important mechanism which facilitates bacterial populations in overcoming antimicrobial treatment. In this study, a total of 120 Escherichia coli and 62 Salmonella enterica subsp. enterica isolates were isolated from broiler chicken farms in Alberta. Fourteen serovars were identified among Salmonella isolates. Thirty one percent of E. coli isolates (37/120) were multiclass drug resistant (resistant to ≥ 3 drug classes), while only about 16% of Salmonella isolates (10/62) were multiclass drug resistant. Among those, eight E. coli isolates had an AmpC-type phenotype, and one Salmonella isolate had an extended-spectrum beta-lactamase (ESBL)-type beta-lactamase phenotype. We identified both AmpC-type (blaCMY-2) and ESBL-type (blaTEM) genes in both E. coli and Salmonella isolates. Plasmids from eight of nine E. coli and Salmonella isolates were transferred to recipient strain E. coli J53 through conjugation. Transferable plasmids in the eight E. coli and Salmonella isolates were also transferred into a lab-made sodium azide-resistant Salmonella recipient through conjugation. The class 1 integrase gene, int1, was detected on plasmids from two E. coli isolates. Further investigation of class 1 integron cassette regions revealed the presence of an aadA gene encoding streptomycin 3''-adenylyltransferase, an aadA1a/aadA2 gene encoding aminoglycoside 3''-O-adenyltransferase, and a putative adenylyltransferase gene. This study provides some insight into potential horizontal gene transfer events of antimicrobial resistance genes between E. coli and Salmonella in broiler chicken production.}, }
@article {pmid33772595, year = {2021}, author = {Castell, C and Rodríguez-Lumbreras, LA and Hervás, M and Fernández-Recio, J and Navarro, JA}, title = {New Insights into the Evolution of the Electron Transfer from Cytochrome f to Photosystem I in the Green and Red Branches of Photosynthetic Eukaryotes.}, journal = {Plant &amp; cell physiology}, volume = {62}, number = {7}, pages = {1082-1093}, pmid = {33772595}, issn = {1471-9053}, support = {BIO2015-64169-P and BIO2016-79930-R//The Spanish Ministry of Economy, Industry and Competitiveness/ ; PAIDI BIO-022//Andalusian Government/ ; //EU FEDER Program/ ; FPU16/04040//FPU Program/ ; //Unit of Information Resources for Research (URICI)/ ; }, mesh = {Chlorophyta/*metabolism ; Cyanobacteria/*metabolism ; Cytochromes f/chemistry/*metabolism ; *Electron Transport ; *Evolution, Molecular ; Kinetics ; Molecular Docking Simulation ; Photosystem I Protein Complex/chemistry/*metabolism ; Protein Structure, Tertiary ; }, abstract = {In cyanobacteria and most green algae of the eukaryotic green lineage, the copper-protein plastocyanin (Pc) alternatively replaces the heme-protein cytochrome c6 (Cc6) as the soluble electron carrier from cytochrome f (Cf) to photosystem I (PSI). The functional and structural equivalence of 'green' Pc and Cc6 has been well established, representing an example of convergent evolution of two unrelated proteins. However, plants only produce Pc, despite having evolved from green algae. On the other hand, Cc6 is the only soluble donor available in most species of the red lineage of photosynthetic organisms, which includes, among others, red algae and diatoms. Interestingly, Pc genes have been identified in oceanic diatoms, probably acquired by horizontal gene transfer from green algae. However, the mechanisms that regulate the expression of a functional Pc in diatoms are still unclear. In the green eukaryotic lineage, the transfer of electrons from Cf to PSI has been characterized in depth. The conclusion is that in the green lineage, this process involves strong electrostatic interactions between partners, which ensure a high affinity and an efficient electron transfer (ET) at the cost of limiting the turnover of the process. In the red lineage, recent kinetic and structural modeling data suggest a different strategy, based on weaker electrostatic interactions between partners, with lower affinity and less efficient ET, but favoring instead the protein exchange and the turnover of the process. Finally, in diatoms the interaction of the acquired green-type Pc with both Cf and PSI may not yet be optimized.}, }
@article {pmid33772086, year = {2021}, author = {Xavier, JC and Gerhards, RE and Wimmer, JLE and Brueckner, J and Tria, FDK and Martin, WF}, title = {The metabolic network of the last bacterial common ancestor.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {413}, pmid = {33772086}, issn = {2399-3642}, mesh = {Bacteria/genetics/*metabolism ; Bacterial Proteins/genetics/*metabolism ; *Energy Metabolism/genetics ; Evolution, Molecular ; Gene Expression Regulation, Bacterial ; *Metabolic Networks and Pathways/genetics ; Phylogeny ; }, abstract = {Bacteria are the most abundant cells on Earth. They are generally regarded as ancient, but due to striking diversity in their metabolic capacities and widespread lateral gene transfer, the physiology of the first bacteria is unknown. From 1089 reference genomes of bacterial anaerobes, we identified 146 protein families that trace to the last bacterial common ancestor, LBCA, and form the conserved predicted core of its metabolic network, which requires only nine genes to encompass all universal metabolites. Our results indicate that LBCA performed gluconeogenesis towards cell wall synthesis, and had numerous RNA modifications and multifunctional enzymes that permitted life with low gene content. In accordance with recent findings for LUCA and LACA, analyses of thousands of individual gene trees indicate that LBCA was rod-shaped and the first lineage to diverge from the ancestral bacterial stem was most similar to modern Clostridia, followed by other autotrophs that harbor the acetyl-CoA pathway.}, }
@article {pmid33771467, year = {2021}, author = {Redkar, A and Sabale, M and Di Pietro, A}, title = {A 'Hydrolase Switch' for Vascular Specialization in Plant Pathogenic Bacteria.}, journal = {Trends in plant science}, volume = {26}, number = {5}, pages = {427-429}, doi = {10.1016/j.tplants.2021.03.002}, pmid = {33771467}, issn = {1878-4372}, mesh = {Bacteria/genetics ; *Hydrolases ; Life Style ; Plant Diseases ; *Xanthomonas/genetics ; }, abstract = {Plant vascular diseases are tissue-specific systemic infections provoked by bacterial and fungal pathogens adapted to thrive in the xylem vessels. A recent report by Gluck-Thaler et al. reveals that, in the phytopathogenic bacterium Xanthomonas, the switch from non-vascular to vascular pathogenesis is determined by a single gene encoding a plant cell wall-degrading hydrolase.}, }
@article {pmid33770502, year = {2021}, author = {Xia, J and Guo, Z and Yang, Z and Han, H and Wang, S and Xu, H and Yang, X and Yang, F and Wu, Q and Xie, W and Zhou, X and Dermauw, W and Turlings, TCJ and Zhang, Y}, title = {Whitefly hijacks a plant detoxification gene that neutralizes plant toxins.}, journal = {Cell}, volume = {184}, number = {7}, pages = {1693-1705.e17}, doi = {10.1016/j.cell.2021.02.014}, pmid = {33770502}, issn = {1097-4172}, mesh = {Animals ; Gene Transfer, Horizontal ; Genes, Plant ; Glucosides/chemistry/metabolism ; Hemiptera/*genetics/physiology ; Herbivory ; Insect Proteins/antagonists &amp; inhibitors/classification/genetics/*metabolism ; Intestinal Mucosa/metabolism ; Solanum lycopersicum/*genetics/metabolism ; Malonyl Coenzyme A/metabolism ; Phylogeny ; Plants, Genetically Modified/genetics/metabolism ; RNA Interference ; RNA, Double-Stranded/metabolism ; Toxins, Biological/chemistry/*metabolism ; }, abstract = {Plants protect themselves with a vast array of toxic secondary metabolites, yet most plants serve as food for insects. The evolutionary processes that allow herbivorous insects to resist plant defenses remain largely unknown. The whitefly Bemisia tabaci is a cosmopolitan, highly polyphagous agricultural pest that vectors several serious plant pathogenic viruses and is an excellent model to probe the molecular mechanisms involved in overcoming plant defenses. Here, we show that, through an exceptional horizontal gene transfer event, the whitefly has acquired the plant-derived phenolic glucoside malonyltransferase gene BtPMaT1. This gene enables whiteflies to neutralize phenolic glucosides. This was confirmed by genetically transforming tomato plants to produce small interfering RNAs that silence BtPMaT1, thus impairing the whiteflies' detoxification ability. These findings reveal an evolutionary scenario whereby herbivores harness the genetic toolkit of their host plants to develop resistance to plant defenses and how this can be exploited for crop protection.}, }
@article {pmid33770290, year = {2021}, author = {Huber, KT and Linz, S and Moulton, V}, title = {The rigid hybrid number for two phylogenetic trees.}, journal = {Journal of mathematical biology}, volume = {82}, number = {5}, pages = {40}, pmid = {33770290}, issn = {1432-1416}, mesh = {Algorithms ; Humans ; Hybridization, Genetic ; *Models, Genetic ; *Phylogeny ; }, abstract = {Recently there has been considerable interest in the problem of finding a phylogenetic network with a minimum number of reticulation vertices which displays a given set of phylogenetic trees, that is, a network with minimum hybrid number. Such networks are useful for representing the evolution of species whose genomes have undergone processes such as lateral gene transfer and recombination that cannot be represented appropriately by a phylogenetic tree. Even so, as was recently pointed out in the literature, insisting that a network displays the set of trees can be an overly restrictive assumption when modeling certain evolutionary phenomena such as incomplete lineage sorting. In this paper, we thus consider the less restrictive notion of rigidly displaying which we introduce and study here. More specifically, we characterize when two trees can be rigidly displayed by a certain type of phylogenetic network called a temporal tree-child network in terms of fork-picking sequences. These are sequences of special subconfigurations of the two trees related to the well-studied cherry-picking sequences. We also show that, in case it exists, the rigid hybrid number for two phylogenetic trees is given by a minimum weight fork-picking sequence for the trees. Finally, we consider the relationship between the rigid hybrid number and three closely related numbers; the weak, beaded, and temporal hybrid numbers. In particular, we show that these numbers can all be different even for a fixed pair of trees, and also present an infinite family of pairs of trees which demonstrates that the difference between the rigid hybrid number and the temporal-hybrid number for two phylogenetic trees on the same set of n leaves can grow at least linearly with n.}, }
@article {pmid33767366, year = {2021}, author = {Steensels, J and Gallone, B and Verstrepen, KJ}, title = {Interspecific hybridization as a driver of fungal evolution and adaptation.}, journal = {Nature reviews. Microbiology}, volume = {19}, number = {8}, pages = {485-500}, pmid = {33767366}, issn = {1740-1534}, mesh = {Adaptation, Physiological ; *Evolution, Molecular ; Fungi/*genetics ; *Gene Transfer, Horizontal ; Genetic Speciation ; *Genome, Fungal ; *Hybridization, Genetic ; }, abstract = {Cross-species gene transfer is often associated with bacteria, which have evolved several mechanisms that facilitate horizontal DNA exchange. However, the increased availability of whole-genome sequences has revealed that fungal species also exchange DNA, leading to intertwined lineages, blurred species boundaries or even novel species. In contrast to prokaryotes, fungal DNA exchange originates from interspecific hybridization, where two genomes are merged into a single, often highly unstable, polyploid genome that evolves rapidly into stabler derivatives. The resulting hybrids can display novel combinations of genetic and phenotypic variation that enhance fitness and allow colonization of new niches. Interspecific hybridization led to the emergence of important pathogens of humans and plants (for example, various Candida and 'powdery mildew' species, respectively) and industrially important yeasts, such as Saccharomyces hybrids that are important in the production of cold-fermented lagers or cold-cellared Belgian ales. In this Review, we discuss the genetic processes and evolutionary implications of fungal interspecific hybridization and highlight some of the best-studied examples. In addition, we explain how hybrids can be used to study molecular mechanisms underlying evolution, adaptation and speciation, and serve as a route towards development of new variants for industrial applications.}, }
@article {pmid33765260, year = {2021}, author = {Bombaywala, S and Mandpe, A and Paliya, S and Kumar, S}, title = {Antibiotic resistance in the environment: a critical insight on its occurrence, fate, and eco-toxicity.}, journal = {Environmental science and pollution research international}, volume = {28}, number = {20}, pages = {24889-24916}, pmid = {33765260}, issn = {1614-7499}, mesh = {Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Anti-Bacterial Agents ; Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; *Wastewater ; }, abstract = {The overuse, misuse, and underuse of antibiotics tend to increase the antibiotic burden in the environment resulting into the evolution in microbial community to possess resistance that renders antibiotics ineffective against them. The current review recapitulates the present state of knowledge about the occurrence and fate of antibiotics in various environmental matrices. Also, the prevalence of antibiotic-resistant bacteria/antibiotic-resistant genes (ARB/ARGs) in various biological and non-biological systems, eco-toxicity of antibiotics on non-target organisms, and remediation methods for antibiotics and ARB/ARGs removal were critically reviewed. Furthermore, a comparison of various technologies for their efficiency to eliminate antibiotic residues and ARB/ARGs is made. The study identified gaps in the investigation of toxic effects of low concentration of antibiotics and the mixture of multiple antibiotics on non-target organisms. The study of antibiotics' phytotoxicity and toxicity towards sediment and soil-dwelling organisms are also recognized as a knowledge gap. The review also details policies implemented across the globe to fight against antibiotic resistance, and the scarcity of data on lab to land transferred remediation technology was identified. The present study entails a critical review of literature providing guidelines for the articulation of policies for prudent use of antibiotics, limits on the amount of antibiotics in pharmaceutical formulations, and regular surveillance in the Indian context.}, }
@article {pmid33760724, year = {2019}, author = {Morinière, L and Lecomte, S and Gueguen, E and Bertolla, F}, title = {In vitro exploration of the Xanthomonas hortorum pv. vitians genome using transposon insertion sequencing and comparative genomics to discriminate between core and contextual essential genes.}, journal = {Microbial genomics}, volume = {7}, number = {6}, pages = {}, pmid = {33760724}, issn = {2057-5858}, abstract = {The essential genome of a bacterium encompasses core genes associated with basic cellular processes and conditionally essential genes dependent upon environmental conditions or the genetic context. Comprehensive knowledge of those gene sets allows for a better understanding of fundamental bacterial biology and offers new perspectives for antimicrobial drug research against detrimental bacteria such as pathogens. We investigated the essential genome of Xanthomonas hortorum pv. vitians, a gammaproteobacterial plant pathogen of lettuce (Lactuca sativa L.) which belongs to the plant-pathogen reservoir genus Xanthomonas and is affiliated to the family Xanthomonadaceae. No practical means of disease control or prevention against this pathogen is currently available, and its molecular biology is virtually unknown. To reach a comprehensive overview of the essential genome of X. hortorum pv. vitians LM16734, we developed a mixed approach combining high-quality full genome sequencing, saturated transposon insertion sequencing (Tn-Seq) in optimal growth conditions, and coupled computational analyses such as comparative genomics, synteny assessment and phylogenomics. Among the 370 essential loci identified by Tn-Seq, a majority was bound to critical cell processes conserved across bacteria. The remaining genes were either related to specific ecological features of Xanthomonas or Xanthomonadaceae species, or acquired through horizontal gene transfer of mobile genetic elements and associated with ancestral parasitic gene behaviour and bacterial defence systems. Our study sheds new light on our usual concepts about gene essentiality and is pioneering in the molecular and genomic study of X. hortorum pv. vitians.}, }
@article {pmid33758084, year = {2021}, author = {Moustafa, AM and Velusamy, SK and Denu, L and Narechania, A and Fine, DH and Planet, PJ}, title = {Adaptation by Ancient Horizontal Acquisition of Butyrate Metabolism Genes in Aggregatibacter actinomycetemcomitans.}, journal = {mBio}, volume = {12}, number = {2}, pages = {}, pmid = {33758084}, issn = {2150-7511}, support = {R01 AI137526/AI/NIAID NIH HHS/United States ; R21 AI144561/AI/NIAID NIH HHS/United States ; }, mesh = {Adaptation, Physiological/*genetics ; Aggregatibacter actinomycetemcomitans/*genetics/*metabolism/pathogenicity ; Anaerobiosis ; Biofilms ; Butyrates/*metabolism ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Time Factors ; }, abstract = {Like the bacterial residents of the human gut, it is likely that many of the species in the human oral microbiota have evolved to better occupy and persist in their niche. Aggregatibacter actinomycetemcomitans (Aa) is both a common colonizer of the oral cavity and has been implicated in the pathogenesis of periodontal disease. Here, we present a whole-genome phylogenetic analysis of Aa isolates from humans and nonhuman primates that revealed an ancient origin for this species and a long history of association with the Catarrhini, the lineage that includes Old World monkeys (OWM) and humans. Further genomic analysis showed a strong association with the presence of a short-chain fatty acid (SCFA) catabolism locus (atoRDAEB) in many human isolates that was absent in almost all nonhuman OWM isolates. We show that this locus was likely acquired through horizontal gene transfer. When grown under conditions that are similar to those at the subgingival site of periodontitis (anaerobic, SCFA replete), Aa strains with atoRDAEB formed robust biofilms and showed upregulation of genes involved in virulence, colonization, and immune evasion. Both an isogenic deletion mutant and nonhuman primate isolates lacking the ato locus failed to grow in a robust biofilm under these conditions, but grew well under the carbohydrate-rich conditions similar to those found above the gumline. We propose that the acquisition of the ato locus was a key evolutionary step allowing Aa to utilize SCFAs, adapt, and modulate subgingival disease.IMPORTANCE There has been considerable interest in the impact of short-chain fatty acids (SCFAs) on inflammatory effects related to the microbiome. Here, we present evidence that SCFAs may also be important in disease by providing an energy source or disease-associated cue for colonizing pathogens. We propose that SCFAs allow Aggregatibacter actinomycetemcomitans (Aa) to adapt to the subgingival anaerobic environment, which is the site of human periodontitis. Under anaerobic, SCFA-rich conditions, human-derived Aa strains that possess butyrate metabolism genes form strong biofilms and upregulate virulence genes. Our phylogenetic analysis highlights a long history of evolution of Aa with its primate hosts and suggests that the acquisition of butyrate metabolism genes may have been a critical step in allowing Aa to colonize a new niche and cause disease in humans. Overall, this study highlights the important role that horizontal gene transfer may play in microbial adaptation and the evolution of infectious disease.}, }
@article {pmid33754381, year = {2021}, author = {Lam, T and Ellison, CK and Eddington, DT and Brun, YV and Dalia, AB and Morrison, DA}, title = {Competence pili in Streptococcus pneumoniae are highly dynamic structures that retract to promote DNA uptake.}, journal = {Molecular microbiology}, volume = {116}, number = {2}, pages = {381-396}, doi = {10.1111/mmi.14718}, pmid = {33754381}, issn = {1365-2958}, support = {R35GM128674/NH/NIH HHS/United States ; R35GM122556/NH/NIH HHS/United States ; R21AI133304/NH/NIH HHS/United States ; }, mesh = {Biological Transport, Active/*physiology ; Cell Wall/metabolism ; DNA Transformation Competence/*physiology ; DNA, Bacterial/*metabolism ; DNA-Binding Proteins/metabolism ; Fimbriae Proteins/metabolism ; Fimbriae, Bacterial/*metabolism ; Streptococcus pneumoniae/*metabolism ; Transformation, Bacterial/genetics/physiology ; }, abstract = {The competence pili of transformable Gram-positive species are phylogenetically related to the diverse and widespread class of extracellular filamentous organelles known as type IV pili. In Gram-negative bacteria, type IV pili act through dynamic cycles of extension and retraction to carry out diverse activities including attachment, motility, protein secretion, and DNA uptake. It remains unclear whether competence pili in Gram-positive species exhibit similar dynamic activity, and their mechanism of action for DNA uptake remains unclear. They are hypothesized to either (1) leave transient cavities in the cell wall that facilitate DNA passage, (2) form static adhesins to enrich DNA near the cell surface for subsequent uptake by membrane-embedded transporters, or (3) play an active role in translocating bound DNA via dynamic activity. Here, we use a recently described pilus labeling approach to demonstrate that competence pili in Streptococcus pneumoniae are highly dynamic structures that rapidly extend and retract from the cell surface. By labeling the principal pilus monomer, ComGC, with bulky adducts, we further demonstrate that pilus retraction is essential for natural transformation. Together, our results suggest that Gram-positive competence pili in other species may also be dynamic and retractile structures that play an active role in DNA uptake.}, }
@article {pmid33753763, year = {2021}, author = {Spadar, A and Perdigão, J and Phelan, J and Charleston, J and Modesto, A and Elias, R and de Sessions, PF and Hibberd, ML and Campino, S and Duarte, A and Clark, TG}, title = {Methylation analysis of Klebsiella pneumoniae from Portuguese hospitals.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {6491}, pmid = {33753763}, issn = {2045-2322}, support = {MR/R025576/1/MRC_/Medical Research Council/United Kingdom ; BB/R013063/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/M01360X/1/MRC_/Medical Research Council/United Kingdom ; MR/R020973/1/MRC_/Medical Research Council/United Kingdom ; MR/N010469/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Bacterial Proteins/genetics ; *DNA Methylation ; DNA Modification Methylases/genetics ; Epigenome ; Humans ; Klebsiella Infections/*microbiology ; Klebsiella pneumoniae/drug effects/*genetics/isolation &amp; purification/pathogenicity ; beta-Lactam Resistance ; }, abstract = {Klebsiella pneumoniae is an important nosocomial infectious agent with a high antimicrobial resistance (AMR) burden. The application of long read sequencing technologies is providing insights into bacterial chromosomal and putative extra-chromosomal genetic elements (PEGEs) associated with AMR, but also epigenetic DNA methylation, which is thought to play a role in cleavage of foreign DNA and expression regulation. Here, we apply the PacBio sequencing platform to eight Portuguese hospital isolates, including one carbapenemase producing isolate, to identify methylation motifs. The resulting assembled chromosomes were between 5.2 and 5.5Mbp in length, and twenty-six PEGEs were found. Four of our eight samples carry blaCTX-M-15, a dominant Extended Spectrum Beta Lactamase in Europe. We identified methylation motifs that control Restriction-Modification systems, including GATC of the DNA adenine methylase (Dam), which methylates N6-methyladenine (m6A) across all our K. pneumoniae assemblies. There was a consistent lack of methylation by Dam of the GATC motif downstream of two genes: fosA, a locus associated with low level fosfomycin resistance, and tnpB transposase on IncFIB(K) plasmids. Overall, we have constructed eight high quality reference genomes of K. pneumoniae, with insights into horizontal gene transfer and methylation m6A motifs.}, }
@article {pmid33753335, year = {2021}, author = {Ortiz de la Rosa, JM and Nordmann, P and Poirel, L}, title = {Antioxidant Molecules as a Source of Mitigation of Antibiotic Resistance Gene Dissemination.}, journal = {Antimicrobial agents and chemotherapy}, volume = {65}, number = {6}, pages = {}, pmid = {33753335}, issn = {1098-6596}, mesh = {*Anti-Bacterial Agents/pharmacology ; Antioxidants/pharmacology ; Drug Resistance, Microbial ; Escherichia coli/genetics ; *Escherichia coli Infections ; Gene Transfer, Horizontal ; Humans ; Plasmids/genetics ; beta-Lactamases/genetics ; }, abstract = {Escherichia coli is the most commonly identified human pathogen and a prominent microorganism of the gut microbiota. Acquired resistance to antibiotics in this species is driven mainly by horizontal gene transfer and plasmid acquisition. Currently, the main concern is the acquisition of extended-spectrum β-lactamases of the CTX-M type in E. coli, a worldwide-observed phenomenon. Plasmids encoding CTX-M enzymes have different scaffolds and conjugate at different frequencies. Here, we show that the conjugation rates of several plasmid types encoding broad-spectrum β-lactamases are increased when the E. coli donor strain is exposed to subinhibitory concentrations of diverse orally given antibiotics, including fluoroquinolones, such as ciprofloxacin and levofloxacin, but also trimethoprim and nitrofurantoin. This study provides insights into underlying mechanisms leading to increased plasmid conjugation frequency in relation to DNA synthesis inhibitor-type antibiotics, involving reactive oxygen species (ROS) production and probably increased expression of genes involved in the SOS response. Furthermore, we show that some antioxidant molecules currently approved for unrelated clinical uses, such as edaravone, p-coumaric acid, and N-acetylcysteine, may antagonize the ability of antibiotics to increase plasmid conjugation rates. These results suggest that several antioxidative molecules might be used in combination with these "inducer" antibiotics to mitigate the unwanted increased resistance plasmid dissemination.}, }
@article {pmid33749577, year = {2021}, author = {Hamidian, M and Hall, RM}, title = {Dissemination of novel Tn7 family transposons carrying genes for synthesis and uptake of fimsbactin siderophores among Acinetobacter baumannii isolates.}, journal = {Microbial genomics}, volume = {7}, number = {3}, pages = {}, pmid = {33749577}, issn = {2057-5858}, mesh = {Acinetobacter baumannii/*genetics/*metabolism ; Bacterial Proteins/*genetics/metabolism ; *DNA Transposable Elements ; Gene Transfer, Horizontal ; Genome, Bacterial ; Phylogeny ; Recombination, Genetic ; Siderophores/*metabolism ; }, abstract = {Acinetobacter baumannii is a successful opportunistic pathogen that can compete for iron under iron-limiting conditions. Here, large novel transposons that carry genes for synthesis and transport of the fimsbactin siderophores present in some A. baumannii strains were examined. Tn6171, originally found in the A. baumannii global clone 1 (GC1) lineage 2 isolate D36, includes tns genes encoding proteins related to the TnsA, TnsB, TnsC transposition proteins (50-59 % identity), TnsD targeting protein (43 % identity) and TnsE (31 % identity) of Tn7, and is found in the chromosome downstream of the glmS gene, the preferred location for Tn7, flanked by a 5 bp target site duplication. Tn6171 is bounded by 29 bp inverted repeats and, like Tn7, includes additional TnsB binding sites at each end. Tn6171 or minor variants were detected in the equivalent location in complete or draft genomes of several further A. baumannii isolates belonging to GC1 [sequence type (ST) 1, ST81, ST94, ST328, ST623, ST717], GC2 (ST2) and ST10. However, in some of these isolates the surrounding glmS region was clearly derived from a different A. baumannii lineage, indicating that the transposon may have been acquired by replacement of a segment of the chromosome. A recombination-free phylogeny revealed that there were several transposon acquisition events in GC1. The GC1 isolates were mainly lineage 2, but a potential third lineage was also detected. A related transposon, designated Tn6552, was detected in ATCC 17978 (ST437) and other ST437 isolates. However, the Tn6552 tnsD targeting gene was interrupted by an ISAba12, and Tn6552 is not downstream of glmS.}, }
@article {pmid33749576, year = {2019}, author = {Lorenzi, JN and Lespinet, O and Leblond, P and Thibessard, A}, title = {Subtelomeres are fast-evolving regions of the Streptomyces linear chromosome.}, journal = {Microbial genomics}, volume = {7}, number = {6}, pages = {}, pmid = {33749576}, issn = {2057-5858}, abstract = {Streptomyces possess a large linear chromosome (6-12 Mb) consisting of a conserved central region flanked by variable arms covering several megabases. In order to study the evolution of the chromosome across evolutionary times, a representative panel of Streptomyces strains and species (125) whose chromosomes are completely sequenced and assembled was selected. The pan-genome of the genus was modelled and shown to be open with a core-genome reaching 1018 genes. The evolution of Streptomyces chromosome was analysed by carrying out pairwise comparisons, and by monitoring indexes measuring the conservation of genes (presence/absence) and their synteny along the chromosome. Using the phylogenetic depth offered by the chosen panel, it was possible to infer that within the central region of the chromosome, the core-genes form a highly conserved organization, which can reveal the existence of an ancestral chromosomal skeleton. Conversely, the chromosomal arms, enriched in variable genes evolved faster than the central region under the combined effect of rearrangements and addition of new information from horizontal gene transfer. The genes hosted in these regions may be localized there because of the adaptive advantage that their rapid evolution may confer. We speculate that (i) within a bacterial population, the variability of these genes may contribute to the establishment of social characters by the production of 'public goods' (ii) at the evolutionary scale, this variability contributes to the diversification of the genetic pool of the bacteria.}, }
@article {pmid33746928, year = {2021}, author = {Huang, L and Liu, M and Zhu, D and Xie, L and Huang, M and Xiang, C and Biville, F and Jia, R and Chen, S and Zhao, X and Yang, Q and Wu, Y and Zhang, S and Huang, J and Ou, X and Mao, S and Gao, Q and Sun, D and Tian, B and Wang, M and Cheng, A}, title = {Natural Transformation of Riemerella columbina and Its Determinants.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {634895}, pmid = {33746928}, issn = {1664-302X}, abstract = {In a previous study, it was shown that Riemerella anatipestifer, a member of Flavobacteriaceae, is naturally competent. However, whether natural competence is universal in Flavobacteriaceae remains unknown. In this study, it was shown for the first time that Riemerella columbina was naturally competent in the laboratory condition; however, Flavobacterium johnsoniae was not naturally competent under the same conditions. The competence of R. columbina was maintained throughout the growth phases, and the transformation frequency was highest during the logarithmic phase. A competition assay revealed that R. columbina preferentially took up its own genomic DNA over heterologous DNA. The natural transformation frequency of R. columbina was significantly increased in GCB medium without peptone or phosphate. Furthermore, natural transformation of R. columbina was inhibited by 0.5 mM EDTA, but could be restored by the addition of CaCl2, MgCl2, ZnCl2, and MnCl2, suggesting that these divalent cations promote the natural transformation of R. columbina. Overall, this study revealed that natural competence is not universal in Flavobacteriaceae members and triggering of competence differs from species to species.}, }
@article {pmid33745750, year = {2021}, author = {Bier, E and Nizet, V}, title = {Driving to Safety: CRISPR-Based Genetic Approaches to Reducing Antibiotic Resistance.}, journal = {Trends in genetics : TIG}, volume = {37}, number = {8}, pages = {745-757}, doi = {10.1016/j.tig.2021.02.007}, pmid = {33745750}, issn = {0168-9525}, mesh = {Anti-Bacterial Agents/adverse effects/*therapeutic use ; CRISPR-Cas Systems/*genetics ; Drug Resistance, Microbial/*genetics ; Gene Editing/methods ; Genome, Bacterial/drug effects/*genetics ; Humans ; }, abstract = {Bacterial resistance to antibiotics has reached critical levels, skyrocketing in hospitals and the environment and posing a major threat to global public health. The complex and challenging problem of reducing antibiotic resistance (AR) requires a network of both societal and science-based solutions to preserve the most lifesaving pharmaceutical intervention known to medicine. In addition to developing new classes of antibiotics, it is essential to safeguard the clinical efficacy of existing drugs. In this review, we examine the potential application of novel CRISPR-based genetic approaches to reducing AR in both environmental and clinical settings and prolonging the utility of vital antibiotics.}, }
@article {pmid33744972, year = {2021}, author = {Spence, MA and Mortimer, MD and Buckle, AM and Minh, BQ and Jackson, CJ}, title = {A Comprehensive Phylogenetic Analysis of the Serpin Superfamily.}, journal = {Molecular biology and evolution}, volume = {38}, number = {7}, pages = {2915-2929}, pmid = {33744972}, issn = {1537-1719}, mesh = {Animals ; Bacteria/genetics ; Chordata/genetics ; *Evolution, Molecular ; Invertebrates/genetics ; *Multigene Family ; *Phylogeny ; Plants/genetics ; Serpins/*genetics ; }, abstract = {Serine protease inhibitors (serpins) are found in all kingdoms of life and play essential roles in multiple physiological processes. Owing to the diversity of the superfamily, phylogenetic analysis is challenging and prokaryotic serpins have been speculated to have been acquired from Metazoa through horizontal gene transfer due to their unexpectedly high homology. Here, we have leveraged a structural alignment of diverse serpins to generate a comprehensive 6,000-sequence phylogeny that encompasses serpins from all kingdoms of life. We show that in addition to a central "hub" of highly conserved serpins, there has been extensive diversification of the superfamily into many novel functional clades. Our analysis indicates that the hub proteins are ancient and are similar because of convergent evolution, rather than the alternative hypothesis of horizontal gene transfer. This work clarifies longstanding questions in the evolution of serpins and provides new directions for research in the field of serpin biology.}, }
@article {pmid33744971, year = {2021}, author = {Negri, A and Werbowy, O and Wons, E and Dersch, S and Hinrichs, R and Graumann, PL and Mruk, I}, title = {Regulator-dependent temporal dynamics of a restriction-modification system's gene expression upon entering new host cells: single-cell and population studies.}, journal = {Nucleic acids research}, volume = {49}, number = {7}, pages = {3826-3840}, pmid = {33744971}, issn = {1362-4962}, mesh = {DNA Restriction-Modification Enzymes/*metabolism ; *Escherichia coli/enzymology/genetics ; Escherichia coli Proteins/*metabolism ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; }, abstract = {Restriction-modification (R-M) systems represent a first line of defense against invasive DNAs, such as bacteriophage DNAs, and are widespread among bacteria and archaea. By acquiring a Type II R-M system via horizontal gene transfer, the new hosts generally become more resistant to phage infection, through the action of a restriction endonuclease (REase), which cleaves DNA at or near specific sequences. A modification methyltransferase (MTase) serves to protect the host genome against its cognate REase activity. The production of R-M system components upon entering a new host cell must be finely tuned to confer protective methylation before the REase acts, to avoid host genome damage. Some type II R-M systems rely on a third component, the controller (C) protein, which is a transcription factor that regulates the production of REase and/or MTase. Previous studies have suggested C protein effects on the dynamics of expression of an R-M system during its establishment in a new host cell. Here, we directly examine these effects. By fluorescently labelling REase and MTase, we demonstrate that lack of a C protein reduces the delay of REase production, to the point of being simultaneous with, or even preceding, production of the MTase. Single molecule tracking suggests that a REase and a MTase employ different strategies for their target search within host cells, with the MTase spending much more time diffusing in proximity to the nucleoid than does the REase. This difference may partially ameliorate the toxic effects of premature REase expression.}, }
@article {pmid33744628, year = {2021}, author = {Sathicq, MB and Sabatino, R and Corno, G and Di Cesare, A}, title = {Are microplastic particles a hotspot for the spread and the persistence of antibiotic resistance in aquatic systems?.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {279}, number = {}, pages = {116896}, doi = {10.1016/j.envpol.2021.116896}, pmid = {33744628}, issn = {1873-6424}, mesh = {Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Attention ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Humans ; *Microplastics ; *Plastics ; }, abstract = {In the last decade, the study of the origin and fate of plastic debris received great attention, leading to a new and broad awareness of the hazard represented by these particles for the environment and the biota. At the same time, the scientific consideration on the leading role of the environment regarding the spread of antibiotic resistant bacteria (ARB) increased. Both, microplastic particles (MPs) and ARB share pollution sources and, in aquatic systems, MPs could act as a novel ecological niche, favouring the survival of pathogens and ARB. MPs can host a specific microbial biofilm, referred to as plastisphere, phylogenetically different from the surrounding planktonic microbial community and from the biofilm growing on other suspended particles. The plastisphere can influence the overall microbiome of a specific habitat, by introducing and supporting different species and by increasing horizontal gene transfer. In this review we collect and analyse the available studies coupling MPs and antibiotic resistance in water, highlighting knowledge gaps to be filled in order to understand if MPs could effectively act as a carrier of ARB and antibiotic resistance genes, and pose a real threat to human health.}, }
@article {pmid33742870, year = {2021}, author = {Huang, FY and Zhu, YG and Su, JQ}, title = {[Diversity and Abundance of Antibiotic Resistance Genes in Tailings Ponds].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {42}, number = {2}, pages = {761-765}, doi = {10.13227/j.hjkx.202008051}, pmid = {33742870}, issn = {0250-3301}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial/genetics ; Humans ; *Ponds ; }, abstract = {Antibiotic resistance genes (ARGs) are considered emerging contaminants posing an increasing threat to the ecological environment and global human health. Profiling ARGs in tailings ponds is essential to better understand their spatial and temporal dynamics. In this study, high-throughput quantitative polymerase chain reaction (PCR) techniques were used to investigate the occurrence, diversity, abundance, and distribution of ARGs in a tailings pond. A total of 97, 52, 44, and 56 ARGs were detected in WK0, WK1, WK2, and HS, respectively, with 11, 6, 3, and 6 mobile genetic elements (MGEs) also being detected, respectively. The absolute abundance of ARGs in the pond water ranged from 6.39×10[7] to 1.75×10[8] copies·L[-1]. Additionally, the abundance of MGEs were higher than ARGs in WK1 and WK2, indicating the potential for horizontal gene transfer (HGT). Furthermore, Cu, TOC, and MGEs were significantly associated with ARGs. Indeed, redundancy analysis (RDA) revealed that Cu, TOC, and MGEs explained 61.64% of the alteration of the ARG profiles, implying their potential roles in the spread and evolution of ARGs in tailings ponds.}, }
@article {pmid33742736, year = {2021}, author = {Ikegaya, M and Miyazaki, T and Park, EY}, title = {Biochemical characterization of Bombyx mori α-N-acetylgalactosaminidase belonging to the glycoside hydrolase family 31.}, journal = {Insect molecular biology}, volume = {30}, number = {4}, pages = {367-378}, doi = {10.1111/imb.12701}, pmid = {33742736}, issn = {1365-2583}, mesh = {Animals ; Biological Evolution ; *Bombyx/genetics/metabolism ; Enterococcus/genetics ; Escherichia coli ; Gene Transfer, Horizontal ; Genes, Bacterial ; Glycoside Hydrolases/metabolism ; Recombinant Proteins/biosynthesis/chemistry/genetics/metabolism ; alpha-N-Acetylgalactosaminidase/*chemistry/genetics/metabolism ; }, abstract = {Horizontal gene transfer is an important evolutionary mechanism not only for bacteria but also for eukaryotes. In the domestic silkworm Bombyx mori, a model species of lepidopteran insects, some enzymes are known to have been acquired by horizontal transfer; however, the enzymatic features of protein BmNag31, belonging to glycoside hydrolase family 31 (GH31) and whose gene was predicted to be transferred from Enterococcus sp. are unknown. In this study, we reveal that the transcription of BmNag31 increases significantly during the prepupal to pupal stage, and decreases in the adult stage. The full-length BmNag31 and its truncated mutants were heterologously expressed in Escherichia coli and characterized. Its catalytic domain exhibits α-N-acetylgalactosaminidase activity and the carbohydrate-binding module family 32 domain shows binding activity towards N-acetylgalactosamine, similar to the Enterococcus faecalis homolog, EfNag31A. Gel filtration chromatography and blue native polyacrylamide gel electrophoresis analyses indicate that BmNag31 forms a hexamer whereas EfNag31A is monomeric. These results provide insights into the function of lepidopteran GH31 α-N-acetylgalactosaminidase.}, }
@article {pmid33740894, year = {2021}, author = {Pyrih, J and Žárský, V and Fellows, JD and Grosche, C and Wloga, D and Striepen, B and Maier, UG and Tachezy, J}, title = {The iron-sulfur scaffold protein HCF101 unveils the complexity of organellar evolution in SAR, Haptista and Cryptista.}, journal = {BMC ecology and evolution}, volume = {21}, number = {1}, pages = {46}, pmid = {33740894}, issn = {2730-7182}, mesh = {Animals ; *Cryptosporidiosis ; *Cryptosporidium ; Iron ; *Iron-Sulfur Proteins/genetics ; Phylogeny ; Sulfur ; }, abstract = {BACKGROUND: Nbp35-like proteins (Nbp35, Cfd1, HCF101, Ind1, and AbpC) are P-loop NTPases that serve as components of iron-sulfur cluster (FeS) assembly machineries. In eukaryotes, Ind1 is present in mitochondria, and its function is associated with the assembly of FeS clusters in subunits of respiratory Complex I, Nbp35 and Cfd1 are the components of the cytosolic FeS assembly (CIA) pathway, and HCF101 is involved in FeS assembly of photosystem I in plastids of plants (chHCF101). The AbpC protein operates in Bacteria and Archaea. To date, the cellular distribution of these proteins is considered to be highly conserved with only a few exceptions.<br><br>RESULTS: We searched for the genes of all members of the Nbp35-like protein family and analyzed their targeting sequences. Nbp35 and Cfd1 were predicted to reside in the cytoplasm with some exceptions of Nbp35 localization to the mitochondria; Ind1was found in the mitochondria, and HCF101 was predicted to reside in plastids (chHCF101) of all photosynthetically active eukaryotes. Surprisingly, we found a second HCF101 paralog in all members of Cryptista, Haptista, and SAR that was predicted to predominantly target mitochondria (mHCF101), whereas Ind1 appeared to be absent in these organisms. We also identified a few exceptions, as apicomplexans possess mHCF101 predicted to localize in the cytosol and Nbp35 in the mitochondria. Our predictions were experimentally confirmed in selected representatives of Apicomplexa (Toxoplasma gondii), Stramenopila (Phaeodactylum tricornutum, Thalassiosira pseudonana), and Ciliophora (Tetrahymena thermophila) by tagging proteins with a transgenic reporter. Phylogenetic analysis suggested that chHCF101 and mHCF101 evolved from a common ancestral HCF101 independently of the Nbp35/Cfd1 and Ind1 proteins. Interestingly, phylogenetic analysis supports rather a lateral gene transfer of ancestral HCF101 from bacteria than its acquisition being associated with either &#x3b1;-proteobacterial or cyanobacterial endosymbionts.<br><br>CONCLUSION: Our searches for Nbp35-like proteins across eukaryotic lineages revealed that SAR, Haptista, and Cryptista possess mitochondrial HCF101. Because plastid localization of HCF101 was only known thus far, the discovery of its mitochondrial paralog explains confusion regarding the presence of HCF101 in organisms that possibly lost secondary plastids (e.g., ciliates, Cryptosporidium) or possess reduced nonphotosynthetic plastids (apicomplexans).}, }
@article {pmid33739418, year = {2021}, author = {Dai, X and Kiuchi, T and Zhou, Y and Jia, S and Xu, Y and Katsuma, S and Shimada, T and Wang, H}, title = {Horizontal Gene Transfer and Gene Duplication of β-Fructofuranosidase Confer Lepidopteran Insects Metabolic Benefits.}, journal = {Molecular biology and evolution}, volume = {38}, number = {7}, pages = {2897-2914}, pmid = {33739418}, issn = {1537-1719}, mesh = {Animals ; *Biological Evolution ; Female ; *Gene Duplication ; *Gene Transfer, Horizontal ; Homeostasis ; Larva/growth &amp; development/metabolism ; Lepidoptera/enzymology/*genetics ; Male ; Sucrase/metabolism ; beta-Fructofuranosidase/*genetics ; }, abstract = {Horizontal gene transfer (HGT) is a potentially critical source of material for ecological adaptation and the evolution of novel genetic traits. However, reports on posttransfer duplication in organism genomes are lacking, and the evolutionary advantages conferred on the recipient are generally poorly understood. Sucrase plays an important role in insect physiological growth and development. Here, we performed a comprehensive analysis of the evolution of insect β-fructofuranosidase transferred from bacteria via HGT. We found that posttransfer duplications of β-fructofuranosidase were widespread in Lepidoptera and sporadic occurrences of β-fructofuranosidase were found in Coleoptera and Hymenoptera. β-fructofuranosidase genes often undergo modifications, such as gene duplication, differential gene loss, and changes in mutation rates. Lepidopteran β-fructofuranosidase gene (SUC) clusters showed marked divergence in gene expression patterns and enzymatic properties in Bombyx mori (moth) and Papilio xuthus (butterfly). We generated SUC1 mutations in B. mori using CRISPR/Cas9 to thoroughly examine the physiological function of SUC. BmSUC1 mutant larvae were viable but displayed delayed growth and reduced sucrase activities that included susceptibility to the sugar mimic alkaloid found in high concentrations in mulberry. BmSUC1 served as a critical sucrase and supported metabolic homeostasis in the larval midgut and silk gland, suggesting that gene transfer of β-fructofuranosidase enhanced the digestive and metabolic adaptation of lepidopteran insects. These findings highlight not only the universal function of β-fructofuranosidase with a link to the maintenance of carbohydrate metabolism but also an underexplored function in the silk gland. This study expands our knowledge of posttransfer duplication and subsequent functional diversification in the adaptive evolution and lineage-specific adaptation of organisms.}, }
@article {pmid33739376, year = {2021}, author = {Tria, FDK and Brueckner, J and Skejo, J and Xavier, JC and Kapust, N and Knopp, M and Wimmer, JLE and Nagies, FSP and Zimorski, V and Gould, SB and Garg, SG and Martin, WF}, title = {Gene Duplications Trace Mitochondria to the Onset of Eukaryote Complexity.}, journal = {Genome biology and evolution}, volume = {13}, number = {5}, pages = {}, pmid = {33739376}, issn = {1759-6653}, mesh = {*Biological Evolution ; Eukaryota/*genetics ; Evolution, Molecular ; *Gene Duplication ; Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; Mitochondria/*genetics ; }, abstract = {The last eukaryote common ancestor (LECA) possessed mitochondria and all key traits that make eukaryotic cells more complex than their prokaryotic ancestors, yet the timing of mitochondrial acquisition and the role of mitochondria in the origin of eukaryote complexity remain debated. Here, we report evidence from gene duplications in LECA indicating an early origin of mitochondria. Among 163,545 duplications in 24,571 gene trees spanning 150 sequenced eukaryotic genomes, we identify 713 gene duplication events that occurred in LECA. LECA's bacterial-derived genes include numerous mitochondrial functions and were duplicated significantly more often than archaeal-derived and eukaryote-specific genes. The surplus of bacterial-derived duplications in LECA most likely reflects the serial copying of genes from the mitochondrial endosymbiont to the archaeal host's chromosomes. Clustering, phylogenies and likelihood ratio tests for 22.4 million genes from 5,655 prokaryotic and 150 eukaryotic genomes reveal no evidence for lineage-specific gene acquisitions in eukaryotes, except from the plastid in the plant lineage. That finding, and the functions of bacterial genes duplicated in LECA, suggests that the bacterial genes in eukaryotes are acquisitions from the mitochondrion, followed by vertical gene evolution and differential loss across eukaryotic lineages, flanked by concomitant lateral gene transfer among prokaryotes. Overall, the data indicate that recurrent gene transfer via the copying of genes from a resident mitochondrial endosymbiont to archaeal host chromosomes preceded the onset of eukaryotic cellular complexity, favoring mitochondria-early over mitochondria-late hypotheses for eukaryote origin.}, }
@article {pmid33737123, year = {2021}, author = {Vargas-Aguilar, AL and Yáñez-Rivera, B and Vega-García, PD and Gomez-Gil, B}, title = {Genomic and molecular evolutionary dynamics of transcriptional response regulator genes in bacterial species of the Harveyi clade of Vibrio.}, journal = {Gene}, volume = {783}, number = {}, pages = {145577}, doi = {10.1016/j.gene.2021.145577}, pmid = {33737123}, issn = {1879-0038}, mesh = {*Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genes, Regulator ; Genome, Bacterial ; Vibrio/*genetics ; }, abstract = {Transcriptional response regulators (TRR) are the most abundant signal transducers in prokaryotic systems that mediate intracellular changes in response to environmental signals. They are involved in a wide range of biological processes that allow bacteria to persist in particular habitats. There is strong evidence that the bacterial habitat and their lifestyle influence the size of their TRR genetic repertoire. Therefore, it would be expected that the evolution of bacterial genomes could be linked to natural selection processes. To test this hypothesis, we explored the evolutionary dynamics of TRR genes of the widely studied Harveyi clade of the genus Vibrio at the molecular and genomic levels. Our results suggest that the TRR genetic repertoire of the species belonging to the Harveyi clade is a product of genomic reduction and expansion. The gene loss and gains that drive their genomic reduction and expansion could be attributed to natural selection and random genetic drift. It seems that natural selection acts to maintain the ancestral state of core TRR genes (shared by all species) by purifying processes and could be driving the loss of some accessory (found in certain species) genes through the diversification of sequences. The neutrality observed in gene gain could be attributed to spontaneous events as horizontal gene transfer driven by stochastic events as occurs in random genetic drift.}, }
@article {pmid33736163, year = {2021}, author = {Zhang, WG and Wen, T and Liu, LZ and Li, JY and Gao, Y and Zhu, D and He, JZ and Zhu, YG}, title = {Agricultural land-use change and rotation system exert considerable influences on the soil antibiotic resistome in Lake Tai Basin.}, journal = {The Science of the total environment}, volume = {771}, number = {}, pages = {144848}, doi = {10.1016/j.scitotenv.2020.144848}, pmid = {33736163}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents ; Genes, Bacterial ; Humans ; *Lakes ; RNA, Ribosomal, 16S/genetics ; Rotation ; *Soil ; Soil Microbiology ; }, abstract = {In this study, we use high-throughput quantitative polymerase chain reaction approaches to comprehensively assess the effects of agricultural land-use change on the antibiotic resistome of agricultural runoffs after rainfalls in Lake Tai Basin. For the first time in this region, our findings show that orchard runoffs harbored more diverse and abundant antibiotic resistance genes (ARGs) than traditional cropland runoffs. Network analysis demonstrated that orchard runoffs possessed a strong ability for ARG dissemination via horizontal gene transfer. These results suggest that residents might be exposed to a higher public health threat than before. Moreover, the present study confirmed that the rice-wheat rotation system plays a key role in regulating the soil antibiotic resistome profile. Using 16S rRNA high-throughput sequencing technology, this study clarified the relationships between the antibiotic resistome and soil microbiome composition. Finally, we discuss the key environmental factors driving changes in the soil antibiotic resistome. In summary, this study gives insight into the dissemination of environmental ARGs to the people living in the Lake Tai Basin.}, }
@article {pmid33732782, year = {2021}, author = {Sagné, E and Citti, C and Dordet-Frisoni, E}, title = {Bacterial Conjugation Protocol for Ruminant Mycoplasmas.}, journal = {Bio-protocol}, volume = {11}, number = {2}, pages = {e3893}, pmid = {33732782}, issn = {2331-8325}, abstract = {In Mycoplasma agalactiae, two simultaneous processes of DNA transfer have been described that require direct cell-to-cell contact and are similar to conjugation. One involves the self-transmission of an integrative conjugative element (ICE) while the second concerns the horizontal transfer of large and small fragments of chromosomal DNA. Here, we describe an optimized conjugation protocol for the horizontal transfer of ICE or chromosomal DNA carrying antibiotic resistance markers (i.e., tetracycline, gentamicin, puromycin) from donor to recipient mycoplasma cells. Calculation of the conjugation frequencies, selection and characterization of transconjugants are detailed. This protocol has been developed with M. agalactiae but has been successfully used for M. bovis and can be adapted to other related mycoplasma species.}, }
@article {pmid33728052, year = {2021}, author = {Li, R and Du, P and Zhang, P and Li, Y and Yang, X and Wang, Z and Wang, J and Bai, L}, title = {Comprehensive Genomic Investigation of Coevolution of mcr genes in Escherichia coli Strains via Nanopore Sequencing.}, journal = {Global challenges (Hoboken, NJ)}, volume = {5}, number = {3}, pages = {2000014}, pmid = {33728052}, issn = {2056-6646}, abstract = {Horizontal gene transfer facilitates the spread of antibiotic resistance genes, which constitutes a global challenge. However, the evolutionary trajectory of the mobile colistin resistome in bacteria is largely unknown. To investigate the coevolution and fitness cost of the colistin resistance genes in wild strains, different assays to uncover the genomic dynamics of mcr-1 and mcr-3 in bacterial populations are utilized. Escherichia coli strains harboring both mcr-1 and mcr-3.1/3.5 are isolated and mcr genes are associated with diverse mobile elements. Under exposure to colistin, the mcr-1-bearing resistome is stably inherited during bacterial replication, but mcr-3 is prone to be eliminated in populations of certain strains. In the absence of colistin, the persistence rates of the mcr-1 and mcr-3-bearing subclones varies depending on the genomic background. The decay of the mcr-bearing bacterial populations can be mediated by the elimination of mcr-containing segments, large genomic deletions, and plasmid loss. Mobile elements, including plasmids and transposons, are double-edged swords in the evolution of the resistome. The findings support the idea that antibiotic overuse accounts for global spread of multidrug-resistant (MDR) bacteria. Therefore, stringent regulation of antibiotic prescription for humans and animals should be performed systematically to alleviate the threat of MDR bacteria.}, }
@article {pmid33727612, year = {2021}, author = {Matriano, DM and Alegado, RA and Conaco, C}, title = {Detection of horizontal gene transfer in the genome of the choanoflagellate Salpingoeca rosetta.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {5993}, pmid = {33727612}, issn = {2045-2322}, mesh = {Choanoflagellata/classification/*genetics ; Computational Biology/methods ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome ; Genomics/methods ; Molecular Sequence Annotation ; Phylogeny ; }, abstract = {Horizontal gene transfer (HGT), the movement of heritable materials between distantly related organisms, is crucial in eukaryotic evolution. However, the scale of HGT in choanoflagellates, the closest unicellular relatives of metazoans, and its possible roles in the evolution of animal multicellularity remains unexplored. We identified at least 175 candidate HGTs in the genome of the colonial choanoflagellate Salpingoeca rosetta using sequence-based tests. The majority of these were orthologous to genes in bacterial and microalgal lineages, yet displayed genomic features consistent with the rest of the S. rosetta genome-evidence of ancient acquisition events. Putative functions include enzymes involved in amino acid and carbohydrate metabolism, cell signaling, and the synthesis of extracellular matrix components. Functions of candidate HGTs may have contributed to the ability of choanoflagellates to assimilate novel metabolites, thereby supporting adaptation, survival in diverse ecological niches, and response to external cues that are possibly critical in the evolution of multicellularity in choanoflagellates.}, }
@article {pmid33727345, year = {2021}, author = {Gago-Córdoba, C and Val-Calvo, J and Abia, D and Díaz-Talavera, A and Miguel-Arribas, A and Aguilar Suárez, R and van Dijl, JM and Wu, LJ and Meijer, WJJ}, title = {A Conserved Class II Type Thioester Domain-Containing Adhesin Is Required for Efficient Conjugation in Bacillus subtilis.}, journal = {mBio}, volume = {12}, number = {2}, pages = {}, pmid = {33727345}, issn = {2150-7511}, support = {/WT_/Wellcome Trust/United Kingdom ; 209500/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Adhesins, Bacterial/*chemistry/*genetics ; Bacillus subtilis/*genetics/pathogenicity ; Bacterial Proteins/*genetics/metabolism ; Conjugation, Genetic/*genetics ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; Operon ; Plasmids/genetics ; }, abstract = {Conjugation, the process by which a DNA element is transferred from a donor to a recipient cell, is the main horizontal gene transfer route responsible for the spread of antibiotic resistance and virulence genes. Contact between a donor and a recipient cell is a prerequisite for conjugation, because conjugative DNA is transferred into the recipient via a channel connecting the two cells. Conjugative elements encode proteins dedicated to facilitating the recognition and attachment to recipient cells, also known as mating pair formation. A subgroup of the conjugative elements is able to mediate efficient conjugation during planktonic growth, and mechanisms facilitating mating pair formation will be particularly important in these cases. Conjugative elements of Gram-negative bacteria encode conjugative pili, also known as sex pili, some of which are retractile. Far less is known about mechanisms that promote mating pair formation in Gram-positive bacteria. The conjugative plasmid pLS20 of the Gram-positive bacterium Bacillus subtilis allows efficient conjugation in liquid medium. Here, we report the identification of an adhesin gene in the pLS20 conjugation operon. The N-terminal region of the adhesin contains a class II type thioester domain (TED) that is essential for efficient conjugation, particularly in liquid medium. We show that TED-containing adhesins are widely conserved in Gram-positive bacteria, including pathogens where they often play crucial roles in pathogenesis. Our study is the first to demonstrate the involvement of a class II type TED-containing adhesin in conjugation.IMPORTANCE Bacterial resistance to antibiotics has become a serious health care problem. The spread of antibiotic resistance genes between bacteria of the same or different species is often mediated by a process named conjugation, where a donor cell transfers DNA to a recipient cell through a connecting channel. The first step in conjugation is recognition and attachment of the donor to a recipient cell. Little is known about this first step, particularly in Gram-positive bacteria. Here, we show that the conjugative plasmid pLS20 of Bacillus subtilis encodes an adhesin protein that is essential for effective conjugation. This adhesin protein has a structural organization similar to adhesins produced by other Gram-positive bacteria, including major pathogens, where the adhesins serve in attachment to host tissues during colonization and infection. Our findings may thus also open novel avenues to design drugs that inhibit the spread of antibiotic resistance by blocking the first recipient-attachment step in conjugation.}, }
@article {pmid33724406, year = {2021}, author = {Haase, MAB and Kominek, J and Opulente, DA and Shen, XX and LaBella, AL and Zhou, X and DeVirgilio, J and Hulfachor, AB and Kurtzman, CP and Rokas, A and Hittinger, CT}, title = {Repeated horizontal gene transfer of GALactose metabolism genes violates Dollo's law of irreversible loss.}, journal = {Genetics}, volume = {217}, number = {2}, pages = {}, pmid = {33724406}, issn = {1943-2631}, support = {R21 AI105619/AI/NIAID NIH HHS/United States ; }, mesh = {*Evolution, Molecular ; Fungal Proteins/*genetics ; Fungi/classification/*genetics ; Galactose/genetics/metabolism ; Galactosidases/*genetics ; *Gene Transfer, Horizontal ; Phylogeny ; }, abstract = {Dollo's law posits that evolutionary losses are irreversible, thereby narrowing the potential paths of evolutionary change. While phenotypic reversals to ancestral states have been observed, little is known about their underlying genetic causes. The genomes of budding yeasts have been shaped by extensive reductive evolution, such as reduced genome sizes and the losses of metabolic capabilities. However, the extent and mechanisms of trait reacquisition after gene loss in yeasts have not been thoroughly studied. Here, through phylogenomic analyses, we reconstructed the evolutionary history of the yeast galactose utilization pathway and observed widespread and repeated losses of the ability to utilize galactose, which occurred concurrently with the losses of GALactose (GAL) utilization genes. Unexpectedly, we detected multiple galactose-utilizing lineages that were deeply embedded within clades that underwent ancient losses of galactose utilization. We show that at least two, and possibly three, lineages reacquired the GAL pathway via yeast-to-yeast horizontal gene transfer. Our results show how trait reacquisition can occur tens of millions of years after an initial loss via horizontal gene transfer from distant relatives. These findings demonstrate that the losses of complex traits and even whole pathways are not always evolutionary dead-ends, highlighting how reversals to ancestral states can occur.}, }
@article {pmid33724360, year = {2021}, author = {Park, HJ and Gokhale, CS and Bertels, F}, title = {How sequence populations persist inside bacterial genomes.}, journal = {Genetics}, volume = {217}, number = {4}, pages = {}, pmid = {33724360}, issn = {1943-2631}, mesh = {DNA Replication ; *DNA Transposable Elements ; Escherichia coli ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Models, Genetic ; }, abstract = {Compared to their eukaryotic counterparts, bacterial genomes are small and contain extremely tightly packed genes. Repetitive sequences are rare but not completely absent. One of the most common repeat families is REPINs. REPINs can replicate in the host genome and form populations that persist for millions of years. Here, we model the interactions of these intragenomic sequence populations with the bacterial host. We first confirm well-established results, in the presence and absence of horizontal gene transfer (hgt) sequence populations either expand until they drive the host to extinction or the sequence population gets purged from the genome. We then show that a sequence population can be stably maintained, when each individual sequence provides a benefit that decreases with increasing sequence population size. Maintaining a sequence population of stable size also requires the replication of the sequence population to be costly to the host, otherwise the sequence population size will increase indefinitely. Surprisingly, in regimes with high hgt rates, the benefit conferred by the sequence population does not have to exceed the damage it causes to its host. Our analyses provide a plausible scenario for the persistence of sequence populations in bacterial genomes. We also hypothesize a limited biologically relevant parameter range for the provided benefit, which can be tested in future experiments.}, }
@article {pmid33722656, year = {2021}, author = {Park, T and Wijeratne, S and Meulia, T and Firkins, JL and Yu, Z}, title = {The macronuclear genome of anaerobic ciliate Entodinium caudatum reveals its biological features adapted to the distinct rumen environment.}, journal = {Genomics}, volume = {113}, number = {3}, pages = {1416-1427}, doi = {10.1016/j.ygeno.2021.03.014}, pmid = {33722656}, issn = {1089-8646}, mesh = {Anaerobiosis ; Animals ; Carbohydrate Metabolism ; *Ciliophora/genetics/metabolism ; *Rumen/metabolism ; Sequence Analysis, DNA ; }, abstract = {Entodinium caudatum is an anaerobic binucleated ciliate representing the most dominant protozoal species in the rumen. However, its biological features are largely unknown due to the inability to establish an axenic culture. In this study, we primally sequenced its macronucleus (MAC) genome to aid the understanding of its metabolism, physiology, ecology. We isolated the MAC of E. caudatum strain MZG-1 and sequenced the MAC genome using Illumina MiSeq, MinION, and PacBio RSII systems. De novo assembly of the MiSeq sequence reads followed with subsequent scaffolding with MinION and PacBio reads resulted in a draft MAC genome about 117 Mbp. A large number of carbohydrate-active enzymes were likely acquired through horizontal gene transfer. About 8.74% of the E. caudatum predicted proteome was predicted as proteases. The MAC genome of E. caudatum will help better understand its important roles in rumen carbohydrate metabolism, and interaction with other members of the rumen microbiome.}, }
@article {pmid33714557, year = {2021}, author = {Graham, LA and Davies, PL}, title = {Horizontal Gene Transfer in Vertebrates: A Fishy Tale.}, journal = {Trends in genetics : TIG}, volume = {37}, number = {6}, pages = {501-503}, doi = {10.1016/j.tig.2021.02.006}, pmid = {33714557}, issn = {0168-9525}, mesh = {Animals ; Antifreeze Proteins/*genetics ; Fish Proteins/*genetics ; Fishes/*genetics ; *Gene Transfer, Horizontal ; Genome ; Vertebrates/genetics ; }, abstract = {The recent assembly of the herring genome suggests this fish acquired its antifreeze protein gene by horizontal transfer and then passed a copy on to the smelt. The direction of gene transfer is confirmed by some accompanying transposable elements and by the breakage of gene synteny.}, }
@article {pmid33713707, year = {2021}, author = {Huang, Y and Song, J and Soyano, K and Ren, Q}, title = {Dorsal regulates the expression of two phage lysozymes acquired via horizontal gene transfer in triangle sail mussel Hyriopsis cumingii.}, journal = {Developmental and comparative immunology}, volume = {120}, number = {}, pages = {104068}, doi = {10.1016/j.dci.2021.104068}, pmid = {33713707}, issn = {1879-0089}, mesh = {Animals ; Bacteriophages/genetics ; Gene Expression Regulation/immunology ; Gene Knockdown Techniques ; Gene Transfer, Horizontal ; Muramidase/*genetics ; Transcription Factors/genetics/*metabolism ; Unionidae/genetics/*immunology/microbiology ; Vibrio parahaemolyticus/immunology ; }, abstract = {Dorsal is a Rel/NF-κB transcription factor, which forms a key part of the Toll pathway. Lysozyme is a ubiquitous enzyme that degrades bacterial cell walls. In this study, a Dorsal homolog was cloned and characterized from triangle sail mussel Hyriopsis cumingii, namely, HcDorsal. Dorsal consisted of 3041 bp, including a 1938 bp open reading frame encoding a 645 amino acid protein. The deduced HcDorsal protein contained a Rel homology domain and an Ig-like, plexin, transcription factor domain. Analysis of expression patterns showed that HcDorsal was highly expressed in the hepatopancreas of H. cumingii. The expression level of HcDorsal continuously increased after Vibrio parahaemolyticus stimulation. When HcDorsal was knocked down by siRNA interference, two phage lysozyme genes (HcLyso1 and HcLyso2) obtained by horizontal gene transfer were significantly downregulated in hemocytes of mussels. Furthermore, knockdown of HcLyso1 and HcLyso2 could weaken V. parahaemolyticus clearance ability. Recombinant HcLyso1 and HcLyso2 proteins accelerated the bacterial clearance in vivo in mussels and evidently inhibited the growth of V. parahaemolyticus. These results suggested that HcDorsal could be activated after V. parahaemolyticus stimulation and then modulate the immune response through the transcriptional regulation of HcLyso1 and HcLyso2, thereby playing a protective role in mussels.}, }
@article {pmid33712424, year = {2021}, author = {Lloyd, CJ and Mejia-Santana, A and Dalia, TN and Dalia, AB and Klose, KE}, title = {Natural Transformation in a Classical-Biotype Vibrio cholerae Strain.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {10}, pages = {}, pmid = {33712424}, issn = {1098-5336}, support = {R35 GM128674/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics ; Chitin ; *Transformation, Bacterial ; Vibrio cholerae O1/*genetics ; }, abstract = {Vibrio cholerae causes the gastrointestinal illness cholera, which spreads throughout the globe in large pandemics. The current pandemic is caused by O1 El Tor biotype strains, whereas previous pandemics were caused by O1 classical biotype strains. El Tor V. cholerae is noted for its ability to acquire exogenous DNA through chitin-induced natural transformation, which has been exploited for genetic manipulation of El Tor strains in the laboratory. In contrast, the prototypical classical strain O395 lacks this ability, which was suspected to be due to a mutation in the regulatory gene hapR HapR and the regulator TfoX control expression of a third competence regulator, QstR. We found that artificial induction of both TfoX and QstR in the presence of HapR in O395 was required for efficient DNA uptake. However, natural transformation in the classical strain is still orders of magnitude below that of an El Tor strain. O395 expressing HapR could also undergo natural transformation after growth on chitin, which could be increased by artificial induction of TfoX and/or QstR. A plasmid that expresses both TfoX and QstR was created that allowed for consistent DNA uptake in O395 carrying a hapR plasmid. This technique was also used to facilitate cotransformation into O395 of unmarked DNA (ΔlacZ, ΔflaA, ΔflgG) for multiplex genome editing by natural transformation (MuGENT). These results demonstrate that the classical biotype O395 strain is functionally capable of DNA uptake, which allows for the rapid genetic manipulation of its genome.IMPORTANCE Natural transformation (uptake of exogenous DNA) in Vibrio cholerae has contributed to the evolution of these human pathogens. Classical biotype V. cholerae strains were responsible for the first six cholera pandemics but were replaced by El Tor biotype V. cholerae in the current pandemic. This study demonstrates that classical V. cholerae is functionally capable of natural transformation, but inactivation of the transformation regulator HapR and inherent levels of transformation that are lower than those of El Tor V. cholerae suggest that the classical biotype may be less able to utilize natural transformation for horizontal gene transfer.}, }
@article {pmid33711060, year = {2021}, author = {Demo, S and Kapinos, A and Bernardino, A and Guardino, K and Hobbs, B and Hoh, K and Lee, E and Vuong, I and Reddi, K and Freise, AC and Moberg Parker, J}, title = {BlueFeather, the singleton that wasn't: Shared gene content analysis supports expansion of Arthrobacter phage Cluster FE.}, journal = {PloS one}, volume = {16}, number = {3}, pages = {e0248418}, pmid = {33711060}, issn = {1932-6203}, support = {S10 RR023057/RR/NCRR NIH HHS/United States ; }, mesh = {Arthrobacter/genetics/*virology ; Bacteriophages/*genetics ; *Gene Transfer, Horizontal ; *Genes, Viral ; *Genetic Variation ; *Phylogeny ; *Sequence Analysis, DNA ; }, abstract = {Bacteriophages (phages) exhibit high genetic diversity, and the mosaic nature of the shared genetic pool makes quantifying phage relatedness a shifting target. Early parameters for clustering of related Mycobacteria and Arthrobacter phage genomes relied on nucleotide identity thresholds but, more recently, clustering of Gordonia and Microbacterium phages has been performed according to shared gene content. Singleton phages lack the nucleotide identity and/or shared gene content required for clustering newly sequenced genomes with known phages. Whole genome metrics of novel Arthrobacter phage BlueFeather, originally designated a putative singleton, showed low nucleotide identity but high amino acid and gene content similarity with Arthrobacter phages originally assigned to Clusters FE and FI. Gene content similarity revealed that BlueFeather shared genes with these phages in excess of the parameter for clustering Gordonia and Microbacterium phages. Single gene analyses revealed evidence of horizontal gene transfer between BlueFeather and phages in unique clusters that infect a variety of bacterial hosts. Our findings highlight the advantage of using shared gene content to study seemingly genetically isolated phages and have resulted in the reclustering of BlueFeather, a putative singleton, as well as former Cluster FI phages, into a newly expanded Cluster FE.}, }
@article {pmid33705557, year = {2021}, author = {Hata, T and Satoh, S and Takada, N and Matsuo, M and Obokata, J}, title = {Kozak Sequence Acts as a Negative Regulator for De Novo Transcription Initiation of Newborn Coding Sequences in the Plant Genome.}, journal = {Molecular biology and evolution}, volume = {38}, number = {7}, pages = {2791-2803}, pmid = {33705557}, issn = {1537-1719}, mesh = {Arabidopsis ; Epigenesis, Genetic ; *Gene Expression Regulation, Plant ; *Gene Transfer, Horizontal ; *Genome, Plant ; *Models, Genetic ; Open Reading Frames ; TATA Box ; *Transcription Initiation Site ; }, abstract = {The manner in which newborn coding sequences and their transcriptional competency emerge during the process of gene evolution remains unclear. Here, we experimentally simulated eukaryotic gene origination processes by mimicking horizontal gene transfer events in the plant genome. We mapped the precise position of the transcription start sites (TSSs) of hundreds of newly introduced promoterless firefly luciferase (LUC) coding sequences in the genome of Arabidopsis thaliana cultured cells. The systematic characterization of the LUC-TSSs revealed that 80% of them occurred under the influence of endogenous promoters, while the remainder underwent de novo activation in the intergenic regions, starting from pyrimidine-purine dinucleotides. These de novo TSSs obeyed unexpected rules; they predominantly occurred ∼100 bp upstream of the LUC inserts and did not overlap with Kozak-containing putative open reading frames (ORFs). These features were the output of the immediate responses to the sequence insertions, rather than a bias in the screening of the LUC gene function. Regarding the wild-type genic TSSs, they appeared to have evolved to lack any ORFs in their vicinities. Therefore, the repulsion by the de novo TSSs of Kozak-containing ORFs described above might be the first selection gate for the occurrence and evolution of TSSs in the plant genome. Based on these results, we characterized the de novo type of TSS identified in the plant genome and discuss its significance in genome evolution.}, }
@article {pmid33693785, year = {2021}, author = {Liu, X and Lin, S and Liu, T and Zhou, Y and Wang, W and Yao, J and Guo, Y and Tang, K and Chen, R and Benedik, MJ and Wang, X}, title = {Xenogeneic silencing relies on temperature-dependent phosphorylation of the host H-NS protein in Shewanella.}, journal = {Nucleic acids research}, volume = {49}, number = {6}, pages = {3427-3440}, pmid = {33693785}, issn = {1362-4962}, mesh = {Bacterial Proteins/chemistry/*metabolism ; Cold Shock Proteins and Peptides/genetics ; DNA-Binding Proteins/chemistry/*metabolism ; *Gene Silencing ; Gene Transfer, Horizontal ; Phosphoprotein Phosphatases/metabolism ; Phosphorylation ; Prophages/genetics ; *Protein Processing, Post-Translational ; Protein Serine-Threonine Kinases/metabolism ; Shewanella/*genetics/metabolism ; *Temperature ; }, abstract = {Lateral gene transfer (LGT) plays a key role in shaping the genome evolution and environmental adaptation of bacteria. Xenogeneic silencing is crucial to ensure the safe acquisition of LGT genes into host pre-existing regulatory networks. We previously found that the host nucleoid structuring protein (H-NS) silences prophage CP4So at warm temperatures yet enables this prophage to excise at cold temperatures in Shewanella oneidensis. However, whether H-NS silences other genes and how bacteria modulate H-NS to regulate the expression of genes have not been fully elucidated. In this study, we discovered that the H-NS silences many LGT genes and the xenogeneic silencing of H-NS relies on a temperature-dependent phosphorylation at warm temperatures in S. oneidensis. Specifically, phosphorylation of H-NS at Ser42 is critical for silencing the cold-inducible genes including the excisionase of CP4So prophage, a cold shock protein, and a stress-related chemosensory system. By contrast, nonphosphorylated H-NS derepresses the promoter activity of these genes/operons to enable their expression at cold temperatures. Taken together, our results reveal that the posttranslational modification of H-NS can function as a regulatory switch to control LGT gene expression in host genomes to enable the host bacterium to react and thrive when environmental temperature changes.}, }
@article {pmid33692486, year = {2021}, author = {Wang, Y and Lu, J and Zhang, S and Li, J and Mao, L and Yuan, Z and Bond, PL and Guo, J}, title = {Non-antibiotic pharmaceuticals promote the transmission of multidrug resistance plasmids through intra- and intergenera conjugation.}, journal = {The ISME journal}, volume = {15}, number = {9}, pages = {2493-2508}, pmid = {33692486}, issn = {1751-7370}, mesh = {*Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; Drug Resistance, Multiple ; Gene Transfer, Horizontal ; Humans ; *Pharmaceutical Preparations ; Plasmids ; }, abstract = {Antibiotic resistance is a global threat to public health. The use of antibiotics at sub-inhibitory concentrations has been recognized as an important factor in disseminating antibiotic resistance via horizontal gene transfer. Although non-antibiotic, human-targeted pharmaceuticals are widely used by society (95% of the pharmaceuticals market), the potential contribution to the spread of antibiotic resistance is not clear. Here, we report that commonly consumed, non-antibiotic pharmaceuticals, including nonsteroidal anti-inflammatories (ibuprofen, naproxen, diclofenac), a lipid-lowering drug (gemfibrozil), and a β-blocker (propranolol), at clinically and environmentally relevant concentrations, significantly accelerated the dissemination of antibiotic resistance via plasmid-borne bacterial conjugation. Various indicators were used to study the bacterial response to these drugs, including monitoring reactive oxygen species (ROS) and cell membrane permeability by flow cytometry, cell arrangement, and whole-genome RNA and protein sequencing. Enhanced conjugation correlated well with increased production of ROS and cell membrane permeability. Additionally, these non-antibiotic pharmaceuticals induced responses similar to those detected when bacteria are exposed to antibiotics, such as inducing the SOS response and enhancing efflux pumps. The findings advance understanding of the transfer of antibiotic resistance genes, emphasizing the concern that non-antibiotic, human-targeted pharmaceuticals enhance the spread of antibiotic resistance among bacterial populations.}, }
@article {pmid33689720, year = {2021}, author = {Westwood, JH}, title = {Plant Biology: Genome Reveals Secrets of the Alien Within.}, journal = {Current biology : CB}, volume = {31}, number = {5}, pages = {R241-R243}, doi = {10.1016/j.cub.2021.01.012}, pmid = {33689720}, issn = {1879-0445}, mesh = {Biology ; DNA Transposable Elements/genetics ; Gene Transfer, Horizontal ; *Genome, Chloroplast ; *Introduced Species ; Plants ; }, abstract = {The genome of the parasitic plant Sapria himalayana reveals extraordinary changes that reflect its endoparasitic lifestyle. The genome has lost many genes, including the entire chloroplast genome, but has gained genes through horizontal gene transfer and repeated transposable elements.}, }
@article {pmid33687766, year = {2021}, author = {Karmakar, R}, title = {State of the art of bacterial chemotaxis.}, journal = {Journal of basic microbiology}, volume = {61}, number = {5}, pages = {366-379}, doi = {10.1002/jobm.202000661}, pmid = {33687766}, issn = {1521-4028}, mesh = {Bacteria/genetics/*metabolism ; *Bacterial Physiological Phenomena ; Bacterial Proteins/genetics ; Chemoreceptor Cells/*metabolism ; *Chemotaxis ; Flagella/*physiology ; Membrane Proteins ; }, abstract = {Bacterial chemotaxis is a biased movement of bacteria toward the beneficial chemical gradient or away from a toxic chemical gradient. This movement is achieved by sensing a chemical gradient by chemoreceptors. In most of the chemotaxis studies, Escherichia coli has been used as a model organism. E. coli have about 4-6 flagella on their surfaces, and the motility is achieved by rotating the flagella. Each flagellum has reversible flagellar motors at its base, which rotate the flagella in counterclockwise and clockwise directions to achieve "run" and "tumble." The chemotaxis of bacteria is regulated by a network of interacting proteins. The sensory signal is processed and transmitted to the flagellar motor by cytoplasmic proteins. Bacterial chemotaxis plays an important role in many biological processes such as biofilm formation, quorum sensing, bacterial pathogenesis, and host infection. Bacterial chemotaxis can be applied for bioremediation, horizontal gene transfer, drug delivery, or maybe some other industry in near future. This review contains an overview of bacterial chemotaxis, recent findings of the physiological importance of bacterial chemotaxis in other biological processes, and the application of bacterial chemotaxis.}, }
@article {pmid33687344, year = {2021}, author = {Beard, S and Ossandon, FJ and Rawlings, DE and Quatrini, R}, title = {The Flexible Genome of Acidophilic Prokaryotes.}, journal = {Current issues in molecular biology}, volume = {40}, number = {}, pages = {231-266}, doi = {10.21775/cimb.040.231}, pmid = {33687344}, issn = {1467-3045}, mesh = {Acidithiobacillus/*genetics ; Adaptation, Physiological/genetics ; Archaeal Viruses/genetics ; DNA Transposable Elements/genetics ; Gene Flow ; Gene Transfer, Horizontal ; *Genome, Archaeal ; *Genome, Bacterial ; Genomics/methods ; Hydrogen-Ion Concentration ; Phylogeny ; Plasmids/genetics ; Sulfolobus/*genetics/virology ; }, abstract = {Over the last couple of decades there has been considerable progress in the identification and understanding of the mobile genetic elements that are exchanged between microbes in extremely acidic environments, and of the genes piggybacking on them. Numerous plasmid families, unique viruses of bizarre morphologies and lyfe cycles, as well as plasmid-virus chimeras, have been isolated from acidophiles and characterized to varying degrees. Growing evidence provided by omic-studies have shown that the mobile elements repertoire is not restricted to plasmids and viruses, but that a plethora of integrative elements ranging from miniature inverted repeat transposable elements to large integrative conjugative elements populate the genomes of acidophilic bacteria and archaea. This article reviews the diversity of elements that have been found to constitute the flexible genome of acidophiles. Special emphasis is put on the knowledge generated for Sulfolobus (archaea) and species of the bacterial genera Acidithiobacillus and Leptospirillum. Also, recent knowledge on the strategies used by acidophiles to contain deletereous exchanges while allowing innovation, and the emerging details of the molecular biology of these systems, are discussed. Major lacunae in our understanding of the mobilome of acidophilic prokaryotes and topics for further investigations are identified.}, }
@article {pmid33679664, year = {2021}, author = {Cestero, JJ and Castanheira, S and Pucciarelli, MG and García-Del Portillo, F}, title = {A Novel Salmonella Periplasmic Protein Controlling Cell Wall Homeostasis and Virulence.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {633701}, pmid = {33679664}, issn = {1664-302X}, abstract = {Horizontal gene transfer has shaped the evolution of Salmonella enterica as pathogen. Some functions acquired by this mechanism include enzymes involved in peptidoglycan (PG) synthesis and remodeling. Here, we report a novel serovar Typhimurium protein that is absent in non-pathogenic bacteria and bears a LprI functional domain, first reported in a Mycobacterium tuberculosis lipoprotein conferring lysozyme resistance. Based on the presence of such domain, we hypothesized a role of this S. Typhimurium protein in PG metabolism. This protein, which we named ScwA for Salmonella cell wall-related regulator-A, controls positively the levels of the murein lytic transglycosylase MltD. In addition, the levels of other enzymes that cleave bonds in the PG lattice were affected in a mutant lacking ScwA, including a soluble lytic tranglycosylase (Slt), the amidase AmiC, and a few endo- and carboxypeptidases (NlpC, PBP4, and AmpH). The scwA gene has lower G+C content than the genomic average (43.1 vs. 52.2%), supporting acquisition by horizontal transfer. ScwA is located in the periplasm, stabilized by two disulfide bridges, produced preferentially in stationary phase and down-regulated following entry of the pathogen into eukaryotic cells. ScwA deficiency, however, results in a hypervirulent phenotype in the murine typhoid model. Based on these findings, we conclude that ScwA may be exploited by S. Typhimurium to ensure cell envelope homeostasis along the infection and to prevent host overt damage. This role could be accomplished by controlling the production or stability of a reduced number of peptidoglycan hydrolases whose activities result in the release of PG fragments.}, }
@article {pmid33679638, year = {2021}, author = {Yoon, EJ and Jeong, SH}, title = {Mobile Carbapenemase Genes in Pseudomonas aeruginosa.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {614058}, pmid = {33679638}, issn = {1664-302X}, abstract = {Carbapenem-resistant Pseudomonas aeruginosa is one of the major concerns in clinical settings impelling a great challenge to antimicrobial therapy for patients with infections caused by the pathogen. While membrane permeability, together with derepression of the intrinsic beta-lactamase gene, is the global prevailing mechanism of carbapenem resistance in P. aeruginosa, the acquired genes for carbapenemases need special attention because horizontal gene transfer through mobile genetic elements, such as integrons, transposons, plasmids, and integrative and conjugative elements, could accelerate the dissemination of the carbapenem-resistant P. aeruginosa. This review aimed to illustrate epidemiologically the carbapenem resistance in P. aeruginosa, including the resistance rates worldwide and the carbapenemase-encoding genes along with the mobile genetic elements responsible for the horizontal dissemination of the drug resistance determinants. Moreover, the modular mobile elements including the carbapenemase-encoding gene, also known as the P. aeruginosa resistance islands, are scrutinized mostly for their structures.}, }
@article {pmid33677562, year = {2021}, author = {Brandis, G}, title = {Reconstructing the Evolutionary History of a Highly Conserved Operon Cluster in Gammaproteobacteria and Bacilli.}, journal = {Genome biology and evolution}, volume = {13}, number = {4}, pages = {}, pmid = {33677562}, issn = {1759-6653}, mesh = {*Evolution, Molecular ; Firmicutes/classification/*genetics ; Gammaproteobacteria/classification/*genetics ; Gene Order ; Gene Transfer, Horizontal ; *Operon ; Phylogeny ; }, abstract = {The evolution of gene order rearrangements within bacterial chromosomes is a fast process. Closely related species can have almost no conservation in long-range gene order. A prominent exception to this rule is a >40 kb long cluster of five core operons (secE-rpoBC-str-S10-spc-alpha) and three variable adjacent operons (cysS, tufB, and ecf) that together contain 57 genes of the transcriptional and translational machinery. Previous studies have indicated that at least part of this operon cluster might have been present in the last common ancestor of bacteria and archaea. Using 204 whole genome sequences, ∼2 Gy of evolution of the operon cluster were reconstructed back to the last common ancestors of the Gammaproteobacteria and of the Bacilli. A total of 163 independent evolutionary events were identified in which the operon cluster was altered. Further examination showed that the process of disconnecting two operons generally follows the same pattern. Initially, a small number of genes is inserted between the operons breaking the concatenation followed by a second event that fully disconnects the operons. While there is a general trend for loss of gene synteny over time, there are examples of increased alteration rates at specific branch points or within specific bacterial orders. This indicates the recurrence of relaxed selection on the gene order within bacterial chromosomes. The analysis of the alternation events indicates that segmental genome duplications and/or transposon-directed recombination play a crucial role in rearrangements of the operon cluster.}, }
@article {pmid33675661, year = {2021}, author = {Sibbald, SJ and Lawton, M and Archibald, JM}, title = {Mitochondrial Genome Evolution in Pelagophyte Algae.}, journal = {Genome biology and evolution}, volume = {13}, number = {3}, pages = {}, pmid = {33675661}, issn = {1759-6653}, mesh = {Base Sequence ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Mitochondrial ; Genomics ; Phylogeny ; RNA, Transfer/genetics ; Stramenopiles/*genetics ; Synteny ; }, abstract = {The Pelagophyceae are marine stramenopile algae that include Aureoumbra lagunensis and Aureococcus anophagefferens, two microbial species notorious for causing harmful algal blooms. Despite their ecological significance, relatively few genomic studies of pelagophytes have been carried out. To improve understanding of the biology and evolution of pelagophyte algae, we sequenced complete mitochondrial genomes for A. lagunensis (CCMP1510), Pelagomonas calceolata (CCMP1756), and five strains of Aureoc. anophagefferens (CCMP1707, CCMP1708, CCMP1850, CCMP1984, and CCMP3368) using Nanopore long-read sequencing. All pelagophyte mitochondrial genomes assembled into single, circular mapping contigs between 39,376 bp (P. calceolata) and 55,968 bp (A. lagunensis) in size. Mitochondrial genomes for the five Aureoc. anophagefferens strains varied slightly in length (42,401-42,621 bp) and were 99.4-100.0% identical. Gene content and order were highly conserved between the Aureoc. anophagefferens and P. calceolata genomes, with the only major difference being a unique region in Aureoc. anophagefferens containingDNA adenine and cytosine methyltransferase (dam/dcm) genes that appear to be the product of lateral gene transfer from a prokaryotic or viral donor. Although the A. lagunensis mitochondrial genome shares seven distinct syntenic blocks with the other pelagophyte genomes, it has a tandem repeat expansion comprising ∼40% of its length, and lacks identifiable rps19 and glycine tRNA genes. Laterally acquired self-splicing introns were also found in the 23S rRNA (rnl) gene of P. calceolata and the coxI gene of the five Aureoc. anophagefferens genomes. Overall, these data provide baseline knowledge about the genetic diversity of bloom-forming pelagophytes relative to nonbloom-forming species.}, }
@article {pmid33673397, year = {2021}, author = {Pathak, A and Stothard, P and Chauhan, A}, title = {Comparative Genomic Analysis of Three Pseudomonas Species Isolated from the Eastern Oyster (Crassostrea virginica) Tissues, Mantle Fluid, and the Overlying Estuarine Water Column.}, journal = {Microorganisms}, volume = {9}, number = {3}, pages = {}, pmid = {33673397}, issn = {2076-2607}, support = {1901371//National Science Foundation/ ; TOA0000456318//Department of Energy/ ; }, abstract = {The eastern oysters serve as important keystone species in the United States, especially in the Gulf of Mexico estuarine waters, and at the same time, provide unparalleled economic, ecological, environmental, and cultural services. One ecosystem service that has garnered recent attention is the ability of oysters to sequester impurities and nutrients, such as nitrogen (N), from the estuarine water that feeds them, via their exceptional filtration mechanism coupled with microbially-mediated denitrification processes. It is the oyster-associated microbiomes that essentially provide these myriads of ecological functions, yet not much is known on these microbiota at the genomic scale, especially from warm temperate and tropical water habitats. Among the suite of bacterial genera that appear to interplay with the oyster host species, pseudomonads deserve further assessment because of their immense metabolic and ecological potential. To obtain a comprehensive understanding on this aspect, we previously reported on the isolation and preliminary genomic characterization of three Pseudomonas species isolated from minced oyster tissue (P. alcaligenes strain OT69); oyster mantle fluid (P. stutzeri strain MF28) and the water collected from top of the oyster reef (P. aeruginosa strain WC55), respectively. In this comparative genomic analysis study conducted on these three targeted pseudomonads, native to the eastern oyster and its surrounding environment, provided further insights into their unique functional traits, conserved gene pools between the selected pseudomonads, as well as genes that render unique characteristics in context to metabolic traits recruited during their evolutionary history via horizontal gene transfer events as well as phage-mediated incorporation of genes. Moreover, the strains also supported extensively developed resistomes, which suggests that environmental microorganisms native to relatively pristine environments, such as Apalachicola Bay, Florida, have also recruited an arsenal of antibiotic resistant gene determinants, thus posing an emerging public health concern.}, }
@article {pmid33668622, year = {2021}, author = {Tyumentseva, M and Mikhaylova, Y and Prelovskaya, A and Tyumentsev, A and Petrova, L and Fomina, V and Zamyatin, M and Shelenkov, A and Akimkin, V}, title = {Genomic and Phenotypic Analysis of Multidrug-Resistant Acinetobacter baumannii Clinical Isolates Carrying Different Types of CRISPR/Cas Systems.}, journal = {Pathogens (Basel, Switzerland)}, volume = {10}, number = {2}, pages = {}, pmid = {33668622}, issn = {2076-0817}, support = {075-15-2019-1666//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {Acinetobacter baumannii is an opportunistic pathogen being one of the most important causative agents of a wide range of nosocomial infections associated with multidrug resistance and high mortality rate. This study presents a multiparametric and correlation analyses of clinical multidrug-resistant A. baumannii isolates using short- and long-read whole-genome sequencing, which allowed us to reveal specific characteristics of the isolates with different CRISPR/Cas systems. We also compared antibiotic resistance and virulence gene acquisition for the groups of the isolates having functional CRISPR/Cas systems, just CRISPR arrays without cas genes, and without detectable CRISPR spacers. The data include three schemes of molecular typing, phenotypic and genotypic antibiotic resistance determination, as well as phylogenetic analysis of full-length cas gene sequences, predicted prophage sequences and CRISPR array type determination. For the first time the differences between the isolates carrying Type I-F1 and Type I-F2 CRISPR/Cas systems were investigated. A. baumannii isolates with Type I-F1 system were shown to have smaller number of reliably detected CRISPR arrays, and thus they could more easily adapt to environmental conditions through acquisition of antibiotic resistance genes, while Type I-F2 A. baumannii might have stronger "immunity" and use CRISPR/Cas system to block the dissemination of these genes. In addition, virulence factors abaI, abaR, bap and bauA were overrepresented in A. baumannii isolates lacking CRISPR/Cas system. This indicates the role of CRISPR/Cas in fighting against phage infections and preventing horizontal gene transfer. We believe that the data presented will contribute to further investigations in the field of antimicrobial resistance and CRISPR/Cas studies.}, }
@article {pmid33667767, year = {2021}, author = {Oliveira, AS and Amorim, CL and Zlopasa, J and van Loosdrecht, M and Castro, PML}, title = {Recovered granular sludge extracellular polymeric substances as carrier for bioaugmentation of granular sludge reactor.}, journal = {Chemosphere}, volume = {275}, number = {}, pages = {130037}, doi = {10.1016/j.chemosphere.2021.130037}, pmid = {33667767}, issn = {1879-1298}, mesh = {Aerobiosis ; Biological Oxygen Demand Analysis ; Bioreactors ; *Extracellular Polymeric Substance Matrix ; *Sewage ; Waste Disposal, Fluid ; Wastewater ; }, abstract = {An increasing amount of industrial chemicals are being released into wastewater collection systems and indigenous microbial communities in treatment plants are not always effective for their removal. In this work, extracellular polymeric substances (EPS) recovered from aerobic granular sludge (AGS) were used as a natural carrier to immobilize a specific microbial strain, Rhodococcus sp. FP1, able to degrade 2-fluorophenol (2-FP). The produced EPS granules exhibited a 2-FP degrading ability of 100% in batch assays, retaining their original activity after up to 2-months storage. Furthermore, EPS granules were added to an AGS reactor intermittently fed with saline wastewater containing 2-FP. Degradation of 2-FP and stoichiometric fluorine release occurred 8 and 35 days after bioaugmentation, respectively. Chemical oxygen demand removal was not significantly impaired by 2-FP or salinity loads. Nutrients removal was impaired by 2-FP load, but after bioaugmentation, the phosphate and ammonium removal efficiency improved from 14 to 46% and from 25 to 42%, respectively. After 2-FP feeding ceased, at low/moderate salinity (0.6-6.0 g L[-1] NaCl), ammonium removal was completely restored, and phosphate removal efficiency increased. After bioaugmentation, 11 bacteria isolated from AGS were able to degrade 2-FP, indicating that horizontal gene transfer could have occurred in the reactor. The improvement of bioreactor performance after bioaugmentation with EPS immobilized bacteria and the maintenance of cell viability through storage are the main advantages of the use of this natural microbial carrier for bioaugmentation, which can benefit wastewater treatment processes.}, }
@article {pmid33663564, year = {2021}, author = {Ten, KE and Md Zoqratt, MZH and Ayub, Q and Tan, HS}, title = {Characterization of multidrug-resistant Acinetobacter baumannii strain ATCC BAA1605 using whole-genome sequencing.}, journal = {BMC research notes}, volume = {14}, number = {1}, pages = {83}, pmid = {33663564}, issn = {1756-0500}, mesh = {*Acinetobacter baumannii/genetics ; Anti-Bacterial Agents/pharmacology ; Genome, Bacterial/genetics ; Plasmids/genetics ; Whole Genome Sequencing ; }, abstract = {OBJECTIVE: The nosocomial pathogen, Acinetobacter baumannii, has acquired clinical significance due to its ability to persist in hospital settings and survive antibiotic treatment, which eventually resulted in the rapid spread of this bacterium with antimicrobial resistance (AMR) phenotypes. This study used a multidrug-resistant A. baumannii (strain ATCC BAA1605) as a model to study the genomic features of this pathogen.<br><br>RESULTS: One circular chromosome and one circular plasmid were discovered in the complete genome of A. baumannii ATCC BAA1605 using whole-genome sequencing. The chromosome is 4,039,171&#xa0;bp long with a GC content of 39.24%. Many AMR genes, which confer resistance to major classes of antibiotics (beta-lactams, aminoglycosides, tetracycline, sulphonamides), were found on the chromosome. Two genomic islands were predicted on the chromosome, one of which (Genomic Island 1) contains a cluster of AMR genes and mobile elements, suggesting the possibility of horizontal gene transfer. A subtype I-F CRISPR-Cas system was also identified on the chromosome of A. baumannii ATCC BAA1605. This study provides valuable genome data that can be used as a reference for future studies on A. baumannii. The genome of A. baumannii ATCC BAA1605 has been deposited at GenBank under accession no. CP058625 and CP058626.}, }
@article {pmid33655883, year = {2021}, author = {Jones, JM and Grinberg, I and Eldar, A and Grossman, AD}, title = {A mobile genetic element increases bacterial host fitness by manipulating development.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {33655883}, issn = {2050-084X}, support = {R01 GM050895/GM/NIGMS NIH HHS/United States ; R35 GM122538/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacillus subtilis/*genetics/*growth &amp; development ; DNA, Bacterial/*genetics ; *Gene Transfer, Horizontal ; *Genetic Fitness ; Host Microbial Interactions ; Interspersed Repetitive Sequences/*physiology ; }, abstract = {Horizontal gene transfer is a major force in bacterial evolution. Mobile genetic elements are responsible for much of horizontal gene transfer and also carry beneficial cargo genes. Uncovering strategies used by mobile genetic elements to benefit host cells is crucial for understanding their stability and spread in populations. We describe a benefit that ICEBs1, an integrative and conjugative element of Bacillus subtilis, provides to its host cells. Activation of ICEBs1 conferred a frequency-dependent selective advantage to host cells during two different developmental processes: biofilm formation and sporulation. These benefits were due to inhibition of biofilm-associated gene expression and delayed sporulation by ICEBs1-containing cells, enabling them to exploit their neighbors and grow more prior to development. A single ICEBs1 gene, devI (formerly ydcO), was both necessary and sufficient for inhibition of development. Manipulation of host developmental programs allows ICEBs1 to increase host fitness, thereby increasing propagation of the element.}, }
@article {pmid33653940, year = {2021}, author = {Whon, TW and Kim, HS and Shin, NR and Sung, H and Kim, MS and Kim, JY and Kang, W and Kim, PS and Hyun, DW and Seong, HJ and Sul, WJ and Roh, SW and Bae, JW}, title = {Calf Diarrhea Caused by Prolonged Expansion of Autochthonous Gut Enterobacteriaceae and Their Lytic Bacteriophages.}, journal = {mSystems}, volume = {6}, number = {2}, pages = {}, pmid = {33653940}, issn = {2379-5077}, abstract = {Neonatal calf diarrhea is a common disease leading to a major economic loss for cattle producers worldwide. Several infectious and noninfectious factors are implicated in calf diarrhea, but disease control remains problematic because of the multifactorial etiology of the disease. Here, we conducted diagnostic multiplex PCR assay and meta-omics analysis (16S rRNA gene-based metataxonomics and untargeted transcriptional profiling) of rectal content of normal and diarrheic beef calves (n = 111). In the diarrheic calf gut, we detected both microbial compositional dysbiosis (i.e., increased abundances of the family Enterobacteriaceae members and their lytic bacteriophages) and functional dysbiosis (i.e., elevated levels of aerobic respiration and virulence potential). The calf diarrheic transcriptome mirrored the gene expression of the bovine host and was enriched in cellular pathways of sulfur metabolism, innate immunity, and gut motility. We then isolated 12 nontoxigenic Enterobacteriaceae strains from the gut of diarrheic calves. Feeding a strain mixture to preweaning mice resulted in a significantly higher level of fecal moisture content, with decreased body weight gain and shortened colon length. The presented findings suggest that gut inflammation followed by a prolonged expansion of nontoxigenic autochthonous Enterobacteriaceae contributes to the onset of diarrhea in preweaning animals.IMPORTANCE Calf diarrhea is the leading cause of death of neonatal calves worldwide. Several infectious and noninfectious factors are implicated in calf diarrhea, but disease control remains problematic because of the multifactorial etiology of the disease. The major finding of the current study centers around the observation of microbial compositional and functional dysbiosis in rectal samples from diarrheic calves. These results highlight the notion that gut inflammation followed by a prolonged expansion of autochthonous Enterobacteriaceae contributes to the onset of calf diarrhea. Moreover, this condition possibly potentiates the risk of invasion of notorious enteric pathogens, including Salmonella spp., and the emergence of inflammation-resistant (or antibiotic-resistant) microbiota via active horizontal gene transfer mediated by lytic bacteriophages.}, }
@article {pmid33653937, year = {2021}, author = {Suresh, A and Shaik, S and Baddam, R and Ranjan, A and Qumar, S and Jadhav, S and Semmler, T and Ghazi, IA and Wieler, LH and Ahmed, N}, title = {Evolutionary Dynamics Based on Comparative Genomics of Pathogenic Escherichia coli Lineages Harboring Polyketide Synthase (pks) Island.}, journal = {mBio}, volume = {12}, number = {1}, pages = {}, pmid = {33653937}, issn = {2150-7511}, mesh = {Computational Biology/methods ; DNA, Intergenic ; Enteropathogenic Escherichia coli/classification/*genetics/pathogenicity ; Escherichia coli Infections/epidemiology/*microbiology ; *Evolution, Molecular ; *Genome, Bacterial ; Genome-Wide Association Study ; *Genomic Islands ; *Genomics ; Phenotype ; Phylogeny ; Prevalence ; Virulence/genetics ; Virulence Factors/genetics ; }, abstract = {The genotoxin colibactin is a secondary metabolite produced by the polyketide synthase (pks) island harbored by extraintestinal pathogenic E. coli (ExPEC) and other members of the Enterobacteriaceae that has been increasingly reported to have critical implications in human health. The present study entails a high-throughput whole-genome comparison and phylogenetic analysis of such pathogenic E. coli isolates to gain insights into the patterns of distribution, horizontal transmission, and evolution of the island. For the current study, 23 pks-positive ExPEC genomes were newly sequenced, and their virulome and resistome profiles indicated a preponderance of virulence encoding genes and a reduced number of genes for antimicrobial resistance. In addition, 4,090 E. coli genomes from the public domain were also analyzed for large-scale screening for pks-positive genomes, out of which a total of 530 pks-positive genomes were studied to understand the subtype-based distribution pattern(s). The pks island showed a significant association with the B2 phylogroup (82.2%) and a high prevalence in sequence type 73 (ST73; n = 179) and ST95 (n = 110) and the O6:H1 (n = 110) serotype. Maximum-likelihood (ML) phylogeny of the core genome and intergenic regions (IGRs) of the ST95 model data set, which was selected because it had both pks-positive and pks-negative genomes, displayed clustering in relation to their carriage of the pks island. Prevalence patterns of genes encoding RM systems in the pks-positive and pks-negative genomes were also analyzed to determine their potential role in pks island acquisition and the maintenance capability of the genomes. Further, the maximum-likelihood phylogeny based on the core genome and pks island sequences from 247 genomes with an intact pks island demonstrated horizontal gene transfer of the island across sequence types and serotypes, with few exceptions. This study vitally contributes to understanding of the lineages and subtypes that have a higher propensity to harbor the pks island-encoded genotoxin with possible clinical implications.IMPORTANCE Extraintestinal pathologies caused by highly virulent strains of E. coli amount to clinical implications with high morbidity and mortality rates. Pathogenic E. coli strains are evolving with the horizontal acquisition of mobile genetic elements, including pathogenicity islands such as the pks island, which produces the genotoxin colibactin, resulting in severe clinical outcomes, including colorectal cancer progression. The current study encompasses high-throughput comparative genomics and phylogenetic analyses to address the questions pertaining to the acquisition and evolution pattern of the genomic island in different E. coli subtypes. It is crucial to gain insights into the distribution, transfer, and maintenance of pathogenic islands, as they harbor multiple virulence genes involved in pathogenesis and clinical implications of the infection.}, }
@article {pmid33649202, year = {2021}, author = {Power, JJ and Pinheiro, F and Pompei, S and Kovacova, V and Yüksel, M and Rathmann, I and Förster, M and Lässig, M and Maier, B}, title = {Adaptive evolution of hybrid bacteria by horizontal gene transfer.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {10}, pages = {}, pmid = {33649202}, issn = {1091-6490}, mesh = {*Adaptation, Physiological ; Bacillus subtilis/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; }, abstract = {Horizontal gene transfer (HGT) is an important factor in bacterial evolution that can act across species boundaries. Yet, we know little about rate and genomic targets of cross-lineage gene transfer and about its effects on the recipient organism's physiology and fitness. Here, we address these questions in a parallel evolution experiment with two Bacillus subtilis lineages of 7% sequence divergence. We observe rapid evolution of hybrid organisms: gene transfer swaps ∼12% of the core genome in just 200 generations, and 60% of core genes are replaced in at least one population. By genomics, transcriptomics, fitness assays, and statistical modeling, we show that transfer generates adaptive evolution and functional alterations in hybrids. Specifically, our experiments reveal a strong, repeatable fitness increase of evolved populations in the stationary growth phase. By genomic analysis of the transfer statistics across replicate populations, we infer that selection on HGT has a broad genetic basis: 40% of the observed transfers are adaptive. At the level of functional gene networks, we find signatures of negative, positive, and epistatic selection, consistent with hybrid incompatibilities and adaptive evolution of network functions. Our results suggest that gene transfer navigates a complex cross-lineage fitness landscape, bridging epistatic barriers along multiple high-fitness paths.}, }
@article {pmid33649151, year = {2021}, author = {Davis, KP and Grossman, AD}, title = {Specificity and Selective Advantage of an Exclusion System in the Integrative and Conjugative Element ICEBs1 of Bacillus subtilis.}, journal = {Journal of bacteriology}, volume = {203}, number = {10}, pages = {}, pmid = {33649151}, issn = {1098-5530}, support = {R01 GM050895/GM/NIGMS NIH HHS/United States ; R35 GM122538/GM/NIGMS NIH HHS/United States ; T32 GM007287/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacillus subtilis/*genetics/physiology ; Bacterial Proteins/*chemistry/*genetics/metabolism ; *Conjugation, Genetic ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences ; Microbial Viability ; Recombinant Fusion Proteins/chemistry/metabolism ; }, abstract = {Integrative and conjugative elements (ICEs) are mobile genetic elements capable of transferring their own and other DNA. They contribute to the spread of antibiotic resistance and other important traits for bacterial evolution. Exclusion is a mechanism used by many conjugative plasmids and a few ICEs to prevent their host cell from acquiring a second copy of the cognate element. ICEBs1 of Bacillus subtilis has an exclusion mechanism whereby the exclusion protein YddJ in a potential recipient inhibits the activity of the ICEBs1-encoded conjugation machinery in a potential donor. The target of YddJ-mediated exclusion is the conjugation protein ConG (a VirB6 homolog). Here, we defined the regions of YddJ and ConG that confer exclusion specificity and determined the importance of exclusion to host cells. Using chimeras that had parts of ConG from ICEBs1 and the closely related ICEBat1, we identified a putative extracellular loop of ConG that conferred specificity for exclusion by the cognate YddJ. Using chimeras of YddJ from ICEBs1 and ICEBat1, we identified two regions in YddJ needed for exclusion specificity. We also found that YddJ-mediated exclusion reduced the death of donor cells following conjugation into recipients. Donor death was dependent on the ability of transconjugants to themselves become donors and was reduced under osmoprotective conditions, indicating that death was likely due to alterations in the donor cell envelope caused by excessive conjugation. We postulate that elements that can have high frequencies of transfer likely evolved exclusion mechanisms to protect the host cells from excessive death.IMPORTANCE Horizontal gene transfer is a driving force in bacterial evolution, responsible for the spread of many traits, including antibiotic and heavy metal resistance. Conjugation, one type of horizontal gene transfer, involves DNA transfer from donor to recipient cells through conjugation machinery and direct cell-cell contact. Exclusion mechanisms allow conjugative elements to prevent their host from acquiring additional copies of the element and are highly specific, enabling hosts to acquire heterologous elements. We defined regions of the exclusion protein and its target in the conjugation machinery that convey high specificity of exclusion. We found that exclusion protects donors from cell death during periods of high transfer. This is likely important for the element to enter new populations of cells.}, }
@article {pmid33649148, year = {2021}, author = {Akanuma, G and Kawamura, F and Watanabe, S and Watanabe, M and Okawa, F and Natori, Y and Nanamiya, H and Asai, K and Chibazakura, T and Yoshikawa, H and Soma, A and Hishida, T and Kato-Yamada, Y}, title = {Evolution of Ribosomal Protein S14 Demonstrated by the Reconstruction of Chimeric Ribosomes in Bacillus subtilis.}, journal = {Journal of bacteriology}, volume = {203}, number = {10}, pages = {}, pmid = {33649148}, issn = {1098-5530}, mesh = {Bacillus subtilis/*chemistry/genetics/growth &amp; development ; Bacterial Proteins/chemistry/genetics/*metabolism ; Binding Sites ; Escherichia coli/chemistry ; *Evolution, Molecular ; Phylogeny ; Protein Biosynthesis ; Ribosomal Proteins/chemistry/genetics/*metabolism ; Ribosome Subunits, Small, Bacterial/metabolism ; Ribosomes/*metabolism ; Spores, Bacterial/physiology ; Synechococcus/chemistry ; Zinc/metabolism ; }, abstract = {Ribosomal protein S14 can be classified into three types. The first, the C+ type has a Zn[2+] binding motif and is ancestral. The second and third are the C- short and C- long types, neither of which contain a Zn[2+] binding motif and which are ca. 90 residues and 100 residues in length, respectively. In the present study, the C+ type S14 from Bacillus subtilis ribosomes (S14BsC+) were completely replaced by the heterologous C- long type of S14 from Escherichia coli (S14Ec) or Synechococcus elongatus (S14Se). Surprisingly, S14Ec and S14Se were incorporated fully into 70S ribosomes in B. subtilis However, the growth rates as well as the sporulation efficiency of the mutants harboring heterologous S14 were significantly decreased. In these mutants, the polysome fraction was decreased and the 30S and 50S subunits accumulated unusually, indicating that cellular translational activity of these mutants was decreased. In vitro analysis showed a reduction in the translational activity of the 70S ribosome fraction purified from these mutants. The abundance of ribosomal proteins S2 and S3 in the 30S fraction in these mutants was reduced while that of S14 was not significantly decreased. It seems likely that binding of heterologous S14 changes the structure of the 30S subunit, which causes a decrease in the assembly efficiency of S2 and S3, which are located near the binding site of S14. Moreover, we found that S3 from S. elongatus cannot function in B. subtilis unless S14Se is present.IMPORTANCE S14, an essential ribosomal protein, may have evolved to adapt bacteria to zinc-limited environments by replacement of a zinc-binding motif with a zinc-independent sequence. It was expected that the bacterial ribosome would be tolerant to replacement of S14 because of the previous prediction that the spread of C- type S14 involved horizontal gene transfer. In this study, we completely replaced the C+ type of S14 in B. subtilis ribosome with the heterologous C- long type of S14 and characterized the resulting chimeric ribosomes. Our results suggest that the B. subtilis ribosome is permissive for the replacement of S14, but coevolution of S3 might be required to utilize the C- long type of S14 more effectively.}, }
@article {pmid33647609, year = {2021}, author = {Ding, Y and Liang, B and Jiang, W and Han, J and Guadie, A and Yun, H and Cheng, H and Yang, R and Liu, SJ and Wang, A and Ren, N}, title = {Effect of preferential UV photolysis on the source control of antibiotic resistome during subsequent biological treatment systems.}, journal = {Journal of hazardous materials}, volume = {414}, number = {}, pages = {125484}, doi = {10.1016/j.jhazmat.2021.125484}, pmid = {33647609}, issn = {1873-3336}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial ; *Genes, Bacterial ; Photolysis ; Sewage ; Wastewater/analysis ; }, abstract = {The environmental spread of antibiotic resistance genes (ARGs) from the direct application of traditional biological treatment systems for antibiotics in water is a potential public health threat. UV photolysis has been proved to be an efficient pretreatment method for antibacterial activity elimination, but the fate of antibiotic resistome in subsequent bioreactors fed with pretreated florfenicol (FLO) in synthetic wastewater is still unknown. Antibacterial activity in synthetic wastewater was effectively eliminated by UV irradiation pretreatment, and the diversity and abundance of detected ARGs in both aerobic and anaerobic bioreactors were significantly lower than those without pretreatment. Meanwhile, UV irradiation pretreatment shaped the structure and composition of sludge microbial communities in the subsequent bioreactors closer to those of the FLO-free groups. The relative abundances of Pseudomonas and Escherichia-Shigella working as the potential hosts of ARGs were significantly reduced in aerobic and anaerobic bioreactors, respectively. The significantly positive correlation between floR and intI1 and the decrease of intI1 abundance in UV photolytic pretreatment groups indicated that the horizontal transfer of floR was decreased. The study provides new insights into the effect of preferential UV photolysis as a pretreatment method on the source control of antibiotic resistome in subsequent biological treatment process.}, }
@article {pmid33646643, year = {2021}, author = {Prensky, H and Gomez-Simmonds, A and Uhlemann, AC and Lopatkin, AJ}, title = {Conjugation dynamics depend on both the plasmid acquisition cost and the fitness cost.}, journal = {Molecular systems biology}, volume = {17}, number = {3}, pages = {e9913}, pmid = {33646643}, issn = {1744-4292}, mesh = {Bacteria/genetics/growth &amp; development ; *Conjugation, Genetic ; Models, Biological ; Plasmids/*genetics ; Time Factors ; }, abstract = {Plasmid conjugation is a major mechanism responsible for the spread of antibiotic resistance. Plasmid fitness costs are known to impact long-term growth dynamics of microbial populations by providing plasmid-carrying cells a relative (dis)advantage compared to plasmid-free counterparts. Separately, plasmid acquisition introduces an immediate, but transient, metabolic perturbation. However, the impact of these short-term effects on subsequent growth dynamics has not previously been established. Here, we observed that de novo transconjugants grew significantly slower and/or with overall prolonged lag times, compared to lineages that had been replicating for several generations, indicating the presence of a plasmid acquisition cost. These effects were general to diverse incompatibility groups, well-characterized and clinically captured plasmids, Gram-negative recipient strains and species, and experimental conditions. Modeling revealed that both fitness and acquisition costs modulate overall conjugation dynamics, validated with previously published data. These results suggest that the hours immediately following conjugation may play a critical role in both short- and long-term plasmid prevalence. This time frame is particularly relevant to microbiomes with high plasmid/strain diversity considered to be hot spots for conjugation.}, }
@article {pmid33646340, year = {2021}, author = {Jani, M and Azad, RK}, title = {Discovery of mosaic genomic islands in Pseudomonas spp.}, journal = {Archives of microbiology}, volume = {203}, number = {5}, pages = {2735-2742}, pmid = {33646340}, issn = {1432-072X}, mesh = {Computational Biology ; Gene Transfer, Horizontal ; Genome, Bacterial/*genetics ; Genomic Islands/*genetics ; Genomics ; Pseudomonas/*genetics ; Software ; }, abstract = {Genomic islands, defined as large clusters of genes mobilized through horizontal gene transfer, have a profound impact on evolution of prokaryotes. Recently, we developed a new program, IslandCafe, for identifying such large localized structures in bacterial genomes. A unique attribute of IslandCafe is its ability to decipher mosaic structures within genomic islands. Mosaic genomic islands have generated immense interest due to novel traits that have been attributed to such islands. To provide the Pseudomonas research community a catalogue of mosaic islands in Pseudomonas spp., we applied IslandCafe to decipher genomic islands in 224 completely sequenced genomes of Pseudomonas spp. We also performed comparative genomic analysis using BLAST to infer potential sources of distinct segments within genomic islands. Of the total 4271 genomic islands identified in Pseudomonas spp., 1036 were found to be mosaic. We also identified drug-resistant and pathogenic genomic islands and their potential donors. Our analysis provides a useful resource for Pseudomonas research community to further examine and interrogate mosaic islands in the genomes of interest and understand their role in the emergence and evolution of novel traits.}, }
@article {pmid33644715, year = {2021}, author = {Zhang, X and Cvetkovska, M and Morgan-Kiss, R and Hüner, NPA and Smith, DR}, title = {Draft genome sequence of the Antarctic green alga Chlamydomonas sp. UWO241.}, journal = {iScience}, volume = {24}, number = {2}, pages = {102084}, pmid = {33644715}, issn = {2589-0042}, abstract = {Antarctica is home to an assortment of psychrophilic algae, which have evolved various survival strategies for coping with their frigid environments. Here, we explore Antarctic psychrophily by examining the ∼212 Mb draft nuclear genome of the green alga Chlamydomonas sp. UWO241, which resides within the water column of a perennially ice-covered, hypersaline lake. Like certain other Antarctic algae, UWO241 encodes a large number (≥37) of ice-binding proteins, putatively originating from horizontal gene transfer. Even more striking, UWO241 harbors hundreds of highly similar duplicated genes involved in diverse cellular processes, some of which we argue are aiding its survival in the Antarctic via gene dosage. Gene and partial gene duplication appear to be an ongoing phenomenon within UWO241, one which might be mediated by retrotransposons. Ultimately, we consider how such a process could be associated with adaptation to extreme environments but explore potential non-adaptive hypotheses as well.}, }
@article {pmid33643369, year = {2021}, author = {Castellani, LG and Luchetti, A and Nilsson, JF and Pérez-Giménez, J and Wegener, C and Schlüter, A and Pühler, A and Lagares, A and Brom, S and Pistorio, M and Niehaus, K and Torres Tejerizo, GA}, title = {Exopolysaccharide Characterization of Rhizobium favelukesii LPU83 and Its Role in the Symbiosis With Alfalfa.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {642576}, pmid = {33643369}, issn = {1664-462X}, abstract = {One of the greatest inputs of available nitrogen into the biosphere occurs through the biological N2-fixation to ammonium as result of the symbiosis between rhizobia and leguminous plants. These interactions allow increased crop yields on nitrogen-poor soils. Exopolysaccharides (EPS) are key components for the establishment of an effective symbiosis between alfalfa and Ensifer meliloti, as bacteria that lack EPS are unable to infect the host plants. Rhizobium favelukesii LPU83 is an acid-tolerant rhizobia strain capable of nodulating alfalfa but inefficient to fix nitrogen. Aiming to identify the molecular determinants that allow R. favelukesii to infect plants, we studied its EPS biosynthesis. LPU83 produces an EPS I identical to the one present in E. meliloti, but the organization of the genes involved in its synthesis is different. The main gene cluster needed for the synthesis of EPS I in E. meliloti, is split into three different sections in R. favelukesii, which probably arose by a recent event of horizontal gene transfer. A R. favelukesii strain devoided of all the genes needed for the synthesis of EPS I is still able to infect and nodulate alfalfa, suggesting that attention should be directed to other molecules involved in the development of the symbiosis.}, }
@article {pmid33640677, year = {2021}, author = {Yi, S and Huang, J and Hu, X and Chen, L and Dai, X and Sun, J and Liu, P and Wang, X and Wen, J and Wang, L}, title = {Nonconservative integration and diversity of a new family of integrative and conjugative elements associated with antibiotic resistance in zoonotic pathogen Streptococcus suis.}, journal = {Veterinary microbiology}, volume = {254}, number = {}, pages = {109009}, doi = {10.1016/j.vetmic.2021.109009}, pmid = {33640677}, issn = {1873-2542}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics ; China ; *Conjugation, Genetic ; Drug Resistance, Microbial/*genetics ; *Genetic Variation ; Interspersed Repetitive Sequences ; Recombination, Genetic ; Streptococcal Infections/microbiology/*veterinary ; Streptococcus suis/drug effects/*genetics/pathogenicity ; Swine/microbiology ; Whole Genome Sequencing ; }, abstract = {Macrolide and tetracycline resistance in streptococci is mainly caused by acquisition of integrative and conjugative elements (ICEs) of the ICESa2603 family carrying erm(B) and tet(O). But the characteristics about the transferability and physiological consequences of ICEs with triplet serine integrases are still rare. This study tested the transferability of ICESsuYZDH1_SSU0877, a novel erm(B)- and tet(O)-carrying ICESa2603 family-like ICE with triplet serine integrases, and evaluated the physiological consequences after ICE transferred and integrated into recipient. The prevalence of ICESsuYZDH1-like ICEs in S. suis was analyzed based on 1334 genomic sequences available in GenBank and examined in 330 clinical isolates in China. Nonconservative transfer was observed by integrating of ICESsuYZDH1 into SSU1797 gene besides the primary SSU0877 site. Imperfect direct repeats of 2-/4-nt (5'-TC-3'/5'-TCCC-3') and (5'-GC-3'/5'-TCCC-3') were observed at SSU0877 and SSU1797 sites, respectively. The transconjugant suffered a weak fitness cost with stunted growth and less competition with recipient strain. Successive passages indicate the ICESsuYZDH1 could be persist and endued stable resistant phenotype. Comprehensive analysis of the ICESsuYZDH1-like ICEs from both public genome database and our clinical isolates revealed the widespread and diversity of the ICEs by integration at the sites of SSU0877, SSU0468, SSU1262, and SSU1797. The ICESsuYZDH1-like ICEs could stably co-exist within the host chromosome at more than one attachment sites, which is probably mediated by the triplet serine integrases. Nonconservative integration and diversity of the ICESsuYZDH1 family of ICEs might have contributed to the evolution of ICEs and the dissemination of macrolide and tetracycline resistance in S. suis.}, }
@article {pmid33637574, year = {2021}, author = {Loftie-Eaton, W and Crabtree, A and Perry, D and Millstein, J and Baytosh, J and Stalder, T and Robison, BD and Forney, LJ and Top, EM}, title = {Contagious Antibiotic Resistance: Plasmid Transfer among Bacterial Residents of the Zebrafish Gut.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {9}, pages = {}, pmid = {33637574}, issn = {1098-5336}, support = {P20 GM103408/GM/NIGMS NIH HHS/United States ; P30 GM103324/GM/NIGMS NIH HHS/United States ; R01 AI084918/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics/isolation &amp; purification ; Drug Resistance, Multiple, Bacterial/*genetics ; Female ; Gastrointestinal Microbiome/*genetics ; Male ; Plasmids ; Zebrafish/*microbiology ; }, abstract = {By characterizing the trajectories of antibiotic resistance gene transfer in bacterial communities such as the gut microbiome, we will better understand the factors that influence this spread of resistance. Our aim was to investigate the host network of a multidrug resistance broad-host-range plasmid in the culturable gut microbiome of zebrafish. This was done through in vitro and in vivo conjugation experiments with Escherichia coli as the donor of the plasmid pB10::gfp When this donor was mixed with the extracted gut microbiome, only transconjugants of Aeromonas veronii were detected. In separate matings between the same donor and four prominent isolates from the gut microbiome, the plasmid transferred to two of these four isolates, A. veronii and Plesiomonas shigelloides, but not to Shewanella putrefaciens and Vibrio mimicus When these A. veronii and P. shigelloides transconjugants were the donors in matings with the same four isolates, the plasmid now also transferred from A. veronii to S. putrefaciensP. shigelloides was unable to donate the plasmid, and V. mimicus was unable to acquire it. Finally, when the E. coli donor was added in vivo to zebrafish through their food, plasmid transfer was observed in the gut, but only to Achromobacter, a rare member of the gut microbiome. This work shows that the success of plasmid-mediated antibiotic resistance spread in a gut microbiome depends on the donor-recipient species combinations and therefore their spatial arrangement. It also suggests that rare gut microbiome members should not be ignored as potential reservoirs of multidrug resistance plasmids from food.IMPORTANCE To understand how antibiotic resistance plasmids end up in human pathogens, it is crucial to learn how, where, and when they are transferred and maintained in members of bacterial communities such as the gut microbiome. To gain insight into the network of plasmid-mediated antibiotic resistance sharing in the gut microbiome, we investigated the transferability and maintenance of a multidrug resistance plasmid among the culturable bacteria of the zebrafish gut. We show that the success of plasmid-mediated antibiotic resistance spread in a gut microbiome can depend on which species are involved, as some are important nodes in the plasmid-host network and others are dead ends. Our findings also suggest that rare gut microbiome members should not be ignored as potential reservoirs of multidrug resistance plasmids from food.}, }
@article {pmid33631686, year = {2021}, author = {Hutinel, M and Fick, J and Larsson, DGJ and Flach, CF}, title = {Investigating the effects of municipal and hospital wastewaters on horizontal gene transfer.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {276}, number = {}, pages = {116733}, doi = {10.1016/j.envpol.2021.116733}, pmid = {33631686}, issn = {1873-6424}, mesh = {Anti-Bacterial Agents ; Escherichia coli/genetics ; *Gene Transfer, Horizontal ; Hospitals ; Humans ; Plasmids ; Sweden ; *Wastewater ; }, abstract = {Horizontal gene transfer (HGT) plays an important role in the dissemination of antibiotic resistance genes. In sewer systems, human-associated and environmental bacteria are mixed together and exposed to many substances known to increase HGT, including various antibacterial compounds. In wastewaters, those substances are most often detected below concentrations known to induce HGT individually. Still, it is possible that such wastewaters induce HGT, for example via mixture effects. Here, a panel of antibiotics, biocides and other pharmaceuticals was measured in filter-sterilized municipal and hospital wastewater samples from Gothenburg, Sweden. The effects on HGT of the chemical mixtures in these samples were investigated by exposing a complex bacterial donor community together with a GFP-tagged E. coli recipient strain. Recipients that captured sulfonamide resistance-conferring mobile genetic elements (MGEs) from the bacterial community were enumerated and characterized by replicon typing, antibiotic susceptibility testing and long read sequencing. While exposure to municipal wastewater did not result in any detectable change in HGT rates, exposure to hospital wastewater was associated with an increase in the proportion of recipients that acquired sulfonamide resistance but also a drastic decrease in the total number of recipients. Although, concentrations were generally higher in hospital than municipal wastewater, none of the measured substances could individually explain the observed effects of hospital wastewater. The great majority of the MGEs captured were IncN plasmids, and resistance to several antibiotics was co-transferred in most cases. Taken together, the data show no evidence that chemicals present in the studied municipal wastewater induce HGT. Still, the increased relative abundance of transconjugants after exposure to hospital wastewater could have implications for the risks of both emergence and transmission of resistant bacteria.}, }
@article {pmid33630832, year = {2021}, author = {Louha, S and Meinersmann, RJ and Glenn, TC}, title = {Whole genome genetic variation and linkage disequilibrium in a diverse collection of Listeria monocytogenes isolates.}, journal = {PloS one}, volume = {16}, number = {2}, pages = {e0242297}, pmid = {33630832}, issn = {1932-6203}, mesh = {Food Microbiology ; Genetic Variation ; *Genome, Bacterial ; Humans ; *Linkage Disequilibrium ; Listeria monocytogenes/*genetics/isolation &amp; purification ; Listeriosis/*microbiology ; Multilocus Sequence Typing ; Phylogeny ; }, abstract = {We performed whole-genome multi-locus sequence typing for 2554 genes in a large and heterogenous panel of 180 Listeria monocytogenes strains having diverse geographical and temporal origins. The subtyping data was used for characterizing genetic variation and evaluating patterns of linkage disequilibrium in the pan-genome of L. monocytogenes. Our analysis revealed the presence of strong linkage disequilibrium in L. monocytogenes, with ~99% of genes showing significant non-random associations with a large majority of other genes in the genome. Twenty-seven loci having lower levels of association with other genes were considered to be potential "hot spots" for horizontal gene transfer (i.e., recombination via conjugation, transduction, and/or transformation). The patterns of linkage disequilibrium in L. monocytogenes suggest limited exchange of foreign genetic material in the genome and can be used as a tool for identifying new recombinant strains. This can help understand processes contributing to the diversification and evolution of this pathogenic bacteria, thereby facilitating development of effective control measures.}, }
@article {pmid33626339, year = {2021}, author = {Gonçalves, OS and Souza, FO and Bruckner, FP and Santana, MF and Alfenas-Zerbini, P}, title = {Widespread distribution of prophages signaling the potential for adaptability and pathogenicity evolution of Ralstonia solanacearum species complex.}, journal = {Genomics}, volume = {113}, number = {3}, pages = {992-1000}, doi = {10.1016/j.ygeno.2021.02.011}, pmid = {33626339}, issn = {1089-8646}, mesh = {Genome, Bacterial ; Humans ; *Prophages/genetics ; *Ralstonia solanacearum/genetics ; Virulence ; Virulence Factors/genetics ; }, abstract = {Integrated bacteriophages (prophages) can impact host cells, affecting their lifestyle, genomic diversity, and fitness. However, many basic aspects of how these organisms affect the host cell remain poorly understood. Ralstonia solanacearum is a gram-negative plant pathogenic bacterium that encompasses a great diversity of ecotypes regarded as a species complex (R. solanacearum Species Complex - RSSC). RSSC genomes have a mosaic structure containing numerous elements, signaling the potential for its evolution through horizontal gene transfer. Here, we analyzed 120 Ralstonia spp. genomes from the public database to identify prophage sequences. In total, 379 prophage-like elements were found in the chromosome and megaplasmid of Ralstonia spp. These elements encode genes related to host fitness, virulence factors, antibiotic resistance, and niche adaptation, which might contribute to RSSC adaptability. Prophage-like elements are widespread into the complex in different species and geographic origins, suggesting that the RSSC phages are ancestrally acquired. Complete prophages belonging to the families Inoviridae, Myoviridae, and Siphoviridae were found, being the members of Inoviridae the most abundant. Analysis of CRISPR-Cas spacer sequences demonstrated the presence of prophages sequences that indicate successive infection events during bacterial evolution. Besides complete prophages, we also demonstrated 14 novel putative prophages integrated into Ralstonia spp. genomes. Altogether, our results provide insights into the diversity of prophages in RSSC genomes and suggest that these elements may deeply affect the virulence and host adaptation and shaping the genomes among the strains of this important pathogen.}, }
@article {pmid33620655, year = {2021}, author = {Golz, JC and Stingl, K}, title = {Natural Competence and Horizontal Gene Transfer in Campylobacter.}, journal = {Current topics in microbiology and immunology}, volume = {431}, number = {}, pages = {265-292}, pmid = {33620655}, issn = {0070-217X}, mesh = {*Bacteriophages/genetics ; *Campylobacter/genetics ; *Campylobacter jejuni/genetics ; Drug Resistance, Microbial ; Gene Transfer, Horizontal ; Humans ; }, abstract = {Thermophilic Campylobacter, in particular Campylobacter jejuni, C. coli and C. lari are the main relevant Campylobacter species for human infections. Due to their high capacity of genetic exchange by horizontal gene transfer (HGT), rapid adaptation to changing environmental and host conditions contribute to successful spreading and persistence of these foodborne pathogens. However, extensive HGT can exert dangerous side effects for the bacterium, such as the incorporation of gene fragments leading to disturbed gene functions. Here we discuss mechanisms of HGT, notably natural transformation, conjugation and bacteriophage transduction and limiting regulatory strategies of gene transfer. In particular, we summarize the current knowledge on how the DNA macromolecule is exchanged between single cells. Mechanisms to stimulate and to limit HGT obviously coevolved and maintained an optimal balance. Chromosomal rearrangements and incorporation of harmful mutations are risk factors for survival and can result in drastic loss of fitness. In Campylobacter, the restricted recognition and preferential uptake of free DNA from relatives are mediated by a short methylated DNA pattern and not by a classical DNA uptake sequence as found in other bacteria. A class two CRISPR-Cas system is present but also other DNases and restriction-modification systems appear to be important for Campylobacter genome integrity. Several lytic and integrated bacteriophages have been identified, which contribute to genome diversity. Furthermore, we focus on the impact of gene transfer on the spread of antibiotic resistance genes (resistome) and persistence factors. We discuss remaining open questions in the HGT field, supposed to be answered in the future by current technologies like whole-genome sequencing and single-cell approaches.}, }
@article {pmid33620648, year = {2021}, author = {Epping, L and Antão, EM and Semmler, T}, title = {Population Biology and Comparative Genomics of Campylobacter Species.}, journal = {Current topics in microbiology and immunology}, volume = {431}, number = {}, pages = {59-78}, pmid = {33620648}, issn = {0070-217X}, mesh = {*Campylobacter/genetics ; *Campylobacter Infections/epidemiology ; *Campylobacter jejuni/genetics ; Genomics ; Humans ; Multilocus Sequence Typing ; Phylogeny ; }, abstract = {The zoonotic pathogen Campylobacter is the leading cause for bacterial foodborne infections in humans. Campylobacters are most commonly transmitted via the consumption of undercooked poultry meat or raw milk products. The decreasing costs of whole genome sequencing enabled large genome-based analyses of the evolution and population structure of this pathogen, as well as the development of novel high-throughput molecular typing methods. Here, we review the evolutionary development and the population diversity of the two most clinically relevant Campylobacter species; C. jejuni and C. coli. The state-of-the-art phylogenetic studies showed clustering of C. jejuni lineages into host specialists and generalists with coexisting lifestyles in chicken and livestock-associated hosts, as well as the separation of C. coli isolates of riparian origin (waterfowl, water) from C. coli isolated from clinical and farm-related samples. We will give an overview of recombination between both species and the potential impact of horizontal gene transfer on host adaptation in Campylobacter. Additionally, this review briefly places the current knowledge of the population structure of other Campylobacter species such as C. lari, C. concisus and C. upsaliensis into perspective. We also provide an overview of how molecular typing methods such as multilocus sequence typing (MLST) and whole genome MLST have been used to detect and trace Campylobacter outbreaks along the food chain.}, }
@article {pmid33617866, year = {2021}, author = {Tong, C and Hu, H and Chen, G and Li, Z and Li, A and Zhang, J}, title = {Disinfectant resistance in bacteria: Mechanisms, spread, and resolution strategies.}, journal = {Environmental research}, volume = {195}, number = {}, pages = {110897}, doi = {10.1016/j.envres.2021.110897}, pmid = {33617866}, issn = {1096-0953}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Biofilms ; *Disinfectants/pharmacology ; Drug Resistance, Bacterial/genetics ; }, abstract = {Disinfectants are widely acknowledged for removing microorganisms from the surface of the objects and transmission media. However, the emergence of disinfectant resistance has become a severe threat to the safety of life and health and the rational allocation of resources due to the reduced disinfectant effectiveness. The horizontal gene transfer (HGT) of disinfectant resistance genes has also expanded the resistant flora, making the situation worse. This review focused on the resistance mechanisms of disinfectant resistant bacteria on biofilms, cell membrane permeability, efflux pumps, degradable enzymes, and disinfectant targets. Efflux can be the fastest and most effective resistance mechanism for bacteria to respond to stress. The qac genes, located on some plasmids which can transmit resistance through conjugative transfer, are the most commonly reported in the study of disinfectant resistance genes. Whether the qac genes can be transferred through transformation or transduction is still unclear. Studying the factors affecting the resistance of bacteria to disinfectants can find breakthrough methods to more adequately deal with the problem of reduced disinfectant effectiveness. It has been confirmed that the interaction of probiotics and bacteria or the addition of 4-oxazolidinone can inhibit the formation of biofilms. Chemicals such as eugenol and indole derivatives can increase bacterial sensitivity by reducing the expression of efflux pumps. The role of these findings in anti-disinfectant resistance has proved invaluable.}, }
@article {pmid33616518, year = {2021}, author = {Senneby, E and Hallström, B and Rasmussen, M}, title = {Genetic relatedness of Streptococcus dysgalactiae isolates causing recurrent bacteraemia.}, journal = {Journal of medical microbiology}, volume = {70}, number = {3}, pages = {}, doi = {10.1099/jmm.0.001330}, pmid = {33616518}, issn = {1473-5644}, mesh = {Antigens, Bacterial/genetics ; Bacteremia/*microbiology ; Bacterial Outer Membrane Proteins/genetics ; Carrier Proteins/genetics ; Genome, Bacterial/genetics ; Humans ; Phylogeny ; Reinfection/*microbiology ; Streptococcal Infections/*microbiology ; Streptococcus/classification/*genetics/isolation &amp; purification ; }, abstract = {Introduction. Streptococcus dysgalactiae subspecies equisimilis (SDSE) is becoming increasingly recognized as an important human pathogen. Recurrent bacteremia with SDSE has been described previously.Aim. The aims of the study were to establish the genetic relatedness of SDSE isolates with emm-type stG643 that had caused recurrent bacteraemia in three patients and to search for signs of horizontal gene transfer of the emm gene in a collection of SDSE stG643 genomes.Hypothesis. Recurring SDSE bacteremia is caused by the same clone in one patient.Methodology. Whole genome sequencing of 22 clinical SDSE stG643 isolates was performed, including three paired blood culture isolates and sixteen isolates from various sites. All assemblies were aligned to a reference assembly and SNPs were extracted. A total of 53 SDSE genomes were downloaded from GenBank. Two phylogenetic trees, including all 75 SDSE isolates, were created. One tree was based on the emm gene only and one tree was based on all variable positions in the genomes.Results. The genomes from the three pairs of SDSE isolates showed high sequence similarity (1-17 SNPs difference between the pairs), whereas the median SNP difference between the 22 isolates in our collection was 1694 (range 1-11257). The paired isolates were retrieved with 7-53 months between episodes. The 22 SDSE isolates from our collection formed a cluster in the phylogenetic tree based on the emm gene, while they were more scattered in the tree based on all variable positions.Conclusions. Our results show that the paired isolates were of the same clonal origin, which in turn supports carriage between bacteraemia episodes. The phylogenetic analysis indicates that horizontal gene transfer of the emm-gene between some of the SDSE isolates has occurred.}, }
@article {pmid33611323, year = {2021}, author = {Schnaars, V and Wöhlbrand, L and Scheve, S and Hinrichs, C and Reinhardt, R and Rabus, R}, title = {Proteogenomic Insights into the Physiology of Marine, Sulfate-Reducing, Filamentous Desulfonema limicola and Desulfonema magnum.}, journal = {Microbial physiology}, volume = {31}, number = {1}, pages = {1-20}, pmid = {33611323}, issn = {2673-1673}, abstract = {The genus Desulfonema belongs to the deltaproteobacterial family Desulfobacteraceae and comprises marine, sulfate-reducing bacteria that form filaments and move by gliding. This study reports on the complete, manually annotated genomes of Dn. limicola 5ac10T (6.91 Mbp; 6,207 CDS) and Dn. magnum 4be13T (8.03 Mbp; 9,970 CDS), integrated with substrate-specific proteome profiles (8 vs. 11). The richness in mobile genetic elements is shared with other Desulfobacteraceae members, corroborating horizontal gene transfer as major driver in shaping the genomes of this family. The catabolic networks of Dn. limicola and Dn. magnum have the following general characteristics: 98 versus 145 genes assigned (having genomic shares of 1.7 vs. 2.2%), 92.5 versus 89.7% proteomic coverage, and scattered gene clusters for substrate degradation and energy metabolism. The Dn. magnum typifying capacity for aromatic compound degradation (e.g., p-cresol, 3-phenylpropionate) requires 48 genes organized in operon-like structures (87.7% proteomic coverage; no homologs in Dn. limicola). The protein complements for aliphatic compound degradation, central pathways, and energy metabolism are highly similar between both genomes and were identified to a large extent (69-96%). The differential protein profiles revealed a high degree of substrate-specificity for peripheral reaction sequences (forming central intermediates), agreeing with the high number of sensory/regulatory proteins predicted for both strains. By contrast, central pathways and modules of the energy metabolism were constitutively formed under the tested substrate conditions. In accord with their natural habitats that are subject to fluctuating changes of physicochemical parameters, both Desulfonema strains are well equipped to cope with various stress conditions. Next to superoxide dismutase and catalase also desulfoferredoxin and rubredoxin oxidoreductase are formed to counter exposure to molecular oxygen. A variety of proteases and chaperones were detected that function in maintaining cellular homeostasis upon heat or cold shock. Furthermore, glycine betaine/proline betaine transport systems can respond to hyperosmotic stress. Gliding movement probably relies on twitching motility via type-IV pili or adventurous motility. Taken together, this proteogenomic study demonstrates the adaptability of Dn. limicola and Dn. magnum to its dynamic habitats by means of flexible catabolism and extensive stress response capacities.}, }
@article {pmid33608721, year = {2021}, author = {Hedenäs, L and Larsson, P and Cronholm, B and Bisang, I}, title = {Evidence of horizontal gene transfer between land plant plastids has surprising conservation implications.}, journal = {Annals of botany}, volume = {127}, number = {7}, pages = {903-908}, pmid = {33608721}, issn = {1095-8290}, mesh = {*Embryophyta ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Plastid/genetics ; Phylogeny ; Plastids/genetics ; }, abstract = {BACKGROUND AND AIMS: Horizontal gene transfer (HGT) is an important evolutionary mechanism because it transfers genetic material that may code for traits or functions between species or genomes. It is frequent in mitochondrial and nuclear genomes but has not been demonstrated between plastid genomes of different green land plant species.<br><br>METHODS: We Sanger-sequenced the nuclear internal transcribed spacers (ITS1 and 2) and the plastid rpl16 G2 intron (rpl16). In five individuals with foreign rpl16 we also sequenced atpB-rbcL and trnLUAA-trnFGAA.<br><br>KEY RESULTS: We discovered 14 individuals of a moss species with typical nuclear ITSs but foreign plastid rpl16 from a species of a distant lineage. None of the individuals with three plastid markers sequenced contained all foreign markers, demonstrating the transfer of plastid fragments rather than the entire plastid genome, i.e. entire plastids were not transferred. The two lineages diverged 165-185 Myr BP. The extended time interval since lineage divergence suggests that the foreign rpl16 is more likely explained by HGT than by hybridization or incomplete lineage sorting.<br><br>CONCLUSIONS: We provide the first conclusive evidence of interspecific plastid-to-plastid HGT among land plants. Two aspects are critical: it occurred at several localities during the massive colonization of recently disturbed open habitats that were created by large-scale liming as a freshwater biodiversity conservation measure; and it involved mosses whose unique life cycle includes spores that first develop a filamentous protonema phase. We hypothesize that gene transfer is facilitated when protonema filaments of different species intermix intimately when colonizing disturbed early succession habitats.}, }
@article {pmid33608287, year = {2021}, author = {Fioriti, S and Coccitto, SN and Cedraro, N and Simoni, S and Morroni, G and Brenciani, A and Mangiaterra, G and Vignaroli, C and Vezzulli, L and Biavasco, F and Giovanetti, E}, title = {Linezolid Resistance Genes in Enterococci Isolated from Sediment and Zooplankton in Two Italian Coastal Areas.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {9}, pages = {}, pmid = {33608287}, issn = {1098-5336}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Bacterial/*genetics ; Enterococcus/drug effects/genetics/*isolation &amp; purification ; Environmental Monitoring ; Genes, Bacterial ; Geologic Sediments/*microbiology ; Italy ; Linezolid/*pharmacology ; Zooplankton/*microbiology ; }, abstract = {Linezolid is a last-resort antibiotic for the treatment of severe infections caused by multidrug-resistant Gram-positive organisms; although linezolid resistance remains uncommon, the number of linezolid-resistant enterococci has increased in recent years due to worldwide spread of acquired resistance genes (cfr, optrA, and poxtA) in clinical, animal, and environmental settings. In this study, we investigated the occurrence of linezolid-resistant enterococci in marine samples from two coastal areas in Italy. Isolates grown on florfenicol-supplemented Slanetz-Bartley agar plates were investigated for their carriage of optrA, poxtA, and cfr genes; optrA was found in one Enterococcus faecalis isolate, poxtA was found in three Enterococcus faecium isolates and two Enterococcus hirae isolates, and cfr was not found. Two of the three poxtA-carrying E. faecium isolates and the two E. hirae isolates showed related pulsed-field gel electrophoresis (PFGE) profiles. Two E. faecium isolates belonged to the new sequence type 1710, which clustered in clonal complex 94, encompassing nosocomial strains. S1 PFGE/hybridization assays showed a double (chromosome and plasmid) location of poxtA and a plasmid location of optrA Whole-genome sequencing revealed that poxtA was contained in a Tn6657-like element carried by two plasmids (pEfm-EF3 and pEh-GE2) of similar size, found in different species, and that poxtA was flanked by two copies of IS1216 in both plasmids. In mating experiments, all but one strain (E. faecalis EN3) were able to transfer the poxtA gene to E. faecium 64/3. The occurrence of linezolid resistance genes in enterococci from marine samples is of great concern and highlights the need to improve practices aimed at limiting the transmission of linezolid-resistant strains to humans from environmental reservoirs.IMPORTANCE Linezolid is one of the few antimicrobials available to treat severe infections due to drug-resistant Gram-positive bacteria; therefore, the emergence of linezolid-resistant enterococci carrying transferable resistance determinants is of great concern for public health. Linezolid resistance genes (cfr, optrA, and poxtA), often plasmid located, can be transmitted via horizontal gene transfer and have the potential to spread globally. This study highlights the detection of enterococci carrying linezolid resistance genes from sediment and zooplankton samples from two coastal urban areas in Italy. The presence of clinically relevant resistant bacteria, such as linezolid-resistant enterococci, in marine environments could reflect their spillover from human and/or animal reservoirs and could indicate that coastal seawaters also might represent a source of these resistance genes.}, }
@article {pmid33606106, year = {2021}, author = {Schaller, D and Geiß, M and Stadler, PF and Hellmuth, M}, title = {Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs.}, journal = {Journal of mathematical biology}, volume = {82}, number = {3}, pages = {20}, pmid = {33606106}, issn = {1432-1416}, mesh = {*Algorithms ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome ; *Models, Biological ; *Phylogeny ; }, abstract = {Genome-scale orthology assignments are usually based on reciprocal best matches. In the absence of horizontal gene transfer (HGT), every pair of orthologs forms a reciprocal best match. Incorrect orthology assignments therefore are always false positives in the reciprocal best match graph. We consider duplication/loss scenarios and characterize unambiguous false-positive (u-fp) orthology assignments, that is, edges in the best match graphs (BMGs) that cannot correspond to orthologs for any gene tree that explains the BMG. Moreover, we provide a polynomial-time algorithm to identify all u-fp orthology assignments in a BMG. Simulations show that at least [Formula: see text] of all incorrect orthology assignments can be detected in this manner. All results rely only on the structure of the BMGs and not on any a priori knowledge about underlying gene or species trees.}, }
@article {pmid33606087, year = {2021}, author = {Dlamini, ST and Jaiswal, SK and Mohammed, M and Dakora, FD}, title = {Studies of Phylogeny, Symbiotic Functioning and Ecological Traits of Indigenous Microsymbionts Nodulating Bambara Groundnut (Vigna subterranea L. Verdc) in Eswatini.}, journal = {Microbial ecology}, volume = {82}, number = {3}, pages = {688-703}, pmid = {33606087}, issn = {1432-184X}, mesh = {Bradyrhizobium ; Eswatini ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Root Nodules, Plant ; *Vigna ; }, abstract = {Rhizobial microsymbionts of grain legumes are ubiquitous in soils and exhibit a wide range of diversity with respect to colony morphology, genetic variability, biochemical characteristics, and phylogenetic relationships. This study assessed the phylogenetic positions of rhizobial microsymbionts of Bambara groundnut from Eswatini exhibiting variations in morpho-physiology, adaptive characteristics, and N2-fixing efficiency. The isolates' ERIC-PCR profiles revealed the presence of high genetic variation among them. These test isolates also exhibited differences in pH tolerance and IAA production. Multilocus sequence analysis based on the 16S rRNA, atpD, glnII, gyrB, and recA gene sequences of representative test isolates closely aligned them to the type strains of Bradyrhizobium arachidis, B. manausense, B. guangdongense, B. elkanii, and B. pachyrhizi. However, some isolates showed a high divergence from the known reference type strains, indicating that they may represent species yet to be properly characterized and described. Functional characterization in the glasshouse revealed that most of the isolates from the contrasting Agro-ecologies of Eswatini were efficient in N2 fixation, and therefore elicited greater stomatal conductance and photosynthetic rates in the homologous Bambara groundnut. Of the 75 isolates tested, 51% were more effective than the commercial Bradyrhizobium sp. strain CB756, with relative symbiotic effectiveness ranging from 138 to 308%. The findings of this study indicated that the analysis of housekeeping genes and functional traits of Bambara-nodulating microsymbionts can provide a clear view for understanding and predicting rhizobial community structure across environmental gradients.}, }
@article {pmid33597173, year = {2021}, author = {Keller, CM and Kendra, CG and Bruna, RE and Craft, D and Pontes, MH}, title = {Genetic Modification of Sodalis Species by DNA Transduction.}, journal = {mSphere}, volume = {6}, number = {1}, pages = {}, pmid = {33597173}, issn = {2379-5042}, support = {R21 AI148774/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteriophages/genetics/metabolism ; DNA, Bacterial/*genetics ; Enterobacteriaceae/classification/*genetics/*virology ; Escherichia coli/genetics ; *Gene Transfer Techniques ; *Genome, Bacterial ; Host Specificity ; Phylogeny ; Symbiosis ; *Transduction, Genetic ; }, abstract = {Bacteriophages (phages) are ubiquitous in nature. These viruses play a number of central roles in microbial ecology and evolution by, for instance, promoting horizontal gene transfer (HGT) among bacterial species. The ability of phages to mediate HGT through transduction has been widely exploited as an experimental tool for the genetic study of bacteria. As such, bacteriophage P1 represents a prototypical generalized transducing phage with a broad host range that has been extensively employed in the genetic manipulation of Escherichia coli and a number of other model bacterial species. Here we demonstrate that P1 is capable of infecting, lysogenizing, and promoting transduction in members of the bacterial genus Sodalis, including the maternally inherited insect endosymbiont Sodalis glossinidius While establishing new tools for the genetic study of these bacterial species, our results suggest that P1 may be used to deliver DNA to many Gram-negative endosymbionts in their insect host, thereby circumventing a culturing requirement to genetically manipulate these organisms.IMPORTANCE A large number of economically important insects maintain intimate associations with maternally inherited endosymbiotic bacteria. Due to the inherent nature of these associations, insect endosymbionts cannot be usually isolated in pure culture or genetically manipulated. Here we use a broad-host-range bacteriophage to deliver exogenous DNA to an insect endosymbiont and a closely related free-living species. Our results suggest that broad-host-range bacteriophages can be used to genetically alter insect endosymbionts in their insect host and, as a result, bypass a culturing requirement to genetically alter these bacteria.}, }
@article {pmid33597171, year = {2021}, author = {Baltrus, DA and Smith, C and Derrick, M and Leligdon, C and Rosenthal, Z and Mollico, M and Moore, A and Clark, M}, title = {Genomic Background Governs Opposing Responses to Nalidixic Acid upon Megaplasmid Acquisition in Pseudomonas.}, journal = {mSphere}, volume = {6}, number = {1}, pages = {}, pmid = {33597171}, issn = {2379-5042}, mesh = {Anti-Bacterial Agents/*pharmacology ; Ciprofloxacin/pharmacology ; Gene Transfer Techniques ; *Genome, Bacterial ; Nalidixic Acid/*pharmacology ; Plasmids/*genetics ; Pseudomonas putida/*drug effects/*genetics ; }, abstract = {Horizontal gene transfer is a significant driver of evolutionary dynamics across microbial populations. Although the benefits of the acquisition of new genetic material are often quite clear, experiments across systems have demonstrated that gene transfer events can cause significant phenotypic changes and entail fitness costs in a way that is dependent on the genomic and environmental context. Here, we test for the generality of one previously identified cost, sensitization of cells to the antibiotic nalidixic acid after acquisition of an ∼1-Mb megaplasmid, across Pseudomonas strains and species. Overall, we find that the presence of this megaplasmid sensitizes many different Pseudomonas strains to nalidixic acid but that this same horizontal gene transfer event increases resistance of Pseudomonas putida KT2440 to nalidixic acid across assays as well as to ciprofloxacin under competitive conditions. These phenotypic results are not easily explained away as secondary consequences of overall fitness effects and appear to occur independently of another cost associated with this megaplasmid, sensitization to higher temperatures. Lastly, we draw parallels between these reported results and the phenomenon of sign epistasis for de novo mutations and explore how context dependence of effects of plasmid acquisition could impact overall evolutionary dynamics and the evolution of antimicrobial resistance.IMPORTANCE Numerous studies have demonstrated that gene transfer events (e.g., plasmid acquisition) can entail a variety of costs that arise as by-products of the incorporation of foreign DNA into established physiological and genetic systems. These costs can be ameliorated through evolutionary time by the occurrence of compensatory mutations, which stabilize the presence of a horizontally transferred region within the genome but which also may skew future adaptive possibilities for these lineages. Here, we demonstrate another possible outcome, that phenotypic changes arising as a consequence of the same horizontal gene transfer (HGT) event are costly to some strains but may actually be beneficial in other genomic backgrounds under the right conditions. These results provide a new viewpoint for considering conditions that promote plasmid maintenance and highlight the influence of genomic and environmental contexts when considering amelioration of fitness costs after HGT events.}, }
@article {pmid33592234, year = {2021}, author = {Cornet, L and Magain, N and Baurain, D and Lutzoni, F}, title = {Exploring syntenic conservation across genomes for phylogenetic studies of organisms subjected to horizontal gene transfers: A case study with Cyanobacteria and cyanolichens.}, journal = {Molecular phylogenetics and evolution}, volume = {162}, number = {}, pages = {107100}, doi = {10.1016/j.ympev.2021.107100}, pmid = {33592234}, issn = {1095-9513}, mesh = {Cyanobacteria/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genomics ; *Phylogeny ; *Synteny ; }, abstract = {Understanding the evolutionary history of symbiotic Cyanobacteria at a fine scale is essential to unveil patterns of associations with their hosts and factors driving their spatiotemporal interactions. As for bacteria in general, Horizontal Gene Transfers (HGT) are expected to be rampant throughout their evolution, which justified the use of single-locus phylogenies in macroevolutionary studies of these photoautotrophic bacteria. Genomic approaches have greatly increased the amount of molecular data available, but the selection of orthologous, congruent genes that are more likely to reflect bacterial macroevolutionary histories remains problematic. In this study, we developed a synteny-based approach and searched for Collinear Orthologous Regions (COR), under the assumption that genes that are present in the same order and orientation across a wide monophyletic clade are less likely to have undergone HGT. We searched sixteen reference Nostocales genomes and identified 99 genes, part of 28 COR comprising three to eight genes each. We then developed a bioinformatic pipeline, designed to minimize inter-genome contamination and processed twelve Nostoc-associated lichen metagenomes. This reduced our original dataset to 90 genes representing 25 COR, which were used to infer phylogenetic relationships within Nostocales and among lichenized Cyanobacteria. This dataset was narrowed down further to 71 genes representing 22 COR by selecting only genes part of one (largest) operon per COR. We found a relatively high level of congruence among trees derived from the 90-gene dataset, but congruence was only slightly higher among genes within a COR compared to genes across COR. However, topological congruence was significantly higher among the 71 genes part of one operon per COR. Nostocales phylogenies resulting from concatenation and species tree approaches based on the 90- and 71-gene datasets were highly congruent, but the most highly supported result was obtained when using synteny, collinearity, and operon information (i.e., 71-gene dataset) as gene selection criteria, which outperformed larger datasets with more genes.}, }
@article {pmid33592101, year = {2021}, author = {Banhart, S and Selb, R and Oehlmann, S and Bender, J and Buder, S and Jansen, K and Heuer, D}, title = {The Mosaic mtr Locus as Major Genetic Determinant of Azithromycin Resistance of Neisseria gonorrhoeae-Germany, 2018.}, journal = {The Journal of infectious diseases}, volume = {224}, number = {8}, pages = {1398-1404}, doi = {10.1093/infdis/jiab091}, pmid = {33592101}, issn = {1537-6613}, mesh = {5-Methyltetrahydrofolate-Homocysteine S-Methyltransferase/*genetics ; Anti-Bacterial Agents/*pharmacology/therapeutic use ; Azithromycin/*pharmacology ; Drug Resistance, Bacterial/drug effects/*genetics ; Germany/epidemiology ; Gonorrhea/*drug therapy/epidemiology ; Humans ; Microbial Sensitivity Tests ; Neisseria gonorrhoeae/*drug effects/*genetics/isolation &amp; purification ; Phylogeny ; Whole Genome Sequencing ; }, abstract = {Within the German Gonococcal Resistance Network's (GORENET) Neisseria gonorrhoeae (NG) sample collection, azithromycin-resistant NG isolates increased from 4.3% in 2016 to 9.2% in 2018. We aim to understand this observed increase using whole genome sequencing of NG isolates combined with epidemiological and clinical data. Reduced susceptibility to azithromycin in 2018 was predominately clonal (NG multiantigen sequence typing G12302) and could mainly be attributed to the recently described mosaic-like mtr locus. Our data suggest that, together with horizontal gene transfer of resistance determinants and well-established point mutations, international spread of resistant lineages plays a major role regarding azithromycin resistance in Germany.}, }
@article {pmid33592098, year = {2021}, author = {Liao, H and Li, X and Yang, Q and Bai, Y and Cui, P and Wen, C and Liu, C and Chen, Z and Tang, J and Che, J and Yu, Z and Geisen, S and Zhou, S and Friman, VP and Zhu, YG}, title = {Herbicide Selection Promotes Antibiotic Resistance in Soil Microbiomes.}, journal = {Molecular biology and evolution}, volume = {38}, number = {6}, pages = {2337-2350}, pmid = {33592098}, issn = {1537-1719}, support = {BB/T010606/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Herbicides ; *Interspersed Repetitive Sequences ; Microbiota ; Mutation ; Plasmids ; *Selection, Genetic ; *Soil Microbiology ; }, abstract = {Herbicides are one of the most widely used chemicals in agriculture. While they are known to be harmful to nontarget organisms, the effects of herbicides on the composition and functioning of soil microbial communities remain unclear. Here we show that application of three widely used herbicides-glyphosate, glufosinate, and dicamba-increase the prevalence of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in soil microbiomes without clear changes in the abundance, diversity and composition of bacterial communities. Mechanistically, these results could be explained by a positive selection for more tolerant genotypes that acquired several mutations in previously well-characterized herbicide and ARGs. Moreover, herbicide exposure increased cell membrane permeability and conjugation frequency of multidrug resistance plasmids, promoting ARG movement between bacteria. A similar pattern was found in agricultural soils across 11 provinces in China, where herbicide application, and the levels of glyphosate residues in soils, were associated with increased ARG and MGE abundances relative to herbicide-free control sites. Together, our results show that herbicide application can enrich ARGs and MGEs by changing the genetic composition of soil microbiomes, potentially contributing to the global antimicrobial resistance problem in agricultural environments.}, }
@article {pmid33589766, year = {2021}, author = {Yu, Z and Wang, Y and Lu, J and Bond, PL and Guo, J}, title = {Nonnutritive sweeteners can promote the dissemination of antibiotic resistance through conjugative gene transfer.}, journal = {The ISME journal}, volume = {15}, number = {7}, pages = {2117-2130}, pmid = {33589766}, issn = {1751-7370}, mesh = {Drug Resistance, Microbial ; Gene Transfer, Horizontal ; Humans ; *Non-Nutritive Sweeteners ; Phylogeny ; Plasmids/genetics ; Sweetening Agents/pharmacology ; }, abstract = {Antimicrobial resistance (AMR) poses a worldwide threat to human health and biosecurity. The spread of antibiotic resistance genes (ARGs) via conjugative plasmid transfer is a major contributor to the evolution of this resistance. Although permitted as safe food additives, compounds such as saccharine, sucralose, aspartame, and acesulfame potassium that are commonly used as nonnutritive sweeteners have recently been associated with shifts in the gut microbiota similar to those caused by antibiotics. As antibiotics can promote the spread of antibiotic resistance genes (ARGs), we hypothesize that these nonnutritive sweeteners could have a similar effect. Here, we demonstrate for the first time that saccharine, sucralose, aspartame, and acesulfame potassium could promote plasmid-mediated conjugative transfer in three established conjugation models between the same and different phylogenetic strains. The real-time dynamic conjugation process was visualized at the single-cell level. Bacteria exposed to the tested compounds exhibited increased reactive oxygen species (ROS) production, the SOS response, and gene transfer. In addition, cell membrane permeability increased in both parental bacteria under exposure to the tested compounds. The expression of genes involved in ROS detoxification, the SOS response, and cell membrane permeability was significantly upregulated under sweetener treatment. In conclusion, exposure to nonnutritive sweeteners enhances conjugation in bacteria. Our findings provide insight into AMR spread and indicate the potential risk associated with the presence of nonnutritive sweeteners.}, }
@article {pmid33584575, year = {2020}, author = {Peng, Z and Liu, G and Huang, K}, title = {Cold Adaptation Mechanisms of a Snow Alga Chlamydomonas nivalis During Temperature Fluctuations.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {611080}, pmid = {33584575}, issn = {1664-302X}, abstract = {Cold environments, such as glaciers and alpine regions, constitute unique habitats for organisms living on Earth. In these harsh ecosystems, snow algae survive, florish, and even become primary producers for microbial communities. How the snow algae maintain physiological activity during violent ambient temperature changes remains unsolved. To explore the cold adaptation mechanisms of the unicellular snow alga Chlamydomonas nivalis, we compared its physiological responses to a model organism from the same genus, Chlamydomonas reinhardtii. When both cell types were exposed to a shift from 22°C to 4°C, C. nivalis exhibited an apparent advantage in cold tolerance over C. reinhardtii, as C. nivalis had both a higher growth rate and photosynthetic efficiency. To determine the cold tolerance mechanisms of C. nivalis, RNA sequencing was used to compare transcriptomes of both species after 1 h of cold treatment, mimicking temperature fluctuations in the polar region. Differential expression analysis showed that C. nivalis had fewer transcriptomic changes and was more stable during rapid temperature decrease relative to C. reinhardtii, especially for the expression of photosynthesis related genes. Additionally, we found that transcription in C. nivalis was precisely regulated by the cold response network, consisting of at least 12 transcription factors and 3 RNA-binding proteins. Moreover, genes participating in nitrogen metabolism, the pentose phosphate pathway, and polysaccharide biosynthesis were upregulated, indicating that increasing resource assimilation and remodeling of metabolisms were critical for cold adaptation in C. nivalis. Furthermore, we identified horizontally transferred genes differentially expressed in C. nivalis, which are critical for cold adaptation in other psychrophiles. Our results reveal that C. nivalis adapts rapid temperature decrease by efficiently regulating transcription of specific genes to optimize resource assimilation and metabolic pathways, providing critical insights into how snow algae survive and propagate in cold environments.}, }
@article {pmid33583353, year = {2021}, author = {Zhao, J and Zhang, Y and Fan, Y and Han, J and Xiong, Z and Liu, X and Li, B and Lu, B and Cao, B}, title = {Characterization of an NDM-5-producing hypervirulent Klebsiella pneumoniae sequence type 65 clone from a lung transplant recipient.}, journal = {Emerging microbes &amp; infections}, volume = {10}, number = {1}, pages = {396-399}, pmid = {33583353}, issn = {2222-1751}, mesh = {Aged ; Animals ; Anti-Bacterial Agents/pharmacology ; Disease Models, Animal ; Fatal Outcome ; Female ; Gene Transfer, Horizontal ; Humans ; Klebsiella Infections/*diagnosis/mortality ; Klebsiella pneumoniae/*classification/genetics/isolation &amp; purification/pathogenicity ; Lung Transplantation/*mortality ; Male ; Mice ; Phylogeny ; Plasmids/genetics ; Shock, Septic/*microbiology/mortality ; Virulence Factors/genetics ; Whole Genome Sequencing ; beta-Lactamases/*genetics ; }, abstract = {The emergence of New Delhi Metallo-β-lactamase (NDM)-producing Klebsiella pneumoniae has aroused critical concern worldwide. Herein, we reported the first emergence of NDM-5-producing K. pneumoniae isolates in a 68-year-old lung transplant recipient, who died of septic shock 13 days after surgery. The K. pneumoniae strain KP22937 isolated from the bloodstream of the patient was analyzed for phenotypes and genotypes. KP22937 belonged to sequence type (ST) 65 and capsule serotype K2, contained iucABCDiutA and iroBCDN virulence clusters, showed high virulence to mice, and was therefore considered a hypervirulent K. pneumoniae. The blaNDM-5 gene was located on a genomic island region of the IncX3-type plasmid pNDM22937, which was successfully transferred to Escherichia coli EC600 with insignificant fitness costs. The transconjugant demonstrated similar antimicrobial susceptibility and growth kinetics to the recipient E. coli EC600. The plasmid pNDM22937 was almost identical to the blaNDM-5-carrying IncX3 plasmids previously reported in K. pneumoniae strains with different ST types and in other species. Our findings raise concerns about the horizontal spread of blaNDM-5 gene mediated by IncX3 plasmid, where hypervirulent K. pneumoniae strains are also involved. Stricter control measures are needed to prevent the dissemination of the novel clone in hospital settings.}, }
@article {pmid33582843, year = {2021}, author = {Vangalis, V and Knop, M and Typas, MA and Papaioannou, IA}, title = {Establishment of conidial fusion in the asexual fungus Verticillium dahliae as a useful system for the study of non-sexual genetic interactions.}, journal = {Current genetics}, volume = {67}, number = {3}, pages = {471-485}, pmid = {33582843}, issn = {1432-0983}, support = {MIS-5000432//State Scholarships Foundation/ ; }, mesh = {Acremonium/*genetics/pathogenicity ; Ascomycota/genetics/pathogenicity ; Cell Nucleus/genetics ; Fungal Proteins/*genetics ; Gene Transfer, Horizontal/genetics ; Genes, Mating Type, Fungal/genetics ; Hyphae/genetics/growth &amp; development ; Mitogen-Activated Protein Kinases/genetics ; NADPH Oxidases/genetics ; Reproduction, Asexual/*genetics ; Saccharomyces cerevisiae Proteins/genetics ; Spores, Fungal/*genetics/growth &amp; development ; }, abstract = {Cell-to-cell fusion is a fundamental biological process across the tree of life. In filamentous fungi, somatic fusion (or anastomosis) is required for the normal development of their syncytial hyphal networks, and it can initiate non-sexual genetic exchange processes, such as horizontal genetic transfer and the parasexual cycle. Although these could be important drivers of the evolution of asexual fungi, this remains a largely unexplored possibility due to the lack of suitable resources for their study in these puzzling organisms. We thus aimed at the characterization of cell fusion in the important asexual fungus Verticillium dahliae via Conidial Anastomosis Tubes (CATs), which can be useful for the analysis of parasexuality. We optimized appropriate procedures for their highly reproducible quantification and live-cell imaging, which were used to characterize their physiology and cell biology, and to start elucidating their underlying genetic machinery. Formation of CATs was shown to depend on growth conditions and require functional Fus3 and Slt2 MAP kinases, as well as the NADPH oxidase NoxA, whereas the GPCR Ste2 and the mating-type protein MAT1-2-1 were dispensable. We show that nuclei and other organelles can migrate through CATs, which often leads to the formation of transient dikaryons. Their nuclei have possible windows of opportunity for genetic interaction before degradation of one by a presumably homeostatic mechanism. We establish here CAT-mediated fusion in V. dahliae as an experimentally convenient system for the cytological analysis of fungal non-sexual genetic interactions. We expect that it will facilitate the dissection of sexual alternatives in asexual fungi.}, }
@article {pmid33582841, year = {2021}, author = {Blake, KS and Choi, J and Dantas, G}, title = {Approaches for characterizing and tracking hospital-associated multidrug-resistant bacteria.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {78}, number = {6}, pages = {2585-2606}, pmid = {33582841}, issn = {1420-9071}, support = {R01OH011578/OH/NIOSH CDC HHS/United States ; T32 DK007130/DK/NIDDK NIH HHS/United States ; R01 AI123394/AI/NIAID NIH HHS/United States ; R01 HD092414/HD/NICHD NIH HHS/United States ; R01 AT009741/AT/NCCIH NIH HHS/United States ; R01 OH011578/OH/NIOSH CDC HHS/United States ; R01AT009741/AT/NCCIH NIH HHS/United States ; P30 DK052574/DK/NIDDK NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/therapeutic use ; Bacteria/classification/*genetics/isolation &amp; purification ; Cross Infection/drug therapy/microbiology/*pathology ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal ; Humans ; Metagenomics ; Plasmids/genetics/metabolism ; RNA, Ribosomal, 16S/chemistry/classification/metabolism ; Whole Genome Sequencing ; }, abstract = {Hospital-associated infections are a major concern for global public health. Infections with antibiotic-resistant pathogens can cause empiric treatment failure, and for infections with multidrug-resistant bacteria which can overcome antibiotics of "last resort" there exists no alternative treatments. Despite extensive sanitization protocols, the hospital environment is a potent reservoir and vector of antibiotic-resistant organisms. Pathogens can persist on hospital surfaces and plumbing for months to years, acquire new antibiotic resistance genes by horizontal gene transfer, and initiate outbreaks of hospital-associated infections by spreading to patients via healthcare workers and visitors. Advancements in next-generation sequencing of bacterial genomes and metagenomes have expanded our ability to (1) identify species and track distinct strains, (2) comprehensively profile antibiotic resistance genes, and (3) resolve the mobile elements that facilitate intra- and intercellular gene transfer. This information can, in turn, be used to characterize the population dynamics of hospital-associated microbiota, track outbreaks to their environmental reservoirs, and inform future interventions. This review provides a detailed overview of the approaches and bioinformatic tools available to study isolates and metagenomes of hospital-associated bacteria, and their multi-layered networks of transmission.}, }
@article {pmid33582235, year = {2021}, author = {Araújo, DS and De-Paula, RB and Tomé, LMR and Quintanilha-Peixoto, G and Salvador-Montoya, CA and Del-Bem, LE and Badotti, F and Azevedo, VAC and Brenig, B and Aguiar, ERGR and Drechsler-Santos, ER and Fonseca, PLC and Góes-Neto, A}, title = {Comparative mitogenomics of Agaricomycetes: Diversity, abundance, impact and coding potential of putative open-reading frames.}, journal = {Mitochondrion}, volume = {58}, number = {}, pages = {1-13}, doi = {10.1016/j.mito.2021.02.002}, pmid = {33582235}, issn = {1872-8278}, mesh = {Basidiomycota/*genetics ; Codon ; DNA, Mitochondrial/genetics ; *Genes, Fungal ; *Genome, Mitochondrial ; Introns ; Open Reading Frames ; Polyporaceae/*genetics ; }, abstract = {The mitochondrion is an organelle found in eukaryote organisms, and it is vital for different cellular pathways. The mitochondrion has its own DNA molecule and, because its genetic content is relatively conserved, despite the variation of size and structure, mitogenome sequences have been widely used as a promising molecular biomarker for taxonomy and evolution in fungi. In this study, the mitogenomes of two fungal species of Agaricomycetes class, Phellinotus piptadeniae and Trametes villosa, were assembled and annotated for the first time. We used these newly sequenced mitogenomes for comparative analyses with other 55 mitogenomes of Agaricomycetes available in public databases. Mitochondrial DNA (mtDNA) size and content are highly variable and non-coding and intronic regions, homing endonucleases (HEGs), and unidentified ORFs (uORFs) significantly contribute to the total size of the mitogenome. Furthermore, accessory genes (most of them as HEGs) are shared between distantly related species, most likely as a consequence of horizontal gene transfer events. Conversely, uORFs are only shared between taxonomically related species, most probably as a result of vertical evolutionary inheritance. Additionally, codon usage varies among mitogenomes and the GC content of mitochondrial features may be used to distinguish coding from non-coding sequences. Our results also indicated that transposition events of mitochondrial genes to the nuclear genome are not common. Despite the variation of size and content of the mitogenomes, mitochondrial genes seemed to be reliable molecular markers in our time-divergence analysis, even though the nucleotide substitution rates of mitochondrial and nuclear genomes of fungi are quite different. We also showed that many events of mitochondrial gene shuffling probably happened amongst the Agaricomycetes during evolution, which created differences in the gene order among species, even those of the same genus. Altogether, our study revealed new information regarding evolutionary dynamics in Agaricomycetes.}, }
@article {pmid33580956, year = {2021}, author = {Kottara, A and Hall, JPJ and Brockhurst, MA}, title = {The proficiency of the original host species determines community-level plasmid dynamics.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {4}, pages = {}, doi = {10.1093/femsec/fiab026}, pmid = {33580956}, issn = {1574-6941}, support = {BB/R018154/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Bacteria/genetics ; Conjugation, Genetic ; *Gene Transfer, Horizontal ; Host Specificity ; Plasmids/genetics ; }, abstract = {Plasmids are common in natural bacterial communities, facilitating bacterial evolution via horizontal gene transfer. Bacterial species vary in their proficiency to host plasmids: whereas plasmids are stably maintained in some species regardless of selection for plasmid-encoded genes, in other species, even beneficial plasmids are rapidly lost. It is, however, unclear how this variation in host proficiency affects plasmid persistence in communities. Here, we test this using multispecies bacterial soil communities comprising species varying in their proficiency to host a large conjugative mercury resistance plasmid, pQBR103. The plasmid reached higher community-level abundance where beneficial and when introduced to the community in a more proficient host species. Proficient plasmid host species were also better able to disseminate the plasmid to a wider diversity of host species. These findings suggest that the dynamics of plasmids in natural bacterial communities depend not only upon the plasmid's attributes and the selective environment but also upon the proficiency of their host species.}, }
@article {pmid33580675, year = {2021}, author = {Kapili, BJ and Dekas, AE}, title = {PPIT: an R package for inferring microbial taxonomy from nifH sequences.}, journal = {Bioinformatics (Oxford, England)}, volume = {37}, number = {16}, pages = {2289-2298}, doi = {10.1093/bioinformatics/btab100}, pmid = {33580675}, issn = {1367-4811}, support = {OCE-1634297//National Science Foundation/ ; //Graduate Research Fellowship/ ; }, abstract = {MOTIVATION: Linking microbial community members to their ecological functions is a central goal of environmental microbiology. When assigned taxonomy, amplicon sequences of metabolic marker genes can suggest such links, thereby offering an overview of the phylogenetic structure underpinning particular ecosystem functions. However, inferring microbial taxonomy from metabolic marker gene sequences remains a challenge, particularly for the frequently sequenced nitrogen fixation marker gene, nitrogenase reductase (nifH). Horizontal gene transfer in recent nifH evolutionary history can confound taxonomic inferences drawn from the pairwise identity methods used in existing software. Other methods for inferring taxonomy are not standardized and require manual inspection that is difficult to scale.<br><br>RESULTS: We present Phylogenetic Placement for Inferring Taxonomy (PPIT), an R package that infers microbial taxonomy from nifH amplicons using both phylogenetic and sequence identity approaches. After users place query sequences on a reference nifH gene tree provided by PPIT (n&#x2009;=&#x2009;6317 full-length nifH sequences), PPIT searches the phylogenetic neighborhood of each query sequence and attempts to infer microbial taxonomy. An inference is drawn only if references in the phylogenetic neighborhood are: (1) taxonomically consistent and (2) share sufficient pairwise identity with the query, thereby avoiding erroneous inferences due to known horizontal gene transfer events. We find that PPIT returns a higher proportion of correct taxonomic inferences than BLAST-based approaches at the cost of fewer total inferences. We demonstrate PPIT on deep-sea sediment and find that Deltaproteobacteria are the most abundant potential diazotrophs. Using this dataset, we show that emending PPIT inferences based on visual inspection of query sequence placement can achieve taxonomic inferences for nearly all sequences in a query set. We additionally discuss how users can apply PPIT to the analysis of other marker genes.<br><br>PPIT is freely available to noncommercial users at https://github.com/bkapili/ppit. Installation includes a vignette that demonstrates package use and reproduces the nifH amplicon analysis discussed here. The raw nifH amplicon sequence data have been deposited in the GenBank, EMBL and DDBJ databases under BioProject number PRJEB37167.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid33578772, year = {2021}, author = {Tagini, F and Pillonel, T and Bertelli, C and Jaton, K and Greub, G}, title = {Pathogenic Determinants of the Mycobacterium kansasii Complex: An Unsuspected Role for Distributive Conjugal Transfer.}, journal = {Microorganisms}, volume = {9}, number = {2}, pages = {}, pmid = {33578772}, issn = {2076-2607}, abstract = {The Mycobacterium kansasii species comprises six subtypes that were recently classified into six closely related species; Mycobacterium kansasii (formerly M. kansasii subtype 1), Mycobacterium persicum (subtype 2), Mycobacterium pseudokansasii (subtype 3), Mycobacterium ostraviense (subtype 4), Mycobacterium innocens (subtype 5) and Mycobacterium attenuatum (subtype 6). Together with Mycobacterium gastri, they form the M. kansasii complex. M. kansasii is the most frequent and most pathogenic species of the complex. M. persicum is classically associated with diseases in immunosuppressed patients, and the other species are mostly colonizers, and are only very rarely reported in ill patients. Comparative genomics was used to assess the genetic determinants leading to the pathogenicity of members of the M. kansasii complex. The genomes of 51 isolates collected from patients with and without disease were sequenced and compared with 24 publicly available genomes. The pathogenicity of each isolate was determined based on the clinical records or public metadata. A comparative genomic analysis showed that all M. persicum, M. ostraviense, M innocens and M. gastri isolates lacked the ESX-1-associated EspACD locus that is thought to play a crucial role in the pathogenicity of M. tuberculosis and other non-tuberculous mycobacteria. Furthermore, M. kansasii was the only species exhibiting a 25-Kb-large genomic island encoding for 17 type-VII secretion system-associated proteins. Finally, a genome-wide association analysis revealed that two consecutive genes encoding a hemerythrin-like protein and a nitroreductase-like protein were significantly associated with pathogenicity. These two genes may be involved in the resistance to reactive oxygen and nitrogen species, a required mechanism for the intracellular survival of bacteria. Three non-pathogenic M. kansasii lacked these genes likely due to two distinct distributive conjugal transfers (DCTs) between M. attenuatum and M. kansasii, and one DCT between M. persicum and M. kansasii. To our knowledge, this is the first study linking DCT to reduced pathogenicity.}, }
@article {pmid33575588, year = {2020}, author = {Gallant, J and Mouton, J and Ummels, R and Ten Hagen-Jongman, C and Kriel, N and Pain, A and Warren, RM and Bitter, W and Heunis, T and Sampson, SL}, title = {Identification of gene fusion events in Mycobacterium tuberculosis that encode chimeric proteins.}, journal = {NAR genomics and bioinformatics}, volume = {2}, number = {2}, pages = {lqaa033}, pmid = {33575588}, issn = {2631-9268}, support = {MR/R005850/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {Mycobacterium tuberculosis is a facultative intracellular pathogen responsible for causing tuberculosis. The harsh environment in which M. tuberculosis survives requires this pathogen to continuously adapt in order to maintain an evolutionary advantage. However, the apparent absence of horizontal gene transfer in M. tuberculosis imposes restrictions in the ways by which evolution can occur. Large-scale changes in the genome can be introduced through genome reduction, recombination events and structural variation. Here, we identify a functional chimeric protein in the ppe38-71 locus, the absence of which is known to have an impact on protein secretion and virulence. To examine whether this approach was used more often by this pathogen, we further develop software that detects potential gene fusion events from multigene deletions using whole genome sequencing data. With this software we could identify a number of other putative gene fusion events within the genomes of M. tuberculosis isolates. We were able to demonstrate the expression of one of these gene fusions at the protein level using mass spectrometry. Therefore, gene fusions may provide an additional means of evolution for M. tuberculosis in its natural environment whereby novel chimeric proteins and functions can arise.}, }
@article {pmid33572638, year = {2021}, author = {Chambers, ST and Slow, S and Scott-Thomas, A and Murdoch, DR}, title = {Legionellosis Caused by Non-Legionella pneumophila Species, with a Focus on Legionella longbeachae.}, journal = {Microorganisms}, volume = {9}, number = {2}, pages = {}, pmid = {33572638}, issn = {2076-2607}, abstract = {Although known as causes of community-acquired pneumonia and Pontiac fever, the global burden of infection caused by Legionella species other than Legionella pneumophila is under-recognised. Non-L. pneumophila legionellae have a worldwide distribution, although common testing strategies for legionellosis favour detection of L. pneumophila over other Legionella species, leading to an inherent diagnostic bias and under-detection of cases. When systematically tested for in Australia and New Zealand, L. longbeachae was shown to be a leading cause of community-acquired pneumonia. Exposure to potting soils and compost is a particular risk for infection from L. longbeachae, and L. longbeachae may be better adapted to soil and composting plant material than other Legionella species. It is possible that the high rate of L. longbeachae reported in Australia and New Zealand is related to the composition of commercial potting soils which, unlike European products, contain pine bark and sawdust. Genetic studies have demonstrated that the Legionella genomes are highly plastic, with areas of the chromosome showing high levels of recombination as well as horizontal gene transfer both within and between species via plasmids. This, combined with various secretion systems and extensive effector repertoires that enable the bacterium to hijack host cell functions and resources, is instrumental in shaping its pathogenesis, survival and growth. Prevention of legionellosis is hampered by surveillance systems that are compromised by ascertainment bias, which limits commitment to an effective public health response. Current prevention strategies in Australia and New Zealand are directed at individual gardeners who use potting soils and compost. This consists of advice to avoid aerosols generated by the use of potting soils and use masks and gloves, but there is little evidence that this is effective. There is a need to better understand the epidemiology of L. longbeachae and other Legionella species in order to develop effective treatment and preventative strategies globally.}, }
@article {pmid33571441, year = {2021}, author = {Cheng, S and Wong, GK and Melkonian, M}, title = {Giant DNA viruses make big strides in eukaryote evolution.}, journal = {Cell host &amp; microbe}, volume = {29}, number = {2}, pages = {152-154}, doi = {10.1016/j.chom.2021.01.008}, pmid = {33571441}, issn = {1934-6069}, mesh = {DNA Viruses/genetics ; Eukaryota/genetics ; Gene Transfer, Horizontal ; *Giant Viruses/genetics ; *Microalgae ; *Viruses/genetics ; }, abstract = {Nucleocytoplasmic large DNA viruses (NCLDVs) are widespread in the biosphere. This issue of Cell Host &amp; Microbe, Nelson et al., and a recent Nature paper, Moniruzzaman et al., show NCLDVs can integrate into host genomes, highlighting a mechanism of large-scale virus-mediated horizontal gene transfer (vHGT) driving eukaryotic evolution.}, }
@article {pmid33571437, year = {2021}, author = {Ulrich, NJ and Uchida, H and Kanesaki, Y and Hirose, E and Murakami, A and Miller, SR}, title = {Reacquisition of light-harvesting genes in a marine cyanobacterium confers a broader solar niche.}, journal = {Current biology : CB}, volume = {31}, number = {7}, pages = {1539-1546.e4}, doi = {10.1016/j.cub.2021.01.047}, pmid = {33571437}, issn = {1879-0445}, mesh = {*Biological Evolution ; Cyanobacteria/*genetics ; Gene Transfer, Horizontal ; *Photosynthesis/genetics ; *Phycocyanin ; }, abstract = {The evolution of phenotypic plasticity, i.e., the environmental induction of alternative phenotypes by the same genotype, can be an important mechanism of biological diversification.[1][,][2] For example, an evolved increase in plasticity may promote ecological niche expansion as well as the innovation of novel traits;[3] however, both the role of phenotypic plasticity in adaptive evolution and its underlying mechanisms are still poorly understood.[4][,][5] Here, we report that the Chlorophyll d-producing marine cyanobacterium Acaryochloris marina strain MBIC11017 has evolved greater photosynthetic plasticity by reacquiring light-harvesting genes via horizontal gene transfer. The genes, which had been lost by the A. marina ancestor, are involved in the production and degradation of the light-harvesting phycobiliprotein phycocyanin. A. marina MBIC11017 exhibits a high degree of wavelength-dependence in phycocyanin production, and this ability enables it to grow with yellow and green light wavelengths that are inaccessible to other A. marina. Consequently, this strain has a broader solar niche than its close relatives. We discuss the role of horizontal gene transfer for regaining a lost phenotype in light of Dollo's Law[6] that the loss of a complex trait is irreversible.}, }
@article {pmid33571292, year = {2021}, author = {Hull, DM and Harrell, E and van Vliet, AHM and Correa, M and Thakur, S}, title = {Antimicrobial resistance and interspecies gene transfer in Campylobacter coli and Campylobacter jejuni isolated from food animals, poultry processing, and retail meat in North Carolina, 2018-2019.}, journal = {PloS one}, volume = {16}, number = {2}, pages = {e0246571}, pmid = {33571292}, issn = {1932-6203}, support = {U01 FD007145/FD/FDA HHS/United States ; U18 FD006194/FD/FDA HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Campylobacter coli/drug effects/*genetics/isolation &amp; purification ; Campylobacter jejuni/drug effects/*genetics/isolation &amp; purification ; *Drug Resistance, Bacterial ; *Gene Transfer, Horizontal ; Meat/microbiology ; North Carolina ; Poultry/microbiology ; }, abstract = {The Center for Disease Control and Prevention identifies antimicrobial resistant (AMR) Campylobacter as a serious threat to U.S. public health due to high community burden, increased transmissibility, and limited treatability. The National Antimicrobial Resistance Monitoring System (NARMS) plays an important role in surveillance of AMR bacterial pathogens in humans, food animals and retail meats. This study investigated C. coli and C. jejuni from live food animals, poultry carcasses at production, and retail meat in North Carolina between January 2018-December 2019. Whole genome sequencing and bioinformatics were used for phenotypic and genotypic characterization to compare AMR profiles, virulence factors associated with Guillain-Barré Syndrome (GBS) (neuABC and cst-II or cst-III), and phylogenic linkage between 541 Campylobacter isolates (C. coli n = 343, C. jejuni n = 198). Overall, 90.4% (489/541) Campylobacter isolates tested positive for AMR genes, while 43% (233/541) carried resistance genes for three or more antibiotic classes and were classified molecularly multidrug resistant. AMR gene frequencies were highest against tetracyclines (64.3%), beta-lactams (63.6%), aminoglycosides (38.6%), macrolides (34.8%), quinolones (24.4%), lincosamides (13.5%), and streptothricins (5%). A total of 57.6% (114/198) C. jejuni carried GBS virulence factors, while three C. coli carried the C. jejuni-like lipooligosaccharide locus, neuABC and cst-II. Further evidence of C. coli and C. jejuni interspecies genomic exchange was observed in identical multilocus sequence typing, shared sequence type (ST) 7818 clonal complex 828, and identical species-indicator genes mapA, ceuE, and hipO. There was a significant increase in novel STs from 2018 to 2019 (2 in 2018 and 21 in 2019, p<0.002), illustrating variable Campylobacter genomes within food animal production. Introgression between C. coli and C. jejuni may aid pathogen adaption, lead to higher AMR and increase Campylobacter persistence in food processing. Future studies should further characterize interspecies gene transfer and evolutionary trends in food animal production to track evolving risks to public health.}, }
@article {pmid33571209, year = {2021}, author = {Ranjan, M and Khokhani, D and Nayaka, S and Srivastava, S and Keyser, ZP and Ranjan, A}, title = {Genomic diversity and organization of complex polysaccharide biosynthesis clusters in the genus Dickeya.}, journal = {PloS one}, volume = {16}, number = {2}, pages = {e0245727}, pmid = {33571209}, issn = {1932-6203}, mesh = {Base Sequence/genetics ; Dickeya/classification/*genetics/*metabolism ; Gene Transfer, Horizontal ; *Genetic Variation ; Genome, Bacterial ; *Multigene Family ; O Antigens/*biosynthesis/*genetics ; Open Reading Frames ; Phylogeny ; Plant Diseases/microbiology ; Sequence Homology ; }, abstract = {The pectinolytic genus Dickeya (formerly Erwinia chrysanthemi) comprises numerous pathogenic species which cause diseases in various crops and ornamental plants across the globe. Their pathogenicity is governed by complex multi-factorial processes of adaptive virulence gene regulation. Extracellular polysaccharides and lipopolysaccharides present on bacterial envelope surface play a significant role in the virulence of phytopathogenic bacteria. However, very little is known about the genomic location, diversity, and organization of the polysaccharide and lipopolysaccharide biosynthetic gene clusters in Dickeya. In the present study, we report the diversity and structural organization of the group 4 capsule (G4C)/O-antigen capsule, putative O-antigen lipopolysaccharide, enterobacterial common antigen, and core lipopolysaccharide biosynthesis clusters from 54 Dickeya strains. The presence of these clusters suggests that Dickeya has both capsule and lipopolysaccharide carrying O-antigen to their external surface. These gene clusters are key regulatory components in the composition and structure of the outer surface of Dickeya. The O-antigen capsule/group 4 capsule (G4C) coding region shows a variation in gene content and organization. Based on nucleotide sequence homology in these Dickeya strains, two distinct groups, G4C group I and G4C group II, exist. However, comparatively less variation is observed in the putative O-antigen lipopolysaccharide cluster in Dickeya spp. except for in Dickeya zeae. Also, enterobacterial common antigen and core lipopolysaccharide biosynthesis clusters are present mostly as conserved genomic regions. The variation in the O-antigen capsule and putative O-antigen lipopolysaccharide coding region in relation to their phylogeny suggests a role of multiple horizontal gene transfer (HGT) events. These multiple HGT processes might have been manifested into the current heterogeneity of O-antigen capsules and O-antigen lipopolysaccharides in Dickeya strains during its evolution.}, }
@article {pmid33570580, year = {2021}, author = {Patil, S and Kondabagil, K}, title = {Coevolutionary and Phylogenetic Analysis of Mimiviral Replication Machinery Suggest the Cellular Origin of Mimiviruses.}, journal = {Molecular biology and evolution}, volume = {38}, number = {5}, pages = {2014-2029}, pmid = {33570580}, issn = {1537-1719}, mesh = {*Biological Coevolution ; Gene Transfer, Horizontal ; Mimiviridae/*genetics ; Multidimensional Scaling Analysis ; Phylogeny ; *Selection, Genetic ; Viral Proteins/*genetics ; Virus Replication/*genetics ; }, abstract = {Mimivirus is one of the most complex and largest viruses known. The origin and evolution of Mimivirus and other giant viruses have been a subject of intense study in the last two decades. The two prevailing hypotheses on the origin of Mimivirus and other viruses are the reduction hypothesis, which posits that viruses emerged from modern unicellular organisms; whereas the virus-first hypothesis proposes viruses as relics of precellular forms of life. In this study, to gain insights into the origin of Mimivirus, we have carried out extensive phylogenetic, correlation, and multidimensional scaling analyses of the putative proteins involved in the replication of its 1.2-Mb large genome. Correlation analysis and multidimensional scaling methods were validated using bacteriophage, bacteria, archaea, and eukaryotic replication proteins before applying to Mimivirus. We show that a large fraction of mimiviral replication proteins, including polymerase B, clamp, and clamp loaders are of eukaryotic origin and are coevolving. Although phylogenetic analysis places some components along the lineages of phage and bacteria, we show that all the replication-related genes have been homogenized and are under purifying selection. Collectively our analysis supports the idea that Mimivirus originated from a complex cellular ancestor. We hypothesize that Mimivirus has largely retained complex replication machinery reminiscent of its progenitor while losing most of the other genes related to processes such as metabolism and translation.}, }
@article {pmid33570565, year = {2021}, author = {Moura de Sousa, JA and Pfeifer, E and Touchon, M and Rocha, EPC}, title = {Causes and Consequences of Bacteriophage Diversification via Genetic Exchanges across Lifestyles and Bacterial Taxa.}, journal = {Molecular biology and evolution}, volume = {38}, number = {6}, pages = {2497-2512}, pmid = {33570565}, issn = {1537-1719}, mesh = {Bacteriophages/*genetics/pathogenicity ; *Biological Evolution ; Gene Flow ; *Gene Transfer, Horizontal ; *Host-Pathogen Interactions ; Recombination, Genetic ; }, abstract = {Bacteriophages (phages) evolve rapidly by acquiring genes from other phages. This results in mosaic genomes. Here, we identify numerous genetic transfers between distantly related phages and aim at understanding their frequency, consequences, and the conditions favoring them. Gene flow tends to occur between phages that are enriched for recombinases, transposases, and nonhomologous end joining, suggesting that both homologous and illegitimate recombination contribute to gene flow. Phage family and host phyla are strong barriers to gene exchange, but phage lifestyle is not. Even if we observe four times more recent transfers between temperate phages than between other pairs, there is extensive gene flow between temperate and virulent phages, and between the latter. These predominantly involve virulent phages with large genomes previously classed as low gene flux, and lead to the preferential transfer of genes encoding functions involved in cell energetics, nucleotide metabolism, DNA packaging and injection, and virion assembly. Such exchanges may contribute to the observed twice larger genomes of virulent phages. We used genetic transfers, which occur upon coinfection of a host, to compare phage host range. We found that virulent phages have broader host ranges and can mediate genetic exchanges between narrow host range temperate phages infecting distant bacterial hosts, thus contributing to gene flow between virulent phages, as well as between temperate phages. This gene flow drastically expands the gene repertoires available for phage and bacterial evolution, including the transfer of functional innovations across taxa.}, }
@article {pmid33568758, year = {2021}, author = {Ormsby, MJ and Davies, RL}, title = {Diversification of OmpA and OmpF of Yersinia ruckeri is independent of the underlying species phylogeny and evidence of virulence-related selection.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {3493}, pmid = {33568758}, issn = {2045-2322}, support = {BB/I01554X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bacterial Outer Membrane Proteins/*metabolism ; Fish Diseases/virology ; Host Specificity/immunology ; Oncorhynchus mykiss/*genetics ; Phylogeny ; Serogroup ; Virulence/genetics/physiology ; Yersinia Infections/*virology ; Yersinia ruckeri/*virology ; }, abstract = {Yersinia ruckeri is the causative agent of enteric redmouth disease (ERM) which causes economically significant losses in farmed salmonids, especially Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss, Walbaum). However, very little is known about the genetic relationships of disease-causing isolates in these two host species or about factors responsible for disease. Phylogenetic analyses of 16 representative isolates based on the nucleotide sequences of 19 housekeeping genes suggests that pathogenic Atlantic salmon and rainbow trout isolates represent distinct host-specific lineages. However, the apparent phylogenies of certain isolates has been influenced by horizontal gene transfer and recombinational exchange. Splits decomposition analysis demonstrated a net-like phylogeny based on the housekeeping genes, characteristic of recombination. Comparative analysis of the distribution of individual housekeeping gene alleles across the isolates demonstrated evidence of genomic mosaicism and recombinational exchange involving certain Atlantic salmon and rainbow trout isolates. Comparative nucleotide sequence analysis of the key outer membrane protein genes ompA and ompF revealed that the corresponding gene trees were both non-congruent with respect to the housekeeping gene phylogenies providing evidence that horizontal gene transfer has influenced the evolution of both these surface protein-encoding genes. Analysis of inferred amino acid sequence variation in OmpA identified a single variant, OmpA.1, that was present in serotype O1 and O8 isolates representing typical pathogenic strains in rainbow trout and Atlantic salmon, respectively. In particular, the sequence of surface-exposed loop 3 differed by seven amino acids to that of other Y. ruckeri isolates. These findings suggest that positive selection has likely influenced the presence of OmpA.1 in these isolates and that loop 3 may play an important role in virulence. Amino acid sequence variation of OmpF was greater than that of OmpA and was similarly restricted mainly to the surface-exposed loops. Two OmpF variants, OmpF.1 and OmpF.2, were associated with pathogenic rainbow trout and Atlantic salmon isolates, respectively. These OmpF proteins had very similar amino acid sequences suggesting that positive evolutionary pressure has also favoured the selection of these variants in pathogenic strains infecting both species.}, }
@article {pmid33565580, year = {2021}, author = {Kloub, L and Gosselin, S and Fullmer, M and Graf, J and Gogarten, JP and Bansal, MS}, title = {Systematic Detection of Large-Scale Multigene Horizontal Transfer in Prokaryotes.}, journal = {Molecular biology and evolution}, volume = {38}, number = {6}, pages = {2639-2659}, pmid = {33565580}, issn = {1537-1719}, mesh = {Aeromonas/*genetics ; *Gene Transfer, Horizontal ; Genomics/*methods ; *Software ; }, abstract = {Horizontal gene transfer (HGT) is central to prokaryotic evolution. However, little is known about the "scale" of individual HGT events. In this work, we introduce the first computational framework to help answer the following fundamental question: How often does more than one gene get horizontally transferred in a single HGT event? Our method, called HoMer, uses phylogenetic reconciliation to infer single-gene HGT events across a given set of species/strains, employs several techniques to account for inference error and uncertainty, combines that information with gene order information from extant genomes, and uses statistical analysis to identify candidate horizontal multigene transfers (HMGTs) in both extant and ancestral species/strains. HoMer is highly scalable and can be easily used to infer HMGTs across hundreds of genomes. We apply HoMer to a genome-scale data set of over 22,000 gene families from 103 Aeromonas genomes and identify a large number of plausible HMGTs of various scales at both small and large phylogenetic distances. Analysis of these HMGTs reveals interesting relationships between gene function, phylogenetic distance, and frequency of multigene transfer. Among other insights, we find that 1) the observed relative frequency of HMGT increases as divergence between genomes increases, 2) HMGTs often have conserved gene functions, and 3) rare genes are frequently acquired through HMGT. We also analyze in detail HMGTs involving the zonula occludens toxin and type III secretion systems. By enabling the systematic inference of HMGTs on a large scale, HoMer will facilitate a more accurate and more complete understanding of HGT and microbial evolution.}, }
@article {pmid33563283, year = {2021}, author = {Sela, I and Wolf, YI and Koonin, EV}, title = {Assessment of assumptions underlying models of prokaryotic pangenome evolution.}, journal = {BMC biology}, volume = {19}, number = {1}, pages = {27}, pmid = {33563283}, issn = {1741-7007}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Evolution, Molecular ; *Metagenome ; Models, Genetic ; }, abstract = {BACKGROUND: The genomes of bacteria and archaea evolve by extensive loss and gain of genes which, for any group of related prokaryotic genomes, result in the formation of a pangenome with the universal, asymmetrical U-shaped distribution of gene commonality. However, the evolutionary factors that define the specific shape of this distribution are not thoroughly understood.<br><br>RESULTS: We investigate the fit of simple models of genome evolution to the empirically observed gene commonality distributions and genome intersections for 33 groups of closely related bacterial genomes. A model with an infinite external gene pool available for gene acquisition and constant genome size (IGP-CGS model), and two gene turnover rates, one for slow- and the other one for fast-evolving genes, allows two approaches to estimate the parameters for gene content dynamics. One is by fitting the model prediction to the distribution of the number of genes shared by precisely k genomes (gene commonality distribution) and another by analyzing the distribution of the number of genes common for k genome sets (k-cores). Both approaches produce a comparable overall quality of fit, although the former significantly overestimates the number of the universally conserved genes, while the latter overestimates the number of singletons. We further explore the effect of dropping each of the assumptions of the IGP-CGS model on the fit to the gene commonality distributions and show that models with either a finite gene pool or unequal rates of gene loss and gain (greater gene loss rate) eliminate the overestimate of the number of singletons or the core genome size.<br><br>CONCLUSIONS: We examine the assumptions that are usually adopted for modeling the evolution of the U-shaped gene commonality distributions in prokaryote genomes, namely, those of infinitely many genes and constant genome size. The combined analysis of genome intersections and gene commonality suggests that at least one of these assumptions is invalid. The violation of both these assumptions reflects the limited ability of prokaryotes to gain new genes. This limitation seems to stem, at least partly, from the horizontal gene transfer barrier, i.e., the cost of accommodation of foreign genes by prokaryotes. Further development of models taking into account the complexity of microbial evolution is necessary for an improved understanding of the evolution of prokaryotes.}, }
@article {pmid33558686, year = {2021}, author = {Song, W and Wemheuer, B and Steinberg, PD and Marzinelli, EM and Thomas, T}, title = {Contribution of horizontal gene transfer to the functionality of microbial biofilm on a macroalgae.}, journal = {The ISME journal}, volume = {15}, number = {3}, pages = {807-817}, pmid = {33558686}, issn = {1751-7370}, mesh = {Bacteria/genetics ; Biofilms ; *Gene Transfer, Horizontal ; Plankton ; *Seaweed ; }, abstract = {Horizontal gene transfer (HGT) is thought to be an important driving force for microbial evolution and niche adaptation and has been show in vitro to occur frequently in biofilm communities. However, the extent to which HGT takes place and what functions are being transferred in more complex and natural biofilm systems remains largely unknown. To address this issue, we investigated here HGT and enrichment of gene functions in the biofilm community of the common kelp (macroalgae) Ecklonia radiata in comparison to microbial communities in the surrounding seawater. We found that HGTs in the macroalgal biofilms were dominated by transfers between bacterial members of the same class or order and frequently involved genes for nutrient transport, sugar and phlorotannin degradation as well as stress responses, all functions that would be considered beneficial for bacteria living in this particular niche. HGT did not appear to be driven by mobile gene elements, indicating rather an involvement of unspecific DNA uptake (e.g. natural transformation). There was also a low overlap between the gene functions subject to HGT and those enriched in the biofilm community in comparison to planktonic community members. This indicates that much of the functionality required for bacteria to live in an E. radiata biofilm might be derived from vertical or environmental transmissions of symbionts. This study enhances our understanding of the relative role of evolutionary and ecological processes in driving community assembly and genomic diversity of biofilm communities.}, }
@article {pmid33558390, year = {2021}, author = {Kuprat, T and Ortjohann, M and Johnsen, U and Schönheit, P}, title = {Glucose Metabolism and Acetate Switch in Archaea: the Enzymes in Haloferax volcanii.}, journal = {Journal of bacteriology}, volume = {203}, number = {8}, pages = {}, pmid = {33558390}, issn = {1098-5530}, mesh = {Acetate-CoA Ligase/genetics/metabolism ; Acetates/*metabolism ; Acetyl Coenzyme A/metabolism ; Archaeal Proteins/genetics/metabolism ; Glucose/*metabolism ; Haloferax volcanii/*enzymology/genetics/growth &amp; development/metabolism ; Phosphoenolpyruvate Carboxylase/genetics/metabolism ; Phosphoglycerate Mutase/genetics/metabolism ; Phosphopyruvate Hydratase/genetics/metabolism ; Pyruvic Acid/metabolism ; }, abstract = {The halophilic archaeon Haloferax volcanii has been proposed to degrade glucose via the semiphosphorylative Entner-Doudoroff (spED) pathway. Following our previous studies on key enzymes of this pathway, we now focus on the characterization of enzymes involved in 3-phosphoglycerate conversion to pyruvate, in anaplerosis, and in acetyl coenzyme A (acetyl-CoA) formation from pyruvate. These enzymes include phosphoglycerate mutase, enolase, pyruvate kinase, phosphoenolpyruvate carboxylase, and pyruvate-ferredoxin oxidoreductase. The essential function of these enzymes were shown by transcript analyses and growth experiments with respective deletion mutants. Furthermore, we show that H. volcanii-during aerobic growth on glucose-excreted significant amounts of acetate, which was consumed in the stationary phase (acetate switch). The enzyme catalyzing the conversion of acetyl-CoA to acetate as part of the acetate overflow mechanism, an ADP-forming acetyl-CoA synthetase (ACD), was characterized. The functional involvement of ACD in acetate formation and of AMP-forming acetyl-CoA synthetases (ACSs) in activation of excreted acetate was proven by using respective deletion mutants. Together, the data provide a comprehensive analysis of enzymes of the spED pathway and of anaplerosis and report the first genetic evidence of the functional involvement of enzymes of the acetate switch in archaea.IMPORTANCE In this work, we provide a comprehensive analysis of glucose degradation via the semiphosphorylative Entner-Doudoroff pathway in the haloarchaeal model organism Haloferax volcanii The study includes transcriptional analyses, growth experiments with deletion mutants. and characterization of all enzymes involved in the conversion of 3-phosphoglycerate to acetyl coenzyme A (acetyl-CoA) and in anaplerosis. Phylogenetic analyses of several enzymes indicate various lateral gene transfer events from bacteria to haloarchaea. Furthermore, we analyzed the key players involved in the acetate switch, i.e., in the formation (overflow) and subsequent consumption of acetate during aerobic growth on glucose. Together, the data provide novel aspects of glucose degradation, anaplerosis, and acetate switch in H. volcanii and thus expand our understanding of the unusual sugar metabolism in archaea.}, }
@article {pmid33558368, year = {2021}, author = {Bowman, JL and Flores Sandoval, E and Kato, H}, title = {On the Evolutionary Origins of Land Plant Auxin Biology.}, journal = {Cold Spring Harbor perspectives in biology}, volume = {13}, number = {6}, pages = {}, pmid = {33558368}, issn = {1943-0264}, mesh = {*Evolution, Molecular ; Indoleacetic Acids/*metabolism ; Plants/enzymology/*genetics ; }, abstract = {Indole-3-acetic acid, that is, auxin, is a molecule found in a broad phylogenetic distribution of organisms, from bacteria to eukaryotes. In the ancestral land plant auxin was co-opted to be the paramount phytohormone mediating tropic responses and acting as a facilitator of developmental decisions throughout the life cycle. The evolutionary origins of land plant auxin biology genes can now be traced with reasonable clarity. Genes encoding the two enzymes of the land plant auxin biosynthetic pathway arose in the ancestral land plant by a combination of horizontal gene transfer from bacteria and possible neofunctionalization following gene duplication. Components of the auxin transcriptional signaling network have their origins in ancestral alga genes, with gene duplication and neofunctionalization of key domains allowing integration of a portion of the preexisting transcriptional network with auxin. Knowledge of the roles of orthologous genes in extant charophycean algae is lacking, but could illuminate the ancestral functions of both auxin and the co-opted transcriptional network.}, }
@article {pmid33556078, year = {2021}, author = {Asplund-Samuelsson, J and Hudson, EP}, title = {Wide range of metabolic adaptations to the acquisition of the Calvin cycle revealed by comparison of microbial genomes.}, journal = {PLoS computational biology}, volume = {17}, number = {2}, pages = {e1008742}, pmid = {33556078}, issn = {1553-7358}, mesh = {Carbon Cycle ; Carbon Dioxide/chemistry ; Escherichia coli/metabolism ; Gene Transfer, Horizontal ; Genetic Engineering/methods ; Genome, Archaeal ; *Genome, Bacterial ; Genome, Microbial ; Open Reading Frames ; Oxygen Consumption ; Photochemistry/methods ; Photosynthesis/*physiology ; Phylogeny ; Reproducibility of Results ; Ribulose-Bisphosphate Carboxylase/metabolism ; }, abstract = {Knowledge of the genetic basis for autotrophic metabolism is valuable since it relates to both the emergence of life and to the metabolic engineering challenge of incorporating CO2 as a potential substrate for biorefining. The most common CO2 fixation pathway is the Calvin cycle, which utilizes Rubisco and phosphoribulokinase enzymes. We searched thousands of microbial genomes and found that 6.0% contained the Calvin cycle. We then contrasted the genomes of Calvin cycle-positive, non-cyanobacterial microbes and their closest relatives by enrichment analysis, ancestral character estimation, and random forest machine learning, to explore genetic adaptations associated with acquisition of the Calvin cycle. The Calvin cycle overlaps with the pentose phosphate pathway and glycolysis, and we could confirm positive associations with fructose-1,6-bisphosphatase, aldolase, and transketolase, constituting a conserved operon, as well as ribulose-phosphate 3-epimerase, ribose-5-phosphate isomerase, and phosphoglycerate kinase. Additionally, carbohydrate storage enzymes, carboxysome proteins (that raise CO2 concentration around Rubisco), and Rubisco activases CbbQ and CbbX accompanied the Calvin cycle. Photorespiration did not appear to be adapted specifically for the Calvin cycle in the non-cyanobacterial microbes under study. Our results suggest that chemoautotrophy in Calvin cycle-positive organisms was commonly enabled by hydrogenase, and less commonly ammonia monooxygenase (nitrification). The enrichment of specific DNA-binding domains indicated Calvin-cycle associated genetic regulation. Metabolic regulatory adaptations were illustrated by negative correlation to AraC and the enzyme arabinose-5-phosphate isomerase, which suggests a downregulation of the metabolite arabinose-5-phosphate, which may interfere with the Calvin cycle through enzyme inhibition and substrate competition. Certain domains of unknown function that were found to be important in the analysis may indicate yet unknown regulatory mechanisms in Calvin cycle-utilizing microbes. Our gene ranking provides targets for experiments seeking to improve CO2 fixation, or engineer novel CO2-fixing organisms.}, }
@article {pmid33555470, year = {2021}, author = {Cheng, J and Tang, X and Liu, C}, title = {Bacterial communities regulate temporal variations of the antibiotic resistome in soil following manure amendment.}, journal = {Environmental science and pollution research international}, volume = {28}, number = {23}, pages = {29241-29252}, pmid = {33555470}, issn = {1614-7499}, support = {2016YFD0800203//National Key Research and Development Program of China/ ; 2018SZDZX0029//Major Science and Technology Program of Sichuan Province/ ; 41771521//National Natural Science Foundation of China/ ; 42007361//National Natural Science Foundation of China/ ; SDS-135-1702//135 Strategic Program of the Institute of Mountain Hazards and Environment/ ; }, mesh = {Animals ; Anti-Bacterial Agents ; Ecosystem ; Genes, Bacterial ; *Manure ; *Soil ; Soil Microbiology ; Swine ; }, abstract = {The increasing emergence of antibiotic-resistant genes (ARGs) represents a global threat to human health. Land application of animal manure is known to contribute considerably to the propagation and dispersal of antibiotic resistance in agro-ecosystems. Yet, the primary determinants of the fate of the soil resistome remain obscure. In this study, a pot experiment was conducted to examine temporal changes in ARGs, mobile genetic elements (MGEs), and bacterial communities in a weakly developed loamy soil (an entisol known as calcareous purple soil) upon addition of pig or chicken manure. On the day of manure application, substantial increases in the diversity and relative abundance of ARGs were observed in soil amended with raw pig manure. At the same time, no obvious changes were observed for soil amended with chicken manure. Antibiotic resistance in pig manure-amended soils rapidly decreased over time to a level that was still higher than that of unamended soil at 100 days after manure application. The results of the Mantel test and Procrustes analysis indicated that ARG profiles in soil were significantly correlated with the structure of the bacterial phylogeny. Variation partitioning analysis further revealed that the bacterial community played a major role in regulating the temporal changes in ARGs in soil following manure application. Increased numbers and relative abundances of MGEs and their significant positive correlations with ARGs were observed, which suggest that a potential contribution from lateral gene transfer to the persistence and spread of ARGs should not be overlooked. Overall, our findings provide a better understanding of the mechanisms underlying the dynamics of ARGs in entisols following manure application and have practical implications for managing manure applications in entisols of the study area and other areas.}, }
@article {pmid33552448, year = {2021}, author = {Yakimov, A and Bakhlanova, I and Baitin, D}, title = {Targeting evolution of antibiotic resistance by SOS response inhibition.}, journal = {Computational and structural biotechnology journal}, volume = {19}, number = {}, pages = {777-783}, pmid = {33552448}, issn = {2001-0370}, abstract = {Antibiotic resistance is acquired in response to antibiotic therapy by activating SOS-depended mutagenesis and horizontal gene transfer pathways. Compounds able to inhibit SOS response are extremely important to develop new combinatorial strategies aimed to block mutagenesis. The regulators of homologous recombination involved in the processes of DNA repair should be considered as potential targets for blocking. This review highlights the current knowledge of the protein targets for the evolution of antibiotic resistance and the inhibitory effects of some new compounds on this pathway.}, }
@article {pmid33552095, year = {2020}, author = {Pratap, A and Das, A and Kumar, S and Gupta, S}, title = {Current Perspectives on Introgression Breeding in Food Legumes.}, journal = {Frontiers in plant science}, volume = {11}, number = {}, pages = {589189}, pmid = {33552095}, issn = {1664-462X}, abstract = {Food legumes are important for defeating malnutrition and sustaining agri-food systems globally. Breeding efforts in legume crops have been largely confined to the exploitation of genetic variation available within the primary genepool, resulting in narrow genetic base. Introgression as a breeding scheme has been remarkably successful for an array of inheritance and molecular studies in food legumes. Crop wild relatives (CWRs), landraces, and exotic germplasm offer great potential for introgression of novel variation not only to widen the genetic base of the elite genepool for continuous incremental gains over breeding cycles but also to discover the cryptic genetic variation hitherto unexpressed. CWRs also harbor positive quantitative trait loci (QTLs) for improving agronomic traits. However, for transferring polygenic traits, "specialized population concept" has been advocated for transferring QTLs from CWR into elite backgrounds. Recently, introgression breeding has been successful in developing improved cultivars in chickpea (Cicer arietinum), pigeonpea (Cajanus cajan), peanut (Arachis hypogaea), lentil (Lens culinaris), mungbean (Vigna radiata), urdbean (Vigna mungo), and common bean (Phaseolus vulgaris). Successful examples indicated that the usable genetic variation could be exploited by unleashing new gene recombination and hidden variability even in late filial generations. In mungbean alone, distant hybridization has been deployed to develop seven improved commercial cultivars, whereas in urdbean, three such cultivars have been reported. Similarly, in chickpea, three superior cultivars have been developed from crosses between C. arietinum and Cicer reticulatum. Pigeonpea has benefited the most where different cytoplasmic male sterility genes have been transferred from CWRs, whereas a number of disease-resistant germplasm have also been developed in Phaseolus. As vertical gene transfer has resulted in most of the useful gene introgressions of practical importance in food legumes, the horizontal gene transfer through transgenic technology, somatic hybridization, and, more recently, intragenesis also offer promise. The gains through introgression breeding are significant and underline the need of bringing it in the purview of mainstream breeding while deploying tools and techniques to increase the recombination rate in wide crosses and reduce the linkage drag. The resurgence of interest in introgression breeding needs to be capitalized for development of commercial food legume cultivars.}, }
@article {pmid33552002, year = {2020}, author = {García-Ulloa, MI and Escalante, AE and Moreno-Letelier, A and Eguiarte, LE and Souza, V}, title = {Evolutionary Rescue of an Environmental Pseudomonas otitidis in Response to Anthropogenic Perturbation.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {563885}, pmid = {33552002}, issn = {1664-302X}, abstract = {Anthropogenic perturbations introduce novel selective pressures to natural environments, impacting the genomic variability of organisms and thus altering the evolutionary trajectory of populations. Water overexploitation for agricultural purposes and defective policies in Cuatro Cienegas, Coahuila, Mexico, have strongly impacted its water reservoir, pushing entire hydrological systems to the brink of extinction along with their native populations. Here, we studied the effects of continuous water overexploitation on an environmental aquatic lineage of Pseudomonas otitidis over a 13-year period which encompasses three desiccation events. By comparing the genomes of a population sample from 2003 (original state) and 2015 (perturbed state), we analyzed the demographic history and evolutionary response to perturbation of this lineage. Through coalescent simulations, we obtained a demographic model of contraction-expansion-contraction which points to the occurrence of an evolutionary rescue event. Loss of genomic and nucleotide variation alongside an increment in mean and variance of Tajima's D, characteristic of sudden population expansions, support this observation. In addition, a significant increase in recombination rate (R/θ) was observed, pointing to horizontal gene transfer playing a role in population recovery. Furthermore, the gain of phosphorylation, DNA recombination, small-molecule metabolism and transport and loss of biosynthetic and regulatory genes suggest a functional shift in response to the environmental perturbation. Despite subsequent sampling events in the studied site, no pseudomonad was found until the lagoon completely dried in 2017. We speculate about the causes of P. otitidis final decline or possible extinction. Overall our results are evidence of adaptive responses at the genomic level of bacterial populations in a heavily exploited aquifer.}, }
@article {pmid33549716, year = {2021}, author = {Gonçalves, OS and Santana, MF}, title = {The coexistence of monopartite integrative and conjugative elements in the genomes of Acidobacteria.}, journal = {Gene}, volume = {777}, number = {}, pages = {145476}, doi = {10.1016/j.gene.2021.145476}, pmid = {33549716}, issn = {1879-0038}, mesh = {Acidobacteria/*genetics ; Conjugation, Genetic/genetics ; DNA Transposable Elements/*genetics ; DNA, Bacterial/genetics ; Databases, Genetic ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {Soil bacteria can rapidly adapt to environmental perturbations through horizontal gene transfer. Acidobacteria is one of the most persistent dominant phyla in the soil. However, the role of these organisms in terrestrial ecosystems remains elusive. Here we identified and describe the integrative and conjugative elements (ICEs) in the published complete genomes of Acidobacteria. In total, ten novel ICEs were identified, in which nine were found integrated as three separated monopartite ICEs in the single chromosome sequences of three Acidobacteria. These ICEs carry a repertoire of genes with potential environmental roles, including heavy metal resistance, iron uptake, secondary metabolism, and antibiotic resistance. To our knowledge, these are the first evidence of three monopartite ICEs identified in the single chromosome, and this might be due to the absence of recognizable entry exclusion systems. We hypothesis that the coexistence of multiples ICEs in the chromosome of Acidobacteria might reflect a major advantage for the survival, resistance, and persistence of phylum in the environment.}, }
@article {pmid33547987, year = {2021}, author = {Aregbesola, OA and Kumar, A and Mokoena, MP and Olaniran, AO}, title = {Whole-genome sequencing, genome mining, metabolic reconstruction and evolution of pentachlorophenol and other xenobiotic degradation pathways in Bacillus tropicus strain AOA-CPS1.}, journal = {Functional &amp; integrative genomics}, volume = {21}, number = {2}, pages = {171-193}, pmid = {33547987}, issn = {1438-7948}, support = {94036//National Research Foundation/ ; 92803//National Research Foundation/ ; }, mesh = {Bacillus/*genetics ; *Biodegradation, Environmental ; Genome, Bacterial/*genetics ; Molecular Sequence Annotation ; Pentachlorophenol/metabolism ; South Africa ; *Whole Genome Sequencing ; Xenobiotics/metabolism ; }, abstract = {A pentachlorophenol degrading bacterium was isolated from effluent of a wastewater treatment plant in Durban, South Africa, and identified as Bacillus tropicus strain AOA-CPS1 (BtAOA). The isolate degraded 29% of pentachlorophenol (PCP) within 9 days at an initial PCP concentration of 100 mg L[-1] and 62% of PCP when the initial concentration was set at 350 mg L[-1]. The whole-genome of BtAOA was sequenced using Pacific Biosciences RS II sequencer with the Single Molecule, Real-Time (SMRT) Link (version 7.0.1.66975) and analysed using the HGAP4-de-novo assembly application. The contigs were annotated at NCBI, RASTtk and PROKKA prokaryotic genome annotation pipelines. The BtAOA genome is comprised of a 5,246,860-bp chromosome and a 58,449-bp plasmid with a GC content of 35.4%. The metabolic reconstruction for BtAOA showed that the organism has been naturally exposed to various chlorophenolic compounds including PCP and other xenobiotics. The chromosome encodes genes for core processes, stress response and PCP catabolic genes. Analogues of PCP catabolic gene (cpsBDCAE, and p450) sequences were identified from the NCBI annotation data, PCR-amplified from the whole genome of BtAOA, cloned into pET15b expression vector, overexpressed in E. coli BL21 (DE3) expression host, purified and characterized. Sequence mining and comparative analysis of the metabolic reconstruction of the BtAOA genome with closely related strains suggests that the operon encoding the first two enzymes in the PCP degradation pathway were acquired from a pre-existing pterin-carbinolamine dehydratase subsystem. The other two enzymes were recruited via horizontal gene transfer (HGT) from the pool of hypothetical proteins with no previous specific function, while the last enzyme was recruited from pre-existing enzymes from the TCA or serine-glyoxalase cycle via HGT events. This study provides a comprehensive understanding of the role of BtAOA in PCP degradation and its potential exploitation for bioremediation of other xenobiotic compounds.}, }
@article {pmid33547293, year = {2021}, author = {Undheim, EAB and Jenner, RA}, title = {Phylogenetic analyses suggest centipede venom arsenals were repeatedly stocked by horizontal gene transfer.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {818}, pmid = {33547293}, issn = {2041-1723}, mesh = {Animals ; Arthropod Proteins/biosynthesis/classification/*genetics ; Arthropod Venoms/biosynthesis/classification/*genetics ; Chilopoda/classification/*genetics/microbiology/pathogenicity ; Gene Expression ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genes, Fungal ; Phylogeny ; Proteomics/methods ; Transcriptome ; }, abstract = {Venoms have evolved over a hundred times in animals. Venom toxins are thought to evolve mostly by recruitment of endogenous proteins with physiological functions. Here we report phylogenetic analyses of venom proteome-annotated venom gland transcriptome data, assisted by genomic analyses, to show that centipede venoms have recruited at least five gene families from bacterial and fungal donors, involving at least eight horizontal gene transfer events. These results establish centipedes as currently the only known animals with venoms used in predation and defence that contain multiple gene families derived from horizontal gene transfer. The results also provide the first evidence for the implication of horizontal gene transfer in the evolutionary origin of venom in an animal lineage. Three of the bacterial gene families encode virulence factors, suggesting that horizontal gene transfer can provide a fast track channel for the evolution of novelty by the exaptation of bacterial weapons into animal venoms.}, }
@article {pmid33545274, year = {2021}, author = {Palazzo, A and Escuder, E and D'Addabbo, P and Lovero, D and Marsano, RM}, title = {A genomic survey of Tc1-mariner transposons in nematodes suggests extensive horizontal transposon transfer events.}, journal = {Molecular phylogenetics and evolution}, volume = {158}, number = {}, pages = {107090}, doi = {10.1016/j.ympev.2021.107090}, pmid = {33545274}, issn = {1095-9513}, mesh = {Animals ; Biological Evolution ; DNA Transposable Elements/*genetics ; Databases, Genetic ; Gene Transfer, Horizontal ; *Genome ; Nematoda/classification/*genetics ; Phylogeny ; RNA, Ribosomal, 18S/classification/genetics ; }, abstract = {The number of reports concerning horizontal transposon transfers (HTT) in metazoan species is considerably increased, alongside with the exponential growth of genomic sequence data However, our understanding of the mechanisms of such phenomenon is still at an early stage. Nematodes constitute an animal phylum successfully adapted to almost every ecosystem and for this reason could potentially contribute to spreading the genetic information through horizontal transfer. To date, few studies describe HTT of nematode retrotransposons. This is due to the lack of annotation of transposable elements in the sequenced nematode genomes, especially DNA transposons, which are acknowledged as the best horizontal travelers among mobile sequences. We have therefore started a survey of DNA transposons and their possible involvement in HTT in sequenced nematode genomes. Here, we describe 83 new Tc1/mariner elements distributed in 17 nematode species. Among them, nine families were possibly horizontally transferred between nematodes and the most diverse animal species, including ants as preferred partner of HTT. The results obtained suggest that HTT events involving nematodes Tc1/mariner elements are not uncommon, and that nematodes could have a possible role as transposon reservoir that, in turn, can be redistributed among animal genomes. Overall, this could be relevant to understand how the inter-species genetic flows shape the landscape of genetic variation of organisms inhabiting specific environmental communities.}, }
@article {pmid33544239, year = {2021}, author = {Djidjou-Demasse, R and Alizon, S and Sofonea, MT}, title = {Within-host bacterial growth dynamics with both mutation and horizontal gene transfer.}, journal = {Journal of mathematical biology}, volume = {82}, number = {3}, pages = {16}, pmid = {33544239}, issn = {1432-1416}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Bacteria/drug effects/genetics/growth &amp; development ; *Bacterial Infections/microbiology ; Drug Resistance, Bacterial/genetics ; *Gene Transfer, Horizontal/genetics ; *Mutation/genetics ; Plasmids ; }, abstract = {The evolution and emergence of antibiotic resistance is a major public health concern. The understanding of the within-host microbial dynamics combining mutational processes, horizontal gene transfer and resource consumption, is one of the keys to solving this problem. We analyze a generic model to rigorously describe interactions dynamics of four bacterial strains: one fully sensitive to the drug, one with mutational resistance only, one with plasmidic resistance only, and one with both resistances. By defining thresholds numbers (i.e. each strain's effective reproduction and each strain's transition threshold numbers), we first express conditions for the existence of non-trivial stationary states. We find that these thresholds mainly depend on bacteria quantitative traits such as nutrient consumption ability, growth conversion factor, death rate, mutation (forward or reverse), and segregational loss of plasmid probabilities (for plasmid-bearing strains). Next, concerning the order in the set of strain's effective reproduction thresholds numbers, we show that the qualitative dynamics of the model range from the extinction of all strains, coexistence of sensitive and mutational resistance strains, to the coexistence of all strains at equilibrium. Finally, we go through some applications of our general analysis depending on whether bacteria strains interact without or with drug action (either cytostatic or cytotoxic).}, }
@article {pmid33542314, year = {2021}, author = {Vezina, B and Al-Harbi, H and Ramay, HR and Soust, M and Moore, RJ and Olchowy, TWJ and Alawneh, JI}, title = {Sequence characterisation and novel insights into bovine mastitis-associated Streptococcus uberis in dairy herds.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {3046}, pmid = {33542314}, issn = {2045-2322}, mesh = {Animals ; Anti-Bacterial Agents/adverse effects/therapeutic use ; Australia/epidemiology ; Cattle ; Dairy Products ; Drug Resistance, Bacterial/*genetics ; Female ; Genotype ; Humans ; Mastitis, Bovine/*genetics/microbiology/prevention &amp; control ; Molecular Epidemiology ; Multilocus Sequence Typing ; Streptococcal Infections/drug therapy/*genetics/microbiology ; Streptococcus/*genetics/pathogenicity ; }, abstract = {Streptococcus uberis is one of the most frequent mastitis-causing pathogens isolated from dairy cows. Further understanding of S. uberis genetics may help elucidate the disease pathogenesis. We compared the genomes of S. uberis isolates cultured from dairy cows located in distinctly different geographic regions of Australia. All isolates had novel multi locus sequence types (MLST) indicating a highly diverse population of S. uberis. Global clonal complexes (GCC) were more conserved. GCC ST86 and GCC ST143 represented 30% of the total isolates (n = 27) and were clustered within different geographic regions. Core genome phylogeny revealed low phylogenetic clustering by region, isolation source, and MLST. Identification of putative sortase (srtA) substrates and generation of a custom putative virulence factor database revealed genes which may explain the affinity of S. uberis for mammary tissue, evasion of antimicrobial efforts and disease pathogenesis. Of 27 isolates, four contained antibiotic resistance genes including an antimicrobial resistance cluster containing mel/mef(A), mrsE, vatD, lnuD, and transposon-mediated lnuC was also identified. These are novel genes for S. uberis, which suggests interspecies lateral gene transfer. The presence of resistance genes across the two geographic regions tested within one country supports the need for a careful, tailored, implementation and monitoring of antimicrobial stewardship.}, }
@article {pmid33541262, year = {2021}, author = {Pischedda, E and Crava, C and Carlassara, M and Zucca, S and Gasmi, L and Bonizzoni, M}, title = {ViR: a tool to solve intrasample variability in the prediction of viral integration sites using whole genome sequencing data.}, journal = {BMC bioinformatics}, volume = {22}, number = {1}, pages = {45}, pmid = {33541262}, issn = {1471-2105}, support = {682394//H2020 European Research Council/ ; R1623HZAH5//MIUR/ ; RGP0007/2017//Human Frontier Science Program/ ; }, mesh = {Animals ; Computational Biology ; Genome, Viral ; Genomics ; Humans ; *Mosquito Vectors ; *Virus Integration/genetics ; *Whole Genome Sequencing ; }, abstract = {BACKGROUND: Several bioinformatics pipelines have been developed to detect sequences from viruses that integrate into the human genome because of the health relevance of these integrations, such as in the persistence of viral infection and/or in generating genotoxic effects, often progressing into cancer. Recent genomics and metagenomics analyses have shown that viruses also integrate into the genome of non-model organisms (i.e., arthropods, fish, plants, vertebrates). However, rarely studies of endogenous viral elements (EVEs) in non-model organisms have gone beyond their characterization from reference genome assemblies. In non-model organisms, we lack a thorough understanding of the widespread occurrence of EVEs and their biological relevance, apart from sporadic cases which nevertheless point to significant roles of EVEs in immunity and regulation of expression. The concomitance of repetitive DNA, duplications and/or assembly fragmentations in a genome sequence and intrasample variability in whole-genome sequencing (WGS) data could determine misalignments when mapping data to a genome assembly. This phenomenon hinders our ability to properly identify integration sites.<br><br>RESULTS: To fill this gap, we developed ViR, a pipeline which solves the dispersion of reads due to intrasample variability in sequencing data from both single and pooled DNA samples thus ameliorating the detection of integration sites. We tested ViR to work with both in silico and real sequencing data from a non-model organism, the arboviral vector Aedes albopictus. Potential viral integrations predicted by ViR were molecularly validated supporting the accuracy of ViR results.<br><br>CONCLUSION: ViR will open new venues to explore the biology of EVEs, especially in non-model organisms. Importantly, while we generated ViR with the identification of EVEs in mind, its application can be extended to detect any lateral transfer event providing an ad-hoc sequence to interrogate.}, }
@article {pmid33540794, year = {2021}, author = {Feng, H and Zhou, D and Daly, P and Wang, X and Wei, L}, title = {Characterization and Functional Importance of Two Glycoside Hydrolase Family 16 Genes from the Rice White Tip Nematode Aphelenchoides besseyi.}, journal = {Animals : an open access journal from MDPI}, volume = {11}, number = {2}, pages = {}, pmid = {33540794}, issn = {2076-2615}, support = {31871943//National Natural Science Foundation of China/ ; 4911406//Key Lab of Food Quality and Safety of Jiangsu Province - State Key Laboratory Breeding Base/ ; }, abstract = {The glycoside hydrolase family 16 (GH16) is widely found in prokaryotes and eukaryotes, and hydrolyzes the β-1,3(4)-linkages in polysaccharides. Notably, the rice white tip nematode Aphelenchoides besseyi harbors a higher number of GH16s compared with other plant-parasitic nematodes. In this work, two GH16 genes, namely AbGH16-1 and AbGH16-2, were isolated and characterized from A. besseyi. The deduced amino acid sequences of AbGH16-1 and AbGH16-2 contained an N-terminal signal peptide and a fungal Lam16A glucanase domain. Phylogenetic analysis revealed that AbGH16-1 and AbGH16-2 clustered with ascomycete GH16s, suggesting AbGH16-1 and AbGH16-2 were acquired by horizontal gene transfer from fungi. In situ hybridization showed that both AbGH16-1 and AbGH16-2 were specifically expressed in the nematode gonads, correlating with qPCR analysis that showed the high transcript levels of the two genes in the female nematodes. AbGH16-1 and AbGH16-2 were also significantly induced in nematodes feeding on Botrytis cinerea. Characterization of the recombinant protein showed AbGH16-1 and AbGH16-2 displayed pronounced inhibition of both conidial germination and germ tube elongation of B. cinerea. In addition, silencing of AbGH16-1 and AbGH16-2 by RNA interference significantly decreased the reproduction ability of A. besseyi and had a profound impact on the development process of offspring in this nematode. These findings have firstly proved that GH16s may play important roles in A.besseyi feeding and reproduction on fungi, which thus provides novel insights into the function of GH16s in plant-parasitic nematodes.}, }
@article {pmid33539346, year = {2021}, author = {Fredericks, LR and Lee, MD and Crabtree, AM and Boyer, JM and Kizer, EA and Taggart, NT and Roslund, CR and Hunter, SS and Kennedy, CB and Willmore, CG and Tebbe, NM and Harris, JS and Brocke, SN and Rowley, PA}, title = {The Species-Specific Acquisition and Diversification of a K1-like Family of Killer Toxins in Budding Yeasts of the Saccharomycotina.}, journal = {PLoS genetics}, volume = {17}, number = {2}, pages = {e1009341}, pmid = {33539346}, issn = {1553-7404}, support = {P20 GM103408/GM/NIGMS NIH HHS/United States ; P20 GM104420/GM/NIGMS NIH HHS/United States ; P30 GM103324/GM/NIGMS NIH HHS/United States ; }, mesh = {Ascomycota/classification/*genetics/virology ; Evolution, Molecular ; Gene Flow ; Gene Transfer, Horizontal ; *Genetic Variation ; Killer Factors, Yeast/*genetics ; Phylogeny ; RNA, Double-Stranded/genetics ; RNA, Viral/genetics ; Saccharomyces/classification/genetics/virology ; Saccharomyces cerevisiae/genetics ; Saccharomycetales/classification/*genetics/virology ; Species Specificity ; Totivirus/genetics ; }, abstract = {Killer toxins are extracellular antifungal proteins that are produced by a wide variety of fungi, including Saccharomyces yeasts. Although many Saccharomyces killer toxins have been previously identified, their evolutionary origins remain uncertain given that many of these genes have been mobilized by double-stranded RNA (dsRNA) viruses. A survey of yeasts from the Saccharomyces genus has identified a novel killer toxin with a unique spectrum of activity produced by Saccharomyces paradoxus. The expression of this killer toxin is associated with the presence of a dsRNA totivirus and a satellite dsRNA. Genetic sequencing of the satellite dsRNA confirmed that it encodes a killer toxin with homology to the canonical ionophoric K1 toxin from Saccharomyces cerevisiae and has been named K1-like (K1L). Genomic homologs of K1L were identified in six non-Saccharomyces yeast species of the Saccharomycotina subphylum, predominantly in subtelomeric regions of the genome. When ectopically expressed in S. cerevisiae from cloned cDNAs, both K1L and its homologs can inhibit the growth of competing yeast species, confirming the discovery of a family of biologically active K1-like killer toxins. The sporadic distribution of these genes supports their acquisition by horizontal gene transfer followed by diversification. The phylogenetic relationship between K1L and its genomic homologs suggests a common ancestry and gene flow via dsRNAs and DNAs across taxonomic divisions. This appears to enable the acquisition of a diverse arsenal of killer toxins by different yeast species for potential use in niche competition.}, }
@article {pmid33537056, year = {2020}, author = {de Abreu, VAC and Perdigão, J and Almeida, S}, title = {Metagenomic Approaches to Analyze Antimicrobial Resistance: An Overview.}, journal = {Frontiers in genetics}, volume = {11}, number = {}, pages = {575592}, pmid = {33537056}, issn = {1664-8021}, abstract = {Antimicrobial resistance is a major global public health problem, which develops when pathogens acquire antimicrobial resistance genes (ARGs), primarily through genetic recombination between commensal and pathogenic microbes. The resistome is a collection of all ARGs. In microorganisms, the primary method of ARG acquisition is horizontal gene transfer (HGT). Thus, understanding and identifying HGTs, can provide insight into the mechanisms of antimicrobial resistance transmission and dissemination. The use of high-throughput sequencing technologies has made the analysis of ARG sequences feasible and accessible. In particular, the metagenomic approach has facilitated the identification of community-based antimicrobial resistance. This approach is useful, as it allows access to the genomic data in an environmental sample without the need to isolate and culture microorganisms prior to analysis. Here, we aimed to reflect on the challenges of analyzing metagenomic data in the three main approaches for studying antimicrobial resistance: (i) analysis of microbial diversity, (ii) functional gene analysis, and (iii) searching the most complete and pertinent resistome databases.}, }
@article {pmid33536483, year = {2021}, author = {Miyokawa, R and Kanaya, HJ and Itoh, TQ and Kobayakawa, Y and Kusumi, J}, title = {Immature symbiotic system between horizontally transmitted green algae and brown hydra.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {2921}, pmid = {33536483}, issn = {2045-2322}, mesh = {Animals ; Chlorophyta/*genetics ; *Gene Transfer, Horizontal ; Hydra/genetics/*microbiology ; Phylogeny ; RNA-Seq ; Symbiosis/genetics ; }, abstract = {Some strains of brown hydra (Hydra vulgaris) are able to harbor the green algae Chlorococcum in their endodermal epithelial cells as symbionts. However, the relationship between brown hydra and chlorococcum is considered to be incipient symbiosis because most artificially introduced symbionts are not stable and because symbiotic H. vulgaris strains are rare in the wild. In this study, we compared the gene expression levels of the newly established symbiotic hydra (strain 105G), the native symbiotic strain (J7), and their non-symbiotic polyps to determine what changes would occur at the early stage of the evolution of symbiosis. We found that both the 105G and J7 strains showed comparable expression patterns, exhibiting upregulation of lysosomal enzymes and downregulation of genes related to nematocyte development and function. Meanwhile, genes involved in translation and the respiratory chain were upregulated only in strain 105G. Furthermore, treatment with rapamycin, which inhibits translation activity, induced the degeneration of the symbiotic strains (105G and J7). This effect was severe in strain 105G. Our results suggested that evolving the ability to balance the cellular metabolism between the host and the symbiont is a key requirement for adapting to endosymbiosis with chlorococcum.}, }
@article {pmid33536414, year = {2021}, author = {Mageiros, L and Méric, G and Bayliss, SC and Pensar, J and Pascoe, B and Mourkas, E and Calland, JK and Yahara, K and Murray, S and Wilkinson, TS and Williams, LK and Hitchings, MD and Porter, J and Kemmett, K and Feil, EJ and Jolley, KA and Williams, NJ and Corander, J and Sheppard, SK}, title = {Genome evolution and the emergence of pathogenicity in avian Escherichia coli.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {765}, pmid = {33536414}, issn = {2041-1723}, support = {/WT_/Wellcome Trust/United Kingdom ; 088786/C/09/Z/WT_/Wellcome Trust/United Kingdom ; MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; MR/M501608/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Chickens ; Escherichia coli/classification/*genetics/pathogenicity ; Escherichia coli Infections/diagnosis/microbiology/*prevention &amp; control ; *Evolution, Molecular ; Genes, Bacterial ; Genetic Variation ; Genome, Bacterial/*genetics ; Genome-Wide Association Study/methods ; Genotype ; Humans ; Phylogeny ; Poultry Diseases/diagnosis/microbiology/*prevention &amp; control ; Virulence/genetics ; }, abstract = {Chickens are the most common birds on Earth and colibacillosis is among the most common diseases affecting them. This major threat to animal welfare and safe sustainable food production is difficult to combat because the etiological agent, avian pathogenic Escherichia coli (APEC), emerges from ubiquitous commensal gut bacteria, with no single virulence gene present in all disease-causing isolates. Here, we address the underlying evolutionary mechanisms of extraintestinal spread and systemic infection in poultry. Combining population scale comparative genomics and pangenome-wide association studies, we compare E. coli from commensal carriage and systemic infections. We identify phylogroup-specific and species-wide genetic elements that are enriched in APEC, including pathogenicity-associated variation in 143 genes that have diverse functions, including genes involved in metabolism, lipopolysaccharide synthesis, heat shock response, antimicrobial resistance and toxicity. We find that horizontal gene transfer spreads pathogenicity elements, allowing divergent clones to cause infection. Finally, a Random Forest model prediction of disease status (carriage vs. disease) identifies pathogenic strains in the emergent ST-117 poultry-associated lineage with 73% accuracy, demonstrating the potential for early identification of emergent APEC in healthy flocks.}, }
@article {pmid33534143, year = {2021}, author = {Panter, F and Bader, CD and Müller, R}, title = {The Sandarazols are Cryptic and Structurally Unique Plasmid-Encoded Toxins from a Rare Myxobacterium*.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {60}, number = {15}, pages = {8081-8088}, pmid = {33534143}, issn = {1521-3773}, mesh = {Molecular Structure ; Multigene Family ; Myxococcales/*chemistry/metabolism ; Toxins, Biological/*chemistry/genetics/metabolism ; }, abstract = {Herein, we describe a new plasmid found in Sandaracinus sp. MSr10575 named pSa001 spanning 209.7 kbp that harbors a cryptic secondary metabolite biosynthesis gene cluster (BGC). Activation of this BGC by homologous-recombination-mediated exchange of the native promoter sequence against a vanillate inducible system led to the production and subsequent isolation and structure elucidation of novel secondary metabolites, the sandarazols A-G. The sandarazols contain intriguing structural features and very reactive functional groups such as an α-chlorinated ketone, an epoxyketone, and a (2R)-2-amino-3-(N,N-dimethylamino)-propionic acid building block. In-depth investigation of the underlying biosynthetic machinery led to a concise biosynthetic model for the new compound family, including several uncommon biosynthetic steps. The chlorinated congener sandarazol C shows an IC50 value of 0.5 μm against HCT 116 cells and a MIC of 14 μm against Mycobacterium smegmatis, which points at the sandarazols' potential function as defensive secondary metabolites or toxins.}, }
@article {pmid33533920, year = {2021}, author = {Tumuluri, VS and Rajgor, V and Xu, SY and Chouhan, OP and Saikrishnan, K}, title = {Mechanism of DNA cleavage by the endonuclease SauUSI: a major barrier to horizontal gene transfer and antibiotic resistance in Staphylococcus aureus.}, journal = {Nucleic acids research}, volume = {49}, number = {4}, pages = {2161-2178}, pmid = {33533920}, issn = {1362-4962}, mesh = {Adenosine Triphosphatases/chemistry/metabolism ; DNA/chemistry ; *DNA Cleavage ; Drug Resistance, Bacterial ; Endodeoxyribonucleases/*chemistry/*metabolism ; Gene Transfer, Horizontal ; Models, Molecular ; Protein Multimerization ; Staphylococcus aureus/drug effects/*enzymology/genetics ; }, abstract = {Acquisition of foreign DNA by Staphylococcus aureus, including vancomycin resistance genes, is thwarted by the ATP-dependent endonuclease SauUSI. Deciphering the mechanism of action of SauUSI could unravel the reason how it singularly plays a major role in preventing horizontal gene transfer (HGT) in S. aureus. Here, we report a detailed biochemical and structural characterization of SauUSI, which reveals that in the presence of ATP, the enzyme can cleave DNA having a single or multiple target site/s. Remarkably, in the case of multiple target sites, the entire region of DNA flanked by two target sites is shred into smaller fragments by SauUSI. Crystal structure of SauUSI reveals a stable dimer held together by the nuclease domains, which are spatially arranged to hydrolyze the phosphodiester bonds of both strands of the duplex. Thus, the architecture of the dimeric SauUSI facilitates cleavage of either single-site or multi-site DNA. The structure also provides insights into the molecular basis of target recognition by SauUSI. We show that target recognition activates ATP hydrolysis by the helicase-like ATPase domain, which powers active directional movement (translocation) of SauUSI along the DNA. We propose that a pile-up of multiple translocating SauUSI molecules against a stationary SauUSI bound to a target site catalyzes random double-stranded breaks causing shredding of the DNA between two target sites. The extensive and irreparable damage of the foreign DNA by shredding makes SauUSI a potent barrier against HGT.}, }
@article {pmid33531821, year = {2021}, author = {Li, Z and Shi, R and Wu, H and Yan, P}, title = {First Identification of a Patient with Prosthesis-Related Infection Caused by an MCR-1.1-Producing ST131 Escherichia coli After Rhinoplasty.}, journal = {Infection and drug resistance}, volume = {14}, number = {}, pages = {249-257}, pmid = {33531821}, issn = {1178-6973}, abstract = {BACKGROUND: The most common procedure of rhinoplasty is the implantation of a synthetic prosthesis. However, the complications, especially postoperative infection, could lead the suboptimal aesthetic outcome, economic losses and health threats. There is currently little literature providing an incidence of rhinoplasty infection and microbiological and antimicrobial resistance situations.<br><br>METHODS: Therefore, we performed a retrospective observational study which included 173 patients who received a rhinoplasty from 1 January 2015, to 31 December 2019, in the department of plastic surgery of a tertiary hospital in Guangzhou, China. The samples from the infection site were collected and performed the bacterial culture. The antimicrobial susceptibility testing was performed by VITEK and minimum inhibition concentration testing. The whole-genome sequencing was performed by Illumina Hiseq4000 platform.<br><br>RESULTS: We found that eight (4.6%) patients were infected by S. aureus (6), E. raffinosus (1) and E. coli (1), of which are susceptible to most antimicrobials. Remarkably, E. coli RS1231 was resistant to colistin and polymyxin B which conferred by mcr-1.1 locating on an IncI2 plasmid with 59,170-bp sequence length. Through sequence comparison, we speculate that the pRS1231S-MCR-1 was derived from animal sources. Besides, E. coli RS1231 belongs to ST131 O25:H4-fimH22 pandemic subclone and phylogroup B2, which can induce a broad variety of infections.<br><br>CONCLUSION: Our study provided a rhinoplasty infection incidence, microbiological and antimicrobial resistance prevalence data, and revealed, to our knowledge, the first case of postoperative infection of rhinoplasty by mcr-1.1-positive, highly susceptible, and remarkably virulent E. coli isolate.}, }
@article {pmid33531404, year = {2021}, author = {Cazares, D and Cazares, A and Figueroa, W and Guarneros, G and Edwards, RA and Vinuesa, P}, title = {A Novel Group of Promiscuous Podophages Infecting Diverse Gammaproteobacteria from River Communities Exhibits Dynamic Intergenus Host Adaptation.}, journal = {mSystems}, volume = {6}, number = {1}, pages = {}, pmid = {33531404}, issn = {2379-5077}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {Phages are generally described as species specific or even strain specific, implying an inherent limitation for some to be maintained and spread in diverse bacterial communities. Moreover, phage isolation and host range determination rarely consider the phage ecological context, likely biasing our notion on phage specificity. Here we isolated and characterized a novel group of six promiscuous phages, named Atoyac, existing in rivers and sewage by using a diverse collection of over 600 bacteria retrieved from the same environments as potential hosts. These podophages isolated from different regions in Mexico display a remarkably broad host range, infecting bacteria from six genera: Aeromonas, Pseudomonas, Yersinia, Hafnia, Escherichia, and Serratia Atoyac phage genomes are ∼42 kb long and highly similar to each other, but not to those currently available in genome and metagenome public databases. Detailed comparison of the phages' efficiency of plating (EOP) revealed variation among bacterial genera, implying a cost associated with infection of distant hosts, and between phages, despite their sequence similarity. We show, through experimental evolution in single or alternate hosts of different genera, that efficiency of plaque production is highly dynamic and tends toward optimization in hosts rendering low plaque formation. However, adaptation to distinct hosts differed between similar phages; whereas one phage optimized its EOP in all tested hosts, the other reduced plaque production in one host, suggesting that propagation in multiple bacteria may be key to maintain promiscuity in some viruses. Our study expands our knowledge of the virosphere and uncovers bacterium-phage interactions overlooked in natural systems.IMPORTANCE In natural environments, phages coexist and interact with a broad variety of bacteria, posing a conundrum for narrow-host-range phage maintenance in diverse communities. This context is rarely considered in the study of host-phage interactions, typically focused on narrow-host-range viruses and their infectivity in target bacteria isolated from sources distinct to where the phages were retrieved from. By studying phage-host interactions in bacteria and viruses isolated from river microbial communities, we show that novel phages with promiscuous host range encompassing multiple bacterial genera can be found in the environment. Assessment of hundreds of interactions in diverse hosts revealed that similar phages exhibit different infection efficiency and adaptation patterns. Understanding host range is fundamental in our knowledge of bacterium-phage interactions and their impact on microbial communities. The dynamic nature of phage promiscuity revealed in our study has implications in different aspects of phage research such as horizontal gene transfer or phage therapy.}, }
@article {pmid33528570, year = {2021}, author = {Žárský, V and Klimeš, V and Pačes, J and Vlček, &#x10c; and Hradilová, M and Beneš, V and Nývltová, E and Hrdý, I and Pyrih, J and Mach, J and Barlow, L and Stairs, CW and Eme, L and Hall, N and Eliáš, M and Dacks, JB and Roger, A and Tachezy, J}, title = {The Mastigamoeba balamuthi Genome and the Nature of the Free-Living Ancestor of Entamoeba.}, journal = {Molecular biology and evolution}, volume = {38}, number = {6}, pages = {2240-2259}, pmid = {33528570}, issn = {1537-1719}, mesh = {Adaptation, Biological/genetics ; Anaerobiosis/genetics ; Animals ; Archamoebae/*genetics/metabolism ; *Biological Evolution ; Entamoeba histolytica/*genetics ; Gene Transfer, Horizontal ; Genome Size ; *Genome, Protozoan ; Parasites/*genetics ; Transcriptome ; }, abstract = {The transition of free-living organisms to parasitic organisms is a mysterious process that occurs in all major eukaryotic lineages. Parasites display seemingly unique features associated with their pathogenicity; however, it is important to distinguish ancestral preconditions to parasitism from truly new parasite-specific functions. Here, we sequenced the genome and transcriptome of anaerobic free-living Mastigamoeba balamuthi and performed phylogenomic analysis of four related members of the Archamoebae, including Entamoeba histolytica, an important intestinal pathogen of humans. We aimed to trace gene histories throughout the adaptation of the aerobic ancestor of Archamoebae to anaerobiosis and throughout the transition from a free-living to a parasitic lifestyle. These events were associated with massive gene losses that, in parasitic lineages, resulted in a reduction in structural features, complete losses of some metabolic pathways, and a reduction in metabolic complexity. By reconstructing the features of the common ancestor of Archamoebae, we estimated preconditions for the evolution of parasitism in this lineage. The ancestor could apparently form chitinous cysts, possessed proteolytic enzyme machinery, compartmentalized the sulfate activation pathway in mitochondrion-related organelles, and possessed the components for anaerobic energy metabolism. After the split of Entamoebidae, this lineage gained genes encoding surface membrane proteins that are involved in host-parasite interactions. In contrast, gene gains identified in the M. balamuthi lineage were predominantly associated with polysaccharide catabolic processes. A phylogenetic analysis of acquired genes suggested an essential role of lateral gene transfer in parasite evolution (Entamoeba) and in adaptation to anaerobic aquatic sediments (Mastigamoeba).}, }
@article {pmid33526659, year = {2021}, author = {Che, Y and Yang, Y and Xu, X and Břinda, K and Polz, MF and Hanage, WP and Zhang, T}, title = {Conjugative plasmids interact with insertion sequences to shape the horizontal transfer of antimicrobial resistance genes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {6}, pages = {}, pmid = {33526659}, issn = {1091-6490}, mesh = {Chromosomes, Bacterial/genetics ; *Conjugation, Genetic ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal/*genetics ; *Genes, Bacterial ; Mosaicism ; Mutagenesis, Insertional/*genetics ; Phylogeny ; Plasmids/*genetics ; Synteny/genetics ; }, abstract = {It is well established that plasmids play an important role in the dissemination of antimicrobial resistance (AMR) genes; however, little is known about the role of the underlying interactions between different plasmid categories and other mobile genetic elements (MGEs) in shaping the promiscuous spread of AMR genes. Here, we developed a tool designed for plasmid classification, AMR gene annotation, and plasmid visualization and found that most plasmid-borne AMR genes, including those localized on class 1 integrons, are enriched in conjugative plasmids. Notably, we report the discovery and characterization of a massive insertion sequence (IS)-associated AMR gene transfer network (245 combinations covering 59 AMR gene subtypes and 53 ISs) linking conjugative plasmids and phylogenetically distant pathogens, suggesting a general evolutionary mechanism for the horizontal transfer of AMR genes mediated by the interaction between conjugative plasmids and ISs. Moreover, our experimental results confirmed the importance of the observed interactions in aiding the horizontal transfer and expanding the genetic range of AMR genes within complex microbial communities.}, }
@article {pmid33526179, year = {2021}, author = {Shimura, Y and Fujisawa, T and Hirose, Y and Misawa, N and Kanesaki, Y and Nakamura, Y and Kawachi, M}, title = {Complete sequence and structure of the genome of the harmful algal bloom-forming cyanobacterium Planktothrix agardhii NIES-204[T] and detailed analysis of secondary metabolite gene clusters.}, journal = {Harmful algae}, volume = {101}, number = {}, pages = {101942}, doi = {10.1016/j.hal.2020.101942}, pmid = {33526179}, issn = {1878-1470}, mesh = {*Cyanobacteria/genetics ; Harmful Algal Bloom ; *Microcystis/genetics ; Multigene Family ; Planktothrix ; }, abstract = {Planktothrix species are distributed worldwide, and these prevalent cyanobacteria occasionally form potentially devastating toxic blooms. Given the ecological and taxonomic importance of Planktothrix agardhii as a bloom species, we set out to determine the complete genome sequence of the type strain Planktothrix agardhii NIES-204. Remarkably, we found that the 5S ribosomal RNA genes are not adjacent to the 16S and 23S ribosomal RNA genes. The genomic structure of P. agardhii NIES-204 is highly similar to that of another P. agardhii strain isolated from a geographically distant site, although they differ distinctly by a large inversion. We identified numerous gene clusters that encode the components of the metabolic pathways that generate secondary metabolites. We found that the aeruginosin biosynthetic gene cluster was more similar to that of another toxic bloom-forming cyanobacterium Microcystis aeruginosa than to that of other strains of Planktothrix, suggesting horizontal gene transfer. Prenyltransferases encoded in the prenylagaramide gene cluster of Planktothrix strains were classified into two phylogenetically distinct types, suggesting a functional difference. In addition to the secondary metabolite gene clusters, we identified genes for inorganic nitrogen and phosphate uptake components and gas vesicles. Our findings contribute to further understanding of the ecologically important genus Planktothrix.}, }
@article {pmid33525600, year = {2021}, author = {Conti, A and Casagrande Pierantoni, D and Robert, V and Cardinali, G and Corte, L}, title = {Homoplasy as an Auxiliary Criterion for Species Delimitation.}, journal = {Microorganisms}, volume = {9}, number = {2}, pages = {}, pmid = {33525600}, issn = {2076-2607}, abstract = {Homoplasy is a sort of noise in phylogenetic reconstructions, due to the accumulation of backmutations, convergent evolution and horizontal gene transfer (HGT), which is considered the major trigger of homoplasy in microorganism for its massive presence. It is also known that homoplasy increases with the complexity of the tree with both real and simulated data. In this paper, we analyzed the variation of homoplasy with the two widely used taxonomic markers ITS and LSU in four taxonomic models characterized by differences in the intra-specific distances. An algorithm (HomoDist) was developed to analyze the homoplasy index (HI) variation upon addition of a single element (strain or species) in increasing distance from a starting element. This algorithm allows to follow changes of the consistency index (CI), complementary to the HI, with the increase of the number of taxa and with the increase of the distance among elements. Results show that homoplasy increases-as expected-with the number of taxa, but also as a function of the overall distance among species, often with an almost linear relationship between distance and HI. No HI change was observed in trees with few taxa spanning through short distances, indicating that this noise is not prohibitive in this context, although the analysis of the ratio between HI and distance can be recommended as a criterion for tree acceptance. The absence of large changes of the HI within the species, and its increase when new species are added by HomoDist, suggest that homoplasy variation can be used as an auxiliary test in distance-based species delimitation with any type of marker.}, }
@article {pmid33522842, year = {2021}, author = {Sacristán, S and Goss, EM and Eves-van den Akker, S}, title = {How Do Pathogens Evolve Novel Virulence Activities?.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {34}, number = {6}, pages = {576-586}, doi = {10.1094/MPMI-09-20-0258-IA}, pmid = {33522842}, issn = {0894-0282}, mesh = {*Adaptation, Physiological ; *Host-Pathogen Interactions ; Phenotype ; Virulence ; }, abstract = {This article is part of the Top 10 Unanswered Questions in MPMI invited review series.We consider the state of knowledge on pathogen evolution of novel virulence activities, broadly defined as anything that increases pathogen fitness with the consequence of causing disease in either the qualitative or quantitative senses, including adaptation of pathogens to host immunity and physiology, host species, genotypes, or tissues, or the environment. The evolution of novel virulence activities as an adaptive trait is based on the selection exerted by hosts on variants that have been generated de novo or arrived from elsewhere. In addition, the biotic and abiotic environment a pathogen experiences beyond the host may influence pathogen virulence activities. We consider host-pathogen evolution, host range expansion, and external factors that can mediate pathogen evolution. We then discuss the mechanisms by which pathogens generate and recombine the genetic variation that leads to novel virulence activities, including DNA point mutation, transposable element activity, gene duplication and neofunctionalization, and genetic exchange. In summary, if there is an (epi)genetic mechanism that can create variation in the genome, it will be used by pathogens to evolve virulence factors. Our knowledge of virulence evolution has been biased by pathogen evolution in response to major gene resistance, leaving other virulence activities underexplored. Understanding the key driving forces that give rise to novel virulence activities and the integration of evolutionary concepts and methods with mechanistic research on plant-microbe interactions can help inform crop protection.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.}, }
@article {pmid33522394, year = {2021}, author = {Wang, S and Huang, J}, title = {Fungal genes in the innovation and evolution of land plants.}, journal = {Plant signaling &amp; behavior}, volume = {16}, number = {4}, pages = {1879534}, pmid = {33522394}, issn = {1559-2324}, mesh = {*Biological Evolution ; Embryophyta/growth &amp; development/*microbiology ; *Genes, Fungal ; Mycorrhizae/genetics ; Stem Cells/metabolism ; }, abstract = {Although fungal association has been instrumental to the evolution of land plants, how genes of fungal origin might have contributed to major plant innovations remains unclear. In a recent study, we showed that a macro2 domain-containing gene likely acquired from mycorrhiza-like fungi is important in gametophore development of mosses, suggesting a role of fungi-derived genes in the three-dimensional growth of land plants.}, }
@article {pmid33519769, year = {2020}, author = {Sivabalasarma, S and Wetzel, H and Nußbaum, P and van der Does, C and Beeby, M and Albers, SV}, title = {Analysis of Cell-Cell Bridges in Haloferax volcanii Using Electron Cryo-Tomography Reveal a Continuous Cytoplasm and S-Layer.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {612239}, pmid = {33519769}, issn = {1664-302X}, abstract = {Halophilic archaea have been proposed to exchange DNA and proteins using a fusion-based mating mechanism. Scanning electron microscopy previously suggested that mating involves an intermediate state, where cells are connected by an intercellular bridge. To better understand this process, we used electron cryo-tomography (cryoET) and fluorescence microscopy to visualize cells forming these intercellular bridges. CryoET showed that the observed bridges were enveloped by an surface layer (S-layer) and connected mating cells via a continuous cytoplasm. Macromolecular complexes like ribosomes and unknown thin filamentous helical structures were visualized in the cytoplasm inside the bridges, demonstrating that these bridges can facilitate exchange of cellular components. We followed formation of a cell-cell bridge by fluorescence time-lapse microscopy between cells at a distance of 1.5 μm. These results shed light on the process of haloarchaeal mating and highlight further mechanistic questions.}, }
@article {pmid33519747, year = {2020}, author = {Harris, HMB and Hill, C}, title = {A Place for Viruses on the Tree of Life.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {604048}, pmid = {33519747}, issn = {1664-302X}, abstract = {Viruses are ubiquitous. They infect almost every species and are probably the most abundant biological entities on the planet, yet they are excluded from the Tree of Life (ToL). However, there can be no doubt that viruses play a significant role in evolution, the force that facilitates all life on Earth. Conceptually, viruses are regarded by many as non-living entities that hijack living cells in order to propagate. A strict separation between living and non-living entities places viruses far from the ToL, but this may be theoretically unsound. Advances in sequencing technology and comparative genomics have expanded our understanding of the evolutionary relationships between viruses and cellular organisms. Genomic and metagenomic data have revealed that co-evolution between viral and cellular genomes involves frequent horizontal gene transfer and the occasional co-option of novel functions over evolutionary time. From the giant, ameba-infecting marine viruses to the tiny Porcine circovirus harboring only two genes, viruses and their cellular hosts are ecologically and evolutionarily intertwined. When deciding how, if, and where viruses should be placed on the ToL, we should remember that the Tree functions best as a model of biological evolution on Earth, and it is important that models themselves evolve with our increasing understanding of biological systems.}, }
@article {pmid33514319, year = {2021}, author = {Makarenkov, V and Mazoure, B and Rabusseau, G and Legendre, P}, title = {Horizontal gene transfer and recombination analysis of SARS-CoV-2 genes helps discover its close relatives and shed light on its origin.}, journal = {BMC ecology and evolution}, volume = {21}, number = {1}, pages = {5}, pmid = {33514319}, issn = {2730-7182}, support = {249644//Natural Sciences and Engineering Research Council of Canada/ ; CF-0136//Canadian Institute for Advanced Research/ ; }, mesh = {Animals ; *COVID-19 ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Viral/genetics ; Humans ; *SARS-CoV-2 ; }, abstract = {BACKGROUND: The SARS-CoV-2 pandemic is one of the greatest global medical and social challenges that have emerged in recent history. Human coronavirus strains discovered during previous SARS outbreaks have been hypothesized to pass from bats to humans using intermediate hosts, e.g. civets for SARS-CoV and camels for MERS-CoV. The discovery of an intermediate host of SARS-CoV-2 and the identification of specific mechanism of its emergence in humans are topics of primary evolutionary importance. In this study we investigate the evolutionary patterns of 11 main genes of SARS-CoV-2. Previous studies suggested that the genome of SARS-CoV-2 is highly similar to the horseshoe bat coronavirus RaTG13 for most of the genes and to some Malayan pangolin coronavirus (CoV) strains for the receptor binding (RB) domain of the spike protein.<br><br>RESULTS: We provide a detailed list of statistically significant horizontal gene transfer and recombination events (both intergenic and intragenic) inferred for each of 11 main genes of the SARS-CoV-2 genome. Our analysis reveals that two continuous regions of genes S and N of SARS-CoV-2 may result from intragenic recombination between RaTG13 and Guangdong (GD) Pangolin CoVs. Statistically significant gene transfer-recombination events between RaTG13 and GD Pangolin CoV have been identified in region [1215-1425] of gene S and region [534-727] of gene N. Moreover, some statistically&#xa0;significant recombination events between the ancestors of SARS-CoV-2, RaTG13, GD Pangolin CoV and bat CoV ZC45-ZXC21 coronaviruses have been identified in genes ORF1ab, S, ORF3a, ORF7a, ORF8 and N. Furthermore, topology-based clustering of gene trees inferred for 25 CoV organisms revealed a three-way evolution of coronavirus genes, with gene phylogenies of ORF1ab, S and N forming the first cluster, gene phylogenies of ORF3a, E, M, ORF6, ORF7a, ORF7b and ORF8 forming the second cluster, and phylogeny of gene ORF10 forming the third cluster.<br><br>CONCLUSIONS: The results of our horizontal gene transfer and recombination analysis suggest that SARS-CoV-2 could not only be a chimera virus&#xa0;resulting from recombination of the bat RaTG13 and Guangdong pangolin coronaviruses but also a close relative of the bat CoV ZC45 and ZXC21 strains. They also indicate that a GD pangolin may be an intermediate host of&#xa0;this dangerous virus.}, }
@article {pmid33511765, year = {2021}, author = {Huang, X and Jiao, N and Zhang, R}, title = {The genomic content and context of auxiliary metabolic genes in roseophages.}, journal = {Environmental microbiology}, volume = {23}, number = {7}, pages = {3743-3757}, doi = {10.1111/1462-2920.15412}, pmid = {33511765}, issn = {1462-2920}, mesh = {*Genome, Viral/genetics ; Genomics ; Phylogeny ; *Roseobacter ; Seawater ; }, abstract = {Marine bacteriophages frequently possess auxiliary metabolic genes (AMGs) that accelerate host metabolism during phage infection. The significance of AMGs in phage infecting the ecologically important Roseobacter clade, found predominantly in marine environments, remains to be determined. Here, we analysed the distribution and genomic context of 180 AMGs, annotated into 20 types, across 50 roseophage genomes. Roseophages share seven high-frequency AMGs (trx, grx, RNR, thyX, DCD, phoH, and mazG)， most of them involved in the nucleotide biosynthesis pathway that represent conserved intra and inter operational taxonomic units (OTUs), and share ≥97% full-length DNA sequence similarity. Sporadic AMGs (dUTPase, lexA, degS, Que, NAPRT, AHL, pcnB, ctrA, RTX, RNR-nrdA, RNR-nrdE, wclP, and flgJ), present in only one or two OTUs, show high functional diversity. The roseophage AMG repertoire weakly correlates with environmental factors, while host range partially explains the sporadic AMG distribution. Locally co-linear blocks distribution index (LDI) analysis indicated that high-frequency roseopodovirus AMGs are restricted to particular genomic islands, possibly originating from limited historical acquisition events. Low-frequency roseopodovirus AMGs and all roseosiphovirus AMGs have high LDI values, implying multiple historical acquisition events. In summary, roseophages have acquired a range of AMGs through horizontal gene transfer, and the forces shaping the evolution of roseophages are described.}, }
@article {pmid33510864, year = {2021}, author = {Zwanzig, M}, title = {The ecology of plasmid-coded antibiotic resistance: a basic framework for experimental research and modeling.}, journal = {Computational and structural biotechnology journal}, volume = {19}, number = {}, pages = {586-599}, pmid = {33510864}, issn = {2001-0370}, abstract = {Many antibiotic resistance genes are associated with plasmids. The ecological success of these mobile genetic elements within microbial communities depends on varying mechanisms to secure their own propagation, not only on environmental selection. Among the most important are the cost of plasmids and their ability to be transferred to new hosts through mechanisms such as conjugation. These are regulated by dynamic control systems of the conjugation machinery and genetic adaptations that plasmid-host pairs can acquire in coevolution. However, in complex communities, these processes and mechanisms are subject to a variety of interactions with other bacterial species and other plasmid types. This article summarizes basic plasmid properties and ecological principles particularly important for understanding the persistence of plasmid-coded antibiotic resistance in aquatic environments. Through selected examples, it further introduces to the features of different types of simulation models such as systems of ordinary differential equations and individual-based models, which are considered to be important tools to understand these complex systems. This ecological perspective aims to improve the way we study and understand the dynamics, diversity and persistence of plasmids and associated antibiotic resistance genes.}, }
@article {pmid33507911, year = {2021}, author = {Ward, LM and Shih, PM}, title = {Granick revisited: Synthesizing evolutionary and ecological evidence for the late origin of bacteriochlorophyll via ghost lineages and horizontal gene transfer.}, journal = {PloS one}, volume = {16}, number = {1}, pages = {e0239248}, pmid = {33507911}, issn = {1932-6203}, mesh = {Bacterial Proteins/genetics ; Bacteriochlorophylls/genetics/*metabolism ; Biological Evolution ; Chlorophyll/metabolism ; Cyanobacteria/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Metabolic Networks and Pathways ; Oxygen/metabolism ; Photosynthesis/genetics/physiology ; Phototrophic Processes/*genetics ; Phylogeny ; }, abstract = {Photosynthesis-both oxygenic and more ancient anoxygenic forms-has fueled the bulk of primary productivity on Earth since it first evolved more than 3.4 billion years ago. However, the early evolutionary history of photosynthesis has been challenging to interpret due to the sparse, scattered distribution of metabolic pathways associated with photosynthesis, long timescales of evolution, and poor sampling of the true environmental diversity of photosynthetic bacteria. Here, we reconsider longstanding hypotheses for the evolutionary history of phototrophy by leveraging recent advances in metagenomic sequencing and phylogenetics to analyze relationships among phototrophic organisms and components of their photosynthesis pathways, including reaction centers and individual proteins and complexes involved in the multi-step synthesis of (bacterio)-chlorophyll pigments. We demonstrate that components of the photosynthetic apparatus have undergone extensive, independent histories of horizontal gene transfer. This suggests an evolutionary mode by which modular components of phototrophy are exchanged between diverse taxa in a piecemeal process that has led to biochemical innovation. We hypothesize that the evolution of extant anoxygenic photosynthetic bacteria has been spurred by ecological competition and restricted niches following the evolution of oxygenic Cyanobacteria and the accumulation of O2 in the atmosphere, leading to the relatively late evolution of bacteriochlorophyll pigments and the radiation of diverse crown group anoxygenic phototrophs. This hypothesis expands on the classic "Granick hypothesis" for the stepwise evolution of biochemical pathways, synthesizing recent expansion in our understanding of the diversity of phototrophic organisms as well as their evolving ecological context through Earth history.}, }
@article {pmid33505361, year = {2020}, author = {Bian, S and Zeng, W and Li, Q and Li, Y and Wong, NK and Jiang, M and Zuo, L and Hu, Q and Li, L}, title = {Genetic Structure, Function, and Evolution of Capsule Biosynthesis Loci in Vibrio parahaemolyticus.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {546150}, pmid = {33505361}, issn = {1664-302X}, abstract = {Capsule-forming extracellular polysaccharides are crucial for bacterial host colonization, invasion, immune evasion, and ultimately pathogenicity. Due to warming ocean waters and human encroachment of coastal ecosystems, Vibrio parahaemolyticus has emerged as a globally important foodborne enteropathogen implicated in acute gastroenteritis, wound infections, and septic shock. Conventionally, the antigenic properties of lipopolysaccharide (LPS, O antigen) and capsular polysaccharide (CPS, K antigen) have provided a basis for serotyping V. parahaemolyticus, whereas disclosure of genetic elements encoding 13 O-serogroups have allowed molecular serotyping methods to be developed. However, the genetic structure of CPS loci for 71 K-serogroups has remained unidentified, limiting progress in understanding its roles in V. parahaemolyticus pathophysiology. In this study, we identified and characterized the genetic structure and their evolutionary relationship of CPS loci of 40 K-serogroups through whole genome sequencing of 443 V. parahaemolyticus strains. We found a distinct pattern of CPS gene cluster across different K-serogroups and expanded its new 3'-border by identifying glpX as a key gene conserved across all K-serogroups. A total of 217 genes involved in CPS biosynthesis were annotated. Functional contents and genetic structure of the 40 K-serogroups were analyzed. Based on inferences from species trees and gene trees, we proposed an evolution model of the CPS gene clusters of 40 K-serogroups. Horizontal gene transfer by recombination from other Vibrio species, gene duplication is likely to play instrumental roles in the evolution of CPS in V. parahaemolyticus. This is the first time, to the best of our knowledge, that a large scale of CPS gene clusters of different K-serogroups in V. parahaemolyticus have been identified and characterized in evolutionary contexts. This work should help advance understanding on the variation of CPS in V. parahaemolyticus and provide a framework for developing diagnostically relevant serotyping methods.}, }
@article {pmid33502308, year = {2021}, author = {Jones, GH}, title = {Acquisition of pcnB [poly(A) polymerase I] genes via horizontal transfer from the β, γ-Proteobacteria.}, journal = {Microbial genomics}, volume = {7}, number = {2}, pages = {}, pmid = {33502308}, issn = {2057-5858}, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics ; Base Composition ; Betaproteobacteria/classification/*enzymology/genetics ; Evolution, Molecular ; Gammaproteobacteria/classification/*enzymology/genetics ; Gene Transfer, Horizontal ; Phylogeny ; Polynucleotide Adenylyltransferase/*genetics ; }, abstract = {Poly(A) polymerases (PAPs) and tRNA nucleotidyltransferases belong to a superfamily of nucleotidyltransferases and modify RNA 3'-ends. The product of the pcnB gene, PAP I, has been characterized in a few β-, γ- and δ-Proteobacteria. Using the PAP I signature sequence, putative PAPs were identified in bacterial species from the α- and ε-Proteobacteria and from four other bacterial phyla (Firmicutes, Actinobacteria, Bacteroidetes and Aquificae). Phylogenetic analysis, alien index and G+C content calculations strongly suggest that the PAPs in the species identified in this study arose by horizontal gene transfer from the β- and γ-Proteobacteria.}, }
@article {pmid33500192, year = {2021}, author = {Maganha de Almeida Kumlien, AC and Borrego, CM and Balcázar, JL}, title = {Antimicrobial Resistance and Bacteriophages: An Overlooked Intersection in Water Disinfection.}, journal = {Trends in microbiology}, volume = {29}, number = {6}, pages = {517-527}, doi = {10.1016/j.tim.2020.12.011}, pmid = {33500192}, issn = {1878-4380}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics ; *Bacteriophages ; Disinfection/*methods ; *Drug Resistance, Bacterial ; Feces ; Genes, Bacterial ; Humans ; Water Purification/*methods ; }, abstract = {This article focuses on how bacteriophages (phages), antibiotic-resistance genes (ARGs), and disinfection practices intersect. Phages are considered to be the most abundant biological entities on Earth and they have the potential to transfer genes (including ARGs) among their bacterial hosts. In the urban water cycle, phages are used as indicators of fecal pollution and surrogates for human viral pathogens but they are also known to withstand common disinfection treatments deployed to produce safe drinking/reclaimed water. Recent studies also suggest that phages have the potential to become an additional footprint to monitor water safety. A precautionary approach should therefore include phages in surveillance programs aimed at monitoring antimicrobial resistance (AMR) in the urban water cycle. This article argues that phages ought to be used to assess the efficiency of disinfection treatments (both classical and novel) on reducing the risk associated with antibiotic resistance. Finally, this article discusses contributions to the advancement of AMR stewardship in aquatic settings and is relevant for researchers and water industry practitioners.}, }
@article {pmid33500005, year = {2020}, author = {Kim, Y and Leung, MHY and Kwok, W and Fournié, G and Li, J and Lee, PKH and Pfeiffer, DU}, title = {Antibiotic resistance gene sharing networks and the effect of dietary nutritional content on the canine and feline gut resistome.}, journal = {Animal microbiome}, volume = {2}, number = {1}, pages = {4}, pmid = {33500005}, issn = {2524-4671}, abstract = {BACKGROUND: As one of the most densely populated microbial communities on Earth, the gut microbiota serves as an important reservoir of antibiotic resistance genes (ARGs), referred to as the gut resistome. Here, we investigated the association of dietary nutritional content with gut ARG diversity and composition, using publicly available shotgun metagenomic sequence data generated from canine and feline fecal samples. Also, based on network theory, we explored ARG-sharing patterns between gut bacterial genera by identifying the linkage structure between metagenomic assemblies and their functional genes obtained from the same data.<br><br>RESULTS: In both canine and feline gut microbiota, an increase in protein and a reduction in carbohydrate in the diet were associated with increased ARG diversity. ARG diversity of the canine gut microbiota also increased, but less strongly, after a reduction in protein and an increase in carbohydrate in the diet. The association between ARG and taxonomic composition suggests that diet-induced changes in the gut microbiota may be responsible for changes in ARG composition, supporting the links between protein metabolism and antibiotic resistance in gut microbes. In the analysis of the ARG-sharing patterns, 22 ARGs were shared among 46 genera in the canine gut microbiota, and 11 ARGs among 28 genera in the feline gut microbiota. Of these ARGs, the tetracycline resistance gene tet(W) was shared among the largest number of genera, predominantly among Firmicutes genera. Bifidobacterium, a genus extensively used in the fermentation of dairy products and as probiotics, shared tet(W) with a wide variety of other genera. Finally, genera from the same phylum were more likely to share ARGs than with those from different phyla.<br><br>CONCLUSIONS: Our findings show that dietary nutritional content, especially protein content, is associated with the gut resistome and suggest future research to explore the impact of dietary intervention on the development of antibiotic resistance in clinically-relevant gut microbes. Our network analysis also reveals that the genetic composition of bacteria acts as an important barrier to the horizontal transfer of ARGs. By capturing the underlying gene-sharing relationships between different bacterial taxa from metagenomes, our network approach improves our understanding of horizontal gene transfer dynamics.}, }
@article {pmid33498266, year = {2021}, author = {Cui, Z and Wang, S and Kakar, KU and Xie, G and Li, B and Chen, G and Zhu, B}, title = {Genome Sequence and Adaptation Analysis of the Human and Rice Pathogenic Strain Burkholderia glumae AU6208.}, journal = {Pathogens (Basel, Switzerland)}, volume = {10}, number = {2}, pages = {}, pmid = {33498266}, issn = {2076-0817}, support = {2018YFD0201202//National Science and Technology Major Project/ ; }, abstract = {Burkholderia glumae causes rice (Oryza sativa) bacterial panicle blight, which is an increasingly economically important disease worldwide. As the first B. glumae strain isolated from patients with chronic infections, AU6208 has been reported as an opportunistic clinic pathogen. However, our understanding of the molecular mechanism underlying human pathogenesis by B. glumae remains rudimentary. In this study, we report the complete genome sequence of the human-isolated B. glumae strain AU6208 and compare this to the genome of the rice-pathogenic B. glumae type strain LMG 2196[T]. Analysis of the average nucleotide identity demonstrated 99.4% similarity between the human- and plant-pathogenic strains. However, the phenotypic results from this study suggest a history of niche adaptation and divergence. In particular, we found 44 genes were predicted to be horizontally transferred into AU6208, and most of these genes were upregulated in conditions that mimic clinical conditions. In these, the gene pair sbnAB encodes key enzymes in antibiotic biosynthesis. These results suggest that horizontal gene transfer in AU6208 may be responsible for selective advantages in its pathogenicity in humans. Our analysis of the AU6208 genome and comparison with that of LMG 2196[T] reveal the evolutionary signatures of B. glumae in the process of switching niches from plants to humans.}, }
@article {pmid33495563, year = {2021}, author = {Heidler, TV and Ernits, K and Ziolkowska, A and Claesson, R and Persson, K}, title = {Porphyromonas gingivalis fimbrial protein Mfa5 contains a von Willebrand factor domain and an intramolecular isopeptide.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {106}, pmid = {33495563}, issn = {2399-3642}, mesh = {Bacterial Proteins/*chemistry ; Fimbriae Proteins/*chemistry ; Gene Transfer, Horizontal ; Molecular Structure ; *Porphyromonas gingivalis ; von Willebrand Factor ; }, abstract = {The Gram-negative bacterium Porphyromonas gingivalis is a secondary colonizer of the oral biofilm and is involved in the onset and progression of periodontitis. Its fimbriae, of type-V, are important for attachment to other microorganisms in the biofilm and for adhesion to host cells. The fimbriae are assembled from five proteins encoded by the mfa1 operon, of which Mfa5 is one of the ancillary tip proteins. Here we report the X-ray structure of the N-terminal half of Mfa5, which reveals a von Willebrand factor domain and two IgG-like domains. One of the IgG-like domains is stabilized by an intramolecular isopeptide bond, which is the first such bond observed in a Gram-negative bacterium. These features make Mfa5 structurally more related to streptococcal adhesins than to the other P. gingivalis Mfa proteins. The structure reported here indicates that horizontal gene transfer has occurred among the bacteria within the oral biofilm.}, }
@article {pmid33495250, year = {2021}, author = {Vesel, N and Blokesch, M}, title = {Pilus Production in Acinetobacter baumannii Is Growth Phase Dependent and Essential for Natural Transformation.}, journal = {Journal of bacteriology}, volume = {203}, number = {8}, pages = {}, pmid = {33495250}, issn = {1098-5530}, mesh = {Acinetobacter baumannii/*genetics/*growth &amp; development/metabolism ; Bacterial Proteins/genetics/metabolism ; DNA, Bacterial/genetics/metabolism ; Fimbriae Proteins/genetics/metabolism ; Fimbriae, Bacterial/genetics/*metabolism ; Gene Transfer, Horizontal ; Pseudomonas aeruginosa/genetics/metabolism ; Transformation, Bacterial ; }, abstract = {Acinetobacter baumannii is a severe threat to human health as a frequently multidrug-resistant hospital-acquired pathogen. Part of the danger from this bacterium comes from its genome plasticity and ability to evolve quickly by taking up and recombining external DNA into its own genome in a process called natural competence for transformation. This mode of horizontal gene transfer is one of the major ways that bacteria can acquire new antimicrobial resistances and toxic traits. Because these processes in A. baumannii are not well studied, we herein characterized new aspects of natural transformability in this species that include the species' competence window. We uncovered a strong correlation with a growth phase-dependent synthesis of a type IV pilus (TFP), which constitutes the central part of competence-induced DNA uptake machinery. We used bacterial genetics and microscopy to demonstrate that the TFP is essential for the natural transformability and surface motility of A. baumannii, whereas pilus-unrelated proteins of the DNA uptake complex do not affect the motility phenotype. Furthermore, TFP biogenesis and assembly is subject to input from two regulatory systems that are homologous to Pseudomonas aeruginosa, namely, the PilSR two-component system and the Pil-Chp chemosensory system. We demonstrated that these systems affect not only the piliation status of cells but also their ability to take up DNA for transformation. Importantly, we report on discrepancies between TFP biogenesis and natural transformability within the same genus by comparing data for our work on A. baumannii to data reported for Acinetobacter baylyi, the latter of which served for decades as a model for natural competence.IMPORTANCE Rapid bacterial evolution has alarming negative impacts on animal and human health which can occur when pathogens acquire antimicrobial resistance traits. As a major cause of antibiotic-resistant opportunistic infections, A. baumannii is a high-priority health threat which has motivated renewed interest in studying how this pathogen acquires new, dangerous traits. In this study, we deciphered a specific time window in which these bacteria can acquire new DNA and correlated that with its ability to produce the external appendages that contribute to the DNA acquisition process. These cell appendages function doubly for motility on surfaces and for DNA uptake. Collectively, we showed that A. baumannii is similar in its TFP production to Pseudomonas aeruginosa, though it differs from the well-studied species A. baylyi.}, }
@article {pmid33489942, year = {2020}, author = {Pan, Q and Cen, S and Yu, L and Tian, F and Zhao, J and Zhang, H and Chen, W and Zhai, Q}, title = {Niche-Specific Adaptive Evolution of Lactobacillus plantarum Strains Isolated From Human Feces and Paocai.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {615876}, pmid = {33489942}, issn = {2235-2988}, support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Feces ; Fermentation ; Genomics ; Humans ; *Lactobacillus plantarum/genetics ; *Probiotics ; }, abstract = {Lactobacillus plantarum, a widely used probiotic in the food industry, exists in diverse habitats, which has led to its niche-specific genetic evolution. However, the relationship between this type of genetic evolution and the bacterial phenotype remains unclear. Here, six L. plantarum strains derived from paocai and human feces were analyzed at the genomic and phenotypic levels to investigate the features of adaptive evolution in different habitats. A comparative genomic analysis showed that 93 metabolism-related genes underwent structural variations (SVs) during adaptive evolution, including genes responsible for carbohydrate, lipid, amino acid, inorganic ion and coenzyme transport and metabolism, and energy production and conversion. Notably, seven virulence factor-related genes in strains from both habitats showed SVs - similar to the pattern found in the orthologous virulence genes of pathogenic bacteria shared similar niches, suggesting the possibility of horizontal gene transfer. These genomic variations further influenced the metabolic abilities of strains and their interactions with the commensal microbiota in the host intestine. Compared with the strains from feces, those from paocai exhibited a shorter stagnation period and a higher growth rate in a diluted paocai solution because of variations in functional genes. In addition, opposite correlations were identified between the relative abundances of L. plantarum strains and the genus Bifidobacterium in two media inoculated with strains from the two habitats. Overall, our findings revealed that the niche-specific genetic evolution of L. plantarum strains is associated with their fermentation abilities and physiological functions in host gut health. This knowledge can help guiding the exploration and application of probiotics from the specific niches-based probiotic exploitation.}, }
@article {pmid33488562, year = {2020}, author = {Wang, B and Artsimovitch, I}, title = {NusG, an Ancient Yet Rapidly Evolving Transcription Factor.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {619618}, pmid = {33488562}, issn = {1664-302X}, support = {R01 GM067153/GM/NIGMS NIH HHS/United States ; }, abstract = {Timely and accurate RNA synthesis depends on accessory proteins that instruct RNA polymerase (RNAP) where and when to start and stop transcription. Among thousands of transcription factors, NusG/Spt5 stand out as the only universally conserved family of regulators. These proteins interact with RNAP to promote uninterrupted RNA synthesis and with diverse cellular partners to couple transcription to RNA processing, modification or translation, or to trigger premature termination of aberrant transcription. NusG homologs are present in all cells that utilize bacterial-type RNAP, from endosymbionts to plants, underscoring their ancient and essential function. Yet, in stark contrast to other core RNAP components, NusG family is actively evolving: horizontal gene transfer and sub-functionalization drive emergence of NusG paralogs, such as bacterial LoaP, RfaH, and UpxY. These specialized regulators activate a few (or just one) operons required for expression of antibiotics, capsules, secretion systems, toxins, and other niche-specific macromolecules. Despite their common origin and binding site on the RNAP, NusG homologs differ in their target selection, interacting partners and effects on RNA synthesis. Even among housekeeping NusGs from diverse bacteria, some factors promote pause-free transcription while others slow the RNAP down. Here, we discuss structure, function, and evolution of NusG proteins, focusing on unique mechanisms that determine their effects on gene expression and enable bacterial adaptation to diverse ecological niches.}, }
@article {pmid33488549, year = {2020}, author = {Luo, ZH and Narsing Rao, MP and Chen, H and Hua, ZS and Li, Q and Hedlund, BP and Dong, ZY and Liu, BB and Guo, SX and Shu, WS and Li, WJ}, title = {Genomic Insights of "Candidatus Nitrosocaldaceae" Based on Nine New Metagenome-Assembled Genomes, Including "Candidatus Nitrosothermus" Gen Nov. and Two New Species of "Candidatus Nitrosocaldus".}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {608832}, pmid = {33488549}, issn = {1664-302X}, abstract = {"Candidatus Nitrosocaldaceae" are globally distributed in neutral or slightly alkaline hot springs and geothermally heated soils. Despite their essential role in the nitrogen cycle in high-temperature ecosystems, they remain poorly understood because they have never been isolated in pure culture, and very few genomes are available. In the present study, a metagenomics approach was employed to obtain "Ca. Nitrosocaldaceae" metagenomic-assembled genomes (MAGs) from hot spring samples collected from India and China. Phylogenomic analysis placed these MAGs within "Ca. Nitrosocaldaceae." Average nucleotide identity and average amino acid identity analysis suggested the new MAGs represent two novel species of "Candidatus Nitrosocaldus" and a novel genus, herein proposed as "Candidatus Nitrosothermus." Key genes responsible for chemolithotrophic ammonia oxidation and a thaumarchaeal 3HP/4HB cycle were detected in all MAGs. Furthermore, genes coding for urea degradation were only present in "Ca. Nitrosocaldus," while biosynthesis of the vitamins, biotin, cobalamin, and riboflavin were detected in almost all MAGs. Comparison of "Ca. Nitrosocaldales/Nitrosocaldaceae" with other AOA revealed 526 specific orthogroups. This included genes related to thermal adaptation (cyclic 2,3-diphosphoglycerate, and S-adenosylmethionine decarboxylase), indicating their importance for life at high temperature. In addition, these MAGs acquired genes from members from archaea (Crenarchaeota) and bacteria (Firmicutes), mainly involved in metabolism and stress responses, which might play a role to allow this group to adapt to thermal habitats.}, }
@article {pmid33486226, year = {2021}, author = {Li, S and Zhang, C and Li, F and Hua, T and Zhou, Q and Ho, SH}, title = {Technologies towards antibiotic resistance genes (ARGs) removal from aquatic environment: A critical review.}, journal = {Journal of hazardous materials}, volume = {411}, number = {}, pages = {125148}, doi = {10.1016/j.jhazmat.2021.125148}, pmid = {33486226}, issn = {1873-3336}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; }, abstract = {Antibiotic resistance genes (ARGs) have been recognized as emerging pollutants that are widely distributed and accumulated in most of aquatic environment. Although many ARGs-removal technologies are employed, a corresponding discussion of merits and limitations of known technologies is still currently lacking. More importantly, the removal mechanisms of ARGs remain unclear, hindering their ecological feasibility. Thus, further in-depth studies are highly required. In this review, the occurrence and risk of ARGs in aquatic environment are introduced, and the main routes and potential impacts of ARGs dissemination are enumerated. In addition, several novel ARGs detection methods are critically reviewed. Notably, to ensure greater applicability of these technologies, systematic information on how recent technologies impact the ARGs removal and control are comprehensively compared and summarized. Finally, future research directions to alleviate the risk of ARGs in aquatic environment are briefly introduced. Taken together, this review provides useful information to facilitate the development of innovative and feasible ARGs removal technologies and increase their economic viability and ecological sustainability.}, }
@article {pmid33485954, year = {2021}, author = {Rana, S and Valentin, K and Riehl, J and Blanfuné, A and Reynes, L and Thibaut, T and Bartsch, I and Eichinger, L and Glöckner, G}, title = {Analysis of organellar genomes in brown algae reveals an independent introduction of similar foreign sequences into the mitochondrial genome.}, journal = {Genomics}, volume = {113}, number = {2}, pages = {646-654}, doi = {10.1016/j.ygeno.2021.01.003}, pmid = {33485954}, issn = {1089-8646}, mesh = {Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Chloroplast ; *Genome, Mitochondrial ; Phaeophyceae/classification/*genetics ; *Phylogeny ; }, abstract = {Kelp species (Laminariales, Phaeophyceae) are globally widespread along temperate to Polar rocky coastal lines. Here we analyse the mitochondrial and chloroplast genomes of Laminaria rodriguezii, in comparison to the organellar genomes of other kelp species. We also provide the complete mitochondrial genome sequence of another endemic kelp species from a Polar habitat, the Arctic Laminaria solidungula. We compare phylogenetic trees derived from twenty complete mitochondrial and seven complete chloroplast kelp genomes. Interestingly, we found a stretch of more than 700 bp in the mitochondrial genome of L.rodriguezii, which is not present in any other yet sequenced member of the Phaeophyceae. This stretch matches a protein coding region in the mitochondrial genome from Desmarestia viridis, another brown seaweed. Their high similarity suggests that these sequences originated through independent introduction into the two species. Their origin could have been by infection by yet unknown similar mitoviruses, currently only known from fungi and plants.}, }
@article {pmid33485466, year = {2021}, author = {Cai, L and Arnold, BJ and Xi, Z and Khost, DE and Patel, N and Hartmann, CB and Manickam, S and Sasirat, S and Nikolov, LA and Mathews, S and Sackton, TB and Davis, CC}, title = {Deeply Altered Genome Architecture in the Endoparasitic Flowering Plant Sapria himalayana Griff. (Rafflesiaceae).}, journal = {Current biology : CB}, volume = {31}, number = {5}, pages = {1002-1011.e9}, doi = {10.1016/j.cub.2020.12.045}, pmid = {33485466}, issn = {1879-0445}, mesh = {Gene Transfer, Horizontal ; Genome, Plant/*genetics ; Magnoliopsida/*genetics ; Phylogeny ; Symbiosis/*genetics ; }, abstract = {Despite more than 2,000-fold variation in genome size, key features of genome architecture are largely conserved across angiosperms. Parasitic plants have elucidated the many ways in which genomes can be modified, yet we still lack comprehensive genome data for species that represent the most extreme form of parasitism. Here, we present the highly modified genome of the iconic endophytic parasite Sapria himalayana Griff. (Rafflesiaceae), which lacks a typical plant body. First, 44% of the genes conserved in eurosids are lost in Sapria, dwarfing previously reported levels of gene loss in vascular plants. These losses demonstrate remarkable functional convergence with other parasitic plants, suggesting a common genetic roadmap underlying the evolution of plant parasitism. Second, we identified extreme disparity in intron size among retained genes. This includes a category of genes with introns longer than any so far observed in angiosperms, nearing 100 kb in some cases, and a second category of genes with exceptionally short or absent introns. Finally, at least 1.2% of the Sapria genome, including both genic and intergenic content, is inferred to be derived from host-to-parasite horizontal gene transfers (HGTs) and includes genes potentially adaptive for parasitism. Focused phylogenomic reconstruction of HGTs reveals a hidden history of former host-parasite associations involving close relatives of Sapria's modern hosts in the grapevine family. Our findings offer a unique perspective into how deeply angiosperm genomes can be altered to fit an extreme form of plant parasitism and demonstrate the value of HGTs as DNA fossils to investigate extinct symbioses.}, }
@article {pmid33484405, year = {2021}, author = {Gabashvili, E and Kobakhidze, S and Koulouris, S and Robinson, T and Kotetishvili, M}, title = {Bi- and Multi-directional Gene Transfer in the Natural Populations of Polyvalent Bacteriophages, and Their Host Species Spectrum Representing Foodborne Versus Other Human and/or Animal Pathogens.}, journal = {Food and environmental virology}, volume = {13}, number = {2}, pages = {179-202}, pmid = {33484405}, issn = {1867-0342}, mesh = {Animals ; Bacteriophages/classification/*genetics/pathogenicity/physiology ; Escherichia coli/virology ; Foodborne Diseases/microbiology ; *Gene Transfer, Horizontal ; *Host Specificity ; Humans ; Phylogeny ; Recombination, Genetic ; Salmonella enterica/virology ; Staphylococcus aureus/virology ; Virulence ; Yersinia pestis/virology ; }, abstract = {Unraveling the trends of phage-host versus phage-phage coevolution is critical for avoiding possible undesirable outcomes from the use of phage preparations intended for therapeutic, food safety or environmental safety purposes. We aimed to investigate a phenomenon of intergeneric recombination and its trajectories across the natural populations of phages predominantly linked to foodborne pathogens. The results from the recombination analyses, using a large array of the recombination detection algorithms imbedded in SplitsTree, RDP4, and Simplot software packages, provided strong evidence (fit: 100; P ≤ 0.014) for both bi- and multi-directional intergeneric recombination of the genetic loci involved collectively in phage morphogenesis, host specificity, virulence, replication, and persistence. Intergeneric recombination was determined to occur not only among conspecifics of the virulent versus temperate phages but also between the phages with these different lifestyles. The recombining polyvalent phages were suggested to interact with fairly large host species networks, including sometimes genetically very distinct species, such as e.g., Salmonella enterica and/or Escherichia coli versus Staphylococcus aureus or Yersinia pestis. Further studies are needed to understand whether phage-driven intergeneric recombination can lead to undesirable changes of intestinal and other microbiota in humans and animals.}, }
@article {pmid33484020, year = {2021}, author = {Mahelka, V and Krak, K and Fehrer, J and Caklová, P and Nagy Nejedlá, M and Čegan, R and Kopecký, D and Šafář, J}, title = {A Panicum-derived chromosomal segment captured by Hordeum a few million years ago preserves a set of stress-related genes.}, journal = {The Plant journal : for cell and molecular biology}, volume = {105}, number = {5}, pages = {1141-1164}, doi = {10.1111/tpj.15167}, pmid = {33484020}, issn = {1365-313X}, mesh = {Chromosomes, Artificial, Bacterial/*genetics ; DNA Transposable Elements/genetics ; Gene Transfer, Horizontal/genetics ; Hordeum/*genetics ; In Situ Hybridization, Fluorescence ; Panicum/*genetics ; }, abstract = {Intra-specific variability is a cornerstone of evolutionary success of species. Acquiring genetic material from distant sources is an important adaptive mechanism in bacteria, but it can also play a role in eukaryotes. In this paper, we investigate the nature and evolution of a chromosomal segment of panicoid (Poaceae, Panicoideae) origin occurring in the nuclear genomes of species of the barley genus Hordeum (Pooideae). The segment, spanning over 440 kb in the Asian Hordeum bogdanii and 219 kb in the South American Hordeum pubiflorum, resides on a pair of nucleolar organizer region (NOR)-bearing chromosomes. Conserved synteny and micro-collinearity of the segment in both species indicate a common origin of the segment, which was acquired before the split of the respective barley lineages 5-1.7 million years ago. A major part of the foreign DNA consists of several approximately 68 kb long repeated blocks containing five stress-related protein-coding genes and transposable elements (TEs). Whereas outside these repeats, the locus was invaded by multiple TEs from the host genome, the repeated blocks are rather intact and appear to be preserved. The protein-coding genes remained partly functional, as indicated by conserved reading frames, a low amount of non-synonymous mutations, and expression of mRNA. A screen across Hordeum species targeting the panicoid protein-coding genes revealed the presence of the genes in all species of the section Stenostachys. In summary, our study shows that grass genomes can contain large genomic segments obtained from distantly related species. These segments usually remain undetected, but they may play an important role in the evolution and adaptation of species.}, }
@article {pmid33483623, year = {2021}, author = {Darphorn, TS and Bel, K and Koenders-van Sint Anneland, BB and Brul, S and Ter Kuile, BH}, title = {Antibiotic resistance plasmid composition and architecture in Escherichia coli isolates from meat.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {2136}, pmid = {33483623}, issn = {2045-2322}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/drug effects/*genetics/isolation &amp; purification ; Escherichia coli Infections/microbiology ; Gene Order ; Gene Transfer, Horizontal/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Meat/*microbiology ; Multigene Family/genetics ; Plasmids/classification/*genetics ; Replicon/genetics ; Tetracycline Resistance/genetics ; }, abstract = {Resistance plasmids play a crucial role in the transfer of antimicrobial resistance from the veterinary sector to human healthcare. In this study plasmids from foodborne Escherichia coli isolates with a known (ES)BL or tetracycline resistance were sequenced entirely with short- and long-read technologies to obtain insight into their composition and to identify driving factors for spreading. Resistant foodborne E. coli isolates often contained several plasmids coding for resistance to various antimicrobials. Most plasmids were large and contained multiple resistance genes in addition to the selected resistance gene. The majority of plasmids belonged to the IncI, IncF and IncX incompatibility groups. Conserved and variable regions could be distinguished in each of the plasmid groups. Clusters containing resistance genes were located in the variable regions. Tetracycline and (extended spectrum) beta-lactamase resistance genes were each situated in separate clusters, but sulphonamide, macrolide and aminoglycoside formed one cluster and lincosamide and aminoglycoside another. In most plasmids, addiction systems were found to maintain presence in the cell.}, }
@article {pmid33483565, year = {2021}, author = {Subramanyam, S and Nemacheck, JA and Bernal-Crespo, V and Sardesai, N}, title = {Insect derived extra oral GH32 plays a role in susceptibility of wheat to Hessian fly.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {2081}, pmid = {33483565}, issn = {2045-2322}, mesh = {Amino Acid Sequence ; Animals ; Diptera/enzymology/growth &amp; development/*physiology ; Gene Transfer, Horizontal ; Glycoside Hydrolases/chemistry/genetics/*metabolism ; Host-Parasite Interactions ; Hydrolases ; Larva/enzymology/growth &amp; development ; Nutrients/metabolism ; Protein Structure, Secondary ; Triticum/*parasitology ; Virulence ; }, abstract = {The Hessian fly is an obligate parasite of wheat causing significant economic damage, and triggers either a resistant or susceptible reaction. However, the molecular mechanisms of susceptibility leading to the establishment of the larvae are unknown. Larval survival on the plant requires the establishment of a steady source of readily available nutrition. Unlike other insect pests, the Hessian fly larvae have minute mandibles and cannot derive their nutrition by chewing tissue or sucking phloem sap. Here, we show that the virulent larvae produce the glycoside hydrolase MdesGH32 extra-orally, that localizes within the leaf tissue being fed upon. MdesGH32 has strong inulinase and invertase activity aiding in the breakdown of the plant cell wall inulin polymer into monomers and converting sucrose, the primary transport sugar in plants, to glucose and fructose, resulting in the formation of a nutrient-rich tissue. Our finding elucidates the molecular mechanism of nutrient sink formation and establishment of susceptibility.}, }
@article {pmid33483311, year = {2021}, author = {McFarland, AG and Bertucci, HK and Littman, E and Shen, J and Huttenhower, C and Hartmann, EM}, title = {Triclosan Tolerance Is Driven by a Conserved Mechanism in Diverse Pseudomonas Species.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {7}, pages = {}, pmid = {33483311}, issn = {1098-5336}, support = {U19 AI135964/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Anti-Infective Agents, Local/*pharmacology ; Drug Resistance, Bacterial/*genetics ; Pseudomonas/drug effects/*genetics ; Species Specificity ; Triclosan/*pharmacology ; }, abstract = {Perturbation of natural microbial communities by antimicrobials, such as triclosan, can result in selection for antibiotic tolerance, which is of particular concern when pathogens are present. Members of the genus Pseudomonas are found in many natural microbial communities and frequently demonstrate increased abundance following triclosan exposure. The pathogen and well-studied model organism Pseudomonas aeruginosa exhibits high triclosan tolerance; however, it is unknown if all Pseudomonas species share this trait or if there are susceptible strains. We characterized the triclosan tolerance phenotypes of diverse Pseudomonas isolates obtained from triclosan-exposed built environments and identified both tolerant and sensitive strains. High tolerance is associated with carriage of the enoyl-acyl carrier reductase (ENR) isozyme gene fabV, compared to the lesser protective effects of efflux or presence of ENRs. Given its unique importance, we examined fabV distribution throughout Pseudomonas species using large-scale phylogenomic analyses. We find fabV presence or absence is largely invariant at the species level but demonstrates multiple gain and loss events in its evolutionary history. We further provide evidence of its presence on mobile genetic elements. Our results demonstrate the surprising variability in triclosan tolerance in Pseudomonas and confirm fabV to be a useful indicator for high triclosan tolerance in Pseudomonas These findings provide a framework for better monitoring of Pseudomonas in triclosan-exposed environments and interpreting effects on species and gene composition.IMPORTANCE Closely related species are typically assumed to demonstrate similar phenotypes driven by underlying conserved genotypes. When monitoring for the effect of antimicrobials on the types of species that may be selected for, this assumption may prove to be incorrect, and identification of additional genetic markers may be necessary. We isolated several phylogenetically diverse members of Pseudomonas from indoor environments and tested their phenotypic tolerance toward the commonly used antimicrobial triclosan. Although Pseudomonas isolates are broadly regarded to be highly triclosan tolerant, we demonstrate the presence of both triclosan-tolerant and -susceptible strains, separated by a difference in tolerance of nearly 3 orders of magnitude. Bioinformatic and experimental investigation demonstrated that the presence of the gene fabV was associated with high tolerance. We demonstrate that fabV is not evenly distributed in all Pseudomonas species and that its presence could be a useful predictor of high triclosan tolerance suitable for antimicrobial monitoring efforts involving triclosan.}, }
@article {pmid33483304, year = {2021}, author = {Nag, A and Mehra, S}, title = {A Major Facilitator Superfamily (MFS) Efflux Pump, SCO4121, from Streptomyces coelicolor with Roles in Multidrug Resistance and Oxidative Stress Tolerance and Its Regulation by a MarR Regulator.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {7}, pages = {}, pmid = {33483304}, issn = {1098-5336}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/*genetics/metabolism ; Chloramphenicol/pharmacology ; Ciprofloxacin/pharmacology ; Drug Resistance, Multiple, Bacterial/*genetics ; Membrane Transport Proteins/*genetics/metabolism ; Oxidative Stress/*genetics ; Streptomyces coelicolor/drug effects/*genetics/metabolism ; }, abstract = {Overexpression of efflux pumps is one of the major determinants of resistance in bacteria. Streptomyces species harbor a large array of efflux pumps that are transcriptionally silenced under laboratory conditions. However, their dissemination results in multidrug resistance in different clinical pathogens. In this study, we have identified an efflux pump from Streptomyces coelicolor, SCO4121, belonging to the major facilitator superfamily (MFS) family of transporters and characterized its role in antibiotic resistance. SCO4121 provided resistance to multiple dissimilar drugs upon overexpression in both native and heterologous hosts. Further, deletion of SCO4121 resulted in increased sensitivity toward ciprofloxacin and chloramphenicol, suggesting the pump to be a major transporter of these substrates. Apart from providing multidrug resistance, SCO4121 imparted increased tolerance against the strong oxidant HOCl. In wild-type Streptomyces coelicolor cells, these drugs were found to transcriptionally regulate the pump in a concentration-dependent manner. Additionally, we identified SCO4122, a MarR regulator that positively regulates SCO4121 in response to various drugs and the oxidant HOCl. Thus, through these studies we present the multiple roles of SCO4121 in S. coelicolor and highlight the intricate mechanisms via which it is regulated in response to antibiotics and oxidative stress.IMPORTANCE One of the key mechanisms of drug resistance in bacteria is overexpression of efflux pumps. Streptomyces species are a reservoir of a large number of efflux pumps, potentially to provide resistance to both endogenous and nonendogenous antibiotics. While many of these pumps are not expressed under standard laboratory conditions, they result in resistance to multiple drugs when spread to other bacterial pathogens through horizontal gene transfer. In this study, we have identified a widely conserved efflux pump SCO4121 from Streptomyces coelicolor with roles in both multidrug resistance and oxidative stress tolerance. We also report the presence of an adjacent MarR regulator, SCO4122, which positively regulates SCO4121 in the presence of diverse substrates in a redox-responsive manner. This study highlights that soil bacteria such as Streptomyces can reveal novel mechanisms of antibiotic resistance that may potentially emerge in clinically important bacteria.}, }
@article {pmid33477134, year = {2021}, author = {Weiten, A and Kalvelage, K and Becker, P and Reinhardt, R and Hurek, T and Reinhold-Hurek, B and Rabus, R}, title = {Complete Genomes of the Anaerobic Degradation Specialists Aromatoleum petrolei ToN1T and Aromatoleum bremense PbN1T.}, journal = {Microbial physiology}, volume = {31}, number = {1}, pages = {16-35}, doi = {10.1159/000513167}, pmid = {33477134}, issn = {2673-1673}, mesh = {Anaerobiosis/*genetics ; Benzene Derivatives/metabolism ; Carbohydrate Metabolism/genetics ; Energy Metabolism/*genetics ; Genetic Techniques ; Genome, Bacterial/*genetics ; Gluconeogenesis/genetics ; Hydrocarbons, Aromatic/metabolism ; Interspersed Repetitive Sequences/genetics ; Multigene Family/genetics ; Nitrogenase/genetics ; Phylogeny ; Rhodocyclaceae/classification/*genetics/*metabolism ; Terpenes/metabolism ; Type VI Secretion Systems/genetics ; Whole Genome Sequencing ; }, abstract = {The betaproteobacterial genus Aromatoleum comprises facultative denitrifiers specialized in the anaerobic degradation of recalcitrant organic compounds (aromatic and terpenoid). This study reports on the complete and manually annotated genomes of Ar. petrolei ToN1T (5.41 Mbp) and Ar. bremense PbN1T (4.38 Mbp), which cover the phylogenetic breadth of the genus Aromatoleum together with previously genome sequenced Ar. aromaticum EbN1T [Rabus et al., Arch Microbiol. 2005 Jan;183(1):27-36]. The gene clusters for the anaerobic degradation of aromatic and terpenoid (strain ToN1T only) compounds are scattered across the genomes of strains ToN1T and PbN1T. The richness in mobile genetic elements is shared with other Aromatoleum spp., substantiating that horizontal gene transfer should have been a major driver in shaping the genomes of this genus. The composite catabolic network of strains ToN1T and PbN1T comprises 88 proteins, the coding genes of which occupy 86.1 and 76.4 kbp (1.59 and 1.75%) of the respective genome. The strain-specific gene clusters for anaerobic degradation of ethyl-/propylbenzene (strain PbN1T) and toluene/monoterpenes (strain ToN1T) share high similarity with their counterparts in Ar. aromaticum strains EbN1T and pCyN1, respectively. Glucose is degraded via the ED-pathway in strain ToN1T, while gluconeogenesis proceeds via the reverse EMP-pathway in strains ToN1T, PbN1T, and EbN1T. The diazotrophic, endophytic lifestyle of closest related genus Azoarcus is known to be associated with nitrogenase and type-6 secretion system (T6SS). By contrast, strains ToN1T, PbN1T, and EbN1T lack nif genes for nitrogenase (including cofactor synthesis and enzyme maturation). Moreover, strains PbN1T and EbN1T do not possess tss genes for T6SS, while strain ToN1T does and facultative endophytic "Aromatoleum" sp. CIB is known to even have both. These findings underpin the functional heterogeneity among Aromatoleum members, correlating with the high plasticity of their genomes.}, }
@article {pmid33472670, year = {2021}, author = {Arredondo-Alonso, S and Top, J and Corander, J and Willems, RJL and Schürch, AC}, title = {Mode and dynamics of vanA-type vancomycin resistance dissemination in Dutch hospitals.}, journal = {Genome medicine}, volume = {13}, number = {1}, pages = {9}, pmid = {33472670}, issn = {1756-994X}, mesh = {Bacterial Proteins/*metabolism ; Base Sequence ; Enterococcus faecium/genetics/physiology ; Gram-Positive Bacterial Infections/*microbiology/*transmission ; *Hospitals ; Humans ; Netherlands/epidemiology ; Plasmids/genetics ; Reproducibility of Results ; Time Factors ; *Vancomycin Resistance ; Vancomycin-Resistant Enterococci/genetics/isolation &amp; purification ; }, abstract = {BACKGROUND: Enterococcus faecium is a commensal of the gastrointestinal tract of animals and humans but also a causative agent of hospital-acquired infections. Resistance against glycopeptides and to vancomycin has motivated the inclusion of E. faecium in the WHO global priority list. Vancomycin resistance can be conferred by the vanA gene cluster on the transposon Tn1546, which is frequently present in plasmids. The vanA gene cluster can be disseminated clonally but also horizontally either by plasmid dissemination or by Tn1546 transposition between different genomic locations.<br><br>METHODS: We performed a retrospective study of the genomic epidemiology of 309 vancomycin-resistant E. faecium (VRE) isolates across 32 Dutch hospitals (2012-2015). Genomic information regarding clonality and Tn1546 characterization was extracted using hierBAPS sequence clusters (SC) and TETyper, respectively. Plasmids were predicted using gplas in combination with a network approach based on shared k-mer content. Next, we conducted a pairwise comparison between isolates sharing a potential epidemiological link to elucidate whether clonal, plasmid, or Tn1546 spread accounted for vanA-type resistance dissemination.<br><br>RESULTS: On average, we estimated that 59% of VRE cases with a potential epidemiological link were unrelated which was defined as VRE pairs with a distinct Tn1546 variant. Clonal dissemination accounted for 32% cases in which the same SC and Tn1546 variants were identified. Horizontal plasmid dissemination accounted for 7% of VRE cases, in which we observed VRE pairs belonging to a distinct SC but carrying an identical plasmid and Tn1546 variant. In 2% of cases, we observed the same Tn1546 variant in distinct SC and plasmid types which could be explained by mixed and consecutive events of clonal and plasmid dissemination.<br><br>CONCLUSIONS: In related VRE cases, the dissemination of the vanA gene cluster in Dutch hospitals between 2012 and 2015 was dominated by clonal spread. However, we also identified outbreak settings with high frequencies of plasmid dissemination in which the spread of resistance was mainly driven by horizontal gene transfer (HGT). This study demonstrates the feasibility of distinguishing between modes of dissemination with short-read data and provides a novel assessment to estimate the relative contribution of nested genomic elements in the dissemination of vanA-type resistance.}, }
@article {pmid33471190, year = {2021}, author = {Kayali, O and Icgen, B}, title = {intI1 Type Mobile Genetic Elements Co-selected Antibiotic-Resistant Genes in Untreated Hospital Wastewaters.}, journal = {Bulletin of environmental contamination and toxicology}, volume = {106}, number = {2}, pages = {399-405}, pmid = {33471190}, issn = {1432-0800}, support = {117Y245//T&#xfc;rkiye Bilimsel ve Teknolojik Ara&#x15f;tirma Kurumu/ ; }, mesh = {*Anti-Bacterial Agents ; Genes, Bacterial ; Hospitals ; Interspersed Repetitive Sequences ; *Wastewater ; }, abstract = {Dissemination of antibiotic-resistant genes (ARGs) from hospital wastewaters (HWWs) is facilitated by the horizontal gene transfer (HGT) and involves association of ARGs with mobile genetic elements (MGEs). In our previous study, HWWs were found to have relatively high copy numbers of ARGs aadA, tetA, cmlA, sul1, and qnrS. In this study, therefore, the same HWWs were also monitored for 3 MGEs class 1 integron (intI1), insertion sequence common region 1 (ISCR1) and conjugative transposon Tn916/Tn1545 by using quantitative polymerase chain reaction. The gene intI1 with 7.4 × 10[2] average copy number/mL was found to be the most prevalent MGE and was up to two orders of magnitude higher than ISCR1 (5.5 × 10[0] average copy number/mL, p < 0.05) and Tn916/Tn1545 (2.3 × 10[0] average copy number/mL, p < 0.05) in all HWWs tested. Positive correlation between intI1 and the aadA, tetA, cmlA and sul1 genes indicated that the MGEs harbouring class1 integron most likely played major role in co-selecting all these ARGs together.}, }
@article {pmid33470507, year = {2021}, author = {Castelli, M and Lanzoni, O and Nardi, T and Lometto, S and Modeo, L and Potekhin, A and Sassera, D and Petroni, G}, title = {'Candidatus Sarmatiella mevalonica' endosymbiont of the ciliate Paramecium provides insights on evolutionary plasticity among Rickettsiales.}, journal = {Environmental microbiology}, volume = {23}, number = {3}, pages = {1684-1701}, doi = {10.1111/1462-2920.15396}, pmid = {33470507}, issn = {1462-2920}, mesh = {*Paramecium ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rickettsiales/genetics ; Symbiosis/genetics ; }, abstract = {Members of the bacterial order Rickettsiales are obligatorily associated with a wide range of eukaryotic hosts. Their evolutionary trajectories, in particular concerning the origin of shared or differential traits among distant sub-lineages, are still poorly understood. Here, we characterized a novel Rickettsiales bacterium associated with the ciliate Paramecium tredecaurelia and phylogenetically related to the Rickettsia genus. Its genome encodes significant lineage-specific features, chiefly the mevalonate pathway gene repertoire, involved in isoprenoid precursor biosynthesis. Not only this pathway has never been described in Rickettsiales, it also is very rare among bacteria, though typical in eukaryotes, thus likely representing a horizontally acquired trait. The presence of these genes could enable an efficient exploitation of host-derived intermediates for isoprenoid synthesis. Moreover, we hypothesize the reversed reactions could have replaced canonical pathways for producing acetyl-CoA, essential for phospholipid biosynthesis. Additionally, we detected phylogenetically unrelated mevalonate pathway genes in metagenome-derived Rickettsiales sequences, likely indicating evolutionary convergent effects of independent horizontal gene transfer events. Accordingly, convergence, involving both gene acquisitions and losses, is highlighted as a relevant evolutionary phenomenon in Rickettsiales, possibly favoured by plasticity and comparable lifestyles, representing a potentially hidden origin of other more nuanced similarities among sub-lineages.}, }
@article {pmid33469168, year = {2021}, author = {Rodríguez-Beltrán, J and DelaFuente, J and León-Sampedro, R and MacLean, RC and San Millán, &#xc1;}, title = {Beyond horizontal gene transfer: the role of plasmids in bacterial evolution.}, journal = {Nature reviews. Microbiology}, volume = {19}, number = {6}, pages = {347-359}, pmid = {33469168}, issn = {1740-1534}, support = {106918/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacteria/*genetics ; *Biological Evolution ; *Gene Transfer, Horizontal ; Genetic Variation ; *Genome, Bacterial ; Plasmids/*physiology ; }, abstract = {Plasmids have a key role in bacterial ecology and evolution because they mobilize accessory genes by horizontal gene transfer. However, recent studies have revealed that the evolutionary impact of plasmids goes above and beyond their being mere gene delivery platforms. Plasmids are usually kept at multiple copies per cell, producing islands of polyploidy in the bacterial genome. As a consequence, the evolution of plasmid-encoded genes is governed by a set of rules different from those affecting chromosomal genes, and these rules are shaped by unusual concepts in bacterial genetics, such as genetic dominance, heteroplasmy or segregational drift. In this Review, we discuss recent advances that underscore the importance of plasmids in bacterial ecology and evolution beyond horizontal gene transfer. We focus on new evidence that suggests that plasmids might accelerate bacterial evolution, mainly by promoting the evolution of plasmid-encoded genes, but also by enhancing the adaptation of their host chromosome. Finally, we integrate the most relevant theoretical and empirical studies providing a global understanding of the forces that govern plasmid-mediated evolution in bacteria.}, }
@article {pmid33468705, year = {2021}, author = {Singh, A and Gaur, M and Sharma, V and Khanna, P and Bothra, A and Bhaduri, A and Mondal, AK and Dash, D and Singh, Y and Misra, R}, title = {Comparative Genomic Analysis of Mycobacteriaceae Reveals Horizontal Gene Transfer-Mediated Evolution of the CRISPR-Cas System in the Mycobacterium tuberculosis Complex.}, journal = {mSystems}, volume = {6}, number = {1}, pages = {}, pmid = {33468705}, issn = {2379-5077}, abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) genes are conserved genetic elements in many prokaryotes, including Mycobacterium tuberculosis, the causative agent of tuberculosis. Although knowledge of CRISPR locus variability has been utilized in M. tuberculosis strain genotyping, its evolutionary path in Mycobacteriaceae is not well understood. In this study, we have performed a comparative analysis of 141 mycobacterial genomes and identified the exclusive presence of the CRISPR-Cas type III-A system in M. tuberculosis complex (MTBC). Our global phylogenetic analysis of CRISPR repeats and Cas10 proteins offers evidence of horizontal gene transfer (HGT) of the CRISPR-Cas module in the last common ancestor of MTBC and Mycobacterium canettii from a Streptococcus-like environmental bacterium. Additionally, our results show that the variation of CRISPR-Cas organization in M. tuberculosis lineages, especially in the Beijing sublineage of lineage 2, is due to the transposition of insertion sequence IS6110 The direct repeat (DR) region of the CRISPR-Cas locus acts as a hot spot for IS6110 insertion. We show in M. tuberculosis H37Rv that the repeat at the 5' end of CRISPR1 of the forward strand is an atypical repeat made up partly of IS-terminal inverted repeat and partly CRISPR DR. By tracing an undetectable spacer sequence in the DR region, the two CRISPR loci could theoretically be joined to reconstruct the ancestral single CRISPR-Cas locus organization, as seen in M. canettii This study retracing the evolutionary events of HGT and IS6110-driven genomic deletions helps us to better understand the strain-specific variations in M. tuberculosis lineages.IMPORTANCE Comparative genomic analysis of prokaryotes has led to a better understanding of the biology of several pathogenic microorganisms. One such clinically important pathogen is M. tuberculosis, the leading cause of bacterial infection worldwide. Recent evidence on the functionality of the CRISPR-Cas system in M. tuberculosis has brought back focus on these conserved genetic elements, present in many prokaryotes. Our study advances understanding of mycobacterial CRISPR-Cas origin and its diversity among the different species. We provide phylogenetic evidence of acquisition of CRISPR-Cas type III-A in the last common ancestor shared between MTBC and M. canettii, by HGT-mediated events. The most likely source of HGT was an environmental Firmicutes bacterium. Genomic mapping of the CRISPR loci showed the IS6110 transposition-driven variations in M. tuberculosis strains. Thus, this study offers insights into events related to the evolution of CRISPR-Cas in M. tuberculosis lineages.}, }
@article {pmid33462639, year = {2021}, author = {Mandal, S and Debnath, U and Sarkar, J}, title = {Structural-Genetic Characterization Of Novel Butaryl co-A Dehydrogenase and Proposition of Butanol Biosynthesis Pathway in Pusillimonas ginsengisoli SBSA.}, journal = {Journal of molecular evolution}, volume = {89}, number = {1-2}, pages = {81-94}, pmid = {33462639}, issn = {1432-1432}, mesh = {*Alcaligenaceae ; Butanols ; Clostridium/genetics ; Phylogeny ; }, abstract = {Despite extensive use in the biofuel industry, only butyryl co-A dehydrogenase enzymes from the Clostridia group have undergone extensive structural and genetic characterization. The present study, portrays the characterization of structural, functional and phylogenetic properties of butyryl co-A dehydrogenase identified within the genome of Pusillimonas ginsengisoli SBSA. In silico characterization, homology modelling and docking data indicates that this protein is a homo-tetramer and 388 amino acid residue long, rich in alanine and leucine residue; having molecular weight of 42347.69 dalton. Its isoelectric point value is 5.78; indicate its neutral nature while 38.38 instability index value indicate its stable nature. Its thermostable nature evidenced by its high aliphatic index (93.14); makes its suitable for industry-based use. The secondary structure prediction analysis of butyryl co-A dehydrogenase unveiled that the proteins has secondary arrangements of 54% α-helix, 13% β-stand and 5% disordered conformation. However, phylogenetic analysis clearly indicates that probably horizontal gene transfer is the primary mechanism of spreading of this gene in this organism. Notably, multiple sequence alignment study of phylogenetically diverse butyryl co-A dehydrogenase sequence highlighted the presence of conserved amino acid residues i.e. YXV/LGXKXWXS/T. Physicochemical characterization of other relevant proteins involved in butanol metabolism of SBSA also has been carried out. However, metabolic construction of functional butanol biosynthesis pathway in SBSA, enlightened its cost-effective potential use in biofuel industry as an alternate to Clostridia system.}, }
@article {pmid33452307, year = {2021}, author = {Cui, H and Ding, Z and Zhu, Q and Wu, Y and Qiu, B and Gao, P}, title = {Comparative analysis of nuclear, chloroplast, and mitochondrial genomes of watermelon and melon provides evidence of gene transfer.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {1595}, pmid = {33452307}, issn = {2045-2322}, mesh = {Biological Evolution ; Cell Nucleus/*genetics ; Citrullus/*genetics ; Cucurbitaceae/*genetics ; DNA, Plant/chemistry/metabolism ; Gene Transfer, Horizontal ; *Genome, Chloroplast ; *Genome, Mitochondrial ; Genome, Plant ; Whole Genome Sequencing ; }, abstract = {During plant evolution, there is genetic communication between organelle and nuclear genomes. A comparative analysis was performed on the organelle and nuclear genomes of the watermelon and melon. In the watermelon, chloroplast-derived sequences accounted for 7.6% of the total length of the mitochondrial genome. In the melon, chloroplast-derived sequences accounted for approximately 2.73% of the total mitochondrial genome. In watermelon and melon, the chloroplast-derived small-fragment sequences are either a subset of large-fragment sequences or appeared multiple times in the mitochondrial genome, indicating that these fragments may have undergone multiple independent migration integrations or emerged in the mitochondrial genome after migration, replication, and reorganization. There was no evidence of migration from the mitochondria to chloroplast genome. A sequence with a total length of about 73 kb (47%) in the watermelon chloroplast genome was homologous to a sequence of about 313 kb in the nuclear genome. About 33% of sequences in the watermelon mitochondrial genome was homologous with a 260 kb sequence in the nuclear genome. A sequence with a total length of about 38 kb (25%) in the melon chloroplast genome was homologous with 461 sequences in the nuclear genome, with a total length of about 301 kb. A 3.4 Mb sequence in the nuclear genome was homologous with a melon mitochondrial sequence. These results indicate that, during the evolution of watermelon and melon, a large amount of genetic material was exchanged between the nuclear genome and the two organelle genomes in the cytoplasm.}, }
@article {pmid33450027, year = {2021}, author = {Lecocq, M and Groussin, M and Gouy, M and Brochier-Armanet, C}, title = {The Molecular Determinants of Thermoadaptation: Methanococcales as a Case Study.}, journal = {Molecular biology and evolution}, volume = {38}, number = {5}, pages = {1761-1776}, pmid = {33450027}, issn = {1537-1719}, mesh = {*Amino Acid Substitution ; Gene Transfer, Horizontal ; Methanococcales/chemistry/*genetics ; Proteome ; Thermotolerance/*genetics ; }, abstract = {Previous reports have shown that environmental temperature impacts proteome evolution in Bacteria and Archaea. However, it is unknown whether thermoadaptation mainly occurs via the sequential accumulation of substitutions, massive horizontal gene transfers, or both. Measuring the real contribution of amino acid substitution to thermoadaptation is challenging, because of confounding environmental and genetic factors (e.g., pH, salinity, genomic G + C content) that also affect proteome evolution. Here, using Methanococcales, a major archaeal lineage, as a study model, we show that optimal growth temperature is the major factor affecting variations in amino acid frequencies of proteomes. By combining phylogenomic and ancestral sequence reconstruction approaches, we disclose a sequential substitutional scheme in which lysine plays a central role by fine tuning the pool of arginine, serine, threonine, glutamine, and asparagine, whose frequencies are strongly correlated with optimal growth temperature. Finally, we show that colonization to new thermal niches is not associated with high amounts of horizontal gene transfers. Altogether, although the acquisition of a few key proteins through horizontal gene transfer may have favored thermoadaptation in Methanococcales, our findings support sequential amino acid substitutions as the main factor driving thermoadaptation.}, }
@article {pmid33446206, year = {2021}, author = {Li, HS and Tang, XF and Huang, YH and Xu, ZY and Chen, ML and Du, XY and Qiu, BY and Chen, PT and Zhang, W and Ślipiński, A and Escalona, HE and Waterhouse, RM and Zwick, A and Pang, H}, title = {Horizontally acquired antibacterial genes associated with adaptive radiation of ladybird beetles.}, journal = {BMC biology}, volume = {19}, number = {1}, pages = {7}, pmid = {33446206}, issn = {1741-7007}, support = {31702012//National Natural Science Foundation of China/ ; 31970439//National Natural Science Foundation of China/ ; 2017B020202006//Science and Technology Planning Project of Guangdong Province, China/ ; 2017YFD0201000//National Key R&amp;D Program of China/ ; 18lgpy50//Basal Research Fund of Sun Yat-sen University/ ; 201904020041//Science and Technology Planning Project of Guangzhou, China/ ; 2018-04//Open Project of the State Key Laboratory of Biocontrol/ ; PP00P3_170664/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {Adaptation, Biological ; Animals ; Antibiosis/*genetics ; *Biological Evolution ; Cell Wall/chemistry/enzymology ; Coleoptera/enzymology/*genetics ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genes, Insect ; Host-Pathogen Interactions ; Hydrolases/genetics ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT) has been documented in many herbivorous insects, conferring the ability to digest plant material and promoting their remarkable ecological diversification. Previous reports suggest HGT of antibacterial enzymes may have contributed to the insect immune response and limit bacterial growth. Carnivorous insects also display many evolutionary successful lineages, but in contrast to the plant feeders, the potential role of HGTs has been less well-studied.<br><br>RESULTS: Using genomic and transcriptomic data from 38 species of ladybird beetles, we identified a set of bacterial cell wall hydrolase (cwh) genes acquired by this group of beetles. Infection with Bacillus subtilis led to upregulated expression of these ladybird cwh genes, and their recombinantly produced proteins limited bacterial proliferation. Moreover, RNAi-mediated cwh knockdown led to downregulation of other antibacterial genes, indicating a role in antibacterial immune defense. cwh genes are rare in eukaryotes, but have been maintained in all tested Coccinellinae species, suggesting that this putative immune-related HGT event played a role in the evolution of this speciose subfamily of predominant predatory ladybirds.<br><br>CONCLUSION: Our work demonstrates that, in a manner analogous to HGT-facilitated plant feeding, enhanced immunity through HGT might have played a key role in the prey adaptation and niche expansion that promoted the diversification of carnivorous beetle lineages. We believe that this represents the first example of immune-related HGT in carnivorous insects with an association with a subsequent successful species radiation.}, }
@article {pmid33445633, year = {2021}, author = {Gwenzi, W and Chaukura, N and Muisa-Zikali, N and Teta, C and Musvuugwa, T and Rzymski, P and Abia, ALK}, title = {Insects, Rodents, and Pets as Reservoirs, Vectors, and Sentinels of Antimicrobial Resistance.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {10}, number = {1}, pages = {}, pmid = {33445633}, issn = {2079-6382}, abstract = {This paper reviews the occurrence of antimicrobial resistance (AMR) in insects, rodents, and pets. Insects (e.g., houseflies, cockroaches), rodents (rats, mice), and pets (dogs, cats) act as reservoirs of AMR for first-line and last-resort antimicrobial agents. AMR proliferates in insects, rodents, and pets, and their skin and gut systems. Subsequently, insects, rodents, and pets act as vectors that disseminate AMR to humans via direct contact, human food contamination, and horizontal gene transfer. Thus, insects, rodents, and pets might act as sentinels or bioindicators of AMR. Human health risks are discussed, including those unique to low-income countries. Current evidence on human health risks is largely inferential and based on qualitative data, but comprehensive statistics based on quantitative microbial risk assessment (QMRA) are still lacking. Hence, tracing human health risks of AMR to insects, rodents, and pets, remains a challenge. To safeguard human health, mitigation measures are proposed, based on the one-health approach. Future research should include human health risk analysis using QMRA, and the application of in-silico techniques, genomics, network analysis, and 'big data' analytical tools to understand the role of household insects, rodents, and pets in the persistence, circulation, and health risks of AMR.}, }
@article {pmid33441407, year = {2021}, author = {Moller, AG and Winston, K and Ji, S and Wang, J and Hargita Davis, MN and Solís-Lemus, CR and Read, TD}, title = {Genes Influencing Phage Host Range in Staphylococcus aureus on a Species-Wide Scale.}, journal = {mSphere}, volume = {6}, number = {1}, pages = {}, pmid = {33441407}, issn = {2379-5042}, support = {R21 AI121860/AI/NIAID NIH HHS/United States ; }, mesh = {Genome, Bacterial ; Genome-Wide Association Study/methods ; Host Specificity/*genetics ; Humans ; Phenotype ; Staphylococcal Infections/microbiology ; Staphylococcus Phages/*physiology ; Staphylococcus aureus/*genetics/*virology ; }, abstract = {Staphylococcus aureus is a human pathogen that causes serious diseases, ranging from skin infections to septic shock. Bacteriophages (phages) are both natural killers of S. aureus, offering therapeutic possibilities, and important vectors of horizontal gene transfer (HGT) in the species. Here, we used high-throughput approaches to understand the genetic basis of strain-to-strain variation in sensitivity to phages, which defines the host range. We screened 259 diverse S. aureus strains covering more than 40 sequence types for sensitivity to eight phages, which were representatives of the three phage classes that infect the species. The phages were variable in host range, each infecting between 73 and 257 strains. Using genome-wide association approaches, we identified putative loci that affect host range and validated their function using USA300 transposon knockouts. In addition to rediscovering known host range determinants, we found several previously unreported genes affecting bacterial growth during phage infection, including trpA, phoR, isdB, sodM, fmtC, and relA We used the data from our host range matrix to develop predictive models that achieved between 40% and 95% accuracy. This work illustrates the complexity of the genetic basis for phage susceptibility in S. aureus but also shows that with more data, we may be able to understand much of the variation. With a knowledge of host range determination, we can rationally design phage therapy cocktails that target the broadest host range of S. aureus strains and address basic questions regarding phage-host interactions, such as the impact of phage on S. aureus evolution.IMPORTANCEStaphylococcus aureus is a widespread, hospital- and community-acquired pathogen, many strains of which are antibiotic resistant. It causes diverse diseases, ranging from local to systemic infection, and affects both the skin and many internal organs, including the heart, lungs, bones, and brain. Its ubiquity, antibiotic resistance, and disease burden make new therapies urgent. One alternative therapy to antibiotics is phage therapy, in which viruses specific to infecting bacteria clear infection. In this work, we identified and validated S. aureus genes that influence phage host range-the number of strains a phage can infect and kill-by testing strains representative of the diversity of the S. aureus species for phage host range and associating the genome sequences of strains with host range. These findings together improved our understanding of how phage therapy works in the bacterium and improve prediction of phage therapy efficacy based on the predicted host range of the infecting strain.}, }
@article {pmid33439117, year = {2021}, author = {Altamia, MA and Shipway, JR and Stein, D and Betcher, MA and Fung, JM and Jospin, G and Eisen, J and Haygood, MG and Distel, DL}, title = {Teredinibacter haidensis sp. nov., Teredinibacter purpureus sp. nov. and Teredinibacter franksiae sp. nov., marine, cellulolytic endosymbiotic bacteria isolated from the gills of the wood-boring mollusc Bankia setacea (Bivalvia: Teredinidae) and emended description of the genus Teredinibacter.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {71}, number = {2}, pages = {}, pmid = {33439117}, issn = {1466-5034}, support = {U19 TW008163/TW/FIC NIH HHS/United States ; }, mesh = {Animals ; Bacterial Typing Techniques ; Base Composition ; Bivalvia/*microbiology ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Gammaproteobacteria/*classification/isolation &amp; purification ; Gills/*microbiology ; Nitrogen Fixation ; Pacific Ocean ; *Phylogeny ; Pigmentation ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Washington ; Wood ; }, abstract = {Here, we describe three endosymbiotic bacterial strains isolated from the gills of the shipworm, Bankia setacea (Teredinidae: Bivalvia). These strains, designated as Bs08[T], Bs12[T] and Bsc2[T], are Gram-stain-negative, microaerobic, gammaproteobacteria that grow on cellulose and a variety of substrates derived from lignocellulose. Phenotypic characterization, phylogeny based on 16S rRNA gene and whole genome sequence data, amino acid identity and percentage of conserved proteins analyses, show that these strains are novel and may be assigned to the genus Teredinibacter. The three strains may be differentiated and distinguished from other previously described Teredinibacter species based on a combination of four characteristics: colony colour (Bs12[T], purple; others beige to brown), marine salt requirement (Bs12[T], Bsc2[T] and Teredinibacter turnerae strains), the capacity for nitrogen fixation (Bs08[T] and T. turnerae strains) and the ability to respire nitrate (Bs08[T]). Based on these findings, we propose the names Teredinibacter haidensis sp. nov. (type strain Bs08[T]=ATCC TSD-121[T]=KCTC 62964[T]), Teredinibacter purpureus sp. nov. (type strain Bs12[T]=ATCC TSD-122[T]=KCTC 62965[T]) and Teredinibacter franksiae sp. nov. (type strain Bsc2[T]=ATCC TSD-123[T]=KCTC 62966[T]).}, }
@article {pmid33439116, year = {2021}, author = {Månsson, E and Bech Johannesen, T and Nilsdotter-Augustinsson, &#xc5; and Söderquist, B and Stegger, M}, title = {Comparative genomics of Staphylococcus epidermidis from prosthetic-joint infections and nares highlights genetic traits associated with antimicrobial resistance, not virulence.}, journal = {Microbial genomics}, volume = {7}, number = {2}, pages = {}, pmid = {33439116}, issn = {2057-5858}, mesh = {Aged ; Aged, 80 and over ; Computational Biology ; *Drug Resistance, Multiple, Bacterial ; Female ; Gene Transfer, Horizontal ; Genomics ; Hip Prosthesis/*microbiology ; Humans ; Knee Prosthesis/*microbiology ; Male ; Middle Aged ; Phylogeny ; Staphylococcal Infections/*microbiology ; Staphylococcus epidermidis/*classification/genetics/isolation &amp; purification/pathogenicity ; Sweden ; Whole Genome Sequencing/*methods ; }, abstract = {There is increased awareness of the worldwide spread of specific epidemic multidrug-resistant (MDR) lineages of the human commensal Staphylococcus epidermidis. Here, using bioinformatic analyses accounting for population structure, we determined genomic traits (genes, SNPs and k-mers) that distinguish S. epidermidis causing prosthetic-joint infections (PJIs) from commensal isolates from nares, by analysing whole-genome sequencing data from S. epidermidis from PJIs prospectively collected over 10 years in Sweden, and contemporary S. epidermidis from the nares of patients scheduled for arthroplasty surgery. Previously suggested virulence determinants and the presence of genes and mutations linked to antimicrobial resistance (AMR) were also investigated. Publicly available S. epidermidis sequences were used for international extrapolation and validation of findings. Our data show that S. epidermidis causing PJIs differed from nasal isolates not by virulence but by traits associated with resistance to compounds used in prevention of PJIs: β-lactams, aminoglycosides and chlorhexidine. Almost a quarter of the PJI isolates did not belong to any of the previously described major nosocomial lineages, but the AMR-related traits were also over-represented in these isolates, as well as in international S. epidermidis isolates originating from PJIs. Genes previously associated with virulence in S. epidermidis were over-represented in individual lineages, but failed to reach statistical significance when adjusted for population structure. Our findings suggest that the current strategies for prevention of PJIs select for nosocomial MDR S. epidermidis lineages that have arisen from horizontal gene transfer of AMR-related traits into multiple genetic backgrounds.}, }
@article {pmid33436516, year = {2021}, author = {Fu, S and Wang, Q and Zhang, Y and Yang, Q and Hao, J and Liu, Y and Pang, B}, title = {Dynamics and Microevolution of Vibrio parahaemolyticus Populations in Shellfish Farms.}, journal = {mSystems}, volume = {6}, number = {1}, pages = {}, pmid = {33436516}, issn = {2379-5077}, abstract = {Vibrio parahaemolyticus is becoming the leading cause of acute bacterial gastroenteritis, but its population dynamics in aquafarms have received limited attention. To address this research gap, we selected three shellfish farms to examine the impacts of ocean currents and the transport of live aquatic animals on the transmission and microevolution of V. parahaemolyticus by using multilocus sequence typing (MLST) and whole-genome sequencing. MLST and genomic analysis revealed that the community structure of V. parahaemolyticus in Dalian and Donggang was relatively stable in the presence of ocean currents; however, horizontal gene transfer of mobile genetic elements (MGEs) between Dalian and Donggang was very common. Further analysis indicated that the transport of live aquatic animals from Dalian to Xiamen not only introduced new V. parahaemolyticus populations but also allowed the exchange of genetic material between the two sites. More interestingly, Dalian-originated strain ST722 was introduced to Xiamen farms, resulting in one MLST allele change and the acquisition of two genomic islands from indigenous isolates in Xiamen within 8 months; such alterations are thought to promote the adaptation of V. parahaemolyticus These results provide direct observations of how ocean currents and the transport of live aquatic animals contribute to the dissemination and genetic mixture of V. parahaemolyticus, which provides insights into the dynamics and microevolution of V. parahaemolyticus in aquacultural environments.IMPORTANCE Globally, V. parahaemolyticus-related gastroenteritis outbreaks caused by seafood consumption represent an increasing threat to human health. Despite advances in our understanding of the global epidemiology of pandemic V. parahaemolyticus, fundamental questions about the key driving forces for the spread of V. parahaemolyticus at regional and national scales remain unanswered. This study revealed that the transregional transport of aquatic animals and the movement of ocean currents both contributed to the mixing of V. parahaemolyticus populations. More importantly, this study demonstrated how genetic mixture occurred between introduced and endemic V. parahaemolyticus populations via the transport of aquatic animals, which accelerated bacterial adaptation by transferring ecologically important functions. These results suggest that human activities entail a risk of the emergence of new virulent populations for both aquatic animals and humans by horizontal gene transfer and provide important insights into the microevolution and population mixing of V. parahaemolyticus.}, }
@article {pmid33432714, year = {2021}, author = {Crava, CM and Varghese, FS and Pischedda, E and Halbach, R and Palatini, U and Marconcini, M and Gasmi, L and Redmond, S and Afrane, Y and Ayala, D and Paupy, C and Carballar-Lejarazu, R and Miesen, P and van Rij, RP and Bonizzoni, M}, title = {Population genomics in the arboviral vector Aedes aegypti reveals the genomic architecture and evolution of endogenous viral elements.}, journal = {Molecular ecology}, volume = {30}, number = {7}, pages = {1594-1611}, pmid = {33432714}, issn = {1365-294X}, mesh = {*Aedes/genetics ; Animals ; Genomics ; Metagenomics ; Mosquito Vectors/genetics ; RNA, Small Interfering/genetics ; }, abstract = {Horizontal gene transfer from viruses to eukaryotic cells is a pervasive phenomenon. Somatic viral integrations are linked to persistent viral infection whereas integrations into germline cells are maintained in host genomes by vertical transmission and may be co-opted for host functions. In the arboviral vector Aedes aegypti, an endogenous viral element from a nonretroviral RNA virus (nrEVE) was shown to produce PIWI-interacting RNAs (piRNAs) to limit infection with a cognate virus. Thus, nrEVEs may constitute a heritable, sequence-specific mechanism for antiviral immunity, analogous to piRNA-mediated silencing of transposable elements. Here, we combine population genomics and evolutionary approaches to analyse the genomic architecture of nrEVEs in A. aegypti. We conducted a genome-wide screen for adaptive nrEVEs and searched for novel population-specific nrEVEs in the genomes of 80 individual wild-caught mosquitoes from five geographical populations. We show a dynamic landscape of nrEVEs in mosquito genomes and identified five novel nrEVEs derived from two currently circulating viruses, providing evidence of the environmental-dependent modification of a piRNA cluster. Overall, our results show that virus endogenization events are complex with only a few nrEVEs contributing to adaptive evolution in A. aegypti.}, }
@article {pmid33432342, year = {2021}, author = {Harada, R and Inagaki, Y}, title = {Phage Origin of Mitochondrion-Localized Family A DNA Polymerases in Kinetoplastids and Diplonemids.}, journal = {Genome biology and evolution}, volume = {13}, number = {2}, pages = {}, pmid = {33432342}, issn = {1759-6653}, mesh = {Bacteriophages/enzymology/*genetics ; DNA-Directed DNA Polymerase/classification/*genetics ; Euglenozoa/enzymology/*genetics ; *Gene Transfer, Horizontal ; Kinetoplastida/enzymology/*genetics ; Mitochondria/enzymology/genetics ; Phylogeny ; }, abstract = {Mitochondria retain their own genomes as other bacterial endosymbiont-derived organelles. Nevertheless, no protein for DNA replication and repair is encoded in any mitochondrial genomes (mtDNAs) assessed to date, suggesting that the nucleus primarily governs the maintenance of mtDNA. As the proteins of diverse evolutionary origins occupy a large proportion of the current mitochondrial proteomes, we anticipate finding the same evolutionary trend in the nucleus-encoded machinery for mtDNA maintenance. Indeed, none of the DNA polymerases (DNAPs) in the mitochondrial endosymbiont, a putative α-proteobacterium, seemingly had been inherited by their descendants (mitochondria), as none of the known types of mitochondrion-localized DNAP showed a specific affinity to the α-proteobacterial DNAPs. Nevertheless, we currently have no concrete idea of how and when the known types of mitochondrion-localized DNAPs emerged. We here explored the origins of mitochondrion-localized DNAPs after the improvement of the samplings of DNAPs from bacteria and phages/viruses. Past studies have revealed that a set of mitochondrion-localized DNAPs in kinetoplastids and diplonemids, namely PolIB, PolIC, PolID, PolI-Perk1/2, and PolI-dipl (henceforth designated collectively as "PolIBCD+") have emerged from a single DNAP. In this study, we recovered an intimate connection between PolIBCD+ and the DNAPs found in a particular group of phages. Thus, the common ancestor of kinetoplastids and diplonemids most likely converted a laterally acquired phage DNAP into a mitochondrion-localized DNAP that was ancestral to PolIBCD+. The phage origin of PolIBCD+ hints at a potentially large contribution of proteins acquired via nonvertical processes to the machinery for mtDNA maintenance in kinetoplastids and diplonemids.}, }
@article {pmid33431897, year = {2021}, author = {Huang, J and Chen, J and Fang, G and Pang, L and Zhou, S and Zhou, Y and Pan, Z and Zhang, Q and Sheng, Y and Lu, Y and Liu, Z and Zhang, Y and Li, G and Shi, M and Chen, X and Zhan, S}, title = {Two novel venom proteins underlie divergent parasitic strategies between a generalist and a specialist parasite.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {234}, pmid = {33431897}, issn = {2041-1723}, mesh = {Animal Structures/metabolism ; Animals ; Drosophila/parasitology ; Genome, Insect ; Host Specificity ; Host-Parasite Interactions ; Immunity ; Insect Proteins/*metabolism ; Male ; Mucins/chemistry ; Parasites/*physiology ; Phylogeny ; Protein Domains ; Species Specificity ; Wasps/genetics/immunology/physiology ; }, abstract = {Parasitoids are ubiquitous in natural ecosystems. Parasitic strategies are highly diverse among parasitoid species, yet their underlying genetic bases are poorly understood. Here, we focus on the divergent adaptation of a specialist and a generalist drosophilid parasitoids. We find that a novel protein (Lar) enables active immune suppression by lysing the host lymph glands, eventually leading to successful parasitism by the generalist. Meanwhile, another novel protein (Warm) contributes to a passive strategy by attaching the laid eggs to the gut and other organs of the host, leading to incomplete encapsulation and helping the specialist escape the host immune response. We find that these diverse parasitic strategies both originated from lateral gene transfer, followed with duplication and specialization, and that they might contribute to the shift in host ranges between parasitoids. Our results increase our understanding of how novel gene functions originate and how they contribute to host adaptation.}, }
@article {pmid33430372, year = {2021}, author = {Firrao, G and Scortichini, M and Pagliari, L}, title = {Orthology-Based Estimate of the Contribution of Horizontal Gene Transfer from Distantly Related Bacteria to the Intraspecific Diversity and Differentiation of Xylella fastidiosa.}, journal = {Pathogens (Basel, Switzerland)}, volume = {10}, number = {1}, pages = {}, pmid = {33430372}, issn = {2076-0817}, abstract = {Xylella fastidiosa is a xylem-limited bacterium phylogenetically related to the xanthomonads, with an unusually large and diversified range of plant hosts. To ascertain the origin of its peculiarities, its pan-genome was scanned to identify the genes that are not coherent with its phylogenetic position within the order Xanthomonadales. The results of the analysis revealed that a large fraction of the genes of the Xylella pan-genome have no ortholog or close paralog in the order Xanthomonadales. For a significant part of the genes, the closest homologue was found in bacteria belonging to distantly related taxonomic groups, most frequently in the Betaproteobacteria. Other species, such as Xanthomonas vasicola and Xanthomonas albilineans which were investigated for comparison, did not show a similar genetic contribution from distant branches of the prokaryotic tree of life. This finding indicates that the process of acquisition of DNA from the environment is still a relevant component of Xylella fastidiosa evolution. Although the ability of Xylella fastidiosa strains to recombine among themselves is well known, the results of the pan-genome analyses stressed the additional relevance of environmental DNA in shaping their genomes, with potential consequences on their phytopathological features.}, }
@article {pmid33430044, year = {2021}, author = {Veschetti, L and Sandri, A and Patuzzo, C and Melotti, P and Malerba, G and Lleò, MM}, title = {Mobilome Analysis of Achromobacter spp. Isolates from Chronic and Occasional Lung Infection in Cystic Fibrosis Patients.}, journal = {Microorganisms}, volume = {9}, number = {1}, pages = {}, pmid = {33430044}, issn = {2076-2607}, support = {FFC#18/2019//Fondazione per la Ricerca sulla Fibrosi Cistica/ ; }, abstract = {Achromobacter spp. is an opportunistic pathogen that can cause lung infections in patients with cystic fibrosis (CF). Although a variety of mobile genetic elements (MGEs) carrying antimicrobial resistance genes have been identified in clinical isolates, little is known about the contribution of Achromobacter spp. mobilome to its pathogenicity. To provide new insights, we performed bioinformatic analyses of 54 whole genome sequences and investigated the presence of phages, insertion sequences (ISs), and integrative and conjugative elements (ICEs). Most of the detected phages were previously described in other pathogens and carried type II toxin-antitoxin systems as well as other pathogenic genes. Interestingly, the partial sequence of phage Bcep176 was found in all the analyzed Achromobacter xylosoxidans genome sequences, suggesting the integration of this phage in an ancestor strain. A wide variety of IS was also identified either inside of or in proximity to pathogenicity islands. Finally, ICEs carrying pathogenic genes were found to be widespread among our isolates and seemed to be involved in transfer events within the CF lung. These results highlight the contribution of MGEs to the pathogenicity of Achromobacter species, their potential to become antimicrobial targets, and the need for further studies to better elucidate their clinical impact.}, }
@article {pmid33429069, year = {2021}, author = {Galetti, R and Filho, RACP and Ferreira, JC and Varani, AM and Sazinas, P and Jelsbak, L and Darini, ALC}, title = {The plasmidome of multidrug-resistant emergent Salmonella serovars isolated from poultry.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {89}, number = {}, pages = {104716}, doi = {10.1016/j.meegid.2021.104716}, pmid = {33429069}, issn = {1567-7257}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/*genetics ; Genes, Bacterial ; *Plasmids ; Poultry/*microbiology ; Salmonella/*drug effects/*genetics ; }, abstract = {The rapid emergence of resistant bacteria is occurring worldwide. The understanding of the dissemination of antimicrobial resistance using high-throughput sequencing and bioinformatics approaches is providing valuable insights into the genetic basis of the horizontal gene transfer and the emergence of the antibiotic resistance threat. This ultimately can offer vital clues to the development of coordinated efforts to implement new policies to continue fighting against bacterial infections. The poultry microbiota is characterized as a potential reservoir of resistance genes, mostly derived from the Enterobacteriaceae which have become increasingly important in human and animal infections. In this work, complete genome sequences were achieved for four multidrug-resistant Salmonella spp. isolated from poultry from different farms in Brazil. We identified highly similar IncHI2-ST2 megaplasmids (larger than 275.000 bp) in all Salmonella isolates studied. These megaplasmids carry a resistome comprised of eleven different resistance genes (aac(6')-Iaa, aadA1b, aph(4)-Ia, aph(6)-Id, aph(3″)-Ib, aph(3')-Ia, aac(3)-Iva, sul1, tetA, tetB and dfrA1b) and four heavy metal tolerance operons (telluride, mercury, silver and copper). In conclusion, the multidrug-resistant plasmids identified in S. enterica serovar Schwarzengrund and Newport isolated from poultry show a variety of antibiotic resistance and heavy metal tolerance genes, providing advantages for the bacteria to survive under extremely unfavorable conditions.}, }
@article {pmid33427605, year = {2021}, author = {Tengs, T and Delwiche, CF and Monceyron Jonassen, C}, title = {A genetic element in the SARS-CoV-2 genome is shared with multiple insect species.}, journal = {The Journal of general virology}, volume = {102}, number = {3}, pages = {}, pmid = {33427605}, issn = {1465-2099}, mesh = {Animals ; Data Mining ; *Gene Transfer, Horizontal ; *Genome, Viral ; Insecta/*genetics ; Phylogeny ; RNA, Viral/genetics ; SARS-CoV-2/*genetics ; }, abstract = {SARS-CoV-2 is a member of the subgenus Sarbecovirus and thus contains the genetic element s2m. We have extensively mined nucleotide data in GenBank in order to obtain a comprehensive list of s2m sequences both in the four virus families where s2m has previously been described and in other groups of organisms. Surprisingly, there seems to be a xenologue of s2m in a large number of insect species. The function of s2m is unknown, but our data show a very high degree of sequence conservation both in insects and in viruses and that the version of s2m found in SARS-CoV-2 has unique features, not seen in any other virus or insect strains.}, }
@article {pmid33424822, year = {2020}, author = {Goldstein, SL and Klassen, JL}, title = {Pseudonocardia Symbionts of Fungus-Growing Ants and the Evolution of Defensive Secondary Metabolism.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {621041}, pmid = {33424822}, issn = {1664-302X}, abstract = {Actinobacteria belonging to the genus Pseudonocardia have evolved a close relationship with multiple species of fungus-growing ants, where these bacteria produce diverse secondary metabolites that protect the ants and their fungal mutualists from disease. Recent research has charted the phylogenetic diversity of this symbiosis, revealing multiple instances where the ants and Pseudonocardia have formed stable relationships in which these bacteria are housed on specific regions of the ant's cuticle. Parallel chemical and genomic analyses have also revealed that symbiotic Pseudonocardia produce diverse secondary metabolites with antifungal and antibacterial bioactivities, and highlighted the importance of plasmid recombination and horizontal gene transfer for maintaining these symbiotic traits. Here, we propose a multi-level model for the evolution of Pseudonocardia and their secondary metabolites that includes symbiont transmission within and between ant colonies, and the potentially independent movement and diversification of their secondary metabolite biosynthetic genes. Because of their well-studied ecology and experimental tractability, Pseudonocardia symbionts of fungus-growing ants are an especially useful model system to understand the evolution of secondary metabolites, and also comprise a significant source of novel antibiotic and antifungal agents.}, }
@article {pmid33419955, year = {2021}, author = {Dorrell, RG and Villain, A and Perez-Lamarque, B and Audren de Kerdrel, G and McCallum, G and Watson, AK and Ait-Mohamed, O and Alberti, A and Corre, E and Frischkorn, KR and Pierella Karlusich, JJ and Pelletier, E and Morlon, H and Bowler, C and Blanc, G}, title = {Phylogenomic fingerprinting of tempo and functions of horizontal gene transfer within ochrophytes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {4}, pages = {}, pmid = {33419955}, issn = {1091-6490}, mesh = {Chloroplasts/genetics ; Cyanobacteria/*genetics ; DNA Fingerprinting/methods ; Diatoms/*genetics ; Gene Transfer, Horizontal/*genetics ; Genome/genetics ; *Phylogeny ; Symbiosis/genetics ; }, abstract = {Horizontal gene transfer (HGT) is an important source of novelty in eukaryotic genomes. This is particularly true for the ochrophytes, a diverse and important group of algae. Previous studies have shown that ochrophytes possess a mosaic of genes derived from bacteria and eukaryotic algae, acquired through chloroplast endosymbiosis and from HGTs, although understanding of the time points and mechanisms underpinning these transfers has been restricted by the depth of taxonomic sampling possible. We harness an expanded set of ochrophyte sequence libraries, alongside automated and manual phylogenetic annotation, in silico modeling, and experimental techniques, to assess the frequency and functions of HGT across this lineage. Through manual annotation of thousands of single-gene trees, we identify continuous bacterial HGT as the predominant source of recently arrived genes in the model diatom Phaeodactylum tricornutum Using a large-scale automated dataset, a multigene ochrophyte reference tree, and mathematical reconciliation of gene trees, we note a probable elevation of bacterial HGTs at foundational points in diatom evolution, following their divergence from other ochrophytes. Finally, we demonstrate that throughout ochrophyte evolutionary history, bacterial HGTs have been enriched in genes encoding secreted proteins. Our study provides insights into the sources and frequency of HGTs, and functional contributions that HGT has made to algal evolution.}, }
@article {pmid33417534, year = {2021}, author = {Horesh, G and Blackwell, GA and Tonkin-Hill, G and Corander, J and Heinz, E and Thomson, NR}, title = {A comprehensive and high-quality collection of Escherichia coli genomes and their genes.}, journal = {Microbial genomics}, volume = {7}, number = {2}, pages = {}, pmid = {33417534}, issn = {2057-5858}, support = {/WT_/Wellcome Trust/United Kingdom ; 206194/WT_/Wellcome Trust/United Kingdom ; 204016/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Access to Information ; Computational Biology/methods ; Data Curation ; *Databases, Genetic ; Escherichia coli/classification/*genetics ; Escherichia coli Proteins/*genetics ; Gene Flow ; Genome, Bacterial ; Shigella/classification/*genetics ; }, abstract = {Escherichia coli is a highly diverse organism that includes a range of commensal and pathogenic variants found across a range of niches and worldwide. In addition to causing severe intestinal and extraintestinal disease, E. coli is considered a priority pathogen due to high levels of observed drug resistance. The diversity in the E. coli population is driven by high genome plasticity and a very large gene pool. All these have made E. coli one of the most well-studied organisms, as well as a commonly used laboratory strain. Today, there are thousands of sequenced E. coli genomes stored in public databases. While data is widely available, accessing the information in order to perform analyses can still be a challenge. Collecting relevant available data requires accessing different sources, where data may be stored in a range of formats, and often requires further manipulation and processing to apply various analyses and extract useful information. In this study, we collated and intensely curated a collection of over 10 000 E. coli and Shigella genomes to provide a single, uniform, high-quality dataset. Shigella were included as they are considered specialized pathovars of E. coli. We provide these data in a number of easily accessible formats that can be used as the foundation for future studies addressing the biological differences between E. coli lineages and the distribution and flow of genes in the E. coli population at a high resolution. The analysis we present emphasizes our lack of understanding of the true diversity of the E. coli species, and the biased nature of our current understanding of the genetic diversity of such a key pathogen.}, }
@article {pmid33413130, year = {2021}, author = {Li, J and Tang, J and Zeng, S and Han, F and Yuan, J and Yu, J}, title = {Comparative plastid genomics of four Pilea (Urticaceae) species: insight into interspecific plastid genome diversity in Pilea.}, journal = {BMC plant biology}, volume = {21}, number = {1}, pages = {25}, pmid = {33413130}, issn = {1471-2229}, support = {31772260//National Natural Science Foundation of China/ ; cx2019052//Chongqing Study Abroad Innovation Project/ ; }, mesh = {China ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; *Genome, Plant ; *Genome, Plastid ; Phylogeny ; Plants, Medicinal/*genetics ; Sequence Analysis, DNA ; Urticaceae/*genetics ; }, abstract = {BACKGROUND: Pilea is a genus of perennial herbs from the family Urticaceae, and some species are used as courtyard ornamentals or for medicinal purposes. At present, there is no information about the plastid genome of Pilea, which limits our understanding of this genus. Here, we report 4 plastid genomes of Pilea taxa (Pilea mollis, Pilea glauca 'Greizy', Pilea peperomioides and Pilea serpyllacea 'Globosa') and performed comprehensive comparative analysis.<br><br>RESULTS: The four plastid genomes all have a typical quartile structure. The lengths of the plastid genomes ranged from 150,398&#x2009;bp to 152,327&#x2009;bp, and each genome contained 113 unique genes, including 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Comparative analysis showed a rather high level of sequence divergence in the four genomes. Moreover, eight hypervariable regions were identified (petN-psbM, psbZ-trnG-GCC, trnT-UGU-trnL-UAA, accD-psbI, ndhF-rpl32, rpl32-trnL-UAG, ndhA-intron and ycf1), which are proposed for use as DNA barcode regions. Phylogenetic relationships based on the plastid genomes of 23 species of 14 genera of Urticaceae resulted in the placement of Pilea in the middle and lower part of the phylogenetic tree, with 100% bootstrap support within Urticaceae.<br><br>CONCLUSION: Our results enrich the resources concerning plastid genomes. Comparative plastome analysis provides insight into the interspecific diversity of the plastid genome of Pilea. The identified hypervariable regions could be used for developing molecular markers applicable in various research areas.}, }
@article {pmid33407536, year = {2021}, author = {Yehouenou, C and Bogaerts, B and Vanneste, K and Roosens, NHC and De Keersmaecker, SCJ and Marchal, K and Affolabi, D and Soleimani, R and Rodriguez-Villalobos, H and Van Bambeke, F and Dalleur, O and Simon, A}, title = {First detection of a plasmid-encoded New-Delhi metallo-beta-lactamase-1 (NDM-1) producing Acinetobacter baumannii using whole genome sequencing, isolated in a clinical setting in Benin.}, journal = {Annals of clinical microbiology and antimicrobials}, volume = {20}, number = {1}, pages = {5}, pmid = {33407536}, issn = {1476-0711}, mesh = {Acinetobacter baumannii/enzymology/genetics/*isolation &amp; purification ; Adult ; Female ; Humans ; Plasmids ; Whole Genome Sequencing/*methods ; beta-Lactamases/*biosynthesis/genetics ; }, abstract = {BACKGROUND: Carbapenem-resistant Acinetobacter baumannii is considered a top priority pathogen by the World Health Organization for combatting increasing antibiotic resistance and development of new drugs. Since it was originally reported in Klebsiella pneumoniae in 2009, the quick spread of the blaNDM-1 gene encoding a New-Delhi metallo-beta-lactamase-1 (NDM-1) is increasingly recognized as a serious threat. This gene is usually carried by large plasmids and has already been documented in diverse bacterial species, including A. baumannii. Here, we report the first detection of a NDM-1-producing A. baumannii strain isolated in Benin.<br><br>CASE PRESENTATION: A 31-year-old woman was admitted to a surgical unit with a diagnosis of post-cesarean hematoma. An extensively-drug resistant A. baumannii strain solely susceptible to amikacin, colistin and ciprofloxacin, and resistant to several other antibiotics including ceftazidime, imipenem, meropenem, gentamicin, tobramycin, ceftazidime/avibactam, and sulfamethoxazole-trimethoprim, was isolated from the wound. Production of NDM-1 was demonstrated by immunochromatographic testing. Whole genome sequencing of the isolate confirmed the presence of blaNDM-1, but also antibiotic resistance genes against multiple beta-lactamases and other classes of antibiotics, in addition to several virulence genes. Moreover, the blaNDM-1 gene was found to be present in a Tn125 transposon integrated on a plasmid.<br><br>CONCLUSIONS: The discovery of this extensively-drug resistant A. baumannii strain carrying blaNDM-1 in Benin is worrying, especially because of its high potential risk of horizontal gene transfer due to being integrated into a transposon located on a plasmid. Strict control and prevention measures should be taken, once NDM-1 positive A. baumannii has been identified to prevent transfer of this resistance gene to other Enterobacterales. Capacity building is required by governmental agencies to provide suitable antibiotic treatment options and strategies, in combination with strengthening laboratory services for detection and surveillance of this pathogen.}, }
@article {pmid33407123, year = {2021}, author = {Montenegro Benavides, NA and Alvarez B, A and Arrieta-Ortiz, ML and Rodriguez-R, LM and Botero, D and Tabima, JF and Castiblanco, L and Trujillo, C and Restrepo, S and Bernal, A}, title = {The type VI secretion system of Xanthomonas phaseoli pv. manihotis is involved in virulence and in vitro motility.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {14}, pmid = {33407123}, issn = {1471-2180}, support = {INV-2019-84-1855//Facultad de Ciencias, Universidad de los Andes/ ; 521-2010//Departamento Administrativo de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n/ ; }, mesh = {Computational Biology/*methods ; Gene Knockout Techniques ; Gene Transfer, Horizontal ; Mutation ; Phylogeny ; Sequence Analysis, DNA ; Type VI Secretion Systems/*genetics ; Virulence ; Xanthomonas/classification/genetics/*pathogenicity/physiology ; }, abstract = {BACKGROUND: The type VI protein secretion system (T6SS) is important in diverse cellular processes in Gram-negative bacteria, including interactions with other bacteria and with eukaryotic hosts. In this study we analyze the evolution of the T6SS in the genus Xanthomonas and evaluate its importance of the T6SS for virulence and in vitro motility in Xanthomonas phaseoli pv. manihotis (Xpm), the causal agent of bacterial blight in cassava (Manihot esculenta). We delineate the organization of the T6SS gene clusters in Xanthomonas and then characterize proteins of this secretion system in Xpm strain CIO151.<br><br>RESULTS: We describe the presence of three different clusters in the genus Xanthomonas that vary in their organization and degree of synteny between species. Using a gene knockout strategy, we also found that vgrG and hcp are required for maximal aggressiveness of Xpm on cassava plants while clpV is important for both motility and maximal aggressiveness.<br><br>CONCLUSION: We characterized the T6SS in 15 different strains in Xanthomonas and our phylogenetic analyses suggest that the T6SS might have been acquired by a very ancient event of horizontal gene transfer and maintained through evolution, hinting at their importance for the adaptation of Xanthomonas to their hosts. Finally, we demonstrated that the T6SS of Xpm is functional, and significantly contributes to virulence and motility. This is the first experimental study that demonstrates the role of the T6SS in the Xpm-cassava interaction and the T6SS organization in the genus Xanthomonas.}, }
@article {pmid33402829, year = {2020}, author = {Donkor, ES and Kotey, FC}, title = {Methicillin-Resistant Staphylococcus aureus in the Oral Cavity: Implications for Antibiotic Prophylaxis and Surveillance.}, journal = {Infectious diseases}, volume = {13}, number = {}, pages = {1178633720976581}, pmid = {33402829}, issn = {1178-6337}, abstract = {The oral cavity harbors a multitude of commensal flora, which may constitute a repository of antibiotic resistance determinants. In the oral cavity, bacteria form biofilms, and this facilitates the acquisition of antibiotic resistance genes through horizontal gene transfer. Recent reports indicate high methicillin-resistant Staphylococcus aureus (MRSA) carriage rates in the oral cavity. Establishment of MRSA in the mouth could be enhanced by the wide usage of antibiotic prophylaxis among at-risk dental procedure candidates. These changes in MRSA epidemiology have important implications for MRSA preventive strategies, clinical practice, as well as the methodological approaches to carriage studies of the organism.}, }
@article {pmid33402066, year = {2021}, author = {Epstein, B and Tiffin, P}, title = {Comparative genomics reveals high rates of horizontal transfer and strong purifying selection on rhizobial symbiosis genes.}, journal = {Proceedings. Biological sciences}, volume = {288}, number = {1942}, pages = {20201804}, pmid = {33402066}, issn = {1471-2954}, mesh = {*Fabaceae/genetics ; Genome-Wide Association Study ; Genomics ; *Rhizobium/genetics ; Symbiosis/genetics ; }, abstract = {Horizontal transfer (HT) alters the repertoire of symbiosis genes in rhizobial genomes and may play an important role in the on-going evolution of the rhizobia-legume symbiosis. To gain insight into the extent of HT of symbiosis genes with different functional roles (nodulation, N-fixation, host benefit and rhizobial fitness), we conducted comparative genomic and selection analyses of the full-genome sequences from 27 rhizobial genomes. We find that symbiosis genes experience high rates of HT among rhizobial lineages but also bear signatures of purifying selection (low Ka : Ks). HT and purifying selection appear to be particularly strong in genes involved in initiating the symbiosis (e.g. nodulation) and in genome-wide association candidates for mediating benefits provided to the host. These patterns are consistent with rhizobia adapting to the host environment through the loss and gain of symbiosis genes, but not with host-imposed positive selection driving divergence of symbiosis genes through recurring bouts of positive selection.}, }
@article {pmid33401101, year = {2021}, author = {Wan, K and Guo, L and Ye, C and Zhu, J and Zhang, M and Yu, X}, title = {Accumulation of antibiotic resistance genes in full-scale drinking water biological activated carbon (BAC) filters during backwash cycles.}, journal = {Water research}, volume = {190}, number = {}, pages = {116744}, doi = {10.1016/j.watres.2020.116744}, pmid = {33401101}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents/pharmacology ; Charcoal/pharmacology ; *Drinking Water/analysis ; Drug Resistance, Microbial ; Genes, Bacterial ; Humans ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Biological activated carbon (BAC) filtration, a process widely used in drinking water treatment, was recently reported to harbor antibiotic resistance genes (ARGs). This emerging contamination is poorly understood. This study was conducted to investigate the occurrence of ARGs and bacterial community in full-scale BAC filters during the backwash cycle using high-throughput qPCR and high-throughput sequencing. A total of 178 ARGs were detected in all biofilm samples, with relative abundance ranging from 0.1 to 1.37 copies per 16S rRNA and absolute abundance ranging from 4.48 × 10[7] to 3.09 × 10[9] copies/g carbon. Biofilms sampled from different filters shared most detected ARGs and dominant genera including Bryobacter, Pedomicrobium, Reyranella, and Terrimonas, though their bacterial community structure differed significantly. After backwashing, the relative ARGs abundance increased by 1.5- to 3.8-folds and the absolute ARGs abundance increased by 0.90- to 1.12-logs in all biofilm samples during filter ripening, indicating that ARGs accumulated in filters during this period. Redundancy analysis suggested that such ARGs accumulation was mainly driven by horizontal gene transfer in winter, but highly correlated with the increasing relative abundance of genera Bryobacter and Acidibacter in summer. It was observed that 80.6 %-89.3% of the detected ARGs persisted in the filters despite of the backwashing. Given the high richness and relative abundance of ARGs in BAC filter and the ineffectiveness of backwashing in ARG removal, more stringent downstream disinfection strategies are deserved and more research is necessary to assess potential human health risks due to the persistence of ARGs in drinking water.}, }
@article {pmid33398069, year = {2021}, author = {Ebmeyer, S and Kristiansson, E and Larsson, DGJ}, title = {A framework for identifying the recent origins of mobile antibiotic resistance genes.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {8}, pmid = {33398069}, issn = {2399-3642}, mesh = {Animals ; DNA Transposable Elements ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genomics/*methods ; Humans ; Proteobacteria/*genetics ; *Software ; }, abstract = {Since the introduction of antibiotics as therapeutic agents, many bacterial pathogens have developed resistance to antibiotics. Mobile resistance genes, acquired through horizontal gene transfer, play an important role in this process. Understanding from which bacterial taxa these genes were mobilized, and whether their origin taxa share common traits, is critical for predicting which environments and conditions contribute to the emergence of novel resistance genes. This knowledge may prove valuable for limiting or delaying future transfer of novel resistance genes into pathogens. The literature on the origins of mobile resistance genes is scattered and based on evidence of variable quality. Here, we summarize, amend and scrutinize the evidence for 37 proposed origins of mobile resistance genes. Using state-of-the-art genomic analyses, we supplement and evaluate the evidence based on well-defined criteria. Nineteen percent of reported origins did not fulfill the criteria to confidently assign the respective origin. Of the curated origin taxa, >90% have been associated with infection in humans or domestic animals, some taxa being the origin of several different resistance genes. The clinical emergence of these resistance genes appears to be a consequence of antibiotic selection pressure on taxa that are permanently or transiently associated with the human/domestic animal microbiome.}, }
@article {pmid33394421, year = {2021}, author = {Maurya, AP and Rajkumari, J and Pandey, P}, title = {Enrichment of antibiotic resistance genes (ARGs) in polyaromatic hydrocarbon-contaminated soils: a major challenge for environmental health.}, journal = {Environmental science and pollution research international}, volume = {28}, number = {10}, pages = {12178-12189}, pmid = {33394421}, issn = {1614-7499}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Environmental Health ; Genes, Bacterial ; Hydrocarbons ; Soil ; *Soil Microbiology ; }, abstract = {Polyaromatic hydrocarbons (PAHs) are widely spread ecological contaminants. Antibiotic resistance genes (ARGs) are present with mobile genetic elements (MGE) in the bacteria. There are molecular evidences that PAHs may induce the development of ARGs in contaminated soils. Also, the abundance of ARGs related to tetracycline, sulfonamides, aminoglycosides, ampicillin, and fluoroquinolones is high in PAH-contaminated environments. Genes encoding the efflux pump are located in the MGE and, along with class 1 integrons, have a significant role as a connecting link between PAH contamination and enrichment of ARGs. The horizontal gene transfer mechanisms further make this interaction more dynamic. Therefore, necessary steps to control ARGs into the environment and risk management plan of PAHs should be enforced. In this review, influence of PAH on evolution of ARGs in the contaminated soil, and its spread in the environment, has been described. The co-occurrence of antibiotic resistance and PAH degradation abilities in bacterial isolates has raised the concerns. Also, presence of ARGs in the microbiome of PAH-contaminated soil has been discussed as environmental hotspots for ARG spread. In addition to this, the possible links of molecular interactions between ARGs and PAHs, and their effect on environmental health has been explored.}, }
@article {pmid33394148, year = {2021}, author = {Lozo, J and Topisirovic, L and Kojic, M}, title = {Natural bacterial isolates as an inexhaustible source of new bacteriocins.}, journal = {Applied microbiology and biotechnology}, volume = {105}, number = {2}, pages = {477-492}, pmid = {33394148}, issn = {1432-0614}, support = {451-03-68/2020-14/ 200178 and 451-03-68/2020-14/ 200042//Ministry of Education, Science and Technological Development of the Republic of Serbia/ ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; *Bacteriocins ; Food Microbiology ; Food Preservatives ; }, abstract = {Microorganisms isolated from various traditionally fermented food products prepared in households without commercial starter cultures are designated as natural isolates. In addition, this term is also used for microorganisms collected from various natural habitats or products (silage, soil, manure, plant and animal material, etc.) that do not contain any commercial starters or bacterial formulations. They are characterized by unique traits that are the result of the selective pressure of environmental conditions, as well as interactions with other organisms. The synthesis of antimicrobial molecules, including bacteriocins, is an evolutionary advantage and an adaptive feature that sets them apart from other microorganisms from a common environment. This review aims to underline the knowledge of bacteriocins produced by natural isolates, with a particular emphasis on the most common location of their genes and operons, plasmids, and the importance of the relationship between the plasmidome and the adaptive potential of the isolate. Applications of bacteriocins, ranging from natural food preservatives to supplements and drugs in pharmacology and medicine, will also be addressed. The latest challenges faced by researchers in isolating new natural isolates with desired characteristics will be discussed, as well as the production of new antimicrobials, nearly one century since the first discovery of colicins in 1925. KEY POINTS: • Natural bacterial isolates harbor unique properties shaped by diverse interactions. • Horizontal gene transfer enables constant engineering of new antimicrobials. • Fermented food products are important source of bacteriocin-producing natural isolates.}, }
@article {pmid33385887, year = {2021}, author = {Kang, JH and Hwang, CY}, title = {One health approach to genetic relatedness in SCCmec between methicillin-resistant Staphylococcus isolates from companion dogs with pyoderma and their owners.}, journal = {Veterinary microbiology}, volume = {253}, number = {}, pages = {108957}, doi = {10.1016/j.vetmic.2020.108957}, pmid = {33385887}, issn = {1873-2542}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Dog Diseases/microbiology ; Dogs/microbiology ; Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; Methicillin-Resistant Staphylococcus aureus/drug effects/*genetics/isolation &amp; purification ; Microbial Sensitivity Tests ; *One Health ; *Ownership ; Pets/*microbiology ; Pyoderma/microbiology/*veterinary ; Skin/*microbiology ; Staphylococcal Infections/microbiology/transmission/*veterinary ; Whole Genome Sequencing ; }, abstract = {Staphylococcal cassette chromosome mec (SCCmec) confers methicillin resistance and shows ability for horizontal transfer. However, little is known about the potential transfer of SCCmec between different species of staphylococci in a clinical setting. In this study, we investigated the genetic relationship of SCCmec between staphylococci isolated from dogs affected with pyoderma and their owners. Clinical isolates were collected from pyoderma lesions of dogs and from the nasal cavity and finger of owners. Clonal lineages were characterized using multi-locus sequence typing. Genetic relatedness of SCCmec in the isolates from dogs and owners was first evaluated with dru and SCCmec typing, and whole-genome sequencing (WGS) was used to confirm the similarity of DNA sequences and the structural composition of SCCmec. A total of 100 Staphylococcus strains were isolated from 31 dog-owner pairs. One pair with isolates carrying the same SCCmec type V and dru type 11a was detected: 18D20-1 (S. pseudintermedius, dog), 18D20-2 (S. schleiferi, dog), and 18H20-F2 (S. epidermidis, dog owner). WGS revealed that these three isolates showed remarkable genetic similarity in SCCmec with respect to DNA sequences, dru type, structure composition of ccrC and the mec complex, and DR-1 in orfX, which is considered to be the insertion site of SCCmec. Entire identical nucleotide sequences of the whole SCCmec region in different Staphylococcus strains were absent between dogs and owners. However, the remarkable genetic similarity of SCCmec from staphylococci isolated from a dog and owner pair emphasizes that antimicrobial resistance surveillance adopted One Health concept should be continuously performed.}, }
@article {pmid33385612, year = {2020}, author = {Jiang, Y and Wang, Y and Hua, X and Qu, Y and Peleg, AY and Yu, Y}, title = {Pooled Plasmid Sequencing Reveals the Relationship Between Mobile Genetic Elements and Antimicrobial Resistance Genes in Clinically Isolated Klebsiella pneumoniae.}, journal = {Genomics, proteomics &amp; bioinformatics}, volume = {18}, number = {5}, pages = {539-548}, pmid = {33385612}, issn = {2210-3244}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Integrons ; *Klebsiella pneumoniae/genetics ; Plasmids/genetics ; }, abstract = {Plasmids remain important microbial components mediating the horizontal gene transfer (HGT) and dissemination of antimicrobial resistance. To systematically explore the relationship between mobile genetic elements (MGEs) and antimicrobial resistance genes (ARGs), a novel strategy using single-molecule real-time (SMRT) sequencing was developed. This approach was applied to pooled conjugative plasmids from clinically isolated multidrug-resistant (MDR) Klebsiella pneumoniae from a tertiary referral hospital over a 9-month period. The conjugative plasmid pool was obtained from transconjugants that acquired antimicrobial resistance after plasmid conjugation with 53 clinical isolates. The plasmid pool was then subjected to SMRT sequencing, and 82 assembled plasmid fragments were obtained. In total, 124 ARGs (responsible for resistance to β-lactam, fluoroquinolone, and aminoglycoside, among others) and 317 MGEs [including transposons (Tns), insertion sequences (ISs), and integrons] were derived from these fragments. Most of these ARGs were linked to MGEs, allowing for the establishment of a relationship network between MGEs and/or ARGs that can be used to describe the dissemination of resistance by mobile elements. Key elements involved in resistance transposition were identified, including IS26, Tn3, IS903B, ISEcp1, and ISKpn19. As the most predominant IS in the network, a typical IS26-mediated multicopy composite transposition event was illustrated by tracing its flanking 8-bp target site duplications (TSDs). The landscape of the pooled plasmid sequences highlights the diversity and complexity of the relationship between MGEs and ARGs, underpinning the clinical value of dominant HGT profiles.}, }
@article {pmid33384459, year = {2020}, author = {Tóth, AG and Csabai, I and Maróti, G and Jerzsele, &#xc1; and Dubecz, A and Patai, &#xc1;V and Judge, MF and Nagy, S&#xc1; and Makrai, L and Bányai, K and Szita, G and Solymosi, N}, title = {A glimpse of antimicrobial resistance gene diversity in kefir and yoghurt.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {22458}, pmid = {33384459}, issn = {2045-2322}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics ; *Drug Resistance, Bacterial ; *Food Microbiology ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Kefir/*microbiology ; Metagenomics/methods ; Microbial Sensitivity Tests ; Yogurt/*microbiology ; }, abstract = {Antimicrobial resistance (AMR) is a global threat gaining more and more practical significance every year. The main determinants of AMR are the antimicrobial resistance genes (ARGs). Since bacteria can share genetic components via horizontal gene transfer, even non-pathogenic bacteria may provide ARG to any pathogens which they become physically close to (e.g. in the human gut). In addition, fermented food naturally contains bacteria in high amounts. In this study, we examined the diversity of ARG content in various kefir and yoghurt samples (products, grains, bacterial strains) using a unified metagenomic approach. We found numerous ARGs of commonly used fermenting bacteria. Even with the strictest filter restrictions, we identified ARGs undermining the efficacy of aminocoumarins, aminoglycosides, carbapenems, cephalosporins, cephamycins, diaminopyrimidines, elfamycins, fluoroquinolones, fosfomycins, glycylcyclines, lincosamides, macrolides, monobactams, nitrofurans, nitroimidazoles, penams, penems, peptides, phenicols, rifamycins, tetracyclines and triclosan. In the case of gene lmrD, we detected genetic environment providing mobility of this ARG. Our findings support the theory that during the fermentation process, the ARG content of foods can grow due to bacterial multiplication. The results presented suggest that the starting culture strains of fermented foods should be monitored and selected in order to decrease the intake of ARGs via foods.}, }
@article {pmid33383865, year = {2020}, author = {Wibberg, D and Price-Carter, M and Rückert, C and Blom, J and Möbius, P}, title = {Complete Genome Sequence of Ovine Mycobacterium avium subsp. paratuberculosis Strain JIII-386 (MAP-S/type III) and Its Comparison to MAP-S/type I, MAP-C, and M. avium Complex Genomes.}, journal = {Microorganisms}, volume = {9}, number = {1}, pages = {}, pmid = {33383865}, issn = {2076-2607}, abstract = {Mycobacterium avium (M. a.) subsp. paratuberculosis (MAP) is a worldwide-distributed obligate pathogen in ruminants causing Johne's disease. Due to a lack of complete subtype III genome sequences, there is not yet conclusive information about genetic differences between strains of cattle (MAP-C, type II) and sheep (MAP-S) type, and especially between MAP-S subtypes I, and III. Here we present the complete, circular genome of MAP-S/type III strain JIII-386 (DE) closed by Nanopore-technology and its comparison with MAP-S/type I closed genome of strain Telford (AUS), MAP-S/type III draft genome of strain S397 (U.S.), twelve closed MAP-C strains, and eight closed M.-a.-complex-strains. Structural comparative alignments revealed clearly the mosaic nature of MAP, emphasized differences between the subtypes and the higher diversity of MAP-S genomes. The comparison of various genomic elements including transposases and genomic islands provide new insights in MAP genomics. MAP type specific phenotypic features may be attributed to genes of known large sequence polymorphisms (LSP[S]s) regions I-IV and deletions #1 and #2, confirmed here, but could also result from identified frameshifts or interruptions of various virulence-associated genes (e.g., mbtC in MAP-S). Comprehensive core and pan genome analysis uncovered unique genes (e.g., cytochromes) and genes probably acquired by horizontal gene transfer in different MAP-types and subtypes, but also emphasized the highly conserved and close relationship, and the complex evolution of M.-a.-strains.}, }
@article {pmid33383765, year = {2020}, author = {Aksomaitiene, J and Novoslavskij, A and Kudirkiene, E and Gabinaitiene, A and Malakauskas, M}, title = {Whole Genome Sequence-Based Prediction of Resistance Determinants in High-Level Multidrug-Resistant Campylobacter jejuni Isolates in Lithuania.}, journal = {Microorganisms}, volume = {9}, number = {1}, pages = {}, pmid = {33383765}, issn = {2076-2607}, abstract = {Spread of antibiotic resistance via mobile genetic elements associates with transfer of genes providing resistance against multiple antibiotics. Use of various comparative genomics analysis techniques enables to find intrinsic and acquired genes associated with phenotypic antimicrobial resistance (AMR) in Campylobacter jejuni genome sequences with exceptionally high-level multidrug resistance. In this study, we used whole genome sequences of seven C. jejuni to identify isolate-specific genomic features associated with resistance and virulence determinants and their role in multidrug resistance (MDR). All isolates were phenotypically highly resistant to tetracycline, ciprofloxacin, and ceftriaxone (MIC range from 64 to ≥256 µg/mL). Besides, two C. jejuni isolates were resistant to gentamicin, and one was resistant to erythromycin. The extensive drug-resistance profiles were confirmed for the two C. jejuni isolates assigned to ST-4447 (CC179). The most occurring genetic antimicrobial-resistance determinants were tetO, beta-lactamase, and multidrug efflux pumps. In this study, mobile genetic elements (MGEs) were detected in genomic islands carrying genes that confer resistance to MDR, underline their importance for disseminating antibiotic resistance in C. jejuni. The genomic approach showed a diverse distribution of virulence markers, including both plasmids and phage sequences that serve as horizontal gene transfer tools. The study findings describe in silico prediction of AMR and virulence genetics determinants combined with phenotypic AMR detection in multidrug-resistant C. jejuni isolates from Lithuania.}, }
@article {pmid33381850, year = {2020}, author = {Bazin, A and Gautreau, G and Médigue, C and Vallenet, D and Calteau, A}, title = {panRGP: a pangenome-based method to predict genomic islands and explore their diversity.}, journal = {Bioinformatics (Oxford, England)}, volume = {36}, number = {Suppl_2}, pages = {i651-i658}, doi = {10.1093/bioinformatics/btaa792}, pmid = {33381850}, issn = {1367-4811}, mesh = {Gene Transfer, Horizontal ; *Genomic Islands/genetics ; Genomics ; Metagenome ; *Software ; }, abstract = {MOTIVATION: Horizontal gene transfer (HGT) is a major source of variability in prokaryotic genomes. Regions of genome plasticity (RGPs) are clusters of genes located in highly variable genomic regions. Most of them arise from HGT and correspond to genomic islands (GIs). The study of those regions at the species level has become increasingly difficult with the data deluge of genomes. To date, no methods are available to identify GIs using hundreds of genomes to explore their diversity.<br><br>RESULTS: We present here the panRGP method that predicts RGPs using pangenome graphs made of all available genomes for a given species. It allows the study of thousands of genomes in order to access the diversity of RGPs and to predict spots of insertions. It gave the best predictions when benchmarked along other GI detection tools against a reference dataset. In addition, we illustrated its use on metagenome assembled genomes by redefining the borders of the leuX tRNA hotspot, a well-studied spot of insertion in Escherichia coli. panRPG is a scalable and reliable tool to predict GIs and spots making it an ideal approach for large comparative studies.<br><br>The methods presented in the current work are available through the following software: https://github.com/labgem/PPanGGOLiN. Detailed results and scripts to compute the benchmark metrics are available at https://github.com/axbazin/panrgp_supdata.}, }
@article {pmid33375502, year = {2020}, author = {Khezri, A and Avershina, E and Ahmad, R}, title = {Plasmid Identification and Plasmid-Mediated Antimicrobial Gene Detection in Norwegian Isolates.}, journal = {Microorganisms}, volume = {9}, number = {1}, pages = {}, pmid = {33375502}, issn = {2076-2607}, support = {273609//Research Council of Norway/ ; }, abstract = {Norway is known for being one of the countries with the lowest levels of antimicrobial resistance (AMR). AMR, through acquired genes located on transposons or conjugative plasmids, is the horizontal transmission of genes required for a given bacteria to withstand antibiotics. In this work, bioinformatic analysis of whole-genome sequences and hybrid assembled data from Escherichia coli, and Klebsiella pneumoniae isolates from Norwegian patients was performed. For detection of putative plasmids in isolates, the plasmid assembly mode in SPAdes was used, followed by annotation of resulting contigs using PlasmidFinder and two curated plasmid databases (Brooks and PLSDB). Furthermore, ResFinder and Comprehensive Antibiotic Resistance Database (CARD) were used for the identification of antibiotic resistance genes (ARGs). The IncFIB plasmid was detected as the most prevalent plasmid in both E. coli, and K. pneumoniae isolates. Furthermore, ARGs such as aph(3″)-Ib, aph(6)-Id, sul1, sul2, tet(D), and qnrS1 were identified as the most abundant plasmid-mediated ARGs in Norwegian E. coli and K. pneumoniae isolates, respectively. Using hybrid assembly, we were able to locate plasmids and predict ARGs more confidently. In conclusion, plasmid identification and ARG detection using whole-genome sequencing data are heavily dependent on the database of choice; therefore, it is best to use several tools and/or hybrid assembly for obtaining reliable identification results.}, }
@article {pmid33374551, year = {2020}, author = {Uruén, C and Chopo-Escuin, G and Tommassen, J and Mainar-Jaime, RC and Arenas, J}, title = {Biofilms as Promoters of Bacterial Antibiotic Resistance and Tolerance.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {10}, number = {1}, pages = {}, pmid = {33374551}, issn = {2079-6382}, abstract = {Multidrug resistant bacteria are a global threat for human and animal health. However, they are only part of the problem of antibiotic failure. Another bacterial strategy that contributes to their capacity to withstand antimicrobials is the formation of biofilms. Biofilms are associations of microorganisms embedded a self-produced extracellular matrix. They create particular environments that confer bacterial tolerance and resistance to antibiotics by different mechanisms that depend upon factors such as biofilm composition, architecture, the stage of biofilm development, and growth conditions. The biofilm structure hinders the penetration of antibiotics and may prevent the accumulation of bactericidal concentrations throughout the entire biofilm. In addition, gradients of dispersion of nutrients and oxygen within the biofilm generate different metabolic states of individual cells and favor the development of antibiotic tolerance and bacterial persistence. Furthermore, antimicrobial resistance may develop within biofilms through a variety of mechanisms. The expression of efflux pumps may be induced in various parts of the biofilm and the mutation frequency is induced, while the presence of extracellular DNA and the close contact between cells favor horizontal gene transfer. A deep understanding of the mechanisms by which biofilms cause tolerance/resistance to antibiotics helps to develop novel strategies to fight these infections.}, }
@article {pmid33372826, year = {2021}, author = {Kim, M and Park, J and Park, W}, title = {Genomic and phenotypic analyses of multidrug-resistant Acinetobacter baumannii NCCP 16007 isolated from a patient with a urinary tract infection.}, journal = {Virulence}, volume = {12}, number = {1}, pages = {150-164}, pmid = {33372826}, issn = {2150-5608}, mesh = {Acinetobacter Infections/microbiology/*urine ; Acinetobacter baumannii/classification/*drug effects/*genetics/pathogenicity ; Animals ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics ; Biofilms ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomics ; Humans ; Larva/microbiology ; Microbial Sensitivity Tests ; Moths/microbiology ; *Phenotype ; Urinary Tract Infections/*microbiology ; }, abstract = {Polymyxin B (PMB) is increasingly used as a last-line antibiotic; however, the emergence of PMB resistance is a serious threat to global health. Here, a total of 40 Acinetobacter baumannii clinical isolates were collected to screen for PMB-resistant strains. Several clinical isolates including NCCP 16007 were far more resistant to PMB (MIC: 128-256 μg/ml) than the ATCC 17978 strain (MIC: 2 μg/ml) and appeared to possess resistance to broad-spectrum antibiotics including meropenem and 12 others. Four highly PMB-resistant strains possessed point mutations in the histidine kinase PmrB, leading to an increased expression of pmrC encoding a phosphoethanolamine transferase. Whole-genome analyses revealed that the NCCP 16007 stain had acquired two additional copies of the pmrC gene with phage integrase and 13 antibiotic resistance genes (ARGs) from other pathogens, including Klebsiella pneumoniae and Pseudomonas aeruginosa. The GC ratios of the ARGs (50-60%) were higher than that of the chromosomal backbone (39.06%), further supporting the horizontal gene transfer of ARGs. Comparative genomics with other multidrug-resistant A. baumannii strains revealed that the NCCP 16007 strain has many additional ARGs and has lost several virulence factors including Csu pili and heme oxygenase but exhibited high pathogenicity in Galleria mellonella-infection models. The observation of condensed biofilm through confocal and scanning electron microscopy suggested that the NCCP 16007 strain may possess high adhesion capacity during urinary tract infection. Therefore, our genomic and phenotypic analyses suggested that the multidrug-resistant A. baumannii NCCP 16007 strain possesses high genome plasticity, natural transformation ability, and pathogenicity.}, }
@article {pmid33372605, year = {2020}, author = {Li, C and Chen, J and Li, SC}, title = {Deep learning for HGT insertion sites recognition.}, journal = {BMC genomics}, volume = {21}, number = {Suppl 11}, pages = {893}, pmid = {33372605}, issn = {1471-2164}, support = {7005215//City University of Hong Kong/ ; }, mesh = {Base Sequence ; *Deep Learning ; *Gene Transfer, Horizontal ; Genome ; Metagenomics ; Phylogeny ; }, abstract = {BACKGROUND: Horizontal Gene Transfer (HGT) refers to the sharing of genetic materials between distant species that are not in a parent-offspring relationship. The HGT insertion sites are important to understand the HGT mechanisms. Recent studies in main agents of HGT, such as transposon and plasmid, demonstrate that insertion sites usually hold specific sequence features. This motivates us to find a method to infer HGT insertion sites according to sequence features.<br><br>RESULTS: In this paper, we propose a deep residual network, DeepHGT, to recognize HGT insertion sites. To train DeepHGT, we extracted about 1.55 million sequence segments as training instances from 262 metagenomic samples, where the ratio between positive instances and negative instances is about 1:1. These segments are randomly partitioned into three subsets: 80% of them as the training set, 10% as the validation set, and the remaining 10% as the test set. The training loss of DeepHGT is 0.4163 and the validation loss is 0.423. On the test set, DeepHGT has achieved the area under curve (AUC) value of 0.8782. Furthermore, in order to further evaluate the generalization of DeepHGT, we constructed an independent test set containing 689,312 sequence segments from another 147 gut metagenomic samples. DeepHGT has achieved the AUC value of 0.8428, which approaches the previous test AUC value. As a comparison, the gradient boosting classifier model implemented in PyFeat achieve an AUC value of 0.694 and 0.686 on the above two test sets, respectively. Furthermore, DeepHGT could learn discriminant sequence features; for example, DeepHGT has learned a sequence pattern of palindromic subsequences as a significantly (P-value=0.0182) local feature. Hence, DeepHGT is a reliable model to recognize the HGT insertion site.<br><br>CONCLUSION: DeepHGT is the first deep learning model that can accurately recognize HGT insertion sites on genomes according to the sequence pattern.}, }
@article {pmid33372588, year = {2020}, author = {Zhang, W and Zhao, Z and Wang, K and Shen, L and Shi, X}, title = {The International Conference on Intelligent Biology and Medicine (ICIBM) 2020: Scalable techniques and algorithms for computational genomics.}, journal = {BMC genomics}, volume = {21}, number = {Suppl 11}, pages = {831}, pmid = {33372588}, issn = {1471-2164}, mesh = {Algorithms ; Computational Biology ; *Genome-Wide Association Study ; Genomics ; *Medicine ; }, abstract = {In this introduction article, we summarize the 2020 International Conference on Intelligent Biology and Medicine (ICIBM 2020) conference which was held on August 9-10, 2020 (virtual conference). We then briefly describe the nine research articles included in this supplement issue. ICIBM 2020 hosted four scientific sections covering current topics in bioinformatics, computational biology, genomics, biomedical informatics, among others. A total of 75 original manuscripts were submitted to ICIBM 2020. All the papers were under rigorous review (at least three reviewers), and highly ranked manuscripts were selected for oral presentation and supplement issues. This genomics supplement issue included nine manuscripts. These articles cover methods and applications for single cell RNA sequencing, multi-omics data integration for gene regulation, gene fusion detection from long-read RNA sequencing, gene co-expression analysis of metabolic pathways in cancer, integrative genome-wide association studies (GWAS) of subcortical imaging phenotype in Alzheimer's disease, as well as deep learning methods for protein structure prediction, metabolic pathway membership inference, and horizontal gene transfer (HGT) insertion sites prediction.}, }
@article {pmid33370695, year = {2021}, author = {Zhou, G and Qiu, X and Wu, X and Lu, S}, title = {Horizontal gene transfer is a key determinant of antibiotic resistance genes profiles during chicken manure composting with the addition of biochar and zeolite.}, journal = {Journal of hazardous materials}, volume = {408}, number = {}, pages = {124883}, doi = {10.1016/j.jhazmat.2020.124883}, pmid = {33370695}, issn = {1873-3336}, mesh = {Animals ; Anti-Bacterial Agents ; Charcoal ; Chickens ; *Composting ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Manure ; *Zeolites ; }, abstract = {Livestock manure is an important reservoir of antibiotic resistance genes (ARGs). Biochar and zeolite are commonly used to improve the quality of compost, however, little is known about the impacts of these additives on the fate of ARGs during composting and the underlying mechanisms involved. In this study, zeolite (ZL), biochar (BC), or zeolite and biochar (ZB) simultaneously were added to chicken manure compost to evaluate their effects on the ARGs patterns. After composting, the abundance of ARGs reduced by 92.6% in control, while the reductions were 95.9%, 98.7% and 98.2% for ZL, BC, ZB, respectively. Co-occurrence network analysis indicated that the potential hosts for most ARGs were predominantly affiliated to Firmicutes such as Lactobacillus and Fastidiosipila. Furthermore, shifts in ARGs were significantly correlated with class 1 integrase gene (intI1), and structural equation models further revealed that intI1 gene contributed most (standardized total effect 0.92) to the ARGs-removal, which was trigged by horizontal gene transfer. Together these results suggest that the addition of zeolite and biochar mitigate the accumulation and spread of ARGs during composting, and the crucial role of horizontal gene transfer (HGT) on the behaviors of ARGs should pay more attention to in the future.}, }
@article {pmid33368983, year = {2021}, author = {Padial, JM and De la Riva, I}, title = {A paradigm shift in our view of species drives current trends in biological classification.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {96}, number = {2}, pages = {731-751}, doi = {10.1111/brv.12676}, pmid = {33368983}, issn = {1469-185X}, support = {CGL2014-56160-P//Spanish Government/ ; PGC2018-097421-B-100//Spanish Government/ ; }, mesh = {*Ecosystem ; *Genetics, Population ; Geography ; Phylogeny ; }, abstract = {Discontent about changes in species classifications has grown in recent years. Many of these changes are seen as arbitrary, stemming from unjustified conceptual and methodological grounds, or leading to species that are less distinct than those recognised in the past. We argue that current trends in species classification are the result of a paradigm shift toward which systematics and population genetics have converged and that regards species as the phylogenetic lineages that form the branches of the Tree of Life. Species delimitation now consists of determining which populations belong to which individual phylogenetic lineage. This requires inferences on the process of lineage splitting and divergence, a process to which we have only partial access through incidental evidence and assumptions that are themselves subject to refutation. This approach is not free of problems, as horizontal gene transfer, introgression, hybridisation, incorrect assumptions, sampling and methodological biases can mislead inferences of phylogenetic lineages. Increasing precision is demanded through the identification of both sister relationships and processes blurring or mimicking phylogeny, which has triggered, on the one hand, the development of methods that explicitly address such processes and, on the other hand, an increase in geographical and character data sampling necessary to infer/test such processes. Although our resolving power has increased, our knowledge of sister relationships - what we designate as species resolution - remains poor for many taxa and areas, which biases species limits and perceptions about how divergent species are or ought to be. We attribute to this conceptual shift the demise of trinominal nomenclature we are witnessing with the rise of subspecies to species or their rejection altogether; subspecies are raised to species if they are found to correspond to phylogenetic lineages, while they are rejected as fabricated taxa if they reflect arbitrary partitions of continuous or non-hereditary variation. Conservation strategies, if based on taxa, should emphasise species and reduce the use of subspecies to avoid preserving arbitrary partitions of continuous variation; local variation is best preserved by focusing on biological processes generating ecosystem resilience and diversity rather than by formally naming diagnosable units of any kind. Since many binomials still designate complexes of species rather than individual species, many species have been discovered but not named, geographical sampling is sparse, gene lineages have been mistaken for species, plenty of species limits remain untested, and many groups and areas lack adequate species resolution, we cannot avoid frequent changes to classifications as we address these problems. Changes will not only affect neglected taxa or areas, but also popular ones and regions where taxonomic research remained dormant for decades and old classifications were taken for granted.}, }
@article {pmid33367488, year = {2021}, author = {Haimovich, G and Dasgupta, S and Gerst, JE}, title = {RNA transfer through tunneling nanotubes.}, journal = {Biochemical Society transactions}, volume = {49}, number = {1}, pages = {145-160}, doi = {10.1042/BST20200113}, pmid = {33367488}, issn = {1470-8752}, mesh = {Animals ; Cell Communication/genetics ; Cell Membrane Structures/metabolism/*physiology ; Gene Transfer, Horizontal/*physiology ; Humans ; Nanotubes ; Organelles/metabolism ; Pseudopodia/metabolism ; RNA/*metabolism ; RNA Transport/physiology ; }, abstract = {It was already suggested in the early '70's that RNA molecules might transfer between mammalian cells in culture. Yet, more direct evidence for RNA transfer in animal and plant cells was only provided decades later, as this field became established. In this mini-review, we will describe evidence for the transfer of different types of RNA between cells through tunneling nanotubes (TNTs). TNTs are long, yet thin, open-ended cellular protrusions that are structurally distinct from filopodia. TNTs connect cells and can transfer many types of cargo, including small molecules, proteins, vesicles, pathogens, and organelles. Recent work has shown that TNTs can also transfer mRNAs, viral RNAs and non-coding RNAs. Here, we will review the evidence for TNT-mediated RNA transfer, discuss the technical challenges in this field, and conjecture about the possible significance of this pathway in health and disease.}, }
@article {pmid33367253, year = {2020}, author = {Zhang, Y and Chen, M and Siemiatkowska, B and Toleco, MR and Jing, Y and Strotmann, V and Zhang, J and Stahl, Y and Fernie, AR}, title = {A Highly Efficient Agrobacterium-Mediated Method for Transient Gene Expression and Functional Studies in Multiple Plant Species.}, journal = {Plant communications}, volume = {1}, number = {5}, pages = {100028}, pmid = {33367253}, issn = {2590-3462}, mesh = {Agrobacterium/*genetics ; Arabidopsis/genetics ; Gene Editing/*methods ; Gene Expression/*genetics ; Gene Expression Regulation, Plant/genetics ; Gene Transfer, Horizontal ; Plant Leaves/genetics/metabolism ; Plants/*genetics ; Tandem Affinity Purification ; Transformation, Genetic ; }, abstract = {Although the use of stable transformation technology has led to great insight into gene function, its application in high-throughput studies remains arduous. Agro-infiltration have been widely used in species such as Nicotiana benthamiana for the rapid detection of gene expression and protein interaction analysis, but this technique does not work efficiently in other plant species, including Arabidopsis thaliana. As an efficient high-throughput transient expression system is currently lacking in the model plant species A. thaliana, we developed a method that is characterized by high efficiency, reproducibility, and suitability for transient expression of a variety of functional proteins in A. thaliana and 7 other plant species, including Brassica oleracea, Capsella rubella, Thellungiella salsuginea, Thellungiella halophila, Solanum tuberosum, Capsicum annuum, and N. benthamiana. Efficiency of this method was independently verified in three independent research facilities, pointing to the robustness of this technique. Furthermore, in addition to demonstrating the utility of this technique in a range of species, we also present a case study employing this method to assess protein-protein interactions in the sucrose biosynthesis pathway in Arabidopsis.}, }
@article {pmid33363055, year = {2020}, author = {Yang, L and Wang, Y and Yu, P and Ren, S and Zhu, Z and Jin, Y and Yan, J and Peng, X and Chen, L}, title = {Prophage-Related Gene VpaChn25_0724 Contributes to Cell Membrane Integrity and Growth of Vibrio parahaemolyticus CHN25.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {595709}, pmid = {33363055}, issn = {2235-2988}, mesh = {Bacterial Proteins/genetics ; Cell Membrane ; Ecosystem ; Humans ; Prophages/genetics ; Transcriptome ; *Vibrio parahaemolyticus/genetics ; }, abstract = {Vibrio parahaemolyticus is a leading seafood-borne pathogen that can cause acute gastroenteritis and even death in humans. In aquatic ecosystems, phages constantly transform bacterial communities by horizontal gene transfer. Nevertheless, biological functions of prophage-related genes in V. parahaemolyticus remain to be fully unveiled. Herein, for the first time, we studied one such gene VpaChn25_0724 encoding an unknown hypothetical protein in V. parahaemolyticus CHN25. This gene deletion mutant ΔVpaChn25_0724 was constructed by homologous recombination, and its complementary mutant ΔVpaChn25_0724-com was also obtained. The ΔVpaChn25_0724 mutant exhibited a sever defect in growth and swimming motility particularly at lower temperatures. Biofilm formation and cytotoxicity capacity of V. parahaemolyticus CHN25 was significantly lowered in the absence of VpaChn25_0724. Comparative secretomic analysis revealed an increase in extracellular proteins of ΔVpaChn25_0724, which likely resulted from its damaged cell membrane. Comparison of transcriptome data showed twelve significantly altered metabolic pathways in ΔVpaChn25_0724, suggesting inactive transport and utilization of carbon sources, repressed energy production and membrane biogenesis in ΔVpaChn25_0724. Comparative transcriptomic analysis also revealed several remarkably down-regulated key regulators in bacterial gene regulatory networks linked to the observed phenotypic variations. Overall, the results here facilitate better understanding of biological significance of prophage-related genes remaining in V. parahaemolyticus.}, }
@article {pmid33362982, year = {2020}, author = {Driscoll, TP and Verhoeve, VI and Brockway, C and Shrewsberry, DL and Plumer, M and Sevdalis, SE and Beckmann, JF and Krueger, LM and Macaluso, KR and Azad, AF and Gillespie, JJ}, title = {Evolution of Wolbachia mutualism and reproductive parasitism: insight from two novel strains that co-infect cat fleas.}, journal = {PeerJ}, volume = {8}, number = {}, pages = {e10646}, pmid = {33362982}, issn = {2167-8359}, support = {R01 AI017828/AI/NIAID NIH HHS/United States ; R01 AI122672/AI/NIAID NIH HHS/United States ; R01 AI126853/AI/NIAID NIH HHS/United States ; R21 AI146773/AI/NIAID NIH HHS/United States ; }, abstract = {Wolbachiae are obligate intracellular bacteria that infect arthropods and certain nematodes. Usually maternally inherited, they may provision nutrients to (mutualism) or alter sexual biology of (reproductive parasitism) their invertebrate hosts. We report the assembly of closed genomes for two novel wolbachiae, wCfeT and wCfeJ, found co-infecting cat fleas (Ctenocephalides felis) of the Elward Laboratory colony (Soquel, CA, USA). wCfeT is basal to nearly all described Wolbachia supergroups, while wCfeJ is related to supergroups C, D and F. Both genomes contain laterally transferred genes that inform on the evolution of Wolbachia host associations. wCfeT carries the Biotin synthesis Operon of Obligate intracellular Microbes (BOOM); our analyses reveal five independent acquisitions of BOOM across the Wolbachia tree, indicating parallel evolution towards mutualism. Alternately, wCfeJ harbors a toxin-antidote operon analogous to the wPip cinAB operon recently characterized as an inducer of cytoplasmic incompatibility (CI) in flies. wCfeJ cinB and three adjacent genes are collectively similar to large modular toxins encoded in CI-like operons of certain Wolbachia strains and Rickettsia species, signifying that CI toxins streamline by fission of large modular toxins. Remarkably, the C. felis genome itself contains two CI-like antidote genes, divergent from wCfeJ cinA, revealing episodic reproductive parasitism in cat fleas and evidencing mobility of CI loci independent of WO-phage. Additional screening revealed predominant co-infection (wCfeT/wCfeJ) amongst C. felis colonies, though fleas in wild populations mostly harbor wCfeT alone. Collectively, genomes of wCfeT, wCfeJ, and their cat flea host supply instances of lateral gene transfers that could drive transitions between parasitism and mutualism.}, }
@article {pmid33361364, year = {2021}, author = {Li, Z and Shi, L and Wang, B and Wei, X and Zhang, J and Guo, T and Kong, J and Wang, M and Xu, H}, title = {In Vitro Assessment of Antimicrobial Resistance Dissemination Dynamics during Multidrug-Resistant-Bacterium Invasion Events by Using a Continuous-Culture Device.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {6}, pages = {}, pmid = {33361364}, issn = {1098-5336}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteriological Techniques ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/drug effects/*genetics/growth &amp; development ; Gene Transfer, Horizontal ; Microbial Interactions ; Microbial Sensitivity Tests ; Phylogeny ; Salmonella enterica/drug effects/*genetics/growth &amp; development ; Tetracycline/pharmacology ; }, abstract = {Antimicrobial-resistant pathogens display significant public health threats by causing difficulties in clinical treatment of bacterial infection. Antimicrobial resistance (AMR) is transmissible between bacteria, significantly increasing the appearance of antimicrobial-resistant pathogens and aggravating the AMR problem. In this work, the dissemination dynamics of AMR from invading multidrug-resistant (MDR) Escherichia coli to a community of pathogenic Salmonella enterica was investigated using a continuous-culture device, and the behaviors of dissemination dynamics under different levels of antibiotic stress were investigated. Three MDR E. coli invasion events were analyzed in this work: MDR E. coli-S. enterica cocolonization, MDR E. coli invasion after antibiotic treatment of S. enterica, and MDR E. coli invasion before antibiotic treatment of S. enterica It was found that both horizontal gene transfer (HGT) and vertical gene transfer (VGT) play significant roles in AMR dissemination, although different processes contribute differently under different circumstances, that environmental levels of antibiotics promote AMR dissemination by enhancing HGT rather than leading to selective advantage for resistant bacteria, and that early invasion of MDR E. coli completely and quickly sabotages the effectiveness of antibiotic treatment. These findings contribute to understanding the drivers of AMR dissemination under different antibiotic stresses, the detrimental impact of environmental tetracycline contamination, and the danger of nosocomial presence and dissemination of MDR nonpathogens.IMPORTANCE Antimicrobial resistance poses a grave threat to public health and reduces the effectiveness of antimicrobial drugs in treating bacterial infections. Antimicrobial resistance is transmissible, either by horizontal gene transfer between bacteria or by vertical gene transfer following inheritance of genetic traits. The dissemination dynamics and behaviors of this threat, however, have not been rigorously investigated. In this work, with a continuous-culture device, we studied antimicrobial resistance dissemination processes by simulating antimicrobial-resistant Escherichia coli invasion to a pathogenic Salmonella enterica community. Using this novel tool, we provide evidence on the drivers of antimicrobial resistance dissemination, on the detrimental impact of environmental antibiotic contamination, and on the danger of antimicrobial resistance in hospitals, even if what harbors the antimicrobial resistance is not a pathogen. This work furthers our understanding of antimicrobial resistance and its dissemination between bacteria and of antibiotic therapy, our most powerful tool against bacterial infection.}, }
@article {pmid33361328, year = {2020}, author = {Alalam, H and Graf, FE and Palm, M and Abadikhah, M and Zackrisson, M and Boström, J and Fransson, A and Hadjineophytou, C and Persson, L and Stenberg, S and Mattsson, M and Ghiaci, P and Sunnerhagen, P and Warringer, J and Farewell, A}, title = {A High-Throughput Method for Screening for Genes Controlling Bacterial Conjugation of Antibiotic Resistance.}, journal = {mSystems}, volume = {5}, number = {6}, pages = {}, pmid = {33361328}, issn = {2379-5077}, abstract = {The rapid horizontal transmission of antibiotic resistance genes on conjugative plasmids between bacterial host cells is a major cause of the accelerating antibiotic resistance crisis. There are currently no experimental platforms for fast and cost-efficient screening of genetic effects on antibiotic resistance transmission by conjugation, which prevents understanding and targeting conjugation. We introduce a novel experimental framework to screen for conjugation-based horizontal transmission of antibiotic resistance between >60,000 pairs of cell populations in parallel. Plasmid-carrying donor strains are constructed in high-throughput. We then mix the resistance plasmid-carrying donors with recipients in a design where only transconjugants can reproduce, measure growth in dense intervals, and extract transmission times as the growth lag. As proof-of-principle, we exhaustively explore chromosomal genes controlling F-plasmid donation within Escherichia coli populations, by screening the Keio deletion collection in high replication. We recover all seven known chromosomal gene mutants affecting conjugation as donors and identify many novel mutants, all of which diminish antibiotic resistance transmission. We validate nine of the novel genes' effects in liquid mating assays and complement one of the novel genes' effect on conjugation (rseA). The new framework holds great potential for exhaustive disclosing of candidate targets for helper drugs that delay resistance development in patients and societies and improve the longevity of current and future antibiotics. Further, the platform can easily be adapted to explore interspecies conjugation, plasmid-borne factors, and experimental evolution and be used for rapid construction of strains.IMPORTANCE The rapid transmission of antibiotic resistance genes on conjugative plasmids between bacterial host cells is a major cause of the accelerating antibiotic resistance crisis. There are currently no experimental platforms for fast and cost-efficient screening of genetic effects on antibiotic resistance transmission by conjugation, which prevents understanding and targeting conjugation. We introduce a novel experimental framework to screen for conjugation-based horizontal transmission of antibiotic resistance between >60,000 pairs of cell populations in parallel. As proof-of-principle, we exhaustively explore chromosomal genes controlling F-plasmid donation within E. coli populations. We recover all previously known and many novel chromosomal gene mutants that affect conjugation efficiency. The new framework holds great potential for rapid screening of compounds that decrease transmission. Further, the platform can easily be adapted to explore interspecies conjugation, plasmid-borne factors, and experimental evolution and be used for rapid construction of strains.}, }
@article {pmid33361320, year = {2020}, author = {Jiménez-González, A and Andersson, JO}, title = {Metabolic Reconstruction Elucidates the Lifestyle of the Last Diplomonadida Common Ancestor.}, journal = {mSystems}, volume = {5}, number = {6}, pages = {}, pmid = {33361320}, issn = {2379-5077}, abstract = {The identification of ancestral traits is essential to understanding the evolution of any group. In the case of parasitic groups, this helps us understand the adaptation to this lifestyle and a particular host. Most diplomonads are parasites, but there are free-living members of the group nested among the host-associated diplomonads. Furthermore, most of the close relatives within Fornicata are free-living organisms. This leaves the lifestyle of the ancestor unclear. Here, we present metabolic maps of four different diplomonad species. We identified 853 metabolic reactions and 147 pathways present in at least one of the analyzed diplomonads. Our study suggests that diplomonads represent a metabolically diverse group in which differences correlate with different environments (e.g., the detoxification of arsenic). Using a parsimonious analysis, we also provide a description of the putative metabolism of the last Diplomonadida common ancestor. Our results show that the acquisition and loss of reactions have shaped metabolism since this common ancestor. There is a net loss of reaction in all branches leading to parasitic diplomonads, suggesting an ongoing reduction in the metabolic capacity. Important traits present in host-associated diplomonads (e.g., virulence factors and the synthesis of UDP-N-acetyl-d-galactosamine) are shared with free-living relatives. The last Diplomonadida common ancestor most likely already had acquired important enzymes for the salvage of nucleotides and had a reduced capacity to synthesize nucleotides, lipids, and amino acids de novo, suggesting that it was an obligate host-associated organism.IMPORTANCE Diplomonads are a group of microbial eukaryotes found in oxygen-poor environments. There are both parasitic (e.g., Giardia intestinalis) and free-living (e.g., Trepomonas) members in the group. Diplomonads are well known for their anaerobic metabolism, which has been studied for many years. Here, we reconstructed whole metabolic networks of four extant diplomonad species as well as their ancestors, using a bioinformatics approach. We show that the metabolism within the group is under constant change throughout evolutionary time, in response to the environments that the different lineages explore. Both gene losses and gains are responsible for the adaptation processes. Interestingly, it appears that the last Diplomonadida common ancestor had a metabolism that is more similar to extant parasitic than free-living diplomonads. This suggests that the host-associated lifestyle of parasitic diplomonads, such as the human parasite G. intestinalis, is an old evolutionary adaptation.}, }
@article {pmid33356195, year = {2021}, author = {Shi, LD and Xu, QJ and Liu, JY and Han, ZX and Zhu, YG and Zhao, HP}, title = {Will a Non-antibiotic Metalloid Enhance the Spread of Antibiotic Resistance Genes: The Selenate Story.}, journal = {Environmental science &amp; technology}, volume = {55}, number = {2}, pages = {1004-1014}, doi = {10.1021/acs.est.0c05698}, pmid = {33356195}, issn = {1520-5851}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Metalloids ; Selenic Acid ; }, abstract = {The rapid emergence of antibiotic resistance genes (ARGs) has become an increasingly serious threat to public health. Previous studies illustrate the antibiotic-like effect of many substances. However, whether and how commonly used or existing non-antibiotic metalloids (e.g., selenate) would enhance ARG spread remains poorly known. Here, we tracked the long-term operation of a bioreactor continuously fed with selenate for more than 1000 days. Metagenomic sequencing identified 191 different ARGs, of which the total abundance increased significantly after the amendment of selenate. Network analyses showed that ARGs resisting multiple drugs had very similar co-occurrence patterns, implying a potentially larger health risk. Host classification not only indicated multidrug-resistant species but also distinguished the mechanism of ARG enrichment for vertical transfer and horizontal gene transfer. Genome reconstruction of an ARG host suggested that selenate and its bioreduction product selenite could stimulate the overproduction of intracellular reactive oxygen species, which was confirmed by the direct measurement. Bacterial membrane permeability, type IV pilus formation, and DNA repair and recombination were also enhanced, together facilitating the horizontal acquirement of ARGs. Overall, this study for the first time highlights the ARG emergence and dissemination induced by a non-antibiotic metalloid and identifies ARG as a factor to consider in selenate bioremediation.}, }
@article {pmid33353175, year = {2020}, author = {Frosini, SM and Bond, R and McCarthy, AJ and Feudi, C and Schwarz, S and Lindsay, JA and Loeffler, A}, title = {Genes on the Move: In Vitro Transduction of Antimicrobial Resistance Genes between Human and Canine Staphylococcal Pathogens.}, journal = {Microorganisms}, volume = {8}, number = {12}, pages = {}, pmid = {33353175}, issn = {2076-2607}, support = {MR/P028225/1/MRC_/Medical Research Council/United Kingdom ; MR/R000042/1/MRC_/Medical Research Council/United Kingdom ; BB/K011952/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {Transmission of methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-resistant Staphylococcus pseudintermedius (MRSP) between people and pets, and their co-carriage, are well-described. Potential exchange of antimicrobial resistance (AMR) genes amongst these staphylococci was investigated in vitro through endogenous bacteriophage-mediated transduction. Bacteriophages were UV-induced from seven donor isolates of canine (MRSP) and human (MRSA) origin, containing tet(M), tet(K), fusB or fusC, and lysates filtered. Twenty-seven tetracycline- and fusidic acid- (FA-) susceptible recipients were used in 122 donor-recipient combinations (22 tetracycline, 100 FA) across 415 assays (115 tetracycline, 300 FA). Bacteriophage lysates were incubated with recipients and presumed transductants quantified on antimicrobial-supplemented agar plates. Tetracycline resistance transduction from MRSP and MRSA to methicillin-susceptible S. pseudintermedius (MSSP) was confirmed by PCR in 15/115 assays. No FA-resistance transfer occurred, confirmed by negative fusB/fusC PCR, but colonies resulting from FA assays had high MICs (≥32 mg/L) and showed mutations in fusA, two at a novel position (F88L), nine at H457[Y/N/L]. Horizontal gene transfer of tetracycline-resistance confirms that resistance genes can be shared between coagulase-positive staphylococci from different hosts. Cross-species AMR transmission highlights the importance of good antimicrobial stewardship across humans and veterinary species to support One Health.}, }
@article {pmid33352125, year = {2020}, author = {Gallot-Lavallée, L and Archibald, JM}, title = {Evolutionary Biology: Viral Rhodopsins Illuminate Algal Evolution.}, journal = {Current biology : CB}, volume = {30}, number = {24}, pages = {R1469-R1471}, doi = {10.1016/j.cub.2020.10.080}, pmid = {33352125}, issn = {1879-0445}, mesh = {Anions ; Channelrhodopsins ; *Chlorophyta/genetics ; Gene Transfer, Horizontal ; *Giant Viruses/metabolism ; Rhodopsin/genetics/metabolism ; }, abstract = {A new metagenomics study has shown that marine viruses recently acquired genes encoding light-gated ion channels from green algae. These so-called channelrhodopsin genes may allow the viruses to manipulate the swimming behavior of the algae they infect.}, }
@article {pmid33352068, year = {2020}, author = {Ghanim, GE and Rio, DC and Teixeira, FK}, title = {Mechanism and regulation of P element transposition.}, journal = {Open biology}, volume = {10}, number = {12}, pages = {200244}, pmid = {33352068}, issn = {2046-2441}, support = {/WT_/Wellcome Trust/United Kingdom ; R21 HG010238/HG/NHGRI NIH HHS/United States ; R35 GM118121/GM/NIGMS NIH HHS/United States ; 206257/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *DNA Transposable Elements ; Drosophila Proteins/chemistry/genetics/metabolism ; Drosophila melanogaster/*genetics ; Gene Expression Regulation ; Gene Transfer, Horizontal ; Germ Cells/metabolism ; Histones/metabolism ; *Hybridization, Genetic ; Maternal Inheritance ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Transport ; RNA Splicing ; RNA, Small Interfering/genetics ; Selection, Genetic ; Transposases/chemistry/genetics/metabolism ; Vertebrates ; }, abstract = {P elements were first discovered in the fruit fly Drosophila melanogaster as the causative agents of a syndrome of aberrant genetic traits called hybrid dysgenesis. This occurs when P element-carrying males mate with females that lack P elements and results in progeny displaying sterility, mutations and chromosomal rearrangements. Since then numerous genetic, developmental, biochemical and structural studies have culminated in a deep understanding of P element transposition: from the cellular regulation and repression of transposition to the mechanistic details of the transposase nucleoprotein complex. Recent studies have revealed how piwi-interacting small RNA pathways can act to control splicing of the P element pre-mRNA to modulate transposase production in the germline. A recent cryo-electron microscopy structure of the P element transpososome reveals an unusual DNA architecture at the transposon termini and shows that the bound GTP cofactor functions to position the transposon ends within the transposase active site. Genome sequencing efforts have shown that there are P element transposase-homologous genes (called THAP9) in other animal genomes, including humans. This review highlights recent and previous studies, which together have led to new insights, and surveys our current understanding of the biology, biochemistry, mechanism and regulation of P element transposition.}, }
@article {pmid33350471, year = {2021}, author = {Hong, K and Beld, J and Davis, TD and Burkart, MD and Palenik, B}, title = {Screening and characterization of polyhydroxyalkanoate granules, and phylogenetic analysis of polyhydroxyalkanoate synthase gene PhaC in cyanobacteria.}, journal = {Journal of phycology}, volume = {57}, number = {3}, pages = {754-765}, doi = {10.1111/jpy.13123}, pmid = {33350471}, issn = {1529-8817}, support = {K12 GM068524/GM/NIGMS NIH HHS/United States ; }, mesh = {Acyltransferases ; *Cyanobacteria/genetics ; Nodularia ; Phormidium ; Phylogeny ; *Polyhydroxyalkanoates ; RNA, Ribosomal, 16S/genetics ; Synechocystis ; }, abstract = {Using Nile Red and BODIPY 493/503 dye-staining and fluorescence microscopy, twenty cyanobacterial strains, including ten commercially available strains and ten environmental isolates from estuaries, freshwater ponds, and lagoons, were screened for the accumulation of ecologically important and potentially biotechnologically significant carbon storage granules such as polyhydroxyalkanoates (PHA). Dye-staining granules were observed in six strains. Three Synechocystis, spp. strains WHSYN, LSNM, and CGF-1, and a Phormidium-like sp. CGFILA were isolated from environmental sources and found to produce granules of polyhydroxyalkanoate (PHA) according to PHA synthase gene (phaC) PCR screening and [1] H NMR analyses. The environmental isolate, Nodularia sp. Las Olas and commercially available Phormidium cf. iriguum CCALA 759 displayed granules but screened negative for PHA according to phaC PCR and [1] H NMR analyses. Partial polyhydroxyalkanoate synthase subunit C (phaC) and 16S rRNA gene sequences obtained from the PHA-accumulating strains and analyzed alongside publicly available phaC, phaE, 16S rRNA, and 23S rRNA data help in understanding the distribution and evolutionary history of PHA biosynthesis within the phylum Cyanobacteria. The data show that the presence of phaC is highly conserved within the genus Synechocystis, and present in at least one isolate of Phormidium. Maximum likelihood analyses and cophylogenetic modeling of PHA synthase gene sequences provide evidence of a recent horizontal gene transfer event between distant genera of cyanobacteria related to Pleurocapsa sp. PCC 7327 and Phormidium-like sp. CGFILA. These findings will help guide additional screening for PHA producers, and may explain why some Phormidium species produce PHAs, while others do not.}, }
@article {pmid33349652, year = {2021}, author = {Wheatley, RM and MacLean, RC}, title = {CRISPR-Cas systems restrict horizontal gene transfer in Pseudomonas aeruginosa.}, journal = {The ISME journal}, volume = {15}, number = {5}, pages = {1420-1433}, pmid = {33349652}, issn = {1751-7370}, support = {/WT_/Wellcome Trust/United Kingdom ; 106918/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Bacteriophages/genetics ; *CRISPR-Cas Systems/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Gene Transfer, Horizontal ; Pseudomonas aeruginosa/genetics ; }, abstract = {CRISPR-Cas systems provide bacteria and archaea with an adaptive immune system that targets foreign DNA. However, the xenogenic nature of immunity provided by CRISPR-Cas raises the possibility that these systems may constrain horizontal gene transfer. Here we test this hypothesis in the opportunistic pathogen Pseudomonas aeruginosa, which has emerged as an important model system for understanding CRISPR-Cas function. Across the diversity of P. aeruginosa, active CRISPR-Cas systems are associated with smaller genomes and higher GC content, suggesting that CRISPR-Cas inhibits the acquisition of foreign DNA. Although phage is the major target of CRISPR-Cas spacers, more than 80% of isolates with an active CRISPR-Cas system have spacers that target integrative conjugative elements (ICE) or the conserved conjugative transfer machinery used by plasmids and ICE. Consistent with these results, genomes containing active CRISPR-Cas systems harbour a lower abundance of both prophage and ICE. Crucially, spacers in genomes with active CRISPR-Cas systems map to ICE and phage that are integrated into the chromosomes of closely related genomes lacking CRISPR-Cas immunity. We propose that CRISPR-Cas acts as an important constraint to horizontal gene transfer, and the evolutionary mechanisms that ensure its maintenance or drive its loss are key to the ability of this pathogen to adapt to new niches and stressors.}, }
@article {pmid33347602, year = {2021}, author = {Wendling, CC and Refardt, D and Hall, AR}, title = {Fitness benefits to bacteria of carrying prophages and prophage-encoded antibiotic-resistance genes peak in different environments.}, journal = {Evolution; international journal of organic evolution}, volume = {75}, number = {2}, pages = {515-528}, pmid = {33347602}, issn = {1558-5646}, mesh = {Anti-Bacterial Agents ; Drug Resistance, Bacterial/*genetics ; Escherichia coli K12/*genetics/virology ; *Gene Transfer, Horizontal ; *Genetic Fitness ; Prophages/*genetics ; }, abstract = {Understanding the role of horizontal gene transfer (HGT) in adaptation is a key challenge in evolutionary biology. In microbes, an important mechanism of HGT is prophage acquisition (phage genomes integrated into bacterial chromosomes). Prophages can influence bacterial fitness via the transfer of beneficial genes (including antibiotic-resistance genes, ARGs), protection from superinfecting phages, or switching to a lytic lifecycle that releases free phages infectious to competitors. We expect these effects to depend on environmental conditions because of, for example, environment-dependent induction of the lytic lifecycle. However, it remains unclear how costs/benefits of prophages vary across environments. Here, studying prophages with/without ARGs in Escherichia coli, we disentangled the effects of prophages alone and adaptive genes they carry. In competition with prophage-free strains, benefits from prophages and ARGs peaked in different environments. Prophages were most beneficial when induction of the lytic lifecycle was common, whereas ARGs were more beneficial upon antibiotic exposure and with reduced prophage induction. Acquisition of prophage-encoded ARGs by competing strains was most common when prophage induction, and therefore free phages, were common. Thus, selection on prophages and adaptive genes they carry varies independently across environments, which is important for predicting the spread of mobile/integrating genetic elements and their role in evolution.}, }
@article {pmid33345705, year = {2021}, author = {Zhang, H and Liu, J and Wang, L and Zhai, Z}, title = {Glyphosate escalates horizontal transfer of conjugative plasmid harboring antibiotic resistance genes.}, journal = {Bioengineered}, volume = {12}, number = {1}, pages = {63-69}, pmid = {33345705}, issn = {2165-5987}, mesh = {Drug Resistance, Bacterial/*drug effects/genetics ; Escherichia coli/genetics ; Gene Transfer, Horizontal/*drug effects/genetics ; Genes, Bacterial/genetics ; Glycine/*analogs &amp; derivatives/pharmacology ; Plasmids/*genetics ; Reactive Oxygen Species/analysis/metabolism ; Glyphosate ; }, abstract = {Glyphosate has been frequently detected in water environments because of the wide use for controlling weed in farm lands and urban areas. Presently, the focus of the majority of studies is placed on the toxicity of glyphosate on humans and animals. However, the effects of glyphosate on horizontal transfer of conjugative plasmid carrying antibiotic resistance gene (ARG) are largely unknown. Here, we explored the ability and potential mechanism of glyphosate for accelerating horizontal transfer of conjugative plasmid-mediated ARG. The results showed that glyphosate can effectively boost horizontal transfer rate of conjugative plasmid carrying ARG. The possible mechanism analysis demonstrated that over-production of reactive oxygen species and reactive nitrogen species effectively regulated expression levels of bacterial outer membrane protein and conjugative transfer-related genes, thereby resulting into elevated horizontal transfer rate of plasmid-mediated ARG. In conclusion, this study casts new understanding into the biological effects of glyphosate on ARG.}, }
@article {pmid33343523, year = {2020}, author = {Loh, B and Chen, J and Manohar, P and Yu, Y and Hua, X and Leptihn, S}, title = {A Biological Inventory of Prophages in A. baumannii Genomes Reveal Distinct Distributions in Classes, Length, and Genomic Positions.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {579802}, pmid = {33343523}, issn = {1664-302X}, abstract = {Acinetobacter baumannii is of major clinical importance as the bacterial pathogen often causes hospital acquired infections, further complicated by the high prevalence of antibiotic resistant strains. Aside from natural tolerance to certain antibiotic classes, resistance is often acquired by the exchange of genetic information via conjugation but also by the high natural competence exhibited by A. baumannii. In addition, bacteriophages are able to introduce resistance genes but also toxins and virulence factors via phage mediated transduction. In this work, we analyzed the complete genomes of 177 A. baumannii strains for the occurrence of prophages, and analyzed their taxonomy, size and positions of insertion. Among all the prophages that were detected, Siphoviridae and Myoviridae were the two most commonly found families, while the average genome size was determined to be approximately 4 Mbp. Our data shows the wide variation in the number of prophages in A. baumannii genomes and the prevalence of certain prophages within strains that are most "successful" or potentially beneficial to the host. Our study also revealed that only two specific sites of insertion within the genome of the host bacterium are being used, with few exceptions only. Lastly, we analyzed the existence of genes that are encoded in the prophages, which may confer antimicrobial resistance (AMR). Several phages carry AMR genes, including OXA-23 and NDM-1, illustrating the importance of lysogenic phages in the acquisition of resistance genes.}, }
@article {pmid33343000, year = {2021}, author = {Dragoš, A and Priyadarshini, B and Hasan, Z and Strube, ML and Kempen, PJ and Maróti, G and Kaspar, C and Bose, B and Burton, BM and Bischofs, IB and Kovács, &#xc1;T}, title = {Pervasive prophage recombination occurs during evolution of spore-forming Bacilli.}, journal = {The ISME journal}, volume = {15}, number = {5}, pages = {1344-1358}, pmid = {33343000}, issn = {1751-7370}, support = {R01 GM121865/GM/NIGMS NIH HHS/United States ; R01GM121865/NH/NIH HHS/United States ; }, mesh = {*Bacillus ; Bacillus subtilis/genetics ; *Bacteriophages/genetics ; Evolution, Molecular ; Prophages/genetics ; Spores, Bacterial/genetics ; }, abstract = {Phages are the main source of within-species bacterial diversity and drivers of horizontal gene transfer, but we know little about the mechanisms that drive genetic diversity of these mobile genetic elements (MGEs). Recently, we showed that a sporulation selection regime promotes evolutionary changes within SPβ prophage of Bacillus subtilis, leading to direct antagonistic interactions within the population. Herein, we reveal that under a sporulation selection regime, SPβ recombines with low copy number phi3Ts phage DNA present within the B. subtilis population. Recombination results in a new prophage occupying a different integration site, as well as the spontaneous release of virulent phage hybrids. Analysis of Bacillus sp. strains suggests that SPβ and phi3T belong to a distinct cluster of unusually large phages inserted into sporulation-related genes that are equipped with a spore-related genetic arsenal. Comparison of Bacillus sp. genomes indicates that similar diversification of SPβ-like phages takes place in nature. Our work is a stepping stone toward empirical studies on phage evolution, and understanding the eco-evolutionary relationships between bacteria and their phages. By capturing the first steps of new phage evolution, we reveal striking relationship between survival strategy of bacteria and evolution of their phages.}, }
@article {pmid33341549, year = {2021}, author = {Zhou, ZC and Shuai, XY and Lin, ZJ and Liu, Y and Zhu, L and Chen, H}, title = {Prevalence of multi-resistant plasmids in hospital inhalable particulate matter (PM) and its impact on horizontal gene transfer.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {270}, number = {}, pages = {116296}, doi = {10.1016/j.envpol.2020.116296}, pmid = {33341549}, issn = {1873-6424}, mesh = {Animals ; Anti-Bacterial Agents ; *Gene Transfer, Horizontal ; Hospitals ; *Particulate Matter ; Plasmids/genetics ; Prevalence ; Swine ; }, abstract = {Antibiotic resistance is exacerbated by the exchange of antibiotic resistance genes (ARGs) between microbes from diverse habitats. Plasmids are important ARGs mobile elements and are spread by horizontal gene transfer (HGT). In this study, we demonstrated the presence of multi-resistant plasmids from inhalable particulate matter (PM) and its effect on gene horizontal transfer. Three transferable multi-resistant plasmids were identified from PM in a hospital, using conjugative mating assays and nanopore sequencing. pTAir-3 contained 26 horizontal transfer elements and 10 ARGs. Importantly pTAir-5 harbored carbapenem resistance gene (blaOXA) which shows homology to plasmids from human and pig commensal bacteria, thus indicating that PM is a media for antibiotic resistant plasmid spread. In addition, 125 μg/mL PM2.5 and PM10 significantly increased the conjugative transfer rate by 110% and 30%, respectively, and augmented reactive oxygen species (ROS) levels. Underlying mechanisms were revealed by identifying the upregulated expressional levels of genes related to ROS, SOS, cell membranes, pilus generation, and transposition via genome-wide RNA sequencing. The study highlights the airborne spread of multi-resistant plasmids and the impact of inhalable PM on the horizontal transfer of antibiotic resistance.}, }
@article {pmid33339886, year = {2020}, author = {Makkay, AM and Louyakis, AS and Ram-Mohan, N and Gophna, U and Gogarten, JP and Papke, RT}, title = {Insights into gene expression changes under conditions that facilitate horizontal gene transfer (mating) of a model archaeon.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {22297}, pmid = {33339886}, issn = {2045-2322}, mesh = {Archaea/*genetics/growth &amp; development ; Archaeal Proteins/genetics ; Biochemical Phenomena/*genetics ; Gene Expression Regulation, Archaeal ; Gene Transfer, Horizontal/*genetics ; Haloferax volcanii/*genetics ; }, abstract = {Horizontal gene transfer is a means by which bacteria, archaea, and eukaryotes are able to trade DNA within and between species. While there are a variety of mechanisms through which this genetic exchange can take place, one means prevalent in the archaeon Haloferax volcanii involves the transient formation of cytoplasmic bridges between cells and is referred to as mating. This process can result in the exchange of very large fragments of DNA between the participating cells. Genes governing the process of mating, including triggers to initiate mating, mechanisms of cell fusion, and DNA exchange, have yet to be characterized. We used a transcriptomic approach to gain a more detailed knowledge of how mating might transpire. By examining the differential expression of genes expressed in cells harvested from mating conditions on a filter over time and comparing them to those expressed in a shaking culture, we were able to identify genes and pathways potentially associated with mating. These analyses provide new insights into both the mechanisms and barriers of mating in Hfx. volcanii.}, }
@article {pmid33335921, year = {2020}, author = {Bose, S and Aggarwal, S and Singh, DV and Acharya, N}, title = {Extracellular vesicles: An emerging platform in gram-positive bacteria.}, journal = {Microbial cell (Graz, Austria)}, volume = {7}, number = {12}, pages = {312-322}, pmid = {33335921}, issn = {2311-2638}, abstract = {Extracellular vesicles (EV), also known as membrane vesicles, are produced as an end product of secretion by both pathogenic and non-pathogenic bacteria. Several reports suggest that archaea, gram-negative bacteria, and eukaryotic cells secrete membrane vesicles as a means for cell-free intercellular communication. EVs influence intercellular communication by transferring a myriad of biomolecules including genetic information. Also, EVs have been implicated in many phenomena such as stress response, intercellular competition, lateral gene transfer, and pathogenicity. However, the cellular process of secreting EVs in gram-positive bacteria is less studied. A notion with the thick cell-walled microbes such as gram-positive bacteria is that the EV release is impossible among them. The role of gram-positive EVs in health and diseases is being studied gradually. Being nano-sized, the EVs from gram-positive bacteria carry a diversity of cargo compounds that have a role in bacterial competition, survival, invasion, host immune evasion, and infection. In this review, we summarise the current understanding of the EVs produced by gram-positive bacteria. Also, we discuss the functional aspects of these components while comparing them with gram-negative bacteria.}, }
@article {pmid33335515, year = {2020}, author = {Luqman, A and Zabel, S and Rahmdel, S and Merz, B and Gruenheit, N and Harter, J and Nieselt, K and Götz, F}, title = {The Neuromodulator-Encoding sadA Gene Is Widely Distributed in the Human Skin Microbiome.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {573679}, pmid = {33335515}, issn = {1664-302X}, abstract = {Trace amines (TA) are endogenously produced in mammals, have a low concentration in the central nervous system (CNS), but trigger a variety of neurological effects and intervene in host cell communication. It emerged that neurotransmitters and TA are produced also by the microbiota. As it has been shown that TA contribute to wound healing, we examined the skin microbiome of probands using shotgun metagenomics. The phyla Actinobacteria, Proteobacteria, Firmicutes, and Bacteroidetes were predominant. Since SadA is a highly promiscuous TA-producing decarboxylase in Firmicutes, the skin microbiome was specifically examined for the presence of sadA-homologous genes. By mapping the reads of certain genes, we found that, although there were less reads mapping to sadA than to ubiquitous housekeeping genes (arcC and mutS), normalized reads counts were still >1000 times higher than those of rare control genes (icaA, icaB, and epiA). At protein sequence level SadA homologs were found in at least 7 phyla: Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, Acidobacteria, Chloroflexi, and Cyanobacteria, and in 23 genera of the phylum Firmicutes. A high proportion of the genera that have a SadA homolog belong to the classical skin and intestinal microbiota. The distribution of sadA in so many different phyla illustrates the importance of horizontal gene transfer (HGT). We show that the sadA gene is widely distributed in the human skin microbiome. When comparing the sadA read counts in the probands, there was no correlation between age and gender, but an enormous difference in the sadA read counts in the microbiome of the individuals. Since sadA is involved in TA synthesis, it is likely that the TA content of the skin is correlated with the amount of TA producing bacteria in the microbiome. In this way, the microbiome-generated TA could influence signal transmission in the epithelial and nervous system.}, }
@article {pmid33329445, year = {2020}, author = {Liang, D and Andersen, CB and Vetukuri, RR and Dou, D and Grenville-Briggs, LJ}, title = {Horizontal Gene Transfer and Tandem Duplication Shape the Unique CAZyme Complement of the Mycoparasitic Oomycetes Pythium oligandrum and Pythium periplocum.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {581698}, pmid = {33329445}, issn = {1664-302X}, abstract = {Crop protection strategies that are effective but that reduce our reliance on chemical pesticides are urgently needed to meet the UN sustainable development goals for global food security. Mycoparasitic oomycetes such as Pythium oligandrum and Pythium periplocum, have potential for the biological control of plant diseases that threaten crops and have attracted much attention due to their abilities to antagonize plant pathogens and modulate plant immunity. Studies of the molecular and genetic determinants of mycoparasitism in these species have been less well developed than those of their fungal counterparts. Carbohydrate-active enzymes (CAZymes) from P. oligandrum and P. periplocum are predicted to be important components of mycoparasitism, being involved in the degradation of the cell wall of their oomycete and fungal prey species. To explore the evolution of CAZymes of these species we performed an in silico identification and comparison of the full CAZyme complement (CAZyome) of the two mycoparasitic Pythium species (P. oligandrum and P. periplocum), with seven other Pythium species, and four Phytophthora species. Twenty CAZy gene families involved in the degradation of cellulose, hemicellulose, glucan, and chitin were expanded in, or unique to, mycoparasitic Pythium species and several of these genes were expressed during mycoparasitic interactions with either oomycete or fungal prey, as revealed by RNA sequencing and quantitative qRT-PCR. Genes from three of the cellulose and chitin degrading CAZy families (namely AA9, GH5_14, and GH19) were expanded via tandem duplication and predominantly located in gene sparse regions of the genome, suggesting these enzymes are putative pathogenicity factors able to undergo rapid evolution. In addition, five of the CAZy gene families were likely to have been obtained from other microbes by horizontal gene transfer events. The mycoparasitic species are able to utilize complex carbohydrates present in fungal cell walls, namely chitin and N-acetylglucosamine for growth, in contrast to their phytopathogenic counterparts. Nonetheless, a preference for the utilization of simple sugars for growth appears to be a common trait within the oomycete lineage.}, }
@article {pmid33329444, year = {2020}, author = {Tang, M and Kong, X and Hao, J and Liu, J}, title = {Epidemiological Characteristics and Formation Mechanisms of Multidrug-Resistant Hypervirulent Klebsiella pneumoniae.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {581543}, pmid = {33329444}, issn = {1664-302X}, abstract = {Multi-drug resistance (MDR) and hypervirulence (hv) were exhibited by different well-separated Klebsiella pneumoniae lineages in the past, but their convergence clones-MDR-hypervirulent K. pneumoniae (HvKPs)-both highly pathogenic and resistant to most available antibiotics, have increasingly been reported. In light of the clonal lineages and molecular characteristics of the studied MDR-HvKP strains found in the literature since 2014, this review discusses the epidemiology of MDR-HvKPs, in particular summarizing the three general aspects of plasmids-associated mechanisms underlying the formation of MDR-HvKPs clones: MDR-classic K. pneumoniae (cKPs) acquiring hv plasmids, hvKPs obtaining MDR plasmids, and the acquisition of hybrid plasmids harboring virulence and resistance determinants. A deeper understanding of epidemiological characteristics and possible formation mechanisms of MDR-HvKPs is greatly needed for the proper surveillance and management of this potential threat.}, }
@article {pmid33329443, year = {2020}, author = {Venice, F and Desirò, A and Silva, G and Salvioli, A and Bonfante, P}, title = {The Mosaic Architecture of NRPS-PKS in the Arbuscular Mycorrhizal Fungus Gigaspora margarita Shows a Domain With Bacterial Signature.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {581313}, pmid = {33329443}, issn = {1664-302X}, abstract = {As obligate biotrophic symbionts, arbuscular mycorrhizal fungi (AMF) live in association with most land plants. Among them, Gigaspora margarita has been deeply investigated because of its peculiar features, i.e., the presence of an intracellular microbiota with endobacteria and viruses. The genome sequencing of this fungus revealed the presence of some hybrid non-ribosomal peptide synthases-polyketide synthases (NRPS-PKS) that have been rarely identified in AMF. The aim of this study is to describe the architecture of these NRPS-PKS sequences and to understand whether they are present in other fungal taxa related to G. margarita. A phylogenetic analysis shows that the ketoacyl synthase (KS) domain of one G. margarita NRPS-PKS clusters with prokaryotic sequences. Since horizontal gene transfer (HGT) has often been advocated as a relevant evolutionary mechanism for the spread of secondary metabolite genes, we hypothesized that a similar event could have interested the KS domain of the PKS module. The bacterial endosymbiont of G. margarita, Candidatus Glomeribacter gigasporarum (CaGg), was the first candidate as a donor, since it possesses a large biosynthetic cluster involving an NRPS-PKS. However, bioinformatics analyses do not confirm the hypothesis of a direct HGT from the endobacterium to the fungal host: indeed, endobacterial and fungal sequences show a different evolution and potentially different donors. Lastly, by amplifying a NRPS-PKS conserved fragment and mining the sequenced AMF genomes, we demonstrate that, irrespective of the presence of CaGg, G. margarita, and some other related Gigasporaceae possess such a sequence.}, }
@article {pmid33323414, year = {2020}, author = {Xia, X and Lee, P and Cheung, S and Lu, Y and Liu, H}, title = {Discovery of Euryhaline Phycoerythrobilin-Containing Synechococcus and Its Mechanisms for Adaptation to Estuarine Environments.}, journal = {mSystems}, volume = {5}, number = {6}, pages = {}, pmid = {33323414}, issn = {2379-5077}, abstract = {Synechococcus are among the most abundant and widely distributed picocyanobacteria on earth. Cluster 5 phycoerythrobilin-containing (PEB-containing) Synechococcus, the major marine Synechococcus, were considered to prefer high salinity, and they are absent in estuarine ecosystems. However, we have detected PEB-containing Synechococcus in some low-salinity (<15-ppt) areas of the Pearl River estuary at an abundance up to 1.0 × 10[5] cells ml[-1] Two PEB-containing Synechococcus strains (HK01 and LTW-R) were isolated, and tests on them revealed their ability to cope with variations in the salinity (from 14 to 44 ppt). Phylogenetic analysis showed that HK01 belonged to a novel Synechococcus clade (HK1), whereas LTW-R was clustered with S5.2 strains. Whole-genome analysis revealed that a membrane channel protein with glycine zipper motifs is unique to euryhaline Synechococcus The upregulation of this protein, the osmotic sensors, and the heat shock protein HSP20 and the downregulation of the osmolyte biosynthesis enable euryhaline Synechococcus to well adapt to the low and fluctuating salinity in the estuarine environment. In addition, decreasing the salinity in LTW-R strongly downregulated several important metabolic pathways, including photosynthesis, and the Calvin-Benson cycle, whereas its growth was not significantly affected. Moreover, obtaining PEB genes from horizontal gene transfer expands the light niche significantly for euryhaline Synechococcus These results provided new insights into the life strategies and ecological function of marine PEB-containing Synechococcus under the unique environmental condition of estuarine waters, particularly in response to salinity variations.IMPORTANCE Understanding the strategies developed by different microbial groups to adapt to specific niches is critical. Through genome and transcriptome analyses of two newly isolated novel euryhaline Synechococcus strains, this study revealed that cluster 5 phycoerythrobilin-containing Synechococcus, which are thought to be strictly marine strains, could be abundant in low-salinity waters of the Pearl River estuary (salinity <15 ppt) and explained the molecular mechanisms that enabled them to adapt the low and fluctuating salinity in the estuarine environment. This study expands current understanding on mechanisms involved in niche separation of marine Synechococcus lineages.}, }
@article {pmid33321973, year = {2020}, author = {Cunha, E and Janela, R and Costa, M and Tavares, L and Veiga, AS and Oliveira, M}, title = {Nisin Influence on the Antimicrobial Resistance Ability of Canine Oral Enterococci.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {9}, number = {12}, pages = {}, pmid = {33321973}, issn = {2079-6382}, support = {SFRH/BD/131384/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/00276/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, abstract = {Periodontal disease (PD) is one of the most common diseases in dogs. Although previous studies have shown the potential of the antimicrobial peptide nisin for PD control, there is no information regarding its influence in the development of antimicrobial resistance or horizontal gene transfer (HGT). Nisin's mutant prevention concentration (MPC) and selection window (MSW) were determined for a collection of canine oral enterococci. Isolates recovered after the determination of the MPC values were characterized for their antimicrobial profile and its nisin minimum inhibitory and bactericidal concentrations. The potential of vanA HGT between Enterococcus faecium CCGU36804 and nine clinical canine staphylococci and enterococci was evaluated. Nisin MPC values ranged from 400 to more than 600 μg/mL. In comparison with the original enterococci collection, the isolates recovered after the determination of the nisin MPC showed increased resistance towards amoxicillin/clavulanate (5%), vancomycin (5%), enrofloxacin (10%), gentamicin (10%) and imipenem (15%). The HGT of vanA gene was not observed. This work showed that nisin selective pressure may induce changes in the bacteria's antimicrobial resistance profile but does not influence horizontal transfer of vanA gene. To our knowledge, this is the first report of nisin's MPC and MSW determination regarding canine enterococci.}, }
@article {pmid33318011, year = {2021}, author = {Somprasong, N and Hall, CM and Webb, JR and Sahl, JW and Wagner, DM and Keim, P and Currie, BJ and Schweizer, HP}, title = {Burkholderia ubonensis High-Level Tetracycline Resistance Is Due to Efflux Pump Synergy Involving a Novel TetA(64) Resistance Determinant.}, journal = {Antimicrobial agents and chemotherapy}, volume = {65}, number = {3}, pages = {}, pmid = {33318011}, issn = {1098-6596}, mesh = {Anti-Bacterial Agents/pharmacology ; Burkholderia ; *Burkholderia cepacia complex/genetics ; Humans ; *Tetracycline/pharmacology ; Tetracycline Resistance/genetics ; }, abstract = {Burkholderia ubonensis, a nonpathogenic soil bacterium belonging to the Burkholderia cepacia complex (Bcc), is highly resistant to some clinically significant antibiotics. The concern is that B. ubonensis may serve as a resistance reservoir for Bcc or B. pseudomallei complex (Bpc) organisms that are opportunistic human pathogens. Using a B. ubonensis strain highly resistant to tetracycline (MIC, ≥256 µg/ml), we identified and characterized tetA(64) that encodes a novel tetracycline-specific efflux pump of the major facilitator superfamily. TetA(64) and associated TetR(64) regulator expression are induced by tetracyclines. Although TetA(64) is the primary tetracycline and doxycycline resistance determinant, maximum tetracycline and doxycycline resistance requires synergy between TetA(64) and the nonspecific AmrAB-OprA resistance nodulation cell division efflux pump. TetA(64) does not efflux minocycline, tigecycline, and eravacycline. Comprehensive screening of genome sequences showed that TetA(64) is unequally distributed in the Bcc and absent from the Bpc. It is present in some major cystic fibrosis pathogens, like Burkholderia cenocepacia, but absent from others like Burkholderia multivorans The tetR(64)-tetA(64) genes are located in a region of chromosome 1 that is highly conserved in Burkholderia sp. Because there is no evidence for transposition, the tetR(64)-tetA(64) genes may have been acquired by homologous recombination after horizontal gene transfer. Although Burkholderia species contain a resident multicomponent efflux pump that allows them to respond to tetracyclines up to a certain concentration, the acquisition of the single-component TetA(64) by some species likely provides the synergy that these bacteria need to defend against high tetracycline concentrations in niche environments.}, }
@article {pmid33316633, year = {2020}, author = {Li, J and Zhou, Y and Yang, D and Zhang, S and Sun, Z and Wang, Y and Wang, S and Wu, C}, title = {Prevalence and antimicrobial susceptibility of Clostridium perfringens in chickens and pigs from Beijing and Shanxi, China.}, journal = {Veterinary microbiology}, volume = {252}, number = {}, pages = {108932}, doi = {10.1016/j.vetmic.2020.108932}, pmid = {33316633}, issn = {1873-2542}, abstract = {The prevalence and antimicrobial susceptibility of Clostridium perfringens (C. perfringens) in chickens and pigs were investigated in Beijing and Shanxi, China. In total, 322 C. perfringens (chicken n = 60 and pig n = 262) were obtained from 620 feces of chickens (n = 256) and pigs (n = 364). Multiplex PCR for toxin typing of C. perfringens revealed that all the isolates belong to type A, with 45.7 % (147/322) isolates carrying beta-2 toxin-encoding gene cpb2. Minimum inhibitory concentrations of 27 antimicrobial agents showed that 91.0 % of the tested C. perfringens isolates were resistant to gentamicin and sulfonamides (sulfisoxazole and trimethoprim-sulfamethoxazole), and little resistance was showed to amoxicillin-clavulanate, ceftiofur, doxycycline, vancomycin and linezolid. Additionally, nosiheptide, avilamycin, virginiamycin and bacitracin exhibited good activity against the tested C. perfringens with low MIC50 (0.06 to ≤4 μg/mL) and MIC90 values (0.25-8 μg/mL). Whole genome sequencing (WGS) of 48 representative isolates from each farm indicated that the C. perfringens contained diverse antimicrobial resistance genes [tetA(P), ant(6)-Ib, erm(Q), etc.] and toxin genes (cpb2, colA, cloSI, pfoA, etc.). By comparative analysis, four C. perfringens isolates from three different pig farms harboured cpb2-carrying plasmid p1 with 100 % nucleotide sequence identity, suggesting horizontal gene transfer among these microorganisms. The further phylogenomic reconstruction, based on the core-genome single nucleotide polymorphisms (SNPs) of the representatives, demonstrating that C. perfringens from the same farms and regions were closely related. These findings expanded our knowledge of C. perfringens isolated from animals in China, which provided scientific basis for efficient intervention or prevention measures of antimicrobial resistance in animal husbandry in China.}, }
@article {pmid33305885, year = {2021}, author = {Ferguson, KB and Visser, S and Dalíková, M and Provazníková, I and Urbaneja, A and Pérez-Hedo, M and Marec, F and Werren, JH and Zwaan, BJ and Pannebakker, BA and Verhulst, EC}, title = {Jekyll or Hyde? The genome (and more) of Nesidiocoris tenuis, a zoophytophagous predatory bug that is both a biological control agent and a pest.}, journal = {Insect molecular biology}, volume = {30}, number = {2}, pages = {188-209}, pmid = {33305885}, issn = {1365-2583}, mesh = {Animals ; Bacteria/genetics ; Biological Control Agents ; Female ; Gene Transfer, Horizontal ; Genome, Insect ; Heteroptera/*genetics/microbiology ; Symbiosis ; }, abstract = {Nesidiocoris tenuis (Reuter) is an efficient predatory biological control agent used throughout the Mediterranean Basin in tomato crops but regarded as a pest in northern European countries. From the family Miridae, it is an economically important insect yet very little is known in terms of genetic information and no genomic or transcriptomic studies have been published. Here, we use a linked-read sequencing strategy on a single female N. tenuis. From this, we assembled the 355 Mbp genome and delivered an ab initio, homology-based and evidence-based annotation. Along the way, the bacterial "contamination" was removed from the assembly. In addition, bacterial lateral gene transfer (LGT) candidates were detected in the N. tenuis genome. The complete gene set is composed of 24 688 genes; the associated proteins were compared to other hemipterans (Cimex lectularis, Halyomorpha halys and Acyrthosiphon pisum). We visualized the genome using various cytogenetic techniques, such as karyotyping, CGH and GISH, indicating a karyotype of 2n = 32. Additional analyses include the localization of 18S rDNA and unique satellite probes as well as pooled sequencing to assess nucleotide diversity and neutrality of the commercial population. This is one of the first mirid genomes to be released and the first of a mirid biological control agent.}, }
@article {pmid33305421, year = {2021}, author = {Richard, D and Pruvost, O and Balloux, F and Boyer, C and Rieux, A and Lefeuvre, P}, title = {Time-calibrated genomic evolution of a monomorphic bacterium during its establishment as an endemic crop pathogen.}, journal = {Molecular ecology}, volume = {30}, number = {8}, pages = {1823-1835}, doi = {10.1111/mec.15770}, pmid = {33305421}, issn = {1365-294X}, mesh = {Bacteria ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Phylogeny ; Plant Diseases/*microbiology ; }, abstract = {Horizontal gene transfer is of major evolutionary importance as it allows for the redistribution of phenotypically important genes among lineages. Such genes with essential functions include those involved in resistance to antimicrobial compounds and virulence factors in pathogenic bacteria. Understanding gene turnover at microevolutionary scales is critical to assess the pace of this evolutionary process. Here, we characterized and quantified gene turnover for the epidemic lineage of a bacterial plant pathogen of major agricultural importance worldwide. Relying on a dense geographic sampling spanning 39 years of evolution, we estimated both the dynamics of single nucleotide polymorphism accumulation and gene content turnover. We identified extensive gene content variation among lineages even at the smallest phylogenetic and geographic scales. Gene turnover rate exceeded nucleotide substitution rate by three orders of magnitude. Accessory genes were found preferentially located on plasmids, but we identified a highly plastic chromosomal region hosting ecologically important genes such as transcription activator-like effectors. Whereas most changes in the gene content are probably transient, the rapid spread of a mobile element conferring resistance to copper compounds widely used for the management of plant bacterial pathogens illustrates how some accessory genes can become ubiquitous within a population over short timeframes.}, }
@article {pmid33304460, year = {2020}, author = {Jiao, J and Tian, CF}, title = {Ancestral zinc-finger bearing protein MucR in alpha-proteobacteria: A novel xenogeneic silencer?.}, journal = {Computational and structural biotechnology journal}, volume = {18}, number = {}, pages = {3623-3631}, pmid = {33304460}, issn = {2001-0370}, abstract = {The MucR/Ros family protein is conserved in alpha-proteobacteria and characterized by its zinc-finger motif that has been proposed as the ancestral domain from which the eukaryotic C2H2 zinc-finger structure evolved. In the past decades, accumulated evidences have revealed MucR as a pleiotropic transcriptional regulator that integrating multiple functions such as virulence, symbiosis, cell cycle and various physiological processes. Scattered reports indicate that MucR mainly acts as a repressor, through oligomerization and binding to multiple sites of AT-rich target promoters. The N-terminal region and zinc-finger bearing C-terminal region of MucR mediate oligomerization and DNA-binding, respectively. These features are convergent to those of xenogeneic silencers such as H-NS, MvaT, Lsr2 and Rok, which are mainly found in other lineages. Phylogenetic analysis of MucR homologs suggests an ancestral origin of MucR in alpha- and delta-proteobacteria. Multiple independent duplication and lateral gene transfer events contribute to the diversity and phyletic distribution of MucR. Finally, we posed questions which remain unexplored regarding the putative roles of MucR as a xenogeneic silencer and a general manager in balancing adaptation and regulatory integration in the pangenome context.}, }
@article {pmid33301090, year = {2021}, author = {Duminil, J and Besnard, G}, title = {Utility of the Mitochondrial Genome in Plant Taxonomic Studies.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2222}, number = {}, pages = {107-118}, pmid = {33301090}, issn = {1940-6029}, mesh = {*DNA Barcoding, Taxonomic ; *Genome, Mitochondrial ; *Genomics/methods ; Phylogeny ; Phylogeography ; Plants/*classification/*genetics ; Polymorphism, Genetic ; Recombination, Genetic ; Sequence Analysis, DNA ; }, abstract = {Size, structure, and sequence content lability of plant mitochondrial genome (mtDNA) across species has sharply limited its use in taxonomic studies. Historically, mtDNA variation has been first investigated with RFLPs, while the development of universal primers then allowed studying sequence polymorphisms within short genomic regions (<3 kb). The recent advent of NGS technologies now offers new opportunities by greatly facilitating the assembly of longer mtDNA regions, and even full mitogenomes. Phylogenetic works aiming at comparing signals from different genomic compartments (i.e., nucleus, chloroplast, and mitochondria) have been developed on a few plant lineages, and have been shown especially relevant in groups with contrasted inheritance of organelle genomes. This chapter first reviews the main characteristics of mtDNA and the application offered in taxonomic studies. It then presents tips for best sequencing protocol based on NGS data to be routinely used in mtDNA-based phylogenetic studies.}, }
@article {pmid33295091, year = {2021}, author = {Hu, W and Pan, J and Wang, B and Guo, J and Li, M and Xu, M}, title = {Metagenomic insights into the metabolism and evolution of a new Thermoplasmata order (Candidatus Gimiplasmatales).}, journal = {Environmental microbiology}, volume = {23}, number = {7}, pages = {3695-3709}, doi = {10.1111/1462-2920.15349}, pmid = {33295091}, issn = {1462-2920}, mesh = {Archaea/genetics ; *Euryarchaeota/genetics ; Metagenome ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Thermoplasmata is a widely distributed and ecologically important archaeal class in the phylum Euryarchaeota. Because few cultures and genomes are available, uncharacterized Thermoplasmata metabolisms remain unexplored. In this study, we obtained four medium- to high-quality archaeal metagenome-assembled genomes (MAGs) from the filamentous fragments of black-odorous aquatic sediments (Foshan, Guangdong, China). Based on their 16S rRNA gene and ribosomal protein phylogenies, the four MAGs belong to the previously unnamed Thermoplasmata UBA10834 clade. We propose that this clade (five reference genomes from the Genome Taxonomy Database (GTDB) and four MAGs from this study) be considered a new order, Candidatus Gimiplasmatales. Metabolic pathway reconstructions indicated that the Ca. Gimiplasmatales MAGs can biosynthesize isoprenoids and nucleotides de novo. Additionally, some taxa have genes for formaldehyde and acetate assimilation, and the Wood-Ljungdahl CO2 -fixation pathway, indicating a mixotrophic lifestyle. Sulfur reduction, hydrogen metabolism, and arsenic detoxification pathways were predicted, indicating sulfur-, hydrogen-, and arsenic-transformation potentials. Comparative genomics indicated that the H4 F Wood-Ljungdahl pathway of both Ca. Gimiplasmatales and Methanomassiliicoccales was likely obtained by the interdomain lateral gene transfer from the Firmicutes. Collectively, this study elucidates the taxonomic and potential metabolic diversity of the new order Ca. Gimiplasmatales and the evolution of this subgroup and its sister lineage Methanomassiliicoccales.}, }
@article {pmid33294522, year = {2020}, author = {Shaikhutdinov, N and Gogoleva, N and Gusev, O and Shagimardanova, E}, title = {Microbiota composition data of imago and larval stage of the anhydrobiotic midge.}, journal = {Data in brief}, volume = {33}, number = {}, pages = {106527}, pmid = {33294522}, issn = {2352-3409}, abstract = {The ability of larvae of a non-biting midge Polypedilum vanderplanki (Chironomidae) to withstand complete desiccation is a remarkable natural example of adaptation to extreme environment. In anhydrobiosis the larvae lose up to 99.2% of water and stay in a dry form until rainfall in natural environment or up to several decades in laboratory maintaining ability to restore activity soon after rehydration [1]. In the desiccated state, the larvae tolerate a variety of abiotic stresses, including high radiation exposure (7000Gry of [60]Co gamma rays) [2]. Such a cross-resistance to desiccation and ionizing radiation is a characteristic of many anhydrobiotic organisms and believed to be based on similar molecular mechanisms. Microorganisms associated with the anhydrobiotic midge can also sustain desiccation and thus be radiation-resistant because desiccation-resistant prokaryotes are shown to be cross-resistant to ionizing radiation [3]. Microorganisms inhabiting larvae of the anhydrobiotic midge can also sustain desiccation and probably can sustain high doses of ionizing radiation. Therefore, it would be of interest to analyze the taxonomic and functional composition of microbiome of the anhydrobiotic midge. Sequencing data for the total DNA of anhydrobiotic organisms, which also contain reads derived from symbiotic microorganisms provide a promising opportunity to identify microorganisms with remarkable adaptation. It is known that at least some protective genes, such as late embryogenesis abundant (LEA) genes appeared in the genome of the midge by probable horizontal gene transfer from bacteria [1]. We performed shotgun sequencing of imago and larvae DNA samples using HiSeq 2000 and Genome Analyzer IIX System platforms. To assess microbiome diversity specific to anhydrobiotic midges, we analyzed Pool-seq data of the natural population of imago and Pool-seq data of final instar larvae. Data has been deposited in NCBI BioProject repository at NCBI under the accession number PRJNA659554 and consists of raw sequence data.}, }
@article {pmid33294248, year = {2021}, author = {Ji, M and Liu, Z and Sun, K and Li, Z and Fan, X and Li, Q}, title = {Bacteriophages in water pollution control: Advantages and limitations.}, journal = {Frontiers of environmental science &amp; engineering}, volume = {15}, number = {5}, pages = {84}, pmid = {33294248}, issn = {2095-2201}, abstract = {Wastewater is a breeding ground for many pathogens, which may pose a threat to human health through various water transmission pathways. Therefore, a simple and effective method is urgently required to monitor and treat wastewater. As bacterial viruses, bacteriophages (phages) are the most widely distributed and abundant organisms in the biosphere. Owing to their capacity to specifically infect bacterial hosts, they have recently been used as novel tools in water pollution control. The purpose of this review is to summarize and evaluate the roles of phages in monitoring pathogens, tracking pollution sources, treating pathogenic bacteria, infecting bloom-forming cyanobacteria, and controlling bulking sludge and biofilm pollution in wastewater treatment systems. We also discuss the limitations of phage usage in water pollution control, including phage-mediated horizontal gene transfer, the evolution of bacterial resistance, and phage concentration decrease. This review provides an integrated outlook on the use of phages in water pollution control.}, }
@article {pmid33293048, year = {2021}, author = {Sorinolu, AJ and Tyagi, N and Kumar, A and Munir, M}, title = {Antibiotic resistance development and human health risks during wastewater reuse and biosolids application in agriculture.}, journal = {Chemosphere}, volume = {265}, number = {}, pages = {129032}, doi = {10.1016/j.chemosphere.2020.129032}, pmid = {33293048}, issn = {1879-1298}, mesh = {Agriculture ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Anti-Bacterial Agents/toxicity ; *Biosolids ; Drug Resistance, Microbial/genetics ; Humans ; *Wastewater ; }, abstract = {The reuse of treated wastewater (TWW) and sewage sludge are considered as solutions to the limited water resource and sludge disposal issues, respectively. The associated environmental and human health risks need to be analyzed to assess whether they are safe solutions or not. This paper discusses issues that relate to the accumulation of antibiotics and antibiotic resistance (AR) determinants in agricultural lands and crops, following TWW irrigation and biosolid amendment. Exposure assessment and dose-response assessment are the two important aspects of risk assessment discussed in this paper. Finally, research gaps in current knowledge that are relevant to a comprehensive and quantitative AR risk assessment were identified which includes: 1.) Studies on soil conditions that increase the frequency of horizontal gene transfer (HGT) between native soil resistome and pathogenic microbes in biosolids and TWW 2.) Holistic studies that examine the accumulation or dissipation of antibiotics, antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) from the irrigation/biosolids application stage to crop consumption stage 3.) The influences of soil environmental conditions (e.g. salinity, nutrients) on the fate of ARB and ARGs in soil and translocation in edible plants 4.) The development of dose-response models that explicitly incorporate the potential for ARGs transfer between microbes when quantifying the risks of infection due to ARB.}, }
@article {pmid33289629, year = {2020}, author = {Heckel, DG}, title = {Does size really matter?.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, pmid = {33289629}, issn = {2050-084X}, mesh = {Animals ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome ; Herbivory ; Phylogeny ; }, abstract = {Analysis of the smallest known arthropod genome reveals a mechanism for genome reduction that appears to be driven by a specialized ecological interaction with plants.}, }
@article {pmid33288624, year = {2021}, author = {Farrera-Calderon, RG and Pallegar, P and Westbye, AB and Wiesmann, C and Lang, AS and Beatty, JT}, title = {The CckA-ChpT-CtrA Phosphorelay Controlling Rhodobacter capsulatus Gene Transfer Agent Production Is Bidirectional and Regulated by Cyclic di-GMP.}, journal = {Journal of bacteriology}, volume = {203}, number = {5}, pages = {}, pmid = {33288624}, issn = {1098-5530}, mesh = {Amino Acid Substitution ; Bacterial Proteins/genetics/isolation &amp; purification/*metabolism ; Cyclic GMP/*analogs &amp; derivatives/metabolism ; Gene Transfer Techniques ; *Gene Transfer, Horizontal ; Histidine Kinase/genetics/isolation &amp; purification/*metabolism ; Phosphorylation ; Phosphotransferases/genetics/isolation &amp; purification/*metabolism ; Recombinant Proteins/genetics/isolation &amp; purification/metabolism ; Rhodobacter capsulatus/*genetics/*metabolism ; Signal Transduction ; Transcription Factors/genetics/isolation &amp; purification/*metabolism ; }, abstract = {Protein phosphorylation is a universal mechanism for transducing cellular signals in prokaryotes and eukaryotes. The histidine kinase CckA, the histidine phosphotransferase ChpT, and the response regulator CtrA are conserved throughout the alphaproteobacteria. In Rhodobacter capsulatus, these proteins are key regulators of the gene transfer agent (RcGTA), which is present in several alphaproteobacteria. Using purified recombinant R. capsulatus proteins, we show in vitro autophosphorylation of CckA protein, and phosphotransfer to ChpT and thence to CtrA, to demonstrate biochemically that they form a phosphorelay. The secondary messenger cyclic di-GMP changed CckA from a kinase to a phosphatase, resulting in reversal of the phosphotransfer flow in the relay. The substitutions of two residues in CckA greatly affected the kinase or phosphatase activity of the protein in vitro, and production of mutant CckA proteins in vivo confirmed the importance of kinase but not phosphatase activity for the lytic release of RcGTA. However, phosphatase activity was needed to produce functional RcGTA particles. The binding of cyclic di-GMP to the wild-type and mutant CckA proteins was evaluated directly using a pulldown assay based on biotinylated cyclic di-GMP and streptavidin-linked beads.IMPORTANCE The CckA, ChpT, and CtrA phosphorelay proteins are widespread in the alphaproteobacteria, and there are two groups of organisms that differ in terms of whether this pathway is essential for cell viability. Little is known about the biochemical function of these proteins in organisms where the pathway is not essential, a group that includes Rhodobacter capsulatus This work demonstrates biochemically that CckA, ChpT, and CtrA also form a functional phosphorelay in the latter group and that the direction of phosphotransfer is reversed by cyclic di-GMP. It is important to improve understanding of more representatives of this pathway in order to obtain deeper insight into the function, composition, and evolutionary significance of a wider range of bacterial regulatory networks.}, }
@article {pmid33283865, year = {2020}, author = {Fagorzi, C and Ilie, A and Decorosi, F and Cangioli, L and Viti, C and Mengoni, A and diCenzo, GC}, title = {Symbiotic and Nonsymbiotic Members of the Genus Ensifer (syn. Sinorhizobium) Are Separated into Two Clades Based on Comparative Genomics and High-Throughput Phenotyping.}, journal = {Genome biology and evolution}, volume = {12}, number = {12}, pages = {2521-2534}, pmid = {33283865}, issn = {1759-6653}, mesh = {Fabaceae/microbiology ; Gene Transfer, Horizontal ; Genome, Bacterial ; Genomics ; Microarray Analysis ; Nitrogen Fixation/*genetics ; *Phylogeny ; Sinorhizobium/classification/*genetics ; Symbiosis/genetics ; }, abstract = {Rhizobium-legume symbioses serve as paradigmatic examples for the study of mutualism evolution. The genus Ensifer (syn. Sinorhizobium) contains diverse plant-associated bacteria, a subset of which can fix nitrogen in symbiosis with legumes. To gain insights into the evolution of symbiotic nitrogen fixation (SNF), and interkingdom mutualisms more generally, we performed extensive phenotypic, genomic, and phylogenetic analyses of the genus Ensifer. The data suggest that SNF likely emerged several times within the genus Ensifer through independent horizontal gene transfer events. Yet, the majority (105 of 106) of the Ensifer strains with the nodABC and nifHDK nodulation and nitrogen fixation genes were found within a single, monophyletic clade. Comparative genomics highlighted several differences between the "symbiotic" and "nonsymbiotic" clades, including divergences in their pangenome content. Additionally, strains of the symbiotic clade carried 325 fewer genes, on average, and appeared to have fewer rRNA operons than strains of the nonsymbiotic clade. Initial characterization of a subset of ten Ensifer strains identified several putative phenotypic differences between the clades. Tested strains of the nonsymbiotic clade could catabolize 25% more carbon sources, on average, than strains of the symbiotic clade, and they were better able to grow in LB medium and tolerate alkaline conditions. On the other hand, the tested strains of the symbiotic clade were better able to tolerate heat stress and acidic conditions. We suggest that these data support the division of the genus Ensifer into two main subgroups, as well as the hypothesis that pre-existing genetic features are required to facilitate the evolution of SNF in bacteria.}, }
@article {pmid33277504, year = {2020}, author = {Tian, L and Wang, XW and Wu, AK and Fan, Y and Friedman, J and Dahlin, A and Waldor, MK and Weinstock, GM and Weiss, ST and Liu, YY}, title = {Deciphering functional redundancy in the human microbiome.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {6217}, pmid = {33277504}, issn = {2041-1723}, support = {K01 HL130629/HL/NHLBI NIH HHS/United States ; R01 AI042347/AI/NIAID NIH HHS/United States ; U19 AI095219/AI/NIAID NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; U01 HL089856/HL/NHLBI NIH HHS/United States ; R01 AI141529/AI/NIAID NIH HHS/United States ; R01 HD093761/HD/NICHD NIH HHS/United States ; UH3 OD023268/OD/NIH HHS/United States ; }, mesh = {Algorithms ; Bacteria/classification/genetics ; Feces/*microbiology ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; Gene Regulatory Networks ; Gene Transfer, Horizontal ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Models, Genetic ; }, abstract = {Although the taxonomic composition of the human microbiome varies tremendously across individuals, its gene composition or functional capacity is highly conserved - implying an ecological property known as functional redundancy. Such functional redundancy has been hypothesized to underlie the stability and resilience of the human microbiome, but this hypothesis has never been quantitatively tested. The origin of functional redundancy is still elusive. Here, we investigate the basis for functional redundancy in the human microbiome by analyzing its genomic content network - a bipartite graph that links microbes to the genes in their genomes. We find that this network exhibits several topological features that favor high functional redundancy. Furthermore, we develop a simple genome evolution model to generate genomic content network, finding that moderate selection pressure and high horizontal gene transfer rate are necessary to generate genomic content networks with key topological features that favor high functional redundancy. Finally, we analyze data from two published studies of fecal microbiota transplantation (FMT), finding that high functional redundancy of the recipient's pre-FMT microbiota raises barriers to donor microbiota engraftment. This work elucidates the potential ecological and evolutionary processes that create and maintain functional redundancy in the human microbiome and contribute to its resilience.}, }
@article {pmid33277004, year = {2021}, author = {Gao, Q and Gao, S and Bates, C and Zeng, Y and Lei, J and Su, H and Dong, Q and Qin, Z and Zhao, J and Zhang, Q and Ning, D and Huang, Y and Zhou, J and Yang, Y}, title = {The microbial network property as a bio-indicator of antibiotic transmission in the environment.}, journal = {The Science of the total environment}, volume = {758}, number = {}, pages = {143712}, doi = {10.1016/j.scitotenv.2020.143712}, pmid = {33277004}, issn = {1879-1026}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; *Composting ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Manure ; RNA, Ribosomal, 16S ; Soil ; Soil Microbiology ; Swine ; }, abstract = {Interspecies interaction is an essential mechanism for bacterial communities to develop antibiotic resistance via horizontal gene transfer. Nonetheless, how bacterial interactions vary along the environmental transmission of antibiotics and the underpinnings remain unclear. To address it, we explore potential microbial associations by analyzing bacterial networks generated from 16S rRNA gene sequences and functional networks containing a large number of antibiotic-resistance genes (ARGs). Antibiotic concentration decreased by more than 4000-fold along the environmental transmission chain from manure samples of swine farms to aerobic compost, compost-amended agricultural soils, and neighboring agricultural soils. Both bacterial and functional networks became larger in nodes and links with decreasing antibiotic concentrations, likely resulting from lower antibiotics stress. Nonetheless, bacterial networks became less clustered with decreasing antibiotic concentrations, while functional networks became more clustered. Modularity, a key topological property that enhances system resilience to antibiotic stress, remained high for functional networks, but the modularity values of bacterial networks were the lowest when antibiotic concentrations were intermediate. To explain it, we identified a clear shift from deterministic processes, particularly variable selection, to stochastic processes at intermediate antibiotic concentrations as the dominant mechanism in shaping bacterial communities. Collectively, our results revealed microbial network dynamics and suggest that the modularity value of association networks could serve as an important indicator of antibiotic concentrations in the environment.}, }
@article {pmid33276454, year = {2020}, author = {Di Nocera, P and De Gregorio, E}, title = {Growth by Insertion: The Family of Bacterial DDxP Proteins.}, journal = {International journal of molecular sciences}, volume = {21}, number = {23}, pages = {}, pmid = {33276454}, issn = {1422-0067}, mesh = {*Amino Acid Motifs ; Amino Acid Sequence ; *Bacterial Physiological Phenomena ; Bacterial Proteins/chemistry/genetics/*metabolism ; Base Sequence ; Calcium/metabolism ; Gene Transfer, Horizontal ; Multigene Family ; Phylogeny ; *Protein Domains ; Repetitive Sequences, Nucleic Acid ; Species Specificity ; Type I Secretion Systems/genetics/metabolism ; }, abstract = {We have identified a variety of proteins in species of the Legionella, Aeromonas, Pseudomonas, Vibrio, Nitrosomonas, Nitrosospira, Variovorax, Halomonas, and Rhizobia genera, which feature repetitive modules of different length and composition, invariably ending at the COOH side with Asp-Asp-x-Pro (DDxP) motifs. DDxP proteins range in size from 900 to 6200 aa (amino acids), and contain 1 to 5 different module types, present in one or multiple copies. We hypothesize that DDxP proteins were modeled by the action of specific endonucleases inserting DNA segments into genes encoding DDxP motifs. Target site duplications (TSDs) formed upon repair of staggered ends generated by endonuclease cleavage would explain the DDxP motifs at repeat ends. TSDs acted eventually as targets for the insertion of more modules of the same or different types. Repeat clusters plausibly resulted from amplification of both repeat and flanking TSDs. The proposed growth shown by the insertion model is supported by the identification of homologous proteins lacking repeats in Pseudomonas and Rhizobium. The 85 DDxP repeats identified in this work vary in length, and can be sorted into short (136-215 aa) and long (243-304 aa) types. Conserved Asp-Gly-Asp-Gly-Asp motifs are located 11-19 aa from the terminal DDxP motifs in all repeats, and far upstream in most long repeats.}, }
@article {pmid33273523, year = {2020}, author = {Kushwaha, SK and Bhavesh, NLS and Abdella, B and Lahiri, C and Marathe, SA}, title = {The phylogenomics of CRISPR-Cas system and revelation of its features in Salmonella.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {21156}, pmid = {33273523}, issn = {2045-2322}, mesh = {CRISPR-Cas Systems/*genetics ; Conserved Sequence/genetics ; DNA, Intergenic/genetics ; Evolution, Molecular ; Genetic Loci ; Interspersed Repetitive Sequences/genetics ; Operon/genetics ; *Phylogeny ; Salmonella/*genetics ; }, abstract = {Salmonellae display intricate evolutionary patterns comprising over 2500 serovars having diverse pathogenic profiles. The acquisition and/or exchange of various virulence factors influences the evolutionary framework. To gain insights into evolution of Salmonella in association with the CRISPR-Cas genes we performed phylogenetic surveillance across strains of 22 Salmonella serovars. The strains differed in their CRISPR1-leader and cas operon features assorting into two main clades, CRISPR1-STY/cas-STY and CRISPR1-STM/cas-STM, comprising majorly typhoidal and non-typhoidal Salmonella serovars respectively. Serovars of these two clades displayed better relatedness, concerning CRISPR1-leader and cas operon, across genera than between themselves. This signifies the acquisition of CRISPR1/Cas region could be through a horizontal gene transfer event owing to the presence of mobile genetic elements flanking CRISPR1 array. Comparison of CRISPR and cas phenograms with that of multilocus sequence typing (MLST) suggests differential evolution of CRISPR/Cas system. As opposed to broad-host-range, the host-specific serovars harbor fewer spacers. Mapping of protospacer sources suggested a partial correlation of spacer content with habitat diversity of the serovars. Some serovars like serovar Enteritidis and Typhimurium that inhabit similar environment/infect similar hosts hardly shared their protospacer sources.}, }
@article {pmid33273480, year = {2020}, author = {Gaba, S and Kumari, A and Medema, M and Kaushik, R}, title = {Pan-genome analysis and ancestral state reconstruction of class halobacteria: probability of a new super-order.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {21205}, pmid = {33273480}, issn = {2045-2322}, mesh = {Datasets as Topic ; Euryarchaeota/classification/*genetics ; *Genome, Archaeal ; *Phylogeny ; Probability ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Halobacteria, a class of Euryarchaeota are extremely halophilic archaea that can adapt to a wide range of salt concentration generally from 10% NaCl to saturated salt concentration of 32% NaCl. It consists of the orders: Halobacteriales, Haloferaciales and Natriabales. Pan-genome analysis of class Halobacteria was done to explore the core (300) and variable components (Softcore: 998, Cloud:36531, Shell:11784). The core component revealed genes of replication, transcription, translation and repair, whereas the variable component had a major portion of environmental information processing. The pan-gene matrix was mapped onto the core-gene tree to find the ancestral (44.8%) and derived genes (55.1%) of the Last Common Ancestor of Halobacteria. A High percentage of derived genes along with presence of transformation and conjugation genes indicate the occurrence of horizontal gene transfer during the evolution of Halobacteria. A Core and pan-gene tree were also constructed to infer a phylogeny which implicated on the new super-order comprising of Natrialbales and Halobacteriales.}, }
@article {pmid33270000, year = {2021}, author = {Kloos, J and Johnsen, PJ and Harms, K}, title = {Tn1 transposition in the course of natural transformation enables horizontal antibiotic resistance spread in Acinetobacter baylyi.}, journal = {Microbiology (Reading, England)}, volume = {167}, number = {1}, pages = {}, pmid = {33270000}, issn = {1465-2080}, mesh = {Acinetobacter/*drug effects/*genetics/isolation &amp; purification ; Anti-Bacterial Agents/pharmacology ; *DNA Transposable Elements ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Plasmids/genetics/metabolism ; *Transformation, Bacterial ; }, abstract = {Transposons are genetic elements that change their intracellular genomic position by transposition and are spread horizontally between bacteria when located on plasmids. It was recently discovered that transposition from fully heterologous DNA also occurs in the course of natural transformation. Here, we characterize the molecular details and constraints of this process using the replicative transposon Tn1 and the naturally competent bacterium Acinetobacter baylyi. We find that chromosomal insertion of Tn1 by transposition occurs at low but detectable frequencies and preferably around the A. baylyi terminus of replication. We show that Tn1 transposition is facilitated by transient expression of the transposase and resolvase encoded by the donor DNA. RecA protein is essential for the formation of a circular, double-stranded cytoplasmic intermediate from incoming donor DNA, and RecO is beneficial but not essential in this process. Absence of the recipient RecBCD nuclease stabilizes the double-stranded intermediate. Based on these results, we suggest a mechanistic model for transposition during natural transformation.}, }
@article {pmid33266460, year = {2020}, author = {Zhang, J and Chen, K and Jiang, C and Yang, W and Gu, S and Wang, G and Lu, Y and Miao, W and Xiong, J}, title = {Bacteria-Derived Hemolysis-Related Genes Widely Exist in Scuticociliates.}, journal = {Microorganisms}, volume = {8}, number = {11}, pages = {}, pmid = {33266460}, issn = {2076-2607}, support = {31525021//National Natural Science Foundation of China/ ; 91631303//National Natural Science Foundation of China/ ; 31672281//National Natural Science Foundation of China/ ; 2019CFB808//Natural Science Foundation of Hubei Province/ ; JCYJ20180507183240459//Shenzhen Science and Technology Project/ ; 2019M652735//China Postdoctoral Science Foundation/ ; }, abstract = {Scuticociliatosis is an invasive external or systemic infection caused by ciliated protozoa, mainly those within the subclass Scuticociliatia (scuticociliates). Many scuticociliates are fish pathogens, including Miamiensis avidus, Philasterides dicentrarchi, Pseudocohnilembus persalinus, and Uronema marinum. Our previous study showed that hemolysis-related genes derived from bacteria through horizontal gene transfer (HGT) may contribute to virulence in P. persalinus. Hemorrhagic lesions are a common feature of scuticociliatosis, but it is not known whether other scuticociliates also have bacteria-derived hemolysis-related genes. In this study, we constructed a high-quality macronuclear genome of another typical pathogenic scuticociliate, U. marinum. A total of 105 HGT genes were identified in this species, of which 35 were homologs of hemolysis-related genes (including hemolysin-like genes) that had previously been identified in P. persalinus. Sequencing of an additional five species from four scuticociliate families showed that bacteria-derived hemolysis-related genes (especially hemolysin-like genes) are widely distributed in scuticociliates. Based on these findings, we suggest that hemolysin-like genes may have originated before the divergence of scuticociliates.}, }
@article {pmid33266251, year = {2020}, author = {Lyall, R and Nikoloski, Z and Gechev, T}, title = {Comparative Analysis of ROS Network Genes in Extremophile Eukaryotes.}, journal = {International journal of molecular sciences}, volume = {21}, number = {23}, pages = {}, pmid = {33266251}, issn = {1422-0067}, support = {SGA-CSA No. 739582//Project PlantaSYST, European Union's Horizon 2020 Research &amp; Innovation Programme/ ; GA No. 823746//Project RESIST, European Union's Horizon 2020 Research &amp; Innovation Programme/ ; BG05M2OP001-1.003-001-C01//European Regional Development Fund/ ; }, mesh = {Biomarkers ; Eukaryota/*genetics/*metabolism ; Extremophiles/*genetics/*metabolism ; Gene Expression Regulation ; Gene Expression Regulation, Enzymologic ; *Gene Regulatory Networks ; Oxidative Stress ; Plants/genetics/metabolism ; Reactive Oxygen Species/*metabolism ; }, abstract = {The reactive oxygen species (ROS) gene network, consisting of both ROS-generating and detoxifying enzymes, adjusts ROS levels in response to various stimuli. We performed a cross-kingdom comparison of ROS gene networks to investigate how they have evolved across all Eukaryotes, including protists, fungi, plants and animals. We included the genomes of 16 extremotolerant Eukaryotes to gain insight into ROS gene evolution in organisms that experience extreme stress conditions. Our analysis focused on ROS genes found in all Eukaryotes (such as catalases, superoxide dismutases, glutathione reductases, peroxidases and glutathione peroxidase/peroxiredoxins) as well as those specific to certain groups, such as ascorbate peroxidases, dehydroascorbate/monodehydroascorbate reductases in plants and other photosynthetic organisms. ROS-producing NADPH oxidases (NOX) were found in most multicellular organisms, although several NOX-like genes were identified in unicellular or filamentous species. However, despite the extreme conditions experienced by extremophile species, we found no evidence for expansion of ROS-related gene families in these species compared to other Eukaryotes. Tardigrades and rotifers do show ROS gene expansions that could be related to their extreme lifestyles, although a high rate of lineage-specific horizontal gene transfer events, coupled with recent tetraploidy in rotifers, could explain this observation. This suggests that the basal Eukaryotic ROS scavenging systems are sufficient to maintain ROS homeostasis even under the most extreme conditions.}, }
@article {pmid33265037, year = {2021}, author = {Hou, L and Zhang, L and Li, F and Huang, S and Yang, J and Ma, C and Zhang, D and Yu, CP and Hu, A}, title = {Urban ponds as hotspots of antibiotic resistome in the urban environment.}, journal = {Journal of hazardous materials}, volume = {403}, number = {}, pages = {124008}, doi = {10.1016/j.jhazmat.2020.124008}, pmid = {33265037}, issn = {1873-3336}, mesh = {*Anti-Bacterial Agents ; China ; Cities ; Ecosystem ; Genes, Bacterial ; *Ponds ; }, abstract = {The occurrence, dissemination and assembly processes of antibiotic resistance genes (ARGs) in urban water ecosystems are far from being understood. Here, we examined the diversity and abundance of ARGs in urban water ecosystems including landscape ponds, drinking water reservoirs, influents (IFs) and effluents (EFs) of wastewater treatment plants of a coastal city, China through high-throughput quantitative PCR. A total of 237 ARGs were identified, where multidrug, aminoglycoside and beta-lactamase resistance genes were the most abundant. Urban ponds had a comparatively high diversity and large numbers of shared ARGs with IFs and EFs. The average absolute abundance of ARGs (1.38 × 10[7] copies/mL) and mobile genetic elements (MGEs) (4.19 × 10[6] copies/mL) in ponds were only one order of magnitude lower than those of IFs, but higher than those of EFs and reservoirs. Stochastic processes dominated the ARG community assembly in IFs and ponds due to the random horizontal gene transfer caused by MGEs. These results imply that urban ponds are hotspots of ARGs. We further identified 25, 3, and 11 indicator ARGs for tracing the ARG contamination from IFs, EFs and ponds, respectively. Our study represents the first to highlight the role of urban ponds in the dissemination of ARGs.}, }
@article {pmid33265028, year = {2021}, author = {Song, M and Song, D and Jiang, L and Zhang, D and Sun, Y and Chen, G and Xu, H and Mei, W and Li, Y and Luo, C and Zhang, G}, title = {Large-scale biogeographical patterns of antibiotic resistome in the forest soils across China.}, journal = {Journal of hazardous materials}, volume = {403}, number = {}, pages = {123990}, doi = {10.1016/j.jhazmat.2020.123990}, pmid = {33265028}, issn = {1873-3336}, mesh = {*Anti-Bacterial Agents ; China ; Forests ; Genes, Bacterial ; *Soil ; Soil Microbiology ; }, abstract = {Soil is a reservoir of environmental resistomes. Information about their distribution, profiles, and driving forces in undisturbed environments is essential for understanding and managing modern antibiotic resistance genes (ARGs) in human disturbed environments. However, knowledge about the resistomes in pristine soils is limited, particularly at national scale. Here, we conducted a national-scale investigation of soil resistomes in pristine forests across China. Although the antibiotics content was low and ranged from below limit of detection (LOD) to 0.290 μg/kg, numerous detected ARGs conferring resistance to major classes of modern antibiotics were identified and indicated forest soils as a potential source of resistance traits. ARGs ranged from 6.20 × 10[-7] to 2.52 × 10[-3] copies/16S-rRNA and were predominated by those resisting aminoglycoside and encoding deactivation mechanisms. Low abundance of mobile genetic elements (MGEs) and its scarcely positive connections with ARGs suggest the low potential of horizontal gene transfer. The geographic patterns of ARGs and ARG-hosts in pristine forest soils were mainly driven by soil physiochemical variables and followed a distance-decay relationship. This work focusing on pristine soils can provide valuably new information for our understanding of the ARGs in human disturbed environments.}, }
@article {pmid33264670, year = {2021}, author = {Chernova, OA and Chernov, VM and Mouzykantov, AA and Baranova, NB and Edelstein, IA and Aminov, RI}, title = {Antimicrobial drug resistance mechanisms among Mollicutes.}, journal = {International journal of antimicrobial agents}, volume = {57}, number = {2}, pages = {106253}, doi = {10.1016/j.ijantimicag.2020.106253}, pmid = {33264670}, issn = {1872-7913}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Bacterial/*genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Mutation ; Tenericutes/*drug effects/genetics ; }, abstract = {Representatives of the Mollicutes class are the smallest, wall-less bacteria capable of independent reproduction. They are widespread in nature, most are commensals, and some are pathogens of humans, animals and plants. They are also the main contaminants of cell cultures and vaccine preparations. Despite limited biosynthetic capabilities, they are highly adaptable and capable of surviving under various stress and extreme conditions, including antimicrobial selective pressure. This review describes current understanding of antibiotic resistance (ABR) mechanisms in Mollicutes. Protective mechanisms in these bacteria include point mutations, which may include non-target genes, and unique gene exchange mechanisms, contributing to transfer of ABR genes. Better understanding of the mechanisms of emergence and dissemination of ABR in Mollicutes is crucial to control these hypermutable bacteria and prevent the occurrence of highly ABR strains.}, }
@article {pmid33263868, year = {2020}, author = {Christensen, S and Serbus, LR}, title = {Gene Transfer Agents in Symbiotic Microbes.}, journal = {Results and problems in cell differentiation}, volume = {69}, number = {}, pages = {25-76}, pmid = {33263868}, issn = {0080-1844}, mesh = {Bacteria/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Symbiosis ; }, abstract = {Prokaryotes commonly undergo genome reduction, particularly in the case of symbiotic bacteria. Genome reductions tend toward the energetically favorable removal of unnecessary, redundant, or nonfunctional genes. However, without mechanisms to compensate for these losses, deleterious mutation and genetic drift might otherwise overwhelm a population. Among the mechanisms employed to counter gene loss and share evolutionary success within a population, gene transfer agents (GTAs) are increasingly becoming recognized as important contributors. Although viral in origin, GTA particles package fragments of their "host" genome for distribution within a population of cells, often in a synchronized manner, rather than selfishly packaging genes necessary for their spread. Microbes as diverse as archaea and alpha-proteobacteria have been known to produce GTA particles, which are capable of transferring selective advantages such as virulence factors and antibiotic resistance. In this review, we discuss the various types of GTAs identified thus far, focusing on a defined set of symbiotic alpha-proteobacteria known to carry them. Drawing attention to the predicted presence of these genes, we discuss their potential within the selective marine and terrestrial environments occupied by mutualistic, parasitic, and endosymbiotic microbes.}, }
@article {pmid33257452, year = {2021}, author = {Lysnyansky, I and Borovok, I}, title = {A GC-Rich Prophage-Like Genomic Region of Mycoplasma bovirhinis HAZ141_2 Carries a Gene Cluster Encoding Resistance to Kanamycin and Neomycin.}, journal = {Antimicrobial agents and chemotherapy}, volume = {65}, number = {2}, pages = {}, pmid = {33257452}, issn = {1098-6596}, mesh = {Anti-Bacterial Agents/pharmacology ; Escherichia coli ; Genomics ; Gram-Negative Bacteria ; Gram-Positive Bacteria ; *Kanamycin/pharmacology ; Multigene Family ; Mycoplasma ; Neomycin ; *Prophages ; }, abstract = {Recently, a complete genome sequence of Mycoplasma bovirhinis HAZ141_2 was published showing the presence of a 54-kB prophage-like region. Bioinformatic analysis revealed that this region has a more than 40% GC content and a chimeric organization with three structural elements-a prophage continuous region, a restriction-modification cassette, and a highly transmittable aadE-sat4-aphA-3 gene cluster found in both Gram-positive and Gram-negative bacteria. It is known that aadE confers resistance to streptomycin, sat4 governs resistance to streptothricin/nourseothricin, and aphA-3 is responsible for resistance to kanamycin and structurally related antibiotics. An aadE-like (aadE*) gene of strain HAZ141_2 encodes a 228-amino acid (aa) polypeptide whose carboxy-terminal domain (positions 44 to 206) is almost identical to that of a functional 302-aa AadE (positions 140 to 302). Transcription analysis of the aadE*-sat4-aphA-3 genes showed their cotranscription in M. bovirhinis HAZ141_2. Moreover, a common promoter for aadE*-sat4-aphA-3 was mapped upstream of aadE* using 5' rapid amplification of cDNA ends analysis. Determination of MICs to aminoglycosides and nourseothricin revealed that M. bovirhinis HAZ141_2 is highly resistant to kanamycin and neomycin (≥512 μg/ml). However, MICs to streptomycin (64 μg/ml) and nourseothricin (16 to 32 μg/ml) were similar to those identified in the prophageless M. bovirhinis type strain PG43 and Israeli field isolate 316981. We cloned the aadE*-sat4-aphA-3 genes into a low-copy-number vector and transferred them into antibiotic-sensitive Escherichia coli cells. While the obtained E. coli transformants were highly resistant to kanamycin, neomycin, and nourseothricin (MICs, ≥256 μg/ml), there were no changes in MICs to streptomycin, suggesting a functional defect of the aadE*.}, }
@article {pmid33255299, year = {2020}, author = {Khaleque, HN and Fathollazadeh, H and González, C and Shafique, R and Kaksonen, AH and Holmes, DS and Watkin, ELJ}, title = {Unlocking Survival Mechanisms for Metal and Oxidative Stress in the Extremely Acidophilic, Halotolerant Acidihalobacter Genus.}, journal = {Genes}, volume = {11}, number = {12}, pages = {}, pmid = {33255299}, issn = {2073-4425}, mesh = {Catalase/genetics ; Copper/*metabolism ; Ectothiorhodospiraceae/*genetics/metabolism ; Genome, Bacterial/*genetics ; Genomics/methods ; Iron/*metabolism ; Oxidative Stress/*genetics ; Phylogeny ; Sulfur/metabolism ; }, abstract = {Microorganisms used for the biohydrometallurgical extraction of metals from minerals must be able to survive high levels of metal and oxidative stress found in bioleaching environments. The Acidihalobacter genus consists of four species of halotolerant, iron-sulfur-oxidizing acidophiles that are unique in their ability to tolerate chloride and acid stress while simultaneously bioleaching minerals. This paper uses bioinformatic tools to predict the genes and mechanisms used by Acidihalobacter members in their defense against a wide range of metals and oxidative stress. Analysis revealed the presence of multiple conserved mechanisms of metal tolerance. Ac. yilgarnensis F5[T], the only member of this genus that oxidizes the mineral chalcopyrite, contained a 39.9 Kb gene cluster consisting of 40 genes encoding mobile elements and an array of proteins with direct functions in copper resistance. The analysis also revealed multiple strategies that the Acidihalobacter members can use to tolerate high levels of oxidative stress. Three of the Acidihalobacter genomes were found to contain genes encoding catalases, which are not common to acidophilic microorganisms. Of particular interest was a rubrerythrin genomic cluster containing genes that have a polyphyletic origin of stress-related functions.}, }
@article {pmid33253164, year = {2020}, author = {Melo, ES and Wallau, GL}, title = {Mosquito genomes are frequently invaded by transposable elements through horizontal transfer.}, journal = {PLoS genetics}, volume = {16}, number = {11}, pages = {e1008946}, pmid = {33253164}, issn = {1553-7404}, mesh = {Animals ; Anopheles/genetics ; Culicidae/*genetics ; DNA Transposable Elements/*genetics ; Databases, Genetic ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome/genetics ; Mosquito Vectors/genetics ; Phylogeny ; Retroelements ; }, abstract = {Transposable elements (TEs) are mobile genetic elements that parasitize basically all eukaryotic species genomes. Due to their complexity, an in-depth TE characterization is only available for a handful of model organisms. In the present study, we performed a de novo and homology-based characterization of TEs in the genomes of 24 mosquito species and investigated their mode of inheritance. More than 40% of the genome of Aedes aegypti, Aedes albopictus, and Culex quinquefasciatus is composed of TEs, while it varied substantially among Anopheles species (0.13%-19.55%). Class I TEs are the most abundant among mosquitoes and at least 24 TE superfamilies were found. Interestingly, TEs have been extensively exchanged by horizontal transfer (172 TE families of 16 different superfamilies) among mosquitoes in the last 30 million years. Horizontally transferred TEs represents around 7% of the genome in Aedes species and a small fraction in Anopheles genomes. Most of these horizontally transferred TEs are from the three ubiquitous LTR superfamilies: Gypsy, Bel-Pao and Copia. Searching more than 32,000 genomes, we also uncovered transfers between mosquitoes and two different Phyla-Cnidaria and Nematoda-and two subphyla-Chelicerata and Crustacea, identifying a vector, the worm Wuchereria bancrofti, that enabled the horizontal spread of a Tc1-mariner element among various Anopheles species. These data also allowed us to reconstruct the horizontal transfer network of this TE involving more than 40 species. In summary, our results suggest that TEs are frequently exchanged by horizontal transfers among mosquitoes, influencing mosquito's genome size and variability.}, }
@article {pmid33250435, year = {2021}, author = {Taylor, SL and Leong, LEX and Sims, SK and Keating, RL and Papanicolas, LE and Richard, A and Mobegi, FM and Wesselingh, S and Burr, LD and Rogers, GB}, title = {The cystic fibrosis gut as a potential source of multidrug resistant pathogens.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {20}, number = {3}, pages = {413-420}, doi = {10.1016/j.jcf.2020.11.009}, pmid = {33250435}, issn = {1873-5010}, mesh = {Adult ; Anti-Bacterial Agents/*pharmacology ; Case-Control Studies ; Cystic Fibrosis/*microbiology ; *Drug Resistance, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Male ; Metagenomics ; Microbial Sensitivity Tests ; Tobramycin/pharmacology ; }, abstract = {BACKGROUND: The emergence of multidrug resistant (MDR) pathogens represents a profound threat to global health. Individuals with CF have amongst the highest cumulative antibiotic exposure of any patient group, including to critically-important last-line agents. While there is little evidence that antibiotic resistance in airway pathogens results in worse clinical outcomes for CF patients, the potential emergence of MDR pathogens in non-respiratory systems, as a consequence of CF care, represents a potential health threat to the wider population, including family and carers.<br><br>METHODS: Stool from 19 adults with CF and 16 healthy adult controls was subjected to metagenomic sequencing, to assess faecal resistome, and culture-based analysis. Resistant isolates were identified phenotypically, and genetic determinants of resistance characterised by whole genome sequencing.<br><br>RESULTS: CF and control faecal resistomes differed significantly (P&#xa0;=&#xa0;0.0003). The proportion of reads that mapped to mobile genetic elements was significantly higher in CF (P&#xa0;=&#xa0;0.014) and the composition was significantly different (P&#xa0;=&#xa0;0.0001). Notably, CF patients displayed higher carriage of plasmid-mediated aminoglycoside-modifying genes ant(6)-Ib, aac(6')-Ip, and aph(3')-IIIa (P&#xa0;<&#xa0;0.01). Culture-based analysis supported higher aminoglycoside resistance, with a higher proportion of aminoglycoside-resistant, Gram-negative bacteria (P&#xa0;<&#xa0;0.0001). Isolated extended spectrum beta lactamase (ESBL)-positive Escherichia coli from CF stool exhibited phenotypic resistance to tobramycin and gentamicin. Genomic analysis showed co-localisation of both aminoglycoside resistance and ESBL genes, consistent with MDR emergence through horizontal gene transfer.<br><br>CONCLUSIONS: The carriage of potentially transmissible resistance within the adult CF gut microbiome is considerably greater than in healthy individuals and could contribute to the emergence and dissemination of MDR pathogens.}, }
@article {pmid33250254, year = {2021}, author = {Ma, J and Wang, P and Gu, W and Su, Y and Wei, H and Xie, B}, title = {Does lipid stress affect performance, fate of antibiotic resistance genes and microbial dynamics during anaerobic digestion of food waste?.}, journal = {The Science of the total environment}, volume = {756}, number = {}, pages = {143846}, doi = {10.1016/j.scitotenv.2020.143846}, pmid = {33250254}, issn = {1879-1026}, mesh = {Anaerobiosis ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Food ; Genes, Bacterial ; Lipids ; *Refuse Disposal ; }, abstract = {The dissemination of antibiotic resistance genes (ARGs) in food waste (FW) disposal can pose severe threats to public health. Lipid is a primary composition in FW, while whether lipid stress can affect ARGs dynamics during anaerobic digestion (AD) process of FW is uncertain. This study focused on the impacts of lipid stress on methane production, fate of ARGs and its microbial mechanisms during AD of FW. Results showed that high lipid content increased methane yield but prolonged hydrolysis and lag time of methane production compared to AD of FW without oil. Moreover, variations of ARGs were more susceptible to lipid stress. Lipid stress could facilitate the reduction of total ARGs abundances compared to the group without oil, particularly restraining the proliferation of sul1, aadA1 and mefA in AD systems (P < 0.05). Mantel test suggested that integrons (intl1 and intl2) were significantly correlated with all detected ARGs (r: 0.33, P < 0.05), indicating that horizontal gene transfer mediated by integrons could be the driving force on ARGs dissemination. Network analysis suggested that Firmicutes, Bacteroidetes, Synergistetes and Proteobacteria were the main potential hosts of ARGs. In addition, under the lipid stress, the reduction of host bacteria was responsible for the elimination of several specific ARGs, thereby affecting ARGs profiles. These findings firstly deciphered ARGs dynamics and their driving factors responding to lipid stress during anaerobic biological treatment of FW.}, }
@article {pmid33247110, year = {2020}, author = {Kermani, AA and Macdonald, CB and Burata, OE and Ben Koff, B and Koide, A and Denbaum, E and Koide, S and Stockbridge, RB}, title = {The structural basis of promiscuity in small multidrug resistance transporters.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {6064}, pmid = {33247110}, issn = {2041-1723}, support = {R01 CA194864/CA/NCI NIH HHS/United States ; R35 GM128768/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Biological Transport ; Crystallography, X-Ray ; *Drug Resistance, Multiple, Bacterial ; Escherichia coli/metabolism ; Gene Transfer, Horizontal ; Guanine/metabolism ; Hydrophobic and Hydrophilic Interactions ; Membrane Transport Proteins/*chemistry/metabolism ; Models, Molecular ; Riboswitch ; Substrate Specificity ; }, abstract = {By providing broad resistance to environmental biocides, transporters from the small multidrug resistance (SMR) family drive the spread of multidrug resistance cassettes among bacterial populations. A fundamental understanding of substrate selectivity by SMR transporters is needed to identify the types of selective pressures that contribute to this process. Using solid-supported membrane electrophysiology, we find that promiscuous transport of hydrophobic substituted cations is a general feature of SMR transporters. To understand the molecular basis for promiscuity, we solved X-ray crystal structures of a SMR transporter Gdx-Clo in complex with substrates to a maximum resolution of 2.3 Å. These structures confirm the family's extremely rare dual topology architecture and reveal a cleft between two helices that provides accommodation in the membrane for the hydrophobic substituents of transported drug-like cations.}, }
@article {pmid33246485, year = {2020}, author = {Hennart, M and Panunzi, LG and Rodrigues, C and Gaday, Q and Baines, SL and Barros-Pinkelnig, M and Carmi-Leroy, A and Dazas, M and Wehenkel, AM and Didelot, X and Toubiana, J and Badell, E and Brisse, S}, title = {Population genomics and antimicrobial resistance in Corynebacterium diphtheriae.}, journal = {Genome medicine}, volume = {12}, number = {1}, pages = {107}, pmid = {33246485}, issn = {1756-994X}, mesh = {Anti-Bacterial Agents/pharmacology ; Corynebacterium diphtheriae/classification/*drug effects/*genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; Diphtheria/microbiology ; Diphtheria Toxin/genetics ; Drug Resistance, Bacterial/*genetics ; Genes, Bacterial/*genetics ; Genome-Wide Association Study ; Genomics ; Humans ; Macrolides/pharmacology ; *Metagenomics ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Phylogeny ; Prospective Studies ; }, abstract = {BACKGROUND: Corynebacterium diphtheriae, the agent of diphtheria, is a genetically diverse bacterial species. Although antimicrobial resistance has emerged against several drugs including first-line penicillin, the genomic determinants and population dynamics of resistance are largely unknown for this neglected human pathogen.<br><br>METHODS: Here, we analyzed the associations of antimicrobial susceptibility phenotypes, diphtheria toxin production, and genomic features in C. diphtheriae. We used 247 strains collected over several decades in multiple world regions, including the 163 clinical isolates collected prospectively from 2008 to 2017 in France mainland and overseas territories.<br><br>RESULTS: Phylogenetic analysis revealed multiple deep-branching sublineages, grouped into a Mitis lineage strongly associated with diphtheria toxin production and a largely toxin gene-negative Gravis lineage with few toxin-producing isolates including the 1990s ex-Soviet Union outbreak strain. The distribution of susceptibility phenotypes allowed proposing ecological cutoffs for most of the 19 agents tested, thereby defining acquired antimicrobial resistance. Penicillin resistance was found in 17.2% of prospective isolates. Seventeen (10.4%) prospective isolates were multidrug-resistant (&#x2265;&#x2009;3 antimicrobial categories), including four isolates resistant to penicillin and macrolides. Homologous recombination was frequent (r/m&#x2009;=&#x2009;5), and horizontal gene transfer contributed to the emergence of antimicrobial resistance in multiple sublineages. Genome-wide association mapping uncovered genetic factors of resistance, including an accessory penicillin-binding protein (PBP2m) located in diverse genomic contexts. Gene pbp2m is widespread in other Corynebacterium species, and its expression in C. glutamicum demonstrated its effect against several beta-lactams. A novel 73-kb C. diphtheriae multiresistance plasmid was discovered.<br><br>CONCLUSIONS: This work uncovers the dynamics of antimicrobial resistance in C. diphtheriae in the context of phylogenetic structure, biovar, and diphtheria toxin production and provides a blueprint to analyze re-emerging diphtheria.}, }
@article {pmid33245329, year = {2020}, author = {Hammond, JA and Gordon, EA and Socarras, KM and Chang Mell, J and Ehrlich, GD}, title = {Beyond the pan-genome: current perspectives on the functional and practical outcomes of the distributed genome hypothesis.}, journal = {Biochemical Society transactions}, volume = {48}, number = {6}, pages = {2437-2455}, pmid = {33245329}, issn = {1470-8752}, support = {P41 RR006009/RR/NCRR NIH HHS/United States ; R01 AI080935/AI/NIAID NIH HHS/United States ; R01 DC002148/DC/NIDCD NIH HHS/United States ; U01 DK082316/DK/NIDDK NIH HHS/United States ; }, mesh = {Algorithms ; Animals ; Bacterial Infections/microbiology ; Bacterial Physiological Phenomena ; Biodiversity ; Ecology ; Evolution, Molecular ; *Genes, Bacterial ; Genetic Variation ; *Genome, Bacterial ; Genome-Wide Association Study ; Genomics ; Genotype ; Humans ; Mice ; Molecular Biology ; Multigene Family ; Phenotype ; Phylogeny ; Symbiosis ; Whole Genome Sequencing ; }, abstract = {The principle of monoclonality with regard to bacterial infections was considered immutable prior to 30 years ago. This view, espoused by Koch for acute infections, has proven inadequate regarding chronic infections as persistence requires multiple forms of heterogeneity among the bacterial population. This understanding of bacterial plurality emerged from a synthesis of what-were-then novel technologies in molecular biology and imaging science. These technologies demonstrated that bacteria have complex life cycles, polymicrobial ecologies, and evolve in situ via the horizontal exchange of genic characters. Thus, there is an ongoing generation of diversity during infection that results in far more highly complex microbial communities than previously envisioned. This perspective is based on the fundamental tenet that the bacteria within an infecting population display genotypic diversity, including gene possession differences, which result from horizontal gene transfer mechanisms including transformation, conjugation, and transduction. This understanding is embodied in the concepts of the supragenome/pan-genome and the distributed genome hypothesis (DGH). These paradigms have fostered multiple researches in diverse areas of bacterial ecology including host-bacterial interactions covering the gamut of symbiotic relationships including mutualism, commensalism, and parasitism. With regard to the human host, within each of these symbiotic relationships all bacterial species possess attributes that contribute to colonization and persistence; those species/strains that are pathogenic also encode traits for invasion and metastases. Herein we provide an update on our understanding of bacterial plurality and discuss potential applications in diagnostics, therapeutics, and vaccinology based on perspectives provided by the DGH with regard to the evolution of pathogenicity.}, }
@article {pmid33242576, year = {2021}, author = {Chen, R and Huangfu, L and Lu, Y and Fang, H and Xu, Y and Li, P and Zhou, Y and Xu, C and Huang, J and Yang, Z}, title = {Adaptive innovation of green plants by horizontal gene transfer.}, journal = {Biotechnology advances}, volume = {46}, number = {}, pages = {107671}, doi = {10.1016/j.biotechadv.2020.107671}, pmid = {33242576}, issn = {1873-1899}, mesh = {Eukaryota ; Evolution, Molecular ; *Gene Transfer, Horizontal/genetics ; Phylogeny ; Plant Breeding ; Plants/genetics ; *Viridiplantae ; }, abstract = {Horizontal gene transfer (HGT) refers to the movement of genetic material between distinct species by means other than sexual reproduction. HGT has contributed tremendously to the genome plasticity and adaptive evolution of prokaryotes and certain unicellular eukaryotes. The evolution of green plants from chlorophyte algae to angiosperms and from water to land represents a process of adaptation to diverse environments, which has been facilitated by acquisition of genetic material from other organisms. In this article, we review the occurrence of HGT in major lineages of green plants, including chlorophyte and charophyte green algae, bryophytes, lycophytes, ferns, and seed plants. In addition, we discuss the significance of horizontally acquired genes in the adaptive innovations of green plants and their potential applications to crop breeding and improvement.}, }
@article {pmid33242487, year = {2021}, author = {Sanz, C and Casado, M and Navarro-Martin, L and Tadić, &#x110; and Parera, J and Tugues, J and Bayona, JM and Piña, B}, title = {Antibiotic and antibiotic-resistant gene loads in swine slurries and their digestates: Implications for their use as fertilizers in agriculture.}, journal = {Environmental research}, volume = {194}, number = {}, pages = {110513}, doi = {10.1016/j.envres.2020.110513}, pmid = {33242487}, issn = {1096-0953}, mesh = {Agriculture ; Animals ; Anti-Bacterial Agents ; *Fertilizers/analysis ; Genes, Bacterial ; *Manure ; Soil ; Soil Microbiology ; Spain ; Swine ; }, abstract = {The spread of antibiotic resistance in bacteria is a matter of global concern, and the identification of possible sources of the associated genetic elements (antibiotic resistance genes -ARGs-, components of the horizontal gene transfer mechanism), is becoming an urgent need. While the transmission of ARGs in medical settings have been adequately characterized, ARG propagation in agroecosystems remains insufficiently studied. Particularly crucial is the determination of potential risks associated to the use of swine slurries and related products as component of organic fertilizers, an increasingly used farming practice. We determined ARGs and antibiotic loads analysed from swine slurries and digestates from eight farms from Catalonia (NE Spain), and compared the results with their microbiome composition. Both ARGs and antibiotic were conspicuous in farm organic wastes, and the levels of some antibiotics exceeded currently accepted minimum inhibitory concentrations. Particularly, the presence of high loads of fluoroquinolones was directly correlated to the prevalence of the related qnrS1 ARG in the slurry. We also found evidence that ARG loads were directly correlated to the prevalence of determined bacterial taxa (Actinobacteria, Proteobacteria, Spirochaeta), a parameter that could be potentially modulated by the processing of the raw slurry prior to their use as fertilizer.}, }
@article {pmid33235212, year = {2020}, author = {Biggel, M and Xavier, BB and Johnson, JR and Nielsen, KL and Frimodt-Møller, N and Matheeussen, V and Goossens, H and Moons, P and Van Puyvelde, S}, title = {Horizontally acquired papGII-containing pathogenicity islands underlie the emergence of invasive uropathogenic Escherichia coli lineages.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {5968}, pmid = {33235212}, issn = {2041-1723}, support = {/WT_/Wellcome Trust/United Kingdom ; I01 CX000920/CX/CSRD VA/United States ; }, mesh = {Adhesins, Escherichia coli/*genetics ; DNA, Bacterial/genetics ; Escherichia coli Infections/microbiology ; Fimbriae, Bacterial/genetics ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial ; Genome-Wide Association Study ; Genomic Islands/*genetics ; Humans ; Phylogeny ; Urinary Tract/microbiology ; Urinary Tract Infections/microbiology ; *Uropathogenic Escherichia coli/genetics/pathogenicity ; Virulence Factors/genetics ; }, abstract = {Escherichia coli is the leading cause of urinary tract infection, one of the most common bacterial infections in humans. Despite this, a genomic perspective is lacking regarding the phylogenetic distribution of isolates associated with different clinical syndromes. Here, we present a large-scale phylogenomic analysis of a spatiotemporally and clinically diverse set of 907 E. coli isolates, including 722 uropathogenic E. coli (UPEC) isolates. A genome-wide association approach identifies the (P-fimbriae-encoding) papGII locus as the key feature distinguishing invasive UPEC, defined as isolates associated with severe UTI, i.e., kidney infection (pyelonephritis) or urinary-source bacteremia, from non-invasive UPEC, defined as isolates associated with asymptomatic bacteriuria or bladder infection (cystitis). Within the E. coli population, distinct invasive UPEC lineages emerged through repeated horizontal acquisition of diverse papGII-containing pathogenicity islands. Our findings elucidate the molecular determinants of severe UTI and have implications for the early detection of this pathogen.}, }
@article {pmid33234688, year = {2020}, author = {Caro, F and Caro, JA and Place, NM and Mekalanos, JJ}, title = {Transcriptional Silencing by TsrA in the Evolution of Pathogenic Vibrio cholerae Biotypes.}, journal = {mBio}, volume = {11}, number = {6}, pages = {}, pmid = {33234688}, issn = {2150-7511}, support = {R01 AI018045/AI/NIAID NIH HHS/United States ; R37 AI018045/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/metabolism ; Cholera/*microbiology ; Cholera Toxin/chemistry/genetics/*metabolism ; Gene Expression Profiling ; *Gene Expression Regulation, Bacterial ; Gene Silencing ; Genomic Islands ; High-Throughput Nucleotide Sequencing ; Models, Molecular ; Protein Conformation ; Transcription Factors/metabolism ; Vibrio cholerae/*physiology ; Virulence/genetics ; Virulence Factors/genetics ; }, abstract = {Vibrio cholerae is a globally important pathogen responsible for the severe epidemic diarrheal disease called cholera. The current and ongoing seventh pandemic of cholera is caused by El Tor strains, which have completely replaced the sixth-pandemic classical strains of V. cholerae To successfully establish infection and disseminate to new victims, V. cholerae relies on key virulence factors encoded on horizontally acquired genetic elements. The expression of these factors relies on the regulatory architecture that coordinates the timely expression of virulence determinants during host infection. Here, we apply transcriptomics and structural modeling to understand how type VI secretion system regulator A (TsrA) affects gene expression in both the classical and El Tor biotypes of V. cholerae We find that TsrA acts as a negative regulator of V. cholerae virulence genes encoded on horizontally acquired genetic elements. The TsrA regulon comprises genes encoding cholera toxin (CT), the toxin-coregulated pilus (TCP), and the type VI secretion system (T6SS), as well as genes involved in biofilm formation. The majority of the TsrA regulon is carried on horizontally acquired AT-rich genetic islands whose loss or acquisition could be directly ascribed to the differences between the classical and El Tor strains studied. Our modeling predicts that the TsrA protein is a structural homolog of the histone-like nucleoid structuring protein (H-NS) oligomerization domain and is likely capable of forming higher-order superhelical structures, potentially with DNA. These findings describe how TsrA can integrate into the intricate V. cholerae virulence gene expression program, controlling gene expression through transcriptional silencing.IMPORTANCE Pathogenic Vibrio cholerae strains express multiple virulence factors that are encoded by bacteriophage and chromosomal islands. These include cholera toxin and the intestinal colonization pilus called the toxin-coregulated pilus, which are essential for causing severe disease in humans. However, it is presently unclear how the expression of these horizontally acquired accessory virulence genes can be efficiently integrated with preexisting transcriptional programs that are presumably fine-tuned for optimal expression in V. cholerae before its conversion to a human pathogen. Here, we report the role of a transcriptional regulator (TsrA) in silencing horizontally acquired genes encoding important virulence factors. We propose that this factor could be critical to the efficient acquisition of accessory virulence genes by silencing their expression until other signals trigger their transcriptional activation within the host.}, }
@article {pmid33230956, year = {2020}, author = {Fambrini, M and Usai, G and Vangelisti, A and Mascagni, F and Pugliesi, C}, title = {The plastic genome: The impact of transposable elements on gene functionality and genomic structural variations.}, journal = {Genesis (New York, N.Y. : 2000)}, volume = {58}, number = {12}, pages = {e23399}, doi = {10.1002/dvg.23399}, pmid = {33230956}, issn = {1526-968X}, mesh = {Animals ; *DNA Transposable Elements ; *Evolution, Molecular ; *Gene Expression Regulation ; Gene Rearrangement ; *Genomic Structural Variation ; Humans ; *Mutation ; Regulatory Sequences, Nucleic Acid ; Stress, Physiological ; }, abstract = {Transposable elements (TEs) are DNA sequences that can change their position within genomes. TEs are present in most organisms and can be an important genomic component. Their activities are manifold: restructuring of genome size, chromosomal rearrangements, induction of gene mutations, and alteration of gene activity by insertion near or within promoters, intronic regions, or enhancer. There are several examples of mutations and other genetic variations determined by the activity of TEs, associated with the evolution of prokaryotic and eukaryotic organisms and the domestication of plants. Generally, TE mobilization occurs when the organism is subjected to stress, which can include both biotic and abiotic stresses, polyploidy conditions, and interspecific hybridizations, very common events in plants. TEs are widely distributed among organisms. TEs also play essential roles in evolution, but most of them are either dormant or inactive. This is mainly determined by epigenetic silencing mechanisms, regulatory systems, and control systems that aim to limit its proliferation. Furthermore, the host has recruited many genes originated from TEs as transcriptional regulators, especially in defense against pathogens and invasive genetic elements; this phenomenon is called molecular domestication. Therefore, TEs are responsible for horizontal gene transfer and the movement of genetic material between organisms, even phylogenetically distant, with a consequent remixing of their gene pools.}, }
@article {pmid33227198, year = {2020}, author = {Rubini, R and Mayer, C}, title = {Addicting Escherichia coli to New-to-Nature Reactions.}, journal = {ACS chemical biology}, volume = {15}, number = {12}, pages = {3093-3098}, pmid = {33227198}, issn = {1554-8937}, mesh = {Culture Media ; Escherichia coli/genetics/growth &amp; development/*metabolism ; Metal Nanoparticles/chemistry ; Organisms, Genetically Modified ; Palladium/chemistry ; Proof of Concept Study ; Synthetic Biology/methods ; Xenobiotics/administration &amp; dosage ; }, abstract = {Biocontainment is an essential feature when deploying genetically modified organisms (GMOs) in open system applications, as variants escaping their intended operating environments could negatively impact ecosystems and human health. To avoid breaches resulting from metabolic cross-feeding, horizontal gene transfer, and/or genetic mutations, synthetic auxotrophs have been engineered to become dependent on exogenously supplied xenobiotics, such as noncanonical amino acids (ncAAs). The incorporation of these abiological building blocks into essential proteins constitutes a first step toward constructing xenobiological barriers between GMOs and their environments. To transition synthetic auxotrophs further away from familiar biology, we demonstrate how bacterial growth can be confined by transition-metal complexes that catalyze the formation of an essential ncAA through new-to-nature reactions. Specifically, using a homogeneous ruthenium complex enabled us to localize bacterial growth on solid media, while heterogeneous palladium nanoparticles could be recycled and deployed up to five consecutive times to ensure the survival of synthetic auxotrophs in liquid cultures.}, }
@article {pmid33221673, year = {2021}, author = {Ekundayo, TC and Igwaran, A and Oluwafemi, YD and Okoh, AI}, title = {Global bibliometric meta-analytic assessment of research trends on microbial chlorine resistance in drinking water/water treatment systems.}, journal = {Journal of environmental management}, volume = {278}, number = {Pt 2}, pages = {111641}, doi = {10.1016/j.jenvman.2020.111641}, pmid = {33221673}, issn = {1095-8630}, mesh = {Bibliometrics ; China ; Chlorine ; *Drinking Water ; Humans ; Japan ; *Water Purification ; }, abstract = {Chlorine is the commonest and cheapest disinfectant used in drinking water and wastewater treatment at household, municipal and industrial levels. However, the uprising of microbial chlorine resistance (MCR) pose critical public health hazard concerns; because, its potentiate exposure to difficult-to-treat resistant pathogens. Therefore, this study aimed at evaluating the burden of MCR in drinking water/wastewater treatment and distribution systems (DWWTDS) via science mapping of research productivity (authors, countries, institutions), thematic conceptual framework, disciplines, research networks and associated intellectual landscape. MCR data were mined from Scopus and Web of Science based on optimized algorithms with the root key term "chlorine* resistant*'' and analysed for pre-set indicator variables. Results revealed 1127 documents from 442 journals and 1430% average growth rate (AGR) of research articles from 2017 to 2019 on MCR. Country-wise, the USA (n = 299), China (n = 119), and Japan (n = 43) ranked in the 1st, 2nd, and 3rd positions respectively, among the top participating countries in MCR research. MCR research had considerable performance in public health and sustainable concern subjects namely, Environmental Sciences &amp; Ecology, Engineering, Microbiology, Water Resources, Biotechnology &amp; Applied Microbiology, Food Science &amp; Technology, Public, Environ &amp; Occupational Health, Chemistry, Infectious Diseases, and Marine &amp; Freshwater Biology; and with noticeable AGR in Environmental Sciences &amp; Ecology (330%) and Infectious Diseases (130%). The study found biofilm-related thrusts (n = 90, 270% AGR) as main research hotspots on MCR. Overall, the study identified and discussed four important thematic areas of public health challenges in MCR that could promote increasing waterborne diseases due to (re)emerging pathogens, enteric viruses and dissemination in DWWTDS. In conclusion, this study provides comprehensive overview of the growing burden of MCR in DWWTDS and standout as a primer of information for researchers on MCR. It recommends direct, intentional and integrated research priorities on MCR to overcome accompanying public health and environmental threats. In addition, chlorine resistance in waterborne fungi have not received research attention. Research activities related to fungal chlorine resistance will be an invaluable future direction in DWWTDS and guide against exposure to waterborne pathogenic fungi and mycotoxins. It is unknown whether chlorine resistance can be acquired by horizontal gene transfer in microorganisms and future research should elucidate this important thrust.}, }
@article {pmid33220599, year = {2020}, author = {Koblížek, M and Dachev, M and Bína, D and Nupur,  and Piwosz, K and Kaftan, D}, title = {Utilization of light energy in phototrophic Gemmatimonadetes.}, journal = {Journal of photochemistry and photobiology. B, Biology}, volume = {213}, number = {}, pages = {112085}, doi = {10.1016/j.jphotobiol.2020.112085}, pmid = {33220599}, issn = {1873-2682}, mesh = {Bacteria/*chemistry/metabolism ; Bacterial Proteins/*chemistry/metabolism ; Bacteriochlorophylls/*chemistry ; Kinetics ; Oxidation-Reduction ; Phosphorylation ; Photolysis ; Photosynthesis ; Photosynthetic Reaction Center Complex Proteins/*chemistry ; Spectrometry, Fluorescence ; }, abstract = {Gemmatimonas phototrophica is, so far, the only described phototrophic species of the bacterial phylum Gemmatimonadetes. Its cells contain a unique type of photosynthetic complex with the reaction center surrounded by a double ring antenna, however they can also grow in the dark using organic carbon substrates. Its photosynthesis genes were received via horizontal gene transfer from Proteobacteria. This raises two questions; how the horizontally transferred photosynthesis apparatus has integrated into the cellular machinery, and how much light-derived energy actually contributes to the cellular metabolism? To address these points, the photosynthetic reactions were studied on several levels, from photophysics of the reaction center to cellular growth. Flash photolysis measurements and bacteriochlorophyll fluorescence kinetic measurements documented the presence of fully functional type-2 reaction centers with a large light harvesting antenna. When illuminated, the bacterial cells reduced their respiration rate by 58 ± 5%, revealing that oxidative phosphorylation was replaced by photophosphorylation. Moreover, illumination also more than doubled the assimilation rates of glucose, a sugar that is mostly used for respiration. Finally, light increased the growth rates of Gemmatimonas phototrophica colonies on agar plates. All the presented data provide evidence that photosynthetic complexes are fully integrated into cellular metabolism of Gemmatimonas phototrophica, and are able to provide a substantial amount of energy for its metabolism and growth.}, }
@article {pmid33211639, year = {2021}, author = {Ebbole, DJ and Chen, M and Zhong, Z and Farmer, N and Zheng, W and Han, Y and Lu, G and Wang, Z}, title = {Evolution and Regulation of a Large Effector Family of Pyricularia oryzae.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {34}, number = {3}, pages = {255-269}, doi = {10.1094/MPMI-07-20-0210-R}, pmid = {33211639}, issn = {0894-0282}, mesh = {*Ascomycota/genetics ; *Evolution, Molecular ; *Gene Expression Regulation, Fungal ; Genes, Fungal/genetics ; Genetic Variation ; *Host-Pathogen Interactions/genetics ; *Oryza/microbiology ; }, abstract = {Plant pathogen effectors play important roles in parasitism, including countering plant immunity. However, investigations of the emergence and diversification of fungal effectors across host-adapted populations has been limited. We previously identified a gene encoding a suppressor of plant cell death in Pyricularia oryzae (syn. Magnaporthe oryzae). Here, we report the gene is one of a 21-member gene family and we characterize sequence diversity in different populations. Within the rice pathogen population, nucleotide diversity is low, however; the majority of gene family members display presence-absence polymorphism or other null alleles. Gene family allelic diversity is greater between host-adapted populations and, thus, we named them host-adapted genes (HAGs). Multiple copies of HAGs were found in some genome assemblies and sequence divergence between the alleles in two cases suggested they were the result of repeat-induced point mutagenesis. Transfer of family members between populations and novel HAG haplotypes resulting from apparent recombination were observed. HAG family transcripts were induced in planta and a subset of HAGs are dependent on a key regulator of pathogenesis, PMK1. We also found differential intron splicing for some HAGs that would prevent ex planta protein expression. For some genes, spliced transcript was expressed in antiphase with an overlapping antisense transcript. Characterization of HAG expression patterns and allelic diversity reveal novel mechanisms for HAG regulation and mechanisms generating sequence diversity and novel allele combinations. This evidence of strong in planta-specific expression and selection operating on the HAG family is suggestive of a role in parasitism.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.}, }
@article {pmid33203689, year = {2020}, author = {Li, L and Liu, Z and Zhang, M and Meng, D and Liu, X and Wang, P and Li, X and Jiang, Z and Zhong, S and Jiang, C and Yin, H}, title = {Insights into the Metabolism and Evolution of the Genus Acidiphilium, a Typical Acidophile in Acid Mine Drainage.}, journal = {mSystems}, volume = {5}, number = {6}, pages = {}, pmid = {33203689}, issn = {2379-5077}, abstract = {Here, we report three new Acidiphilium genomes, reclassified existing Acidiphilium species, and performed the first comparative genomic analysis on Acidiphilium in an attempt to address the metabolic potential, ecological functions, and evolutionary history of the genus Acidiphilium In the genomes of Acidiphilium, we found an abundant repertoire of horizontally transferred genes (HTGs) contributing to environmental adaption and metabolic expansion, including genes conferring photosynthesis (puf, puh), CO2 assimilation (rbc), capacity for methane metabolism (mmo, mdh, frm), nitrogen source utilization (nar, cyn, hmp), sulfur compound utilization (sox, psr, sqr), and multiple metal and osmotic stress resistance capacities (czc, cop, ect). Additionally, the predicted donors of horizontal gene transfer were present in a cooccurrence network of Acidiphilium Genome-scale positive selection analysis revealed that 15 genes contained adaptive mutations, most of which were multifunctional and played critical roles in the survival of extreme conditions. We proposed that Acidiphilium originated in mild conditions and adapted to extreme environments such as acidic mineral sites after the acquisition of many essential functions.IMPORTANCE Extremophiles, organisms that thrive in extreme environments, are key models for research on biological adaption. They can provide hints for the origin and evolution of life, as well as improve the understanding of biogeochemical cycling of elements. Extremely acidophilic bacteria such as Acidiphilium are widespread in acid mine drainage (AMD) systems, but the metabolic potential, ecological functions, and evolutionary history of this genus are still ambiguous. Here, we sequenced the genomes of three new Acidiphilium strains and performed comparative genomic analysis on this extremely acidophilic bacterial genus. We found in the genomes of Acidiphilium an abundant repertoire of horizontally transferred genes (HTGs) contributing to environmental adaption and metabolic ability expansion, as indicated by phylogenetic reconstruction and gene context comparison. This study has advanced our understanding of microbial evolution and biogeochemical cycling in extreme niches.}, }
@article {pmid33203384, year = {2020}, author = {Aljahdali, NH and Sanad, YM and Han, J and Foley, SL}, title = {Current knowledge and perspectives of potential impacts of Salmonella enterica on the profile of the gut microbiota.}, journal = {BMC microbiology}, volume = {20}, number = {1}, pages = {353}, pmid = {33203384}, issn = {1471-2180}, mesh = {Animals ; Gastroenteritis/microbiology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/immunology/microbiology ; Gene Transfer, Horizontal ; Host-Pathogen Interactions ; Humans ; Microbial Interactions ; Salmonella Infections/*microbiology ; Salmonella enterica/*physiology ; }, abstract = {In the past decade, the initial studies of the gut microbiota started focusing on the correlation of the composition of the gut microbiota and the health or diseases of the host, and there are extensive literature reviews pertaining to this theme. However, little is known about the association between the microbiota, the host, and pathogenic bacteria, such as Salmonella enterica, which is among the most important foodborne pathogens and identified as the source of multiple outbreaks linked to contaminated foods causing salmonellosis. Secretion systems, flagella, fimbriae, endotoxins, and exotoxins are factors that play the most important roles in the successful infection of the host cell by Salmonella. Infections with S. enterica, which is a threat to human health, can alter the genomic, taxonomic, and functional traits of the gut microbiota. The purpose of this review is to outline the state of knowledge on the impacts of S. enterica on the intestinal microbiota and highlight the need to identify the gut bacteria that could contribute to salmonellosis.}, }
@article {pmid33202889, year = {2020}, author = {Grynberg, P and Coiti Togawa, R and Dias de Freitas, L and Antonino, JD and Rancurel, C and Mota do Carmo Costa, M and Grossi-de-Sa, MF and Miller, RNG and Brasileiro, ACM and Messenberg Guimaraes, P and Danchin, EGJ}, title = {Comparative Genomics Reveals Novel Target Genes towards Specific Control of Plant-Parasitic Nematodes.}, journal = {Genes}, volume = {11}, number = {11}, pages = {}, pmid = {33202889}, issn = {2073-4425}, mesh = {Animals ; Computer Simulation ; Gene Expression Regulation ; Gene Ontology ; Gene Transfer, Horizontal ; Genome, Helminth/genetics ; Genomics/methods ; Helminth Proteins/*genetics ; Host-Parasite Interactions/genetics ; Nematoda/genetics/pathogenicity ; Phylogeny ; Plant Diseases/parasitology ; Plants/*parasitology ; Tylenchoidea/*genetics/pathogenicity ; }, abstract = {Plant-parasitic nematodes cause extensive annual yield losses to worldwide agricultural production. Most cultivated plants have no known resistance against nematodes and the few bearing a resistance gene can be overcome by certain species. Chemical methods that have been deployed to control nematodes have largely been banned from use due to their poor specificity and high toxicity. Hence, there is an urgent need for the development of cleaner and more specific control methods. Recent advances in nematode genomics, including in phytoparasitic species, provide an unprecedented opportunity to identify genes and functions specific to these pests. Using phylogenomics, we compared 61 nematode genomes, including 16 for plant-parasitic species and identified more than 24,000 protein families specific to these parasites. In the genome of Meloidogyne incognita, one of the most devastating plant parasites, we found ca. 10,000 proteins with orthologs restricted only to phytoparasitic species and no further homology in protein databases. Among these phytoparasite-specific proteins, ca. 1000 shared the same properties as known secreted effectors involved in essential parasitic functions. Of these, 68 were novel and showed strong expression during the endophytic phase of the nematode life cycle, based on both RNA-seq and RT-qPCR analyses. Besides effector candidates, transcription-related and neuro-perception functions were enriched in phytoparasite-specific proteins, revealing interesting targets for nematode control methods. This phylogenomics analysis constitutes a unique resource for the further understanding of the genetic basis of nematode adaptation to phytoparasitism and for the development of more efficient control methods.}, }
@article {pmid33202061, year = {2021}, author = {Mutuku, JM and Cui, S and Yoshida, S and Shirasu, K}, title = {Orobanchaceae parasite-host interactions.}, journal = {The New phytologist}, volume = {230}, number = {1}, pages = {46-59}, doi = {10.1111/nph.17083}, pmid = {33202061}, issn = {1469-8137}, support = {BB/P023223/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *Arabidopsis/genetics ; Host-Parasite Interactions ; *Orobanchaceae/genetics ; Plant Roots ; *Striga ; }, abstract = {Parasitic plants in the family Orobanchaceae, such as Striga, Orobanche and Phelipanche, often cause significant damage to agricultural crops. The Orobanchaceae family comprises more than 2000 species in about 100 genera, providing an excellent system for studying the molecular basis of parasitism and its evolution. Notably, the establishment of model Orobanchaceae parasites, such as Triphysaria versicolor and Phtheirospermum japonicum, that can infect the model host Arabidopsis, has greatly facilitated transgenic analyses of genes important for parasitism. In addition, recent genomic and transcriptomic analyses of several Orobanchaceae parasites have revealed fascinating molecular insights into the evolution of parasitism and strategies for adaptation in this family. This review highlights recent progress in understanding how Orobanchaceae parasites attack their hosts and how the hosts mount a defense against the threats.}, }
@article {pmid33199756, year = {2020}, author = {Shinozuka, H and Shinozuka, M and de Vries, EM and Sawbridge, TI and Spangenberg, GC and Cocks, BG}, title = {Fungus-originated genes in the genomes of cereal and pasture grasses acquired through ancient lateral transfer.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {19883}, pmid = {33199756}, issn = {2045-2322}, mesh = {Avena/genetics ; Edible Grain/*genetics ; Endophytes/genetics ; Epichloe/*genetics ; Evolution, Molecular ; Fungal Proteins/*genetics ; Gene Transfer, Horizontal ; High-Throughput Nucleotide Sequencing ; Hordeum/genetics ; Phylogeny ; Plant Proteins/*genetics ; Poaceae/*genetics ; Sequence Analysis, DNA ; Sequence Analysis, RNA ; Triticum/genetics ; }, abstract = {Evidence for ancestral gene transfer between Epichloë fungal endophyte ancestors and their host grass species is described. From genomes of cool-season grasses (the Poeae tribe), two Epichloë-originated genes were identified through DNA sequence similarity analysis. The two genes showed 96% and 85% DNA sequence identities between the corresponding Epichloë genes. One of the genes was specific to the Loliinae sub-tribe. The other gene was more widely conserved in the Poeae and Triticeae tribes, including wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.). The genes were independently transferred during the last 39 million years. The transferred genes were expressed in plant tissues, presumably retaining molecular functions. Multiple gene transfer events between the specific plant and fungal lineages are unique. A range of cereal crops is included in the Poeae and Triticeae tribes, and the Loliinae sub-tribe is consisted of economically important pasture and forage crops. Identification and characterisation of the 'natural' adaptation transgenes in the genomes of cereals, and pasture and forage grasses, that worldwide underpin the production of major foods, such as bread, meat, and milk, may change the 'unnatural' perception status of transgenic and gene-edited plants.}, }
@article {pmid33199394, year = {2021}, author = {An, J and Guo, G and Yu, D and Zhu, K and Zhang, C and Li, Y}, title = {ICEHpsaHPS7, a Novel Multiple Drug Resistance Integrative Conjugative Element in Glaesserella parasuis.}, journal = {Antimicrobial agents and chemotherapy}, volume = {65}, number = {2}, pages = {}, pmid = {33199394}, issn = {1098-6596}, mesh = {Conjugation, Genetic ; *Drug Resistance, Multiple ; *Gene Transfer, Horizontal ; Serogroup ; }, abstract = {Integrative conjugative elements (ICEs) are a kind of novel self-transmissible mobile genetic element. In this study, a novel ICE was identified in Glaesserella (Haemophilus) parasuis We confirmed that it could mediate the migration of antimicrobial resistance genes in G. parasuis and found that there may have been a transferring potential between different serovar strains of G. parasuis These findings demonstrate that the ICE is crucial to the horizontal transfer of antimicrobial resistance among G. parasuis strains.}, }
@article {pmid33198099, year = {2020}, author = {Shelenkov, A and Petrova, L and Fomina, V and Zamyatin, M and Mikhaylova, Y and Akimkin, V}, title = {Multidrug-Resistant Proteus mirabilis Strain with Cointegrate Plasmid.}, journal = {Microorganisms}, volume = {8}, number = {11}, pages = {}, pmid = {33198099}, issn = {2076-2607}, support = {075-15-2019-1666//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {Proteus mirabilis is a component of the normal intestinal microflora of humans and animals, but can cause urinary tract infections and even sepsis in hospital settings. In recent years, the number of multidrug-resistant P. mirabilis isolates, including the ones producing extended-spectrum β-lactamases (ESBLs), is increasing worldwide. However, the number of investigations dedicated to this species, especially, whole-genome sequencing, is much lower in comparison to the members of the ESKAPE pathogens group. This study presents a detailed analysis of clinical multidrug-resistant ESBL-producing P. mirabilis isolate using short- and long-read whole-genome sequencing, which allowed us to reveal possible horizontal gene transfer between Klebsiella pneumoniae and P. mirabilis plasmids and to locate the CRISPR-Cas system in the genome together with its probable phage targets, as well as multiple virulence genes. We believe that the data presented will contribute to the understanding of antibiotic resistance acquisition and virulence mechanisms for this important pathogen.}, }
@article {pmid33196407, year = {2021}, author = {Juscamayta-López, E and Valdivia, F and Morales, S and Donaires, LF and Fiestas-Solórzano, V and Oré, M and Pachas, P and León-Janampa, N and Gavilán, R}, title = {Emergence of ciprofloxacin-resistant Neisseria meningitidis B from asymptomatic carriers during an outbreak in Peru, 2017.}, journal = {Journal of medical microbiology}, volume = {70}, number = {1}, pages = {}, doi = {10.1099/jmm.0.001245}, pmid = {33196407}, issn = {1473-5644}, mesh = {Anti-Bacterial Agents/*pharmacology ; Carrier State/epidemiology/*microbiology ; Ciprofloxacin/*pharmacology ; *Drug Resistance, Bacterial ; Humans ; Meningococcal Infections/epidemiology/*microbiology ; Microbial Sensitivity Tests ; Neisseria meningitidis/classification/drug effects/genetics/*isolation &amp; purification ; Peru/epidemiology ; Phylogeny ; }, abstract = {Asymptomatic carriers are a likely source of transmission of Neisseria meningitidis to close contacts who are placed at a higher risk for invasive meningococcal disease (IMD). Although N. meningitidis ciprofloxacin-resistance is rare, there have been an increase in the reports of resistant isolates mainly in patients diagnosed with IMD, and little is known about the N. meningitidis ciprofloxacin-resistance in the carrier populations. We performed a pharyngeal carriage study during a 2017 military setting outbreak in Peru, caused by a ciprofloxacin-resistant N. meningitidis B. The isolates analysed came from two hospitalized cases and six asymptomatic carriers. Whole-genome sequence-based analysis was performed and showed that strains carrying the Thr91Ile mutation, in the gene encoding for subunit A of DNA gyrase (gyrA), were responsible for the fluoroquinolone resistance (MICs ≥0.256 µg ml[-1]) and were closely related to highly virulent strains from France, Norway and the UK. Phylogenetic analysis of the gyrA gene revealed that likely these Peruvian isolates acquired resistance through horizontal gene transfer from Neisseria lactamica. Our study provides evidence for the emergence and propagation of ciprofloxacin-resistant N. meningitidis B from asymptomatic carriers, and recommends the introduction of serogroup B vaccines for high-risk populations.}, }
@article {pmid33193572, year = {2020}, author = {Giannakou, K and Cotterrell, M and Delneri, D}, title = {Genomic Adaptation of Saccharomyces Species to Industrial Environments.}, journal = {Frontiers in genetics}, volume = {11}, number = {}, pages = {916}, pmid = {33193572}, issn = {1664-8021}, support = {BB/M017702/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {The budding yeast has been extensively studied for its physiological performance in fermentative environments and, due to its remarkable plasticity, is used in numerous industrial applications like in brewing, baking and wine fermentations. Furthermore, thanks to its small and relatively simple eukaryotic genome, the molecular mechanisms behind its evolution and domestication are more easily explored. Considerable work has been directed into examining the industrial adaptation processes that shaped the genotypes of species and hybrids belonging to the Saccharomyces group, specifically in relation to beverage fermentation performances. A variety of genetic mechanisms are responsible for the yeast response to stress conditions, such as genome duplication, chromosomal re-arrangements, hybridization and horizontal gene transfer, and these genetic alterations are also contributing to the diversity in the Saccharomyces industrial strains. Here, we review the recent genetic and evolutionary studies exploring domestication and biodiversity of yeast strains.}, }
@article {pmid33193265, year = {2020}, author = {Liu, M and Huang, M and Wang, M and Zhu, D and Jia, R and Chen, S and Zhang, L and Pan, L and Cheng, A}, title = {The Clustered Regularly Interspaced Short Palindromic Repeat System and Argonaute: An Emerging Bacterial Immunity System for Defense Against Natural Transformation?.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {593301}, pmid = {33193265}, issn = {1664-302X}, abstract = {Clustered regularly interspaced short palindromic repeat (CRISPR) systems and prokaryotic Argonaute proteins (Agos) have been shown to defend bacterial and archaeal cells against invading nucleic acids. Indeed, they are important elements for inhibiting horizontal gene transfer between bacterial and archaeal cells. The CRISPR system employs an RNA-guide complex to target invading DNA or RNA, while Agos target DNA using single stranded DNA or RNA as guides. Thus, the CRISPR and Agos systems defend against exogenous nucleic acids by different mechanisms. It is not fully understood how antagonization of these systems occurs during natural transformation, wherein exogenous DNA enters a host cell as single stranded DNA and is then integrated into the host genome. In this review, we discuss the functions and mechanisms of the CRISPR system and Agos in cellular defense against natural transformation.}, }
@article {pmid33193153, year = {2020}, author = {Li, L and Hassan, KA and Tetu, SG and Naidu, V and Pokhrel, A and Cain, AK and Paulsen, IT}, title = {The Transcriptomic Signature of Tigecycline in Acinetobacter baumannii.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {565438}, pmid = {33193153}, issn = {1664-302X}, abstract = {Tigecycline, a protein translation inhibitor, is a treatment of last resort for infections caused by the opportunistic multidrug resistance human pathogen Acinetobacter baumannii. However, strains resistant to tigecycline were reported not long after its clinical introduction. Translation inhibitor antibiotics perturb ribosome function and induce the reduction of (p)ppGpp, an alarmone involved in the stringent response that negatively modulates ribosome production. Through RNA sequencing, this study revealed a significant reduction in the transcription of genes in citric acid cycle and cell respiration, suggesting tigecycline inhibits or slows down bacterial growth. Our results indicated that the drug-induced reduction of (p)ppGpp level promoted the production but diminished the degradation of ribosomes, which mitigates the translational inhibition effect by tigecycline. The reduction of (p)ppGpp also led to a decrease of transcription coupled nucleotide excision repair which likely increases the chances of development of tigecycline resistant mutants. Increased expression of genes linked to horizontal gene transfer were also observed. The most upregulated gene, rtcB, involving in RNA repair, is either a direct tigecycline stress response or is in response to the transcription de-repression of a toxin-antitoxin system. The most down-regulated genes encode two β-lactamases, which is a possible by-product of tigecycline-induced reduction in transcription of genes associated with peptidoglycan biogenesis. This transcriptomics study provides a global genetic view of why A. baumannii is able to rapidly develop tigecycline resistance.}, }
@article {pmid33191749, year = {2020}, author = {Jong, MC and Harwood, CR and Blackburn, A and Snape, JR and Graham, DW}, title = {Impact of Redox Conditions on Antibiotic Resistance Conjugative Gene Transfer Frequency and Plasmid Fate in Wastewater Ecosystems.}, journal = {Environmental science &amp; technology}, volume = {54}, number = {23}, pages = {14984-14993}, doi = {10.1021/acs.est.0c03714}, pmid = {33191749}, issn = {1520-5851}, mesh = {Drug Resistance, Microbial/genetics ; *Ecosystem ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Oxidation-Reduction ; Plasmids/genetics ; *Wastewater ; }, abstract = {Wastewater is a common pathway for the spread of antibiotic resistance (AR) genes and bacteria into the environment. Biological treatment can mitigate this path, but horizontal gene transfer (HGT) between bacteria also occurs in such processes, although the influence of bioreactor habitat and ecology on HGT frequency is not well understood. Here, we quantified how oxidation-reduction (redox) conditions impact the fate of a Green fluorescent protein (Gfp)-tagged AR plasmid (pRP4-gfp) within an E. coli host (EcoFJ1) in the liquid phase and biofilms in bioreactors. Replicate reactors treating domestic wastewater were operated under stable aerobic (+195 ± 25 mV), anoxic (-15 ± 50 mV), and anaerobic (-195 ± 15 mV) conditions, and flow cytometry and selective plating were used to quantify donor strain, EcoFJ1(pRP4-gfp), and putative transconjugants over time. Plasmid pRP4-gfp-bearing cells disappeared rapidly in aerobic ecosystems (∼2.0 log reduction after 72 h), especially in the liquid phase. In contrast, EcoFJ1(pRP4-gfp) and putative transconjugants persisted much longer in anaerobic biofilms (∼1.0 log reduction, after 72 h). Plasmid transfer frequencies were also higher under anaerobic conditions. In parallel, protozoan abundances were over 20 times higher in aerobic reactors relative to anaerobic reactors, and protozoa numbers significantly inversely correlated with pRP4-gfp signals across all reactors (p < 0.05). Taken together, observed HGT frequency and plasmid retention are impacted by habitat conditions and trophic effects, especially oxygen conditions and apparent predation. New aerobic bioreactor designs are needed, ideally employing passive aeration to save energy, to minimize resistance HGT in biological wastewater treatment processes.}, }
@article {pmid33190645, year = {2020}, author = {Kleiner, M and Bushnell, B and Sanderson, KE and Hooper, LV and Duerkop, BA}, title = {Transductomics: sequencing-based detection and analysis of transduced DNA in pure cultures and microbial communities.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {158}, pmid = {33190645}, issn = {2049-2618}, support = {K01 DK102436/DK/NIDDK NIH HHS/United States ; R01 AI141479/AI/NIAID NIH HHS/United States ; R01 DK070855/DK/NIDDK NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; DNA, Bacterial/*analysis/*genetics ; Gastrointestinal Microbiome/genetics ; Gene Transfer, Horizontal/*genetics ; *Genomics ; Male ; Mice ; Mice, Inbred C57BL ; Microbiota/*genetics ; Reproducibility of Results ; *Transduction, Genetic ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT) plays a central role in microbial evolution. Our understanding of the mechanisms, frequency, and taxonomic range of HGT in polymicrobial environments is limited, as we currently rely on historical HGT events inferred from genome sequencing and studies involving cultured microorganisms. We lack approaches to observe ongoing HGT in microbial communities.<br><br>RESULTS: To address this knowledge gap, we developed a DNA sequencing-based "transductomics" approach that detects and characterizes microbial DNA transferred via transduction. We validated our approach using model systems representing a range of transduction modes and show that we can detect numerous classes of transducing DNA. Additionally, we show that we can use this methodology to obtain insights into DNA transduction among all major taxonomic groups of the intestinal microbiome.<br><br>CONCLUSIONS: The transductomics approach that we present here allows for the detection and characterization of genes that are potentially transferred between microbes in complex microbial communities at the time of measurement and thus provides insights into real-time ongoing horizontal gene transfer. This work extends the genomic toolkit for the broader study of mobile DNA within microbial communities and could be used to understand how phenotypes spread within microbiomes. Video Abstract.}, }
@article {pmid33187698, year = {2021}, author = {Zheng, Z and Li, L and Makhalanyane, TP and Xu, C and Li, K and Xue, K and Xu, C and Qian, R and Zhang, B and Du, J and Yu, H and Cui, X and Wang, Y and Hao, Y}, title = {The composition of antibiotic resistance genes is not affected by grazing but is determined by microorganisms in grassland soils.}, journal = {The Science of the total environment}, volume = {761}, number = {}, pages = {143205}, doi = {10.1016/j.scitotenv.2020.143205}, pmid = {33187698}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents ; Drug Resistance, Microbial/genetics ; Ecosystem ; Genes, Bacterial ; *Grassland ; *Soil ; Soil Microbiology ; }, abstract = {Grazing is expected to exert a substantial influence on antibiotic resistance genes (ARGs) in grassland ecosystems. However, the precise effects of grazing on the composition of ARGs in grassland soils remain unclear. This is especially the case for grassland soils subject to long-term grazing. Here, we investigated ARGs and bacterial community composition in soils subject to long-term historic grazing (13-39 years) and corresponding ungrazed samples. Using a combination of shotgun metagenomics, amplicon analyses and associated soil physicochemical data, we provide novel insights regarding the structure of ARGs in grassland soils. Interestingly, our analysis revealed that long-term historic grazing had no impacts on the composition of ARGs in grassland soils. An average of 378 ARGs, conferring resistance to 14 major categories of antibiotics (80%), were identified in both grazing and ungrazed sites. Actinobacteria, Proteobacteria and Acidobacteria were the most prevalent predicted hosts in these soils and were also shown to harbour genetic capacity for multiple-resistant ARGs. Our results suggested that positive effects of bacterial community composition on ARGs could potentially be controlled by affecting MGEs. Soil properties had direct effects on the composition of ARGs through affecting the frequency of horizontal gene transfer among bacteria. Twelve novel ARGs were found in S. grandis steppe grasslands, indicating that different vegetation types might induce shifts in soil ARGs. Collectively, these findings suggest that soil properties, plants and microorganisms play critical roles in shaping ARG patterns in grasslands. Together, these data establish a solid baseline for understanding environmental antibiotic resistance in grasslands.}, }
@article {pmid33185664, year = {2021}, author = {Goughenour, KD and Whalin, J and Slot, JC and Rappleye, CA}, title = {Diversification of Fungal Chitinases and Their Functional Differentiation in Histoplasma capsulatum.}, journal = {Molecular biology and evolution}, volume = {38}, number = {4}, pages = {1339-1355}, pmid = {33185664}, issn = {1537-1719}, support = {R21 AI117122/AI/NIAID NIH HHS/United States ; T32 AI112542/AI/NIAID NIH HHS/United States ; }, mesh = {Chitinases/*genetics/metabolism ; *Evolution, Molecular ; Fungal Proteins/*genetics/metabolism ; *Genome, Fungal ; Histoplasma/enzymology/*genetics ; Protein Domains ; }, abstract = {Chitinases enzymatically hydrolyze chitin, a highly abundant and utilized polymer of N-acetyl-glucosamine. Fungi are a rich source of chitinases; however, the phylogenetic and functional diversity of fungal chitinases are not well understood. We surveyed fungal chitinases from 373 publicly available genomes, characterized domain architecture, and conducted phylogenetic analyses of the glycoside hydrolase (GH18) domain. This large-scale analysis does not support the previous division of fungal chitinases into three major clades (A, B, C) as chitinases previously assigned to the "C" clade are not resolved as distinct from the "A" clade. Fungal chitinase diversity was partly shaped by horizontal gene transfer, and at least one clade of bacterial origin occurs among chitinases previously assigned to the "B" clade. Furthermore, chitin-binding domains (including the LysM domain) do not define specific clades, but instead are found more broadly across clades of chitinases. To gain insight into biological function diversity, we characterized all eight chitinases (Cts) from the thermally dimorphic fungus, Histoplasma capsulatum: six A clade, one B clade, and one formerly classified C clade chitinases. Expression analyses showed variable induction of chitinase genes in the presence of chitin but preferential expression of CTS3 in the mycelial stage. Activity assays demonstrated that Cts1 (B-I), Cts2 (A-V), Cts3 (A-V), Cts4 (A-V) have endochitinase activities with varying degrees of chitobiosidase function. Cts6 (C-I) has activity consistent with N-acetyl-glucosaminidase exochitinase function and Cts8 (A-II) has chitobiase activity. These results suggest chitinase activity is variable even within subclades and that predictions of functionality require more sophisticated models.}, }
@article {pmid33185245, year = {2020}, author = {Rao, RT and Sharma, S and Sivakumar, N and Jayakumar, K}, title = {Genomic islands and the evolution of livestock-associated Staphylococcus aureus genomes.}, journal = {Bioscience reports}, volume = {40}, number = {11}, pages = {}, pmid = {33185245}, issn = {1573-4935}, mesh = {Animals ; Computational Biology ; Databases, Genetic ; *Evolution, Molecular ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genomic Islands ; Livestock/*microbiology ; Staphylococcal Infections/genetics/microbiology/*veterinary ; Staphylococcus aureus/*genetics/isolation &amp; purification/pathogenicity ; Virulence ; }, abstract = {BACKGROUND: Genomic Islands (GIs) are commonly believed to be relics of horizontal transfer and associated with specific metabolic capacities, including virulence of the strain. Horizontal gene transfer (HGT) plays a vital role in the acquisition of GIs and the evolution and adaptation of bacterial genomes.<br><br>OBJECTIVE: The present study was designed to predict the GIs and role of HGT in evolution of livestock-associated Staphylococcus aureus (LA-SA).<br><br>METHODS: GIs were predicted with two methods namely, Ensemble algorithm for Genomic Island Detection (EGID) tool, and Seq word Sniffer script. Functional characterization of GI elements was performed with clustering of orthologs. The putative donor predictions of GIs was done with the aid of the pre_GI database.<br><br>RESULTS: The present study predicted a pan of 46 GIs across the LA-SA genomes. Functional characterization of GI sequences revealed few unique results like the presence of metabolic operons like leuABCD and folPK genes in GIs and showed the importance of GIs in the adaptation to the host niche. The developed framework for GI donor prediction results revealed Rickettsia and Mycoplasma as the major donors of GI elements.<br><br>CONCLUSIONS: The role of GIs during the evolutionary race of LA-SA could be concluded from the present study. Niche adaptation of LA-SA enhanced presumably due to these GIs. Future studies could focus on the evolutionary relationships between Rickettsia and Mycoplasma sp. with S. aureus and also the evolution of Leucine/Isoleucine mosaic operon (leuABCD).}, }
@article {pmid33184734, year = {2021}, author = {Sun, Y and Guo, G and Tian, F and Chen, H and Liu, W and Li, M and Wang, S}, title = {Antibiotic resistance genes and bacterial community on the surfaces of five cultivars of fresh tomatoes.}, journal = {Ecotoxicology (London, England)}, volume = {30}, number = {8}, pages = {1550-1558}, pmid = {33184734}, issn = {1573-3017}, support = {31770152//National Natural Science Foundation of China/ ; }, mesh = {Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Humans ; *Solanum lycopersicum/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Antibiotic resistance genes and bacteria (ARGs and ARB) in vegetable or fruit pose risks to ecological environment health. However, the assessment of ARGs and ARB from one popular vegetable, fresh tomato, has not been carried out before. In this study, high-throughput quantitative PCR and 16S rRNA gene Illumina sequencing technology were used to explore the antibiotic resistance characteristics of bacteria on five common cultivars of fresh tomatoes from supermarket. A total of 191 ARGs and 10 mobile genetic elements (MGEs) were detected on the tomato surfaces. The distribution profile of ARGs and MGEs was different among samples, with the organic tomatoes showing more ARGs and MGEs number and relative abundance. Aminoglycoside resistance genes strA and strB, sulfonamide resistance gene sul1, and multidrug resistance gene qacΔ1-01 were the predominant ARGs. Dominant MGEs were transposase genes, which might promote horizontal gene transfer (HGT) of ARGs. Network analysis indicated that fifteen bacterial families might be the potential hosts of ARGs, and the detected MGEs might have positive correlation with ARGs. These results revealed the bacterial ARGs and MGEs from fresh tomato, which might help guide human to pay more attention to ecological environment impacts of ARGs and ARB on the surfaces of vegetable or fruit.}, }
@article {pmid33180493, year = {2020}, author = {Wang, Z and Wang, K and Bravo, A and Soberón, M and Cai, J and Shu, C and Zhang, J}, title = {Coexistence of cry9 with the vip3A Gene in an Identical Plasmid of Bacillus thuringiensis Indicates Their Synergistic Insecticidal Toxicity.}, journal = {Journal of agricultural and food chemistry}, volume = {68}, number = {47}, pages = {14081-14090}, doi = {10.1021/acs.jafc.0c05304}, pmid = {33180493}, issn = {1520-5118}, mesh = {Animals ; *Bacillus thuringiensis/genetics ; Bacterial Proteins/genetics ; Insecta ; *Insecticides/toxicity ; Pest Control, Biological ; Plasmids/genetics ; }, abstract = {Bacillus thuringiensis (Bt) strains may express several insecticidal proteins with synergistic features, achieving high insecticidal toxicity and delaying development of resistance in insect pests. Previous work showed that Cry9Aa and Vip3Aa proteins present synergistic activity against Chilo suppressalis. In this study, genome-wide analysis of 489 Bt genomes revealed that cry9A was associated with the vip3A gene in seven Bt strains. Among all Bt genomes analyzed, not a single strain was found to have the cry9A gene alone without the presence of the vip3A gene. The complete genome sequencing of two Bt strains, 4AP1 and 4AO1, revealed that cry9A and vip3A genes were located in the same plasmid in both strains. The genome context analysis suggested a recombination mechanism responsible for the insertion of the cry9A gene into the plasmid containing vip3A. The coexistence of Cry9A with Vip3A proteins in strain 4AP1 was confirmed by liquid chromatography-tandem mass spectrometry and western blot analyses. Furthermore, another Cry9 protein codified by the gene in the identical plasmid also showed synergistic activity with the Vip3A protein. Overall, our results support that cry9 genes coexisted with vip3A and that complete genome sequencing combined with protein expression analysis may be used to identify associations of insecticidal proteins with potential synergistic toxicity.}, }
@article {pmid33180321, year = {2021}, author = {Wasfi, R and Rasslan, F and Hassan, SS and Ashour, HM and Abd El-Rahman, OA}, title = {Co-Existence of Carbapenemase-Encoding Genes in Acinetobacter baumannii from Cancer Patients.}, journal = {Infectious diseases and therapy}, volume = {10}, number = {1}, pages = {291-305}, pmid = {33180321}, issn = {2193-8229}, abstract = {INTRODUCTION: Acinetobacter baumannii is an opportunistic pathogen, which can acquire new resistance genes. Infections by carbapenem-resistant A. baumannii (CRAB) in cancer patients cause high mortality.<br><br>METHODS: CRAB isolates from cancer patients were screened for carbapenemase-encoding genes that belong to Ambler classes (A), (B), and (D), followed by genotypic characterization by enterobacterial-repetitive-Intergenic-consensus-polymerase chain reaction (ERIC-PCR) and multilocus-sequence-typing (MLST).<br><br>RESULTS: A total of 94.1% of CRAB isolates co-harbored more than one carbapenemase-encoding gene. The genes blaNDM, blaOXA-23-like, and blaKPC showed the&#xa0;highest prevalence, with rates of 23 (67.7%), 19 (55.9%), and 17 (50%), respectively. ERIC-PCR revealed 19 patterns (grouped into 9 clusters). MLST analysis identified different sequence types (STs) (ST-268, ST-195, ST-1114, and ST-1632) that belong to the highly resistant easily spreadable International clone II (IC II). Genotype diversity indicated the&#xa0;dissemination of carbapenem-hydrolyzing, &#x3b2;-lactamase-encoding genes among genetically unrelated isolates. We observed a&#xa0;high prevalence of metallo-&#x3b2;-lactamase (MBL)-encoding genes (including the highly-resistant blaNDM gene that is capable of horizontal gene transfer) and of isolates harboring multiple carbapenemase-encoding genes from different classes.<br><br>CONCLUSION: The findings are alarming and call for measures to prevent and control the spread of MBL-encoding genes among bacteria causing infections in cancer patients and other immunocompromised patient populations.}, }
@article {pmid33178155, year = {2020}, author = {Foka, FET and Mienie, C and Bezuidenhout, CC and Ateba, CN}, title = {Complete Genomic Analysis of VRE From a Cattle Feedlot: Focus on 2 Antibiotic Resistance.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {571958}, pmid = {33178155}, issn = {1664-302X}, abstract = {Practices in intensive animal farming such as the extensive use of antimicrobials have significant impacts on the genetic make-up of bacterial communities, especially on that of human/animal commensals. In this report, whole genome sequencing of two vancomycin-resistant enterococci (VRE) isolates from a cattle feedlot in the North West Province, South Africa, was used to highlight the threats that extensive antimicrobial usage in intensive animal rearing represents for environmental microbiomes and the food chain. The genomic DNA of the studied strains was extracted using a DNA extraction kit. Whole-genome sequencing was performed through next-generation sequencing. The genomes of Enterococcus durans strain NWUTAL1 and Enterococcus gallinarum strain S52016 consisted of 3,279,618 and 2,374,946 bp, respectively with G + C contents of 40.76 and 43.13%, respectively. Antibiotic resistance genes (ARG), plasmids and virulence factors (involved in biofilm formation, colonization and copper/silver efflux system), were detected in the genomes of both strains. The presence of these genetic determinants in the studied strains is a cause for concern as they may disseminate and find their way into the food chain via horizontal gene transfer amongst bacteria of the different ecological niches. Issues of this nature cannot be undermined and are relevant as far as food safety is concerned.}, }
@article {pmid33177216, year = {2020}, author = {Molina-Quiroz, RC and Dalia, TN and Camilli, A and Dalia, AB and Silva-Valenzuela, CA}, title = {Prophage-Dependent Neighbor Predation Fosters Horizontal Gene Transfer by Natural Transformation.}, journal = {mSphere}, volume = {5}, number = {6}, pages = {}, pmid = {33177216}, issn = {2379-5042}, support = {R01 AI055058/AI/NIAID NIH HHS/United States ; R35 GM128674/GM/NIGMS NIH HHS/United States ; R37 AI055058/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Chitin/metabolism ; Gene Transfer, Horizontal ; Predatory Behavior ; Prophages/*genetics/growth &amp; development ; Vibrio cholerae/*genetics/pathogenicity/*virology ; Virulence ; }, abstract = {Natural transformation is a broadly conserved mechanism of horizontal gene transfer (HGT) in bacteria that can shape their evolution through the acquisition of genes that promote virulence, antibiotic resistance, and other traits. Recent work has established that neighbor predation via type VI secretion systems, bacteriocins, and virulent phages plays an important role in promoting HGT. Here, we demonstrate that in chitin estuary microcosms, Vibrio cholerae K139 lysogens exhibit prophage-dependent neighbor predation of nonlysogens to enhance HGT. Through predation of nonlysogens, K139 lysogens also have a fitness advantage under these microcosm conditions. The ecological strategy revealed by our work provides a better understanding of the evolutionary mechanisms used by bacteria to adapt in their natural setting and contributes to our understanding of the selective pressures that may drive prophage maintenance in bacterial genomes.IMPORTANCE Prophages are nearly ubiquitous in bacterial species. These integrated phage elements have previously been implicated in horizontal gene transfer (HGT) largely through their ability to carry out transduction (generalized or specialized). Here, we show that prophage-encoded viral particles promote neighbor predation leading to enhanced HGT by natural transformation in the waterborne pathogen Vibrio cholerae Our findings contribute to a comprehensive understanding of the dynamic forces involved in prophage maintenance which ultimately drive the evolution of naturally competent bacteria in their natural environment.}, }
@article {pmid33171625, year = {2020}, author = {Abd El-Aziz, NK and Ammar, AM and Hamdy, MM and Gobouri, AA and Azab, E and Sewid, AH}, title = {First Report of aacC5-aadA7Δ4 Gene Cassette Array and Phage Tail Tape Measure Protein on Class 1 Integrons of Campylobacter Species Isolated from Animal and Human Sources in Egypt.}, journal = {Animals : an open access journal from MDPI}, volume = {10}, number = {11}, pages = {}, pmid = {33171625}, issn = {2076-2615}, abstract = {Campylobacter species are common commensals in the gastrointestinal tract of livestock animals; thus, animal-to-human transmission occurs frequently. We investigated for the first time, class 1 integrons and associated gene cassettes among pan drug-resistant (PDR), extensively drug-resistant (XDR), and multidrug-resistant (MDR) Campylobacter species isolated from livestock animals and humans in Egypt. Campylobacter species were detected in 58.11% of the analyzed chicken samples represented as 67.53% Campylobacter jejuni(C. jejuni) and 32.47% Campylobacter coli (C. coli). C. jejuni isolates were reported in 51.42%, 74.28%, and 66.67% of examined minced meat, raw milk, and human stool samples, respectively. Variable antimicrobial resistance phenotypes; PDR (2.55%), XDR (68.94%), and MDR (28.5%) campylobacters were reported. Molecular analysis revealed that 97.36% of examined campylobacters were integrase gene-positive; all harbored the class 1 integrons, except one possessed an empty integron structure. DNA sequence analysis revealed the predominance of aadA (81.08%) and dfrA (67.56%) alleles accounting for resistance to aminoglycosides and trimethoprim, respectively. This is the first report of aacC5-aadA7Δ4 gene cassette array and a putative phage tail tape measure protein on class 1 integrons of Campylobacter isolates. Evidence from this study showed the possibility of Campylobacter-bacteriophage interactions and treatment failure in animals and humans due to horizontal gene transfer mediated by class 1 integrons.}, }
@article {pmid33171385, year = {2020}, author = {Paulitsch, F and Delamuta, JRM and Ribeiro, RA and da Silva Batista, JS and Hungria, M}, title = {Phylogeny of symbiotic genes reveals symbiovars within legume-nodulating Paraburkholderia species.}, journal = {Systematic and applied microbiology}, volume = {43}, number = {6}, pages = {126151}, doi = {10.1016/j.syapm.2020.126151}, pmid = {33171385}, issn = {1618-0984}, mesh = {Bacterial Typing Techniques ; Brazil ; Burkholderiaceae/*classification/isolation &amp; purification ; DNA, Bacterial/genetics ; Fabaceae/*microbiology ; Genes, Bacterial ; Mimosa/microbiology ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Root Nodules, Plant/*microbiology ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {Bacteria belonging to the genus Paraburkholderia are capable of establishing symbiotic relationships with plants belonging to the Fabaceae (=Leguminosae) family and fixing the atmospheric nitrogen in specialized structures in the roots called nodules, in a process known as biological nitrogen fixation (BNF). In the nodulation and BNF processes several bacterial symbiotic genes are involved, but the relations between symbiotic, core genes and host specificity are still poorly studied and understood in Paraburkholderia. In this study, eight strains of nodulating nitrogen-fixing Paraburkholderia isolated in Brazil, together with described species and other reference strains were used to infer the relatedness between core (16S rDNA, recA) and symbiotic (nod, nif, fix) genes. The diversity of genes involved in the nodulation (nodAC) and nitrogen fixation (nifH) abilities was investigated. Only two groups, one containing three Paraburkholderia species symbionts of Mimosa, and another one with P. ribeironis strains presented similar phylogenetic patterns in the analysis of core and symbiotic genes. In three other groups events of horizontal gene transfer of symbiotic genes were detected. Paraburkholderia strains with available genomes were used in the complementary analysis of nifHDK and fixABC and confirmed well-defined phylogenetic positions of symbiotic genes. In all analyses of nod, nif and fix genes the strains were distributed into five clades with high bootstrap support, allowing the proposal of five symbiovars in nodulating nitrogen-fixing Paraburkholderia, designated as mimosae, africana, tropicalis, atlantica and piptadeniae. Phylogenetic inferences within each symbiovar are discussed.}, }
@article {pmid33170167, year = {2020}, author = {Naureen, Z and Dautaj, A and Anpilogov, K and Camilleri, G and Dhuli, K and Tanzi, B and Maltese, PE and Cristofoli, F and De Antoni, L and Beccari, T and Dundar, M and Bertelli, M}, title = {Bacteriophages presence in nature and their role in the natural selection of bacterial populations.}, journal = {Acta bio-medica : Atenei Parmensis}, volume = {91}, number = {13-S}, pages = {e2020024}, pmid = {33170167}, issn = {2531-6745}, mesh = {Bacteria ; *Bacteriophages ; *Microbiota ; Selection, Genetic ; }, abstract = {Phages are the obligate parasite of bacteria and have complex interactions with their hosts. Phages can live in, modify, and shape bacterial communities by bringing about changes in their abundance, diversity, physiology, and virulence. In addition, phages mediate lateral gene transfer, modify host metabolism and reallocate bacterially-derived biochemical compounds through cell lysis, thus playing an important role in ecosystem. Phages coexist and coevolve with bacteria and have developed several antidefense mechanisms in response to bacterial defense strategies against them. Phages owe their existence to their bacterial hosts, therefore they bring about alterations in their host genomes by transferring resistance genes and genes encoding toxins in order to improve the fitness of the hosts. Application of phages in biotechnology, environment, agriculture and medicines demands a deep insight into the myriad of phage-bacteria interactions. However, to understand their complex interactions, we need to know how unique phages are to their bacterial hosts and how they exert a selective pressure on the microbial communities in nature. Consequently, the present review focuses on phage biology with respect to natural selection of bacterial populations.}, }
@article {pmid33169907, year = {2021}, author = {Aulestia, M and Flores, A and Mangas, EL and Pérez-Pulido, AJ and Santero, E and Camacho, EM}, title = {Isolation and genomic characterization of the ibuprofen-degrading bacterium Sphingomonas strain MPO218.}, journal = {Environmental microbiology}, volume = {23}, number = {1}, pages = {267-280}, doi = {10.1111/1462-2920.15309}, pmid = {33169907}, issn = {1462-2920}, support = {BIO2014-57545-R//Ministerio de Ciencia e Innovaci&#xf3;n/ ; }, mesh = {*Biodegradation, Environmental ; Gene Transfer, Horizontal ; Genomics ; Ibuprofen/*metabolism ; Plasmids/*genetics ; Sphingomonadaceae/genetics ; Sphingomonas/*metabolism ; Water Pollutants, Chemical/*metabolism ; Water Pollution, Chemical/analysis ; Water Purification ; }, abstract = {The presence of pharmaceutical compounds in waters and soils is of particular concern because these compounds can be biologically active, even at environmental concentrations. Most pharmaceutical contaminants result from inefficient removal of these compounds during wastewater treatment. Although microorganisms able to biodegrade pharmaceuticals compounds have been described, the isolation and characterization of new bacterial strains capable of degrading drugs remain important to improve the removal of this pollutant. In this work, we describe the Sphingomonas wittichii strain MPO218 as able to use ibuprofen as the sole carbon and energy source. The genome of MPO218 consists of a circular chromosome and two circular plasmids. Our analysis shows that the largest plasmid, named pIBU218, is conjugative and can horizontally transfer the capability of growing on ibuprofen after conjugation with another related bacterium, Sphingopyxis granuli TFA. This plasmid appears to be unstable since it undergoes different deletions in absence of selection when growth on ibuprofen is not selected. This is the first described example of a natural and conjugative plasmid that enables growth on ibuprofen and is another example of how horizontal gene transfer plays a crucial role in the evolution of bacteria.}, }
@article {pmid33169795, year = {2021}, author = {Li, Q and Scornavacca, C and Galtier, N and Chan, YB}, title = {The Multilocus Multispecies Coalescent: A Flexible New Model of Gene Family Evolution.}, journal = {Systematic biology}, volume = {70}, number = {4}, pages = {822-837}, doi = {10.1093/sysbio/syaa084}, pmid = {33169795}, issn = {1076-836X}, mesh = {Computer Simulation ; *Evolution, Molecular ; *Gene Duplication ; Gene Transfer, Horizontal ; Genetic Speciation ; *Models, Genetic ; *Multigene Family ; Phylogeny ; }, abstract = {Incomplete lineage sorting (ILS), the interaction between coalescence and speciation, can generate incongruence between gene trees and species trees, as can gene duplication (D), transfer (T), and loss (L). These processes are usually modeled independently, but in reality, ILS can affect gene copy number polymorphism, that is, interfere with DTL. This has been previously recognized, but not treated in a satisfactory way, mainly because DTL events are naturally modeled forward-in-time, while ILS is naturally modeled backward-in-time with the coalescent. Here, we consider the joint action of ILS and DTL on the gene tree/species tree problem in all its complexity. In particular, we show that the interaction between ILS and duplications/transfers (without losses) can result in patterns usually interpreted as resulting from gene loss, and that the realized rate of D, T, and L becomes nonhomogeneous in time when ILS is taken into account. We introduce algorithmic solutions to these problems. Our new model, the multilocus multispecies coalescent, which also accounts for any level of linkage between loci, generalizes the multispecies coalescent (MSC) model and offers a versatile, powerful framework for proper simulation, and inference of gene family evolution. [Gene duplication; gene loss; horizontal gene transfer; incomplete lineage sorting; multispecies coalescent; hemiplasy; recombination.].}, }
@article {pmid33168636, year = {2021}, author = {Hardy, L and Juan, PA and Coupat-Goutaland, B and Charpentier, X}, title = {Transposon Insertion Sequencing in a Clinical Isolate of Legionella pneumophila Identifies Essential Genes and Determinants of Natural Transformation.}, journal = {Journal of bacteriology}, volume = {203}, number = {3}, pages = {}, pmid = {33168636}, issn = {1098-5530}, mesh = {Cell Survival ; DNA Transposable Elements/*genetics ; Gene Library ; Gene Transfer, Horizontal ; *Genes, Essential ; Legionella ; Legionella pneumophila/*genetics/*isolation &amp; purification ; Mutagenesis ; }, abstract = {Legionella pneumophila is a Gram-negative bacterium ubiquitous in freshwater environments which, if inhaled, can cause a severe pneumonia in humans. The emergence of L. pneumophila is linked to several traits selected in the environment, the acquisition of some of which involved intra- and interkingdom horizontal gene transfer events. Transposon insertion sequencing (TIS) is a powerful method to identify the genetic basis of selectable traits as well as to identify fitness determinants and essential genes, which are possible antibiotic targets. TIS has not yet been used to its full power in L. pneumophila, possibly because of the difficulty of obtaining a high-saturation transposon insertion library. Indeed, we found that isolates of sequence type 1 (ST1), which includes the commonly used laboratory strains, are poorly permissive to saturating mutagenesis by conjugation-mediated transposon delivery. In contrast, we obtained high-saturation libraries in non-ST1 clinical isolates, offering the prospect of using TIS on unaltered L. pneumophila strains. Focusing on one of them, we then used TIS to identify essential genes in L. pneumophila We also revealed that TIS could be used to identify genes controlling vertical transmission of mobile genetic elements. We then applied TIS to identify all the genes required for L. pneumophila to develop competence and undergo natural transformation, defining the set of major and minor type IV pilins that are engaged in DNA uptake. This work paves the way for the functional exploration of the L. pneumophila genome by TIS and the identification of the genetic basis of other life traits of this species.IMPORTANCELegionella pneumophila is the etiologic agent of a severe form of nosocomial and community-acquired pneumonia in humans. The environmental life traits of L. pneumophila are essential to its ability to accidentally infect humans. A comprehensive identification of their genetic basis could be obtained through the use of transposon insertion sequencing. However, this powerful approach had not been fully implemented in L. pneumophila Here, we describe the successful implementation of the transposon-sequencing approach in a clinical isolate of L. pneumophila We identify essential genes, potential drug targets, and genes required for horizontal gene transfer by natural transformation. This work represents an important step toward identifying the genetic basis of the many life traits of this environmental and pathogenic species.}, }
@article {pmid33165775, year = {2021}, author = {Chenthamara, K and Druzhinina, IS and Rahimi, MJ and Grujic, M and Cai, F}, title = {Ecological Genomics and Evolution of Trichoderma reesei.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2234}, number = {}, pages = {1-21}, doi = {10.1007/978-1-0716-1048-0_1}, pmid = {33165775}, issn = {1940-6029}, mesh = {Animals ; *Biological Evolution ; *Ecological and Environmental Phenomena ; Genome, Fungal ; Genomics/*methods ; Hypocreales/*genetics ; Likelihood Functions ; Parasites/genetics ; Phylogeny ; }, abstract = {The filamentous fungus Trichoderma reesei (Hypocreales, Ascomycota) is an efficient industrial cell factory for the production of cellulolytic enzymes used for biofuel and other applications. Therefore, researches addressing T. reesei are relatively advanced compared to other Trichoderma spp. because of the significant bulk of available knowledge, multiple genomic data, and gene manipulation techniques. However, the established role of T. reesei in industry has resulted in a frequently biased understanding of the biology of this fungus. Thus, the recent studies unexpectedly show that the superior cellulolytic activity of T. reesei and other Trichoderma species evolved due to multiple lateral gene transfer events, while the innate ability to parasitize other fungi (mycoparasitism) was maintained in the genus, including T. reesei. In this chapter, we will follow the concept of ecological genomics and describe the ecology, distribution, and evolution of T. reesei, as well as critically discuss several common misconceptions that originate from the success of this species in applied sciences and industry.}, }
@article {pmid33162948, year = {2020}, author = {Das, B and Bhadra, RK}, title = {(p)ppGpp Metabolism and Antimicrobial Resistance in Bacterial Pathogens.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {563944}, pmid = {33162948}, issn = {1664-302X}, abstract = {Single cell microorganisms including pathogens relentlessly face myriads of physicochemical stresses in their living environment. In order to survive and multiply under such unfavorable conditions, microbes have evolved with complex genetic networks, which allow them to sense and respond against these stresses. Stringent response is one such adaptive mechanism where bacteria can survive under nutrient starvation and other related stresses. The effector molecules for the stringent response are guanosine-5'-triphosphate 3'-diphosphate (pppGpp) and guanosine-3', 5'-bis(diphosphate) (ppGpp), together called (p)ppGpp. These effector molecules are now emerging as master regulators for several physiological processes of bacteria including virulence, persistence, and antimicrobial resistance. (p)ppGpp may work independently or along with its cofactor DksA to modulate the activities of its prime target RNA polymerase and other metabolic enzymes, which are involved in different biosynthetic pathways. Enzymes involved in (p)ppGpp metabolisms are ubiquitously present in bacteria and categorized them into three classes, i.e., canonical (p)ppGpp synthetase (RelA), (p)ppGpp hydrolase/synthetase (SpoT/Rel/RSH), and small alarmone synthetases (SAS). While RelA gets activated in response to amino acid starvation, enzymes belonging to SpoT/Rel/RSH and SAS family can synthesize (p)ppGpp in response to glucose starvation and several other stress conditions. In this review, we will discuss about the current status of the following aspects: (i) diversity of (p)ppGpp biosynthetic enzymes among different bacterial species including enteropathogens, (ii) signals that modulate the activity of (p)ppGpp synthetase and hydrolase, (iii) effect of (p)ppGpp in the production of antibiotics, and (iv) role of (p)ppGpp in the emergence of antibiotic resistant pathogens. Emphasis has been given to the cholera pathogen Vibrio cholerae due to its sophisticated and complex (p)ppGpp metabolic pathways, rapid mutational rate, and acquisition of antimicrobial resistance determinants through horizontal gene transfer. Finally, we discuss the prospect of (p)ppGpp metabolic enzymes as potential targets for developing antibiotic adjuvants and tackling persistence of infections.}, }
@article {pmid33160787, year = {2021}, author = {Wang, L and Yuan, L and Li, ZH and Zhang, X and Sheng, GP}, title = {Quantifying the occurrence and transformation potential of extracellular polymeric substances (EPS)-associated antibiotic resistance genes in activated sludge.}, journal = {Journal of hazardous materials}, volume = {408}, number = {}, pages = {124428}, doi = {10.1016/j.jhazmat.2020.124428}, pmid = {33160787}, issn = {1873-3336}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; *Extracellular Polymeric Substance Matrix/genetics ; Genes, Bacterial ; *Sewage ; Wastewater ; }, abstract = {Antibiotic resistance has been regarded as a global concern and biological wastewater treatment plants (WWTPs) are ideal hotbeds for the emergence and propagation of antibiotic resistance genes (ARGs). Extracellular polymeric substances (EPS), one of the primary components of activated sludge, might affect the distribution of extracellular ARGs in supernatant and EPS matrix, and thus alter their uptake potential by microbial cells. Herein, the presence and significance of EPS-associated ARGs in activated sludge from four WWTPs were assessed. Seven typical ARGs (sulI, sulII, blaTEM-1, tetA, tetO, tetQ, tetW) and class I integron (intI1) in EPS-associated, cell-free, and intracellular DNA were quantified. Results show that the absolute abundances of EPS-associated, cell-free, and intracellular ARGs were 5.90 × 10[6]-6.45 × 10[9], 5.53 × 10[4]-4.58 × 10[6], and 2.68 × 10[8]-1.79 × 10[11] copies/g-volatile suspended solids, respectively. The absolute abundances of EPS-associated ARGs were 0.2-4.6 orders of magnitude higher than those of the corresponding cell-free ARGs. Considering the higher DNA contents in EPS, the transformation abilities of EPS-associated ARGs were 3.3-236.3 folds higher than those of cell-free ARGs. Therefore, EPS-associated ARGs are an important source of extracellular ARGs, and it may play a crucial role in horizontal gene transfer via transformation in WWTPs.}, }
@article {pmid33159845, year = {2021}, author = {Gawryluk, RMR and Stairs, CW}, title = {Diversity of electron transport chains in anaerobic protists.}, journal = {Biochimica et biophysica acta. Bioenergetics}, volume = {1862}, number = {1}, pages = {148334}, doi = {10.1016/j.bbabio.2020.148334}, pmid = {33159845}, issn = {1879-2650}, mesh = {Anaerobiosis ; *Biological Evolution ; Electron Transport Chain Complex Proteins/*metabolism ; Eukaryota/*enzymology ; Mitochondrial Proteins/*metabolism ; }, abstract = {Eukaryotic microbes (protists) that occupy low-oxygen environments often have drastically different mitochondrial metabolism compared to their aerobic relatives. A common theme among many anaerobic protists is the serial loss of components of the electron transport chain (ETC). Here, we discuss the diversity of the ETC across the tree of eukaryotes and review hypotheses for how ETCs are modified, and ultimately lost, in protists. We find that while protists have converged to some of the same metabolism as anaerobic animals, there are clear protist-specific strategies to thrive without oxygen.}, }
@article {pmid33158891, year = {2021}, author = {Raymond, JA and Janech, MG and Mangiagalli, M}, title = {Ice-Binding Proteins Associated with an Antarctic Cyanobacterium, Nostoc sp. HG1.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {2}, pages = {}, pmid = {33158891}, issn = {1098-5336}, mesh = {Antarctic Regions ; Bacterial Proteins/chemistry/*genetics ; Carrier Proteins/chemistry/*genetics ; *Ice ; Metagenome ; Nostoc/*genetics ; }, abstract = {Ice-binding proteins (IBPs) have been identified in numerous polar algae and bacteria, but so far not in any cyanobacteria, despite the abundance of cyanobacteria in polar regions. We previously reported strong IBP activity associated with an Antarctic Nostoc species. In this study, to identify the proteins responsible, as well as elucidate their origin, we sequenced the DNA of an environmental sample of this species, designated Nostoc sp. HG1, and its bacterial community and attempted to identify IBPs by looking for known IBPs in the metagenome and by looking for novel IBPs by tandem mass spectrometry (MS/MS) proteomics analyses of ice affinity-purified proteins. The metagenome contained over 116 DUF3494-type IBP genes, the most common type of IBP identified so far. One of the IBPs could be confidently assigned to Nostoc, while the others could be attributed to diverse bacteria, which, surprisingly, accounted for the great majority of the metagenome. Recombinant Nostoc IBPs (nIBPs) had strong ice-structuring activities, and their circular dichroism spectra were consistent with the secondary structure of a DUF3494-type IBP. nIBP is unusual in that it is the only IBP identified so far to have a PEP (amino acid motif) C-terminal signal, a signal that has been associated with anchoring to the outer cell membrane. These results suggest that the observed IBP activity of Nostoc sp. HG1 was due to a combination of endogenous and exogenous IBPs. Amino acid and nucleotide sequence analyses of nIBP raise the possibility that it was acquired from a planctomycete.IMPORTANCE The horizontal transfer of genes encoding ice-binding proteins (IBPs), proteins that confer freeze-thaw tolerance, has allowed many microorganisms to expand their ranges into polar regions. One group of microorganisms for which nothing is known about its IBPs is cyanobacteria. In this study, we identified a cyanobacterial IBP and showed that it was likely acquired from another bacterium, probably a planctomycete. We also showed that a consortium of IBP-producing bacteria living with the Nostoc contribute to its IBP activity.}, }
@article {pmid33158887, year = {2021}, author = {Shi, Y and Queller, DC and Tian, Y and Zhang, S and Yan, Q and He, Z and He, Z and Wu, C and Wang, C and Shu, L}, title = {The Ecology and Evolution of Amoeba-Bacterium Interactions.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {2}, pages = {}, pmid = {33158887}, issn = {1098-5336}, mesh = {Amoeba/*physiology ; Bacteria ; *Bacterial Physiological Phenomena ; *Microbial Interactions ; }, abstract = {Amoebae are protists that have complicated relationships with bacteria, covering the whole spectrum of symbiosis. Amoeba-bacterium interactions contribute to the study of predation, symbiosis, pathogenesis, and human health. Given the complexity of their relationships, it is necessary to understand the ecology and evolution of their interactions. In this paper, we provide an updated review of the current understanding of amoeba-bacterium interactions. We start by discussing the diversity of amoebae and their bacterial partners. We also define three types of ecological interactions between amoebae and bacteria and discuss their different outcomes. Finally, we focus on the implications of amoeba-bacterium interactions on human health, horizontal gene transfer, drinking water safety, and the evolution of symbiosis. In conclusion, amoeba-bacterium interactions are excellent model systems to investigate a wide range of scientific questions. Future studies should utilize advanced techniques to address research gaps, such as detecting hidden diversity, lack of amoeba genomes, and the impacts of amoeba predation on the microbiome.}, }
@article {pmid33158886, year = {2021}, author = {Wurlitzer, JM and Stanišić, A and Wasmuth, I and Jungmann, S and Fischer, D and Kries, H and Gressler, M}, title = {Bacterial-Like Nonribosomal Peptide Synthetases Produce Cyclopeptides in the Zygomycetous Fungus Mortierella alpina.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {3}, pages = {}, pmid = {33158886}, issn = {1098-5336}, mesh = {Fungal Proteins/genetics/*metabolism ; Mortierella/*enzymology/genetics ; Peptide Synthases/genetics/*metabolism ; Peptides, Cyclic/*metabolism ; Phylogeny ; }, abstract = {Fungi are traditionally considered a reservoir of biologically active natural products. However, an active secondary metabolism has long not been attributed to early-diverging fungi such as Mortierella Here, we report on the biosynthesis of two series of cyclic pentapeptides, the malpicyclins and malpibaldins, as products of Mortierella alpina ATCC 32222. The molecular structures of malpicyclins were elucidated by high-resolution tandem mass spectrometry (HR-MS/MS), Marfey's method, and one-dimensional (1D) and 2D nuclear magnetic resonance (NMR) spectroscopy. In addition, malpibaldin biosynthesis was confirmed by HR-MS. Genome mining and comparative quantitative real-time PCR (qRT-PCR) expression analysis pointed at two pentamodular nonribosomal peptide synthetases (NRPSs), malpicyclin synthetase MpcA and malpibaldin synthetase MpbA, as candidate biosynthetic enzymes. Heterologous production of the respective adenylation domains and substrate specificity assays proved promiscuous substrate selection and confirmed their respective biosynthetic roles. In stark contrast to known fungal NRPSs, MpbA and MpcA contain bacterial-like dual epimerase/condensation domains allowing the racemization of enzyme-tethered l-amino acids and the subsequent incorporation of d-amino acids into the metabolites. Phylogenetic analyses of both NRPS genes indicated a bacterial origin and a horizontal gene transfer into the fungal genome. We report on the as-yet-unexplored nonribosomal peptide biosynthesis in basal fungi which highlights this paraphylum as a novel and underrated resource of natural products.IMPORTANCE Fungal natural compounds are industrially produced, with application in antibiotic treatment, cancer medications, and crop plant protection. Traditionally, higher fungi have been intensively investigated concerning their metabolic potential, but reidentification of already known compounds is frequently observed. Hence, alternative strategies to acquire novel bioactive molecules are required. We present the genus Mortierella as representative of the early-diverging fungi as an underestimated resource of natural products. Mortierella alpina produces two families of cyclopeptides, designated malpicyclins and malpibaldins, respectively, via two pentamodular nonribosomal peptide synthetases (NRPSs). These enzymes are much more closely related to bacterial than to other fungal NRPSs, suggesting a bacterial origin of these NRPS genes in Mortierella Both enzymes were biochemically characterized and are involved in as-yet-unknown biosynthetic pathways of natural products in basal fungi. Hence, this report establishes early-diverging fungi as prolific natural compound producers and sheds light on the origin of their biosynthetic capacity.}, }
@article {pmid33158244, year = {2020}, author = {Sánchez-Costa, M and Blesa, A and Berenguer, J}, title = {Nitrate Respiration in Thermus thermophilus NAR1: from Horizontal Gene Transfer to Internal Evolution.}, journal = {Genes}, volume = {11}, number = {11}, pages = {}, pmid = {33158244}, issn = {2073-4425}, mesh = {Bacterial Proteins/genetics ; DNA Transposable Elements/genetics ; Gene Transfer, Horizontal/genetics ; Nitrate Reductases/genetics/*metabolism ; Nitrates/*metabolism ; Nitrites/metabolism ; Nitrogen Oxides/metabolism ; Operon/genetics ; Plasmids/genetics ; Thermus thermophilus/genetics/*metabolism ; }, abstract = {Genes coding for enzymes of the denitrification pathway appear randomly distributed among isolates of the ancestral genus Thermus, but only in few strains of the species Thermus thermophilus has the pathway been studied to a certain detail. Here, we review the enzymes involved in this pathway present in T. thermophilus NAR1, a strain extensively employed as a model for nitrate respiration, in the light of its full sequence recently assembled through a combination of PacBio and Illumina technologies in order to counteract the systematic errors introduced by the former technique. The genome of this strain is divided in four replicons, a chromosome of 2,021,843 bp, two megaplasmids of 370,865 and 77,135 bp and a small plasmid of 9799 pb. Nitrate respiration is encoded in the largest megaplasmid, pTTHNP4, within a region that includes operons for O2 and nitrate sensory systems, a nitrate reductase, nitrate and nitrite transporters and a nitrate specific NADH dehydrogenase, in addition to multiple insertion sequences (IS), suggesting its mobility-prone nature. Despite nitrite is the final product of nitrate respiration in this strain, the megaplasmid encodes two putative nitrite reductases of the cd1 and Cu-containing types, apparently inactivated by IS. No nitric oxide reductase genes have been found within this region, although the NorR sensory gene, needed for its expression, is found near the inactive nitrite respiration system. These data clearly support that partial denitrification in this strain is the consequence of recent deletions and IS insertions in genes involved in nitrite respiration. Based on these data, the capability of this strain to transfer or acquire denitrification clusters by horizontal gene transfer is discussed.}, }
@article {pmid33157023, year = {2021}, author = {Köstlbacher, S and Collingro, A and Halter, T and Domman, D and Horn, M}, title = {Coevolving Plasmids Drive Gene Flow and Genome Plasticity in Host-Associated Intracellular Bacteria.}, journal = {Current biology : CB}, volume = {31}, number = {2}, pages = {346-357.e3}, pmid = {33157023}, issn = {1879-0445}, support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Adaptation, Physiological/*genetics ; Chlamydia/*genetics/pathogenicity ; Chromosomes, Bacterial/genetics ; DNA, Bacterial/genetics ; *Evolution, Molecular ; *Gene Flow ; Gene Transfer, Horizontal ; Genome, Bacterial/genetics ; Host Microbial Interactions/genetics ; Plasmids/*genetics ; }, abstract = {Plasmids are important in microbial evolution and adaptation to new environments. Yet, carrying a plasmid can be costly, and long-term association of plasmids with their hosts is poorly understood. Here, we provide evidence that the Chlamydiae, a phylum of strictly host-associated intracellular bacteria, have coevolved with their plasmids since their last common ancestor. Current chlamydial plasmids are amalgamations of at least one ancestral plasmid and a bacteriophage. We show that the majority of plasmid genes are also found on chromosomes of extant chlamydiae. The most conserved plasmid gene families are predominantly vertically inherited, while accessory plasmid gene families show significantly increased mobility. We reconstructed the evolutionary history of plasmid gene content of an entire bacterial phylum over a period of around one billion years. Frequent horizontal gene transfer and chromosomal integration events illustrate the pronounced impact of coevolution with these extrachromosomal elements on bacterial genome dynamics in host-dependent microbes.}, }
@article {pmid33156617, year = {2020}, author = {Torbøl Pedersen, J and De Loma, J and Levi, M and Palmgren, M and Broberg, K}, title = {Predicted AS3MT Proteins Methylate Arsenic and Support Two Major Phylogenetic AS3MT Groups.}, journal = {Chemical research in toxicology}, volume = {33}, number = {12}, pages = {3041-3047}, pmid = {33156617}, issn = {1520-5010}, mesh = {Animals ; Arsenic/*metabolism ; Faecalibacterium prausnitzii/enzymology ; Gastrointestinal Microbiome ; Humans ; Hydra/enzymology ; Methylation ; Methyltransferases/genetics/*metabolism ; Phylogeny ; Rhodopseudomonas/enzymology ; }, abstract = {Inorganic arsenic is one of the most toxic and carcinogenic substances in the environment, but many organisms, including humans, methylate inorganic arsenic to mono-, di-, and trimethylated arsenic metabolites, which the organism can excrete. In humans and other eukaryotic organisms, the arsenite methyltransferase (AS3MT) protein methylates arsenite. AS3MT sequences from eukaryotic organisms group phylogenetically with predicted eubacterial AS3MT sequences, which has led to the suggestion that AS3MT was acquired from eubacteria by multiple events of horizontal gene transfer. In this study, we evaluated whether 55 (out of which 47 were predicted based on protein sequence similarity) sequences encoding putative AS3MT orthologues in 47 species from different kingdoms can indeed methylate arsenic. Fifty-three of the proteins showed arsenic methylating capacity. For example, the predicted AS3MT of the human gut bacterium Faecalibacterium prausnitzii methylated arsenic efficiently. We performed a kinetic analysis of 14 AS3MT proteins representing two phylogenetically distinct clades (Group 1 and 2) that each contain both eubacterial and eukaryotic sequences. We found that animal and bacterial AS3MTs in Group 1 rarely produce trimethylated arsenic, whereas Hydra vulgaris and the bacterium Rhodopseudomonas palustris in Group 2 produce trimethylated arsenic metabolites. These findings suggest that animals during evolution have acquired different arsenic methylating phenotypes from different bacteria. Further, it shows that humans carry two bacterial systems for arsenic methylation: one bacterium-derived AS3MT from Group 1 incorporated in the human genome and one from Group 2 in F. prausnitzii present in the gut microbiome.}, }
@article {pmid33155112, year = {2021}, author = {Galitskaya, P and Biktasheva, L and Kuryntseva, P and Selivanovskaya, S}, title = {Response of soil bacterial communities to high petroleum content in the absence of remediation procedures.}, journal = {Environmental science and pollution research international}, volume = {28}, number = {8}, pages = {9610-9627}, pmid = {33155112}, issn = {1614-7499}, support = {17-74-20183//Russian Science Foundation/ ; }, mesh = {Biodegradation, Environmental ; Hydrocarbons ; *Petroleum ; *Petroleum Pollution ; RNA, Ribosomal, 16S/genetics ; Soil ; Soil Microbiology ; *Soil Pollutants/analysis ; }, abstract = {Oil spills are events that frequently lead to petroleum pollution. This pollution may cause stress to microbial communities, which require long adaption periods. Soil petroleum pollution is currently considered one of the most serious environmental problems. In the present work, processes occurring in the bacterial communities of three soil samples with different physicochemical characteristics, artificially polluted with 12% of crude oil, were investigated in 120-day laboratory experiment. It was found that the total petroleum hydrocarbon content did not decrease during this time; however, the proportion of petroleum fractions was altered. Petroleum pollution led to a short-term decrease in the bacterial 16S rRNA gene copy number. On the basis of amplicon sequencing analysis, it was concluded that bacterial community successions were similar in the three soils investigated. Thus, the phyla Actinobacteria and Proteobacteria and candidate TM7 phylum (Saccaribacteria) were predominant with relative abundances ranging from 35 to 58%, 25 to 30%, and 15 to 35% in different samples, respectively. The predominant operational taxonomic units (OTUs) after pollution belonged to the genera Rhodococcus and Mycobacterium, families Nocardioidaceae and Sinobacteraceae, and candidate class ТМ7-3. Genes from the alkIII group encoding monoxygenases were the most abundant compared with other catabolic genes from the alkI, alkII, GN-PAH, and GP-PAH groups, and their copy number significantly increased after pollution. The copy numbers of expressed genes involved in the horizontal transfer of catabolic genes, FlgC, TraG, and OmpF, also increased after pollution by 11-33, 16-63, and 11-71 times, respectively. The bacterial community structure after a high level of petroleum pollution changed because of proliferation of the cells that initially were able to decompose hydrocarbons, and in the second place, because proliferation of the cells that received these catabolic genes through horizontal transfer.}, }
@article {pmid33154257, year = {2020}, author = {Modgil, V and Kaur, H and Mohan, B and Taneja, N}, title = {Molecular, phylogenetic and antibiotic resistance analysis of enteroaggregative escherichia coli/uropathogenic Escherichia coli hybrid genotypes causing urinary tract infections.}, journal = {Indian journal of medical microbiology}, volume = {38}, number = {3 &amp; 4}, pages = {421-429}, doi = {10.4103/ijmm.IJMM_20_365}, pmid = {33154257}, issn = {1998-3646}, mesh = {Drug Resistance, Microbial ; Enteropathogenic Escherichia coli/*classification/drug effects/genetics ; Genotype ; Humans ; Phylogeny ; Urinary Tract Infections/*microbiology ; Uropathogenic Escherichia coli/*classification/drug effects/genetics ; }, abstract = {BACKGROUND: Horizontal gene transfer of virulence genes (VGs) from different Escherichia coli pathotypes results in the evolution of hybrid strains. Hybrid genotypes of enteroaggregative E. coli and uropathogenic E. coli (EAEC/UPEC) have been reported in sporadic infections and outbreaks of extraintestinal origin. Yet, their association with routine infections is still underrated.<br><br>MATERIALS AND METHODS: In this study, we analysed 163 isolates of E. coli from cases of urinary tract infection seeking hybrid (EAEC/UPEC) strains. Using multiplex polymerase chain reaction, we investigated VGs (adhesive and toxin genes) of UPEC along with EAEC marker genes (aap and agg R), ast A (toxin genes) and serine protease autotransporters of Enterobacteriaceae, pet (plasmid-encoded toxin) and pic (mucinase gene). Those UPEC strains which had characteristic defining genes of EAEC (agg R/aap or their combination) were considered UPEC/EAEC hybrids.<br><br>RESULTS: Molecular predictors of EAEC (aap and aggR) were detected in 20.2% (33/163) of the strains. The pap C was also detected in 36% of the EAEC/UPEC hybrid strains. Phylogenetic analysis revealed that hybrid strains belonged to Group D (60.6%). Nearly 73.8% of UPEC and 75.7% of UPEC/EAEC hybrid strains were multidrug-resistant. Among UPEC isolates, 72.3% and in hybrid UPEC/EAEC, 78.7% isolates were able to produce biofilm.<br><br>CONCLUSIONS: Our results indicated a closer relationship among EAEC and UPEC, which suggested that some EAEC strains can be potential uropathogens. Ours is a first study documenting the existence of EAEC pathotypes VGs in UPEC strains of nosocomial origin; further studies are required to understand the diarrhoeagenic potential of these hybrids.}, }
@article {pmid33151628, year = {2021}, author = {Soberón-Chávez, G and González-Valdez, A and Soto-Aceves, MP and Cocotl-Yañez, M}, title = {Rhamnolipids produced by Pseudomonas: from molecular genetics to the market.}, journal = {Microbial biotechnology}, volume = {14}, number = {1}, pages = {136-146}, pmid = {33151628}, issn = {1751-7915}, mesh = {Glycolipids ; Molecular Biology ; *Pseudomonas ; Pseudomonas aeruginosa/genetics ; *Pseudomonas putida ; Surface-Active Agents ; }, abstract = {Rhamnolipids are biosurfactants with a wide range of industrial applications that entered into the market a decade ago. They are naturally produced by Pseudomonas aeruginosa and some Burkholderia species. Occasionally, some strains of different bacterial species, like Pseudomonas chlororaphis NRRL B-30761, which have acquired RL-producing ability by horizontal gene transfer, have been described. P. aeruginosa, the ubiquitous opportunistic pathogenic bacterium, is the best rhamnolipids producer, but Pseudomonas putida has been used as heterologous host for the production of this biosurfactant with relatively good yields. The molecular genetics of rhamnolipids production by P. aeruginosa has been widely studied not only due to the interest in developing overproducing strains, but because it is coordinately regulated with the expression of different virulence-related traits by the quorum-sensing response. Here, we highlight how the research of the molecular mechanisms involved in rhamnolipid production have impacted the development of strains that are suitable for industrial production of this biosurfactant, as well as some perspectives to improve these industrial useful strains.}, }
@article {pmid33149210, year = {2021}, author = {Benz, F and Huisman, JS and Bakkeren, E and Herter, JA and Stadler, T and Ackermann, M and Diard, M and Egli, A and Hall, AR and Hardt, WD and Bonhoeffer, S}, title = {Plasmid- and strain-specific factors drive variation in ESBL-plasmid spread in vitro and in vivo.}, journal = {The ISME journal}, volume = {15}, number = {3}, pages = {862-878}, pmid = {33149210}, issn = {1751-7370}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; *Escherichia coli/genetics ; Gene Transfer, Horizontal ; Mice ; Plasmids/genetics ; *Salmonella enterica/genetics ; beta-Lactamases/genetics ; }, abstract = {Horizontal gene transfer, mediated by conjugative plasmids, is a major driver of the global rise of antibiotic resistance. However, the relative contributions of factors that underlie the spread of plasmids and their roles in conjugation in vivo are unclear. To address this, we investigated the spread of clinical Extended Spectrum Beta-Lactamase (ESBL)-producing plasmids in the absence of antibiotics in vitro and in the mouse intestine. We hypothesised that plasmid properties would be the primary determinants of plasmid spread and that bacterial strain identity would also contribute. We found clinical Escherichia coli strains natively associated with ESBL-plasmids conjugated to three distinct E. coli strains and one Salmonella enterica serovar Typhimurium strain. Final transconjugant frequencies varied across plasmid, donor, and recipient combinations, with qualitative consistency when comparing transfer in vitro and in vivo in mice. In both environments, transconjugant frequencies for these natural strains and plasmids covaried with the presence/absence of transfer genes on ESBL-plasmids and were affected by plasmid incompatibility. By moving ESBL-plasmids out of their native hosts, we showed that donor and recipient strains also modulated transconjugant frequencies. This suggests that plasmid spread in the complex gut environment of animals and humans can be predicted based on in vitro testing and genetic data.}, }
@article {pmid33148824, year = {2020}, author = {Zhu, W and Wang, X and Qin, J and Liang, W and Shen, Z}, title = {Dissemination and Stability of the blaNDM-5-Carrying IncX3-Type Plasmid among Multiclonal Klebsiella pneumoniae Isolates.}, journal = {mSphere}, volume = {5}, number = {6}, pages = {}, pmid = {33148824}, issn = {2379-5042}, mesh = {Anti-Bacterial Agents/*pharmacology ; Carbapenems/*pharmacology ; Child ; Conjugation, Genetic ; Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Humans ; Klebsiella Infections/microbiology ; Klebsiella pneumoniae/classification/*drug effects/*genetics ; Microbial Sensitivity Tests ; Plasmids/*genetics ; beta-Lactamases/classification/*genetics ; }, abstract = {NDM-5 carbapenemase was mainly identified in Escherichia coli, while the rapid transmission of blaNDM-5 among Enterobacteriaceae has raised serious public attention. This study identified 14 NDM-5-producing Klebsiella pneumoniae isolates from 107 carbapenem-resistant K. pneumoniae isolates, recovered from blood, urine, and normally sterile body fluids of pediatric patients from January 2016 to December 2018. All NDM-5-producing isolates were highly resistant to β-lactams, while tigecycline and polymyxin B exhibited excellent antimicrobial activity. These 14 strains belonged to 9 different sequence types (STs) and displayed various pulsed-field gel electrophoresis (PFGE) patterns, suggesting that they were not clonally related. S1-PFGE followed by Southern blotting showed that the blaNDM-5 gene was located on an ∼46-kb IncX3 plasmid in all strains. All blaNDM-5-carrying plasmids were successfully transferred into recipient E. coli J53. PCR-based sequencing demonstrated that all of the blaNDM-5-carrying plasmids shared highly similar backbones, with nucleotide sequence identity of >99%. Moreover, this plasmid displayed high sequence similarity to the previously reported epidemic IncX3 blaNDM-5-carrying plasmids, with dynamic changes observed only in blaNDM-5-surrounding elements. Interestingly, the IncX3 blaNDM-5-carrying plasmids showed strong stability in clinical isolates when cultured in antibiotic-free medium. However, after the conjugation inhibitor linoleic acid was added, a gradual increase in the level of IncX3 plasmid loss could be observed. Clinical isolates displayed 10% to 15% blaNDM-5-carrying plasmid loss after coculture with linoleic acid for 5 days. These results showed that the IncX3 plasmid facilitated the dissemination of blaNDM-5 among multiclonal K. pneumoniae strains in children and that conjugal transfer contributed significantly to IncX3 plasmid stability within K. pneumoniaeIMPORTANCE The emergence and spread of New Delhi metallo-β-lactamase (NDM)-producing Enterobacteriaceae have been a serious challenge to public health, and NDM-5 shows increased resistance to carbapenems compared with other variants. NDM-5 has been identified mostly in E. coli but has rarely been described in K. pneumoniae and other Enterobacteriaceae isolates. Here, we present the dissemination of highly similar 46-kb IncX3 blaNDM-5-carrying plasmids among multiclonal K. pneumoniae strains in children, highlighting the horizontal gene transfer of blaNDM-5 among K. pneumoniae strains via the IncX3 plasmid. Moreover, the IncX3 blaNDM-5-carrying plasmids displayed strong stability in clinical strains when cultured in antibiotic-free medium, and the plasmid maintenance was attributed partly to conjugal transfer. Plasmid conjugation is mediated by the type IV secretion system (T4SS), and T4SS is conserved among all epidemic IncX3 blaNDM-5-carrying plasmids. Therefore, combining conjugation inhibition and promotion of plasmid loss would be an effective strategy to limit the conjugation-assisted persistence of IncX3 blaNDM-5-carrying plasmids.}, }
@article {pmid33144944, year = {2020}, author = {Phan, NT and Orjuela, J and Danchin, EGJ and Klopp, C and Perfus-Barbeoch, L and Kozlowski, DK and Koutsovoulos, GD and Lopez-Roques, C and Bouchez, O and Zahm, M and Besnard, G and Bellafiore, S}, title = {Genome structure and content of the rice root-knot nematode (Meloidogyne graminicola).}, journal = {Ecology and evolution}, volume = {10}, number = {20}, pages = {11006-11021}, pmid = {33144944}, issn = {2045-7758}, abstract = {Discovered in the 1960s, Meloidogyne graminicola is a root-knot nematode species considered as a major threat to rice production. Yet, its origin, genomic structure, and intraspecific diversity are poorly understood. So far, such studies have been limited by the unavailability of a sufficiently complete and well-assembled genome. In this study, using a combination of Oxford Nanopore Technologies and Illumina sequencing data, we generated a highly contiguous reference genome (283 scaffolds with an N50 length of 294 kb, totaling 41.5 Mb). The completeness scores of our assembly are among the highest currently published for Meloidogyne genomes. We predicted 10,284 protein-coding genes spanning 75.5% of the genome. Among them, 67 are identified as possibly originating from horizontal gene transfers (mostly from bacteria), which supposedly contribute to nematode infection, nutrient processing, and plant defense manipulation. Besides, we detected 575 canonical transposable elements (TEs) belonging to seven orders and spanning 2.61% of the genome. These TEs might promote genomic plasticity putatively related to the evolution of M. graminicola parasitism. This high-quality genome assembly constitutes a major improvement regarding previously available versions and represents a valuable molecular resource for future phylogenomic studies of Meloidogyne species. In particular, this will foster comparative genomic studies to trace back the evolutionary history of M. graminicola and its closest relatives.}, }
@article {pmid33139761, year = {2020}, author = {Chen, YM and Holmes, EC and Chen, X and Tian, JH and Lin, XD and Qin, XC and Gao, WH and Liu, J and Wu, ZD and Zhang, YZ}, title = {Diverse and abundant resistome in terrestrial and aquatic vertebrates revealed by transcriptional analysis.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {18870}, pmid = {33139761}, issn = {2045-2322}, mesh = {Animals ; Aquatic Organisms/*genetics ; Drug Resistance, Microbial/*genetics ; Fishes/*genetics ; Gene Expression Profiling ; Gene Transfer, Horizontal/genetics ; Humans ; Metagenome/genetics ; Metagenomics ; Transcriptome/*genetics ; }, abstract = {Despite increasing evidence that antibiotic resistant pathogens are shared among humans and animals, the diversity, abundance and patterns of spread of antibiotic resistance genes (ARGs) in wildlife remains unclear. We identified 194 ARGs associated with phenotypic resistance to 13 types of antibiotic in meta-transcriptomic data generated from a broad range of lower vertebrates residing in both terrestrial and aquatic habitats. These ARGs, confirmed by PCR, included those that shared high sequence similarity to clinical isolates of public health concern. Notably, the lower vertebrate resistome varied by ecological niche of the host sampled. The resistomes in marine fish shared high similarity and were characterized by very high abundance, distinct from that observed in other habitats. An assessment of ARG mobility found that ARGs in marine fish were frequently co-localized with mobile elements, indicating that they were likely spread by horizontal gene transfer. Together, these data reveal the remarkable diversity and transcriptional levels of ARGs in lower vertebrates, and suggest that these wildlife species might play an important role in the global spread of ARGs.}, }
@article {pmid33137105, year = {2020}, author = {Nagies, FSP and Brueckner, J and Tria, FDK and Martin, WF}, title = {A spectrum of verticality across genes.}, journal = {PLoS genetics}, volume = {16}, number = {11}, pages = {e1009200}, pmid = {33137105}, issn = {1553-7404}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Archaeal/genetics ; Genome, Bacterial/genetics ; Phylogeny ; }, abstract = {Lateral gene transfer (LGT) has impacted prokaryotic genome evolution, yet the extent to which LGT compromises vertical evolution across individual genes and individual phyla is unknown, as are the factors that govern LGT frequency across genes. Estimating LGT frequency from tree comparisons is problematic when thousands of genomes are compared, because LGT becomes difficult to distinguish from phylogenetic artefacts. Here we report quantitative estimates for verticality across all genes and genomes, leveraging a well-known property of phylogenetic inference: phylogeny works best at the tips of trees. From terminal (tip) phylum level relationships, we calculate the verticality for 19,050,992 genes from 101,422 clusters in 5,655 prokaryotic genomes and rank them by their verticality. Among functional classes, translation, followed by nucleotide and cofactor biosynthesis, and DNA replication and repair are the most vertical. The most vertically evolving lineages are those rich in ecological specialists such as Acidithiobacilli, Chlamydiae, Chlorobi and Methanococcales. Lineages most affected by LGT are the α-, β-, γ-, and δ- classes of Proteobacteria and the Firmicutes. The 2,587 eukaryotic clusters in our sample having prokaryotic homologues fail to reject eukaryotic monophyly using the likelihood ratio test. The low verticality of α-proteobacterial and cyanobacterial genomes requires only three partners-an archaeal host, a mitochondrial symbiont, and a plastid ancestor-each with mosaic chromosomes, to directly account for the prokaryotic origin of eukaryotic genes. In terms of phylogeny, the 100 most vertically evolving prokaryotic genes are neither representative nor predictive for the remaining 97% of an average genome. In search of factors that govern LGT frequency, we find a simple but natural principle: Verticality correlates strongly with gene distribution density, LGT being least likely for intruding genes that must replace a preexisting homologue in recipient chromosomes. LGT is most likely for novel genetic material, intruding genes that encounter no competing copy.}, }
@article {pmid33133037, year = {2020}, author = {McMillan, EA and Jackson, CR and Frye, JG}, title = {Transferable Plasmids of Salmonella enterica Associated With Antibiotic Resistance Genes.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {562181}, pmid = {33133037}, issn = {1664-302X}, abstract = {Salmonella enterica is a common foodborne illness in the United States and globally. An increasing number of Salmonella infections are resistant to antibiotics, and many of the genes responsible for those resistances are carried by plasmids. Plasmids are important mediators of horizontal gene exchange, which could potentially increase the spread of antibiotic resistance (AR) genes. Twenty-eight different incompatibility groups of plasmids have been described in Enterobacteriaceae. Incompatibility groups differ in their accessory gene content, replication mechanisms, and their associations with Salmonella serotypes and animal sources. Plasmids also differ in their ability to conjugate or be mobilized, essential genes, and conditions required for transfer. It is important to understand the differences in gene content and transfer mechanisms to accurately determine the impact of plasmids on the dissemination and persistence of antibiotic resistance genes. This review will cover the most common plasmid incompatibility groups present in S. enterica with a focus on the transfer mechanisms and associated antibiotic resistance genes.}, }
@article {pmid33132139, year = {2020}, author = {Miyazaki, T and Oba, N and Park, EY}, title = {Structural insight into the substrate specificity of Bombyx mori β-fructofuranosidase belonging to the glycoside hydrolase family 32.}, journal = {Insect biochemistry and molecular biology}, volume = {127}, number = {}, pages = {103494}, doi = {10.1016/j.ibmb.2020.103494}, pmid = {33132139}, issn = {1879-0240}, mesh = {Amino Acid Sequence ; Animals ; Bombyx/*genetics/growth &amp; development/metabolism ; Glycoside Hydrolases/classification ; Insect Proteins/chemistry/classification/*genetics/metabolism ; Larva/genetics/growth &amp; development/metabolism ; Multigene Family ; Phylogeny ; Sequence Alignment ; Substrate Specificity ; beta-Fructofuranosidase/chemistry/classification/*genetics/metabolism ; }, abstract = {Sucrose-hydrolyzing enzymes are largely divided into β-fructofuranosidase and sucrose α-glucosidase. The domestic silkworm Bombyx mori possesses both enzymes, BmSUC1 and BmSUH, belonging to the glycoside hydrolase family 32 (GH32) and GH13, respectively. BmSUC1 was presumed to be acquired by horizontal gene transfer from bacteria based on phylogenetic analysis and related to tolerance to sugar-mimic alkaloids contained in mulberry latex. Here we investigated the substrate specificity of recombinant BmSUC1 that can hydrolyze not only sucrose but also fructooligosaccharides and fructans, and revealed that the enzyme was competitively inhibited by 1,4-dideoxy-1,4-imino-D-arabinitol, one of the alkaloids. Moreover, the crystal structures of BmSUC1 in apo form and complex with sucrose were determined, and the active site pocket was shallow and suitable for shorter substrates but was related to more relaxed substrate specificity than the strict sucrose α-glucosidase BmSUH. Considering together with the distribution of BmSUC1-orthologous genes in many lepidopterans, our results suggest that BmSUC1 contributes to the digestion of fructooligosaccharides and fructans derived from feed plants.}, }
@article {pmid33130070, year = {2020}, author = {Vos, M}, title = {The evolution of bacterial pathogens in the Anthropocene.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {86}, number = {}, pages = {104611}, doi = {10.1016/j.meegid.2020.104611}, pmid = {33130070}, issn = {1567-7257}, mesh = {*Bacteria ; *Biological Evolution ; *Climate Change ; Disease Susceptibility ; *Environment ; *Environmental Microbiology ; Gene Transfer, Horizontal ; Gene-Environment Interaction ; Host-Pathogen Interactions ; Humans ; Mutation ; }, abstract = {Humankind has become a primary driver of global environmental and climate change. The extent of planetary change is such that it has been proposed to classify the current geological age as the 'Anthropocene'. Anthropogenic environmental degradation presents numerous threats to human health and wellbeing, including an increased risk of infectious disease. This review focuses on how processes such as pollution, climate change and human-mediated dispersal could affect the evolution of bacterial pathogens. Effects of environmental change on the 'big five' of evolution: mutation rate, recombination (horizontal gene transfer), migration, selection and drift are discussed. Microplastic pollution is used as a case study to highlight the combined effects of some of these processes on the evolutionary diversification of human pathogens. Although the evidence is still incomplete, a picture is emerging that environmental pathogens could evolve at increased rates in the Anthropocene, with potential consequences for human infection.}, }
@article {pmid33127989, year = {2020}, author = {Li, Y and Mohanty, S and Nilsson, D and Hansson, B and Mao, K and Irbäck, A}, title = {When a foreign gene meets its native counterpart: computational biophysics analysis of two PgiC loci in the grass Festuca ovina.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {18752}, pmid = {33127989}, issn = {2045-2322}, mesh = {Evolution, Molecular ; Festuca/genetics/*metabolism ; Gene Transfer, Horizontal ; Plant Proteins/genetics/metabolism ; }, abstract = {Duplicative horizontal gene transfer may bring two previously separated homologous genes together, which may raise questions about the interplay between the gene products. One such gene pair is the "native" PgiC1 and "foreign" PgiC2 in the perennial grass Festuca ovina. Both PgiC1 and PgiC2 encode cytosolic phosphoglucose isomerase, a dimeric enzyme whose proper binding is functionally essential. Here, we use biophysical simulations to explore the inter-monomer binding of the two homodimers and the heterodimer that can be produced by PgiC1 and PgiC2 in F. ovina. Using simulated native-state ensembles, we examine the structural properties and binding tightness of the dimers. In addition, we investigate their ability to withstand dissociation when pulled by a force. Our results suggest that the inter-monomer binding is tighter in the PgiC2 than the PgiC1 homodimer, which could explain the more frequent occurrence of the foreign PgiC2 homodimer in dry habitats. We further find that the PgiC1 and PgiC2 monomers are compatible with heterodimer formation; the computed binding tightness is comparable to that of the PgiC1 homodimer. Enhanced homodimer stability and capability of heterodimer formation with PgiC1 are properties of PgiC2 that may contribute to the retaining of the otherwise redundant PgiC2 gene.}, }
@article {pmid33127909, year = {2020}, author = {Martijn, J and Schön, ME and Lind, AE and Vosseberg, J and Williams, TA and Spang, A and Ettema, TJG}, title = {Hikarchaeia demonstrate an intermediate stage in the methanogen-to-halophile transition.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {5490}, pmid = {33127909}, issn = {2041-1723}, mesh = {Archaea/*classification/*genetics/metabolism ; Archaeal Proteins/metabolism ; Euryarchaeota/classification/*genetics/metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Archaeal ; Metagenomics ; Methane/metabolism ; Multigene Family ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Halobacteria (henceforth: Haloarchaea) are predominantly aerobic halophiles that are thought to have evolved from anaerobic methanogens. This remarkable transformation most likely involved an extensive influx of bacterial genes. Whether it entailed a single massive transfer event or a gradual stream of transfers remains a matter of debate. To address this, genomes that descend from methanogen-to-halophile intermediates are necessary. Here, we present five such near-complete genomes of Marine Group IV archaea (Hikarchaeia), the closest known relatives of Haloarchaea. Their inclusion in gene tree-aware ancestral reconstructions reveals an intermediate stage that had already lost a large number of genes, including nearly all of those involved in methanogenesis and the Wood-Ljungdahl pathway. In contrast, the last Haloarchaea common ancestor gained a large number of genes and expanded its aerobic respiration and salt/UV resistance gene repertoire. Our results suggest that complex and gradual patterns of gain and loss shaped the methanogen-to-halophile transition.}, }
@article {pmid33127895, year = {2020}, author = {Sheridan, PO and Raguideau, S and Quince, C and Holden, J and Zhang, L and ,  and Williams, TA and Gubry-Rangin, C}, title = {Gene duplication drives genome expansion in a major lineage of Thaumarchaeota.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {5494}, pmid = {33127895}, issn = {2041-1723}, support = {MR/M50161X/1/MRC_/Medical Research Council/United Kingdom ; MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; BB/R015171/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Archaea/*classification/*genetics/metabolism ; Ecosystem ; Evolution, Molecular ; *Gene Duplication ; Gene Transfer, Horizontal ; *Genome, Archaeal ; Metagenomics ; *Phylogeny ; Proteome ; }, abstract = {Ammonia-oxidising archaea of the phylum Thaumarchaeota are important organisms in the nitrogen cycle, but the mechanisms driving their radiation into diverse ecosystems remain underexplored. Here, existing thaumarchaeotal genomes are complemented with 12 genomes belonging to the previously under-sampled Nitrososphaerales to investigate the impact of lateral gene transfer (LGT), gene duplication and loss across thaumarchaeotal evolution. We reveal a major role for gene duplication in driving genome expansion subsequent to early LGT. In particular, two large LGT events are identified into Nitrososphaerales and the fate of these gene families is highly lineage-specific, being lost in some descendant lineages, but undergoing extensive duplication in others, suggesting niche-specific roles. Notably, some genes involved in carbohydrate transport or coenzyme metabolism were duplicated, likely facilitating niche specialisation in soils and sediments. Overall, our results suggest that LGT followed by gene duplication drives Nitrososphaerales evolution, highlighting a previously under-appreciated mechanism of genome expansion in archaea.}, }
@article {pmid33125394, year = {2020}, author = {Monte, DFM and Sellera, FP and Lopes, R and Keelara, S and Landgraf, M and Greene, S and Fedorka-Cray, PJ and Thakur, S}, title = {Class 1 integron-borne cassettes harboring blaCARB-2 gene in multidrug-resistant and virulent Salmonella Typhimurium ST19 strains recovered from clinical human stool samples, United States.}, journal = {PloS one}, volume = {15}, number = {10}, pages = {e0240978}, pmid = {33125394}, issn = {1932-6203}, support = {U18 FD006194/FD/FDA HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Multiple, Bacterial ; Genome, Bacterial ; Humans ; Integrons ; Microbial Sensitivity Tests ; Phylogeny ; Plasmids/genetics ; Salmonella Infections/*microbiology ; Salmonella typhimurium/*classification/genetics/isolation &amp; purification/pathogenicity ; United States ; Virulence Factors/*genetics ; Whole Genome Sequencing ; beta-Lactamases/*genetics ; }, abstract = {International lineages, such as Salmonella Typhimurium sequence type (ST) 19, are most often associated with foodborne diseases and deaths in humans. In this study, we compared the whole-genome sequences of five S. Typhimurium strains belonging to ST19 recovered from clinical human stool samples in North Carolina, United States. Overall, S. Typhimurium strains displayed multidrug-resistant profile, being resistance to critically and highly important antimicrobials including ampicillin, ticarcillin/clavulanic acid, streptomycin and sulfisoxazole, chloramphenicol, tetracycline, respectively. Interestingly, all S. Typhimurium strains carried class 1 integron (intl1) and we were able to describe two genomic regions surrounding blaCARB-2 gene, size 4,062 bp and 4,422 bp for S. Typhimurium strains (HS5344, HS5437, and HS5478) and (HS5302 and HS5368), respectively. Genomic analysis for antimicrobial resistome confirmed the presence of clinically important genes, including blaCARB-2, aac(6')-Iaa, aadA2b, sul1, tetG, floR, and biocide resistance genes (qacEΔ1). S. Typhimurium strains harbored IncFIB plasmid containing spvRABCD operon, as well as rck and pef virulence genes, which constitute an important apparatus for spreading the virulence plasmid. In addition, we identified several virulence genes, chromosomally located, while the phylogenetic analysis revealed clonal relatedness among these strains with S. enterica isolated from human and non-human sources obtained in European and Asian countries. Our results provide new insights into this unusual class 1 integron in virulent S. Typhimurium strains that harbors a pool of genes acting as potential hotspots for horizontal gene transfer providing readily adaptation to new surrounds, as well as being crucially required for virulence in vivo. Therefore, continuous genomic surveillance is an important tool for safeguarding human health.}, }
@article {pmid33125315, year = {2020}, author = {Berglund, F and Böhm, ME and Martinsson, A and Ebmeyer, S and Österlund, T and Johnning, A and Larsson, DGJ and Kristiansson, E}, title = {Comprehensive screening of genomic and metagenomic data reveals a large diversity of tetracycline resistance genes.}, journal = {Microbial genomics}, volume = {6}, number = {11}, pages = {}, pmid = {33125315}, issn = {2057-5858}, mesh = {Anti-Bacterial Agents/*pharmacology ; Escherichia coli/*drug effects/*genetics/isolation &amp; purification ; Gene Transfer, Horizontal/genetics ; Humans ; Interspersed Repetitive Sequences/genetics ; Membrane Transport Proteins/genetics ; Metagenome/genetics ; Phylogeny ; Ribosomal Proteins/genetics ; Tetracycline/*pharmacology ; Tetracycline Resistance/*genetics ; }, abstract = {Tetracyclines are broad-spectrum antibiotics used to prevent or treat a variety of bacterial infections. Resistance is often mediated through mobile resistance genes, which encode one of the three main mechanisms: active efflux, ribosomal target protection or enzymatic degradation. In the last few decades, a large number of new tetracycline-resistance genes have been discovered in clinical settings. These genes are hypothesized to originate from environmental and commensal bacteria, but the diversity of tetracycline-resistance determinants that have not yet been mobilized into pathogens is unknown. In this study, we aimed to characterize the potential tetracycline resistome by screening genomic and metagenomic data for novel resistance genes. By using probabilistic models, we predicted 1254 unique putative tetracycline resistance genes, representing 195 gene families (<70 % amino acid sequence identity), whereof 164 families had not been described previously. Out of 17 predicted genes selected for experimental verification, 7 induced a resistance phenotype in an Escherichia coli host. Several of the predicted genes were located on mobile genetic elements or in regions that indicated mobility, suggesting that they easily can be shared between bacteria. Furthermore, phylogenetic analysis indicated several events of horizontal gene transfer between bacterial phyla. Our results also suggested that acquired efflux pumps originate from proteobacterial species, while ribosomal protection genes have been mobilized from Firmicutes and Actinobacteria. This study significantly expands the knowledge of known and putatively novel tetracycline resistance genes, their mobility and evolutionary history. The study also provides insights into the unknown resistome and genes that may be encountered in clinical settings in the future.}, }
@article {pmid33124350, year = {2020}, author = {Yuan, QY and Chen, HJ and Laurence, H and He, YL}, title = {[Antibiotics Induce Horizontal Gene Transfer of Resistance at Sublethal Concentrations].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {41}, number = {8}, pages = {3748-3757}, doi = {10.13227/j.hjkx.201912015}, pmid = {33124350}, issn = {0250-3301}, mesh = {*Anti-Bacterial Agents/toxicity ; Ceftazidime ; Escherichia coli/genetics ; *Gene Transfer, Horizontal ; Plasmids/genetics ; beta-Lactamases/genetics ; }, abstract = {In order to explore the conjugation of genes encoding extended-spectrum β-lactamase (ESBL), ESBL-expressing P. aeruginosa and E.coli strains isolated from the wastewater of major hospitals in Singapore were used as donors. gfp-tagged E.coli SCC1 strains resistant to chloramphenicol (CHL) were chosen as recipients. Using response surface analysis, we detected and analyzed the induction of conjugal transfer under single-exposure and co-exposure of tetracycline (TC), sulfamethoxazole (SMZ), and ceftazidime (CAZ) at sublethal concentrations. It was found that the ESBL plasmid could be conjugal transferred from P. aeruginosa and E.coli strains to the recipient E.coli SCC1 strains at an average frequency of 0.0015 and 0.0042, respectively, without stress from inducing antibiotics, thus showing a low fitness cost and higher conjugal frequency between E.coli strains under the exposure of sub-MIC antibiotics. A significant conjugation between E.coli strains occurred under the single-exposure or co-exposure of a TC concentration of <0.03 mg·L[-1] and a CAZ concentration of <0.002 mg·L[-1], as inhibited by a sub-MIC level of TC. The conjugation between P. aeruginosa and E.coli strains was stimulated under the exposure of TC and CAZ with concentrations 5-times larger than the MIC, while no significant induction was detected from the sub-MIC antibiotics.}, }
@article {pmid33124288, year = {2020}, author = {Zhou, XY and Wang, YZ and Su, JQ and Huang, FY}, title = {[Microplastics-Induced Shifts of Diversity and Abundance of Antibiotic Resistance Genes in River Water].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {41}, number = {9}, pages = {4076-4080}, doi = {10.13227/j.hjkx.202003146}, pmid = {33124288}, issn = {0250-3301}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial/genetics ; Humans ; Microplastics ; *Plastics ; Rivers ; }, abstract = {Microplastics (MPs) and antibiotic resistance genes (ARGs) are both considered emerging contaminants of increasing concern because their combined pollution poses a serious risk to the ecological environment and human health. In this study, high-throughput quantitative PCR techniques were used to investigate the diversity and abundance of ARGs in river water, to which two different microplastics (PVC and PVA) were added for aerated incubation. The results showed that ARGs in river water were diverse, and microplastics could induce more types of ARGs. Although the number and abundance of ARGs decreased in all three treatments, which were cultivated for 14 d by aeration, compared to those in non-treated samples, the total abundance of ARGs in treatments aerated with MPs were higher than those aerated without MPs, especially in the samples treated with water-soluble microplastics (PVA). Significant correlations between the abundance of ARGs and mobile genetic elements (MGEs) were observed, implying that the occurrence of MGEs may potentially affect the transmission and distribution of ARGs through horizontal gene transfer (HGT) in river water.}, }
@article {pmid33123928, year = {2021}, author = {Lin, Z and Yuan, T and Zhou, L and Cheng, S and Qu, X and Lu, P and Feng, Q}, title = {Impact factors of the accumulation, migration and spread of antibiotic resistance in the environment.}, journal = {Environmental geochemistry and health}, volume = {43}, number = {5}, pages = {1741-1758}, doi = {10.1007/s10653-020-00759-0}, pmid = {33123928}, issn = {1573-2983}, support = {2019B003//Jiangsu Key Laboratory of Coal-based Greenhouse Gas Control and Utilization/ ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Biodiversity ; Drug Resistance, Bacterial ; *Drug Resistance, Microbial/drug effects/genetics ; Environmental Pollutants ; *Gene Transfer, Horizontal ; Metals, Heavy/pharmacology ; Microbiota ; }, abstract = {Antibiotic resistance is a great concern, which leads to global public health risks and ecological and environmental risks. The presence of antibiotic-resistant genes and antibiotic-resistant bacteria in the environment exacerbates the risk of spreading antibiotic resistance. Among them, horizontal gene transfer is an important mode in the spread of antibiotic resistance genes, and it is one of the reasons that the antibiotic resistance pollution has become increasingly serious. At the same time, free antibiotic resistance genes and resistance gene host bacterial also exist in the natural environment. They can not only affect horizontal gene transfer, but can also migrate and aggregate among environmental media in many ways and then continue to affect the proliferate and transfer of antibiotic resistance genes. All this shows the seriousness of antibiotic resistance pollution. Therefore, in this review, we reveal the sensitive factors affecting the distribution and spread of antibiotic resistance through three aspects: the influencing factors of horizontal gene transfer, the host bacteria of resistance genes and the migration of antibiotic resistance between environmental media. This review reveals the huge role of environmental migration in the spread of antibiotic resistance, and the environmental behavior of antibiotic resistance deserves wider attention. Meanwhile, extracellular antibiotic resistance genes and intracellular antibiotic resistance genes play different roles, so they should be studied separately.}, }
@article {pmid33123750, year = {2021}, author = {Xu, F and Yan, H and Liu, Y and Zhao, S and Song, S and Gu, T and Song, Z and Xie, J and Rong, C}, title = {A Re-evaluation of the Taxonomy and Classification of the Type III Secretion System in a Pathogenic Bacterium Causing Soft Rot Disease of Pleurotus eryngii.}, journal = {Current microbiology}, volume = {78}, number = {1}, pages = {179-189}, pmid = {33123750}, issn = {1432-0991}, support = {31701975//National Natural Science Foundation of China (CN)/ ; }, mesh = {Bacterial Proteins/genetics ; China ; Enterobacteriaceae ; Pantoea ; Phylogeny ; *Pleurotus/genetics ; *Type III Secretion Systems/genetics ; }, abstract = {Pantoea beijingensis, a gram-negative pathogenic bacterium, causes soft rot disease in the fungus Pleurotus eryngii in China. However, the taxonomic classification of this pathogen is controversial due to close relationships between bacteria of the genera Pantoea and Erwinia. This study aimed to resolve the identity of P. beijingensis using phylogenomic and systematic analyses of Pantoea and Erwinia by whole-genome sequencing. Single-copy orthologs identified from the Erwinia/Pantoea core genomes were used to delineate Erwinia/Pantoea phylogeny. P. beijingensis LMG27579[T] clustered within a single Erwinia clade. A whole-genome-based phylogenetic tree and average nucleotide and amino-acid identity values indicate that P. beijingensis LMG27579[T] should be renamed Erwinia beijingensis. The hrp/hrc genes encoding type III secretion system (T3SS) proteins in Erwinia and Pantoea were divided into five groups according to gene contents and organization. Neighbor-joining-inferred phylogenetic trees based on concatenated HrcU, HrcN, and HrcR in the main hrp/hrc cluster showed that E. beijingensis T3SS proteins are closely related to those in Ewingella americana, implying that E. beijingensis and E. americana have a recent common hrp/hrc gene ancestor. Furthermore, T3SS proteins of Erwinia and Pantoea were clustered in different clades separated by other bacterial T3SS proteins. Thus, T3SS genes in Pantoea and Erwinia strains might have been acquired by horizontal gene transfer. Overall, our findings clarify the taxonomy of the bacterium causing soft rot in P. eryngii, as well as the genetic structure and classification of the hrp/hrc T3SS virulence factor. We propose that T3SS acquisition is important for E. beijingensis emergence and pathogenesis.}, }
@article {pmid33123110, year = {2020}, author = {Alves-Barroco, C and Rivas-García, L and Fernandes, AR and Baptista, PV}, title = {Tackling Multidrug Resistance in Streptococci - From Novel Biotherapeutic Strategies to Nanomedicines.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {579916}, pmid = {33123110}, issn = {1664-302X}, abstract = {The pyogenic streptococci group includes pathogenic species for humans and other animals and has been associated with enduring morbidity and high mortality. The main reason for the treatment failure of streptococcal infections is the increased resistance to antibiotics. In recent years, infectious diseases caused by pyogenic streptococci resistant to multiple antibiotics have been raising with a significant impact to public health and veterinary industry. The rise of antibiotic-resistant streptococci has been associated to diverse mechanisms, such as efflux pumps and modifications of the antimicrobial target. Among streptococci, antibiotic resistance emerges from previously sensitive populations as result of horizontal gene transfer or chromosomal point mutations due to excessive use of antimicrobials. Streptococci strains are also recognized as biofilm producers. The increased resistance of biofilms to antibiotics among streptococci promote persistent infection, which comprise circa 80% of microbial infections in humans. Therefore, to overcome drug resistance, new strategies, including new antibacterial and antibiofilm agents, have been studied. Interestingly, the use of systems based on nanoparticles have been applied to tackle infection and reduce the emergence of drug resistance. Herein, we present a synopsis of mechanisms associated to drug resistance in (pyogenic) streptococci and discuss some innovative strategies as alternative to conventional antibiotics, such as bacteriocins, bacteriophage, and phage lysins, and metal nanoparticles. We shall provide focused discussion on the advantages and limitations of agents considering application, efficacy and safety in the context of impact to the host and evolution of bacterial resistance.}, }
@article {pmid33123100, year = {2020}, author = {Gionfriddo, CM and Wymore, AM and Jones, DS and Wilpiszeski, RL and Lynes, MM and Christensen, GA and Soren, A and Gilmour, CC and Podar, M and Elias, DA}, title = {An Improved hgcAB Primer Set and Direct High-Throughput Sequencing Expand Hg-Methylator Diversity in Nature.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {541554}, pmid = {33123100}, issn = {1664-302X}, abstract = {The gene pair hgcAB is essential for microbial mercury methylation. Our understanding of its abundance and diversity in nature is rapidly evolving. In this study we developed a new broad-range primer set for hgcAB, plus an expanded hgcAB reference library, and used these to characterize Hg-methylating communities from diverse environments. We applied this new Hg-methylator database to assign taxonomy to hgcA sequences from clone, amplicon, and metagenomic datasets. We evaluated potential biases introduced in primer design, sequence length, and classification, and suggest best practices for studying Hg-methylator diversity. Our study confirms the emerging picture of an expanded diversity of HgcAB-encoding microbes in many types of ecosystems, with abundant putative mercury methylators Nitrospirae and Chloroflexi in several new environments including salt marsh and peat soils. Other common microbes encoding HgcAB included Phycisphaerae, Aminicenantes, Spirochaetes, and Elusimicrobia. Combined with high-throughput amplicon specific sequencing, the new primer set also indentified novel hgcAB sequences similar to Lentisphaerae, Bacteroidetes, Atribacteria, and candidate phyla WOR-3 and KSB1 bacteria. Gene abundance data also corroborate the important role of two "classic" groups of methylators (Deltaproteobacteria and Methanomicrobia) in many environments, but generally show a scarcity of hgcAB+ Firmicutes. The new primer set was developed to specifically target hgcAB sequences found in nature, reducing degeneracy and providing increased sensitivity while maintaining broad diversity capture. We evaluated mock communities to confirm primer improvements, including culture spikes to environmental samples with variable DNA extraction and PCR amplification efficiencies. For select sites, this new workflow was combined with direct high-throughput hgcAB sequencing. The hgcAB diversity generated by direct amplicon sequencing confirmed the potential for novel Hg-methylators previously identified using metagenomic screens. A new phylogenetic analysis using sequences from freshwater, saline, and terrestrial environments showed Deltaproteobacteria HgcA sequences generally clustered among themselves, while metagenome-resolved HgcA sequences in other phyla tended to cluster by environment, suggesting horizontal gene transfer into many clades. HgcA from marine metagenomes often formed distinct subtrees from those sequenced from freshwater ecosystems. Overall the majority of HgcA sequences branch from a cluster of HgcAB fused proteins related to Thermococci, Atribacteria (candidate division OP9), Aminicenantes (OP8), and Chloroflexi. The improved primer set and library, combined with direct amplicon sequencing, provide a significantly improved assessment of the abundance and diversity of hgcAB+ microbes in nature.}, }
@article {pmid33122675, year = {2020}, author = {Kohler, P and Tijet, N and Kim, HC and Johnstone, J and Edge, T and Patel, SN and Seah, C and Willey, B and Coleman, B and Green, K and Armstrong, I and Katz, K and Muller, MP and Powis, J and Poutanen, SM and Richardson, D and Sarabia, A and Simor, A and McGeer, A and Melano, RG and , }, title = {Dissemination of Verona Integron-encoded Metallo-β-lactamase among clinical and environmental Enterobacteriaceae isolates in Ontario, Canada.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {18580}, pmid = {33122675}, issn = {2045-2322}, support = {158728/SNSF_/Swiss National Science Foundation/Switzerland ; 313039//CIHR/Canada ; }, mesh = {Case-Control Studies ; Drug Resistance, Multiple, Bacterial ; Enterobacteriaceae/*enzymology/genetics/isolation &amp; purification ; Enterobacteriaceae Infections/enzymology/*epidemiology/microbiology ; Humans ; Ontario/epidemiology ; Whole Genome Sequencing ; beta-Lactamases/genetics/metabolism ; }, abstract = {Surveillance data from Southern Ontario show that a majority of Verona Integron-encoded Metallo-β-lactamase (VIM)-producing Enterobacteriaceae are locally acquired. To better understand the local epidemiology, we analysed clinical and environmental blaVIM-positive Enterobacteriaceae from the area. Clinical samples were collected within the Toronto Invasive Bacterial Diseases Network (2010-2016); environmental water samples were collected in 2015. We gathered patient information on place of residence and hospital admissions prior to the diagnosis. Patients with and without plausible source of acquisition were compared regarding risk exposures. Microbiological isolates underwent whole-genome sequencing (WGS); blaVIM carrying plasmids were characterized. We identified 15 patients, thereof 11 with blaVIM-1-positive Enterobacter hormaechei within two genetic clusters based on WGS. Whereas no obvious epidemiologic link was identified among cluster I patients, those in cluster II were connected to a hospital outbreak. Except for patients with probable acquisition abroad, we did not identify any further risk exposures. Two blaVIM-1-positive E. hormaechei from environmental waters matched with the clinical clusters; plasmid sequencing suggested a common ancestor plasmid for the two clusters. These data show that both clonal spread and horizontal gene transfer are drivers of the dissemination of blaVIM-1-carrying Enterobacter hormaechei in hospitals and the aquatic environment in Southern Ontario, Canada.}, }
@article {pmid33122438, year = {2020}, author = {Westra, ER and Levin, BR}, title = {It is unclear how important CRISPR-Cas systems are for protecting natural populations of bacteria against infections by mobile genetic elements.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {45}, pages = {27777-27785}, pmid = {33122438}, issn = {1091-6490}, support = {R01 GM091875/GM/NIGMS NIH HHS/United States ; R35 GM136407/GM/NIGMS NIH HHS/United States ; BB/N017412/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Archaea/genetics ; Bacteria/*genetics ; Bacteriophages/genetics ; CRISPR-Cas Systems/*physiology ; Computer Simulation ; Evolution, Molecular ; Gene Transfer, Horizontal ; Interspersed Repetitive Sequences ; Models, Theoretical ; Plasmids/*genetics ; Viruses/genetics ; }, abstract = {Articles on CRISPR commonly open with some variant of the phrase "these short palindromic repeats and their associated endonucleases (Cas) are an adaptive immune system that exists to protect bacteria and archaea from viruses and infections with other mobile genetic elements." There is an abundance of genomic data consistent with the hypothesis that CRISPR plays this role in natural populations of bacteria and archaea, and experimental demonstrations with a few species of bacteria and their phage and plasmids show that CRISPR-Cas systems can play this role in vitro. Not at all clear are the ubiquity, magnitude, and nature of the contribution of CRISPR-Cas systems to the ecology and evolution of natural populations of microbes and the strength of selection mediated by different types of phage and plasmids to the evolution and maintenance of CRISPR-Cas systems. In this perspective, with the aid of heuristic mathematical-computer simulation models, we explore the a priori conditions under which exposure to lytic and temperate phage and conjugative plasmids will select for and maintain CRISPR-Cas systems in populations of bacteria and archaea. We review the existing literature addressing these ecological and evolutionary questions and highlight the experimental and other evidence needed to fully understand the conditions responsible for the evolution and maintenance of CRISPR-Cas systems and the contribution of these systems to the ecology and evolution of bacteria, archaea, and the mobile genetic elements that infect them.}, }
@article {pmid33121492, year = {2020}, author = {Silva, MF and Duarte, A and Pereira, G and Mateus, L and Lopes-da-Costa, L and Silva, E}, title = {Assessment of Campylobacter fetus subsp. venerealis molecular diagnosis using clinical samples of bulls.}, journal = {BMC veterinary research}, volume = {16}, number = {1}, pages = {410}, pmid = {33121492}, issn = {1746-6148}, support = {PTDC/CVT-CVT/30145/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDP/CVT/00276/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; SFRH/BD/125657/2016//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; SFRH/BD/130923/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; DL57/2016/CP1438/CT0001//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, mesh = {Animals ; Bacterial Typing Techniques/veterinary ; Campylobacter/genetics/*isolation &amp; purification ; Campylobacter Infections/diagnosis/microbiology/*veterinary ; Cattle ; Cattle Diseases/*diagnosis/*microbiology ; Foreskin/microbiology ; Male ; Real-Time Polymerase Chain Reaction/veterinary ; }, abstract = {BACKGROUND: Campylobacter fetus subsp. venerealis (Cfv) is the pathogen responsible for Bovine Genital Campylobacteriosis (BGC), a venereal disease of cattle associated with impaired reproductive performance. Although several PCR assays were developed to identify this pathogen, most of them are still poorly evaluated in clinical samples. This study evaluated real-time PCR assays for Cfv detection in preputial samples of bulls (n = 308).<br><br>RESULTS: The detection at the subspecies level (Cfv) compared four assays: two targeting ISCfe1 and two targeting parA gene. The detection at the species level (C. fetus) considered an assay targeting the nahE gene and a commercial kit for C. fetus identification. At the subspecies level, assays directed either to different targets (parA and ISCfe1), or to the same target (ISCfe1 or parA), showed a high percentage of disagreeing results. All samples positive at the subspecies level (n&#x2009;=&#x2009;169) were negative in C. fetus detection assays, which strongly suggests the horizontal gene transfer of ISCfe1 and parA to other bacterial species. This was confirmed by microbiological isolation of three Campylobacter portucalensis strains responsible for false positive results. Sequences with a high level of identity with ISCfe1 and parA gene of Cfv were identified in C. portucalensis genome.<br><br>CONCLUSIONS: Overall, this study reveals that PCR assays solely directed to a subspecies target originate a high rate of false positive results, due to the presence of parA and ISCfe1 homologous sequences in other bacterial species, namely of the genus Campylobacter. Although the specificity of these methods may be higher if applied to bulls from herds with clinical features of BGC or in other geographical regions, current PCR diagnosis should couple subspecies and species targets, and further research must be envisaged to identify Cfv specific molecular targets.}, }
@article {pmid33121146, year = {2020}, author = {Otinov, GD and Lokteva, AV and Petrova, AD and Zinchenko, IV and Isaeva, MV and Kovtunov, EA and Koshel, EI}, title = {Positive and Negative Effects of Metal Oxide Nanoparticles on Antibiotic Resistance Genes Transfer.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {9}, number = {11}, pages = {}, pmid = {33121146}, issn = {2079-6382}, support = {19-74-00125//Russian Science Foundation/ ; }, abstract = {Rapid development of antibiotic resistance in bacteria is a critical public health problem in the world. One of the main routes of resistance development is the transfer of genes containing antibiotic resistance cassettes. Gene transfer can be done through horizontal transfer of genes: transduction, conjugation, and transformation. Many factors in the environment influence these processes, and one of them is the action of metal oxide nanoparticles (MONPs), which can appear in the milieu through both biological synthesis and the release of engineered nanomaterial. In this study, the effect of AlOOH, CuO, Fe3O4, TiO2, and ZnO MONPs on the transformation (heat shock transformation) of bacteria Escherichia coli K12, and the conjugation between E. coli cc118 and E. coli Nova Blue were studied. The MONPs were synthesized by one method and fully characterized. ZnO nanoparticles (NPs) have significantly increased the efficiency of transformation (more than 9-fold), while the other NPs have reduced it to 31 times (TiO2 NPs). AlOOH NPs increased the number of transconjugants more than 1.5-fold, while CuO and Fe3O4 NPs did not have a significant effect on transformation and conjugation. Thus, the data shows that different types of MONPs can enhance or inhibit different gene transfer mechanisms, affecting the spread of antibiotic resistance genes.}, }
@article {pmid33120155, year = {2021}, author = {Pu, Q and Fan, XT and Li, H and An, XL and Lassen, SB and Su, JQ}, title = {Cadmium enhances conjugative plasmid transfer to a fresh water microbial community.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {268}, number = {Pt B}, pages = {115903}, doi = {10.1016/j.envpol.2020.115903}, pmid = {33120155}, issn = {1873-6424}, mesh = {Cadmium ; *Conjugation, Genetic ; Fresh Water ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Microbiota ; Phylogeny ; Plasmids/genetics ; }, abstract = {Co-selection of antibiotic resistance genes (ARGs) by heavy metals might facilitate the spread of ARGs in the environments. Cadmium contamination is ubiquitous, while, it remains unknown the extent to which cadmium (Cd[2+]) impact plasmid-mediated transfer of ARGs in aquatic bacterial communities. In the present study, we found that Cd[2+] amendment at sub-inhibitory concentration significantly increased conjugation frequency of RP4 plasmid from Pseudomonas putida KT2442 to a fresh water microbial community by liquid mating method. Cd[2+] treatment (1-100 mg/L) significantly increased the cell membrane permeability and antioxidant activities of conjugation mixtures. Amendments of 10 and 100 mg/L Cd[2+] significantly enhanced the mRNA expression levels of mating pair formation gene (trbBp) and the DNA transfer and replication gene (trfAp) due to the repression of regulatory genes (korA, korB and trbA). Phylogenetic analysis of transconjugants indicated that Proteobacteria was the dominant recipients and high concentration of Cd[2+] treatment resulted in expanded recipient taxa. This study suggested that sub-inhibitory Cd[2+] contamination would facilitate plasmid conjugation and contributed to the maintenance and spread of plasmid associated ARGs, and highlighted the urgent need for effective remediation of Cd[2+] in aquatic environments.}, }
@article {pmid33115833, year = {2020}, author = {Zukancic, A and Khan, MA and Gurmen, SJ and Gliniecki, QM and Moritz-Kinkade, DL and Maddox, CW and Alam, MT}, title = {Staphylococcal Protein A (spa) Locus Is a Hot Spot for Recombination and Horizontal Gene Transfer in Staphylococcus pseudintermedius.}, journal = {mSphere}, volume = {5}, number = {5}, pages = {}, pmid = {33115833}, issn = {2379-5042}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Dogs ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Genomics ; Microbial Sensitivity Tests ; *Recombination, Genetic ; Staphylococcal Infections/microbiology/*veterinary ; Staphylococcal Protein A/*genetics ; Staphylococcus/drug effects/*genetics ; Virulence Factors/*genetics ; Whole Genome Sequencing ; }, abstract = {Staphylococcus pseudintermedius is a major canine pathogen but also occasionally colonizes and infects humans. Multidrug-resistant methicillin-resistant S. pseudintermedius (MDR MRSP) strains have emerged globally, making treatment and control of this pathogen challenging. Sequence type 71 (ST71), ST68, and ST45 are the most widespread and successful MDR MRSP clones. The potential genetic factors underlying the clonal success of these and other predominant clones remain unknown. Characterization of the pangenome, lineage-associated accessory genes, and genes acquired through horizontal gene transfer from other bacteria is important for identifying such factors. Here, we analyzed genome sequence data from 622 S. pseudintermedius isolates to investigate the evolution of pathogenicity across lineages. We show that the predominant clones carry one or more lineage-associated virulence genes. The gene encoding staphylococcal protein A (SpA), a key virulence factor involved in immune evasion and a potential vaccine antigen, is deleted in 62% of isolates. Most importantly, we have discovered that the spa locus is a hot spot for recombination and horizontal gene transfer in S. pseudintermedius, where genes related to restriction modification, prophage immunity, mercury resistance, and nucleotide and carbohydrate metabolism have been acquired in different lineages. Our study also establishes that ST45 is composed of two distinct sublineages that differ in their accessory gene content and virulence potential. Collectively, this study reports several previously undetected lineage-associated genetic factors that may have a role in the clonal success of the major MDR MRSP clones. These data provide a framework for future experimental studies on S. pseudintermedius pathogenesis and for developing novel therapeutics against this pathogen.IMPORTANCEStaphylococcus pseudintermedius is a major canine pathogen but can also occasionally infect humans. Identification of genetic factors contributing to the virulence and clonal success of multidrug-resistant S. pseudintermedius clones is critical for the development of therapeutics against this pathogen. Here, we characterized the genome sequences of a global collection of 622 S. pseudintermedius isolates. We show that all major clones, besides carrying core virulence genes, which are present in all strains, carry one or more lineage-specific genes. Many of these genes have been acquired from other bacterial species through a horizontal gene transfer mechanism. Importantly, we have discovered that the staphylococcal protein A gene (spa), a widely used marker for molecular typing of S. pseudintermedius strains and a potential vaccine candidate antigen, is deleted in 62% of strains. Furthermore, the spa locus in S. pseudintermedius acts as a reservoir to accumulate lineage-associated genes with adaptive functions.}, }
@article {pmid33115402, year = {2020}, author = {Acar Kirit, H and Lagator, M and Bollback, JP}, title = {Experimental determination of evolutionary barriers to horizontal gene transfer.}, journal = {BMC microbiology}, volume = {20}, number = {1}, pages = {326}, pmid = {33115402}, issn = {1471-2180}, support = {/WT_/Wellcome Trust/United Kingdom ; 216779/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Escherichia coli/*genetics/metabolism ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Fitness ; *Models, Genetic ; Salmonella typhimurium/*genetics/metabolism ; }, abstract = {BACKGROUND: Horizontal gene transfer, the acquisition of genes across species boundaries, is a major source of novel phenotypes that enables microbes to rapidly adapt to new environments. How the transferred gene alters the growth - fitness - of the new host affects the success of the horizontal gene transfer event and how rapidly the gene spreads in the population. Several selective barriers - factors that impact the fitness effect of the transferred gene - have been suggested to impede the likelihood of horizontal transmission, however experimental evidence is scarce. The objective of this study was to determine the fitness effects of orthologous genes transferred from Salmonella enterica serovar Typhimurium to Escherichia coli to identify the selective barriers using highly precise experimental measurements.<br><br>RESULTS: We found that most gene transfers result in strong fitness costs. Previously identified evolutionary barriers - gene function and the number of protein-protein interactions - did not predict the fitness effects of transferred genes. In contrast, dosage sensitivity, gene length, and the intrinsic protein disorder significantly impact the likelihood of a successful horizontal transfer.<br><br>CONCLUSION: While computational approaches have been successful in describing long-term barriers to horizontal gene transfer, our experimental results identified previously underappreciated barriers that determine the fitness effects of newly transferred genes, and hence their short-term eco-evolutionary dynamics.}, }
@article {pmid33114362, year = {2020}, author = {Poole, TL and Schlosser, WD and Anderson, RC and Norman, KN and Beier, RC and Nisbet, DJ}, title = {Whole-Genome Sequence of Aeromonas hydrophila CVM861 Isolated from Diarrhetic Neonatal Swine.}, journal = {Microorganisms}, volume = {8}, number = {11}, pages = {}, pmid = {33114362}, issn = {2076-2607}, abstract = {Aeromonas hydrophila are ubiquitous in the environment and are highly distributed in aquatic habitats. They have long been known as fish pathogens but are opportunistic human pathogens. Aeromonas spp. have persisted through food-processing safeguards and have been isolated from fresh grocery vegetables, dairy, beef, pork, poultry products and packaged ready-to-eat meats, thus providing an avenue to foodborne illness. A beta-hemolytic, putative Escherichia coli strain collected from diarrheic neonatal pigs in Oklahoma was subsequently identified as A. hydrophila, and designated CVM861. Here we report the whole-genome sequence of A. hydrophila CVM861, SRA accession number, SRR12574563; BioSample number, SAMN1590692; Genbank accession number SRX9061579. The sequence data for CVM861 revealed four Aeromonas-specific virulence genes: lipase (lip), hemolysin (hlyA), cytonic enterotoxin (ast) and phospholipid-cholesterolacyltransferase (GCAT). There were no alignments to any virulence genes in VirulenceFinder. CVM861 contained an E. coli resistance plasmid identified as IncQ1_1__M28829. There were five aminoglycoside, three beta-lactam, and one each of macrolide, phenicol, sulfonamide, tetracycline and trimethoprim resistance genes, all with over 95% identity to genes in the ResFinder database. Additionally, there were 36 alignments to mobile genetic elements using MobileElementFinder. This shows that an aquatic pathogen, rarely considered in human disease, contributes to the resistome reservoir and may be capable of transferring resistance and virulence genes to other more prevalent foodborne strains such as E. coli or Salmonella in swine or other food production systems.}, }
@article {pmid33114079, year = {2020}, author = {Sivalingam, P and Poté, J and Prabakar, K}, title = {Extracellular DNA (eDNA): Neglected and Potential Sources of Antibiotic Resistant Genes (ARGs) in the Aquatic Environments.}, journal = {Pathogens (Basel, Switzerland)}, volume = {9}, number = {11}, pages = {}, pmid = {33114079}, issn = {2076-0817}, abstract = {Over the past decades, the rising antibiotic resistance bacteria (ARB) are continuing to emerge as a global threat due to potential public health risk. Rapidly evolving antibiotic resistance and its persistence in the environment, have underpinned the need for more studies to identify the possible sources and limit the spread. In this context, not commonly studied and a neglected genetic material called extracellular DNA (eDNA) is gaining increased attention as it can be one of the significant drivers for transmission of extracellular ARGS (eARGs) via horizontal gene transfer (HGT) to competent environmental bacteria and diverse sources of antibiotic-resistance genes (ARGs) in the environment. Consequently, this review highlights the studies that address the environmental occurrence of eDNA and encoding eARGs and its impact on the environmental resistome. In this review, we also brief the recent dedicated technological advancements that are accelerating extraction of eDNA and the efficiency of treatment technologies in reducing eDNA that focuses on environmental antibiotic resistance and potential ecological health risk.}, }
@article {pmid33112226, year = {2020}, author = {Tassinari, E and Bawn, M and Thilliez, G and Charity, O and Acton, L and Kirkwood, M and Petrovska, L and Dallman, T and Burgess, CM and Hall, N and Duffy, G and Kingsley, RA}, title = {Whole-genome epidemiology links phage-mediated acquisition of a virulence gene to the clonal expansion of a pandemic Salmonella enterica serovar Typhimurium clone.}, journal = {Microbial genomics}, volume = {6}, number = {11}, pages = {}, pmid = {33112226}, issn = {2057-5858}, support = {BB/N007964/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M025489/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012504/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10348/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10349/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bacterial Proteins/*genetics ; Bacteriophages/*genetics ; Clonal Evolution/genetics ; Genome, Bacterial/*genetics ; Guanine Nucleotide Exchange Factors/genetics ; Salmonella Infections, Animal/microbiology ; Salmonella typhimurium/*genetics/isolation &amp; purification/pathogenicity ; Swine ; Swine Diseases/microbiology ; Virulence/genetics ; Virulence Factors/genetics ; Whole Genome Sequencing ; }, abstract = {Epidemic and pandemic clones of bacterial pathogens with distinct characteristics continually emerge, replacing those previously dominant through mechanisms that remain poorly characterized. Here, whole-genome-sequencing-powered epidemiology linked horizontal transfer of a virulence gene, sopE, to the emergence and clonal expansion of a new epidemic Salmonella enterica serovar Typhimurium (S. Typhimurium) clone. The sopE gene is sporadically distributed within the genus Salmonella and rare in S. enterica Typhimurium lineages, but was acquired multiple times during clonal expansion of the currently dominant pandemic monophasic S. Typhimurium sequence type (ST) 34 clone. Ancestral state reconstruction and time-scaled phylogenetic analysis indicated that sopE was not present in the common ancestor of the epidemic clade, but later acquisition resulted in increased clonal expansion of sopE-containing clones that was temporally associated with emergence of the epidemic, consistent with increased fitness. The sopE gene was mainly associated with a temperate bacteriophage mTmV, but recombination with other bacteriophage and apparent horizontal gene transfer of the sopE gene cassette resulted in distribution among at least four mobile genetic elements within the monophasic S. enterica Typhimurium ST34 epidemic clade. The mTmV prophage lysogenic transfer to other S. enterica serovars in vitro was limited, but included the common pig-associated S. enterica Derby (S. Derby). This may explain mTmV in S. Derby co-circulating on farms with monophasic S. Typhimurium ST34, highlighting the potential for further transfer of the sopE virulence gene in nature. We conclude that whole-genome epidemiology pinpoints potential drivers of evolutionary and epidemiological dynamics during pathogen emergence, and identifies targets for subsequent research in epidemiology and bacterial pathogenesis.}, }
@article {pmid33111499, year = {2020}, author = {Zrimec, J}, title = {Multiple plasmid origin-of-transfer regions might aid the spread of antimicrobial resistance to human pathogens.}, journal = {MicrobiologyOpen}, volume = {9}, number = {12}, pages = {e1129}, pmid = {33111499}, issn = {2045-8827}, mesh = {Algorithms ; Bacteria/drug effects/*genetics ; Conjugation, Genetic/*genetics ; Databases, Genetic ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal/*genetics ; Humans ; Nucleic Acid Conformation ; Plasmids/*genetics ; Sequence Alignment ; Transformation, Bacterial/*genetics ; }, abstract = {Antimicrobial resistance poses a great danger to humanity, in part due to the widespread horizontal gene transfer of plasmids via conjugation. Modeling of plasmid transfer is essential to uncovering the fundamentals of resistance transfer and for the development of predictive measures to limit the spread of resistance. However, a major limitation in the current understanding of plasmids is the incomplete characterization of the conjugative DNA transfer mechanisms, which conceals the actual potential for plasmid transfer in nature. Here, we consider that the plasmid-borne origin-of-transfer substrates encode specific DNA structural properties that can facilitate finding these regions in large datasets and develop a DNA structure-based alignment procedure for typing the transfer substrates that outperforms sequence-based approaches. Thousands of putative DNA transfer substrates are identified, showing that plasmid mobility can be twofold higher and span almost twofold more host species than is currently known. Over half of all putative mobile plasmids contain the means for mobilization by conjugation systems belonging to different mobility groups, which can hypothetically link previously confined host ranges across ecological habitats into a robust plasmid transfer network. This hypothetical network is found to facilitate the transfer of antimicrobial resistance from environmental genetic reservoirs to human pathogens, which might be an important driver of the observed rapid resistance development in humans and thus an important point of focus for future prevention measures.}, }
@article {pmid33111162, year = {2021}, author = {Inglis, PW and Santos, LAVM and Craveiro, SR and Ribeiro, BM and Castro, MEB}, title = {Mosaic genome evolution and phylogenetics of Chrysodeixis includens nucleopolyhedrovirus (ChinNPV) and virulence of seven new isolates from the Brazilian states of Minas Gerais and Mato Grosso.}, journal = {Archives of virology}, volume = {166}, number = {1}, pages = {125-138}, pmid = {33111162}, issn = {1432-8798}, support = {193.001532/2016//Funda&#xe7;&#xe3;o de Apoio &#xe0; Pesquisa do Distrito Federal/ ; 305756/2017-6//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 193.001531/2016-PRONEX//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Animals ; Baculoviridae/genetics ; Base Sequence ; Brazil ; Evolution, Molecular ; Genome, Viral/*genetics ; Larva/virology ; Moths/virology ; Nucleopolyhedroviruses/*genetics ; Pest Control, Biological ; Phylogeny ; Glycine max/virology ; Virulence/*genetics ; }, abstract = {In a comparative analysis of genome sequences from isolates of the baculovirus Chrysodeixis includens nucleopolyhedrovirus (ChinNPV) from Brazil and Guatemala, we identified a subset of isolates possessing chimeric genomes. We identified six distinct phylogenetically incongruous regions (PIRs) dispersed in the genomes, of between 279 and 3345 bp in length. The individual PIRs possessed high sequence similarity among the affected ChinNPV isolates but varied in coverage in some instances. The donor for four of the PIRs implicated in horizontal gene transfer (HGT) was identified as Trichoplusia ni single nucleopolyhedrovirus (TnSNPV), an alphabaculovirus closely related to ChinNPV, or another unknown but closely related virus. BLAST searches of the other two PIRs returned only ChinNPV sequences, but HGT from an unknown donor baculovirus cannot be excluded. Although Chrysodeixis includens and Trichoplusia ni are frequently co-collected from soybean fields in Brazil, pathogenicity data suggest that natural coinfection of C. includens larvae with ChinNPV and TnSNPV is probably uncommon. Additionally, since the chimeric ChinNPV genomes with tracts of TnSNPV sequence were restricted to a single monophyletic lineage of closely related isolates, a model of progressive restoration of the native DNA sequence by recombination with ChinNPV possessing a fully or partially non-chimeric genome is reasonable. However, multiple independent HGT from TnSNPV to ChinNPV during the evolution of these isolates cannot be excluded. Mortality data suggest that the ChinNPV isolates with chimeric genomes are not significantly different in pathogenicity towards C. includens when compared to most other ChinNPV isolates. Exclusion of the PIRs prior to phylogenetic analysis had a large impact on the topology of part of the maximum-likelihood tree, revealing a homogenous clade of three isolates (IB, IC and ID) from Paraná state in Brazil collected in 2006, together with an isolate from Guatemala collected in 1972 (IA), comprising the lineage uniquely affected by HGT from TnSNPV. The other 10 Brazilian ChinNPV isolates from Paraná, Mato Grosso, and Minas Gerais states showed higher variability, where only three isolates from Paraná state formed a monophyletic group correlating with geographical origin.}, }
@article {pmid33108120, year = {2020}, author = {Ropars, J and Caron, T and Lo, YC and Bennetot, B and Giraud, T}, title = {[The domestication of Penicillium cheese fungi].}, journal = {Comptes rendus biologies}, volume = {343}, number = {2}, pages = {155-176}, doi = {10.5802/crbiol.15}, pmid = {33108120}, issn = {1768-3238}, mesh = {Cheese/*microbiology ; Domestication ; Gene Transfer, Horizontal ; Humans ; Penicillium/*genetics ; }, abstract = {Domestication is the process of organism evolution under selection by humans, and as such has been a model for studying adaptation since Charles Darwin. Here we review recent studies on the genomics of adaptation and domestication syndrome in two cheese-making fungal lineages, Penicillium roqueforti used for maturing blue cheeses, and the Penicillium camemberti species complex used for making soft cheeses such as Camembert and Brie. Comparative genomics have revealed horizontal gene transfers involved in convergent adaptation to cheese. Population genomics have identified differentiated populations with contrasted traits, several populations having independently been domesticated for cheese making in both P. roqueforti and the Penicillium camemberti species complex, and having undergone bottlenecks. The different cheese populations have acquired traits beneficial for cheese making in comparison to non-cheese populations, regarding color, spore production, growth rates on cheese, salt tolerance, lipolysis, proteolysis, volatile compound or toxin production and/or competitive ability. The cheese populations also show degeneration for some unused functions such as decreased ability of sexual reproduction or of growth under harsh conditions. These recent findings have fundamental importance for our understanding of adaptation and have applied interest for strain improvement.}, }
@article {pmid33108117, year = {2020}, author = {Pelletier, G}, title = {[Plants that capture fungus genes to protect themselves from fungi].}, journal = {Comptes rendus biologies}, volume = {343}, number = {2}, pages = {131-133}, doi = {10.5802/crbiol.19}, pmid = {33108117}, issn = {1768-3238}, mesh = {Fungi/genetics ; *Fusarium ; Gene Transfer, Horizontal ; *Triticum ; }, }
@article {pmid33108025, year = {2021}, author = {Parsons, C and Stüeken, EE and Rosen, CJ and Mateos, K and Anderson, RE}, title = {Radiation of nitrogen-metabolizing enzymes across the tree of life tracks environmental transitions in Earth history.}, journal = {Geobiology}, volume = {19}, number = {1}, pages = {18-34}, pmid = {33108025}, issn = {1472-4669}, support = {80NSSC18K0829/ImNASA/Intramural NASA/United States ; }, mesh = {*Ammonium Compounds ; Biological Evolution ; Denitrification ; *Enzymes ; Nitrates ; Nitrogen ; Oxidation-Reduction ; *Radiation ; }, abstract = {Nitrogen is an essential element to life and exerts a strong control on global biological productivity. The rise and spread of nitrogen-utilizing microbial metabolisms profoundly shaped the biosphere on the early Earth. Here, we reconciled gene and species trees to identify birth and horizontal gene transfer events for key nitrogen-cycling genes, dated with a time-calibrated tree of life, in order to examine the timing of the proliferation of these metabolisms across the tree of life. Our results provide new insights into the evolution of the early nitrogen cycle that expand on geochemical reconstructions. We observed widespread horizontal gene transfer of molybdenum-based nitrogenase back to the Archean, minor horizontal transfer of genes for nitrate reduction in the Archean, and an increase in the proliferation of genes metabolizing nitrite around the time of the Mesoproterozoic (~1.5 Ga). The latter coincides with recent geochemical evidence for a mid-Proterozoic rise in oxygen levels. Geochemical evidence of biological nitrate utilization in the Archean and early Proterozoic may reflect at least some contribution of dissimilatory nitrate reduction to ammonium (DNRA) rather than pure denitrification to N2 . Our results thus help unravel the relative dominance of two metabolic pathways that are not distinguishable with current geochemical tools. Overall, our findings thus provide novel constraints for understanding the evolution of the nitrogen cycle over time and provide insights into the bioavailability of various nitrogen sources in the early Earth with possible implications for the emergence of eukaryotic life.}, }
@article {pmid33105683, year = {2020}, author = {Abushattal, S and Vences, A and Barca, AV and Osorio, CR}, title = {Diverse Horizontally-Acquired Gene Clusters Confer Sucrose Utilization to Different Lineages of the Marine Pathogen Photobacterium damselae subsp. damselae.}, journal = {Genes}, volume = {11}, number = {11}, pages = {}, pmid = {33105683}, issn = {2073-4425}, mesh = {Fructokinases/genetics ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/genetics ; Genes, Essential/genetics ; Genome, Bacterial/genetics ; Multigene Family/*genetics ; Phosphoenolpyruvate Sugar Phosphotransferase System/genetics ; Photobacterium/*genetics/isolation &amp; purification/*metabolism ; Sucrose/*metabolism ; beta-Fructofuranosidase/genetics ; }, abstract = {The ability to metabolize sucrose is a variable trait within the family Vibrionaceae. The marine bacterium Photobacterium damselae subsp. damselae (Pdd), pathogenic for marine animals and humans, is generally described as negative for sucrose utilization (Scr[-]). Previous studies have reported sucrose-utilizing isolates (Scr[+]), but the genetic basis of this variable phenotype remains uncharacterized. Here, we carried out the genome sequencing of five Scr[+] and two Scr[-] Pdd isolates and conducted a comparative genomics analysis with sixteen additional Pdd genomes sequenced in previous studies. We identified two different versions of a four-gene cluster (scr cluster) exclusive of Scr[+] isolates encoding a PTS system sucrose-specific IIBC component (scrA), a fructokinase (scrK), a sucrose-6-phosphate hydrolase (scrB), and a sucrose operon repressor (scrR). A scrA deletion mutant did not ferment sucrose and was impaired for growth with sucrose as carbon source. Comparative genomics analyses suggested that scr clusters were acquired by horizontal transfer by different lineages of Pdd and were inserted into a recombination hot-spot in the Pdd genome. The incongruence of phylogenies based on housekeeping genes and on scr genes revealed that phylogenetically diverse gene clusters for sucrose utilization have undergone extensive horizontal transfer among species of Vibrio and Photobacterium.}, }
@article {pmid33105659, year = {2020}, author = {Puinongpo, W and Singchat, W and Petpradub, S and Kraichak, E and Nunome, M and Laopichienpong, N and Thongchum, R and Intarasorn, T and Sillapaprayoon, S and Indananda, C and Muangmai, N and Suntrarachun, S and Baicharoen, S and Chanhome, L and Peyachoknagul, S and Srikulnath, K}, title = {Existence of Bov-B LINE Retrotransposons in Snake Lineages Reveals Recent Multiple Horizontal Gene Transfers with Copy Number Variation.}, journal = {Genes}, volume = {11}, number = {11}, pages = {}, pmid = {33105659}, issn = {2073-4425}, mesh = {Animals ; Base Sequence ; DNA/genetics ; DNA Copy Number Variations/*genetics ; Evolution, Molecular ; Female ; Gene Transfer, Horizontal/*genetics ; Genetic Variation/genetics ; Genome/genetics ; Long Interspersed Nucleotide Elements/*genetics ; Male ; Mutation Rate ; Sequence Alignment ; Snakes/*genetics ; Thailand ; }, abstract = {Transposable elements (TEs) are dynamic elements present in all eukaryotic genomes. They can "jump" and amplify within the genome and promote segmental genome rearrangements on both autosomes and sex chromosomes by disruption of gene structures. The Bovine-B long interspersed nuclear element (Bov-B LINE) is among the most abundant TE-retrotransposon families in vertebrates due to horizontal transfer (HT) among vertebrate lineages. Recent studies have shown multiple HTs or the presence of diverse Bov-B LINE groups in the snake lineage. It is hypothesized that Bov-B LINEs are highly dynamic and that the diversity reflects multiple HTs in snake lineages. Partial sequences of Bov-B LINE from 23 snake species were characterized. Phylogenetic analysis resolved at least two Bov-B LINE groups that might correspond to henophidian and caenophidian snakes; however, the tree topology differed from that based on functional nuclear and mitochondrial gene sequences. Several Bov-B LINEs of snakes showed greater than 80% similarity to sequences obtained from insects, whereas the two Bov-B LINE groups as well as sequences from the same snake species classified in different Bov-B LINE groups showed sequence similarities of less than 80%. Calculation of estimated divergence time and pairwise divergence between all individual Bov-B LINE copies suggest invasion times ranging from 79.19 to 98.8 million years ago in snakes. Accumulation of elements in a lineage-specific fashion ranged from 9 × 10[-6]% to 5.63 × 10[-2]% per genome. The genomic proportion of Bov-B LINEs varied among snake species but was not directly associated with genome size or invasion time. No differentiation in Bov-B LINE copy number between males and females was observed in any of the snake species examined. Incongruence in tree topology between Bov-B LINEs and other snake phylogenies may reflect past HT events. Sequence divergence of Bov-B LINEs between copies suggests that recent multiple HTs occurred within the same evolutionary timeframe in the snake lineage. The proportion of Bov-B LINEs varies among species, reflecting species specificity in TE invasion. The rapid speciation of snakes, coinciding with Bov-B LINE invasion in snake genomes, leads us to better understand the effect of Bov-B LINEs on snake genome evolution.}, }
@article {pmid33105635, year = {2020}, author = {Virolle, C and Goldlust, K and Djermoun, S and Bigot, S and Lesterlin, C}, title = {Plasmid Transfer by Conjugation in Gram-Negative Bacteria: From the Cellular to the Community Level.}, journal = {Genes}, volume = {11}, number = {11}, pages = {}, pmid = {33105635}, issn = {2073-4425}, mesh = {Biofilms/*growth &amp; development ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/*genetics ; F Factor/*genetics/physiology ; Fimbriae, Bacterial/metabolism ; Gene Transfer, Horizontal/*genetics ; Gram-Negative Bacteria/*genetics ; }, abstract = {Bacterial conjugation, also referred to as bacterial sex, is a major horizontal gene transfer mechanism through which DNA is transferred from a donor to a recipient bacterium by direct contact. Conjugation is universally conserved among bacteria and occurs in a wide range of environments (soil, plant surfaces, water, sewage, biofilms, and host-associated bacterial communities). Within these habitats, conjugation drives the rapid evolution and adaptation of bacterial strains by mediating the propagation of various metabolic properties, including symbiotic lifestyle, virulence, biofilm formation, resistance to heavy metals, and, most importantly, resistance to antibiotics. These properties make conjugation a fundamentally important process, and it is thus the focus of extensive study. Here, we review the key steps of plasmid transfer by conjugation in Gram-negative bacteria, by following the life cycle of the F factor during its transfer from the donor to the recipient cell. We also discuss our current knowledge of the extent and impact of conjugation within an environmentally and clinically relevant bacterial habitat, bacterial biofilms.}, }
@article {pmid33104745, year = {2020}, author = {Samarth, DP and Kwon, YM}, title = {Horizontal genetic exchange of chromosomally encoded markers between Campylobacter jejuni cells.}, journal = {PloS one}, volume = {15}, number = {10}, pages = {e0241058}, pmid = {33104745}, issn = {1932-6203}, mesh = {Animals ; Campylobacter Infections/microbiology ; Campylobacter jejuni/*genetics ; Chickens ; Chloramphenicol Resistance/*genetics ; DNA, Bacterial ; *Gene Transfer, Horizontal ; Genetic Markers ; Genome, Bacterial ; Homologous Recombination ; Kanamycin Resistance/*genetics ; }, abstract = {Many epidemiological studies provide us with the evidence of horizontal gene transfer (HGT) contributing to the bacterial genomic diversity that benefits the bacterial populations with increased ability to adapt to the dynamic environments. Campylobacter jejuni, a major cause of acute enteritis in the U.S., often linked with severe post-infection neuropathies, has been reported to exhibit a non-clonal population structure and comparatively higher strain-level genetic variation. In this study, we provide evidence of the HGT of chromosomally encoded genetic markers between C. jejuni cells in the biphasic MH medium. We used two C. jejuni NCTC-11168 mutants harbouring distinct antibiotic-resistance genes [chloramphenicol (Cm) and kanamycin (Km)] present at two different neutral genomic loci. Cultures of both marker strains were mixed together and incubated for 5 hrs, then plated on MH agar plates supplemented with both antibiotics. The recombinant cells with double antibiotic markers were generated at the frequency of 0.02811 ± 0.0035% of the parental strains. PCR assays using locus-specific primers confirmed that transfer of the antibiotic-resistance genes was through homologous recombination. Also, the addition of chicken cecal content increased the recombination efficiency approximately up to 10-fold as compared to the biphasic MH medium (control) at P < 0.05. Furthermore, treating the co-culture with DNase I decreased the available DNA, which in turn significantly reduced recombination efficiency by 99.92% (P < 0.05). We used the cell-free supernatant of 16 hrs-culture of Wild-type C. jejuni as a template for PCR and found DNA sequences from six different genomic regions were easily amplified, indicating the presence of released chromosomal DNA in the culture supernatant. Our findings suggest that HGT in C. jejuni is facilitated in the chicken gut environment contributing to in vivo genomic diversity. Additionally, C. jejuni might have an active mechanism to release its chromosomal DNA into the extracellular environment, further expediting HGT in C. jejuni populations.}, }
@article {pmid33103573, year = {2020}, author = {Zhang, J and Liu, G and Zhang, X and Chang, Y and Wang, S and He, W and Sun, W and Chen, D and Murchie, AIH}, title = {Aminoglycoside riboswitch control of the expression of integron associated aminoglycoside resistance adenyltransferases.}, journal = {Virulence}, volume = {11}, number = {1}, pages = {1432-1442}, pmid = {33103573}, issn = {2150-5608}, mesh = {Acetyltransferases/*genetics ; Aminoglycosides/*genetics/metabolism ; Base Sequence ; DNA, Bacterial/genetics ; Drug Resistance, Microbial/*genetics ; Integrons/*genetics ; Pseudomonas fluorescens/genetics/pathogenicity ; Recombination, Genetic ; *Riboswitch ; }, abstract = {The proliferation of antibiotic resistance has its origins in horizontal gene transfer. The class 1 integrons mediate gene transfer by assimilating antibiotic-resistance genes through site-specific recombination. For the class 1 integrons the first assimilated gene normally encodes an aminoglycoside antibiotic resistance protein which is either an aminoglycoside acetyltransferase (AAC), nucleotidyltransferase - (ANT), or adenyl transferase (AAD). An aminoglycoside-sensing riboswitch RNA in the leader RNA of AAC/AAD that controls the expression of aminoglycoside resistance genes has been previously described. Here we explore the relationship between the recombinant products of integron recombination and a series of candidate riboswitch RNAs in the 5' UTR of aad (aminoglycoside adenyltransferases) genes. The RNA sequences from the 5' UTR of the aad genes from pathogenic strains that are the products of site-specific DNA recombination by class 1 integrons were investigated. Reporter assays, MicroScale Thermophoresis (MST) and covariance analysis revealed that a functional aminoglycoside-sensing riboswitch was selected at the DNA level through integron-mediated site-specific recombination. This study explains the close association between integron recombination and the aminoglycoside-sensing riboswitch RNA.}, }
@article {pmid33099099, year = {2020}, author = {Gong, P and Liu, H and Xin, Y and Wang, G and Dai, X and Yao, J}, title = {Composting of oxytetracycline fermentation residue in combination with hydrothermal pretreatment for reducing antibiotic resistance genes enrichment.}, journal = {Bioresource technology}, volume = {318}, number = {}, pages = {124271}, doi = {10.1016/j.biortech.2020.124271}, pmid = {33099099}, issn = {1873-2976}, mesh = {Anti-Bacterial Agents/pharmacology ; *Composting ; Drug Resistance, Microbial/genetics ; Fermentation ; Genes, Bacterial/genetics ; Manure ; *Oxytetracycline ; }, abstract = {Hydrothermal pretreatment can efficiently remove the residual antibiotics in oxytetracycline fermentation residue (OFR), but its effect on antibiotic resistance genes (ARGs) during composting remains unclear. This study compared the shifts in bacterial community and evolutions in ARGs and integrons during different composting processes of OFRs with and without hydrothermal pretreatment. The results demonstrated that hydrothermal pretreatment increased the bacterial alpha diversity at the initial phase, and increased the relative abundances of Proteobacteria and Actinobacteria but decreased that of Bacteroidetes at the final phase by inactivating mycelia and removing residual oxytetracycline. Composting process inevitably elevated the abundance and relative abundance of ARGs. However, the increase in ARGs was significantly reduced by hydrothermal pretreatment, because the removal of oxytetracycline decreased their potential host bacteria and inhibited their horizontal gene transfer. The results demonstrated that hydrothermal pretreatment is an efficient strategy to reduce the enrichment of ARGs during the OFR composting.}, }
@article {pmid33098671, year = {2021}, author = {Taylor, EA and Ossa-Trujillo, C and Vinasco, J and Jordan, ER and García Buitrago, JA and Hagevoort, R and Norman, KN and Lawhon, SD and Piñeiro, JM and Levent, G and Scott, HM}, title = {Use of critically important antimicrobial classes early in life may adversely impact bacterial resistance profiles during adult years: potential co-selection for plasmid-borne fluoroquinolone and macrolide resistance via extended-spectrum beta-lactam use in dairy cattle.}, journal = {Letters in applied microbiology}, volume = {72}, number = {3}, pages = {220-224}, doi = {10.1111/lam.13419}, pmid = {33098671}, issn = {1472-765X}, support = {2016-68003-24607//National Institute of Food and Agriculture/ ; //United States Department of Agriculture/ ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Cattle ; Cattle Diseases/drug therapy/microbiology ; Cephalosporin Resistance/*genetics ; Cephalosporins/*pharmacology ; Drug Resistance, Multiple, Bacterial/*drug effects/genetics ; Escherichia coli/*drug effects/genetics/isolation &amp; purification ; Escherichia coli Infections/microbiology/veterinary ; Fluoroquinolones/pharmacology ; Gene Transfer, Horizontal/genetics ; Longitudinal Studies ; Macrolides/pharmacology ; Plasmids/genetics ; Selection, Genetic/*drug effects/genetics ; United States ; }, abstract = {The transfer of antimicrobial resistance genes commonly occurs via vertical and horizontal gene transfer, as such genes are often found on the same mobile genetic element. This occurrence can lead to the co-selection of resistance to antimicrobials without their application. Dairy cattle located in the south-western United States were enrolled in a matched-pair longitudinal study to evaluate the effects of a two-dose ceftiofur treatment for metritis on levels of third-generation cephalosporin resistance among faecal Escherichia coli temporally. Escherichia coli chosen for further investigation were isolated on selective media, harboured extended-spectrum beta-lactam, fluoroquinolone and macrolide resistance genes. This combination has previously been unreported; importantly, it included genes encoding for resistance to antibiotics that can only be used in dairy cattle less than 20 months of age. Fluoroquinolones, macrolides and third and higher generation cephalosporins are considered critically important and highest priority for human medicine by the World Health Organization.}, }
@article {pmid33095240, year = {2021}, author = {Erber, L and Betat, H and Mörl, M}, title = {CCA-Addition Gone Wild: Unusual Occurrence and Phylogeny of Four Different tRNA Nucleotidyltransferases in Acanthamoeba castellanii.}, journal = {Molecular biology and evolution}, volume = {38}, number = {3}, pages = {1006-1017}, pmid = {33095240}, issn = {1537-1719}, mesh = {Acanthamoeba castellanii/*enzymology/genetics ; Desulfovibrio/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Multigene Family ; Phylogeny ; RNA Nucleotidyltransferases/genetics/*metabolism ; }, abstract = {tRNAs are important players in the protein synthesis machinery, where they act as adapter molecules for translating the mRNA codons into the corresponding amino acid sequence. In a series of highly conserved maturation steps, the primary transcripts are converted into mature tRNAs. In the amoebozoan Acanthamoeba castellanii, a highly unusual evolution of some of these processing steps was identified that are based on unconventional RNA polymerase activities. In this context, we investigated the synthesis of the 3'-terminal CCA-end that is added posttranscriptionally by a specialized polymerase, the tRNA nucleotidyltransferase (CCA-adding enzyme). The majority of eukaryotic organisms carry only a single gene for a CCA-adding enzyme that acts on both the cytosolic and the mitochondrial tRNA pool. In a bioinformatic analysis of the genome of this organism, we identified a surprising multitude of genes for enzymes that contain the active site signature of eukaryotic/eubacterial tRNA nucleotidyltransferases. In vitro activity analyses of these enzymes revealed that two proteins represent bona fide CCA-adding enzymes, one of them carrying an N-terminal sequence corresponding to a putative mitochondrial target signal. The other enzymes have restricted activities and represent CC- and A-adding enzymes, respectively. The A-adding enzyme is of particular interest, as its sequence is closely related to corresponding enzymes from Proteobacteria, indicating a horizontal gene transfer. Interestingly, this unusual diversity of nucleotidyltransferase genes is not restricted to Acanthamoeba castellanii but is also present in other members of the Acanthamoeba genus, indicating an ancient evolutionary trait.}, }
@article {pmid33095158, year = {2020}, author = {Greenhalgh, R and Dermauw, W and Glas, JJ and Rombauts, S and Wybouw, N and Thomas, J and Alba, JM and Pritham, EJ and Legarrea, S and Feyereisen, R and Van de Peer, Y and Van Leeuwen, T and Clark, RM and Kant, MR}, title = {Genome streamlining in a minute herbivore that manipulates its host plant.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, pmid = {33095158}, issn = {2050-084X}, support = {773902-SuperPests//Horizon 2020 - Research and Innovation Framework Programme/International ; STW-GAP/13550//Netherlands Organisation for Scientific Research/International ; 12T9818N//Research Foundation Flanders/International ; 772026-POLYADAPT//European Union Horizon 2020 research and innovation program/International ; 1457346//USA National Science Foundation/International ; 1274917N//Research Foundation Flanders/International ; 1457346//National Science Foundation/International ; T32 GM007464/GM/NIGMS NIH HHS/United States ; STW-VIDI/13492//Netherlands Organisation for Scientific Research/International ; 773902-SuperPests//European Union Horizon 2020 research and innovation program/International ; }, mesh = {Animals ; Evolution, Molecular ; *Genome ; *Herbivory ; Host-Pathogen Interactions ; Solanum lycopersicum/*parasitology ; Mites/*genetics ; Phylogeny ; }, abstract = {The tomato russet mite, Aculops lycopersici, is among the smallest animals on earth. It is a worldwide pest on tomato and can potently suppress the host's natural resistance. We sequenced its genome, the first of an eriophyoid, and explored whether there are genomic features associated with the mite's minute size and lifestyle. At only 32.5 Mb, the genome is the smallest yet reported for any arthropod and, reminiscent of microbial eukaryotes, exceptionally streamlined. It has few transposable elements, tiny intergenic regions, and is remarkably intron-poor, as more than 80% of coding genes are intronless. Furthermore, in accordance with ecological specialization theory, this defense-suppressing herbivore has extremely reduced environmental response gene families such as those involved in chemoreception and detoxification. Other losses associate with this species' highly derived body plan. Our findings accelerate the understanding of evolutionary forces underpinning metazoan life at the limits of small physical and genome size.}, }
@article {pmid33091798, year = {2020}, author = {Yu, H and Yang, J and Cui, H and Li, Z and Jia, F and Chen, J and Li, X}, title = {Effects of plant density on tillering in the weed grass Aegilops tauschii Coss. and its phytohormonal regulation.}, journal = {Plant physiology and biochemistry : PPB}, volume = {157}, number = {}, pages = {70-78}, doi = {10.1016/j.plaphy.2020.10.013}, pmid = {33091798}, issn = {1873-2690}, mesh = {Aegilops/*physiology ; China ; Plant Growth Regulators/*physiology ; Plant Weeds/*physiology ; Seeds/*physiology ; }, abstract = {Aegilops tauschii Coss, a notorious wheat field weed, poses a serious threat to wheat in China. Tillers are an important agronomic tool for yield. In this study, a total of 12 Ae. tauschii populations were collected from China to investigate the effect of plant density on tiller occurrence and its phytohormonal regulation. We assayed the growth parameters of Ae. tauschii and the levels of endogenous hormones at different plant densities. The results showed that plant density had a significant effect on the quantity and quality of Ae. tauschii seeds produced per plant. In particular, the tiller and spike numbers per plant were negatively affected by plant density (P < 0.0001). The contents of 13 endogenous hormones in the tiller nodes changed in response to plant density. Among them, indole-3-acetic acid (IAA) and gibberellin (GA) positively responded to plant density. However, the reverse result was found for cytokinin (CTK). Interestingly, phylogenetic tree analysis of auxin (AeYUCCA), CK (AeIPT) and GA (AeCPS) biosynthesis related genes found that phylogenies in the Gramineae for the three different genes were various, hinting at horizontal gene transfer. Moreover, the dynamics of the expression of AeYUCCA, AeIPT and AeCPS were roughly consistent with their phytohormone contents during tillering stage. When externally sprayed on plants of Ae. tauschii, 2,4-D isooctyl ester and GA3 markedly reduced its tillering while 6-BA had no significant effect.}, }
@article {pmid33085588, year = {2020}, author = {Gurung, D and Blumenthal, RM}, title = {Distribution of RecBCD and AddAB recombination-associated genes among bacteria in 33 phyla.}, journal = {Microbiology (Reading, England)}, volume = {166}, number = {11}, pages = {1047-1064}, doi = {10.1099/mic.0.000980}, pmid = {33085588}, issn = {1465-2080}, mesh = {Amino Acid Sequence ; Bacteria/classification/*genetics ; Base Sequence ; Conserved Sequence ; DNA, Bacterial/genetics ; Evolution, Molecular ; Exodeoxyribonuclease V/*genetics ; Exodeoxyribonucleases/*genetics ; Gene Transfer, Horizontal/genetics ; Phylogeny ; Rec A Recombinases/genetics ; Recombination, Genetic/*genetics ; }, abstract = {Homologous recombination plays key roles in fundamental processes such as recovery from DNA damage and in bacterial horizontal gene transfer, yet there are still open questions about the distribution of recognized components of recombination machinery among bacteria and archaea. RecBCD helicase-nuclease plays a central role in recombination among Gammaproteobacteria like Escherichia coli; while bacteria in other phyla, like the Firmicute Bacillus subtilis, use the related AddAB complex. The activity of at least some of these complexes is controlled by short DNA sequences called crossover hotspot instigator (Chi) sites. When RecBCD or AddAB complexes encounter an autologous Chi site during unwinding, they introduce a nick such that ssDNA with a free end is available to invade another duplex. If homologous DNA is present, RecA-dependent homologous recombination is promoted; if not (or if no autologous Chi site is present) the RecBCD/AddAB complex eventually degrades the DNA. We examined the distribution of recBCD and addAB genes among bacteria, and sought ways to distinguish them unambiguously. We examined bacterial species among 33 phyla, finding some unexpected distribution patterns. RecBCD and addAB are less conserved than recA, with the orthologous recB and addA genes more conserved than the recC or addB genes. We were able to classify RecB vs. AddA and RecC vs. AddB in some bacteria where this had not previously been done. We used logo analysis to identify sequence segments that are conserved, but differ between the RecBC and AddAB proteins, to help future differentiation between members of these two families.}, }
@article {pmid33082253, year = {2020}, author = {Ghanem, M and Dubé, JY and Wang, J and McIntosh, F and Houle, D and Domenech, P and Reed, MB and Raman, S and Buter, J and Minnaard, AJ and Moody, DB and Behr, MA}, title = {Heterologous Production of 1-Tuberculosinyladenosine in Mycobacterium kansasii Models Pathoevolution towards the Transcellular Lifestyle of Mycobacterium tuberculosis.}, journal = {mBio}, volume = {11}, number = {5}, pages = {}, pmid = {33082253}, issn = {2150-7511}, support = {FND-148362//CIHR/Canada ; }, mesh = {Animals ; Culture Media/chemistry ; Evolution, Molecular ; Female ; Hydrogen-Ion Concentration ; Lipids/*biosynthesis ; Lung/microbiology ; Macrophages/microbiology ; Male ; Mice ; Mice, Inbred C57BL ; Mycobacterium kansasii/*genetics/physiology ; Mycobacterium tuberculosis/*genetics/physiology ; Tuberculosis/microbiology ; }, abstract = {Mycobacterium kansasii is an environmental nontuberculous mycobacterium that causes opportunistic tuberculosis-like disease. It is one of the most closely related species to the Mycobacterium tuberculosis complex. Using M. kansasii as a proxy for the M. kansasii-M. tuberculosis common ancestor, we asked whether introducing the M. tuberculosis-specific gene pair Rv3377c-Rv3378c into M. kansasii affects the course of experimental infection. Expression of these genes resulted in the production of an adenosine-linked lipid species, known as 1-tuberculosinyladenosine (1-TbAd), but did not alter growth in vitro under standard conditions. Production of 1-TbAd enhanced growth of M. kansasii under acidic conditions through a bacterial cell-intrinsic mechanism independent of controlling pH in the bulk extracellular and intracellular spaces. Production of 1-TbAd led to greater burden of M. kansasii in the lungs of C57BL/6 mice during the first 24 h after infection, and ex vivo infections of alveolar macrophages recapitulated this phenotype within the same time frame. However, in long-term infections, production of 1-TbAd resulted in impaired bacterial survival in both C57BL/6 mice and Ccr2[-/-] mice. We have demonstrated that M. kansasii is a valid surrogate of M. tuberculosis to study virulence factors acquired by the latter organism, yet shown the challenge inherent to studying the complex evolution of mycobacterial pathogenicity with isolated gene complementation.IMPORTANCE This work sheds light on the role of the lipid 1-tuberculosinyladenosine in the evolution of an environmental ancestor to M. tuberculosis On a larger scale, it reinforces the importance of horizontal gene transfer in bacterial evolution and examines novel models and methods to provide a better understanding of the subtle effects of individual M. tuberculosis-specific virulence factors in infection settings that are relevant to the pathogen.}, }
@article {pmid33081925, year = {2020}, author = {Wickramasinghe, NC and Steele, EJ and Klyce, B and Tokoro, G and Wickramasinghe, DT}, title = {The sociology of science and generality of the DNA/RNA/protein paradigm throughout the cosmos.}, journal = {Advances in genetics}, volume = {106}, number = {}, pages = {45-60}, doi = {10.1016/bs.adgen.2020.03.005}, pmid = {33081925}, issn = {0065-2660}, mesh = {Animals ; Biological Evolution ; DNA/*genetics ; Earth, Planet ; Gene Transfer, Horizontal/genetics ; Humans ; Proteins/*genetics ; RNA/*genetics ; Retroviridae/genetics ; Sociology ; }, abstract = {The theory of cometary panspermia argues that life cannot have originated on Earth in the time available. It must have an ultimate, but still undiscovered cosmological source. The origin of life remains an open question. Life on Earth was introduced by impacting comets, and its further evolution was driven by the subsequent acquisition of cosmically derived genes. Explicit predictions of this theory stating how the acquisition of new genes drives evolution, are compared with recent developments in relation to horizontal gene transfer, and the role of retroviruses in evolution. Precisely stated predictions of the theory of cometary panspermia are shown to have been verified.}, }
@article {pmid33081846, year = {2020}, author = {Bowler, P and Murphy, C and Wolcott, R}, title = {Biofilm exacerbates antibiotic resistance: Is this a current oversight in antimicrobial stewardship?.}, journal = {Antimicrobial resistance and infection control}, volume = {9}, number = {1}, pages = {162}, pmid = {33081846}, issn = {2047-2994}, mesh = {Anti-Bacterial Agents/pharmacology ; Antimicrobial Stewardship/*methods ; Biofilms/*growth &amp; development ; Cross Infection/drug therapy/*prevention &amp; control ; *Drug Resistance, Microbial ; Gene Transfer, Horizontal ; Humans ; Mutation ; }, abstract = {OBJECTIVE: To raise awareness of the role of environmental biofilm in the emergence and spread of antibiotic resistance and its consideration in antimicrobial stewardship.<br><br>BACKGROUND: Antibiotic resistance is a major threat to public health. Overuse of antibiotics, increased international travel, and genetic promiscuity amongst bacteria have contributed to antibiotic resistance, and global containment efforts have so far met with limited success. Antibiotic resistance is a natural mechanism by which bacteria have adapted to environmental threats over billions of years and is caused either by genetic mutations or by horizontal gene transfer. Another ancient survival strategy involves bacteria existing within a self-produced polymeric matrix, which today is termed biofilm. Biofilm similarly enables bacterial tolerance to environmental threats, and also encourages the transfer of antibiotic resistance genes between bacterial species. This natural and ubiquitous mode of bacterial life has not been considered amongst strategies to tackle antibiotic resistance in healthcare facilities, despite its ability to significantly enhance bacterial survival and persistence, and to encourage antibiotic resistance.<br><br>CONCLUSION: Biofilm must be considered synonymously with antibiotic resistance because of its proficiency in transferring resistance genes as well as its innate phenotypic tolerance to antibiotics. Although biofilm falls outside of the current definition of antimicrobial stewardship, greater awareness of the existence, ubiquity, and consequences of environmental biofilm amongst healthcare practitioners is crucial to improving hygiene practices and controlling the emergence and spread of antibiotic resistance in healthcare facilities.}, }
@article {pmid33081703, year = {2020}, author = {Duplouy, A and Pranter, R and Warren-Gash, H and Tropek, R and Wahlberg, N}, title = {Towards unravelling Wolbachia global exchange: a contribution from the Bicyclus and Mylothris butterflies in the Afrotropics.}, journal = {BMC microbiology}, volume = {20}, number = {1}, pages = {319}, pmid = {33081703}, issn = {1471-2180}, support = {790531//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; 1328944//Academy of Finland/ ; UNCE204069//Charles University/ ; PRIMUS/17/SCI/8//Charles University/ ; Waitt Grant W163-11//National Geographic Society/ ; 2015-04441//Swedish Research Council/ ; }, mesh = {Africa ; Animals ; Biodiversity ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Geography ; Lepidoptera/genetics/*physiology ; Phylogeny ; *Symbiosis ; Wolbachia/genetics/*physiology ; }, abstract = {BACKGROUND: Phylogenetically closely related strains of maternally inherited endosymbiotic bacteria are often found in phylogenetically divergent, and geographically distant insect host species. The interspecies transfer of the symbiont Wolbachia has been thought to have occurred repeatedly, facilitating its observed global pandemic. Few ecological interactions have been proposed as potential routes for the horizontal transfer of Wolbachia within natural insect communities. These routes are however likely to act only at the local scale, but how they may support the global distribution of some Wolbachia strains remains unclear.<br><br>RESULTS: Here, we characterize the Wolbachia diversity in butterflies from the tropical forest regions of central Africa to discuss transfer at both local and global scales. We show that numerous species from both the Mylothris (family Pieridae) and Bicyclus (family Nymphalidae) butterfly genera are infected with similar Wolbachia strains, despite only minor interclade contacts across the life cycles of the species within their partially overlapping ecological niches. The phylogenetic distance and differences in resource use between these genera rule out the role of ancestry, hybridization, and shared host-plants in the interspecies transfer of the symbiont. Furthermore, we could not identify any shared ecological factors to explain the presence of the strains in other arthropod species from other habitats, or even ecoregions.<br><br>CONCLUSION: Only the systematic surveys of the Wolbachia strains from entire species communities may offer the material currently lacking for understanding how Wolbachia may transfer between highly different and unrelated hosts, as well as across environmental scales.}, }
@article {pmid33081159, year = {2020}, author = {Daniel, S and Goldlust, K and Quebre, V and Shen, M and Lesterlin, C and Bouet, JY and Yamaichi, Y}, title = {Vertical and Horizontal Transmission of ESBL Plasmid from Escherichia coli O104:H4.}, journal = {Genes}, volume = {11}, number = {10}, pages = {}, pmid = {33081159}, issn = {2073-4425}, mesh = {Anti-Bacterial Agents/pharmacology ; *Conjugation, Genetic ; Escherichia coli Infections/microbiology/*transmission ; Escherichia coli O104/*genetics ; Escherichia coli Proteins/*genetics ; *Gene Transfer, Horizontal ; Humans ; Plasmids/*genetics ; Toxin-Antitoxin Systems/genetics ; beta-Lactam Resistance/*genetics ; }, abstract = {Multidrug resistance (MDR) often results from the acquisition of mobile genetic elements (MGEs) that encode MDR gene(s), such as conjugative plasmids. The spread of MDR plasmids is founded on their ability of horizontal transference, as well as their faithful inheritance in progeny cells. Here, we investigated the genetic factors involved in the prevalence of the IncI conjugative plasmid pESBL, which was isolated from the Escherichia coli O104:H4 outbreak strain in Germany in 2011. Using transposon-insertion sequencing, we identified the pESBL partitioning locus (par). Genetic, biochemical and microscopic approaches allowed pESBL to be characterized as a new member of the Type Ib partitioning system. Inactivation of par caused mis-segregation of pESBL followed by post-segregational killing (PSK), resulting in a great fitness disadvantage but apparent plasmid stability in the population of viable cells. We constructed a variety of pESBL derivatives with different combinations of mutations in par, conjugational transfer (oriT) and pnd toxin-antitoxin (TA) genes. Only the triple mutant exhibited plasmid-free cells in viable cell populations. Time-lapse tracking of plasmid dynamics in microfluidics indicated that inactivation of pnd improved the survival of plasmid-free cells and allowed oriT-dependent re-acquisition of the plasmid. Altogether, the three factors-active partitioning, toxin-antitoxin and conjugational transfer-are all involved in the prevalence of pESBL in the E. coli population.}, }
@article {pmid33079312, year = {2021}, author = {Lee, GE and Kim, JJ and Kim, HS and Sul, WJ}, title = {Metagenomic analysis of the dust particles collected from the suction tube and the suction funnel of a dermatological laser smoke evacuator system.}, journal = {Lasers in medical science}, volume = {36}, number = {6}, pages = {1249-1260}, pmid = {33079312}, issn = {1435-604X}, support = {Graduate Research Scholarship in 2017//Chung-Ang University/ ; 2019R1A4A1024764//National Research Foundation of Korea/ ; 2020R1F1A1048238//National Research Foundation of Korea/ ; }, mesh = {Actinobacteria ; Brevibacterium ; Dust ; Humans ; Laser Therapy/instrumentation ; *Metagenome ; Smoke ; Suction/instrumentation ; }, abstract = {In the last few decades, there has essentially been an explosion in the use of lasers in medicine, especially in the area of cosmetic dermatology. Potentially harmful substances are liberated when tissues are vaporized with laser. This creates numerous risks, including the spread of infectious disease. Smoke evacuators are devices that capture and filter laser plume, thereby maintaining a safe environment for the surgical team and patient. Our aim was to characterize the microbial community structure within the suction tube and funnel of the smoke evacuator system, identify their origin, and evaluate pathogenicity. Dust particles were collected from the instruments with a cotton swab. DNA was extracted from the swabs and the transport media, and sequencing was performed using the Illumina HiSeq Xplatform. Metagenomic analysis was conducted using the Empowering the Development of Genomics Expertise (EDGE) Bioinformatics pipeline and custom Python scripts. The most abundant bacterial species were Micrococcus luteus and Brevibacterium casei in the suction tube, and Dermacoccus sp. Ellin 185 and Janibacter hoylei in the suction funnel. A total of 15 medium- to high-quality metagenome-assembled genomes (MAGs) were constructed where we found 104 antibiotic-resistant genes (ARGs) and 741 virulence factors. Findings indicate that the suction tube and funnel are likely a reservoir of virulence factor genes and ARGs, which can possibly be passed on to other bacteria via horizontal gene transfer. We would like to emphasize the health risk these microorganisms pose and the need to reevaluate the current hygiene standards with regard to the smoke evacuator system.}, }
@article {pmid33078828, year = {2020}, author = {Sharda, M and Badrinarayanan, A and Seshasayee, ASN}, title = {Evolutionary and Comparative Analysis of Bacterial Nonhomologous End Joining Repair.}, journal = {Genome biology and evolution}, volume = {12}, number = {12}, pages = {2450-2466}, pmid = {33078828}, issn = {1759-6653}, support = {//Wellcome Trust/United Kingdom ; IA/I/16/2/502711/WTDBT_/DBT-Wellcome Trust India Alliance/India ; }, mesh = {Bacteria/*genetics ; Base Composition ; *Biological Evolution ; *DNA End-Joining Repair ; Gene Transfer, Horizontal ; Genome Size ; *Selection, Genetic ; }, abstract = {DNA double-strand breaks (DSBs) are a threat to genome stability. In all domains of life, DSBs are faithfully fixed via homologous recombination. Recombination requires the presence of an uncut copy of duplex DNA which is used as a template for repair. Alternatively, in the absence of a template, cells utilize error-prone nonhomologous end joining (NHEJ). Although ubiquitously found in eukaryotes, NHEJ is not universally present in bacteria. It is unclear as to why many prokaryotes lack this pathway. Toward understanding what could have led to the current distribution of bacterial NHEJ, we carried out comparative genomics and phylogenetic analysis across ∼6,000 genomes. Our results show that this pathway is sporadically distributed across the phylogeny. Ancestral reconstruction further suggests that NHEJ was absent in the eubacterial ancestor and can be acquired via specific routes. Integrating NHEJ occurrence data for archaea, we also find evidence for extensive horizontal exchange of NHEJ genes between the two kingdoms as well as across bacterial clades. The pattern of occurrence in bacteria is consistent with correlated evolution of NHEJ with key genome characteristics of genome size and growth rate; NHEJ presence is associated with large genome sizes and/or slow growth rates, with the former being the dominant correlate. Given the central role these traits play in determining the ability to carry out recombination, it is possible that the evolutionary history of bacterial NHEJ may have been shaped by requirement for efficient DSB repair.}, }
@article {pmid33076221, year = {2020}, author = {Hammer-Dedet, F and Jumas-Bilak, E and Licznar-Fajardo, P}, title = {The Hydric Environment: A Hub for Clinically Relevant Carbapenemase Encoding Genes.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {9}, number = {10}, pages = {}, pmid = {33076221}, issn = {2079-6382}, abstract = {Carbapenems are β-lactams antimicrobials presenting a broad activity spectrum and are considered as last-resort antibiotic. Since the 2000s, carbapenemase producing Enterobacterales (CPE) have emerged and are been quickly globally spreading. The global dissemination of carbapenemase encoding genes (CEG) within clinical relevant bacteria is attributed in part to its location onto mobile genetic elements. During the last decade, carbapenemase producing bacteria have been isolated from non-human sources including the aquatic environment. Aquatic ecosystems are particularly impacted by anthropic activities, which conduce to a bidirectional exchange between aquatic environments and human beings and therefore the aquatic environment may constitute a hub for CPE and CEG. More recently, the isolation of autochtonous aquatic bacteria carrying acquired CEG have been reported and suggest that CEG exchange by horizontal gene transfer occurred between allochtonous and autochtonous bacteria. Hence, aquatic environment plays a central role in persistence, dissemination and emergence of CEG both within environmental ecosystem and human beings, and deserves to be studied with particular attention.}, }
@article {pmid33075053, year = {2020}, author = {Nguyen, M and Olson, R and Shukla, M and VanOeffelen, M and Davis, JJ}, title = {Predicting antimicrobial resistance using conserved genes.}, journal = {PLoS computational biology}, volume = {16}, number = {10}, pages = {e1008319}, pmid = {33075053}, issn = {1553-7358}, support = {75N93019C00076/AI/NIAID NIH HHS/United States ; }, mesh = {Algorithms ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics ; Conserved Sequence/*genetics ; Drug Resistance, Bacterial/*genetics ; Genome, Bacterial/*genetics ; Genomics/*methods ; *Machine Learning ; Phenotype ; }, abstract = {A growing number of studies are using machine learning models to accurately predict antimicrobial resistance (AMR) phenotypes from bacterial sequence data. Although these studies are showing promise, the models are typically trained using features derived from comprehensive sets of AMR genes or whole genome sequences and may not be suitable for use when genomes are incomplete. In this study, we explore the possibility of predicting AMR phenotypes using incomplete genome sequence data. Models were built from small sets of randomly-selected core genes after removing the AMR genes. For Klebsiella pneumoniae, Mycobacterium tuberculosis, Salmonella enterica, and Staphylococcus aureus, we report that it is possible to classify susceptible and resistant phenotypes with average F1 scores ranging from 0.80-0.89 with as few as 100 conserved non-AMR genes, with very major error rates ranging from 0.11-0.23 and major error rates ranging from 0.10-0.20. Models built from core genes have predictive power in cases where the primary AMR mechanisms result from SNPs or horizontal gene transfer. By randomly sampling non-overlapping sets of core genes, we show that F1 scores and error rates are stable and have little variance between replicates. Although these small core gene models have lower accuracies and higher error rates than models built from the corresponding assembled genomes, the results suggest that sufficient variation exists in the core non-AMR genes of a species for predicting AMR phenotypes.}, }
@article {pmid33074084, year = {2020}, author = {Fang, Z and Zhou, H}, title = {Identification of the conjugative and mobilizable plasmid fragments in the plasmidome using sequence signatures.}, journal = {Microbial genomics}, volume = {6}, number = {11}, pages = {}, pmid = {33074084}, issn = {2057-5858}, mesh = {Bacteria/*genetics ; Base Sequence/genetics ; Computational Biology/*methods ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial/genetics ; Microbiota/genetics ; Plasmids/*genetics ; Sequence Analysis, DNA ; }, abstract = {Plasmids are the key element in horizontal gene transfer in the microbial community. Recently, a large number of experimental and computational methods have been developed to obtain the plasmidomes of microbial communities. Distinguishing transmissible plasmid sequences, which are derived from conjugative or at least mobilizable plasmids, from non-transmissible plasmid sequences in the plasmidome is essential for understanding the diversity of plasmids and how they regulate the microbial community. Unfortunately, due to the highly fragmented characteristics of DNA sequences in the plasmidome, effective identification methods are lacking. In this work, we used information entropy from information theory to assess the randomness of synonymous codon usage over 4424 plasmid genomes. The results showed that for all amino acids, the choice of a synonymous codon in conjugative and mobilizable plasmids is more random than that in non-transmissible plasmids, indicating that transmissible plasmids have different sequence signatures from non-transmissible plasmids. Inspired by this phenomenon, we further developed a novel algorithm named PlasTrans. PlasTrans takes the triplet code sequences and base sequences of plasmid DNA fragments as input and uses the convolutional neural network of the deep learning technique to further extract the more complex signatures of the plasmid sequences and identify the conjugative and mobilizable DNA fragments. Tests showed that PlasTrans could achieve an AUC of as high as 84-91%, even though the fragments only contained hundreds of base pairs. To the best of our knowledge, this is the first quantitative analysis of the difference in sequence signatures between transmissible and non-transmissible plasmids, and we developed the first tool to perform transferability annotation for DNA fragments in the plasmidome. We expect that PlasTrans will be a useful tool for researchers who analyse the properties of novel plasmids in the microbial community and horizontal gene transfer, especially the spread of resistance genes and virulence factors associated with plasmids. PlasTrans is freely available via https://github.com/zhenchengfang/PlasTrans.}, }
@article {pmid33067437, year = {2020}, author = {Scholz, M and Albanese, D and Tuohy, K and Donati, C and Segata, N and Rota-Stabelli, O}, title = {Large scale genome reconstructions illuminate Wolbachia evolution.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {5235}, pmid = {33067437}, issn = {2041-1723}, mesh = {Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Host Specificity ; Phylogeny ; Wolbachia/classification/*genetics/physiology ; }, abstract = {Wolbachia is an iconic example of a successful intracellular bacterium. Despite its importance as a manipulator of invertebrate biology, its evolutionary dynamics have been poorly studied from a genomic viewpoint. To expand the number of Wolbachia genomes, we screen over 30,000 publicly available shotgun DNA sequencing samples from 500 hosts. By assembling over 1000 Wolbachia genomes, we provide a substantial increase in host representation. Our phylogenies based on both core-genome and gene content provide a robust reference for future studies, support new strains in model organisms, and reveal recent horizontal transfers amongst distantly related hosts. We find various instances of gene function gains and losses in different super-groups and in cytoplasmic incompatibility inducing strains. Our Wolbachia-host co-phylogenies indicate that horizontal transmission is widespread at the host intraspecific level and that there is no support for a general Wolbachia-mitochondrial synchronous divergence.}, }
@article {pmid33066635, year = {2020}, author = {Dedeo, CL and Teschke, CM and Alexandrescu, AT}, title = {Keeping It Together: Structures, Functions, and Applications of Viral Decoration Proteins.}, journal = {Viruses}, volume = {12}, number = {10}, pages = {}, pmid = {33066635}, issn = {1999-4915}, support = {R01 GM076661/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Capsid/chemistry ; Capsid Proteins/chemistry/genetics ; DNA Packaging ; DNA Viruses/*genetics ; DNA, Viral ; Gene Transfer, Horizontal ; Host-Pathogen Interactions ; Mice ; Models, Molecular ; Protein Folding ; Structure-Activity Relationship ; Viral Proteins/*chemistry/*genetics ; Virion ; Virus Assembly ; }, abstract = {Decoration proteins are viral accessory gene products that adorn the surfaces of some phages and viral capsids, particularly tailed dsDNA phages. These proteins often play a "cementing" role, reinforcing capsids against accumulating internal pressure due to genome packaging, or environmental insults such as extremes of temperature or pH. Many decoration proteins serve alternative functions, including target cell recognition, participation in viral assembly, capsid size determination, or modulation of host gene expression. Examples that currently have structures characterized to high-resolution fall into five main folding motifs: β-tulip, β-tadpole, OB-fold, Ig-like, and a rare knotted α-helical fold. Most of these folding motifs have structure homologs in virus and target cell proteins, suggesting horizontal gene transfer was important in their evolution. Oligomerization states of decoration proteins range from monomers to trimers, with the latter most typical. Decoration proteins bind to a variety of loci on capsids that include icosahedral 2-, 3-, and 5-fold symmetry axes, as well as pseudo-symmetry sites. These binding sites often correspond to "weak points" on the capsid lattice. Because of their unique abilities to bind virus surfaces noncovalently, decoration proteins are increasingly exploited for technology, with uses including phage display, viral functionalization, vaccination, and improved nanoparticle design for imaging and drug delivery. These applications will undoubtedly benefit from further advances in our understanding of these versatile augmenters of viral functions.}, }
@article {pmid33066176, year = {2020}, author = {Wysocka, M and Zamudio, R and Oggioni, MR and Gołębiewska, J and Dudziak, A and Krawczyk, B}, title = {The New Klebsiellapneumoniae ST152 Variants with Hypermucoviscous Phenotype Isolated from Renal Transplant Recipients with Asymptomatic Bacteriuria-Genetic Characteristics by WGS.}, journal = {Genes}, volume = {11}, number = {10}, pages = {}, pmid = {33066176}, issn = {2073-4425}, mesh = {Bacterial Proteins/*genetics ; Bacteriuria/etiology/*pathology ; *Genetic Variation ; Humans ; Kidney Transplantation/*adverse effects ; Klebsiella Infections/*complications/microbiology ; Klebsiella pneumoniae/*genetics/isolation &amp; purification ; Phenotype ; Virulence Factors/*genetics ; Whole Genome Sequencing ; }, abstract = {Klebsiellapneumoniae (Kp) is one of the most important etiological factors of urinary tract infections in renal transplant (RTx) recipients. We described the antimicrobial susceptibility phenotypes and genomic features of two hypermucoviscous (HM) Kp isolates recovered from RTx recipients with asymptomatic bacteriuria (ABU). Using whole genome sequencing (WGS) data, we showed that the strains belong to the ST152 lineage with the KL149 capsular serotype, but without rmpA/magA genes, which is typical for HM+ hypervirulent Kp. These new strains carried virulence-associated genes that predispose for urinary tract infections (UTIs). Likewise, both strains carried the ecp gene encoding pilus common for extended-spectrum β-lactamase (ESBL) Escherichiacoli. Although the two ST152 isolates were closely related and differed by only nine single nucleotide polymorphisms (SNPs) in their chromosomes, they had different plasmid compositions and chromosomal elements, with isolate KP28872 carrying an ESBL plasmid and an integrative conjugative element. These two isolates are an example of the high plasticity of the K. pneumoniae accessory genome. The identification of patients with ABU matched with the correct epidemiological profiling of isolates could facilitate interventions to prevent or rapidly treat K. pneumoniae infections.}, }
@article {pmid33065245, year = {2020}, author = {Yang, J and Yuan, B and Wu, Y and Li, M and Li, J and Xu, D and Gao, ZH and Ma, G and Zhou, Y and Zuo, Y and Wang, J and Guo, Y}, title = {The wide distribution and horizontal transfers of beta satellite DNA in eukaryotes.}, journal = {Genomics}, volume = {112}, number = {6}, pages = {5295-5304}, doi = {10.1016/j.ygeno.2020.10.006}, pmid = {33065245}, issn = {1089-8646}, mesh = {Animals ; DNA, Satellite/*chemistry ; Eukaryota/genetics ; Gene Transfer, Horizontal ; Genetic Variation ; Genome ; Genome, Archaeal ; Genome, Bacterial ; Humans ; Polymerase Chain Reaction ; Primates/genetics ; Whole Genome Sequencing ; }, abstract = {Beta satellite DNA (satDNA), also known as Sau3A sequences, are repetitive DNA sequences reported in human and primate genomes. It is previously thought that beta satDNAs originated in old world monkeys and bursted in great apes. In this study, we searched 7821 genome assemblies of 3767 eukaryotic species and found that beta satDNAs are widely distributed across eukaryotes. The four major branches of eukaryotes, animals, fungi, plants and Harosa/SAR, all have multiple clades containing beta satDNAs. These results were also confirmed by searching whole genome sequencing data (SRA) and PCR assay. Beta satDNA sequences were found in all the primate clades, as well as in Dermoptera and Scandentia, indicating that the beta satDNAs in primates might originate in the common ancestor of Primatomorpha or Euarchonta. In contrast, the widely patchy distribution of beta satDNAs across eukaryotes presents a typical scenario of multiple horizontal transfers.}, }
@article {pmid33065010, year = {2020}, author = {Rozenberg, A and Oppermann, J and Wietek, J and Fernandez Lahore, RG and Sandaa, RA and Bratbak, G and Hegemann, P and Béjà, O}, title = {Lateral Gene Transfer of Anion-Conducting Channelrhodopsins between Green Algae and Giant Viruses.}, journal = {Current biology : CB}, volume = {30}, number = {24}, pages = {4910-4920.e5}, doi = {10.1016/j.cub.2020.09.056}, pmid = {33065010}, issn = {1879-0445}, mesh = {Animals ; Anions/metabolism ; Cell Line ; Channelrhodopsins/*genetics/metabolism ; Chlorophyta/*genetics/metabolism/radiation effects/virology ; *Gene Transfer, Horizontal ; *Genes, Viral ; Giant Viruses/*genetics/metabolism ; Hybrid Cells ; Light ; Metagenomics ; Mice ; Optogenetics ; Phylogeny ; Rats ; }, abstract = {Channelrhodopsins (ChRs) are light-gated ion channels widely used as optogenetic tools for manipulating neuronal activity. The currently characterized ChR families include green algal and cryptophyte cation-conducting ChRs (CCRs) and cryptophyte, haptophyte, and stramenopile anion-conducting ChRs (ACRs). Here, we report the discovery of a new family of phylogenetically distinct ChRs encoded by marine giant viruses and acquired from their unicellular green algal hosts. These previously unknown viral and green algal ChRs act as ACRs when expressed in cultured neuroblastoma-derived cells and are likely involved in behavioral responses to light.}, }
@article {pmid33062657, year = {2020}, author = {Hernandez, BG and Vinithakumari, AA and Sponseller, B and Tangudu, C and Mooyottu, S}, title = {Prevalence, Colonization, Epidemiology, and Public Health Significance of Clostridioides difficile in Companion Animals.}, journal = {Frontiers in veterinary science}, volume = {7}, number = {}, pages = {512551}, pmid = {33062657}, issn = {2297-1769}, abstract = {Clostridioides difficile, previously Clostrdium difficile, is a major cause of antibiotic-associated enteric disease in humans in hospital settings. Increased incidence of C. difficile infection (CDI) in community settings raises concerns over an alternative source of CDI for humans. The detection of genetically similar and toxigenic C. difficile isolates in companion animals, including asymptomatic pets, suggests the potential role of household pets as a source of community-associated CDI. The close association between companion animals and humans, in addition to the use of similar antibiotics in both species, could provide a selective advantage for the emergence of new C. difficile strains and thus increase the incidental transmission of CDI to humans. Therefore, screening household pets for C. difficile is becoming increasingly important from a public health standpoint and may become a part of routine testing in the future, for the benefit of susceptible or infected individuals within a household. In this review, we analyze available information on prevalence, pathophysiology, epidemiology, and molecular genetics of C. difficile infection, focusing on companion animals and evaluate the risk of pet-borne transmission of CDI as an emerging public health concern. Molecular epidemiological characterization of companion animal C. difficile strains could provide further insights into the interspecies transmission of CDI. The mosaic nature of C. difficile genomes and their susceptibility to horizontal gene transfer may facilitate the inter-mixing of genetic material, which could increase the possibility of the emergence of new community-associated CDI strains. However, detailed genome-wide characterization and comparative genome analysis are warranted to confirm this hypothesis.}, }
@article {pmid33058346, year = {2020}, author = {Stevison, LS and McGaugh, SE}, title = {It's time to stop sweeping recombination rate under the genome scan rug.}, journal = {Molecular ecology}, volume = {29}, number = {22}, pages = {4249-4253}, doi = {10.1111/mec.15690}, pmid = {33058346}, issn = {1365-294X}, mesh = {*Genome ; Genomics ; Hybridization, Genetic ; Recombination, Genetic ; *Selection, Genetic ; }, abstract = {Different parts of the genome can vary widely in their evolutionary histories and sequence divergence from other species. Indeed, some of the most interesting biology (e.g., hybridization, horizontal gene transfer, variable mutation rates across the genome) is revealed by the discordant relationships between taxa across the genome. The goal for much of evolutionary genetics is centred on understanding the evolutionary processes by which such varied signatures arise and are maintained. Many evolutionary genetics studies seek to identify signatures of positive selection between two closely related ecotypes or taxa by delineating regions with particularly high divergence relative to a genome-wide average, often termed "divergence outliers." In a From the Cover article in this issue of Molecular Ecology, Booker et al. take a major step forward in showing that recombination rate differences are sufficient to create false positive divergence outliers, even under neutrality. They demonstrate that the variance of genome scan metrics is especially high in regions with low recombination rates, consistent with previous work. Furthermore, they show that both relative and absolute measures of divergence (FST and DXY , respectively) as well as other commonly used statistics in genome scans (e.g., πW , Tajima's D and H12) all have similar covariance between variance and local recombination rate. Finally, Booker et al. show that low recombination regions will tend to produce more outliers if genome-wide averages are used as cut-offs to define genomic outliers. Booker et al.'s results suggest that recombination rate variation, even under neutral conditions, can shape genome scans for selection, and this important variable can no longer be ignored.}, }
@article {pmid33055207, year = {2020}, author = {Woods, LC and Gorrell, RJ and Taylor, F and Connallon, T and Kwok, T and McDonald, MJ}, title = {Horizontal gene transfer potentiates adaptation by reducing selective constraints on the spread of genetic variation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {43}, pages = {26868-26875}, pmid = {33055207}, issn = {1091-6490}, mesh = {Adaptation, Physiological/*genetics ; Anti-Bacterial Agents ; *Biological Evolution ; Drug Resistance, Bacterial/*genetics ; Gene Flow ; *Gene Transfer, Horizontal ; Genetic Fitness ; Genetic Variation ; Helicobacter pylori/*genetics ; Metronidazole ; Selection, Genetic ; }, abstract = {Horizontal gene transfer (HGT) confers the rapid acquisition of novel traits and is pervasive throughout microbial evolution. Despite the central role of HGT, the evolutionary forces that drive the dynamics of HGT alleles in evolving populations are poorly understood. Here, we show that HGT alters the evolutionary dynamics of genetic variation, so that deleterious genetic variants, including antibiotic resistance genes, can establish in populations without selection. We evolve antibiotic-sensitive populations of the human pathogen Helicobacter pylori in an environment without antibiotic but with HGT from an antibiotic-resistant isolate of H. pylori We find that HGT increases the rate of adaptation, with most horizontally transferred genetic variants establishing at a low frequency in the population. When challenged with antibiotic, this low-level variation potentiates adaptation, with HGT populations flourishing in conditions where nonpotentiated populations go extinct. By extending previous models of evolution under HGT, we evaluated the conditions for the establishment and spread of HGT-acquired alleles into recipient populations. We then used our model to estimate parameters of HGT and selection from our experimental evolution data. Together, our findings show how HGT can act as an evolutionary force that facilitates the spread of nonselected genetic variation and expands the adaptive potential of microbial populations.}, }
@article {pmid33055096, year = {2020}, author = {Zhou, Z and Charlesworth, J and Achtman, M}, title = {Accurate reconstruction of bacterial pan- and core genomes with PEPPAN.}, journal = {Genome research}, volume = {30}, number = {11}, pages = {1667-1679}, pmid = {33055096}, issn = {1549-5469}, support = {//Wellcome Trust/United Kingdom ; 202792/Z/16/Z//Wellcome Trust/United Kingdom ; BB/L020319/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Algorithms ; Bacteria/*classification ; Genes, Bacterial ; *Genome, Bacterial ; Genomics/*methods ; *Phylogeny ; Pseudogenes ; Software ; Streptococcus/classification/genetics ; }, abstract = {Bacterial genomes can contain traces of a complex evolutionary history, including extensive homologous recombination, gene loss, gene duplications, and horizontal gene transfer. To reconstruct the phylogenetic and population history of a set of multiple bacteria, it is necessary to examine their pangenome, the composite of all the genes in the set. Here we introduce PEPPAN, a novel pipeline that can reliably construct pangenomes from thousands of genetically diverse bacterial genomes that represent the diversity of an entire genus. PEPPAN outperforms existing pangenome methods by providing consistent gene and pseudogene annotations extended by similarity-based gene predictions, and identifying and excluding paralogs by combining tree- and synteny-based approaches. The PEPPAN package additionally includes PEPPAN_parser, which implements additional downstream analyses, including the calculation of trees based on accessory gene content or allelic differences between core genes. To test the accuracy of PEPPAN, we implemented SimPan, a novel pipeline for simulating the evolution of bacterial pangenomes. We compared the accuracy and speed of PEPPAN with four state-of-the-art pangenome pipelines using both empirical and simulated data sets. PEPPAN was more accurate and more specific than any of the other pipelines and was almost as fast as any of them. As a case study, we used PEPPAN to construct a pangenome of approximately 40,000 genes from 3052 representative genomes spanning at least 80 species of Streptococcus The resulting gene and allelic trees provide an unprecedented overview of the genomic diversity of the entire Streptococcus genus.}, }
@article {pmid33052805, year = {2020}, author = {Secaira-Morocho, H and Castillo, JA and Driks, A}, title = {Diversity and evolutionary dynamics of spore-coat proteins in spore-forming species of Bacillales.}, journal = {Microbial genomics}, volume = {6}, number = {11}, pages = {}, pmid = {33052805}, issn = {2057-5858}, mesh = {Bacillus subtilis/*genetics/metabolism ; Bacterial Proteins/*genetics/*metabolism ; Biological Evolution ; Genes, Bacterial/genetics ; Genome, Bacterial/genetics ; Phylogeny ; Spores, Bacterial/*genetics ; }, abstract = {Among members of the Bacillales order, there are several species capable of forming a structure called an endospore. Endospores enable bacteria to survive under unfavourable growth conditions and germinate when environmental conditions are favourable again. Spore-coat proteins are found in a multilayered proteinaceous structure encasing the spore core and the cortex. They are involved in coat assembly, cortex synthesis and germination. Here, we aimed to determine the diversity and evolutionary processes that have influenced spore-coat genes in various spore-forming species of Bacillales using an in silico approach. For this, we used sequence similarity searching algorithms to determine the diversity of coat genes across 161 genomes of Bacillales. The results suggest that among Bacillales, there is a well-conserved core genome, composed mainly by morphogenetic coat proteins and spore-coat proteins involved in germination. However, some spore-coat proteins are taxa-specific. The best-conserved genes among different species may promote adaptation to changeable environmental conditions. Because most of the Bacillus species harbour complete or almost complete sets of spore-coat genes, we focused on this genus in greater depth. Phylogenetic reconstruction revealed eight monophyletic groups in the Bacillus genus, of which three are newly discovered. We estimated the selection pressures acting over spore-coat genes in these monophyletic groups using classical and modern approaches and detected horizontal gene transfer (HGT) events, which have been further confirmed by scanning the genomes to find traces of insertion sequences. Although most of the genes are under purifying selection, there are several cases with individual sites evolving under positive selection. Finally, the HGT results confirm that sporulation is an ancestral feature in Bacillus.}, }
@article {pmid33052487, year = {2021}, author = {Matsushima, N and Miyashita, H and Tamaki, S and Kretsinger, RH}, title = {Shrinking of repeating unit length in leucine-rich repeats from double-stranded DNA viruses.}, journal = {Archives of virology}, volume = {166}, number = {1}, pages = {43-64}, pmid = {33052487}, issn = {1432-8798}, mesh = {Archaea/virology ; Bacteria/virology ; Consensus Sequence/genetics ; DNA/*genetics ; Eukaryota/virology ; Leucine/*genetics ; Phylogeny ; Repetitive Sequences, Amino Acid/*genetics ; Viral Proteins/genetics ; Viruses/*genetics ; }, abstract = {Leucine-rich repeats (LRRs) are present in over 563,000 proteins from viruses to eukaryotes. LRRs repeat in tandem and have been classified into fifteen classes in which the repeat unit lengths range from 20 to 29 residues. Most LRR proteins are involved in protein-protein or ligand interactions. The amount of genome sequence data from viruses is increasing rapidly, and although viral LRR proteins have been identified, a comprehensive sequence analysis has not yet been done, and their structures, functions, and evolution are still unknown. In the present study, we characterized viral LRRs by sequence analysis and identified over 600 LRR proteins from 89 virus species. Most of these proteins were from double-stranded DNA (dsDNA) viruses, including nucleocytoplasmic large dsDNA viruses (NCLDVs). We found that the repeating unit lengths of 11 types are one to five residues shorter than those of the seven known corresponding LRR classes. The repeating units of six types are 19 residues long and are thus the shortest among all LRRs. In addition, two of the LRR types are unique and have not been observed in bacteria, archae or eukaryotes. Conserved strongly hydrophobic residues such as Leu, Val or Ile in the consensus sequences are replaced by Cys with high frequency. Phylogenetic analysis indicated that horizontal gene transfer of some viral LRR genes had occurred between the virus and its host. We suggest that the shortening might contribute to the survival strategy of viruses. The present findings provide a new perspective on the origin and evolution of LRRs.}, }
@article {pmid33049532, year = {2021}, author = {Mazhar, SH and Li, X and Rashid, A and Su, J and Xu, J and Brejnrod, AD and Su, JQ and Wu, Y and Zhu, YG and Zhou, SG and Feng, R and Rensing, C}, title = {Co-selection of antibiotic resistance genes, and mobile genetic elements in the presence of heavy metals in poultry farm environments.}, journal = {The Science of the total environment}, volume = {755}, number = {Pt 2}, pages = {142702}, doi = {10.1016/j.scitotenv.2020.142702}, pmid = {33049532}, issn = {1879-1026}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Farms ; Genes, Bacterial ; Interspersed Repetitive Sequences ; Manure ; *Metals, Heavy ; Poultry ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Environmental selection of antibiotic resistance genes (ARGs) is considered to be caused by antibiotic or metal residues, frequently used in livestock. In this study we examined three commercial poultry farms to correlate the co-occurrence patterns of antibiotic and metal residues to the presence of ARGs. We quantified 283 ARGs, 12 mobile genetic elements (MGEs), 49 targeted antibiotics, 7 heavy metals and sequenced 16S rRNA genes. The abundance and type of ARG were significantly enriched in manure while soil harbored the most diverse bacterial community. Procrustes analysis displayed significant correlations between ARGs/MGEs and the microbiome. Cadmium (Cd), arsenic (As), zinc (Zn), copper (Cu) and lead (Pb) were responsible for a majority of positive correlations to ARGs when compared to antibiotics. Integrons and transposons co-occurred with ARGs corresponding to 9 classes of antibiotics, especially Class1 integrase intI-1LC. Redundancy analysis (RDA) and Variance partitioning analysis (VPA) showed that antibiotics, metals, MGEs and bacteria explain solely 0.7%, 5.7%, 12.4%, and 21.9% of variances of ARGs in the microbial community, respectively. These results suggested that bacterial composition and horizontal gene transfer were the major factors shaping the composition of ARGs; Metals had a bigger effect on ARG profile than detected antibiotics in this study.}, }
@article {pmid33048442, year = {2021}, author = {Wang, M and Nie, Y and Wu, XL}, title = {Membrane vesicles from a Dietzia bacterium containing multiple cargoes and their roles in iron delivery.}, journal = {Environmental microbiology}, volume = {23}, number = {2}, pages = {1009-1019}, doi = {10.1111/1462-2920.15278}, pmid = {33048442}, issn = {1462-2920}, support = {2018YFA0902100//National Key R&amp;D Program of China/ ; 2018YFA0902103//National Key R&amp;D Program of China/ ; 31761133006//National Natural Science Foundation of China/ ; 31770118//National Natural Science Foundation of China/ ; 31770120//National Natural Science Foundation of China/ ; }, mesh = {Actinomycetales/cytology/genetics/*metabolism ; Canthaxanthin/metabolism ; DNA, Bacterial/metabolism ; Extracellular Vesicles/*metabolism ; Gene Transfer, Horizontal ; Iron/*metabolism ; Microbial Interactions ; Siderophores/metabolism ; Species Specificity ; }, abstract = {Membrane vesicles (MVs) released from bacteria act as extracellular vehicles carrying various functional cargoes between cells. MVs with different cargoes play multiple roles in stress adaptation, nutrient acquisition and microbial interactions. However, previous studies have primarily focused on MVs from Gram-negative bacteria, while the characteristics of cargoes in MVs from Gram-positive bacteria and their involvement in microbial interactions remain to be elucidated. Here, we used a Gram-positive strain, Dietzia sp. DQ12-45-1b from Corynebacteriales, to analyse the characteristics and functions of MVs. We identified the 'antioxidant' canthaxanthin is stored within MVs by LC-MS/MS. In addition, nearly the entire genomic content of strain DQ12-45-1b are evenly distributed in MVs, suggesting that MVs from DQ12-45-1b might involve in horizontal gene transfer. Finally, the mycobactin-type siderophores were detected in MVs. The iron-loaded MVs effectively mediate iron binding and delivery to homologous bacteria from the order Corynebacteriales, but not to more distantly related species from the orders Pseudomonadales, Bacillales and Enterobacterales. These results revealed that the iron-loaded MVs are shared between homologous species. Together, we report the Gram-positive bacterium Dietzia sp. DQ12-45-1b released MVs that contain canthaxanthin, DNA and siderophores and prove that MVs act as public goods between closely related species.}, }
@article {pmid33047414, year = {2020}, author = {Stoy, KS and Gibson, AK and Gerardo, NM and Morran, LT}, title = {A need to consider the evolutionary genetics of host-symbiont mutualisms.}, journal = {Journal of evolutionary biology}, volume = {33}, number = {12}, pages = {1656-1668}, doi = {10.1111/jeb.13715}, pmid = {33047414}, issn = {1420-9101}, support = {R35 GM137975/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Biological Coevolution/*genetics ; Gene Transfer, Horizontal ; Genetic Variation ; Host-Parasite Interactions/genetics ; Models, Genetic ; Recombination, Genetic ; Symbiosis/*genetics ; }, abstract = {Despite the ubiquity and importance of mutualistic interactions, we know little about the evolutionary genetics underlying their long-term persistence. As in antagonistic interactions, mutualistic symbioses are characterized by substantial levels of phenotypic and genetic diversity. In contrast to antagonistic interactions, however, we, by and large, do not understand how this variation arises, how it is maintained, nor its implications for future evolutionary change. Currently, we rely on phenotypic models to address the persistence of mutualistic symbioses, but the success of an interaction almost certainly depends heavily on genetic interactions. In this review, we argue that evolutionary genetic models could provide a framework for understanding the causes and consequences of diversity and why selection may favour processes that maintain variation in mutualistic interactions.}, }
@article {pmid33045730, year = {2020}, author = {Choi, J and Groisman, EA}, title = {Horizontally acquired regulatory gene activates ancestral regulatory system to promote Salmonella virulence.}, journal = {Nucleic acids research}, volume = {48}, number = {19}, pages = {10832-10847}, pmid = {33045730}, issn = {1362-4962}, support = {R01 AI120558/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacterial Proteins/*genetics/metabolism ; Cell Line ; Evolution, Molecular ; Female ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Membrane Proteins/*genetics/metabolism ; Mice ; Mice, Inbred BALB C ; Promoter Regions, Genetic ; Salmonella typhimurium/*genetics/pathogenicity ; Transcription Factors/*genetics/metabolism ; Transcriptional Activation ; Virulence/genetics ; }, abstract = {Horizontally acquired genes are typically regulated by ancestral regulators. This regulation enables expression of horizontally acquired genes to be coordinated with that of preexisting genes. Here, we report a singular example of the opposite regulation: a horizontally acquired gene that controls an ancestral regulator, thereby promoting bacterial virulence. We establish that the horizontally acquired regulatory gene ssrB is necessary to activate the ancestral regulatory system PhoP/PhoQ of Salmonella enterica serovar Typhimurium (S. Typhimurium) in mildly acidic pH, which S. Typhimurium experiences inside macrophages. SsrB promotes phoP transcription by binding upstream of the phoP promoter. SsrB also increases ugtL transcription by binding to the ugtL promoter region, where it overcomes gene silencing by the heat-stable nucleoid structuring protein H-NS, enhancing virulence. The largely non-pathogenic species S. bongori failed to activate PhoP/PhoQ in mildly acidic pH because it lacks both the ssrB gene and the SsrB binding site in the target promoter. Low Mg2+ activated PhoP/PhoQ in both S. bongori and ssrB-lacking S. Typhimurium, indicating that the SsrB requirement for PhoP/PhoQ activation is signal-dependent. By controlling the ancestral genome, horizontally acquired genes are responsible for more crucial abilities, including virulence, than currently thought.}, }
@article {pmid33045347, year = {2020}, author = {Del Barrio-Tofiño, E and López-Causapé, C and Oliver, A}, title = {Pseudomonas aeruginosa epidemic high-risk clones and their association with horizontally-acquired β-lactamases: 2020 update.}, journal = {International journal of antimicrobial agents}, volume = {56}, number = {6}, pages = {106196}, doi = {10.1016/j.ijantimicag.2020.106196}, pmid = {33045347}, issn = {1872-7913}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics ; Brazil/epidemiology ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal/*genetics ; Humans ; Microbial Sensitivity Tests ; Molecular Epidemiology ; Pseudomonas Infections/drug therapy/epidemiology/microbiology ; Pseudomonas aeruginosa/drug effects/*genetics/isolation &amp; purification ; beta-Lactamases/*genetics ; }, abstract = {Pseudomonas aeruginosa global clones associated with multidrug-resistant (MDR) and extensively drug-resistant (XDR) phenotypes, denominated high-risk clones, are a growing threat in hospitals worldwide. Here we provide a 2020 update on nosocomial MDR/XDR high-risk P. aeruginosa clones. According to their prevalence, global spread and association with MDR/XDR profiles and regarding extended-spectrum β-lactamases (ESBLs) and carbapenemases, the worldwide top 10 P. aeruginosa high-risk clones includes ST235, ST111, ST233, ST244, ST357, ST308, ST175, ST277, ST654 and ST298. ST235 is certainly the most relevant high-risk clone, showing a worldwide dissemination associated with over 60 different β-lactamase variants, including multiple carbapenemases from classes A and B. Moreover, ST235 shows a highly virulent phenotype associated with a high mortality rate, likely due to the production of the ExoU cytotoxin. ST111 and ST233 are also worldwide disseminated MDR/XDR clones, particularly linked to VIM-2 metallo-β-lactamase (MBL), whereas ST244 is a very prevalent clone not always associated with MDR/XDR profiles. ST357, ST308 and ST298 are also exoU+ and are therefore potentially associated with higher virulence. In contrast, ST175, prevalent in some European countries, shows a MDR/XDR phenotype frequently caused by specific chromosomal mutations and is associated with lower virulence. Finally, ST277 is highly prevalent in Brazil and is specifically associated with the SPM MBL. A deeper understanding of the underlying factors driving the success of high-risk clones, including the reported increased capacity for acquiring exogenous determinants, increased spontaneous mutation rates or greater ability to develop biofilms, is required to develop global strategies to combat them.}, }
@article {pmid33038622, year = {2020}, author = {Zheng, H and Wang, R and Zhang, Q and Zhao, J and Li, F and Luo, X and Xing, B}, title = {Pyroligneous acid mitigated dissemination of antibiotic resistance genes in soil.}, journal = {Environment international}, volume = {145}, number = {}, pages = {106158}, doi = {10.1016/j.envint.2020.106158}, pmid = {33038622}, issn = {1873-6750}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Humans ; *Soil ; Soil Microbiology ; Terpenes ; }, abstract = {Strategies to mitigate the spread of antibiotic resistance genes (ARGs) in soils are urgently needed. Therefore, a pristine pyroligneous acid (PA) from pyrolyzing blended woody waste at 450 °C and its three fractions distilled at 98, 130, and 220 °C (F1, F2, and F3) were used to evaluate their feasibility of reducing ARGs in soil. Application of PA, F2, and F3 effectively decreased the relative ARG abundance by 22.4-75.4% and 39.7-66.7% in the rhizosphere and bulk soil relative to control, respectively, and the removal efficiency followed an order of F3 > PA > F2. Contrarily, F1 increased the abundance of ARGs. The decreased abundance of two mobile genetic elements and impaired conjugative transfer of RP4 plasmid in the presence of PA, F2 and F3 demonstrated that the weakened horizontal gene transfer (HGT) contributed to the reduced ARG level. Variation partitioning analysis and structural equation models confirmed that ARG reduction was primarily driven by the weakened HGT, followed by the decreased co-selection of heavy metals and shifted bacterial community (e.g., reduced potential host bacteria of ARGs). Our findings provide practical and technical support for developing PA-based technology in remediating ARG-contaminated soil to ensure food safety and protect human health.}, }
@article {pmid33036450, year = {2020}, author = {Kwon, HJ and Chen, Z and Evans, P and Meng, J and Chen, Y}, title = {Characterization of Mobile Genetic Elements Using Long-Read Sequencing for Tracking Listeria monocytogenes from Food Processing Environments.}, journal = {Pathogens (Basel, Switzerland)}, volume = {9}, number = {10}, pages = {}, pmid = {33036450}, issn = {2076-0817}, abstract = {Recently developed nanopore sequencing technologies offer a unique opportunity to rapidly close the genome and to identify complete sequences of mobile genetic elements (MGEs). In this study, 17 isolates of Listeria monocytogenes (Lm) epidemic clone II (ECII) from seven ready-to-eat meat or poultry processing facilities, not known to be associated with outbreaks, were shotgun sequenced, and among them, five isolates were further subjected to long-read sequencing. Additionally, 26 genomes of Lm ECII isolates associated with three listeriosis outbreaks in the U.S. and South Africa were obtained from the National Center for Biotechnology Information (NCBI) database and analyzed to evaluate if MGEs may be used as a high-resolution genetic marker for identifying and sourcing the origin of Lm. The analyses identified four comK prophages in 11 non-outbreak isolates from four facilities and three comK prophages in 20 isolates associated with two outbreaks that occurred in the U.S. In addition, three different plasmids were identified among 10 non-outbreak isolates and 14 outbreak isolates. Each comK prophage and plasmid was conserved among the isolates sharing it. Different prophages from different facilities or outbreaks had significant genetic variations, possibly due to horizontal gene transfer. Phylogenetic analysis showed that isolates from the same facility or the same outbreak always closely clustered. The time of most recent common ancestor of the Lm ECII isolates was estimated to be in March 1816 with the average nucleotide substitution rate of 3.1 × 10[-7] substitutions per site per year. This study showed that complete MGE sequences provide a good signal to determine the genetic relatedness of Lm isolates, to identify persistence or repeated contamination that occurred within food processing environment, and to study the evolutionary history among closely related isolates.}, }
@article {pmid33034112, year = {2021}, author = {Li, G and Xia, LJ and Zhou, SY and Wang, XR and Cui, CY and He, YZ and Diao, XY and Liu, M and Lian, XL and Kreiswirth, BN and Liu, YH and Liao, XP and Chen, L and Sun, J}, title = {Linoleic acid and α-linolenic acid inhibit conjugative transfer of an IncX4 plasmid carrying mcr-1.}, journal = {Journal of applied microbiology}, volume = {130}, number = {6}, pages = {1893-1901}, doi = {10.1111/jam.14885}, pmid = {33034112}, issn = {1365-2672}, support = {2016YFD0501300//National Key Research and Development Program of China/ ; 31972735//National Natural Science Foundation of China/ ; R21AI135250//National Institute of Allergy and Infectious Diseases/ ; D20008//Higher Education Discipline Innovation Project/ ; R21 AI106551/AI/NIAID NIH HHS/United States ; IRT_17R39//the Program for Innovative Research Team in the University of Ministry of Education of China/ ; R01AI090155//National Institute of Allergy and Infectious Diseases/ ; }, mesh = {Adenosine Triphosphatases/chemistry/genetics ; Colistin/pharmacology ; Conjugation, Genetic ; Drug Resistance, Bacterial ; Escherichia coli/classification/*genetics ; Escherichia coli Proteins/chemistry/genetics ; Gene Expression/drug effects ; Gene Transfer, Horizontal/*drug effects ; Linoleic Acid/chemistry/metabolism/*pharmacology ; Molecular Docking Simulation ; Plasmids/genetics ; alpha-Linolenic Acid/chemistry/metabolism/*pharmacology ; }, abstract = {AIMS: The aim of this study was to determine the effects of unsaturated fatty acids on clinical plasmids.<br><br>METHODS AND RESULTS: Two unsaturated fatty acids, linoleic acid (LA) and &#x3b1;-linolenic acid (ALA) at final concentration 0, 0&#xb7;03, 0&#xb7;3 and 3&#xa0;mmol&#xa0;l[-1] , respectively, were used to assess the effects on conjugative transfer of a mcr-1-harbouring plasmid pCSZ4 (IncX4) in conjugation experiment. The inhibitory mechanisms were analysed by molecular docking and the gene expression of virB11 was quantitated by qRT-PCR. Target plasmid diversity was carried out by TrwD/VirB11 homology protein sequence prediction analysis. Our results showed that LA and ALA inhibit plasmid pCSZ4 transfer by binding to the amino acid residues (Phe124 and Thr125) of VirB11 with dose-dependent effects. The expression levels of virB11 gene were also significantly inhibited by LA and ALA treatment. Protein homology analysis revealed a wide distribution of TrwD/VirB11-like genes among over 37 classes of plasmids originated from both Gram-negative and Gram-positive bacteria.<br><br>CONCLUSIONS: This study demonstrates representing a diversity of plasmids that may be potentially inhibited by unsaturated fatty acids.<br><br>Our work reported here provides additional support for application of curbing the spread of multiple plasmids by unsaturated fatty acids.}, }
@article {pmid33033577, year = {2020}, author = {Pérez, J and Contreras-Moreno, FJ and Marcos-Torres, FJ and Moraleda-Muñoz, A and Muñoz-Dorado, J}, title = {The antibiotic crisis: How bacterial predators can help.}, journal = {Computational and structural biotechnology journal}, volume = {18}, number = {}, pages = {2547-2555}, pmid = {33033577}, issn = {2001-0370}, abstract = {Discovery of antimicrobials in the past century represented one of the most important advances in public health. Unfortunately, the massive use of these compounds in medicine and other human activities has promoted the selection of pathogens that are resistant to one or several antibiotics. The current antibiotic crisis is creating an urgent need for research into new biological weapons with the ability to kill these superbugs. Although a proper solution requires this problem to be addressed in a variety of ways, the use of bacterial predators is emerging as an excellent strategy, especially when used as whole cell therapeutic agents, as a source of new antimicrobial agents by awakening silent metabolic pathways in axenic cultures, or as biocontrol agents. Moreover, studies on their prey are uncovering mechanisms of resistance that can be shared by pathogens, representing new targets for novel antimicrobial agents. In this review we discuss potential of the studies on predator-prey interaction to provide alternative solutions to the problem of antibiotic resistance.}, }
@article {pmid33033258, year = {2020}, author = {Weaver, SJ and Ortega, DR and Sazinsky, MH and Dalia, TN and Dalia, AB and Jensen, GJ}, title = {CryoEM structure of the type IVa pilus secretin required for natural competence in Vibrio cholerae.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {5080}, pmid = {33033258}, issn = {2041-1723}, support = {R01 AI127401/AI/NIAID NIH HHS/United States ; R35 GM128674/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Bacterial Secretion Systems/*ultrastructure ; *Cryoelectron Microscopy ; Cysteine/genetics ; Fimbriae, Bacterial/*ultrastructure ; Membrane Proteins/ultrastructure ; Models, Molecular ; Mutation/genetics ; Phylogeny ; Protein Domains ; Secretin/*chemistry ; Transformation, Bacterial ; Vibrio cholerae/*metabolism/*ultrastructure ; }, abstract = {Natural transformation is the process by which bacteria take up genetic material from their environment and integrate it into their genome by homologous recombination. It represents one mode of horizontal gene transfer and contributes to the spread of traits like antibiotic resistance. In Vibrio cholerae, a type IVa pilus (T4aP) is thought to facilitate natural transformation by extending from the cell surface, binding to exogenous DNA, and retracting to thread this DNA through the outer membrane secretin, PilQ. Here, we use a functional tagged allele of VcPilQ purified from native V. cholerae cells to determine the cryoEM structure of the VcPilQ secretin in amphipol to ~2.7 Å. We use bioinformatics to examine the domain architecture and gene neighborhood of T4aP secretins in Proteobacteria in comparison with VcPilQ. This structure highlights differences in the architecture of the T4aP secretin from the type II and type III secretion system secretins. Based on our cryoEM structure, we design a series of mutants to reversibly regulate VcPilQ gate dynamics. These experiments support the idea of VcPilQ as a potential druggable target and provide insight into the channel that DNA likely traverses to promote the spread of antibiotic resistance via horizontal gene transfer by natural transformation.}, }
@article {pmid33031917, year = {2020}, author = {Kanao, T and Sharmin, S and Tokuhisa, M and Otsuki, M and Kamimura, K}, title = {Identification of a gene encoding a novel thiosulfate:quinone oxidoreductase in marine Acidithiobacillus sp. strain SH.}, journal = {Research in microbiology}, volume = {171}, number = {7}, pages = {281-286}, doi = {10.1016/j.resmic.2020.09.004}, pmid = {33031917}, issn = {1769-7123}, mesh = {Acidithiobacillus thiooxidans/*enzymology/*genetics ; Amino Acid Sequence/genetics ; Base Sequence ; DNA, Bacterial/genetics ; Genome, Bacterial/genetics ; Oxidation-Reduction ; Quinone Reductases/*genetics ; Quinones/*metabolism ; Sulfurtransferases/genetics ; Thiosulfates/*metabolism ; }, abstract = {Sulfur-oxidizing bacteria that are halophilic and acidophilic have gained interest because of their potential use in bioleaching operations in salt-containing environments. Acidithiobacillus sp. strain SH, which was previously identified as Acidithiobacillus thiooxidans based on its 16S rRNA gene sequence, is a chemolithoautotrophic marine bacterium exhibiting sodium chloride-stimulated thiosulfate-oxidizing activities. A novel thiosulfate:quinone oxidoreductase from strain SH (SH-TQO) has been purified from its solubilized membrane fraction. The gene for SH-TQO was determined from the draft genome sequence of the strain SH. Amino acid sequences of peptides generated by the in-gel trypsin digestion of SH-TQO were found in a protein encoded by locus tag B1757_09800 of the genome of the strain SH. The gene encoded 444 amino acids with a signal peptide of 29 amino acids and was annotated to encode a porin. The gene was located in a unique genomic region, not found in A. thiooxidans strains, suggesting that the strain SH acquired this region through a horizontal gene transfer. A protein-protein basic local alignment search revealed that sulfur-oxidizing bacteria, such as Acidithiobacillus species have proteins homologous to SH-TQO, though the degree of homologies was relatively low. The protein, DoxXA, which is homologous to TQO from Acidianus amvibalens, was also found in the genomic region.}, }
@article {pmid33031891, year = {2021}, author = {Gao, JG}, title = {Tracking the evolutionary innovations of plant terrestrialization.}, journal = {Gene}, volume = {769}, number = {}, pages = {145203}, doi = {10.1016/j.gene.2020.145203}, pmid = {33031891}, issn = {1879-0038}, mesh = {*Biological Evolution ; Bryophyta/genetics/physiology ; Gene Transfer, Horizontal ; Genome, Plant ; *Plant Physiological Phenomena ; Plants/genetics ; }, abstract = {The gradual transition of the algal ancestor from the freshwater to land has always attracted evolutionary biologists. The recent report of high-quality reference genomes of five Charophyta algae (Spirogloea muscicola, Mesotaenium endlicherianum, Mesostigma viride, Chlorokybus atmophyticus and Penium margaritaceum) and one hornwort (Anthoceros angustus) species sheds light on this fascinating transition. These early diverging plants and algae could have gained new genes from soil bacteria and fungi through horizontal gene transfer (HGT), which was so common during plant terrestrialization and may outrun our expectations. Through reviewing and critical thinking about the advancements on these plant genomes, here, I propose three prospective research directions that need to address in the future: (i) due to the ubiquitous nature of viruses that is similar to soil bacteria and fungi, there is less attention to viruses that probably also play an important role in the genome evolution of plants via HGT; (ii) multicellularity has occurred many times independently, but we still know a little about the biological and ecological mechanisms leading to multi-cellularity in Streptophyta; (iii) and most importantly, the quantitative relationships between genetic innovations and environmental variables such as temperature, precipitation and solar radiation, need pioneering research collaborated by biological evolutionists, computer scientists, and ecologists, which are crucial for understanding the macroevolution of plants and could also be used to simulate the evolution of plants under future climate change.}, }
@article {pmid33027508, year = {2021}, author = {Cai, R and Ané, C}, title = {Assessing the fit of the multi-species network coalescent to multi-locus data.}, journal = {Bioinformatics (Oxford, England)}, volume = {37}, number = {5}, pages = {634-641}, doi = {10.1093/bioinformatics/btaa863}, pmid = {33027508}, issn = {1367-4811}, mesh = {*Genome ; High-Throughput Nucleotide Sequencing ; Likelihood Functions ; Phylogeny ; *Software ; }, abstract = {MOTIVATION: With growing genome-wide molecular datasets from next-generation sequencing, phylogenetic networks can be estimated using a variety of approaches. These phylogenetic networks include events like hybridization, gene flow or horizontal gene transfer explicitly. However, the most accurate network inference methods are computationally heavy. Methods that scale to larger datasets do not calculate a full likelihood, such that traditional likelihood-based tools for model selection are not applicable to decide how many past hybridization events best fit the data. We propose here a goodness-of-fit test to quantify the fit between data observed from genome-wide multi-locus data, and patterns expected under the multi-species coalescent model on a candidate phylogenetic network.<br><br>RESULTS: We identified weaknesses in the previously proposed TICR test, and proposed corrections. The performance of our new test was validated by simulations on real-world phylogenetic networks. Our test provides one of the first rigorous tools for model selection, to select the adequate network complexity for the data at hand. The test can also work for identifying poorly inferred areas on a network.<br><br>Software for the goodness-of-fit test is available as a Julia package at https://github.com/cecileane/QuartetNetworkGoodnessFit.jl.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid33023469, year = {2020}, author = {Peoples, LM and Kyaw, TS and Ugalde, JA and Mullane, KK and Chastain, RA and Yayanos, AA and Kusube, M and Methé, BA and Bartlett, DH}, title = {Distinctive gene and protein characteristics of extremely piezophilic Colwellia.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {692}, pmid = {33023469}, issn = {1471-2164}, support = {1536776//National Science Foundation/ ; NNX11AG10G/NASA/NASA/United States ; Project 1265//Prince Albert II of Monaco Foundation/ ; }, mesh = {*Adaptation, Physiological ; Alanine Dehydrogenase/genetics/metabolism ; Alteromonadaceae/classification/*genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Cell Respiration ; *Extreme Environments ; *Genome, Bacterial ; Hydrostatic Pressure ; Membrane Fluidity ; Methylamines/metabolism ; Nitrites/metabolism ; Peptide Synthases/genetics/metabolism ; Phylogeny ; *Proteome ; Transposases/genetics/metabolism ; }, abstract = {BACKGROUND: The deep ocean is characterized by low temperatures, high hydrostatic pressures, and low concentrations of organic matter. While these conditions likely select for distinct genomic characteristics within prokaryotes, the attributes facilitating adaptation to the deep ocean are relatively unexplored. In this study, we compared the genomes of seven strains within the genus Colwellia, including some of the most piezophilic microbes known, to identify genomic features that enable life in the deep sea.<br><br>RESULTS: Significant differences were found to exist between piezophilic and non-piezophilic strains of Colwellia. Piezophilic Colwellia have a more basic and hydrophobic proteome. The piezophilic abyssal and hadal isolates have more genes involved in replication/recombination/repair, cell wall/membrane biogenesis, and cell motility. The characteristics of respiration, pilus generation, and membrane fluidity adjustment vary between the strains, with operons for a nuo dehydrogenase and a tad pilus only present in the piezophiles. In contrast, the piezosensitive members are unique in having the capacity for dissimilatory nitrite and TMAO reduction. A number of genes exist only within deep-sea adapted species, such as those encoding d-alanine-d-alanine ligase for peptidoglycan formation, alanine dehydrogenase for NADH/NAD[+] homeostasis, and a SAM methyltransferase for tRNA modification. Many of these piezophile-specific genes are in variable regions of the genome near genomic islands, transposases, and toxin-antitoxin systems.<br><br>CONCLUSIONS: We identified a number of adaptations that may facilitate deep-sea radiation in members of the genus Colwellia, as well as in other piezophilic bacteria. An enrichment in more basic and hydrophobic amino acids could help piezophiles stabilize and limit water intrusion into proteins as a result of high pressure. Variations in genes associated with the membrane, including those involved in unsaturated fatty acid production and respiration, indicate that membrane-based adaptations are critical for coping with high pressure. The presence of many piezophile-specific genes near genomic islands highlights that adaptation to the deep ocean may be facilitated by horizontal gene transfer through transposases or other mobile elements. Some of these genes are amenable to further study in genetically tractable piezophilic and piezotolerant deep-sea microorganisms.}, }
@article {pmid33022046, year = {2020}, author = {Galbraith, JD and Ludington, AJ and Suh, A and Sanders, KL and Adelson, DL}, title = {New Environment, New Invaders-Repeated Horizontal Transfer of LINEs to Sea Snakes.}, journal = {Genome biology and evolution}, volume = {12}, number = {12}, pages = {2370-2383}, pmid = {33022046}, issn = {1759-6653}, mesh = {Animals ; *Biological Evolution ; Ecosystem ; *Gene Transfer, Horizontal ; Hydrophiidae/*genetics ; *Long Interspersed Nucleotide Elements ; Seawater ; }, abstract = {Although numerous studies have found horizontal transposon transfer (HTT) to be widespread across metazoans, few have focused on HTT in marine ecosystems. To investigate potential recent HTTs into marine species, we searched for novel repetitive elements in sea snakes, a group of elapids which transitioned to a marine habitat at most 18 Ma. Our analysis uncovered repeated HTTs into sea snakes following their marine transition. The seven subfamilies of horizontally transferred LINE retrotransposons we identified in the olive sea snake (Aipysurus laevis) are transcribed, and hence are likely still active and expanding across the genome. A search of 600 metazoan genomes found all seven were absent from other amniotes, including terrestrial elapids, with the most similar LINEs present in fish and marine invertebrates. The one exception was a similar LINE found in sea kraits, a lineage of amphibious elapids which independently transitioned to a marine environment 25 Ma. Our finding of repeated horizontal transfer events into marine snakes greatly expands past findings that the marine environment promotes the transfer of transposons. Transposons are drivers of evolution as sources of genomic sequence and hence genomic novelty. We identified 13 candidate genes for HTT-induced adaptive change based on internal or neighboring HTT LINE insertions. One of these, ADCY4, is of particular interest as a part of the KEGG adaptation pathway "Circadian Entrainment." This provides evidence of the ecological interactions between species influencing evolution of metazoans not only through specific selection pressures, but also by contributing novel genomic material.}, }
@article {pmid33016310, year = {2020}, author = {Bamba, M and Aoki, S and Kajita, T and Setoguchi, H and Watano, Y and Sato, S and Tsuchimatsu, T}, title = {Massive rhizobial genomic variation associated with partner quality in Lotus-Mesorhizobium symbiosis.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {12}, pages = {}, doi = {10.1093/femsec/fiaa202}, pmid = {33016310}, issn = {1574-6941}, mesh = {Genomics ; *Lotus ; *Mesorhizobium/genetics ; *Rhizobium/genetics ; Symbiosis ; }, abstract = {Variation in partner quality is commonly observed in diverse cooperative relationships, despite the theoretical prediction that selection favoring high-quality partners should eliminate such variation. Here, we investigated how genetic variation in partner quality could be maintained in the nitrogen-fixing mutualism between Lotus japonicus and Mesorhizobium bacteria. We reconstructed de novo assembled full-genome sequences from nine rhizobial symbionts, finding massive variation in the core genome and the similar symbiotic islands, indicating recent horizontal gene transfer (HGT) of the symbiosis islands into diverse Mesorhizobium lineages. A cross-inoculation experiment using 9 sequenced rhizobial symbionts and 15 L. japonicus accessions revealed extensive quality variation represented by plant growth phenotypes, including genotype-by-genotype interactions. Variation in quality was not associated with the presence/absence variation in known symbiosis-related genes in the symbiosis island; rather, it showed significant correlation with the core genome variation. Given the recurrent HGT of the symbiosis islands into diverse Mesorhizobium strains, local Mesorhizobium communities could serve as a major source of variation for core genomes, which might prevent variation in partner quality from fixing, even in the presence of selection favoring high-quality partners. These findings highlight the novel role of HGT of symbiosis islands in maintaining partner quality variation in the legume-rhizobia symbiosis.}, }
@article {pmid33014261, year = {2020}, author = {Barreto, HC and Frazão, N and Sousa, A and Konrad, A and Gordo, I}, title = {Mutation accumulation and horizontal gene transfer in Escherichia coli colonizing the gut of old mice.}, journal = {Communicative &amp; integrative biology}, volume = {13}, number = {1}, pages = {89-96}, pmid = {33014261}, issn = {1942-0889}, abstract = {The ecology and environment of the microbes that inhabit the mammalian intestine undergoes several changes as the host ages. Here, we ask if the selection pressure experienced by a new strain colonizing the aging gut differs from that in the gut of young adults. Using experimental evolution in mice after a short antibiotic treatment, as a model for a common clinical situation, we show that a new colonizing E. coli strain rapidly adapts to the aging gut via both mutation accumulation and bacteriophage-mediated horizontal gene transfer (HGT). The pattern of evolution of E. coli in aging mice is characterized by a larger number of transposable element insertions and intergenic mutations compared to that in young mice, which is consistent with the gut of aging hosts harboring a stressful and iron limiting environment.}, }
@article {pmid33013812, year = {2020}, author = {Riva, F and Riva, V and Eckert, EM and Colinas, N and Di Cesare, A and Borin, S and Mapelli, F and Crotti, E}, title = {An Environmental Escherichia coli Strain Is Naturally Competent to Acquire Exogenous DNA.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {574301}, pmid = {33013812}, issn = {1664-302X}, abstract = {The diffusion of antibiotic resistance determinants in different environments, e.g., soil and water, has become a public concern for global health and food safety and many efforts are currently devoted to clarify this complex ecological and evolutionary issue. Horizontal gene transfer (HGT) has an important role in the spread of antibiotic resistance genes (ARGs). However, among the different HGT mechanisms, the capacity of environmental bacteria to acquire naked exogenous DNA by natural competence is still poorly investigated. This study aimed to characterize the ability of the environmental Escherichia coli strain ED1, isolated from the crustacean Daphnia sp., to acquire exogenous DNA by natural competence. Transformation experiments were carried out varying different parameters, i.e., cell growth phase, amount of exogenous DNA and exposition to artificial lake water (ALW) and treated wastewater to mimic environmental-like conditions that may be encountered in the agri-food system. Results were compared with those showed by the laboratory E. coli strain DH5α. Our experimental data, supported by genomic sequencing, showed that, when exposed to pure water, ED1 strain was able to acquire exogenous DNA with frequencies (10[-8]-10[-9]) statistically higher than the ones observed for DH5α strain (10[-10]). Interestingly, higher values were retrieved for ED1 than DH5α strains exposed to ALW (10[-7] vs. 10[-9], respectively) or treated wastewater (10[-8] vs. 10[-10], respectively). We tested, therefore, ED1 strain ability to colonize the rhizosphere of lettuce, a model plant representative of raw-consumed vegetables of high economic importance in the ready-to-eat food industry. Results showed that ED1 strain was able to efficiently colonize lettuce rhizosphere, revealing a stable colonization for 14 days-long period. In conclusion, ED1 strain ability to acquire exogenous DNA in environmental-like conditions by natural competence, combined with its ability to efficiently and stably colonize plant rhizosphere, poses the attention to food and human safety showing a possible route of diffusion of antibiotic resistance in the agri-food system, sustaining the "One Health" warnings related to the antibiotic spread.}, }
@article {pmid33013753, year = {2020}, author = {Hülter, NF and Wein, T and Effe, J and Garoña, A and Dagan, T}, title = {Intracellular Competitions Reveal Determinants of Plasmid Evolutionary Success.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {2062}, pmid = {33013753}, issn = {1664-302X}, abstract = {Plasmids are autonomously replicating genetic elements that are ubiquitous in all taxa and habitats where they constitute an integral part of microbial genomes. The stable inheritance of plasmids depends on their segregation during cell division and their long-term persistence in a host population is thought to largely depend on their impact on the host fitness. Nonetheless, many plasmids found in nature are lacking a clear trait that is advantageous to their host; the determinants of plasmid evolutionary success in the absence of plasmid benefit to the host remain understudied. Here we show that stable plasmid inheritance is an important determinant of plasmid evolutionary success. Borrowing terminology from evolutionary biology of cellular living forms, we hypothesize that Darwinian fitness is key for the plasmid evolutionary success. Performing intracellular plasmid competitions between non-mobile plasmids enables us to compare the evolutionary success of plasmid genotypes within the host, i.e., the plasmid fitness. Intracellular head-to-head competitions between stable and unstable variants of the same model plasmid revealed that the stable plasmid variant has a higher fitness in comparison to the unstable plasmid. Preemptive plasmid competitions reveal that plasmid fitness may depend on the order of plasmid arrival in the host. Competitions between plasmids characterized by similar stability of inheritance reveal plasmid fitness differences depending on the plasmid-encoded trait. Our results further reveal that competing plasmids can be maintained in coexistence following plasmid fusions that maintain unstable plasmid variants over time. Plasmids are not only useful accessory genetic elements to their host but they are also evolving and replicating entities, similarly to cellular living forms. There is a clear link between plasmid genetics and plasmid evolutionary success - hence plasmids are evolving entities whose fitness is quantifiable.}, }
@article {pmid33012528, year = {2020}, author = {Van Etten, J and Bhattacharya, D}, title = {Horizontal Gene Transfer in Eukaryotes: Not if, but How Much?.}, journal = {Trends in genetics : TIG}, volume = {36}, number = {12}, pages = {915-925}, doi = {10.1016/j.tig.2020.08.006}, pmid = {33012528}, issn = {0168-9525}, mesh = {Eukaryota/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; }, abstract = {Horizontal gene transfer (HGT), the movement of genetic material across branches of the tree of life, is well established in prokaryotes and uncontroversial. This is explained in part by relatively compact prokaryote genomes that facilitate assembly and gene prediction, resulting in thousands of complete genomes for analysis. By contrast, their large and often complex genome structure have thwarted HGT studies of eukaryotes. The tide has recently turned with the availability of sufficient high-quality genome data to address quantity and quality of HGT in these taxa. Here, we argue that HGT is a small but significant player in the evolution of microbial eukaryotes and provide examples where HGT has facilitated gain of adaptive functions and in some cases, underpinned major lifestyle transitions.}, }
@article {pmid33011835, year = {2020}, author = {Chen, S and Feng, H and Li, X and Chao, HJ and Wu, J and Liu, J and Zhu, WJ and Yan, DZ}, title = {The Complete Genome Sequence of a Bacterial Strain with High Alkalic Xylanase Activity Isolated from the Sludge Near a Papermill.}, journal = {Current microbiology}, volume = {77}, number = {12}, pages = {3945-3952}, doi = {10.1007/s00284-020-02227-5}, pmid = {33011835}, issn = {1432-0991}, support = {31770119//National Natural Science Foundation of China/ ; 31800111//National Natural Science Foundation of China/ ; }, mesh = {DNA, Bacterial/genetics ; *Fatty Acids ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Sewage ; }, abstract = {Many organisms secrete xylanase, an import group of proteins hydrolyzing xylan, and thus are able to use xylan as their carbon source. In this study, we sequenced the whole genome of a bacterial strain, YD01, which was isolated from the sludge near the sewage discharge outlet of a papermill and showed high alkalic xylanase activity. Its genome consists of a chromosome and two plasmids. Six rRNA genes, 46 tRNA genes, 3136 CDSs as well as 955 repetitive sequences were predicted. 3046 CDSs were functionally annotated. Phylogenetic analysis on 16S rRNA shows that YD01 is a new species in Microbacterium genus and is taxonomically close to M. jejuense THG-C31[T] and M. kyungheense THG-C26[T]. A comparative study on phylogenetic trees of 16S rRNA and xylanase genes suggests that xylanase genes in YD01 may originate from horizontal gene transfer instead of ancestral gene duplication.}, }
@article {pmid33007823, year = {2020}, author = {Fiore, MA and Raisman, JC and Wong, NH and Hudson, AO and Wadsworth, CB}, title = {Exploration of the Neisseria Resistome Reveals Resistance Mechanisms in Commensals That May Be Acquired by N. gonorrhoeae through Horizontal Gene Transfer.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {9}, number = {10}, pages = {}, pmid = {33007823}, issn = {2079-6382}, abstract = {Nonpathogenic Neisseria transfer mutations encoding antibiotic resistance to their pathogenic relative Neisseria gonorrhoeae. However, the resistance genotypes and subsequent phenotypes of nonpathogens within the genus have been described infrequently. Here, we characterize the minimum inhibitory concentrations (MICs) of a panel of Neisseria (n = 26)-including several commensal species-to a suite of diverse antibiotics. We furthermore use whole genome sequencing and the Comprehensive Antibiotic Resistance Database Resistance Gene Identifier (RGI) platform to predict putative resistance-encoding mutations. Resistant isolates to all tested antimicrobials including penicillin (n = 5/26), ceftriaxone (n = 2/26), cefixime (n = 3/26), tetracycline (n = 10/26), azithromycin (n = 11/26), and ciprofloxacin (n = 4/26) were found. In total, 63 distinct mutations were predicted by RGI to be involved in resistance. The presence of several mutations had clear associations with increased MIC such as DNA gyrase subunit A (gyrA) (S91F) and ciprofloxacin, tetracycline resistance protein (tetM) and 30S ribosomal protein S10 (rpsJ) (V57M) and tetracycline, and TEM-type β-lactamases and penicillin. However, mutations with strong associations to macrolide and cephalosporin resistance were not conclusive. This work serves as an initial exploration into the resistance-encoding mutations harbored by nonpathogenic Neisseria, which will ultimately aid in prospective surveillance for novel resistance mechanisms that may be rapidly acquired by N. gonorrhoeae.}, }
@article {pmid33003637, year = {2020}, author = {Kukovetz, K and Hertel, B and Schvarcz, CR and Saponaro, A and Manthey, M and Burk, U and Greiner, T and Steward, GF and Van Etten, JL and Moroni, A and Thiel, G and Rauh, O}, title = {A Functional K[+] Channel from Tetraselmis Virus 1, a Member of the Mimiviridae.}, journal = {Viruses}, volume = {12}, number = {10}, pages = {}, pmid = {33003637}, issn = {1999-4915}, mesh = {Amino Acid Sequence ; Evolution, Molecular ; Genome, Viral ; Ion Channels ; Lipid Bilayers ; Mimiviridae/genetics/*physiology ; Phycodnaviridae/genetics ; Phylogeny ; Potassium/*metabolism ; Potassium Channels/classification/genetics/*physiology ; Sequence Alignment ; Sequence Analysis ; Sodium/metabolism ; Sodium Channels ; Viruses, Unclassified/genetics/*physiology ; }, abstract = {Potassium ion (K[+]) channels have been observed in diverse viruses that infect eukaryotic marine and freshwater algae. However, experimental evidence for functional K[+] channels among these alga-infecting viruses has thus far been restricted to members of the family Phycodnaviridae, which are large, double-stranded DNA viruses within the phylum Nucleocytoviricota. Recent sequencing projects revealed that alga-infecting members of Mimiviridae, another family within this phylum, may also contain genes encoding K[+] channels. Here we examine the structural features and the functional properties of putative K[+] channels from four cultivated members of Mimiviridae. While all four proteins contain variations of the conserved selectivity filter sequence of K[+] channels, structural prediction algorithms suggest that only two of them have the required number and position of two transmembrane domains that are present in all K[+] channels. After in vitro translation and reconstitution of the four proteins in planar lipid bilayers, we confirmed that one of them, a 79 amino acid protein from the virus Tetraselmis virus 1 (TetV-1), forms a functional ion channel with a distinct selectivity for K[+] over Na[+] and a sensitivity to Ba[2+]. Thus, virus-encoded K[+] channels are not limited to Phycodnaviridae but also occur in the members of Mimiviridae. The large sequence diversity among the viral K[+] channels implies multiple events of lateral gene transfer.}, }
@article {pmid33002118, year = {2020}, author = {Song, J and Klümper, U and Riber, L and Dechesne, A and Smets, BF and Sørensen, SJ and Brandt, KK}, title = {A converging subset of soil bacterial taxa is permissive to the IncP-1 plasmid pKJK5 across a range of soil copper contamination.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {11}, pages = {}, doi = {10.1093/femsec/fiaa200}, pmid = {33002118}, issn = {1574-6941}, mesh = {*Conjugation, Genetic ; *Copper ; Permissiveness ; Plasmids/genetics ; RNA, Ribosomal, 16S/genetics ; Soil ; Soil Microbiology ; }, abstract = {Stressors like metals or antibiotics can affect bacterial community permissiveness for plasmid uptake, but there is little knowledge about long-term effects of such stressors on the evolution of community permissiveness. We assessed the effect of more than 90 years of soil Cu contamination on bacterial community permissiveness (i.e. uptake ability) toward a gfp-tagged IncP-1 plasmid (pKJK5) introduced via an Escherichia coli donor. Plasmid transfer events from the donor to the recipient soil bacterial community were quantified and transconjugants were subsequently isolated by fluorescence activated cell sorting and identified by 16S rRNA gene amplicon sequencing. Transfer frequency of plasmid pKJK5 was reduced in bacterial communities extracted from highly Cu contaminated (4526 mg kg-1) soil compared to corresponding communities extracted from moderately (458 mg kg-1) Cu contaminated soil and a low Cu reference soil (15 mg kg-1). The taxonomic composition of the transconjugal pools showed remarkable similarities irrespective of the degree of soil Cu contamination and despite contrasting compositions of the extracted recipient communities and the original soil communities. Permissiveness assessed at the level of individual operational taxonomic units (OTUs; 16S rRNA gene 97% sequence similarity threshold) was only slightly affected by soil Cu level and high replicate variability of OTU-level permissiveness indicated a role of stochastic events in IncP-1 plasmid transfer or strain-to-strain permissiveness variability.}, }
@article {pmid32999421, year = {2021}, author = {Chu, X and Li, S and Wang, S and Luo, D and Luo, H}, title = {Gene loss through pseudogenization contributes to the ecological diversification of a generalist Roseobacter lineage.}, journal = {The ISME journal}, volume = {15}, number = {2}, pages = {489-502}, pmid = {32999421}, issn = {1751-7370}, mesh = {Ecosystem ; Genome, Bacterial ; Phylogeny ; *Roseobacter/genetics ; }, abstract = {Ecologically relevant genes generally show patchy distributions among related bacterial genomes. This is commonly attributed to lateral gene transfer, whereas the opposite mechanism-gene loss-has rarely been explored. Pseudogenization is a major mechanism underlying gene loss, and pseudogenes are best characterized by comparing closely related genomes because of their short life spans. To explore the role of pseudogenization in microbial ecological diversification, we apply rigorous methods to characterize pseudogenes in the 279 newly sequenced Ruegeria isolates of the globally abundant Roseobacter group collected from two typical coastal habitats in Hong Kong, the coral Platygyra acuta and the macroalga Sargassum hemiphyllum. Pseudogenes contribute to ~16% of the accessory genomes of these strains. Ancestral state reconstruction reveals that many pseudogenization events are correlated with ancestral niche shifts. Specifically, genes related to resource scavenging and energy acquisition were often pseudogenized when roseobacters inhabiting carbon-limited and energy-poor coral skeleton switched to other resource-richer niches. For roseobacters inhabiting the macroalgal niches, genes for nitrogen regulation and carbohydrate utilization were important but became dispensable upon shift to coral skeleton where nitrate is abundant but carbohydrates are less available. Whereas low-energy-demanding secondary transporters are more favorable in coral skeleton, ATP-driven primary transporters are preferentially kept in the energy-replete macroalgal niches. Moreover, a large proportion of these families mediate organismal interactions, suggesting their rapid losses by pseudogenization as a potential response to host and niche shift. These findings illustrate an important role of pseudogenization in shaping genome content and driving ecological diversification of marine roseobacters.}, }
@article {pmid32992519, year = {2020}, author = {Kollarcikova, M and Faldynova, M and Matiasovicova, J and Jahodarova, E and Kubasova, T and Seidlerova, Z and Babak, V and Videnska, P and Cizek, A and Rychlik, I}, title = {Different Bacteroides Species Colonise Human and Chicken Intestinal Tract.}, journal = {Microorganisms}, volume = {8}, number = {10}, pages = {}, pmid = {32992519}, issn = {2076-2607}, support = {RVO0518//Ministerstvo Zem&#x11b;d&#x11b;lstv&#xed;/ ; CZ.02.1.01/0.0/0.0/16_025/0007404//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy/ ; }, abstract = {Bacteroidaceae are common gut microbiota members in all warm-blooded animals. However, if Bacteroidaceae are to be used as probiotics, the species selected for different hosts should reflect the natural distribution. In this study, we therefore evaluated host adaptation of bacterial species belonging to the family Bacteroidaceae. B. dorei, B. uniformis, B. xylanisolvens, B. ovatus, B. clarus, B. thetaiotaomicron and B. vulgatus represented human-adapted species while B. gallinaceum, B. caecigallinarum, B. mediterraneensis, B. caecicola, M. massiliensis, B. plebeius and B. coprocola were commonly detected in chicken but not human gut microbiota. There were 29 genes which were present in all human-adapted Bacteroides but absent from the genomes of all chicken isolates, and these included genes required for the pentose cycle and glutamate or histidine metabolism. These genes were expressed during an in vitro competitive assay, in which human-adapted Bacteroides species overgrew the chicken-adapted isolates. Not a single gene specific for the chicken-adapted species was found. Instead, chicken-adapted species exhibited signs of frequent horizontal gene transfer, of KUP, linA and sugE genes in particular. The differences in host adaptation should be considered when the new generation of probiotics for humans or chickens is designed.}, }
@article {pmid32990598, year = {2020}, author = {Colnaghi, M and Lane, N and Pomiankowski, A}, title = {Genome expansion in early eukaryotes drove the transition from lateral gene transfer to meiotic sex.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, pmid = {32990598}, issn = {2050-084X}, support = {EP/F500351/1//Engineering and Physical Sciences Research Council/International ; EP/I017909/1//Engineering and Physical Sciences Research Council/International ; NE/R010579/1//Natural Environment Research Council/International ; BB/S003681/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Eukaryota/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome/genetics ; Haploidy ; Meiosis/*genetics ; Models, Genetic ; Mutation Rate ; Prokaryotic Cells ; Reproduction/genetics ; }, abstract = {Prokaryotes acquire genes from the environment via lateral gene transfer (LGT). Recombination of environmental DNA can prevent the accumulation of deleterious mutations, but LGT was abandoned by the first eukaryotes in favour of sexual reproduction. Here we develop a theoretical model of a haploid population undergoing LGT which includes two new parameters, genome size and recombination length, neglected by previous theoretical models. The greater complexity of eukaryotes is linked with larger genomes and we demonstrate that the benefit of LGT declines rapidly with genome size. The degeneration of larger genomes can only be resisted by increases in recombination length, to the same order as genome size - as occurs in meiosis. Our results can explain the strong selective pressure towards the evolution of sexual cell fusion and reciprocal recombination during early eukaryotic evolution - the origin of meiotic sex.}, }
@article {pmid32988548, year = {2020}, author = {Marin, C and Sevilla-Navarro, S and Lonjedo, R and Catalá-Gregori, P and Ferrús, MA and Vega, S and Jiménez-Belenguer, A}, title = {Genotyping and molecular characterization of antimicrobial resistance in thermophilic Campylobacter isolated from poultry breeders and their progeny in Eastern Spain.}, journal = {Poultry science}, volume = {99}, number = {10}, pages = {5096-5104}, pmid = {32988548}, issn = {1525-3171}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Breeding ; *Campylobacter/drug effects/genetics ; *Campylobacter Infections/epidemiology/veterinary ; Chickens ; *Drug Resistance, Bacterial/genetics ; Genotype ; Poultry ; *Poultry Diseases/microbiology ; Spain ; }, abstract = {Thermophilic Campylobacter spp. are recognized as a major cause of acute bacterial diarrhea in humans, with broiler meat being the most common source of human infection. Antibiotic therapy is usually necessary for severe or prolonged infections, especially in immunocompromised populations such as young or elderly individuals. However, different studies have demonstrated a close association between antibiotic use in animal production and antimicrobial resistance (AMR) in humans. In this sense, there is social pressure to reduce antibiotic administration and find adequate alternatives to control the presence of bacterial infections in farms. However, there is a lack of information related to Campylobacter AMR dynamics through the entire production system from breeders to their progeny. It is unknown if resistance genes are a result of adaptation through chromosomal mutation or through horizontal gene transfer, instead of vertical transmission of DNA from the parent to their progeny. Thus, the main objectives of this study were to assess the main AMR rates present in a poultry production system, to study the relationship between Campylobacter AMR profiles from breeders and their progeny, and to study the presence and distribution of antibiotic resistance genes in poultry production. Regarding AMR rates, ciprofloxacin was classified as extremely high, followed by nalidixic acid and tetracyclines that were classified as very high. Moreover, this study demonstrated a relationship between the AMR patterns and genes found from Campylobacter strains isolated in breeders and those present in their progeny.}, }
@article {pmid32986560, year = {2022}, author = {Tavernelli, D and Calamoneri, T and Vocca, P}, title = {Linear Time Reconciliation With Bounded Transfers of Genes.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {19}, number = {2}, pages = {1009-1017}, doi = {10.1109/TCBB.2020.3027207}, pmid = {32986560}, issn = {1557-9964}, mesh = {*Algorithms ; *Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal/genetics ; Phylogeny ; }, abstract = {Tree reconciliation is a general framework for investigating the mutual influence between gene and species trees according to the parsimony principle, that is, to each evolutionary event a cost is assigned and the goal is to find a reconciliation of minimum total cost. The resulting optimization problem is known as the reconciliation problem. Usually, the considered events are: co-divergence, gene Duplication, horizontal gene Transfer, and gene Loss (DTL model), while in a more conservative setting, gene transfers are not allowed (DL model). The reconciliation problem requires, in the DL model, time linear in the dimension of the two trees and at least quadratic time in the DTL model. Hence, it is reasonable to argue that the introduction of horizontal gene transfers increases the complexity of the problem. Instead, we introduce horizontal gene transfers with some constraints and prove that the problem is still linear in the dimension of the trees. Namely, we allow gene transfers of length bounded by k=2, on the basis of the observation that transfers are more likely to occur between closely related species than between distantly related ones. Then we extend the same reasonings to the case in which under additional constrains. In this paper we study also another problem related to the reconciliation one, that is optimally rooting one of the two trees when it is not, and also for it we prove similar results. The relevance of this contribution lies in showing that, in the transit from the DL to the DTL model, the computational time does not increase suddenly to quadratic but remains linear in the case when gene transfers are very short (i.e., happening between very close genes).}, }
@article {pmid32985658, year = {2021}, author = {Jaron, KS and Bast, J and Nowell, RW and Ranallo-Benavidez, TR and Robinson-Rechavi, M and Schwander, T}, title = {Genomic Features of Parthenogenetic Animals.}, journal = {The Journal of heredity}, volume = {112}, number = {1}, pages = {19-33}, pmid = {32985658}, issn = {1465-7333}, support = {T32 GM007057/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; DNA Transposable Elements ; Gene Transfer, Horizontal ; Genome ; Inverted Repeat Sequences ; Mutation ; Parthenogenesis/*genetics ; Selection, Genetic ; }, abstract = {Evolution without sex is predicted to impact genomes in numerous ways. Case studies of individual parthenogenetic animals have reported peculiar genomic features that were suggested to be caused by their mode of reproduction, including high heterozygosity, a high abundance of horizontally acquired genes, a low transposable element load, or the presence of palindromes. We systematically characterized these genomic features in published genomes of 26 parthenogenetic animals representing at least 18 independent transitions to asexuality. Surprisingly, not a single feature was systematically replicated across a majority of these transitions, suggesting that previously reported patterns were lineage-specific rather than illustrating the general consequences of parthenogenesis. We found that only parthenogens of hybrid origin were characterized by high heterozygosity levels. Parthenogens that were not of hybrid origin appeared to be largely homozygous, independent of the cellular mechanism underlying parthenogenesis. Overall, despite the importance of recombination rate variation for the evolution of sexual animal genomes, the genome-wide absence of recombination does not appear to have had the dramatic effects which are expected from classical theoretical models. The reasons for this are probably a combination of lineage-specific patterns, the impact of the origin of parthenogenesis, and a survivorship bias of parthenogenetic lineages.}, }
@article {pmid32979568, year = {2020}, author = {Wee, BA and Muloi, DM and van Bunnik, BAD}, title = {Quantifying the transmission of antimicrobial resistance at the human and livestock interface with genomics.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {26}, number = {12}, pages = {1612-1616}, pmid = {32979568}, issn = {1469-0691}, support = {MR/R000093/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; *Bacterial Zoonoses/genetics/microbiology ; *Drug Resistance, Bacterial/drug effects/genetics ; Escherichia coli/drug effects/pathogenicity ; Escherichia coli Infections/genetics/microbiology ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/genetics ; *Genomics ; Humans ; Livestock/*microbiology ; Plasmids/genetics ; }, abstract = {BACKGROUND: Livestock have been implicated as a reservoir for antimicrobial resistance (AMR) that can spread to humans. Close proximity and ecological interfaces involving livestock have been posited as risk factors for the transmission of AMR. In spite of this, there are sparse data and limited agreement on the transmission dynamics that occur.<br><br>OBJECTIVES: To identify how genome sequencing approaches can be used to quantify the dynamics of AMR transmission at the human-livestock interface, and where current knowledge can be improved to better understand the impact of transmission on the spread of AMR.<br><br>SOURCES: Key articles investigating various aspects of AMR transmission at the human-livestock interface are discussed, with a focus on Escherichia coli.<br><br>CONTENT: We recapitulate the current understanding of the transmission of AMR between humans and livestock based on current genomic and epidemiological approaches. We discuss how the use of well-designed, high-resolution genome sequencing studies can improve our understanding of the human-livestock interface.<br><br>IMPLICATIONS: A better understanding of the human-livestock interface will aid in the development of evidence-based and effective One Health interventions that can ultimately reduce the burden of AMR in humans.}, }
@article {pmid32979052, year = {2020}, author = {Miles, JA and Davies, TA and Hayman, RD and Lorenzen, G and Taylor, J and Anjarwalla, M and Allen, SJR and Graham, JWD and Taylor, PC}, title = {A Case Study of Eukaryogenesis: The Evolution of Photoreception by Photolyase/Cryptochrome Proteins.}, journal = {Journal of molecular evolution}, volume = {88}, number = {8-9}, pages = {662-673}, pmid = {32979052}, issn = {1432-1432}, mesh = {Amino Acid Sequence ; *Cryptochromes/genetics ; *Deoxyribodipyrimidine Photo-Lyase/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Photoreceptors, Microbial/*genetics ; *Phylogeny ; Tryptophan ; }, abstract = {Eukaryogenesis, the origin of the eukaryotes, is still poorly understood. Herein, we show how a detailed all-kingdom phylogenetic analysis overlaid with a map of key biochemical features can provide valuable clues. The photolyase/cryptochrome family of proteins are well known to repair DNA in response to potentially harmful effects of sunlight and to entrain circadian rhythms. Phylogenetic analysis of photolyase/cryptochrome protein sequences from a wide range of prokaryotes and eukaryotes points to a number of horizontal gene transfer events between ancestral bacteria and ancestral eukaryotes. Previous experimental research has characterised patterns of tryptophan residues in these proteins that are important for photoreception, specifically a tryptophan dyad, a canonical tryptophan triad, an alternative tryptophan triad, a tryptophan tetrad and an alternative tetrad. Our results suggest that the spread of the different triad and tetrad motifs across the kingdoms of life accompanied the putative horizontal gene transfers and is consistent with multiple bacterial contributions to eukaryogenesis.}, }
@article {pmid32976806, year = {2020}, author = {Ropars, J and Didiot, E and Rodríguez de la Vega, RC and Bennetot, B and Coton, M and Poirier, E and Coton, E and Snirc, A and Le Prieur, S and Giraud, T}, title = {Domestication of the Emblematic White Cheese-Making Fungus Penicillium camemberti and Its Diversification into Two Varieties.}, journal = {Current biology : CB}, volume = {30}, number = {22}, pages = {4441-4453.e4}, doi = {10.1016/j.cub.2020.08.082}, pmid = {32976806}, issn = {1879-0445}, mesh = {Cheese/*microbiology ; Food Microbiology/*methods ; Genetic Variation ; Genome, Fungal ; Penicillium/*genetics ; Phenotype ; }, abstract = {Domestication involves recent adaptation under strong human selection and rapid diversification and therefore constitutes a good model for studies of these processes. We studied the domestication of the emblematic white mold Penicillium camemberti, used for the maturation of soft cheeses, such as Camembert and Brie, about which surprisingly little was known, despite its economic and cultural importance. Whole-genome-based analyses of genetic relationships and diversity revealed that an ancient domestication event led to the emergence of the gray-green P. biforme mold used in cheese making, by divergence from the blue-green wild P. fuscoglaucum fungus. Another much more recent domestication event led to the generation of the P. camemberti clonal lineage as a sister group to P. biforme. Penicillium biforme displayed signs of phenotypic adaptation to cheese making relative to P. fuscoglaucum, in terms of whiter color, faster growth on cheese medium under cave conditions, lower amounts of toxin production, and greater ability to prevent the growth of other fungi. The P. camemberti lineage displayed even stronger signs of domestication for all these phenotypic features. We also identified two differentiated P. camemberti varieties, apparently associated with different kinds of cheeses and with contrasted phenotypic features in terms of color, growth, toxin production, and competitive ability. We have thus identified footprints of domestication in these fungi, with genetic differentiation between cheese and wild populations, bottlenecks, and specific phenotypic traits beneficial for cheese making. This study has not only fundamental implications for our understanding of domestication but can also have important effects on cheese making.}, }
@article {pmid32974587, year = {2020}, author = {Schniete, JK and Reumerman, R and Kerr, L and Tucker, NP and Hunter, IS and Herron, PR and Hoskisson, PA}, title = {Differential transcription of expanded gene families in central carbon metabolism of Streptomyces coelicolor A3(2).}, journal = {Access microbiology}, volume = {2}, number = {6}, pages = {acmi000122}, pmid = {32974587}, issn = {2516-8290}, abstract = {BACKGROUND: Streptomycete bacteria are prolific producers of specialized metabolites, many of which have clinically relevant bioactivity. A striking feature of their genomes is the expansion of gene families that encode the same enzymatic function. Genes that undergo expansion events, either by horizontal gene transfer or duplication, can have a range of fates: genes can be lost, or they can undergo neo-functionalization or sub-functionalization. To test whether expanded gene families in Streptomyces exhibit differential expression, an RNA-Seq approach was used to examine cultures of wild-type Streptomyces coelicolor grown with either glucose or tween as the sole carbon source.<br><br>RESULTS: RNA-Seq analysis showed that two-thirds of genes within expanded gene families show transcriptional differences when strains were grown on tween compared to glucose. In addition, expression of specialized metabolite gene clusters (actinorhodin, isorenieratane, coelichelin and a cryptic NRPS) was also influenced by carbon source.<br><br>CONCLUSIONS: Expression of genes encoding the same enzymatic function had transcriptional differences when grown on different carbon sources. This transcriptional divergence enables partitioning to function under different physiological conditions. These approaches can inform metabolic engineering of industrial Streptomyces strains and may help develop cultivation conditions to activate the so-called silent biosynthetic gene clusters.}, }
@article {pmid32974563, year = {2019}, author = {Kaur, A and Bansal, K and Kumar, S and Sonti, RV and Patil, PB}, title = {Complete genome dynamics of a dominant-lineage strain of Xanthomonas oryzae pv. oryzae harbouring a novel plasmid encoding a type IV secretion system.}, journal = {Access microbiology}, volume = {1}, number = {9}, pages = {e000063}, pmid = {32974563}, issn = {2516-8290}, abstract = {Xanthomonas oryzae pv. oryzae (Xoo) is a serious pathogen causing bacterial blight disease in rice. Population genomic studies have revealed that rampant inter-strain rather than inter-lineage differences are contributing to the evolutionary success of this pathogen. Here, we report the complete genome sequence of BXO1, a strain of Xoo belonging to a dominant lineage from India. A complete genome-based investigation revealed the presence of two plasmids, pBXO1-1 (66.7 kb) and pBXO1-2 (25.6 kb). The pBXO1-1 plasmid encodes 71 genes, 38 of which encode hypothetical proteins of unknown function. However, these hypothetical genes possess atypical GC content, pointing towards their acquisition and movement through horizontal gene transfer. Interestingly, pBXO1-2 encodes a type IV secretion system (T4SS), which is known to play an important role in the conjugative transfer of genetic material, and also provides fitness to pathogenic bacteria for their enhanced survival. Neither plasmid has been reported previously in any other complete Xoo genome published to date. Our analysis also revealed that the pBXO1-2 plasmid is present in Xanthomonas albilineans str. GPE PC73, which is known to cause leaf scald, a lethal disease in sugarcane. Our complete genome sequence analysis of BXO1 has provided us with detailed insights into the two novel strain-specific plasmids, in addition to decoding their functional capabilities, which were not assessable when using the draft genome sequence of the strain. Overall, our study has revealed the mobility of a novel T4SS in two pathogenic species of Xanthomonas that infect the vascular tissues of two economically important monocot plants, i.e. rice and sugarcane.}, }
@article {pmid32974097, year = {2020}, author = {Hernández, L and Vicens, A and Eguiarte, LE and Souza, V and De Anda, V and González, JM}, title = {Evolutionary history of dimethylsulfoniopropionate (DMSP) demethylation enzyme DmdA in marine bacteria.}, journal = {PeerJ}, volume = {8}, number = {}, pages = {e9861}, pmid = {32974097}, issn = {2167-8359}, abstract = {Dimethylsulfoniopropionate (DMSP), an osmolyte produced by oceanic phytoplankton and bacteria, is primarily degraded by bacteria belonging to the Roseobacter lineage and other marine Alphaproteobacteria via DMSP-dependent demethylase A protein (DmdA). To date, the evolutionary history of DmdA gene family is unclear. Some studies indicate a common ancestry between DmdA and GcvT gene families and a co-evolution between Roseobacter and the DMSP-producing-phytoplankton around 250 million years ago (Mya). In this work, we analyzed the evolution of DmdA under three possible evolutionary scenarios: (1) a recent common ancestor of DmdA and GcvT, (2) a coevolution between Roseobacter and the DMSP-producing-phytoplankton, and (3) an enzymatic adaptation for utilizing DMSP in marine bacteria prior to Roseobacter origin. Our analyses indicate that DmdA is a new gene family originated from GcvT genes by duplication and functional divergence driven by positive selection before a coevolution between Roseobacter and phytoplankton. Our data suggest that Roseobacter acquired dmdA by horizontal gene transfer prior to an environment with higher DMSP. Here, we propose that the ancestor that carried the DMSP demethylation pathway genes evolved in the Archean, and was exposed to a higher concentration of DMSP in a sulfur-rich atmosphere and anoxic ocean, compared to recent Roseobacter eco-orthologs (orthologs performing the same function under different conditions), which should be adapted to lower concentrations of DMSP.}, }
@article {pmid32973725, year = {2020}, author = {Prussing, C and Snavely, EA and Singh, N and Lapierre, P and Lasek-Nesselquist, E and Mitchell, K and Haas, W and Owsiak, R and Nazarian, E and Musser, KA}, title = {Nanopore MinION Sequencing Reveals Possible Transfer of bla KPC-2 Plasmid Across Bacterial Species in Two Healthcare Facilities.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {2007}, pmid = {32973725}, issn = {1664-302X}, support = {NU50CK000516/CC/CDC HHS/United States ; U60 OE000103/OE/OSELS CDC HHS/United States ; }, abstract = {Carbapenemase-producing Enterobacteriaceae are a major threat to global public health. Klebsiella pneumoniae carbapenemase (KPC) is the most commonly identified carbapenemase in the United States and is frequently found on mobile genetic elements including plasmids, which can be horizontally transmitted between bacteria of the same or different species. Here we describe the results of an epidemiological investigation of KPC-producing bacteria at two healthcare facilities. Using a combination of short-read and long-read whole-genome sequencing, we identified an identical 44 kilobase plasmid carrying the bla KPC-2 gene in four bacterial isolates belonging to three different species (Citrobacter freundii, Klebsiella pneumoniae, and Escherichia coli). The isolates in this investigation were collected from patients who were epidemiologically linked in a region in which KPC was uncommon, suggesting that the antibiotic resistance plasmid was transmitted between these bacterial species. This investigation highlights the importance of long-read sequencing in investigating the relatedness of bacterial plasmids, and in elucidating potential plasmid-mediated outbreaks caused by antibiotic resistant bacteria.}, }
@article {pmid32972363, year = {2020}, author = {Wan, Y and Wick, RR and Zobel, J and Ingle, DJ and Inouye, M and Holt, KE}, title = {GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {658}, pmid = {32972363}, issn = {1471-2164}, support = {1/CX/CSRD VA/United States ; 1/CX/CSRD VA/United States ; 1/CX/CSRD VA/United States ; }, mesh = {Escherichia coli/genetics ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Salmonella typhimurium/genetics ; *Software ; Whole Genome Sequencing/methods ; }, abstract = {BACKGROUND: Horizontal gene transfer contributes to bacterial evolution through mobilising genes across various taxonomical boundaries. It is frequently mediated by mobile genetic elements (MGEs), which may capture, maintain, and rearrange mobile genes and co-mobilise them between bacteria, causing horizontal gene co-transfer (HGcoT). This physical linkage between mobile genes poses a great threat to public health as it facilitates dissemination and co-selection of clinically important genes amongst bacteria. Although rapid accumulation of bacterial whole-genome sequencing data since the 2000s enables study of HGcoT at the population level, results based on genetic co-occurrence counts and simple association tests are usually confounded by bacterial population structure when sampled bacteria belong to the same species, leading to spurious conclusions.<br><br>RESULTS: We have developed a network approach to explore WGS data for evidence of intraspecies HGcoT and have implemented it in R package GeneMates (github.com/wanyuac/GeneMates). The package takes as input an allelic presence-absence matrix of interested genes and a matrix of core-genome single-nucleotide polymorphisms, performs association tests with linear mixed models controlled for population structure, produces a network of significantly associated alleles, and identifies clusters within the network as plausible co-transferred alleles. GeneMates users may choose to score consistency of allelic physical distances measured in genome assemblies using a novel approach we have developed and overlay scores to the network for further evidence of HGcoT. Validation studies of GeneMates on known acquired antimicrobial resistance genes in Escherichia coli and Salmonella Typhimurium show advantages of our network approach over simple association analysis: (1) distinguishing between allelic co-occurrence driven by HGcoT and that driven by clonal reproduction, (2) evaluating effects of population structure on allelic co-occurrence, and (3) direct links between allele clusters in the network and MGEs when physical distances are incorporated.<br><br>CONCLUSION: GeneMates offers an effective approach to detection of intraspecies HGcoT using WGS data.}, }
@article {pmid32971865, year = {2020}, author = {Roy, NK and Murphy, A and Costa, M}, title = {Arsenic Methyltransferase and Methylation of Inorganic Arsenic.}, journal = {Biomolecules}, volume = {10}, number = {9}, pages = {}, pmid = {32971865}, issn = {2218-273X}, support = {P30 ES000260/ES/NIEHS NIH HHS/United States ; R01 ES022935/ES/NIEHS NIH HHS/United States ; ES026138/NH/NIH HHS/United States ; }, mesh = {Animals ; Arsenic/*metabolism ; Cysteine/genetics/*metabolism ; Humans ; Methylation ; Methyltransferases/classification/genetics/*metabolism ; Phylogeny ; Polymorphism, Single Nucleotide ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Arsenic occurs naturally in the environment, and exists predominantly as inorganic arsenite (As (III) and arsenate As (V)). Arsenic contamination of drinking water has long been recognized as a major global health concern. Arsenic exposure causes changes in skin color and lesions, and more severe health conditions such as black foot disease as well as various cancers originating in the lungs, skin, and bladder. In order to efficiently metabolize and excrete arsenic, it is methylated to monomethylarsonic and dimethylarsinic acid. One single enzyme, arsenic methyltransferase (AS3MT) is responsible for generating both metabolites. AS3MT has been purified from several mammalian and nonmammalian species, and its mRNA sequences were determined from amino acid sequences. With the advent of genome technology, mRNA sequences of AS3MT have been predicted from many species throughout the animal kingdom. Horizontal gene transfer had been postulated for this gene through phylogenetic studies, which suggests the importance of this gene in appropriately handling arsenic exposures in various organisms. An altered ability to methylate arsenic is dependent on specific single nucleotide polymorphisms (SNPs) in AS3MT. Reduced AS3MT activity resulting in poor metabolism of iAs has been shown to reduce expression of the tumor suppressor gene, p16, which is a potential pathway in arsenic carcinogenesis. Arsenic is also known to induce oxidative stress in cells. However, the presence of antioxidant response elements (AREs) in the promoter sequences of AS3MT in several species does not correlate with the ability to methylate arsenic. ARE elements are known to bind NRF2 and induce antioxidant enzymes to combat oxidative stress. NRF2 may be partly responsible for the biotransformation of iAs and the generation of methylated arsenic species via AS3MT. In this article, arsenic metabolism, excretion, and toxicity, a discussion of the AS3MT gene and its evolutionary history, and DNA methylation resulting from arsenic exposure have been reviewed.}, }
@article {pmid32968092, year = {2020}, author = {Lapadula, WJ and Mascotti, ML and Juri Ayub, M}, title = {Whitefly genomes contain ribotoxin coding genes acquired from plants.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {15503}, pmid = {32968092}, issn = {2045-2322}, mesh = {Animals ; Gene Expression Profiling ; Gene Transfer, Horizontal/*genetics ; Genes, Insect/*genetics ; Genes, Plant/*genetics ; Genome, Insect/*genetics ; Hemiptera/*genetics ; Phylogeny ; RNA, Ribosomal, 28S/genetics ; Ribosome Inactivating Proteins/*genetics ; Selection, Genetic/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Ribosome inactivating proteins (RIPs) are RNA N-glycosidases that depurinate a specific adenine residue in the conserved sarcin/ricin loop of 28S rRNA. These enzymes are widely distributed among plants and bacteria. Previously, we have described for the first time RIP genes in mosquitoes belonging to the Culicidae family. We showed that these genes are derived from a single event of horizontal gene transfer (HGT) from a prokaryotic donor. Mosquito RIP genes are evolving under purifying selection, strongly suggesting that these toxins have acquired a functional role. In this work, we show the existence of two RIP encoding genes in the genome of the whitefly Bemisia tabaci, a hemiptera species belonging to the Aleyrodidae family distantly related to mosquitoes. Contamination artifacts were ruled out analyzing three independent B. tabaci genome databases. In contrast to mosquito RIPs, whitefly genes harbor introns and according to transcriptomic evidence are transcribed and spliced. Phylogeny and the taxonomic distribution strongly support that whitefly RIP genes are derived from an independent HGT event from a plant source. These results, along with our previous description of RIPs in Diptera, suggest that the acquired genes are functional in these insects and confer some fitness advantage.}, }
@article {pmid32966583, year = {2020}, author = {Carreira, C and Lønborg, C and Kühl, M and Lillebø, AI and Sandaa, RA and Villanueva, L and Cruz, S}, title = {Fungi and viruses as important players in microbial mats.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {11}, pages = {}, doi = {10.1093/femsec/fiaa187}, pmid = {32966583}, issn = {1574-6941}, mesh = {*Ecosystem ; Food Chain ; Fresh Water ; Fungi/genetics ; *Viruses/genetics ; }, abstract = {Microbial mats are compacted, surface-associated microbial ecosystems reminiscent of the first living communities on early Earth. While often considered predominantly prokaryotic, recent findings show that both fungi and viruses are ubiquitous in microbial mats, albeit their functional roles remain unknown. Fungal research has mostly focused on terrestrial and freshwater ecosystems where fungi are known as important recyclers of organic matter, whereas viruses are exceptionally abundant and important in aquatic ecosystems. Here, viruses have shown to affect organic matter cycling and the diversity of microbial communities by facilitating horizontal gene transfer and cell lysis. We hypothesise fungi and viruses to have similar roles in microbial mats. Based on the analysis of previous research in terrestrial and aquatic ecosystems, we outline novel hypotheses proposing strong impacts of fungi and viruses on element cycling, food web structure and function in microbial mats, and outline experimental approaches for studies needed to understand these interactions.}, }
@article {pmid32965219, year = {2020}, author = {Kurushima, J and Campo, N and van Raaphorst, R and Cerckel, G and Polard, P and Veening, JW}, title = {Unbiased homeologous recombination during pneumococcal transformation allows for multiple chromosomal integration events.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, pmid = {32965219}, issn = {2050-084X}, support = {31003A_172861//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/International ; 771534- PneumoCaTChER.//European Commission/International ; ANR-10-BLAN-1331//Agence Nationale de la Recherche/International ; 40AR40_185533//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/International ; EXStasis-17-CE13-0031-01//Agence Nationale de la Recherche/International ; }, mesh = {Drug Resistance, Bacterial/genetics ; *Homologous Recombination ; Single-Cell Analysis ; Streptococcus pneumoniae/*genetics ; }, abstract = {The spread of antimicrobial resistance and vaccine escape in the human pathogen Streptococcus pneumoniae can be largely attributed to competence-induced transformation. Here, we studied this process at the single-cell level. We show that within isogenic populations, all cells become naturally competent and bind exogenous DNA. We find that transformation is highly efficient and that the chromosomal location of the integration site or whether the transformed gene is encoded on the leading or lagging strand has limited influence on recombination efficiency. Indeed, we have observed multiple recombination events in single recipients in real-time. However, because of saturation and because a single-stranded donor DNA replaces the original allele, transformation efficiency has an upper threshold of approximately 50% of the population. The fixed mechanism of transformation results in a fail-safe strategy for the population as half of the population generally keeps an intact copy of the original genome.}, }
@article {pmid32963323, year = {2020}, author = {Neil, K and Allard, N and Grenier, F and Burrus, V and Rodrigue, S}, title = {Highly efficient gene transfer in the mouse gut microbiota is enabled by the Incl2 conjugative plasmid TP114.}, journal = {Communications biology}, volume = {3}, number = {1}, pages = {523}, pmid = {32963323}, issn = {2399-3642}, support = {159817//CIHR/Canada ; 414079//CIHR/Canada ; }, mesh = {Animals ; Conjugation, Genetic/*genetics ; DNA Transposable Elements/genetics ; DNA, Bacterial/genetics ; Enterobacteriaceae/genetics ; Escherichia coli/genetics ; Female ; Gastrointestinal Microbiome/*genetics ; Gene Library ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/genetics ; Mice ; Mice, Inbred C57BL ; Plasmids/*genetics ; }, abstract = {The gut microbiota is a suspected hotspot for bacterial conjugation due to its high density and diversity of microorganisms. However, the contribution of different conjugative plasmid families to horizontal gene transfer in this environment remains poorly characterized. Here, we systematically quantified the transfer rates in the mouse intestinal tract for 13 conjugative plasmids encompassing 10 major incompatibility groups. The vast majority of these plasmids were unable to perform conjugation in situ or only reached relatively low transfer rates. Surprisingly, IncI2 conjugative plasmid TP114 was identified as a proficient DNA delivery system in this environment, with the ability to transfer to virtually 100% of the probed recipient bacteria. We also show that a type IV pilus present in I-complex conjugative plasmids plays a crucial role for the transfer of TP114 in the mouse intestinal microbiota, most likely by contributing to mating pair stabilization. These results provide new insights on the mobility of genes in the gut microbiota and highlights TP114 as a very efficient DNA delivery system of interest for microbiome editing tools.}, }
@article {pmid32958711, year = {2020}, author = {Rada, AM and De La Cadena, E and Agudelo, C and Capataz, C and Orozco, N and Pallares, C and Dinh, AQ and Panesso, D and Ríos, R and Diaz, L and Correa, A and Hanson, BM and Villegas, MV and Arias, CA and Restrepo, E}, title = {Dynamics of blaKPC-2 Dissemination from Non-CG258 Klebsiella pneumoniae to Other Enterobacterales via IncN Plasmids in an Area of High Endemicity.}, journal = {Antimicrobial agents and chemotherapy}, volume = {64}, number = {12}, pages = {}, pmid = {32958711}, issn = {1098-6596}, support = {P01 AI152999/AI/NIAID NIH HHS/United States ; R21 AI143229/AI/NIAID NIH HHS/United States ; R01 AI134637/AI/NIAID NIH HHS/United States ; K24 AI121296/AI/NIAID NIH HHS/United States ; R01 AI093749/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics ; Carbapenems ; Colombia/epidemiology ; Humans ; Infant, Newborn ; *Klebsiella Infections/epidemiology ; *Klebsiella pneumoniae/genetics ; Plasmids/genetics ; beta-Lactamases/genetics ; }, abstract = {Carbapenem-resistant Enterobacterales (CRE) pose a significant threat to global public health. The most important mechanism for carbapenem resistance is the production of carbapenemases. Klebsiella pneumoniae carbapenemase (KPC) represents one of the main carbapenemases worldwide. Complex mechanisms of blaKPC dissemination have been reported in Colombia, a country with a high endemicity of carbapenem resistance. Here, we characterized the dynamics of dissemination of blaKPC gene among CRE infecting and colonizing patients in three hospitals localized in a highly endemic area of Colombia (2013 and 2015). We identified the genomic characteristics of KPC-producing Enterobacterales recovered from patients infected/colonized and reconstructed the dynamics of dissemination of blaKPC-2 using both short and long read sequencing. We found that spread of blaKPC-2 among Enterobacterales in the participating hospitals was due to intra- and interspecies horizontal gene transfer (HGT) mediated by promiscuous plasmids associated with transposable elements that was originated from a multispecies outbreak of KPC-producing Enterobacterales in a neonatal intensive care unit. The plasmids were detected in isolates recovered in other units within the same hospital and nearby hospitals. The gene "epidemic" was driven by IncN-pST15-type plasmids carrying a novel Tn4401b structure and non-Tn4401 elements (NTEKPC) in Klebsiella spp., Escherichia coli, Enterobacter spp., and Citrobacter spp. Of note, mcr-9 was found to coexist with blaKPC-2 in species of the Enterobacter cloacae complex. Our findings suggest that the main mechanism for dissemination of blaKPC-2 is HGT mediated by highly transferable plasmids among species of Enterobacterales in infected/colonized patients, presenting a major challenge for public health interventions in developing countries such as Colombia.}, }
@article {pmid32958633, year = {2020}, author = {Kibby, EM and Whiteley, AT}, title = {The Linguistics of Bacterial Conflict Systems Reveal Ancient Origins of Eukaryotic Innate Immunity.}, journal = {Journal of bacteriology}, volume = {202}, number = {24}, pages = {}, pmid = {32958633}, issn = {1098-5530}, support = {T32 GM008759/GM/NIGMS NIH HHS/United States ; }, mesh = {*Bacteria/genetics ; *Eukaryota ; Immune System ; Immunity, Innate ; Linguistics ; }, abstract = {The arms race between bacteria and their competitors has produced an astounding variety of conflict systems that are shared via horizontal gene transfer across bacterial populations. In this issue of the Journal of Bacteriology, Burroughs and Aravind investigate how these biological conflict systems have been mixed and matched into new configurations, often with novel protein domains (A. M. Burroughs and L. Aravind, J Bacteriol 202:e00365-20, 2020, https://doi.org/10.1128/JB.00365-20). The authors additionally characterize the evolutionary history of genes in eukaryotes that appear to have been acquired from these prokaryotic defense systems.}, }
@article {pmid32956455, year = {2021}, author = {Ip, JC and Xu, T and Sun, J and Li, R and Chen, C and Lan, Y and Han, Z and Zhang, H and Wei, J and Wang, H and Tao, J and Cai, Z and Qian, PY and Qiu, JW}, title = {Host-Endosymbiont Genome Integration in a Deep-Sea Chemosymbiotic Clam.}, journal = {Molecular biology and evolution}, volume = {38}, number = {2}, pages = {502-518}, pmid = {32956455}, issn = {1537-1719}, support = {EP-C-18-007/EPA/EPA/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Bivalvia/*microbiology/physiology ; *Gene Transfer, Horizontal ; *Genome ; Hemoglobins/chemistry/genetics ; Hydrothermal Vents/*microbiology ; Immune System ; Phylogeny ; Piscirickettsiaceae/genetics ; *Symbiosis ; }, abstract = {Endosymbiosis with chemosynthetic bacteria has enabled many deep-sea invertebrates to thrive at hydrothermal vents and cold seeps, but most previous studies on this mutualism have focused on the bacteria only. Vesicomyid clams dominate global deep-sea chemosynthesis-based ecosystems. They differ from most deep-sea symbiotic animals in passing their symbionts from parent to offspring, enabling intricate coevolution between the host and the symbiont. Here, we sequenced the genomes of the clam Archivesica marissinica (Bivalvia: Vesicomyidae) and its bacterial symbiont to understand the genomic/metabolic integration behind this symbiosis. At 1.52 Gb, the clam genome encodes 28 genes horizontally transferred from bacteria, a large number of pseudogenes and transposable elements whose massive expansion corresponded to the timing of the rise and subsequent divergence of symbiont-bearing vesicomyids. The genome exhibits gene family expansion in cellular processes that likely facilitate chemoautotrophy, including gas delivery to support energy and carbon production, metabolite exchange with the symbiont, and regulation of the bacteriocyte population. Contraction in cellulase genes is likely adaptive to the shift from phytoplankton-derived to bacteria-based food. It also shows contraction in bacterial recognition gene families, indicative of suppressed immune response to the endosymbiont. The gammaproteobacterium endosymbiont has a reduced genome of 1.03 Mb but retains complete pathways for sulfur oxidation, carbon fixation, and biosynthesis of 20 common amino acids, indicating the host's high dependence on the symbiont for nutrition. Overall, the host-symbiont genomes show not only tight metabolic complementarity but also distinct signatures of coevolution allowing the vesicomyids to thrive in chemosynthesis-based ecosystems.}, }
@article {pmid32954887, year = {2020}, author = {Nadeem, SF and Gohar, UF and Tahir, SF and Mukhtar, H and Pornpukdeewattana, S and Nukthamna, P and Moula Ali, AM and Bavisetty, SCB and Massa, S}, title = {Antimicrobial resistance: more than 70 years of war between humans and bacteria.}, journal = {Critical reviews in microbiology}, volume = {46}, number = {5}, pages = {578-599}, doi = {10.1080/1040841X.2020.1813687}, pmid = {32954887}, issn = {1549-7828}, mesh = {Animals ; Anti-Bacterial Agents/history/*pharmacology ; Bacteria/*drug effects/genetics ; Bacterial Infections/drug therapy/history/*microbiology ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; History, 20th Century ; History, 21st Century ; Humans ; Plasmids/genetics/metabolism ; }, abstract = {Development of antibiotic resistance in bacteria is one of the major issues in the present world and one of the greatest threats faced by mankind. Resistance is spread through both vertical gene transfer (parent to offspring) as well as by horizontal gene transfer like transformation, transduction and conjugation. The main mechanisms of resistance are limiting uptake of a drug, modification of a drug target, inactivation of a drug, and active efflux of a drug. The highest quantities of antibiotic concentrations are usually found in areas with strong anthropogenic pressures, for example medical source (e.g., hospitals) effluents, pharmaceutical industries, wastewater influents, soils treated with manure, animal husbandry and aquaculture (where antibiotics are generally used as in-feed preparations). Hence, the strong selective pressure applied by antimicrobial use has forced microorganisms to evolve for survival. The guts of animals and humans, wastewater treatment plants, hospital and community effluents, animal husbandry and aquaculture runoffs have been designated as "hotspots for AMR genes" because the high density of bacteria, phages, and plasmids in these settings allows significant genetic exchange and recombination. Evidence from the literature suggests that the knowledge of antibiotic resistance in the population is still scarce. Tackling antimicrobial resistance requires a wide range of strategies, for example, more research in antibiotic production, the need of educating patients and the general public, as well as developing alternatives to antibiotics (briefly discussed in the conclusions of this article).}, }
@article {pmid32943748, year = {2021}, author = {Chen, MY and Teng, WK and Zhao, L and Hu, CX and Zhou, YK and Han, BP and Song, LR and Shu, WS}, title = {Comparative genomics reveals insights into cyanobacterial evolution and habitat adaptation.}, journal = {The ISME journal}, volume = {15}, number = {1}, pages = {211-227}, pmid = {32943748}, issn = {1751-7370}, mesh = {Adaptation, Physiological/genetics ; *Cyanobacteria/genetics ; Ecosystem ; Genomics ; Humans ; Phylogeny ; }, abstract = {Cyanobacteria are photosynthetic prokaryotes that inhabit diverse aquatic and terrestrial environments. However, the evolutionary mechanisms involved in the cyanobacterial habitat adaptation remain poorly understood. Here, based on phylogenetic and comparative genomic analyses of 650 cyanobacterial genomes, we investigated the genetic basis of cyanobacterial habitat adaptation (marine, freshwater, and terrestrial). We show: (1) the expansion of gene families is a common strategy whereby terrestrial cyanobacteria cope with fluctuating environments, whereas the genomes of many marine strains have undergone contraction to adapt to nutrient-poor conditions. (2) Hundreds of genes are strongly associated with specific habitats. Genes that are differentially abundant in genomes of marine, freshwater, and terrestrial cyanobacteria were found to be involved in light sensing and absorption, chemotaxis, nutrient transporters, responses to osmotic stress, etc., indicating the importance of these genes in the survival and adaptation of organisms in specific habitats. (3) A substantial fraction of genes that facilitate the adaptation of Cyanobacteria to specific habitats are contributed by horizontal gene transfer, and such genetic exchanges are more frequent in terrestrial cyanobacteria. Collectively, our results further our understandings of the adaptations of Cyanobacteria to different environments, highlighting the importance of ecological constraints imposed by the environment in shaping the evolution of Cyanobacteria.}, }
@article {pmid32941984, year = {2020}, author = {Wang, M and Ruan, R}, title = {Genome-wide identification and functional analysis of the horizontally transferred genes in Penicillium.}, journal = {Genomics}, volume = {112}, number = {6}, pages = {5037-5043}, doi = {10.1016/j.ygeno.2020.09.025}, pmid = {32941984}, issn = {1089-8646}, mesh = {Gene Expression ; *Gene Transfer, Horizontal ; Genome, Fungal ; Metabolic Networks and Pathways/genetics ; Penicillium/*genetics/metabolism ; }, abstract = {Horizontal gene transfer (HGT) is the transmission of genetic material between different evolutionary lineages and is believed to be an important source of genomic innovation in fungi. In this study, we searched for prokaryotic-derived HGTs in 23 fully sequenced genomes using a comprehensive phylogenomic pipeline followed by manual curation. We found strong support for 60 HGT events comprising 190 genes putatively acquired from bacteria. HGT affected all Penicillium species to various degrees. Gene duplication events happened to 3 HGT genes after the transmission. Most HGT events include genes encoding a variety of enzymes, which are associated with sugar, amino acid, and lipid metabolism. Transcriptome data from 6 Penicillium species revealed that 33 of 35 HGT genes showed expression under the conditions tested and 16 genes were differentially expressed. Our results suggest an important role for inter-domain gene transfers in shaping the genome of Penicillium fungi.}, }
@article {pmid32938241, year = {2020}, author = {Daniali, M and Nikfar, S and Abdollahi, M}, title = {Antibiotic resistance propagation through probiotics.}, journal = {Expert opinion on drug metabolism &amp; toxicology}, volume = {16}, number = {12}, pages = {1207-1215}, doi = {10.1080/17425255.2020.1825682}, pmid = {32938241}, issn = {1744-7607}, mesh = {Animals ; Anti-Infective Agents/*pharmacology ; Drug Resistance, Microbial/*genetics ; Gastrointestinal Microbiome/physiology ; Gastrointestinal Tract/microbiology ; Gene Transfer, Horizontal ; Genetic Therapy/methods ; Humans ; Precision Medicine ; Probiotics/administration &amp; dosage/*adverse effects ; }, abstract = {INTRODUCTION: The widespread use of probiotics globally has established an argument against their safety profile. Recent studies investigated the gastrointestinal tract (GIT) as a reservoir for antibiotic resistance genes and horizontal gene transfer (HGT) amongst opportunistic pathogens, probiotics, and the normal microbiota which might cause severe clinical implications.<br><br>AREAS COVERED: In this review, we aimed to discuss the potential role of probiotics in spreading antibiotic resistance. All relevant data were found through online/updated databases such as PubMed, Google Scholar, and Clinicaltrials.gov. This review is based on the studies undertaken over the past two decades (2000-2020).<br><br>EXPERT OPINION: Microorganisms are capable of transferring resistance genes to survive against antimicrobial medications. Transference of resistance genes among pathogens, probiotics, and gut microbiota in the GIT through HGT endow probiotics as a possible source for antimicrobial resistance genes, which is responsible for the development of the antibiotic resistance crisis. According to the expression of genes in mechanisms of antibiotics resistance and probiotics HGT, the hypothesis of the role of these microorganisms in personalized medicine and gene therapy could also be considered.}, }
@article {pmid32935885, year = {2021}, author = {Raut, P and Glass, JB and Lieberman, RL}, title = {Archaeal roots of intramembrane aspartyl protease siblings signal peptide peptidase and presenilin.}, journal = {Proteins}, volume = {89}, number = {2}, pages = {232-241}, doi = {10.1002/prot.26009}, pmid = {32935885}, issn = {1097-0134}, support = {80NSSC19K0477/NASA/NASA/United States ; }, mesh = {Amino Acid Sequence ; Aspartic Acid Proteases/chemistry/*genetics/metabolism ; Bacteria/classification/enzymology/*genetics ; Biological Evolution ; Catalytic Domain ; Computational Biology/methods ; Conserved Sequence ; Crenarchaeota/classification/enzymology/*genetics ; Euryarchaeota/classification/enzymology/*genetics ; Gene Expression ; Humans ; Isoenzymes/chemistry/genetics/metabolism ; Nanoarchaeota/classification/enzymology/*genetics ; Phylogeny ; Presenilins/chemistry/*genetics/metabolism ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Sorting Signals/genetics ; Sequence Alignment ; Sequence Analysis, Protein ; Sequence Homology, Amino Acid ; }, abstract = {Signal peptides help newly synthesized proteins reach the cell membrane or be secreted. As part of a biological process key to immune response and surveillance in humans, and associated with diseases, for example, Alzheimer, remnant signal peptides and other transmembrane segments are proteolyzed by the intramembrane aspartyl protease (IAP) enzyme family. Here, we identified IAP orthologs throughout the tree of life. In addition to eukaryotes, IAPs are encoded in metabolically diverse archaea from a wide range of environments. We found three distinct clades of archaeal IAPs: (a) Euryarchaeota (eg, halophilic Halobacteriales, methanogenic Methanosarcinales and Methanomicrobiales, marine Poseidoniales, acidophilic Thermoplasmatales, hyperthermophilic Archaeoglobus spp.), (b) DPANN, and (c) Bathyarchaeota, Crenarchaeota, and Asgard. IAPs were also present in bacterial genomes from uncultivated members of Candidate Phylum Radiation, perhaps due to horizontal gene transfer from DPANN archaeal lineages. Sequence analysis of the catalytic motif YD…GXGD (where X is any amino acid) in IAPs from archaea and bacteria reveals WD in Lokiarchaeota and many residue types in the X position. Gene neighborhood analysis in halophilic archaea shows IAP genes near corrinoid transporters (btuCDF genes). In marine Euryarchaeota, a putative BtuF-like domain is found in N-terminus of the IAP gene, suggesting a role for these IAPs in metal ion cofactor or other nutrient scavenging. Interestingly, eukaryotic IAP family members appear to have evolved either from Euryarchaeota or from Asgard archaea. Taken together, our phylogenetic and bioinformatics analysis should prompt experiments to probe the biological roles of IAPs in prokaryotic secretomes.}, }
@article {pmid32934307, year = {2020}, author = {French, KE and Zhou, Z and Terry, N}, title = {Horizontal 'gene drives' harness indigenous bacteria for bioremediation.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {15091}, pmid = {32934307}, issn = {2045-2322}, support = {S10 OD018136/OD/NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; *Biodegradation, Environmental ; Ecosystem ; Escherichia coli/genetics ; Escherichia coli Proteins/genetics ; Hydrocarbons/metabolism ; Petroleum/metabolism ; Petroleum Pollution ; Soil/chemistry ; Soil Microbiology ; Soil Pollutants/chemistry ; }, abstract = {Engineering bacteria to clean-up oil spills is rapidly advancing but faces regulatory hurdles and environmental concerns. Here, we develop a new technology to harness indigenous soil microbial communities for bioremediation by flooding local populations with catabolic genes for petroleum hydrocarbon degradation. Overexpressing three enzymes (almA, xylE, p450cam) in Escherichia coli led to degradation of 60-99% of target hydrocarbon substrates. Mating experiments, fluorescence microscopy and TEM revealed indigenous bacteria could obtain these vectors from E. coli through several mechanisms of horizontal gene transfer (HGT), including conjugation and cytoplasmic exchange through nanotubes. Inoculating petroleum-polluted sediments with E. coli carrying the vector pSF-OXB15-p450camfusion showed that the E. coli cells died after five days but a variety of bacteria received and carried the vector for over 60 days after inoculation. Within 60 days, the total petroleum hydrocarbon content of the polluted soil was reduced by 46%. Pilot experiments show that vectors only persist in indigenous populations when under selection pressure, disappearing when this carbon source is removed. This approach to remediation could prime indigenous bacteria for degrading pollutants while providing minimal ecosystem disturbance.}, }
@article {pmid32934114, year = {2020}, author = {Yin, Z and Zhang, S and Wei, Y and Wang, M and Ma, S and Yang, S and Wang, J and Yuan, C and Jiang, L and Du, Y}, title = {Horizontal Gene Transfer Clarifies Taxonomic Confusion and Promotes the Genetic Diversity and Pathogenicity of Plesiomonas shigelloides.}, journal = {mSystems}, volume = {5}, number = {5}, pages = {}, pmid = {32934114}, issn = {2379-5077}, abstract = {Plesiomonas shigelloides is an emerging pathogen that has been shown to be involved in gastrointestinal diseases and extraintestinal infections in humans. However, the taxonomic position, evolutionary dynamics, and pathogenesis of P. shigelloides remain unclear. We reported the draft genome sequences of 12 P. shigelloides strains representing different serogroups. We were able to determine a clear distinction between P. shigelloides and other members of Enterobacterales via core genome phylogeny, Neighbor-Net network, and average genome identity analysis. The pan-genome analysis of P. shigelloides revealed extensive genetic diversity and presented large flexible gene repertoires, while the core genome phylogeny exhibited a low level of clonality. The discordance between the core genome phylogeny and the pan-genome phylogeny indicated that flexible accessory genomes account for an important proportion of the evolution of P. shigelloides, which was subsequently characterized by determinations of hundreds of horizontally transferred genes (horizontal genes), massive gene expansions and contractions, and diverse mobile genetic elements (MGEs). The apparently high levels of horizontal gene transfer (HGT) in P. shigelloides were conferred from bacteria with novel properties from other taxa (mainly Vibrionaceae and Aeromonadaceae), which caused the historical taxonomic confusion and shaped the virulence gene pools. Furthermore, P. shigelloides genomes contain many macromolecular secretion system genes, virulence factor genes, and resistance genes, indicating its potential to cause intestinal and invasive infections. Collectively, our work provides insights into the phylogenetic position, evolutionary dynamic, and pathogenesis of P. shigelloides at the genomic level, which could facilitate the observation and research of this important pathogen.IMPORTANCE The taxonomic position of P. shigelloides has been the subject of debate for a long time, and until now, the evolutionary dynamics and pathogenesis of P. shigelloides were unclear. In this study, pan-genome analysis indicated extensive genetic diversity and the presence of large and variable gene repertoires. Our results revealed that horizontal gene transfer was the focal driving force for the genetic diversity of the P. shigelloides pan-genome and might have contributed to the emergence of novel properties. Vibrionaceae and Aeromonadaceae were found to be the predominant donor taxa for horizontal genes, which might have caused the taxonomic confusion historically. Comparative genomic analysis revealed the potential of P. shigelloides to cause intestinal and invasive diseases. Our results could advance the understanding of the evolution and pathogenesis of P. shigelloides, particularly in elucidating the role of horizontal gene transfer and investigating virulence-related elements.}, }
@article {pmid32933329, year = {2021}, author = {Wakade, VS and Shende, P}, title = {Strategic advancements and multimodal applications of biofilm therapy.}, journal = {Expert opinion on biological therapy}, volume = {21}, number = {3}, pages = {395-412}, doi = {10.1080/14712598.2020.1822319}, pmid = {32933329}, issn = {1744-7682}, mesh = {Bacteria ; *Biofilms ; Humans ; *Quorum Sensing ; }, abstract = {INTRODUCTION: Biofilm is a layer of mucilage consisting of bacterial species like Escherichia coli and Streptococcus aureus adhering to the solid cell surface. Biofilm is an important and novel approach in a delivery system consisting of six elements that includes extracellular DNA, enzymes, proteins, bacteria, exopolysaccharides and water channels. The biofilm formation is based on two mechanisms: extra polymeric substance and quorum sensing. The microbes present in biofilm prevent direct interaction between the cell surface and foreign materials, like allergens, or toxic gases, like carbon-monoxide and chlorofluorocarbon, entering the body.<br><br>AREAS COVERED: The authors focus on the novel applications of biofilms such as adhesives, tissue engineering, targeted delivery system, probiotics, nutrients delivery, etc. Moreover, the information of the factors for biofilm formation, techniques useful in biofilm formation, and clinical studies are also covered in this article.<br><br>EXPERT OPINION: Many people believe that biofilms have a negative impact on human health, but the expert opinion states that biofilm is a futuristic approach useful in therapeutics for the treatment of tumors and cancer. Biofilms can be combined with novel delivery systems such as nanoparticles, microparticles, etc. for better therapeutic action.}, }
@article {pmid32931580, year = {2021}, author = {Chernomor, O and Peters, L and Schneidewind, J and Loeschcke, A and Knieps-Grünhagen, E and Schmitz, F and von Lieres, E and Kutta, RJ and Svensson, V and Jaeger, KE and Drepper, T and von Haeseler, A and Krauss, U}, title = {Complex Evolution of Light-Dependent Protochlorophyllide Oxidoreductases in Aerobic Anoxygenic Phototrophs: Origin, Phylogeny, and Function.}, journal = {Molecular biology and evolution}, volume = {38}, number = {3}, pages = {819-837}, pmid = {32931580}, issn = {1537-1719}, mesh = {*Evolution, Molecular ; Molecular Structure ; Oxidoreductases Acting on CH-CH Group Donors/chemistry/*genetics/metabolism ; Photosynthesis ; Phylogeny ; Proteobacteria/*enzymology/*genetics ; Rhodobacteraceae ; }, abstract = {Light-dependent protochlorophyllide oxidoreductase (LPOR) and dark-operative protochlorophyllide oxidoreductase are evolutionary and structurally distinct enzymes that are essential for the synthesis of (bacterio)chlorophyll, the primary pigment needed for both anoxygenic and oxygenic photosynthesis. In contrast to the long-held hypothesis that LPORs are only present in oxygenic phototrophs, we recently identified a functional LPOR in the aerobic anoxygenic phototrophic bacterium (AAPB) Dinoroseobacter shibae and attributed its presence to a single horizontal gene transfer event from cyanobacteria. Here, we provide evidence for the more widespread presence of genuine LPOR enzymes in AAPBs. An exhaustive bioinformatics search identified 36 putative LPORs outside of oxygenic phototrophic bacteria (cyanobacteria) with the majority being AAPBs. Using in vitro and in vivo assays, we show that the large majority of the tested AAPB enzymes are genuine LPORs. Solution structural analyses, performed for two of the AAPB LPORs, revealed a globally conserved structure when compared with a well-characterized cyanobacterial LPOR. Phylogenetic analyses suggest that LPORs were transferred not only from cyanobacteria but also subsequently between proteobacteria and from proteobacteria to Gemmatimonadetes. Our study thus provides another interesting example for the complex evolutionary processes that govern the evolution of bacteria, involving multiple horizontal gene transfer events that likely occurred at different time points and involved different donors.}, }
@article {pmid32929737, year = {2021}, author = {Garcia, LE and Edera, AA and Palmer, JD and Sato, H and Sanchez-Puerta, MV}, title = {Horizontal gene transfers dominate the functional mitochondrial gene space of a holoparasitic plant.}, journal = {The New phytologist}, volume = {229}, number = {3}, pages = {1701-1714}, doi = {10.1111/nph.16926}, pmid = {32929737}, issn = {1469-8137}, mesh = {DNA, Mitochondrial ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; *Genes, Mitochondrial ; *Genome, Mitochondrial ; Phylogeny ; }, abstract = {Although horizontal gene transfer (HGT) is common in angiosperm mitochondrial DNAs (mtDNAs), few cases of functional foreign genes have been identified. The one outstanding candidate for large-scale functional HGT is the holoparasite Lophophytum mirabile, whose mtDNA has lost most native genes but contains intact foreign homologs acquired from legume host plants. To investigate the extent to which this situation results from functional replacement of native by foreign genes, functional mitochondrial gene transfer to the nucleus, and/or loss of mitochondrial biochemical function in the context of extreme parasitism, we examined the Lophophytum mitochondrial and nuclear transcriptomes by deep paired-end RNA sequencing. Most foreign mitochondrial genes in Lophophytum are highly transcribed, accurately spliced, and efficiently RNA edited. By contrast, we found no evidence for functional gene transfer to the nucleus or loss of mitochondrial functions in Lophophytum. Many functional replacements occurred via the physical replacement of native genes by foreign genes. Some of these events probably occurred as the final act of HGT itself. Lophophytum mtDNA has experienced an unprecedented level of functional replacement of native genes by foreign copies. This raises important questions concerning population-genetic and molecular regimes that underlie such a high level of foreign gene takeover.}, }
@article {pmid32929209, year = {2021}, author = {Laurenceau, R and Raho, N and Forget, M and Arellano, AA and Chisholm, SW}, title = {Frequency of mispackaging of Prochlorococcus DNA by cyanophage.}, journal = {The ISME journal}, volume = {15}, number = {1}, pages = {129-140}, pmid = {32929209}, issn = {1751-7370}, mesh = {*Bacteriophages/genetics ; DNA ; Gene Transfer, Horizontal ; Genome, Viral ; *Prochlorococcus/genetics ; }, abstract = {Prochlorococcus cells are the numerically dominant phototrophs in the open ocean. Cyanophages that infect them are a notable fraction of the total viral population in the euphotic zone, and, as vehicles of horizontal gene transfer, appear to drive their evolution. Here we examine the propensity of three cyanophages-a podovirus, a siphovirus, and a myovirus-to mispackage host DNA in their capsids while infecting Prochlorococcus, the first step in phage-mediated horizontal gene transfer. We find the mispackaging frequencies are distinctly different among the three phages. Myoviruses mispackage host DNA at low and seemingly fixed frequencies, while podo- and siphoviruses vary in their mispackaging frequencies by orders of magnitude depending on growth light intensity. We link this difference to the concentration of intracellular reactive oxygen species and protein synthesis rates, both parameters increasing in response to higher light intensity. Based on our findings, we propose a model of mispackaging frequency determined by the imbalance between the production of capsids and the number of phage genome copies during infection: when protein synthesis rate increase to levels that the phage cannot regulate, they lead to an accumulation of empty capsids, in turn triggering more frequent host DNA mispackaging errors.}, }
@article {pmid32929149, year = {2020}, author = {Yang, F and Han, B and Gu, Y and Zhang, K}, title = {Swine liquid manure: a hotspot of mobile genetic elements and antibiotic resistance genes.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {15037}, pmid = {32929149}, issn = {2045-2322}, mesh = {Animal Husbandry/methods ; Animals ; *DNA Transposable Elements ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Manure/*microbiology ; Microbiota ; Swine/*microbiology/physiology ; }, abstract = {The overuse or abuse of antibiotics as veterinary medicine and growth promoters accelerates antibiotic resistance, creating a serious threat to public health in the world. Swine liquid manure as an important reservoir of antibiotic resistance genes (ARGs) has received much attention, but little information is known regarding the occurrence, persistence and fate of ARGs-associated mobile genetic elements (MGEs) in swine farms, especially their change patterns and removal in full-scale piggery wastewater treatment systems (PWWTSs). In this study, we searched the presence and distribution of MGEs and associated ARGs in swine farms, and addressed their fate and seasonal variation in full-scale PWWTSs by real-time quantitative PCR (qPCR). Our results revealed class 1 integrons, class 2 integrons and conjugative plasmids were prevalent in pig feces and piggery wastewater. A clear pattern of these MGE levels in swine liquid manure was also observed, i.e., intI1 > intI2 > traA (p < 0.01), and their absolute abundances in winter were all higher than that in summer with 0.07-2.23 logs. Notably, MGEs and ARGs prevailed through various treatment units of PWWTSs, and considerable levels of them were present in the treated effluent discharged from swine farms (up to 10[1]-10[7] copies/mL for MGEs and 10[3]-10[8] copies/mL for ARGs). There were significant correlations between most ARG abundance and MGE levels (p < 0.05), such as tetQ and traA (r = 0.775), sul1 and intI1 (r = 0.847), qnrS and inI2 (r = 0.859), suggesting the potential of ARGs-horizontal transfer. Thus the high prevalence and enrichment of MGEs and ARGs occurred in pig feces and piggery wastewater, also implicating that swine liquid manure could be a hotspot for horizontal transfer of ARGs.}, }
@article {pmid32926145, year = {2020}, author = {Wang, YW and Hess, J and Slot, JC and Pringle, A}, title = {De Novo Gene Birth, Horizontal Gene Transfer, and Gene Duplication as Sources of New Gene Families Associated with the Origin of Symbiosis in Amanita.}, journal = {Genome biology and evolution}, volume = {12}, number = {11}, pages = {2168-2182}, pmid = {32926145}, issn = {1759-6653}, mesh = {Amanita/*genetics ; *Gene Duplication ; *Gene Transfer, Horizontal ; Multigene Family ; Mycorrhizae/*genetics ; Phylogeny ; Selection, Genetic ; Symbiosis/*genetics ; }, abstract = {By introducing novel capacities and functions, new genes and gene families may play a crucial role in ecological transitions. Mechanisms generating new gene families include de novo gene birth, horizontal gene transfer, and neofunctionalization following a duplication event. The ectomycorrhizal (ECM) symbiosis is a ubiquitous mutualism and the association has evolved repeatedly and independently many times among the fungi, but the evolutionary dynamics enabling its emergence remain elusive. We developed a phylogenetic workflow to first understand if gene families unique to ECM Amanita fungi and absent from closely related asymbiotic species are functionally relevant to the symbiosis, and then to systematically infer their origins. We identified 109 gene families unique to ECM Amanita species. Genes belonging to unique gene families are under strong purifying selection and are upregulated during symbiosis, compared with genes of conserved or orphan gene families. The origins of seven of the unique gene families are strongly supported as either de novo gene birth (two gene families), horizontal gene transfer (four), or gene duplication (one). An additional 34 families appear new because of their selective retention within symbiotic species. Among the 109 unique gene families, the most upregulated gene in symbiotic cultures encodes a 1-aminocyclopropane-1-carboxylate deaminase, an enzyme capable of downregulating the synthesis of the plant hormone ethylene, a common negative regulator of plant-microbial mutualisms.}, }
@article {pmid32925946, year = {2020}, author = {Marcelli, B and Karsens, H and Nijland, M and Oudshoorn, R and Kuipers, OP and Kok, J}, title = {Employing lytic phage-mediated horizontal gene transfer in Lactococcus lactis.}, journal = {PloS one}, volume = {15}, number = {9}, pages = {e0238988}, pmid = {32925946}, issn = {1932-6203}, mesh = {Bacteriophages/*genetics ; Cheese/microbiology ; Dairy Products/microbiology ; Food Microbiology/*methods ; Gene Transfer Techniques ; Lactococcus lactis/*genetics ; Plasmids/genetics ; }, abstract = {Lactococcus lactis is a lactic acid bacterium widely used as a starter culture in the manufacture of dairy products, especially a wide variety of cheeses. Improved industrial strains would help to manufacture better food products that can meet the industry's and consumer's demands with respect to e.g. quality, taste, texture and shelf life. Bacteriophage infection of L. lactis starter cultures represents one of the main causes of fermentation failure and consequent economic losses for the dairy industry. In this study, however, we aim at employing bacteriophages for beneficial purposes. We developed an experimental setup to assess whether phage-mediated horizontal gene transfer could be used to enhance the genetic characteristics of L. lactis strains in accordance with the European law regarding the use of genetically modified organisms (GMOs) in the food industry. Although we could not show the transfer of chromosomal DNA we did successfully transduce two dissimilar plasmids from L. lactis strain MG1363 to one of its derivatives employing three different lactococcal bacteriophages.}, }
@article {pmid32925914, year = {2020}, author = {Moffat, J and Chalmers, G and Reid-Smith, R and Mulvey, MR and Agunos, A and Calvert, J and Cormier, A and Ricker, N and Weese, JS and Boerlin, P}, title = {Resistance to extended-spectrum cephalosporins in Escherichia coli and other Enterobacterales from Canadian turkeys.}, journal = {PloS one}, volume = {15}, number = {9}, pages = {e0236442}, pmid = {32925914}, issn = {1932-6203}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology/therapeutic use ; Cephalosporins/*pharmacology/therapeutic use ; Drug Resistance, Bacterial ; Enterobacteriaceae/*drug effects/genetics/isolation &amp; purification ; Enterobacteriaceae Infections/drug therapy/*veterinary ; Escherichia coli/drug effects/genetics/isolation &amp; purification ; Poultry Diseases/*drug therapy/microbiology ; Turkeys/*microbiology ; }, abstract = {The goal of this study was to determine the frequency of resistance to extended-spectrum cephalosporins (ESCs) in Escherichia coli and other Enterobacterales from turkeys in Canada and characterize the associated resistance determinants. Pooled fecal samples were collected in 77 turkey farms across British Columbia, Québec, and Ontario. Isolates were obtained with and without selective enrichment cultures and compared to isolates from diagnostic submissions of suspected colibacillosis cases in Ontario. Isolates were identified using MALDI-TOF and susceptibility to ESCs was assessed by disk diffusion. The presence of blaCMY, blaCTX-M, blaTEM, and blaSHV was tested by PCR. Transformation experiments were used to characterize blaCMY plasmids. Genome sequencing with short and long reads was performed on a representative sample of blaCTX-M-positive isolates to assess isolates relatedness and characterize blaCTX-M plasmids. For the positive enrichment cultures (67% of total samples), 93% (587/610) were identified as E. coli, with only a few other Enterobacterales species identified. The frequency of ESC resistance was low in E. coli isolates from diagnostic submission (4%) and fecal samples without selective enrichment (5%). Of the ESC-resistant Enterobacterales isolates from selective enrichments, 71%, 18%, 14%, and 8% were positive for blaCMY, blaTEM, blaCTX-M, and blaSHV, respectively. IncI1 followed by IncK were the main incompatibility groups identified for blaCMY plasmids. The blaCTX-M-1 gene was found repeatedly on IncI1 plasmids of the pMLST type 3, while blaCTX-M-15, blaCTX-M-55, and blaCTX-M-65 were associated with a variety of IncF plasmids. Clonal spread of strains carrying blaCTX-M genes between turkey farms was observed, as well as the presence of an epidemic blaCTX-M-1 plasmid in unrelated E. coli strains. In conclusion, Enterobacterales resistant to ESCs were still widespread at low concentration in turkey feces two years after the cessation of ceftiofur use. Although blaCMY-2 is the main ESC resistance determinant in E. coli from Canadian turkeys, blaCTX-M genes also occur which are often carried by multidrug resistance plasmids. Both clonal spread and horizontal gene transfer are involved in parallel in the spread of blaCTX-M genes in Enterobacterales from Canadian turkeys.}, }
@article {pmid32918458, year = {2020}, author = {Vancaester, E and Depuydt, T and Osuna-Cruz, CM and Vandepoele, K}, title = {Comprehensive and Functional Analysis of Horizontal Gene Transfer Events in Diatoms.}, journal = {Molecular biology and evolution}, volume = {37}, number = {11}, pages = {3243-3257}, doi = {10.1093/molbev/msaa182}, pmid = {32918458}, issn = {1537-1719}, mesh = {Adaptation, Biological ; Diatoms/*genetics/metabolism ; Gene Regulatory Networks ; *Gene Transfer, Horizontal ; Phylogeny ; Selection, Genetic ; Vitamin B 12/metabolism ; }, abstract = {Diatoms are a diverse group of mainly photosynthetic algae, responsible for 20% of worldwide oxygen production, which can rapidly respond to favorable conditions and often outcompete other phytoplankton. We investigated the contribution of horizontal gene transfer (HGT) to its ecological success. A large-scale phylogeny-based prokaryotic HGT detection procedure across nine sequenced diatoms showed that 3-5% of their proteome has a horizontal origin and a large influx occurred at the ancestor of diatoms. More than 90% of HGT genes are expressed, and species-specific HGT genes in Phaeodactylum tricornutum undergo strong purifying selection. Genes derived from HGT are implicated in several processes including environmental sensing and expand the metabolic toolbox. Cobalamin (vitamin B12) is an essential cofactor for roughly half of the diatoms and is only produced by bacteria. Five consecutive genes involved in the final synthesis of the cobalamin biosynthetic pathway, which could function as scavenging and repair genes, were detected as HGT. The full suite of these genes was detected in the cold-adapted diatom Fragilariopsis cylindrus. This might give diatoms originating from the Southern Ocean, a region typically depleted in cobalamin, a competitive advantage. Overall, we show that HGT is a prevalent mechanism that is actively used in diatoms to expand its adaptive capabilities.}, }
@article {pmid32916483, year = {2021}, author = {Xu, F and Du, W and Carter, LJ and Xu, M and Wang, G and Qiu, L and Zhu, J and Zhu, C and Yin, Y and Ji, R and Banwart, SA and Guo, H}, title = {Elevated CO2 concentration modifies the effects of organic fertilizer substitution on rice yield and soil ARGs.}, journal = {The Science of the total environment}, volume = {754}, number = {}, pages = {141898}, doi = {10.1016/j.scitotenv.2020.141898}, pmid = {32916483}, issn = {1879-1026}, support = {MR/S032126/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Anti-Bacterial Agents ; Carbon Dioxide/analysis ; Drug Resistance, Microbial/genetics ; *Fertilizers/analysis ; *Oryza ; Soil ; }, abstract = {Antibiotic resistance and rising CO2 levels are considered among the most significant challenges we will face in terms of global development over the following decades. However, the impact of elevated CO2 on soil antibiotic resistance has rarely been investigated. We used a free-air CO2 enrichment system to investigate the potential risks posed by applying mineral and organic fertilizers to paddy soil at current CO2 concentration (370 ppm) and future elevated CO2 (eCO2, 570 ppm predicted for 2100). Organic fertilizer substitution (substituting the mineral fertilizer by 50% N) alone increased the plant uptake and soil residue of sulfamethazine, and enriched sulfonamide resistance genes (sul1, sul2), tetracycline resistance genes (tetG, tetM) and class 1 integron (intl1). But it decreased the rice grain yield (by 7.6%). Comparatively, eCO2 decreased the sul2, tetG and intl1 gene abundances by organic fertilizer substitution, and meanwhile increased grain yield (by 8.4%). Proteobacteria and Nitrospirae were potential hosts of antibiotic resistance genes (ARGs). Horizontal gene transfer via intl1 may play an important role in ARGs spread under eCO2. Results indicated that future elevated CO2 concentration could modify the effects of organic fertilizer substitution on rice yield and soil ARGs, with unknown implications for future medicine and human health.}, }
@article {pmid32916103, year = {2020}, author = {Zheng, W and Pena, A and Low, WW and Wong, JLC and Frankel, G and Egelman, EH}, title = {Cryoelectron-Microscopic Structure of the pKpQIL Conjugative Pili from Carbapenem-Resistant Klebsiella pneumoniae.}, journal = {Structure (London, England : 1993)}, volume = {28}, number = {12}, pages = {1321-1328.e2}, pmid = {32916103}, issn = {1878-4186}, support = {107057/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; G20 RR031199/RR/NCRR NIH HHS/United States ; R35 GM122510/GM/NIGMS NIH HHS/United States ; MR/P028225/1/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Carbapenem-Resistant Enterobacteriaceae/*chemistry ; Cryoelectron Microscopy ; Klebsiella pneumoniae/*chemistry ; Pili, Sex/*chemistry ; Protein Domains ; }, abstract = {Conjugative pili are important in mediating bacterial conjugation and horizontal gene transfer. Since plasmid transfer can include antibiotic-resistance genes, conjugation is an important mechanism in the spread of antibiotic resistance. Filamentous bacteriophages have been shown to exist in two different structural classes: those with a 5-fold rotational symmetry and those with a one-start helix with approximately 5 subunits per turn. Structures for the F and the F-like pED208 conjugation pilus have shown that they have 5-fold rotational symmetry. Here, we report the cryoelectron-microscopic structure of conjugative pili from carbapenem-resistant Klebsiella pneumoniae, encoded on the IncFIIK pKpQIL plasmid, at 3.9 Å resolution and show that it has a one-start helix. These results establish that conjugation pili can exist in at least two structural classes, consistent with other results showing that relatively small perturbations are needed to change the helical symmetry of polymers.}, }
@article {pmid32915993, year = {2020}, author = {Li, X and Cheng, J and Liu, X and Guo, X and Liu, Y and Fan, W and Lu, L and Ma, Y and Liu, T and Tao, S and Jiang, H}, title = {Origin and Evolution of Fusidane-Type Antibiotics Biosynthetic Pathway through Multiple Horizontal Gene Transfers.}, journal = {Genome biology and evolution}, volume = {12}, number = {10}, pages = {1830-1840}, pmid = {32915993}, issn = {1759-6653}, mesh = {Anti-Bacterial Agents/biosynthesis ; *Biological Evolution ; Biosynthetic Pathways ; Cytochrome P-450 Enzyme System/genetics ; Fungi/*genetics ; Fusidic Acid/*metabolism ; *Gene Transfer, Horizontal ; *Genome, Fungal ; Intramolecular Transferases/genetics ; Multigene Family ; }, abstract = {Fusidane-type antibiotics represented by fusidic acid, helvolic acid, and cephalosporin P1 have very similar core structures, but they are produced by fungi belonging to different taxonomic groups. The origin and evolution of fusidane-type antibiotics biosynthetic gene clusters (BGCs) in different antibiotics producing strains remained an enigma. In this study, we investigated the distribution and evolution of the fusidane BGCs in 1,284 fungal genomes. We identified 12 helvolic acid BGCs, 4 fusidic acid BGCs, and 1 cephalosporin P1 BGC in Pezizomycotina fungi. Phylogenetic analyses indicated six horizontal gene transfer (HGT) events in the evolutionary trajectory of the BGCs, including 1) three transfers across Eurotiomycetes and Sordariomycetes classes; 2) one transfer between genera under Sordariomycetes class; and 3) two transfers within Aspergillus genus under Eurotiomycetes classes. Finally, we proposed that the ancestor of fusidane BGCs would be originated from the Zoopagomycota by ancient HGT events according to the phylogenetic trees of key enzymes in fusidane BGCs (OSC and P450 genes). Our results extensively clarify the evolutionary trajectory of fusidane BGCs by HGT among distantly related fungi and provide new insights into the evolutionary mechanisms of metabolic pathways in fungi.}, }
@article {pmid32909073, year = {2021}, author = {Mootapally, C and Mahajan, MS and Nathani, NM}, title = {Sediment Plasmidome of the Gulfs of Kathiawar Peninsula and Arabian Sea: Insights Gained from Metagenomics Data.}, journal = {Microbial ecology}, volume = {81}, number = {2}, pages = {540-548}, pmid = {32909073}, issn = {1432-184X}, support = {PDF/2016/001239//Science and Engineering Research Board/ ; PDF/2016/000190//Science and Engineering Research Board/ ; }, mesh = {Bacteria/classification/genetics/isolation &amp; purification ; Drug Resistance, Bacterial/genetics ; Ecosystem ; Genes, Bacterial/genetics ; Geologic Sediments/*microbiology ; Metagenome/*genetics ; Oceans and Seas ; Plasmids/*genetics ; Seawater/*microbiology ; Virulence Factors/genetics ; }, abstract = {Plasmidomes have become the research area of interest for ecologists exploring bacteria rich ecosystems. Marine environments are among such niche that host a huge number of microbes and have a complex environment which pose the need to study these bacterial indicators of horizontal gene transfer events for survival and stability. The plasmid content of the metagenomics data from 8 sediment samples of the Gulfs of Kathiawar and an open Arabian Sea sample was screened. The reads corresponding to hits against the plasmid database were assembled and studied for diversity using Kraken and functional content using MG-RAST. The sequences were also checked for resistome and virulence factors. The replicon hosts were overall dominated by Proteobacteria, Firmicutes, and Actinobacteria while red algae specific to the Kutch samples. The genes encoded were dominant in the flagella motility and type VI secretion systems. Overall, results from the study confirmed that the plasmids encoded traits for metal, antibiotic, and phage resistance along with virulence systems, and these would be conferring benefit to the hosts. The study throws insights into the environmental role of the plasmidome in adaptation of the microbes in the studied sites to the environmental stresses.}, }
@article {pmid32908149, year = {2020}, author = {Weinheimer, AR and Aylward, FO}, title = {A distinct lineage of Caudovirales that encodes a deeply branching multi-subunit RNA polymerase.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {4506}, pmid = {32908149}, issn = {2041-1723}, mesh = {*Biological Evolution ; Caudovirales/*genetics ; DNA, Viral/genetics ; DNA-Directed RNA Polymerases/*genetics ; Datasets as Topic ; Gene Transfer, Horizontal ; Metagenomics ; Phylogeny ; Protein Subunits/*genetics ; Sequence Analysis, DNA ; Viral Proteins/*genetics ; }, abstract = {Bacteriophages play critical roles in the biosphere, but their vast genomic diversity has obscured their evolutionary origins, and phylogenetic analyses have traditionally been hindered by their lack of universal phylogenetic marker genes. In this study we mine metagenomic data and identify a clade of Caudovirales that encodes the β and β' subunits of multi-subunit RNA polymerase (RNAP), a high-resolution phylogenetic marker which enables detailed evolutionary analyses. Our RNAP phylogeny revealed that the Caudovirales RNAP forms a clade distinct from cellular homologs, suggesting an ancient acquisition of this enzyme. Within these multimeric RNAP-encoding Caudovirales (mReC), we find that the similarity of major capsid proteins and terminase large subunits further suggests they form a distinct clade with common evolutionary origin. Our study characterizes a clade of RNAP-encoding Caudovirales and suggests the ancient origin of this enzyme in this group, underscoring the important role of viruses in the early evolution of life on Earth.}, }
@article {pmid32884309, year = {2020}, author = {Khurshid, M and Rasool, MH and Ashfaq, UA and Aslam, B and Waseem, M and Ali, MA and Almatroudi, A and Rasheed, F and Saeed, M and Guo, Q and Wang, M}, title = {Acinetobacter baumannii Sequence Types Harboring Genes Encoding Aminoglycoside Modifying Enzymes and 16SrRNA Methylase; a Multicenter Study from Pakistan.}, journal = {Infection and drug resistance}, volume = {13}, number = {}, pages = {2855-2862}, pmid = {32884309}, issn = {1178-6973}, abstract = {INTRODUCTION: The aminoglycosides are widely used for the therapeutic management of infections caused by gram-negative bacteria, including the Acinetobacter baumannii strains. However, the resistance to the members of the aminoglycoside family, such as amikacin, gentamicin, and tobramycin, is increasingly being common among the clinical isolates.<br><br>PURPOSE: This study aimed to investigate the presence of 16SrRNA methylases and aminoglycoside modifying enzymes (AMEs) genes among aminoglycoside resistant A. baumannii isolates and to study the genetic diversity of the clinical population of A. baumannii in local hospitals.<br><br>MATERIAL AND METHODS: The 143 A. baumannii clinical strains were analyzed for antimicrobial susceptibility, genetic screening for enzymes conferring aminoglycosides resistance followed by the multilocus sequence typing.<br><br>RESULTS: The 133/143 (93%) isolates were non-susceptible to at least one of the tested aminoglycosides, including amikacin, gentamicin, and tobramycin. The MIC distribution has shown that 87.486.7% strains were resistant to amikacin and gentamicin, respectively. The aphA6, aadB, aacC1, and aphA1 were found in 74.1%, 59.4%, 16.1%, and 11.2% isolates, respectively, whereas the armA was found in 28% of the strains having a higher MIC value (MIC; &#x2265;256&#xb5;g/mL). The MLST data have shown that the ST589 and ST2 were the most common STs and corresponded to 51 (35.7%) and 38 (26.6%) isolates, respectively, and few of the isolates corresponding to these STs were found to harbor the armA gene with a variable genotypic profile for AMEs.<br><br>DISCUSSION: The study has reported the incidence of various enzymes conferring aminoglycoside resistance among the A. baumannii clones for the first time from Pakistan. The findings suggest the possibility of transmission of aminoglycoside resistance determinants through the lateral gene transfer as well as clonal dissemination.}, }
@article {pmid32882137, year = {2020}, author = {Fujino, T and Tozaki, M and Murakami, H}, title = {An Amino Acid-Swapped Genetic Code.}, journal = {ACS synthetic biology}, volume = {9}, number = {10}, pages = {2703-2713}, doi = {10.1021/acssynbio.0c00196}, pmid = {32882137}, issn = {2161-5063}, mesh = {Amino Acid Substitution ; Amino Acids/*genetics ; Amino Acyl-tRNA Synthetases/metabolism ; Cell-Free System ; Codon/genetics ; Escherichia coli/enzymology/*genetics ; Escherichia coli Proteins/metabolism ; Gene Transfer, Horizontal ; *Genetic Code ; Genetic Engineering/*methods ; Organisms, Genetically Modified ; Protein Biosynthesis/*genetics ; RNA, Messenger/genetics ; }, abstract = {Preventing the escape of hazardous genes from genetically modified organisms (GMOs) into the environment is one of the most important issues in biotechnology research. Various strategies were developed to create "genetic firewalls" that prevent the leakage of GMOs; however, they were not specially designed to prevent the escape of genes. To address this issue, we developed amino acid (AA)-swapped genetic codes orthogonal to the standard genetic code, namely SL (Ser and Leu were swapped) and SLA genetic codes (Ser, Leu, and Ala were swapped). From mRNAs encoded by the AA-swapped genetic codes, functional proteins were only synthesized in translation systems featuring the corresponding genetic codes. These results clearly demonstrated the orthogonality of the AA-swapped genetic codes against the standard genetic code and their potential to function as "genetic firewalls for genes". Furthermore, we propose "a codon-bypass strategy" to develop a GMO with an AA-swapped genetic code.}, }
@article {pmid32880674, year = {2020}, author = {van Dijk, B}, title = {Can mobile genetic elements rescue genes from extinction?.}, journal = {Current genetics}, volume = {66}, number = {6}, pages = {1069-1071}, pmid = {32880674}, issn = {1432-0983}, mesh = {Bacteria/*genetics ; Chromosomes, Bacterial/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Interspersed Repetitive Sequences/*genetics ; Prokaryotic Cells ; }, abstract = {Bacteria and other prokaryotes evolve primarily through rapid changes in their gene content by quickly losing and gaining genes whenever an ecological opportunity emerges. As gene loss and horizontal gene transfer (HGT) appear to be the most common events across the prokaryotic tree of life, we need to think beyond gradual sequence evolution if we wish to understand the microbial world. Especially genes that reside on mobile genetic elements (MGEs) may spread much more rapidly through a microbial population than genes that reside on the bacterial chromosome. This raises the question: why are some genes associated with MGEs, while others are not? Here, I briefly review a recently proposed class of genes for which we have coined the term "rescuable genes". The fitness effect of carrying these genes is so small, either constantly or on average, that they are prone to be lost from a microbial population. I argue that HGT, even when costly to the individual cells, may play an important role in maintaining these rescuable genes in microbial communities.}, }
@article {pmid32879312, year = {2020}, author = {Bellas, CM and Schroeder, DC and Edwards, A and Barker, G and Anesio, AM}, title = {Flexible genes establish widespread bacteriophage pan-genomes in cryoconite hole ecosystems.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {4403}, pmid = {32879312}, issn = {2041-1723}, support = {M 2299/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Bacteriophages/*genetics ; Cyanobacteria/virology ; Ecosystem ; Gene Transfer, Horizontal ; Genes, Viral ; Genome, Viral ; Host Microbial Interactions/genetics ; Ice Cover/microbiology/*virology ; *Metagenome ; Metagenomics ; Phylogeny ; }, abstract = {Bacteriophage genomes rapidly evolve via mutation and horizontal gene transfer to counter evolving bacterial host defenses; such arms race dynamics should lead to divergence between phages from similar, geographically isolated ecosystems. However, near-identical phage genomes can reoccur over large geographical distances and several years apart, conversely suggesting many are stably maintained. Here, we show that phages with near-identical core genomes in distant, discrete aquatic ecosystems maintain diversity by possession of numerous flexible gene modules, where homologous genes present in the pan-genome interchange to create new phage variants. By repeatedly reconstructing the core and flexible regions of phage genomes from different metagenomes, we show a pool of homologous gene variants co-exist for each module in each location, however, the dominant variant shuffles independently in each module. These results suggest that in a natural community, recombination is the largest contributor to phage diversity, allowing a variety of host recognition receptors and genes to counter bacterial defenses to co-exist for each phage.}, }
@article {pmid32877528, year = {2021}, author = {Shinzato, C and Khalturin, K and Inoue, J and Zayasu, Y and Kanda, M and Kawamitsu, M and Yoshioka, Y and Yamashita, H and Suzuki, G and Satoh, N}, title = {Eighteen Coral Genomes Reveal the Evolutionary Origin of Acropora Strategies to Accommodate Environmental Changes.}, journal = {Molecular biology and evolution}, volume = {38}, number = {1}, pages = {16-30}, pmid = {32877528}, issn = {1537-1719}, mesh = {*Adaptation, Biological ; Animals ; Anthozoa/*genetics ; *Biological Evolution ; *Climate Change ; *Fossils ; Genome ; }, abstract = {The genus Acropora comprises the most diverse and abundant scleractinian corals (Anthozoa, Cnidaria) in coral reefs, the most diverse marine ecosystems on Earth. However, the genetic basis for the success and wide distribution of Acropora are unknown. Here, we sequenced complete genomes of 15 Acropora species and 3 other acroporid taxa belonging to the genera Montipora and Astreopora to examine genomic novelties that explain their evolutionary success. We successfully obtained reasonable draft genomes of all 18 species. Molecular dating indicates that the Acropora ancestor survived warm periods without sea ice from the mid or late Cretaceous to the Early Eocene and that diversification of Acropora may have been enhanced by subsequent cooling periods. In general, the scleractinian gene repertoire is highly conserved; however, coral- or cnidarian-specific possible stress response genes are tandemly duplicated in Acropora. Enzymes that cleave dimethlysulfonioproprionate into dimethyl sulfide, which promotes cloud formation and combats greenhouse gasses, are the most duplicated genes in the Acropora ancestor. These may have been acquired by horizontal gene transfer from algal symbionts belonging to the family Symbiodiniaceae, or from coccolithophores, suggesting that although functions of this enzyme in Acropora are unclear, Acropora may have survived warmer marine environments in the past by enhancing cloud formation. In addition, possible antimicrobial peptides and symbiosis-related genes are under positive selection in Acropora, perhaps enabling adaptation to diverse environments. Our results suggest unique Acropora adaptations to ancient, warm marine environments and provide insights into its capacity to adjust to rising seawater temperatures.}, }
@article {pmid32875793, year = {2020}, author = {Zarei-Baygi, A and Wang, P and Harb, M and Stadler, LB and Smith, AL}, title = {Membrane Fouling Inversely Impacts Intracellular and Extracellular Antibiotic Resistance Gene Abundances in the Effluent of an Anaerobic Membrane Bioreactor.}, journal = {Environmental science &amp; technology}, volume = {54}, number = {19}, pages = {12742-12751}, doi = {10.1021/acs.est.0c04787}, pmid = {32875793}, issn = {1520-5851}, mesh = {Anaerobiosis ; *Anti-Bacterial Agents/pharmacology ; Bioreactors ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Membranes, Artificial ; *Wastewater ; }, abstract = {Anaerobic membrane bioreactors (AnMBRs) can significantly reduce the release of antibiotic resistance elements to the environment. The purpose of this study was to elucidate the role of membrane fouling layers (biofilms) in mitigating the release of intracellular and extracellular antibiotic resistance genes (iARGs and eARGs) from an AnMBR. The AnMBR was equipped with three membrane modules, each exhibiting a different level of fouling. Results showed that the absolute abundance of ARGs decreased gradually in the suspended biomass during operation of the AnMBR. Normalized abundances of targeted ARGs and intI1 were found to be significantly higher in the fouling layers compared to the suspended biomass, implying adsorption or an increased potential for horizontal gene transfer of ARGs in the biofilm. Effluent ARG data revealed that the highly fouled (HF) membrane significantly reduced the absolute abundance of eARGs. However, the HF membrane effluent concomitantly had the highest absolute abundance of iARGs. Nevertheless, total ARG abundance (sum of iARG and eARG) in the effluent of the AnMBR was not impacted by the extent of fouling. These results suggest a need for a combination of different treatment technologies to effectively prevent antibiotic resistance proliferation associated with these two ARG fractions.}, }
@article {pmid32873785, year = {2020}, author = {Kent, AG and Vill, AC and Shi, Q and Satlin, MJ and Brito, IL}, title = {Widespread transfer of mobile antibiotic resistance genes within individual gut microbiomes revealed through bacterial Hi-C.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {4379}, pmid = {32873785}, issn = {2041-1723}, support = {DP2 HL141007/HL/NHLBI NIH HHS/United States ; K23 AI114994/AI/NIAID NIH HHS/United States ; }, mesh = {Adult ; Aged ; Anti-Bacterial Agents/*pharmacology/therapeutic use ; DNA, Bacterial/genetics/isolation &amp; purification ; Drug Resistance, Bacterial/*genetics ; Gastrointestinal Microbiome/drug effects/*genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial/*drug effects ; High-Throughput Nucleotide Sequencing ; Humans ; Interspersed Repetitive Sequences/drug effects ; Middle Aged ; }, abstract = {The gut microbiome harbors a 'silent reservoir' of antibiotic resistance (AR) genes that is thought to contribute to the emergence of multidrug-resistant pathogens through horizontal gene transfer (HGT). To counteract the spread of AR, it is paramount to know which organisms harbor mobile AR genes and which organisms engage in HGT. Despite methods that characterize the overall abundance of AR genes in the gut, technological limitations of short-read sequencing have precluded linking bacterial taxa to specific mobile genetic elements (MGEs) encoding AR genes. Here, we apply Hi-C, a high-throughput, culture-independent method, to surveil the bacterial carriage of MGEs. We compare two healthy individuals with seven neutropenic patients undergoing hematopoietic stem cell transplantation, who receive multiple courses of antibiotics, and are acutely vulnerable to the threat of multidrug-resistant infections. We find distinct networks of HGT across individuals, though AR and mobile genes are associated with more diverse taxa within the neutropenic patients than the healthy subjects. Our data further suggest that HGT occurs frequently over a several-week period in both cohorts. Whereas most efforts to understand the spread of AR genes have focused on pathogenic species, our findings shed light on the role of the human gut microbiome in this process.}, }
@article {pmid32873755, year = {2020}, author = {de la Higuera, I and Kasun, GW and Torrance, EL and Pratt, AA and Maluenda, A and Colombet, J and Bisseux, M and Ravet, V and Dayaram, A and Stainton, D and Kraberger, S and Zawar-Reza, P and Goldstien, S and Briskie, JV and White, R and Taylor, H and Gomez, C and Ainley, DG and Harding, JS and Fontenele, RS and Schreck, J and Ribeiro, SG and Oswald, SA and Arnold, JM and Enault, F and Varsani, A and Stedman, KM}, title = {Unveiling Crucivirus Diversity by Mining Metagenomic Data.}, journal = {mBio}, volume = {11}, number = {5}, pages = {}, pmid = {32873755}, issn = {2150-7511}, support = {80NSSC17K0301/ImNASA/Intramural NASA/United States ; RL5 GM118963/GM/NIGMS NIH HHS/United States ; TL4 GM118965/GM/NIGMS NIH HHS/United States ; UL1 GM118964/GM/NIGMS NIH HHS/United States ; }, mesh = {Capsid Proteins/genetics ; DNA Viruses/*classification/genetics ; *Data Mining ; *Genome, Viral ; *Metagenome ; Metagenomics ; RNA Viruses/classification/genetics ; Tombusviridae/classification/genetics ; }, abstract = {The discovery of cruciviruses revealed the most explicit example of a common protein homologue between DNA and RNA viruses to date. Cruciviruses are a novel group of circular Rep-encoding single-stranded DNA (ssDNA) (CRESS-DNA) viruses that encode capsid proteins that are most closely related to those encoded by RNA viruses in the family Tombusviridae The apparent chimeric nature of the two core proteins encoded by crucivirus genomes suggests horizontal gene transfer of capsid genes between DNA and RNA viruses. Here, we identified and characterized 451 new crucivirus genomes and 10 capsid-encoding circular genetic elements through de novo assembly and mining of metagenomic data. These genomes are highly diverse, as demonstrated by sequence comparisons and phylogenetic analysis of subsets of the protein sequences they encode. Most of the variation is reflected in the replication-associated protein (Rep) sequences, and much of the sequence diversity appears to be due to recombination. Our results suggest that recombination tends to occur more frequently among groups of cruciviruses with relatively similar capsid proteins and that the exchange of Rep protein domains between cruciviruses is rarer than intergenic recombination. Additionally, we suggest members of the stramenopiles/alveolates/Rhizaria supergroup as possible crucivirus hosts. Altogether, we provide a comprehensive and descriptive characterization of cruciviruses.IMPORTANCE Viruses are the most abundant biological entities on Earth. In addition to their impact on animal and plant health, viruses have important roles in ecosystem dynamics as well as in the evolution of the biosphere. Circular Rep-encoding single-stranded (CRESS) DNA viruses are ubiquitous in nature, many are agriculturally important, and they appear to have multiple origins from prokaryotic plasmids. A subset of CRESS-DNA viruses, the cruciviruses, have homologues of capsid proteins encoded by RNA viruses. The genetic structure of cruciviruses attests to the transfer of capsid genes between disparate groups of viruses. However, the evolutionary history of cruciviruses is still unclear. By collecting and analyzing cruciviral sequence data, we provide a deeper insight into the evolutionary intricacies of cruciviruses. Our results reveal an unexpected diversity of this virus group, with frequent recombination as an important determinant of variability.}, }
@article {pmid32873199, year = {2020}, author = {Brückner, A and Kaltenpoth, M and Heethoff, M}, title = {De novo biosynthesis of simple aromatic compounds by an arthropod (Archegozetes longisetosus).}, journal = {Proceedings. Biological sciences}, volume = {287}, number = {1934}, pages = {20201429}, pmid = {32873199}, issn = {1471-2954}, mesh = {Animals ; Arthropods/enzymology/metabolism ; Fungi ; Mites/*physiology ; Organic Chemicals ; Polyketide Synthases/metabolism ; Symbiosis ; }, abstract = {The ability to synthesize simple aromatic compounds is well known from bacteria, fungi and plants, which all share an exclusive biosynthetic route-the shikimic acid pathway. Some of these organisms further evolved the polyketide pathway to form core benzenoids via a head-to-tail condensation of polyketide precursors. Arthropods supposedly lack the ability to synthesize aromatics and instead rely on aromatic amino acids acquired from food, or from symbiotic microorganisms. The few studies purportedly showing de novo biosynthesis via the polyketide synthase (PKS) pathway failed to exclude endosymbiotic bacteria, so their results are inconclusive. We investigated the biosynthesis of aromatic compounds in defence secretions of the oribatid mite Archegozetes longisetosus. Exposing the mites to a diet containing high concentrations of antibiotics removed potential microbial partners but did not affect the production of defensive benzenoids. To gain insights into benzenoid biosynthesis, we fed mites with stable-isotope labelled precursors and monitored incorporation with mass spectrometry. Glucose, malonic acid and acetate, but not phenylalanine, were incorporated into the benzenoids, further evidencing autogenous biosynthesis. Whole-transcriptome sequencing with hidden Markov model profile search of protein domain families and subsequent phylogenetic analysis revealed a putative PKS domain similar to an actinobacterial PKS, possibly indicating a horizontal gene transfer.}, }
@article {pmid32870981, year = {2020}, author = {Smith, EA and Newton, ILG}, title = {Genomic Signatures of Honey Bee Association in an Acetic Acid Symbiont.}, journal = {Genome biology and evolution}, volume = {12}, number = {10}, pages = {1882-1894}, pmid = {32870981}, issn = {1759-6653}, mesh = {Acetic Acid/metabolism ; Acetobacteraceae/*genetics/metabolism ; Animals ; Bees/*microbiology ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Phylogeny ; Symbiosis/*genetics ; }, abstract = {Recent declines in the health of the honey bee have startled researchers and lay people alike as honey bees are agriculture's most important pollinator. Honey bees are important pollinators of many major crops and add billions of dollars annually to the US economy through their services. One factor that may influence colony health is the microbial community. Indeed, the honey bee worker digestive tract harbors a characteristic community of bee-specific microbes, and the composition of this community is known to impact honey bee health. However, the honey bee is a superorganism, a colony of eusocial insects with overlapping generations where nestmates cooperate, building a hive, gathering and storing food, and raising brood. In contrast to what is known regarding the honey bee worker gut microbiome, less is known of the microbes associated with developing brood, with food stores, and with the rest of the built hive environment. More recently, the microbe Bombella apis was identified as associated with nectar, with developing larvae, and with honey bee queens. This bacterium is related to flower-associated microbes such as Saccharibacter floricola and other species in the genus Saccharibacter, and initial phylogenetic analyses placed it as sister to these environmental bacteria. Here, we used comparative genomics of multiple honey bee-associated strains and the nectar-associated Saccharibacter to identify genomic changes that may be associated with the ecological transition to honey bee association. We identified several genomic differences in the honey bee-associated strains, including a complete CRISPR/Cas system. Many of the changes we note here are predicted to confer upon Bombella the ability to survive in royal jelly and defend themselves against mobile elements, including phages. Our results are a first step toward identifying potential function of this microbe in the honey bee superorganism.}, }
@article {pmid32867033, year = {2020}, author = {Bulavaitė, A and Dalgediene, I and Michailoviene, V and Pleckaityte, M}, title = {Type II Restriction-Modification System from Gardnerella vaginalis ATCC 14018.}, journal = {Pathogens (Basel, Switzerland)}, volume = {9}, number = {9}, pages = {}, pmid = {32867033}, issn = {2076-0817}, support = {S-MIP-17-49//Lietuvos Mokslo Taryba/ ; }, abstract = {Intensive horizontal gene transfer may generate diversity and heterogeneity within the genus Gardnerella. Restriction-modification (R-M) systems and CRISPR-Cas are the principal defense tools against foreign DNA in bacteria. Nearly half of the tested Gardnerella spp. isolates harbored the CRISPR-Cas system. Several putative R-M systems of Gardnerella spp. strains were identified in the REBASE database. However, there was no experimental evidence for restriction endonuclease (REase) activity in the isolates. We showed that G. vaginalis strain ATCC 14018 contains the REase R.Gva14018I, which recognizes GGCC and most probably generates blunt ends on cleavage. Bioinformatics evidence and the activity of recombinant methyltransferase M.Gva14018I in vivo indicate that ATCC 14018 possesses a HaeIII-like R-M system. The truncated R.Gva14018I-4 lacking the C-terminal region was expressed in Escherichia coli and displayed wild-type REase specificity. Polyclonal antibodies against R.Gva14018I-4 detected the wild-type REase in the cell lysate of ATCC 14018. The cofactor requirements for activity and bioinformatics analysis indicated that R.Gva14018I belongs to the PD-(D/E)XK family of REases. The REase-like activity was observed in 5 of 31 tested Gardnerella spp. strains, although none of these matched the DNA digestion pattern of R.Gva14018I.}, }
@article {pmid32861499, year = {2020}, author = {Taher, EM and Hemmatzadeh, F and Aly, SA and Elesswy, HA and Petrovski, KR}, title = {Molecular characterization of antimicrobial resistance genes on farms and in commercial milk with emphasis on the effect of currently practiced heat treatments on viable but nonculturable formation.}, journal = {Journal of dairy science}, volume = {103}, number = {11}, pages = {9936-9945}, doi = {10.3168/jds.2020-18631}, pmid = {32861499}, issn = {1525-3198}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/*genetics ; *Bacterial Physiological Phenomena ; Drug Resistance, Bacterial/*genetics ; Farms ; Genome, Bacterial/*genetics ; Hot Temperature ; Milk/*microbiology ; Pasteurization ; Plasmids/*genetics ; }, abstract = {Despite the considerable advances that have been made to improve dairy food safety, there is rising concern that pasteurization is not sufficient for the destruction of plasmid-mediated antimicrobial resistance (AMR) genes of resistant bacteria and could stimulate bacteria to enter into a viable but nonculturable (VBNC) state. In the current study, we surveyed the prevalence of 1 genomic and 9 plasmid-mediated AMR genes in 100 samples (bulk tank milk and milk filter socks) at the farm level and 152 commercial milk samples (pasteurized and UHT milks) and assessed the VBNC state in dairy bacteria. Results revealed that sul2 was the most prevalent plasmid-mediated gene in milk filter socks (96%), bulk tank milk (48%), pasteurized milk (68%), and UHT (43%) milk; in contrast, mecA was not detected in any sample. Additionally, commercial pasteurization (as currently practiced) failed to decrease the prevalence of the blaTEM-B1 (43%), tetK (30%), and tetA (55%) plasmid-mediated AMR genes; thus, commercial pasteurization may be one of the factors creating the VBNC state in some dairy bacteria. Continued research is necessary to identify bacterial species entering the VBNC state after pasteurization, to assess their potential hazard level and shed more light on the expression and possibility of horizontal gene transfer of those plasmid-mediated AMR genes.}, }
@article {pmid32860774, year = {2020}, author = {Schmitt, A and Hirt, H and Järvå, MA and Sun, WS and Ter Beek, J and Dunny, GM and Berntsson, RP}, title = {Enterococcal PrgA Extends Far Outside the Cell and Provides Surface Exclusion to Protect against Unwanted Conjugation.}, journal = {Journal of molecular biology}, volume = {432}, number = {20}, pages = {5681-5695}, doi = {10.1016/j.jmb.2020.08.018}, pmid = {32860774}, issn = {1089-8638}, support = {R35 GM118079/GM/NIGMS NIH HHS/United States ; }, mesh = {Adhesins, Bacterial/metabolism ; Bacterial Proteins/chemistry/*metabolism ; DNA, Bacterial/metabolism ; Enterococcus/genetics/*metabolism ; Enterococcus faecalis/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Membrane Proteins/metabolism ; Plasmids ; Type IV Secretion Systems ; Virulence ; Virulence Factors/*metabolism ; }, abstract = {Horizontal gene transfer between Gram-positive bacteria leads to a rapid spread of virulence factors and antibiotic resistance. This transfer is often facilitated via type 4 secretion systems (T4SS), which frequently are encoded on conjugative plasmids. However, donor cells that already contain a particular conjugative plasmid resist acquisition of a second copy of said plasmid. They utilize different mechanisms, including surface exclusion for this purpose. Enterococcus faecalis PrgA, encoded by the conjugative plasmid pCF10, is a surface protein that has been implicated to play a role in both virulence and surface exclusion, but the mechanism by which this is achieved has not been fully explained. Here, we report the structure of full-length PrgA, which shows that PrgA protrudes far out from the cell wall (approximately 40 nm), where it presents a protease domain. In vivo experiments show that PrgA provides a physical barrier to cellular adhesion, thereby reducing cellular aggregation. This function of PrgA contributes to surface exclusion, reducing the uptake of its cognate plasmid by approximately one order of magnitude. Using variants of PrgA with mutations in the catalytic site we show that the surface exclusion effect is dependent on the activity of the protease domain of PrgA. In silico analysis suggests that PrgA can interact with another enterococcal adhesin, PrgB, and that these two proteins have co-evolved. PrgB is a strong virulence factor, and PrgA is involved in post-translational processing of PrgB. Finally, competition mating experiments show that PrgA provides a significant fitness advantage to plasmid-carrying cells.}, }
@article {pmid32860228, year = {2020}, author = {Gabaldón, T}, title = {Patterns and impacts of nonvertical evolution in eukaryotes: a paradigm shift.}, journal = {Annals of the New York Academy of Sciences}, volume = {1476}, number = {1}, pages = {78-92}, pmid = {32860228}, issn = {1749-6632}, mesh = {Eukaryota/*genetics/metabolism ; Eukaryotic Cells/*physiology ; *Evolution, Molecular ; Gene Transfer, Horizontal/*physiology ; Genomics/methods ; Phylogeny ; }, abstract = {Evolution of eukaryotic species and their genomes has been traditionally understood as a vertical process in which genetic material is transmitted from parents to offspring along a lineage, and in which genetic exchange is restricted within species boundaries. However, mounting evidence from comparative genomics indicates that this paradigm is often violated. Horizontal gene transfer and mating between diverged lineages blur species boundaries and challenge the reconstruction of evolutionary histories of species and their genomes. Nonvertical evolution might be more restricted in eukaryotes than in prokaryotes, yet it is not negligible and can be common in certain groups. Recognition of such processes brings about the need to incorporate this complexity into our models, as well as to conceptually reframe eukaryotic diversity and evolution. Here, I review the recent work from genomics studies that supports the effects of nonvertical modes of evolution including introgression, hybridization, and horizontal gene transfer in different eukaryotic groups. I then discuss emerging patterns and effects, illustrated by specific examples, that support the conclusion that nonvertical processes are often at the root of important evolutionary transitions and adaptations. I will argue that a paradigm shift is needed to naturally accommodate nonvertical processes in eukaryotic evolution.}, }
@article {pmid32858915, year = {2020}, author = {Lao, J and Guédon, G and Lacroix, T and Charron-Bourgoin, F and Libante, V and Loux, V and Chiapello, H and Payot, S and Leblond-Bourget, N}, title = {Abundance, Diversity and Role of ICEs and IMEs in the Adaptation of Streptococcus salivarius to the Environment.}, journal = {Genes}, volume = {11}, number = {9}, pages = {}, pmid = {32858915}, issn = {2073-4425}, mesh = {*Adaptation, Physiological ; *Conjugation, Genetic ; *DNA Transposable Elements ; Environment ; Evolution, Molecular ; *Genetic Variation ; *Genome, Bacterial ; Genomics ; Humans ; *Interspersed Repetitive Sequences ; Streptococcus salivarius/*genetics/physiology ; }, abstract = {Streptococcus salivarius is a significant contributor to the human oral, pharyngeal and gut microbiomes that contribute to the maintenance of health. The high genomic diversity observed in this species is mainly caused by horizontal gene transfer. This work aimed to evaluate the contribution of integrative and conjugative elements (ICEs) and integrative and mobilizable elements (IMEs) in S. salivarius genome diversity. For this purpose, we performed an in-depth analysis of 75 genomes of S. salivarius and searched for signature genes of conjugative and mobilizable elements. This analysis led to the retrieval of 69 ICEs, 165 IMEs and many decayed elements showing their high prevalence in S. salivarius genomes. The identification of almost all ICE and IME boundaries allowed the identification of the genes in which these elements are inserted. Furthermore, the exhaustive analysis of the adaptation genes carried by these elements showed that they encode numerous functions such as resistance to stress, to antibiotics or to toxic compounds, and numerous enzymes involved in diverse cellular metabolic pathways. These data support the idea that not only ICEs but also IMEs and decayed elements play an important role in S. salivarius adaptation to the environment.}, }
@article {pmid32857738, year = {2020}, author = {Wang, J and Zhou, J}, title = {The effects of offshore petroleum exploitation on microbial community and antibiotic resistome of adjacent marine sediments.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {81}, number = {12}, pages = {2501-2510}, doi = {10.2166/wst.2020.289}, pmid = {32857738}, issn = {0273-1223}, mesh = {Anti-Bacterial Agents ; Bacteria/genetics ; Genes, Bacterial ; Geologic Sediments ; Humans ; *Microbiota ; *Petroleum ; }, abstract = {The exploitation of petroleum in offshore areas is becoming more prosperous due to the increasing human demand for oil. However, the effects of offshore petroleum exploitation on the microbial community in the surrounding environment are still not adequately understood. In the present study, variations in the composition, function, and antibiotic resistance of the microbial community in marine sediments adjacent to an offshore petroleum exploitation platform were analyzed by a metagenomics-based method. Significant shifts in the microbial community composition were observed in sediments impacted by offshore petroleum exploitation. Nitrosopumilales was enriched in marine sediments with the activities of offshore petroleum exploitation compared to the control sediments. The abundances of function genes involved in carbon, butanoate, methane, and fatty acid metabolism in sediment microbial communities also increased due to the offshore petroleum exploitation. Offshore petroleum exploitation resulted in the propagation of some antibiotic resistance genes (ARGs), including a multidrug transporter, smeE, and arnA, in marine sediments via horizontal gene transfer mediated by class I integrons. However, the total abundance and diversity of ARGs in marine sediments were not significantly affected by offshore petroleum exploitation. This study is the first attempt to analyze the impact of offshore petroleum exploitation on the spread of antibiotic resistance.}, }
@article {pmid32854417, year = {2020}, author = {Turnaev, II and Gunbin, KV and Suslov, VV and Akberdin, IR and Kolchanov, NA and Afonnikov, DA}, title = {The Phylogeny of Class B Flavoprotein Monooxygenases and the Origin of the YUCCA Protein Family.}, journal = {Plants (Basel, Switzerland)}, volume = {9}, number = {9}, pages = {}, pmid = {32854417}, issn = {2223-7747}, support = {0324-2019-0040-C-01//Russian State Budget Project/ ; }, abstract = {YUCCA (YUCCA flavin-dependent monooxygenase) is one of the two enzymes of the main auxin biosynthesis pathway (tryptophan aminotransferase enzyme (TAA)/YUCCA) in land plants. The evolutionary origin of the YUCCA family is currently controversial: YUCCAs are assumed to have emerged via a horizontal gene transfer (HGT) from bacteria to the most recent common ancestor (MRCA) of land plants or to have inherited it from their ancestor, the charophyte algae. To refine YUCCA origin, we performed a phylogenetic analysis of the class B flavoprotein monooxygenases and comparative analysis of the sequences belonging to different families of this protein class. We distinguished a new protein family, named type IIb flavin-containing monooxygenases (FMOs), which comprises homologs of YUCCA from Rhodophyta, Chlorophyta, and Charophyta, land plant proteins, and FMO-E, -F, and -G of the bacterium Rhodococcus jostii RHA1. The type IIb FMOs differ considerably in the sites and domain composition from the other families of class B flavoprotein monooxygenases, YUCCAs included. The phylogenetic analysis also demonstrated that the type IIb FMO clade is not a sibling clade of YUCCAs. We have also identified the bacterial protein group named YUC-like FMOs as the closest to YUCCA homologs. Our results support the hypothesis of the emergence of YUCCA via HGT from bacteria to MRCA of land plants.}, }
@article {pmid32851833, year = {2020}, author = {Isernia, C and Malgieri, G and Russo, L and D'Abrosca, G and Baglivo, I and Pedone, PV and Fattorusso, R}, title = {Zinc Fingers.}, journal = {Metal ions in life sciences}, volume = {20}, number = {}, pages = {}, doi = {10.1515/9783110589757-018}, pmid = {32851833}, issn = {1559-0836}, mesh = {Agrobacterium tumefaciens ; Amino Acid Sequence ; Humans ; Proteins ; Zinc ; *Zinc Fingers ; }, abstract = {Zinc finger (ZF) domains, that represent the majority of the DNA-binding motifs in eukaryotes, are involved in several processes ranging from RNA packaging to transcriptional activation, regulation of apoptosis, protein folding and assembly, and lipid binding. While their amino acid composition varies from one domain to the other, a shared feature is the coordination of a zinc ion, with a structural role, by a different combination of cysteines and histidines. The classical zinc finger domain (also called Cys2His2) that represents the most common class, uses two cysteines and two histidines to coordinate the metal ion, and forms a compact ββα architecture consisting in a β-sheet and an α-helix. GAG-knuckle resembles the classical ZF, treble clef and zinc ribbon are also well represented in the human genome. Zinc fingers are also present in prokaryotes. The first prokaryotic ZF domain found in the transcriptional regulator Ros protein was identified in Agrobacterium tumefaciens. It shows a Cys2His2 metal ion coordination sphere and folds in a domain significantly larger than its eukaryotic counterpart arranged in a βββαα topology. Interestingly, this domain does not strictly require the metal ion coordination to achieve the functional fold. Here, we report what is known on the main classes of eukaryotic and prokarotic ZFs, focusing our attention to the role of the metal ion, the folding mechanism, and the DNA binding. The hypothesis of a horizontal gene transfer from prokaryotes to eukaryotes is also discussed.}, }
@article {pmid32849481, year = {2020}, author = {Li, C and Li, C and Li, L and Yang, X and Chen, S and Qi, B and Zhao, Y}, title = {Comparative Genomic and Secretomic Analysis Provide Insights Into Unique Agar Degradation Function of Marine Bacterium Vibrio fluvialis A8 Through Horizontal Gene Transfer.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1934}, pmid = {32849481}, issn = {1664-302X}, abstract = {Agarose-oligosaccharide production from agar degradation by agarase exhibits lots of advantages and good application prospects. In this study, a novel agar-degrading bacterium Vibrio sp. A8 was isolated from a red algae in the South China Sea. The whole genome sequencing with comparative genomic and secretomic analysis were used to better understand its genetic components about agar degradation. This strain exhibited good agarase production in artificial seawater after culture optimization. The complete genome (4.88 Mb) of this strain comprised two circular chromosomes (3.19 and 1.69 Mb) containing 4,572 protein-coding genes, 108 tRNA genes and 31 rRNA genes. This strain was identified as Vibrio fluvialis A8 by comparative genomic analysis based on genome phylogenetic tree and average nucleotide identity (ANI) similarity. Different from other 20 similar strains including three strains of the same species, V. fluvialis A8 possessed unique agar degradation ability with four β-agarases (GH50) and one α-1,3-L-NA2 hydrolase (GH117) due to the horizontal gene transfer. Secretomic analysis showed that only β-agarase (gene 3152) was abundantly expressed in the secretome of V. fluvialis A8. This agarase had a good substrate specificity and wide work conditions in complex environments, suggesting its potential application for agarose-oligosaccharide production.}, }
@article {pmid32849443, year = {2020}, author = {Hall, JPJ and Harrison, E and Pärnänen, K and Virta, M and Brockhurst, MA}, title = {The Impact of Mercury Selection and Conjugative Genetic Elements on Community Structure and Resistance Gene Transfer.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1846}, pmid = {32849443}, issn = {1664-302X}, abstract = {Carriage of resistance genes can underpin bacterial survival, and by spreading these genes between species, mobile genetic elements (MGEs) can potentially protect diversity within microbial communities. The spread of MGEs could be affected by environmental factors such as selection for resistance, and biological factors such as plasmid host range, with consequences for individual species and for community structure. Here we cultured a focal bacterial strain, Pseudomonas fluorescens SBW25, embedded within a soil microbial community, with and without mercury selection, and with and without mercury resistance plasmids (pQBR57 or pQBR103), to investigate the effects of selection and resistance gene introduction on (1) the focal species; (2) the community as a whole; (3) the spread of the introduced mer resistance operon. We found that P. fluorescens SBW25 only escaped competitive exclusion by other members of community under mercury selection, even when it did not begin with a mercury resistance plasmid, due to its propensity to acquire resistance from the community by horizontal gene transfer. Mercury pollution had a significant effect on community structure, decreasing alpha diversity within communities while increasing beta diversity between communities, a pattern that was not affected by the introduction of mercury resistance plasmids by P. fluorescens SBW25. Nevertheless, the introduced merA gene spread to a phylogenetically diverse set of recipients over the 5 weeks of the experiment, as assessed by epicPCR. Our data demonstrates how the effects of MGEs can be experimentally assessed for individual lineages, the wider community, and for the spread of adaptive traits.}, }
@article {pmid32849368, year = {2020}, author = {Yin, M and Zhang, Z and Xuan, M and Feng, H and Ye, W and Zheng, X and Wang, Y}, title = {Conserved Subgroups of the Plant-Specific RWP-RK Transcription Factor Family Are Present in Oomycete Pathogens.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1724}, pmid = {32849368}, issn = {1664-302X}, abstract = {Nitrogen is a major constituent of proteins, chlorophyll, nucleotides, and hormones and has profound effects on plant growth and productivity. RWP-RK family transcription factors (TFs) are key regulators that bind to cis-acting elements in the promoter regions of nitrogen use efficiency-related genes and genes responsible for gametogenesis and embryogenesis. The proteins share a conserved RWPxRK motif; have been found in all vascular plants, green algae, and slime molds; and are considered to be a plant-specific TF family. In this study, we show that RWP-RK proteins are also widely present in the Stramenopila kingdom, particularly among the oomycetes, with 12-15 members per species. These proteins form three distinct phylogenetic subgroups, two of which are relatively closely related to the nodule inception (NIN)-like protein (NLP) or the RWP-RK domain protein (RKD) subfamilies of plant RWP-RK proteins. The donor for horizontal gene transfer of RWP-RK domains to slime molds is likely to have been among the Stramenopila, predating the divide between brown algae and oomycetes. The RWP-RK domain has secondary structures that are conserved across plants and oomycetes, but several amino acids that may affect DNA-binding affinity differ. The transcriptional activities of orthologous RWP-RK genes were found to be conserved in oomycetes. Our results demonstrate that RWP-RK family TF genes are present in the oomycetes and form specific subgroups with functions that are likely conserved. Our results provide new insights for further understanding the evolution and function of this TF family in specific eukaryotic organisms.}, }
@article {pmid32849358, year = {2020}, author = {Bannantine, JP and Conde, C and Bayles, DO and Branger, M and Biet, F}, title = {Genetic Diversity Among Mycobacterium avium Subspecies Revealed by Analysis of Complete Genome Sequences.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1701}, pmid = {32849358}, issn = {1664-302X}, abstract = {Mycobacterium avium comprises four subspecies that contain both human and veterinary pathogens. At the inception of this study, twenty-eight M. avium genomes had been annotated as RefSeq genomes, facilitating direct comparisons. These genomes represent strains from around the world and provided a unique opportunity to examine genome dynamics in this species. Each genome was confirmed to be classified correctly based on SNP genotyping, nucleotide identity and presence/absence of repetitive elements or other typing methods. The Mycobacterium avium subspecies paratuberculosis (Map) genome size and organization was remarkably consistent, averaging 4.8 Mb with a variance of only 29.6 kb among the 13 strains. Comparing recombination events along with the larger genome size and variance observed among Mycobacterium avium subspecies avium (Maa) and Mycobacterium avium subspecies hominissuis (Mah) strains (collectively termed non-Map) suggests horizontal gene transfer occurs in non-Map, but not in Map strains. Overall, M. avium subspecies could be divided into two major sub-divisions, with the Map type II (bovine strains) clustering tightly on one end of a phylogenetic spectrum and Mah strains clustering more loosely together on the other end. The most evolutionarily distinct Map strain was an ovine strain, designated Telford, which had >1,000 SNPs and showed large rearrangements compared to the bovine type II strains. The Telford strain clustered with Maa strains as an intermediate between Map type II and Mah. SNP analysis and genome organization analyses repeatedly demonstrated the conserved nature of Map versus the mosaic nature of non-Map M. avium strains. Finally, core and pangenomes were developed for Map and non-Map strains. A total of 80% Map genes belonged to the Map core genome, while only 40% of non-Map genes belonged to the non-Map core genome. These genomes provide a more complete and detailed comparison of these subspecies strains as well as a blueprint for how genetic diversity originated.}, }
@article {pmid32849327, year = {2020}, author = {Hall, RJ and Whelan, FJ and McInerney, JO and Ou, Y and Domingo-Sananes, MR}, title = {Horizontal Gene Transfer as a Source of Conflict and Cooperation in Prokaryotes.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1569}, pmid = {32849327}, issn = {1664-302X}, abstract = {Horizontal gene transfer (HGT) is one of the most important processes in prokaryote evolution. The sharing of DNA can spread neutral or beneficial genes, as well as genetic parasites across populations and communities, creating a large proportion of the variability acted on by natural selection. Here, we highlight the role of HGT in enhancing the opportunities for conflict and cooperation within and between prokaryote genomes. We discuss how horizontally acquired genes can cooperate or conflict both with each other and with a recipient genome, resulting in signature patterns of gene co-occurrence, avoidance, and dependence. We then describe how interactions involving horizontally transferred genes may influence cooperation and conflict at higher levels (populations, communities, and symbioses). Finally, we consider the benefits and drawbacks of HGT for prokaryotes and its fundamental role in understanding conflict and cooperation from the gene-gene to the microbiome level.}, }
@article {pmid32848007, year = {2020}, author = {Rivard, N and Colwell, RR and Burrus, V}, title = {Antibiotic Resistance in Vibrio cholerae: Mechanistic Insights from IncC Plasmid-Mediated Dissemination of a Novel Family of Genomic Islands Inserted at trmE.}, journal = {mSphere}, volume = {5}, number = {4}, pages = {}, pmid = {32848007}, issn = {2379-5042}, support = {PJT-153071//CIHR/Canada ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics ; Cholera/microbiology ; Computer Simulation ; Conjugation, Genetic ; Drug Resistance, Multiple, Bacterial/*genetics ; Gammaproteobacteria/genetics ; Gene Transfer, Horizontal ; Genome, Bacterial ; *Genomic Islands ; Haiti ; Humans ; Plasmids/*genetics ; Vibrio cholerae/*drug effects/*genetics ; }, abstract = {Cholera remains a formidable disease, and reports of multidrug-resistant strains of the causative agent Vibrio cholerae have become common during the last 3 decades. The pervasiveness of resistance determinants has largely been ascribed to mobile genetic elements, including SXT/R391 integrative conjugative elements, IncC plasmids, and genomic islands (GIs). Conjugative transfer of IncC plasmids is activated by the master activator AcaCD whose regulatory network extends to chromosomally integrated GIs. MGIVchHai6 is a multidrug resistance GI integrated at the 3' end of trmE (mnmE or thdF) in chromosome 1 of non-O1/non-O139 V. cholerae clinical isolates from the 2010 Haitian cholera outbreak. In the presence of an IncC plasmid expressing AcaCD, MGIVchHai6 excises from the chromosome and transfers at high frequency. Herein, the mechanism of mobilization of MGIVchHai6 GIs by IncC plasmids was dissected. Our results show that AcaCD drives expression of GI-borne genes, including xis and mobIM , involved in excision and mobilization. A 49-bp fragment upstream of mobIM was found to serve as the minimal origin of transfer (oriT) of MGIVchHai6. The direction of transfer initiated at oriT was determined using IncC plasmid-driven mobilization of chromosomal markers via MGIVchHai6. In addition, IncC plasmid-encoded factors, including the relaxase TraI, were found to be required for GI transfer. Finally, in silico exploration of Gammaproteobacteria genomes identified 47 novel related and potentially AcaCD-responsive GIs in 13 different genera. Despite sharing conserved features, these GIs integrate at trmE, yicC, or dusA and carry a diverse cargo of genes involved in phage resistance.IMPORTANCE The increasing association of the etiological agent of cholera, Vibrio cholerae serogroup O1 and O139, with multiple antibiotic resistance threatens to deprive health practitioners of this effective tool. Drug resistance in cholera results mainly from acquisition of mobile genetic elements. Genomic islands conferring multidrug resistance and mobilizable by IncC conjugative plasmids were reported to circulate in non-O1/non-O139 V. cholerae clinical strains isolated from the 2010 Haitian cholera outbreak. As these genomic islands can be transmitted to pandemic V. cholerae serogroups, their mechanism of transmission needed to be investigated. Our research revealed plasmid- and genomic island-encoded factors required for the resistance island excision, mobilization, and integration, as well as regulation of these functions. The discovery of related genomic islands carrying diverse phage resistance genes but lacking antibiotic resistance-conferring genes in a wide range of marine dwelling bacteria suggests that these elements are ancient and recently acquired drug resistance genes.}, }
@article {pmid32847815, year = {2020}, author = {Slomka, S and Françoise, I and Hornung, G and Asraf, O and Biniashvili, T and Pilpel, Y and Dahan, O}, title = {Experimental Evolution of Bacillus subtilis Reveals the Evolutionary Dynamics of Horizontal Gene Transfer and Suggests Adaptive and Neutral Effects.}, journal = {Genetics}, volume = {216}, number = {2}, pages = {543-558}, pmid = {32847815}, issn = {1943-2631}, mesh = {Bacillus subtilis/*genetics/metabolism ; *Directed Molecular Evolution ; *Gene Transfer, Horizontal ; *Salt Tolerance ; Selection, Genetic ; }, abstract = {Tracing evolutionary processes that lead to fixation of genomic variation in wild bacterial populations is a prime challenge in molecular evolution. In particular, the relative contribution of horizontal gene transfer (HGT) vs.de novo mutations during adaptation to a new environment is poorly understood. To gain a better understanding of the dynamics of HGT and its effect on adaptation, we subjected several populations of competent Bacillus subtilis to a serial dilution evolution on a high-salt-containing medium, either with or without foreign DNA from diverse pre-adapted or naturally salt tolerant species. Following 504 generations of evolution, all populations improved growth yield on the medium. Sequencing of evolved populations revealed extensive acquisition of foreign DNA from close Bacillus donors but not from more remote donors. HGT occurred in bursts, whereby a single bacterial cell appears to have acquired dozens of fragments at once. In the largest burst, close to 2% of the genome has been replaced by HGT. Acquired segments tend to be clustered in integration hotspots. Other than HGT, genomes also acquired spontaneous mutations. Many of these mutations occurred within, and seem to alter, the sequence of flagellar proteins. Finally, we show that, while some HGT fragments could be neutral, others are adaptive and accelerate evolution.}, }
@article {pmid32847015, year = {2020}, author = {Blanco-Picazo, P and Roscales, G and Toribio-Avedillo, D and Gómez-Gómez, C and Avila, C and Ballesté, E and Muniesa, M and Rodríguez-Rubio, L}, title = {Antibiotic Resistance Genes in Phage Particles from Antarctic and Mediterranean Seawater Ecosystems.}, journal = {Microorganisms}, volume = {8}, number = {9}, pages = {}, pmid = {32847015}, issn = {2076-2607}, support = {AGL2016-75536-P//Ministerio de Ciencia e Innovaci&#xf3;n/ ; BES-2017-081296//Ministerio de Econom&#xed;a, Industria y Competitividad, Gobierno de Espa&#xf1;a/ ; 2017SGR170//Generalitat de Catalunya/ ; CTM2016-78901/ANT//Ministerio de Ciencia e Innovaci&#xf3;n/ ; }, abstract = {Anthropogenic activities are a key factor in the development of antibiotic resistance in bacteria, a growing problem worldwide. Nevertheless, antibiotics and resistances were being generated by bacterial communities long before their discovery by humankind, and might occur in areas without human influence. Bacteriophages are known to play a relevant role in the dissemination of antibiotic resistance genes (ARGs) in aquatic environments. In this study, five ARGs (blaTEM, blaCTX-M-1, blaCTX-M-9, sul1 and tetW) were monitored in phage particles isolated from seawater of two different locations: (i) the Mediterranean coast, subjected to high anthropogenic pressure, and (ii) the Antarctic coast, where the anthropogenic impact is low. Although found in lower quantities, ARG-containing phage particles were more prevalent among the Antarctic than the Mediterranean seawater samples and Antarctic bacterial communities were confirmed as their source. In the Mediterranean area, ARG-containing phages from anthropogenic fecal pollution might allow ARG transmission through the food chain. ARGs were detected in phage particles isolated from fish (Mediterranean, Atlantic, farmed, and frozen), the most abundant being β-lactamases. Some of these particles were infectious in cultures of the fecal bacteria Escherichia coli. By serving as ARG reservoirs in marine environments, including those with low human activity, such as the Antarctic, phages could contribute to ARG transmission between bacterial communities.}, }
@article {pmid32846568, year = {2020}, author = {Campos Calero, G and Caballero Gómez, N and Lavilla Lerma, L and Benomar, N and Knapp, CW and Abriouel, H}, title = {In silico mapping of microbial communities and stress responses in a porcine slaughterhouse and pork products through its production chain, and the efficacy of HLE disinfectant.}, journal = {Food research international (Ottawa, Ont.)}, volume = {136}, number = {}, pages = {109486}, doi = {10.1016/j.foodres.2020.109486}, pmid = {32846568}, issn = {1873-7145}, mesh = {Abattoirs ; Animals ; Computer Simulation ; *Disinfectants ; Humans ; *Meat Products ; *Microbiota ; *Red Meat ; Swine ; }, abstract = {The use of shotgun metagenomic sequencing to understand ecological-level spread of microbes and their genes has provided new insights for the prevention, surveillance and control of microbial contaminants in the slaughterhouse environment. Here, microbial samples were collected from products and surrounding areas though a porcine slaughter process; shotgun metagenomic DNA-sequencing of these samples revealed a high community diversity within the porcine slaughterhouse and pork products, in zones originating from animal arrival through to the sale zones. Bacteria were more prevalent in the first zones, such as arrival- and anesthesia-zones, and DNA viruses were prevalent in the scorching-and-whip zone, animal products and sale zone. Data revealed the dominance of Firmicutes and Proteobacteria phyla followed by Actinobacteria, with a clear shift in the relative abundance of lactic acid bacteria (mainly Lactobacillus sp.) from early slaughtering steps to Proteobacteria and then to viruses suggesting site-specific community compositions occur in the slaughterhouse. Porcine-type-C oncovirus was the main virus found in slaughterhouse, which causes malignant diseases in animals and humans. As such, to guarantee food safety in a slaughterhouse, a better decipher of ecology and adaptation strategies of microbes becomes crucial. Analysis of functional genes further revealed high abundance of diverse genes associated with stress, especially in early zones (animal and environmental surfaces of arrival zone with 57,710 and 40,806 genes, respectively); SOS responsive genes represented the most prevalent, possibly associated with genomic changes responsible of biofilm formation, stringent response, heat shock, antimicrobial production and antibiotic response. The presence of several antibiotic resistance genes suggests horizontal gene transfer, thus increasing the likelihood for resistance selection in human pathogens. These findings are of great concern, with the suggestion to focus control measures and establish good disinfection strategies to avoid gene spread and microbial contaminants (bacteria and viruses) from the animal surface into the food chain and environment, which was achieved by applying HLE disinfectant after washing with detergent.}, }
@article {pmid32845827, year = {2020}, author = {Calder, A and Menkiti, CJ and Çağdaş, A and Lisboa Santos, J and Streich, R and Wong, A and Avini, AH and Bojang, E and Yogamanoharan, K and Sivanesan, N and Ali, B and Ashrafi, M and Issa, A and Kaur, T and Latif, A and Mohamed, HAS and Maqsood, A and Tamang, L and Swager, E and Stringer, AJ and Snyder, LAS}, title = {Virulence genes and previously unexplored gene clusters in four commensal Neisseria spp. isolated from the human throat expand the neisserial gene repertoire.}, journal = {Microbial genomics}, volume = {6}, number = {9}, pages = {}, pmid = {32845827}, issn = {2057-5858}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacterial Proteins/*genetics ; Gene Transfer, Horizontal ; Healthy Volunteers ; High-Throughput Nucleotide Sequencing ; Humans ; Multigene Family ; Neisseria/*classification/genetics/isolation &amp; purification/pathogenicity ; Pharynx/*microbiology ; Phylogeny ; Symbiosis ; Type VI Secretion Systems/genetics ; Virulence Factors/genetics ; Whole Genome Sequencing/*methods ; }, abstract = {Commensal non-pathogenic Neisseria spp. live within the human host alongside the pathogenic Neisseria meningitidis and Neisseria gonorrhoeae and due to natural competence, horizontal gene transfer within the genus is possible and has been observed. Four distinct Neisseria spp. isolates taken from the throats of two human volunteers have been assessed here using a combination of microbiological and bioinformatics techniques. Three of the isolates have been identified as Neisseria subflava biovar perflava and one as Neisseria cinerea. Specific gene clusters have been identified within these commensal isolate genome sequences that are believed to encode a Type VI Secretion System, a newly identified CRISPR system, a Type IV Secretion System unlike that in other Neisseria spp., a hemin transporter, and a haem acquisition and utilization system. This investigation is the first to investigate these systems in either the non-pathogenic or pathogenic Neisseria spp. In addition, the N. subflava biovar perflava possess previously unreported capsule loci and sequences have been identified in all four isolates that are similar to genes seen within the pathogens that are associated with virulence. These data from the four commensal isolates provide further evidence for a Neisseria spp. gene pool and highlight the presence of systems within the commensals with functions still to be explored.}, }
@article {pmid32843891, year = {2020}, author = {Lafond, M and Hellmuth, M}, title = {Reconstruction of time-consistent species trees.}, journal = {Algorithms for molecular biology : AMB}, volume = {15}, number = {}, pages = {16}, pmid = {32843891}, issn = {1748-7188}, abstract = {BACKGROUND: The history of gene families-which are equivalent to event-labeled gene trees-can to some extent be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes. The question then arises as whether inferred event-labeled gene trees are "biologically feasible" which is the case if one can find a species tree with which the gene tree can be reconciled in a time-consistent way.<br><br>RESULTS: In this contribution, we consider event-labeled gene trees that contain speciations, duplications as well as horizontal gene transfer (HGT) and we assume that the species tree is unknown. Although many problems become NP-hard as soon as HGT and time-consistency are involved, we show, in contrast, that the problem of finding a time-consistent species tree for a given event-labeled gene can be solved in polynomial-time. We provide a cubic-time algorithm to decide whether a "time-consistent" species tree for a given event-labeled gene tree exists and, in the affirmative case, to construct the species tree within the same time-complexity.}, }
@article {pmid32841233, year = {2020}, author = {Russell, SL and Pepper-Tunick, E and Svedberg, J and Byrne, A and Ruelas Castillo, J and Vollmers, C and Beinart, RA and Corbett-Detig, R}, title = {Horizontal transmission and recombination maintain forever young bacterial symbiont genomes.}, journal = {PLoS genetics}, volume = {16}, number = {8}, pages = {e1008935}, pmid = {32841233}, issn = {1553-7404}, support = {R25 GM058903/GM/NIGMS NIH HHS/United States ; R35 GM128932/GM/NIGMS NIH HHS/United States ; T32 HG008345/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics/*pathogenicity ; Bivalvia/genetics/*microbiology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genetic Variation ; *Genome, Bacterial ; *Recombination, Genetic ; Symbiosis/*genetics ; }, abstract = {Bacterial symbionts bring a wealth of functions to the associations they participate in, but by doing so, they endanger the genes and genomes underlying these abilities. When bacterial symbionts become obligately associated with their hosts, their genomes are thought to decay towards an organelle-like fate due to decreased homologous recombination and inefficient selection. However, numerous associations exist that counter these expectations, especially in marine environments, possibly due to ongoing horizontal gene flow. Despite extensive theoretical treatment, no empirical study thus far has connected these underlying population genetic processes with long-term evolutionary outcomes. By sampling marine chemosynthetic bacterial-bivalve endosymbioses that range from primarily vertical to strictly horizontal transmission, we tested this canonical theory. We found that transmission mode strongly predicts homologous recombination rates, and that exceedingly low recombination rates are associated with moderate genome degradation in the marine symbionts with nearly strict vertical transmission. Nonetheless, even the most degraded marine endosymbiont genomes are occasionally horizontally transmitted and are much larger than their terrestrial insect symbiont counterparts. Therefore, horizontal transmission and recombination enable efficient natural selection to maintain intermediate symbiont genome sizes and substantial functional genetic variation.}, }
@article {pmid32841111, year = {2020}, author = {Botelho, J and Mourão, J and Roberts, AP and Peixe, L}, title = {Comprehensive genome data analysis establishes a triple whammy of carbapenemases, ICEs and multiple clinically relevant bacteria.}, journal = {Microbial genomics}, volume = {6}, number = {10}, pages = {}, pmid = {32841111}, issn = {2057-5858}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics ; Computer Simulation ; DNA Transposable Elements/*genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/drug effects/*genetics ; Genome, Bacterial/genetics ; Humans ; Klebsiella pneumoniae/drug effects/*genetics ; Microbial Sensitivity Tests ; Pseudomonas aeruginosa/drug effects/*genetics ; beta-Lactamases/*genetics ; beta-Lactams/pharmacology ; }, abstract = {Carbapenemases inactivate most β-lactam antibiotics, including carbapenems, and have frequently been reported among Enterobacteriaceae, Acinetobacter spp. and Pseudomonas spp. Traditionally, the horizontal gene transfer of carbapenemase-encoding genes (CEGs) has been linked to plasmids. However, given that integrative and conjugative elements (ICEs) are possibly the most abundant conjugative elements among prokaryotes, we conducted an in silico analysis to ascertain the likely role of ICEs in the spread of CEGs among all bacterial genomes (n=182 663). We detected 17 520 CEGs, of which 66 were located within putative ICEs among several bacterial species (including clinically relevant bacteria, such as Pseudomonas aeruginosa, Klebsiella pneumoniae and Escherichia coli). Most CEGs detected within ICEs belong to the IMP, NDM and SPM metallo-beta-lactamase families, and the serine beta-lactamase KPC and GES families. Different mechanisms were likely responsible for acquisition of these genes. The majority of CEG-bearing ICEs belong to the MPFG, MPFT and MPFF classes and often encode resistance to other antibiotics (e.g. aminoglycosides and fluoroquinolones). This study provides a snapshot of the different CEGs associated with ICEs among available bacterial genomes and sheds light on the underappreciated contribution of ICEs to the spread of carbapenem resistance globally.}, }
@article {pmid32839909, year = {2021}, author = {Wang, Y and Chen, Z and Wen, Q and Ji, Y}, title = {Variation of heavy metal speciation, antibiotic degradation, and potential horizontal gene transfer during pig manure composting under different chlortetracycline concentration.}, journal = {Environmental science and pollution research international}, volume = {28}, number = {1}, pages = {1224-1234}, doi = {10.1007/s11356-020-10557-x}, pmid = {32839909}, issn = {1614-7499}, support = {51878214//National Natural Science Foundation of China/ ; 2019TS03//State Key Laboratory of Urban Water Resource and Environment/ ; UTF-2016-longterm/ 10042//Senter for Internasjonalisering av Utdanning/ ; }, mesh = {Animals ; Anti-Bacterial Agents ; *Chlortetracycline ; *Composting ; Gene Transfer, Horizontal ; Genes, Bacterial ; Manure ; *Metals, Heavy ; Swine ; }, abstract = {Overuse of heavy metal and antibiotics in livestock husbandry has led to the accumulation of heavy metal resistance genes (HMRGs) and antibiotic resistance genes (ARGs) in environment. This research aims to reveal the variation of heavy metal speciation and potential horizontal gene transfer (HGT) of HMRGs and ARGs in manure composting under different initial chlortetracycline (CTC) concentrations. Treatments spiked with 20 mg/kg CTC (treatment P1), 100 mg/kg CTC (treatment P2), and the control (treatment CK) were operated. Results showed that CTC could be completely removed in the thermophilic phase of all the treatments despite of the initial concentrations. Bioavailable Cu in treatments CK, P1, and P2 declined by 14.5%, 27.1%, and 26.7% and bioavailable Zn declined by 15.3%, 29.5%, and 12.1%, respectively, after the composting, respectively. Relative abundance of HMRGs decreased by 6.49 log, 8.88 log, and 5.77 log, respectively, in treatments CK, P1, and P2. Relative abundance of ARGs decreased by 3.37 log, 4.86 log, and 3.32 log, respectively, in treatments CK, P1, and P2. Composting could effectively reduce genes pcoD, pcoA, zntA, tetQ, and tetA, which might locate on the same plasmid. CTC of 100 mg/kg promoted the co-selection of ARGs and HMRGs and increased the potential HGT of gene cusA.}, }
@article {pmid32836113, year = {2020}, author = {Gwenzi, W}, title = {The 'thanato-resistome' - The funeral industry as a potential reservoir of antibiotic resistance: Early insights and perspectives.}, journal = {The Science of the total environment}, volume = {749}, number = {}, pages = {141120}, pmid = {32836113}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; *Ecosystem ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; }, abstract = {The funeral industry is a potential reservoir of antibiotic resistance. The occurrence, human exposure and health risks of antibiotic resistance in the funeral industry were examined. The funeral industry harbours antibiotic resistance to multiple common and last-resort antibiotics, hence constitutes the 'thanato-resistome'. Hydrological processes, air-borne particulates and vectors disseminate antibiotic resistance, while horizontal gene transfer circulates antibiotic resistance among resistomes, forming a complex network. Ingestion, inhalation of air-borne particulates, dermal intake and clothes of workers contribute to human exposure. Human health risks include; development of drug resistance in previously susceptible pathogens, and increased morbidity and mortality caused by increased pathogenicity and outbreaks of multi-drug resistant infections. Ecological risks include the proliferation of resistant organisms at the expense of susceptible ones, thereby disrupting ecosystem structure and function, including biogeochemical cycles. Barring inferential data, quantitative evidence linking antibiotic resistance to human infections is weak. This reflects the lack of systematic quantitative studies, rather than the absence of such health risks. Quantitative risk assessment is constrained by lack of quantitative data on antibiotic resistance in various reservoirs and exposure routes. A framework for risk assessment and mitigation is proposed. Finally, ten hypotheses and emerging tools such as genomics, in silico techniques and big data analytics are highlighted.}, }
@article {pmid32835992, year = {2021}, author = {Jiang, W and Liu, Y and Ke, Z and Zhang, L and Zhang, M and Zhou, Y and Wang, H and Wu, C and Qiu, J and Hong, Q}, title = {Substrate preference of carbamate hydrolase CehA reveals its environmental behavior.}, journal = {Journal of hazardous materials}, volume = {403}, number = {}, pages = {123677}, doi = {10.1016/j.jhazmat.2020.123677}, pmid = {32835992}, issn = {1873-3336}, mesh = {Carbaryl ; *Carbofuran ; Carboxylic Ester Hydrolases ; *Insecticides ; }, abstract = {The cehA gene is the earliest reported and most widely found carbaryl hydrolase gene. CehA detoxifies carbaryl and other carbamate pesticides via de-esterification. Currently, there is no systematic research available on substrate preference or the mechanism of CehA action in different hosts. In this study, we found that CehA from different hosts is highly conserved, with more than 99% amino acid sequence similarity, and that transposable elements exist in both the upstream and downstream regions of cehA. By introducing point mutations into the cehA gene of Sphingobium sp. CFD-1, we obtained and heterologously expressed all reported CehA(CehAS) encoding genes. Assays to determine enzymatic properties and substrate profiles of CehAS showed that each CehA has a significant substrate preference for different carbamate insecticides. Specifically, CehA152Phe/Leu determines the catalytic preference for bicyclic carbamate substrates (carbofuran, carbaryl), while CehA494Thr/Ala and 570Thr/Ile determine the preference for monocyclic carbamate substrates (isoprocarb, propoxur) and linear carbamate substrates (oxamyl, aldicarb), respectively. Considering the existence of transposable elements in the flanking regions of cehA, we speculate that the cehA hosts may have acquired the hydrolysis ability, as well as substrate preference for carbamate pesticides, through horizontal gene transfer and genetic copying errors.}, }
@article {pmid32831012, year = {2020}, author = {Palmieri, N and Hess, C and Hess, M and Alispahic, M}, title = {Sequencing of five poultry strains elucidates phylogenetic relationships and divergence in virulence genes in Morganella morganii.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {579}, pmid = {32831012}, issn = {1471-2164}, mesh = {Animals ; Anti-Bacterial Agents ; Humans ; *Morganella morganii/genetics ; Phylogeny ; Poultry ; Virulence/genetics ; beta-Lactamases/genetics ; beta-Lactams ; }, abstract = {BACKGROUND: M. morganii is a bacterium frequently associated with urinary infections in humans. While many human strains are sequenced, only the genomes of few poultry strains are available. Here, we performed a detailed characterization of five highly resistant Morganella morganii strains isolated in association with Escherichia coli from diseased domestic Austrian poultry flocks, namely geese, turkeys and chicken layers. Additionally, we sequenced the genomes of these strains by NGS and analyzed phylogenetic clustering, resistance and virulence genes in the context of host-specificity.<br><br>RESULTS: Two strains were identified to be Extended Spectrum Beta Lactamase (ESBL) and one as AmpC beta-lactamases (AMP-C) phenotype, while two were ESBL negative. By integrating the genome sequences of these five poultry strains with all the available M. morganii genomes, we constructed a phylogenetic tree that clearly separates the Morganella genus into two clusters (M1 and M2), which approximately reflect the proposed subspecies classification (morganii and sibonii). Additionally, we found no association between phylogenetic structure and host, suggesting interspecies transmission. All five poultry strains contained genes for resistance to aminocoumarins, beta-lactams, colistin, elfamycins, fluoroquinolones, phenicol, rifampin and tetracycline. A comparative genomics analysis of virulence genes showed acquisition of novel virulence genes involved in secretion system and adherence in cluster M2. We showed that some of these genes were acquired by horizontal gene transfer from closely related Morganellaceae species and propose that novel virulence genes could be responsible for expansion of tissue tropism in M. morganii. Finally, we detected variability in copy number and high sequence divergence in toxin genes and provided evidence for positive selection in insecticidal toxins genes, likely reflecting host-related adaptations.<br><br>CONCLUSIONS: In summary, this study describes i) the first isolation and characterization of M. morganii from goose and turkey, ii) a large-scale genetic analysis of M. morganii and an attempt to generate a global picture of the M. morganii intraspecific phylogenetic structure.}, }
@article {pmid32828660, year = {2020}, author = {Sibbald, SJ and Eme, L and Archibald, JM and Roger, AJ}, title = {Lateral Gene Transfer Mechanisms and Pan-genomes in Eukaryotes.}, journal = {Trends in parasitology}, volume = {36}, number = {11}, pages = {927-941}, doi = {10.1016/j.pt.2020.07.014}, pmid = {32828660}, issn = {1471-5007}, mesh = {Eukaryota/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome/*genetics ; Genome, Protozoan/genetics ; Host-Parasite Interactions/genetics ; }, abstract = {Lateral gene transfer (LGT) is well known as an important driver of genome evolution in bacteria and archaea, but its importance in eukaryote evolution has yet to be fully elucidated. There is now abundant evidence indicating that LGT has played a role in the adaptation of eukaryotes to new environments and conditions, including host-parasite interactions. However, the mechanisms and frequency of LGT across the tree of eukaryotes remain poorly understood. Here we review evidence for known and potential mechanisms of LGT into diverse eukaryote lineages with a particular focus on protists, and we discuss trends emerging from recently reported examples. We also explore the potential role of LGT in generating 'pan-genomes' in diverse eukaryotic species.}, }
@article {pmid32827633, year = {2020}, author = {Esch, T and Kream, RM and Stefano, GB}, title = {Emerging regulatory roles of opioid peptides, endogenous morphine, and opioid receptor subtypes in immunomodulatory processes: Metabolic, behavioral, and evolutionary perspectives.}, journal = {Immunology letters}, volume = {227}, number = {}, pages = {28-33}, doi = {10.1016/j.imlet.2020.08.007}, pmid = {32827633}, issn = {1879-0542}, mesh = {Animals ; Behavior ; Biological Evolution ; Humans ; Immunity ; Immunomodulation ; Inflammation/*metabolism ; Morphine/*metabolism ; Nitric Oxide/metabolism ; Opioid Peptides/*metabolism ; Pain/*metabolism ; Receptors, Opioid/genetics/*metabolism ; }, abstract = {Integrated behavioral paradigms such as nociceptive processing coupled to anti-nociceptive responsiveness include systemically-mediated states of alertness, vigilance, motivation, and avoidance. Within a historical and cultural context, opium and its biologically active compounds, codeine and morphine, have been widely used as frontline anti-nociceptive agents. In eukaryotic cells, opiate alkaloids and opioid peptides were evolutionarily fashioned as regulatory factors in neuroimmune, vascular immune, and systemic immune communication and auto-immunoregulation. The significance of opioidergic regulation of immune function was validated by the identification of novel μ and δ opioid receptors on circulating leukocytes. The novel μ3 opioid receptor subtype has been characterized as an opioid peptide-insensitive and opiate alkaloid-selective G protein-coupled receptor (GPCR) that is functionally linked to the activation of constitutive nitric oxide synthase (cNOS). Opioid peptides stimulate granulocyte and immunocyte activation and chemotaxis via activation of a novel leukocyte δ2 receptor subtype. However, opiate alkaloid μ3 receptor agonists inhibit these same cellular activities. Opiate coupling to cNOS and subsequent production and release of mitochondrial nitric oxide (NO) suggests an evolutionary linkage to similar physiological events in prokaryotic cells. A subpopulation of immunocytes from Mytilus edulis and Leucophaea maderae and human granulocytes respond to low opioid concentrations, mediated by the adherence-promoting role of (D-Ala2-D-Met5)-enkephalinamide (DAMA), which is blocked by naloxone in a dose-dependent manner. Neutral endopeptidase 24.11 (NEP), or enkephalinase (CD10), is present on both human and invertebrate immunocytes. Alkaloids, including morphine, are found in both prokaryotic and eukaryotic cells and may have evolved much later in evolution through horizontal gene transfer. It is possible that opioid-mediated regulatory activities were conserved and elaborated during evolution as the central nervous system (CNS) became immunologically isolated by the blood-brain barrier. Thus, opioid receptor coupling became significant for cognitive and behavioural processes. Although opioid peptides and alkaloids work synergistically to suppress nociception, they mediate different actions in immune surveillance. Increased understanding of the evolutionary development of opioid receptors, nociceptive and anti-nociceptive pathways, and immunomodulation may help in the understanding of the development of tolerance to the clinical use of opiates for pain management. The significance of endogenous morphine's importance to evolution can be ascertained by the number of physiological tissues and systems that can be affected by this chemical messenger mechanism, which transcends pain. An integrated review is presented of opioid and opiate receptors, immunomodulation, and pain associated with inflammation, from an evolutionary perspective.}, }
@article {pmid32823766, year = {2020}, author = {Li, KL and Nakashima, K and Inoue, J and Satoh, N}, title = {Phylogenetic Analyses of Glycosyl Hydrolase Family 6 Genes in Tunicates: Possible Horizontal Transfer.}, journal = {Genes}, volume = {11}, number = {8}, pages = {}, pmid = {32823766}, issn = {2073-4425}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Bacteria/genetics ; Binding Sites ; Catalytic Domain ; Chromosome Mapping ; Conserved Sequence ; Evolution, Molecular ; Fungi/genetics ; Gene Transfer, Horizontal ; Glucosyltransferases/genetics ; *Multigene Family ; N-Glycosyl Hydrolases/chemistry/*genetics ; *Phylogeny ; Protein Binding ; Protein Domains ; RNA Splice Sites ; Urochordata/*classification/*genetics ; }, abstract = {Horizontal gene transfer (HGT) is the movement of genetic material between different species. Although HGT is less frequent in eukaryotes than in bacteria, several instances of HGT have apparently shaped animal evolution. One well-known example is the tunicate cellulose synthase gene, CesA, in which a gene, probably transferred from bacteria, greatly impacted tunicate evolution. A Glycosyl Hydrolase Family 6 (GH6) hydrolase-like domain exists at the C-terminus of tunicate CesA, but not in cellulose synthases of other organisms. The recent discovery of another GH6 hydrolase-like gene (GH6-1) in tunicate genomes further raises the question of how tunicates acquired GH6. To examine the probable origin of these genes, we analyzed the phylogenetic relationship of GH6 proteins in tunicates and other organisms. Our analyses show that tunicate GH6s, the GH6-1 gene, and the GH6 part of the CesA gene, form two independent, monophyletic gene groups. We also compared their sequence signatures and exon splice sites. All tunicate species examined have shared splice sites in GH6-containing genes, implying ancient intron acquisitions. It is likely that the tunicate CesA and GH6-1 genes existed in the common ancestor of all extant tunicates.}, }
@article {pmid32823495, year = {2020}, author = {Lima, T and Domingues, S and Da Silva, GJ}, title = {Manure as a Potential Hotspot for Antibiotic Resistance Dissemination by Horizontal Gene Transfer Events.}, journal = {Veterinary sciences}, volume = {7}, number = {3}, pages = {}, pmid = {32823495}, issn = {2306-7381}, abstract = {The increasing demand for animal-derived foods has led to intensive and large-scale livestock production with the consequent formation of large amounts of manure. Livestock manure is widely used in agricultural practices as soil fertilizer worldwide. However, several antibiotic residues, antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria are frequently detected in manure and manure-amended soils. This review explores the role of manure in the persistence and dissemination of ARGs in the environment, analyzes the procedures used to decrease antimicrobial resistance in manure and the potential impact of manure application in public health. We highlight that manure shows unique features as a hotspot for antimicrobial gene dissemination by horizontal transfer events: richness in nutrients, a high abundance and diversity of bacteria populations and antibiotic residues that may exert a selective pressure on bacteria and trigger gene mobilization; reduction methodologies are able to reduce the concentrations of some, but not all, antimicrobials and microorganisms. Conjugation events are often seen in the manure environment, even after composting. Antibiotic resistance is considered a growing threat to human, animal and environmental health. Therefore, it is crucial to reduce the amount of antimicrobials and the load of antimicrobial resistant bacteria that end up in soil.}, }
@article {pmid32818733, year = {2020}, author = {Wang, H and Wang, J and Li, S and Ding, G and Wang, K and Zhuang, T and Huang, X and Wang, X}, title = {Synergistic effect of UV/chlorine in bacterial inactivation, resistance gene removal, and gene conjugative transfer blocking.}, journal = {Water research}, volume = {185}, number = {}, pages = {116290}, doi = {10.1016/j.watres.2020.116290}, pmid = {32818733}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics ; *Chlorine ; Disinfection ; Drug Resistance, Bacterial ; Drug Resistance, Microbial ; Genes, Bacterial ; Wastewater ; }, abstract = {Antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) were investigated from effluent of two hospital and two municipal wastewater treatment plants (WWTPs) before and after disinfection. The results of network analysis showed that 8 genera were identified to be the main potential hosts of ARGs, including Mycobacterium, Ferruginibacter, Thermomonas, Morganella, Enterococcus, Bacteroides, Myroides and Romboutsia. The removal of ARGs and their possible bacterialhosts were synchronous and consistent by chlorine or ultraviolet (UV) disinfection in WWTPs. The mechanisms of ARB and ARGs removal, and conjugation transfer of RP4 plasmids by UV, chlorine and synergistic UV/chlorine disinfection was revealed. Compared to UV alone, ARB inactivation was improved 1.4 log and photoreactivation was overcomeeffectively by UV/chlorine combination (8 mJ/cm[2], chlorine 2 mg/L). However, ARGs degradation was more difficult than ARB inactivation. Until UV dosage enhanced to 320 mJ/cm[2], ARGs achieved 0.58-1.60 log removal. Meanwhile, when 2 mg/L of chlorine was combined with UV combination, ARGs removal enhanced 1-1.5 log. The synergistic effect of adding low-dose chlorine (1-2 mg/L) during UV radiation effectively improved ARB and ARGs removal simultaneously. The same synergistic effect also occurred in the horizontal gene transfer (HGT). Non-lethal dose chlorine (0.5 mg/L) increased the conjugation transfer frequency,which confirmed that the mRNA expression levels of type IV secretion system (T4SS) proteins vir4D, vir5B and vir10B were significantly enhanced. The risk of RP4 plasmid conjugation transfer was significantly reduced with UV/chlorine (UV ≥ 4 mJ/cm[2], chlorine ≥ 1 mg/L). These findings may serve as valuable implications for assessing and controlling the risk of ARGs transfer and propagation in the environment.}, }
@article {pmid32818425, year = {2020}, author = {Ramírez-Vargas, G and Rodríguez, C}, title = {Putative Conjugative Plasmids with tcdB and cdtAB Genes in Clostridioides difficile.}, journal = {Emerging infectious diseases}, volume = {26}, number = {9}, pages = {2287-2290}, pmid = {32818425}, issn = {1080-6059}, mesh = {Bacterial Proteins/genetics ; *Bacterial Toxins/genetics ; Clostridioides ; *Clostridioides difficile/genetics ; Enterotoxins ; Plasmids/genetics ; }, abstract = {The major toxins of Clostridioides difficile (TcdA, TcdB, CDT) are chromosomally encoded in nearly all known strains. Following up on previous findings, we identified 5 examples of a family of putative conjugative plasmids with tcdB and cdtAB in clinical C. difficile isolates from multilocus sequence typing clades C-I, 2, and 4.}, }
@article {pmid32817383, year = {2020}, author = {McDaniel, EA and Peterson, BD and Stevens, SLR and Tran, PQ and Anantharaman, K and McMahon, KD}, title = {Expanded Phylogenetic Diversity and Metabolic Flexibility of Mercury-Methylating Microorganisms.}, journal = {mSystems}, volume = {5}, number = {4}, pages = {}, pmid = {32817383}, issn = {2379-5077}, abstract = {Methylmercury is a potent bioaccumulating neurotoxin that is produced by specific microorganisms that methylate inorganic mercury. Methylmercury production in diverse anaerobic bacteria and archaea was recently linked to the hgcAB genes. However, the full phylogenetic and metabolic diversity of mercury-methylating microorganisms has not been fully unraveled due to the limited number of cultured experimentally verified methylators and the limitations of primer-based molecular methods. Here, we describe the phylogenetic diversity and metabolic flexibility of putative mercury-methylating microorganisms by hgcAB identification in publicly available isolate genomes and metagenome-assembled genomes (MAGs) as well as novel freshwater MAGs. We demonstrate that putative mercury methylators are much more phylogenetically diverse than previously known and that hgcAB distribution among genomes is most likely due to several independent horizontal gene transfer events. The microorganisms we identified possess diverse metabolic capabilities spanning carbon fixation, sulfate reduction, nitrogen fixation, and metal resistance pathways. We identified 111 putative mercury methylators in a set of previously published permafrost metatranscriptomes and demonstrated that different methylating taxa may contribute to hgcA expression at different depths. Overall, we provide a framework for illuminating the microbial basis of mercury methylation using genome-resolved metagenomics and metatranscriptomics to identify putative methylators based upon hgcAB presence and describe their putative functions in the environment.IMPORTANCE Accurately assessing the production of bioaccumulative neurotoxic methylmercury by characterizing the phylogenetic diversity, metabolic functions, and activity of methylators in the environment is crucial for understanding constraints on the mercury cycle. Much of our understanding of methylmercury production is based on cultured anaerobic microorganisms within the Deltaproteobacteria, Firmicutes, and Euryarchaeota. Advances in next-generation sequencing technologies have enabled large-scale cultivation-independent surveys of diverse and poorly characterized microorganisms from numerous ecosystems. We used genome-resolved metagenomics and metatranscriptomics to highlight the vast phylogenetic and metabolic diversity of putative mercury methylators and their depth-discrete activities in thawing permafrost. This work underscores the importance of using genome-resolved metagenomics to survey specific putative methylating populations of a given mercury-impacted ecosystem.}, }
@article {pmid32817379, year = {2020}, author = {Peter, S and Bosio, M and Gross, C and Bezdan, D and Gutierrez, J and Oberhettinger, P and Liese, J and Vogel, W and Dörfel, D and Berger, L and Marschal, M and Willmann, M and Gut, I and Gut, M and Autenrieth, I and Ossowski, S}, title = {Tracking of Antibiotic Resistance Transfer and Rapid Plasmid Evolution in a Hospital Setting by Nanopore Sequencing.}, journal = {mSphere}, volume = {5}, number = {4}, pages = {}, pmid = {32817379}, issn = {2379-5042}, mesh = {Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Multiple, Bacterial ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genomics ; Hospitals ; Humans ; *Nanopore Sequencing ; Plasmids/*genetics ; Pseudomonas aeruginosa/drug effects/enzymology/genetics ; Sequence Analysis, DNA/*methods ; beta-Lactamases/genetics ; }, abstract = {Infections with multidrug-resistant bacteria often leave limited or no treatment options. The transfer of antimicrobial resistance genes (ARG) carrying plasmids between bacterial species by horizontal gene transfer represents an important mode of expansion of ARGs. Here, we demonstrate the application of Nanopore sequencing in a hospital setting for monitoring transfer and rapid evolution of antibiotic resistance plasmids within and across multiple species. In 2009, we experienced an outbreak with extensively multidrug-resistant Pseudomonas aeruginosa harboring the carbapenemase-encoding blaIMP-8 gene. In 2012, the first Citrobacter freundii and Citrobacter cronae strains harboring the same gene were detected. Using Nanopore and Illumina sequencing, we conducted comparative analysis of all blaIMP-8 bacteria isolated in our hospital over a 6-year period (n = 54). We developed the computational platform plasmIDent for Nanopore-based characterization of clinical isolates and monitoring of ARG transfer, comprising de novo assembly of genomes and plasmids, plasmid circularization, ARG annotation, comparative genome analysis of multiple isolates, and visualization of results. Using plasmIDent, we identified a 40-kb plasmid carrying blaIMP-8 in P. aeruginosa and C. freundii, verifying the plasmid transfer. Within C. freundii, the plasmid underwent further evolution and plasmid fusion, resulting in a 164-kb megaplasmid, which was transferred to C. cronae Multiple rearrangements of the multidrug resistance gene cassette were detected in P. aeruginosa, including deletions and translocations of complete ARGs. In summary, plasmid transfer, plasmid fusion, and rearrangement of the ARG cassette mediated the rapid evolution of opportunistic pathogens in our hospital. We demonstrated the feasibility of near-real-time monitoring of plasmid evolution and ARG transfer in clinical settings, enabling successful countermeasures to contain plasmid-mediated outbreaks.IMPORTANCE Infections with multidrug-resistant bacteria represent a major threat to global health. While the spread of multidrug-resistant bacterial clones is frequently studied in the hospital setting, surveillance of the transfer of mobile genetic elements between different bacterial species was difficult until recent advances in sequencing technologies. Nanopore sequencing technology was applied to track antimicrobial gene transfer in a long-term outbreak of multidrug-resistant Pseudomonas aeruginosa, Citrobacter freundii, and Citrobacter cronae in a German hospital over 6 years. We developed a novel computational pipeline, pathoLogic, which enables de novo assembly of genomes and plasmids, antimicrobial resistance gene annotation and visualization, and comparative analysis. Applying this approach, we detected plasmid transfer between different bacterial species as well as plasmid fusion and frequent rearrangements of the antimicrobial resistance gene cassette. This study demonstrated the feasibility of near-real-time tracking of plasmid-based antimicrobial resistance gene transfer in hospitals, enabling countermeasures to contain plasmid-mediated outbreaks.}, }
@article {pmid32817089, year = {2020}, author = {Fonseca, DR and Halim, MFA and Holten, MP and Costa, KC}, title = {Type IV-Like Pili Facilitate Transformation in Naturally Competent Archaea.}, journal = {Journal of bacteriology}, volume = {202}, number = {21}, pages = {}, pmid = {32817089}, issn = {1098-5530}, mesh = {Archaeal Proteins/*metabolism ; *DNA, Archaeal ; *Gene Transfer, Horizontal ; Methanococcus/*genetics ; Methanomicrobiaceae/*genetics ; }, abstract = {Naturally competent organisms are capable of DNA uptake directly from the environment through the process of transformation. Despite the importance of transformation to microbial evolution, DNA uptake remains poorly characterized outside of the bacterial domain. Here, we identify the pilus as a necessary component of the transformation machinery in archaea. We describe two naturally competent organisms, Methanococcus maripaludis and Methanoculleus thermophilus In M. maripaludis, replicative vectors were transferred with an average efficiency of 2.4 × 10[3] transformants μg[-1] DNA. In M. thermophilus, integrative vectors were transferred with an average efficiency of 2.7 × 10[3] transformants μg[-1] DNA. Additionally, natural transformation of M. thermophilus could be used to introduce chromosomal mutations. To our knowledge, this is the first demonstration of a method to introduce targeted mutations in a member of the order Methanomicrobiales For both organisms, mutants lacking structural components of the type IV-like pilus filament were defective for DNA uptake, demonstrating the importance of pili for natural transformation. Interestingly, competence could be induced in a noncompetent strain of M. maripaludis by expressing pilin genes from a replicative vector. These results expand the known natural competence pili to include examples from the archaeal domain and highlight the importance of pili for DNA uptake in diverse microbial organisms.IMPORTANCE Microbial organisms adapt and evolve by acquiring new genetic material through horizontal gene transfer. One way that this occurs is natural transformation, the direct uptake and genomic incorporation of environmental DNA by competent organisms. Archaea represent up to a third of the biodiversity on Earth, yet little is known about transformation in these organisms. Here, we provide the first characterization of a component of the archaeal DNA uptake machinery. We show that the type IV-like pilus is essential for natural transformation in two archaeal species. This suggests that pili are important for transformation across the tree of life and further expands our understanding of gene flow in archaea.}, }
@article {pmid32816017, year = {2020}, author = {Li, B and Chen, Z and Zhang, F and Liu, Y and Yan, T}, title = {Abundance, diversity and mobility potential of antibiotic resistance genes in pristine Tibetan Plateau soil as revealed by soil metagenomics.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {10}, pages = {}, doi = {10.1093/femsec/fiaa172}, pmid = {32816017}, issn = {1574-6941}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial ; Genes, Bacterial ; *Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Soil ; Tibet ; }, abstract = {Widespread occurrence of antibiotic resistance genes (ARGs) has become an important clinical issue. Studying ARGs in pristine soil environments can help to better understand the intrinsic soil resistome. In this study, 10 soil samples were collected from a high elevation and relatively pristine Tibetan area, and metagenomic sequencing and bioinformatic analyses were conducted to investigate the microbial diversity, the abundance and diversity of ARGs and the mobility potential of ARGs as indicated by different mobile genetic elements (MGEs). A total of 48 ARG types with a relative abundance of 0.05-0.28 copies of ARG/copy of 16S rRNA genes were detected in Tibetan soil samples. The observed ARGs were mainly associated with antibiotics that included glycopeptide and rifamycin; the most abundant ARGs were vanRO and vanSO. Low abundance of MGEs and potentially plasmid-related ARGs indicated a low horizontal gene transfer risk of ARGs in the pristine soil. Pearson correlation and redundancy analyses showed that temperature and total organic carbon were the major environmental factors controlling both microbial diversity and ARG abundance and diversity.}, }
@article {pmid32813310, year = {2020}, author = {Iwabuchi, N and Kitazawa, Y and Maejima, K and Koinuma, H and Miyazaki, A and Matsumoto, O and Suzuki, T and Nijo, T and Oshima, K and Namba, S and Yamaji, Y}, title = {Functional variation in phyllogen, a phyllody-inducing phytoplasma effector family, attributable to a single amino acid polymorphism.}, journal = {Molecular plant pathology}, volume = {21}, number = {10}, pages = {1322-1336}, pmid = {32813310}, issn = {1364-3703}, mesh = {Amino Acids/genetics ; *Bacterial Proteins/genetics/metabolism ; Flowers/growth &amp; development/microbiology ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genes, Bacterial ; MADS Domain Proteins/metabolism ; Phylogeny ; *Phytoplasma/genetics/metabolism/pathogenicity ; Plant Diseases/etiology/microbiology ; Polymorphism, Single Nucleotide ; Transcription Factors/metabolism ; }, abstract = {Flower malformation represented by phyllody is a common symptom of phytoplasma infection induced by a novel family of phytoplasma effectors called phyllogens. Despite the accumulation of functional and structural phyllogen information, the molecular mechanisms of phyllody have not yet been integrated with their evolutionary aspects due to the limited data on their homologs across diverse phytoplasma lineages. Here, we developed a novel universal PCR-based approach to identify 25 phytoplasma phyllogens related to nine "Candidatus Phytoplasma" species, including four species whose phyllogens have not yet been identified. Phylogenetic analyses showed that the phyllogen family consists of four groups (phyl-A, -B, -C, and -D) and that the evolutionary relationships of phyllogens were significantly distinct from those of phytoplasmas, suggesting that phyllogens were transferred horizontally among phytoplasma strains and species. Although phyllogens belonging to the phyl-A, -C, and -D groups induced phyllody, the phyl-B group lacked the ability to induce phyllody. Comparative functional analyses of phyllogens revealed that a single amino acid polymorphism in phyl-B group phyllogens prevented interactions between phyllogens and A- and E-class MADS domain transcription factors (MTFs), resulting in the inability to degrade several MTFs and induce phyllody. Our finding of natural variation in the function of phytoplasma effectors provides new insights into molecular mechanisms underlying the aetiology of phytoplasma diseases.}, }
@article {pmid32807206, year = {2020}, author = {Glickman, C and Kammlade, SM and Hasan, NA and Epperson, LE and Davidson, RM and Strong, M}, title = {Characterization of integrated prophages within diverse species of clinical nontuberculous mycobacteria.}, journal = {Virology journal}, volume = {17}, number = {1}, pages = {124}, pmid = {32807206}, issn = {1743-422X}, support = {T15 LM009451/LM/NLM NIH HHS/United States ; }, mesh = {*Genome, Bacterial ; Humans ; *Lysogeny ; Mycobacterium Infections, Nontuberculous/*microbiology ; Nontuberculous Mycobacteria/genetics/growth &amp; development/pathogenicity/*virology ; Prophages/*genetics ; Virulence ; }, abstract = {BACKGROUND: Nontuberculous mycobacterial (NTM) infections are increasing in prevalence, with current estimates suggesting that over 100,000 people in the United States are affected each year. It is unclear how certain species of mycobacteria transition from environmental bacteria to clinical pathogens, or what genetic elements influence the differences in virulence among strains of the same species. A potential mechanism of genetic evolution and diversity within mycobacteria is the presence of integrated viruses called prophages in the host genome. Prophages may act as carriers of bacterial genes, with the potential of altering bacterial fitness through horizontal gene transfer. In this study, we quantify the frequency and composition of prophages within mycobacteria isolated from clinical samples and compare them against the composition of PhagesDB, an environmental mycobacteriophage database.<br><br>METHODS: Prophages were predicted by agreement between two discovery tools, VirSorter and Phaster, and the frequencies of integrated prophages were compared by growth rate. Prophages were assigned to PhagesDB lettered clusters. Bacterial virulence gene frequency was calculated using a combination of the Virulence Factor Database (VFDB) and the Pathosystems Resource Integration Center virulence database (Patric-VF) within the gene annotation software Prokka. CRISPR elements were discovered using CRT. ARAGORN was used to quantify tRNAs.<br><br>RESULTS: Rapidly growing mycobacteria (RGM) were more likely to contain prophage than slowly growing mycobacteria (SGM). CRISPR elements were not associated with prophage abundance in mycobacteria. The abundance of tRNAs was enriched in SGM compared to RGM. We compared the abundance of bacterial virulence genes within prophage genomes from clinical isolates to mycobacteriophages from PhagesDB. Our data suggests that prophages from clinical mycobacteria are enriched for bacterial virulence genes relative to environmental mycobacteriophage from PhagesDB.<br><br>CONCLUSION: Prophages are present in clinical NTM isolates. Prophages are more likely to be present in RGM compared to SGM genomes. The mechanism and selective advantage of this enrichment by growth rate remain unclear. In addition, the frequency of bacterial virulence genes in prophages from clinical NTM is enriched relative to the PhagesDB environmental proxy. This suggests prophages may act as a reservoir of genetic elements bacteria could use to thrive within a clinical environment.}, }
@article {pmid32806781, year = {2020}, author = {Carraro, N and Sentchilo, V and Polák, L and Bertelli, C and van der Meer, JR}, title = {Insights into Mobile Genetic Elements of the Biocide-Degrading Bacterium Pseudomonas nitroreducens HBP-1.}, journal = {Genes}, volume = {11}, number = {8}, pages = {}, pmid = {32806781}, issn = {2073-4425}, mesh = {Computational Biology/methods ; Conjugation, Genetic ; *DNA Transposable Elements ; DNA, Bacterial ; Disinfectants/*pharmacology ; Fatty Acids/metabolism ; Gene Order ; Gene Transfer, Horizontal ; Genome, Bacterial ; Genomic Islands ; Genomics/methods ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Plasmids/genetics ; Prophages ; Pseudomonas/*drug effects/*genetics/virology ; }, abstract = {The sewage sludge isolate Pseudomonas nitroreducens HBP-1 was the first bacterium known to completely degrade the fungicide 2-hydroxybiphenyl. PacBio and Illumina whole-genome sequencing revealed three circular DNA replicons: a chromosome and two plasmids. Plasmids were shown to code for putative adaptive functions such as heavy metal resistance, but with unclarified ability for self-transfer. About one-tenth of strain HBP-1's chromosomal genes are likely of recent horizontal influx, being part of genomic islands, prophages and integrative and conjugative elements (ICEs). P. nitroreducens carries two large ICEs with different functional specialization, but with homologous core structures to the well-known ICEclc of Pseudomonas knackmussii B13. The variable regions of ICEPni1 (96 kb) code for, among others, heavy metal resistances and formaldehyde detoxification, whereas those of ICEPni2 (171 kb) encodes complete meta-cleavage pathways for catabolism of 2-hydroxybiphenyl and salicylate, a protocatechuate pathway and peripheral enzymes for 4-hydroxybenzoate, ferulate, vanillin and vanillate transformation. Both ICEs transferred at frequencies of 10[-6]-10[-8] per P. nitroreducens HBP-1 donor into Pseudomonas putida, where they integrated site specifically into tRNA[Gly]-gene targets, as expected. Our study highlights the underlying determinants and mechanisms driving dissemination of adaptive properties allowing bacterial strains to cope with polluted environments.}, }
@article {pmid32806463, year = {2020}, author = {Li, H and Xu, H and Song, HL and Lu, Y and Yang, XL}, title = {Antibiotic resistance genes, bacterial communities, and functions in constructed wetland-microbial fuel cells: Responses to the co-stresses of antibiotics and zinc.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {265}, number = {Pt B}, pages = {115084}, doi = {10.1016/j.envpol.2020.115084}, pmid = {32806463}, issn = {1873-6424}, mesh = {Anti-Bacterial Agents/pharmacology ; *Bioelectric Energy Sources ; Drug Resistance, Microbial/drug effects ; Genes, Bacterial/drug effects ; Wetlands ; Zinc ; }, abstract = {The effects of the continuous accumulation of Zinc (Zn) on the fate of antibiotic resistance genes (ARGs) in constructed wetland-microbial fuel cells (CW-MFCs) remain unclear. In this study, the impacts of Zn addition and a circuit mode on antibiotic removal, occurrence of ARGs, the bacterial community, and bacterial functions were investigated in three groups of CW-MFCs. The results showed that continuous Zn exposure enriched the target ARGs during the initial stage, while excessive Zn accumulation decreased antibiotic removal and the abundance of ARGs. A principal component analysis demonstrated that ARGs and the bacterial community distribution characteristics were significantly impacted by the mass accumulation of antibiotics and Zn, as well as the circuit mode. A redundancy analysis, partial least squares path modeling, and Procrustes analysis revealed that the accumulation of antibiotics and Zn, the composition of the bacterial community, the circuit mode, and the abundance of intI associated with horizontal gene transfer jointly contributed to the distributions of ARGs in the electrodes and effluent. Moreover, continuous exposure to Zn decreased the bacterial diversity and changed the composition and function of the bacterial community predicted using PICRUSt tool. The co-occurrence of ARGs, their potential hosts and bacterial functions were further revealed using a network analysis. A variation partition analysis also showed that the accumulation of target pollutants and the circuit mode had a significant impact on the bacterial community composition and functions. Therefore, the interaction among ARGs, the bacterial community, bacterial functions, and pollutant accumulations in the CW-MFC was complex. This study provides useful implications for the application of CW-MFCs for the treatment of wastewater contaminated with antibiotics and heavy metals.}, }
@article {pmid32804963, year = {2020}, author = {Laverty, AL and Primpke, S and Lorenz, C and Gerdts, G and Dobbs, FC}, title = {Bacterial biofilms colonizing plastics in estuarine waters, with an emphasis on Vibrio spp. and their antibacterial resistance.}, journal = {PloS one}, volume = {15}, number = {8}, pages = {e0237704}, pmid = {32804963}, issn = {1932-6203}, mesh = {Anti-Bacterial Agents/pharmacology ; Atlantic Ocean ; Biofilms/*drug effects ; DNA, Bacterial/isolation &amp; purification ; Drug Resistance, Bacterial/genetics ; *Estuaries ; Gene Transfer, Horizontal ; *Plastics ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Vibrio/drug effects/genetics/*isolation &amp; purification ; *Water Pollutants ; }, abstract = {Since plastics degrade very slowly, they remain in the environment on much longer timescales than most natural organic substrates and provide a novel habitat for colonization by bacterial communities. The spectrum of relationships between plastics and bacteria, however, is little understood. The first objective of this study was to examine plastics as substrates for communities of Bacteria in estuarine surface waters. We used next-generation sequencing of the 16S rRNA gene to characterize communities from plastics collected in the field, and over the course of two colonization experiments, from biofilms that developed on plastic (low-density polyethylene, high-density polyethylene, polypropylene, polycarbonate, polystyrene) and glass substrates placed in the environment. Both field sampling and colonization experiments were conducted in estuarine tributaries of the lower Chesapeake Bay. As a second objective, we concomitantly analyzed biofilms on plastic substrates to ascertain the presence and abundance of Vibrio spp. bacteria, then isolated three human pathogens, V. cholerae, V. parahaemolyticus, and V. vulnificus, and determined their antibiotic-resistant profiles. In both components of this study, we compared our results with analyses conducted on paired samples of estuarine water. This research adds to a nascent literature that suggests environmental factors govern the development of bacterial communities on plastics, more so than the characteristics of the plastic substrates themselves. In addition, this study is the first to culture three pathogenic vibrios from plastics in estuaries, reinforcing and expanding upon earlier reports of plastic pollution as a habitat for Vibrio species. The antibiotic resistance detected among the isolates, coupled with the longevity of plastics in the aqueous environment, suggests biofilms on plastics have potential to persist and serve as focal points of potential pathogens and horizontal gene transfer.}, }
@article {pmid32803348, year = {2021}, author = {Preena, PG and Dharmaratnam, A and Raj, NS and Raja, SA and Nair, RR and Swaminathan, TR}, title = {Antibiotic-resistant Enterobacteriaceae from diseased freshwater goldfish.}, journal = {Archives of microbiology}, volume = {203}, number = {1}, pages = {219-231}, pmid = {32803348}, issn = {1432-072X}, support = {PDF/2017/000378//Science and Engineering Board, Department of Science and Technology/ ; F. No Agri.edn.27/2/2015//Indian Council of Agriculture Research/ ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Bacterial/genetics ; Enterobacteriaceae/*drug effects/*genetics/isolation &amp; purification ; Enterobacteriaceae Infections/microbiology/*veterinary ; Fish Diseases/*microbiology ; Fresh Water ; Gene Transfer, Horizontal/drug effects ; Goldfish/*microbiology ; Humans ; Microbial Sensitivity Tests ; Plasmids/genetics ; beta-Lactamases/genetics ; }, abstract = {Goldfish farming gained more attention among the ornamental fishes in aquaculture industry. The occurrence of bacterial infections and further antimicrobial treatment lead to the major crisis of antibiotic resistance in aquaculture. We have isolated diverse enterobacteriaceae groups which affect the goldfish and identified their response towards 46 antimicrobials of 15 different classes. Thirteen significant bacterial isolates such as Edwardsiella tarda, Serratia marcescens, Klebsiella aerogenes, Proteus penneri, P. hauseri, Enterobacter cloacae, E. cancerogenus, E. ludwigii, Citrobacter freundii, E. coli, Kluyvera cryocrescens, Plesiomonas shigelloides and Providencia vermicola were recovered from the infected fish with the Shannon-wiener diversity index of 2.556. Multiple antibiotic resistance (MAR) index was found to be maximum for P. penneri (0.87) and minimum for C. freundii and E. cloacae (0.22), highlighting the hyper antibiotic selection pressure in the farm. The minimum concentration of antibiotics required to inhibit most of the resistant isolates was found to be > 256 mcg/ml. All the isolates were susceptible towards ciprofloxacin. Plasmid curing and further AMR tests could reveal the location of antibiotic resistance genes mainly as plasmids which determine the large extent of AMR spread through horizontal gene transfer. This study is the first of its kind to investigate the antimicrobial resistance profile of enterobacteriaceae recovered from goldfish, before and after plasmid curing.}, }
@article {pmid32802718, year = {2020}, author = {Sharma, V and Mobeen, F and Prakash, T}, title = {In silico functional and evolutionary analyses of rubber oxygenases (RoxA and RoxB).}, journal = {3 Biotech}, volume = {10}, number = {9}, pages = {376}, pmid = {32802718}, issn = {2190-572X}, abstract = {The study presents an in silico identification of poly (cis-1,4-isoprene) cleaving enzymes, viz., RoxA and RoxB in bacteria, followed by their functional and evolutionary exploration using comparative genomics. The orthologs of these proteins were found to be restricted to Gram-negative beta-, gamma-, and delta-proteobacteria. Toward the evolutionary propagation, the RoxA and RoxB genes were predicted to have evolved via a common interclass route of horizontal gene transfer in the phylum Proteobacteria (delta → gamma → beta). Besides, recombination, mutation, and gene conversion were also detected in both the genes leading to their diversification. Further, the differential selective pressure is predicted to be operating on entire RoxA and RoxB genes such that the former is diversifying further, whereas the latter is evolving to reduce its genetic diversity. However, the structurally and functionally important sites/residues of these genes were found to be preventing changes implying their evolutionary conservation. Further, the phylogenetic analysis demonstrated a sharp split between the RoxA and RoxB orthologs and indicated the emergence of their variant as another type of putative rubber oxygenase (RoxC) in the class Gammaproteobacteria. A detailed in silico analysis of the signature motifs and residues of Rox sequences exhibited important differences as well as similarities among the RoxA, RoxB, and putative RoxC sequences. Although RoxC appears to be a hybrid of RoxA and RoxB, the signature motifs and residues of RoxC are more similar to RoxB.}, }
@article {pmid32799172, year = {2020}, author = {Birk, T and Fuentes, MAF and Aabo, S and Jensen, LB}, title = {Horizontal transmission of antimicrobial resistance genes from E. coli to Serratia spp. in minced meat using a gfp tagged plasmid.}, journal = {Research in veterinary science}, volume = {132}, number = {}, pages = {481-484}, doi = {10.1016/j.rvsc.2020.07.025}, pmid = {32799172}, issn = {1532-2661}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Bacterial/genetics ; Enterobacteriaceae/drug effects ; Escherichia coli/*drug effects/*genetics ; Food Microbiology ; Gene Transfer, Horizontal ; Meat/*microbiology ; Microbial Sensitivity Tests/veterinary ; Plasmids ; RNA, Ribosomal, 16S/genetics ; Serratia/*drug effects/*genetics ; Swine ; }, abstract = {The transmission of antimicrobial resistance genes from enteric bacteria from the animal reservoir to indigenous bacteria in meat is a serious concern, as it can contribute to human exposure to antimicrobial resistance genes. The aim of this study was to investigate plasmid-mediated horizontal transfer of antimicrobial resistance genes from Escherichia coli to indigenous environmental bacteria in minced pork stored at 10 and 37 °C. E. coli MG1555 containing a gfp-tagged plasmid carrying tetracycline, kanamycin and streptomycin resistance genes was used as the donor with the indigenous bacteria in minced pork acting as potential recipients. The results demonstrated that enteric members of the pork meat microbiota were able to receive gfp-plasmids from the E. coli donor strain at both 10 and 37 °C. The majority of transconjugants were identified as Serratia spp. through sequencing of their 16S rRNA genes. This indicates that environmental Serratia spp. and other Enterobacteriaceae may play a role as carrier of antimicrobial resistance genes through the meat production chain to the consumer.}, }
@article {pmid32797039, year = {2020}, author = {Banderas, A and Carcano, A and Sia, E and Li, S and Lindner, AB}, title = {Ratiometric quorum sensing governs the trade-off between bacterial vertical and horizontal antibiotic resistance propagation.}, journal = {PLoS biology}, volume = {18}, number = {8}, pages = {e3000814}, pmid = {32797039}, issn = {1545-7885}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Load ; Bacterial Proteins/*genetics/metabolism ; Conjugation, Genetic ; Drug Resistance, Microbial/*genetics ; Enterococcus faecalis/drug effects/*genetics/growth &amp; development/metabolism ; Gene Expression ; *Gene Transfer, Horizontal ; Genetic Fitness ; Models, Statistical ; Pheromones/biosynthesis/*genetics ; Plasmids/chemistry/metabolism ; Quorum Sensing/*drug effects/genetics ; Virulence ; }, abstract = {Plasmid-mediated horizontal gene transfer of antibiotic resistance and virulence in pathogenic bacteria underlies a major public health issue. Understanding how, in the absence of antibiotic-mediated selection, plasmid-bearing cells avoid being outnumbered by plasmid-free cells is key to developing counterstrategies. Here, we quantified the induction of the plasmidial sex pheromone pathway of Enterococcus faecalis to show that the integration of the stimulatory (mate-sensing) and inhibitory (self-sensing) signaling modules from the pCF10 conjugative plasmid provides a precise measure of the recipient-to-donor ratio, agnostic to variations in population size. Such ratiometric control of conjugation favors vertical plasmid transfer under low mating likelihood and allows activation of conjugation functions only under high mating likelihood. We further show that this strategy constitutes a cost-effective investment into mating effort because overstimulation produces unproductive self-aggregation and growth rate reduction. A mathematical model suggests that ratiometric control of conjugation increases plasmid fitness and predicts a robust long-term, stable coexistence of donors and recipients. Our results demonstrate how population-level parameters can control transfer of antibiotic resistance in bacteria, opening the door for biotic control strategies.}, }
@article {pmid32796589, year = {2020}, author = {Berbers, B and Ceyssens, PJ and Bogaerts, P and Vanneste, K and Roosens, NHC and Marchal, K and De Keersmaecker, SCJ}, title = {Development of an NGS-Based Workflow for Improved Monitoring of Circulating Plasmids in Support of Risk Assessment of Antimicrobial Resistance Gene Dissemination.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {9}, number = {8}, pages = {}, pmid = {32796589}, issn = {2079-6382}, support = {Ylieff project - AMRSeq//Belgian Federal Science Policy Office (BELSPO)/ ; .Be READY project//Sciensano/ ; }, abstract = {Antimicrobial resistance (AMR) is one of the most prominent public health threats. AMR genes localized on plasmids can be easily transferred between bacterial isolates by horizontal gene transfer, thereby contributing to the spread of AMR. Next-generation sequencing (NGS) technologies are ideal for the detection of AMR genes; however, reliable reconstruction of plasmids is still a challenge due to large repetitive regions. This study proposes a workflow to reconstruct plasmids with NGS data in view of AMR gene localization, i.e., chromosomal or on a plasmid. Whole-genome and plasmid DNA extraction methods were compared, as were assemblies consisting of short reads (Illumina MiSeq), long reads (Oxford Nanopore Technologies) and a combination of both (hybrid). Furthermore, the added value of conjugation of a plasmid to a known host was evaluated. As a case study, an isolate harboring a large, low-copy mcr-1-carrying plasmid (>200 kb) was used. Hybrid assemblies of NGS data obtained from whole-genome DNA extractions of the original isolates resulted in the most complete reconstruction of plasmids. The optimal workflow was successfully applied to multidrug-resistant Salmonella Kentucky isolates, where the transfer of an ESBL-gene-containing fragment from a plasmid to the chromosome was detected. This study highlights a strategy including wet and dry lab parameters that allows accurate plasmid reconstruction, which will contribute to an improved monitoring of circulating plasmids and the assessment of their risk of transfer.}, }
@article {pmid32788591, year = {2020}, author = {Wang, D and Yu, X and Xu, K and Bi, G and Cao, M and Zelzion, E and Fu, C and Sun, P and Liu, Y and Kong, F and Du, G and Tang, X and Yang, R and Wang, J and Tang, L and Wang, L and Zhao, Y and Ge, Y and Zhuang, Y and Mo, Z and Chen, Y and Gao, T and Guan, X and Chen, R and Qu, W and Sun, B and Bhattacharya, D and Mao, Y}, title = {Pyropia yezoensis genome reveals diverse mechanisms of carbon acquisition in the intertidal environment.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {4028}, pmid = {32788591}, issn = {2041-1723}, mesh = {Animal Shells/chemistry ; Animals ; Antioxidants/pharmacology ; Base Composition/genetics ; Biological Evolution ; Calcium Carbonate/metabolism ; Carbon/*metabolism ; Carbonic Anhydrases/genetics/metabolism ; Cell Nucleus/genetics ; Gene Dosage ; Gene Expression Profiling ; Gene Transfer, Horizontal/genetics ; *Genome ; Mollusca ; Photosynthesis/drug effects ; Ploidies ; Rhodophyta/drug effects/*genetics/*metabolism ; Superoxide Dismutase/genetics ; Transcription, Genetic/drug effects ; *Water Movements ; }, abstract = {Changes in atmospheric CO2 concentration have played a central role in algal and plant adaptation and evolution. The commercially important red algal genus, Pyropia (Bangiales) appears to have responded to inorganic carbon (Ci) availability by evolving alternating heteromorphic generations that occupy distinct habitats. The leafy gametophyte inhabits the intertidal zone that undergoes frequent emersion, whereas the sporophyte conchocelis bores into mollusk shells. Here, we analyze a high-quality genome assembly of Pyropia yezoensis to elucidate the interplay between Ci availability and life cycle evolution. We find horizontal gene transfers from bacteria and expansion of gene families (e.g. carbonic anhydrase, anti-oxidative related genes), many of which show gametophyte-specific expression or significant up-regulation in gametophyte in response to dehydration. In conchocelis, the release of HCO3[-] from shell promoted by carbonic anhydrase provides a source of Ci. This hypothesis is supported by the incorporation of [13]C isotope by conchocelis when co-cultured with [13]C-labeled CaCO3.}, }
@article {pmid32787773, year = {2020}, author = {Khurana, H and Singh, DN and Singh, A and Singh, Y and Lal, R and Negi, RK}, title = {Gut microbiome of endangered Tor putitora (Ham.) as a reservoir of antibiotic resistance genes and pathogens associated with fish health.}, journal = {BMC microbiology}, volume = {20}, number = {1}, pages = {249}, pmid = {32787773}, issn = {1471-2180}, support = {NBAIM/AMAAS/2017-20/GF/1a//National Bureau of Agriculturally Important Microorganisms/International ; }, mesh = {Animals ; Bacteria/*classification/genetics/isolation &amp; purification/pathogenicity ; Bacterial Proteins/genetics ; *Drug Resistance, Bacterial ; Endangered Species ; Fishes/*microbiology ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; Phylogeny ; Sequence Analysis, DNA ; Virulence Factors/genetics ; }, abstract = {BACKGROUND: Tor putitora, the largest freshwater fish of the Indian subcontinent, is an endangered species. Several factors have been attributed towards its continuous population decrease, but very little is known about the gut microbiome of this fish. Also, the fish gut microbiome serves as a reservoir of virulence factors and antibiotic resistance determinants. Therefore, the shotgun metagenomic approach was employed to investigate the taxonomic composition and functional potential of microbial communities present in the gut of Tor putitora, as well as the detection of virulence and antibiotic resistance genes in the microbiome.<br><br>RESULTS: The analysis of bacterial diversity showed that Proteobacteria was predominant phylum, followed by Chloroflexi, Bacteroidetes, and Actinobacteria. Within Proteobacteria, Aeromonas and Caulobacter were chiefly present; also, Klebsiella, Escherichia, and plant symbionts were noticeably detected. Functional characterization of gut microbes endowed the virulence determinants, while surveillance of antibiotic resistance genes showed the dominance of &#x3b2;-lactamase variants. The antibiotic-resistant Klebsiella pneumoniae and Escherichia coli pathovars were also detected. Microbial genome reconstruction and comparative genomics confirmed the presence of Aeromonads, the predominant fish pathogens.<br><br>CONCLUSIONS: Gut microbiome of endangered Tor putitora consisted of both commensals and opportunistic pathogens, implying that factors adversely affecting the non-pathogenic population would allow colonization and proliferation of pathogens causing diseased state in asymptomatic Tor putitora. The presence of virulence factors and antibiotic resistance genes suggested the potential risk of dissemination to other bacteria due to horizontal gene transfer, thereby posing a threat to fish and human health. The preservation of healthy gut microflora and limited use of antibiotics are some of the prerequisites for the conservation of this imperilled species.}, }
@article {pmid32784449, year = {2020}, author = {Liu, Y and Tong, Z and Shi, J and Jia, Y and Yang, K and Wang, Z}, title = {Correlation between Exogenous Compounds and the Horizontal Transfer of Plasmid-Borne Antibiotic Resistance Genes.}, journal = {Microorganisms}, volume = {8}, number = {8}, pages = {}, pmid = {32784449}, issn = {2076-2607}, support = {2018YFA0903400//National Key Research and Development Program of China/ ; BK20190893//Natural Science Foundation of Jiangsu Province of China/ ; 2019M651984//China Postdoctoral Science Foundation/ ; 2019//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; 2019//Lift Engineering of Young Talents of Jiangsu Association for Science and Technology/ ; }, abstract = {The global spread of antibiotic resistance has posed a serious threat to public healthcare and undermined decades of progress made in the fight against bacterial infections. It has been demonstrated that the lack of novel effective antibiotics and rapid spread of antibiotic resistance genes via horizontal transfer in the ecosystem are mainly responsible for this crisis. Notably, plasmid-mediated horizontal transfer of antibiotic resistance genes (ARGs) is recognized as the most dominant dissemination pathway of ARGs in humans, animals and environmental settings. Antibiotic selective pressure has always been regarded as one of the crucial contributors to promoting the dissemination of antibiotic resistance through horizontal gene transfer (HGT). However, the roles of exogenous compounds and particularly non-antibiotic drugs in the spread of ARGs are still underappreciated. In this review, we first summarize the major pathways of HGT in bacteria, including conjugation, transformation, transduction and vesiduction. Subsequently, an overview of these compounds capable of promoting the HGT is presented, which guides to the formulation of more reasonable dosing regimens and drug residue standards in clinical practice. By contrast, these compounds that display an inhibition effect on HGT are also highlighted, which provides a unique strategy to minimize the spread of ARGs. Lastly, we discuss the implementations and challenges in bringing these HGT inhibitors into clinical trials.}, }
@article {pmid32782278, year = {2020}, author = {Minami, A and Ugai, T and Ozaki, T and Oikawa, H}, title = {Predicting the chemical space of fungal polyketides by phylogeny-based bioinformatics analysis of polyketide synthase-nonribosomal peptide synthetase and its modification enzymes.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {13556}, pmid = {32782278}, issn = {2045-2322}, mesh = {Computational Biology/*methods ; Fungi/genetics/*metabolism ; *Multigene Family ; Peptide Synthases/genetics/*metabolism ; Phylogeny ; Polyketide Synthases/genetics/*metabolism ; Polyketides/*chemistry/*metabolism ; }, abstract = {Fungal polyketide synthase (PKS)-nonribosomal peptide synthetase (NRPS) hybrids are key enzymes for synthesizing structurally diverse hybrid natural products (NPs) with characteristic biological activities. Predicting their chemical space is of particular importance in the field of natural product chemistry. However, the unexplored programming rule of the PKS module has prevented prediction of its chemical structure based on amino acid sequences. Here, we conducted a phylogenetic analysis of 884 PKS-NRPS hybrids and a modification enzyme analysis of the corresponding biosynthetic gene cluster, revealing a hidden relationship between its genealogy and core structures. This unexpected result allowed us to predict 18 biosynthetic gene cluster (BGC) groups producing known carbon skeletons (number of BGCs; 489) and 11 uncharacterized BGC groups (171). The limited number of carbon skeletons suggests that fungi tend to select PK skeletons for survival during their evolution. The possible involvement of a horizontal gene transfer event leading to the diverse distribution of PKS-NRPS genes among fungal species is also proposed. This study provides insight into the chemical space of fungal PKs and the distribution of their biosynthetic gene clusters.}, }
@article {pmid32778753, year = {2020}, author = {Sandberg, TE and Szubin, R and Phaneuf, PV and Palsson, BO}, title = {Synthetic cross-phyla gene replacement and evolutionary assimilation of major enzymes.}, journal = {Nature ecology &amp; evolution}, volume = {4}, number = {10}, pages = {1402-1409}, pmid = {32778753}, issn = {2397-334X}, support = {R01 GM057089/GM/NIGMS NIH HHS/United States ; }, mesh = {Escherichia coli/genetics ; *Gene Transfer, Horizontal ; *Genome ; Genomics ; Humans ; Sequence Analysis, DNA ; }, abstract = {The ability of DNA to produce a functional protein even after transfer to a foreign host is of fundamental importance in both evolutionary biology and biotechnology, enabling horizontal gene transfer in the wild and heterologous expression in the lab. However, the influence of genetic particulars on DNA functionality in a new host is poorly understood, as are the evolutionary mechanisms of assimilation and refinement. Here, we describe an automation-enabled large-scale experiment wherein Escherichia coli strains were evolved in parallel after replacement of the genes pgi or tpiA with orthologous DNA from donor species spanning all domains of life, from humans to hyperthermophilic archaea. Via analysis of hundreds of clones evolved for 50,000+ cumulative generations across dozens of independent lineages, we show that orthogene-upregulating mutations can completely mitigate fitness defects that result from initial non-functionality, with coding sequence changes unnecessary. Gene target, donor species and genomic location of the swap all influenced outcomes-both the nature of adaptive mutations (often synonymous) and the frequency with which strains successfully evolved to assimilate the foreign DNA. Additionally, time series DNA sequencing and replay evolution experiments revealed transient copy number expansions, the contingency of lineage outcome on first-step mutations and the ability for strains to escape from suboptimal local fitness maxima. Overall, this study establishes the influence of various DNA and protein features on cross-species genetic interchangeability and evolutionary outcomes, with implications for both horizontal gene transfer and rational strain design.}, }
@article {pmid32774329, year = {2020}, author = {Brito, &#xc2; and Vieira, J and Vieira, CP and Zhu, T and Leão, PN and Ramos, V and Lu, X and Vasconcelos, VM and Gugger, M and Tamagnini, P}, title = {Comparative Genomics Discloses the Uniqueness and the Biosynthetic Potential of the Marine Cyanobacterium Hyella patelloides.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1527}, pmid = {32774329}, issn = {1664-302X}, abstract = {Baeocytous cyanobacteria (Pleurocapsales/Subsection II) can thrive in a wide range of habitats on Earth but, compared to other cyanobacterial lineages, they remain poorly studied at genomic level. In this study, we sequenced the first genome from a member of the Hyella genus - H. patelloides LEGE 07179, a recently described species isolated from the Portuguese foreshore. This genome is the largest of the thirteen baeocyte-forming cyanobacterial genomes sequenced so far, and diverges from the most closely related strains. Comparative analysis revealed strain-specific genes and horizontal gene transfer events between H. patelloides and its closest relatives. Moreover, H. patelloides genome is distinctive by the number and diversity of natural product biosynthetic gene clusters (BGCs). The majority of these clusters are strain-specific BGCs with a high probability of synthesizing novel natural products. One BGC was identified as being putatively involved in the production of terminal olefin. Our results showed that, H. patelloides produces hydrocarbon with C15 chain length, and synthesizes C14, C16, and C18 fatty acids exceeding 4% of the dry cell weight. Overall, our data contributed to increase the information on baeocytous cyanobacteria, and shed light on H. patelloides evolution, phylogeny and natural product biosynthetic potential.}, }
@article {pmid32772672, year = {2020}, author = {van Oppen, MJH and Medina, M}, title = {Coral evolutionary responses to microbial symbioses.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1808}, pages = {20190591}, pmid = {32772672}, issn = {1471-2970}, mesh = {Animals ; Anthozoa/metabolism/*microbiology ; *Biological Evolution ; Dinoflagellida/*physiology ; Global Warming ; *Microbiota ; *Symbiosis ; }, abstract = {This review explores how microbial symbioses may have influenced and continue to influence the evolution of reef-building corals (Cnidaria; Scleractinia). The coral holobiont comprises a diverse microbiome including dinoflagellate algae (Dinophyceae; Symbiodiniaceae), bacteria, archaea, fungi and viruses, but here we focus on the Symbiodiniaceae as knowledge of the impact of other microbial symbionts on coral evolution is scant. Symbiosis with Symbiodiniaceae has extended the coral's metabolic capacity through metabolic handoffs and horizontal gene transfer (HGT) and has contributed to the ecological success of these iconic organisms. It necessitated the prior existence or the evolution of a series of adaptations of the host to attract and select the right symbionts, to provide them with a suitable environment and to remove disfunctional symbionts. Signatures of microbial symbiosis in the coral genome include HGT from Symbiodiniaceae and bacteria, gene family expansions, and a broad repertoire of oxidative stress response and innate immunity genes. Symbiosis with Symbiodiniaceae has permitted corals to occupy oligotrophic waters as the algae provide most corals with the majority of their nutrition. However, the coral-Symbiodiniaceae symbiosis is sensitive to climate warming, which disrupts this intimate relationship, causing coral bleaching, mortality and a worldwide decline of coral reefs. This article is part of the theme issue 'The role of the microbiome in host evolution'.}, }
@article {pmid32770105, year = {2020}, author = {Dombrowski, N and Williams, TA and Sun, J and Woodcroft, BJ and Lee, JH and Minh, BQ and Rinke, C and Spang, A}, title = {Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {3939}, pmid = {32770105}, issn = {2041-1723}, mesh = {Archaea/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Archaeal ; Phylogeny ; Symbiosis/*genetics ; }, abstract = {The recently discovered DPANN archaea are a potentially deep-branching, monophyletic radiation of organisms with small cells and genomes. However, the monophyly and early emergence of the various DPANN clades and their role in life's evolution are debated. Here, we reconstructed and analysed genomes of an uncharacterized archaeal phylum (Candidatus Undinarchaeota), revealing that its members have small genomes and, while potentially being able to conserve energy through fermentation, likely depend on partner organisms for the acquisition of certain metabolites. Our phylogenomic analyses robustly place Undinarchaeota as an independent lineage between two highly supported 'DPANN' clans. Further, our analyses suggest that DPANN have exchanged core genes with their hosts, adding to the difficulty of placing DPANN in the tree of life. This pattern can be sufficiently dominant to allow identifying known symbiont-host clades based on routes of gene transfer. Together, our work provides insights into the origins and evolution of DPANN and their hosts.}, }
@article {pmid32768779, year = {2020}, author = {Subirats, J and Murray, R and Scott, A and Lau, CH and Topp, E}, title = {Composting of chicken litter from commercial broiler farms reduces the abundance of viable enteric bacteria, Firmicutes, and selected antibiotic resistance genes.}, journal = {The Science of the total environment}, volume = {746}, number = {}, pages = {141113}, doi = {10.1016/j.scitotenv.2020.141113}, pmid = {32768779}, issn = {1879-1026}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Chickens ; *Composting ; Drug Resistance, Microbial/drug effects/genetics ; Farms ; Firmicutes ; Gastrointestinal Microbiome/*drug effects ; Genes, Bacterial/drug effects ; Manure ; RNA, Ribosomal, 16S/genetics ; }, abstract = {We examined the ability of composting to remove ARGs and enteric bacteria in litter obtained from broiler chickens fed with a diet supplemented with Bacitracin methylene disalicylate (BDM) (conventional chicken litter), or an antibiotic-free diet (raised without antibiotic (RWA) chicken litter). This was done by evaluating the litter before and after composting for the abundance of ten gene targets associated with antibiotic resistance or horizontal gene transfer, the composition of the bacterial communities, and the abundance of viable enteric bacteria. The abundance of gene targets was determined by qPCR and the microbial community composition of chicken litter determined by 16S rRNA gene amplicon sequencing. Enteric bacteria were enumerated by viable plate count. A majority of the gene targets were more abundant in conventional than in RWA litter. In both litter types, the absolute abundance of all of the target genes decreased after composting except sul1, intI1, incW and erm(F) that remained stable. Composting significantly reduced the abundance of enteric bacteria, including those carrying antibiotic resistance. The major difference in bacterial community composition between conventional and RWA litter was due to members affiliated to the genus Pseudomonas, which were 28% more abundant in conventional than in RWA litter. Composting favoured the presence of thermophilic bacteria, such as those affiliated with the genus Truepera, but decreased the abundance of those bacterial genera associated with cold-adapted species, such as Carnobacterium, Psychrobacter and Oceanisphaera. The present study shows that chicken litter from broilers fed with a diet supplemented with antibiotic has an increased abundance of some ARGs, even after composting. However, we can conclude that fertilization with composted litter represents a reduced risk of transmission of antibiotic resistance genes and enteric bacteria of poultry origin to soil and crops than will fertilization with raw litter.}, }
@article {pmid32763695, year = {2021}, author = {Liu, W and Ling, N and Guo, J and Ruan, Y and Wang, M and Shen, Q and Guo, S}, title = {Dynamics of the antibiotic resistome in agricultural soils amended with different sources of animal manures over three consecutive years.}, journal = {Journal of hazardous materials}, volume = {401}, number = {}, pages = {123399}, doi = {10.1016/j.jhazmat.2020.123399}, pmid = {32763695}, issn = {1873-3336}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Ecosystem ; Genes, Bacterial ; *Manure ; *Soil ; Soil Microbiology ; Swine ; }, abstract = {The application of animal manure is generally considered an important transmission pathway for antibiotic resistance genes (ARGs) in soil. Nevertheless, the fate of ARGs in soil where manure from different sources has been repeatedly implemented is not fully understood. Thus, the succession of ARGs and bacterial communities following the repeated application of three types of animal manures (pig, chicken, and cow manure) to agricultural soil were investigated using Illumina sequencing analysis and high-throughput qPCR. Results showed that manure application remarkably increased the abundance of soil ARGs by increasing the enrichment of indigenous ARGs and introducing extrinsic ARGs. There were no prominent differences in the abundance or diversity of ARGs among the three different manured soils. The abundance and diversity of ARGs in manured soils increased over three consecutive years. Additionally, the abundance of mobile gene elements (MGEs) and bacteria were positively correlated with ARGs, while the changes in the ARG profiles were dramatically associated with the MGEs and bacterial communities. These findings imply that repeated manure application may facilitate to the accumulation and persistence of the soil resistome by regulation of the bacterial community and horizontal gene transfer, providing better insights into the temporal dynamics of soil ARGs in agro-ecosystems.}, }
@article {pmid32761262, year = {2020}, author = {Sutter, JM and Johnsen, U and Reinhardt, A and Schönheit, P}, title = {Pentose degradation in archaea: Halorhabdus species degrade D-xylose, L-arabinose and D-ribose via bacterial-type pathways.}, journal = {Extremophiles : life under extreme conditions}, volume = {24}, number = {5}, pages = {759-772}, pmid = {32761262}, issn = {1433-4909}, support = {SCHO 316/11-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Arabinose/metabolism ; Bacteria ; *Halobacteriaceae/enzymology ; Pentoses ; Ribose ; *Xylose/metabolism ; }, abstract = {The degradation of the pentoses D-xylose, L-arabinose and D-ribose in the domain of archaea, in Haloferax volcanii and in Haloarcula and Sulfolobus species, has been shown to proceed via oxidative pathways to generate α-ketoglutarate. Here, we report that the haloarchaeal Halorhabdus species utilize the bacterial-type non-oxidative degradation pathways for pentoses generating xylulose-5-phosphate. The genes of these pathways are each clustered and were constitutively expressed. Selected enzymes involved in D-xylose degradation, xylose isomerase and xylulokinase, and those involved in L-arabinose degradation, arabinose isomerase and ribulokinase, were characterized. Further, D-ribose degradation in Halorhabdus species involves ribokinase, ribose-5-phosphate isomerase and D-ribulose-5-phosphate-3-epimerase. Ribokinase of Halorhabdus tiamatea and ribose-5-phosphate isomerase of Halorhabdus utahensis were characterized. This is the first report of pentose degradation via the bacterial-type pathways in archaea, in Halorhabdus species that likely acquired these pathways from bacteria. The utilization of bacterial-type pathways of pentose degradation rather than the archaeal oxidative pathways generating α-ketoglutarate might be explained by an incomplete gluconeogenesis in Halorhabdus species preventing the utilization of α-ketoglutarate in the anabolism.}, }
@article {pmid32759337, year = {2020}, author = {Stephens, C and Arismendi, T and Wright, M and Hartman, A and Gonzalez, A and Gill, M and Pandori, M and Hess, D}, title = {F Plasmids Are the Major Carriers of Antibiotic Resistance Genes in Human-Associated Commensal Escherichia coli.}, journal = {mSphere}, volume = {5}, number = {4}, pages = {}, pmid = {32759337}, issn = {2379-5042}, support = {R15 AI130816/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/drug effects/*genetics ; Escherichia coli Infections/microbiology ; F Factor/*genetics ; Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; Microbial Sensitivity Tests ; Sequence Analysis, DNA ; *Symbiosis ; Young Adult ; }, abstract = {The evolution and propagation of antibiotic resistance by bacterial pathogens are significant threats to global public health. Contemporary DNA sequencing tools were applied here to gain insight into carriage of antibiotic resistance genes in Escherichia coli, a ubiquitous commensal bacterium in the gut microbiome in humans and many animals, and a common pathogen. Draft genome sequences generated for a collection of 101 E. coli strains isolated from healthy undergraduate students showed that horizontally acquired antibiotic resistance genes accounted for most resistance phenotypes, the primary exception being resistance to quinolones due to chromosomal mutations. A subset of 29 diverse isolates carrying acquired resistance genes and 21 control isolates lacking such genes were further subjected to long-read DNA sequencing to enable complete or nearly complete genome assembly. Acquired resistance genes primarily resided on F plasmids (101/153 [67%]), with smaller numbers on chromosomes (30/153 [20%]), IncI complex plasmids (15/153 [10%]), and small mobilizable plasmids (5/153 [3%]). Nearly all resistance genes were found in the context of known transposable elements. Very few structurally conserved plasmids with antibiotic resistance genes were identified, with the exception of an ∼90-kb F plasmid in sequence type 1193 (ST1193) isolates that appears to serve as a platform for resistance genes and may have virulence-related functions as well. Carriage of antibiotic resistance genes on transposable elements and mobile plasmids in commensal E. coli renders the resistome highly dynamic.IMPORTANCE Rising antibiotic resistance in human-associated bacterial pathogens is a serious threat to our ability to treat many infectious diseases. It is critical to understand how acquired resistance genes move in and through bacteria associated with humans, particularly for species such as Escherichia coli that are very common in the human gut but can also be dangerous pathogens. This work combined two distinct DNA sequencing approaches to allow us to explore the genomes of E. coli from college students to show that the antibiotic resistance genes these bacteria have acquired are usually carried on a specific type of plasmid that is naturally transferrable to other E. coli, and likely to other related bacteria.}, }
@article {pmid32756562, year = {2020}, author = {Ali, J and Awan, MOU and Akca, G and Zeb, I and Amin, BA and Ahmad, R and Shah, MM and Nazir, R}, title = {Prevalence of diversified antibiotic resistant bacteria within sanitation related facilities of human populated workplaces in Abbottabad.}, journal = {PloS one}, volume = {15}, number = {8}, pages = {e0233325}, pmid = {32756562}, issn = {1932-6203}, mesh = {Bacteria/*drug effects/genetics/*isolation &amp; purification ; *Drug Resistance, Multiple, Bacterial/genetics ; Environmental Microbiology ; Female ; Humans ; Hygiene ; Male ; Occupational Exposure ; Pakistan ; Phylogeny ; Plasmids ; Prevalence ; R Factors ; RNA, Ribosomal, 16S/genetics ; Sanitation ; *Toilet Facilities ; *Workplace ; }, abstract = {Antibiotics discovery was a significant breakthrough in the field of therapeutic medicines, but the over (mis)use of such antibiotics (in parallel) caused the increasing number of resistant bacterial species at an ever-higher rate. This study was thus devised to assess the multi-drug resistant bacteria present in sanitation-related facilities in human workplaces. In this regard, samples were collected from different gender, location, and source-based facilities, and subsequent antibiotic sensitivity testing was performed on isolated bacterial strains. Four classes of the most commonly used antibiotics i.e., β-lactam, Aminoglycosides, Macrolides, and Sulphonamides, were evaluated against the isolated bacteria. The antibiotic resistance profile of different (70) bacterial strains showed that the antibiotic resistance-based clusters also followed the grouping based on their isolation sources, mainly the gender. Twenty-three bacterial strains were further selected for their 16s rRNA gene based molecular identification and for phylogenetic analysis to evaluate the taxonomic evolution of antibiotic resistant bacteria (ARB). Moreover, the bacterial resistance to Sulphonamides and beta lactam was observed to be the most and to Aminoglycosides and macrolides as the least. Plasmid curing was also performed for multidrug resistant (MDR) bacterial strains, which significantly abolished the resistance potential of bacterial strains for different antibiotics. These curing results suggested that the antibiotic resistance determinants in these purified bacterial strains are present on respective plasmids. Altogether, the data suggested that the human workplaces are the hotspot for the prevalence of MDR bacteria and thus may serve as the source of horizontal gene transfer and further transmission to other environments.}, }
@article {pmid32756444, year = {2020}, author = {DeSalle, R and Riley, M}, title = {Should Networks Supplant Tree Building?.}, journal = {Microorganisms}, volume = {8}, number = {8}, pages = {}, pmid = {32756444}, issn = {2076-2607}, abstract = {Recent studies suggested that network methods should supplant tree building as the basis of genealogical analysis. This proposition is based upon two arguments. First is the observation that bacterial and archaeal lineages experience processes oppositional to bifurcation and hence the representation of the evolutionary process in a tree like structure is illogical. Second is the argument tree building approaches are circular-you ask for a tree and you get one, which pins a verificationist label on tree building that, if correct, should be the end of phylogenetic analysis as we currently know it. In this review, we examine these questions and suggest that rumors of the death of the bacterial tree of life are exaggerated at best.}, }
@article {pmid32749953, year = {2020}, author = {Nolan, LM and Turnbull, L and Katrib, M and Osvath, SR and Losa, D and Lazenby, JJ and Whitchurch, CB}, title = {Pseudomonas aeruginosa is capable of natural transformation in biofilms.}, journal = {Microbiology (Reading, England)}, volume = {166}, number = {10}, pages = {995-1003}, pmid = {32749953}, issn = {1465-2080}, mesh = {Bacterial Proteins/genetics/metabolism ; *Biofilms/growth &amp; development ; DNA/metabolism ; Fimbriae, Bacterial/genetics/metabolism ; Pseudomonas aeruginosa/genetics/*physiology ; *Transformation, Bacterial ; }, abstract = {Natural transformation is a mechanism that enables competent bacteria to acquire naked, exogenous DNA from the environment. It is a key process that facilitates the dissemination of antibiotic resistance and virulence determinants throughout bacterial populations. Pseudomonas aeruginosa is an opportunistic Gram-negative pathogen that produces large quantities of extracellular DNA (eDNA) that is required for biofilm formation. P. aeruginosa has a remarkable level of genome plasticity and diversity that suggests a high degree of horizontal gene transfer and recombination but is thought to be incapable of natural transformation. Here we show that P. aeruginosa possesses homologues of all proteins known to be involved in natural transformation in other bacterial species. We found that P. aeruginosa in biofilms is competent for natural transformation of both genomic and plasmid DNA. Furthermore, we demonstrate that type-IV pili (T4P) facilitate but are not absolutely essential for natural transformation in P. aeruginosa.}, }
@article {pmid32727926, year = {2020}, author = {Crane, A and Abaidoo, J and Beltran, G and Fry, D and Furey, C and Green, N and Johal, R and La Rosa, B and Jimenez, CL and Luong, L and Maag, G and Porche, J and Reyes, L and Robinson, A and Sabbara, S and Herrera, LS and Negrete, AU and Wilson, P and Geiler-Samerotte, K and Pfeifer, SP}, title = {The Complete Genome Sequence of the Staphylococcus Bacteriophage Metroid.}, journal = {G3 (Bethesda, Md.)}, volume = {10}, number = {9}, pages = {2975-2979}, pmid = {32727926}, issn = {2160-1836}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Genome Size ; *Genome, Viral ; Staphylococcus/genetics ; *Staphylococcus Phages/genetics ; }, abstract = {Phages infecting bacteria of the genus Staphylococcus play an important role in their host's ecology and evolution. On one hand, horizontal gene transfer from phage can encourage the rapid adaptation of pathogenic Staphylococcus enabling them to escape host immunity or access novel environments. On the other hand, lytic phages are promising agents for the treatment of bacterial infections, especially those resistant to antibiotics. As part of an ongoing effort to gain novel insights into bacteriophage diversity, we characterized the complete genome of the Staphylococcus bacteriophage Metroid, a cluster C phage with a genome size of 151kb, encompassing 254 predicted protein-coding genes as well as 4 tRNAs. A comparative genomic analysis highlights strong similarities - including a conservation of the lysis cassette - with other Staphylococcus cluster C bacteriophages, several of which were previously characterized for therapeutic applications.}, }
@article {pmid32727924, year = {2020}, author = {Tabima, JF and Trautman, IA and Chang, Y and Wang, Y and Mondo, S and Kuo, A and Salamov, A and Grigoriev, IV and Stajich, JE and Spatafora, JW}, title = {Phylogenomic Analyses of Non-Dikarya Fungi Supports Horizontal Gene Transfer Driving Diversification of Secondary Metabolism in the Amphibian Gastrointestinal Symbiont, Basidiobolus.}, journal = {G3 (Bethesda, Md.)}, volume = {10}, number = {9}, pages = {3417-3433}, pmid = {32727924}, issn = {2160-1836}, mesh = {Amphibians ; Animals ; *Entomophthorales ; Fungi ; *Gene Transfer, Horizontal ; Phylogeny ; Secondary Metabolism ; }, abstract = {Research into secondary metabolism (SM) production by fungi has resulted in the discovery of diverse, biologically active compounds with significant medicinal applications. The fungi rich in SM production are taxonomically concentrated in the subkingdom Dikarya, which comprises the phyla Ascomycota and Basidiomycota. Here, we explore the potential for SM production in Mucoromycota and Zoopagomycota, two phyla of nonflagellated fungi that are not members of Dikarya, by predicting and identifying core genes and gene clusters involved in SM. The majority of non-Dikarya have few genes and gene clusters involved in SM production except for the amphibian gut symbionts in the genus BasidiobolusBasidiobolus genomes exhibit an enrichment of SM genes involved in siderophore, surfactin-like, and terpene cyclase production, all these with evidence of constitutive gene expression. Gene expression and chemical assays also confirm that Basidiobolus has significant siderophore activity. The expansion of SMs in Basidiobolus are partially due to horizontal gene transfer from bacteria, likely as a consequence of its ecology as an amphibian gut endosymbiont.}, }
@article {pmid32723693, year = {2020}, author = {Wang, Q and Huang, J}, title = {Fungal Genes in Plants: Impact and Potential Applications.}, journal = {Trends in plant science}, volume = {25}, number = {11}, pages = {1064-1067}, doi = {10.1016/j.tplants.2020.07.005}, pmid = {32723693}, issn = {1878-4372}, mesh = {Fungi/genetics ; *Fusarium ; Gene Transfer, Horizontal ; Genes, Fungal ; Plant Diseases/genetics ; *Triticum ; }, abstract = {Although there is accumulating evidence for the role of foreign genes in plant development and adaptation, many issues remain. A recent study by Wang et al. on a gene of fungal origin in wheatgrass disease resistance highlights the potential application of fungal genes in crop improvement and related areas.}, }
@article {pmid32720896, year = {2020}, author = {Carraro, N and Richard, X and Sulser, S and Delavat, F and Mazza, C and van der Meer, JR}, title = {An analog to digital converter controls bistable transfer competence development of a widespread bacterial integrative and conjugative element.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, pmid = {32720896}, issn = {2050-084X}, support = {Interdisciplinary Grant//SystemsX.ch/International ; 31003A_175638/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {Bacteria/*genetics ; Bacterial Outer Membrane Proteins/*genetics/*metabolism ; Conjugation, Genetic/*physiology ; DNA Transposable Elements ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genome, Bacterial ; Pseudomonas/*genetics/*metabolism ; Transcription Factors/*metabolism ; }, abstract = {Conjugative transfer of the integrative and conjugative element ICEclc in Pseudomonas requires development of a transfer competence state in stationary phase, which arises only in 3-5% of individual cells. The mechanisms controlling this bistable switch between non-active and transfer competent cells have long remained enigmatic. Using a variety of genetic tools and epistasis experiments in P. putida, we uncovered an 'upstream' cascade of three consecutive transcription factor-nodes, which controls transfer competence initiation. One of the uncovered transcription factors (named BisR) is representative for a new regulator family. Initiation activates a feedback loop, controlled by a second hitherto unrecognized heteromeric transcription factor named BisDC. Stochastic modelling and experimental data demonstrated the feedback loop to act as a scalable converter of unimodal (population-wide or 'analog') input to bistable (subpopulation-specific or 'digital') output. The feedback loop further enables prolonged production of BisDC, which ensures expression of the 'downstream' functions mediating ICE transfer competence in activated cells. Phylogenetic analyses showed that the ICEclc regulatory constellation with BisR and BisDC is widespread among Gamma- and Beta-proteobacteria, including various pathogenic strains, highlighting its evolutionary conservation and prime importance to control the behaviour of this wide family of conjugative elements.}, }
@article {pmid32719664, year = {2020}, author = {Abe, T and Akazawa, Y and Toyoda, A and Niki, H and Baba, T}, title = {Batch-Learning Self-Organizing Map Identifies Horizontal Gene Transfer Candidates and Their Origins in Entire Genomes.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1486}, pmid = {32719664}, issn = {1664-302X}, abstract = {Horizontal gene transfer (HGT) has been widely suggested to play a critical role in the environmental adaptation of microbes; however, the number and origin of the genes in microbial genomes obtained through HGT remain unknown as the frequency of detected HGT events is generally underestimated, particularly in the absence of information on donor sequences. As an alternative to phylogeny-based methods that rely on sequence alignments, we have developed an alignment-free clustering method on the basis of an unsupervised neural network "Batch-Learning Self-Organizing Map (BLSOM)" in which sequence fragments are clustered based solely on oligonucleotide similarity without taxonomical information, to detect HGT candidates and their origin in entire genomes. By mapping the microbial genomic sequences on large-scale BLSOMs constructed with nearly all prokaryotic genomes, HGT candidates can be identified, and their origin assigned comprehensively, even for microbial genomes that exhibit high novelty. By focusing on two types of Alphaproteobacteria, specifically psychrotolerant Sphingomonas strains from an Antarctic lake, we detected HGT candidates using BLSOM and found higher proportions of HGT candidates from organisms belonging to Betaproteobacteria in the genomes of these two Antarctic strains compared with those of continental strains. Further, an origin difference was noted in the HGT candidates found in the two Antarctic strains. Although their origins were highly diversified, gene functions related to the cell wall or membrane biogenesis were shared among the HGT candidates. Moreover, analyses of amino acid frequency suggested that housekeeping genes and some HGT candidates of the Antarctic strains exhibited different characteristics to other continental strains. Lys, Ser, Thr, and Val were the amino acids found to be increased in the Antarctic strains, whereas Ala, Arg, Glu, and Leu were decreased. Our findings strongly suggest a low-temperature adaptation process for microbes that may have arisen convergently as an independent evolutionary strategy in each Antarctic strain. Hence, BLSOM analysis could serve as a powerful tool in not only detecting HGT candidates and their origins in entire genomes, but also in providing novel perspectives into the environmental adaptations of microbes.}, }
@article {pmid32719325, year = {2020}, author = {Marasini, D and Karki, AB and Bryant, JM and Sheaff, RJ and Fakhr, MK}, title = {Molecular characterization of megaplasmids encoding the type VI secretion system in Campylobacter jejuni isolated from chicken livers and gizzards.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {12514}, pmid = {32719325}, issn = {2045-2322}, mesh = {Animals ; Campylobacter jejuni/*genetics/*isolation &amp; purification ; Cell Death ; Cell Survival ; Chickens/*microbiology ; Chromosomes, Bacterial/genetics ; DNA, Bacterial/genetics ; Erythrocytes/metabolism ; Genome, Bacterial ; Gizzard, Avian/*microbiology ; HEK293 Cells ; Hemolysis ; Horses ; Humans ; Liver/*microbiology ; Plasmids/*genetics ; Tetracycline Resistance ; Type VI Secretion Systems/*genetics ; }, abstract = {Megaplasmids in Campylobacter spp. likely play important roles in antibiotic resistance, virulence, and horizontal gene transfer. In this study, megaplasmids pCJDM202 (119 kb) and pCJDM67L (116 kb) from C. jejuni strains WP2-202 and OD2-67, respectively, were sequenced and characterized. These megaplasmids contained genes for tetracycline resistance [tet(O)], the Type IV secretion system, conjugative transfer and the Type VI secretion system (T6SS). The T6SS genes in Campylobacter plasmids encoded genes and proteins that were similar to those identified in Campylobacter chromosomal DNA. When the megaplasmid pCJDM202 from C. jejuni WP2-202 was transferred via conjugation to C. jejuni NCTC11168 Nal[+], transconconjugants acquired tetracycline resistance and enhanced cytotoxicity towards red blood cells. A T6SS mutant of strain WP2-202 was generated and designated Δhcp3; the mutant was significantly impaired in its ability to lyse red blood cells and survive in defibrinated blood. The cytotoxicity of Campylobacter strains towards the human embryonic kidney cell line HEK 293 was not impacted by the T6SS. In summary, the T6SS encoded by Campylobacter megaplasmids mediates lysis of RBCs and likely contributes to survival on retail meats where blood cells are abundant.}, }
@article {pmid32715552, year = {2021}, author = {Fang, H and Xu, JB and Nie, Y and Wu, XL}, title = {Pan-genomic analysis reveals that the evolution of Dietzia species depends on their living habitats.}, journal = {Environmental microbiology}, volume = {23}, number = {2}, pages = {861-877}, doi = {10.1111/1462-2920.15176}, pmid = {32715552}, issn = {1462-2920}, support = {2018YFA0902100//National Key R&amp;D Program of China/ ; 2018YFA0902103//National Key R&amp;D Program of China/ ; 31770118//National Natural Science Foundation of China/ ; 31770120//National Natural Science Foundation of China/ ; }, mesh = {Actinobacteria/classification/*genetics/isolation &amp; purification/metabolism ; Bacterial Proteins/genetics/metabolism ; *Ecosystem ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomics ; Phylogeny ; }, abstract = {The bacterial genus Dietzia is widely distributed in various environments. The genomes of 26 diverse strains of Dietzia, including almost all the type strains, were analysed in this study. This analysis revealed a lipid metabolism gene richness, which could explain the ability of Dietzia to live in oil related environments. The pan-genome consists of 83,976 genes assigned into 10,327 gene families, 792 of which are shared by all the genomes of Dietzia. Mathematical extrapolation of the data suggests that the Dietzia pan-genome is open. Both gene duplication and gene loss contributed to the open pan-genome, while horizontal gene transfer was limited. Dietzia strains primarily gained their diverse metabolic capacity through more ancient gene duplications. Phylogenetic analysis of Dietzia isolated from aquatic and terrestrial environments showed two distinct clades from the same ancestor. The genome sizes of Dietzia strains from aquatic environments were significantly larger than those from terrestrial environments, which was mainly due to the occurrence of more gene loss events during the evolutionary progress of the strains from terrestrial environments. The evolutionary history of Dietzia was tightly coupled to environmental conditions, and iron concentrations should be one of the key factors shaping the genomes of the Dietzia lineages.}, }
@article {pmid32709941, year = {2020}, author = {Avni, E and Snir, S}, title = {A New Phylogenomic Approach For Quantifying Horizontal Gene Transfer Trends in Prokaryotes.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {12425}, pmid = {32709941}, issn = {2045-2322}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Models, Genetic ; Phylogeny ; }, abstract = {It is well established nowadays that among prokaryotes, various families of orthologous genes exhibit conflicting evolutionary history. A prime factor for this conflict is horizontal gene transfer (HGT) - the transfer of genetic material not via vertical descent. Thus, the prevalence of HGT is challenging the meaningfulness of the classical Tree of Life concept. Here we present a comprehensive study of HGT representing the entire prokaryotic world. We mainly rely on a novel analytic approach for analyzing an aggregate of gene histories, by means of the quartet plurality distribution (QPD) that we develop. Through the analysis of real and simulated data, QPD is used to reveal evidence of a barrier against HGT, separating the archaea from the bacteria and making HGT between the two domains, in general, quite rare. In contrast, bacteria's confined HGT is substantially more frequent than archaea's. Our approach also reveals that despite intensive HGT, a strong tree-like signal can be extracted, corroborating several previous works. Thus, QPD, which enables one to analytically combine information from an aggregate of gene trees, can be used for understanding patterns and rates of HGT in prokaryotes, as well as for validating or refuting models of horizontal genetic transfers and evolution in general.}, }
@article {pmid32709619, year = {2020}, author = {Roberts, WR and Downey, KM and Ruck, EC and Traller, JC and Alverson, AJ}, title = {Improved Reference Genome for Cyclotella cryptica CCMP332, a Model for Cell Wall Morphogenesis, Salinity Adaptation, and Lipid Production in Diatoms (Bacillariophyta).}, journal = {G3 (Bethesda, Md.)}, volume = {10}, number = {9}, pages = {2965-2974}, pmid = {32709619}, issn = {2160-1836}, mesh = {Cell Wall ; *Diatoms/genetics ; Lipids ; Morphogenesis ; Salinity ; }, abstract = {The diatom, Cyclotella cryptica, is a well-established model species for physiological studies and biotechnology applications of diatoms. To further facilitate its use as a model diatom, we report an improved reference genome assembly and annotation for C. cryptica strain CCMP332. We used a combination of long- and short-read sequencing to assemble a high-quality and contaminant-free genome. The genome is 171 Mb in size and consists of 662 scaffolds with a scaffold N50 of 494 kb. This represents a 176-fold decrease in scaffold number and 41-fold increase in scaffold N50 compared to the previous assembly. The genome contains 21,250 predicted genes, 75% of which were assigned putative functions. Repetitive DNA comprises 59% of the genome, and an improved classification of repetitive elements indicated that a historically steady accumulation of transposable elements has contributed to the relatively large size of the C. cryptica genome. The high-quality C. cryptica genome will serve as a valuable reference for ecological, genetic, and biotechnology studies of diatoms.}, }
@article {pmid32707922, year = {2020}, author = {Citti, C and Baranowski, E and Dordet-Frisoni, E and Faucher, M and Nouvel, LX}, title = {Genomic Islands in Mycoplasmas.}, journal = {Genes}, volume = {11}, number = {8}, pages = {}, pmid = {32707922}, issn = {2073-4425}, mesh = {Animals ; *Evolution, Molecular ; *Genome, Bacterial ; *Genomic Islands ; Humans ; Mycoplasma/*genetics/growth &amp; development ; }, abstract = {Bacteria of the Mycoplasma genus are characterized by the lack of a cell-wall, the use of UGA as tryptophan codon instead of a universal stop, and their simplified metabolic pathways. Most of these features are due to the small-size and limited-content of their genomes (580-1840 Kbp; 482-2050 CDS). Yet, the Mycoplasma genus encompasses over 200 species living in close contact with a wide range of animal hosts and man. These include pathogens, pathobionts, or commensals that have retained the full capacity to synthesize DNA, RNA, and all proteins required to sustain a parasitic life-style, with most being able to grow under laboratory conditions without host cells. Over the last 10 years, comparative genome analyses of multiple species and strains unveiled some of the dynamics of mycoplasma genomes. This review summarizes our current knowledge of genomic islands (GIs) found in mycoplasmas, with a focus on pathogenicity islands, integrative and conjugative elements (ICEs), and prophages. Here, we discuss how GIs contribute to the dynamics of mycoplasma genomes and how they participate in the evolution of these minimal organisms.}, }
@article {pmid32703812, year = {2020}, author = {Alexander, HK and MacLean, RC}, title = {Stochastic bacterial population dynamics restrict the establishment of antibiotic resistance from single cells.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {32}, pages = {19455-19464}, pmid = {32703812}, issn = {1091-6490}, support = {/WT_/Wellcome Trust/United Kingdom ; 106918/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Dose-Response Relationship, Drug ; Drug Resistance, Bacterial/*drug effects/genetics ; Microbial Sensitivity Tests ; Microbial Viability/drug effects ; Models, Theoretical ; Plasmids/genetics ; Pseudomonas aeruginosa/*drug effects/genetics/growth &amp; development ; Single-Cell Analysis ; Stochastic Processes ; }, abstract = {A better understanding of how antibiotic exposure impacts the evolution of resistance in bacterial populations is crucial for designing more sustainable treatment strategies. The conventional approach to this question is to measure the range of concentrations over which resistant strain(s) are selectively favored over a sensitive strain. Here, we instead investigate how antibiotic concentration impacts the initial establishment of resistance from single cells, mimicking the clonal expansion of a resistant lineage following mutation or horizontal gene transfer. Using two Pseudomonas aeruginosa strains carrying resistance plasmids, we show that single resistant cells have <5% probability of detectable outgrowth at antibiotic concentrations as low as one-eighth of the resistant strain's minimum inhibitory concentration (MIC). This low probability of establishment is due to detrimental effects of antibiotics on resistant cells, coupled with the inherently stochastic nature of cell division and death on the single-cell level, which leads to loss of many nascent resistant lineages. Our findings suggest that moderate doses of antibiotics, well below the MIC of resistant strains, may effectively restrict de novo emergence of resistance even though they cannot clear already-large resistant populations.}, }
@article {pmid32703190, year = {2020}, author = {Daugavet, MA and Shabelnikov, SV and Podgornaya, OI}, title = {Amino acid sequence associated with bacteriophage recombination site helps to reveal genes potentially acquired through horizontal gene transfer.}, journal = {BMC bioinformatics}, volume = {21}, number = {Suppl 12}, pages = {305}, pmid = {32703190}, issn = {1471-2105}, support = {19-74-20102//Russian Science Foundation/ ; }, mesh = {Amino Acid Sequence ; Bacteriophages/*genetics ; Base Sequence ; Conserved Sequence ; Gene Transfer, Horizontal/*genetics ; *Genes, Viral ; Protein Domains ; Recombination, Genetic/*genetics ; Viral Proteins/*chemistry/classification ; }, abstract = {BACKGROUND: Horizontal gene transfer, i.e. the acquisition of genetic material from nonparent organism, is considered an important force driving species evolution. Many cases of horizontal gene transfer from prokaryotes to eukaryotes have been registered, but no transfer mechanism has been deciphered so far, although viruses were proposed as possible vectors in several studies. In agreement with this idea, in our previous study we discovered that in two eukaryotic proteins bacteriophage recombination site (AttP) was adjacent to the regions originating via horizontal gene transfer. In one of those cases AttP site was present inside the introns of cysteine-rich repeats. In the present study we aimed to apply computational tools for finding multiple horizontal gene transfer events in large genome databases. For that purpose we used a sequence of cysteine-rich repeats to identify genes potentially acquired through horizontal transfer.<br><br>RESULTS: HMMER remote similarity search significantly detected 382 proteins containing cysteine-rich repeats. All of them, except 8 sequences, belong to eukaryotes. In 124 proteins the presence of conserved structural domains was predicted. In spite of the fact that cysteine-rich repeats are found almost exclusively in eukaryotic proteins, many predicted domains are most common for prokaryotes or bacteriophages. Ninety-eight proteins out of 124 contain typical prokaryotic domains. In those cases proteins were considered as potentially originating via horizontal transfer. In addition, HHblits search revealed that two domains of the same fungal protein, Glycoside hydrolase and Peptidase M15, have high similarity with proteins of two different prokaryotic species, hinting at independent horizontal gene transfer events.<br><br>CONCLUSIONS: Cysteine-rich repeats in eukaryotic proteins are usually accompanied by conserved domains typical for prokaryotes or bacteriophages. These proteins, containing both cysteine-rich repeats, and characteristic prokaryotic domains, might represent multiple independent horizontal gene transfer events from prokaryotes to eukaryotes. We believe that the presence of bacteriophage recombination site inside cysteine-rich repeat coding sequence may facilitate horizontal genes transfer. Thus computational approach, described in the present study, can help finding multiple sequences originated from horizontal transfer in eukaryotic genomes.}, }
@article {pmid32703172, year = {2020}, author = {Kim, HS and Lohmar, JM and Busman, M and Brown, DW and Naumann, TA and Divon, HH and Lysøe, E and Uhlig, S and Proctor, RH}, title = {Identification and distribution of gene clusters required for synthesis of sphingolipid metabolism inhibitors in diverse species of the filamentous fungus Fusarium.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {510}, pmid = {32703172}, issn = {1471-2164}, mesh = {*Fumonisins ; Fungi ; *Fusarium/genetics ; Multigene Family ; Sphingolipids ; }, abstract = {BACKGROUND: Sphingolipids are structural components and signaling molecules in eukaryotic membranes, and many organisms produce compounds that inhibit sphingolipid metabolism. Some of the inhibitors are structurally similar to the sphingolipid biosynthetic intermediate sphinganine and are referred to as sphinganine-analog metabolites (SAMs). The mycotoxins fumonisins, which are frequent contaminants in maize, are one family of SAMs. Due to food and feed safety concerns, fumonisin biosynthesis has been investigated extensively, including characterization of the fumonisin biosynthetic gene cluster in the agriculturally important fungi Aspergillus and Fusarium. Production of several other SAMs has also been reported in fungi, but there is almost no information on their biosynthesis. There is also little information on how widely SAM production occurs in fungi or on the extent of structural variation of fungal SAMs.<br><br>RESULTS: Using fumonisin biosynthesis as a model, we predicted that SAM biosynthetic gene clusters in fungi should include a polyketide synthase&#xa0;(PKS), an aminotransferase and a dehydrogenase gene. Surveys of genome sequences identified five putative clusters with this three-gene combination in 92 of 186 Fusarium species examined. Collectively, the putative SAM clusters were distributed widely but discontinuously among the species. We propose that the SAM5 cluster confers production of a previously reported Fusarium SAM, 2-amino-14,16-dimethyloctadecan-3-ol (AOD), based on the occurrence of AOD production only in species with the cluster and on deletion analysis of the SAM5 cluster PKS gene. We also identified SAM clusters in 24 species of other fungal genera, and propose that one of the clusters confers production of sphingofungin, a previously reported Aspergillus SAM.<br><br>CONCLUSION: Our results provide a genomics approach to identify novel SAM biosynthetic gene clusters in fungi, which should in turn contribute to identification of novel SAMs with applications in medicine and other fields. Information about novel SAMs could also provide insights into the role of SAMs in the ecology of fungi. Such insights have potential to contribute to strategies to reduce fumonisin contamination in crops and to control crop diseases caused by SAM-producing fungi.}, }
@article {pmid32698896, year = {2020}, author = {Tonkin-Hill, G and MacAlasdair, N and Ruis, C and Weimann, A and Horesh, G and Lees, JA and Gladstone, RA and Lo, S and Beaudoin, C and Floto, RA and Frost, SDW and Corander, J and Bentley, SD and Parkhill, J}, title = {Producing polished prokaryotic pangenomes with the Panaroo pipeline.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {180}, pmid = {32698896}, issn = {1474-760X}, support = {206194/WT_/Wellcome Trust/United Kingdom ; 107032/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; 204016/WT_/Wellcome Trust/United Kingdom ; MR/R015600/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Algorithms ; Biological Evolution ; Drug Resistance, Bacterial/genetics ; *Genome, Bacterial ; Genomics/*methods ; Klebsiella pneumoniae/genetics ; Mycobacterium tuberculosis/genetics ; *Software ; }, abstract = {Population-level comparisons of prokaryotic genomes must take into account the substantial differences in gene content resulting from horizontal gene transfer, gene duplication and gene loss. However, the automated annotation of prokaryotic genomes is imperfect, and errors due to fragmented assemblies, contamination, diverse gene families and mis-assemblies accumulate over the population, leading to profound consequences when analysing the set of all genes found in a species. Here, we introduce Panaroo, a graph-based pangenome clustering tool that is able to account for many of the sources of error introduced during the annotation of prokaryotic genome assemblies. Panaroo is available at https://github.com/gtonkinhill/panaroo .}, }
@article {pmid32695079, year = {2020}, author = {Slizovskiy, IB and Mukherjee, K and Dean, CJ and Boucher, C and Noyes, NR}, title = {Mobilization of Antibiotic Resistance: Are Current Approaches for Colocalizing Resistomes and Mobilomes Useful?.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1376}, pmid = {32695079}, issn = {1664-302X}, support = {R01 AI141810/AI/NIAID NIH HHS/United States ; }, abstract = {Antimicrobial resistance (AMR) poses a global human and animal health threat, and predicting AMR persistence and transmission remains an intractable challenge. Shotgun metagenomic sequencing can help overcome this by enabling characterization of AMR genes within all bacterial taxa, most of which are uncultivatable in laboratory settings. Shotgun sequencing, therefore, provides a more comprehensive glance at AMR "potential" within samples, i.e., the "resistome." However, the risk inherent within a given resistome is predicated on the genomic context of various AMR genes, including their presence within mobile genetic elements (MGEs). Therefore, resistome risk stratification can be advanced if AMR profiles are considered in light of the flanking mobilizable genomic milieu (e.g., plasmids, integrative conjugative elements (ICEs), phages, and other MGEs). Because such mediators of horizontal gene transfer (HGT) are involved in uptake by pathogens, investigators are increasingly interested in characterizing that resistome fraction in genomic proximity to HGT mediators, i.e., the "mobilome"; we term this "colocalization." We explored the utility of common colocalization approaches using alignment- and assembly-based techniques, on clinical (human) and agricultural (cattle) fecal metagenomes, obtained from antimicrobial use trials. Ordination revealed that tulathromycin-treated cattle experienced a shift in ICE and plasmid composition versus untreated animals, though the resistome was unaffected during the monitoring period. Contrarily, the human resistome and mobilome composition both shifted shortly after antimicrobial administration, though this rebounded to pre-treatment status. Bayesian networks revealed statistical AMR-MGE co-occurrence in 19 and 2% of edges from the cattle and human networks, respectively, suggesting a putatively greater mobility potential of AMR in cattle feces. Conversely, using Mobility Index (MI) and overlap analysis, abundance of de novo-assembled contigs supporting resistomes flanked by MGE increased shortly post-exposure within human metagenomes, though > 40 days after peak dose such contigs were rare (∼2%). MI was not substantially altered by antimicrobial exposure across all cattle metagenomes, ranging 0.5-4.0%. We highlight that current alignment- and assembly-based methods estimating resistome mobility yield contradictory and incomplete results, likely constrained by approach-specific data inputs, and bioinformatic limitations. We discuss recent laboratory and computational advancements that may enhance resistome risk analysis in clinical, regulatory, and commercial applications.}, }
@article {pmid32693346, year = {2020}, author = {Zhang, X and Li, R}, title = {Variation and distribution of antibiotic resistance genes and their potential hosts in microbial electrolysis cells treating sewage sludge.}, journal = {Bioresource technology}, volume = {315}, number = {}, pages = {123838}, doi = {10.1016/j.biortech.2020.123838}, pmid = {32693346}, issn = {1873-2976}, mesh = {Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Microbial/drug effects ; Electrolysis ; Genes, Bacterial ; *Sewage ; }, abstract = {Microbial electrolysis cells (MECs) system is an emerging pollution control technology. However, information on the variation of antibiotic resistance genes (ARGs) in MECs treating sewage sludge is still very limited. In this study, the fate of ARGs and their correlation with microbes in MECs under different applied voltages (0-1.5 V) were studied. Most target ARGs were effectively removed, but tetB, tetM and tetQ were enriched up to 2.05 log units in suspended sludge. Most ARGs were mainly distributed on electrodes, except tetQ and tetM enriched in suspended sludge. The selective pressure of residual antibiotics in the sewage sludge was negligible. Horizontal gene transfer was validated for the spread of sul1, sul2, tetA and tetC in MECs. Network analysis revealed that the potential hosts of ARGs mainly belonged to Bacteroidetes, Firmicutes and Proteobacteria. Some genera related to electron transfer were newly found to be the potential ARGs hosts in MECs.}, }
@article {pmid32690555, year = {2020}, author = {Huszczynski, SM and Hao, Y and Lam, JS and Khursigara, CM}, title = {Identification of the Pseudomonas aeruginosa O17 and O15 O-Specific Antigen Biosynthesis Loci Reveals an ABC Transporter-Dependent Synthesis Pathway and Mechanisms of Genetic Diversity.}, journal = {Journal of bacteriology}, volume = {202}, number = {19}, pages = {}, pmid = {32690555}, issn = {1098-5530}, support = {PJT 156111//CIHR/Canada ; MOP-14687//CIHR/Canada ; }, mesh = {ATP-Binding Cassette Transporters/*genetics/*metabolism ; Gene Knockout Techniques ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; *Genetic Variation ; Lipopolysaccharides/metabolism ; Methyltransferases ; O Antigens/*biosynthesis/*genetics ; Phylogeny ; Polysaccharides, Bacterial/metabolism ; Pseudomonas aeruginosa/classification/*genetics/*isolation &amp; purification ; Serogroup ; }, abstract = {Many bacterial cell surface glycans, such as the O antigen component of lipopolysaccharide (LPS), are produced via the so-called Wzx/Wzy- or ABC transporter-dependent pathways. O antigens are highly diverse polysaccharides that protect bacteria from their environment and engage in important host-pathogen interactions. The specific structure and composition of O antigens are the basis of classifying bacteria into O serotypes. In the opportunistic pathogen Pseudomonas aeruginosa, there are currently 20 known O-specific antigen (OSA) structures. The clusters of genes responsible for 18 of these O antigens have been identified, all of which follow the Wzx/Wzy-dependent pathway and are located at a common locus. In this study, we located the two unidentified O antigen biosynthesis clusters responsible for the synthesis of the O15 and the O17 OSA structures by analyzing published whole-genome sequence data. Intriguingly, these clusters were found outside the conserved OSA biosynthesis locus and were likely acquired through multiple horizontal gene transfer events. Based on data from knockout and overexpression studies, we determined that the synthesis of these O antigens follows an ABC transporter-dependent rather than a Wzx/Wzy-dependent pathway. In addition, we collected evidence to show that the O15 and O17 polysaccharide chain lengths are regulated by molecular rulers with distinct and variable domain architectures. The findings in this report are critical for a comprehensive understanding of O antigen biosynthesis in P. aeruginosa and provide a framework for future studies.IMPORTANCEP. aeruginosa is a problematic opportunistic pathogen that causes diseases in those with compromised host defenses, such as those suffering from cystic fibrosis. This bacterium produces a number of virulence factors, including a serotype-specific O antigen. Here, we identified and characterized the gene clusters that produce the O15 and O17 O antigens and show that they utilize a pathway for synthesis that is distinct from that of the 18 other known serotypes. We also provide evidence that these clusters have acquired mutations in specific biosynthesis genes and have undergone extensive horizontal gene transfer within the P. aeruginosa population. These findings expand on our understanding of O antigen biosynthesis in Gram-negative bacteria and the mechanisms that drive O antigen diversity.}, }
@article {pmid34368692, year = {2020}, author = {Al-Hassan, LL and Al-Madboly, LA}, title = {Molecular characterisation of an Acinetobacter baumannii outbreak.}, journal = {Infection prevention in practice}, volume = {2}, number = {2}, pages = {100040}, pmid = {34368692}, issn = {2590-0889}, abstract = {BACKGROUND: Acinetobacter baumannii are problematic hospital pathogens, and the increased incidence of multi drug resistance has significantly limited treatment options. The global epidemiology is not fully characterised due to large data gaps from low- and middle-income countries. This study characterised the molecular epidemiology of an A. baumanniii outbreak in Egypt.<br><br>METHODS: Fifty-four A.&#xa0;baumannii isolates were recovered from a 4-month-outbreak at Tanta University Hospitals (TUH). Associated clinical and demographic data, and the antibiograms were analysed, and Carbapenem resistant isolates were screened for acquired carbapenemase genes by PCR and sequencing. Epidemiological typing was performed by single-locus sequencing of bla OXA-51-like and Multi Locus Sequence Typing (MLST), and sequence types (STs) were analysed based on maximum-likelihood phylogeny (PhyML) to identify relatedness.<br><br>FINDINGS: Immune suppression and ICU admission were the most common co-morbidity and risk factor. Carbapenem resistance accounted for 81%, and correlated with the presence of OXA-23, NDM-1 and -2, and VIM-1 and -2 carbapenemases. Nine different bla OXA-51-like genes were identified which corresponded to 22 different Sequence Types (STs), including 10 novel. International clone (IC2) was the predominant clone. PhyML analysis revealed the presence of 2 distinct clones with multiple sub-lineages.<br><br>CONCLUSION: Given the short duration of the study, there was a rare heterogeneous population in the hospital. Carbapenem resistance is mediated by acquired carbapenemases in diverse lineages indicating the possibility of horizontal gene transfer. The diversity indicates the influx of multiple lineages of IC2 into TUH from unknown sources. Molecular epidemiological studies are essential for infection prevention and control measures.}, }
@article {pmid34618927, year = {2019}, author = {Miyagi, M and Wheeler, WC}, title = {Comparing and displaying phylogenetic trees using edge union networks.}, journal = {Cladistics : the international journal of the Willi Hennig Society}, volume = {35}, number = {6}, pages = {688-694}, doi = {10.1111/cla.12374}, pmid = {34618927}, issn = {1096-0031}, support = {SIMPLEX N66001-15-C-4039//DARPA/ ; REU DBI-1358465//NSF/ ; }, abstract = {The general problem of representing collections of trees as a single graph has led to many tree summary techniques. Many consensus approaches take sets of trees (either inferred as separate gene trees or gleaned from the posterior of a Bayesian analysis) and produce a single "best" tree. In scenarios where horizontal gene transfer or hybridization are suspected, networks may be preferred, which allow for nodes to have two parents, representing the fusion of lineages. One such construct is the cluster union network (CUN), which is constructed using the union of all clusters in the input trees. The CUN has a number of mathematically desirable properties, but can also present edges not observed in the input trees. In this paper we define a new network construction, the edge union network (EUN), which displays edges if and only if they are contained in the input trees. We also demonstrate that this object can be constructed with polynomial time complexity given arbitrary phylogenetic input trees, and so can be used in conjunction with network analysis techniques for further phylogenetic hypothesis testing.}, }
@article {pmid34179812, year = {2019}, author = {Kwon, KM and Bekal, S and Domier, LL and Lambert, KN}, title = {Active and inactive forms of biotin synthase occur in Heterodera glycines.}, journal = {Journal of nematology}, volume = {51}, number = {}, pages = {}, pmid = {34179812}, issn = {0022-300X}, abstract = {Heterodera glycines, the soybean cyst nematode (SCN), is a plant-parasitic nematode capable of manipulating host plant biochemistry and development. Many studies have suggested that the nematode has acquired genes from bacteria via horizontal gene transfer events (HGTs) that have the potential to enhance nematode parasitism. A recent allelic imbalance analysis identified two candidate virulence genes, which also appear to have entered the SCN genome through HGTs. One of the candidate genes, H. glycines biotin synthase (HgBioB), contained sequence polymorphisms between avirulent and virulent inbred SCN strains. To test the function of these HgBioB alleles, a complementation experiment using biotin synthase-deficient Escherichia coli was conducted. Here, we report that avirulent nematodes produce an active biotin synthase while virulent ones contain an inactive form of the enzyme. Moreover, sequencing analysis of HgBioB genes from SCN field populations indicates the presence of diverse mixture of HgBioB alleles with the virulent form being the most prevalent. We hypothesize that the mutations in the inactive HgBioB allele within the virulent SCN could result in a change in protein function that in some unknown way bolster its parasitic lifestyle.}, }
@article {pmid34103738, year = {2019}, author = {Lowerre, KM and Espinosa, A and Paz-Y-Miño-C, G and Hemme, C}, title = {Bioinformatics Structural and Phylogenetic Characterization of Entamoeba histolytica Alcohol Dehydrogenase 2 (EhADH2).}, journal = {Bios}, volume = {90}, number = {1}, pages = {30-41}, pmid = {34103738}, issn = {0005-3155}, support = {P20 GM103430/GM/NIGMS NIH HHS/United States ; }, abstract = {An amitochondriate parasite, Entamoeba histolytica, has a bifunctional ADHE enzyme (EhADH2) that contains separate acetaldehyde (ALDH) and alcohol (ADH) dehydrogenase activities. In a cluster of 25 bifunctional enzymes of single cell eukaryotes and bacteria, we present a phylogenetic analysis that suggests a lateral gene transfer event (prokaryotic ancestor to single-cell eukaryotic ancestor) and a complex structure that aligns with key homologs in the ADHE evolutionary history based on their similarity with bacterial alcohol dehydrogenases. We show that the ADHE in Entamoeba lineage diverged independently but shows significant similarities to the structure of ADHE in Fusobacterium, and a complex model that maps its ALDH and ADH domain well with bacteria such as Geobaccillus thermoglucosidasius. Our analyses likely support a lateral acquisition of an EhADH2-like ancestral gene from bacteria. Several evolutionary analyses software programs reveal that the enzyme structure is highly conserved, and maintains a similar function within a diverse set of pathogens, including Escherichia coli and Clostridium spp.}, }
@article {pmid34532552, year = {2018}, author = {Loyo, CL and Burton, BM}, title = {Quantitative Transformation Efficiency Assay for Bacillus subtilis.}, journal = {Bio-protocol}, volume = {8}, number = {23}, pages = {e3109}, pmid = {34532552}, issn = {2331-8325}, abstract = {Bacillus subtilis (B. subtilis) is a model Gram-positive organism used to study a variety of physiological states and stress responses, one of which is the development of competence. Competence refers to the physiological state of a cell which allows it to be transformed naturally. Through induction of competence, the efficiency of natural transformation can be quantified by plating colony forming units (CFU) and transforming units (TFU). Here we describe a protocol for quantifying relative transformability using B. subtilis.}, }
@article {pmid34532544, year = {2018}, author = {Zhao, M and Zhang, B and Ma, J and Lisch, D}, title = {Genome-wide Estimation of Evolutionary Distance and Phylogenetic Analysis of Homologous Genes.}, journal = {Bio-protocol}, volume = {8}, number = {23}, pages = {e3097}, pmid = {34532544}, issn = {2331-8325}, abstract = {Homologous genes, including paralogs and orthologs, are genes that share sequence homologies within or between different species. Homologous genes originate from a common origin through speciation, genetic duplication or horizontal gene transfer. Estimation of the sequence divergence of homologous genes help us to understand divergence time, which makes it possible to understand the evolutionary patterns of speciation, gene duplication and gene transfer events. This protocol will provide a detailed bioinformatics pipeline on how to identify the homologous genes, compare their sequence divergence and phylogenetic relationships, focusing on homologous genes that show syntenic relationships using soybean (Glycine max) and common bean (Phaseolus vulgaris) as example species.}, }
@article {pmid33350166, year = {2018}, author = {Olaimat, AN and Al-Holy, MA and Shahbaz, HM and Al-Nabulsi, AA and Abu Ghoush, MH and Osaili, TM and Ayyash, MM and Holley, RA}, title = {Emergence of Antibiotic Resistance in Listeria monocytogenes Isolated from Food Products: A Comprehensive Review.}, journal = {Comprehensive reviews in food science and food safety}, volume = {17}, number = {5}, pages = {1277-1292}, doi = {10.1111/1541-4337.12387}, pmid = {33350166}, issn = {1541-4337}, support = {//Hashemite University/ ; }, abstract = {Listeria monocytogenes is an opportunistic pathogen that has been involved in several deadly illness outbreaks. Future outbreaks may be more difficult to manage because of the emergence of antibiotic resistance among L. monocytogenes strains isolated from food products. The present review summarizes the available evidence on the emergence of antibiotic resistance among L. monocytogenes strains isolated from food products and the possible ways this resistance has developed. Furthermore, the resistance of food L. monocytogenes isolates to antibiotics currently used in the treatment of human listeriosis such as penicillin, ampicillin, tetracycline, and gentamicin, has been documented. Acquisition of movable genetic elements is considered the major mechanism of antibiotic resistance development in L. monocytogenes. Efflux pumps have also been linked with resistance of L. monocytogenes to some antibiotics including fluoroquinolones. Some L. monocytogenes strains isolated from food products are intrinsically resistant to several antibiotics. However, factors in food processing chains and environments (from farm to table) including extensive or sub-inhibitory antibiotics use, horizontal gene transfer, exposure to environmental stresses, biofilm formation, and presence of persister cells play crucial roles in the development of antibiotic resistance by L. monocytogenes.}, }
@article {pmid33579083, year = {2016}, author = {Loong, SK and Che Mat Seri, NAA and Mahfodz, NH and Ahmad Nasrah, SN and Teoh, BT and AbuBakar, S}, title = {Emergence of Enterococcus gallinarum carrying vanA gene cluster displaying atypical phenotypes.}, journal = {Tropical biomedicine}, volume = {33}, number = {4}, pages = {837-841}, pmid = {33579083}, issn = {2521-9855}, abstract = {Motile enterococci such as Enterococcus gallinarum has the ability to acquire and transfer antibiotic resistance genes to other enterococci. Even though infections caused by E. gallinarum are rare, the discovery of this bacteria in food sources and in clinical environments is disturbing. Here, we report the isolation and identification of E. gallinarum from the wound of a hospital in-patient. The isolate was identified using 16S rDNA sequencing. Isolate 146 harboured the vanA and vanC1 gene clusters, was vancomycin-susceptible, and displayed resistance to ampicillin, penicillin, erythromycin and teicoplanin. This isolate also showed intermediate resistance to linezolid and sequencing of the 23S rRNA peptidyl transferase region did not unveil any known mutations associated to the conferment of linezolid resistance. The presence of vanA did not confer resistance to vancomycin. Structural analyses into the Tn1546 transposon carrying the vanA gene revealed distinct genetic variations in the vanS, vanY and vanS-vanH intergenic region that could be associated to the atypical antibiotic resistance phenotypes of isolate 146. Finding from this study are suggestive of the occurrence of interspecies horizontal gene transfer and that similarities in genotypic characteristic may not necessarily correlate with actual antibiotic resistance pattern of E. gallinarum.}, }
@article {pmid32846688, year = {2015}, author = {Heidel-Fischer, HM and Vogel, H}, title = {Molecular mechanisms of insect adaptation to plant secondary compounds.}, journal = {Current opinion in insect science}, volume = {8}, number = {}, pages = {8-14}, doi = {10.1016/j.cois.2015.02.004}, pmid = {32846688}, issn = {2214-5753}, abstract = {During feeding, herbivorous insects are exposed to an array of plant defensive compounds. In this review, we examine molecular mechanisms of insect adaptation to these toxic metabolites. We discuss both the importance of evolutionary variation of existing detoxification gene families, as well as the evolution of novel mechanisms through gene recruitment, neofunctionalization and horizontal gene transfer. The ability of insects to cope with the chemical diversity of their host plants and the different mechanisms that insects use to resist these toxins open new avenues for understanding fundamental aspects of insect-plant coevolutionary adaptation.}, }
@article {pmid33065890, year = {2012}, author = {Campocasso, A and La Scola, B}, title = {Virus géants associés aux amibes.}, journal = {Virologie (Montrouge, France)}, volume = {16}, number = {1}, pages = {6-17}, doi = {10.1684/vir.2012.0432}, pmid = {33065890}, issn = {1267-8694}, abstract = {The discovery of Acanthamoeba polyphaga Mimivirus, a giant amoeba-associated virus less than a decade ago, has shattered the definition of what is a virus. With an exceptional size of 500 nm, a genome of more than 1 Mb, a particle containing both DNA and RNA, possibility to be infected by another virus are unusual characteristics that make it immediately exceptional. Since then, several giant viruses have been isolated such as Marseillevirus. It is highly probable that closely related viruses will be isolated as it is now understood that they were not previously isolated because they are not filterable. Environmental metagenomic studies suggest that these viruses are ubiquitous. The discovery of virophages, small viruses able to infect Mimivirus as bacteriophage infect bacteria, fuel the debate about the nature of viruses and their place in the evolution of life. Current works, especially genome sequencing of these new viruses, open new perspectives about evolution and lateral gene transfer with their host but also with bacteria and other viruses. The knowledge about these viruses is only at the first step and increasing interest for it suggests that we are only at the dawn of the understanding of their role in evolution and ecosystems regulation.}, }
@article {pmid33873367, year = {2003}, author = {Cobbett, CS and Hussain, D and Haydon, MJ}, title = {Structural and functional relationships between type 1B heavy metal-transporting P-type ATPases in Arabidopsis.}, journal = {The New phytologist}, volume = {159}, number = {2}, pages = {315-321}, pmid = {33873367}, issn = {1469-8137}, abstract = {Arabidopsis is remarkable for having eight members of the type 1B heavy metal-transporting P-type ATPase subfamily. Sequence analyses indicate that four, two of which may be targeted to plastids, are related to known Cu(I) transporters and contain N-terminal metal-binding site (MBS) motifs similar to those identified in other organisms. The remaining four are more closely related to known divalent cation transporters of prokaryotes. Three of these form a closely related group and are believed to be Zn(II) transporters. These contain a predicted N-terminal MBS that is a variant of those found in Cu transporters in addition to extended C-terminal regions that contain likely metal-binding sequences. Our current limited knowledge of the physiological roles of these transporters is reviewed and their evolutionary relationships are explored, including an hypothesis that some, particularly the putative divalent cation transporters, are derived from horizontal gene transfer events.}, }
@article {pmid33873398, year = {2003}, author = {Van Elsas, JD and Turner, S and Bailey, MJ}, title = {Horizontal gene transfer in the phytosphere.}, journal = {The New phytologist}, volume = {157}, number = {3}, pages = {525-537}, pmid = {33873398}, issn = {1469-8137}, abstract = {Here, the ecological aspects of gene transfer processes between bacteria in the phytosphere are examined in the context of emerging evidence for the dominant role that horizontal gene transfer (HGT) has played in the evolutionary shaping of bacterial communities. Moreover, the impact of the putative capture of genetic material by bacteria from plants is discussed. Examples are provided that illustrate how mobile genetic elements (MGEs) influence the behaviour of bacteria in their natural habitat, especially in structured communities such as biofilms on plant surfaces. This community behaviour is used as a framework to pose questions on the evolutionary role and significance of gene transfer processes in plant-associated habitats. Selection within the highly structured phytosphere is likely to represent a dominant force shaping the genetic make-up of plant-associated bacterial communities. Current understanding of the triggering and impact of horizontal gene transfer, however, remains limited by our lack of understanding of the nature of the selective forces that act on bacteria in situ. The individual, colony, population and community level selection benefits imposed by the ability to use specific carbon sources or survive selective compounds are clear, but it is not always possible to assess what drives gene transfer and persistence. The role of HGT in the adaptation of host bacteria to their environmental niche is still not fully understood.}, }
@article {pmid34644923, year = {1999}, author = {Schwarz, S and Noble, WC}, title = {Aspects of bacterial resistance to antimicrobials used in veterinary dermatological practice.}, journal = {Veterinary dermatology}, volume = {10}, number = {3}, pages = {163-176}, doi = {10.1046/j.1365-3164.1999.00170.x}, pmid = {34644923}, issn = {1365-3164}, abstract = {Aspects of bacterial resistance to the major classes of antimicrobials used in veterinary dermatology are presented in this review. Resistance of gram-positive and gram-negative bacteria to tetracyclines, macrolide-lincosamide-streptogramin antibiotics, chloramphenicol, mupirocin, sulphonamides, trimethoprim, aminoglycosides, fluoroquinolones and β-lactam antibiotics are depicted with respect to the different mechanisms of acquired and intrinsic resistance. Examples are given for the three major resistance mechanisms, enzymatic inactivation, decreased intracellular drug accumulation and target modification. In addition, basic information about mobile genetic elements which carry resistance genes, such as plasmids, transposons and gene cassettes, and their modes of spreading via transduction, conjugation, mobilization and transformation is provided.}, }
@article {pmid32689930, year = {2020}, author = {Buongermino Pereira, M and Österlund, T and Eriksson, KM and Backhaus, T and Axelson-Fisk, M and Kristiansson, E}, title = {A comprehensive survey of integron-associated genes present in metagenomes.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {495}, pmid = {32689930}, issn = {1471-2164}, mesh = {Bacteria/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; *Integrons/genetics ; *Metagenome ; }, abstract = {BACKGROUND: Integrons are genomic elements that mediate horizontal gene transfer by inserting and removing genetic material using site-specific recombination. Integrons are commonly found in bacterial genomes, where they maintain a large and diverse set of genes that plays an important role in adaptation and evolution. Previous studies have started to characterize the wide range of biological functions present in integrons. However, the efforts have so far mainly been limited to genomes from cultivable bacteria and amplicons generated by PCR, thus targeting only a small part of the total integron diversity. Metagenomic data, generated by direct sequencing of environmental and clinical samples, provides a more holistic and unbiased analysis of integron-associated genes. However, the fragmented nature of metagenomic data has previously made such analysis highly challenging.<br><br>RESULTS: Here, we present a systematic survey of integron-associated genes in metagenomic data. The analysis was based on a newly developed computational method where integron-associated genes were identified by detecting their associated recombination sites. By processing contiguous sequences assembled from more than 10 terabases of metagenomic data, we were able to identify 13,397 unique integron-associated genes. Metagenomes from marine microbial communities had the highest occurrence of integron-associated genes with levels more than 100-fold higher than in the human microbiome. The identified genes had a large functional diversity spanning over several functional classes. Genes associated with defense mechanisms and mobility facilitators were most overrepresented and more than five times as common in integrons compared to other bacterial genes. As many as two thirds of the genes were found to encode proteins of unknown function. Less than 1% of the genes were associated with antibiotic resistance, of which several were novel, previously undescribed, resistance gene variants.<br><br>CONCLUSIONS: Our results highlight the large functional diversity maintained by integrons present in unculturable bacteria and significantly expands the number of described integron-associated genes.}, }
@article {pmid32687170, year = {2020}, author = {Yang, LL and Jiang, Z and Li, Y and Wang, ET and Zhi, XY}, title = {Plasmids Related to the Symbiotic Nitrogen Fixation Are Not Only Cooperated Functionally but Also May Have Evolved over a Time Span in Family Rhizobiaceae.}, journal = {Genome biology and evolution}, volume = {12}, number = {11}, pages = {2002-2014}, pmid = {32687170}, issn = {1759-6653}, mesh = {*Evolution, Molecular ; Genome, Bacterial ; Nitrogen Fixation/*genetics ; Phylogeny ; *Plasmids ; Rhizobiaceae/*genetics ; Symbiosis/*genetics ; }, abstract = {Rhizobia are soil bacteria capable of forming symbiotic nitrogen-fixing nodules associated with leguminous plants. In fast-growing legume-nodulating rhizobia, such as the species in the family Rhizobiaceae, the symbiotic plasmid is the main genetic basis for nitrogen-fixing symbiosis, and is susceptible to horizontal gene transfer. To further understand the symbioses evolution in Rhizobiaceae, we analyzed the pan-genome of this family based on 92 genomes of type/reference strains and reconstructed its phylogeny using a phylogenomics approach. Intriguingly, although the genetic expansion that occurred in chromosomal regions was the main reason for the high proportion of low-frequency flexible gene families in the pan-genome, gene gain events associated with accessory plasmids introduced more genes into the genomes of nitrogen-fixing species. For symbiotic plasmids, although horizontal gene transfer frequently occurred, transfer may be impeded by, such as, the host's physical isolation and soil conditions, even among phylogenetically close species. During coevolution with leguminous hosts, the plasmid system, including accessory and symbiotic plasmids, may have evolved over a time span, and provided rhizobial species with the ability to adapt to various environmental conditions and helped them achieve nitrogen fixation. These findings provide new insights into the phylogeny of Rhizobiaceae and advance our understanding of the evolution of symbiotic nitrogen fixation.}, }
@article {pmid32681114, year = {2020}, author = {Redondo-Salvo, S and Fernández-López, R and Ruiz, R and Vielva, L and de Toro, M and Rocha, EPC and Garcillán-Barcia, MP and de la Cruz, F}, title = {Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {3602}, pmid = {32681114}, issn = {2041-1723}, mesh = {Algorithms ; Gammaproteobacteria/classification/*genetics ; *Gene Transfer, Horizontal ; Genomics ; Phylogeny ; Plasmids/*genetics ; }, abstract = {Plasmids can mediate horizontal gene transfer of antibiotic resistance, virulence genes, and other adaptive factors across bacterial populations. Here, we analyze genomic composition and pairwise sequence identity for over 10,000 reference plasmids to obtain a global map of the prokaryotic plasmidome. Plasmids in this map organize into discrete clusters, which we call plasmid taxonomic units (PTUs), with high average nucleotide identity between its members. We identify 83 PTUs in the order Enterobacterales, 28 of them corresponding to previously described archetypes. Furthermore, we develop an automated algorithm for PTU identification, and validate its performance using stochastic blockmodeling. The algorithm reveals a total of 276 PTUs in the bacterial domain. Each PTU exhibits a characteristic host distribution, organized into a six-grade scale (I-VI), ranging from plasmids restricted to a single host species (grade I) to plasmids able to colonize species from different phyla (grade VI). More than 60% of the plasmids in the global map are in groups with host ranges beyond the species barrier.}, }
@article {pmid32680451, year = {2020}, author = {Ruhe, ZC and Low, DA and Hayes, CS}, title = {Polymorphic Toxins and Their Immunity Proteins: Diversity, Evolution, and Mechanisms of Delivery.}, journal = {Annual review of microbiology}, volume = {74}, number = {}, pages = {497-520}, pmid = {32680451}, issn = {1545-3251}, support = {R01 GM117373/GM/NIGMS NIH HHS/United States ; R01 GM117930/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/genetics/*immunology ; Bacterial Proteins/metabolism ; Bacterial Toxins/*genetics/*immunology/metabolism ; *Gene Transfer, Horizontal ; *Microbial Interactions ; Type VI Secretion Systems/genetics/immunology ; }, abstract = {All bacteria must compete for growth niches and other limited environmental resources. These existential battles are waged at several levels, but one common strategy entails the transfer of growth-inhibitory protein toxins between competing cells. These antibacterial effectors are invariably encoded with immunity proteins that protect cells from intoxication by neighboring siblings. Several effector classes have been described, each designed to breach the cell envelope of target bacteria. Although effector architectures and export pathways tend to be clade specific, phylogenetically distant species often deploy closely related toxin domains. Thus, diverse competition systems are linked through a common reservoir of toxin-immunity pairs that is shared via horizontal gene transfer. These toxin-immunity protein pairs are extraordinarily diverse in sequence, and this polymorphism underpins an important mechanism of self/nonself discrimination in bacteria. This review focuses on the structures, functions, and delivery mechanisms of polymorphic toxin effectors that mediate bacterial competition.}, }
@article {pmid32679802, year = {2020}, author = {Kami, D and Gojo, S}, title = {From Cell Entry to Engraftment of Exogenous Mitochondria.}, journal = {International journal of molecular sciences}, volume = {21}, number = {14}, pages = {}, pmid = {32679802}, issn = {1422-0067}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Endocytosis ; Endosomes/genetics ; Gene Transfer, Horizontal ; Humans ; Mitochondria/genetics/*transplantation ; Pinocytosis ; Symbiosis ; }, abstract = {Mitochondrial transfer has been recognized to play a role in a variety of processes, ranging from fertilization to cancer and neurodegenerative diseases as well as mammalian horizontal gene transfer. It is achieved through either exogeneous or intercellular mitochondrial transfer. From the viewpoint of evolution, exogeneous mitochondrial transfer is quite akin to the initial process of symbiosis between α-protobacterium and archaea, although the progeny have developed more sophisticated machinery to engulf environmental materials, including nutrients, bacteria, and viruses. A molecular-based knowledge of endocytosis, including macropinocytosis and endosomal escape involving bacteria and viruses, could provide mechanistic insights into exogeneous mitochondrial transfer. We focus on exogeneous mitochondrial transfer in this review to facilitate the clinical development of the use of isolated mitochondria to treat various pathological conditions. Several kinds of novel procedures to enhance exogeneous mitochondrial transfer have been developed and are summarized in this review.}, }
@article {pmid32676056, year = {2020}, author = {Jiang, H and Yu, T and Yang, Y and Yu, S and Wu, J and Lin, R and Li, Y and Fang, J and Zhu, C}, title = {Co-occurrence of Antibiotic and Heavy Metal Resistance and Sequence Type Diversity of Vibrio parahaemolyticus Isolated From Penaeus vannamei at Freshwater Farms, Seawater Farms, and Markets in Zhejiang Province, China.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1294}, pmid = {32676056}, issn = {1664-302X}, abstract = {Vibrio parahaemolyticus is the leading cause of seafood-borne bacterial poisoning in China and is a threat to human health worldwide. The aim of this study was to assess the antibiotic resistance profiles and distribution of heavy metal resistance of V. parahaemolyticus isolates from Penaeus vannamei from freshwater farms, seawater farms, and their corresponding markets in Zhejiang, China and to assess the relationship between multidrug resistance (MDR) and multi-heavy metal resistance (MHMR). Of the 360 P. vannamei samples that we tested, 90 (25.00%) were V. parahaemolyticus positive, but the occurrence of pathogenic isolates carrying the toxin genes tdh (4.44%) and trh (3.33%) was low. None of the tested isolates harbored both the tdh and trh genes. However, antibiotic resistance profiles varied among different sampling locations, levels of resistance to the antibiotics ampicillin (76.67%) and streptomycin (74.44%) were high overall, and MDR isolates were common (40.00% of all isolates). Heavy metal resistance patterns were similar among the different sampling locations. Overall, the majority of V. parahaemolyticus isolates displayed tolerance to Cd[2+] (60.00%), and fewer were resistant to Cu[2+] (40.00%), Zn[2+] (38.89%), Ni[2+] (24.44%), Cr[3+] (14.44%), and Co[2+] (8.89%). In addition, 34.44% (31/90) of isolates tested in this study were found to be MHMR. Using Pearson's correlation analysis, MDR and MHMR were found to be positively correlated (P = 0.004; R = 0.759). The 18 V. parahaemolyticus isolates that were both MDR and MHMR represented 18 sequence types, of which 12 were novel to the PubMLST database, and displayed a high level of genetic diversity, suggesting that dissemination may be affected by mobile genetic elements via horizontal gene transfer. However, a low percentage of class 1 integrons without gene cassettes and no class 2 or 3 integrons were detected in the 18 MDR and MHMR isolates or in the 90 V. parahaemolyticus isolates overall. Thus, we suggest that future research focus on elucidating the mechanisms that lead to a high prevalence of resistance determinants in V. parahaemolyticus. The results of this study provide data that will support aquatic animal health management and food safety risk assessments in the aquaculture industry.}, }
@article {pmid32673374, year = {2020}, author = {Yan, Q and Rogan, CJ and Pang, YY and Davis, EW and Anderson, JC}, title = {Ancient co-option of an amino acid ABC transporter locus in Pseudomonas syringae for host signal-dependent virulence gene regulation.}, journal = {PLoS pathogens}, volume = {16}, number = {7}, pages = {e1008680}, pmid = {32673374}, issn = {1553-7374}, mesh = {Arabidopsis/*microbiology ; Gene Expression Regulation, Bacterial/*physiology ; Plant Diseases/microbiology ; Pseudomonas syringae/*pathogenicity ; Type III Secretion Systems/*physiology ; Virulence/*physiology ; }, abstract = {Pathogenic bacteria frequently acquire virulence traits via horizontal gene transfer, yet additional evolutionary innovations may be necessary to integrate newly acquired genes into existing regulatory pathways. The plant bacterial pathogen Pseudomonas syringae relies on a horizontally acquired type III secretion system (T3SS) to cause disease. T3SS-encoding genes are induced by plant-derived metabolites, yet how this regulation occurs, and how it evolved, is poorly understood. Here we report that the two-component system AauS-AauR and substrate-binding protein AatJ, proteins encoded by an acidic amino acid-transport (aat) and -utilization (aau) locus in P. syringae, directly regulate T3SS-encoding genes in response to host aspartate and glutamate signals. Mutants of P. syringae strain DC3000 lacking aauS, aauR or aatJ expressed lower levels of T3SS genes in response to aspartate and glutamate, and had decreased T3SS deployment and virulence during infection of Arabidopsis. We identified an AauR-binding motif (Rbm) upstream of genes encoding T3SS regulators HrpR and HrpS, and demonstrated that this Rbm is required for maximal T3SS deployment and virulence of DC3000. The Rbm upstream of hrpRS is conserved in all P. syringae strains with a canonical T3SS, suggesting AauR regulation of hrpRS is ancient. Consistent with a model of conserved function, an aauR deletion mutant of P. syringae strain B728a, a bean pathogen, had decreased T3SS expression and growth in host plants. Together, our data suggest that, upon acquisition of T3SS-encoding genes, a strain ancestral to P. syringae co-opted an existing AatJ-AauS-AauR pathway to regulate T3SS deployment in response to specific host metabolite signals.}, }
@article {pmid32672812, year = {2020}, author = {Saak, CC and Dinh, CB and Dutton, RJ}, title = {Experimental approaches to tracking mobile genetic elements in microbial communities.}, journal = {FEMS microbiology reviews}, volume = {44}, number = {5}, pages = {606-630}, pmid = {32672812}, issn = {1574-6976}, support = {DP2 AT010401/AT/NCCIH NIH HHS/United States ; T32 GM007198/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; Environmental Microbiology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Microbiological Techniques/*trends ; Microbiota/*genetics ; }, abstract = {Horizontal gene transfer is an important mechanism of microbial evolution and is often driven by the movement of mobile genetic elements between cells. Due to the fact that microbes live within communities, various mechanisms of horizontal gene transfer and types of mobile elements can co-occur. However, the ways in which horizontal gene transfer impacts and is impacted by communities containing diverse mobile elements has been challenging to address. Thus, the field would benefit from incorporating community-level information and novel approaches alongside existing methods. Emerging technologies for tracking mobile elements and assigning them to host organisms provide promise for understanding the web of potential DNA transfers in diverse microbial communities more comprehensively. Compared to existing experimental approaches, chromosome conformation capture and methylome analyses have the potential to simultaneously study various types of mobile elements and their associated hosts. We also briefly discuss how fermented food microbiomes, given their experimental tractability and moderate species complexity, make ideal models to which to apply the techniques discussed herein and how they can be used to address outstanding questions in the field of horizontal gene transfer in microbial communities.}, }
@article {pmid32671212, year = {2020}, author = {Lehtinen, S and Chewapreecha, C and Lees, J and Hanage, WP and Lipsitch, M and Croucher, NJ and Bentley, SD and Turner, P and Fraser, C and Mostowy, RJ}, title = {Horizontal gene transfer rate is not the primary determinant of observed antibiotic resistance frequencies in Streptococcus pneumoniae.}, journal = {Science advances}, volume = {6}, number = {21}, pages = {eaaz6137}, pmid = {32671212}, issn = {2375-2548}, support = {R01 AI106786/AI/NIAID NIH HHS/United States ; U01 GM110721/GM/NIGMS NIH HHS/United States ; T32 AI007535/AI/NIAID NIH HHS/United States ; U54 GM088558/GM/NIGMS NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; MR/R015600/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {The extent to which evolution is constrained by the rate at which horizontal gene transfer (HGT) allows DNA to move between genetic lineages is an open question, which we address in the context of antibiotic resistance in Streptococcus pneumoniae. We analyze microbiological, genomic, and epidemiological data from the largest-to-date sequenced pneumococcal carriage study in 955 infants from a refugee camp on the Thailand-Myanmar border. Using a unified framework, we simultaneously test prior hypotheses on rates of HGT and a key evolutionary covariate (duration of carriage) as determinants of resistance frequencies. We conclude that in this setting, there is little evidence of HGT playing a major role in determining resistance frequencies. Instead, observed resistance frequencies are best explained as the outcome of selection acting on a pool of variants, irrespective of the rate at which resistance determinants move between genetic lineages.}, }
@article {pmid32670414, year = {2020}, author = {Li, C and Chen, J and Li, SC}, title = {Understanding Horizontal Gene Transfer network in human gut microbiota.}, journal = {Gut pathogens}, volume = {12}, number = {}, pages = {33}, pmid = {32670414}, issn = {1757-4749}, abstract = {BACKGROUND: Horizontal Gene Transfer (HGT) is the process of transferring genetic materials between species. Through sharing genetic materials, microorganisms in the human microbiota form a network. The network can provide insights into understanding the microbiota. Here, we constructed the HGT networks from the gut microbiota sequencing data and performed network analysis to characterize the HGT networks of gut microbiota.<br><br>RESULTS: We constructed the HGT network and perform the network analysis to two typical gut microbiota datasets, a 283-sample dataset of Mother-to-Child and a 148-sample dataset of longitudinal inflammatory bowel disease (IBD) metagenome. The results indicated that (1) the HGT networks are scale-free. (2) The networks expand their complexities, sizes, and edge numbers, accompanying the early stage of lives; and microbiota established in children shared high similarity as their mother (p-value&#xa0;=&#xa0;0.0138), supporting the transmission of microbiota from mother to child. (3) Groups harbor group-specific network edges, and network communities, which can potentially serve as biomarkers. For instances, IBD patient group harbors highly abundant communities of Proteobacteria (p-value&#xa0;=&#xa0;0.0194) and Actinobacteria (p-value&#xa0;=&#xa0;0.0316); children host highly abundant communities of Proteobacteria (p-value&#xa0;=&#xa0;2.8785 e - 5) and Actinobacteria (p-value&#xa0;=&#xa0;0.0015), and the mothers host highly abundant communities of Firmicutes (p-value&#xa0;=&#xa0;8.0091 e - 7). IBD patient networks contain more HGT edges in pathogenic genus, including Mycobacterium, Sutterella, and Pseudomonas. Children's networks contain more edges from Bifidobacterium and Escherichia.<br><br>CONCLUSION: Hence, we proposed the HGT network constructions from the gut microbiota sequencing data. The HGT networks capture the host state and the response of microbiota to the environmental and host changes, and they are essential to understand the human microbiota.}, }
@article {pmid32670207, year = {2020}, author = {Castro-Jaimes, S and Bello-López, E and Velázquez-Acosta, C and Volkow-Fernández, P and Lozano-Zarain, P and Castillo-Ramírez, S and Cevallos, MA}, title = {Chromosome Architecture and Gene Content of the Emergent Pathogen Acinetobacter haemolyticus.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {926}, pmid = {32670207}, issn = {1664-302X}, abstract = {Acinetobacter haemolyticus is a Gammaproteobacterium that has been involved in serious diseases frequently linked to the nosocomial environment. Most of the strains causing such infections are sensitive to a wide variety of antibiotics, but recent reports indicate that this pathogen is acquiring very efficiently carbapenem-resistance determinants like the blaNDM-1 gene, all over the world. With this work we contribute with a collection set of 31 newly sequenced nosocomial A. haemolyticus isolates. Genome analysis of these sequences and others collected from RefSeq indicates that their chromosomes are organized in 12 syntenic blocks that contain most of the core genome genes. These blocks are separated by hypervariable regions that are rich in unique gene families, but also have signals of horizontal gene transfer. Genes involved in virulence or encoding different secretion systems are located inside syntenic regions and have recombination signals. The relative order of the synthetic blocks along the A. haemolyticus chromosome can change, indicating that they have been subject to several kinds of inversions. Genomes of this microorganism show large differences in gene content even if they are in the same clade. Here we also show that A. haemolyticus has an open pan-genome.}, }
@article {pmid32669470, year = {2020}, author = {Pedersen, T and Tellevik, MG and Kommedal, &#xd8; and Lindemann, PC and Moyo, SJ and Janice, J and Blomberg, B and Samuelsen, &#xd8; and Langeland, N}, title = {Horizontal Plasmid Transfer among Klebsiella pneumoniae Isolates Is the Key Factor for Dissemination of Extended-Spectrum β-Lactamases among Children in Tanzania.}, journal = {mSphere}, volume = {5}, number = {4}, pages = {}, pmid = {32669470}, issn = {2379-5042}, mesh = {Bacterial Typing Techniques ; DNA, Bacterial/genetics ; Disease Outbreaks ; Drug Resistance, Multiple, Bacterial ; Female ; Gene Transfer, Horizontal ; Hospitalization ; Humans ; Infant ; Klebsiella Infections/*epidemiology/microbiology ; Klebsiella pneumoniae/*enzymology/*genetics ; Male ; Multilocus Sequence Typing ; Phylogeny ; Plasmids/genetics ; Tanzania/epidemiology ; Whole Genome Sequencing ; beta-Lactamases/*genetics ; }, abstract = {Increased knowledge about the role of horizontal gene transfer is key to improve our understanding of the spread of antimicrobial resistance (AMR) in human populations. We therefore studied the dissemination of the blaCTX-M-15 extended-spectrum-β-lactamase (ESBL) gene in Klebsiella pneumoniae isolates obtained from stool samples from hospitalized children and healthy controls below 2 years of age in Dar es Salaam, Tanzania, from August 2010 to July 2011. We performed Illumina whole-genome sequencing (WGS) to characterize resistance genes, multilocus sequence type (MLST), plasmid incompatibility group (Inc), and plasmid MLST of 128 isolates of K. pneumoniae with blaCTX-M-15 recovered from both healthy and hospitalized children. We assessed the phylogenetic relationship using single nucleotide polymorphism (SNP)-based analysis and resolved the sequences of five reference plasmids by Oxford Nanopore technology to investigate plasmid dissemination. The WGS analyses revealed the presence of a blaCTX-M-15-positive IncFIIK5/IncR plasmid with a highly conserved backbone in 70% (90/128) of the isolates. This plasmid, harboring genes encoding resistance to most β-lactams, aminoglycosides, trimethoprim-sulfamethoxazole, and chloramphenicol, was present in phylogenetically very diverse K. pneumoniae strains (48 different MLSTs) carried by both hospitalized and healthy children. Our data strongly suggest widespread horizontal transfer of this ESBL-carrying plasmid both in hospitals and in the general population.IMPORTANCE Horizontal spread of plasmids carrying multiple resistance genes is considered an important mechanism behind the global health problem caused by multidrug-resistant bacteria. Nevertheless, knowledge about spread of plasmids in a community is limited. Our detailed molecular analyses of K. pneumoniae isolated from hospitalized and healthy children in Tanzania disclosed an epidemic spread of a resistance plasmid. In this study population, we revealed horizontal plasmid transfer among K. pneumoniae as the key factor for dissemination of ESBLs. Traditional outbreak investigation and surveillance focus on the spread of bacterial clones, and short-read sequencing can result in erroneous plasmid composition. Our approach using long-read sequencing reveals horizontal gene transfer of antimicrobial resistance, and therefore has a potential impact on outbreak investigations and approaches to limit spread of AMR.}, }
@article {pmid32669211, year = {2020}, author = {Pachanon, R and Koide, K and Kongsoi, S and Nakajima, C and Kapalamula, TF and Suthienkul, O and Suzuki, Y}, title = {Interaction of the plasmid-encoded quinolone resistance protein QnrB19 with Salmonella Typhimurium DNA gyrase.}, journal = {Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy}, volume = {26}, number = {11}, pages = {1139-1145}, doi = {10.1016/j.jiac.2020.06.002}, pmid = {32669211}, issn = {1437-7780}, mesh = {Anti-Bacterial Agents/pharmacology ; *DNA Gyrase/genetics ; Drug Resistance, Bacterial/genetics ; Escherichia coli/genetics ; Humans ; Microbial Sensitivity Tests ; Plasmids/genetics ; *Quinolones/pharmacology ; Salmonella typhimurium/genetics ; }, abstract = {BACKGROUND: Plasmid-encoded quinolone resistance protein Qnr is an important factor in bacterial resistance to quinolones. Qnr interacts with DNA gyrase and reduces susceptibility to quinolones. The gene qnr likely spreads rapidly among Enterobacteriaceae via horizontal gene transfer. Though the vast amounts of epidemiological data are available, molecular details of the contribution of QnrB19, the predominant Qnr in Salmonella spp., to the acquisition of quinolone resistance has not yet been understood well.<br><br>OBJECTIVE: We aimed to examine the role of QnrB19 in quinolone resistance acquisition using recombinant Salmonella Typhimurium DNA gyrases and QnrB19.<br><br>MATERIALS AND METHODS: Recombinant QnrB19 was expressed in E.&#xa0;coli and purified by Ni-NTA agarose column chromatography. DNA supercoiling activities of recombinant Salmonella Typhimurium DNA gyrase were assessed with or without QnrB19 under the existence of three quinolones to measure IC50s, the concentration of each quinolone required for 50% inhibition in&#xa0;vitro.<br><br>RESULTS: The IC50s of norfloxacin, ciprofloxacin and nalidixic acid against DNA gyrases were measured to be 0.30, 0.16 and 17.7&#xa0;&#x3bc;g/mL, respectively. The addition of QnrB19 increased the IC50s of norfloxacin and ciprofloxacin to be 0.81 and 0.48&#xa0;&#x3bc;g/mL, respectively, where no effect of QnrB19 was observed on the IC50 of nalidixic acid.<br><br>CONCLUSION: QnrB19 was shown for the first time in&#xa0;vitro to have ability to grant non-classical quinolone resistance to S. Typhimurium DNA gyrase. Structural insight on quinolones in this study may contribute to investigate drugs useful for preventing the spread of plasmid carrying PMQR along with other factors associating with antimicrobial resistance in S. Typhimurium and other bacteria.}, }
@article {pmid32668354, year = {2020}, author = {Wang, J and Qin, X and Guo, J and Jia, W and Wang, Q and Zhang, M and Huang, Y}, title = {Evidence of selective enrichment of bacterial assemblages and antibiotic resistant genes by microplastics in urban rivers.}, journal = {Water research}, volume = {183}, number = {}, pages = {116113}, doi = {10.1016/j.watres.2020.116113}, pmid = {32668354}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents ; Bacteria ; China ; *Drug Resistance, Bacterial/genetics ; Ecosystem ; Environmental Monitoring ; Genes, Bacterial ; Humans ; Microplastics ; Plastics ; *Rivers ; Water Pollutants, Chemical/*analysis ; }, abstract = {The ubiquitous presence of microplastics in aquatic environments has recently drawn considerable attention due to their potential threat to the entire ecosystem. The colonization of bacterial communities on microplastics is an important ecological linkage for microplastics in aquatic ecosystems, which is yet poorly understood. In this study, microplastic particles were sampled in two urbanized rivers in Jiaxing, Zhejiang, China, and the differences between bacterial assemblages colonizing microplastics and planktonic bacteria were estimated. Results from high-throughput sequencing showed that the bacterial communities on microplastics were less rich and diverse compared to those from the freshwater samples, with a significantly distinct taxonomic composition. The predicted functional profiles also indicated significant differences between microplastic and water samples. The functions related to biofilm formation and human diseases were relatively higher for the bacterial communities on the microplastics. Network analyses suggested that microplastic bacterial communities possessed higher average path length, clustering coefficient, and modularity compared to those in water samples. Additionally, quantitative PCR results showed microplastics selectively enriched antibiotic resistant genes (ARGs), and a good-fit correlation between ARG profiles and bacterial community composition was observed. The relative abundances of integron-integrase gene classes 1 and 2 were greater on microplastics, potentially suggesting a higher level of horizontal gene transfer. Findings of this study suggested microplastics are a novel microbial niche and may serve as hotspots for microbial interaction, potentially increasing risks to freshwater ecosystems and human health.}, }
@article {pmid32667508, year = {2020}, author = {Forero, D and Campos, LA and Castro-Huertas, V and Bianchi, FM}, title = {Evolutionary mechanisms for camouflage in Cladomorphus phyllinus (Phasmatodea): A reflection on the role of evidence for hypotheses proposition.}, journal = {Anais da Academia Brasileira de Ciencias}, volume = {92}, number = {2}, pages = {e20200197}, doi = {10.1590/0001-3765202020200197}, pmid = {32667508}, issn = {1678-2690}, mesh = {*Biological Evolution ; }, abstract = {We address and discuss some of the many flaws exhibited by Costa et al. (2019) which tried to explain the twig-like camouflage of Cladomorphus phyllinus. Given the lack of both empirical and theoretical underpinnings in Costa et al. (2019), we call into question the validity of their conclusions, in particular, that horizontal gene transfer is a causal mechanism for the camouflage in C. phyllinus.}, }
@article {pmid32665274, year = {2020}, author = {Kogay, R and Wolf, YI and Koonin, EV and Zhaxybayeva, O}, title = {Selection for Reducing Energy Cost of Protein Production Drives the GC Content and Amino Acid Composition Bias in Gene Transfer Agents.}, journal = {mBio}, volume = {11}, number = {4}, pages = {}, pmid = {32665274}, issn = {2150-7511}, mesh = {Alphaproteobacteria/*genetics ; Amino Acids ; Bacterial Proteins/*genetics ; Bacteriophages/genetics ; Base Composition ; *Gene Transfer, Horizontal ; Genes, Viral ; Genome, Bacterial ; Prophages/genetics ; }, abstract = {Gene transfer agents (GTAs) are virus-like elements integrated into bacterial genomes, particularly, those of Alphaproteobacteria The GTAs can be induced under conditions of nutritional stress, incorporate random fragments of bacterial DNA into miniphage particles, lyse the host cells, and infect neighboring bacteria, thus enhancing horizontal gene transfer. We show that GTA genes evolve under conditions of pronounced positive selection for the reduction of the energy cost of protein production as shown by comparison of the amino acid compositions with those of both homologous viral genes and host genes. The energy saving in GTA genes is comparable to or even more pronounced than that in the genes encoding the most abundant, essential bacterial proteins. In cases in which viruses acquire genes from GTAs, the bias in amino acid composition disappears in the course of evolution, showing that reduction of the energy cost of protein production is an important factor of evolution of GTAs but not bacterial viruses. These findings strongly suggest that GTAs represent bacterial adaptations rather than selfish, virus-like elements. Because GTA production kills the host cell and does not propagate the GTA genome, it appears likely that the GTAs are retained in the course of evolution via kin or group selection. Therefore, we hypothesize that GTAs facilitate the survival of bacterial populations under energy-limiting conditions through the spread of metabolic and transport capabilities via horizontal gene transfer and increases in nutrient availability resulting from the altruistic suicide of GTA-producing cells.IMPORTANCE Kin selection and group selection remain controversial topics in evolutionary biology. We argue that these types of selection are likely to operate in bacterial populations by showing that bacterial gene transfer agents (GTAs), but not related viruses, evolve under conditions of positive selection for the reduction of the energy cost of GTA particle production. We hypothesize that GTAs are dedicated devices mediating the survival of bacteria under conditions of nutrient limitation. The benefits conferred by GTAs under nutritional stress conditions appear to include horizontal dissemination of genes that could provide bacteria with enhanced capabilities for nutrient utilization and increases of nutrient availability occurring through the lysis of GTA-producing bacteria.}, }
@article {pmid32658920, year = {2020}, author = {Grace, CA and Carr, M}, title = {The evolutionary history of mariner elements in stalk-eyed flies reveals the horizontal transfer of transposons from insects into the genome of the cnidarian Hydra vulgaris.}, journal = {PloS one}, volume = {15}, number = {7}, pages = {e0235984}, pmid = {32658920}, issn = {1932-6203}, mesh = {Animals ; *DNA Transposable Elements ; Diptera/classification/*genetics ; *Evolution, Molecular ; Eye/anatomy &amp; histology/growth &amp; development/metabolism ; *Gene Transfer, Horizontal ; *Genome ; Host-Pathogen Interactions/*genetics ; Hydra/physiology ; Insect Proteins/*genetics ; Phylogeny ; }, abstract = {The stalk-eyed flies (Diopsidae, Diptera) are a family of approximately 100 species of calypterate dipterans, characterised by extended head capsules. Species within the family have previously been shown to possess six subfamilies of mariner transposons, with nucleotide substitution patterns suggesting that at least two subfamilies are currently active. The vertumnana subfamily has been shown to have been involved in a horizontal transfer event involving Diopsidae and a second dipteran family in the Tephritidae. Presented here are cloned and sequenced mariner elements from three further diopsid species, in addition to a bioinformatic analysis of mariner elements identified in transcriptomic and genomic data from the genus Teleopsis. The newly identified mariner elements predominantly fall into previously recognised subfamilies, however the publicly available Teleopsis data also revealed a novel subfamily. Three of the seven identified subfamilies are shown to have undergone horizontal transfer, two of which appear to involve diopsid donor species. One recipient group of a diopsid mariner is the Bactrocera genus of tephritid flies, the transfer of which was previously proposed in an earlier study of diopsid mariner elements. The second horizontal transfer, of the mauritiana subfamily, can be traced from the Teleopsis genus to the cnidarian Hydra vulgaris. The mauritiana elements are shown to be active in the recipient H. vulgaris and transposase expression is observed in all body tissues examined in both species. The increased diversity of diopsid mariner elements points to a minimum of four subfamilies being present in the ancestral genome. Both vertical inheritance and stochastic loss of TEs have subsequently occurred within the diopsid radiation. The TE complement of H. vulgaris contains at least two mariner subfamilies of insect origin. Despite the phylogenetic distance between donor and recipient species, both subfamilies are shown to be active and proliferating within H. vulgaris.}, }
@article {pmid32658259, year = {2020}, author = {Hollensteiner, J and Schneider, D and Poehlein, A and Daniel, R}, title = {Complete Genome of Roseobacter ponti DSM 106830T.}, journal = {Genome biology and evolution}, volume = {12}, number = {7}, pages = {1013-1018}, pmid = {32658259}, issn = {1759-6653}, mesh = {Gene Transfer, Horizontal ; *Genome, Bacterial ; Phylogeny ; Roseobacter/*genetics/metabolism ; }, abstract = {Members of the Roseobacter group are known for their different ecologically relevant metabolic traits and high abundance in many marine environments. This includes traits like carbon monoxide oxidation, sulfur oxidation, nitrogen oxidation, DMSP demethylation, denitrification, and production of bioactive compounds. Nevertheless, their role in the marine biogeochemical cycles remains to be elucidated. Roseobacter ponti DSM 106830T, also designated strain MM-7T (=KCTC 52469T =NBRC 112431T), is a novel type strain of the Roseobacter group, which was proposed as new Roseobacter species. It was isolated from seawater of the Yellow Sea in South Korea. We report the complete genome sequence of R. ponti DSM 106830T, which belongs to the family Rhodobacteraceae. The genome of R. ponti DSM 106830T comprises a single circular chromosome (3,861,689 bp) with a GC content of 60.52% and an additional circular plasmid (p1) of 100,942 bp with a GC content of 61.51%. The genome encodes 3,812 putative genes, including 3 rRNA, 42 tRNA, 1 tmRNA, and 3 ncRNA. The genome information was used to perform a phylogenetic analysis, which confirmed that the strain represents a new species. Moreover, the genome sequence enabled the investigation of the metabolic capabilities and versatility of R. ponti DSM 106830T. Finally, it provided insight into the high niche adaptation potential of Roseobacter group members.}, }
@article {pmid32656745, year = {2020}, author = {Brovedan, MA and Cameranesi, MM and Limansky, AS and Morán-Barrio, J and Marchiaro, P and Repizo, GD}, title = {What do we know about plasmids carried by members of the Acinetobacter genus?.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {36}, number = {8}, pages = {109}, doi = {10.1007/s11274-020-02890-7}, pmid = {32656745}, issn = {1573-0972}, support = {PICT-2017-3536//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; PIP2017-11220170100377CO//Consejo Nacional de Investigaciones Cient&#xed;ficas y T&#xe9;cnicas (AR)/ ; }, mesh = {Acinetobacter baumannii/*genetics ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics/metabolism ; DNA, Bacterial/*genetics/isolation &amp; purification ; Drug Resistance, Multiple, Bacterial/genetics ; Plasmids/*genetics ; Sequence Analysis, DNA ; }, abstract = {Several Acinetobacter spp. act as opportunistic pathogens causing healthcare-associated infections worldwide, and in this respect their ability to resist antimicrobial compounds has certainly boosted up their global propagation. Acinetobacter clinical strains have demonstrated a remarkable ability to evolve and become resistant to almost all available drugs in the antimicrobial arsenal, including the last-resort carbapenem β-lactams. The dissemination of antimicrobial resistant genes (ARG), heavy metals-detoxification systems and other traits such as virulence factors is facilitated by mobile genetic elements (MGE) through horizontal gene transfer. Among them, plasmids have been shown to play a critical role in this genus. Despite the continuous increase of Acinetobacter plasmid sequences present in databases, there are no reports describing the basic traits carried by these MGE. To fill this gap, a broad analysis of the Acinetobacter plasmidome was performed. A search for Acinetobacter complete plasmids indicated that 905 sequences have been deposited in the NCBI-GenBank public database, of which 492 are harbored by Acinetobacter baumannii strains. Plasmid-classification schemes based on Rep proteins homology have so far described 23 different groups for A. baumannii (GR1-23), and 16 Acinetobacter Rep3 Groups (AR3G1-16) for the complete genus. Acinetobacter plasmids size ranges from 1.3 to 400 kb. Interestingly, widespread plasmids which are < 20 kb make up 56% of the total present in members of this genus. This led to the proposal of Acinetobacter plasmid assignation to two groups according to their size (< 20 kb and > 20 kb). Usually, smaller plasmids are not self-transmissible, and thereby employ alternative mechanisms of dissemination. For instance, a subgroup of < 20 kb-plasmids belonging to the pRAY-family, lack a rep gene, but encode a relaxase enabling their mobilization by conjugative plasmids. Other subgroup, including small GR2 Acinetobacter plasmids, does not encode a relaxase gene. However, they could still be mobilized by conjugative plasmids which recognize an oriT region carried by these small plasmids. Also, these < 20 kb-plasmids usually carry accessory genes bordered by XerC/D-recombinases recognition sites which have been hypothesized to mediate plasmid plasticity. Conversely, many cases of larger plasmids are self-transmissible and might encode virulence factors and their regulators, thus controlling strain pathogenicity. The ARGs carried by the > 20 kb-plasmids are usually encoded within other MGEs such as transposons, or as part of integrons. It has been recently noted that some of the > 20 kb-plasmids are derived from excised phages, and thus dubbed as phage-like plasmids. All in all, the plethora of plasmids found in strains of this genus and the multiple strategies promoting their evolution and dissemination have certainly contributed to survival of the Acinetobacter members in different habitats, including the clinical environment.}, }
@article {pmid32656099, year = {2020}, author = {Bohr, LL and Mortimer, TD and Pepperell, CS}, title = {Lateral Gene Transfer Shapes Diversity of Gardnerella spp.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {293}, pmid = {32656099}, issn = {2235-2988}, support = {R01 AI113287/AI/NIAID NIH HHS/United States ; T32 GM007215/GM/NIGMS NIH HHS/United States ; }, mesh = {Female ; Gardnerella ; Gene Transfer, Horizontal ; Humans ; Infant, Newborn ; *Microbiota/genetics ; Pregnancy ; *Premature Birth ; *Vaginosis, Bacterial ; }, abstract = {Gardnerella spp. are pathognomonic for bacterial vaginosis, which increases the risk of preterm birth and the transmission of sexually transmitted infections. Gardnerella spp. are genetically diverse, comprising what have recently been defined as distinct species with differing functional capacities. Disease associations with Gardnerella spp. are not straightforward: patients with BV are usually infected with multiple species, and Gardnerella spp. are also found in the vaginal microbiome of healthy women. Genome comparisons of Gardnerella spp. show evidence of lateral gene transfer (LGT), but patterns of LGT have not been characterized in detail. Here we sought to define the role of LGT in shaping the genetic structure of Gardnerella spp. We analyzed whole genome sequencing data for 106 Gardnerella strains and used these data for pan genome analysis and to characterize LGT in the core and accessory genomes, over recent and remote timescales. In our diverse sample of Gardnerella strains, we found that both the core and accessory genomes are clearly differentiated in accordance with newly defined species designations. We identified putative competence and pilus assembly genes across most species; we also found them to be differentiated between species. Competence machinery has diverged in parallel with the core genome, with selection against deleterious mutations as a predominant influence on their evolution. By contrast, the virulence factor vaginolysin, which encodes a toxin, appears to be readily exchanged among species. We identified five distinct prophage clusters in Gardnerella genomes, two of which appear to be exchanged between Gardnerella species. Differences among species are apparent in their patterns of LGT, including their exchange with diverse gene pools. Despite frequent LGT and co-localization in the same niche, our results show that Gardnerella spp. are clearly genetically differentiated and yet capable of exchanging specific genetic material. This likely reflects complex interactions within bacterial communities associated with the vaginal microbiome. Our results provide insight into how such interactions evolve and are maintained, allowing these multi-species communities to colonize and invade human tissues and adapt to antibiotics and other stressors.}, }
@article {pmid32655527, year = {2020}, author = {Kawano, H and Suzuki-Minakuchi, C and Sugiyama, D and Watanabe, N and Takahashi, Y and Okada, K and Nojiri, H}, title = {A Novel Small RNA on the Pseudomonas putida KT2440 Chromosome Is Involved in the Fitness Cost Imposed by IncP-1 Plasmid RP4.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1328}, pmid = {32655527}, issn = {1664-302X}, abstract = {Plasmids can provide advantageous traits to host bacteria, although they may impose a fitness cost. Chromosome-encoded factors are important for regulating the expression of genes on plasmids, and host chromosomes may differ in terms of their interactions with a given plasmid. Accordingly, differences in fitness cost loading and compensatory co-evolution may occur for various host chromosome/plasmid combinations. However, the mechanisms of compensatory evolution are highly divergent and require further insights. Here, we reveal novel evolutionally mechanisms of Pseudomonas putida KT2440 to improve the fitness cost imposed by the incompatibility P-1 (IncP-1) multidrug resistance plasmid RP4. A mixed culture of RP4-harboring and -free KT2440 cells was serially transferred every 24 h under non-selective conditions. Initially, the proportion of RP4-harboring cells decreased rapidly, but it immediately recovered, suggesting that the fitness of RP4-harboring strains improved during cultivation. Larger-sized colonies appeared during 144-h mixed culture, and evolved strains isolated from larger-sized colonies showed higher growth rates and fitness than those of the ancestral strain. Whole-genome sequencing revealed that evolved strains had one of two mutations in the same intergenic region of the chromosome. Based on the research of another group, this region is predicted to contain a stress-inducible small RNA (sRNA). Identification of the transcriptional start site in this sRNA indicated that one mutation occurred within the sRNA region, whereas the other was in its promoter region. Quantitative reverse-transcription PCR showed that the expression of this sRNA was strongly induced by RP4 carriage in the ancestral strain but repressed in the evolved strains. When the sRNA region was overexpressed in the RP4-free strain, the fitness decreased, and the colony size became smaller. Using transcriptome analysis, we also showed that the genes involved in amino acid metabolism and stress responses were differentially transcribed by overexpression of the sRNA region. These results indicate that the RP4-inducible chromosomal sRNA was responsible for the fitness cost of RP4 on KT2440 cells, where this sRNA is of key importance in host evolution toward rapid amelioration of the cost.}, }
@article {pmid32655523, year = {2020}, author = {Maruyama, H and Prieto, EI and Nambu, T and Mashimo, C and Kashiwagi, K and Okinaga, T and Atomi, H and Takeyasu, K}, title = {Different Proteins Mediate Step-Wise Chromosome Architectures in Thermoplasma acidophilum and Pyrobaculum calidifontis.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1247}, pmid = {32655523}, issn = {1664-302X}, abstract = {Archaeal species encode a variety of distinct lineage-specific chromosomal proteins. We have previously shown that in Thermococcus kodakarensis, histone, Alba, and TrmBL2 play distinct roles in chromosome organization. Although our understanding of individual archaeal chromosomal proteins has been advancing, how archaeal chromosomes are folded into higher-order structures and how they are regulated are largely unknown. Here, we investigated the primary and higher-order structures of archaeal chromosomes from different archaeal lineages. Atomic force microscopy of chromosome spreads out of Thermoplasma acidophilum and Pyrobaculum calidifontis cells revealed 10-nm fibers and 30-40-nm globular structures, suggesting the occurrence of higher-order chromosomal folding. Our results also indicated that chromosome compaction occurs toward the stationary phase. Micrococcal nuclease digestion indicated that fundamental structural units of the chromosome exist in T. acidophilum and T. kodakarensis but not in P. calidifontis or Sulfolobus solfataricus. In vitro reconstitution showed that, in T. acidophilum, the bacterial HU protein homolog HTa formed a 6-nm fiber by wrapping DNA, and that Alba was responsible for the formation of the 10-nm fiber by binding along the DNA without wrapping. Remarkably, Alba could form different higher-order complexes with histone or HTa on DNA in vitro. Mass spectrometry detected HTa and Rad50 in the T. acidophilum chromosome but not in other species. A putative transcriptional regulator of the AsnC/Lrp family (Pcal_1183) was detected on the P. calidifontis chromosome, but not on that of other species studied. Putative membrane-associated proteins were detected in the chromosomes of the three archaeal species studied, including T. acidophilum, P. calidifontis, and T. kodakarensis. Collectively, our data show that Archaea use different combinations of proteins to achieve chromosomal architecture and functional regulation.}, }
@article {pmid32655516, year = {2020}, author = {Wang, P and Li, LZ and Qin, YL and Liang, ZL and Li, XT and Yin, HQ and Liu, LJ and Liu, SJ and Jiang, CY}, title = {Comparative Genomic Analysis Reveals the Metabolism and Evolution of the Thermophilic Archaeal Genus Metallosphaera.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1192}, pmid = {32655516}, issn = {1664-302X}, abstract = {Members of the genus Metallosphaera are widely found in sulfur-rich and metal-laden environments, but their physiological and ecological roles remain poorly understood. Here, we sequenced Metallosphaera tengchongensis Ric-A, a strain isolated from the Tengchong hot spring in Yunnan Province, China, and performed a comparative genome analysis with other Metallosphaera genomes. The genome of M. tengchongensis had an average nucleotide identity (ANI) of approximately 70% to that of Metallosphaera cuprina. Genes sqr, tth, sir, tqo, hdr, tst, soe, and sdo associated with sulfur oxidation, and gene clusters fox and cbs involved in iron oxidation existed in all Metallosphaera genomes. However, the adenosine-5'-phosphosulfate (APS) pathway was only detected in Metallosphaera sedula and Metallosphaera yellowstonensis, and several subunits of fox cluster were lost in M. cuprina. The complete 3-hydroxypropionate/4-hydroxybutyrate cycle and dicarboxylate/4-hydroxybutyrate cycle involved in carbon fixation were found in all Metallosphaera genomes. A large number of gene family gain events occurred in M. yellowstonensis and M. sedula, whereas gene family loss events occurred frequently in M. cuprina. Pervasive strong purifying selection was found acting on the gene families of Metallosphaera, of which transcription-related genes underwent the strongest purifying selection. In contrast, genes related to prophages, transposons, and defense mechanisms were under weaker purifying pressure. Taken together, this study expands knowledge of the genomic traits of Metallosphaera species and sheds light on their evolution.}, }
@article {pmid32655502, year = {2020}, author = {Yu, X and Xu, J and Gu, Y and Zhang, R and Zhu, Y and Liu, X}, title = {Molecular Characterization and Comparative Genomic Analysis of vB_PaeP_YA3, a Novel Temperate Bacteriophage of Pseudomonas aeruginosa.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {947}, pmid = {32655502}, issn = {1664-302X}, abstract = {It is well known that bacteriophages play crucial roles in many aspects, such as controlling the number and the diversity of bacteria and participating in horizontal gene transfer, which is a key process in the evolution of bacteria. However, so far, the number of temperate bacteriophages is still limited, and their life processes are severely unknown, except for members of the lambdoid family of coliphages. In this study, a novel temperate phage of Pseudomonas aeruginosa, YA3 (vB_PaeP_YA3), was isolated from waste water. The morphology of YA3 suggested that it is a Podoviridae. The YA3 genome is a circular double-stranded DNA of 45,253 bp, with an average G + C content of 57.2%. A total of 65 open reading frames (ORFs) were predicted according to the sequence of YA3's genome, of which only 32 (49.2%) ORFs were assigned with putative functions and 13 ORFs were confirmed by the structural proteome. Genome and proteome analyses confirmed the lysogenic nature of this phage, which encodes the typical lysogen-related proteins integrase, CI, Cro, and Q protein. The genome of YA3 is most closely related with that of temperate phage vB_PaeP_Tr60_Ab31, whereas the homology coverage is just 48%. There are many critical differences between their genomes, involving promoters, lysis pathways, and regulation patterns. YA3 is capable of stably lysogenizing its host P. aeruginosa PA14, targeting the integration site within the serine tRNA gene (PA14_RS20820), which is similar with phage vB_PaeP_Tr60_Ab31. The phylogenetic analysis is more complicated than we thought. Based on phage terminase large subunit (TerL) and CI proteins, phage YA3 is related with phage lambda, while their genome coverage is extremely low (<1%). Therefore, phage YA3 is a considerably novel lambda-like temperate phage, and a further study of its genome may deepen our understanding of the interaction between lysogenic phages and their bacterial hosts.}, }
@article {pmid32652213, year = {2020}, author = {Kocer, K and Boutin, S and Probst, K and Heeg, K and Nurjadi, D}, title = {Whole-genome sequencing disproves two suspected transmission events of blaNDM between Pseudomonas aeruginosa and Enterobacterales in hospitalized patients.}, journal = {The Journal of hospital infection}, volume = {106}, number = {2}, pages = {372-375}, doi = {10.1016/j.jhin.2020.07.006}, pmid = {32652213}, issn = {1532-2939}, mesh = {Aged ; Anti-Bacterial Agents/pharmacology ; Coinfection/*microbiology ; Drug Resistance, Multiple, Bacterial/*genetics ; Enterobacteriaceae/drug effects/*genetics ; *Gene Transfer, Horizontal ; Gram-Negative Bacterial Infections/microbiology ; Hospitalization ; Humans ; Male ; Middle Aged ; Plasmids/genetics ; Pseudomonas Infections/microbiology ; Pseudomonas aeruginosa/drug effects/enzymology/*genetics ; Retrospective Studies ; Whole Genome Sequencing ; beta-Lactamases/genetics ; }, abstract = {New Delhi metallo-β-lactamase (blaNDM) acquisition by Gram-negative bacteria is a primary concern due to its broad-host-range distribution. This study investigated two potential in-vivo horizontal gene transfers (HGTs) of blaNDM between Enterobacterales and Pseudomonas aeruginosa, initially indicated by polymerase chain reaction. Whole-genome sequencing showed independent parallel acquisition of two different blaNDM variants (NDM-1 and NDM-5) in P. aeruginosa and Enterobacterales, respectively. The data show that short-read sequencing provides the necessary resolution to confirm or dispute HGT by the comparison of genetic elements surrounding the gene of interest, and thus provide a timely response to potential outbreaks.}, }
@article {pmid32650149, year = {2020}, author = {Xu, L and Campos, LC and Canales, M and Ciric, L}, title = {Drinking water biofiltration: Behaviour of antibiotic resistance genes and the association with bacterial community.}, journal = {Water research}, volume = {182}, number = {}, pages = {115954}, doi = {10.1016/j.watres.2020.115954}, pmid = {32650149}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drinking Water/*analysis ; Drug Resistance, Microbial/drug effects ; Genes, Bacterial/drug effects ; }, abstract = {Antibiotic resistance genes (ARGs) are being detected in drinking water frequently, constituting a major public health issue. As a typical drinking water treatment process, the biofilter may harbour various ARGs due to the filter biofilms established during the filtration process. The objective of this study was to investigate the behaviour of ARGs (blaCTX-M, blaOXA-1, blaTEM, ermB, tetA, tetG, tetQ, tetW, tetX, sul 1, sul 2, dfrA1 and dfrA12) and their possible association with bacteria in a bench-scale biofiltration system. The impact of filter media on horizontal gene transfer (HGT) was also explored using a model conjugative plasmid, RP1. The biofiltration system comprised four types of biofilters, including sand, granular activated carbon (GAC), GAC sandwich, and anthracite-sand biofilters. Results showed that although the absolute abundance of ARGs decreased (0.97-log reduction on average), the ARGs' abundance normalised to bacterial numbers showed an increasing trend in the filtered water. Biofilms collected from the surface layer revealed the lowest relative abundance of ARGs (p < 0.01) compared to the deeper layer biofilms, indicating that the proportion of ARG-carrying bacteria was greater in the lower position. Most chosen ARG numbers correlated to Proteobacteria, Acidobacteria and Nitrospirae phyla, which accounted for 51.9%, 5.2% and 2.0% of the biofilm communities, respectively. GAC media revealed the highest transfer frequency (2.60 × 10[-5]), followed by anthracite (5.31 × 10[-6]) and sand (2.47 × 10[-6]). Backwashing can reduce the transferability of RP1 plasmid significantly in biofilms but introduces more transconjugants into the planktonic phase. Overall, the results of this study could enhance our understanding of the prevalence of ARGs in drinking water biofiltration treatment.}, }
@article {pmid32648520, year = {2020}, author = {Shrestha, P and Ni, J and Wong, TY}, title = {Synergistic and antagonistic interactions of triclosan with various antibiotics in bacteria.}, journal = {Journal of environmental science and health. Part C, Toxicology and carcinogenesis}, volume = {38}, number = {3}, pages = {187-203}, doi = {10.1080/26896583.2020.1781494}, pmid = {32648520}, issn = {2689-6591}, mesh = {Anti-Bacterial Agents/*toxicity ; *Bacteria ; Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Phylogeny ; Triclosan/toxicity ; }, abstract = {Triclosan (TCS), a well-studied antimicrobial compound and an environmental pollutant, is present in many household products. A systematic survey of TCS-antibiotic-bacteria interactions is lacking. We wish to understand the origin of such interactions by testing 16 phylogenetically well-characterized bacteria for their sensitivities to 6 different classes of antibiotics with or without the presence of TCS. Our results show that TCS interacts synergistically with some antibiotics against some Bacilli species. TCS could also interact antagonistically with other antibiotics against certain bacteria, including pathogens such as Pseudomonas aeruginosa and Stenotrophomonas maltophilia. Antagonism between drugs often coincided with the concomitant enhanced removal of Ethidium bromide (EtBr) from the cells. Enterococcus faecalis shows a unique response to TCS. High levels of TCS inhibits E. faecalis. Cells survive at lower TCS concentrations, and these cells can remove EtBr more readily than unexposed cells. At even lower TCS concentration, cell-growth is inhibited again, causing the culture to exhibit a unique extra inhibition zone around the TCS-disk. The TCS-antibiotic-bacteria interaction profiles of some bacteria do not follow their bacterial phylogenetic relations. This suggests that such interactions may be related to horizontal gene transfer among different bacteria.}, }
@article {pmid32647212, year = {2021}, author = {Ogawara, H}, title = {Possible drugs for the treatment of bacterial infections in the future: anti-virulence drugs.}, journal = {The Journal of antibiotics}, volume = {74}, number = {1}, pages = {24-41}, pmid = {32647212}, issn = {1881-1469}, mesh = {Animals ; Anti-Bacterial Agents/*chemistry/classification/history/*therapeutic use ; Bacteria/*drug effects/*pathogenicity ; Bacterial Infections/*drug therapy/microbiology ; Drug Resistance, Bacterial ; History, 20th Century ; History, 21st Century ; Humans ; Virulence ; Virulence Factors/*antagonists &amp; inhibitors ; }, abstract = {Antibiotic resistance is a global threat that should be urgently resolved. Finding a new antibiotic is one way, whereas the repression of the dissemination of virulent pathogenic bacteria is another. From this point of view, this paper summarizes first the mechanisms of conjugation and transformation, two important processes of horizontal gene transfer, and then discusses the approaches for disarming virulent pathogenic bacteria, that is, virulence factor inhibitors. In contrast to antibiotics, anti-virulence drugs do not impose a high selective pressure on a bacterial population, and repress the dissemination of antibiotic resistance and virulence genes. Disarmed virulence factors make virulent pathogens avirulent bacteria or pathobionts, so that we human will be able to coexist with these disarmed bacteria peacefully.}, }
@article {pmid32645885, year = {2020}, author = {Sánchez-Soto, D and Agüero-Chapin, G and Armijos-Jaramillo, V and Perez-Castillo, Y and Tejera, E and Antunes, A and Sánchez-Rodríguez, A}, title = {ShadowCaster: Compositional Methods under the Shadow of Phylogenetic Models to Detect Horizontal Gene Transfers in Prokaryotes.}, journal = {Genes}, volume = {11}, number = {7}, pages = {}, pmid = {32645885}, issn = {2073-4425}, mesh = {Gammaproteobacteria/classification/genetics ; *Gene Transfer, Horizontal ; *Genome, Archaeal ; *Genome, Bacterial ; Genomics/*methods ; Phylogeny ; *Software ; Support Vector Machine ; }, abstract = {Horizontal gene transfer (HGT) plays an important role for evolutionary innovations within prokaryotic communities and is a crucial event for their survival. Several computational approaches have arisen to identify HGT events in recipient genomes. However, this has been proven to be a complex task due to the generation of a great number of false positives and the prediction disagreement among the existing methods. Phylogenetic reconstruction methods turned out to be the most reliable ones, but they are not extensible to all genes/species and are computationally demanding when dealing with large datasets. In contrast, the so-called surrogate methods that use heuristic solutions either based on nucleotide composition patterns or phyletic distribution of BLAST hits can be applied easily to the genomic scale, but they fail in identifying common HGT events. Here, we present ShadowCaster, a hybrid approach that sequentially combines nucleotide composition-based predictions by support vector machines (SVMs) under the shadow of phylogenetic models independent of tree reconstruction, to improve the detection of HGT events in prokaryotes. ShadowCaster successfully predicted close and distant HGT events in both artificial and bacterial genomes. ShadowCaster detected HGT related to heavy metal resistance in the genome of Rhodanobacter denitrificans with higher accuracy than the most popular state-of-the-art computational approaches, encompassing most of the predicted cases made by other methods. ShadowCaster is released at the GitHub platform as an open-source software under the GPLv3 license.}, }
@article {pmid32640584, year = {2020}, author = {Mauritzen, JJ and Castillo, D and Tan, D and Svenningsen, SL and Middelboe, M}, title = {Beyond Cholera: Characterization of zot-Encoding Filamentous Phages in the Marine Fish Pathogen Vibrio anguillarum.}, journal = {Viruses}, volume = {12}, number = {7}, pages = {}, pmid = {32640584}, issn = {1999-4915}, mesh = {Animals ; Endotoxins/*genetics ; Fish Diseases/microbiology ; Genome, Viral/genetics ; Inovirus/*genetics ; Lysogeny/genetics ; Microscopy, Electron, Transmission ; Oncorhynchus mykiss/microbiology/virology ; Open Reading Frames/genetics ; Phylogeny ; Polymerase Chain Reaction ; Salmon/microbiology/virology ; Sequence Analysis, DNA ; Vibrio/*virology ; Vibrio Infections/microbiology/veterinary ; }, abstract = {Zonula occludens toxin (Zot) is a conserved protein in filamentous vibriophages and has been reported as a putative toxin in Vibrio cholerae. Recently, widespread distribution of zot-encoding prophages was found among marine Vibrio species, including environmental isolates. However, little is known about the dynamics of these prophages beyond V. cholerae. In this study, we characterized and quantified the zot-encoding filamentous phage VAIϕ, spontaneously induced from the fish pathogen V. anguillarum. VAIϕ contained 6117 bp encoding 11 ORFs, including ORF8[pVAI], exhibiting 27%-73% amino acid identity to Inovirus Zot-like proteins. A qPCR method revealed an average of four VAIϕ genomes per host genome during host exponential growth phase, and PCR demonstrated dissemination of induced VAIϕ to other V. anguillarum strains through re-integration in non-lysogens. VAIϕ integrated into both chromosomes of V. anguillarum by recombination, causing changes in a putative ORF in the phage genome. Phylogenetic analysis of the V. anguillarumInoviridae elements revealed mosaic genome structures related to mainly V. cholerae. Altogether, this study contributes to the understanding of Inovirus infection dynamics and mobilization of zot-like genes beyond human pathogenic vibrios, and discusses their potential role in the evolution of the fish pathogen V. anguillarum.}, }
@article {pmid32636337, year = {2020}, author = {DuPai, CD and Wilke, CO and Davies, BW}, title = {A Comprehensive Coexpression Network Analysis in Vibrio cholerae.}, journal = {mSystems}, volume = {5}, number = {4}, pages = {}, pmid = {32636337}, issn = {2379-5077}, support = {R01 AI125337/AI/NIAID NIH HHS/United States ; R21 AI137546/AI/NIAID NIH HHS/United States ; }, abstract = {Research into the evolution and pathogenesis of Vibrio cholerae has benefited greatly from the generation of high-throughput sequencing data to drive molecular analyses. The steady accumulation of these data sets now provides a unique opportunity for in silico hypothesis generation via coexpression analysis. Here, we leverage all published V. cholerae RNA sequencing data, in combination with select data from other platforms, to generate a gene coexpression network that validates known gene interactions and identifies novel genetic partners across the entire V. cholerae genome. This network provides direct insights into genes influencing pathogenicity, metabolism, and transcriptional regulation, further clarifies results from previous sequencing experiments in V. cholerae (e.g., transposon insertion sequencing [Tn-seq] and chromatin immunoprecipitation sequencing [ChIP-seq]), and expands upon microarray-based findings in related Gram-negative bacteria.IMPORTANCE Cholera is a devastating illness that kills tens of thousands of people annually. Vibrio cholerae, the causative agent of cholera, is an important model organism to investigate both bacterial pathogenesis and the impact of horizontal gene transfer on the emergence and dissemination of new virulent strains. Despite the importance of this pathogen, roughly one-third of V. cholerae genes are functionally unannotated, leaving large gaps in our understanding of this microbe. Through coexpression network analysis of existing RNA sequencing data, this work develops an approach to uncover novel gene-gene relationships and contextualize genes with no known function, which will advance our understanding of V. cholerae virulence and evolution.}, }
@article {pmid32635298, year = {2020}, author = {Wang, HC and Lin, SJ and Mohapatra, A and Kumar, R and Wang, HC}, title = {A Review of the Functional Annotations of Important Genes in the AHPND-Causing pVA1 Plasmid.}, journal = {Microorganisms}, volume = {8}, number = {7}, pages = {}, pmid = {32635298}, issn = {2076-2607}, support = {MOST106-2313-B-038-004-MY3//Ministry of Science and Technology, Taiwan/ ; MOST108-2314-B-006-096-MY3//Ministry of Science and Technology, Taiwan/ ; MOST109-2634-F-006-022//Ministry of Science and Technology, Taiwan/ ; NTOU-TMU-109-01//University System of Taipei Joint Research Program/ ; }, abstract = {Acute hepatopancreatic necrosis disease (AHPND) is a lethal shrimp disease. The pathogenic agent of this disease is a special Vibrio parahaemolyticus strain that contains a pVA1 plasmid. The protein products of two toxin genes in pVA1, pirA[vp] and pirB[vp], targeted the shrimp's hepatopancreatic cells and were identified as the major virulence factors. However, in addition to pirA[vp] and pirB[vp], pVA1 also contains about ~90 other open-reading frames (ORFs), which may encode functional proteins. NCBI BLASTp annotations of the functional roles of 40 pVA1 genes reveal transposases, conjugation factors, and antirestriction proteins that are involved in horizontal gene transfer, plasmid transmission, and maintenance, as well as components of type II and III secretion systems that may facilitate the toxic effects of pVA1-containing Vibrio spp. There is also evidence of a post-segregational killing (PSK) system that would ensure that only pVA1 plasmid-containing bacteria could survive after segregation. Here, in this review, we assess the functional importance of these pVA1 genes and consider those which might be worthy of further study.}, }
@article {pmid32634380, year = {2020}, author = {Pallegar, P and Canuti, M and Langille, E and Peña-Castillo, L and Lang, AS}, title = {A Two-Component System Acquired by Horizontal Gene Transfer Modulates Gene Transfer and Motility via Cyclic Dimeric GMP.}, journal = {Journal of molecular biology}, volume = {432}, number = {17}, pages = {4840-4855}, doi = {10.1016/j.jmb.2020.07.001}, pmid = {32634380}, issn = {1089-8638}, mesh = {Bacterial Proteins/*chemistry/genetics/*metabolism ; Cyclic GMP/*analogs &amp; derivatives/metabolism ; Escherichia coli Proteins/metabolism ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Histidine Kinase/metabolism ; Phosphoric Diester Hydrolases/metabolism ; Phosphorus-Oxygen Lyases/metabolism ; Phosphorylation ; Protein Domains ; Rhodobacter capsulatus/genetics/*metabolism ; }, abstract = {Bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) is an important intracellular signaling molecule that affects diverse physiological processes in bacteria. The intracellular levels of c-di-GMP are controlled by proteins acting as diguanylate cyclase (DGC) and phosphodiesterase (PDE) enzymes that synthesize and degrade c-di-GMP, respectively. In the alphaproteobacterium Rhodobacter capsulatus, flagellar motility and gene exchange via production of the gene transfer agent RcGTA are regulated by c-di-GMP. One of the R. capsulatus proteins involved in this regulation is Rcc00620, which contains an N-terminal two-component system response regulator receiver (REC) domain and C-terminal DGC and PDE domains. We demonstrate that the enzymatic activity of Rcc00620 is regulated through the phosphorylation status of its REC domain, which is controlled by a cognate histidine kinase protein, Rcc00621. In this system, the phosphorylated form of Rcc00620 is active as a PDE enzyme and stimulates gene transfer and motility. In addition, we discovered that the rcc00620 and rcc00621 genes are present in only one lineage within the genus Rhodobacter and were acquired via horizontal gene transfer from a distantly related alphaproteobacterium in the order Sphingomonadales. Therefore, a horizontally acquired regulatory system regulates gene transfer in the recipient organism.}, }
@article {pmid32626197, year = {2019}, author = {,  and Koutsoumanis, K and Allende, A and Alvarez-Ordóñez, A and Bolton, D and Bover-Cid, S and Chemaly, M and Davies, R and De Cesare, A and Hilbert, F and Lindqvist, R and Nauta, M and Peixe, L and Ru, G and Simmons, M and Skandamis, P and Suffredini, E and Jenkins, C and Malorny, B and Ribeiro Duarte, AS and Torpdahl, M and da Silva Felício, MT and Guerra, B and Rossi, M and Herman, L}, title = {Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food-borne microorganisms.}, journal = {EFSA journal. European Food Safety Authority}, volume = {17}, number = {12}, pages = {e05898}, pmid = {32626197}, issn = {1831-4732}, abstract = {This Opinion considers the application of whole genome sequencing (WGS) and metagenomics for outbreak investigation, source attribution and risk assessment of food-borne pathogens. WGS offers the highest level of bacterial strain discrimination for food-borne outbreak investigation and source-attribution as well as potential for more precise hazard identification, thereby facilitating more targeted risk assessment and risk management. WGS improves linking of sporadic cases associated with different food products and geographical regions to a point source outbreak and can facilitate epidemiological investigations, allowing also the use of previously sequenced genomes. Source attribution may be favoured by improved identification of transmission pathways, through the integration of spatial-temporal factors and the detection of multidirectional transmission and pathogen-host interactions. Metagenomics has potential, especially in relation to the detection and characterisation of non-culturable, difficult-to-culture or slow-growing microorganisms, for tracking of hazard-related genetic determinants and the dynamic evaluation of the composition and functionality of complex microbial communities. A SWOT analysis is provided on the use of WGS and metagenomics for Salmonella and Shigatoxin-producing Escherichia coli (STEC) serotyping and the identification of antimicrobial resistance determinants in bacteria. Close agreement between phenotypic and WGS-based genotyping data has been observed. WGS provides additional information on the nature and localisation of antimicrobial resistance determinants and on their dissemination potential by horizontal gene transfer, as well as on genes relating to virulence and biological fitness. Interoperable data will play a major role in the future use of WGS and metagenomic data. Capacity building based on harmonised, quality controlled operational systems within European laboratories and worldwide is essential for the investigation of cross-border outbreaks and for the development of international standardised risk assessments of food-borne microorganisms.}, }
@article {pmid32625182, year = {2020}, author = {Ithurbide, S and Coste, G and Lisboa, J and Eugénie, N and Bentchikou, E and Bouthier de la Tour, C and Liger, D and Confalonieri, F and Sommer, S and Quevillon-Cheruel, S and Servant, P}, title = {Natural Transformation in Deinococcus radiodurans: A Genetic Analysis Reveals the Major Roles of DprA, DdrB, RecA, RecF, and RecO Proteins.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1253}, pmid = {32625182}, issn = {1664-302X}, abstract = {Horizontal gene transfer is a major driver of bacterial evolution and adaptation to environmental stresses, occurring notably via transformation of naturally competent organisms. The Deinococcus radiodurans bacterium, characterized by its extreme radioresistance, is also naturally competent. Here, we investigated the role of D. radiodurans players involved in different steps of natural transformation. First, we identified the factors (PilQ, PilD, type IV pilins, PilB, PilT, ComEC-ComEA, and ComF) involved in DNA uptake and DNA translocation across the external and cytoplasmic membranes and showed that the DNA-uptake machinery is similar to that described in the Gram negative bacterium Vibrio cholerae. Then, we studied the involvement of recombination and DNA repair proteins, RecA, RecF, RecO, DprA, and DdrB into the DNA processing steps of D. radiodurans transformation by plasmid and genomic DNA. The transformation frequency of the cells devoid of DprA, a highly conserved protein among competent species, strongly decreased but was not completely abolished whereas it was completely abolished in ΔdprA ΔrecF, ΔdprA ΔrecO, and ΔdprA ΔddrB double mutants. We propose that RecF and RecO, belonging to the recombination mediator complex, and DdrB, a specific deinococcal DNA binding protein, can replace a function played by DprA, or alternatively, act at a different step of recombination with DprA. We also demonstrated that a ΔdprA mutant is as resistant as wild type to various doses of γ-irradiation, suggesting that DprA, and potentially transformation, do not play a major role in D. radiodurans radioresistance.}, }
@article {pmid32625173, year = {2020}, author = {Miyakoshi, M and Ohtsubo, Y and Nagata, Y and Tsuda, M}, title = {Transcriptome Analysis of Zygotic Induction During Conjugative Transfer of Plasmid RP4.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1125}, pmid = {32625173}, issn = {1664-302X}, abstract = {Conjugative transfer of bacterial plasmid is one of the major mechanisms of horizontal gene transfer, which is mediated by direct contact between donor and recipient cells. Gene expression of a conjugative plasmid is tightly regulated mostly by plasmid-encoded transcriptional regulators, but it remains obscure how differently plasmid genes are expressed in each cell during the conjugation event. Here, we report a comprehensive analysis of gene expression during conjugative transfer of plasmid RP4, which is transferred between isogenic strains of Pseudomonas putida KT2440 at very high frequency. To discriminate the expression changes in the donor and recipient cells, we took advantage of conjugation in the presence of rifampicin (Rif). Within 10 min of mating, we successfully detected transient transcription of plasmid genes in the resultant transconjugant cells. This phenomenon known as zygotic induction is likely attributed to derepression of multiple RP4-encoded repressors. Interestingly, we also observed that the traJIH operon encoding relaxase and its auxiliary proteins were upregulated specifically in the donor cells. Identification of the 5' end of the zygotically induced traJ mRNA confirmed that the transcription start site of traJ was located 24-nt upstream of the nick site in the origin of transfer (oriT) as previously reported. Since the traJ promoter is encoded on the region to be transferred first, the relaxase may be expressed in the donor cell after regeneration of the oriT-flanking region, which in itself is likely to displace the autogenous repressors around oriT. This study provides new insights into the regulation of plasmid transfer processes.}, }
@article {pmid32619486, year = {2020}, author = {Zhang, Z and Qu, C and Zhang, K and He, Y and Zhao, X and Yang, L and Zheng, Z and Ma, X and Wang, X and Wang, W and Wang, K and Li, D and Zhang, L and Zhang, X and Su, D and Chang, X and Zhou, M and Gao, D and Jiang, W and Leliaert, F and Bhattacharya, D and De Clerck, O and Zhong, B and Miao, J}, title = {Adaptation to Extreme Antarctic Environments Revealed by the Genome of a Sea Ice Green Alga.}, journal = {Current biology : CB}, volume = {30}, number = {17}, pages = {3330-3341.e7}, doi = {10.1016/j.cub.2020.06.029}, pmid = {32619486}, issn = {1879-0445}, mesh = {*Adaptation, Physiological ; Algal Proteins/*genetics/metabolism ; Antarctic Regions ; Chlamydomonas/genetics/*physiology ; *Extreme Environments ; *Gene Expression Regulation ; *Genome ; Ice Cover ; Phylogeny ; Salinity ; *Transcriptome ; Whole Genome Sequencing ; }, abstract = {The unicellular green alga Chlamydomonas sp. ICE-L thrives in polar sea ice, where it tolerates extreme low temperatures, high salinity, and broad seasonal fluctuations in light conditions. Despite the high interest in biotechnological uses of this species, little is known about the adaptations that allow it to thrive in this harsh and complex environment. Here, we assembled a high-quality genome sequence of ∼542 Mb and found that retrotransposon proliferation contributed to the relatively large genome size of ICE-L when compared to other chlorophytes. Genomic features that may support the extremophilic lifestyle of this sea ice alga include massively expanded gene families involved in unsaturated fatty acid biosynthesis, DNA repair, photoprotection, ionic homeostasis, osmotic homeostasis, and reactive oxygen species detoxification. The acquisition of multiple ice binding proteins through putative horizontal gene transfer likely contributed to the origin of the psychrophilic lifestyle in ICE-L. Additional innovations include the significant upregulation under abiotic stress of several expanded ICE-L gene families, likely reflecting adaptive changes among diverse metabolic processes. Our analyses of the genome, transcriptome, and functional assays advance general understanding of the Antarctic green algae and offer potential explanations for how green plants adapt to extreme environments.}, }
@article {pmid32618561, year = {2020}, author = {Xu, F and Jiménez-González, A and Einarsson, E and Ástvaldsson, &#xc1; and Peirasmaki, D and Eckmann, L and Andersson, JO and Svärd, SG and Jerlström-Hultqvist, J}, title = {The compact genome of Giardia muris reveals important steps in the evolution of intestinal protozoan parasites.}, journal = {Microbial genomics}, volume = {6}, number = {8}, pages = {}, pmid = {32618561}, issn = {2057-5858}, support = {P30 DK120515/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Antigens, Protozoan/*genetics ; *Biological Evolution ; Genome, Protozoan ; *Giardia/genetics/immunology ; Giardiasis/*parasitology ; Host-Pathogen Interactions ; Humans ; Mice ; *Protozoan Proteins/genetics/immunology ; Species Specificity ; *Virulence Factors/genetics/immunology ; }, abstract = {Diplomonad parasites of the genus Giardia have adapted to colonizing different hosts, most notably the intestinal tract of mammals. The human-pathogenic Giardia species, Giardia intestinalis, has been extensively studied at the genome and gene expression level, but no such information is available for other Giardia species. Comparative data would be particularly valuable for Giardia muris, which colonizes mice and is commonly used as a prototypic in vivo model for investigating host responses to intestinal parasitic infection. Here we report the draft-genome of G. muris. We discovered a highly streamlined genome, amongst the most densely encoded ever described for a nuclear eukaryotic genome. G. muris and G. intestinalis share many known or predicted virulence factors, including cysteine proteases and a large repertoire of cysteine-rich surface proteins involved in antigenic variation. Different to G. intestinalis, G. muris maintains tandem arrays of pseudogenized surface antigens at the telomeres, whereas intact surface antigens are present centrally in the chromosomes. The two classes of surface antigens engage in genetic exchange. Reconstruction of metabolic pathways from the G. muris genome suggest significant metabolic differences to G. intestinalis. Additionally, G. muris encodes proteins that might be used to modulate the prokaryotic microbiota. The responsible genes have been introduced in the Giardia genus via lateral gene transfer from prokaryotic sources. Our findings point to important evolutionary steps in the Giardia genus as it adapted to different hosts and it provides a powerful foundation for mechanistic exploration of host-pathogen interaction in the G. muris-mouse pathosystem.}, }
@article {pmid32617187, year = {2020}, author = {Emrizal, R and Nor Muhammad, NA}, title = {Phylogenetic comparison between Type IX Secretion System (T9SS) protein components suggests evidence of horizontal gene transfer.}, journal = {PeerJ}, volume = {8}, number = {}, pages = {e9019}, pmid = {32617187}, issn = {2167-8359}, abstract = {Porphyromonas gingivalis is one of the major bacteria that causes periodontitis. Chronic periodontitis is a severe form of periodontal disease that ultimately leads to tooth loss. Virulence factors that contribute to periodontitis are secreted by Type IX Secretion System (T9SS). There are aspects of T9SS protein components that have yet to be characterised. Thus, the aim of this study is to investigate the phylogenetic relationship between members of 20 T9SS component protein families. The Bayesian Inference (BI) trees for 19 T9SS protein components exhibit monophyletic clades for all major classes under Bacteroidetes with strong support for the monophyletic clades or its subclades that is consistent with phylogeny exhibited by the constructed BI tree of 16S rRNA. The BI tree of PorR is different from the 19 BI trees of T9SS protein components as it does not exhibit monophyletic clades for all major classes under Bacteroidetes. There is strong support for the phylogeny exhibited by the BI tree of PorR which deviates from the phylogeny based on 16S rRNA. Hence, it is possible that the porR gene is subjected to horizontal transfer as it is known that virulence factor genes could be horizontally transferred. Seven genes (porR included) that are involved in the biosynthesis of A-LPS are found to be flanked by insertion sequences (IS5 family transposons). Therefore, the intervening DNA segment that contains the porR gene might be transposed and subjected to conjugative transfer. Thus, the seven genes can be co-transferred via horizontal gene transfer. The BI tree of UgdA does not exhibit monophyletic clades for all major classes under Bacteroidetes which is similar to the BI tree of PorR (both are a part of the seven genes). Both BI trees also exhibit similar topology as the four identified clusters with strong support and have similar relative positions to each other in both BI trees. This reinforces the possibility that porR and the other six genes might be horizontally transferred. Other than the BI tree of PorR, the 19 other BI trees of T9SS protein components also exhibit evidence of horizontal gene transfer. However, their genes might undergo horizontal gene transfer less frequently compared to porR because the intervening DNA segment that contains porR is easily exchanged between bacteria under Bacteroidetes due to the presence of insertion sequences (IS5 family transposons) that flank it. In conclusion, this study can provide a better understanding about the phylogeny of T9SS protein components.}, }
@article {pmid32611704, year = {2020}, author = {Castillo-Ramírez, S and Mateo-Estrada, V and Gonzalez-Rocha, G and Opazo-Capurro, A}, title = {Phylogeographical Analyses and Antibiotic Resistance Genes of Acinetobacter johnsonii Highlight Its Clinical Relevance.}, journal = {mSphere}, volume = {5}, number = {4}, pages = {}, pmid = {32611704}, issn = {2379-5042}, mesh = {Acinetobacter/*drug effects/*genetics ; Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genetic Variation ; *Genome, Bacterial ; Phylogeny ; Phylogeography ; }, abstract = {Acinetobacter johnsonii has been severely understudied and its population structure and the presence of antibiotic resistance genes (ARGs) are very much uncertain. Our phylogeographical analysis shows that intercontinental transmission has occurred frequently and that different lineages are circulating within single countries; notably, clinical and nonclinical strains are not well differentiated from one another. Importantly, in this species recombination is a significant source of single nucleotide polymorphisms. Furthermore, our results show this species could be an important reservoir of ARGs since it has a significant amount of ARGs, and many of them show signals of horizontal gene transfer. Thus, this study clearly points out the clinical importance of A. johnsonii and the urgent need to better appreciate its genomic diversity.}, }
@article {pmid32611311, year = {2020}, author = {Li, X and Fang, C and Zhao, JP and Zhou, XY and Ni, Z and Niu, DK}, title = {Desiccation does not drastically increase the accessibility of exogenous DNA to nuclear genomes: evidence from the frequency of endosymbiotic DNA transfer.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {452}, pmid = {32611311}, issn = {1471-2164}, support = {31671321//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Cell Nucleus/*genetics ; DNA, Mitochondrial ; *Desiccation ; *Gene Transfer, Horizontal ; Genome ; Plants/genetics ; Plastids/genetics ; Rotifera/genetics ; Tardigrada/genetics ; }, abstract = {BACKGROUND: Although horizontal gene transfer (HGT) is a widely accepted force in the evolution of prokaryotic genomes, its role in the evolution of eukaryotic genomes remains hotly debated. Some bdelloid rotifers that are resistant to extreme desiccation and radiation undergo a very high level of HGT, whereas in another desiccation-resistant invertebrate, the tardigrade, the pattern does not exist. Overall, the DNA double-strand breaks (DSBs) induced by prolonged desiccation have been postulated to open a gateway to the nuclear genome for exogenous DNA integration and thus to facilitate the HGT process, thereby enhancing the rate of endosymbiotic DNA transfer (EDT).<br><br>RESULTS: We first surveyed the abundance of nuclear mitochondrial DNAs (NUMTs) and nuclear plastid DNAs (NUPTs) in five eukaryotes that are highly resistant to desiccation: the bdelloid rotifers Adineta vaga and Adineta ricciae, the tardigrade Ramazzottius varieornatus, and the resurrection plants Dorcoceras hygrometricum and Selaginella tamariscina. Excessive NUMTs or NUPTs were not detected. Furthermore, we compared 24 groups of desiccation-tolerant organisms with their relatively less desiccation-tolerant relatives but did not find a significant difference in NUMT/NUPT contents.<br><br>CONCLUSIONS: Desiccation may induce DSBs, but it is unlikely to dramatically increase the frequency of exogenous sequence integration in most eukaryotes. The capture of exogenous DNA sequences is possible only when DSBs are repaired through a subtype of non-homologous end joining, named alternative end joining (alt-EJ). Due to the deleterious effects of the resulting insertion mutations, alt-EJ is less frequently initiated than other mechanisms.}, }
@article {pmid32606838, year = {2020}, author = {Nazir, A and Zhao, Y and Li, M and Manzoor, R and Tahir, RA and Zhang, X and Qing, H and Tong, Y}, title = {Structural Genomics of repA, repB 1-Carrying IncFIB Family pA1705-qnrS, P911021-tetA, and P1642-tetA, Multidrug-Resistant Plasmids from Klebsiella pneumoniae.}, journal = {Infection and drug resistance}, volume = {13}, number = {}, pages = {1889-1903}, pmid = {32606838}, issn = {1178-6973}, abstract = {BACKGROUND: Multidrug-resistant plasmids carrying replication genes have been widely present in various strains of Klebsiella pneumoniae. RepA and repB1 were found in plasmids belong to the IncFIB, but their detailed structural and genomic characterization was not reported yet. This is the first study that delivers structural and functional insights of repA- and repB1-carrying IncFIB plasmids.<br><br>METHODS: Klebsiella pneumoniae strains A1705, 911021, and 1642 were isolated from the human urine samples and bronchoalveolar fluids collected from different hospitals of China. Antibacterial susceptibility and plasmid transfer ability were tested to characterize the resistant phenotypes mediated by the pA1705-qnrS, p911021-tetA, and p1642-tetA. The complete nucleotide sequences of these plasmids were determined through high-throughput sequencing technology and comparative genomic analyses of plasmids belong to the same incompatibility group were executed to extract the genomic variations and features.<br><br>RESULTS: The pA1705-qnrS, p911021-tetA, and p1642-tetA are defined as non-conjugative plasmids, having two replication genes, repA and repB1 associated with IncFIB family, and unknown incompatible group, respectively. Comparative genomic analysis revealed that relatively small backbones of IncFIB plasmids integrated massive accessory module at one "hotspot" that was located between orf312 and repB1. These IncFIB plasmids exhibited the distinct profiles of accessory modules including one or two multidrug-resistant regions, many complete and remnant mobile elements comprising integrons, transposons and insertion sequences. The clusters of resistant genes were recognized in this study against different classes of antibiotics including &#x3b2;-lactam, phenicol, aminoglycoside, tetracycline, quinolone, trimethoprim, sulfonamide, tunicamycin, and macrolide. It has been observed that all resistant genes were located in multidrug resistance regions.<br><br>CONCLUSION: It is concluded that multidrug-resistant repA and repB1-carrying IncFIB plasmids are a key source to mediate the resistance through mobile elements among Klebsiella pneumoniae. Current findings provide a deep understanding of horizontal gene transfer among plasmids of the IncFIB family via mobile elements that will be utilized in further in vitro studies.}, }
@article {pmid32605988, year = {2020}, author = {Leu, AO and McIlroy, SJ and Ye, J and Parks, DH and Orphan, VJ and Tyson, GW}, title = {Lateral Gene Transfer Drives Metabolic Flexibility in the Anaerobic Methane-Oxidizing Archaeal Family Methanoperedenaceae.}, journal = {mBio}, volume = {11}, number = {3}, pages = {}, pmid = {32605988}, issn = {2150-7511}, mesh = {Anaerobiosis ; Archaea/*genetics/*metabolism ; Gene Regulatory Networks ; *Gene Transfer, Horizontal ; Genomics ; Geologic Sediments/microbiology ; Hydrogen/metabolism ; *Metagenome ; Methane/*metabolism ; Nitrates/metabolism ; Oxidation-Reduction ; }, abstract = {Anaerobic oxidation of methane (AOM) is an important biological process responsible for controlling the flux of methane into the atmosphere. Members of the archaeal family Methanoperedenaceae (formerly ANME-2d) have been demonstrated to couple AOM to the reduction of nitrate, iron, and manganese. Here, comparative genomic analysis of 16 Methanoperedenaceae metagenome-assembled genomes (MAGs), recovered from diverse environments, revealed novel respiratory strategies acquired through lateral gene transfer (LGT) events from diverse archaea and bacteria. Comprehensive phylogenetic analyses suggests that LGT has allowed members of the Methanoperedenaceae to acquire genes for the oxidation of hydrogen and formate and the reduction of arsenate, selenate, and elemental sulfur. Numerous membrane-bound multiheme c-type cytochrome complexes also appear to have been laterally acquired, which may be involved in the direct transfer of electrons to metal oxides, humic substances, and syntrophic partners.IMPORTANCE AOM by microorganisms limits the atmospheric release of the potent greenhouse gas methane and has consequent importance for the global carbon cycle and climate change modeling. While the oxidation of methane coupled to sulfate by consortia of anaerobic methanotrophic (ANME) archaea and bacteria is well documented, several other potential electron acceptors have also been reported to support AOM. In this study, we identify a number of novel respiratory strategies that appear to have been laterally acquired by members of the Methanoperedenaceae, as they are absent from related archaea and other ANME lineages. Expanding the known metabolic potential for members of the Methanoperedenaceae provides important insight into their ecology and suggests their role in linking methane oxidation to several global biogeochemical cycles.}, }
@article {pmid32605600, year = {2020}, author = {Lefoulon, E and Clark, T and Borveto, F and Perriat-Sanguinet, M and Moulia, C and Slatko, BE and Gavotte, L}, title = {Pseudoscorpion Wolbachia symbionts: diversity and evidence for a new supergroup S.}, journal = {BMC microbiology}, volume = {20}, number = {1}, pages = {188}, pmid = {32605600}, issn = {1471-2180}, support = {-//New England Biolabs/International ; }, mesh = {Animals ; Arachnida/*microbiology ; Biotin/*genetics ; Gene Transfer, Horizontal ; Genome Size ; Genome, Bacterial ; Molecular Sequence Annotation ; Multilocus Sequence Typing ; Operon ; Phylogeny ; Symbiosis ; Whole Genome Sequencing/*methods ; Wolbachia/*classification/genetics/isolation &amp; purification ; }, abstract = {BACKGROUND: Wolbachia are the most widely spread endosymbiotic bacteria, present in a wide variety of insects and two families of nematodes. As of now, however, relatively little genomic data has been available. The Wolbachia symbiont can be parasitic, as described for many arthropod systems, an obligate mutualist, as in filarial nematodes or a combination of both in some organisms. They are currently classified into 16 monophyletic lineage groups ("supergroups"). Although the nature of these symbioses remains largely unknown, expanded Wolbachia genomic data will contribute to understanding their diverse symbiotic mechanisms and evolution.<br><br>RESULTS: This report focuses on Wolbachia infections in three pseudoscorpion species infected by two distinct groups of Wolbachia strains, based upon multi-locus phylogenies. Geogarypus minor harbours wGmin and Chthonius ischnocheles harbours wCisc, both closely related to supergroup H, while Atemnus politus harbours wApol, a member of a novel supergroup S along with Wolbachia from the pseudoscorpion Cordylochernes scorpioides (wCsco). Wolbachia supergroup S is most closely related to Wolbachia supergroups C and F. Using target enrichment by hybridization with Wolbachia-specific biotinylated probes to capture large fragments of Wolbachia DNA, we produced two draft genomes of wApol. Annotation of wApol highlights presence of a biotin operon, which is incomplete in many sequenced Wolbachia genomes.<br><br>CONCLUSIONS: The present study highlights at least two symbiont acquisition events among pseudoscorpion species. Phylogenomic analysis indicates that the Wolbachia from Atemnus politus (wApol), forms a separate supergroup ("S") with the Wolbachia from Cordylochernes scorpioides (wCsco). Interestingly, the biotin operon, present in wApol, appears to have been horizontally transferred multiple times along Wolbachia evolutionary history.}, }
@article {pmid32604730, year = {2020}, author = {Kim, CH}, title = {SARS-CoV-2 Evolutionary Adaptation toward Host Entry and Recognition of Receptor O-Acetyl Sialylation in Virus-Host Interaction.}, journal = {International journal of molecular sciences}, volume = {21}, number = {12}, pages = {}, pmid = {32604730}, issn = {1422-0067}, mesh = {Acetylesterase/metabolism ; Animals ; Betacoronavirus/genetics/*metabolism ; Binding Sites ; COVID-19 ; Cell Line ; Coronavirus/genetics ; Coronavirus Infections/*virology ; Esterases ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Glycosaminoglycans/metabolism ; Hemagglutinins, Viral/genetics ; Host Microbial Interactions/*physiology ; Humans ; Lectins/metabolism ; Pandemics ; Pneumonia, Viral/*virology ; Polysaccharides ; Receptors, Virus/chemistry/*metabolism ; SARS-CoV-2 ; Sialic Acids/chemistry/metabolism ; Spike Glycoprotein, Coronavirus/chemistry/physiology ; Torovirus ; Viral Fusion Proteins/genetics ; *Virus Internalization ; }, abstract = {The recently emerged SARS-CoV-2 is the cause of the global health crisis of the coronavirus disease 2019 (COVID-19) pandemic. No evidence is yet available for CoV infection into hosts upon zoonotic disease outbreak, although the CoV epidemy resembles influenza viruses, which use sialic acid (SA). Currently, information on SARS-CoV-2 and its receptors is limited. O-acetylated SAs interact with the lectin-like spike glycoprotein of SARS CoV-2 for the initial attachment of viruses to enter into the host cells. SARS-CoV-2 hemagglutinin-esterase (HE) acts as the classical glycan-binding lectin and receptor-degrading enzyme. Most β-CoVs recognize 9-O-acetyl-SAs but switched to recognizing the 4-O-acetyl-SA form during evolution of CoVs. Type I HE is specific for the 9-O-Ac-SAs and type II HE is specific for 4-O-Ac-SAs. The SA-binding shift proceeds through quasi-synchronous adaptations of the SA-recognition sites of the lectin and esterase domains. The molecular switching of HE acquisition of 4-O-acetyl binding from 9-O-acetyl SA binding is caused by protein-carbohydrate interaction (PCI) or lectin-carbohydrate interaction (LCI). The HE gene was transmitted to a β-CoV lineage A progenitor by horizontal gene transfer from a 9-O-Ac-SA-specific HEF, as in influenza virus C/D. HE acquisition, and expansion takes place by cross-species transmission over HE evolution. This reflects viral evolutionary adaptation to host SA-containing glycans. Therefore, CoV HE receptor switching precedes virus evolution driven by the SA-glycan diversity of the hosts. The PCI or LCI stereochemistry potentiates the SA-ligand switch by a simple conformational shift of the lectin and esterase domains. Therefore, examination of new emerging viruses can lead to better understanding of virus evolution toward transitional host tropism. A clear example of HE gene transfer is found in the BCoV HE, which prefers 7,9-di-O-Ac-SAs, which is also known to be a target of the bovine torovirus HE. A more exciting case of such a switching event occurs in the murine CoVs, with the example of the β-CoV lineage A type binding with two different subtypes of the typical 9-O-Ac-SA (type I) and the exclusive 4-O-Ac-SA (type II) attachment factors. The protein structure data for type II HE also imply the virus switching to binding 4-O acetyl SA from 9-O acetyl SA. Principles of the protein-glycan interaction and PCI stereochemistry potentiate the SA-ligand switch via simple conformational shifts of the lectin and esterase domains. Thus, our understanding of natural adaptation can be specified to how carbohydrate/glycan-recognizing proteins/molecules contribute to virus evolution toward host tropism. Under the current circumstances where reliable antiviral therapeutics or vaccination tools are lacking, several trials are underway to examine viral agents. As expected, structural and non-structural proteins of SARS-CoV-2 are currently being targeted for viral therapeutic designation and development. However, the modern global society needs SARS-CoV-2 preventive and therapeutic drugs for infected patients. In this review, the structure and sialobiology of SARS-CoV-2 are discussed in order to encourage and activate public research on glycan-specific interaction-based drug creation in the near future.}, }
@article {pmid32602886, year = {2020}, author = {Shen, D and Gao, B and Miskey, C and Chen, C and Sang, Y and Zong, W and Wang, S and Wang, Y and Wang, X and Ivics, Z and Song, C}, title = {Multiple Invasions of Visitor, a DD41D Family of Tc1/mariner Transposons, throughout the Evolution of Vertebrates.}, journal = {Genome biology and evolution}, volume = {12}, number = {7}, pages = {1060-1073}, pmid = {32602886}, issn = {1759-6653}, mesh = {Animals ; *Biological Evolution ; *DNA Transposable Elements ; DNA-Binding Proteins ; Gene Transfer, Horizontal ; Invertebrates/*genetics ; Transposases ; Vertebrates/*genetics ; }, abstract = {Although the DD41D (named as Visitor, VS) family of Tc1/mariner transposons was discovered in Arthropods and Mollusca, the evolution profile of this family is still largely unknown. We found that VS is widespread in the animal kingdom, including 140 species of 18 orders in invertebrates and 30 species of 12 orders in vertebrates, and one land plant species. Our data revealed multiple horizontal transfer events in both invertebrates and vertebrates and invasion into multiple lineages of mammals, including Chiroptera (seven species), Dasyuromorphia/Marsupialia (one species), Didelphimorphia/Marsupialia (one species), Diprotodontia/Marsupialia (two species), and Primates (one species). Phylogenetic analysis revealed a close relationship of VSs to DD37D/maT and DD34D/mariner and confirmed that VSs with the DD40D signature identified previously are not a distinct family but originated from DD41D/VS. Age analysis revealed that the most recent invasion of VSs was found in ray-finned fishes and a toad, followed by relatively young invasions in bats and marsupials, whereas VSs in mammals, jawless fishes, and lizards were mainly represented by ancient copies, suggesting old age. Phylogenetic analyses and comparison of pairwise distances between VSs and recombination-activating gene 1 (RAG1) support horizontal transfer events of VSs in vertebrates. The intact VSs from bats were nonfunctional as determined by the transposition activity assay. Some vertebrate lineages and species were identified as the hot hosts of Tc1/mariner transposons. Overall, our study presents the evolution profile of VSs and suggests that VSs play roles in diversifying and shaping the genomes of diverse animal lineages.}, }
@article {pmid32601732, year = {2020}, author = {Amorim, IC and Melo, ES and Moura, RC and Wallau, GL}, title = {Diverse mobilome of Dichotomius (Luederwaldtinia) schiffleri (Coleoptera: Scarabaeidae) reveals long-range horizontal transfer events of DNA transposons.}, journal = {Molecular genetics and genomics : MGG}, volume = {295}, number = {6}, pages = {1339-1353}, doi = {10.1007/s00438-020-01703-8}, pmid = {32601732}, issn = {1617-4623}, support = {0777-2.02/15//Funda&#xe7;&#xe3;o de Amparo &#xe0; Ci&#xea;ncia e Tecnologia do Estado de Pernambuco/ ; }, mesh = {Animals ; Coleoptera/*genetics ; DNA Transposable Elements/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome/*genetics ; *Phylogeny ; }, abstract = {Transposable elements (TEs) are mobile DNA sequences that are able to move from one genomic location to another. These selfish elements are known as genomic parasites, since they hijack the host molecular machinery to generate new copies of themselves. The mobilization of TEs can be seen as a natural mutagen because new TE copies can insert into different loci and impact host genomic structure through different mechanisms. Although our knowledge about TEs is improving with new genomes available, there is still very limited data about the mobilome of species from the Coleoptera order, the most diverse order of insects, including species from the Scarabaeidae family. Therefore, the main goal of this study was to characterize the mobilome of D. (Luederwaldtinia) schiffleri, based on low-coverage genome sequencing, and reconstruct their evolutionary history. We used a combination of four different approaches for TE characterization and maximum likelihood phylogenetic analysis to study their evolution. We found a large and diverse mobilome composed of 38 TE superfamilies, 20 DNA transposon and 18 retrotransposons, accounting for 21% of the genome. Moreover, we found a number of incongruences between the TE and host phylogenetic trees in three DNA transposon TE superfamilies, which represents five TE families, suggesting possible horizontal transfer events between highly divergent taxa. In summary, we found an abundant and diverse mobilome and a number of horizontal transfer events that have shaped the evolutionary history of this species.}, }
@article {pmid32601550, year = {2020}, author = {Shtratnikova, VY and Schelkunov, MI and Penin, AA and Logacheva, MD}, title = {Mitochondrial genome of the nonphotosynthetic mycoheterotrophic plant Hypopitys monotropa, its structure, gene expression and RNA editing.}, journal = {PeerJ}, volume = {8}, number = {}, pages = {e9309}, pmid = {32601550}, issn = {2167-8359}, abstract = {Heterotrophic plants-plants that have lost the ability to photosynthesize-are characterized by a number of changes at all levels of organization. Heterotrophic plants are divided into two large categories-parasitic and mycoheterotrophic (MHT). The question of to what extent such changes are similar in these two categories is still open. The plastid genomes of nonphotosynthetic plants are well characterized, and they exhibit similar patterns of reduction in the two groups. In contrast, little is known about the mitochondrial genomes of MHT plants. We report the structure of the mitochondrial genome of Hypopitys monotropa, a MHT member of Ericaceae, and the expression of its genes. In contrast to its highly reduced plastid genome, the mitochondrial genome of H. monotropa is larger than that of its photosynthetic relative Vaccinium macrocarpon, and its complete size is ~810 Kb. We observed an unusually long repeat-rich structure of the genome that suggests the existence of linear fragments. Despite this unique feature, the gene content of the H. monotropa mitogenome is typical of flowering plants. No acceleration of substitution rates is observed in mitochondrial genes, in contrast to previous observations in parasitic non-photosynthetic plants. Transcriptome sequencing revealed the trans-splicing of several genes and RNA editing in 33 of 38 genes. Notably, we did not find any traces of horizontal gene transfer from fungi, in contrast to plant parasites, which extensively integrate genetic material from their hosts.}, }
@article {pmid32597553, year = {2020}, author = {Algar, E and Al-Ramahi, Y and de Lorenzo, V and Martínez-García, E}, title = {Environmental Performance of Pseudomonas putida with a Uracylated Genome.}, journal = {Chembiochem : a European journal of chemical biology}, volume = {21}, number = {22}, pages = {3255-3265}, doi = {10.1002/cbic.202000330}, pmid = {32597553}, issn = {1439-7633}, mesh = {DNA, Bacterial/genetics ; Hydrolases/*genetics/metabolism ; Mutation ; Nucleic Acid Conformation ; Pseudomonas putida/enzymology/*genetics ; Uracil/*chemistry ; Uracil-DNA Glycosidase/*genetics/metabolism ; }, abstract = {A variant of the soil bacterium Pseudomonas putida with a genome containing a ∼20 % replacement of the whole of thymine (T) by uracil (U) was made by deleting genes ung (uracil DNA glycosylase) and dut (deoxyuridine 5'-triphosphate nucleotide hydrolase). Proteomic comparisons revealed that, of 281 up-regulated and 96 down-regulated proteins in the Δung Δdut cells, as compared to the wild-type, many were involved in nucleotide metabolism. Unexpectedly, genome uracylation did not greatly change the gross environmental endurance profile of P. putida, increased spontaneous mutagenesis by only twofold and supported expression of heterologous proteins well. As U-enriched DNA is potentially degraded by the base excision repair of recipients encoding a uracil DNA glycosylase, we then tested the spread potential of genetic material originating in the Δung Δdut cells either within the same species or in a commonly used Escherichia coli strain. Transformation and conjugation experiments revealed that horizontal gene transfer of U-containing plasmids fared worse than those made of standard DNA by two orders of magnitude. Although this figure does not guarantee the certainty of containment, it suggests a general strategy for curbing the dispersal of recombinant genetic constructs.}, }
@article {pmid32595626, year = {2020}, author = {Bischof, K and Schiffer, D and Trunk, S and Höfler, T and Hopfer, A and Rechberger, G and Koraimann, G}, title = {Regulation of R1 Plasmid Transfer by H-NS, ArcA, TraJ, and DNA Sequence Elements.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1254}, pmid = {32595626}, issn = {1664-302X}, abstract = {In conjugative elements such as integrating conjugative elements (ICEs) or conjugative plasmids (CPs) transcription of DNA transfer genes is a prerequisite for cells to become transfer competent, i.e., capable of delivering plasmid DNA via bacterial conjugation into new host bacteria. In the large family of F-like plasmids belonging to the MobF12A group, transcription of DNA transfer genes is tightly controlled and dependent on the activation of a single promoter, designated PY. Plasmid encoded TraJ and chromosomally encoded ArcA proteins are known activators, whereas the nucleoid associated protein heat-stable nucleoid structuring (H-NS) silences the PY promoter. To better understand the role of these proteins in PY promoter activation, we performed in vitro DNA binding studies using purified H-NS, ArcA, and TraJR 1 (TraJ encoded by the conjugative resistance plasmid R1). All proteins could bind to R1PY DNA with high affinities; however, only ArcA was found to be highly sequence specific. DNase I footprinting studies revealed three H-NS binding sites, confirmed the binding site for ArcA, and suggested that TraJ contacts a dyad symmetry DNA sequence located between -51 and -38 in the R1PY promoter region. Moreover, TraJR 1 and ArcA supplied together changed the H-NS specific protection pattern suggesting that these proteins are able to replace H-NS from R1PY regions proximal to the transcription start site. Our findings were corroborated by PY-lacZ reporter fusions with a series of site specific R1PY promoter mutations. Sequential changes of some critical DNA bases in the TraJ binding site (jbs) from plasmid R1 to plasmid F led to a remarkable specificity switch: The PY promoter became activatable by F encoded TraJ whereas TraJR 1 lost its activation function. The R1PY mutagenesis approach also confirmed the requirement for the host-encoded response-regulator ArcA and indicated that the sequence context, especially in the -35 region is critical for PY regulation and function.}, }
@article {pmid32592387, year = {2020}, author = {Pongchaikul, P and Santanirand, P and Antonyuk, S and Winstanley, C and Darby, AC}, title = {AcGI1, a novel genomic island carrying antibiotic resistance integron In687 in multidrug resistant Achromobacter xylosoxidans in a teaching hospital in Thailand.}, journal = {FEMS microbiology letters}, volume = {367}, number = {14}, pages = {}, pmid = {32592387}, issn = {1574-6968}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Achromobacter denitrificans/classification/drug effects/*genetics/isolation &amp; purification ; Aminoglycosides/pharmacology ; Anti-Bacterial Agents/*pharmacology ; *Drug Resistance, Multiple, Bacterial ; Fluoroquinolones/pharmacology ; *Genomic Islands ; Gram-Negative Bacterial Infections/*microbiology ; Hospitals, Teaching ; Humans ; *Integrons ; Microbial Sensitivity Tests ; Phylogeny ; Sequence Analysis, DNA ; Thailand ; }, abstract = {This study investigated the genetic basis of multidrug resistance in two strains of Achromobacter xylosoxidans isolated from patients attending a hospital in Thailand in 2012. These isolates were highly resistant to cephalosporins, aminoglycosides, fluoroquinolones, co-trimoxazole and carbapenems. Whole genome sequencing revealed that the two isolates were not clonally related and identified a carbapenem resistance gene-habouring integron (In687), residing in a novel genomic island, AcGI1. This In687 shares 100% identical nucleotide sequence with ones found in Acinetobacter baumannii Aci 16, isolated from the same hospital in 2007. We report the first analysis of multidrug-resistant A. xylosoxidans isolated in Thailand, and the first example of this island in A. xylosoxidans. Our data support the idea that resistance has spread in Thailand via horizontal gene transfer between species and suggest the possibility of A. xylosoxidans may serve as a reservoir of antibiotic resistance, especially in hospital setting.}, }
@article {pmid32591385, year = {2020}, author = {Dmowski, M and Kern-Zdanowicz, I}, title = {A Novel Mobilizing Tool Based on the Conjugative Transfer System of the IncM Plasmid pCTX-M3.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {17}, pages = {}, pmid = {32591385}, issn = {1098-5336}, mesh = {Bacillus subtilis/*genetics ; Citrobacter freundii/*genetics ; Conjugation, Genetic ; DNA, Bacterial/genetics ; Escherichia coli/*genetics ; *Gene Transfer, Horizontal ; Lactococcus lactis/*genetics ; Plasmids/*genetics ; }, abstract = {Conjugative plasmids are the main players in horizontal gene transfer in Gram-negative bacteria. DNA transfer tools constructed on the basis of such plasmids enable gene manipulation even in strains of clinical or environmental origin, which are often difficult to work with. The conjugation system of the IncM plasmid pCTX-M3 isolated from a clinical strain of Citrobacter freundii has been shown to enable efficient mobilization of oriTpCTX-M3-bearing plasmids into a broad range of hosts comprising Alpha-, Beta-, and Gammaproteobacteria We constructed a helper plasmid, pMOBS, mediating such mobilization with an efficiency up to 1,000-fold higher than that achieved with native pCTX-M3. We also constructed Escherichia coli donor strains with chromosome-integrated conjugative transfer genes: S14 and S15, devoid of one putative regulator (orf35) of the pCTX-M3 tra genes, and S25 and S26, devoid of two putative regulators (orf35 and orf36) of the pCTX-M3 tra genes. Strains S14 and S15 and strains S25 and S26 are, respectively, up to 100 and 1,000 times more efficient in mobilization than pCTX-M3. Moreover, they also enable plasmid mobilization into the Gram-positive bacteria Bacillus subtilis and Lactococcus lactis Additionally, the constructed E. coli strains carried no antibiotic resistance genes that are present in pCTX-M3 to facilitate manipulations with antibiotic-resistant recipient strains, such as those of clinical origin. To demonstrate possible application of the constructed tool, an antibacterial conjugation-based system was designed. Strain S26 was used for introduction of a mobilizable plasmid coding for a toxin, resulting in the elimination of over 90% of recipient E. coli cells.IMPORTANCE The conjugation of donor and recipient bacterial cells resulting in conjugative transfer of mobilizable plasmids is the preferred method enabling the introduction of DNA into strains for which other transfer methods are difficult to establish (e.g., clinical strains). We have constructed E. coli strains carrying the conjugation system of the IncM plasmid pCTX-M3 integrated into the chromosome. To increase the mobilization efficiency up to 1,000-fold, two putative regulators of this system, orf35 and orf36, were disabled. The constructed strains broaden the repertoire of tools for the introduction of DNA into the Gram-negative Alpha-, Beta-, and Gammaproteobacteria, as well as into Gram-positive bacteria such as Bacillus subtilis and Lactococcus lactis The antibacterial procedure based on conjugation with the use of the orf35- and orf36-deficient strain lowered the recipient cell number by over 90% owing to the mobilizable plasmid-encoded toxin.}, }
@article {pmid32591383, year = {2020}, author = {Headd, B and Bradford, SA}, title = {The Conjugation Window in an Escherichia coli K-12 Strain with an IncFII Plasmid.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {17}, pages = {}, pmid = {32591383}, issn = {1098-5336}, mesh = {Anti-Bacterial Agents/pharmacology ; *Conjugation, Genetic ; Drug Resistance, Microbial/*genetics ; Escherichia coli K12/drug effects/*genetics ; Plasmids/genetics/*physiology ; }, abstract = {Many studies have examined the role that conjugation plays in disseminating antibiotic resistance genes in bacteria. However, relatively little research has quantitively examined and modeled the dynamics of conjugation under growing and nongrowing conditions beyond a couple of hours. We therefore examined growing and nongrowing cultures of Escherichia coli over a 24-h period to understand the dynamics of bacterial conjugation in the presence and absence of antibiotics with pUUH239.2, an IncFII plasmid containing multiantibiotic- and metal-resistant genes. Our data indicate that conjugation occurs after E. coli cells divide and before they have transitioned to a nongrowing phase. The result is that there is only a small window of opportunity for E. coli to conjugate with pUUH239.2 under both growing and nongrowing conditions. Only a very small percentage of the donor cells likely are capable of even undergoing conjugation, and not all transconjugants can become donor cells due to molecular regulatory controls and not being in the correct growth phase. Once a growing culture enters stationary phase, the number of capable donor cells decreases rapidly and conjugation slows to produce a plateau. Published models did not provide accurate descriptions of conjugation under nongrowing conditions. We present here a modified modeling approach that accurately describes observed conjugation behavior under growing and nongrowing conditions.IMPORTANCE There has been growing interest in horizontal gene transfer of antibiotic resistance plasmids as the antibiotic resistance crisis has worsened over the years. Most studies examining conjugation of bacterial plasmids focus on growing cultures of bacteria for short periods, but in the environment, most bacteria grow episodically and at much lower rates than in the laboratory. We examined conjugation of an IncFII antibiotic resistance plasmid in E. coli under growing and nongrowing conditions to understand the dynamics of conjugation under which the plasmid is transferred. We found that conjugation occurs in a narrow time frame when E. coli is transitioning from a growing to nongrowing phase and that the conjugation plateau develops because of a lack of capable donor cells in growing cultures. From an environmental aspect, our results suggest that episodic growth in nutrient-depleted environments could result in more conjugation than sustained growth in a nutrient rich environment.}, }
@article {pmid32590929, year = {2020}, author = {He, Z and Long, P and Fang, F and Li, S and Zhang, P and Chen, Z}, title = {Diversity of MSDIN family members in amanitin-producing mushrooms and the phylogeny of the MSDIN and prolyl oligopeptidase genes.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {440}, pmid = {32590929}, issn = {1471-2164}, support = {Grant No. 31872616//National Natural Science Foundation of China/ ; Grant no. 18A026//Scientific Research Foundation of Hunan Provincial Education Department/ ; }, mesh = {Agaricales/*classification/genetics/metabolism ; Amanitins/biosynthesis ; Asia ; Evolution, Molecular ; Fungal Proteins/*genetics/metabolism ; Gene Expression Profiling/*methods ; Gene Expression Regulation, Fungal ; Gene Transfer, Horizontal ; Multigene Family ; North America ; Peptides, Cyclic/*biosynthesis ; Phylogeny ; Prolyl Oligopeptidases/genetics/metabolism ; Species Specificity ; }, abstract = {BACKGROUND: Amanitin-producing mushrooms, mainly distributed in the genera Amanita, Galerina and Lepiota, possess MSDIN gene family for the biosynthesis of many cyclopeptides catalysed by prolyl oligopeptidase (POP). Recently, transcriptome sequencing has proven to be an efficient way to mine MSDIN and POP genes in these lethal mushrooms. Thus far, only A. palloides and A. bisporigera from North America and A. exitialis and A. rimosa from Asia have been studied based on transcriptome analysis. However, the MSDIN and POP genes of many amanitin-producing mushrooms in China remain unstudied; hence, the transcriptomes of these speices deserve to be analysed.<br><br>RESULTS: In this study, the MSDIN and POP genes from ten Amanita species, two Galerina species and Lepiota venenata were studied and the phylogenetic relationships of their MSDIN and POP genes were analysed. Through transcriptome sequencing and PCR cloning, 19 POP genes and 151 MSDIN genes predicted to encode 98 non-duplicated cyclopeptides, including &#x3b1;-amanitin, &#x3b2;-amanitin, phallacidin, phalloidin and 94 unknown peptides, were found in these species. Phylogenetic analysis showed that (1) MSDIN genes generally clustered depending on the taxonomy of the genus, while Amanita MSDIN genes clustered depending on the chemical substance; and (2) the POPA genes of Amanita, Galerina and Lepiota clustered and were separated into three different groups, but the POPB genes of the three distinct genera were clustered in a highly supported monophyletic group.<br><br>CONCLUSIONS: These results indicate that lethal Amanita species have the genetic capacity to produce numerous cyclopeptides, most of which are unknown, while lethal Galerina and Lepiota species seem to only have the genetic capacity to produce &#x3b1;-amanitin. Additionally, the POPB phylogeny of Amanita, Galerina and Lepiota conflicts with the taxonomic status of the three genera, suggesting that underlying horizontal gene transfer has occurred among these three genera.}, }
@article {pmid32590051, year = {2020}, author = {Hu, W and Feng, S and Tong, Y and Zhang, H and Yang, H}, title = {Adaptive defensive mechanism of bioleaching microorganisms under extremely environmental acid stress: Advances and perspectives.}, journal = {Biotechnology advances}, volume = {42}, number = {}, pages = {107580}, doi = {10.1016/j.biotechadv.2020.107580}, pmid = {32590051}, issn = {1873-1899}, mesh = {*Adaptation, Physiological ; *Stress, Physiological ; }, abstract = {Bioleaching microorganisms inhabit extremely acidic environments (pH < 3.0) and can be used in the biohydrometallurgical industry. They employ several strategies, such as biofilms formation, mechanical defense, membrane reversal potential, proton efflux, intracellular buffering, and protection, or repair mechanism of biomacromolecules, to maintain their intracellular pH within a narrow range, which is close to neutral, for conducting normal physiological activity. In this review, we describe the effects of these strategies on the homeostasis of intracellular pH of bioleaching microorganisms and the relevant energy metabolism. The potential significance of horizontal gene transfer and gene loss in their adaptation to the environment, and the prospect of new technologies, such as cryo EM technology, in revealing the potential acid-resistant components have also been discussed.}, }
@article {pmid32587604, year = {2020}, author = {Becerra-Rodríguez, C and Marsit, S and Galeote, V}, title = {Diversity of Oligopeptide Transport in Yeast and Its Impact on Adaptation to Winemaking Conditions.}, journal = {Frontiers in genetics}, volume = {11}, number = {}, pages = {602}, pmid = {32587604}, issn = {1664-8021}, abstract = {Nitrogen is an essential nutrient for yeasts and its relative abundance is an important modulator of fermentation kinetics. The main sources of nitrogen in food are ammonium and free amino acids, however, secondary sources such as oligopeptides are also important contributors to the nitrogen supply. In yeast, oligopeptide uptake is driven by different families of proton-coupled transporters whose specificity depends on peptide length. Proton-dependent Oligopeptide Transporters (POT) are specific to di- and tri-peptides, whereas the Oligopeptide Transport (OPT) family members import tetra- and pentapeptides. Recently, the novel family of Fungal Oligopeptide Transporters (FOT) has been identified in Saccharomyces cerevisiae wine strains as a result of a horizontal gene transfer from Torulaspora microellipsoides. In natural grape must fermentations with S. cerevisiae, Fots have a broader range of oligopeptide utilization in comparison with non-Fot strains, leading to higher biomass production and better fermentation efficiency. In this review we present the current knowledge on the diversity of oligopeptide transporters in yeast, also discussing how the consumption of oligopeptides provides an adaptive advantage to yeasts within the wine environment.}, }
@article {pmid32585032, year = {2020}, author = {Megarioti, AH and Kouvelis, VN}, title = {The Coevolution of Fungal Mitochondrial Introns and Their Homing Endonucleases (GIY-YIG and LAGLIDADG).}, journal = {Genome biology and evolution}, volume = {12}, number = {8}, pages = {1337-1354}, pmid = {32585032}, issn = {1759-6653}, mesh = {*Biological Coevolution ; Endonucleases/*genetics ; Fungi/enzymology/*genetics ; Gene Transfer, Horizontal ; *Genes, Mitochondrial ; Genome, Mitochondrial ; Introns/*genetics ; Phylogeny ; }, abstract = {Fungal mitochondrial (mt) genomes exhibit great diversity in size which is partially attributed to their variable intergenic regions and most importantly to the inclusion of introns within their genes. These introns belong to group I or II, and both of them are self-splicing. The majority of them carry genes encoding homing endonucleases, either LAGLIDADG or GIY-YIG. In this study, it was found that these intronic homing endonucleases genes (HEGs) may originate from mt free-standing open reading frames which can be found nowadays in species belonging to Early Diverging Fungi as "living fossils." A total of 487 introns carrying HEGs which were located in the publicly available mt genomes of representative species belonging to orders from all fungal phyla was analyzed. Their distribution in the mt genes, their insertion target sequence, and the phylogenetic analyses of the HEGs showed that these introns along with their HEGs form a composite structure in which both selfish elements coevolved. The invasion of the ancestral free-standing HEGs in the introns occurred through a perpetual mechanism, called in this study as "aenaon" hypothesis. It is based on recombination, transpositions, and horizontal gene transfer events throughout evolution. HEGs phylogenetically clustered primarily according to their intron hosts and secondarily to the mt genes carrying the introns and their HEGs. The evolutionary models created revealed an "intron-early" evolution which was enriched by "intron-late" events through many different independent recombinational events which resulted from both vertical and horizontal gene transfers.}, }
@article {pmid32582449, year = {2020}, author = {Putra, RD and Lyrawati, D}, title = {Interactions between Bacteriophages and Eukaryotic Cells.}, journal = {Scientifica}, volume = {2020}, number = {}, pages = {3589316}, pmid = {32582449}, issn = {2090-908X}, abstract = {As the name implies, bacteriophage is a bacterium-specific virus. It infects and kills the bacterial host. Bacteriophages have gained attention as alternative antimicrobial entities in the science community in the western world since the alarming rise of antibiotic resistance among microbes. Although generally considered as prokaryote-specific viruses, recent studies indicate that bacteriophages can interact with eukaryotic organisms, including humans. In the current review, these interactions are divided into two categories, i.e., indirect and direct interactions, with the involvement of bacteriophages, bacteria, and eukaryotes. We discuss bacteriophage-related diseases, transcytosis of bacteriophages, bacteriophage interactions with cancer cells, collaboration of bacteriophages and eukaryotes against bacterial infections, and horizontal gene transfer between bacteriophages and eukaryotes. Such interactions are crucial for understanding and developing bacteriophages as the therapeutic agents and pharmaceutical delivery systems. With the advancement and combination of in silico, in vitro, and in vivo approaches and clinical trials, bacteriophages definitely serve as useful repertoire for biologic target-based drug development to manage many complex diseases in the future.}, }
@article {pmid32582169, year = {2020}, author = {Rosini, R and Nicchi, S and Pizza, M and Rappuoli, R}, title = {Vaccines Against Antimicrobial Resistance.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {1048}, pmid = {32582169}, issn = {1664-3224}, mesh = {Antibodies, Monoclonal/therapeutic use ; Bacterial Infections/drug therapy/immunology/therapy ; Biotechnology/methods/trends ; Drug Resistance, Bacterial/immunology ; Drug Resistance, Microbial/*immunology ; Host Microbial Interactions/drug effects/immunology ; Humans ; Infections/drug therapy/immunology/therapy ; Models, Immunological ; Vaccines/immunology/*therapeutic use ; Vaccines, Synthetic/immunology/therapeutic use ; mRNA Vaccines ; }, abstract = {In the last century, life expectancy has increased considerably, thanks to the introduction of antibiotics, hygiene and vaccines that have contributed to the cure and prevention of many infectious diseases. The era of antimicrobial therapy started in the nineteenth century with the identification of chemical compounds with antimicrobial properties. However, immediately after the introduction of these novel drugs, microorganisms started to become resistant through different strategies. Although resistance mechanisms were already present before antibiotic introduction, their large-scale use and mis-use have increased the number of resistant microorganisms. Rapid spreading of mobile elements by horizontal gene transfer such as plasmids and integrative conjugative elements (ICE) carrying multiple resistance genes has dramatically increased the worldwide prevalence of relevant multi drug-resistant human pathogens such as Staphylococcus aureus, Neisseria gonorrhoeae, and Enterobacteriaceae. Today, antimicrobial resistance (AMR) remains one of the major global concerns to be addressed and only global efforts could help in finding a solution. In terms of magnitude the economic impact of AMR is estimated to be comparable to that of climate global change in 2030. Although antibiotics continue to be essential to treat such infections, non-antibiotic therapies will play an important role in limiting the increase of antibiotic resistant microorganisms. Among non-antibiotic strategies, vaccines and therapeutic monoclonal antibodies (mAbs) play a strategic role. In this review, we will summarize the evolution and the mechanisms of antibiotic resistance, and the impact of AMR on life expectancy and economics.}, }
@article {pmid32582111, year = {2020}, author = {Tokuda, M and Suzuki, H and Yanagiya, K and Yuki, M and Inoue, K and Ohkuma, M and Kimbara, K and Shintani, M}, title = {Determination of Plasmid pSN1216-29 Host Range and the Similarity in Oligonucleotide Composition Between Plasmid and Host Chromosomes.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1187}, pmid = {32582111}, issn = {1664-302X}, abstract = {Plasmids are extrachromosomal DNA that can be horizontally transferred between different bacterial cells by conjugation. Horizontal gene transfer of plasmids can promote rapid evolution and adaptation of bacteria by imparting various traits involved in antibiotic resistance, virulence, and metabolism to their hosts. The host range of plasmids is an important feature for understanding how they spread in environmental microbial communities. Earlier bioinformatics studies have demonstrated that plasmids are likely to have similar oligonucleotide (k-mer) compositions to their host chromosomes and that evolutionary host ranges of plasmids could be predicted from this similarity. However, there are no complementary studies to assess the consistency between the predicted evolutionary host range and experimentally determined replication/transfer host range of a plasmid. In the present study, the replication/transfer host range of a model plasmid, pSN1216-29, exogenously isolated from cow manure as a newly discovered self-transmissible plasmid, was experimentally determined within microbial communities extracted from soil and cow manure. In silico prediction of evolutionary host range was performed with the pSN1216-29 using its oligonucleotide compositions independently. The results showed that oligonucleotide compositions of the plasmid pSN1216-29 had more similarities to those of hosts (transconjugants genera) than those of non-hosts (other genera). These findings can contribute to the understanding of how plasmids behave in microbial communities, and aid in the designing of appropriate plasmid vectors for different bacteria.}, }
@article {pmid32582074, year = {2020}, author = {Brankovics, B and van Diepeningen, AD and de Hoog, GS and van der Lee, TAJ and Waalwijk, C}, title = {Detecting Introgression Between Members of the Fusarium fujikuroi and F. oxysporum Species Complexes by Comparative Mitogenomics.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1092}, pmid = {32582074}, issn = {1664-302X}, abstract = {The Fusarium fujikuroi species complex (FFSC) and F. oxysporum species complex (FOSC) are two related groups of plant pathogens causing a wide diversity of diseases in agricultural crops world wide. The aims of this study are (1) to clarify the phylogeny of the FFSC, (2) to identify potential deviation from tree-like evolution, (3) to explore the value of using mitogenomes for these kinds of analyses, and (4) to better understand mitogenome evolution. In total, we have sequenced 24 species from the FFSC and a representative set of recently analyzed FOSC strains was chosen, while F. redolens was used as outgroup for the two species complexes. A species tree was constructed based on the concatenated alignment of seven nuclear genes and the mitogenome, which was contrasted to individual gene trees to identify potential conflicts. These comparisons indicated conflicts especially within the previously described African clade of the FFSC. Furthermore, the analysis of the mitogenomes revealed the presence of a variant of the large variable (LV) region in FFSC which was previously only reported for FOSC. The distribution of this variant and the results of sequence comparisons indicate horizontal genetic transfer between members of the two species complexes, most probably through introgression. In addition, a duplication of atp9 was found inside an intron of cob, which suggests that even highly conserved mitochondrial genes can have paralogs. Paralogization in turn may lead to inaccurate single gene phylogenies. In conclusion, mitochondrial genomes provide a robust basis for phylogeny. Comparative phylogenetic analysis indicated that gene flow among and between members of FFSC and FOSC has played an important role in the evolutionary history of these two groups. Since mitogenomes show greater levels of conservation and synteny than nuclear regions, they are more likely to be compatible for recombination than nuclear regions. Therefore, mitogenomes can be used as indicators to detect interspecies gene flow.}, }
@article {pmid32581279, year = {2020}, author = {Hazzouri, KM and Sudalaimuthuasari, N and Kundu, B and Nelson, D and Al-Deeb, MA and Le Mansour, A and Spencer, JJ and Desplan, C and Amiri, KMA}, title = {The genome of pest Rhynchophorus ferrugineus reveals gene families important at the plant-beetle interface.}, journal = {Communications biology}, volume = {3}, number = {1}, pages = {323}, pmid = {32581279}, issn = {2399-3642}, mesh = {Animals ; Biological Evolution ; Cytochrome P-450 Enzyme System/genetics ; DNA Transposable Elements ; Female ; Gene Transfer, Horizontal ; *Genome, Insect ; Insect Proteins/*genetics ; Male ; Molecular Sequence Annotation ; *Multigene Family ; Plants ; Population Density ; Receptors, Odorant/genetics ; Sex Chromosomes ; Synteny ; Weevils/*genetics ; }, abstract = {The red palm weevil, Rhynchophorus ferrugineus, infests palm plantations, leading to large financial losses and soil erosion. Pest-host interactions are poorly understood in R. ferrugineus, but the analysis of genetic diversity and pest origins will help advance efforts to eradicate this pest. We sequenced the genome of R. ferrugineus using a combination of paired-end Illumina sequencing (150 bp), Oxford Nanopore long reads, 10X Genomics and synteny analysis to produce an assembly with a scaffold N50 of ~60 Mb. Structural variations showed duplication of detoxifying and insecticide resistance genes (e.g., glutathione S-transferase, P450, Rdl). Furthermore, the evolution of gene families identified those under positive selection including one glycosyl hydrolase (GH16) gene family, which appears to result from horizontal gene transfer. This genome will be a valuable resource to understand insect evolution and behavior and to allow the genetic modification of key genes that will help control this pest.}, }
@article {pmid32581135, year = {2020}, author = {Schrader, SM and Vaubourgeix, J and Nathan, C}, title = {Biology of antimicrobial resistance and approaches to combat it.}, journal = {Science translational medicine}, volume = {12}, number = {549}, pages = {}, pmid = {32581135}, issn = {1946-6242}, support = {F30 AI140623/AI/NIAID NIH HHS/United States ; MR/P028225/1/MRC_/Medical Research Council/United Kingdom ; T32 GM007739/GM/NIGMS NIH HHS/United States ; U19 AI111143/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; *Anti-Infective Agents/pharmacology/therapeutic use ; Bacteria/genetics ; Biology ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Insufficient development of new antibiotics and the rising resistance of bacteria to those that we have are putting the world at risk of losing the most widely curative class of medicines currently available. Preventing deaths from antimicrobial resistance (AMR) will require exploiting emerging knowledge not only about genetic AMR conferred by horizontal gene transfer or de novo mutations but also about phenotypic AMR, which lacks a stably heritable basis. This Review summarizes recent advances and continuing limitations in our understanding of AMR and suggests approaches for combating its clinical consequences, including identification of previously unexploited bacterial targets, new antimicrobial compounds, and improved combination drug regimens.}, }
@article {pmid32578878, year = {2020}, author = {Sun, G and Bai, S and Guan, Y and Wang, S and Wang, Q and Liu, Y and Liu, H and Goffinet, B and Zhou, Y and Paoletti, M and Hu, X and Haas, FB and Fernandez-Pozo, N and Czyrt, A and Sun, H and Rensing, SA and Huang, J}, title = {Are fungi-derived genomic regions related to antagonism towards fungi in mosses?.}, journal = {The New phytologist}, volume = {228}, number = {4}, pages = {1169-1175}, doi = {10.1111/nph.16776}, pmid = {32578878}, issn = {1469-8137}, mesh = {*Bryophyta/genetics ; Fungi/genetics ; Genome, Fungal ; Genomics ; *Mycorrhizae ; Symbiosis ; }, }
@article {pmid32576860, year = {2020}, author = {John, MS and Nagoth, JA and Ramasamy, KP and Ballarini, P and Mozzicafreddo, M and Mancini, A and Telatin, A and Liò, P and Giuli, G and Natalello, A and Miceli, C and Pucciarelli, S}, title = {Horizontal gene transfer and silver nanoparticles production in a new Marinomonas strain isolated from the Antarctic psychrophilic ciliate Euplotes focardii.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {10218}, pmid = {32576860}, issn = {2045-2322}, support = {MR/T030062/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Anti-Bacterial Agents/*administration &amp; dosage/chemistry/metabolism ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Euplotes/physiology ; Fibroblasts/cytology/*drug effects ; *Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Genome, Bacterial ; Humans ; Marinomonas/classification/genetics/*isolation &amp; purification/metabolism ; Metal Nanoparticles/*administration &amp; dosage/chemistry ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Silver/*chemistry ; }, abstract = {We isolated a novel bacterial strain from a prokaryotic consortium associated to the psychrophilic marine ciliate Euplotes focardii, endemic of the Antarctic coastal seawater. The 16S rDNA sequencing and the phylogenetic analysis revealed the close evolutionary relationship to the Antarctic marine bacterium Marinomonas sp. BSw10506 and the sub antarctic Marinomonas polaris. We named this new strain Marinomonas sp. ef1. The optimal growth temperature in LB medium was 22 °C. Whole genome sequencing and analysis showed a reduced gene loss limited to regions encoding for transposases. Additionally, five genomic islands, e.g. DNA fragments that facilitate horizontal gene transfer phenomena, were identified. Two open reading frames predicted from the genomic islands coded for enzymes belonging to the Nitro-FMN-reductase superfamily. One of these, the putative NAD(P)H nitroreductase YfkO, has been reported to be involved in the bioreduction of silver (Ag) ions and the production of silver nanoparticles (AgNPs). After the Marinomonas sp. ef1 biomass incubation with 1 mM of AgNO3 at 22 °C, we obtained AgNPs within 24 h. The AgNPs were relatively small in size (50 nm) and had a strong antimicrobial activity against twelve common nosocomial pathogenic microorganisms including Staphylococcus aureus and two Candida strains. To our knowledge, this is the first report of AgNPs biosynthesis by a Marinomonas strain. This biosynthesis may play a dual role in detoxification from silver nitrate and protection from pathogens for the bacterium and potentially for the associated ciliate. Biosynthetic AgNPs also represent a promising alternative to conventional antibiotics against common pathogens.}, }
@article {pmid32576698, year = {2020}, author = {Ianiri, G and Coelho, MA and Ruchti, F and Sparber, F and McMahon, TJ and Fu, C and Bolejack, M and Donovan, O and Smutney, H and Myler, P and Dietrich, F and Fox, D and LeibundGut-Landmann, S and Heitman, J}, title = {HGT in the human and skin commensal Malassezia: A bacterially derived flavohemoglobin is required for NO resistance and host interaction.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {27}, pages = {15884-15894}, pmid = {32576698}, issn = {1091-6490}, support = {R37 AI039115/AI/NIAID NIH HHS/United States ; R01 AI039115/AI/NIAID NIH HHS/United States ; HHSN272200700057C/AI/NIAID NIH HHS/United States ; I01 BX003478/BX/BLRD VA/United States ; HHSN272201700059C/AI/NIAID NIH HHS/United States ; HHSN272201200025C/AI/NIAID NIH HHS/United States ; R01 AI050113/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*genetics/metabolism ; Crystallography, X-Ray ; Ergosterol/biosynthesis ; Evolution, Molecular ; Fungal Proteins/genetics/metabolism ; Gene Deletion ; Gene Expression Regulation, Fungal ; Gene Transfer, Horizontal ; Hemeproteins/chemistry/*genetics/metabolism ; Host Microbial Interactions/*physiology ; Humans ; Malassezia/classification/*genetics/*metabolism ; Models, Molecular ; Nitric Oxide/*metabolism ; Oxidative Stress/genetics/physiology ; Phylogeny ; Skin/metabolism/*microbiology ; Symbiosis ; }, abstract = {The skin of humans and animals is colonized by commensal and pathogenic fungi and bacteria that share this ecological niche and have established microbial interactions. Malassezia are the most abundant fungal skin inhabitant of warm-blooded animals and have been implicated in skin diseases and systemic disorders, including Crohn's disease and pancreatic cancer. Flavohemoglobin is a key enzyme involved in microbial nitrosative stress resistance and nitric oxide degradation. Comparative genomics and phylogenetic analyses within the Malassezia genus revealed that flavohemoglobin-encoding genes were acquired through independent horizontal gene transfer events from different donor bacteria that are part of the mammalian microbiome. Through targeted gene deletion and functional complementation in Malassezia sympodialis, we demonstrated that bacterially derived flavohemoglobins are cytoplasmic proteins required for nitric oxide detoxification and nitrosative stress resistance under aerobic conditions. RNA-sequencing analysis revealed that endogenous accumulation of nitric oxide resulted in up-regulation of genes involved in stress response and down-regulation of the MalaS7 allergen-encoding genes. Solution of the high-resolution X-ray crystal structure of Malassezia flavohemoglobin revealed features conserved with both bacterial and fungal flavohemoglobins. In vivo pathogenesis is independent of Malassezia flavohemoglobin. Lastly, we identified an additional 30 genus- and species-specific horizontal gene transfer candidates that might have contributed to the evolution of this genus as the most common inhabitants of animal skin.}, }
@article {pmid32575751, year = {2020}, author = {Mortier-Barrière, I and Polard, P and Campo, N}, title = {Direct Visualization of Horizontal Gene Transfer by Transformation in Live Pneumococcal Cells Using Microfluidics.}, journal = {Genes}, volume = {11}, number = {6}, pages = {}, pmid = {32575751}, issn = {2073-4425}, mesh = {Bacterial Proteins/*genetics ; Chromosomes/genetics ; DNA Transformation Competence/genetics ; DNA, Bacterial/genetics ; Gene Expression Regulation, Bacterial/genetics ; Gene Transfer, Horizontal/*genetics ; Microfluidics/methods ; Pneumococcal Infections/*genetics/microbiology ; Streptococcus pneumoniae/*genetics/pathogenicity ; Transformation, Bacterial/genetics ; }, abstract = {Natural genetic transformation is a programmed mechanism of horizontal gene transfer in bacteria. It requires the development of competence, a specialized physiological state during which proteins involved in DNA uptake and chromosomal integration are produced. In Streptococcus pneumoniae, competence is transient. It is controlled by a secreted peptide pheromone, the competence-stimulating peptide (CSP) that triggers the sequential transcription of two sets of genes termed early and late competence genes, respectively. Here, we used a microfluidic system with fluorescence microscopy to monitor pneumococcal competence development and transformation, in live cells at the single cell level. We present the conditions to grow this microaerophilic bacterium under continuous flow, with a similar doubling time as in batch liquid culture. We show that perfusion of CSP in the microfluidic chamber results in the same reduction of the growth rate of individual cells as observed in competent pneumococcal cultures. We also describe newly designed fluorescent reporters to distinguish the expression of competence genes with temporally distinct expression profiles. Finally, we exploit the microfluidic technology to inject both CSP and transforming DNA in the microfluidic channels and perform near real time-tracking of transformation in live cells. We show that this approach is well suited to investigating the onset of pneumococcal competence together with the appearance and the fate of transformants in individual cells.}, }
@article {pmid32572143, year = {2020}, author = {Ren, FR and Sun, X and Wang, TY and Yao, YL and Huang, YZ and Zhang, X and Luan, JB}, title = {Biotin provisioning by horizontally transferred genes from bacteria confers animal fitness benefits.}, journal = {The ISME journal}, volume = {14}, number = {10}, pages = {2542-2553}, pmid = {32572143}, issn = {1751-7370}, mesh = {Animals ; Bacteria/genetics ; *Biotin ; Escherichia coli ; *Hemiptera ; Symbiosis ; }, abstract = {Insect symbionts are widespread in nature and lateral gene transfer is prevalent in insect symbiosis. However, the function of horizontally transferred genes (HTGs) in insect symbiosis remains speculative, including the mechanism that enables insects to feed on plant phloem deficient in B vitamins. Previously, we found there is redundancy in biotin synthesis pathways from both whitefly Bemisia tabaci and symbiotic Hamiltonella due to the presence of whitefly HTGs. Here, we demonstrate that elimination of Hamiltonella decreased biotin levels but elevated the expression of horizontally transferred biotin genes in whiteflies. HTGs proteins exhibit specific expression patterns in specialized insect cells called bacteriocytes housing symbionts. Complementation with whitefly HTGs rescued E. coli biotin gene knockout mutants. Furthermore, silencing whitefly HTGs in Hamiltonella-infected whiteflies reduced biotin levels and hindered adult survival and fecundity, which was partially rescued by biotin supplementation. Each of horizontally transferred biotin genes are conserved in various laboratory cultures and species of whiteflies with geographically diverse distributions, which shares an evolutionary origin. We provide the first experimental evidence that biotin synthesized through acquired HTGs is important in whiteflies and may be as well in other animals. Our findings suggest that B vitamin provisioning in animal-microbe symbiosis frequently evolved from bacterial symbionts to animal hosts through horizontal gene transfer events. This study will also shed light on how the animal genomes evolve through functional transfer of genes with bacterial origin in the wider contexts of microbial ecology.}, }
@article {pmid32571917, year = {2020}, author = {Rodríguez-Beltrán, J and Sørum, V and Toll-Riera, M and de la Vega, C and Peña-Miller, R and San Millán, &#xc1;}, title = {Genetic dominance governs the evolution and spread of mobile genetic elements in bacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {27}, pages = {15755-15762}, pmid = {32571917}, issn = {1091-6490}, mesh = {Bacteria/*genetics ; Drug Resistance, Bacterial/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Humans ; Interspersed Repetitive Sequences/*genetics ; Plasmids/genetics ; Virulence/genetics ; }, abstract = {Mobile genetic elements (MGEs), such as plasmids, promote bacterial evolution through horizontal gene transfer (HGT). However, the rules governing the repertoire of traits encoded on MGEs remain unclear. In this study, we uncovered the central role of genetic dominance shaping genetic cargo in MGEs, using antibiotic resistance as a model system. MGEs are typically present in more than one copy per host bacterium, and as a consequence, genetic dominance favors the fixation of dominant mutations over recessive ones. In addition, genetic dominance also determines the phenotypic effects of horizontally acquired MGE-encoded genes, silencing recessive alleles if the recipient bacterium already carries a wild-type copy of the gene. The combination of these two effects governs the catalog of genes encoded on MGEs. Our results help to understand how MGEs evolve and spread, uncovering the neglected influence of genetic dominance on bacterial evolution. Moreover, our findings offer a framework to forecast the spread and evolvability of MGE-encoded genes, which encode traits of key human interest, such as virulence or antibiotic resistance.}, }
@article {pmid32571204, year = {2020}, author = {Vázquez-Rosas-Landa, M and Ponce-Soto, GY and Aguirre-Liguori, JA and Thakur, S and Scheinvar, E and Barrera-Redondo, J and Ibarra-Laclette, E and Guttman, DS and Eguiarte, LE and Souza, V}, title = {Population genomics of Vibrionaceae isolated from an endangered oasis reveals local adaptation after an environmental perturbation.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {418}, pmid = {32571204}, issn = {1471-2164}, support = {IG200215//PAPIIT/ ; 238245//CONACYT/ ; }, mesh = {Adaptation, Physiological ; Gene Transfer, Horizontal ; Genetics, Population ; Genome, Bacterial ; Multigene Family ; Mutation ; Phylogeny ; *Polymorphism, Single Nucleotide ; Population Density ; Selection, Genetic ; Vibrionaceae/*classification/genetics/isolation &amp; purification/*physiology ; Whole Genome Sequencing/*methods ; }, abstract = {BACKGROUND: In bacteria, pan-genomes are the result of an evolutionary "tug of war" between selection and horizontal gene transfer (HGT). High rates of HGT increase the genetic pool and the effective population size (Ne), resulting in open pan-genomes. In contrast, selective pressures can lead to local adaptation by purging the variation introduced by HGT and mutation, resulting in closed pan-genomes and clonal lineages. In this study, we explored both hypotheses, elucidating the pan-genome of Vibrionaceae isolates after a perturbation event in the endangered oasis of Cuatro Ciénegas Basin (CCB), Mexico, and looking for signals of adaptation to the environments in their genomes.<br><br>RESULTS: We obtained 42 genomes of Vibrionaceae distributed in six lineages, two of them did not showed any close reference strain in databases. Five of the lineages showed closed pan-genomes and were associated to either water or sediment environment; their high Ne estimates suggest that these lineages are not from a recent origin. The only clade with an open pan-genome was found in both environments and was formed by ten genetic groups with low Ne, suggesting a recent origin. The recombination and mutation estimators (r/m) ranged from 0.005 to 2.725, which are similar to oceanic Vibrionaceae estimations. However, we identified 367 gene families with signals of positive selection, most of them found in the core genome; suggesting that despite recombination, natural selection moves the Vibrionaceae CCB lineages to local adaptation, purging the genomes and keeping closed pan-genome patterns. Moreover, we identify 598 SNPs associated with an unstructured environment; some of the genes associated with these SNPs were related to sodium transport.<br><br>CONCLUSIONS: Different lines of evidence suggest that the sampled Vibrionaceae, are part of the rare biosphere usually living under famine conditions. Two of these lineages were reported for the first time. Most Vibrionaceae lineages of CCB are adapted to their micro-habitats rather than to the sampled environments. This pattern of adaptation is concordant with the association of closed pan-genomes and local adaptation.}, }
@article {pmid32566125, year = {2020}, author = {Gacesa, R and Hung, JY and Bourne, DG and Long, PF}, title = {Horizontal transfer of a natterin-like toxin encoding gene within the holobiont of the reef building coral Acropora digitifera (Cnidaria: Anthozoa: Scleractinia) and across multiple animal linages.}, journal = {Journal of venom research}, volume = {10}, number = {}, pages = {7-12}, pmid = {32566125}, issn = {2044-0324}, abstract = {Phylogenetic evidence is provided for horizontal transfer of a natterin-like toxin encoding gene from fungi into the genome of the coral Acropora digitifera. Sequencing analysis of the coral tissues supported that a fungal taxon predicted to be the most likely gene donor was represented in the coral microbiome. Further bioinformatics data suggested widespread recruitment of the natterin-like gene into venomous terrestrial invertebrates, and repositioning of this gene to non-toxic functions in non-venomous teleost fish.}, }
@article {pmid32565537, year = {2020}, author = {Vassallo, CN and Troselj, V and Weltzer, ML and Wall, D}, title = {Rapid diversification of wild social groups driven by toxin-immunity loci on mobile genetic elements.}, journal = {The ISME journal}, volume = {14}, number = {10}, pages = {2474-2487}, pmid = {32565537}, issn = {1751-7370}, support = {R01 GM101449/GM/NIGMS NIH HHS/United States ; }, mesh = {Alleles ; Biological Evolution ; Genomics ; Humans ; Interspersed Repetitive Sequences ; *Myxococcus xanthus/genetics ; }, abstract = {Many species form distinct social groups that provide fitness advantages to individuals. However, the evolutionary processes that generate new social groups are not well understood. Here we examined recently diverged natural isolates of the model social bacterium, Myxococcus xanthus, to probe the genetic mechanisms and evolutionary processes of kin discrimination that occurred naturally in soil. We show that social incompatibilities were formed from horizontal gene transfer of effectors belonging to three distinct polymorphic toxin systems; outer membrane exchange, type VI secretion and rearrangement hotspot systems. Strikingly, the unique toxin effectors and their respective immunity genes that are responsible for social incompatibilities reside on mobile genetic elements, which make up nearly all of the genotypic variation between isolates within clades. By disrupting these three toxin systems, we engineered social harmony between strains that were originally incompatible. In addition, a horizontal allele swap of a single kin recognition receptor changed social interactions and competition outcomes. Our results provide a case study for how horizontal gene transfer led to social diversification in a natural context. Finally, we show how genomic information of kin discriminatory loci can be used to predict social interactions.}, }
@article {pmid32563696, year = {2021}, author = {Hwang, K and Choe, H and Nasir, A and Kim, KM}, title = {Complete genome of Polaromonas vacuolata KCTC 22033[T] isolated from beneath Antarctic Sea ice.}, journal = {Marine genomics}, volume = {55}, number = {}, pages = {100790}, doi = {10.1016/j.margen.2020.100790}, pmid = {32563696}, issn = {1876-7478}, mesh = {Antarctic Regions ; Aquatic Organisms/genetics ; Comamonadaceae/*genetics ; *Genome, Bacterial ; Whole Genome Sequencing ; }, abstract = {Polaromonas vacuolata KCTC 22033[T] is an obligate aerobic, Gram-negative, psychrophilic and rod-shaped bacterium isolated from beneath the sea ice off the coast of the Palmer Peninsula, Anvers Islands, Antarctica. P. vacuolata is the type species of Polaromonas genus and the first example of gas vacuolate Betaproteobacteria isolated from marine habitats. Here, we report a complete genome of P. vacuolata KCTC 22033[T], which consists of 3,837,686 bp (G + C content of 52.07%) with a single chromosome, 3461 protein-coding genes, 56 tRNAs and 6 rRNA operons. Genomic analysis revealed the presence of genes involved in bacterial adaptation under saline conditions, cold adaptation via the production of gas vesicles and cell adhesion proteins, and a photoheterotrophic lifestyle when challenged by starvation. Intriguingly, several of these genes were likely acquired from species outside the Polaromonas genus. The genomic information therefore describes the unique evolution and adaptation of P. vacuolata to its extraordinary habitat, i.e., beneath the Antarctic sea ice.}, }
@article {pmid32561581, year = {2020}, author = {Wiersma, SJ and Mooiman, C and Giera, M and Pronk, JT}, title = {Squalene-Tetrahymanol Cyclase Expression Enables Sterol-Independent Growth of Saccharomyces cerevisiae.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {17}, pages = {}, pmid = {32561581}, issn = {1098-5336}, mesh = {Biological Evolution ; *Gene Expression ; Gene Transfer, Horizontal ; Lyases/*genetics/metabolism ; Microorganisms, Genetically-Modified/genetics/metabolism ; Protozoan Proteins/*genetics/metabolism ; Saccharomyces cerevisiae/*genetics/growth &amp; development ; Sterols/metabolism ; Tetrahymena thermophila/*genetics ; }, abstract = {Biosynthesis of sterols, which are considered essential components of virtually all eukaryotic membranes, requires molecular oxygen. Anaerobic growth of the yeast Saccharomyces cerevisiae therefore strictly depends on sterol supplementation of synthetic growth media. Neocallimastigomycota are a group of strictly anaerobic fungi which, instead of containing sterols, contain the pentacyclic triterpenoid "sterol surrogate" tetrahymanol, which is formed by cyclization of squalene. Here, we demonstrate that expression of the squalene-tetrahymanol cyclase gene TtTHC1 from the ciliate Tetrahymena thermophila enables synthesis of tetrahymanol by S. cerevisiae Moreover, expression of TtTHC1 enabled exponential growth of anaerobic S. cerevisiae cultures in sterol-free synthetic media. After deletion of the ERG1 gene from a TtTHC1-expressing S. cerevisiae strain, native sterol synthesis was abolished and sustained sterol-free growth was demonstrated under anaerobic as well as aerobic conditions. Anaerobic cultures of TtTHC1-expressing S. cerevisiae on sterol-free medium showed lower specific growth rates and biomass yields than ergosterol-supplemented cultures, while their ethanol yield was higher. This study demonstrated that acquisition of a functional squalene-tetrahymanol cyclase gene offers an immediate growth advantage to S. cerevisiae under anaerobic, sterol-limited conditions and provides the basis for a metabolic engineering strategy to eliminate the oxygen requirements associated with sterol synthesis in yeasts.IMPORTANCE The laboratory experiments described in this report simulate a proposed horizontal gene transfer event during the evolution of strictly anaerobic fungi. The demonstration that expression of a single heterologous gene sufficed to eliminate anaerobic sterol requirements in the model eukaryote Saccharomyces cerevisiae therefore contributes to our understanding of how sterol-independent eukaryotes evolved in anoxic environments. This report provides a proof of principle for a metabolic engineering strategy to eliminate sterol requirements in yeast strains that are applied in large-scale anaerobic industrial processes. The sterol-independent yeast strains described in this report provide a valuable platform for further studies on the physiological roles and impacts of sterols and sterol surrogates in eukaryotic cells.}, }
@article {pmid32560683, year = {2020}, author = {Jaffe, AL and Castelle, CJ and Matheus Carnevali, PB and Gribaldo, S and Banfield, JF}, title = {The rise of diversity in metabolic platforms across the Candidate Phyla Radiation.}, journal = {BMC biology}, volume = {18}, number = {1}, pages = {69}, pmid = {32560683}, issn = {1741-7007}, mesh = {Bacteria/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; *Phylogeny ; }, abstract = {BACKGROUND: A unifying feature of the bacterial Candidate Phyla Radiation (CPR) is a limited and highly variable repertoire of biosynthetic capabilities. However, the distribution of metabolic traits across the CPR and the evolutionary processes underlying them are incompletely resolved.<br><br>RESULTS: Here, we selected ~&#x2009;1000 genomes of CPR bacteria from diverse environments to construct a robust internal phylogeny that was consistent across two unlinked marker sets. Mapping of glycolysis, the pentose phosphate pathway, and pyruvate metabolism onto the tree showed that some components of these pathways are sparsely distributed and that similarity between metabolic platforms is only partially predicted by phylogenetic relationships. To evaluate the extent to which gene loss and lateral gene transfer have shaped trait distribution, we analyzed the patchiness of gene presence in a phylogenetic context, examined the phylogenetic depth of clades with shared traits, and compared the reference tree topology with those of specific metabolic proteins. While the central glycolytic pathway in CPR is widely conserved and has likely been shaped primarily by vertical transmission, there is evidence for both gene loss and transfer especially in steps that convert glucose into fructose 1,6-bisphosphate and glycerate 3P into pyruvate. Additionally, the distribution of Group 3 and Group 4-related NiFe hydrogenases is patchy and suggests multiple events of ancient gene transfer.<br><br>CONCLUSIONS: We infer that patterns of gene gain and loss in CPR, including acquisition of accessory traits in independent transfer events, could have been driven by shifts in host-derived resources and led to sparse but varied genetic inventories.}, }
@article {pmid32559326, year = {2020}, author = {Da Ines, O and Michard, R and Fayos, I and Bastianelli, G and Nicolas, A and Guiderdoni, E and White, C and Sourdille, P}, title = {Bread wheat TaSPO11-1 exhibits evolutionarily conserved function in meiotic recombination across distant plant species.}, journal = {The Plant journal : for cell and molecular biology}, volume = {103}, number = {6}, pages = {2052-2068}, doi = {10.1111/tpj.14882}, pmid = {32559326}, issn = {1365-313X}, mesh = {Aegilops/genetics ; Arabidopsis Proteins/genetics ; Conserved Sequence/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genes, Plant/*genetics ; Meiosis/genetics ; Oryza/genetics ; Plant Proteins/*genetics ; Sequence Alignment ; Triticum/*genetics ; }, abstract = {The manipulation of meiotic recombination in crops is essential to develop new plant varieties rapidly, helping to produce more cultivars in a sustainable manner. One option is to control the formation and repair of the meiosis-specific DNA double-strand breaks (DSBs) that initiate recombination between the homologous chromosomes and ultimately lead to crossovers. These DSBs are introduced by the evolutionarily conserved topoisomerase-like protein SPO11 and associated proteins. Here, we characterized the homoeologous copies of the SPO11-1 protein in hexaploid bread wheat (Triticum aestivum). The genome contains three SPO11-1 gene copies that exhibit 93-95% identity at the nucleotide level, and clearly the A and D copies originated from the diploid ancestors Triticum urartu and Aegilops tauschii, respectively. Furthermore, phylogenetic analysis of 105 plant genomes revealed a clear partitioning between monocots and dicots, with the seven main motifs being almost fully conserved, even between clades. The functional similarity of the proteins among monocots was confirmed through complementation analysis of the Oryza sativa (rice) spo11-1 mutant by the wheat TaSPO11-1-5D coding sequence. Also, remarkably, although the wheat and Arabidopsis SPO11-1 proteins share only 55% identity and the partner proteins also differ, the TaSPO11-1-5D cDNA significantly restored the fertility of the Arabidopsis spo11-1 mutant, indicating a robust functional conservation of the SPO11-1 protein activity across distant plants. These successful heterologous complementation assays, using both Arabidopsis and rice hosts, are good surrogates to validate the functionality of candidate genes and cDNA, as well as variant constructs, when the transformation and mutant production in wheat is much longer and more tedious.}, }
@article {pmid32556263, year = {2020}, author = {Roy, D and Huguet, KT and Grenier, F and Burrus, V}, title = {IncC conjugative plasmids and SXT/R391 elements repair double-strand breaks caused by CRISPR-Cas during conjugation.}, journal = {Nucleic acids research}, volume = {48}, number = {16}, pages = {8815-8827}, pmid = {32556263}, issn = {1362-4962}, support = {PJT-153071//CIHR/Canada ; }, mesh = {Bacteriophage lambda/genetics ; *CRISPR-Cas Systems ; *Conjugation, Genetic ; DNA Restriction-Modification Enzymes/*genetics ; Escherichia coli/*genetics ; Gene Transfer, Horizontal ; Operon ; Plasmids/*genetics ; Vibrio cholerae/*genetics ; }, abstract = {Bacteria have evolved defence mechanisms against bacteriophages. Restriction-modification systems provide innate immunity by degrading invading DNAs that lack proper methylation. CRISPR-Cas systems provide adaptive immunity by sampling the genome of past invaders and cutting the DNA of closely related DNA molecules. These barriers also restrict horizontal gene transfer mediated by conjugative plasmids. IncC conjugative plasmids are important contributors to the global dissemination of multidrug resistance among pathogenic bacteria infecting animals and humans. Here, we show that IncC conjugative plasmids are highly resilient to host defence systems during entry into a new host by conjugation. Using a TnSeq strategy, we uncover a conserved operon containing five genes (vcrx089-vcrx093) that confer a novel host defence evasion (hde) phenotype. We show that vcrx089-vcrx090 promote resistance against type I restriction-modification, whereas vcrx091-vcxr093 promote CRISPR-Cas evasion by repairing double-strand DNA breaks via recombination between short sequence repeats. vcrx091, vcrx092 and vcrx093 encode a single-strand binding protein, and a single-strand annealing recombinase and double-strand exonuclease related to Redβ and λExo of bacteriophage λ, respectively. Homologous genes of the integrative and conjugative element R391 also provide CRISPR-Cas evasion. Hence, the conserved hde operon considerably broadens the host range of large families of mobile elements spreading multidrug resistance.}, }
@article {pmid32547503, year = {2020}, author = {Solgi, H and Nematzadeh, S and Giske, CG and Badmasti, F and Westerlund, F and Lin, YL and Goyal, G and Nikbin, VS and Nemati, AH and Shahcheraghi, F}, title = {Molecular Epidemiology of OXA-48 and NDM-1 Producing Enterobacterales Species at a University Hospital in Tehran, Iran, Between 2015 and 2016.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {936}, pmid = {32547503}, issn = {1664-302X}, abstract = {Carbapenem-resistant Enterobacterales (CRE) is an increasing problem worldwide. Here, we examined the clonal relatedness of 71 non-repetitive CRE isolates collected in a university hospital in Tehran, Iran, between February 2015 and March 2016. Pulsed-field gel electrophoresis (PFGE) and MLST were used for epidemiological analysis. Screening for antibiotic resistance genes, PCR-based replicon typing, conjugation experiments, and optical DNA mapping were also performed. Among all 71 isolates, 47 isolates of Klebsiella pneumoniae (66.2%), eight Escherichia coli (11.2%), five Serratia marcescens (7%), and two Enterobacter cloacae (2.8%) harbored bla NDM-1 and bla OXA-48 genes together or alone. PFGE analysis revealed that most of the OXA-48- and NDM-1-producing K. pneumoniae and all of OXA-48-producing S. marcescens were clonally related, while all eight E. coli and two E. cloacae isolates were clonally unrelated. The predominant clones of carbapenemase-producing K. pneumoniae associated with outbreaks within the hospital were ST147 (n = 13) and ST893 (n = 10). Plasmids carrying bla NDM-1 and bla OXA-48 were successfully transferred to an E. coli K12-recipient strain. The bla OXA-48 gene was located on an IncL/M conjugative plasmid, while the bla NDM-1 gene was located on both IncFII ∼86-kb to ∼140-kb and IncA/C conjugative plasmids. Our findings provide novel epidemiologic data on carbapenemase-producing Enterobacterales (CPE) in Iran and highlight the importance of horizontal gene transfer in the dissemination of bla NDM-1 and bla OXA-48 genes. The occurrence and transmission of distinct K. pneumoniae clones call for improved infection control to prevent further spread of these pathogens in Iran.}, }
@article {pmid32546745, year = {2020}, author = {Pirritano, M and Zaburannyi, N and Grosser, K and Gasparoni, G and Müller, R and Simon, M and Schrallhammer, M}, title = {Dual-Seq reveals genome and transcriptome of Caedibacter taeniospiralis, obligate endosymbiont of Paramecium.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {9727}, pmid = {32546745}, issn = {2045-2322}, mesh = {Animals ; Bacteria/genetics ; Evolution, Molecular ; Gammaproteobacteria/*genetics/pathogenicity ; Genome, Bacterial/genetics ; Paramecium/genetics/*microbiology ; Phenotype ; Phylogeny ; Symbiosis/*genetics/physiology ; Transcriptome ; }, abstract = {Interest in host-symbiont interactions is continuously increasing, not only due to the growing recognition of the importance of microbiomes. Starting with the detection and description of novel symbionts, attention moves to the molecular consequences and innovations of symbioses. However, molecular analysis requires genomic data which is difficult to obtain from obligate intracellular and uncultivated bacteria. We report the identification of the Caedibacter genome, an obligate symbiont of the ciliate Paramecium. The infection does not only confer the host with the ability to kill other cells but also renders them immune against this effect. We obtained the C. taeniospiralis genome and transcriptome by dual-Seq of DNA and RNA from infected paramecia. Comparison of codon usage and expression level indicates that genes necessary for a specific trait of this symbiosis, i.e. the delivery of an unknown toxin, result from horizontal gene transfer hinting to the relevance of DNA transfer for acquiring new characters. Prediction of secreted proteins of Caedibacter as major agents of contact with the host implies, next to several toxin candidates, a rather uncharacterized secretome which appears to be highly adapted to this symbiosis. Our data provides new insights into the molecular establishment and evolution of this obligate symbiosis and for the pathway characterization of toxicity and immunity.}, }
@article {pmid32546718, year = {2020}, author = {Strakova, A and Nicholls, TJ and Baez-Ortega, A and Ní Leathlobhair, M and Sampson, AT and Hughes, K and Bolton, IAG and Gori, K and Wang, J and Airikkala-Otter, I and Allen, JL and Allum, KM and Arnold, CL and Bansse-Issa, L and Bhutia, TN and Bisson, JL and Blank, K and Briceño, C and Castillo Domracheva, A and Corrigan, AM and Cran, HR and Crawford, JT and Cutter, SM and Davis, E and de Castro, KF and De Nardi, AB and de Vos, AP and Delgadillo Keenan, L and Donelan, EM and Espinoza Huerta, AR and Faramade, IA and Fazil, M and Fotopoulou, E and Fruean, SN and Gallardo-Arrieta, F and Glebova, O and Gouletsou, PG and Häfelin Manrique, RF and Henriques, JJGP and Horta, RS and Ignatenko, N and Kane, Y and King, C and Koenig, D and Krupa, A and Kruzeniski, SJ and Lanza-Perea, M and Lazyan, M and Lopez Quintana, AM and Losfelt, T and Marino, G and Martínez Castañeda, S and Martínez-López, MF and Masuruli, BM and Meyer, M and Migneco, EJ and Nakanwagi, B and Neal, KB and Neunzig, W and Nixon, SJ and Ortega-Pacheco, A and Pedraza-Ordoñez, F and Peleteiro, MC and Polak, K and Pye, RJ and Ramirez-Ante, JC and Reece, JF and Rojas Gutierrez, J and Sadia, H and Schmeling, SK and Shamanova, O and Sherlock, AG and Steenland-Smit, AE and Svitich, A and Tapia Martínez, LJ and Thoya Ngoka, I and Torres, CG and Tudor, EM and van der Wel, MG and Vițălaru, BA and Vural, SA and Walkinton, O and Wehrle-Martinez, AS and Widdowson, SAE and Zvarich, I and Chinnery, PF and Falkenberg, M and Gustafsson, CM and Murchison, EP}, title = {Recurrent horizontal transfer identifies mitochondrial positive selection in a transmissible cancer.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {3059}, pmid = {32546718}, issn = {2041-1723}, support = {212219/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; 213464/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; /DH_/Department of Health/United Kingdom ; MC_UP_1501/2/MRC_/Medical Research Council/United Kingdom ; 102942/Z/13/A/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Dog Diseases/*genetics ; Dogs ; Gene Transfer, Horizontal ; *Haplotypes ; Phylogeny ; Polymorphism, Genetic ; Recurrence ; Selection, Genetic ; Venereal Tumors, Veterinary/*genetics ; }, abstract = {Autonomous replication and segregation of mitochondrial DNA (mtDNA) creates the potential for evolutionary conflict driven by emergence of haplotypes under positive selection for 'selfish' traits, such as replicative advantage. However, few cases of this phenomenon arising within natural populations have been described. Here, we survey the frequency of mtDNA horizontal transfer within the canine transmissible venereal tumour (CTVT), a contagious cancer clone that occasionally acquires mtDNA from its hosts. Remarkably, one canine mtDNA haplotype, A1d1a, has repeatedly and recently colonised CTVT cells, recurrently replacing incumbent CTVT haplotypes. An A1d1a control region polymorphism predicted to influence transcription is fixed in the products of an A1d1a recombination event and occurs somatically on other CTVT mtDNA backgrounds. We present a model whereby 'selfish' positive selection acting on a regulatory variant drives repeated fixation of A1d1a within CTVT cells.}, }
@article {pmid32546670, year = {2020}, author = {Zhong, ZP and Rapp, JZ and Wainaina, JM and Solonenko, NE and Maughan, H and Carpenter, SD and Cooper, ZS and Jang, HB and Bolduc, B and Deming, JW and Sullivan, MB}, title = {Viral Ecogenomics of Arctic Cryopeg Brine and Sea Ice.}, journal = {mSystems}, volume = {5}, number = {3}, pages = {}, pmid = {32546670}, issn = {2379-5077}, abstract = {Arctic regions, which are changing rapidly as they warm 2 to 3 times faster than the global average, still retain microbial habitats that serve as natural laboratories for understanding mechanisms of microbial adaptation to extreme conditions. Seawater-derived brines within both sea ice (sea-ice brine) and ancient layers of permafrost (cryopeg brine) support diverse microbes adapted to subzero temperatures and high salinities, yet little is known about viruses in these extreme environments, which, if analogous to other systems, could play important evolutionary and ecosystem roles. Here, we characterized viral communities and their functions in samples of cryopeg brine, sea-ice brine, and melted sea ice. Viral abundance was high in cryopeg brine (1.2 × 10[8] ml[-1]) and much lower in sea-ice brine (1.3 × 10[5] to 2.1 × 10[5] ml[-1]), which roughly paralleled the differences in cell concentrations in these samples. Five low-input, quantitative viral metagenomes were sequenced to yield 476 viral populations (i.e., species level; ≥10 kb), only 12% of which could be assigned taxonomy by traditional database approaches, indicating a high degree of novelty. Additional analyses revealed that these viruses: (i) formed communities that differed between sample type and vertically with sea-ice depth; (ii) infected hosts that dominated these extreme ecosystems, including Marinobacter, Glaciecola, and Colwellia; and (iii) encoded fatty acid desaturase (FAD) genes that likely helped their hosts overcome cold and salt stress during infection, as well as mediated horizontal gene transfer of FAD genes between microbes. Together, these findings contribute to understanding viral abundances and communities and how viruses impact their microbial hosts in subzero brines and sea ice.IMPORTANCE This study explores viral community structure and function in remote and extreme Arctic environments, including subzero brines within marine layers of permafrost and sea ice, using a modern viral ecogenomics toolkit for the first time. In addition to providing foundational data sets for these climate-threatened habitats, we found evidence that the viruses had habitat specificity, infected dominant microbial hosts, encoded host-derived metabolic genes, and mediated horizontal gene transfer among hosts. These results advance our understanding of the virosphere and how viruses influence extreme ecosystems. More broadly, the evidence that virally mediated gene transfers may be limited by host range in these extreme habitats contributes to a mechanistic understanding of genetic exchange among microbes under stressful conditions in other systems.}, }
@article {pmid32544567, year = {2020}, author = {Zhou, Y and Tian, D and Tang, Y and Yu, L and Huang, Y and Li, G and Li, M and Wang, Y and Yang, Z and Poirel, L and Jiang, X}, title = {High-risk KPC-producing Klebsiella pneumoniae lack type I R-M systems.}, journal = {International journal of antimicrobial agents}, volume = {56}, number = {2}, pages = {106050}, doi = {10.1016/j.ijantimicag.2020.106050}, pmid = {32544567}, issn = {1872-7913}, mesh = {Bacterial Proteins/*genetics ; Deoxyribonucleases, Type I Site-Specific/*genetics ; Drug Resistance, Multiple, Bacterial/genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; Interspersed Repetitive Sequences ; Klebsiella Infections/microbiology ; Klebsiella pneumoniae/classification/*genetics ; Plasmids/genetics ; Polymorphism, Genetic ; Whole Genome Sequencing ; beta-Lactamases/*genetics ; }, abstract = {Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae (KPC-KP) have disseminated worldwide and are a major threat to public health. The multidrug-resistant (MDR)-phenotype of KPC-KP are commonly associated with the presence of high molecular weight blaKPC plasmids. Restriction-modification (R-M) systems provide bacteria with innate defense against plasmids or other infectious gene elements. As blaKPC plasmids are favored by such MDR K. pneumoniae, it was of interest to examine the co-distribution of R-M and acquired blaKPC plasmids in KPC-KP. A total of 459 clinical K. pneumoniae isolates in China and 217 global whole-genome sequences in GenBank were collected to determine the prevalence of type I R-M systems. The type I R-M systems were scarce in the KPC-positive group and high-risk Klebsiella pneumoniae clonal group 258 (CG258). The polymorphisms of type I R-M observed in K. pneumoniae revealed the ubiquity of their recognition sequences in DNA; therefore, the type I R-M systems could attack most invading DNA elements, such as blaKPC genes. Overall, this work indicated the type I R-M systems may impact the acquisition of blaKPC genes in K. pneumoniae.}, }
@article {pmid32541663, year = {2020}, author = {Bárdy, P and Füzik, T and Hrebík, D and Pantůček, R and Thomas Beatty, J and Plevka, P}, title = {Structure and mechanism of DNA delivery of a gene transfer agent.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {3034}, pmid = {32541663}, issn = {2041-1723}, mesh = {Bacteriophages/genetics/*physiology/ultrastructure ; Cryoelectron Microscopy ; DNA, Bacterial/genetics ; Gene Expression Regulation, Bacterial ; *Gene Transfer Techniques ; Gene Transfer, Horizontal ; Rhodobacter capsulatus/*genetics/*virology ; Siphoviridae/genetics/*physiology/ultrastructure ; }, abstract = {Alphaproteobacteria, which are the most abundant microorganisms of temperate oceans, produce phage-like particles called gene transfer agents (GTAs) that mediate lateral gene exchange. However, the mechanism by which GTAs deliver DNA into cells is unknown. Here we present the structure of the GTA of Rhodobacter capsulatus (RcGTA) and describe the conformational changes required for its DNA ejection. The structure of RcGTA resembles that of a tailed phage, but it has an oblate head shortened in the direction of the tail axis, which limits its packaging capacity to less than 4,500 base pairs of linear double-stranded DNA. The tail channel of RcGTA contains a trimer of proteins that possess features of both tape measure proteins of long-tailed phages from the family Siphoviridae and tail needle proteins of short-tailed phages from the family Podoviridae. The opening of a constriction within the RcGTA baseplate enables the ejection of DNA into bacterial periplasm.}, }
@article {pmid32540654, year = {2020}, author = {Lin, Y and Dong, X and Sun, R and Wu, J and Tian, L and Rao, D and Zhang, L and Yang, K}, title = {Migratory birds-one major source of environmental antibiotic resistance around Qinghai Lake, China.}, journal = {The Science of the total environment}, volume = {739}, number = {}, pages = {139758}, pmid = {32540654}, issn = {1879-1026}, mesh = {Animals ; Anti-Bacterial Agents ; Bacteria/genetics ; Birds ; China ; *Genes, Bacterial ; *Lakes ; }, abstract = {Migratory birds are potential transmitters of bacterial antibiotic resistance. However, their role in the environmental dissemination of bacterial antibiotic resistance and the extent of their impact on the environment are not yet clear. Qinghai Lake is one of the most important breeding and stopover ground for the migratory birds along the Central Asian Flyway. Here, we investigated the bacterial antibiotic resistance in the environment and among the migratory birds around the lake. The results of culture-based analysis of bacterial antibiotic resistance, quantitative PCR and metagenomic sequencing indicate that migratory birds are one major source of bacterial antibiotic resistance in the environment around Qinghai Lake. Network analysis reveals the co-occurrence patterns of antibiotic resistance genes (ARGs) and bacterial genera. Genetic co-localization analysis suggests high co-selection potential (with incidence of 35.8%) among different ARGs, but limited linkage (with incidence of only 3.7%) between ARGs and biocide/metal resistance genes (BMRGs). The high genetic linkage between ARGs and mobile genetic elements (MGEs) is still largely confined to the bacterial community in migratory birds (accounting for 96.0% of sequencing reads of MGE-linked ARGs), which indicates limited horizontal transfer of ARGs to the environment. Nevertheless, the antibiotic resistance determinants carried by migratory birds and their specific genetic properties (high co-selection and mobility potential of the ARGs) remind us that the role of migratory birds in the environmental dissemination of bacterial antibiotic resistance deserves more attention.}, }
@article {pmid32540473, year = {2020}, author = {Prasad, B and Richter, P and Vadakedath, N and Mancinelli, R and Krüger, M and Strauch, SM and Grimm, D and Darriet, P and Chapel, JP and Cohen, J and Lebert, M}, title = {Exploration of space to achieve scientific breakthroughs.}, journal = {Biotechnology advances}, volume = {43}, number = {}, pages = {107572}, doi = {10.1016/j.biotechadv.2020.107572}, pmid = {32540473}, issn = {1873-1899}, mesh = {Adaptation, Physiological ; Agriculture ; *Space Flight ; Stress, Physiological ; *Weightlessness ; }, abstract = {Living organisms adapt to changing environments using their amazing flexibility to remodel themselves by a process called evolution. Environmental stress causes selective pressure and is associated with genetic and phenotypic shifts for better modifications, maintenance, and functioning of organismal systems. The natural evolution process can be used in complement to rational strain engineering for the development of desired traits or phenotypes as well as for the production of novel biomaterials through the imposition of one or more selective pressures. Space provides a unique environment of stressors (e.g., weightlessness and high radiation) that organisms have never experienced on Earth. Cells in the outer space reorganize and develop or activate a range of molecular responses that lead to changes in cellular properties. Exposure of cells to the outer space will lead to the development of novel variants more efficiently than on Earth. For instance, natural crop varieties can be generated with higher nutrition value, yield, and improved features, such as resistance against high and low temperatures, salt stress, and microbial and pest attacks. The review summarizes the literature on the parameters of outer space that affect the growth and behavior of cells and organisms as well as complex colloidal systems. We illustrate an understanding of gravity-related basic biological mechanisms and enlighten the possibility to explore the outer space environment for application-oriented aspects. This will stimulate biological research in the pursuit of innovative approaches for the future of agriculture and health on Earth.}, }
@article {pmid32535196, year = {2020}, author = {Pietsch, F and O'Neill, AJ and Ivask, A and Jenssen, H and Inkinen, J and Kahru, A and Ahonen, M and Schreiber, F}, title = {Selection of resistance by antimicrobial coatings in the healthcare setting.}, journal = {The Journal of hospital infection}, volume = {106}, number = {1}, pages = {115-125}, doi = {10.1016/j.jhin.2020.06.006}, pmid = {32535196}, issn = {1532-2939}, mesh = {Anti-Bacterial Agents/*pharmacology ; Anti-Infective Agents/*pharmacology ; Bacteria/*drug effects/genetics ; Biofilms/drug effects ; Coated Materials, Biocompatible ; Copper/pharmacology ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; *Health Facilities ; Humans ; Mutation ; Pore Forming Cytotoxic Proteins/pharmacology ; Silver/pharmacology ; Surface Properties ; }, abstract = {Antimicrobial touch surfaces have been introduced in healthcare settings with the aim of supporting existing hygiene procedures, and to help combat the increasing threat of antimicrobial resistance. However, concerns have been raised over the potential selection pressure exerted by such surfaces, which may drive the evolution and spread of antimicrobial resistance. This review highlights studies that indicate risks associated with resistance on antimicrobial surfaces by different processes, including evolution by de-novo mutation and horizontal gene transfer, and species sorting of inherently resistant bacteria dispersed on to antimicrobial surfaces. The review focuses on antimicrobial surfaces made of copper, silver and antimicrobial peptides because of the practical application of copper and silver, and the promising characteristics of antimicrobial peptides. The available data point to a potential for resistance selection and a subsequent increase in resistant strains via cross-resistance and co-resistance conferred by metal and antibiotic resistance traits. However, translational studies describing the development of resistance to antimicrobial touch surfaces in healthcare-related environments are rare, and will be needed to assess whether and how antimicrobial surfaces lead to resistance selection in these settings. Such studies will need to consider numerous variables, including the antimicrobial concentrations present in coatings, the occurrence of biofilms on surfaces, and the humidity relevant to dry-surface environments. On-site tests on the efficacy of antimicrobial coatings should routinely evaluate the risk of selection associated with their use.}, }
@article {pmid32532873, year = {2020}, author = {Nagasawa, R and Sato, T and Nomura, N and Nakamura, T and Senpuku, H}, title = {Potential Risk of Spreading Resistance Genes within Extracellular-DNA-Dependent Biofilms of Streptococcus mutans in Response to Cell Envelope Stress Induced by Sub-MICs of Bacitracin.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {16}, pages = {}, pmid = {32532873}, issn = {1098-5336}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacitracin/*pharmacology ; *Biofilms ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/*physiology ; Genes, MDR/genetics ; Microbial Sensitivity Tests ; Streptococcus mutans/genetics/*physiology ; Stress, Physiological ; }, abstract = {Antibiotics are used to treat or prevent some types of bacterial infection. The inappropriate use of antibiotics unnecessarily promotes antibiotic resistance and increases resistant bacteria, and controlling these bacteria is difficult. While the emergence of drug-resistant bacteria is a serious problem, the behavior of drug-resistant bacteria is not fully understood. In this study, we investigated the behavior of Streptococcus mutans, a major etiological agent of dental caries that is resistant to bacitracin, which is a cell wall-targeting antibiotic, and focused on biofilm formation in the presence of bacitracin. S. mutans UA159 most strongly induced extracellular DNA (eDNA)-dependent biofilm formation in the presence of bacitracin at 1/8× MIC. The ΔmbrC and ΔmbrD mutant strains, which lack bacitracin resistance, also formed biofilms in the presence of bacitracin at 1/2× MIC. This difference between the wild type and the mutants was caused by the induction of atlA expression in the mid-log phase. We also revealed that certain rgp genes involved in the synthesis of rhamnose-glucose polysaccharide related to cell wall synthesis were downregulated by bacitracin. In addition, glucosyltransferase-I was also involved in eDNA-dependent biofilm formation. The biofilm led to increased transformation efficiencies and promoted horizontal gene transfer. Biofilms were also induced by ampicillin and vancomycin, antibiotics targeting cell wall synthesis, suggesting that cell envelope stress triggers biofilm formation. Therefore, the expression of the atlA and rgp genes is regulated by S. mutans, which forms eDNA-dependent biofilms, promoting horizontal gene transfer in response to cell envelope stress induced by sub-MICs of antibiotics.IMPORTANCE Antibiotics have been reported to induce biofilm formation in many bacteria at subinhibitory concentrations. Accordingly, it is conceivable that the MIC against drug-sensitive bacteria may promote biofilm formation of resistant bacteria. Since drug-resistant bacteria have spread, it is important to understand the behavior of resistant bacteria. Streptococcus mutans is bacitracin resistant, and the 1/8× MIC of bacitracin, which is a cell wall-targeted antibiotic, induced eDNA-dependent biofilm formation. The ΔmbrC and ΔmbrD strains, which are not resistant to bacitracin, also formed biofilms in the presence of bacitracin at 1/2× MIC, and biofilms of both the wild type and mutants promoted horizontal gene transfer. Another cell wall-targeted antibiotic, vancomycin, showed effects on biofilms and gene transfer similar to those of bacitracin. Thus, treatment with cell wall-targeted antibiotics may promote the spread of drug-resistant genes in biofilms. Therefore, the behavior of resistant bacteria in the presence of antibiotics at sub-MICs should be investigated when using antibiotics.}, }
@article {pmid32531733, year = {2020}, author = {Jang, HM and Lee, J and Shin, SG and Shin, J and Kim, YM}, title = {Comparing the fate of antibiotic resistance genes in two full-scale thermophilic anaerobic digestion plants treating food wastewater.}, journal = {Bioresource technology}, volume = {312}, number = {}, pages = {123577}, doi = {10.1016/j.biortech.2020.123577}, pmid = {32531733}, issn = {1873-2976}, mesh = {Anaerobiosis ; *Anti-Bacterial Agents ; Drug Resistance, Bacterial ; Genes, Bacterial ; Macrolides ; *Wastewater ; }, abstract = {This study focus on the fate of ARGs in the full-scale AD of food wastewater (FWW). Residue was collected from two different full-scale thermophilic AD treating FWW. Ten selected ARGs, including tetracycline resistance genes (tetM, tetX, tetQ, tetH and tetG), sulfonamide resistance genes (sul1 and sul2), quinolone resistance genes (qnrD) and macrolide resistance genes (ermB and ermC), were amplified using quantitative polymerase chain reaction (qPCR). Furthermore, the class 1 integron-integrase gene (intI1) was selected as a representative mobile gene element. Remarkable reduction in the ARGs and intI1 was observed in two-stage (acidogenic-methanogenic) AD, particularly, tetG, tetH, tetM, tetQ, tetX and intI1 not detected. Additionally, significant positive correlation (p < 0.01) between ARGs and intI1 suggested a strong likelihood of horizontal gene transfer (HGT). Furthermore, stepwise multiple linear regression analysis revealed significant factors related to the fate of individual ARGs and intI1 during AD.}, }
@article {pmid32530914, year = {2020}, author = {Touchon, M and Perrin, A and de Sousa, JAM and Vangchhia, B and Burn, S and O'Brien, CL and Denamur, E and Gordon, D and Rocha, EP}, title = {Phylogenetic background and habitat drive the genetic diversification of Escherichia coli.}, journal = {PLoS genetics}, volume = {16}, number = {6}, pages = {e1008866}, pmid = {32530914}, issn = {1553-7404}, mesh = {Animals ; Animals, Wild/microbiology ; Australia ; Chickens/microbiology ; Drug Resistance, Bacterial/genetics ; Escherichia coli/*genetics/isolation &amp; purification/pathogenicity ; *Evolution, Molecular ; Feces/microbiology ; Fresh Water/microbiology ; *Gene Transfer, Horizontal ; *Genetic Variation ; Genome Size ; Genome, Bacterial/*genetics ; Humans ; Inflammatory Bowel Diseases/microbiology ; Interspersed Repetitive Sequences/genetics ; Intestinal Mucosa/microbiology ; Meat/microbiology ; Molecular Sequence Annotation ; Phylogeny ; Soil Microbiology ; Virulence Factors/genetics ; Whole Genome Sequencing ; }, abstract = {Escherichia coli is mostly a commensal of birds and mammals, including humans, where it can act as an opportunistic pathogen. It is also found in water and sediments. We investigated the phylogeny, genetic diversification, and habitat-association of 1,294 isolates representative of the phylogenetic diversity of more than 5,000 isolates from the Australian continent. Since many previous studies focused on clinical isolates, we investigated mostly other isolates originating from humans, poultry, wild animals and water. These strains represent the species genetic diversity and reveal widespread associations between phylogroups and isolation sources. The analysis of strains from the same sequence types revealed very rapid change of gene repertoires in the very early stages of divergence, driven by the acquisition of many different types of mobile genetic elements. These elements also lead to rapid variations in genome size, even if few of their genes rise to high frequency in the species. Variations in genome size are associated with phylogroup and isolation sources, but the latter determine the number of MGEs, a marker of recent transfer, suggesting that gene flow reinforces the association of certain genetic backgrounds with specific habitats. After a while, the divergence of gene repertoires becomes linear with phylogenetic distance, presumably reflecting the continuous turnover of mobile element and the occasional acquisition of adaptive genes. Surprisingly, the phylogroups with smallest genomes have the highest rates of gene repertoire diversification and fewer but more diverse mobile genetic elements. This suggests that smaller genomes are associated with higher, not lower, turnover of genetic information. Many of these genomes are from freshwater isolates and have peculiar traits, including a specific capsule, suggesting adaptation to this environment. Altogether, these data contribute to explain why epidemiological clones tend to emerge from specific phylogenetic groups in the presence of pervasive horizontal gene transfer across the species.}, }
@article {pmid32525727, year = {2020}, author = {Gong, L and Liu, Y and Xiong, Y and Li, T and Yin, C and Zhao, J and Yu, J and Yin, Q and Gupta, VK and Jiang, Y and Duan, X}, title = {New insights into the evolution of host specificity of three Penicillium species and the pathogenicity of P. Italicum involving the infection of Valencia orange (Citrus sinensis).}, journal = {Virulence}, volume = {11}, number = {1}, pages = {748-768}, pmid = {32525727}, issn = {2150-5608}, mesh = {China ; Citrus sinensis/*microbiology ; Computational Biology ; Gene Expression Profiling ; *Genome, Fungal ; Genomics ; *Host Specificity ; Penicillium/classification/*pathogenicity ; Plant Diseases/*microbiology ; Transcriptome ; Virulence ; }, abstract = {UNLABELLED: Blue and green molds, the common phenotypes of post-harvest diseases in fruits, are mainly caused by Penicillium fungal species, including P. italicum, P. digitatum, and P. expansum. We sequenced and assembled the genome of a P. italicum strain, which contains 31,034,623 bp with 361 scaffolds and 627 contigs. The mechanisms underlying the evolution of host specificity among the analyzed Penicillium species were associated with the expansion of protein families, genome restructuring, horizontal gene transfer, and positive selection pressure. A dual-transcriptome analysis following the infection of Valencia orange (Citrus sinensis) by P. italicum resulted in the annotation of 9,307 P. italicum genes and 24,591 Valencia orange genes. The pathogenicity of P. italicum may be due to the activation of effectors, including 51 small secreted cysteine-rich proteins, 110 carbohydrate-active enzymes, and 12 G protein-coupled receptors. Additionally, 211 metabolites related to the interactions between P. italicum and Valencia orange were identified by gas chromatography-time of flight mass spectrography, three of which were further confirmed by ultra-high performance liquid chromatography triple quadrupole mass spectrometry. A metabolomics analysis indicated that P. italicum pathogenicity is associated with the sphingolipid and salicylic acid signaling pathways. Moreover, a correlation analysis between the metabolite contents and gene expression levels suggested that P. italicum induces carbohydrate metabolism in Valencia orange fruits as part of its infection strategy. This study provides useful information regarding the genomic determinants that drive the evolution of host specificity in Penicillium species and clarifies the host-plant specificity during the infection of Valencia orange by P. italicum.<br><br>IMPORTANCE: P. italicum GL_Gan1, a local strain in Guangzhou, China, was sequenced. Comparison of the genome of P. italicum GL_Gan1 with other pathogenic Penicillium species, P. digitatum and P. expansum, revealed that the expansion of protein families, genome restructuring, HGT, and positive selection pressure were related to the host range expansion of the analyzed Penicillium species. Moreover, gene gains or losses might be associated with the speciation of these Penicillium species. In addition, the molecular basis of host-plant specificity during the infection of Valencia orange (Citrus sinensis) by P. italicum was also elucidated by transcriptomic and metabolomics analysis. The data presented herein may be useful for further elucidating the molecular basis of the evolution of host specificity of Penicillium species and for illustrating the host-plant specificity during the infection of Valencia orange by P. italicum.}, }
@article {pmid32522962, year = {2020}, author = {Lee, M and Choi, TJ}, title = {Species Transferability of Klebsiella pneumoniae Carbapenemase-2 Isolated from a High-Risk Clone of Escherichia coli ST410.}, journal = {Journal of microbiology and biotechnology}, volume = {30}, number = {7}, pages = {974-981}, pmid = {32522962}, issn = {1738-8872}, mesh = {Aged ; Bacterial Outer Membrane Proteins ; Bacterial Proteins/*genetics ; Clone Cells ; Cross Infection/microbiology ; Escherichia coli/enzymology/genetics/isolation &amp; purification ; Escherichia coli Infections/microbiology ; *Gene Transfer, Horizontal ; Genotype ; Humans ; Klebsiella Infections/microbiology ; Klebsiella pneumoniae/enzymology/*genetics/isolation &amp; purification ; Male ; Microbial Sensitivity Tests ; Molecular Typing ; Multilocus Sequence Typing ; Plasmids ; Renal Insufficiency, Chronic/microbiology ; Whole Genome Sequencing ; beta-Lactamases/*genetics ; }, abstract = {Sequence type 410 (ST410) of Escherichia coli is an extraintestinal pathogen associated with multi drug resistance. In this study, we aimed to investigate the horizontal propagation pathway of a highrisk clone of E. coli ST410 that produces Klebsiella pneumoniae carbapenemase (KPC). blaKPCencoding E. coli and K. pneumoniae isolates were evaluated, and complete sequencing and comparative analysis of blaKPC-encoding plasmids from E. coli and K. pneumoniae, antimicrobial susceptibility tests, polymerase chain reaction, multilocus sequence typing, and conjugal transfer of plasmids were performed. Whole-genome sequencing was performed for plasmids mediating KPC-2 production in E. coli and K. pneumoniae clinical isolates. Strains E. coli CPEc171209 and K. pneumoniae CPKp171210 were identified as ST410 and ST307, respectively. CPEc171209 harbored five plasmids belonging to serotype O8:H21, which is in the antimicrobial-resistant clade C4/H24. The CPKp171210 isolate harbored three plasmids. Both strains harbored various additional antimicrobial resistance genes. The IncX3 plasmid pECBHS_9_5 harbored blaKPC-2 within a truncated Tn4401a transposon, which also contains blaSHV-182 with duplicated conjugative elements. This plasmid displayed 100% identity with the IncX3 plasmid pKPBHS_10_3 from the K. pneumoniae CPKp171210 ST307 strain. The genes responsible for the conjugal transfer of the IncX3 plasmid included tra/trb clusters and pil genes coding the type IV pilus. ST410 can be transmitted between patients, posing an elevated risk in clinical settings. The emergence of a KPC-producing E. coli strain (ST410) is concerning because the blaKPC-2-bearing plasmids may carry treatment resistance across species barriers. Transgenic translocation occurs among carbapenem-resistant bacteria, which may spread rapidly via horizontal migration.}, }
@article {pmid32521746, year = {2020}, author = {Lynch, CT and Lynch, H and Burke, S and Hawkins, K and Buttimer, C and Mc Carthy, C and Egan, J and Whyte, P and Bolton, D and Coffey, A and Lucey, B}, title = {Antimicrobial Resistance Determinants Circulating among Thermophilic Campylobacter Isolates Recovered from Broilers in Ireland Over a One-Year Period.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {9}, number = {6}, pages = {}, pmid = {32521746}, issn = {2079-6382}, support = {15F641//Department of Agriculture Food and the Marine, Food Institutional Research Measure/ ; }, abstract = {Campylobacteriosis is the leading cause of human bacterial gastroenteritis, very often associated with poultry consumption. Thermophilic Campylobacter (Campylobacter jejuni and Campylobacter coli) isolates (n = 158) recovered from broiler neck skin and caecal contents in Ireland over a one-year period, resistant to at least one of three clinically relevant antimicrobial classes, were screened for resistance determinants. All ciprofloxacin-resistant isolates (n = 99) harboured the C257T nucleotide mutation (conferring the Thr-86-Ile substitution) in conjunction with other synonymous and nonsynonymous mutations, which may have epidemiological value. The A2075G nucleotide mutation and amino acid substitutions in L4 and L22 were detected in all erythromycin-resistant isolates (n = 5). The tetO gene was detected in 100% (n = 119) of tetracycline-resistant isolates and three of which were found to harbour the mosaic tetracycline resistance gene tetO/32/O. Two streptomycin-resistant C. jejuni isolates (isolated from the same flock) harboured ant(6)-Ib, located in a multidrug resistance genomic island, containing aminoglycoside, streptothricin (satA) and tetracycline resistance genes (truncated tetO and mosaic tetO/32/O). The ant(6)-Ie gene was identified in two streptomycin-resistant C. coli isolates. This study highlights the widespread acquisition of antimicrobial resistance determinants among chicken-associated Campylobacter isolates, through horizontal gene transfer or clonal expansion of resistant lineages. The stability of such resistance determinants is compounded by the fluidity of mobile genetic element.}, }
@article {pmid32521019, year = {2020}, author = {Phansopa, C and Dunning, LT and Reid, JD and Christin, PA}, title = {Lateral Gene Transfer Acts As an Evolutionary Shortcut to Efficient C4 Biochemistry.}, journal = {Molecular biology and evolution}, volume = {37}, number = {11}, pages = {3094-3104}, pmid = {32521019}, issn = {1537-1719}, mesh = {Amino Acid Substitution ; *Biological Evolution ; *Gene Transfer, Horizontal ; Phosphoenolpyruvate Carboxylase/*genetics ; Photosynthesis/*genetics ; Poaceae/enzymology/*genetics ; }, abstract = {The adaptation of proteins for novel functions often requires changes in their kinetics via amino acid replacement. This process can require multiple mutations, and therefore extended periods of selection. The transfer of genes among distinct species might speed up the process, by providing proteins already adapted for the novel function. However, this hypothesis remains untested in multicellular eukaryotes. The grass Alloteropsis is an ideal system to test this hypothesis due to its diversity of genes encoding phosphoenolpyruvate carboxylase, an enzyme that catalyzes one of the key reactions in the C4 pathway. Different accessions of Alloteropsis either use native isoforms relatively recently co-opted from other functions or isoforms that were laterally acquired from distantly related species that evolved the C4 trait much earlier. By comparing the enzyme kinetics, we show that native isoforms with few amino acid replacements have substrate KM values similar to the non-C4 ancestral form, but exhibit marked increases in catalytic efficiency. The co-option of native isoforms was therefore followed by rapid catalytic improvements, which appear to rely on standing genetic variation observed within one species. Native C4 isoforms with more amino acid replacements exhibit additional changes in affinities, suggesting that the initial catalytic improvements are followed by gradual modifications. Finally, laterally acquired genes show both strong increases in catalytic efficiency and important changes in substrate handling. We conclude that the transfer of genes among distant species sharing the same physiological novelty creates an evolutionary shortcut toward more efficient enzymes, effectively accelerating evolution.}, }
@article {pmid32520697, year = {2020}, author = {Andrade-Oliveira, AL and Rossi, CC and Souza-Silva, T and Giambiagi-deMarval, M}, title = {Staphylococcus nepalensis, a commensal of the oral microbiota of domestic cats, is a reservoir of transferrable antimicrobial resistance.}, journal = {Microbiology (Reading, England)}, volume = {166}, number = {8}, pages = {727-734}, doi = {10.1099/mic.0.000940}, pmid = {32520697}, issn = {1465-2080}, mesh = {Animals ; Animals, Domestic ; Anti-Bacterial Agents/pharmacology ; Cats ; Disease Reservoirs/microbiology/*veterinary ; Drug Resistance, Bacterial/drug effects/*genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Variation ; Microbial Sensitivity Tests ; Plasmids/drug effects/genetics ; Staphylococcal Infections/microbiology/veterinary ; Staphylococcus/drug effects/genetics/isolation &amp; purification/*physiology ; Staphylococcus aureus/genetics ; }, abstract = {Staphylococcus nepalensis is a commensal bacterium from the oral microbiota of domestic cats, with a still obscure clinical importance. In this work, we analysed the ability of feline strains of S. nepalensis to transfer antimicrobial resistance genes to Staphylococcus aureus isolated from humans through plasmids. To this end, we first analysed all publicly available genomes from cat staphylococci using computational methods to build a pan-resistome. Genes that encode resistance to erythromycin, gentamicin, mupirocin and tetracycline, common to human and cat staphylococci and previously described to be located in mobile genetic elements, were chosen for the next analyses. We studied 15 strains of S. nepalensis, which were shown to be genetically different by GTG5-PCR. As observed by disc diffusion, resistance to tetracycline was widespread (80 %), followed by resistance to erythromycin (40 %), gentamicin (27 %) and mupirocin (7 %). The strains were positive for several antimicrobial resistance genes and more than half of them harboured plasmids. The loss of plasmids and resistance genes in some strains were induced by stress with SDS. Through conjugation experiments, we observed that these plasmids can be transferred to S. aureus, thus increasing its potential to resist drug therapy. Our findings show that S. nepalensis, an underestimated inhabitant of the cat microbiota, can be a reservoir of antimicrobial resistance genes for S. aureus and, like many other staphylococci, be an overlooked and silent threat to their animal hosts and humans living with them.}, }
@article {pmid32518725, year = {2020}, author = {Alvarenga, DO and Franco, MW and Sivonen, K and Fiore, MF and Varani, AM}, title = {Evaluating Eucalyptus leaf colonization by Brasilonema octagenarum (Cyanobacteria, Scytonemataceae) using in planta experiments and genomics.}, journal = {PeerJ}, volume = {8}, number = {}, pages = {e9158}, pmid = {32518725}, issn = {2167-8359}, abstract = {BACKGROUND: Brasilonema is a cyanobacterial genus found on the surface of mineral substrates and plants such as bromeliads, orchids and eucalyptus. B. octagenarum stands out among cyanobacteria due to causing damage to the leaves of its host in an interaction not yet observed in other cyanobacteria. Previous studies revealed that B. octagenaum UFV-E1 is capable of leading eucalyptus leaves to suffer internal tissue damage and necrosis by unknown mechanisms. This work aimed to investigate the effects of B. octagenarum UFV-E1 inoculation on Eucalyptus urograndis and to uncover molecular mechanisms potentially involved in leaf damage by these cyanobacteria using a comparative genomics approach.<br><br>RESULTS: Leaves from E. urograndis saplings were exposed for 30 days to B. octagenarum UFV-E1, which was followed by the characterization of its genome and its comparison with the genomes of four other Brasilonema strains isolated from phyllosphere and the surface of mineral substrates. While UFV-E1 inoculation caused an increase in root and stem dry mass of the host plants, the sites colonized by cyanobacteria on leaves presented a significant decrease in pigmentation, showing that the cyanobacterial mats have an effect on leaf cell structure. Genomic analyses revealed that all evaluated Brasilonema genomes harbored genes encoding molecules possibly involved in plant-pathogen interactions, such as hydrolases targeting plant cell walls and proteins similar to known virulence factors from plant pathogens. However, sequences related to the type III secretory system and effectors were not detected, suggesting that, even if any virulence factors could be expressed in contact with their hosts, they would not have the structural means to actively reach plant cytoplasm.<br><br>CONCLUSIONS: Leaf damage by this species is likely related to the blockage of access to sunlight by the efficient growth of cyanobacterial mats on the phyllosphere, which may hinder the photosynthetic machinery and prevent access to some essential molecules. These results reveal that the presence of cyanobacteria on leaf surfaces is not as universally beneficial as previously thought, since they may not merely provide the products of nitrogen fixation to their hosts in exchange for physical support, but in some cases also hinder regular leaf physiology leading to tissue damage.}, }
@article {pmid32514119, year = {2020}, author = {Gomes, ALC and Johns, NI and Yang, A and Velez-Cortes, F and Smillie, CS and Smith, MB and Alm, EJ and Wang, HH}, title = {Genome and sequence determinants governing the expression of horizontally acquired DNA in bacteria.}, journal = {The ISME journal}, volume = {14}, number = {9}, pages = {2347-2357}, pmid = {32514119}, issn = {1751-7370}, support = {DP5 OD009172/OD/NIH HHS/United States ; T32 GM087237/GM/NIGMS NIH HHS/United States ; R01 AI132403/AI/NIAID NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; U01 GM110714/GM/NIGMS NIH HHS/United States ; }, mesh = {*Bacteria/genetics ; Base Composition ; DNA ; *Gene Transfer, Horizontal ; Genome, Bacterial/genetics ; Transcription Initiation Site ; }, abstract = {While horizontal gene transfer is prevalent across the biosphere, the regulatory features that enable expression and functionalization of foreign DNA remain poorly understood. Here, we combine high-throughput promoter activity measurements and large-scale genomic analysis of regulatory regions to investigate the cross-compatibility of regulatory elements (REs) in bacteria. Functional characterization of thousands of natural REs in three distinct bacterial species revealed distinct expression patterns according to RE and recipient phylogeny. Host capacity to activate foreign promoters was proportional to their genomic GC content, while many low GC regulatory elements were both broadly active and had more transcription start sites across hosts. The difference in expression capabilities could be explained by the influence of the host GC content on the stringency of the AT-rich canonical σ70 motif necessary for transcription initiation. We further confirm the generalizability of this model and find widespread GC content adaptation of the σ70 motif in a set of 1,545 genomes from all major bacterial phyla. Our analysis identifies a key mechanism by which the strength of the AT-rich σ70 motif relative to a host's genomic GC content governs the capacity for expression of acquired DNA. These findings shed light on regulatory adaptation in the context of evolving genomic composition.}, }
@article {pmid32514117, year = {2020}, author = {Nishimura, Y and Otagiri, M and Yuki, M and Shimizu, M and Inoue, JI and Moriya, S and Ohkuma, M}, title = {Division of functional roles for termite gut protists revealed by single-cell transcriptomes.}, journal = {The ISME journal}, volume = {14}, number = {10}, pages = {2449-2460}, pmid = {32514117}, issn = {1751-7370}, mesh = {Animals ; Eukaryota ; *Gastrointestinal Microbiome ; *Isoptera ; Phylogeny ; Symbiosis ; Transcriptome ; }, abstract = {The microbiome in the hindgut of wood-feeding termites comprises various species of bacteria, archaea, and protists. This gut community is indispensable for the termite, which thrives solely on recalcitrant and nitrogen-poor wood. However, the difficulty in culturing these microorganisms has hindered our understanding of the function of each species in the gut. Although protists predominate in the termite gut microbiome and play a major role in wood digestion, very few culture-independent studies have explored the contribution of each species to digestion. Here, we report single-cell transcriptomes of four protists species comprising the protist population in worldwide pest Coptotermes formosanus. Comparative transcriptomic analysis revealed that the expression patterns of the genes involved in wood digestion were different among species, reinforcing their division of roles in wood degradation. Transcriptomes, together with enzyme assays, also suggested that one of the protists, Cononympha leidyi, actively degrades chitin and assimilates it into amino acids. We propose that C. leidyi contributes to nitrogen recycling and inhibiting infection from entomopathogenic fungi through chitin degradation. Two of the genes for chitin degradation were further revealed to be acquired via lateral gene transfer (LGT) implying the importance of LGT in the evolution of symbiosis. Our single-cell-based approach successfully characterized the function of each protist in termite hindgut and explained why the gut community includes multiple species.}, }
@article {pmid32513960, year = {2020}, author = {Rosendahl, S and Tamman, H and Brauer, A and Remm, M and Hõrak, R}, title = {Chromosomal toxin-antitoxin systems in Pseudomonas putida are rather selfish than beneficial.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {9230}, pmid = {32513960}, issn = {2045-2322}, mesh = {Anti-Bacterial Agents/pharmacology ; Antitoxins/genetics ; Bacterial Proteins/metabolism ; Bacterial Toxins/genetics/metabolism ; Biofilms/drug effects ; Databases, Factual ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Genetic Loci ; Phylogeny ; Proteomics ; Pseudomonas putida/classification/genetics/*physiology ; Stress, Physiological ; Toxin-Antitoxin Systems/drug effects/genetics/*physiology ; }, abstract = {Chromosomal toxin-antitoxin (TA) systems are widespread genetic elements among bacteria, yet, despite extensive studies in the last decade, their biological importance remains ambivalent. The ability of TA-encoded toxins to affect stress tolerance when overexpressed supports the hypothesis of TA systems being associated with stress adaptation. However, the deletion of TA genes has usually no effects on stress tolerance, supporting the selfish elements hypothesis. Here, we aimed to evaluate the cost and benefits of chromosomal TA systems to Pseudomonas putida. We show that multiple TA systems do not confer fitness benefits to this bacterium as deletion of 13 TA loci does not influence stress tolerance, persistence or biofilm formation. Our results instead show that TA loci are costly and decrease the competitive fitness of P. putida. Still, the cost of multiple TA systems is low and detectable in certain conditions only. Construction of antitoxin deletion strains showed that only five TA systems code for toxic proteins, while other TA loci have evolved towards reduced toxicity and encode non-toxic or moderately potent proteins. Analysis of P. putida TA systems' homologs among fully sequenced Pseudomonads suggests that the TA loci have been subjected to purifying selection and that TA systems spread among bacteria by horizontal gene transfer.}, }
@article {pmid32512856, year = {2020}, author = {Arhab, Y and Bulakhov, AG and Pestova, TV and Hellen, CUT}, title = {Dissemination of Internal Ribosomal Entry Sites (IRES) Between Viruses by Horizontal Gene Transfer.}, journal = {Viruses}, volume = {12}, number = {6}, pages = {}, pmid = {32512856}, issn = {1999-4915}, support = {R01 AI123406/AI/NIAID NIH HHS/United States ; R35 GM122602/GM/NIGMS NIH HHS/United States ; }, mesh = {5' Untranslated Regions ; Animals ; Gene Expression Regulation, Viral ; *Gene Transfer, Horizontal ; Humans ; *Internal Ribosome Entry Sites ; Protein Biosynthesis ; RNA, Viral/genetics/metabolism ; Virus Diseases/virology ; Viruses/*genetics/growth &amp; development/metabolism ; }, abstract = {Members of Picornaviridae and of the Hepacivirus, Pegivirus and Pestivirus genera of Flaviviridae all contain an internal ribosomal entry site (IRES) in the 5'-untranslated region (5'UTR) of their genomes. Each class of IRES has a conserved structure and promotes 5'-end-independent initiation of translation by a different mechanism. Picornavirus 5'UTRs, including the IRES, evolve independently of other parts of the genome and can move between genomes, most commonly by intratypic recombination. We review accumulating evidence that IRESs are genetic entities that can also move between members of different genera and even between families. Type IV IRESs, first identified in the Hepacivirus genus, have subsequently been identified in over 25 genera of Picornaviridae, juxtaposed against diverse coding sequences. In several genera, members have either type IV IRES or an IRES of type I, II or III. Similarly, in the genus Pegivirus, members contain either a type IV IRES or an unrelated type; both classes of IRES also occur in members of the genus Hepacivirus. IRESs utilize different mechanisms, have different factor requirements and contain determinants of viral growth, pathogenesis and cell type specificity. Their dissemination between viruses by horizontal gene transfer has unexpectedly emerged as an important facet of viral evolution.}, }
@article {pmid32512822, year = {2020}, author = {Oscarsson, J and DiRienzo, J and Johansson, A}, title = {Editorial Comments to the Special Issue: "Aggregatibacter actinomycetemcomitans-Gram-Negative Bacterial Pathogen".}, journal = {Pathogens (Basel, Switzerland)}, volume = {9}, number = {6}, pages = {}, pmid = {32512822}, issn = {2076-0817}, abstract = {Aggregatibacter actinomycetemcomitans is a periodontal pathogen colonizing the oral cavity in many individuals of the human population. It is equipped with several potent virulence factors that can cause cell death and induce or evade the host inflammatory response. Both harmless and highly virulent genotypes of the bacterium have emerged because of the large genetic diversity within the species. The oral condition and age, as well as the geographic origin of the individual, influence the risk to be colonized by a virulent genotype of the bacterium. In the present editorial, the different genetic and virulence properties of A. actinomycetemcomitans will be addressed in relation to the publications in this Special Issue.}, }
@article {pmid32512159, year = {2020}, author = {Lapadula, WJ and Marcet, PL and Taracena, ML and Lenhart, A and Juri Ayub, M}, title = {Characterization of horizontally acquired ribotoxin encoding genes and their transcripts in Aedes aegypti.}, journal = {Gene}, volume = {754}, number = {}, pages = {144857}, doi = {10.1016/j.gene.2020.144857}, pmid = {32512159}, issn = {1879-0038}, mesh = {Aedes/*genetics/physiology ; Animals ; Base Sequence ; Protein Synthesis Inhibitors/*metabolism ; Ribosome Inactivating Proteins/genetics/*metabolism ; Ribosomes/*metabolism ; Sequence Homology ; Toxins, Biological/genetics/*metabolism ; }, abstract = {Ribosome Inactivating Proteins (RIPs) are RNA N-glycosidases that depurinate a specific adenine residue in the conserved sarcin/ricin loop of the 28S rRNA. The occurrence of RIP genes has been described in a wide range of plant taxa, as well as in several species of bacteria and fungi. A remarkable case is the presence of these genes in metazoans belonging to the Culicinae subfamily. We reported that these genes are derived from a single horizontal gene transfer event, most likely from a bacterial donor species. Moreover, we have shown evidence that mosquito RIP genes are evolving under purifying selection, suggesting that these toxins have acquired a functional role in these organisms. In the present work, we characterized the intra-specific sequence variability of Aedes aegypti RIP genes (RIPAe1, RIPAe2, and RIPAe3) and tested their expression at the mRNA level. Our results show that RIPAe2 and RIPAe3 are transcribed and polyadenylated, and their expression levels are modulated across the developmental stages. Varibility among genes was observed, including the existence of null alleles for RIPAe1 and RIPAe2, with variants showing partial deletions. These results further support the existence of a physiological function for these foreign genes in mosquitoes. The possible nature of this functionality is discussed.}, }
@article {pmid32510809, year = {2020}, author = {Tolosi, R and Apostolakos, I and Laconi, A and Carraro, L and Grilli, G and Cagnardi, P and Piccirillo, A}, title = {Rapid detection and quantification of plasmid-mediated colistin resistance genes (mcr-1 to mcr-5) by real-time PCR in bacterial and environmental samples.}, journal = {Journal of applied microbiology}, volume = {129}, number = {6}, pages = {1523-1529}, doi = {10.1111/jam.14738}, pmid = {32510809}, issn = {1365-2672}, support = {2015KA3XFH//Italian Ministry of Research and University/ ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics/*isolation &amp; purification ; Bacterial Proteins/*genetics ; Colistin/*pharmacology ; Drug Resistance, Bacterial/*genetics ; Humans ; Limit of Detection ; Plasmids/*genetics ; Real-Time Polymerase Chain Reaction ; }, abstract = {AIM: The aim of the study was to validate a rapid method to detect and quantify colistin resistance genes (mcr-1 to mcr-5) by real-time polymerase chain reaction (RT-PCR) in diverse matrices.<br><br>METHODS AND RESULTS: The detection limit of two newly designed SYBR Green real-time PCR assays for mcr-4 and mcr-5 and of previously published protocols for mcr-1 to mcr-3 was assessed using serial dilutions of reference strains. The assays could detect all five mcr genes with the lower limit of 10[2] copy numbers. Escherichia coli isolates (n&#xa0;=&#xa0;1062) and environmental samples (n&#xa0;=&#xa0;93) were tested for the presence of mcr genes. The assays enabled the detection of colistin resistance genes both in bacterial isolates and in complex environmental samples.<br><br>CONCLUSIONS: This method represents a set of sensitive, rapid and effective assays for the screening of colistin resistance directly from the environment.<br><br>Colistin is an antimicrobial commonly used in animals and has recently emerged as a last-resort treatment in humans. Plasmid-mediated mcr genes confer resistance to colistin and represent a major threat for public health since they can be easily disseminated through horizontal gene transfer. The rapid and sensitive detection of mcr genes is of utmost necessity.}, }
@article {pmid32509768, year = {2020}, author = {Emamalipour, M and Seidi, K and Zununi Vahed, S and Jahanban-Esfahlan, A and Jaymand, M and Majdi, H and Amoozgar, Z and Chitkushev, LT and Javaheri, T and Jahanban-Esfahlan, R and Zare, P}, title = {Horizontal Gene Transfer: From Evolutionary Flexibility to Disease Progression.}, journal = {Frontiers in cell and developmental biology}, volume = {8}, number = {}, pages = {229}, pmid = {32509768}, issn = {2296-634X}, abstract = {Flexibility in the exchange of genetic material takes place between different organisms of the same or different species. This phenomenon is known to play a key role in the genetic, physiological, and ecological performance of the host. Exchange of genetic materials can cause both beneficial and/or adverse biological consequences. Horizontal gene transfer (HGT) or lateral gene transfer (LGT) as a general mechanism leads to biodiversity and biological innovations in nature. HGT mediators are one of the genetic engineering tools used for selective introduction of desired changes in the genome for gene/cell therapy purposes. HGT, however, is crucial in development, emergence, and recurrence of various human-related diseases, such as cancer, genetic-, metabolic-, and neurodegenerative disorders and can negatively affect the therapeutic outcome by promoting resistant forms or disrupting the performance of genome editing toolkits. Because of the importance of HGT and its vital physio- and pathological roles, here the variety of HGT mechanisms are reviewed, ranging from extracellular vesicles (EVs) and nanotubes in prokaryotes to cell-free DNA and apoptotic bodies in eukaryotes. Next, we argue that HGT plays a role both in the development of useful features and in pathological states associated with emerging and recurrent forms of the disease. A better understanding of the different HGT mediators and their genome-altering effects/potentials may pave the way for the development of more effective therapeutic and diagnostic regimes.}, }
@article {pmid32509595, year = {2020}, author = {Gonzales-Siles, L and Karlsson, R and Schmidt, P and Salvà-Serra, F and Jaén-Luchoro, D and Skovbjerg, S and Moore, ERB and Gomila, M}, title = {A Pangenome Approach for Discerning Species-Unique Gene Markers for Identifications of Streptococcus pneumoniae and Streptococcus pseudopneumoniae.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {222}, pmid = {32509595}, issn = {2235-2988}, mesh = {*Genomics ; Genotype ; *Streptococcus/genetics ; *Streptococcus pneumoniae/genetics ; }, abstract = {Correct identifications of isolates and strains of the Mitis-Group of the genus Streptococcus are particularly difficult, due to high genetic similarity, resulting from horizontal gene transfer and homologous recombination, and unreliable phenotypic and genotypic biomarkers for differentiating the species. Streptococcus pneumoniae and Streptococcus pseudopneumoniae are the most closely related species of the clade. In this study, publicly-available genome sequences for Streptococcus pneumoniae and S. pseudopneumoniae were analyzed, using a pangenomic approach, to find candidates for species-unique gene markers; ten species-unique genes for S. pneumoniae and nine for S. pseudopneumoniae were identified. These species-unique gene marker candidates were verified by PCR assays for identifying S. pneumoniae and S. pseudopneumoniae strains isolated from clinical samples. All determined species-level unique gene markers for S. pneumoniae were detected in all S. pneumoniae clinical isolates, whereas fewer of the unique S. pseudopneumoniae gene markers were present in more than 95% of the clinical isolates. In parallel, taxonomic identifications of the clinical isolates were confirmed, using conventional optochin sensitivity testing, targeted PCR-detection for the "Xisco" gene, as well as genomic ANIb similarity analyses for the genome sequences of selected strains. Using mass spectrometry-proteomics, species-specific peptide matches were observed for four of the S. pneumoniae gene markers and for three of the S. pseudopneumoniae gene markers. Application of multiple species-level unique biomarkers of S. pneumoniae and S. pseudopneumoniae, is proposed as a protocol for the routine clinical laboratory for improved, reliable differentiation, and identification of these pathogenic and commensal species.}, }
@article {pmid32502238, year = {2020}, author = {Morel, B and Kozlov, AM and Stamatakis, A and Szöllősi, GJ}, title = {GeneRax: A Tool for Species-Tree-Aware Maximum Likelihood-Based Gene Family Tree Inference under Gene Duplication, Transfer, and Loss.}, journal = {Molecular biology and evolution}, volume = {37}, number = {9}, pages = {2763-2774}, pmid = {32502238}, issn = {1537-1719}, support = {714774/ERC_/European Research Council/International ; }, mesh = {Cyanobacteria/genetics ; Gene Deletion ; *Gene Duplication ; Gene Transfer, Horizontal ; *Genetic Techniques ; *Phylogeny ; *Software ; }, abstract = {Inferring phylogenetic trees for individual homologous gene families is difficult because alignments are often too short, and thus contain insufficient signal, while substitution models inevitably fail to capture the complexity of the evolutionary processes. To overcome these challenges, species-tree-aware methods also leverage information from a putative species tree. However, only few methods are available that implement a full likelihood framework or account for horizontal gene transfers. Furthermore, these methods often require expensive data preprocessing (e.g., computing bootstrap trees) and rely on approximations and heuristics that limit the degree of tree space exploration. Here, we present GeneRax, the first maximum likelihood species-tree-aware phylogenetic inference software. It simultaneously accounts for substitutions at the sequence level as well as gene level events, such as duplication, transfer, and loss relying on established maximum likelihood optimization algorithms. GeneRax can infer rooted phylogenetic trees for multiple gene families, directly from the per-gene sequence alignments and a rooted, yet undated, species tree. We show that compared with competing tools, on simulated data GeneRax infers trees that are the closest to the true tree in 90% of the simulations in terms of relative Robinson-Foulds distance. On empirical data sets, GeneRax is the fastest among all tested methods when starting from aligned sequences, and it infers trees with the highest likelihood score, based on our model. GeneRax completed tree inferences and reconciliations for 1,099 Cyanobacteria families in 8 min on 512 CPU cores. Thus, its parallelization scheme enables large-scale analyses. GeneRax is available under GNU GPL at https://github.com/BenoitMorel/GeneRax (last accessed June 17, 2020).}, }
@article {pmid32500473, year = {2020}, author = {Donassolo, RA and Ferreira, MRA and Moreira, C and Dos Santos, LM and Griep, E and Moreira, GMSG and Rodrigues, RR and Moreira, &#xc2;N and Conceição, FR}, title = {Formaldehyde effects on kanamycin resistance gene of inactivated recombinant Escherichia coli vaccines.}, journal = {Biotechnology letters}, volume = {42}, number = {11}, pages = {2223-2230}, pmid = {32500473}, issn = {1573-6776}, mesh = {Escherichia coli/drug effects/*genetics ; Escherichia coli Vaccines/adverse effects/genetics ; Formaldehyde/*pharmacology ; Gene Transfer, Horizontal/drug effects ; Kanamycin Resistance/*drug effects ; Plasmids/*drug effects/genetics ; Vaccines, Inactivated ; Vaccines, Synthetic ; }, abstract = {OBJECTIVES: Earlier studies have demonstrated the use of inactivated recombinant E. coli (bacterins), to protect against Clostridium spp. in vaccinated animals. These bacterins have a simpler, safer, and faster production process. However, these bacterins carry expression plasmids, containing antibiotic resistance gene, which could be assimilate accidentally by environmental microorganisms. Considering this, we aimed to impair this plasmids using formaldehyde at different concentrations.<br><br>RESULTS: This compound inactivated the highest density of cells in 24 h. KanR cassette amplification was found to be impaired with 0.8% for 24 h or 0.4% for 72 h. Upon electroporation, E. coli DH5&#x3b1; ultracompetent cells were unable to acquire the plasmids extracted from the bacterins after inactivation procedure. Formaldehyde-treated bacterins were incubated with other viable strains of E. coli, leading to no detectable gene transfer.<br><br>CONCLUSIONS: We found that this compound is effective as an inactivation agent. Here we demonstrate the biosafety involving antibiotic resistance gene of recombinant E. coli vaccines allowing to industrial production and animal application.}, }
@article {pmid32500263, year = {2020}, author = {Fischer, M and Francis, A}, title = {The Space of Tree-Based Phylogenetic Networks.}, journal = {Bulletin of mathematical biology}, volume = {82}, number = {6}, pages = {70}, doi = {10.1007/s11538-020-00744-9}, pmid = {32500263}, issn = {1522-9602}, mesh = {Algorithms ; *Biological Evolution ; Cluster Analysis ; Computational Biology ; Evolution, Molecular ; Gene Transfer, Horizontal ; Hybridization, Genetic ; Mathematical Concepts ; Models, Biological ; *Models, Genetic ; *Phylogeny ; }, abstract = {Phylogenetic networks are generalizations of phylogenetic trees that allow the representation of reticulation events such as horizontal gene transfer or hybridization, and can also represent uncertainty in inference. A subclass of these, tree-based phylogenetic networks, have been introduced to capture the extent to which reticulate evolution nevertheless broadly follows tree-like patterns. Several important operations that change a general phylogenetic network have been developed in recent years and are important for allowing algorithms to move around spaces of networks; a vital ingredient in finding an optimal network given some biological data. A key such operation is the nearest neighbour interchange, or NNI. While it is already known that the space of unrooted phylogenetic networks is connected under NNI, it has been unclear whether this also holds for the subspace of tree-based networks. In this paper, we show that the space of unrooted tree-based phylogenetic networks is indeed connected under the NNI operation. We do so by explicitly showing how to get from one such network to another one without losing tree-basedness along the way. Moreover, we introduce some new concepts, for instance "shoat networks", and derive some interesting aspects concerning tree-basedness. Last, we use our results to derive an upper bound on the size of the space of tree-based networks.}, }
@article {pmid32496186, year = {2020}, author = {Morgado, SM and Paulo Vicente, AC}, title = {Genomics of Atlantic Forest Mycobacteriaceae strains unravels a mobilome diversity with a novel integrative conjugative element and plasmids harbouring T7SS.}, journal = {Microbial genomics}, volume = {6}, number = {7}, pages = {}, pmid = {32496186}, issn = {2057-5858}, mesh = {Brazil ; Conjugation, Genetic ; Forests ; Gene Transfer, Horizontal ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; *Interspersed Repetitive Sequences ; Mycobacteriaceae/*classification/genetics ; Phylogeny ; Plasmids/*genetics ; Sequence Analysis, DNA/*methods ; Soil Microbiology ; }, abstract = {Mobile genetic elements (MGEs) are agents of bacterial evolution and adaptation. Genome sequencing provides an unbiased approach that has revealed an abundance of MGEs in prokaryotes, mainly plasmids and integrative conjugative elements. Nevertheless, many mobilomes, particularly those from environmental bacteria, remain underexplored despite their representing a reservoir of genes that can later emerge in the clinic. Here, we explored the mobilome of the Mycobacteriaceae family, focusing on strains from Brazilian Atlantic Forest soil. Novel Mycolicibacterium and Mycobacteroides strains were identified, with the former ones harbouring linear and circular plasmids encoding the specialized type-VII secretion system (T7SS) and mobility-associated genes. In addition, we also identified a T4SS-mediated integrative conjugative element (ICEMyc226) encoding two T7SSs and a number of xenobiotic degrading genes. Our study uncovers the diversity of the Mycobacteriaceae mobilome, providing the evidence of an ICE in this bacterial family. Moreover, the presence of T7SS genes in an ICE, as well as plasmids, highlights the role of these mobile genetic elements in the dispersion of T7SS.}, }
@article {pmid32494685, year = {2020}, author = {Fan, X and Qiu, H and Han, W and Wang, Y and Xu, D and Zhang, X and Bhattacharya, D and Ye, N}, title = {Phytoplankton pangenome reveals extensive prokaryotic horizontal gene transfer of diverse functions.}, journal = {Science advances}, volume = {6}, number = {18}, pages = {eaba0111}, pmid = {32494685}, issn = {2375-2548}, abstract = {The extent and role of horizontal gene transfer (HGT) in phytoplankton and, more broadly, eukaryotic evolution remain controversial topics. Recent studies substantiate the importance of HGT in modifying or expanding functions such as metal or reactive species detoxification and buttressing halotolerance. Yet, the potential of HGT to significantly alter the fate of species in a major eukaryotic assemblage remains to be established. We provide such an example for the ecologically important lineages encompassed by cryptophytes, rhizarians, alveolates, stramenopiles, and haptophytes ("CRASH" taxa). We describe robust evidence of prokaryotic HGTs in these taxa affecting functions such as polysaccharide biosynthesis. Numbers of HGTs range from 0.16 to 1.44% of CRASH species gene inventories, comparable to the ca. 1% prokaryote-derived HGTs found in the genomes of extremophilic red algae. Our results substantially expand the impact of HGT in eukaryotes and define a set of general principles for prokaryotic gene fixation in phytoplankton genomes.}, }
@article {pmid32494170, year = {2020}, author = {Lin, M and Yang, Y and Yang, Y and Chen, G and He, R and Wu, Y and Zhong, LL and El-Sayed Ahmed, MAE and Feng, S and Shen, C and Wen, X and Huang, J and Li, H and Zheng, X and Tian, GB}, title = {Co-Occurrence of mcr-9 and bla NDM-1 in Enterobacter cloacae Isolated from a Patient with Bloodstream Infection.}, journal = {Infection and drug resistance}, volume = {13}, number = {}, pages = {1397-1402}, pmid = {32494170}, issn = {1178-6973}, abstract = {BACKGROUND: Bloodstream infection (BSI) caused by carbapenem-resistant Enterobacteriaceae are potentially life-threatening related to poorer outcomes. Colistin is considered one of the last-resort treatments against human infections caused by multidrug-resistant (MDR) Gram-negative bacteria. Therefore, emergence of strains from the blood that co-harboring mcr and carbapenem resistance genes were considered as a serious problem.<br><br>PURPOSE: In this study, two mcr-9-harboring MDR Enterobacter cloacae isolates BSI034 and BSI072 recovered from BSI patients were identified, one of which co-harbored mcr-9 and bla NDM-1. The genetic characteristics of the MDR plasmid needed to be clarified.<br><br>METHODS: S1-PFGE and Southern blotting were conducted to determine the location of mcr-9. Whole-genome sequencing was performed to obtain the complete genome and plasmid sequences. The resistome and virulence genes of the strains, accompanied by the genetic characteristics of mcr-9- and bla NDM-1-harboring plasmids, were analyzed.<br><br>RESULTS: Whole-genome sequencing showed that BSI034 harbored mcr-9-carrying IncHI2-type pBSI034-MCR9 and bla NDM-1-carrying IncX3-type pBSI034-NDM1. The 278,517 bp pBSI034-MCR9 carried mcr-9 along with the other 19 resistance genes. mcr-9 was flanked by IS903B (1057 bp) and IS26 (820 bp) in the same orientation. In addition to resistance genes, strain BSI034 also carried a chromosome-located Yersinia high-pathogenicity island, which harbored genes of yersiniabactin biosynthesis operon ybtSXQPAUTE, irp1/2, and fyuA.<br><br>CONCLUSION: We described the complete genome and mcr-9/bla NDM-1-co-harboring plasmid of E. cloacae from a BSI patient. Notable differences were observed within mosaic modules between pBSI034-MCR9 and other mcr-9-harboring plasmids due to extensive recombination via horizontal gene transfer.}, }
@article {pmid32493722, year = {2020}, author = {Nett, RS and Nguyen, H and Nagel, R and Marcassa, A and Charles, TC and Friedberg, I and Peters, RJ}, title = {Unraveling a Tangled Skein: Evolutionary Analysis of the Bacterial Gibberellin Biosynthetic Operon.}, journal = {mSphere}, volume = {5}, number = {3}, pages = {}, pmid = {32493722}, issn = {2379-5042}, support = {R01 GM076324/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*genetics/*metabolism ; Biosynthetic Pathways ; *Evolution, Molecular ; Gibberellins/*metabolism ; Multigene Family ; *Operon ; Plant Growth Regulators/biosynthesis ; Plants/microbiology ; Symbiosis ; }, abstract = {Gibberellin (GA) phytohormones are ubiquitous regulators of growth and developmental processes in vascular plants. The convergent evolution of GA production by plant-associated bacteria, including both symbiotic nitrogen-fixing rhizobia and phytopathogens, suggests that manipulation of GA signaling is a powerful mechanism for microbes to gain an advantage in these interactions. Although orthologous operons encode GA biosynthetic enzymes in both rhizobia and phytopathogens, notable genetic heterogeneity and scattered operon distribution in these lineages, including loss of the gene for the final biosynthetic step in most rhizobia, suggest varied functions for GA in these distinct plant-microbe interactions. Therefore, deciphering GA operon evolutionary history should provide crucial evidence toward understanding the distinct biological roles for bacterial GA production. To further establish the genetic composition of the GA operon, two operon-associated genes that exhibit limited distribution among rhizobia were biochemically characterized, verifying their roles in GA biosynthesis. This enabled employment of a maximum parsimony ancestral gene block reconstruction algorithm to characterize loss, gain, and horizontal gene transfer (HGT) of GA operon genes within alphaproteobacterial rhizobia, which exhibit the most heterogeneity among the bacteria containing this biosynthetic gene cluster. Collectively, this evolutionary analysis reveals a complex history for HGT of the entire GA operon, as well as the individual genes therein, and ultimately provides a basis for linking genetic content to bacterial GA functions in diverse plant-microbe interactions, including insight into the subtleties of the coevolving molecular interactions between rhizobia and their leguminous host plants.IMPORTANCE While production of phytohormones by plant-associated microbes has long been appreciated, identification of the gibberellin (GA) biosynthetic operon in plant-associated bacteria has revealed surprising genetic heterogeneity. Notably, this heterogeneity seems to be associated with the lifestyle of the microbe; while the GA operon in phytopathogenic bacteria does not seem to vary to any significant degree, thus enabling production of bioactive GA, symbiotic rhizobia exhibit a number of GA operon gene loss and gain events. This suggests that a unique set of selective pressures are exerted on this biosynthetic gene cluster in rhizobia. Through analysis of the evolutionary history of the GA operon in alphaproteobacterial rhizobia, which display substantial diversity in their GA operon structure and gene content, we provide insight into the effect of lifestyle and host interactions on the production of this phytohormone by plant-associated bacteria.}, }
@article {pmid32490527, year = {2020}, author = {Luévano-Martínez, LA and Duncan, AL}, title = {Origin and diversification of the cardiolipin biosynthetic pathway in the Eukarya domain.}, journal = {Biochemical Society transactions}, volume = {48}, number = {3}, pages = {1035-1046}, doi = {10.1042/BST20190967}, pmid = {32490527}, issn = {1470-8752}, support = {BB/R00126X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Archaea/*enzymology ; Bacteria/*enzymology ; Binding Sites ; Biosynthetic Pathways ; Cardiolipins/*biosynthesis ; Catalysis ; Eukaryota/*enzymology ; Evolution, Molecular ; Gene Transfer, Horizontal ; Hydrolases/metabolism ; Mitochondria/metabolism ; Models, Molecular ; Phosphatidylglycerols/*metabolism ; Phospholipids/metabolism ; Phosphoric Monoester Hydrolases/metabolism ; Phylogeny ; }, abstract = {Cardiolipin (CL) and its precursor phosphatidylglycerol (PG) are important anionic phospholipids widely distributed throughout all domains of life. They have key roles in several cellular processes by shaping membranes and modulating the activity of the proteins inserted into those membranes. They are synthesized by two main pathways, the so-called eukaryotic pathway, exclusively found in mitochondria, and the prokaryotic pathway, present in most bacteria and archaea. In the prokaryotic pathway, the first and the third reactions are catalyzed by phosphatidylglycerol phosphate synthase (Pgps) belonging to the transferase family and cardiolipin synthase (Cls) belonging to the hydrolase family, while in the eukaryotic pathway, those same reactions are catalyzed by unrelated homonymous enzymes: Pgps of the hydrolase family and Cls of the transferase family. Because of the enzymatic arrangement found in both pathways, it seems that the eukaryotic pathway evolved by convergence to the prokaryotic pathway. However, since mitochondria evolved from a bacterial endosymbiont, it would suggest that the eukaryotic pathway arose from the prokaryotic pathway. In this review, it is proposed that the eukaryote pathway evolved directly from a prokaryotic pathway by the neofunctionalization of the bacterial enzymes. Moreover, after the eukaryotic radiation, this pathway was reshaped by horizontal gene transfers or subsequent endosymbiotic processes.}, }
@article {pmid32487758, year = {2020}, author = {Semini, G and Paape, D and Blume, M and Sernee, MF and Peres-Alonso, D and Calvignac-Spencer, S and Döllinger, J and Jehle, S and Saunders, E and McConville, MJ and Aebischer, T}, title = {Leishmania Encodes a Bacterium-like 2,4-Dienoyl-Coenzyme A Reductase That Is Required for Fatty Acid β-Oxidation and Intracellular Parasite Survival.}, journal = {mBio}, volume = {11}, number = {3}, pages = {}, pmid = {32487758}, issn = {2150-7511}, mesh = {Amino Acid Sequence ; Animals ; Fatty Acid Desaturases/genetics/*metabolism ; Fatty Acids/*metabolism ; Female ; Leishmania major/*enzymology/*genetics/growth &amp; development ; Leishmania mexicana/genetics ; Macrophages/parasitology ; Mice ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; Oxidation-Reduction ; Phylogeny ; }, abstract = {Leishmania spp. are protozoan parasites that cause a spectrum of important diseases in humans. These parasites develop as extracellular promastigotes in the digestive tract of their insect vectors and as obligate intracellular amastigotes that infect macrophages and other phagocytic cells in their vertebrate hosts. Promastigote-to-amastigote differentiation is associated with marked changes in metabolism, including the upregulation of enzymes involved in fatty acid β-oxidation, which may reflect adaptation to the intracellular niche. Here, we have investigated the function of one of these enzymes, a putative 2,4-dienoyl-coenzyme A (CoA) reductase (DECR), which is specifically required for the β-oxidation of polyunsaturated fatty acids. The Leishmania DECR shows close homology to bacterial DECR proteins, suggesting that it was acquired by lateral gene transfer. It is present in other trypanosomatids that have obligate intracellular stages (i.e., Trypanosoma cruzi and Angomonas) but is absent from dixenous parasites with an exclusively extracellular lifestyle (i.e., Trypanosoma brucei). A DECR-green fluorescent protein (GFP) fusion protein was localized to the mitochondrion in both promastigote and amastigote stages, and the levels of expression increased in the latter stages. A Leishmania major Δdecr null mutant was unable to catabolize unsaturated fatty acids and accumulated the intermediate 2,4-decadienoyl-CoA, confirming DECR's role in β-oxidation. Strikingly, the L. major Δdecr mutant was unable to survive in macrophages and was avirulent in BALB/c mice. These findings suggest that β-oxidation of polyunsaturated fatty acids is essential for intracellular parasite survival and that the bacterial origin of key enzymes in this pathway could be exploited in developing new therapies.IMPORTANCE The Trypanosomatidae are protozoan parasites that infect insects, plants, and animals and have evolved complex monoxenous (single host) and dixenous (two hosts) lifestyles. A number of species of Trypanosomatidae, including Leishmania spp., have evolved the capacity to survive within intracellular niches in vertebrate hosts. The adaptations, metabolic and other, that are associated with development of intracellular lifestyles remain poorly defined. We show that genomes of Leishmania and Trypanosomatidae that can survive intracellularly encode a 2,4-dienoyl-CoA reductase that is involved in catabolism of a subclass of fatty acids. The trypanosomatid enzyme shows closest similarity to the corresponding bacterial enzymes and is located in the mitochondrion and essential for intracellular growth of Leishmania The findings suggest that acquisition of this gene by lateral gene transfer from bacteria by ancestral monoxenous Trypanosomatidae likely contributed to the development of a dixenous lifestyle of these parasites.}, }
@article {pmid32483914, year = {2020}, author = {Zamudio, R and Haigh, RD and Ralph, JD and De Ste Croix, M and Tasara, T and Zurfluh, K and Kwun, MJ and Millard, AD and Bentley, SD and Croucher, NJ and Stephan, R and Oggioni, MR}, title = {Lineage-specific evolution and gene flow in Listeria monocytogenes are independent of bacteriophages.}, journal = {Environmental microbiology}, volume = {22}, number = {12}, pages = {5058-5072}, pmid = {32483914}, issn = {1462-2920}, support = {BB/N002903/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 104169/Z/14/Z/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; BB/P504737/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/R015600/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Bacteriophages/*physiology ; *Evolution, Molecular ; *Gene Flow ; Gene Transfer, Horizontal ; Genetic Variation ; Genome, Bacterial/genetics ; Listeria monocytogenes/classification/*genetics/isolation &amp; purification/virology ; Listeriosis/epidemiology/microbiology ; Multilocus Sequence Typing ; Phylogeny ; Polymorphism, Single Nucleotide ; Recombination, Genetic ; }, abstract = {Listeria monocytogenes is a foodborne pathogen causing systemic infection with high mortality. To allow efficient tracking of outbreaks a clear definition of the genomic signature of a cluster of related isolates is required, but lineage-specific characteristics call for a more detailed understanding of evolution. In our work, we used core genome MLST (cgMLST) to identify new outbreaks combined to core genome SNP analysis to characterize the population structure and gene flow between lineages. Whilst analysing differences between the four lineages of L. monocytogenes we have detected differences in the recombination rate, and interestingly also divergence in the SNP differences between sub-lineages. In addition, the exchange of core genome variation between the lineages exhibited a distinct pattern, with lineage III being the best donor for horizontal gene transfer. Whilst attempting to link bacteriophage-mediated transduction to observed gene transfer, we found an inverse correlation between phage presence in a lineage and the extent of recombination. Irrespective of the profound differences in recombination rates observed between sub-lineages and lineages, we found that the previously proposed cut-off of 10 allelic differences in cgMLST can be still considered valid for the definition of a foodborne outbreak cluster of L. monocytogenes.}, }
@article {pmid32483324, year = {2020}, author = {van Bergeijk, DA and Terlouw, BR and Medema, MH and van Wezel, GP}, title = {Ecology and genomics of Actinobacteria: new concepts for natural product discovery.}, journal = {Nature reviews. Microbiology}, volume = {18}, number = {10}, pages = {546-558}, pmid = {32483324}, issn = {1740-1534}, mesh = {Actinobacteria/*genetics/metabolism ; Anti-Bacterial Agents/biosynthesis/*isolation &amp; purification/pharmacology ; Biological Products/*isolation &amp; purification/metabolism/pharmacology ; Drug Discovery ; Ecology ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genome, Bacterial ; Genomics/methods ; Humans ; Metabolic Networks and Pathways/genetics ; Multigene Family ; }, abstract = {Actinobacteria constitute a highly diverse bacterial phylum with an unrivalled metabolic versatility. They produce most of the clinically used antibiotics and a plethora of other natural products with medical or agricultural applications. Modern 'omics'-based technologies have revealed that the genomic potential of Actinobacteria greatly outmatches the known chemical space. In this Review, we argue that combining insights into actinobacterial ecology with state-of-the-art computational approaches holds great promise to unlock this unexplored reservoir of actinobacterial metabolism. This enables the identification of small molecules and other stimuli that elicit the induction of poorly expressed biosynthetic gene clusters, which should help reinvigorate screening efforts for their precious bioactive natural products.}, }
@article {pmid32482165, year = {2020}, author = {Moon, K and Jeon, JH and Kang, I and Park, KS and Lee, K and Cha, CJ and Lee, SH and Cho, JC}, title = {Freshwater viral metagenome reveals novel and functional phage-borne antibiotic resistance genes.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {75}, pmid = {32482165}, issn = {2049-2618}, support = {2016001350004//Ministry of Environment (KR)/International ; 2016001350004//Ministry of Environment (KR)/International ; NRF-2018R1A5A1025077//National Research Foundation of Korea/International ; NRF-2019R1I1A1A01062072//National Research Foundation of Korea/International ; NRF-2017M3A9E4078014//National Research Foundation of Korea/International ; }, mesh = {Anti-Bacterial Agents/pharmacology ; *Bacteriophages/genetics ; Drug Resistance, Bacterial/genetics ; Escherichia coli/drug effects/genetics ; Fresh Water/virology ; *Metagenome/drug effects ; Metagenomics ; Viruses/genetics ; }, abstract = {BACKGROUND: Antibiotic resistance developed by bacteria is a significant threat to global health. Antibiotic resistance genes (ARGs) spread across different bacterial populations through multiple dissemination routes, including horizontal gene transfer mediated by bacteriophages. ARGs carried by bacteriophages are considered especially threatening due to their prolonged persistence in the environment, fast replication rates, and ability to infect diverse bacterial hosts. Several studies employing qPCR and viral metagenomics have shown that viral fraction and viral sequence reads in clinical and environmental samples carry many ARGs. However, only a few ARGs have been found in viral contigs assembled from metagenome reads, with most of these genes lacking effective antibiotic resistance phenotypes. Owing to the wide application of viral metagenomics, nevertheless, different classes of ARGs are being continuously found in viral metagenomes acquired from diverse environments. As such, the presence and functionality of ARGs encoded by bacteriophages remain up for debate.<br><br>RESULTS: We evaluated ARGs excavated from viral contigs recovered from urban surface water viral metagenome data. In virome reads and contigs, diverse ARGs, including polymyxin resistance genes, multidrug efflux proteins, and &#x3b2;-lactamases, were identified. In particular, when a lenient threshold of e value of &#x2264; 1 &#xd7; e[-5] and query coverage of &#x2265; 60% were employed in the Resfams database, the novel &#x3b2;-lactamases blaHRV-1 and blaHRVM-1 were found. These genes had unique sequences, forming distinct clades of class A and subclass B3 &#x3b2;-lactamases, respectively. Minimum inhibitory concentration analyses for E. coli strains harboring blaHRV-1 and blaHRVM-1 and catalytic kinetics of purified HRV-1 and HRVM-1 showed reduced susceptibility to penicillin, narrow- and extended-spectrum cephalosporins, and carbapenems. These genes were also found in bacterial metagenomes, indicating that they were harbored by actively infecting phages.<br><br>CONCLUSION: Our results showed that viruses in the environment carry as-yet-unreported functional ARGs, albeit in small quantities. We thereby suggest that environmental bacteriophages could be reservoirs of widely variable, unknown ARGs that could be disseminated via virus-host interactions. Video abstract.}, }
@article {pmid32474783, year = {2020}, author = {Révész, F and Farkas, M and Kriszt, B and Szoboszlay, S and Benedek, T and Táncsics, A}, title = {Effect of oxygen limitation on the enrichment of bacteria degrading either benzene or toluene and the identification of Malikia spinosa (Comamonadaceae) as prominent aerobic benzene-, toluene-, and ethylbenzene-degrading bacterium: enrichment, isolation and whole-genome analysis.}, journal = {Environmental science and pollution research international}, volume = {27}, number = {25}, pages = {31130-31142}, pmid = {32474783}, issn = {1614-7499}, support = {NKFIH-831-10/2019//Ministry for Innovation and Technology (HU)/ ; }, mesh = {Benzene ; Benzene Derivatives ; Biodegradation, Environmental ; *Comamonadaceae ; Oxygen ; Pseudomonas ; *Toluene ; Xylenes ; }, abstract = {The primary aims of this present study were to evaluate the effect of oxygen limitation on the bacterial community structure of enrichment cultures degrading either benzene or toluene and to clarify the role of Malikia-related bacteria in the aerobic degradation of BTEX compounds. Accordingly, parallel aerobic and microaerobic enrichment cultures were set up and the bacterial communities were investigated through cultivation and 16S rDNA Illumina amplicon sequencing. In the aerobic benzene-degrading enrichment cultures, the overwhelming dominance of Malikia spinosa was observed and it was abundant in the aerobic toluene-degrading enrichment cultures as well. Successful isolation of a Malikia spinosa strain shed light on the fact that this bacterium harbours a catechol 2,3-dioxygenase (C23O) gene encoding a subfamily I.2.C-type extradiol dioxygenase and it is able to degrade benzene, toluene and ethylbenzene under clear aerobic conditions. While quick degradation of the aromatic substrates was observable in the case of the aerobic enrichments, no significant benzene degradation, and the slow degradation of toluene was observed in the microaerobic enrichments. Despite harbouring a subfamily I.2.C-type C23O gene, Malikia spinosa was not found in the microaerobic enrichments; instead, members of the Pseudomonas veronii/extremaustralis lineage dominated these communities. Whole-genome analysis of M. spinosa strain AB6 revealed that the C23O gene was part of a phenol-degrading gene cluster, which was acquired by the strain through a horizontal gene transfer event. Results of the present study revealed that bacteria, which encode subfamily I.2.C-type extradiol dioxygenase enzyme, will not be automatically able to degrade monoaromatic hydrocarbons under microaerobic conditions.}, }
@article {pmid32474215, year = {2020}, author = {Huyan, J and Tian, Z and Zhang, Y and Zhang, H and Shi, Y and Gillings, MR and Yang, M}, title = {Dynamics of class 1 integrons in aerobic biofilm reactors spiked with antibiotics.}, journal = {Environment international}, volume = {140}, number = {}, pages = {105816}, doi = {10.1016/j.envint.2020.105816}, pmid = {32474215}, issn = {1873-6750}, mesh = {*Anti-Bacterial Agents/pharmacology ; Bacteria ; Biofilms ; Drug Resistance, Microbial/genetics ; *Integrons/genetics ; }, abstract = {Class 1 integrons are strongly associated with the dissemination of antibiotic resistance in bacteria. However, little is known about whether the presence of antibiotics affects the abundance of integrons and antibiotic resistance genes during biological wastewater treatment. To explore the roles of class 1 integrons in spreading antibiotic resistance genes in environmental compartments, the dynamics of integrons were followed in biofilm reactors treating synthetic wastewater respectively spiked with streptomycin (STM) and oxytetracycline (OTC). The relative abundance of the integron-integrase gene (intI1) increased 12 or 29-fold respectively when treated with STM or OTC, under incrementally increasing dosage regimes from 0 to 50 mg L[-1]. Significant increases in intI1 abundance initially occurred at an antibiotic dose of 0.1 mg L[-1]. At the beginning of the experiment, 51% to 64% of integrons carried no gene cassettes. In STM and OTC spiked systems, there was a significant increase in the proportion of integrons that contained resistance gene cassettes, particularly at intermediate and higher antibiotic concentrations. Gene cassettes encoding resistance to aminoglycosides, trimethoprim, beta-lactam, erythromycin, and quaternary ammonium compounds were all detected in the treated systems. Three tetracycline resistance genes (tetA, tetC, tetG) were significantly correlated with the abundance of intI1 (p < 0.01), despite no tet resistance being present as a gene cassette. Genome sequencing of isolates showed synteny between the tet resistance genes and intI1, mediated through linkage to transposable elements including Tn3, IS26 and ISCR3. Class 1 integrons appeared to be under positive selection in the presence of antibiotics, and might have actively acquired new gene cassettes during the experiment.}, }
@article {pmid32471348, year = {2020}, author = {Silva, SS and Monfardini, MV and Scaletsky, ICA}, title = {Large plasmids encoding antibiotic resistance and localized-like adherence in atypical enteropathogenic Escherichia coli strains.}, journal = {BMC microbiology}, volume = {20}, number = {1}, pages = {138}, pmid = {32471348}, issn = {1471-2180}, mesh = {Ampicillin/pharmacology ; Anti-Bacterial Agents/*pharmacology ; Bacterial Adhesion ; Conjugation, Genetic ; *Drug Resistance, Bacterial ; Enteropathogenic Escherichia coli/drug effects/*genetics/isolation &amp; purification ; Escherichia coli Proteins/*genetics ; Fimbriae Proteins/genetics ; Gene Transfer, Horizontal ; HeLa Cells ; Humans ; Kanamycin/pharmacology ; Microbial Sensitivity Tests ; Mutagenesis, Insertional ; Plasmids/*genetics ; Tetracycline/pharmacology ; }, abstract = {BACKGROUND: In previous studies, we have shown that atypical enteropathogenic Escherichia coli (aEPEC) strains are important diarrheal pathogens among Brazilian children. In the characterization of a collection of 126 aEPEC strains, we identified 29 strains expressing the localized-like adherence (LAL) pattern on HEp-2 cells and harboring large plasmids in the range of 60 to 98 MDa. In this study, we examined 18 of these strains for their ability to transfer the LAL phenotype to a E. coli K-12 C600 strain.<br><br>RESULTS: In conjugation experiments, using eight strains which were resistant to one or more antimicrobials and positive for F-pili genes (traA), we were able to cotransfer antimicrobial resistance markers along with adhesion genes. By transforming E. coli DH5&#x3b1; with plasmid DNA from strains A46 (pIS46), A66 (pIS66) and A102 (pIS102), we were able to demonstrate that genes encoding ampicillin, tetracycline and LAL were encoded on a 98-MDa conjugative plasmid. To identify a gene responsible for LAL, we constructed a transposon mutant library of A102 strain. Among 18 mutants that did not adhere to HeLa cells, four carried insertions within fimbrial genes (fimA and traJ) and agglutinin genes (tia and hek). Using these Tn5 mutants as donors, we were able to obtain kanamycin-resistant E. coli MA3456 transconjugants. Sequence analysis of the plasmid genes revealed a region exhibit to 80 and 73% amino acid similarities to the agglutinins Tia and Hek, respectively.<br><br>CONCLUSION: In this study, we have identified three large conjugative plasmids, pIS46, pIS66 and pIS102, coding for antimicrobial resistance and localized-like adherence (LAL) to HeLa cells. In addition, we identified a tia/hek homolog encoded on the pIS102 plasmid, which seems to be involved in adhesion of A102 strain.}, }
@article {pmid32470826, year = {2020}, author = {Li, D and Gao, J and Dai, H and Wang, Z and Duan, W}, title = {Long-term responses of antibiotic resistance genes under high concentration of enrofloxacin, sulfadiazine and triclosan in aerobic granular sludge system.}, journal = {Bioresource technology}, volume = {312}, number = {}, pages = {123567}, doi = {10.1016/j.biortech.2020.123567}, pmid = {32470826}, issn = {1873-2976}, mesh = {Anti-Bacterial Agents ; Drug Resistance, Microbial ; Enrofloxacin ; Genes, Bacterial ; Sewage ; Sulfadiazine ; *Triclosan ; }, abstract = {It is worth to reveal the long-term responses of antibiotic resistance genes (ARGs) in aerobic granular sludge (AGS) system exposed to high level enrofloxacin (ENR), sulfadiazine (SDZ) and triclosan (TCS). In present study, ppm level ENR, SDZ and TCS were added into three AGS reactors, respectively. ARGs in ENR and SDZ systems showed trends of increasing first and then decreasing, which were contrary to that in TCS system. 80%, 56% and 40% ARGs in ENR, SDZ and TCS systems, respectively, were enriched after loading, but several ARGs still kept high enrichment values after the withdrawn of loadings. The dominant bacteria in ENR (Flavobacterium), SDZ (Candidatus_Competibacter and Defluviicoccus) and TCS (Defluviicoccus) systems might contribute to the reductions of ARGs. IntI1 altered the overall ARGs profiles through horizontal gene transfer. The interactions of bacterial communities and environmental factors might be responsible for the different ARGs patterns in ENR, SDZ and TCS systems.}, }
@article {pmid32470517, year = {2020}, author = {Piper, P and Begres, B and Snider, M and Fraga, D}, title = {Two cryptosporidia species encode active creatine kinases that are not seen in other apicomplexa species.}, journal = {Comparative biochemistry and physiology. Part B, Biochemistry &amp; molecular biology}, volume = {246-247}, number = {}, pages = {110459}, doi = {10.1016/j.cbpb.2020.110459}, pmid = {32470517}, issn = {1879-1107}, mesh = {Amino Acid Sequence ; Creatine/metabolism ; Creatine Kinase/genetics/*metabolism ; Cryptosporidium/enzymology/genetics/*metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal ; Glycine/analogs &amp; derivatives/metabolism ; Kinetics ; Magnetic Resonance Spectroscopy ; Phylogeny ; Sequence Alignment ; Substrate Specificity ; }, abstract = {A gene encoding creatine kinase was identified in two cryptosporidia species, Cryptosporidium muris and C. andersonii. They were syntenic and shared 91% identity 94% identity at the amino acid level and nucleotide levels respectively. The C. muris creatine kinase was characterized biochemically and shown to phosphorylate both creatine and glycocyamine with a 20-fold greater preference for creatine. The observed catalytic turnover with creatine was kcat = 30 s[-1] with a catalytic efficiency of 15.4 mM[-1] s[-1]. These values were within the range observed for other creatine kinases. A search of all the apicomplexa genomes available on EuPathDB did not reveal any other phosphagen kinase genes raising the possibility of horizontal gene transfer. However, no definitive conclusion could be drawn regarding this hypothesis given the massive amount of gene loss in the apicomplexa species which are primarily parasitic species. The implications of a creatine kinase in the parasites' infection cycle are discussed.}, }
@article {pmid32461272, year = {2020}, author = {Maeusli, M and Lee, B and Miller, S and Reyna, Z and Lu, P and Yan, J and Ulhaq, A and Skandalis, N and Spellberg, B and Luna, B}, title = {Horizontal Gene Transfer of Antibiotic Resistance from Acinetobacter baylyi to Escherichia coli on Lettuce and Subsequent Antibiotic Resistance Transmission to the Gut Microbiome.}, journal = {mSphere}, volume = {5}, number = {3}, pages = {}, pmid = {32461272}, issn = {2379-5042}, support = {R01 AI139052/AI/NIAID NIH HHS/United States ; R01 AI130060/AI/NIAID NIH HHS/United States ; R21 AI132923/AI/NIAID NIH HHS/United States ; R01 AI117211/AI/NIAID NIH HHS/United States ; }, mesh = {Acinetobacter/*genetics ; Animals ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/drug effects/*genetics ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; *Gene Transfer, Horizontal ; Klebsiella pneumoniae/genetics ; Lactuca/*microbiology ; Mice ; Mice, Inbred BALB C ; Plasmids/genetics ; Specific Pathogen-Free Organisms ; }, abstract = {Agricultural use of antibiotics is recognized by the U.S. Centers for Disease Control and Prevention as a major contributor to antibiotic-resistant infections. While most One Health attention has been on the potential for antibiotic resistance transmission from livestock and contaminated meat products to people, plant foods are fundamental to the food chain for meat eaters and vegetarians alike. We hypothesized that environmental bacteria that colonize plant foods may serve as platforms for the persistence of antibiotic-resistant bacteria and for horizontal gene transfer of antibiotic-resistant genes. Donor Acinetobacter baylyi and recipient Escherichia coli were cocultured in vitro, in planta on lettuce, and in vivo in BALB/c mice. We showed that nonpathogenic, environmental A. baylyi is capable of transferring plasmids conferring antibiotic resistance to E. coli clinical isolates on lettuce leaf discs. Furthermore, transformant E. coli from the in planta assay could then colonize the mouse gut microbiome. The target antibiotic resistance plasmid was identified in mouse feces up to 5 days postinfection. We specifically identified in vivo transfer of the plasmid to resident Klebsiella pneumoniae in the mouse gut. Our findings highlight the potential for environmental bacteria exposed to antibiotics to transmit resistance genes to mammalian pathogens during ingestion of leafy greens.IMPORTANCE Previous efforts have correlated antibiotic-fed livestock and meat products with respective antibiotic resistance genes, but virtually no research has been conducted on the transmission of antibiotic resistance from plant foods to the mammalian gut (C. S. Hölzel, J. L. Tetens, and K. Schwaiger, Pathog Dis 15:671-688, 2018, https://doi.org/10.1089/fpd.2018.2501; C. M. Liu et al., mBio 9:e00470-19, 2018, https://doi.org/10.1128/mBio.00470-18; B. Spellberg et al., NAM Perspectives, 2016, https://doi.org/10.31478/201606d; J. O'Neill, Antimicrobials in agriculture and the environment, 2015; Centers for Disease Control and Prevention, Antibiotic resistance threats in the United States, 2019). Here, we sought to determine if horizontal transmission of antibiotic resistance genes can occur between lettuce and the mammalian gut microbiome, using a mouse model. Furthermore, we have created a new model to study horizontal gene transfer on lettuce leaves using an antibiotic-resistant transformant of A. baylyi (Ab[zeoR]).}, }
@article {pmid32459899, year = {2020}, author = {Davidovich, NV and Kukalevskaya, NN and Bashilova, EN and Bazhukova, TA}, title = {[General principles of antibiotic resistance evolution in bacteria (review of literature).].}, journal = {Klinicheskaia laboratornaia diagnostika}, volume = {65}, number = {6}, pages = {387-393}, doi = {10.18821/0869-2084-2020-65-6-387-393}, pmid = {32459899}, issn = {0869-2084}, mesh = {Anti-Bacterial Agents ; Bacteria/*drug effects/*genetics ; *Drug Resistance, Bacterial ; Ecosystem ; *Evolution, Molecular ; Gene Transfer, Horizontal ; }, abstract = {Currently, the impact of antibiotic resistance on human health is a worldwide problem and its study is of great interest from a molecular genetic, environmental and clinical view-point. This review summarizes the latest data about antibiotic resistance, the classification of microorganisms as sensitive and resistant to the action of antibiotics, reveals the concept of minimum inhibitory concentration from modern positions. The resistance of microorganisms to antibacterial agents can be intrinsic and acquired, as well as being one of the examples of evolution that are currently available for study. Modern methods of whole-genome sequencing and complex databases of nucleotide-tagged libraries give an idea of the multifaceted nature of the mechanisms of intrinsic resistance to antibiotics and are able to provide information on genes encoding metabolic enzymes and proteins that regulate the basic processes of the physiology of bacteria. The article describes the main ways of spreading the resistance of microorganisms, reflects the concepts of "founder effect" and the fitness cost of bacteria, which underlie the emergence and evolution of antibiotic resistance. It is shown that the origin of antibiotic resistance genes that human pathogens currently possess can be traced by studying the surrounding not only clinical, but also non-clinical (ecological) habitats. As well as microorganisms of the surrounding ecosystems are the donors of resistance genes in horizontal gene transfer.}, }
@article {pmid32457503, year = {2020}, author = {Antonaru, LA and Cardona, T and Larkum, AWD and Nürnberg, DJ}, title = {Global distribution of a chlorophyll f cyanobacterial marker.}, journal = {The ISME journal}, volume = {14}, number = {9}, pages = {2275-2287}, pmid = {32457503}, issn = {1751-7370}, support = {BB/L011506/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R001383/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Antarctic Regions ; Arctic Regions ; *Chlorophyll/analogs &amp; derivatives ; Chlorophyll A ; *Cyanobacteria/genetics ; Light ; Photosynthesis ; Phylogeny ; }, abstract = {Some cyanobacteria use light outside the visible spectrum for oxygenic photosynthesis. The far-red light (FRL) region is made accessible through a complex acclimation process that involves the formation of new phycobilisomes and photosystems containing chlorophyll f. Diverse cyanobacteria ranging from unicellular to branched-filamentous forms show this response. These organisms have been isolated from shaded environments such as microbial mats, soil, rock, and stromatolites. However, the full spread of chlorophyll f-containing species in nature is still unknown. Currently, discovering new chlorophyll f cyanobacteria involves lengthy incubation times under selective far-red light. We have used a marker gene to detect chlorophyll f organisms in environmental samples and metagenomic data. This marker, apcE2, encodes a phycobilisome linker associated with FRL-photosynthesis. By focusing on a far-red motif within the sequence, degenerate PCR and BLAST searches can effectively discriminate against the normal chlorophyll a-associated apcE. Even short recovered sequences carry enough information for phylogenetic placement. Markers of chlorophyll f photosynthesis were found in metagenomic datasets from diverse environments around the globe, including cyanobacterial symbionts, hypersaline lakes, corals, and the Arctic/Antarctic regions. This additional information enabled higher phylogenetic resolution supporting the hypothesis that vertical descent, as opposed to horizontal gene transfer, is largely responsible for this phenotype's distribution.}, }
@article {pmid32456625, year = {2020}, author = {Alderliesten, JB and Duxbury, SJN and Zwart, MP and de Visser, JAGM and Stegeman, A and Fischer, EAJ}, title = {Effect of donor-recipient relatedness on the plasmid conjugation frequency: a meta-analysis.}, journal = {BMC microbiology}, volume = {20}, number = {1}, pages = {135}, pmid = {32456625}, issn = {1471-2180}, support = {50-54100-98-1 19//ZonMw/International ; }, mesh = {Bacteria/*classification/genetics ; Bacterial Physiological Phenomena ; Conjugation, Genetic ; Drug Resistance, Bacterial ; Escherichia coli/genetics/*growth &amp; development ; Escherichia coli Proteins/genetics ; Phylogeny ; Plasmids/*genetics ; Species Specificity ; }, abstract = {BACKGROUND: Conjugation plays a major role in the transmission of plasmids encoding antibiotic resistance genes in both clinical and general settings. The conjugation efficiency is influenced by many biotic and abiotic factors, one of which is the taxonomic relatedness between donor and recipient bacteria. A comprehensive overview of the influence of donor-recipient relatedness on conjugation is still lacking, but such an overview is important to quantitatively assess the risk of plasmid transfer and the effect of interventions which limit the spread of antibiotic resistance, and to obtain parameter values for conjugation in mathematical models. Therefore, we performed a meta-analysis on reported conjugation frequencies from Escherichia coli donors to various recipient species.<br><br>RESULTS: Thirty-two studies reporting 313 conjugation frequencies for liquid broth matings and 270 conjugation frequencies for filter matings were included in our meta-analysis. The reported conjugation frequencies varied over 11 orders of magnitude. Decreasing taxonomic relatedness between donor and recipient bacteria, when adjusted for confounding factors, was associated with a lower conjugation frequency in liquid matings. The mean conjugation frequency for bacteria of the same order, the same class, and other classes was 10, 20, and 789 times lower than the mean conjugation frequency within the same species, respectively. This association between relatedness and conjugation frequency was not found for filter matings. The conjugation frequency was furthermore found to be influenced by temperature in both types of mating experiments, and in addition by plasmid incompatibility group in liquid matings, and by recipient origin and mating time in filter matings.<br><br>CONCLUSIONS: In our meta-analysis, taxonomic relatedness is limiting conjugation in liquid matings, but not in filter matings, suggesting that taxonomic relatedness is not a limiting factor for conjugation in environments where bacteria are fixed in space.}, }
@article {pmid32453777, year = {2020}, author = {Krawczyk, B and Wysocka, M and Kotłowski, R and Bronk, M and Michalik, M and Samet, A}, title = {Linezolid-resistant Enterococcus faecium strains isolated from one hospital in Poland -commensals or hospital-adapted pathogens?.}, journal = {PloS one}, volume = {15}, number = {5}, pages = {e0233504}, pmid = {32453777}, issn = {1932-6203}, mesh = {*Drug Resistance, Bacterial ; Enterococcus faecium/*classification/genetics/isolation &amp; purification ; Evolution, Molecular ; Female ; Gene Transfer, Horizontal ; Genotyping Techniques ; Gram-Positive Bacterial Infections/*microbiology ; Humans ; Linezolid/*pharmacology ; Male ; Phylogeny ; Point Mutation ; Poland ; RNA, Ribosomal, 23S/genetics ; Sequence Analysis, DNA ; Symbiosis ; Virulence Factors/genetics ; }, abstract = {One of the most pressing problems of enterococci infections is occurring resistance to linezolid, which is an antibiotic used in the treatment of infections caused by vancomycin-resistant strains (VRE). The main objective of our research was to investigate the relationship of 19 linezolid-resistant E. faecium isolates from 18 patients hospitalized at Clinical Hospital in Gdansk (Poland). One of the LZDREF was isolated in 2003 (K2003), and another 18 were collected from 2013 to 2017. Genotyping with PCR MP method indicated 14 main unrelated genetic profiles and no association with K2003 strain. Two isolates with the same genotype and genetically closely related two sub-types (2 isolates for each sub-type) were hospital-derived colonizations of patients. The other unrelated genotypes were discussed in the context of colonization, nosocomial infections, and commensal origin, taking into account prior exposure to linezolid. We determined the presence of a point mutation G2576T in six loci of 23S rDNA. There was also a significant correlation (p<0.0015) between the presence of MIC>32 value and the presence of G2576T point mutation on the sixth rrn. We also detected 5 virulence genes for all isolates: gelE, cylA, asa1, hyl, esp. Correlation (p≤0.0001) was observed between the presence of gelE gene encoding gelatinase and two other genes: cylA and asa1 encoding cytolysin and collagen binding protein responsible for aggregation of bacterial cells, respectively. Significant correlation was also observed between asa1 and cfr genes encoding 23S rRNA rybonuclease responsible for resistance to PhLOPSA antibiotics (p = 0.0004). The multidimensional analysis has also shown the correlation between cfr gene and GI-tract (p = 0, 0491), which suggests horizontal gene transfer inside the gut microbiota and the risk of colonization with linezolid-resistant strains without previously being treated with the antibiotic. The patient could have been colonized with LZDRVREF strains which in the absence of competitive microbiota quickly settle in ecological niches favourable for them and pose a risk for the patient.}, }
@article {pmid32450799, year = {2020}, author = {Saliu, EM and Zentek, J and Vahjen, W}, title = {In vitro conjugation kinetics of AmpC, broad spectrum and extended-spectrum beta-lactamase-producing Escherichia coli donors and various Enterobacteriaceae recipients.}, journal = {BMC microbiology}, volume = {20}, number = {1}, pages = {133}, pmid = {32450799}, issn = {1471-2180}, mesh = {Animals ; Bacterial Proteins/*genetics ; Conjugation, Genetic ; Enterobacteriaceae/classification/*genetics/isolation &amp; purification ; Escherichia coli/classification/*genetics ; Escherichia coli Proteins/genetics ; In Vitro Techniques ; Kinetics ; Plasmids/genetics ; Poultry/microbiology ; Species Specificity ; beta-Lactamases/*genetics ; }, abstract = {BACKGROUND: Extended spectrum beta-lactamase (ESBL)-producing enterobacteria pose a major hazard to public health. Due to the possibility of genetic transfer, ESBL genes might spread to pathogenic enterobacterial strains. Thus, information on possible genetic transfer between enterobacteria is of high interest. It was therefore the aim of this in vitro study to screen the capacity of a wide range of Enterobacteriaceae for differences in conjugation at different time points with five ESBL-producing Escherichia coli strains.<br><br>RESULTS: Conjugation frequencies for five potential E. coli donor strains producing the enzymes CTX-M-1, CTX-M-15, SHV-12, TEM-1, TEM-52 and CMY-2, and six potential recipient strains commonly detected in the gastrointestinal tract of poultry (E. coli, Serratia marcescens subsp. marcescens, Enterobacter cloacae, Salmonella (S.) enterica serovar Typhimurium and Proteus mirabilis) were obtained. Different combinations of donor and recipient strains were co-incubated for between 0 and 22&#x2009;h and spread on selective agar. Conjugation frequencies were calculated as transconjugants per donor. Some donor and recipient strain combinations did not perform plasmid transfer within 22&#x2009;h. Hence, the recipient Proteus mirabilis did not accept plasmids from any of the given donors and the E. coli ESBL10716 donor was unable to transfer its plasmid to any recipient. Enterobacter cloacae only accepted the plasmids from the donors E. coli ESBL10708 and E. coli ESBL10716 while E. coli ESBL10708 did not transfer its plasmid to Serratia marcescens subsp. marcescens. E. coli IMT11716 on the other hand did not perform conjugation with the donor E. coli ESBL10689. The remaining mating pairs differed in conjugation frequency, ranging from 10[-&#x2009;5] to 10[-&#x2009;9] transconjugants/donor. The earliest conjugation events were detected after 4&#x2009;h. However, some mating pairs turned positive only after 22&#x2009;h of coincubation.<br><br>CONCLUSION: A suitable mating pair for future in vivo studies to combat transfer of antibiotic resistance to pathogenic bacteria in broiler chicken was determined. The results of this study also suggest that the kinetic of conjugation differs between mating pairs and is independent of species origin. This should be considered when performing conjugation experiments.}, }
@article {pmid32448450, year = {2020}, author = {Zolfaghari Emameh, R and Masoori, L and Taheri, RA and Falak, R}, title = {Identification and characterization of parvalbumin-like protein in Trichophyton violaceum.}, journal = {Fungal biology}, volume = {124}, number = {6}, pages = {592-600}, doi = {10.1016/j.funbio.2020.02.014}, pmid = {32448450}, issn = {1878-6146}, mesh = {Animals ; Antigens, Fungal ; Arthrodermataceae/*chemistry/*genetics ; Evolution, Molecular ; Fish Proteins/chemistry/genetics ; Fishes ; Fungal Proteins/analysis/chemistry/*genetics/immunology ; Genes, Fungal ; Parvalbumins/analysis/chemistry/*genetics/immunology ; Phylogeny ; }, abstract = {Parvalbumins play crucial physiological roles in neuromuscular systems of vertebrates, such as cell-cycle, development of neurons, contraction of muscles, and regulation of intracellular calcium. To perform these neuromuscular functions, parvalbumin may be in associated with other proteins including calbindin, carbonic anhydrase, and cytochrome oxidase. Humans may show an IgE-specific hypersensitivity to parvalbumins after consumption of some distinct fish species. While this protein is abundant in fish muscles, literature review of publications related to fish parvalbumins, do not point to the presence of parvalbumins in eukaryotic microbes. In this study, we propose that distantly related parvalbumins may be found in some non-fish species. Bioinformatics studies such as multiple sequence alignment (MSA), phylogenetic analysis as well as molecular-based experiments indicate that, at least two parvalbumins sequences (UniProt IDs: A0A178F775 and A0A178F7E4) with EF-hand domains and Ca[2+]-binding sites could be identified in Trichophyton violaceum, a pathogenic fungal species. It was determined that both genes consisted of a single exon and encoded for parvalbumin proteins possessing conserved amino acid motifs. Antigenicity prediction revealed antigenic sites located in both sides of the Ca[2+]-binding site of the first EF-hand domain. Our phylogenetic analysis revealed that one of parvalbumins (UniProt ID: 0A178F775) can be evolved to other parvalbumins in T. violaceum (UniProt ID: A0A178F7E4) and fish species through evolutionary phenomenon. To confirm our in-silico findings, we designed three primer pairs to detect one of the T. violaceum parvalbumins (UniProt ID: A0A178F7E4) by polymerase chain reaction (PCR); one primer pair showed a strong and specific band in agarose gel electrophoresis. To evaluate the specificity of the method, the primers were tested on extracted DNA from Trichophyton rubrum and T. mentagrophytes. The results demonstrated that the evaluated parvalbumin gene (UniProt ID: A0A178F7E4) was T. violaceum-specific and this pathogenic fungus can be differentiated from T. rubrum and T. mentagrophytes through identification of parvalbumin genes. Further studies are necessary to unravel the biochemical and physiological functions of parvalbumins in T. violaceum.}, }
@article {pmid32442459, year = {2020}, author = {Neveu, E and Khalifeh, D and Salamin, N and Fasshauer, D}, title = {Prototypic SNARE Proteins Are Encoded in the Genomes of Heimdallarchaeota, Potentially Bridging the Gap between the Prokaryotes and Eukaryotes.}, journal = {Current biology : CB}, volume = {30}, number = {13}, pages = {2468-2480.e5}, doi = {10.1016/j.cub.2020.04.060}, pmid = {32442459}, issn = {1879-0445}, mesh = {Amino Acid Sequence ; Archaea/*genetics/metabolism ; Archaeal Proteins/chemistry/*genetics/metabolism ; *Evolution, Molecular ; Genome, Archaeal ; SNARE Proteins/chemistry/*genetics/metabolism ; }, abstract = {A defining feature of eukaryotic cells is the presence of numerous membrane-bound organelles that subdivide the intracellular space into distinct compartments. How the eukaryotic cell acquired its internal complexity is still poorly understood. Material exchange among most organelles occurs via vesicles that bud off from a source and specifically fuse with a target compartment. Central players in the vesicle fusion process are the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins. These small tail-anchored (TA) membrane proteins zipper into elongated four-helix bundles that pull membranes together. SNARE proteins are highly conserved among eukaryotes but are thought to be absent in prokaryotes. Here, we identified SNARE-like factors in the genomes of uncultured organisms of Asgard archaea of the Heimdallarchaeota clade, which are thought to be the closest living relatives of eukaryotes. Biochemical experiments show that the archaeal SNARE-like proteins can interact with eukaryotic SNARE proteins. We did not detect SNAREs in α-proteobacteria, the closest relatives of mitochondria, but identified several genes encoding for SNARE proteins in γ-proteobacteria of the order Legionellales, pathogens that live inside eukaryotic cells. Very probably, their SNAREs stem from lateral gene transfer from eukaryotes. Together, this suggests that the diverse set of eukaryotic SNAREs evolved from an archaeal precursor. However, whether Heimdallarchaeota actually have a simplified endomembrane system will only be seen when we succeed studying these organisms under the microscope.}, }
@article {pmid32440763, year = {2020}, author = {Roulet, ME and Garcia, LE and Gandini, CL and Sato, H and Ponce, G and Sanchez-Puerta, MV}, title = {Multichromosomal structure and foreign tracts in the Ombrophytum subterraneum (Balanophoraceae) mitochondrial genome.}, journal = {Plant molecular biology}, volume = {103}, number = {6}, pages = {623-638}, doi = {10.1007/s11103-020-01014-x}, pmid = {32440763}, issn = {1573-5028}, support = {PICT-0691//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; 06/A724//Universidad Nacional de Cuyo/ ; 1062432//National Science Foundation/ ; }, mesh = {Balanophoraceae/*genetics ; DNA, Mitochondrial/*genetics ; Gene Transfer, Horizontal ; Genome, Mitochondrial/*genetics ; }, abstract = {Horizontal gene transfer (HGT) is frequent in parasitic plant mitochondria as a result of vascular connections established in host-parasite relationships. Recent studies of the holoparasitic plant Lophophytum mirabile (Balanophoraceae) revealed the unprecedented acquisition of a large amount of mitochondrial sequences from its legume host. We focused on a close relative, the generalist holoparasite Ombrophytum subterraneum, to examine the incidence of HGT events in the mitochondrial genome (mtDNA). The mtDNA of O. subterraneum assembles into 54 circular chromosomes, only 34 of which contain the 51 full-length coding regions. Numerous foreign tracts (totaling almost 100 kb, ~ 14% of the mtDNA), including 12 intact genes, were acquired by HGT from the Asteraceae hosts. Nine chromosomes concentrate most of those regions and eight are almost entirely foreign. Native homologs of each foreign gene coexist in the mtDNA and are potentially functional. A large proportion of shorter regions were related to the Fabaceae (a total of ~ 110 kb, 15.4%), some of which were shared with L. mirabile. We also found evidence of foreign sequences donated by angiosperm lineages not reported as hosts (Apocynaceae, Euphorbiaceae, Lamiaceae, and Malvales). We propose an evolutionary hypothesis that involves ancient transfers from legume hosts in the common ancestor of Ombrophytum and Lophophytum followed by more recent transfer events in L. mirabile. Besides, the O. subterraneum mtDNA was also subjected to additional HGT events from diverse angiosperm lineages, including large and recent transfers from the Asteraceae, and also from Lamiaceae.}, }
@article {pmid32439778, year = {2020}, author = {Wulff, BBH and Jones, JDG}, title = {Breeding a fungal gene into wheat.}, journal = {Science (New York, N.Y.)}, volume = {368}, number = {6493}, pages = {822-823}, doi = {10.1126/science.abb9991}, pmid = {32439778}, issn = {1095-9203}, mesh = {Breeding ; *Fusarium ; Gene Transfer, Horizontal ; Genes, Fungal ; Triticum/*genetics ; }, }
@article {pmid32438044, year = {2020}, author = {Herzog, S and Brinkmann, H and Vences, M and Fleißner, A}, title = {Evidence of repeated horizontal transfer of sterol C-5 desaturase encoding genes among dikarya fungi.}, journal = {Molecular phylogenetics and evolution}, volume = {150}, number = {}, pages = {106850}, doi = {10.1016/j.ympev.2020.106850}, pmid = {32438044}, issn = {1095-9513}, mesh = {Ascomycota/enzymology/*genetics ; Basidiomycota/enzymology/*genetics ; Databases, Genetic ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Oxidoreductases/classification/*genetics ; Phylogeny ; RNA, Ribosomal, 18S/classification/genetics ; }, abstract = {Gene duplication and horizontal gene transfer (HGT) are two important but different forces for adaptive genome evolution. In eukaryotic organisms, gene duplication is considered to play a more important evolutionary role than HGT. However, certain fungal lineages have developed highly efficient mechanisms that avoid the occurrence of duplicated gene sequences within their genomes. While these mechanisms likely originated as a defense against harmful mobile genetic elements, they come with an evolutionary cost. A prominent example for a genome defense system is the RIP mechanism of the ascomycete fungus Neurospora crassa, which efficiently prevents sequence duplication within the genome and functional redundancy of the subsequent paralogs. Despite this tight control, the fungus possesses two functionally redundant sterol C-5 desaturase enzymes, ERG-10a and ERG-10b, that catalyze the same step during ergosterol biosynthesis. In this study, we addressed this conundrum by phylogenetic analysis of the two proteins and supporting topology tests. We obtained evidence that a primary HGT of a sterol C-5 desaturase gene from Tremellales (an order of Basidiomycota) into a representative of the Pezizomycotina (a subphylum of Ascomycota) is the origin of the ERG-10b sequence. The reconstructed phylogenies suggest that this HGT event was followed by multiple HGT events among other members of the Pezizomycotina, thereby generating a diverse group with members in the four classes Sordariomycetes, Xylonomycetes, Eurotiomycetes and Dothideomycetes, which all harbor the second sterol C-5 desaturase or maintained in some cases only the ERG-10b version of this enzyme. These results furnish an example for a gene present in numerous ascomycetous fungi but primarily acquired by an ancestral HGT event from another fungal phylum. Furthermore, these data indicate that HGT represents one mechanism to generate functional redundancy in organisms with a strict avoidance of gene duplications.}, }
@article {pmid32436087, year = {2020}, author = {Cheng, J and Tang, X and Liu, C}, title = {Occurrence and distribution of antibiotic resistance genes in various rural environmental media.}, journal = {Environmental science and pollution research international}, volume = {27}, number = {23}, pages = {29191-29203}, doi = {10.1007/s11356-020-09287-x}, pmid = {32436087}, issn = {1614-7499}, support = {41790431//National Natural Science Foundation of China/ ; 41771521//National Natural Science Foundation of China (CN)/ ; SDS-135-1702//Institute of Mountain Hazards and Environment/ ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/drug effects ; Genes, Bacterial/*drug effects ; Rivers ; }, abstract = {Antibiotic resistance genes (ARGs) in rural environments have been poorly characterized in the literature. In this study, the diversity, abundance, and distribution of ARGs in surface waters, soils, and sediments of a typical hilly rural area in the Upper Yangtze River watershed were investigated using the high-throughput quantitative polymerase chain reaction, and their relationships with chemical properties of the samples were analyzed. No significant differences in the diversity and abundance of ARGs were observed among the three medium types while the ARG distribution pattern in the sediments was obviously different from that of the surface waters. According to the co-occurrence pattern of ARGs subtypes obtained by network analysis, blaOXA10-02, blaPSE, lnuB-02, and qacEΔ1-01 can be used to estimate the relative abundance of total ARGs for the study area. It appeared that the prevalence of ARGs in the sediments was promoted by the horizontal gene transfer (HGT) and vertical gene transfer together, while their spread in the surface waters and soils were facilitated by the supply of biogenic elements and HGT, respectively. Mobile genetic elements (MGEs) were abundant and detected in all samples, and their abundance was significantly and positively correlated with that of ARGs, implying that the potential horizontal transfer of ARGs to other bacteria and pathogens in rural environments should not be overlooked.}, }
@article {pmid32435238, year = {2020}, author = {Vrancianu, CO and Popa, LI and Bleotu, C and Chifiriuc, MC}, title = {Targeting Plasmids to Limit Acquisition and Transmission of Antimicrobial Resistance.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {761}, pmid = {32435238}, issn = {1664-302X}, abstract = {Antimicrobial resistance (AMR) is a significant global threat to both public health and the environment. The emergence and expansion of AMR is sustained by the enormous diversity and mobility of antimicrobial resistance genes (ARGs). Different mechanisms of horizontal gene transfer (HGT), including conjugation, transduction, and transformation, have facilitated the accumulation and dissemination of ARGs in Gram-negative and Gram-positive bacteria. This has resulted in the development of multidrug resistance in some bacteria. The most clinically significant ARGs are usually located on different mobile genetic elements (MGEs) that can move intracellularly (between the bacterial chromosome and plasmids) or intercellularly (within the same species or between different species or genera). Resistance plasmids play a central role both in HGT and as support elements for other MGEs, in which ARGs are assembled by transposition and recombination mechanisms. Considering the crucial role of MGEs in the acquisition and transmission of ARGs, a potential strategy to control AMR is to eliminate MGEs. This review discusses current progress on the development of chemical and biological approaches for the elimination of ARG carriers.}, }
@article {pmid32432548, year = {2020}, author = {van Dijk, B and Hogeweg, P and Doekes, HM and Takeuchi, N}, title = {Slightly beneficial genes are retained by bacteria evolving DNA uptake despite selfish elements.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, pmid = {32432548}, issn = {2050-084X}, support = {ICT-610427//Seventh Framework Programme/International ; RGY0072/2015//Human Frontier Science Program/International ; }, mesh = {Bacteria/*genetics/growth &amp; development/metabolism ; DNA, Bacterial/*genetics/metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal ; }, abstract = {Horizontal gene transfer (HGT) and gene loss result in rapid changes in the gene content of bacteria. While HGT aids bacteria to adapt to new environments, it also carries risks such as selfish genetic elements (SGEs). Here, we use modelling to study how HGT of slightly beneficial genes impacts growth rates of bacterial populations, and if bacterial collectives can evolve to take up DNA despite selfish elements. We find four classes of slightly beneficial genes: indispensable, enrichable, rescuable, and unrescuable genes. Rescuable genes - genes with small fitness benefits that are lost from the population without HGT - can be collectively retained by a community that engages in costly HGT. While this 'gene-sharing' cannot evolve in well-mixed cultures, it does evolve in a spatial population like a biofilm. Despite enabling infection by harmful SGEs, the uptake of foreign DNA is evolutionarily maintained by the hosts, explaining the coexistence of bacteria and SGEs.}, }
@article {pmid32429345, year = {2020}, author = {Miller, C and Gilmore, J}, title = {Detection of Quorum-Sensing Molecules for Pathogenic Molecules Using Cell-Based and Cell-Free Biosensors.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {9}, number = {5}, pages = {}, pmid = {32429345}, issn = {2079-6382}, abstract = {Since the discovery and subsequent use of penicillin, antibiotics have been used to treat most bacterial infections in the U.S. Over time, the repeated prescription of many antibiotics has given rise to many antibiotic-resistant microbes. A bacterial strain becomes resistant by horizontal gene transfer, where surviving microbes acquire genetic material or DNA fragments from adjacent bacteria that encode for resistance. In order to avoid significant bacterial resistance, novel and target therapeutics are needed. Further advancement of diagnostic technologies could be used to develop novel treatment strategies. The use of biosensors to detect quorum-sensing signaling molecules has the potential to provide timely diagnostic information toward mitigating the multidrug-resistant bacteria epidemic. Resistance and pathogenesis are controlled by quorum-sensing (QS) circuits. QS systems secrete or passively release signaling molecules when the bacterial concentration reaches a certain threshold. Signaling molecules give an early indication of virulence. Detection of these compounds in vitro or in vivo can be used to identify the onset of infection. Whole-cell and cell-free biosensors have been developed to detect quorum-sensing signaling molecules. This review will give an overview of quorum networks in the most common pathogens found in chronic and acute infections. Additionally, the current state of research surrounding the detection of quorum-sensing molecules will be reviewed. Followed by a discussion of future works toward the advancement of technologies to quantify quorum signaling molecules in chronic and acute infections.}, }
@article {pmid32429344, year = {2020}, author = {Sariola, S and Gilbert, SF}, title = {Toward a Symbiotic Perspective on Public Health: Recognizing the Ambivalence of Microbes in the Anthropocene.}, journal = {Microorganisms}, volume = {8}, number = {5}, pages = {}, pmid = {32429344}, issn = {2076-2607}, support = {316941//Academy of Finland/ ; SFG//Swarthmore College Faculty Research/ ; }, abstract = {Microbes evolve in complex environments that are often fashioned, in part, by human desires. In a global perspective, public health has played major roles in structuring how microbes are perceived, cultivated, and destroyed. The germ theory of disease cast microbes as enemies of the body and the body politic. Antibiotics have altered microbial development by providing stringent natural selection on bacterial species, and this has led to the formation of antibiotic-resistant bacterial strains. Public health perspectives such as "Precision Public Health" and "One Health" have recently been proposed to further manage microbial populations. However, neither of these take into account the symbiotic relationships that exist between bacterial species and between bacteria, viruses, and their eukaryotic hosts. We propose a perspective on public health that recognizes microbial evolution through symbiotic associations (the hologenome theory) and through lateral gene transfer. This perspective has the advantage of including both the pathogenic and beneficial interactions of humans with bacteria, as well as combining the outlook of the "One Health" model with the genomic methodologies utilized in the "Precision Public Health" model. In the Anthropocene, the conditions for microbial evolution have been altered by human interventions, and public health initiatives must recognize both the beneficial (indeed, necessary) interactions of microbes with their hosts as well as their pathogenic interactions.}, }
@article {pmid32427317, year = {2020}, author = {Mungan, MD and Alanjary, M and Blin, K and Weber, T and Medema, MH and Ziemert, N}, title = {ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining.}, journal = {Nucleic acids research}, volume = {48}, number = {W1}, pages = {W546-W552}, pmid = {32427317}, issn = {1362-4962}, mesh = {Biosynthetic Pathways/genetics ; Data Mining ; Drug Resistance, Bacterial/*genetics ; Genes, Bacterial ; *Genome, Bacterial ; Metagenomics ; *Software ; }, abstract = {Multi-drug resistant pathogens have become a major threat to human health and new antibiotics are urgently needed. Most antibiotics are derived from secondary metabolites produced by bacteria. In order to avoid suicide, these bacteria usually encode resistance genes, in some cases within the biosynthetic gene cluster (BGC) of the respective antibiotic compound. Modern genome mining tools enable researchers to computationally detect and predict BGCs that encode the biosynthesis of secondary metabolites. The major challenge now is the prioritization of the most promising BGCs encoding antibiotics with novel modes of action. A recently developed target-directed genome mining approach allows researchers to predict the mode of action of the encoded compound of an uncharacterized BGC based on the presence of resistant target genes. In 2017, we introduced the 'Antibiotic Resistant Target Seeker' (ARTS). ARTS allows for specific and efficient genome mining for antibiotics with interesting and novel targets by rapidly linking housekeeping and known resistance genes to BGC proximity, duplication and horizontal gene transfer (HGT) events. Here, we present ARTS 2.0 available at http://arts.ziemertlab.com. ARTS 2.0 now includes options for automated target directed genome mining in all bacterial taxa as well as metagenomic data. Furthermore, it enables comparison of similar BGCs from different genomes and their putative resistance genes.}, }
@article {pmid32425968, year = {2020}, author = {Devia, J and Bastías, C and Kessi-Pérez, EI and Villarroel, CA and De Chiara, M and Cubillos, FA and Liti, G and Martínez, C and Salinas, F}, title = {Transcriptional Activity and Protein Levels of Horizontally Acquired Genes in Yeast Reveal Hallmarks of Adaptation to Fermentative Environments.}, journal = {Frontiers in genetics}, volume = {11}, number = {}, pages = {293}, pmid = {32425968}, issn = {1664-8021}, abstract = {In the past decade, the sequencing of large cohorts of Saccharomyces cerevisiae strains has revealed a landscape of genomic regions acquired by Horizontal Gene Transfer (HGT). The genes acquired by HGT play important roles in yeast adaptation to the fermentation process, improving nitrogen and carbon source utilization. However, the functional characterization of these genes at the molecular level has been poorly attended. In this work, we carried out a systematic analysis of the promoter activity and protein level of 30 genes contained in three horizontally acquired regions commonly known as regions A, B, and C. In three strains (one for each region), we used the luciferase reporter gene and the mCherry fluorescent protein to quantify the transcriptional and translational activity of these genes, respectively. We assayed the strains generated in four different culture conditions; all showed low levels of transcriptional and translational activity across these environments. However, we observed an increase in protein levels under low nitrogen culture conditions, suggesting a possible role of the horizontally acquired genes in the adaptation to nitrogen-limited environments. Furthermore, since the strains carrying the luciferase reporter gene are null mutants for the horizontally acquired genes, we assayed growth parameters (latency time, growth rate, and efficiency) and the fermentation kinetics in this set of deletion strains. The results showed that single deletion of 20 horizontally acquired genes modified the growth parameters, whereas the deletion of five of them altered the maximal CO2 production rate (Vmax). Interestingly, we observed a correlation between growth parameters and Vmax for an ORF within region A, encoding an ortholog to a thiamine (vitamin B1) transporter whose deletion decreased the growth rate, growth efficiency, and CO2 production. Altogether, our results provided molecular and phenotypic evidence highlighting the importance of horizontally acquired genes in yeast adaptation to fermentative environments.}, }
@article {pmid32424779, year = {2020}, author = {Cao, J and Liu, F and Zhu, B and Shi, Y and Gao, GF}, title = {Diversity and abundance of resistome in rhizosphere soil.}, journal = {Science China. Life sciences}, volume = {63}, number = {12}, pages = {1946-1949}, pmid = {32424779}, issn = {1869-1889}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/classification/drug effects/genetics/isolation &amp; purification ; Biodiversity ; Citrus/microbiology ; Drug Resistance, Bacterial/drug effects/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Metagenome/*genetics ; Phylogeny ; *Rhizosphere ; *Soil Microbiology ; }, }
@article {pmid32424247, year = {2020}, author = {Wang, Y and Lu, J and Engelstädter, J and Zhang, S and Ding, P and Mao, L and Yuan, Z and Bond, PL and Guo, J}, title = {Non-antibiotic pharmaceuticals enhance the transmission of exogenous antibiotic resistance genes through bacterial transformation.}, journal = {The ISME journal}, volume = {14}, number = {8}, pages = {2179-2196}, pmid = {32424247}, issn = {1751-7370}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; Drug Resistance, Microbial ; Genes, Bacterial ; *Pharmaceutical Preparations ; Proteomics ; Transformation, Bacterial ; }, abstract = {Antibiotic resistance is a serious global threat for public health. Considering the high abundance of cell-free DNA encoding antibiotic resistance genes (ARGs) in both clinical and environmental settings, natural transformation is an important horizontal gene transfer pathway to transmit antibiotic resistance. It is acknowledged that antibiotics are key drivers for disseminating antibiotic resistance, yet the contributions of non-antibiotic pharmaceuticals on transformation of ARGs are overlooked. In this study, we report that some commonly consumed non-antibiotic pharmaceuticals, at clinically and environmentally relevant concentrations, significantly facilitated the spread of antibiotic resistance through the uptake of exogenous ARGs. This included nonsteroidal anti-inflammatories, ibuprofen, naproxen, diclofenac, the lipid-lowering drug, gemfibrozil, and the β-blocker propranolol. Based on the results of flow cytometry, whole-genome RNA sequencing and proteomic analysis, the enhanced transformation of ARGs was affiliated with promoted bacterial competence, enhanced stress levels, over-produced reactive oxygen species and increased cell membrane permeability. In addition, a mathematical model was proposed and calibrated to predict the dynamics of transformation during exposure to non-antibiotic pharmaceuticals. Given the high consumption of non-antibiotic pharmaceuticals, these findings reveal new concerns regarding antibiotic resistance dissemination exacerbated by non-antibiotic pharmaceuticals.}, }
@article {pmid32424207, year = {2020}, author = {Lira, F and Vaz-Moreira, I and Tamames, J and Manaia, CM and Martínez, JL}, title = {Metagenomic analysis of an urban resistome before and after wastewater treatment.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {8174}, pmid = {32424207}, issn = {2045-2322}, abstract = {Determining the effect of wastewater treatment in water resistome is a topic of interest for water quality, mainly under re-use and One-Health perspectives. The resistome, the plasmidome, and the bacterial community composition of samples from influents and treated effluents from a wastewater treatment plant located in Northern Portugal were studied using metagenomic techniques. Wastewater treatment contributed to reduce the abundance of resistance genes and of plasmid replicons, coinciding with a decline in the number of intrinsic resistance genes from Enterobacteriaceae, as well as with a reduction in the relative abundance of Firmicutes and Proteobacteria after treatment. These taxons comprise bacterial pathogens, including those belonging to the ESKAPE group, which encompasses bacteria with the highest risk of acquiring antibiotic resistance, being the most relevant hosts of resistance genes acquired through horizontal gene transfer. Our results support that wastewater treatment efficiently removes the hosts of antibiotic resistance genes and, consequently, the harboured antibiotic resistance genes. Principal component analysis indicates that the resistome and the bacterial composition clustered together in influent samples, while did not cluster in final effluent samples. Our results suggest that wastewater treatment mitigates the environmental dissemination of urban resistome, through the removal of the hosts harbouring mobile resistance genes.}, }
@article {pmid32415210, year = {2020}, author = {Acman, M and van Dorp, L and Santini, JM and Balloux, F}, title = {Large-scale network analysis captures biological features of bacterial plasmids.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {2452}, pmid = {32415210}, issn = {2041-1723}, support = {BB/R01356X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /DH_/Department of Health/United Kingdom ; 19RX03/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MR/P007597/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Algorithms ; Bacteria/*genetics ; Base Composition/genetics ; Databases, Genetic ; *Gene Regulatory Networks ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial ; Phylogeny ; Plasmids/*genetics ; Replicon/genetics ; }, abstract = {Many bacteria can exchange genetic material through horizontal gene transfer (HGT) mediated by plasmids and plasmid-borne transposable elements. Here, we study the population structure and dynamics of over 10,000 bacterial plasmids, by quantifying their genetic similarities and reconstructing a network based on their shared k-mer content. We use a community detection algorithm to assign plasmids into cliques, which correlate with plasmid gene content, bacterial host range, GC content, and existing classifications based on replicon and mobility (MOB) types. Further analysis of plasmid population structure allows us to uncover candidates for yet undescribed replicon genes, and to identify transposable elements as the main drivers of HGT at broad phylogenetic scales. Our work illustrates the potential of network-based analyses of the bacterial 'mobilome' and opens up the prospect of a natural, exhaustive classification framework for bacterial plasmids.}, }
@article {pmid32414799, year = {2020}, author = {Storck, V and Gallego, S and Vasileiadis, S and Hussain, S and Béguet, J and Rouard, N and Baguelin, C and Perruchon, C and Devers-Lamrani, M and Karpouzas, DG and Martin-Laurent, F}, title = {Insights into the Function and Horizontal Transfer of Isoproturon Degradation Genes (pdmAB) in a Biobed System.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {14}, pages = {}, pmid = {32414799}, issn = {1098-5336}, mesh = {Biodegradation, Environmental ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Herbicides/*metabolism ; Phenylurea Compounds/*metabolism ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Sphingomonas/*genetics/metabolism ; }, abstract = {Biobeds, designed to minimize pesticide point source contamination, rely mainly on biodegradation processes. We studied the interactions of a biobed microbial community with the herbicide isoproturon (IPU) to explore the role of the pdmA gene, encoding the large subunit of an N-demethylase responsible for the initial demethylation of IPU, via quantitative PCR (qPCR) and reverse transcription-PCR (RT-qPCR) and the effect of IPU on the diversity of the total bacterial community and its active fraction through amplicon sequencing of DNA and RNA, respectively. We further investigated the localization and dispersal mechanisms of pdmAB in the biobed packing material by measuring the abundance of the plasmid pSH (harboring pdmAB) of the IPU-degrading Sphingomonas sp. strain SH (previously isolated from the soil used in the biobed) compared with the abundance of the pdmA gene and metagenomic fosmid library screening. pdmA abundance and expression increased concomitantly with IPU mineralization, verifying its major role in IPU transformation in the biobed system. DNA- and RNA-based 16S rRNA gene sequencing analysis showed no effects on bacterial diversity. The pdmAB-harboring plasmid pSH showed a consistently lower abundance than pdmA, suggesting the localization of pdmAB in replicons other than pSH. Metagenomic analysis identified four pdmAB-carrying fosmids. In three of these fosmids, the pdmAB genes were organized in a well-conserved operon carried by sphingomonad plasmids with low synteny with pSH, while the fourth fosmid contained an incomplete pdmAB cassette localized in a genomic fragment of a Rhodanobacter strain. Further analysis suggested a potentially crucial role of IS6 and IS256 in the transposition and activation of the pdmAB operon.IMPORTANCE Our study provides novel insights into the interactions of IPU with the bacterial community of biobed systems, reinforces the assumption of a transposable nature of IPU-degrading genes, and verifies that on-farm biobed systems are hot spots for the evolution of pesticide catabolic traits.}, }
@article {pmid32413061, year = {2020}, author = {Wade, T and Rangel, LT and Kundu, S and Fournier, GP and Bansal, MS}, title = {Assessing the accuracy of phylogenetic rooting methods on prokaryotic gene families.}, journal = {PloS one}, volume = {15}, number = {5}, pages = {e0232950}, pmid = {32413061}, issn = {1932-6203}, mesh = {Algorithms ; Biological Evolution ; Computational Biology/*methods ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Models, Genetic ; Phylogeny ; Prokaryotic Cells ; }, abstract = {Almost all standard phylogenetic methods for reconstructing gene trees result in unrooted trees; yet, many of the most useful applications of gene trees require that the gene trees be correctly rooted. As a result, several computational methods have been developed for inferring the root of unrooted gene trees. However, the accuracy of such methods has never been systematically evaluated on prokaryotic gene families, where horizontal gene transfer is often one of the dominant evolutionary events driving gene family evolution. In this work, we address this gap by conducting a thorough comparative evaluation of five different rooting methods using large collections of both simulated and empirical prokaryotic gene trees. Our simulation study is based on 6000 true and reconstructed gene trees on 100 species and characterizes the rooting accuracy of the four methods under 36 different evolutionary conditions and 3 levels of gene tree reconstruction error. The empirical study is based on a large, carefully designed data set of 3098 gene trees from 504 bacterial species (406 Alphaproteobacteria and 98 Cyanobacteria) and reveals insights that supplement those gleaned from the simulation study. Overall, this work provides several valuable insights into the accuracy of the considered methods that will help inform the choice of rooting methods to use when studying microbial gene family evolution. Among other findings, this study identifies parsimonious Duplication-Transfer-Loss (DTL) rooting and Minimal Ancestor Deviation (MAD) rooting as two of the most accurate gene tree rooting methods for prokaryotes and specifies the evolutionary conditions under which these methods are most accurate, demonstrates that DTL rooting is highly sensitive to high evolutionary rates and gene tree error, and that rooting methods based on branch-lengths are generally robust to gene tree reconstruction error.}, }
@article {pmid32411103, year = {2020}, author = {Williams, CL and Thomas, BJ and McEwan, NR and Rees Stevens, P and Creevey, CJ and Huws, SA}, title = {Rumen Protozoa Play a Significant Role in Fungal Predation and Plant Carbohydrate Breakdown.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {720}, pmid = {32411103}, issn = {1664-302X}, abstract = {The rumen protozoa, alongside fungi, comprise the eukaryotic portion of the rumen microbiome. Rumen protozoa may account for up to 50% of biomass, yet their role in this ecosystem remains unclear. Early experiments inferred a role in carbohydrate and protein metabolism, but due to their close association with bacteria, definitively attributing these functions to the protozoa was challenging. The advent of 'omic technologies has created opportunities to broaden our understanding of the rumen protozoa. This study aimed to utilize these methods to further our understanding of the role that protozoa play in the rumen in terms of their metabolic capacities, and in doing so, contribute valuable sequence data to reduce the chance of mis or under-representation of the rumen protozoa in meta'omic datasets. Rumen protozoa were isolated and purified using glucose-based sedimentation and differential centrifugation, extracted RNA was Poly(A) fraction enriched and DNase treated before use in a phage-based, cDNA metatranscriptomic library. Biochemical activity testing of the phage library showed 6 putatively positive plaques in response to carboxymethyl cellulose agar (indicative of cellulose activity), and no positive results for tributyrin (indicative of esterase/lipase activity) or egg yolk agar (indicative of proteolysis). Direct sequencing of the cDNA was also conducted using the Illumina HiSeq 2500. The metatranscriptome identified a wealth of carbohydrate-active enzymes which accounted for 8% of total reads. The most highly expressed carbohydrate-active enzymes were glycosyl hydrolases 5 and 11, polysaccharide lyases and deacetylases, xylanases and enzymes active against pectin, mannan and chitin; the latter likely used to digest rumen fungi which contain a chitin-rich cell membrane. Codon usage analysis of expressed genes also showed evidence of horizontal gene transfer, suggesting that many of these enzymes were acquired from the rumen bacteria in an evolutionary response to the carbohydrate-rich environment of the rumen. This study provides evidence of the significant contribution that the protozoa make to carbohydrate breakdown in the rumen, potentially using horizontally acquired genes, and highlights their predatory capacity.}, }
@article {pmid32408484, year = {2020}, author = {Wu, X and Zhou, H and Li, L and Wang, E and Zhou, X and Gu, Y and Wu, X and Shen, L and Zeng, W}, title = {Whole Genome Sequencing and Comparative Genomic Analyses of Lysinibacillus pakistanensis LZH-9, a Halotolerant Strain with Excellent COD Removal Capability.}, journal = {Microorganisms}, volume = {8}, number = {5}, pages = {}, pmid = {32408484}, issn = {2076-2607}, support = {No. 31470230, 51320105006, 51604308//National Natural Science Foundation of China/ ; No. 2017RS3003//Youth Talent Foundation of Hunan Province of China/ ; No.2018JJ2486//Natural Science Foundation of Hunan Province of China/ ; 2018WK2012//Key Research and Development Projects in Hunan Province/ ; No. 2019zzts707//Fundamental Research Funds for the Central Universities of Central South University/ ; }, abstract = {Halotolerant microorganisms are promising in bio-treatment of hypersaline industrial wastewater. Four halotolerant bacteria strains were isolated from wastewater treatment plant, of which a strain LZH-9 could grow in the presence of up to 14% (w/v) NaCl, and it removed 81.9% chemical oxygen demand (COD) at 96 h after optimization. Whole genome sequencing of Lysinibacillus pakistanensis LZH-9 and comparative genomic analysis revealed metabolic versatility of different species of Lysinibacillus, and abundant genes involved in xenobiotics biodegradation, resistance to toxic compound, and salinity were found in all tested species of Lysinibacillus, in which Horizontal Gene Transfer (HGT) contributed to the acquisition of many important properties of Lysinibacillus spp. such as toxic compound resistance and osmotic stress resistance as revealed by phylogenetic analyses. Besides, genome wide positive selection analyses revealed seven genes that contained adaptive mutations in Lysinibacillus spp., most of which were multifunctional. Further expression assessment with Codon Adaption Index (CAI) also reflected the high metabolic rate of L. pakistanensis to digest potential carbon or nitrogen sources in organic contaminants, which was closely linked with efficient COD removal ability of strain LZH-9. The high COD removal efficiency and halotolerance as well as genomic evidences suggested that L. pakistanensis LZH-9 was promising in treating hypersaline industrial wastewater.}, }
@article {pmid32403359, year = {2020}, author = {Wang, M and Zhu, H and Kong, Z and Li, T and Ma, L and Liu, D and Shen, Q}, title = {Pan-Genome Analyses of Geobacillus spp. Reveal Genetic Characteristics and Composting Potential.}, journal = {International journal of molecular sciences}, volume = {21}, number = {9}, pages = {}, pmid = {32403359}, issn = {1422-0067}, support = {2018YFD0500201//National Key R&amp;D Program of China/ ; 31972513//National Natural Science Foundation of China/ ; BK20150059//Jiangsu Province Natural Sciences Fund Subsidization Project/ ; KYZ201716//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Agriculture/methods ; Biotechnology/methods ; Composting/*methods ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Genome, Bacterial/*genetics ; Genomics/*methods ; Geobacillus/classification/*genetics ; Phylogeny ; Species Specificity ; }, abstract = {The genus Geobacillus is abundant in ecological diversity and is also well-known as an authoritative source for producing various thermostable enzymes. Although it is clear now that Geobacillus evolved from Bacillus, relatively little knowledge has been obtained regarding its evolutionary mechanism, which might also contribute to its ecological diversity and biotechnology potential. Here, a statistical comparison of thirty-two Geobacillus genomes was performed with a specific focus on pan- and core genomes. The pan-genome of this set of Geobacillus strains contained 14,913 genes, and the core genome contained 940 genes. The Clusters of Orthologous Groups (COG) and Carbohydrate-Active Enzymes (CAZymes) analysis revealed that the Geobacillus strains had huge potential industrial application in composting for agricultural waste management. Detailed comparative analyses showed that basic functional classes and housekeeping genes were conserved in the core genome, while genes associated with environmental interaction or energy metabolism were more enriched in the pan-genome. Therefore, the evolution of Geobacillus seems to be guided by environmental parameters. In addition, horizontal gene transfer (HGT) events among different Geobacillus species were detected. Altogether, pan-genome analysis was a useful method for detecting the evolutionary mechanism, and Geobacillus' evolution was directed by the environment and HGT events.}, }
@article {pmid32393168, year = {2020}, author = {Chibani, CM and Roth, O and Liesegang, H and Wendling, CC}, title = {Genomic variation among closely related Vibrio alginolyticus strains is located on mobile genetic elements.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {354}, pmid = {32393168}, issn = {1471-2164}, support = {WE 5822/ 1-1//Deutsche Forschungsgemeinschaft/ ; WE5822/1-2//Deutsche Forschungsgemeinschaft/ ; RO462/4-2//Deutsche Forschungsgemeinschaft/ ; na//KAAD/ ; }, mesh = {Drug Resistance/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Variation ; *Genome, Bacterial ; Genomic Islands ; Phylogeny ; Vibrio alginolyticus/classification/*genetics/isolation &amp; purification/pathogenicity ; Virulence/genetics ; }, abstract = {BACKGROUND: Species of the genus Vibrio, one of the most diverse bacteria genera, have undergone niche adaptation followed by clonal expansion. Niche adaptation and ultimately the formation of ecotypes and speciation in this genus has been suggested to be mainly driven by horizontal gene transfer (HGT) through mobile genetic elements (MGEs). Our knowledge about the diversity and distribution of Vibrio MGEs is heavily biased towards human pathogens and our understanding of the distribution of core genomic signatures and accessory genes encoded on MGEs within specific Vibrio clades is still incomplete. We used nine different strains of the marine bacterium Vibrio alginolyticus isolated from pipefish in the Kiel-Fjord to perform a multiscale-comparative genomic approach that allowed us to investigate [1] those genomic signatures that characterize a habitat-specific ecotype and [2] the source of genomic variation within this ecotype.<br><br>RESULTS: We found that the nine isolates from the Kiel-Fjord have a closed-pangenome and did not differ based on core-genomic signatures. Unique genomic regions and a unique repertoire of MGEs within the Kiel-Fjord isolates suggest that the acquisition of gene-blocks by HGT played an important role in the evolution of this ecotype. Additionally, we found that ~&#x2009;90% of the genomic variation among the nine isolates is encoded on MGEs, which supports ongoing theory that accessory genes are predominately located on MGEs and shared by HGT. Lastly, we could show that these nine isolates share a unique virulence and resistance profile which clearly separates them from all other investigated V. alginolyticus strains and suggests that these are habitat-specific genes, required for a successful colonization of the pipefish, the niche of this ecotype.<br><br>CONCLUSION: We conclude that all nine V. alginolyticus strains from the Kiel-Fjord belong to a unique ecotype, which we named the Kiel-alginolyticus ecotype. The low sequence variation of the core-genome in combination with the presence of MGE encoded relevant traits, as well as the presence of a suitable niche (here the pipefish), suggest, that this ecotype might have evolved from a clonal expansion following HGT driven niche-adaptation.}, }
@article {pmid32393110, year = {2020}, author = {Zhou, Y and Tang, Y and Fu, P and Tian, D and Yu, L and Huang, Y and Li, G and Li, M and Wang, Y and Yang, Z and Xu, X and Yin, Z and Zhou, D and Poirel, L and Jiang, X}, title = {The type I-E CRISPR-Cas system influences the acquisition of blaKPC-IncF plasmid in Klebsiella pneumonia.}, journal = {Emerging microbes &amp; infections}, volume = {9}, number = {1}, pages = {1011-1022}, pmid = {32393110}, issn = {2222-1751}, mesh = {Bacterial Proteins/genetics/isolation &amp; purification ; *CRISPR-Cas Systems ; *Carbapenem-Resistant Enterobacteriaceae/genetics/isolation &amp; purification ; China/epidemiology ; *Gene Transfer, Horizontal ; Humans ; Klebsiella Infections/epidemiology ; Klebsiella pneumoniae/*genetics/isolation &amp; purification ; Molecular Epidemiology ; Plasmids/isolation &amp; purification ; Pneumonia/epidemiology/microbiology ; beta-Lactamases/genetics/isolation &amp; purification ; }, abstract = {Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae (KPC-KP) have disseminated worldwide and emerged as major threats to public health. Of epidemiological significance, the international pandemic of KPC-KP is primarily associated with CG258 isolates and blaKPC-IncF plasmids. CRISPR-Cas system is an adaptive immune system that can hinder gene expansion driven by horizontal gene transfer. Because of blaKPC-IncF plasmids are favored by CG258 K. pneumoniae, it was of interest to examine the co-distribution of CRISPR and blaKPC-IncF plasmids in such isolates. We collected 459 clinical K. pneumoniae isolates in China and collected 203 global whole-genome sequences in GenBank to determine the prevalence of CRISPR-Cas systems. We observed that CRISPR-Cas system was significantly scarce in the CG258 lineage and blaKPC-positive isolates. Furthermore, the results of conjugation and plasmid stability assay fully demonstrated the CRIPSR-Cas system in K. pneumoniae could effectively hindered blaKPC-IncF plasmids invasion and existence. Notably, most blaKPC-IncF plasmids were also proved to be good targets of CRISPR owing to carry matched and functional protospacers and PAMs. Overall, our work suggests that type I-E CRISPR-Cas systems could impact the spread of blaKPC in K. pneumoniae populations, and the scarcity of CRISPR-Cas system was one of potential factors leading to the propagation of blaKPC-IncF plasmids in CG258 K. pneumoniae.}, }
@article {pmid32390973, year = {2020}, author = {Woegerbauer, M and Bellanger, X and Merlin, C}, title = {Cell-Free DNA: An Underestimated Source of Antibiotic Resistance Gene Dissemination at the Interface Between Human Activities and Downstream Environments in the Context of Wastewater Reuse.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {671}, pmid = {32390973}, issn = {1664-302X}, abstract = {The dissemination of antimicrobial resistance (AMR) is one of the biggest challenges faced by mankind in the public health domains. It is currently favored by a lack of confinement between waste disposal and food production in the environmental compartment. To date, much effort has been devoted into the elucidation and control of cell-associated propagation of AMR. However, substantial knowledge gaps remain on the contribution of cell-free DNA to promote horizontal transfers of resistance genes in wastewater and downstream environments. Cell free DNA, which covers free extracellular DNA (exDNA) as well as DNA encapsulated in vesicles or bacteriophages, can persist after disinfection and promote gene transfer in the absence of physical and temporal contact between a donor and recipient bacteria. The increasing water scarcity associated to climatic change requires developing innovative wastewater reuse practices and, concomitantly, a robust evaluation of AMR occurrence by implementing treatment technologies able to exert a stringent control on AMR propagation in downstream environments exposed to treated or non-treated wastewater. This necessarily implies understanding the fate of ARGs on various forms of cell-free DNA, especially during treatment processes that are permissive to their formation. We propose that comprehensive approaches, investigating both the occurrence of ARGs and their compartmentalization in different forms of cellular or cell-free associated DNA should be established for each treatment technology. This should then allow selecting and tuning technologies for their capacity to limit the propagation of ARGs in any of their forms.}, }
@article {pmid32390273, year = {2020}, author = {Cartwright, A and Arnscheidt, J and Conwell, M and Dooley, JSG and McGonigle, C and Naughton, PJ}, title = {Effects of freshwater sponge Ephydatia fluviatilis on conjugative transfer of antimicrobial resistance in Enterococcus faecalis strains in aquatic environments.}, journal = {Letters in applied microbiology}, volume = {71}, number = {1}, pages = {39-45}, doi = {10.1111/lam.13310}, pmid = {32390273}, issn = {1472-765X}, support = {//Department for the Economy/ ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Conjugation, Genetic/*genetics ; Drug Resistance, Bacterial/*genetics ; Enterococcus faecalis/drug effects/*genetics ; Fresh Water ; In Situ Hybridization, Fluorescence ; Pheromones/pharmacology ; Plasmids/genetics ; Porifera/*microbiology ; Vancomycin/pharmacology ; Vancomycin Resistance/*genetics ; }, abstract = {Filter feeding is a biotic process that brings waterborne bacteria in close contact with each other and may thus support the horizontal transfer of their antimicrobial resistance genes. This laboratory study investigated whether the freshwater sponge Ephydatia fluviatilis supported the transfer of vancomycin resistance between two Enterococcus faecalis strains that we previously demonstrated to exhibit pheromone responsive plasmid conjugation. Microcosm experiments exposed live and dead colonies of laboratory-grown sponges to a vancomycin-resistant donor strain and a rifampicin-resistant recipient strain of Ent. faecalis. Enterococci with both resistance phenotypes were detected on double selection plates. In comparison to controls, abundance of these presumed transconjugants increased significantly in water from sponge microcosms. Homogenized suspensions of sponge cells also yielded presumed transconjugants; however, there was no significant difference between samples from live or dead sponges. Fluorescent in situ hybridization analysis of the sponge cell matrix using species-specific probes revealed the presence of enterococci clusters with cells adjacent to each other. The results demonstrated that sponge colonies can support the horizontal transfer of antimicrobial resistance although the mechanism underlying this process, such as binding of the bacteria to the sponge collagen matrix, has yet to be fully elucidated.}, }
@article {pmid32388614, year = {2020}, author = {Siddique, AB}, title = {Viruses of endophytic and pathogenic forest fungi.}, journal = {Virus genes}, volume = {56}, number = {4}, pages = {407-416}, pmid = {32388614}, issn = {1572-994X}, mesh = {Forests ; Fungal Viruses/*genetics/pathogenicity ; Fungi/genetics/pathogenicity/*virology ; *Metagenomics ; Plant Diseases/genetics/*microbiology/virology ; Plants/genetics/microbiology/virology ; }, abstract = {Mycoviruses, just as the fungal endophytes they infect, are ubiquitous biological entities on Earth. Mycoviruses constitute a diverse group of viruses, and metagenomic approaches have-through recent discoveries of been mycoviruses-only recently began to provide evidence of this astonishing diversity. The current review presents (1) various mycoviruses which infect fungal endophytes and forest pathogens, (2) their presumed origins and interactions with fungi, plants and the environment, (3) high-throughput sequencing techniques that can be used to explore the horizontal gene transfer of mycoviruses, and (4) how the hypo- and hypervirulence induced by mycoviral infection is relevant to the biological control of pathogenic fungi.}, }
@article {pmid32382084, year = {2020}, author = {Tidjani, AR and Bontemps, C and Leblond, P}, title = {Telomeric and sub-telomeric regions undergo rapid turnover within a Streptomyces population.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {7720}, pmid = {32382084}, issn = {2045-2322}, mesh = {Amino Acid Sequence/genetics ; Chromosomes, Bacterial/*genetics ; DNA Replication/*genetics ; Genetic Variation ; Plasmids/genetics ; Recombination, Genetic/genetics ; Replicon/genetics ; Soil Microbiology ; Streptomyces/*genetics ; Telomere/*genetics ; Terminal Repeat Sequences/genetics ; }, abstract = {Genome dynamics was investigated within natural populations of the soil bacterium Streptomyces. The exploration of a set of closely related strains isolated from micro-habitats of a forest soil exhibited a strong diversity of the terminal structures of the linear chromosome, i.e. terminal inverted repeats (TIRs). Large insertions, deletions and translocations could be observed along with evidence of transfer events between strains. In addition, the telomere and its cognate terminal protein complexes required for terminal replication and chromosome maintenance, were shown to be variable within the population probably reflecting telomere exchanges between the chromosome and other linear replicons (i.e., plasmids). Considering the close genetic relatedness of the strains, these data suggest that the terminal regions are prone to a high turnover due to a high recombination associated with extensive horizontal gene transfer.}, }
@article {pmid32380667, year = {2020}, author = {Pettis, GS and Mukerji, AS}, title = {Structure, Function, and Regulation of the Essential Virulence Factor Capsular Polysaccharide of Vibrio vulnificus.}, journal = {International journal of molecular sciences}, volume = {21}, number = {9}, pages = {}, pmid = {32380667}, issn = {1422-0067}, support = {NA06OAR4170022, project no. R/PMO-21//National Oceanic and Atmospheric Administration/ ; }, mesh = {Antigens, Bacterial/*chemistry/immunology ; Bacterial Capsules/*chemistry/immunology ; Gene Expression ; Gene Expression Regulation, Bacterial ; Humans ; Operon ; Phenotype ; Polysaccharides, Bacterial/*chemistry/immunology/metabolism ; Structure-Activity Relationship ; Vibrio Infections/immunology/microbiology ; Vibrio vulnificus/genetics/immunology/*pathogenicity ; Virulence ; *Virulence Factors ; }, abstract = {Vibrio vulnificus populates coastal waters around the world, where it exists freely or becomes concentrated in filter feeding mollusks. It also causes rapid and life-threatening sepsis and wound infections in humans. Of its many virulence factors, it is the V. vulnificus capsule, composed of capsular polysaccharide (CPS), that plays a critical role in evasion of the host innate immune system by conferring antiphagocytic ability and resistance to complement-mediated killing. CPS may also provoke a portion of the host inflammatory cytokine response to this bacterium. CPS production is biochemically and genetically diverse among strains of V. vulnificus, and the carbohydrate diversity of CPS is likely affected by horizontal gene transfer events that result in new combinations of biosynthetic genes. Phase variation between virulent encapsulated opaque colonial variants and attenuated translucent colonial variants, which have little or no CPS, is a common phenotype among strains of this species. One mechanism for generating acapsular variants likely involves homologous recombination between repeat sequences flanking the wzb phosphatase gene within the Group 1 CPS biosynthetic and transport operon. A considerable number of environmental, genetic, and regulatory factors have now been identified that affect CPS gene expression and CPS production in this pathogen.}, }
@article {pmid32379323, year = {2020}, author = {Dong, X and Qu, G and Piazza, CL and Belfort, M}, title = {Group II intron as cold sensor for self-preservation and bacterial conjugation.}, journal = {Nucleic acids research}, volume = {48}, number = {11}, pages = {6198-6209}, pmid = {32379323}, issn = {1362-4962}, support = {R01 GM039422/GM/NIGMS NIH HHS/United States ; R01 GM044844/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Sequence ; *Cold Temperature ; Cold-Shock Response ; *Conjugation, Genetic ; DNA Nucleotidyltransferases/metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal ; Introns/*genetics ; Lactococcus lactis/*genetics ; Plasmids/genetics/metabolism ; *RNA Splicing ; RNA, Catalytic/metabolism ; RNA, Messenger/genetics/metabolism ; Retroelements ; }, abstract = {Group II introns are self-splicing ribozymes and mobile genetic elements. Splicing is required for both expression of the interrupted host gene and intron retromobility. For the pRS01 plasmid-encoded Lactococcus lactis group II intron, Ll.LtrB, splicing enables expression of the intron's host relaxase protein. Relaxase, in turn, initiates horizontal transfer of the conjugative pRS01 plasmid and stimulates retrotransposition of the intron. Little is known about how splicing of bacterial group II introns is influenced by environmental conditions. Here, we show that low temperatures can inhibit Ll.LtrB intron splicing. Whereas autocatalysis is abolished in the cold, splicing is partially restored by the intron-encoded protein (IEP). Structure profiling reveals cold-induced disruptions of key tertiary interactions, suggesting that a kinetic trap prevents the intron RNA from assuming its native state. Interestingly, while reduced levels of transcription and splicing lead to a paucity of excised intron in the cold, levels of relaxase mRNA are maintained, partially due to diminished intron-mediated mRNA targeting, allowing intron spread by conjugal transfer. Taken together, this study demonstrates not only the intrinsic cold sensitivity of group II intron splicing and the role of the IEP for cold-stress adaptation, but also maintenance of horizontal plasmid and intron transfer under cold-shock.}, }
@article {pmid32376847, year = {2020}, author = {Taxt, AM and Avershina, E and Frye, SA and Naseer, U and Ahmad, R}, title = {Rapid identification of pathogens, antibiotic resistance genes and plasmids in blood cultures by nanopore sequencing.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {7622}, pmid = {32376847}, issn = {2045-2322}, mesh = {Blood Culture/*methods ; DNA, Bacterial/genetics/isolation &amp; purification ; Drug Resistance, Microbial/*genetics ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Nanopore Sequencing/*methods ; Plasmids/*genetics ; Salmonella/genetics ; Time Factors ; }, abstract = {Bloodstream infections (BSI) and sepsis are major causes of morbidity and mortality worldwide. Blood culture-based diagnostics usually requires 1-2 days for identification of bacterial agent and an additional 2-3 days for phenotypic determination of antibiotic susceptibility pattern. With the escalating burden of antimicrobial resistance (AMR) rapid diagnostics becomes increasingly important to secure adequate antibiotic therapy. Real-time whole genome sequencing represents a genotypic diagnostic approach with the ability to rapidly identify pathogens and AMR-encoding genes. Here we have used nanopore sequencing of bacterial DNA extracted from positive blood cultures for identification of pathogens, detection of plasmids and AMR-encoding genes. To our knowledge, this is the first study to gather the above-mentioned information from nanopore sequencing and conduct a comprehensive analysis for diagnostic purposes in real-time. Identification of pathogens was possible after 10 minutes of sequencing and all predefined AMR-encoding genes and plasmids from monoculture experiments were detected within one hour using raw nanopore sequencing data. Furthermore, we demonstrate the correct identification of plasmids and blaCTX-M subtypes using de novo assembled nanopore contigs. Results from this study hold great promise for future applications in clinical microbiology and for health care surveillance purposes.}, }
@article {pmid32375974, year = {2020}, author = {Hughes-Games, A and Roberts, AP and Davis, SA and Hill, DJ}, title = {Identification of integrative and conjugative elements in pathogenic and commensal Neisseriaceae species via genomic distributions of DNA uptake sequence dialects.}, journal = {Microbial genomics}, volume = {6}, number = {5}, pages = {}, pmid = {32375974}, issn = {2057-5858}, mesh = {Chromosomes, Bacterial/*genetics ; Conjugation, Genetic ; *DNA Transposable Elements ; Drug Resistance, Multiple, Bacterial ; Evolution, Molecular ; Gene Transfer, Horizontal ; High-Throughput Nucleotide Sequencing ; Neisseriaceae/*classification/genetics/isolation &amp; purification/pathogenicity ; Phenotype ; Phylogeny ; Plasmids/*genetics ; Sequence Analysis, DNA/*methods ; Symbiosis ; Virulence Factors/genetics ; Vocabulary ; }, abstract = {Mobile genetic elements (MGEs) are key factors responsible for dissemination of virulence determinants and antimicrobial-resistance genes amongst pathogenic bacteria. Conjugative MGEs are notable for their high gene loads donated per transfer event, broad host ranges and phylogenetic ubiquity amongst prokaryotes, with the subclass of chromosomally inserted integrative and conjugative elements (ICEs) being particularly abundant. The focus on a small number of model systems has biased the study of ICEs towards those conferring readily selectable phenotypes to host cells, whereas the identification and characterization of integrated cryptic elements remains challenging. Even though antimicrobial resistance and horizontally acquired virulence genes are major factors aggravating neisserial infection, conjugative MGEs of Neisseria gonorrhoeae and Neisseria meningitidis remain poorly characterized. Using a phenotype-independent approach based on atypical distributions of DNA uptake sequences (DUSs) in MGEs relative to the chromosomal background, we have identified two groups of chromosomally integrated conjugative elements in Neisseria: one found almost exclusively in pathogenic species possibly deriving from the genus Kingella, the other belonging to a group of Neisseria mucosa-like commensals. The former element appears to enable transfer of traditionally gonococcal-specific loci such as the virulence-associated toxin-antitoxin system fitAB to N. meningitidis chromosomes, whilst the circular form of the latter possesses a unique attachment site (attP) sequence seemingly adapted to exploit DUS motifs as chromosomal integration sites. In addition to validating the use of DUS distributions in Neisseriaceae MGE identification, the >170 identified ICE sequences provide a valuable resource for future studies of ICE evolution and host adaptation.}, }
@article {pmid32375954, year = {2020}, author = {Silva, LAD and Ardisson-Araújo, DMP and de Camargo, BR and de Souza, ML and Ribeiro, BM}, title = {A novel cypovirus found in a betabaculovirus co-infection context contains a poxvirus immune nuclease (poxin)-related gene.}, journal = {The Journal of general virology}, volume = {101}, number = {6}, pages = {667-675}, doi = {10.1099/jgv.0.001413}, pmid = {32375954}, issn = {1465-2099}, mesh = {Animals ; Brazil ; Coinfection/*genetics ; Cyclic GMP/genetics ; Deoxyribonucleases/*genetics ; Genome, Viral/genetics ; Granulovirus/*genetics ; Larva/virology ; Lepidoptera/virology ; Moths/virology ; Occlusion Bodies, Viral/genetics ; Phylogeny ; Poxviridae/*genetics ; Reoviridae/*genetics ; }, abstract = {The cassava hornworm Erinnyis ello ello (Lepidoptera: Sphingidae) is an important pest in Brazil. This insect feeds on host plants of several species, especially Manihot esculenta (cassava) and Hevia brasiliensis (rubber tree). Cassava hornworm outbreaks are quite common in Brazil and can cause great impact over crop production. Granulare and polyhedral-shaped occlusion bodies (OBs) were observed in extracts of dead E. ello larvae from rubber-tree plantations by light and scanning electron microscopy (SEM), suggesting a mixed infection. The polyhedral-shaped OB surface revealed indentations that resemble those found in cypovirus polyhedra. After OB nucleic acid extraction followed by cDNA production and Illumina deep-sequencing analysis, the results confirmed for the presence of a putative novel cypovirus that carries ten segments and also a betabaculovirus (Erinnyis ello granulovirus, ErelGV). Phylogenetic analysis of the predicted segment 1-enconded RdRP showed that the new cypovirus isolate is closely related to a member of species Cypovirus 2, which was isolated from Inachis io (Lepidoptera: Nymphalidae). Therefore, we named this new isolate Erinnyis ello cypovirus 2 (ErelCPV-2). Genome in silico analyses showed that ErelCPV-2 segment 8 (S8) has a predicted amino acid identity of 35.82 % to a hypothetical protein of betabaculoviruses. This putative protein has a cGAMP-specific nuclease domain related to the poxvirus immune nucleases (poxins) from the 2',3'-cGAMP-degrading enzyme family.}, }
@article {pmid32371951, year = {2020}, author = {Tan, JL and Simbun, A and Chan, KG and Ngeow, YF}, title = {Genome sequence analysis of multidrug-resistant Mycobacterium tuberculosis from Malaysia.}, journal = {Scientific data}, volume = {7}, number = {1}, pages = {135}, pmid = {32371951}, issn = {2052-4463}, mesh = {Gene Transfer, Horizontal ; Humans ; Malaysia ; Molecular Sequence Annotation ; Mutation ; Mycobacterium tuberculosis/*genetics ; Tuberculosis, Multidrug-Resistant/*microbiology ; }, abstract = {Mycobacterium tuberculosis (MTB) is commonly used as a model to study pathogenicity and multiple drug resistance in bacteria. These MTB characteristics are highly dependent on the evolution and phylogeography of the bacterium. In this paper, we describe 15 new genomes of multidrug-resistant MTB (MDRTB) from Malaysia. The assessments and annotations on the genome assemblies suggest that strain differences are due to lineages and horizontal gene transfer during the course of evolution. The genomes show mutations listed in current drug resistance databases and global MTB collections. This genome data will augment existing information available for comparative genomic studies to understand MTB drug resistance mechanisms and evolution.}, }
@article {pmid32369929, year = {2020}, author = {Chon, JW and Lee, UJ and Bensen, R and West, S and Paredes, A and Lim, J and Khan, S and Hart, ME and Phillips, KS and Sung, K}, title = {Virulence Characteristics of mecA-Positive Multidrug-Resistant Clinical Coagulase-Negative Staphylococci.}, journal = {Microorganisms}, volume = {8}, number = {5}, pages = {}, pmid = {32369929}, issn = {2076-2607}, abstract = {Coagulase-negative staphylococci (CoNS) are an important group of opportunistic pathogenic microorganisms that cause infections in hospital settings and are generally resistant to many antimicrobial agents. We report on phenotypic and genotypic virulence characteristics of a select group of clinical, mecA-positive (encoding penicillin-binding protein 2a) CoNS isolates. All CoNS were resistant to two or more antimicrobials with S. epidermidis strain 214EP, showing resistance to fifteen of the sixteen antimicrobial agents tested. Aminoglycoside-resistance genes were the ones most commonly detected. The presence of megaplasmids containing both horizontal gene transfer and antimicrobial resistance genetic determinants indicates that CoNS may disseminate antibiotic resistance to other bacteria. Staphylococcus sciuri species produced six virulence enzymes, including a DNase, gelatinase, lipase, phosphatase, and protease that are suspected to degrade tissues into nutrients for bacterial growth and contribute to the pathogenicity of CoNS. The PCR assay for the detection of biofilm-associated genes found the eno (encoding laminin-binding protein) gene in all isolates. Measurement of their biofilm-forming ability and Spearman's rank correlation coefficient analyses revealed that the results of crystal violet (CV) and extracellular polymeric substances (EPS) assays were significantly correlated (ρ = 0.9153, P = 3.612e-12). The presence of virulence factors, biofilm-formation capability, extracellular enzymes, multidrug resistance, and gene transfer markers in mecA-positive CoNS clinical strains used in this study makes them powerful opportunistic pathogens. The study also warrants a careful evaluation of nosocomial infections caused by CoNS and may be useful in studying the mechanism of virulence and factors associated with their pathogenicity in vivo and developing effective strategies for mitigation.}, }
@article {pmid32369588, year = {2020}, author = {Bhattacharjee, S and Mishra, AK}, title = {The tale of caspase homologues and their evolutionary outlook: deciphering programmed cell death in cyanobacteria.}, journal = {Journal of experimental botany}, volume = {71}, number = {16}, pages = {4639-4657}, pmid = {32369588}, issn = {1460-2431}, mesh = {*Apoptosis ; Biological Evolution ; Caspases/genetics/metabolism ; *Cyanobacteria/genetics/metabolism ; Proteolysis ; }, abstract = {Programmed cell death (PCD), a genetically orchestrated mechanism of cellular demise, is paradoxically required to support life. As in lower eukaryotes and bacteria, PCD in cyanobacteria is poorly appreciated, despite recent biochemical and molecular evidence that supports its existence. Cyanobacterial PCD is an altruistic reaction to stressful conditions that significantly enhances genetic diversity and inclusive fitness of the population. Recent bioinformatic analysis has revealed an abundance of death-related proteases, i.e. orthocaspases (OCAs) and their mutated variants, in cyanobacteria, with the larger genomes of morphologically complex strains harbouring most of them. Sequence analysis has depicted crucial accessory domains along with the proteolytic p20-like sub-domain in OCAs, predicting their functional versatility. However, the cascades involved in sensing death signals, their transduction, and the downstream expression and activation of OCAs remain to be elucidated. Here, we provide a comprehensive description of the attempts to identify mechanisms of PCD and the existence and importance of OCAs based on in silico approaches. We also review the evolutionary and ecological significance of PCD in cyanobacteria. In the future, the analysis of cyanobacterial PCD will identify novel proteins that have varied functional roles in signalling cascades and also help in understanding the incipient mechanism of PCD morphotype(s) from where eukaryotic PCD might have originated.}, }
@article {pmid32366826, year = {2020}, author = {Tóth, AG and Csabai, I and Krikó, E and Tőzsér, D and Maróti, G and Patai, &#xc1;V and Makrai, L and Szita, G and Solymosi, N}, title = {Antimicrobial resistance genes in raw milk for human consumption.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {7464}, pmid = {32366826}, issn = {2045-2322}, mesh = {Animals ; Bacteria/*genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; *Gene Transfer, Horizontal ; Humans ; Milk/*microbiology ; }, abstract = {The increasing prevalence of antimicrobial resistance (AMR) is a significant threat to global health. More and more multi-drug-resistant bacterial strains cause life-threatening infections and the death of thousands of people each year. Beyond disease control animals are often given antibiotics for growth promotion or increased feed efficiency, which further increase the chance of the development of multi-resistant strains. After the consumption of unprocessed animal products, these strains may meet the human bacteriota. Among the foodborne and the human populations, antimicrobial resistance genes (ARGs) may be shared by horizontal gene transfer. This study aims to test the presence of antimicrobial resistance genes in milk metagenome, investigate their genetic position and their linkage to mobile genetic elements. We have analyzed raw milk samples from public markets sold for human consumption. The milk samples contained genetic material from various bacterial species and the in-depth analysis uncovered the presence of several antimicrobial resistance genes. The samples contained complete ARGs influencing the effectiveness of acridine dye, cephalosporin, cephamycin, fluoroquinolone, penam, peptide antibiotics and tetracycline. One of the ARGs, PC1 beta-lactamase may also be a mobile element that facilitates the transfer of resistance genes to other bacteria, e.g. to the ones living in the human gut.}, }
@article {pmid32366649, year = {2020}, author = {Mourkas, E and Taylor, AJ and Méric, G and Bayliss, SC and Pascoe, B and Mageiros, L and Calland, JK and Hitchings, MD and Ridley, A and Vidal, A and Forbes, KJ and Strachan, NJC and Parker, CT and Parkhill, J and Jolley, KA and Cody, AJ and Maiden, MCJ and Kelly, DJ and Sheppard, SK}, title = {Agricultural intensification and the evolution of host specialism in the enteric pathogen Campylobacter jejuni.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {20}, pages = {11018-11028}, pmid = {32366649}, issn = {1091-6490}, support = {BB/R003491/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/I02464X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 088786/C/09/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Adaptation, Physiological/genetics ; *Agriculture ; Animals ; Biofilms ; Campylobacter jejuni/*genetics/*physiology ; Cattle/microbiology/physiology ; Diet ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genomics ; Homologous Recombination ; *Host Specificity ; Hydrophobic and Hydrophilic Interactions ; Mutagenesis ; Phenotype ; Recombination, Genetic ; *Specialization ; }, abstract = {Modern agriculture has dramatically changed the distribution of animal species on Earth. Changes to host ecology have a major impact on the microbiota, potentially increasing the risk of zoonotic pathogens being transmitted to humans, but the impact of intensive livestock production on host-associated bacteria has rarely been studied. Here, we use large isolate collections and comparative genomics techniques, linked to phenotype studies, to understand the timescale and genomic adaptations associated with the proliferation of the most common food-born bacterial pathogen (Campylobacter jejuni) in the most prolific agricultural mammal (cattle). Our findings reveal the emergence of cattle specialist C. jejuni lineages from a background of host generalist strains that coincided with the dramatic rise in cattle numbers in the 20th century. Cattle adaptation was associated with horizontal gene transfer and significant gene gain and loss. This may be related to differences in host diet, anatomy, and physiology, leading to the proliferation of globally disseminated cattle specialists of major public health importance. This work highlights how genomic plasticity can allow important zoonotic pathogens to exploit altered niches in the face of anthropogenic change and provides information for mitigating some of the risks posed by modern agricultural systems.}, }
@article {pmid32363801, year = {2020}, author = {Soler, N and Forterre, P}, title = {Vesiduction: the fourth way of HGT.}, journal = {Environmental microbiology}, volume = {22}, number = {7}, pages = {2457-2460}, doi = {10.1111/1462-2920.15056}, pmid = {32363801}, issn = {1462-2920}, support = {340440//H2020 European Research Council/International ; }, mesh = {Archaea/genetics/*physiology ; Bacteria/genetics ; *Bacterial Physiological Phenomena ; DNA/metabolism ; Extracellular Vesicles/genetics/*physiology ; Gene Transfer, Horizontal/*physiology ; }, abstract = {Besides the canonical gene transfer mechanisms transformation, transduction and conjugation, DNA transfer involving extracellular vesicles is still under appreciated. However, this widespread phenomenon has been observed in the three domains of life. Here, we propose the term 'Vesiduction' as a fourth mode of intercellular DNA transfer.}, }
@article {pmid32359160, year = {2020}, author = {Öztürk, B and Werner, J and Meier-Kolthoff, JP and Bunk, B and Spröer, C and Springael, D}, title = {Comparative Genomics Suggests Mechanisms of Genetic Adaptation toward the Catabolism of the Phenylurea Herbicide Linuron in Variovorax.}, journal = {Genome biology and evolution}, volume = {12}, number = {6}, pages = {827-841}, pmid = {32359160}, issn = {1759-6653}, mesh = {Adaptation, Biological/*genetics ; Comamonadaceae/*genetics/metabolism ; Genome, Bacterial ; Herbicides/*metabolism ; Linuron/*metabolism ; Phylogeny ; *Plasmids ; }, abstract = {Biodegradation of the phenylurea herbicide linuron appears a specialization within a specific clade of the Variovorax genus. The linuron catabolic ability is likely acquired by horizontal gene transfer but the mechanisms involved are not known. The full-genome sequences of six linuron-degrading Variovorax strains isolated from geographically distant locations were analyzed to acquire insight into the mechanisms of genetic adaptation toward linuron metabolism. Whole-genome sequence analysis confirmed the phylogenetic position of the linuron degraders in a separate clade within Variovorax and indicated that they unlikely originate from a common ancestral linuron degrader. The linuron degraders differentiated from Variovorax strains that do not degrade linuron by the presence of multiple plasmids of 20-839 kb, including plasmids of unknown plasmid groups. The linuron catabolic gene clusters showed 1) high conservation and synteny and 2) strain-dependent distribution among the different plasmids. Most of them were bordered by IS1071 elements forming composite transposon structures, often in a multimeric array configuration, appointing IS1071 as a key element in the recruitment of linuron catabolic genes in Variovorax. Most of the strains carried at least one (catabolic) broad host range plasmid that might have been a second instrument for catabolic gene acquisition. We conclude that clade 1 Variovorax strains, despite their different geographical origin, made use of a limited genetic repertoire regarding both catabolic functions and vehicles to acquire linuron biodegradation.}, }
@article {pmid32357498, year = {2020}, author = {Rolland, S and Mengue, L and Noël, C and Crapart, S and Mercier, A and Aucher, W and Héchard, Y and Samba-Louaka, A}, title = {Encystment Induces Down-Regulation of an Acetyltransferase-Like Gene in Acanthamoeba castellanii.}, journal = {Pathogens (Basel, Switzerland)}, volume = {9}, number = {5}, pages = {}, pmid = {32357498}, issn = {2076-0817}, support = {ANR-17-CE13-00001-01 "Amocyst"//Agence Nationale de la Recherche/ ; }, abstract = {Acanthamoeba castellanii is a ubiquitous free-living amoeba. Pathogenic strains are causative agents of Acanthamoeba keratitis and granulomatous amoebic encephalitis. In response to adverse conditions, A. castellanii differentiate into cysts, which are metabolically inactive and resistant cells. This process, also named encystment, involves biochemical and genetic modifications that remain largely unknown. This study characterizes the role of the ACA1_384820 Acanthamoeba gene during encystment. This gene encodes a putative N-acetyltransferase, belonging to the Gcn5-related N-acetyltransferase (GNAT) family. We showed that expression of the ACA1_384820 gene was down-regulated as early as two hours after induction of encystment in A. castellanii. Interestingly, overexpression of the ACA1_384820 gene affects formation of cysts. Unexpectedly, the search of homologs of ACA1_384820 in the Eukaryota gene datasets failed, except for some species in the Acanthamoeba genus. Bioinformatics analysis suggested a possible lateral acquisition of this gene from prokaryotic cells. This study enabled us to describe a new Acanthamoeba gene that is down-regulated during encystment.}, }
@article {pmid32357453, year = {2020}, author = {Lange, J and Heidenreich, K and Higelin, K and Dyck, K and Marx, V and Reichel, C and Wamel, WV and Reijer, MD and Görlich, D and Kahl, BC}, title = {Staphylococcus aureus Pathogenicity in Cystic Fibrosis Patients-Results from an Observational Prospective Multicenter Study Concerning Virulence Genes, Phylogeny, and Gene Plasticity.}, journal = {Toxins}, volume = {12}, number = {5}, pages = {}, pmid = {32357453}, issn = {2072-6651}, support = {S05/07//Mukoviszidose e.V./International ; TRR34//Deutsche Forschungsgemeinschaft/International ; Kah2/016/16//Interdisziplin&#xe4;res Zentrum f&#xfc;r Klinische Forschung/International ; }, mesh = {Austria ; Cystic Fibrosis/diagnosis/*microbiology/physiopathology ; Disease Progression ; Female ; Gene Expression Regulation, Bacterial ; Germany ; Host-Pathogen Interactions ; Humans ; Longitudinal Studies ; Lung/*microbiology/physiopathology ; Male ; *Phylogeny ; Prospective Studies ; Respiratory Tract Infections/diagnosis/*microbiology/physiopathology ; Staphylococcal Infections/diagnosis/*microbiology/physiopathology ; Staphylococcus aureus/*genetics/*pathogenicity ; Time Factors ; Virulence/genetics ; Virulence Factors/*genetics ; }, abstract = {Staphylococcus aureus and cystic fibrosis (CF) are closely interlinked. To date, however, the impact of S. aureus culture in CF airways on lung function and disease progression has only been elucidated to a limited degree. This analysis aims to identify bacterial factors associated to clinical deterioration. Data were collected during an observational prospective multi-center study following 195 patients from 17 centers. The average follow-up time was 80 weeks. S. aureus isolates (n = 3180) were scanned for the presence of 25 virulence genes and agr-types using single and multiplex PCR. The presence of specific virulence genes was not associated to clinical deterioration. For the agr-types 1 and 4, however, a link to the subjects' clinical status became evident. Furthermore, a significant longitudinal decrease in the virulence gene quantity was observed. Analyses of the plasticity of the virulence genes revealed significantly increased plasticity rates in the presence of environmental stress. The results suggest that the phylogenetic background defines S. aureus pathogenicity rather than specific virulence genes. The longitudinal loss of virulence genes most likely reflects the adaptation process directed towards a persistent and colonizing rather than infecting lifestyle.}, }
@article {pmid32354325, year = {2020}, author = {Li, J and Gu, T and Li, L and Wu, X and Shen, L and Yu, R and Liu, Y and Qiu, G and Zeng, W}, title = {Complete genome sequencing and comparative genomic analyses of Bacillus sp. S3, a novel hyper Sb(III)-oxidizing bacterium.}, journal = {BMC microbiology}, volume = {20}, number = {1}, pages = {106}, pmid = {32354325}, issn = {1471-2180}, support = {2019JJ40361//Natural Science Foundation of Hunan Province of China/International ; 31470230, 51320105006, 51604308//National Natural Science Foundation of China/International ; 2018WK2012//Key Research and Development Projects in Hunan Province/International ; 2019zzts687//Fundamental Research Funds for the Central University of Central South University/International ; 2017RS3003//Youth Talent Foundation of Hunan Province of China/International ; }, mesh = {Antimony/*metabolism ; Bacillus/*genetics/metabolism ; Base Composition ; Biodegradation, Environmental ; Chromosomes, Bacterial/genetics ; Evolution, Molecular ; Genome Size ; Genome, Bacterial ; Genomics ; Molecular Sequence Annotation ; Phylogeny ; Plasmids/genetics ; Whole Genome Sequencing/*methods ; }, abstract = {BACKGROUND: Antimonite [Sb(III)]-oxidizing bacterium has great potential in the environmental bioremediation of Sb-polluted sites. Bacillus sp. S3 that was previously isolated from antimony-contaminated soil displayed high Sb(III) resistance and Sb(III) oxidation efficiency. However, the genomic information and evolutionary feature of Bacillus sp. S3 are very scarce.<br><br>RESULTS: Here, we identified a 5,436,472&#x2009;bp chromosome with 40.30% GC content and a 241,339&#x2009;bp plasmid with 36.74% GC content in the complete genome of Bacillus sp. S3. Genomic annotation showed that Bacillus sp. S3 contained a key aioB gene potentially encoding As (III)/Sb(III) oxidase, which was not shared with other Bacillus strains. Furthermore, a wide variety of genes associated with Sb(III) and other heavy metal (loid) s were also ascertained in Bacillus sp. S3, reflecting its adaptive advantage for growth in the harsh eco-environment. Based on the analysis of phylogenetic relationship and the average nucleotide identities (ANI), Bacillus sp. S3 was proved to a novel species within the Bacillus genus. The majority of mobile genetic elements (MGEs) mainly distributed on chromosomes within the Bacillus genus. Pan-genome analysis showed that the 45 genomes contained 554 core genes and many unique genes were dissected in analyzed genomes. Whole genomic alignment showed that Bacillus genus underwent frequently large-scale evolutionary events. In addition, the origin and evolution analysis of Sb(III)-resistance genes revealed the evolutionary relationships and horizontal gene transfer (HGT) events among the Bacillus genus. The assessment of functionality of heavy metal (loid) s resistance genes emphasized its indispensable role in the harsh eco-environment of Bacillus genus. Real-time quantitative PCR (RT-qPCR) analysis indicated that Sb(III)-related genes were all induced under the Sb(III) stress, while arsC gene was down-regulated.<br><br>CONCLUSIONS: The results in this study shed light on the molecular mechanisms of Bacillus sp. S3 coping with Sb(III), extended our understanding on the evolutionary relationships between Bacillus sp. S3 and other closely related species, and further enriched the Sb(III) resistance genetic data sources.}, }
@article {pmid32354184, year = {2020}, author = {Loayza, F and Graham, JP and Trueba, G}, title = {Factors Obscuring the Role of E. coli from Domestic Animals in the Global Antimicrobial Resistance Crisis: An Evidence-Based Review.}, journal = {International journal of environmental research and public health}, volume = {17}, number = {9}, pages = {}, pmid = {32354184}, issn = {1660-4601}, support = {R01 AI135118/AI/NIAID NIH HHS/United States ; R01AI135118/NH/NIH HHS/United States ; }, mesh = {Animals ; *Animals, Domestic/microbiology ; Anti-Bacterial Agents ; *Drug Resistance, Bacterial ; *Escherichia coli/drug effects/genetics/pathogenicity ; *Escherichia coli Infections ; Humans ; }, abstract = {Recent studies have found limited associations between antimicrobial resistance (AMR) in domestic animals (and animal products), and AMR in human clinical settings. These studies have primarily used Escherichia coli, a critically important bacterial species associated with significant human morbidity and mortality. E. coli is found in domestic animals and the environment, and it can be easily transmitted between these compartments. Additionally, the World Health Organization has highlighted E. coli as a "highly relevant and representative indicator of the magnitude and the leading edge of the global antimicrobial resistance (AMR) problem". In this paper, we discuss the weaknesses of current research that aims to link E. coli from domestic animals to the current AMR crisis in humans. Fundamental gaps remain in our understanding the complexities of E. coli population genetics and the magnitude of phenomena such as horizontal gene transfer (HGT) or DNA rearrangements (transposition and recombination). The dynamic and intricate interplay between bacterial clones, plasmids, transposons, and genes likely blur the evidence of AMR transmission from E. coli in domestic animals to human microbiota and vice versa. We describe key factors that are frequently neglected when carrying out studies of AMR sources and transmission dynamics.}, }
@article {pmid32353032, year = {2020}, author = {Heß, S and Hiltunen, T and Berendonk, TU and Kneis, D}, title = {High variability of plasmid uptake rates in Escherichia coli isolated from sewage and river sediments.}, journal = {PloS one}, volume = {15}, number = {4}, pages = {e0232130}, pmid = {32353032}, issn = {1932-6203}, mesh = {Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic/*drug effects ; Drug Resistance, Microbial/drug effects/genetics ; Escherichia coli/genetics/metabolism ; Gene Transfer, Horizontal/*drug effects/genetics ; Plasmids/*drug effects/genetics/metabolism ; Rivers ; Serratia marcescens/genetics ; Sewage ; }, abstract = {The horizontal transfer of plasmids is a key mechanism behind the spread of antibiotic resistance in bacteria. So far, transfer rate constants were measured for a variety of plasmids, donors and recipients. The employed strains typically had a long history in laboratories. Existing data are, therefore, not necessarily representative for real-world environments. Moreover, information on the inter-strain variability of plasmid transfer rates is scarce. Using a high-throughput approach, we studied the uptake of RP4 by various Escherichia coli recipients using Serratia marcescens as the donor. The recipient strains were isolated from human-borne sewage and river sediments. The rate constants of plasmid transfer generally followed a log-normal distribution with considerable variance. The rate constants for good and poor recipients (95 and 5% quantile) differed by more than three orders of magnitude. Specifically, the inter-strain variability of the rate constant was large in comparison to alterations induced by low-level antibiotic exposure. We did not find evidence for diverging efficiencies of plasmid uptake between E. coli recipients of different origin. On average, strains isolated from river bottom sediments were equally efficient in the acquisition of RP4 as isolates extracted from sewage. We conclude that E. coli strains persisting in the aquatic environment and those of direct human origin share a similar intrinsic potential for the conjugative uptake of certain plasmids. In view of the large inter-strain variability, we propose to work towards probabilistic modeling of the environmental spread of antibiotic resistance.}, }
@article {pmid32345784, year = {2020}, author = {Brandsch, R and Mihasan, M}, title = {A soil bacterial catabolic pathway on the move: Transfer of nicotine catabolic genes between Arthrobacter genus megaplasmids and invasion by mobile elements.}, journal = {Journal of biosciences}, volume = {45}, number = {}, pages = {}, pmid = {32345784}, issn = {0973-7138}, mesh = {Arthrobacter/*enzymology/*genetics/metabolism ; Bacterial Proteins/*genetics/metabolism ; Chromosomes, Bacterial ; *DNA Transposable Elements ; Gene Transfer, Horizontal ; Genes, Bacterial ; Integrases/genetics ; Micrococcaceae/genetics ; Nicotine/*metabolism ; Plasmids ; Soil Microbiology ; }, abstract = {The 165,137 bp plasmid pAO1 of Paenarthrobacter nicotinovorans carries the genes of a nicotine catabolic pathway. The genes are organized into several gene modules responsible for the catabolism of L- and D-nicotine to nicotine blue, alpha-ketoglutarate and succinate. Various modules of these genes have been shown to be present in gram-positive (Gram?) soil bacteria. The presence of the identical pAO1 nic-genes on the 288,370 bp plasmid pZXY21 of Arthrobacter sp. ZXY2 (96 percent to 100 percent at the nucleotide level) permitted the identification of the limits of this DNA fragment. At the 5' end of the nic-genes are located the ORFs of two predicted integrases of the tyrosine recombinase family with conserved R, H, R and Y catalytic residues and that of a small transposase with a predicted leucine zipper motive. They are related to Tn554A, Tn554B and Tn554C of Staphylococcus aureus and suggest that the entire nic-genes DNA fragment represents a large catabolic transposon. Surprisingly the nic-genes on pZXY21 were found to be interspersed by mobile elements encoding transposases of various IS families. Insertion of these IS elements disrupts nicotine degradation and divide the nic-genes DNA into potentially new transposons. This finding may illustrate how nicotine catabolic genes can be mobilized and spread by horizontal gene transfer to other soil bacteria.}, }
@article {pmid32344121, year = {2020}, author = {Najar, IN and Sherpa, MT and Das, S and Das, S and Thakur, N}, title = {Diversity analysis and metagenomic insights into antibiotic and metal resistance among Himalayan hot spring bacteriobiome insinuating inherent environmental baseline levels of antibiotic and metal tolerance.}, journal = {Journal of global antimicrobial resistance}, volume = {21}, number = {}, pages = {342-352}, doi = {10.1016/j.jgar.2020.03.026}, pmid = {32344121}, issn = {2213-7173}, mesh = {Anti-Bacterial Agents/pharmacology ; Genes, Bacterial/genetics ; *Hot Springs ; Metagenome ; *Metagenomics ; }, abstract = {OBJECTIVES: Mechanisms of occurrence and expression of antibiotic resistance genes (ARGs) in thermophilic bacteria are still unknown owing to limited research and data. In this research, comparative profiling of ARGs and metal tolerance genes among thermophilic bacteria has been done by functional metagenomic methods.<br><br>METHODS: Shotgun metagenomic sequence data were generated using Illumina HiSeq 4000. Putative ARGs from the PROKKA predicted genes were identified with the ardbAnno V.1.0 script available from the ARDB (Antibiotic Resistance Genes Database) consortium using the non-redundant resistance genes as a reference. Putative metal resistance genes (MRGs) were identified by using BacMetScan V.1.0. The whole-genome sequencing for bacterial isolates was performed using Illumina HiSeq 4000 sequencing technology with a paired-end sequencing module.<br><br>RESULTS: Metagenomic analysis showed the dominance of Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes in two hot springs of Sikkim. ARG analysis through shotgun gene sequencing was found to be negative in the case of thermophilic bacteria. However, few genes were detected but they showed maximum similarity with mesophilic bacteria. Concurrently, MRGs were also detected in the metagenome sequence of isolates from hot springs. Detection of MRGs and absence of ARGs investigated by whole-genome sequencing in the reference genome sequence of thermophilic Geobacillus also conveyed the same message.<br><br>CONCLUSION: The study of ARGs and MRGs (Heavy metal resistance gene) among culturable and non-culturable bacteria from the hot springs of Sikkim via metagenomics showed a preferential selection of MRGs over ARGs. The absence of ARGs also does not support the co-selection of ARGs and MRGs in these environments. This evolutionary selection of metal resistance over antibiotic genes may have been necessary to survive in the geological craters which have an abundance of different metals from earth sediments rather than antibiotics. Furthermore, the selection could be environment driven depending on the susceptibility of ARGs in a thermophilic environments as it reduces the chances of horizontal gene transfer.}, }
@article {pmid32339850, year = {2020}, author = {Chotinantakul, K and Chansiw, N and Okada, S}, title = {Biofilm formation and transfer of a streptomycin resistance gene in enterococci from fermented pork.}, journal = {Journal of global antimicrobial resistance}, volume = {22}, number = {}, pages = {434-440}, doi = {10.1016/j.jgar.2020.04.016}, pmid = {32339850}, issn = {2213-7173}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Biofilms ; Drug Resistance, Bacterial ; Enterococcus/genetics ; Humans ; *Pork Meat ; *Red Meat ; Streptomycin/pharmacology ; Swine ; }, abstract = {OBJECTIVES: Multidrug-resistant (MDR) enterococci are found extensively in food samples. This study characterized the phenotypic virulence factors and the ability of horizontal gene transfer of a streptomycin resistance gene among enterococci isolated from fermented pork.<br><br>METHODS: Thirty-six MDR enterococci were subjected to screening of gelatinase, biofilm formation at various temperatures (4 &#xb0;C, 25 &#xb0;C and 37 &#xb0;C), clumping ability and conjugation.<br><br>RESULTS: All gelatinase-positive and clumping-positive strains were Enterococcus faecalis (41.7% and 38.9%, respectively). None of Enterococcus faecium and Enterococcus hirae demonstrated both phenotypes. Moderate and strong biofilm formations were found mostly at optimal temperatures in all the three species tested. However, moderate and weak biofilm formations could be found in 52.8% at 4 &#xb0;C. No association was observed between biofilm formation and asa1, efaA, gelE and esp genes. Surprisingly, our data revealed evidence of the streptomycin resistance gene (aadE) being transferred among meat E. faecalis isolates as characterized by the pheromone-clumping response.<br><br>CONCLUSIONS: Here we report the co-existence of some virulence factors and MDR enterococci from fermented pork. Our data demonstrated for the first time that the aadE gene could be transferred via conjugation among enterococci isolated from meat, contributing to streptomycin resistance. This study highlights the importance of horizontal gene transfer within the food chain reservoir and that transfer to humans might be possible, causing harm or untreatable diseases.}, }
@article {pmid32337781, year = {2020}, author = {Vezzulli, L and Baker-Austin, C and Kirschner, A and Pruzzo, C and Martinez-Urtaza, J}, title = {Global emergence of environmental non-O1/O139 Vibrio cholerae infections linked with climate change: a neglected research field?.}, journal = {Environmental microbiology}, volume = {22}, number = {10}, pages = {4342-4355}, doi = {10.1111/1462-2920.15040}, pmid = {32337781}, issn = {1462-2920}, support = {311846//European FP7 project 'Protecting the health of Europeans by improving methods for the detection of pathogens in drinking water and water used in food preparation AQUAVALENS/International ; LSC17-007//NFB GmbH/International ; }, mesh = {*Climate Change ; Disease Outbreaks ; Ecology ; *Ecosystem ; Gastroenteritis/microbiology/*pathology ; Gene Transfer, Horizontal ; Humans ; Seawater/microbiology ; Vibrio Infections/microbiology/*pathology ; Vibrio cholerae non-O1/classification/genetics/*pathogenicity ; }, abstract = {The bacterium Vibrio cholerae is a natural inhabitant of aquatic ecosystems across the planet. V. cholerae serogroups O1 and O139 are responsible for cholera outbreaks in developing countries accounting for 3-5 million infections worldwide and 28.800-130.000 deaths per year according to the World Health Organization. In contrast, V. cholerae serogroups other than O1 and O139, also designated as V. cholerae non-O1/O139 (NOVC), are not associated with epidemic cholera but can cause other illnesses that may range in severity from mild (e.g. gastroenteritis, otitis, etc.) to life-threatening (e.g. necrotizing fasciitis). Although generally neglected, NOVC-related infections are on the rise and represent one of the most striking examples of emerging human diseases linked to climate change. NOVC strains are also believed to potentially contribute to the emergence of new pathogenic strains including strains with epidemic potential as a direct consequence of genetic exchange mechanisms such as horizontal gene transfer and genetic recombination. Besides general features concerning the biology and ecology of NOVC strains and their associated diseases, this review aims to highlight the most relevant aspects related to the emergence and potential threat posed by NOVC strains under a rapidly changing environmental and climatic scenario.}, }
@article {pmid32335280, year = {2020}, author = {Chen, L and Han, D and Tang, Z and Hao, J and Xiong, W and Zeng, Z}, title = {Co-existence of the oxazolidinone resistance genes cfr and optrA on two transferable multi-resistance plasmids in one Enterococcus faecalis isolate from swine.}, journal = {International journal of antimicrobial agents}, volume = {56}, number = {1}, pages = {105993}, doi = {10.1016/j.ijantimicag.2020.105993}, pmid = {32335280}, issn = {1872-7913}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Conjugation, Genetic/genetics ; Drug Resistance, Bacterial/*genetics ; Enterococcus/drug effects/*genetics/isolation &amp; purification ; Enterococcus faecalis/drug effects/*genetics/isolation &amp; purification ; Gene Transfer, Horizontal/genetics ; Gram-Positive Bacterial Infections/drug therapy/microbiology/veterinary ; Methyltransferases/genetics ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Oxazolidinones/*pharmacology ; Swine ; }, abstract = {OBJECTIVES: To identify and characterize oxazolidinone resistance genes cfr and optrA in enterococcal isolates.<br><br>METHODS: Two hundred and ninety-three enterococcal isolates were screened for the presence of cfr and optrA by polymerase chain reaction. The transferability of cfr and optrA was examined by conjugation. S1 nuclease pulsed-field gel electrophoresis and Southern blotting were used to identify the location of cfr and optrA. One Enterococcus faecalis isolate carrying both cfr and optrA was sequenced in full.<br><br>RESULTS: cfr and optrA were detected in 16 (5.5%) and 170 (58.0%) enterococcal isolates, respectively. Sixteen enterococcal isolates (E. faecalis n=13, Enterococcus avium n=2, Enterococcus mundtii n=1) carried both cfr and optrA. The cfr-carrying fragment between res and theta in plasmid p4 showed 98.9% identity to the corresponding region of plasmid pEF120805 from vancomycin-resistant Enterococcus faecium. The optrA-carrying segment between tnpB and optrA in plasmid p1 showed >99.9% identity to the corresponding region of genomic DNA from E. faecalis A101. Plasmid p4 and plasmid p1 were simultaneously conjugated to E. faecalis JH2-2.<br><br>CONCLUSIONS: One hundred and seventy optrA-positive enterococci were identified in 293 enterococcal isolates from swine and the farm environment. The co-existence of cfr and optrA in E. avium and E. mundtii has been identified previously. cfr and optrA were identified on two new conjugative plasmids from one E. faecalis isolate. The optrA-carrying segment (IS1216E-optrA-IS1216E) was reported initially. Among different types of enterococcal plasmids, ISEnfa5 and IS1216E elements may play a vital role in the dissemination of cfr and optrA, respectively.}, }
@article {pmid32334350, year = {2020}, author = {Furlan, JPR and Dos Santos, LDR and Moretto, JAS and Ramos, MS and Gallo, IFL and Alves, GAD and Paulelli, AC and Rocha, CCS and Cesila, CA and Gallimberti, M and Devóz, PP and Júnior, FB and Stehling, EG}, title = {Occurrence and abundance of clinically relevant antimicrobial resistance genes in environmental samples after the Brumadinho dam disaster, Brazil.}, journal = {The Science of the total environment}, volume = {726}, number = {}, pages = {138100}, doi = {10.1016/j.scitotenv.2020.138100}, pmid = {32334350}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents/*pharmacology ; Brazil ; Cities ; *Disasters ; Drug Resistance, Bacterial/drug effects ; Genes, Bacterial/drug effects ; }, abstract = {On January 25th 2019, the structure damming a pond containing ore mining wastes and iron burst at Brumadinho City, Brazil. About 11.7 million m[3] of a tailings-mud mixture was released from the dam, causing destruction along 300 km of the Paraopeba River toward the São Francisco River. The environments with a high content of metals may provide a suitable environment for horizontal gene transfer, including antimicrobial resistance genes (ARGs). Therefore, this study aimed to detect and quantify clinically relevant ARGs in environmental samples after the Brumadinho dam disaster. Soil, sediment, and water samples were collected within 300 km of the Brumadinho dam disaster at unaffected and affected sites. Physical-chemical parameters of water samples were measured. Total DNA was extracted and 65 clinically relevant ARGs were researched by PCR. The most prevalent ARGs were selected for real-time quantitative PCR analysis. The average of the physical-chemical parameters was higher in the affected sites when compared to the unaffected sites, especially turbidity, concentration of Fe and Al. A total of 387 amplicons from 29 ARGs were detected, which confer resistance to β-lactams, quinolones, aminoglycosides, tetracyclines, sulphonamides, phenicols, macrolides, glycopeptides, and polymyxins, including extended-spectrum β-lactamases-encoding genes, and mcr-7.1. The sul1 gene had higher total concentrations than blaTEM, tetB and qnrB in the environmental samples, and the diversity and abundance of ARGs increased at the sites affected by the Brumadinho dam disaster. Therefore, we point out that the contamination by the Brumadinho dam disaster tailings resulted in an increase in the amount and abundance of ARGs in the environment.}, }
@article {pmid32332135, year = {2020}, author = {Gao, R and Ding, M and Jiang, S and Zhao, Z and Chenthamara, K and Shen, Q and Cai, F and Druzhinina, IS}, title = {The Evolutionary and Functional Paradox of Cerato-platanins in Fungi.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {13}, pages = {}, pmid = {32332135}, issn = {1098-5336}, mesh = {*Evolution, Molecular ; Fungal Proteins/*genetics/metabolism ; Fungi/genetics/metabolism ; Gene Transfer, Horizontal ; Genome, Fungal ; Solanum lycopersicum/microbiology ; *Multigene Family ; Plant Roots/microbiology ; Trichoderma/*genetics/metabolism ; }, abstract = {Cerato-platanins (CPs) form a family of fungal small secreted cysteine-rich proteins (SSCPs) and are of particular interest not only because of their surface activity but also their abundant secretion by fungi. We performed an evolutionary analysis of 283 CPs from 157 fungal genomes with the focus on the environmental opportunistic plant-beneficial and mycoparasitic fungus Trichoderma Our results revealed a long evolutionary history of CPs in Dikarya fungi that have undergone several events of lateral gene transfer and gene duplication. Three genes were maintained in the core genome of Trichoderma, while some species have up to four CP-encoding genes. All Trichoderma CPs evolve under stabilizing natural selection pressure. The functional genomic analysis of CPs in Trichoderma guizhouense and Trichoderma harzianum revealed that only epl1 is active at all stages of development but that it plays a minor role in interactions with other fungi and bacteria. The deletion of this gene results in increased colonization of tomato roots by Trichoderma spp. Similarly, biochemical tests of EPL1 heterologously produced by Pichia pastoris support the claims described above. Based on the results obtained, we conclude that the function of CPs is probably linked to their surfactant properties and the ability to modify the hyphosphere of submerged mycelia and, thus, facilitate the nutritional versatility of fungi. The effector-like functions do not sufficiently describe the diversity and evolution of these proteins in fungi, as they are also maintained, duplicated, or laterally transferred in the genomes of nonherbivore fungi.IMPORTANCE Cerato-platanins (CPs) are surface-active small proteins abundantly secreted by filamentous fungi. Consequently, immune systems of plants and other organisms recognize CPs and activate defense mechanisms. Some CPs are toxic to plants and act as virulence factors in plant-pathogenic fungi. Our analysis, however, demonstrates that the interactions with plants do not explain the origin and evolution of CPs in the fungal kingdom. We revealed a long evolutionary history of CPs with multiple cases of gene duplication and events of interfungal lateral gene transfers. In the mycoparasitic Trichoderma spp., CPs evolve under stabilizing natural selection and hamper the colonization of roots. We propose that the ability to modify the hydrophobicity of the fungal hyphosphere is a key to unlock the evolutionary and functional paradox of these proteins.}, }
@article {pmid32330583, year = {2020}, author = {Moure, Z and Lara, N and Marín, M and Sola-Campoy, PJ and Bautista, V and Gómez-Bertomeu, F and Gómez-Dominguez, C and Pérez-Vázquez, M and Aracil, B and Campos, J and Cercenado, E and Oteo-Iglesias, J and , }, title = {Interregional spread in Spain of linezolid-resistant Enterococcus spp. isolates carrying the optrA and poxtA genes.}, journal = {International journal of antimicrobial agents}, volume = {55}, number = {6}, pages = {105977}, doi = {10.1016/j.ijantimicag.2020.105977}, pmid = {32330583}, issn = {1872-7913}, mesh = {Aged ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/*genetics ; Enterococcus faecalis/drug effects/*genetics/isolation &amp; purification ; Enterococcus faecium/drug effects/*genetics/isolation &amp; purification ; Female ; Gene Transfer, Horizontal ; Genome, Bacterial ; Gram-Positive Bacterial Infections/*epidemiology/*microbiology ; Humans ; Linezolid/*pharmacology ; Male ; Molecular Epidemiology ; Multilocus Sequence Typing ; Mutation ; Plasmids ; Spain/epidemiology ; Whole Genome Sequencing ; }, abstract = {The emergence of linezolid-resistant Enterococcus spp. (LRE) due to transferable resistance determinants is a matter of concern. To understand the contribution of the plasmid-encoded optrA and poxtA genes to the emergence of LRE, clinical isolates from different Spanish hospitals submitted to the Spanish Reference Laboratory from 2015-2018 were analysed. Linezolid resistance mechanisms were screened in all isolates by PCR and sequencing. Genetic relatedness of Enterococcus spp. carrying optrA and poxtA was studied by PFGE and MLST. Antimicrobial susceptibility was tested by broth microdilution using EUCAST standards. A total of 97 LRE isolates were studied, in 94 (96.9%) of which at least one resistance determinant was detected; 84/97 isolates (86.6%) presented a single resistance mechanism as follows: 45/84 (53.6%) carried the optrA gene, 38/84 (45.2%) carried the G2576T mutation and 1/84 (1.2%) carried the poxtA gene. In addition, 5/97 isolates (5.2%) carried both optrA and the G2576T mutation and 5/97 (5.2%) carried both optrA and poxtA. The optrA gene was more frequent in Enterococcus faecalis (83.6%) than Enterococcus faecium (11.1%) and was mainly associated with community-acquired urinary tract infections. Carriage of the poxtA gene was more frequent in E. faecium (13.9%) than E. faecalis (1.6%). Among the optrA-positive E. faecalis isolates, two main clusters were detected by PFGE. These two clusters belonged to ST585 and ST480 and were distributed throughout 11 and 6 Spanish provinces, respectively. This is the first description of LRE carrying the poxtA gene in Spain, including the co-existence of optrA and poxtA in five isolates.}, }
@article {pmid32327734, year = {2020}, author = {Mahendra, C and Christie, KA and Osuna, BA and Pinilla-Redondo, R and Kleinstiver, BP and Bondy-Denomy, J}, title = {Author Correction: Broad-spectrum anti-CRISPR proteins facilitate horizontal gene transfer.}, journal = {Nature microbiology}, volume = {5}, number = {6}, pages = {872}, doi = {10.1038/s41564-020-0726-9}, pmid = {32327734}, issn = {2058-5276}, abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.}, }
@article {pmid32326434, year = {2020}, author = {Pérez-Etayo, L and González, D and Vitas, AI}, title = {The Aquatic Ecosystem, a Good Environment for the Horizontal Transfer of Antimicrobial Resistance and Virulence-Associated Factors Among Extended Spectrum β-lactamases Producing E. coli.}, journal = {Microorganisms}, volume = {8}, number = {4}, pages = {}, pmid = {32326434}, issn = {2076-2607}, abstract = {One of the main public health problems nowadays is the increase of antimicrobial resistance, both in the hospital environment and outside it (animal environment, food and aquatic ecosystems, among others). It is necessary to investigate the virulence-associated factors and the ability of horizontal gene transfer among bacteria for a better understanding of the pathogenicity and the mechanisms of dissemination of resistant bacteria. Therefore, the objective of this work was to detect several virulence factors genes (fimA, papC, papG III, cnf1, hlyA and aer) and to determine the conjugative capacity in a wide collection of extended-spectrum β-lactamases-producing E. coli isolated from different sources (human, food, farms, rivers, and wastewater treatment plants). Regarding virulence genes, fimA, papC, and aer were distributed throughout all the studied environments, papG III was mostly related to clinical strains and wastewater is a route of dissemination for cnf1 and hlyA. Strains isolated from aquatic environments showed an average conjugation frequencies of 1.15 × 10[-1] ± 5 × 10[-1], being significantly higher than those observed in strains isolated from farms and food (p < 0.05), with frequencies of 1.53 × 10[-4] ± 2.85 × 10[-4] and 9.61 × 10[-4] ± 1.96 × 10[-3], respectively. The reported data suggest the importance that the aquatic environment (especially WWTPs) acquires for the exchange of genes and the dispersion of resistance. Therefore, specific surveillance programs of AMR indicators in wastewaters from animal or human origin are needed, in order to apply sanitation measures to reduce the burden of resistant bacteria arriving to risky environments as WWTPs.}, }
@article {pmid32319739, year = {2020}, author = {Rova, M and Hellberg Lindqvist, M and Goetelen, T and Blomqvist, S and Nilsson, T}, title = {Heterologous expression of the gene for chlorite dismutase from Ideonella dechloratans is induced by an FNR-type transcription factor.}, journal = {MicrobiologyOpen}, volume = {9}, number = {7}, pages = {e1049}, pmid = {32319739}, issn = {2045-8827}, mesh = {Burkholderiales/enzymology/*genetics/*metabolism ; Escherichia coli/genetics ; Escherichia coli Proteins/genetics ; Gene Expression Regulation, Bacterial/*genetics ; Iron-Sulfur Proteins/genetics ; Oxidoreductases/*biosynthesis/*genetics ; Perchlorates/metabolism ; Promoter Regions, Genetic/genetics ; }, abstract = {Regulation of the expression of the gene for chlorite dismutase (cld), located on the chlorate reduction composite transposon of the chlorate reducer Ideonella dechloratans, was studied. A 200 bp upstream sequence of the cld gene, and mutated and truncated versions thereof, was used in a reporter system in Escherichia coli. It was found that a sequence within this upstream region, which is nearly identical to the canonical FNR-binding sequence of E. coli, is necessary for anaerobic induction of the reporter gene. Anaerobic induction was regained in an FNR-deficient strain of E. coli when supplemented either with the fnr gene from E. coli or with a candidate fnr gene cloned from I. dechloratans. In vivo transcription of the suggested fnr gene of I. dechloratans was demonstrated by qRT-PCR. Based on these results, the cld promoter of I. dechloratans is suggested to be a class II-activated promoter regulated by an FNR-type protein of I. dechloratans. No fnr-type genes have been found on the chlorate reduction composite transposon of I. dechloratans, making anaerobic upregulation of the cld gene after a gene transfer event dependent on the presence of an fnr-type gene in the recipient.}, }
@article {pmid32316688, year = {2020}, author = {Santero, E and Díaz, E}, title = {Special Issue: Genetics of Biodegradation and Bioremediation.}, journal = {Genes}, volume = {11}, number = {4}, pages = {}, pmid = {32316688}, issn = {2073-4425}, mesh = {Bacteria/*genetics/metabolism ; Bacterial Proteins/*genetics/metabolism ; *Biodegradation, Environmental ; Environmental Pollutants/*metabolism ; *Gene Expression Regulation, Bacterial ; }, abstract = {Many different biodegradation pathways, both aerobic and anaerobic, have already been characterised, and the phylogenetic relationships among catabolic genes within the different types of pathways have been studied. However, new biodegradation activities and their coding genes are continuously being reported, including those involved in the catabolism of emerging contaminants or those generally regarded as non-biodegradable. Gene regulation is also an important issue for the efficient biodegradation of contaminants. Specific induction by the substrate and over-imposed global regulatory networks adjust the expression of the biodegradation genes to the bacterial physiological needs. New biodegradation pathways can be assembled in a particular strain or in a bacterial consortium by recruiting biodegradation genes from different origins through horizontal gene transfer. The abundance and diversity of biodegradation genes, analysed by either genomic or metagenomic approaches, constitute valuable indicators of the biodegradation potential of a particular environmental niche. This knowledge paves the way to systems metabolic engineering approaches to valorise biowaste for the production of value-added products.}, }
@article {pmid32316316, year = {2020}, author = {Berckx, F and Wibberg, D and Kalinowski, J and Pawlowski, K}, title = {The Peptidoglycan Biosynthesis Gene murC in Frankia: Actinorhizal vs. Plant Type.}, journal = {Genes}, volume = {11}, number = {4}, pages = {}, pmid = {32316316}, issn = {2073-4425}, mesh = {Bacterial Proteins/genetics/*metabolism ; Frankia/classification/*growth &amp; development ; *Multigene Family ; Nitrogen Fixation ; Peptidoglycan/*biosynthesis ; Phylogeny ; Rhamnaceae/genetics/*metabolism/microbiology ; Root Nodules, Plant/genetics/*metabolism/microbiology ; Symbiosis ; }, abstract = {Nitrogen-fixing Actinobacteria of the genus Frankia can be subdivided into four phylogenetically distinct clades; members of clusters one to three engage in nitrogen-fixing root nodule symbioses with actinorhizal plants. Mur enzymes are responsible for the biosynthesis of the peptidoglycan layer of bacteria. The four Mur ligases,MurC, MurD, MurE, and MurF, catalyse the addition of a short polypeptide to UDP-N-acetylmuramic acid. Frankia strains of cluster-2 and cluster-3 contain two copies of murC, while the strains of cluster-1 and cluster-4 contain only one. Phylogenetically, the protein encoded by the murC gene shared only by cluster-2 and cluster-3, termed MurC1, groups with MurC proteins of other Actinobacteria. The protein encoded by the murC gene found in all Frankia strains, MurC2, shows a higher similarity to the MurC proteins of plants than of Actinobacteria. MurC2 could have been either acquired via horizontal gene transfer or via gene duplication and convergent evolution, while murC1 was subsequently lost in the cluster-1 and cluster-4 strains. In the nodules induced by the cluster-2 strains, the expression levels of murC2 were significantly higher than those of murC1. Thus, there is clear sequence divergence between both types of Frankia MurC, and Frankia murC1 is in the process of being replaced by murC2, indicating selection in favour of murC2. Nevertheless, protein modelling showed no major structural differences between the MurCs from any phylogenetic group examined.}, }
@article {pmid32311501, year = {2020}, author = {Li, C and Ma, G and Yang, T and Wen, X and Qin, C and Yue, L and Jia, X and Shen, Y and Lu, D and Wang, L and Shen, D and Chen, F}, title = {A rare carbapenem-resistant hypervirulent K1/ST1265 Klebsiella pneumoniae with an untypeable blaKPC-harboured conjugative plasmid.}, journal = {Journal of global antimicrobial resistance}, volume = {22}, number = {}, pages = {426-433}, doi = {10.1016/j.jgar.2020.04.009}, pmid = {32311501}, issn = {2213-7173}, mesh = {Acute Disease ; Carbapenems/pharmacology ; Humans ; *Klebsiella Infections ; Klebsiella pneumoniae/genetics ; *Pancreatitis ; Phylogeny ; Plasmids/genetics ; beta-Lactamases/genetics ; }, abstract = {OBJECTIVE: We investigated the pathogenesis of a patient with severe acute pancreatitis by comprehensively analysing a rare carbapenem-resistant hypervirulent K1/ST1265 Klebsiella pneumoniae (CR-HvKP) strain.<br><br>METHODS: We conducted virulence and multidrug-resistance phenotypic characterization and identified a CR-HvKP strain from the patient. It was subjected to Pacbio sequencing, and subsequent analysis of virulence, resistance genes and mobile genetic elements.<br><br>RESULTS: We described the phenotype and genotype of a rare CR-HvKP strain with an untypeable blaKPC-harboured conjugative plasmid and a pLVPK-like virulent plasmid. Resistance gene analysis showed that the untypeable blaKPC-2-harboured plasmid was formed by IS26-mediated recombination of blaKPC-embedded transposon Tn6500 into pCN061p4 from Escherichia coli. Interestingly, it had an R-M system that might protect plasmid from cleavage. This may facilitate the stabilization of plasmids in bacteria in the event of missing CR-plasmid during transmission. Virulence gene analysis indicated 78 virulence genes on the genome, including 67 on the chromosome (37 in high-pathogenic island) and 11 on the pLVPK-like virulence plasmid (harbouring rmpA/rmpA2). Further phylogenetic analysis revealed that the CR-HvKP evolved from HvKP through acquiring an antimicrobial-resistance plasmid.<br><br>CONCLUSION: Our research, to our knowledge, first reported a ST1265/K1 CR-HvKP strain with an untypeable blaKPC-harboured plasmid. The trend that HvKP could evolve into CR-HvKP by obtaining stabilized/conjugative blaKPC-carrying plasmids is a considerable threat to public health and should be closely supervised.}, }
@article {pmid32310121, year = {2020}, author = {Peng, H and Gu, J and Wang, X and Wang, Q and Sun, W and Hu, T and Guo, H and Ma, J and Bao, J}, title = {Insight into the fate of antibiotic resistance genes and bacterial community in co-composting green tea residues with swine manure.}, journal = {Journal of environmental management}, volume = {266}, number = {}, pages = {110581}, doi = {10.1016/j.jenvman.2020.110581}, pmid = {32310121}, issn = {1095-8630}, mesh = {Animals ; Anti-Bacterial Agents ; Bacteria ; *Composting ; Drug Resistance, Microbial ; Genes, Bacterial ; Manure ; Swine ; Tea ; }, abstract = {Green tea residues (GTRs) are byproducts of tea production and processing, and this type of agricultural waste retains nutritious components. This study investigated the co-composting of GTRs with swine manure, as well as the effects of GTRs on antibiotic resistance genes (ARGs) and the bacterial community during co-composting. The temperature and C/N ratio indicate compost was mature after processing. The addition of GTRs effectively promoted the reduction in the abundances of most targeted ARGs (tet and sul genes), mobile genetic element (MGE; intI1), and metal resistance genes (MRGs; pcoA and tcrB). Redundancy analysis (RDA) showed that GTRs can reduce the abundance of MRGs and ARGs by reducing the bioavailability of heavy metals. Network analysis shows that Firmicutes and Actinobacteria were the main hosts of ARGs and ARGs, MGEs, and MRGs shared the same potential host bacteria. Adding GTRs during composting may reduce ARGs transmission through horizontal gene transfer (HGT). GTRs affected the bacterial community, thereby influencing the variations in the ARG profiles and reducing the potential risk associated with the compost product.}, }
@article {pmid32308441, year = {2020}, author = {Xu, Q and Fu, Y and Zhao, F and Jiang, Y and Yu, Y}, title = {Molecular Characterization of Carbapenem-Resistant Serratia marcescens Clinical Isolates in a Tertiary Hospital in Hangzhou, China.}, journal = {Infection and drug resistance}, volume = {13}, number = {}, pages = {999-1008}, pmid = {32308441}, issn = {1178-6973}, abstract = {INTRODUCTION: Although carbapenem-resistant Enterobacteriaceae (CRE) have been thoroughly investigated as the pathogens most commonly associated with clinical infections, data on Serratia marcescens are inadequate and superficial.<br><br>METHODS: In this study, we characterized 36 carbapenem-resistant Serratia marcescens (CRSM) isolates in our hospital from April 2018 to March 2019 by analysing whole-genome sequencing (WGS) data. The molecular typing of the isolates was performed using both pulsed-field gel electrophoresis (PFGE) and core genome multilocus sequence typing (cgMLST).<br><br>RESULTS: Thirty-three of the 36 isolates showed carbapenem resistance conferred by a bla KPC-2-harbouring plasmid, while the remaining three isolates were characterized by overexpression of beta-lactamase combined with porin loss. The bla KPC-2 genes in all the isolates were located on a plasmid of ~103 kb, except one, which was on a plasmid of ~94 kb. The gene structure surrounding bla KPC-2 in the plasmids was confirmed by integration of a partial Tn4401 structure and an intact IS26 as previously reported. Most of the plasmids also contained a mobile genetic element (MGE) comprising qnr and ISKpn19, which provided evidence of horizontal transfer of antibiotic resistance genes.<br><br>CONCLUSION: The thirty-six CRSM isolates were mainly clonally disseminated with a bla KPC-2-harbouring plasmid in our hospital. The gene structure surrounding bla KPC-2 as an MGE, as well as the qnr segment, might be acquired by horizontal gene transfer, and it could aggravate the infection and increase the difficulty of clinical treatment.}, }
@article {pmid32304827, year = {2020}, author = {Harris, AJ and Goldman, AD}, title = {The complex phylogenetic relationships of a 4mC/6mA DNA methyltransferase in prokaryotes.}, journal = {Molecular phylogenetics and evolution}, volume = {149}, number = {}, pages = {106837}, doi = {10.1016/j.ympev.2020.106837}, pmid = {32304827}, issn = {1095-9513}, mesh = {DNA/*metabolism ; DNA Methylation/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Likelihood Functions ; Methyltransferases/*classification/genetics ; Multigene Family ; *Phylogeny ; Prokaryotic Cells/*enzymology ; }, abstract = {DNA methyltransferases are proteins that modify DNA via attachment of methyl groups to nucleobases and are ubiquitous across the bacterial, archaeal, and eukaryotic domains of life. Here, we investigated the complex evolutionary history of the large and consequential 4mC/6mA DNA methyltransferase protein family using phylogenetic reconstruction of amino acid sequences. We present a well-supported phylogeny of this family based on systematic sampling of taxa across superphyla of bacteria and archaea. We compared the phylogeny to a current representation of the species tree of life and found that the 4mC/6mA methyltransferase family has a strikingly complex evolutionary history that likely began sometime after the last universal common ancestor of life diverged into the bacterial and archaeal lineages and probably involved many horizontal gene transfers within and between domains. Despite the complexity of its evolutionary history, we inferred that only one significant shift in molecular evolutionary rate characterizes the diversification of this protein family.}, }
@article {pmid32302381, year = {2020}, author = {Riedel, T and Neumann-Schaal, M and Wittmann, J and Schober, I and Hofmann, JD and Lu, CW and Dannheim, A and Zimmermann, O and Lochner, M and Groß, U and Overmann, J}, title = {Characterization of Clostridioides difficile DSM 101085 with A-B-CDT+ Phenotype from a Late Recurrent Colonization.}, journal = {Genome biology and evolution}, volume = {12}, number = {5}, pages = {566-577}, pmid = {32302381}, issn = {1759-6653}, mesh = {ADP Ribose Transferases/*genetics/metabolism ; Aged ; Bacterial Proteins/*genetics/metabolism ; Bacterial Toxins/*genetics/metabolism ; Clostridioides/*genetics/metabolism/*pathogenicity ; Enterotoxins/*genetics/metabolism ; *Evolution, Molecular ; Humans ; Metabolome ; *Phenotype ; *Virulence ; }, abstract = {During the last decades, hypervirulent strains of Clostridioides difficile with frequent disease recurrence and increased mortality appeared. Clostridioides difficile DSM 101085 was isolated from a patient who suffered from several recurrent infections and colonizations, likely contributing to a fatal outcome. Analysis of the toxin repertoire revealed the presence of a complete binary toxin locus and an atypical pathogenicity locus consisting of only a tcdA pseudogene and a disrupted tcdC gene sequence. The pathogenicity locus shows upstream a transposon and has been subject to homologous recombination or lateral gene transfer events. Matching the results of the genome analysis, neither TcdA nor TcdB production but the expression of cdtA and cdtB was detected. This highlights a potential role of the binary toxin C. difficile toxin in this recurrent colonization and possibly further in a host-dependent virulence. Compared with the C. difficile metabolic model strains DSM 28645 (630Δerm) and DSM 27147 (R20291), strain DSM 101085 showed a specific metabolic profile, featuring changes in the threonine degradation pathways and alterations in the central carbon metabolism. Moreover, products originating from Stickland pathways processing leucine, aromatic amino acids, and methionine were more abundant in strain DSM 101085, indicating a more efficient use of these substrates. The particular characteristics of strain C. difficile DSM 101085 may represent an adaptation to a low-protein diet in a patient with recurrent infections.}, }
@article {pmid32298615, year = {2020}, author = {Denise, R and Abby, SS and Rocha, EPC}, title = {The Evolution of Protein Secretion Systems by Co-option and Tinkering of Cellular Machineries.}, journal = {Trends in microbiology}, volume = {28}, number = {5}, pages = {372-386}, doi = {10.1016/j.tim.2020.01.005}, pmid = {32298615}, issn = {1878-4380}, mesh = {Archaea/*genetics/metabolism ; Bacteria/*genetics/metabolism ; Bacterial Secretion Systems/*genetics/*metabolism ; Bacteriophages/genetics ; *Biological Evolution ; Protein Transport/genetics/physiology ; }, abstract = {Protein secretion is important for many biotic and abiotic interactions. The evolution of protein secretion systems of bacteria, and related nanomachines, occurred by the co-option of machineries for motility, conjugation, injection, or adhesion. Some of these secretion systems emerged many times, whereas others are unique. In most cases, their evolution occurred by successive rounds of gene accretion, deletion, and horizontal transfer, resulting in machines that can be very different from the original ones. The frequency with which such co-option processes occurred seems to depend on the complexity of the systems, their differences to the ancestral machines, the availability of genetic material to tinker with, and possibly on the mechanisms of effector recognition. Understanding the evolution of secretion systems illuminates their functional diversification and could drive the discovery of novel systems.}, }
@article {pmid32297955, year = {2020}, author = {Warman, EA and Singh, SS and Gubieda, AG and Grainger, DC}, title = {A non-canonical promoter element drives spurious transcription of horizontally acquired bacterial genes.}, journal = {Nucleic acids research}, volume = {48}, number = {9}, pages = {4891-4901}, pmid = {32297955}, issn = {1362-4962}, support = {/WT_/Wellcome Trust/United Kingdom ; 212193/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {AT Rich Sequence ; Bacterial Proteins/metabolism ; DNA/chemistry ; DNA-Binding Proteins/metabolism ; DNA-Directed RNA Polymerases/chemistry/*metabolism ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; *Promoter Regions, Genetic ; Sigma Factor/chemistry/metabolism ; Transcription, Genetic ; *Transcriptional Activation ; }, abstract = {RNA polymerases initiate transcription at DNA sequences called promoters. In bacteria, the best conserved promoter feature is the AT-rich -10 element; a sequence essential for DNA unwinding. Further elements, and gene regulatory proteins, are needed to recruit RNA polymerase to the -10 sequence. Hence, -10 elements cannot function in isolation. Many horizontally acquired genes also have a high AT-content. Consequently, sequences that resemble the -10 element occur frequently. As a result, foreign genes are predisposed to spurious transcription. However, it is not clear how RNA polymerase initially recognizes such sequences. Here, we identify a non-canonical promoter element that plays a key role. The sequence, itself a short AT-tract, resides 5 base pairs upstream of otherwise cryptic -10 elements. The AT-tract alters DNA conformation and enhances contacts between the DNA backbone and RNA polymerase.}, }
@article {pmid32296407, year = {2020}, author = {García López, E and Martín-Galiano, AJ}, title = {The Versatility of Opportunistic Infections Caused by Gemella Isolates Is Supported by the Carriage of Virulence Factors From Multiple Origins.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {524}, pmid = {32296407}, issn = {1664-302X}, abstract = {The molecular basis of the pathogenesis of the opportunistic invasive infections caused by isolates of the Gemella genus remains largely unknown. Moreover, inconsistencies in the current species assignation were detected after genome-level comparison of 16 public Gemella isolates. A literature search detected that, between the two most pathogenic species, Gemella morbillorum causes about twice the number of cases compared to Gemella haemolysans. These two species shared their mean diseases - sepsis and endocarditis - but differed in causing other syndromes. A number of well-known virulence factors were harbored by all species, such as a manganese transport/adhesin sharing 83% identity from oral endocarditis-causing streptococci. Likewise, all Gemellae carried the genes required for incorporating phosphorylcholine into their cell walls and encoded some choline-binding proteins. In contrast, other proteins were species-specific, which may justify the known epidemiological differences. G. haemolysans, but not G. morbillorum, harbor a gene cluster potentially encoding a polysaccharidic capsule. Species-specific surface determinants also included Rib and MucBP repeats, hemoglobin-binding NEAT domains, peptidases of C5a complement factor and domains that recognize extracellular matrix molecules exposed in damaged heart valves, such as collagen and fibronectin. Surface virulence determinants were associated with several taxonomically dispersed opportunistic genera of the oral microbiota, such as Granulicatella, Parvimonas, and Streptococcus, suggesting the existence of a horizontally transferrable gene reservoir in the oral environment, likely facilitated by close proximity in biofilms and ultimately linked to endocarditis. The identification of the Gemella virulence pool should be implemented in whole genome-based protocols to rationally predict the pathogenic potential in ongoing clinical infections caused by these poorly known bacterial pathogens.}, }
@article {pmid32296121, year = {2020}, author = {Monteil, CL and Grouzdev, DS and Perrière, G and Alonso, B and Rouy, Z and Cruveiller, S and Ginet, N and Pignol, D and Lefevre, CT}, title = {Repeated horizontal gene transfers triggered parallel evolution of magnetotaxis in two evolutionary divergent lineages of magnetotactic bacteria.}, journal = {The ISME journal}, volume = {14}, number = {7}, pages = {1783-1794}, pmid = {32296121}, issn = {1751-7370}, mesh = {*Alphaproteobacteria ; Bacteria/genetics ; Gene Transfer, Horizontal ; Gram-Negative Bacteria ; *Magnetospirillum/genetics ; }, abstract = {Under the same selection pressures, two genetically divergent populations may evolve in parallel toward the same adaptive solutions. Here, we hypothesized that magnetotaxis (i.e., magnetically guided chemotaxis) represents a key adaptation to micro-oxic habitats in aquatic sediments and that its parallel evolution homogenized the phenotypes of two evolutionary divergent clusters of freshwater spirilla. All magnetotactic bacteria affiliated to the Magnetospirillum genus (Alphaproteobacteria class) biomineralize the same magnetic particle chains and share highly similar physiological and ultrastructural features. We looked for the processes that could have contributed at shaping such an evolutionary pattern by reconciling species and gene trees using newly sequenced genomes of Magnetospirillum related bacteria. We showed that repeated horizontal gene transfers and homologous recombination of entire operons contributed to the parallel evolution of magnetotaxis. We propose that such processes could represent a more parsimonious and rapid solution for adaptation compared with independent and repeated de novo mutations, especially in the case of traits as complex as magnetotaxis involving tens of interacting proteins. Besides strengthening the idea about the importance of such a function in micro-oxic habitats, these results reinforce previous observations in experimental evolution suggesting that gene flow could alleviate clonal interference and speed up adaptation under some circumstances.}, }
@article {pmid32293532, year = {2020}, author = {Tao, Y and Zhou, K and Xie, L and Xu, Y and Han, L and Ni, Y and Qu, J and Sun, J}, title = {Emerging coexistence of three PMQR genes on a multiple resistance plasmid with a new surrounding genetic structure of qnrS2 in E. coli in China.}, journal = {Antimicrobial resistance and infection control}, volume = {9}, number = {1}, pages = {52}, pmid = {32293532}, issn = {2047-2994}, mesh = {Anti-Bacterial Agents/*pharmacology ; Cefepime/pharmacology ; Ceftazidime/pharmacology ; Ceftriaxone/pharmacology ; China ; Ciprofloxacin/pharmacology ; *Drug Resistance, Multiple, Bacterial ; Escherichia coli/*classification/drug effects/genetics ; Escherichia coli Proteins/*genetics ; Genome Size ; Levofloxacin/pharmacology ; Microbial Sensitivity Tests ; Mutation ; Plasmids/*genetics ; Whole Genome Sequencing/methods ; }, abstract = {BACKGROUND: Quinolones are commonly used for treatment of infections by bacteria of the Enterobacteriaceae family. However, the rising resistance to quinolones worldwide poses a major clinical and public health risk. This study aimed to characterise a novel multiple resistance plasmid carrying three plasmid-mediated quinolone resistance genes in Escherichia coli clinical stain RJ749.<br><br>METHODS: MICs of ceftriaxone, cefepime, ceftazidime, ciprofloxacin, and levofloxacin for RJ749 and transconjugant c749 were determined by the Etest method. Conjugation was performed using sodium azide-resistant E. coli J53 strain as a recipient. The quinolone resistance-determining regions of gyrA, gyrB, parC, and parE were PCR-amplified.<br><br>RESULTS: RJ749 was highly resistant to quinolones, while c749 showed low-level resistance. S1-nuclease pulsed-field gel electrophoresis revealed that RJ749 and c749 both harboured a plasmid. PCR presented chromosomal mutation sites of the quinolone resistance-determining region, which mediated quinolone resistance. The c749 genome comprised a single plasmid, pRJ749, with a multiple resistance region, including three plasmid-mediated quinolone resistance (PMQR) genes (aac (6')-Ib-cr, qnrS2, and oqxAB) and ten acquired resistance genes. One of the genes, qnrS2, was shown for the first time to be flanked by two IS26s. Three IS26-mediated circular molecules carrying the PMQR genes were detected.<br><br>CONCLUSIONS: We revealed the coexistence of three PMQR genes on a multiple resistance plasmid and a new surrounding genetic structure of qnrS2 flanked by IS26 elements. IS26 plays an important role in horizontal spread of quinolone resistance.}, }
@article {pmid32293157, year = {2020}, author = {Cheng, X and Garcés-Carrera, S and Whitworth, RJ and Fellers, JP and Park, Y and Chen, MS}, title = {A Horizontal Gene Transfer Led to the Acquisition of a Fructan Metabolic Pathway in a Gall Midge.}, journal = {Advanced biosystems}, volume = {4}, number = {4}, pages = {e1900275}, doi = {10.1002/adbi.201900275}, pmid = {32293157}, issn = {2366-7478}, mesh = {Animals ; Bacterial Proteins/genetics ; *Diptera/enzymology/genetics ; Fructans/*metabolism ; *Gene Transfer, Horizontal ; *Glycoside Hydrolases/genetics/metabolism ; *Insect Proteins/genetics/metabolism ; }, abstract = {Animals are thought to use only glucose polymers (glycogen) as energy reserve, whereas both glucose (starch) and fructose polymers (fructans) are used by microbes and plants. Here, it is reported that the gall midge Mayetiola destructor, and likely other herbivorous animal species, gained the ability to utilize dietary fructans directly as storage polysaccharides by a single horizontal gene transfer (HGT) of bacterial levanase/inulinase gene followed by gene expansion and differentiation. Multiple genes encoding levanases/inulinases have their origin in a single HGT event from a bacterium and they show high expression levels and enzymatic activities in different tissues of the gall midge, including nondigestive fat bodies and eggs, both of which contained significant amounts of fructans. This study provides evidence that animals can also use fructans as energy reserve by incorporating bacterial genes in their genomes.}, }
@article {pmid32291839, year = {2020}, author = {Huber, L and Giguère, S and Slovis, NM and Álvarez-Narváez, S and Hart, KA and Greiter, M and Morris, ERA and Cohen, ND}, title = {The novel and transferable erm(51) gene confers macrolides, lincosamides and streptogramins B (MLSB) resistance to clonal Rhodococcus equi in the environment.}, journal = {Environmental microbiology}, volume = {22}, number = {7}, pages = {2858-2869}, doi = {10.1111/1462-2920.15020}, pmid = {32291839}, issn = {1462-2920}, support = {//Grayson-Jockey Club Research Foundation/International ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; DNA Transposable Elements/genetics ; Drug Resistance, Bacterial/*genetics ; Farms ; Gene Transfer, Horizontal ; Genome, Bacterial/genetics ; Horses ; Lincosamides/pharmacology ; Macrolides/pharmacology ; Microbial Sensitivity Tests ; Plasmids/genetics ; Rhodococcus equi/*drug effects/*genetics ; Streptogramin B/pharmacology ; Streptogramin Group B/pharmacology ; Virginiamycin/pharmacology ; }, abstract = {The use of mass antimicrobial treatment has been linked to the emergence of antimicrobial resistance in human and animal pathogens. Using whole-genome single-molecule real-time (SMRT) sequencing, we characterized genomic variability of multidrug-resistant Rhodococcus equi isolated from soil samples from 100 farms endemic for R. equi infections in Kentucky. We discovered the novel erm(51)-encoding resistance to MLSB in R. equi isolates from soil of horse-breeding farms. Erm(51) is inserted in a transposon (TnErm51) that is associated with a putative conjugative plasmid (pRErm51), a mobilizable plasmid (pMobErm51), or both enabling horizontal gene transfer to susceptible organisms and conferring high levels of resistance against MLSB in vitro. This new resistant genotype also carries a previously unidentified rpoB mutation conferring resistance to rifampicin. Isolates carrying both vapA and erm(51) were rarely found, indicating either a recent acquisition of erm(51) and/or impaired survival when isolates carry both genes. Isolates carrying erm(51) are closely related genetically and were likely selected by antimicrobial exposure in the environment.}, }
@article {pmid32291353, year = {2020}, author = {Moulana, A and Anderson, RE and Fortunato, CS and Huber, JA}, title = {Selection Is a Significant Driver of Gene Gain and Loss in the Pangenome of the Bacterial Genus Sulfurovum in Geographically Distinct Deep-Sea Hydrothermal Vents.}, journal = {mSystems}, volume = {5}, number = {2}, pages = {}, pmid = {32291353}, issn = {2379-5077}, abstract = {Microbial genomes have highly variable gene content, and the evolutionary history of microbial populations is shaped by gene gain and loss mediated by horizontal gene transfer and selection. To evaluate the influence of selection on gene content variation in hydrothermal vent microbial populations, we examined 22 metagenome-assembled genomes (MAGs) (70 to 97% complete) from the ubiquitous vent Epsilonbacteraeota genus Sulfurovum that were recovered from two deep-sea hydrothermal vent regions, Axial Seamount in the northeastern Pacific Ocean (13 MAGs) and the Mid-Cayman Rise in the Caribbean Sea (9 MAGs). Genes involved in housekeeping functions were highly conserved across Sulfurovum lineages. However, genes involved in environment-specific functions, and in particular phosphate regulation, were found mostly in Sulfurovum genomes from the Mid-Cayman Rise in the low-phosphate Atlantic Ocean environment, suggesting that nutrient limitation is an important selective pressure for these bacteria. Furthermore, genes that were rare within the pangenome were more likely to undergo positive selection than genes that were highly conserved in the pangenome, and they also appeared to have experienced gene-specific sweeps. Our results suggest that selection is a significant driver of gene gain and loss for dominant microbial lineages in hydrothermal vents and highlight the importance of factors like nutrient limitation in driving microbial adaptation and evolution.IMPORTANCE Microbes can alter their gene content through the gain and loss of genes. However, there is some debate as to whether natural selection or neutral processes play a stronger role in molding the gene content of microbial genomes. In this study, we examined variation in gene content for the Epsilonbacteraeota genus Sulfurovum from deep-sea hydrothermal vents, which are dynamic habitats known for extensive horizontal gene transfer within microbial populations. Our results show that natural selection is a strong driver of Sulfurovum gene content and that nutrient limitation in particular has shaped the Sulfurovum genome, leading to differences in gene content between ocean basins. Our results also suggest that recently acquired genes undergo stronger selection than genes that were acquired in the more distant past. Overall, our results highlight the importance of natural selection in driving the evolution of microbial populations in these dynamic habitats.}, }
@article {pmid32285801, year = {2020}, author = {Evans, DR and Griffith, MP and Sundermann, AJ and Shutt, KA and Saul, MI and Mustapha, MM and Marsh, JW and Cooper, VS and Harrison, LH and Van Tyne, D}, title = {Systematic detection of horizontal gene transfer across genera among multidrug-resistant bacteria in a single hospital.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, pmid = {32285801}, issn = {2050-084X}, support = {R00 EY028222/EY/NEI NIH HHS/United States ; R01 AI127472/AI/NIAID NIH HHS/United States ; U01 AI124302/AI/NIAID NIH HHS/United States ; R21 AI109459/AI/NIAID NIH HHS/United States ; R01 AI127472/AI/NIAID NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Bacterial Infections/*genetics/*transmission ; Cross Infection/*genetics/*transmission ; Disease Transmission, Infectious ; Drug Resistance, Multiple, Bacterial/*genetics ; Female ; Gene Transfer, Horizontal/*genetics ; Hospitals ; Humans ; Interspersed Repetitive Sequences/genetics ; Male ; Middle Aged ; Plasmids/genetics ; Young Adult ; }, abstract = {Multidrug-resistant bacteria pose a serious health threat, especially in hospitals. Horizontal gene transfer (HGT) of mobile genetic elements (MGEs) facilitates the spread of antibiotic resistance, virulence, and environmental persistence genes between nosocomial pathogens. We screened the genomes of 2173 bacterial isolates from healthcare-associated infections from a single hospital over 18 months, and identified identical nucleotide regions in bacteria belonging to distinct genera. To further resolve these shared sequences, we performed long-read sequencing on a subset of isolates and generated highly contiguous genomes. We then tracked the appearance of ten different plasmids in all 2173 genomes, and found evidence of plasmid transfer independent from bacterial transmission. Finally, we identified two instances of likely plasmid transfer within individual patients, including one plasmid that likely transferred to a second patient. This work expands our understanding of HGT in healthcare settings, and can inform efforts to limit the spread of drug-resistant pathogens in hospitals.}, }
@article {pmid32283399, year = {2020}, author = {Zhang, WZ and Gao, JF and Duan, WJ and Zhang, D and Jia, JX and Wang, YW}, title = {Sulfidated nanoscale zero-valent iron is an efficient material for the removal and regrowth inhibition of antibiotic resistance genes.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {263}, number = {Pt B}, pages = {114508}, doi = {10.1016/j.envpol.2020.114508}, pmid = {32283399}, issn = {1873-6424}, mesh = {*Anti-Bacterial Agents ; Drug Resistance, Microbial ; Genes, Bacterial ; *Iron ; RNA, Ribosomal, 16S ; }, abstract = {Antibiotic resistance genes (ARGs) and mobile gene elements (MGEs), the emerging genetic contaminants, are regarded as severe risks to public health for impairing the inactivation efficacy of antibiotics. Secondary effluents from wastewater treatment plants are the hotspots for spreading these menaces. Herein, sulfidated nanoscale zero-valent iron (S-nZVI) was occupied to remove ARGs and MGEs in secondary effluents and weaken the regrowth capacity of their bacterial carriers. The effects of S/Fe molar ratios (S/Fe), initial pH and dosages on 16S rRNA and ARGs removal were also investigated. Characterization, mass balance and scavenging experiments were conducted to explore the mechanisms of the gene removal. Quantitative PCR (qPCR) and high throughput fluorescence qPCR showed more than 3 log unit of 16S rRNA and seven out of 10 ARGs existed in secondary effluent could be removed after S-nZVI treatment. The mechanisms might be that DNA accepted the electron provided by the Fe[0] core of S-nZVI after being adsorbed onto S-nZVI surface, causing the decrease of 16S rRNA, ARGs and lost their regrowth capacity, especially for typical MGE (intI1) and further inhibiting the vertical gene transfer (VGT) and intI1-induced horizontal gene transfer (HGT). Fe[0] core was oxidized to iron oxides and hydroxides at the same time. High throughput sequencing, network analysis and variation partitioning analysis revealed the complex correlations between bacteria and ARGs in secondary effluent, S/Fe could directly influence ARGs variations, and bacterial genera made the greatest contribution to ARGs variations, followed by MGEs and operational parameters. As a result, S-nZVI could be an available reductive approach to deal with bacteria and ARGs.}, }
@article {pmid32273397, year = {2020}, author = {Wang, H and Sun, S and Ge, W and Zhao, L and Hou, B and Wang, K and Lyu, Z and Chen, L and Xu, S and Guo, J and Li, M and Su, P and Li, X and Wang, G and Bo, C and Fang, X and Zhuang, W and Cheng, X and Wu, J and Dong, L and Chen, W and Li, W and Xiao, G and Zhao, J and Hao, Y and Xu, Y and Gao, Y and Liu, W and Liu, Y and Yin, H and Li, J and Li, X and Zhao, Y and Wang, X and Ni, F and Ma, X and Li, A and Xu, SS and Bai, G and Nevo, E and Gao, C and Ohm, H and Kong, L}, title = {Horizontal gene transfer of Fhb7 from fungus underlies Fusarium head blight resistance in wheat.}, journal = {Science (New York, N.Y.)}, volume = {368}, number = {6493}, pages = {}, doi = {10.1126/science.aba5435}, pmid = {32273397}, issn = {1095-9203}, mesh = {Cloning, Molecular ; Disease Resistance/*genetics ; Epichloe/*genetics ; Fusarium/*pathogenicity ; *Gene Transfer, Horizontal ; Glutathione Transferase/*genetics ; Plant Breeding ; Plant Diseases/*microbiology ; Poaceae/genetics ; Triticum/*genetics/*microbiology ; }, abstract = {Fusarium head blight (FHB), a fungal disease caused by Fusarium species that produce food toxins, currently devastates wheat production worldwide, yet few resistance resources have been discovered in wheat germplasm. Here, we cloned the FHB resistance gene Fhb7 by assembling the genome of Thinopyrum elongatum, a species used in wheat distant hybridization breeding. Fhb7 encodes a glutathione S-transferase (GST) and confers broad resistance to Fusarium species by detoxifying trichothecenes through de-epoxidation. Fhb7 GST homologs are absent in plants, and our evidence supports that Th. elongatum has gained Fhb7 through horizontal gene transfer (HGT) from an endophytic Epichloë species. Fhb7 introgressions in wheat confers resistance to both FHB and crown rot in diverse wheat backgrounds without yield penalty, providing a solution for Fusarium resistance breeding.}, }
@article {pmid32273343, year = {2020}, author = {Sheppard, D and Berry, JL and Denise, R and Rocha, EPC and Matthews, S and Pelicic, V}, title = {The major subunit of widespread competence pili exhibits a novel and conserved type IV pilin fold.}, journal = {The Journal of biological chemistry}, volume = {295}, number = {19}, pages = {6594-6604}, pmid = {32273343}, issn = {1083-351X}, support = {MR/P022197/1/MRC_/Medical Research Council/United Kingdom ; MR/P028225/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Fimbriae Proteins/*chemistry/genetics ; Fimbriae, Bacterial/*chemistry/genetics ; *Protein Folding ; Streptococcus pneumoniae/*chemistry/genetics ; Streptococcus sanguis/*chemistry/genetics ; }, abstract = {Type IV filaments (T4F), which are helical assemblies of type IV pilins, constitute a superfamily of filamentous nanomachines virtually ubiquitous in prokaryotes that mediate a wide variety of functions. The competence (Com) pilus is a widespread T4F, mediating DNA uptake (the first step in natural transformation) in bacteria with one membrane (monoderms), an important mechanism of horizontal gene transfer. Here, we report the results of genomic, phylogenetic, and structural analyses of ComGC, the major pilin subunit of Com pili. By performing a global comparative analysis, we show that Com pili genes are virtually ubiquitous in Bacilli, a major monoderm class of Firmicutes. This also revealed that ComGC displays extensive sequence conservation, defining a monophyletic group among type IV pilins. We further report ComGC solution structures from two naturally competent human pathogens, Streptococcus sanguinis (ComGCSS) and Streptococcus pneumoniae (ComGCSP), revealing that this pilin displays extensive structural conservation. Strikingly, ComGCSS and ComGCSP exhibit a novel type IV pilin fold that is purely helical. Results from homology modeling analyses suggest that the unusual structure of ComGC is compatible with helical filament assembly. Because ComGC displays such a widespread distribution, these results have implications for hundreds of monoderm species.}, }
@article {pmid32273005, year = {2020}, author = {Baron, S and Le Devendec, L and Lucas, P and Larvor, E and Jové, T and Kempf, I}, title = {Characterisation of plasmids harbouring extended-spectrum cephalosporin resistance genes in Escherichia coli from French rivers.}, journal = {Veterinary microbiology}, volume = {243}, number = {}, pages = {108619}, doi = {10.1016/j.vetmic.2020.108619}, pmid = {32273005}, issn = {1873-2542}, mesh = {Anti-Bacterial Agents/*pharmacology ; Cephalosporin Resistance/*genetics ; Escherichia coli/classification/*drug effects/*genetics ; France ; Gene Transfer, Horizontal ; Genetic Variation ; Multilocus Sequence Typing ; Plasmids/*genetics ; Rivers/*microbiology ; beta-Lactamases/genetics ; }, abstract = {Antimicrobial resistance is a "One Health" issue that requires improved knowledge of the presence and abundance of resistant bacteria in the environment. Extended-spectrum cephalosporins (ESCs) are critically important antibiotics (CIAs), and resistance to these CIAs is often encoded by beta-lactamase genes borne on conjugative plasmids. We thus decided to characterise 21 plasmids of ESC-resistant Escherichia coli randomly selected from isolates previously obtained from river water collected in a rural area in western France. The plasmids encoding ESC resistance were sequenced to investigate the diversity of the genes encoding ESC resistance and their genetic context. Sequences revealed that eleven IncI1 pMLST3 plasmids carried the blaCTX-M-1 and sul2 genes, and some of them also had the tet(A), aadA5 or dfrA17 genes. The blaCTX-M-1 gene was also detected on an IncN plasmid. Five plasmids obtained from four rivers contained blaCTX-M-14, either on IncI1 or on IncFII plasmids. Two strains from two rivers contained blaCTX-M-15 on IncN pMLST7 plasmids, with qnrS1 and dfrA14 genes. One plasmid contained the blaCTX-M-55, a blaTEM-1B-like, and fosA genes. One plasmid contained the blaCMY-2 gene. The diversity of the genes and plasmids of the resistant bacteria isolated from French rivers is probably related to the various animal and human origins of the isolated bacteria.}, }
@article {pmid32272070, year = {2020}, author = {Rosch, JW and Tuomanen, EI}, title = {Caging and COM-Bating Antibiotic Resistance.}, journal = {Cell host &amp; microbe}, volume = {27}, number = {4}, pages = {489-490}, doi = {10.1016/j.chom.2020.03.013}, pmid = {32272070}, issn = {1934-6069}, mesh = {Bacteria/genetics ; Drug Resistance, Microbial ; *Gene Transfer, Horizontal ; Plasmids ; *Proton-Motive Force ; }, abstract = {Horizontal gene transfer (HGT) facilitates spead of antibiotic resistance elements. In this issue of Cell Host &amp; Microbe, Domenech et al. discover that compounds disrupting proton motive force block natural competence (COM) and interrupt intraspecies HGT and exchange of antibiotic resistance. Such strategies might minimize clinical spread of antibiotic resistance.}, }
@article {pmid32271821, year = {2020}, author = {Li, Q and Zhang, Q}, title = {Prevalence and pollution characteristics of antibiotic resistant genes in one high anthropogenically-impacted river.}, journal = {PloS one}, volume = {15}, number = {4}, pages = {e0231128}, pmid = {32271821}, issn = {1932-6203}, mesh = {Anti-Bacterial Agents/analysis ; Biofilms ; China ; Drug Resistance, Microbial/*genetics ; Ecosystem ; Feces/microbiology ; Geography ; Geologic Sediments/chemistry ; *Human Activities ; Humans ; Prevalence ; RNA, Ribosomal, 16S/genetics ; *Rivers ; Water Pollutants, Chemical/analysis ; Water Pollution/*analysis ; }, abstract = {The objectives of this study were to comprehensively investigate the occurrence, distribution, and mobility of antibiotic resistant genes (ARGs) in the biofilm, water, and sediment from a section of the Weihe-river, in the northern Henan province, China. The abundances of nine ARGs belonging to four commonly used antibiotic classes (tetracyclines, sulfonamides, fluoroquinolones, and multidrug) and class 1 integron-integrase gene (intI1) were quantified. Sulfonamides gene (sulI) accounted for the highest percentage of detected ARGs in most sampling sites, including in water, biofilm, and sediment. Among the resistance genes, IntI1 and sul1 were significantly correlated (r>0.800, p<0.01) with a fecal coliform (FC) detected in the biofilm, and there was also a significantly positive correlation between the abundances of 16SrRNA and intI1 in the biofilms. Compared with the sediment and water samples, the biofilms contained sufficient nutrients to promote bacterial reproduction. Under sufficient total nitrogen and phosphorus concentrations, the horizontal gene transfer due to intI1 plays a key role in the formation and migration of ARGs within biofilms.}, }
@article {pmid32270947, year = {2020}, author = {Tekeli, A and Öcal, DN and Dolapçı, &#x130;}, title = {Detection of sasX Gene and Distribution of SCCmec Types in Invasive and Non-invasive Coagulase-negative Staphylococci.}, journal = {Balkan medical journal}, volume = {37}, number = {4}, pages = {215-221}, pmid = {32270947}, issn = {2146-3131}, mesh = {Coagulase/*analysis/blood/metabolism ; Cross-Sectional Studies ; Humans ; Microbial Sensitivity Tests/methods ; Staphylococcus/*genetics/isolation &amp; purification/*metabolism ; Staphylococcus capitis/genetics/isolation &amp; purification ; Staphylococcus epidermidis/genetics/isolation &amp; purification ; Staphylococcus haemolyticus/genetics/isolation &amp; purification ; Staphylococcus hominis/genetics/isolation &amp; purification ; Staphylococcus lugdunensis/genetics/isolation &amp; purification ; Staphylococcus saprophyticus/genetics/isolation &amp; purification ; }, abstract = {BACKGROUND: Coagulase-negative staphylococci, which belong to the normal microbiota of the skin and mucous membranes, are opportunistic pathogens. sasX, a newly described protein, is thought to play an important role in nasal colonization and methicillin-resistant Staphylococcus aureus virulence, and it may be acquired from coagulase-negative staphylococci by horizontal gene transfer. It has been considered that understanding the function of sasX gene may help clarify the relevance of the different adhesion mechanisms in the pathogenesis of infections associated with biofilm.<br><br>AIMS: To investigate the sasX gene presence, staphylococcal cassette chromosome mec types, and antimicrobial resistance patterns of invasive and noninvasive coagulase-negative staphylococci isolates.<br><br>STUDY DESIGN: Cross-sectional study.<br><br>METHODS: The study included a total of 180 coagulase-negative staphylococci strains. Non-invasive isolates (n=91) were obtained from the hands of healthy volunteers who do not work at the hospital (n=30), the nasal vestibule of healthy volunteer hospital workers (n=26), and central venous catheter (n=35). Invasive isolates (n=89) were isolated from peripheral blood cultures of inpatients who do not have catheters. All isolates were identified by conventional microbiological methods, automated systems, and, if needed, with matrix-assisted laser desorption/ionization-time of flight. Staphylococcal cassette chromosome mec typing, sasX and mec gene detection, antibiotic susceptibility, and sasX gene sequence analysis were performed.<br><br>RESULTS: Peripheral blood, central venous catheter colonization, and nasal vestibule isolates were positive for the sasX gene, whereas hand isolates were negative. sasX gene was present in 17 isolates, and no statistical significance was found between invasive and noninvasive isolates (p=0.173). Sequence analysis of the sasX genes showed high homology to related proteins of Staphylococcus phage SPbeta-like and Staphylococcus epidermidis RP62A. staphylococcal cassette chromosome mec type V was the most prevalent regardless of species. staphylococcal cassette chromosome mec type II was more frequent in invasive isolates and found to be statistically important for invasive and noninvasive S. epidermidis isolates (p=0.029). Staphylococcus haemolyticus isolates had the overall highest resistance rates. Resistance to ciprofloxacin, trimethoprim-sulfamethoxazole, and erythromycin was found to be higher in isolates from catheter and blood culture. Staphylococcus hominis isolates had the highest rate for inducible clindamycin resistance. None of the isolates were resistant to vancomycin, teicoplanin, and linezolid.<br><br>CONCLUSION: The sasX gene is detected in 9.44% of the isolates. There is no statistical difference between the sasX-positive and -negative isolates in terms of antibacterial resistance and the presence of sasX and SCCmec types. Further studies about the role of sasX at virulence in coagulase-negative staphylococci, especially from clinical samples such as tracheal aspirate and abscess isolates, and distribution of staphylococcal cassette chromosome mec types are needed.}, }
@article {pmid32269157, year = {2020}, author = {Drott, MT and Bastos, RW and Rokas, A and Ries, LNA and Gabaldón, T and Goldman, GH and Keller, NP and Greco, C}, title = {Diversity of Secondary Metabolism in Aspergillus nidulans Clinical Isolates.}, journal = {mSphere}, volume = {5}, number = {2}, pages = {}, pmid = {32269157}, issn = {2379-5042}, support = {R01 AI065728/AI/NIAID NIH HHS/United States ; R01 GM112739/GM/NIGMS NIH HHS/United States ; T32 ES007015/ES/NIEHS NIH HHS/United States ; }, mesh = {Aspergillosis/*microbiology ; Aspergillus nidulans/*genetics/*metabolism ; Fungal Proteins/genetics ; Gene Expression Regulation, Fungal ; Gene Transfer, Horizontal ; Genetic Variation ; Genome, Fungal ; *Multigene Family ; Mutation ; *Secondary Metabolism ; Sterigmatocystin/biosynthesis ; }, abstract = {The filamentous fungus Aspergillus nidulans has been a primary workhorse used to understand fungal genetics. Much of this work has focused on elucidating the genetics of biosynthetic gene clusters (BGCs) and the secondary metabolites (SMs) they produce. SMs are both niche defining in fungi and of great economic importance to humans. Despite the focus on A. nidulans, very little is known about the natural diversity in secondary metabolism within this species. We determined the BGC content and looked for evolutionary patterns in BGCs from whole-genome sequences of two clinical isolates and the A4 reference genome of A. nidulans Differences in BGC content were used to explain SM profiles determined using liquid chromatography-high-resolution mass spectrometry. We found that in addition to genetic variation of BGCs contained by all isolates, nine BGCs varied by presence/absence. We discovered the viridicatumtoxin BGC in A. nidulans and suggest that this BGC has undergone a horizontal gene transfer from the Aspergillus section Nigri lineage into Penicillium sometime after the sections Nigri and Nidulantes diverged. We identified the production of viridicatumtoxin and several other compounds previously not known to be produced by A. nidulans One isolate showed a lack of sterigmatocystin production even though it contained an apparently intact sterigmatocystin BGC, raising questions about other genes and processes known to regulate this BGC. Altogether, our work uncovers a large degree of intraspecies diversity in BGC and SM production in this genetic model species and offers new avenues to understand the evolution and regulation of secondary metabolism.IMPORTANCE Much of what we know about the genetics underlying secondary metabolite (SM) production and the function of SMs in the model fungus Aspergillus nidulans comes from a single reference genome. A growing body of research indicates the importance of biosynthetic gene cluster (BGC) and SM diversity within a species. However, there is no information about the natural diversity of secondary metabolism in A. nidulans We discovered six novel clusters that contribute to the considerable variation in both BGC content and SM production within A. nidulans We characterize a diverse set of mutations and emphasize how findings of single nucleotide polymorphisms (SNPs), deletions, and differences in evolutionary history encompass much of the variation observed in nonmodel systems. Our results emphasize that A. nidulans may also be a strong model to use within-species diversity to elucidate regulatory cross talk, fungal ecology, and drug discovery systems.}, }
@article {pmid32269153, year = {2020}, author = {Hashimoto, Y and Kita, I and Suzuki, M and Hirakawa, H and Ohtaki, H and Tomita, H}, title = {First Report of the Local Spread of Vancomycin-Resistant Enterococci Ascribed to the Interspecies Transmission of a vanA Gene Cluster-Carrying Linear Plasmid.}, journal = {mSphere}, volume = {5}, number = {2}, pages = {}, pmid = {32269153}, issn = {2379-5042}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics ; Carbon-Oxygen Ligases/*genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Electrophoresis, Gel, Pulsed-Field ; Enterococcus/genetics ; Enterococcus faecium/genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Gram-Positive Bacterial Infections/microbiology ; Humans ; Microbial Sensitivity Tests ; *Multigene Family ; Plasmids/*genetics ; Vancomycin Resistance/*genetics ; Vancomycin-Resistant Enterococci/classification/*genetics/pathogenicity ; Whole Genome Sequencing ; }, abstract = {Vancomycin-resistant enterococci pose a threat in the clinical setting and have been linked to hospital outbreaks worldwide. In 2017, a local spread of VanA-type vancomycin-resistant enterococci (VRE) occurred in Japan, and 25 enterococcal isolates, including 14 Enterococcus faecium, 8 E. raffinosus, and 3 E. casseliflavus isolates, were identified from four inpatients. Molecular analysis of the multispecies of VanA-type VRE revealed the involvement of both the dissemination of clonally related VRE strains between patients and the horizontal transfer of plasmids harboring the vanA gene cluster between Enterococcus spp. Pulsed-field gel electrophoresis showed that the plasmid DNAs without S1 nuclease treatment were able to migrate into the gel, suggesting that the topology of the plasmid was linear. Whole-genome sequencing revealed that this plasmid, designated pELF2, was 108,102 bp long and encoded multiple antimicrobial resistance genes, including ermA and ant(9). The amino acid sequences of putative replication- and transfer-related genes were highly conserved between pELF2 and pELF1, the latter of which was the first identified enterococcal conjugative linear plasmid. On comparing the genomic structure, pELF2 showed the presence of a backbone similar to that of pELF1, especially with respect to the nucleotide sequences of both terminal ends, indicating a hybrid-type linear plasmid, possessing two different terminal structures. pELF2 possessed a broad host range and high conjugation frequencies for enterococci. The easy transfer of pELF2 to different Enterococcus spp. in vitro might explain this local spread of multiple species, highlighting the clinical threat from the spread of antimicrobial resistance by an enterococcal linear plasmid.IMPORTANCE Increasing multidrug resistance, including vancomycin resistance, in enterococci is a major concern in clinical settings. Horizontal gene transfer, such as via plasmids, has been shown to play a crucial role in the acquisition of vancomycin resistance. Among vancomycin resistance types, the VanA type is one of the most prevalent, and outbreaks caused by VanA-type vancomycin-resistant enterococci (VRE) have occurred worldwide. Here, we describe an enterococcal linear plasmid responsible for multispecies local spread of VanA-type VRE. Such a study is important because although hospital outbreaks caused by mixed enterococcal species have been reported, this particular spread indicates plasmid transfer across species. This is a crucial finding because the high risk for such a spread of antimicrobial resistance calls for regular monitoring and surveillance.}, }
@article {pmid32260256, year = {2020}, author = {Vergara, E and Neira, G and González, C and Cortez, D and Dopson, M and Holmes, DS}, title = {Evolution of Predicted Acid Resistance Mechanisms in the Extremely Acidophilic Leptospirillum Genus.}, journal = {Genes}, volume = {11}, number = {4}, pages = {}, pmid = {32260256}, issn = {2073-4425}, mesh = {Acids/metabolism/*toxicity ; Bacteria/*genetics/metabolism ; Ferric Compounds/metabolism ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/drug effects/*genetics ; *Genomics ; Hydrogen-Ion Concentration ; Iron/metabolism ; Phylogeny ; }, abstract = {Organisms that thrive in extremely acidic environments (≤pH 3.5) are of widespread importance in industrial applications, environmental issues, and evolutionary studies. Leptospirillum spp. constitute the only extremely acidophilic microbes in the phylogenetically deep-rooted bacterial phylum Nitrospirae. Leptospirilli are Gram-negative, obligatory chemolithoautotrophic, aerobic, ferrous iron oxidizers. This paper predicts genes that Leptospirilli use to survive at low pH and infers their evolutionary trajectory. Phylogenetic and other bioinformatic approaches suggest that these genes can be classified into (i) "first line of defense", involved in the prevention of the entry of protons into the cell, and (ii) neutralization or expulsion of protons that enter the cell. The first line of defense includes potassium transporters, predicted to form an inside positive membrane potential, spermidines, hopanoids, and Slps (starvation-inducible outer membrane proteins). The "second line of defense" includes proton pumps and enzymes that consume protons. Maximum parsimony, clustering methods, and gene alignments are used to infer the evolutionary trajectory that potentially enabled the ancestral Leptospirillum to transition from a postulated circum-neutral pH environment to an extremely acidic one. The hypothesized trajectory includes gene gains/loss events driven extensively by horizontal gene transfer, gene duplications, gene mutations, and genomic rearrangements.}, }
@article {pmid32256483, year = {2020}, author = {Guerrero-Garzón, JF and Zehl, M and Schneider, O and Rückert, C and Busche, T and Kalinowski, J and Bredholt, H and Zotchev, SB}, title = {Streptomyces spp. From the Marine Sponge Antho dichotoma: Analyses of Secondary Metabolite Biosynthesis Gene Clusters and Some of Their Products.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {437}, pmid = {32256483}, issn = {1664-302X}, abstract = {Actinomycete bacteria from marine environments represent a potential source for new antibiotics and anti-tumor drugs. Ten strains belonging to the genus Streptomyces isolated from the marine sponge Antho dichotoma collected at the bottom of the Trondheim fjord (Norway) were screened for antibiotic activity. Since only few isolates proved to be bioactive in the conditions tested, we decided to gain an insight into their biosynthetic potential using genome sequencing and analysis. Draft genomes were analyzed for the presence of secondary metabolite biosynthesis gene clusters (BGCs) using antiSMASH software. BGCs specifying both known and potentially novel secondary metabolites were identified, suggesting that these isolates might be sources for new bioactive compounds. The results of this analysis also implied horizontal transfer of several gene clusters between the studied isolates, which was especially evident for the lantibiotic- and thiopeptide-encoding BGCs. The latter implies the significance of particular secondary metabolites for the adaptation of Streptomyces to the spatially enclosed marine environments such as marine sponges. Two bioactive isolates, one showing activity against both yeast and Bacillus subtilis, and one only against yeast were analyzed in details, leading to the identification of cycloheximide, linearmycins, and echinomycins that are presumably responsible for the observed bioactivities.}, }
@article {pmid32255846, year = {2020}, author = {Dafale, NA and Srivastava, S and Purohit, HJ}, title = {Zoonosis: An Emerging Link to Antibiotic Resistance Under "One Health Approach".}, journal = {Indian journal of microbiology}, volume = {60}, number = {2}, pages = {139-152}, pmid = {32255846}, issn = {0046-8991}, abstract = {Current scenario in communicable diseases has generated new era that identifies the "One health" approach to understand the sharing and management of etiological agents with its impact on ecosystem. Under this context the relevance of zoonotic diseases generates major concern. The indiscriminate and higher use of antibiotics in animal husbandry creates substantial pressure on the gut microbiome for development of resistance due to shorter generation time and high density. Thus, gut works as a bioreactor for the breeding of ARBs in this scenario and are continuously released in different niches. These ARBs transfer resistance genes among native flora through horizontal gene transfer events, vectors and quorum sensing. About 60% of infectious diseases in human are caused by zoonotic pathogens have potential to carry ARGs which could be transmitted to humans. The well documented zoonotic diseases are anthrax cause by Bacillus anthracis, bovine tuberculosis by Mycobacterium tuberculosis, brucellosis by Brucella abortus, and hemorrhagic colitis by Escherichia coli. Similarly, most of the antibiotics are not completely metabolized and released in unmetabolized forms which enters the food chain and affect various ecological niches through bioaccumulation. The persistence period of antibiotics ranges from < 1 to 3466 days in environment. The consequences of misusing the antibiotic in livestock and their fate in various ecological niches have been discussed in this review. Further the light sheds on antibiotics persistence and it biodegradation through different abiotic and biotic approaches in environment. The knowledge on personnel hygiene and strong surveillance system for zoonotic disease including ARBs transmission, prevention and control measures should be established to regulate the spread of AMR in the environment and subsequently to the human being through a food web.}, }
@article {pmid32253194, year = {2020}, author = {Arlt, MF and Brogley, MA and Stark-Dykema, ER and Hu, YC and Mueller, JL}, title = {Genomic Structure, Evolutionary Origins, and Reproductive Function of a Large Amplified Intrinsically Disordered Protein-Coding Gene on the X Chromosome (Laidx) in Mice.}, journal = {G3 (Bethesda, Md.)}, volume = {10}, number = {6}, pages = {1997-2005}, pmid = {32253194}, issn = {2160-1836}, support = {R01 HD094736/HD/NICHD NIH HHS/United States ; }, mesh = {Animals ; Genomics ; *Intrinsically Disordered Proteins ; Male ; Mice ; Rats ; Spermatids ; X Chromosome/genetics ; Y Chromosome/genetics ; }, abstract = {Mouse sex chromosomes are enriched for co-amplified gene families, present in tens to hundreds of copies. Co-amplification of Slx/Slxl1 on the X chromosome and Sly on the Y chromosome are involved in dose-dependent meiotic drive, however the role of other co-amplified genes remains poorly understood. Here we demonstrate that the co-amplified gene family on the X chromosome, Srsx, along with two additional partial gene annotations, is actually part of a larger transcription unit, which we name LaidxLaidx is harbored in a 229 kb amplicon that represents the ancestral state as compared to a 525 kb Y-amplicon containing the rearranged LaidyLaidx contains a 25,011 nucleotide open reading frame, predominantly expressed in round spermatids, predicted to encode an 871 kD protein. Laidx has orthologous copies with the rat and also the 825-MY diverged parasitic Chinese liver fluke, Clonorchis sinensis, the likely result of a horizontal gene transfer of rodent Laidx to an ancestor of the liver fluke. To assess the male reproductive functions of Laidx, we generated mice carrying a multi-megabase deletion of the Laidx-ampliconic region. Laidx-deficient male mice do not show detectable reproductive defects in fertility, fecundity, testis histology, and offspring sex ratio. We speculate that Laidx and Laidy represent a now inactive X vs. Y chromosome conflict that occurred in an ancestor of present day mice.}, }
@article {pmid32251355, year = {2020}, author = {Oghenekaro, AO and Kovalchuk, A and Raffaello, T and Camarero, S and Gressler, M and Henrissat, B and Lee, J and Liu, M and Martínez, AT and Miettinen, O and Mihaltcheva, S and Pangilinan, J and Ren, F and Riley, R and Ruiz-Dueñas, FJ and Serrano, A and Thon, MR and Wen, Z and Zeng, Z and Barry, K and Grigoriev, IV and Martin, F and Asiegbu, FO}, title = {Genome sequencing of Rigidoporus microporus provides insights on genes important for wood decay, latex tolerance and interspecific fungal interactions.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {5250}, pmid = {32251355}, issn = {2045-2322}, mesh = {Cell Wall/metabolism/microbiology ; Enzymes/genetics/metabolism ; Fungal Proteins/*genetics ; Gene Expression Regulation, Fungal ; Gene Transfer, Horizontal ; Genome, Fungal ; Host-Pathogen Interactions/genetics ; Latex/*metabolism ; Microbial Interactions/genetics ; Phylogeny ; Polyporales/*genetics/metabolism/*pathogenicity ; Secondary Metabolism ; Wood/metabolism/*microbiology ; }, abstract = {Fungal plant pathogens remain a serious threat to the sustainable agriculture and forestry, despite the extensive efforts undertaken to control their spread. White root rot disease is threatening rubber tree (Hevea brasiliensis) plantations throughout South and Southeast Asia and Western Africa, causing tree mortality and severe yield losses. Here, we report the complete genome sequence of the basidiomycete fungus Rigidoporus microporus, a causative agent of the disease. Our phylogenetic analysis confirmed the position of R. microporus among the members of Hymenochaetales, an understudied group of basidiomycetes. Our analysis further identified pathogen's genes with a predicted role in the decay of plant cell wall polymers, in the utilization of latex components and in interspecific interactions between the pathogen and other fungi. We also detected putative horizontal gene transfer events in the genome of R. microporus. The reported first genome sequence of a tropical rubber tree pathogen R. microporus should contribute to the better understanding of how the fungus is able to facilitate wood decay and nutrient cycling as well as tolerate latex and utilize resinous extractives.}, }
@article {pmid32249619, year = {2020}, author = {Redfern, J and Enright, MC}, title = {Further understanding of Pseudomonas aeruginosa's ability to horizontally acquire virulence: possible intervention strategies.}, journal = {Expert review of anti-infective therapy}, volume = {18}, number = {6}, pages = {539-549}, doi = {10.1080/14787210.2020.1751610}, pmid = {32249619}, issn = {1744-8336}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Multiple, Bacterial ; Gene Transfer, Horizontal ; Humans ; Pseudomonas Infections/*drug therapy/microbiology ; Pseudomonas aeruginosa/drug effects/genetics/*pathogenicity ; Quorum Sensing ; Virulence ; }, abstract = {Introduction: Pseudomonas aeruginosa is a common, ubiquitous bacterium that is found in natural environments but is also a successful opportunistic pathogen of humans and plants. The reasons for this flexibility and evolutionary success can be attributed to its ability to readily acquire new genes to ensure its survival enabling it to survive desiccation, the action of antimicrobial compounds and invade new territories such as modern hospitals with high levels of antibiotic usage.Areas covered: Literature was searched using PubMed and Web of science (05/19 to 05/20). Identified studies paint a picture of a dynamic, highly variable population shaped by frequent intra- and inter-species horizontal gene transfer resulting in a species able to resist the action of antibiotics and deploy multiple virulence strategies controlled by complex quorum-sensing systems. We investigate possible control measures including anti-virulence and environmental control measures.Expert opinion: P.aeruginosa is a resilient, richly diverse species but also a global health threat due to the emergence and global dissemination of successful multiresistant clones that resist all antibiotics. Genomics offers the potential for rapid identification of 'high-risk' clones to guide chemotherapy, but novel control measures are also required to slow the species progression to pan-resistance.}, }
@article {pmid32249276, year = {2020}, author = {Holt, KE and Lassalle, F and Wyres, KL and Wick, R and Mostowy, RJ}, title = {Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales.}, journal = {The ISME journal}, volume = {14}, number = {7}, pages = {1713-1730}, pmid = {32249276}, issn = {1751-7370}, support = {MR/N010760/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Enterobacter ; Enterobacteriaceae/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; }, abstract = {Bacterial capsules and lipopolysaccharides are diverse surface polysaccharides (SPs) that serve as the frontline for interactions with the outside world. While SPs can evolve rapidly, their diversity and evolutionary dynamics across different taxonomic scales has not been investigated in detail. Here, we focused on the bacterial order Enterobacteriales (including the medically relevant Enterobacteriaceae), to carry out comparative genomics of two SP locus synthesis regions, cps and kps, using 27,334 genomes from 45 genera. We identified high-quality cps loci in 22 genera and kps in 11 genera, around 4% of which were detected in multiple species. We found SP loci to be highly dynamic genetic entities: their evolution was driven by high rates of horizontal gene transfer (HGT), both of whole loci and component genes, and relaxed purifying selection, yielding large repertoires of SP diversity. In spite of that, we found the presence of (near-)identical locus structures in distant taxonomic backgrounds that could not be explained by recent exchange, pointing to long-term selective preservation of locus structures in some populations. Our results reveal differences in evolutionary dynamics driving SP diversity within different bacterial species, with lineages of Escherichia coli, Enterobacter hormaechei and Klebsiella aerogenes most likely to share SP loci via recent exchange; and lineages of Salmonella enterica, Citrobacter sakazakii and Serratia marcescens most likely to share SP loci via other mechanisms such as long-term preservation. Overall, the evolution of SP loci in Enterobacteriales is driven by a range of evolutionary forces and their dynamics and relative importance varies between different species.}, }
@article {pmid32248555, year = {2020}, author = {Preena, PG and Swaminathan, TR and Rejish Kumar, VJ and Bright Singh, IS}, title = {Unravelling the menace: detection of antimicrobial resistance in aquaculture.}, journal = {Letters in applied microbiology}, volume = {71}, number = {1}, pages = {26-38}, doi = {10.1111/lam.13292}, pmid = {32248555}, issn = {1472-765X}, support = {PDF/2017/000378//Science and Engineering Board (SERB) Department of Science and Technology (DST)/ ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Aquaculture ; Bacteria/*drug effects/genetics ; Bacterial Infections/drug therapy/veterinary ; Drug Resistance, Bacterial/*genetics ; Fish Diseases/*microbiology ; Fishes/*microbiology ; Gene Transfer, Horizontal ; Integrons/genetics ; Plasmids/genetics ; Prescription Drug Overuse ; }, abstract = {One of the major problems to be addressed in aquaculture is the prominence of antimicrobial resistance (AMR). The occurrence of bacterial infections in cultured fishes promotes the continuous use of antibiotics in aquaculture, which results in the selection of proliferated antibiotic-resistant bacteria and increases the possibility of transfer to the whole environment through horizontal gene transfer. Hence, the accurate cultivation-dependent and cultivation-independent detection methods are very much crucial for the immediate and proper management of this menace. Antimicrobial resistance determinants carrying mobile genetic transfer elements such as transposons, plasmids, integrons and gene cassettes need to be specifically analysed through molecular detection techniques. The susceptibility of microbes to antibiotics should be tested at regular intervals along with various biochemical assays and conjugation studies so as to determine the extent of spread of AMR. Advanced omic-based and bioinformatic tools can also be incorporated for understanding of genetic diversity. The present review focuses on different detection methods to unearth the complexity of AMR in aquaculture. This monitoring helps the authorities to curb the use of antibiotics, commencement of appropriate management measures and adequate substitute strategies in aquaculture. The long battle of AMR could be overcome by the sincere implementation of One Health approach. SIGNIFICANCE AND IMPACT OF THE STUDY: The use of antibiotics and increased antimicrobial resistance (AMR) are of major concerns in aquaculture industry. This could result in global health risks through direct consumption of cultured fishes and dissemination of AMR to natural environment through horizontal gene transfer. Hence, timely detection of the antimicrobial-resistant pathogens and continuous monitoring programmes are inevitable. Advanced microbiological, molecular biological and omic-based tools can unravel the menace to a great extent. This will help the authorities to curb the use of antibiotics and implement appropriate management measures to overcome the threat.}, }
@article {pmid32246084, year = {2020}, author = {Chelkha, N and Hasni, I and Louazani, AC and Levasseur, A and La Scola, B and Colson, P}, title = {Vermamoeba vermiformis CDC-19 draft genome sequence reveals considerable gene trafficking including with candidate phyla radiation and giant viruses.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {5928}, pmid = {32246084}, issn = {2045-2322}, mesh = {Amoeba/classification/*genetics/microbiology ; Bacteria/*genetics ; Base Sequence/genetics ; DNA Barcoding, Taxonomic ; Disease Resistance/genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Genes, Viral/genetics ; Genome, Protozoan/*genetics ; Giant Viruses/*genetics ; Humans ; Phylogeny ; Sequence Homology ; }, abstract = {Vermamoeba vermiformis is a predominant free-living amoeba in human environments and amongst the most common amoebae that can cause severe infections in humans. It is a niche for numerous amoeba-resisting microorganisms such as bacteria and giant viruses. Differences in the susceptibility to these giant viruses have been observed. V. vermiformis and amoeba-resisting microorganisms share a sympatric lifestyle that can promote exchanges of genetic material. This work analyzed the first draft genome sequence of a V. vermiformis strain (CDC-19) through comparative genomic, transcriptomic and phylogenetic analyses. The genome of V. vermiformis is 59.5 megabase pairs in size, and 22,483 genes were predicted. A high proportion (10% (n = 2,295)) of putative genes encoded proteins showed the highest sequence homology with a bacterial sequence. The expression of these genes was demonstrated for some bacterial homologous genes. In addition, for 30 genes, we detected best BLAST hits with members of the Candidate Phyla Radiation. Moreover, 185 genes (0.8%) best matched with giant viruses, mostly those related to the subfamily Klosneuvirinae (101 genes), in particular Bodo saltans virus (69 genes). Lateral sequence transfers between V. vermiformis and amoeba-resisting microorganisms were strengthened by Sanger sequencing, transcriptomic and phylogenetic analyses. This work provides important insights and genetic data for further studies about this amoeba and its interactions with microorganisms.}, }
@article {pmid32245943, year = {2020}, author = {Taton, A and Erikson, C and Yang, Y and Rubin, BE and Rifkin, SA and Golden, JW and Golden, SS}, title = {The circadian clock and darkness control natural competence in cyanobacteria.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {1688}, pmid = {32245943}, issn = {2041-1723}, support = {R01 GM118815/GM/NIGMS NIH HHS/United States ; R35 GM118290/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Physiological/genetics ; Bacterial Proteins/genetics/metabolism ; Circadian Clocks/*physiology ; Circadian Rhythm Signaling Peptides and Proteins/genetics/metabolism ; DNA Transposable Elements/genetics ; Darkness ; Fimbriae, Bacterial/*metabolism ; Gene Expression Regulation, Bacterial/physiology ; Gene Transfer, Horizontal ; Models, Biological ; Mutation ; Seasons ; Synechococcus/*physiology ; Transcription Factors/metabolism ; Transformation, Bacterial/*physiology ; }, abstract = {The cyanobacterium Synechococcus elongatus is a model organism for the study of circadian rhythms. It is naturally competent for transformation-that is, it takes up DNA from the environment, but the underlying mechanisms are unclear. Here, we use a genome-wide screen to identify genes required for natural transformation in S. elongatus, including genes encoding a conserved Type IV pilus, genes known to be associated with competence in other bacteria, and others. Pilus biogenesis occurs daily in the morning, while natural transformation is maximal when the onset of darkness coincides with the dusk circadian peak. Thus, the competence state in cyanobacteria is regulated by the circadian clock and can adapt to seasonal changes of day length.}, }
@article {pmid32245640, year = {2020}, author = {Wu, D and Wang, H and Zhu, F and Jiang, S and Sun, L and Zhao, F and Yu, Y and Chen, Y}, title = {Characterization of an ST5-SCCmec II-t311 methicillin-resistant Staphylococcus aureus strain with a widespread cfr-positive plasmid.}, journal = {Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy}, volume = {26}, number = {7}, pages = {699-705}, doi = {10.1016/j.jiac.2020.02.018}, pmid = {32245640}, issn = {1437-7780}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology/therapeutic use ; Bacterial Proteins/genetics/isolation &amp; purification ; China/epidemiology ; Gene Transfer, Horizontal ; Genetic Variation ; Genome, Bacterial/genetics ; Genomic Islands/genetics ; Humans ; Methicillin/pharmacology/therapeutic use ; Methicillin Resistance/*genetics ; Methicillin-Resistant Staphylococcus aureus/drug effects/*genetics/isolation &amp; purification/pathogenicity ; Mutation ; Plasmids/*genetics/isolation &amp; purification ; Staphylococcal Infections/*drug therapy/epidemiology/microbiology/veterinary ; Staphylococcus/genetics/isolation &amp; purification/pathogenicity ; Swine/microbiology ; Virulence Factors/genetics ; }, abstract = {PURPOSE: To determine the genetic characteristics of the Chinese epidemic ST5-SCCmec II-t311 methicillin-resistant Staphylococcus aureus (MRSA) clone and to investigate the transmission characteristics of the cfr-positive plasmid.<br><br>METHODS: The complete genome of SR153 was sequenced. Genomic comparison with MRSA strains of other lineages was performed. The cfr-positive plasmid was investigated and compared with other cfr-positive plasmids from different origins and different areas.<br><br>RESULTS: The cfr-positive MRSA strain SR153 was a Chinese epidemic ST5-SCCmec II-t311 strain. It clustered much closer to the Japanese ST5-SCCmec II clone than to the European and American ST5-SCCmec II clones. The genome of SR153 contains one circular chromosome and three plasmids. It harbors the genomic islands &#x3bd;Sa&#x3b1;, &#x3bd;Sa&#x3b2;, &#x3bd;Sa&#x3b3;, &#x3a6;Sa1 and &#x3a6;Sa3, the pathogenicity island &#x3bd;Sa4, and genes encoding virulence factors such as tst and many enterotoxins. The SR153 genome also contains several resistance genes and mutations, such as ermA, aadD, spc, aacA-aphD, lnuA, tetK, blaZ and mutations in grlA and gyrA. SR153 harbors a cfr-positive plasmid, pSR01, which is highly similar to pSX01 from a Staphylococcus xylosus of pig origin from Henan Province. pSR01 was also highly similar to pXWZ from a Staphylococcus capitis and pLRSA417 from S.&#xa0;aureus. Both were obtained from geographically separated hospitals in Zhejiang Province.<br><br>CONCLUSIONS: SR153, which clustered closely to the Japanese ST5-SCCmec II clone, is more resistant than N315. A pSR01-like cfr-positive plasmid was widespread among different Staphylococcus species of both human and animal origin in different hospitals and areas.}, }
@article {pmid32239586, year = {2020}, author = {Lan, N and Perlatti, B and Kvitek, DJ and Wiemann, P and Harvey, CJB and Frisvad, J and An, Z and Bills, GF}, title = {Acrophiarin (antibiotic S31794/F-1) from Penicillium arenicola shares biosynthetic features with both Aspergillus- and Leotiomycete-type echinocandins.}, journal = {Environmental microbiology}, volume = {22}, number = {6}, pages = {2292-2311}, pmid = {32239586}, issn = {1462-2920}, support = {R01 GM121458/GM/NIGMS NIH HHS/United States ; //Ben and Kay Fortson Endowment/International ; }, mesh = {Anti-Infective Agents/*metabolism ; *Ascomycota/genetics ; *Aspergillus/genetics ; *Echinocandins/biosynthesis/genetics ; *Lipopeptides/biosynthesis/genetics ; Multigene Family ; *Penicillium/genetics ; }, abstract = {The antifungal echinocandin lipopeptide, acrophiarin, was circumscribed in a patent in 1979. We confirmed that the producing strain NRRL 8095 is Penicillium arenicola and other strains of P. arenicola produced acrophiarin and acrophiarin analogues. Genome sequencing of NRRL 8095 identified the acrophiarin gene cluster. Penicillium arenicola and echinocandin-producing Aspergillus species belong to the family Aspergillaceae of the Eurotiomycetes, but several features of acrophiarin and its gene cluster suggest a closer relationship with echinocandins from Leotiomycete fungi. These features include hydroxy-glutamine in the peptide core instead of a serine or threonine residue, the inclusion of a non-heme iron, α-ketoglutarate-dependent oxygenase for hydroxylation of the C3 of the glutamine, and a thioesterase. In addition, P. arenicola bears similarity to Leotiomycete echinocandin-producing species because it exhibits self-resistance to exogenous echinocandins. Phylogenetic analysis of the genes of the echinocandin biosynthetic family indicated that most of the predicted proteins of acrophiarin gene cluster exhibited higher similarity to the predicted proteins of the pneumocandin gene cluster of the Leotiomycete Glarea lozoyensis than to those of the echinocandin B gene cluster from A. pachycristatus. The fellutamide gene cluster and related gene clusters are recognized as relatives of the echinocandins. Inclusion of the acrophiarin gene cluster into a comprehensive phylogenetic analysis of echinocandin gene clusters indicated the divergent evolutionary lineages of echinocandin gene clusters are descendants from a common ancestral progenitor. The minimal 10-gene cluster may have undergone multiple gene acquisitions or losses and possibly horizontal gene transfer after the ancestral separation of the two lineages.}, }
@article {pmid32236187, year = {2020}, author = {Cunningham, CJ and Kuyukina, MS and Ivshina, IB and Konev, AI and Peshkur, TA and Knapp, CW}, title = {Potential risks of antibiotic resistant bacteria and genes in bioremediation of petroleum hydrocarbon contaminated soils.}, journal = {Environmental science. Processes &amp; impacts}, volume = {22}, number = {5}, pages = {1110-1124}, doi = {10.1039/c9em00606k}, pmid = {32236187}, issn = {2050-7895}, mesh = {*Anti-Bacterial Agents ; Bacteria ; Biodegradation, Environmental ; *Drug Resistance, Bacterial/genetics ; Hydrocarbons ; *Petroleum ; Soil ; Soil Microbiology ; *Soil Pollutants ; }, abstract = {Bioremediation represents a sustainable approach to remediating petroleum hydrocarbon contaminated soils. One aspect of sustainability includes the sourcing of nutrients used to stimulate hydrocarbon-degrading microbial populations. Organic nutrients such as animal manure and sewage sludge may be perceived as more sustainable than conventional inorganic fertilizers. However, organic nutrients often contain antibiotic residues and resistant bacteria (along with resistance genes and mobile genetic elements). This is further exacerbated since antibiotic resistant bacteria may become more abundant in contaminated soils due to co-selection pressures from pollutants such as metals and hydrocarbons. We review the issues surrounding bioremediation of petroleum-hydrocarbon contaminated soils, as an example, and consider the potential human-health risks from antibiotic resistant bacteria. While awareness is coming to light, the relationship between contaminated land and antibiotic resistance remains largely under-explored. The risk of horizontal gene transfer between soil microorganisms, commensal bacteria and/or human pathogens needs to be further elucidated, and the environmental triggers for gene transfer need to be better understood. Findings of antibiotic resistance from animal manures are emerging, but even fewer bioremediation studies using sewage sludge have made any reference to antibiotic resistance. Resistance mechanisms, including those to antibiotics, have been considered by some authors to be a positive trait associated with resilience in strains intended for bioremediation. Nevertheless, recognition of the potential risks associated with antibiotic resistant bacteria and genes in contaminated soils appears to be increasing and requires further investigation. Careful selection of bacterial candidates for bioremediation possessing minimal antibiotic resistance as well as pre-treatment of organic wastes to reduce selective pressures (e.g., antibiotic residues) are suggested to prevent environmental contamination with antibiotic-resistant bacteria and genes.}, }
@article {pmid32234815, year = {2020}, author = {Lima-Mendez, G and Oliveira Alvarenga, D and Ross, K and Hallet, B and Van Melderen, L and Varani, AM and Chandler, M}, title = {Toxin-Antitoxin Gene Pairs Found in Tn3 Family Transposons Appear To Be an Integral Part of the Transposition Module.}, journal = {mBio}, volume = {11}, number = {2}, pages = {}, pmid = {32234815}, issn = {2150-7511}, mesh = {Bacteria/classification/*genetics ; *DNA Transposable Elements ; Gene Expression Regulation, Bacterial ; Gene Order ; Genes, Bacterial ; Models, Biological ; *Multigene Family ; Phylogeny ; Promoter Regions, Genetic ; Recombination, Genetic ; Toxin-Antitoxin Systems/*genetics ; }, abstract = {Much of the diversity of prokaryotic genomes is contributed by the tightly controlled recombination activity of transposons (Tns). The Tn3 family is arguably one of the most widespread transposon families. Members carry a large range of passenger genes incorporated into their structures. Family members undergo replicative transposition using a DDE transposase to generate a cointegrate structure which is then resolved by site-specific recombination between specific DNA sequences (res) on each of the two Tn copies in the cointegrate. These sites also carry promoters controlling expression of the recombinase and transposase. We report here that a number of Tn3 members encode a type II toxin-antitoxin (TA) system, typically composed of a stable toxin and a labile antitoxin that binds the toxin and inhibits its lethal activity. This system serves to improve plasmid maintenance in a bacterial population and, until recently, was believed to be associated with bacterial persistence. At least six different TA gene pairs are associated with various Tn3 members. Our data suggest that several independent acquisition events have occurred. In contrast to most Tn3 family passenger genes, which are generally located away from the transposition module, the TA gene pairs abut the res site upstream of the resolvase genes. Although their role when part of Tn3 family transposons is unclear, this finding suggests a potential role for the embedded TA in stabilizing the associated transposon with the possibility that TA expression is coupled to expression of transposase and resolvase during the transposition process itself.IMPORTANCE Transposable elements (TEs) are important in genetic diversification due to their recombination properties and their ability to promote horizontal gene transfer. Over the last decades, much effort has been made to understand TE transposition mechanisms and their impact on prokaryotic genomes. For example, the Tn3 family is ubiquitous in bacteria, molding their host genomes by the paste-and-copy mechanism. In addition to the transposition module, Tn3 members often carry additional passenger genes (e.g., conferring antibiotic or heavy metal resistance and virulence), and three were previously known to carry a toxin-antitoxin (TA) system often associated with plasmid maintenance; however, the role of TA systems within the Tn3 family is unknown. The genetic context of TA systems in Tn3 members suggests that they may play a regulatory role in ensuring stable invasion of these Tns during transposition.}, }
@article {pmid32234751, year = {2020}, author = {Borlinghaus, J and Bolger, A and Schier, C and Vogel, A and Usadel, B and Gruhlke, MC and Slusarenko, AJ}, title = {Genetic and molecular characterization of multicomponent resistance of Pseudomonas against allicin.}, journal = {Life science alliance}, volume = {3}, number = {5}, pages = {}, pmid = {32234751}, issn = {2575-1077}, mesh = {Anti-Bacterial Agents/metabolism ; Disulfides/metabolism/*pharmacology ; Drug Resistance, Bacterial/*genetics ; Garlic/metabolism ; Glutathione/metabolism ; Oxidation-Reduction ; Pseudomonas/*genetics ; Sulfinic Acids/metabolism/*pharmacology ; }, abstract = {The common foodstuff garlic produces the potent antibiotic defense substance allicin after tissue damage. Allicin is a redox toxin that oxidizes glutathione and cellular proteins and makes garlic a highly hostile environment for non-adapted microbes. Genomic clones from a highly allicin-resistant Pseudomonas fluorescens (PfAR-1), which was isolated from garlic, conferred allicin resistance to Pseudomonas syringae and even to Escherichia coli Resistance-conferring genes had redox-related functions and were on core fragments from three similar genomic islands identified by sequencing and in silico analysis. Transposon mutagenesis and overexpression analyses revealed the contribution of individual candidate genes to allicin resistance. Taken together, our data define a multicomponent resistance mechanism against allicin in PfAR-1, achieved through horizontal gene transfer.}, }
@article {pmid32224234, year = {2020}, author = {Petersen, G and Anderson, B and Braun, HP and Meyer, EH and Møller, IM}, title = {Mitochondria in parasitic plants.}, journal = {Mitochondrion}, volume = {52}, number = {}, pages = {173-182}, doi = {10.1016/j.mito.2020.03.008}, pmid = {32224234}, issn = {1872-8278}, mesh = {Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; *Genome, Mitochondrial ; Magnoliopsida/*genetics ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {Plant mitochondrial genomes are renowned for their structural complexity, extreme variation in size and mutation rates, and ability to incorporate foreign DNA. Parasitic flowering plants are no exception, and the close association between parasite and host may even enhance the likelihood of horizontal gene transfer (HGT) between them. Recent studies on mistletoes (Viscum) have revealed that these parasites have lost an exceptional number of mitochondrial genes, including all complex I genes of the respiratory chain. At the same time, an altered respiratory pathway has been demonstrated. Here we review the current understanding of mitochondrial evolution in parasitic plants with a special emphasis on HGT to and from parasite mitochondrial genomes, as well as the uniquely altered mitochondria in Viscum and related plants.}, }
@article {pmid32224105, year = {2020}, author = {Mikhailovsky, G and Gordon, R}, title = {Shuffling type of biological evolution based on horizontal gene transfer and the biosphere gene pool hypothesis.}, journal = {Bio Systems}, volume = {193-194}, number = {}, pages = {104131}, doi = {10.1016/j.biosystems.2020.104131}, pmid = {32224105}, issn = {1872-8324}, mesh = {*Biological Evolution ; DNA Shuffling/*methods ; Eukaryota/genetics ; *Evolution, Molecular ; *Gene Pool ; Gene Transfer, Horizontal/*genetics ; Prokaryotic Cells/physiology ; }, abstract = {Widespread horizontal gene transfer (HGT) may appear a significant factor that accelerates biological evolution. Here we look at HGT primarily from the point of view of prokaryote clones, which we take as the descendants of a single cell, all of whom have exactly the same nucleotide sequence. Any novelty that emerges as a random mutation, creating a new clone, could either disappear before its first HGT, or survive for a period and be transferred to another clone. Due to the chain character of HGT, each gene with an adaptive mutation is thus spread among numerous existing clones, creating further new clones in the process. This makes propagation far faster than elimination, and such genes become practically immortal and form a kind of "biosphere gene pool" (BGP). Not all of these genes exist in every clone, and moreover not all of them are expressed. A significant fraction of the BGP includes of genes repressed by regulatory genes. However, these genes express often enough to be subject to natural selection. In a changing environment, both repressed and expressed genes, after transferring to another clone, may prove useful in an alternative environment, and this will give rise to new clones. This mechanism for testing repressed genes for adaptability can be thought as a "shuffle of a deck of genes" by analogy with shuffling a deck of cards. In the Archean and Proterozoic eons, both BGP and the operational part of each genome were rather poor, and the probability of incorporation of randomly expressed genes into the operational part of each genome was very small. Accordingly, biological evolution during these eons was slow due to rare adaptive mutations. This explains why the realm of prokaryotes as the sole organisms on Earth lasted so long. However, over about 3.5 billion years before the Phanerozoic eon, the BGP gradually accumulated a huge number of genes. Each of them was useful in a certain environment of past eras. We suggest that multicellular eukaryotes that appeared at the end of the Proterozoic eon could shuffle these genes accumulated in BGP via HGT from prokaryotes that live in these multicellular organisms. Perhaps this was the cause of the "Cambrian explosion" and the high (and increasing) rate of evolution in the Phanerozoic eon compared with the Archean and Proterozoic.}, }
@article {pmid32222331, year = {2020}, author = {Eda, R and Nakamura, M and Takayama, Y and Maehana, S and Nakano, R and Yano, H and Kitasato, H}, title = {Trends and molecular characteristics of carbapenemase-producing Enterobacteriaceae in Japanese hospital from 2006 to 2015.}, journal = {Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy}, volume = {26}, number = {7}, pages = {667-671}, doi = {10.1016/j.jiac.2020.02.002}, pmid = {32222331}, issn = {1437-7780}, mesh = {Anti-Bacterial Agents/*pharmacology/therapeutic use ; Bacterial Proteins/genetics/isolation &amp; purification ; Carbapenem-Resistant Enterobacteriaceae/drug effects/genetics/*isolation &amp; purification ; Ceftazidime/pharmacology/therapeutic use ; Citrobacter freundii/drug effects/genetics/isolation &amp; purification ; DNA, Bacterial/genetics/isolation &amp; purification ; Enterobacteriaceae Infections/*drug therapy/epidemiology/microbiology ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Hospitals/statistics &amp; numerical data/*trends ; Humans ; Imipenem/pharmacology/therapeutic use ; Japan/epidemiology ; Klebsiella pneumoniae/drug effects/genetics/isolation &amp; purification ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Plasmids/genetics/isolation &amp; purification ; Polymerase Chain Reaction ; Prevalence ; beta-Lactam Resistance/*genetics ; beta-Lactamases/genetics/isolation &amp; purification ; }, abstract = {BACKGROUND: The increasing number of carbapenemase-producing Enterobacteriaceae (CPE) has become a global problem. Most carbapenemases detected in Japan are imipenemase, which is an imipenem-degrading enzyme with low ability; thus, CPE could have been overlooked. Therefore, this study aimed to detect and analyze CPE, without overlooking CPE showing the low minimum inhibitory concentration phenotype.<br><br>METHODS: CPE screening was conducted on 531 ceftazidime-resistant Enterobacteriaceae isolated from Kitasato University Hospital during 2006-2015. We confirmed the presence of the carbapenemase genes (blaIMP, blaVIM, blaKPC, blaNDM, and blaOXA-48) by multiplex polymerase chain reaction. The detected CPE strains were analyzed by antimicrobial susceptibility testing, multilocus sequence typing, conjugal experiments, replicon typing, and plasmid profiling by restriction enzyme treatment.<br><br>RESULTS: The CPE detection rate in Kitasato University Hospital within the past 10 years was 0.0003% (nine CPE strains). These nine CPE strains were identified to harbor 8 blaIMP-1 or 1 blaNDM-5. The CPE strains consisted of five species including Klebsiella pneumoniae and Citrobacter freundii. Six of eight blaIMP-1 were coded by IncHI2 plasmid, and the other two were coded by IncA/C plasmid. Plasmid profiling revealed that K.&#xa0;pneumoniae and C.&#xa0;freundii isolated from the same patient harbored the same plasmid.<br><br>CONCLUSION: The CPE detection rate in this study was significantly lower than those previously reported in Japan. In one case, IncA/C plasmid transmission through different bacterial species within the body was speculated. Although the number of CPE detected was low, these results indicated that the resistance plasmid could spread to other bacterial species.}, }
@article {pmid32218510, year = {2020}, author = {Mahendra, C and Christie, KA and Osuna, BA and Pinilla-Redondo, R and Kleinstiver, BP and Bondy-Denomy, J}, title = {Broad-spectrum anti-CRISPR proteins facilitate horizontal gene transfer.}, journal = {Nature microbiology}, volume = {5}, number = {4}, pages = {620-629}, pmid = {32218510}, issn = {2058-5276}, support = {R01GM127489//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/International ; DP5 OD021344/OD/NIH HHS/United States ; P01 HL142494/HL/NHLBI NIH HHS/United States ; R00-CA218870//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/International ; R01 GM127489/GM/NIGMS NIH HHS/United States ; R00 CA218870/CA/NCI NIH HHS/United States ; }, mesh = {CRISPR-Associated Protein 9/*antagonists &amp; inhibitors/genetics/metabolism ; *CRISPR-Cas Systems ; Clustered Regularly Interspaced Short Palindromic Repeats ; Conjugation, Genetic ; DNA/antagonists &amp; inhibitors/genetics/metabolism ; Enterococcus/genetics/virology ; *Gene Transfer, Horizontal ; HEK293 Cells ; Humans ; Listeria/genetics/virology ; Plasmids/chemistry/*metabolism ; Protein Binding ; RNA, Guide, CRISPR-Cas Systems/*antagonists &amp; inhibitors/genetics/metabolism ; Staphylococcus/genetics/virology ; Streptococcus/genetics/virology ; }, abstract = {CRISPR-Cas adaptive immune systems protect bacteria and archaea against their invading genetic parasites, including bacteriophages/viruses and plasmids. In response to this immunity, many phages have anti-CRISPR (Acr) proteins that inhibit CRISPR-Cas targeting. To date, anti-CRISPR genes have primarily been discovered in phage or prophage genomes. Here, we uncovered acr loci on plasmids and other conjugative elements present in Firmicutes using the Listeria acrIIA1 gene as a marker. The four identified genes, found in Listeria, Enterococcus, Streptococcus and Staphylococcus genomes, can inhibit type II-A SpyCas9 or SauCas9, and are thus named acrIIA16-19. In Enterococcus faecalis, conjugation of a Cas9-targeted plasmid was enhanced by anti-CRISPRs derived from Enterococcus conjugative elements, highlighting a role for Acrs in the dissemination of plasmids. Reciprocal co-immunoprecipitation showed that each Acr protein interacts with Cas9, and Cas9-Acr complexes were unable to cleave DNA. Northern blotting suggests that these anti-CRISPRs manipulate single guide RNA length, loading or stability. Mirroring their activity in bacteria, AcrIIA16 and AcrIIA17 provide robust and highly potent broad-spectrum inhibition of distinct Cas9 proteins in human cells (for example, SpyCas9, SauCas9, SthCas9, NmeCas9 and CjeCas9). This work presents a focused analysis of non-phage Acr proteins, demonstrating a role in horizontal gene transfer bolstered by broad-spectrum CRISPR-Cas9 inhibition.}, }
@article {pmid32217404, year = {2020}, author = {Zhang, P and Liu, M and Fu, J and Zhong, C and Zong, G and Cao, G}, title = {Identification of a mobilizable, multidrug-resistant genomic island in Myroides odoratimimus isolated from Tibetan pasture.}, journal = {The Science of the total environment}, volume = {723}, number = {}, pages = {137970}, doi = {10.1016/j.scitotenv.2020.137970}, pmid = {32217404}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents/pharmacology ; China ; Drug Resistance, Multiple, Bacterial ; Escherichia coli/drug effects ; Flavobacteriaceae ; Flavobacteriaceae Infections/*drug therapy ; Genomic Islands/*drug effects ; Humans ; Tibet ; }, abstract = {Strains of the environmental bacterium Myroides odoratimimus can cause human infections. However, treating M. odoratimimus infections can be difficult because of multidrug resistance in this organism. In this study, we isolated strain M. odoratimimus G13 from pastureland in Tibet, China. The minimum inhibitory concentration analysis suggested that strain G13 has resistance to multiple antibiotics, with an MIC for tetracycline of 168 mg/L. Whole-genome sequencing and bioinformatic analysis revealed that the genome of G13 was rich in virulence factor-encoding genes and antibiotic resistance genes (ARGs). The mobilizable genomic island MGI1313 was also identified and characterized, and six resistance genes related to four types of antibiotics were annotated in MGI1313. Conjugation assays indicated that MGI1313 could be transferred from G13 to Escherichia coli 25DN by horizontal gene transfer, resulting in multidrug-resistant E. coli conjugants. In conclusion, multidrug-resistant M. odoratimimus G13 and the mobility of MGI1313 raise the risk of difficult-to-treat bacterial infections and should be under close surveillance.}, }
@article {pmid32213257, year = {2020}, author = {Terrat, Y and Farnaes, L and Bradley, J and Tromas, N and Shapiro, BJ}, title = {Two cases of type-a Haemophilus influenzae meningitis within the same week in the same hospital are phylogenetically unrelated but recently exchanged capsule genes.}, journal = {Microbial genomics}, volume = {6}, number = {4}, pages = {}, pmid = {32213257}, issn = {2057-5858}, support = {//CIHR/Canada ; }, mesh = {Bacterial Capsules/*genetics ; California ; Child, Preschool ; Evolution, Molecular ; Gene Transfer, Horizontal ; Haemophilus influenzae/*classification/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Humans ; Meningitis, Haemophilus/*microbiology/transmission ; Phylogeny ; Whole Genome Sequencing/*methods ; }, abstract = {Haemophilus influenzae causes common and sometimes severe adult and pediatric disease including chronic obstructive respiratory disease, otitis media and infections of the central nervous system. Serotype b strains, with a b-type capsule, have been the historical cause of invasive disease, and the introduction of a serotype b-specific vaccine has led to their decline. However, unencapsulated or non-b-type H. influenzae infections are not prevented by the vaccine and appear to be increasing in frequency. Here we report two pediatric cases of severe central nervous system H. influenzae infection presenting to the same hospital in San Diego, California during the same week in January 2016. Due to good vaccine coverage in this part of the world, H. influenzae cases are normally rare and seeing two cases in the same week was unexpected. We thus suspected a recent transmission chain, and possible local outbreak. To test this hypothesis, we isolated and sequenced whole genomes from each patient and placed them in a phylogenetic tree spanning the known diversity of H. influenzae. Surprisingly, we found that the two isolates (SD2016_1 and SD2016_2) belonged to distantly related lineages, suggesting two independent transmission events and ruling out a local outbreak. Despite being distantly related, the two isolates belong to two different lineages that have exchanged capsule loci in the recent past. Therefore, as in other bacterial pathogens, capsule switching by horizontal gene transfer may be an important evolutionary mechanism of vaccine evasion in H. influenzae.}, }
@article {pmid32210943, year = {2020}, author = {Lin, Y and Dong, X and Wu, J and Rao, D and Zhang, L and Faraj, Y and Yang, K}, title = {Metadata Analysis of mcr-1-Bearing Plasmids Inspired by the Sequencing Evidence for Horizontal Transfer of Antibiotic Resistance Genes Between Polluted River and Wild Birds.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {352}, pmid = {32210943}, issn = {1664-302X}, abstract = {We sequenced the whole genomes of three mcr-1-positive multidrug-resistant E. coli strains, which were previously isolated from the environment of egret habitat (polluted river) and egret feces. The results exhibit high correlation between antibiotic-resistant phenotype and genotype among the three strains. Most of the mobilized antibiotic resistance genes (ARGs) are distributed on plasmids in the forms of transposons or integrons. Multidrug-resistant (MDR) regions of high homology are detected on plasmids of different E. coli isolates. Therefore, horizontal transfer of resistance genes has facilitated the transmission of antibiotic resistance between the environmental and avian bacteria, and the transfer of ARGs have involved multiple embedded genetic levels (transposons, integrons, plasmids, and bacterial lineages). Inspired by this, systematic metadata analysis was performed for the available sequences of mcr-1-bearing plasmids. Among these plasmids, IncHI2 plasmids carry the most additional ARGs. The composition of these additional ARGs varies according to their geographical distribution. The phylogenetic reconstruction of IncI2 and IncX4 plasmids provides the evidence for their multiregional evolution. Phylogenetic analysis at the level of mobile genetic element (plasmid) provides important epidemiological information for the global dissemination of mcr-1 gene. Highly homologous mcr-1-bearing IncI2 plasmids have been isolated from different regions along the East Asian-Australasian Flyway, suggesting that migratory birds may mediate the intercontinental transportation of ARGs.}, }
@article {pmid32210932, year = {2020}, author = {Korry, BJ and Cabral, DJ and Belenky, P}, title = {Metatranscriptomics Reveals Antibiotic-Induced Resistance Gene Expression in the Murine Gut Microbiota.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {322}, pmid = {32210932}, issn = {1664-302X}, support = {P20 GM109035/GM/NIGMS NIH HHS/United States ; P20 GM121344/GM/NIGMS NIH HHS/United States ; R21 AT010366/AT/NCCIH NIH HHS/United States ; }, abstract = {Antibiotic resistance is a current and expanding threat to the practice of modern medicine. Antibiotic therapy has been shown to perturb the composition of the host microbiome with significant health consequences. In addition, the gut microbiome is known to be a reservoir of antibiotic resistance genes. Work has demonstrated that antibiotics can alter the collection of antibiotic resistance genes within the microbiome through selection and horizontal gene transfer. While antibiotics also have the potential to impact the expression of resistance genes, metagenomic-based pipelines currently lack the ability to detect these shifts. Here, we utilized a dual sequencing approach combining shotgun metagenomics and metatranscriptomics to profile how three antibiotics, amoxicillin, doxycycline, and ciprofloxacin, impact the murine gut resistome at the DNA and RNA level. We found that each antibiotic induced broad, but untargeted impacts on the gene content of the resistome. In contrast, changes in ARG transcript abundance were more targeted to the antibiotic treatment. Doxycycline and amoxicillin induced the expression of tetracycline and beta-lactamase resistance genes, respectively. Furthermore, the increased beta-lactamase resistance gene transcripts could contribute to an observed bloom of Bacteroides thetaiotaomicron during amoxicillin treatment. Based on these findings, we propose that the utilization of a dual sequencing methodology provides a unique capacity to fully understand the response of the resistome to antibiotic perturbation. In particular, the analysis of transcripts reveals that the expression and utilization of resistance genes is far narrower than their abundance at the genomic level would suggest.}, }
@article {pmid32209693, year = {2020}, author = {Green, LR and Al-Rubaiawi, AA and Al-Maeni, MARM and Harrison, OB and Blades, M and Oldfield, NJ and Turner, DPJ and Maiden, MCJ and Bayliss, CD}, title = {Localized Hypermutation is the Major Driver of Meningococcal Genetic Variability during Persistent Asymptomatic Carriage.}, journal = {mBio}, volume = {11}, number = {2}, pages = {}, pmid = {32209693}, issn = {2150-7511}, support = {MR/M020193/1/MRC_/Medical Research Council/United Kingdom ; 104992/Z/14/Z/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 087622/Z/08/A/WT_/Wellcome Trust/United Kingdom ; MR/S009264/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Alleles ; Antigenic Variation ; *Asymptomatic Infections ; Bacterial Adhesion ; Fimbriae Proteins/genetics ; Fimbriae, Bacterial/genetics ; Gene Transfer, Horizontal ; *Genetic Variation ; Humans ; Longitudinal Studies ; *Mutation ; Neisseria meningitidis/*genetics ; Phenotype ; Whole Genome Sequencing ; }, abstract = {Host persistence of bacteria is facilitated by mutational and recombinatorial processes that counteract loss of genetic variation during transmission and selection from evolving host responses. Genetic variation was investigated during persistent asymptomatic carriage of Neisseria meningitidis Interrogation of whole-genome sequences for paired isolates from 25 carriers showed that de novo mutations were infrequent, while horizontal gene transfer occurred in 16% of carriers. Examination of multiple isolates per time point enabled separation of sporadic and transient allelic variation from directional variation. A comprehensive comparative analysis of directional allelic variation with hypermutation of simple sequence repeats and hyperrecombination of class 1 type IV pilus genes detected an average of seven events per carrier and 2:1 bias for changes due to localized hypermutation. Directional genetic variation was focused on the outer membrane with 69% of events occurring in genes encoding enzymatic modifiers of surface structures or outer membrane proteins. Multiple carriers exhibited directional and opposed switching of allelic variants of the surface-located Opa proteins that enables continuous expression of these adhesins alongside antigenic variation. A trend for switching from PilC1 to PilC2 expression was detected, indicating selection for specific alterations in the activities of the type IV pilus, whereas phase variation of restriction modification (RM) systems, as well as associated phasevarions, was infrequent. We conclude that asymptomatic meningococcal carriage on mucosal surfaces is facilitated by frequent localized hypermutation and horizontal gene transfer affecting genes encoding surface modifiers such that optimization of adhesive functions occurs alongside escape of immune responses by antigenic variation.IMPORTANCE Many bacterial pathogens coexist with host organisms, rarely causing disease while adapting to host responses. Neisseria meningitidis, a major cause of meningitis and septicemia, is a frequent persistent colonizer of asymptomatic teenagers/young adults. To assess how genetic variation contributes to host persistence, whole-genome sequencing and hypermutable sequence analyses were performed on multiple isolates obtained from students naturally colonized with meningococci. High frequencies of gene transfer were observed, occurring in 16% of carriers and affecting 51% of all nonhypermutable variable genes. Comparative analyses showed that hypermutable sequences were the major mechanism of variation, causing 2-fold more changes in gene function than other mechanisms. Genetic variation was focused on genes affecting the outer membrane, with directional changes in proteins responsible for bacterial adhesion to host surfaces. This comprehensive examination of genetic plasticity in individual hosts provides a significant new platform for rationale design of approaches to prevent the spread of this pathogen.}, }
@article {pmid32209690, year = {2020}, author = {Frost, CL and Siozios, S and Nadal-Jimenez, P and Brockhurst, MA and King, KC and Darby, AC and Hurst, GDD}, title = {The Hypercomplex Genome of an Insect Reproductive Parasite Highlights the Importance of Lateral Gene Transfer in Symbiont Biology.}, journal = {mBio}, volume = {11}, number = {2}, pages = {}, pmid = {32209690}, issn = {2150-7511}, support = {BB/L024209/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bacteriophages/genetics ; Gammaproteobacteria/*genetics ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomics ; *Interspersed Repetitive Sequences ; Phylogeny ; Repetitive Sequences, Nucleic Acid ; Symbiosis/*genetics ; Wasps/*microbiology ; }, abstract = {Mobile elements-plasmids and phages-are important components of microbial function and evolution via traits that they encode and their capacity to shuttle genetic material between species. We here report the unusually rich array of mobile elements within the genome of Arsenophonus nasoniae, the son-killer symbiont of the parasitic wasp Nasonia vitripennis This microbe's genome has the highest prophage complement reported to date, with over 50 genomic regions that represent either intact or degraded phage material. Moreover, the genome is predicted to include 17 extrachromosomal genetic elements, which carry many genes predicted to be important at the microbe-host interface, derived from a diverse assemblage of insect-associated gammaproteobacteria. In our system, this diversity was previously masked by repetitive mobile elements that broke the assembly derived from short reads. These findings suggest that other complex bacterial genomes will be revealed in the era of long-read sequencing.IMPORTANCE The biology of many bacteria is critically dependent on genes carried on plasmid and phage mobile elements. These elements shuttle between microbial species, thus providing an important source of biological innovation across taxa. It has recently been recognized that mobile elements are also important in symbiotic bacteria, which form long-lasting interactions with their host. In this study, we report a bacterial symbiont genome that carries a highly complex array of these elements. Arsenophonus nasoniae is the son-killer microbe of the parasitic wasp Nasonia vitripennis and exists with the wasp throughout its life cycle. We completed its genome with the aid of recently developed long-read technology. This assembly contained over 50 chromosomal regions of phage origin and 17 extrachromosomal elements within the genome, encoding many important traits at the host-microbe interface. Thus, the biology of this symbiont is enabled by a complex array of mobile elements.}, }
@article {pmid32209674, year = {2020}, author = {Choi, J and Groisman, EA}, title = {Salmonella expresses foreign genes during infection by degrading their silencer.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {14}, pages = {8074-8082}, pmid = {32209674}, issn = {1091-6490}, support = {R01 AI120558/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacterial Proteins/*metabolism ; Cell Line ; DNA-Binding Proteins/*metabolism ; *Gene Expression Regulation, Bacterial ; Gene Silencing ; Gene Transfer, Horizontal ; Macrophages/*microbiology ; Mice ; Protease La/*metabolism ; Proteolysis ; Salmonella Infections/*microbiology ; Salmonella typhimurium/genetics/metabolism/*pathogenicity ; Transcription, Genetic ; Virulence/genetics ; Virulence Factors/genetics/metabolism ; }, abstract = {The heat-stable nucleoid structuring (H-NS, also referred to as histone-like nucleoid structuring) protein silences transcription of foreign genes in a variety of Gram-negative bacterial species. To take advantage of the products encoded in foreign genes, bacteria must overcome the silencing effects of H-NS. Because H-NS amounts are believed to remain constant, overcoming gene silencing has largely been ascribed to proteins that outcompete H-NS for binding to AT-rich foreign DNA. However, we report here that the facultative intracellular pathogen Salmonella enterica serovar Typhimurium decreases H-NS amounts 16-fold when inside macrophages. This decrease requires both the protease Lon and the DNA-binding virulence regulator PhoP. The decrease in H-NS abundance reduces H-NS binding to foreign DNA, allowing transcription of foreign genes, including those required for intramacrophage survival. The purified Lon protease degraded free H-NS but not DNA-bound H-NS. By displacing H-NS from DNA, the PhoP protein promoted H-NS proteolysis, thereby de-repressing foreign genes-even those whose regulatory sequences are not bound by PhoP. The uncovered mechanism enables a pathogen to express foreign virulence genes during infection without the need to evolve binding sites for antisilencing proteins at each foreign gene.}, }
@article {pmid32209379, year = {2020}, author = {Bai, L and Zhang, S and Deng, Y and Song, C and Kang, G and Dong, Y and Wang, Y and Gao, F and Huang, H}, title = {Comparative genomics analysis of Acinetobacter haemolyticus isolates from sputum samples of respiratory patients.}, journal = {Genomics}, volume = {112}, number = {4}, pages = {2784-2793}, doi = {10.1016/j.ygeno.2020.03.016}, pmid = {32209379}, issn = {1089-8646}, mesh = {Acinetobacter/*genetics/isolation &amp; purification/metabolism/pathogenicity ; Bacterial Proteins/genetics ; Drug Resistance, Bacterial ; Genes, Bacterial ; *Genome, Bacterial ; Genomics ; Humans ; Molecular Sequence Annotation ; Phylogeny ; Respiratory Tract Infections/microbiology ; Sputum/microbiology ; Virulence Factors/genetics ; }, abstract = {Acinetobacter haemolyticus (A. haemolyticus) is a significant Acinetobacter pathogen, and the resistance of A. haemolyticus continues to rise due to abuse of antibiotics and the frequent gene exchange between bacteria in hospital. In this study, we performed complete genome sequencing of two A. haemolyticus strains TJR01 and TJS01 to improve our understanding of pathogenic and resistance of A. haemolyticus. Both TJR01 and TJS01 contain one chromosome and two plasmids. Compared to TJS01, more virulence factors (VFs) associated pathogenicity and resistant genes were predicted in TJR01 due to T4SS and integron associated with combination and transport. Antimicrobial susceptibility results were consistent with sequencing. We suppose TJS01 was a susceptive strain and TJR01 was an acquired multidrug resistance strain due to plasmid-mediated horizontal gene transfer. We hope these findings may be helpful for clinical treatment of A. haemolyticus infection and reduce the risk of potential outbreak infection.}, }
@article {pmid32205462, year = {2020}, author = {Martínez-Chavarría, LC and Sagawa, J and Irons, J and Hinz, AK and Lemon, A and Graça, T and Downs, DM and Vadyvaloo, V}, title = {Putative Horizontally Acquired Genes, Highly Transcribed during Yersinia pestis Flea Infection, Are Induced by Hyperosmotic Stress and Function in Aromatic Amino Acid Metabolism.}, journal = {Journal of bacteriology}, volume = {202}, number = {11}, pages = {}, pmid = {32205462}, issn = {1098-5530}, support = {R01 AI117016/AI/NIAID NIH HHS/United States ; R01 GM095837/GM/NIGMS NIH HHS/United States ; R21 AI097974/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acids, Aromatic/*metabolism ; Animals ; Bacterial Proteins/genetics/metabolism ; Gene Transfer, Horizontal ; Operon ; Siphonaptera/*microbiology ; Yersinia pestis/genetics/growth &amp; development/*metabolism ; }, abstract = {While alternating between insects and mammals during its life cycle, Yersinia pestis, the flea-transmitted bacterium that causes plague, regulates its gene expression appropriately to adapt to these two physiologically disparate host environments. In fleas competent to transmit Y. pestis, low-GC-content genes y3555, y3551, and y3550 are highly transcribed, suggesting that these genes have a highly prioritized role in flea infection. Here, we demonstrate that y3555, y3551, and y3550 are transcribed as part of a single polycistronic mRNA comprising the y3555, y3554, y3553, y355x, y3551, and y3550 genes. Additionally, y355x-y3551-y3550 compose another operon, while y3550 can be also transcribed as a monocistronic mRNA. The expression of these genes is induced by hyperosmotic salinity stress, which serves as an explicit environmental stimulus that initiates transcriptional activity from the predicted y3550 promoter. Y3555 has homology to pyridoxal 5'-phosphate (PLP)-dependent aromatic aminotransferases, while Y3550 and Y3551 are homologous to the Rid protein superfamily (YjgF/YER057c/UK114) members that forestall damage caused by reactive intermediates formed during PLP-dependent enzymatic activity. We demonstrate that y3551 specifically encodes an archetypal RidA protein with 2-aminoacrylate deaminase activity but Y3550 lacks Rid deaminase function. Heterologous expression of y3555 generates a critical aspartate requirement in a Salmonella entericaaspC mutant, while its in vitro expression, and specifically its heterologous coexpression with y3550, enhances the growth rate of an Escherichia coli ΔaspC ΔtyrB mutant in a defined minimal amino acid-supplemented medium. Our data suggest that the y3555, y3551, and y3550 genes operate cooperatively to optimize aromatic amino acid metabolism and are induced under conditions of hyperosmotic salinity stress.IMPORTANCE Distinct gene repertoires are expressed during Y. pestis infection of its flea and mammalian hosts. The functions of many of these genes remain predicted or unknown, necessitating their characterization, as this may provide a better understanding of Y. pestis specialized biological adaptations to the discrete environments of its two hosts. This study provides functional context to adjacently clustered horizontally acquired genes predominantly expressed in the flea host by deciphering their fundamental processes with regard to (i) transcriptional organization, (ii) transcription activation signals, and (iii) biochemical function. Our data support a role for these genes in osmoadaptation and aromatic amino acid metabolism, highlighting these as preferential processes by which Y. pestis gene expression is modulated during flea infection.}, }
@article {pmid32203124, year = {2020}, author = {Liang, JL and Liu, J and Jia, P and Yang, TT and Zeng, QW and Zhang, SC and Liao, B and Shu, WS and Li, JT}, title = {Novel phosphate-solubilizing bacteria enhance soil phosphorus cycling following ecological restoration of land degraded by mining.}, journal = {The ISME journal}, volume = {14}, number = {6}, pages = {1600-1613}, pmid = {32203124}, issn = {1751-7370}, mesh = {Bacteria/genetics ; China ; Microbiota ; *Mining ; Phosphates/metabolism ; Phosphorus/*metabolism ; Plants/metabolism ; Soil ; *Soil Microbiology ; }, abstract = {Little is known about the changes in soil microbial phosphorus (P) cycling potential during terrestrial ecosystem management and restoration, although much research aims to enhance soil P cycling. Here, we used metagenomic sequencing to analyse 18 soil microbial communities at a P-deficient degraded mine site in southern China where ecological restoration was implemented using two soil ameliorants and eight plant species. Our results show that the relative abundances of key genes governing soil microbial P-cycling potential were higher at the restored site than at the unrestored site, indicating enhancement of soil P cycling following restoration. The gcd gene, encoding an enzyme that mediates inorganic P solubilization, was predominant across soil samples and was a major determinant of bioavailable soil P. We reconstructed 39 near-complete bacterial genomes harboring gcd, which represented diverse novel phosphate-solubilizing microbial taxa. Strong correlations were found between the relative abundance of these genomes and bioavailable soil P, suggesting their contributions to the enhancement of soil P cycling. Moreover, 84 mobile genetic elements were detected in the scaffolds containing gcd in the 39 genomes, providing evidence for the role of phage-related horizontal gene transfer in assisting soil microbes to acquire new metabolic potential related to P cycling.}, }
@article {pmid32200751, year = {2020}, author = {Quistad, SD and Doulcier, G and Rainey, PB}, title = {Experimental manipulation of selfish genetic elements links genes to microbial community function.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1798}, pages = {20190681}, pmid = {32200751}, issn = {1471-2970}, mesh = {Bacteria/*genetics ; Metagenome ; Metagenomics ; Microbiota/*genetics ; *Repetitive Sequences, Nucleic Acid ; *Soil Microbiology ; }, abstract = {Microbial communities underpin the Earth's biological and geochemical processes, but their complexity hampers understanding. Motivated by the challenge of diversity and the need to forge ways of capturing dynamical behaviour connecting genes to function, biologically independent experimental communities comprising hundreds of microbial genera were established from garden compost and propagated on nitrogen-limited minimal medium with cellulose (paper) as sole carbon source. After 1 year of bi-weekly transfer, communities retained hundreds of genera. To connect genes to function, we used a simple experimental manipulation that involved the periodic collection of selfish genetic elements (SGEs) from separate communities, followed by pooling and redistribution across communities. The treatment was predicted to promote amplification and dissemination of SGEs and thus horizontal gene transfer. Confirmation came from comparative metagenomics, which showed the substantive movement of ecologically significant genes whose dynamic across space and time could be followed. Enrichment of genes implicated in nitrogen metabolism, and particularly ammonification, prompted biochemical assays that revealed a measurable impact on community function. Our simple experimental strategy offers a conceptually new approach for unravelling dynamical processes affecting microbial community function. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.}, }
@article {pmid32200735, year = {2020}, author = {Rainey, PB and Quistad, SD}, title = {Toward a dynamical understanding of microbial communities.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1798}, pages = {20190248}, pmid = {32200735}, issn = {1471-2970}, mesh = {Bacteria/*genetics ; *Bacterial Physiological Phenomena/genetics ; *Biological Evolution ; *Gene Transfer, Horizontal ; *Metagenome ; *Microbiota ; }, abstract = {The challenge of moving beyond descriptions of microbial community composition to the point where understanding underlying eco-evolutionary dynamics emerges is daunting. While it is tempting to simplify through use of model communities composed of a small number of types, there is a risk that such strategies fail to capture processes that might be specific and intrinsic to complexity of the community itself. Here, we describe approaches that embrace this complexity and show that, in combination with metagenomic strategies, dynamical insight is increasingly possible. Arising from these studies is mounting evidence of rapid eco-evolutionary change among lineages and a sense that processes, particularly those mediated by horizontal gene transfer, not only are integral to system function, but are central to long-term persistence. That such dynamic, systems-level insight is now possible, means that the study and manipulation of microbial communities can move to new levels of inquiry. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.}, }
@article {pmid32198762, year = {2020}, author = {Dunning, LT and Christin, PA}, title = {Reticulate evolution, lateral gene transfer, and innovation in plants.}, journal = {American journal of botany}, volume = {107}, number = {4}, pages = {541-544}, doi = {10.1002/ajb2.1452}, pmid = {32198762}, issn = {1537-2197}, mesh = {Evolution, Molecular ; *Gene Transfer, Horizontal ; Phylogeny ; *Plants ; }, }
@article {pmid32196086, year = {2020}, author = {Talagrand-Reboul, E and Colston, SM and Graf, J and Lamy, B and Jumas-Bilak, E}, title = {Comparative and Evolutionary Genomics of Isolates Provide Insight into the Pathoadaptation of Aeromonas.}, journal = {Genome biology and evolution}, volume = {12}, number = {5}, pages = {535-552}, pmid = {32196086}, issn = {1759-6653}, mesh = {*Adaptation, Physiological ; Aeromonas/*genetics/isolation &amp; purification/*pathogenicity ; *Biological Evolution ; *Genome, Bacterial ; Genomics/*methods ; Genotype ; Humans ; Phenotype ; Phylogeny ; Virulence ; Virulence Factors/*genetics ; }, abstract = {Aeromonads are ubiquitous aquatic bacteria that cause opportunistic infections in humans, but their pathogenesis remains poorly understood. A pathogenomic approach was undertaken to provide insights into the emergence and evolution of pathogenic traits in aeromonads. The genomes of 64 Aeromonas strains representative of the whole genus were analyzed to study the distribution, phylogeny, and synteny of the flanking sequences of 13 virulence-associated genes. The reconstructed evolutionary histories varied markedly depending on the gene analyzed and ranged from vertical evolution, which followed the core genome evolution (alt and colAh), to complex evolution, involving gene loss by insertion sequence-driven gene disruption, horizontal gene transfer, and paraphyly with some virulence genes associated with a phylogroup (aer, ser, and type 3 secretion system components) or no phylogroup (type 3 secretion system effectors, Ast, ExoA, and RtxA toxins). The general pathogenomic overview of aeromonads showed great complexity with diverse evolution modes and gene organization and uneven distribution of virulence genes in the genus; the results provided insights into aeromonad pathoadaptation or the ability of members of this group to emerge as pathogens. Finally, these findings suggest that aeromonad virulence-associated genes should be examined at the population level and that studies performed on type or model strains at the species level cannot be generalized to the whole species.}, }
@article {pmid32189080, year = {2020}, author = {Dodueva, IE and Lebedeva, MA and Kuznetsova, KA and Gancheva, MS and Paponova, SS and Lutova, LL}, title = {Plant tumors: a hundred years of study.}, journal = {Planta}, volume = {251}, number = {4}, pages = {82}, pmid = {32189080}, issn = {1432-2048}, support = {16-16-10011//Russian Science Foundation/ ; 18-04-01107//&#x420;&#x43e;&#x441;&#x441;&#x438;&#x439;&#x441;&#x43a;&#x438;&#x439; &#x424;&#x43e;&#x43d;&#x434; &#x424;&#x443;&#x43d;&#x434;&#x430;&#x43c;&#x435;&#x43d;&#x442;&#x430;&#x43b;&#x44c;&#x43d;&#x44b;&#x445; &#x418;&#x441;&#x441;&#x43b;&#x435;&#x434;&#x43e;&#x432;&#x430;&#x43d;&#x438;&#x439; (&#x420;&#x424;&#x424;&#x418;)/ ; }, mesh = {Animals ; Bacteria/metabolism ; Fungi/metabolism ; Host-Pathogen Interactions ; Insecta/metabolism ; Meristem/growth &amp; development/microbiology ; Plant Cells/metabolism ; Plant Development ; Plant Growth Regulators/metabolism ; Plant Tumors/*microbiology ; Viruses/metabolism ; }, abstract = {The review provides information on the mechanisms underlying the development of spontaneous and pathogen-induced tumors in higher plants. The activation of meristem-specific regulators in plant tumors of various origins suggests the meristem-like nature of abnormal plant hyperplasia. Plant tumor formation has more than a century of research history. The study of this phenomenon has led to a number of important discoveries, including the development of the Agrobacterium-mediated transformation technique and the discovery of horizontal gene transfer from bacteria to plants. There are two main groups of plant tumors: pathogen-induced tumors (e.g., tumors induced by bacteria, viruses, fungi, insects, etc.), and spontaneous ones, which are formed in the absence of any pathogen in plants with certain genotypes (e.g., interspecific hybrids, inbred lines, and mutants). The causes of the transition of plant cells to tumor growth are different from those in animals, and they include the disturbance of phytohormonal balance and the acquisition of meristematic characteristics by differentiated cells. The aim of this review is to discuss the mechanisms underlying the development of most known examples of plant tumors.}, }
@article {pmid32189025, year = {2020}, author = {Zhang, C and Ma, H and Sanchez-Puerta, MV and Li, L and Xiao, J and Liu, Z and Ci, X and Li, J}, title = {Horizontal Gene Transfer has Impacted cox1 Gene Evolution in Cassytha filiformis.}, journal = {Journal of molecular evolution}, volume = {88}, number = {4}, pages = {361-371}, pmid = {32189025}, issn = {1432-1432}, support = {2017XTBG-T03//CAS 135 program/International ; 31500311//National Natural Science Foundation of China/International ; }, mesh = {Cyclooxygenase 1/*genetics ; *Gene Transfer, Horizontal ; Introns ; *Lauraceae/enzymology/genetics ; Phylogeny ; Plant Proteins/*genetics ; }, abstract = {The gene cox1 is one of the most reported mitochondrial genes involved in horizontal gene transfer among angiosperms. However, whether different cox1 copies exist in different populations of a species and whether any other novel way except intron homing exists for cox1 intron acquisition is less understood. In this study, we chose Cassytha filiformis, a parasitic plant from the angiosperm family Lauraceae, as an example to study cox1 variation and evolution. We identified the stable and inheritable co-occurrence of two copies of cox1 genes, which were different in base composition and insertion/deletion among samples of a single species, C. filiformis. The bioinformatic analyses revealed that Type I copy had intact open reading frames, but type II copy had premature stop codons and was a pseudogene. Further INDEL characterization, phylogenetic analyses, and CCT comparisons consistently support two different origins for the two types of C. filiformis cox1 genes. Type I cox1 was likely vertically inherited within the magnoliids but it has captured an intron from another species, whereas the entire type II intron-containing cox1 has most likely been transferred integrally from Cuscuta or other Convolvulaceae species. The finding of the two independent horizontal gene transfer events associated with C. filiformis cox1 genes not only promotes our understanding of the evolutionary history of C. filiformis, but also leaves intriguing evolutionary questions that merits further efforts.}, }
@article {pmid32188438, year = {2020}, author = {Liang, P and Zhang, Y and Xu, B and Zhao, Y and Liu, X and Gao, W and Ma, T and Yang, C and Wang, S and Liu, R}, title = {Deletion of genomic islands in the Pseudomonas putida KT2440 genome can create an optimal chassis for synthetic biology applications.}, journal = {Microbial cell factories}, volume = {19}, number = {1}, pages = {70}, pmid = {32188438}, issn = {1475-2859}, support = {No. 2018YFA0900100//National Key Research and Development Program of China/ ; 31570035//National Natural Science Funding of China/ ; 31670093//National Natural Science Funding of China/ ; 17JCZDJC32100//the Tianjin Natural Science Funding/ ; 18JCYBJC24500//the Tianjin Natural Science Funding/ ; }, mesh = {Base Sequence ; Biodegradation, Environmental ; Biosynthetic Pathways ; Biotransformation ; Carbon/metabolism ; DNA, Bacterial/genetics ; *Genomic Islands ; Metabolic Engineering ; Pseudomonas putida/*genetics ; *Sequence Deletion ; *Synthetic Biology ; }, abstract = {BACKGROUND: Genome streamlining is a feasible strategy for constructing an optimum microbial chassis for synthetic biology applications. Genomic islands (GIs) are usually regarded as foreign DNA sequences, which can be obtained by horizontal gene transfer among microorganisms. A model strain Pseudomonas putida KT2440 has broad applications in biocatalysis, biotransformation and biodegradation.<br><br>RESULTS: In this study, the identified GIs in P. putida KT2440 accounting for 4.12% of the total genome size were deleted to generate a series of genome-reduced strains. The mutant KTU-U13 with the largest deletion was advantageous over the original strain KTU in several physiological characteristics evaluated. The mutant KTU-U13 showed high plasmid transformation efficiency and heterologous protein expression capacity compared with the original strain KTU. The metabolic phenotype analysis showed that the types of carbon sources utilized by the mutant KTU-U13 and the utilization capabilities for certain carbon sources were increased greatly. The polyhydroxyalkanoate (PHA) yield and cell dry weight of the mutant KTU-U13 were improved significantly compared with the original strain KTU. The chromosomal integration efficiencies for the &#x3b3;-hexachlorocyclohexane (&#x3b3;-HCH) and 1,2,3-trichloropropane (TCP) biodegradation pathways were improved greatly when using the mutant KTU-U13 as the recipient cell and enhanced degradation of &#x3b3;-HCH and TCP by the mutant KTU-U13 was also observed. The mutant KTU-U13 was able to stably express a plasmid-borne zeaxanthin biosynthetic pathway, suggesting the excellent genetic stability of the mutant.<br><br>CONCLUSIONS: These desirable traits make the GIs-deleted mutant KTU-U13 an optimum chassis for synthetic biology applications. The present study suggests that the systematic deletion of GIs in bacteria may be a useful approach for generating an optimal chassis for the construction of microbial cell factories.}, }
@article {pmid32188136, year = {2020}, author = {Focardi, A and Ostrowski, M and Goossen, K and Brown, MV and Paulsen, I}, title = {Investigating the Diversity of Marine Bacteriophage in Contrasting Water Masses Associated with the East Australian Current (EAC) System.}, journal = {Viruses}, volume = {12}, number = {3}, pages = {}, pmid = {32188136}, issn = {1999-4915}, mesh = {Australia ; Bacteriophages/*classification/*genetics/isolation &amp; purification ; *Biodiversity ; DNA Viruses/genetics ; DNA, Viral ; Genes, Viral/genetics ; Metagenome ; Microbiota ; Oceans and Seas ; Phylogeny ; Seawater/*virology ; }, abstract = {Virus- and bacteriophage-induced mortality can have a significant impact on marine productivity and alter the flux of nutrients in marine microbial food-webs. Viral mediated horizontal gene transfer can also influence host fitness and community composition. However, there are very few studies of marine viral diversity in the Southern Hemisphere, which hampers our ability to fully understand the complex interplay of biotic and abiotic factors that shape microbial communities. We carried out the first genetic study of bacteriophage communities within a dynamic western boundary current (WBC) system, the east Australian current (EAC). Virus DNA sequences were extracted from 63 assembled metagenomes and six metaviromes obtained from various depths at 24 different locations. More than 1700 bacteriophage genomic fragments (>9 kbps) were recovered from the assembled sequences. Bacteriophage diversity displayed distinct depth and regional patterns. There were clear differences in the bacteriophage populations associated with the EAC and Tasman Sea euphotic zones, at both the taxonomic and functional level. In contrast, bathypelagic phages were similar across the two oceanic regions. These data provide the first characterisation of viral diversity across a dynamic western boundary current, which is an emerging model for studying the response of microbial communities to climate change.}, }
@article {pmid32186700, year = {2020}, author = {Coimbra, NDR and Goes-Neto, A and Azevedo, V and Ouangraoua, A}, title = {Reconstructing the Phylogeny of Corynebacteriales while Accounting for Horizontal Gene Transfer.}, journal = {Genome biology and evolution}, volume = {12}, number = {4}, pages = {381-395}, pmid = {32186700}, issn = {1759-6653}, mesh = {Corynebacterium/*genetics/growth &amp; development ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomics ; *Models, Genetic ; *Phylogeny ; Species Specificity ; }, abstract = {Horizontal gene transfer is a common mechanism in Bacteria that has contributed to the genomic content of existing organisms. Traditional methods for estimating bacterial phylogeny, however, assume only vertical inheritance in the evolution of homologous genes, which may result in errors in the estimated phylogenies. We present a new method for estimating bacterial phylogeny that accounts for the presence of genes acquired by horizontal gene transfer between genomes. The method identifies and corrects putative transferred genes in gene families, before applying a gene tree-based summary method to estimate bacterial species trees. The method was applied to estimate the phylogeny of the order Corynebacteriales, which is the largest clade in the phylum Actinobacteria. We report a collection of 14 phylogenetic trees on 360 Corynebacteriales genomes. All estimated trees display each genus as a monophyletic clade. The trees also display several relationships proposed by past studies, as well as new relevant relationships between and within the main genera of Corynebacteriales: Corynebacterium, Mycobacterium, Nocardia, Rhodococcus, and Gordonia. An implementation of the method in Python is available on GitHub at https://github.com/UdeS-CoBIUS/EXECT (last accessed April 2, 2020).}, }
@article {pmid32184766, year = {2020}, author = {Hu, T and Cui, Y and Zhang, Y and Qu, X and Zhao, C}, title = {Genome Analysis and Physiological Characterization of Four Streptococcus thermophilus Strains Isolated From Chinese Traditional Fermented Milk.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {184}, pmid = {32184766}, issn = {1664-302X}, abstract = {Streptococcus thermophilus plays important roles in the dairy industry and is widely used as a dairy starter in the production of fermented dairy products. The genomes of S. thermophilus strains CS5, CS9, CS18, and CS20 from fermented milk in China were sequenced and used for biodiversity analysis. In the present study, the phylogenetic analysis of all 34 S. thermophilus genomes publicly available including these four strains reveals that the phylogenetic reconstruction does not match geographic distribution as strains isolated from the same continent are not even clustered on the nearby branches. The core and variable genes were also identified, which vary among strains from 0 to 202. CS9 strain contained 127 unique genes from a variety of distantly related species. It was speculated that CS9 had undergone horizontal gene transfer (HGT) during the long evolutionary process. The safety evaluation of these four strains indicated that none of them contains antibiotic resistance genes and that they are all sensitive to multiple antibiotics. In addition, the strains do not contain any pathogenic virulence factors or plasmids and thus can be considered safe. Furthermore, these strains were investigated in terms of their technological properties including milk acidification, exopolysaccharide (EPS) and γ-aminobutyric acid (GABA) production, and in vitro survival capacity in the gastrointestinal tract. CS9 possesses a special eps gene cluster containing significant traces of HGT, while the eps gene clusters of CS5, CS18, and CS20 are almost the same. The monosaccharide compositional analysis indicated that crude EPS-CS5, EPS-CS9, EPS-CS18, and EPS-CS20 contain similar monosaccharide compositions with different ratios. Furthermore, CS9 was one of a few GABA-producing strains that could ferment glutamate to produce GABA, which is beneficial for improving the acid tolerance of the strain. CS18 has the most potential for the production of fermented food among these four strains because of its fast growth rate, rapid acidifying capacity, and stronger acid and bile salt resistance capacity. This study focused on the genome analysis of the four new S. thermophilus strains to investigate the diversity of strains and provides a reference for selecting excellent strains by use of the genome data.}, }
@article {pmid32184760, year = {2020}, author = {Wang, Y and Jiang, Y and Deng, Y and Yi, C and Wang, Y and Ding, M and Liu, J and Jin, X and Shen, L and He, Y and Wu, X and Chen, X and Sun, C and Zheng, M and Zhang, R and Ye, H and An, H and Wong, A}, title = {Probiotic Supplements: Hope or Hype?.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {160}, pmid = {32184760}, issn = {1664-302X}, abstract = {Probiotic bacteria have been associated with various health benefits and included in overwhelming number of foods. Today, probiotic supplements are consumed with increasing regularity and record a rapidly growing economic value. With billions of heterogeneous populations of probiotics per serving, probiotic supplements contain the largest quantity of probiotics across all functional foods. They often carry antibiotic-resistant determinants that can be transferred to and accumulate in resident bacteria of the gastrointestinal tract and risk their acquisitions by opportunistic pathogens. While the health benefits of probiotics have been widely publicized, this health risk, however, is underrepresented in both scientific studies and public awareness. On the other hand, the human gut presents conditions that are unfavorable for bacteria, including probiotics. It remains uncertain if probiotics from supplements can tolerate acids and bile salts that may undermine their effectiveness in conferring health benefits. Here, we put into perspective the perceived health benefits and the long-term safety of consuming probiotic supplements, specifically bringing intolerance to acids and bile salts, and the long-standing issue of antibiotic-resistant gene transfer into sharp focus. We report that probiotics from supplements examined in this study have poor tolerance to acids and bile salts while also displaying resistance to multiple antibiotics. They could also adapt and gain resistance to streptomycin in vitro. In an environment where consuming supplements is considered a norm, our results and that of others will put in perspective the persisting concerns surrounding probiotic supplements so that the current hype does not overpower the hope.}, }
@article {pmid32184369, year = {2020}, author = {Liu, YF and Chen, J and Zaramela, LS and Wang, LY and Mbadinga, SM and Hou, ZW and Wu, XL and Gu, JD and Zengler, K and Mu, BZ}, title = {Genomic and Transcriptomic Evidence Supports Methane Metabolism in Archaeoglobi.}, journal = {mSystems}, volume = {5}, number = {2}, pages = {}, pmid = {32184369}, issn = {2379-5077}, abstract = {Euryarchaeal lineages have been believed to have a methanogenic last common ancestor. However, members of euryarchaeal Archaeoglobi have long been considered nonmethanogenic and their evolutionary history remains elusive. Here, three high-quality metagenomic-assembled genomes (MAGs) retrieved from high-temperature oil reservoir and hot springs, together with three newly assembled Archaeoglobi MAGs from previously reported hot spring metagenomes, are demonstrated to represent a novel genus of Archaeoglobaceae, "Candidatus Methanomixophus." All "Ca Methanomixophus" MAGs encode an M methyltransferase (MTR) complex and a traditional type of methyl-coenzyme M reductase (MCR) complex, which is different from the divergent MCR complexes found in "Ca Polytropus marinifundus." In addition, "Ca Methanomixophus dualitatem" MAGs preserve the genomic capacity for dissimilatory sulfate reduction. Comparative phylogenetic analysis supports a laterally transferred origin for an MCR complex and vertical heritage of the MTR complex in this lineage. Metatranscriptomic analysis revealed concomitant in situ activity of hydrogen-dependent methylotrophic methanogenesis and heterotrophic fermentation within populations of "Ca Methanomixophus hydrogenotrophicum" in a high-temperature oil reservoir.IMPORTANCE Current understanding of the diversity, biology, and ecology of Archaea is very limited, especially considering how few of the known phyla have been cultured or genomically explored. The reconstruction of "Ca Methanomixophus" MAGs not only expands the known range of metabolic versatility of the members of Archaeoglobi but also suggests that the phylogenetic distribution of MCR and MTR complexes is even wider than previously anticipated.}, }
@article {pmid32184120, year = {2020}, author = {Warren, JM and Sloan, DB}, title = {Interchangeable parts: The evolutionarily dynamic tRNA population in plant mitochondria.}, journal = {Mitochondrion}, volume = {52}, number = {}, pages = {144-156}, doi = {10.1016/j.mito.2020.03.007}, pmid = {32184120}, issn = {1872-8278}, mesh = {Evolution, Molecular ; Genetic Variation ; Mitochondria/*genetics ; Phylogeny ; Plants/*genetics ; RNA, Mitochondrial/genetics ; RNA, Transfer/*genetics ; Sequence Analysis, RNA ; }, abstract = {Transfer RNAs (tRNAs) remain one of the very few classes of genes still encoded in the mitochondrial genome. These key components of the protein translation system must interact with a large enzymatic network of nuclear-encoded gene products to maintain mitochondrial function. Plants have an evolutionarily dynamic mitochondrial tRNA population, including ongoing tRNA gene loss and replacement by both horizontal gene transfer from diverse sources and import of nuclear-expressed tRNAs from the cytosol. Thus, plant mitochondria represent an excellent model for understanding how anciently divergent genes can act as "interchangeable parts" during the evolution of complex molecular systems. In particular, understanding the integration of the mitochondrial translation system with elements of the corresponding machinery used in cytosolic protein synthesis is a key area for eukaryotic cellular evolution. Here, we review the increasingly detailed phylogenetic data about the evolutionary history of mitochondrial tRNA gene loss, transfer, and functional replacement that has created extreme variation in mitochondrial tRNA populations across plant species. We describe emerging tRNA-seq methods with promise for refining our understanding of the expression and subcellular localization of tRNAs. Finally, we summarize current evidence and identify open questions related to coevolutionary changes in nuclear-encoded enzymes that have accompanied turnover in mitochondrial tRNA populations.}, }
@article {pmid32182360, year = {2020}, author = {Ali, F and Seshasayee, ASN}, title = {Dynamics of genetic variation in transcription factors and its implications for the evolution of regulatory networks in Bacteria.}, journal = {Nucleic acids research}, volume = {48}, number = {8}, pages = {4100-4114}, pmid = {32182360}, issn = {1362-4962}, support = {IA/I/16/2/502711/WTDBT_/DBT-Wellcome Trust India Alliance/India ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Escherichia coli/genetics ; *Evolution, Molecular ; *Gene Expression Regulation, Bacterial ; *Gene Regulatory Networks ; Genes, Bacterial ; Mutation ; *Point Mutation ; Transcription Factors/*genetics/physiology ; }, abstract = {The evolution of regulatory networks in Bacteria has largely been explained at macroevolutionary scales through lateral gene transfer and gene duplication. Transcription factors (TF) have been found to be less conserved across species than their target genes (TG). This would be expected if TFs accumulate mutations faster than TGs. This hypothesis is supported by several lab evolution studies which found TFs, especially global regulators, to be frequently mutated. Despite these studies, the contribution of point mutations in TFs to the evolution of regulatory network is poorly understood. We tested if TFs show greater genetic variation than their TGs using whole-genome sequencing data from a large collection of Escherichia coli isolates. TFs were less diverse than their TGs across natural isolates, with TFs of large regulons being more conserved. In contrast, TFs showed higher mutation frequency in adaptive laboratory evolution experiments. However, over long-term laboratory evolution spanning 60 000 generations, mutation frequency in TFs gradually declined after a rapid initial burst. Extrapolating the dynamics of genetic variation from long-term laboratory evolution to natural populations, we propose that point mutations, conferring large-scale gene expression changes, may drive the early stages of adaptation but gene regulation is subjected to stronger purifying selection post adaptation.}, }
@article {pmid32176784, year = {2020}, author = {Liu, B and Shui, L and Zhou, K and Jiang, Y and Li, X and Guan, J and Li, Q and Zhuo, C}, title = {Impact of Plasmid-Encoded H-NS-like Protein on blaNDM-1-Bearing IncX3 Plasmid in Escherichia coli.}, journal = {The Journal of infectious diseases}, volume = {221}, number = {Suppl 2}, pages = {S229-S236}, doi = {10.1093/infdis/jiz567}, pmid = {32176784}, issn = {1537-6613}, mesh = {Anti-Bacterial Agents/therapeutic use ; Bacterial Proteins/genetics ; Carbapenem-Resistant Enterobacteriaceae/genetics ; China ; Drug Resistance, Multiple, Bacterial/*genetics ; Enterobacteriaceae Infections/microbiology ; Escherichia coli/drug effects/*genetics/isolation &amp; purification ; Escherichia coli Infections/microbiology ; Gene Transfer, Horizontal/*genetics ; Humans ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Plasmids/*genetics ; Virulence/genetics ; beta-Lactamases/*genetics ; }, abstract = {BACKGROUND: This study was performed to assess the role of the histone-like nucleoid-structuring (H-NS)-like protein, carried by blaNDM-1-encoding IncX3-type plasmids, in the dissemination of IncX3 plasmids.<br><br>METHODS: The blaNDM-1-encoding IncX3 plasmids were analyzed using southern blot, conjugation, and competition assays. Virulence was evaluated with a Galleria mellonella infection model. An hns-knockout IncX3 plasmid was also constructed to identify the functions of plasmid-borne H-NS-like protein in Escherichia coli.<br><br>RESULTS: The assasys detected blaNDM-1-encoding IncX3-type plasmids with similar fingerprint patterns in all New Delhi metallo-&#x3b2;-lactamase (NDM) 1-producing carbapenem-resistant Enterobacteriaceae. The IncX3 plasmid conferred a fitness advantage to E. coli J53 but had no effect on host virulence. Moreover, the transconjugation frequency of the hns-null IncX3 plasmid pHN330-&#x25b3;hns was increased by 2.5-fold compared with the wild type. This was caused by up-regulation of conjugation-related plasmid-borne genes and the partition-related gene, in the J330-pHN330-&#x25b3;hns strain. In addition, decreased virulence was detected with this variant.<br><br>CONCLUSIONS: Our results highlight the important role of IncX3 plasmids in the dissemination of blaNDM-1 in south China. Plasmid-encoded H-NS-like protein can inhibit plasmid conjugation, partition, and the expression of related genes, in addition to promoting virulence in the host.}, }
@article {pmid32175329, year = {2020}, author = {Bykov, A and Glazunova, O and Alikina, O and Sukharicheva, N and Masulis, I and Shavkunov, K and Ozoline, O}, title = {Excessive Promoters as Silencers of Genes Horizontally Acquired by Escherichia coli.}, journal = {Frontiers in molecular biosciences}, volume = {7}, number = {}, pages = {28}, pmid = {32175329}, issn = {2296-889X}, abstract = {Horizontally acquired genes are usually transcriptionally inactive, although most of them are associated with genomic loci enriched with promoter-like sequences forming "promoter islands." We hypothesized that lateral DNA transfer induces local mutagenesis, accumulating AT base pairs and creating promoter-like sequences, whose occupancy with RNA polymerase and a specific silencer H-NS suppresses the transcription of foreign genes. Error-prone mutagenesis was implemented for the "promoter island" of a foreign gene appY and the promoter region of an inherent gene dps. Derivatives with changed transcriptional activity were selected using a reporter plasmid pET28_eGFP. Only one cycle of mutagenesis with negative selection suppressed the activity of the main dps promoter to the background level due to a single substitution in its -10 element, while positive selection gave a sequence with improved -35 element, thus testifying feasibility of the approach. The same suppression for appY was achieved by three cycles, while eightfold transcription activation required nine iterations of mutagenesis. In both cases, the number of potential start points decreased resulting in an ordinary regulatory region with only one dominant promoter in the case of positive selection. Efficiency of H-NS binding remained virtually unchanged in all mutant constructs. Based on these findings we conclude that excessive promoters can adversely affect transcription by providing a platform for interference between several RNA polymerase molecules, which can act as a silencer at promoter-dense regions.}, }
@article {pmid32172042, year = {2020}, author = {Cen, T and Zhang, X and Xie, S and Li, D}, title = {Preservatives accelerate the horizontal transfer of plasmid-mediated antimicrobial resistance genes via differential mechanisms.}, journal = {Environment international}, volume = {138}, number = {}, pages = {105544}, doi = {10.1016/j.envint.2020.105544}, pmid = {32172042}, issn = {1873-6750}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Plasmids ; }, abstract = {Increasing concentrations of preservatives have been detected in environments due to the overuse and misuse of preservatives in food and personal care products. Recent studies have relied heavily on the toxicity, biodegradability, and fate of preservatives in the environment. However, the biological effects of preservatives on antimicrobial resistance, which poses great threats to public health worldwide, are largely unknown. This study investigated three preservatives for their ability and mechanisms of promoting horizontal transfer of antimicrobial resistance genes (ARGs). The results demonstrated that these preservatives (sodium nitrite, sodium benzoate, and triclocarbon), under daily-use concentrations, led to concentration-dependent increases in conjugative transfer by 1.24-2.63, 6.79-7.05, and 2.17-4.31 folds compared with the control group. Even these three preservatives had different patterns on generating intracellular reactive oxidative species (ROS) and reactive nitrogen species (RNS), all of them could stimulate radical-induced RpoS regulon and SOS response, increase cell membrane permeability, and regulate conjugative transfer-related genes, subsequently promoting horizontal transfer of ARGs. The present results expanded the understanding of biological effects induced by preservatives, and provided mechanistic insight into the preservatives-induced resistance. This study also opens an intriguing question on the roles of emerging contaminants including preservatives in the emerging and spread of ARGs in various environments.}, }
@article {pmid32171258, year = {2020}, author = {Sparks, ME and Bansal, R and Benoit, JB and Blackburn, MB and Chao, H and Chen, M and Cheng, S and Childers, C and Dinh, H and Doddapaneni, HV and Dugan, S and Elpidina, EN and Farrow, DW and Friedrich, M and Gibbs, RA and Hall, B and Han, Y and Hardy, RW and Holmes, CJ and Hughes, DST and Ioannidis, P and Cheatle Jarvela, AM and Johnston, JS and Jones, JW and Kronmiller, BA and Kung, F and Lee, SL and Martynov, AG and Masterson, P and Maumus, F and Munoz-Torres, M and Murali, SC and Murphy, TD and Muzny, DM and Nelson, DR and Oppert, B and Panfilio, KA and Paula, DP and Pick, L and Poelchau, MF and Qu, J and Reding, K and Rhoades, JH and Rhodes, A and Richards, S and Richter, R and Robertson, HM and Rosendale, AJ and Tu, ZJ and Velamuri, AS and Waterhouse, RM and Weirauch, MT and Wells, JT and Werren, JH and Worley, KC and Zdobnov, EM and Gundersen-Rindal, DE}, title = {Brown marmorated stink bug, Halyomorpha halys (Stål), genome: putative underpinnings of polyphagy, insecticide resistance potential and biology of a top worldwide pest.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {227}, pmid = {32171258}, issn = {1471-2164}, support = {R01 GM113230/GM/NIGMS NIH HHS/United States ; U54 HG003273/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Ecosystem ; Gene Transfer, Horizontal ; Genome Size ; Heteroptera/classification/*genetics ; Insect Proteins/*genetics ; *Insecticide Resistance ; Introduced Species ; Phylogeny ; Whole Genome Sequencing/*methods ; }, abstract = {BACKGROUND: Halyomorpha halys (Stål), the brown marmorated stink bug, is a highly invasive insect species due in part to its exceptionally high levels of polyphagy. This species is also a nuisance due to overwintering in human-made structures. It has caused significant agricultural losses in recent years along the Atlantic seaboard of North America and in continental Europe. Genomic resources will assist with determining the molecular basis for this species' feeding and habitat traits, defining potential targets for pest management strategies.<br><br>RESULTS: Analysis of the 1.15-Gb draft genome assembly has identified a wide variety of genetic elements underpinning the biological characteristics of this formidable pest species, encompassing the roles of sensory functions, digestion, immunity, detoxification and development, all of which likely support H. halys' capacity for invasiveness. Many of the genes identified herein have potential for biomolecular pesticide applications.<br><br>CONCLUSIONS: Availability of the H. halys genome sequence will be useful for the development of environmentally friendly biomolecular pesticides to be applied in concert with more traditional, synthetic chemical-based controls.}, }
@article {pmid32170101, year = {2020}, author = {Zhang, HH and Peccoud, J and Xu, MR and Zhang, XG and Gilbert, C}, title = {Horizontal transfer and evolution of transposable elements in vertebrates.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {1362}, pmid = {32170101}, issn = {2041-1723}, mesh = {Animals ; Computational Biology ; *DNA Transposable Elements ; Eukaryota/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome ; Mammals/genetics ; Mutation Rate ; Retroelements ; Vertebrates/*genetics ; }, abstract = {Horizontal transfer of transposable elements (HTT) is an important process shaping eukaryote genomes, yet very few studies have quantified this phenomenon on a large scale or have evaluated the selective constraints acting on transposable elements (TEs) during vertical and horizontal transmission. Here we screen 307 vertebrate genomes and infer a minimum of 975 independent HTT events between lineages that diverged more than 120 million years ago. HTT distribution greatly differs from null expectations, with 93.7% of these transfers involving ray-finned fishes and less than 3% involving mammals and birds. HTT incurs purifying selection (conserved protein evolution) on all TEs, confirming that producing functional transposition proteins is required for a TE to invade new genomes. In the absence of HTT, DNA transposons appear to evolve neutrally within genomes, unlike most retrotransposons, which evolve under purifying selection. This selection regime indicates that proteins of most retrotransposon families tend to process their own encoding RNA (cis-preference), which helps retrotransposons to persist within host lineages over long time periods.}, }
@article {pmid32169935, year = {2020}, author = {Álvarez-Narváez, S and Giguère, S and Berghaus, LJ and Dailey, C and Vázquez-Boland, JA}, title = {Horizontal Spread of Rhodococcus equi Macrolide Resistance Plasmid pRErm46 across Environmental Actinobacteria.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {9}, pages = {}, pmid = {32169935}, issn = {1098-5336}, mesh = {Actinobacteria/genetics ; Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Bacterial/*genetics ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Macrolides/*pharmacology ; Plasmids/genetics ; Rhodococcus equi/*genetics ; }, abstract = {Conjugation is one of the main mechanisms involved in the spread and maintenance of antibiotic resistance in bacterial populations. We recently showed that the emerging macrolide resistance in the soilborne equine and zoonotic pathogen Rhodococcus equi is conferred by the erm(46) gene carried on the 87-kb conjugative plasmid pRErm46. Here, we investigated the conjugal transferability of pRErm46 to 14 representative bacteria likely encountered by R. equi in the environmental habitat. In vitro mating experiments demonstrated conjugation to different members of the genus Rhodococcus as well as to Nocardia and Arthrobacter spp. at frequencies ranging from ∼10[-2] to 10[-6] pRErm46 transfer was also observed in mating experiments in soil and horse manure, albeit at a low frequency and after prolonged incubation at 22 to 30°C (environmental temperatures), not 37°C. All transconjugants were able to transfer pRErm46 back to R. equi Conjugation could not be detected with Mycobacterium or Corynebacterium spp. or several members of the more distant phylum Firmicutes such as Enterococcus, Streptococcus, or Staphylococcus Thus, the pRErm46 host range appears to span several actinobacterial orders with certain host restriction within the Corynebacteriales All bacterial species that acquired pRErm46 expressed increased macrolide resistance with no significant deleterious impact on fitness, except in the case of Rhodococcus rhodnii Our results indicate that actinobacterial members of the environmental microbiota can both acquire and transmit the R. equi pRErm46 plasmid and thus potentially contribute to the maintenance and spread of erm(46)-mediated macrolide resistance in equine farms.IMPORTANCE This study demonstrates the efficient horizontal transfer of the Rhodococcus equi conjugative plasmid pRErm46, recently identified as the cause of the emerging macrolide resistance among equine isolates of this pathogen, to and from different environmental Actinobacteria, including a variety of rhodococci as well as Nocardia and Arthrobacter spp. The reported data support the notion that environmental microbiotas may act as reservoirs for the endemic maintenance of antimicrobial resistance in an antibiotic pressurized farm habitat.}, }
@article {pmid32163577, year = {2020}, author = {Cehovin, A and Jolley, KA and Maiden, MCJ and Harrison, OB and Tang, CM}, title = {Association of Neisseria gonorrhoeae Plasmids With Distinct Lineages and The Economic Status of Their Country of Origin.}, journal = {The Journal of infectious diseases}, volume = {222}, number = {11}, pages = {1826-1836}, pmid = {32163577}, issn = {1537-6613}, support = {/WT_/Wellcome Trust/United Kingdom ; 102908/Z/13/Z/WT_/Wellcome Trust/United Kingdom ; 214374/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; 104992/Z/14/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Anti-Bacterial Agents ; Drug Resistance, Bacterial/genetics ; *Economic Status ; Gene Transfer, Horizontal ; Genomics ; Gonorrhea/microbiology ; Humans ; Neisseria gonorrhoeae/classification/*genetics/isolation &amp; purification ; Phylogeny ; Plasmids/*chemistry ; Type IV Secretion Systems/genetics ; Whole Genome Sequencing ; beta-Lactamases/genetics ; }, abstract = {Plasmids are vehicles for horizontal gene transfer between bacteria, and in Neisseria gonorrhoeae plasmids can mediate high-level antimicrobial resistance (AMR). Using genomic and phylogenetic analyses, we show that plasmids are widespread in a collection of 3724 gonococcal isolates from 56 countries, and characterized the conjugative, β-lactamase and cryptic plasmids. We found that variants of the conjugative plasmid (which can mediate tetracycline resistance) and the β-lactamase plasmid expressing TEM-135 are associated with distinct gonococcal lineages. Furthermore, AMR plasmids are significantly more prevalent in gonococci from less wealthy countries, highlighting the need for further studies. More than 94% of gonococci possess the cryptic plasmid, with its absence correlated with the presence of a novel chromosomal type IV secretion system. Our results reveal the extent of plasmid-mediated AMR in the gonococcus, particularly in less wealthy countries, where diagnostic and therapeutic options can be limited, and highlight the risk of their global spread.}, }
@article {pmid32163188, year = {2020}, author = {Chadha, S and Sharma, M}, title = {Genetic differentiation and phylogenetic potential of Ty3/Gypsy LTR retrotransposon markers in soil and plant pathogenic fungi.}, journal = {Journal of basic microbiology}, volume = {60}, number = {6}, pages = {508-516}, doi = {10.1002/jobm.201900487}, pmid = {32163188}, issn = {1521-4028}, mesh = {DNA, Fungal/genetics ; Fungi/classification/*genetics ; Gene Transfer, Horizontal ; Genetic Markers ; Genetic Variation ; Genome, Fungal/genetics ; Genotype ; Phylogeny ; Plant Diseases/microbiology ; Retroelements/*genetics ; Soil Microbiology ; Terminal Repeat Sequences/*genetics ; }, abstract = {Genetic diversity studies are crucial for understanding the genetic structure and evolutionary dynamics of fungal species and communities. Fungal genomes are often reshaped by their repetitive components such as transposable elements. These elements are key players in genomic rearrangements and are ideal targets for genetic diversity and evolutionary studies. Herein, we used three Ty3/Gypsy long terminal repeat retrotransposons, Grasshopper, Maggy, and Pyret, for genetic differentiation and diversity in soil and plant pathogenic fungi, representing diverse species, order, and phyla. Pyret DNA markers showed the highest gene diversity and Shannon's information indices, followed by Maggy and Grasshopper. The observed high levels of multilocus polymorphism indicate the continuous mobility of these elements after their transfer in the new host. In conclusion, this study presents novel markers for genetic differentiation and evolutionary studies of fungi, and sheds light on the prevalence of gene acquisition phenomenon in field fungi.}, }
@article {pmid32163141, year = {2020}, author = {Greshake Tzovaras, B and Segers, FHID and Bicker, A and Dal Grande, F and Otte, J and Anvar, SY and Hankeln, T and Schmitt, I and Ebersberger, I}, title = {What Is in Umbilicaria pustulata? A Metagenomic Approach to Reconstruct the Holo-Genome of a Lichen.}, journal = {Genome biology and evolution}, volume = {12}, number = {4}, pages = {309-324}, pmid = {32163141}, issn = {1759-6653}, mesh = {Ascomycota/*genetics/growth &amp; development ; *Genome, Fungal ; Lichens/*genetics/growth &amp; development ; *Metagenome ; Phylogeny ; *Symbiosis ; }, abstract = {Lichens are valuable models in symbiosis research and promising sources of biosynthetic genes for biotechnological applications. Most lichenized fungi grow slowly, resist aposymbiotic cultivation, and are poor candidates for experimentation. Obtaining contiguous, high-quality genomes for such symbiotic communities is technically challenging. Here, we present the first assembly of a lichen holo-genome from metagenomic whole-genome shotgun data comprising both PacBio long reads and Illumina short reads. The nuclear genomes of the two primary components of the lichen symbiosis-the fungus Umbilicaria pustulata (33 Mb) and the green alga Trebouxia sp. (53 Mb)-were assembled at contiguities comparable to single-species assemblies. The analysis of the read coverage pattern revealed a relative abundance of fungal to algal nuclei of ∼20:1. Gap-free, circular sequences for all organellar genomes were obtained. The bacterial community is dominated by Acidobacteriaceae and encompasses strains closely related to bacteria isolated from other lichens. Gene set analyses showed no evidence of horizontal gene transfer from algae or bacteria into the fungal genome. Our data suggest a lineage-specific loss of a putative gibberellin-20-oxidase in the fungus, a gene fusion in the fungal mitochondrion, and a relocation of an algal chloroplast gene to the algal nucleus. Major technical obstacles during reconstruction of the holo-genome were coverage differences among individual genomes surpassing three orders of magnitude. Moreover, we show that GC-rich inverted repeats paired with nonrandom sequencing error in PacBio data can result in missing gene predictions. This likely poses a general problem for genome assemblies based on long reads.}, }
@article {pmid32160146, year = {2020}, author = {Goswami, C and Fox, S and Holden, MTG and Connor, M and Leanord, A and Evans, TJ}, title = {Origin, maintenance and spread of antibiotic resistance genes within plasmids and chromosomes of bloodstream isolates of Escherichia coli.}, journal = {Microbial genomics}, volume = {6}, number = {4}, pages = {}, pmid = {32160146}, issn = {2057-5858}, support = {/CSO_/Chief Scientist Office/United Kingdom ; }, mesh = {Chromosomes, Bacterial/genetics ; *Drug Resistance, Bacterial ; Escherichia coli/*classification/genetics/isolation &amp; purification ; Escherichia coli Infections/*microbiology ; Escherichia coli Proteins/*genetics ; Gene Transfer, Horizontal ; Humans ; Phylogeny ; Plasmids/genetics ; Sepsis/*microbiology ; United Kingdom ; Whole Genome Sequencing ; }, abstract = {Blood stream invasion by Escherichia coli is the commonest cause of bacteremia in the UK and elsewhere with an attributable mortality of about 15-20 %; antibiotic resistance to multiple agents is common in this microbe and is associated with worse outcomes. Genes conferring antimicrobial resistance, and their frequent location on horizontally transferred genetic elements is well-recognised, but the origin of these determinants, and their ability to be maintained and spread within clinically-relevant bacterial populations is unclear. Here, we set out to examine the distribution of antimicrobial resistance genes in chromosomes and plasmids of 16 bloodstream isolates of E. coli from patients within Scotland, and how these genes are maintained and spread. Using a combination of short and long-read whole genome sequencing methods, we were able to assemble complete sequences of 44 plasmids, with 16 Inc group F and 20 col plasmids; antibiotic resistance genes located almost exclusively within the F group. blaCTX-M15 genes had re-arranged in some strains into the chromosome alone (five strains), while others contained plasmid copies alone (two strains). Integrons containing multiple antibiotic genes were widespread in plasmids, notably many with a dfrA7 gene encoding resistance to trimethoprim, thus linking trimethoprim resistance to the other antibiotic resistance genes within the plasmids. This will allow even narrow spectrum antibiotics such as trimethoprim to act as a selective agent for plasmids containing antibiotic resistance genes mediating much broader resistance, including blaCTX-M15. To our knowledge, this is the first analysis to provide complete sequence data of chromosomes and plasmids in a collection of pathogenic human bloodstream isolates of E. coli. Our findings reveal the interplay between plasmids and integrative and conjugative elements in the maintenance and spread of antibiotic resistance genes within pathogenic E. coli.}, }
@article {pmid32156029, year = {2020}, author = {Amaretti, A and Righini, L and Candeliere, F and Musmeci, E and Bonvicini, F and Gentilomi, GA and Rossi, M and Raimondi, S}, title = {Antibiotic Resistance, Virulence Factors, Phenotyping, and Genotyping of Non-Escherichia coli Enterobacterales from the Gut Microbiota of Healthy Subjects.}, journal = {International journal of molecular sciences}, volume = {21}, number = {5}, pages = {}, pmid = {32156029}, issn = {1422-0067}, mesh = {Amoxicillin-Potassium Clavulanate Combination/*pharmacology ; Anti-Bacterial Agents/*pharmacology ; Citrobacter/drug effects/genetics/pathogenicity ; Cronobacter/drug effects/genetics/pathogenicity ; Drug Resistance, Multiple, Bacterial/*genetics ; Enterobacter/drug effects/genetics/pathogenicity ; Enterobacteriaceae/*drug effects/genetics/pathogenicity ; Gastrointestinal Microbiome/*drug effects/genetics ; Healthy Volunteers ; Humans ; Klebsiella/drug effects/genetics/pathogenicity ; Microbial Sensitivity Tests ; RNA, Ribosomal, 16S/genetics ; Virulence/genetics ; Virulence Factors/genetics ; beta-Lactamase Inhibitors/*pharmacology ; }, abstract = {Non-Escherichia coli Enterobacterales (NECE) can colonize the human gut and may present virulence determinants and phenotypes that represent severe heath concerns. Most information is available for virulent NECE strains, isolated from patients with an ongoing infection, while the commensal NECE population of healthy subjects is understudied. In this study, 32 NECE strains were isolated from the feces of 20 healthy adults. 16S rRNA gene sequencing and mass spectrometry attributed the isolates to Klebsiella pneumoniae, Klebsiella oxytoca, Enterobacter cloacae, Enterobacter aerogenes, Enterobacter kobei, Citrobacter freundii, Citrobacter amalonaticus, Cronobacter sp., and Hafnia alvei, Morganella morganii, and Serratia liquefaciens. Multiplex PCR revealed that K. pneumoniae harbored virulence genes for adhesins (mrkD, ycfM, and kpn) and enterobactin (entB) and, in one case, also for yersiniabactin (ybtS, irp1, irp2, and fyuA). Virulence genes were less numerous in the other NECE species. Biofilm formation was spread across all the species, while curli and cellulose were mainly produced by Citrobacter and Enterobacter. Among the most common antibiotics, amoxicillin-clavulanic acid was the sole against which resistance was observed, only Klebsiella strains being susceptible. The NECE inhabiting the intestine of healthy subjects have traits that may pose a health threat, taking into account the possibility of horizontal gene transfer.}, }
@article {pmid32150264, year = {2020}, author = {Yang, L and Yang, D and Yang, Q and Cheng, F and Huang, Y}, title = {Extracellular DNA in blood products and its potential effects on transfusion.}, journal = {Bioscience reports}, volume = {40}, number = {3}, pages = {}, pmid = {32150264}, issn = {1573-4935}, mesh = {Blood Transfusion/*methods ; Cell-Free Nucleic Acids/*genetics ; DNA, Mitochondrial/genetics ; Humans ; Transfusion Reaction/*genetics ; }, abstract = {Blood transfusions are sometimes necessary after a high loss of blood due to injury or surgery. Some people need regular transfusions due to medical conditions such as haemophilia or cancer. Studies have suggested that extracellular DNA including mitochondrial DNA present in the extracellular milieu of transfused blood products has biological actions that are capable of activating the innate immune systems and potentially contribute to some adverse reactions in transfusion. From the present work, it becomes increasingly clear that extracellular DNA encompassed mitochondrial DNA is far from being biologically inert in blood products. It has been demonstrated to be present in eligible blood products and thus can be transfused to blood recipients. Although the presence of extracellular DNA in human plasma was initially detected in 1948, some aspects have not been fully elucidated. In this review, we summarize the potential origins, clearance mechanisms, relevant structures, and potential role of extracellular DNA in the innate immune responses and its relationship with individual adverse reactions in transfusion.}, }
@article {pmid32149072, year = {2020}, author = {Prado, IGO and da Silva, GC and Crispim, JS and Vidigal, PMP and Nascimento, M and Santana, MF and Bazzolli, DMS}, title = {Comparative Genomics of Actinobacillus pleuropneumoniae Serotype 8 Reveals the Importance of Prophages in the Genetic Variability of the Species.}, journal = {International journal of genomics}, volume = {2020}, number = {}, pages = {9354204}, pmid = {32149072}, issn = {2314-4378}, abstract = {Actinobacillus pleuropneumoniae is the etiologic agent of porcine pleuropneumonia. Currently, there are 18 different serotypes; the serotype 8 is the most widely distributed in the United States, Canada, United Kingdom, and southeastern Brazil. In this study, genomes of seven A. pleuropneumoniae serotype 8 clinical isolates were compared to the other genomes of twelve serotypes. The analyses of serotype 8 genomes resulted in a set of 2352 protein-coding sequences. Of these sequences, 76.6% are present in all serotypes, 18.5% are shared with some serotypes, and 4.9% were differential. This differential portion was characterized as a series of hypothetical and regulatory protein sequences: mobile element sequence. Synteny analysis demonstrated possible events of gene recombination and acquisition by horizontal gene transfer (HGT) in this species. A total of 30 sequences related to prophages were identified in the genomes. These sequences represented 0.3 to 3.5% of the genome of the strains analyzed, and 16 of them contained complete prophages. Similarity analysis between complete prophage sequences evidenced a possible HGT with species belonging to the family Pasteurellaceae. Thus, mobile genetic elements, such as prophages, are important components of the differential portion of the A. pleuropneumoniae genome and demonstrate a central role in the evolution of the species. This study represents the first study done to understand the genome of A. pleuropneumoniae serotype 8.}, }
@article {pmid32143559, year = {2020}, author = {Klonowska, A and Moulin, L and Ardley, JK and Braun, F and Gollagher, MM and Zandberg, JD and Marinova, DV and Huntemann, M and Reddy, TBK and Varghese, NJ and Woyke, T and Ivanova, N and Seshadri, R and Kyrpides, N and Reeve, WG}, title = {Novel heavy metal resistance gene clusters are present in the genome of Cupriavidus neocaledonicus STM 6070, a new species of Mimosa pudica microsymbiont isolated from heavy-metal-rich mining site soil.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {214}, pmid = {32143559}, issn = {1471-2164}, support = {DE-AC02-05CH11231//Biological and Environmental Research/ ; BETASYM ANR-09-JCJ-0046//Agence Nationale de la Recherche/ ; }, mesh = {Cadmium/metabolism ; Cupriavidus/*drug effects/*genetics ; Metals, Heavy/*toxicity ; Mimosa/*microbiology ; Multigene Family ; Nickel/toxicity ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhizobium/drug effects/genetics ; Soil ; Soil Microbiology ; Symbiosis ; Synteny/genetics ; Zinc/toxicity ; }, abstract = {BACKGROUND: Cupriavidus strain STM 6070 was isolated from nickel-rich soil collected near Koniambo massif, New Caledonia, using the invasive legume trap host Mimosa pudica. STM 6070 is a heavy metal-tolerant strain that is highly effective at fixing nitrogen with M. pudica. Here we have provided an updated taxonomy for STM 6070 and described salient features of the annotated genome, focusing on heavy metal resistance (HMR) loci and heavy metal efflux (HME) systems.<br><br>RESULTS: The 6,771,773&#x2009;bp high-quality-draft genome consists of 107 scaffolds containing 6118 protein-coding genes. ANI values show that STM 6070 is a new species of Cupriavidus. The STM 6070 symbiotic region was syntenic with that of the M. pudica-nodulating Cupriavidus taiwanensis LMG 19424[T]. In contrast to the nickel and zinc sensitivity of C. taiwanensis strains, STM 6070 grew at high Ni[2+] and Zn[2+] concentrations. The STM 6070 genome contains 55 genes, located in 12 clusters, that encode HMR structural proteins belonging to the RND, MFS, CHR, ARC3, CDF and P-ATPase protein superfamilies. These HMR molecular determinants are putatively involved in arsenic (ars), chromium (chr), cobalt-zinc-cadmium (czc), copper (cop, cup), nickel (nie and nre), and silver and/or copper (sil) resistance. Seven of these HMR clusters were common to symbiotic and non-symbiotic Cupriavidus species, while four clusters were specific to STM 6070, with three of these being associated with insertion sequences. Within the specific STM 6070 HMR clusters, three novel HME-RND systems (nieIC cep nieBA, czcC2B2A2, and hmxB zneAC zneR hmxS) were identified, which constitute new candidate genes for nickel and zinc resistance.<br><br>CONCLUSIONS: STM 6070 belongs to a new Cupriavidus species, for which we have proposed the name Cupriavidus neocaledonicus sp. nov.. STM6070 harbours a pSym with a high degree of gene conservation to the pSyms of M. pudica-nodulating C. taiwanensis strains, probably as a result of recent horizontal transfer. The presence of specific HMR clusters, associated with transposase genes, suggests that the selection pressure of the New Caledonian ultramafic soils has driven the specific adaptation of STM 6070 to heavy-metal-rich soils via horizontal gene transfer.}, }
@article {pmid32143027, year = {2020}, author = {McInnes, RS and McCallum, GE and Lamberte, LE and van Schaik, W}, title = {Horizontal transfer of antibiotic resistance genes in the human gut microbiome.}, journal = {Current opinion in microbiology}, volume = {53}, number = {}, pages = {35-43}, doi = {10.1016/j.mib.2020.02.002}, pmid = {32143027}, issn = {1879-0364}, support = {215154/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; MR/N013913/1/MRC_/Medical Research Council/United Kingdom ; BB/S017941/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/*genetics/isolation &amp; purification/metabolism ; Bacterial Proteins/genetics/metabolism ; *Drug Resistance, Bacterial ; Gastrointestinal Microbiome/*drug effects ; Gene Transfer, Horizontal ; Humans ; }, abstract = {Infections caused by antibiotic-resistant bacteria are a major threat to public health. The pathogens causing these infections can acquire antibiotic resistance genes in a process termed horizontal gene transfer (HGT). HGT is a common event in the human gut microbiome, that is, the microbial ecosystem of the human intestinal tract. HGT in the gut microbiome can occur via different mechanisms of which transduction and conjugation have been best characterised. Novel bioinformatic tools and experimental approaches have been developed to determine the association of antibiotic resistance genes with their microbial hosts and to quantify the extent of HGT in the gut microbiome. Insights from studies into HGT in the gut microbiome may lead to the development of novel interventions to minimise the spread of antibiotic resistance genes among commensals and opportunistic pathogens.}, }
@article {pmid32140835, year = {2020}, author = {Chen, Y and Guo, X and Wu, J and Jin, M and Zeng, R}, title = {A novel deep-sea bacteriophage possesses features of Wbeta-like viruses and prophages.}, journal = {Archives of virology}, volume = {165}, number = {5}, pages = {1219-1223}, doi = {10.1007/s00705-020-04579-6}, pmid = {32140835}, issn = {1432-8798}, support = {DY135-B-04//China Ocean Mineral Resources Research and Development Association/ ; 2019013//Scientific Research Foundation of Third Institute of Oceanography, MNR/ ; 41976084//National Natural Science Foundation of China/ ; 31702372//National Natural Science Foundation of China (CN)/ ; }, mesh = {Bacillus Phages/*classification/genetics/growth &amp; development/*isolation &amp; purification ; Bacillus cereus/*virology ; Bacteriolysis ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Viral ; Lysogeny ; Recombination, Genetic ; Seawater/*virology ; Sequence Analysis, DNA ; }, abstract = {As the most abundant biological entities, viruses are major players in marine ecosystems. However, our knowledge about virus-host interactions and viral ecology in the deep sea remains very limited. In this study, a novel bacteriophage (designated as phage BVE2) infecting Bacillus cereus group bacteria, was isolated from deep-sea sediments. Phage BVE2 caused host lysis within 1.5 h after infection. However, the presence of two integrase-encoding genes in the BVE2 genome suggested that BVE2 may also follow a temperate strategy. The genome of phage BVE2 is approximately 20 kb in length and is predicted to encode 28 proteins. Genomic and phylogenetic analysis suggested that BVE2 is a highly mosaic phage that has inherited genetic features from Wbeta-like viruses, B. cereus prophages, and its host, suggesting that frequent horizontal gene transfer events occurred during its evolution. This study will help to reveal the evolutionary history of Wbeta-like viruses and improve our understanding of viral diversity and virus-host interactions in the deep sea.}, }
@article {pmid32139767, year = {2020}, author = {Hassan, R and Tantawy, M and Gouda, NA and Elzayat, MG and Gabra, S and Nabih, A and Diab, AA and El-Hadidi, M and Bakry, U and Shoeb, MR and Elanany, M and Shalaby, L and Sayed, AA}, title = {Genotypic characterization of multiple drug resistant Escherichia coli isolates from a pediatric cancer hospital in Egypt.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {4165}, pmid = {32139767}, issn = {2045-2322}, mesh = {Anti-Bacterial Agents/*pharmacokinetics ; Cancer Care Facilities/statistics &amp; numerical data ; Drug Resistance, Multiple, Bacterial/genetics ; Egypt ; Escherichia coli/*drug effects/*genetics ; Escherichia coli Proteins/genetics/*metabolism ; Genotype ; Humans ; Microbial Sensitivity Tests ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; }, abstract = {Infection with multiple drug resistant (MDR) Escherichia coli poses a life threat to immunocompromised pediatric cancer patients. Our aim is to genotypically characterize the plasmids harbored in MDR E. coli isolates recovered from bacteremic patients of Children's Cancer Hospital in Egypt 57357 (CCHE 57357). In this study, 21 carbapenem-resistant E. coli (CRE) isolates were selected that exhibit Quinolones and Aminoglycosides resistance. Plasmid shot-gun sequencing was performed using Illumina next- generation sequencing platform. Isolates demonstrated resistant to all beta-lactams, carbapenems, aminoglycosides and quinolones. Of the 32 antimicrobial resistant genes identified that exceeded the analysis cutoff coverage, the highest represented genes were aph(6)-Id, sul2, aph(3″)-Ib, aph(3')-Ia, sul1, dfrA12, TEM-220, NDM-11. Isolates employed a wide array of resistance mechanisms including antibiotic efflux, antibiotic inactivation, antibiotic target replacements and antibiotic target alteration. Sequenced isolates displayed diverse insertion sequences, including IS26, suggesting dynamic reshuffling of the harbored plasmids. Most isolates carried plasmids originating from other bacterial species suggesting a possible horizontal gene transfer. Only two isolates showed virulence factors with iroA gene cluster which was found in only one of them. Outside the realms of nosocomial infections among patients in hospitals, our results indicate a transfer of resistant genes and plasmids across different organisms.}, }
@article {pmid32138652, year = {2020}, author = {Sevillya, G and Adato, O and Snir, S}, title = {Detecting horizontal gene transfer: a probabilistic approach.}, journal = {BMC genomics}, volume = {21}, number = {Suppl 1}, pages = {106}, pmid = {32138652}, issn = {1471-2164}, mesh = {Algorithms ; Bacteria/*genetics ; Computational Biology/*methods ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genetic Speciation ; Phylogeny ; Viruses/*genetics ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT) is the event of a DNA sequence being transferred between species not by inheritance. HGT is a crucial factor in prokaryotic evolution and is a significant source for genomic novelty resulting in antibiotic resistance or the outbreak of virulent strains. Detection of HGT and the mechanisms responsible and enabling it, is hence of prime importance.Existing algorithms rely on a strong phylogenetic signal distinguishing the transferred sequence from its recipient genome. Closely related species pose an even greater challenge as most genes are very similar and therefore, the phylogenetic signal is weak anyhow. Notwithstanding, the importance of detecting HGT between such organisms is extremely high for the role of HGT in the emergence of new highly virulent strains.<br><br>RESULTS: In a recent work we devised a novel technique that relies on loss of synteny around a gene as a witness for HGT. We used a novel heuristic for synteny measurement, SI (Syntent Index), and the technique was tested on both simulated and real data and was found to provide a greater sensitivity than other HGT techniques. This synteny-based approach suffers low specificity, in particular more closely related species. Here we devise an adaptive approach to cope with this by varying the criteria according to species distance. The new approach is doubly adaptive as it also considers the lengths of the genes being transferred. In particular, we use Chernoff bound to decree HGT both in simulations and real bacterial genomes taken from EggNog database.<br><br>CONCLUSIONS: Here we show empirically that this approach is more conservative than the previous &#x3c7;[2] based approach and provides a lower false positive rate, especially for closely related species and under wide range of genome parameters.}, }
@article {pmid32133212, year = {2019}, author = {Sharma, VK and Yu, X and McDonald, TJ and Jinadatha, C and Dionysiou, DD and Feng, M}, title = {Elimination of antibiotic resistance genes and control of horizontal transfer risk by UV-based treatment of drinking water: A mini review.}, journal = {Frontiers of environmental science &amp; engineering}, volume = {13}, number = {3}, pages = {}, pmid = {32133212}, issn = {2095-2201}, support = {P42 ES027704/ES/NIEHS NIH HHS/United States ; }, abstract = {Antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) have been recognized as one of the biggest public health issues of the 21st century. Both ARB and ARGs have been determined in water after treatment with conventional disinfectants. Ultraviolet (UV) technology has been seen growth in application to disinfect the water. However, UV method alone is not adequate to degrade ARGs in water. Researchers are investigating the combination of UV with other oxidants (chlorine, hydrogen peroxide (H2O2), peroxymonosulfate (PMS), and photocatalysts) to harness the high reactivity of produced reactive species (Cl·, ClO·, Cl2·[-], ·OH, and SO4·[-]) in such processes with constituents of cell (e.g., deoxyribonucleic acid (DNA) and its components) in order to increase the degradation efficiency of ARGs. This paper briefly reviews the current status of different UV-based treatments (UV/chlorination, UV/H2O2, UV/PMS, and UV-photocatalysis) to degrade ARGs and to control horizontal gene transfer (HGT) in water. The review also provides discussion on the mechanism of degradation of ARGs and application of q-PCR and gel electrophoresis to obtain insights of the fate of ARGs during UV-based treatment processes.}, }
@article {pmid32132980, year = {2020}, author = {Werner, J and Nour, E and Bunk, B and Spröer, C and Smalla, K and Springael, D and Öztürk, B}, title = {PromA Plasmids Are Instrumental in the Dissemination of Linuron Catabolic Genes Between Different Genera.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {149}, pmid = {32132980}, issn = {1664-302X}, abstract = {PromA plasmids are broad host range (BHR) plasmids, which are often cryptic and hence have an uncertain ecological role. We present three novel PromA γ plasmids which carry genes associated with degradation of the phenylurea herbicide linuron, two of which originated from unrelated Hydrogenophaga hosts isolated from different environments (pPBL-H3-2 and pBPS33-2), and one (pEN1) which was exogenously captured from an on-farm biopurification system (BPS). Hydrogenophaga sp. plasmid pBPS33-2 carries all three necessary gene clusters (hylA, dca, ccd) determining the three main steps for conversion of linuron to Krebs cycle intermediates, while pEN1 only determines the initial linuron hydrolysis step. Hydrogenophaga sp. plasmid pPBL-H3-2 exists as two variants, both containing ccd but with the hylA and dca gene modules interchanged between each other at exactly the same location. Linuron catabolic gene clusters that determine the same step were identical on all plasmids, encompassed in differently arranged constellations and characterized by the presence of multiple IS1071 elements. In all plasmids except pEN1, the insertion spot of the catabolic genes in the PromA γ plasmids was the same. Highly similar PromA plasmids carrying the linuron degrading gene cargo at the same insertion spot were previously identified in linuron degrading Variovorax sp. Interestingly, in both Hydrogenophaga populations not every PromA plasmid copy carries catabolic genes. The results indicate that PromA plasmids are important vehicles of linuron catabolic gene dissemination, rather than being cryptic and only important for the mobilization of other plasmids.}, }
@article {pmid32132663, year = {2020}, author = {Zheng, Z and Zhang, Y and Liu, Z and Dong, Z and Xie, C and Bravo, A and Soberón, M and Mahillon, J and Sun, M and Peng, D}, title = {The CRISPR-Cas systems were selectively inactivated during evolution of Bacillus cereus group for adaptation to diverse environments.}, journal = {The ISME journal}, volume = {14}, number = {6}, pages = {1479-1493}, pmid = {32132663}, issn = {1751-7370}, mesh = {Acclimatization ; Bacillus ; Bacillus cereus/*physiology ; *CRISPR-Cas Systems ; Environment ; Gene Transfer, Horizontal ; }, abstract = {CRISPR-Cas systems are considered as barriers to horizontal gene transfer (HGT). However, the influence of such systems on HGT within species is unclear. Also, little is known about the impact of CRISPR-Cas systems on bacterial evolution at the population level. Here, using Bacillus cereus sensu lato as model, we investigate the interplay between CRISPR-Cas systems and HGT at the population scale. We found that only a small fraction of the strains have CRISPR-Cas systems (13.9% of 1871), and most of such systems are defective based on their gene content analysis. Comparative genomic analysis revealed that the CRISPR-Cas systems are barriers to HGT within this group, since strains harboring active systems contain less mobile genetic elements (MGEs), have lower fraction of unique genes and also display limited environmental distributions than strains without active CRISPR-Cas systems. The introduction of a functional CRISPR-Cas system into a strain lacking the system resulted in reduced adaptability to various stresses and decreased pathogenicity of the transformant strain, indicating that B. cereus group strains could benefit from inactivating such systems. Our work provides a large-scale case to support that the CRISPR-Cas systems are barriers to HGT within species, and that in the B. cereus group the inactivation of CRISPR-Cas systems correlated with acquisition of MGEs that could result in better adaptation to diverse environments.}, }
@article {pmid32130952, year = {2020}, author = {Domenech, A and Brochado, AR and Sender, V and Hentrich, K and Henriques-Normark, B and Typas, A and Veening, JW}, title = {Proton Motive Force Disruptors Block Bacterial Competence and Horizontal Gene Transfer.}, journal = {Cell host &amp; microbe}, volume = {27}, number = {4}, pages = {544-555.e3}, doi = {10.1016/j.chom.2020.02.002}, pmid = {32130952}, issn = {1934-6069}, support = {/SNSF_/Swiss National Science Foundation/Switzerland ; //Swedish Foundation for Strategic Research/International ; }, mesh = {Animals ; Anti-Bacterial Agents/adverse effects/pharmacology ; Bacterial Proteins/*antagonists &amp; inhibitors/drug effects ; Drug Resistance, Microbial/drug effects ; Drug Resistance, Multiple/drug effects ; *Gene Transfer, Horizontal/drug effects ; Humans ; Mice ; *Proton-Motive Force ; Quorum Sensing/drug effects ; *Streptococcus pneumoniae/drug effects/metabolism ; Virulence Factors ; }, abstract = {Streptococcus pneumoniae is a commensal of the human nasopharynx that can also cause severe antibiotic-resistant infections. Antibiotics drive the spread of resistance by inducing S. pneumoniae competence, in which bacteria express the transformation machinery that facilitates uptake of exogenous DNA and horizontal gene transfer (HGT). We performed a high-throughput screen and identified potent inhibitors of S. pneumoniae competence, called COM-blockers. COM-blockers limit competence by inhibiting the proton motive force (PMF), thereby disrupting export of a quorum-sensing peptide that regulates the transformation machinery. Known chemical PMF disruptors and alterations in pH homeostasis similarly inhibit competence. COM-blockers limit transformation of clinical multi-drug-resistant strains and HGT in infected mice. At their active concentrations, COM-blockers do not affect growth, compromise antibiotic activity, or elicit detectable resistance. COM-blockers provide an experimental tool to inhibit competence and other PMF-involved processes and could help reduce the spread of virulence factors and antibiotic resistance in bacteria. VIDEO ABSTRACT.}, }
@article {pmid32127605, year = {2020}, author = {Wang, Z and Li, W and Li, H and Zheng, W and Guo, F}, title = {Phylogenomics of Rhodocyclales and its distribution in wastewater treatment systems.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {3883}, pmid = {32127605}, issn = {2045-2322}, mesh = {Betaproteobacteria/genetics/*isolation &amp; purification ; Denitrification ; Gene Transfer, Horizontal ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Temperature ; *Waste Disposal, Fluid ; Wastewater/*microbiology ; }, abstract = {Rhodocyclales is an abundant bacterial order in wastewater treatment systems and putatively plays key roles in multiple functions. Its phylogenomics, prevalence of denitrifying genes in sub-lineages and distribution in wastewater treatment plants (WWTPs) worldwide have not been well characterized. In the present study, we collected 78 Rhodocyclales genomes, including 17 from type strains, non-type strains and genome bins contributed by this study. Phylogenomics indicated that the order could be divided into five family-level lineages. With only a few exceptions (mostly in Rhodocyclaceae), nirS-containing genomes in this order usually contained the downstream genes of norB and nosZ. Multicopy of denitrifying genes occurred frequently and events of within-order horizontal transfer of denitrifying genes were phylogenetically deduced. The distribution of Rhodocyclaceae, Zoogloeaceae and Azonexaceae in global WWTPs were significantly governed by temperature, mixed liquor suspended solids, etc. Metagenomic survey showed that the order generally ranked at the top or second for different denitrifying genes in wastewater treatment systems. Our results provided comprehensive genomic insights into the phylogeny and features of denitrifying genes of Rhodocyclales. Its contribution to the denitrifying gene pool in WWTPs was proved.}, }
@article {pmid32127449, year = {2020}, author = {Carvalho, G and Fouchet, D and Danesh, G and Godeux, AS and Laaberki, MH and Pontier, D and Charpentier, X and Venner, S}, title = {Bacterial Transformation Buffers Environmental Fluctuations through the Reversible Integration of Mobile Genetic Elements.}, journal = {mBio}, volume = {11}, number = {2}, pages = {}, pmid = {32127449}, issn = {2150-7511}, mesh = {Bacteria/*genetics ; *Computer Simulation ; Environmental Microbiology ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Interspersed Repetitive Sequences ; *Transformation, Bacterial ; }, abstract = {Horizontal gene transfer (HGT) promotes the spread of genes within bacterial communities. Among the HGT mechanisms, natural transformation stands out as being encoded by the bacterial core genome. Natural transformation is often viewed as a way to acquire new genes and to generate genetic mixing within bacterial populations. Another recently proposed function is the curing of bacterial genomes of their infectious parasitic mobile genetic elements (MGEs). Here, we propose that these seemingly opposing theoretical points of view can be unified. Although costly for bacterial cells, MGEs can carry functions that are at points in time beneficial to bacteria under stressful conditions (e.g., antibiotic resistance genes). Using computational modeling, we show that, in stochastic environments, an intermediate transformation rate maximizes bacterial fitness by allowing the reversible integration of MGEs carrying resistance genes, although these MGEs are costly for host cell replication. Based on this dual function (MGE acquisition and removal), transformation would be a key mechanism for stabilizing the bacterial genome in the long term, and this would explain its striking conservation.IMPORTANCE Natural transformation is the acquisition, controlled by bacteria, of extracellular DNA and is one of the most common mechanisms of horizontal gene transfer, promoting the spread of resistance genes. However, its evolutionary function remains elusive, and two main roles have been proposed: (i) the new gene acquisition and genetic mixing within bacterial populations and (ii) the removal of infectious parasitic mobile genetic elements (MGEs). While the first one promotes genetic diversification, the other one promotes the removal of foreign DNA and thus genome stability, making these two functions apparently antagonistic. Using a computational model, we show that intermediate transformation rates, commonly observed in bacteria, allow the acquisition then removal of MGEs. The transient acquisition of costly MGEs with resistance genes maximizes bacterial fitness in environments with stochastic stress exposure. Thus, transformation would ensure both a strong dynamic of the bacterial genome in the short term and its long-term stabilization.}, }
@article {pmid32125435, year = {2020}, author = {Santana-Molina, C and Rivas-Marin, E and Rojas, AM and Devos, DP}, title = {Origin and Evolution of Polycyclic Triterpene Synthesis.}, journal = {Molecular biology and evolution}, volume = {37}, number = {7}, pages = {1925-1941}, pmid = {32125435}, issn = {1537-1719}, mesh = {Carotenoids/*metabolism ; Eukaryota/metabolism ; *Evolution, Molecular ; Farnesyl-Diphosphate Farnesyltransferase/*genetics/metabolism ; Genes, Bacterial ; *Phylogeny ; Squalene/*metabolism ; Sterols/biosynthesis ; }, abstract = {Polycyclic triterpenes are members of the terpene family produced by the cyclization of squalene. The most representative polycyclic triterpenes are hopanoids and sterols, the former are mostly found in bacteria, whereas the latter are largely limited to eukaryotes, albeit with a growing number of bacterial exceptions. Given their important role and omnipresence in most eukaryotes, contrasting with their scant representation in bacteria, sterol biosynthesis was long thought to be a eukaryotic innovation. Thus, their presence in some bacteria was deemed to be the result of lateral gene transfer from eukaryotes. Elucidating the origin and evolution of the polycyclic triterpene synthetic pathways is important to understand the role of these compounds in eukaryogenesis and their geobiological value as biomarkers in fossil records. Here, we have revisited the phylogenies of the main enzymes involved in triterpene synthesis, performing gene neighborhood analysis and phylogenetic profiling. Squalene can be biosynthesized by two different pathways containing the HpnCDE or Sqs proteins. Our results suggest that the HpnCDE enzymes are derived from carotenoid biosynthesis ones and that they assembled in an ancestral squalene pathway in bacteria, while remaining metabolically versatile. Conversely, the Sqs enzyme is prone to be involved in lateral gene transfer, and its emergence is possibly related to the specialization of squalene biosynthesis. The biosynthesis of hopanoids seems to be ancestral in the Bacteria domain. Moreover, no triterpene cyclases are found in Archaea, invoking a potential scenario in which eukaryotic genes for sterol biosynthesis assembled from ancestral bacterial contributions in early eukaryotic lineages.}, }
@article {pmid32122894, year = {2020}, author = {Cui, CY and Chen, C and Liu, BT and He, Q and Wu, XT and Sun, RY and Zhang, Y and Cui, ZH and Guo, WY and Jia, QL and Li, C and Kreiswirth, BN and Liao, XP and Chen, L and Liu, YH and Sun, J}, title = {Co-occurrence of Plasmid-Mediated Tigecycline and Carbapenem Resistance in Acinetobacter spp. from Waterfowls and Their Neighboring Environment.}, journal = {Antimicrobial agents and chemotherapy}, volume = {64}, number = {5}, pages = {}, pmid = {32122894}, issn = {1098-6596}, support = {R01 AI090155/AI/NIAID NIH HHS/United States ; }, mesh = {Acinetobacter/*drug effects ; Acinetobacter Infections/epidemiology/*microbiology/*veterinary ; Animals ; Anti-Bacterial Agents/*pharmacology ; Bird Diseases/epidemiology/*microbiology ; Birds/*microbiology ; Carbapenems/*pharmacology ; China ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Molecular Epidemiology ; Plasmids ; Tetracycline Resistance/*genetics ; Tigecycline/*pharmacology ; Whole Genome Sequencing ; }, abstract = {Tigecycline serves as one of the antibiotics of last resort to treat multidrug-resistant (including carbapenem-resistant) pathogens. However, the recently emerged plasmid-mediated tigecycline resistance mechanism, Tet(X), challenges the clinical efficacy of this class of antibiotics. In this study, we detected 180 tet(X)-harboring Acinetobacter isolates (8.9%, n = 180) from 2,018 samples collected from avian farms and adjacent environments in China. Eighteen tet(X)-harboring isolates (10.0%) were found to cocarry the carbapenemase gene blaNDM-1, mostly from waterfowl samples (94.4%, 17/18). Interestingly, among six Acinetobacter strains, tet(X) and blaNDM-1 were found to colocalize on the same plasmids. Moreover, whole-genome sequencing (WGS) revealed a novel orthologue of tet(X) in the six isolates coharboring tet(X) and blaNDM-1 Inverse PCR suggested that the two tet(X) genes form a single transposable unit and may be cotransferred. Sequence comparison between six tet(X)- and blaNDM-1-coharboring plasmids showed that they shared a highly homologous plasmid backbone even though they were isolated from different Acinetobacter species (three from Acinetobacter indicus, two from Acinetobacter schindleri, and one from Acinetobacter lwoffii) from various sources and from different geological regions, suggesting the horizontal genetic transfer of a common tet(X)- and blaNDM-1-coharboring plasmid among Acinetobacter species in China. Emergence and spread of such plasmids and strains are of great clinical concern, and measures must be implemented to avoid their dissemination.}, }
@article {pmid32122606, year = {2020}, author = {Dong, WL and Xu, QJ and Atiah, LA and Odah, KA and Gao, YH and Kong, LC and Ma, HX}, title = {Genomic island type IV secretion system and transposons in genomic islands involved in antimicrobial resistance in Trueperella pyogenes.}, journal = {Veterinary microbiology}, volume = {242}, number = {}, pages = {108602}, doi = {10.1016/j.vetmic.2020.108602}, pmid = {32122606}, issn = {1873-2542}, mesh = {Actinomycetaceae/*drug effects/*genetics ; Animals ; Anti-Bacterial Agents/*pharmacology ; *DNA Transposable Elements ; Drug Resistance, Multiple, Bacterial/*genetics ; *Genomic Islands ; Lung/microbiology ; Microbial Sensitivity Tests ; Swine/microbiology ; Tetracycline Resistance/genetics ; Type IV Secretion Systems/*genetics ; Whole Genome Sequencing ; }, abstract = {Trueperella pyogenes (T. pyogenes) is a well-known opportunistic pathogen of many animal species. It can cause a variety of suppurative infections. The objective of this research was to get insight into the gene context and the location of the antimicrobial resistance determinants in the two multi-resistant T. pyogenes isolates TP3 and TP4. Comparative analysis of key factors leading to antimicrobial resistance was performed. Both isolates were resistant to erythromycin, azithromycin and tetracycline, and susceptible to ciprofloxacin, enrofloxacin, cefazolin and florfenicol. In addition, TP4 was resistant to amikacin and gentamicin. Whole-genome analyses revealed that both TP3 and TP4 contained two different genomic islands (TP3-GI1, TP3-GI5, TP4-GI5 and TP4-GI8) involved in multi-drug resistance. There is a common region in TP3-GI1 and TP4-GI5, containing the tetracycline resistance gene tet(W) and a series of genes involved in type IV secretion systems. Several genes located on TP3-GI5 and TP4-GI8 are highly homologous. Tetracycline-resistance gene tet(33) was potentially acquired by horizontal gene transfer via IS6100 located on 57,936 bp TP3-GI5. The macrolide resistance gene erm(X) was located near the end of the TP3-GI5. The sequence analysis of TP4-GI8 showed that two copies of erm(X) and two IS1634 elements located in the same orientation may have formed a composite transposon. GI-type T4SS, transposons and multiple resistance genes located on GIs play a key role in multiple drug resistance of TP3 and TP4.}, }
@article {pmid32122298, year = {2020}, author = {Roach, MJ and Borneman, AR}, title = {New genome assemblies reveal patterns of domestication and adaptation across Brettanomyces (Dekkera) species.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {194}, pmid = {32122298}, issn = {1471-2164}, mesh = {Adaptation, Physiological ; Brettanomyces/classification/genetics/*physiology ; Evolution, Molecular ; Fermentation ; Gene Transfer, Horizontal ; *Genome, Fungal ; Phylogeny ; Sequence Analysis, DNA/*methods ; Species Specificity ; }, abstract = {BACKGROUND: Yeasts of the genus Brettanomyces are of significant interest, both for their capacity to spoil, as well as their potential to positively contribute to different industrial fermentations. However, considerable variance exists in the depth of research and knowledgebase of the five currently known species of Brettanomyces. For instance, Brettanomyces bruxellensis has been heavily studied and many resources are available for this species, whereas Brettanomyces nanus is rarely studied and lacks a publicly available genome assembly altogether. The purpose of this study is to fill this knowledge gap and explore the genomic adaptations that have shaped the evolution of this genus.<br><br>RESULTS: Strains for each of the five widely accepted species of Brettanomyces (Brettanomyces anomalus, B. bruxellensis, Brettanomyces custersianus, Brettanomyces naardenensis, and B. nanus) were sequenced using a combination of long- and short-read sequencing technologies. Highly contiguous assemblies were produced for each species. Structural differences between the species' genomes were observed with gene expansions in fermentation-relevant genes (particularly in B. bruxellensis and B. nanus) identified. Numerous horizontal gene transfer (HGT) events in all Brettanomyces species', including an HGT event that is probably responsible for allowing B. bruxellensis and B. anomalus to utilize sucrose were also observed.<br><br>CONCLUSIONS: Genomic adaptations and some evidence of domestication that have taken place in Brettanomyces are outlined. These new genome assemblies form a valuable resource for future research in Brettanomyces.}, }
@article {pmid32121565, year = {2020}, author = {Tiwari, P and Bae, H}, title = {Horizontal Gene Transfer and Endophytes: An Implication for the Acquisition of Novel Traits.}, journal = {Plants (Basel, Switzerland)}, volume = {9}, number = {3}, pages = {}, pmid = {32121565}, issn = {2223-7747}, support = {PJ013655022020//Rural Development Administration/ ; }, abstract = {Horizontal gene transfer (HGT), an important evolutionary mechanism observed in prokaryotes, is the transmission of genetic material across phylogenetically distant species. In recent years, the availability of complete genomes has facilitated the comprehensive analysis of HGT and highlighted its emerging role in the adaptation and evolution of eukaryotes. Endophytes represent an ecologically favored association, which highlights its beneficial attributes to the environment, in agriculture and in healthcare. The HGT phenomenon in endophytes, which features an important biological mechanism for their evolutionary adaptation within the host plant and simultaneously confers "novel traits" to the associated microbes, is not yet completely understood. With a focus on the emerging implications of HGT events in the evolution of biological species, the present review discusses the occurrence of HGT in endophytes and its socio-economic importance in the current perspective. To our knowledge, this review is the first report that provides a comprehensive insight into the impact of HGT in the adaptation and evolution of endophytes.}, }
@article {pmid32117108, year = {2020}, author = {Wang, F and Han, W and Chen, S and Dong, W and Qiao, M and Hu, C and Liu, B}, title = {Fifteen-Year Application of Manure and Chemical Fertilizers Differently Impacts Soil ARGs and Microbial Community Structure.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {62}, pmid = {32117108}, issn = {1664-302X}, abstract = {Manure, which contains large amounts of antibiotics and antibiotic resistance genes (ARGs), is widely used in agricultural soils and may lead to the evolution and dispersal of ARGs in the soil environment. In the present study, soils that received manure or chemical fertilizers for 15 years were sampled on the North China Plain (NCP), which is one of the primary areas of intensive agriculture in China. High-throughput quantitative PCR and sequencing technologies were employed to assess the effects of long-term manure or chemical fertilizer application on the distribution of ARGs and microbial communities. A total of 114 unique ARGs were successfully amplified from all soil samples. Manure application markedly increased the relative abundance and detectable numbers of ARGs, with up to 0.23 copies/16S rRNA gene and 81 unique ARGs. The increased abundance of ARGs in manure-fertilized soil was mainly due to the manure increasing the abundance of indigenous soil ARGs. In contrast, chemical fertilizers only moderately affected the diversity of ARGs and had no significant effect on the relative abundance of the total ARGs. In addition, manure application increased the abundance of mobile genetic elements (MGEs), which were significantly and positively correlated with most types of ARGs, indicating that horizontal gene transfer via MGEs may play an important role in the spread of ARGs. Furthermore, the application of manure and chemical fertilizers significantly affected microbial community structure, and variation partitioning analysis showed that microbial community shifts represented the major driver shaping the antibiotic resistome. Taken together, our results provide insight into the long-term effects of manure and chemical fertilization on the dissemination of ARGs in intensive agricultural ecosystems.}, }
@article {pmid32117100, year = {2020}, author = {Mazhar, SH and Herzberg, M and Ben Fekih, I and Zhang, C and Bello, SK and Li, YP and Su, J and Xu, J and Feng, R and Zhou, S and Rensing, C}, title = {Comparative Insights Into the Complete Genome Sequence of Highly Metal Resistant Cupriavidus metallidurans Strain BS1 Isolated From a Gold-Copper Mine.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {47}, pmid = {32117100}, issn = {1664-302X}, abstract = {The highly heavy metal resistant strain Cupriavidus metallidurans BS1 was isolated from the Zijin gold-copper mine in China. This was of particular interest since the extensively studied, closely related strain, C. metallidurans CH34 was shown to not be only highly heavy metal resistant but also able to reduce metal complexes and biomineralizing them into metallic nanoparticles including gold nanoparticles. After isolation, C. metallidurans BS1 was characterized and complete genome sequenced using PacBio and compared to CH34. Many heavy metal resistance determinants were identified and shown to have wide-ranging similarities to those of CH34. However, both BS1 and CH34 displayed extensive genome plasticity, probably responsible for significant differences between those strains. BS1 was shown to contain three prophages, not present in CH34, that appear intact and might be responsible for shifting major heavy metal resistance determinants from plasmid to chromid (CHR2) in C. metallidurans BS1. Surprisingly, the single plasmid - pBS1 (364.4 kbp) of BS1 contains only a single heavy metal resistance determinant, the czc determinant representing RND-type efflux system conferring resistance to cobalt, zinc and cadmium, shown here to be highly similar to that determinant located on pMOL30 in C. metallidurans CH34. However, in BS1 another homologous czc determinant was identified on the chromid, most similar to the czc determinant from pMOL30 in CH34. Other heavy metal resistance determinants such as cnr and chr determinants, located on megaplasmid pMOL28 in CH34, were shown to be adjacent to the czc determinant on chromid (CHR2) in BS1. Additionally, other heavy metal resistance determinants such as pbr, cop, sil, and ars were located on the chromid (CHR2) and not on pBS1 in BS1. A diverse range of genomic rearrangements occurred in this strain, isolated from a habitat of constant exposure to high concentrations of copper, gold and other heavy metals. In contrast, the megaplasmid in BS1 contains mostly genes encoding unknown functions, thus might be more of an evolutionary playground where useful genes could be acquired by horizontal gene transfer and possibly reshuffled to help C. metallidurans BS1 withstand the intense pressure of extreme concentrations of heavy metals in its environment.}, }
@article {pmid32114122, year = {2020}, author = {Zhen, Z and Yan, C and Zhao, Y}, title = {Influence of epiphytic bacteria on arsenic metabolism in Hydrilla verticillata.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {261}, number = {}, pages = {114232}, doi = {10.1016/j.envpol.2020.114232}, pmid = {32114122}, issn = {1873-6424}, mesh = {*Arsenic/metabolism ; *Bacteria/genetics/metabolism ; Gene Transfer, Horizontal ; *Hydrocharitaceae/microbiology ; Phylogeny ; }, abstract = {Microbial assemblages such as biofilms around aquatic plants play a major role in arsenic (As) cycling, which has often been overlooked in previous studies. In this study, arsenite (As(III))-oxidizing, arsenate (As(V))-reducing and As(III)-methylating bacteria were found to coexist in the phyllosphere of Hydrilla verticillata, and their relative activities were shown to determine As speciation, accumulation and efflux. When exposed to As(III), As(III) oxidation was not observed in treatment H(III)-B, whereas treatment H(III)+B showed a significant As(III) oxidation ability, thereby indicating that epiphytic bacteria displayed a substantial As(III) oxidation ability. When exposed to As(V), the medium only contained 5.89% As(III) after 48 h of treatment H(V)-B, while an As(III) content of 86.72% was observed after treatment H(V)+B, thereby indicating that the elevated As(III) in the medium probably originated from As(V) reduction by epiphytic bacteria. Our data also indicated that oxidizing bacteria decreased the As accumulation (by approximately 64.44% compared with that of treatment H(III)-B) in plants, while reducing bacteria played a critical role in increasing As accumulation (by approximately 3.31-fold compared with that of treatment H(V)-B) in plants. Regardless of whether As(III) or As(V) was supplied, As(III) was dominant in the plant tissue (over 75%). Furthermore, the presence of epiphytic bacteria enhanced As efflux by approximately 9-fold. Metagenomic analysis revealed highly diverse As metabolism genes in epiphytic bacterial community, particularly those related to energetic metabolism (aioAB), and As resistance (arsABCR, acr3, arsM). Phylogenetic analysis of As metabolism genes revealed evidence of both vertical inheritance and horizontal gene transfer, which might have contributed to the evolution of the As metabolism genes. Taken together, our research suggested that the diversity of As metabolism genes in epiphytic bacterial community is associated with aquatic submerged macrophytes which may play an important role in As biogeochemistry in aquatic environments.}, }
@article {pmid32112190, year = {2020}, author = {Lang, SA and McIlroy, P and Shain, DH}, title = {Structural Evolution of the Glacier Ice Worm Fo ATP Synthase Complex.}, journal = {The protein journal}, volume = {39}, number = {2}, pages = {152-159}, pmid = {32112190}, issn = {1875-8355}, support = {ARRA NIH R15GM093685/NH/NIH HHS/United States ; }, mesh = {ATP Synthetase Complexes/*chemistry/genetics ; Adaptation, Biological ; Animals ; Cold Temperature ; Energy Metabolism ; *Evolution, Molecular ; Oligochaeta/*enzymology/genetics ; Protein Domains ; }, abstract = {The segmented annelid worm, Mesenchytraeus solifugus, is a permanent resident of temperate, maritime glaciers in the Pacific northwestern region of North America, displaying atypically high intracellular ATP levels which have been linked to its unusual ability to thrive in hydrated glacier ice. We have shown previously that ice worms contain a highly basic, carboxy terminal extension on their ATP6 regulatory subunit, likely acquired by horizontal gene transfer from a microbial dietary source. Here we examine the full complement of F1F0 ATP synthase structural subunits with attention to non-conservative, ice worm-specific structural modifications. Our genomics analyses and molecular models identify putative proton shuttling domains on either side of the F0 hemichannel, which predictably function to enhance proton flow across the mitochondrial membrane. Other components of the ice worm ATP synthase complex have remained largely unchanged in the context of Metazoan evolution.}, }
@article {pmid32111893, year = {2020}, author = {Golz, JC and Epping, L and Knüver, MT and Borowiak, M and Hartkopf, F and Deneke, C and Malorny, B and Semmler, T and Stingl, K}, title = {Whole genome sequencing reveals extended natural transformation in Campylobacter impacting diagnostics and the pathogens adaptive potential.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {3686}, pmid = {32111893}, issn = {2045-2322}, mesh = {Animals ; Campylobacter Infections/diagnosis/*genetics/microbiology ; Campylobacter coli/*genetics/pathogenicity ; Campylobacter jejuni/*growth &amp; development/pathogenicity ; Gastroenteritis/diagnosis/*genetics/microbiology ; *Genetic Variation ; *Genome, Bacterial ; Humans ; *Recombination, Genetic ; Whole Genome Sequencing ; }, abstract = {Campylobacter is the major bacterial agent of human gastroenteritis worldwide and represents a crucial global public health burden. Species differentiation of C. jejuni and C. coli and phylogenetic analysis is challenged by inter-species horizontal gene transfer. Routine real-time PCR on more than 4000 C. jejuni and C. coli field strains identified isolates with ambiguous PCR results for species differentiation, in particular, from the isolation source eggs. K-mer analysis of whole genome sequencing data indicated the presence of C. coli hybrid strains with huge amounts of C. jejuni introgression. Recombination events were distributed over the whole chromosome. MLST typing was impaired, since C. jejuni sequences were also found in six of the seven housekeeping genes. cgMLST suggested that the strains were phylogenetically unrelated. Intriguingly, the strains shared a stress response set of C. jejuni variant genes, with proposed roles in oxidative, osmotic and general stress defence, chromosome maintenance and repair, membrane transport, cell wall and capsular biosynthesis and chemotaxis. The results have practical impact on routine typing and on the understanding of the functional adaption to harsh environments, enabling successful spreading and persistence of Campylobacter.}, }
@article {pmid32110912, year = {2020}, author = {Saliu, EM and Ren, H and Boroojeni, FG and Zentek, J and Vahjen, W}, title = {The Impact of Direct-Fed Microbials and Phytogenic Feed Additives on Prevalence and Transfer of Extended-Spectrum Beta-Lactamase Genes in Broiler Chicken.}, journal = {Microorganisms}, volume = {8}, number = {3}, pages = {}, pmid = {32110912}, issn = {2076-2607}, support = {No. 2817701014//undefined &lt;span style="color:gray;font-size:10px;"&gt;undefined&lt;/span&gt;/ ; }, abstract = {Poultry frequently account for the highest prevalence of extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae in livestock. To investigate the impact of direct-fed microbials (DFM) and phytobiotic feed additives on prevalence and conjugation of extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae, an animal trial was conducted. Lactobacillus agilis LA73 and Lactobacillus salivarius LS1 and two commercial phytogenic feed additives (consisting of carvacrol, cinnamaldehyde, and eugenol) were used as feed additives either alone or as a combination of DFM and phytogenic feed additive. An ESBL-producing E. coli donor and a potentially pathogenic Salmonella Typhimurium recipient were inoculated at 5 × 10[9] cells/mL in cecal contents from 2-week-old broilers. Conjugation frequencies were determined after 4 h aerobic co-incubation at 37 °C and corrected for the impact of the sample matrix on bacterial growth of donor and recipient. Surprisingly, indigenous Enterobacteriaceae acted as recipients instead of the anticipated Salmonella recipient. The observed increase in conjugation frequency was most obvious in the groups fed the combinations of DFM and phytogenic product, but merely up to 0.6 log units. Further, cecal samples were examined for ESBL-producing Enterobacteriaceae on five consecutive days in broilers aged 27-31 days. All samples derived from animals fed the experimental diet showed lower ESBL-prevalence than the control. It is concluded that Lactobacillus spp. and essential oils may help to reduce the prevalence of ESBL-harboring plasmids in broilers, while the effect on horizontal gene transfer is less obvious.}, }
@article {pmid32109282, year = {2020}, author = {Abe, K and Nomura, N and Suzuki, S}, title = {Biofilms: hot spots of horizontal gene transfer (HGT) in aquatic environments, with a focus on a new HGT mechanism.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {5}, pages = {}, pmid = {32109282}, issn = {1574-6941}, mesh = {Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics ; Biofilms ; Drug Resistance, Microbial ; *Gene Transfer, Horizontal ; }, abstract = {Biofilms in water environments are thought to be hot spots for horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). ARGs can be spread via HGT, though mechanisms are known and have been shown to depend on the environment, bacterial communities and mobile genetic elements. Classically, HGT mechanisms include conjugation, transformation and transduction; more recently, membrane vesicles (MVs) have been reported as DNA reservoirs implicated in interspecies HGT. Here, we review the current knowledge on the HGT mechanisms with a focus on the role of MVs and the methodological innovations in the HGT research.}, }
@article {pmid32106817, year = {2020}, author = {Tong, W and Li, X and Wang, E and Cao, Y and Chen, W and Tao, S and Wei, G}, title = {Genomic insight into the origins and evolution of symbiosis genes in Phaseolus vulgaris microsymbionts.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {186}, pmid = {32106817}, issn = {1471-2164}, support = {2016YFD0200308//National Key Research &amp; Development Program/ ; }, mesh = {Bradyrhizobium/*classification/genetics/physiology ; Chromosomes, Bacterial/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Phaseolus/*microbiology ; Phylogeny ; Plasmids/genetics ; Rhizobium phaseoli/*classification/genetics/physiology ; Root Nodules, Plant/microbiology ; Sinorhizobium/*classification/genetics/physiology ; Symbiosis ; Whole Genome Sequencing/*methods ; }, abstract = {BACKGROUND: Phaseolus vulgaris (common bean) microsymbionts belonging to the bacterial genera Rhizobium, Bradyrhizobium, and Ensifer (Sinorhizobium) have been isolated across the globe. Individual symbiosis genes (e.g., nodC) of these rhizobia can be different within each genus and among distinct genera. Little information is available about the symbiotic structure of indigenous Rhizobium strains nodulating introduced bean plants or the emergence of a symbiotic ability to associate with bean plants in Bradyrhizobium and Ensifer strains. Here, we sequenced the genomes of 29 representative bean microsymbionts (21 Rhizobium, four Ensifer, and four Bradyrhizobium) and compared them with closely related reference strains to estimate the origins of symbiosis genes among these Chinese bean microsymbionts.<br><br>RESULTS: Comparative genomics demonstrated horizontal gene transfer exclusively at the plasmid level, leading to expanded diversity of bean-nodulating Rhizobium strains. Analysis of vertically transferred genes uncovered 191 (out of the 2654) single-copy core genes with phylogenies strictly consistent with the taxonomic status of bacterial species, but none were found on symbiosis plasmids. A common symbiotic region was wholly conserved within the Rhizobium genus yet different from those of the other two genera. A single strain of Ensifer and two Bradyrhizobium strains shared similar gene content with soybean microsymbionts in both chromosomes and symbiotic regions.<br><br>CONCLUSIONS: The 19 native bean Rhizobium microsymbionts were assigned to four defined species and six putative novel species. The symbiosis genes of R. phaseoli, R. sophoriradicis, and R. esperanzae strains that originated from Mexican bean-nodulating strains were possibly introduced alongside bean seeds. R. anhuiense strains displayed distinct host ranges, indicating transition into bean microsymbionts. Among the six putative novel species exclusive to China, horizontal transfer of symbiosis genes suggested symbiosis with other indigenous legumes and loss of originally symbiotic regions or non-symbionts before the introduction of common bean into China. Genome data for Ensifer and Bradyrhizobium strains indicated symbiotic compatibility between microsymbionts of common bean and other hosts such as soybean.}, }
@article {pmid32106595, year = {2020}, author = {Fouz, N and Pangesti, KNA and Yasir, M and Al-Malki, AL and Azhar, EI and Hill-Cawthorne, GA and Abd El Ghany, M}, title = {The Contribution of Wastewater to the Transmission of Antimicrobial Resistance in the Environment: Implications of Mass Gathering Settings.}, journal = {Tropical medicine and infectious disease}, volume = {5}, number = {1}, pages = {}, pmid = {32106595}, issn = {2414-6366}, abstract = {Antimicrobial resistance (AMR) is the major issue posing a serious global health threat. Low- and middle-income countries are likely to be the most affected, both in terms of impact on public health and economic burden. Recent studies highlighted the role of resistance networks on the transmission of AMR organisms, with this network being driven by complex interactions between clinical (e.g., human health, animal husbandry and veterinary medicine) and other components, including environmental factors (e.g., persistence of AMR in wastewater). Many studies have highlighted the role of wastewater as a significant environmental reservoir of AMR as it represents an ideal environment for AMR bacteria (ARB) and antimicrobial resistant genes (ARGs) to persist. Although the treatment process can help in removing or reducing the ARB load, it has limited impact on ARGs. ARGs are not degradable; therefore, they can be spread among microbial communities in the environment through horizontal gene transfer, which is the main resistance mechanism in most Gram-negative bacteria. Here we analysed the recent literature to highlight the contribution of wastewater to the emergence, persistence and transmission of AMR under different settings, particularly those associated with mass gathering events (e.g., Hajj and Kumbh Mela).}, }
@article {pmid32103021, year = {2020}, author = {Oliveira, PH and Touchon, M and Cury, J and Rocha, EPC}, title = {Author Correction: The chromosomal organization of horizontal gene transfer in bacteria.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {1155}, doi = {10.1038/s41467-020-15091-5}, pmid = {32103021}, issn = {2041-1723}, abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.}, }
@article {pmid32102454, year = {2020}, author = {Khaledian, E and Brayton, KA and Broschat, SL}, title = {A Systematic Approach to Bacterial Phylogeny Using Order Level Sampling and Identification of HGT Using Network Science.}, journal = {Microorganisms}, volume = {8}, number = {2}, pages = {}, pmid = {32102454}, issn = {2076-2607}, support = {1262664//National Stroke Foundation/ ; }, abstract = {Reconstructing and visualizing phylogenetic relationships among living organisms is a fundamental challenge because not all organisms share the same genes. As a result, the first phylogenetic visualizations employed a single gene, e.g., rRNA genes, sufficiently conserved to be present in all organisms but divergent enough to provide discrimination between groups. As more genome data became available, researchers began concatenating different combinations of genes or proteins to construct phylogenetic trees believed to be more robust because they incorporated more information. However, the genes or proteins chosen were based on ad hoc approaches. The large number of complete genome sequences available today allows the use of whole genomes to analyze relationships among organisms rather than using an ad hoc set of genes. We present a systematic approach for constructing a phylogenetic tree based on simultaneously clustering the complete proteomes of 360 bacterial species. From the homologous clusters, we identify 49 protein sequences shared by 99% of the organisms to build a tree. Of the 49 sequences, 47 have homologous sequences in both archaea and eukarya. The clusters are also used to create a network from which bacterial species with horizontally-transferred genes from other phyla are identified.}, }
@article {pmid32100706, year = {2020}, author = {Whelan, FJ and Rusilowicz, M and McInerney, JO}, title = {Coinfinder: detecting significant associations and dissociations in pangenomes.}, journal = {Microbial genomics}, volume = {6}, number = {3}, pages = {}, pmid = {32100706}, issn = {2057-5858}, support = {BB/N018044/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Computational Biology ; *Genome ; Phylogeny ; *Software ; Streptococcus pneumoniae/genetics ; }, abstract = {The accessory genes of prokaryote and eukaryote pangenomes accumulate by horizontal gene transfer, differential gene loss, and the effects of selection and drift. We have developed Coinfinder, a software program that assesses whether sets of homologous genes (gene families) in pangenomes associate or dissociate with each other (i.e. are 'coincident') more often than would be expected by chance. Coinfinder employs a user-supplied phylogenetic tree in order to assess the lineage-dependence (i.e. the phylogenetic distribution) of each accessory gene, allowing Coinfinder to focus on coincident gene pairs whose joint presence is not simply because they happened to appear in the same clade, but rather that they tend to appear together more often than expected across the phylogeny. Coinfinder is implemented in C++, Python3 and R and is freely available under the GNU license from https://github.com/fwhelan/coinfinder.}, }
@article {pmid32098822, year = {2020}, author = {Buckner, MMC and Ciusa, ML and Meek, RW and Moorey, AR and McCallum, GE and Prentice, EL and Reid, JP and Alderwick, LJ and Di Maio, A and Piddock, LJV}, title = {HIV Drugs Inhibit Transfer of Plasmids Carrying Extended-Spectrum β-Lactamase and Carbapenemase Genes.}, journal = {mBio}, volume = {11}, number = {1}, pages = {}, pmid = {32098822}, issn = {2150-7511}, support = {/WT_/Wellcome Trust/United Kingdom ; MR/N012933/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Anti-HIV Agents/*pharmacology ; Bacterial Proteins/*genetics ; Dideoxynucleosides ; Drug Resistance, Bacterial/drug effects ; Enterobacteriaceae/genetics ; Escherichia coli/genetics ; Gene Transfer, Horizontal/*drug effects ; HIV Infections/drug therapy ; HIV Integrase Inhibitors ; Klebsiella pneumoniae/genetics ; Plasmids/*genetics ; Zidovudine ; beta-Lactamases/*genetics ; }, abstract = {Antimicrobial-resistant (AMR) infections pose a serious risk to human and animal health. A major factor contributing to this global crisis is the sharing of resistance genes between different bacteria via plasmids. The WHO lists Enterobacteriaceae, such as Escherichia coli and Klebsiella pneumoniae, producing extended-spectrum β-lactamases (ESBL) and carbapenemases as "critical" priorities for new drug development. These resistance genes are most often shared via plasmid transfer. However, finding methods to prevent resistance gene sharing has been hampered by the lack of screening systems for medium-/high-throughput approaches. Here, we have used an ESBL-producing plasmid, pCT, and a carbapenemase-producing plasmid, pKpQIL, in two different Gram-negative bacteria, E. coli and K. pneumoniae Using these critical resistance-pathogen combinations, we developed an assay using fluorescent proteins, flow cytometry, and confocal microscopy to assess plasmid transmission inhibition within bacterial populations in a medium-throughput manner. Three compounds with some reports of antiplasmid properties were tested; chlorpromazine reduced transmission of both plasmids and linoleic acid reduced transmission of pCT. We screened the Prestwick library of over 1,200 FDA-approved drugs/compounds. From this, we found two nucleoside analogue drugs used to treat HIV, abacavir and azidothymidine (AZT), which reduced plasmid transmission (AZT, e.g., at 0.25 μg/ml reduced pCT transmission in E. coli by 83.3% and pKpQIL transmission in K. pneumoniae by 80.8% compared to untreated controls). Plasmid transmission was reduced by concentrations of the drugs which are below peak serum concentrations and are achievable in the gastrointestinal tract. These drugs could be used to decolonize humans, animals, or the environment from AMR plasmids.IMPORTANCE More and more bacterial infections are becoming resistant to antibiotics. This has made treatment of many infections very difficult. One of the reasons this is such a large problem is that bacteria are able to share their genetic material with other bacteria, and these shared genes often include resistance to a variety of antibiotics, including some of our drugs of last resort. We are addressing this problem by using a fluorescence-based system to search for drugs that will stop bacteria from sharing resistance genes. We uncovered a new role for two drugs used to treat HIV and show that they are able to prevent the sharing of two different types of resistance genes in two unique bacterial strains. This work lays the foundation for future work to reduce the prevalence of resistant infections.}, }
@article {pmid32098813, year = {2020}, author = {Waterworth, SC and Flórez, LV and Rees, ER and Hertweck, C and Kaltenpoth, M and Kwan, JC}, title = {Horizontal Gene Transfer to a Defensive Symbiont with a Reduced Genome in a Multipartite Beetle Microbiome.}, journal = {mBio}, volume = {11}, number = {1}, pages = {}, pmid = {32098813}, issn = {2150-7511}, support = {T32 GM008349/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics ; Biological Products ; Burkholderia/genetics ; Coleoptera/*microbiology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome Size ; Genome, Bacterial/*genetics ; Metagenomics ; Microbiota/*genetics ; Multigene Family ; Symbiosis/*genetics/physiology ; }, abstract = {Symbiotic mutualisms of bacteria and animals are ubiquitous in nature, running a continuum from facultative to obligate from the perspectives of both partners. The loss of functions required for living independently but not within a host gives rise to reduced genomes in many symbionts. Although the phenomenon of genome reduction can be explained by existing evolutionary models, the initiation of the process is not well understood. Here, we describe the microbiome associated with the eggs of the beetle Lagria villosa, consisting of multiple bacterial symbionts related to Burkholderia gladioli, including a reduced-genome symbiont thought to be the exclusive producer of the defensive compound lagriamide. We show that the putative lagriamide-producing symbiont is the only member of the microbiome undergoing genome reduction and that it has already lost the majority of its primary metabolism and DNA repair pathways. The key step preceding genome reduction in the symbiont was likely the horizontal acquisition of the putative lagriamide lga biosynthetic gene cluster. Unexpectedly, we uncovered evidence of additional horizontal transfers to the symbiont's genome while genome reduction was occurring and despite a current lack of genes needed for homologous recombination. These gene gains may have given the genome-reduced symbiont a selective advantage in the microbiome, especially given the maintenance of the large lga gene cluster despite ongoing genome reduction.IMPORTANCE Associations between microorganisms and an animal, plant, or fungal host can result in increased dependence over time. This process is due partly to the bacterium not needing to produce nutrients that the host provides, leading to loss of genes that it would need to live independently and to a consequent reduction in genome size. It is often thought that genome reduction is aided by genetic isolation-bacteria that live in monocultures in special host organs, or inside host cells, have less access to other bacterial species from which they can obtain genes. Here, we describe exposure of a genome-reduced beetle symbiont to a community of related bacteria with nonreduced genomes. We show that the symbiont has acquired genes from other bacteria despite going through genome reduction, suggesting that isolation has not yet played a major role in this case of genome reduction, with horizontal gene gains still offering a potential route for adaptation.}, }
@article {pmid32093600, year = {2020}, author = {Cahill, SM and Arbatsky, NP and Shashkov, AS and Shneider, MM and Popova, AV and Hall, RM and Kenyon, JJ and Knirel, YA}, title = {Elucidation of the K32 Capsular Polysaccharide Structure and Characterization of the KL32 Gene Cluster of Acinetobacter baumannii LUH5549.}, journal = {Biochemistry. Biokhimiia}, volume = {85}, number = {2}, pages = {241-247}, doi = {10.1134/S000629792002011X}, pmid = {32093600}, issn = {1608-3040}, mesh = {Acinetobacter baumannii/*genetics ; Bacterial Capsules/chemistry/genetics/metabolism ; Carbohydrate Conformation ; Computational Biology ; Multigene Family/*genetics ; Polysaccharides, Bacterial/*chemistry/isolation &amp; purification/*metabolism ; }, abstract = {Capsular polysaccharide (CPS), isolated from Acinetobacter baumannii LUH5549 carrying the KL32 capsule biosynthesis gene cluster, was studied by sugar analysis, Smith degradation, and one- and two-dimensional [1]H and [13]C NMR spectroscopy. The K32 CPS was found to be composed of branched pentasaccharide repeats (K units) containing two residues of β-D-GalpNAc and one residue of β-D-GlcpA (β-D-glucuronic acid) in the main chain and one residue each of β-D-Glcp and α-D-GlcpNAc in the disaccharide side chain. Consistent with the established CPS structure, the KL32 gene cluster includes genes for a UDP-glucose 6-dehydrogenase (Ugd3) responsible for D-GlcA synthesis and four glycosyltransferases that were assigned to specific linkages. Genes encoding an acetyltransferase and an unknown protein product were not involved in CPS biosynthesis. Whilst the KL32 gene cluster has previously been found in the global clone 2 (GC2) lineage, LUH5549 belongs to the sequence type ST354, thus demonstrating horizontal gene transfer between these lineages.}, }
@article {pmid32091394, year = {2020}, author = {Blondel, L and Jones, TE and Extavour, CG}, title = {Bacterial contribution to genesis of the novel germ line determinant oskar.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, pmid = {32091394}, issn = {2050-084X}, mesh = {Animals ; *Bacterial Physiological Phenomena ; Bayes Theorem ; Drosophila Proteins/biosynthesis/*genetics ; Drosophila melanogaster/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Germ Cells/*microbiology ; Likelihood Functions ; Phylogeny ; }, abstract = {New cellular functions and developmental processes can evolve by modifying existing genes or creating novel genes. Novel genes can arise not only via duplication or mutation but also by acquiring foreign DNA, also called horizontal gene transfer (HGT). Here we show that HGT likely contributed to the creation of a novel gene indispensable for reproduction in some insects. Long considered a novel gene with unknown origin, oskar has evolved to fulfil a crucial role in insect germ cell formation. Our analysis of over 100 insect Oskar sequences suggests that oskar arose de novo via fusion of eukaryotic and prokaryotic sequences. This work shows that highly unusual gene origin processes can give rise to novel genes that may facilitate evolution of novel developmental mechanisms.}, }
@article {pmid32089519, year = {2021}, author = {Fischer, MG}, title = {The Virophage Family Lavidaviridae.}, journal = {Current issues in molecular biology}, volume = {40}, number = {}, pages = {1-24}, doi = {10.21775/cimb.040.001}, pmid = {32089519}, issn = {1467-3045}, mesh = {Capsid/chemistry ; Coinfection ; DNA, Viral/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Variation ; *Genome, Viral ; Giant Viruses/classification/genetics ; Host Microbial Interactions ; Host Specificity ; *Metagenome ; Metagenomics/methods ; Phylogeny ; Virophages/*classification/*genetics ; Virus Replication ; }, abstract = {Double-stranded (ds) DNA viruses of the family Lavidaviridae, commonly known as virophages, are a fascinating group of eukaryotic viruses that depend on a coinfecting giant dsDNA virus of the Mimiviridae for their propagation. Instead of replicating in the nucleus, virophages multiply in the cytoplasmic virion factory of a coinfecting giant virus inside a phototrophic or heterotrophic protistal host cell. Virophages are parasites of giant viruses and can inhibit their replication, which may lead to increased survival rates of the infected host cell population. The genomes of virophages are 17-33 kilobase pairs (kbp) long and encode 16-34 proteins. Genetic signatures of virophages can be found in metagenomic datasets from various saltwater and freshwater environments around the planet. Most virophages share a set of conserved genes that code for a major and a minor capsid protein, a cysteine protease, a genome-packaging ATPase, and a superfamily 3 helicase, although the genomes are otherwise diverse and variable. Lavidaviruses share genes with other mobile genetic elements, suggesting that horizontal gene transfer and recombination have been major forces in shaping these viral genomes. Integrases are occasionally found in virophage genomes and enable these DNA viruses to persist as provirophages in the chromosomes of their viral and cellular hosts. As we watch the genetic diversity of this new viral family unfold through metagenomics, additional isolates are still lacking and critical questions regarding their infection cycle, host range, and ecology remain to be answered.}, }
@article {pmid32084126, year = {2020}, author = {Czaja, W and Bensasson, D and Ahn, HW and Garfinkel, DJ and Bergman, CM}, title = {Evolution of Ty1 copy number control in yeast by horizontal transfer and recombination.}, journal = {PLoS genetics}, volume = {16}, number = {2}, pages = {e1008632}, pmid = {32084126}, issn = {1553-7404}, support = {R01 GM095622/GM/NIGMS NIH HHS/United States ; R01 GM124216/GM/NIGMS NIH HHS/United States ; }, mesh = {*DNA Copy Number Variations ; DNA, Fungal/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Fungal/*genetics ; Retroelements/*genetics ; Saccharomyces cerevisiae/*genetics ; Sympatry/genetics ; }, abstract = {Transposable elements constitute a large fraction of most eukaryotic genomes. Insertion of mobile DNA sequences typically has deleterious effects on host fitness, and thus diverse mechanisms have evolved to control mobile element proliferation. Mobility of the Ty1 retrotransposon in Saccharomyces yeasts is regulated by copy number control (CNC) mediated by a self-encoded restriction factor derived from the Ty1 gag capsid gene that inhibits virus-like particle function. Here, we survey a panel of wild and human-associated strains of S. cerevisiae and S. paradoxus to investigate how genomic Ty1 content influences variation in Ty1 mobility. We observe high levels of mobility for a tester element with a gag sequence from the canonical Ty1 subfamily in permissive strains that either lack full-length Ty1 elements or only contain full-length copies of the Ty1' subfamily that have a divergent gag sequence. In contrast, low levels of canonical Ty1 mobility are observed in restrictive strains carrying full-length Ty1 elements containing a canonical gag sequence. Phylogenomic analysis of full-length Ty1 elements revealed that Ty1' is the ancestral subfamily present in wild strains of S. cerevisiae, and that canonical Ty1 in S. cerevisiae is a derived subfamily that acquired gag from S. paradoxus by horizontal transfer and recombination. Our results provide evidence that variation in the ability of S. cerevisiae and S. paradoxus strains to repress canonical Ty1 transposition via CNC is regulated by the genomic content of different Ty1 subfamilies, and that self-encoded forms of transposon control can spread across species boundaries by horizontal transfer.}, }
@article {pmid32080746, year = {2020}, author = {Di Giovanni, D and Lepetit, D and Guinet, B and Bennetot, B and Boulesteix, M and Couté, Y and Bouchez, O and Ravallec, M and Varaldi, J}, title = {A Behavior-Manipulating Virus Relative as a Source of Adaptive Genes for Drosophila Parasitoids.}, journal = {Molecular biology and evolution}, volume = {37}, number = {10}, pages = {2791-2807}, doi = {10.1093/molbev/msaa030}, pmid = {32080746}, issn = {1537-1719}, mesh = {Adaptation, Biological ; Animals ; Behavior, Animal ; Drosophila/*parasitology ; Female ; *Gene Transfer, Horizontal ; *Genes, Viral ; Genome, Insect ; Larva/parasitology ; Selection, Genetic ; Wasps/*genetics/ultrastructure/*virology ; }, abstract = {Some species of parasitic wasps have domesticated viral machineries to deliver immunosuppressive factors to their hosts. Up to now, all described cases fall into the Ichneumonoidea superfamily, which only represents around 10% of hymenoptera diversity, raising the question of whether such domestication occurred outside this clade. Furthermore, the biology of the ancestral donor viruses is completely unknown. Since the 1980s, we know that Drosophila parasitoids belonging to the Leptopilina genus, which diverged from the Ichneumonoidea superfamily 225 Ma, do produce immunosuppressive virus-like structure in their reproductive apparatus. However, the viral origin of these structures has been the subject of debate. In this article, we provide genomic and experimental evidence that those structures do derive from an ancestral virus endogenization event. Interestingly, its close relatives induce a behavior manipulation in present-day wasps. Thus, we conclude that virus domestication is more prevalent than previously thought and that behavior manipulation may have been instrumental in the birth of such associations.}, }
@article {pmid32079043, year = {2020}, author = {Dziuba, MV and Zwiener, T and Uebe, R and Schüler, D}, title = {Single-step transfer of biosynthetic operons endows a non-magnetotactic Magnetospirillum strain from wetland with magnetosome biosynthesis.}, journal = {Environmental microbiology}, volume = {22}, number = {4}, pages = {1603-1618}, doi = {10.1111/1462-2920.14950}, pmid = {32079043}, issn = {1462-2920}, support = {91578115//Deutscher Akademischer Austauschdienst/International ; 692637//H2020 European Research Council/International ; }, mesh = {Gene Transfer, Horizontal ; Magnetosomes/*metabolism ; Magnetospirillum/*genetics/*metabolism ; Multigene Family ; *Operon ; Phylogeny ; Wetlands ; }, abstract = {The magnetotactic lifestyle represents one of the most complex traits found in many bacteria from aquatic environments and depends on magnetic organelles, the magnetosomes. Genetic transfer of magnetosome biosynthesis operons to a non-magnetotactic bacterium has only been reported once so far, but it is unclear whether this may also occur in other recipients. Besides magnetotactic species from freshwater, the genus Magnetospirillum of the Alphaproteobacteria also comprises a number of strains lacking magnetosomes, which are abundant in diverse microbial communities. Their close phylogenetic interrelationships raise the question whether the non-magnetotactic magnetospirilla may have the potential to (re)gain a magnetotactic lifestyle upon acquisition of magnetosome gene clusters. Here, we studied the transfer of magnetosome gene operons into several non-magnetotactic environmental magnetospirilla. Single-step transfer of a compact vector harbouring >30 major magnetosome genes from M. gryphiswaldense induced magnetosome biosynthesis in a Magnetospirillum strain from a constructed wetland. However, the resulting magnetic cellular alignment was insufficient for efficient magnetotaxis under conditions mimicking the weak geomagnetic field. Our work provides insights into possible evolutionary scenarios and potential limitations for the dissemination of magnetotaxis by horizontal gene transfer and expands the range of foreign recipients that can be genetically magnetized.}, }
@article {pmid32076126, year = {2020}, author = {Mao, M and Bennett, GM}, title = {Symbiont replacements reset the co-evolutionary relationship between insects and their heritable bacteria.}, journal = {The ISME journal}, volume = {14}, number = {6}, pages = {1384-1395}, pmid = {32076126}, issn = {1751-7370}, mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification ; *Bacterial Physiological Phenomena ; *Biological Evolution ; Gene Transfer, Horizontal ; Genome, Bacterial ; Hemiptera/genetics/*microbiology ; Phylogeny ; *Symbiosis ; }, abstract = {Auchenorrhynchan insects (Hemiptera) generally depend on two bacterial symbionts for nutrition. These bacteria experience extreme genome reduction and loss of essential cell functions that require direct host support, or the replacement of failing symbionts with more capable ones. However, it remains unclear how hosts adapt to integrate symbionts into their systems, particularly when they are replaced. Here, we comparatively investigated the evolution of host-support mechanisms in the glassy-winged sharpshooter, Homalodisca vitripennis (GWSS), and the aster leafhopper, Macrosteles quadrilineatus (ALF). ALF harbors the ancestral co-symbionts of the Auchenorrhyncha that have tiny genomes, Sulcia (190 kb) and Nasuia (112 kb). In GWSS, Sulcia retains an expanded genome (245 kb), but Nasuia was replaced by the more capable Baumannia (686 kb). To support their symbionts, GWSS and ALF have evolved novel mechanisms via horizontal gene transfer, gene duplication, and co-option of mitochondrial support genes. However, GWSS has fewer support systems targeting essential bacterial processes. In particular, although both hosts use ancestral mechanisms to support Sulcia, GWSS does not encode all of the same support genes required to sustain Sulcia-ALF or Nasuia. Moreover, GWSS support of Baumannia is far more limited and tailored to its expanded capabilities. Our results demonstrate how symbiont replacements shape host genomes and the co-evolutionary process.}, }
@article {pmid32075851, year = {2020}, author = {Beaulaurier, J and Luo, E and Eppley, JM and Uyl, PD and Dai, X and Burger, A and Turner, DJ and Pendelton, M and Juul, S and Harrington, E and DeLong, EF}, title = {Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities.}, journal = {Genome research}, volume = {30}, number = {3}, pages = {437-446}, pmid = {32075851}, issn = {1549-5469}, mesh = {Bacteriophages/genetics ; DNA Packaging ; *Genome, Viral ; Metagenomics ; Nanopore Sequencing/*methods ; Seawater/virology ; }, abstract = {Viruses are the most abundant biological entities on Earth and play key roles in host ecology, evolution, and horizontal gene transfer. Despite recent progress in viral metagenomics, the inherent genetic complexity of virus populations still poses technical difficulties for recovering complete virus genomes from natural assemblages. To address these challenges, we developed an assembly-free, single-molecule nanopore sequencing approach, enabling direct recovery of complete virus genome sequences from environmental samples. Our method yielded thousands of full-length, high-quality draft virus genome sequences that were not recovered using standard short-read assembly approaches. Additionally, our analyses discriminated between populations whose genomes had identical direct terminal repeats versus those with circularly permuted repeats at their termini, thus providing new insight into native virus reproduction and genome packaging. Novel DNA sequences were discovered, whose repeat structures, gene contents, and concatemer lengths suggest they are phage-inducible chromosomal islands, which are packaged as concatemers in phage particles, with lengths that match the size ranges of co-occurring phage genomes. Our new virus sequencing strategy can provide previously unavailable information about the genome structures, population biology, and ecology of naturally occurring viruses and viral parasites.}, }
@article {pmid32074088, year = {2019}, author = {Asgin, N and Otlu, B and Cakmakliogullari, EK and Celik, B}, title = {High prevalence of TEM, VIM, and OXA-2 beta-lactamases and clonal diversity among Acinetobacter baumannii isolates in Turkey.}, journal = {Journal of infection in developing countries}, volume = {13}, number = {9}, pages = {794-801}, doi = {10.3855/jidc.11684}, pmid = {32074088}, issn = {1972-2680}, mesh = {Acinetobacter Infections/epidemiology/*microbiology ; Acinetobacter baumannii/drug effects/*genetics/isolation &amp; purification/metabolism ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Humans ; Prevalence ; Turkey/epidemiology ; beta-Lactam Resistance/genetics ; beta-Lactamases/*metabolism ; }, abstract = {INTRODUCTION: Acinetobacter baumannii is an opportunistic pathogen that causes nosocomial infections with high mortality. Treatment options are limited owing to its resistance to numerous antibiotics. Here, we sought to determine the antibiotic susceptibilities of A. baumannii isolates, investigate clonal relationship among the strains, and determine the frequency of beta-lactamase resistance genes.<br><br>METHODOLOGY: The identification and antibiotic susceptibilities of 69 A. baumannii strains were determined using a BD-Phoenix automated system. The presence of blaOXA-2, blaOXA-10, blaOXA-23, blaOXA-24/40, blaOXA-51, blaOXA-58, blaTEM, blaSHV, blaIMP, blaVIM, and blaGIM genes were investigated using polymerase chain reaction (PCR), and clonal relatioships among the isolates were determined using pulsed-field gel electrophoresis (PFGE).<br><br>RESULTS: All strains were resistant to ampicillin-sulbactam, gentamicin, cefepime, ciprofloxacin, and ceftriaxone. While 65 of the 69 strains (94.2%) were resistant to piperacillin-tazobactam, amikacin, imipenem, and meropenem, all strains were susceptible to tigecycline and colistin. The frequencies of blaOXA-51, blaOXA-23, blaTEM, blaOXA-2, blaVIM, and blaSHV were 100%, 94.2%, 53.6%, 21.7%, 14.5%, and 2.9%, respectively. Based on PFGE results, 56 of the 69 strains were clonally related, and the clustering rate was 81.2%. No common outbreak isolate was detected.<br><br>CONCLUSIONS: The most prevalent OXA genes were blaOXA-51, blaOXA-23, and blaOXA-2. Furthermore, blaTEM, blaSHV, and blaVIM, which are common in Enterobacterales and Pseudomonas spp, were detected, suggesting horizontal gene transfer had occurred between bacteria. No single clone outbreak was detected by PFGE. However, multiclonal spread and the high clustering rate suggest cross-contamination. Therefore, in future, more effective infection control measures must be implemented.}, }
@article {pmid32071159, year = {2020}, author = {Brooks, MR and Padilla-Vélez, L and Khan, TA and Qureshi, AA and Pieper, JB and Maddox, CW and Alam, MT}, title = {Prophage-Mediated Disruption of Genetic Competence in Staphylococcus pseudintermedius.}, journal = {mSystems}, volume = {5}, number = {1}, pages = {}, pmid = {32071159}, issn = {2379-5077}, support = {T35 OD011145/OD/NIH HHS/United States ; }, abstract = {Methicillin-resistant Staphylococcus pseudintermedius (MRSP) is a major cause of soft tissue infections in dogs and occasionally infects humans. Hypervirulent multidrug-resistant (MDR) MRSP clones have emerged globally. The sequence types ST71 and ST68, the major epidemic clones of Europe and North America, respectively, have spread to other regions. The genetic factors underlying the success of these clones have not been investigated thoroughly. Here, we performed a comprehensive genomic analysis of 371 S. pseudintermedius isolates to dissect the differences between major clonal lineages. We show that the prevalence of genes associated with antibiotic resistance, virulence, prophages, restriction-modification (RM), and CRISPR/Cas systems differs significantly among MRSP clones. The isolates with GyrA+GrlA mutations, conferring fluoroquinolone resistance, carry more of these genes than those without GyrA+GrlA mutations. ST71 and ST68 clones carry lineage-specific prophages with genes that are likely associated with their increased fitness and virulence. We have discovered that a prophage, SpST71A, is inserted within the comGA gene of the late competence operon comG in the ST71 lineage. A functional comG is essential for natural genetic competence, which is one of the major modes of horizontal gene transfer (HGT) in bacteria. The RM and CRISPR/Cas systems, both major genetic barriers to HGT, are also lineage specific. Clones harboring CRISPR/Cas or a prophage-disrupted comG exhibited less genetic diversity and lower rates of recombination than clones lacking these systems. After Listeria monocytogenes, this is the second example of prophage-mediated competence disruption reported in any bacteria. These findings are important for understanding the evolution and clonal expansion of MDR MRSP clones.IMPORTANCE Staphylococcus pseudintermedius is a bacterium responsible for clinically important infections in dogs and can infect humans. In this study, we performed genomic analysis of 371 S. pseudintermedius isolates to understand the evolution of antibiotic resistance and virulence in this organism. The analysis covered significant reported clones, including ST71 and ST68, the major epidemic clones of Europe and North America, respectively. We show that the prevalence of genes associated with antibiotic resistance, virulence, prophages, and horizontal gene transfer differs among clones. ST71 and ST68 carry prophages with novel virulence and antibiotic resistance genes. Importantly, site-specific integration of a prophage, SpST71A, has led to the disruption of the genetic competence operon comG in ST71 clone. A functional comG is essential for the natural uptake of foreign DNA and thus plays an important role in the evolution of bacteria. This study provides insight into the emergence and evolution of antibiotic resistance and virulence in S. pseudintermedius, which may help in efforts to combat this pathogen.}, }
@article {pmid32069326, year = {2020}, author = {Kizziah, JL and Manning, KA and Dearborn, AD and Dokland, T}, title = {Structure of the host cell recognition and penetration machinery of a Staphylococcus aureus bacteriophage.}, journal = {PLoS pathogens}, volume = {16}, number = {2}, pages = {e1008314}, pmid = {32069326}, issn = {1553-7374}, support = {R01 AI083255/AI/NIAID NIH HHS/United States ; U24 GM116788/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteriophages/genetics/*metabolism/*ultrastructure ; Cryoelectron Microscopy/methods ; Gene Transfer, Horizontal/genetics ; Humans ; Models, Molecular ; Protein Binding/genetics ; Protein Conformation ; Staphylococcus aureus/*genetics/ultrastructure/virology ; Virion/genetics ; }, abstract = {Staphylococcus aureus is a common cause of infections in humans. The emergence of virulent, antibiotic-resistant strains of S. aureus is a significant public health concern. Most virulence and resistance factors in S. aureus are encoded by mobile genetic elements, and transduction by bacteriophages represents the main mechanism for horizontal gene transfer. The baseplate is a specialized structure at the tip of bacteriophage tails that plays key roles in host recognition, cell wall penetration, and DNA ejection. We have used high-resolution cryo-electron microscopy to determine the structure of the S. aureus bacteriophage 80α baseplate at 3.75 Å resolution, allowing atomic models to be built for most of the major tail and baseplate proteins, including two tail fibers, the receptor binding protein, and part of the tape measure protein. Our structure provides a structural basis for understanding host recognition, cell wall penetration and DNA ejection in viruses infecting Gram-positive bacteria. Comparison to other phages demonstrates the modular design of baseplate proteins, and the adaptations to the host that take place during the evolution of staphylococci and other pathogens.}, }
@article {pmid32065888, year = {2020}, author = {Wang, Q and Liu, L and Hou, Z and Wang, L and Ma, D and Yang, G and Guo, S and Luo, J and Qi, L and Luo, Y}, title = {Heavy metal copper accelerates the conjugative transfer of antibiotic resistance genes in freshwater microcosms.}, journal = {The Science of the total environment}, volume = {717}, number = {}, pages = {137055}, doi = {10.1016/j.scitotenv.2020.137055}, pmid = {32065888}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents ; Copper ; Drug Resistance, Microbial ; Fresh Water/*chemistry ; Genes, Bacterial ; }, abstract = {Recent studies have consistently demonstrated increasing abundances of antibiotic resistance genes (ARGs) in the absence of antibiotic use. There is a large amount of quantitative data that has correlated the elevated ARGs levels with the concentrations of heavy metals in environments with anthropogenic impact. However, the mechanisms by which heavy metals facilitate the proliferation and horizontal gene transfer of ARGs among environmental bacteria were still unknown. This study validated effects of four typical heavy metals (Cu, Cd, Pb, Zn) on the plasmid RP4 mediated conjugative transfer of ARGs in freshwater microcosms. The results suggested that the typical heavy metals including Cu, Pb and Zn would promote conjugative transfer of the plasmid RP4, and Cu (5.0 μg/L) had the greatest ability to increase conjugative transfer by 16-fold higher than the control groups. In conjugative transfer microcosms, the species of each cultivable transconjugant were isolated, and their minimum inhibitory concentrations (MICs) were assessed via antibiotic susceptibility testing. The mechanism of the increased conjugative transfer of Cu was that Cu induced cell damage and the reduced conjugative transfer of Cd was that Cd increased the content of extracellular polymers substances (EPS). This study confirms that heavy metal Cu facilitates the conjugative transfer of environmental-mediated plasmid RP4 by cell damage effect, therefore accelerating the transmission and proliferation of ARGs.}, }
@article {pmid32062436, year = {2020}, author = {Deng, C and Liu, X and Li, L and Shi, J and Guo, W and Xue, J}, title = {Temporal dynamics of antibiotic resistant genes and their association with the bacterial community in a water-sediment mesocosm under selection by 14 antibiotics.}, journal = {Environment international}, volume = {137}, number = {}, pages = {105554}, doi = {10.1016/j.envint.2020.105554}, pmid = {32062436}, issn = {1873-6750}, mesh = {*Anti-Bacterial Agents ; Bacteria/genetics ; *Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; Time Factors ; Water ; }, abstract = {Antibiotics in aquatic environments at high concentrations and sub-inhibitory concentrations potentially select for the evolution of antibiotic resistant genes (ARGs), posing a potential risk to aquatic ecological safety. Our knowledge of the temporal and successive dynamics of ARGs and bacterial community under the selective pressure of antibiotics in natural water-sediment system was limited. This study used a 120-d operating hydrodynamic mesocosm to explore the temporal dynamics of ARGs in water-sediment systems, and the main selective mechanisms following the attenuation and transport of 14 commonly used antibiotics. Under the selective pressures by antibiotics, ARGs propagated transiently, and persisted after antibiotic removal; the bacterial community structures likewise changed. Mantel test and network analysis indicated that ARGs significantly correlated with the bacterial community in the water and surface sediments. Structural equation model (SEM) further revealed that the evolution of ARGs was mainly due to the direct effect of the change in bacterial community and horizontal gene transfer (HGT) via the class 1 integron-integrase gene (intI1), but antibiotics indirectly influenced ARG profiles. The migration of ARGs in deep layer sediments was not related to the bacterial community and intI1, but may be explained by antibiotic selective effects and ARG transformation.}, }
@article {pmid32061337, year = {2020}, author = {Ishibashi, K and Tanaka, Y and Morishita, Y}, title = {Perspectives on the evolution of aquaporin superfamily.}, journal = {Vitamins and hormones}, volume = {112}, number = {}, pages = {1-27}, doi = {10.1016/bs.vh.2019.08.001}, pmid = {32061337}, issn = {0083-6729}, mesh = {Amino Acid Sequence ; *Aquaporins/genetics/metabolism ; *Phylogeny ; Water ; }, abstract = {Aquaporins (AQPs) belong to a transmembrane protein superfamily composed of an internal repeat of a three membrane-spanning domain and each has a highly conserved NPA box. Based on the more variable carboxyl-terminal NPA box, AQPs can be divided into three subfamilies: (1) glycerol-channel aquaglyceroporin (gAQP) (2) water-selective AQP (wAQP), and (3) deviated superaquaporin (sAQP) in the order of passible evolution. This classification has functional and localization relevance: most wAQPs transports water selectively whereas gAQPs and sAQPs also transport small molecules with sAQPs mostly localized inside the cell. As this classification is not based on the function, some wAQPs functioning as glycerol channels will not be included in gAQPs. AQP ancestors may have first originated in eubacteria as gAQPs to transport small molecules such as glycerol. Later some of them may have acquired a water-selective filter to become wAQPs. Although AQPs are absent in many bacteria, especially in archaea, both gAQPs and wAQPs may have been carried over to eukaryotes or horizontally transferred. Finally, multicellular organisms have obtained new sAQPs, which are curiously absent in fungi and plants. Interestingly, both plants and higher insects independently have lost gAQPs, whose functions, however, have been taken over by functionally modified wAQPs partly obtained by horizontal gene transfers from bacteria. This evolutionary viewpoints on AQPs will facilitate further functional analysis of AQP-like sequences and expand our viewpoints on AQP superfamily.}, }
@article {pmid32061177, year = {2020}, author = {Gonçalves, P and Gonçalves, C and Brito, PH and Sampaio, JP}, title = {The Wickerhamiella/Starmerella clade-A treasure trove for the study of the evolution of yeast metabolism.}, journal = {Yeast (Chichester, England)}, volume = {37}, number = {4}, pages = {313-320}, doi = {10.1002/yea.3463}, pmid = {32061177}, issn = {1097-0061}, mesh = {Animals ; DNA, Fungal/genetics/*isolation &amp; purification ; Evolution, Molecular ; Flowers/microbiology ; Gene Transfer, Horizontal ; Glycolipids/biosynthesis/genetics ; Insecta/microbiology ; Metabolic Networks and Pathways ; Phylogeny ; Saccharomycetales/*classification/*genetics/isolation &amp; purification ; }, abstract = {The Wickerhamiella and Starmerella genera form a clade (W/S clade) that branches close to Yarrowia lipolytica in the Saccharomycotina species tree. It comprises approximately 90 recognized species and 50 putative new species not formally described yet. The large majority of the members of the W/S clade are ecologically associated with flowers and floricolous insects. Many species exhibit unusual metabolic traits, like fructophily and the production of sophorolipids, which are glycolipids that can be used as environmentally friendly biosurfactants. Genomic data have not only firmly established the W/S clade but have also revealed a tumultuous evolution of metabolism marked by losses and gains of important metabolic pathways, among which alcoholic fermentation. Possibly the most surprising finding brought to light by comparative genomics concerned the large number of genes acquired by some species of the W/S clade from bacteria through horizontal gene transfer, many of which were shown to be functional in their new setting. This was facilitated by the genetic tractability of one species in the clade, Starmerella bombicola, which is used for the industrial production of sophorolipids. We suggest that high-density coverage of genome sequencing in this clade, combined with the possibility to conduct molecular genetics experiments in at least one species, has the potential to set the stage for yet more exciting discoveries concerning the evolution of yeast metabolism.}, }
@article {pmid32061118, year = {2020}, author = {Madikonda, AK and Shaikh, A and Khanra, S and Yakkala, H and Yellaboina, S and Lin-Chao, S and Siddavattam, D}, title = {Metabolic remodeling in Escherichia coli MG1655. A prophage e14-encoded small RNA, co293, post-transcriptionally regulates transcription factors HcaR and FadR.}, journal = {The FEBS journal}, volume = {287}, number = {21}, pages = {4767-4782}, doi = {10.1111/febs.15247}, pmid = {32061118}, issn = {1742-4658}, mesh = {Base Sequence ; Carbon/metabolism ; Escherichia coli/*genetics/metabolism/virology ; Escherichia coli Proteins/*genetics/metabolism ; Esterases/genetics/metabolism ; *Gene Expression Regulation, Bacterial ; Metabolic Networks and Pathways/genetics ; Operon ; Prophages/*genetics/metabolism ; RNA/*genetics/metabolism ; Sphingomonadaceae/genetics/metabolism ; Transcription Factors/*genetics/metabolism ; }, abstract = {In previous studies, we have shown the existence of metabolic remodeling in glucose-grown Escherichia coli MG1655 cells expressing the esterase Orf306 from the opd island of Sphingobium fuliginis. We now show that Orf306-dependent metabolic remodeling is due to regulation of a novel small RNA (sRNA). Endogenous propionate, produced due to the esterase/lipase activity of Orf306, repressed expression of a novel E. coli sRNA, co293. This sRNA post-transcriptionally regulates expression of the transcription factors HcaR and FadR either by inhibiting translation or by destabilizing their transcripts. Hence, repression of co293 expression elevates the levels of HcaR and FadR with consequent activation of alternative carbon catabolic pathways. HcaR activates the hca and MHP operons leading to upregulation of the phenyl propionate and hydroxy phenyl propionate (HPP) degradation pathways. Similarly, FadR stimulates the expression of the transcription factor IclR which negatively regulates the glyoxylate bypass pathway genes, aceBAK.}, }
@article {pmid32060618, year = {2020}, author = {Chauve, C and Ponty, Y and Wallner, M}, title = {Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer models.}, journal = {Journal of mathematical biology}, volume = {80}, number = {5}, pages = {1353-1388}, pmid = {32060618}, issn = {1432-1416}, mesh = {Algorithms ; Computational Biology ; Computer Simulation ; *Evolution, Molecular ; Gene Deletion ; Gene Duplication ; Gene Transfer, Horizontal ; Genetic Speciation ; Mathematical Concepts ; *Models, Genetic ; Multigene Family ; Phylogeny ; }, abstract = {Given a set of species whose evolution is represented by a species tree, a gene family is a group of genes having evolved from a single ancestral gene. A gene family evolves along the branches of a species tree through various mechanisms, including-but not limited to-speciation ([Formula: see text]), gene duplication ([Formula: see text]), gene loss ([Formula: see text]), and horizontal gene transfer ([Formula: see text]). The reconstruction of a gene tree representing the evolution of a gene family constrained by a species tree is an important problem in phylogenomics. However, unlike in the multispecies coalescent evolutionary model that considers only speciation and incomplete lineage sorting events, very little is known about the search space for gene family histories accounting for gene duplication, gene loss and horizontal gene transfer (the [Formula: see text]-model). In this work, we introduce the notion of evolutionary histories defined as a binary ordered rooted tree describing the evolution of a gene family, constrained by a species tree in the [Formula: see text]-model. We provide formal grammars describing the set of all evolutionary histories that are compatible with a given species tree, whether it is ranked or unranked. These grammars allow us, using either analytic combinatorics or dynamic programming, to efficiently compute the number of histories of a given size, and also to generate random histories of a given size under the uniform distribution. We apply these tools to obtain exact asymptotics for the number of gene family histories for two species trees, the rooted caterpillar and complete binary tree, as well as estimates of the range of the exponential growth factor of the number of histories for random species trees of size up to 25. Our results show that including horizontal gene transfers induce a dramatic increase of the number of evolutionary histories. We also show that, within ranked species trees, the number of evolutionary histories in the [Formula: see text]-model is almost independent of the species tree topology. These results establish firm foundations for the development of ensemble methods for the prediction of reconciliations.}, }
@article {pmid32059297, year = {2020}, author = {Makowska, N and Zawierucha, K and Nadobna, P and Piątek-Bajan, K and Krajewska, A and Szwedyk, J and Iwasieczko, P and Mokracka, J and Koczura, R}, title = {Occurrence of integrons and antibiotic resistance genes in cryoconite and ice of Svalbard, Greenland, and the Caucasus glaciers.}, journal = {The Science of the total environment}, volume = {716}, number = {}, pages = {137022}, doi = {10.1016/j.scitotenv.2020.137022}, pmid = {32059297}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents ; Arctic Regions ; Drug Resistance, Microbial ; Ecosystem ; Greenland ; *Ice Cover ; Integrons ; Svalbard ; }, abstract = {The prevalence of integrons and antibiotic resistance genes (ARGs) is a serious threat for public health in the new millennium. Although commonly detected in sites affected by strong anthropogenic pressure, in remote areas their occurrence, dissemination, and transfer to other ecosystems is poorly recognized. Remote sites are considered as a benchmark for human-induced contamination on Earth. For years glaciers were considered pristine, now they are regarded as reservoirs of contaminants, thus studies on contamination of glaciers, which may be released to other ecosystems, are highly needed. Therefore, in this study we evaluated the occurrence and frequency of clinically relevant ARGs and resistance integrons in the genomes of culturable bacteria and class 1 integron-integrase gene copy number in the metagenome of cryoconite, ice and supraglacial gravel collected on two Arctic (South-West Greenland and Svalbard) and two High Mountain (the Caucasus) glaciers. Altogether, 36 strains with intI1 integron-integrase gene were isolated. Presence of class 1 integron-integrase gene was also recorded in metagenomic DNA from all sampling localities. The mean values of relative abundance of intI1 gene varied among samples and ranged from 0.7% in cryoconite from Adishi Glacier (the Caucasus) to 16.3% in cryoconite from Greenland. Moreover, antibiotic-resistant strains were isolated from all regions. Genes conferring resistance to β-lactams (blaSHV, blaTEM, blaOXA, blaCMY), fluoroquinolones (qepA, qnrC), and chloramphenicol (cat, cmr) were detected in the genomes of bacterial isolates.}, }
@article {pmid32056705, year = {2020}, author = {Montánchez, I and Kaberdin, VR}, title = {Vibrio harveyi: A brief survey of general characteristics and recent epidemiological traits associated with climate change.}, journal = {Marine environmental research}, volume = {154}, number = {}, pages = {104850}, doi = {10.1016/j.marenvres.2019.104850}, pmid = {32056705}, issn = {1879-0291}, mesh = {Adaptation, Physiological ; Animals ; *Climate Change ; Humans ; *Vibrio/pathogenicity/physiology ; Virulence ; }, abstract = {Here we briefly review the major characteristics of the emerging pathogen Vibrio harveyi and discuss survival strategies and adaptation mechanisms underlying the capacity of this marine bacterium to thrive in natural and artificial aquatic settings. Recent studies suggest that some adaptation mechanisms can easily be acquired by V. harveyi and other members of the Vibrionaceae family owing to efficient horizontal gene transfer and elevated mutation rate. While discussing the main factors in charge of the expansion of Vibrio spp. habitats and concomitant spread of Vibrio-associated diseases under climate change, this review highlights the need for future studies able to address the joint impact of environmental and anthropogenic factors on the long-term dynamics and virulence of V. harveyi populations at the global scale.}, }
@article {pmid32056367, year = {2020}, author = {Ding, BY and Niu, J and Shang, F and Yang, L and Zhang, W and Smagghe, G and Wang, JJ}, title = {Parental silencing of a horizontally transferred carotenoid desaturase gene causes a reduction of red pigment and fitness in the pea aphid.}, journal = {Pest management science}, volume = {76}, number = {7}, pages = {2423-2433}, doi = {10.1002/ps.5783}, pmid = {32056367}, issn = {1526-4998}, support = {XmT2018063//Chongqing Special Postdoctoral Science Foundation/ ; 2017YFD0200900//National Key R&amp;D Program of China/ ; CARS-26//The earmarked fund for Modern Agro-industry Technology Research System of China/ ; //111 Project (B18044)/ ; 2018M640894//China Postdoctoral Science Foundation/ ; //The Foundation Project of Southwest University (SWU019033)/ ; }, mesh = {Animals ; *Aphids ; Oxidoreductases ; Pisum sativum ; Pigmentation ; }, abstract = {BACKGROUND: Aphids obtained carotenoid biosynthesis genes via horizontal gene transfers from fungi. However, the roles of these genes in the contributions of in aphids'adaptation and whether these genes could be used as RNAi-based pest control targets are not yet clear. Thus, in this study we used parental RNAi to analyze the potential function of a carotenoid desaturase gene (CdeB) by combined molecular and chemical approaches in the pea aphid (Acyrthosiphon pisum).<br><br>RESULTS: Transcriptional analyses showed that CdeB was significantly more highly expressed in the red morphs compared to the green ones and was associated with the production of red carotenoid. Co-transferring of pET28a-CdeB (the CdeB gene was cloned into pET28a) and pACCRT-EIB (produced lycopene) showed a deep red color in the bacterial precipitate and produced more of a red pigment, lycopene, in vitro. Parental gene-silencing of CdeB resulted in a lower body color intensity in the treated aphids and following generations in vivo. Interestingly, the dsCdeB treatment also reduced aphid performance as reflected by a delay in nymphal developmental duration, lower weight, smaller number, and altered age structure of the population.<br><br>CONCLUSION: Our results demonstrate that CdeB is involved in red color formation and the silencing of this gene by parental RNAi reduced fitness in the pea aphid. The results enhance our understanding of the biosynthesis of carotenoid in aphids and provide insights into the potential ecological significance of carotenoids in the adaptation of the aphid's biology to the environment and developing environmentally friendly control strategies for this pest.}, }
@article {pmid32052827, year = {2020}, author = {Rossi, CC and Pereira, MF and Giambiagi-deMarval, M}, title = {Underrated Staphylococcus species and their role in antimicrobial resistance spreading.}, journal = {Genetics and molecular biology}, volume = {43}, number = {1 suppl 2}, pages = {e20190065}, pmid = {32052827}, issn = {1415-4757}, abstract = {The increasing threat of antimicrobial resistance has shed light on the interconnection between humans, animals, the environment, and their roles in the exchange and spreading of resistance genes. In this review, we present evidences that show that Staphylococcus species, usually referred to as harmless or opportunistic pathogens, represent a threat to human and animal health for acting as reservoirs of antimicrobial resistance genes. The capacity of genetic exchange between isolates of different sources and species of the Staphylococcus genus is discussed with emphasis on mobile genetic elements, the contribution of biofilm formation, and evidences obtained either experimentally or through genome analyses. We also discuss the involvement of CRISPR-Cas systems in the limitation of horizontal gene transfer and its suitability as a molecular clock to describe the history of genetic exchange between staphylococci.}, }
@article {pmid32047136, year = {2020}, author = {Arredondo-Alonso, S and Top, J and McNally, A and Puranen, S and Pesonen, M and Pensar, J and Marttinen, P and Braat, JC and Rogers, MRC and van Schaik, W and Kaski, S and Willems, RJL and Corander, J and Schürch, AC}, title = {Plasmids Shaped the Recent Emergence of the Major Nosocomial Pathogen Enterococcus faecium.}, journal = {mBio}, volume = {11}, number = {1}, pages = {}, pmid = {32047136}, issn = {2150-7511}, mesh = {Anti-Bacterial Agents/pharmacology ; Cross Infection/*microbiology ; DNA Transposable Elements/genetics ; Enterococcus faecium/drug effects/*genetics/*pathogenicity ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomics ; Gram-Positive Bacterial Infections/microbiology/transmission ; Hospitals ; Humans ; Phylogeny ; Plasmids/*genetics ; Sequence Analysis, DNA ; Whole Genome Sequencing ; }, abstract = {Enterococcus faecium is a gut commensal of humans and animals but is also listed on the WHO global priority list of multidrug-resistant pathogens. Many of its antibiotic resistance traits reside on plasmids and have the potential to be disseminated by horizontal gene transfer. Here, we present the first comprehensive population-wide analysis of the pan-plasmidome of a clinically important bacterium, by whole-genome sequence analysis of 1,644 isolates from hospital, commensal, and animal sources of E. faecium Long-read sequencing on a selection of isolates resulted in the completion of 305 plasmids that exhibited high levels of sequence modularity. We further investigated the entirety of all plasmids of each isolate (plasmidome) using a combination of short-read sequencing and machine-learning classifiers. Clustering of the plasmid sequences unraveled different E. faecium populations with a clear association with hospitalized patient isolates, suggesting different optimal configurations of plasmids in the hospital environment. The characterization of these populations allowed us to identify common mechanisms of plasmid stabilization such as toxin-antitoxin systems and genes exclusively present in particular plasmidome populations exemplified by copper resistance, phosphotransferase systems, or bacteriocin genes potentially involved in niche adaptation. Based on the distribution of k-mer distances between isolates, we concluded that plasmidomes rather than chromosomes are most informative for source specificity of E. faeciumIMPORTANCEEnterococcus faecium is one of the most frequent nosocomial pathogens of hospital-acquired infections. E. faecium has gained resistance against most commonly available antibiotics, most notably, against ampicillin, gentamicin, and vancomycin, which renders infections difficult to treat. Many antibiotic resistance traits, in particular, vancomycin resistance, can be encoded in autonomous and extrachromosomal elements called plasmids. These sequences can be disseminated to other isolates by horizontal gene transfer and confer novel mechanisms to source specificity. In our study, we elucidated the total plasmid content, referred to as the plasmidome, of 1,644 E. faecium isolates by using short- and long-read whole-genome technologies with the combination of a machine-learning classifier. This was fundamental to investigate the full collection of plasmid sequences present in our collection (pan-plasmidome) and to observe the potential transfer of plasmid sequences between E. faecium hosts. We observed that E. faecium isolates from hospitalized patients carried a larger number of plasmid sequences compared to that from other sources, and they elucidated different configurations of plasmidome populations in the hospital environment. We assessed the contribution of different genomic components and observed that plasmid sequences have the highest contribution to source specificity. Our study suggests that E. faecium plasmids are regulated by complex ecological constraints rather than physical interaction between hosts.}, }
@article {pmid32046678, year = {2020}, author = {Szemraj, M and Grazul, M and Balcerczak, E and Szewczyk, EM}, title = {Staphylococcal species less frequently isolated from human clinical specimens - are they a threat for hospital patients?.}, journal = {BMC infectious diseases}, volume = {20}, number = {1}, pages = {128}, pmid = {32046678}, issn = {1471-2334}, support = {502-03/3-012-03/503-31-011//Uniwersytet Medyczny w Lodzi (PL)/ ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteremia/microbiology ; Bacterial Proteins/genetics ; Biofilms ; Coagulase/metabolism ; Drug Resistance, Bacterial/*drug effects/genetics ; Enterotoxins/genetics ; Gene Expression Regulation, Bacterial ; Hospitals ; Humans ; Microbial Sensitivity Tests ; Staphylococcal Infections/*microbiology ; Staphylococcus/drug effects/*genetics/*isolation &amp; purification/pathogenicity ; Staphylococcus aureus/genetics/metabolism/pathogenicity ; Virulence Factors/genetics/metabolism ; }, abstract = {BACKGROUND: Coagulase-negative staphylococci belonging to S. haemolyticus, S. hominis subsp. hominis, S. simulans, and S. warneri are often described as etiological factors of infections. Staphylococci are a phylogenetically coherent group; nevertheless, there are differences among the species which may be important to clinicians.<br><br>METHODS: We investigated selected virulence factors and antibiotic resistance that were phenotypically demonstrated, the presence and expression of genes encoding the virulence factors, and the type of the SCCmec cassette.<br><br>RESULTS: The differences between the tested species were revealed. A great number of isolates produced a biofilm and many of them contained single icaADBC operon genes. Clear differences between species in the lipolytic activity spectrum could be related to their ability to cause various types of infections. Our studies also revealed the presence of genes encoding virulence factors homologous to S. aureus in the analysed species such as enterotoxin and pvl genes, which were also expressed in single isolates of S. simulans and S. warneri. S. haemolyticus and S. hominis subsp. hominis isolates were resistant to all clinically important antibiotics including &#xdf;-lactams. The identified SCCmec cassettes belonged to IV, V, VII, and IX type but most of the detected cassettes were non-typeable. Among the investigated species, S. hominis subsp. hominis isolates accumulated virulence genes typical for S. aureus in the most efficient way and were widely resistant to antibiotics.<br><br>CONCLUSIONS: Our results clearly indicated significant differences between the tested species, which might be a result of the horizontal gene transfer (HGT) and can lead to the formation and selection of multi-drug resistant strains as well as strains with new virulence features. Such strains can have a new clinical relevance.}, }
@article {pmid32044654, year = {2020}, author = {Will, WR and Fang, FC}, title = {The evolution of MarR family transcription factors as counter-silencers in regulatory networks.}, journal = {Current opinion in microbiology}, volume = {55}, number = {}, pages = {1-8}, pmid = {32044654}, issn = {1879-0364}, support = {R01 AI112640/AI/NIAID NIH HHS/United States ; R01 AI039557/AI/NIAID NIH HHS/United States ; R56 AI112640/AI/NIAID NIH HHS/United States ; R01 AI044486/AI/NIAID NIH HHS/United States ; R01 AI118962/AI/NIAID NIH HHS/United States ; R01 AI150041/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; Bacterial Proteins/*genetics ; DNA-Binding Proteins/*genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Escherichia coli Proteins/genetics ; Evolution, Molecular ; Gene Expression Regulation, Bacterial ; *Multigene Family ; Repressor Proteins/genetics ; Transcription Factors/*genetics ; }, abstract = {Gene duplication facilitates the evolution of biological complexity, as one copy of a gene retains its original function while a duplicate copy can acquire mutations that would otherwise diminish fitness. Duplication has played a particularly important role in the evolution of regulatory networks by permitting novel regulatory interactions and responses to stimuli. The diverse MarR family of transcription factors (MFTFs) illustrate this concept, ranging from highly specific repressors of single operons to pleiotropic global regulators controlling hundreds of genes. MFTFs are often genetically and functionally linked to antimicrobial efflux systems. However, the SlyA MFTF lineage in the Enterobacteriaceae plays little or no role in regulating efflux but rather functions as transcriptional counter-silencers, which alleviate xenogeneic silencing of horizontally acquired genes and facilitate bacterial evolution by horizontal gene transfer. This review will explore recent advances in our understanding of MFTF traits that have contributed to their functional evolution.}, }
@article {pmid32042895, year = {2020}, author = {Bethke, JH and Davidovich, A and Cheng, L and Lopatkin, AJ and Song, W and Thaden, JT and Fowler, VG and Xiao, M and You, L}, title = {Environmental and genetic determinants of plasmid mobility in pathogenic Escherichia coli.}, journal = {Science advances}, volume = {6}, number = {4}, pages = {eaax3173}, pmid = {32042895}, issn = {2375-2548}, support = {R01 AI125604/AI/NIAID NIH HHS/United States ; R01 GM098642/GM/NIGMS NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; *Conjugation, Genetic ; Drug Resistance, Bacterial/drug effects/*genetics ; Escherichia coli/*genetics ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Plasmids/*genetics ; Whole Genome Sequencing ; }, abstract = {Plasmids are key vehicles of horizontal gene transfer (HGT), mobilizing antibiotic resistance, virulence, and other traits among bacterial populations. The environmental and genetic forces that drive plasmid transfer are poorly understood, however, due to the lack of definitive quantification coupled with genomic analysis. Here, we integrate conjugative phenotype with plasmid genotype to provide quantitative analysis of HGT in clinical Escherichia coli pathogens. We find a substantial proportion of these pathogens (>25%) able to readily spread resistance to the most common classes of antibiotics. Antibiotics of varied modes of action had less than a 5-fold effect on conjugation efficiency in general, with one exception displaying 31-fold promotion upon exposure to macrolides and chloramphenicol. In contrast, genome sequencing reveals plasmid incompatibility group strongly correlates with transfer efficiency. Our findings offer new insights into the determinants of plasmid mobility and have implications for the development of treatments that target HGT.}, }
@article {pmid32042448, year = {2020}, author = {Brito, AF and Pinney, JW}, title = {The evolution of protein domain repertoires: Shedding light on the origins of the Herpesviridae family.}, journal = {Virus evolution}, volume = {6}, number = {1}, pages = {veaa001}, pmid = {32042448}, issn = {2057-1577}, abstract = {Herpesviruses (HVs, Family: Herpesviridae) have large genomes that encode hundreds of proteins. Apart from amino acid mutations, protein domain acquisitions, duplications and losses are also common modes of evolution. HV domain repertoires differ across species, and only a core set is shared among all species, aspect that raises a question: How have HV domain repertoires diverged while keeping some similarities? To answer such question, we used profile Hidden Markov Models (HMMs) to search for domains in all possible translated open reading frames (ORFs) of fully sequenced HV genomes. With at least 274 domains being identified, we built a matrix of domain counts per species, and applied a parsimony method to reconstruct the ancestral states of these domains along the HV phylogeny. It revealed events of domain gain, duplication, and loss over more than 400 millions of years, where Alpha-, Beta-, and GammaHVs expanded and condensed their domain repertoires at distinct rates. Most of the acquired domains perform 'Modulation and Control', 'Envelope', or 'Auxiliary' functions, categories that showed high flexibility (number of domains) and redundancy (number of copies). Conversely, few gains and duplications were observed for domains involved in 'Capsid assembly and structure', and 'DNA Replication, recombination and metabolism'. Among the forty-one primordial domains encoded by Herpesviridae ancestors, twenty-eight are still found in all present-day HVs. Because of their distinct evolutionary strategies, HV domain repertoires are very specific at the subfamily, genus and species levels. Differences in domain composition may not only explain HV host range and tissue tropism, but also provide hints to the origins of HVs.}, }
@article {pmid32041869, year = {2020}, author = {Ribeiro, CL and Conde, D and Balmant, KM and Dervinis, C and Johnson, MG and McGrath, AP and Szewczyk, P and Unda, F and Finegan, CA and Schmidt, HW and Miles, B and Drost, DR and Novaes, E and Gonzalez-Benecke, CA and Peter, GF and Burleigh, JG and Martin, TA and Mansfield, SD and Chang, G and Wickett, NJ and Kirst, M}, title = {The uncharacterized gene EVE contributes to vessel element dimensions in Populus.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {9}, pages = {5059-5066}, pmid = {32041869}, issn = {1091-6490}, mesh = {Biological Evolution ; Cell Membrane ; Gene Expression Regulation, Developmental ; Gene Expression Regulation, Plant ; Magnoliopsida/*metabolism ; Photosynthesis ; Phycodnaviridae ; Plant Proteins/*genetics/*metabolism ; Plants, Genetically Modified ; Populus/*genetics/*metabolism ; Potassium/metabolism ; Water/metabolism ; Xylem/cytology/metabolism ; }, abstract = {The radiation of angiosperms led to the emergence of the vast majority of today's plant species and all our major food crops. Their extraordinary diversification occurred in conjunction with the evolution of a more efficient vascular system for the transport of water, composed of vessel elements. The physical dimensions of these water-conducting specialized cells have played a critical role in angiosperm evolution; they determine resistance to water flow, influence photosynthesis rate, and contribute to plant stature. However, the genetic factors that determine their dimensions are unclear. Here we show that a previously uncharacterized gene, ENLARGED VESSEL ELEMENT (EVE), contributes to the dimensions of vessel elements in Populus, impacting hydraulic conductivity. Our data suggest that EVE is localized in the plasma membrane and is involved in potassium uptake of differentiating xylem cells during vessel development. In plants, EVE first emerged in streptophyte algae, but expanded dramatically among vessel-containing angiosperms. The phylogeny, structure and composition of EVE indicates that it may have been involved in an ancient horizontal gene-transfer event.}, }
@article {pmid32041484, year = {2020}, author = {Nazareth, T and Craveiro, I and Moutinho, A and Seixas, G and Gonçalves, C and Gonçalves, L and Teodósio, R and Sousa, CA}, title = {What happens when we modify mosquitoes for disease prevention? A systematic review.}, journal = {Emerging microbes &amp; infections}, volume = {9}, number = {1}, pages = {348-365}, pmid = {32041484}, issn = {2222-1751}, mesh = {Animals ; *Animals, Genetically Modified ; Gene Transfer, Horizontal ; Mosquito Control/*methods ; Mosquito Vectors/*genetics/microbiology ; Wolbachia ; }, abstract = {The release of modified mosquitoes to suppress/replace vectors constitutes a promising tool for vector control and disease prevention. Evidence regarding these innovative modification techniques is scarce and disperse. This work conducted a systematic review, gathering and analysing research articles from PubMed and Biblioteca Virtual em Saúde databases whose results report efficacy and non-target effects of using modified insects for disease prevention, until 2016. More than 1500 publications were screened and 349 were analysed. Only 12/3.4% articles reported field-based evidence and 41/11.7% covered modification strategies' post-release efficacy. Variability in the effective results (90/25.7%) questioned its reproducibility in different settings. We also found publications reporting reversal outcomes 38/10.9%, (e.g. post-release increase of vector population). Ecological effects were also reported, such as horizontal transfer events (54/15.5%), and worsening pathogenesis induced by natural wolbachia (10/2.9%). Present work revealed promising outcomes of modifying strategies. However, it also revealed a need for field-based evidence mainly regarding epidemiologic and long-term impact. It pointed out some eventual irreversible and important effects that must not be ignored when considering open-field releases, and that may constitute constraints to generate the missing field evidence. Present work constitutes a baseline of knowledge, offering also a methodological approach that may facilitate future updates.}, }
@article {pmid32040377, year = {2020}, author = {Perez-Quintero, AL and Ortiz-Castro, M and Lang, JM and Rieux, A and Wu, G and Liu, S and Chapman, TA and Chang, C and Ziegle, J and Peng, Z and White, FF and Plazas, MC and Leach, JE and Broders, K}, title = {Genomic Acquisitions in Emerging Populations of Xanthomonas vasicola pv. vasculorum Infecting Corn in the United States and Argentina.}, journal = {Phytopathology}, volume = {110}, number = {6}, pages = {1161-1173}, doi = {10.1094/PHYTO-03-19-0077-R}, pmid = {32040377}, issn = {0031-949X}, mesh = {Argentina ; Genomics ; Phylogeny ; Plant Diseases ; South Africa ; South America ; United States ; *Xanthomonas ; Zea mays ; }, abstract = {Xanthomonas vasicola pv. vasculorum is an emerging bacterial plant pathogen that causes bacterial leaf streak on corn. First described in South Africa in 1949, reports of this pathogen have greatly increased in the past years in South America and in the United States. The rapid spread of this disease in North and South America may be due to more favorable environmental conditions, susceptible hosts and/or genomic changes that favored the spread. To understand whether genetic mechanisms exist behind the recent spread of X. vasicola pv. vasculorum, we used comparative genomics to identify gene acquisitions in X. vasicola pv. vasculorum genomes from the United States and Argentina. We sequenced 41 genomes of X. vasicola pv. vasculorum and the related sorghum-infecting X. vasicola pv. holcicola and performed comparative analyses against all available X. vasicola genomes. Time-measured phylogenetic analyses showed that X. vasicola pv. vasculorum strains from the United States and Argentina are closely related and arose from two introductions to North and South America. Gene content comparisons identified clusters of genes enriched in corn X. vasicola pv. vasculorum that showed evidence of horizontal transfer including one cluster corresponding to a prophage found in all X. vasicola pv. vasculorum strains from the United States and Argentina as well as in X. vasicola pv. holcicola strains. In this work, we explore the genomes of an emerging phytopathogen population as a first step toward identifying genetic changes associated with the emergence. The acquisitions identified may contain virulence determinants or other factors associated with the spread of X. vasicola pv. vasculorum in North and South America and will be the subject of future work.}, }
@article {pmid32038518, year = {2019}, author = {Bachmann, NL and Salamzade, R and Manson, AL and Whittington, R and Sintchenko, V and Earl, AM and Marais, BJ}, title = {Key Transitions in the Evolution of Rapid and Slow Growing Mycobacteria Identified by Comparative Genomics.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {3019}, pmid = {32038518}, issn = {1664-302X}, support = {U19 AI110818/AI/NIAID NIH HHS/United States ; }, abstract = {Mycobacteria have been classified into rapid and slow growing phenotypes, but the genetic factors that underlie these growth rate differences are not well understood. We compared the genomes of 157 mycobacterial species, representing all major branches of the mycobacterial phylogenetic tree to identify genes and operons enriched among rapid and slow growing mycobacteria. Overlaying growth phenotype on a phylogenetic tree based on 304 core genes suggested that ancestral mycobacteria had a rapid growth phenotype with a single major evolutionary separation into rapid and slow growing sub-genera. We identified 293 genes enriched among rapid growing sub-genera, including genes encoding for amino acid transport/metabolism (e.g., livFGMH operon) and transcription, as well as novel ABC transporters. Loss of the livFGMH and ABC transporter operons among slow growing species suggests that reduced cellular amino acid transport may be growth limiting. Comparative genomic analysis suggests that horizontal gene transfer, from non-mycobacterial genera, may have contributed to niche adaptation and pathogenicity, especially among slow growing species. Interestingly, the mammalian cell entry (mce) operon was found to be ubiquitous, irrespective of growth phenotype or pathogenicity, although protein sequence homology between rapid and slow growing species was low (<50%). This suggests that the mce operon was present in ancestral rapid growing species, but later adapted by slow growing species for use as a mechanism to establish an intra-cellular lifestyle.}, }
@article {pmid32038517, year = {2019}, author = {Navarro-Muñoz, JC and Collemare, J}, title = {Evolutionary Histories of Type III Polyketide Synthases in Fungi.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {3018}, pmid = {32038517}, issn = {1664-302X}, abstract = {Type III polyketide synthases (PKSs) produce secondary metabolites with diverse biological activities, including antimicrobials. While they have been extensively studied in plants and bacteria, only a handful of type III PKSs from fungi has been characterized in the last 15 years. The exploitation of fungal type III PKSs to produce novel bioactive compounds requires understanding the diversity of these enzymes, as well as of their biosynthetic pathways. Here, phylogenetic and reconciliation analyses of 522 type III PKSs from 1,193 fungal genomes revealed complex evolutionary histories with massive gene duplications and losses, explaining their discontinuous distribution in the fungal tree of life. In addition, horizontal gene transfer events from bacteria to fungi and, to a lower extent, between fungi, could be inferred. Ancestral gene duplication events have resulted in the divergence of eight phylogenetic clades. Especially, two clades show ancestral linkage and functional co-evolution between a type III PKS and a reducing PKS genes. Investigation of the occurrence of protein domains in fungal type III PKS predicted gene clusters highlighted the diversity of biosynthetic pathways, likely reflecting a large chemical landscape. Type III PKS genes are most often located next to genes encoding cytochrome P450s, MFS transporters and transcription factors, defining ancestral core gene clusters. This analysis also allowed predicting gene clusters for the characterized fungal type III PKSs and provides working hypotheses for the elucidation of the full biosynthetic pathways. Altogether, our analyses provide the fundamental knowledge to motivate further characterization and exploitation of fungal type III PKS biosynthetic pathways.}, }
@article {pmid32032776, year = {2020}, author = {Li, DC and Gao, JF and Zhang, SJ and Gao, YQ and Sun, LX}, title = {Emergence and spread patterns of antibiotic resistance genes during two different aerobic granular sludge cultivation processes.}, journal = {Environment international}, volume = {137}, number = {}, pages = {105540}, doi = {10.1016/j.envint.2020.105540}, pmid = {32032776}, issn = {1873-6750}, mesh = {*Anti-Bacterial Agents ; *Drug Resistance, Microbial/genetics ; Environmental Health ; *Genes, Bacterial ; Humans ; *Sewage/microbiology ; Wastewater ; }, abstract = {The prevalence and accumulation of antibiotic resistance genes (ARGs) were frequently detected in biological wastewater treatment processes, which might cause potential health crisis to human. In present study, the fates of ARGs during two different aerobic granular sludge (AGS) cultivation processes were investigated. The results showed that traditional AGS (T-AGS) cultivation process and enhanced AGS (E-AGS) cultivation process had significant differences (P < 0.005) in ARGs shift patterns. E-AGS process had higher average relative abundance (0.280 ± 0.079) of ARGs than T-AGS process (0.130 ± 0.041), while the intensity of ARGs enrichment during E-AGS (1.52-5.29 fold) was lower than T-AGS (3.79-75.31 fold) process. TnpA and intI1 as two different types of mobile genetic elements (MGEs) carrying ARGs, were observed to contribute significantly to the horizontal gene transfer (HGT) during T-AGS (r = 0.902, P < 0.050) and E-AGS (r = 0.823, P < 0.001) processes, respectively. Higher HGT level took place and more possible potential hosts (25 hosts) harboring ARGs were detected during E-AGS process comparing with T-AGS process (17 hosts). Meanwhile, over large AGS might increase the propagation of several antibiotic deactivation ARGs, so it was not advised. Overall, whether during T-AGS or during E-AGS process which was applied in a pilot-scale sequencing batch reactor treating municipal wastewater, the accumulation and spread of ARGs were inevitable. It should be valued that some suitable pre-treatments of seed sludge should be executed, meanwhile, advanced treatment for removing of ARGs in AGS should be conducted to maintain the relative abundances of ARGs at relatively low level.}, }
@article {pmid32031723, year = {2020}, author = {Zhang, W and Yu, H and Lv, Y and Bushley, KE and Wickham, JD and Gao, S and Hu, S and Zhao, L and Sun, J}, title = {Gene family expansion of pinewood nematode to detoxify its host defence chemicals.}, journal = {Molecular ecology}, volume = {29}, number = {5}, pages = {940-955}, doi = {10.1111/mec.15378}, pmid = {32031723}, issn = {1365-294X}, mesh = {Adaptation, Biological/*genetics ; Animals ; Gene Duplication ; Gene Transfer, Horizontal ; Genes, Helminth ; Inactivation, Metabolic ; *Multigene Family ; Pinus/chemistry/*parasitology ; Plant Diseases/*parasitology ; Terpenes/*metabolism ; Transcriptome ; Tylenchida/*genetics ; }, abstract = {Gene gain/loss in the context of gene family dynamics plays an important role in evolutionary processes as organisms, particularly invasive species, adapt to new environments or niches. One notable example of this is the duplication of digestive proteases in some parasitic insects and helminths to meet nutritional requirements during animal parasitism. However, whether gene family expansion participates in the adaptation of a plant parasite nematode to its host remains unknown. Here, we compared the newly sequenced genomes of the pinewood nematode, Bursaphelenchus xylophilus, with the genomes of free-living, animal-parasitic and plant-parasitic nematodes. The results showed gene expansions occurring in 51 gene families in B. xylophilus, especially in xenobiotic detoxification pathways, including flavin monooxygenase (FMO), cytochrome P450 (CYP450), short chain dehydrogenase (SDR), alcohol dehydrogenase (ADH), aldehyde dehydrogenase (ALDH), UDP-glucuronosyltransferase (UGT) and glutathione S-transferase (GST). Although a majority of these expansions probably resulted from gene duplications, nine ADH genes were potentially acquired by horizontal gene transfer (HGT) from fungi. From the transcriptomes of B. xylophilus treated with pine saplings and terpenes, candidate xenobiotic detoxification genes were identified. We propose that host defence chemicals led to gene family expansions of xenobiotic detoxification pathways in B. xylophilus facilitating its survival in pine resin ducts. This study contributes to a better understanding of how a parasitic nematode adapts to its host.}, }
@article {pmid32031617, year = {2020}, author = {Al Suwayyid, BA and Rankine-Wilson, L and Speers, DJ and Wise, MJ and Coombs, GW and Kahler, CM}, title = {Meningococcal Disease-Associated Prophage-Like Elements Are Present in Neisseria gonorrhoeae and Some Commensal Neisseria Species.}, journal = {Genome biology and evolution}, volume = {12}, number = {2}, pages = {3938-3950}, pmid = {32031617}, issn = {1759-6653}, mesh = {Gene Transfer, Horizontal/genetics/physiology ; Inovirus/genetics ; Meningococcal Infections/*virology ; Neisseria/*virology ; Neisseria cinerea/virology ; Neisseria gonorrhoeae/virology ; Neisseria lactamica/virology ; Phylogeny ; Prophages/*genetics ; }, abstract = {Neisseria spp. possess four genogroups of filamentous prophages, termed Nf1 to 4. A filamentous bacteriophage from the Nf1 genogroup termed meningococcal disease-associated phage (MDA φ) is associated with clonal complexes of Neisseria meningitidis that cause invasive meningococcal disease. Recently, we recovered an isolate of Neisseria gonorrhoeae (ExNg63) from a rare case of gonococcal meningitis, and found that it possessed a region with 90% similarity to Nf1 prophages, specifically, the meningococcal MDA φ. This led to the hypothesis that the Nf1 prophage may be more widely distributed amongst the genus Neisseria. An analysis of 92 reference genomes revealed the presence of intact Nf1 prophages in the commensal species, Neisseria lactamica and Neisseria cinerea in addition to the pathogen N. gonorrhoeae. In N. gonorrhoeae, Nf1 prophages had a restricted distribution but were present in all representatives of MLST ST1918. Of the 160 phage integration sites identified, only one common insertion site was found between one isolate of N. gonorrhoeae and N. meningitidis. There was an absence of any obvious conservation of the receptor for prophage entry, PilE, suggesting that the phage may have been obtained by natural transformation. An examination of the restriction modification systems and mutated mismatch repair systems with prophage presence suggested that there was no obvious preference for these hosts. A timed phylogeny inferred that N. meningitidis was the donor of the Nf1 prophages in N. lactamica and N. gonorrhoeae. Further work is required to determine whether Nf1 prophages are active and can act as accessory colonization factors in these species.}, }
@article {pmid32028892, year = {2020}, author = {Palma, F and Brauge, T and Radomski, N and Mallet, L and Felten, A and Mistou, MY and Brisabois, A and Guillier, L and Midelet-Bourdin, G}, title = {Dynamics of mobile genetic elements of Listeria monocytogenes persisting in ready-to-eat seafood processing plants in France.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {130}, pmid = {32028892}, issn = {1471-2164}, support = {643476//Horizon 2020 Research and Innovation Program: COMPARE/ ; }, mesh = {*Food-Processing Industry ; France ; Genes, Bacterial ; Genome, Bacterial ; *Interspersed Repetitive Sequences ; Listeria monocytogenes/classification/*genetics/isolation &amp; purification ; Phylogeny ; Plasmids/genetics ; Polymorphism, Single Nucleotide ; Prophages/genetics ; Seafood/*microbiology ; Stress, Physiological/genetics ; }, abstract = {BACKGROUND: Listeria monocytogenes Clonal Complexes (CCs) have been epidemiologically associated with foods, especially ready-to-eat (RTE) products for which the most likely source of contamination depends on the occurrence of persisting clones in food-processing environments (FPEs). As the ability of L. monocytogenes to adapt to environmental stressors met in the food chain challenges the efforts to its eradication from FPEs, the threat of persistent strains to the food industry and public health authorities continues to rise. In this study, 94 food and FPEs L. monocytogenes isolates, representing persistent subtypes contaminating three French seafood facilities over 2-6 years, were whole-genome sequenced to characterize their genetic diversity and determine the biomarkers associated with long-term survival in FPEs.<br><br>RESULTS: Food and FPEs isolates belonged to five CCs, comprising long-term intra- and inter-plant persisting clones. Mobile genetic elements (MGEs) such as plasmids, prophages and transposons were highly conserved within CCs, some of which harboured genes for resistance to chemical compounds and biocides used in the processing plants. Some of these genes were found in a 90.8 kbp plasmid, predicted to be" mobilizable", identical in isolates from CC204 and CC155, and highly similar to an 81.6 kbp plasmid from isolates belonging to CC7. These similarities suggest horizontal transfer between isolates, accompanied by deletion and homologous recombination in isolates from CC7. Prophage profiles characterized persistent clonal strains and several prophage-loci were plant-associated. Notably, a persistent clone from CC101 harboured a novel 31.5 kbp genomic island that we named Listeria genomic island 3 (LGI3), composed by plant-associated loci and chromosomally integrating cadmium-resistance determinants cadA1C.<br><br>CONCLUSIONS: Genome-wide analysis indicated that inter- and intra-plant persisting clones harbour conserved MGEs, likely acquired in FPEs and maintained by selective pressures. The presence of closely related plasmids in L. monocytogenes CCs supports the hypothesis of horizontal gene transfer conferring enhanced survival to FPE-associated stressors, especially in hard-to-clean harbourage sites. Investigating the MGEs evolutionary and transmission dynamics provides additional resolution to trace-back potentially persistent clones. The biomarkers herein discovered provide new tools for better designing effective strategies for the removal or reduction of resident L. monocytogenes in FPEs to prevent contamination of RTE seafood.}, }
@article {pmid32027370, year = {2020}, author = {Stalder, T and Cornwell, B and Lacroix, J and Kohler, B and Dixon, S and Yano, H and Kerr, B and Forney, LJ and Top, EM}, title = {Evolving Populations in Biofilms Contain More Persistent Plasmids.}, journal = {Molecular biology and evolution}, volume = {37}, number = {6}, pages = {1563-1576}, pmid = {32027370}, issn = {1537-1719}, support = {P20 GM103408/GM/NIGMS NIH HHS/United States ; P30 GM103324/GM/NIGMS NIH HHS/United States ; R01 AI084918/AI/NIAID NIH HHS/United States ; }, mesh = {*Biofilms ; *Biological Evolution ; *Plasmids ; Shewanella/*genetics ; Whole Genome Sequencing ; }, abstract = {Bacterial plasmids substantially contribute to the rapid spread of antibiotic resistance, which is a crisis in healthcare today. Coevolution of plasmids and their hosts promotes this spread of resistance by ameliorating the cost of plasmid carriage. However, our knowledge of plasmid-bacteria coevolution is solely based on studies done in well-mixed liquid cultures, even though biofilms represent the main way of bacterial life on Earth and are responsible for most infections. The spatial structure and the heterogeneity provided by biofilms are known to lead to increased genetic diversity as compared with well-mixed liquids. Therefore, we expect that growth in this complex environment could affect the evolutionary trajectories of plasmid-host dyads. We experimentally evolved Shewanella oneidensis MR-1 with plasmid pBP136Gm in biofilms and chemostats and sequenced the genomes of clones and populations. Biofilm populations not only maintained a higher diversity of mutations than chemostat populations but contained a few clones with markedly more persistent plasmids that evolved via multiple distinct trajectories. These included the acquisition of a putative toxin-antitoxin transposon by the plasmid and chromosomal mutations. Some of these genetic changes resulted in loss of plasmid transferability or decrease in plasmid cost. Growth in chemostats led to a higher proportion of variants with decreased plasmid persistence, a phenomenon not detected in biofilms. We suggest that the presence of more stable plasmid-host dyads in biofilms reflects higher genetic diversity and possibly unknown selection pressures. Overall, this study underscores the importance of the mode of growth in the evolution of antibiotic-resistant bacteria.}, }
@article {pmid32020051, year = {2020}, author = {Li, L and Dechesne, A and Madsen, JS and Nesme, J and Sørensen, SJ and Smets, BF}, title = {Plasmids persist in a microbial community by providing fitness benefit to multiple phylotypes.}, journal = {The ISME journal}, volume = {14}, number = {5}, pages = {1170-1181}, pmid = {32020051}, issn = {1751-7370}, mesh = {Anti-Bacterial Agents ; Bacteria/genetics ; Drug Resistance, Microbial ; Gene Transfer, Horizontal ; Host Specificity ; *Microbiota ; *Plasmids ; Pseudomonas/genetics ; }, abstract = {The current epidemic of antibiotic resistance has been facilitated by the wide and rapid horizontal dissemination of antibiotic resistance genes (ARGs) in microbial communities. Indeed, ARGs are often located on plasmids, which can efficiently shuttle genes across diverse taxa. While the existence conditions of plasmids have been extensively studied in a few model bacterial populations, their fate in complex bacterial communities is poorly understood. Here, we coupled plasmid transfer assays with serial growth experiments to investigate the persistence of the broad-host-range IncP-1 plasmid pKJK5 in microbial communities derived from a sewage treatment plant. The cultivation conditions combined different nutrient and oxygen levels, and were non-selective and non-conducive for liquid-phase conjugal transfer. Following initial transfer, the plasmid persisted in almost all conditions during a 10-day serial growth experiment (equivalent to 60 generations), with a transient transconjugant incidence up to 30%. By combining cell enumeration and sorting with amplicon sequencing, we mapped plasmid fitness effects across taxa of the microbial community. Unexpected plasmid fitness benefits were observed in multiple phylotypes of Aeromonas, Enterobacteriaceae, and Pseudomonas, which resulted in community-level plasmid persistence. We demonstrate, for the first time, that plasmid fitness effects across community members can be estimated in high-throughput without prior isolation. By gaining a fitness benefit when carrying plasmids, members within complex microbial communities might have a hitherto unrecognised potential to maintain plasmids for long-term community-wide access.}, }
@article {pmid32019787, year = {2020}, author = {Wiechert, J and Filipchyk, A and Hünnefeld, M and Gätgens, C and Brehm, J and Heermann, R and Frunzke, J}, title = {Deciphering the Rules Underlying Xenogeneic Silencing and Counter-Silencing of Lsr2-like Proteins Using CgpS of Corynebacterium glutamicum as a Model.}, journal = {mBio}, volume = {11}, number = {1}, pages = {}, pmid = {32019787}, issn = {2150-7511}, mesh = {Bacterial Proteins/*genetics/metabolism ; Corynebacterium glutamicum/*genetics ; DNA-Binding Proteins/genetics/metabolism ; *Gene Silencing ; Gene Transfer, Horizontal ; Protein Binding ; Transcription Factors/genetics/metabolism ; }, abstract = {Lsr2-like nucleoid-associated proteins play an important role as xenogeneic silencers (XS) of horizontally acquired genomic regions in actinobacteria. In this study, we systematically analyzed the in vivo constraints underlying silencing and counter-silencing of the Lsr2-like protein CgpS in Corynebacterium glutamicum Genome-wide analysis revealed binding of CgpS to regions featuring a distinct drop in GC profile close to the transcription start site (TSS) but also identified an overrepresented motif with multiple A/T steps at the nucleation site of the nucleoprotein complex. Binding of specific transcription factors (TFs) may oppose XS activity, leading to counter-silencing. Following a synthetic counter-silencing approach, target gene activation was realized by inserting operator sites of an effector-responsive TF within various CgpS target promoters, resulting in increased promoter activity upon TF binding. Analysis of reporter constructs revealed maximal counter-silencing when the TF operator site was inserted at the position of maximal CgpS coverage. This principle was implemented in a synthetic toggle switch, which features a robust and reversible response to effector availability, highlighting the potential for biotechnological applications. Together, our results provide comprehensive insights into how Lsr2 silencing and counter-silencing shape evolutionary network expansion in this medically and biotechnologically relevant bacterial phylum.IMPORTANCE In actinobacteria, Lsr2-like nucleoid-associated proteins function as xenogeneic silencers (XS) of horizontally acquired genomic regions, including viral elements, virulence gene clusters in Mycobacterium tuberculosis, and genes involved in cryptic specialized metabolism in Streptomyces species. Consequently, a detailed mechanistic understanding of Lsr2 binding in vivo is relevant as a potential drug target and for the identification of novel bioactive compounds. Here, we followed an in vivo approach to investigate the rules underlying xenogeneic silencing and counter-silencing of the Lsr2-like XS CgpS from Corynebacterium glutamicum Our results demonstrated that CgpS distinguishes between self and foreign by recognizing a distinct drop in GC profile in combination with a short, sequence-specific motif at the nucleation site. Following a synthetic counter-silencer approach, we studied the potential and constraints of transcription factors to counteract CgpS silencing, thereby facilitating the integration of new genetic traits into host regulatory networks.}, }
@article {pmid32019196, year = {2020}, author = {Willms, IM and Yuan, J and Penone, C and Goldmann, K and Vogt, J and Wubet, T and Schöning, I and Schrumpf, M and Buscot, F and Nacke, H}, title = {Distribution of Medically Relevant Antibiotic Resistance Genes and Mobile Genetic Elements in Soils of Temperate Forests and Grasslands Varying in Land Use.}, journal = {Genes}, volume = {11}, number = {2}, pages = {}, pmid = {32019196}, issn = {2073-4425}, mesh = {Agriculture ; Bacteria/genetics/*growth &amp; development ; Bacterial Proteins/genetics ; *Drug Resistance, Microbial ; Environmental Monitoring ; Forests ; Fungal Proteins/genetics ; Fungi/genetics/*growth &amp; development ; Grassland ; *Integrons ; Macrolides/pharmacology ; Plasmids/*genetics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Soil Microbiology ; }, abstract = {Antibiotic-resistant pathogens claim the lives of thousands of people each year and are currently considered as one of the most serious threats to public health. Apart from clinical environments, soil ecosystems also represent a major source of antibiotic resistance determinants, which can potentially disseminate across distinct microbial habitats and be acquired by human pathogens via horizontal gene transfer. Therefore, it is of global importance to retrieve comprehensive information on environmental factors, contributing to an accumulation of antibiotic resistance genes and mobile genetic elements in these ecosystems. Here, medically relevant antibiotic resistance genes, class 1 integrons and IncP-1 plasmids were quantified via real time quantitative PCR in soils derived from temperate grasslands and forests, varying in land use over a large spatial scale. The generated dataset allowed an analysis, decoupled from regional influences, and enabled the identification of land use practices and soil characteristics elevating the abundance of antibiotic resistance genes and mobile genetic elements. In grassland soils, the abundance of the macrolide resistance gene mefA as well as the sulfonamide resistance gene sul2 was positively correlated with organic fertilization and the abundance of aac(6')-lb, conferring resistance to different aminoglycosides, increased with mowing frequency. With respect to forest soils, the beta-lactam resistance gene blaIMP-12 was significantly correlated with fungal diversity which might be due to the fact that different fungal species can produce beta-lactams. Furthermore, except blaIMP-5 and blaIMP-12, the analyzed antibiotic resistance genes as well as IncP-1 plasmids and class-1 integrons were detected less frequently in forest soils than in soils derived from grassland that are commonly in closer proximity to human activities.}, }
@article {pmid32019018, year = {2020}, author = {Lu, J and Wang, Y and Zhang, S and Bond, P and Yuan, Z and Guo, J}, title = {Triclosan at environmental concentrations can enhance the spread of extracellular antibiotic resistance genes through transformation.}, journal = {The Science of the total environment}, volume = {713}, number = {}, pages = {136621}, doi = {10.1016/j.scitotenv.2020.136621}, pmid = {32019018}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents ; *Drug Resistance, Bacterial ; Ecosystem ; Escherichia coli ; Genes, Bacterial ; Proteomics ; Triclosan ; }, abstract = {The dissemination of antibiotic resistance mediated by horizontal transfer of antibiotic resistance genes (ARGs) is exacerbating the global antibiotic crisis. Currently, little is known about whether non-antibiotic, anti-microbial (NAAM) chemicals are associated with the dissemination of ARGs in the environment. In this study, we aimed to evaluate whether a ubiquitous NAAM chemical, triclosan (TCS), is able to promote the transformation of plasmid-borne antibiotic resistance genes (ARGs). By using the plasmid pUC19 carrying ampicillin resistance genes as the extracellular ARG and a model microorganism Escherichia coli DH5ɑ as the recipient, we found that TCS at environmentally detected concentrations (0.2 μg/L to 20 μg/L) significantly enhanced the transformation of plasmid-borne ARGs into E. coli DH5ɑ for up to 1.4-fold. The combination of phenotypic experiments, genome-wide RNA sequencing and proteomic analyses revealed that TCS exposure stimulated the reactive oxygen species (ROS) production for 1.3- to 1.5-fold, induced bacterial membrane damage and up-regulated the translation of outer membrane porin. Moreover, general secretion system Sec (1.4-fold), twin arginine translocation system Tat (1.2-fold) and type IV pilus secretion systems (2.5-fold) were enhanced by TCS, which might contribute to the DNA searching/capture by pilus. Together, TCS might increase the transformation frequency of ARGs into E. coli DH5ɑ by ROS over-production, damaging cell membrane barrier, mediating the pilus capture of plasmid and the translocation of plasmid via cell membrane channels. This study reports that TCS could accelerate the transformation of extracellular ARGs to competent bacteria at environmentally relevant concentrations. The findings advance our understanding of the fate of ARGs in ecosystems and call for risk assessments of NAAM chemicals on disseminating antibiotic resistance.}, }
@article {pmid32015881, year = {2020}, author = {Sawa, T and Kooguchi, K and Moriyama, K}, title = {Molecular diversity of extended-spectrum β-lactamases and carbapenemases, and antimicrobial resistance.}, journal = {Journal of intensive care}, volume = {8}, number = {}, pages = {13}, pmid = {32015881}, issn = {2052-0492}, abstract = {Along with the recent spread of multidrug-resistant bacteria, outbreaks of extended-spectrum β-lactamase (ESBL) and carbapenemase-producing bacteria present a serious challenge to clinicians. β-lactam antibiotics are the most frequently used antibacterial agents and ESBLs, and carbapenemases confer resistance not only to carbapenem antibiotics but also to penicillin and cephem antibiotics. The mechanism of β-lactam resistance involves an efflux pump, reduced permeability, altered transpeptidases, and inactivation by β-lactamases. Horizontal gene transfer is the most common mechanism associated with the spread of extended-spectrum β-lactam- and carbapenem resistance among pathogenic bacterial species. Along with the increase in antimicrobial resistance, many different types of ESBLs and carbapenemases have emerged with different enzymatic characteristics. For example, carbapenemases are represented across classes A to D of the Ambler classification system. Because bacteria harboring different types of ESBLs and carbapenemases require specific therapeutic strategies, it is essential for clinicians to understand the characteristics of infecting pathogens. In this review, we summarize the current knowledge on carbapenem resistance by ESBLs and carbapenemases, such as class A carbapenemases, class C extended-spectrum AmpC (ESAC), carbapenem-hydrolyzing class D β-lactamases (CHDLs), and class B metallo-β-lactamases, with the aim of aiding critical care clinicians in their therapeutic decision making.}, }
@article {pmid32015529, year = {2020}, author = {Dion, MB and Oechslin, F and Moineau, S}, title = {Phage diversity, genomics and phylogeny.}, journal = {Nature reviews. Microbiology}, volume = {18}, number = {3}, pages = {125-138}, pmid = {32015529}, issn = {1740-1534}, mesh = {Bacteriophages/*classification/*genetics/ultrastructure ; *Biodiversity ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Viral ; Host Microbial Interactions ; Metagenomics ; *Phylogeny ; Recombination, Genetic ; Viral Proteins/genetics ; Virion/ultrastructure ; }, abstract = {Recent advances in viral metagenomics have enabled the rapid discovery of an unprecedented catalogue of phages in numerous environments, from the human gut to the deep ocean. Although these advances have expanded our understanding of phage genomic diversity, they also revealed that we have only scratched the surface in the discovery of novel viruses. Yet, despite the remarkable diversity of phages at the nucleotide sequence level, the structural proteins that form viral particles show strong similarities and conservation. Phages are uniquely interconnected from an evolutionary perspective and undergo multiple events of genetic exchange in response to the selective pressure of their hosts, which drives their diversity. In this Review, we explore phage diversity at the structural, genomic and community levels as well as the complex evolutionary relationships between phages, moulded by the mosaicity of their genomes.}, }
@article {pmid32015144, year = {2020}, author = {Matsutani, M and Matsumoto, N and Hirakawa, H and Shiwa, Y and Yoshikawa, H and Okamoto-Kainuma, A and Ishikawa, M and Kataoka, N and Yakushi, T and Matsushita, K}, title = {Comparative Genomic Analysis of Closely Related Acetobacter pasteurianus Strains Provides Evidence of Horizontal Gene Transfer and Reveals Factors Necessary for Thermotolerance.}, journal = {Journal of bacteriology}, volume = {202}, number = {8}, pages = {}, pmid = {32015144}, issn = {1098-5530}, mesh = {Acetobacter/classification/*genetics/physiology ; Bacterial Proteins/genetics/metabolism ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Hot Temperature ; Phenotype ; }, abstract = {Acetobacter pasteurianus is an industrial strain used for the vinegar production. Many A. pasteurianus strains with different phenotypic characteristics have been isolated so far. To understand the genetic background underpinning these phenotypes, a comparative genomic analysis of A. pasteurianus strains was conducted. Based on bioinformatics and experimental results, we report the following. (i) The gene repertoire related to the respiratory chains showed that several horizontal gene transfer events occurred after the divergence of these strains, indicating that the respiratory chain in A. pasteurianus has the diversity to adapt to its environment. (ii) There is a clear difference in thermotolerance even between 12 closely related strains. NBRC 3279, NBRC 3284, and NBRC 3283, in particular, which have only 55 mutations in total, showed differences in thermotolerance. The Na[+]/H[+] antiporter gene nhaK2 was mutated in the thermosensitive NBRC 3279 and NBRC 3284 strains and not in the thermotolerant NBRC 3283 strain. The Na[+]/H[+] antiporter activity of the three strains and expression of nhaK2 gene from NBRC 3283 in the two thermosensitive strains showed that these mutations are critical for thermotolerance. These results suggested that horizontal gene transfer events and several mutations have affected the phenotypes of these closely related strains.IMPORTANCEAcetobacter pasteurianus, an industrial vinegar-producing strain, exhibits diverse phenotypic differences such as respiratory activity related to acetic acid production, acetic acid resistance, or thermotolerance. In this study, we investigated the correlations between genome sequences and phenotypes among closely related A. pasteurianus strains. The gene repertoire related to the respiratory chains showed that the respiratory components of A. pasteurianus has a diversity caused by several horizontal gene transfers and mutations. In three closely related strains with clear differences in their thermotolerances, we found that the insertion or deletion that occurred in the Na[+]/H[+] antiporter gene nhaK2 is directly related to their thermotolerance. Our study suggests that a relatively quick mutation has occurred in the closely related A. pasteurianus due to its genetic instability and that this has largely affected its phenotype.}, }
@article {pmid32013150, year = {2020}, author = {Piña-Iturbe, A and Suazo, ID and Hoppe-Elsholz, G and Ulloa-Allendes, D and González, PA and Kalergis, AM and Bueno, SM}, title = {Horizontally Acquired Homologs of Xenogeneic Silencers: Modulators of Gene Expression Encoded by Plasmids, Phages and Genomic Islands.}, journal = {Genes}, volume = {11}, number = {2}, pages = {}, pmid = {32013150}, issn = {2073-4425}, mesh = {Bacteria/*genetics/virology ; Bacterial Proteins/*genetics ; Bacteriophages/*genetics ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genetic Fitness ; Genomic Islands ; Plasmids/*genetics ; }, abstract = {Acquisition of mobile elements by horizontal gene transfer can play a major role in bacterial adaptation and genome evolution by providing traits that contribute to bacterial fitness. However, gaining foreign DNA can also impose significant fitness costs to the host bacteria and can even produce detrimental effects. The efficiency of horizontal acquisition of DNA is thought to be improved by the activity of xenogeneic silencers. These molecules are a functionally related group of proteins that possess affinity for the acquired DNA. Binding of xenogeneic silencers suppresses the otherwise uncontrolled expression of genes from the newly acquired nucleic acid, facilitating their integration to the bacterial regulatory networks. Even when the genes encoding for xenogeneic silencers are part of the core genome, homologs encoded by horizontally acquired elements have also been identified and studied. In this article, we discuss the current knowledge about horizontally acquired xenogeneic silencer homologs, focusing on those encoded by genomic islands, highlighting their distribution and the major traits that allow these proteins to become part of the host regulatory networks.}, }
@article {pmid32011709, year = {2020}, author = {Miller, WG and Yee, E and Bono, JL}, title = {Complete Genome Sequencing of Four Arcobacter Species Reveals a Diverse Suite of Mobile Elements.}, journal = {Genome biology and evolution}, volume = {12}, number = {2}, pages = {3850-3856}, pmid = {32011709}, issn = {1759-6653}, mesh = {Arcobacter/*genetics ; DNA Transposable Elements/genetics ; Interspersed Repetitive Sequences/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; Whole Genome Sequencing/*methods ; }, abstract = {Arcobacter species are recovered from a wide variety of sources, including animals, food, and both fresh and marine waters. Several Arcobacter species have also been recovered from human clinical samples and are thus associated tentatively with food- and water-borne human illnesses. Genome sequencing of the poultry isolate Arcobacter cibarius H743 and the Arcobacter acticola, Arcobacter pacificus, and Arcobacter porcinus type strains identified a large number and variety of insertion sequences. This study presents an analysis of these A. acticola, A. cibarius, A. pacificus, and A. porcinus IS elements. The four genomes sequenced here contain 276 complete and degenerate IS elements, representing 13 of the current 29 prokaryotic IS element families. Expansion of the analysis to include 15 other previously sequenced Arcobacter spp. added 73 complete and degenerate IS elements. Several of these IS elements were identified in two or more Arcobacter species, suggesting movement by horizontal gene transfer between the arcobacters. These IS elements are putatively associated with intragenomic deletions and inversions, and tentative movement of antimicrobial resistance genes. The A. cibarius strain H743 megaplasmid contains multiple IS elements common to the chromosome and, unusually, a complete ribosomal RNA locus, indicating that larger scale genomic rearrangements, potentially resulting from IS element-mediated megaplasmid cointegration and resolution may be occurring within A. cibarius and possibly other arcobacters. The presence of such a large and varied suite of mobile elements could have profound effects on Arcobacter biology and evolution.}, }
@article {pmid32004459, year = {2020}, author = {Zhou, W and Spoto, M and Hardy, R and Guan, C and Fleming, E and Larson, PJ and Brown, JS and Oh, J}, title = {Host-Specific Evolutionary and Transmission Dynamics Shape the Functional Diversification of Staphylococcus epidermidis in Human Skin.}, journal = {Cell}, volume = {180}, number = {3}, pages = {454-470.e18}, pmid = {32004459}, issn = {1097-4172}, support = {U19 AI142733/AI/NIAID NIH HHS/United States ; P30 CA034196/CA/NCI NIH HHS/United States ; R43 AR073562/AR/NIAMS NIH HHS/United States ; F30 DE027870/DE/NIDCR NIH HHS/United States ; R90 DE022526/DE/NIDCR NIH HHS/United States ; T90 DE021989/DE/NIDCR NIH HHS/United States ; K22 AI119231/AI/NIAID NIH HHS/United States ; U54 NS105539/NS/NINDS NIH HHS/United States ; R21 AR075174/AR/NIAMS NIH HHS/United States ; DP2 GM126893/GM/NIGMS NIH HHS/United States ; }, mesh = {Adult ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; *Evolution, Molecular ; Female ; *Gene Transfer, Horizontal ; Healthy Volunteers ; Host Microbial Interactions/*genetics ; Humans ; Male ; Microbiota/*genetics ; Middle Aged ; Phylogeny ; *Polymorphism, Single Nucleotide ; Skin/*microbiology ; Staphylococcus epidermidis/*genetics/isolation &amp; purification/pathogenicity ; Virulence/genetics ; Young Adult ; }, abstract = {Metagenomic inferences of bacterial strain diversity and infectious disease transmission studies largely assume a dominant, within-individual haplotype. We hypothesize that within-individual bacterial population diversity is critical for homeostasis of a healthy microbiome and infection risk. We characterized the evolutionary trajectory and functional distribution of Staphylococcus epidermidis-a keystone skin microbe and opportunistic pathogen. Analyzing 1,482 S. epidermidis genomes from 5 healthy individuals, we found that skin S. epidermidis isolates coalesce into multiple founder lineages rather than a single colonizer. Transmission events, natural selection, and pervasive horizontal gene transfer result in population admixture within skin sites and dissemination of antibiotic resistance genes within-individual. We provide experimental evidence for how admixture can modulate virulence and metabolism. Leveraging data on the contextual microbiome, we assess how interspecies interactions can shape genetic diversity and mobile gene elements. Our study provides insights into how within-individual evolution of human skin microbes shapes their functional diversification.}, }
@article {pmid32002743, year = {2020}, author = {Balcázar, JL}, title = {Implications of bacteriophages on the acquisition and spread of antibiotic resistance in the environment.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {23}, number = {4}, pages = {475-479}, doi = {10.1007/s10123-020-00121-5}, pmid = {32002743}, issn = {1618-1905}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics/virology ; Bacteriophages/*genetics ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/physiology ; }, abstract = {Although bacteriophages (or simply phages) are the most abundant biological entities and have the potential to transfer genetic material between bacterial hosts, their contribution to the acquisition and spread of antibiotic resistance genes in the environment has not been extensively studied. The environment is continually exposed to a wide variety of pollutants from anthropogenic sources, which may promote horizontal gene transfer events, including those mediated by phages. Considering the significant and growing concern of antibiotic resistance, phages should be taken into consideration during the implementation of mitigation measures. This review is focused on the emergence and spread of antibiotic resistance in the environment, with a special emphasis on the role of phages.}, }
@article {pmid32002659, year = {2020}, author = {Geiß, M and Laffitte, MEG and Sánchez, AL and Valdivia, DI and Hellmuth, M and Rosales, MH and Stadler, PF}, title = {Best match graphs and reconciliation of gene trees with species trees.}, journal = {Journal of mathematical biology}, volume = {80}, number = {5}, pages = {1459-1495}, pmid = {32002659}, issn = {1432-1416}, mesh = {Algorithms ; Computational Biology ; Computer Graphics ; Computer Simulation ; *Evolution, Molecular ; Gene Deletion ; Gene Duplication ; Gene Transfer, Horizontal ; *Genetic Speciation ; Mathematical Concepts ; *Models, Genetic ; *Phylogeny ; }, abstract = {A wide variety of problems in computational biology, most notably the assessment of orthology, are solved with the help of reciprocal best matches. Using an evolutionary definition of best matches that captures the intuition behind the concept we clarify rigorously the relationships between reciprocal best matches, orthology, and evolutionary events under the assumption of duplication/loss scenarios. We show that the orthology graph is a subgraph of the reciprocal best match graph (RBMG). We furthermore give conditions under which an RBMG that is a cograph identifies the correct orthlogy relation. Using computer simulations we find that most false positive orthology assignments can be identified as so-called good quartets-and thus corrected-in the absence of horizontal transfer. Horizontal transfer, however, may introduce also false-negative orthology assignments.}, }
@article {pmid32001686, year = {2020}, author = {Boekhoud, IM and Hornung, BVH and Sevilla, E and Harmanus, C and Bos-Sanders, IMJG and Terveer, EM and Bolea, R and Corver, J and Kuijper, EJ and Smits, WK}, title = {Plasmid-mediated metronidazole resistance in Clostridioides difficile.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {598}, pmid = {32001686}, issn = {2041-1723}, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Clostridioides difficile/drug effects/genetics/growth &amp; development/*physiology ; Clostridium Infections/drug therapy/microbiology ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/*drug effects/genetics ; Feces/microbiology ; Gene Dosage ; Gene Transfer, Horizontal/genetics ; Humans ; Metronidazole/*pharmacology/therapeutic use ; Plasmids/*genetics ; Polymorphism, Single Nucleotide/genetics ; Replicon/genetics ; }, abstract = {Metronidazole was until recently used as a first-line treatment for potentially life-threatening Clostridioides difficile (CD) infection. Although cases of metronidazole resistance have been documented, no clear mechanism for metronidazole resistance or a role for plasmids in antimicrobial resistance has been described for CD. Here, we report genome sequences of seven susceptible and sixteen resistant CD isolates from human and animal sources, including isolates from a patient with recurrent CD infection by a PCR ribotype (RT) 020 strain, which developed resistance to metronidazole over the course of treatment (minimal inhibitory concentration [MIC] = 8 mg L[-1]). Metronidazole resistance correlates with the presence of a 7-kb plasmid, pCD-METRO. pCD-METRO is present in toxigenic and non-toxigenic resistant (n = 23), but not susceptible (n = 563), isolates from multiple countries. Introduction of a pCD-METRO-derived vector into a susceptible strain increases the MIC 25-fold. Our finding of plasmid-mediated resistance can impact diagnostics and treatment of CD infections.}, }
@article {pmid32000682, year = {2020}, author = {De Maayer, P and Pillay, T and Coutinho, TA}, title = {Comparative genomic analysis of the secondary flagellar (flag-2) system in the order Enterobacterales.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {100}, pmid = {32000682}, issn = {1471-2164}, mesh = {Bacterial Proteins/*genetics ; Enterobacteriaceae/*classification/genetics ; Evolution, Molecular ; Flagella/*genetics ; Gene Transfer, Horizontal ; Multigene Family ; Phylogeny ; }, abstract = {BACKGROUND: The order Enterobacterales encompasses a broad range of metabolically and ecologically versatile bacterial taxa, most of which are motile by means of peritrichous flagella. Flagellar biosynthesis has been linked to a primary flagella locus, flag-1, encompassing ~ 50 genes. A discrete locus, flag-2, encoding a distinct flagellar system, has been observed in a limited number of enterobacterial taxa, but its function remains largely uncharacterized.<br><br>RESULTS: Comparative genomic analyses showed that orthologous flag-2 loci are present in 592/4028 taxa belonging to 5/8 and 31/76 families and genera, respectively, in the order Enterobacterales. Furthermore, the presence of only the outermost flag-2 genes in many taxa suggests that this locus was far more prevalent and has subsequently been lost through gene deletion events. The flag-2 loci range in size from ~&#x2009;3.4 to 81.1 kilobases and code for between five and 102 distinct proteins. The discrepancy in size and protein number can be attributed to the presence of cargo gene islands within the loci. Evolutionary analyses revealed a complex evolutionary history for the flag-2 loci, representing ancestral elements in some taxa, while showing evidence of recent horizontal acquisition in other enterobacteria.<br><br>CONCLUSIONS: The flag-2 flagellar system is a fairly common, but highly variable feature among members of the Enterobacterales. Given the energetic burden of flagellar biosynthesis and functioning, the prevalence of a second flagellar system suggests it plays important biological roles in the enterobacteria and we postulate on its potential role as locomotory organ or as secretion system.}, }
@article {pmid31999971, year = {2020}, author = {Li, G and Chen, X and Yin, H and Wang, W and Wong, PK and An, T}, title = {Natural sphalerite nanoparticles can accelerate horizontal transfer of plasmid-mediated antibiotic-resistance genes.}, journal = {Environment international}, volume = {136}, number = {}, pages = {105497}, doi = {10.1016/j.envint.2020.105497}, pmid = {31999971}, issn = {1873-6750}, mesh = {*Anti-Bacterial Agents ; Escherichia coli ; *Gene Transfer, Horizontal ; Genes, Bacterial ; *Nanoparticles ; Plasmids ; Sulfides ; Zinc Compounds ; }, abstract = {Minerals and microorganisms are integral parts of natural environments, and they inevitably interact. Antibiotic-resistance genes (ARGs) significantly threaten modern healthcare. However, the effects of natural minerals on ARG propagation in aquatic systems are not fully understood. The present work studied the effects of natural sphalerite (NS) nanoparticles on the horizontal transfer of ARGs from Escherichia coli DH5α (CTX) (donor) to E. coli C600 (Sm) (recipient), and from E. coli DH5α (MCR) (donor) to E. coli C600 (Sm), and their underlying mechanisms. NS particles (0.5-50 mg L[-1]) induced an NS-concentration-dependent increase in conjugative transfer frequency. The underlying mechanisms associated with the facilitated ARG transfer included the production of intracellular reactive oxygen species, the SOS response, changes in bacterial cell morphology, and alteration of mRNA levels of bacterial cell membrane protein-related genes and genes associated with conjugative ARG transfer. The information herein offers new mechanistic understanding of risks of bacterial resistance resulting from NS.}, }
@article {pmid31997351, year = {2020}, author = {de Vries, S and Stukenbrock, EH and Rose, LE}, title = {Rapid evolution in plant-microbe interactions - an evolutionary genomics perspective.}, journal = {The New phytologist}, volume = {226}, number = {5}, pages = {1256-1262}, doi = {10.1111/nph.16458}, pmid = {31997351}, issn = {1469-8137}, mesh = {Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome ; *Genomics ; Hybridization, Genetic ; Selection, Genetic ; }, abstract = {Access to greater genomic resolution through new sequencing technologies is transforming the field of plant pathology. As scientists embrace these new methods, some overarching patterns and observations come into focus. Evolutionary genomic studies are used to determine not only the origins of pathogen lineages and geographic patterns of genetic diversity, but also to discern how natural selection structures genetic variation across the genome. With greater and greater resolution, we can now pinpoint the targets of selection on a large scale. At multiple levels, crypsis and convergent evolution are evident. Host jumps and shifts may be more pervasive than once believed, and hybridization and horizontal gene transfer (HGT) likely play important roles in the emergence of genetic novelty.}, }
@article {pmid31996416, year = {2020}, author = {Hegstad, K and Mylvaganam, H and Janice, J and Josefsen, E and Sivertsen, A and Skaare, D}, title = {Role of Horizontal Gene Transfer in the Development of Multidrug Resistance in Haemophilus influenzae.}, journal = {mSphere}, volume = {5}, number = {1}, pages = {}, pmid = {31996416}, issn = {2379-5042}, mesh = {Alleles ; Bacterial Typing Techniques ; Drug Resistance, Multiple, Bacterial/*genetics ; *Gene Transfer, Horizontal ; Haemophilus influenzae/*drug effects/*genetics ; Norway ; Phylogeny ; Plasmids/genetics ; Polymorphism, Single Nucleotide ; beta-Lactams/pharmacology ; }, abstract = {Haemophilus influenzae colonizes the respiratory tract in humans and causes both invasive and noninvasive infections. Resistance to extended-spectrum cephalosporins in H. influenzae is rare in Europe. In this study, we defined acquired resistance gene loci and ftsI mutations in multidrug-resistant (MDR) and/or PBP3-mediated beta-lactam-resistant (rPBP3) H. influenzae strains, intending to understand the mode of spread of antibiotic resistance determinants in this species. Horizontal transfer of mobile genetic elements and transformation with resistance-conferring ftsI alleles were contributory. We found one small plasmid and three novel integrative conjugative elements (ICEs) which carry different combinations of resistance genes. Demonstration of transfer and/or ICE circular forms showed that the ICEs are functional. Two extensively MDR genetically unrelated H. influenzae strains (F and G) from the same geographical region shared an identical novel MDR ICE (Tn6686) harboring bla TEM-1, catA2-like, and tet(B). The first Nordic case of MDR H. influenzae septicemia, strain 0, originating from the same geographical area as these strains, had a similar resistance pattern but contained another ICE [Tn6687 with bla TEM-1, catP and tet(B)] with an overall structure quite similar to that of Tn6686. Comparison of the complete ftsI genes among rPBP3 strains revealed that the entire gene or certain regions of it are identical in genetically unrelated strains, indicating horizontal gene transfer. Our findings illustrate that H. influenzae is capable of acquiring resistance against a wide range of commonly used antibiotics through horizontal gene transfer, in terms of conjugative transfer of ICEs and transformation of chromosomal genes.IMPORTANCE Haemophilus influenzae colonizes the respiratory tract in humans and causes both invasive and noninvasive infections. As a threat to treatment, resistance against critically important antibiotics is on the rise in H. influenzae Identifying mechanisms for horizontal acquisition of resistance genes is important to understand how multidrug resistance develops. The present study explores the antimicrobial resistance genes and their context in beta-lactam-resistant H. influenzae with coresistance to up to four non-beta-lactam groups. The results reveal that this organism is capable of acquiring resistance to a wide range of commonly used antibiotics through conjugative transfer of mobile genetic elements and transformation of chromosomal genes, resulting in mosaic genes with a broader resistance spectrum. Strains with chromosomally mediated resistance to extended-spectrum cephalosporins, co-trimoxazole, and quinolones combined with mobile genetic elements carrying genes mediating resistance to ampicillin, tetracyclines, and chloramphenicol have been reported, and further dissemination of such strains represents a particular concern.}, }
@article {pmid31996415, year = {2020}, author = {Ott, LC and Stromberg, ZR and Redweik, GAJ and Wannemuehler, MJ and Mellata, M}, title = {Mouse Genetic Background Affects Transfer of an Antibiotic Resistance Plasmid in the Gastrointestinal Tract.}, journal = {mSphere}, volume = {5}, number = {1}, pages = {}, pmid = {31996415}, issn = {2379-5042}, support = {R01 GM099537/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/drug effects/*genetics ; Female ; *Gastrointestinal Microbiome ; Gene Transfer, Horizontal ; Intestines/microbiology ; Male ; Mice ; Mice, 129 Strain/genetics ; Mice, Inbred C3H/genetics ; Mice, Knockout/genetics ; Plasmids/*genetics ; Salmonella enterica/drug effects/*genetics ; }, abstract = {Dissemination of antibiotic resistance (AR) genes, often on plasmids, leads to antibiotic-resistant bacterial infections, which is a major problem for animal and public health. Bacterial conjugation is the primary route of AR gene transfer in the mammalian gastrointestinal tract. Significant gaps in knowledge about which gastrointestinal communities and host factors promote plasmid transfer remain. Here, we used Salmonella enterica serovar Kentucky strain CVM29188 carrying plasmid pCVM29188_146 (harboring streptomycin and tetracycline resistance genes) to assess plasmid transfer to Escherichia coli under in vitro conditions and in various mouse strains with a conventional or defined microbiota. As an initial test, the transfer of pCVM29188_146 to the E. coli strains was confirmed in vitro Colonization resistance and, therefore, a lack of plasmid transfer were found in wild-type mice harboring a conventional microbiota. Thus, mice harboring the altered Schaedler flora (ASF), or ASF mice, were used to probe for host factors in the context of a defined microbiota. To assess the influence of inflammation on plasmid transfer, we compared interleukin-10 gene-deficient 129S6/SvEv ASF mice (proinflammatory environment) to wild-type 129S6/SvEv ASF mice and found no difference in transconjugant yields. In contrast, the mouse strain influenced plasmid transfer, as C3H/HeN ASF mice had significantly lower levels of transconjugants than 129S6/SvEv ASF mice. Although gastrointestinal members were identical between the ASF mouse strains, a few differences from C3H/HeN ASF mice were detected, with C3H/HeN ASF mice having significantly lower abundances of ASF members 356 (Clostridium sp.), 492 (Eubacterium plexicaudatum), and 502 (Clostridium sp.) than 129S6/SvEv ASF mice. Overall, we demonstrate that microbiota complexity and mouse genetic background influence in vivo plasmid transfer.IMPORTANCE Antibiotic resistance is a threat to public health. Many clinically relevant antibiotic resistance genes are carried on plasmids that can be transferred to other bacterial members in the gastrointestinal tract. The current study used a murine model to study the transfer of a large antibiotic resistance plasmid from a foodborne Salmonella strain to a gut commensal E. coli strain in the gastrointestinal tract. We found that different mouse genetic backgrounds and a different diversity of microbial communities influenced the level of Escherichia coli that acquired the plasmid in the gastrointestinal tract. This study suggests that the complexity of the microbial community and host genetics influence plasmid transfer from donor to recipient bacteria.}, }
@article {pmid31994769, year = {2020}, author = {Chalmers, TJ and Wu, LE}, title = {Transposable Elements Cross Kingdom Boundaries and Contribute to Inflammation and Ageing: Somatic Acquisition of Foreign Transposable Elements as a Catalyst of Genome Instability, Epigenetic Dysregulation, Inflammation, Senescence, and Ageing.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {42}, number = {3}, pages = {e1900197}, doi = {10.1002/bies.201900197}, pmid = {31994769}, issn = {1521-1878}, support = {APP1127821//National Health and Medical Research Council/International ; }, mesh = {Aging/*genetics ; Animals ; DNA Transposable Elements/*genetics ; *Epigenesis, Genetic ; Evolution, Molecular ; Gastrointestinal Microbiome/genetics ; *Gene Transfer, Horizontal ; Genomic Instability/*genetics ; Host Microbial Interactions/*genetics ; Humans ; Inflammation/genetics ; Mammals/*genetics ; Prokaryotic Cells/metabolism ; }, abstract = {The de-repression of transposable elements (TEs) in mammalian genomes is thought to contribute to genome instability, inflammation, and ageing, yet is viewed as a cell-autonomous event. In contrast to mammalian cells, prokaryotes constantly exchange genetic material through TEs, crossing both cell and species barriers, contributing to rapid microbial evolution and diversity in complex communities such as the mammalian gut. Here, it is proposed that TEs released from prokaryotes in the microbiome or from pathogenic infections regularly cross the kingdom barrier to the somatic cells of their eukaryotic hosts. It is proposed this horizontal transfer of TEs from microbe to host is a stochastic, ongoing catalyst of genome destabilization, resulting in structural and epigenetic variations, and activation of well-evolved host defense mechanisms contributing to inflammation, senescence, and biological ageing. It is proposed that innate immunity pathways defend against the horizontal acquisition of microbial TEs, and that activation of this pathway during horizontal transposon transfer promotes chronic inflammation during ageing. Finally, it is suggested that horizontal acquisition of prokaryotic TEs into mammalian genomes has been masked and subsequently under-reported due to flaws in current sequencing pipelines, and new strategies to uncover these events are proposed.}, }
@article {pmid31992633, year = {2020}, author = {Cao, C and Wang, J and Liu, Y and Kwok, LY and Zhang, H and Zhang, W}, title = {Adaptation of Lactobacillus plantarum to Ampicillin Involves Mechanisms That Maintain Protein Homeostasis.}, journal = {mSystems}, volume = {5}, number = {1}, pages = {}, pmid = {31992633}, issn = {2379-5077}, abstract = {The widespread use of antibiotics has caused great concern in the biosafety of probiotics. In this study, we conducted a 12-month adaptive laboratory evolution (ALE) experiment to select for antibiotics-adapted Lactobacillus plantarum P-8, a dairy-originated probiotic bacterium. During the ALE process, the ampicillin MIC for the parental L. plantarum P-8 strain increased gradually and reached the maximum level of bacterial fitness. To elucidate the molecular mechanisms underlying the ampicillin-resistant phenotype, we comparatively analyzed the genomes and proteomes of the parental strain (L. plantarum P-8) and two adapted lines (L. plantarum 400g and L. plantarum 1600g). The adapted lines showed alterations in their carbon, amino acid, and cell surface-associated metabolic pathways. Then, gene disruption mutants were created to determine the role of six highly expressed genes in contributing to the enhanced ampicillin resistance. Inactivation of an ATP-dependent Clp protease/the ATP-binding subunit ClpL, a small heat shock protein, or a hypothetical protein resulted in partial but significant phenotypic reversion, confirming their necessary roles in the bacterial adaptation to ampicillin. Genomic analysis confirmed that none of the ampicillin-specific differential expressed genes were flanked by any mobile genetic elements; thus, even though long-term exposure to ampicillin upregulated their expression, there is low risk of spread of these genes and adapted drug resistance to other bacteria via horizontal gene transfer. Our study has provided evidence of the biosafety of probiotics even when used in the presence of antibiotics.IMPORTANCE Antibiotic resistance acquired by adaptation to certain antibiotics has led to growing public concerns. Here, a long-term evolution experiment was used together with proteomic analysis to identify genes/proteins responsible for the adaptive phenotype. This work has provided novel insights into the biosafety of new probiotics with high tolerance to antibiotics.}, }
@article {pmid31992632, year = {2020}, author = {Bellieny-Rabelo, D and Nkomo, NP and Shyntum, DY and Moleleki, LN}, title = {Horizontally Acquired Quorum-Sensing Regulators Recruited by the PhoP Regulatory Network Expand the Host Adaptation Repertoire in the Phytopathogen Pectobacterium brasiliense.}, journal = {mSystems}, volume = {5}, number = {1}, pages = {}, pmid = {31992632}, issn = {2379-5077}, abstract = {In this study, we examine the impact of transcriptional network rearrangements driven by horizontal gene acquisition in PhoP and SlyA regulons using as a case study a phytopathosystem comprised of potato tubers and the soft-rot pathogen Pectobacterium brasiliense 1692 (Pb1692). Genome simulations and statistical analyses uncovered the tendency of PhoP and SlyA networks to mobilize lineage-specific traits predicted as horizontal gene transfer at late infection, highlighting the prominence of regulatory network rearrangements in this stage of infection. The evidence further supports the circumscription of two horizontally acquired quorum-sensing regulators (carR and expR1) by the PhoP network. By recruiting carR and expR1, the PhoP network also impacts certain host adaptation- and bacterial competition-related systems, seemingly in a quorum sensing-dependent manner, such as the type VI secretion system, carbapenem biosynthesis, and plant cell wall-degrading enzymes (PCWDE) like cellulases and pectate lyases. Conversely, polygalacturonases and the type III secretion system (T3SS) exhibit a transcriptional pattern that suggests quorum-sensing-independent regulation by the PhoP network. This includes an uncharacterized novel phage-related gene family within the T3SS gene cluster that has been recently acquired by two Pectobacterium species. The evidence further suggests a PhoP-dependent regulation of carbapenem- and PCWDE-encoding genes based on the synthesized products' optimum pH. The PhoP network also controls slyA expression in planta, which seems to impact carbohydrate metabolism regulation, especially at early infection, when 76.2% of the SlyA-regulated genes from that category also require PhoP to achieve normal expression levels.IMPORTANCE Exchanging genetic material through horizontal transfer is a critical mechanism that drives bacteria to efficiently adapt to host defenses. In this report, we demonstrate that a specific plant-pathogenic species (from the Pectobacterium genus) successfully integrated a population density-based behavior system (quorum sensing) acquired through horizontal transfer into a resident stress-response gene regulatory network controlled by the PhoP protein. Evidence found here underscores that subsets of bacterial weaponry critical for colonization, typically known to respond to quorum sensing, are also controlled by PhoP. Some of these traits include different types of enzymes that can efficiently break down plant cell walls depending on the environmental acidity level. Thus, we hypothesize that PhoP's ability to elicit regulatory responses based on acidity and nutrient availability fluctuations has strongly impacted the fixation of its regulatory connection with quorum sensing. In addition, another global gene regulator, known as SlyA, was found under the PhoP regulatory network. The SlyA regulator controls a series of carbohydrate metabolism-related traits, which also seem to be regulated by PhoP. By centralizing quorum sensing and slyA under PhoP scrutiny, Pectobacterium cells added an advantageous layer of control over those two networks that potentially enhances colonization efficiency.}, }
@article {pmid31992628, year = {2020}, author = {Linsky, M and Vitkin, Y and Segal, G}, title = {A Novel Legionella Genomic Island Encodes a Copper-Responsive Regulatory System and a Single Icm/Dot Effector Protein Transcriptionally Activated by Copper.}, journal = {mBio}, volume = {11}, number = {1}, pages = {}, pmid = {31992628}, issn = {2150-7511}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/*genetics/metabolism ; Copper/*metabolism ; Escherichia coli/genetics/metabolism ; *Gene Expression Regulation, Bacterial ; Gene Order ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genomic Islands ; Legionella/classification/*genetics/*metabolism ; Legionella pneumophila/classification/genetics/metabolism ; Phylogeny ; Protein Binding ; Transcription, Genetic ; }, abstract = {The intracellular pathogen Legionella pneumophila utilizes the Icm/Dot type IV secretion system to translocate >300 effector proteins into host cells during infection. The regulation of some of these effector-encoding genes was previously shown to be coordinated by several global regulators, including three two-component systems (TCSs) found in all the Legionella species examined. Here, we describe the first Legionella genomic island encoding a single Icm/Dot effector and a dedicated TCS, which regulates its expression. This genomic island, which we named Lci, undergoes horizontal gene transfer in the Legionella genus, and the TCS encoded from this island (LciRS) is homologous to TCSs that control the expression of various metal resistance systems found in other bacteria. We found that the L. pneumophila sensor histidine kinase LciS is specifically activated by copper via a unique, small periplasmic sensing domain. Upon activation by LciS, the response regulator LciR directly binds to a conserved regulatory element and activates the expression of the adjacently located lciE effector-encoding gene. Thus, LciR represents the first local regulator of effectors identified in L. pneumophila Moreover, we found that the expression of the lciRS operon is repressed by the Fis1 and Fis3 regulators, leading to Fis-mediated effects on copper induction of LciE and silencing of the expression of this genomic island in the absence of copper. This island represents a novel type of effector regulation in Legionella, shedding new light on the ways by which the Legionella pathogenesis system evolves its effector repertoire and expands its activating signals.IMPORTANCELegionella pneumophila is an intracellular human pathogen that utilizes amoebae as its environmental host. The adaptation of L. pneumophila to the intracellular environment requires coordination of expression of its multicomponent pathogenesis system, which is composed of a secretion system and effector proteins. However, the regulatory factors controlling the expression of this pathogenesis system are only partially uncovered. Here, we discovered a novel regulatory system that is activated by copper and controls the expression of a single effector protein. The genes encoding both the regulatory system and the effector protein are located on a genomic island that undergoes horizontal gene transfer within the Legionella genus. This regulator-effector genomic island represents the first reported case of local regulation of effectors in Legionella The discovery of this regulatory mechanism is an important step forward in the understanding of how the regulatory network of effectors functions and evolves in the Legionella genus.}, }
@article {pmid31990919, year = {2020}, author = {Ely, B}, title = {Recombination and gene loss occur simultaneously during bacterial horizontal gene transfer.}, journal = {PloS one}, volume = {15}, number = {1}, pages = {e0227987}, pmid = {31990919}, issn = {1932-6203}, mesh = {Base Sequence ; Caulobacter crescentus/classification/*genetics/metabolism ; Chromosome Mapping ; *Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; *Mutagenesis, Insertional ; Phylogeny ; *Recombination, Genetic ; Whole Genome Sequencing ; }, abstract = {Bacteria can acquire new genes by incorporating environmental DNA into their genomes, yet genome sizes stay relatively constant. In nature, gene acquisition is a rare event so it is difficult to observe. However, the Caulobacter crescentus CB2A genome contains 114 insertions of genetic material from the closely-related NA1000 strain, providing a unique opportunity to analyze the horizontal transfer of genetic material. Analyses of these insertions led to a new model that involves preferential recombination at non-homologous regions that are flanked by regions of homology and does not involve any mutational processes. The net result is the replacement of segments of the recipient genome instead of the simple addition of genetic material during horizontal gene transfer. Analyses of the genomes of closely related strains of other bacterial and archaea genera, suggested that horizontal gene transfer occurs preferentially in non-homologous regions in these organisms as well. Thus, it appears to be a general phenomenon that prokaryotic horizontal gene transfer occurs preferentially at sites where the incoming DNA contains a non-homologous region that is flanked by regions of homology. Therefore, gene replacement is a common phenomenon during horizontal gene transfer.}, }
@article {pmid31990351, year = {2019}, author = {Lam, T and Maienschein-Cline, M and Eddington, DT and Morrison, DA}, title = {Multiplex gene transfer by genetic transformation between isolated S. pneumoniae cells confined in microfluidic droplets.}, journal = {Integrative biology : quantitative biosciences from nano to macro}, volume = {11}, number = {12}, pages = {415-424}, pmid = {31990351}, issn = {1757-9708}, support = {R21 AI133304/AI/NIAID NIH HHS/United States ; UL1 TR002003/TR/NCATS NIH HHS/United States ; }, mesh = {Biofilms ; Drug Resistance, Bacterial ; Drug Resistance, Microbial ; *Gene Transfer Techniques ; Genomics ; *Microfluidics ; *Streptococcus pneumoniae ; *Transformation, Bacterial ; Whole Genome Sequencing ; }, abstract = {Gene exchange via genetic transformation makes major contributions to antibiotic resistance of the human pathogen, Streptococcus pneumoniae (pneumococcus). The transfers begin when a pneumococcal cell, in a transient specialized physiological state called competence, attacks and lyses another cell, takes up fragments of the liberated DNA, and integrates divergent genes into its genome. Recently, it has been demonstrated that the pneumococcal cells can be enclosed in femtoliter-scale droplets for study of the transformation mechanism, offering the ability to characterize individual cell-cell interactions and overcome the limitations of current methods involving bulk mixed cultures. To determine the relevance and reliability of this new method for study of bacterial genetic transformation, we compared recombination events occurring in 44 recombinants recovered after competence-mediated gene exchange between pairs of cells confined in femtoliter-scale droplets vs. those occurring in exchanges in parallel bulk culture mixtures. The pattern of recombination events in both contexts exhibited the hallmarks of the macro-recombination exchanges previously observed within the more complex natural contexts of biofilms and long-term evolution in the human host.}, }
@article {pmid31982569, year = {2020}, author = {Raheem, MA and Xue, M and Ahmad, HI and Ahmad, MZ and Tipu, MY and Afzal, G and Song, X and Rahim, MA and Qi, K}, title = {Adaptation to host-specific bacterial pathogens drive rapid evolution of novel PhoP/PhoQ regulation pathway modulating the virulence.}, journal = {Microbial pathogenesis}, volume = {141}, number = {}, pages = {103997}, doi = {10.1016/j.micpath.2020.103997}, pmid = {31982569}, issn = {1096-1208}, mesh = {Bacterial Proteins/*genetics ; Biological Evolution ; *Enterobacteriaceae/genetics/pathogenicity ; Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Host Microbial Interactions ; Models, Theoretical ; Transcription Factors/genetics ; Virulence/*genetics ; }, abstract = {The presence of the PhoP-PhoQ system is usually different in various bacterial groups, suggesting that PhoP can control the expression of different genes in species. However, little is known about the evolution of the PhoP-PhoQ system among bacterial pathogens. Here, we study the evolution of PhoP and PhoQ regulation in 15 species of Enterobacteriaceae family. We have determined that the regulatory objectives adopted by PhoP and PhoQ are mainly different, due to the result of horizontal gene transfer events and even the change in the genetic content between closely related species. We have compared many possibilities tests (M1 vs. M2 and M7 with M8) to determine the positive selection. Estimating parameters at M1 and M2, with positive selection in M2 of the two proteins. The proportions of positive selection sites significant with ω = 4.53076 for PhoP and ω = 4.21041 PhQ. M8 was significant for PhoP and PhQ proteins. To further confirm the positive selection results, we used the Selecton server to confer positive selection on individual sites using the Mechanistic-Empirical Combination model, and we noticed that several sites had been identified under selection pressure during the evolution. There was a strong indication for the positive selection in bacterial genes of PhoP and PhoQ showed the results. By the use of REL and IFEL, the positive selection for PhoP was detected 14 and 11 sites respectively at different codon positions. The positively selected sites of amino acids such as Arginine, Alanine, Lysine, and Leucine are more important for the production of signals. Our results suggest that the positive selection of PhoP-PhoQ genes in host adaptation during evolution raises an intriguing possibility causes subtle variations in actions of PhoP-PhoQ and also increases the opportunities that cause modification in protein structure for the evolution of increasing pathogenicity in bacterial pathogens.}, }
@article {pmid31981830, year = {2020}, author = {Jin, N and Morais, CLM and Martin, FL and Zhang, D}, title = {Spectrochemical identification of kanamycin resistance genes in artificial microbial communities using Clover-assay.}, journal = {Journal of pharmaceutical and biomedical analysis}, volume = {181}, number = {}, pages = {113108}, doi = {10.1016/j.jpba.2020.113108}, pmid = {31981830}, issn = {1873-264X}, mesh = {Deuterium Oxide/*chemistry ; *Genetic Techniques ; Kanamycin Resistance/*genetics ; Microbiota/*genetics ; Spectrum Analysis, Raman/*methods ; }, abstract = {Persistent abuse and overuse of antibiotics induces a widespread bloom of antibiotic resistance genes (ARGs) and the emergence of superbugs. A method designed to rapidly quantify ARGs in real-world scenarios is urgently needed. Here, we present an orthogonal test of heavy water and kanamycin exposure, namely, a "clover-assay", to reveal the capability of state-of-the-art Raman microspectroscopy to identify ARGs within microbial communities. This assay successfully recognizes the discriminating spectral alterations from two genetically identical strains that differ only in terms of the expression of one kanamycin resistance gene. In addition to the previously reported Raman shift at carbon-deuterium vibration bands (2,040-2,300 cm[-1]), we identify two new peak shifts (970-990 cm[-1]) and (1,110-1,130 cm[-1]) associated with deuterium labelling. Notably, the spectral alterations from 1,110-1,130 cm[-1] strongly correlate with kanamycin exposure. By introducing dispersion index (DI) and clover assay index (CAI) as indicators, this assay is able to quantify the abundance of kanamycin resistance genes within artificial microbiotas. Based on our results, the biospectral clover assay is a powerful tool for the in situ interrogation of the occurrence of ARGs within microbial communities, which displays great potential to eliminate the need for culture protocols in the future. Due to the non-destructive and non-intrusive features, this approach may therefore potentially be able to diagnose horizontal gene transfer (HGT) in real time.}, }
@article {pmid31979031, year = {2020}, author = {Luziatelli, F and Ficca, AG and Cardarelli, M and Melini, F and Cavalieri, A and Ruzzi, M}, title = {Genome Sequencing of Pantoea agglomerans C1 Provides Insights into Molecular and Genetic Mechanisms of Plant Growth-Promotion and Tolerance to Heavy Metals.}, journal = {Microorganisms}, volume = {8}, number = {2}, pages = {}, pmid = {31979031}, issn = {2076-2607}, abstract = {Distinctive strains of Pantoea are used as soil inoculants for their ability to promote plant growth. Pantoea agglomerans strain C1, previously isolated from the phyllosphere of lettuce, can produce indole-3-acetic acid (IAA), solubilize phosphate, and inhibit plant pathogens, such as Erwinia amylovora. In this paper, the complete genome sequence of strain C1 is reported. In addition, experimental evidence is provided on how the strain tolerates arsenate As (V) up to 100 mM, and on how secreted metabolites like IAA and siderophores act as biostimulants in tomato cuttings. The strain has a circular chromosome and two prophages for a total genome of 4,846,925-bp, with a DNA G+C content of 55.2%. Genes related to plant growth promotion and biocontrol activity, such as those associated with IAA and spermidine synthesis, solubilization of inorganic phosphate, acquisition of ferrous iron, and production of volatile organic compounds, siderophores and GABA, were found in the genome of strain C1. Genome analysis also provided better understanding of the mechanisms underlying strain resistance to multiple toxic heavy metals and transmission of these genes by horizontal gene transfer. Findings suggested that strain C1 exhibits high biotechnological potential as plant growth-promoting bacterium in heavy metal polluted soils.}, }
@article {pmid31977149, year = {2020}, author = {Bauer, R and Neffgen, N and Grempels, A and Furitsch, M and Mauerer, S and Barbaqadze, S and Haase, G and Kestler, H and Spellerberg, B}, title = {Heterogeneity of Streptococcus anginosus ß-hemolysis in relation to CRISPR/Cas.}, journal = {Molecular oral microbiology}, volume = {35}, number = {2}, pages = {56-65}, doi = {10.1111/omi.12278}, pmid = {31977149}, issn = {2041-1014}, mesh = {*Clustered Regularly Interspaced Short Palindromic Repeats ; Hemolysis ; Humans ; Phylogeny ; Streptococcus/genetics ; *Streptococcus anginosus/genetics ; }, abstract = {Streptococcus anginosus is a commensal of the oral mucosa that can cause severe invasive infections. A considerable proportion of Streptococcus anginosus strains are ß-hemolytic due to the presence of an SLS-like gene cluster. However, the majority of strains do not display ß-hemolysis. To investigate ß-hemolysin heterogeneity in S. anginosus, we determined the presence of sag genes and correlated it with the presence of CRISPR/Cas genes in a collection of ß-hemolytic and non-ß-hemolytic strains. All of the ß-hemolytic strains carried the sag gene cluster. In contrast to other streptococci, clinical S. anginosus strains that do not display ß-hemolysis do not harbor sag genes. Phylogenetic analysis of the ß-hemolytic strains revealed that they belong to two previously defined clusters within S. anginosus. Correlation with CRISPR/Cas genes showed a significant difference for the presence of CRISPR/Cas in ß-hemolytic versus non-ß-hemolytic isolates. The presence of the CRISPR/Cas type IIA or type IIC locus is associated with the absence of sag genes; in 65% of the non-ß-hemolytic strains a CRISPR/Cas locus was found, while only 24% of ß-hemolytic strains carry CRISPR/Cas genes. Further analysis of the spacer content of the CRISPR systems revealed the presence of multiple self-targeting sequences directed against S. anginosus genes. These results support the hypothesis that horizontal gene transfer is involved in the acquisition of ß-hemolysin genes and that CRISPR/Cas may limit DNA uptake in S. anginosus.}, }
@article {pmid31971995, year = {2020}, author = {Ben Maamar, S and Glawe, AJ and Brown, TK and Hellgeth, N and Hu, J and Wang, JP and Huttenhower, C and Hartmann, EM}, title = {Mobilizable antibiotic resistance genes are present in dust microbial communities.}, journal = {PLoS pathogens}, volume = {16}, number = {1}, pages = {e1008211}, pmid = {31971995}, issn = {1553-7374}, support = {U19 AI135964/AI/NIAID NIH HHS/United States ; }, mesh = {*Air Pollution, Indoor ; Drug Resistance, Microbial/*genetics ; *Dust ; Environmental Microbiology ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genome, Bacterial ; Metagenomics ; Microbiota/*genetics ; }, abstract = {The decades-long global trend of urbanization has led to a population that spends increasing amounts of time indoors. Exposure to microbes in buildings, and specifically in dust, is thus also increasing, and has been linked to various health outcomes and to antibiotic resistance genes (ARGs). These are most efficiently screened using DNA sequencing, but this method does not determine which microbes are viable, nor does it reveal whether their ARGs can actually disseminate to other microbes. We have thus performed the first study to: 1) examine the potential for ARG dissemination in indoor dust microbial communities, and 2) validate the presence of detected mobile ARGs in viable dust bacteria. Specifically, we integrated 166 dust metagenomes from 43 different buildings. Sequences were assembled, annotated, and screened for potential integrons, transposons, plasmids, and associated ARGs. The same dust samples were further investigated using cultivation and isolate genome and plasmid sequencing. Potential ARGs were detected in dust isolate genomes, and we confirmed their placement on mobile genetic elements using long-read sequencing. We found 183 ARGs, of which 52 were potentially mobile (associated with a putative plasmid, transposon or integron). One dust isolate related to Staphylococcus equorum proved to contain a plasmid carrying an ARG that was detected metagenomically and confirmed through whole genome and plasmid sequencing. This study thus highlights the power of combining cultivation with metagenomics to assess the risk of potentially mobile ARGs for public health.}, }
@article {pmid31971565, year = {2020}, author = {Xing, H and Kembel, SW and Makarenkov, V}, title = {Transfer index, NetUniFrac and some useful shortest path-based distances for community analysis in sequence similarity networks.}, journal = {Bioinformatics (Oxford, England)}, volume = {36}, number = {9}, pages = {2740-2749}, doi = {10.1093/bioinformatics/btaa043}, pmid = {31971565}, issn = {1367-4811}, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal ; Genome ; Phylogeny ; *Software ; }, abstract = {MOTIVATION: Phylogenetic trees and the methods for their analysis have played a key role in many evolutionary, ecological and bioinformatics studies. Alternatively, phylogenetic networks have been widely used to analyze and represent complex reticulate evolutionary processes which cannot be adequately studied using traditional phylogenetic methods. These processes include, among others, hybridization, horizontal gene transfer, and genetic recombination. Nowadays, sequence similarity and genome similarity networks have become an efficient tool for community analysis of large molecular datasets in comparative studies. These networks can be used for tackling a variety of complex evolutionary problems such as the identification of horizontal gene transfer events, the recovery of mosaic genes and genomes, and the study of holobionts.<br><br>RESULTS: The shortest path in a phylogenetic tree is used to estimate evolutionary distances between species. We show how the shortest path concept can be extended to sequence similarity networks by defining five new distances, NetUniFrac, Spp, Spep, Spelp and Spinp, and the Transfer index, between species communities present in the network. These new distances can be seen as network analogs of the traditional UniFrac distance used to assess dissimilarity between species communities in a phylogenetic tree, whereas the Transfer index is intended for estimating the rate and direction of gene transfers, or species dispersal, between different phylogenetic, or ecological, species communities. Moreover, NetUniFrac and the Transfer index can be computed in linear time with respect to the number of edges in the network. We show how these new measures can be used to analyze microbiota and antibiotic resistance gene similarity networks.<br><br>Our NetFrac program, implemented in R and C, along with its source code, is freely available on Github at the following URL address: https://github.com/XPHenry/Netfrac.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid31970482, year = {2020}, author = {Wang, P and Wang, Y and Guo, X and Huang, S and Zhu, G}, title = {Biochemical and phylogenetic characterization of a monomeric isocitrate dehydrogenase from a marine methanogenic archaeon Methanococcoides methylutens.}, journal = {Extremophiles : life under extreme conditions}, volume = {24}, number = {2}, pages = {319-328}, pmid = {31970482}, issn = {1433-4909}, mesh = {Amino Acid Sequence ; Isocitrate Dehydrogenase/*genetics ; Kinetics ; *Methanosarcinaceae/genetics ; NADP ; *Phylogeny ; }, abstract = {Monomeric isocitrate dehydrogenase (IDH) stands for a separated subgroup among IDH protein family. Up to now, all reported monomeric IDHs are from prokaryotes. Here, a monomeric IDH from a marine methanogenic archaeon Methanococcoides methylutens (MmIDH) was reported for the first time. BLAST search demonstrated that only a few marine archaea encode the monomeric IDH and all these organisms are methylotrophic. MmIDH shows the highest homology (~ 70%) to the monomeric IDHs from some marine bacteria, suggesting a lateral gene transfer event between marine bacteria and archaea. The monomeric state of MmIDH was determined by size exclusion chromatography. MmIDH is divalent cation-dependent and Mn[2+] is the most favored. Kinetic analysis showed that MmIDH is highly specific to NADP[+] and cannot utilize the NAD[+]. The optimal temperature for MmIDH activity is 50 °C and the optimal pH is 8.2. Heat inactivation assay revealed that MmIDH is a mesophilic enzyme. It sustained 50% activity after incubation at 39 °C for 20 min. Moreover, the putative coenzyme binding residues (His590, Arg601, and Arg650) of MmIDH were explored by mutagenesis. The triple mutant H590L/R601D/R650S displayed a 5.93-fold preference for NAD[+] over NADP[+], indicating that the coenzyme specificity of MmIDH was significantly switched from NADP[+] to NAD[+] by three key mutations.}, }
@article {pmid31968709, year = {2020}, author = {Hu, Y and Xing, W and Hu, Z and Liu, G}, title = {Phylogenetic Analysis and Substitution Rate Estimation of Colonial Volvocine Algae Based on Mitochondrial Genomes.}, journal = {Genes}, volume = {11}, number = {1}, pages = {}, pmid = {31968709}, issn = {2073-4425}, mesh = {Chlorophyceae/classification/*genetics ; *Evolution, Molecular ; *Genome, Mitochondrial ; *Genome, Plant ; Mitochondrial Proteins/*genetics ; *Phylogeny ; Plant Proteins/*genetics ; }, abstract = {We sequenced the mitochondrial genome of six colonial volvocine algae, namely: Pandorina morum, Pandorina colemaniae, Volvulina compacta, Colemanosphaera angeleri, Colemanosphaera charkowiensi, and Yamagishiella unicocca. Previous studies have typically reconstructed the phylogenetic relationship between colonial volvocine algae based on chloroplast or nuclear genes. Here, we explore the validity of phylogenetic analysis based on mitochondrial protein-coding genes. We found phylogenetic incongruence of the genera Yamagishiella and Colemanosphaera. In Yamagishiella, the stochastic error and linkage group formed by the mitochondrial protein-coding genes prevent phylogenetic analyses from reflecting the true relationship. In Colemanosphaera, a different reconstruction approach revealed a different phylogenetic relationship. This incongruence may be because of the influence of biological factors, such as incomplete lineage sorting or horizontal gene transfer. We also analyzed the substitution rates in the mitochondrial and chloroplast genomes between colonial volvocine algae. Our results showed that all volvocine species showed significantly higher substitution rates for the mitochondrial genome compared with the chloroplast genome. The nonsynonymous substitution (dN)/synonymous substitution (dS) ratio is similar in the genomes of both organelles in most volvocine species, suggesting that the two counterparts are under a similar selection pressure. We also identified a few chloroplast protein-coding genes that showed high dN/dS ratios in some species, resulting in a significant dN/dS ratio difference between the mitochondrial and chloroplast genomes.}, }
@article {pmid31968354, year = {2020}, author = {Schulz, F and Roux, S and Paez-Espino, D and Jungbluth, S and Walsh, DA and Denef, VJ and McMahon, KD and Konstantinidis, KT and Eloe-Fadrosh, EA and Kyrpides, NC and Woyke, T}, title = {Giant virus diversity and host interactions through global metagenomics.}, journal = {Nature}, volume = {578}, number = {7795}, pages = {432-436}, pmid = {31968354}, issn = {1476-4687}, mesh = {Animals ; *Biodiversity ; Capsid Proteins/genetics ; DNA Viruses/*classification/*genetics ; Eukaryotic Cells/*metabolism/*virology ; Gene Transfer, Horizontal ; Genome, Viral/genetics ; Giant Viruses/classification/genetics ; Host Microbial Interactions/*genetics ; *Metagenomics ; Phylogeny ; }, abstract = {Our current knowledge about nucleocytoplasmic large DNA viruses (NCLDVs) is largely derived from viral isolates that are co-cultivated with protists and algae. Here we reconstructed 2,074 NCLDV genomes from sampling sites across the globe by building on the rapidly increasing amount of publicly available metagenome data. This led to an 11-fold increase in phylogenetic diversity and a parallel 10-fold expansion in functional diversity. Analysis of 58,023 major capsid proteins from large and giant viruses using metagenomic data revealed the global distribution patterns and cosmopolitan nature of these viruses. The discovered viral genomes encoded a wide range of proteins with putative roles in photosynthesis and diverse substrate transport processes, indicating that host reprogramming is probably a common strategy in the NCLDVs. Furthermore, inferences of horizontal gene transfer connected viral lineages to diverse eukaryotic hosts. We anticipate that the global diversity of NCLDVs that we describe here will establish giant viruses-which are associated with most major eukaryotic lineages-as important players in ecosystems across Earth's biomes.}, }
@article {pmid31965613, year = {2020}, author = {Sawa, T and Momiyama, K and Mihara, T and Kainuma, A and Kinoshita, M and Moriyama, K}, title = {Molecular epidemiology of clinically high-risk Pseudomonas aeruginosa strains: Practical overview.}, journal = {Microbiology and immunology}, volume = {64}, number = {5}, pages = {331-344}, doi = {10.1111/1348-0421.12776}, pmid = {31965613}, issn = {1348-0421}, support = {15H05008//Ministry of Education, Culture, Sports, Science and Technology Japan Society for the Promotion of Science/ ; 18H02905//Ministry of Education, Culture, Sports, Science and Technology Japan Society for the Promotion of Science/ ; 18K16521//Ministry of Education, Culture, Sports, Science and Technology Japan Society for the Promotion of Science/ ; 24390403//Ministry of Education, Culture, Sports, Science and Technology Japan Society for the Promotion of Science/ ; 26670791//Ministry of Education, Culture, Sports, Science and Technology Japan Society for the Promotion of Science/ ; //Japan Society for the Promotion of Science/ ; }, mesh = {Bacterial Typing Techniques ; DNA, Bacterial/genetics ; Disease Outbreaks ; Drug Resistance, Multiple, Bacterial/*genetics ; Humans ; Molecular Epidemiology ; Multilocus Sequence Typing ; Multiplex Polymerase Chain Reaction ; Phylogeny ; Pseudomonas Infections/*epidemiology ; Pseudomonas aeruginosa/*classification/isolation &amp; purification ; Software ; }, abstract = {In recent years, numerous outbreaks of multidrug-resistant Pseudomonas aeruginosa have been reported across the world. Once an outbreak occurs, besides routinely testing isolates for susceptibility to antimicrobials, it is required to check their virulence genotypes and clonality profiles. Replacing pulsed-field gel electrophoresis DNA fingerprinting are faster, easier-to-use, and less expensive polymerase chain reaction (PCR)-based methods for characterizing hospital isolates. P. aeruginosa possesses a mosaic genome structure and a highly conserved core genome displaying low sequence diversity and a highly variable accessory genome that communicates with other Pseudomonas species via horizontal gene transfer. Multiple-locus variable-number tandem-repeat analysis and multilocus sequence typing methods allow for phylogenetic analysis of isolates by PCR amplification of target genes with the support of Internet-based services. The target genes located in the core genome regions usually contain low-frequency mutations, allowing the resulting phylogenetic trees to infer evolutionary processes. The multiplex PCR-based open reading frame typing (POT) method, integron PCR, and exoenzyme genotyping can determine a genotype by PCR amplifying a specific insertion gene in the accessory genome region using a single or a multiple primer set. Thus, analyzing P. aeruginosa isolates for their clonality, virulence factors, and resistance characteristics is achievable by combining the clonality evaluation of the core genome based on multiple-locus targeting methods with other methods that can identify specific virulence and antimicrobial genes. Software packages such as eBURST, R, and Dendroscope, which are powerful tools for phylogenetic analyses, enable researchers and clinicians to visualize clonality associations in clinical isolates.}, }
@article {pmid31964746, year = {2020}, author = {Gjonbalaj, M and Keith, JW and Do, MH and Hohl, TM and Pamer, EG and Becattini, S}, title = {Antibiotic Degradation by Commensal Microbes Shields Pathogens.}, journal = {Infection and immunity}, volume = {88}, number = {4}, pages = {}, pmid = {31964746}, issn = {1098-5522}, support = {P30 CA008748/CA/NCI NIH HHS/United States ; R01 AI042135/AI/NIAID NIH HHS/United States ; U01 AI124275/AI/NIAID NIH HHS/United States ; }, mesh = {Ampicillin/administration &amp; dosage/*metabolism/pharmacology ; Animals ; Anti-Bacterial Agents/administration &amp; dosage/*metabolism/pharmacology ; Clostridioides difficile/*drug effects/growth &amp; development ; Drug Resistance, Bacterial ; Escherichia coli/enzymology/growth &amp; development/*metabolism ; Hydrolysis ; Intestines/*microbiology ; Listeria monocytogenes/*drug effects ; Mice ; Microbial Interactions ; Microbial Viability/drug effects ; beta-Lactamases/*metabolism ; }, abstract = {The complex bacterial populations that constitute the gut microbiota can harbor antibiotic resistance genes (ARGs), including those encoding β-lactamase enzymes (BLA), which degrade commonly prescribed antibiotics such as ampicillin. The prevalence of such genes in commensal bacteria has been increased in recent years by the wide use of antibiotics in human populations and in livestock. While transfer of ARGs between bacterial species has well-established dramatic public health implications, these genes can also function in trans within bacterial consortia, where antibiotic-resistant bacteria can provide antibiotic-sensitive neighbors with leaky protection from drugs, as shown both in vitro and in vivo, in models of lung and subcutaneous coinfection. However, whether the expression of ARGs by harmless commensal bacterial species can destroy antibiotics in the intestinal lumen and shield antibiotic-sensitive pathogens is unknown. To address this question, we colonized germfree or wild-type mice with a model intestinal commensal strain of Escherichia coli that produces either functional or defective BLA. Mice were subsequently infected with Listeria monocytogenes or Clostridioides difficile, followed by treatment with oral ampicillin. The production of functional BLA by commensal E. coli markedly reduced clearance of these pathogens and enhanced systemic dissemination during ampicillin treatment. Pathogen resistance was independent of ARG acquisition via horizontal gene transfer but instead relied on antibiotic degradation in the intestinal lumen by BLA. We conclude that commensal bacteria that have acquired ARGs can mediate shielding of pathogens from the bactericidal effects of antibiotics.}, }
@article {pmid31964505, year = {2020}, author = {Saroj, DB and Gupta, AK}, title = {Genome based safety assessment for Bacillus coagulans strain LBSC (DSM 17654) for probiotic application.}, journal = {International journal of food microbiology}, volume = {318}, number = {}, pages = {108523}, doi = {10.1016/j.ijfoodmicro.2020.108523}, pmid = {31964505}, issn = {1879-3460}, mesh = {Bacillus coagulans/*genetics ; Bacterial Proteins/genetics ; Base Sequence ; Consumer Product Safety ; DNA, Bacterial/genetics ; Genome, Bacterial/*genetics ; Genomic Instability ; *Probiotics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The present study on Bacillus coagulans strain LBSC (DSM 17654) describes the use of whole genome sequencing, in correlation with the phenotypic properties to assess the safety of the strain. Analysis of the 16S rRNA sequence of the B. coagulans strain LBSC (DSM 17654), showed 100% homology with 99% coverage with B. coagulans strain HM-08. BLAT (BLAST Like Analysis Tool) analysis for whole genome comparison with B. coagulans ATCC 7050, B. coagulans HM-08 and B. coagulans Slac showed 96%, 99% and 99% sequence identity respectively. Whole genome sequencing results demonstrated a single scaffold of 36,35,902 bp and 3331 coding sequences. Gene ontology segregated the proteins as those with molecular function, cellular component and biological process of the predicted genes from assembled genome. Risk associated sequences like antibiotic resistance genes, biogenic amine producing genes, virulence factor genes and other safety related genes were identified with focus on horizontal gene transfer and its non-functionality. The absence of mobile elements in the vicinity of the genes, render it non-transferable and non-toxic phenotypic properties confirm the non-functionality of the genes. Absence of functional genes of concern and confirmation of absence of mobile elements in the vicinity of other non-clinically significant genes indicated no safety concern. The absence of complete and functional prophage sequences which are deleterious for the genome stability and presence of CRISPR system which are advantageous for genome stability by acting as a barrier to entry of foreign DNA elements indicated the stability of the genome. The molecular approach used in this study satisfies the requirements for the safety assessment of the probiotic strain which could indicate it to be potentially safe.}, }
@article {pmid31961790, year = {2020}, author = {Mohanraj, RS and Samanta, P and Mukhopadhyay, AK and Mandal, J}, title = {Haitian-like genetic traits with creeping MIC of Azithromycin in Vibrio cholerae O1 isolates from Puducherry, India.}, journal = {Journal of medical microbiology}, volume = {69}, number = {3}, pages = {372-378}, doi = {10.1099/jmm.0.001131}, pmid = {31961790}, issn = {1473-5644}, mesh = {Alleles ; Anti-Bacterial Agents/*pharmacology ; Azithromycin/*pharmacology ; Cholera/*epidemiology/microbiology ; Ciprofloxacin/pharmacology ; Drug Resistance, Bacterial/*genetics ; Feces/microbiology ; Gene Transfer, Horizontal ; Genotype ; Haiti ; Humans ; India/epidemiology ; Microbial Sensitivity Tests ; Mutation ; Phenotype ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Tetracycline/pharmacology ; Vibrio cholerae O1/*genetics/isolation &amp; purification ; }, abstract = {Introduction. The emergence of novel strains of Vibrio cholerae O1 El Tor biotype has gained attention due to causing several epidemics around the world. Variant strains have evolved as a result of the acquisition of genes that confer extended virulence and pathogenicity.Aim. This study aimed to determine the presence of the most recently emerging Haitian-like genetic traits among the isolates from Jawaharlal Institute of Postgraduate Medical Education and Research, Pondicherry, Southern India. We also wanted to detect the prevalence of the sulfamethoxazole and trimethoprim (SXT) element, which is an integrating conjugative element (ICE) and the antimicrobial resistance genes present in our isolates.Methodology. Identification of Haitian-specific alleles was done by mismatched amplification mutation assay PCR (MAMA-PCR). The presence of SXT elements was carried out by PCR by detecting int, eex, att-prfC and setR genes. Detection of antibiotic resistance determinant, sul(1,2,3); dfr(A1,18,5) for trimethoprim resistance, tet(A,B,C,D,E,Y,G,M), tet34 for tetracycline resistance and erm(A,B,C), mph(A,B), ere(A,B), msr(A,D) for azithromycin resistance were targeted by PCR. The MIC of tetracycline, ciprofloxacin and azithromycin was determined by the E-test method.Results. Of the 95 isolates, 60 % of the isolates were found to carry Haitian-specific alleles of ctxB, tcpA and rtxA gene, 100 % of the isolates were found to carry SXT elements. All the isolates harboured the four conserved genes of the SXT element, except one which had only eex, att-prfC, setR genes. About 99 % harboured sul2 and dfrA1 genes. No tet and macrolide genes were detected. We observed a progressive increase in the MIC of azithromycin ranging from 0.75 µg ml[-1] to 2 µg ml[-1].Conclusion. None of the isolates were the prototype El Tor biotype. All the isolates were a Haitian variant. The presence of SXT elements across all our isolates and their creeping MIC of azithromycin is a matter of concern. Further testing for other genetic determinants of resistance will be carried out in our future studies.}, }
@article {pmid31960565, year = {2020}, author = {Dumas, E and Feurtey, A and Rodríguez de la Vega, RC and Le Prieur, S and Snirc, A and Coton, M and Thierry, A and Coton, E and Le Piver, M and Roueyre, D and Ropars, J and Branca, A and Giraud, T}, title = {Independent domestication events in the blue-cheese fungus Penicillium roqueforti.}, journal = {Molecular ecology}, volume = {29}, number = {14}, pages = {2639-2660}, pmid = {31960565}, issn = {1365-294X}, mesh = {Cheese/*microbiology ; Domestication ; *Food Microbiology ; Gene Transfer, Horizontal ; Genome, Fungal ; Penicillium/*genetics ; Phenotype ; }, abstract = {Domestication provides an excellent framework for studying adaptive divergence. Using population genomics and phenotypic assays, we reconstructed the domestication history of the blue cheese mould Penicillium roqueforti. We showed that this fungus was domesticated twice independently. The population used in Roquefort originated from an old domestication event associated with weak bottlenecks and exhibited traits beneficial for pre-industrial cheese production (slower growth in cheese and greater spore production on bread, the traditional multiplication medium). The other cheese population originated more recently from the selection of a single clonal lineage, was associated with all types of blue cheese worldwide except Roquefort, and displayed phenotypes more suited for industrial cheese production (high lipolytic activity, efficient cheese cavity colonization ability and salt tolerance). We detected genomic regions affected by recent positive selection and putative horizontal gene transfers. This study sheds light on the processes of rapid adaptation and raises questions about genetic resource conservation.}, }
@article {pmid31960057, year = {2020}, author = {Yousuf, M and Iuliani, I and Veetil, RT and Seshasayee, ASN and Sclavi, B and Cosentino Lagomarsino, M}, title = {Early fate of exogenous promoters in E. coli.}, journal = {Nucleic acids research}, volume = {48}, number = {5}, pages = {2348-2356}, pmid = {31960057}, issn = {1362-4962}, support = {/WT_/Wellcome Trust/United Kingdom ; IA/I/16/2/502711/WTDBT_/DBT-Wellcome Trust India Alliance/India ; }, mesh = {Chromatin/chemistry/metabolism ; Escherichia coli/*genetics/metabolism ; Escherichia coli Proteins/*genetics/metabolism ; Fimbriae Proteins/*genetics/metabolism ; Gene Dosage ; *Gene Expression Regulation, Bacterial ; Gene Silencing ; Gene Transfer, Horizontal ; Genes, Reporter ; Green Fluorescent Proteins/genetics/metabolism ; *Mutagenesis, Insertional ; *Promoter Regions, Genetic ; Protein Binding ; Protein Biosynthesis ; Transgenes ; }, abstract = {Gene gain by horizontal gene transfer is a major pathway of genome innovation in bacteria. The current view posits that acquired genes initially need to be silenced and that a bacterial chromatin protein, H-NS, plays a role in this silencing. However, we lack direct observation of the early fate of a horizontally transferred gene to prove this theory. We combine sequencing, flow cytometry and sorting, followed by microscopy to monitor gene expression and its variability after large-scale random insertions of a reporter gene in a population of Escherichia coli bacteria. We find that inserted promoters have a wide range of gene-expression variability related to their location. We find that high-expression clones carry insertions that are not correlated with H-NS binding. Conversely, binding of H-NS correlates with silencing. Finally, while most promoters show a common level of extrinsic noise, some insertions show higher noise levels. Analysis of these high-noise clones supports a scenario of switching due to transcriptional interference from divergent ribosomal promoters. Altogether, our findings point to evolutionary pathways where newly-acquired genes are not necessarily silenced, but may immediately explore a wide range of expression levels to probe the optimal ones.}, }
@article {pmid31956321, year = {2019}, author = {Alexandraki, V and Kazou, M and Blom, J and Pot, B and Papadimitriou, K and Tsakalidou, E}, title = {Comparative Genomics of Streptococcus thermophilus Support Important Traits Concerning the Evolution, Biology and Technological Properties of the Species.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2916}, pmid = {31956321}, issn = {1664-302X}, abstract = {Streptococcus thermophilus is a major starter for the dairy industry with great economic importance. In this study we analyzed 23 fully sequenced genomes of S. thermophilus to highlight novel aspects of the evolution, biology and technological properties of this species. Pan/core genome analysis revealed that the species has an important number of conserved genes and that the pan genome is probably going to be closed soon. According to whole genome phylogeny and average nucleotide identity (ANI) analysis, most S. thermophilus strains were grouped in two major clusters (i.e., clusters A and B). More specifically, cluster A includes strains with chromosomes above 1.83 Mbp, while cluster B includes chromosomes below this threshold. This observation suggests that strains belonging to the two clusters may be differentiated by gene gain or gene loss events. Furthermore, certain strains of cluster A could be further subdivided in subgroups, i.e., subgroup I (ASCC 1275, DGCC 7710, KLDS SM, MN-BM-A02, and ND07), II (MN-BM-A01 and MN-ZLW-002), III (LMD-9 and SMQ-301), and IV (APC151 and ND03). In cluster B certain strains formed one distinct subgroup, i.e., subgroup I (CNRZ1066, CS8, EPS, and S9). Clusters and subgroups observed for S. thermophilus indicate the existence of lineages within the species, an observation which was further supported to a variable degree by the distribution and/or the architecture of several genomic traits. These would include exopolysaccharide (EPS) gene clusters, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)-CRISPR associated (Cas) systems, as well as restriction-modification (R-M) systems and genomic islands (GIs). Of note, the histidine biosynthetic cluster was found present in all cluster A strains (plus strain NCTC12958[T]) but was absent from all strains in cluster B. Other loci related to lactose/galactose catabolism and urea metabolism, aminopeptidases, the majority of amino acid and peptide transporters, as well as amino acid biosynthetic pathways were found to be conserved in all strains suggesting their central role for the species. Our study highlights the necessity of sequencing and analyzing more S. thermophilus complete genomes to further elucidate important aspects of strain diversity within this starter culture that may be related to its application in the dairy industry.}, }
@article {pmid31956023, year = {2020}, author = {Bowles, AMC and Bechtold, U and Paps, J}, title = {The Origin of Land Plants Is Rooted in Two Bursts of Genomic Novelty.}, journal = {Current biology : CB}, volume = {30}, number = {3}, pages = {530-536.e2}, doi = {10.1016/j.cub.2019.11.090}, pmid = {31956023}, issn = {1879-0445}, support = {BB/N016831/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Biological Evolution ; Embryophyta/*genetics ; *Evolution, Molecular ; *Genome, Plant ; Phylogeny ; }, abstract = {Over the last 470 Ma, plant evolution has seen major evolutionary transitions, such as the move from water to land and the origins of vascular tissues, seeds, and flowers [1]. These have resulted in the evolution of terrestrial flora that has shaped modern ecosystems and the diversification of the Plant Kingdom, Viridiplantae, into over 374,000 described species [2]. Each of these transitions was accompanied by the gain and loss of genes in plant genomes. For example, whole-genome duplications are known to be fundamental to the origins of both seed and flowering plants [3, 4]. With the ever-increasing quality and quantity of whole-genome data, evolutionary insight into origins of distinct plant groups using comparative genomic techniques is now feasible. Here, using an evolutionary genomics pipeline to compare 208 complete genomes, we analyze the gene content of the ancestral genomes of the last common ancestor of land plants and all other major groups of plant. This approach reveals an unprecedented level of fundamental genomic novelties in two nodes related to the origin of land plants: the first in the origin of streptophytes during the Ediacaran and another in the ancestor of land plants in the Ordovician. Our findings highlight the biological processes that evolved with the origin of land plants and emphasize the importance of conserved gene novelties in plant diversification. Comparisons to other eukaryotic studies suggest a separation of the genomic origins of multicellularity and terrestrialization in plants.}, }
@article {pmid31955713, year = {2020}, author = {Patiño-Navarrete, R and Rosinski-Chupin, I and Cabanel, N and Gauthier, L and Takissian, J and Madec, JY and Hamze, M and Bonnin, RA and Naas, T and Glaser, P}, title = {Stepwise evolution and convergent recombination underlie the global dissemination of carbapenemase-producing Escherichia coli.}, journal = {Genome medicine}, volume = {12}, number = {1}, pages = {10}, pmid = {31955713}, issn = {1756-994X}, mesh = {Bacterial Proteins/*genetics/metabolism ; Enteropathogenic Escherichia coli/classification/drug effects/*genetics ; Escherichia coli Proteins/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Mutation ; Penicillin-Binding Proteins/genetics ; Peptidoglycan Glycosyltransferase/genetics ; Phylogeny ; Porins/genetics ; *beta-Lactam Resistance ; beta-Lactamases/*genetics/metabolism ; }, abstract = {BACKGROUND: Carbapenem-resistant Enterobacteriaceae are considered by WHO as "critical" priority pathogens for which novel antibiotics are urgently needed. The dissemination of carbapenemase-producing Escherichia coli (CP-Ec) in the community is a major public health concern. However, the global molecular epidemiology of CP-Ec isolates remains largely unknown as well as factors contributing to the acquisition of carbapenemase genes.<br><br>METHODS: We first analyzed the whole-genome sequence and the evolution of the E. coli sequence type (ST) 410 and its disseminated clade expressing the carbapenemase OXA-181. We reconstructed the phylogeny of 19 E. coli ST enriched in CP-Ec and corresponding to a total of 2026 non-redundant isolates. Using the EpiCs software, we determined the significance of the association between specific mutations and the acquisition of a carbapenemase gene and the most probable order of events. The impact of the identified mutations was assessed experimentally by genetic manipulations and phenotypic testing.<br><br>RESULTS: In 13 of the studied STs, acquisition of carbapenemase genes occurred in multidrug-resistant lineages characterized by a combination of mutations in ftsI encoding the penicillin-binding protein 3 and in the porin genes ompC and ompF. Mutated ftsI genes and a specific ompC allele related to that from ST38 inducing reduced susceptibility to diverse &#x3b2;-lactams spread across the species by recombination. We showed that these mutations precede in most cases the acquisition of a carbapenemase gene. The ompC allele from ST38 might have contributed to the selection of CP-Ec disseminated lineages within this ST. On the other hand, in the pandemic ST131 lineage, CP-Ec were not associated with mutations in ompC or ftsI and show no signs of dissemination.<br><br>CONCLUSIONS: Lineages of CP-Ec have started to disseminate globally. However, their selection is a multistep process involving mutations, recombination, acquisition of antibiotic resistance genes, and selection by &#x3b2;-lactams from diverse families. This process did not yet occur in the high-risk lineage ST131.}, }
@article {pmid31954307, year = {2020}, author = {Zhou, CS and Wu, JW and Dong, LL and Liu, BF and Xing, DF and Yang, SS and Wu, XK and Wang, Q and Fan, JN and Feng, LP and Cao, GL}, title = {Removal of antibiotic resistant bacteria and antibiotic resistance genes in wastewater effluent by UV-activated persulfate.}, journal = {Journal of hazardous materials}, volume = {388}, number = {}, pages = {122070}, doi = {10.1016/j.jhazmat.2020.122070}, pmid = {31954307}, issn = {1873-3336}, mesh = {Anti-Bacterial Agents ; Bacteria/drug effects/radiation effects ; Drug Resistance, Bacterial/*genetics ; *Genes, Bacterial ; Macrolides ; Quinolones ; Sulfates/*pharmacology ; Sulfonamides ; Tetracyclines ; *Ultraviolet Rays ; Wastewater ; *Water Pollutants ; Water Purification/*methods ; }, abstract = {The emerging antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are increasingly appreciated to be as important as microbial contaminants. This paper focused on UV-activated persulfate (UV/PS), an advanced oxidation process, in removing ARB and ARGs from secondary wastewater effluent. Results showed that the inactivation efficiency of macrolides-resistant bacteria (MRB), sulfonamides-resistant bacteria (SRB), tetracyclines-resistant bacteria (TRB) and quinolones-resistant bacteria (QRB) by UV/PS reached 96.6 %, 94.7 %, 98.0 % and 99.9 % in 10 min, respectively. UV/PS also showed significant removal efficiency on ARGs. The reduction of total ARGs reached 3.84 orders of magnitude in UV/PS which is more than that in UV by 0.56 log. Particularly, the removal of mobile genetic elements (MGE) which might favor the horizontal gene transfer of ARGs among different microbial achieved 76.09 % by UV/PS. High-throughput sequencing revealed that UV/PS changed the microbial community. The proportions of Proteobacteria and Actinobacteria that pose human health risks were 4.25 % and 1.6 % less than UV, respectively. Co-occurrence analyzes indicated that ARGs were differentially contributed by bacterial taxa. In UV/PS system, hydroxyl radical and sulfate radical contributed to the removal of bacteria and ARGs. Our study provided a new method of UV/PS to remove ARGs and ARB for wastewater treatment.}, }
@article {pmid31944684, year = {2020}, author = {Wang, X and Chen, Z and Mu, Q and Wu, X and Zhang, J and Mao, D and Luo, Y and Alvarez, PJJ}, title = {Ionic Liquid Enriches the Antibiotic Resistome, Especially Efflux Pump Genes, Before Significantly Affecting Microbial Community Structure.}, journal = {Environmental science &amp; technology}, volume = {54}, number = {7}, pages = {4305-4315}, doi = {10.1021/acs.est.9b04116}, pmid = {31944684}, issn = {1520-5851}, mesh = {Anti-Bacterial Agents ; Drug Resistance, Microbial ; Genes, Bacterial ; *Ionic Liquids ; *Microbiota ; }, abstract = {An expanding list of chemicals may permeabilize bacterial cells and facilitate horizontal gene transfer (HGT), which enhances propagation of antibiotic resistance genes (ARGs) in the environment. Previous studies showed that 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIm][PF6]), an ionic liquid, can facilitate HGT of some ARGs among bacteria. However, the dynamic response of a wider range of ARGs and associated mobile genetic elements (MGEs) in different environments is unknown. Here, we used metagenomic tools to study shifts of the resistome and microbiome in both sediments and freshwater microcosms exposed to [BMIm][PF6]. Exposure for 16 h to 0.1 or 1.0 g/L significantly enriched more than 207 ARG subtypes primarily encoding efflux pumps in freshwater microcosms as well as cultivable antibiotic-resistant bacteria. This resistome enrichment was attributed to HGT facilitated by MGEs (428 plasmids, 61 integron-integrase genes, and 45 gene cassettes were enriched) as well as to HGT-related functional genes. Interestingly, resistome enrichment occurred fast (within 16 h) after [BMIm][PF6] exposure, before any significant changes in bacterial community structure. Similar ARG enrichment occurred in sediment microcosms exposed to [BMIm][PF6] for 28 d, and this longer exposure affected the microbial community structure (e.g., Proteobacteria abundance increased significantly). Overall, this study suggests that [BMIm][PF6] releases could rapidly enrich the antibiotic resistome in receiving environments by increasing HGT and fortuitously selecting for efflux pump genes, thus contributing to ARG propagation.}, }
@article {pmid31941435, year = {2020}, author = {He, Y and Zhou, X and Chen, Z and Deng, X and Gehring, A and Ou, H and Zhang, L and Shi, X}, title = {PRAP: Pan Resistome analysis pipeline.}, journal = {BMC bioinformatics}, volume = {21}, number = {1}, pages = {20}, pmid = {31941435}, issn = {1471-2105}, support = {2017YFC1601200//Key Technologies Research and Development Program/ ; 31601562//National Natural Science Foundation of China/ ; }, mesh = {Alleles ; China ; Drug Resistance, Microbial/*genetics ; Salmonella enterica/genetics ; *Software ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: Antibiotic resistance genes (ARGs) can spread among pathogens via horizontal gene transfer, resulting in imparities in their distribution even within the same species. Therefore, a pan-genome approach to analyzing resistomes is necessary for thoroughly characterizing patterns of ARGs distribution within particular pathogen populations. Software tools are readily available for either ARGs identification or pan-genome analysis, but few exist to combine the two functions.<br><br>RESULTS: We developed Pan Resistome Analysis Pipeline (PRAP) for the rapid identification of antibiotic resistance genes from various formats of whole genome sequences based on the CARD or ResFinder databases. Detailed annotations were used to analyze pan-resistome features and characterize distributions of ARGs. The contribution of different alleles to antibiotic resistance was predicted by a random forest classifier. Results of analysis were presented in browsable files along with a variety of visualization options. We demonstrated the performance of PRAP by analyzing the genomes of 26&#x2009;Salmonella enterica isolates from Shanghai, China.<br><br>CONCLUSIONS: PRAP was effective for identifying ARGs and visualizing pan-resistome features, therefore facilitating pan-genomic investigation of ARGs. This tool has the ability to further excavate potential relationships between antibiotic resistance genes and their phenotypic traits.}, }
@article {pmid31937678, year = {2020}, author = {Olm, MR and Crits-Christoph, A and Diamond, S and Lavy, A and Matheus Carnevali, PB and Banfield, JF}, title = {Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries.}, journal = {mSystems}, volume = {5}, number = {1}, pages = {}, pmid = {31937678}, issn = {2379-5077}, support = {R01 AI092531/AI/NIAID NIH HHS/United States ; }, abstract = {Longstanding questions relate to the existence of naturally distinct bacterial species and genetic approaches to distinguish them. Bacterial genomes in public databases form distinct groups, but these databases are subject to isolation and deposition biases. To avoid these biases, we compared 5,203 bacterial genomes from 1,457 environmental metagenomic samples to test for distinct clouds of diversity and evaluated metrics that could be used to define the species boundary. Bacterial genomes from the human gut, soil, and the ocean all exhibited gaps in whole-genome average nucleotide identities (ANI) near the previously suggested species threshold of 95% ANI. While genome-wide ratios of nonsynonymous and synonymous nucleotide differences (dN/dS) decrease until ANI values approach ∼98%, two methods for estimating homologous recombination approached zero at ∼95% ANI, supporting breakdown of recombination due to sequence divergence as a species-forming force. We evaluated 107 genome-based metrics for their ability to distinguish species when full genomes are not recovered. Full-length 16S rRNA genes were least useful, in part because they were underrecovered from metagenomes. However, many ribosomal proteins displayed both high metagenomic recoverability and species discrimination power. Taken together, our results verify the existence of sequence-discrete microbial species in metagenome-derived genomes and highlight the usefulness of ribosomal genes for gene-level species discrimination.IMPORTANCE There is controversy about whether bacterial diversity is clustered into distinct species groups or exists as a continuum. To address this issue, we analyzed bacterial genome databases and reports from several previous large-scale environment studies and identified clear discrete groups of species-level bacterial diversity in all cases. Genetic analysis further revealed that quasi-sexual reproduction via horizontal gene transfer is likely a key evolutionary force that maintains bacterial species integrity. We next benchmarked over 100 metrics to distinguish these bacterial species from each other and identified several genes encoding ribosomal proteins with high species discrimination power. Overall, the results from this study provide best practices for bacterial species delineation based on genome content and insight into the nature of bacterial species population genetics.}, }
@article {pmid31935189, year = {2020}, author = {Wathugala, ND and Hemananda, KM and Yip, CB and Hynes, MF}, title = {Defining the requirements for the conjugative transfer of Rhizobium leguminosarum plasmid pRleVF39b.}, journal = {Microbiology (Reading, England)}, volume = {166}, number = {3}, pages = {318-331}, doi = {10.1099/mic.0.000885}, pmid = {31935189}, issn = {1465-2080}, mesh = {Bacterial Proteins/genetics ; Conjugation, Genetic/*genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial ; *Plasmids ; Rhizobium leguminosarum/*genetics ; }, abstract = {Rhizobium leguminosarum strain VF39 contains a plasmid, pRleVF39b, which encodes a distinctive type of conjugation system (rhizobial type IVa) that is relatively widespread among rhizobial genomes. The cluster of genes encoding the transfer functions lacks orthologs to genes such as traCD, traF and traB, but contains 15 conserved genes of unknown function. We determined the importance of these genes in conjugation by constructing marked and unmarked mutations in each gene, and established that six genes, now designated trcA-F, played a significant role in plasmid transfer. Like the relaxase gene, traA, and the genes encoding the MPF system (trb genes), five of these genes, located in two divergently transcribed operons, are regulated by the Xre family repressor TrbR. The other gene, trcF encodes a protein with similarity to histidinol phosphatases, and its role in conjugation is unclear, but mutations in trcF are severely impaired for conjugation. TrcF does not play a role in regulation of other conjugation genes.}, }
@article {pmid31931516, year = {2020}, author = {Findlay Black, H and Mastromatteo, S and Sinha, S and Ehrlich, RL and Nislow, C and Chang Mell, J and Redfield, RJ}, title = {A competence-regulated toxin-antitoxin system in Haemophilus influenzae.}, journal = {PloS one}, volume = {15}, number = {1}, pages = {e0217255}, pmid = {31931516}, issn = {1932-6203}, support = {F32 AI084427/AI/NIAID NIH HHS/United States ; R01 DC002148/DC/NIDCD NIH HHS/United States ; //CIHR/Canada ; }, mesh = {Antitoxins/genetics ; DNA/*genetics/metabolism ; Escherichia coli/genetics ; Gene Expression Regulation, Bacterial/genetics ; Gene Transfer, Horizontal/genetics ; Haemophilus influenzae/*genetics ; Operon/genetics ; Promoter Regions, Genetic ; Protein Biosynthesis/genetics ; RNA-Seq ; Streptococcus/*genetics ; Toxin-Antitoxin Systems/*genetics ; Trans-Activators/genetics ; Transcription Factors/*genetics ; Transformation, Bacterial/genetics ; }, abstract = {Natural competence allows bacteria to respond to environmental and nutritional cues by taking up free DNA from their surroundings, thus gaining both nutrients and genetic information. In the Gram-negative bacterium Haemophilus influenzae, the genes needed for DNA uptake are induced by the CRP and Sxy transcription factors in response to lack of preferred carbon sources and nucleotide precursors. Here we show that one of these genes, HI0659, encodes the antitoxin of a competence-regulated toxin-antitoxin operon ('toxTA'), likely acquired by horizontal gene transfer from a Streptococcus species. Deletion of the putative toxin (HI0660) restores uptake to the antitoxin mutant. The full toxTA operon was present in only 17 of the 181 strains we examined; complete deletion was seen in 22 strains and deletions removing parts of the toxin gene in 142 others. In addition to the expected Sxy- and CRP-dependent-competence promoter, HI0659/660 transcript analysis using RNA-seq identified an internal antitoxin-repressed promoter whose transcription starts within toxT and will yield nonfunctional protein. We propose that the most likely effect of unopposed toxin expression is non-specific cleavage of mRNAs and arrest or death of competent cells in the culture. Although the high frequency of toxT and toxTA deletions suggests that this competence-regulated toxin-antitoxin system may be mildly deleterious, it could also facilitate downregulation of protein synthesis and recycling of nucleotides under starvation conditions. Although our analyses were focused on the effects of toxTA, the RNA-seq dataset will be a useful resource for further investigations into competence regulation.}, }
@article {pmid31930503, year = {2020}, author = {Chase, WR and Zhaxybayeva, O and Rocha, J and Cosgrove, DJ and Shapiro, LR}, title = {Global cellulose biomass, horizontal gene transfers and domain fusions drive microbial expansin evolution.}, journal = {The New phytologist}, volume = {226}, number = {3}, pages = {921-938}, doi = {10.1111/nph.16428}, pmid = {31930503}, issn = {1469-8137}, mesh = {Biomass ; Cell Wall ; *Cellulose ; *Gene Transfer, Horizontal ; Phylogeny ; Plant Proteins/genetics ; }, abstract = {Plants must rearrange the network of complex carbohydrates in their cell walls during normal growth and development. To accomplish this, all plants depend on proteins called expansins that nonenzymatically loosen noncovalent bonding between cellulose microfibrils. Surprisingly, expansin genes have more recently been found in some bacteria and microbial eukaryotes, where their biological functions are largely unknown. Here, we reconstruct a comprehensive phylogeny of microbial expansin genes. We find these genes in all eukaryotic microorganisms that have structural cell wall cellulose, suggesting expansins evolved in ancient marine microorganisms long before the evolution of land plants. We also find expansins in an unexpectedly high diversity of bacteria and fungi that do not have cellulosic cell walls. These bacteria and fungi inhabit varied ecological contexts, mirroring the diversity of terrestrial and aquatic niches where plant and/or algal cellulosic cell walls are present. The microbial expansin phylogeny shows evidence of multiple horizontal gene transfer events within and between bacterial and eukaryotic microbial lineages, which may in part underlie their unusually broad phylogenetic distribution. Overall, expansins are unexpectedly widespread in bacteria and eukaryotes, and the contribution of these genes to microbial ecological interactions with plants and algae has probbaly been underappreciated.}, }
@article {pmid31929575, year = {2020}, author = {Umeda, K and Nakamura, H and Fukuda, A and Yamaguchi, T and Matsumoto, Y and Motooka, D and Nakamura, S and Kawahara, R}, title = {Molecular characterization of blaKHM-1 encoding plasmid in an Enterobacter hormaechei subsp. hoffmannii isolate from blood culture.}, journal = {PloS one}, volume = {15}, number = {1}, pages = {e0227605}, pmid = {31929575}, issn = {1932-6203}, mesh = {Anti-Bacterial Agents/therapeutic use ; Bacterial Proteins/genetics/metabolism ; Blood/microbiology ; Blood Culture ; Conserved Sequence ; Drug Resistance, Multiple, Bacterial ; Enterobacter/*genetics/metabolism ; Enterobacteriaceae Infections/blood/drug therapy/*microbiology ; Gene Transfer, Horizontal ; Humans ; Plasmids/*genetics/metabolism ; Whole Genome Sequencing ; beta-Lactamases/genetics/metabolism ; }, abstract = {KHM-1 was first reported in 1997 in Japan as a novel metallo-β-lactamase mediated by Citrobacter freundii carrying pKHM-1 plasmid. There have been few reports in the clinical field since then. A blaKHM-1-positive Enterobacter hormaechei subsp. hoffmannii in E. cloacae complex, isolate OIPH-N069 was isolated from an inpatient blood culture in 2016. The isolate was characterized by whole-genome sequencing, comparative analysis of the blaKHM-1 encoding plasmid, antimicrobial susceptibility tests, and bacterial conjugation. OIPH-N069 was classified into ST78 of E. cloacae complex, and was multidrug resistant because of the presence of antimicrobial resistance genes in addition to blaKHM-1 on its chromosome and plasmids. blaKHM-1 was located on 136,816 bp of the IncA/C2 plasmid pN069-1, which could be transferred to different bacterial species. The backbone structure, genetic arrangement of the class 1 integron cassette, and the blaKHM-1 gene located downstream of the IncA/C2 antibiotic resistance island, ARI-A, in pN069-1 and pKHM-1 were identical. Horizontal gene transfer of the blaCTX-M-2-ISEcp1 resistance gene module only occurred with pN069-1. The study findings indicate not only the structural conservation of blaKHM-1 encoding plasmids over time and across species, but also the risk of the spread of blaKHM-1 encoding plasmids to other bacterial species and the accumulation of additional resistance genes.}, }
@article {pmid31926878, year = {2020}, author = {Sheppard, RJ and Beddis, AE and Barraclough, TG}, title = {The role of hosts, plasmids and environment in determining plasmid transfer rates: A meta-analysis.}, journal = {Plasmid}, volume = {108}, number = {}, pages = {102489}, doi = {10.1016/j.plasmid.2020.102489}, pmid = {31926878}, issn = {1095-9890}, support = {BB/M011178/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Algorithms ; Bacteria/genetics ; *Conjugation, Genetic ; Escherichia coli/genetics ; *Gene Transfer, Horizontal ; Models, Biological ; Plasmids/*genetics ; }, abstract = {Plasmids transfer at highly variable rates that spread over 10 orders of magnitude. While rates have been measured for decades and it is known that the rates are affected bysome biotic and abiotic factors, it is unclear how and to what extent these factors determine the rates of transfer. We performed a meta-analysis of 1224 published transfer rates from 33 papers (filtered to 612 transfer rates) to assess this variation. Over three quarters of the variation can be predicted, with plasmid repression and media type (solid versus liquid) identified as general variables explaining the most variation. Of the host and plasmid identities, identity of the recipient bacterium explained the most variation, up to 34% in some models, and more than any other explanatory variable. These results emphasize the role of the recipient in determining the rate of transfer, and show an improved range of transfer values and their correlates that can be used in future when modeling plasmid persistence.}, }
@article {pmid31926423, year = {2020}, author = {Zhang, X and Yang, F and Chen, L and Feng, H and Yin, S and Chen, M}, title = {Insights into ecological roles and potential evolution of Mlr-dependent microcystin-degrading bacteria.}, journal = {The Science of the total environment}, volume = {710}, number = {}, pages = {136401}, doi = {10.1016/j.scitotenv.2019.136401}, pmid = {31926423}, issn = {1879-1026}, mesh = {*Bacteria ; Biodegradation, Environmental ; Microcystins ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {Over decades many studies have focused on the biodegradation of microcystins (MCs), and some Mlr-dependent MC-degrading bacteria were recorded, but the ecological functions, metabolic traits, and potential evolution of these organisms remain poorly understood. In this study, 16S rRNA-based phylogeny unraveled a wide range of genetic diversity across bacterial lineage, accompanied by re-evaluation of taxonomic placement of some MC-degrading species. Genome-wide comparison showed that considerable genes unique in individual organisms were identified, suggesting genetic differentiation among these Mlr-dependent MC-degrading bacteria. Notably, analyses of metabolic profiles first revealed the presence of functional genes involved in phenylacetate biodegradation in the specialized genomic regions, and mlr gene cluster was located around the neighborhood. The identification of transposable elements further indicated that these genomic regions might undergo horizontal gene transfer events to recruit novel functionalities, suggesting an adaptive force driving genome evolution of these organisms. In short, phylogenetic and genetic content analyses of Mlr-dependent MC-degraders shed light on their metabolic potential, ecological roles, and bacterial evolution, and expand the understanding of ecological status of MCs biodegradation.}, }
@article {pmid31926390, year = {2020}, author = {Zhang, H and Chen, S and Zhang, Q and Long, Z and Yu, Y and Fang, H}, title = {Fungicides enhanced the abundance of antibiotic resistance genes in greenhouse soil.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {259}, number = {}, pages = {113877}, doi = {10.1016/j.envpol.2019.113877}, pmid = {31926390}, issn = {1873-6424}, mesh = {Agriculture ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/drug effects/genetics ; *Fungicides, Industrial/pharmacology ; Genes, Bacterial/genetics ; *Soil Microbiology ; }, abstract = {Long-term substantial application of fungicides in greenhouse cultivation led to residual pollution in soils and then altered soil microbial community. However, it is unclear whether residual fungicides could affect the diversity and abundance of antibiotic resistance genes (ARGs) in greenhouse soils. Here, the dissipation of fungicides and its impact on the abundance of ARGs were determined using shotgun metagenomic sequencing in the greenhouse and mountain soils under laboratory conditions. Our results showed the greenhouse soils harbored more diverse and abundant ARGs than the mountain soils. The application of carbendazim, azoxystrobin, and chlorothalonil could increase the abundance of total ARGs in the greenhouse soils, especially for those dominant ARG subtypes including sul2, sul1, aadA, tet(L), tetA(G), and tetX2. The abundant ARGs were significantly correlated with mobile genetic elements (MGEs, e.g. intI1and R485) in the greenhouse soils but no significant relationship in the mountain soils. Meanwhile, the co-occurrence patterns of ARGs and MGEs, e.g., sul2 and R485, sul1 and transposase, were further verified via the genetic arrangement of genes on the metagenome-assembled contigs in the greenhouse soils. Additionally, host tracking analysis indicated that ARGs were mainly carried by enterobacteria in the greenhouse soils but actinomyces in the mountain soils. These findings confirmed that some fungicides might serve as the co-selectors of ARGs and elevated their abundance via MGEs-mediated horizontal gene transfer in the greenhouse soils.}, }
@article {pmid31924623, year = {2020}, author = {Germer, A and Tiso, T and Müller, C and Behrens, B and Vosse, C and Scholz, K and Froning, M and Hayen, H and Blank, LM}, title = {Exploiting the Natural Diversity of RhlA Acyltransferases for the Synthesis of the Rhamnolipid Precursor 3-(3-Hydroxyalkanoyloxy)Alkanoic Acid.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {6}, pages = {}, pmid = {31924623}, issn = {1098-5336}, mesh = {Acyltransferases/*genetics/metabolism ; Bacteria/*genetics/metabolism ; Bacterial Proteins/*genetics/metabolism ; Carboxylic Acids/*metabolism ; Glycolipids/biosynthesis/*metabolism ; }, abstract = {While rhamnolipids of the Pseudomonas aeruginosa type are commercially available, the natural diversity of rhamnolipids and their origin have barely been investigated. Here, we collected known and identified new rhlA genes encoding the acyltransferase responsible for the synthesis of the lipophilic rhamnolipid precursor 3-(3-hydroxyalkanoyloxy)alkanoic acid (HAA). Generally, all homologs were found in Betaproteobacteria and Gammaproteobacteria A likely horizontal gene transfer event into Actinobacteria is the only identified exception. The phylogeny of the RhlA homologs from Pseudomonas and Burkholderia species is consistent with the organism phylogeny, and genes involved in rhamnolipid synthesis are located in operons. In contrast, RhlA homologs from the Enterobacterales do not follow the organisms' phylogeny but form their own branch. Furthermore, in many Enterobacterales and Halomonas from the Oceanospirillales, an isolated rhlA homolog can be found in the genome. The RhlAs from Pseudomonas aeruginosa PA01, Pseudomonas fluorescens LMG 05825, Pantoea ananatis LMG 20103, Burkholderia plantarii PG1, Burkholderia ambifaria LMG 19182, Halomonas sp. strain R57-5, Dickeya dadantii Ech586, and Serratia plymuthica PRI-2C were expressed in Escherichia coli and tested for HAA production. Indeed, except for the Serratia RhlA, HAAs were produced with the engineered strains. A detailed analysis of the produced HAA congeners by high-performance liquid chromatography coupled to tandem mass spectrometry (HPLC-MS/MS) highlights the congener specificity of the RhlA proteins. The congener length varies from 4 to 18 carbon atoms, with the main congeners consisting of different combinations of saturated or monounsaturated C10, C12, and C14 fatty acids. The results are discussed in the context of the phylogeny of this unusual enzymatic activity.IMPORTANCE The RhlA specificity explains the observed differences in 3-(3-hydroxyalkanoyloxy)alkanoic acid (HAA) congeners. Whole-cell catalysts can now be designed for the synthesis of different congener mixtures of HAAs and rhamnolipids, thereby contributing to the envisaged synthesis of designer HAAs.}, }
@article {pmid31924580, year = {2020}, author = {Dang, C and Xia, Y and Zheng, M and Liu, T and Liu, W and Chen, Q and Ni, J}, title = {Metagenomic insights into the profile of antibiotic resistomes in a large drinking water reservoir.}, journal = {Environment international}, volume = {136}, number = {}, pages = {105449}, doi = {10.1016/j.envint.2019.105449}, pmid = {31924580}, issn = {1873-6750}, mesh = {*Anti-Bacterial Agents ; China ; *Drinking Water ; *Drug Resistance, Microbial ; Environmental Monitoring ; Genes, Bacterial ; }, abstract = {Reservoirs play a vital role in the control and management of surface water resources. However, the long water residence time in the reservoir potentially increases the storage and accumulation of antibiotic resistant genes (ARGs). The full profiles and potential health risks of antibiotic resistomes in reservoirs are largely unknown. In this study, we investigated the antibiotic resistomes of water and sediment during different seasons in the Danjiangkou Reservoir, which is one of the largest reservoirs in China, using a metagenomic sequencing approach. A total of 436 ARG subtypes belonging to 20 ARG types were detected from 24 water and 18 sediment samples, with an average abundance of 0.138 copies/cell. The overall ARG abundance in the sediment was higher than that in the water, and bacitracin and vancomycin resistance genes were the predominant ARG types in the water and sediment, respectively. The overall ARG abundance in the dry season was higher than that in the wet season, and a significant difference in ARG subtype compositions was observed in water, but not in the sediment, between the different seasons. The potential horizontal gene transfer frequency in the water was higher than that in the sediment, and the ARGs in water mainly came from the sediment upstream of the reservoir. The metagenomic assembly identified 14 contigs as ARG-carrying pathogens including Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa, and 3 of 14 carried virulence factors. Overall, the potential public health risks posed by resistomes in the water of the Danjiangkou Reservoir were higher in the dry season than in the wet season. Based on these results, strategies including sediment control and pathogen monitoring are suggested for water safety management in drinking water reservoirs.}, }
@article {pmid31922542, year = {2020}, author = {Kanger, K and Guilford, NGH and Lee, H and Nesbø, CL and Truu, J and Edwards, EA}, title = {Antibiotic resistome and microbial community structure during anaerobic co-digestion of food waste, paper and cardboard.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {2}, pages = {}, doi = {10.1093/femsec/fiaa006}, pmid = {31922542}, issn = {1574-6941}, mesh = {Anaerobiosis ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/*genetics ; Food ; Food Microbiology ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Metagenome ; *Microbiota/genetics ; Plasmids ; RNA, Ribosomal, 16S ; *Waste Products ; }, abstract = {Solid organic waste is a significant source of antibiotic resistance genes (ARGs) and effective treatment strategies are urgently required to limit the spread of antimicrobial resistance. Here, we studied ARG diversity and abundance as well as the relationship between antibiotic resistome and microbial community structure within a lab-scale solid-state anaerobic digester treating a mixture of food waste, paper and cardboard. A total of 10 samples from digester feed and digestion products were collected for microbial community analysis including small subunit rRNA gene sequencing, total community metagenome sequencing and high-throughput quantitative PCR. We observed a significant shift in microbial community composition and a reduction in ARG diversity and abundance after 6 weeks of digestion. ARGs were identified in all samples with multidrug resistance being the most abundant ARG type. Thirty-two per cent of ARGs detected in digester feed were located on plasmids indicating potential for horizontal gene transfer. Using metagenomic assembly and binning, we detected potential bacterial hosts of ARGs in digester feed, which included Erwinia, Bifidobacteriaceae, Lactococcus lactis and Lactobacillus. Our results indicate that the process of sequential solid-state anaerobic digestion of food waste, paper and cardboard tested herein provides a significant reduction in the relative abundance of ARGs per 16S rRNA gene.}, }
@article {pmid31921015, year = {2019}, author = {Weber, RE and Pietsch, M and Frühauf, A and Pfeifer, Y and Martin, M and Luft, D and Gatermann, S and Pfennigwerth, N and Kaase, M and Werner, G and Fuchs, S}, title = {IS26-Mediated Transfer of bla NDM-1 as the Main Route of Resistance Transmission During a Polyclonal, Multispecies Outbreak in a German Hospital.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2817}, pmid = {31921015}, issn = {1664-302X}, abstract = {One of the most demanding challenges in infection control is the worldwide dissemination of multidrug-resistant (MDR) bacteria in clinical settings. Especially the increasing prevalence of carbapenemase producing Gram-negative pathogens poses an urgent threat to public health, as these enzymes confer resistance to almost all β-lactam antibiotics including carbapenems. In this study, we report a prolonged nosocomial outbreak of various NDM-1-producing Enterobacterales species due to clonal spread and cross-species exchange of plasmids and possibly transposons. Between July 2015 and September 2017, a total of 51 carbapenemase-positive isolates were collected from 38 patients and three environmental sources in a single German hospital. Combining molecular typing methods and whole genome sequencing, the metallo-β-lactamase gene bla NDM-1 was found to be present in 35 isolates of which seven additionally carried the carbapenemase gene bla KPC-2. Core genome MLST (cgMLST) revealed different clusters of closely related isolates of Escherichia coli, Klebsiella pneumoniae, Citrobacter freundii, Morganella morganii or Enterobacter cloacae indicating clonal spread. The detailed reconstruction of the plasmid sequences revealed that in all outbreak-associated isolates blaNDM-1 was located on similar composite transposons, which were also very similar to Tn125 previously described for Acinetobacter baumannii. In contrast to Tn125, these structures were flanked by IS26 elements, which could facilitate horizontal gene transfer. Moreover, the identical plasmid was found to be shared by E. coli and M. morganii isolates. Our results highlight the importance of detailed genome-based analyses for complex nosocomial outbreaks, allowing the identification of causal genetic determinants and providing insights into potential mechanisms involved in the dissemination of antibiotic resistances between different bacterial species.}, }
@article {pmid31917785, year = {2020}, author = {Jones, K and Burgess, G and Budd, AM and Huerlimann, R and Mashkour, N and Ariel, E}, title = {Molecular evidence for horizontal transmission of chelonid alphaherpesvirus 5 at green turtle (Chelonia mydas) foraging grounds in Queensland, Australia.}, journal = {PloS one}, volume = {15}, number = {1}, pages = {e0227268}, pmid = {31917785}, issn = {1932-6203}, mesh = {Alphaherpesvirinae/genetics/isolation &amp; purification/*pathogenicity ; Animals ; Aquatic Organisms/*virology ; DNA, Viral/genetics/isolation &amp; purification ; Datasets as Topic ; *Endangered Species ; Gene Transfer, Horizontal ; Herpesviridae Infections/transmission/*veterinary/virology ; Pacific Ocean ; Phylogeny ; Polymerase Chain Reaction ; Queensland ; Turtles/*virology ; }, abstract = {Fibropapillomatosis (FP) is a marine turtle disease recognised by benign tumours on the skin, eyes, shell, oral cavity and/or viscera. Despite being a globally distributed disease that affects an endangered species, research on FP and its likely causative agent chelonid alphaherpesvirus 5 (ChHV5) in Australia is limited. Here we present improved molecular assays developed for detection of ChHV5, in combination with a robust molecular and phylogenetic analysis of ChHV5 variants. This approach utilised a multi-gene assay to detect ChHV5 in all FP tumors sampled from 62 marine turtles found at six foraging grounds along the Great Barrier Reef. Six distinct variants of ChHV5 were identified and the distribution of these variants was associated with host foraging ground. Conversely, no association between host genetic origin and ChHV5 viral variant was found. Together this evidence supports the hypothesis that marine turtles undergo horizontal transmission of ChHV5 at foraging grounds and are unlikely to be contracting the disease at rookeries, either during mating or vertically from parent to offspring.}, }
@article {pmid31915216, year = {2020}, author = {Tian, D and Wang, B and Zhang, H and Pan, F and Wang, C and Shi, Y and Sun, Y}, title = {Dissemination of the blaNDM-5 Gene via IncX3-Type Plasmid among Enterobacteriaceae in Children.}, journal = {mSphere}, volume = {5}, number = {1}, pages = {}, pmid = {31915216}, issn = {2379-5042}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics ; Carbapenems/pharmacology ; Child ; *Drug Resistance, Multiple, Bacterial ; Enterobacteriaceae/drug effects/enzymology/*genetics ; Enterobacteriaceae Infections/microbiology/transmission ; Escherichia coli/genetics ; *Gene Transfer, Horizontal ; Humans ; Klebsiella pneumoniae/genetics ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Plasmids/*genetics ; beta-Lactamases/*genetics ; }, abstract = {The continuous emergence of novel New Delhi metallo-β-lactamase-5 (NDM-5)-producing Enterobacteriaceae isolates is receiving more and more public attention. Twenty-two NDM-5-producing strains were identified from 146 carbapenemase-producing Enterobacteriaceae (CRE) strains isolated from pediatric patients between January and March 2017, indicating that the blaNDM-5 gene has spread to children. All 22 isolates, including 16 Klebsiella pneumoniae strains, four Klebsiella aerogenes strains, and two Escherichia coli strains, showed significantly high resistance to β-lactam antibiotics (except aztreonam) but remained susceptible to tigecycline and colistin. K. pneumoniae and K. aerogenes strains were respectively defined as homologous clonal isolates by pulsed-field gel electrophoresis (PFGE). Multilocus sequence typing (MLST) results confirmed the genetic relatedness with all K. pneumoniae strains belonging to sequence type (ST) 48. Two E. coli isolates (ST617 and ST1236) were considered genetically unrelated. Twenty-two blaNDM-5 plasmids were positive for the IncX3 amplicon and showed almost identical profiles after digestion with HindIII and EcoRI. Four representative strains (K. pneumoniae K725, K. aerogenes CR33, E. coli Z214, and E. coli Z244) were selected for further study. Plasmids harboring blaNDM-5 showed strong stability in both clinical isolates and transconjugants, without apparent plasmid loss after 100 serial generations. S1-PFGE followed by Southern blot analysis demonstrated that the blaNDM-5 gene was located on an ∼46-kb plasmid. Plasmid sequences of pNDM-K725, pNDM-CR33, and pNDM-Z214 were almost identical but were slightly different from that of pNDM-Z244. Compared with pNDM-Z244, ΔISAba125 and partial copies of IS3000 were missing. The genetic backgrounds of the blaNDM-5 gene in four strains were slightly different from that of the typical pNDM_MGR194. This study comprehensively characterized the horizontal gene transfer of the blaNDM-5 gene among different Enterobacteriaceae isolates in pediatric patients, and the IncX3-type plasmid was responsible for the spread.IMPORTANCE The emergence of CRE strains resistant to multiple antibiotics is considered a substantial threat to human health. Therefore, all the efforts to provide a detailed molecular transmission mechanism of specific drug resistance can contribute positively to prevent the further spread of multidrug-resistant bacteria. Although the new superbug harboring blaNDM-5 has been reported in many countries, it was mostly identified among E. coli strains, and the gene transfer mechanism has not been fully recognized and studied. In this work, we identified 22 blaNDM-5-positive strains in different species of Enterobacteriaceae, including 16 Klebsiella pneumoniae strains, four Klebsiella aerogenes strains, and two Escherichia coli strains, which indicated the horizontal gene transfer of blaNDM-5 among Enterobacteriaceae strains in pediatric patients. Moreover, blaNDM-5 was located on a 46-kb IncX3 plasmid, which is possibly responsible for this widespread horizontal gene transfer. The different genetic contexts of the blaNDM-5 gene indicated some minor evolutions of the plasmid, based on the complete sequences of the blaNDM-5 plasmids. These findings are of great significance to understand the transmission mechanism of drug resistance genes, develop anti-infection treatment, and take effective infection control measures.}, }
@article {pmid31911812, year = {2020}, author = {Christensen, S and Molloy, EK and Vachaspati, P and Yammanuru, A and Warnow, T}, title = {Non-parametric correction of estimated gene trees using TRACTION.}, journal = {Algorithms for molecular biology : AMB}, volume = {15}, number = {}, pages = {1}, pmid = {31911812}, issn = {1748-7188}, abstract = {MOTIVATION: Estimated gene trees are often inaccurate, due to insufficient phylogenetic signal in the single gene alignment, among other causes. Gene tree correction aims to improve the accuracy of an estimated gene tree by using computational techniques along with auxiliary information, such as a reference species tree or sequencing data. However, gene trees and species trees can differ as a result of gene duplication and loss (GDL), incomplete lineage sorting (ILS), and other biological processes. Thus gene tree correction methods need to take estimation error as well as gene tree heterogeneity into account. Many prior gene tree correction methods have been developed for the case where GDL is present.<br><br>RESULTS: Here, we study the problem of gene tree correction where gene tree heterogeneity is instead due to ILS and/or HGT. We introduce TRACTION, a simple polynomial time method that provably finds an optimal solution to the RF-optimal tree refinement and completion (RF-OTRC) Problem, which seeks a refinement and completion of a singly-labeled gene tree with respect to a given singly-labeled species tree so as to minimize the Robinson-Foulds (RF) distance. Our extensive simulation study on 68,000 estimated gene trees shows that TRACTION matches or improves on the accuracy of well-established methods from the GDL literature when HGT and ILS are both present, and ties for best under the ILS-only conditions. Furthermore, TRACTION ties for fastest on these datasets. We also show that a naive generalization of the RF-OTRC problem to multi-labeled trees is possible, but can produce misleading results where gene tree heterogeneity is due to GDL.}, }
@article {pmid31911609, year = {2020}, author = {Munck, C and Sheth, RU and Freedberg, DE and Wang, HH}, title = {Recording mobile DNA in the gut microbiota using an Escherichia coli CRISPR-Cas spacer acquisition platform.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {95}, pmid = {31911609}, issn = {2041-1723}, support = {R01 AI132403/AI/NIAID NIH HHS/United States ; }, mesh = {CRISPR-Cas Systems ; Computational Biology ; DNA, Bacterial/*genetics/metabolism ; Escherichia coli/*genetics/metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome ; Gene Transfer, Horizontal ; Humans ; *Interspersed Repetitive Sequences ; Plasmids/genetics/metabolism ; }, abstract = {The flow of genetic material between bacteria is central to the adaptation and evolution of bacterial genomes. However, our knowledge about DNA transfer within complex microbiomes is lacking, with most studies of horizontal gene transfer (HGT) relying on bioinformatic analyses of genetic elements maintained on evolutionary timescales or experimental measurements of phenotypically trackable markers. Here, we utilize the CRISPR-Cas spacer acquisition process to detect DNA acquisition events from complex microbiota in real-time and at nucleotide resolution. In this system, an E. coli recording strain is exposed to a microbial sample and spacers are acquired from transferred plasmids and permanently stored in genomic CRISPR arrays. Sequencing and analysis of acquired spacers enables identification of the transferred plasmids. This approach allowed us to identify individual mobile elements without relying on phenotypic markers or post-transfer replication. We found that HGT into the recording strain in human clinical fecal samples can be extensive and is driven by different plasmid types, with the IncX type being the most actively transferred.}, }
@article {pmid31911466, year = {2020}, author = {Zhou, Z and Liu, Y and Xu, W and Pan, J and Luo, ZH and Li, M}, title = {Genome- and Community-Level Interaction Insights into Carbon Utilization and Element Cycling Functions of Hydrothermarchaeota in Hydrothermal Sediment.}, journal = {mSystems}, volume = {5}, number = {1}, pages = {}, pmid = {31911466}, issn = {2379-5077}, abstract = {Hydrothermal vents release reduced compounds and small organic carbon compounds into the surrounding seawater, providing essential substrates for microbial growth and bioenergy transformations. Despite the wide distribution of the marine benthic group E archaea (referred to as Hydrothermarchaeota) in the hydrothermal environment, little is known about their genomic repertoires and biogeochemical significance. Here, we studied four highly complete (>80%) metagenome-assembled genomes (MAGs) from a black smoker chimney and the surrounding sulfur-rich sediments on the South Atlantic Mid-Ocean Ridge and publicly available data sets (the Integrated Microbial Genomes system of the U.S. Department of Energy-Joint Genome Institute and NCBI SRA data sets). Genomic analysis suggested a wide carbon metabolic diversity of Hydrothermarchaeota members, including the utilization of proteins, lactate, and acetate; the anaerobic degradation of aromatics; the oxidation of C1 compounds (CO, formate, and formaldehyde); the utilization of methyl compounds; CO2 incorporation by the tetrahydromethanopterin-based Wood-Ljungdahl pathway; and participation in the type III ribulose-1,5-bisphosphate carboxylase/oxygenase-based Calvin-Benson-Bassham cycle. These microbes also potentially oxidize sulfur, arsenic, and hydrogen and engage in anaerobic respiration based on sulfate reduction and denitrification. Among the 140 MAGs reconstructed from the black smoker chimney microbial community (including Hydrothermarchaeota MAGs), community-level metabolic predictions suggested a redundancy of carbon utilization and element cycling functions and interactive syntrophic and sequential utilization of substrates. These processes might make various carbon and energy sources widely accessible to the microorganisms. Further, the analysis suggested that Hydrothermarchaeota members contained important functional components obtained from the community via lateral gene transfer, becoming a distinctive clade. This might serve as a niche-adaptive strategy for metabolizing heavy metals, C1 compounds, and reduced sulfur compounds. Collectively, the analysis provides comprehensive metabolic insights into the Hydrothermarchaeota IMPORTANCE This study provides comprehensive metabolic insights into the Hydrothermarchaeota from comparative genomics, evolution, and community-level perspectives. Members of the Hydrothermarchaeota synergistically participate in a wide range of carbon-utilizing and element cycling processes with other microorganisms in the community. We expand the current understanding of community interactions within the hydrothermal sediment and chimney, suggesting that microbial interactions based on sequential substrate metabolism are essential to nutrient and element cycling.}, }
@article {pmid31910889, year = {2020}, author = {Lee, K and Kim, DW and Lee, DH and Kim, YS and Bu, JH and Cha, JH and Thawng, CN and Hwang, EM and Seong, HJ and Sul, WJ and Wellington, EMH and Quince, C and Cha, CJ}, title = {Mobile resistome of human gut and pathogen drives anthropogenic bloom of antibiotic resistance.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {2}, pmid = {31910889}, issn = {2049-2618}, support = {MR/M50161X/1/MRC_/Medical Research Council/United Kingdom ; MR/S037195/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics/pathogenicity ; Drug Resistance, Bacterial/*genetics ; Feces/microbiology ; *Gastrointestinal Microbiome ; Gene Transfer, Horizontal ; *Genes, MDR ; Humans ; Interspersed Repetitive Sequences ; Metagenome ; Republic of Korea ; Rivers/*microbiology ; Sewage/microbiology ; }, abstract = {BACKGROUND: The impact of human activities on the environmental resistome has been documented in many studies, but there remains the controversial question of whether the increased antibiotic resistance observed in anthropogenically impacted environments is just a result of contamination by resistant fecal microbes or is mediated by indigenous environmental organisms. Here, to determine exactly how anthropogenic influences shape the environmental resistome, we resolved the microbiome, resistome, and mobilome of the planktonic microbial communities along a single river, the Han, which spans a gradient of human activities.<br><br>RESULTS: The bloom of antibiotic resistance genes (ARGs) was evident in the downstream regions and distinct successional dynamics of the river resistome occurred across the spatial continuum. We identified a number of widespread ARG sequences shared between the river, human gut, and pathogenic bacteria. These human-related ARGs were largely associated with mobile genetic elements rather than particular gut taxa and mainly responsible for anthropogenically driven bloom of the downstream river resistome. Furthermore, both sequence- and phenotype-based analyses revealed environmental relatives of clinically important proteobacteria as major carriers of these ARGs.<br><br>CONCLUSIONS: Our results demonstrate a more nuanced view of the impact of anthropogenic activities on the river resistome: fecal contamination is present and allows the transmission of ARGs to the environmental resistome, but these mobile genes rather than resistant fecal bacteria proliferate in environmental relatives of their original hosts. Video abstract.}, }
@article {pmid31908502, year = {2019}, author = {Dadgostar, P}, title = {Antimicrobial Resistance: Implications and Costs.}, journal = {Infection and drug resistance}, volume = {12}, number = {}, pages = {3903-3910}, pmid = {31908502}, issn = {1178-6973}, abstract = {Antimicrobial resistance (AMR) has developed as one of the major urgent threats to public health causing serious issues to successful prevention and treatment of persistent diseases. In spite of different actions taken in recent decades to tackle this issue, the trends of global AMR demonstrate no signs of slowing down. Misusing and overusing different antibacterial agents in the health care setting as well as in the agricultural industry are considered the major reasons behind the emergence of antimicrobial resistance. In addition, the spontaneous evolution, mutation of bacteria, and passing the resistant genes through horizontal gene transfer are significant contributors to antimicrobial resistance. Many studies have demonstrated the disastrous financial consequences of AMR including extremely high healthcare costs due to an increase in hospital admissions and drug usage. The literature review, which included articles published after the year 2012, was performed using Scopus, PubMed and Google Scholar with the utilization of keyword searches. Results indicated that the multifactorial threat of antimicrobial resistance has resulted in different complex issues affecting countries across the globe. These impacts found in the sources are categorized into three different levels: patient, healthcare, and economic. Although gaps in knowledge about AMR and areas for improvement are obvious, there is not any clearly understood progress to put an end to the persistent trends of antimicrobial resistance.}, }
@article {pmid31907602, year = {2020}, author = {Chen, G and Song, W and Ying, X}, title = {Horizontal Gene Transfer of Short-Chain Dehydrogenase Coding Genes Contribute to the Biofilm Formation and Pathogenicity on Mycobacterium grossiae sp. nov. PB739[T] (=DSM 104744[T]).}, journal = {Current microbiology}, volume = {77}, number = {4}, pages = {528-533}, pmid = {31907602}, issn = {1432-0991}, support = {2016F10025//Science and technology department of Zhejiang Province/ ; }, mesh = {Aged ; Base Composition ; Biofilms/*growth &amp; development ; DNA, Bacterial/genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Genomics ; Humans ; Male ; Mycobacterium/enzymology/*genetics/*pathogenicity ; Mycobacterium Infections/microbiology ; Oxidoreductases/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Virulence ; }, abstract = {Mycobacterium grossiae sp. nov. of type strain PB739[T] is a Gram-positive acid-alcohol-fast rod-shaped bacterium, which was recently isolated from a 76-year-old male who suffered from a 1-year history of hemoptysis. This strain was described as novel species in Mycobacterium genus. In this study, its genome was completely sequenced by PacBio technology, analyzed, and compared with other selected complete genome sequences of Mycobacterium to elucidate the distinct pathogenic features of the strain. The genomic analysis revealed that the genome of PB739[T] consists of one circular DNA chromosome of 5,637,923 bp with a GC content of 70.48% and one plasmid of 43,679 bp with a GC content of 66.24%. The entire genome contains 5434 predicted coding genes, 48 tRNAs, and 6 rRNA genes. Genome and comparative genomics against M. grossiae SCH identified three tandem short-chain dehydrogenase (SDR) genes which only exist in PB739[T]. These three tandem SDR genes locate in a Genomic island which was identified by Island Viewer. These SDR genes were predicted to be horizontally transferred from a Streptomyces ancestor based on phylogeny. Analysis of the mutant ΔSDR confirmed the relationship between these tandem genes with biofilm and pathogenicity. This report will provide us with an extended understanding of M. grossiae at the genomic level and would be helpful for understanding the evolution of Mycobacterium genus.}, }
@article {pmid31906858, year = {2020}, author = {Kawalek, A and Kotecka, K and Modrzejewska, M and Gawor, J and Jagura-Burdzy, G and Bartosik, AA}, title = {Genome sequence of Pseudomonas aeruginosa PAO1161, a PAO1 derivative with the ICEPae1161 integrative and conjugative element.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {14}, pmid = {31906858}, issn = {1471-2164}, support = {2015/18/E/NZ2/00675//National Science Centre, Poland/ ; 2013/11/B/NZ2/02555//National Science Centre, Poland/ ; }, mesh = {Conjugation, Genetic/*genetics ; Drug Resistance, Microbial/drug effects/genetics ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/*genetics ; Humans ; Mercury/pharmacology ; Mutation ; Operon ; Phenotype ; Plasmids/*genetics ; Polymorphism, Single Nucleotide ; Pseudomonas aeruginosa/classification/*genetics ; Pseudomonas putida/genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {BACKGROUND: Pseudomonas aeruginosa is a cause of nosocomial infections, especially in patients with cystic fibrosis and burn wounds. PAO1 strain and its derivatives are widely used to study the biology of this bacterium, however recent studies demonstrated differences in the genomes and phenotypes of derivatives from different laboratories.<br><br>RESULTS: Here we report the genome sequence of P. aeruginosa PAO1161 laboratory strain, a leu-, Rif[R], restriction-modification defective PAO1 derivative, described as the host of IncP-8 plasmid FP2, conferring the resistance to mercury. Comparison of PAO1161 genome with PAO1-UW sequence revealed lack of an inversion of a large genome segment between rRNA operons and 100 nucleotide polymorphisms, short insertions and deletions. These included a change in leuA, resulting in E108K substitution, which caused leucine auxotrophy and a mutation in rpoB, likely responsible for the rifampicin resistance. Nonsense mutations were detected in PA2735 and PA1939 encoding a DNA methyltransferase and a putative OLD family endonuclease, respectively. Analysis of revertants in these two genes showed that PA2735 is a component of a restriction-modification system, independent of PA1939. Moreover, a 12&#x2009;kb RPG42 prophage and a novel 108&#x2009;kb PAPI-1 like integrative conjugative element (ICE) encompassing a mercury resistance operon were identified. The ICEPae1161 was transferred to Pseudomonas putida cells, where it integrated in the genome and conferred the mercury resistance.<br><br>CONCLUSIONS: The high-quality P. aeruginosa PAO1161 genome sequence provides a reference for further research including e.g. investigation of horizontal gene transfer or comparative genomics. The strain was found to carry ICEPae1161, a functional PAPI-1 family integrative conjugative element, containing loci conferring mercury resistance, in the past attributed to the FP2 plasmid of IncP-8 incompatibility group. This indicates that the&#xa0;only known member of IncP-8 is in fact an ICE.}, }
@article {pmid31904319, year = {2020}, author = {Bielli, A and Piazza, A and Cento, V and Comandatore, F and Lepera, V and Gatti, M and Brioschi, P and Vismara, C and Bandi, C and Perno, CF}, title = {In vivo acquisition and risk of inter-species spread of bla KPC-3-plasmid from Klebsiella pneumoniae to Serratia marcescens in the lower respiratory tract.}, journal = {Journal of medical microbiology}, volume = {69}, number = {1}, pages = {82-86}, doi = {10.1099/jmm.0.001113}, pmid = {31904319}, issn = {1473-5644}, mesh = {Adult ; Bacterial Proteins/*genetics ; Cross Infection/microbiology ; *Gene Transfer, Horizontal ; Humans ; Intensive Care Units ; Klebsiella Infections/microbiology ; Klebsiella pneumoniae/*enzymology/*genetics ; Male ; *Plasmids ; Respiratory Tract Infections/microbiology ; Serratia Infections/microbiology ; Serratia marcescens/*enzymology/*genetics ; Whole Genome Sequencing ; beta-Lactamases/*genetics ; }, abstract = {In recent years, Serratia marcescens has emerged as an important agent of hospital-acquired infections, such as pneumonia, urinary tract infection, septicaemia and meningitis, particularly in vulnerable patients. Compared to Klebsiella pneumoniae and Escherichia coli, S. marcescens is less commonly associated with bla KPC genes, yet few cases of plasmid transmission at the gastrointestinal level from K. pneumoniae carbapenemase (KPC)-producing Enterobacterales to S. marcescens have been described. Here we report a case of in vivo acquisition, during a 3-month period of hospitalization in the intensive care unit, of a bla KPC-3 gene carried by a pKpQIL-IT plasmid, and its probable transmission at the bronchial level among different species of Enterobacterales, including K. pneumoniae and S. marcescens. By using whole genome sequence analyses we were able provide insight into the dynamics of carbapenem-resistance determinants acquisition in the lower respiratory tract, a novel anatomical region for such plasmid transmission events, that usually involve the gastrointestinal tract. The co-presence at the same time of both wild-type and resistant Enterobacterales could have been the critical factor leading to the spread of plasmids harbouring carbapenem-resistance genes, of particular importance during surveillance screenings. The possibility of such an event may have significant consequences in terms of antimicrobial treatment, with a potential limitation of therapeutic options, thereby further complicating the clinical management of high-risk critically ill patients.}, }
@article {pmid31903215, year = {2019}, author = {Goehlich, H and Roth, O and Wendling, CC}, title = {Filamentous phages reduce bacterial growth in low salinities.}, journal = {Royal Society open science}, volume = {6}, number = {12}, pages = {191669}, pmid = {31903215}, issn = {2054-5703}, abstract = {Being non-lytic, filamentous phages can replicate at high frequencies and often carry virulence factors, which are important in the evolution and emergence of novel pathogens. However, their net effect on bacterial fitness remains unknown. To understand the ecology and evolution between filamentous phages and their hosts, it is important to assess (i) fitness effects of filamentous phages on their hosts and (ii) how these effects depend on the environment. To determine how the net effect on bacterial fitness by filamentous phages changes across environments, we constructed phage-bacteria infection networks at ambient 15 practical salinity units (PSU) and stressful salinities (11 and 7 PSU) using the marine bacterium, Vibrio alginolyticus and its derived filamentous phages as model system. We observed no significant difference in network structure at 15 and 11 PSU. However, at 7 PSU phages significantly reduced bacterial growth changing network structure. This pattern was mainly driven by a significant increase in bacterial susceptibility. Our findings suggest that filamentous phages decrease bacterial growth, an indirect measure of fitness in stressful environmental conditions, which might impact bacterial communities, alter horizontal gene transfer events and possibly favour the emergence of novel pathogens in environmental Vibrios.}, }
@article {pmid31902033, year = {2020}, author = {Zhang, Y and Wang, D and Wang, Y and Dong, H and Yuan, Y and Yang, W and Lai, D and Zhang, M and Jiang, L and Li, Z}, title = {Parasitic plant dodder (Cuscuta spp.): A new natural Agrobacterium-to-plant horizontal gene transfer species.}, journal = {Science China. Life sciences}, volume = {63}, number = {2}, pages = {312-316}, doi = {10.1007/s11427-019-1588-x}, pmid = {31902033}, issn = {1869-1889}, mesh = {Agrobacterium/*genetics ; Cuscuta/*genetics ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Gene Transfer, Horizontal/*genetics ; Genes, Plant ; Genomics ; Host-Parasite Interactions/*genetics ; Sequence Analysis ; }, }
@article {pmid31900308, year = {2020}, author = {Madhav, M and Parry, R and Morgan, JAT and James, P and Asgari, S}, title = {Wolbachia Endosymbiont of the Horn Fly (Haematobia irritans irritans): a Supergroup A Strain with Multiple Horizontally Acquired Cytoplasmic Incompatibility Genes.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {6}, pages = {}, pmid = {31900308}, issn = {1098-5336}, mesh = {Animals ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Muscidae/*microbiology ; *Symbiosis/genetics ; Wolbachia/genetics/*physiology ; }, abstract = {The horn fly, Haematobia irritansirritans, is a hematophagous parasite of livestock distributed throughout Europe, Africa, Asia, and the Americas. Welfare losses on livestock due to horn fly infestation are estimated to cost between $1 billion and $2.5 billion (U.S. dollars) annually in North America and Brazil. The endosymbiotic bacterium Wolbachia pipientis is a maternally inherited manipulator of reproductive biology in arthropods and naturally infects laboratory colonies of horn flies from Kerrville, TX, and Alberta, Canada, but it has also been identified in wild-caught samples from Canada, the United States, Mexico, and Hungary. Reassembly of PacBio long-read and Illumina genomic DNA libraries from the Kerrville H. i. irritans genome project allowed for a complete and circularized 1.3-Mb Wolbachia genome (wIrr). Annotation of wIrr yielded 1,249 coding genes, 34 tRNAs, 3 rRNAs, and 5 prophage regions. Comparative genomics and whole-genome Bayesian evolutionary analysis of wIrr compared to published Wolbachia genomes suggested that wIrr is most closely related to and diverged from Wolbachia supergroup A strains known to infect Drosophila spp. Whole-genome synteny analyses between wIrr and closely related genomes indicated that wIrr has undergone significant genome rearrangements while maintaining high nucleotide identity. Comparative analysis of the cytoplasmic incompatibility (CI) genes of wIrr suggested two phylogenetically distinct CI loci and acquisition of another cifB homolog from phylogenetically distant supergroup A Wolbachia strains, suggesting horizontal acquisition of these loci. The wIrr genome provides a resource for future examination of the impact Wolbachia may have in both biocontrol and potential insecticide resistance of horn flies.IMPORTANCE Horn flies, Haematobia irritans irritans, are obligate hematophagous parasites of cattle having significant effects on production and animal welfare. Control of horn flies mainly relies on the use of insecticides, but issues with resistance have increased interest in development of alternative means of control. Wolbachia pipientis is an endosymbiont bacterium known to have a range of effects on host reproduction, such as induction of cytoplasmic incompatibility, feminization, male killing, and also impacts vector transmission. These characteristics of Wolbachia have been exploited in biological control approaches for a range of insect pests. Here we report the assembly and annotation of the circular genome of the Wolbachia strain of the Kerrville, TX, horn fly (wIrr). Annotation of wIrr suggests its unique features, including the horizontal acquisition of additional transcriptionally active cytoplasmic incompatibility loci. This study provides the foundation for future studies of Wolbachia-induced biological effects for control of horn flies.}, }
@article {pmid31898704, year = {2020}, author = {Rokas, A and Mead, ME and Steenwyk, JL and Raja, HA and Oberlies, NH}, title = {Biosynthetic gene clusters and the evolution of fungal chemodiversity.}, journal = {Natural product reports}, volume = {37}, number = {7}, pages = {868-878}, pmid = {31898704}, issn = {1460-4752}, support = {P01 CA125066/CA/NCI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Biosynthetic Pathways/genetics ; *Evolution, Molecular ; Fungi/genetics/*metabolism ; Gene Transfer, Horizontal ; *Genes, Fungal ; Humans ; *Multigene Family ; Secondary Metabolism ; Species Specificity ; }, abstract = {Covering: up to 2019Fungi produce a remarkable diversity of secondary metabolites: small, bioactive molecules not required for growth but which are essential to their ecological interactions with other organisms. Genes that participate in the same secondary metabolic pathway typically reside next to each other in fungal genomes and form biosynthetic gene clusters (BGCs). By synthesizing state-of-the-art knowledge on the evolution of BGCs in fungi, we propose that fungal chemodiversity stems from three molecular evolutionary processes involving BGCs: functional divergence, horizontal transfer, and de novo assembly. We provide examples of how these processes have contributed to the generation of fungal chemodiversity, discuss their relative importance, and outline major, outstanding questions in the field.}, }
@article {pmid31896482, year = {2020}, author = {Khan, H and Miao, X and Liu, M and Ahmad, S and Bai, X}, title = {Behavior of last resort antibiotic resistance genes (mcr-1 and blaNDM-1) in a drinking water supply system and their possible acquisition by the mouse gut flora.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {259}, number = {}, pages = {113818}, doi = {10.1016/j.envpol.2019.113818}, pmid = {31896482}, issn = {1873-6424}, mesh = {Animals ; Anti-Bacterial Agents ; Drinking Water/*microbiology ; Drug Resistance, Microbial/*genetics ; Gastrointestinal Microbiome/*physiology ; Genes, Bacterial ; Mice ; Water Supply ; beta-Lactamases ; }, abstract = {Mcr-1 and blaNDM-1 antibiotic resistance genes (ARGs) confer resistance to colistins and carbapenems, which are often antibiotics used as a last resort in tertiary care hospitals. Dissemination of these two ARGs in drinking water supply systems and their effect on healthy gut bacteria are poorly studied. In this study, the dissemination of mcr-1 and blaNDM-1 in a drinking water supply system, and their effect on the antibiotic resistance of mouse gut bacteria are explored. Metagenome analysis revealed that source water (Taipu river and Jinze reservoir) was polluted with ARGs. Mcr-1 and blaNDM-1 can be disseminated through the water distribution system. Even advanced water treatments (ozone and biological activated carbon (BAC)) could not effectively remove mcr-1 and blaNDM-1. Low concentrations of chloramine disinfectants in the water distribution system were not effective at limiting ARG abundance. Mobile genetic elements were also found to play a major role in the dissemination of ARGs via horizontal gene transfer (HGT) throughout the water supply system. Statistical analysis revealed that there was no effect of temperature on the abundance of mcr-1 and blaNDM-1 throughout the water supply system. A last resort ARG, mcr-1 can disseminate from drinking water to the healthy mouse gut. The presence of mcr-1 in a strain belonging to Enterococcus hirae, which is different from the strain belonging to the Bacillus cereus group isolated from drinking water, strongly supports the phenomena of HGT inside the gut. This research provides novel insights into the role of drinking water in disseminating ARGs to the gut and strongly suggests that drinking water may also play a major role apart from other factors known to be involved in the prevalence of last resort ARGs in the gut.}, }
@article {pmid31896018, year = {2020}, author = {Yuan, W and Tian, T and Yang, Q and Riaz, L}, title = {Transfer potentials of antibiotic resistance genes in Escherichia spp. strains from different sources.}, journal = {Chemosphere}, volume = {246}, number = {}, pages = {125736}, doi = {10.1016/j.chemosphere.2019.125736}, pmid = {31896018}, issn = {1879-1298}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects ; Drug Resistance, Microbial/*genetics ; *Environmental Monitoring ; Escherichia ; *Genes, Bacterial ; Humans ; Livestock ; Manure/microbiology ; Metals, Heavy ; Plasmids ; Wastewater/microbiology ; }, abstract = {Multidrug-resistant Escherichia coli and antibiotic-resistance genes (ARGs) present a danger to public health. However, information on the dissemination potentials of antibiotic resistance among bacteria from different environments is lacking. We isolated multiple antibiotic-resistant Escherichia spp. from animal farms, hospitals, and municipal wastewater-treatment plants (MWWTPs) using culture-based methods, and carried out resistance phenotype and gene analyses. Thirty-five isolates of multiple antibiotic-resistant Escherichia spp. were further screened to detect 61 ARGs, 18 mobile genetic elements (MGEs), and gene cassettes. The isolates from livestock manure and MWWTPs showed greater diversity in plasmid profiling than hospital wastewater. Each Escherichia sp. carried 21-26 ARGs and 8-12 MGEs. In addition, 11 gene cassettes were detected in 34 Escherichia isolates, with greater diversity in livestock manure and MWWTPs than in hospital wastewater. The results indicated that the potential for ARG transfer was higher in livestock manure and MWWTPs compared with human clinical sources, possibly related to the high occurrence of both residual antibiotics and heavy metals in these environments.}, }
@article {pmid31888149, year = {2019}, author = {Meroni, G and Soares Filipe, JF and Drago, L and Martino, PA}, title = {Investigation on Antibiotic-Resistance, Biofilm Formation and Virulence Factors in Multi Drug Resistant and Non Multi Drug Resistant Staphylococcus pseudintermedius.}, journal = {Microorganisms}, volume = {7}, number = {12}, pages = {}, pmid = {31888149}, issn = {2076-2607}, abstract = {Staphylococcus pseudintermedius is a commensal bacterium frequently isolated from canine skin and recognized as a zoonotic agent especially for dog-owners. This study focused on (a) the antibiotic-resistance phenotypes; (b) the ability to produce biofilm (slime); and (c) the dissemination of virulence factors in S. pseudintermedius strains. Seventy-three S. pseudintermedius strains were screened for antibiotic-resistance against 22 different molecules by means of Kirby-Bauer assay. The ability to produce biofilm was investigated using the microtiter plate assay (MtP) and the amplification of icaA and icaD genes. Virulence factors such as cytotoxins (lukI), enterotoxins (seC), and exfoliative toxins (siet, expA, and expB) were evaluated. The antibiotic-resistance profiles revealed 42/73 (57%) multi-drug resistant (MDR) strains and 31/73 (43%) not-MDR. All the MDR strains and 8/31 (27%) of not-MDR resulted in biofilm producers. Leukotoxin LukI was found in 70/73 (96%) of the isolates. Moreover, the enterotoxin gene seC was detected in 47/73 (64%) of the strains. All the isolates carried the siet gene, whereas expA and expB were found in 3/73 (4%) and 5/73 (7%), respectively. In conclusion, S. pseudintermedius should be considered a potential zoonotic and human agent able to carry different virulence determinants and capable of producing biofilm which facilitates horizontal gene transfer.}, }
@article {pmid31885375, year = {2019}, author = {Wein, T and Stücker, FT and Hülter, NF and Dagan, T}, title = {Quantification of Plasmid-Mediated Antibiotic Resistance in an Experimental Evolution Approach.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {154}, pages = {}, doi = {10.3791/60749}, pmid = {31885375}, issn = {1940-087X}, mesh = {Drug Resistance, Microbial/*genetics ; Evolution, Molecular ; *Plasmids ; }, abstract = {Plasmids play a major role in microbial ecology and evolution as vehicles of lateral gene transfer and reservoirs of accessory gene functions in microbial populations. This is especially the case under rapidly changing environments such as fluctuating antibiotics exposure. We recently showed that plasmids maintain antibiotic resistance genes in Escherichia coli without positive selection for the plasmid presence. Here we describe an experimental system that allows following both the plasmid genotype and phenotype in long-term evolution experiments. We use molecular techniques to design a model plasmid that is subsequently introduced to an experimental evolution batch system approach in an E. coli host. We follow the plasmid frequency over time by applying replica plating of the E. coli populations while quantifying the antibiotic resistance persistence. In addition, we monitor the conformation of plasmids in host cells by analyzing the extent of plasmid multimer formation by plasmid nicking and agarose gel electrophoresis. Such an approach allows us to visualize not only the genome size of evolving plasmids but also their topological conformation-a factor highly important for plasmid inheritance. Our system combines molecular strategies with traditional microbiology approaches and provides a set-up to follow plasmids in bacterial populations over a long time. The presented approach can be applied to study a wide range of mobile genetic elements in the future.}, }
@article {pmid31881904, year = {2019}, author = {Li, C and Jiang, Y and Li, S}, title = {LEMON: a method to construct the local strains at horizontal gene transfer sites in gut metagenomics.}, journal = {BMC bioinformatics}, volume = {20}, number = {Suppl 23}, pages = {702}, pmid = {31881904}, issn = {1471-2105}, mesh = {Bacteria/genetics ; Computer Simulation ; Databases, Genetic ; Gastrointestinal Tract/*microbiology ; Gene Fusion ; Gene Transfer, Horizontal/*genetics ; Humans ; *Metagenomics ; *Software ; Transcriptome/genetics ; }, abstract = {BACKGROUND: Horizontal Gene Transfer (HGT) refers to the transfer of genetic materials between organisms through mechanisms other than parent-offspring inheritance. HGTs may affect human health through a large number of microorganisms, especially the gut microbiomes which the human body harbors. The transferred segments may lead to complicated local genome structural variations. Details of the local genome structure can elucidate the effects of the HGTs.<br><br>RESULTS: In this work, we propose a graph-based method to reconstruct the local strains from the gut metagenomics data at the HGT sites. The method is implemented in a package named LEMON. The simulated results indicate that the method can identify transferred segments accurately on reference sequences of the microbiome. Simulation results illustrate that LEMON could recover local strains with complicated structure variation. Furthermore, the gene fusion points detected in real data near HGT breakpoints validate the accuracy of LEMON. Some strains reconstructed by LEMON have a replication time profile with lower standard error, which demonstrates HGT events recovered by LEMON is reliable.<br><br>CONCLUSIONS: Through LEMON we could reconstruct the sequence structure of bacteria, which harbors HGT events. This helps us to study gene flow among different microbial species.}, }
@article {pmid31873203, year = {2020}, author = {Yaffe, E and Relman, DA}, title = {Tracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence and adaptation.}, journal = {Nature microbiology}, volume = {5}, number = {2}, pages = {343-353}, pmid = {31873203}, issn = {2058-5276}, support = {R01 AI112401/AI/NIAID NIH HHS/United States ; R01 AI147023/AI/NIAID NIH HHS/United States ; R56 AI147023/AI/NIAID NIH HHS/United States ; }, mesh = {Adaptation, Physiological/genetics ; Adult ; Computer Simulation ; Evolution, Molecular ; Gastrointestinal Microbiome/*genetics/*physiology ; Gene Transfer, Horizontal ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenome ; Models, Genetic ; Phylogeny ; Time Factors ; }, abstract = {Despite the importance of horizontal gene transfer for rapid bacterial evolution, reliable assignment of mobile genetic elements to their microbial hosts in natural communities such as the human gut microbiota is lacking. We used high-throughput chromosomal conformation capture coupled with probabilistic modelling of experimental noise to resolve 88 strain-level metagenome-assembled genomes of distal gut bacteria from two participants, including 12,251 accessory elements. Comparisons of two samples collected 10 years apart for each of the participants revealed extensive in situ exchange of accessory elements as well as evidence of adaptive evolution in core genomes. Accessory elements were predominantly promiscuous and prevalent in the distal gut metagenomes of 218 adult individuals. This research provides a foundation and approach for studying microbial evolution in natural environments.}, }
@article {pmid31871091, year = {2020}, author = {Li, Q and Zhao, P and Li, L and Zhao, H and Shi, L and Tian, P}, title = {Engineering a CRISPR Interference System To Repress a Class 1 Integron in Escherichia coli.}, journal = {Antimicrobial agents and chemotherapy}, volume = {64}, number = {3}, pages = {}, pmid = {31871091}, issn = {1098-6596}, mesh = {Anti-Bacterial Agents/*pharmacology ; Base Sequence ; *CRISPR-Cas Systems ; Conjugation, Genetic ; Drug Resistance, Multiple, Bacterial/genetics ; Escherichia coli/*drug effects/genetics/metabolism ; Escherichia coli Proteins/genetics/metabolism ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genetic Engineering/*methods ; Integrases/genetics/metabolism ; *Integrons ; Plasmids/chemistry/metabolism ; RNA, Guide, CRISPR-Cas Systems/genetics/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Sulfamethoxazole/pharmacology ; Trimethoprim/pharmacology ; }, abstract = {Microbial multidrug resistance (MDR) poses a huge threat to human health. Bacterial acquisition of MDR relies primarily on class 1 integron-involved horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). To date, no strategies other than the use of antibiotics can efficiently cope with MDR. Here, we report that an engineered CRISPR interference (CRISPRi) system can markedly reduce MDR by blocking a class 1 integron in Escherichia coli Using CRISPRi to block plasmid R388 class 1 integron, E. coli recombinants showed halted growth upon exposure to relevant antibiotics. A microplate alamarBlue assay showed that both subgenomic RNAs (sgRNAs) R3 and R6 led to 8- and 32-fold decreases in half-maximal inhibitory concentrations (IC50) for trimethoprim and sulfamethoxazole, respectively. Reverse transcription and quantitative PCR (RT-qPCR) revealed that the strain employing sgRNA R6 exhibited 97% and 84% decreases in the transcriptional levels of the dfrB2 cassette and sul1, two typical ARGs, respectively. RT-qPCR analysis also demonstrated that the strain recruiting sgRNA R3 showed a 96% decrease in the transcriptional level of intI1, and a conjugation assay revealed a 1,000-fold decrease in HGT rates of ARGs. Overall, the sgRNA R3 targeting the 31 bp downstream of the Pc promoter on the intI1 nontemplate strand outperformed other sgRNAs in reducing integron activity. Furthermore, this CRISPRi system is reversible, genetically stable, and titratable by varying the concentration of the inducer. To our knowledge, this is the first report on exploiting a CRISPRi system to reduce the class 1 integron in E. coli This study provides valuable insights for future development of CRISPRi-based antimicrobial agents and cellular therapy to suppress MDR.}, }
@article {pmid31870298, year = {2019}, author = {Asimakis, ED and Doudoumis, V and Hadapad, AB and Hire, RS and Batargias, C and Niu, C and Khan, M and Bourtzis, K and Tsiamis, G}, title = {Detection and characterization of bacterial endosymbionts in Southeast Asian tephritid fruit fly populations.}, journal = {BMC microbiology}, volume = {19}, number = {Suppl 1}, pages = {290}, pmid = {31870298}, issn = {1471-2180}, mesh = {Animals ; Bacteria/*classification/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Gene Transfer, Horizontal ; Pest Control, Biological ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Symbiosis ; Tephritidae/*microbiology ; }, abstract = {BACKGROUND: Various endosymbiotic bacteria, including Wolbachia of the Alphaproteobacteria, infect a wide range of insects and are capable of inducing reproductive abnormalities to their hosts such as cytoplasmic incompatibility (CI), parthenogenesis, feminization and male-killing. These extended phenotypes can be potentially exploited in enhancing environmentally friendly methods, such as the sterile insect technique (SIT), for controlling natural populations of agricultural pests. The goal of the present study is to investigate the presence of Wolbachia, Spiroplasma, Arsenophonus and Cardinium among Bactrocera, Dacus and Zeugodacus flies of Southeast Asian populations, and to genotype any detected Wolbachia strains.<br><br>RESULTS: A specific 16S rRNA PCR assay was used to investigate the presence of reproductive parasites in natural populations of nine different tephritid species originating from three Asian countries, Bangladesh, China and India. Wolbachia infections were identified in Bactrocera dorsalis, B. correcta, B. scutellaris and B. zonata, with 12.2-42.9% occurrence, Entomoplasmatales in B. dorsalis, B. correcta, B. scutellaris, B. zonata, Zeugodacus cucurbitae and Z. tau (0.8-14.3%) and Cardinium in B. dorsalis and Z. tau (0.9-5.8%), while none of the species tested, harbored infections with Arsenophonus. Infected populations showed a medium (between 10 and 90%) or low (<&#x2009;10%) prevalence, ranging from 3 to 80% for Wolbachia, 2 to 33% for Entomoplasmatales and 5 to 45% for Cardinium. Wolbachia and Entomoplasmatales infections were found both in tropical and subtropical populations, the former mostly in India and the latter in various regions of India and Bangladesh. Cardinium infections were identified in both countries but only in subtropical populations. Phylogenetic analysis revealed the presence of Wolbachia with some strains belonging either to supergroup B or supergroup A. Sequence analysis revealed deletions of variable length and nucleotide variation in three Wolbachia genes. Spiroplasma strains were characterized as citri-chrysopicola-mirum and ixodetis strains while the remaining Entomoplasmatales to the Mycoides-Entomoplasmataceae clade. Cardinium strains were characterized as group A, similar to strains infecting Encarsia pergandiella.<br><br>CONCLUSIONS: Our results indicated that in the Southeast natural populations examined, supergroup A Wolbachia strain infections were the most common, followed by Entomoplasmatales and Cardinium. In terms of diversity, most strains of each bacterial genus detected clustered in a common group. Interestingly, the deletions detected in three Wolbachia genes were either new or similar to those of previously identified pseudogenes that were integrated in the host genome indicating putative horizontal gene transfer events in B. dorsalis, B. correcta and B. zonata.}, }
@article {pmid31866140, year = {2020}, author = {Papale, F and Saget, J and Bapteste, &#xc9;}, title = {Networks Consolidate the Core Concepts of Evolution by Natural Selection.}, journal = {Trends in microbiology}, volume = {28}, number = {4}, pages = {254-265}, doi = {10.1016/j.tim.2019.11.006}, pmid = {31866140}, issn = {1878-4380}, mesh = {Bacteria ; Biofilms ; *Biological Evolution ; Gene Transfer Techniques ; Microbiology ; Microbiota ; Protein Interaction Maps ; *Selection, Genetic ; Transcriptome ; }, abstract = {Microbiology has unraveled rich evidence of ongoing reticulate evolutionary processes and complex interactions both within and between cells. These phenomena feature real biological networks, which can logically be analyzed using network-based tools. It is thus not surprising that network sciences, a field independent from evolutionary biology and microbiology, have recently pervasively infused their methods into both fields. Importantly, network tools bring forward observations enhancing the understanding of three core evolutionary concepts: variation, fitness, and heredity. Consequently, our work shows how network sciences can enhance evolutionary theory by explaining the evolution by natural selection of a broad diversity of units of selection, while updating the popular figure of Darwin's tree of life with a comprehensive sketch of the networks of evolution.}, }
@article {pmid31863068, year = {2019}, author = {Zhang, X and Deatherage, DE and Zheng, H and Georgoulis, SJ and Barrick, JE}, title = {Evolution of satellite plasmids can prolong the maintenance of newly acquired accessory genes in bacteria.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {5809}, pmid = {31863068}, issn = {2041-1723}, mesh = {Animals ; Bees/microbiology ; DNA Replication ; Escherichia coli/*genetics ; *Evolution, Molecular ; Gastrointestinal Microbiome/genetics ; *Gene Transfer, Horizontal ; Neisseriaceae/*genetics ; Plasmids/*genetics ; }, abstract = {Transmissible plasmids spread genes encoding antibiotic resistance and other traits to new bacterial species. Here we report that laboratory populations of Escherichia coli with a newly acquired IncQ plasmid often evolve 'satellite plasmids' with deletions of accessory genes and genes required for plasmid replication. Satellite plasmids are molecular parasites: their presence reduces the copy number of the full-length plasmid on which they rely for their continued replication. Cells with satellite plasmids gain an immediate fitness advantage from reducing burdensome expression of accessory genes. Yet, they maintain copies of these genes and the complete plasmid, which potentially enables them to benefit from and transmit the traits they encode in the future. Evolution of satellite plasmids is transient. Cells that entirely lose accessory gene function or plasmid mobility dominate in the long run. Satellite plasmids also evolve in Snodgrassella alvi colonizing the honey bee gut, suggesting that this mechanism may broadly contribute to the importance of IncQ plasmids as agents of bacterial gene transfer in nature.}, }
@article {pmid31862787, year = {2020}, author = {Francois, CM and Durand, F and Figuet, E and Galtier, N}, title = {Prevalence and Implications of Contamination in Public Genomic Resources: A Case Study of 43 Reference Arthropod Assemblies.}, journal = {G3 (Bethesda, Md.)}, volume = {10}, number = {2}, pages = {721-730}, pmid = {31862787}, issn = {2160-1836}, mesh = {Animals ; Arthropods/*genetics ; Computational Biology/methods ; *DNA Contamination ; Databases, Genetic ; *Genome ; Genome, Insect ; *Genomics/methods ; High-Throughput Nucleotide Sequencing ; Humans ; Molecular Sequence Annotation ; Phylogeny ; Reproducibility of Results ; Sequence Analysis, DNA ; }, abstract = {Thanks to huge advances in sequencing technologies, genomic resources are increasingly being generated and shared by the scientific community. The quality of such public resources are therefore of critical importance. Errors due to contamination are particularly worrying; they are widespread, propagate across databases, and can compromise downstream analyses, especially the detection of horizontally-transferred sequences. However we still lack consistent and comprehensive assessments of contamination prevalence in public genomic data. Here we applied a standardized procedure for foreign sequence annotation to 43 published arthropod genomes from the widely used Ensembl Metazoa database. This method combines information on sequence similarity and synteny to identify contaminant and putative horizontally-transferred sequences in any genome assembly, provided that an adequate reference database is available. We uncovered considerable heterogeneity in quality among arthropod assemblies, some being devoid of contaminant sequences, whereas others included hundreds of contaminant genes. Contaminants far outnumbered horizontally-transferred genes and were a major confounder of their detection, quantification and analysis. We strongly recommend that automated standardized decontamination procedures be systematically embedded into the submission process to genomic databases.}, }
@article {pmid31861375, year = {2019}, author = {Hughes, AC and Zhang, Y and Bai, X and Xiong, Y and Wang, Y and Yang, X and Xu, Q and He, X}, title = {Structural and Functional Characterization of Stx2k, a New Subtype of Shiga Toxin 2.}, journal = {Microorganisms}, volume = {8}, number = {1}, pages = {}, pmid = {31861375}, issn = {2076-2607}, abstract = {Shiga toxin (Stx) is the major virulence factor of Shiga toxin-producing Escherichia coli (STEC). Stx evolves rapidly and, as such, new subtypes continue to emerge that challenge the efficacy of existing disease management and surveillance strategies. A new subtype, Stx2k, was recently identified in E. coli isolated from a wide range of sources including diarrheal patients, animals, and raw meats, and was poorly detected by existing immunoassays. In this study, the structure of Stx2kE167Q was determined at 2.29 Å resolution and the conservation of structure with Stx2a was revealed. A novel polyclonal antibody capable of neutralizing Stx2k and an immunoassay, with a 10-fold increase in sensitivity compared to assays using extant antibodies, were developed. Stx2k is less toxic than Stx2a in Vero cell assays but is similar to Stx2a in receptor-binding preference, thermostability, and acid tolerance. Although Stx2k does not appear to be as potent as Stx2a to Vero cells, the wide distribution and blended virulence profiles of the Stx2k-producing strains suggest that horizontal gene transfer through Stx2k-converting phages could result in the emergence of new and highly virulent pathogens. This study provides useful information and tools for early detection and control of Stx2k-producing E. coli, which could reduce public risk of infection by less-known STECs.}, }
@article {pmid31858709, year = {2020}, author = {Glasner, ME and Truong, DP and Morse, BC}, title = {How enzyme promiscuity and horizontal gene transfer contribute to metabolic innovation.}, journal = {The FEBS journal}, volume = {287}, number = {7}, pages = {1323-1342}, pmid = {31858709}, issn = {1742-4658}, support = {R01 GM124409/GM/NIGMS NIH HHS/United States ; }, mesh = {Aldehyde-Lyases/genetics/*metabolism ; *Gene Transfer, Horizontal ; Oxidoreductases/genetics/*metabolism ; Oxidoreductases Acting on CH-CH Group Donors/genetics/*metabolism ; Substrate Specificity ; }, abstract = {Promiscuity is the coincidental ability of an enzyme to catalyze its native reaction and additional reactions that are not biological functions in the same active site. Promiscuity plays a central role in enzyme evolution and is thus a useful property for protein and metabolic engineering. This review examines enzyme evolution holistically, beginning with evaluating biochemical support for four enzyme evolution models. As expected, there is strong biochemical support for the subfunctionalization and innovation-amplification-divergence models, in which promiscuity is a central feature. In many cases, however, enzyme evolution is more complex than the models indicate, suggesting much is yet to be learned about selective pressures on enzyme function. A complete understanding of enzyme evolution must also explain the ability of metabolic networks to integrate new enzyme activities. Hidden within metabolic networks are underground metabolic pathways constructed from promiscuous activities. We discuss efforts to determine the diversity and pervasiveness of underground metabolism. Remarkably, several studies have discovered that some metabolic defects can be repaired via multiple underground routes. In prokaryotes, metabolic innovation is driven by connecting enzymes acquired by horizontal gene transfer (HGT) into the metabolic network. Thus, we end the review by discussing how the combination of promiscuity and HGT contribute to evolution of metabolism in prokaryotes. Future studies investigating the contribution of promiscuity to enzyme and metabolic evolution will need to integrate deeper probes into the influence of evolution on protein biophysics, enzymology, and metabolism with more complex and realistic evolutionary models. ENZYMES: lactate dehydrogenase (EC 1.1.1.27), malate dehydrogenase (EC 1.1.1.37), OSBS (EC 4.2.1.113), HisA (EC 5.3.1.16), TrpF, PriA (EC 5.3.1.24), R-mandelonitrile lyase (EC 4.1.2.10), Maleylacetate reductase (EC 1.3.1.32).}, }
@article {pmid31849914, year = {2019}, author = {Nasir, A and Caetano-Anollés, G and Claverie, JM}, title = {Editorial: Viruses, Genetic Exchange, and the Tree of Life.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2782}, doi = {10.3389/fmicb.2019.02782}, pmid = {31849914}, issn = {1664-302X}, }
@article {pmid31849866, year = {2019}, author = {Raymond, JA and Remias, D}, title = {Ice-Binding Proteins in a Chrysophycean Snow Alga: Acquisition of an Essential Gene by Horizontal Gene Transfer.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2697}, pmid = {31849866}, issn = {1664-302X}, support = {P 29959/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {All ice-associated algae examined so far have genes for ice-binding proteins (IBPs), which suggest that these proteins are essential for survival in icy habitats. The most common type of IBP, type 1 IBPs (also referred to as DUF3494 IBPs), is also found in ice-associated bacteria and fungi. Previous studies have suggested that algal IBP genes were acquired by horizontal transfer from other microorganisms (probably bacteria). However, it remains unclear whether this is also the case for algae distantly related to the ones examined so far and whether microorganisms other than bacteria could be the donors. Furthermore, there is only limited evidence that these proteins are expressed at low temperature. Here, we show that Kremastochrysopsis austriaca (Chrysophyceae), an Austrian snow alga that is not closely related to any of the ice-associated algae examined so far, also produces IBPs, although their activity was weak. Sequencing the algal genome and the transcriptomes of cells grown at 1 and 15°C revealed three isoforms of a type 1 IBP. In agreement with their putative function, the three isoforms were strongly upregulated by one to two orders of magnitude at 1°C compared to 15°C. In a phylogenetic tree, the K. austriaca IBPs were distant from other algal IBPs, with the closest matches being bacterial proteins. These results suggest that the K. austriaca IBPs were derived from a gene that was acquired from a bacterium unrelated to other IBP donor bacteria and confirm by their presence in yet another alga the essential role of algal IBPs.}, }
@article {pmid31849846, year = {2019}, author = {Toyohara, D and Yokoi, Y and Inoue, G and Muraoka, T and Mori, T}, title = {Abiotic Factors Promote Cell Penetrating Peptide Permeability in Enterobacteriaceae Models.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2534}, pmid = {31849846}, issn = {1664-302X}, abstract = {Conventionally, the delivery of biomolecules into bacteria for the generation of characterized or functional mutants has relied greatly on horizontal gene transfer techniques. However, the low compatibility of these techniques with novel or hard-to-transform bacteria currently serves as a challenge to the bioengineering field. Here, we explored the use of cell penetrating peptides (CPPs) as an alternative biomolecule delivery approach by investigating the effects of the abiotic factors during CPP permeation. Using the (KFF)3K-FAM conjugate and Escherichia coli as models, we evaluated four abiotic factors where two of these factors, temperature and solution tonicity, promoted (KFF)3K-FAM permeation efficiency. Our data show that optimal (KFF)3K-FAM permeation efficiency was achieved for E. coli at approximately 98.1% under conditions of 37°C (growth optimal temperature) and 50% PBS concentration. Based on these conditions, we subsequently tested the applicability of CPP permeation in various bacterial strains by treating 10 bacterial strains from the Enterobacteriaceae family among which seven strains have no CPP permeation records with (KFF)3K-FAM. Interestingly, when compared with non-optimized conditions, all 10 strains showed a marked increase in CPP permeation ranging between 20 and 90% efficiency. Although using strains within Enterobacteriaceae that are phylogenetically close, our results hinted on the possibility that with proper optimization of the abiotic factors, CPPs could be compatible with a broad range of bacterial strains. Our efforts suggest that CPP could serve as an effective alternative approach for mutant generation and for biomolecule delivery into novel or hard-to-transform bacteria.}, }
@article {pmid31849833, year = {2019}, author = {Sutton, TDS and Hill, C}, title = {Gut Bacteriophage: Current Understanding and Challenges.}, journal = {Frontiers in endocrinology}, volume = {10}, number = {}, pages = {784}, pmid = {31849833}, issn = {1664-2392}, abstract = {The gut microbiome is widely accepted to have a significant impact on human health yet, despite years of research on this complex ecosystem, the contributions of different forces driving microbial population structure remain to be fully elucidated. The viral component of the human gut microbiome is dominated by bacteriophage, which are known to play crucial roles in shaping microbial composition, driving bacterial diversity, and facilitating horizontal gene transfer. Bacteriophage are also one of the most poorly understood components of the human gut microbiome, with the vast majority of viral sequences sharing little to no homology to reference databases. If we are to understand the dynamics of bacteriophage populations, their interaction with the human microbiome and ultimately their influence on human health, we will depend heavily on sequence based approaches and in silico tools. This is complicated by the fact that, as with any research field in its infancy, methods of analyses vary and this can impede our ability to compare the outputs of different studies. Here, we discuss the major findings to date regarding the human virome and reflect on our current understanding of how gut bacteriophage shape the microbiome. We consider whether or not the virome field is built on unstable foundations and if so, how can we provide a solid basis for future experimentation. The virome is a challenging yet crucial piece of the human microbiome puzzle. In order to develop our understanding, we will discuss the need to underpin future studies with robust research methods and suggest some solutions to existing challenges.}, }
@article {pmid31848306, year = {2019}, author = {Kothari, A and Soneja, D and Tang, A and Carlson, HK and Deutschbauer, AM and Mukhopadhyay, A}, title = {Native Plasmid-Encoded Mercury Resistance Genes Are Functional and Demonstrate Natural Transformation in Environmental Bacterial Isolates.}, journal = {mSystems}, volume = {4}, number = {6}, pages = {}, pmid = {31848306}, issn = {2379-5077}, abstract = {Plasmid-mediated horizontal gene transfer (HGT) is a major driver of genetic diversity in bacteria. We experimentally validated the function of a putative mercury resistance operon present on an abundant 8-kbp native plasmid found in groundwater samples without detectable levels of mercury. Phylogenetic analyses of the plasmid-encoded mercury reductases from the studied groundwater site show them to be distinct from those reported in proximal metal-contaminated sites. We synthesized the entire native plasmid and demonstrated that the plasmid was sufficient to confer functional mercury resistance in Escherichia coli Given the possibility that natural transformation is a prevalent HGT mechanism in the low-cell-density environments of groundwaters, we also assayed bacterial strains from this environment for competence. We used the native plasmid-encoded metal resistance to design a screen and identified 17 strains positive for natural transformation. We selected 2 of the positive strains along with a model bacterium to fully confirm HGT via natural transformation. From an ecological perspective, the role of the native plasmid population in providing advantageous traits combined with the microbiome's capacity to take up environmental DNA enables rapid adaptation to environmental stresses.IMPORTANCE Horizontal transfer of mobile genetic elements via natural transformation has been poorly understood in environmental microbes. Here, we confirm the functionality of a native plasmid-encoded mercury resistance operon in a model microbe and then query for the dissemination of this resistance trait via natural transformation into environmental bacterial isolates. We identified 17 strains including Gram-positive and Gram-negative bacteria to be naturally competent. These strains were able to successfully take up the plasmid DNA and obtain a clear growth advantage in the presence of mercury. Our study provides important insights into gene dissemination via natural transformation enabling rapid adaptation to dynamic stresses in groundwater environments.}, }
@article {pmid31848285, year = {2019}, author = {Simpson, CA and Podicheti, R and Rusch, DB and Dalia, AB and van Kessel, JC}, title = {Diversity in Natural Transformation Frequencies and Regulation across Vibrio Species.}, journal = {mBio}, volume = {10}, number = {6}, pages = {}, pmid = {31848285}, issn = {2150-7511}, support = {R35 GM124698/GM/NIGMS NIH HHS/United States ; R35 GM128674/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics ; DNA Transformation Competence/genetics ; DNA, Bacterial ; Gene Expression ; *Gene Expression Regulation, Bacterial ; Humans ; Models, Biological ; Phenotype ; Phylogeny ; Quorum Sensing ; Trans-Activators/genetics ; *Transformation, Bacterial ; Vibrio/classification/*physiology ; }, abstract = {In Vibrio species, chitin-induced natural transformation enables bacteria to take up DNA from the external environment and integrate it into their genome. Expression of the master competence regulator TfoX bypasses the need for chitin induction and drives expression of the genes required for competence in several Vibrio species. Here, we show that TfoX expression in Vibrio campbellii strains DS40M4 and NBRC 15631 enables high natural transformation frequencies. Conversely, transformation was not achieved in the model quorum-sensing strain V. campbellii BB120 (previously classified as Vibrio harveyi). Surprisingly, we find that quorum sensing is not required for transformation in V. campbellii DS40M4 or Vibrio parahaemolyticus in contrast to the established regulatory pathway in Vibrio cholerae in which quorum sensing is required to activate the competence regulator QstR. Similar to V. cholerae, expression of both QstR and TfoX is necessary for transformation in DS40M4. There is a wide disparity in transformation frequencies among even closely related Vibrio strains, with V. vulnificus having the lowest functional transformation frequency. Ectopic expression of both TfoX and QstR is sufficient to produce a significant increase in transformation frequency in Vibrio vulnificus To explore differences in competence regulation, we used previously studied V. cholerae competence genes to inform a comparative genomics analysis coupled with transcriptomics. We find that transformation capability cannot necessarily be predicted by the level of gene conservation but rather correlates with competence gene expression following TfoX induction. Thus, we have uncovered notable species- and strain-level variations in the competence gene regulation pathway across the Vibrio genus.IMPORTANCE Naturally transformable, or competent, bacteria are able to take up DNA from their environment, a key method of horizontal gene transfer for acquisition of new DNA sequences. Our research shows that Vibrio species that inhabit marine environments exhibit a wide diversity in natural transformation capability ranging from nontransformability to high transformation rates in which 10% of cells measurably incorporate new DNA. We show that the role of regulatory systems controlling the expression of competence genes (e.g., quorum sensing) differs throughout both the species and strain levels. We explore natural transformation capabilities of Vibrio campbellii species which have been thus far uncharacterized and find novel regulation of competence. Expression of two key transcription factors, TfoX and QstR, is necessary to stimulate high levels of transformation in Vibrio campbellii and recover low rates of transformation in Vibrio vulnificus.}, }
@article {pmid31845962, year = {2020}, author = {Sevillya, G and Doerr, D and Lerner, Y and Stoye, J and Steel, M and Snir, S}, title = {Horizontal Gene Transfer Phylogenetics: A Random Walk Approach.}, journal = {Molecular biology and evolution}, volume = {37}, number = {5}, pages = {1470-1479}, doi = {10.1093/molbev/msz302}, pmid = {31845962}, issn = {1537-1719}, mesh = {*Gene Transfer, Horizontal ; *Genetic Techniques ; Genome, Microbial ; *Models, Genetic ; Phylogeny ; *Synteny ; }, abstract = {The dramatic decrease in time and cost for generating genetic sequence data has opened up vast opportunities in molecular systematics, one of which is the ability to decipher the evolutionary history of strains of a species. Under this fine systematic resolution, the standard markers are too crude to provide a phylogenetic signal. Nevertheless, among prokaryotes, genome dynamics in the form of horizontal gene transfer (HGT) between organisms and gene loss seem to provide far richer information by affecting both gene order and gene content. The "synteny index" (SI) between a pair of genomes combines these latter two factors, allowing comparison of genomes with unequal gene content, together with order considerations of their common genes. Although this approach is useful for classifying close relatives, no rigorous statistical modeling for it has been suggested. Such modeling is valuable, as it allows observed measures to be transformed into estimates of time periods during evolution, yielding the "additivity" of the measure. To the best of our knowledge, there is no other additivity proof for other gene order/content measures under HGT. Here, we provide a first statistical model and analysis for the SI measure. We model the "gene neighborhood" as a "birth-death-immigration" process affected by the HGT activity over the genome, and analytically relate the HGT rate and time to the expected SI. This model is asymptotic and thus provides accurate results, assuming infinite size genomes. Therefore, we also developed a heuristic model following an "exponential decay" function, accounting for biologically realistic values, which performed well in simulations. Applying this model to 1,133 prokaryotes partitioned to 39 clusters by the rank of genus yields that the average number of genome dynamics events per gene in the phylogenetic depth of genus is around half with significant variability between genera. This result extends and confirms similar results obtained for individual genera in different manners.}, }
@article {pmid31844709, year = {2019}, author = {Astorga, F and Navarrete-Talloni, MJ and Miró, MP and Bravo, V and Toro, M and Blondel, CJ and Hervé-Claude, LP}, title = {Antimicrobial resistance in E. coli isolated from dairy calves and bedding material.}, journal = {Heliyon}, volume = {5}, number = {11}, pages = {e02773}, pmid = {31844709}, issn = {2405-8440}, abstract = {INTRODUCTION: E. coli is a ubiquitous bacterium commonly used as a sentinel in antimicrobial resistance studies. Here, E. coli was isolated from three groups (sick calves, healthy calves and bedding material), to assess the presence of antimicrobial resistance, describe resistance profiles, and compare these resistances among groups.<br><br>MATERIAL AND METHODS: Samples were collected from calves and calving pens from 20 dairy farms. Using the disc diffusion method, E.&#xa0;coli isolates were screened for antimicrobial resistance against seven antimicrobials: Amoxicillin, Ceftiofur, Gentamicin, Enrofloxacin, Trimethoprim-sulfamethoxazole, Florfenicol and Oxytetracycline. Isolates resistant to all these seven antimicrobials were tested again against an extended 19 antimicrobial drug panel and for the presence of the most common E.&#xa0;coli pathogenicity genes through PCR.<br><br>RESULTS &amp; DISCUSSION: Three hundred forty-nine E.&#xa0;coli isolates were obtained; most isolates were resistant to a single antimicrobial, but 2.3% (8) were resistant to 16 to 19 of the antimicrobials tested. The group with the highest percentage of multiresistant isolates was the calves with diarrhea group. Younger calves provided samples with higher antimicrobial resistance levels.<br><br>CONCLUSIONS: There is a high rate of antimicrobial resistance in dairy farms calving pens. These bacteria could not only be a resistance gene reservoir, but also could have the potential to spread these determinants through horizontal gene transfer to other susceptible bacteria. Measures should be taken to protect colonization of younger calves, based on hygienic measures and proper management.}, }
@article {pmid31844016, year = {2020}, author = {Aoki, S and Nakase, K and Nakaminami, H and Wajima, T and Hayashi, N and Noguchi, N}, title = {Transferable Multidrug-Resistance Plasmid Carrying a Novel Macrolide-Clindamycin Resistance Gene, erm(50), in Cutibacterium acnes.}, journal = {Antimicrobial agents and chemotherapy}, volume = {64}, number = {3}, pages = {}, pmid = {31844016}, issn = {1098-6596}, mesh = {Acne Vulgaris/microbiology ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics/metabolism ; Clindamycin/*pharmacology ; Conjugation, Genetic ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Expression ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; Macrolides/*pharmacology ; Microbial Sensitivity Tests ; Phylogeny ; Plasmids/*chemistry/metabolism ; Propionibacteriaceae/classification/drug effects/*genetics/isolation &amp; purification ; RNA, Ribosomal, 23S/genetics/metabolism ; Tetracycline Resistance/genetics ; Tetracyclines/pharmacology ; Whole Genome Sequencing ; }, abstract = {Antimicrobial-resistant Cutibacterium acnes strains have emerged and disseminated throughout the world. The 23S rRNA mutation and erm(X) gene are known as the major resistance determinants of macrolides and clindamycin in C. acnes We isolated eight high-level macrolide-clindamycin-resistant C. acnes strains with no known resistance determinants, such as 23S rRNA mutation and erm(X), from different acne patients in 2008 between 2013 and 2015. The aim of this study was to identify the novel mechanisms of resistance in C. acnes Whole-genome sequencing revealed the existence of a plasmid DNA, denoted pTZC1 (length, 31,440 bp), carrying the novel macrolide-clindamycin resistance gene erm(50) and tetracycline resistance gene tet(W). pTZC1 was detected in all C. acnes isolates (eight strains) exhibiting high-level macrolide-clindamycin resistance, with no known resistance determinants (MIC of clarithromycin, ≥256 μg/ml; clindamycin, ≥256 μg/ml). Transconjugation experiments demonstrated that the pTZC1 was horizontally transferred among C. acnes strains and conferred resistance to macrolides, clindamycin, and tetracyclines. Our data showed, for the first time, the existence of a transferable multidrug-resistant plasmid in C. acnes Increased prevalence of this plasmid will be a great threat to antimicrobial therapy for acne vulgaris.}, }
@article {pmid31841712, year = {2020}, author = {Loayza-Villa, F and Salinas, L and Tijet, N and Villavicencio, F and Tamayo, R and Salas, S and Rivera, R and Villacis, J and Satan, C and Ushiña, L and Muñoz, O and Zurita, J and Melano, R and Reyes, J and Trueba, GA}, title = {Diverse Escherichia coli lineages from domestic animals carrying colistin resistance gene mcr-1 in an Ecuadorian household.}, journal = {Journal of global antimicrobial resistance}, volume = {22}, number = {}, pages = {63-67}, doi = {10.1016/j.jgar.2019.12.002}, pmid = {31841712}, issn = {2213-7173}, mesh = {Animals ; Animals, Domestic/*microbiology ; Anti-Bacterial Agents/pharmacology ; Chickens/microbiology ; *Colistin/pharmacology ; Cross-Sectional Studies ; Dogs/microbiology ; Ecuador ; Escherichia coli/genetics ; *Escherichia coli Proteins/genetics ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; }, abstract = {OBJECTIVE: The aim of this study was to detect potential animal reservoirs of Escherichia coli carrying the mcr-1 gene in an Ecuadorian household.<br><br>METHODS: The mobile colistin-resistance gene, mcr-1, was first detected in Ecuador in a commensal E. coli isolate from a boy. A cross-sectional study was performed to detect the possible source of colistin-resistant E. coli in the boy's household. Faecal swabs and soil faecal samples were collected from companion animals. Samples were plated on selective media to isolate colistin-resistant E. coli and isolates were submitted to PCR detection of mcr-1, pulsed field gel electrophoresis (PFGE), and multi-locus sequences typing (MLST). Moreover, the genomes of all the isolates were sequenced.<br><br>RESULTS: Three different colistin-resistant E. coli sequence types (ST3941, 1630 and 2170), corresponding to three PFGE patterns, were obtained from a chicken and two dogs; these isolates were different from the human isolate (ST609). By whole-genome sequencing, the mcr-1.1 gene was found on IncI2 plasmids with very high nucleotide identity.<br><br>CONCLUSIONS: Our results indicate a polyclonal dissemination of mcr-1.1 in the environment surrounding the first MCR-producing E. coli strain reported in Ecuador. Our findings support the idea of lateral dissemination of mcr-1.1 gene between unrelated E. coli isolates.}, }
@article {pmid31838385, year = {2020}, author = {Xu, L and Zhou, Z and Zhu, L and Han, Y and Lin, Z and Feng, W and Liu, Y and Shuai, X and Chen, H}, title = {Antibiotic resistance genes and microcystins in a drinking water treatment plant.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {258}, number = {}, pages = {113718}, doi = {10.1016/j.envpol.2019.113718}, pmid = {31838385}, issn = {1873-6424}, mesh = {Anti-Bacterial Agents ; Drinking Water/*analysis ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Microcystins/*analysis ; *Water Purification ; }, abstract = {Problems with antibiotic resistance genes (ARGs) and secondary pollution from microcystins (MCs), caused by cyanobacterial blooms have become significant global issues. These two pollutants co-occur in drinking water treatment plants (DWTPs), but the exact relationships between them requires further clarification. Here, a high-throughput quantitative real-time PCR and enzyme-linked immunosorbent assay were used to investigate the behavior of ARGs and MCs in a practical DWTP in the first place. After the on-site investigation, the effect of MCs on the horizontal transfer of ARGs was studied under laboratory conditions, and mechanisms explored at both cellular and molecular levels. MCs could promote the spread of ARGs, especially in relatively stationary and stable environments such as biofilms. MC-LR was the most efficient microcystin subtype promoting conjugative transfer, which was 25.13 times higher than for the control group. MCs affected the horizontal transfer of ARGs by regulating a series of gene systems involved in conjugative transfer, stimulating the formation of reactive oxygen species (ROS), and increasing cell membrane permeability. This study can provide a theoretical basis for the control of ARGs and MCs in DWTPs, which is of great significance for the scientific assessment of drinking water safety.}, }
@article {pmid31838265, year = {2020}, author = {Zheng, W and Huyan, J and Tian, Z and Zhang, Y and Wen, X}, title = {Clinical class 1 integron-integrase gene - A promising indicator to monitor the abundance and elimination of antibiotic resistance genes in an urban wastewater treatment plant.}, journal = {Environment international}, volume = {135}, number = {}, pages = {105372}, doi = {10.1016/j.envint.2019.105372}, pmid = {31838265}, issn = {1873-6750}, mesh = {Anti-Bacterial Agents ; Drug Resistance, Microbial ; Genes, Bacterial ; Humans ; Integrases ; Integrons ; *Wastewater ; }, abstract = {In this study, 295 antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) from the influent, activated sludge (AS), and membrane bioreactor (MBR) permeate were primarily examined in the wastewater treatment plant (WWTP) biweekly over 13 months. The absolute concentrations of ARGs and MGEs respectively ranged from 1.27 × 10[10] to 1.94 × 10[11] and 8.00 × 10[9] to 1.24 × 10[11] copies/L in the influent, of which were reduced by 2 to 3 orders of magnitude in the permeate. No significant seasonal variation of ARGs and MGEs was found in the WWTP, except that the absolute abundance of ARGs and MGEs in the AS was peaked during spring. The antibiotics affected neither ARGs nor MGEs significantly, suggesting their concentrations may be not high enough to pose a selective pressure. In contrast, the bacterial community had direct effect on the MGEs variation, meanwhile the MGEs influenced the ARG abundance directly. Class 1 integron-integrase gene (intI1), clinical intI1, and Tn21 associated more frequently with ARGs in the AS over long-term, suggesting the potential of them involved in horizontal gene transfer. Both intI1 and clinical intI1 had significantly positive associations with the overall abundance of ARGs, as well as significantly negative relationships with the overall removal rates of ARGs in the MBR. However, the abundances between intI1 and clinical intI1 were significantly different. Meanwhile, clinical intI1 remained rather consistent proportion with the ARG abundance in the AS and permeate, was stronger correlated with human pathogens, and was associated with greater number of ARGs over time. Moreover, clinical intI1 was significantly associated with the removal efficiency of ARGs from all classes. Taken together, clinical intI1 can be adopted as an indicator for the abundance and removal efficiency of ARGs in the WWTP.}, }
@article {pmid31835720, year = {2019}, author = {Imchen, M and Vennapu, RK and Ghosh, P and Kumavath, R}, title = {Insights into Antagonistic Interactions of Multidrug Resistant Bacteria in Mangrove Sediments from the South Indian State of Kerala.}, journal = {Microorganisms}, volume = {7}, number = {12}, pages = {}, pmid = {31835720}, issn = {2076-2607}, support = {EMEQ/051/2014//Science and Engineering Research Board/ ; EEQ/2018/001085//Science and Engineering Research Board/ ; }, abstract = {Antibiotic resistance is a global issue which is magnified by interspecies horizontal gene transfer. Understanding antibiotic resistance in bacteria in a natural setting is crucial to check whether they are multidrug resistant (MDR) and possibly avoid outbreaks. In this study, we have isolated several antibiotic-resistant bacteria (ARB) (n = 128) from the mangroves in Kerala, India. ARBs were distributed based on antibiotics (p = 1.6 × 10[-5]). The 16S rRNA gene characterization revealed dominance by Bacillaceae (45%), Planococcaceae (22.5%), and Enterobacteriaceae (17.5%). A high proportion of the isolates were MDR (75%) with maximum resistance to methicillin (70%). Four isolates affiliated to plant-growth promoters, probiotics, food, and human pathogens were resistant to all antibiotics indicating the seriousness and prevalence of MDR. A significant correlation (R = 0.66; p = 2.5 × 10[-6]) was observed between MDR and biofilm formation. Antagonist activity was observed in 62.5% isolates. Gram-positive isolates were more susceptible to antagonism (75.86%) than gram-negative (36.36%) isolates. Antagonism interactions against gram-negative isolates were lower (9.42%) when compared to gram-positive isolates (89.85%). Such strong antagonist activity can be harnessed for inspection of novel antimicrobial mechanisms and drugs. Our study shows that MDR with strong biofilm formation is prevalent in natural habitat and if acquired by deadly pathogens may create havoc in public health.}, }
@article {pmid31835029, year = {2019}, author = {Dalia, AB and Dalia, TN}, title = {Spatiotemporal Analysis of DNA Integration during Natural Transformation Reveals a Mode of Nongenetic Inheritance in Bacteria.}, journal = {Cell}, volume = {179}, number = {7}, pages = {1499-1511.e10}, pmid = {31835029}, issn = {1097-4172}, support = {K22 AI118863/AI/NIAID NIH HHS/United States ; R35 GM128674/GM/NIGMS NIH HHS/United States ; }, mesh = {DNA Replication ; Drug Resistance, Bacterial/genetics ; *Gene Transfer, Horizontal ; *Homologous Recombination ; Streptococcus pneumoniae/*genetics ; *Transformation, Genetic ; Vibrio cholerae/*genetics ; }, abstract = {Natural transformation (NT) is a major mechanism of horizontal gene transfer in microbial species that promotes the spread of antibiotic-resistance determinants and virulence factors. Here, we develop a cell biological approach to characterize the spatiotemporal dynamics of homologous recombination during NT in Vibrio cholerae. Our results directly demonstrate (1) that transforming DNA efficiently integrates into the genome as single-stranded DNA, (2) that the resulting heteroduplexes are resolved by chromosome replication and segregation, and (3) that integrated DNA is rapidly expressed prior to cell division. We show that the combination of these properties results in the nongenetic transfer of gene products within transformed populations, which can support phenotypic inheritance of antibiotic resistance in both V. cholerae and Streptococcus pneumoniae. Thus, beyond the genetic acquisition of novel DNA sequences, NT can also promote the nongenetic inheritance of traits during this conserved mechanism of horizontal gene transfer.}, }
@article {pmid31830246, year = {2020}, author = {Blow, F and Gioti, A and Goodhead, IB and Kalyva, M and Kampouraki, A and Vontas, J and Darby, AC}, title = {Functional Genomics of a Symbiotic Community: Shared Traits in the Olive Fruit Fly Gut Microbiota.}, journal = {Genome biology and evolution}, volume = {12}, number = {2}, pages = {3778-3791}, pmid = {31830246}, issn = {1759-6653}, support = {BB/K501773/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Gastrointestinal Microbiome/genetics/*physiology ; Gene Transfer, Horizontal ; Genomics/methods ; Olea/*parasitology ; Symbiosis/genetics/*physiology ; Tephritidae/genetics/*metabolism/*microbiology ; Urease/genetics/metabolism ; }, abstract = {The olive fruit fly Bactrocera oleae is a major pest of olives worldwide and houses a specialized gut microbiota dominated by the obligate symbiont "Candidatus Erwinia dacicola." Candidatus Erwinia dacicola is thought to supplement dietary nitrogen to the host, with only indirect evidence for this hypothesis so far. Here, we sought to investigate the contribution of the symbiosis to insect fitness and explore the ecology of the insect gut. For this purpose, we examined the composition of bacterial communities associated with Cretan olive fruit fly populations, and inspected several genomes and one transcriptome assembly. We identified, and reconstructed the genome of, a novel component of the gut microbiota, Tatumella sp. TA1, which is stably associated with Mediterranean olive fruit fly populations. We also reconstructed a number of pathways related to nitrogen assimilation and interactions with the host. The results show that, despite variation in taxa composition of the gut microbial community, core functions related to the symbiosis are maintained. Functional redundancy between different microbial taxa was observed for genes involved in urea hydrolysis. The latter is encoded in the obligate symbiont genome by a conserved urease operon, likely acquired by horizontal gene transfer, based on phylogenetic evidence. A potential underlying mechanism is the action of mobile elements, especially abundant in the Ca. E. dacicola genome. This finding, along with the identification, in the studied genomes, of extracellular surface structure components that may mediate interactions within the gut community, suggest that ongoing and past genetic exchanges between microbes may have shaped the symbiosis.}, }
@article {pmid31828082, year = {2019}, author = {Zhou, W and Chen, Q and Qian, C and Shen, K and Zhu, X and Zhou, D and Lu, W and Sun, Z and Liu, H and Li, K and Xu, T and Bao, Q and Lu, J}, title = {In Vitro Susceptibility and Florfenicol Resistance in Citrobacter Isolates and Whole-Genome Analysis of Multidrug-Resistant Citrobacter freundii.}, journal = {International journal of genomics}, volume = {2019}, number = {}, pages = {7191935}, pmid = {31828082}, issn = {2314-4378}, abstract = {The genus Citrobacter is an opportunistic pathogen causing infections in animals, and the published data for its resistance to florfenicol are scarce. In this study, we investigated the antimicrobial susceptibility and molecular characteristics of florfenicol resistance genes among Citrobacter isolates from animal and relevant environmental samples and conducted a comparative analysis of a multidrug-resistant Citrobacter freundii strain isolated from a rabbit. Among 20 Citrobacter strains isolated from animal samples, resistance was most commonly observed to ampicillin (100%), tetracycline (75%), streptomycin (65%), florfenicol (60%), chloramphenicol (60%), and aztreonam (50%), while all the strains found in environmental samples were resistant to few antibiotics. The florfenicol resistance gene floR was detected in 12 isolates (48%, 12/25) from animal samples, and all of the floR-positive isolates were resistant to florfenicol with minimum inhibitory concentration (MIC) values ≥256 μg/mL. Sequencing and comparative analysis of the plasmids from a multidrug-resistant C. freundii isolate named R47 showed that the floR-containing region in the plasmid pR47-54 was a truncated transposon-like structure and could be found on both plasmids and chromosomes of bacteria of either animal or human origin. Furthermore, a range of antimicrobial and metal resistance genes associated with mobile genetic elements could be identified in pR47-54 and the other plasmid pR47-309 of C. freundii R47. These results provide in-depth views into the phenotypic and molecular characteristics of Citrobacter isolates recovered from animal and relevant environmental samples, as well as highlight the role horizontal gene transfer plays in the dissemination of plasmid-encoded resistance genes.}, }
@article {pmid31827592, year = {2019}, author = {Allman, ES and Baños, H and Rhodes, JA}, title = {NANUQ: a method for inferring species networks from gene trees under the coalescent model.}, journal = {Algorithms for molecular biology : AMB}, volume = {14}, number = {}, pages = {24}, pmid = {31827592}, issn = {1748-7188}, support = {R01 GM117590/GM/NIGMS NIH HHS/United States ; }, abstract = {Species networks generalize the notion of species trees to allow for hybridization or other lateral gene transfer. Under the network multispecies coalescent model, individual gene trees arising from a network can have any topology, but arise with frequencies dependent on the network structure and numerical parameters. We propose a new algorithm for statistical inference of a level-1 species network under this model, from data consisting of gene tree topologies, and provide the theoretical justification for it. The algorithm is based on an analysis of quartets displayed on gene trees, combining several statistical hypothesis tests with combinatorial ideas such as a quartet-based intertaxon distance appropriate to networks, the NeighborNet algorithm for circular split systems, and the Circular Network algorithm for constructing a splits graph.}, }
@article {pmid31825517, year = {2020}, author = {Moreira, SM and de Oliveira Mendes, TA and Santanta, MF and Huws, SA and Creevey, CJ and Mantovani, HC}, title = {Genomic and gene expression evidence of nonribosomal peptide and polyketide production among ruminal bacteria: a potential role in niche colonization?.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {2}, pages = {}, doi = {10.1093/femsec/fiz198}, pmid = {31825517}, issn = {1574-6941}, mesh = {Animals ; Bacteria/classification/genetics/*metabolism ; Feces/microbiology ; Gastrointestinal Microbiome ; Gene Expression Profiling ; Genomics ; *Peptide Biosynthesis, Nucleic Acid-Independent ; Peptide Synthases/genetics ; Phylogeny ; Polyketide Synthases/genetics ; Polyketides/*metabolism ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Ruminants ; }, abstract = {Genomic and transcriptomic analyses were performed to investigate nonribosomal peptide synthetases (NRPS) and polyketide synthases (PKS) in 310 genomes of ruminal/fecal microorganisms. A total of 119 biosynthetic genes potentially encoding distinct nonribosomal peptides (NRPs) and polyketides (PKs) were predicted in the ruminal microbial genomes and functional annotation separated these genes into 19 functional categories. The phylogenetic reconstruction of the 16S rRNA sequences coupled to the distribution of the three 'backbone' genes involved in NRPS and PKS biosyntheses suggested that these genes were not acquired through horizontal gene transfer. Metatranscriptomic analyses revealed that the predominant genes involved in the synthesis of NRPs and PKs were more abundant in sheep rumen datasets. Reads mapping to the NRPS and PKS biosynthetic genes were represented in the active ruminal microbial community, with transcripts being highly expressed in the bacterial community attached to perennial ryegrass, and following the main changes occurring between primary and secondary colonization of the forage incubated with ruminal fluid. This study is the first comprehensive characterization demonstrating the rich genetic capacity for NRPS and PKS biosyntheses within rumen bacterial genomes, which highlights the potential functional roles of secondary metabolites in the rumen ecosystem.}, }
@article {pmid31825473, year = {2020}, author = {Haag, KL and Pombert, JF and Sun, Y and de Albuquerque, NRM and Batliner, B and Fields, P and Lopes, TF and Ebert, D}, title = {Microsporidia with Vertical Transmission Were Likely Shaped by Nonadaptive Processes.}, journal = {Genome biology and evolution}, volume = {12}, number = {1}, pages = {3599-3614}, pmid = {31825473}, issn = {1759-6653}, support = {R15 AI128627/AI/NIAID NIH HHS/United States ; }, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Drift ; *Genome, Fungal ; Microsporidia/*genetics ; Recombination, Genetic ; Selection, Genetic ; }, abstract = {Microsporidia have the leanest genomes among eukaryotes, and their physiological and genomic simplicity has been attributed to their intracellular, obligate parasitic life-style. However, not all microsporidia genomes are small or lean, with the largest dwarfing the smallest ones by at least an order of magnitude. To better understand the evolutionary mechanisms behind this genomic diversification, we explore here two clades of microsporidia with distinct life histories, Ordospora and Hamiltosporidium, parasitizing the same host species, Daphnia magna. Based on seven newly assembled genomes, we show that mixed-mode transmission (the combination of horizontal and vertical transmission), which occurs in Hamiltosporidium, is found to be associated with larger and AT-biased genomes, more genes, and longer intergenic regions, as compared with the exclusively horizontally transmitted Ordospora. Furthermore, the Hamiltosporidium genome assemblies contain a variety of repetitive elements and long segmental duplications. We show that there is an excess of nonsynonymous substitutions in the microsporidia with mixed-mode transmission, which cannot be solely attributed to the lack of recombination, suggesting that bursts of genome size in these microsporidia result primarily from genetic drift. Overall, these findings suggest that the switch from a horizontal-only to a mixed mode of transmission likely produces population bottlenecks in Hamiltosporidium species, therefore reducing the effectiveness of natural selection, and allowing their genomic features to be largely shaped by nonadaptive processes.}, }
@article {pmid31824468, year = {2019}, author = {Ipoutcha, T and Tsarmpopoulos, I and Talenton, V and Gaspin, C and Moisan, A and Walker, CA and Brownlie, J and Blanchard, A and Thebault, P and Sirand-Pugnet, P}, title = {Multiple Origins and Specific Evolution of CRISPR/Cas9 Systems in Minimal Bacteria (Mollicutes).}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2701}, pmid = {31824468}, issn = {1664-302X}, abstract = {CRISPR/Cas systems provide adaptive defense mechanisms against invading nucleic acids in prokaryotes. Because of its interest as a genetic tool, the Type II CRISPR/Cas9 system from Streptococcus pyogenes has been extensively studied. It includes the Cas9 endonuclease that is dependent on a dual-guide RNA made of a tracrRNA and a crRNA. Target recognition relies on crRNA annealing and the presence of a protospacer adjacent motif (PAM). Mollicutes are currently the bacteria with the smallest genome in which CRISPR/Cas systems have been reported. Many of them are pathogenic to humans and animals (mycoplasmas and ureaplasmas) or plants (phytoplasmas and some spiroplasmas). A global survey was conducted to identify and compare CRISPR/Cas systems found in the genome of these minimal bacteria. Complete or degraded systems classified as Type II-A and less frequently as Type II-C were found in the genome of 21 out of 52 representative mollicutes species. Phylogenetic reconstructions predicted a common origin of all CRISPR/Cas systems of mycoplasmas and at least two origins were suggested for spiroplasmas systems. Cas9 in mollicutes were structurally related to the S. aureus Cas9 except the PI domain involved in the interaction with the PAM, suggesting various PAM might be recognized by Cas9 of different mollicutes. Structure of the predicted crRNA/tracrRNA hybrids was conserved and showed typical stem-loop structures pairing the Direct Repeat part of crRNAs with the 5' region of tracrRNAs. Most mollicutes crRNA/tracrRNAs showed G + C% significantly higher than the genome, suggesting a selective pressure for maintaining stability of these secondary structures. Examples of CRISPR spacers matching with mollicutes phages were found, including the textbook case of Mycoplasma cynos strain C142 having no prophage sequence but a CRISPR/Cas system with spacers targeting prophage sequences that were found in the genome of another M. cynos strain that is devoid of a CRISPR system. Despite their small genome size, mollicutes have maintained protective means against invading DNAs, including restriction/modification and CRISPR/Cas systems. The apparent lack of CRISPR/Cas systems in several groups of species including main pathogens of humans, ruminants, and plants suggests different evolutionary routes or a lower risk of phage infection in specific ecological niches.}, }
@article {pmid31822981, year = {2020}, author = {Wang, S and Li, S and Du, D and Wang, D and Yan, W}, title = {Conjugative transfer of Megaplasmids pND6-1 and pND6-2 enhancing naphthalene degradation in aqueous environment: characterization and bioaugmentation prospects.}, journal = {Applied microbiology and biotechnology}, volume = {104}, number = {2}, pages = {861-871}, doi = {10.1007/s00253-019-10273-8}, pmid = {31822981}, issn = {1432-0614}, mesh = {Biotransformation ; Conjugation, Genetic ; *Gene Transfer, Horizontal ; Genomic Instability ; Metabolic Engineering/*methods ; Metabolic Networks and Pathways/genetics ; Naphthalenes/*metabolism ; *Plasmids ; Pseudomonas putida/genetics/growth &amp; development/*metabolism ; *Water Microbiology ; Water Pollutants, Chemical/*metabolism ; }, abstract = {INTRODUCTION: Naphthalene catabolic strain Pseudomonas putida ND6 harbors two megaplasmids pND6-1 and pND6-2; naphthalene-degrading associated genes are located on pND6-1, while plasmid pND6-2 possesses potential coding genes for conjugative transfer.<br><br>METHODS: In this study, the recombinant ND6 in which pND6-1 and pND6-2 were labeled with gentamicin and kanamycin-encoding genes, respectively, was constructed to investigate the conjugative transfer behavior of the two plasmids in distinct aqueous matrices.<br><br>RESULTS: The results indicated that both pND6-1 and pND6-2 plasmids could transfer from donor strain ND6 to a recipient strain P. putida KT2440, while the transfer frequency of pND6-2 (1.90&#x2009;&#xd7;&#x2009;10[-&#x2009;2]) was significantly higher than that of pND6-1 (3.12&#x2009;&#xd7;&#x2009;10[-&#x2009;9]). Furthermore, the concomitant transfer of pND6-1 and pND6-2 was confirmed at a lower frequency of 10[-&#x2009;9] colonies per recipient similar with that of pND6-1. The conjugative transfer efficiency was obviously affected by the initial inoculum and the stability of microbes. Moreover, more than 90% of the transconjugants lost the plasmids after 20 generations cultivation without resistance pressure, suggesting the importance of selective pressure to maintain the plasmid stability. Finally, the naphthalene degradation analysis by mixed ND6 and KT2440 revealed that conjugative transfer of catabolic plasmids contributed to the rapid dispersion of the degradation genes on plasmids and enhanced the naphthalene removal.}, }
@article {pmid31818620, year = {2020}, author = {Liu, C and Chen, Y and Li, X and Zhang, Y and Ye, J and Huang, H and Zhu, C}, title = {Temporal effects of repeated application of biogas slurry on soil antibiotic resistance genes and their potential bacterial hosts.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {258}, number = {}, pages = {113652}, doi = {10.1016/j.envpol.2019.113652}, pmid = {31818620}, issn = {1873-6424}, mesh = {Animals ; Bacteria ; *Biofuels ; Drug Resistance, Microbial/*genetics ; *Genes, Bacterial ; Manure ; Soil ; *Soil Microbiology ; }, abstract = {Biogas slurry, a liquid end product of animal manure fermentation, is widely used as fertilizer in crop fields. Land application may introduce antibiotics and related resistance genes from livestock production into agricultural soil. Nevertheless, changes in antimicrobial resistance in soil where biogas slurry has been repeatedly applied are not fully understood. In the present study, 13 veterinary antibiotics were analyzed in soils that were repeatedly sprayed with biogas slurry, and simultaneously, temporal changes in antibiotic resistance genes (ARGs) and bacterial community composition were investigated using a real-time quantitative PCR assay and MiSeq sequencing. Long-term repeated application of biogas slurry did not result in excessive accumulation of antibiotic residuals in the soil but increased the abundance of ARGs and facilitated ARG transfer among potential hosts. Although the quantitative PCR assay showed a decreasing trend for the relative abundance of ARGs over time, a relevance network analysis revealed highly complex bacteria-ARG co-occurrence after long-term application, which implied that repeated application might intensify horizontal gene transfer (HGT) of ARGs among different bacterial hosts in soil. The increased relative abundance of the intl1 gene supported the shift in ARG-bacteria co-occurrence. Furthermore, ordination analysis showed that the distributions of antibiotic resistance bacteria (ARB) and ARGs were closely related to application duration than to the influence of antibiotic residuals in the biogas slurry-treated soil environment. Additionally, natural level of ARG abundance in untreated soils indirectly suggested the presence/absence of antibiotics was not a key determinant causing the spread of antimicrobial resistance. This study provides improved insight into the effects of long-term repeated application of biogas slurry on the shift in ARG abundances and bacteria-ARG co-occurrence in soils, highlighting the need to focus on the influence of changed soil environment on the ARG transfer.}, }
@article {pmid31818598, year = {2020}, author = {Nguyen, BT and Chen, QL and He, JZ and Hu, HW}, title = {Microbial regulation of natural antibiotic resistance: Understanding the protist-bacteria interactions for evolution of soil resistome.}, journal = {The Science of the total environment}, volume = {705}, number = {}, pages = {135882}, doi = {10.1016/j.scitotenv.2019.135882}, pmid = {31818598}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents ; Bacteria ; Drug Resistance, Microbial ; Genes, Bacterial ; Humans ; *Soil ; Soil Microbiology ; }, abstract = {The emergence, evolution and spread of antibiotic resistance genes (ARGs) in the environment represent a global threat to human health. Our knowledge of antibiotic resistance in human-impacted ecosystems is rapidly growing with antibiotic use, organic fertilization and wastewater irrigation identified as key selection pressures. However, the importance of biological interactions, especially predation and competition, as a potential driver of antibiotic resistance in the natural environment with limited anthropogenic disturbance remains largely overlooked. Stress-affected bacteria develop resistance to maximize competition and survival, and similarly bacteria may develop resistance to fight stress under the predation pressure of protists, an essential component of the soil microbiome. In this article, we summarized the major findings for the prevalence of natural ARGs on our planet and discussed the potential selection pressures driving the evolution and development of antibiotic resistance in natural settings. This is the first article that reviewed the potential links between protists and the antibiotic resistance of bacteria, and highlighted the importance of predation by protists as a crucial selection pressure of antibiotic resistance in the absence of anthropogenic disturbance. We conclude that an improved ecological understanding of the protists-bacteria interactions and other biological relationships would greatly expand our ability to predict and mitigate the environmental antibiotic resistance under the context of global change.}, }
@article {pmid31818316, year = {2019}, author = {Zeng, Q and Liao, C and Terhune, J and Wang, L}, title = {Impacts of florfenicol on the microbiota landscape and resistome as revealed by metagenomic analysis.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {155}, pmid = {31818316}, issn = {2049-2618}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Aquaculture ; Drug Resistance, Bacterial/*genetics ; Fish Diseases/*microbiology ; Fresh Water ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/genetics ; Ictaluridae/*microbiology ; Microbiota/*drug effects/genetics ; Sepsis/*veterinary ; Thiamphenicol/*analogs &amp; derivatives/pharmacology ; }, abstract = {BACKGROUND: Drug-resistant fish pathogens can cause significant economic loss to fish farmers. Since 2012, florfenicol has become an approved drug for treating both septicemia and columnaris diseases in freshwater fish. Due to the limited drug options available for aquaculture, the impact of the therapeutical florfenicol treatment on the microbiota landscape as well as the resistome present in the aquaculture farm environment needs to be evaluated.<br><br>RESULTS: Time-series metagenomic analyses were conducted to the aquatic microbiota present in the tank-based catfish production systems, in which catfish received standard therapeutic 10-day florfenicol treatment following the federal veterinary regulations. Results showed that the florfenicol treatment shifted the structure of the microbiota and reduced the biodiversity of it by acting as a strong stressor. Planctomycetes, Chloroflexi, and 13 other phyla were susceptible to the florfenicol treatment and their abundance was inhibited by the treatment. In contrast, the abundance of several bacteria belonging to the Proteobacteria, Bacteroidetes, Actinobacteria, and Verrucomicrobia phyla increased. These bacteria with increased abundance either harbor florfenicol-resistant genes (FRGs) or had beneficial mutations. The florfenicol treatment promoted the proliferation of florfenicol-resistant genes. The copy number of phenicol-specific resistance genes as well as multiple classes of antibiotic-resistant genes (ARGs) exhibited strong correlations across different genetic exchange communities (p&#x2009;<&#x2009;0.05), indicating the horizontal transfer of florfenicol-resistant genes among these bacterial species or genera. Florfenicol treatment also induced mutation-driven resistance. Significant changes in single-nucleotide polymorphism (SNP) allele frequencies were observed in membrane transporters, genes involved in recombination, and in genes with primary functions of a resistance phenotype.<br><br>CONCLUSIONS: The therapeutical level of florfenicol treatment significantly altered the microbiome and resistome present in catfish tanks. Both intra-population and inter-population horizontal ARG transfer was observed, with the intra-population transfer being more common. The oxazolidinone/phenicol-resistant gene optrA was the most prevalent transferred ARG. In addition to horizontal gene transfer, bacteria could also acquire florfenicol resistance by regulating the innate efflux systems via mutations. The observations made by this study are of great importance for guiding the strategic use of florfenicol, thus preventing the formation, persistence, and spreading of florfenicol-resistant bacteria and resistance genes in aquaculture.}, }
@article {pmid31812729, year = {2020}, author = {Cordeiro, NF and Iriarte, A and Yim, L and Betancor, L and Chabalgoity, JA and Camou, T and Vignoli, R}, title = {Plasmidome of a multiresistant Salmonella enterica serovar Typhimurium isolate from Uruguay.}, journal = {Journal of global antimicrobial resistance}, volume = {20}, number = {}, pages = {84-86}, doi = {10.1016/j.jgar.2019.11.019}, pmid = {31812729}, issn = {2213-7173}, mesh = {Bacterial Proteins/genetics ; Computational Biology/methods ; *Drug Resistance, Multiple, Bacterial ; Gene Transfer, Horizontal ; HIV Infections/*microbiology ; Humans ; Plasmids/*genetics ; Salmonella typhimurium/classification/*genetics/isolation &amp; purification ; Uruguay ; }, }
@article {pmid31810981, year = {2020}, author = {Desiderato, A and Barbeitos, M and Gilbert, C and Da Lage, JL}, title = {Horizontal Transfer and Gene Loss Shaped the Evolution of Alpha-Amylases in Bilaterians.}, journal = {G3 (Bethesda, Md.)}, volume = {10}, number = {2}, pages = {709-719}, pmid = {31810981}, issn = {2160-1836}, mesh = {Basidiomycota/*genetics/metabolism ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Fungal ; Introns ; Phylogeny ; *Transformation, Genetic ; alpha-Amylases/*genetics ; }, abstract = {The subfamily GH13_1 of alpha-amylases is typical of Fungi, but it is also found in some unicellular eukaryotes (e.g., Amoebozoa, choanoflagellates) and non-bilaterian Metazoa. Since a previous study in 2007, GH13_1 amylases were considered ancestral to the Unikonts, including animals, except Bilateria, such that it was thought to have been lost in the ancestor of this clade. The only alpha-amylases known to be present in Bilateria so far belong to the GH13_15 and 24 subfamilies (commonly called bilaterian alpha-amylases) and were likely acquired by horizontal transfer from a proteobacterium. The taxonomic scope of Eukaryota genomes in databases has been greatly increased ever since 2007. We have surveyed GH13_1 sequences in recent data from ca. 1600 bilaterian species, 60 non-bilaterian animals and also in unicellular eukaryotes. As expected, we found a number of those sequences in non-bilaterians: Anthozoa (Cnidaria) and in sponges, confirming the previous observations, but none in jellyfishes and in Ctenophora. Our main and unexpected finding is that such fungal (also called Dictyo-type) amylases were also consistently retrieved in several bilaterian phyla: hemichordates (deuterostomes), brachiopods and related phyla, some molluscs and some annelids (protostomes). We discuss evolutionary hypotheses possibly explaining the scattered distribution of GH13_1 across bilaterians, namely, the retention of the ancestral gene in those phyla only and/or horizontal transfers from non-bilaterian donors.}, }
@article {pmid31810689, year = {2020}, author = {Cheng, X and Delanka-Pedige, HMK and Munasinghe-Arachchige, SP and Abeysiriwardana-Arachchige, ISA and Smith, GB and Nirmalakhandan, N and Zhang, Y}, title = {Removal of antibiotic resistance genes in an algal-based wastewater treatment system employing Galdieria sulphuraria: A comparative study.}, journal = {The Science of the total environment}, volume = {711}, number = {}, pages = {134435}, pmid = {31810689}, issn = {1879-1026}, support = {SC2 GM130432/GM/NIGMS NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents ; Drug Resistance, Microbial ; Genes, Bacterial ; Waste Disposal, Fluid ; Wastewater/*chemistry ; }, abstract = {In this study, we compared removal of antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs) in two wastewater treatment systems fed with the same primary effluent: a conventional wastewater treatment system (consisting of a trickling filter followed by an activated sludge process) versus an algal-based system, employing an extremophilic alga, Galdieria sulphuraria. Our results demonstrated that the algal system can reduce concentrations of erythromycin- and sulfamethoxazole-resistant bacteria in the effluent more effectively than the conventional treatment system. A decreasing trend of total bacteria and ARGs was observed in both the treatment systems. However, the relative ratio of most ARGs (qnrA, qnrB, qnrS, sul1) and intI1 in the surviving bacteria increased in the conventional system; whereas, the algal system reduced more of the relative abundance of qnrA, qnrS, tetW and intⅠ1 in the surviving bacteria. The role of bacteriophages in horizontal gene transfer (HGT) of ARGs in the two systems was indicated by a positive correlation between ARG absolute abundance in bacteriophage and ARG relative abundance in the bacteria. Four of the five detectable genes (qnrS, tetW, sul1 and intI1) were significantly reduced in the algal system in bacteriophage phase which signified a decrease in phage-mediated ARG transfer in the algal system. Results of this study demonstrate the feasibility of the algal-based wastewater treatment system in decreasing ARGs and ARB and in minimizing the spread of antibiotic resistance to the environment.}, }
@article {pmid31810287, year = {2019}, author = {Mancino, W and Lugli, GA and Sinderen, DV and Ventura, M and Turroni, F}, title = {Mobilome and Resistome Reconstruction from Genomes Belonging to Members of the Bifidobacterium Genus.}, journal = {Microorganisms}, volume = {7}, number = {12}, pages = {}, pmid = {31810287}, issn = {2076-2607}, support = {15/JP-HDHL/3280//Joint Programming Initiative A healthy diet for a healthy life/ ; SFI/12/RC/2273-P1//Irish Government's National Development Plan/ ; SFI/12/RC/2273-P2//SFI through the Irish Government's National Development Plan/ ; }, abstract = {Specific members of the genus Bifidobacterium are among the first colonizers of the human/animal gut, where they act as important intestinal commensals associated with host health. As part of the gut microbiota, bifidobacteria may be exposed to antibiotics, used in particular for intrapartum prophylaxis, especially to prevent Streptococcus infections, or in the very early stages of life after the birth. In the current study, we reconstructed the in silico resistome of the Bifidobacterium genus, analyzing a database composed of 625 bifidobacterial genomes, including partial assembled strains with less than 100 genomic sequences. Furthermore, we screened bifidobacterial genomes for mobile genetic elements, such as transposases and prophage-like elements, in order to investigate the correlation between the bifido-mobilome and the bifido-resistome, also identifying genetic insertion hotspots that appear to be prone to horizontal gene transfer (HGT) events. These insertion hotspots were shown to be widely distributed among analyzed bifidobacterial genomes, and suggest the acquisition of antibiotic resistance genes through HGT events. These data were further corroborated by growth experiments directed to evaluate bacitracin A resistance in Bifidobacterium spp., a property that was predicted by in silico analyses to be part of the HGT-acquired resistome.}, }
@article {pmid31805640, year = {2019}, author = {Chirak, ER and Kimeklis, AK and Karasev, ES and Kopat, VV and Safronova, VI and Belimov, AA and Aksenova, TS and Kabilov, MR and Provorov, NA and Andronov, EE}, title = {Search for Ancestral Features in Genomes of Rhizobium leguminosarum bv. viciae Strains Isolated from the Relict Legume Vavilovia formosa.}, journal = {Genes}, volume = {10}, number = {12}, pages = {}, pmid = {31805640}, issn = {2073-4425}, mesh = {Bacterial Proteins/genetics ; DNA, Bacterial/*genetics ; *Evolution, Molecular ; Fabaceae/*microbiology ; *Genes, Bacterial ; Rhizobium leguminosarum/*genetics/isolation &amp; purification ; Species Specificity ; Symbiosis/*genetics ; }, abstract = {Vavilovia formosa is a relict leguminous plant growing in hard-to-reach habitats in the rocky highlands of the Caucasus and Middle East, and it is considered as the putative closest living relative of the last common ancestor (LCA) of the Fabeae tribe. Symbionts of Vavilovia belonging to Rhizobium leguminosarum bv. viciae compose a discrete group that differs from the other strains, especially in the nucleotide sequences of the symbiotically specialised (sym) genes. Comparison of the genomes of Vavilovia strains with the reference group composed of R. leguminosarum bv. viciae strains isolated from Pisum and Vicia demonstrated that the vavilovia strains have a set of genomic features, probably indicating the important stages of microevolution of the symbiotic system. Specifically, symbionts of Vavilovia (considered as an ancestral group) demonstrated a scattered arrangement of sym genes (>90 kb cluster on pSym), with the location of nodT gene outside of the other nod operons, the presence of nodX and fixW, and the absence of chromosomal fixNOPQ copies. In contrast, the reference (derived) group harboured sym genes as a compact cluster (<60 kb) on a single pSym, lacking nodX and fixW, with nodT between nodN and nodO, and possessing chromosomal fixNOPQ copies. The TOM strain, obtained from nodules of the primitive "Afghan" peas, occupied an intermediate position because it has the chromosomal fixNOPQ copy, while the other features, the most important of which is presence of nodX and fixW, were similar to the Vavilovia strains. We suggest that genome evolution from the ancestral to the derived R. leguminosarum bv. viciae groups follows the "gain-and-loss of sym genes" and the "compaction of sym cluster" strategies, which are common for the macro-evolutionary and micro-evolutionary processes. The revealed genomic features are in concordance with a relict status of the vavilovia strains, indicating that V. formosa coexists with ancestral microsymbionts, which are presumably close to the LCA of R. leguminosarum bv. viciae.}, }
@article {pmid31799257, year = {2019}, author = {Peñil-Celis, A and Garcillán-Barcia, MP}, title = {Crosstalk Between Type VI Secretion System and Mobile Genetic Elements.}, journal = {Frontiers in molecular biosciences}, volume = {6}, number = {}, pages = {126}, pmid = {31799257}, issn = {2296-889X}, abstract = {Many bacterial processes require cell-cell contacts. Such are the cases of bacterial conjugation, one of the main horizontal gene transfer mechanisms that physically spreads DNA, and the type VI secretion systems (T6SSs), which deploy antibacterial activity. Bacteria depend on conjugation to adapt to changing environments, while T6SS killing activity could pose a threat to mating partners. Here we review the experimental evidences of overlapping and interaction between the T6SSs, bacterial conjugation, and conjugative genetic elements.}, }
@article {pmid31797948, year = {2019}, author = {Hasni, I and Chelkha, N and Baptiste, E and Mameri, MR and Lachuer, J and Plasson, F and Colson, P and La Scola, B}, title = {Investigation of potential pathogenicity of Willaertia magna by investigating the transfer of bacteria pathogenicity genes into its genome.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {18318}, pmid = {31797948}, issn = {2045-2322}, mesh = {Animals ; Cell Line ; Chlorocebus aethiops ; Disinfectants/*pharmacology ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Legionella pneumophila/drug effects ; Legionellosis/prevention &amp; control ; *Schizopyrenida/genetics/pathogenicity ; Vero Cells ; Virulence Factors/*genetics ; Water Purification ; Water Quality ; Waterborne Diseases/prevention &amp; control ; }, abstract = {Willaertia magna c2c maky is a thermophilic amoeba closely related to the genus Naegleria. This free-living amoeba has the ability to eliminate Legionella pneumophila, which is an amoeba-resisting bacterium living in an aquatic environment. To prevent the proliferation of L. pneumophila in cooling towers, the use of W. magna as natural biocide has been proposed. To provide a better understanding of the W. magna genome, whole-genome sequencing was performed through the study of virulence factors and lateral gene transfers. This amoeba harbors a genome of 36.5 megabases with 18,519 predicted genes. BLASTp analyses reported protein homology between 136 W. magna sequences and amoeba-resistant microorganisms. Horizontal gene transfers were observed based on the basis of the phylogenetic reconstruction hypothesis. We detected 15 homologs of N. fowleri genes related to virulence, although these latter were also found in the genome of N. gruberi, which is a non-pathogenic amoeba. Furthermore, the cytotoxicity test performed on human cells supports the hypothesis that the strain c2c maky is a non-pathogenic amoeba. This work explores the genomic repertory for the first draft genome of genus Willaertia and provides genomic data for further comparative studies on virulence of related pathogenic amoeba, N. fowleri.}, }
@article {pmid31795918, year = {2019}, author = {Qin, L and Erkelens, AM and Ben Bdira, F and Dame, RT}, title = {The architects of bacterial DNA bridges: a structurally and functionally conserved family of proteins.}, journal = {Open biology}, volume = {9}, number = {12}, pages = {190223}, pmid = {31795918}, issn = {2046-2441}, mesh = {Bacteria/*genetics/metabolism ; Bacterial Proteins/*chemistry/metabolism ; Chromatin/genetics/metabolism ; DNA, Bacterial/*chemistry ; DNA-Binding Proteins/chemistry/metabolism ; Gene Transfer, Horizontal ; Models, Molecular ; Nucleic Acid Conformation ; Protein Binding ; Protein Conformation ; Protein Interaction Domains and Motifs ; Structure-Activity Relationship ; }, abstract = {Every organism across the tree of life compacts and organizes its genome with architectural chromatin proteins. While eukaryotes and archaea express histone proteins, the organization of bacterial chromosomes is dependent on nucleoid-associated proteins. In Escherichia coli and other proteobacteria, the histone-like nucleoid structuring protein (H-NS) acts as a global genome organizer and gene regulator. Functional analogues of H-NS have been found in other bacterial species: MvaT in Pseudomonas species, Lsr2 in actinomycetes and Rok in Bacillus species. These proteins complement hns[-] phenotypes and have similar DNA-binding properties, despite their lack of sequence homology. In this review, we focus on the structural and functional characteristics of these four architectural proteins. They are able to bridge DNA duplexes, which is key to genome compaction, gene regulation and their response to changing conditions in the environment. Structurally the domain organization and charge distribution of these proteins are conserved, which we suggest is at the basis of their conserved environment responsive behaviour. These observations could be used to find and validate new members of this protein family and to predict their response to environmental changes.}, }
@article {pmid31791228, year = {2019}, author = {Salazar, AN and Gorter de Vries, AR and van den Broek, M and Brouwers, N and de la Torre Cortès, P and Kuijpers, NGA and Daran, JG and Abeel, T}, title = {Chromosome level assembly and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {916}, pmid = {31791228}, issn = {1471-2164}, mesh = {Beer ; Chromosomes, Fungal ; *Genome, Fungal ; Haploidy ; High-Throughput Nucleotide Sequencing ; Hybridization, Genetic ; Nanopore Sequencing ; Saccharomyces/*genetics ; Saccharomyces cerevisiae/*genetics ; }, abstract = {BACKGROUND: The lager brewing yeast, S. pastorianus, is a hybrid between S. cerevisiae and S. eubayanus with extensive chromosome aneuploidy. S. pastorianus is subdivided into Group 1 and Group 2 strains, where Group 2 strains have higher copy number and a larger degree of heterozygosity for S. cerevisiae chromosomes. As a result, Group 2 strains were hypothesized to have emerged from a hybridization event distinct from Group 1 strains. Current genome assemblies of S. pastorianus strains are incomplete and highly fragmented, limiting our ability to investigate their evolutionary history.<br><br>RESULTS: To fill this gap, we generated a chromosome-level genome assembly of the S. pastorianus strain CBS 1483 from Oxford Nanopore MinION DNA sequencing data and analysed the newly assembled subtelomeric regions and chromosome heterozygosity. To analyse the evolutionary history of S. pastorianus strains, we developed Alpaca: a method to compute sequence similarity between genomes without assuming linear evolution. Alpaca revealed high similarities between the S. cerevisiae subgenomes of Group 1 and 2 strains, and marked differences from sequenced S. cerevisiae strains.<br><br>CONCLUSIONS: Our findings suggest that Group 1 and Group 2 strains originated from a single hybridization involving a heterozygous S. cerevisiae strain, followed by different evolutionary trajectories. The clear differences between both groups may originate from a severe population bottleneck caused by the isolation of the first pure cultures. Alpaca provides a computationally inexpensive method to analyse evolutionary relationships while considering non-linear evolution such as horizontal gene transfer and sexual reproduction, providing a complementary viewpoint beyond traditional phylogenetic approaches.}, }
@article {pmid31788034, year = {2019}, author = {Southworth, J and Grace, CA and Marron, AO and Fatima, N and Carr, M}, title = {A genomic survey of transposable elements in the choanoflagellate Salpingoeca rosetta reveals selection on codon usage.}, journal = {Mobile DNA}, volume = {10}, number = {}, pages = {44}, pmid = {31788034}, issn = {1759-8753}, abstract = {BACKGROUND: Unicellular species make up the majority of eukaryotic diversity, however most studies on transposable elements (TEs) have centred on multicellular host species. Such studies may have therefore provided a limited picture of how transposable elements evolve across eukaryotes. The choanoflagellates, as the sister group to Metazoa, are an important study group for investigating unicellular to multicellular transitions. A previous survey of the choanoflagellate Monosiga brevicollis revealed the presence of only three families of LTR retrotransposons, all of which appeared to be active. Salpingoeca rosetta is the second choanoflagellate to have its whole genome sequenced and provides further insight into the evolution and population biology of transposable elements in the closest relative of metazoans.<br><br>RESULTS: Screening the genome revealed the presence of a minimum of 20 TE families. Seven of the annotated families are DNA transposons and the remaining 13 families are LTR retrotransposons. Evidence for two putative non-LTR retrotransposons was also uncovered, but full-length sequences could not be determined. Superfamily phylogenetic trees indicate that vertical inheritance and, in the case of one family, horizontal transfer have been involved in the evolution of the choanoflagellates TEs. Phylogenetic analyses of individual families highlight recent element activity in the genome, however six families did not show evidence of current transposition. The majority of families possess young insertions and the expression levels of TE genes vary by four orders of magnitude across families. In contrast to previous studies on TEs, the families present in S. rosetta show the signature of selection on codon usage, with families favouring codons that are adapted to the host translational machinery. Selection is stronger in LTR retrotransposons than DNA transposons, with highly expressed families showing stronger codon usage bias. Mutation pressure towards guanosine and cytosine also appears to contribute to TE codon usage.<br><br>CONCLUSIONS: S. rosetta increases the known diversity of choanoflagellate TEs and the complement further highlights the role of horizontal gene transfer from prey species in choanoflagellate genome evolution. Unlike previously studied TEs, the S. rosetta families show evidence for selection on their codon usage, which is shown to act via translational efficiency and translational accuracy.}, }
@article {pmid31784663, year = {2019}, author = {Caneschi, WL and Sanchez, AB and Felestrino, &#xc9;B and Lemes, CGC and Cordeiro, IF and Fonseca, NP and Villa, MM and Vieira, IT and Moraes, L&#xc2;G and Assis, RAB and do Carmo, FF and Kamino, LHY and Silva, RS and Ferro, JA and Ferro, MIT and Ferreira, RM and Santos, VL and Silva, UCM and Almeida, NF and Varani, AM and Garcia, CCM and Setubal, JC and Moreira, LM}, title = {Serratia liquefaciens FG3 isolated from a metallophyte plant sheds light on the evolution and mechanisms of adaptive traits in extreme environments.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {18006}, pmid = {31784663}, issn = {2045-2322}, mesh = {Acclimatization/*genetics ; *Biological Evolution ; Brazil ; Extreme Environments ; Extremophiles/*genetics/isolation &amp; purification ; Flowers/microbiology ; Genes, Bacterial ; Genomic Islands ; Genomics ; Lamiales/*microbiology ; Phylogeny ; Plasmids/genetics ; Serratia liquefaciens/*genetics/isolation &amp; purification ; }, abstract = {Serratia liquefaciens strain FG3 (SlFG3), isolated from the flower of Stachytarpheta glabra in the Brazilian ferruginous fields, has distinctive genomic, adaptive, and biotechnological potential. Herein, using a combination of genomics and molecular approaches, we unlocked the evolution of the adaptive traits acquired by S1FG3, which exhibits the second largest chromosome containing the largest conjugative plasmids described for Serratia. Comparative analysis revealed the presence of 18 genomic islands and 311 unique protein families involved in distinct adaptive features. S1FG3 has a diversified repertoire of genes associated with Nonribosomal peptides (NRPs/PKS), a complete and functional cluster related to cellulose synthesis, and an extensive and functional repertoire of oxidative metabolism genes. In addition, S1FG3 possesses a complete pathway related to protocatecuate and chloroaromatic degradation, and a complete repertoire of genes related to DNA repair and protection that includes mechanisms related to UV light tolerance, redox process resistance, and a laterally acquired capacity to protect DNA using phosphorothioation. These findings summarize that SlFG3 is well-adapted to different biotic and abiotic stress situations imposed by extreme conditions associated with ferruginous fields, unlocking the impact of the lateral gene transfer to adjust the genome for extreme environments, and providing insight into the evolution of prokaryotes.}, }
@article {pmid31783256, year = {2020}, author = {Lu, J and Wang, Y and Jin, M and Yuan, Z and Bond, P and Guo, J}, title = {Both silver ions and silver nanoparticles facilitate the horizontal transfer of plasmid-mediated antibiotic resistance genes.}, journal = {Water research}, volume = {169}, number = {}, pages = {115229}, doi = {10.1016/j.watres.2019.115229}, pmid = {31783256}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents ; Drug Resistance, Microbial ; *Escherichia coli K12 ; Gene Transfer, Horizontal ; Humans ; Ions ; *Metal Nanoparticles ; Plasmids ; Proteomics ; Silver ; }, abstract = {Antibiotic resistance in bacteria is a growing threat to global human health. Horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) is recognized as the primary contributor to antibiotic resistance dissemination. Silver nanoparticles (AgNPs) are widely used in personal care products as antimicrobial agents. While heavy metals are known to induce antibiotic resistance in bacteria, it is not known whether AgNPs in the environment can stimulate the HGT of ARGs. Here, we report that both AgNPs and ionic silver Ag[+], at environmentally relevant and sub-lethal concentrations, facilitate the conjugative transfer of plasmid-borne ARGs across bacterial genera (from the donor Escherichia coli K-12 LE392 to the recipient Pseudomonas putida KT2440). The underlying mechanisms of the Ag[+]- or AgNPs-promoted HGT were unveiled by detecting oxidative stress and cell membrane permeability, combined with genome-wide RNA sequencing and proteomic analyses. It was found that both Ag[+] and AgNPs exposure induced various bacterial responses that included reactive oxygen species (ROS) generation, membrane damage and the SOS response. This study exposes the potential ecological risks of environmental levels of AgNPs and Ag[+] for promoting the spread of ARGs and highlights concerns regarding the management of nanoparticles and heavy metals.}, }
@article {pmid31781082, year = {2019}, author = {Cameron, A and Zaheer, R and McAllister, TA}, title = {Emerging Variants of the Integrative and Conjugant Element ICEMh1 in Livestock Pathogens: Structural Insights, Potential Host Range, and Implications for Bacterial Fitness and Antimicrobial Therapy.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2608}, pmid = {31781082}, issn = {1664-302X}, abstract = {Horizontal gene transfer of integrative and conjugative elements (ICE) in bacterial pathogens of the bovine respiratory disease (BRD) complex has emerged as a significant cause of antimicrobial resistance (AMR) and therapeutic failure and mortalities in cattle. The aim of this study was to assess an AMR ICE occurring in Pasteurella multocida from a case of BRD, designated ICEMh1 [PM22] for its structure and host genome insertion site, and to identify consequences for host fitness and antimicrobial therapy. The modular structure of ICEMh1-like elements found in several related livestock pathogens was compared to ICEMh1 [PM22], and the repertoire of cargo genes in variable ICE modules was functionally categorized. AMR genes were identified as frequent additions to the variable modules of ICEMh1-like elements. Random PCR-based mapping of ICEMh1 [PM22]-genome junctions in transconjugants provided evidence that ICEMh1 [PM22] integrates into the tRNA-leu for the UUG codon, and not into tRNA-leu for other codons. This was separately confirmed in the genomes of ICEMh1-like-harboring livestock pathogens. Bacterial genera harboring receptive tRNA-leu[UUG] were identified to establish the potential host range of ICEMh1-like elements. ICEMh1 [PM22]-carrying transconjugants in P. multocida and Mannheimia haemolytica were less fit than isogenic strains without the ICE when grown without antimicrobial selection. This fitness cost was abrogated in the presence of subinhibitory concentrations of antimicrobials. Despite this cost, ICEMh1 [PM22] was retained in transconjugants in extended culture. To identify possible therapeutic efficiencies, antimicrobial combinations were screened for synergistic interactions against AMR ICEMh1 [PM22]-carrying transconjugants. No antimicrobial combination tested exhibited synergistic interactions against AMR P. multocida or M. haemolytica harboring ICEMh1 [PM22]. In conclusion, this study provided information on the structural variation of ICEMh1-like elements, refined the ICE insertion site and potential host range, and demonstrated the risk and consequences for AMR following horizontal transfer of ICE into BRD pathogens.}, }
@article {pmid31781067, year = {2019}, author = {Garcillán-Barcia, MP and Cuartas-Lanza, R and Cuevas, A and de la Cruz, F}, title = {Cis-Acting Relaxases Guarantee Independent Mobilization of MOBQ 4 Plasmids.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2557}, pmid = {31781067}, issn = {1664-302X}, abstract = {Plasmids are key vehicles of horizontal gene transfer and contribute greatly to bacterial genome plasticity. In this work, we studied a group of plasmids from enterobacteria that encode phylogenetically related mobilization functions that populate the previously non-described MOBQ 4 relaxase family. These plasmids encode two transfer genes: mobA coding for the MOBQ 4 relaxase; and mobC, which is non-essential but enhances the plasmid mobilization frequency. The origin of transfer is located between these two divergently transcribed mob genes. We found that MPFI conjugative plasmids were the most efficient helpers for MOBQ 4 conjugative dissemination among clinically relevant enterobacteria. While highly similar in their mobilization module, two sub-groups with unrelated replicons (Rep_3 and ColE2) can be distinguished in this plasmid family. These subgroups can stably coexist (are compatible) and transfer independently, despite origin-of-transfer cross-recognition by their relaxases. Specific discrimination among their highly similar oriT sequences is guaranteed by the preferential cis activity of the MOBQ 4 relaxases. Such a strategy would be biologically relevant in a scenario of co-residence of non-divergent elements to favor self-dissemination.}, }
@article {pmid31780956, year = {2019}, author = {Ding, BY and Niu, J and Shang, F and Yang, L and Chang, TY and Wang, JJ}, title = {Characterization of the Geranylgeranyl Diphosphate Synthase Gene in Acyrthosiphon pisum (Hemiptera: Aphididae) and Its Association With Carotenoid Biosynthesis.}, journal = {Frontiers in physiology}, volume = {10}, number = {}, pages = {1398}, pmid = {31780956}, issn = {1664-042X}, abstract = {Carotenoids play many crucial roles in organisms. Recently, the de novo synthesis of carotenoids has been reported in pea aphid (Acyrthosiphon pisum) through horizontally transferred genes. However, their upstream pathway in the pea aphid is poorly understood. Geranylgeranyl diphosphate synthase (GGPPS) is the functional enzyme in the synthesis of geranylgeranyl diphosphate (GGPP) which is a precursor for the biosynthesis of many biological metabolites, including carotenoid synthesis. In this study, we performed a series of experiments to characterize GGPPS gene and its association with carotenoid biosynthesis. (1) determining the transcript abundance and carotenoid content in two geographical strain with red and green morphs, and (2) examining the abundance of carotenoid related genes and carotenoid levels after silencing of GGPPS in both red and green morphs. We observed that GGPPS was more highly expressed in the green morph than in the red morph of two strains of the pea aphid. The total level of carotenoids was also higher in green morphs than in red morphs in both strains. In addition to the total carotenoid difference, the carotenoids found in the two morphs also differed. There were α-carotene, β-carotene, and γ-carotene in the green morphs, but three additional carotenoids, including cis-torulene[∗], trans-torulene[∗], and 3,4-didehydrolycopene[∗], were present in the red morphs. Silencing the GGPPS by RNAi in both the red and green morphs decreased the expression of some carotenoid biosynthesis-related genes, including carotenoid synthase/cyclase genes and carotenoid desaturase genes in green morphs. Carotenoid levels were decreased in both green and red morphs. However, the specific carotenoids present were not changed after silencing GGPPS. These results demonstrated that GGPPS may act as the upstream enzyme to influence the synthesis of the total amount of carotenoids. The present study provided important molecular evidence for the conserved roles of GGPPS associated with carotenoids biosynthesis and will enhance further investigation on the mechanisms of carotenoid biosynthesis in pea aphid.}, }
@article {pmid31777397, year = {2019}, author = {Carrillo-Méndez, G and Zermeño-Cervantes, LA and Venancio-Landeros, AA and Díaz, SF and Cardona-Félix, CS}, title = {Natural genetic transformation of Vibrio parahaemolyticus via pVA1 plasmid acquisition as a potential mechanism causing AHPND.}, journal = {Diseases of aquatic organisms}, volume = {137}, number = {1}, pages = {33-40}, doi = {10.3354/dao03420}, pmid = {31777397}, issn = {0177-5103}, mesh = {Animals ; Aquaculture ; Penaeidae ; Plasmids ; Transformation, Genetic ; *Vibrio parahaemolyticus ; }, abstract = {Vibrio parahaemolyticus is the causative bacterium of acute hepatopancreatic necrosis disease (AHPND) in white shrimp Litopenaeus vannamei. This bacterium secretes protein toxins whose genes are encoded in an auto-transmissible plasmid called pVA1. The presence of this plasmid in V. parahaemolyticus is determinant for disease development. Its propagation is not only linked to bacterial colonisation capacity but also to horizontal gene transfer mechanisms. Nevertheless, the active uptake of plasmid, which is known as natural genetic transformation (NGT), has not yet been proposed as a possible acquisition mechanism of the pVA1 plasmid among Vibrio species. Previous studies suggest that some Vibrio species have the ability to undergo NGT in the presence of chitin. Therefore, the objective of this study was to evaluate the induction of NGT mediated by chitin in V. parahaemolyticus (ATCC-17802) through its ability to incorporate and express the pVA1 plasmid. The results showed that a reference strain that does not initially contain the plasmid can incorporate the plasmid under the appropriate transformation conditions, and cause mortality in white shrimp similar to that observed for pathogenic strains isolated from infectious outbreaks. Given the management and conditions of a shrimp farm with large amounts of chitinous exoskeletons, it is feasible that NGT could be a possible acquisition mechanism of plasmid pVA1 among Vibrio species, turning a non-causative strain of V. parahaemolyticus into a causative strain. With this study, we have expanded the knowledge of the pathogenesis process mediated by NGT and the understanding of the possible propagation mechanisms of emerging diseases in the aquaculture sector.}, }
@article {pmid31776415, year = {2019}, author = {Uygur, B and Melikov, K and Arakelyan, A and Margolis, LB and Chernomordik, LV}, title = {Syncytin 1 dependent horizontal transfer of marker genes from retrovirally transduced cells.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {17637}, pmid = {31776415}, issn = {2045-2322}, mesh = {Animals ; Blotting, Western ; Cell Line ; Gene Products, env/*metabolism ; Genetic Markers/genetics ; Green Fluorescent Proteins/genetics ; Humans ; Pregnancy Proteins/*metabolism ; Retroviridae/*genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Transduction, Genetic/*methods ; }, abstract = {Retroviral transduction is routinely used to generate cell lines expressing exogenous non-viral genes. Here, we show that human cells transduced to stably express GFP transfer GFP gene to non-transduced cells. This horizontal gene transfer was mediated by a fraction of extracellular membrane vesicles that were released by the transduced cells. These vesicles carried endogenous retroviral envelope protein syncytin 1 and essentially acted as replication-competent retroviruses. The ability to transfer the GFP gene correlated with the levels of syncytin 1 expression in the transduced cells and depended on the fusogenic activity of this protein, substantiating the hypothesis that endogenous syncytin 1 mediates fusion stage in the delivery of extracellular vesicle cargo into target cells. Our findings suggest that testing for replication-competent retroviruses, a routine safety test for transduced cell products in clinical studies, should be also carried out for cell lines generated by retroviral vectors in in vitro studies.}, }
@article {pmid31775552, year = {2019}, author = {Mohan Raj, JR and Karunasagar, I}, title = {Phages amid antimicrobial resistance.}, journal = {Critical reviews in microbiology}, volume = {45}, number = {5-6}, pages = {701-711}, doi = {10.1080/1040841X.2019.1691973}, pmid = {31775552}, issn = {1549-7828}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/*genetics/virology ; Bacterial Infections/*microbiology/therapy ; Bacteriophages/*genetics/physiology ; *Drug Resistance, Bacterial ; Humans ; Phage Therapy ; Transduction, Genetic ; }, abstract = {Increasing levels of resistance to antimicrobial agents have created chaos in the health sector, with several infections not responding to antibiotic treatments. Search for alternative strategies has looked at bacteriophages as potential therapeutics and in the last couple of years. There are reports of phages being successfully used to treat life-threatening infections. Phages are also mobile elements that exchange genes between and within different bacterial species and account significantly for strain differences across and within a species. A gap in metagenomics analysis and conservative methods of detection have failed to give an accurate account of the role of bacteriophages in antimicrobial resistance. Recent studies have focussed on the role of bacteriophages in the adaptation of pathogens to new hosts and the emergence of multidrug-resistance, which are a significant concern against phage therapy. This article presents a comprehensive account of weighing the odds of phage therapy verses phage-mediated antimicrobial resistance.}, }
@article {pmid31775114, year = {2020}, author = {Liu, Y and Wu, F and Chen, Q and Ying, Y and Jiang, Y and Lu, J and Lin, X and Li, K and Xu, T and Bao, Q and Ni, L}, title = {Comparative genomics analysis of Raoultella planticola S25 isolated from duck in China, with florfenicol resistance.}, journal = {Comparative immunology, microbiology and infectious diseases}, volume = {68}, number = {}, pages = {101398}, doi = {10.1016/j.cimid.2019.101398}, pmid = {31775114}, issn = {1878-1667}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; China ; Cloning, Molecular ; DNA, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Ducks/microbiology ; Enterobacteriaceae/*drug effects/*genetics ; Feces/microbiology ; Gene Transfer, Horizontal ; Genome, Bacterial ; Genomics ; Klebsiella pneumoniae/genetics ; Microbial Sensitivity Tests ; Plasmids/genetics ; Sequence Analysis, DNA ; Thiamphenicol/*analogs &amp; derivatives/pharmacology ; }, abstract = {To characterize the florfenicol resistance gene and analyze the structure of the resistance gene-related sequence of an Raoultella planticola strain S25 isolated from a duck fecal sample from a farm in South China. Molecular cloning was performed to clone the resistance genes such as mdfA, floR and so on, and the minimum inhibitory concentrations (MICs) were quantified to determine the resistance levels generated by the cloned genes and the related strains. Sequencing and comparative genomics methods were used to analyze the structure of the resistance gene-related sequence. The result showed that the genome of R. planticola S25 consists of a 5.47 Mb chromosome encoding 4962 predicted coding sequence (CDS) and a 68,566 bp plasmid, pS25-68, encoding 84 ORFs. The plasmid sharing the greatest sequence identity with the floR-carrying plasmid pS25-68 is plasmid1 in Klebsiella pneumoniae strain blaNDM-1, which was isolated from a patient in Canada. The mdfA1 gene encoded on the chromosome generated resistance to florfenicol in addition to chloramphenicol. Comparative genomic analysis of the floR-related transposon-like fragment of pS25-68 showed that an approximately 3 kb sequence encoding IS91-virD2-floR-lysR was conserved and presented in the majority of the sequences (84.5 %, 169/200) collected from the database. The results of this work demonstrated that horizontal transfer of the florfenicol resistance gene floR occurred widely between the bacteria of different species and with different origins and that additional florfenicol resistance genes may be present in the bacterial population.}, }
@article {pmid31774316, year = {2020}, author = {Racewicz, P and Majewski, M and Madeja, ZE and Łukomska, A and Kubiak, M}, title = {Role of integrons in the proliferation of multiple drug resistance in selected bacteria occurring in poultry production.}, journal = {British poultry science}, volume = {61}, number = {2}, pages = {122-131}, doi = {10.1080/00071668.2019.1697426}, pmid = {31774316}, issn = {1466-1799}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects ; Cell Proliferation ; Chickens ; Drug Resistance, Multiple/drug effects ; Drug Resistance, Multiple, Bacterial/drug effects ; *Integrons ; Microbial Sensitivity Tests/veterinary ; *Poultry ; }, abstract = {1. The increase in microbial resistance, and in particular multiple drug resistance (MDR), is an increasing threat to public health. The uncontrolled use of antibiotics and antibacterial chemotherapeutics in the poultry industry, especially in concentrations too low to cause inhibition, and the occurrence of residues in feed and in the environment play a significant role in the development of resistance among zoonotic food-borne microorganisms.2. Determining the presence and transmission methods of resistance in bacteria is crucial for tracking and preventing antibiotic resistance. Horizontal transfer of genetic elements responsible for drug resistance is considered to be the main mechanism for the spread of antibiotic resistance.3. Of the many well-known genetic elements responsible for horizontal gene transfer, integrons are among the most important factors contributing to multiple drug resistance. The mechanism of bacterial drug resistance acquisition through integrons is one of the essential elements of MDR prevention in animal production.}, }
@article {pmid31771466, year = {2019}, author = {Gerdol, M and Sollitto, M and Pallavicini, A and Castellano, I}, title = {The complex evolutionary history of sulfoxide synthase in ovothiol biosynthesis.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1916}, pages = {20191812}, pmid = {31771466}, issn = {1471-2954}, mesh = {Animals ; Bacteria/enzymology ; *Biological Evolution ; Ergothioneine/biosynthesis/metabolism ; Fungi/enzymology ; Gene Transfer, Horizontal ; Methylhistidines ; Sulfoxides/*metabolism ; }, abstract = {Sulfoxide synthases are enzymes involved in the biosynthesis of small sulfur-containing natural products. Their enzymatic activity represents a unique sulfur transfer strategy in nature that is the insertion of a sulfur atom on the imidazole ring of histidine. To date, only two enzymes are known to carry out this function: the sulfoxide synthase EgtB, involved in the biosynthesis of ergothioneine in fungi and bacteria, and the 5-histidylcysteine sulfoxide synthase OvoA, involved in the biosynthesis of ovothiols, found in the eggs and biological fluids of marine invertebrates, some proteobacteria and protists. In particular, ovothiols, thanks to their unique redox properties, are probably the most intriguing marine sulfur-containing molecules. Although they have long been considered as cellular protective molecules, new evidence suggest that their biological activities and ecological role might be more complex than originally thought. Here, we investigate the evolutionary history of OvoA in Metazoa, reporting its monophyletic ancient origins, which could be traced back to the latest common ancestor of Choanozoa. Nevertheless, we show that OvoA is missing in several major extant taxa and we discuss this patchy distribution in the light of the massive genome reduction events documented in Metazoa. We also highlight two interesting cases of secondary acquisition through horizontal gene transfer, which occurred in hydrozoans and bdelloid rotifers. The evolutionary success of this metabolic pathway is probably ascribable to its role in the maintenance of cellular redox homeostasis, which enables organisms to survive in different environmental niches.}, }
@article {pmid31771223, year = {2019}, author = {Hur, Y and Chalita, M and Ha, SM and Baek, I and Chun, J}, title = {VCGIDB: A Database and Web Resource for the Genomic Islands from Vibrio Cholerae.}, journal = {Pathogens (Basel, Switzerland)}, volume = {8}, number = {4}, pages = {}, pmid = {31771223}, issn = {2076-0817}, support = {918013-04-2-SB010//Ministry of Agriculture, Food and Rural Affairs (MAFRA) of Korea/ ; NRF- 2014M3C9A3063541//Ministry of Science and ICT, South Korea/ ; }, abstract = {Vibrio cholerae is the causative agent of cholera, which is a severe, life-threatening diarrheal disease. The current seventh pandemic has not been eradicated and the outbreak is still ongoing around the world. The evolution of the pandemic-causing strain has been greatly influenced by lateral gene transfer, and the mechanisms of acquisition of pathogenicity in V. cholerae are mainly involved with genomic islands (GIs). Thus, detecting GIs and their comprehensive information is necessary to understand the continuing resurgence and newly emerging pathogenic V. cholerae strains. In this study, 798 V. cholerae strains were tested using the GI-Scanner algorithm, which was developed to detect candidate GIs and identify them in a comparative genomics approach. The algorithm predicted 435 highly possible genomic islands, and we built a database, called Vibrio cholerae Genomic Island Database (VCGIDB). This database shows advanced results that were acquired from a large genome set using phylogeny-based predictions. Moreover, VCGIDB is a highly expendable database that does not require intensive computation, which enables us to update it with a greater number of genomes using a novel genomic island prediction method. The VCGIDB website allows the user to browse the data and presents the results in a visual manner.}, }
@article {pmid31768302, year = {2019}, author = {Cabrera-Contreras, R and Santamaría, RI and Bustos, P and Martínez-Flores, I and Meléndez-Herrada, E and Morelos-Ramírez, R and Barbosa-Amezcua, M and González-Covarrubias, V and Silva-Herzog, E and Soberón, X and González, V}, title = {Genomic diversity of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated from a Children's Hospital in México City in an eight-years survey.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e8068}, pmid = {31768302}, issn = {2167-8359}, abstract = {Staphylococcus epidermidis is a human commensal and pathogen worldwide distributed. In this work, we surveyed for multi-resistant S. epidermidis strains in eight years at a children's health-care unit in México City. Multidrug-resistant S. epidermidis were present in all years of the study, including resistance to methicillin, beta-lactams, fluoroquinolones, and macrolides. To understand the genetic basis of antibiotic resistance and its association with virulence and gene exchange, we sequenced the genomes of 17 S. epidermidis isolates. Whole-genome nucleotide identities between all the pairs of S. epidermidis strains were about 97% to 99%. We inferred a clonal structure and eight Multilocus Sequence Types (MLSTs) in the S. epidermidis sequenced collection. The profile of virulence includes genes involved in biofilm formation and phenol-soluble modulins (PSMs). Half of the S. epidermidis analyzed lacked the ica operon for biofilm formation. Likely, they are commensal S. epidermidis strains but multi-antibiotic resistant. Uneven distribution of insertion sequences, phages, and CRISPR-Cas immunity phage systems suggest frequent horizontal gene transfer. Rates of recombination between S. epidermidis strains were more prevalent than the mutation rate and affected the whole genome. Therefore, the multidrug resistance, independently of the pathogenic traits, might explain the persistence of specific highly adapted S. epidermidis clonal lineages in nosocomial settings.}, }
@article {pmid31767852, year = {2019}, author = {Damke, PP and Di Guilmi, AM and Varela, PF and Velours, C and Marsin, S and Veaute, X and Machouri, M and Gunjal, GV and Rao, DN and Charbonnier, JB and Radicella, JP}, title = {Identification of the periplasmic DNA receptor for natural transformation of Helicobacter pylori.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {5357}, pmid = {31767852}, issn = {2041-1723}, mesh = {Bacterial Proteins/genetics/*metabolism ; Biological Transport ; DNA/genetics/metabolism ; DNA, Bacterial/genetics/*metabolism ; *Gene Transfer, Horizontal ; Helicobacter pylori/genetics/*metabolism ; Periplasm/genetics/*metabolism ; Receptors, Cell Surface/genetics/*metabolism ; *Transformation, Bacterial ; }, abstract = {Horizontal gene transfer through natural transformation is a major driver of antibiotic resistance spreading in many pathogenic bacterial species. In the case of Gram-negative bacteria, and in particular of Helicobacter pylori, the mechanisms underlying the handling of the incoming DNA within the periplasm are poorly understood. Here we identify the protein ComH as the periplasmic receptor for the transforming DNA during natural transformation in H. pylori. ComH is a DNA-binding protein required for the import of DNA into the periplasm. Its C-terminal domain displays strong affinity for double-stranded DNA and is sufficient for the accumulation of DNA in the periplasm, but not for DNA internalisation into the cytoplasm. The N-terminal region of the protein allows the interaction of ComH with a periplasmic domain of the inner-membrane channel ComEC, which is known to mediate the translocation of DNA into the cytoplasm. Our results indicate that ComH is involved in the import of DNA into the periplasm and its delivery to the inner membrane translocator ComEC.}, }
@article {pmid31767779, year = {2020}, author = {Zarrella, TM and Yang, J and Metzger, DW and Bai, G}, title = {Bacterial Second Messenger Cyclic di-AMP Modulates the Competence State in Streptococcus pneumoniae.}, journal = {Journal of bacteriology}, volume = {202}, number = {4}, pages = {}, pmid = {31767779}, issn = {1098-5530}, support = {R01 DC006917/DC/NIDCD NIH HHS/United States ; R01 HL140496/HL/NHLBI NIH HHS/United States ; R35 HL135756/HL/NHLBI NIH HHS/United States ; R56 AI122763/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/physiology ; DNA-Binding Proteins/physiology ; Dinucleoside Phosphates/*physiology ; Glycine/pharmacology ; Hydrogen-Ion Concentration ; Potassium/metabolism ; Second Messenger Systems/*physiology ; Sequence Analysis, RNA ; Streptococcus pneumoniae/genetics/*physiology ; Transcriptome ; }, abstract = {Streptococcus pneumoniae (the pneumococcus) is a naturally competent organism that causes diseases such as pneumonia, otitis media, and bacteremia. The essential bacterial second messenger cyclic di-AMP (c-di-AMP) is an emerging player in the stress responses of many pathogens. In S. pneumoniae, c-di-AMP is produced by a diadenylate cyclase, CdaA, and cleaved by phosphodiesterases Pde1 and Pde2. c-di-AMP binds a transporter of K[+] (Trk) family protein, CabP, which subsequently halts K[+] uptake via the transporter TrkH. Recently, it was reported that Pde1 and Pde2 are essential for pneumococcal virulence in mouse models of disease. To elucidate c-di-AMP-mediated transcription that may lead to changes in pathogenesis, we compared the transcriptomes of wild-type (WT) and Δpde1 Δpde2 strains by transcriptome sequencing (RNA-Seq) analysis. Notably, we found that many competence-associated genes are significantly upregulated in the Δpde1 Δpde2 strain compared to the WT. These genes play a role in DNA uptake, recombination, and autolysis. Competence is induced by a quorum-sensing mechanism initiated by the secreted factor competence-stimulating peptide (CSP). Surprisingly, the Δpde1 Δpde2 strain exhibited reduced transformation efficiency compared to WT bacteria, which was c-di-AMP dependent. Transformation efficiency was also directly related to the [K[+]] in the medium, suggesting a link between c-di-AMP function and the pneumococcal competence state. We found that a strain that possesses a V76G variation in CdaA produced less c-di-AMP and was highly susceptible to CSP. Deletion of cabP and trkH restored the growth of these bacteria in medium with CSP. Overall, our study demonstrates a novel role for c-di-AMP in the competence program of S. pneumoniaeIMPORTANCE Genetic competence in bacteria leads to horizontal gene transfer, which can ultimately affect antibiotic resistance, adaptation to stress conditions, and virulence. While the mechanisms of pneumococcal competence signaling cascades have been well characterized, the molecular mechanism behind competence regulation is not fully understood. The bacterial second messenger c-di-AMP has previously been shown to play a role in bacterial physiology and pathogenesis. In this study, we provide compelling evidence for the interplay between c-di-AMP and the pneumococcal competence state. These findings not only attribute a new biological function to this dinucleotide as a regulator of competence, transformation, and survival under stress conditions in pneumococci but also provide new insights into how pneumococcal competence is modulated.}, }
@article {pmid31767064, year = {2019}, author = {Rohde, J and Rubin, JE and Kulathunga, DGRS and Hill, JE and Habighorst-Blome, K and Hampson, DJ and La, T}, title = {Identification of Brachyspira species by cpn60 universal target sequencing is superior to NADH oxidase gene sequencing.}, journal = {Veterinary microbiology}, volume = {239}, number = {}, pages = {108454}, doi = {10.1016/j.vetmic.2019.108454}, pmid = {31767064}, issn = {1873-2542}, mesh = {Bacterial Typing Techniques/*standards ; Brachyspira/*classification/*genetics ; Genes, Bacterial/*genetics ; Molecular Typing/standards ; Multienzyme Complexes/genetics ; NADH, NADPH Oxidoreductases/genetics ; *Phylogeny ; Species Specificity ; }, abstract = {The pig colon is the habitat of diverse Brachyspira species, of which only a few are of clinical importance. Methods for identification have shifted from phenotypic to molecular testing over the last two decades. Following the emergence of B. hampsonii it became evident that relying on species-specific PCRs carries the risk of overlooking important new species. Consequently, sequencing was proposed as an unbiased alternative for identification of isolates. So far, the main target for identification across species has been the NADH oxidase gene (nox). However, multiple copies of this gene in the genome and potential lateral gene transfer reduce confidence when using this gene. This study compared identification and phylogentic relationship inferred from nox sequencing to that inferred from sequencing of the cpn60 universal target using a collection of 168 isolates from different Brachyspira species. The majority of isolates had an identical identification with both methods. There were a few outliers in the trees with uncertain assignment to a species by BLAST analysis. A few major discrepancies pertained to the pathogenic species B. hampsonii (2), B. pilosicoli (1) and B. suanatina (1). Weakly haemolytic variants of B. hyodysenteriae were assigned to the correct species by both methods. Some of the isolates identified as B. hampsonii also had a weakly haemolytic phenotype.}, }
@article {pmid31764979, year = {2019}, author = {Wang, M and Fu, H and Ruan, R}, title = {A Small Horizontally Transferred Gene Cluster Contributes to the Sporulation of Alternaria alternata.}, journal = {Genome biology and evolution}, volume = {11}, number = {12}, pages = {3436-3444}, pmid = {31764979}, issn = {1759-6653}, mesh = {Alternaria/classification/genetics/*physiology ; Ascomycota/classification/genetics ; Basidiomycota/classification/genetics ; Citrus/microbiology ; Evolution, Molecular ; Fungal Proteins/*genetics/*metabolism ; Gene Deletion ; *Gene Transfer, Horizontal ; *Multigene Family ; Phylogeny ; Plant Diseases/microbiology ; Spores, Fungal/classification/genetics/physiology ; }, abstract = {Horizontal gene transfer (HGT) has been identified as an important source of genomic innovation in fungi. However, how HGT drove the evolution of Alternaria alternata, a necrotrophic fungus which can be ubiquitously isolated from soil and various plants and decaying plant materials is largely known. In this study, we identified 12 protein-encoding genes that are likely acquired from lineages outside Pezizomycotina. Phylogenetic trees and approximately unbiased comparative topology tests strongly supported the evolutionary origin of these genes. According to their predicted functions, these HGT candidates are involved in nitrogen and carbohydrate metabolism. Especially, five genes of them were likely transferred as a physically linked cluster from Tremellales (Basidiomycota). Functionally knocking out the five-gene cluster in an A. alternata isolate causing citrus brown spot resulted in an 80% decrease in asexual spore production in the deletion mutant. We further knocked out each of these five genes in this cluster and the resultant single-gene deletion mutants exhibited a various degree of reduction in spore production. Except for conidiation, functions of these genes associated with vegetative growth, stress tolerance, and virulence are very limited. Our results provide new evidence that HGT has played important roles over the course of the evolution of filamentous fungi.}, }
@article {pmid31762502, year = {2019}, author = {Das, L and Virmani, R and Sharma, V and Rawat, D and Singh, Y}, title = {Human Milk Microbiota: Transferring the Antibiotic Resistome to Infants.}, journal = {Indian journal of microbiology}, volume = {59}, number = {4}, pages = {410-416}, pmid = {31762502}, issn = {0046-8991}, abstract = {Commensal bacterial population is believed to be a reservoir for antibiotic resistance genes (ARGs). The infant gut microbiota has relatively higher abundance of ARGs than the adults. These genes can get transferred from commensals to pathogens by horizontal gene transfer, which magnifies the spectrum of antibiotic resistance in the environment. The presence of ARGs in neo-nates and infants, with no prior antibiotic exposure, questions their origin in the naïve commensal population. Breast milk microbiota that is responsible for the initial seeding of infant gut microbiota has also been found to harbour a vast array of ARGs. This review discusses the recent findings that indicate the potential of breast milk microbiota to act as a vehicle for transmission of ARGs to infants.}, }
@article {pmid31759330, year = {2019}, author = {Schiffer, PH and Danchin, EGJ and Burnell, AM and Creevey, CJ and Wong, S and Dix, I and O'Mahony, G and Culleton, BA and Rancurel, C and Stier, G and Martínez-Salazar, EA and Marconi, A and Trivedi, U and Kroiher, M and Thorne, MAS and Schierenberg, E and Wiehe, T and Blaxter, M}, title = {Signatures of the Evolution of Parthenogenesis and Cryptobiosis in the Genomes of Panagrolaimid Nematodes.}, journal = {iScience}, volume = {21}, number = {}, pages = {587-602}, pmid = {31759330}, issn = {2589-0042}, support = {REI18431/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {Most animal species reproduce sexually and fully parthenogenetic lineages are usually short lived in evolution. Still, parthenogenesis may be advantageous as it avoids the cost of sex and permits colonization by single individuals. Panagrolaimid nematodes have colonized environments ranging from arid deserts to Arctic and Antarctic biomes. Many are obligatory meiotic parthenogens, and most have cryptobiotic abilities, being able to survive repeated cycles of complete desiccation and freezing. To identify systems that may contribute to these striking abilities, we sequenced and compared the genomes and transcriptomes of parthenogenetic and outcrossing panagrolaimid species, including cryptobionts and non-cryptobionts. The parthenogens are triploids, most likely originating through hybridization. Adaptation to cryptobiosis shaped the genomes of panagrolaimid nematodes and is associated with the expansion of gene families and signatures of selection on genes involved in cryptobiosis. All panagrolaimids have acquired genes through horizontal gene transfer, some of which are likely to contribute to cryptobiosis.}, }
@article {pmid31757820, year = {2020}, author = {Cusick, KD and Polson, SW and Duran, G and Hill, RT}, title = {Multiple Megaplasmids Confer Extremely High Levels of Metal Tolerance in Alteromonas Strains.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {3}, pages = {}, pmid = {31757820}, issn = {1098-5336}, support = {P20 GM103446/GM/NIGMS NIH HHS/United States ; }, mesh = {Alteromonas/drug effects/*genetics ; *Drug Tolerance ; Electrophoresis, Gel, Pulsed-Field/*methods ; Metals/*adverse effects ; Plasmids/*physiology ; Whole Genome Sequencing ; }, abstract = {Alteromonas is a widely distributed genus of marine Gammaproteobacteria, with representatives shown to be key players in diverse processes, including biogeochemical cycling and biofouling of marine substrata. While Alteromonas spp. are early colonizers of copper-based antifouling paints on marine vessels, their mechanism of tolerance is poorly understood. PacBio whole-genome sequencing of Alteromonas macleodii strains CUKW and KCC02, isolated from Cu/Ni alloy test coupons submerged in oligotrophic coastal waters, indicated the presence of multiple megaplasmids (ca. 200 kb) in both. A pulsed-field gel electrophoresis method was developed and used to confirm the presence of multiple megaplasmids in these two strains; it was then used to screen additional Alteromonas strains for which little to no sequencing data exist. Plasmids were not detected in any of the other strains. Bioinformatic analysis of the CUKW and KCC02 plasmids identified numerous genes associated with metal resistance. Copper resistance orthologs from both the Escherichia coli Cue and Cus and Pseudomonas syringae Cop systems were present, at times as multiple copies. Metal growth assays in the presence of copper, cobalt, manganese, and zinc performed with 10 Alteromonas strains demonstrated the ability of CUKW and KCC02 to grow at metal concentrations inhibitory to all the other strains tested. This study reports multiple megaplasmids in Alteromonas strains. Bioinformatic analysis of the CUKW and KCC02 plasmids indicate that they harbor elements of the Tra system conjugation apparatus, although their type of mobility remains to be experimentally verified.IMPORTANCE Copper is commonly used as an antifouling agent on ship hulls. Alteromonas spp. are early colonizers of copper-based antifouling paint, but their mechanism of tolerance is poorly understood. Sequencing of A. macleodii strains isolated from copper test materials for marine ships indicated the presence of multiple megaplasmids. Plasmids serve as key vectors in horizontal gene transfer and confer traits such as metal resistance, detoxification, ecological interaction, and antibiotic resistance. Bioinformatic analysis identified many metal resistance genes and genes associated with mobility. Understanding the molecular mechanisms and capacity for gene transfer within marine biofilms provides a platform for the development of novel antifouling solutions targeting genes involved in copper tolerance and biofilm formation.}, }
@article {pmid31756888, year = {2019}, author = {Arizala, D and Arif, M}, title = {Genome-Wide Analyses Revealed Remarkable Heterogeneity in Pathogenicity Determinants, Antimicrobial Compounds, and CRISPR-Cas Systems of Complex Phytopathogenic Genus Pectobacterium.}, journal = {Pathogens (Basel, Switzerland)}, volume = {8}, number = {4}, pages = {}, pmid = {31756888}, issn = {2076-0817}, support = {Hatch project 9038H//National Institute of Food and Agriculture/ ; }, abstract = {The Pectobacterium genus comprises pectolytic enterobacteria defined as the causal agents of soft rot, blackleg, and aerial stem rot diseases of potato and economically important crops. In this study, we undertook extensive genome-wide comparative analyses of twelve species that conform the Pectobacterium genus. Bioinformatics approaches outlined a low nucleotide identity of P. parmentieri and P. wasabiae with other species, while P. carotovorum subsp. odoriferum was shown to harbor numerous pseudogenes, which suggests low coding capacity and genomic degradation. The genome atlases allowed for distinguishing distinct DNA structures and highlighted suspicious high transcription zones. The analyses unveiled a noteworthy heterogeneity in the pathogenicity determinants. Specifically, phytotoxins, polysaccharides, iron uptake systems, and the type secretion systems III-V were observed in just some species. Likewise, a comparison of gene clusters encoding antimicrobial compounds put in evidence for high conservation of carotovoricin, whereas a few species possessed the phenazine, carbapenem, and carocins. Moreover, three clustered regularly interspaced short palindromic repeats-Cas (CRISPR-Cas) systems: I-E, I-F, and III-A were identified. Surrounding some CRISPR-Cas regions, different toxin and antitoxin systems were found, which suggests bacterial suicide in the case of an immune system failure. Multiple whole-genome alignments shed light on to the presence of a novel cellobiose phosphotransferase system (PTS) exclusive to P. parmenteri, and an unreported T5SS conserved in almost all species. Several regions that were associated with virulence, microbe antagonism, and adaptive immune systems were predicted within genomic islands, which underscored the essential role that horizontal gene transfer has imparted in the dynamic evolution and speciation of Pectobacterium species. Overall, the results decipher the different strategies that each species has developed to infect their hosts, outcompete for food resources, and defend against bacteriophages. Our investigation provides novel genetic insights that will assist in understanding the pathogenic lifestyle of Pectobacterium, a genus that jeopardizes the agriculture sustainability of important crops worldwide.}, }
@article {pmid31754824, year = {2020}, author = {Gabashvili, E and Osepashvili, M and Koulouris, S and Ujmajuridze, L and Tskhitishvili, Z and Kotetishvili, M}, title = {Phage Transduction is Involved in the Intergeneric Spread of Antibiotic Resistance-Associated blaCTX-M, mel, and tetM Loci in Natural Populations of Some Human and Animal Bacterial Pathogens.}, journal = {Current microbiology}, volume = {77}, number = {2}, pages = {185-193}, pmid = {31754824}, issn = {1432-0991}, support = {PhDF2016_97//Shota Rustaveli National Science Foundation/ ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/drug effects/*genetics/virology ; Bacteriophages/*genetics ; DNA, Intergenic ; Databases, Genetic ; Drug Resistance, Microbial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Viral ; *Transduction, Genetic ; beta-Lactamases/*genetics ; }, abstract = {The horizontal genetic transfer (HGT) of antibiotic resistance genes (ARGs) mediated by species-specific bacteriophages contributes to the emergence of antibiotic-resistant strains in natural populations of human and animal bacterial pathogens posing a significant threat to global public health. However, it is unclear and needs to be determined whether polyvalent bacteriophages play any role in the intergeneric transmission of ARGs. In this study, we examined the genome sequences of 2239 bacteriophages from different sources for the presence of ARGs. The identified ARG-carrying bacteriophages were then analyzed by PHACTS, PHAST, and HostPhinder programs to determine their lifestyles, genes coding for bacterial cell lysis, recombinases, and a spectrum of their potential host species, respectively. We employed the SplitsTree, RDP4 and SimPlot software packages in recombination tests to identify HGT events of ARGs between these bacteriophages and bacteria. In our analyses, some ARG-carrying bacteriophages exhibited temperate and/or polyvalent patterns. The bootstrap values (97-100) for the SplitsTree-generated parallelograms, fit values (97-100) for splits networks, Phi P values (< 10[-17] to 3.9 × 10[-16]), RDP4 P values (≤ 7.8 × 10[-03]), and the SimPlot results, provided strong statistical evidence for the phage transduction events of blaCTX-M, mel, and tetM loci on inter-species level. These events involved several host species such as Escherichia coli, Salmonella enterica, Shigella sonnei, Streptococcus pneumoniae and Bacillus coagulans. HGT of mel loci between Erysipelothrix and Streptococcus phages were also detected. These results firmly suggest that certain bacteriophages possibly with temperate properties induce the intergeneric dissemination of blaCTX-M, mel and tetM in the above species.}, }
@article {pmid31754114, year = {2019}, author = {Weinstein, DJ and Allen, SE and Lau, MCY and Erasmus, M and Asalone, KC and Walters-Conte, K and Deikus, G and Sebra, R and Borgonie, G and van Heerden, E and Onstott, TC and Bracht, JR}, title = {The genome of a subterrestrial nematode reveals adaptations to heat.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {5268}, pmid = {31754114}, issn = {2041-1723}, support = {K22 CA184297/CA/NCI NIH HHS/United States ; }, mesh = {Adaptation, Physiological/*genetics ; Animals ; Ecosystem ; Gene Expression Regulation ; Gene Ontology ; Gene Transfer, Horizontal ; Genome, Helminth/*genetics ; HSP70 Heat-Shock Proteins/genetics ; *Heat-Shock Response ; Helminth Proteins/genetics ; Nematoda/classification/*genetics ; Phylogeny ; Soil/parasitology ; Stress, Physiological ; Transcriptome ; }, abstract = {The nematode Halicephalobus mephisto was originally discovered inhabiting a deep terrestrial aquifer 1.3 km underground. H. mephisto can thrive under conditions of abiotic stress including heat and minimal oxygen, where it feeds on a community of both chemolithotrophic and heterotrophic prokaryotes in an unusual ecosystem isolated from the surface biosphere. Here we report the comprehensive genome and transcriptome of this organism, identifying a signature of adaptation: an expanded repertoire of 70 kilodalton heat-shock proteins (Hsp70) and avrRpt2 induced gene 1 (AIG1) proteins. The expanded Hsp70 genes are transcriptionally induced upon growth under heat stress, and we find that positive selection is detectable in several members of this family. We further show that AIG1 may have been acquired by horizontal gene transfer (HGT) from a rhizobial fungus. Over one-third of the genes of H. mephisto are novel, highlighting the divergence of this nematode from other sequenced organisms. This work sheds light on the genomic basis of heat tolerance in a complete subterrestrial eukaryotic genome.}, }
@article {pmid31748247, year = {2019}, author = {Feng, C and Wen, P and Xu, H and Chi, X and Li, S and Yu, X and Lin, X and Wu, S and Zheng, B}, title = {Emergence and Comparative Genomics Analysis of Extended-Spectrum-β-Lactamase-Producing Escherichia coli Carrying mcr-1 in Fennec Fox Imported from Sudan to China.}, journal = {mSphere}, volume = {4}, number = {6}, pages = {}, pmid = {31748247}, issn = {2379-5042}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteriological Techniques ; China ; Communicable Diseases, Imported/microbiology/veterinary ; Conjugation, Genetic ; Culture Media/chemistry ; Drug Resistance, Bacterial ; Escherichia coli/*enzymology/*genetics/isolation &amp; purification ; Escherichia coli Infections/microbiology/*veterinary ; Escherichia coli Proteins/*genetics ; Feces/microbiology ; Foxes/*microbiology ; Gene Transfer, Horizontal ; *Genomics ; Genotype ; Plasmids/analysis ; Sequence Analysis, DNA ; Sudan ; beta-Lactamases/*genetics ; }, abstract = {The aim of this study was to investigate the occurrence and genomic characteristics of extended-spectrum-β-lactamase-producing Escherichia coli (ESBL-EC) in fennec fox imported from Sudan to China. We screened 88 fecal samples from fennec fox for ESBL-EC, using cefotaxime- and meropenem-supplemented selective medium. Antimicrobial susceptibility testing was performed by the agar dilution method except for colistin and tigecycline; for colistin and tigecycline, testing was conducted by the broth microdilution method. ESBL-EC bacteria were sequenced, and their genomes were characterized. Plasmid conjugation, S1 nuclease pulsed-field gel electrophoresis (PFGE), and Southern blotting were performed for a MCR-1-producing isolate. The genetic environment of mcr-1 and ESBL genes was also investigated. A total of 29 ESBL-EC bacteria were isolated from 88 fennec fox (32.9%), while no carbapenemase producers were found. The most prevalent genotypes were the blaCTX-M-55 and blaCTX-M-14 genes, followed by blaCTX-M-15 and blaCTX-M-64 We detected nine sequence types among 29 ESBL-EC. Furthermore, the mcr-1 gene was detected in isolate EcFF273. Conjugation analysis confirmed that the mcr-1 gene was transferable. S1 PFGE, Southern blotting, and whole-genome sequencing revealed that mcr-1 and blaCTX-M-64 were both located on a 65-kb IncI2 plasmid. This study reports for the first time the occurrence of ESBL-EC in fennec fox. The high prevalence of ESBL producers and the occurrence of MCR-1 producer in fennec fox imported into China from Sudan are unexpected. In addition, it clearly demonstrated that commensal E. coli strains can be reservoirs of blaCTX-M and mcr-1, potentially contributing to the dissemination and transfer of such genes to pathogenic bacteria among fennec fox. Our results support the implication of fennec fox as a biological vector for ESBL-producing members of the Enterobacteriaceae family.IMPORTANCE The extended-spectrum-β-lactamase (ESBL)-producing members of the Enterobacteriaceae family are a global concern for both animal and human health. There is some information indicating a high prevalence of ESBL producers in food animals. Moreover, there have been an increasing number of reports on ESBL-producing strains resistant to the last-resort antibiotic colistin with the global dissemination of the plasmid-mediated mcr-1 gene, which is believed to have originated in animal breeding. However, little is known regarding the burden of ESBL-producing Enterobacteriaceae on wild animals. No data were available on the prevalence of antimicrobial resistance (AMR) among wild animals imported into China. This is the first study to investigate the microbiological and genomics surveillance investigation of ESBL colonization among fennec fox (Vulpes zerda) imported from Sudan to China, and we uncovered a high prevalence of ESBL-EC. Furthermore, the underlying mechanism of colistin resistance in an isolate that harbored mcr-1 was also investigated. Results of characterization and analysis of 29 ESBL-producing E. coli may have important implications on our understanding of the transmission dynamics of these bacteria. We emphasize the importance of improved multisectoral surveillance for colistin-resistant E. coli in this region.}, }
@article {pmid31747398, year = {2019}, author = {Mackow, NA and Shen, J and Adnan, M and Khan, AS and Fries, BC and Diago-Navarro, E}, title = {CRISPR-Cas influences the acquisition of antibiotic resistance in Klebsiella pneumoniae.}, journal = {PloS one}, volume = {14}, number = {11}, pages = {e0225131}, pmid = {31747398}, issn = {1932-6203}, support = {I01 BX003741/BX/BLRD VA/United States ; R21 AI114259/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/toxicity ; Bacterial Proteins/genetics ; CRISPR-Cas Systems ; Carbapenems/toxicity ; *Drug Resistance, Bacterial ; Klebsiella pneumoniae/drug effects/*genetics/pathogenicity ; beta-Lactamases/genetics ; }, abstract = {In the US Carbapenem resistance in Klebsiella pneumoniae (Kp) is primarily attributed to the presence of the genes blaKPC-2 and blaKPC-3, which are transmitted via plasmids. Carbapenem-resistant Kp (CR-Kp) infections are associated with hospital outbreaks. They are difficult to treat, and associated with high mortality rates prompting studies of how resistance is obtained. In this study, we determined the presence of CRISPR-Cas in 304 clinical Kp strains. The CRISPR-Cas system has been found to prevent the spread of plasmids and bacteriophages, and therefore limits the horizontal gene transfer mediated by these mobile genetic elements. Here, we hypothesized that only those Kp strains that lack CRISPR-Cas can acquire CR plasmids, while those strains that have CRISPR-Cas are protected from gaining these plasmids and thus maintain sensitivity to antimicrobials. Our results show that CRISPR-Cas is absent in most clinical Kp strains including the clinically important ST258 clone. ST258 strains that continue to be sensitive to carbapenems also lack CRISPR-Cas. Interestingly, CRISPR-Cas positive strains, all non-ST258, exhibit lower resistance rates to antimicrobials than CRISPR-Cas negative strains. Importantly, we demonstrate that the presence of CRISPR-Cas appears to inhibit the acquisition of blaKPC plasmids in 7 Kp strains. Furthermore, we show that strains that are unable to acquire blaKPC plasmids contain CRISPR spacer sequences highly identical to those found in previously published multidrug-resistance-containing plasmids. Lastly, to our knowledge this is the first paper demonstrating that resistance to blaKPC plasmid invasion in a CRISPR-containing Kp strain can be reversed by deleting the CRISPR-cas cassette.}, }
@article {pmid31745096, year = {2019}, author = {Chandrasekaran, S and Jiang, SC}, title = {A dose response model for quantifying the infection risk of antibiotic-resistant bacteria.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {17093}, pmid = {31745096}, issn = {2045-2322}, mesh = {Anti-Bacterial Agents/*administration &amp; dosage ; Bacteria/*drug effects/isolation &amp; purification ; Bacterial Infections/*drug therapy/microbiology ; Dose-Response Relationship, Drug ; *Drug Resistance, Bacterial ; Humans ; *Models, Statistical ; }, abstract = {Quantifying the human health risk of microbial infection helps inform regulatory policies concerning pathogens, and the associated public health measures. Estimating the infection risk requires knowledge of the probability of a person being infected by a given quantity of pathogens, and this relationship is modeled using pathogen specific dose response models (DRMs). However, risk quantification for antibiotic-resistant bacteria (ARB) has been hindered by the absence of suitable DRMs for ARB. A new approach to DRMs is introduced to capture ARB and antibiotic-susceptible bacteria (ASB) dynamics as a stochastic simple death (SD) process. By bridging SD with data from bench experiments, we demonstrate methods to (1) account for the effect of antibiotic concentrations and horizontal gene transfer on risk; (2) compute total risk for samples containing multiple bacterial types (e.g., ASB, ARB); and (3) predict if illness is treatable with antibiotics. We present a case study of exposure to a mixed population of Gentamicin-susceptible and resistant Escherichia coli and predict the health outcomes for varying Gentamicin concentrations. Thus, this research establishes a new framework to quantify the risk posed by ARB and antibiotics.}, }
@article {pmid31744234, year = {2019}, author = {Kraeva, N and Leštinová, T and Ishemgulova, A and Majerová, K and Butenko, A and Vaselek, S and Bespyatykh, J and Charyyeva, A and Spitzová, T and Kostygov, AY and Lukeš, J and Volf, P and Votýpka, J and Yurchenko, V}, title = {LmxM.22.0250-Encoded Dual Specificity Protein/Lipid Phosphatase Impairs Leishmania mexicana Virulence In Vitro.}, journal = {Pathogens (Basel, Switzerland)}, volume = {8}, number = {4}, pages = {}, pmid = {31744234}, issn = {2076-0817}, support = {17-10656S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 19-15- 00054//Russian Science Foundation/ ; CZ LL1601/ERC_/European Research Council/International ; CZ.02.1.01/0.0/ 0.0/16_019/0000759//European Regional Development Fund/ ; UNCE 20472//Grantov&#xe1; Agentura, Univerzita Karlova/ ; }, abstract = {Protein phosphorylation/dephosphorylation is an important regulatory mechanism that controls many key physiological processes. Numerous pathogens successfully use kinases and phosphatases to internalize, replicate, and survive, modifying the host's phosphorylation profile or signal transduction pathways. Multiple phosphatases and kinases from diverse bacterial pathogens have been implicated in human infections before. In this work, we have identified and characterized the dual specificity protein/lipid phosphatase LmDUSP1 as a novel virulence factor governing Leishmania mexicana infection. The LmDUSP1-encoding gene (LmxM.22.0250 in L. mexicana) has been acquired from bacteria via horizontal gene transfer. Importantly, its orthologues have been associated with virulence in several bacterial species, such as Mycobacterium tuberculosis and Listeria monocytogenes. Leishmania mexicana with ablated LmxM.22.0250 demonstrated severely attenuated virulence in the experimental infection of primary mouse macrophages, suggesting that this gene facilitates Leishmania pathogenicity in vertebrates. Despite significant upregulation of LmxM.22.0250 expression in metacyclic promastigotes, its ablation did not affect the ability of mutant cells to differentiate into virulent stages in insects. It remains to be further investigated which specific biochemical pathways involve LmDUSP1 and how this facilitates the parasite's survival in the host. One of the interesting possibilities is that LmDUSP1 may target host's substrate(s), thereby affecting its signal transduction pathways.}, }
@article {pmid31744069, year = {2019}, author = {Chien, MF and Ho, YN and Yang, HE and Narita, M and Miyauchi, K and Endo, G and Huang, CC}, title = {Identification of A Novel Arsenic Resistance Transposon Nested in A Mercury Resistance Transposon of Bacillus sp. MB24.}, journal = {Microorganisms}, volume = {7}, number = {11}, pages = {}, pmid = {31744069}, issn = {2076-2607}, support = {19H02654, 18F18393//Japan Society for the Promotion of Science/ ; }, abstract = {A novel TnMERI1-like transposon designated as TnMARS1 was identified from mercury resistant Bacilli isolated from Minamata Bay sediment. Two adjacent ars operon-like gene clusters, ars1 and ars2, flanked by a pair of 78-bp inverted repeat sequences, which resulted in a 13.8-kbp transposon-like fragment, were found to be sandwiched between two transposable genes of the TnMERI1-like transposon of a mercury resistant bacterium, Bacillus sp. MB24. The presence of a single transcription start site in each cluster determined by 5'-RACE suggested that both are operons. Quantitative real time RT-PCR showed that the transcription of the arsR genes contained in each operon was induced by arsenite, while arsR2 responded to arsenite more sensitively and strikingly than arsR1 did. Further, arsenic resistance complementary experiments showed that the ars2 operon conferred arsenate and arsenite resistance to an arsB-knocked out Bacillus host, while the ars1 operon only raised arsenite resistance slightly. This transposon nested in TnMARS1 was designated as TnARS1. Multi-gene cluster blast against bacteria and Bacilli whole genome sequence databases suggested that TnMARS1 is the first case of a TnMERI1-like transposon combined with an arsenic resistance transposon. The findings of this study suggested that TnMERI1-like transposons could recruit other mobile elements into its genetic structure, and subsequently cause horizontal dissemination of both mercury and arsenic resistances among Bacilli in Minamata Bay.}, }
@article {pmid31741007, year = {2020}, author = {Hayek, M and Baraquet, C and Lami, R and Blache, Y and Molmeret, M}, title = {The Marine Bacterium Shewanella woodyi Produces C8-HSL to Regulate Bioluminescence.}, journal = {Microbial ecology}, volume = {79}, number = {4}, pages = {865-881}, doi = {10.1007/s00248-019-01454-z}, pmid = {31741007}, issn = {1432-184X}, mesh = {Homoserine/*analogs &amp; derivatives/biosynthesis ; Lactones ; *Luminescence ; *Quorum Sensing ; Shewanella/*physiology ; }, abstract = {Quorum sensing (QS), a cell-to-cell communication system involved in the synchronization of bacterial behavior in a cell-density-dependent manner has been shown to control phenotypes such as luminescence, virulence, and biofilm formation. The marine strain, Shewanella woodyi MS32 has been identified as a luminous bacterium. Very little information is known on this bacterium, in particular if its luminescence and biofilm formation are controlled by QS. In this study, we have demonstrated that S. woodyi MS32 emits luminescence in planktonic and sessile conditions. The putative QS regulatory genes homologous to luxI and luxR identified in the S. woodyi MS32 genome, named swoI and swoR, are divergently transcribed and are not genetically linked to the lux operon in contrast with its closest parent Shewanella hanedai and with Aliivibrio fischeri. Interestingly, the phylogenetic analysis based on the SwoI and SwoR sequences shows that a separate horizontal gene transfer (HGT) occurred for the regulatory genes and for the lux operon. Functional analyses demonstrate that the swoI and swoR mutants were non-luminescent. Expression of lux genes was impaired in the QS regulatory mutants. N-octanoyl-L-homoserine lactone (C8-HSL) identified using liquid chromatography mass spectrometry in the wild-type strain (but not in ΔswoI) can induce S. woodyi luminescence. No significant difference has been detected between the wild-type and mutants on adhesion and biofilm formation in the conditions tested. Therefore, we have demonstrated that the luxCDABEG genes of S. woodyi MS32 are involved in luminescence emission and that the swoR/swoI genes, originated from a separate HGT, regulate luminescence through C8-HSL production.}, }
@article {pmid31740605, year = {2019}, author = {McKenna, DD and Shin, S and Ahrens, D and Balke, M and Beza-Beza, C and Clarke, DJ and Donath, A and Escalona, HE and Friedrich, F and Letsch, H and Liu, S and Maddison, D and Mayer, C and Misof, B and Murin, PJ and Niehuis, O and Peters, RS and Podsiadlowski, L and Pohl, H and Scully, ED and Yan, EV and Zhou, X and Ślipiński, A and Beutel, RG}, title = {The evolution and genomic basis of beetle diversity.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {49}, pages = {24729-24737}, pmid = {31740605}, issn = {1091-6490}, mesh = {Animals ; Bacteria/enzymology/genetics ; Bacterial Proteins/genetics/metabolism ; *Biodiversity ; *Biological Evolution ; Cell Wall/chemistry/metabolism ; Cellulases/genetics/metabolism ; Coleoptera/enzymology/*genetics/microbiology ; Fungal Proteins/genetics/metabolism ; Fungi/enzymology/genetics ; *Gene Transfer, Horizontal ; *Genome, Insect ; Herbivory/genetics ; Insect Proteins/genetics/metabolism ; Lignin/chemistry/metabolism ; Phylogeny ; Plants/chemistry ; Polysaccharide-Lyases/genetics/metabolism ; Polysaccharides/chemistry/metabolism ; }, abstract = {The order Coleoptera (beetles) is arguably the most speciose group of animals, but the evolutionary history of beetles, including the impacts of plant feeding (herbivory) on beetle diversification, remain poorly understood. We inferred the phylogeny of beetles using 4,818 genes for 146 species, estimated timing and rates of beetle diversification using 89 genes for 521 species representing all major lineages and traced the evolution of beetle genes enabling symbiont-independent digestion of lignocellulose using 154 genomes or transcriptomes. Phylogenomic analyses of these uniquely comprehensive datasets resolved previously controversial beetle relationships, dated the origin of Coleoptera to the Carboniferous, and supported the codiversification of beetles and angiosperms. Moreover, plant cell wall-degrading enzymes (PCWDEs) obtained from bacteria and fungi via horizontal gene transfers may have been key to the Mesozoic diversification of herbivorous beetles-remarkably, both major independent origins of specialized herbivory in beetles coincide with the first appearances of an arsenal of PCWDEs encoded in their genomes. Furthermore, corresponding (Jurassic) diversification rate increases suggest that these novel genes triggered adaptive radiations that resulted in nearly half of all living beetle species. We propose that PCWDEs enabled efficient digestion of plant tissues, including lignocellulose in cell walls, facilitating the evolution of uniquely specialized plant-feeding habits, such as leaf mining and stem and wood boring. Beetle diversity thus appears to have resulted from multiple factors, including low extinction rates over a long evolutionary history, codiversification with angiosperms, and adaptive radiations of specialized herbivorous beetles following convergent horizontal transfers of microbial genes encoding PCWDEs.}, }
@article {pmid31740556, year = {2020}, author = {Chen, M and Zhang, C and Zhang, X and Chen, M}, title = {Meningococcal Quinolone Resistance Originated from Several Commensal Neisseria Species.}, journal = {Antimicrobial agents and chemotherapy}, volume = {64}, number = {2}, pages = {}, pmid = {31740556}, issn = {1098-6596}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; China/epidemiology ; Ciprofloxacin/pharmacology ; DNA Gyrase/genetics ; DNA Topoisomerase IV/genetics ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; Mutation/genetics ; Neisseria/*drug effects/genetics ; Neisseria meningitidis/*drug effects/*genetics ; Phylogeny ; Prevalence ; Quinolones/*pharmacology ; Transformation, Bacterial/genetics ; }, abstract = {Quinolone resistance is increasing in Neisseria meningitidis, with its prevalence in China being high (>70%), but its origin remains unknown. The aim of this study was to investigate the donors of mutation-harboring gyrA alleles in N. meningitidis A total of 198 N. meningitidis isolates and 293 commensal Neisseria isolates were collected between 2005 and 2018 in Shanghai, China. The MICs of ciprofloxacin were determined using the agar dilution method. The resistance-associated genes gyrA and parC were sequenced for all isolates, while a few isolates were sequenced on the Illumina platform. The prevalences of quinolone resistance in the N. meningitidis and commensal Neisseria isolates were 67.7% (134/198) and 99.3% (291/293), respectively. All 134 quinolone-resistant N. meningitidis isolates possessed mutations in T91 (n = 123) and/or D95 (n = 12) of GyrA, with 7 isolates also harboring ParC mutations and exhibiting higher MICs. Phylogenetic analysis of the gyrA sequence identified six clusters. Among the 71 mutation-harboring gyrA alleles found in 221 N. meningitidis isolates and genomes (n = 221), 12 alleles (n = 103, 46.6%) were included in the N. meningitidis cluster, while 20 alleles (n = 56) were included in the N. lactamica cluster, 27 alleles (n = 49) were included in the N. cinerea cluster, and 9 alleles (n = 10) were included in the N. subflava cluster. Genomic analyses identified the exact N. lactamica donors of seven mutation-harboring gyrA alleles (gyrA92, gyrA97, gyrA98, gyrA114, gyrA116, gyrA151, and gyrA230) and the N. subflava donor isolate of gyrA171, with the sizes of the recombinant fragments ranging from 634 to 7,499 bp. Transformation of gyrA fragments from these donor strains into a meningococcal isolate increased its ciprofloxacin MIC from 0.004 μg/ml to 0.125 or 0.19 μg/ml and to 0.5 μg/ml with further transformation of an additional ParC mutation. Over half of the quinolone-resistant N. meningitidis isolates acquired resistance by horizontal gene transfer from three commensal Neisseria species. Quinolone resistance in N. meningitidis increases in a stepwise manner.}, }
@article {pmid31740334, year = {2020}, author = {Feng, JM and Jiang, CQ and Sun, ZY and Hua, CJ and Wen, JF and Miao, W and Xiong, J}, title = {Single-cell transcriptome sequencing of rumen ciliates provides insight into their molecular adaptations to the anaerobic and carbohydrate-rich rumen microenvironment.}, journal = {Molecular phylogenetics and evolution}, volume = {143}, number = {}, pages = {106687}, doi = {10.1016/j.ympev.2019.106687}, pmid = {31740334}, issn = {1095-9513}, mesh = {Adaptation, Physiological ; Anaerobiosis ; Animals ; Carbohydrate Metabolism ; Cellulases/genetics ; Ciliophora/classification/*genetics/physiology ; Gene Transfer, Horizontal ; Glycoside Hydrolases/genetics ; Phylogeny ; Polygalacturonase/genetics ; RNA-Seq ; Rumen/metabolism/*parasitology ; Single-Cell Analysis ; *Transcriptome ; }, abstract = {Rumen ciliates are a specialized group of ciliates exclusively found in the anaerobic, carbohydrate-rich rumen microenvironment. However, the molecular and mechanistic basis of the physiological and behavioral adaptation of ciliates to the rumen microenvironment is undefined. We used single-cell transcriptome sequencing to explore the adaptive evolution of three rumen ciliates: two entodiniomorphids, Entodinium furca and Diplodinium dentatum; and one vestibuliferid, Isotricha intestinalis. We found that all three species are members of monophyletic orders within the class Litostomatea, with E. furca and D. dentatum in Entodiniomorphida and I. intestinalis in Vestibuliferida. The two entodiniomorphids might use H2-producing mitochondria and the vestibuliferid might use anaerobic mitochondria to survive under strictly anaerobic conditions. Moreover, carbohydrate-active enzyme (CAZyme) genes were identified in all three species, including cellulases, hemicellulases, and pectinases. The evidence that all three species have acquired prokaryote-derived genes by horizontal gene transfer (HGT) to digest plant biomass includes a significant enrichment of gene ontology categories such as cell wall macromolecule catabolic process and carbohydrate catabolic process and the identification of genes in common between CAZyme and HGT groups. These findings suggest that HGT might be an important mechanism in the adaptive evolution of ciliates to the rumen microenvironment.}, }
@article {pmid31738764, year = {2019}, author = {Robertson, J and Lin, J and Wren-Hedgus, A and Arya, G and Carrillo, C and Nash, JHE}, title = {Development of a multi-locus typing scheme for an Enterobacteriaceae linear plasmid that mediates inter-species transfer of flagella.}, journal = {PloS one}, volume = {14}, number = {11}, pages = {e0218638}, pmid = {31738764}, issn = {1932-6203}, mesh = {Enterobacteriaceae/classification/*genetics ; Flagella/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Multilocus Sequence Typing/*methods ; Phylogeny ; Plasmids/classification/genetics ; Salmonella typhi/classification/genetics ; Serogroup ; Species Specificity ; }, abstract = {Due to the public health importance of flagellar genes for typing, it is important to understand mechanisms that could alter their expression or presence. Phenotypic novelty in flagellar genes arise predominately through accumulation of mutations but horizontal transfer is known to occur. A linear plasmid termed pBSSB1 previously identified in Salmonella Typhi, was found to encode a flagellar operon that can mediate phase variation, which results in the rare z66 flagella phenotype. The identification and tracking of homologs of pBSSB1 is limited because it falls outside the normal replicon typing schemes for plasmids. Here we report the generation of nine new pBSSB1-family sequences using Illumina and Nanopore sequence data. Homologs of pBSSB1 were identified in 154 genomes representing 25 distinct serotypes from 67,758 Salmonella public genomes. Pangenome analysis of pBSSB1-family contigs was performed using roary and we identified three core genes amenable to a minimal pMLST scheme. Population structure analysis based on the newly developed pMLST scheme identified three major lineages representing 35 sequence types, and the distribution of these sequence types was found to span multiple serovars across the globe. This in silico pMLST scheme has shown utility in tracking and subtyping pBSSB1-family plasmids and it has been incorporated into the plasmid MLST database under the name "pBSSB1-family".}, }
@article {pmid31738701, year = {2019}, author = {Ooka, T and Seto, K and Ogura, Y and Nakamura, K and Iguchi, A and Gotoh, Y and Honda, M and Etoh, Y and Ikeda, T and Sugitani, W and Konno, T and Kawano, K and Imuta, N and Yoshiie, K and Hara-Kudo, Y and Murakami, K and Hayashi, T and Nishi, J}, title = {O-antigen biosynthesis gene clusters of Escherichia albertii: their diversity and similarity to Escherichia coli gene clusters and the development of an O-genotyping method.}, journal = {Microbial genomics}, volume = {5}, number = {11}, pages = {}, pmid = {31738701}, issn = {2057-5858}, mesh = {Base Sequence/genetics ; Escherichia/*genetics/metabolism ; Escherichia coli/genetics ; Genome, Bacterial/genetics ; Genotype ; Humans ; Multigene Family/genetics ; O Antigens/biosynthesis/*genetics ; Phylogeny ; Serotyping/methods ; }, abstract = {Escherichia albertii is a recently recognized human enteropathogen that is closely related to Escherichia coli. In many Gram-negative bacteria, including E. coli, O-antigen variation has long been used for the serotyping of strains. In E. albertii, while eight O-serotypes unique to this species have been identified, some strains have been shown to exhibit genetic or serological similarity to known E. coli/Shigella O-serotypes. However, the diversity of O-serotypes and O-antigen biosynthesis gene clusters (O-AGCs) of E. albertii remains to be systematically investigated. Here, we analysed the O-AGCs of 65 E. albertii strains and identified 40 E. albertii O-genotypes (EAOgs) (named EAOg1-EAOg40). Analyses of the 40 EAOgs revealed that as many as 20 EAOgs exhibited significant genetic and serological similarity to the O-AGCs of known E. coli/Shigella O-serotypes, and provided evidence for the inter-species horizontal gene transfer of O-AGCs between E. albertii and E. coli. Based on the sequence variation in the wzx gene among the 40 EAOgs, we developed a multiplex PCR-based O-genotyping system for E. albertii (EAO-genotyping PCR) and verified its usefulness by genotyping 278 E. albertii strains from various sources. Although 225 (80.9 %) of the 278 strains could be genotyped, 51 were not assigned to any of the 40 EAOgs, indicating that further analyses are required to better understand the diversity of O-AGCs in E. albertii and improve the EAO-genotyping PCR method. A phylogenetic view of E. albertii strains sequenced so far is also presented with the distribution of the 40 EAOgs, which provided multiple examples for the intra-species horizontal transfer of O-AGCs in E. albertii.}, }
@article {pmid31736930, year = {2019}, author = {Gonçalves, C and Ferreira, C and Gonçalves, LG and Turner, DL and Leandro, MJ and Salema-Oom, M and Santos, H and Gonçalves, P}, title = {A New Pathway for Mannitol Metabolism in Yeasts Suggests a Link to the Evolution of Alcoholic Fermentation.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2510}, pmid = {31736930}, issn = {1664-302X}, abstract = {The yeasts belonging to the Wickerhamiella and Starmerella genera (W/S clade) share a distinctive evolutionary history marked by loss and subsequent reinstatement of alcoholic fermentation mediated by horizontal gene transfer events. Species in this clade also share unusual features of metabolism, namely the preference for fructose over glucose as carbon source, a rare trait known as fructophily. Here we show that fructose may be the preferred sugar in W/S-clade species because, unlike glucose, it can be converted directly to mannitol in a reaction with impact on redox balance. According to our results, mannitol is excreted to the growth medium in appreciable amounts along with other fermentation products such as glycerol and ethanol but unlike the latter metabolites mannitol production increases with temperature. We used comparative genomics to find genes involved in mannitol metabolism and established the mannitol biosynthesis pathway in W/S-clade species Starmerella bombicola using molecular genetics tools. Surprisingly, mannitol production seems to be so important that St. bombicola (and other W/S-clade species) deploys a novel pathway to mediate the conversion of glucose to fructose, thereby allowing cells to produce mannitol even when glucose is the sole carbon source. Using targeted mutations and [13]C-labeled glucose followed by NMR analysis of end-products, we showed that the novel mannitol biosynthesis pathway involves fructose-6-phosphate as an intermediate, implying a key role for a yet unknown fructose-6-P phosphatase. We hypothesize that mannitol production contributed to mitigate the negative effects on redox balance of the ancient loss of alcoholic fermentation in the W/S clade. Presently, mannitol also seems to play a role in stress protection.}, }
@article {pmid31736929, year = {2019}, author = {Hamprecht, A and Sommer, J and Willmann, M and Brender, C and Stelzer, Y and Krause, FF and Tsvetkov, T and Wild, F and Riedel-Christ, S and Kutschenreuter, J and Imirzalioglu, C and Gonzaga, A and Nübel, U and Göttig, S}, title = {Pathogenicity of Clinical OXA-48 Isolates and Impact of the OXA-48 IncL Plasmid on Virulence and Bacterial Fitness.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2509}, pmid = {31736929}, issn = {1664-302X}, abstract = {OXA-48 is the most common carbapenemase in Enterobacterales in Germany and one of the most frequent carbapenemases worldwide. Several reports have associated bla OXA - 48 with a virulent host phenotype. To challenge this hypothesis, 35 OXA-48-producing clinical isolates of Escherichia coli (n = 15) and Klebsiella pneumoniae (n = 20) were studied in vitro, in vivo employing the Galleria mellonella infection model and by whole-genome sequencing. Clinical isolates belonged to 7 different sequence types (STs) in E. coli and 12 different STs in K. pneumoniae. In 26/35 isolates bla OXA- 48 was located on a 63 kb IncL plasmid. Horizontal gene transfer (HGT) to E. coli J53 was high in isolates with the 63 kb IncL plasmid (transconjugation frequency: ∼10[3]/donor) but low in isolates with non-IncL plasmids (<10[-6]/donor). Several clinical isolates were both highly cytotoxic against human cells and virulent in vivo. However, 63 kb IncL transconjugants generated from these highly virulent isolates were not more cytotoxic or virulent when compared to the recipient strain. Additionally, no genes associated with virulence were detected by in silico analysis of OXA-48 plasmids. The 63 kb plasmid was highly stable and did not impair growth or fitness in E. coli J53. In conclusion, OXA-48 clinical isolates in Germany are diverse but typically harbor the same 63 kb IncL plasmid which has been reported worldwide. We demonstrate that this 63 kb IncL plasmid has a low fitness burden, high plasmid stability and can be transferred by highly efficient HGT which is likely the cause of the rapid dissemination of OXA-48 rather than the expansion of a single clone or gain of virulence.}, }
@article {pmid31733995, year = {2020}, author = {Li, S and Yao, Q and Liu, J and Wei, D and Zhou, B and Zhu, P and Cui, X and Jin, J and Liu, X and Wang, G}, title = {Profiles of antibiotic resistome with animal manure application in black soils of northeast China.}, journal = {Journal of hazardous materials}, volume = {384}, number = {}, pages = {121216}, doi = {10.1016/j.jhazmat.2019.121216}, pmid = {31733995}, issn = {1873-3336}, mesh = {Animals ; Cattle ; Chickens ; China ; Drug Resistance, Microbial/*genetics ; Drug Resistance, Multiple/*genetics ; Environmental Monitoring ; *Genes, Bacterial ; *Manure ; Soil ; *Soil Microbiology ; Swine ; }, abstract = {Black soils (Mollisols) are important soil resources for crop production and maintain food safety in China. For keeping soil fertility, the application of animal manure is commonly practiced in black soils. However, the impact of this application on abundance and diversity of antibiotic resistance genes (ARGs) in black soils of China remains unclear. Here, we surveyed the profiles of ARGs in 72 soil samples collected from four long-term experimental stations with different fertilization regimes and from open farmlands in two sites across northeast China using high-throughput quantitative PCR. Results showed that a total of 178 ARGs including mobile genetic elements (MGEs) were detected, and the diversity and abundance of ARGs were significantly increased with manure application. Additionally, the finding of a significant positive correlation between relative abundance of ARGs and MGEs (P < 0.0001), suggesting that horizontal gene transfer may potentially impact the transmission of ARGs. Furthermore, two genes aadA-1-01 and mexF, encoding resistance to aminoglycoside and multidrug, respectively, were recognized as indicators to estimate the abundance of other co-occurring ARGs. These findings provided insights into the soil resistome in black soils of northeast China and also highlighted the environmental risks caused by manure application should not be ignored.}, }
@article {pmid31732826, year = {2020}, author = {Xu, G}, title = {Evolution of LuxR solos in bacterial communication: receptors and signals.}, journal = {Biotechnology letters}, volume = {42}, number = {2}, pages = {181-186}, doi = {10.1007/s10529-019-02763-6}, pmid = {31732826}, issn = {1573-6776}, support = {31570038//National Natural Science Foundation of China/ ; }, mesh = {Acyl-Butyrolactones/metabolism ; Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Gram-Negative Bacteria/metabolism/*physiology ; Quorum Sensing ; Repressor Proteins/*genetics/*metabolism ; Trans-Activators/*genetics/*metabolism ; }, abstract = {Cell-cell communication in bacteria needs chemical signals and cognate receptors. Many Gram-negative bacteria use acyl-homoserine lactones (AHLs) and cognate LuxR-type receptors to regulate their quorum sensing (QS) systems. The signal synthase-receptor (LuxI-LuxR) pairs may have co-evolved together. However, many LuxR solo (orphan LuxR) regulators sense more signals than just AHLs, and expand the regulatory networks for inter-species and inter-kingdom communication. Moreover, there are also some QS regulators from the TetR family. LuxR solo regulators might have evolved by gene duplication and horizontal gene transfer. An increased understanding of the evolutionary roles of QS regulators would be helpful for engineering of cell-cell communication circuits in bacteria.}, }
@article {pmid31731444, year = {2019}, author = {Ghosh, S and Sarangi, AN and Mukherjee, M and Bhowmick, S and Tripathy, S}, title = {Reanalysis of Lactobacillus paracasei Lbs2 Strain and Large-Scale Comparative Genomics Places Many Strains into Their Correct Taxonomic Position.}, journal = {Microorganisms}, volume = {7}, number = {11}, pages = {}, pmid = {31731444}, issn = {2076-2607}, abstract = {Lactobacillus paracasei are diverse Gram-positive bacteria that are very closely related to Lactobacillus casei, belonging to the Lactobacillus casei group. Due to extreme genome similarities between L. casei and L. paracasei, many strains have been cross placed in the other group. We had earlier sequenced and analyzed the genome of Lactobacillus paracasei Lbs2, but mistakenly identified it as L. casei. We re-analyzed Lbs2 reads into a 2.5 MB genome that is 91.28% complete with 0.8% contamination, which is now suitably placed under L. paracasei based on Average Nucleotide Identity and Average Amino Acid Identity. We took 74 sequenced genomes of L. paracasei from GenBank with assembly sizes ranging from 2.3 to 3.3 MB and genome completeness between 88% and 100% for comparison. The pan-genome of 75 L. paracasei strains hold 15,945 gene families (21,5232 genes), while the core genome contained about 8.4% of the total genes (243 gene families with 18,225 genes) of pan-genome. Phylogenomic analysis based on core gene families revealed that the Lbs2 strain has a closer relationship with L. paracasei subsp. tolerans DSM20258. Finally, the in-silico analysis of the L. paracasei Lbs2 genome revealed an important pathway that could underpin the production of thiamin, which may contribute to the host energy metabolism.}, }
@article {pmid31730849, year = {2019}, author = {Cheng, S and Xian, W and Fu, Y and Marin, B and Keller, J and Wu, T and Sun, W and Li, X and Xu, Y and Zhang, Y and Wittek, S and Reder, T and Günther, G and Gontcharov, A and Wang, S and Li, L and Liu, X and Wang, J and Yang, H and Xu, X and Delaux, PM and Melkonian, B and Wong, GK and Melkonian, M}, title = {Genomes of Subaerial Zygnematophyceae Provide Insights into Land Plant Evolution.}, journal = {Cell}, volume = {179}, number = {5}, pages = {1057-1067.e14}, doi = {10.1016/j.cell.2019.10.019}, pmid = {31730849}, issn = {1097-4172}, mesh = {Abscisic Acid/pharmacology ; Amino Acid Sequence ; *Biological Evolution ; Embryophyta/*genetics ; *Genome, Plant ; Multigene Family ; Phylogeny ; Plant Proteins/chemistry ; Protein Domains ; Streptophyta/classification/*genetics ; Symbiosis/genetics ; Synteny/genetics ; }, abstract = {The transition to a terrestrial environment, termed terrestrialization, is generally regarded as a pivotal event in the evolution and diversification of the land plant flora that changed the surface of our planet. Through phylogenomic studies, a group of streptophyte algae, the Zygnematophyceae, have recently been recognized as the likely sister group to land plants (embryophytes). Here, we report genome sequences and analyses of two early diverging Zygnematophyceae (Spirogloea muscicola gen. nov. and Mesotaenium endlicherianum) that share the same subaerial/terrestrial habitat with the earliest-diverging embryophytes, the bryophytes. We provide evidence that genes (i.e., GRAS and PYR/PYL/RCAR) that increase resistance to biotic and abiotic stresses in land plants, in particular desiccation, originated or expanded in the common ancestor of Zygnematophyceae and embryophytes, and were gained by horizontal gene transfer (HGT) from soil bacteria. These two Zygnematophyceae genomes represent a cornerstone for future studies to understand the underlying molecular mechanism and process of plant terrestrialization.}, }
@article {pmid31730154, year = {2019}, author = {Andolfo, G and Di Donato, A and Chiaiese, P and De Natale, A and Pollio, A and Jones, JDG and Frusciante, L and Ercolano, MR}, title = {Alien Domains Shaped the Modular Structure of Plant NLR Proteins.}, journal = {Genome biology and evolution}, volume = {11}, number = {12}, pages = {3466-3477}, pmid = {31730154}, issn = {1759-6653}, support = {BB/H019820/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/K003550/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M008193/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P021646/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Chlorophyta/classification/genetics ; Disease Resistance/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Plant/genetics ; Genomics ; NLR Proteins/*genetics/metabolism ; Nucleotide Motifs ; Operon ; Phylogeny ; Plant Immunity ; Plant Proteins/*genetics/metabolism ; Plants/classification/genetics ; Protein Domains/*genetics ; }, abstract = {Plant innate immunity mostly relies on nucleotide-binding (NB) and leucine-rich repeat (LRR) intracellular receptors to detect pathogen-derived molecules and to induce defense responses. A multitaxa reconstruction of NB-domain associations allowed us to identify the first NB-LRR arrangement in the Chlorophyta division of the Viridiplantae. Our analysis points out that the basic NOD-like receptor (NLR) unit emerged in Chlorophytes by horizontal transfer and its diversification started from Toll/interleukin receptor-NB-LRR members. The operon-based genomic structure of Chromochloris zofingiensis NLR copies suggests a functional origin of NLR clusters. Moreover, the transmembrane signatures of NLR proteins in the unicellular alga C. zofingiensis support the hypothesis that the NLR-based immunity system of plants derives from a cell-surface surveillance system. Taken together, our findings suggest that NLRs originated in unicellular algae and may have a common origin with cell-surface LRR receptors.}, }
@article {pmid31728272, year = {2019}, author = {Wayne, EC and Long, C and Haney, MJ and Batrakova, EV and Leisner, TM and Parise, LV and Kabanov, AV}, title = {Targeted Delivery of siRNA Lipoplexes to Cancer Cells Using Macrophage Transient Horizontal Gene Transfer.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {6}, number = {21}, pages = {1900582}, pmid = {31728272}, issn = {2198-3844}, support = {P30 CA016086/CA/NCI NIH HHS/United States ; R01 CA184088/CA/NCI NIH HHS/United States ; R01 NS102412/NS/NINDS NIH HHS/United States ; T32 CA196589/CA/NCI NIH HHS/United States ; }, abstract = {Delivery of nucleic acids into solid tumor environments remains a pressing challenge. This study examines the ability of macrophages to horizontally transfer small interfering RNA (siRNA) lipoplexes to cancer cells. Macrophages are a natural candidate for a drug carrier because of their ability to accumulate at high densities into many cancer types, including, breast, prostate, brain, and colon cancer. Here, it is demonstrated that macrophages can horizontally transfer siRNA to cancer cells during in vitro coculture. The amount of transfer can be dosed depending on the amount of siRNA loaded and total number of macrophages delivered. Macrophages loaded with calcium integrin binding protein-1 (CIB1)-siRNA result in decreased tumorsphere growth and decreased mRNA expression of CIB1 and KI67 in MDA-MB-468 human breast cancer cells. Adoptive transfer of macrophages transfected with CIB1-siRNA localizes to the orthotopic MDA-MB-468 tumor. Furthermore, it is reported that macrophage activation can modulate this transfer process as well as intracellular trafficking protein Rab27a. As macrophages are heavily involved in tumor progression, understanding how to use macrophages for drug delivery can substantially benefit the treatment of tumors.}, }
@article {pmid31723216, year = {2020}, author = {Yamagishi, J and Hayashida, K and Matsuo, J and Okubo, T and Kuroda, M and Nagai, H and Sekizuka, T and Yamaguchi, H and Sugimoto, C}, title = {Complete genome and bimodal genomic structure of the amoebal symbiont Neochlamydia strain S13 revealed by ultra-long reads obtained from MinION.}, journal = {Journal of human genetics}, volume = {65}, number = {1}, pages = {41-48}, pmid = {31723216}, issn = {1435-232X}, mesh = {Acanthamoeba/microbiology ; *Genome, Bacterial ; Genomics/methods ; Gram-Negative Bacteria/*genetics/growth &amp; development/isolation &amp; purification ; Phylogeny ; Sequence Analysis, DNA/*instrumentation/methods ; }, abstract = {Neochlamydia strain S13 is an amoebal symbiont of an Acanthamoeba sp. The symbiont confers resistance to Legionella pneumophila on its host; however, the molecular mechanism underlying this resistance is not completely understood. Genome analyses have been crucial for understanding the complicated host-symbiont relationship but segregating the host's genome DNA from the symbiont's DNA is often challenging. In this study, we successfully identified a bimodal genomic structure in Neochlamydia strain S13 using PacBio RS II supported by ultra-long reads derived from MinION. One mode consisted of circular sequences of 2,586,667 and 231,307 bp; the other was an integrated sequence of the two via long homologous regions. They encoded 2175 protein-coding regions, some of which were implied to be acquired via horizontal gene transfer. They were specifically conserved in the genus Neochlamydia and formed a cluster in the genome, presumably by multiplication through genome replication. Moreover, it was notable that the sequenced DNA was obtained without segregating the symbiont DNA from the host. This is an easy and versatile technique that facilitates the characterization of diverse hosts and symbionts in nature.}, }
@article {pmid31722662, year = {2019}, author = {Theobald, S and Vesth, TC and Andersen, MR}, title = {Genus level analysis of PKS-NRPS and NRPS-PKS hybrids reveals their origin in Aspergilli.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {847}, pmid = {31722662}, issn = {1471-2164}, mesh = {Aspergillus/classification/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Penicillium chrysogenum/genetics ; Peptide Synthases/classification/*genetics ; Phylogeny ; Polyketide Synthases/classification/*genetics ; }, abstract = {BACKGROUND: Filamentous fungi produce a vast amount of bioactive secondary metabolites (SMs) synthesized by e.g. hybrid polyketide synthase-nonribosomal peptide synthetase enzymes (PKS-NRPS; NRPS-PKS). While their domain structure suggests a common ancestor with other SM proteins, their evolutionary origin and dynamics in fungi are still unclear. Recent rational engineering approaches highlighted the possibility to reassemble hybrids into chimeras - suggesting molecular recombination as diversifying mechanism.<br><br>RESULTS: Phylogenetic analysis of hybrids in 37 species - spanning 9 sections of Aspergillus and Penicillium chrysogenum - let us describe their dynamics throughout the genus Aspergillus. The tree topology indicates that three groups of PKS-NRPS as well as one group of NRPS-PKS hybrids developed independently from each other. Comparison to other SM genes lead to the conclusion that hybrids in Aspergilli have several PKS ancestors; in contrast, hybrids are monophyletic when compared to available NRPS genes - with the exception of a small group of NRPSs. Our analysis also revealed that certain NRPS-likes are derived from NRPSs, suggesting that the NRPS/NRPS-like relationship is dynamic and proteins can diverge from one function to another. An extended phylogenetic analysis including bacterial and fungal taxa revealed multiple ancestors of hybrids. Homologous hybrids are present in all sections which suggests frequent horizontal gene transfer between genera and a finite number of hybrids in fungi.<br><br>CONCLUSION: Phylogenetic distances between hybrids provide us with evidence for their evolution: Large inter-group distances indicate multiple independent events leading to the generation of hybrids, while short intra-group distances of hybrids from different taxonomic sections indicate frequent horizontal gene transfer. Our results are further supported by adding bacterial and fungal genera. Presence of related hybrid genes in all Ascomycetes suggests a frequent horizontal gene transfer between genera and a finite diversity of hybrids - also explaining their scarcity. The provided insights into relations of hybrids and other SM genes will serve in rational design of new hybrid enzymes.}, }
@article {pmid31719176, year = {2019}, author = {Phillips, KN and Widmann, S and Lai, HY and Nguyen, J and Ray, JCJ and Balázsi, G and Cooper, TF}, title = {Diversity in lac Operon Regulation among Diverse Escherichia coli Isolates Depends on the Broader Genetic Background but Is Not Explained by Genetic Relatedness.}, journal = {mBio}, volume = {10}, number = {6}, pages = {}, pmid = {31719176}, issn = {2150-7511}, mesh = {Escherichia coli/*classification/*genetics/isolation &amp; purification ; Evolution, Molecular ; *Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Genes, Regulator ; *Genetic Background ; *Genetic Variation ; *Lac Operon ; Mutation ; Phenotype ; Phylogeny ; Polymorphism, Genetic ; }, abstract = {Transcription of bacterial genes is controlled by the coordinated action of cis- and trans-acting regulators. The activity and mode of action of these regulators can reflect different requirements for gene products in different environments. A well-studied example is the regulatory function that integrates the environmental availability of glucose and lactose to control the Escherichia colilac operon. Most studies of lac operon regulation have focused on a few closely related strains. To determine the range of natural variation in lac regulatory function, we introduced a reporter construct into 23 diverse E. coli strains and measured expression with combinations of inducer concentrations. We found a wide range of regulatory functions. Several functions were similar to the one observed in a reference lab strain, whereas others depended weakly on the presence of cAMP. Some characteristics of the regulatory function were explained by the genetic relatedness of strains, indicating that differences varied on relatively short time scales. The regulatory characteristics explained by genetic relatedness were among those that best predicted the initial growth of strains following transition to a lactose environment, suggesting a role for selection. Finally, we transferred the lac operon, with the lacI regulatory gene, from five natural isolate strains into a reference lab strain. The regulatory function of these hybrid strains revealed the effect of local and global regulatory elements in controlling expression. Together, this work demonstrates that regulatory functions can be varied within a species and that there is variation within a species to best match a function to particular environments.IMPORTANCE The lac operon of Escherichia coli is a classic model for studying gene regulation. This study has uncovered features such as the environmental input logic controlling gene expression, as well as gene expression bistability and hysteresis. Most lac operon studies have focused on a few lab strains, and it is not known how generally those findings apply to the diversity of E. coli strains. We examined the environmental dependence of lac gene regulation in 20 natural isolates of E. coli and found a wide range of regulatory responses. By transferring lac genes from natural isolate strains into a common reference strain, we found that regulation depends on both the lac genes themselves and on the broader genetic background, indicating potential for still-greater regulatory diversity following horizontal gene transfer. Our results reveal that there is substantial natural variation in the regulation of the lac operon and indicate that this variation can be ecologically meaningful.}, }
@article {pmid31717440, year = {2019}, author = {Cheepudom, J and Lin, TL and Lee, CC and Meng, M}, title = {Characterization of a Novel Thermobifida fusca Bacteriophage P318.}, journal = {Viruses}, volume = {11}, number = {11}, pages = {}, pmid = {31717440}, issn = {1999-4915}, mesh = {Actinobacteria/*virology ; Bacteriophages/genetics/*isolation &amp; purification ; DNA, Viral ; Gene Ontology ; Gene Transfer, Horizontal ; Genome, Viral/physiology ; Phylogeny ; Siphoviridae/genetics/*isolation &amp; purification ; Thermobifida ; Viral Proteins/genetics ; }, abstract = {Thermobifida fusca is of biotechnological interest due to its ability to produce an array of plant cell wall hydrolytic enzymes. Nonetheless, only one T. fusca bacteriophage with genome information has been reported to date. This study was aimed at discovering more relevant bacteriophages to expand the existing knowledge of phage diversity for this host species. With this end in view, a thermostable T. fusca bacteriophage P318, which belongs to the Siphoviridae family, was isolated and characterized. P318 has a double-stranded DNA genome of 48,045 base pairs with 3'-extended COS ends, on which 52 putative ORFs are organized into clusters responsible for the order of genome replication, virion morphogenesis, and the regulation of the lytic/lysogenic cycle. In comparison with T. fusca and the previously discovered bacteriophage P1312, P318 has a much lower G+C content in its genome except at the region encompassing ORF42, which produced a protein with unknown function. P1312 and P318 share very few similarities in their genomes except for the regions encompassing ORF42 of P318 and ORF51 of P1312 that are homologous. Thus, acquisition of ORF42 by lateral gene transfer might be an important step in the evolution of P318.}, }
@article {pmid31711966, year = {2019}, author = {Hendriksen, M and Francis, A}, title = {Tree-metrizable HGT networks.}, journal = {Mathematical biosciences}, volume = {318}, number = {}, pages = {108283}, doi = {10.1016/j.mbs.2019.108283}, pmid = {31711966}, issn = {1879-3134}, mesh = {*Gene Transfer, Horizontal ; *Models, Genetic ; *Phylogeny ; }, abstract = {Phylogenetic trees are often constructed by using a metric on the set of taxa that label the leaves of the tree. While there are a number of methods for constructing a tree using a given metric, such trees will only display the metric if it satisfies the so-called "four point condition", established by Buneman in 1971. While this condition guarantees that a unique tree will display the metric, meaning that the distance between any two leaves can be found by adding the distances on arcs in the path between the leaves, it doesn't exclude the possibility that a phylogenetic network might also display the metric. This possibility was recently pointed out and "tree-metrized" networks - that display a tree metric - with a single reticulation were characterized. In this paper, we show that in the case of HGT (horizontal gene transfer) networks, in fact there are tree-metrized networks containing many reticulations.}, }
@article {pmid31708906, year = {2019}, author = {Dordet-Frisoni, E and Faucher, M and Sagné, E and Baranowski, E and Tardy, F and Nouvel, LX and Citti, C}, title = {Mycoplasma Chromosomal Transfer: A Distributive, Conjugative Process Creating an Infinite Variety of Mosaic Genomes.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2441}, pmid = {31708906}, issn = {1664-302X}, abstract = {The capacity of Mycoplasmas to engage in horizontal gene transfers has recently been highlighted. Despite their small genome, some of these wall-less bacteria are able to exchange multiple, large portions of their chromosome via a conjugative mechanism that does not conform to canonical Hfr/oriT models. To understand the exact features underlying mycoplasma chromosomal transfer (MCT), extensive genomic analyses were performed at the nucleotide level, using individual mating progenies derived from our model organism, Mycoplasma agalactiae. Genome reconstruction showed that MCT resulted in the distributive transfer of multiple chromosomal DNA fragments and generated progenies composed of a variety of mosaic genomes, each being unique. Analyses of macro- and micro-events resulting from MCT revealed that the vast majority of the acquired fragments were unrelated and co-transferred independently from the selection marker, these resulted in up to 17% of the genome being exchanged. Housekeeping and accessory genes were equally affected by MCT, with up to 35 CDSs being gained or lost. This efficient HGT process also created a number of chimeric genes and genetic micro-variations that may impact gene regulation and/or expression. Our study unraveled the tremendous plasticity of M. agalactiae genome and point toward MCT as a major player in diversification and adaptation to changing environments, offering a significant advantage to this minimal pathogen.}, }
@article {pmid31706562, year = {2020}, author = {Kalita, M and Małek, W}, title = {Root nodules of Genista germanica harbor Bradyrhizobium and Rhizobium bacteria exchanging nodC and nodZ genes.}, journal = {Systematic and applied microbiology}, volume = {43}, number = {1}, pages = {126026}, doi = {10.1016/j.syapm.2019.126026}, pmid = {31706562}, issn = {1618-0984}, mesh = {Bacteria/classification/genetics/isolation &amp; purification ; Bacterial Proteins/genetics ; Bradyrhizobium/classification/*genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; Genes, Essential/genetics ; Genetic Variation ; Genista/*microbiology ; Host Specificity ; Phylogeny ; Plant Root Nodulation/*genetics ; RNA, Ribosomal, 16S/genetics ; Rhizobium/classification/*genetics/isolation &amp; purification ; Root Nodules, Plant/*microbiology ; Sequence Analysis, DNA ; Symbiosis/genetics ; }, abstract = {A collection of 18 previously unstudied strains isolated from root nodules of Genista germanica (German greenweed) grown in southeast Poland was evaluated for the level of genetic diversity using the BOX-PCR technique and the phylogenetic relationship based on both core (16S rRNA, dnaK, ftsA, glnII, gyrB, recA, rpoB) and nodulation (nodC and nodZ) gene sequences. Each of the 18 G. germanica root nodule isolates displayed unique BOX-PCR patterns, indicating their high level of genomic heterogeneity. Based on the comparative 16S rDNA sequence analysis, 12 isolates were affiliated to the Bradyrhizobium genus and the other strains were most similar to Rhizobium species. Phylogenetic analysis of the core gene sequences indicated that the studied Bradyrhizobium bacteria were most closely related to Bradyrhizobium japonicum, whereas Rhizobium isolates were most closely related to Rhizobium lusitanum and R. leguminosarum. The phylogenies of nodC and nodZ for the Rhizobium strains were incongruent with each other and with the phylogenies inferred from the core gene sequences. All Rhizobium nodZ gene sequences acquired in this study were grouped with the sequences of Bradyrhizobium strains. Some of the studied Rhizobium isolates were placed in the nodC phylogenetic tree together with reference Rhizobium species, while the others were closely related to Bradyrhizobium bacteria. The results provided evidence for horizontal transfer of nodulation genes between Bradyrhizobium and Rhizobium. However, the horizontal transfer of nod genes was not sufficient for Rhizobium strains to form nodules on G. germanica roots, suggesting that symbiotic genes have to be adapted to the bacterial genome.}, }
@article {pmid31705134, year = {2020}, author = {Caugant, DA and Brynildsrud, OB}, title = {Neisseria meningitidis: using genomics to understand diversity, evolution and pathogenesis.}, journal = {Nature reviews. Microbiology}, volume = {18}, number = {2}, pages = {84-96}, pmid = {31705134}, issn = {1740-1534}, mesh = {*Biological Evolution ; Gene Expression Regulation, Bacterial/*physiology ; *Genetic Variation ; *Genomics ; Gonorrhea/microbiology ; Humans ; Neisseria meningitidis/*genetics/*pathogenicity ; }, abstract = {Meningococcal disease remains an important cause of morbidity and death worldwide despite the development and increasing implementation of effective vaccines. Elimination of the disease is hampered by the enormous diversity and antigenic variability of the causative agent, Neisseria meningitidis, one of the most variable bacteria in nature. These features are attained mainly through high rates of horizontal gene transfer and alteration of protein expression through phase variation. The recent availability of whole-genome sequencing (WGS) of large-scale collections of N. meningitidis isolates from various origins, databases to facilitate storage and sharing of WGS data and the concomitant development of effective bioinformatics tools have led to a much more thorough understanding of the diversity of the species, its evolution and population structure and how virulent traits may emerge. Implementation of WGS is already contributing to enhanced epidemiological surveillance and is essential to ascertain the impact of vaccination strategies. This Review summarizes the recent advances provided by WGS studies in our understanding of the biology of N. meningitidis and the epidemiology of meningococcal disease.}, }
@article {pmid31704048, year = {2020}, author = {Dow, L and Morrissey, KL and Willems, A and Kroth, PG}, title = {Complete genome sequence of Dyadobacter sp. 32, isolated from a culture of the freshwater diatom Cymbella microcephala.}, journal = {Marine genomics}, volume = {52}, number = {}, pages = {100720}, doi = {10.1016/j.margen.2019.100720}, pmid = {31704048}, issn = {1876-7478}, mesh = {Austria ; *Biofilms ; Cytophagaceae/*genetics ; Diatoms/microbiology/*physiology ; *Genome, Bacterial ; Germany ; Lakes ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Switzerland ; Whole Genome Sequencing ; }, abstract = {Bacteria have been shown to be involved in different species-specific interactions with eukaryotic algae such as diatoms, impacting important ecosystem processes. Recently, a strain assigned to Dyadobacter, named 'species 32', has been shown to be involved in a number of ecologically relevant diatom processes, such as biofilm formation or growth enhancement, depending on the diatom species. This bacterium was originally isolated from a culture of freshwater benthic diatoms that originated from an epilithic biofilm, in which both bacteria and diatoms coexist. A single complete circular chromosome of Dyadobacter sp. 32 was assembled with a length of 7,101,228 bp, containing 6062 protein coding genes and 3 rRNA operons. A number of interesting genetic features were found, such as a putative zeaxanthin biosynthetic gene cluster. A large number of polysaccharide utilizing gene clusters were also detected, along with genes potentially acquired from other bacteria through horizontal gene transfer, and genes previously identified in other algae-bacteria interactions. These data serve to increase our understanding of specific interactions within freshwater biofilms, and identify a number of gene targets with which to study the molecular basis of diatom-bacteria interactions.}, }
@article {pmid31702138, year = {2020}, author = {Niu, B and Cai, J and Song, W and Zhao, G}, title = {Novel Electrochemical Pretreatment for Preferential Removal of Nonylphenol in Industrial Wastewater: Biodegradability Improvement and Toxicity Reduction.}, journal = {Environmental science &amp; technology}, volume = {54}, number = {2}, pages = {1258-1266}, doi = {10.1021/acs.est.9b03153}, pmid = {31702138}, issn = {1520-5851}, mesh = {Biological Oxygen Demand Analysis ; Industrial Waste ; Oxidation-Reduction ; Phenols ; Waste Disposal, Fluid ; *Wastewater ; *Water Pollutants, Chemical ; }, abstract = {Preferential pretreatment of nonylphenol (NP) before biological treatment is of great significance due to its horizontal gene transfer effect and endocrine disruption activity. A novel molecular imprinting high-index facet SnO2 (MI-SnO2, HIF) electrode is designed. NP was effectively removed from industrial wastewater at 1.8 V with totally suppressing human estrogen activity. The ratio of 5 day biological oxygen demand to chemical oxygen demand (BOD5/CODCr) was enhanced to 0.412 from 0.186 after preferential pretreatment. The effluent concentration of NP was 6.4 μg L[-1] after further simulating anaerobic-anoxic-oxic treatment, which was about 1/10 of that without pretreatment. This preferential electrochemical pretreatment is interpreted as prior adsorption and enrichment of target pollutants on the MI-SnO2, HIF surface. The reactive oxygen species and subsequent oxidation products were investigated by in situ electron paramagnetic resonance and electrochemical infrared spectroscopy. The degradation pathway of NP was further analyzed by liquid chromatography-mass spectrometry. This unique pretreatment method for a complex tannery wastewater system has irreplaceable status because no methods with similar advantages have been reported, expecting to be widely used in preferential pretreatment of toxic contaminants blended with highly concentrated nontoxic organics.}, }
@article {pmid31698835, year = {2019}, author = {Belibasakis, GN and Maula, T and Bao, K and Lindholm, M and Bostanci, N and Oscarsson, J and Ihalin, R and Johansson, A}, title = {Virulence and Pathogenicity Properties of Aggregatibacter actinomycetemcomitans.}, journal = {Pathogens (Basel, Switzerland)}, volume = {8}, number = {4}, pages = {}, pmid = {31698835}, issn = {2076-0817}, abstract = {Aggregatibacter actinomycetemcomitans is a periodontal pathogen colonizing the oral cavity of a large proportion of the human population. It is equipped with several potent virulence factors that can cause cell death and induce or evade inflammation. Because of the large genetic diversity within the species, both harmless and highly virulent genotypes of the bacterium have emerged. The oral condition and age, as well as the geographic origin of the individual, influence the risk to be colonized by a virulent genotype of the bacterium. In the present review, the virulence and pathogenicity properties of A. actinomycetemcomitans will be addressed.}, }
@article {pmid31695182, year = {2020}, author = {Bernheim, A and Sorek, R}, title = {The pan-immune system of bacteria: antiviral defence as a community resource.}, journal = {Nature reviews. Microbiology}, volume = {18}, number = {2}, pages = {113-119}, pmid = {31695182}, issn = {1740-1534}, mesh = {Bacteria/immunology/*virology ; Bacteriophages/*physiology ; }, abstract = {Viruses and their hosts are engaged in a constant arms race leading to the evolution of antiviral defence mechanisms. Recent studies have revealed that the immune arsenal of bacteria against bacteriophages is much more diverse than previously envisioned. These discoveries have led to seemingly contradictory observations: on one hand, individual microorganisms often encode multiple distinct defence systems, some of which are acquired by horizontal gene transfer, alluding to their fitness benefit. On the other hand, defence systems are frequently lost from prokaryotic genomes on short evolutionary time scales, suggesting that they impose a fitness cost. In this Perspective article, we present the 'pan-immune system' model in which we suggest that, although a single strain cannot carry all possible defence systems owing to their burden on fitness, it can employ horizontal gene transfer to access immune defence mechanisms encoded by closely related strains. Thus, the 'effective' immune system is not the one encoded by the genome of a single microorganism but rather by its pan-genome, comprising the sum of all immune systems available for a microorganism to horizontally acquire and use.}, }
@article {pmid31693795, year = {2020}, author = {Fewer, DP and Metsä-Ketelä, M}, title = {A pharmaceutical model for the molecular evolution of microbial natural products.}, journal = {The FEBS journal}, volume = {287}, number = {7}, pages = {1429-1449}, doi = {10.1111/febs.15129}, pmid = {31693795}, issn = {1742-4658}, mesh = {Biological Products/chemistry/*metabolism/*pharmacology ; *Evolution, Molecular ; *Metabolic Networks and Pathways ; Molecular Structure ; *Synthetic Biology ; }, abstract = {Microbes are talented chemists with the ability to generate tremendously complex and diverse natural products which harbor potent biological activities. Natural products are produced using sets of specialized biosynthetic enzymes encoded by secondary metabolism pathways. Here, we present a two-step evolutionary model to explain the diversification of biosynthetic pathways that account for the proliferation of these molecules. We argue that the appearance of natural product families has been a slow and infrequent process. The first step led to the original emergence of bioactive molecules and different classes of natural products. However, much of the chemical diversity observed today has resulted from the endless modification of the ancestral biosynthetic pathways. The second step rapidly modulates the pre-existing biological activities to increase their potency and to adapt to changing environmental conditions. We highlight the importance of enzyme promiscuity in this process, as it facilitates both the incorporation of horizontally transferred genes into secondary metabolic pathways and the functional differentiation of proteins to catalyze novel chemistry. We provide examples where single point mutations or recombination events have been sufficient for new enzymatic activities to emerge. A unique feature in the evolution of microbial secondary metabolism is that gene duplication is not essential but offers opportunities to synthesize more complex metabolites. Microbial natural products are highly important for the pharmaceutical industry due to their unique bioactivities. Therefore, understanding the natural mechanisms leading to the formation of diverse metabolic pathways is vital for future attempts to utilize synthetic biology for the generation of novel molecules.}, }
@article {pmid31693153, year = {2020}, author = {Yubuki, N and Galindo, LJ and Reboul, G and López-García, P and Brown, MW and Pollet, N and Moreira, D}, title = {Ancient Adaptive Lateral Gene Transfers in the Symbiotic Opalina-Blastocystis Stramenopile Lineage.}, journal = {Molecular biology and evolution}, volume = {37}, number = {3}, pages = {651-659}, doi = {10.1093/molbev/msz250}, pmid = {31693153}, issn = {1537-1719}, mesh = {Algal Proteins/*genetics ; Animals ; Bacteria/*genetics ; Blastocystis/classification/*genetics ; Evolution, Molecular ; Gene Expression Profiling ; Gene Transfer, Horizontal ; Genes, Bacterial ; Phylogeny ; Ranidae/parasitology ; Stramenopiles/classification/*genetics ; Xenopus/parasitology ; }, abstract = {Lateral gene transfer is a very common process in bacterial and archaeal evolution, playing an important role in the adaptation to new environments. In eukaryotes, its role and frequency remain highly debated, although recent research supports that gene transfer from bacteria to diverse eukaryotes may be much more common than previously appreciated. However, most of this research focused on animals and the true phylogenetic and functional impact of bacterial genes in less-studied microbial eukaryotic groups remains largely unknown. Here, we have analyzed transcriptome data from the deep-branching stramenopile Opalinidae, common members of frog gut microbiomes, and distantly related to the well-known genus Blastocystis. Phylogenetic analyses suggest the early acquisition of several bacterial genes in a common ancestor of both lineages. Those lateral gene transfers most likely facilitated the adaptation of the free-living ancestor of the Opalinidae-Blastocystis symbiotic group to new niches in the oxygen-depleted animal gut environment.}, }
@article {pmid31686120, year = {2020}, author = {Deng, ZS and Kong, ZY and Zhang, BC and Zhao, LF}, title = {Insights into non-symbiotic plant growth promotion bacteria associated with nodules of Sphaerophysa salsula growing in northwestern China.}, journal = {Archives of microbiology}, volume = {202}, number = {2}, pages = {399-409}, doi = {10.1007/s00203-019-01752-7}, pmid = {31686120}, issn = {1432-072X}, support = {31660106//National Outstanding Youth Science Fund Project of National Natural Science Foundation of China/ ; }, mesh = {Bacillus pumilus/*metabolism ; Carbon-Carbon Lyases ; China ; Endophytes/isolation &amp; purification ; Fabaceae/*growth &amp; development/*microbiology ; Gene Transfer, Horizontal ; Mesorhizobium/genetics/*metabolism ; Nitrogen Fixation ; Phylogeny ; Plant Development/physiology ; Root Nodules, Plant/*microbiology ; Siderophores ; Streptomyces/*metabolism ; }, abstract = {In addition to rhizobia, other non-symbiotic endophytic bacteria also have been simultaneously isolated from the same root nodules. The existence of non-symbiotic endophytic bacteria in leguminous root nodules is a universal phenomenon. The vast majority of studies have detected endophytic bacteria in other plant tissues. In contrast, little systemic observation has been made on the non-symbiotic endophytic bacteria within leguminous root nodules. The present investigation was carried out to isolate plant growth-promoting endophytic non-symbiotic bacteria from indigenous leguminous Sphaerophysa salsula and their influence on plant growth. A total of 65 endophytic root nodule-associated bacteria were isolated from indigenous legume S. salsula growing in the northwestern arid regions of China. When combining our previous work with the current study, sequence analysis of the nifH gene revealed that the strain belonging to non-nodulating Bacillus pumilus Qtx-10 had genes similar to those of Rhizobium leguminosarum Qtx-10-1. The results indicated that horizontal gene transfer could have occurred between rhizobia and non-symbiotic endophyties. Under pot culture conditions, out of the 20 representative endophytic isolates, 15 with plant growth-promoting traits, such as IAA production, ACC deaminase, phosphate solubilization, chitinase, siderophore, and fungal inhibition activity showed plant growth-promoting activity with respect to various plant parameters such as chlorophyll content, fresh weight of plant, shoot length, nodule number per plant and average nodule weight per plant when co-inoculated with rhizobial bioinoculant Mesorhizobium sp. Zw-19 under N-free culture conditions. Among them, Bacillus pumilus Qtx-10 and Streptomyces bottropensis Gt-10 were excellent plant growth-promoting bacteria, which enhanced the seeding fresh weight by 87.5% and the shoot length by 89.4%, respectively. The number of nodules grew more than 31.89% under field conditions. Our findings indicate the frequent presence of these non-symbiotic endophytic bacteria within root nodules, and that they help to improve nodulation and nitrogen fixation in legume plants through synergistic interactions with rhizobia.}, }
@article {pmid31683155, year = {2019}, author = {Yin, X and Deng, Y and Ma, L and Wang, Y and Chan, LYL and Zhang, T}, title = {Exploration of the antibiotic resistome in a wastewater treatment plant by a nine-year longitudinal metagenomic study.}, journal = {Environment international}, volume = {133}, number = {Pt B}, pages = {105270}, doi = {10.1016/j.envint.2019.105270}, pmid = {31683155}, issn = {1873-6750}, mesh = {Anti-Bacterial Agents/chemistry/*pharmacology ; Drug Resistance, Bacterial/*drug effects ; Ecosystem ; Genes, Bacterial ; Hong Kong ; Humans ; Longitudinal Studies ; Metagenome ; Methicillin-Resistant Staphylococcus aureus/*drug effects ; Sewage/microbiology ; Wastewater/*microbiology ; }, abstract = {The spread of antibiotic resistance genes (ARGs) is a growing global problem. Activated sludge (AS) in wastewater treatment plants (WWTPs) has been proposed as a hotspot for ARGs. However, few studies have been conducted to uncover the temporal dynamics of the resistome of AS in WWTPs by long-term longitudinal sampling. In this study, we quantified ARGs and identified their host microbiome in a Hong Kong WWTP in 97 monthly AS samples spanning 9 years. Throughout this analysis, we demonstrated that both the abundance and structures of the resistome changed significantly every two to three years, implying that there was a successive selection of resistomes in the AS system over the study period. The detection of genes of antibiotic-resistant pathogens that are emerging major threats to public health in the AS samples, including mcr, CRE (carbapenem-resistant Enterobacteriaceae) and MRSA (methicillin-resistant Staphylococcus aureus)-related genes, highlight the role of WWTPs as reservoirs of ARGs. In addition, the core resistome (abundant and persistent genes) in AS were found to overlap with those in other ecosystems such as urban sewage, livestock feces, and fishpond sediments, revealing the broad dissemination of ARGs in WWTPs and other environments. Annual variation of resistomes were explained via structural equation modeling (SEM), which deciphered the structural linkages of determining factors such as the operational parameters, microbial community composition and horizontal gene transfer (HGT). Specifically, potentially relevant antibiotic resistance bacteria (ARBs) were explored and discussed based on assembly-based analyses and network correlations. Moreover, consistent with the clear relationship between resistomes and mobile genetic elements (MGEs), it was found that there was a relatively high potential for gene exchange in AS in comparison with soil genomes, which could be explained by the engineering features of WWTPs. Based on these findings, longitudinal monitoring of WWTPs is warranted for risk assessment to reveal emerging ARGs, resistome evolution, correlations with ARBs, and the potential for spread in downstream environments and concomitant exposure risks for humans.}, }
@article {pmid31682962, year = {2020}, author = {Arushothy, R and Ramasamy, H and Hashim, R and Raj A S, S and Amran, F and Samsuddin, N and Ahmad, N}, title = {Multidrug-resistant Streptococcus pneumoniae causing invasive pneumococcal disease isolated from a paediatric patient.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {90}, number = {}, pages = {219-222}, doi = {10.1016/j.ijid.2019.10.037}, pmid = {31682962}, issn = {1878-3511}, mesh = {Anti-Bacterial Agents/pharmacology ; Cefotaxime/pharmacology ; Ceftriaxone/pharmacology ; *Drug Resistance, Multiple, Bacterial ; Erythromycin/pharmacology ; Female ; Gene Transfer, Horizontal ; Humans ; Infant ; Penicillins/pharmacology ; Pneumococcal Infections/epidemiology/*microbiology ; Serogroup ; Serotyping ; Streptococcus pneumoniae/classification/drug effects/genetics/*physiology ; }, abstract = {The emergence of non-vaccine multidrug-resistant Streptococcus pneumoniae serotypes is on rise. This study was performed to investigate a highly resistant serotype 15A S. pneumoniae isolated from the blood specimen of a 20-month-old patient who died of her infection. The SS40_16 isolate was resistant to erythromycin, co-trimoxazole, tetracycline, and chloramphenicol, as well as to penicillin, ceftriaxone, and cefotaxime (using meningitis cut-off points, Clinical and Laboratory Standards Institute). The isolate belonged to sequence type 1591 (ST1591) and was related to CC81 clonal complex, suggesting the possibility of horizontal gene transfer. Scanning electron microscopy comparison between resistant and sensitive pneumococcal isolates also indicated similar phenotypic characteristics that confer high resistance. The emergence of highly resistant non-vaccine pneumococci is of great concern to public health and in the clinical setting. Pneumococcal surveillance programs represent a crucial tool, not only for determining the impact of pneumococcal conjugate vaccines, but also for monitoring the selective pressure of serotype replacement with regard to the treatment of invasive pneumococcal disease.}, }
@article {pmid31681239, year = {2019}, author = {Meygret, A and Peuchant, O and Dordet-Frisoni, E and Sirand-Pugnet, P and Citti, C and Bébéar, C and Béven, L and Pereyre, S}, title = {High Prevalence of Integrative and Conjugative Elements Encoding Transcription Activator-Like Effector Repeats in Mycoplasma hominis.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2385}, pmid = {31681239}, issn = {1664-302X}, abstract = {Integrative and conjugative elements (ICEs) are modular mobile genetic elements that can disseminate through excision, circularization, and transfer. Mycoplasma ICEs have recently been found distributed among some mycoplasma species and there is accumulating evidence that they play a pivotal role in horizontal gene transfers. The occurrence of ICEs has not been documented in Mycoplasma hominis, a human urogenital pathogen responsible for urogenital infections, neonatal infections and extragenital infections. In this study, we searched for, characterized, and compared ICEs by genome analyses of 12 strains of M. hominis. ICEs of 27-30 kb were found in one or two copies in seven of the 12 M. hominis strains sequenced. Only five of these ICEs seemed to be functional, as assessed by detection of circular forms of extrachromosomal ICE. Moreover, the prevalence of ICEs in M. hominis was estimated to be 45% in a collection of 120 clinical isolates of M. hominis, including 27 tetracycline-resistant tet(M)-positive isolates. The proportion of ICEs was not higher in isolates carrying the tet(M) gene, suggesting that ICEs are not involved in tetracycline resistance. Notably, all M. hominis ICEs had a very similar structure, consisting of a 4.0-5.1 kb unusual module composed of five to six juxtaposed CDSs. All the genes forming this module were specific to M. hominis ICEs as they had no homologs in other mycoplasma ICEs. In each M. hominis ICE, one to three CDSs encode proteins that share common structural features with transcription activator-like (TAL) effectors involved in polynucleotide recognition and signal transduction in symbiotic plant pathogen bacteria. The conserved and specific structure of M. hominis ICEs and the high prevalence in clinical strains suggest that these ICEs may confer a selective advantage for the physiology or pathogenicity of this human pathogenic bacterium. These data open the way for further studies aiming at unraveling horizontal gene transfers and virulence factors in M. hominis.}, }
@article {pmid31681190, year = {2019}, author = {Gao, NL and Chen, J and Wang, T and Lercher, MJ and Chen, WH}, title = {Prokaryotic Genome Expansion Is Facilitated by Phages and Plasmids but Impaired by CRISPR.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2254}, pmid = {31681190}, issn = {1664-302X}, abstract = {Viruses and plasmids can introduce novel DNA into bacterial cells, thereby creating an opportunity for genome expansion; conversely, CRISPR, the prokaryotic adaptive immune system, which targets and eliminates foreign DNAs, may impair genome expansions. Recent studies presented conflicting results over the impact of CRISPR on genome expansion. In this study, we constructed a comprehensive dataset of prokaryotic genomes and identified their associations with viruses and plasmids. We found that genomes associated with viruses and/or plasmids were significantly larger than those without, indicating that both viruses and plasmids contribute to genome expansion. Genomes were increasingly larger with increasing numbers of associated viruses or plasmids. Conversely, genomes with CRISPR systems were significantly smaller than those without, indicating that CRISPR has a negative impact on genome size. These results confirmed that on evolutionary timescales, viruses and plasmids facilitate genome expansion, while CRISPR impairs such a process in prokaryotes. Furthermore, our results also revealed that CRISPR systems show a preference for targeting viruses over plasmids.}, }
@article {pmid31679927, year = {2019}, author = {Olofsson, JK and Dunning, LT and Lundgren, MR and Barton, HJ and Thompson, J and Cuff, N and Ariyarathne, M and Yakandawala, D and Sotelo, G and Zeng, K and Osborne, CP and Nosil, P and Christin, PA}, title = {Population-Specific Selection on Standing Variation Generated by Lateral Gene Transfers in a Grass.}, journal = {Current biology : CB}, volume = {29}, number = {22}, pages = {3921-3927.e5}, doi = {10.1016/j.cub.2019.09.023}, pmid = {31679927}, issn = {1879-0445}, support = {MR/K001744/1/MRC_/Medical Research Council/United Kingdom ; BB/J004243/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Biological Evolution ; Evolution, Molecular ; Gene Expression Regulation, Plant/genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Plant/genetics ; Genome/genetics ; Phylogeny ; Poaceae/*genetics ; }, abstract = {Evidence of eukaryote-to-eukaryote lateral gene transfer (LGT) has accumulated in recent years [1-14], but the selective pressures governing the evolutionary fate of these genes within recipient species remain largely unexplored [15, 16]. Among non-parasitic plants, successful LGT has been reported between different grass species [5, 8, 11, 16-19]. Here, we use the grass Alloteropsis semialata, a species that possesses multigene LGT fragments that were acquired recently from distantly related grass species [5, 11, 16], to test the hypothesis that the successful LGT conferred an advantage and were thus rapidly swept into the recipient species. Combining whole-genome and population-level RAD sequencing, we show that the multigene LGT fragments were rapidly integrated in the recipient genome, likely due to positive selection for genes encoding proteins that added novel functions. These fragments also contained physically linked hitchhiking protein-coding genes, and subsequent genomic erosion has generated gene presence-absence polymorphisms that persist in multiple geographic locations, becoming part of the standing genetic variation. Importantly, one of the hitchhiking genes underwent a secondary rapid spread in some populations. This shows that eukaryotic LGT can have a delayed impact, contributing to local adaptation and intraspecific ecological diversification. Therefore, while short-term LGT integration is mediated by positive selection on some of the transferred genes, physically linked hitchhikers can remain functional and augment the standing genetic variation with delayed adaptive consequences.}, }
@article {pmid31679813, year = {2019}, author = {Ophinni, Y and Palatini, U and Hayashi, Y and Parrish, NF}, title = {piRNA-Guided CRISPR-like Immunity in Eukaryotes.}, journal = {Trends in immunology}, volume = {40}, number = {11}, pages = {998-1010}, doi = {10.1016/j.it.2019.09.003}, pmid = {31679813}, issn = {1471-4981}, mesh = {Animals ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; DNA Transposable Elements/*genetics ; Drosophila melanogaster ; Endogenous Retroviruses/*genetics ; Epigenesis, Genetic ; Eukaryota ; Gene Transfer, Horizontal ; Germ Cells/*physiology ; Humans ; Immunity/*genetics ; RNA, Small Interfering/*genetics ; }, abstract = {Eukaryotic genomes contain virus-derived sequences called endogenous virus elements (EVEs). The majority of EVEs are related to retroviruses, which integrate into the host genome in order to replicate. Some retroviral EVEs encode a function; for example, some produce proteins that block infection by related viruses. EVEs derived from nonretroviral viruses - also recently found in many eukaryotic genomes - are more enigmatic. Here, we summarize the evidence that EVEs can act as templates to generate Piwi-interacting RNAs (piRNAs), whose canonical function is sequence-specific silencing of transposable elements (TEs) to maintain genomic integrity. We argue that EVEs may thus enable heritable, sequence-specific antiviral immune memory in eukaryotes - analogous to CRISPR-Cas immunity in prokaryotes.}, }
@article {pmid31676475, year = {2019}, author = {Caldera, EJ and Chevrette, MG and McDonald, BR and Currie, CR}, title = {Local Adaptation of Bacterial Symbionts within a Geographic Mosaic of Antibiotic Coevolution.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {24}, pages = {}, pmid = {31676475}, issn = {1098-5336}, support = {T32 GM008505/GM/NIGMS NIH HHS/United States ; U19 TW009872/TW/FIC NIH HHS/United States ; U19 AI109673/AI/NIAID NIH HHS/United States ; }, mesh = {Acclimatization/*physiology ; Actinobacteria/genetics/*metabolism ; Animals ; Anti-Bacterial Agents/*metabolism/pharmacology ; Ants/microbiology ; *Biological Coevolution ; Biosynthetic Pathways/genetics ; Costa Rica ; Host Microbial Interactions/physiology ; Hypocreales/drug effects/pathogenicity ; Secondary Metabolism/genetics ; Symbiosis/genetics/*physiology ; }, abstract = {The geographic mosaic theory of coevolution (GMC) posits that coevolutionary dynamics go beyond local coevolution and are comprised of the following three components: geographic selection mosaics, coevolutionary hot spots, and trait remixing. It is unclear whether the GMC applies to bacteria, as horizontal gene transfer and cosmopolitan dispersal may violate theoretical assumptions. Here, we test key GMC predictions in an antibiotic-producing bacterial symbiont (genus Pseudonocardia) that protects the crops of neotropical fungus-farming ants (Apterostigma dentigerum) from a specialized pathogen (genus Escovopsis). We found that Pseudonocardia antibiotic inhibition of common Escovopsis pathogens was elevated in A. dentigerum colonies from Panama compared to those from Costa Rica. Furthermore, a Panama Canal Zone population of Pseudonocardia on Barro Colorado Island (BCI) was locally adapted, whereas two neighboring populations were not, consistent with a GMC-predicted selection mosaic and a hot spot of adaptation surrounded by areas of maladaptation. Maladaptation was shaped by incongruent Pseudonocardia-Escovopsis population genetic structure, whereas local adaptation was facilitated by geographic isolation on BCI after the flooding of the Panama Canal. Genomic assessments of antibiotic potential of 29 Pseudonocardia strains identified diverse and unique biosynthetic gene clusters in BCI strains despite low genetic diversity in the core genome. The strength of antibiotic inhibition was not correlated with the presence/absence of individual biosynthetic gene clusters or with parasite location. Rather, biosynthetic gene clusters have undergone selective sweeps, suggesting that the trait remixing dynamics conferring the long-term maintenance of antibiotic potency rely on evolutionary genetic changes within already-present biosynthetic gene clusters and not simply on the horizontal acquisition of novel genetic elements or pathways.IMPORTANCE Recently, coevolutionary theory in macroorganisms has been advanced by the geographic mosaic theory of coevolution (GMC), which considers how geography and local adaptation shape coevolutionary dynamics. Here, we test GMC in an ancient symbiosis in which the ant Apterostigma dentigerum cultivates fungi in an agricultural system analogous to human farming. The cultivars are parasitized by the fungus Escovopsis The ants maintain symbiotic actinobacteria with antibiotic properties that help combat Escovopsis infection. This antibiotic symbiosis has persisted for tens of millions of years, raising the question of how antibiotic potency is maintained over these time scales. Our study tests the GMC in a bacterial defensive symbiosis and in a multipartite symbiosis framework. Our results show that this multipartite symbiotic system conforms to the GMC and demonstrate that this theory is applicable in both microbes and indirect symbiont-symbiont interactions.}, }
@article {pmid31675559, year = {2019}, author = {Sui, Q and Chen, Y and Yu, D and Wang, T and Hai, Y and Zhang, J and Chen, M and Wei, Y}, title = {Fates of intracellular and extracellular antibiotic resistance genes and microbial community structures in typical swine wastewater treatment processes.}, journal = {Environment international}, volume = {133}, number = {Pt B}, pages = {105183}, doi = {10.1016/j.envint.2019.105183}, pmid = {31675559}, issn = {1873-6750}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bioreactors ; DNA, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Swine ; Wastewater ; }, abstract = {Swine wastewater is an important reservoir of spread antibiotic resistance to the environment. Intra- and extracellular antibiotic resistance genes (iARGs and eARGs) were quantified during two typical swine wastewater treatment processes including a sequencing membrane bioreactor (SMBR) at pilot-scale and anaerobic-anoxic-oxic (A[2]O) at full-scale. The concentrations of iARGs and eARGs in raw wastewater were 3.42E+09 and 3.79E+07 copies/mL, respectively. The compositions were different between iARGs and eARGs. SMBR showed 0.63 log higher removals in the concentrations of iARG than A[2]O, while similar removal effects (3.01-3.44 log copies/mL) of eARGs were performed by the two processes. It suggested that membrane separation had advantages in the concentration removals of iARG rather than eARG. sul1 took the dominance in eARGs in effluent and had positive correlations with intI1, which indicated the risk of horizontal gene transfer of eARGs after wastewater discharge. Microbial community structures were estimated by 16S rRNA gene sequencing with both intra- and extracellular DNA (iDNA and eDNA). Compared between the effluent samples of the two treatment processes, microbial community structures estimated by iDNA had great differences, however which were similar for eDNA. Microbial community and water-quality parameters were the major influencing factors on ARG occurrences during swine wastewater treatment.}, }
@article {pmid31665678, year = {2019}, author = {Liao, H and Zhao, Q and Cui, P and Chen, Z and Yu, Z and Geisen, S and Friman, VP and Zhou, S}, title = {Efficient reduction of antibiotic residues and associated resistance genes in tylosin antibiotic fermentation waste using hyperthermophilic composting.}, journal = {Environment international}, volume = {133}, number = {Pt B}, pages = {105203}, doi = {10.1016/j.envint.2019.105203}, pmid = {31665678}, issn = {1873-6750}, support = {105624/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Anti-Bacterial Agents/*analysis ; Bacteria/genetics ; *Composting ; Drug Resistance, Microbial/*genetics ; Fermentation ; *Genes, Bacterial ; Tylosin/*analysis ; }, abstract = {Insufficient removal of antibiotics and antibiotic resistance genes (ARGs) from waste products can increase the risk of selection for antibiotic resistance in non-clinical environments. While composting is an efficient way to reduce ARGs, most conventional methods are ineffective at processing highly contaminated antibiotic fermentation waste. Here we explored the efficacy and underlying mechanisms of hyperthermophilic composting at removing tylosin antibiotic fermentation residues (TFR) and associated ARGs and mobile genetic elements (MGEs; plasmids, integrons and transposon). Hyperthermophilic composting removed 95.0% of TFR, 75.8% of ARGs and 98.5% of MGEs and this reduction mainly occurred after extended exposure to temperatures above 60 °C for at least 6 days. Based on sequencing and culture-dependent experiments, reduction in ARGs and MGEs was strongly associated with a decrease in the number of bacterial taxa that were initially associated with ARGs and MGEs. Moreover, we found 94.1% reduction in plasmid genes abundances (ISCR1 and IncQ-oriV) that significantly correlated with reduced ARGs during the composting, which suggests that plasmids were the main carriers for ARGs. We verified this using direct culturing to show that ARGs were more often found in plasmids during the early phase of composting. Together these results suggest that hyperthermophilic composting is efficient at removing ARGs and associated resistance genes from antibiotic fermentation waste by decreasing the abundance of antibiotic resistance plasmids and associated host bacteria.}, }
@article {pmid31662278, year = {2019}, author = {Zhang, K and Beverley, SM}, title = {Mannogen-ing Central Carbon Metabolism by Leishmania.}, journal = {Trends in parasitology}, volume = {35}, number = {12}, pages = {947-949}, pmid = {31662278}, issn = {1471-5007}, support = {R01 AI031078/AI/NIAID NIH HHS/United States ; R01 AI099380/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Carbon ; Glycosyltransferases ; *Leishmania ; *Parasites ; Phosphorylases ; Virulence ; }, abstract = {Leishmania parasites synthesize mannogens, a unique type of storage carbohydrate, from finely tuned interactions between synthesis and degradation by a family of mannosyltransferase/phosphorylases (MTPs) newly discovered by Sernee et al. The crucial roles of mannogen in regulating central carbon metabolism and in vivo virulence suggest the potential of MTPs as promising drug targets.}, }
@article {pmid31661914, year = {2019}, author = {Arber, W}, title = {Self-Organization of the Biological Evolution.}, journal = {Genes}, volume = {10}, number = {11}, pages = {}, doi = {10.3390/genes10110854}, pmid = {31661914}, issn = {2073-4425}, mesh = {Bacteriophages/genetics/pathogenicity ; Escherichia coli/*genetics/virology ; *Evolution, Molecular ; Mutation ; Polymorphism, Genetic ; Selection, Genetic ; }, abstract = {We report here experiments carried out with nonpathogenic Escherichia coli bacterial strains and their phages. This research yielded interesting insights into their activities, occasionally producing genetic variants of different types. In order to not interfere with the genetic stability of the parental strains involved, we found that the bacteria are genetically equipped to only rarely produce a genetic variant, which may occur by a number of different approaches. On the one hand, the genes of relevance for the production of specific genetic variants are relatively rarely expressed. On the other hand, other gene products act as moderators of the frequencies that produce genetic variants. We call the genes producing genetic variants and those moderating the frequencies of genetic variation "evolution genes". Their products are generally not required for daily bacterial life. We can, therefore, conclude that the bacterial genome has a duality. Some of the bacterial enzymes involved in biological evolution have become useful tools (e.g., restriction endonucleases) for molecular genetic research involving the genetic set-up of any living organism.}, }
@article {pmid31661808, year = {2019}, author = {Romaniuk, K and Styczynski, M and Decewicz, P and Buraczewska, O and Uhrynowski, W and Fondi, M and Wolosiewicz, M and Szuplewska, M and Dziewit, L}, title = {Diversity and Horizontal Transfer of Antarctic Pseudomonas spp. Plasmids.}, journal = {Genes}, volume = {10}, number = {11}, pages = {}, pmid = {31661808}, issn = {2073-4425}, mesh = {Antarctic Regions ; Biofilms ; DNA Transposable Elements ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Microbiota ; *Phylogeny ; Plasmids/genetics ; Pseudomonas/classification/*genetics/physiology ; }, abstract = {Pseudomonas spp. are widely distributed in various environments around the world. They are also common in the Antarctic regions. To date, almost 200 plasmids of Pseudomonas spp. have been sequenced, but only 12 of them were isolated from psychrotolerant strains. In this study, 15 novel plasmids of cold-active Pseudomonas spp. originating from the King George Island (Antarctica) were characterized using a combined, structural and functional approach, including thorough genomic analyses, functional analyses of selected genetic modules, and identification of active transposable elements localized within the plasmids and comparative genomics. The analyses performed in this study increased the understanding of the horizontal transfer of plasmids found within Pseudomonas populations inhabiting Antarctic soils. It was shown that the majority of the studied plasmids are narrow-host-range replicons, whose transfer across taxonomic boundaries may be limited. Moreover, structural and functional analyses enabled identification and characterization of various accessory genetic modules, including genes encoding major pilin protein (PilA), that enhance biofilm formation, as well as active transposable elements. Furthermore, comparative genomic analyses revealed that the studied plasmids of Antarctic Pseudomonas spp. are unique, as they are highly dissimilar to the other known plasmids of Pseudomonas spp.}, }
@article {pmid31659841, year = {2019}, author = {Wilkins, LGE}, title = {Can interspecies affairs in the dark lead to evolutionary innovation?.}, journal = {Molecular ecology}, volume = {28}, number = {21}, pages = {4693-4696}, doi = {10.1111/mec.15262}, pmid = {31659841}, issn = {1365-294X}, mesh = {Alleles ; Animals ; Ecology ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genetic Variation/genetics ; Genome, Bacterial/genetics ; Symbiosis/genetics ; }, abstract = {Evolutionary adaptation is the adjustment of species to a new or changing environment. Engaging in mutualistic microbial symbioses has been put forward as a key trait that promotes the differential, evolutionary success of many animal and plant lineages (McFall-Ngai, 2008). Microbial mutualists allow these organisms to occupy new ecological niches where they could not have persisted on their own or would have been constrained by competitors. Vertical transmission of beneficial microbial symbionts from parents to the offspring is expected to link the adaptive association between a given host and microbe, and it can lead to coevolution and sometimes even cospeciation (Fisher, Henry, Cornwallis, Kiers, &amp; West, 2017). Vertical transmission also causes bottlenecks that strongly reduce the effective population size and genetic diversity of the symbiont population. Moreover, vertically transmitted symbionts are assumed to have fewer opportunities to exchange genes with relatives in the environment. In a "From the Cover" article in this issue of Molecular Ecology, Breusing, Johnson, Vrijenhoek, and Young (2019) investigated whether hybridization among different host species could lead to interspecies exchange of otherwise strictly vertically transmitted symbionts. Hybridization of divergent lineages can potentially cause intrinsic and extrinsic incompatibilities, swamp rare alleles, and lead to population extinctions. In some cases, however, it might also create novel trait combinations that lead to evolutionary innovation (Marques, Meier, &amp; Seehausen, 2019). Breusing et al. (2019) linked the concept of hybridization to symbiont transmission, and their findings have significant implications for the study of evolution of vertically transmitted symbionts and their hosts.}, }
@article {pmid31659382, year = {2020}, author = {Rocha, G and Le Queré, A and Medina, A and Cuéllar, A and Contreras, JL and Carreño, R and Bustillos, R and Muñoz-Rojas, J and Villegas, MDC and Chaintreuil, C and Dreyfus, B and Munive, JA}, title = {Diversity and phenotypic analyses of salt- and heat-tolerant wild bean Phaseolus filiformis rhizobia native of a sand beach in Baja California and description of Ensifer aridi sp. nov.}, journal = {Archives of microbiology}, volume = {202}, number = {2}, pages = {309-322}, pmid = {31659382}, issn = {1432-072X}, support = {242743//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; 273344//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; 220636//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; VIEP00075//Benem&#xe9;rita Universidad Aut&#xf3;noma de Puebla/ ; M08-A02//SEP-CONACYT-ANUIES-ECOS NORD France/ ; }, mesh = {DNA, Bacterial/genetics ; Hot Temperature ; Mexico ; Phaseolus/growth &amp; development/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhizobiaceae/*classification/genetics/*isolation &amp; purification ; Root Nodules, Plant/*microbiology ; Salt Tolerance/genetics ; Sand ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {In northern Mexico, aridity, salinity and high temperatures limit areas that can be cultivated. To investigate the nature of nitrogen-fixing symbionts of Phaseolus filiformis, an adapted wild bean species native to this region, their phylogenies were inferred by MLSA. Most rhizobia recovered belong to the proposed new species Ensifer aridi. Phylogenetic analyses of nodC and nifH show that Mexican isolates carry symbiotic genes acquired through horizontal gene transfer that are divergent from those previously characterized among bean symbionts. These strains are salt tolerant, able to grow in alkaline conditions, high temperatures, and capable of utilizing a wide range of carbohydrates and organic acids as carbon sources for growth. This study improves the knowledge on diversity, geographic distribution and evolution of bean-nodulating rhizobia in Mexico and further enlarges the spectrum of microsymbiont with which Phaseolus species can interact with, including cultivated bean varieties, notably under stressed environments. Here, the species Ensifer aridi sp. nov. is proposed as strain type of the Moroccan isolate LMR001[T] (= LMG 31426[T]; = HAMBI 3707[T]) recovered from desert sand dune.}, }
@article {pmid31659012, year = {2020}, author = {Pallegar, P and Peña-Castillo, L and Langille, E and Gomelsky, M and Lang, AS}, title = {Cyclic di-GMP-Mediated Regulation of Gene Transfer and Motility in Rhodobacter capsulatus.}, journal = {Journal of bacteriology}, volume = {202}, number = {2}, pages = {}, pmid = {31659012}, issn = {1098-5530}, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics/metabolism ; Cyclic GMP/*analogs &amp; derivatives/metabolism ; Escherichia coli Proteins/metabolism ; Gene Expression Regulation, Bacterial/drug effects ; Gene Transfer, Horizontal/drug effects ; Molecular Sequence Data ; Phosphoric Diester Hydrolases/genetics/metabolism ; Phosphorus-Oxygen Lyases/metabolism ; Rhodobacter capsulatus/drug effects/*metabolism ; Signal Transduction/drug effects/genetics ; }, abstract = {Gene transfer agents (GTAs) are bacteriophage-like particles produced by several bacterial and archaeal lineages that contain small pieces of the producing cells' genomes that can be transferred to other cells in a process similar to transduction. One well-studied GTA is RcGTA, produced by the alphaproteobacterium Rhodobacter capsulatus RcGTA gene expression is regulated by several cellular regulatory systems, including the CckA-ChpT-CtrA phosphorelay. The transcription of multiple other regulator-encoding genes is affected by the response regulator CtrA, including genes encoding putative enzymes involved in the synthesis and hydrolysis of the second messenger bis-(3'-5')-cyclic dimeric GMP (c-di-GMP). To investigate whether c-di-GMP signaling plays a role in RcGTA production, we disrupted the CtrA-affected genes potentially involved in this process. We found that disruption of four of these genes affected RcGTA gene expression and production. We performed site-directed mutagenesis of key catalytic residues in the GGDEF and EAL domains responsible for diguanylate cyclase (DGC) and c-di-GMP phosphodiesterase (PDE) activities and analyzed the functions of the wild-type and mutant proteins. We also measured RcGTA production in R. capsulatus strains where intracellular levels of c-di-GMP were altered by the expression of either a heterologous DGC or a heterologous PDE. This adds c-di-GMP signaling to the collection of cellular regulatory systems controlling gene transfer in this bacterium. Furthermore, the heterologous gene expression and the four gene disruptions had similar effects on R. capsulatus flagellar motility as found for gene transfer, and we conclude that c-di-GMP inhibits both RcGTA production and flagellar motility in R. capsulatusIMPORTANCE Gene transfer agents (GTAs) are virus-like particles that move cellular DNA between cells. In the alphaproteobacterium Rhodobacter capsulatus, GTA production is affected by the activities of multiple cellular regulatory systems, to which we have now added signaling via the second messenger dinucleotide molecule bis-(3'-5')-cyclic dimeric GMP (c-di-GMP). Similar to the CtrA phosphorelay, c-di-GMP also affects R. capsulatus flagellar motility in addition to GTA production, with lower levels of intracellular c-di-GMP favoring increased flagellar motility and gene transfer. These findings further illustrate the interconnection of GTA production with global systems of regulation in R. capsulatus, providing additional support for the notion that the production of GTAs has been maintained in this and related bacteria because it provides a benefit to the producing organisms.}, }
@article {pmid31654794, year = {2020}, author = {Kocer, K and Boutin, S and Dalpke, AH and Heeg, K and Mutters, NT and Nurjadi, D}, title = {Comparative genomic analysis reveals a high prevalence of inter-species in vivo transfer of carbapenem-resistance plasmids in patients with haematological malignancies.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {26}, number = {6}, pages = {780.e1-780.e8}, doi = {10.1016/j.cmi.2019.10.014}, pmid = {31654794}, issn = {1469-0691}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Carbapenem-Resistant Enterobacteriaceae/*genetics/*isolation &amp; purification ; Carbapenems/pharmacology ; Child ; Child, Preschool ; Enterobacteriaceae Infections/microbiology/transmission ; Female ; *Gene Transfer, Horizontal ; Genomics ; Gram-Negative Bacteria/drug effects ; Hematologic Neoplasms/*microbiology ; Humans ; Infant ; Male ; Middle Aged ; Plasmids/*genetics ; Prevalence ; Retrospective Studies ; Whole Genome Sequencing ; Young Adult ; }, abstract = {OBJECTIVES: Conjugative gene transfer has been considered as one of the driving factors in the transmission and dissemination of multidrug resistance in bacteria. The abundance of antimicrobial resistance genes and bacteria in the gut microbiome may provide the ideal platform for plasmid exchange. Systematic data on in vivo horizontal gene transfer (HGT) and its frequency are scarce.<br><br>MATERIALS AND METHODS: One hundred and ninety-six carbapenem-resistant gram-negative bacilli (CRGNBs) from 179 patients (158 inpatients and 21 outpatients) between January 2016 and April 2017 were analysed retrospectively. Alignment of plasmid content for 32 isolates from 16 patients with multiple CRGNB species was performed from whole-genome sequencing (WGS) data.<br><br>RESULTS: Sixteen of the 179 patients (8.9%) were colonized and/or infected with more than one CRGNB species; 11/179 (6.1%) were colonized by multiple carbapenem-resistant Enterobacteriaceae (CREs) and 5/179 (2.8%) by carbapenem-resistant non-fermenters (CRNFs) and CREs. WGS suggested interspecies transfer as the predominant mechanism rather than independent acquisition in 8/10 patients (80%, one non-recoverable isolate) with multiple CREs but not in CRNF-CRE combinations; 30/158 inpatients (20%) had underlying haematological malignancies, and they are more likely to exhibit multiple CRGNB strains (OR 3.0, 95%CI 0.98-8.89, p 0.05) and CRE strains (OR 3.9, 95%CI 1.02-14.58, p 0.04) during hospital stay compared to other patient groups.<br><br>CONCLUSION: Our data give insight into the occurrence of natural in&#xa0;vivo HGT in a clinical setting. Better understanding of HGT will help optimize containment measures and may guide antibiotic stewardship programmes.}, }
@article {pmid31654228, year = {2020}, author = {Zhu, D and Yang, Z and Xu, J and Wang, M and Jia, R and Chen, S and Liu, M and Zhao, X and Yang, Q and Wu, Y and Zhang, S and Liu, Y and Zhang, L and Yu, Y and Chen, X and Cheng, A}, title = {Pan-genome analysis of Riemerella anatipestifer reveals its genomic diversity and acquired antibiotic resistance associated with genomic islands.}, journal = {Functional &amp; integrative genomics}, volume = {20}, number = {3}, pages = {307-320}, pmid = {31654228}, issn = {1438-7948}, support = {2017YFD050080//National Key Research and Development Program of China/ ; CARS-42-17//China Agricultural Research System/ ; 2017HH0026//International S&amp;T Cooperation Program of Sichuan Province/ ; (2017)03//Science and Technology Innovation Program of Guizhou Academy of Agricultural Science/ ; CARS-SVDIP//Sichuan Veterinary Medicine and Drug Innovation Group of China Agricultural Research System/ ; }, mesh = {*Drug Resistance, Bacterial ; Flavobacteriaceae/classification/*genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Phylogeny ; Virulence Factors/genetics ; }, abstract = {Riemerella anatipestifer is a gram-negative bacterium that leads to severe contagious septicemia in ducks, turkeys, chickens, and wild waterfowl. Here, a pan-genome with 32 R. anatipestifer genomes is re-established, and the mathematical model is calculated to evaluate the expansion of R. anatipestifer genomes, which were determined to be open. Average nucleotide identity (ANI) and phylogenetic analysis preliminarily clarify intraspecies variation and distance. Comparative genomic analysis of R. anatipestifer found that horizontal gene transfer events, which provide an expressway for the recruitment of novel functionalities and facilitate genetic diversity in microbial genomes, play a key role in the process of acquiring and transmitting antibiotic-resistance genes in R. anatipestifer. Furthermore, a new antibiotic-resistance gene cluster was identified in the same loci in 14 genomes. The uneven distribution of virulence factors was also confirmed by our results. Our study suggests that the ability to acquire foreign genes (such as antibiotic-resistance genes) increases the adaptability of R. anatipestifer, and the virulence genes with little mobility are highly conserved in R. anatipestifer.}, }
@article {pmid31653201, year = {2019}, author = {Choi, IS and Schwarz, EN and Ruhlman, TA and Khiyami, MA and Sabir, JSM and Hajarah, NH and Sabir, MJ and Rabah, SO and Jansen, RK}, title = {Fluctuations in Fabaceae mitochondrial genome size and content are both ancient and recent.}, journal = {BMC plant biology}, volume = {19}, number = {1}, pages = {448}, pmid = {31653201}, issn = {1471-2229}, mesh = {Fabaceae/*genetics ; *Genome Size ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; }, abstract = {BACKGROUND: Organelle genome studies of Fabaceae, an economically and ecologically important plant family, have been biased towards the plastid genome (plastome). Thus far, less than 15 mitochondrial genome (mitogenome) sequences of Fabaceae have been published, all but four of which belong to the subfamily Papilionoideae, limiting the understanding of size variation and content across the family. To address this, four mitogenomes were sequenced and assembled from three different subfamilies (Cercidoideae, Detarioideae and Caesalpinioideae).<br><br>RESULTS: Phylogenetic analysis based on shared mitochondrial protein coding regions produced a fully resolved and well-supported phylogeny that was completely congruent with the plastome tree. Comparative analyses suggest that two kinds of mitogenome expansions have occurred in Fabaceae. Size expansion of four genera (Tamarindus, Libidibia, Haematoxylum, and Leucaena) in two subfamilies (Detarioideae and Caesalpinioideae) occurred in relatively deep nodes, and was mainly caused by intercellular gene transfer and/or interspecific horizontal gene transfer (HGT). The second, more recent expansion occurred in the Papilionoideae as a result of duplication of native mitochondrial sequences. Family-wide gene content analysis revealed 11 gene losses, four (rps2, 7, 11 and 13) of which occurred in the ancestor of Fabaceae. Losses of the remaining seven genes (cox2, rpl2, rpl10, rps1, rps19, sdh3, sdh4) were restricted to specific lineages or occurred independently in different clades. Introns of three genes (cox2, ccmFc and rps10) showed extensive lineage-specific length variation due to large sequence insertions and deletions. Shared DNA analysis among Fabaceae mitogenomes demonstrated a substantial decay of intergenic spacers and provided further insight into HGT between the mimosoid clade of Caesalpinioideae and the holoparasitic Lophophytum (Balanophoraceae).<br><br>CONCLUSION: This study represents the most exhaustive analysis of Fabaceae mitogenomes so far, and extends the understanding the dynamic variation in size and gene/intron content. The four newly sequenced mitogenomes reported here expands the phylogenetic coverage to four subfamilies. The family has experienced multiple mitogenome size fluctuations in both ancient and recent times. The causes of these size variations are distinct in different lineages. Fabaceae mitogenomes experienced extensive size fluctuation by recruitment of exogenous DNA and duplication of native mitochondrial DNA.}, }
@article {pmid31649084, year = {2019}, author = {Gasser, MT and Chung, M and Bromley, RE and Nadendla, S and Dunning Hotopp, JC}, title = {Complete Genome Sequence of wAna, the Wolbachia Endosymbiont of Drosophila ananassae.}, journal = {Microbiology resource announcements}, volume = {8}, number = {43}, pages = {}, pmid = {31649084}, issn = {2576-098X}, support = {R01 CA206188/CA/NCI NIH HHS/United States ; U19 AI110820/AI/NIAID NIH HHS/United States ; }, abstract = {Here, we present the complete genome sequence of the Wolbachia endosymbiont wAna, isolated from Drosophila ananassae and derived from Oxford Nanopore and Illumina sequencing. We anticipate that this will aid in Wolbachia comparative genomics and the assembly of D. ananassae specifically in regions containing extensive lateral gene transfer events.}, }
@article {pmid31647561, year = {2020}, author = {Lewis, WH and Lind, AE and Sendra, KM and Onsbring, H and Williams, TA and Esteban, GF and Hirt, RP and Ettema, TJG and Embley, TM}, title = {Convergent Evolution of Hydrogenosomes from Mitochondria by Gene Transfer and Loss.}, journal = {Molecular biology and evolution}, volume = {37}, number = {2}, pages = {524-539}, pmid = {31647561}, issn = {1537-1719}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Aerobiosis ; Anaerobiosis ; Ciliophora/*classification/physiology ; Evolution, Molecular ; Gene Expression Profiling/*methods ; Gene Transfer, Horizontal ; Genome, Mitochondrial ; Hydrogen/metabolism ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; Sequence Analysis, RNA ; }, abstract = {Hydrogenosomes are H2-producing mitochondrial homologs found in some anaerobic microbial eukaryotes that provide a rare intracellular niche for H2-utilizing endosymbiotic archaea. Among ciliates, anaerobic and aerobic lineages are interspersed, demonstrating that the switch to an anaerobic lifestyle with hydrogenosomes has occurred repeatedly and independently. To investigate the molecular details of this transition, we generated genomic and transcriptomic data sets from anaerobic ciliates representing three distinct lineages. Our data demonstrate that hydrogenosomes have evolved from ancestral mitochondria in each case and reveal different degrees of independent mitochondrial genome and proteome reductive evolution, including the first example of complete mitochondrial genome loss in ciliates. Intriguingly, the FeFe-hydrogenase used for generating H2 has a unique domain structure among eukaryotes and appears to have been present, potentially through a single lateral gene transfer from an unknown donor, in the common aerobic ancestor of all three lineages. The early acquisition and retention of FeFe-hydrogenase helps to explain the facility whereby mitochondrial function can be so radically modified within this diverse and ecologically important group of microbial eukaryotes.}, }
@article {pmid31645564, year = {2019}, author = {Lee, J and Kim, D and Bhattacharya, D and Yoon, HS}, title = {Expansion of phycobilisome linker gene families in mesophilic red algae.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {4823}, pmid = {31645564}, issn = {2041-1723}, mesh = {Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; Genome, Plastid ; Genomics ; Photosynthesis/*genetics ; Phycobilisomes/*genetics ; Phylogeny ; Plastids/genetics ; Porphyridium/*genetics ; Rhodophyta/genetics ; Symbiosis ; }, abstract = {The common ancestor of red algae (Rhodophyta) has undergone massive genome reduction, whereby 25% of the gene inventory has been lost, followed by its split into the species-poor extremophilic Cyanidiophytina and the broadly distributed mesophilic red algae. Success of the mesophile radiation is surprising given their highly reduced gene inventory. To address this latter issue, we combine an improved genome assembly from the unicellular red alga Porphyridium purpureum with a diverse collection of other algal genomes to reconstruct ancient endosymbiotic gene transfers (EGTs) and gene duplications. We find EGTs associated with the core photosynthetic machinery that may have played important roles in plastid establishment. More significant are the extensive duplications and diversification of nuclear gene families encoding phycobilisome linker proteins that stabilize light-harvesting functions. We speculate that the origin of these complex families in mesophilic red algae may have contributed to their adaptation to a diversity of light environments.}, }
@article {pmid31641046, year = {2019}, author = {Zhong, C and Han, M and Yang, P and Chen, C and Yu, H and Wang, L and Ning, K}, title = {Comprehensive Analysis Reveals the Evolution and Pathogenicity of Aeromonas, Viewed from Both Single Isolated Species and Microbial Communities.}, journal = {mSystems}, volume = {4}, number = {5}, pages = {}, pmid = {31641046}, issn = {2379-5077}, abstract = {The genus Aeromonas is a common gastrointestinal pathogen associated with human and animal infections. Due to the high level of cross-species similarity, their evolutionary dynamics and genetic diversity are still fragmented. Hereby, we investigated the pan-genomes of 29 Aeromonas species, as well as Aeromonas species in microbial communities, to clarify their evolutionary dynamics and genetic diversity, with special focus on virulence factors and horizontal gene transfer events. Our study revealed an open pan-genome of Aeromonas containing 10,144 gene families. These Aeromonas species exhibited different functional constraints, with the single-copy core genes and most accessory genes experiencing purifying selection. The significant congruence between core genome and pan-genome trees revealed that core genes mainly affected evolutionary divergences of Aeromonas species. Gene gains and losses revealed a high level of genome plasticity, exhibited by hundreds of gene expansions and contractions, horizontally transferred genes, and mobile genetic elements. The selective constraints shaped virulence gene pools of these Aeromonas strains, where genes encoding hemolysin were ubiquitous. Of these strains, Aeromonas aquatica MX16A seemed to be more resistant, as it harbored most resistance genes. Finally, the virulence factors of Aeromonas in microbial communities were quite dynamic in response to environment changes. For example, the virulence diversity of Aeromonas in microbial communities could reach levels that match some of the most virulent Aeromonas species (such as A. hydrophila) in penetrated-air and modified-air packaging. Our work shed some light onto genetic diversity, evolutionary history, and functional features of Aeromonas, which could facilitate the detection and prevention of infections.IMPORTANCE Aeromonas has long been known as a gastrointestinal pathogen, yet it has many species whose evolutionary dynamics and genetic diversity had been unclear until now. We have conducted pan-genome analysis for 29 Aeromonas species and revealed a high level of genome plasticity exhibited by hundreds of gene expansions and contractions, horizontally transferred genes, and mobile genetic elements. These species also contained many virulence factors both identified from single isolated species and microbial community. This pan-genome study could elevate the level for detection and prevention of Aeromonas infections.}, }
@article {pmid31640552, year = {2019}, author = {Deng, Y and Xu, H and Su, Y and Liu, S and Xu, L and Guo, Z and Wu, J and Cheng, C and Feng, J}, title = {Horizontal gene transfer contributes to virulence and antibiotic resistance of Vibrio harveyi 345 based on complete genome sequence analysis.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {761}, pmid = {31640552}, issn = {1471-2164}, support = {319QN336)//the Hainan Provincial Natural Science Foundation of China/ ; 2018A030310695//Natural Science Foundation of Guangdong Province/ ; 31902415//National Natural Science Foundation of China/ ; 41806147//National Natural Science Foundation of China/ ; 2016YT03H038//Guangdong YangFan Innovative &amp; Entepreneurial Research Team Program/ ; CARS-48//the China Agriculture Research System/ ; }, mesh = {Drug Resistance, Microbial/*genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial/*genetics ; Genomic Islands/genetics ; Molecular Sequence Annotation ; Multigene Family ; Phylogeny ; Plasmids/genetics ; Prophages/genetics ; Species Specificity ; Vibrio/classification/*genetics/*pathogenicity/physiology ; Virulence/genetics ; Virulence Factors ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT), which is affected by environmental pollution and climate change, promotes genetic communication, changing bacterial pathogenicity and drug resistance. However, few studies have been conducted on the effect of HGT on the high pathogenicity and drug resistance of the opportunistic pathogen Vibrio harveyi.<br><br>RESULTS: V. harveyi 345 that was multidrug resistant and infected Epinephelus oanceolutus was isolated from a diseased organism in Shenzhen, Southern China, an important and contaminated aquaculture area. Analysis of the entire genome sequence predicted 5678 genes including 487 virulence genes contributing to bacterial pathogenesis and 25 antibiotic-resistance genes (ARGs) contributing to antimicrobial resistance. Five ARGs (tetm, tetb, qnrs, dfra17, and sul2) and one virulence gene (CU052_28670) on the pAQU-type plasmid p345-185, provided direct evidence for HGT. Comparative genome analysis of 31&#x2009;V. harveyi strains indicated that 217 genes and 7 gene families, including a class C beta-lactamase gene, a virulence-associated protein D gene, and an OmpA family protein gene were specific to strain V. harveyi 345. These genes could contribute to HGT or be horizontally transferred from other bacteria to enhance the virulence or antibiotic resistance of 345. Mobile genetic elements in 71 genomic islands encoding virulence factors for three type III secretion proteins and 13 type VI secretion system proteins, and two incomplete prophage sequences were detected that could be HGT transfer tools. Evaluation of the complete genome of V. harveyi 345 and comparative genomics indicated genomic exchange, especially exchange of pathogenic genes and drug-resistance genes by HGT contributing to pathogenicity and drug resistance. Climate change and continued environmental deterioration are expected to accelerate the HGT of V. harveyi, increasing its pathogenicity and drug resistance.<br><br>CONCLUSION: This study provides timely information for further analysis of V. harveyi pathogenesis and antimicrobial resistance and developing pollution control measurements for coastal areas.}, }
@article {pmid31639358, year = {2019}, author = {Brockhurst, MA and Harrison, E and Hall, JPJ and Richards, T and McNally, A and MacLean, C}, title = {The Ecology and Evolution of Pangenomes.}, journal = {Current biology : CB}, volume = {29}, number = {20}, pages = {R1094-R1103}, doi = {10.1016/j.cub.2019.08.012}, pmid = {31639358}, issn = {1879-0445}, support = {BB/R006253/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R014884/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 106918/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; BB/R006261/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Biological Evolution ; Evolution, Molecular ; *Genome, Bacterial ; *Metagenome ; Phylogeny ; }, abstract = {Since the first genome-scale comparisons, it has been evident that the genomes of many species are unbound by strict vertical descent: Large differences in gene content can occur among genomes belonging to the same prokaryotic species, with only a fraction of genes being universal to all genomes. These insights gave rise to the pangenome concept. The pangenome is defined as the set of all the genes present in a given species and can be subdivided into the accessory genome, present in only some of the genomes, and the core genome, present in all the genomes. Pangenomes arise due to gene gain by genomes from other species through horizontal gene transfer and differential gene loss among genomes, and have been described in both prokaryotes and eukaryotes. Our current view of pangenome variation is phenomenological and incomplete. In this review, we outline the mechanistic, ecological and evolutionary drivers of and barriers to horizontal gene transfer that are likely to structure pangenomes. We highlight the key role of conflict between the host chromosome(s) and the mobile genetic elements that mediate gene exchange. We identify shortcomings in our current models of pangenome evolution and suggest directions for future research to allow a more complete understanding of how and why pangenomes evolve.}, }
@article {pmid31639075, year = {2019}, author = {Booth, SC and Turner, RJ}, title = {Phylogenetic characterization of the energy taxis receptor Aer in Pseudomonas and phenotypic characterization in Pseudomonas pseudoalcaligenes KF707.}, journal = {Microbiology (Reading, England)}, volume = {165}, number = {12}, pages = {1331-1344}, doi = {10.1099/mic.0.000864}, pmid = {31639075}, issn = {1465-2080}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/genetics/*metabolism ; Gene Transfer, Horizontal ; Genetic Variation ; Membrane Proteins/chemistry/genetics/*metabolism ; Phenotype ; *Phylogeny ; Pseudomonas/classification/genetics/physiology ; Pseudomonas pseudoalcaligenes/*classification/genetics/*physiology ; Signal Transduction/genetics ; Species Specificity ; Taxis Response ; }, abstract = {Chemotaxis allows bacteria to sense gradients in their environment and respond by directing their swimming. Aer is a receptor that, instead of responding to a specific chemoattractant, allows bacteria to sense cellular energy levels and move towards favourable environments. In Pseudomonas, the number of apparent Aer homologues differs between the only two species it has been characterized in, Pseudomonas aeruginosa and Pseudomonas putida. Here we combined bioinformatic approaches with deletional mutagenesis in Pseudomonas pseudoalcaligenes KF707 to further characterize Aer. It was determined that the number of Aer homologues varies between zero and four throughout the genus Pseudomonas, and they were phylogenetically classified into five subgroups. We also used sequence analysis to show that these homologous receptors differ in their HAMP signal transduction domains. Genetic analysis also indicated that some Aer homologues have likely been subject to horizontal transfer. P. pseudoalcaligenes KF707 was unique among strains for having three Aer homologues as well as the receptors CttP and McpB. Phenotypic characterization in this strain showed that the most prevalent homologue of Aer was key, but not essential, for energy taxis. This study demonstrates that energy taxis in Pseudomonas varies between species and provides a new naming convention and associated phylogenetic details for Aer chemoreceptors.}, }
@article {pmid31635920, year = {2019}, author = {Wideman, JG and Richards, TA}, title = {Editorial overview: Investigating phenotype evolution in the post-genomic era.}, journal = {Current opinion in genetics &amp; development}, volume = {58-59}, number = {}, pages = {iii-v}, doi = {10.1016/j.gde.2019.09.006}, pmid = {31635920}, issn = {1879-0380}, mesh = {Bacteria/genetics/metabolism ; Eukaryota/genetics/metabolism ; *Evolution, Molecular ; Fungi/genetics/metabolism ; Gene Fusion ; Gene Transfer, Horizontal ; Genome ; *Genomics ; Phenotype ; *Proteomics ; Recombination, Genetic ; }, }
@article {pmid31635268, year = {2019}, author = {Fouladkhah, AC and Thompson, B and Camp, JS}, title = {Safety of Food and Water Supplies in the Landscape of Changing Climate.}, journal = {Microorganisms}, volume = {7}, number = {10}, pages = {}, pmid = {31635268}, issn = {2076-2607}, abstract = {In response to evolving environmental, production, and processing conditions, microbial communities have tremendous abilities to move toward increased diversity and fitness by various pathways such as vertical and horizontal gene transfer mechanisms, biofilm formation, and quorum sensing [...].}, }
@article {pmid31634801, year = {2020}, author = {Zhang, J and Buhe, C and Yu, D and Zhong, H and Wei, Y}, title = {Ammonia stress reduces antibiotic efflux but enriches horizontal gene transfer of antibiotic resistance genes in anaerobic digestion.}, journal = {Bioresource technology}, volume = {295}, number = {}, pages = {122191}, doi = {10.1016/j.biortech.2019.122191}, pmid = {31634801}, issn = {1873-2976}, mesh = {Ammonia ; Anaerobiosis ; *Anti-Bacterial Agents ; Drug Resistance, Microbial ; *Gene Transfer, Horizontal ; Genes, Bacterial ; }, abstract = {The dynamics of antibiotic resistance genes (ARGs) response to ammonia stress were evaluated using metagenomics and quantitative PCR (qPCR) in anaerobic digestion (AD). Ammonia stress reduced ARGs associated with antibiotic efflux, especially the major facilitator superfamily (MFS) of tet(L), due to free ammonia (FA) that changed the proton gradient of efflux system. Nonetheless, ARGs of antibiotic target alteration, especially ermB, were enriched under ammonia stress, which could be attributed to the initiation of the internal enhancer of the transferability of the broad host range plasmid, pAMbeta1. Statistical analysis elucidated the significant changes of ARGs are directly attributed to the mobile genetic elements (MGEs), but the little affected ARGs are mainly determined by the functional microbes reflected by nitrogen cycling genes (NCyc). This study deciphered the profiles of ARGs response to ammonia stress in AD, which indicated the importance of alleviation of ammonia inhibition for the mitigation of ARGs dissemination.}, }
@article {pmid31632385, year = {2019}, author = {Koziaeva, V and Dziuba, M and Leão, P and Uzun, M and Krutkina, M and Grouzdev, D}, title = {Genome-Based Metabolic Reconstruction of a Novel Uncultivated Freshwater Magnetotactic coccus "Ca. Magnetaquicoccus inordinatus" UR-1, and Proposal of a Candidate Family "Ca. Magnetaquicoccaceae".}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2290}, pmid = {31632385}, issn = {1664-302X}, abstract = {Magnetotactic bacteria are widely represented microorganisms that have the ability to synthesize magnetosomes. The magnetotactic cocci of the order Magnetococcales are the most frequently identified, but their classification remains unclear due to the low number of cultivated representatives. This paper reports the analysis of an uncultivated magnetotactic coccus UR-1 collected from the Uda River (in eastern Siberia). Genome analyses of this bacterium and comparison to the available Magnetococcales genomes identified a novel species called "Ca. Magnetaquicoccus inordinatus," and a delineated candidate family "Ca. Magnetaquicoccaceae" within the order Magnetococcales is proposed. We used average amino acid identity values <55-56% and <64-65% as thresholds for the separation of families and genera, respectively, within the order Magnetococcales. Analyses of the genome sequence of UR-1 revealed a potential ability for a chemolithoautotrophic lifestyle, with the oxidation of a reduced sulfur compound and carbon assimilation by rTCA. A nearly complete magnetosome genome island, containing a set of mam and mms genes, was also identified. Further comparative analyses of the magnetosome genes showed vertical inheritance as well as horizontal gene transfer as the evolutionary drivers of magnetosome biomineralization genes in strains of the order Magnetococcales.}, }
@article {pmid31632374, year = {2019}, author = {Song, D and Chen, X and Xu, M and Hai, R and Zhou, A and Tian, R and Van Nostrand, JD and Kempher, ML and Guo, J and Sun, G and Zhou, J}, title = {Adaptive Evolution of Sphingobium hydrophobicum C1[T] in Electronic Waste Contaminated River Sediment.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2263}, pmid = {31632374}, issn = {1664-302X}, abstract = {Electronic waste (e-waste) has caused a severe worldwide pollution problem. Despite increasing isolation of degradative microorganisms from e-waste contaminated environments, the mechanisms underlying their adaptive evolution in such habitats remain unclear. Sphingomonads generally have xenobiotic-degrading ability and may play important roles in bioremediation. Sphingobium hydrophobicum C1[T], characterized with superior cell surface hydrophobicity, was recently isolated from e-waste contaminated river sediment. To dissect the mechanisms driving its adaptive evolution, we evaluated its stress resistance, sequenced its genome and performed comparative genomic analysis with 19 other Sphingobium strains. Strain C1[T] can feed on several kinds of e-waste-derived xenobiotics, exhibits a great resistance to heavy metals and possesses a high colonization ability. It harbors abundant genes involved in environmental adaptation, some of which are intrinsic prior to experiencing e-waste contamination. The extensive genomic variations between strain C1[T] and other Sphingobium strains, numerous C1[T]-unique genes, massive mobile elements and frequent genome rearrangements reflect a high genome plasticity. Positive selection, gene duplication, and especially horizontal gene transfer drive the adaptive evolution of strain C1[T]. Moreover, presence of type IV secretion systems may allow strain C1[T] to be a source of beneficial genes for surrounding microorganisms. This study provides new insights into the adaptive evolution of sphingomonads, and potentially guides bioremediation strategies.}, }
@article {pmid31631079, year = {2019}, author = {Kohyama, Y and Suzuki, S}, title = {Conjugative Gene Transfer between Nourished and Starved Cells of Photobacterium damselae ssp. damselae and Escherichia coli.}, journal = {Microbes and environments}, volume = {34}, number = {4}, pages = {388-392}, pmid = {31631079}, issn = {1347-4405}, mesh = {Conjugation, Genetic/drug effects ; Culture Media/chemistry ; Drug Resistance, Multiple, Bacterial/genetics ; Escherichia coli/drug effects/*genetics ; Gene Transfer, Horizontal/*drug effects ; Genes, Bacterial/genetics ; Nutrients/analysis/*pharmacology ; Photobacterium/drug effects/*genetics ; Plasmids/genetics ; Transcription, Genetic/drug effects ; }, abstract = {Horizontal gene transfer (HGT) between bacteria with different habitats and nutritional requirements is important for the spread of antibiotic resistance genes (ARG). The objective of the present study was to clarify the effects of organic matter on HGT between nourished and starved bacteria. We demonstrated that conjugation ability is affected by the nutritional conditions of the cell and environment. A filter mating HGT experiment was performed using Photobacterium damselae ssp. damselae, strain 04Ya311, a marine-origin bacterium possessing the multidrug-resistance plasmid pAQU1, as the donor, and Escherichia coli as the recipient. The donor and recipient were both prepared as nutrient-rich cultured and starved cells. Filter mating was performed on agar plates with and without organic nutrients. The transcription of the plasmid-borne genes tet(M) and traI was quantitated under eutrophic and oligotrophic conditions. The donor P. damselae transferred the plasmid to E. coli at a transfer rate of 10[-4] under oligotrophic and eutrophic conditions. However, when the donor was starved, HGT was not detected under oligotrophic conditions. The addition of organic matter to starved cells restored conjugative HGT even after 6 d of starvation. The transcription of traI was not detected in starved cells, but was restored upon the addition of organic matter. The HGT rate appears to be affected by the transcription of plasmid-associated genes. The present results suggest that the HGT rate is low in starved donors under oligotrophic conditions, but is restored by the addition of organic matter.}, }
@article {pmid31629970, year = {2020}, author = {Wang, H and Qi, H and Gong, S and Huang, Z and Meng, C and Zhang, Y and Chen, X and Jiao, X}, title = {Fe3O4 composited with MoS2 blocks horizontal gene transfer.}, journal = {Colloids and surfaces. B, Biointerfaces}, volume = {185}, number = {}, pages = {110569}, doi = {10.1016/j.colsurfb.2019.110569}, pmid = {31629970}, issn = {1873-4367}, mesh = {Animals ; Catalysis ; Cell Membrane/drug effects/metabolism ; DNA Replication/drug effects/genetics ; Disulfides/*chemistry/toxicity ; Ferric Compounds/*chemistry/toxicity ; Gene Expression Regulation/drug effects ; *Gene Transfer, Horizontal ; Hydrogen-Ion Concentration ; Molybdenum/*chemistry/toxicity ; Plasmids/genetics ; RNA, Messenger/genetics/metabolism ; Zebrafish/genetics ; }, abstract = {In this study, we found that Fe3O4 promoted horizontal gene transfer (HGT), but when Fe3O4 was composited with MoS2, the Fe3O4@MoS2 nanocomposite interacting with bacteria significantly blocked the HGT in the conjugation system. qPCR was used to analyze the expression of genes belonging to the chromosome and plasmid in the conjugation system. Results demonstrated that Fe3O4@MoS2 inhibited conjugation by promoting the expression of the global regulatory gene (trbA) and inhibiting the expression of conjugative transfer genes involved in mating pair formation (traF, trbB), DNA replication (trfA), and porins (outer membrane protein (omp) A and ompC). All of these genes are related to the permeability of the cell membrane, except for trfA. The results showed that Fe3O4@MoS2 interacted with bacteria to decrease their permeability against exogenous DNA. MoS2 may play an essential role in the HGT-inhibiting activity of Fe3O4@MoS2. This study highlights the diverse biological properties of nano-materials and provides clues for nano-scientists to develop environmentally friendly materials.}, }
@article {pmid31626631, year = {2019}, author = {Chlebek, JL and Hughes, HQ and Ratkiewicz, AS and Rayyan, R and Wang, JC and Herrin, BE and Dalia, TN and Biais, N and Dalia, AB}, title = {PilT and PilU are homohexameric ATPases that coordinate to retract type IVa pili.}, journal = {PLoS genetics}, volume = {15}, number = {10}, pages = {e1008448}, pmid = {31626631}, issn = {1553-7404}, support = {K22 AI118863/AI/NIAID NIH HHS/United States ; R35 GM128674/GM/NIGMS NIH HHS/United States ; SC2 AI116566/AI/NIAID NIH HHS/United States ; }, mesh = {Acinetobacter/physiology ; Adenosine Triphosphatases/*physiology ; Fimbriae Proteins/*physiology ; Fimbriae, Bacterial/*enzymology ; Mutation ; Protein Multimerization/physiology ; Vibrio cholerae/physiology ; }, abstract = {Bacterial type IV pili are critical for diverse biological processes including horizontal gene transfer, surface sensing, biofilm formation, adherence, motility, and virulence. These dynamic appendages extend and retract from the cell surface. In many type IVa pilus systems, extension occurs through the action of an extension ATPase, often called PilB, while optimal retraction requires the action of a retraction ATPase, PilT. Many type IVa systems also encode a homolog of PilT called PilU. However, the function of this protein has remained unclear because pilU mutants exhibit inconsistent phenotypes among type IV pilus systems and because it is relatively understudied compared to PilT. Here, we study the type IVa competence pilus of Vibrio cholerae as a model system to define the role of PilU. We show that the ATPase activity of PilU is critical for pilus retraction in PilT Walker A and/or Walker B mutants. PilU does not, however, contribute to pilus retraction in ΔpilT strains. Thus, these data suggest that PilU is a bona fide retraction ATPase that supports pilus retraction in a PilT-dependent manner. We also found that a ΔpilU mutant exhibited a reduction in the force of retraction suggesting that PilU is important for generating maximal retraction forces. Additional in vitro and in vivo data show that PilT and PilU act as independent homo-hexamers that may form a complex to facilitate pilus retraction. Finally, we demonstrate that the role of PilU as a PilT-dependent retraction ATPase is conserved in Acinetobacter baylyi, suggesting that the role of PilU described here may be broadly applicable to other type IVa pilus systems.}, }
@article {pmid31625443, year = {2019}, author = {Bosch, T and Schade, R and Landman, F and Schouls, L and Dijk, KV}, title = {A blaVIM-1 positive Aeromonas hydrophila strain in a near-drowning patient: evidence for interspecies plasmid transfer within the patient.}, journal = {Future microbiology}, volume = {14}, number = {}, pages = {1191-1197}, doi = {10.2217/fmb-2019-0091}, pmid = {31625443}, issn = {1746-0921}, mesh = {Aeromonas hydrophila/*drug effects/*genetics ; Carbapenems/*pharmacology ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Gram-Negative Bacterial Infections/diagnosis/microbiology ; Humans ; Male ; Microbial Sensitivity Tests ; Near Drowning ; Plasmids/*genetics ; Pneumonia/diagnosis/microbiology ; Sequence Analysis, DNA ; Whole Genome Sequencing ; beta-Lactamases/*genetics ; }, abstract = {Aim: To show that a strain of Aeromonas hydrophila became resistant to carbapenems by interspecies transfer of a plasmid using long-read sequencing. Material &amp; methods: Whole genome sequencing of the four isolates was done using Illumina Hiseq, while the plasmid was reconstructed using the MinION sequencer. The resistome was identified with ResFinder. Results: Whole genome sequencing and long-read sequencing showed that all isolates carried a blaVIM-1 gene located on a 165 kb incA/C plasmid. ResFinder confirmed that the resistome of the plasmid, comprising 13 resistance genes, was identical within all isolates. Discussion: Long-read sequencing using the MinION successfully reconstructed a plasmid that was identical in all isolates, providing evidence for horizontal gene transfer of this blaVIM-1 gene carrying plasmid within the patient.}, }
@article {pmid31624505, year = {2019}, author = {Tansirichaiya, S and Rahman, MA and Roberts, AP}, title = {The Transposon Registry.}, journal = {Mobile DNA}, volume = {10}, number = {}, pages = {40}, pmid = {31624505}, issn = {1759-8753}, abstract = {Transposable elements in prokaryotes are found in many forms and therefore a robust nomenclature system is needed in order to allow researchers to describe and search for them in publications and databases. Here we provide an update on The Transposon Registry which allocates numbers to any prokaryotic transposable element. Additionally, we present the completion of registry records for all transposons assigned Tn numbers from Tn1 onwards where sequence data or publications exist.}, }
@article {pmid31624345, year = {2020}, author = {Manzano-Marı N, A and Coeur d'acier, A and Clamens, AL and Orvain, C and Cruaud, C and Barbe, V and Jousselin, E}, title = {Serial horizontal transfer of vitamin-biosynthetic genes enables the establishment of new nutritional symbionts in aphids' di-symbiotic systems.}, journal = {The ISME journal}, volume = {14}, number = {1}, pages = {259-273}, pmid = {31624345}, issn = {1751-7370}, mesh = {Animals ; Aphids/*microbiology ; Buchnera/*genetics ; Erwinia/*genetics ; *Gene Transfer, Horizontal ; Symbiosis/*genetics ; Vitamins/biosynthesis ; }, abstract = {Many insects depend on obligate mutualistic bacteria to provide essential nutrients lacking from their diet. Most aphids, whose diet consists of phloem, rely on the bacterial endosymbiont Buchnera aphidicola to supply essential amino acids and B vitamins. However, in some aphid species, provision of these nutrients is partitioned between Buchnera and a younger bacterial partner, whose identity varies across aphid lineages. Little is known about the origin and the evolutionary stability of these di-symbiotic systems. It is also unclear whether the novel symbionts merely compensate for losses in Buchnera or carry new nutritional functions. Using whole-genome endosymbiont sequences of nine Cinara aphids that harbour an Erwinia-related symbiont to complement Buchnera, we show that the Erwinia association arose from a single event of symbiont lifestyle shift, from a free-living to an obligate intracellular one. This event resulted in drastic genome reduction, long-term genome stasis, and co-divergence with aphids. Fluorescence in situ hybridisation reveals that Erwinia inhabits its own bacteriocytes near Buchnera's. Altogether these results depict a scenario for the establishment of Erwinia as an obligate symbiont that mirrors Buchnera's. Additionally, we found that the Erwinia vitamin-biosynthetic genes not only compensate for Buchnera's deficiencies, but also provide a new nutritional function; whose genes have been horizontally acquired from a Sodalis-related bacterium. A subset of these genes have been subsequently transferred to a new Hamiltonella co-obligate symbiont in one specific Cinara lineage. These results show that the establishment and dynamics of multi-partner endosymbioses can be mediated by lateral gene transfers between co-ocurring symbionts.}, }
@article {pmid31622879, year = {2019}, author = {Wang, H and Qi, H and Zhu, M and Gong, S and Huang, Z and Zhang, Y and Chen, X and Jiao, X}, title = {MoS2 decorated nanocomposite: Fe2O3@MoS2 inhibits the conjugative transfer of antibiotic resistance genes.}, journal = {Ecotoxicology and environmental safety}, volume = {186}, number = {}, pages = {109781}, doi = {10.1016/j.ecoenv.2019.109781}, pmid = {31622879}, issn = {1090-2414}, mesh = {Anti-Bacterial Agents/pharmacology ; Candida albicans/drug effects/genetics ; Conjugation, Genetic/*drug effects/genetics ; Disulfides/*chemistry/pharmacology ; Drug Resistance, Microbial/*drug effects/genetics ; Escherichia coli/drug effects/genetics ; Ferric Compounds/*chemistry/pharmacology ; Gene Transfer, Horizontal/*drug effects ; Genes, Microbial ; Molybdenum/*chemistry/pharmacology ; Nanocomposites/*chemistry ; Plasmids ; Staphylococcus aureus/drug effects/genetics ; }, abstract = {Nanomaterials of Al2O3 and TiO2 have been proved to promote the spread of antibiotic resistance genes (ARGs) by horizontal gene transfer. In this work, we found that Fe2O3@MoS2 nanocomposite inhibited the horizontal gene transfer (HGT) by inhibiting the conjugative transfer mediated by RP4-7 plasmid. To discover the mechanism of Fe2O3@MoS2 inhibiting HGT, the bacterial cells were collected under the optimal mating conditions. The collected bacterial cells were used for analyzing the expression levels of genes unique to the plasmid and the bacterial chromosome in the conjugation system by qPCR. The results of genes expression demonstrated that the mechanism of Fe2O3@MoS2 inhibited conjugation by promoting the expression of global regulatory gene (trbA) and inhibiting the expression of conjugative transfer genes involved in mating pair formation (traF, trbB) and DNA replication (trfA). The risk assessment of Fe2O3@MoS2 showed that it had very low toxicity to organisms. The findings of this paper showed that Fe2O3@MoS2, as an inhibitor of horizontal gene transfer, is an environment-friendly material.}, }
@article {pmid31622701, year = {2020}, author = {Imbs, TI and Zvyagintseva, TN and Ermakova, SP}, title = {Is the transformation of fucoidans in human body possible?.}, journal = {International journal of biological macromolecules}, volume = {142}, number = {}, pages = {778-781}, doi = {10.1016/j.ijbiomac.2019.10.018}, pmid = {31622701}, issn = {1879-0003}, mesh = {Animals ; Epithelial Cells/drug effects ; Gastrointestinal Microbiome/genetics ; Humans ; Intestinal Absorption ; Liver ; Macrophages ; Metabolome ; Molecular Weight ; Phaeophyceae/*chemistry ; Plant Extracts/blood/*chemistry/*metabolism/urine ; Polysaccharides/blood/*chemistry/*metabolism/urine ; }, abstract = {Fucoidans are a group of homo-and hetero-polysaccharides, which necessarily contains residues of sulfated α-L-fucose. Fucoidans are found only in brown algae. These polysaccharides exhibit a wide spectrum of biological activity and have a great therapeutic potential. Enzymes capable of catalyzing the degradation of fucoidans are absent in the mammalian enzyme system. The question arises: is the transformation of fucoidan in mammals, particularly in human possible? Studies in vivo (in situ) and in vitro have demonstrated that high molecular weight fucoidans are absorbed across rat intestinal epithelial cells, accumulated by liver macrophages, and characterized by low levels in blood and urine. Using the example of the Okinawa Prefecture (Japan) residents, it was shown that Cladosiphon okamuranus alga is digested and the fucoidan contained in this alga is absorbed in the human body.}, }
@article {pmid31621176, year = {2020}, author = {Venice, F and Ghignone, S and Salvioli di Fossalunga, A and Amselem, J and Novero, M and Xianan, X and Sędzielewska Toro, K and Morin, E and Lipzen, A and Grigoriev, IV and Henrissat, B and Martin, FM and Bonfante, P}, title = {At the nexus of three kingdoms: the genome of the mycorrhizal fungus Gigaspora margarita provides insights into plant, endobacterial and fungal interactions.}, journal = {Environmental microbiology}, volume = {22}, number = {1}, pages = {122-141}, doi = {10.1111/1462-2920.14827}, pmid = {31621176}, issn = {1462-2920}, mesh = {Bacteria/classification/genetics ; *Bacterial Physiological Phenomena ; Base Sequence ; Gene Transfer, Horizontal ; Genome, Fungal/genetics ; Glomeromycota/genetics/*physiology ; Microbiota/genetics ; Mycorrhizae/*physiology ; Plant Roots/*microbiology ; Plants/*microbiology ; Symbiosis/*physiology ; }, abstract = {As members of the plant microbiota, arbuscular mycorrhizal fungi (AMF, Glomeromycotina) symbiotically colonize plant roots. AMF also possess their own microbiota, hosting some uncultivable endobacteria. Ongoing research has revealed the genetics underlying plant responses to colonization by AMF, but the fungal side of the relationship remains in the dark. Here, we sequenced the genome of Gigaspora margarita, a member of the Gigasporaceae in an early diverging group of the Glomeromycotina. In contrast to other AMF, G. margarita may host distinct endobacterial populations and possesses the largest fungal genome so far annotated (773.104 Mbp), with more than 64% transposable elements. Other unique traits of the G. margarita genome include the expansion of genes for inorganic phosphate metabolism, the presence of genes for production of secondary metabolites and a considerable number of potential horizontal gene transfer events. The sequencing of G. margarita genome reveals the importance of its immune system, shedding light on the evolutionary pathways that allowed early diverging fungi to interact with both plants and bacteria.}, }
@article {pmid31619192, year = {2019}, author = {Aruhomukama, D and Najjuka, CF and Kajumbula, H and Okee, M and Mboowa, G and Sserwadda, I and Mayanja, R and Joloba, ML and Kateete, DP}, title = {blaVIM- and blaOXA-mediated carbapenem resistance among Acinetobacter baumannii and Pseudomonas aeruginosa isolates from the Mulago hospital intensive care unit in Kampala, Uganda.}, journal = {BMC infectious diseases}, volume = {19}, number = {1}, pages = {853}, pmid = {31619192}, issn = {1471-2334}, mesh = {Acinetobacter Infections/*microbiology ; *Acinetobacter baumannii/drug effects/enzymology ; Cross Infection/*microbiology ; Humans ; Intensive Care Units ; Microbial Sensitivity Tests ; Pseudomonas Infections/*microbiology ; *Pseudomonas aeruginosa/drug effects/enzymology ; Uganda ; *beta-Lactam Resistance ; beta-Lactamases ; }, abstract = {BACKGROUND: Between January 2015 and July 2017, we investigated the frequency of carbapenem resistant Acinetobacter baumannii (CRAB) and carbapenem resistant Pseudomonas aeruginosa (CRPA) at the Mulago Hospital intensive care unit (ICU) in Kampala, Uganda. Carbapenemase production and carbapenemase gene carriage among CRAB and CRPA were determined; mobility potential of carbapenemase genes via horizontal gene transfer processes was also studied.<br><br>METHODS: Clinical specimens from 9269 patients were processed for isolation of CRAB and CRPA. Drug susceptibility testing was performed with the disk diffusion method. Carriage of carbapenemase genes and class 1 integrons was determined by PCR. Conjugation experiments that involved blaVIM positive CRAB/CRPA (donors) and sodium azide resistant Escherichia coli J53 (recipient) were performed.<br><br>RESULTS: The 9269 specimens processed yielded 1077 and 488 isolates of Acinetobacter baumannii and Pseudomonas aeruginosa, respectively. Of these, 2.7% (29/1077) and 7.4% (36/488) were confirmed to be CRAB and CRPA respectively, but 46 were available for analysis (21 CRAB and 25 CRPA). Majority of specimens yielding CRAB and CRPA were from the ICU (78%) while 20 and 2% were from the ENT (Ear Nose &amp; Throat) Department and the Burns Unit, respectively. Carbapenemase assays performed with the MHT assay showed that 40 and 33% of CRPA and CRAB isolates respectively, were carbapenemase producers. Also, 72 and 48% of CRPA and CRAB isolates respectively, were metallo-beta-lactamase producers. All the carbapenemase producing isolates were multidrug resistant but susceptible to colistin. blaVIM was the most prevalent carbapenemase gene, and it was detected in all CRAB and CRPA isolates while blaOXA-23 and blaOXA-24 were detected in 29 and 24% of CRAB isolates, respectively. Co-carriage of blaOXA-23 and blaOXA-24 occurred in 14% of CRAB isolates. Moreover, 63% of the study isolates carried class 1 integrons; of these 31% successfully transferred blaVIM to E. coli J53.<br><br>CONCLUSIONS: CRAB and CRPA prevalence at the Mulago Hospital ICU is relatively low but carbapenemase genes especially blaVIM and blaOXA-23 are prevalent among them. This requires strengthening of infection control practices to curb selection and transmission of these strains in the hospital.}, }
@article {pmid31618878, year = {2019}, author = {Dieser, M and Smith, HJ and Ramaraj, T and Foreman, CM}, title = {Janthinobacterium CG23_2: Comparative Genome Analysis Reveals Enhanced Environmental Sensing and Transcriptional Regulation for Adaptation to Life in an Antarctic Supraglacial Stream.}, journal = {Microorganisms}, volume = {7}, number = {10}, pages = {}, pmid = {31618878}, issn = {2076-2607}, support = {ANT-0838970//National Science Foundation/ ; }, abstract = {As many bacteria detected in Antarctic environments are neither true psychrophiles nor endemic species, their proliferation in spite of environmental extremes gives rise to genome adaptations. Janthinobacterium sp. CG23_2 is a bacterial isolate from the Cotton Glacier stream, Antarctica. To understand how Janthinobacterium sp. CG23_2 has adapted to its environment, we investigated its genomic traits in comparison to genomes of 35 published Janthinobacterium species. While we hypothesized that genome shrinkage and specialization to narrow ecological niches would be energetically favorable for dwelling in an ephemeral Antarctic stream, the genome of Janthinobacterium sp. CG23_2 was on average 1.7 ± 0.6 Mb larger and predicted 1411 ± 499 more coding sequences compared to the other Janthinobacterium spp. Putatively identified horizontal gene transfer events contributed 0.92 Mb to the genome size expansion of Janthinobacterium sp. CG23_2. Genes with high copy numbers in the species-specific accessory genome of Janthinobacterium sp. CG23_2 were associated with environmental sensing, locomotion, response and transcriptional regulation, stress response, and mobile elements-functional categories which also showed molecular adaptation to cold. Our data suggest that genome plasticity and the abundant complementary genes for sensing and responding to the extracellular environment supported the adaptation of Janthinobacterium sp. CG23_2 to this extreme environment.}, }
@article {pmid31615877, year = {2019}, author = {Deng, J and Auchtung, JM and Konstantinidis, KT and Brettar, I and Höfle, MG and Tiedje, JM}, title = {Genomic Variations Underlying Speciation and Niche Specialization of Shewanella baltica.}, journal = {mSystems}, volume = {4}, number = {5}, pages = {}, pmid = {31615877}, issn = {2379-5077}, abstract = {Shewanella baltica was the dominant culturable nitrate-reducing bacterium in the eutrophic and strongly stratified Baltic Sea in the 1980s, where it primarily inhabited the oxic-anoxic transition zone. The genomic structures of 46 of these isolates were investigated through comparative genomic hybridization (CGH), which revealed a gradient of genomic similarity, ranging from 65% to as high as 99%. The core genome of the S. baltica species was enriched in anaerobic respiration-associated genes. Auxiliary genes, most of which locate within a few genomic islands (GIs), were nonuniformly distributed among the isolates. Specifically, hypothetical and mobile genetic element (MGE)-associated genes dominated intraclade gene content differences, whereas gain/loss of functional genes drove gene content differences among less related strains. Among the major S. baltica clades, gene signatures related to specific redox-driven and spatial niches within the water column were identified. For instance, genes involved in anaerobic respiration of sulfur compounds may provide key adaptive advantages for clade A strains in anoxic waters where sulfur-containing electron acceptors are present. Genes involved in cell motility, in particular, a secondary flagellar biosynthesis system, may be associated with the free-living lifestyle by clade E strains. Collectively, this study revealed characteristics of genome variations present in the water column and active speciation of S. baltica strains, driven by niche partitioning and horizontal gene transfer (HGT).IMPORTANCE Speciation in nature is a fundamental process driving the formation of the vast microbial diversity on Earth. In the central Baltic Sea, the long-term stratification of water led to formation of a large-scale vertical redoxcline that provided a gradient of environmental niches with respect to the availability of electron acceptors and donors. The region was home to Shewanella baltica populations, which composed the dominant culturable nitrate-reducing bacteria, particularly in the oxic-anoxic transition zone. Using the collection of S. baltica isolates as a model system, genomic variations showed contrasting gene-sharing patterns within versus among S. baltica clades and revealed genomic signatures of S. baltica clades related to redox niche specialization as well as particle association. This study provides important insights into genomic mechanisms underlying bacterial speciation within this unique natural redoxcline.}, }
@article {pmid31615674, year = {2019}, author = {Khalil, AB and Qarawi, S and Sivakumar, N}, title = {Genomic comparison of anoxybacillus flavithermus AK1, a thermophilic bacteria, with other strains.}, journal = {Enzyme and microbial technology}, volume = {131}, number = {}, pages = {109385}, doi = {10.1016/j.enzmictec.2019.109385}, pmid = {31615674}, issn = {1879-0909}, mesh = {Anoxybacillus/*genetics/isolation &amp; purification ; Base Composition ; *Genome, Bacterial ; *Genomics ; Genotype ; Hot Springs ; Saudi Arabia ; }, abstract = {From ecological and industrial perspectives, Anoxybacillus flavithermus species that lives in a thermophilic environment, are extremely important bacteria due to their potential in producing highly interesting compounds and enzymes. In order to understand the genetic makeup of these thermophiles, we have performed a comparative genomics study of 12 genome-sequenced strains of Anoxybacillus flavithermus bacteria. The genome size of Anoxybacillus flavithermus strains is from 2.5Mbp to 3.7Mbp and on average containing a low percentage of G + C genomic content (˜41.9%). We show that, on the basis of the total gene-content, Anoxybacillus flavithermus strains are grouped in three different subgroups. In the future, it would be interesting to explore these strain subgroups to further understand the lifestyle of thermophilic bacteria. Focussing on the Anoxybacillus flavithermus AK1 strain, which was isolated from a Hot Spring in Saudi Arabia and closely related to A. flavithermus NBRC strain, we identified a unique list of 75 genes specific to AK1 strain, of which 63 of them have homologs in other taxonomically related species. We speculate that these AK1-specific genes might be resulted due to horizontal gene transfer from other bacteria in order to adapt to the extreme environmental conditions. Moreover, we predicted three potential secondary metabolite gene clusters in the AK1 strain that further need to be experimentally characterised. Genomic annotation, secondary metabolite gene clusters and outcomes of the strain genomic comparisons from this study would be the basis for the strain-specific mathematical model for exploiting the metabolism for the industrial and ecological applications.}, }
@article {pmid31613206, year = {2020}, author = {Hall, JPJ and Wright, RCT and Guymer, D and Harrison, E and Brockhurst, MA}, title = {Extremely fast amelioration of plasmid fitness costs by multiple functionally diverse pathways.}, journal = {Microbiology (Reading, England)}, volume = {166}, number = {1}, pages = {56-62}, doi = {10.1099/mic.0.000862}, pmid = {31613206}, issn = {1465-2080}, mesh = {Bacterial Proteins/*genetics/metabolism ; Biological Evolution ; Gene Transfer, Horizontal ; Genetic Fitness ; Genome, Bacterial/genetics ; *Mutation ; Phenotype ; Plasmids/genetics/*physiology ; Pseudomonas fluorescens/*genetics ; }, abstract = {The acquisition of plasmids is often accompanied by fitness costs such that compensatory evolution is required to allow plasmid survival, but it is unclear whether compensatory evolution can be extensive or rapid enough to maintain plasmids when they are very costly. The mercury-resistance plasmid pQBR55 drastically reduced the growth of its host, Pseudomonas fluorescens SBW25, immediately after acquisition, causing a small colony phenotype. However, within 48 h of growth on agar plates we observed restoration of the ancestral large colony morphology, suggesting that compensatory mutations had occurred. Relative fitness of these evolved strains, in lab media and in soil microcosms, varied between replicates, indicating different mutational mechanisms. Using genome sequencing we identified that restoration was associated with chromosomal mutations in either a hypothetical DNA-binding protein PFLU4242, RNA polymerase or the GacA/S two-component system. Targeted deletions in PFLU4242, gacA or gacS recapitulated the ameliorated phenotype upon plasmid acquisition, indicating three distinct mutational pathways to compensation. Our data shows that plasmid compensatory evolution is fast enough to allow survival of a plasmid despite it imposing very high fitness costs upon its host, and indeed may regularly occur during the process of isolating and selecting individual plasmid-containing clones.}, }
@article {pmid31611667, year = {2020}, author = {Koonin, EV and Makarova, KS and Wolf, YI and Krupovic, M}, title = {Evolutionary entanglement of mobile genetic elements and host defence systems: guns for hire.}, journal = {Nature reviews. Genetics}, volume = {21}, number = {2}, pages = {119-131}, pmid = {31611667}, issn = {1471-0064}, mesh = {Biological Evolution ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Host-Pathogen Interactions ; *Interspersed Repetitive Sequences ; }, abstract = {All cellular life forms are afflicted by diverse genetic parasites, including viruses and other types of mobile genetic elements (MGEs), and have evolved multiple, diverse defence systems that protect them from MGE assault via different mechanisms. Here, we provide our perspectives on how recent evidence points to tight evolutionary connections between MGEs and defence systems that reach far beyond the proverbial arms race. Defence systems incur a fitness cost for the hosts; therefore, at least in prokaryotes, horizontal mobility of defence systems, mediated primarily by MGEs, is essential for their persistence. Moreover, defence systems themselves possess certain features of selfish elements. Common components of MGEs, such as site-specific nucleases, are 'guns for hire' that can also function as parts of defence mechanisms and are often shuttled between MGEs and defence systems. Thus, evolutionary and molecular factors converge to mould the multifaceted, inextricable connection between MGEs and anti-MGE defence systems.}, }
@article {pmid31611373, year = {2019}, author = {Gonçalves, C and Gonçalves, P}, title = {Multilayered horizontal operon transfers from bacteria reconstruct a thiamine salvage pathway in yeasts.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {44}, pages = {22219-22228}, pmid = {31611373}, issn = {1091-6490}, mesh = {Bacteria/genetics ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; *Operon ; Saccharomycetales/*genetics ; Thiamine/*genetics/metabolism ; }, abstract = {Horizontal acquisition of bacterial genes is presently recognized as an important contribution to the adaptation and evolution of eukaryotic genomes. However, the mechanisms underlying expression and consequent selection and fixation of the prokaryotic genes in the new eukaryotic setting are largely unknown. Here we show that genes composing the pathway for the synthesis of the essential vitamin B1 (thiamine) were lost in an ancestor of a yeast lineage, the Wickerhamiella/Starmerella (W/S) clade, known to harbor an unusually large number of genes of alien origin. The thiamine pathway was subsequently reassembled, at least twice, by multiple HGT events from different bacterial donors involving both single genes and entire operons. In the W/S-clade species Starmerella bombicola we obtained direct genetic evidence that all bacterial genes of the thiamine pathway are functional. The reconstructed pathway is composed by yeast and bacterial genes operating coordinately to scavenge thiamine derivatives from the environment. The adaptation of the newly acquired operons to the eukaryotic setting involved a repertoire of mechanisms until now only sparsely documented, namely longer intergenic regions, post-horizontal gene transfer (HGT) gene fusions fostering coordinated expression, gene relocation, and possibly recombination generating mosaic genes. The results provide additional evidence that HGT occurred recurrently in this yeast lineage and was crucial for the reestablishment of lost functions and that similar mechanisms are used across a broad range of eukaryotic microbes to promote adaptation of prokaryotic genes to their new environment.}, }
@article {pmid31611352, year = {2019}, author = {Wang, L and Liu, D and Lv, Y and Cui, L and Li, Y and Li, T and Song, H and Hao, Y and Shen, J and Wang, Y and Walsh, TR}, title = {Novel Plasmid-Mediated tet(X5) Gene Conferring Resistance to Tigecycline, Eravacycline, and Omadacycline in a Clinical Acinetobacter baumannii Isolate.}, journal = {Antimicrobial agents and chemotherapy}, volume = {64}, number = {1}, pages = {}, pmid = {31611352}, issn = {1098-6596}, support = {G1100135/MRC_/Medical Research Council/United Kingdom ; MR/N028317/1/MRC_/Medical Research Council/United Kingdom ; MR/P007295/1/MRC_/Medical Research Council/United Kingdom ; MR/S013768/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Acinetobacter Infections/drug therapy/microbiology ; Acinetobacter baumannii/*drug effects/*genetics/isolation &amp; purification ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/chemistry/genetics ; China ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Microbial Sensitivity Tests ; Models, Genetic ; Models, Molecular ; Molecular Docking Simulation ; Plasmids/genetics ; Tetracycline Resistance/genetics ; Tetracyclines/pharmacology ; Tigecycline/pharmacology ; }, abstract = {A novel, plasmid-mediated, high-level tigecycline resistance tet(X) gene variant, tet(X5), was detected in a clinical Acinetobacter baumannii isolate from China in 2017. Tet(X5) shows 84.5% and 90.5% amino acid identity to Tet(X3) and Tet(X4), respectively, with similar binding sites and a comparable affinity for tetracyclines. The tet(X5)-containing plasmid could only be transferred to A. baumannii via electrotransformation. This report follows the recent study describing the identification of tet(X3) and tet(X4).}, }
@article {pmid31609967, year = {2019}, author = {Takano, S and Fukuda, K and Koto, A and Miyazaki, R}, title = {A novel system of bacterial cell division arrest implicated in horizontal transmission of an integrative and conjugative element.}, journal = {PLoS genetics}, volume = {15}, number = {10}, pages = {e1008445}, pmid = {31609967}, issn = {1553-7404}, mesh = {Bacterial Proteins/*genetics ; Cell Division/*genetics ; Conjugation, Genetic ; DNA Transposable Elements/*genetics ; *Gene Transfer, Horizontal ; Genetic Loci ; Mutation ; Pseudomonas putida/*genetics ; S Phase Cell Cycle Checkpoints/genetics ; }, abstract = {Integrative and conjugative elements (ICEs) are widespread mobile DNA elements in the prokaryotic world. ICEs are usually retained within the bacterial chromosome, but can be excised and transferred from a donor to a new recipient cell, even of another species. Horizontal transmission of ICEclc, a prevalent ICE in proteobacteria, only occurs from developed specialized transfer competent (tc) cells in the donor population. tc cells become entirely dedicated to the ICE transmission at the cost of cell proliferation. The cell growth impairment is mediated by two ICEclc located genes, parA and shi, but the mechanistic and dynamic details of this process are unknown. To better understand the function of ParA and Shi, we followed their intracellular behavior from fluorescent protein fusions, and studied host cell division at single-cell level. Superresolution imaging revealed that ParA-mCherry colocalized with the host nucleoid while Shi-GFP was enriched at the membrane during the growth impairment. Despite being enriched at different cellular locations, the two proteins showed in vivo interactions, and mutations in the Walker A motif of ParA dislocalized both ParA and Shi. In addition, ParA mutations in the ATPase motif abolished the growth arrest on the host cell. Time-lapse microscopy revealed that ParA and Shi initially delay cell division, suggesting an extension of the S phase of cells, but eventually completely inhibit cell elongation. The parA-shi locus is highly conserved in other ICEclc-related elements, and expressing ParA-Shi from ICEclc in other proteobacterial species caused similar growth arrest, suggesting that the system functions similarly across hosts. The results of our study provide mechanistic insight into the novel and unique system on ICEs and help to understand such epistatic interaction between ICE genes and host physiology that entails efficient horizontal gene transfer.}, }
@article {pmid31609418, year = {2019}, author = {Tralamazza, SM and Rocha, LO and Oggenfuss, U and Corrêa, B and Croll, D}, title = {Complex Evolutionary Origins of Specialized Metabolite Gene Cluster Diversity among the Plant Pathogenic Fungi of the Fusarium graminearum Species Complex.}, journal = {Genome biology and evolution}, volume = {11}, number = {11}, pages = {3106-3122}, pmid = {31609418}, issn = {1759-6653}, mesh = {DNA Transposable Elements ; Evolution, Molecular ; Fungi/genetics ; Fusariosis/*microbiology ; Fusarium/*genetics ; Gene Transfer, Horizontal ; *Genome, Fungal ; *Multigene Family ; Plant Diseases/microbiology ; Secondary Metabolism/*genetics ; Triticum/microbiology ; }, abstract = {Fungal genomes encode highly organized gene clusters that underlie the production of specialized (or secondary) metabolites. Gene clusters encode key functions to exploit plant hosts or environmental niches. Promiscuous exchange among species and frequent reconfigurations make gene clusters some of the most dynamic elements of fungal genomes. Despite evidence for high diversity in gene cluster content among closely related strains, the microevolutionary processes driving gene cluster gain, loss, and neofunctionalization are largely unknown. We analyzed the Fusarium graminearum species complex (FGSC) composed of plant pathogens producing potent mycotoxins and causing Fusarium head blight on cereals. We de novo assembled genomes of previously uncharacterized FGSC members (two strains of F. austroamericanum, F. cortaderiae, and F. meridionale). Our analyses of 8 species of the FGSC in addition to 15 other Fusarium species identified a pangenome of 54 gene clusters within FGSC. We found that multiple independent losses were a key factor generating extant cluster diversity within the FGSC and the Fusarium genus. We identified a modular gene cluster conserved among distantly related fungi, which was likely reconfigured to encode different functions. We also found strong evidence that a rare cluster in FGSC was gained through an ancient horizontal transfer between bacteria and fungi. Chromosomal rearrangements underlying cluster loss were often complex and were likely facilitated by an enrichment in specific transposable elements. Our findings identify important transitory stages in the birth and death process of specialized metabolism gene clusters among very closely related species.}, }
@article {pmid31608043, year = {2019}, author = {Gifford, I and Vance, S and Nguyen, G and Berry, AM}, title = {A Stable Genetic Transformation System and Implications of the Type IV Restriction System in the Nitrogen-Fixing Plant Endosymbiont Frankia alni ACN14a.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2230}, pmid = {31608043}, issn = {1664-302X}, abstract = {Genus Frankia is comprised primarily of nitrogen-fixing actinobacteria that form root nodule symbioses with a group of hosts known as the actinorhizal plants. These plants are evolutionarily closely related to the legumes that are nodulated by the rhizobia. Both host groups utilize homologs of nodulation genes for root-nodule symbiosis, derived from common plant ancestors. The corresponding endosymbionts, Frankia and the rhizobia, however, are distantly related groups of bacteria, leading to questions about their symbiotic mechanisms and evolutionary history. To date, a stable system of electrotransformation has been lacking in Frankia despite numerous attempts by research groups worldwide. We have identified type IV methyl-directed restriction systems, highly-expressed in a range of actinobacteria, as a likely barrier to Frankia transformation. Here we report the successful electrotransformation of the model strain F. alni ACN14a with an unmethylated, broad host-range replicating plasmid, expressing chloramphenicol-resistance for selection and GFP as a marker of gene expression. This system circumvented the type IV restriction barrier and allowed the stable maintenance of the plasmid. During nitrogen limitation, Frankia differentiates into two cell types: the vegetative hyphae and nitrogen-fixing vesicles. When the expression of egfp under the control of the nif gene cluster promoter was localized using fluorescence imaging, the expression of nitrogen fixation in nitrogen-limited culture was localized in Frankia vesicles but not in hyphae. The ability to separate gene expression patterns between Frankia hyphae and vesicles will enable deeper comparisons of molecular signaling and metabolic exchange between Frankia-actinorhizal and rhizobia-legume symbioses to be made, and may broaden potential applications in agriculture. Further downstream applications are possible, including gene knock-outs and complementation, to open up a range of experiments in Frankia and its symbioses. Additionally, in the transcriptome of F. alni ACN14a, type IV restriction enzymes were highly expressed in nitrogen-replete culture but their expression strongly decreased during symbiosis. The down-regulation of type IV restriction enzymes in symbiosis suggests that horizontal gene transfer may occur more frequently inside the nodule, with possible new implications for the evolution of Frankia.}, }
@article {pmid31605997, year = {2020}, author = {Riva, V and Riva, F and Vergani, L and Crotti, E and Borin, S and Mapelli, F}, title = {Microbial assisted phytodepuration for water reclamation: Environmental benefits and threats.}, journal = {Chemosphere}, volume = {241}, number = {}, pages = {124843}, doi = {10.1016/j.chemosphere.2019.124843}, pmid = {31605997}, issn = {1879-1298}, mesh = {Bacteria/genetics/*metabolism ; *Biodegradation, Environmental ; Drug Resistance, Microbial/genetics ; Humans ; Waste Disposal, Fluid/methods ; Wastewater/analysis/chemistry ; Water Purification/*methods ; *Wetlands ; }, abstract = {Climate changes push for water reuse as a priority to counteract water scarcity and minimize water footprint especially in agriculture, one of the highest water consuming human activities. Phytodepuration is indicated as a promising technology for water reclamation, also in the light of its economic and ecological sustainability, and the use of specific bacterial inocula for microbial assisted phytodepuration has been proposed as a further advance for its implementation. Here we provided an overview on the selection and use of plant growth promoting bacteria in Constructed Wetland (CW) systems, showing their advantages in terms of plant growth support and pollutant degradation abilities. Moreover, CWs are also proposed for the removal of emerging organic pollutants like antibiotics from urban wastewaters. We focused on this issue, still debated in the literature, revealing the necessity to deepen the knowledge on the antibiotic resistance spread into the environment in relation to treated wastewater release and reuse. In addition, given the presence in the plant system of microhabitats (e.g. rhizosphere) that are hot spot for Horizontal Gene Transfer, we highlighted the importance of gene exchange to understand if these events can promote the diffusion of antibiotic resistance genes and antibiotic resistant bacteria, possibly entering in the food production chain when treated wastewater is used for irrigation. Ideally, this new knowledge will lead to improve the design of phytodepuration systems to maximize the quality and safety of the treated effluents in compliance with the 'One Health' concept.}, }
@article {pmid31603209, year = {2019}, author = {Feurtey, A and Stevens, DM and Stephan, W and Stukenbrock, EH}, title = {Interspecific Gene Exchange Introduces High Genetic Variability in Crop Pathogen.}, journal = {Genome biology and evolution}, volume = {11}, number = {11}, pages = {3095-3105}, pmid = {31603209}, issn = {1759-6653}, mesh = {Ascomycota/*genetics/pathogenicity ; DNA Transposable Elements/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Introgression ; *Genetic Variation ; Genome, Fungal ; Haplotypes ; Plant Diseases/*genetics/microbiology ; Triticum/*microbiology ; Virulence Factors/genetics ; }, abstract = {Genome analyses have revealed a profound role of hybridization and introgression in the evolution of many eukaryote lineages, including fungi. The impact of recurrent introgression on fungal evolution however remains elusive. Here, we analyzed signatures of introgression along the genome of the fungal wheat pathogen Zymoseptoria tritici. We applied a comparative population genomics approach, including genome data from five Zymoseptoria species, to characterize the distribution and composition of introgressed regions representing segments with an exceptional haplotype pattern. These regions are found throughout the genome, comprising 5% of the total genome and overlapping with > 1,000 predicted genes. We performed window-based phylogenetic analyses along the genome to distinguish regions which have a monophyletic or nonmonophyletic origin with Z. tritici sequences. A majority of nonmonophyletic windows overlap with the highly variable regions suggesting that these originate from introgression. We verified that incongruent gene genealogies do not result from incomplete lineage sorting by comparing the observed and expected length distribution of haplotype blocks resulting from incomplete lineage sorting. Although protein-coding genes are not enriched in these regions, we identify 18 that encode putative virulence determinants. Moreover, we find an enrichment of transposable elements in these regions implying that hybridization may contribute to the horizontal spread of transposable elements. We detected a similar pattern in the closely related species Zymoseptoria ardabiliae, suggesting that hybridization is widespread among these closely related grass pathogens. Overall, our results demonstrate a significant impact of recurrent hybridization on overall genome evolution of this important wheat pathogen.}, }
@article {pmid31602783, year = {2020}, author = {Brown Kav, A and Rozov, R and Bogumil, D and Sørensen, SJ and Hansen, LH and Benhar, I and Halperin, E and Shamir, R and Mizrahi, I}, title = {Unravelling plasmidome distribution and interaction with its hosting microbiome.}, journal = {Environmental microbiology}, volume = {22}, number = {1}, pages = {32-44}, doi = {10.1111/1462-2920.14813}, pmid = {31602783}, issn = {1462-2920}, support = {640384//H2020 European Research Council/International ; 1947/19//Israel Science FoundationFundRef Organization Name: Israel Science/International ; }, mesh = {Animals ; Bacteria/*genetics ; Gene Transfer, Horizontal ; Microbiota/*genetics ; Plasmids/*genetics ; Rumen/*microbiology ; }, abstract = {Horizontal gene transfer via plasmids plays a pivotal role in microbial evolution. The forces that shape plasmidomes functionality and distribution in natural environments are insufficiently understood. Here, we present a comparative study of plasmidomes across adjacent microbial environments present in different individual rumen microbiomes. Our findings show that the rumen plasmidome displays enormous unknown functional potential currently unannotated in available databases. Nevertheless, this unknown functionality is conserved and shared with published rat gut plasmidome data. Moreover, the rumen plasmidome is highly diverse compared with the microbiome that hosts these plasmids, across both similar and different rumen habitats. Our analysis demonstrates that its structure is shaped more by stochasticity than selection. Nevertheless, the plasmidome is an active partner in its intricate relationship with the host microbiome with both interacting with and responding to their environment.}, }
@article {pmid31601908, year = {2019}, author = {Stsiapanava, A and Selmer, M}, title = {Crystal structure of ErmE - 23S rRNA methyltransferase in macrolide resistance.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {14607}, pmid = {31601908}, issn = {2045-2322}, mesh = {Anti-Bacterial Agents/pharmacology ; Arginine/chemistry ; Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; *Drug Resistance, Bacterial ; Fluorometry ; Glycine/chemistry ; Macrolides/*pharmacology ; Methyltransferases/*chemistry ; RNA, Bacterial/chemistry ; RNA, Ribosomal, 23S/*chemistry ; Saccharopolyspora/*enzymology ; Substrate Specificity ; }, abstract = {Pathogens often receive antibiotic resistance genes through horizontal gene transfer from bacteria that produce natural antibiotics. ErmE is a methyltransferase (MTase) from Saccharopolyspora erythraea that dimethylates A2058 in 23S rRNA using S-adenosyl methionine (SAM) as methyl donor, protecting the ribosomes from macrolide binding. To gain insights into the mechanism of macrolide resistance, the crystal structure of ErmE was determined to 1.75 Å resolution. ErmE consists of an N-terminal Rossmann-like α/ß catalytic domain and a C-terminal helical domain. Comparison with ErmC' that despite only 24% sequence identity has the same function, reveals highly similar catalytic domains. Accordingly, superposition with the catalytic domain of ErmC' in complex with SAM suggests that the cofactor binding site is conserved. The two structures mainly differ in the C-terminal domain, which in ErmE contains a longer loop harboring an additional 310 helix that interacts with the catalytic domain to stabilize the tertiary structure. Notably, ErmE also differs from ErmC' by having long disordered extensions at its N- and C-termini. A C-terminal disordered region rich in arginine and glycine is also a present in two other MTases, PikR1 and PikR2, which share about 30% sequence identity with ErmE and methylate the same nucleotide in 23S rRNA.}, }
@article {pmid31600629, year = {2019}, author = {Medina, EM and Walsh, E and Buchler, NE}, title = {Evolutionary innovation, fungal cell biology, and the lateral gene transfer of a viral KilA-N domain.}, journal = {Current opinion in genetics &amp; development}, volume = {58-59}, number = {}, pages = {103-110}, doi = {10.1016/j.gde.2019.08.004}, pmid = {31600629}, issn = {1879-0380}, mesh = {DNA-Binding Proteins/chemistry/genetics/metabolism ; Evolution, Molecular ; Fungi/*genetics/metabolism ; Gene Transfer, Horizontal/*physiology ; Membrane Proteins/chemistry/genetics/metabolism ; Nuclear Proteins/chemistry/genetics/metabolism ; Phylogeny ; Protein Conformation ; Protein Domains/*genetics ; Repressor Proteins/chemistry/genetics/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/genetics/metabolism ; Schizosaccharomyces pombe Proteins/chemistry/genetics/metabolism ; Transcription Factors/chemistry/*genetics/metabolism ; Viral Regulatory and Accessory Proteins/*genetics ; }, abstract = {Fungi are found in diverse ecological niches as primary decomposers, mutualists, or parasites of plants and animals. Although animals and fungi share a common ancestor, fungi dramatically diversified their life cycle, cell biology, and metabolism as they evolved and colonized new niches. This review focuses on a family of fungal transcription factors (Swi4/Mbp1, APSES, Xbp1, Bqt4) derived from the lateral gene transfer of a KilA-N domain commonly found in prokaryotic and eukaryotic DNA viruses. These virus-derived fungal regulators play central roles in cell cycle, morphogenesis, sexual differentiation, and quiescence. We consider the possible origins of KilA-N and how this viral DNA binding domain came to be intimately associated with fungal processes.}, }
@article {pmid31595505, year = {2020}, author = {Rockwell, NC and Lagarias, JC}, title = {Phytochrome evolution in 3D: deletion, duplication, and diversification.}, journal = {The New phytologist}, volume = {225}, number = {6}, pages = {2283-2300}, pmid = {31595505}, issn = {1469-8137}, support = {R01 GM068552/GM/NIGMS NIH HHS/United States ; }, mesh = {*Biological Evolution ; Cyanobacteria/*genetics ; Gene Duplication ; Gene Transfer, Horizontal ; *Genes, Plant ; *Phylogeny ; Phytochrome/*genetics/metabolism ; Plant Physiological Phenomena/*genetics ; Plants/*genetics/metabolism ; Sequence Deletion ; Symbiosis ; }, abstract = {Canonical plant phytochromes are master regulators of photomorphogenesis and the shade avoidance response. They are also part of a widespread superfamily of photoreceptors with diverse spectral and biochemical properties. Plant phytochromes belong to a clade including other phytochromes from glaucophyte, prasinophyte, and streptophyte algae (all members of the Archaeplastida) and those from cryptophyte algae. This is consistent with recent analyses supporting the existence of an AC (Archaeplastida + Cryptista) clade. AC phytochromes have been proposed to arise from ancestral cyanobacterial genes via endosymbiotic gene transfer (EGT), but most recent studies instead support multiple horizontal gene transfer (HGT) events to generate extant eukaryotic phytochromes. In principle, this scenario would be compared to the emerging understanding of early events in eukaryotic evolution to generate a coherent picture. Unfortunately, there is currently a major discrepancy between the evolution of phytochromes and the evolution of eukaryotes; phytochrome evolution is thus not a solved problem. We therefore examine phytochrome evolution in a broader context. Within this context, we can identify three important themes in phytochrome evolution: deletion, duplication, and diversification. These themes drive phytochrome evolution as organisms evolve in response to environmental challenges.}, }
@article {pmid31594929, year = {2019}, author = {Hua, ZS and Wang, YL and Evans, PN and Qu, YN and Goh, KM and Rao, YZ and Qi, YL and Li, YX and Huang, MJ and Jiao, JY and Chen, YT and Mao, YP and Shu, WS and Hozzein, W and Hedlund, BP and Tyson, GW and Zhang, T and Li, WJ}, title = {Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {4574}, pmid = {31594929}, issn = {2041-1723}, mesh = {Alkanes/metabolism ; Archaea/enzymology/*genetics/isolation &amp; purification ; *Biological Evolution ; China ; Computational Biology ; Genome, Archaeal ; Hot Springs/*microbiology ; Hot Temperature ; Metabolic Networks and Pathways/genetics ; *Metagenome ; Methane/metabolism ; Multigene Family/genetics ; Oxidoreductases/*genetics/metabolism ; Phylogeny ; }, abstract = {Several recent studies have shown the presence of genes for the key enzyme associated with archaeal methane/alkane metabolism, methyl-coenzyme M reductase (Mcr), in metagenome-assembled genomes (MAGs) divergent to existing archaeal lineages. Here, we study the mcr-containing archaeal MAGs from several hot springs, which reveal further expansion in the diversity of archaeal organisms performing methane/alkane metabolism. Significantly, an MAG basal to organisms from the phylum Thaumarchaeota that contains mcr genes, but not those for ammonia oxidation or aerobic metabolism, is identified. Together, our phylogenetic analyses and ancestral state reconstructions suggest a mostly vertical evolution of mcrABG genes among methanogens and methanotrophs, along with frequent horizontal gene transfer of mcr genes between alkanotrophs. Analysis of all mcr-containing archaeal MAGs/genomes suggests a hydrothermal origin for these microorganisms based on optimal growth temperature predictions. These results also suggest methane/alkane oxidation or methanogenesis at high temperature likely existed in a common archaeal ancestor.}, }
@article {pmid31594809, year = {2019}, author = {Conlan, S and Lau, AF and Deming, C and Spalding, CD and Lee-Lin, S and Thomas, PJ and Park, M and Dekker, JP and Frank, KM and Palmore, TN and Segre, JA}, title = {Plasmid Dissemination and Selection of a Multidrug-Resistant Klebsiella pneumoniae Strain during Transplant-Associated Antibiotic Therapy.}, journal = {mBio}, volume = {10}, number = {5}, pages = {}, pmid = {31594809}, issn = {2150-7511}, support = {ZIA CL004042/ImNIH/Intramural NIH HHS/United States ; ZIA CL080018/ImNIH/Intramural NIH HHS/United States ; ZIA HG200382/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*administration &amp; dosage ; Antibiotic Prophylaxis/methods ; *Drug Resistance, Multiple, Bacterial ; *Gene Transfer, Horizontal ; Hematopoietic Stem Cell Transplantation ; Humans ; Klebsiella Infections/*microbiology ; Klebsiella pneumoniae/*drug effects/isolation &amp; purification ; Plasmids/*analysis ; Selection, Genetic ; Transplant Recipients ; }, abstract = {Antibiotics, which are used both to prevent and to treat infections, are a mainstay therapy for lifesaving procedures such as transplantation. For this reason, and many others, increased antibiotic resistance among human-associated pathogens, such as the carbapenem-resistant Enterobacteriaceae species, is of grave concern. In this study, we report on a hematopoietic stem cell transplant recipient in whom cultures detected the emergence of carbapenem resistance and spread across five strains of bacteria that persisted for over a year. Carbapenem resistance in Citrobacter freundii, Enterobacter cloacae, Klebsiella aerogenes, and Klebsiella pneumoniae was linked to a pair of plasmids, each carrying the Klebsiella pneumoniae carbapenemase gene (blaKPC). Surveillance cultures identified a carbapenem-susceptible strain of Citrobacter freundii that may have become resistant through horizontal gene transfer of these plasmids. Selection of a multidrug-resistant Klebsiella pneumoniae strain was also detected following combination antibiotic therapy. Here we report a plasmid carrying the blaKPC gene with broad host range that poses the additional threat of spreading to endogenous members of the human gut microbiome.IMPORTANCE Antibiotic-resistant bacteria are a serious threat to medically fragile patient populations. The spread of antibiotic resistance through plasmid-mediated mechanisms is of grave concern as it can lead to the conversion of endogenous patient-associated strains to difficult-to-treat pathogens.}, }
@article {pmid31592759, year = {2019}, author = {Williams, LE and Cullen, N and DeGiorgis, JA and Martinez, KJ and Mellone, J and Oser, M and Wang, J and Zhang, Y}, title = {Variation in genome content and predatory phenotypes between Bdellovibrio sp. NC01 isolated from soil and B. bacteriovorus type strain HD100.}, journal = {Microbiology (Reading, England)}, volume = {165}, number = {12}, pages = {1315-1330}, pmid = {31592759}, issn = {1465-2080}, support = {P20 GM103430/GM/NIGMS NIH HHS/United States ; }, mesh = {Antibiosis/genetics ; Bacterial Proteins/genetics ; Bdellovibrio/classification/genetics/*physiology ; Escherichia coli/physiology ; Gene Deletion ; Gene Transfer, Horizontal ; Genome, Bacterial/*genetics ; Gram-Negative Bacteria/physiology ; Microbial Viability ; Phenotype ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {Defining phenotypic and associated genotypic variation among Bdellovibrio may further our understanding of how this genus attacks and kills different Gram-negative bacteria. We isolated Bdellovibrio sp. NC01 from soil. Analysis of 16S rRNA gene sequences and average amino acid identity showed that NC01 belongs to a different species than the type species bacteriovorus. By clustering amino acid sequences from completely sequenced Bdellovibrio and comparing the resulting orthologue groups to a previously published analysis, we defined a 'core genome' of 778 protein-coding genes and identified four protein-coding genes that appeared to be missing only in NC01. To determine how horizontal gene transfer (HGT) may have impacted NC01 genome evolution, we performed genome-wide comparisons of Bdellovibrio nucleotide sequences, which indicated that eight NC01 genomic regions were likely acquired by HGT. To investigate how genome variation may impact predation, we compared protein-coding gene content between NC01 and the B. bacteriovorus type strain HD100, focusing on genes implicated as important in successful killing of prey. Of these, NC01 is missing ten genes that may play roles in lytic activity during predation. Compared to HD100, NC01 kills fewer tested prey strains and kills Escherichia coli ML35 less efficiently. NC01 causes a smaller log reduction in ML35, after which the prey population recovers and the NC01 population decreases. In addition, NC01 forms turbid plaques on lawns of E. coli ML35, in contrast to clear plaques formed by HD100. Linking phenotypic variation in interactions between Bdellovibrio and Gram-negative bacteria with underlying Bdellovibrio genome variation is valuable for understanding the ecological significance of predatory bacteria and evaluating their effectiveness in clinical applications.}, }
@article {pmid31591493, year = {2020}, author = {Ben Maamar, S and Hu, J and Hartmann, EM}, title = {Implications of indoor microbial ecology and evolution on antibiotic resistance.}, journal = {Journal of exposure science &amp; environmental epidemiology}, volume = {30}, number = {1}, pages = {1-15}, pmid = {31591493}, issn = {1559-064X}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics/*physiology ; Ecology ; Gene Transfer, Horizontal ; Humans ; }, abstract = {The indoor environment is an important source of microbial exposures for its human occupants. While we naturally want to favor positive health outcomes, built environment design and operation may counter-intuitively favor negative health outcomes, particularly with regard to antibiotic resistance. Indoor environments contain microbes from both human and non-human origins, providing a unique venue for microbial interactions, including horizontal gene transfer. Furthermore, stressors present in the built environment could favor the exchange of genetic material in general and the retention of antibiotic resistance genes in particular. Intrinsic and acquired antibiotic resistance both pose a potential threat to human health; these phenomena need to be considered and controlled separately. The presence of both environmental and human-associated microbes, along with their associated antibiotic resistance genes, in the face of stressors, including antimicrobial chemicals, creates a unique opportunity for the undesirable spread of antibiotic resistance. In this review, we summarize studies and findings related to various interactions between human-associated bacteria, environmental bacteria, and built environment conditions, and particularly their relation to antibiotic resistance, aiming to guide "healthy" building design.}, }
@article {pmid31589312, year = {2020}, author = {Arnold, B and Sohail, M and Wadsworth, C and Corander, J and Hanage, WP and Sunyaev, S and Grad, YH}, title = {Fine-Scale Haplotype Structure Reveals Strong Signatures of Positive Selection in a Recombining Bacterial Pathogen.}, journal = {Molecular biology and evolution}, volume = {37}, number = {2}, pages = {417-428}, pmid = {31589312}, issn = {1537-1719}, support = {F32 GM120839/GM/NIGMS NIH HHS/United States ; R01 AI106786/AI/NIAID NIH HHS/United States ; T32 AI007535/AI/NIAID NIH HHS/United States ; U54 GM088558/GM/NIGMS NIH HHS/United States ; R01 AI132606/AI/NIAID NIH HHS/United States ; }, mesh = {Evolution, Molecular ; Gene Frequency ; Gene Transfer, Horizontal ; *Genetic Variation ; Haplotypes ; Linkage Disequilibrium ; Neisseria gonorrhoeae/*genetics ; Recombination, Genetic ; Selection, Genetic ; Sequence Analysis, DNA/*methods ; }, abstract = {Identifying genetic variation in bacteria that has been shaped by ecological differences remains an important challenge. For recombining bacteria, the sign and strength of linkage provide a unique lens into ongoing selection. We show that derived alleles <300 bp apart in Neisseria gonorrhoeae exhibit more coupling linkage than repulsion linkage, a pattern that cannot be explained by limited recombination or neutrality as these couplings are significantly stronger for nonsynonymous alleles than synonymous alleles. This general pattern is driven by a small fraction of highly diverse genes, many of which exhibit evidence of interspecies horizontal gene transfer and an excess of intermediate frequency alleles. Extensive simulations show that two distinct forms of positive selection can create these patterns of genetic variation: directional selection on horizontally transferred alleles or balancing selection that maintains distinct haplotypes in the presence of recombination. Our results establish a framework for identifying patterns of selection in fine-scale haplotype structure that indicate specific ecological processes in species that recombine with distantly related lineages or possess coexisting adaptive haplotypes.}, }
@article {pmid31589296, year = {2019}, author = {John, J and George, S and Nori, SRC and Nelson-Sathi, S}, title = {Phylogenomic Analysis Reveals the Evolutionary Route of Resistant Genes in Staphylococcus aureus.}, journal = {Genome biology and evolution}, volume = {11}, number = {10}, pages = {2917-2926}, pmid = {31589296}, issn = {1759-6653}, mesh = {Drug Resistance, Bacterial/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial ; Phylogeny ; Staphylococcus aureus/classification/drug effects/*genetics ; }, abstract = {Multidrug-resistant Staphylococcus aureus is a leading concern worldwide. Coagulase-Negative Staphylococci are claimed to be the reservoir and source of important resistant elements in S. aureus. However, the origin and evolutionary route of resistant genes in S. aureus are still remaining unknown. Here, we performed a detailed phylogenomic analysis of 152 completely sequenced S. aureus strains in comparison with 7,529 non-Staphylococcus aureus reference bacterial genomes. Our results reveal that S. aureus has a large open pan-genome where 97 (55%) of its known resistant-related genes belonging to its accessory genome. Among these genes, 47 (27%) were located within the Staphylococcal Cassette Chromosome mec (SCCmec), a transposable element responsible for resistance against major classes of antibiotics including beta-lactams, macrolides, and aminoglycosides. However, the physically linked mec-box genes (MecA-MecR-MecI) that are responsible for the maintenance of SCCmec elements is not unique to S. aureus, instead it is widely distributed within Staphylococcaceae family. The phyletic patterns of SCCmec-encoded resistant genes in Staphylococcus species are significantly different from that of its core genes indicating frequent exchange of these genes between Staphylococcus species. Our in-depth analysis of SCCmec-resistant gene phylogenies reveals that genes such as blaZ, ble, kmA, and tetK that are responsible for beta-lactam, bleomycin, kanamycin, and tetracycline resistance in S. aureus were laterally transferred from non-Staphylococcus sources. In addition, at least 11 non-SCCmec-encoded resistant genes in S. aureus, were laterally acquired from distantly related species. Our study evidently shows that gene transfers played a crucial role in shaping the evolution of antibiotic resistance in S. aureus.}, }
@article {pmid31587897, year = {2019}, author = {Bublitz, DC and Chadwick, GL and Magyar, JS and Sandoz, KM and Brooks, DM and Mesnage, S and Ladinsky, MS and Garber, AI and Bjorkman, PJ and Orphan, VJ and McCutcheon, JP}, title = {Peptidoglycan Production by an Insect-Bacterial Mosaic.}, journal = {Cell}, volume = {179}, number = {3}, pages = {703-712.e7}, pmid = {31587897}, issn = {1097-4172}, support = {MR/S009272/1/MRC_/Medical Research Council/United Kingdom ; P20 GM103546/GM/NIGMS NIH HHS/United States ; S10 OD021806/OD/NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*genetics/pathogenicity ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Hemiptera/*genetics/microbiology ; Host-Pathogen Interactions ; Insect Proteins/genetics/metabolism ; Peptidoglycan/*biosynthesis/genetics ; *Symbiosis ; }, abstract = {Peptidoglycan (PG) is a defining feature of bacteria, involved in cell division, shape, and integrity. We previously reported that several genes related to PG biosynthesis were horizontally transferred from bacteria to the nuclear genome of mealybugs. Mealybugs are notable for containing a nested bacteria-within-bacterium endosymbiotic structure in specialized insect cells, where one bacterium, Moranella, lives in the cytoplasm of another bacterium, Tremblaya. Here we show that horizontally transferred genes on the mealybug genome work together with genes retained on the Moranella genome to produce a PG layer exclusively at the Moranella cell periphery. Furthermore, we show that an insect protein encoded by a horizontally transferred gene of bacterial origin is transported into the Moranella cytoplasm. These results provide a striking parallel to the genetic and biochemical mosaicism found in organelles, and prove that multiple horizontally transferred genes can become integrated into a functional pathway distributed between animal and bacterial endosymbiont genomes.}, }
@article {pmid31586462, year = {2020}, author = {Shen, Y and Chen, M}, title = {Prevalence, sequence type, and quinolone resistance of Neisseria lactamica carried in children younger than 15 years in Shanghai, China.}, journal = {The Journal of infection}, volume = {80}, number = {1}, pages = {61-68}, doi = {10.1016/j.jinf.2019.08.020}, pmid = {31586462}, issn = {1532-2742}, mesh = {Child ; China/epidemiology ; Drug Resistance, Bacterial ; Humans ; Microbial Sensitivity Tests ; *Neisseria lactamica ; *Neisseria meningitidis/genetics ; Prevalence ; *Quinolones/pharmacology ; }, abstract = {OBJECTIVE: Neisseria lactamica has an important influence on carriage and antimicrobial susceptibility of N. meningitidis, a major pathogen of septicemia and meningitis. In China, quinolone resistance is highly prevalent in N. meningitidis but unknown in N. lactamica. This study investigates the carriage rate, sequence type, and ciprofloxacin resistance of N. lactamica in children in China.<br><br>METHODS: During 2014-2016, throat swabs were collected from 2,239 children in Shanghai. The ciprofloxacin minimum inhibitory concentrations of the isolates were determined by the agar dilution method.<br><br>RESULTS: The overall carriage rate of N. lactamica was higher (8.9%) than that of N. meningitidis (0.9%) and peaked at two years (37.1%). The resistance frequency of N. lactamica to ciprofloxacin was 98.5% (197/200). There were 65 sequence types (STs). Clonal complex (cc) 640 (45.5%) dominated, while ST-14031 was predominant (37%, 74/200). All isolates possessed a GyrA mutation; 17 isolates (8.5%) harbored additionally a ParC mutation. Assigned to 39 different alleles, the gyrA sequences from these N. lactamica isolates formed an N. lactamica cluster, which also included eight alleles from N. meningitidis.<br><br>CONCLUSION: The N. lactamica isolates in China showed distinct characteristics with lower genetic diversity and a much higher prevalence of quinolone resistance than in other countries.}, }
@article {pmid31584178, year = {2020}, author = {Güell, M}, title = {Conjugative Assembly Genome Engineering (CAGE).}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2075}, number = {}, pages = {399-409}, doi = {10.1007/978-1-4939-9877-7_28}, pmid = {31584178}, issn = {1940-6029}, mesh = {Alleles ; Bacteria/genetics ; *Conjugation, Genetic ; DNA, Bacterial ; *Gene Transfer, Horizontal ; *Genetic Engineering ; Genetic Markers ; Genetic Testing ; *Genome, Bacterial ; Genomics/methods ; Genotyping Techniques ; Plasmids/genetics ; Recombination, Genetic ; Whole Genome Sequencing ; }, abstract = {Conjugative assembly genome engineering (CAGE) enables the transfer of large chromosomal regions from a donor to a recipient. Specific regions of the donor chromosome can be introduced in the recipient genome by the directed insertion of an origin of transfer and two selection cassettes. Multiple paired CAGE experiments can be combined to generate chimeric chromosomes from different donor strains.}, }
@article {pmid31584176, year = {2020}, author = {DelaFuente, J and Rodriguez-Beltran, J and San Millan, A}, title = {Methods to Study Fitness and Compensatory Adaptation in Plasmid-Carrying Bacteria.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2075}, number = {}, pages = {371-382}, doi = {10.1007/978-1-4939-9877-7_26}, pmid = {31584176}, issn = {1940-6029}, mesh = {*Adaptation, Biological ; Bacteria/drug effects/*genetics ; DNA Transposable Elements ; Databases, Genetic ; Drug Resistance, Microbial ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Fitness ; Plasmids/*genetics ; Web Browser ; Workflow ; }, abstract = {Mobile genetic elements such as plasmids mediate horizontal gene transfer in prokaryotes, promoting bacterial adaptation and evolution. Despite the potential advantages conferred by these genetic elements, plasmids can also produce a fitness cost when they arrive to a new host. This initial burden is one of the main limits to the spread of plasmids in bacterial populations. However, plasmid costs can be ameliorated over time through compensatory mutations in the plasmid or the chromosome (compensatory adaptation). Understanding the origin of the cost produced by plasmids and the potential for compensatory adaptation is crucial to predict the spread and evolution of plasmid-mediated traits, such as antibiotic resistance. Here, we describe a simple protocol designed to analyze the fitness effects of a plasmid in a new host bacterium. We also provide a method to examine the potential for compensatory adaptation, using experimental evolution, and to elucidate if compensation originates in the plasmid, the bacterium, or both.}, }
@article {pmid31584175, year = {2020}, author = {Delaye, L and Vargas, C and Latorre, A and Moya, A}, title = {Inferring Horizontal Gene Transfer with DarkHorse, Phylomizer, and ETE Toolkits.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2075}, number = {}, pages = {355-369}, doi = {10.1007/978-1-4939-9877-7_25}, pmid = {31584175}, issn = {1940-6029}, mesh = {*Computational Biology/methods ; Databases, Genetic ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genomics/methods ; Phylogeny ; *Software ; Web Browser ; }, abstract = {In this chapter, we describe how to use DarkHorse2.0 to search for xenologs in the genome of the cyanobacterium Synechococcus elongatus PCC 7942. DarkHorse is an implicit phylogenetic method that uses BLAST searches to identify proteins having close homologs of unexpected taxonomic affiliation. Once a set of putative xenologs are identified, Phylomizer is used to reconstruct phylogenetic trees. Phylomizer reproduces all the necessary steps to perform a basic phylogenetic analysis. The combined use of DarkHorse and Phylomizer allows the identification of genes incorporated into a given genome by HGT.}, }
@article {pmid31584171, year = {2020}, author = {Garcillán-Barcia, MP and Redondo-Salvo, S and Vielva, L and de la Cruz, F}, title = {MOBscan: Automated Annotation of MOB Relaxases.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2075}, number = {}, pages = {295-308}, doi = {10.1007/978-1-4939-9877-7_21}, pmid = {31584171}, issn = {1940-6029}, mesh = {Computational Biology/*methods ; *Conjugation, Genetic ; DNA Topoisomerases, Type I/genetics/*metabolism ; Databases, Genetic ; *Gene Transfer, Horizontal ; Multigene Family ; *Software ; Web Browser ; }, abstract = {Relaxase-based plasmid classification has become popular in the past 10 years. Nevertheless, it is not obvious how to assign a query protein to a relaxase MOB family. Automated protein annotation is commonly used to classify them into families, gathering evolutionarily related proteins that likely perform the same function, while circumventing the problem of different naming conventions. Here, we implement an automated method, MOBscan, to identify relaxases and classify them into any of the nine MOB families. MOBscan is a web tool that carries out a HMMER search against a curated database of MOB profile Hidden Markov models. It is freely available at https://castillo.dicom.unican.es/mobscan/ .}, }
@article {pmid31584169, year = {2020}, author = {Cury, J and Abby, SS and Doppelt-Azeroual, O and Néron, B and Rocha, EPC}, title = {Identifying Conjugative Plasmids and Integrative Conjugative Elements with CONJscan.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2075}, number = {}, pages = {265-283}, doi = {10.1007/978-1-4939-9877-7_19}, pmid = {31584169}, issn = {1940-6029}, mesh = {Computational Biology/*methods ; *Conjugation, Genetic ; DNA Transposable Elements ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Genomic Islands ; Genomics ; Plasmids/*genetics ; *Software ; }, abstract = {We present a computational method to identify conjugative systems in plasmids and chromosomes using the CONJscan module of MacSyFinder. The method relies on the identification of the protein components of the system using hidden Markov model profiles and then checking that the composition and genetic organization of the system is consistent with that expected from a conjugative system. The method can be assessed online using the Galaxy workflow or locally using a standalone software. The latter version allows to modify the models of the module (i.e., to change the expected components, their number, and their organization).CONJscan identifies conjugative systems, but when the mobile genetic element is integrative (ICE), one often also wants to delimit it from the chromosome. We present a method, with a script, to use the results of CONJscan and comparative genomics to delimit ICE in chromosomes. The method provides a visual representation of the ICE location. Together, these methods facilitate the identification of conjugative elements in bacterial genomes.}, }
@article {pmid31584168, year = {2020}, author = {Browne, PD and Kot, W and Jørgensen, TS and Hansen, LH}, title = {The Mobilome: Metagenomic Analysis of Circular Plasmids, Viruses, and Other Extrachromosomal Elements.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2075}, number = {}, pages = {253-264}, doi = {10.1007/978-1-4939-9877-7_18}, pmid = {31584168}, issn = {1940-6029}, mesh = {Computational Biology/methods ; *DNA Transposable Elements ; DNA, Circular ; Databases, Genetic ; Escherichia coli/genetics ; Gene Library ; Gene Transfer, Horizontal ; *Metagenome ; *Metagenomics/methods ; Plasmids/*genetics ; Viruses/*genetics ; }, abstract = {Isolation, sequencing, and analysis of circular genetic elements bring new insights to mobile genetic elements related to microbial ecology. One method used to study circular plasmids, viruses, and other elements is called the mobilome method. The mobilome method presented here is an unamplified mobilome approach allowing fast isolation of circular DNA elements from a variety of samples followed by directly building unamplified Illumina-compatible sequencing libraries using enzymatic tagging and fragmentation. Several methods for bioinformatic analysis of mobilome data are also suggested.}, }
@article {pmid31584167, year = {2020}, author = {Calvo-Villamañán, A and Bernheim, A and Bikard, D}, title = {Methods for the Analysis and Characterization of Defense Mechanisms Against Horizontal Gene Transfer: CRISPR Systems.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2075}, number = {}, pages = {235-249}, doi = {10.1007/978-1-4939-9877-7_17}, pmid = {31584167}, issn = {1940-6029}, mesh = {Bacteriophages/physiology ; *CRISPR-Cas Systems ; *Clustered Regularly Interspaced Short Palindromic Repeats ; *Defense Mechanisms ; *Gene Transfer, Horizontal ; Host-Pathogen Interactions ; Plasmids/genetics ; }, abstract = {CRISPR-Cas systems provide RNA-guided adaptive immunity to the majority of archaea and many bacteria. They are able to capture pieces of invading genetic elements in the form of novel spacers in an array of repeats. These elements can then be used as a memory to destroy incoming DNA through the action of RNA-guided nucleases. This chapter describes general procedures to determine the ability of CRISPR-Cas systems to capture novel sequences and to use them to block phages and horizontal gene transfer. All protocols are performed in Staphylococcus aureus using Type II-A CRISPR-Cas systems. Nonetheless, the protocols provided can be adapted to work with other bacteria and other types of CRISPR-Cas systems.}, }
@article {pmid31584165, year = {2020}, author = {Blesa, A and Berenguer, J}, title = {Methods to Identify and Analyze Vesicle-Protected DNA Transfer.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2075}, number = {}, pages = {209-221}, doi = {10.1007/978-1-4939-9877-7_15}, pmid = {31584165}, issn = {1940-6029}, mesh = {Biological Transport ; DNA/genetics/metabolism ; *Extracellular Vesicles/ultrastructure ; *Gene Transfer, Horizontal ; Thermus/*genetics/*metabolism/ultrastructure ; Transformation, Bacterial ; }, abstract = {Conjugation, transformation, and transduction constitute the three classical mechanisms involved in horizontal gene transfer (HGT) among prokaryotes. In addition, alternative HGT mechanisms exist in groups of organisms. Among them, the use of DNA-containing membrane vesicles as shuttle elements for HGT has been described for a number of microorganisms, including both thermophiles and mesophiles. Here we describe the methods followed to detect, purify, and analyze these vesicles.}, }
@article {pmid31584164, year = {2020}, author = {Vit, C and Loot, C and Escudero, JA and Nivina, A and Mazel, D}, title = {Integron Identification in Bacterial Genomes and Cassette Recombination Assays.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2075}, number = {}, pages = {189-208}, doi = {10.1007/978-1-4939-9877-7_14}, pmid = {31584164}, issn = {1940-6029}, mesh = {Bacteria/*genetics ; Chromosome Deletion ; Computational Biology/*methods ; Conjugation, Genetic ; DNA Transposable Elements ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Integrons ; *Recombination, Genetic ; *Software ; }, abstract = {Integrons are genetic elements involved in bacterial adaptation to the environment. Sedentary chromosomal integrons (SCIs) can stockpile and rearrange a myriad of different functions encoded in gene cassettes. Through their association with transposable elements and conjugative plasmids, some SCIs have acquired mobility and are now termed Mobile Integrons (MIs). MIs have reached the hospitals and are involved in the rise and spread of antibiotic resistance genes through horizontal gene transfer among numerous bacterial species. Here we aimed at describing methods for the detection of integrons in sequenced bacterial genomes as well as for the experimental characterization of the activity of their different components: the integrase and the recombination sites.}, }
@article {pmid31584159, year = {2020}, author = {Clark, RR and Gray, TA and Derbyshire, KM}, title = {Quantifying and Characterizing Distributive Conjugal Transfer in Mycobacterium smegmatis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2075}, number = {}, pages = {123-134}, doi = {10.1007/978-1-4939-9877-7_9}, pmid = {31584159}, issn = {1940-6029}, mesh = {Bacterial Physiological Phenomena ; *Conjugation, Genetic ; DNA, Bacterial ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Bacterial ; High-Throughput Screening Assays ; Mycobacterium smegmatis/*genetics ; }, abstract = {Horizontal gene transfer (HGT) in prokaryotes disseminates genetic information throughout a population and can facilitate adaptation and evolution of the species. Mycobacteria utilize an atypical method of conjugation called distributive conjugal transfer (DCT), which results in mosaic genomes and the potential for accelerated evolution beyond that enabled by the more classical oriT-mediated conjugation. The following is a description of the basic DCT protocol, some possible variations of the assay, and examples of downstream applications to better understand mycobacterial functions.}, }
@article {pmid31584158, year = {2020}, author = {Novais, C and Freitas, AR and León-Sampedro, R and Peixe, L and Coque, TM}, title = {Methods to Quantify DNA Transfer in Enterococcus.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2075}, number = {}, pages = {111-122}, doi = {10.1007/978-1-4939-9877-7_8}, pmid = {31584158}, issn = {1940-6029}, mesh = {*Conjugation, Genetic ; *DNA Transposable Elements ; *DNA, Bacterial ; Enterococcus/*genetics ; Gene Transfer, Horizontal ; }, abstract = {DNA uptake in Enterococcus normally occurs by conjugation, a natural process that is replicated in biomedical research to assess the transferability of different mobile genetic elements and chromosomal regions as well as to study the host range of plasmids and other conjugative elements. More efficient artificial methods to transform cells with foreign DNA as chemotransformation and electroporation are widely used in molecular genetics. Here, we described conjugation protocols to quantify DNA transfer among Enterococcus and revise current perspectives and lab strains. Protocols of electrotransformation have been previously described in this series.}, }
@article {pmid31584154, year = {2020}, author = {Jofre, J and Muniesa, M}, title = {Bacteriophage Isolation and Characterization: Phages of Escherichia coli.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2075}, number = {}, pages = {61-79}, doi = {10.1007/978-1-4939-9877-7_4}, pmid = {31584154}, issn = {1940-6029}, mesh = {Bacteriolysis ; Bacteriophages/*isolation &amp; purification/*physiology/ultrastructure ; Centrifugation, Density Gradient/methods ; Cesium ; Chlorides ; Environmental Microbiology ; Escherichia coli/virology ; Host-Pathogen Interactions ; Sewage/virology ; Viral Plaque Assay ; }, abstract = {Here we introduce methods for the detection, enumeration, and isolation of bacteriophages from Escherichia coli. In bacteria, horizontal gene transfer may be mediated by virulent and temperate phages. Strict virulent phages, able to propagate in a suitable strain following the lytic pathway, can be isolated directly from different natural environments. In temperate phages, the lytic cycle must be activated, and phages are detected after their induction. In both cases, detection is based on the production of visible plaques in a confluent lawn of the host strain using a double agar layer method. Further purification and characterization are achieved by density gradients, electron microscopy studies, and genomic analysis. This straightforward methodology can be applied to the detection, enumeration, and isolation of bacteriophages from any bacterial species, using the appropriate host strain, media, and culture conditions.}, }
@article {pmid31581193, year = {2019}, author = {Fang, Y and Wang, H and Liu, X and Xin, D and Rao, Y and Zhu, B}, title = {Transcriptome analysis of Xanthomonas oryzae pv. oryzicola exposed to H2O2 reveals horizontal gene transfer contributes to its oxidative stress response.}, journal = {PloS one}, volume = {14}, number = {10}, pages = {e0218844}, pmid = {31581193}, issn = {1932-6203}, mesh = {*Gene Expression Profiling ; Gene Expression Regulation, Bacterial/*drug effects ; *Gene Transfer, Horizontal ; Hydrogen Peroxide/*pharmacology ; Oxidative Stress/*drug effects ; *Xanthomonas/genetics/metabolism ; }, abstract = {Xanthomonas oryzae pv. oryzicola (Xoc), the causal agent of bacterial leaf streak, is one of the most severe seed-borne bacterial diseases of rice. However, the molecular mechanisms underlying Xoc in response to oxidative stress are still unknown. In this study, we performed a time-course RNA-seq analysis on the Xoc in response to H2O2, aiming to reveal its oxidative response network. Overall, our RNA sequence analysis of Xoc revealed a significant global gene expression profile when it was exposed to H2O2. There were 7, 177, and 246 genes that were differentially regulated at the early, middle, and late stages after exposure, respectively. Three genes (xoc_1643, xoc_1946, xoc_3249) showing significantly different expression levels had proven relationships with oxidative stress response and pathogenesis. Moreover, a hypothetical protein (XOC_2868) showed significantly differential expression, and the xoc_2868 mutants clearly displayed a greater H2O2 sensitivity and decreased pathogenicity than those of the wild-type. Gene localization and phylogeny analysis strongly suggests that this gene may have been horizontally transferred from a Burkholderiaceae ancestor. Our study not only provides a first glance of Xoc's global response against oxidative stress, but also reveals the impact of horizontal gene transfer in the evolutionary history of Xoc.}, }
@article {pmid31580486, year = {2020}, author = {Novák Vanclová, AMG and Zoltner, M and Kelly, S and Soukal, P and Záhonová, K and Füssy, Z and Ebenezer, TE and Lacová Dobáková, E and Eliáš, M and Lukeš, J and Field, MC and Hampl, V}, title = {Metabolic quirks and the colourful history of the Euglena gracilis secondary plastid.}, journal = {The New phytologist}, volume = {225}, number = {4}, pages = {1578-1592}, doi = {10.1111/nph.16237}, pmid = {31580486}, issn = {1469-8137}, support = {P009018/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Biological Evolution ; Euglena gracilis/*metabolism ; Gene Expression Regulation ; Gene Transfer, Horizontal ; Plastids ; Proteins/genetics/*metabolism ; *Proteome ; }, abstract = {Euglena spp. are phototrophic flagellates with considerable ecological presence and impact. Euglena gracilis harbours secondary green plastids, but an incompletely characterised proteome precludes accurate understanding of both plastid function and evolutionary history. Using subcellular fractionation, an improved sequence database and MS we determined the composition, evolutionary relationships and hence predicted functions of the E. gracilis plastid proteome. We confidently identified 1345 distinct plastid protein groups and found that at least 100 proteins represent horizontal acquisitions from organisms other than green algae or prokaryotes. Metabolic reconstruction confirmed previously studied/predicted enzymes/pathways and provided evidence for multiple unusual features, including uncoupling of carotenoid and phytol metabolism, a limited role in amino acid metabolism, and dual sets of the SUF pathway for FeS cluster assembly, one of which was acquired by lateral gene transfer from Chlamydiae. Plastid paralogues of trafficking-associated proteins potentially mediating fusion of transport vesicles with the outermost plastid membrane were identified, together with derlin-related proteins, potential translocases across the middle membrane, and an extremely simplified TIC complex. The Euglena plastid, as the product of many genomes, combines novel and conserved features of metabolism and transport.}, }
@article {pmid31574422, year = {2019}, author = {Wideman, JG and Novick, A and Muñoz-Gómez, SA and Doolittle, WF}, title = {Neutral evolution of cellular phenotypes.}, journal = {Current opinion in genetics &amp; development}, volume = {58-59}, number = {}, pages = {87-94}, doi = {10.1016/j.gde.2019.09.004}, pmid = {31574422}, issn = {1879-0380}, mesh = {Eukaryota/*genetics/metabolism ; *Evolution, Molecular ; Gene Deletion ; Gene Duplication/physiology ; Gene Transfer, Horizontal/physiology ; Genetic Drift ; Genetic Variation/*physiology ; Genotype ; Mutation ; Organelles/genetics/metabolism ; Phenotype ; Trypanosoma/genetics/physiology ; Yeasts/genetics/metabolism ; }, abstract = {Eukaryotes exhibit a great diversity of cellular and subcellular morphologies, but their basic underlying architecture is fairly constant. All have a nucleus, Golgi, cytoskeleton, plasma membrane, vesicles, ribosomes, and all known lineages but one have mitochondrion-related organelles. Moreover, most eukaryotes undergo processes such as mitosis, meiosis, DNA recombination, and often perform feats such as phagocytosis, and amoeboid and flagellar movement. With all of these commonalities, it is obvious that eukaryotes evolved from a common ancestor, but it is not obvious how eukaryotes came to have their diverse structural phenotypes. Are these phenotypes adaptations to particular niches, their evolution dominated by positive natural selection? Or is eukaryotic cellular diversity substantially the product of neutral evolutionary processes, with adaptation either illusory or a secondary consequence? In this paper, we outline how a hierarchical view of phenotype can be used to articulate a neutral theory of phenotypic evolution, involving processes such as gene loss, gene replacement by homologues or analogues, gene duplication followed by subfunctionalization, and constructive neutral evolution. We suggest that neutral iterations of these processes followed by entrenchment of their products can explain much of the diversity of cellular, developmental, and biochemical phenotypes of unicellular eukaryotes and should be explored in addition to adaptive explanations.}, }
@article {pmid31570405, year = {2019}, author = {Hao, G and Chen, AI and Liu, M and Zhou, H and Egan, M and Yang, X and Kan, B and Wang, H and Goulian, M and Zhu, J}, title = {Colistin-resistance-mediated bacterial surface modification sensitizes phage infection.}, journal = {Antimicrobial agents and chemotherapy}, volume = {63}, number = {12}, pages = {}, pmid = {31570405}, issn = {1098-6596}, support = {R01 AI120489/AI/NIAID NIH HHS/United States ; R01 GM080279/GM/NIGMS NIH HHS/United States ; R21 AI125814/AI/NIAID NIH HHS/United States ; }, abstract = {Colistin is a drug of last resort for the treatment of many multidrug resistant Gram-negative bacteria, including Klebsiella pneumoniae However, bacteria readily acquire resistance to this antibiotic via lipopolysaccharide modifications caused by spontaneous mutations or from enzymes acquired by lateral gene transfer. The fitness cost associated with these modifications remains poorly understood. In this study, we show that colistin-resistant K. pneumoniae are more susceptible to killing by a newly isolated lytic phage than the colistin sensitive parent strain. We observe this behavior for colistin-resistance conferred by a horizontally transferred mcr-1 containing plasmid and also from the inactivation of the chromosomal gene mgrB By measuring zeta potentials, we found that the phage particles were negatively charged at neutral pH and that colistin-resistant bacteria had less negative zeta potentials than did wildtype. These results suggest that the decreased negative surface charge of colistin-resistant cells lowers the electrostatic repulsion between the phage and bacteria, thereby promoting phage adherence and subsequent infection. To further explore this, we tested the effect of phage treatment on K. pneumoniae growing in several different environments. We found that colistin-resistant cells were more susceptible to phage than were the wildtype cells when growing in biofilms or infected moth larvae and when colonizing the mammalian gut. A better understanding of these fitness costs may lead to new treatment approaches that minimize the emergence and spread of colistin-resistant pathogens in human and environmental reservoirs.}, }
@article {pmid31563088, year = {2020}, author = {Cyriaque, V and Jacquiod, S and Riber, L and Abu Al-Soud, W and Gillan, DC and Sørensen, SJ and Wattiez, R}, title = {Selection and propagation of IncP conjugative plasmids following long-term anthropogenic metal pollution in river sediments.}, journal = {Journal of hazardous materials}, volume = {382}, number = {}, pages = {121173}, doi = {10.1016/j.jhazmat.2019.121173}, pmid = {31563088}, issn = {1873-3336}, mesh = {Gene Transfer, Horizontal ; Geologic Sediments/*microbiology ; Metals ; Microbiota ; *Plasmids ; RNA, Ribosomal, 16S ; Real-Time Polymerase Chain Reaction ; Rivers/*microbiology ; Water Pollutants, Chemical ; Water Pollution ; }, abstract = {For a century, the MetalEurop foundry released metals into the river "La Deûle". Previous work revealed higher microbial diversity in metal impacted sediments, and horizontal gene transfer mediated by conjugative plasmids was suggested to drive the community adaptation to metals. We used an integrative state-of-the-art molecular approach coupling quantitative PCR, conjugation assays, flow cytometry, fluorescence activated cell sorting and 16S rRNA gene amplicon sequencing to investigate the presence of conjugative plasmids and their propagation patterns in sediment microbiomes. We highlighted the existence of a native broad-host range IncP conjugative plasmid population in polluted sediments, confirming their ecological importance for microbial adaptation. However, despite incompatibilities and decreased transfer frequencies with our own alien IncP plasmid, we evidenced that a wide diversity of bacterial members was still prone to uptake the plasmid, indicating that sediment microbial communities are still inclined to receive conjugative plasmids from the same group. We observed that metal pollution favoured exogenous plasmid transfer to specific metal-selected bacteria, which are likely coming from upstream sources (e.g. wastewater treatment plant, farms…). Altogether, our results suggest that MetalEurop sediments are hotspots for gene transfer via plasmids, acting as an "environmental reservoir" for microbes and mobile elements released by human activities.}, }
@article {pmid31562736, year = {2019}, author = {Ingmer, H and Gerlach, D and Wolz, C}, title = {Temperate Phages of Staphylococcus aureus.}, journal = {Microbiology spectrum}, volume = {7}, number = {5}, pages = {}, pmid = {31562736}, issn = {2165-0497}, mesh = {Animals ; Gene Transfer, Horizontal ; Host Specificity ; Host-Pathogen Interactions/physiology ; Humans ; Immune Evasion ; Podoviridae ; Staphylococcal Infections/*microbiology/*virology ; Staphylococcus Phages/classification/*genetics/*physiology ; Staphylococcus aureus/*genetics/*virology ; Teichoic Acids/metabolism ; Transduction, Genetic ; Virulence/genetics ; Virulence Factors/genetics ; Virus Integration ; }, abstract = {Most Staphylococcus aureus isolates carry multiple bacteriophages in their genome, which provide the pathogen with traits important for niche adaptation. Such temperate S. aureus phages often encode a variety of accessory factors that influence virulence, immune evasion and host preference of the bacterial lysogen. Moreover, transducing phages are primary vehicles for horizontal gene transfer. Wall teichoic acid (WTA) acts as a common phage receptor for staphylococcal phages and structural variations of WTA govern phage-host specificity thereby shaping gene transfer across clonal lineages and even species. Thus, bacteriophages are central for the success of S. aureus as a human pathogen.}, }
@article {pmid31562168, year = {2019}, author = {Schmithausen, RM and Sib, E and Exner, M and Hack, S and Rösing, C and Ciorba, P and Bierbaum, G and Savin, M and Bloomfield, SF and Kaase, M and Jacobshagen, A and Gemein, S and Gebel, J and Engelhart, S and Exner, D}, title = {The Washing Machine as a Reservoir for Transmission of Extended-Spectrum-Beta-Lactamase (CTX-M-15)-Producing Klebsiella oxytoca ST201 to Newborns.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {22}, pages = {}, pmid = {31562168}, issn = {1098-5336}, mesh = {Anti-Bacterial Agents/pharmacology ; Cross Infection/microbiology/transmission ; Disease Outbreaks/prevention &amp; control/statistics &amp; numerical data ; *Drug Resistance, Multiple, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Environmental Microbiology ; Equipment Contamination ; Fomites/*microbiology ; Germany ; Humans ; Infant, Newborn ; Intensive Care Units, Neonatal ; Klebsiella Infections/prevention &amp; control/*transmission ; Klebsiella oxytoca/drug effects/enzymology/isolation &amp; purification ; *Laundry Service, Hospital ; Multilocus Sequence Typing ; *Rubber ; *Water Microbiology ; beta-Lactamases ; }, abstract = {During the period from April 2012 to May 2013, 13 newborns (1 to 4 weeks of age) and 1 child in a pediatric hospital ward in Germany were colonized with Klebsiella oxytoca producing an extended-spectrum beta-lactamase (ESBL) (CTX-M-15). A microbiological source-tracking analysis with human and environmental samples was carried out to identify the source and transmission pathways of the K. oxytoca clone. In addition, different hygienic intervention methods were evaluated. K. oxytoca isolates were detected in the detergent drawer and on the rubber door seal of a domestic washer-extractor machine that was used in the same ward to wash laundry for the newborns, as well as in two sinks. These strains were typed using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing. The environmental findings were compared with those for the human strains and the isolates detected on clothing. The results from both techniques showed that the strains were identical (sequence type 201 and PFGE type 00531, a clone specific to this hospital and not previously isolated in Germany), emphasizing the washing machine as a reservoir and fomite for the transmission of these multidrug-resistant bacteria. After the washing machine was taken out of use, no further colonizations were detected during the subsequent 4-year period.IMPORTANCE Washing machines should be further investigated as possible sites for horizontal gene transfer (ESBL genes) and cross-contamination with clinically important Gram-negative strains. Particularly in the health care sector, the knowledge of possible (re-)contamination of laundry (patients' clothes and staff uniforms) with multidrug-resistant Gram-negative bacteria could help to prevent and to control nosocomial infections. This report describes an outbreak with a single strain of a multidrug-resistant bacterium (Klebsiella oxytoca sequence type 201) in a neonatal intensive care unit that was terminated only when the washing machine was removed. In addition, the study implies that changes in washing machine design and processing are required to prevent accumulation of residual water where microbial growth can occur and contaminate clothes.}, }
@article {pmid31554924, year = {2019}, author = {Farzand, R and Rajakumar, K and Zamudio, R and Oggioni, MR and Barer, MR and O'Hare, HM}, title = {ICEKp2: description of an integrative and conjugative element in Klebsiella pneumoniae, co-occurring and interacting with ICEKp1.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {13892}, pmid = {31554924}, issn = {2045-2322}, mesh = {Bacterial Proteins/*genetics ; China ; Drug Resistance, Multiple, Bacterial/genetics ; Escherichia coli/genetics ; Gene Transfer, Horizontal/genetics ; Humans ; Klebsiella Infections/microbiology ; Klebsiella pneumoniae/*genetics ; Mutation/genetics ; Plasmids/genetics ; Pseudomonas aeruginosa/genetics ; Virulence/genetics ; }, abstract = {Klebsiella pneumoniae is a human pathogen, prominent in antimicrobial-resistant and nosocomial infection. The integrative and conjugative element ICEKp1 is present in a third of clinical isolates and more prevalent in invasive disease; it provides genetic diversity and enables the spread of virulence-associated genes. We report a second integrative conjugative element that can co-occur with ICEKp1 in K. pneumoniae. This element, ICEKp2, is similar to the Pseudomonas aeruginosa pathogenicity island PAPI. We identified ICEKp2 in K. pneumoniae sequence types ST11, ST258 and ST512, which are associated with carbapenem-resistant outbreaks in China and the US, including isolates with and without ICEKp1. ICEKp2 was competent for excision, but self-mobilisation to recipient Escherichia coli was not detected. In an isolate with both elements, ICEKp2 positively influenced the efficiency of plasmid mobilisation driven by ICEKp1. We propose a putative mechanism, in which a Mob2 ATPase of ICEKp2 may contribute to the ICEKp1 conjugation machinery. Supporting this mechanism, mob2, but not a variant with mutations in the ATPase motif, restored transfer efficiency to an ICEKp2 knockout. This is the first demonstration of the interaction between integrative and conjugative genetic elements in a single Gram-negative bacterium with implications for understanding evolution by horizontal gene transfer.}, }
@article {pmid31554719, year = {2019}, author = {Suzuki, Y and Ida, M and Kubota, H and Ariyoshi, T and Murakami, K and Kobayashi, M and Kato, R and Hirai, A and Suzuki, J and Sadamasu, K}, title = {Multiple β-Lactam Resistance Gene-Carrying Plasmid Harbored by Klebsiella quasipneumoniae Isolated from Urban Sewage in Japan.}, journal = {mSphere}, volume = {4}, number = {5}, pages = {}, pmid = {31554719}, issn = {2379-5042}, mesh = {Anti-Bacterial Agents/pharmacology ; Carbapenems ; Conjugation, Genetic ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Japan ; Klebsiella/*drug effects/*genetics ; Microbial Sensitivity Tests ; Phylogeny ; Plasmids/*genetics ; Public Health ; Sewage/*microbiology ; Urban Renewal ; *beta-Lactam Resistance ; beta-Lactamases/genetics ; beta-Lactams/*pharmacology ; }, abstract = {The continuous emergence of carbapenemase-producing Enterobacteriaceae (CPE) presents a great public health challenge. Mitigation of CPE spread in the environment is crucial, particularly from a One Health perspective. Here we describe the isolation of CPE strain SNI47 from influent water of a sewage treatment plant in Japan. SNI47 was identified as Klebsiella quasipneumoniae subsp. quasipneumoniae by phylogenetic analysis and was resistant to β-lactams, including carbapenems. Of four plasmids detected from SNI47, the 185,311-bp IncA/C2 plasmid (pTMSNI47-1), which carried 10 drug resistance genes, including genes for four β-lactamases (blaCTX-M-2, blaDHA-1, blaKHM-1, and blaOXA-10), was transferred to Escherichia coli J53 via conjugation. The MICs of all tested β-lactams for the transconjugant were higher than for the recipient. We constructed recombinant plasmids, into which each β-lactamase gene was inserted, and used them to transform E. coli DH5α cells, demonstrating that KHM-1 enhanced carbapenem resistance. In addition, these β-lactamases were responsible for a wide-spectrum β-lactam resistance acquisition with mutual compensation. KHM-1, recognized as a rare type of metallo-β-lactamase, was detected in a transferable plasmid, from a sewage treatment plant, involved in horizontal gene transfer. The detection of such plasmids raises a health risk alarm for CPE dissemination.IMPORTANCE In our investigation of urban wastewater in Japan, carbapenem-resistant Klebsiella quasipneumoniae subsp. quasipneumoniae was isolated that carried the pTMSNI47-1 plasmid, which carries four β-lactamase genes and has transferability among Enterobacteriaceae pTMSNI47-1 was found to encode a rarely reported carbapenemase, KHM-1. Cooperative effects of β-lactamases encoded by pTMSNI47-1 appeared to have broad-spectrum resistance to β-lactams. The detection of the KHM-1 gene in urban wastewater suggests that such a rare antimicrobial resistance (AMR) gene can be pooled in the environment, potentially emerging as an AMR determinant in a pathogen. When the number of β-lactamase resistance genes is increased in one plasmid, the transfer of this plasmid can confer broad-spectrum resistance to β-lactams, even if the individual gene confers narrow-spectrum resistance. The present study adds important information about the potential risk of sewage treatment plants as reservoirs and environmental suppliers of AMR genes, contributing to the public health from a One Health perspective.}, }
@article {pmid31553893, year = {2019}, author = {Orrego, LM and Cabello-Donayre, M and Vargas, P and Martínez-García, M and Sánchez, C and Pineda-Molina, E and Jiménez, M and Molina, R and Pérez-Victoria, JM}, title = {Heme synthesis through the life cycle of the heme auxotrophic parasite Leishmania major.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {33}, number = {12}, pages = {13367-13385}, doi = {10.1096/fj.201901274RR}, pmid = {31553893}, issn = {1530-6860}, mesh = {Amino Acid Sequence ; Animals ; Coproporphyrinogen Oxidase/metabolism ; Female ; Ferrochelatase/chemistry/genetics/*metabolism ; Heme/*biosynthesis ; Leishmania major/*growth &amp; development ; Leishmaniasis, Cutaneous/*metabolism/parasitology ; Macrophages/metabolism/parasitology ; Male ; Mice ; Mice, Inbred BALB C ; Protein Conformation ; Protoporphyrinogen Oxidase/metabolism ; Protozoan Proteins/chemistry/genetics/*metabolism ; Psychodidae/*metabolism/parasitology ; Sequence Homology ; *Virulence ; }, abstract = {Heme is an essential molecule synthetized through a broadly conserved 8-step route that has been lost in trypanosomatid parasites. Interestingly, Leishmania reacquired by horizontal gene transfer from γ-proteobacteria the genes coding for the last 3 enzymes of the pathway. Here we show that intracellular amastigotes of Leishmania major can scavenge heme precursors from the host cell to fulfill their heme requirements, demonstrating the functionality of this partial pathway. To dissect its role throughout the L. major life cycle, the significance of L. major ferrochelatase (LmFeCH), the terminal enzyme of the route, was evaluated. LmFeCH expression in a heterologous system demonstrated its activity. Knockout promastigotes lacking lmfech were not able to use the ferrochelatase substrate protoporphyrin IX as a source of heme. In vivo infection of Phlebotomus perniciosus with knockout promastigotes shows that LmFeCH is not required for their development in the sandfly. In contrast, the replication of intracellular amastigotes was hampered in vitro by the deletion of lmfech. However, LmFeCH[-/-] parasites produced disease in a cutaneous leishmaniasis murine model in a similar way as control parasites. Therefore, although L. major can synthesize de novo heme from macrophage precursors, this activity is dispensable being an unsuited target for leishmaniasis treatment.-Orrego, L. M., Cabello-Donayre, M., Vargas, P., Martínez-García, M., Sánchez, C., Pineda-Molina, E., Jiménez, M., Molina, R., Pérez-Victoria, J. M. Heme synthesis through the life cycle of the heme auxotrophic parasite Leishmania major.}, }
@article {pmid31552071, year = {2019}, author = {Liu, S and Wu, B and Lv, S and Shen, Z and Li, R and Yi, G and Li, C and Guo, X}, title = {Genetic Diversity in FUB Genes of Fusarium oxysporum f. sp. cubense Suggests Horizontal Gene Transfer.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {1069}, pmid = {31552071}, issn = {1664-462X}, abstract = {Fusaric acid (FA) is an important secondary metabolite of many Fusarium species and involved in the wilt symptoms caused in banana by Fusarium oxysporum f. sp. cubense (Foc). To investigate the evolution characteristics of the 12 Foc FA biosynthetic genes (FUB), coding sequences of the 12 FUB genes and three housekeeping genes, EF-1α/RPB1/RPB2 (translation elongation factor-1α/RNA polymerase II subunit I/RNA polymerase II subunit II), were subjected to genetic diversity analysis, phylogenetic analysis, recombination detection, and selective pressure analysis. The results of selective pressure analysis showed that the 15 genes were mainly subjected to negative selection. However, a significantly higher number of silent mutations, which could not be simply explained by selective pressure difference, were observed in the 12 FUB genes in Foc than in the three housekeeping genes. Infraspecies phylogeny and recombination detection analysis showed that significantly more horizontal gene transfer (HGT) events (normalized) had occurred in the FUB genes than in the three housekeeping genes. In addition, many of these events involved outgroup isolates and significantly increased the genetic diversity of FUB genes in Foc. The infraspecies phylogenetic analysis suggested that the polyphyletic phylogeny proposed for Foc requires further discussion, and the divergence of race 1, race 4, and the common ancestor of several F. oxysporum (Fo) isolates pathogenic to nonbanana plants should have diverged over a short period. Finally, our results suggest that the FUB genes in Fo should have benefited from HGT to gain a relatively high genetic diversity to respond to different host plants and environments despite mainly being subject to negative selection.}, }
@article {pmid31551977, year = {2019}, author = {Bouznif, B and Guefrachi, I and Rodríguez de la Vega, RC and Hungria, M and Mars, M and Alunni, B and Shykoff, JA}, title = {Phylogeography of the Bradyrhizobium spp. Associated With Peanut, Arachis hypogaea: Fellow Travelers or New Associations?.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2041}, pmid = {31551977}, issn = {1664-302X}, abstract = {Legume plants have colonized almost all terrestrial biotopes. Their ecological success is partly due to the selective advantage provided by their symbiotic association with nitrogen-fixing bacteria called rhizobia, which allow legumes to thrive on marginal lands and nitrogen depleted soils where non-symbiotic plants cannot grow. Additionally, their symbiotic capacities result in a high protein content in their aerial parts and seeds. This interesting nutritional value has led to the domestication and agricultural exploitation of several legumes grown for seeds and/or fodder for human and domestic animal consumption. Several cultivated legume species are thus grown far beyond their natural geographic range. Other legume species have become invasives, spreading into new habitats. The cultivation and establishment of legume species outside of their original range requires either that they are introduced or cultivated along with their original symbiotic partner or that they find an efficient symbiotic partner in their introduced habitat. The peanut, Arachis hypogaea, a native of South America, is now cultivated throughout the world. This species forms root nodules with Bradyrhizobium, but it is unclear whether these came with the seeds from their native range or were acquired locally. Here we propose to investigate the phylogeography of Bradyrhizobium spp. associated with a number of different wild and cultivated legume species from a range of geographical areas, including numerous strains isolated from peanut roots across the areas of peanut cultivation. This will allow us to address the question of whether introduced/cultivated peanuts associate with bacteria from their original geographic range, i.e., were introduced together with their original bacterial symbionts, or whether they acquired their current associations de novo from the bacterial community within the area of introduction. We will base the phylogenetic analysis on sequence data from both housekeeping and core genes and a symbiotic gene (nif). Differences between the phylogenetic signal of symbiotic and non-symbiotic genes could result from horizontal transfer of symbiosis capacity. Thus this study will also allow us to elucidate the processes by which this symbiotic association has evolved within this group of Bradyrhizobium spp.}, }
@article {pmid31551333, year = {2019}, author = {O'Neal, L and Gullett, JM and Aksenova, A and Hubler, A and Briegel, A and Ortega, D and Kjær, A and Jensen, G and Alexandre, G}, title = {Distinct Chemotaxis Protein Paralogs Assemble into Chemoreceptor Signaling Arrays To Coordinate Signaling Output.}, journal = {mBio}, volume = {10}, number = {5}, pages = {}, pmid = {31551333}, issn = {2150-7511}, mesh = {Bacterial Proteins/*metabolism ; Carrier Proteins/*metabolism ; Chemoreceptor Cells/*physiology ; Chemotaxis/*physiology ; Membrane Proteins/*metabolism ; Methyl-Accepting Chemotaxis Proteins/*metabolism ; Signal Transduction/*physiology ; }, abstract = {Most chemotactic motile bacteria possess multiple chemotaxis signaling systems, the functions of which are not well characterized. Chemotaxis signaling is initiated by chemoreceptors that assemble as large arrays, together with chemotaxis coupling proteins (CheW) and histidine kinase proteins (CheA), which form a baseplate with the cytoplasmic tips of receptors. These cell pole-localized arrays mediate sensing, signaling, and signal amplification during chemotaxis responses. Membrane-bound chemoreceptors with different cytoplasmic domain lengths segregate into distinct arrays. Here, we show that a bacterium, Azospirillum brasilense, which utilizes two chemotaxis signaling systems controlling distinct motility parameters, coordinates its chemotactic responses through the production of two separate membrane-bound chemoreceptor arrays by mixing paralogs within chemotaxis baseplates. The polar localization of chemoreceptors of different length classes is maintained in strains that had baseplate signaling proteins from either chemotaxis system but was lost when both systems were deleted. Chemotaxis proteins (CheA and CheW) from each of the chemotaxis signaling systems (Che1 and Che4) could physically interact with one another, and chemoreceptors from both classes present in A. brasilense could interact with Che1 and Che4 proteins. The assembly of paralogs from distinct chemotaxis pathways into baseplates provides a straightforward mechanism for coordinating signaling from distinct pathways, which we predict is not unique to this system given the propensity of chemotaxis systems for horizontal gene transfer.IMPORTANCE The assembly of chemotaxis receptors and signaling proteins into polar arrays is universal in motile chemotactic bacteria. Comparative genome analyses indicate that most motile bacteria possess multiple chemotaxis signaling systems, and experimental evidence suggests that signaling from distinct chemotaxis systems is integrated. Here, we identify one such mechanism. We show that paralogs from two chemotaxis systems assemble together into chemoreceptor arrays, forming baseplates comprised of proteins from both chemotaxis systems. These mixed arrays provide a straightforward mechanism for signal integration and coordinated response output from distinct chemotaxis systems. Given that most chemotactic bacteria encode multiple chemotaxis systems and the propensity for these systems to be laterally transferred, this mechanism may be common to ensure chemotaxis signal integration occurs.}, }
@article {pmid31550387, year = {2020}, author = {Pommerrenig, B and Diehn, TA and Bernhardt, N and Bienert, MD and Mitani-Ueno, N and Fuge, J and Bieber, A and Spitzer, C and Bräutigam, A and Ma, JF and Chaumont, F and Bienert, GP}, title = {Functional evolution of nodulin 26-like intrinsic proteins: from bacterial arsenic detoxification to plant nutrient transport.}, journal = {The New phytologist}, volume = {225}, number = {3}, pages = {1383-1396}, doi = {10.1111/nph.16217}, pmid = {31550387}, issn = {1469-8137}, mesh = {Animals ; Aquaporins/metabolism ; Arsenic/*metabolism ; Bacteria/metabolism ; Biodegradation, Environmental ; Biological Transport ; Boric Acids/metabolism ; Boron/metabolism ; Bryophyta/metabolism ; Cell Membrane/metabolism ; Diffusion ; *Evolution, Molecular ; Membrane Proteins/*genetics ; Metalloids/metabolism ; Mutation/genetics ; Nitrogen/*metabolism ; Oocytes/metabolism ; Phenotype ; Phosphorus/*metabolism ; Phylogeny ; Plant Proteins/*genetics ; Plants/*metabolism ; Recombinant Fusion Proteins/metabolism ; Silicic Acid/metabolism ; Water/metabolism ; Xenopus/metabolism ; }, abstract = {Nodulin 26-like intrinsic proteins (NIPs) play essential roles in transporting the nutrients silicon and boron in seed plants, but the evolutionary origin of this transport function and the co-permeability to toxic arsenic remains enigmatic. Horizontal gene transfer of a yet uncharacterised bacterial AqpN-aquaporin group was the starting-point for plant NIP evolution. We combined intense sequence, phylogenetic and genetic context analyses and a mutational approach with various transport assays in oocytes and plants to resolve the transorganismal and functional evolution of bacterial and algal and terrestrial plant NIPs and to reveal their molecular transport specificity features. We discovered that aqpN genes are prevalently located in arsenic resistance operons of various prokaryotic phyla. We provided genetic and functional evidence that these proteins contribute to the arsenic detoxification machinery. We identified NIPs with the ancestral bacterial AqpN selectivity filter composition in algae, liverworts, moss, hornworts and ferns and demonstrated that these archetype plant NIPs and their prokaryotic progenitors are almost impermeable to water and silicon but transport arsenic and boron. With a mutational approach, we demonstrated that during evolution, ancestral NIP selectivity shifted to allow subfunctionalisations. Together, our data provided evidence that evolution converted bacterial arsenic efflux channels into essential seed plant nutrient transporters.}, }
@article {pmid31548387, year = {2019}, author = {Petersen, J and Vollmers, J and Ringel, V and Brinkmann, H and Ellebrandt-Sperling, C and Spröer, C and Howat, AM and Murrell, JC and Kaster, AK}, title = {A marine plasmid hitchhiking vast phylogenetic and geographic distances.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {41}, pages = {20568-20573}, pmid = {31548387}, issn = {1091-6490}, mesh = {Bacterial Proteins/*genetics ; *Environment ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Geography ; Phylogeny ; Plasmids/*genetics ; Recombination, Genetic ; Roseobacter/classification/*genetics ; }, abstract = {Horizontal gene transfer (HGT) plays an important role in bacterial evolution and serves as a driving force for bacterial diversity and versatility. HGT events often involve mobile genetic elements like plasmids, which can promote their own dissemination by associating with adaptive traits in the gene pool of the so-called mobilome. Novel traits that evolve through HGT can therefore lead to the exploitation of new ecological niches, prompting an adaptive radiation of bacterial species. In this study, we present phylogenetic, biogeographic, and functional analyses of a previously unrecognized RepL-type plasmid found in diverse members of the marine Roseobacter group across the globe. Noteworthy, 100% identical plasmids were detected in phylogenetically and geographically distant bacteria, revealing a so-far overlooked, but environmentally highly relevant vector for HGT. The genomic and functional characterization of this plasmid showed a completely conserved backbone dedicated to replication, stability, and mobilization as well as an interchangeable gene cassette with highly diverse, but recurring motifs. The majority of the latter appear to be involved in mechanisms coping with toxins and/or pollutants in the marine environment. Furthermore, we provide experimental evidence that the plasmid has the potential to be transmitted across bacterial orders, thereby increasing our understanding of evolution and microbial niche adaptation in the environment.}, }
@article {pmid31546588, year = {2019}, author = {Mi-Ichi, F and Yoshida, H}, title = {Unique Features of Entamoeba Sulfur Metabolism; Compartmentalization, Physiological Roles of Terminal Products, Evolution and Pharmaceutical Exploitation.}, journal = {International journal of molecular sciences}, volume = {20}, number = {19}, pages = {}, pmid = {31546588}, issn = {1422-0067}, support = {18H04675//Grants-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology of Japan/ ; 18K07087//Grants-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology of Japan/ ; 16K08842//Grants-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology of Japan/ ; JP19fm0208025//AMED-J-PRIDE/ ; }, mesh = {Antiprotozoal Agents/pharmacology ; Biological Evolution ; Entamoeba/drug effects/genetics/growth &amp; development/*metabolism ; Entamoebiasis/parasitology ; Gene Transfer, Horizontal ; Humans ; Lipid Metabolism ; Parasite Encystment ; Protozoan Proteins/metabolism ; Sulfatases/metabolism ; Sulfotransferases/metabolism ; Sulfur/*metabolism ; }, abstract = {Sulfur metabolism is essential for all living organisms. Recently, unique features of the Entamoeba metabolic pathway for sulfated biomolecules have been described. Entamoeba is a genus in the phylum Amoebozoa and includes the causative agent for amoebiasis, a global public health problem. This review gives an overview of the general features of the synthesis and degradation of sulfated biomolecules, and then highlights the characteristics that are unique to Entamoeba. Future biological and pharmaceutical perspectives are also discussed.}, }
@article {pmid31543875, year = {2019}, author = {Søndberg, E and Sinha, AK and Gerdes, K and Semsey, S}, title = {CRP Interacts Specifically With Sxy to Activate Transcription in Escherichia coli.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2053}, pmid = {31543875}, issn = {1664-302X}, abstract = {Horizontal gene transfer through natural competence is an important driving force of bacterial evolution and antibiotic resistance development. In several Gram-negative pathogens natural competence is regulated by the concerted action of cAMP receptor protein (CRP) and the transcriptional co-regulator Sxy through a subset of CRP-binding sites (CRP-S sites) at genes encoding competence factors. Despite the wealth of knowledge on CRP's structure and function it is not known how CRP and Sxy act together to activate transcription. In order to get an insight into the regulatory mechanism by which these two proteins activate gene expression, we performed a series of mutational analyses on CRP and Sxy. We found that CRP contains a previously uncharacterized region necessary for Sxy dependent induction of CRP-S sites, here named "Sxy Interacting Region" (SIR) encompassing residues Q194 and L196. Lost promoter induction in SIR mutants could be restored in the presence of specific complementary Sxy mutants, presenting evidence for a direct interaction of CRP and Sxy proteins in transcriptional activation. Moreover, we identified constitutive mutants of Sxy causing higher levels of CRP-S site promoter activation than wild-type Sxy. Both suppressor and constitutive mutations are located within the same area of Sxy.}, }
@article {pmid31543869, year = {2019}, author = {Navarro-Garcia, F and Ruiz-Perez, F and Cataldi, &#xc1; and Larzábal, M}, title = {Type VI Secretion System in Pathogenic Escherichia coli: Structure, Role in Virulence, and Acquisition.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1965}, pmid = {31543869}, issn = {1664-302X}, abstract = {Bacterial pathogens utilize a myriad of mechanisms to invade mammalian hosts, damage tissue sites, and evade the immune system. One essential strategy of Gram-negative bacteria is the secretion of virulence factors through both inner and outer membranes to reach a potential target. Most secretion systems are harbored in mobile elements including transposons, plasmids, pathogenicity islands, and phages, and Escherichia coli is one of the more versatile bacteria adopting this genetic information by horizontal gene transfer. Additionally, E. coli is a bacterial species with members of the commensal intestinal microbiota and pathogens associated with numerous types of infections such as intestinal, urinary, and systemic in humans and other animals. T6SS cluster plasticity suggests evolutionarily divergent systems were acquired horizontally. T6SS is a secretion nanomachine that is extended through the bacterial double membrane; from this apparatus, substrates are conveyed straight from the cytoplasm of the bacterium into a target cell or to the extracellular space. This nanomachine consists of three main complexes: proteins in the inner membrane that are T4SS component-like, the baseplate complex, and the tail complex, which are formed by components evolutionarily related to contractile bacteriophage tails. Advances in the T6SS understanding include the functional and structural characterization of at least 13 subunits (so-called core components), which are thought to comprise the minimal apparatus. So far, the main role of T6SS is on bacterial competition by using it to kill neighboring non-immune bacteria for which antibacterial proteins are secreted directly into the periplasm of the bacterial target after cell-cell contact. Interestingly, a few T6SSs have been associated directly to pathogenesis, e.g., roles in biofilm formation and macrophage survival. Here, we focus on the advances on T6SS from the perspective of E. coli pathotypes with emphasis in the secretion apparatus architecture, the mechanisms of pathogenicity of effector proteins, and the events of lateral gene transfer that led to its spread.}, }
@article {pmid31542868, year = {2019}, author = {Matveeva, TV and Otten, L}, title = {Widespread occurrence of natural genetic transformation of plants by Agrobacterium.}, journal = {Plant molecular biology}, volume = {101}, number = {4-5}, pages = {415-437}, pmid = {31542868}, issn = {1573-5028}, support = {16-16-10010//Russian Science Foundation/ ; }, mesh = {Agrobacterium/*genetics ; Biological Evolution ; DNA, Bacterial/chemistry ; DNA, Plant/chemistry ; Gene Transfer, Horizontal ; *Genome, Plant ; Plants, Genetically Modified/genetics ; Sequence Analysis, DNA ; Transcriptome ; *Transformation, Genetic ; }, abstract = {Naturally transgenic plant species occur on an unexpectedly large scale. Agrobacterium-mediated gene transfer leads to the formation of crown galls or hairy roots, due to expression of transferred T-DNA genes. Spontaneous regeneration of transformed cells can produce natural transformants carrying cellular T-DNA (cT-DNA) sequences of bacterial origin. This particular type of horizontal gene transfer (HGT) could play a role in plant evolution. However, the material available today is not enough for generalizations concerning the role of Agrobacterium in HGT from bacteria to plants. In this study, we searched for T-DNA-like genes in the sequenced genomes of dicots and monocots. We demonstrate the presence of cT-DNAs in 23 out of 275 dicot species, within genera Eutrema, Arachis, Nissolia, Quillaja, Euphorbia, Parasponia, Trema, Humulus, Psidium, Eugenia, Juglans, Azadirachta, Silene, Dianthus, Vaccinium, Camellia, and Cuscuta. Analysis of transcriptome data of 356 dicot species yielded 16 additional naturally transgenic species. Thus, HGT from Agrobacterium to dicots is remarkably widespread. Opine synthesis genes are most frequent, followed by plast genes. Species in the genera Parasponia, Trema, Camellia, Azadirachta, Quillaja, and Diospyros contain a combination of plast and opine genes. Some are intact and expressed, but the majority have internal stop codons. Among the sequenced monocot species, Dioscorea alata (greater yam) and Musa acuminata (banana) also contain T-DNA-like sequences. The identified examples are valuable material for future research on the role of Agrobacterium-derived genes in plant evolution, for investigations on Agrobacterium strain diversity, and for studies on the function and evolution of cT-DNA genes in natural transformants.}, }
@article {pmid31541308, year = {2020}, author = {Thomas-Vaslin, V}, title = {Individuation and the Organization in Complex Living Ecosystem: Recursive Integration and Self-assertion by Holon-Lymphocytes.}, journal = {Acta biotheoretica}, volume = {68}, number = {1}, pages = {171-199}, doi = {10.1007/s10441-019-09364-w}, pmid = {31541308}, issn = {1572-8358}, mesh = {Aging/genetics ; *Ecosystem ; Environment ; *Feedback ; *Gene Transfer, Horizontal ; Humans ; *Identification, Psychological ; Immune System/*immunology/metabolism ; *Individuation ; Lymphocytes/*immunology ; }, abstract = {Individuation and organization in complex living multi-level ecosystem occurs as dynamical processes from early ontogeny. The notion of living "holon" displaying dynamic self-assertion and integration is used here to explain the ecosystems dynamic processes. The update of the living holon state according to the continuous change of the dynamic system allows for its viability. This is interpreted as adaptation, selection and organization by the human that observes the system a posteriori from its level. Our model concerns the complex dynamics of the adaptive immune system, integrating holon-lymphocytes that collectively preserve the identity and integrity of the organism. Each lymphocyte individualizes as a dynamic holon-lymphocyte, with somatic gene individuation leading to an individual, singular antigen immunoreceptor type, promoting the self-assertion. In turn, the "Immunoception" allows for perception of the environmental antigenic context, thus integration of the holon in its environment. The self-assertion/integration of holon-lymphocyte starts from fetal stages and is influenced by mother Lamarckian acquired historicity transmissions, a requisite for the integrity of the holobiont-organism. We propose a dynamic model of the perception by holon-lymphocyte, and at the supra-clonal level of the immune system functions that sustain the identity and integrity of the holon-holobiont organism.}, }
@article {pmid31540994, year = {2019}, author = {Ganter, S and Miotello, G and Manso-Silván, L and Armengaud, J and Tardy, F and Gaurivaud, P and Thiaucourt, F}, title = {Proteases as Secreted Exoproteins in Mycoplasmas from Ruminant Lungs and Their Impact on Surface-Exposed Proteins.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {23}, pages = {}, pmid = {31540994}, issn = {1098-5336}, mesh = {Animals ; Lung/*microbiology ; Membrane Proteins/metabolism ; Mycoplasma/*enzymology ; Peptide Hydrolases/*metabolism ; Ruminants/*microbiology ; }, abstract = {Many mycoplasma species are isolated from the ruminant lungs as either saprophytes or true pathogens. These wall-less bacteria possess a minimal genome and reduced metabolic capabilities. Accordingly, they rely heavily on their hosts for the supply of essential metabolites and, notably, peptides. Seven of 13 ruminant lung-associated Mycoplasma (sub)species were shown to possess caseinolytic activity when grown in rich media and assessed with a quantitative fluorescence test. For some species, this activity was detected in spent medium, an indication that proteases were secreted outside the mycoplasma cells. To identify these proteases, we incubated concentrated washed cell pellets in a defined medium and analyzed the supernatants by tandem mass spectrometry. Secreted-protease activity was detected mostly in the species belonging to the Mycoplasma mycoides cluster (MMC) and, to a lesser extent, in Mycoplasma bovirhinis Analyzing a Mycoplasma mycoides subsp. capri strain, chosen as a model, we identified 35 expressed proteases among 55 predicted coding genes, of which 5 were preferentially found in the supernatant. Serine protease S41, acquired by horizontal gene transfer, was responsible for the caseinolytic activity, as demonstrated by zymography and mutant analysis. In an M. capricolum mutant, inactivation of the S41 protease resulted in marked modification of the expression or secretion of 17 predicted surface-exposed proteins. This is an indication that the S41 protease could have a role in posttranslational cleavage of surface-exposed proteins and ectodomain shedding, whose physiological impacts still need to be explored.IMPORTANCE Few studies pertaining to proteases in ruminant mycoplasmas have been reported. Here, we focus on proteases that are secreted outside the mycoplasma cell using a mass spectrometry approach. The most striking result is the identification, within the Mycoplasma mycoides cluster, of a serine protease that is exclusively detected outside the mycoplasma cells and is responsible for casein digestion. This protease may also be involved in the posttranslational processing of surface proteins, as suggested by analysis of mutants showing a marked reduction in the secretion of extracellular proteins. By analogy, this finding may help increase understanding of the mechanisms underlying this ectodomain shedding in other mycoplasma species. The gene encoding this protease is likely to have been acquired via horizontal gene transfer from Gram-positive bacteria and sortase-associated surface proteases. Whether this protease and the associated ectodomain shedding are related to virulence has yet to be ascertained.}, }
@article {pmid31540466, year = {2019}, author = {Bello-López, JM and Cabrero-Martínez, OA and Ibáñez-Cervantes, G and Hernández-Cortez, C and Pelcastre-Rodríguez, LI and Gonzalez-Avila, LU and Castro-Escarpulli, G}, title = {Horizontal Gene Transfer and Its Association with Antibiotic Resistance in the Genus Aeromonas spp.}, journal = {Microorganisms}, volume = {7}, number = {9}, pages = {}, pmid = {31540466}, issn = {2076-2607}, abstract = {The evolution of multidrug resistant bacteria to the most diverse antimicrobials known so far pose a serious problem to global public health. Currently, microorganisms that develop resistant phenotypes to multiple drugs are associated with high morbidity and mortality. This resistance is encoded by a group of genes termed 'bacterial resistome', divided in intrinsic and extrinsic resistome. The first one refers to the resistance displayed on an organism without previous exposure to an antibiotic not involving horizontal genetic transfer, and it can be acquired via mutations. The latter, on the contrary, is acquired exclusively via horizontal genetic transfer involving mobile genetic elements that constitute the 'bacterial mobilome'. This transfer is mediated by three different mechanisms: transduction, transformation, and conjugation. Recently, a problem of public health due to implications in the emergence of multi-drug resistance in Aeromonas spp. strains in water environments has been described. This is derived from the genetic material transfer via conjugation events. This is important, since bacteria that have acquired antibiotic resistance in natural environments can cause infections derived from their ingestion or direct contact with open wounds or mucosal tissue, which in turn, by their resistant nature, makes their eradication complex. Implications of the emergence of resistance in Aeromonas spp. by horizontal gene transfer on public health are discussed.}, }
@article {pmid31540216, year = {2019}, author = {Kwun, MJ and Oggioni, MR and Bentley, SD and Fraser, C and Croucher, NJ}, title = {Synergistic Activity of Mobile Genetic Element Defences in Streptococcus pneumoniae.}, journal = {Genes}, volume = {10}, number = {9}, pages = {}, pmid = {31540216}, issn = {2073-4425}, support = {MR/M003078/1/MRC_/Medical Research Council/United Kingdom ; MR/R015600/1/MRC_/Medical Research Council/United Kingdom ; BB/N002903/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 104169/Z/14/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {DNA Restriction-Modification Enzymes/*genetics ; Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences ; Streptococcus pneumoniae/enzymology/*genetics ; Transformation, Bacterial ; }, abstract = {A diverse set of mobile genetic elements (MGEs) transmit between Streptococcus pneumoniae cells, but many isolates remain uninfected. The best-characterised defences against horizontal transmission of MGEs are restriction-modification systems (RMSs), of which there are two phase-variable examples in S. pneumoniae. Additionally, the transformation machinery has been proposed to limit vertical transmission of chromosomally integrated MGEs. This work describes how these mechanisms can act in concert. Experimental data demonstrate RMS phase variation occurs at a sub-maximal rate. Simulations suggest this may be optimal if MGEs are sometimes vertically inherited, as it reduces the probability that an infected cell will switch between RMS variants while the MGE is invading the population, and thereby undermine the restriction barrier. Such vertically inherited MGEs can be deleted by transformation. The lack of between-strain transformation hotspots at known prophage att sites suggests transformation cannot remove an MGE from a strain in which it is fixed. However, simulations confirmed that transformation was nevertheless effective at preventing the spread of MGEs into a previously uninfected cell population, if a recombination barrier existed between co-colonising strains. Further simulations combining these effects of phase variable RMSs and transformation found they synergistically inhibited MGEs spreading, through limiting both vertical and horizontal transmission.}, }
@article {pmid31539947, year = {2019}, author = {Yadav, S and Kapley, A}, title = {Exploration of activated sludge resistome using metagenomics.}, journal = {The Science of the total environment}, volume = {692}, number = {}, pages = {1155-1164}, doi = {10.1016/j.scitotenv.2019.07.267}, pmid = {31539947}, issn = {1879-1026}, mesh = {Bacteria ; Drug Resistance, Microbial/*genetics ; Gene Transfer, Horizontal ; India ; *Metagenome ; Metagenomics ; Plasmids ; Sewage/*microbiology ; }, abstract = {Antibiotic resistance is a global problem. In India poor waste management and inadequate sanitary are key factors which encourage the dissemination of antimicrobial resistance. Microbial biodiversity serves as an invaluable source for diverse types of bioactive compounds that encompass most of the pharmaceuticals to date. Therefore, in this study, we used the metagenomic approach for the surveillance of antibiotic resistance genes, drug resistant microbes and mobile-genetic elements in two activated sludge metagenome samples collected from Ankleshwar, Gujarat, India. Proteobacteria were found to be the most abundant bacteria among the metagenome analyzed. Twenty-four genes conferring resistance to antibiotics and heavy metals were found. Multidrug resistant "ESKAPE pathogens" were also abundant in the sludge metagenome. Mobile genetic elements like IncP-1 plasmid pKJK5, IncP-1beta multi resistance plasmid and pB8 were also noticed in the higher abundance. These plasmids play an important role in the spread of antibiotic resistance by the horizontal gene transfer. Statistical analysis of both metagenome using STAMP software confirmed presence of mobile genetic elements such as gene transfer agents, phages, Prophages etc. which also play important role in the dissemination of antibiotic resistant genes.}, }
@article {pmid31536887, year = {2019}, author = {Young, S and Rohr, JR and Harwood, VJ}, title = {Vancomycin resistance plasmids affect persistence of Enterococcus faecium in water.}, journal = {Water research}, volume = {166}, number = {}, pages = {115069}, doi = {10.1016/j.watres.2019.115069}, pmid = {31536887}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents ; Bacterial Proteins ; *Enterococcus faecium ; *Gram-Positive Bacterial Infections ; Humans ; Microbial Sensitivity Tests ; Plasmids ; Vancomycin Resistance ; }, abstract = {Vancomycin resistant enterococci (VRE) cause 20,000 infections annually in the United States, most of which are nosocomial. Recent findings of VRE in sewage-contaminated surface waters demonstrate an alternate route of human exposure, and a possible setting for horizontal gene exchange facilitated by plasmids and other mobile genetic elements. Maintenance of antibiotic resistance genes and proteins may, however, present a fitness cost in the absence of selective pressure, particularly in habitats such as environmental waters that are not optimal for gut-associated bacteria. Nutrient levels, which are transiently elevated following sewage spills, may also affect survival. We tested the hypotheses that nutrients and/or plasmids conferring vancomycin resistance affect Enterococcus faecium survival in river water by measuring decay of strains that differed only by their plasmid, under natural and augmented nutrient conditions. In natural river water, decay rate (log10 reduction) correlated directly with plasmid size; however, plasmid presence and size had no effect on decay rate when nutrients levels were augmented. Under natural nutrient levels, the vancomycin-resistant strain with the largest plasmid (200 kb) decayed significantly more rapidly than the plasmid-less, susceptible parent strain, in contrast to similar decay rates among strains under augmented nutrient conditions. This work is among the first to show that plasmids conferring antibiotic resistance affect fitness of Enterococcus species in secondary habitats such as surface water. The nutrient-dependent nature of the fitness cost suggests that conveyance of VRE to environmental waters in nutrient-rich sewage may prolong survival of these pathogens, providing greater opportunity for host infection and/or horizontal gene transfer.}, }
@article {pmid31536878, year = {2019}, author = {Lambrecht, E and Van Coillie, E and Van Meervenne, E and Boon, N and Heyndrickx, M and Van de Wiele, T}, title = {Commensal E. coli rapidly transfer antibiotic resistance genes to human intestinal microbiota in the Mucosal Simulator of the Human Intestinal Microbial Ecosystem (M-SHIME).}, journal = {International journal of food microbiology}, volume = {311}, number = {}, pages = {108357}, doi = {10.1016/j.ijfoodmicro.2019.108357}, pmid = {31536878}, issn = {1879-3460}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Cefotaxime/pharmacology ; Chickens/microbiology ; *Computer Simulation ; Conjugation, Genetic/*genetics ; Drug Resistance, Bacterial/*genetics ; Ecosystem ; Escherichia coli/drug effects/*genetics ; Gastrointestinal Microbiome/drug effects/genetics ; Gene Transfer, Horizontal/*genetics ; Humans ; Intestinal Mucosa/*microbiology ; Intestines/microbiology ; Plasmids/genetics ; }, abstract = {Food-producing animals are indicated as a reservoir of antibiotic resistance genes and a potential vector for transmission of plasmid-encoded antibiotic resistance genes by conjugation to the human intestinal microbiota. In this study, transfer of an antibiotic resistance plasmid from a commensal E. coli originating from a broiler chicken towards the human intestinal microbiota was assessed by using a Mucosal Simulator of the Human Intestinal Microbial Ecosystem (M-SHIME). This in vitro model mimics the human intestinal ecosystem and received a single dose of 10[9]E. coli MB6212, which harbors a plasmid known to confer resistance towards several antibiotics including tetracycline, sulfamethoxazole and cefotaxime. Since the degree of stress imposed by stomach pH and bile acids vary with the consumed meal size, the effect of meal size on E. coli donor survival and on plasmid transfer towards lumen and mucosal coliforms and anaerobes was determined. The administered commensal E. coli strain survived stomach acid and bile salt stress and was able to grow in the colon environment during the timeframe of the experiment (72 h). Transfer of antibiotic resistance was observed rapidly since cultivable transconjugant coliforms and anaerobes were already detected in the lumen and mucosa after 2 h in the simulated proximal colon. The presence of the resistance plasmid in the transconjugants was confirmed by PCR. Differences in meal size and adapted digestion had neither a detectable impact on antibiotic resistance transfer, nor on the survival of the E. coli donor strain, nor on short chain fatty acid profiles. The median number of resistant indigenous coliforms in the lumen of the inoculated colon vessels was 5.00 × 10[5] cfu/ml [min - max: 3.47 × 10[4]-3.70 × 10[8] cfu/ml], and on the mucosa 1.44 × 10[7] cfu/g [min-max: 4.00 × 10[3]-4.00 × 10[8] cfu/g]. Exact quantification of the anaerobic transconjugants was difficult, as (intrinsic) resistant anaerobic background microbiota were present. QPCR data supported the observation of plasmid transfer in the simulated colon. Moreover, inoculation of E. coli MB6212 had no significant impact on the microbial diversity in the lumen as determined by 16 S ribosomal gene based next generation sequencing on lumen samples. This study demonstrates that a commensal, antibiotic resistant E. coli strain present in food can transfer its antibiotic resistance plasmid relatively quickly to intestinal microbiota in the M-SHIME. The spread and persistence of antibiotic resistance genes and resistant bacteria in our intestinal system is an alarming scenario which might present clinical challenges, since it implies a potential reservoir for dissemination to pathogenic bacteria.}, }
@article {pmid31534648, year = {2019}, author = {Craft, KM and Nguyen, JM and Berg, LJ and Townsend, SD}, title = {Methicillin-resistant Staphylococcus aureus (MRSA): antibiotic-resistance and the biofilm phenotype.}, journal = {MedChemComm}, volume = {10}, number = {8}, pages = {1231-1241}, pmid = {31534648}, issn = {2040-2511}, support = {T32 GM065086/GM/NIGMS NIH HHS/United States ; }, abstract = {Staphylococcus aureus (S. aureus) is an asymptomatic colonizer of 30% of all human beings. While generally benign, antibiotic resistance contributes to the success of S. aureus as a human pathogen. Resistance is rapidly evolved through a wide portfolio of mechanisms including horizontal gene transfer and chromosomal mutation. In addition to traditional resistance mechanisms, a special feature of S. aureus pathogenesis is its ability to survive on both biotic and abiotic surfaces in the biofilm state. Due to this characteristic, S. aureus is a leading cause of human infection. Methicillin-resistant S. aureus (MRSA) in particular has emerged as a widespread cause of both community- and hospital-acquired infections. Currently, MRSA is responsible for 10-fold more infections than all multi-drug resistant (MDR) Gram-negative pathogens combined. Recently, MRSA was classified by the World Health Organization (WHO) as one of twelve priority pathogens that threaten human health. In this targeted mini-review, we discuss MRSA biofilm production, the relationship of biofilm production to antibiotic resistance, and front-line techniques to defeat the biofilm-resistance system.}, }
@article {pmid31534034, year = {2019}, author = {Sherlock, D and Leong, JX and Fogg, PCM}, title = {Identification of the First Gene Transfer Agent (GTA) Small Terminase in Rhodobacter capsulatus and Its Role in GTA Production and Packaging of DNA.}, journal = {Journal of virology}, volume = {93}, number = {23}, pages = {}, pmid = {31534034}, issn = {1098-5514}, support = {/WT_/Wellcome Trust/United Kingdom ; 109363/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacteriophages/genetics ; Capsid Proteins/genetics ; DNA ; *DNA Packaging ; DNA-Binding Proteins ; Drug Resistance, Bacterial ; Endodeoxyribonucleases/*genetics/metabolism ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Multigene Family ; Rhodobacter capsulatus/*genetics/virology ; Sequence Alignment ; Sequence Analysis, Protein ; Transduction, Genetic ; Virus Assembly ; }, abstract = {Genetic exchange mediated by viruses of bacteria (bacteriophages) is the primary driver of rapid bacterial evolution. The priority of viruses is usually to propagate themselves. Most bacteriophages use the small terminase protein to identify their own genome and direct its inclusion into phage capsids. Gene transfer agents (GTAs) are descended from bacteriophages, but they instead package fragments of the entire bacterial genome without preference for their own genes. GTAs do not selectively target specific DNA, and no GTA small terminases are known. Here, we identified the small terminase from the model Rhodobacter capsulatus GTA, which then allowed prediction of analogues in other species. We examined the role of the small terminase in GTA production and propose a structural basis for random DNA packaging.IMPORTANCE Random transfer of any and all genes between bacteria could be influential in the spread of virulence or antimicrobial resistance genes. Discovery of the true prevalence of GTAs in sequenced genomes is hampered by their apparent similarity to bacteriophages. Our data allowed the prediction of small terminases in diverse GTA producer species, and defining the characteristics of a "GTA-type" terminase could be an important step toward novel GTA identification. Importantly, the GTA small terminase shares many features with its phage counterpart. We propose that the GTA terminase complex could become a streamlined model system to answer fundamental questions about double-stranded DNA (dsDNA) packaging by viruses that have not been forthcoming to date.}, }
@article {pmid31533074, year = {2020}, author = {Li, XP and Sun, RY and Song, JQ and Fang, LX and Zhang, RM and Lian, XL and Liao, XP and Liu, YH and Lin, J and Sun, J}, title = {Within-host heterogeneity and flexibility of mcr-1 transmission in chicken gut.}, journal = {International journal of antimicrobial agents}, volume = {55}, number = {1}, pages = {105806}, doi = {10.1016/j.ijantimicag.2019.09.010}, pmid = {31533074}, issn = {1872-7913}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Cecum/microbiology ; Chickens/*microbiology ; China/epidemiology ; Colistin/pharmacology ; Drug Resistance, Bacterial/genetics ; Electrophoresis, Gel, Pulsed-Field/veterinary ; Enterobacteriaceae/drug effects/*enzymology/genetics ; Enterobacteriaceae Infections/epidemiology/*microbiology ; Escherichia coli/drug effects/*enzymology/genetics ; Escherichia coli Infections/epidemiology/*microbiology ; Escherichia coli Proteins/*genetics ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests/veterinary ; Plasmids/genetics ; Poultry Diseases/epidemiology/*microbiology ; Whole Genome Sequencing/veterinary ; }, abstract = {OBJECTIVES: To characterize the colistin-resistant bacterial population in the gut and assess diversity of mcr-1 transmission within a single individual.<br><br>METHODS: Large numbers of isolates (>100 colonies/chicken cecum sample) were collected from nine randomly selected mcr-1-positive chickens in China and used for comprehensive microbiological, molecular and comparative genomics analyses.<br><br>RESULTS: Of 1273 colonies, 968 were mcr-1 positive (962 Escherichia coli, two Escherichia fergusonii, two Klebsiella pneumoniae and two Klebsiella quasipneumoniae). One to six colistin-resistant species and three to 10 E. coli pulsed-field gel electrophoresis (PFGE) clusters could be identified from each sample. Whole-genome sequencing (WGS) analysis of the representative E. coli strains revealed three to nine sequence types observed in a single chicken host. The mcr-1 genes are located in either chromosomes or plasmids of different types, including IncI2 (n=30), IncHI2 (n=14), IncX4 (n=4), p0111(n=2) and IncHI1(n=1). Strikingly, in single cecum samples, one to five Inc type plasmids harbouring mcr-1 could be identified. Great diversity was also observed for the same IncI2 plasmid within a single chicken host. In addition, up to eight genetic contexts of the mcr-1 gene occurred within a single chicken.<br><br>CONCLUSIONS: There is extensive heterogeneity and flexibility of mcr-1 transmission in chicken gut due to bacterial species differences, distant clonal relatedness of isolates, many types and variations of mcr-positive plasmids, and the flexible genetic context of the mcr-1 gene. These compelling findings indicate that the gut is a 'melting pot' for active horizontal transfer of the mcr-1 gene.}, }
@article {pmid31532038, year = {2019}, author = {Close, DM and Cooper, CJ and Wang, X and Chirania, P and Gupta, M and Ossyra, JR and Giannone, RJ and Engle, N and Tschaplinski, TJ and Smith, JC and Hedstrom, L and Parks, JM and Michener, JK}, title = {Horizontal transfer of a pathway for coumarate catabolism unexpectedly inhibits purine nucleotide biosynthesis.}, journal = {Molecular microbiology}, volume = {112}, number = {6}, pages = {1784-1797}, pmid = {31532038}, issn = {1365-2958}, support = {R01 GM054403/GM/NIGMS NIH HHS/United States ; R25 GM086761/GM/NIGMS NIH HHS/United States ; }, mesh = {Acinetobacter baumannii/metabolism ; Coumaric Acids/*metabolism ; Escherichia coli/genetics ; Evolution, Molecular ; Gene Transfer Techniques ; Gene Transfer, Horizontal ; IMP Dehydrogenase/genetics/metabolism ; Metabolic Networks and Pathways/genetics ; Molecular Dynamics Simulation ; Mutation ; Purine Nucleotides/antagonists &amp; inhibitors/*biosynthesis/genetics ; }, abstract = {A microbe's ecological niche and biotechnological utility are determined by its specific set of co-evolved metabolic pathways. The acquisition of new pathways, through horizontal gene transfer or genetic engineering, can have unpredictable consequences. Here we show that two different pathways for coumarate catabolism failed to function when initially transferred into Escherichia coli. Using laboratory evolution, we elucidated the factors limiting activity of the newly acquired pathways and the modifications required to overcome these limitations. Both pathways required host mutations to enable effective growth with coumarate, but the necessary mutations differed. In one case, a pathway intermediate inhibited purine nucleotide biosynthesis, and this inhibition was relieved by single amino acid replacements in IMP dehydrogenase. A strain that natively contains this coumarate catabolism pathway, Acinetobacter baumannii, is resistant to inhibition by the relevant intermediate, suggesting that natural pathway transfers have faced and overcome similar challenges. Molecular dynamics simulation of the wild type and a representative single-residue mutant provide insight into the structural and dynamic changes that relieve inhibition. These results demonstrate how deleterious interactions can limit pathway transfer, that these interactions can be traced to specific molecular interactions between host and pathway, and how evolution or engineering can alleviate these limitations.}, }
@article {pmid31527797, year = {2019}, author = {Marcet-Houben, M and Gabaldón, T}, title = {Evolutionary and functional patterns of shared gene neighbourhood in fungi.}, journal = {Nature microbiology}, volume = {4}, number = {12}, pages = {2383-2392}, pmid = {31527797}, issn = {2058-5276}, mesh = {Eukaryota/genetics ; *Evolution, Molecular ; Fungal Proteins/genetics ; Fungi/classification/*genetics ; Gene Transfer, Horizontal ; *Genome, Fungal ; Genomics ; *Multigene Family ; Phylogeny ; Secondary Metabolism/genetics ; }, abstract = {Gene clusters comprise genomically co-localized and potentially co-regulated genes that tend to be conserved across species. In eukaryotes, multiple examples of metabolic gene clusters are known, particularly among fungi and plants. However, little is known about how gene clustering patterns vary among taxa or with respect to functional roles. Furthermore, mechanisms of the formation, maintenance and evolution of gene clusters remain unknown. We surveyed 341 fungal genomes to discover gene clusters shared by different species, independently of their functions. We inferred 12,120 cluster families, which comprised roughly one third of the gene space and were enriched in genes associated with diverse cellular functions. Additionally, most clusters did not encode transcription factors, suggesting that they are regulated distally. We used phylogenomics to characterize the evolutionary history of these clusters. We found that most clusters originated once and were transmitted vertically, coupled to differential loss. However, convergent evolution-that is, independent appearance of the same cluster-was more prevalent than anticipated. Finally, horizontal gene transfer of entire clusters was somewhat restricted, with the exception of those associated with secondary metabolism. Altogether, our results provide insights on the evolution of gene clustering as well as a broad catalogue of evolutionarily conserved gene clusters whose function remains to be elucidated.}, }
@article {pmid31522940, year = {2019}, author = {Yoshida, S and Kim, S and Wafula, EK and Tanskanen, J and Kim, YM and Honaas, L and Yang, Z and Spallek, T and Conn, CE and Ichihashi, Y and Cheong, K and Cui, S and Der, JP and Gundlach, H and Jiao, Y and Hori, C and Ishida, JK and Kasahara, H and Kiba, T and Kim, MS and Koo, N and Laohavisit, A and Lee, YH and Lumba, S and McCourt, P and Mortimer, JC and Mutuku, JM and Nomura, T and Sasaki-Sekimoto, Y and Seto, Y and Wang, Y and Wakatake, T and Sakakibara, H and Demura, T and Yamaguchi, S and Yoneyama, K and Manabe, RI and Nelson, DC and Schulman, AH and Timko, MP and dePamphilis, CW and Choi, D and Shirasu, K}, title = {Genome Sequence of Striga asiatica Provides Insight into the Evolution of Plant Parasitism.}, journal = {Current biology : CB}, volume = {29}, number = {18}, pages = {3041-3052.e4}, doi = {10.1016/j.cub.2019.07.086}, pmid = {31522940}, issn = {1879-0445}, mesh = {Animals ; Biological Evolution ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Germination ; Host-Parasite Interactions/*genetics ; Orobanchaceae/genetics ; Parasites/genetics/metabolism ; Plant Roots ; Seeds ; Striga/*genetics ; Symbiosis ; }, abstract = {Parasitic plants in the genus Striga, commonly known as witchweeds, cause major crop losses in sub-Saharan Africa and pose a threat to agriculture worldwide. An understanding of Striga parasite biology, which could lead to agricultural solutions, has been hampered by the lack of genome information. Here, we report the draft genome sequence of Striga asiatica with 34,577 predicted protein-coding genes, which reflects gene family contractions and expansions that are consistent with a three-phase model of parasitic plant genome evolution. Striga seeds germinate in response to host-derived strigolactones (SLs) and then develop a specialized penetration structure, the haustorium, to invade the host root. A family of SL receptors has undergone a striking expansion, suggesting a molecular basis for the evolution of broad host range among Striga spp. We found that genes involved in lateral root development in non-parasitic model species are coordinately induced during haustorium development in Striga, suggesting a pathway that was partly co-opted during the evolution of the haustorium. In addition, we found evidence for horizontal transfer of host genes as well as retrotransposons, indicating gene flow to S. asiatica from hosts. Our results provide valuable insights into the evolution of parasitism and a key resource for the future development of Striga control strategies.}, }
@article {pmid31520936, year = {2020}, author = {Lu, XM and Lu, PZ}, title = {Seasonal variations in antibiotic resistance genes in estuarine sediments and the driving mechanisms.}, journal = {Journal of hazardous materials}, volume = {383}, number = {}, pages = {121164}, doi = {10.1016/j.jhazmat.2019.121164}, pmid = {31520936}, issn = {1873-3336}, mesh = {*Anti-Bacterial Agents/analysis ; Cities ; Drug Resistance, Microbial/genetics ; Estuaries ; *Genes, Bacterial ; Geologic Sediments ; Seasons ; }, abstract = {Estuary sediments are chemically contaminated by adjacent coastal industrial cities, but the impact of organic pollutants on antibiotic resistance genes (ARGs) in estuarine sediments is unknown. We comprehensively analyzed the complex interactions between chemical pollutants (heavy metals and organic pollutants), mobile genetic elements (MGEs), and ARGs in estuarine sediments during various seasons. The results indicate that under the effects of the chemically polluted river water, the number of different estuarine sediment ARGs increased by 76.9%-92.3% in summer and 5.9%-35.3% in winter, and the abundance of these ARGs increased by 29-5195 times in summer and 48-239 times in winter. The abundance of sediment ARGs in distinct estuaries showed different seasonal trends. Seasonal changes had a greater impact on the abundance of estuarine sediment ARGs than on their diversity. The diversity of estuarine sediment ARGs was positively correlated with the chemical pollution levels. Furthermore, chemical pollution was positively correlated with MGEs, and MGEs were correlated with ARG abundance. These results indicate that ARGs are enriched in bacteria via horizontal gene transfer triggered by chemical pollution, promoting multi-antibiotic resistance in estuarine sediment bacteria. These findings have implications for our understanding of the distribution and propagation of ARGs in chemically polluted estuarine sediments.}, }
@article {pmid31520716, year = {2019}, author = {Waldron, R and McGowan, J and Gordon, N and Mitchell, EB and Fitzpatrick, DA and Doyle, S}, title = {Characterisation of three novel β-1,3 glucanases from the medically important house dust mite Dermatophagoides pteronyssinus (airmid).}, journal = {Insect biochemistry and molecular biology}, volume = {115}, number = {}, pages = {103242}, doi = {10.1016/j.ibmb.2019.103242}, pmid = {31520716}, issn = {1879-0240}, mesh = {Amino Acid Sequence ; Animals ; Dermatophagoides pteronyssinus/*enzymology/genetics ; Endo-1,3(4)-beta-Glucanase/genetics/isolation &amp; purification/*metabolism ; }, abstract = {The European house dust mite, Dermatophagoides pteronyssinus is a major source of airborne allergens worldwide and is found in half of European homes. Interactions between microbes and house dust mites (HDM) are considered important factors that allow them to persist in the home. Laboratory studies indicate the European HDM, D. pteronyssinus is a mycophagous mite, capable of utilising a variety of fungi for nutrients, however specific mycolytic digestive enzymes are unknown. Our previous work identified a number of putative glycosyl hydrolases present in the predicted proteome of D. pteronyssinus airmid and validated the expression of 42 of these. Of note, three GH16 proteins with predicted β-1,3 glucanase activity were found to be consistently present in the mite body and excretome. Here, we performed an extensive bioinformatic, proteomic and biochemical study to characterize three-novel β-1,3 glucanases from this medically important house dust mite. The genes encoding novel β-1,3 glucanases designated Glu1, Glu2 and Glu3 were identified in D. pteronyssinus airmid, each exhibited more than 59% amino acid identity to one another. These enzymes are encoded by Glu genes present in a tri-gene cluster and protein homologs are found in other acari. The patchy phyletic distribution of Glu proteins means their evolutionary history remains elusive, however horizontal gene transfer cannot be completely excluded. Recombinant Glu1 and Glu2 exhibit hydrolytic activity toward laminarin, pachyman and barley glucan. Excreted β-1,3 glucanase activity was increased in response to D. pteronyssinus airmid feeding on baker's yeast. Active β-1,3 glucanases are expressed and excreted in the faeces of D. pteronyssinus airmid indicating they are digestive enzymes capable of breaking down β-1,3 glucans of fungi present in house dust.}, }
@article {pmid31519332, year = {2020}, author = {Dorman, CJ and Ní Bhriain, N}, title = {CRISPR-Cas, DNA Supercoiling, and Nucleoid-Associated Proteins.}, journal = {Trends in microbiology}, volume = {28}, number = {1}, pages = {19-27}, doi = {10.1016/j.tim.2019.08.004}, pmid = {31519332}, issn = {1878-4380}, mesh = {Bacteria/*genetics ; Bacterial Physiological Phenomena ; Bacterial Proteins/*genetics/metabolism ; CRISPR-Cas Systems ; *Clustered Regularly Interspaced Short Palindromic Repeats ; *DNA ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Immunity ; Integration Host Factors ; Interspersed Repetitive Sequences ; Promoter Regions, Genetic ; Transcription Factors ; Transcriptome ; }, abstract = {In this opinion article we highlight links between the H-NS nucleoid-associated protein, variable DNA topology, the regulation of CRISPR-cas locus expression, CRISPR-Cas activity, and the recruitment of novel genetic information by the CRISPR array. We propose that the requirement that the invading mobile genetic element be negatively supercoiled limits effective CRISPR action to a window in the bacterial growth cycle when DNA topology is optimal, and that this same window is used for the efficient integration of new spacer sequences at the CRISPR array. H-NS silences CRISPR promoters, and we propose that antagonists of H-NS, such as the LeuO transcription factor, provide a basis for a stochastic genetic switch that acts at random in each cell in the bacterial population. In addition, we wish to propose a mechanism by which mobile genetic elements can suppress CRISPR-cas transcription using H-NS homologues. Although the individual components of this network are known, we propose a new model in which they are integrated and linked to the physiological state of the bacterium. The model provides a basis for cell-to-cell variation in the expression and performance of CRISPR systems in bacterial populations.}, }
@article {pmid31519331, year = {2020}, author = {Baker-Austin, C and Oliver, JD}, title = {Vibrio vulnificus.}, journal = {Trends in microbiology}, volume = {28}, number = {1}, pages = {81-82}, doi = {10.1016/j.tim.2019.08.006}, pmid = {31519331}, issn = {1878-4380}, mesh = {Foodborne Diseases/microbiology ; Gene Transfer, Horizontal ; Genome, Bacterial ; Hemorrhagic Septicemia ; Humans ; Phylogeny ; Vibrio Infections/*microbiology ; *Vibrio vulnificus/classification/genetics ; Wound Infection ; }, }
@article {pmid31518354, year = {2019}, author = {Kim, BJ and Kim, GN and Kim, BR and Shim, TS and Kook, YH and Kim, BJ}, title = {New Mycobacteroides abscessus subsp. massiliense strains with recombinant hsp65 gene laterally transferred from Mycobacteroides abscessus subsp. abscessus: Potential for misidentification of M. abscessus strains with the hsp65-based method.}, journal = {PloS one}, volume = {14}, number = {9}, pages = {e0220312}, pmid = {31518354}, issn = {1932-6203}, mesh = {Bacterial Proteins/*genetics ; Chaperonin 60/*genetics ; *Gene Transfer, Horizontal ; Humans ; Mycobacterium Infections, Nontuberculous/*microbiology ; Mycobacterium abscessus/*classification/*genetics ; Nontuberculous Mycobacteria/classification/genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {It has been reported that lateral gene transfer (LGT) events among Mycobacteroides abscessus strains are prevalent. The hsp65 gene, a chronometer gene for bacterial phylogenetic analysis, is resistant to LGT events, particularly among mycobacterial strains, rendering the hsp65-targeting method the most widely used method for mycobacterial detection. To determine the prevalence of M. abscessus strains that are subject to hsp65 LGT, we applied rpoB typing to 100 clinically isolated Korean strains of M. abscessus that had been identified by hsp65 sequence analysis. The analysis indicated the presence of 2 rough strains, showing a discrepancy between the 2 typing methods. MLST analysis based on the partial sequencing of seven housekeeping genes, erm(41) PCR and further hsp65 PCR-restriction enzyme and polymorphism analysis (PRA) were conducted to identify the two strains. The MLST results showed that the two strains belong to M. abscessus subsp. massiliense and not to M. abscessus subsp. abscessus, as indicated by the rpoB-based analysis, suggesting that their hsp65 genes are subject to LGT from M. abscessus subsp. abscessus. Further analysis of these strains using the hsp65 PRA method indicated that these strains possess a PRA pattern identical to that of M. abscessus subsp. abscessus and distinct from that of M. abscessus subsp. massiliense. In conclusion, we identified two M. abscessus subsp. massiliense rough strains from Korean patients with hsp65 genes that might be laterally transferred from M. abscessus subsp. abscessus. To the best of our knowledge, this is the first demonstration of possible LGT events associated with the hsp65 gene in mycobacteria. Our results also suggest that there is the potential for misidentification when the hsp65-based protocol is used for mycobacterial identification.}, }
@article {pmid31515374, year = {2019}, author = {MacLean, RC and San Millan, A}, title = {The evolution of antibiotic resistance.}, journal = {Science (New York, N.Y.)}, volume = {365}, number = {6458}, pages = {1082-1083}, doi = {10.1126/science.aax3879}, pmid = {31515374}, issn = {1095-9203}, support = {/WT_/Wellcome Trust/United Kingdom ; /ERC_/European Research Council/International ; }, mesh = {Bacteria/drug effects/*genetics ; Bacterial Infections/drug therapy ; Conjugation, Genetic ; Drug Resistance, Bacterial/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; Plasmids/genetics ; Transduction, Genetic ; }, }
@article {pmid31513773, year = {2019}, author = {Sernee, MF and Ralton, JE and Nero, TL and Sobala, LF and Kloehn, J and Vieira-Lara, MA and Cobbold, SA and Stanton, L and Pires, DEV and Hanssen, E and Males, A and Ward, T and Bastidas, LM and van der Peet, PL and Parker, MW and Ascher, DB and Williams, SJ and Davies, GJ and McConville, MJ}, title = {A Family of Dual-Activity Glycosyltransferase-Phosphorylases Mediates Mannogen Turnover and Virulence in Leishmania Parasites.}, journal = {Cell host &amp; microbe}, volume = {26}, number = {3}, pages = {385-399.e9}, doi = {10.1016/j.chom.2019.08.009}, pmid = {31513773}, issn = {1934-6069}, mesh = {Crystallography, X-Ray ; Gene Transfer, Horizontal ; Glycosyltransferases/chemistry/*classification/genetics/*metabolism ; Leishmania/*enzymology ; Mannans ; Mannosyltransferases/chemistry/genetics/*metabolism ; Models, Molecular ; Oligosaccharides ; Phosphorylases/chemistry/*classification/genetics/*metabolism ; Protein Conformation ; Thermotolerance ; Virulence ; }, abstract = {Parasitic protists belonging to the genus Leishmania synthesize the non-canonical carbohydrate reserve, mannogen, which is composed of β-1,2-mannan oligosaccharides. Here, we identify a class of dual-activity mannosyltransferase/phosphorylases (MTPs) that catalyze both the sugar nucleotide-dependent biosynthesis and phosphorolytic turnover of mannogen. Structural and phylogenic analysis shows that while the MTPs are structurally related to bacterial mannan phosphorylases, they constitute a distinct family of glycosyltransferases (GT108) that have likely been acquired by horizontal gene transfer from gram-positive bacteria. The seven MTPs catalyze the constitutive synthesis and turnover of mannogen. This metabolic rheostat protects obligate intracellular parasite stages from nutrient excess, and is essential for thermotolerance and parasite infectivity in the mammalian host. Our results suggest that the acquisition and expansion of the MTP family in Leishmania increased the metabolic flexibility of these protists and contributed to their capacity to colonize new host niches.}, }
@article {pmid31511878, year = {2019}, author = {Ten Doesschate, T and Abbott, IJ and Willems, RJL and Top, J and Rogers, MRC and Bonten, MM and Paganelli, FL}, title = {In vivo acquisition of fosfomycin resistance in Escherichia coli by fosA transmission from commensal flora.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {74}, number = {12}, pages = {3630-3632}, pmid = {31511878}, issn = {1460-2091}, mesh = {Aged ; Anti-Bacterial Agents/*pharmacology ; Bacteremia/drug therapy ; *Drug Resistance, Bacterial ; Escherichia coli/*drug effects/genetics ; Escherichia coli Infections/drug therapy ; Escherichia coli Proteins/*genetics ; Fosfomycin/*pharmacology ; *Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; *Symbiosis ; }, }
@article {pmid31508512, year = {2019}, author = {Huang, GD and Liu, XM and Huang, TL and Xia, LC}, title = {The statistical power of k-mer based aggregative statistics for alignment-free detection of horizontal gene transfer.}, journal = {Synthetic and systems biotechnology}, volume = {4}, number = {3}, pages = {150-156}, pmid = {31508512}, issn = {2405-805X}, abstract = {Alignment-based database search and sequence comparison are commonly used to detect horizontal gene transfer (HGT). However, with the rapid increase of sequencing depth, hundreds of thousands of contigs are routinely assembled from metagenomics studies, which challenges alignment-based HGT analysis by overwhelming the known reference sequences. Detecting HGT by k-mer statistics thus becomes an attractive alternative. These alignment-free statistics have been demonstrated in high performance and efficiency in whole-genome and transcriptome comparisons. To adapt k-mer statistics for HGT detection, we developed two aggregative statistics T s u m S and T s u m * , which subsample metagenome contigs by their representative regions, and summarize the regional D 2 S and D 2 * metrics by their upper bounds. We systematically studied the aggregative statistics' power at different k-mer size using simulations. Our analysis showed that, in general, the power of T s u m S and T s u m * increases with sequencing coverage, and reaches a maximum power >80% at k = 6, with 5% Type-I error and the coverage ratio >0.2x. The statistical power of T s u m S and T s u m * was evaluated with realistic simulations of HGT mechanism, sequencing depth, read length, and base error. We expect these statistics to be useful distance metrics for identifying HGT in metagenomic studies.}, }
@article {pmid31507555, year = {2019}, author = {Sun, D and Jeannot, K and Xiao, Y and Knapp, CW}, title = {Editorial: Horizontal Gene Transfer Mediated Bacterial Antibiotic Resistance.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1933}, pmid = {31507555}, issn = {1664-302X}, }
@article {pmid31507546, year = {2019}, author = {Olekhnovich, EI and Manolov, AI and Samoilov, AE and Prianichnikov, NA and Malakhova, MV and Tyakht, AV and Pavlenko, AV and Babenko, VV and Larin, AK and Kovarsky, BA and Starikova, EV and Glushchenko, OE and Safina, DD and Markelova, MI and Boulygina, EA and Khusnutdinova, DR and Malanin, SY and Abdulkhakov, SR and Abdulkhakov, RA and Grigoryeva, TV and Kostryukova, ES and Govorun, VM and Ilina, EN}, title = {Shifts in the Human Gut Microbiota Structure Caused by Quadruple Helicobacter pylori Eradication Therapy.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1902}, pmid = {31507546}, issn = {1664-302X}, abstract = {The human gut microbiome plays an important role both in health and disease. Use of antibiotics can alter gut microbiota composition, which can lead to various deleterious events. Here we report a whole genome sequencing metagenomic/genomic study of the intestinal microbiota changes caused by Helicobacter pylori (HP) eradication therapy. Using approaches for metagenomic data analysis we revealed a statistically significant decrease in alpha-diversity and relative abundance of Bifidobacterium adolescentis due to HP eradication therapy, while the relative abundance of Enterococcus faecium increased. We have detected changes in general metagenome resistome profiles as well: after HP eradication therapy, the ermB, CFX group, and tetQ genes were overrepresented, while tetO and tetW genes were underrepresented. We have confirmed these results with genome-resolved metagenomic approaches. MAG (metagenome-assembled genomes) abundance profiles have changed dramatically after HP eradication therapy. Focusing on ermB gene conferring resistance to macrolides, which were included in the HP eradication therapy scheme, we have shown a connection between antibiotic resistance genes (ARGs) and some overrepresented MAGs. Moreover, some E. faecium strains isolated from stool samples obtained after HP eradication have manifested greater antibiotic resistance in vitro in comparison to other isolates, as well as the higher number of ARGs conferring resistance to macrolides and tetracyclines.}, }
@article {pmid31506307, year = {2019}, author = {McDonald, MC and Taranto, AP and Hill, E and Schwessinger, B and Liu, Z and Simpfendorfer, S and Milgate, A and Solomon, PS}, title = {Transposon-Mediated Horizontal Transfer of the Host-Specific Virulence Protein ToxA between Three Fungal Wheat Pathogens.}, journal = {mBio}, volume = {10}, number = {5}, pages = {}, pmid = {31506307}, issn = {2150-7511}, mesh = {Ascomycota/*genetics ; Base Sequence ; DNA Transposable Elements/*genetics ; Evolution, Molecular ; Fungal Proteins/*genetics ; *Gene Transfer, Horizontal ; Host-Pathogen Interactions/genetics ; Mycotoxins/*genetics ; Plant Diseases/*microbiology ; Sequence Alignment ; Triticum/*microbiology ; Virulence/genetics ; }, abstract = {Most known examples of horizontal gene transfer (HGT) between eukaryotes are ancient. These events are identified primarily using phylogenetic methods on coding regions alone. Only rarely are there examples of HGT where noncoding DNA is also reported. The gene encoding the wheat virulence protein ToxA and the surrounding 14 kb is one of these rare examples. ToxA has been horizontally transferred between three fungal wheat pathogens (Parastagonospora nodorum, Pyrenophora tritici-repentis, and Bipolaris sorokiniana) as part of a conserved ∼14 kb element which contains coding and noncoding regions. Here we used long-read sequencing to define the extent of HGT between these three fungal species. Construction of near-chromosomal-level assemblies enabled identification of terminal inverted repeats on either end of the 14 kb region, typical of a type II DNA transposon. This is the first description of ToxA with complete transposon features, which we call ToxhAT. In all three species, ToxhAT resides in a large (140-to-250 kb) transposon-rich genomic island which is absent in isolates that do not carry the gene (annotated here as toxa[-]). We demonstrate that the horizontal transfer of ToxhAT between P. tritici-repentis and P. nodorum occurred as part of a large (∼80 kb) HGT which is now undergoing extensive decay. In B. sorokiniana, in contrast, ToxhAT and its resident genomic island are mobile within the genome. Together, these data provide insight into the noncoding regions that facilitate HGT between eukaryotes and into the genomic processes which mask the extent of HGT between these species.IMPORTANCE This work dissects the tripartite horizontal transfer of ToxA, a gene that has a direct negative impact on global wheat yields. Defining the extent of horizontally transferred DNA is important because it can provide clues to the mechanisms that facilitate HGT. Our analysis of ToxA and its surrounding 14 kb suggests that this gene was horizontally transferred in two independent events, with one event likely facilitated by a type II DNA transposon. These horizontal transfer events are now in various processes of decay in each species due to the repeated insertion of new transposons and subsequent rounds of targeted mutation by a fungal genome defense mechanism known as repeat induced point mutation. This work highlights the role that HGT plays in the evolution of host adaptation in eukaryotic pathogens. It also increases the growing body of evidence indicating that transposons facilitate adaptive HGT events between fungi present in similar environments and hosts.}, }
@article {pmid31504747, year = {2020}, author = {Sinn, BT and Barrett, CF}, title = {Ancient Mitochondrial Gene Transfer between Fungi and the Orchids.}, journal = {Molecular biology and evolution}, volume = {37}, number = {1}, pages = {44-57}, doi = {10.1093/molbev/msz198}, pmid = {31504747}, issn = {1537-1719}, mesh = {Basidiomycota/*genetics ; *Gene Transfer, Horizontal ; *Genome, Mitochondrial ; Genome, Plant ; Orchidaceae/*genetics ; Phylogeny ; Sequence Analysis, RNA ; }, abstract = {The mitochondrial genomes (mitogenomes) of plants are known to incorporate and accumulate DNA from intra- and extracellular donors. Despite the intimate relationships formed between flowing plants (angiosperms) and fungi, lengthy fungal-like sequence has not been identified in angiosperm mitogenomes to date. Here, we present multiple lines of evidence documenting horizontal gene transfer (HGT) between the mitogenomes of fungi and the ancestors of the orchids, plants that are obligate parasites of fungi during their early development. We show that the ancestor of the orchids acquired an ∼270-bp fungal mitogenomic region containing three transfer RNA genes. We propose that the short HGT was later replaced by a second HGT event transferring >8 kb and 14 genes from a fungal mitogenome to that of the ancestor of the largest orchid subfamily, Epidendroideae. Our results represent the first evidence of genomic-scale HGT between fungal and angiosperm mitogenomes and demonstrate that the length intergenic spacer regions of angiosperm mitogenomes can effectively fossilize the genomic remains of ancient, nonplant organisms.}, }
@article {pmid31504731, year = {2019}, author = {Catchpole, RJ and Forterre, P}, title = {The Evolution of Reverse Gyrase Suggests a Nonhyperthermophilic Last Universal Common Ancestor.}, journal = {Molecular biology and evolution}, volume = {36}, number = {12}, pages = {2737-2747}, pmid = {31504731}, issn = {1537-1719}, mesh = {DNA Topoisomerases, Type I/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Origin of Life ; *Phylogeny ; }, abstract = {Reverse gyrase (RG) is the only protein found ubiquitously in hyperthermophilic organisms, but absent from mesophiles. As such, its simple presence or absence allows us to deduce information about the optimal growth temperature of long-extinct organisms, even as far as the last universal common ancestor of extant life (LUCA). The growth environment and gene content of the LUCA has long been a source of debate in which RG often features. In an attempt to settle this debate, we carried out an exhaustive search for RG proteins, generating the largest RG data set to date. Comprising 376 sequences, our data set allows for phylogenetic reconstructions of RG with unprecedented size and detail. These RG phylogenies are strikingly different from those of universal proteins inferred to be present in the LUCA, even when using the same set of species. Unlike such proteins, RG does not form monophyletic archaeal and bacterial clades, suggesting RG emergence after the formation of these domains, and/or significant horizontal gene transfer. Additionally, the branch lengths separating archaeal and bacterial groups are very short, inconsistent with the tempo of evolution from the time of the LUCA. Despite this, phylogenies limited to archaeal RG resolve most archaeal phyla, suggesting predominantly vertical evolution since the time of the last archaeal ancestor. In contrast, bacterial RG indicates emergence after the last bacterial ancestor followed by significant horizontal transfer. Taken together, these results suggest a nonhyperthermophilic LUCA and bacterial ancestor, with hyperthermophily emerging early in the evolution of the archaeal and bacterial domains.}, }
@article {pmid31504492, year = {2019}, author = {Jiménez-González, A and Xu, F and Andersson, JO}, title = {Lateral Acquisitions Repeatedly Remodel the Oxygen Detoxification Pathway in Diplomonads and Relatives.}, journal = {Genome biology and evolution}, volume = {11}, number = {9}, pages = {2542-2556}, pmid = {31504492}, issn = {1759-6653}, mesh = {Anaerobiosis ; Biological Evolution ; Diplomonadida/genetics/*metabolism ; Hemeproteins/metabolism ; Hydrogen Peroxide/metabolism ; *Metabolic Networks and Pathways ; Oxygen/*metabolism ; Phylogeny ; Reactive Oxygen Species/metabolism ; Superoxides/metabolism ; Water/metabolism ; }, abstract = {Oxygen and reactive oxygen species (ROS) are important stress factors for cells because they can oxidize many large molecules. Fornicata, a group of flagellated protists that includes diplomonads, have anaerobic metabolism but are still able to tolerate fluctuating levels of oxygen. We identified 25 protein families putatively involved in detoxification of oxygen and ROS in this group using a bioinformatics approach and propose how these interact in an oxygen detoxification pathway. These protein families were divided into a central oxygen detoxification pathway and accessory pathways for the synthesis of nonprotein thiols. We then used a phylogenetic approach to investigate the evolutionary origin of the components of this putative pathway in Diplomonadida and other Fornicata species. Our analyses suggested that the diplomonad ancestor was adapted to low-oxygen levels, was able to reduce O2 to H2O in a manner similar to extant diplomonads, and was able to synthesize glutathione and l-cysteine. Several genes involved in the pathway have complex evolutionary histories and have apparently been repeatedly acquired through lateral gene transfer and subsequently lost. At least seven genes were acquired independently in different Fornicata lineages, leading to evolutionary convergences. It is likely that acquiring these oxygen detoxification proteins helped anaerobic organisms (like the parasitic Giardia intestinalis) adapt to low-oxygen environments (such as the digestive tract of aerobic hosts).}, }
@article {pmid31504488, year = {2019}, author = {Douglas, GM and Langille, MGI}, title = {Current and Promising Approaches to Identify Horizontal Gene Transfer Events in Metagenomes.}, journal = {Genome biology and evolution}, volume = {11}, number = {10}, pages = {2750-2766}, pmid = {31504488}, issn = {1759-6653}, mesh = {Gene Duplication ; *Gene Transfer, Horizontal ; *Metagenome ; Phylogeny ; }, abstract = {High-throughput shotgun metagenomics sequencing has enabled the profiling of myriad natural communities. These data are commonly used to identify gene families and pathways that were potentially gained or lost in an environment and which may be involved in microbial adaptation. Despite the widespread interest in these events, there are no established best practices for identifying gene gain and loss in metagenomics data. Horizontal gene transfer (HGT) represents several mechanisms of gene gain that are especially of interest in clinical microbiology due to the rapid spread of antibiotic resistance genes in natural communities. Several additional mechanisms of gene gain and loss, including gene duplication, gene loss-of-function events, and de novo gene birth are also important to consider in the context of metagenomes but have been less studied. This review is largely focused on detecting HGT in prokaryotic metagenomes, but methods for detecting these other mechanisms are first discussed. For this article to be self-contained, we provide a general background on HGT and the different possible signatures of this process. Lastly, we discuss how improved assembly of genomes from metagenomes would be the most straight-forward approach for improving the inference of gene gain and loss events. Several recent technological advances could help improve metagenome assemblies: long-read sequencing, determining the physical proximity of contigs, optical mapping of short sequences along chromosomes, and single-cell metagenomics. The benefits and limitations of these advances are discussed and open questions in this area are highlighted.}, }
@article {pmid31504476, year = {2019}, author = {Azam, S and Parthasarathy, S and Singh, C and Kumar, S and Siddavattam, D}, title = {Genome Organization and Adaptive Potential of Archetypal Organophosphate Degrading Sphingobium fuliginis ATCC 27551.}, journal = {Genome biology and evolution}, volume = {11}, number = {9}, pages = {2557-2562}, pmid = {31504476}, issn = {1759-6653}, mesh = {*Genome, Bacterial ; Molecular Sequence Annotation ; Phylogeny ; Plasmids/genetics ; Sphingomonadaceae/*genetics ; Whole Genome Sequencing ; }, abstract = {Sphingobium fuliginis ATCC 27551, previously classified as Flavobacterium sp. ATCC 27551, degrades neurotoxic organophosphate insecticides and nerve agents through the activity of a membrane-associated organophosphate hydrolase. This study was designed to determine the complete genome sequence of S. fuliginis ATCC 27551 to unravel its degradative potential and adaptability to harsh environments. The 5,414,624 bp genome with a GC content of 64.4% is distributed between two chromosomes and four plasmids and encodes 5,557 proteins. Of the four plasmids, designated as pSF1, pSF2, pSF3, and pSF4, only two (pSF1 and pSF2) are self-transmissible and contained the complete genetic repertoire for a T4SS. The other two plasmids (pSF3 and pSF4) are mobilizable and both showed the presence of an oriT and relaxase-encoding sequences. The sequence of plasmid pSF3 coincided with the previously determined sequence of pPDL2 and included an opd gene encoding organophosphate hydrolase as a part of the mobile element. About 15,455 orthologous clusters were identified from among the cumulatively annotated genes of 49 Sphingobium species. Phylogenetic analysis done using the core genome consisting of 802 orthologous clusters revealed a close relationship between S. fuliginis ATCC 27551 and bacteria capable of degradation of polyaromatic hydrocarbon compounds. Genes coding for transposases, efflux pumps conferring resistance to heavy metals, and TonR-type outer membrane receptors are selectively enriched in the genome of S. fuliginis ATCC 27551 and appear to contribute to the adaptive potential of the organism to challenging and harsh environments.}, }
@article {pmid31501287, year = {2019}, author = {Ding, H and Grüll, MP and Mulligan, ME and Lang, AS and Beatty, JT}, title = {Induction of Rhodobacter capsulatus Gene Transfer Agent Gene Expression Is a Bistable Stochastic Process Repressed by an Extracellular Calcium-Binding RTX Protein Homologue.}, journal = {Journal of bacteriology}, volume = {201}, number = {23}, pages = {}, pmid = {31501287}, issn = {1098-5530}, mesh = {Bacterial Proteins/*genetics/metabolism ; Calcium/*metabolism ; Calcium-Binding Proteins/*genetics/metabolism ; Cell Division ; DNA Transposable Elements ; Escherichia coli ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Genes, Reporter ; Luminescent Proteins/genetics/metabolism ; Mutagenesis ; Mutation ; Phylogeny ; Plasmids/chemistry/metabolism ; Quorum Sensing/genetics ; Rhodobacter capsulatus/*genetics/metabolism ; Stochastic Processes ; Whole Genome Sequencing ; Red Fluorescent Protein ; }, abstract = {Bacteriophage-like gene transfer agents (GTAs) have been discovered in both of the prokaryotic branches of the three-domain phylogenetic tree of life. The production of a GTA (RcGTA) by the phototrophic alphaproteobacterium Rhodobacter capsulatus is regulated by quorum sensing and a phosphorelay homologous to systems in other species that control essential functions such as the initiation of chromosome replication and cell division. In wild-type strains, RcGTA is produced in <3% of cells in laboratory cultures. Mutants of R. capsulatus that exhibit greatly elevated production of RcGTA were created decades ago by chemical mutagenesis, but the nature and molecular consequences of the mutation were unknown. We show that the number of cells in a population that go on to express RcGTA genes is controlled by a stochastic process, in contrast to a genetic process. We used transposon mutagenesis along with a fluorescent protein reporter system and genome sequence data to identify a gene, rcc00280, that encodes an RTX family calcium-binding protein homologue. The Rc280 protein acts as an extracellular repressor of RcGTA gene expression by decreasing the percentage of cells that induce the production of RcGTA.IMPORTANCE GTAs catalyze horizontal gene transfer (HGT), which is important for genomic evolution because the majority of genes found in bacterial genomes have undergone HGT at some point in their evolution. Therefore, it is important to determine how the production of GTAs is regulated to understand the factors that modulate the frequency of gene transfer and thereby specify the tempo of evolution. This work describes a new type of genetic regulation in which an extracellular calcium-binding protein homologue represses the induction of the Rhodobacter capsulatus GTA, RcGTA.}, }
@article {pmid31501285, year = {2019}, author = {Suchland, RJ and Carrell, SJ and Wang, Y and Hybiske, K and Kim, DB and Dimond, ZE and Hefty, PS and Rockey, DD}, title = {Chromosomal Recombination Targets in Chlamydia Interspecies Lateral Gene Transfer.}, journal = {Journal of bacteriology}, volume = {201}, number = {23}, pages = {}, pmid = {31501285}, issn = {1098-5530}, support = {P20 GM113117/GM/NIGMS NIH HHS/United States ; R01 AI126785/AI/NIAID NIH HHS/United States ; R21 AI125929/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Base Sequence ; Chlamydia muridarum/drug effects/*genetics/metabolism ; Chlamydia trachomatis/drug effects/*genetics/metabolism ; Chromosomes, Bacterial/*chemistry/metabolism ; Crosses, Genetic ; DNA Transposable Elements ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Plasmids/chemistry/metabolism ; *Recombination, Genetic ; Tetracycline/pharmacology ; Tetracycline Resistance/genetics ; }, abstract = {Lateral gene transfer (LGT) among Chlamydia trachomatis strains is common, in both isolates generated in the laboratory and those examined directly from patients. In contrast, there are very few examples of recent acquisition of DNA by any Chlamydia spp. from any other species. Interspecies LGT in this system was analyzed using crosses of tetracycline (Tc)-resistant C. trachomatis L2/434 and chloramphenicol (Cam)-resistant C. muridarum VR-123. Parental C. muridarum strains were created using a plasmid-based Himar transposition system, which led to integration of the Cam[r] marker randomly across the chromosome. Fragments encompassing 79% of the C. muridarum chromosome were introduced into a C. trachomatis background, with the total coverage contained on 142 independent recombinant clones. Genome sequence analysis of progeny strains identified candidate recombination hot spots, a property not consistent with in vitroC. trachomatis × C. trachomatis (intraspecies) crosses. In both interspecies and intraspecies crosses, there were examples of duplications, mosaic recombination endpoints, and recombined sequences that were not linked to the selection marker. Quantitative analysis of the distribution and constitution of inserted sequences indicated that there are different constraints on interspecies LGT than on intraspecies crosses. These constraints may help explain why there is so little evidence of interspecies genetic exchange in this system, which is in contrast to very widespread intraspecies exchange in C. trachomatisIMPORTANCE Genome sequence analysis has demonstrated that there is widespread lateral gene transfer among strains within the species C. trachomatis and with other closely related Chlamydia species in laboratory experiments. This is in contrast to the complete absence of foreign DNA in the genomes of sequenced clinical C. trachomatis strains. There is no understanding of any mechanisms of genetic transfer in this important group of pathogens. In this report, we demonstrate that interspecies genetic exchange can occur but that the nature of the fragments exchanged is different than those observed in intraspecies crosses. We also generated a large hybrid strain library that can be exploited to examine important aspects of chlamydial disease.}, }
@article {pmid31498841, year = {2019}, author = {Martino, F and Tijet, N and Melano, R and Petroni, A and Heinz, E and De Belder, D and Faccone, D and Rapoport, M and Biondi, E and Rodrigo, V and Vazquez, M and Pasteran, F and Thomson, NR and Corso, A and Gomez, SA}, title = {Isolation of five Enterobacteriaceae species harbouring blaNDM-1 and mcr-1 plasmids from a single paediatric patient.}, journal = {PloS one}, volume = {14}, number = {9}, pages = {e0221960}, pmid = {31498841}, issn = {1932-6203}, mesh = {Anti-Bacterial Agents/pharmacology ; Child ; Child, Preschool ; Drug Resistance, Bacterial/genetics ; Enterobacteriaceae/classification/drug effects/*genetics/*isolation &amp; purification ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Hospitals ; Humans ; Phylogeny ; Plasmids/*genetics ; Psoriasis/microbiology ; }, abstract = {In Argentina, NDM metallo-β-lactamase was first reported in 2013. By now, it has disseminated throughout the country in diverse Gram negative bacteria. Here, we report the case of a paediatric patient that underwent a 1-year hospitalisation due to erythrodermic psoriasis in 2014 and received multiple antimicrobial treatments. During his stay, five isolates were obtained from rectal swabs (rs) or blood culture (bc) suspicious of carbapenemase production: a K. quasipneumoniae subsp. quasipneumoniae (rs), Citrobacter freundii (rs), Escherichia coli (bc), Enterobacter cloacae (rs), and a Serratia marcescens (bc). The isolates were studied with broth microdilution, biparental conjugation and plasmid and whole genome sequencing (Illumina). All isolates harboured an 138,998-bp type 1 IncC plasmid that carried blaNDM-1, bleMBL, blaCMY-6, rmtC, aac(6')-Ib, and sul1 resistance genes. Additionally, the blaNDM-plasmids contained ISKpn8 an insertion sequence previously described as associated only to blaKPC. One isolate, a colistin-resistant E. coli, also carried a mcr-1-containing an IncI2 plasmid, which did not harbour additional resistance. The whole genome of K. quasipneumoniae subsp. quasipneumoniae isolate was fully sequenced. This isolate harboured, additionally to blaNDM, three plasmid-mediated quinolone resistance genes: qnrB4, qnrB52 and aac(6')-Ib-cr1. The E. cloacae isolate also harboured qnrA1. These findings alert to the underestimated horizontal dissemination of multidrug-resistant plasmids limiting treatment options with last resort antimicrobials.}, }
@article {pmid31497375, year = {2019}, author = {Fuentes, MD and Gutierrez, S and Sahagun, D and Gomez, J and Mendoza, J and Ellis, CC and Bauer, S and Blattner, J and Lee, WY and Alvarez, M and Domínguez, DC}, title = {Assessment of Antibiotic Levels, Multi-Drug Resistant Bacteria and Genetic Biomarkers in the Waters of the Rio Grande River Between the United States-Mexico Border.}, journal = {Journal of health &amp; pollution}, volume = {9}, number = {23}, pages = {190912}, pmid = {31497375}, issn = {2156-9614}, support = {R25 GM060424/GM/NIGMS NIH HHS/United States ; R25 GM123928/GM/NIGMS NIH HHS/United States ; }, abstract = {BACKGROUND: The worldwide emergence of multi-drug resistant bacteria has become a health crisis, as fewer or sometimes no antimicrobial agents are effective against these bacteria. The Rio Grande River is the natural boundary between the United States (US) and Mexico. It spans a border region between Texas, New Mexico and Mexico. Underserved populations on the Mexican side use the river for recreational purposes, while on the US side, the river is used for irrigation and as a source of drinking water.<br><br>OBJECTIVES: The purpose of the present study was to evaluate the concentration of antibiotic residues, to determine the presence of genetic elements conferring antibiotic resistance and to characterize multi-drug resistant bacteria in the waters of the Rio Grande River.<br><br>METHODS: Water samples were obtained from the Rio Grande River. Deoxyribonucleic acid (DNA) was extracted from both isolated bacteria and directly from the water. Amplification of selected genetic elements was accomplished by polymerase chain reaction. Identification and isolation of bacteria was performed through MicroScan autoSCAN-4. Fecal contamination was assessed by IDEXX Colilert. Antibiotic residues were determined by liquid chromatography and mass spectrometry.<br><br>RESULTS: Antibiotics were found in 92% of both water and sediment samples. Antibiotic concentrations ranged from 0.38 ng/L - 742.73 ng/L and 0.39 ng/l - 66.3 ng/g dry weight in water and sediment samples, respectively. Genetic elements conferring resistance were recovered from all collection sites. Of the isolated bacteria, 91 (64.08%) were resistant to at least two synergistic antibiotic combinations and 11 (14.79%) were found to be resistant to 20 or more individual antibiotics. Fecal contamination was higher during the months of April and July.<br><br>CONCLUSIONS: The 26 km segment of the Rio Grande River from Sunland Park NM to El Paso, TX and Juarez, Mexico is an area of concern due to poor water quality. The presence of multidrug resistant bacteria, antibiotics and mobile genetic elements may be a health hazard for the surrounding populations of this binational border region. Policies need to be developed for the appropriate management of the environmental natural resources in this border region.<br><br>COMPETING INTERESTS: The authors declare no competing financial interests.}, }
@article {pmid31496755, year = {2019}, author = {Thingholm, KR and Hertz, FB and Løbner-Olesen, A and Frimodt-Møller, N and Nielsen, KL}, title = {Escherichia coli belonging to ST131 rarely transfers bla ctx-m-15 to fecal Escherichia coli.}, journal = {Infection and drug resistance}, volume = {12}, number = {}, pages = {2429-2435}, pmid = {31496755}, issn = {1178-6973}, abstract = {BACKGROUND: Extended spectrum beta-lactamase (ESBL)-producing Escherichia coli (E. coli) causing urinary tract infections often belong to sequence type 131 (ST131), serotype O25, carrying bla CTX-M-15.<br><br>AIM: The main aim of this study was to examine the conjugational frequencies of E. coli with plasmids carrying bla CTX-M-15 to E. coli isolates from the fecal flora of healthy humans to determine whether ST131 is more likely to uptake or donate ESBL resistance compared to other E. coli clones.<br><br>METHODS: &#xa0;Donors and recipients were all clinical isolates and did not harbor plasmids with identical incompatibility groups (Inc-groups) based on in silico analyses of Inc-groups and restriction/modification systems (R/M-systems). The in vitro conjugation experiments were performed as filter conjugation with verification of transconjugants by random amplified polymorphic DNA (RAPD) PCR and bla CTX-M-15 PCR.<br><br>RESULTS: The frequencies of conjugation with bla CTX-M-15-carrying plasmids were found to be very rare with detectable conjugation frequencies in the range of 4x10[-9]-7x10[-7] transconjugants/recipient. Recipients of O25/ST131 type yielded significantly lower conjugation frequencies compared to recipients of other O-types (P=0.004). The applied ST131/O25 donors did not yield detectable levels of transconjugants regardless of the applied recipient. Presence of sub-MIC levels of ampicillin increased plasmid transfer frequencies x100 fold (P=0.07).<br><br>CONCLUSION: The results indicate that bla CTX-M-15 is rarely transferred by conjugation to E. coli isolates of the intestinal flora, even when the gene is plasmid-borne.}, }
@article {pmid31495055, year = {2019}, author = {Boto, L and Pineda, M and Pineda, R}, title = {Potential impacts of horizontal gene transfer on human health and physiology and how anthropogenic activity can affect it.}, journal = {The FEBS journal}, volume = {286}, number = {20}, pages = {3959-3967}, doi = {10.1111/febs.15054}, pmid = {31495055}, issn = {1742-4658}, support = {CGL2016-75262-P//Direcci&#xf3;n General de Investigaci&#xf3;n Cient&#xed;fica y T&#xe9;cnica/International ; }, mesh = {Bacteria/*genetics ; Bacterial Proteins/*genetics ; Biodiversity ; Gene Transfer, Horizontal/*genetics ; *Genome, Bacterial ; Humans ; Microbiota/*physiology ; }, abstract = {Horizontal gene transfer (HGT) is widespread among prokaryotes driving their evolution. In this paper, we review the potential impact in humans of the HGT between prokaryotes living in close association with humans in two scenarios: horizontal transfer in human microbiomes and transfer between microbes living in human managed environments. Although our vision is focused on the possible impact of these transfers in the propagation of antibiotic resistance genes or pathogenicity determinants, we also discuss possible human physiological adaptations via gene transfer between resident and occasional bacteria in the human microbiome.}, }
@article {pmid31493990, year = {2019}, author = {Vos, M and Buckling, A and Kuijper, B}, title = {Sexual Selection in Bacteria?.}, journal = {Trends in microbiology}, volume = {27}, number = {12}, pages = {972-981}, doi = {10.1016/j.tim.2019.07.009}, pmid = {31493990}, issn = {1878-4380}, mesh = {Bacteria/*genetics ; Biological Evolution ; *Gene Transfer, Horizontal ; Genetic Fitness ; *Selection, Genetic ; Transformation, Bacterial ; }, abstract = {A main mechanism of lateral gene transfer in bacteria is transformation, where cells take up free DNA from the environment which subsequently can be recombined into the genome. Bacteria are also known to actively release DNA into the environment through secretion or lysis, which could aid uptake via transformation. Various evolutionary benefits of DNA uptake and DNA release have been proposed but these have all been framed in the context of natural selection. Here, we interpret bacterial DNA uptake and release in the context of sexual selection theory, which has been central to our understanding of the bewildering diversity of traits associated with sexual reproduction in the eukaryote world but has never been applied to prokaryotes. Specifically, we explore potential scenarios where bacteria releasing DNA into the environment could compete for successful uptake by other cells, or where bacteria could selectively take up DNA to enhance their fitness. We conclude that there is potential for sexual selection to act in bacteria, and that this might in part explain the considerable diversity in transformation-related behaviours.}, }
@article {pmid31493577, year = {2020}, author = {Zhu, L and Chen, T and Xu, L and Zhou, Z and Feng, W and Liu, Y and Chen, H}, title = {Effect and mechanism of quorum sensing on horizontal transfer of multidrug plasmid RP4 in BAC biofilm.}, journal = {The Science of the total environment}, volume = {698}, number = {}, pages = {134236}, doi = {10.1016/j.scitotenv.2019.134236}, pmid = {31493577}, issn = {1879-1026}, mesh = {Acyl-Butyrolactones/*metabolism ; *Biofilms ; Charcoal ; Drinking Water/microbiology ; Gene Transfer, Horizontal ; Plasmids ; *Quorum Sensing ; }, abstract = {The widespread emergence of antibiotic resistance genes (ARGs) in drinking water systems endangers human health, and may be exacerbated by their horizontal gene transfer (HGT) among microbiota. In our previous study, Quorum sensing (QS) molecules produced by bacteria from biological activated carbon (BAC) biofilms were demonstrated to influence the transfer efficiency of a model conjugative plasmid, here RP4. In this study, we further explored the effect and mechanism of QS on conjugation transfer. The results revealed that Acyl-homoserine lactones producing (AHL-producing) bacteria isolated from BAC biofilm play a role in the propagation of ARGs. We selected several quorum sensing inhibitors (QSIs) to study their effects on AHL-producing bacteria, including the formation of biofilm and the regulating effect on conjugation transfer. In addition, the possible molecular mechanisms for AHLs that promote conjugative transfer were attributable to enhancing the mRNA expression, which involved altered expressions of conjugation-related genes. We also found that QSIs could inhibit conjugative transfer by downregulating the conjugation-relevant genes. We believe that this is the first insightful exploration of the mechanism by which AHLs will facilitate and QSIs will inhibit the conjugative transfer of ARGs. These results provide creative insight into ARG pollution control that involves blocking QS during BAC treatment in drinking water systems.}, }
@article {pmid31492517, year = {2019}, author = {Botelho, J and Grosso, F and Peixe, L}, title = {Antibiotic resistance in Pseudomonas aeruginosa - Mechanisms, epidemiology and evolution.}, journal = {Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy}, volume = {44}, number = {}, pages = {100640}, doi = {10.1016/j.drup.2019.07.002}, pmid = {31492517}, issn = {1532-2084}, mesh = {Anti-Bacterial Agents/*therapeutic use ; Clone Cells ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genetic Fitness ; *Genome, Bacterial ; Genomic Islands ; Host-Pathogen Interactions/genetics ; Humans ; Interspersed Repetitive Sequences ; Molecular Epidemiology ; Opportunistic Infections/*drug therapy/epidemiology/microbiology ; Plasmids/chemistry/metabolism ; Pseudomonas Infections/*drug therapy/epidemiology/microbiology ; Pseudomonas aeruginosa/drug effects/*genetics/growth &amp; development/pathogenicity ; beta-Lactamases/genetics/metabolism ; }, abstract = {Antibiotics are powerful drugs used in the treatment of bacterial infections. The inappropriate use of these medicines has driven the dissemination of antibiotic resistance (AR) in most bacteria. Pseudomonas aeruginosa is an opportunistic pathogen commonly involved in environmental- and difficult-to-treat hospital-acquired infections. This species is frequently resistant to several antibiotics, being in the "critical" category of the WHO's priority pathogens list for research and development of new antibiotics. In addition to a remarkable intrinsic resistance to several antibiotics, P. aeruginosa can acquire resistance through chromosomal mutations and acquisition of AR genes. P. aeruginosa has one of the largest bacterial genomes and possesses a significant assortment of genes acquired by horizontal gene transfer (HGT), which are frequently localized within integrons and mobile genetic elements (MGEs), such as transposons, insertion sequences, genomic islands, phages, plasmids and integrative and conjugative elements (ICEs). This genomic diversity results in a non-clonal population structure, punctuated by specific clones that are associated with significant morbidity and mortality worldwide, the so-called high-risk clones. Acquisition of MGEs produces a fitness cost in the host, that can be eased over time by compensatory mutations during MGE-host coevolution. Even though plasmids and ICEs are important drivers of AR, the underlying evolutionary traits that promote this dissemination are poorly understood. In this review, we provide a comprehensive description of the main strategies involved in AR in P. aeruginosa and the leading drivers of HGT in this species. The most recently developed genomic tools that allowed a better understanding of the features contributing for the success of P. aeruginosa are discussed.}, }
@article {pmid31486763, year = {2019}, author = {Urquiaga, MCO and Klepa, MS and Somasegaran, P and Ribeiro, RA and Delamuta, JRM and Hungria, M}, title = {Bradyrhizobium frederickii sp. nov., a nitrogen-fixing lineage isolated from nodules of the caesalpinioid species Chamaecrista fasciculata and characterized by tolerance to high temperature in vitro.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {69}, number = {12}, pages = {3863-3877}, doi = {10.1099/ijsem.0.003697}, pmid = {31486763}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; Bradyrhizobium/*classification/isolation &amp; purification ; Chamaecrista/*microbiology ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Missouri ; Multilocus Sequence Typing ; Nebraska ; Nitrogen Fixation ; Nucleic Acid Hybridization ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Root Nodules, Plant/*microbiology ; Sequence Analysis, DNA ; Symbiosis ; Temperature ; }, abstract = {The symbioses between legumes and nitrogen-fixing rhizobia make the greatest contribution to the global nitrogen input via the process of biological nitrogen fixation (BNF). Bradyrhizobium stands out as the main genus nodulating basal Caesalpinioideae. We performed a polyphasic study with 11 strains isolated from root nodules of Chamaecristafasciculata, an annual multi-functional native legume of the USA. In the 16S rRNA gene phylogeny the strains were clustered in the Bradyrhizobium japonicumsuperclade. The results of analysis of the intergenic transcribed spacer (ITS) indicated less than 89.9 % similarity to other Bradyrhizobium species. Multilocus sequence analysis (MLSA) with four housekeeping genes (glnII, gyrB, recA and rpoB) confirmed the new group, sharing less than 95.2 % nucleotide identity with other species. The MLSA with 10 housekeeping genes (atpD, dnaK, gap, glnII, gltA, gyrB, pnp, recA, rpoB and thrC) indicated Bradyrhizobium daqingense as the closest species. Noteworthy, high genetic diversity among the strains was confirmed in the analyses of ITS, MLSA and BOX-PCR. Average nucleotide identity and digital DNA-DNA hybridization values were below the threshold of described Bradyrhizobium species, of 89.7 and 40 %, respectively. In the nifH and nodC phylogenies, the strains were grouped together, but with an indication of horizontal gene transfer, showing higher similarity to Bradyrhizobium arachidis and Bradyrhizobium forestalis. Other phenotypic, genotypic and symbiotic properties were evaluated, and the results altogether support the description of the CNPSo strains as representatives of the new species Bradyrhizobiumfrederickii sp. nov., with CNPSo 3426[T] (=USDA 10052[T]=U686[T]=CL 20[T]) as the type strain.}, }
@article {pmid31485711, year = {2020}, author = {Akiyama, K and Fujisawa, K and Kondo, H and Netsu, Y and Nishikawa, K and Takata, Y and Nakamura, Y and Kino, Y and Ayukawa, S and Yamamura, M and Hayashi, N and Tagawa, YI and Nakashima, N}, title = {MazF activation causes ACA sequence-independent and selective alterations in RNA levels in Escherichia coli.}, journal = {Archives of microbiology}, volume = {202}, number = {1}, pages = {105-114}, doi = {10.1007/s00203-019-01726-9}, pmid = {31485711}, issn = {1432-072X}, support = {17K07714//Japan Society for the Promotion of Science/ ; }, mesh = {DNA-Binding Proteins/genetics/*metabolism ; Endoribonucleases/genetics/*metabolism ; Escherichia coli/*genetics/*metabolism ; Escherichia coli K12/genetics/metabolism ; Escherichia coli Proteins/*genetics/*metabolism ; Gene Expression Regulation, Bacterial/*genetics ; RNA/chemistry/*genetics ; }, abstract = {Escherichia coli MazF is a toxin protein that cleaves RNA at ACA sequences. Its activation has been thought to cause growth inhibition, primarily through indiscriminate cleavage of RNA. To investigate responses following MazF activation, transcriptomic profiles of mazF-overexpressing and non-overexpressing E. coli K12 cells were compared. Analyses of differentially expressed genes demonstrated that the presence and the number of ACA trimers in RNA was unrelated to cellular RNA levels. Mapping differentially expressed genes onto the chromosome identified two chromosomal segments in which upregulated genes formed clusters, and these segments were absent in the chromosomes of E. coli strains other than K12. These results suggest that MazF regulates selective, rather than indiscriminate, categories of genes, and is involved in the regulation of horizontally acquired genes. We conclude that the primary role of MazF is not only cleaving RNA indiscriminately but also generating a specific cellular state.}, }
@article {pmid31485077, year = {2019}, author = {Bakkeren, E and Huisman, JS and Fattinger, SA and Hausmann, A and Furter, M and Egli, A and Slack, E and Sellin, ME and Bonhoeffer, S and Regoes, RR and Diard, M and Hardt, WD}, title = {Salmonella persisters promote the spread of antibiotic resistance plasmids in the gut.}, journal = {Nature}, volume = {573}, number = {7773}, pages = {276-280}, pmid = {31485077}, issn = {1476-4687}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/drug effects/*genetics ; Feces/microbiology ; Gastrointestinal Microbiome/drug effects/*genetics ; *Gene Transfer, Horizontal ; Intestinal Mucosa/*microbiology ; Mice ; Models, Theoretical ; Plasmids/*genetics ; Salmonella typhimurium/drug effects/*genetics ; Vaccination ; }, abstract = {The emergence of antibiotic-resistant bacteria through mutations or the acquisition of genetic material such as resistance plasmids represents a major public health issue[1,2]. Persisters are subpopulations of bacteria that survive antibiotics by reversibly adapting their physiology[3-10], and can promote the emergence of antibiotic-resistant mutants[11]. We investigated whether persisters can also promote the spread of resistance plasmids. In contrast to mutations, the transfer of resistance plasmids requires the co-occurrence of both a donor and a recipient bacterial strain. For our experiments, we chose the facultative intracellular entero-pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium) and Escherichia coli, a common member of the microbiota[12]. S. Typhimurium forms persisters that survive antibiotic therapy in several host tissues. Here we show that tissue-associated S. Typhimurium persisters represent long-lived reservoirs of plasmid donors or recipients. The formation of reservoirs of S. Typhimurium persisters requires Salmonella pathogenicity island (SPI)-1 and/or SPI-2 in gut-associated tissues, or SPI-2 at systemic sites. The re-seeding of these persister bacteria into the gut lumen enables the co-occurrence of donors with gut-resident recipients, and thereby favours plasmid transfer between various strains of Enterobacteriaceae. We observe up to 99% transconjugants within two to three days of re-seeding. Mathematical modelling shows that rare re-seeding events may suffice for a high frequency of conjugation. Vaccination reduces the formation of reservoirs of persisters after oral infection with S. Typhimurium, as well as subsequent plasmid transfer. We conclude that-even without selection for plasmid-encoded resistance genes-small reservoirs of pathogen persisters can foster the spread of promiscuous resistance plasmids in the gut.}, }
@article {pmid31481382, year = {2019}, author = {Tidjani, AR and Lorenzi, JN and Toussaint, M and van Dijk, E and Naquin, D and Lespinet, O and Bontemps, C and Leblond, P}, title = {Massive Gene Flux Drives Genome Diversity between Sympatric Streptomyces Conspecifics.}, journal = {mBio}, volume = {10}, number = {5}, pages = {}, pmid = {31481382}, issn = {2150-7511}, mesh = {Actinobacteria/genetics ; Biosynthetic Pathways/genetics ; Chromosomes, Bacterial ; Conjugation, Genetic ; DNA, Bacterial/genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; *Genetic Variation ; Genome, Bacterial ; Multigene Family ; Multilocus Sequence Typing ; Phylogeny ; Plasmids ; Streptomyces/*genetics ; }, abstract = {In this work, by comparing genomes of closely related individuals of Streptomyces isolated at a spatial microscale (millimeters or centimeters), we investigated the extent and impact of horizontal gene transfer in the diversification of a natural Streptomyces population. We show that despite these conspecific strains sharing a recent common ancestor, all harbored significantly different gene contents, implying massive and rapid gene flux. The accessory genome of the strains was distributed across insertion/deletion events (indels) ranging from one to several hundreds of genes. Indels were preferentially located in the arms of the linear chromosomes (ca. 12 Mb) and appeared to form recombination hot spots. Some of them harbored biosynthetic gene clusters (BGCs) whose products confer an inhibitory capacity and may constitute public goods that can favor the cohesiveness of the bacterial population. Moreover, a significant proportion of these variable genes were either plasmid borne or harbored signatures of actinomycete integrative and conjugative elements (AICEs). We propose that conjugation is the main driver for the indel flux and diversity in Streptomyces populations.IMPORTANCE Horizontal gene transfer is a rapid and efficient way to diversify bacterial gene pools. Currently, little is known about this gene flux within natural soil populations. Using comparative genomics of Streptomyces strains belonging to the same species and isolated at microscale, we reveal frequent transfer of a significant fraction of the pangenome. We show that it occurs at a time scale enabling the population to diversify and to cope with its changing environment, notably, through the production of public goods.}, }
@article {pmid31478834, year = {2019}, author = {Matthey, N and Stutzmann, S and Stoudmann, C and Guex, N and Iseli, C and Blokesch, M}, title = {Neighbor predation linked to natural competence fosters the transfer of large genomic regions in Vibrio cholerae.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, pmid = {31478834}, issn = {2050-084X}, support = {31003A_162551/SNSF_/Swiss National Science Foundation/Switzerland ; 309064-VIR4ENV//Seventh Framework Programme/International ; 724630-CholeraIndex//H2020 European Research Council/International ; 55008726/HHMI/Howard Hughes Medical Institute/United States ; 31003A_162551//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/International ; }, mesh = {*DNA Transformation Competence ; DNA, Bacterial/genetics/*metabolism ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Vibrio cholerae/*genetics ; }, abstract = {Natural competence for transformation is a primary mode of horizontal gene transfer. Competent bacteria are able to absorb free DNA from their surroundings and exchange this DNA against pieces of their own genome when sufficiently homologous. However, the prevalence of non-degraded DNA with sufficient coding capacity is not well understood. In this context, we previously showed that naturally competent Vibrio cholerae use their type VI secretion system (T6SS) to actively acquire DNA from non-kin neighbors. Here, we explored the conditions of the DNA released through T6SS-mediated killing versus passive cell lysis and the extent of the transfers that occur due to these conditions. We show that competent V. cholerae acquire DNA fragments with a length exceeding 150 kbp in a T6SS-dependent manner. Collectively, our data support the notion that the environmental lifestyle of V. cholerae fosters the exchange of genetic material with sufficient coding capacity to significantly accelerate bacterial evolution.}, }
@article {pmid31476715, year = {2019}, author = {Dunn, CD and Paavilainen, VO}, title = {Wherever I may roam: organellar protein targeting and evolvability.}, journal = {Current opinion in genetics &amp; development}, volume = {58-59}, number = {}, pages = {9-16}, doi = {10.1016/j.gde.2019.07.012}, pmid = {31476715}, issn = {1879-0380}, support = {R01 GM132649/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence/genetics ; Amoeba/genetics/metabolism ; Endoplasmic Reticulum/metabolism ; Eukaryota/*genetics/metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Mitochondria/genetics/*metabolism ; Molecular Chaperones/genetics/metabolism ; Phylogeny ; Protein Sorting Signals/*genetics/physiology ; Protein Transport/genetics/physiology ; }, abstract = {Many functions of eukaryotic cells are compartmentalized within membrane-bound organelles. One or more cis-encoded signals within a polypeptide sequence typically govern protein targeting to and within destination organelles. Perhaps unexpectedly, organelle targeting does not occur with high specificity, but instead is characterized by considerable degeneracy and inefficiency. Indeed, the same peptide signals can target proteins to more than one location, randomized sequences can easily direct proteins to organelles, and many enzymes appear to traverse different subcellular settings across eukaryotic phylogeny. We discuss the potential benefits provided by flexibility in organelle targeting, with a special emphasis on horizontally transferred and de novo proteins. Moreover, we consider how these new organelle residents can be protected and maintained before they contribute to the needs of the cell and promote fitness.}, }
@article {pmid31474968, year = {2019}, author = {Tan, X and Qiu, H and Li, F and Cheng, D and Zheng, X and Wang, B and Huang, M and Li, W and Li, Y and Sang, K and Song, B and Du, J and Chen, H and Xie, C}, title = {Complete Genome Sequence of Sequevar 14M Ralstonia solanacearum Strain HA4-1 Reveals Novel Type III Effectors Acquired Through Horizontal Gene Transfer.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1893}, pmid = {31474968}, issn = {1664-302X}, abstract = {Ralstonia solanacearum, which causes bacterial wilt in a broad range of plants, is considered a "species complex" due to its significant genetic diversity. Recently, we have isolated a new R. solanacearum strain HA4-1 from Hong'an county in Hubei province of China and identified it being phylotype I, sequevar 14M (phylotype I-14M). Interestingly, we found that it can cause various disease symptoms among different potato genotypes and display different pathogenic behavior compared to a phylogenetically related strain, GMI1000. To dissect the pathogenic mechanisms of HA4-1, we sequenced its whole genome by combined sequencing technologies including Illumina HiSeq2000, PacBio RS II, and BAC-end sequencing. Genome assembly results revealed the presence of a conventional chromosome, a megaplasmid as well as a 143 kb plasmid in HA4-1. Comparative genome analysis between HA4-1 and GMI1000 shows high conservation of the general virulence factors such as secretion systems, motility, exopolysaccharides (EPS), and key regulatory factors, but significant variation in the repertoire and structure of type III effectors, which could be the determinants of their differential pathogenesis in certain potato species or genotypes. We have identified two novel type III effectors that were probably acquired through horizontal gene transfer (HGT). These novel R. solanacearum effectors display homology to several YopJ and XopAC family members. We named them as RipBR and RipBS. Notably, the copy of RipBR on the plasmid is a pseudogene, while the other on the megaplasmid is normal. For RipBS, there are three copies located in the megaplasmid and plasmid, respectively. Our results have not only enriched the genome information on R. solanacearum species complex by sequencing the first sequevar 14M strain and the largest plasmid reported in R. solanacearum to date but also revealed the variation in the repertoire of type III effectors. This will greatly contribute to the future studies on the pathogenic evolution, host adaptation, and interaction between R. solanacearum and potato.}, }
@article {pmid31474367, year = {2019}, author = {Stanley, SY and Borges, AL and Chen, KH and Swaney, DL and Krogan, NJ and Bondy-Denomy, J and Davidson, AR}, title = {Anti-CRISPR-Associated Proteins Are Crucial Repressors of Anti-CRISPR Transcription.}, journal = {Cell}, volume = {178}, number = {6}, pages = {1452-1464.e13}, pmid = {31474367}, issn = {1097-4172}, support = {T32 AI060537/AI/NIAID NIH HHS/United States ; R01 GM127489/GM/NIGMS NIH HHS/United States ; DP5 OD021344/OD/NIH HHS/United States ; U01 MH115747/MH/NIMH NIH HHS/United States ; P50 GM082250/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteriophages/*genetics ; CRISPR-Associated Proteins/genetics ; CRISPR-Cas Systems/*genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/*genetics ; Escherichia coli/virology ; Promoter Regions, Genetic/genetics ; Pseudomonas aeruginosa/virology ; Transcription Factors/genetics ; Transcription, Genetic ; Viral Proteins/*genetics ; }, abstract = {Phages express anti-CRISPR (Acr) proteins to inhibit CRISPR-Cas systems that would otherwise destroy their genomes. Most acr genes are located adjacent to anti-CRISPR-associated (aca) genes, which encode proteins with a helix-turn-helix DNA-binding motif. The conservation of aca genes has served as a signpost for the identification of acr genes, but the function of the proteins encoded by these genes has not been investigated. Here we reveal that an acr-associated promoter drives high levels of acr transcription immediately after phage DNA injection and that Aca proteins subsequently repress this transcription. Without Aca activity, this strong transcription is lethal to a phage. Our results demonstrate how sufficient levels of Acr proteins accumulate early in the infection process to inhibit existing CRISPR-Cas complexes in the host cell. They also imply that the conserved role of Aca proteins is to mitigate the deleterious effects of strong constitutive transcription from acr promoters.}, }
@article {pmid31472442, year = {2019}, author = {Zhao, JH and Guo, HS}, title = {Trans-kingdom RNA interactions drive the evolutionary arms race between hosts and pathogens.}, journal = {Current opinion in genetics &amp; development}, volume = {58-59}, number = {}, pages = {62-69}, doi = {10.1016/j.gde.2019.07.019}, pmid = {31472442}, issn = {1879-0380}, mesh = {Arabidopsis/*genetics/metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal/immunology ; Host-Pathogen Interactions/*genetics/immunology ; MicroRNAs/*genetics/metabolism ; Plant Diseases/genetics/immunology ; RNA, Small Interfering/*genetics/metabolism ; Virulence/genetics/immunology ; }, abstract = {Trans-kingdom RNA plays a key role in host-parasite interactions. Hosts export specific endogenous microRNAs (miRNAs) into pathogens to target pathogen virulence genes and inhibit their invasion. In addition, trans-kingdom sRNAs produced by parasites may function as RNA effectors to suppress host immunity. Here, we summarize recent, important findings regarding trans-kingdom RNA and focus on the roles of trans-kingdom RNA in driving an evolutionary arms race between host and pathogen. We suggest that trans-kingdom RNA is a new platform for such arms races. Furthermore, we conjecture that trans-kingdom RNA contributes to horizontal gene transfer (HGT) involved in host-pathogen interactions. In addition, we propose that trans-kingdom RNA exchange and RNA driven HGT can have a great impact on the evolutionary ecology of interacting species.}, }
@article {pmid31471306, year = {2019}, author = {Oladeinde, A and Cook, K and Lakin, SM and Woyda, R and Abdo, Z and Looft, T and Herrington, K and Zock, G and Lawrence, JP and Thomas, JC and Beaudry, MS and Glenn, T}, title = {Horizontal Gene Transfer and Acquired Antibiotic Resistance in Salmonella enterica Serovar Heidelberg following In Vitro Incubation in Broiler Ceca.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {22}, pages = {}, pmid = {31471306}, issn = {1098-5336}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Cecum/*microbiology ; Chickens/microbiology ; Drug Resistance, Multiple, Bacterial/*genetics ; *Gastrointestinal Microbiome ; *Gene Transfer Techniques ; Interspersed Repetitive Sequences ; Plasmids/genetics ; Salmonella enterica/drug effects/*genetics ; Serogroup ; Whole Genome Sequencing ; beta-Lactamases/genetics ; }, abstract = {The chicken gastrointestinal tract harbors microorganisms that play a role in the health and disease status of the host. The cecum is the part of the gut that carries the highest microbial densities, has the longest residence time of digesta, and is a vital site for urea recycling and water regulation. Therefore, the cecum provides a rich environment for bacteria to horizontally transfer genes between one another via mobile genetic elements such as plasmids and bacteriophages. In this study, we used broiler chicken cecum as a model to investigate antibiotic resistance genes that can be transferred in vitro from cecal flora to Salmonella enterica serovar Heidelberg. We used whole-genome sequencing and resistome enrichment to decipher the interactions between S Heidelberg, the gut microbiome, and acquired antibiotic resistance. After 48 h of incubation of ceca under microaerophilic conditions, we recovered one S Heidelberg isolate with an acquired IncK2 plasmid (88 kb) carrying an extended-spectrum-β-lactamase gene (blaCMY-2). In vitro, this plasmid was transferable between Escherichia coli and S Heidelberg strains but transfer was unsuccessful between S Heidelberg strains. An in-depth genetic characterization of transferred plasmids suggests that they share significant homology with P1-like phages. This study contributes to our understanding of horizontal gene transfer between an important foodborne pathogen and the chicken gut microbiome.IMPORTANCES. Heidelberg is a clinically important serovar, linked to foodborne illness and among the top 5 serovars isolated from poultry in the United States and Canada. Acquisition of new genetic material from the microbial flora in the gastrointestinal tract of food animals, including broilers, may contribute to increased fitness of pathogens like S. Heidelberg and may increase their level of antibiotic tolerance. Therefore, it is critical to gain a better understanding of the interactions that occur between important pathogens and the commensals present in the animal gut and other agroecosystems. In this report, we show that the native flora in broiler ceca were capable of transferring mobile genetic elements carrying the AmpC β-lactamase (blaCMY-2) gene to an important foodborne pathogen, S Heidelberg. The potential role for bacteriophage transduction is also discussed.}, }
@article {pmid31470481, year = {2019}, author = {Han, YH and Yin, DX and Jia, MR and Wang, SS and Chen, Y and Rathinasabapathi, B and Chen, DL and Ma, LQ}, title = {Arsenic-resistance mechanisms in bacterium Leclercia adecarboxylata strain As3-1: Biochemical and genomic analyses.}, journal = {The Science of the total environment}, volume = {690}, number = {}, pages = {1178-1189}, doi = {10.1016/j.scitotenv.2019.07.098}, pmid = {31470481}, issn = {1879-1026}, mesh = {Adaptation, Physiological ; Arsenic/*metabolism ; Bacterial Proteins/genetics ; Enterobacteriaceae/genetics/*physiology ; Environmental Pollutants/*metabolism ; Genomics ; }, abstract = {Microbial arsenic transformation is important in As biogeochemical cycles in the environment. In this study, a new As-resistant bacterial strain Leclercia adecarboxylata As3-1 was isolated and its associated mechanisms in As resistance and detoxification were evaluated based on genome sequencing and gene annotations. After subjecting strain As3-1 to medium containing arsenate (AsV), AsV reduction occurred and an AsV-enhanced bacterial growth was observed. Strain As3-1 lacked arsenite (AsIII) oxidation ability and displayed lower AsIII resistance than AsV, probably due to its higher AsIII accumulation. Polymerase chain reaction and phylogenetic analysis showed that strain As3-1 harbored a typical AsV reductase gene (arsC) on the plasmids. Genome sequencing and gene annotations identified four operons phoUpstBACS, arsHRBC, arsCRDABC and ttrRSBCA, with 8 additional genes outside the operons that might have involved in As resistance and detoxification in strain As3-1. These included 5 arsC genes explaining why strain As3-1 tolerated high AsV concentrations. Besides ArsC, TtrB, TtrC and TtrA proteins could also be involved in AsV reduction and consequent energy acquisition for bacterial growth. Our data provided a new example of diverse As-regulating systems and AsV-enhanced growth without ArrA in bacteria. The information helps to understand the role of As in selecting microbial systems that can transform and utilize As.}, }
@article {pmid31467320, year = {2019}, author = {Quispe-Huamanquispe, DG and Gheysen, G and Yang, J and Jarret, R and Rossel, G and Kreuze, JF}, title = {The horizontal gene transfer of Agrobacterium T-DNAs into the series Batatas (Genus Ipomoea) genome is not confined to hexaploid sweetpotato.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {12584}, pmid = {31467320}, issn = {2045-2322}, mesh = {Agrobacterium/*genetics ; DNA, Bacterial/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Plant/*genetics ; Ipomoea batatas/*genetics ; Phylogeny ; *Polyploidy ; }, abstract = {The discovery of the insertion of IbT-DNA1 and IbT-DNA2 into the cultivated (hexaploid) sweetpotato [Ipomoea batatas (L.) Lam.] genome constitutes a clear example of an ancient event of Horizontal Gene Transfer (HGT). However, it remains unknown whether the acquisition of both IbT-DNAs by the cultivated sweetpotato occurred before or after its speciation. Therefore, this study aims to evaluate the presence of IbT-DNAs in the genomes of sweetpotato's wild relatives belonging to the taxonomic group series Batatas. Both IbT-DNA1 and IbT-DNA2 were found in tetraploid I. batatas (L.) Lam. and had highly similar sequences and at the same locus to those found in the cultivated sweetpotato. Moreover, IbT-DNA1 was also found in I. cordatotriloba and I. tenuissima while IbT-DNA2 was detected in I. trifida. This demonstrates that genome integrated IbT-DNAs are not restricted to the cultivated sweetpotato but are also present in tetraploid I. batatas and other related species.}, }
@article {pmid31467246, year = {2019}, author = {Li, B and Kurihara, S and Kim, SH and Liang, J and Michael, AJ}, title = {A polyamine-independent role for S-adenosylmethionine decarboxylase.}, journal = {The Biochemical journal}, volume = {476}, number = {18}, pages = {2579-2594}, doi = {10.1042/BCJ20190561}, pmid = {31467246}, issn = {1470-8728}, mesh = {Adenosylmethionine Decarboxylase/chemistry/genetics/*metabolism ; Arabidopsis/enzymology/genetics ; Arabidopsis Proteins/chemistry/genetics/metabolism ; Putrescine/chemistry/*metabolism ; Ralstonia pickettii/*enzymology/genetics ; Saccharomyces cerevisiae/enzymology/genetics ; Saccharomyces cerevisiae Proteins/chemistry/genetics/metabolism ; Shewanella/*enzymology/genetics ; Spermidine/chemistry/*metabolism ; }, abstract = {The only known function of S-adenosylmethionine decarboxylase (AdoMetDC) is to supply, with its partner aminopropyltransferase enzymes such as spermidine synthase (SpdSyn), the aminopropyl donor for polyamine biosynthesis. Polyamine spermidine is probably essential for the growth of all eukaryotes, most archaea and many bacteria. Two classes of AdoMetDC exist, the prokaryotic class 1a and 1b forms, and the eukaryotic class 2 enzyme, which is derived from an ancient fusion of two prokaryotic class 1b genes. Herein, we show that 'eukaryotic' class 2 AdoMetDCs are found in bacteria and are enzymatically functional. However, the bacterial AdoMetDC class 2 genes are phylogenetically limited and were likely acquired from a eukaryotic source via transdomain horizontal gene transfer, consistent with the class 2 form of AdoMetDC being a eukaryotic invention. We found that some class 2 and thousands of class 1b AdoMetDC homologues are present in bacterial genomes that also encode a gene fusion of an N-terminal membrane protein of the Major Facilitator Superfamily (MFS) class of transporters and a C-terminal SpdSyn-like domain. Although these AdoMetDCs are enzymatically functional, spermidine is absent, and an entire fusion protein or its SpdSyn-like domain only, does not biochemically complement a SpdSyn deletion strain of E. coli This suggests that the fusion protein aminopropylates a substrate other than putrescine, and has a role outside of polyamine biosynthesis. Another integral membrane protein found clustered with these genes is DUF350, which is also found in other gene clusters containing a homologue of the glutathionylspermidine synthetase family and occasionally other polyamine biosynthetic enzymes.}, }
@article {pmid31467106, year = {2019}, author = {Dunning Hotopp, JC and Matsumura, J and Bromley, RE and Riley, DR and Agrawal, S and Sparklin, B and Mattick, J and Crabtree, J and Mahurkar, A}, title = {TwinBLAST: When Two Is Better than One.}, journal = {Microbiology resource announcements}, volume = {8}, number = {35}, pages = {}, pmid = {31467106}, issn = {2576-098X}, support = {R01 CA206188/CA/NCI NIH HHS/United States ; }, abstract = {Analysis of sequence read pairs can be essential for characterizing structural variation, including junction-spanning pairs of reads (JSPRs) suggesting recent lateral/horizontal gene transfer. TwinBLAST can be used to facilitate this analysis of JSPRs by enabling the visualization and curation of two BLAST reports side by side in a single interface.}, }
@article {pmid31462912, year = {2019}, author = {Pruvost, O and Boyer, K and Ravigné, V and Richard, D and Vernière, C}, title = {Deciphering how plant pathogenic bacteria disperse and meet: Molecular epidemiology of Xanthomonas citri pv. citri at microgeographic scales in a tropical area of Asiatic citrus canker endemicity.}, journal = {Evolutionary applications}, volume = {12}, number = {8}, pages = {1523-1538}, pmid = {31462912}, issn = {1752-4571}, abstract = {Although some plant pathogenic bacteria represent a significant threat to agriculture, the determinants of their ecological success and evolutionary potential are still poorly understood. Refining our understanding of bacterial strain circulation at small spatial scales and the biological significance and evolutionary consequences of co-infections are key questions. The study of bacterial population biology can be challenging, because it requires high-resolution markers that can be genotyped with a high throughput. Here, we overcame this difficulty for Xanthomonas citri pv. citri, a genetically monomorphic bacterium causing Asiatic citrus canker (ACC). Using a genotyping method that did not require cultivating the bacterium or purifying DNA, we deciphered the pathogen's spatial genetic structure at several microgeographic scales, down to single lesion, in a situation of ACC endemicity. In a grove where copper was recurrently applied for ACC management, copper-susceptible and copper-resistant X. citri pv. citri coexisted and the bacterial population structured as three genetic clusters, suggesting a polyclonal contamination. The range of spatial dependency, estimated for the two largest clusters, was four times greater for the cluster predominantly composed of copper-resistant bacteria. Consistently, the evenness value calculated for this cluster was indicative of increased transmission. Linkage disequilibrium was high even at a tree scale, probably due to a combination of clonality and admixture. Approximately 1% of samples exhibited within-lesion multilocus polymorphism, explained at least in part by polyclonal infections. Canker lesions, which are of major biological significance as an inoculum source, may also represent a preferred niche for horizontal gene transfer. This study points out the potential of genotyping data for estimating the range of spatial dependency of plant bacterial pathogens, an important parameter for guiding disease management strategies.}, }
@article {pmid31462749, year = {2019}, author = {Xu, Y and Wang, S and Li, L and Sahu, SK and Petersen, M and Liu, X and Melkonian, M and Zhang, G and Liu, H}, title = {Molecular evidence for origin, diversification and ancient gene duplication of plant subtilases (SBTs).}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {12485}, pmid = {31462749}, issn = {2045-2322}, mesh = {*Evolution, Molecular ; *Gene Duplication ; *Gene Transfer, Horizontal ; *Genes, Plant ; *Phylogeny ; Plants/*genetics ; }, abstract = {Plant subtilases (SBTs) are a widely distributed family of serine proteases which participates in plant developmental processes and immune responses. Although SBTs are divided into seven subgroups in plants, their origin and evolution, particularly in green algae remain elusive. Here, we present a comprehensive large-scale evolutionary analysis of all subtilases. The plant subtilases SBT1-5 were found to be monophyletic, nested within a larger radiation of bacteria suggesting that they originated from bacteria by a single horizontal gene transfer (HGT) event. A group of bacterial subtilases comprising representatives from four phyla was identified as a sister group to SBT1-5. The phylogenetic analyses, based on evaluation of novel streptophyte algal genomes, suggested that the recipient of the HGT of bacterial subtilases was the common ancestor of Coleochaetophyceae, Zygnematophyceae and embryophytes. Following the HGT, the subtilase gene duplicated in the common ancestor and the two genes diversified into SBT2 and SBT1, 3-5 respectively. Comparative structural analysis of homology-modeled SBT2 proteins also showed their conservation from bacteria to embryophytes. Our study provides the first molecular evidence about the evolution of plant subtilases via HGT followed by a first gene duplication in the common ancestor of Coleochaetophyceae, Zygnematophyceae, and embryophytes, and subsequent expansion in embryophytes.}, }
@article {pmid31462715, year = {2019}, author = {Wang, B and Qin, W and Ren, Y and Zhou, X and Jung, MY and Han, P and Eloe-Fadrosh, EA and Li, M and Zheng, Y and Lu, L and Yan, X and Ji, J and Liu, Y and Liu, L and Heiner, C and Hall, R and Martens-Habbena, W and Herbold, CW and Rhee, SK and Bartlett, DH and Huang, L and Ingalls, AE and Wagner, M and Stahl, DA and Jia, Z}, title = {Expansion of Thaumarchaeota habitat range is correlated with horizontal transfer of ATPase operons.}, journal = {The ISME journal}, volume = {13}, number = {12}, pages = {3067-3079}, pmid = {31462715}, issn = {1751-7370}, mesh = {Adenosine Triphosphatases/*genetics/metabolism ; Ammonium Compounds/metabolism ; Archaea/classification/enzymology/*genetics/isolation &amp; purification ; Archaeal Proteins/*genetics/metabolism ; Ecosystem ; Escherichia coli/metabolism ; *Gene Transfer, Horizontal ; Hydrogen-Ion Concentration ; *Operon ; Oxidation-Reduction ; Phylogeny ; Soil Microbiology ; }, abstract = {Thaumarchaeota are responsible for a significant fraction of ammonia oxidation in the oceans and in soils that range from alkaline to acidic. However, the adaptive mechanisms underpinning their habitat expansion remain poorly understood. Here we show that expansion into acidic soils and the high pressures of the hadopelagic zone of the oceans is tightly linked to the acquisition of a variant of the energy-yielding ATPases via horizontal transfer. Whereas the ATPase genealogy of neutrophilic Thaumarchaeota is congruent with their organismal genealogy inferred from concatenated conserved proteins, a common clade of V-type ATPases unites phylogenetically distinct clades of acidophilic/acid-tolerant and piezophilic/piezotolerant species. A presumptive function of pumping cytoplasmic protons at low pH is consistent with the experimentally observed increased expression of the V-ATPase in an acid-tolerant thaumarchaeote at low pH. Consistently, heterologous expression of the thaumarchaeotal V-ATPase significantly increased the growth rate of E. coli at low pH. Its adaptive significance to growth in ocean trenches may relate to pressure-related changes in membrane structure in which this complex molecular machine must function. Together, our findings reveal that the habitat expansion of Thaumarchaeota is tightly correlated with extensive horizontal transfer of atp operons.}, }
@article {pmid31455740, year = {2019}, author = {Durieux, I and Ginevra, C and Attaiech, L and Picq, K and Juan, PA and Jarraud, S and Charpentier, X}, title = {Diverse conjugative elements silence natural transformation in Legionella species.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {37}, pages = {18613-18618}, pmid = {31455740}, issn = {1091-6490}, mesh = {Bacterial Proteins/genetics/metabolism ; DNA-Binding Proteins/genetics/metabolism ; Gene Silencing ; *Gene Transfer, Horizontal ; Genome-Wide Association Study ; Legionella pneumophila/*genetics ; Molecular Chaperones/genetics/metabolism ; Plasmids/*genetics ; RNA ; RNA, Small Untranslated/*genetics/metabolism ; *Transformation, Bacterial ; }, abstract = {Natural transformation (i.e., the uptake of DNA and its stable integration in the chromosome) is a major mechanism of horizontal gene transfer in bacteria. Although the vast majority of bacterial genomes carry the genes involved in natural transformation, close relatives of naturally transformable species often appear not competent for natural transformation. In addition, unexplained extensive variations in the natural transformation phenotype have been reported in several species. Here, we addressed this phenomenon by conducting a genome-wide association study (GWAS) on a panel of isolates of the opportunistic pathogen Legionella pneumophila GWAS revealed that the absence of the transformation phenotype is associated with the conjugative plasmid pLPL. The plasmid inhibits transformation by simultaneously silencing the genes required for DNA uptake and recombination. We identified a small RNA (sRNA), RocRp, as the sole plasmid-encoded factor responsible for the silencing of natural transformation. RocRp is homologous to the highly conserved and chromosome-encoded sRNA RocR which controls the transient expression of the DNA uptake system. Assisted by the ProQ/FinO-domain RNA chaperone RocC, RocRp acts as a substitute of RocR, ensuring that the bacterial host of the conjugative plasmid does not become naturally transformable. Distinct homologs of this plasmid-encoded sRNA are found in diverse conjugative elements in other Legionella species. Their low to high prevalence may result in the lack of transformability of some isolates up to the apparent absence of natural transformation in the species. Generally, our work suggests that conjugative elements obscure the widespread occurrence of natural transformability in bacteria.}, }
@article {pmid31455637, year = {2019}, author = {Wang, Y and Youssef, NH and Couger, MB and Hanafy, RA and Elshahed, MS and Stajich, JE}, title = {Molecular Dating of the Emergence of Anaerobic Rumen Fungi and the Impact of Laterally Acquired Genes.}, journal = {mSystems}, volume = {4}, number = {4}, pages = {}, pmid = {31455637}, issn = {2379-5077}, support = {S10 OD016290/OD/NIH HHS/United States ; }, abstract = {The anaerobic gut fungi (AGF), or Neocallimastigomycota, inhabit the rumen and alimentary tract of herbivorous mammals, where they play important roles in the degradation of plant fiber. Comparative genomic and phylogenomic analyses of the AGF have long been hampered by their fastidious growth condition, as well as their large (up to 200 Mb) and AT-biased (78 to 84%) genomes. We sequenced 21 AGF transcriptomes and combined them with 5 available AGF genome sequences to explore their evolutionary relationships, time their divergence, and characterize gene gain/loss patterns associated with their evolution. We estimate that the most recent common ancestor of the AGF diverged 66 (±10) million years ago, a time frame that coincides with the evolution of grasses (Poaceae), as well as the mammalian transition from insectivory to herbivory. The concordance of independent estimations suggests that AGF have been important in shaping the success of mammalian herbivory transition by improving the efficiency of energy acquisition from recalcitrant plant materials. Comparative genomics identified multiple lineage-specific genes in the AGF, two of which were acquired from rumen gut bacteria and animal hosts via horizontal gene transfer (HGT). A third AGF domain, plant-like polysaccharide lyase, represents a novel gene in fungi that potentially aids AGF to degrade pectin. Analysis of genomic and transcriptomic sequences confirmed both the presence and expression of these lineage-specific genes in nearly all AGF clades. These genetic elements may contribute to the exceptional abilities of AGF to degrade plant biomass and enable metabolism of the rumen microbes and animal hosts.IMPORTANCE Anaerobic fungi living in the rumen of herbivorous mammals possess an extraordinary ability to degrade plant biomass. We examined the origin and genomic composition of these poorly characterized anaerobic gut fungi using both transcriptome and genomic data. Phylogenomics and molecular dating analyses found remarkable concurrence of the divergence times of the rumen fungi, the forage grasses, and the dietary shift of ancestral mammals from primarily insectivory to herbivory. Comparative genomics identified unique machinery in these fungi to utilize plant polysaccharides. The rumen fungi were also identified with the ability to code for three protein domains with putative functions in plant pectin degradation and microbial defense, which were absent from all other fungal organisms (examined over 1,000 fungal genomes). Two of these domains were likely acquired from rumen gut bacteria and animal hosts separately via horizontal gene transfer. The third one is a plant-like polysaccharide lyase, representing a unique fungal enzyme with potential pectin breakdown abilities.}, }
@article {pmid31452874, year = {2019}, author = {Yuan, Y and Li, Y and Wang, G and Li, C and Chang, YF and Chen, W and Nian, S and Mao, Y and Zhang, J and Zhong, F and Zhang, L}, title = {blaNDM-5 carried by a hypervirulent Klebsiella pneumoniae with sequence type 29.}, journal = {Antimicrobial resistance and infection control}, volume = {8}, number = {}, pages = {140}, pmid = {31452874}, issn = {2047-2994}, mesh = {Animals ; Carbapenem-Resistant Enterobacteriaceae/genetics/isolation &amp; purification/*pathogenicity ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; Klebsiella Infections/*microbiology ; Klebsiella pneumoniae/genetics/isolation &amp; purification/*pathogenicity ; Moths/microbiology ; Phylogeny ; Plasmids/genetics ; Sequence Analysis, DNA ; Sputum/microbiology ; Virulence ; Whole Genome Sequencing/*methods ; beta-Lactamases/*genetics ; }, abstract = {BACKGROUND: A carbapenem-resistant hypermucoviscous Klebsiella pneumoniae isolate was recovered from human sputum.<br><br>METHODS: Whole genome sequencing of this isolate was carried out to reveal its clonal background, antimicrobial resistance determinants and virulence factors. Virulence assays were performed using wax moth larvae. The transfer of blaNDM-5 between bacterial strains was tested using conjugation. 59 genome assemblies of ST29 K. pneumoniae and 230 IncX3 plasmids regardless of the carriage of resistance gene were employed for phylogenetic analysis, respectively.<br><br>RESULTS: The strain carried a virulence plasmid pVir-SCNJ1 bearing the virulence gene rmpA and exhibited a high virulence in wax moth. This hypervirulent strain belongs to sequence type 29 and carries blaNDM-5, which is located on a conjugative plasmid, designated pNDM5-SCNJ1, belonging to type IncX3. pNDM5-SCNJ1 was fully sequenced and shows high similarity with pNDM_MGR194, except some deletion inside the ISAba125 region. Phylogenetic analysis of IncX3 plasmids revealed that although blaNDM-5 can be evolved from blaNDM-1 via point mutations within some IncX3 plasmids, most of blaNDM-5-carrying IncX3 plasmids probably have acquired blaNDM-5 in multiple events.<br><br>CONCLUSIONS: In this study, we characterized a blaNDM-5-positive hypervirulent K. pneumoniae of sequence type 29 in China. Our results highlight the need for active surveillance on this lineage of carbapenem-resistant K. pneumoniae.}, }
@article {pmid31451772, year = {2019}, author = {Adam, PS and Borrel, G and Gribaldo, S}, title = {An archaeal origin of the Wood-Ljungdahl H4MPT branch and the emergence of bacterial methylotrophy.}, journal = {Nature microbiology}, volume = {4}, number = {12}, pages = {2155-2163}, pmid = {31451772}, issn = {2058-5276}, mesh = {Archaea/*classification ; Bacteria/*classification/enzymology ; Carbon/metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Archaeal ; Genome, Archaeal ; Genome, Bacterial ; Methane/*metabolism ; Phylogeny ; Pterins/*metabolism ; Wood/metabolism ; }, abstract = {The tetrahydromethanopterin (H4MPT) methyl branch of the Wood-Ljungdahl pathway is shared by archaeal and bacterial metabolisms that greatly contribute to the global carbon budget and greenhouse gas fluxes: methanogenesis and methylotrophy, including methanotrophy[1-3]. It has been proposed that the H4MPT branch dates back to the last universal common ancestor[4-6]. Interestingly, it has been identified in numerous recently sequenced and mostly uncultured non-methanogenic and non-methylotrophic archaeal and bacterial lineages, where its function remains unclear[5,7]. Here, we have examined the distribution and phylogeny of the enzymes involved in the H4MPT branch and the biosynthesis of its cofactors in over 6,400 archaeal and bacterial genomes. We find that a full Wood-Ljungdahl H4MPT pathway is widespread in Archaea and is likely ancestral to this domain, whereas this is not the case for Bacteria. Moreover, the inclusion of recently sequenced lineages leads to an important shortening of the branch separating Archaea and Bacteria with respect to previous phylogenies of the H4MPT branch. Finally, the genes for the pathway are colocalized in many of the recently sequenced archaeal lineages, similar to bacteria. Together, these results weaken the last universal common ancestor hypothesis and rather favour an origin of the H4MPT branch in Archaea and its subsequent transfer to Bacteria. We propose a scenario for its potential initial role in the first bacterial recipients and its evolution up to the emergence of aerobic methylotrophy. Finally, we discuss how an ancient horizontal transfer not only triggered the emergence of key metabolic processes but also important transitions in Earth's history.}, }
@article {pmid31448067, year = {2019}, author = {Kawamura, Y and Sanchez Calle, A and Yamamoto, Y and Sato, TA and Ochiya, T}, title = {Extracellular vesicles mediate the horizontal transfer of an active LINE-1 retrotransposon.}, journal = {Journal of extracellular vesicles}, volume = {8}, number = {1}, pages = {1643214}, pmid = {31448067}, issn = {2001-3078}, abstract = {Long interspersed element-1 (LINE-1 or L1) retrotransposons replicate through a copy-and-paste mechanism using an RNA intermediate. However, little is known about the physical transmission of retrotransposon RNA between cells. To examine the horizontal transfer of an active human L1 retrotransposon mediated by extracellular vesicles (EVs), human cancer cells were transfected with an expression construct containing a retrotransposition-competent human L1 tagged with a reporter gene. Using this model, active retrotransposition events were detected by screening for the expression of the reporter gene inserted into the host genome by retrotransposition. EVs including exosomes and microvesicles were isolated from cells by differential centrifugation. The enrichment of L1-derived reporter RNA transcripts were detected in EVs isolated from cells expressing active L1 retrotransposition. The delivery of reporter RNA was confirmed in recipient cells, and reporter genes were detected in the genome of recipient cells. Additionally, employing qRT-PCR, we found that host-encoded factors are activated in response to increased exposure to L1-derived RNA transcripts in recipient cells. Our results suggest that the horizontal transfer of retrotransposons can occur through the incorporation of RNA intermediates delivered via EVs and may have important implications for the intercellular regulation of gene expression and gene function.}, }
@article {pmid31448060, year = {2019}, author = {Arredondo, A and Àlvarez, G and Nart, J and Mor, C and Blanc, V and León, R}, title = {Detection and expression analysis of tet(B) in Streptococcus oralis.}, journal = {Journal of oral microbiology}, volume = {11}, number = {1}, pages = {1643204}, pmid = {31448060}, issn = {2000-2297}, abstract = {Tetracycline resistance can be achieved through tet genes, which code for efflux pumps, ribosomal protection proteins and inactivation enzymes. Some of these genes have only been described in either Gram-positive or Gram-negative bacteria. This is the case of tet(B), which codes for an efflux pump and, so far, had only been found in Gram-negative bacteria. In this study, tet(B) was detected in two clinical Streptococcus oralis strains isolated from the gingival sulci of two subjects. In both cases, the gene was completely sequenced, yielding 100% shared identity and coverage with other previously published sequences of tet(B). Moreover, we studied the expression of tet(B) using RT-qPCR in the isolates grown with and without tetracycline, detecting constitutive expression in only one of the isolates, with no signs of expression in the other one. This is the first time that the presence and expression of the tet(B) gene has been confirmed in Gram-positive bacteria, which highlights the potential of the genus Streptococcus to become a reservoir and a disseminator of antibiotic resistance genes in an environment so prone to horizontal gene transfer as is the oral biofilm.}, }
@article {pmid31441977, year = {2019}, author = {de Reus, E and Nielsen, MR and Frandsen, RJN}, title = {Metabolic and regulatory insights from the experimental horizontal gene transfer of the aurofusarin and bikaverin gene clusters to Aspergillus nidulans.}, journal = {Molecular microbiology}, volume = {112}, number = {6}, pages = {1684-1700}, doi = {10.1111/mmi.14376}, pmid = {31441977}, issn = {1365-2958}, mesh = {Aspergillus nidulans/*genetics/metabolism ; Fungal Proteins/metabolism ; Fusarium/*genetics/metabolism ; Gene Expression Regulation, Fungal/genetics ; Gene Transfer Techniques ; Multigene Family/*genetics/physiology ; Naphthoquinones/metabolism ; Xanthones/metabolism ; }, abstract = {We staged the transfer of the aurofusarin and bikaverin biosynthetic gene clusters (BGCs) to Aspergillus nidulans with the aim of gaining functional insights into dynamics immediately following a horizontal gene transfer (HGT) event. While the introduction of both BGCs resulted in the production of detectable pathway metabolites in A. nidulans, the transferred aurofusarin BGC formed dimeric shunt products instead of aurofusarin. This was linked to low transcription of the cluster activator and insufficient activity of tailoring enzymes, demonstrating how a shift of the pathway bottleneck after HGT can result in metabolic innovation. The transferred bikaverin BGC readily produced bikaverin, providing a model system for studying the conservation of regulatory responses to environmental cues. Conserved PacC-mediated pH regulation of the bikaverin BGC was observed between original host Fusarium fujikuroi and A. nidulans. Contrary to strong nitrogen responses described in other hosts, the BGC appeared unresponsive to environmental nitrogen in A. nidulans. While F. fujikuroi and A. nidulans both form chlamydospore-like structures when exposed to ralsolamycin, specific induction of the bikaverin BGC was not observed in A. nidulans. We propose that the presence of compatible cis-regulatory elements in BGCs facilitates regulatory conservation after transfer, without which the chromosomal context would dictate expression.}, }
@article {pmid31440214, year = {2019}, author = {Buhl, M and Kästle, C and Geyer, A and Autenrieth, IB and Peter, S and Willmann, M}, title = {Molecular Evolution of Extensively Drug-Resistant (XDR) Pseudomonas aeruginosa Strains From Patients and Hospital Environment in a Prolonged Outbreak.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1742}, pmid = {31440214}, issn = {1664-302X}, abstract = {In this study, we aimed to elucidate a prolonged outbreak of extensively drug-resistant (XDR) Pseudomonas aeruginosa, at two adjacent hospitals over a time course of 4 years. Since all strains exhibited a similar antibiotic susceptibility pattern and carried the carbapenemase gene blaVIM, a monoclonal outbreak was assumed. To shed light on the intra-hospital evolution of these strains over time, whole genome sequence (WGS) analysis of 100 clinical and environmental outbreak strains was employed. Phylogenetic analysis of the core genome revealed the outbreak to be polyclonal, rather than monoclonal as initially suggested. The vast majority of strains fell into one of two major clusters, composed of 27 and 59 strains, and their accessory genome each revealed over 400 and 600 accessory genes, respectively, thus indicating an unexpectedly high structural diversity among phylogenetically clustered strains. Further analyses focused on the cluster with 59 strains, representing the hospital from which both clinical and environmental strains were available. Our investigation clearly shows both accumulation and loss of genes occur very frequently over time, as reflected by analysis of protein enrichment as well as functional enrichment. In addition, we investigated adaptation through single nucleotide polymorphisms (SNPs). Among the genes affected by SNPs, there are a multidrug efflux pump (mexZ) and a mercury detoxification operon (merR) with deleterious mutations, potentially leading to loss of repression with resistance against antibiotics and disinfectants. Our results not only confirm WGS to be a powerful tool for epidemiologic analyses, but also provide insights into molecular evolution during an XDR P. aeruginosa hospital outbreak. Genome mutation unveiled a striking genetic plasticity on an unexpectedly high level, mostly driven by horizontal gene transfer. Our study adds valuable information to the molecular understanding of "real-world" Intra-hospital P. aeruginosa evolution and is a step forward toward more personalized medicine in infection control.}, }
@article {pmid31437318, year = {2019}, author = {Cecchin, M and Marcolungo, L and Rossato, M and Girolomoni, L and Cosentino, E and Cuine, S and Li-Beisson, Y and Delledonne, M and Ballottari, M}, title = {Chlorella vulgaris genome assembly and annotation reveals the molecular basis for metabolic acclimation to high light conditions.}, journal = {The Plant journal : for cell and molecular biology}, volume = {100}, number = {6}, pages = {1289-1305}, pmid = {31437318}, issn = {1365-313X}, support = {679814/ERC_/European Research Council/International ; }, mesh = {Acclimatization/*genetics/*radiation effects ; Base Sequence ; Biofuels ; Biomass ; Biosynthetic Pathways/genetics/physiology/radiation effects ; Biotechnology ; Chlorella vulgaris/*genetics/growth &amp; development/*metabolism/*radiation effects ; Fatty Acid Synthases/genetics/metabolism ; Fatty Acids/biosynthesis ; Gene Expression Regulation, Plant/radiation effects ; Gene Ontology ; Gene Transfer, Horizontal ; Genome, Mitochondrial ; Genome, Plant ; *Light ; Lipids/biosynthesis ; Meiosis ; *Molecular Sequence Annotation ; Phylogeny ; Transcriptome ; Triglycerides/biosynthesis ; }, abstract = {Chlorella vulgaris is a fast-growing fresh-water microalga cultivated on the industrial scale for applications ranging from food to biofuel production. To advance our understanding of its biology and to establish genetics tools for biotechnological manipulation, we sequenced the nuclear and organelle genomes of Chlorella vulgaris 211/11P by combining next generation sequencing and optical mapping of isolated DNA molecules. This hybrid approach allowed us to assemble the nuclear genome in 14 pseudo-molecules with an N50 of 2.8 Mb and 98.9% of scaffolded genome. The integration of RNA-seq data obtained at two different irradiances of growth (high light, HL versus low light, LL) enabled us to identify 10 724 nuclear genes, coding for 11 082 transcripts. Moreover, 121 and 48 genes, respectively, were found in the chloroplast and mitochondrial genome. Functional annotation and expression analysis of nuclear, chloroplast and mitochondrial genome sequences revealed particular features of Chlorella vulgaris. Evidence of horizontal gene transfers from chloroplast to mitochondrial genome was observed. Furthermore, comparative transcriptomic analyses of LL versus HL provided insights into the molecular basis for metabolic rearrangement under HL versus LL conditions leading to enhanced de novo fatty acid biosynthesis and triacylglycerol accumulation. The occurrence of a cytosolic fatty acid biosynthetic pathway could be predicted and its upregulation upon HL exposure was observed, consistent with the increased lipid amount under HL conditions. These data provide a rich genetic resource for future genome editing studies, and potential targets for biotechnological manipulation of Chlorella vulgaris or other microalgae species to improve biomass and lipid productivity.}, }
@article {pmid31435688, year = {2019}, author = {Jones, GH}, title = {Phylogeny and Evolution of RNA 3'-Nucleotidyltransferases in Bacteria.}, journal = {Journal of molecular evolution}, volume = {87}, number = {7-8}, pages = {254-270}, pmid = {31435688}, issn = {1432-1432}, mesh = {Amino Acid Sequence/genetics ; Bacteria/genetics ; Bacterial Proteins/genetics ; Biological Evolution ; Evolution, Molecular ; Phylogeny ; Polynucleotide Adenylyltransferase/genetics/metabolism ; RNA/genetics/metabolism ; RNA Nucleotidyltransferases/*genetics/metabolism ; RNA, Transfer/metabolism ; Sequence Homology, Amino Acid ; }, abstract = {The tRNA nucleotidyltransferases and poly(A) polymerases belong to a superfamily of nucleotidyltransferases. The amino acid sequences of a number of bacterial tRNA nucleotidyltransferases and poly(A) polymerases have been used to construct a rooted, neighbor-joining phylogenetic tree. Using information gleaned from that analysis, along with data from the rRNA-based phylogenetic tree, structural data available on a number of members of the superfamily and other biochemical information on the superfamily, it is possible to suggest a scheme for the evolution of the bacterial tRNA nucleotidyltransferases and poly(A) polymerases from ancestral species. Elements of that scheme are discussed along with questions arising from the scheme which can be explored experimentally.}, }
@article {pmid31433955, year = {2019}, author = {Dubnau, D and Blokesch, M}, title = {Mechanisms of DNA Uptake by Naturally Competent Bacteria.}, journal = {Annual review of genetics}, volume = {53}, number = {}, pages = {217-237}, doi = {10.1146/annurev-genet-112618-043641}, pmid = {31433955}, issn = {1545-2948}, support = {R01 GM043756/GM/NIGMS NIH HHS/United States ; R01 GM057720/GM/NIGMS NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/cytology/drug effects/*genetics ; Bacterial Proteins/genetics/metabolism ; DNA, Bacterial/genetics/metabolism ; DNA-Binding Proteins/genetics/metabolism ; *Gene Transfer, Horizontal ; Helicobacter pylori/genetics/metabolism ; Membrane Proteins/genetics/metabolism ; Transformation, Bacterial/*genetics ; Type IV Secretion Systems ; }, abstract = {Transformation is a widespread mechanism of horizontal gene transfer in bacteria. DNA uptake to the periplasmic compartment requires a DNA-uptake pilus and the DNA-binding protein ComEA. In the gram-negative bacteria, DNA is first pulled toward the outer membrane by retraction of the pilus and then taken up by binding to periplasmic ComEA, acting as a Brownian ratchet to prevent backward diffusion. A similar mechanism probably operates in the gram-positive bacteria as well, but these systems have been less well characterized. Transport, defined as movement of a single strand of transforming DNA to the cytosol, requires the channel protein ComEC. Although less is understood about this process, it may be driven by proton symport. In this review we also describe various phenomena that are coordinated with the expression of competence for transformation, such as fratricide, the kin-discriminatory killing of neighboring cells, and competence-mediated growth arrest.}, }
@article {pmid31432082, year = {2019}, author = {Obata, D and Takabayashi, A and Tanaka, R and Tanaka, A and Ito, H}, title = {Horizontal Transfer of Promiscuous Activity from Nonphotosynthetic Bacteria Contributed to Evolution of Chlorophyll Degradation Pathway.}, journal = {Molecular biology and evolution}, volume = {36}, number = {12}, pages = {2830-2841}, doi = {10.1093/molbev/msz193}, pmid = {31432082}, issn = {1537-1719}, mesh = {Arabidopsis Proteins/*genetics/metabolism ; Bacterial Proteins/*genetics/metabolism ; Chlorophyll/*metabolism ; Chloroplast Proteins/*genetics/metabolism ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Magnesium/metabolism ; Phylogeny ; Substrate Specificity ; }, abstract = {The relationship between enzymes and substrates does not perfectly match the "lock and key" model, because enzymes act on molecules other than their true substrate in different catalytic reactions. Such biologically nonfunctional reactions are called "promiscuous activities." Promiscuous activities are apparently useless, but they can be an important starting point for enzyme evolution. It has been hypothesized that enzymes with low promiscuous activity will show enhanced promiscuous activity under selection pressure and become new specialists through gene duplication. Although this is the prevailing scenario, there are two major problems: 1) it would not apply to prokaryotes because horizontal gene transfer is more significant than gene duplication and 2) there is no direct evidence that promiscuous activity is low without selection pressure. We propose a new scenario including various levels of promiscuous activity throughout a clade and horizontal gene transfer. STAY-GREEN (SGR), a chlorophyll a-Mg dechelating enzyme, has homologous genes in bacteria lacking chlorophyll. We found that some bacterial SGR homologs have much higher Mg-dechelating activities than those of green plant SGRs, while others have no activity, indicating that the level of promiscuous activity varies. A phylogenetic analysis suggests that a bacterial SGR homolog with high dechelating activity was horizontally transferred to a photosynthetic eukaryote. Some SGR homologs acted on various chlorophyll molecules that are not used as substrates by green plant SGRs, indicating that SGR acquired substrate specificity after transfer to eukaryotes. We propose that horizontal transfer of high promiscuous activity is one process of new enzyme acquisition.}, }
@article {pmid31431529, year = {2019}, author = {Frazão, N and Sousa, A and Lässig, M and Gordo, I}, title = {Horizontal gene transfer overrides mutation in Escherichia coli colonizing the mammalian gut.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {36}, pages = {17906-17915}, pmid = {31431529}, issn = {1091-6490}, mesh = {Algorithms ; Animals ; Bacteriophages/physiology ; Biological Evolution ; Escherichia coli/*genetics/virology ; Gastrointestinal Microbiome ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Genomics ; Intestinal Mucosa/*metabolism/*microbiology ; Mice ; Models, Biological ; *Mutation ; Symbiosis ; }, abstract = {Bacteria evolve by mutation accumulation in laboratory experiments, but tempo and mode of evolution in natural environments are largely unknown. Here, we study the ubiquitous natural process of host colonization by commensal bacteria. We show, by experimental evolution of Escherichia coli in the mouse intestine, that the ecology of the gut controls the pace and mode of evolution of a new invading bacterial strain. If a resident E. coli strain is present in the gut, the invading strain evolves by rapid horizontal gene transfer (HGT), which precedes and outweighs evolution by accumulation of mutations. HGT is driven by 2 bacteriophages carried by the resident strain, which cause an epidemic phage infection of the invader. These dynamics are followed by subsequent evolution by clonal interference of genetically diverse lineages of phage-carrying (lysogenic) bacteria. We show that the genes uptaken by HGT enhance the metabolism of specific gut carbon sources and provide a fitness advantage to lysogenic invader lineages. A minimal dynamical model explains the temporal pattern of phage epidemics and the complex evolutionary outcome of phage-mediated selection. We conclude that phage-driven HGT is a key eco-evolutionary driving force of gut colonization-it accelerates evolution and promotes genetic diversity of commensal bacteria.}, }
@article {pmid31430481, year = {2019}, author = {Keeling, PJ and Burki, F}, title = {Progress towards the Tree of Eukaryotes.}, journal = {Current biology : CB}, volume = {29}, number = {16}, pages = {R808-R817}, doi = {10.1016/j.cub.2019.07.031}, pmid = {31430481}, issn = {1879-0445}, mesh = {Eukaryota/*classification/genetics ; *Evolution, Molecular ; *Genome ; *Phylogeny ; }, abstract = {Developing a detailed understanding of how all known forms of life are related to one another in the tree of life has been a major preoccupation of biology since the idea of tree-like evolution first took hold. Since most life is microbial, our intuitive use of morphological comparisons to infer relatedness only goes so far, and molecular sequence data, most recently from genomes and transcriptomes, has been the primary means to infer these relationships. For prokaryotes this presented new challenges, since the degree of horizontal gene transfer led some to question the tree-like depiction of evolution altogether. Most eukaryotes are also microbial, but in contrast to prokaryotic life, the application of large-scale molecular data to the tree of eukaryotes has largely been a constructive process, leading to a small number of very diverse lineages, or 'supergroups'. The tree is not completely resolved, and contentious problems remain, but many well-established supergroups now encompass much more diversity than the traditional kingdoms. Some of the most exciting recent developments come from the discovery of branches in the tree that we previously had no inkling even existed, many of which are of great ecological or evolutionary interest. These new branches highlight the need for more exploration, by high-throughput molecular surveys, but also more traditional means of observations and cultivation.}, }
@article {pmid31430401, year = {2019}, author = {Mathé-Hubert, H and Kaech, H and Hertaeg, C and Jaenike, J and Vorburger, C}, title = {Nonrandom associations of maternally transmitted symbionts in insects: The roles of drift versus biased cotransmission and selection.}, journal = {Molecular ecology}, volume = {28}, number = {24}, pages = {5330-5346}, doi = {10.1111/mec.15206}, pmid = {31430401}, issn = {1365-294X}, mesh = {Animals ; Aphids/*genetics/microbiology ; Bayes Theorem ; Drosophila/genetics/microbiology ; Gene Transfer, Horizontal/genetics ; Maternal Inheritance/genetics ; Microbiota/genetics ; Phylogeny ; Spiroplasma/*genetics ; Symbiosis/*genetics ; Wolbachia/*genetics ; }, abstract = {Virtually all higher organisms form holobionts with associated microbiota. To understand the biology of holobionts we need to know how species assemble and interact. Controlled experiments are suited to study interactions between particular symbionts, but they only accommodate a tiny portion of the diversity within each species. Alternatively, interactions can be inferred by testing if associations among symbionts in the field are more or less frequent than expected under random assortment. However, random assortment may not be a valid null hypothesis for maternally transmitted symbionts since drift alone can result in associations. Here, we analyse a European field survey of endosymbionts in pea aphids (Acyrthosiphon pisum), confirming that symbiont associations are pervasive. To interpret them, we develop a model simulating the effect of drift on symbiont associations. We show that drift induces apparently nonrandom assortment, even though horizontal transmissions and maternal transmission failures tend to randomise symbiont associations. We also use this model in the approximate Bayesian computation framework to revisit the association between Spiroplasma and Wolbachia in Drosophila neotestacea. New field data reported here reveal that this association has disappeared in the investigated location, yet a significant interaction between Spiroplasma and Wolbachia can still be inferred. Our study confirms that negative and positive associations are pervasive and often induced by symbiont-symbiont interactions. Nevertheless, some associations are also likely to be driven by drift. This possibility needs to be considered when performing such analyses, and our model is helpful for this purpose.}, }
@article {pmid31429177, year = {2019}, author = {Fernandez-Garcia, L and Kim, JS and Tomas, M and Wood, TK}, title = {Toxins of toxin/antitoxin systems are inactivated primarily through promoter mutations.}, journal = {Journal of applied microbiology}, volume = {127}, number = {6}, pages = {1859-1868}, doi = {10.1111/jam.14414}, pmid = {31429177}, issn = {1365-2672}, support = {PI16/01163//National Plan for Scientific Research, Technological Development and Innovation 2008-2011/ ; GAIN, Axencia de Innovaci&#xf3;n//Xunta de Galicia/ ; KRIBB Initiative Research Program//Xunta de Galicia/ ; }, mesh = {Bacterial Toxins/*genetics/*metabolism ; Chromosomes, Bacterial/genetics ; Escherichia coli/genetics/growth &amp; development/physiology ; Escherichia coli Proteins/genetics ; Mutation/*genetics ; Plasmids/genetics ; Promoter Regions, Genetic/*genetics ; Toxin-Antitoxin Systems/*genetics ; }, abstract = {AIMS: Given the extreme toxicity of some of the toxins of toxin-antitoxin (TA) systems, we were curious how the cell silences toxins, if the antitoxin is inactivated or independent toxins are obtained via horizontal gene transfer.<br><br>METHODS AND RESULTS: Growth curves of Escherichia coli K12 BW25113 harbouring plasmid pCA24N to produce RalR, MqsR, GhoT or Hha toxins, showed toxin inactivation after 3&#xa0;h. Sequencing plasmids from these cultures revealed toxin inactivation occurred primarily due to consistent deletions in the promoter. The lack of mutation in the structural genes was corroborated by a bioinformatics analysis of 1000 E. coli genomes which showed both conservation and little variability in the four toxin genes. For those strains that lacked a mutation in the plasmid, single nucleotide polymorphism analysis was performed to identify that chromosomal mutations iraM and mhpR inactivate the toxins GhoT and MqsR/GhoT respectively.<br><br>CONCLUSION: We find that the RalR (type I), MqsR (type II), GhoT (type V) and Hha (type VII) toxins are inactivated primarily by a mutation that inactivates the toxin promoter or via the chromosomal mutations iraM and mhpR.<br><br>This study demonstrates toxins of TA systems may be inactivated by mutations that primarily affect the toxin gene promoter instead of the toxin structural gene.}, }
@article {pmid31428076, year = {2019}, author = {Jiang, H and Cheng, H and Liang, Y and Yu, S and Yu, T and Fang, J and Zhu, C}, title = {Diverse Mobile Genetic Elements and Conjugal Transferability of Sulfonamide Resistance Genes (sul1, sul2, and sul3) in Escherichia coli Isolates From Penaeus vannamei and Pork From Large Markets in Zhejiang, China.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1787}, pmid = {31428076}, issn = {1664-302X}, abstract = {High prevalence rates of sulfonamide resistance genes sul1, sul2, and sul3 have been observed in Gram-negative bacteria isolated from humans, domestic animals, and aquaculture species worldwide. We investigated the distribution characteristics, location, conjugative transferability, and genetic environments of sul genes from Escherichia coli isolates collected from Penaeus vannamei and pork samples from three large markets in Zhejiang, China. The prevalence rates of sul genes in sulfonamide-resistant E. coli isolates from P. vannamei and pork samples were 90.0 and 88.6%, respectively, and the prevalence of sul1 and sul2 was significantly higher than that of sul3 (p < 0.05). Twenty-four representative sul-positive E. coli isolates were analyzed in detail. Southern blot hybridization confirmed that sul genes of E. coli isolates were located on plasmids and/or chromosomes. Transfer of resistance through conjugation was observed in all 18 E. coli isolates harboring sul genes on plasmids. Replicon typing identified seven different incompatibility groups and IncF was the dominant replicon type among sul gene-containing plasmids from both sources. PCR walking analysis indicated that 87.5% (35/40) of sul gene-related fragments carried insertion sequences (ISs) belonging to a variety of families in diverse sites, with IS26 occurring most frequently. In addition, the sul1 gene was detected mainly in fragments carrying class 1 integrons. Co-location on the same fragment with resistance genes that may contribute to the persistence and dissemination of sul1 and/or sul2 genes. The diversity of mobile genetic elements and resistance genes adjacent to sul3 was much lower than those adjacent to sul1 and sul2, especially those located in chromosomes, which reduced the transmission potential of the sul3 gene. In conclusion, combined with the results of clonal relatedness analysis by PFGE and MLST of 24 representative E. coli isolates from P. vannamei and pork samples, it showed that a small number of sul genes were vertically transmitted among E. coli from P. vannamei and that horizontal gene transfer was likely the main transmission mechanism of sul genes from both sources. Our results provide important information to better understand the risk of transmission of sul genes from seafood and meat to humans.}, }
@article {pmid31427514, year = {2019}, author = {Kjeldsen, KU and Schreiber, L and Thorup, CA and Boesen, T and Bjerg, JT and Yang, T and Dueholm, MS and Larsen, S and Risgaard-Petersen, N and Nierychlo, M and Schmid, M and Bøggild, A and van de Vossenberg, J and Geelhoed, JS and Meysman, FJR and Wagner, M and Nielsen, PH and Nielsen, LP and Schramm, A}, title = {On the evolution and physiology of cable bacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {38}, pages = {19116-19125}, pmid = {31427514}, issn = {1091-6490}, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics/*metabolism ; *Biological Evolution ; Carbon Cycle ; Cell Movement ; Chemotaxis ; Cytochromes/metabolism ; Deltaproteobacteria/classification/*genetics/*physiology ; Electron Transport ; *Genome, Bacterial ; Geologic Sediments/microbiology ; Nitrates/metabolism ; Oxidation-Reduction ; Oxygen/metabolism ; Phylogeny ; Proteome/*analysis ; Sequence Homology ; Sulfides/metabolism ; }, abstract = {Cable bacteria of the family Desulfobulbaceae form centimeter-long filaments comprising thousands of cells. They occur worldwide in the surface of aquatic sediments, where they connect sulfide oxidation with oxygen or nitrate reduction via long-distance electron transport. In the absence of pure cultures, we used single-filament genomics and metagenomics to retrieve draft genomes of 3 marine Candidatus Electrothrix and 1 freshwater Ca. Electronema species. These genomes contain >50% unknown genes but still share their core genomic makeup with sulfate-reducing and sulfur-disproportionating Desulfobulbaceae, with few core genes lost and 212 unique genes (from 197 gene families) conserved among cable bacteria. Last common ancestor analysis indicates gene divergence and lateral gene transfer as equally important origins of these unique genes. With support from metaproteomics of a Ca. Electronema enrichment, the genomes suggest that cable bacteria oxidize sulfide by reversing the canonical sulfate reduction pathway and fix CO2 using the Wood-Ljungdahl pathway. Cable bacteria show limited organotrophic potential, may assimilate smaller organic acids and alcohols, fix N2, and synthesize polyphosphates and polyglucose as storage compounds; several of these traits were confirmed by cell-level experimental analyses. We propose a model for electron flow from sulfide to oxygen that involves periplasmic cytochromes, yet-unidentified conductive periplasmic fibers, and periplasmic oxygen reduction. This model proposes that an active cable bacterium gains energy in the anodic, sulfide-oxidizing cells, whereas cells in the oxic zone flare off electrons through intense cathodic oxygen respiration without energy conservation; this peculiar form of multicellularity seems unparalleled in the microbial world.}, }
@article {pmid31427512, year = {2019}, author = {Hehenberger, E and Gast, RJ and Keeling, PJ}, title = {A kleptoplastidic dinoflagellate and the tipping point between transient and fully integrated plastid endosymbiosis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {36}, pages = {17934-17942}, pmid = {31427512}, issn = {1091-6490}, mesh = {Dinoflagellida/*physiology ; Electron Transport ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; *Gene Transfer, Horizontal ; Models, Biological ; *Mutagenesis, Insertional ; Plastids/*genetics ; *Symbiosis ; }, abstract = {Plastid endosymbiosis has been a major force in the evolution of eukaryotic cellular complexity, but how endosymbionts are integrated is still poorly understood at a mechanistic level. Dinoflagellates, an ecologically important protist lineage, represent a unique model to study this process because dinoflagellate plastids have repeatedly been reduced, lost, and replaced by new plastids, leading to a spectrum of ages and integration levels. Here we describe deep-transcriptomic analyses of the Antarctic Ross Sea dinoflagellate (RSD), which harbors long-term but temporary kleptoplasts stolen from haptophyte prey, and is closely related to dinoflagellates with fully integrated plastids derived from different haptophytes. In some members of this lineage, called the Kareniaceae, their tertiary haptophyte plastids have crossed a tipping point to stable integration, but RSD has not, and may therefore reveal the order of events leading up to endosymbiotic integration. We show that RSD has retained its ancestral secondary plastid and has partitioned functions between this plastid and the kleptoplast. It has also obtained genes for kleptoplast-targeted proteins via horizontal gene transfer (HGT) that are not derived from the kleptoplast lineage. Importantly, many of these HGTs are also found in the related species with fully integrated plastids, which provides direct evidence that genetic integration preceded organelle fixation. Finally, we find that expression of kleptoplast-targeted genes is unaffected by environmental parameters, unlike prey-encoded homologs, suggesting that kleptoplast-targeted HGTs have adapted to posttranscriptional regulation mechanisms of the host.}, }
@article {pmid31425984, year = {2019}, author = {Lin, H and Jiang, L and Li, B and Dong, Y and He, Y and Qiu, Y}, title = {Screening and evaluation of heavy metals facilitating antibiotic resistance gene transfer in a sludge bacterial community.}, journal = {The Science of the total environment}, volume = {695}, number = {}, pages = {133862}, doi = {10.1016/j.scitotenv.2019.133862}, pmid = {31425984}, issn = {1879-1026}, mesh = {Drug Resistance, Microbial/*genetics ; Environmental Monitoring ; Gene Transfer, Horizontal ; Metals, Heavy/*toxicity ; Sewage/chemistry/*microbiology ; Water Pollutants, Chemical/*toxicity ; }, abstract = {Recent growing evidence suggests that heavy metals can stimulate the transfer of antibiotic resistance genes (ARGs) between bacteria. However, most previous studies focused on pure strains, the effect of heavy metals on ARG transfer in bacterial communities, especially in activated sludge, has not been clearly explored. In this study, a high-throughput method, combining computerized incubator (Bioscreen C) and flow cytometry, was developed to evaluate different concentrations of heavy metals influencing ARG transfer in sludge bacteria communities. By using Escherichia coli MG1655 as the donor of broad-host range IncP-1 plasmid pKJK5, it was found that 0.5 mmol/L Pb, 0.1 mmol/L As and 0.005 mmol/L Hg could obviously promote ARG transfer in sludge bacteria communities. Furthermore, mating assays on microfluidic chips also proved higher transfer frequencies in attached communities under the above heavy metal stresses. Transconjugants under Pb, As and Hg stresses were isolated and phylogenetically described. For As and Hg, the dominant genus was Pseudomonas, accounting for 88% and 96%, respectively. While under Pb stress, the genera Aeromonas and Enterobacter were the main transconjugants, accounting for 56% and 32% respectively. Moreover, ABC transporters and Amino acid metabolism, which were related to heavy metal transport and cellular metabolism, were dominant in the prediction of microbial metabolic function of transconjugants. This study can be helpful for risk assessment and control of ARG spreading in WWTPs.}, }
@article {pmid31424971, year = {2019}, author = {Gaut, BS and Miller, AJ and Seymour, DK}, title = {Living with Two Genomes: Grafting and Its Implications for Plant Genome-to-Genome Interactions, Phenotypic Variation, and Evolution.}, journal = {Annual review of genetics}, volume = {53}, number = {}, pages = {195-215}, doi = {10.1146/annurev-genet-112618-043545}, pmid = {31424971}, issn = {1545-2948}, mesh = {Biological Evolution ; Biological Variation, Population ; Chimera ; Epigenesis, Genetic ; Gene Expression Regulation, Plant ; *Genome, Plant ; Host-Parasite Interactions/*genetics ; Plant Breeding/*methods ; Plant Growth Regulators/physiology ; Plant Roots/physiology ; Plants/genetics/*parasitology ; }, abstract = {Plant genomes interact when genetically distinct individuals join, or are joined, together. Individuals can fuse in three contexts: artificial grafts, natural grafts, and host-parasite interactions. Artificial grafts have been studied for decades and are important platforms for studying the movement of RNA, DNA, and protein. Yet several mysteries about artificial grafts remain, including the factors that contribute to graft incompatibility, the prevalence of genetic and epigenetic modifications caused by exchanges between graft partners, and the long-term effects of these modifications on phenotype. Host-parasite interactions also lead to the exchange of materials, and RNA exchange actively contributes to an ongoing arms race between parasite virulence and host resistance. Little is known about natural grafts except that they can be frequent and may provide opportunities for evolutionary innovation through genome exchange. In this review, we survey our current understanding about these three mechanisms of contact, the genomic interactions that result, and the potential evolutionary implications.}, }
@article {pmid31422229, year = {2019}, author = {Mukhtar, S and Ahmad, S and Bashir, A and Mehnaz, S and Mirza, MS and Malik, KA}, title = {Identification of plasmid encoded osmoregulatory genes from halophilic bacteria isolated from the rhizosphere of halophytes.}, journal = {Microbiological research}, volume = {228}, number = {}, pages = {126307}, doi = {10.1016/j.micres.2019.126307}, pmid = {31422229}, issn = {1618-0623}, mesh = {Alanine/metabolism ; Amino Acids, Diamino/metabolism ; Anti-Bacterial Agents/pharmacology ; Atriplex/microbiology ; Bacteria/classification/drug effects/*genetics/isolation &amp; purification ; Bacterial Proteins/genetics ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; Osmoregulation/*genetics ; Oxidoreductases ; Peptide Hydrolases ; Phylogeny ; Plasmids/*genetics/*isolation &amp; purification ; Porins/metabolism ; Proline/metabolism ; *Rhizosphere ; Salt Tolerance/*genetics ; Salt-Tolerant Plants/*microbiology ; Sodium Chloride ; Soil ; Soil Microbiology ; Trehalose/metabolism ; }, abstract = {Bacterial plasmids carry genes that code for additional traits such as osmoregulation, CO2 fixation, antibiotic and heavy metal resistance, root nodulation and nitrogen fixation. The main objective of the current study was to identify plasmid-conferring osmoregulatory genes in bacteria isolated from rhizospheric and non-rhizospheric soils of halophytes (Salsola stocksii and Atriplex amnicola). More than 55% of halophilic bacteria from the rhizosphere and 70% from non-rhizospheric soils were able to grow at 3 M salt concentrations. All the strains showed optimum growth at 1.5-3.0 M NaCl. Bacterial strains from the Salsola rhizosphere showed maximum (31%) plasmid elimination during curing experiments as compared to bacterial strains from the Atriplex rhizosphere and non-rhizospheric soils. Two plasmid cured strains Bacillus HL2HP6 and Oceanobacillus HL2RP7 lost their ability to grow in halophilic medium, but they grew well on LB medium. The plasmid cured strains also showed a change in sensitivity to specific antibiotics. These plasmids were isolated and transformed into E. coli strains and growth response of wild-type and transformed E. coli strains was compared at 1.5-4 M NaCl concentrations. Chromosomal DNA and plasmids from Bacillus filamentosus HL2HP6 were sequenced by using high throughput sequencing approach. Results of functional analysis of plasmid sequences showed different proteins and enzymes involved in osmoregulation of bacteria, such as trehalose, ectoine synthetase, porins, proline, alanine, inorganic ion transporters, dehydrogenases and peptidases. Our results suggested that plasmid conferring osmoregulatory genes play a vital role to maintain internal osmotic balance of bacterial cells and these genes can be used to develop salt tolerant transgenic crops.}, }
@article {pmid31420127, year = {2019}, author = {Claessen, D and Errington, J}, title = {Cell Wall Deficiency as a Coping Strategy for Stress.}, journal = {Trends in microbiology}, volume = {27}, number = {12}, pages = {1025-1033}, doi = {10.1016/j.tim.2019.07.008}, pmid = {31420127}, issn = {1878-4380}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics ; Bacterial Physiological Phenomena/drug effects ; Bacterial Proteins/metabolism ; Cell Wall/*drug effects/*physiology ; Eukaryota ; Gene Transfer, Horizontal ; Host Microbial Interactions ; *Stress, Physiological ; beta-Lactams/pharmacology ; }, abstract = {The cell wall is a surface layer located outside the cell membrane of almost all bacteria; it protects cells from environmental stresses and gives them their typical shape. The cell wall is highly conserved in bacteria and is the target for some of our best antibiotics. Surprisingly, some bacteria are able to shed their wall under the influence of stress, yielding cells that are cell-wall-deficient. Notably, wall-deficient cells are flexible and are able to maneuver through narrow spaces, insensitive to wall-targeting antibiotics, and capable of taking up and exchanging DNA. Moreover, given that wall-associated epitopes are often recognized by host defense systems, wall deficiency provides a plausible explanation for how some bacteria may hide in their host. In this review we focus on this paradoxical stress response, which provides cells with unique opportunities that are unavailable to walled cells.}, }
@article {pmid31418013, year = {2019}, author = {Lee, HH and Ke, HM and Lin, CI and Lee, TJ and Chung, CL and Tsai, IJ}, title = {Evidence of Extensive Intraspecific Noncoding Reshuffling in a 169-kb Mitochondrial Genome of a Basidiomycetous Fungus.}, journal = {Genome biology and evolution}, volume = {11}, number = {10}, pages = {2774-2788}, pmid = {31418013}, issn = {1759-6653}, mesh = {Basidiomycota/*genetics ; *Evolution, Molecular ; Genome Size ; *Genome, Fungal ; *Genome, Mitochondrial ; Introns ; Molecular Sequence Annotation ; Polymorphism, Genetic ; Synteny ; }, abstract = {Comparative genomics of fungal mitochondrial genomes (mitogenomes) have revealed a remarkable pattern of rearrangement between and within major phyla owing to horizontal gene transfer and recombination. The role of recombination was exemplified at a finer evolutionary time scale in basidiomycetes group of fungi as they display a diversity of mitochondrial DNA inheritance patterns. Here, we assembled mitogenomes of six species from the Hymenochaetales order of basidiomycetes and examined 59 mitogenomes from 2 genetic lineages of Phellinus noxius. Gene order is largely collinear, while intergene regions are major determinants of mitogenome size variation. Substantial sequence divergence was found in shared introns consistent with high horizontal gene transfer frequency observed in yeasts, but we also identified a rare case where an intron was retained in five species since speciation. In contrast to the hyperdiversity observed in nuclear genomes of Phellinus noxius, mitogenomes' intraspecific polymorphisms at protein-coding sequences are extremely low. Phylogeny network based on introns revealed turnover as well as exchange of introns between two lineages. Strikingly, some strains harbor a mosaic origin of introns from both lineages. Analysis of intergenic sequence indicated substantial differences between and within lineages, and an expansion may be ongoing as a result of exchange between distal intergenes. These findings suggest that the evolution in mitochondrial DNAs is usually lineage specific but chimeric mitotypes are frequently observed, thus capturing the possible evolutionary processes shaping mitogenomes in a basidiomycete. The large mitogenome sizes reported in various basidiomycetes appear to be a result of interspecific reshuffling of intergenes.}, }
@article {pmid31409239, year = {2019}, author = {Leclerc, QJ and Lindsay, JA and Knight, GM}, title = {Mathematical modelling to study the horizontal transfer of antimicrobial resistance genes in bacteria: current state of the field and recommendations.}, journal = {Journal of the Royal Society, Interface}, volume = {16}, number = {157}, pages = {20190260}, pmid = {31409239}, issn = {1742-5662}, support = {MR/P014658/1/MRC_/Medical Research Council/United Kingdom ; MR/P028322/1/MRC_/Medical Research Council/United Kingdom ; MR/N013638/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/*genetics ; Drug Resistance, Bacterial/*genetics ; *Gene Transfer, Horizontal ; *Models, Biological ; }, abstract = {Antimicrobial resistance (AMR) is one of the greatest public health challenges we are currently facing. To develop effective interventions against this, it is essential to understand the processes behind the spread of AMR. These are partly dependent on the dynamics of horizontal transfer of resistance genes between bacteria, which can occur by conjugation (direct contact), transformation (uptake from the environment) or transduction (mediated by bacteriophages). Mathematical modelling is a powerful tool to investigate the dynamics of AMR; however, the extent of its use to study the horizontal transfer of AMR genes is currently unclear. In this systematic review, we searched for mathematical modelling studies that focused on horizontal transfer of AMR genes. We compared their aims and methods using a list of predetermined criteria and used our results to assess the current state of this research field. Of the 43 studies we identified, most focused on the transfer of single genes by conjugation in Escherichia coli in culture and its impact on the bacterial evolutionary dynamics. Our findings highlight the existence of an important research gap in the dynamics of transformation and transduction and the overall public health implications of horizontal transfer of AMR genes. To further develop this field and improve our ability to control AMR, it is essential that we clarify the structural complexity required to study the dynamics of horizontal gene transfer, which will require cooperation between microbiologists and modellers.}, }
@article {pmid31408698, year = {2019}, author = {Schmidt, M}, title = {A metric space for semantic containment: Towards the implementation of genetic firewalls.}, journal = {Bio Systems}, volume = {185}, number = {}, pages = {104015}, doi = {10.1016/j.biosystems.2019.104015}, pmid = {31408698}, issn = {1872-8324}, mesh = {Amino Acids/*genetics ; Codon/*genetics ; DNA/*genetics ; Genetic Code/*genetics ; Genetic Engineering/methods ; *Mutation ; Semantics ; Synthetic Biology/*methods ; }, abstract = {Analysing or engineering the genetic code has mainly been considered as an approach to reduce or increase the mutational robustness of the genetic code, i.e. the error tolerance in DNA mutations, or to enable the incorporation of non-canonical amino acids. The approach of "semantic containment", however, is less interested in altering the mutational tolerance of the standard code, but to create synthetic alternative genetic codes that limit or all together impede horizontal gene transfer between a natural and genomically recoded organisms (GRO). A major claim or conjecture of semantic containment is: "the farther, the safer", meaning, the less similarity there is between two codes, the less chance of a horizontal gene transfer, and the stronger the genetic firewall. So far, no metrics were available to measure and quantify the "genetic distance" between different genetic codes. Such a metric, however, is iis paramount to allow the experimental testing and evaluation of the validity of semantic biocontainment for the first time. Here, we introduce a metric space to measure exactly the distance (dissimilarity) between different genetic codes, in order to provide a framework to evaluate the relation between distance and strength of a genetic firewall. Results are presented that incorporate bespoken metrics when producing alternative genetic codes according to predefined goals, specifications and limitations. Finally, as an outlook, implications and challenges for genetic firewall(s) are discussed for dual- and multi-code systems.}, }
@article {pmid31404169, year = {2019}, author = {Almeida, EL and Carrillo Rincón, AF and Jackson, SA and Dobson, ADW}, title = {Comparative Genomics of Marine Sponge-Derived Streptomyces spp. Isolates SM17 and SM18 With Their Closest Terrestrial Relatives Provides Novel Insights Into Environmental Niche Adaptations and Secondary Metabolite Biosynthesis Potential.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1713}, pmid = {31404169}, issn = {1664-302X}, abstract = {The emergence of antibiotic resistant microorganisms has led to an increased need for the discovery and development of novel antimicrobial compounds. Frequent rediscovery of the same natural products (NPs) continues to decrease the likelihood of the discovery of new compounds from soil bacteria. Thus, efforts have shifted toward investigating microorganisms and their secondary metabolite biosynthesis potential, from diverse niche environments, such as those isolated from marine sponges. Here we investigated at the genomic level two Streptomyces spp. strains, namely SM17 and SM18, isolated from the marine sponge Haliclona simulans, with previously reported antimicrobial activity against clinically relevant pathogens; using single molecule real-time (SMRT) sequencing. We performed a series of comparative genomic analyses on SM17 and SM18 with their closest terrestrial relatives, namely S. albus J1074 and S. pratensis ATCC 33331 respectively; in an effort to provide further insights into potential environmental niche adaptations (ENAs) of marine sponge-associated Streptomyces, and on how these adaptations might be linked to their secondary metabolite biosynthesis potential. Prediction of secondary metabolite biosynthetic gene clusters (smBGCs) indicated that, even though the marine isolates are closely related to their terrestrial counterparts at a genomic level; they potentially produce different compounds. SM17 and SM18 displayed a better ability to grow in high salinity medium when compared to their terrestrial counterparts, and further analysis of their genomes indicated that they possess a pool of 29 potential ENA genes that are absent in S. albus J1074 and S. pratensis ATCC 33331. This ENA gene pool included functional categories of genes that are likely to be related to niche adaptations and which could be grouped based on potential biological functions such as osmotic stress, defense; transcriptional regulation; symbiotic interactions; antimicrobial compound production and resistance; ABC transporters; together with horizontal gene transfer and defense-related features.}, }
@article {pmid31399023, year = {2019}, author = {Kruse, T and Ratnadevi, CM and Erikstad, HA and Birkeland, NK}, title = {Complete genome sequence analysis of the thermoacidophilic verrucomicrobial methanotroph "Candidatus Methylacidiphilum kamchatkense" strain Kam1 and comparison with its closest relatives.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {642}, pmid = {31399023}, issn = {1471-2164}, support = {261923//Norges Forskningsr&#xe5;d/ ; }, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/genetics ; Biomass ; Genome, Bacterial/genetics ; *Genomics ; Phylogeny ; Species Specificity ; Verrucomicrobia/*genetics/metabolism ; }, abstract = {BACKGROUND: The candidate genus "Methylacidiphilum" comprises thermoacidophilic aerobic methane oxidizers belonging to the Verrucomicrobia phylum. These are the first described non-proteobacterial aerobic methane oxidizers. The genes pmoCAB, encoding the particulate methane monooxygenase do not originate from horizontal gene transfer from proteobacteria. Instead, the "Ca. Methylacidiphilum" and the sister genus "Ca. Methylacidimicrobium" represent a novel and hitherto understudied evolutionary lineage of aerobic methane oxidizers. Obtaining and comparing the full genome sequences is an important step towards understanding the evolution and physiology of this novel group of organisms.<br><br>RESULTS: Here we present the closed genome of "Ca. Methylacidiphilum kamchatkense" strain Kam1 and a comparison with the genomes of its two closest relatives "Ca. Methylacidiphilum fumariolicum" strain SolV and "Ca. Methylacidiphilum infernorum" strain V4. The genome consists of a single 2,2 Mbp chromosome with 2119 predicted protein coding sequences. Genome analysis showed that the majority of the genes connected with metabolic traits described for one member of "Ca. Methylacidiphilum" is conserved between all three genomes. All three strains encode class I CRISPR-cas systems. The average nucleotide identity between "Ca. M. kamchatkense" strain Kam1 and strains SolV and V4 is &#x2264;95% showing that they should be regarded as separate species. Whole genome comparison revealed a high degree of synteny between the genomes of strains Kam1 and SolV. In contrast, comparison of the genomes of strains Kam1 and V4 revealed a number of rearrangements. There are large differences in the numbers of transposable elements found in the genomes of the three strains with 12, 37 and 80 transposable elements in the genomes of strains Kam1, V4 and SolV respectively. Genomic rearrangements and the activity of transposable elements explain much of the genomic differences between strains. For example, a type 1h uptake hydrogenase is conserved between strains Kam1 and SolV but seems to have been lost from strain V4 due to genomic rearrangements.<br><br>CONCLUSIONS: Comparing three closed genomes of "Ca. Methylacidiphilum" spp. has given new insights into the evolution of these organisms and revealed large differences in numbers of transposable elements between strains, the activity of these explains much of the genomic differences between strains.}, }
@article {pmid31398983, year = {2019}, author = {Polcarová, P and Hobzová, L and Kukla, R and Skořepa, P and Smetana, J and Šošovičková, R and Chlíbek, R}, title = {In-vivo interspecies transmission of carbapenemase KPC in a long-term treated female patient.}, journal = {Epidemiologie, mikrobiologie, imunologie : casopis Spolecnosti pro epidemiologii a mikrobiologii Ceske lekarske spolecnosti J.E. Purkyne}, volume = {68}, number = {2}, pages = {99-102}, pmid = {31398983}, issn = {1210-7913}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Bacteria/drug effects/enzymology ; *Bacterial Infections/microbiology ; Bacterial Proteins/genetics ; Coinfection/microbiology ; *Cross Infection/microbiology ; Drug Resistance, Bacterial/genetics ; Female ; Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; Plasmids/genetics ; *beta-Lactamases/genetics ; }, abstract = {The increasing incidence of multiresistant bacterial strains is currently a serious health concern. These pathogens are often the cause of nosocomial infections with limited treatment options and high fatality rates. A case report is presented of an uncommon detection of four different species (Citrobacter freundii, Klebsiella pneumoniae, Escherichia coli, and Morganella morganii) producing the same type of carbapenemase, KPC-2, in a female patient during her complicated long-term hospital stay. Resistance was probably spread to other species by horizontal transmission of plasmids carrying the blaKPC-2 genes. The implementation of strict anti-epidemic measures prevented further spread of these carbapenem-resistant bacteria.}, }
@article {pmid31398493, year = {2020}, author = {Gajamer, VR and Bhattacharjee, A and Paul, D and Ingti, B and Sarkar, A and Kapil, J and Singh, AK and Pradhan, N and Tiwari, HK}, title = {High prevalence of carbapenemase, AmpC β-lactamase and aminoglycoside resistance genes in extended-spectrum β-lactamase-positive uropathogens from Northern India.}, journal = {Journal of global antimicrobial resistance}, volume = {20}, number = {}, pages = {197-203}, doi = {10.1016/j.jgar.2019.07.029}, pmid = {31398493}, issn = {2213-7173}, mesh = {Aminoglycosides/*genetics/pharmacology ; Bacteria/*classification/drug effects/genetics ; Bacterial Proteins/*genetics ; Drug Resistance, Multiple, Bacterial ; Gene Transfer, Horizontal ; Humans ; India ; Microbial Sensitivity Tests ; Plasmids/genetics ; Prevalence ; Urinary Tract Infections/*microbiology ; Urine/microbiology ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: This study investigated the occurrence of extended-spectrum β-lactamase (ESBL) genes coexisting with carbapenemase, AmpC and aminoglycoside resistance gene in uropathogens in India.<br><br>METHODS: Antimicrobial susceptibility testing was performed by disk diffusion. Antimicrobial resistance genes were detected by multiplex PCR.<br><br>RESULTS: Of 1516 consecutive urine samples, 454 (29.9%) showed significant bacteriuria with a single micro-organism, predominantly Escherichia coli (n=343), followed by Klebsiella pneumoniae (n=92), Pseudomonas aeruginosa (n=10) and Proteus mirabilis (n=9). Among the uropathogens, 61 ESBL-producers were identified containing blaCTX-M-15 (n=32), blaCTX-M-15+blaOXA-2 (n=15), blaCTX-M-15+blaOXA-2+blaTEM-1 (n=6), blaOXA-2 (n=5), blaOXA-2+blaSHV-76 (n=1), blaTEM-1+blaSHV-76 (n=1) and blaTEM-1 (n=1). All ESBL genes were located on horizontally transferable plasmids of incompatibility types HI1, I1, FIA+FIB, FIA and Y. Among the 61 ESBL-producers, 59 harboured carbapenemase genes, including blaNDM-5 (n=48), blaNDM-5+blaOXA-48 (n=5), blaNDM-5+blaIMP (n=5) and blaNDM-5+blaIMP+blaVIM (n=1). ESBL-producing uropathogens also harboured 16S rRNA methylase genes, including rmtB (n=9), rmtA (n=4), rmtC (n=1) and armA (n=1). ESBL-positive isolates also contained AmpC genes, including blaCIT (n=8) and blaDHA-1 (n=1). Imipenem and gentamicin had the lowest resistance rates against the uropathogens.<br><br>CONCLUSION: This is the first report showing the high prevalence of carbapenemases in ESBL-positive isolates in this area. Regular surveillance for such resistance mechanisms will be useful for health personnel to treat infections by these multidrug-resistant pathogens.}, }
@article {pmid31398339, year = {2019}, author = {Arevalo, P and VanInsberghe, D and Elsherbini, J and Gore, J and Polz, MF}, title = {A Reverse Ecology Approach Based on a Biological Definition of Microbial Populations.}, journal = {Cell}, volume = {178}, number = {4}, pages = {820-834.e14}, doi = {10.1016/j.cell.2019.06.033}, pmid = {31398339}, issn = {1097-4172}, mesh = {Adaptation, Physiological/genetics ; Alleles ; Clostridiales/*genetics ; Colitis, Ulcerative/microbiology ; Crohn Disease/microbiology ; *Gene Flow ; Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; Microbiota/*genetics ; Models, Genetic ; Mutation Rate ; Phylogeny ; Polymorphism, Single Nucleotide ; Prochlorococcus/genetics ; Sulfolobus/genetics ; Vibrio/genetics ; }, abstract = {Delineating ecologically meaningful populations among microbes is important for identifying their roles in environmental and host-associated microbiomes. Here, we introduce a metric of recent gene flow, which when applied to co-existing microbes, identifies congruent genetic and ecological units separated by strong gene flow discontinuities from their next of kin. We then develop a pipeline to identify genome regions within these units that show differential adaptation and allow mapping of populations onto environmental variables or host associations. Using this reverse ecology approach, we show that the human commensal bacterium Ruminococcus gnavus breaks up into sharply delineated populations that show different associations with health and disease. Defining populations by recent gene flow in this way will facilitate the analysis of bacterial and archaeal genomes using ecological and evolutionary theory developed for plants and animals, thus allowing for testing unifying principles across all biology.}, }
@article {pmid31397624, year = {2020}, author = {Khalid, S and Ahmad, N and Ali, SM and Khan, AU}, title = {Outbreak of Efficiently Transferred Carbapenem-Resistant blaNDM-Producing Gram-Negative Bacilli Isolated from Neonatal Intensive Care Unit of an Indian Hospital.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {26}, number = {3}, pages = {284-289}, doi = {10.1089/mdr.2019.0092}, pmid = {31397624}, issn = {1931-8448}, mesh = {Acinetobacter/drug effects/enzymology/genetics/isolation &amp; purification ; Acinetobacter baumannii/drug effects/enzymology/genetics/isolation &amp; purification ; Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; *Disease Outbreaks ; Drug Resistance, Multiple, Bacterial/*genetics ; Enterobacter aerogenes/drug effects/enzymology/genetics/isolation &amp; purification ; Enterobacter cloacae/drug effects/enzymology/genetics/isolation &amp; purification ; Enterobacteriaceae/drug effects/enzymology/genetics/isolation &amp; purification ; Escherichia coli/drug effects/enzymology/genetics/isolation &amp; purification ; Gene Expression ; *Gene Transfer, Horizontal ; Gram-Negative Bacterial Infections/drug therapy/*epidemiology/microbiology/*transmission ; Humans ; India/epidemiology ; Infant, Newborn ; Intensive Care Units, Neonatal ; Klebsiella pneumoniae/drug effects/enzymology/genetics/isolation &amp; purification ; Microbial Sensitivity Tests ; Plasmids ; beta-Lactamases/*genetics ; }, abstract = {The emergence of blaNDM particularly in Gram-negative bacteria is a burden on the health care system in developing countries. Hence, this study was initiated to screen New Delhi Metallo-β-lactamase (NDM)-producing Gram-negative bacterial strains from neonatal intensive care unit (NICU) of an Indian Hospital. A total of 18 blaNDM-producing isolates were detected in the present study. Out of 18 blaNDM variant isolates, 6 were Klebsiella pneumoniae, 4 Escherichia coli, 2 Enterobacter aerogenes, 1 Acinetobacter lwoffii, 1 Enterobacter cloacae, 3 Acinobacter baumannii, and 1 Cedecea davisae from NICU, showing resistance against all antibiotics, except colistin and polymixin. The transferability of resistance determinants was tested by conjugation. Transfer of blaNDM-producing strains was successful in all 18 strains. In the case of transconjugants, the minimum inhibitory concentration values were found to decrease. The blaNDM-producing isolates contained detectable plasmids of size 66, 38, and 6 kb. Plasmi/d-based replicon typing revealed the incompatibility types Inc (A/C, FIIA, FIC, K, F, W, FIA, P, X, FIB, B/O) in blaNDM-carrying isolates. This study revealed the outbreak of multiple variants of blaNDM (13 NDM-1, 4 NDM-5, and 1 NDM-7). Moreover, other resistance markers, viz. blaOXA-1, blaCMY-1, blaVIM-1, and blaSHV-1 coassociated with blaNDM were also found. In this study, we reported NDM-producing C. davisae as a first report to the best of our knowledge. This study is an attempt to reveal the dissemination of blaNDM isolated from neonates in NICU and their efficient transferability among Gram-negative bacilli through horizontal gene transfer.}, }
@article {pmid31396996, year = {2019}, author = {Liu, Y and Zeng, Y and Huang, Y and Gu, L and Wang, S and Li, C and Morrison, DA and Deng, H and Zhang, JR}, title = {HtrA-mediated selective degradation of DNA uptake apparatus accelerates termination of pneumococcal transformation.}, journal = {Molecular microbiology}, volume = {112}, number = {4}, pages = {1308-1325}, doi = {10.1111/mmi.14364}, pmid = {31396996}, issn = {1365-2958}, mesh = {Bacterial Proteins/genetics/metabolism ; DNA/metabolism ; Gene Transfer, Horizontal ; Proteomics ; Serine Endopeptidases/genetics/*metabolism ; Serine Proteases/metabolism ; Streptococcus pneumoniae/genetics/metabolism ; Transcriptome/genetics ; Transformation, Bacterial/*genetics ; Transformation, Genetic/genetics ; Virulence/genetics ; }, abstract = {Natural transformation mediates horizontal gene transfer, and thereby promotes exchange of antibiotic resistance and virulence traits among bacteria. Streptococcus pneumoniae, the first known transformable bacterium, rapidly activates and then terminates the transformation state, but it is unclear how the bacterium accomplishes this rapid turn-around at the protein level. This work determined the transcriptomic and proteomic dynamics during the window of pneumococcal transformation. RNA sequencing revealed a nearly uniform temporal pattern of rapid transcriptional activation and subsequent shutdown for the genes encoding transformation proteins. In contrast, mass spectrometry analysis showed that the majority of transformation proteins were substantially preserved beyond the window of transformation. However, ComEA and ComEC, major components of the DNA uptake apparatus for transformation, were completely degraded at the end of transformation. Further mutagenesis screening revealed that the membrane-associated serine protease HtrA mediates selective degradation of ComEA and ComEC, strongly suggesting that breakdown of the DNA uptake apparatus by HtrA is an important mechanism for termination of pneumococcal transformation. Finally, our mutagenesis analysis showed that HtrA inhibits natural transformation of Streptococcus mitis and Streptococcus gordonii. Together, this work has revealed that HtrA regulates the level and duration of natural transformation in multiple streptococcal species.}, }
@article {pmid31396256, year = {2019}, author = {Tan, M and Long, H and Liao, B and Cao, Z and Yuan, D and Tian, G and Zhuang, J and Yang, J}, title = {QS-Net: Reconstructing Phylogenetic Networks Based on Quartet and Sextet.}, journal = {Frontiers in genetics}, volume = {10}, number = {}, pages = {607}, pmid = {31396256}, issn = {1664-8021}, abstract = {Phylogenetic networks are used to estimate evolutionary relationships among biological entities or taxa involving reticulate events such as horizontal gene transfer, hybridization, recombination, and reassortment. In the past decade, many phylogenetic tree and network reconstruction methods have been proposed. Despite that they are highly accurate in reconstructing simple to moderate complex reticulate events, the performance decreases when several reticulate events are present simultaneously. In this paper, we proposed QS-Net, a phylogenetic network reconstruction method taking advantage of information on the relationship among six taxa. To evaluate the performance of QS-Net, we conducted experiments on three artificial sequence data simulated from an evolutionary tree, an evolutionary network involving three reticulate events, and a complex evolutionary network involving five reticulate events. Comparison with popular phylogenetic methods including Neighbor-Joining, Split-Decomposition, Neighbor-Net, and Quartet-Net suggests that QS-Net is comparable with other methods in reconstructing tree-like evolutionary histories, while it outperforms them in reconstructing reticulate events. In addition, we also applied QS-Net in real data including a bacterial taxonomy data consisting of 36 bacterial species and the whole genome sequences of 22 H7N9 influenza A viruses. The results indicate that QS-Net is capable of inferring commonly believed bacterial taxonomy and influenza evolution as well as identifying novel reticulate events. The software QS-Net is publically available at https://github.com/Tmyiri/QS-Net.}, }
@article {pmid31396099, year = {2019}, author = {Cambier, S and Ginis, O and Moreau, SJM and Gayral, P and Hearn, J and Stone, GN and Giron, D and Huguet, E and Drezen, JM}, title = {Gall Wasp Transcriptomes Unravel Potential Effectors Involved in Molecular Dialogues With Oak and Rose.}, journal = {Frontiers in physiology}, volume = {10}, number = {}, pages = {926}, pmid = {31396099}, issn = {1664-042X}, abstract = {To gain insight into wasp factors that might be involved in the initial induction of galls on woody plants, we performed high throughput (454) transcriptome analysis of ovaries and venom glands of two cynipid gall wasps, Biorhiza pallida and Diplolepis rosae, inducing galls on oak and rose, respectively. De novo assembled and annotated contigs were compared to sequences from phylogenetically related parasitoid wasps. The relative expression levels of contigs were estimated to identify the most expressed gene sequences in each tissue. We identify for the first time a set of maternally expressed gall wasp proteins potentially involved in the interaction with the plant. Some genes highly expressed in venom glands and ovaries may act to suppress early plant defense signaling. We also identify gall wasp cellulases that could be involved in observed local lysis of plant tissue following oviposition, and which may have been acquired from bacteria by horizontal gene transfer. We find no evidence of virus-related gene expression, in contrast to many non-cynipid parasitoid wasps. By exploring gall wasp effectors, this study is a first step toward understanding the molecular mechanisms underlying cynipid gall induction in woody plants, and the recent sequencing of oak and rose genomes will enable study of plant responses to these factors.}, }
@article {pmid31394466, year = {2019}, author = {Slipko, K and Reif, D and Wögerbauer, M and Hufnagl, P and Krampe, J and Kreuzinger, N}, title = {Removal of extracellular free DNA and antibiotic resistance genes from water and wastewater by membranes ranging from microfiltration to reverse osmosis.}, journal = {Water research}, volume = {164}, number = {}, pages = {114916}, doi = {10.1016/j.watres.2019.114916}, pmid = {31394466}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents ; DNA ; Drug Resistance, Microbial ; Genes, Bacterial ; Humans ; Osmosis ; *Wastewater ; Water ; *Water Purification ; }, abstract = {Free DNA in the effluent from wastewater treatment plants has recently been observed to contain antibiotic resistance genes (ARGs), which may contribute to the spread of antibiotic resistance via horizontal gene transfer in the receiving environment. Technical membrane systems applied in wastewater and drinking water treatment are situated at central nodes between the environmental and human related aspects of the "One Health" approach and are considered as effective barriers for antibiotic resistant bacteria. However, they are not evaluated for their permeability for ARGs encoded in free DNA, which may result, for example, from the release of free DNA after bacterial die-off during particular treatment processes. This study examined the potential and principle mechanisms for the removal of free DNA containing ARGs by technical membrane filtration. Ten different membranes, varied by the charge (neutral and negative) and the molecular weight cut off (in a range from microfiltration to reverse osmosis), were tested for the removal of free DNA (pure supercoiled and linearized plasmids encoding for ARGs and free linear chromosomal DNA with a broader fragment size spectrum) in different water matrices (distilled water and wastewater treatment plant effluent). Our results showed that membranes with a molecular weight cut off smaller than 5000 Da (ultrafiltration, nanofiltration and reverse osmosis) could retain ≥99.80% of free DNA, both pure plasmid and linear fragments of different sizes, whereas microfiltration commonly applied in wastewater treatment showed no retention. Size exclusion was identified as the main retention mechanism. Additionally, surface charging of the membrane and adsorption of free DNA on the membrane surface played a key role in prevention of free DNA permeation. Currently, majority of the applied membranes is negatively charged to prevent adsorption of natural organic matter. In our study, negatively charged membranes showed lower retention of free DNA compared to neutral ones due to repulsion of free DNA molecules, reduced adsorption and decreased blockage of the membrane surface. Therefore, the applied membrane may not be as an effective barrier for ARGs encoded in free DNA, as it would be predicted based only on the molecular weight cut off. Thus, careful considerations of membrane's specifications (molecular weight cut-off and charge) are required during design of a filtration system for retention of free DNA.}, }
@article {pmid31387908, year = {2019}, author = {LaBrie, SD and Dimond, ZE and Harrison, KS and Baid, S and Wickstrum, J and Suchland, RJ and Hefty, PS}, title = {Transposon Mutagenesis in Chlamydia trachomatis Identifies CT339 as a ComEC Homolog Important for DNA Uptake and Lateral Gene Transfer.}, journal = {mBio}, volume = {10}, number = {4}, pages = {}, pmid = {31387908}, issn = {2150-7511}, support = {P20 GM103638/GM/NIGMS NIH HHS/United States ; P20 GM113117/GM/NIGMS NIH HHS/United States ; R01 AI126785/AI/NIAID NIH HHS/United States ; R21 AI125929/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacterial Proteins/genetics/*metabolism ; Chlamydia Infections/*microbiology ; Chlamydia trachomatis/*genetics/*metabolism ; DNA Transposable Elements ; DNA, Bacterial/*genetics/metabolism ; Female ; *Gene Transfer, Horizontal ; Humans ; Mice ; Mice, Inbred C57BL ; Mutagenesis, Insertional ; Mutation ; }, abstract = {Transposon mutagenesis is a widely applied and powerful genetic tool for the discovery of genes associated with selected phenotypes. Chlamydia trachomatis is a clinically significant, obligate intracellular bacterium for which many conventional genetic tools and capabilities have been developed only recently. This report describes the successful development and application of a Himar transposon mutagenesis system for generating single-insertion mutant clones of C. trachomatis This system was used to generate a pool of 105 transposon mutant clones that included insertions in genes encoding flavin adenine dinucleotide (FAD)-dependent monooxygenase (C. trachomatis148 [ct148]), deubiquitinase (ct868), and competence-associated (ct339) proteins. A subset of Tn mutant clones was evaluated for growth differences under cell culture conditions, revealing that most phenocopied the parental strain; however, some strains displayed subtle and yet significant differences in infectious progeny production and inclusion sizes. Bacterial burden studies in mice also supported the idea that a FAD-dependent monooxygenase (ct148) and a deubiquitinase (ct868) were important for these infections. The ct339 gene encodes a hypothetical protein with limited sequence similarity to the DNA-uptake protein ComEC. A transposon insertion in ct339 rendered the mutant incapable of DNA acquisition during recombination experiments. This observation, along with in situ structural analysis, supports the idea that this protein is playing a role in the fundamental process of lateral gene transfer similar to that of ComEC. In all, the development of the Himar transposon system for Chlamydia provides an effective genetic tool for further discovery of genes that are important for basic biology and pathogenesis aspects.IMPORTANCEChlamydia trachomatis infections have an immense impact on public health; however, understanding the basic biology and pathogenesis of this organism has been stalled by the limited repertoire of genetic tools. This report describes the successful adaptation of an important tool that has been lacking in Chlamydia studies: transposon mutagenesis. This advance enabled the generation of 105 insertional mutants, demonstrating that numerous gene products are not essential for in vitro growth. Mammalian infections using these mutants revealed that several gene products are important for infections in vivo Moreover, this tool enabled the investigation and discovery of a gene critical for lateral gene transfer; a process fundamental to the evolution of bacteria and likely for Chlamydia as well. The development of transposon mutagenesis for Chlamydia has broad impact for the field and for the discovery of genes associated with selected phenotypes, providing an additional avenue for the discovery of molecular mechanisms used for pathogenesis and for a more thorough understanding of this important pathogen.}, }
@article {pmid31387857, year = {2019}, author = {Jani, M and Azad, RK}, title = {IslandCafe: Compositional Anomaly and Feature Enrichment Assessment for Delineation of Genomic Islands.}, journal = {G3 (Bethesda, Md.)}, volume = {9}, number = {10}, pages = {3273-3285}, pmid = {31387857}, issn = {2160-1836}, mesh = {Algorithms ; Bacteria/*genetics ; Computational Biology/*methods ; DNA Transposable Elements ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genomic Islands ; Genomics/*methods ; Reproducibility of Results ; }, abstract = {One of the evolutionary forces driving bacterial genome evolution is the acquisition of clusters of genes through horizontal gene transfer (HGT). These genomic islands may confer adaptive advantages to the recipient bacteria, such as, the ability to thwart antibiotics, become virulent or hypervirulent, or acquire novel metabolic traits. Methods for detecting genomic islands either search for markers or features typical of islands or examine anomaly in oligonucleotide composition against the genome background. The former tends to underestimate, missing islands that have the markers either lost or degraded, while the latter tends to overestimate, due to their inability to discriminate compositional atypicality arising because of HGT from those that are a consequence of other biological factors. We propose here a framework that exploits the strengths of both these approaches while bypassing the pitfalls of either. Genomic islands lacking markers are identified by their association with genomic islands with markers. This was made possible by performing marker enrichment and phyletic pattern analyses within an integrated framework of recursive segmentation and clustering. The proposed method, IslandCafe, compared favorably with frequently used methods for genomic island detection on synthetic test datasets and on a test-set of known islands from 15 well-characterized bacterial species. Furthermore, IslandCafe identified novel islands with imprints of likely horizontal acquisition.}, }
@article {pmid31385413, year = {2019}, author = {Mourkas, E and Florez-Cuadrado, D and Pascoe, B and Calland, JK and Bayliss, SC and Mageiros, L and Méric, G and Hitchings, MD and Quesada, A and Porrero, C and Ugarte-Ruiz, M and Gutiérrez-Fernández, J and Domínguez, L and Sheppard, SK}, title = {Gene pool transmission of multidrug resistance among Campylobacter from livestock, sewage and human disease.}, journal = {Environmental microbiology}, volume = {21}, number = {12}, pages = {4597-4613}, pmid = {31385413}, issn = {1462-2920}, support = {FS246004//Food Standards Agency/International ; MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; BB/I02464X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BES-2013-065003//Spanish Ministry of Economy and Competitiveness/International ; /WT_/Wellcome Trust/United Kingdom ; 088786/C/09/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Campylobacter Infections/microbiology ; Campylobacter coli/drug effects/*genetics ; Campylobacter jejuni/*genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; *Gene Pool ; *Gene Transfer, Horizontal ; Humans ; Livestock/*microbiology ; Microbial Sensitivity Tests ; Poultry/microbiology ; Sewage/*microbiology ; Spain ; }, abstract = {The use of antimicrobials in human and veterinary medicine has coincided with a rise in antimicrobial resistance (AMR) in the food-borne pathogens Campylobacter jejuni and Campylobacter coli. Faecal contamination from the main reservoir hosts (livestock, especially poultry) is the principal route of human infection but little is known about the spread of AMR among source and sink populations. In particular, questions remain about how Campylobacter resistomes interact between species and hosts, and the potential role of sewage as a conduit for the spread of AMR. Here, we investigate the genomic variation associated with AMR in 168 C. jejuni and 92 C. coli strains isolated from humans, livestock and urban effluents in Spain. AMR was tested in vitro and isolate genomes were sequenced and screened for putative AMR genes and alleles. Genes associated with resistance to multiple drug classes were observed in both species and were commonly present in multidrug-resistant genomic islands (GIs), often located on plasmids or mobile elements. In many cases, these loci had alleles that were shared among C. jejuni and C. coli consistent with horizontal transfer. Our results suggest that specific antibiotic resistance genes have spread among Campylobacter isolated from humans, animals and the environment.}, }
@article {pmid31384000, year = {2019}, author = {Džunková, M and Low, SJ and Daly, JN and Deng, L and Rinke, C and Hugenholtz, P}, title = {Defining the human gut host-phage network through single-cell viral tagging.}, journal = {Nature microbiology}, volume = {4}, number = {12}, pages = {2192-2203}, pmid = {31384000}, issn = {2058-5276}, mesh = {Bacteria/genetics/virology ; Bacteriophages/genetics/isolation &amp; purification/*physiology ; Feces/microbiology ; Gastrointestinal Microbiome/genetics/*physiology ; Gene Transfer, Horizontal ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; Host Microbial Interactions/genetics/*physiology ; Humans ; Metagenome ; Microbial Interactions/genetics/*physiology ; Sequence Analysis, DNA ; Species Specificity ; Viruses/genetics ; }, abstract = {Viral discovery is accelerating at an unprecedented rate due to continuing advances in culture-independent sequence-based analyses. One important facet of this discovery is identification of the hosts of these recently characterized uncultured viruses. To this end, we have adapted the viral tagging approach, which bypasses the need for culture-based methods to identify host-phage pairings. Fluorescently labelled anonymous virions adsorb to unlabelled anonymous bacterial host cells, which are then individually sorted as host-phage pairs, followed by genome amplification and high-throughput sequencing to establish the identities of both the host and the attached virus(es). We demonstrate single-cell viral tagging using the faecal microbiome, including cross-tagging of viruses and bacteria between human subjects. A total of 363 unique host-phage pairings were predicted, most of which were subject-specific and involved previously uncharacterized viruses despite the majority of their bacterial hosts having known taxonomy. One-fifth of these pairs were confirmed by multiple individual tagged cells. Viruses targeting more than one bacterial species were conspicuously absent in the host-phage network, suggesting that phages are not major vectors of inter-species horizontal gene transfer in the human gut. A high level of cross-reactivity between phages and bacteria from different subjects was noted despite subject-specific viral profiles, which has implications for faecal microbiota transplant therapy.}, }
@article {pmid31383764, year = {2019}, author = {Zborowsky, S and Lindell, D}, title = {Resistance in marine cyanobacteria differs against specialist and generalist cyanophages.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {34}, pages = {16899-16908}, pmid = {31383764}, issn = {1091-6490}, mesh = {*Aquatic Organisms/growth &amp; development/virology ; Bacteriophages/*physiology ; *Models, Biological ; *Prochlorococcus/growth &amp; development/virology ; *Synechococcus/growth &amp; development/virology ; }, abstract = {Long-term coexistence between unicellular cyanobacteria and their lytic viruses (cyanophages) in the oceans is thought to be due to the presence of sensitive cells in which cyanophages reproduce, ultimately killing the cell, while other cyanobacteria survive due to resistance to infection. Here, we investigated resistance in marine cyanobacteria from the genera Synechococcus and Prochlorococcus and compared modes of resistance against specialist and generalist cyanophages belonging to the T7-like and T4-like cyanophage families. Resistance was extracellular in most interactions against specialist cyanophages irrespective of the phage family, preventing entry into the cell. In contrast, resistance was intracellular in practically all interactions against generalist T4-like cyanophages. The stage of intracellular arrest was interaction-specific, halting at various stages of the infection cycle. Incomplete infection cycles proceeded to various degrees of phage genome transcription and translation as well as phage genome replication in numerous interactions. In a particularly intriguing case, intracellular capsid assembly was observed, but the phage genome was not packaged. The cyanobacteria survived the encounter despite late-stage infection and partial genome degradation. We hypothesize that this is tolerated due to genome polyploidy, which we found for certain strains of both Synechococcus and Prochlorococcus Our findings unveil a heavy cost of promiscuous entry of generalist phages into nonhost cells that is rarely paid by specialist phages and suggests the presence of unknown mechanisms of intracellular resistance in the marine unicellular cyanobacteria. Furthermore, these findings indicate that the range for virus-mediated horizontal gene transfer extends beyond hosts to nonhost cyanobacterial cells.}, }
@article {pmid31379767, year = {2019}, author = {He, Y and Wang, S and Zhang, J and Zhang, X and Sun, F and He, B and Liu, X}, title = {Integrative and Conjugative Elements-Positive Vibrio parahaemolyticus Isolated From Aquaculture Shrimp in Jiangsu, China.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1574}, pmid = {31379767}, issn = {1664-302X}, abstract = {The development of multidrug- and toxin-resistant bacteria as a result of increasing industrialization and sustained and intense antimicrobial use in aquaculture results in human health problems through increased incidence of food-borne illnesses. Integrative and conjugative elements (ICEs) are self-transmissible mobile genetic elements that allow bacteria to acquire complex new traits through horizontal gene transfer and encode a wide variety of genetic information, including resistance to antibiotics and heavy metals; however, there is a lack of studies of ICEs of environmental origin in Asia. Here, we determined the prevalence, genotypes, heavy metal resistance and antimicrobial susceptibility of 997 presumptive strains of Vibrio parahaemolyticus (tlh [+], tdh [-]), a Gram-negative bacterium that causes gastrointestinal illness in humans, isolated from four species of aquaculture shrimp in Jiangsu, China. We found that 59 of the 997 isolates (5.9%) were ICE-positive, and of these, 9 isolates tested positive for all resistance genes. BLAST analysis showed that similarity for the eight strains to V. parahaemolyticus was 99%. Tracing the V. parahaemolyticus genotypes, showed no significant relevance of genotype among the antimicrobial resistance strains bearing the ICEs or not. Thus, in aquaculture, ICEs are not the major transmission mediators of resistance to antibiotics or heavy metals. We suggest future research to elucidate mechanisms that drive transmission of resistance determinants in V. parahaemolyticus.}, }
@article {pmid31377583, year = {2019}, author = {Cerqueira, F and Matamoros, V and Bayona, JM and Berendonk, TU and Elsinga, G and Hornstra, LM and Piña, B}, title = {Antibiotic resistance gene distribution in agricultural fields and crops. A soil-to-food analysis.}, journal = {Environmental research}, volume = {177}, number = {}, pages = {108608}, doi = {10.1016/j.envres.2019.108608}, pmid = {31377583}, issn = {1096-0953}, mesh = {Agriculture ; Anti-Bacterial Agents ; Drug Resistance, Microbial/*genetics ; Food Analysis ; *Genes, Bacterial ; RNA, Ribosomal, 16S ; Soil ; Soil Microbiology ; Spain ; }, abstract = {Despite the social concern about the generalization of antibiotic resistance hotspots worldwide, very little is known about the contribution of different potential sources to the global risk. Here we present a quantitative analysis of the distribution of Antibiotic Resistance Genes (ARGs) in soil, rhizospheric soil, roots, leaves and beans in tomato, lettuce and broad beans crops (165 samples in total), grown in nine commercial plots distributed in four geographical zones in the vicinity of Barcelona (North East Spain). We also analyzed five soil samples from a nearby forest, with no record of agricultural activities. DNA samples were analyzed for their content in the ARGs sul1, tetM, qnrS1, blaCTX-M-32, blaOXA-58, mecA, and blaTEM, plus the integron intI1, using qPCR methods. In addition, soil microbiomes from the different plots were analyzed by amplicon-targeted 16S rRNA gene sequencing. Our data show a decreasing gradient of ARG loads from soil to fruits and beans, the latter showing only from 0.1 to 0.01% of the abundance values in soil. The type of crop was the main determinant for both ARG distribution and microbiome composition among the different plots, with minor contributions of geographic location and irrigation water source. We propose that soil amendment and/or fertilization, more than irrigation water, are the main drivers of ARG loads on the edible parts of the crop, and that they should therefore be specifically controlled.}, }
@article {pmid31377529, year = {2019}, author = {Marano, RBM and Zolti, A and Jurkevitch, E and Cytryn, E}, title = {Antibiotic resistance and class 1 integron gene dynamics along effluent, reclaimed wastewater irrigated soil, crop continua: elucidating potential risks and ecological constraints.}, journal = {Water research}, volume = {164}, number = {}, pages = {114906}, doi = {10.1016/j.watres.2019.114906}, pmid = {31377529}, issn = {1879-2448}, mesh = {Agricultural Irrigation ; Drug Resistance, Microbial ; Genes, Bacterial ; *Integrons ; Soil ; Waste Disposal, Fluid ; *Wastewater ; }, abstract = {Reuse of municipal wastewater is a growing global trend, but currently there is lack of consensus regarding the potential dissemination of antibiotic resistance elements by treated wastewater irrigation. We tracked intI1, a proxy for anthropogenic pollution, and an assemblage of antibiotic resistance genes associated with mobile elements and/or wastewater (blaGES, blaOXA2, blaOXA10, blaTEM, blaCTX-M-32 and qnrS) in treated wastewater effluents, effluent stabilization reservoirs, and along irrigation water-soil-crop continua in experimental lysimeters and large-scale commercial fields. While several of the targeted antibiotic resistance genes were profuse in effluents, there was almost no correlation between gene abundance in irrigation water and those detected in soil, and no evidence of systematic gene transfer to irrigated soil or crops. In contrast, soil intI1 abundance correlated strongly to irrigation water levels in lysimeters and sandy field soils, but this was not the case for clay-rich soils or for most of the analyzed crops, suggesting that intI1 may not always be a reliable marker for tracking the impact of treated wastewater irrigation. We hypothesize that "ecological boundaries" expedited by biotic and abiotic factors constrain dissemination of antibiotic resistance elements, and assert that a more holistic perception of these factors is crucial for understanding and managing antibiotic resistance dissemination.}, }
@article {pmid31377195, year = {2019}, author = {Rawlings, ND and Bateman, A}, title = {Origins of peptidases.}, journal = {Biochimie}, volume = {166}, number = {}, pages = {4-18}, pmid = {31377195}, issn = {1638-6183}, mesh = {Animals ; Archaea/*enzymology ; Bacteria/*enzymology ; Databases, Protein ; Eukaryota/*enzymology ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Peptide Hydrolases/classification/genetics ; Phylogeny ; Viruses/*enzymology ; }, abstract = {The distribution of all peptidase homologues across all phyla of organisms was analysed to determine within which kingdom each of the 271 families originated. No family was found to be ubiquitous and even peptidases thought to be essential for life, such as signal peptidase and methionyl aminopeptides are missing from some clades. There are 33 peptidase families common to archaea, bacteria and eukaryotes and are assumed to have originated in the last universal common ancestor (LUCA). These include peptidases with different catalytic types, exo- and endopeptidases, peptidases with different tertiary structures and peptidases from different families but with similar structures. This implies that the different catalytic types and structures pre-date LUCA. Other families have had their origins in the ancestors of viruses, archaea, bacteria, fungi, plants and animals, and a number of families have had their origins in the ancestors of particular phyla. The evolution of peptidases is compared to recent hypotheses about the evolution of organisms.}, }
@article {pmid31375780, year = {2019}, author = {Miyazaki, K and Tomariguchi, N}, title = {Occurrence of randomly recombined functional 16S rRNA genes in Thermus thermophilus suggests genetic interoperability and promiscuity of bacterial 16S rRNAs.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {11233}, pmid = {31375780}, issn = {2045-2322}, mesh = {Adaptation, Physiological ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/genetics ; RNA, Ribosomal, 16S/*genetics ; Thermus thermophilus/*genetics ; }, abstract = {Based on the structural complexity of ribosomes, 16S rRNA genes are considered species-specific and hence used for bacterial phylogenetic analysis. However, a growing number of reports suggest the occurrence of horizontal gene transfer, raising genealogical questions. Here we show the genetic interoperability and promiscuity of 16S rRNA in the ribosomes of an extremely thermophilic bacterium, Thermus thermophilus. The gene in this thermophile was systematically replaced with a diverse array of heterologous genes, resulting in the discovery of various genes that supported growth, some of which were from different phyla. Moreover, numerous functional chimeras were spontaneously generated. Remarkably, cold-adapted mutants were obtained carrying chimeric or full-length heterologous genes, indicating that horizontal gene transfer promoted adaptive evolution. The ribosome may well be understood as a patchworked supramolecule comprising patchworked components. We here propose the "random patch model" for ribosomal evolution.}, }
@article {pmid31375493, year = {2019}, author = {Schwendener, S and Nigg, A and Collaud, A and Overesch, G and Kittl, S and Phumthanakorn, N and Perreten, V}, title = {Typing of mecD Islands in Genetically Diverse Methicillin-Resistant Macrococcus caseolyticus Strains from Cattle.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {19}, pages = {}, pmid = {31375493}, issn = {1098-5336}, mesh = {Animals ; Bacterial Typing Techniques ; Cattle ; Chromosomes, Bacterial/genetics ; England ; Female ; Genes, Bacterial ; *Genetic Variation ; *Genomic Islands ; Methicillin Resistance/*genetics ; Microbial Sensitivity Tests ; Milk/microbiology ; Multilocus Sequence Typing ; Phylogeny ; Staphylococcaceae/*drug effects/*genetics ; Wales ; }, abstract = {Macrococcus caseolyticus belongs to the normal bacterial flora of dairy cows and does not usually cause disease. However, methicillin-resistant M. caseolyticus strains were isolated from bovine mastitis milk. These bacteria had acquired a chromosomal island (McRI mecD -1 or McRI mecD -2) carrying the methicillin resistance gene mecD To gain insight into the distribution of McRI mecD types in M. caseolyticus from cattle, 33 mecD-containing strains from Switzerland were characterized using molecular techniques, including multilocus sequence typing, antibiotic resistance gene identification, and PCR-based McRI mecD typing. In addition, the same genetic features were analyzed in 27 mecD-containing M. caseolyticus strains isolated from bovine bulk milk in England/Wales using publicly available whole-genome sequences. The 60 strains belonged to 24 different sequence types (STs), with strains belonging to ST5, ST6, ST21, and ST26 observed in both Switzerland and England/Wales. McRI mecD -1 was found in different STs from Switzerland (n = 19) and England/Wales (n = 4). McRI mecD -2 was only found in 7 strains from Switzerland, all of which belonged to ST6. A novel island, McRI mecD -3, which contains a complete mecD operon (mecD-mecR1m-mecIm [where the subscript m indicates Macrococcus]) combined with the left part of McRI mecD -2 and the right part of McRI mecD -1, was found in heterogeneous STs from both collections (Switzerland, n = 7; England/Wales, n = 21). Two strains from England/Wales carried a truncated McRI mecD -3. Phylogenetic analyses revealed no clustering of strains according to geographical origin or carriage of McRI mecD -1 and McRI mecD -3. Circular excisions were also detected for McRI mecD -1 and McRI mecD -3 by PCR. The analyses indicate that these islands are mobile and may spread by horizontal gene transfer between genetically diverse M. caseolyticus strains.IMPORTANCE Since its first description in 2017, the methicillin resistance gene mecD has been detected in M. caseolyticus strains from different cattle sources and countries. Our study provides new insights into the molecular diversity of mecD-carrying M. caseolyticus strains by using two approaches to characterize mecD elements: (i) multiplex PCR for molecular typing of McRI mecD and (ii) read mapping against reference sequences to identify McRI mecD types in silico In combination with multilocus sequence typing, this approach can be used for molecular characterization and surveillance of M. caseolyticus carrying mecD.}, }
@article {pmid31375487, year = {2019}, author = {Li, Z and Schottroff, F and Simpson, DJ and Gänzle, MG}, title = {The Copy Number of the spoVA[2mob] Operon Determines Pressure Resistance of Bacillus Endospores.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {19}, pages = {}, pmid = {31375487}, issn = {1098-5336}, mesh = {Bacillus/*genetics ; Bacterial Proteins/genetics ; *DNA Copy Number Variations ; Food Microbiology/methods ; Genome, Bacterial ; *Operon ; Polymerase Chain Reaction ; *Pressure ; Spores, Bacterial/*genetics/growth &amp; development ; Stress, Physiological ; Whole Genome Sequencing ; }, abstract = {The spoVA[2mob] operon confers heat resistance to Bacillus spp., and the resistance correlates to the copy number of the operon. Bacillus endospores also exhibit a strong variation in resistance to pressure, but the underlying mechanisms of endospore resistance to pressure are not fully understood. We determined the effects of multiple spoVA[2mob] operons on high-pressure resistance in Bacillus endospores. The copy numbers of the spoVA[2mob] operon in 17 strains of Bacillus subtilis, Bacillus amyloliquefaciens, Bacillus cereus, Bacillus velezensis, and Bacillus pumilus were determined via droplet digital PCR (ddPCR) and genome sequencing. These strains contained between 0 and 3 copies of the spoVA[2mob] operon; the quantification of the gene copy number by ddPCR was as accurate as whole-genome sequencing. We further tested the pressure resistance of 17 Bacillus endospores at 600 MPa and 80°C. Strains with one or no spoVA[2mob] operon had significantly lower pressure resistance than strains with two or three copies of the operons (P < 0.001), indicating that redundant spoVA[2mob] operons in Bacillus contributed to higher pressure resistance of endospores. The copy number of the spoVA[2mob] operon was not related to the dipicolinic acid (DPA) content of endospores. Overall, the copy number of the spoVA[2mob] operon contributes to pressure resistance of Bacillus endospores. This improves our understanding of the pressure resistance mechanisms in Bacillus spp. and may inform the development of high-pressure sterilization in food processing.IMPORTANCEBacillus spp. are considered pressure-resistant microorganisms, but the resistance mechanisms remain unknown. The spoVA[2mob] operon is a mobile genetic element, and it can transfer to pathogenic or spoilage organisms by horizontal gene transfer. Results in this study indicate that multiple copies of the spoVA[2mob] operon mediate high-pressure resistance of Bacillus endospores, and it might contribute to the identification of the source of pressure-resistant pathogens and spoilage organisms that may contaminate the food supply. The droplet digital PCR (ddPCR) system is well suited for analysis in some human diseases due to its high efficiency and capability to provide high precision; however, no relevant studies in food microbiology have been reported so far. This study demonstrates a novel application of ddPCR in food microbiology.}, }
@article {pmid31375138, year = {2019}, author = {Bickhart, DM and Watson, M and Koren, S and Panke-Buisse, K and Cersosimo, LM and Press, MO and Van Tassell, CP and Van Kessel, JAS and Haley, BJ and Kim, SW and Heiner, C and Suen, G and Bakshy, K and Liachko, I and Sullivan, ST and Myer, PR and Ghurye, J and Pop, M and Weimer, PJ and Phillippy, AM and Smith, TPL}, title = {Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {153}, pmid = {31375138}, issn = {1474-760X}, support = {R43 AI122654/AI/NIAID NIH HHS/United States ; R44 AI122654/AI/NIAID NIH HHS/United States ; R44 AI150008/AI/NIAID NIH HHS/United States ; R44AI122654-02A1//National Institute of Allergy and Infectious Diseases (US)/International ; }, mesh = {Animals ; Cattle ; Clustered Regularly Interspaced Short Palindromic Repeats ; Drug Resistance, Microbial/*genetics ; Gene Transfer, Horizontal ; Genes, Microbial ; Metagenomics/*methods ; Microbiota/*genetics ; Open Reading Frames ; Prophages/genetics ; Rumen/microbiology/virology ; Sequence Analysis, DNA/*methods ; Viruses/*genetics/isolation &amp; purification ; }, abstract = {We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattle rumen microbial community, and provide a comparison to short read-based methods. Long-read alignments and Hi-C linkage between contigs support the identification of 188 novel virus-host associations and the determination of phage life cycle states in the rumen microbial community. The long-read assembly also identifies 94 antimicrobial resistance genes, compared to only seven alleles in the short-read assembly. We demonstrate novel techniques that work synergistically to improve characterization of biological features in a highly complex rumen microbial community.}, }
@article {pmid31372643, year = {2019}, author = {Negri, A and Jąkalski, M and Szczuka, A and Pryszcz, LP and Mruk, I}, title = {Transcriptome analyses of cells carrying the Type II Csp231I restriction-modification system reveal cross-talk between two unrelated transcription factors: C protein and the Rac prophage repressor.}, journal = {Nucleic acids research}, volume = {47}, number = {18}, pages = {9542-9556}, pmid = {31372643}, issn = {1362-4962}, mesh = {Amino Acid Sequence/genetics ; Bacteriophages/*genetics/pathogenicity ; Citrobacter/genetics ; DNA Restriction Enzymes/genetics ; DNA Restriction-Modification Enzymes/*genetics ; DNA, Bacterial/chemistry/genetics ; Deoxyribonucleases, Type II Site-Specific/genetics ; Escherichia coli/*genetics/virology ; Gene Expression Profiling/methods ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal/genetics ; Host-Pathogen Interactions/*genetics ; Phenotype ; Transcription Factors/genetics ; Viral Proteins/genetics ; }, abstract = {Restriction-modification (R-M) systems represent an effective mechanism of defence against invading bacteriophages, and are widely spread among bacteria and archaea. In acquiring a Type II R-M system via horizontal gene transfer, the new hosts become more resistant to phage infection, through the action of a restriction endonuclease (REase), which recognizes and cleaves specific target DNAs. To protect the host cell's DNA, there is also a methyltransferase (MTase), which prevents DNA cleavage by the cognate REase. In some R-M systems, the host also accepts a cis-acting transcription factor (C protein), which regulates the counteracting activities of REase and MTase to avoid host self-restriction. Our study characterized the unexpected phenotype of Escherichia coli cells, which manifested as extensive cell filamentation triggered by acquiring the Csp231I R-M system from Citrobacter sp. Surprisingly, we found that the cell morphology defect was solely dependent on the C regulator. Our transcriptome analysis supported by in vivo and in vitro assays showed that C protein directly silenced the expression of the RacR repressor to affect the Rac prophage-related genes. The rac locus ydaST genes, when derepressed, exerted a toxicity indicated by cell filamentation through an unknown mechanism. These results provide an apparent example of transcription factor cross-talk, which can have significant consequences for the host, and may represent a constraint on lateral gene transfer.}, }
@article {pmid31371723, year = {2019}, author = {Coyne, MJ and Béchon, N and Matano, LM and McEneany, VL and Chatzidaki-Livanis, M and Comstock, LE}, title = {A family of anti-Bacteroidales peptide toxins wide-spread in the human gut microbiota.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {3460}, pmid = {31371723}, issn = {2041-1723}, support = {P30 DK034854/DK/NIDDK NIH HHS/United States ; R01 AI093771/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*biosynthesis/pharmacology ; Bacterial Proteins/biosynthesis/genetics/pharmacology ; Bacterial Toxins/*biosynthesis/genetics/pharmacology ; Bacteriocins/*biosynthesis/*genetics/pharmacology ; Bacteroidetes/drug effects/genetics/*metabolism ; Base Sequence ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Gastrointestinal Tract/microbiology ; Gene Transfer, Horizontal/genetics ; Humans ; Interspersed Repetitive Sequences ; Metagenomics ; Microbial Sensitivity Tests ; Peptides/genetics/*metabolism/pharmacology ; Prevotella/drug effects ; Sequence Analysis, Protein ; Vaginosis, Bacterial ; }, abstract = {Bacteria often produce antimicrobial toxins to compete in microbial communities. Here we identify a family of broad-spectrum peptide toxins, named bacteroidetocins, produced by Bacteroidetes species. We study this toxin family using phenotypic, mutational, bioinformatic, and human metagenomic analyses. Bacteroidetocins are related to class IIa bacteriocins of Gram-positive bacteria and kill members of the Bacteroidetes phylum, including Bacteroides, Parabacteroides, and Prevotella gut species, as well as pathogenic Prevotella species. The bacteroidetocin biosynthesis genes are found in horizontally acquired mobile elements, which likely allow dissemination within the gut microbiota and may explain their wide distribution in human populations. Bacteroidetocins may have potential applications in microbiome engineering and as therapeutics for polymicrobial diseases such as bacterial vaginosis and periodontal disease.}, }
@article {pmid31370208, year = {2019}, author = {Saliu, EM and Eitinger, M and Zentek, J and Vahjen, W}, title = {Nutrition Related Stress Factors Reduce the Transfer of Extended-Spectrum Beta-Lactamase Resistance Genes between an Escherichia coli Donor and a Salmonella Typhimurium Recipient In Vitro.}, journal = {Biomolecules}, volume = {9}, number = {8}, pages = {}, pmid = {31370208}, issn = {2218-273X}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Copper/pharmacology ; Escherichia coli/*genetics ; Fatty Acids, Volatile/pharmacology ; *Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Hydrogen-Ion Concentration ; Nutrients/*pharmacology ; Osmolar Concentration ; Salmonella typhimurium/*drug effects/*genetics/growth &amp; development/physiology ; *Stress, Physiological ; Zinc/pharmacology ; beta-Lactam Resistance/*genetics ; }, abstract = {The transfer of extended spectrum β-lactamase (ESBL)-genes occurs frequently between different bacteria species. The aim of this study was to investigate the impact of nutrition related stress factors on this transfer. Thus, an Escherichia coli donor and a Salmonella Typhimurium recipient were co-incubated for 4 h in media containing different levels of the stress factors' pH, osmolality, copper, zinc and acetic, propionic, lactic, and n-butyric acid, as well as subtherapeutic levels of cefotaxime, sulfamethoxazole/trimethoprim, and nitrofurantoin. Conjugation frequencies were calculated as transconjugants per donor, recipient, and total bacterial count. A correction factor for the stress impact on bacterial growth was used. Acetic, lactic, and n-butyric, acid, as well as pH, showed no significant impact. In contrast, increasing concentrations of propionate, zinc, copper, and nitrofurantoin, as well as increased osmolality reduced conjugation frequencies. Sulfamethoxazole/trimethoprim and cefotaxime showed increased transconjugants per donor, which decreased after correction for stress. This study showed, for the model mating pair, that conjugation frequencies decreased under different physiological stress conditions, and, thus, the hypothesis that stress factors may enhance conjugation should be viewed with caution. Furthermore, for studies on in vitro gene transfer, it is vital to consider the impact of studied stressors on bacterial growth.}, }
@article {pmid31368488, year = {2019}, author = {Sapriel, G and Brosch, R}, title = {Shared Pathogenomic Patterns Characterize a New Phylotype, Revealing Transition toward Host-Adaptation Long before Speciation of Mycobacterium tuberculosis.}, journal = {Genome biology and evolution}, volume = {11}, number = {8}, pages = {2420-2438}, pmid = {31368488}, issn = {1759-6653}, mesh = {Adaptation, Physiological/*genetics ; Bacterial Proteins/genetics ; *Evolution, Molecular ; *Genome, Bacterial ; Humans ; Mycobacterium tuberculosis/classification/*genetics/*pathogenicity ; *Phylogeny ; Tuberculosis/*microbiology ; Virulence Factors/genetics ; }, abstract = {Tuberculosis remains one of the deadliest infectious diseases of humanity. To better understand the evolutionary history of host-adaptation of tubercle bacilli (MTB), we sought for mycobacterial species that were more closely related to MTB than the previously used comparator species Mycobacterium marinum and Mycobacterium kansasii. Our phylogenomic approach revealed some recently sequenced opportunistic mycobacterial pathogens, Mycobacterium decipiens, Mycobacterium lacus, Mycobacterium riyadhense, and Mycobacterium shinjukuense, to constitute a common clade with MTB, hereafter called MTB-associated phylotype (MTBAP), from which MTB have emerged. Multivariate and clustering analyses of genomic functional content revealed that the MTBAP lineage forms a clearly distinct cluster of species that share common genomic characteristics, such as loss of core genes, shift in dN/dS ratios, and massive expansion of toxin-antitoxin systems. Consistently, analysis of predicted horizontal gene transfer regions suggests that putative functions acquired by MTBAP members were markedly associated with changes in microbial ecology, for example adaption to intracellular stress resistance. Our study thus considerably deepens our view on MTB evolutionary history, unveiling a decisive shift that promoted conversion to host-adaptation among ancestral founders of the MTBAP lineage long before Mycobacterium tuberculosis has adapted to the human host.}, }
@article {pmid31363851, year = {2019}, author = {Beyer, HM and Mikula, KM and Kudling, TV and Iwaï, H}, title = {Crystal structures of CDC21-1 inteins from hyperthermophilic archaea reveal the selection mechanism for the highly conserved homing endonuclease insertion site.}, journal = {Extremophiles : life under extreme conditions}, volume = {23}, number = {6}, pages = {669-679}, pmid = {31363851}, issn = {1433-4909}, support = {131413//Biotieteiden ja Ymp&#xe4;rist&#xf6;n Tutkimuksen Toimikunta/ ; 137995//Biotieteiden ja Ymp&#xe4;rist&#xf6;n Tutkimuksen Toimikunta/ ; 277335//Biotieteiden ja Ymp&#xe4;rist&#xf6;n Tutkimuksen Toimikunta/ ; NNF17OC0025402//Novo Nordisk Foundation/ ; NNF17OC0027550//Novo Nordisk Foundation/ ; }, mesh = {Archaeal Proteins/*chemistry/genetics ; Endonucleases/*chemistry/genetics ; Enzyme Stability ; Hot Temperature ; *Inteins ; Protein Domains ; Pyrococcus abyssi/*enzymology/genetics ; Pyrococcus horikoshii/*enzymology/genetics ; }, abstract = {Self-splicing inteins are mobile genetic elements invading host genes via nested homing endonuclease (HEN) domains. All HEN domains residing within inteins are inserted at a highly conserved insertion site. A purifying selection mechanism directing the location of the HEN insertion site has not yet been identified. In this work, we solved the three-dimensional crystal structures of two inteins inserted in the cell division control protein 21 of the hyperthermophilic archaea Pyrococcus abyssi and Pyrococcus horikoshii. A comparison between the structures provides the structural basis for the thermo-stabilization mechanism of inteins that have lost the HEN domain during evolution. The presence of an entire extein domain in the intein structure from Pyrococcus horikoshii suggests the selection mechanism for the highly conserved HEN insertion point.}, }
@article {pmid31361051, year = {2019}, author = {Avello, M and Davis, KP and Grossman, AD}, title = {Identification, characterization and benefits of an exclusion system in an integrative and conjugative element of Bacillus subtilis.}, journal = {Molecular microbiology}, volume = {112}, number = {4}, pages = {1066-1082}, pmid = {31361051}, issn = {1365-2958}, support = {R01 GM050895/GM/NIGMS NIH HHS/United States ; R35 GM122538/GM/NIGMS NIH HHS/United States ; T32 GM007287/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacillus subtilis/*genetics ; Bacterial Proteins/genetics ; Chromosomes, Bacterial/genetics ; Conjugation, Genetic/*genetics ; DNA Replication/genetics ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal/*genetics ; Integration Host Factors/genetics ; Plasmids/genetics ; }, abstract = {Integrative and conjugative elements (ICEs) are mobile genetic elements that transfer from cell to cell by conjugation (like plasmids) and integrate into the chromosomes of bacterial hosts (like lysogenic phages or transposons). ICEs are prevalent in bacterial chromosomes and play a major role in bacterial evolution by promoting horizontal gene transfer. Exclusion prevents the redundant transfer of conjugative elements into host cells that already contain a copy of the element. Exclusion has been characterized mostly for conjugative elements of Gram-negative bacteria. Here, we report the identification and characterization of an exclusion mechanism in ICEBs1 from the Gram-positive bacterium Bacillus subtilis. We found that cells containing ICEBs1 inhibit the activity of the ICEBs1-encoded conjugation machinery in other cells. This inhibition (exclusion) was specific to the cognate conjugation machinery and the ICEBs1 gene yddJ was both necessary and sufficient to mediate exclusion by recipient cells. Through a mutagenesis and enrichment screen, we identified exclusion-resistant mutations in the ICEBs1 gene conG. Using genes from a heterologous but related ICE, we found that the exclusion specificity was determined by ConG and YddJ. Finally, we found that under conditions that support conjugation, exclusion provides a selective advantage to the element and its host cells.}, }
@article {pmid31358910, year = {2019}, author = {Debroas, D and Siguret, C}, title = {Viruses as key reservoirs of antibiotic resistance genes in the environment.}, journal = {The ISME journal}, volume = {13}, number = {11}, pages = {2856-2867}, pmid = {31358910}, issn = {1751-7370}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics/metabolism ; Bacterial Infections/*microbiology/*veterinary ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; Plasmids/genetics/metabolism ; Swine ; Swine Diseases/*microbiology ; Viruses/*genetics/metabolism ; }, abstract = {Antibiotic resistance is a rapidly growing health care problem globally and causes many illnesses and deaths. Bacteria can acquire antibiotic resistance genes (ARGs) by horizontal transfer mediated by mobile genetic elements, where the role of phages in their dissemination in natural environments has not yet been clearly resolved. From metagenomic studies, we showed that the mean proportion of predicted ARGs found in prophages (0-0.0028%) was lower than those present in the free viruses (0.001-0.1%). Beta-lactamase, from viruses in the swine gut, represented 0.10 % of the predicted genes. Overall, in the environment, the ARG distribution associated with viruses was strongly linked to human activity, and the low dN/dS ratio observed advocated for a negative selection of the ARGs harbored by the viruses. Our network approach showed that viruses were linked to putative pathogens (Enterobacterales and vibrionaceae) and were considered key vehicles in ARG transfer, similar to plasmids. Therefore, these ARGs could then be disseminated at larger temporal and spatial scales than those included in the bacterial genomes, allowing for time-delayed genetic exchanges.}, }
@article {pmid31357661, year = {2019}, author = {Phale, PS and Shah, BA and Malhotra, H}, title = {Variability in Assembly of Degradation Operons for Naphthalene and its derivative, Carbaryl, Suggests Mobilization through Horizontal Gene Transfer.}, journal = {Genes}, volume = {10}, number = {8}, pages = {}, pmid = {31357661}, issn = {2073-4425}, mesh = {Bacteria/genetics/metabolism ; Carbaryl/*metabolism ; Evolution, Molecular ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; *Operon ; *Polymorphism, Genetic ; }, abstract = {In the biosphere, the largest biological laboratory, increased anthropogenic activities have led microbes to evolve and adapt to the changes occurring in the environment. Compounds, specifically xenobiotics, released due to such activities persist in nature and undergo bio-magnification in the food web. Some of these compounds act as potent endocrine disrupters, mutagens or carcinogens, and therefore their removal from the environment is essential. Due to their persistence, microbial communities have evolved to metabolize them partially or completely. Diverse biochemical pathways have evolved or been assembled by exchange of genetic material (horizontal gene transfer) through various mobile genetic elements like conjugative and non-conjugative plasmids, transposons, phages and prophages, genomic islands and integrative conjugative elements. These elements provide an unlimited opportunity for genetic material to be exchanged across various genera, thus accelerating the evolution of a new xenobiotic degrading phenotype. In this article, we illustrate examples of the assembly of metabolic pathways involved in the degradation of naphthalene and its derivative, Carbaryl, which are speculated to have evolved or adapted through the above-mentioned processes.}, }
@article {pmid31355850, year = {2019}, author = {D'Andrea, MM and Antonelli, A and Brenciani, A and Di Pilato, V and Morroni, G and Pollini, S and Fioriti, S and Giovanetti, E and Rossolini, GM}, title = {Characterization of Tn6349, a novel mosaic transposon carrying poxtA, cfr and other resistance determinants, inserted in the chromosome of an ST5-MRSA-II strain of clinical origin.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {74}, number = {10}, pages = {2870-2875}, doi = {10.1093/jac/dkz278}, pmid = {31355850}, issn = {1460-2091}, mesh = {*Chromosomes, Bacterial ; Computational Biology ; Conjugation, Genetic ; Cystic Fibrosis/complications ; *DNA Transposable Elements ; *Drug Resistance, Multiple, Bacterial ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Methicillin-Resistant Staphylococcus aureus/*genetics/*isolation &amp; purification ; Pneumonia, Staphylococcal/microbiology ; Prophages/isolation &amp; purification ; Sequence Analysis, DNA ; Transformation, Bacterial ; }, abstract = {OBJECTIVES: To characterize the genetic element carrying the poxtA oxazolidinone resistance gene found in the poxtA index strain Staphylococcus aureus AOUC-0915 isolated from a cystic fibrosis patient.<br><br>METHODS: The genetic context of poxtA was investigated by bioinformatics analysis of WGS data of strain AOUC-0915, followed by PCR and confirmatory Sanger sequencing for repetitive regions. Conjugation and electrotransformation experiments were carried out to assess horizontal transferability using S. aureus and Enterococcus faecalis recipients. Production of phage particles was evaluated by PCR using DNA preparations obtained after phage induction. Excision of the transposon carrying poxtA was evaluated by inverse PCR experiments for detection of circular intermediates.<br><br>RESULTS: poxtA was found to be associated with a 48&#x2009;kb composite transposon of original structure, named Tn6349, inserted into a &#x3c6;N315-like prophage. The transposon was bounded by two IS1216 insertion sequences, carried several resistance genes [erm(B), cfr, poxtA and fexB] and exhibited a mosaic structure made by a derivative of plasmid pE35048-oc (previously described in an Enterococcus faecium clinical isolate) and Tn6657, a novel composite transposon carrying the poxtA and fexB genes. Excision ability of Tn6349 as a circular intermediate was demonstrated. Transferability of Tn6349 or modules thereof to S. aureus or E. faecalis by either conjugation or electrotransformation was not detected. Induction of the &#x3c6;N315-like prophage carrying Tn6349 was not observed.<br><br>CONCLUSIONS: This study describes the structure of Tn6349, a novel composite transposon carrying several resistance determinants to anti-ribosomal drugs, including cfr and poxtA, from an oxazolidinone-resistant MRSA strain. Analysis of Tn6349 revealed a modular structure that could favour the mobilization of its resistance determinants.}, }
@article {pmid31354668, year = {2019}, author = {Shen, JP and Li, ZM and Hu, HW and Zeng, J and Zhang, LM and Du, S and He, JZ}, title = {Distribution and Succession Feature of Antibiotic Resistance Genes Along a Soil Development Chronosequence in Urumqi No.1 Glacier of China.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1569}, pmid = {31354668}, issn = {1664-302X}, abstract = {Primary succession of plant and microbial communities in the glacier retreating foreland has been extensively studied, but shifts of antibiotic resistance genes (ARGs) with the glacier retreating due to global warming remain elusive. Unraveling the diversity and succession features of ARGs in pristine soil during glacier retreating could contribute to a mechanistic understanding of the evolution and development of soil resistome. In this study, we quantified the abundance and diversity of ARGs along a 50-year soil development chronosequence by using a high-throughput quantitative PCR (HT-qPCR) technique. A total of 24 ARGs and two mobile genetic elements (MGEs) were detected from all the glacier samples, and the numbers of detected ARGs showed a unimodal pattern with an increasing trend at the early stage (0∼8 years) but no significant change at later stages (17∼50 years). The oprJ and mexF genes encoding multidrug resistance were the only two ARGs that were detected across all the succession ages, and the mexF gene showed an increasing trend along the succession time. Structural equation models indicated the predominant role of the intI1 gene encoding the Class 1 integron-integrase in shaping the variation of ARG profiles. These findings suggested the presence of ARGs in pristine soils devoid of anthropogenic impacts, and horizontal gene transfer mediated by MGEs may contribute to the succession patterns of ARGs during the initial soil formation stage along the chronosequence.}, }
@article {pmid31354647, year = {2019}, author = {Gago-Córdoba, C and Val-Calvo, J and Miguel-Arribas, A and Serrano, E and Singh, PK and Abia, D and Wu, LJ and Meijer, WJJ}, title = {Surface Exclusion Revisited: Function Related to Differential Expression of the Surface Exclusion System of Bacillus subtilis Plasmid pLS20.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1502}, pmid = {31354647}, issn = {1664-302X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {During conjugation a genetic element is transferred from a bacterial donor to a recipient cell via a connecting channel. It is the major route responsible for the spread of antibiotic resistance. Conjugative elements can contain exclusion system(s) that inhibit its transfer to a cell already harboring the element. Our limited knowledge on exclusion systems is mainly based on plasmids of Gram-negative bacteria. Here we studied the conjugative plasmid pLS20 of the Gram-positive Bacillus subtilis. We demonstrate that pLS20 contains an exclusion system and identified the single gene responsible for exclusion, named sespLS20 , which is embedded in the conjugation operon. SespLS20 is the founding member of a novel family of surface exclusion proteins encoded by conjugative elements of Gram-positive origin. We show that the extent of surface exclusion correlates with the level of sespLS20 expression, and that sespLS20 is expressed at basal low-levels in all donor cells but becomes highly expressed in conjugating cells. Accordingly, the transfer of pLS20 from a conjugation-primed donor cell to an un-primed or conjugation-primed donor is inhibited moderately and very efficiently, respectively. The consequences of this differential regulation, which appears to be a conserved feature of surface exclusion systems of Gram-positive and Gram-negative origin, are discussed.}, }
@article {pmid31351286, year = {2019}, author = {Lu, XM and Lu, PZ}, title = {Distribution of antibiotic resistance genes in soil amended using Azolla imbricata and its driving mechanisms.}, journal = {The Science of the total environment}, volume = {692}, number = {}, pages = {422-431}, doi = {10.1016/j.scitotenv.2019.07.285}, pmid = {31351286}, issn = {1879-1026}, mesh = {China ; Drug Resistance, Microbial/*genetics ; Ferns/*chemistry ; Fertilizers/*analysis ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {The floating aquatic plant of Azolla imbricata has an outstanding purification capability for polluted river water, and it is also employed to improve soil fertility. However, the occurrence and distribution of antibiotic resistance genes (ARGs) in soil amended using A.imbricata remain unclear. In the soil amendment with A. imbricata, heavy metals, antibiotics, transposase genes, ARGs, and bacterial communities in the soil were determined in this study. The results indicated that the diversity of bacteria and ARGs increased, while the diversity of ARGs decreased under the amendment using an appropriate amount of A. imbricata. The Firmicutes, Chloroflexi, Actinobacteria, and Cyanobacteria were the main host bacteria of ARGs. The vertical gene transfer of ARGs was weak, and the horizontal gene transfer became the dominant transfer pathway of ARGs. The amendment with A. imbricata altered the distribution of heavy metals, antibiotics, transposase genes, ARGs, and dominant bacteria. The amendment using A. imbricata promoted the degradation of antibiotics, decreased the concentrations of available heavy metals, and eliminated the abundance of ARGs and transposase genes. Our findings suggested a comprehensive effect of multiple stresses on the fate of ARGs in soil amended with A. imbricata, providing an insight into the distribution and propagation of ARGs in soil amended using plant residues.}, }
@article {pmid31350897, year = {2019}, author = {Ramos-Silva, P and Serrano, M and Henriques, AO}, title = {From Root to Tips: Sporulation Evolution and Specialization in Bacillus subtilis and the Intestinal Pathogen Clostridioides difficile.}, journal = {Molecular biology and evolution}, volume = {36}, number = {12}, pages = {2714-2736}, pmid = {31350897}, issn = {1537-1719}, mesh = {Amino Acid Sequence ; Bacillus subtilis/*genetics ; *Biological Evolution ; Clostridioides difficile/*genetics ; Genes, Bacterial ; *Spores, Bacterial ; }, abstract = {Bacteria of the Firmicutes phylum are able to enter a developmental pathway that culminates with the formation of highly resistant, dormant endospores. Endospores allow environmental persistence, dissemination and for pathogens, are also infection vehicles. In both the model Bacillus subtilis, an aerobic organism, and in the intestinal pathogen Clostridioides difficile, an obligate anaerobe, sporulation mobilizes hundreds of genes. Their expression is coordinated between the forespore and the mother cell, the two cells that participate in the process, and is kept in close register with the course of morphogenesis. The evolutionary mechanisms by which sporulation emerged and evolved in these two species, and more broadly across Firmicutes, remain largely unknown. Here, we trace the origin and evolution of sporulation using the genes known to be involved in the process in B. subtilis and C. difficile, and estimating their gain-loss dynamics in a comprehensive bacterial macroevolutionary framework. We show that sporulation evolution was driven by two major gene gain events, the first at the base of the Firmicutes and the second at the base of the B. subtilis group and within the Peptostreptococcaceae family, which includes C. difficile. We also show that early and late sporulation regulons have been coevolving and that sporulation genes entail greater innovation in B. subtilis with many Bacilli lineage-restricted genes. In contrast, C. difficile more often recruits new sporulation genes by horizontal gene transfer, which reflects both its highly mobile genome, the complexity of the gut microbiota, and an adjustment of sporulation to the gut ecosystem.}, }
@article {pmid31347197, year = {2020}, author = {Wickell, DA and Li, FW}, title = {On the evolutionary significance of horizontal gene transfers in plants.}, journal = {The New phytologist}, volume = {225}, number = {1}, pages = {113-117}, doi = {10.1111/nph.16022}, pmid = {31347197}, issn = {1469-8137}, mesh = {Adaptation, Biological ; *Biological Evolution ; Ferns/genetics/physiology ; Gene Transfer, Horizontal/*genetics ; Photosynthesis ; Plant Physiological Phenomena ; Plants/*genetics ; }, abstract = {Horizontal gene transfer (HGT) has long been seen as a crucial process in the evolution of prokaryotic species, but until recently it was thought to have little, if any, effect on the evolution of eukaryotic life forms. Detecting and describing HGT events in eukaryotes is difficult, making this phenomenon at times controversial. However, modern advances in genomics and bioinformatics have radically altered our view of HGT in eukaryotes, especially in plants. It now appears that HGT to and from plant lineages is more common than previously suspected. Importantly, the transfer of functional nuclear genes with adaptive significance has been reported in numerous taxa. Here we review several recent studies that have found evidence of the horizontal transfer of nuclear genes, and argue that HGT has undoubtedly had profound impacts on plant evolution as a whole.}, }
@article {pmid31345254, year = {2019}, author = {Zielezinski, A and Girgis, HZ and Bernard, G and Leimeister, CA and Tang, K and Dencker, T and Lau, AK and Röhling, S and Choi, JJ and Waterman, MS and Comin, M and Kim, SH and Vinga, S and Almeida, JS and Chan, CX and James, BT and Sun, F and Morgenstern, B and Karlowski, WM}, title = {Benchmarking of alignment-free sequence comparison methods.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {144}, pmid = {31345254}, issn = {1474-760X}, support = {R01 GM120624/GM/NIGMS NIH HHS/United States ; R01GM120624/NH/NIH HHS/United States ; }, mesh = {Benchmarking ; Gene Transfer, Horizontal ; Internet ; Phylogeny ; Regulatory Sequences, Nucleic Acid ; Sequence Alignment ; *Sequence Analysis ; Sequence Analysis, Protein ; Software ; }, abstract = {BACKGROUND: Alignment-free (AF) sequence comparison is attracting persistent interest driven by data-intensive applications. Hence, many AF procedures have been proposed in recent years, but a lack of a clearly defined benchmarking consensus hampers their performance assessment.<br><br>RESULTS: Here, we present a community resource (http://afproject.org) to establish standards for comparing alignment-free approaches across different areas of sequence-based research. We characterize 74 AF methods available in 24 software tools for five research applications, namely, protein sequence classification, gene tree inference, regulatory element detection, genome-based phylogenetic inference, and reconstruction of species trees under horizontal gene transfer and recombination events.<br><br>CONCLUSION: The interactive web service allows researchers to explore the performance of alignment-free tools relevant to their data types and analytical goals. It also allows method developers to assess their own algorithms and compare them with current state-of-the-art tools, accelerating the development of new, more accurate AF solutions.}, }
@article {pmid31341074, year = {2019}, author = {Price, VJ and McBride, SW and Hullahalli, K and Chatterjee, A and Duerkop, BA and Palmer, KL}, title = {Enterococcus faecalis CRISPR-Cas Is a Robust Barrier to Conjugative Antibiotic Resistance Dissemination in the Murine Intestine.}, journal = {mSphere}, volume = {4}, number = {4}, pages = {}, pmid = {31341074}, issn = {2379-5042}, support = {K01 DK102436/DK/NIDDK NIH HHS/United States ; R01 AI116610/AI/NIAID NIH HHS/United States ; R01 AI141479/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *CRISPR-Cas Systems ; *Conjugation, Genetic ; *Drug Resistance, Bacterial ; Enterococcus faecalis/drug effects/*genetics ; *Gene Transfer, Horizontal ; Intestines/*microbiology ; Mice ; Mice, Inbred C57BL ; Plasmids/genetics ; }, abstract = {CRISPR-Cas systems are barriers to horizontal gene transfer (HGT) in bacteria. Little is known about CRISPR-Cas interactions with conjugative plasmids, and studies investigating CRISPR-Cas/plasmid interactions in in vivo models relevant to infectious disease are lacking. These are significant gaps in knowledge because conjugative plasmids disseminate antibiotic resistance genes among pathogens in vivo, and it is essential to identify strategies to reduce the spread of these elements. We use enterococci as models to understand the interactions of CRISPR-Cas with conjugative plasmids. Enterococcus faecalis is a native colonizer of the mammalian intestine and harbors pheromone-responsive plasmids (PRPs). PRPs mediate inter- and intraspecies transfer of antibiotic resistance genes. We assessed E. faecalis CRISPR-Cas anti-PRP activity in the mouse intestine and under different in vitro conditions. We observed striking differences in CRISPR-Cas efficiency in vitro versus in vivo With few exceptions, CRISPR-Cas blocked intestinal PRP dissemination, while in vitro, the PRP frequently escaped CRISPR-Cas defense. Our results further the understanding of CRISPR-Cas biology by demonstrating that standard in vitro experiments do not adequately model the in vivo antiplasmid activity of CRISPR-Cas. Additionally, our work identifies several variables that impact the apparent in vitro antiplasmid activity of CRISPR-Cas, including planktonic versus biofilm settings, different donor-to-recipient ratios, production of a plasmid-encoded bacteriocin, and the time point at which matings are sampled. Our results are clinically significant because they demonstrate that barriers to HGT encoded by normal (healthy) human microbiota can have significant impacts on in vivo antibiotic resistance dissemination.IMPORTANCE CRISPR-Cas is a type of immune system in bacteria that is hypothesized to be a natural impediment to the spread of antibiotic resistance genes. In this study, we directly assessed the impact of CRISPR-Cas on antibiotic resistance dissemination in the mammalian intestine and under different in vitro conditions. We observed a robust effect of CRISPR-Cas on in vivo but not in vitro dissemination of antibiotic resistance plasmids in the native mammalian intestinal colonizer Enterococcus faecalis We conclude that standard in vitro experiments currently do not appropriately model the in vivo conditions where antibiotic resistance dissemination occurs between E. faecalis strains in the intestine. Moreover, our results demonstrate that CRISPR-Cas present in native members of the mammalian intestinal microbiota can block the spread of antibiotic resistance plasmids.}, }
@article {pmid31337658, year = {2019}, author = {Villada, JC and Duran, MF and Lee, PKH}, title = {Genomic Evidence for Simultaneous Optimization of Transcription and Translation through Codon Variants in the pmoCAB Operon of Type Ia Methanotrophs.}, journal = {mSystems}, volume = {4}, number = {4}, pages = {}, pmid = {31337658}, issn = {2379-5077}, abstract = {Understanding the interplay between genotype and phenotype is a fundamental goal of functional genomics. Methane oxidation is a microbial phenotype with global-scale significance as part of the carbon biogeochemical cycle and a sink for greenhouse gas. Microorganisms that oxidize methane (methanotrophs) are taxonomically diverse and widespread around the globe. In methanotrophic bacteria, enzymes in the methane oxidation metabolic module (KEGG module M00174, conversion of methane to formaldehyde) are encoded in four operons (pmoCAB, mmoXYZBCD, mxaFI, and xoxF). Recent reports have suggested that methanotrophs in Proteobacteria acquired methane monooxygenases through horizontal gene transfer. Here, we used a genomic meta-analysis to infer the transcriptional and translational advantages of coding sequences from the methane oxidation metabolic modules of different types of methanotrophs. By analyzing isolate and metagenome-assembled genomes from phylogenetically and geographically diverse sources, we detected an anomalous nucleotide composition bias in the coding sequences of particulate methane monooxygenase genes (pmoCAB) from type Ia methanotrophs. We found that this nucleotide bias increases the level of codon bias by decreasing the GC content in the third base of codons, a strategy that contrasts with that of other coding sequences in the module. Further codon usage analyses uncovered that codon variants of the type Ia pmoCAB coding sequences deviate from the genomic signature to match ribosomal protein-coding sequences. Subsequently, computation of transcription and translation metrics revealed that the pmoCAB coding sequences of type Ia methanotrophs optimize the usage of codon variants to maximize translation efficiency and accuracy, while minimizing the synthesis cost of transcripts and proteins.IMPORTANCE Microbial methane oxidation plays a fundamental role in the biogeochemical cycle of Earth's system. Recent reports have provided evidence for the acquisition of methane monooxygenases by horizontal gene transfer in methane-oxidizing bacteria from different environments, but how evolution has shaped the coding sequences to execute methanotrophy efficiently remains unexplored. In this work, we provide genomic evidence that among the different types of methanotrophs, type Ia methanotrophs possess a unique coding sequence of the pmoCAB operon that is under positive selection for optimal resource allocation and efficient synthesis of transcripts and proteins. This adaptive trait possibly enables type Ia methanotrophs to respond robustly to fluctuating methane availability and explains their global prevalence.}, }
@article {pmid31337355, year = {2019}, author = {Armaleo, D and Müller, O and Lutzoni, F and Andrésson, &#xd3;S and Blanc, G and Bode, HB and Collart, FR and Dal Grande, F and Dietrich, F and Grigoriev, IV and Joneson, S and Kuo, A and Larsen, PE and Logsdon, JM and Lopez, D and Martin, F and May, SP and McDonald, TR and Merchant, SS and Miao, V and Morin, E and Oono, R and Pellegrini, M and Rubinstein, N and Sanchez-Puerta, MV and Savelkoul, E and Schmitt, I and Slot, JC and Soanes, D and Szövényi, P and Talbot, NJ and Veneault-Fourrey, C and Xavier, BB}, title = {The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {605}, pmid = {31337355}, issn = {1471-2164}, support = {IGSP 2008001//Duke Institute for Genomic Sciences and Policy/ ; FWP 61327//U.S. Department of Energy/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; DE-FC02-02ER63421//U.S. Department of Energy/ ; 112442//U.S. Department of Energy/ ; 1011101//National Science Foundation/ ; }, mesh = {Ascomycota/*genetics ; Chlorophyta/*genetics ; Gene Transfer, Horizontal ; Genome, Fungal ; Lichens/*genetics ; Symbiosis/*genetics ; }, abstract = {BACKGROUND: Lichens, encompassing 20,000 known species, are symbioses between specialized fungi (mycobionts), mostly ascomycetes, and unicellular green algae or cyanobacteria (photobionts). Here we describe the first parallel genomic analysis of the mycobiont Cladonia grayi and of its green algal photobiont Asterochloris glomerata. We focus on genes/predicted proteins of potential symbiotic significance, sought by surveying proteins differentially activated during early stages of mycobiont and photobiont interaction in coculture, expanded or contracted protein families, and proteins with differential rates of evolution.<br><br>RESULTS: A) In coculture, the fungus upregulated small secreted proteins, membrane transport proteins, signal transduction components, extracellular hydrolases and, notably, a ribitol transporter and an ammonium transporter, and the alga activated DNA metabolism, signal transduction, and expression of flagellar components. B) Expanded fungal protein families include heterokaryon incompatibility proteins, polyketide synthases, and a unique set of G-protein &#x3b1; subunit paralogs. Expanded algal protein families include carbohydrate active enzymes and a specific subclass of cytoplasmic carbonic anhydrases. The alga also appears to have acquired by horizontal gene transfer from prokaryotes novel archaeal ATPases and Desiccation-Related Proteins. Expanded in both symbionts are signal transduction components, ankyrin domain proteins and transcription factors involved in chromatin remodeling and stress responses. The fungal transportome is contracted, as are algal nitrate assimilation genes. C) In the mycobiont, slow-evolving proteins were enriched for components involved in protein translation, translocation and sorting.<br><br>CONCLUSIONS: The surveyed genes affect stress resistance, signaling, genome reprogramming, nutritional and structural interactions. The alga carries many genes likely transferred horizontally through viruses, yet we found no evidence of inter-symbiont gene transfer. The presence in the photobiont of meiosis-specific genes supports the notion that sexual reproduction occurs in Asterochloris while they are free-living, a phenomenon with implications for the adaptability of lichens and the persistent autonomy of the symbionts. The diversity of the genes affecting the symbiosis suggests that lichens evolved by accretion of many scattered regulatory and structural changes rather than through introduction of a few key innovations. This predicts that paths to lichenization were variable in different phyla, which is consistent with the emerging consensus that ascolichens could have had a few independent origins.}, }
@article {pmid31336172, year = {2020}, author = {Papa-Ezdra, R and Grill Diaz, F and Vieytes, M and García-Fulgueiras, V and Caiata, L and Ávila, P and Brasesco, M and Christophersen, I and Cordeiro, NF and Algorta, G and Galiana, A and Vignoli, R}, title = {First three Escherichia coli isolates harbouring mcr-1 in Uruguay.}, journal = {Journal of global antimicrobial resistance}, volume = {20}, number = {}, pages = {187-190}, doi = {10.1016/j.jgar.2019.07.016}, pmid = {31336172}, issn = {2213-7173}, mesh = {Adult ; Aged, 80 and over ; Cephalosporins/pharmacology ; Colistin/pharmacology ; *Drug Resistance, Bacterial ; Escherichia coli/*classification/drug effects/genetics/isolation &amp; purification ; Escherichia coli Infections/blood/*microbiology/urine ; Escherichia coli Proteins/*genetics ; Female ; Gene Transfer, Horizontal ; Humans ; Male ; Multilocus Sequence Typing ; Rectum/microbiology ; Retrospective Studies ; Uruguay/epidemiology ; }, abstract = {OBJECTIVE: This report described the first Escherichia coli (E. coli) isolates harbouring mcr-1 in Uruguay.<br><br>METHODS: Three E. coli isolates were obtained from blood, urine and rectal swabs from different patients in two hospitals. Extended-spectrum &#x3b2;-lactamases (ESBL), plasmid-encoded (pAmpC) &#x3b2;-lactamases, plasmid-mediated quinolone resistance (PMQR) genes, class 1 integrons, and mcr-1, mcr-2 and mcr-3 were sought and characterised in three E. coli isolates. Transfer of resistance determinants was assessed by conjugation. Clonality was analysed by multilocus sequence typing.<br><br>RESULTS: All isolates were categorised as being colistin-resistant and the mcr-1 gene was detected. Two isolates were also resistant to oxyimino cephalosporins: one on account of blaCMY-2 and the other due to blaCTX-M-15, the latter also harbouring transferable quinolone-resistance genes (aac(6')Ib-cr and qnrB). All mcr-1 genes were transferred by conjugation to recipient strains. The mcr-1-bearing isolates belonged to sequence types ST10, ST93 and ST5442.<br><br>CONCLUSIONS: ST10 is considered as a high-risk clone worldwide. This type of mcr-1-harbouring clone is a major concern for human and animal health and must be under close surveillance. This study detected the presence of mcr-1 for the first time in Uruguay, albeit in an allodemic manner, associated with different antibiotic-resistance genes and from diverse clinical contexts. Considering that colistin is often the last therapeutic option available for multidrug-resistant Gram-negative bacilli infections, it is important to maximise precautions to avoid dissemination of isolates carrying mcr-1.}, }
@article {pmid31335917, year = {2019}, author = {Seiler, E and Trappe, K and Renard, BY}, title = {Where did you come from, where did you go: Refining metagenomic analysis tools for horizontal gene transfer characterisation.}, journal = {PLoS computational biology}, volume = {15}, number = {7}, pages = {e1007208}, pmid = {31335917}, issn = {1553-7358}, mesh = {Computational Biology ; Computer Simulation ; Databases, Genetic/statistics &amp; numerical data ; Disease Outbreaks/statistics &amp; numerical data ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genetic Variation ; Genome, Bacterial ; Helicobacter pylori/genetics ; Humans ; *Metagenome ; Metagenomics/*methods/statistics &amp; numerical data ; Methicillin-Resistant Staphylococcus aureus/genetics ; *Models, Genetic ; Mutation ; Staphylococcal Infections/epidemiology/microbiology ; }, abstract = {Horizontal gene transfer (HGT) has changed the way we regard evolution. Instead of waiting for the next generation to establish new traits, especially bacteria are able to take a shortcut via HGT that enables them to pass on genes from one individual to another, even across species boundaries. The tool Daisy offers the first HGT detection approach based on read mapping that provides complementary evidence compared to existing methods. However, Daisy relies on the acceptor and donor organism involved in the HGT being known. We introduce DaisyGPS, a mapping-based pipeline that is able to identify acceptor and donor reference candidates of an HGT event based on sequencing reads. Acceptor and donor identification is akin to species identification in metagenomic samples based on sequencing reads, a problem addressed by metagenomic profiling tools. However, acceptor and donor references have certain properties such that these methods cannot be directly applied. DaisyGPS uses MicrobeGPS, a metagenomic profiling tool tailored towards estimating the genomic distance between organisms in the sample and the reference database. We enhance the underlying scoring system of MicrobeGPS to account for the sequence patterns in terms of mapping coverage of an acceptor and donor involved in an HGT event, and report a ranked list of reference candidates. These candidates can then be further evaluated by tools like Daisy to establish HGT regions. We successfully validated our approach on both simulated and real data, and show its benefits in an investigation of an outbreak involving Methicillin-resistant Staphylococcus aureus data.}, }
@article {pmid31333625, year = {2019}, author = {Kim, BJ and Cha, GY and Kim, BR and Kook, YH and Kim, BJ}, title = {Insights From the Genome Sequence of Mycobacterium paragordonae, a Potential Novel Live Vaccine for Preventing Mycobacterial Infections: The Putative Role of Type VII Secretion Systems for an Intracellular Lifestyle Within Free-Living Environmental Predators.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1524}, pmid = {31333625}, issn = {1664-302X}, abstract = {Mycobacterium paragordonae (Mpg) is a temperature-sensitive Mycobacterium species that can grow at permissive temperatures but fails to grow above 37°C. Due to this unique growth trait, Mpg has recently been proposed as a novel live vaccine candidate for the prevention of mycobacterial infections. Furthermore, the increasing frequency of the isolation of Mpg from water supply systems led us to hypothesize that the free-living amoeba system is the natural reservoir of Mpg. In this study, we report the complete 6.7-Mb genome sequence of Mpg and show that this genome comprises four different plasmids with lengths of 305 kb (pMpg-1), 144 kb (pMpg-2), 26 kb (pMpg-3), and 17 kb (pMpg-4). The first two plasmids, pMpg-1 and -2, encode distinct Type VII secretion systems (T7SS), ESX-P5 and ESX-2, respectively. Genome-based phylogeny indicated that Mpg is the closest relative to M. gordonae, which has a 7.7-Mb genome; phylogenetic analysis revealed an average of 86.68% nucleotide identity between these two species. The most important feature of Mpg genome is the acquisition of massive genes related to T7SS, which may have had effect on adaptation to their intracellular lifestyle within free-living environmental predators, such as amoeba. Comparisons of the resistance to bacterial killing within amoeba indicated that Mpg exhibited stronger resistance to amoeba killing compared to M. gordonae and M. marinum, further supporting our genome-based findings indicating the special adaptation of Mpg to free-living amoeba. We also determined that, among the strains studied, there were more shared CDS between M. tuberculosis and Mpg. In addition, the presence of diverse T7SSs in the Mpg genome, including an intact ESX-1, may suggest the feasibility of Mpg as a novel tuberculosis vaccine. Our data highlight a significant role of lateral gene transfer in the evolution of mycobacteria for niche diversification and for increasing the intracellular survival capacity.}, }
@article {pmid31332314, year = {2019}, author = {Yang, Z and Wafula, EK and Kim, G and Shahid, S and McNeal, JR and Ralph, PE and Timilsena, PR and Yu, WB and Kelly, EA and Zhang, H and Person, TN and Altman, NS and Axtell, MJ and Westwood, JH and dePamphilis, CW}, title = {Convergent horizontal gene transfer and cross-talk of mobile nucleic acids in parasitic plants.}, journal = {Nature plants}, volume = {5}, number = {9}, pages = {991-1001}, pmid = {31332314}, issn = {2055-0278}, mesh = {Chromosome Mapping ; Cuscuta/*genetics/*physiology ; *Gene Transfer, Horizontal ; Host-Parasite Interactions ; Nucleic Acids/*physiology ; }, abstract = {Horizontal gene transfer (HGT), the movement and genomic integration of DNA across species boundaries, is commonly associated with bacteria and other microorganisms, but functional HGT (fHGT) is increasingly being recognized in heterotrophic parasitic plants that obtain their nutrients and water from their host plants through direct haustorial feeding. Here, in the holoparasitic stem parasite Cuscuta, we identify 108 transcribed and probably functional HGT events in Cuscuta campestris and related species, plus 42 additional regions with host-derived transposon, pseudogene and non-coding sequences. Surprisingly, 18 Cuscuta fHGTs were acquired from the same gene families by independent HGT events in Orobanchaceae parasites, and the majority are highly expressed in the haustorial feeding structures in both lineages. Convergent retention and expression of HGT sequences suggests an adaptive role for specific additional genes in parasite biology. Between 16 and 20 of the transcribed HGT events are inferred as ancestral in Cuscuta based on transcriptome sequences from species across the phylogenetic range of the genus, implicating fHGT in the successful radiation of Cuscuta parasites. Genome sequencing of C. campestris supports transfer of genomic DNA-rather than retroprocessed RNA-as the mechanism of fHGT. Many of the C. campestris genes horizontally acquired are also frequent sources of 24-nucleotide small RNAs that are typically associated with RNA-directed DNA methylation. One HGT encoding a leucine-rich repeat protein kinase overlaps with a microRNA that has been shown to regulate host gene expression, suggesting that HGT-derived parasite small RNAs may function in the parasite-host interaction. This study enriches our understanding of HGT by describing a parasite-host system with unprecedented gene exchange that points to convergent evolution of HGT events and the functional importance of horizontally transferred coding and non-coding sequences.}, }
@article {pmid31330692, year = {2019}, author = {Saakian, DB and Koh, JM and Cheong, KH}, title = {Approximate perturbative solutions of quasispecies model with recombination.}, journal = {Physical review. E}, volume = {99}, number = {6-1}, pages = {062407}, doi = {10.1103/PhysRevE.99.062407}, pmid = {31330692}, issn = {2470-0053}, abstract = {Despite the major roles played by genetic recombination in ecoevolutionary processes, limited progress has been made in analyzing realistic recombination models to date, due largely to the complexity of the associated mechanisms and the strongly nonlinear nature of the dynamical differential systems. In this paper, we consider a many-loci genomic model with fitness dependent on the Hamming distance from a reference genome, and adopt a Hamilton-Jacobi formulation to derive perturbative solutions for general linear fitness landscapes. The horizontal gene transfer model is used to describe recombination processes. Cases of weak selection and weak recombination with simultaneous mutation and selection are examined, yielding semianalytical solutions for the distribution surplus of O(1/N) accuracy, where N is the number of nucleotides in the genome.}, }
@article {pmid31330386, year = {2019}, author = {Guo, MT and Tian, XB}, title = {Impacts on antibiotic-resistant bacteria and their horizontal gene transfer by graphene-based TiO2&amp;Ag composite photocatalysts under solar irradiation.}, journal = {Journal of hazardous materials}, volume = {380}, number = {}, pages = {120877}, doi = {10.1016/j.jhazmat.2019.120877}, pmid = {31330386}, issn = {1873-3336}, mesh = {Anti-Bacterial Agents/pharmacology ; Catalysis ; Drug Resistance, Microbial/*genetics ; Gene Transfer, Horizontal/*drug effects ; Graphite/*pharmacology ; Photochemical Processes ; Silver/*pharmacology ; *Sunlight ; Titanium/*pharmacology ; }, abstract = {In recent years, photocatalysis has been considered as a promising method, which provides measures to environmental pollution. Antibiotic resistant bacteria (ARB) and their antibiotic resistance genes (ARGs), as the emerging environmental pollutants, are released into the environment, resulting in antibiotic resistance spread. TiO2-based nanocomposites, as the most common photocatalytic material, may influence ARB and ARGs under photocatalytic conditions. However, the research on this aspect is rare. A novel nanocomposite synthesized from Ag, TiO2 and graphene oxide (GO), was selected as a representative of nanomaterials for investigation. The experimental results indicated that TiO2/Ag/GO nanocomposites significantly affected ARB vitality. 100 mg/L TiO2/Ag/GO will reduce bacterial survival to 12.2% in 10 min under simulated sunlight irradiation. Chloramphenicol as the most representative antibiotic in the water, reduces the effect of ARB inactivation under photocatalytic conditions. The addition of TiO2/Ag/GO could affect tetracycline antibiotic resistance. The level of bacterial tolerance to tetracycline had a significant reduction. The horizontal gene transfer was promoted from 1 to 2 folds with the addition of TiO2/Ag/GO. Even high TiO2/Ag/GO concentration (100 mg/L) sample had a limited promotion, suggesting that TiO2/Ag/GO will not increase the risk of antibiotic resistance spread compared to other nano materials.}, }
@article {pmid31326825, year = {2019}, author = {Li, B and Qiu, Y and Song, Y and Lin, H and Yin, H}, title = {Dissecting horizontal and vertical gene transfer of antibiotic resistance plasmid in bacterial community using microfluidics.}, journal = {Environment international}, volume = {131}, number = {}, pages = {105007}, doi = {10.1016/j.envint.2019.105007}, pmid = {31326825}, issn = {1873-6750}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/*genetics ; *Conjugation, Genetic ; Drug Resistance, Bacterial/*genetics ; Escherichia coli ; *Gene Transfer, Horizontal ; Humans ; Microbiota ; Microfluidics ; Plasmids/*genetics ; Sewage/microbiology ; }, abstract = {The spread of antibiotic resistance genes (ARGs) has become an emerging threat to the global health. Although horizontal gene transfer (HGT) is regarded as one of the major pathways, more evidence has shown the significant involvement of vertical gene transfer (VGT). However, traditional cultivation-based methods cannot distinguish HGT and VGT, resulting in often contradictory conclusions. Here, single-cell microfluidics with time-lapse imaging has been successfully employed to dissect the contribution of plasmid-mediated HGT and VGT to ARG transmission in an environmental community. Using Escherichia coli with an ARG-coded plasmid pKJK5 with trimethoprim resistance as the donor, we quantified the effects of three representative antibiotics (trimethoprim, tetracycline and amoxicillin) on the ARG transfer process in an activated sludge bacterial community. It was found that HGT was influenced by the inhibitory mechanism of an antibiotic and its targets (donor, recipient alone or together), whereas VGT contributes significantly to the formation of transconjugants and consequently ARG spreading. Trimethoprim is highly resisted by the donor and transconjugants, and its presence significantly increased both the HGT and VGT rates. Although tetracycline and amoxicillin both inhibit the donor, they showed different effects on HGT rate as a result of different inhibitory mechanisms. Furthermore, we show the kinetics of HGT in a community can be described using an epidemic infection model, which in combination with quantitative measure of HGT and VGT on chip provides a promising tool to study and predict the dynamics of ARG spread in real-world communities.}, }
@article {pmid31325664, year = {2019}, author = {Dunn, SJ and Connor, C and McNally, A}, title = {The evolution and transmission of multi-drug resistant Escherichia coli and Klebsiella pneumoniae: the complexity of clones and plasmids.}, journal = {Current opinion in microbiology}, volume = {51}, number = {}, pages = {51-56}, doi = {10.1016/j.mib.2019.06.004}, pmid = {31325664}, issn = {1879-0364}, support = {BB/R006261/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 203821/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; MR/S013660/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Multiple, Bacterial ; Escherichia coli/drug effects/*genetics/isolation &amp; purification ; Escherichia coli Infections/*microbiology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Humans ; Klebsiella Infections/*microbiology ; Klebsiella pneumoniae/drug effects/*genetics/isolation &amp; purification ; Plasmids/*genetics/metabolism ; }, abstract = {The vast majority of Escherichia coli and Klebsiella pneumoniae isolated from human clinical extra-intestinal infections are now multi-drug resistant (MDR). Extended Spectrum Beta Lactamase (ESBL) carriage in clinical isolates of these bacteria is now commonplace, and carriage of carbapenemases is continuing to increase. MDR is primarily concentrated in a small number of globally disseminated clones, which generally differ between ESBL and carbapenemase carrying-clones in E. coli, but seem to converge in K. pneumoniae. In both species MDR is mediated by acquisition and maintenance of MDR plasmids. The plasmids associated with ESBL and carbapenemases also differ, and when both resistances are present in the same strain they are generally on distinct plasmids. Recent research is attempting to provide clues as to why some lineages appear better suited to acquisition and maintenance of these plasmids without a fitness cost. Central to this is the appearance of adaptive mutations in intergenic regions, and selection on genes involved in anaerobic metabolism, hinting at a process whereby these clones can outcompete commensal strains of the same species to initiate long-term intestinal colonization.}, }
@article {pmid31325615, year = {2020}, author = {Tchuinte, PLS and Rabenandrasana, MAN and Ramparany, L and Ratsima, E and Enouf, V and Randrianirina, F and Collard, JM}, title = {Genome-based insights into the resistomes and mobilomes of two Providencia rettgeri strains isolated from wound infections in Madagascar.}, journal = {Journal of global antimicrobial resistance}, volume = {20}, number = {}, pages = {178-182}, doi = {10.1016/j.jgar.2019.07.013}, pmid = {31325615}, issn = {2213-7173}, mesh = {Anti-Bacterial Agents/*pharmacology ; *Drug Resistance, Multiple, Bacterial ; Gene Transfer, Horizontal ; Genome, Bacterial ; Genomic Islands ; High-Throughput Nucleotide Sequencing ; Humans ; Interspersed Repetitive Sequences ; Madagascar ; Microbial Sensitivity Tests ; Phylogeny ; Plasmids/genetics ; Providencia/*classification/drug effects/genetics/isolation &amp; purification ; Spain ; United States ; Whole Genome Sequencing/*methods ; Wound Infection/*microbiology ; }, abstract = {OBJECTIVES: A molecular analysis was performed of two Providencia rettgeri (P. rettgeri) strains (Pr 297 and Pr 269) collected in 2007 and 2009 from wound swabs of patients admitted to the intensive care units at Joseph Ravoangy Andrianavalona hospital and the Military Hospital in Antananarivo, Madagascar.<br><br>METHODS: The two P. rettgeri isolates were subjected to susceptibility testing. Whole genome sequencing was performed to characterise the antibiotic resistance genes, genomic islands and mobilomes (integrons, plasmids and insertion sequences).<br><br>RESULTS: All isolates were found to be multidrug-resistant. Antibiotic-resistant genes described were amongst eight different classes of antimicrobial agents. Thirty insertion sequences and twelve genomic islands were predicted in each genome. Class 1 and class 2 integrons were found in both genomes, with gene cassette regions encompassing arr-2 - cmlA5 - blaOXA-10 - ant (3")-Ia and dfrA1 - sat2 - ant (3")-Ia - orfX, respectively. IncA/C2, ColM and ColE1-like plasmids were described harbouring blaCMY-30, qnrD and aac(6')-Ib-cr4 genes, respectively. Phylogenetic analysis showed that Pr 297 and Pr 269 isolates were genetically identical and clustered with P. rettgeri strains described in the USA and Spain.<br><br>CONCLUSIONS: It is believed that this is the first molecular characterisation of wound infection pathogens from Madagascan patients and the first description of P. rettgeri co-producing CMY-30, OXA-10 and AAC(6')-Ib-cr4 enzymes. The diversity of the resistance determinants and mobile genetic elements was probably due to extensive horizontal gene transfer events, highlighting the need to conduct further molecular monitoring studies to understand the genomic plasticity of resistant bacteria in Madagascan hospitals.}, }
@article {pmid31325209, year = {2020}, author = {Rosenberg, E and Zilber-Rosenberg, I}, title = {The hologenome concept of evolution: do mothers matter most?.}, journal = {BJOG : an international journal of obstetrics and gynaecology}, volume = {127}, number = {2}, pages = {129-137}, doi = {10.1111/1471-0528.15882}, pmid = {31325209}, issn = {1471-0528}, mesh = {Adaptation, Biological/genetics/*physiology ; Adaptation, Physiological/genetics/*physiology ; Adult ; Animals ; Biological Evolution ; Evolution, Molecular ; Female ; Gene Transfer, Horizontal/*genetics ; Genetic Speciation ; Genetic Variation ; Heredity ; Host Microbial Interactions/*physiology ; Humans ; Male ; Microbiota/genetics/*physiology ; *Mothers ; Plants ; Pregnancy ; }, abstract = {The hologenome concept of evolution is discussed, with special emphasis placed upon the microbiome of women. The microbiome is dynamic, changing under different conditions, and differs between women and men. Genetic variation occurs not only in the host, but also in the microbiome by the acquisition of novel microbes, the amplification of specific microbes, and horizontal gene transfer. The majority of unique genes in human holobionts are found in microbiomes, and mothers are responsible for transferring most of these to their offspring during birth, breastfeeding, and physical contact. Thus, mothers are likely to be the primary providers of the majority of genetic information to offspring via mitochondria and the microbiome. TWEETABLE ABSTRACT: Microbiomes differ between women and men. Most genes in humans are in the microbiome. Mothers transfer most of these genes to offspring.}, }
@article {pmid31323140, year = {2019}, author = {Hao, K and Ullah, H and Jarwar, AR and Nong, X and Tu, X and Zhang, Z}, title = {Molecular identification and diapause-related functional characterization of a novel dual-specificity kinase gene, MPKL, in Locusta migratoria.}, journal = {FEBS letters}, volume = {593}, number = {21}, pages = {3064-3074}, doi = {10.1002/1873-3468.13544}, pmid = {31323140}, issn = {1873-3468}, support = {CARS-34-07B//China Agriculture Research System/International ; 61661136004//National Natural Science Foundation of China/International ; No. ST/N006712/1//STFC Newton Agritech Programme of UK/International ; }, mesh = {Animals ; Cloning, Molecular/*methods ; Diapause ; Evolution, Molecular ; Female ; Forkhead Transcription Factors/metabolism ; Gene Transfer, Horizontal ; Insect Proteins/genetics/metabolism ; Locusta migratoria/enzymology/*physiology ; Ovary/metabolism ; Photoperiod ; Phylogeny ; Protein Kinases/*genetics/*metabolism ; Proto-Oncogene Proteins c-akt/metabolism ; }, abstract = {Diapause is an important overwintering strategy enabling Locusta migratoria to survive under stressed conditions. We identified a novel dual-specificity kinase gene that is differentially expressed between long and short day-treated L. migratoria. To determine its function on photoperiodic diapause induction, we cloned the specific gene. Interestingly, phylogenetic analysis shows that this dual-specificity kinase is of the mycetozoa protein kinase-like (MPKL) type and may have been transferred horizontally from Mycetozoa to L. migratoria. RNA interference results confirm that MPKL promotes photoperiodic diapause induction of L. migratoria. Furthermore, MPKL significantly inhibits Akt and FOXO (i.e. forkhead box protein O) phosphorylation levels in ovaries, and also enhances reactive oxygen species, superoxide dismutase and catalase activities, whereas peroxidase activity is decreased under both photoperiodic regimes. The findings of the present study offer insight into the molecular mechanism responsible for dual-specificity kinase-induced diapause in insects.}, }
@article {pmid31323028, year = {2019}, author = {Denise, R and Abby, SS and Rocha, EPC}, title = {Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility.}, journal = {PLoS biology}, volume = {17}, number = {7}, pages = {e3000390}, pmid = {31323028}, issn = {1545-7885}, mesh = {Archaea/classification/genetics/metabolism ; Bacteria/classification/genetics/metabolism ; Cell Adhesion/genetics ; Cytoskeleton/*genetics/metabolism ; DNA/genetics/*metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Intermediate Filament Proteins/classification/*genetics/metabolism ; Intermediate Filaments/classification/*genetics/metabolism ; Movement ; Phylogeny ; Protein Transport/genetics ; }, abstract = {Processes of molecular innovation require tinkering and shifting in the function of existing genes. How this occurs in terms of molecular evolution at long evolutionary scales remains poorly understood. Here, we analyse the natural history of a vast group of membrane-associated molecular systems in Bacteria and Archaea-the type IV filament (TFF) superfamily-that diversified in systems involved in flagellar or twitching motility, adhesion, protein secretion, and DNA uptake. The phylogeny of the thousands of detected systems suggests they may have been present in the last universal common ancestor. From there, two lineages-a bacterial and an archaeal-diversified by multiple gene duplications, gene fissions and deletions, and accretion of novel components. Surprisingly, we find that the 'tight adherence' (Tad) systems originated from the interkingdom transfer from Archaea to Bacteria of a system resembling the 'EppA-dependent' (Epd) pilus and were associated with the acquisition of a secretin. The phylogeny and content of ancestral systems suggest that initial bacterial pili were engaged in cell motility and/or DNA uptake. In contrast, specialised protein secretion systems arose several times independently and much later in natural history. The functional diversification of the TFF superfamily was accompanied by genetic rearrangements with implications for genetic regulation and horizontal gene transfer: systems encoded in fewer loci were more frequently exchanged between taxa. This may have contributed to their rapid evolution and spread across Bacteria and Archaea. Hence, the evolutionary history of the superfamily reveals an impressive catalogue of molecular evolution mechanisms that resulted in remarkable functional innovation and specialisation from a relatively small set of components.}, }
@article {pmid31314095, year = {2019}, author = {Shang, Y and Li, D and Hao, W and Schwarz, S and Shan, X and Liu, B and Zhang, SM and Li, XS and Du, XD}, title = {A prophage and two ICESa2603-family integrative and conjugative elements (ICEs) carrying optrA in Streptococcus suis.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {74}, number = {10}, pages = {2876-2879}, doi = {10.1093/jac/dkz309}, pmid = {31314095}, issn = {1460-2091}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Chloramphenicol/pharmacology ; Conjugation, Genetic ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Interspersed Repetitive Sequences ; Microbial Sensitivity Tests ; Oxazolidinones/pharmacology ; Polymerase Chain Reaction ; Prophages/genetics/*isolation &amp; purification ; Streptococcal Infections/veterinary ; Streptococcus suis/drug effects/*genetics/isolation &amp; purification ; Swine ; Swine Diseases/microbiology ; Whole Genome Sequencing ; }, abstract = {OBJECTIVES: To investigate the presence and transfer of the oxazolidinone/phenicol resistance gene optrA and identify the genetic elements involved in the horizontal transfer of the optrA gene in Streptococcus suis.<br><br>METHODS: A total of 237 S. suis isolates were screened for the presence of the optrA gene by PCR. Whole-genome DNA of three optrA-positive strains was completely sequenced using the Illumina MiSeq and Pacbio RSII platforms. MICs were determined by broth microdilution. Transferability of the optrA gene in S. suis was investigated by conjugation. The presence of circular intermediates was examined by inverse PCR.<br><br>RESULTS: The optrA gene was present in 11.8% (28/237) of the S. suis strains. In three strains, the optrA gene was flanked by two copies of IS1216 elements in the same orientation, located either on a prophage or on ICESa2603-family integrative and conjugative elements (ICEs), including one tandem ICE. In one isolate, the optrA-carrying ICE transferred with a frequency of 2.1&#x205f;&#xd7;&#x205f;10-8. After the transfer, the transconjugant displayed elevated MICs of the respective antimicrobial agents. Inverse PCRs revealed that circular intermediates of different sizes were formed in the three optrA-carrying strains, containing one copy of the IS1216E element and the optrA gene alone or in combination with other resistance genes.<br><br>CONCLUSIONS: A prophage and two ICESa2603-family ICEs (including one tandem ICE) associated with the optrA gene were identified in S. suis. The association of the optrA gene with the IS1216E elements and its location on either a prophage or ICEs will aid its horizontal transfer.}, }
@article {pmid31309702, year = {2019}, author = {Luque, A and Paytubi, S and Sánchez-Montejo, J and Gibert, M and Balsalobre, C and Madrid, C}, title = {Crosstalk between bacterial conjugation and motility is mediated by plasmid-borne regulators.}, journal = {Environmental microbiology reports}, volume = {11}, number = {5}, pages = {708-717}, doi = {10.1111/1758-2229.12784}, pmid = {31309702}, issn = {1758-2229}, support = {2017 SGR 499//Generalitat de Catalunya/International ; AGL2013-45339-R//Spanish Ministry of Science and Innovation/International ; //Spanish Ministry of Science/International ; PGC2018-096958-B-I00//Innovation and Universities/International ; }, mesh = {Bacterial Proteins/genetics ; *Conjugation, Genetic ; Escherichia coli/*genetics/physiology ; Flagella/genetics ; *Gene Expression Regulation, Bacterial ; Movement ; Plasmids/*genetics ; }, abstract = {Plasmid conjugation is a major horizontal gene transfer mechanism. The acquisition of a plasmid may cause a perturbation of the cell functions in addition to provide advantageous properties for the recipient cell, such as the gaining of antibiotic resistances. The interplay between plasmid and chromosomal functions has been studied using the IncHI1 plasmid R27. Plasmids of the incompatibility group HI1, isolated from several Gram-negative pathogens, are associated with the spread of multidrug resistance. Their conjugation is tightly regulated by temperature, being repressed at temperatures within the host (37°C). In this report, we described that at permissive temperature, when conjugation of plasmid R27 is prompted, a reduction in the motility of the cells is observed. This reduction is mediated by the plasmid-encoded regulators TrhR/TrhY, which together with HtdA form a plasmid-borne regulatory circuit controlling R27 conjugation. TrhR/TrhY, required to induce R27 conjugation, is responsible for the downregulation of the flagella synthesis and the consequent decrease in motility. TrhR/TrhY repress, direct or indirectly, the expression of the specific flagellar sigma subunit FliA and, consequently, the expression of all genes located bellow in the flagellar expression cascade.}, }
@article {pmid31309043, year = {2019}, author = {Lee, JW}, title = {Protocol measuring horizontal gene transfer from algae to non-photosynthetic organisms.}, journal = {MethodsX}, volume = {6}, number = {}, pages = {1564-1574}, pmid = {31309043}, issn = {2215-0161}, abstract = {Horizontal gene transfer (HGT) is a natural process for an organism to transfer genetic material to another organism that is a completely different species, for example, from a blue-green alga to a non-photosynthetic bacterium. The phenomenon of HGT is not only of an interest to the science of molecular genetics and biology, but also to the biosafety issue of genetic engineering. The novel protocol reported here for the first time teaches how to measure HGT from a genetically engineered (GE) blue-green alga (gene donor) to wild-type E. coli (recipient). This novel protocol can be used to measure HGT frequency for both plasmid transgenes and/or genomic transgenes from a donor to recipient organism. •According to this novel protocol, the HGT frequency may be calculated from the number of HGT recipient colonies observed, the number of recipient cells plated, and the donor-recipient co-incubation time.•This approach can also help test the possible HGT routes to assess whether a HGT is through a direct cell-to-cell interaction or by an indirect cell-to-liquid environment-to-cell process.•The protocol may be applied in full and/or in part with adjustments to measure HGT for a wide range of donor and recipient organisms of interest.}, }
@article {pmid31309007, year = {2019}, author = {Trubl, G and Roux, S and Solonenko, N and Li, YF and Bolduc, B and Rodríguez-Ramos, J and Eloe-Fadrosh, EA and Rich, VI and Sullivan, MB}, title = {Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e7265}, pmid = {31309007}, issn = {2167-8359}, abstract = {Soils impact global carbon cycling and their resident microbes are critical to their biogeochemical processing and ecosystem outputs. Based on studies in marine systems, viruses infecting soil microbes likely modulate host activities via mortality, horizontal gene transfer, and metabolic control. However, their roles remain largely unexplored due to technical challenges with separating, isolating, and extracting DNA from viruses in soils. Some of these challenges have been overcome by using whole genome amplification methods and while these have allowed insights into the identities of soil viruses and their genomes, their inherit biases have prevented meaningful ecological interpretations. Here we experimentally optimized steps for generating quantitatively-amplified viral metagenomes to better capture both ssDNA and dsDNA viruses across three distinct soil habitats along a permafrost thaw gradient. First, we assessed differing DNA extraction methods (PowerSoil, Wizard mini columns, and cetyl trimethylammonium bromide) for quantity and quality of viral DNA. This established PowerSoil as best for yield and quality of DNA from our samples, though ∼1/3 of the viral populations captured by each extraction kit were unique, suggesting appreciable differential biases among DNA extraction kits. Second, we evaluated the impact of purifying viral particles after resuspension (by cesium chloride gradients; CsCl) and of viral lysis method (heat vs bead-beating) on the resultant viromes. DNA yields after CsCl particle-purification were largely non-detectable, while unpurified samples yielded 1-2-fold more DNA after lysis by heat than by bead-beating. Virome quality was assessed by the number and size of metagenome-assembled viral contigs, which showed no increase after CsCl-purification, but did from heat lysis relative to bead-beating. We also evaluated sample preparation protocols for ssDNA virus recovery. In both CsCl-purified and non-purified samples, ssDNA viruses were successfully recovered by using the Accel-NGS 1S Plus Library Kit. While ssDNA viruses were identified in all three soil types, none were identified in the samples that used bead-beating, suggesting this lysis method may impact recovery. Further, 13 ssDNA vOTUs were identified compared to 582 dsDNA vOTUs, and the ssDNA vOTUs only accounted for ∼4% of the assembled reads, implying dsDNA viruses were dominant in these samples. This optimized approach was combined with the previously published viral resuspension protocol into a sample-to-virome protocol for soils now available at protocols.io, where community feedback creates 'living' protocols. This collective approach will be particularly valuable given the high physicochemical variability of soils, which will may require considerable soil type-specific optimization. This optimized protocol provides a starting place for developing quantitatively-amplified viromic datasets and will help enable viral ecogenomic studies on organic-rich soils.}, }
@article {pmid31305242, year = {2019}, author = {Kobras, CM and Falush, D}, title = {Adapting for life in the extreme.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, pmid = {31305242}, issn = {2050-084X}, mesh = {Archaea/genetics ; *Gene Transfer, Horizontal ; Genome ; Phylogeny ; *Rhodophyta ; }, abstract = {Red algae have adapted to extreme environments by acquiring genes from bacteria and archaea.}, }
@article {pmid31301509, year = {2019}, author = {Suzuki, Y and Hashimoto, R and Xie, H and Nishimura, E and Nishiyama, M and Nukazawa, K and Ishii, S}, title = {Growth and antibiotic resistance acquisition of Escherichia coli in a river that receives treated sewage effluent.}, journal = {The Science of the total environment}, volume = {690}, number = {}, pages = {696-704}, doi = {10.1016/j.scitotenv.2019.07.050}, pmid = {31301509}, issn = {1879-1026}, mesh = {Drug Resistance, Bacterial/*genetics ; *Environmental Monitoring ; Escherichia coli/*growth &amp; development ; Rivers/*microbiology ; Sewage/microbiology ; *Waste Disposal, Fluid ; }, abstract = {Wastewater treatment plants could discharge Escherichia coli and antibiotic resistant bacteria to the environment adjacent to, or downstream of their discharge point. However, their discharge also contains nutrients which could promote growth of E. coli in water environments. This study was done to clarify the potential of growth and antibiotic resistance acquisition of E. coli in a river environment. Levels of E. coli were monitored in a river that receives treated sewage effluent for over four years. River water, periphyton and sediment samples were collected at sites upstream and downstream of treated sewage inflow. Concentrations of E. coli increased in river water and periphyton at the sites downstream of the treated sewage inflow, although levels of E. coli were very low or below detection limit in the treated sewage samples. Concentrations of Chlorophyll a increased at the downstream sites, likely due to nutrient input from the treated sewage. Based on pulsed field gel electrophoresis, identical genotype occurred at multiple sites both upstream and downstream of the treated sewage inflow. However, strains resistant to antibiotics such as ampicillin, cefazolin, ciprofloxacin, and chloramphenicol were more frequently obtained from the downstream sites than the upstream sites. Multidrug resistant E. coli strains were detected in periphyton and sediment samples collected at the downstream sites. Non-resistant strains with PDGE genotype identical to the multi-drug strains were also detected, indicating that E. coli might have become resistant to antibiotics by acquiring resistance genes via horizontal gene transfer. Laboratory incubation experiment showed the growth of E. coli in periphyton or sediment-fed river water samples. These results suggest that the wastewater treatment inflow did not directly provide E. coli to the river water, but could promote the growth of periphyton, which could lead to the elevated levels of E. coli and the emergence of antibiotic resistant E. coli.}, }
@article {pmid31297970, year = {2019}, author = {Wang, M and Fu, H and Shen, XX and Ruan, R and Rokas, A and Li, H}, title = {Genomic features and evolution of the conditionally dispensable chromosome in the tangerine pathotype of Alternaria alternata.}, journal = {Molecular plant pathology}, volume = {20}, number = {10}, pages = {1425-1438}, pmid = {31297970}, issn = {1364-3703}, mesh = {Alternaria/genetics/metabolism/*pathogenicity ; Chromosomes, Fungal/genetics ; Citrus/*microbiology ; Fungal Proteins/genetics/metabolism ; Genome, Fungal/genetics ; Plant Diseases/microbiology ; }, abstract = {The tangerine pathotype of the ascomycete fungus Alternaria alternata is the causal agent of citrus brown spot, which can result in significant losses of both yield and marketability for tangerines worldwide. A conditionally dispensable chromosome (CDC), which harbours the host-selective ACT toxin gene cluster, is required for tangerine pathogenicity of A. alternata. To understand the genetic makeup and evolution of the tangerine pathotype CDC, we isolated and sequenced the CDCs of the A. alternata Z7 strain and analysed the function and evolution of their genes. The A. alternata Z7 strain has two CDCs (~1.1 and ~0.8 Mb, respectively), and the longer Z7 CDC contains all but one contig of the shorter one. Z7 CDCs contain 254 predicted protein-coding genes, which are enriched in functional categories associated with 'metabolic process' (55 genes, P = 0.037). Relatively few of the CDC genes can be classified as carbohydrate-active enzymes (CAZymes) (4) and transporters (19) and none as kinases. Evolutionary analysis of the 254 CDC proteins showed that their evolutionary conservation tends to be restricted within the genus Alternaria and that the CDC genes evolve faster than genes in the essential chromosomes, likely due to fewer selective constraints. Interestingly, phylogenetic analysis suggested that four of the 25 genes responsible for the ACT toxin production were likely transferred from Colletotrichum (Sordariomycetes). Functional experiments showed that two of them are essential for the virulence of the tangerine pathotype of A. alternata. These results provide new insights into the function and evolution of CDC genes in Alternaria.}, }
@article {pmid31295654, year = {2019}, author = {Quintela-Baluja, M and Abouelnaga, M and Romalde, J and Su, JQ and Yu, Y and Gomez-Lopez, M and Smets, B and Zhu, YG and Graham, DW}, title = {Spatial ecology of a wastewater network defines the antibiotic resistance genes in downstream receiving waters.}, journal = {Water research}, volume = {162}, number = {}, pages = {347-357}, pmid = {31295654}, issn = {1879-2448}, support = {MR/P028195/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Anti-Bacterial Agents ; Drug Resistance, Microbial ; Genes, Bacterial ; RNA, Ribosomal, 16S ; Spain ; *Wastewater ; }, abstract = {Wastewater treatment plants (WWTPs) are an effective barrier in the protection of human and environment health around the world, although WWTPs also are suggested to be selectors and-or reservoirs of antibiotic resistance genes (ARGs) before entering the environment. The dogma about WWTPs as "ARG selectors" presumes that biotreatment compartments (e.g., activated sludge; AS) are single densely populated ecosystems with elevated horizontal gene transfer. However, recent work has suggested WWTP biotreatment compartments may be different than previously believed relative to antibiotic resistance (AR) fate, and other process factors, such as bacterial separation and specific waste sources, may be key to ARGs released to the environment. Here we combined 16S rRNA metagenomic sequencing and high-throughput qPCR to characterise microbial communities and ARGs across a wastewater network in Spain that includes both community (i.e., non-clinical urban) and hospital sources. Contrary to expectations, ARGs found in downstream receiving waters were not dominated by AS biosolids (RAS), but more resembled raw wastewater sources. In fact, ARGs and microbial communities in liquid-phase WWTP effluents and RAS were significantly different (Bray-Curtis dissimilarity index = 0.66 ± 0.11), with a consequential fraction of influent ARGs and organisms passing directly through the WWTP with limited association with RAS. Instead, ARGs and organisms in the RAS may be more defined by biosolids separation and biophysical traits, such as flocculation, rather than ARG carriage. This explains why RAS has significantly lower ARG richness (47 ± 4 ARGs) than liquid-phase effluents (104 ± 5 ARGs), and downstream water column (135 ± 4 ARGs) and river sediments (120 ± 5 ARGs) (Tukey's test, p < 0.001). These data suggest RAS and liquid-phase WWTP effluents may reflect two parallel ecosystems with potentially limited ARG exchange. As such, ARG mitigation in WWTPs should more focus on removing bacterial hosts from the liquid phase, AR source reduction, and possibly disinfection to reduce ARG releases to the environment.}, }
@article {pmid31294043, year = {2019}, author = {Kampf, G}, title = {Adaptive bacterial response to low level chlorhexidine exposure and its implications for hand hygiene.}, journal = {Microbial cell (Graz, Austria)}, volume = {6}, number = {7}, pages = {307-320}, pmid = {31294043}, issn = {2311-2638}, abstract = {Chlorhexidine digluconate (CHG) is commonly used in healthcare, e.g. in skin antiseptics, antimicrobial soaps, alcohol-based hand rubs and oral or wound antiseptics. Aim of the literature review was to evaluate the potential of bacteria to adapt to low level CHG exposure. A maximum 4fold MIC increase to CHG was found after low level exposure in most of the 71 evaluated bacterial species. A strong adaptive mostly stable MIC change was described in strains or isolates of the healthcare-associated species E. coli, S. marcescens and P. aeruginosa (up to 500fold, 128fold or 32fold, respectively). The highest MIC values after adaptation were 2,048 mg/l (S. marcescens) and 1,024 mg/l (P. aeruginosa). A new resistance to tetracycline, gentamicin, meropeneme or triclosan was found in some adapted isolates. In E. coli horizontal gene transfer was induced (sulfonamide resistance by conjugation), pointing out an additional risk of sublethal CHG. The use of CHG in patient care - but also all other settings such as consumer products and households - should therefore be critically assessed and restricted to indications with a proven health benefit or justifiable public health benefits. Additional CHG has no health benefit when used in alcohol-based hand rubs and is not recommended by the WHO. For routine hand washing of soiled hands the use of plain soap is sufficient, CHG in soaps has no health benefit. In surgical hand antisepsis alcohol-based hand rubs should be preferred to CHG soaps. Implementation of these principles will help to reduce avoidable selection pressure.}, }
@article {pmid31293838, year = {2019}, author = {Vigué, L and Eyre-Walker, A}, title = {The comparative population genetics of Neisseria meningitidis and Neisseria gonorrhoeae.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e7216}, pmid = {31293838}, issn = {2167-8359}, abstract = {Neisseria meningitidis and N. gonorrhoeae are closely related pathogenic bacteria. To compare their population genetics, we compiled a dataset of 1,145 genes found across 20 N. meningitidis and 15 N. gonorrhoeae genomes. We find that N. meningitidis is seven-times more diverse than N. gonorrhoeae in their combined core genome. Both species have acquired the majority of their diversity by recombination with divergent strains, however, we find that N. meningitidis has acquired more of its diversity by recombination than N. gonorrhoeae. We find that linkage disequilibrium (LD) declines rapidly across the genomes of both species. Several observations suggest that N. meningitidis has a higher effective population size than N. gonorrhoeae; it is more diverse, the ratio of non-synonymous to synonymous polymorphism is lower, and LD declines more rapidly to a lower asymptote in N. meningitidis. The two species share a modest amount of variation, half of which seems to have been acquired by lateral gene transfer and half from their common ancestor. We investigate whether diversity varies across the genome of each species and find that it does. Much of this variation is due to different levels of lateral gene transfer. However, we also find some evidence that the effective population size varies across the genome. We test for adaptive evolution in the core genome using a McDonald-Kreitman test and by considering the diversity around non-synonymous sites that are fixed for different alleles in the two species. We find some evidence for adaptive evolution using both approaches.}, }
@article {pmid31293547, year = {2019}, author = {Passera, A and Compant, S and Casati, P and Maturo, MG and Battelli, G and Quaglino, F and Antonielli, L and Salerno, D and Brasca, M and Toffolatti, SL and Mantegazza, F and Delledonne, M and Mitter, B}, title = {Not Just a Pathogen? Description of a Plant-Beneficial Pseudomonas syringae Strain.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1409}, pmid = {31293547}, issn = {1664-302X}, abstract = {Plants develop in a microbe-rich environment and must interact with a plethora of microorganisms, both pathogenic and beneficial. Indeed, such is the case of Pseudomonas, and its model organisms P. fluorescens and P. syringae, a bacterial genus that has received particular attention because of its beneficial effect on plants and its pathogenic strains. The present study aims to compare plant-beneficial and pathogenic strains belonging to the P. syringae species to get new insights into the distinction between the two types of plant-microbe interactions. In assays carried out under greenhouse conditions, P. syringae pv. syringae strain 260-02 was shown to promote plant-growth and to exert biocontrol of P. syringae pv. tomato strain DC3000, against the Botrytis cinerea fungus and the Cymbidium Ringspot Virus. This P. syringae strain also had a distinct volatile emission profile, as well as a different plant-colonization pattern, visualized by confocal microscopy and gfp labeled strains, compared to strain DC3000. Despite the different behavior, the P. syringae strain 260-02 showed great similarity to pathogenic strains at a genomic level. However, genome analyses highlighted a few differences that form the basis for the following hypotheses regarding strain 260-02. P. syringae strain 260-02: (i) possesses non-functional virulence genes, like the mangotoxin-producing operon Mbo; (ii) has different regulation pathways, suggested by the difference in the autoinducer system and the lack of a virulence activator gene; (iii) has genes encoding DNA methylases different from those found in other P. syringae strains, suggested by the presence of horizontal-gene-transfer-obtained methylases that could affect gene expression.}, }
@article {pmid31292537, year = {2019}, author = {Salcher, MM and Schaefle, D and Kaspar, M and Neuenschwander, SM and Ghai, R}, title = {Evolution in action: habitat transition from sediment to the pelagial leads to genome streamlining in Methylophilaceae.}, journal = {The ISME journal}, volume = {13}, number = {11}, pages = {2764-2777}, pmid = {31292537}, issn = {1751-7370}, mesh = {Adaptation, Physiological ; *Ecosystem ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome Size ; *Genome, Bacterial ; Geologic Sediments/*microbiology ; Lakes/*microbiology ; Methylophilaceae/classification/*genetics/isolation &amp; purification/physiology ; Phylogeny ; Seawater/*microbiology ; }, abstract = {The most abundant aquatic microbes are small in cell and genome size. Genome-streamlining theory predicts gene loss caused by evolutionary selection driven by environmental factors, favouring superior competitors for limiting resources. However, evolutionary histories of such abundant, genome-streamlined microbes remain largely unknown. Here we reconstruct the series of steps in the evolution of some of the most abundant genome-streamlined microbes in freshwaters ("Ca. Methylopumilus") and oceans (marine lineage OM43). A broad genomic spectrum is visible in the family Methylophilaceae (Betaproteobacteria), from sediment microbes with medium-sized genomes (2-3 Mbp genome size), an occasionally blooming pelagic intermediate (1.7 Mbp), and the most reduced pelagic forms (1.3 Mbp). We show that a habitat transition from freshwater sediment to the relatively oligotrophic pelagial was accompanied by progressive gene loss and adaptive gains. Gene loss has mainly affected functions not necessarily required or advantageous in the pelagial or is encoded by redundant pathways. Likewise, we identified genes providing adaptations to oligotrophic conditions that have been transmitted horizontally from pelagic freshwater microbes. Remarkably, the secondary transition from the pelagial of lakes to the oceans required only slight modifications, i.e., adaptations to higher salinity, gained via horizontal gene transfer from indigenous microbes. Our study provides first genomic evidence of genome reduction taking place during habitat transitions. In this regard, the family Methylophilaceae is an exceptional model for tracing the evolutionary history of genome streamlining as such a collection of evolutionarily related microbes from different habitats is rare in the microbial world.}, }
@article {pmid31291702, year = {2019}, author = {Callier, V}, title = {Core Concept: Gene transfers from bacteria and viruses may be shaping complex organisms.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {28}, pages = {13714-13716}, pmid = {31291702}, issn = {1091-6490}, mesh = {Bacteria/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome/*genetics ; Genomics ; Viruses/*genetics ; }, }
@article {pmid31289171, year = {2019}, author = {Bikkarolla, SK and Nordberg, V and Rajer, F and Müller, V and Kabir, MH and Kk, S and Dvirnas, A and Ambjörnsson, T and Giske, CG and Navér, L and Sandegren, L and Westerlund, F}, title = {Optical DNA Mapping Combined with Cas9-Targeted Resistance Gene Identification for Rapid Tracking of Resistance Plasmids in a Neonatal Intensive Care Unit Outbreak.}, journal = {mBio}, volume = {10}, number = {4}, pages = {}, pmid = {31289171}, issn = {2150-7511}, mesh = {CRISPR-Associated Protein 9/*genetics ; Child, Preschool ; Chromosome Mapping ; Disease Outbreaks ; Drug Resistance, Multiple, Bacterial/*genetics ; Fluorescence ; Follow-Up Studies ; Humans ; Infant ; Infant, Newborn ; *Intensive Care Units, Neonatal ; Klebsiella Infections/microbiology ; Klebsiella pneumoniae/enzymology/*genetics ; Plasmids/*genetics ; Sweden ; beta-Lactamases/genetics ; }, abstract = {The global spread of antibiotic resistance among Enterobacteriaceae is largely due to multidrug resistance plasmids that can transfer between different bacterial strains and species. Horizontal gene transfer of resistance plasmids can complicate hospital outbreaks and cause problems in epidemiological tracing, since tracing is usually based on bacterial clonality. We have developed a method, based on optical DNA mapping combined with Cas9-assisted identification of resistance genes, which is used here to characterize plasmids during an extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae outbreak at a Swedish neonatal intensive care unit. The outbreak included 17 neonates initially colonized with ESBL-producing Klebsiella pneumoniae (ESBL-KP), some of which were found to carry additional ESBL-producing Escherichia coli (ESBL-EC) in follow-up samples. We demonstrate that all ESBL-KP isolates contained two plasmids with the blaCTX-M-15 gene located on the smaller one (~80 kbp). The same ESBL-KP clone was present in follow-up samples for up to 2 years in some patients, and the plasmid carrying the blaCTX-M-15 gene was stable throughout this time period. However, extensive genetic rearrangements within the second plasmid were observed in the optical DNA maps for several of the ESBL-KP isolates. Optical mapping also demonstrated that even though other bacterial clones and species carrying blaCTX-M group 1 genes were found in some neonates, no transfer of resistance plasmids had occurred. The data instead pointed toward unrelated acquisition of ESBL-producing Enterobacteriaceae (EPE). In addition to revealing important information about the specific outbreak, the method presented is a promising tool for surveillance and infection control in clinical settings.IMPORTANCE This study presents how a novel method, based on visualizing single plasmids using sequence-specific fluorescent labeling, could be used to analyze the genetic dynamics of an outbreak of resistant bacteria in a neonatal intensive care unit at a Swedish hospital. Plasmids are a central reason for the rapid global spread of bacterial resistance to antibiotics. In a single experimental procedure, this method replaces many traditional plasmid analysis techniques that together provide limited details and are slow to perform. The method is much faster than long-read whole-genome sequencing and offers direct genetic comparison of patient samples. We could conclude that no transfer of resistance plasmids had occurred between different bacteria during the outbreak and that secondary cases of ESBL-producing Enterobacteriaceae carriage were instead likely due to influx of new strains. We believe that the method offers potential in improving surveillance and infection control of resistant bacteria in hospitals.}, }
@article {pmid31288975, year = {2019}, author = {Morley, VJ and Woods, RJ and Read, AF}, title = {Bystander Selection for Antimicrobial Resistance: Implications for Patient Health.}, journal = {Trends in microbiology}, volume = {27}, number = {10}, pages = {864-877}, pmid = {31288975}, issn = {1878-4380}, support = {K08 AI119182/AI/NIAID NIH HHS/United States ; L30 AI113834/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Infective Agents/*therapeutic use ; Bacterial Infections/drug therapy ; Cross Infection/drug therapy/microbiology ; Drug Resistance, Bacterial/*drug effects ; Gene Transfer, Horizontal ; Humans ; Microbiota/*drug effects/physiology ; Risk Factors ; }, abstract = {Antimicrobial therapy promotes resistance emergence in target infections and in off-target microbiota. Off-target resistance emergence threatens patient health when off-target populations are a source of future infections, as they are for many important drug-resistant pathogens. However, the health risks of antimicrobial exposure in off-target populations remain largely unquantified, making rational antibiotic stewardship challenging. Here, we discuss the contribution of bystander antimicrobial exposure to the resistance crisis, the implications for antimicrobial stewardship, and some novel opportunities to limit resistance evolution while treating target pathogens.}, }
@article {pmid31285337, year = {2019}, author = {Greenlon, A and Chang, PL and Damtew, ZM and Muleta, A and Carrasquilla-Garcia, N and Kim, D and Nguyen, HP and Suryawanshi, V and Krieg, CP and Yadav, SK and Patel, JS and Mukherjee, A and Udupa, S and Benjelloun, I and Thami-Alami, I and Yasin, M and Patil, B and Singh, S and Sarma, BK and von Wettberg, EJB and Kahraman, A and Bukun, B and Assefa, F and Tesfaye, K and Fikre, A and Cook, DR}, title = {Global-level population genomics reveals differential effects of geography and phylogeny on horizontal gene transfer in soil bacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {30}, pages = {15200-15209}, pmid = {31285337}, issn = {1091-6490}, mesh = {Biological Evolution ; Cicer/*microbiology ; Conjugation, Genetic ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Mesorhizobium/classification/*genetics ; Metagenomics/methods ; Microbial Consortia/*genetics ; Nitrogen Fixation/physiology ; Phylogeny ; Phylogeography ; Soil/classification ; Soil Microbiology ; Symbiosis/genetics ; }, abstract = {Although microorganisms are known to dominate Earth's biospheres and drive biogeochemical cycling, little is known about the geographic distributions of microbial populations or the environmental factors that pattern those distributions. We used a global-level hierarchical sampling scheme to comprehensively characterize the evolutionary relationships and distributional limitations of the nitrogen-fixing bacterial symbionts of the crop chickpea, generating 1,027 draft whole-genome sequences at the level of bacterial populations, including 14 high-quality PacBio genomes from a phylogenetically representative subset. We find that diverse Mesorhizobium taxa perform symbiosis with chickpea and have largely overlapping global distributions. However, sampled locations cluster based on the phylogenetic diversity of Mesorhizobium populations, and diversity clusters correspond to edaphic and environmental factors, primarily soil type and latitude. Despite long-standing evolutionary divergence and geographic isolation, the diverse taxa observed to nodulate chickpea share a set of integrative conjugative elements (ICEs) that encode the major functions of the symbiosis. This symbiosis ICE takes 2 forms in the bacterial chromosome-tripartite and monopartite-with tripartite ICEs confined to a broadly distributed superspecies clade. The pairwise evolutionary relatedness of these elements is controlled as much by geographic distance as by the evolutionary relatedness of the background genome. In contrast, diversity in the broader gene content of Mesorhizobium genomes follows a tight linear relationship with core genome phylogenetic distance, with little detectable effect of geography. These results illustrate how geography and demography can operate differentially on the evolution of bacterial genomes and offer useful insights for the development of improved technologies for sustainable agriculture.}, }
@article {pmid31283433, year = {2019}, author = {Thapa, SP and Davis, EW and Lyu, Q and Weisberg, AJ and Stevens, DM and Clarke, CR and Coaker, G and Chang, JH}, title = {The Evolution, Ecology, and Mechanisms of Infection by Gram-Positive, Plant-Associated Bacteria.}, journal = {Annual review of phytopathology}, volume = {57}, number = {}, pages = {341-365}, doi = {10.1146/annurev-phyto-082718-100124}, pmid = {31283433}, issn = {1545-2107}, mesh = {Ecology ; Gram-Positive Bacteria ; Humans ; *Infections ; Plants ; *Symbiosis ; }, abstract = {Gram-positive bacteria are prominent members of plant-associated microbial communities. Although many are hypothesized to be beneficial, some are causative agents of economically important diseases of crop plants. Because the features of Gram-positive bacteria are fundamentally different relative to those of Gram-negative bacteria, the evolution and ecology as well as the mechanisms used to colonize and infect plants also differ. Here, we discuss recent advances in our understanding of Gram-positive, plant-associated bacteria and provide a framework for future research directions on these important plant symbionts.}, }
@article {pmid31282048, year = {2019}, author = {Depotter, JRL and Shi-Kunne, X and Missonnier, H and Liu, T and Faino, L and van den Berg, GCM and Wood, TA and Zhang, B and Jacques, A and Seidl, MF and Thomma, BPHJ}, title = {Dynamic virulence-related regions of the plant pathogenic fungus Verticillium dahliae display enhanced sequence conservation.}, journal = {Molecular ecology}, volume = {28}, number = {15}, pages = {3482-3495}, pmid = {31282048}, issn = {1365-294X}, mesh = {Base Sequence ; Conserved Sequence/*genetics ; Gene Transfer, Horizontal/genetics ; *Genome, Fungal ; Haploidy ; Models, Genetic ; Phylogeny ; Plants/*microbiology ; Selection, Genetic ; Species Specificity ; Verticillium/*genetics/*pathogenicity ; Virulence/genetics ; }, abstract = {Plant pathogens continuously evolve to evade host immune responses. During host colonization, many fungal pathogens secrete effectors to perturb such responses, but these in turn may become recognized by host immune receptors. To facilitate the evolution of effector repertoires, such as the elimination of recognized effectors, effector genes often reside in genomic regions that display increased plasticity, a phenomenon that is captured in the two-speed genome hypothesis. The genome of the vascular wilt fungus Verticillium dahliae displays regions with extensive presence/absence polymorphisms, so-called lineage-specific regions, that are enriched in in planta-induced putative effector genes. As expected, comparative genomics reveals differential degrees of sequence divergence between lineage-specific regions and the core genome. Unanticipated, lineage-specific regions display markedly higher sequence conservation in coding as well as noncoding regions than the core genome. We provide evidence that disqualifies horizontal transfer to explain the observed sequence conservation and conclude that sequence divergence occurs at a slower pace in lineage-specific regions of the V. dahliae genome. We hypothesize that differences in chromatin organisation may explain lower nucleotide substitution rates in the plastic, lineage-specific regions of V. dahliae.}, }
@article {pmid31280161, year = {2019}, author = {Wang, Z and Song, G and Li, Y and Yu, G and Hou, X and Gan, Z and Li, R}, title = {The diversity, origin, and evolutionary analysis of geosmin synthase gene in cyanobacteria.}, journal = {The Science of the total environment}, volume = {689}, number = {}, pages = {789-796}, doi = {10.1016/j.scitotenv.2019.06.468}, pmid = {31280161}, issn = {1879-1026}, mesh = {Bacterial Proteins/*genetics/metabolism ; Cyanobacteria/*genetics/metabolism ; DNA, Bacterial/analysis ; *Evolution, Molecular ; *Genetic Variation ; Naphthols/*metabolism ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {The sesquiterpene geosmin, mainly originating from cyanobacteria, is considered one of the problematic odor compounds responsible for unpleasant-tasting and -smelling water episodes in freshwater supplies. The biochemistry and genetics of geosmin synthesis in cyanobacteria is well-elucidated and the geosmin synthase gene (geo) has been cloned and characterized in recent years. However, understanding the diversity, origin, and evolution of geo has been hindered by the limited availability of geo sequences to date. On the basis of the cloned geo sequences from16 filamentous geosmin-producing cyanobacterial species, representing 11 genera in Nostocales and Oscillatoriales, the diversity and evolution of geo in cyanobacteria was systematically analyzed in this study. Homologous alignment revealed that geo is highly conserved among the examined cyanobacterial species, with DNA sequence identities >0.72. Phylogenetic reconstruction and codon bias analysis based on geo suggest that cyanobacterial geo form a monophyletic branch with a common origin and ancestor for cyanobacteria, actinomycetes, and myxobacteria. The global ratio of nonsynonymous/synonymous nucleotide substitutions (dN/dS) was 0.125, which is substantially <1 and indicates strong purifying selection in the evolution of cyanobacterial geo. To add to further interest, horizontal gene transfer of cyanobacterial geo in evolutionary history was confirmed by the discovery of an incongruent coevolutionary relationship between geo and housekeeping genes 16S rDNA and rpoC. The present study enhances the fundamental understanding of cyanobacterial geo in diversity and evolution, and sheds light on the development of molecular assays for detection and molecular ecology research of geosmin-producing cyanobacteria.}, }
@article {pmid31279547, year = {2019}, author = {Selle, K and Andersen, JM and Barrangou, R}, title = {Short communication: Transcriptional response to a large genomic island deletion in the dairy starter culture Streptococcus thermophilus.}, journal = {Journal of dairy science}, volume = {102}, number = {9}, pages = {7800-7806}, doi = {10.3168/jds.2019-16397}, pmid = {31279547}, issn = {1525-3198}, mesh = {Animals ; Clustered Regularly Interspaced Short Palindromic Repeats ; Fermentation ; Gene Deletion ; Gene Expression Regulation, Bacterial/physiology ; *Genomic Islands ; Genomics ; Lactic Acid/metabolism ; Lactobacillus delbrueckii/metabolism ; Milk/*microbiology ; Streptococcus thermophilus/genetics/*metabolism ; Transcriptome ; Yogurt/*microbiology ; }, abstract = {Streptococcus thermophilus is a lactic acid bacterium widely used in the syntrophic fermentation of milk into yogurt and cheese. Streptococcus thermophilus has adapted to ferment milk primarily through reductive genome evolution but also through acquisition of genes conferring proto-cooperation with Lactobacillus bulgaricus and efficient metabolism of milk macronutrients. Genomic analysis of Strep. thermophilus strains suggests that mobile genetic elements have contributed to genomic evolution through horizontal gene transfer and genomic plasticity. We previously used the endogenous type II CRISPR-Cas [clustered regularly interspaced short palindromic repeats (CRISPR) with CRISPR-associated sequences (Cas)] system in Strep. thermophilus to isolate derivatives lacking the chromosomal mobile genetic element and expandable island that display decreased fitness under routine culturing conditions. Of note, the Lac operon and Leloir pathway genes were deleted in the largest expendable genomic island (102 kbp), rendering the strain incapable of acidifying milk. However, the removal of other open reading frames in the same island had unclear effects on the fitness and regulatory networks of Strep. thermophilus. To uncover the physiological basis for the observed phenotypic changes and underlying regulatory networks affected by deletion of the 102-kbp genomic island in Strep. thermophilus, we analyzed the transcriptome of the mutant that lacked ∼5% of its genome. In addition to the loss of transcripts encoded by the deleted material, we detected a total of 56 genes that were differentially expressed, primarily encompassing 10 select operons. Several predicted metabolic pathways were affected, including amino acid and purine metabolism, oligopeptide transport, and iron transport. Collectively, these results suggest that deletion of a 102-kb genomic island in Strep. thermophilus influences compensatory transcription of starvation stress response genes and metabolic pathways involved in important niche-related adaptation.}, }
@article {pmid31279132, year = {2020}, author = {Martins, ER and Bueno, MFC and Francisco, GR and Casella, T and de Oliveira Garcia, D and Cerdeira, LT and Gerber, AL and de Almeida, LGP and Lincopan, N and de Vasconcelos, ATR and Nogueira, MCL and Estofolete, CF}, title = {Genome and plasmid context of two rmtG-carrying Enterobacter hormaechei isolated from urinary tract infections in Brazil.}, journal = {Journal of global antimicrobial resistance}, volume = {20}, number = {}, pages = {36-40}, doi = {10.1016/j.jgar.2019.06.020}, pmid = {31279132}, issn = {2213-7173}, mesh = {Bacterial Proteins/genetics ; Brazil ; Chromosomes, Bacterial/*genetics ; Enterobacter/classification/genetics/*isolation &amp; purification ; Enterobacteriaceae Infections/*diagnosis ; Gene Transfer, Horizontal ; High-Throughput Nucleotide Sequencing ; Humans ; Methyltransferases/*genetics ; Plasmids/*genetics ; Urinary Tract Infections/*microbiology ; Whole Genome Sequencing ; }, abstract = {OBJECTIVES: Enterobacter hormaechei is an important causative agent of severe infections in critically ill patients. Aminoglycosides are among the main antibiotics for the treatment of E. hormaechei infections, however the development of antimicrobial resistance is an increasing problem. RmtG is a 16S rRNA methyltransferase, a class of enzymes conferring high-level resistance to clinically relevant aminoglycosides. The aim of this study was to characterise the full genetic context of plasmids harbouring the rmtG gene in two aminoglycoside-resistant E. hormaechei isolated in Brazil.<br><br>METHODS: ThermtG-harbouring plasmids were transferred to an Escherichia coli J53 recipient strain and were fully sequenced using a MiSeq sequencing system. Complete genome assemblies were accomplished using a combination of Newbler v.3.0, SPAdes 3.10.0 and phrap/cross_match programs. Plasmid sequences were annotated using RAST server and were then manually curated using BLAST databases and ISfinder. Easyfig 2.0 was used to map and compare regions of interest containing rmtG in both plasmids.<br><br>RESULTS: Both isolates carried thermtG gene on an IncA/C plasmid of &#x2dc;152kb and &#x2dc;235kb, respectively, associated with a Tn3 transposon. The plasmids contain a transfer region as well as genes involved in plasmid stability and resistance to &#x3b2;-lactams, sulfonamides and quaternary ammonium compounds. One of the plasmids also carried the mrk operon encoding type 3 fimbriae.<br><br>CONCLUSION: This first detection ofrmtG in E. hormaechei supports the ability for horizontal transfer. The location in complex genetic platforms carried by Tn3 transposons in IncA/C plasmids may facilitate dissemination to other Gram-negative pathogens, further limiting treatment options.}, }
@article {pmid31278791, year = {2019}, author = {Dunny, GM and Hirt, H}, title = {A new flavor of entry exclusion in ICE elements provides a selective advantage for the element and its host.}, journal = {Molecular microbiology}, volume = {112}, number = {4}, pages = {1061-1065}, pmid = {31278791}, issn = {1365-2958}, support = {R35 GM118079/GM/NIGMS NIH HHS/United States ; }, mesh = {*Bacillus subtilis ; Conjugation, Genetic ; *Gene Transfer, Horizontal ; }, abstract = {Entry exclusion has been described in many bacterial conjugation systems, but their molecular mechanisms are not well understood. In the current issue, Avello et al. describe a new exclusion system in the conjugative element ICEBs1. They identify the yddJ gene as the functional exclusion gene and its target as the protein product of the conG gene. They provide evidence for a possible mechanism and for the contribution of the system to reduce fitness costs of ICE expression.}, }
@article {pmid31278675, year = {2019}, author = {Guio, L and González, J}, title = {New Insights on the Evolution of Genome Content: Population Dynamics of Transposable Elements in Flies and Humans.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1910}, number = {}, pages = {505-530}, doi = {10.1007/978-1-4939-9074-0_16}, pmid = {31278675}, issn = {1940-6029}, mesh = {Animals ; *DNA Transposable Elements ; Drosophila/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; Genetics, Population ; *Genome ; *Genomics/methods ; Humans ; Mutagenesis, Insertional ; Mutation Rate ; Population Dynamics ; }, abstract = {Understanding the abundance, diversity, and distribution of TEs in genomes is crucial to understand genome structure, function, and evolution. Advances in whole-genome sequencing techniques, as well as in bioinformatics tools, have increased our ability to detect and analyze the transposable element content in genomes. In addition to reference genomes, we now have access to population datasets in which multiple individuals within a species are sequenced. In this chapter, we highlight the recent advances in the study of TE population dynamics focusing on fruit flies and humans, which represent two extremes in terms of TE abundance, diversity, and activity. We review the most recent methodological approaches applied to the study of TE dynamics as well as the new knowledge on host factors involved in the regulation of TE activity. In addition to transposition rates, we also focus on TE deletion rates and on the selective forces that affect the dynamics of TEs in genomes.}, }
@article {pmid31278668, year = {2019}, author = {Watson, AK and Lannes, R and Pathmanathan, JS and Méheust, R and Karkar, S and Colson, P and Corel, E and Lopez, P and Bapteste, E}, title = {The Methodology Behind Network Thinking: Graphs to Analyze Microbial Complexity and Evolution.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1910}, number = {}, pages = {271-308}, doi = {10.1007/978-1-4939-9074-0_9}, pmid = {31278668}, issn = {1940-6029}, mesh = {Biodiversity ; Biological Evolution ; Computational Biology/methods ; Ecosystem ; Evolution, Molecular ; Gene Ontology ; Gene Regulatory Networks ; High-Throughput Nucleotide Sequencing ; *Metagenome ; *Metagenomics/methods ; Microbiota ; Molecular Sequence Annotation ; Multigene Family ; }, abstract = {In the post genomic era, large and complex molecular datasets from genome and metagenome sequencing projects expand the limits of what is possible for bioinformatic analyses. Network-based methods are increasingly used to complement phylogenetic analysis in studies in molecular evolution, including comparative genomics, classification, and ecological studies. Using network methods, the vertical and horizontal relationships between all genes or genomes, whether they are from cellular chromosomes or mobile genetic elements, can be explored in a single expandable graph. In recent years, development of new methods for the construction and analysis of networks has helped to broaden the availability of these approaches from programmers to a diversity of users. This chapter introduces the different kinds of networks based on sequence similarity that are already available to tackle a wide range of biological questions, including sequence similarity networks, gene-sharing networks and bipartite graphs, and a guide for their construction and analyses.}, }
@article {pmid31278667, year = {2019}, author = {Puigbò, P and Wolf, YI and Koonin, EV}, title = {Genome-Wide Comparative Analysis of Phylogenetic Trees: The Prokaryotic Forest of Life.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1910}, number = {}, pages = {241-269}, doi = {10.1007/978-1-4939-9074-0_8}, pmid = {31278667}, issn = {1940-6029}, mesh = {Algorithms ; Biological Evolution ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome-Wide Association Study/methods ; *Genomics/methods ; Models, Genetic ; *Phylogeny ; Prokaryotic Cells/*classification ; }, abstract = {Genome-wide comparison of phylogenetic trees is becoming an increasingly common approach in evolutionary genomics, and a variety of approaches for such comparison have been developed. In this article we present several methods for comparative analysis of large numbers of phylogenetic trees. To compare phylogenetic trees taking into account the bootstrap support for each internal branch, the boot-split distance (BSD) method is introduced as an extension of the previously developed split distance (SD) method for tree comparison. The BSD method implements the straightforward idea that comparison of phylogenetic trees can be made more robust by treating tree splits differentially depending on the bootstrap support. Approaches are also introduced for detecting treelike and netlike evolutionary trends in the phylogenetic Forest of Life (FOL), i.e., the entirety of the phylogenetic trees for conserved genes of prokaryotes. The principal method employed for this purpose includes mapping quartets of species onto trees to calculate the support of each quartet topology and so to quantify the tree and net contributions to the distances between species. We describe the applications methods used to analyze the FOL and the results obtained with these methods. These results support the concept of the Tree of Life (TOL) as a central evolutionary trend in the FOL as opposed to the traditional view of the TOL as a "species tree."}, }
@article {pmid31278666, year = {2019}, author = {Liu, L and Anderson, C and Pearl, D and Edwards, SV}, title = {Modern Phylogenomics: Building Phylogenetic Trees Using the Multispecies Coalescent Model.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1910}, number = {}, pages = {211-239}, doi = {10.1007/978-1-4939-9074-0_7}, pmid = {31278666}, issn = {1940-6029}, mesh = {Evolution, Molecular ; Gene Duplication ; Gene Flow ; Gene Transfer, Horizontal ; Genetic Heterogeneity ; Genetic Loci ; *Genomics/methods ; *Models, Genetic ; Multilocus Sequence Typing/methods ; *Phylogeny ; }, abstract = {The multispecies coalescent (MSC) model provides a compelling framework for building phylogenetic trees from multilocus DNA sequence data. The pure MSC is best thought of as a special case of so-called "multispecies network coalescent" models, in which gene flow is allowed among branches of the tree, whereas MSC methods assume there is no gene flow between diverging species. Early implementations of the MSC, such as "parsimony" or "democratic vote" approaches to combining information from multiple gene trees, as well as concatenation, in which DNA sequences from multiple gene trees are combined into a single "supergene," were quickly shown to be inconsistent in some regions of tree space, in so far as they converged on the incorrect species tree as more gene trees and sequence data were accumulated. The anomaly zone, a region of tree space in which the most frequent gene tree is different from the species tree, is one such region where many so-called "coalescent" methods are inconsistent. Second-generation implementations of the MSC employed Bayesian or likelihood models; these are consistent in all regions of gene tree space, but Bayesian methods in particular are incapable of handling the large phylogenomic data sets currently available. Two-step methods, such as MP-EST and ASTRAL, in which gene trees are first estimated and then combined to estimate an overarching species tree, are currently popular in part because they can handle large phylogenomic data sets. These methods are consistent in the anomaly zone but can sometimes provide inappropriate measures of tree support or apportion error and signal in the data inappropriately. MP-EST in particular employs a likelihood model which can be conveniently manipulated to perform statistical tests of competing species trees, incorporating the likelihood of the collected gene trees on each species tree in a likelihood ratio test. Such tests provide a useful alternative to the multilocus bootstrap, which only indirectly tests the appropriateness of competing species trees. We illustrate these tests and implementations of the MSC with examples and suggest that MSC methods are a useful class of models effectively using information from multiple loci to build phylogenetic trees.}, }
@article {pmid31276345, year = {2019}, author = {Molina-Romero, C and Arrieta, O and Hernández-Pando, R}, title = {Tuberculosis and lung cancer.}, journal = {Salud publica de Mexico}, volume = {61}, number = {3}, pages = {286-291}, doi = {10.21149/10090}, pmid = {31276345}, issn = {1606-7916}, mesh = {Humans ; Lung Neoplasms/*complications/*epidemiology ; Tuberculosis, Pulmonary/*complications/*epidemiology ; }, abstract = {OBJECTIVE: To describe the epidemiological studies about the relationship between lung cancer (LC) and pulmonary tuberculosis (Tb) and its possible molecular mechanisms.<br><br>MATERIALS AND METHODS: We reviewed research databases in search of publications that included keywords LC and Tb.<br><br>RESULTS: It has been proposed that chronic inflammation in the lungs due to Tb could cause clastogenic activity in the DNA of bronchial epithelium. Another possibility is lateral gene transfer; since Mycobacterium tuberculosis (MTb) is an intracellular organism, bacterial DNA could integrate to bronchial epithelial cells inducing neoplastic transformation.<br><br>CONCLUSIONS: There are epidemiological reports, particularly from Asian countries, which confirm a relationship between LC and Tb. MTb could play an active role in cellular transformation and it is important to elucidate the mecha- nism involved.}, }
@article {pmid31273387, year = {2019}, author = {Kopejtka, K and Lin, Y and Jakubovičová, M and Koblížek, M and Tomasch, J}, title = {Clustered Core- and Pan-Genome Content on Rhodobacteraceae Chromosomes.}, journal = {Genome biology and evolution}, volume = {11}, number = {8}, pages = {2208-2217}, pmid = {31273387}, issn = {1759-6653}, mesh = {Bacterial Proteins/*genetics ; Chromosomes, Bacterial/*genetics ; DNA Replication ; Gene Expression Regulation, Bacterial ; *Genome, Bacterial ; *Phylogeny ; Rhodobacteraceae/*genetics ; }, abstract = {In Bacteria, chromosome replication starts at a single origin of replication and proceeds on both replichores. Due to its asymmetric nature, replication influences chromosome structure and gene organization, mutation rate, and expression. To date, little is known about the distribution of highly conserved genes over the bacterial chromosome. Here, we used a set of 101 fully sequenced Rhodobacteraceae representatives to analyze the relationship between conservation of genes within this family and their distance from the origin of replication. Twenty-two of the analyzed species had core genes clustered significantly closer to the origin of replication with representatives of the genus Celeribacter being the most apparent example. Interestingly, there were also eight species with the opposite organization. In particular, Rhodobaca barguzinensis and Loktanella vestfoldensis showed a significant increase of core genes with distance from the origin of replication. The uneven distribution of low-conserved regions is in particular pronounced for genomes in which the halves of one replichore differ in their conserved gene content. Phage integration and horizontal gene transfer partially explain the scattered nature of Rhodobacteraceae genomes. Our findings lay the foundation for a better understanding of bacterial genome evolution and the role of replication therein.}, }
@article {pmid31266954, year = {2019}, author = {Rivas-Marin, E and Stettner, S and Gottshall, EY and Santana-Molina, C and Helling, M and Basile, F and Ward, NL and Devos, DP}, title = {Essentiality of sterol synthesis genes in the planctomycete bacterium Gemmata obscuriglobus.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {2916}, pmid = {31266954}, issn = {2041-1723}, support = {P20 GM103432/GM/NIGMS NIH HHS/United States ; P20 RR016474/RR/NCRR NIH HHS/United States ; }, mesh = {Bacterial Proteins/*genetics/metabolism ; Biological Evolution ; Planctomycetales/genetics/growth &amp; development/*metabolism ; Sterols/*biosynthesis ; }, abstract = {Sterols and hopanoids are chemically and structurally related lipids mostly found in eukaryotic and bacterial cell membranes. Few bacterial species have been reported to produce sterols and this anomaly had originally been ascribed to lateral gene transfer (LGT) from eukaryotes. In addition, the functions of sterols in these bacteria are unknown and the functional overlap between sterols and hopanoids is still unclear. Gemmata obscuriglobus is a bacterium from the Planctomycetes phylum that synthesizes sterols, in contrast to its hopanoid-producing relatives. Here we show that sterols are essential for growth of G. obscuriglobus, and that sterol depletion leads to aberrant membrane structures and defects in budding cell division. This report of sterol essentiality in a prokaryotic species advances our understanding of sterol distribution and function, and provides a foundation to pursue fundamental questions in evolutionary cell biology.}, }
@article {pmid31262826, year = {2019}, author = {Tchesnokova, V and Radey, M and Chattopadhyay, S and Larson, L and Weaver, JL and Kisiela, D and Sokurenko, EV}, title = {Pandemic fluoroquinolone resistant Escherichia coli clone ST1193 emerged via simultaneous homologous recombinations in 11 gene loci.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {29}, pages = {14740-14748}, pmid = {31262826}, issn = {1091-6490}, support = {R01 AI106007/AI/NIAID NIH HHS/United States ; R41 AI116114/AI/NIAID NIH HHS/United States ; R42 AI116114/AI/NIAID NIH HHS/United States ; }, mesh = {Chromosomes, Bacterial/genetics ; DNA Gyrase/genetics ; DNA Topoisomerase IV/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli Proteins/genetics ; Fluoroquinolones/*pharmacology/therapeutic use ; Gene Transfer, Horizontal ; *Genetic Loci ; *Homologous Recombination ; Humans ; Microbial Sensitivity Tests ; Mutation ; Pandemics ; Urinary Tract Infections/drug therapy/epidemiology/microbiology ; Uropathogenic Escherichia coli/*genetics/pathogenicity ; }, abstract = {Global growth in antibiotic resistance is a major social problem. A high level of resistance to fluoroquinolones requires the concurrent presence of at least 3 mutations in the target proteins-2 in DNA gyrase (GyrA) and 1 in topoisomerase IV (ParC), which occur in a stepwise manner. In the Escherichia coli chromosome, the gyrA and parC loci are positioned about 1 Mb away from each other. Here we show that the 3 fluoroquinolone resistance mutations are tightly associated genetically in naturally occurring strains. In the latest pandemic uropathogenic and multidrug-resistant E. coli clonal group ST1193, the mutant variants of gyrA and parC were acquired not by a typical gradual, stepwise evolution but all at once. This happened as part of 11 simultaneous homologous recombination events involving 2 phylogenetically distant strains of E. coli, from an uropathogenic clonal complex ST14 and fluoroquinolone-resistant ST10. The gene exchanges swapped regions between 0.5 and 139 Kb in length (183 Kb total) spread along 976 Kb of chromosomal DNA around and between gyrA and parC loci. As a result, all 3 fluoroquinolone resistance mutations in GyrA and ParC have simultaneously appeared in ST1193. Based on molecular clock estimates, this potentially happened as recently as <12 y ago. Thus, naturally occurring homologous recombination events between 2 strains can involve numerous chromosomal gene locations simultaneously, resulting in the transfer of distant but tightly associated genetic mutations and emergence of a both highly pathogenic and antibiotic-resistant strain with a rapid global spread capability.}, }
@article {pmid31261372, year = {2020}, author = {Hagbø, M and Ravi, A and Angell, IL and Sunde, M and Ludvigsen, J and Diep, DB and Foley, SL and Vento, M and Collado, MC and Perez-Martinez, G and Rudi, K}, title = {Experimental support for multidrug resistance transfer potential in the preterm infant gut microbiota.}, journal = {Pediatric research}, volume = {88}, number = {1}, pages = {57-65}, pmid = {31261372}, issn = {1530-0447}, mesh = {Animals ; Anti-Bacterial Agents ; Bacteriophages ; Chickens ; Contig Mapping ; DNA Transposable Elements ; DNA, Bacterial/analysis ; Enterococcus/genetics ; Escherichia coli/genetics ; *Gastrointestinal Microbiome ; *Gene Transfer Techniques ; *Gene Transfer, Horizontal ; Humans ; Infant, Newborn ; Infant, Premature ; *Multigene Family ; Plasmids/genetics ; Prevalence ; Prospective Studies ; Sequence Analysis, DNA ; Staphylococcus epidermidis/genetics ; Twins ; }, abstract = {BACKGROUND: There is currently a lack of experimental evidence for horizontal gene transfer (HGT) mechanisms in the human gut microbiota. The aim of this study was therefore to experimentally determine the HGT potential in the microbiota of a healthy preterm infant twin pair and to evaluate the global occurrence of the mobilized elements.<br><br>METHODS: Stool samples were collected. Both shotgun metagenome sequencing and bacterial culturing were done for the same samples. A range of experimental conditions were used to test DNA transfer for the cultured isolates. Searches for global distribution of transferable elements were done for the ~120,000 metagenomic samples in the Sequence Read Archive (SRA) database.<br><br>RESULTS: DNA transfer experiments demonstrated frequent transmission of an ESBL encoding IncI1 plasmid, a high copy number ColEI plasmid, and bacteriophage P1. Both IncI1 and ColE1 were abundant in the stool samples. In vitro competition experiments showed that transconjugants containing IncI1 plasmids outcompeted the recipient strain in the absence of antibiotic selection. The SRA searches indicated a global distribution of the mobilizable elements, with chicken identified as a possible reservoir for the IncI1 ESBL encoding plasmid.<br><br>CONCLUSION: Our results experimentally support a major horizontal transmission and persistence potential of the preterm infant gut microbiota mobilome involving genes encoding ESBL.}, }
@article {pmid31260828, year = {2019}, author = {Chen, Y and Li, P and Huang, Y and Yu, K and Chen, H and Cui, K and Huang, Q and Zhang, J and Yew-Hoong Gin, K and He, Y}, title = {Environmental media exert a bottleneck in driving the dynamics of antibiotic resistance genes in modern aquatic environment.}, journal = {Water research}, volume = {162}, number = {}, pages = {127-138}, doi = {10.1016/j.watres.2019.06.047}, pmid = {31260828}, issn = {1879-2448}, mesh = {*Anti-Bacterial Agents ; Bacteria ; Drug Resistance, Microbial ; *Genes, Bacterial ; Soil ; }, abstract = {With the rapid construction of dams worldwide, reservoir system has become a representation of modern aquatic environment. However, the profiles of antibiotic resistance genes (ARGs) and associated factor influencing their dynamics in modern aquatic environment (e.g., water phase, sediment phase, and soil phase) are largely unknown. Here, we comprehensively characterized the diversity, abundance, distribution of ARGs in a large drinking water reservoir using high-throughput quantitative PCR, as well as ranked the factors (e.g., mobile genetic elements (MGEs), bacteria community, bacterial biomass, antibiotics, and basic properties) influencing the profiles of ARGs on the basis of structural equation models (SEMs). Water phase was prone to harbor more diverse ARGs as compared to sediment phase and soil phase, and soil phase in drawdown area was a potential reservoir and hotspot for ARGs. Environmental media partially affected the ARG diversity in modern aquatic environment, while it observably influenced the distributions of ARGs and MGEs and their co-occurrence patterns. The pathways for the proliferation and spread of ARGs in water phase were both the horizontal gene transfer (HGT) and vertical gene transfer (VGT), while the dominant pathways in sediment phase and soil phase were the HGT and VGT, respectively. The SEMs demonstrated that MGEs contributed the most to drive the ARG dynamics in both water phase and sediment phase, while the most dominant factor for this in soil phase was bacterial community. Overall, environmental media exerted a bottleneck in driving the dynamics of ARGs in modern aquatic environment probably via diversifying the MGEs, bacterial community, bacterial biomass, antibiotics and basic properties.}, }
@article {pmid31252216, year = {2019}, author = {Gomez-Valero, L and Buchrieser, C}, title = {Intracellular parasitism, the driving force of evolution of Legionella pneumophila and the genus Legionella.}, journal = {Microbes and infection}, volume = {21}, number = {5-6}, pages = {230-236}, doi = {10.1016/j.micinf.2019.06.012}, pmid = {31252216}, issn = {1769-714X}, abstract = {Legionella pneumophila is an intracellular pathogen that causes a severe pneumonia called Legionnaires' disease that is often fatal when not promptly diagnosed and treated. Legionella parasitize aquatic protozoa with which it co-evolved over an evolutionary long time. The close relationship between hosts and pathogens, their co-evolution, led to molecular interactions such as the exchange of genetic material through horizontal gene transfer (HGT). Genome sequencing of L. pneumophila and of the entire genus Legionella that comprises over 60 species revealed that Legionellae have co-opted genes and thus cellular functions from their eukaryotic hosts to a surprisingly high extent. Acquisition and loss of these eukaryotic-like genes and domains is an on-going process underlining the highly dynamic nature of the Legionella genomes. Although the large amount and diversity of HGT in Legionella seems to be unique in the prokaryotic world the analyses of more and more genomes from environmental organisms and symbionts of amoeba revealed that such genetic exchanges occur among all amoeba associated bacteria and also among the different microorganisms that infect amoeba. This dynamic reshuffling and gene-acquisition has led to the emergence of Legionella as human pathogen and may lead to the emergence of new human pathogens from the environment.}, }
@article {pmid31251650, year = {2019}, author = {Ram, Y and Hadany, L}, title = {Evolution of Stress-Induced Mutagenesis in the Presence of Horizontal Gene Transfer.}, journal = {The American naturalist}, volume = {194}, number = {1}, pages = {73-89}, doi = {10.1086/703457}, pmid = {31251650}, issn = {1537-5323}, mesh = {Alleles ; *Gene Transfer, Horizontal ; *Models, Genetic ; *Mutagenesis ; *Stress, Physiological ; }, abstract = {Stress-induced mutagenesis has been observed in multiple species of bacteria and yeast. It has been suggested that in asexual populations, a mutator allele that increases the mutation rate during stress can sweep to fixation with the beneficial mutations it generates. However, even asexual microbes can undergo horizontal gene transfer and rare recombination, which typically interfere with the spread of mutator alleles. Here we examine the effect of horizontal gene transfer on the evolutionary advantage of stress-induced mutator alleles. Our results demonstrate that stress-induced mutator alleles are favored by selection even in the presence of horizontal gene transfer and more so when the mutator alleles also increase the rate of horizontal gene transfer. We suggest that when regulated by stress, mutation and horizontal gene transfer can be complementary rather than competing adaptive strategies and that stress-induced mutagenesis has important implications for evolutionary biology, ecology, and epidemiology, even in the presence of horizontal gene transfer and rare recombination.}, }
@article {pmid31247332, year = {2020}, author = {Alvarado, G and Holland, SR and DePerez-Rasmussen, J and Jarvis, BA and Telander, T and Wagner, N and Waring, AL and Anast, A and Davis, B and Frank, A and Genenbacher, K and Larson, J and Mathis, C and Oates, AE and Rhoades, NA and Scott, L and Young, J and Mortimer, NT}, title = {Bioinformatic analysis suggests potential mechanisms underlying parasitoid venom evolution and function.}, journal = {Genomics}, volume = {112}, number = {2}, pages = {1096-1104}, doi = {10.1016/j.ygeno.2019.06.022}, pmid = {31247332}, issn = {1089-8646}, mesh = {Animals ; Arthropod Venoms/*genetics/metabolism ; Drosophila melanogaster/immunology/parasitology ; *Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; Immune Evasion ; Proteome/genetics/metabolism ; Wasps/*genetics/pathogenicity ; }, abstract = {Hymenopteran parasitoid wasps are a diverse collection of species that infect arthropod hosts and use factors found in their venoms to manipulate host immune responses, physiology, and behaviour. Whole parasitoid venoms have been profiled using proteomic approaches, and here we present a bioinformatic characterization of the venom protein content from Ganaspis sp. 1, a parasitoid that infects flies of the genus Drosophila. We find evidence that diverse evolutionary processes including multifunctionalization, co-option, gene duplication, and horizontal gene transfer may be acting in concert to drive venom gene evolution in Ganaspis sp.1. One major role of parasitoid wasp venom is host immune evasion. We previously demonstrated that Ganaspis sp. 1 venom inhibits immune cell activation in infected Drosophila melanogaster hosts, and our current analysis has uncovered additional predicted virulence functions. Overall, this analysis represents an important step towards understanding the composition and activity of parasitoid wasp venoms.}, }
@article {pmid31247256, year = {2019}, author = {Poey, ME and Azpiroz, MF and Laviña, M}, title = {On sulfonamide resistance, sul genes, class 1 integrons and their horizontal transfer in Escherichia coli.}, journal = {Microbial pathogenesis}, volume = {135}, number = {}, pages = {103611}, doi = {10.1016/j.micpath.2019.103611}, pmid = {31247256}, issn = {1096-1208}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Carrier Proteins/genetics ; Conjugation, Genetic/drug effects ; Drug Combinations ; Drug Resistance, Bacterial/drug effects/*genetics ; Escherichia coli K12/drug effects/*genetics ; Escherichia coli Proteins/*genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial ; Integrons/*genetics ; Microbial Sensitivity Tests ; Microbial Viability/drug effects/genetics ; Plasmids/genetics ; Sulfamethoxazole/pharmacology ; Sulfonamides/*pharmacology ; Trimethoprim, Sulfamethoxazole Drug Combination/pharmacology ; Uropathogenic Escherichia coli/drug effects/genetics ; }, abstract = {Class 1 integrons (Int1) contribute to antibiotic multiresistance in Gram-negative bacteria. Being frequently carried by conjugative plasmids, their spread would depend to some extent on their horizontal transfer to other bacteria. This was the main issue that was addressed in this work: the analysis of Int1 lateral transfer in the presence of different antibiotic pressures. Strains from a previously obtained collection of Escherichia coli K12 carrying natural Int1[+] conjugative plasmids were employed as Int1 donors in conjugation experiments. Two recipient strains were used: an E. coli K12 and an uropathogenic E. coli isolate. The four antibiotics employed to select transconjugants in LB solid medium were ampicillin, trimethoprim, sulfamethoxazole, and co-trimoxazole. For this purpose, adequate final concentrations of the three last antibiotics had to be determined. Abundant transconjugants resulted from the mating experiments and appeared in most -but not all-selective plates. In those supplemented with sulfamethoxazole or co-trimoxazole, transconjugants grew or not depending on the genetic context of the recipient strain and on the type of gene conferring sulfonamide resistance (sul1 or sul2) carried by the Int1[+] plasmid. The horizontal transfer of a recombinant plasmid bearing an Int1 was also assayed by transformation and these experiments provided further information on the viability of the Int1[+] clones. Overall, results point to the existence of constraints for the lateral transfer of Int1 among E. coli bacteria, which are particularly evidenced under the antibiotic pressure of sulfamethoxazole or of its combined formula co-trimoxazole.}, }
@article {pmid31247085, year = {2020}, author = {Velasco, JM and Valderama, MT and Margulieux, K and Diones, PC and Peacock, T and Navarro, FC and Liao, C and Chua, D and Macareo, L and Crawford, J and Swierczewski, B}, title = {Comparison of Carbapenem-Resistant Microbial Pathogens in Combat and Non-combat Wounds of Military and Civilian Patients Seen at a Tertiary Military Hospital, Philippines (2013-2017).}, journal = {Military medicine}, volume = {185}, number = {1-2}, pages = {e197-e202}, doi = {10.1093/milmed/usz148}, pmid = {31247085}, issn = {1930-613X}, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Carbapenems ; Escherichia coli/genetics ; Hospitals, Military ; Humans ; Microbial Sensitivity Tests ; *Military Personnel ; Philippines/epidemiology ; Prospective Studies ; Tertiary Care Centers ; United States ; }, abstract = {INTRODUCTION: Bacterial wound infections are a danger to both military and civilian populations. The nature of injury and infection associated with combat related wounds are important in guiding antibiotic prophylaxis and empiric treatment guidelines.<br><br>MATERIALS AND METHODS: The isolates were screened for drug-resistance by the MicroScan Walkaway Plus System using either the Negative Breakpoint Combo Panel (NBCP) 30 or 34 or Positive Breakpoint Combo Panel (PBPC) 20 or 23. Isolates with a minimum inhibitory concentration (MIC) of &#x2265;8 &#x3bc;g/mL to imipenem and/or meropenem were tested for both carbapenemase production using the CarbaNP test and real-time PCR to determine molecular resistance mechanisms. Plasmid conjugation analysis was performed to define potential for horizontal gene transfer.<br><br>RESULTS: We characterized 634 bacterial wound isolates collected from September 2013 to December 2017 from patients seen at a Philippine military tertiary hospital presenting with combat or non-combat injuries [354 (military) and 280 (civilians)]. Staphylococcus aureus was the most predominant bacterial species isolated from wounds in both populations (104/634, 16%). A variety of Gram-negative bacterial species comprised 442/634 (70%) of the isolates identified, with the most prevalent shown to be Pseudomonas aeruginosa, Enterobacter cloacae, Klebsiella pneumoniae, Escherichia coli, and Acinetobacter sp. Carbapenemase production was detected in 34/442 (8%) Gram-negative isolates. Testing for molecular resistance mechanisms showed 32/34 (17 military, 15 civilian) wound isolates were blaNDM positive and 2 were blaVIM positive, with the two blaVIM isolates found in the civilian population. Plasmid conjugation of 14 blaNDM and 2 blaVIM positive wound isolates representatives showed 2/16 (13%) produced E. coli J53 transconjugants (E. coli from a civilian; E. cloacae from a military).<br><br>CONCLUSION: We describe in this study the wound bacterial and antibiotic resistance profile in the military (combat vs non-combat associated) and civilian population. We observed that, with the exception of Acinetobacter sp., resistance of prevalent Gram-negative bacterial species to imipenem or meropenem were not significantly different between the military and civilian populations. We also presented data on the prevalent bacterial species isolated from both combat and non-combat wounds in a military tertiary care hospital setting as well as the carbapenemase-encoding gene primarily responsible for carbapenem resistance as well as evidence of horizontal transfer via mobile genetic elements. Clinicians may use this information to guide empiric antibiotic coverage for the predominant organisms if wound culture results are not readily available.A prospective, longitudinal evaluation of the wound bacterial profile documenting the changing bacterial flora using higher resolution molecular strategies can provide a more comprehensive understanding of the diversity, composition, and abundance of bacterial composition of the wound microbial community from the time of injury, during the course of evacuation from the field to higher level of care facilities, and up to wound resolution.}, }
@article {pmid31244798, year = {2019}, author = {Levesque, S and de Melo, AG and Labrie, SJ and Moineau, S}, title = {Mobilome of Brevibacterium aurantiacum Sheds Light on Its Genetic Diversity and Its Adaptation to Smear-Ripened Cheeses.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1270}, pmid = {31244798}, issn = {1664-302X}, abstract = {Brevibacterium aurantiacum is an actinobacterium that confers key organoleptic properties to washed-rind cheeses during the ripening process. Although this industrially relevant species has been gaining an increasing attention in the past years, its genome plasticity is still understudied due to the unavailability of complete genomic sequences. To add insights on the mobilome of this group, we sequenced the complete genomes of five dairy Brevibacterium strains and one non-dairy strain using PacBio RSII. We performed phylogenetic and pan-genome analyses, including comparisons with other publicly available Brevibacterium genomic sequences. Our phylogenetic analysis revealed that these five dairy strains, previously identified as Brevibacterium linens, belong instead to the B. aurantiacum species. A high number of transposases and integrases were observed in the Brevibacterium spp. strains. In addition, we identified 14 and 12 new insertion sequences (IS) in B. aurantiacum and B. linens genomes, respectively. Several stretches of homologous DNA sequences were also found between B. aurantiacum and other cheese rind actinobacteria, suggesting horizontal gene transfer (HGT). A HGT region from an iRon Uptake/Siderophore Transport Island (RUSTI) and an iron uptake composite transposon were found in five B. aurantiacum genomes. These findings suggest that low iron availability in milk is a driving force in the adaptation of this bacterial species to this niche. Moreover, the exchange of iron uptake systems suggests cooperative evolution between cheese rind actinobacteria. We also demonstrated that the integrative and conjugative element BreLI (Brevibacterium Lanthipeptide Island) can excise from B. aurantiacum SMQ-1417 chromosome. Our comparative genomic analysis suggests that mobile genetic elements played an important role into the adaptation of B. aurantiacum to cheese ecosystems.}, }
@article {pmid31244796, year = {2019}, author = {Labonté, JM and Pachiadaki, M and Fergusson, E and McNichol, J and Grosche, A and Gulmann, LK and Vetriani, C and Sievert, SM and Stepanauskas, R}, title = {Single Cell Genomics-Based Analysis of Gene Content and Expression of Prophages in a Diffuse-Flow Deep-Sea Hydrothermal System.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1262}, pmid = {31244796}, issn = {1664-302X}, abstract = {Phage-host interactions likely play a major role in the composition and functioning of many microbiomes, yet remain poorly understood. Here, we employed single cell genomics to investigate phage-host interactions in a diffuse-flow, low-temperature hydrothermal vent that may be reflective of a broadly distributed biosphere in the subseafloor. We identified putative prophages in 13 of 126 sequenced single amplified genomes (SAGs), with no evidence for lytic infections, which is in stark contrast to findings in the surface ocean. Most were distantly related to known prophages, while their hosts included bacterial phyla Campylobacterota, Bacteroidetes, Chlorobi, Proteobacteria, Lentisphaerae, Spirochaetes, and Thermotogae. Our results suggest the predominance of lysogeny over lytic interaction in diffuse-flow, deep-sea hydrothermal vents, despite the high activity of the dominant Campylobacteria that would favor lytic infections. We show that some of the identified lysogens have co-evolved with their host over geological time scales and that their genes are transcribed in the environment. Functional annotations of lysogeny-related genes suggest involvement in horizontal gene transfer enabling host's protection against toxic metals and antibacterial compounds.}, }
@article {pmid31241141, year = {2019}, author = {Glover, N and Dessimoz, C and Ebersberger, I and Forslund, SK and Gabaldón, T and Huerta-Cepas, J and Martin, MJ and Muffato, M and Patricio, M and Pereira, C and da Silva, AS and Wang, Y and Sonnhammer, E and Thomas, PD}, title = {Advances and Applications in the Quest for Orthologs.}, journal = {Molecular biology and evolution}, volume = {36}, number = {10}, pages = {2157-2164}, pmid = {31241141}, issn = {1537-1719}, support = {R01 DK110520/DK/NIDDK NIH HHS/United States ; R01 HD085901/HD/NICHD NIH HHS/United States ; R35 GM122480/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Animals ; *Evolution, Molecular ; Genomics/methods/*trends ; Humans ; *Multigene Family ; }, abstract = {Gene families evolve by the processes of speciation (creating orthologs), gene duplication (paralogs), and horizontal gene transfer (xenologs), in addition to sequence divergence and gene loss. Orthologs in particular play an essential role in comparative genomics and phylogenomic analyses. With the continued sequencing of organisms across the tree of life, the data are available to reconstruct the unique evolutionary histories of tens of thousands of gene families. Accurate reconstruction of these histories, however, is a challenging computational problem, and the focus of the Quest for Orthologs Consortium. We review the recent advances and outstanding challenges in this field, as revealed at a symposium and meeting held at the University of Southern California in 2017. Key advances have been made both at the level of orthology algorithm development and with respect to coordination across the community of algorithm developers and orthology end-users. Applications spanned a broad range, including gene function prediction, phylostratigraphy, genome evolution, and phylogenomics. The meetings highlighted the increasing use of meta-analyses integrating results from multiple different algorithms, and discussed ongoing challenges in orthology inference as well as the next steps toward improvement and integration of orthology resources.}, }
@article {pmid31239482, year = {2019}, author = {Jia, Q and Chen, X and Köllner, TG and Rinkel, J and Fu, J and Labbé, J and Xiong, W and Dickschat, JS and Gershenzon, J and Chen, F}, title = {Terpene Synthase Genes Originated from Bacteria through Horizontal Gene Transfer Contribute to Terpenoid Diversity in Fungi.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {9223}, pmid = {31239482}, issn = {2045-2322}, mesh = {Alkyl and Aryl Transferases/*genetics/metabolism ; Bacteria/enzymology/*genetics ; Biocatalysis ; *Gene Transfer, Horizontal ; Genome, Fungal/genetics ; Hypocreales/*genetics/*metabolism ; Phylogeny ; Terpenes/*metabolism ; }, abstract = {Fungi are successful eukaryotes of wide distribution. They are known as rich producers of secondary metabolites, especially terpenoids, which are important for fungi-environment interactions. Horizontal gene transfer (HGT) is an important mechanism contributing to genetic innovation of fungi. However, it remains unclear whether HGT has played a role in creating the enormous chemical diversity of fungal terpenoids. Here we report that fungi have acquired terpene synthase genes (TPSs), which encode pivotal enzymes for terpenoid biosynthesis, from bacteria through HGT. Phylogenetic analysis placed the majority of fungal and bacterial TPS genes from diverse taxa into two clades, indicating ancient divergence. Nested in the bacterial TPS clade is a number of fungal TPS genes that are inferred as the outcome of HGT. These include a monophyletic clade of nine fungal TPS genes, designated as BTPSL for bacterial TPS-like genes, from eight species of related entomopathogenic fungi, including seven TPSs from six species in the genus Metarhizium. In vitro enzyme assays demonstrate that all seven BTPSL genes from the genus Metarhizium encode active enzymes with sesquiterpene synthase activities of two general product profiles. By analyzing the catalytic activity of two resurrected ancestral BTPSLs and one closely related bacterial TPS, the trajectory of functional evolution of BTPSLs after HGT from bacteria to fungi and functional divergence within Metarhizium could be traced. Using M. brunneum as a model species, both BTPSLs and typical fungal TPSs were demonstrated to be involved in the in vivo production of terpenoids, illustrating the general importance of HGT of TPS genes from bacteria as a mechanism contributing to terpenoid diversity in fungi.}, }
@article {pmid31238848, year = {2019}, author = {Dimitriu, T and Marchant, L and Buckling, A and Raymond, B}, title = {Bacteria from natural populations transfer plasmids mostly towards their kin.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1905}, pages = {20191110}, pmid = {31238848}, issn = {1471-2954}, support = {MR/N013824/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Bacteria/genetics ; Bacterial Physiological Phenomena ; Conjugation, Genetic ; Escherichia coli/*genetics ; Gene Transfer, Horizontal ; *Plasmids ; }, abstract = {Plasmids play a key role in microbial ecology and evolution, yet the determinants of plasmid transfer rates are poorly understood. Particularly, interactions between donor hosts and potential recipients are understudied. Here, we investigate the importance of genetic similarity between naturally co-occurring Escherichia coli isolates in plasmid transfer. We uncover extensive variability, spanning over five orders of magnitude, in the ability of isolates to donate and receive two different plasmids, R1 and RP4. Overall, transfer is strongly biased towards clone-mates, but not correlated to genetic distance when donors and recipients are not clone-mates. Transfer is limited by the presence of a functional restriction-modification system in recipients, suggesting sharing of strain-specific defence systems contributes to bias towards kin. Such restriction of transfer to kin sets the stage for longer-term coevolutionary interactions leading to mutualism between plasmids and bacterial hosts in natural communities.}, }
@article {pmid31236589, year = {2019}, author = {Verster, KI and Wisecaver, JH and Karageorgi, M and Duncan, RP and Gloss, AD and Armstrong, EE and Price, DK and Menon, AR and Ali, ZM and Whiteman, NK}, title = {Horizontal Transfer of Bacterial Cytolethal Distending Toxin B Genes to Insects.}, journal = {Molecular biology and evolution}, volume = {36}, number = {10}, pages = {2105-2110}, pmid = {31236589}, issn = {1537-1719}, support = {R35 GM119816/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Aphids/*genetics/microbiology ; Bacterial Toxins/*genetics ; Deoxyribonucleases/genetics ; Drosophila/*genetics/microbiology ; *Gene Transfer, Horizontal ; }, abstract = {Horizontal gene transfer events have played a major role in the evolution of microbial species, but their importance in animals is less clear. Here, we report horizontal gene transfer of cytolethal distending toxin B (cdtB), prokaryotic genes encoding eukaryote-targeting DNase I toxins, into the genomes of vinegar flies (Diptera: Drosophilidae) and aphids (Hemiptera: Aphididae). We found insect-encoded cdtB genes are most closely related to orthologs from bacteriophage that infect Candidatus Hamiltonella defensa, a bacterial mutualistic symbiont of aphids that confers resistance to parasitoid wasps. In drosophilids, cdtB orthologs are highly expressed during the parasitoid-prone larval stage and encode a protein with ancestral DNase activity. We show that cdtB has been domesticated by diverse insects and hypothesize that it functions in defense against their natural enemies.}, }
@article {pmid31231937, year = {2019}, author = {Québatte, M and Dehio, C}, title = {Bartonella gene transfer agent: Evolution, function, and proposed role in host adaptation.}, journal = {Cellular microbiology}, volume = {21}, number = {11}, pages = {e13068}, pmid = {31231937}, issn = {1462-5822}, support = {31003A_173119/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {Adaptation, Physiological/genetics ; Animals ; Bacterial Proteins/genetics ; Bartonella/*genetics/growth &amp; development/metabolism/*pathogenicity ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics/physiology ; Host Microbial Interactions ; Mutation ; Recombination, Genetic/genetics ; Replication Origin/genetics ; Type IV Secretion Systems/genetics/metabolism ; }, abstract = {The processes underlying host adaptation by bacterial pathogens remain a fundamental question with relevant clinical, ecological, and evolutionary implications. Zoonotic pathogens of the genus Bartonella constitute an exceptional model to study these aspects. Bartonellae have undergone a spectacular diversification into multiple species resulting from adaptive radiation. Specific adaptations of a complex facultative intracellular lifestyle have enabled the colonisation of distinct mammalian reservoir hosts. This remarkable host adaptability has a multifactorial basis and is thought to be driven by horizontal gene transfer (HGT) and recombination among a limited genus-specific pan genome. Recent functional and evolutionary studies revealed that the conserved Bartonella gene transfer agent (BaGTA) mediates highly efficient HGT and could thus drive this evolution. Here, we review the recent progress made towards understanding BaGTA evolution, function, and its role in the evolution and pathogenesis of Bartonella spp. We notably discuss how BaGTA could have contributed to genome diversification through recombination of beneficial traits that underlie host adaptability. We further address how BaGTA may counter the accumulation of deleterious mutations in clonal populations (Muller's ratchet), which are expected to occur through the recurrent transmission bottlenecks during the complex infection cycle of these pathogens in their mammalian reservoir hosts and arthropod vectors.}, }
@article {pmid31231618, year = {2019}, author = {Dong, X and Song, J and Chen, J and Bi, D and Wang, W and Ren, Y and Wang, H and Wang, G and Tang, KFJ and Wang, X and Huang, J}, title = {Conjugative Transfer of the pVA1-Type Plasmid Carrying the pirAB[vp] Genes Results in the Formation of New AHPND-Causing Vibrio.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {195}, pmid = {31231618}, issn = {2235-2988}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Aquaculture ; Conjugation, Genetic ; *Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Microbial Sensitivity Tests ; Penaeidae/microbiology ; Plasmids/*genetics ; Vibrio/drug effects/*genetics ; }, abstract = {Acute hepatopancreatic necrosis disease (AHPND) has caused sharp declines in aquaculture industries of whiteleg shrimp Penaeus vannamei in Asia and the Americas since 2010. Vibrio parahaemolyticus, V. campbellii, V. owensii, and V. punensis have been proved to cause AHPND. However, the mechanisms underlying the burgeoning number of Vibrio species that cause AHPND is not known. All of AHPND-causing Vibrio bacteria (VAHPND) harbor a highly homologous plasmid (designated as pVA1-type) carrying pirAB[vp] toxin genes. In this study, we demonstrate conclusively that the pVA1-type plasmid can be transferred from VAHPND to non-pathogenic bacteria. We constructed a pVPGX1-Cm[r] plasmid (a pVA1-type plasmid) by adding a chloramphenicol resistance gene as a marker in a donor AHPND-causing V. parahaemolyticus 20130629002S01 (Vp2S01). Horizontal transfer of this plasmid was successfully performed from the AHPND-Vp2S01 to a non-pathogenic strain of V. campbellii at the transfer efficiency of 2.6×10[-8] transconjugant/recipient, and DNase I treatment did not eliminate the transfer. The recipient V. campbellii acquired the pVA1-type plasmid and was shown to produce pirAB[vp] RNA and proteins. Challenge studies using the transconjugant caused 100% mortality in exposed groups of P. vannamei. The challenged shrimp, infected with the transconjugant bacteria, showed typical gross signs and histological lesions of AHPND. These results demonstrated the conjugative transfer of an AHPND pVA1-type plasmid. It provides timely information for explaining the increased species of AHPND-causing Vibrio bacteria and will be useful in the development of management strategies leading to the prevention and control of AHPND.}, }
@article {pmid31231332, year = {2019}, author = {Dong, Y and Zhang, F and Wang, B and Gao, J and Zhang, J and Shao, Y}, title = {Laboratory Evolution Assays and Whole-Genome Sequencing for the Development and Safety Evaluation of Lactobacillus plantarum With Stable Resistance to Gentamicin.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1235}, pmid = {31231332}, issn = {1664-302X}, abstract = {The goal of this work was to use laboratory evolution assays and whole-genome sequencing to develop and test the safety of a probiotic, Lactobacillus plantarum, with high-level of resistance to gentamicin. The evolution of L. plantarum was evaluated under the selective pressure from gentamicin and subsequently when the selective pressure was removed. After 30 days of selective pressure from gentamicin, the minimum inhibitory concentration (MIC) of L. plantarum to gentamicin increased from 4 to 512 μg/mL and remained stable at this level. After removing the selective pressure, the resistance of L. plantarum to gentamicin decreased to 64 μg/mL after 20 days, and remained stable thereafter. Although the MIC declined it was still higher than the cut-off value recommended by EFSA, indicating that the acquisition of gentamicin-resistance was an irreversible process. Using whole-genome sequencing, gene mutations were identified in the strains that had undergone selection pressure from gentamicin as well as in the strains where the selection pressure was subsequently removed. Specifically, four non-synonymous mutations were detected including one single nucleotide polymorphism (SNP), one insertion, and two structural variants (SVs), of which the mutations in genes encoding the drug resistance MFS transporter and transcriptional regulator of AraC family were only detected in the strains under selective pressure from gentamicin. The results indicate that these mutations play an important role in increasing the resistant levels of L. plantarum to gentamicin. The mobility analysis of mutant genes confirmed that they were not located on mobile elements of the genome of highly resistant L. plantarum, indicating that horizontal gene transfer was not possible.}, }
@article {pmid31229670, year = {2019}, author = {Barros, J and Melo, LDR and Poeta, P and Igrejas, G and Ferraz, MP and Azeredo, J and Monteiro, FJ}, title = {Lytic bacteriophages against multidrug-resistant Staphylococcus aureus, Enterococcus faecalis and Escherichia coli isolates from orthopaedic implant-associated infections.}, journal = {International journal of antimicrobial agents}, volume = {54}, number = {3}, pages = {329-337}, doi = {10.1016/j.ijantimicag.2019.06.007}, pmid = {31229670}, issn = {1872-7913}, mesh = {Adult ; Aged ; Aged, 80 and over ; *Bacteriolysis ; Bacteriophages/growth &amp; development/*isolation &amp; purification ; Drug Resistance, Multiple, Bacterial ; Enterococcus faecalis/drug effects/isolation &amp; purification/pathogenicity/virology ; Escherichia coli/drug effects/isolation &amp; purification/pathogenicity/virology ; Escherichia coli Infections/*therapy ; Female ; Gram-Positive Bacterial Infections/microbiology/*therapy ; Humans ; Male ; Middle Aged ; Orthopedic Procedures/adverse effects ; Phage Therapy/*methods ; Prosthesis-Related Infections/microbiology/*therapy ; Staphylococcus aureus/drug effects/isolation &amp; purification/pathogenicity/virology ; }, abstract = {Orthopaedic implant-associated infections are a devastating complication of orthopaedic surgery with a significant impact on patients and healthcare systems. The aims of this work were to describe the patterns of antimicrobial resistance, pathogenicity and virulence of clinical bacterial isolates from orthopaedic implant-associated infections and to further isolate and characterise bacteriophages that are efficient in controlling these bacteria. Staphylococcus aureus, Enterococcus faecalis and Escherichia coli isolated from orthopaedic infections showed multiresistance patterns to the most frequently used antibiotics in clinical settings. The presence of mobile genetic elements (mecA, Tn916/Tn1545 and intl1) and virulence determinants (icaB, cna, hlb, cylLs, cylM, agg, gelE, fsr and fimA) highlighted the pathogenicity of these isolates. Moreover, the isolates belonged to clonal complexes associated with the acquisition of pathogenicity islands and antimicrobial resistance genes by recombination and horizontal gene transfer. Bacteriophages vB_SauM_LM12, vB_EfaS_LM99 and vB_EcoM_JB75 were characterised and their ability to infect clinical isolates of S. aureus, E. faecalis and E. coli, respectively, was assessed. Morphological and genomic analyses revealed that vB_EfaS_LM99 and vB_EcoM_JB75 belong to the Siphoviridae and Myoviridae families, respectively, and no genes associated with lysogeny were found. The bacteriophages showed low latent periods, high burst sizes, broad host ranges and tolerance to several environmental conditions. Moreover, they showed high efficiency and specificity to infect and reduce clinical bacteria, including methicillin-resistant S. aureus and vancomycin-resistant enterococci. Therefore, the results obtained suggest that the bacteriophages used in this work are a promising approach to control these pathogens involved in orthopaedic implant-associated infections.}, }
@article {pmid31228823, year = {2019}, author = {Cai, X and Zheng, X and Zhang, D and Iqbal, W and Liu, C and Yang, B and Zhao, X and Lu, X and Mao, Y}, title = {Microbial characterization of heavy metal resistant bacterial strains isolated from an electroplating wastewater treatment plant.}, journal = {Ecotoxicology and environmental safety}, volume = {181}, number = {}, pages = {472-480}, doi = {10.1016/j.ecoenv.2019.06.036}, pmid = {31228823}, issn = {1090-2414}, mesh = {Bacteria/drug effects/genetics/isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Drug Resistance, Multiple, Bacterial/genetics ; *Electroplating ; Gene Transfer, Horizontal ; Humans ; Metals, Heavy/*metabolism/pharmacology ; Sewage/chemistry/microbiology ; Wastewater/*microbiology ; Water Pollutants, Chemical/analysis/*metabolism/pharmacology ; }, abstract = {Heavy metal pollution is one of the most widespread and complex environmental issues globally, posing a great threat to the ecosystem as well as human health. Bioremediation through heavy metal-resistant bacteria (HMRB) is currently the most promising technology to address this issue. To obtain HMRB to remediate heavy metal pollution potentially, 15 culturable HMRB strains were isolated from the sludge samples of an electroplating wastewater treatment plant (EWWTP), which belonged to the Bacillus, Shewanella, Lysinibacillus, and Acinetobacter genera. Their maximum tolerance concentrations to Cu[2+], Ni[2+], Mn[2+], Co[2+], and Cr2O7[2-] were 40 mM, 10 mM, 200 mM, 40 mM, and 10 mM, respectively, and strain Mn1-4 showed much higher Mn[2+] tolerance and removal effectiveness (3.355 g/L) than previously published reports. Moreover, multiple heavy metal-resistant genotypes and phenotypes were identified among these strains, of which strain Co1-1 carried the most of resistant gene sequences (10) and exhibited resistance to 7 categories of heavy metals, and the co-occurrence of heavy metal and antibiotic resistance were clearly observed in strain Ni1-3. In addition, flanked insert sequence (IS) elements on the heavy metal resistant genes (HMRGs) suggested that horizontal gene transfer (HGT) events may have resulted in multiple heavy metal resistance phenotypes and genotypes in these strains, and IS982 family transposase was presumed to result in the high Ni[2+] tolerance in strain Ni1-3. This study expands our understanding of bacterial heavy metal resistance and provides promising candidates for heavy metal bioremediation.}, }
@article {pmid31227737, year = {2019}, author = {Hongo, Y and Yabuki, A and Fujikura, K and Nagai, S}, title = {Genes functioned in kleptoplastids of Dinophysis are derived from haptophytes rather than from cryptophytes.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {9009}, pmid = {31227737}, issn = {2045-2322}, mesh = {Chloroplast Proteins/classification/*genetics/metabolism ; Cryptophyta/*genetics/metabolism ; Dinoflagellida/classification/*genetics/metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genes, Protozoan/*genetics ; Haptophyta/*genetics/metabolism ; Phylogeny ; Pigments, Biological/biosynthesis ; Plastids/*genetics/metabolism ; Sequence Analysis, DNA ; }, abstract = {Toxic dinoflagellates belonging to the genus Dinophysis acquire plastids indirectly from cryptophytes through the consumption of the ciliate Mesodinium rubrum. Dinophysis acuminata harbours three genes encoding plastid-related proteins, which are thought to have originated from fucoxanthin dinoflagellates, haptophytes and cryptophytes via lateral gene transfer (LGT). Here, we investigate the origin of these plastid proteins via RNA sequencing of species related to D. fortii. We identified 58 gene products involved in porphyrin, chlorophyll, isoprenoid and carotenoid biosyntheses as well as in photosynthesis. Phylogenetic analysis revealed that the genes associated with chlorophyll and carotenoid biosyntheses and photosynthesis originated from fucoxanthin dinoflagellates, haptophytes, chlorarachniophytes, cyanobacteria and cryptophytes. Furthermore, nine genes were laterally transferred from fucoxanthin dinoflagellates, whose plastids were derived from haptophytes. Notably, transcription levels of different plastid protein isoforms varied significantly. Based on these findings, we put forth a novel hypothesis regarding the evolution of Dinophysis plastids that ancestral Dinophysis species acquired plastids from haptophytes or fucoxanthin dinoflagellates, whereas LGT from cryptophytes occurred more recently. Therefore, the evolutionary convergence of genes following LGT may be unlikely in most cases.}, }
@article {pmid31227544, year = {2019}, author = {Cooper, BS and Vanderpool, D and Conner, WR and Matute, DR and Turelli, M}, title = {Wolbachia Acquisition by Drosophila yakuba-Clade Hosts and Transfer of Incompatibility Loci Between Distantly Related Wolbachia.}, journal = {Genetics}, volume = {212}, number = {4}, pages = {1399-1419}, pmid = {31227544}, issn = {1943-2631}, support = {R01 GM104325/GM/NIGMS NIH HHS/United States ; R01 GM121750/GM/NIGMS NIH HHS/United States ; R35 GM124701/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Drosophila/*genetics/microbiology/physiology ; Female ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Genome, Insect ; Genome, Mitochondrial ; Host-Pathogen Interactions ; Infertility/*genetics ; Male ; Phylogeny ; Wolbachia/*genetics/pathogenicity ; }, abstract = {Maternally transmitted Wolbachia infect about half of insect species, yet the predominant mode(s) of Wolbachia acquisition remains uncertain. Species-specific associations could be old, with Wolbachia and hosts codiversifying (i.e., cladogenic acquisition), or relatively young and acquired by horizontal transfer or introgression. The three Drosophila yakuba-clade hosts [(D. santomea, D. yakuba) D. teissieri] diverged ∼3 MYA and currently hybridize on the West African islands Bioko and São Tomé. Each species is polymorphic for nearly identical Wolbachia that cause weak cytoplasmic incompatibility (CI)-reduced egg hatch when uninfected females mate with infected males. D. yakuba-clade Wolbachia are closely related to wMel, globally polymorphic in D. melanogaster We use draft Wolbachia and mitochondrial genomes to demonstrate that D. yakuba-clade phylogenies for Wolbachia and mitochondria tend to follow host nuclear phylogenies. However, roughly half of D. santomea individuals, sampled both inside and outside of the São Tomé hybrid zone, have introgressed D. yakuba mitochondria. Both mitochondria and Wolbachia possess far more recent common ancestors than the bulk of the host nuclear genomes, precluding cladogenic Wolbachia acquisition. General concordance of Wolbachia and mitochondrial phylogenies suggests that horizontal transmission is rare, but varying relative rates of molecular divergence complicate chronogram-based statistical tests. Loci that cause CI in wMel are disrupted in D. yakuba-clade Wolbachia; but a second set of loci predicted to cause CI are located in the same WO prophage region. These alternative CI loci seem to have been acquired horizontally from distantly related Wolbachia, with transfer mediated by flanking Wolbachia-specific ISWpi1 transposons.}, }
@article {pmid31226841, year = {2019}, author = {Liang, H and Wei, T and Xu, Y and Li, L and Kumar Sahu, S and Wang, H and Li, H and Fu, X and Zhang, G and Melkonian, M and Liu, X and Wang, S and Liu, H}, title = {Phylogenomics Provides New Insights into Gains and Losses of Selenoproteins among Archaeplastida.}, journal = {International journal of molecular sciences}, volume = {20}, number = {12}, pages = {}, pmid = {31226841}, issn = {1422-0067}, support = {2017YFB0403904//National Key Research and Development Program of China/ ; JCYJ20151015162041454//Shenzhen Municipal Government of China/ ; JCYJ20160331150739027//Shenzhen Municipal Government of China/ ; 2017B030301011//Guangdong Provincial Key Laboratory of Genome Read and Write/ ; }, mesh = {Chlorophyta/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genomics ; Phylogeny ; Plant Proteins/*genetics ; Rhodophyta/*genetics ; Selenocysteine/genetics ; Selenoproteins/*genetics ; Streptophyta/*genetics ; Transcriptome ; }, abstract = {Selenoproteins that contain selenocysteine (Sec) are found in all kingdoms of life. Although they constitute a small proportion of the proteome, selenoproteins play essential roles in many organisms. In photosynthetic eukaryotes, selenoproteins have been found in algae but are missing in land plants (embryophytes). In this study, we explored the evolutionary dynamics of Sec incorporation by conveying a genomic search for the Sec machinery and selenoproteins across Archaeplastida. We identified a complete Sec machinery and variable sizes of selenoproteomes in the main algal lineages. However, the entire Sec machinery was missing in the Bangiophyceae-Florideophyceae clade (BV) of Rhodoplantae (red algae) and only partial machinery was found in three species of Archaeplastida, indicating parallel loss of Sec incorporation in different groups of algae. Further analysis of genome and transcriptome data suggests that all major lineages of streptophyte algae display a complete Sec machinery, although the number of selenoproteins is low in this group, especially in subaerial taxa. We conclude that selenoproteins tend to be lost in Archaeplastida upon adaptation to a subaerial or acidic environment. The high number of redox-active selenoproteins found in some bloom-forming marine microalgae may be related to defense against viral infections. Some of the selenoproteins in these organisms may have been gained by horizontal gene transfer from bacteria.}, }
@article {pmid31226672, year = {2019}, author = {Chen, Y and Huang, H and Zheng, X}, title = {Fate of sulfonamide resistance genes during sludge anaerobic fermentation: Roles of sludge components and fermentation pHs.}, journal = {Bioresource technology}, volume = {289}, number = {}, pages = {121636}, doi = {10.1016/j.biortech.2019.121636}, pmid = {31226672}, issn = {1873-2976}, mesh = {Anaerobiosis ; Fermentation ; Hydrogen-Ion Concentration ; *Sewage ; *Sulfonamides ; }, abstract = {This study assessed potential effects of two neglected factors (sludge components and pH values) on the fate of sulfonamide (sul) resistance genes during sludge anaerobic fermentation. It was found that sludge with different contents of protein, carbohydrate and humic acid caused no significant changes in the abundances of sul genes. Nevertheless, sul genes were sensitive to pHs (4-10), and the maximum attenuations (0.8-1.1 log unit) were obtained at pH 10. Mechanism exploration indicated that pHs drove the community evolution of sulfonamide resistant bacteria (SRB), most of which were affiliated to the pH-enriched phyla but not the pH-enriched dominant genera. In addition, the relative abundances of SRB were decreased under both acidic and alkaline conditions. Furthermore, the abundances of intI 1 as well as the sul-carrying abilities of plasmid and extracellular DNA were all reduced at test pHs, indicating that the potential of horizontal gene transfer among bacteria was restricted.}, }
@article {pmid31226020, year = {2019}, author = {Lacroix, B and Citovsky, V}, title = {Pathways of DNA Transfer to Plants from Agrobacterium tumefaciens and Related Bacterial Species.}, journal = {Annual review of phytopathology}, volume = {57}, number = {}, pages = {231-251}, pmid = {31226020}, issn = {1545-2107}, support = {R01 GM050224/GM/NIGMS NIH HHS/United States ; }, mesh = {*Agrobacterium tumefaciens ; Bacteria ; Bacterial Proteins ; DNA, Bacterial ; Gene Transfer, Horizontal ; *Plants ; Virulence ; }, abstract = {Genetic transformation of host plants by Agrobacterium tumefaciens and related species represents a unique model for natural horizontal gene transfer. Almost five decades of studying the molecular interactions between Agrobacterium and its host cells have yielded countless fundamental insights into bacterial and plant biology, even though several steps of the DNA transfer process remain poorly understood. Agrobacterium spp. may utilize different pathways for transferring DNA, which likely reflects the very wide host range of Agrobacterium. Furthermore, closely related bacterial species, such as rhizobia, are able to transfer DNA to host plant cells when they are provided with Agrobacterium DNA transfer machinery and T-DNA. Homologs of Agrobacterium virulence genes are found in many bacterial genomes, but only one non-Agrobacterium bacterial strain, Rhizobium etli CFN42, harbors a complete set of virulence genes and can mediate plant genetic transformation when carrying a T-DNA-containing plasmid.}, }
@article {pmid31222994, year = {2019}, author = {Ren, Y and Li, Y and Han, G and Zhu, F and Liu, C and Song, J}, title = {[Research advances in drug resistance of Aeromonas hydrophila in fishery].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {35}, number = {5}, pages = {759-765}, doi = {10.13345/j.cjb.180399}, pmid = {31222994}, issn = {1872-2075}, mesh = {*Aeromonas hydrophila/drug effects ; Animals ; *Anti-Bacterial Agents/pharmacology ; China/epidemiology ; *Drug Resistance, Bacterial ; *Fish Diseases/epidemiology/microbiology ; Fisheries ; Fishes ; *Gram-Negative Bacterial Infections/epidemiology/microbiology ; Research ; }, abstract = {As one of the most common pathogens in aquatic animals, Aeromonas hydrophila exhibits a wide range of pathogenicity. Due to factors like unreasonable use of antibiotics and horizontal gene transfer mediated by plasmids, many resistant strains of Aeromonas hydrophila were isolated from ready-to-eat seafood products in retail markets, supermarkets and restaurants. These strains carry many resistance genes. Therefore, it is essential to explore the key control points, and seek for prevention and control strategies so as to effectively alleviate antibiotic resistance. We review here the prevalence of drug resistance of Aeromonas hydrophila in China, and its main infection and resistance mechanisms, and the main means and strategies for reducing and preventing drug resistance. We also address further research directions and focus on drug resistance in Aeromonas hydrophila of the aquatic product.}, }
@article {pmid31222493, year = {2019}, author = {de Santana Lopes, A and Gomes Pacheco, T and Nascimento da Silva, O and Magalhães Cruz, L and Balsanelli, E and Maltempi de Souza, E and de Oliveira Pedrosa, F and Rogalski, M}, title = {The plastomes of Astrocaryum aculeatum G. Mey. and A. murumuru Mart. show a flip-flop recombination between two short inverted repeats.}, journal = {Planta}, volume = {250}, number = {4}, pages = {1229-1246}, pmid = {31222493}, issn = {1432-2048}, support = {CNPq//CNPq/ ; Grant 459698/2014-1//CNPq/ ; }, mesh = {Arecaceae/*genetics ; Evolution, Molecular ; Inverted Repeat Sequences/*genetics ; Phylogeny ; Plastids/*genetics ; RNA Editing ; Recombination, Genetic ; }, abstract = {The plastomes of Astrocaryum murumuru and A. aculeatum revealed a lineage-specific structural feature originated by flip-flop recombination, non-synonymous substitutions in conserved genes and several molecular markers. Astrocaryum murumuru Mart. and A. aculeatum G.Mey. are two palm species of Amazon forest that are economically important as source of food, oil and raw material for several applications. Genetic studies aiming to establish strategies for conservation and domestication of both species are still in the beginning given that the exploitation is mostly by extractive activity. The identification and characterization of molecular markers are essential to assess the genetic diversity of natural populations of both species. Therefore, we sequenced and characterized in detail the plastome of both species. We compared both species and identified 32 polymorphic SSR loci, 150 SNPs, 46 indels and eight hotspots of nucleotide diversity. Additionally, we reported a specific RNA editing site found in the ccsA gene, which is exclusive to A. murumuru. Moreover, the structural analysis in the plastomes of both species revealed a 4.6-kb inversion encompassing a set of genes involved in chlororespiration and plastid translation. This 4.6-kb inversion is a lineage-specific structural feature of the genus Astrocaryum originated by flip-flop recombination between two short inverted repeats. Furthermore, our phylogenetic analysis using whole plastomes of 39 Arecaceae species placed the Astrocaryum species sister to Acrocomia within the tribe Cocoseae. Finally, our data indicated substantial changes in the plastome structure and sequence of both species of the genus Astrocaryum, bringing new molecular markers, several structural and evolving features, which can be applied in several areas such as genetic, evolution, breeding, phylogeny and conservation strategies for both species.}, }
@article {pmid31222169, year = {2019}, author = {Weiss, E and Spicher, C and Haas, R and Fischer, W}, title = {Excision and transfer of an integrating and conjugative element in a bacterial species with high recombination efficiency.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {8915}, pmid = {31222169}, issn = {2045-2322}, mesh = {Bacteria/*genetics ; Chromosomes, Bacterial ; *Conjugation, Genetic ; Gene Transfer, Horizontal ; *Homologous Recombination ; }, abstract = {Horizontal transfer of mobile genetic elements, such as integrating and conjugative elements (ICEs), plays an important role in generating diversity and maintaining comprehensive pan-genomes in bacterial populations. The human gastric pathogen Helicobacter pylori, which is known for its extreme genetic diversity, possesses highly efficient transformation and recombination systems to achieve this diversity, but it is unclear to what extent these systems influence ICE physiology. In this study, we have examined the excision/integration and horizontal transfer characteristics of an ICE (termed ICEHptfs4) in these bacteria. We show that transfer of ICEHptfs4 DNA during mating between donor and recipient strains is independent of its conjugation genes, and that homologous recombination is much more efficient than site-specific integration into the recipient chromosome. Nevertheless, ICEHptfs4 excision by site-specific recombination occurs permanently in a subpopulation of cells and involves relocation of a circularization-dependent promoter. Selection experiments for excision indicate that the circular form of ICEHptfs4 is not replicative, but readily reintegrates by site-specific recombination. Thus, although ICEHptfs4 harbours all essential transfer genes, and typical ICE functions such as site-specific integration are active in H. pylori, canonical ICE transfer is subordinate to the more efficient general DNA uptake and homologous recombination machineries in these bacteria.}, }
@article {pmid31220250, year = {2019}, author = {Fang, Z and Tan, J and Wu, S and Li, M and Xu, C and Xie, Z and Zhu, H}, title = {PPR-Meta: a tool for identifying phages and plasmids from metagenomic fragments using deep learning.}, journal = {GigaScience}, volume = {8}, number = {6}, pages = {}, pmid = {31220250}, issn = {2047-217X}, mesh = {Bacteriophages/genetics/*isolation &amp; purification ; *Deep Learning ; Metagenome ; Metagenomics/*methods ; Plasmids/genetics/*isolation &amp; purification ; *Software ; }, abstract = {BACKGROUND: Phages and plasmids are the major components of mobile genetic elements, and fragments from such elements generally co-exist with chromosome-derived fragments in sequenced metagenomic data. However, there is a lack of efficient methods that can simultaneously identify phages and plasmids in metagenomic data, and the existing tools identifying either phages or plasmids have not yet presented satisfactory performance.<br><br>FINDINGS: We present PPR-Meta, a 3-class classifier that allows simultaneous identification of both phage and plasmid fragments from metagenomic assemblies. PPR-Meta consists of several modules for predicting sequences of different lengths. Using deep learning, a novel network architecture, referred to as the Bi-path Convolutional Neural Network, is designed to improve the performance for short fragments. PPR-Meta demonstrates much better performance than currently available similar tools individually for phage or plasmid identification, while testing on both artificial contigs and real metagenomic data. PPR-Meta is freely available via http://cqb.pku.edu.cn/ZhuLab/PPR_Meta or https://github.com/zhenchengfang/PPR-Meta.<br><br>CONCLUSIONS: To the best of our knowledge, PPR-Meta is the first tool that can simultaneously identify phage and plasmid fragments efficiently and reliably. The software is optimized and can be easily run on a local PC by non-computer professionals. We developed PPR-Meta to promote the research on mobile genetic elements and horizontal gene transfer.}, }
@article {pmid31219097, year = {2019}, author = {Mohan Raj, JR and Vittal, R and Shivakumaraswamy, SK and Deekshit, VK and Chakraborty, A and Karunasagar, I}, title = {Presence &amp; mobility of antimicrobial resistance in Gram-negative bacteria from environmental samples in coastal Karnataka, India.}, journal = {The Indian journal of medical research}, volume = {149}, number = {2}, pages = {290-294}, pmid = {31219097}, issn = {0971-5916}, mesh = {Animals ; Anti-Bacterial Agents/adverse effects/therapeutic use ; Bacterial Infections/drug therapy/*epidemiology/genetics/microbiology ; Drug Resistance, Bacterial/*genetics ; *Environmental Microbiology ; Gene Transfer, Horizontal/genetics ; Gram-Negative Bacteria/drug effects/genetics/pathogenicity ; Humans ; India/epidemiology ; Microbial Sensitivity Tests ; Plasmids/genetics ; beta-Lactamases/*genetics ; }, abstract = {To understand antimicrobial resistance (AMR) patterns and mechanisms of horizontal gene transfer in human-associated environments is essential to AMR surveillance. Gram-negative bacteria (1122 isolates) from food-animal environments were characterized for antimicrobial susceptibility and AMR genes. Seventy five per cent of the isolates (837 of 1122) were resistant to at least one of the antibiotics tested. Resistance to more than three groups of antimicrobials (multidrug resistance) was observed in 43 isolates with most often encountered (12 of 43) resistance to β-lactams, tetracycline, quinolones and nitrofurantoin. The profile of frequently reported plasmid-mediated resistance gene in these isolates was determined. The mobility of these elements as plasmids or phages was examined. The blaCTX-M gene was present in the plasmid of 61 per cent and packed in induced phage fractions in 72 per cent of the isolates and blaTEMin 69 per cent phage fractions compared to 15 per cent presence in the plasmid.}, }
@article {pmid31219087, year = {2019}, author = {Ragupathi, NKD and Bakthavatchalam, YD and Mathur, P and Pragasam, AK and Walia, K and Ohri, VC and Veeraraghavan, B}, title = {Plasmid profiles among some ESKAPE pathogens in a tertiary care centre in south India.}, journal = {The Indian journal of medical research}, volume = {149}, number = {2}, pages = {222-231}, pmid = {31219087}, issn = {0971-5916}, mesh = {Acinetobacter baumannii/drug effects/genetics/pathogenicity ; Anti-Bacterial Agents/adverse effects/*therapeutic use ; Cross Infection/*drug therapy/epidemiology/genetics/microbiology ; Drug Resistance, Multiple, Bacterial/*genetics ; Enterobacter/drug effects/genetics/pathogenicity ; Enterococcus faecium/drug effects/genetics/pathogenicity ; Gene Transfer, Horizontal/genetics ; Humans ; India/epidemiology ; Klebsiella pneumoniae/drug effects/genetics/pathogenicity ; Plasmids/drug effects/*genetics ; Pseudomonas aeruginosa/drug effects/genetics/pathogenicity ; Staphylococcus aureus/drug effects/genetics/pathogenicity ; beta-Lactamases/genetics ; }, abstract = {BACKGROUND &amp; OBJECTIVES: Plasmid has led to increase in resistant bacterial pathogens through the exchange of antimicrobial resistance (AMR) genetic determinants through horizontal gene transfer. Baseline data on the occurrence of plasmids carrying AMR genes are lacking in India. This study was aimed to identify the plasmids associated with AMR genetic determinants in ESKAPE pathogens.<br><br>METHODS: A total of 112 ESKAPE isolates including Escherichia coli (n=37), Klebsiella pneumoniae (n=48, including 7 pan-drug susceptible isolates), Acinetobacter baumannii (n=8), Pseudomonas aeruginosa (n=1) and Staphylococcus aureus (n=18) were analyzed in the study. Isolates were screened for antimicrobial susceptibility and whole genome sequencing of isolates was performed using Ion Torrent (PGM) sequencer. Downstream data analysis was done using PATRIC, ResFinder, PlasmidFinder and MLSTFinder databases. All 88 whole genome sequences (WGS) were deposited at GenBank.<br><br>RESULTS: Most of the study isolates showed resistant phenotypes. As analyzed from WGS, the isolates included both known and unknown sequence types. The plasmid analysis revealed the presence of single or multiple plasmids in the isolates. Plasmid types such as IncHI1B(pNDM-MAR), IncFII(pRSB107), IncFIB(Mar), IncFIB(pQil), IncFIA, IncFII(K), IncR, ColKP3 and ColpVC were present in K. pneumoniae. In E. coli, IncFIA, IncFII, IncFIB, Col(BS512), IncL1, IncX3 and IncH were present along with other types. S. aureus harboured seven different plasmid groups pMW2 (rep 5), pSAS1 (rep 7), pDLK1 (rep 10), pUB110 (rep US12), Saa6159 (rep 16), pKH12 (rep 21) and pSA1308 (rep 21). The overall incidence of IncF type plasmids was 56.5 per cent followed by Col type plasmids 18.3 per cent and IncX 5.3 per cent. Other plasmid types identified were <5 per cent.<br><br>Results from the study may serve as a baseline data for the occurrence of AMR genes and plasmids in India. Information on the association between phenotypic and genotypic expression of AMR was deciphered from the data. Further studies on the mechanism of antibiotic resistance dissemination are essential for enhancing clinical lifetime of antibiotics.}, }
@article {pmid31215866, year = {2019}, author = {Gehrke, EJ and Zhang, X and Pimentel-Elardo, SM and Johnson, AR and Rees, CA and Jones, SE and Hindra,  and Gehrke, SS and Turvey, S and Boursalie, S and Hill, JE and Carlson, EE and Nodwell, JR and Elliot, MA}, title = {Silencing cryptic specialized metabolism in Streptomyces by the nucleoid-associated protein Lsr2.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, pmid = {31215866}, issn = {2050-084X}, mesh = {Anti-Bacterial Agents/biosynthesis ; Bacterial Proteins/genetics/*metabolism ; Binding Sites ; Biosynthetic Pathways/genetics ; Cell Nucleus/*metabolism ; Chromosomes, Bacterial/genetics ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial ; Metabolome/genetics ; Mutation/genetics ; Phenotype ; Streptomyces/genetics/*metabolism ; Volatilization ; }, abstract = {Lsr2 is a nucleoid-associated protein conserved throughout the actinobacteria, including the antibiotic-producing Streptomyces. Streptomyces species encode paralogous Lsr2 proteins (Lsr2 and Lsr2-like, or LsrL), and we show here that of the two, Lsr2 has greater functional significance. We found that Lsr2 binds AT-rich sequences throughout the chromosome, and broadly represses gene expression. Strikingly, specialized metabolic clusters were over-represented amongst its targets, and the cryptic nature of many of these clusters appears to stem from Lsr2-mediated repression. Manipulating Lsr2 activity in model species and uncharacterized isolates resulted in the production of new metabolites not seen in wild type strains. Our results suggest that the transcriptional silencing of biosynthetic clusters by Lsr2 may protect Streptomyces from the inappropriate expression of specialized metabolites, and provide global control over Streptomyces' arsenal of signaling and antagonistic compounds.}, }
@article {pmid31215393, year = {2019}, author = {Behra, PRK and Pettersson, BMF and Das, S and Dasgupta, S and Kirsebom, LA}, title = {Comparative genomics of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members emphasizing tRNA and non-coding RNA.}, journal = {BMC evolutionary biology}, volume = {19}, number = {1}, pages = {124}, pmid = {31215393}, issn = {1471-2148}, mesh = {Amino Acyl-tRNA Synthetases/genetics ; Bacteriophages/genetics ; Genome Size ; *Genome, Bacterial ; Genomics ; Molecular Sequence Annotation ; Mycobacterium/classification/*genetics/*growth &amp; development ; Phylogeny ; Plasmids/genetics ; RNA, Bacterial/*genetics ; RNA, Transfer/*genetics ; RNA, Untranslated/chemistry/*genetics ; Ribonuclease P/genetics ; Sequence Inversion ; }, abstract = {BACKGROUND: Mycobacteria occupy various ecological niches and can be isolated from soil, tap water and ground water. Several cause diseases in humans and animals. To get deeper insight into our understanding of mycobacterial evolution focusing on tRNA and non-coding (nc)RNA, we conducted a comparative genome analysis of Mycobacterium mucogenicum (Mmuc) and Mycobacterium neoaurum (Mneo) clade members.<br><br>RESULTS: Genome sizes for Mmuc- and Mneo-clade members vary between 5.4 and 6.5 Mbps with the complete Mmuc[T] (type strain) genome encompassing 6.1 Mbp. The number of tRNA genes range between 46 and 79 (including one pseudo tRNA gene) with 39 tRNA genes common among the members of these clades, while additional tRNA genes were probably acquired through horizontal gene transfer. Selected tRNAs and ncRNAs (RNase P RNA, tmRNA, 4.5S RNA, Ms1 RNA and 6C RNA) are expressed, and the levels for several of these are higher in stationary phase compared to exponentially growing cells. The rare tRNA[Ile]TAT isoacceptor and two for mycobacteria novel ncRNAs: the Lactobacillales-derived GOLLD RNA and a homolog to the antisense Salmonella typhimurium phage Sar RNA, were shown to be present and expressed in certain Mmuc-clade members.<br><br>CONCLUSIONS: Phages, IS elements, horizontally transferred tRNA gene clusters, and phage-derived ncRNAs appears to have influenced the evolution of the Mmuc- and Mneo-clades. While the number of predicted coding sequences correlates with genome size, the number of tRNA coding genes does not. The majority of the tRNA genes in mycobacteria are transcribed mainly from single genes and the levels of certain ncRNAs, including RNase P RNA (essential for the processing of tRNAs), are higher at stationary phase compared to exponentially growing cells. We provide supporting evidence that Ms1 RNA represents a mycobacterial 6S RNA variant. The evolutionary routes for the ncRNAs RNase P RNA, tmRNA and Ms1 RNA are different from that of the core genes.}, }
@article {pmid31211676, year = {2019}, author = {Langelier, C and Graves, M and Kalantar, K and Caldera, S and Durrant, R and Fisher, M and Backman, R and Tanner, W and DeRisi, JL and Leung, DT}, title = {Microbiome and Antimicrobial Resistance Gene Dynamics in International Travelers.}, journal = {Emerging infectious diseases}, volume = {25}, number = {7}, pages = {1380-1383}, pmid = {31211676}, issn = {1080-6059}, support = {K23 HL138461/HL/NHLBI NIH HHS/United States ; }, mesh = {Biodiversity ; Communicable Diseases/*epidemiology/*microbiology ; Computational Biology/methods ; Databases, Genetic ; *Drug Resistance, Microbial ; Gene Transfer, Horizontal ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; *Metagenomics/methods ; *Microbiota/drug effects/genetics ; *Travel ; *Travel-Related Illness ; }, abstract = {We used metagenomic next-generation sequencing to longitudinally assess the gut microbiota and antimicrobial resistomes of international travelers to clarify global exchange of resistant organisms. Travel resulted in an increase in antimicrobial resistance genes and a greater proportion of Escherichia species within gut microbial communities without impacting diversity.}, }
@article {pmid31207872, year = {2019}, author = {Lerner, A and Ramesh, A and Matthias, T}, title = {The Revival of the Battle between David and Goliath in the Enteric Viruses and Microbiota Struggle: Potential Implication for Celiac Disease.}, journal = {Microorganisms}, volume = {7}, number = {6}, pages = {}, pmid = {31207872}, issn = {2076-2607}, abstract = {The human gut is inhabited by overcrowded prokaryotic communities, a major component of which is the virome, comprised of viruses, bacteriophages, archaea, eukaryotes and bacteria. The virome is required for luminal homeostasis and, by their lytic or synergic capacities, they can regulate the microbial community structure and activity. Dysbiosis is associated with numerous chronic human diseases. Since the virome can impact microbial genetics and behavior, understanding its biology, composition, cellular cycle, regulation, mode of action and potential beneficial or hostile activities can change the present paradigm of the cross-talks in the luminal gut compartment. Celiac disease is a frequent autoimmune disease in which viruses can play a role in disease development. Based on the current knowledge on the enteric virome, in relation to celiac disease pathophysiological evolvement, the current review summarizes the potential interphases between the two. Exploring and understanding the role of the enteric virome in gluten-dependent enteropathy might bring new therapeutic strategies to change the luminal eco-event for the patient's benefit.}, }
@article {pmid31206984, year = {2019}, author = {Hernández-Cabanyero, C and Lee, CT and Tolosa-Enguis, V and Sanjuán, E and Pajuelo, D and Reyes-López, F and Tort, L and Amaro, C}, title = {Adaptation to host in Vibrio vulnificus, a zoonotic pathogen that causes septicemia in fish and humans.}, journal = {Environmental microbiology}, volume = {21}, number = {8}, pages = {3118-3139}, doi = {10.1111/1462-2920.14714}, pmid = {31206984}, issn = {1462-2920}, support = {AICO/2018/123//Generalitat Valenciana/International ; AGL2017-87723-P//Ministry of Science, Innovation and Universities/International ; BES-2015-073117//Ministry of Science, Innovation and Universities/International ; }, mesh = {Acclimatization ; Animals ; Fish Diseases/*microbiology ; Fishes ; Gene Transfer, Horizontal ; Humans ; Immunity, Innate ; Iron/metabolism ; Phylogeny ; Sepsis/microbiology/*veterinary ; Vibrio Infections/microbiology/*veterinary ; Vibrio vulnificus/genetics/*physiology ; *Zoonoses ; }, abstract = {Vibrio vulnificus is a siderophilic pathogen spreading due to global warming. The zoonotic strains constitute a clonal-complex related to fish farms that are distributed worldwide. In this study, we applied a transcriptomic and single gene approach and discover that the zoonotic strains bypassed the iron requirement of the species thanks to the acquisition of two iron-regulated outer membrane proteins (IROMPs) involved in resistance to fish innate immunity. Both proteins have been acquired by horizontal gene transfer and are contributing to the successful spreading of this clonal-complex. We have also discovered that the zoonotic strains express a virulent phenotype in the blood of its main susceptible hosts (iron-overloaded humans and healthy eels) by combining a host-specific protective envelope with the common expression of two toxins (VvhA and RtxA1), one of which (RtxA1) is directly involved in sepsis. Finally, we found that both IROMPs are also present in other fish pathogenic species and have recently been transmitted to the phylogenetic lineage involved in human primary sepsis after raw seafood ingestion. Together our results highlight the potential hazard that the aquaculture industry poses to public health, which is of particular relevance in the context of a warming world.}, }
@article {pmid31204704, year = {2019}, author = {Mothay, D and Ramesh, KV}, title = {Evolutionary history and genetic diversity study of heat-shock protein 60 of Rhizophagus irregularis.}, journal = {Journal of genetics}, volume = {98}, number = {2}, pages = {}, pmid = {31204704}, issn = {0973-7731}, mesh = {Chaperonin 60/*genetics/metabolism ; Codon ; Databases, Genetic ; Dyslexia/genetics ; *Evolution, Molecular ; *Genetic Variation ; Genetics, Population ; Glomeromycota/classification/*genetics/metabolism ; Humans ; Meta-Analysis as Topic ; Mitochondria/genetics/metabolism ; Odds Ratio ; Phylogeny ; Polymorphism, Genetic ; Synteny ; }, abstract = {Despite the ubiquitous occurrence of heat-shock protein 60 (Hsp60) and their role in maintenance of cell activity and integrity, this protein remains poorly characterized in many of the symbiotic soil mycorrhizal fungi such as Rhizophagus irregularis. Thus, in the current study, an attempt has been made to elucidate the evolutionary history, time of divergence followed by estimation of population genetic parameters of hsp60 using R. irregularis as a model organism. Sequence alignment reported here identified several close homologues for hsp60 (gene) and Hsp60 (protein) from diverse taxa, while the output from protein-based phylogenetic tree indicates that mitochondrial Hsp60 of R. irregularis shares close evolutionary relationship with classical α-proteobacteria. This is perhaps the first line of evidence elucidating the likelihood of hsp60 from fungal taxa sharing a close evolutionary relationship with classical α-proteobacteria as a common ancestor. Comprehensive analysis of mitochondrial hsp60 from selected fungal taxa from the evolutionary point of view explains the possibility of gene duplication and or horizontal gene transfer of this gene across various fungal species. Synteny relationships and population genetics credibly explain high genetic variability associated with fungal hsp60 presumably brought by random genetic recombination events. The results presented here also confirm a high level of genetic differentiation of hsp60 among all the three fungal populations analysed. In this context, the outcome of the current study, basedon computational approach, stands as a testimony for explaining the possibility of increased genetic differentiation experienced by hsp60 of R. irregularis.}, }
@article {pmid31199267, year = {2021}, author = {Du, H and Ong, YS and Knittel, M and Mawhorter, R and Liu, N and Gross, G and Tojo, R and Libeskind-Hadas, R and Wu, YC}, title = {Multiple Optimal Reconciliations Under the Duplication-Loss-Coalescence Model.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {18}, number = {6}, pages = {2144-2156}, doi = {10.1109/TCBB.2019.2922337}, pmid = {31199267}, issn = {1557-9964}, mesh = {*Algorithms ; Gene Duplication/*genetics ; Gene Transfer, Horizontal/genetics ; Genes, Fungal/genetics ; Genomics/*methods ; *Models, Genetic ; *Phylogeny ; }, abstract = {Gene trees can differ from species trees due to a variety of biological phenomena, the most prevalent being gene duplication, horizontal gene transfer, gene loss, and coalescence. To explain topological incongruence between the two trees, researchers apply reconciliation methods, often relying on a maximum parsimony framework. However, while several studies have investigated the space of maximum parsimony reconciliations (MPRs) under the duplication-loss and duplication-transfer-loss models, the space of MPRs under the duplication-loss-coalescence (DLC) model remains poorly understood. To address this problem, we present new algorithms for computing the size of MPR space under the DLC model and sampling from this space uniformly at random. Our algorithms are efficient in practice, with runtime polynomial in the size of the species and gene tree when the number of genes that map to any given species is fixed, thus proving that the MPR problem is fixed-parameter tractable. We have applied our methods to a biological data set of 16 fungal species to provide the first key insights in the space of MPRs under the DLC model. Our results show that a plurality reconciliation, and underlying events, are likely to be representative of MPR space.}, }
@article {pmid31197715, year = {2019}, author = {Khajanchi, BK and Kaldhone, PR and Foley, SL}, title = {Protocols of Conjugative Plasmid Transfer in Salmonella: Plate, Broth, and Filter Mating Approaches.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2016}, number = {}, pages = {129-139}, doi = {10.1007/978-1-4939-9570-7_12}, pmid = {31197715}, issn = {1940-6029}, mesh = {*Conjugation, Genetic ; DNA Transposable Elements ; *Gene Transfer Techniques ; Gene Transfer, Horizontal ; Humans ; Plasmids/*genetics ; Salmonella/*genetics ; Salmonella Infections/microbiology ; }, abstract = {Bacterial conjugation is a natural process that allows for horizontal transmission of DNA from one bacterium to another. Several plasmids carry transposons that encode multiple antimicrobial and metal resistance genes. Conjugative plasmid transfer requires intimate cell-to-cell contacts between the donor and the recipient. Self-conjugative plasmids harbor tra genes which facilitate plasmid transfer from donor to recipient bacterial strain. Here we describe different methods of conjugative plasmid transfers via conjugation.}, }
@article {pmid31195017, year = {2019}, author = {Lemmens, L and Maklad, HR and Bervoets, I and Peeters, E}, title = {Transcription Regulators in Archaea: Homologies and Differences with Bacterial Regulators.}, journal = {Journal of molecular biology}, volume = {431}, number = {20}, pages = {4132-4146}, doi = {10.1016/j.jmb.2019.05.045}, pmid = {31195017}, issn = {1089-8638}, mesh = {Archaea/*genetics/metabolism ; Evolution, Molecular ; Gene Expression Regulation, Archaeal ; Transcription Factors/genetics/*metabolism ; *Transcription, Genetic ; }, abstract = {The fitness and survival of prokaryotic microorganisms depends on their ability to adequately respond to environmental changes, sudden stress conditions and metabolic shifts. An important mechanism underlying this response is the regulation of gene expression mediated by transcription factors that are responsive to small-molecule ligands or other intracellular signals. Despite constituting a distinct domain of life from bacteria and harboring a eukaryotic-like basal transcription apparatus, it is well established that archaea have similar transcription factors pointing to the existence of shared ancestral proteins and to the occurrence of inter-domain horizontal gene transfer events. However, while global structural features of bacterial and archaeal transcription factors are indeed similar, other characteristics imply that archaeal regulators have undergone independent evolution. Here, we discuss the characteristics of Lrp/AsnC, MarR, ArsR/SmtB and TrmB families of transcription factors, which are the dominant families that constitute the transcription factor repertoire in archaea. We exemplify the evolutionary expansion of these families in archaeal lineages by emphasizing homologies and differences with bacterial counterparts in terms of ligand or signal response, physiological functions and mechanistic principles of regulation. As such, we aim to define future research approaches that enable further characterization of the functions and mechanisms of archaeal transcription factors.}, }
@article {pmid31194018, year = {2019}, author = {Pachori, P and Gothalwal, R and Gandhi, P}, title = {Emergence of antibiotic resistance Pseudomonas aeruginosa in intensive care unit; a critical review.}, journal = {Genes &amp; diseases}, volume = {6}, number = {2}, pages = {109-119}, pmid = {31194018}, issn = {2352-3042}, abstract = {The emergence of antibiotic resistant bacteria in the healthcare is a serious concern. In the Healthcare premises precisely intensive care unit are major sources of microbial diversity. Recent findings have demonstrated not only microbial diversity but also drug resistant microbes largely habitat in ICU. Pseudomonas aeruginosa found as a part of normal intestinal flora and a significant pathogen responsible for wide range of ICU acquired infection in critically ill patients. Nosocomial infection associated with this organism including gastrointestinal infection, urinary tract infections and blood stream infection. Infection caused by this organism are difficult to treat because of the presence of its innate resistance to many antibiotics (β-lactam and penem group of antibiotics), and its ability to acquire further resistance mechanism to multiple class of antibiotics, including Beta-lactams, aminoglycosides and fluoroquinolones. In the molecular evolution microbes adopted several mechanism to maintain genomic plasticity. The tool microbe use for its survival is mainly biofilm formation, quorum sensing, and horizontal gene transfer and enzyme promiscuity. Such genomic plasticity provide an ideal habitat to grow and survive in hearse environment mainly antibiotics pressure. This review focus on infection caused by Pseudomonas aeruginosa, its mechanisms of resistance and available treatment options. The present study provides a systemic review on major source of Pseudomonas aeruginosa in ICU. Further, study also emphasizes virulence gene/s associated with Pseudomonas aeruginosa genome for extended drug resistance. Study gives detailed overview of antibiotic drug resistance mechanism.}, }
@article {pmid31186329, year = {2019}, author = {Delavat, F and Moritz, R and van der Meer, JR}, title = {Transient Replication in Specialized Cells Favors Transfer of an Integrative and Conjugative Element.}, journal = {mBio}, volume = {10}, number = {3}, pages = {}, pmid = {31186329}, issn = {2150-7511}, mesh = {Bacterial Proteins/genetics ; *Conjugation, Genetic ; DNA Replication ; *DNA Transposable Elements ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genetic Fitness ; Genome, Bacterial ; Pseudomonas putida/*genetics ; }, abstract = {Integrative and conjugative elements (ICEs) are widespread mobile DNA within bacterial genomes, whose lifestyle is relatively poorly understood. ICEs transmit vertically through donor cell chromosome replication, but in order to transfer, they have to excise from the chromosome. The excision step makes ICEs prone to loss, in case the donor cell divides and the ICE is not replicated. By adapting the system of LacI-cyan fluorescent protein (CFP) binding to lacO operator arrays, we analyze here the process of excision and transfer of the ICE for 3-chlorobenzoate degradation (ICEclc) in individual cells of the bacterium Pseudomonas putida We provide evidence that ICEclc excises exclusively in a subset of specialized transfer-competent cells. ICEclc copy numbers in transfer-competent cells were higher than in regular nontransferring cells but were reduced in mutants lacking the ICE oriT1 origin of transfer, the ICE DNA relaxase, or the excision recombination sites. Consistently, transfer-competent cells showed a higher proportion without any observable LacI-CFP foci, suggesting ICEclc loss, but this proportion was independent of the ICE relaxase or the ICE origins of transfer. Our results thus indicated that the excised ICE becomes transiently replicated in transfer-competent cells, with up to six observable copies from LacI-CFP fluorescent focus measurements. Most of the observed ICEclc transfer to ICE-free P. putida recipients occurred from donors displaying 3 to 4 ICE copies, which constitute a minority among all transfer-competent cells. This finding suggests, therefore, that replication of the excised ICEclc in donors is beneficial for transfer fitness to recipient cells.IMPORTANCE Bacterial evolution is driven to a large extent by horizontal gene transfer (HGT)-the processes that distribute genetic material between species rather than by vertical descent. The different elements and processes mediating HGT have been characterized in great molecular detail. In contrast, very little is known on adaptive features selecting HGT evolvability and fitness optimization. By studying the molecular behavior of an integrated mobile DNA of the class of integrative and conjugative elements in individual Pseudomonas putida donor bacteria, we report here how transient replication of the element after its excision from the chromosome is favorable for its transfer success. Since successful transfer into a new recipient is a measure of the element's fitness, transient replication may have been selected as an adaptive benefit for more-optimal transfer.}, }
@article {pmid31184285, year = {2020}, author = {Rahman, M and Khan, MKA}, title = {In silico based unraveling of New Delhi metallo-β-lactamase (NDM-1) inhibitors from natural compounds: a molecular docking and molecular dynamics simulation study.}, journal = {Journal of biomolecular structure &amp; dynamics}, volume = {38}, number = {7}, pages = {2093-2103}, doi = {10.1080/07391102.2019.1627248}, pmid = {31184285}, issn = {1538-0254}, mesh = {Anti-Bacterial Agents/pharmacology ; Meropenem ; Molecular Docking Simulation ; *Molecular Dynamics Simulation ; *beta-Lactamases/metabolism ; }, abstract = {The development of pathogenic microbial resistance toward antibiotics has become a global clinical concern. New Delhi metallo-β-lactmase-1 (NDM-1) and its variants have recently drawn immense attention for its biological ability to catalyze the hydrolysis of almost all of β-lactam antibiotics including the Carbapenems which are generally considered as the last-resort antibiotics. Also, the horizontal gene transfer is expediting the rapid spread of NDM-1 in bacteria. In the wake of this serious antibiotic resistance problem it becomes imperative to find inhibitors which can render the present antibiotics functional and useful. In the present study, we have used Molecular docking and Molecular Dynamics (MD) simulation approach to find out suitable inhibitors against NDM-1 from an array of different natural compounds. We have screened unique natural compounds from ZINC database and also a set of standard antibiotics and inhibitors. Based upon the highest binding affinity demonstrated by docking with NDM-1, the best binding antibiotic Meropenem and the top five natural compounds, viz., Withaferin A, Beta-Sitosterol, Aristolochic acid, Diosgenin and Guggulsterone E were selected and subjected to MD simulations study. The docked NDM-1 complex with withaferin A, beta-sitosterol and diosgenin were found to be more stable as compared to the one with meropenem throughout the MD simulation process with the relative RMSD and RMSF in acceptable range. In conclusion, these compounds can be readily tested in vitro and in vivo to fully establish and confirm their inhibition potentiality and can also serve as lead molecules for the development of future functional inhibitors.Communicated by Ramaswamy H. Sarma.}, }
@article {pmid31182035, year = {2019}, author = {Brown, BP and Wernegreen, JJ}, title = {Genomic erosion and extensive horizontal gene transfer in gut-associated Acetobacteraceae.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {472}, pmid = {31182035}, issn = {1471-2164}, support = {S10 OD018164/OD/NIH HHS/United States ; 1106401//National Science Foundation/ ; MCB-1103113//National Science Foundation/ ; R01GM062626//National Institutes of Health/ ; }, mesh = {Acetobacteraceae/classification/*genetics/metabolism ; Animals ; Ants/microbiology ; Evolution, Molecular ; Gastrointestinal Tract/microbiology ; *Gene Transfer, Horizontal ; Genomics ; Metabolic Networks and Pathways/genetics ; Phylogeny ; Symbiosis/genetics ; }, abstract = {BACKGROUND: Symbiotic relationships between animals and bacteria have profound impacts on the evolutionary trajectories of each partner. Animals and gut bacteria engage in a variety of relationships, occasionally persisting over evolutionary timescales. Ants are a diverse group of animals that engage in many types of associations with taxonomically distinct groups of bacterial associates. Here, we bring into culture and characterize two closely-related strains of gut associated Acetobacteraceae (AAB) of the red carpenter ant, Camponotus chromaiodes.<br><br>RESULTS: Genome sequencing, assembly, and annotation of both strains delineate stark patterns of genomic erosion and sequence divergence in gut associated AAB. We found widespread horizontal gene transfer (HGT) in these bacterial associates and report elevated gene acquisition associated with energy production and conversion, amino acid and coenzyme transport and metabolism, defense mechanisms, and lysine export. Both strains have acquired the complete NADH-quinone oxidoreductase complex, plausibly from an Enterobacteriaceae origin, likely facilitating energy production under diverse conditions. Conservation of several lysine biosynthetic and salvage pathways and accumulation of lysine export genes via HGT implicate L-lysine supplementation by both strains as a potential functional benefit for the host. These trends are contrasted by genome-wide erosion of several amino acid biosynthetic pathways and pathways in central metabolism. We perform phylogenomic analyses on both strains as well as several free living and host associated AAB. Based on their monophyly and deep divergence from other AAB, these C. chromaiodes gut associates may represent a novel genus. Together, our results demonstrate how extensive horizontal transfer between gut associates along with genome-wide deletions leads to mosaic metabolic pathways. More broadly, these patterns demonstrate that HGT and genomic erosion shape metabolic capabilities of persistent gut associates and influence their genomic evolution.<br><br>CONCLUSIONS: Using comparative genomics, our study reveals substantial changes in genomic content in persistent associates of the insect gastrointestinal tract and provides evidence for the evolutionary pressures inherent to this environment. We describe patterns of genomic erosion and horizontal acquisition that result in mosaic metabolic pathways. Accordingly, the phylogenetic position of both strains of these associates form a divergent, monophyletic clade sister to gut associates of honey bees and more distantly to Gluconobacter.}, }
@article {pmid31178319, year = {2019}, author = {Parker, BJ and Brisson, JA}, title = {A Laterally Transferred Viral Gene Modifies Aphid Wing Plasticity.}, journal = {Current biology : CB}, volume = {29}, number = {12}, pages = {2098-2103.e5}, pmid = {31178319}, issn = {1879-0445}, support = {R01 GM116867/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Physiological/*genetics ; Animals ; Aphids/genetics/*growth &amp; development/virology ; Female ; *Gene Transfer, Horizontal ; Genes, Viral/*physiology ; Genotype ; Wings, Animal/*growth &amp; development/virology ; }, abstract = {Organisms often respond to changing environments by altering development of particular traits. These plastic traits exhibit genetic variation; i.e., genotypes respond differently to the same environmental cues. Theoretical studies have demonstrated the importance of this variation, which is targeted by natural selection, in adapting plastic responses to maximize fitness [1, 2]. However, little is known about the underlying genetic mechanisms. We identify two laterally transferred genes that contribute to variation in a classic example of phenotypic plasticity: the pea aphid's ability to produce winged offspring in response to crowding. We discovered that aphid genotypes vary extensively for this trait and that aphid genes of viral origin are upregulated in response to crowding solely in highly inducible genotypes. We knocked down expression of these genes to demonstrate their functional role in wing plasticity. Through phylogenetic analysis, we found that these genes likely originated from a virus that infects rosy apple aphids and causes their hosts to produce winged offspring [3]. The function of these genes has therefore been retained following transfer to pea aphids. Our results uncover a novel role for co-opted viral genes, demonstrating that they are used to modulate ecologically relevant, plastic phenotypes. Our findings also address a critical question about the evolution of environmentally sensitive traits: whether the genes that control the expression of plastic traits also underlie variation in plasticity. The genes we identify originated from outside aphids themselves, and thus, our work shows that genes formerly unrelated to plasticity can fine-tune the strength of plastic responses to the environment.}, }
@article {pmid31177378, year = {2019}, author = {Subhadra, B and Surendran, S and Lim, BR and Yim, JS and Kim, DH and Woo, K and Han, K and Oh, MH and Choi, CH}, title = {Complete genome sequence and phylogenetic analysis of nosocomial pathogen Acinetobacter nosocomialis strain NCTC 8102.}, journal = {Genes &amp; genomics}, volume = {41}, number = {9}, pages = {1063-1075}, pmid = {31177378}, issn = {2092-9293}, mesh = {Acinetobacter/classification/*genetics/pathogenicity ; Biofilms ; *Genome, Bacterial ; Genomic Islands ; Molecular Sequence Annotation ; *Phylogeny ; Prophages/genetics ; Virulence/genetics ; }, abstract = {BACKGROUND: Acinetobacter has emerged recently as one of the most challenging nosocomial pathogens because of its increased rate of antimicrobial resistance. The genetic complexity and genome diversity, as well as the lack of adequate knowledge on the pathogenic determinants of Acinetobacter strains often hinder with pathogenesis studies for the development of better therapeutics to tackle this nosocomial pathogen.<br><br>OBJECTIVES: In this study, we comparatively analyzed the whole genome sequence of a virulent Acinetobacternosocomialis strain NCTC 8102.<br><br>METHODS: The genomic DNA of A. nosocomialis NCTC 8102 was isolated and sequenced using PacBio RS II platform. The sequenced genome was functionally annotated and gene prediction was carried out using the program, Glimmer 3. The phylogenetic analysis of the genome was performed using Mega 6 program and the comparative genome analysis was carried out by BLAST (Basic Local Alignment Search Tool).<br><br>RESULTS: The complete genome analysis depicted that the genome consists of a circular chromosome with an average G&#x2009;+&#x2009;C content of 38.7%. The genome comprises 3700 protein-coding genes, 96 RNA genes (18 rRNA, 74 tRNA and 4 ncRNA genes), and 91 pseudogenes. In addition, 6 prophage regions comprising 2 intact, 1 incomplete and 3 questionable ones and 18 genomic islands were identified in the genome, suggesting the possible occurrence of horizontal gene transfer in this strain. Comparative genome analysis of A. nosocomialis NCTC 8102 genome with the already sequenced A. nosocomialis strain SSA3 showed an average nucleotide identity of 99.0%. In addition, the number of prophages and genomic islands were higher in the A. nosocomialis NCTC 8102 genome compared to that of the strain SSA3. 14 of the genomic islands were unique to A. nosocomialis NCTC 8102 compared to strain SSA3 and they harbored genes which are involved in virulence, multidrug resistance, biofilm formation and bacterial pathogenesis.<br><br>CONCLUSION: We sequenced the whole genome of A. nosocomialis strain NCTC 8102 followed by comparatively genome analysis. The study provides valuable information on the genetic features of A. nosocomialis strain and the data from this study would assist in further studies for the development of control measures for this nosocomial pathogen.}, }
@article {pmid31176414, year = {2019}, author = {Karkaba, A and Hill, K and Benschop, J and Pleydell, E and Grinberg, A}, title = {Carriage and population genetics of extended spectrum β-lactamase-producing Escherichia coli in cats and dogs in New Zealand.}, journal = {Veterinary microbiology}, volume = {233}, number = {}, pages = {61-67}, doi = {10.1016/j.vetmic.2019.04.015}, pmid = {31176414}, issn = {1873-2542}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Carrier State/epidemiology/*veterinary ; Cats/microbiology ; Dogs/microbiology ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/enzymology/*genetics ; Escherichia coli Infections/epidemiology/*veterinary ; Feces/microbiology ; Female ; Gene Transfer, Horizontal ; Genetics, Population ; Genotype ; Hospitals, Animal ; Humans ; Male ; Multilocus Sequence Typing ; New Zealand/epidemiology ; Pets/*microbiology ; Prevalence ; beta-Lactamases/biosynthesis/*genetics ; }, abstract = {The incidence of infections with extended spectrum β-lactamase producing Escherichia coli (ESBL-E) is increasing both in humans and animals. There is a paucity of data about the rate of faecal carriage of ESBL-E in pets. In this study, faecal swabs collected from 586 pets (225 cats; 361 dogs) in Auckland, New Zealand, were analysed for the presence of ESBL-E by culture, and a questionnaire was delivered to the owners. The ESBL-E were characterised and data elicited by the questionnaires were used for a multivariable analysis, to investigate the factors associated with faecal ESBL-E carriage. The prevalence of ESBL-E in faecal swabs was 6.4%. The β-lactamase genes detected in the ESBL-E were the blaCTX-M-14 (n = 2) and blaCMY-2 (n = 34). Several isolates displayed multilocus sequence types (ST) associated with human and animal infections. Multiple isolates sharing the same ST displayed different antibiograms and β-lactamase genes, reflecting horizontal gene transfer between and within ST. Variables independently associated with increased odds of ESBL-E carriage were: animal received systemic antimicrobial treatment in the six months before the sampling; presence of household members working in veterinary clinics; presence of household members travelling overseas in the six months before the sampling. We conclude that pets are colonised by ESBL-E which are genotypically similar to the bacteria found to infect humans and animals. The statistical analysis suggested a number of eco-epidemiological factors associated with ESBL-E carriage. In particular, they suggest veterinary clinics may represent hot-spots of antimicrobial resistance.}, }
@article {pmid31176227, year = {2019}, author = {Zhang, C and Brown, PJB and Hu, Z}, title = {Higher functionality of bacterial plasmid DNA in water after peracetic acid disinfection compared with chlorination.}, journal = {The Science of the total environment}, volume = {685}, number = {}, pages = {419-427}, doi = {10.1016/j.scitotenv.2019.05.074}, pmid = {31176227}, issn = {1879-1026}, mesh = {DNA, Bacterial ; Disinfectants/*analysis ; Disinfection/*methods ; Halogenation ; Peracetic Acid/*analysis ; Plasmids/genetics ; Water Purification/*methods ; }, abstract = {Peracetic acid (PAA) is an emerging disinfectant with a low disinfection by-product formation potential, but how PAA destroys gene function after killing bacteria remains to be studied. Bacterial plasmid DNA is a mobile genetic element that often harbors undesirable genes encoding antibiotic resistance and virulence factors. Even though PAA efficiently kills bacteria, bacterial plasmids and other mobile genetic elements might still be intact and functional after PAA disinfection, posing potential public health and environmental risks. This study evaluated the impact of PAA disinfection on the functionality of plasmid DNA in vivo and compared the results with those from chlorination. We delivered a plasmid DNA harboring two antibiotic resistance genes to Escherichia coli TOP10 to form an antibiotic-resistant bacterium (ARB). The planktonic ARB was treated with PAA and chlorine to find the minimum doses inhibiting the regrowth of the strain. PAA and chlorine stopped the regrowth at 8 ± 1 mg PAA·L[-1] and 20 ± 9 mg Cl2·L[-1], respectively. The functionality of the plasmid DNA after PAA and chlorine disinfection was then determined at higher doses in vivo. Neither PAA nor chlorine completely destroyed the plasmid DNA. However, chlorine was more efficient than PAA in eliminating the plasmid DNA. PAA at 25 mg PAA·L[-1] reduced the transforming activity of the plasmid DNA by less than 0.3 log10 units, whereas chlorine at 25 mg Cl2·L[-1] reduced the transforming activity by approximately 1.7 log10 units. Chlorine had a more pronounced impact on the functionality of the plasmid DNA because it oxidizes or destroys bacterial components including plasmid DNA faster than PAA. In addition, environmental scanning electron microscopy shows that chlorination desiccated the cells resulting in the flat cellular structure and possibly more complete loss of plasmid DNA, whereas PAA disinfection had a less impact on cell structure and morphology. This study demonstrates that more plasmid DNA remains functional in water after PAA disinfection than after chlorination. These functional genetic elements could be acquired by other microorganisms via horizontal gene transfer to pose potential public health and environmental risks.}, }
@article {pmid31174603, year = {2019}, author = {Arango-Argoty, GA and Dai, D and Pruden, A and Vikesland, P and Heath, LS and Zhang, L}, title = {NanoARG: a web service for detecting and contextualizing antimicrobial resistance genes from nanopore-derived metagenomes.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {88}, pmid = {31174603}, issn = {2049-2618}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/*drug effects/*genetics ; Base Sequence ; Computational Biology ; Drug Resistance, Bacterial/*genetics ; Genes, Bacterial ; High-Throughput Nucleotide Sequencing ; Humans ; Internet ; *Metagenome ; Metagenomics ; *Nanopores ; *Software ; }, abstract = {BACKGROUND: Direct and indirect selection pressures imposed by antibiotics and co-selective agents and horizontal gene transfer are fundamental drivers of the evolution and spread of antibiotic resistance. Therefore, effective environmental monitoring tools should ideally capture not only antibiotic resistance genes (ARGs), but also mobile genetic elements (MGEs) and indicators of co-selective forces, such as metal resistance genes (MRGs). A major challenge towards characterizing the potential human health risk of antibiotic resistance is the ability to identify ARG-carrying microorganisms, of which human pathogens are arguably of greatest risk. Historically, short reads produced by next-generation sequencing technologies have hampered confidence in assemblies for achieving these purposes.<br><br>RESULTS: Here, we introduce NanoARG, an online computational resource that takes advantage of the long reads produced by nanopore sequencing technology. Specifically, long nanopore reads enable identification of ARGs in the context of relevant neighboring genes, thus providing valuable insight into mobility, co-selection, and pathogenicity. NanoARG was applied to study a variety of nanopore sequencing data to demonstrate its functionality. NanoARG was further validated through characterizing its ability to correctly identify ARGs in sequences of varying lengths and a range of sequencing error rates.<br><br>CONCLUSIONS: NanoARG allows users to upload sequence data online and provides various means to analyze and visualize the data, including quantitative and simultaneous profiling of ARGs, MRGs, MGEs, and putative pathogens. A user-friendly interface allows users the analysis of long DNA sequences (including assembled contigs), facilitating data processing, analysis, and visualization. NanoARG is publicly available and freely accessible at https://bench.cs.vt.edu/nanoarg .}, }
@article {pmid31174336, year = {2019}, author = {Sottorff, I and Wiese, J and Lipfert, M and Preußke, N and Sönnichsen, FD and Imhoff, JF}, title = {Different Secondary Metabolite Profiles of Phylogenetically almost Identical Streptomyces griseus Strains Originating from Geographically Remote Locations.}, journal = {Microorganisms}, volume = {7}, number = {6}, pages = {}, pmid = {31174336}, issn = {2076-2607}, abstract = {As Streptomyces have shown an outstanding capacity for drug production, different campaigns in geographically distant locations currently aim to isolate new antibiotic producers. However, many of these newly isolated Streptomyces strains are classified as identical to already described species. Nevertheless, as discrepancies in terms of secondary metabolites and morphology are possible, we compared two Streptomyces strains with identical 16S rRNA gene sequences but geographically distant origins. Chosen were an Easter Island Streptomyces isolate (Streptomyces sp. SN25_8.1) and the next related type strain, which is Streptomyces griseus subsp. griseus DSM 40236[T] isolated from Russian garden soil. Compared traits included phylogenetic relatedness based on 16S rRNA gene sequences, macro and microscopic morphology, antibiotic activity and secondary metabolite profiles. Both Streptomyces strains shared several common features, such as morphology and core secondary metabolite production. They revealed differences in pigmentation and in the production of accessory secondary metabolites which appear to be strain-specific. In conclusion, despite identical 16S rRNA classification Streptomyces strains can present different secondary metabolite profiles and may well be valuable for consideration in processes for drug discovery.}, }
@article {pmid31172913, year = {2019}, author = {Novick, RP}, title = {Pathogenicity Islands and Their Role in Staphylococcal Biology.}, journal = {Microbiology spectrum}, volume = {7}, number = {3}, pages = {}, pmid = {31172913}, issn = {2165-0497}, mesh = {Animals ; Bacteriophages/genetics ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Genome, Bacterial ; Genomic Islands/*genetics ; Humans ; Staphylococcal Infections/microbiology ; Staphylococcus/*genetics/*physiology/virology ; Staphylococcus aureus/genetics ; Virulence/genetics ; Virulence Factors/*genetics ; }, abstract = {Pathogenicity islands are members of a vast collection of genomic islands that encode important virulence, antibiotic resistance and other accessory functions and have a critical role in bacterial gene transfer. Staphylococcus aureus is host to a large family of such islands, known as SaPIs, which encode super antigen and other virulence determinants, are mobilized by helper phages and transferred at extremely high frequencies. They benefit their host cells by interfering with phage predation and enhancing horizontal gene transfer. This chapter describes their life cycle, the bases of their phage interference mechanisms, their transfer system and their conversion to antibacterial agents for treatment ofstaphylococcal infections.}, }
@article {pmid31171857, year = {2019}, author = {Kato, S and Itoh, T and Yuki, M and Nagamori, M and Ohnishi, M and Uematsu, K and Suzuki, K and Takashina, T and Ohkuma, M}, title = {Isolation and characterization of a thermophilic sulfur- and iron-reducing thaumarchaeote from a terrestrial acidic hot spring.}, journal = {The ISME journal}, volume = {13}, number = {10}, pages = {2465-2474}, pmid = {31171857}, issn = {1751-7370}, mesh = {Archaea/classification/genetics/isolation &amp; purification/*metabolism ; DNA, Bacterial/genetics ; Hot Springs/chemistry/*microbiology ; Hot Temperature ; Iron/*metabolism ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sulfur/*metabolism ; }, abstract = {A deep-branching clade of Thaumarchaeota, conventionally called Terrestrial hot spring creanarchaeotic group (THSCG), is a missing link between thaumarchaeotic ammonia oxidizers and the deeper-branching non-ammonia oxidizers, such as Crenarchaeota and Candidatus Korarchaeota. Here, we report isolation of the first cultivated representative from the THSCG, named as NAS-02. Physiological characterization demonstrated that the isolate was a thermoacidophilic, sulfur- and iron-reducing organoheterotroph, which was supported by gene contents encoded in its complete genome. There was no evidence for ammonia oxidation by the isolate. Members in THSCG are likely thermophiles, and may play roles in degrading cell debris as a scavenger and in biogeochemical cycling of sulfur and iron in the hot environments, as suggested by the physiological characteristics of the isolate and the geographical distribution of the 16S rRNA gene sequences of THSCG in terrestrial hot springs and marine hydrothermal fields. Phylogenetic analysis suggests that the THSCG lineage represented by NAS-02 has gained the ability of sulfur reduction via horizontal gene transfer. Based on the phylogeny and physiology, we propose the name Conexivisphaera calidus gen. nov., sp. nov. to accommodate the isolate.}, }
@article {pmid31166888, year = {2019}, author = {Bayjanov, JR and Baan, J and Rogers, MRC and Troelstra, A and Willems, RJL and van Schaik, W}, title = {Enterococcus faecium genome dynamics during long-term asymptomatic patient gut colonization.}, journal = {Microbial genomics}, volume = {5}, number = {7}, pages = {}, pmid = {31166888}, issn = {2057-5858}, mesh = {Cross Infection/*microbiology ; DNA Transposable Elements/*genetics ; DNA, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Enterococcus faecium/*genetics/isolation &amp; purification ; Evolution, Molecular ; Gastrointestinal Microbiome/*genetics ; Genome, Bacterial/*genetics ; Gram-Positive Bacterial Infections/*microbiology ; Humans ; Recombination, Genetic/genetics ; }, abstract = {Enterococcus faecium is a gut commensal of humans and animals. In addition, it has recently emerged as an important nosocomial pathogen through the acquisition of genetic elements that confer resistance to antibiotics and virulence. We performed a whole-genome sequencing-based study on 96 multidrug-resistant E. faecium strains that asymptomatically colonized five patients with the aim of describing the genome dynamics of this species. The patients were hospitalized on multiple occasions and isolates were collected over periods ranging from 15 months to 6.5 years. Ninety-five of the sequenced isolates belonged to E. faecium clade A1, which was previously determined to be responsible for the vast majority of clinical infections. The clade A1 strains clustered into six clonal groups of highly similar isolates, three of which consisted entirely of isolates from a single patient. We also found evidence of concurrent colonization of patients by multiple distinct lineages and transfer of strains between patients during hospitalization. We estimated the evolutionary rate of two clonal groups that each colonized single patients at 12.6 and 25.2 single-nucleotide polymorphisms (SNPs)/genome/year. A detailed analysis of the accessory genome of one of the clonal groups revealed considerable variation due to gene gain and loss events, including the chromosomal acquisition of a 37 kbp prophage and the loss of an element containing carbohydrate metabolism-related genes. We determined the presence and location of 12 different insertion sequence (IS) elements, with ISEfa5 showing a unique pattern of location in 24 of the 25 isolates, suggesting widespread ISEfa5 excision and insertion into the genome during gut colonization. Our findings show that the E. faecium genome is highly dynamic during asymptomatic colonization of the human gut. We observed considerable genomic flexibility due to frequent horizontal gene transfer and recombination, which can contribute to the generation of genetic diversity within the species and, ultimately, can contribute to its success as a nosocomial pathogen.}, }
@article {pmid31166197, year = {2019}, author = {Marx, CJ}, title = {Experimental Evolution of Methylobacterium: 15 Years of Planned Experiments and Surprise Findings.}, journal = {Current issues in molecular biology}, volume = {33}, number = {}, pages = {249-266}, doi = {10.21775/cimb.033.249}, pmid = {31166197}, issn = {1467-3045}, mesh = {*Directed Molecular Evolution/methods/trends ; Epistasis, Genetic/physiology ; Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Gene Transfer Techniques ; *Metabolic Engineering/methods/trends ; Metabolic Networks and Pathways/genetics ; *Methylobacterium/genetics/metabolism ; Models, Biological ; Organisms, Genetically Modified ; Research/trends ; }, abstract = {Experimental evolution has become an increasingly common approach for studying evolutionary phenomena, as well as uncovering physiological connections in a manner complementary to traditional genetics. Here I describe the development of Methylobacterium as a model system for using experimental evolution to study questions at the intersection of metabolism and evolution. Each experiment was initiated to address a particular question inspired by patterns in natural methylotrophs, such as tradeoffs between single-carbon and multi-carbon growth, or the challenges involved in incorporating novel metabolic pathways or genes with poor codon usage that are acquired via horizontal gene transfer. What I could not have appreciated initially, however, was just how many fortuitous surprise findings would emerge. These have ranged from the repeatability of evolution, complex dynamics within populations, epistasis between beneficial mutations, and even the ability to use simple mathematical models to generate testable, quantitative hypotheses about the fitness landscape.}, }
@article {pmid31166175, year = {2019}, author = {Liao, M and Tong, T and Zong, Y and Zhou, X and Cheng, L and Huang, R and Ren, B and Alterovitz, G}, title = {Application of Omics and Bioinformatics Tools in Streptococcus Research.}, journal = {Current issues in molecular biology}, volume = {32}, number = {}, pages = {327-376}, doi = {10.21775/cimb.032.327}, pmid = {31166175}, issn = {1467-3045}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics/metabolism ; CRISPR-Cas Systems ; Chromosome Mapping ; Computational Biology/*methods ; DNA, Bacterial/genetics/metabolism ; Drug Resistance, Multiple, Bacterial/*genetics ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Host-Pathogen Interactions/genetics ; Humans ; Phylogeny ; Streptococcal Infections/drug therapy/microbiology/pathology ; Streptococcus/classification/drug effects/*genetics/pathogenicity ; Virulence ; }, abstract = {Researchers used to focus on analyzing single gene or protein expression of the microbes. But recently, genome, transcriptome, proteome and metabolome have gained more and more attention. Based on technologies of omics, including genomics, transcriptomics and metabolomics, a large quantity of information about cells, microbes and human, such as the information about phylogeny, virulence, antibiotic resistance and other aspects, has been revealed. Genus Streptococcus is one of the most invasive groups of bacteria that cause both human and animal diseases, threatening public health. In this review, we summarize the application of omics to analyze this genus-Streptococcus.}, }
@article {pmid31166171, year = {2019}, author = {Lu, M and Gong, T and Zhang, A and Tang, B and Chen, J and Zhang, Z and Li, Y and Zhou, X}, title = {Mobile Genetic Elements in Streptococci.}, journal = {Current issues in molecular biology}, volume = {32}, number = {}, pages = {123-166}, doi = {10.21775/cimb.032.123}, pmid = {31166171}, issn = {1467-3045}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics/metabolism ; Conjugation, Genetic ; Drug Resistance, Multiple, Bacterial/*genetics ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genome, Bacterial ; Host-Pathogen Interactions/genetics ; Humans ; *Interspersed Repetitive Sequences ; Streptococcal Infections/drug therapy/microbiology/pathology ; Streptococcus pneumoniae/drug effects/*genetics/metabolism/pathogenicity ; Streptococcus pyogenes/drug effects/*genetics/metabolism/pathogenicity ; Transformation, Bacterial ; Virulence ; }, abstract = {Streptococci are a group of Gram-positive bacteria belonging to the family Streptococcaceae, which are responsible of multiple diseases. Some of these species can cause invasive infection that may result in life-threatening illness. Moreover, antibiotic-resistant bacteria are considerably increasing, thus imposing a global consideration. One of the main causes of this resistance is the horizontal gene transfer (HGT), associated to gene transfer agents including transposons, integrons, plasmids and bacteriophages. These agents, which are called mobile genetic elements (MGEs), encode proteins able to mediate DNA movements. This review briefly describes MGEs in streptococci, focusing on their structure and properties related to HGT and antibiotic resistance.}, }
@article {pmid31166168, year = {2019}, author = {Gong, T and Lu, M and Zhou, X and Zhang, A and Tang, B and Chen, J and Jing, M and Li, Y}, title = {CRISPR-Cas Systems in Streptococci.}, journal = {Current issues in molecular biology}, volume = {32}, number = {}, pages = {1-38}, doi = {10.21775/cimb.032.001}, pmid = {31166168}, issn = {1467-3045}, mesh = {CRISPR-Associated Protein 9/*genetics/metabolism ; *CRISPR-Cas Systems ; Clustered Regularly Interspaced Short Palindromic Repeats ; Conjugation, Genetic ; Gene Editing/methods ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genetic Therapy/methods ; Genome, Bacterial ; Humans ; Interspersed Repetitive Sequences ; Isoenzymes/genetics/metabolism ; RNA, Circular/genetics/metabolism ; RNA, Guide, CRISPR-Cas Systems/*genetics/metabolism ; Streptococcus/*genetics/immunology/virology ; Streptococcus Phages/*genetics/metabolism ; }, abstract = {Streptococci are one of the most important and common constituents of the host's microbiota and can colonize and live in the upper respiratory and urogenital tract of humans and animals. The CRISPR-Cas systems (i.e., clustered regularly interspaced short palindromic repeat, with CRISPR-associated proteins) found in bacteria and archaea provide sequence-based adaptive immunity against mobile genetic elements, especially in the streptococci. Here, recent research progress on CRISPR-Cas systems in the streptococci is reviewed, including their classification (mainly type I, type II, and type III), physiological function, defense mechanism (CRISPR adaptation, crRNA biogenesis, and target interference) and applications, which are useful for a better understanding of the functions of such systems. Finally, the advances that have been made in streptococci may help in the discovery of further novel CRISPR-Cas systems for use in new technologies and applications in other species.}, }
@article {pmid31165781, year = {2019}, author = {Faure, G and Shmakov, SA and Yan, WX and Cheng, DR and Scott, DA and Peters, JE and Makarova, KS and Koonin, EV}, title = {CRISPR-Cas in mobile genetic elements: counter-defence and beyond.}, journal = {Nature reviews. Microbiology}, volume = {17}, number = {8}, pages = {513-525}, pmid = {31165781}, issn = {1740-1534}, support = {ZIA LM000073/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Archaea/genetics ; Bacteria/genetics ; Bacteriophages/genetics ; *CRISPR-Cas Systems ; DNA Transposable Elements ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences ; Plasmids ; *Recombination, Genetic ; }, abstract = {The principal function of CRISPR-Cas systems in archaea and bacteria is defence against mobile genetic elements (MGEs), including viruses, plasmids and transposons. However, the relationships between CRISPR-Cas and MGEs are far more complex. Several classes of MGE contributed to the origin and evolution of CRISPR-Cas, and, conversely, CRISPR-Cas systems and their components were recruited by various MGEs for functions that remain largely uncharacterized. In this Analysis article, we investigate and substantially expand the range of CRISPR-Cas components carried by MGEs. Three groups of Tn7-like transposable elements encode 'minimal' type I CRISPR-Cas derivatives capable of target recognition but not cleavage, and another group encodes an inactivated type V variant. These partially inactivated CRISPR-Cas variants might mediate guide RNA-dependent integration of the respective transposons. Numerous plasmids and some prophages encode type IV systems, with similar predicted properties, that appear to contribute to competition among plasmids and between plasmids and viruses. Many prokaryotic viruses also carry CRISPR mini-arrays, some of which recognize other viruses and are implicated in inter-virus conflicts, and solitary repeat units, which could inhibit host CRISPR-Cas systems.}, }
@article {pmid31164464, year = {2019}, author = {Knopp, M and Gudmundsdottir, JS and Nilsson, T and König, F and Warsi, O and Rajer, F and Ädelroth, P and Andersson, DI}, title = {De Novo Emergence of Peptides That Confer Antibiotic Resistance.}, journal = {mBio}, volume = {10}, number = {3}, pages = {}, pmid = {31164464}, issn = {2150-7511}, mesh = {Aminoglycosides/pharmacology ; Drug Resistance, Microbial/*genetics ; Escherichia coli/*drug effects/genetics ; *Evolution, Molecular ; Gene Library ; Genomics ; Open Reading Frames ; Peptides/*genetics ; Phenotype ; Phylogeny ; RNA, Untranslated/*genetics ; }, abstract = {The origin of novel genes and beneficial functions is of fundamental interest in evolutionary biology. New genes can originate from different mechanisms, including horizontal gene transfer, duplication-divergence, and de novo from noncoding DNA sequences. Comparative genomics has generated strong evidence for de novo emergence of genes in various organisms, but experimental demonstration of this process has been limited to localized randomization in preexisting structural scaffolds. This bypasses the basic requirement of de novo gene emergence, i.e., lack of an ancestral gene. We constructed highly diverse plasmid libraries encoding randomly generated open reading frames and expressed them in Escherichia coli to identify short peptides that could confer a beneficial and selectable phenotype in vivo (in a living cell). Selections on antibiotic-containing agar plates resulted in the identification of three peptides that increased aminoglycoside resistance up to 48-fold. Combining genetic and functional analyses, we show that the peptides are highly hydrophobic, and by inserting into the membrane, they reduce membrane potential, decrease aminoglycoside uptake, and thereby confer high-level resistance. This study demonstrates that randomized DNA sequences can encode peptides that confer selective benefits and illustrates how expression of random sequences could spark the origination of new genes. In addition, our results also show that this question can be addressed experimentally by expression of highly diverse sequence libraries and subsequent selection for specific functions, such as resistance to toxic compounds, the ability to rescue auxotrophic/temperature-sensitive mutants, and growth on normally nonused carbon sources, allowing the exploration of many different phenotypes.IMPORTANCEDe novo gene origination from nonfunctional DNA sequences was long assumed to be implausible. However, recent studies have shown that large fractions of genomic noncoding DNA are transcribed and translated, potentially generating new genes. Experimental validation of this process so far has been limited to comparative genomics, in vitro selections, or partial randomizations. Here, we describe selection of novel peptides in vivo using fully random synthetic expression libraries. The peptides confer aminoglycoside resistance by inserting into the bacterial membrane and thereby partly reducing membrane potential and decreasing drug uptake. Our results show that beneficial peptides can be selected from random sequence pools in vivo and support the idea that expression of noncoding sequences could spark the origination of new genes.}, }
@article {pmid31162871, year = {2019}, author = {León-Sampedro, R and Del Campo, R and Rodriguez-Baños, M and Lanza, VF and Pozuelo, MJ and Francés-Cuesta, C and Tedim, AP and Freitas, AR and Novais, C and Peixe, L and Willems, RJL and Corander, J and González Candelas, F and Baquero, F and Coque, TM}, title = {Phylogenomics of Enterococcus faecalis from wild birds: new insights into host-associated differences in core and accessory genomes of the species.}, journal = {Environmental microbiology}, volume = {21}, number = {8}, pages = {3046-3062}, doi = {10.1111/1462-2920.14702}, pmid = {31162871}, issn = {1462-2920}, support = {//Instituto de Salud Carlos III of Spain/Ministry of Economy and Competitiveness/International ; //European Development Regional Fund 'A way to achieve Europe' (ERDF)/International ; PI15-0512//Spanish R&amp;D National Plan Estatal de I + D + i 2013-2016/International ; JPIAMR2016-AC16/00039//Joint Programming Initiative in Antimicrobial Resistance (JPIAMR)/International ; //Sociedad Espa&#xf1;ola de Enfermedades Infecciosas y Microbiolog&#xed;a Cl&#xed;nica (SEIMC)/International ; }, mesh = {Animals ; Animals, Wild ; Birds/*microbiology ; Enterococcus faecalis/*genetics ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genome, Bacterial ; Host Specificity ; *Phylogeny ; }, abstract = {Wild birds have been suggested to be reservoirs of antimicrobial resistant and/or pathogenic Enterococcus faecalis (Efs) strains, but the scarcity of studies and available sequences limit our understanding of the population structure of the species in these hosts. Here, we analysed the clonal and plasmid diversity of 97 Efs isolates from wild migratory birds. We found a high diversity, with most sequence types (STs) being firstly described here, while others were found in other hosts including some predominant in poultry. We found that pheromone-responsive plasmids predominate in wild bird Efs while 35% of the isolates entirely lack plasmids. Then, to better understand the ecology of the species, the whole genome of fivestrains with known STs (ST82, ST170, ST16 and ST55) were sequenced and compared with all the Efs genomes available in public databases. Using several methods to analyse core and accessory genomes (AccNET, PLACNET, hierBAPS and PANINI), we detected differences in the accessory genome of some lineages (e.g. ST82) demonstrating specific associations with birds. Conversely, the genomes of other Efs lineages exhibited divergence in core and accessory genomes, reflecting different adaptive trajectories in various hosts. This pangenome divergence, horizontal gene transfer events and occasional epidemic peaks could explain the population structure of the species.}, }
@article {pmid31161945, year = {2019}, author = {Shurina, BA and Page, RC}, title = {Influence of substrates and inhibitors on the structure of Klebsiella pneumoniae carbapenemase-2.}, journal = {Experimental biology and medicine (Maywood, N.J.)}, volume = {244}, number = {17}, pages = {1596-1604}, pmid = {31161945}, issn = {1535-3699}, mesh = {Bacterial Proteins/*antagonists &amp; inhibitors ; Enzyme Inhibitors/*pharmacology ; Humans ; Klebsiella pneumoniae/*drug effects/*metabolism ; beta-Lactamases ; }, abstract = {UNLABELLED: The hydrolysis of last resort carbapenem antibiotics by Klebsiella pneumoniae carbapenemase-2 (KPC-2) presents a significant danger to global health. Combined with horizontal gene transfer, the emergence KPC-2 threatens to quickly expand carbapenemase activity to ever increasing numbers of pathogens. Our understanding of KPC-2 has greatly increased over the past decade thanks, in great part, to 20 crystal structures solved by groups around the world. These include apo KPC-2 structures, along with structures featuring a library of 10 different inhibitors representing diverse structural and functional classes. Herein we focus on cataloging the available KPC-2 structures and presenting a discussion of key aspects of each structure and important relationships between structures. Although the available structures do not provide information on dynamic motions with KPC-2, and the family of structures indicates small conformational changes across a wide array of bound inhibitors, substrates, and products, the structures provide a strong foundation for additional studies in the coming years to discover new KPC-2 inhibitors.<br><br>IMPACT STATEMENT: The work herein is important to the field as it provides a clear and succinct accounting of available KPC-2 structures. The work advances the field by collecting and analyzing differences and similarities across the available structures. This work features new analyses and interpretations of the existing structures which will impact the field in a positive way by making structural insights more widely available among the beta-lactamase community.}, }
@article {pmid31161186, year = {2019}, author = {Uskoković, V and Tang, S and Wu, VM}, title = {Targeted magnetic separation of biomolecules and cells using earthicle-based ferrofluids.}, journal = {Nanoscale}, volume = {11}, number = {23}, pages = {11236-11253}, doi = {10.1039/c9nr01579e}, pmid = {31161186}, issn = {2040-3372}, mesh = {Animals ; Bacteria/*isolation &amp; purification ; Cell Line ; *Cell Separation ; Colloids ; Ferric Compounds/*chemistry ; *Fibroblasts/cytology/metabolism ; *Magnetic Fields ; Magnetite Nanoparticles/*chemistry ; Mice ; Muramidase/*isolation &amp; purification ; }, abstract = {Targeting specific molecular or cell populations within single tissues or multicomponent in vitro systems is a most sought goal in biomedicine. Here we report on targeted magnetic separation of cells and biomolecules using a ferrofluid comprising superparamagnetic iron-oxide/silicate/carbon core/shell/crust nanoparticles in combination with a handheld, 2.5 cm[3] NdFeB magnet (≤180 mT) and one minute exposure time. Ferrofluids were highly effective at separating (i) biomolecules, (ii) bacteria and (iii) eukaryotic cells from solutions, and they also exhibited selectivity in the separation of all three families of entities. Specifically, they were more effective at separating the negatively charged protein, albumin in the presence of the external magnetic field, but were more effective at precipitating the positively charged protein, lysozyme without the application of the external field. Because of the more effective sorption of proteins than carbohydrates on carbon and the shielding of peptidoglycans by the transmembrane proteins and hydrophilic heads of the outer membrane amphiphiles in Gram-negative bacteria, they were separated more effectively than their Gram-positive counterparts. Ferrofluids were also more efficient at separating the clinical isolate, methicillin-resistant version of S. aureus (MRSA) than its regular, lab strain and the effect is thought to be due to structural changes to the cell envelope caused by the overexpression of efflux pumps or by the higher rate of conjugation conditioning horizontal gene transfer in MRSA than in the regular, nonresistant strain. Ferrofluids also displayed a greater affinity for the cancer cells than for the normal, primary cells and allowed for targeted separation of the former after the cells were allowed to uptake the nanoparticles for 24 h. This selectivity should allow for an effective separation of cancer cells interspersed within a healthy cell population. Interaction with bacterial and eukaryotic cells was driven neither by electrostatic attraction nor chemisorption, but by weaker, van der Waals and π-interactions. Adsorption was also endothermic, irreversible for the most part, and more favorable at high concentrations, as inferred by comparison with Langmuir, Freundlich, Temkin and Dubinin-Radushkevich isotherms. These targeted effects are relevant for numerous fields of biomedicine and biotechnologies and require further insight for optimization and translation.}, }
@article {pmid31160340, year = {2019}, author = {Inniss, NL and Prehna, G and Morrison, DA}, title = {The pneumococcal σ[X] activator, ComW, is a DNA-binding protein critical for natural transformation.}, journal = {The Journal of biological chemistry}, volume = {294}, number = {29}, pages = {11101-11118}, pmid = {31160340}, issn = {1083-351X}, support = {R03 AI128228/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/genetics/*metabolism ; Biopolymers/chemistry/metabolism ; DNA, Bacterial/metabolism ; DNA-Binding Proteins/chemistry/genetics/*metabolism ; Gene Transfer, Horizontal ; Genes, Bacterial ; Models, Molecular ; Mutation ; Promoter Regions, Genetic ; Protein Binding ; Sequence Homology, Amino Acid ; Sigma Factor/chemistry/genetics/*metabolism ; Streptococcus pneumoniae/genetics/*metabolism ; *Transformation, Genetic ; }, abstract = {Natural genetic transformation via horizontal gene transfer enables rapid adaptation to dynamic environments and contributes to both antibiotic resistance and vaccine evasion among bacterial populations. In Streptococcus pneumoniae (pneumococcus), transformation occurs when cells enter competence, a transient state in which cells express the competence master regulator, SigX (σ[Χ]), an alternative σ factor (σ), and a competence co-regulator, ComW. Together, ComW and σ[X] facilitate expression of the genes required for DNA uptake and genetic recombination. SigX activity depends on ComW, as ΔcomW cells transcribe late genes and transform at levels 10- and 10,000-fold below that of WT cells, respectively. Previous findings suggest that ComW functions during assembly of the RNA polymerase-σ[X] holoenzyme to help promote transcription from σ[X]-targeted promoters. However, it remains unknown how ComW facilitates holoenzyme assembly. As ComW seems to be unique to Gram-positive cocci and has no sequence similarity with known transcriptional activators, here we used Rosetta to generate an ab initio model of pneumococcal ComW's 3D-structure. Using this model as a basis for further biochemical, biophysical, and genetic investigations into the molecular features important for its function, we report that ComW is a predicted globular protein and that it interacts with DNA, independently of DNA sequence. We also identified conserved motifs in ComW and show that key residues in these motifs contribute to DNA binding. Lastly, we provide evidence that ComW's DNA-binding activity is important for transformation in pneumococcus. Our findings begin to fill the gaps in understanding how ComW regulates σ[Χ] activity during bacterial natural transformation.}, }
@article {pmid31158594, year = {2019}, author = {Zhang, S and Wang, Y and Song, H and Lu, J and Yuan, Z and Guo, J}, title = {Copper nanoparticles and copper ions promote horizontal transfer of plasmid-mediated multi-antibiotic resistance genes across bacterial genera.}, journal = {Environment international}, volume = {129}, number = {}, pages = {478-487}, doi = {10.1016/j.envint.2019.05.054}, pmid = {31158594}, issn = {1873-6750}, mesh = {Bacteria/*drug effects/genetics ; Copper/*chemistry/pharmacology ; Drug Resistance, Bacterial/*genetics ; *Gene Transfer, Horizontal ; Metal Nanoparticles/*chemistry ; Metals, Heavy/chemistry/pharmacology ; Plasmids/*genetics ; }, abstract = {The spread of antibiotic resistance has become a major concern for public health. As emerging contaminants, various metallic nanoparticles (NPs) and ionic heavy metals have been ubiquitously detected in various environments. Although previous studies have indicated NPs and ionic heavy metals could exhibit co-selection effects for antibiotic resistance, little is known about whether and how they could promote antibiotic resistance spread via horizontal gene transfer across bacterial genera. This study, we report both CuO NPs and copper ions (Cu[2+]) could stimulate the conjugative transfer of multiple-drug resistance genes. When exposing bacteria to CuO NPs or Cu[2+] at environmental-relevant and sub-inhibitory concentrations (e.g., 1-100 μmol/L), conjugation frequencies of plasmid-encoded antibiotic resistance genes across genera (i.e., from Escherichia coli to Pseudomonas putida) were significantly enhanced (p < 0.05). The over-production of reactive oxygen species played a crucial role in promoting conjugative transfer. Genome-wide RNA and protein sequencing suggested expressional levels of genes and proteins related to oxidative stress, cell membrane permeability, and pilus generation were significantly up-regulated under CuO NPs and Cu[2+] exposure (p < 0.05). This study provides insights in the contributions of NPs and heavy metals on the spread of antibiotic resistance.}, }
@article {pmid31157229, year = {2019}, author = {Cirrincione, S and Neumann, B and Zühlke, D and Riedel, K and Pessione, E}, title = {Detailed Soluble Proteome Analyses of a Dairy-Isolated Enterococcus faecalis: A Possible Approach to Assess Food Safety and Potential Probiotic Value.}, journal = {Frontiers in nutrition}, volume = {6}, number = {}, pages = {71}, pmid = {31157229}, issn = {2296-861X}, abstract = {Enterococci are common inhabitants of the gastrointestinal tracts of humans and animals and thanks to their capability to tolerate different environmental conditions and their high rates of gene transfer, they are able to colonize various ecological niches, as food matrices. Enterococcus faecalis bacteria are defined as controversial microorganisms. From one side they are used as food starters, bio-control agents and probiotics to improve human or animal health. From the other side, in the last two decades enterococci have emerged as important nosocomial pathogens, because bearing high-level of resistance to antibiotics and several putative virulence factors. In this study, the soluble proteome quantitation data (LC-MS/MS) of the food-isolated strain E. faecalis D27 (dairy-isolate) was compared with the soluble proteome quantitation data of the pathogenic E. faecalis UW3114 (urinary tract infection isolate) and with the one of the health promoting strain E. faecalis Symbioflor1, respectively. The comparison of cytosolic protein expression profiles highlighted statistically significant changes in the abundance of proteins mainly involved in specific metabolic pathways, nutrient transport, stress response, and cell wall modulation. Moreover, especially in the dairy isolate and the clinical isolate, several proteins with potential pathogenic implications were found, such as serine proteases, von Willebrand factor, serine hydrolase with beta lactamase activity, efflux transporter, and proteins involved in horizontal gene transfer. The analysis of the extracellular proteome provided interesting results concerning proteins involved in bacterial communication, such as pheromones and conjugative elements and also proteins able to interact with human components. The phenotypic characterization evaluating (i) biofilm formation (ii) hemolytic activity on blood agar plates (iii) protease activity (iv) gelatinase (v) antibiotic resistance pattern, enabled us to elucidate the risks associated with the poor characterized foodborne E. faecalis D27.}, }
@article {pmid31155362, year = {2019}, author = {Russell, SL and Chappell, L and Sullivan, W}, title = {A symbiont's guide to the germline.}, journal = {Current topics in developmental biology}, volume = {135}, number = {}, pages = {315-351}, doi = {10.1016/bs.ctdb.2019.04.007}, pmid = {31155362}, issn = {1557-8933}, mesh = {Animals ; Cell Movement ; Embryo, Nonmammalian/microbiology ; Germ Cells/*physiology ; Stem Cells/cytology ; *Symbiosis ; }, abstract = {Microbial symbioses exhibit astounding adaptations, yet all symbionts face the problem of how to reliably associate with host offspring every generation. A common strategy is vertical transmission, in which symbionts are directly transmitted from the female to her offspring. The diversity of symbionts and vertical transmission mechanisms is as expansive as the diversity of eukaryotic host taxa that house them. However, there are several common themes among these mechanisms based on the degree to which symbionts associate with the host germline during transmission. In this review, we detail three distinct vertical transmission strategies, starting with associations that are transmitted from host somatic cells to offspring somatic cells, either due to lacking a germline or avoiding it. A second strategy involves somatically-localized symbionts that migrate into the germline during host development. The third strategy we discuss is one in which the symbiont maintains continuous association with the germline throughout development. Unexpectedly, the vast majority of documented vertically inherited symbionts rely on the second strategy: soma-to-germline migration. Given that not all eukaryotes contain a sequestered germline and instead produce offspring from somatic stem cell lineages, this soma-to-germline migration is discussed in the context of multicellular evolution. Lastly, as recent genomics data have revealed an abundance of horizontal gene transfer events from symbiotic and non-symbiotic bacteria to host genomes, we discuss their impact on eukaryotic host evolution.}, }
@article {pmid31149898, year = {2019}, author = {Rossoni, AW and Price, DC and Seger, M and Lyska, D and Lammers, P and Bhattacharya, D and Weber, AP}, title = {The genomes of polyextremophilic cyanidiales contain 1% horizontally transferred genes with diverse adaptive functions.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, pmid = {31149898}, issn = {2050-084X}, support = {EXC 1028//Deutsche Forschungsgemeinschaft/International ; WE 2231/21-1//Deutsche Forschungsgemeinschaft/International ; }, mesh = {*Adaptation, Biological ; Algal Proteins/genetics ; DNA, Algal/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Rhodophyta/*genetics ; }, abstract = {The role and extent of horizontal gene transfer (HGT) in eukaryotes are hotly disputed topics that impact our understanding of the origin of metabolic processes and the role of organelles in cellular evolution. We addressed this issue by analyzing 10 novel Cyanidiales genomes and determined that 1% of their gene inventory is HGT-derived. Numerous HGT candidates share a close phylogenetic relationship with prokaryotes that live in similar habitats as the Cyanidiales and encode functions related to polyextremophily. HGT candidates differ from native genes in GC-content, number of splice sites, and gene expression. HGT candidates are more prone to loss, which may explain the absence of a eukaryotic pan-genome. Therefore, the lack of a pan-genome and cumulative effects fail to provide substantive arguments against our hypothesis of recurring HGT followed by differential loss in eukaryotes. The maintenance of 1% HGTs, even under selection for genome reduction, underlines the importance of non-endosymbiosis related foreign gene acquisition.}, }
@article {pmid31146755, year = {2019}, author = {Dunivin, TK and Yeh, SY and Shade, A}, title = {A global survey of arsenic-related genes in soil microbiomes.}, journal = {BMC biology}, volume = {17}, number = {1}, pages = {45}, pmid = {31146755}, issn = {1741-7007}, support = {R25 GM115335/GM/NIGMS NIH HHS/United States ; }, mesh = {Access to Information ; Arsenic/*adverse effects/metabolism ; Bacteria/*drug effects/genetics/metabolism ; Drug Resistance, Bacterial/*genetics ; Microbiota/*drug effects/genetics ; *Soil Microbiology ; Soil Pollutants/*adverse effects ; }, abstract = {BACKGROUND: Environmental resistomes include transferable microbial genes. One important resistome component is resistance to arsenic, a ubiquitous and toxic metalloid that can have negative and chronic consequences for human and animal health. The distribution of arsenic resistance and metabolism genes in the environment is not well understood. However, microbial communities and their resistomes mediate key transformations of arsenic that are expected to impact both biogeochemistry and local toxicity.<br><br>RESULTS: We examined the phylogenetic diversity, genomic location (chromosome or plasmid), and biogeography of arsenic resistance and metabolism genes in 922 soil genomes and 38 metagenomes. To do so, we developed a bioinformatic toolkit that includes BLAST databases, hidden Markov models and resources for gene-targeted assembly of nine arsenic resistance and metabolism genes: acr3, aioA, arsB, arsC (grx), arsC (trx), arsD, arsM, arrA, and arxA. Though arsenic-related genes were common, they were not universally detected, contradicting the common conjecture that all organisms have them. From major clades of arsenic-related genes, we inferred their potential for horizontal and vertical transfer. Different types and proportions of genes were detected across soils, suggesting microbial community composition will, in part, determine local arsenic toxicity and biogeochemistry. While arsenic-related genes were globally distributed, particular sequence variants were highly endemic (e.g., acr3), suggesting dispersal limitation. The gene encoding arsenic methylase arsM was unexpectedly abundant in soil metagenomes (median 48%), suggesting that it plays a prominent role in global arsenic biogeochemistry.<br><br>CONCLUSIONS: Our analysis advances understanding of arsenic resistance, metabolism, and biogeochemistry, and our approach provides a roadmap for the ecological investigation of environmental resistomes.}, }
@article {pmid31146680, year = {2019}, author = {Zhang, X and Liu, X and Li, L and Wei, G and Zhang, D and Liang, Y and Miao, B}, title = {Phylogeny, Divergent Evolution, and Speciation of Sulfur-Oxidizing Acidithiobacillus Populations.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {438}, pmid = {31146680}, issn = {1471-2164}, support = {31570113//National Natural Science Foundation of China/ ; }, mesh = {Acidithiobacillus/*classification/*genetics/metabolism ; *Evolution, Molecular ; Genes, Bacterial ; Genetic Speciation ; Genome Size ; *Genome, Bacterial ; Interspersed Repetitive Sequences ; Oxidation-Reduction ; Phylogeny ; Sulfur/metabolism ; }, abstract = {BACKGROUND: Habitats colonized by acidophiles as an ideal physical barrier may induce genetic exchange of microbial members within the common communities, but little is known about how species in extremely acidic environments diverge and evolve.<br><br>RESULTS: Using the acidophilic sulfur-oxidizer Acidithiobacillus as a case study, taxonomic reclassifications of many isolates provides novel insights into their phylogenetic lineage. Whole-genome-based comparisons were attempted to investigate the intra- and inter-species divergence. Recent studies clarified that functional and structural specificities of bacterial strains might provide opportunities for adaptive evolution responding to local environmental conditions. Acidophilic microorganisms play a key role in the acidification of natural waters and thus the formation of extremely acidic environments, and the feedbacks of the latter might confer the distinct evolutionary patterns of Acidithiobacillus spp. Varied horizontal gene transfer events occurred in different bacterial strains, probably resulting in the expansion of Acidithiobacillus genomes. Gene loss as another evolutionary force might cause the adaptive phenotypic diversity. A conceptual model for potential community-dependent evolutionary adaptation was thus proposed to illustrate the observed genome differentiation.<br><br>CONCLUSIONS: Collectively, the findings shed light on the phylogeny and divergent evolution of Acidithiobacillus strains, and provided a useful reference for evolutionary studies of other extremophiles.}, }
@article {pmid31143827, year = {2019}, author = {Malathi, VG and Renuka Devi, P}, title = {ssDNA viruses: key players in global virome.}, journal = {Virusdisease}, volume = {30}, number = {1}, pages = {3-12}, pmid = {31143827}, issn = {2347-3584}, abstract = {Single-stranded (ss)DNA viruses are extremely widespread, infect diverse hosts from all three domains of life and include important pathogens. Most ssDNA viruses possess small genomes that replicate by the rolling-circle-like mechanism initiated by a distinct virus-encoded endonuclease. High throughput genome sequencing and improved bioinformatics tools have yielded vast information on presence of ssDNA viruses in diverse habitats. The simple genome of ssDNA viruses have high propensity to undergo mutation and recombination often emerging as threat to human civilization. Interestingly their genome is found embedded in fossils dating back to million years. The unusual evolutionary history of ssDNA viruses reveal evidences of horizontal gene transfer, sometimes between different species and genera.}, }
@article {pmid31142760, year = {2019}, author = {Parmeciano DI Noto, G and Iriarte, A and Ramírez, MS and Centrón, D and Quiroga, C}, title = {ICE SXT vs. ICESh95: Co-existence of Integrative and Conjugative Elements and Competition for a New Host.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {8045}, pmid = {31142760}, issn = {2045-2322}, support = {BID/OC ANPCyT (2013&#x2013;1978)//Ministry of Science, Technology and Productive Innovation, Argentina | Agencia Nacional de Promoci&#x00F3;n Cient&#x00ED;fica y Tecnol&#x00F3;gica (National Agency for Science and Technology, Argentina)/International ; }, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacterial Proteins/genetics ; Conjugation, Genetic/drug effects/genetics ; DNA Transposable Elements/*genetics ; DNA, Bacterial/genetics/isolation &amp; purification ; Drug Resistance, Multiple, Bacterial/drug effects/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/drug effects/*genetics ; Genetic Variation/drug effects ; Genome, Bacterial/genetics ; Gram-Negative Bacterial Infections/*drug therapy/microbiology ; Host Specificity/genetics ; Humans ; Integrases/genetics ; Molecular Sequence Annotation ; Phylogeny ; Sequence Analysis, DNA ; Shewanella/drug effects/*genetics/isolation &amp; purification ; }, abstract = {Integrative and conjugative elements (ICEs) are mobile genetic elements that contribute to horizontal gene transfer. The aim of this work was to study different types of ICEs in clinical isolates of the emergent pathogen Shewanella spp., to compare their transfer efficiency and their ability to integrate a new host. Here we show that 3 out of 10 clinical isolates contained an ICE. Two of these elements were similar to ICEs from the SXT/R391 family and the other one was similar to ICESh95, a hybrid platform. Mating assays showed that these elements co-exist for several generations in the same host. Furthermore, transfer rates and competition assays between ICESh95 and ICESh392, an SXT-like element, suggest that the latter has evolved into a well-oiled machine that efficiently spread to different bacteria. Our results provide strong evidence of the role that ICEs play in the dissemination of genetic traits in nature and the implications that they have in the global threat of antimicrobial resistance.}, }
@article {pmid31138576, year = {2019}, author = {Wachino, JI and Jin, W and Kimura, K and Arakawa, Y}, title = {Intercellular Transfer of Chromosomal Antimicrobial Resistance Genes between Acinetobacter baumannii Strains Mediated by Prophages.}, journal = {Antimicrobial agents and chemotherapy}, volume = {63}, number = {8}, pages = {}, pmid = {31138576}, issn = {1098-6596}, mesh = {Acinetobacter baumannii/*genetics ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics ; Capsid ; Chromosomes, Bacterial ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Plasmids ; Prophages/*genetics ; Transduction, Genetic ; beta-Lactamases/genetics ; }, abstract = {The spread of antimicrobial resistance genes (ARGs) among Gram-negative pathogens, including Acinetobacter baumannii, is primarily mediated by transferable plasmids; however, ARGs are frequently integrated into its chromosome. How ARG gets horizontally incorporated into the chromosome of A. baumannii, and whether it functions as a cause for further spread of ARG, remains unknown. Here, we demonstrated intercellular prophage-mediated transfer of chromosomal ARGs without direct cell-cell interaction in A. baumannii We prepared ARG-harboring extracellular DNA (eDNA) components from the culture supernatant of a multidrug-resistant (MDR) A. baumannii NU-60 strain and exposed an antimicrobial-susceptible (AS) A. baumannii ATCC 17978 strain to the eDNA components. The antimicrobial-resistant (AR) A. baumannii ATCC 17978 derivatives appeared to acquire various ARGs, originating from dispersed loci of the MDR A. baumannii chromosome, along with their surrounding regions, by homologous recombination, with the ARGs including armA (aminoglycoside resistance), blaTEM-1 (β-lactam resistance), tet(B) (tetracycline resistance), and gyrA-81L (nalidixic acid resistance) genes. Notably, the eDNAs conferring antimicrobial resistance were enveloped in specific capsid proteins consisting of phage particles, thereby protecting the eDNAs from detergent and DNase treatments. The phages containing ARGs were likely released into the extracellular space from MDR A. baumannii, thereby transducing ARGs into AS A. baumannii, resulting in the acquisition of AR properties by the recipient. We concluded that the generalized transduction, in which phages were capable of carrying random pieces of A. baumannii genomic DNAs, enabled efficacious intercellular transfer of chromosomal ARGs between A. baumannii strains without direct cell-cell interaction.}, }
@article {pmid31138439, year = {2019}, author = {Hashimoto, M and Hasegawa, H and Maeda, S}, title = {High temperatures promote cell-to-cell plasmid transformation in Escherichia coli.}, journal = {Biochemical and biophysical research communications}, volume = {515}, number = {1}, pages = {196-200}, doi = {10.1016/j.bbrc.2019.05.134}, pmid = {31138439}, issn = {1090-2104}, mesh = {Bacteriological Techniques/methods ; Biofilms ; DNA, Bacterial/genetics/metabolism ; Deoxyribonucleases/metabolism ; Escherichia coli/classification/*genetics/physiology ; *Gene Transfer, Horizontal ; *Hot Temperature ; Plasmids/*genetics ; Transformation, Bacterial/*genetics ; }, abstract = {Bacteria continuously change their genetic characteristics to adapt to the changing environment by means of horizontal gene transfer. Although three conventional mechanisms of horizontal gene transfer are well known (transformation, transduction, and conjugation), new variations of these mechanisms have also been described. We previously reported that DNase-sensitive cell-to-cell transfer of non-conjugative plasmids, termed as "cell-to-cell transformation," occurs between the cells of two Escherichia coli strains in a co-culture. In this study, to further investigate the mechanism of cell-to-cell transformation, we constructed a new experimental system for cell-to-cell transformation. By using this system, we found that high temperatures of approximately 41ºC-45 °C significantly promote cell-to-cell plasmid transformation. This transfer was much more frequent in solid-air biofilms than in liquid culture, suggesting an importance of biofilm environment. Plasmid transfer frequency reached over 10[-7]/cell under the optimal strain-plasmid combination and conditions tested. DNase sensitivity test and plasmid isolation from the transformants confirmed the horizontal transfer of full-length plasmids via transformation. Comparative natural transformation experiments, which used similar strains and plasmids under equivalent culture conditions, revealed that cell-to-cell transformation occurs approximately 10[3] times more frequently than natural transformation, indicating the uniqueness and effectiveness of the cell-to-cell transformation mechanism. As temperatures of approximately 41ºC-45 °C are common in the avian intestines and under some other environmental situations, the phenomenon demonstrated here can occur efficiently in such locations. To the best of our knowledge, this is the first study to demonstrate the enhancing effect of high temperatures on cell-to-cell plasmid transformation in E. coli.}, }
@article {pmid31136832, year = {2019}, author = {Kang, ZZ and Lei, CW and Kong, LH and Wang, YL and Ye, XL and Ma, BH and Wang, XC and Li, C and Zhang, Y and Wang, HN}, title = {Detection of transferable oxazolidinone resistance determinants in Enterococcus faecalis and Enterococcus faecium of swine origin in Sichuan Province, China.}, journal = {Journal of global antimicrobial resistance}, volume = {19}, number = {}, pages = {333-337}, doi = {10.1016/j.jgar.2019.05.021}, pmid = {31136832}, issn = {2213-7173}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; China ; Drug Resistance, Bacterial/*genetics ; Enterococcus faecalis/*drug effects/genetics ; Enterococcus faecium/*drug effects/genetics ; Farms ; Feces/microbiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Interspersed Repetitive Sequences ; Microbial Sensitivity Tests ; Oxazolidinones/*pharmacology ; Swine ; Swine Diseases/microbiology ; Whole Genome Sequencing ; }, abstract = {OBJECTIVES: The aim of this study was to detect transferable oxazolidinone resistance determinants (cfr, optrA and poxtA) in Enterococcus faecalis and Enterococcus faecium isolates of swine origin in Sichuan Province, China.<br><br>METHODS: A total of 158 enterococcal isolates (93 E. faecalis and 65 E. faecium) isolated from 25 large-scale swine farms (2016-2017) were screened for the presence of cfr, optrA and poxtA by PCR. The genetic environments of cfr, optrA and poxtA were characterised by whole-genome sequencing. Transfer of oxazolidinone resistance determinants was determined by conjugation or electrotransformation experiments.<br><br>RESULTS: The transferable oxazolidinone resistance determinants cfr, optrA and poxtA were detected in zero, six and one enterococcal isolates, respectively. The poxtA gene in one E. faecalis isolate was located on a 37 990-bp plasmid that co-harboured fexB, cat, tet(L) and tet(M) and could be conjugated to E. faecalis JH2-2. One E. faecalis isolate harboured two different OptrA variants, including one variant with a single substitution (Q219H) that has not been reported previously. Two optrA-carrying plasmids, pC25-1 (45 581bp) and pC54 (64 500bp), shared a 40 494-bp identical region containing the genetic context IS1216E-fexA-optrA-erm(A)-IS1216E that could be electrotransformed into Staphylococcus aureus. Four different chromosomal optrA gene clusters were found in five strains, in which optrA was associated with Tn554 or Tn558 inserted into the radC gene.<br><br>CONCLUSION: This study highlights the fact that mobile genetic elements, such as plasmids, IS1216E, Tn554 and Tn558, may facilitate the horizontal transmission of optrA and poxtA genes.}, }
@article {pmid31136784, year = {2019}, author = {Khanppnavar, B and Chatterjee, R and Choudhury, GB and Datta, S}, title = {Genome-wide survey and crystallographic analysis suggests a role for both horizontal gene transfer and duplication in pantothenate biosynthesis pathways.}, journal = {Biochimica et biophysica acta. General subjects}, volume = {1863}, number = {10}, pages = {1547-1559}, doi = {10.1016/j.bbagen.2019.05.017}, pmid = {31136784}, issn = {1872-8006}, mesh = {Allosteric Regulation ; Catalysis ; Crystallography, X-Ray ; Gene Dosage ; *Gene Duplication ; *Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome ; Oxidation-Reduction ; Pantothenic Acid/*biosynthesis ; Surveys and Questionnaires ; }, abstract = {Pantothenate is the metabolic precursor of Coenzyme A, an indispensable cofactor for many fundamental cellular processes. In this study, we show that many bacterial species have acquired multiple copies of pantothenate biosynthesis pathway genes via horizontal and vertical gene transfer events. Some bacterial species were also found to lack panE and panD genes, and depended on alternative enzymes/metabolic sources for pantothenate production. To shed light on the factors responsible for such dynamic evolutionary selections, the structural and functional characteristics of P. aeruginosa ketopantoate reductase (KPR), an enzyme that catalyzes the rate-limiting step and also the most duplicated, was investigated. A comparative analysis of apo and NADP+ bound crystal structures of P. aeruginosa KPR with orthologs, revealed that the residues involved in the interaction with specific phosphate moiety of NADP+ are relatively less conserved, suggesting dynamic evolutionary trajectories in KPRs for redox cofactor selection. Our structural and biochemical data also show that the specific conformational changes mediated by NADPH binding facilitate the cooperative binding of ketopantoate. From drastically reduced catalytic activity for NADH catalyzed the reaction with significantly higher KM of ketopantoate, it appears that the binding of ketopantoate is allosterically regulated to confer redox cofactor specificity. Altogether, our results, in compliance with earlier studies, not only depict the role of lateral gene transfer events in many bacterial species for enhancing pantothenate production but also highlight the possible role of redox cofactor balance in the regulation of pantothenate biosynthesis pathways.}, }
@article {pmid31135958, year = {2019}, author = {Ponce-Toledo, RI and López-García, P and Moreira, D}, title = {Horizontal and endosymbiotic gene transfer in early plastid evolution.}, journal = {The New phytologist}, volume = {224}, number = {2}, pages = {618-624}, pmid = {31135958}, issn = {1469-8137}, support = {322669/ERC_/European Research Council/International ; }, mesh = {*Biological Evolution ; Gene Expression Regulation/physiology ; Gene Transfer, Horizontal ; Photosynthesis/genetics/physiology ; Plastids/*genetics/*physiology ; Symbiosis/*physiology ; }, abstract = {Plastids evolved from a cyanobacterium that was engulfed by a heterotrophic eukaryotic host and became a stable organelle. Some of the resulting eukaryotic algae entered into a number of secondary endosymbioses with diverse eukaryotic hosts. These events had major consequences on the evolution and diversification of life on Earth. Although almost all plastid diversity derives from a single endosymbiotic event, the analysis of nuclear genomes of plastid-bearing lineages has revealed a mosaic origin of plastid-related genes. In addition to cyanobacterial genes, plastids recruited for their functioning eukaryotic proteins encoded by the host nucleus and also bacterial proteins of noncyanobacterial origin. Therefore, plastid proteins and plastid-localised metabolic pathways evolved by tinkering and using gene toolkits from different sources. This mixed heritage seems especially complex in secondary algae containing green plastids, the acquisition of which appears to have been facilitated by many previous acquisitions of red algal genes (the 'red carpet hypothesis').}, }
@article {pmid31134321, year = {2019}, author = {Long, J and Xu, Y and Ou, L and Yang, H and Xi, Y and Chen, S and Duan, G}, title = {Diversity of CRISPR/Cas system in Clostridium perfringens.}, journal = {Molecular genetics and genomics : MGG}, volume = {294}, number = {5}, pages = {1263-1275}, pmid = {31134321}, issn = {1617-4623}, support = {2018ZX10301407//National Science and Technology Specific Projects/ ; 2013ZX10004607//National Science and Technology Specific Projects/ ; 17HASTIT045//Henan Province University Science and Technology Innovation Talent Projects/ ; }, mesh = {Bacteriophages/genetics ; CRISPR-Cas Systems/*genetics ; Clostridium perfringens/*genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/*genetics ; Computational Biology/methods ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/genetics ; Phylogeny ; Plasmids/genetics ; Polymorphism, Genetic/genetics ; }, abstract = {Clostridium perfringens is an important pathogen of human and livestock infections, posing a threat to health. The horizontal gene transfer (HGT) of plasmids that carry toxin-related genes is involved in C. perfringens pathogenicity. The CRISPR/Cas system, which has been identified in a wide range of prokaryotes, provides acquired immunity against HGT. However, information about the CRISPR/Cas system in Clostridium perfringens is still limited. In this study, 111 C. perfringens strains with publicly available genomes were used to analyze the occurrence and diversity of CRISPR/Cas system and evaluate the potential of CRISPR-based genotyping in this multi-host pathogen. A total of 59 out of the 111 genomes harbored at least one confirmed CRISPR array. Four CRISPR/Cas system subtypes, including subtypes IB, IIA, IIC, and IIID systems, were identified in 32 strains. Subtype IB system was the most prevalent in this species, which was subdivided into four subgroups displaying subgroup specificity in terms of cas gene content, repeat sequence content, and PAM. We showed that the CRISPR spacer polymorphism can be used for evolutionary studies, and that it can provide discriminatory power for typing strains. Nevertheless, the application of this approach was largely limited to strains that contain the CRISPR/Cas system. Spacer origin analysis revealed that approximately one-fifth of spacers showed significant matches to plasmids and phages, thereby suggesting the implication of CRISPR/Cas systems in controlling HGT. Collectively, our results provide new insights into the diversity and evolution of CRISPR/Cas system in C. perfringens.}, }
@article {pmid31133029, year = {2019}, author = {Regmi, A and Boyd, EF}, title = {Carbohydrate metabolic systems present on genomic islands are lost and gained in Vibrio parahaemolyticus.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {112}, pmid = {31133029}, issn = {1471-2180}, mesh = {Bacterial Proteins/genetics ; Carbohydrate Metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genomic Islands ; Multigene Family ; Phylogeny ; Symporters/*genetics ; Vibrio parahaemolyticus/classification/*genetics ; }, abstract = {BACKGROUND: Utilizing unique carbohydrates or utilizing them more efficiently help bacteria expand and colonize new niches. Horizontal gene transfer (HGT) of catabolic systems is a powerful mechanism by which bacteria can acquire new phenotypic traits that can increase survival and fitness in different niches. In this work, we examined carbon catabolism diversity among Vibrio parahaemolyticus, a marine species that is also an important human and fish pathogen.<br><br>RESULTS: Phenotypic differences in carbon utilization between Vibrio parahaemolyticus strains lead us to examine genotypic differences in this species and the family Vibrionaceae in general. Bioinformatics analysis showed that the ability to utilize D-galactose was present in all V. parahaemolyticus but at least two distinct transporters were present; a major facilitator superfamily (MFS) transporter and a sodium/galactose transporter (SGLT). Growth and genetic analyses demonstrated that SGLT was a more efficient transporter of D-galactose and was the predominant type among strains. Phylogenetic analysis showed that D-galactose gene galM was acquired multiples times within the family Vibrionaceae and was transferred between distantly related species. The ability to utilize D-gluconate was universal within the species. Deletion of eda (VP0065), which encodes aldolase, a key enzyme in the Entner-Doudoroff (ED) pathway, reached a similar biomass to wild type when grown on D-gluconate as a sole carbon source. Two additional eda genes were identified, VPA1708 (eda2) associated with a D-glucuronate cluster and VPA0083 (eda3) that clustered with an oligogalacturonide (OGA) metabolism cluster. EDA2 and EDA3 were variably distributed among the species. A metabolic island was identified that contained citrate fermentation, L-rhamnose and OGA metabolism clusters as well as a CRISPR-Cas system. Phylogenetic analysis showed that CitF and RhaA had a limited distribution among V. parahaemolyticus, and RhaA was acquired at least three times. Within V. parahaemolyticus, two different regions contained the gene for L-arabinose catabolism and most strains had the ability to catabolism this sugar.<br><br>CONCLUSION: Our data suggest that horizontal transfer of metabolic systems among Vibrionaceae is an important source of metabolic diversity. This work identified four EDA homologues suggesting that the ED pathway plays a significant role in metabolism. We describe previously uncharacterized metabolism islands that were hotspots for the gain and loss of functional modules likely mediated by transposons.}, }
@article {pmid31132519, year = {2019}, author = {Chen, R and Yao, Y and Fang, H and Zhang, E and Li, P and Xu, Y and Yin, S and Huangfu, L and Sun, G and Xu, C and Zhou, Y and Yang, Z}, title = {Origin, evolution and functional characterization of the land plant glycoside hydrolase subfamily GH5_11.}, journal = {Molecular phylogenetics and evolution}, volume = {138}, number = {}, pages = {205-218}, doi = {10.1016/j.ympev.2019.05.031}, pmid = {31132519}, issn = {1095-9513}, mesh = {Arabidopsis/*enzymology/*genetics ; Cellulose/metabolism ; *Evolution, Molecular ; Gene Duplication ; Gene Expression Regulation, Plant ; Gene Transfer, Horizontal/genetics ; Genes, Plant ; Glycoside Hydrolases/*genetics/*metabolism ; Mutagenesis/genetics ; Mutation/genetics ; Phenotype ; Phylogeny ; Selection, Genetic ; }, abstract = {Colonization of the land by plants was a critical event in the establishment of modern terrestrial ecosystems, and many characteristics of land plants originated during this process, including the emergence of rosette terminal cellulose-synthesizing complexes. Cellulases are non-homologous isofunctional enzymes, encoded by glycosyl hydrolase (GH) gene families. Although the plant GH5_11 gene subfamily is presumed to encode a cell-wall degrading enzyme, its evolutionary and functional characteristics remain unclear. In the present study, we report the evolution of the land plant GH5_11 subfamily, and the functions of its members in terms of cellulase activity, through comprehensive phylogenetic analyses and observation of Arabidopsis mutants. Phylogenetic and sequence similarity analyses reveal that the ancestor of land plants acquired the GH5_11 gene from fungi through a horizontal gene transfer (HGT) event. Subsequently, positive selection with massive gene duplication and loss events contributed to the evolution of this subfamily in land plants. In Arabidopsis and rice, expression of GH5_11 genes are regulated by multiple abiotic stresses, the duplicated genes showing different patterns of expression. The Arabidopsis mutants atgh5_11a and atgh5_11c display low levels of cellulase and endoglucanase activities, with correspondingly high levels of cellulose, implying that the encoded proteins may function as endoglucanases. However, atgh5_11a and atgh5_11c also display an enlarged rosette leaf phenotype, and atgh5_11c is late-flowering under short photoperiods. These observations suggest that plant GH5_11s possess more functions beyond being endonucleases. To summarize, we demonstrate that the ancestor of land plants has acquired GH5_11 gene through HGT, which extends the cellulose degradation complexity. Our investigations illuminate features of part of the molecular framework underlying the origin of land plants and provide a focus on the cellulose degradation pathway.}, }
@article {pmid31132119, year = {2019}, author = {Heo, S and Bae, T and Lee, JH and Jeong, DW}, title = {Transfer of a lincomycin-resistant plasmid between coagulase-negative staphylococci during soybean fermentation and mouse intestine passage.}, journal = {FEMS microbiology letters}, volume = {366}, number = {10}, pages = {}, doi = {10.1093/femsle/fnz113}, pmid = {31132119}, issn = {1574-6968}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Coagulase/analysis ; Drug Resistance, Microbial/*genetics ; Female ; Fermented Foods/microbiology ; Gene Transfer Techniques ; Interspersed Repetitive Sequences ; Intestines/*microbiology ; Lincomycin/*pharmacology ; Male ; Mice ; Mice, Inbred C57BL ; Plasmids/*genetics ; Glycine max/metabolism/*microbiology ; Staphylococcus saprophyticus/drug effects/*genetics ; }, abstract = {Staphylococcus equorum is a benign bacterium and the predominant species in high-salt fermented food. Some strains of S. equorum contain antibiotic-resistance plasmids, such as pSELNU1 that contains a lincosamide nucleotidyltransferase (lnuA) gene and confers resistance to lincomycin. Previously, we showed that pSELNU1 is transferred to other bacteria under laboratory growth conditions. However, it is not known if the plasmid can be transferred to other bacteria during food fermentation (in situ) or during passage through animal intestines (in vivo). In this study, we examined the in situ and in vivo transfer of pSELNU1 using Staphylococcus saprophyticus as a recipient. During soybean fermentation, pSELNU1 was transferred to S. saprophyticus at a rate of 1.9 × 10-5-5.6 × 10-6 per recipient in the presence of lincomycin. However, during passage through murine intestines, the plasmid was transferred at similar rates (1.3 × 10-5 per recipient) in the absence of lincomycin, indicating that the plasmid transfer is much more efficient under in vivo conditions. Based on these results, we conclude that it is prudent to examine food fermentation starter candidates for the presence of mobile genetic elements containing antibiotic resistance genes and to select candidates lacking these genes.}, }
@article {pmid31131182, year = {2019}, author = {Tashiro, Y and Takaki, K and Futamata, H}, title = {Targeted delivery using membrane vesicles in prokaryotes.}, journal = {Biophysics and physicobiology}, volume = {16}, number = {}, pages = {114-120}, pmid = {31131182}, issn = {2189-4779}, abstract = {Membrane vesicles (MVs) are lumen-containing spheres of lipid bilayers secreted by all prokaryotes into the extracellular milieu. They have multifunctional roles in stress response, virulence transfer, biofilm formation, and microbial interactions. Remarkably, MVs contain various components, including lytic enzymes, genetic materials, and hydrophobic signals, at high concentrations and transfer them effectively to the target microbial cells. Therefore, MVs act as carriers for bactericidal effects, horizontal gene transfer, and quorum sensing. Although the purpose of secreted MVs remains unclear, recent reports have provided evidence that MVs selectively interact with microbial cells in order to transfer their content to the target species. Herein, we review microbial interactions using MVs and discuss MV-mediated selective delivery of their content to target microbial cells.}, }
@article {pmid31130940, year = {2019}, author = {Newberry, EA and Ebrahim, M and Timilsina, S and Zlatković, N and Obradović, A and Bull, CT and Goss, EM and Huguet-Tapia, JC and Paret, ML and Jones, JB and Potnis, N}, title = {Corrigendum: Inference of Convergent Gene Acquisition Among Pseudomonas syringae Strains Isolated From Watermelon, Cantaloupe, and Squash.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {963}, doi = {10.3389/fmicb.2019.00963}, pmid = {31130940}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2019.00270.].}, }
@article {pmid31130838, year = {2019}, author = {Sita, LV and Diniz, GB and Horta-Junior, JAC and Casatti, CA and Bittencourt, JC}, title = {Nomenclature and Comparative Morphology of the Teneurin/TCAP/ADGRL Protein Families.}, journal = {Frontiers in neuroscience}, volume = {13}, number = {}, pages = {425}, pmid = {31130838}, issn = {1662-4548}, abstract = {The teneurins are a family of glycosylated type II transmembrane proteins synthesized in several tissue from both vertebrate and invertebrate species. These proteins interact with the latrophilins, a group of adhesion G protein-coupled receptors. Both teneurins and latrophilins may have been acquired by choanoflagellates through horizontal gene transfer from a toxin-target system present in prokaryotes. Teneurins are highly conserved in eukaryotes, with four paralogs (TEN1, TEN2, TEN3, and TEN4) in most vertebrates playing a role in the normal neural development, axonal guiding, synapse formation and synaptic maintenance. In this review, we summarize the main findings concerning the distribution and morphology of the teneurins and latrophilins, both during development and in adult animals. We also briefly discuss the current knowledge in the distribution of the teneurin C-terminal associated protein (TCAP), a peptidergic sequence at the terminal portion of teneurins that may be independently processed and secreted. Through the analysis of anatomical data, we draw parallels to the evolution of those proteins and the increasing complexity of this system, which mirrors the increase in metazoan sensory complexity. This review underscores the need for further studies investigating the distribution of teneurins and latrophilins and the use of different animal models.}, }
@article {pmid31129322, year = {2019}, author = {Xie, S and Gu, AZ and Cen, T and Li, D and Chen, J}, title = {The effect and mechanism of urban fine particulate matter (PM2.5) on horizontal transfer of plasmid-mediated antimicrobial resistance genes.}, journal = {The Science of the total environment}, volume = {683}, number = {}, pages = {116-123}, doi = {10.1016/j.scitotenv.2019.05.115}, pmid = {31129322}, issn = {1879-1026}, mesh = {Air Pollutants/*adverse effects ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/*genetics ; Environmental Monitoring ; Escherichia coli/drug effects/*genetics ; *Gene Transfer, Horizontal ; Particulate Matter/*adverse effects ; Plasmids ; }, abstract = {Fine particulate matter (PM2.5) and antimicrobial resistance are two major threats to public health worldwide. Current air pollution studies rely heavily on the assessment of PM2.5 chemistry and toxicity. However, whether and how PM2.5 affects the proliferation and transfer of antimicrobial resistance genes (ARGs) in various environments has remained unanswered. This study investigated the effects and potential mechanisms of urban PM2.5 on the horizontal transfer of ARGs between opportunistic Escherichia coli (E. coli) strains. The results showed that urban PM2.5 samples collected from Xi'an (XA), Shanghai (SH), and Shijiazhuang (SJZ) in China induced location- and concentration-dependent promotion of conjugative transfer frequencies compared to the control group. The relevant mechanisms were also explored, including the formation of intracellular reactive oxygen species (ROS) and the subsequent induction of oxidative stress, SOS response, changes in membrane permeability, and alternations in mRNA expression of genes involved in horizontal transfer. This study highlights the effect of PM2.5 on promoting the horizontal transfer of ARGs and elucidates the mechanism of the antimicrobial-resistance risks posed by urban PM2.5. These findings are of great value in understanding the transmission of antimicrobial resistance in various environments and provide valuable information for re-evaluating air quality assessment practices.}, }
@article {pmid31128867, year = {2019}, author = {Reichler, SJ and Martin, NH and Evanowski, RL and Kovac, J and Wiedmann, M and Orsi, RH}, title = {A century of gray: A genomic locus found in 2 distinct Pseudomonas spp. is associated with historical and contemporary color defects in dairy products worldwide.}, journal = {Journal of dairy science}, volume = {102}, number = {7}, pages = {5979-6000}, doi = {10.3168/jds.2018-16192}, pmid = {31128867}, issn = {1525-3198}, mesh = {Animals ; Cheese/*analysis/microbiology ; Color ; Genetic Loci/physiology ; Genome, Bacterial/*physiology ; Genomics ; Italy ; Milk/*chemistry/microbiology ; Phenotype ; Pigmentation ; Pigments, Biological/biosynthesis ; Pseudomonas fluorescens/*genetics/metabolism ; Pseudomonas putida/*genetics/metabolism ; }, abstract = {Some gram-negative bacteria, including Pseudomonas spp., can grow at refrigeration temperatures and cause flavor, odor, and texture defects in fluid milk. Historical and modern cases exist of gray and blue color defects in fluid milk due to Pseudomonas, and several recent reports have detailed fresh cheese spoilage associated with blue-pigment-forming Pseudomonas. Our goal was to investigate the genomes of pigmented Pseudomonas isolates responsible for historical and modern pigmented spoilage of dairy products in the United States to determine the genetic basis of pigment-forming phenotypes. We performed whole genome sequencing of 9 Pseudomonas isolates: 3 from recent incidents of gray-pigmented fluid milk (Pseudomonas fluorescens group), 1 from blue-pigmented cheese (P. fluorescens group), 2 from a historical blue milk spoilage incident (Pseudomonas putida group), and 3 with no evidence for blue or gray pigment formation (2 from P. fluorescens group and 1 from Pseudomonas chlororaphis group). All 6 isolates collected from products with a gray or blue pigment defect were confirmed to produce pigment using potato dextrose agar or pasteurized milk. A subset of 2 isolates was selected for inoculation into milk and onto the surface of a model cheese for subsequent color measurement. These isolates produced different colors on potato dextrose agar, but produced nearly identical color defects in milk and on model cheese. For the same subset of 2 isolates, the gray color defect in milk was produced only in containers with ample headspace and not in full containers, suggesting that oxygen is vital for pigment formation. This work also demonstrated that a Pseudomonas isolate from cheese can produce a pigment defect in milk, and vice versa. Comparative genomics identified an accessory locus encoding tryptophan biosynthesis genes that was present in all isolates that produced gray or blue pigment under laboratory conditions and was only previously reported in 2 P. fluorescens isolates responsible for blue mozzarella in Italy. Because this locus was found in genetically distant isolates belonging to different Pseudomonas species groups, it may have been acquired via horizontal gene transfer. These data suggest that several past and present gray- or blue-pigmented dairy spoilage events share a common genetic etiology that transcends species-level identification and merits further investigation to determine mechanistic details and modes of prevention.}, }
@article {pmid31126947, year = {2019}, author = {Murphy, CL and Youssef, NH and Hanafy, RA and Couger, MB and Stajich, JE and Wang, Y and Baker, K and Dagar, SS and Griffith, GW and Farag, IF and Callaghan, TM and Elshahed, MS}, title = {Horizontal Gene Transfer as an Indispensable Driver for Evolution of Neocallimastigomycota into a Distinct Gut-Dwelling Fungal Lineage.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {15}, pages = {}, pmid = {31126947}, issn = {1098-5336}, mesh = {Animals ; Biological Evolution ; Cattle/microbiology ; *Evolution, Molecular ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; *Gene Transfer, Horizontal ; Genome, Fungal ; Goats/microbiology ; Neocallimastigomycota/*genetics/physiology ; Sheep/microbiology ; }, abstract = {Survival and growth of the anaerobic gut fungi (AGF; Neocallimastigomycota) in the herbivorous gut necessitate the possession of multiple abilities absent in other fungal lineages. We hypothesized that horizontal gene transfer (HGT) was instrumental in forging the evolution of AGF into a phylogenetically distinct gut-dwelling fungal lineage. The patterns of HGT were evaluated in the transcriptomes of 27 AGF strains, 22 of which were isolated and sequenced in this study, and 4 AGF genomes broadly covering the breadth of AGF diversity. We identified 277 distinct incidents of HGT in AGF transcriptomes, with subsequent gene duplication resulting in an HGT frequency of 2 to 3.5% in AGF genomes. The majority of HGT events were AGF specific (91.7%) and wide (70.8%), indicating their occurrence at early stages of AGF evolution. The acquired genes allowed AGF to expand their substrate utilization range, provided new venues for electron disposal, augmented their biosynthetic capabilities, and facilitated their adaptation to anaerobiosis. The majority of donors were anaerobic fermentative bacteria prevalent in the herbivorous gut. This study strongly indicates that HGT indispensably forged the evolution of AGF as a distinct fungal phylum and provides a unique example of the role of HGT in shaping the evolution of a high-rank taxonomic eukaryotic lineage.IMPORTANCE The anaerobic gut fungi (AGF) represent a distinct basal phylum lineage (Neocallimastigomycota) commonly encountered in the rumen and alimentary tracts of herbivores. Survival and growth of anaerobic gut fungi in these anaerobic, eutrophic, and prokaryote-dominated habitats necessitates the acquisition of several traits absent in other fungal lineages. We assess here the role of horizontal gene transfer as a relatively fast mechanism for trait acquisition by the Neocallimastigomycota postsequestration in the herbivorous gut. Analysis of 27 transcriptomes that represent the broad diversity of Neocallimastigomycota identified 277 distinct HGT events, with subsequent gene duplication resulting in an HGT frequency of 2 to 3.5% in AGF genomes. These HGT events have allowed AGF to survive in the herbivorous gut by expanding their substrate utilization range, augmenting their biosynthetic pathway, providing new routes for electron disposal by expanding fermentative capacities, and facilitating their adaptation to anaerobiosis. HGT in the AGF is also shown to be mainly a cross-kingdom affair, with the majority of donors belonging to the bacteria. This study represents a unique example of the role of HGT in shaping the evolution of a high-rank taxonomic eukaryotic lineage.}, }
@article {pmid31123134, year = {2019}, author = {Nolivos, S and Cayron, J and Dedieu, A and Page, A and Delolme, F and Lesterlin, C}, title = {Role of AcrAB-TolC multidrug efflux pump in drug-resistance acquisition by plasmid transfer.}, journal = {Science (New York, N.Y.)}, volume = {364}, number = {6442}, pages = {778-782}, doi = {10.1126/science.aav6390}, pmid = {31123134}, issn = {1095-9203}, mesh = {Anti-Bacterial Agents/pharmacology ; Antiporters/antagonists &amp; inhibitors/biosynthesis/genetics ; Bacterial Proteins/antagonists &amp; inhibitors/biosynthesis/genetics ; Carrier Proteins/genetics/*physiology ; Conjugation, Genetic ; DNA, Single-Stranded ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/drug effects/genetics/*physiology ; Escherichia coli Proteins/genetics/*physiology ; F Factor/genetics/*physiology ; Microscopy ; Protein Biosynthesis/drug effects ; Tetracycline/pharmacology ; }, abstract = {Drug-resistance dissemination by horizontal gene transfer remains poorly understood at the cellular scale. Using live-cell microscopy, we reveal the dynamics of resistance acquisition by transfer of the Escherichia coli fertility factor-conjugation plasmid encoding the tetracycline-efflux pump TetA. The entry of the single-stranded DNA plasmid into the recipient cell is rapidly followed by complementary-strand synthesis, plasmid-gene expression, and production of TetA. In the presence of translation-inhibiting antibiotics, resistance acquisition depends on the AcrAB-TolC multidrug efflux pump, because it reduces tetracycline concentrations in the cell. Protein synthesis can thus persist and TetA expression can be initiated immediately after plasmid acquisition. AcrAB-TolC efflux activity can also preserve resistance acquisition by plasmid transfer in the presence of antibiotics with other modes of action.}, }
@article {pmid31119503, year = {2019}, author = {Jung, CM and Carr, M and Blakeney, GA and Indest, KJ}, title = {Enhanced plasmid-mediated bioaugmentation of RDX-contaminated matrices in column studies using donor strain Gordonia sp. KTR9.}, journal = {Journal of industrial microbiology &amp; biotechnology}, volume = {46}, number = {9-10}, pages = {1273-1281}, pmid = {31119503}, issn = {1476-5535}, mesh = {Gordonia Bacterium/genetics/*metabolism ; Nitrogen/metabolism ; Plasmids/genetics ; Rhodococcus/genetics ; Triazines/*metabolism ; }, abstract = {Horizontal gene transfer (HGT) is the lateral movement of genetic material between organisms. The RDX explosive-degrading bacterium Gordonia sp. KTR9 has been shown previously to transfer the pGKT2 plasmid containing the RDX degradative genes (xplAB) by HGT. Overall, fitness costs to the transconjugants to maintain pGKT2 was determined through growth and survivability assessments. Rhodococcus jostii RHA1 transconjugants demonstrated a fitness cost while other strains showed minimal cost. Biogeochemical parameters that stimulate HGT of pGKT2 were evaluated in soil slurry mating experiments and the absence of nitrogen was found to increase HGT events three orders of magnitude. Experiments evaluating RDX degradation in flow-through soil columns containing mating pairs showed 20% greater degradation than columns with only the donor KTR9 strain. Understanding the factors governing HGT will benefit bioaugmentation efforts where beneficial bacteria with transferrable traits could be used to more efficiently degrade contaminants through gene transfer to native populations.}, }
@article {pmid31118304, year = {2019}, author = {Salinas, L and Cárdenas, P and Johnson, TJ and Vasco, K and Graham, J and Trueba, G}, title = {Diverse Commensal Escherichia coli Clones and Plasmids Disseminate Antimicrobial Resistance Genes in Domestic Animals and Children in a Semirural Community in Ecuador.}, journal = {mSphere}, volume = {4}, number = {3}, pages = {}, pmid = {31118304}, issn = {2379-5042}, support = {R01 AI135118/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Animals, Domestic/*microbiology ; Anti-Bacterial Agents/pharmacology ; Child, Preschool ; Drug Resistance, Bacterial ; Ecuador ; Escherichia coli/drug effects/*genetics ; Escherichia coli Infections/microbiology/*veterinary ; Feces/microbiology ; *Gene Transfer, Horizontal ; *Genes, MDR ; Humans ; Infant ; Microbial Sensitivity Tests ; Plasmids/genetics ; Rural Population ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {The increased prevalence of antimicrobial resistance (AMR) among Enterobacteriaceae has had major clinical and economic impacts on human medicine. Many of the multidrug-resistant (multiresistant) Enterobacteriaceae found in humans are community acquired, and some of them are possibly linked to food animals (i.e., livestock raised for meat and dairy products). In this study, we examined whether numerically dominant commensal Escherichia coli strains from humans (n = 63 isolates) and domestic animals (n = 174 isolates) in the same community and with matching phenotypic AMR patterns were clonally related or shared the same plasmids. We identified 25 multiresistant isolates (i.e., isolates resistant to more than one antimicrobial) that shared identical phenotypic resistance patterns. We then investigated the diversity of E. coli clones, AMR genes, and plasmids carrying the AMR genes using conjugation, replicon typing, and whole-genome sequencing. All of the multiresistant E. coli isolates (from children and domestic animals) analyzed had at least 90 or more whole-genome SNP differences between one another, suggesting that none of the strains was recently transferred. While the majority of isolates shared the same antimicrobial resistance genes and replicons, DNA sequencing indicated that these genes and replicons were found on different plasmid structures. We did not find evidence of the clonal spread of AMR in this community: instead, AMR genes were carried on diverse clones and plasmids. This presents a significant challenge for understanding the movement of AMR in a community.IMPORTANCE Even though Escherichia coli strains may share nearly identical phenotypic AMR profiles and AMR genes and overlap in space and time, the diversity of clones and plasmids challenges research that aims to identify sources of AMR. Horizontal gene transfer appears to play a more significant role than clonal expansion in the spread of AMR in this community.}, }
@article {pmid31118300, year = {2019}, author = {Cummins, ML and Roy Chowdhury, P and Marenda, MS and Browning, GF and Djordjevic, SP}, title = {Salmonella Genomic Island 1B Variant Found in a Sequence Type 117 Avian Pathogenic Escherichia coli Isolate.}, journal = {mSphere}, volume = {4}, number = {3}, pages = {}, pmid = {31118300}, issn = {2379-5042}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Australia ; Birds/microbiology ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/*genetics/pathogenicity ; *Gene Transfer, Horizontal ; *Genomic Islands ; Salmonella enterica/*genetics ; Whole Genome Sequencing ; }, abstract = {Salmonella genomic island 1 (SGI1) is an integrative genetic island first described in Salmonella enterica serovars Typhimurium DT104 and Agona in 2000. Variants of it have since been described in multiple serovars of S. enterica, as well as in Proteus mirabilis, Acinetobacter baumannii, Morganella morganii, and several other genera. The island typically confers resistance to older, first-generation antimicrobials; however, some variants carry blaNDM-1, blaVEB-6, and blaCTX-M15 genes that encode resistance to frontline, clinically important antibiotics, including third-generation cephalosporins. Genome sequencing studies of avian pathogenic Escherichia coli (APEC) identified a sequence type 117 (ST117) isolate (AVC96) with genetic features found in SGI1. The complete genome sequence of AVC96 was assembled from a combination of Illumina and single-molecule real-time (SMRT) sequence data. Analysis of the AVC96 chromosome identified a variant of SGI1-B located 18 bp from the 3' end of trmE, also known as the attB site, a known hot spot for the integration of genomic islands. This is the first report of SGI1 in wild-type E. coli The variant, here named SGI1-B-Ec1, was otherwise unremarkable, apart from the identification of ISEc43 in open reading frame (ORF) S023.IMPORTANCE SGI1 and variants of it carry a variety of antimicrobial resistance genes, including those conferring resistance to extended-spectrum β-lactams and carbapenems, and have been found in diverse S. enterica serovars, Acinetobacter baumannii, and other members of the Enterobacteriaceae SGI1 integrates into Gram-negative pathogenic bacteria by targeting a conserved site 18 bp from the 3' end of trmE For the first time, we describe a novel variant of SGI1 in an avian pathogenic Escherichia coli isolate. The presence of SGI1 in E. coli is significant because it represents yet another lateral gene transfer mechanism to enhancing the capacity of E. coli to acquire and propagate antimicrobial resistance and putative virulence genes. This finding underscores the importance of whole-genome sequencing (WGS) to microbial genomic epidemiology, particularly within a One Health context. Further studies are needed to determine how widespread SGI1 and variants of it may be in Australia.}, }
@article {pmid31116476, year = {2019}, author = {Baltrus, DA and Clark, M}, title = {A complete genome sequence for Pseudomonas syringae pv. pisi PP1 highlights the importance of multiple modes of horizontal gene transfer during phytopathogen evolution.}, journal = {Molecular plant pathology}, volume = {20}, number = {7}, pages = {1013-1018}, pmid = {31116476}, issn = {1364-3703}, mesh = {Base Sequence ; *Biological Evolution ; Chromosomes, Bacterial/genetics ; Gene Transfer, Horizontal/*genetics ; Genetic Loci ; *Genome, Bacterial ; Phylogeny ; Plants/*microbiology ; Pseudomonas syringae/*genetics ; Synteny/genetics ; }, abstract = {Hybrid assembly strategies that combine long-read sequencing reads from Oxford Nanopore's MinION device combined with high-depth Illumina paired-end reads have enabled completion and circularization of both plasmids and chromosomes from multiple bacterial strains. Here we demonstrate the utility of supplementing Illumina paired-end reads from a previously published draft genome of P. syringae pv. pisi PP1 with long reads to generate a complete genome sequence for this strain. The phylogenetic placement and genomic repertoire of virulence factors within this strain provides a unique perspective on virulence evolution within P. syringae phylogroup 2, and highlights that strains can rapidly acquire virulence factors through horizontal gene transfer by acquisition of plasmids as well as through chromosomal recombination.}, }
@article {pmid31113374, year = {2019}, author = {Zhao, Y and Hu, K and Zhang, J and Guo, Y and Fan, X and Wang, Y and Mensah, SD and Zhang, X}, title = {Outbreak of carbapenem-resistant Acinetobacter baumannii carrying the carbapenemase OXA-23 in ICU of the eastern Heilongjiang Province, China.}, journal = {BMC infectious diseases}, volume = {19}, number = {1}, pages = {452}, pmid = {31113374}, issn = {1471-2334}, support = {D201224//Natural Science Foundation of Heilongjiang Province/ ; 2017-405//Health and Family Planning Commission of Guangdong Province (CN)/ ; }, mesh = {Acinetobacter Infections/drug therapy/*epidemiology/microbiology/prevention &amp; control ; Acinetobacter baumannii/*drug effects/genetics/isolation &amp; purification ; Adult ; Aged ; Aged, 80 and over ; Anti-Bacterial Agents/therapeutic use ; Bacterial Proteins/*genetics ; Carbapenems/pharmacology ; China/epidemiology ; Cross Infection/prevention &amp; control ; Disease Outbreaks ; Drug Resistance, Bacterial/drug effects/*genetics ; Enterobacteriaceae/genetics ; Female ; Gene Transfer, Horizontal ; Humans ; Infection Control/methods ; Intensive Care Units/statistics &amp; numerical data ; Male ; Microbial Sensitivity Tests ; Middle Aged ; beta-Lactamases/*genetics ; }, abstract = {BACKGROUND: To investigate the carbapenem resistance mechanisms and clonal relationship of carbapenem-resistant Acinetobacter baumannii (CRAB) strains isolated in the intensive care unit (ICU) of the First Affiliated Hospital of Jiamusi University, management approaches to ICU clonal CRAB outbreaks were described.<br><br>METHODS: The sensitivity of the antibiotic was determined using the VITEK-2 automated system. Carbapenemase genes (blaTEM, blaSHV, blaKPC, blaNDM, blaIMP-4, blaVIM, blaOXA-23, blaOXA-24, blaOXA-51, and blaOXA-58), AmpC enzyme genes (blaACC, blaDHA, blaADC), and ISAba1 were assessed for all collected isolates using polymerase chain reaction (PCR). The transfer of resistance genes was investigated via conjugation experiments. The clonal relationship of isolates was determined via enterobacterial repetitive intergenic consensus (ERIC)-PCR and multilocus sequence typing (MLST). When the detection rate of CRAB increased from 25% in 2010 to 92% in 2014, a number of actions were initiated, including enhanced infection control, staff education, and the cleaning of the hospital environment.<br><br>RESULTS: Clinical isolates were positive for the following genes: blaOXA23, blaOXA51, blaOXA24, blaADC, blaTEM, ISAba1, ISA-23, and ISA-ADC; however, blaOXA58, ISA-51, blaNDM, blaIMP, blaKPC, blaTEM, blaSHV, blaVIM, and blaACC were not detected. Four carbapenem-resistant isolates successfully transferred plasmids from A. baumannii isolates to E. coli J53. MLST showed that all strains belonged to ST2 except for one isolate, which belonged to the new genotype ST1199. The ERIC-PCR method found the following three genotypes: type A in 8, type B in 12, type C in 1, and two profiles (A, B) belonged to ST2. After taking control measures, the prevalence of CRAB isolates decreased, and the discovery rate of CRAB dropped to 11.4% in 2017.<br><br>CONCLUSION: The obtained result suggests that blaOXA-23-producing CC2 isolates were prevalent in the ICU of the First Affiliated Hospital of Jiamusi University. Targeted surveillance was implemented to identify the current situation of the ICU and the further implementation of infection control effectively prevented the spread of nosocomial infection.}, }
@article {pmid31111820, year = {2019}, author = {McShan, WM and McCullor, KA and Nguyen, SV}, title = {The Bacteriophages of Streptococcus pyogenes.}, journal = {Microbiology spectrum}, volume = {7}, number = {3}, pages = {}, pmid = {31111820}, issn = {2165-0497}, mesh = {Bacterial Toxins/genetics ; Bacteriophages/*genetics ; Drug Resistance, Bacterial/genetics ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genome, Bacterial ; Genome, Viral ; Humans ; Phenotype ; Prophages/genetics ; Serogroup ; Streptococcus pyogenes/*genetics/*virology ; Transduction, Genetic ; Virulence/genetics ; Virulence Factors/genetics ; }, abstract = {The bacteriophages of Streptococcus pyogenes (group A streptococcus) play a key role in population shaping, genetic transfer, and virulence of this bacterial pathogen. Lytic phages like A25 can alter population distributions through elimination of susceptible serotypes but also serve as key mediators for genetic transfer of virulence genes and antibiotic resistance via generalized transduction. The sequencing of multiple S. pyogenes genomes has uncovered a large and diverse population of endogenous prophages that are vectors for toxins and other virulence factors and occupy multiple attachment sites in the bacterial genomes. Some of these sites for integration appear to have the potential to alter the bacterial phenotype through gene disruption. Remarkably, the phage-like chromosomal islands (SpyCI), which share many characteristics with endogenous prophages, have evolved to mediate a growth-dependent mutator phenotype while acting as global transcriptional regulators. The diverse population of prophages appears to share a large pool of genetic modules that promotes novel combinations that may help disseminate virulence factors to different subpopulations of S. pyogenes. The study of the bacteriophages of this pathogen, both lytic and lysogenic, will continue to be an important endeavor for our understanding of how S. pyogenes continues to be a significant cause of human disease.}, }
@article {pmid31111818, year = {2019}, author = {Turner, CE and Bubba, L and Efstratiou, A}, title = {Pathogenicity Factors in Group C and G Streptococci.}, journal = {Microbiology spectrum}, volume = {7}, number = {3}, pages = {}, pmid = {31111818}, issn = {2165-0497}, mesh = {Adhesins, Bacterial ; Animals ; Bacterial Proteins ; Bacterial Toxins ; Gene Transfer, Horizontal ; Humans ; Streptococcal Infections/immunology/*microbiology ; Streptococcus/*classification/enzymology/genetics/*pathogenicity ; Streptococcus pyogenes ; Virulence/genetics ; *Virulence Factors ; }, abstract = {Initially recognized zoonoses, streptococci belonging to Lancefield group C (GCS) and G (GGS) were subsequently recognised as human pathogens causing a diverse range of symptoms, from asymptomatic carriage to life threatening diseases. Their taxonomy has changed during the last decade. Asymptomatic carriage is <4% amongst the human population and invasive infections are often in association with chronic diseases such as diabetes, cardiovascular diseases or chronic skin infections. Other clinical manifestations include acute pharyngitis, pneumonia, endocarditis, bacteraemia and toxic-shock syndrome. Post streptococcal sequalae such as rheumatic fever and acute glomerulonephritis have also been described but mainly in developed countries and amongst specific populations. Putative virulence determinants for these organisms include adhesins, toxins, and other factors that are essential for dissemination in human tissues and for interference with the host immune responses. High nucleotide similarities among virulence genes and their association with mobile genetic elements supports the hypothesis of extensive horizontal gene transfer events between the various pyogenic streptococcal species belonging to Lancefield groups A, C and G. A better understanding of the mechanisms of pathogenesis should be apparent by whole-genome sequencing, and this would result in more effective clinical strategies for the pyogenic group in general.}, }
@article {pmid31111814, year = {2019}, author = {Santoro, F and Iannelli, F and Pozzi, G}, title = {Genomics and Genetics of Streptococcus pneumoniae.}, journal = {Microbiology spectrum}, volume = {7}, number = {3}, pages = {}, pmid = {31111814}, issn = {2165-0497}, mesh = {Bacterial Proteins/genetics ; Bacteriophages ; DNA Repair ; DNA Restriction-Modification Enzymes ; Gene Transfer, Horizontal ; Genetic Engineering ; *Genome, Bacterial ; *Genomics ; Humans ; Plasmids ; Promoter Regions, Genetic ; Streptococcus pneumoniae/*genetics ; Transformation, Genetic ; }, abstract = {Ninety years after the discovery of pneumococcal Transformation, and 74 years after the work of Avery and colleagues that identified DNA as the genetic material, Streptococcus pneumoniae is still one of the most important model organism to understand Bacterial Genetics and Genomics. In this Chapter special emphasis has been given to Genomics and to Mobile Genetic Elements (the Mobilome) which greatly contribute to the dynamic variation of pneumococcal genomes by horizontal gene transfer. Other topics include molecular mechanisms of Genetic Transformation, Restriction/Modification Systems, Mismatch DNA Repair, and techniques for construction of genetically engineered pneumococcal strains.}, }
@article {pmid31111195, year = {2019}, author = {Hellmuth, M and Seemann, CR}, title = {Alternative characterizations of Fitch's xenology relation.}, journal = {Journal of mathematical biology}, volume = {79}, number = {3}, pages = {969-986}, pmid = {31111195}, issn = {1432-1416}, mesh = {Animals ; Eukaryotic Cells/*metabolism ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Humans ; *Models, Statistical ; *Phylogeny ; Prokaryotic Cells/*metabolism ; }, abstract = {Horizontal gene transfer (HGT) is an important factor for the evolution of prokaryotes as well as eukaryotes. According to Walter M. Fitch, two genes are xenologs if they are separated by at least one HGT. This concept is formalized through Fitch relations, which are defined as binary relations that comprise all pairs (x, y) of genes x and y for which y has been horizontally transferred at least once since it diverged from the last common ancestor of x and y. This definition, in particular, preserves the directional character of the transfer. Fitch relations are characterized by a small set of forbidden induced subgraphs on three vertices and can be recognized in linear time. The mathematical characterization of Fitch relations is crucial to understand whether putative xenology relations are at least to some extent "biologically feasible". In this contribution, we provide two novel characterizations of Fitch relations. In particular, these results allow us directly to reconstruct gene trees (together with the location of the horizontal transfer events) that explain the underlying Fitch relation. As a biological side result, we can conclude that the phylogenetic signal to infer these gene trees is entirely contained in those pairs of genes x and y for which no directional transfer has been taken place in the common history of y and the last common ancestor of x and y. In other words, non-HGT events provide the essential information about the gene trees. In addition, we utilize the new characterizations to present an alternative, short and elegant proof of the characterization theorem established by Geiß et al. (J Math Bio 77(5), 2018).}, }
@article {pmid31110497, year = {2019}, author = {Pan, D and Morono, Y and Inagaki, F and Takai, K}, title = {An Improved Method for Extracting Viruses From Sediment: Detection of Far More Viruses in the Subseafloor Than Previously Reported.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {878}, pmid = {31110497}, issn = {1664-302X}, abstract = {Viruses are the most abundant biological entities on Earth and perform essential ecological functions in aquatic environments by mediating biogeochemical cycling and lateral gene transfer. Cellular life as well as viruses have been found in deep subseafloor sediment. However, the study of deep sediment viruses has been hampered by the complexities involved in efficiently extracting viruses from a sediment matrix. Here, we developed a new method for the extraction of viruses from sediment based on density separation using a Nycodenz density step gradient. The density separation method resulted in up to 2 orders of magnitude greater recovery of viruses from diverse subseafloor sediments compared to conventional methods. The density separation method also showed more consistent performance between samples of different sediment lithology, whereas conventional virus extraction methods were highly inconsistent. Using this new method, we show that previously published virus counts have underestimated viral abundances by up to 2 orders of magnitude. These improvements suggest that the carbon contained within viral biomass in the subseafloor environment may potentially be revised upward to 0.8-3.7 Gt from current estimates of 0.2 Gt. The vastly improved recovery of viruses indicate that viruses represent a far larger pool of organic carbon in subseafloor environments than previously estimated.}, }
@article {pmid31107962, year = {2020}, author = {Schmid, DS}, title = {Mixing It Up: New Insights Into Interspecies Recombination Between Herpes Simplex Virus Type 1 and 2.}, journal = {The Journal of infectious diseases}, volume = {221}, number = {8}, pages = {1208-1209}, pmid = {31107962}, issn = {1537-6613}, support = {CC999999/ImCDC/Intramural CDC HHS/United States ; }, mesh = {Gene Transfer, Horizontal ; *Herpes Simplex ; *Herpesvirus 1, Human/genetics ; Humans ; Simplexvirus ; }, abstract = {Herpes simplex viruses (HSV-1 and HSV-2) are closely related alphaherpesviruses, with more than 80% identity at the deoxyribonucleic acid (DNA) sequence level [1]. More than two thirds of the world’s population is estimated to have been infected with one or both viruses. The divergence of the common ancestor to these viruses is thought to have coincided with the separation of the human and chimpanzee lineages approximately 6 million years ago, leading to separate evolution of HSV-1 and HSV-2, respectively. Zoonotic transmission of HSV-2 to an extinct early hominid occurred approximately one and a half million years ago [2]. No other primate species are known to serve as common hosts for 2 distinct herpes simplex species.}, }
@article {pmid31106958, year = {2019}, author = {Wang, D and Xu, Z and Zhang, G and Xia, L and Dong, X and Li, Q and Liles, MR and Shao, J and Shen, Q and Zhang, R}, title = {A genomic island in a plant beneficial rhizobacterium encodes novel antimicrobial fatty acids and a self-protection shield to enhance its competition.}, journal = {Environmental microbiology}, volume = {21}, number = {9}, pages = {3455-3471}, doi = {10.1111/1462-2920.14683}, pmid = {31106958}, issn = {1462-2920}, support = {973 program, 2015CB150505//National Key Basic Research Program of China/ ; KJQN201667//Fundamental Research Funds for the Central Universities/ ; B12009//111 Project/ ; //Priority Academic Program Development (PAPD) of Jiangsu Higher Education Institutions/ ; 31870096//National Natural Science Foundation of China/ ; 31572214//National Natural Science Foundation of China/ ; 31501833//National Natural Science Foundation of China/ ; 2016YFD0200305//National Key Research and Development Program/ ; 2017YFD0200805//National Key Research and Development Program/ ; }, abstract = {Rhizobacteria devote a relatively large percentage of their genomes to encode bioactive natural products that are important for competition in the rhizosphere. In this study, a plant beneficial rhizobacterium Bacillus velezensis SQR9 was discovered to produce novel antibacterial fatty acids, Bacillunoic acids, which are encoded on a genomic island (GI). This GI contains a hybrid type I fatty acid synthase (FAS)-polyketide synthase (PKS) system and an ABC transporter. The FAS was predicted to synthesize a primer that was transferred to the PKS to synthesize Bacillunoic acids. The synthesized Bacillunoic acids inhibit the growth of diverse bacteria, with the strongest activity against closely related Bacillus strains, the ABC transporter exported the toxic Bacillunoic acids upon their induction for protecting the producing strain. The inhibition of other Bacillus strains by Bacillunoic acids extended the antimicrobial spectrum of SQR9 and enhanced its competition with closely related root-associated bacteria. So, through the obtaining of this GI by horizontal gene transfer, strain SQR9 not only acquired a competitive weapon but also acquired a self-protecting shield, which increased its competition with other rhizobacteria.}, }
@article {pmid31106341, year = {2019}, author = {Li, Z and Bock, R}, title = {Rapid functional activation of a horizontally transferred eukaryotic gene in a bacterial genome in the absence of selection.}, journal = {Nucleic acids research}, volume = {47}, number = {12}, pages = {6351-6359}, pmid = {31106341}, issn = {1362-4962}, support = {669982/ERC_/European Research Council/International ; }, mesh = {Escherichia coli/genetics ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Mutation ; Porphyridium/genetics ; Promoter Regions, Genetic ; *Transcriptional Activation ; }, abstract = {Horizontal gene transfer has occurred between organisms of all domains of life and contributed substantially to genome evolution in both prokaryotes and eukaryotes. Phylogenetic evidence suggests that eukaryotic genes horizontally transferred to bacteria provided useful new gene functions that improved metabolic plasticity and facilitated adaptation to new environments. How these eukaryotic genes evolved into functional bacterial genes is not known. Here, we have conducted a genetic screen to identify the mechanisms involved in functional activation of a eukaryotic gene after its transfer into a bacterial genome. We integrated a eukaryotic selectable marker gene cassette driven by expression elements from the red alga Porphyridium purpureum into the genome of Escherichia coli. Following growth under non-selective conditions, gene activation events were indentified by antibiotic selection. We show that gene activation in the bacterial recipient occurs at high frequency and involves two major types of spontaneous mutations: deletion and gene amplification. We further show that both mechanisms result in promoter capture and are frequently triggered by microhomology-mediated recombination. Our data suggest that horizontally transferred genes have a high probability of acquiring functionality, resulting in their maintenance if they confer a selective advantage.}, }
@article {pmid31103521, year = {2019}, author = {Guzmán-Herrador, DL and Llosa, M}, title = {The secret life of conjugative relaxases.}, journal = {Plasmid}, volume = {104}, number = {}, pages = {102415}, doi = {10.1016/j.plasmid.2019.102415}, pmid = {31103521}, issn = {1095-9890}, mesh = {Bacteria/enzymology/*genetics/*metabolism ; Biotechnology ; *Conjugation, Genetic ; DNA Replication ; DNA, Bacterial ; Endonucleases/chemistry/genetics/*metabolism ; Plasmids/*genetics/*metabolism ; Recombination, Genetic ; }, abstract = {Conjugative relaxases are well-characterized proteins responsible for the site- and strand-specific endonucleolytic cleavage and strand transfer reactions taking place at the start and end of the conjugative DNA transfer process. Most of the relaxases characterized biochemically and structurally belong to the HUH family of endonucleases. However, an increasing number of new families of relaxases are revealing a variety of protein folds and catalytic alternatives to accomplish conjugative DNA processing. Relaxases show high specificity for their cognate target DNA sequences, but several recent reports underscore the importance of their activity on secondary targets, leading to widespread mobilization of plasmids containing an oriT-like sequence. Some relaxases perform other functions associated with their nicking and strand transfer ability, such as catalyzing site-specific recombination or initiation of plasmid replication. They perform these roles in the absence of conjugation, and the validation of these functions in several systems strongly suggest that they are not mere artifactual laboratory observations. Other unexpected roles recently assigned to relaxases include controlling plasmid copy number and promoting retrotransposition. Their capacity to mediate promiscuous mobilization and genetic reorganizations can be exploited for a number of imaginative biotechnological applications. Overall, there is increasing evidence that conjugative relaxases are not only key enzymes for horizontal gene transfer, but may have been adapted to perform other roles which contribute to prokaryotic genetic plasticity. Relaxed target specificity may be key to this versatility.}, }
@article {pmid31100670, year = {2019}, author = {Zheng, F and Zhu, D and Giles, M and Daniell, T and Neilson, R and Zhu, YG and Yang, XR}, title = {Mineral and organic fertilization alters the microbiome of a soil nematode Dorylaimus stagnalis and its resistome.}, journal = {The Science of the total environment}, volume = {680}, number = {}, pages = {70-78}, doi = {10.1016/j.scitotenv.2019.04.384}, pmid = {31100670}, issn = {1879-1026}, mesh = {Agriculture/*methods ; Animals ; Anti-Bacterial Agents/analysis ; Environmental Monitoring ; *Fertilizers ; Helminths/*microbiology ; Manure ; Microbiota ; Minerals ; Nematoda ; Soil ; *Soil Microbiology ; Soil Pollutants/analysis ; Swine ; }, abstract = {Although the effects of fertilization on the abundance and diversity of soil nematodes have been widely studied, the impact of fertilization on soil nematode microbiomes remains largely unknown. Here, we investigated how different fertilizers: no fertilizer, mineral fertilizer, clean slurry (pig manure with a reduced antibiotic burden) and dirty slurry (pig manure with antibiotics) affect the microbiome of a dominant soil nematode and its associated antibiotic resistance genes (ARGs). The results of 16S rRNA gene high throughput sequencing showed that the microbiome of the soil nematode Dorylaimus stagnalis is diverse (Shannon index: 9.95) and dominated by Proteobacteria (40.3%). Application of mineral fertilizers significantly reduced the diversity of the nematode microbiome (by 28.2%; P < 0.05) but increased the abundance of Proteobacteria (by 70.1%; P = 0.001). Microbial community analysis, using a null hypothesis model, indicated that microbiomes associated with the nematode are not neutrally assembled. Organic fertilizers also altered the diversity of the nematode microbiome, but had no impact on its composition as illustrated by principal coordinates analysis (PCoA). Interestingly, although no change of total ARGs was observed in the nematode microbiome and no significant relationship existed between nematode microbiome and resistome, the abundance of 48 out of a total of 75 ARGs was enriched in the organic fertilizer treatments. Thus, the data suggests that ARGs in the nematode microbiome still had a risk of horizontal gene transfer under fertilization and nematodes might be a potential refuge for ARGs.}, }
@article {pmid31097577, year = {2019}, author = {Brumley, DR and Carrara, F and Hein, AM and Yawata, Y and Levin, SA and Stocker, R}, title = {Bacteria push the limits of chemotactic precision to navigate dynamic chemical gradients.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {22}, pages = {10792-10797}, pmid = {31097577}, issn = {1091-6490}, mesh = {*Bacteria/drug effects/metabolism ; Chemotactic Factors/pharmacology ; Chemotaxis/*physiology ; Computer Simulation ; Environment ; *Models, Biological ; Signal-To-Noise Ratio ; Vibrio/drug effects/physiology ; }, abstract = {Ephemeral aggregations of bacteria are ubiquitous in the environment, where they serve as hotbeds of metabolic activity, nutrient cycling, and horizontal gene transfer. In many cases, these regions of high bacterial concentration are thought to form when motile cells use chemotaxis to navigate to chemical hotspots. However, what governs the dynamics of bacterial aggregations is unclear. Here, we use an experimental platform to create realistic submillimeter-scale nutrient pulses with controlled nutrient concentrations. By combining experiments, mathematical theory, and agent-based simulations, we show that individual Vibrio ordalii bacteria begin chemotaxis toward hotspots of dissolved organic matter (DOM) when the magnitude of the chemical gradient rises sufficiently far above the sensory noise that is generated by stochastic encounters with chemoattractant molecules. Each DOM hotspot is surrounded by a dynamic ring of chemotaxing cells, which congregate in regions of high DOM concentration before dispersing as DOM diffuses and gradients become too noisy for cells to respond to. We demonstrate that V. ordalii operates close to the theoretical limits on chemotactic precision. Numerical simulations of chemotactic bacteria, in which molecule counting noise is explicitly taken into account, point at a tradeoff between nutrient acquisition and the cost of chemotactic precision. More generally, our results illustrate how limits on sensory precision can be used to understand the location, spatial extent, and lifespan of bacterial behavioral responses in ecologically relevant environments.}, }
@article {pmid31096330, year = {2019}, author = {Olanrewaju, TO and McCarron, M and Dooley, JSG and Arnscheidt, J}, title = {Transfer of antibiotic resistance genes between Enterococcus faecalis strains in filter feeding zooplankton Daphnia magna and Daphnia pulex.}, journal = {The Science of the total environment}, volume = {659}, number = {}, pages = {1168-1175}, doi = {10.1016/j.scitotenv.2018.12.314}, pmid = {31096330}, issn = {1879-1026}, mesh = {Animals ; Daphnia/*physiology ; Drug Resistance, Bacterial/*genetics ; Enterococcus faecalis/*physiology ; Environmental Monitoring ; Gene Transfer, Horizontal ; Plasmids ; Vancomycin ; Vancomycin Resistance ; Zooplankton/physiology ; }, abstract = {Antibiotic resistant bacteria from faecal pollution sources are pervasive in aquatic environments. A facilitating role for the emergence of waterborne, multi-drug resistant bacterial pathogens has been attributed to biofiltration but had not yet been substantiated. This study investigated the effect of filtration and gut passage in Daphnia spp. on conjugal transfer of resistance genes in Enterococcus faecalis. In vivo conjugation experiments involved a vancomycin-resistant donor strain bearing a plasmid-borne vanA resistance gene, and two vancomycin-susceptible and rifampicin-resistant recipient strains in the presence of Daphnia magna or Daphnia pulex. Results showed successful transfer of the vanA resistance gene from donor to recipient; gene identity was confirmed by PCR and DNA sequencing. There was no significant difference in the number of transconjugants recovered from D. magna and D. pulex. However, transconjugant numbers differed by one order of magnitude between recipient strains. Transconjugant numbers from D. magna were also significantly different between treatments with ingestion of individual phytoplankton species before filtration of bacteria. The highest transfer efficiency calculated from excreted transconjugants was 2.5 × 10[-6]. This proof of concept for facilitation of horizontal gene transfer by a filter feeding organism provides evidence that Daphnia can disseminate antibiotic resistant transconjugants in the environment.}, }
@article {pmid31095296, year = {2019}, author = {Dabo, M and Jaiswal, SK and Dakora, FD}, title = {Phylogenetic evidence of allopatric speciation of bradyrhizobia nodulating cowpea (Vigna unguiculata L. walp) in South African and Mozambican soils.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {6}, pages = {}, pmid = {31095296}, issn = {1574-6941}, mesh = {Bradyrhizobium/*classification/genetics ; DNA, Bacterial ; *Genetic Speciation ; Molecular Typing ; Mozambique ; Phylogeny ; Phylogeography ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S ; Root Nodules, Plant/*microbiology ; *Soil ; Soil Microbiology ; South Africa ; Symbiosis ; Vigna/*microbiology ; }, abstract = {The legume host and soil environment play a major role in establishing effective symbiosis with diverse rhizobia for plant growth promotion and nodule formation. The aim of this study was to assess the morpho-physiology, distribution and phylogenetic position of rhizobia nodulating cowpea from South Africa and Mozambique. The results showed that the isolates were highly diverse in their appearance on yeast mannitol agar plates. The isolates tested also showed an ability to produce IAA at concentrations ranging from 0.64 to 56.46 μg.ml-1 and to solubilise phosphorus at levels from 0 to 3.55 index. Canonical correspondence analysis showed that soil pH and mineral nutrients significantly influenced bradyrhizobial distribution. Analysis of BOX-PCR placed the isolates in eight major clusters with 0.01 to 1.00 similarity coefficient which resulted in 45 unique BOX-types. Phylogenetic analyses based on 16S rRNA, atpD, glnII, gyrB and recA gene sequences showed distinct novel evolutionary lineages within the genus Bradyrhizobium, with some of them being closely related to Bradyrhizobium kavangense, B. subterraneum and B. pachyrhizi. Furthermore, symbiotic gene phylogenies suggested that the isolates' sym loci probably relates to the isolates' geographical origin. The results indicated that geographical origin did affect the isolates' phylogenetic placement and could be the basis for allopatric speciation.}, }
@article {pmid31093491, year = {2019}, author = {Evanovich, E and de Souza Mendonça Mattos, PJ and Guerreiro, JF}, title = {Comparative Genomic Analysis of Lactobacillus plantarum: An Overview.}, journal = {International journal of genomics}, volume = {2019}, number = {}, pages = {4973214}, pmid = {31093491}, issn = {2314-436X}, abstract = {BACKGROUND: Lactobacillus plantarum is widely used in the manufacture of dairy products, fermented foods, and bacteriocins. The genomes of the strains contain multiple genes which may have been acquired by horizontal gene transfer. Many of these genes are important for the regulation, metabolism, and transport of various sugars; however, other genes may carry and spread virulence and antibiotic resistance determinants. In this way, monitoring these genomes is essential to the manufacture of food. In this study, we aim to provide an overview of the genomic properties of L. plantarum based on approaches of comparative genomics.<br><br>RESULTS: The finding of the current study indicates that the core genome of L. plantarum presents 1425 protein-coding genes and is mostly related to the metabolic process. The accessory genome has on average 1320 genes that encodes protein involved in processes as the formation of bacteriocins, degradation of halogen, arsenic detoxification, and nisin resistance. Most of the strains show an ancestral synteny, similar to the one described in the genomes of L. pentosus KCA1 and L. plantarum WCFS1. The lifestyle island analyses did not show a pattern of arrangement or gene content according to habitat.<br><br>CONCLUSIONS: Our results suggest that there is a high rate of transfer of genetic material between the strains. We did not identify any virulence factors and antibiotic resistance genes on the genomes. Thus, the strains may be useful for the biotechnology, bioremediation, and production of bacteriocins. The potential applications are, however, restricted to particular strains.}, }
@article {pmid31091487, year = {2019}, author = {Zhang, J and Lu, T and Shen, P and Sui, Q and Zhong, H and Liu, J and Tong, J and Wei, Y}, title = {The role of substrate types and substrate microbial community on the fate of antibiotic resistance genes during anaerobic digestion.}, journal = {Chemosphere}, volume = {229}, number = {}, pages = {461-470}, doi = {10.1016/j.chemosphere.2019.05.036}, pmid = {31091487}, issn = {1879-1298}, mesh = {Anaerobiosis/drug effects/genetics ; Animals ; Anti-Bacterial Agents/analysis ; Bacteria/drug effects/genetics ; Chickens ; Drug Resistance, Microbial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial/drug effects ; Manure/analysis/*microbiology ; Metals, Heavy/pharmacology ; Microbiota/drug effects/*genetics ; Sewage/microbiology ; Swine ; Waste Disposal, Fluid/instrumentation/*methods ; beta-Lactamases/genetics ; }, abstract = {Anaerobic digestion (AD) is regarded as a promising technology in energy recovery and the spread mitigation of antibiotic resistance. However, the performance of AD is dependent on various factors, and substrate type is one of the most important. In this study, the fate of antibiotic resistance genes (ARGs) response to the substrate types was investigated, and three typical environmental reservoirs of ARGs (pig manure, chicken manure and sewage sludge) were selected. The role of substrate microbial community on the fate of ARGs was clarified through the comparison between the AD of the substrates with and without a prior autoclave-disinfected step. Results showed that substrate types significantly influenced the fate of ARGs, while the influence from the substrate microbial community was limited. The concentration of antibiotics, the horizontal gene transfer reflected by intI1 and co-selection from heavy metals reflected by metal resistance genes (MRGs) were all reduced effectively. Microbial community varied from substrate types and dominated the ARGs fate concerning the standardized total effects through the mantel test and SEM analysis. The fate of tetX, ermF, tetM and ermB was mainly determined by the physicochemical parameters and the phyla of Firmicutes and Bacteroides. The phyla of Actinobacteria, pcoA and czcA contributed most to the reduction of blaTEM and mcr-1, and the phyla of Proteobacteria, Chloroflexi, Synergistetes, Euryarchaeote, intI1 and merA correlated significantly with the fate of blaCTX-M, ereA, tetG and sulI. This study highlighted the importance of substrate types when considering the fate of ARGs during AD.}, }
@article {pmid31091181, year = {2019}, author = {Joyce, A and McCarthy, CGP and Murphy, S and Walsh, F}, title = {Antibiotic resistomes of healthy pig faecal metagenomes.}, journal = {Microbial genomics}, volume = {5}, number = {5}, pages = {}, pmid = {31091181}, issn = {2057-5858}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/drug effects/genetics/isolation &amp; purification ; Cluster Analysis ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial/*genetics ; Feces/*microbiology ; Gastrointestinal Microbiome/drug effects/genetics ; Gastrointestinal Tract/microbiology ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Genome, Bacterial ; Humans ; Ireland ; Metagenome/*genetics ; Metagenomics ; Swine ; }, abstract = {Antibiotic resistance reservoirs within food-producing animals are thought to be a risk to animal and human health. This study describes the minimum natural resistome of pig faeces as the bacteria are under no direct antibiotic selective pressure. The faecal resistome of 257 different genes comprised 56 core and 201 accessory resistance genes. The genes present at the highest relative abundances across all samples were tetW, tetQ, tet44, tet37, tet40, mefA, aadE, ant(9)-1, ermB and cfxA2. This study characterized the baseline resistome, the microbiome composition and the metabolic components described by the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in healthy pig faeces, without antibiotic selective pressures. The microbiome hierarchical analysis resulted in a cluster tree with a highly similar pattern to that of the accessory resistome cluster tree. Functional capacity profiling identified genes associated with horizontal gene transfer. We identified a statistically significant positive correlation between the total antibiotic resistome and suggested indicator genes, which agree with using these genes as indicators of the total resistomes. The correlation between total resistome and total microbiome in this study was positive and statistically significant. Therefore, the microbiome composition influenced the resistome composition. This study identified a core and accessory resistome present in a cohort of healthy pigs, in the same conditions without antibiotics. It highlights the presence of antibiotic resistance in the absence of antibiotic selective pressure and the variability between animals even under the same housing, food and living conditions. Antibiotic resistance will remain in the healthy pig gut even when antibiotics are not used. Therefore, the risk of antibiotic resistance transfer from animal faeces to human pathogens or the environment will remain in the absence of antibiotics.}, }
@article {pmid31087504, year = {2019}, author = {Marín, P and Martirani-Von Abercron, SM and Urbina, L and Pacheco-Sánchez, D and Castañeda-Cataña, MA and Retegi, A and Eceiza, A and Marqués, S}, title = {Bacterial nanocellulose production from naphthalene.}, journal = {Microbial biotechnology}, volume = {12}, number = {4}, pages = {662-676}, pmid = {31087504}, issn = {1751-7915}, mesh = {Alphaproteobacteria/growth &amp; development/*metabolism ; Carbon/metabolism ; Cellulose/*metabolism ; Gas Chromatography-Mass Spectrometry ; Industrial Microbiology/methods ; Microscopy, Electron, Scanning ; *Nanostructures ; Naphthalenes/*metabolism ; }, abstract = {Polycyclic aromatic compounds (PAHs) are toxic compounds that are released in the environment as a consequence of industrial activities. The restoration of PAH-polluted sites considers the use of bacteria capable of degrading aromatic compounds to carbon dioxide and water. Here we characterize a new Xanthobacteraceae strain, Starkeya sp. strain N1B, previously isolated during enrichment under microaerophilic conditions, which is capable of using naphthalene crystals as the sole carbon source. The strain produced a structured biofilm when grown on naphthalene crystals, which had the shape of a half-sphere organized over the crystal. Scanning electron microscopy (SEM) and GC-MS analysis indicated that the biofilm was essentially made of cellulose, composed of several micron-long nanofibrils of 60 nm diameter. A cellulosic biofilm was also formed when the cells grew with glucose as the carbon source. Fourier transformed infrared spectroscopy (FTIR) confirmed that the polymer was type I cellulose in both cases, although the crystallinity of the material greatly depended on the carbon source used for growth. Using genome mining and mutant analysis, we identified the genetic complements required for the transformation of naphthalene into cellulose, which seemed to have been successively acquired through horizontal gene transfer. The capacity to develop the biofilm around the crystal was found to be dispensable for growth when naphthalene was used as the carbon source, suggesting that the function of this structure is more intricate than initially thought. This is the first example of the use of toxic aromatic hydrocarbons as the carbon source for bacterial cellulose production. Application of this capacity would allow the remediation of a PAH into such a value-added polymer with multiple biotechnological usages.}, }
@article {pmid31086216, year = {2019}, author = {Agamennone, V and Le, NG and van Straalen, NM and Brouwer, A and Roelofs, D}, title = {Antimicrobial activity and carbohydrate metabolism in the bacterial metagenome of the soil-living invertebrate Folsomia candida.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {7308}, pmid = {31086216}, issn = {2045-2322}, mesh = {Animals ; Carbohydrate Metabolism/*genetics ; DNA, Bacterial/genetics/isolation &amp; purification ; Disease Resistance/*genetics ; Gastrointestinal Microbiome/*genetics ; Gene Transfer, Horizontal ; Host Microbial Interactions/genetics ; Insecta/*genetics/metabolism/microbiology ; Metagenome/*physiology ; Metagenomics ; Polysaccharides/metabolism ; Sequence Analysis, DNA ; Soil/chemistry ; Soil Microbiology ; }, abstract = {The microbiome associated with an animal's gut and other organs is considered an integral part of its ecological functions and adaptive capacity. To better understand how microbial communities influence activities and capacities of the host, we need more information on the functions that are encoded in a microbiome. Until now, the information about soil invertebrate microbiomes is mostly based on taxonomic characterization, achieved through culturing and amplicon sequencing. Using shotgun sequencing and various bioinformatics approaches we explored functions in the bacterial metagenome associated with the soil invertebrate Folsomia candida, an established model organism in soil ecology with a fully sequenced, high-quality genome assembly. Our metagenome analysis revealed a remarkable diversity of genes associated with antimicrobial activity and carbohydrate metabolism. The microbiome also contains several homologs to F. candida genes that were previously identified as candidates for horizontal gene transfer (HGT). We suggest that the carbohydrate- and antimicrobial-related functions encoded by Folsomia's metagenome play a role in the digestion of recalcitrant soil-born polysaccharides and the defense against pathogens, thereby significantly contributing to the adaptation of these animals to life in the soil. Furthermore, the transfer of genes from the microbiome may constitute an important source of new functions for the springtail.}, }
@article {pmid31086114, year = {2019}, author = {Qin, L and Zhang, X and Chen, X and Wang, K and Shen, Y and Li, D}, title = {Isolation of a Novel Microcystin-Degrading Bacterium and the Evolutionary Origin of mlr Gene Cluster.}, journal = {Toxins}, volume = {11}, number = {5}, pages = {}, pmid = {31086114}, issn = {2072-6651}, mesh = {Bacterial Proteins/*genetics ; Biodegradation, Environmental ; DNA, Ribosomal/genetics ; Genes, Bacterial ; Marine Toxins ; Microcystins/*metabolism ; Multigene Family ; Phylogeny ; Sphingomonadaceae/*genetics/*metabolism ; }, abstract = {The mlr-dependent biodegradation plays an essential role in the natural attenuation of microcystins (MCs) in eutrophic freshwater ecosystems. However, their evolutionary origin is still unclear due to the lack of mlr gene cluster sequences. In this study, a Sphingopyxis sp. strain X20 with high MC-degrading ability was isolated, and the mlrA gene activity was verified by heterologous expression. The whole sequence of the mlr gene cluster in strain X20 was obtained through PCR and thermal asymmetric interlaced (TAIL)-PCR, and then used for evolutionary origin analyses together with the sequences available in GenBank. Phylogenetic analyses of mlr gene clusters suggested that the four mlr genes had the same origin and evolutionary history. Genomic island analyses showed that there is a genomic island on the genome of sphingomonads that is capable of degrading MCs, on which the mlr gene cluster anchors. The concentrated distribution of the mlr gene cluster in sphingomonads implied that these genes have likely been present in the sphingomonads gene pool for a considerable time. Therefore, the mlr gene cluster may have initially entered into the genome of sphingomonads together with the genomic island by a horizontal gene transfer event, and then become inherited by some sphingomonads. The species other than sphingomonads have likely acquired mlr genes from sphingomonads by recently horizontal gene transfer due to the sporadic distribution of MC-degrading species and the mlr genes in them. Our results shed new light on the evolutionary origin of the mlr cluster and thus facilitate the interpretation of characteristic distribution of the mlr gene in bacteria and the understanding of whole mlr pathway.}, }
@article {pmid31085389, year = {2019}, author = {Li, ZH and Yuan, L and Gao, SX and Wang, L and Sheng, GP}, title = {Mitigated membrane fouling and enhanced removal of extracellular antibiotic resistance genes from wastewater effluent via an integrated pre-coagulation and microfiltration process.}, journal = {Water research}, volume = {159}, number = {}, pages = {145-152}, doi = {10.1016/j.watres.2019.05.005}, pmid = {31085389}, issn = {1879-2448}, mesh = {*Anti-Bacterial Agents ; Bacteria ; Drug Resistance, Microbial ; Genes, Bacterial ; Humans ; *Wastewater ; }, abstract = {Antibiotic resistance genes (ARGs) have been regarded as an emerging pollutant in municipal wastewater treatment plant (WWTP) effluents due to their potential risk to human health and ecological safety when reused for landscape and irrigation. Conventional wastewater treatment processes generally fail to effectively reduce ARGs, especially extracellular ARGs (eARGs), which are persistent in the environment and play an important role in horizontal gene transfer via transformation. Herein, an integrated process of pre-coagulation and microfiltration was developed for removal of ARGs, especially eARGs, from wastewater effluent. Results show that the integrated process could effectively reduce the absolute abundances of total ARGs (tARGs) (>2.9 logs) and eARGs (>5.2 logs) from the effluent. The excellent performance could be mainly attributed to the capture of antibiotic resistant bacteria (ARB) and eARGs by pre-coagulation and co-rejection during subsequent microfiltration. Moreover, the integrated process exhibited a good performance on removing common pollutants (e.g., dissolved organic carbon and phosphate) from the effluent to improve water quality. Besides, the integrated process also greatly reduced membrane fouling compared with microfiltration. These findings suggest that the integrated process of pre-coagulation and microfiltration is a promising advanced wastewater treatment technology for ARGs (especially eARGs) removal from WWTP effluents to ensure water reuse security.}, }
@article {pmid31081928, year = {2019}, author = {Cusimano, N and Renner, SS}, title = {Sequential horizontal gene transfers from different hosts in a widespread Eurasian parasitic plant, Cynomorium coccineum.}, journal = {American journal of botany}, volume = {106}, number = {5}, pages = {679-689}, doi = {10.1002/ajb2.1286}, pmid = {31081928}, issn = {1537-2197}, mesh = {Cynomorium/*genetics ; *Gene Transfer, Horizontal ; Genes, Mitochondrial ; *Genes, Plant ; *Genome, Mitochondrial ; *Genome, Plastid ; Italy ; Plant Dispersal/*genetics ; }, abstract = {PREMISE: Parasitic plants with large geographic ranges, and different hosts in parts of their range, may acquire horizontally transferred genes (HGTs), which might sometimes leave a footprint of gradual host and range expansion. Cynomorium coccineum, the only member of the Saxifragales family Cynomoriaceae, is a root holoparasite that occurs in water-stressed habitats from western China to the Canary Islands. It parasitizes at least 10 angiosperm families from different orders, some of them only in parts of its range. This parasite therefore offers an opportunity to trace HGTs as long as parasite-host pairs can be obtained and sequenced.<br><br>METHODS: By sequencing mitochondrial, plastid, and nuclear loci from parasite-host pairs from throughout the parasite's range and with prior information from completely assembled mitochondrial and plastid genomes, we detected 10 HGTs of five mitochondrial genes.<br><br>RESULTS: The 10 HGTs appear to have occurred sequentially as C. coccineum expanded from East to West. Molecular-clock models yield Cynomorium stem ages between 66 and 156 Myr, with relaxed clocks converging on 66-67 Myr. Chinese Sapindales, probably Nitraria, were the first source of transferred genes, followed by Iranian and Mediterranean Caryophyllales. The most recently acquired gene appears to come from a Tamarix host in the Iberian Peninsula.<br><br>CONCLUSIONS: Data on HGTs that have accumulated over the past 15 years, along with this discovery of multiple HGTs within a single widespread species, underline the need for more whole-genome data from parasite-host pairs to investigate whether and how transferred copies coexist with, or replace, native functional genes.}, }
@article {pmid31081040, year = {2019}, author = {Mendler, K and Chen, H and Parks, DH and Lobb, B and Hug, LA and Doxey, AC}, title = {AnnoTree: visualization and exploration of a functionally annotated microbial tree of life.}, journal = {Nucleic acids research}, volume = {47}, number = {9}, pages = {4442-4448}, pmid = {31081040}, issn = {1362-4962}, mesh = {Archaea/classification/*genetics ; Bacteria/classification/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genome, Archaeal/genetics ; Genome, Bacterial/genetics ; Genomics ; *Molecular Sequence Annotation ; Phylogeny ; }, abstract = {Bacterial genomics has revolutionized our understanding of the microbial tree of life; however, mapping and visualizing the distribution of functional traits across bacteria remains a challenge. Here, we introduce AnnoTree-an interactive, functionally annotated bacterial tree of life that integrates taxonomic, phylogenetic and functional annotation data from over 27 000 bacterial and 1500 archaeal genomes. AnnoTree enables visualization of millions of precomputed genome annotations across the bacterial and archaeal phylogenies, thereby allowing users to explore gene distributions as well as patterns of gene gain and loss in prokaryotes. Using AnnoTree, we examined the phylogenomic distributions of 28 311 gene/protein families, and measured their phylogenetic conservation, patchiness, and lineage-specificity within bacteria. Our analyses revealed widespread phylogenetic patchiness among bacterial gene families, reflecting the dynamic evolution of prokaryotic genomes. Genes involved in phage infection/defense, mobile elements, and antibiotic resistance dominated the list of most patchy traits, as well as numerous intriguing metabolic enzymes that appear to have undergone frequent horizontal transfer. We anticipate that AnnoTree will be a valuable resource for exploring prokaryotic gene histories, and will act as a catalyst for biological and evolutionary hypothesis generation. AnnoTree is freely available at http://annotree.uwaterloo.ca.}, }
@article {pmid31078715, year = {2020}, author = {Huang, T and Xiong, T and Peng, Z and Xiao, YS and Liu, ZG and Hu, M and Xie, MY}, title = {Genomic analysis revealed adaptive mechanism to plant-related fermentation of Lactobacillus plantarum NCU116 and Lactobacillus spp.}, journal = {Genomics}, volume = {112}, number = {1}, pages = {703-711}, doi = {10.1016/j.ygeno.2019.05.004}, pmid = {31078715}, issn = {1089-8646}, mesh = {Adaptation, Physiological/*genetics ; Bacterial Proteins/*genetics ; *Genetic Loci ; *Genome, Bacterial ; Genomics ; Lactobacillus plantarum/*genetics ; }, abstract = {Lactobacillus plantarum NCU116 is the first sequenced strain derived from traditional Chinese sauerkraut (TCS). Since NCU116 manifested outstanding probiotic effects in vitro and in vivo, it is crucial to comprehend a clear genetic background for NCU116. Functional re-annotation and comparative analysis were performed to excavate the unique and representative genes in NCU116, in order to investigate its metabolic preference and adaptive mechanism. Horizontal gene transfer (HGT) seemed to occur frequently, which endows NCU116 with a strong ability to transport carbohydrates, as a strain-specific fructose/mannose-PTS was identified, and opu and osmC coding genes were retrieved as NCU116-specific. In addition, a strain-specific type I R/M system and several prophage loci were found in NCU116, which could play vital roles in self-defense mechanism. Pathways of bacterial metabolism on plant-related substrates fermentation were then generated by reconstruction of associated pathways. Moreover, a unique potential plantaricin-producing locus with high homology to that of JDM1 was defined in the genome of NCU116, which could be very important for the preservation of fermented-food. Our results would provide critical basis for the application of NCU116 in food and pharmaceuticals industries.}, }
@article {pmid31078551, year = {2019}, author = {Verdonk, CJ and Sullivan, JT and Williman, KM and Nicholson, L and Bastholm, TR and Hynes, MF and Ronson, CW and Bond, CS and Ramsay, JP}, title = {Delineation of the integrase-attachment and origin-of-transfer regions of the symbiosis island ICEMlSym[R7A].}, journal = {Plasmid}, volume = {104}, number = {}, pages = {102416}, doi = {10.1016/j.plasmid.2019.102416}, pmid = {31078551}, issn = {1095-9890}, mesh = {Base Sequence ; Binding Sites ; Cloning, Molecular ; *Conjugation, Genetic ; DNA Nucleotidyltransferases ; *DNA Transposable Elements ; Gene Order ; Gene Transfer, Horizontal ; *Genomic Islands ; Integrases/*metabolism ; Nucleotide Motifs ; Protein Binding ; Recombination, Genetic ; *Replication Origin ; Symbiosis ; Viral Proteins ; }, abstract = {Integrative and conjugative elements (ICEs) are chromosomally-integrated mobile genetic elements that excise from their host chromosome and transfer to other bacteria via conjugation. ICEMlSym[R7A] is the prototypical member of a large family of "symbiosis ICEs" which confer upon their hosts the ability to form a nitrogen-fixing symbiosis with a variety of legume species. Mesorhizobial symbiosis ICEs carry a common core of mobilisation genes required for integration, excision and conjugative transfer. IntS of ICEMlSym[R7A] enables recombination between the ICEMlSym[R7A] attachment site attP and the 3' end of the phe-tRNA gene. Here we identified putative IntS attP arm (P) sites within the attP region and demonstrated that the outermost P1 and P5 sites demarcated the minimal region for efficient IntS-mediated integration. We also identified the ICEMlSym[R7A] origin-of-transfer (oriT) site directly upstream of the relaxase-gene rlxS. The ICEMlSym[R7A] conjugation system mobilised a plasmid carrying the cloned oriT to Escherichia coli in an rlxS-dependent manner. Surprisingly, an in-frame, markerless deletion mutation in the ICEMlSym[R7A] recombination directionality factor (excisionase) gene rdfS, but not a mutation in intS, abolished mobilisation, suggesting the rdfS deletion tentatively has downstream effects on conjugation or its regulation. In summary, this work defines two critical cis-acting regions required for excision and transfer of ICEMlSym[R7A] and related ICEs.}, }
@article {pmid31077860, year = {2019}, author = {Papagiannitsis, CC and Bitar, I and Malli, E and Tsilipounidaki, K and Hrabak, J and Petinaki, E}, title = {IncC blaKPC-2-positive plasmid characterised from ST648 Escherichia coli.}, journal = {Journal of global antimicrobial resistance}, volume = {19}, number = {}, pages = {73-77}, doi = {10.1016/j.jgar.2019.05.001}, pmid = {31077860}, issn = {2213-7173}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics ; Base Sequence ; DNA Transposable Elements ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/drug effects/*genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; Greece/epidemiology ; Humans ; Klebsiella Infections ; Klebsiella pneumoniae/genetics ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; *Plasmids ; Whole Genome Sequencing ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: This study describes the characterisation of type 2 IncC plasmids pC-Ec20-KPC and pC-Ec2-KPC, carrying theblaKPC-2 gene, from two multiresistant Escherichia coli recovered in University Hospital of Larissa (Greece) in 2018.<br><br>METHODS: E. coli strains Ec-2Lar and Ec-20Lar were recovered from rectal swabs of two patients during monthly surveillance cultures. Transfer experiments by conjugation were carried out using rifampicin-resistant E. coli A15 laboratory strain as recipient. blaKPC-carrying plasmids were characterised by S1 profiling. Isolates were typed by MLST. Whole-genome sequencing was performed using the Sequel platform.<br><br>RESULTS: Both E. coli isolates, belonging to ST648, transferred blaKPC-2 to E. coli A15 by conjugation. Plasmid analysis revealed that the transconjugants harboured blaKPC-positive plasmids of different sizes. Analysis of plasmid sequences showed that in both isolates the blaKPC-2 gene was carried on a type 2 IncC plasmid (pC-Ec20-KPC and pC-Ec2-KPC, respectively). Both plasmids carried the ARI-B resistance island consisting of several resistance genes, intact and truncated copies of several mobile elements, and a 25 571-bp segment harbouring coding sequences for an iron transporter. The blaKPC-2 gene was part of transposon Tn4401a, which was bounded by 5-bp direct repeats (TCCTT) suggesting its transposition into the IncC plasmids.<br><br>CONCLUSION: To our knowledge, this is the first report on complete nucleotide sequences of type 2 IncC plasmids. These findings, which hypothesise the acquisition of KPC-2-encoding transposon Tn4401a by an IncC replicon, indicate the ongoing need for molecular surveillance studies of multidrug-resistant pathogens. In addition, they underline the increasing clinical importance of the IncC plasmid family.}, }
@article {pmid31077680, year = {2019}, author = {Erdős, PL and Semple, C and Steel, M}, title = {A class of phylogenetic networks reconstructable from ancestral profiles.}, journal = {Mathematical biosciences}, volume = {313}, number = {}, pages = {33-40}, doi = {10.1016/j.mbs.2019.04.009}, pmid = {31077680}, issn = {1879-3134}, mesh = {*Models, Biological ; *Phylogeny ; }, abstract = {Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set X of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate processes (for example, hybrid evolution, endosymbiosis, and lateral gene transfer). A major goal in systematic biology is to infer evolutionary relationships, and while phylogenetic trees can be uniquely determined from various simple combinatorial data on X, for networks the reconstruction question is much more subtle. Here we ask when can a network be uniquely reconstructed from its 'ancestral profile' (the number of paths from each ancestral vertex to each element in X). We show that reconstruction holds (even within the class of all networks) for a class of networks we call 'orchard networks', and we provide a polynomial-time algorithm for reconstructing any orchard network from its ancestral profile. Our approach relies on establishing a structural theorem for orchard networks, which also provides for a fast (polynomial-time) algorithm to test if any given network is of orchard type. Since the class of orchard networks includes tree-sibling tree-consistent networks and tree-child networks, our result generalise reconstruction results from 2008 and 2009. Orchard networks allow for an unbounded number k of reticulation vertices, in contrast to tree-sibling tree-consistent networks and tree-child networks for which k is at most 2|X|-4 and |X|-1, respectively.}, }
@article {pmid31077129, year = {2019}, author = {Busch, A and Danchin, EGJ and Pauchet, Y}, title = {Functional diversification of horizontally acquired glycoside hydrolase family 45 (GH45) proteins in Phytophaga beetles.}, journal = {BMC evolutionary biology}, volume = {19}, number = {1}, pages = {100}, pmid = {31077129}, issn = {1471-2148}, mesh = {Amino Acid Sequence ; Animals ; Biocatalysis ; Coleoptera/*enzymology/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Insect ; Glycoside Hydrolases/chemistry/*genetics ; Insect Proteins/chemistry/genetics ; *Multigene Family ; Phylogeny ; }, abstract = {BACKGROUND: Cellulose, a major polysaccharide of the plant cell wall, consists of β-1,4-linked glucose moieties forming a molecular network recalcitrant to enzymatic breakdown. Although cellulose is potentially a rich source of energy, the ability to degrade it is rare in animals and was believed to be present only in cellulolytic microbes. Recently, it has become clear that some animals encode endogenous cellulases belonging to several glycoside hydrolase families (GHs), including GH45. GH45s are distributed patchily among the Metazoa and, in insects, are encoded only by the genomes of Phytophaga beetles. This study aims to understand both the enzymatic functions and the evolutionary history of GH45s in these beetles.<br><br>RESULTS: To this end, we biochemically assessed the enzymatic activities of 37 GH45s derived from five species of Phytophaga beetles and discovered that beetle-derived GH45s degrade three different substrates: amorphous cellulose, xyloglucan and glucomannan. Our phylogenetic and gene structure analyses indicate that at least one gene encoding a putative cellulolytic GH45 was present in the last common ancestor of the Phytophaga, and that GH45 xyloglucanases evolved several times independently in these beetles. The most closely related clade to Phytophaga GH45s was composed of fungal sequences, suggesting this GH family was acquired by horizontal gene transfer from fungi. Besides the insects, other arthropod GH45s do not share a common origin and appear to have emerged at least three times independently.<br><br>CONCLUSION: The rise of functional innovation from gene duplication events has been a fundamental process in the evolution of GH45s in Phytophaga beetles. Both, enzymatic activity and ancestral origin suggest that GH45s were likely an essential prerequisite for the adaptation allowing Phytophaga beetles to feed on plants.}, }
@article {pmid31072320, year = {2019}, author = {Oliveira, H and Sampaio, M and Melo, LDR and Dias, O and Pope, WH and Hatfull, GF and Azeredo, J}, title = {Staphylococci phages display vast genomic diversity and evolutionary relationships.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {357}, pmid = {31072320}, issn = {1471-2164}, support = {R01 GM116884/GM/NIGMS NIH HHS/United States ; SFRH/BPD/111653/2015//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 54308198//Howard Hughes Medical Institute/United States ; GM116884//National Institutes of Health/ ; POCI-01-0145-FEDER-006684//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, mesh = {Chromosome Mapping ; *Evolution, Molecular ; *Genetic Variation ; *Genome, Viral ; Genomics/*methods ; Humans ; Phylogeny ; Staphylococcus Phages/*classification/*genetics ; Viral Proteins/*genetics ; }, abstract = {BACKGROUND: Bacteriophages are the most abundant and diverse entities in the biosphere, and this diversity is driven by constant predator-prey evolutionary dynamics and horizontal gene transfer. Phage genome sequences are under-sampled and therefore present an untapped and uncharacterized source of genetic diversity, typically characterized by highly mosaic genomes and no universal genes. To better understand the diversity and relationships among phages infecting human pathogens, we have analysed the complete genome sequences of 205 phages of Staphylococcus sp.<br><br>RESULTS: These are predicted to encode 20,579 proteins, which can be sorted into 2139 phamilies (phams) of related sequences; 745 of these are orphams and possess only a single gene. Based on shared gene content, these phages were grouped into four clusters (A, B, C and D), 27 subclusters (A1-A2, B1-B17, C1-C6 and D1-D2) and one singleton. However, the genomes have mosaic architectures and individual genes with common ancestors are positioned in distinct genomic contexts in different clusters. The staphylococcal Cluster B siphoviridae are predicted to be temperate, and the integration cassettes are often closely-linked to genes implicated in bacterial virulence determinants. There are four unusual endolysin organization strategies found in Staphylococcus phage genomes, with endolysins predicted to be encoded as single genes, two genes spliced, two genes adjacent and as a single gene with inter-lytic-domain secondary translational start site. Comparison of the endolysins reveals multi-domain modularity, with conservation of the SH3 cell wall binding domain.<br><br>CONCLUSIONS: This study provides a high-resolution view of staphylococcal viral genetic diversity, and insights into their gene flux patterns within and across different phage groups (cluster and subclusters) providing insights into their evolution.}, }
@article {pmid31071205, year = {2019}, author = {Kim, KG and Jeong, J and Kim, MJ and Park, DW and Shin, JH and Park, HJ and Chung, JK and Kee, HY}, title = {Prevalence and molecular epidemiology of ESBLs, plasmid-determined AmpC-type β-lactamases and carbapenemases among diarrhoeagenic Escherichia coli isolates from children in Gwangju, Korea: 2007-16.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {74}, number = {8}, pages = {2181-2187}, doi = {10.1093/jac/dkz175}, pmid = {31071205}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics ; Child ; Child, Preschool ; DNA, Bacterial/genetics ; Diarrhea/*microbiology ; Drug Resistance, Multiple, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/drug effects/enzymology/*genetics ; Escherichia coli Infections/*epidemiology/microbiology ; Female ; Gene Transfer, Horizontal ; Hospitals/statistics &amp; numerical data ; Humans ; Male ; Microbial Sensitivity Tests ; Prevalence ; Republic of Korea/epidemiology ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: Young children could act as important carriers of cefotaxime-resistant Enterobacteriaceae. However, most studies on these bacteria have focused on hospitalized adults. Therefore, we determined the prevalence and characteristics of ESBL-, plasmid-determined AmpC-type β-lactamase (PABL)- and carbapenemase-producing diarrhoeagenic Escherichia coli isolates mainly from infants and children in the south-west region of Korea over a 10 year period.<br><br>METHODS: Non-duplicate E. coli clinical isolates were recovered from diarrhoeagenic patient specimens at 12 hospitals in Gwangju, Korea, between January 2007 and December 2016. Antimicrobial susceptibilities and molecular features of ESBL- and carbapenemase-producing isolates were determined.<br><br>RESULTS: A total of 1047 pathogenic E. coli isolates were collected and 58 cefotaxime-resistant E. coli isolates (5.5%) were identified. The prevalence and types of &#x3b2;-lactamase genes increased steadily from 5.7% in 2007 to 11.6% in 2016 with some fluctuations. CTX-M-14 (53.4%) was the predominant CTX-M genotype. PFGE revealed high genetic heterogeneities among diarrhoeagenic E. coli isolates, suggesting horizontal transfer of antibiotic resistance genes, which was also proved by conjugation assay.<br><br>CONCLUSIONS: Progressive increases in carriage rates and the number of &#x3b2;-lactamase types, and the possibility of community outbreaks of these food-borne bacteria in young children, may pose tangible public health threats.}, }
@article {pmid31068910, year = {2019}, author = {Bukowski, M and Piwowarczyk, R and Madry, A and Zagorski-Przybylo, R and Hydzik, M and Wladyka, B}, title = {Prevalence of Antibiotic and Heavy Metal Resistance Determinants and Virulence-Related Genetic Elements in Plasmids of Staphylococcus aureus.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {805}, pmid = {31068910}, issn = {1664-302X}, abstract = {The use of antibiotics on a mass scale, particularly in farming, and their release into the environment has led to a rapid emergence of resistant bacteria. Once emerged, resistance determinants are spread by horizontal gene transfer among strains of the same as well as disparate bacterial species. Their accumulation in free-living as well as livestock and community-associated strains results in the widespread multiple-drug resistance among clinically relevant species posing an increasingly pressing problem in healthcare. One of these clinically relevant species is Staphylococcus aureus, a common cause of hospital and community outbreaks. Among the rich diversity of mobile genetic elements regularly occurring in S. aureus such as phages, pathogenicity islands, and staphylococcal cassette chromosomes, plasmids are the major mean for dissemination of resistance determinants and virulence factors. Unfortunately, a vast number of whole-genome sequencing projects does not aim for complete sequence determination, which results in a disproportionately low number of known complete plasmid sequences. To address this problem we determined complete plasmid sequences derived from 18 poultry S. aureus strains and analyzed the prevalence of antibiotic and heavy metal resistance determinants, genes of virulence factors, as well as genetic elements relevant for their maintenance. Some of the plasmids have been reported before and are being found in clinical isolates of strains typical for humans or human ones of livestock origin. This shows that livestock-associated staphylococci are a significant reservoir of resistance determinants and virulence factors. Nevertheless, nearly half of the plasmids were unknown to date. In this group we found a potentially mobilizable plasmid pPA3 being a unique example of accumulation of resistance determinants and virulence factors likely stabilized by a presence of a toxin-antitoxin system.}, }
@article {pmid31064835, year = {2019}, author = {Carroll, LM and Gaballa, A and Guldimann, C and Sullivan, G and Henderson, LO and Wiedmann, M}, title = {Identification of Novel Mobilized Colistin Resistance Gene mcr-9 in a Multidrug-Resistant, Colistin-Susceptible Salmonella enterica Serotype Typhimurium Isolate.}, journal = {mBio}, volume = {10}, number = {3}, pages = {}, pmid = {31064835}, issn = {2150-7511}, mesh = {Anti-Bacterial Agents/*pharmacology ; Colistin/*pharmacology ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Salmonella typhimurium/*drug effects/*genetics ; Serogroup ; }, abstract = {Mobilized colistin resistance (mcr) genes are plasmid-borne genes that confer resistance to colistin, an antibiotic used to treat severe bacterial infections. To date, eight known mcr homologues have been described (mcr-1 to -8). Here, we describe mcr-9, a novel mcr homologue detected during routine in silico screening of sequenced Salmonella genomes for antimicrobial resistance genes. The amino acid sequence of mcr-9, detected in a multidrug-resistant (MDR) Salmonella enterica serotype Typhimurium (S Typhimurium) strain isolated from a human patient in Washington State in 2010, most closely resembled mcr-3, aligning with 64.5% amino acid identity and 99.5% coverage using Translated Nucleotide BLAST (tblastn). The S. Typhimurium strain was tested for phenotypic resistance to colistin and was found to be sensitive at the 2-mg/liter European Committee on Antimicrobial Susceptibility Testing breakpoint under the tested conditions. mcr-9 was cloned in colistin-susceptible Escherichia coli NEB5α under an IPTG (isopropyl-β-d-thiogalactopyranoside)-induced promoter to determine whether it was capable of conferring resistance to colistin when expressed in a heterologous host. Expression of mcr-9 conferred resistance to colistin in E. coli NEB5α at 1, 2, and 2.5 mg/liter colistin, albeit at a lower level than mcr-3 Pairwise comparisons of the predicted protein structures associated with all nine mcr homologues (Mcr-1 to -9) revealed that Mcr-9, Mcr-3, Mcr-4, and Mcr-7 share a high degree of similarity at the structural level. Our results indicate that mcr-9 is capable of conferring phenotypic resistance to colistin in Enterobacteriaceae and should be immediately considered when monitoring plasmid-mediated colistin resistance.IMPORTANCE Colistin is a last-resort antibiotic that is used to treat severe infections caused by MDR and extensively drug-resistant (XDR) bacteria. The World Health Organization (WHO) has designated colistin as a "highest priority critically important antimicrobial for human medicine" (WHO, Critically Important Antimicrobials for Human Medicine, 5th revision, 2017, https://www.who.int/foodsafety/publications/antimicrobials-fifth/en/), as it is often one of the only therapies available for treating serious bacterial infections in critically ill patients. Plasmid-borne mcr genes that confer resistance to colistin pose a threat to public health at an international scale, as they can be transmitted via horizontal gene transfer and have the potential to spread globally. Therefore, the establishment of a complete reference of mcr genes that can be used to screen for plasmid-mediated colistin resistance is essential for developing effective control strategies.}, }
@article {pmid31064110, year = {2019}, author = {Floriano, B and Santero, E and Reyes-Ramírez, F}, title = {Biodegradation of Tetralin: Genomics, Gene Function and Regulation.}, journal = {Genes}, volume = {10}, number = {5}, pages = {}, pmid = {31064110}, issn = {2073-4425}, mesh = {Biodegradation, Environmental ; *Genomics ; Humans ; Petroleum/metabolism/toxicity ; Rhodococcus/genetics/growth &amp; development/*metabolism ; Sphingomonadaceae/genetics/growth &amp; development/*metabolism ; Tetrahydronaphthalenes/*metabolism/toxicity ; }, abstract = {Tetralin (1,2,3,4-tetrahydonaphthalene) is a recalcitrant compound that consists of an aromatic and an alicyclic ring. It is found in crude oils, produced industrially from naphthalene or anthracene, and widely used as an organic solvent. Its toxicity is due to the alteration of biological membranes by its hydrophobic character and to the formation of toxic hydroperoxides. Two unrelated bacteria, Sphingopyxis granuli strain TFA and Rhodococcus sp. strain TFB were isolated from the same niche as able to grow on tetralin as the sole source of carbon and energy. In this review, we provide an overview of current knowledge on tetralin catabolism at biochemical, genetic and regulatory levels in both strains. Although they share the same biodegradation strategy and enzymatic activities, no evidences of horizontal gene transfer between both bacteria have been found. Moreover, the regulatory elements that control the expression of the gene clusters are completely different in each strain. A special consideration is given to the complex regulation discovered in TFA since three regulatory systems, one of them involving an unprecedented communication between the catabolic pathway and the regulatory elements, act together at transcriptional and posttranscriptional levels to optimize tetralin biodegradation gene expression to the environmental conditions.}, }
@article {pmid31063791, year = {2019}, author = {Selão, TT and Włodarczyk, A and Nixon, PJ and Norling, B}, title = {Growth and selection of the cyanobacterium Synechococcus sp. PCC 7002 using alternative nitrogen and phosphorus sources.}, journal = {Metabolic engineering}, volume = {54}, number = {}, pages = {255-263}, doi = {10.1016/j.ymben.2019.04.013}, pmid = {31063791}, issn = {1096-7184}, mesh = {*Nitrogen/chemistry/metabolism/pharmacology ; *Phosphorus/chemistry/metabolism/pharmacology ; Synechococcus/genetics/*growth &amp; development ; }, abstract = {Cyanobacteria, such as Synechococcus sp. PCC 7002 (Syn7002), are promising chassis strains for "green" biotechnological applications as they can be grown in seawater using oxygenic photosynthesis to fix carbon dioxide into biomass. Their other major nutritional requirements for efficient growth are sources of nitrogen (N) and phosphorus (P). As these organisms are more economically cultivated in outdoor open systems, there is a need to develop cost-effective approaches to prevent the growth of contaminating organisms, especially as the use of antibiotic selection markers is neither economically feasible nor ecologically desirable due to the risk of horizontal gene transfer. Here we have introduced a synthetic melamine degradation pathway into Syn7002 and evolved the resulting strain to efficiently use the nitrogen-rich xenobiotic compound melamine as the sole N source. We also show that expression of phosphite dehydrogenase in the absence of its cognate phosphite transporter permits growth of Syn7002 on phosphite and can be used as a selectable marker in Syn7002. We combined these two strategies to generate a strain that can grow on melamine and phosphite as sole N and P sources, respectively. This strain is able to resist deliberate contamination in large excess and should be a useful chassis for metabolic engineering and biotechnological applications using cyanobacteria.}, }
@article {pmid31063253, year = {2019}, author = {Nagata, Y and Kato, H and Ohtsubo, Y and Tsuda, M}, title = {Lessons from the genomes of lindane-degrading sphingomonads.}, journal = {Environmental microbiology reports}, volume = {11}, number = {5}, pages = {630-644}, doi = {10.1111/1758-2229.12762}, pmid = {31063253}, issn = {1758-2229}, support = {//Ministry of Education, Culture, Sports, Science and Technology of Japan/International ; //Institute for Fermentation, Osaka (IFO), Japan/International ; }, mesh = {Bacterial Proteins/genetics ; *Biodegradation, Environmental ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; Hexachlorocyclohexane/*metabolism ; Phylogeny ; Plasmids ; Sphingomonadaceae/*genetics/*metabolism ; }, abstract = {Bacterial strains capable of degrading man-made xenobiotic compounds are good materials to study bacterial evolution towards new metabolic functions. Lindane (γ-hexachlorocyclohexane, γ-HCH, or γ-BHC) is an especially good target compound for the purpose, because it is relatively recalcitrant but can be degraded by a limited range of bacterial strains. A comparison of the complete genome sequences of lindane-degrading sphingomonad strains clearly demonstrated that (i) lindane-degrading strains emerged from a number of different ancestral hosts that have recruited lin genes encoding enzymes that are able to channel lindane to central metabolites, (ii) in sphingomonads lin genes have been acquired by horizontal gene transfer mediated by different plasmids and in which IS6100 plays a role in recruitment and distribution of genes, and (iii) IS6100 plays a role in dynamic genome rearrangements providing genetic diversity to different strains and ability to evolve to other states. Lindane-degrading bacteria whose genomes change so easily and quickly are also fascinating starting materials for tracing the bacterial evolution process experimentally in a relatively short time period. As the origin of the specific lin genes remains a mystery, such genes will be useful probes for exploring the cryptic 'gene pool' available to bacteria.}, }
@article {pmid31060509, year = {2019}, author = {Gonnella, G and Adam, N and Perner, M}, title = {Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {339}, pmid = {31060509}, issn = {1471-2164}, support = {PE1549-6/3//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Acclimatization ; Bacterial Proteins/genetics/metabolism ; *Ecosystem ; Genome, Bacterial ; Hydrogen/*metabolism ; Hydrogenase/genetics/metabolism ; Molecular Sequence Annotation ; Piscirickettsiaceae/classification/*genetics ; }, abstract = {BACKGROUND: Obligate sulfur oxidizing chemolithoauthotrophic strains of Hydrogenovibrio crunogenus have been isolated from multiple hydrothermal vent associated habitats. However, a hydrogenase gene cluster (encoding the hydrogen converting enzyme and its maturation/assembly machinery) detected on the first sequenced H. crunogenus strain (XCL-2) suggested that hydrogen conversion may also play a role in this organism. Yet, numerous experiments have underlined XCL-2's inability to consume hydrogen under the tested conditions. A recent study showed that the closely related strain SP-41 contains a homolog of the XCL-2 hydrogenase (a group 1b [NiFe]-hydrogenase), but that it can indeed use hydrogen. Hence, the question remained unresolved, why SP-41 is capable of using hydrogen, while XCL-2 is not.<br><br>RESULTS: Here, we present the genome sequence of the SP-41 strain and compare it to that of the XCL-2 strain. We show that the chromosome of SP-41 codes for a further hydrogenase gene cluster, including two additional hydrogenases: the first appears to be a group 1d periplasmic membrane-anchored hydrogenase, and the second a group 2b sensory hydrogenase. The region where these genes are located was likely acquired horizontally and exhibits similarity to other Hydrogenovibrio species (H. thermophilus MA2-6 and H. marinus MH-110 [T]) and other hydrogen oxidizing Proteobacteria (Cupriavidus necator H16 and Ghiorsea bivora TAG-1 [T]). The genomes of XCL-2 and SP-41 show a strong conservation in gene order. However, several short genomic regions are not contained in the genome of the other strain. These exclusive regions are often associated with signs of DNA mobility, such as genes coding for transposases. They code for transport systems and/or extend the metabolic potential of the strains.<br><br>CONCLUSIONS: Our results suggest that horizontal gene transfer plays an important role in shaping the genomes of these strains, as a likely mechanism for habitat adaptation, including, but not limited to the transfer of the hydrogen conversion ability.}, }
@article {pmid31058854, year = {2019}, author = {Blumenstiel, JP}, title = {Birth, School, Work, Death, and Resurrection: The Life Stages and Dynamics of Transposable Element Proliferation.}, journal = {Genes}, volume = {10}, number = {5}, pages = {}, pmid = {31058854}, issn = {2073-4425}, mesh = {Alu Elements/genetics ; Animals ; Cell Proliferation/*genetics ; DNA Transposable Elements/*genetics ; Drosophila Proteins/genetics ; Drosophila melanogaster/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Long Interspersed Nucleotide Elements/genetics ; Transposases/genetics ; }, abstract = {Transposable elements (TEs) can be maintained in sexually reproducing species even if they are harmful. However, the evolutionary strategies that TEs employ during proliferation can modulate their impact. In this review, I outline the different life stages of a TE lineage, from birth to proliferation to extinction. Through their interactions with the host, TEs can exploit diverse strategies that range from long-term coexistence to recurrent movement across species boundaries by horizontal transfer. TEs can also engage in a poorly understood phenomenon of TE resurrection, where TE lineages can apparently go extinct, only to proliferate again. By determining how this is possible, we may obtain new insights into the evolutionary dynamics of TEs and how they shape the genomes of their hosts.}, }
@article {pmid31057498, year = {2019}, author = {Hu, X and Kang, F and Yang, B and Zhang, W and Qin, C and Gao, Y}, title = {Extracellular Polymeric Substances Acting as a Permeable Barrier Hinder the Lateral Transfer of Antibiotic Resistance Genes.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {736}, pmid = {31057498}, issn = {1664-302X}, abstract = {Antibiotic resistance genes (ARGs) in bacteria are emerging contaminants as their proliferation in the environment poses significant threats to human health. It is well recognized that extracellular polymeric substances (EPS) can protect microorganisms against stress or damage from exogenous contaminants. However, it is not clear whether EPS could affect the lateral transfer of ARGs into bacteria, which is one of the major processes for the dissemination of ARGs. This study investigated the lateral transfer of ARGs carried by plasmids (pUC19, pHSG298, and pHSG396) into competent Escherichia coli cells with and without EPS. Transformant numbers and transformation efficiency for E. coli without EPS were up to 29 times of those with EPS at pH 7.0 in an aqueous system. The EPS removal further increased cell permeability in addition to the enhanced cell permeability by Ca[2+], which could be responsible for the enhanced lateral transfer of ARGs. The fluorescence quenching experiments showed that EPS could strongly bind to plasmid DNA in the presence of Ca[2+] and the binding strength (LogK A = 10.65-15.80 L mol[-1]) between EPS and plasmids was positively correlated with the enhancement percentage of transformation efficiency resulting from the EPS removal. X-ray photoelectron spectroscopy (XPS) analyses and model computation further showed that Ca[2+] could electrostatically bind with EPS mainly through the carboxyl group, hydroxyl group, and RC-O-CR in glucoside, thus bridging the plasmid and EPS. As a result, the binding of plasmids with EPS hindered the lateral transfer of plasmid-borne ARGs. This study improved our understanding on the function of EPS in controlling the fate and transport of ARGs on the molecular and cellular scales.}, }
@article {pmid31056439, year = {2019}, author = {Maori, E and Garbian, Y and Kunik, V and Mozes-Koch, R and Malka, O and Kalev, H and Sabath, N and Sela, I and Shafir, S}, title = {A Transmissible RNA Pathway in Honey Bees.}, journal = {Cell reports}, volume = {27}, number = {7}, pages = {1949-1959.e6}, doi = {10.1016/j.celrep.2019.04.073}, pmid = {31056439}, issn = {2211-1247}, mesh = {Animals ; Bees/*genetics ; Fatty Acids/genetics/physiology ; Gene Transfer, Horizontal/physiology ; Larva/genetics/metabolism/physiology ; RNA Interference/*physiology ; RNA, Double-Stranded/*genetics/physiology ; Signal Transduction/*genetics ; }, abstract = {Systemic RNAi, initiated by double-stranded RNA (dsRNA) ingestion, has been reported in diverse invertebrates, including honey bees, demonstrating environmental RNA uptake that undermines homologous gene expression. However, the question why any organism would take up RNA from the environment has remained largely unanswered. Here, we report on horizontal RNA flow among honey bees mediated by secretion and ingestion of worker and royal jelly diets. We demonstrate that transmission of jelly-secreted dsRNA to larvae is biologically active and triggers gene knockdown that lasts into adulthood. Worker and royal jellies harbor differential naturally occurring RNA populations. Jelly RNAs corresponded to honey bee protein-coding genes, transposable elements, and non-coding RNA, as well as bacteria, fungi, and viruses. These results reveal an inherent property of honey bees to share RNA among individuals and generations. Our findings suggest a transmissible RNA pathway, playing a role in social immunity and signaling between members of the hive.}, }
@article {pmid31054238, year = {2019}, author = {Kang, CS and Dunfield, PF and Semrau, JD}, title = {The origin of aerobic methanotrophy within the Proteobacteria.}, journal = {FEMS microbiology letters}, volume = {366}, number = {9}, pages = {}, doi = {10.1093/femsle/fnz096}, pmid = {31054238}, issn = {1574-6968}, mesh = {Aerobiosis ; Alcohol Oxidoreductases/genetics/metabolism ; Copper/metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome ; *Genome, Bacterial ; Methane/*metabolism ; Methanol/metabolism ; Oxygenases/genetics/metabolism ; Phylogeny ; Proteobacteria/*classification/*enzymology ; }, abstract = {Aerobic methanotrophs play critical roles in the global carbon cycle, but despite their environmental ubiquity, they are phylogenetically restricted. Via bioinformatic analyses, it is shown that methanotrophy likely arose from methylotrophy from the lateral gene transfer of either of the two known forms of methane monooxygenase (particulate and soluble methane monooxygenases). Moreover, it appears that both known forms of pyrroloquinoline quinone-dependent methanol dehydrogenase (MeDH) found in methanotrophs-the calcium-containing Mxa-MeDH and the rare earth element-containing Xox-MeDH-were likely encoded in the genomes before the acquisition of the methane monooxygenases (MMOs), but that some methanotrophs subsequently received an additional copy of Xox-MeDH-encoding genes via lateral gene transfer. Further, data are presented that indicate the evolution of methanotrophy from methylotrophy not only required lateral transfer of genes encoding for methane monooxygenases, but also likely the pre-existence of a means of collecting copper. Given the emerging interest in valorizing methane via biological platforms, it is recommended that future strategies for heterologous expression of methane monooxygenase for conversion of methane to methanol also include cloning of genes encoding mechanism(s) of copper uptake, especially for expression of particulate methane monooxygenase.}, }
@article {pmid31053752, year = {2019}, author = {Gomez-Valero, L and Buchrieser, C}, title = {Intracellular parasitism, the driving force of evolution of Legionella pneumophila and the genus Legionella.}, journal = {Genes and immunity}, volume = {20}, number = {5}, pages = {394-402}, doi = {10.1038/s41435-019-0074-z}, pmid = {31053752}, issn = {1476-5470}, mesh = {Amoeba/genetics/microbiology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Host-Pathogen Interactions/*genetics ; Legionella pneumophila/genetics/*pathogenicity ; }, abstract = {Legionella pneumophila is an intracellular pathogen that causes a severe pneumonia called Legionnaires' disease that is often fatal when not promptly diagnosed and treated. However, L. pneumophila is mainly an environmental pathogen of protozoa. This bacterium parasitizes free-living amoeba and other aquatic protozoa with which it co-evolved over an evolutionary long time. Due to the close relationship between hosts and pathogens, their co-evolution leads to molecular interactions such as the exchange of genetic material through horizontal gene transfer (HGT). Those genes that confer an advantage to the bacteria were fixed in their genomes and help these pathogens to subvert host functions to their advantage. Genome sequencing of L. pneumophila and recently of the entire genus Legionella that comprises over 60 species revealed that Legionellae have co-opted genes and thus cellular functions from their eukaryotic hosts to a surprisingly high extent never observed before for an prokaryotic organism. Acquisition and loss of these eukaryotic-like genes and eukaryotic domains is an ongoing process underlining the highly dynamic nature of the Legionella genomes. Although the large amount and diversity of HGT that occurred between Legionella and their protozoan hosts seems to be unique in the prokaryotic world, the analyses of more and more genomes from environmental organisms and symbionts of amoeba revealed that such genetic exchanges occur among all amoeba-associated bacteria and also among the different microorganisms that infect amoeba such as viruses. This dynamic reshuffling and gene-acquisition has led to the emergence of major human pathogens such as Legionella and may lead to the emergence of new human pathogens from the environment.}, }
@article {pmid31051140, year = {2019}, author = {Maori, E and Navarro, IC and Boncristiani, H and Seilly, DJ and Rudolph, KLM and Sapetschnig, A and Lin, CC and Ladbury, JE and Evans, JD and Heeney, JL and Miska, EA}, title = {A Secreted RNA Binding Protein Forms RNA-Stabilizing Granules in the Honeybee Royal Jelly.}, journal = {Molecular cell}, volume = {74}, number = {3}, pages = {598-608.e6}, pmid = {31051140}, issn = {1097-4164}, support = {104640/Z/14/Z/WT_/Wellcome Trust/United Kingdom ; C6946/A14492/CRUK_/Cancer Research UK/United Kingdom ; 092096/Z/10/Z/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; C13474/A18583/CRUK_/Cancer Research UK/United Kingdom ; 18583/CRUK_/Cancer Research UK/United Kingdom ; C57233/A22356/CRUK_/Cancer Research UK/United Kingdom ; }, mesh = {Animals ; Bees/*genetics ; Fatty Acids/biosynthesis/*genetics ; Gene Transfer, Horizontal/*genetics ; Glycoproteins/*genetics ; Insect Proteins/*genetics ; Phase Transition ; RNA/genetics ; RNA Transport/genetics ; RNA-Binding Proteins/genetics ; }, abstract = {RNA flow between organisms has been documented within and among different kingdoms of life. Recently, we demonstrated horizontal RNA transfer between honeybees involving secretion and ingestion of worker and royal jellies. However, how the jelly facilitates transfer of RNA is still unknown. Here, we show that worker and royal jellies harbor robust RNA-binding activity. We report that a highly abundant jelly component, major royal jelly protein 3 (MRJP-3), acts as an extracellular non-sequence-specific RNA-aggregating factor. Multivalent RNA binding stimulates higher-order assembly of MRJP-3 into extracellular ribonucleoprotein granules that protect RNA from degradation and enhance RNA bioavailability. These findings reveal that honeybees have evolved a secreted dietary RNA-binding factor to concentrate, stabilize, and share RNA among individuals. Our work identifies high-order ribonucleoprotein assemblies with functions outside cells and organisms.}, }
@article {pmid31050420, year = {2019}, author = {Mantilla-Calderon, D and Plewa, MJ and Michoud, G and Fodelianakis, S and Daffonchio, D and Hong, PY}, title = {Water Disinfection Byproducts Increase Natural Transformation Rates of Environmental DNA in Acinetobacter baylyi ADP1.}, journal = {Environmental science &amp; technology}, volume = {53}, number = {11}, pages = {6520-6528}, doi = {10.1021/acs.est.9b00692}, pmid = {31050420}, issn = {1520-5851}, mesh = {*Acinetobacter ; DNA ; DNA Damage ; Disinfection ; Water ; }, abstract = {The process of natural transformation allows for the stable uptake, integration, and functional expression of extracellular DNA. This mechanism of horizontal gene transfer has been widely linked to the acquisition of antibiotic resistance and virulence factors. Here, we demonstrate that bromoacetic acid (BAA)-a regulated drinking water disinfection byproduct (DBP)-can stimulate natural transformation rates in the model organism Acinetobacter baylyi ADP1. We demonstrate that transformation stimulation in response to BAA is concentration-dependent and is linked to the ability of this compound to generate DNA damage via oxidative stress. In presence of BAA, transcription of recA was upregulated 20-40% compared to the nontreated controls, indicating that this component of the DNA damage response could be associated with the increase in transformation. Other genes associated with DNA translocation across the cytoplasmic membrane (i.e., pilX, comA) did not exhibit increased transcription in the presence of BAA, indicating that the enhancement of transformation is not associated with increased translocation rates of environmental DNA. Overall, these results lead us to speculate that elevated recA transcription levels could lead to increased integration rates of foreign DNA within the recipient cell during DNA repair. Lastly, we show that an artificial DBP cocktail simulating the environmental concentrations of five water DBP classes stimulates natural transformation by almost 2-fold. The results of this study suggest that mutagens like DBPs may play an important role in enhancing the fixation rates of extracellular DNA in the environmental metagenome.}, }
@article {pmid31037350, year = {2019}, author = {Dávila Felipe, M and Domelevo Entfellner, JB and Lemoine, F and Truszkowski, J and Gascuel, O}, title = {Distribution and asymptotic behavior of the phylogenetic transfer distance.}, journal = {Journal of mathematical biology}, volume = {79}, number = {2}, pages = {485-508}, pmid = {31037350}, issn = {1432-1416}, support = {VIROGENESIS 634650//H2020 European Research Council/International ; VIROGENESIS 634650//H2020 European Research Council/International ; INCEPTION PIA/ANR-16-CONV-0005//Agence Nationale de la Recherche/International ; INCEPTION PIA/ANR-16-CONV-0005//Agence Nationale de la Recherche/International ; INCEPTION PIA/ANR-16-CONV-0005//Agence Nationale de la Recherche/International ; }, mesh = {Algorithms ; Computer Simulation ; *Gene Transfer, Horizontal ; *Models, Genetic ; *Phylogeny ; }, abstract = {The transfer distance (TD) was introduced in the classification framework and studied in the context of phylogenetic tree matching. Recently, Lemoine et al. (Nature 556(7702):452-456, 2018. https://doi.org/10.1038/s41586-018-0043-0) showed that TD can be a powerful tool to assess the branch support on large phylogenies, thus providing a relevant alternative to Felsenstein's bootstrap. This distance allows a reference branch[Formula: see text] in a reference tree [Formula: see text] to be compared to a branch b from another tree T (typically a bootstrap tree), both on the same set of n taxa. The TD between these branches is the number of taxa that must be transferred from one side of b to the other in order to obtain [Formula: see text]. By taking the minimum TD from [Formula: see text] to all branches in T we define the transfer index, denoted by [Formula: see text], measuring the degree of agreement of T with [Formula: see text]. Let us consider a reference branch [Formula: see text] having p tips on its light side and define the transfer support (TS) as [Formula: see text]. Lemoine et al. (2018) used computer simulations to show that the TS defined in this manner is close to 0 for random "bootstrap" trees. In this paper, we demonstrate that result mathematically: when T is randomly drawn, TS converges in probability to 0 when n tends to [Formula: see text]. Moreover, we fully characterize the distribution of [Formula: see text] on caterpillar trees, indicating that the convergence is fast, and that even when n is small, moderate levels of branch support cannot appear by chance.}, }
@article {pmid31032941, year = {2019}, author = {Broecker, F and Moelling, K}, title = {What viruses tell us about evolution and immunity: beyond Darwin?.}, journal = {Annals of the New York Academy of Sciences}, volume = {1447}, number = {1}, pages = {53-68}, pmid = {31032941}, issn = {1749-6632}, mesh = {Animals ; Epigenesis, Genetic/genetics/immunology ; *Evolution, Molecular ; Humans ; Immunity, Cellular/*genetics/*immunology ; Phylogeny ; Protein Structure, Secondary ; RNA, Circular/genetics/immunology ; Viruses/*genetics/*immunology ; }, abstract = {We describe mechanisms of genetic innovation mediated by viruses and related elements that, during evolution, caused major genetic changes beyond what was anticipated by Charles Darwin. Viruses and related elements introduced genetic information and have shaped the genomes and immune systems of all cellular life forms. None of these mechanisms contradict Darwin's theory of evolution but extend it by means of sequence information that has recently become available. Not only do small increments of genetic information contribute to evolution, but also do major events such as infection by viruses or bacteria, which can supply new genetic information to a host by horizontal gene transfer. Thereby, viruses and virus-like elements act as major drivers of evolution.}, }
@article {pmid31031724, year = {2019}, author = {Schwartz, K and Hammerl, JA and Göllner, C and Strauch, E}, title = {Environmental and Clinical Strains of Vibrio cholerae Non-O1, Non-O139 From Germany Possess Similar Virulence Gene Profiles.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {733}, pmid = {31031724}, issn = {1664-302X}, abstract = {Vibrio cholerae is a natural inhabitant of aquatic ecosystems globally. Strains of the serogroups O1 and O139 cause the epidemic diarrheal disease cholera. In Northern European waters, V. cholerae bacteria belonging to other serogroups (designated non-O1, non-O139) are present, of which some strains have been associated with gastrointestinal infections or extraintestinal infections, like wound infections or otitis. For this study, environmental strains from the German coastal waters of the North Sea and the Baltic Sea were selected (100 strains) and compared to clinical strains (10 isolates) that were from patients who contracted the infections in the same geographical region. The strains were characterized by MLST and examined by PCR for the presence of virulence genes encoding the cholera toxin, the toxin-coregulated pilus (TCP), and other virulence-associated accessory factors. The latter group comprised hemolysins, RTX toxins, cholix toxin, pandemic islands, and type III secretion system (TTSS). Phenotypic assays for hemolytic activity against human and sheep erythrocytes were also performed. The results of the MLST analysis revealed a considerable heterogeneity of sequence types (in total 74 STs). The presence of virulence genes was also variable and 30 profiles were obtained by PCR. One profile was found in 38 environmental strains and six clinical strains. Whole genome sequencing (WGS) was performed on 15 environmental and 7 clinical strains that were ST locus variants in one, two, or three alleles. Comparison of WGS results revealed that a set of virulence genes found in some clinical strains is also present in most environmental strains irrespective of the ST. In few strains, more virulence factors are acquired through horizontal gene transfer (i.e., TTSS, genomic islands). A distinction between clinical and environmental strains based on virulence gene profiles is not possible for our strains. Probably, many virulence traits of V. cholerae evolved in response to biotic and abiotic pressure and serve adaptation purposes in the natural aquatic environment, but provide a prerequisite for infection of susceptible human hosts. These findings indicate the need for surveillance of Vibrio spp. in Germany, as due to global warming abundance of Vibrio will rise and infections are predicted to increase.}, }
@article {pmid31030846, year = {2019}, author = {Rossi, CC and Andrade-Oliveira, AL and Giambiagi-deMarval, M}, title = {CRISPR tracking reveals global spreading of antimicrobial resistance genes by Staphylococcus of canine origin.}, journal = {Veterinary microbiology}, volume = {232}, number = {}, pages = {65-69}, doi = {10.1016/j.vetmic.2019.04.009}, pmid = {31030846}, issn = {1873-2542}, mesh = {Animals ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Disease Reservoirs/microbiology ; Dogs/microbiology ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; Methicillin Resistance/genetics ; Microbial Sensitivity Tests ; Pets/microbiology ; Plasmids ; Staphylococcal Infections/transmission/*veterinary ; Staphylococcus/*genetics/isolation &amp; purification ; }, abstract = {The close contact between pets and their owners is a potential source for microorganisms and genetic material exchange. Staphylococcus species considered as harmless inhabitants of animals' and humans' microbiota can act as reservoirs of antimicrobial resistance genes to more virulent species, thereby increasing their potential to resist drug therapy. This process could be inhibited by the antiplasmid immunity conferred by CRISPR systems. On the other hand, CRISPR spacer sequences can be explored as molecular clocks to track the history of genetic invasion suffered by a bacterial strain. To understand better the role of domestic dogs in human health as an antimicrobial resistance genes source, we analyzed 129 genomes of Staphylococcus strains of canine origin for the presence of CRISPR systems. Only 8% of the strains were positive for CRISPR, which is consistent with Staphylococcus role as gene reservoirs. The plasmidial origin or some spacers confirms the unsuccessful attempt of plasmid exchange in strains carrying CRISPRs. Some of these systems are within a staphylococcal cassette chromosome mec (SCCmec), sharing 98% of identity between their harboring strains. These CRISPRs' spacers reveal that this SCCmec was transferred between canine S. pseudintermedius strains, then to S. schleiferi and to Staphylococcus strains isolated from human beings. Our findings shows genetic evidence for the global spreading of pathogenic bacteria and the antimicrobial resistance genes carried by them and reinforce that, in the age of antimicrobial resistance, it is imperative that drug therapies consider the integrated nature of the relationship between pets and humans.}, }
@article {pmid31029811, year = {2019}, author = {Johnson, NR and Axtell, MJ}, title = {Small RNA warfare: exploring origins and function of trans-species microRNAs from the parasitic plant Cuscuta.}, journal = {Current opinion in plant biology}, volume = {50}, number = {}, pages = {76-81}, doi = {10.1016/j.pbi.2019.03.014}, pmid = {31029811}, issn = {1879-0356}, mesh = {*Cuscuta ; Host-Parasite Interactions ; *MicroRNAs ; Plants ; RNA, Plant ; }, abstract = {Parasitic plants make direct contact with their host's vasculature. In parasitism by Cuscuta, RNA and other macromolecules regularly move between host and parasite. Recently, trans-species microRNA from Cuscuta have been shown to functionally target host genes which have essential roles in host defense. Known pathways for the evolution of microRNAs, and the prevalence of horizontal gene transfer events in the Cuscuta lineage, hint that trans-species microRNAs could originate from captured host genes. It is unknown how the delivery of microRNAs from the parasite to the host takes place. One exciting possibility is through apoplastic export using extracellular vesicles, a process which has recently been shown to transport select small RNAs in plants and fungi. These discoveries represent the initial findings of what may be a widespread mechanism of interactions between species.}, }
@article {pmid31028704, year = {2019}, author = {Kuzmanović, N and Puławska, J}, title = {Evolutionary Relatedness and Classification of Tumor-Inducing and Opine-Catabolic Plasmids in Three Rhizobium rhizogenes Strains Isolated from the Same Crown Gall Tumor.}, journal = {Genome biology and evolution}, volume = {11}, number = {6}, pages = {1525-1540}, pmid = {31028704}, issn = {1759-6653}, mesh = {Arginine/analogs &amp; derivatives/metabolism ; Conjugation, Genetic ; Oxazines/*metabolism ; Plant Tumors/*microbiology ; *Plasmids ; Rhizobium/classification/*genetics/pathogenicity ; Virulence ; }, abstract = {Plasmids play a crucial role in the ecology of agrobacteria. In this study, we sequenced tumor-inducing (Ti) and opine-catabolic (OC) plasmids in three Rhizobium rhizogenes (Agrobacterium biovar 2) strains isolated from the same crown gall tumor on "Colt" cherry rootstock and conducted comparative genomic analyses. Tumorigenic strains C5.7 and C6.5 carry nopaline-type Ti plasmids pTiC5.7/pTiC6.5, whereas the nonpathogenic strain Colt5.8 carries the nopaline-type OC plasmid pOC-Colt5.8. Overall, comparative genomic analysis indicated that pTiC5.7/pTiC6.5 and related Ti plasmids described before (pTiC58 and pTi-SAKURA) originate from a common ancestor, although they have diverged during evolution. On the other hand, plasmid pOC-Colt5.8 was most closely related to the well-known OC plasmid pAtK84b; however, analysis suggested that they had different evolutionary histories and seem to share a more distant common ancestor. Although the reconstruction of the evolutionary history of Ti and OC plasmids is still speculative, we hypothesized that nopaline-type Ti plasmid might originate from the nopaline-type OC plasmid. Our results suggested that OC plasmids are widespread and closely associated with crown gall tumors. Finally, we proposed a thorough scheme for classification of Ti and OC plasmids that is based on separate comparative analysis of each functional element of the plasmid studied.}, }
@article {pmid31028389, year = {2019}, author = {Tsushima, A and Gan, P and Kumakura, N and Narusaka, M and Takano, Y and Narusaka, Y and Shirasu, K}, title = {Genomic Plasticity Mediated by Transposable Elements in the Plant Pathogenic Fungus Colletotrichum higginsianum.}, journal = {Genome biology and evolution}, volume = {11}, number = {5}, pages = {1487-1500}, pmid = {31028389}, issn = {1759-6653}, mesh = {Arabidopsis ; Colletotrichum/*genetics/pathogenicity ; *DNA Transposable Elements ; Genes, Essential ; Genetic Variation ; *Genome, Fungal ; Plant Diseases ; Synteny ; Virulence ; }, abstract = {Phytopathogen genomes are under constant pressure to change, as pathogens are locked in an evolutionary arms race with their hosts, where pathogens evolve effector genes to manipulate their hosts, whereas the hosts evolve immune components to recognize the products of these genes. Colletotrichum higginsianum (Ch), a fungal pathogen with no known sexual morph, infects Brassicaceae plants including Arabidopsis thaliana. Previous studies revealed that Ch differs in its virulence toward various Arabidopsis thaliana ecotypes, indicating the existence of coevolutionary selective pressures. However, between-strain genomic variations in Ch have not been studied. Here, we sequenced and assembled the genome of a Ch strain, resulting in a highly contiguous genome assembly, which was compared with the chromosome-level genome assembly of another strain to identify genomic variations between strains. We found that the two closely related strains vary in terms of large-scale rearrangements, the existence of strain-specific regions, and effector candidate gene sets and that these variations are frequently associated with transposable elements (TEs). Ch has a compartmentalized genome consisting of gene-sparse, TE-dense regions with more effector candidate genes and gene-dense, TE-sparse regions harboring conserved genes. Additionally, analysis of the conservation patterns and syntenic regions of effector candidate genes indicated that the two strains vary in their effector candidate gene sets because of de novo evolution, horizontal gene transfer, or gene loss after divergence. Our results reveal mechanisms for generating genomic diversity in this asexual pathogen, which are important for understanding its adaption to hosts.}, }
@article {pmid31028374, year = {2019}, author = {Ellison, CK and Dalia, TN and Dalia, AB and Brun, YV}, title = {Real-time microscopy and physical perturbation of bacterial pili using maleimide-conjugated molecules.}, journal = {Nature protocols}, volume = {14}, number = {6}, pages = {1803-1819}, pmid = {31028374}, issn = {1750-2799}, support = {K22 AI118863/AI/NIAID NIH HHS/United States ; R35 GM122556/GM/NIGMS NIH HHS/United States ; R35 GM128674/GM/NIGMS NIH HHS/United States ; }, mesh = {Biotin/chemistry ; Caulobacter/chemistry/*ultrastructure ; Cysteine/chemistry ; Fimbriae, Bacterial/chemistry/*ultrastructure ; Fluorescent Dyes/*chemistry ; Maleimides/*chemistry ; Microscopy, Fluorescence/*methods ; Models, Molecular ; Optical Imaging/methods ; Staining and Labeling/methods ; Vibrio cholerae/chemistry/*ultrastructure ; }, abstract = {Bacteria use surface-exposed, proteinaceous fibers called pili for diverse behaviors, including horizontal gene transfer, surface sensing, motility, and pathogenicity. Visualization of these filamentous nanomachines and their activity in live cells has proven challenging, largely due to their small size. Here, we describe a broadly applicable method for labeling and imaging pili and other surface-exposed nanomachines in live cells. This technique uses a combination of genetics and maleimide-based click chemistry in which a cysteine substitution is made in the major pilin subunit for subsequent labeling with thiol-reactive maleimide dyes. Large maleimide-conjugated molecules can also be used to physically interfere with the dynamic activity of filamentous nanomachines. We describe parameters for selecting cysteine substitution positions, optimized labeling conditions for epifluorescence imaging of pilus fibers, and methods for impeding pilus activity. After cysteine knock-in strains have been generated, this protocol can be completed within 30 min to a few hours, depending on the species and the experiment of choice. Visualization of extracellular nanomachines such as pili using this approach can provide a more comprehensive understanding of the role played by these structures in distinct bacterial behaviors.}, }
@article {pmid31028028, year = {2019}, author = {Herzog, PL and Sützl, L and Eisenhut, B and Maresch, D and Haltrich, D and Obinger, C and Peterbauer, CK}, title = {Versatile Oxidase and Dehydrogenase Activities of Bacterial Pyranose 2-Oxidase Facilitate Redox Cycling with Manganese Peroxidase In Vitro.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {13}, pages = {}, pmid = {31028028}, issn = {1098-5336}, support = {W 1224/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Bacterial Proteins/*genetics/metabolism ; Carbohydrate Dehydrogenases/*genetics/metabolism ; Oxidation-Reduction ; Oxidoreductases/metabolism ; Peroxidases/*genetics/metabolism ; Streptomycetaceae/enzymology/*genetics/metabolism ; }, abstract = {Pyranose 2-oxidase (POx) has long been accredited a physiological role in lignin degradation, but evidence to provide insights into the biochemical mechanisms and interactions is insufficient. There are ample data in the literature on the oxidase and dehydrogenase activities of POx, yet the biological relevance of this duality could not be established conclusively. Here we present a comprehensive biochemical and phylogenetic characterization of a novel pyranose 2-oxidase from the actinomycetous bacterium Kitasatospora aureofaciens (KaPOx) as well as a possible biomolecular synergism of this enzyme with peroxidases using phenolic model substrates in vitro A phylogenetic analysis of both fungal and bacterial putative POx-encoding sequences revealed their close evolutionary relationship and supports a late horizontal gene transfer of ancestral POx sequences. We successfully expressed and characterized a novel bacterial POx gene from K. aureofaciens, one of the putative POx genes closely related to well-known fungal POx genes. Its biochemical characteristics comply with most of the classical hallmarks of known fungal pyranose 2-oxidases, i.e., reactivity with a range of different monosaccharides as electron donors as well as activity with oxygen, various quinones, and complexed metal ions as electron acceptors. Thus, KaPOx shows the pronounced duality of oxidase and dehydrogenase similar to that of fungal POx. We further performed efficient redox cycling of aromatic lignin model compounds between KaPOx and manganese peroxidase (MnP). In addition, we found a Mn(III) reduction activity in KaPOx, which, in combination with its ability to provide H2O2, implies this and potentially other POx as complementary enzymatic tools for oxidative lignin degradation by specialized peroxidases.IMPORTANCE Establishment of a mechanistic synergism between pyranose oxidase and (manganese) peroxidases represents a vital step in the course of elucidating microbial lignin degradation. Here, the comprehensive characterization of a bacterial pyranose 2-oxidase from Kitasatospora aureofaciens is of particular interest for several reasons. First, the phylogenetic analysis of putative pyranose oxidase genes reveals a widespread occurrence of highly similar enzymes in bacteria. Still, there is only a single report on a bacterial pyranose oxidase, stressing the need of closing this gap in the scientific literature. In addition, the relatively small K. aureofaciens proteome supposedly supplies a limited set of enzymatic functions to realize lignocellulosic biomass degradation. Both enzyme and organism therefore present a viable model to study the mechanisms of bacterial lignin decomposition, elucidate physiologically relevant interactions with specialized peroxidases, and potentially realize biotechnological applications.}, }
@article {pmid31028005, year = {2019}, author = {Zhao, S and Lieberman, TD and Poyet, M and Kauffman, KM and Gibbons, SM and Groussin, M and Xavier, RJ and Alm, EJ}, title = {Adaptive Evolution within Gut Microbiomes of Healthy People.}, journal = {Cell host &amp; microbe}, volume = {25}, number = {5}, pages = {656-667.e8}, pmid = {31028005}, issn = {1934-6069}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; }, mesh = {*Adaptation, Biological ; Adult ; Bacteroides fragilis/*genetics/*growth &amp; development ; Female ; *Gastrointestinal Microbiome ; Genetics, Population ; Healthy Volunteers ; Humans ; Male ; Metagenomics ; *Microbiota ; Mutation ; Selection, Genetic ; Young Adult ; }, abstract = {Natural selection shapes bacterial evolution in all environments. However, the extent to which commensal bacteria diversify and adapt within the human gut remains unclear. Here, we combine culture-based population genomics and metagenomics to investigate the within-microbiome evolution of Bacteroides fragilis. We find that intra-individual B. fragilis populations contain substantial de novo nucleotide and mobile element diversity, preserving years of within-person history. This history reveals multiple signatures of within-person adaptation, including parallel evolution in sixteen genes. Many of these genes are implicated in cell-envelope biosynthesis and polysaccharide utilization. Tracking evolutionary trajectories using near-daily metagenomic sampling, we find evidence for years-long coexistence in one subject despite adaptive dynamics. We used public metagenomes to investigate one adaptive mutation common in our cohort and found that it emerges frequently in Western, but not Chinese, microbiomes. Collectively, these results demonstrate that B. fragilis adapts within individual microbiomes, pointing to factors that promote long-term gut colonization.}, }
@article {pmid31027795, year = {2019}, author = {Aijuka, M and Buys, EM}, title = {Persistence of foodborne diarrheagenic Escherichia coli in the agricultural and food production environment: Implications for food safety and public health.}, journal = {Food microbiology}, volume = {82}, number = {}, pages = {363-370}, doi = {10.1016/j.fm.2019.03.018}, pmid = {31027795}, issn = {1095-9998}, mesh = {Adaptation, Physiological ; Bacterial Adhesion ; Biofilms/growth &amp; development ; Diarrhea/*microbiology/prevention &amp; control ; Environmental Microbiology ; Escherichia coli/genetics/growth &amp; development/*physiology ; Escherichia coli Infections/*microbiology/prevention &amp; control ; *Food Microbiology ; Foodborne Diseases/*microbiology/prevention &amp; control ; Gene Transfer, Horizontal ; Humans ; }, abstract = {Diarrheagenic Escherichia coli (DEC) is a leading cause of foodborne illness associated with intestinal disease. While known over the years that contamination of food sources occurs via the oral faecal-route, the mechanisms underlying its persistence within the open environments including the food chain remains virtually unknown. Therefore, in this mini-review we will shed light on bacterial processes such as initial attachment, biofilm formation, horizontal gene transfer and response to environmental stresses. These factors may enable persistence of DEC as well as the emergence of potentially more virulent strains within the agricultural and food production environment. Mechanistic studies in clinical microbiology and immunology have elucidated infection pathways in the human and other animal bodies leading to diagnostic and treatment solutions. Therefore, understanding DEC behaviour in the agricultural and food production environment is crucial for ensuring food safety and public health by reducing the burden of foodborne illnesses.}, }
@article {pmid31026582, year = {2019}, author = {Li, J and Rettedal, EA and van der Helm, E and Ellabaan, M and Panagiotou, G and Sommer, MOA}, title = {Antibiotic Treatment Drives the Diversification of the Human Gut Resistome.}, journal = {Genomics, proteomics &amp; bioinformatics}, volume = {17}, number = {1}, pages = {39-51}, pmid = {31026582}, issn = {2210-3244}, mesh = {Adult ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/isolation &amp; purification ; Drug Resistance, Bacterial/*genetics ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Metagenomics ; Prospective Studies ; }, abstract = {Despite the documented antibiotic-induced disruption of the gut microbiota, the impact of antibiotic intake on strain-level dynamics, evolution of resistance genes, and factors influencing resistance dissemination potential remains poorly understood. To address this gap we analyzed public metagenomic datasets from 24 antibiotic treated subjects and controls, combined with an in-depth prospective functional study with two subjects investigating the bacterial community dynamics based on cultivation-dependent and independent methods. We observed that short-term antibiotic treatment shifted and diversified the resistome composition, increased the average copy number of antibiotic resistance genes, and altered the dominant strain genotypes in an individual-specific manner. More than 30% of the resistance genes underwent strong differentiation at the single nucleotide level during antibiotic treatment. We found that the increased potential for horizontal gene transfer, due to antibiotic administration, was ∼3-fold stronger in the differentiated resistance genes than the non-differentiated ones. This study highlights how antibiotic treatment has individualized impacts on the resistome and strain level composition, and drives the adaptive evolution of the gut microbiota.}, }
@article {pmid31024929, year = {2019}, author = {Müller, AU and Weber-Ban, E}, title = {The Bacterial Proteasome at the Core of Diverse Degradation Pathways.}, journal = {Frontiers in molecular biosciences}, volume = {6}, number = {}, pages = {23}, pmid = {31024929}, issn = {2296-889X}, abstract = {Proteasomal protein degradation exists in mycobacteria and other actinobacteria, and expands their repertoire of compartmentalizing protein degradation pathways beyond the usual bacterial types. A product of horizontal gene transfer, bacterial proteasomes have evolved to support the organism's survival under challenging environmental conditions like nutrient starvation and physical or chemical stresses. Like the eukaryotic 20S proteasome, the bacterial core particle is gated and must associate with a regulator complex to form a fully active protease capable of recruiting and internalizing substrate proteins. By association with diverse regulator complexes that employ different recruitment strategies, the bacterial 20S core particle is able to act in different cellular degradation pathways. In association with the mycobacterial proteasomal ATPase Mpa, the proteasome degrades substrates post-translationally modified with prokaryotic, ubiquitin-like protein Pup in a process called pupylation. Upon interaction with the ATP-independent bacterial proteasome activator Bpa, poorly structured substrates are recruited for proteasomal degradation. A potential third degradation route might employ a Cdc48-like protein of actinobacteria (Cpa), for which interaction with the 20S core was recently demonstrated but no degradation substrates have been identified yet. The alternative interaction partners and wide range of substrate proteins suggest that the bacterial proteasome is a modular, functionally flexible and conditionally regulated degradation machine in bacteria that encounter rapidly changing and challenging conditions.}, }
@article {pmid31024760, year = {2019}, author = {Palmer, M and Venter, SN and McTaggart, AR and Coetzee, MPA and Van Wyk, S and Avontuur, JR and Beukes, CW and Fourie, G and Santana, QC and Van Der Nest, MA and Blom, J and Steenkamp, ET}, title = {The synergistic effect of concatenation in phylogenomics: the case in Pantoea.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6698}, pmid = {31024760}, issn = {2167-8359}, abstract = {With the increased availability of genome sequences for bacteria, it has become routine practice to construct genome-based phylogenies. These phylogenies have formed the basis for various taxonomic decisions, especially for resolving problematic relationships between taxa. Despite the popularity of concatenating shared genes to obtain well-supported phylogenies, various issues regarding this combined-evidence approach have been raised. These include the introduction of phylogenetic error into datasets, as well as incongruence due to organism-level evolutionary processes, particularly horizontal gene transfer and incomplete lineage sorting. Because of the huge effect that this could have on phylogenies, we evaluated the impact of phylogenetic conflict caused by organism-level evolutionary processes on the established species phylogeny for Pantoea, a member of the Enterobacterales. We explored the presence and distribution of phylogenetic conflict at the gene partition and nucleotide levels, by identifying putative inter-lineage recombination events that might have contributed to such conflict. Furthermore, we determined whether smaller, randomly constructed datasets had sufficient signal to reconstruct the current species tree hypothesis or if they would be overshadowed by phylogenetic incongruence. We found that no individual gene tree was fully congruent with the species phylogeny of Pantoea, although many of the expected nodes were supported by various individual genes across the genome. Evidence of recombination was found across all lineages within Pantoea, and provides support for organism-level evolutionary processes as a potential source of phylogenetic conflict. The phylogenetic signal from at least 70 random genes recovered robust, well-supported phylogenies for the backbone and most species relationships of Pantoea, and was unaffected by phylogenetic conflict within the dataset. Furthermore, despite providing limited resolution among taxa at the level of single gene trees, concatenated analyses of genes that were identified as having no signal resulted in a phylogeny that resembled the species phylogeny of Pantoea. This distribution of signal and noise across the genome presents the ideal situation for phylogenetic inference, as the topology from a ≥70-gene concatenated species phylogeny is not driven by single genes, and our data suggests that this finding may also hold true for smaller datasets. We thus argue that, by using a concatenation-based approach in phylogenomics, one can obtain robust phylogenies due to the synergistic effect of the combined signal obtained from multiple genes.}, }
@article {pmid31024611, year = {2019}, author = {Janwa, H and Massey, SE and Velev, J and Mishra, B}, title = {On the Origin of Biomolecular Networks.}, journal = {Frontiers in genetics}, volume = {10}, number = {}, pages = {240}, pmid = {31024611}, issn = {1664-8021}, support = {U54 CA193313/CA/NCI NIH HHS/United States ; }, abstract = {Biomolecular networks have already found great utility in characterizing complex biological systems arising from pairwise interactions amongst biomolecules. Here, we explore the important and hitherto neglected role of information asymmetry in the genesis and evolution of such pairwise biomolecular interactions. Information asymmetry between sender and receiver genes is identified as a key feature distinguishing early biochemical reactions from abiotic chemistry, and a driver of network topology as biomolecular systems become more complex. In this context, we review how graph theoretical approaches can be applied not only for a better understanding of various proximate (mechanistic) relations, but also, ultimate (evolutionary) structures encoded in such networks from among all types of variations they induce. Among many possible variations, we emphasize particularly the essential role of gene duplication in terms of signaling game theory, whereby sender and receiver gene players accrue benefit from gene duplication, leading to a preferential attachment mode of network growth. The study of the resulting dynamics suggests many mathematical/computational problems, the majority of which are intractable yet yield to efficient approximation algorithms, when studied through an algebraic graph theoretic lens. We relegate for future work the role of other possible generalizations, additionally involving horizontal gene transfer, sexual recombination, endo-symbiosis, etc., which enrich the underlying graph theory even further.}, }
@article {pmid31024592, year = {2019}, author = {Dillon, MM and Almeida, RND and Laflamme, B and Martel, A and Weir, BS and Desveaux, D and Guttman, DS}, title = {Molecular Evolution of Pseudomonas syringae Type III Secreted Effector Proteins.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {418}, pmid = {31024592}, issn = {1664-462X}, abstract = {Diverse Gram-negative pathogens like Pseudomonas syringae employ type III secreted effector (T3SE) proteins as primary virulence factors that combat host immunity and promote disease. T3SEs can also be recognized by plant hosts and activate an effector triggered immune (ETI) response that shifts the interaction back toward plant immunity. Consequently, T3SEs are pivotal in determining the virulence potential of individual P. syringae strains, and ultimately help to restrict P. syringae pathogens to a subset of potential hosts that are unable to recognize their repertoires of T3SEs. While a number of effector families are known to be present in the P. syringae species complex, one of the most persistent challenges has been documenting the complex variation in T3SE contents across a diverse collection of strains. Using the entire pan-genome of 494 P. syringae strains isolated from more than 100 hosts, we conducted a global analysis of all known and putative T3SEs. We identified a total of 14,613 putative T3SEs, 4,636 of which were unique at the amino acid level, and show that T3SE repertoires of different P. syringae strains vary dramatically, even among strains isolated from the same hosts. We also find substantial diversification within many T3SE families, and in many cases find strong signatures of positive selection. Furthermore, we identify multiple gene gain and loss events for several families, demonstrating an important role of horizontal gene transfer (HGT) in the evolution of P. syringae T3SEs. These analyses provide insight into the evolutionary history of P. syringae T3SEs as they co-evolve with the host immune system, and dramatically expand the database of P. syringae T3SEs alleles.}, }
@article {pmid31024512, year = {2019}, author = {Panzetta, ME and Luján, AL and Bastidas, RJ and Damiani, MT and Valdivia, RH and Saka, HA}, title = {Ptr/CTL0175 Is Required for the Efficient Recovery of Chlamydia trachomatis From Stress Induced by Gamma-Interferon.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {756}, pmid = {31024512}, issn = {1664-302X}, support = {S10 OD018164/OD/NIH HHS/United States ; }, abstract = {Chlamydia trachomatis is the most common sexually transmitted bacterial pathogen in humans and a frequent cause of asymptomatic, persistent infections leading to serious complications, particularly in young women. Chlamydia displays a unique obligate intracellular lifestyle involving the infectious elementary body and the replicative reticulate body. In the presence of stressors such as gamma-interferon (IFNγ) or beta-lactam antibiotics, C. trachomatis undergoes an interruption in its replication cycle and enters a viable but non-cultivable state. Upon removal of the stressors, surviving C. trachomatis resume cell division and developmental transitions. In this report, we describe a genetic screen to identify C. trachomatis mutants with defects in recovery from IFNγ- and/or penicillin-induced stress and characterized a chemically derived C. trachomatis mutant strain that exhibited a significant decrease in recovery from IFNγ- but not penicillin-induced stress. Through lateral gene transfer and targeted insertional gene inactivation we identified ptr, encoding a predicted protease, as a gene required for recovery from IFNγ-induced stress. A C. trachomatis LGV-L2 ptr-null strain displayed reduced generation of infectious progeny and impaired genome replication upon removal of IFNγ. This defect was restored by introducing a wild type copy of ptr on a plasmid, indicating that Ptr is required for a rapid growth upon removal of IFNγ. Ptr was expressed throughout the developmental cycle and localized to the inclusion lumen. Overall, our findings indicate that the putative secreted protease Ptr is required for C. trachomatis to specifically recover from IFNγ- but not penicillin-induced stress.}, }
@article {pmid31021234, year = {2019}, author = {Hwang, S and Maxwell, KL}, title = {Meet the Anti-CRISPRs: Widespread Protein Inhibitors of CRISPR-Cas Systems.}, journal = {The CRISPR journal}, volume = {2}, number = {1}, pages = {23-30}, doi = {10.1089/crispr.2018.0052}, pmid = {31021234}, issn = {2573-1602}, mesh = {Archaea/genetics/immunology/*virology ; Bacteria/genetics/immunology/*virology ; Bacteriophages/*genetics/metabolism ; CRISPR-Associated Protein 9/genetics/immunology ; *CRISPR-Cas Systems ; Clustered Regularly Interspaced Short Palindromic Repeats/immunology ; Computational Biology/methods ; DNA Transposable Elements ; Evolution, Molecular ; Gene Editing/methods ; *Genome, Viral ; Plasmids/metabolism ; Prophages/genetics/metabolism ; Pseudomonas Phages/*genetics/metabolism ; Viral Proteins/*genetics/metabolism ; }, abstract = {The constant selective pressure exerted by phages, the viruses that infect bacteria, has led to the evolution of a wide range of anti-phage defenses. One of these defense mechanisms, CRISPR-Cas, provides an adaptive immune system to battle phage infection and inhibit horizontal gene transfer by plasmids, transposons, and other mobile genetic elements. Although CRISPR-Cas systems are widespread in bacteria and archaea, they appear to have minimal long-term evolutionary effects with respect to limiting horizontal gene transfer. One factor that may contribute to this may be the presence of potent inhibitors of CRISPR-Cas systems, known as anti-CRISPR proteins. Forty unique families of anti-CRISPR proteins have been described to date. These inhibitors, which are active against both Class 1 and 2 CRISPR-Cas systems, have a wide range of mechanisms of activity. Studies of these proteins have provided important insight into the evolutionary arms race between bacteria and phages, and have contributed to the development of biotechnological tools that can be harnessed for control of CRISPR-Cas genome editing.}, }
@article {pmid31018602, year = {2019}, author = {Zeng, J and Gupta, VK and Jiang, Y and Yang, B and Gong, L and Zhu, H}, title = {Cross-Kingdom Small RNAs Among Animals, Plants and Microbes.}, journal = {Cells}, volume = {8}, number = {4}, pages = {}, pmid = {31018602}, issn = {2073-4409}, mesh = {Animals ; Bacteria/genetics ; Gene Expression Regulation/*genetics ; Gene Silencing ; Gene Transfer, Horizontal/*genetics/physiology ; Humans ; MicroRNAs/genetics/metabolism ; Plants/genetics ; RNA, Bacterial/genetics ; RNA, Plant/genetics ; RNA, Small Interfering/genetics ; RNA, Small Untranslated/*genetics/metabolism ; }, abstract = {Small RNAs (sRNAs), a class of regulatory non-coding RNAs around 20~30-nt long, including small interfering RNAs (siRNAs) and microRNAs (miRNAs), are critical regulators of gene expression. Recently, accumulating evidence indicates that sRNAs can be transferred not only within cells and tissues of individual organisms, but also across different eukaryotic species, serving as a bond connecting the animal, plant, and microbial worlds. In this review, we summarize the results from recent studies on cross-kingdom sRNA communication. We not only review the horizontal transfer of sRNAs among animals, plants and microbes, but also discuss the mechanism of RNA interference (RNAi) signal transmission via cross-kingdom sRNAs. We also compare the advantages of host-induced gene silencing (HIGS) and spray-induced gene silencing (SIGS) technology and look forward to their applicable prospects in controlling fungal diseases.}, }
@article {pmid31018106, year = {2019}, author = {Silva, JK and Marques, LM and Timenetsky, J and de Farias, ST}, title = {Ureaplasma diversum protein interaction networks: evidence of horizontal gene transfer and evolution of reduced genomes among Mollicutes.}, journal = {Canadian journal of microbiology}, volume = {65}, number = {8}, pages = {596-612}, doi = {10.1139/cjm-2018-0688}, pmid = {31018106}, issn = {1480-3275}, mesh = {Animals ; Bacterial Proteins/genetics/*metabolism ; Cattle ; Corynebacterium/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome Size ; *Genome, Bacterial ; Genomics ; Metabolic Networks and Pathways ; *Protein Interaction Maps ; Purines/metabolism ; Pyrimidines/metabolism ; Staphylococcus aureus/genetics ; Tenericutes/classification/*genetics/metabolism ; Ureaplasma/classification/*genetics/metabolism ; Virulence ; }, abstract = {Ureaplasma diversum is a member of the Mollicutes class responsible for urogenital tract infection in cattle and small ruminants. Studies indicate that the process of horizontal gene transfer, the exchange of genetic material among different species, has a crucial role in mollicute evolution, affecting the group's characteristic genomic reduction process and simplification of metabolic pathways. Using bioinformatics tools and the STRING database of known and predicted protein interactions, we constructed the protein-protein interaction network of U. diversum and compared it with the networks of other members of the Mollicutes class. We also investigated horizontal gene transfer events in subnetworks of interest involved in purine and pyrimidine metabolism and urease function, chosen because of their intrinsic importance for host colonization and virulence. We identified horizontal gene transfer events among Mollicutes and from Ureaplasma to Staphylococcus aureus and Corynebacterium, bacterial groups that colonize the urogenital niche. The overall tendency of genome reduction and simplification in the Mollicutes is echoed in their protein interaction networks, which tend to be more generalized and less selective. Our data suggest that the process was permitted (or enabled) by an increase in host dependence and the available gene repertoire in the urogenital tract shared via horizontal gene transfer.}, }
@article {pmid31016356, year = {2019}, author = {Li, J and Wang, J and Li, S and Yi, F and Xu, J and Shu, M and Shen, M and Jiao, Y and Tao, F and Zhu, C and Zhang, H and Qian, S and Zhong, W}, title = {Co-occurrence of functional modules derived from nicotine-degrading gene clusters confers additive effects in Pseudomonas sp. JY-Q.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {11}, pages = {4499-4510}, doi = {10.1007/s00253-019-09800-4}, pmid = {31016356}, issn = {1432-0614}, support = {31670115//National Natural Science Foundation of China/ ; 31800118//National Natural Science Foundation of China/ ; 2017M621965//China Postdoctoral Science Foundation/ ; }, mesh = {Adaptation, Biological ; Biotransformation ; Gene Deletion ; Gene Duplication ; Gene Transfer, Horizontal ; Metabolic Networks and Pathways/*genetics ; *Multigene Family ; Nicotine/*metabolism ; Pseudomonas/*genetics/isolation &amp; purification/*metabolism ; }, abstract = {Pseudomonas sp. JY-Q was isolated from nicotine-rich environment and could degrade and tolerate high-content nicotine. Its specific genetic architecture comprised duplicated homologous nicotine-degrading clusters for different functional modules on the whole pathway. Its adaptive and genomic properties caused our concern whether the duplicated homologous gene clusters confer additive effects on nicotine degradation and result in strain JY-Q strong capability. After deletion of representative genes from duplicated homologous gene clusters of upstream module Nic1, midstream module Spm, and downstream module Nic2, the nicotine degradation efficiency of the wild type and mutant strains were examined. As the first genes of clusters Nic1-1 and Nic1-2, nicA2 and nox are both involved in nicotine degradation, but nox exhibited more contribution to nicotine metabolism due to the higher transcriptional amount of nox than that of nicA2. Likewise, the sub-clusters spm1 and spm2 showed additive effect on nicotine metabolism. As two hpo-like genes of clusters Nic2-1 and Nic2-2, hpo1, and hpo2 also showed additive effect on the nicotine degrading, but hpo1 provided more contribution than hpo2. The third hpo-like gene in cluster NA (nicotinic acid degrading), nicX is not necessary for 2,5-dihydroxypyridine transformation when hpo1 and hpo2 exist. A variety of transposases and integrases observed around Nic1 and Nic2 cluster genes suggests that the duplicated genes could evolve from horizontal gene transfer (HGT)-related dissemination. This study provide an insight into a novel adaptability mechanism of strains in extreme environment such as high nicotine concentration, and potential novel targets to enhance strain synthesis/degradation ability for future applications.}, }
@article {pmid31014248, year = {2019}, author = {Villani, A and Proctor, RH and Kim, HS and Brown, DW and Logrieco, AF and Amatulli, MT and Moretti, A and Susca, A}, title = {Variation in secondary metabolite production potential in the Fusarium incarnatum-equiseti species complex revealed by comparative analysis of 13 genomes.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {314}, pmid = {31014248}, issn = {1471-2164}, support = {678781//Horizon 2020 Framework Programme/ ; }, mesh = {Evolution, Molecular ; Fusarium/*genetics/*metabolism ; Genes, Fungal/genetics ; Genome, Fungal/*genetics ; Genomics ; Multigene Family/genetics ; Phylogeny ; Sequence Homology, Nucleic Acid ; }, abstract = {BACKGROUND: The Fusarium incarnatum-equiseti species complex (FIESC) comprises 33 phylogenetically distinct species that have been recovered from diverse biological sources, but have been most often isolated from agricultural plants and soils. Collectively, members of FIESC can produce diverse mycotoxins. However, because the species diversity of FIESC has been recognized only recently, the potential of species to cause mycotoxin contamination of crop plants is unclear. In this study, therefore, we used comparative genomics to investigate the distribution of and variation in genes and gene clusters responsible for the synthesis of mycotoxins and other secondary metabolites (SMs) in FIESC.<br><br>RESULTS: We examined genomes of 13 members of FIESC that were selected based primarily on their phylogenetic diversity and/or occurrence on crops. The presence and absence of SM biosynthetic gene clusters varied markedly among the genomes. For example, the trichothecene mycotoxin as well as the carotenoid and fusarubin pigment clusters were present in all genomes examined, whereas the enniatin, fusarin, and zearalenone mycotoxin clusters were present in only some genomes. Some clusters exhibited discontinuous patterns of distribution in that their presence and absence was not correlated with the phylogenetic relationships of species. We also found evidence that cluster loss and horizontal gene transfer have contributed to such distribution patterns. For example, a combination of multiple phylogenetic analyses suggest that five NRPS and seven PKS genes were introduced into FIESC from other Fusarium lineages.<br><br>CONCLUSION: Our results suggest that although the portion of the genome devoted to SM biosynthesis has remained similar during the evolutionary diversification of FIESC, the ability to produce SMs could be affected by the different distribution of related functional and complete gene clusters.}, }
@article {pmid31009683, year = {2019}, author = {Kabbara, S and Bidon, B and Kilani, J and Dugé de Bernonville, T and Clastre, M and Courdavault, V and Cock, JM and Papon, N}, title = {Megaviruses: An involvement in phytohormone receptor gene transfer in brown algae?.}, journal = {Gene}, volume = {704}, number = {}, pages = {149-151}, doi = {10.1016/j.gene.2019.04.055}, pmid = {31009683}, issn = {1879-0038}, mesh = {*Cytokinins/genetics/metabolism ; *Gene Transfer, Horizontal ; *Phaeophyceae/genetics/metabolism/virology ; Phycodnaviridae/*physiology ; *Plant Proteins/genetics/metabolism ; *Receptors, Cell Surface/genetics/metabolism ; }, }
@article {pmid31004458, year = {2019}, author = {Liu, J and Zeng, Q and Wang, M and Cheng, A and Liu, M and Zhu, D and Chen, S and Jia, R and Zhao, XX and Wu, Y and Yang, Q and Zhang, S and Liu, Y and Yu, Y and Zhang, L and Chen, X}, title = {Comparative genome-scale modelling of the pathogenic Flavobacteriaceae species Riemerella anatipestifer in China.}, journal = {Environmental microbiology}, volume = {21}, number = {8}, pages = {2836-2851}, doi = {10.1111/1462-2920.14635}, pmid = {31004458}, issn = {1462-2920}, support = {CARS-42-17//China Agricultural Research System/International ; 2017YFD0500800//National Key Research and Development Program of China/International ; CARS-SVDIP//Sichuan Veterinary Medicine and Drug Innovation Group of China Agricultural Research System/International ; 2016JPT0004//Special Fund for Key Laboratory of Animal Disease and Human Health of Sichuan Province/International ; }, mesh = {Animals ; China ; Genetic Variation ; Genome, Bacterial ; Genomics ; Models, Genetic ; Multilocus Sequence Typing ; Riemerella/*genetics/pathogenicity ; Virulence ; }, abstract = {Riemerella anatipestifer (RA) is a gram-negative bacterium that has a high potential to infect waterfowl. Although more and more genomes of RA have been generated comparaed to genomic analysis of RA still remains at the level of individual species. In this study, we analysed the pan-genome of 27 RA virulent isolates to reveal the intraspecies genomic diversity from various aspects. The multi-locus sequence typing (MLST) analysis suggests that the geographic origin of R. anatipestifer is Guangdong province, China. Results of pan-genome analysis revealed an open pan-genome for all 27 species with the sizes of 2967 genes. We identified 387 genes among 555 unique genes originated by horizontal gene transfer. Further studies showed 204 strain-specific HGT genes were predicted as virulent proteins. Screening the 1113 core genes in RA through subtractive genomic approach, 70 putative vaccine targets out of 125 non-cytoplasmic proteins have been predicted. Further analysis of these non A. platyrhynchos homologous proteins predicted that 56 essential proteins as drug target with more interaction partners were involved in unique metabolic pathways of RA. In conclusion, the present study indicated the essence and the diversity of RA and also provides useful information for identification of vaccine and drugs candidates in future.}, }
@article {pmid31001492, year = {2019}, author = {Salvadori, G and Junges, R and Morrison, DA and Petersen, FC}, title = {Competence in Streptococcus pneumoniae and Close Commensal Relatives: Mechanisms and Implications.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {94}, pmid = {31001492}, issn = {2235-2988}, mesh = {*DNA Transformation Competence ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Streptococcus mitis/*genetics ; Streptococcus pneumoniae/*genetics ; *Transformation, Bacterial ; }, abstract = {The mitis group of streptococci comprises species that are common colonizers of the naso-oral-pharyngeal tract of humans. Streptococcus pneumoniae and Streptococcus mitis are close relatives and share ~60-80% of orthologous genes, but still present striking differences in pathogenic potential toward the human host. S. mitis has long been recognized as a reservoir of antibiotic resistance genes for S. pneumoniae, as well as a source for capsule polysaccharide variation, leading to resistance and vaccine escape. Both species share the ability to become naturally competent, and in this context, competence-associated killing mechanisms such as fratricide are thought to play an important role in interspecies gene exchange. Here, we explore the general mechanism of natural genetic transformation in the two species and touch upon the fundamental clinical and evolutionary implications of sharing similar competence, fratricide mechanisms, and a large fraction of their genomic DNA.}, }
@article {pmid31000782, year = {2019}, author = {Ramo-Fernández, L and Boeck, C and Koenig, AM and Schury, K and Binder, EB and Gündel, H and Fegert, JM and Karabatsiakis, A and Kolassa, IT}, title = {The effects of childhood maltreatment on epigenetic regulation of stress-response associated genes: an intergenerational approach.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {983}, pmid = {31000782}, issn = {2045-2322}, mesh = {Adult ; Adverse Childhood Experiences ; Cells, Cultured ; Child Abuse ; DNA Methylation ; Epigenesis, Genetic ; Female ; Gene Transfer, Horizontal ; Gene-Environment Interaction ; *Genotype ; Humans ; Immunity, Cellular ; Infant, Newborn ; Male ; Mother-Child Relations ; Mothers ; Polymorphism, Single Nucleotide ; Receptors, Corticotropin-Releasing Hormone/*genetics ; Receptors, Glucocorticoid/*genetics ; Stress, Psychological/*genetics ; Tacrolimus Binding Proteins/*genetics ; CRF Receptor, Type 1 ; }, abstract = {While biological alterations associated with childhood maltreatment (CM) have been found in affected individuals, it remains unknown to what degree these alterations are biologically transmitted to the next generation. We investigated intergenerational effects of maternal CM on DNA methylation and gene expression in N = 113 mother-infant dyads shortly after parturition, additionally accounting for the role of the FKBP5 rs1360780 genotype. Using mass array spectrometry, we assessed the DNA methylation of selected stress-response-associated genes (FK506 binding protein 51 [FKBP5], glucocorticoid receptor [NR3C1], corticotropin-releasing hormone receptor 1 [CRHR1]) in isolated immune cells from maternal blood and neonatal umbilical cord blood. In mothers, CM was associated with decreased levels of DNA methylation of FKBP5 and CRHR1 and increased NR3C1 methylation, but not with changes in gene expression profiles. Rs1360780 moderated the FKBP5 epigenetic CM-associated regulation profiles in a gene × environment interaction. In newborns, we found no evidence for any intergenerational transmission of CM-related methylation profiles for any of the investigated epigenetic sites. These findings support the hypothesis of a long-lasting impact of CM on the biological epigenetic regulation of stress-response mediators and suggest for the first time that these specific epigenetic patterns might not be directly transmitted to the next generation.}, }
@article {pmid30997667, year = {2019}, author = {Sandoval-Vargas, JM and Jiménez-Clemente, LA and Macedo-Osorio, KS and Oliver-Salvador, MC and Fernández-Linares, LC and Durán-Figueroa, NV and Badillo-Corona, JA}, title = {Use of the ptxD gene as a portable selectable marker for chloroplast transformation in Chlamydomonas reinhardtii.}, journal = {Molecular biotechnology}, volume = {61}, number = {6}, pages = {461-468}, pmid = {30997667}, issn = {1559-0305}, mesh = {Algal Proteins/genetics/metabolism ; Bacterial Proteins/*genetics/metabolism ; Chlamydomonas reinhardtii/*genetics/metabolism ; Chloroplasts/*genetics/metabolism ; Genetic Engineering/methods ; Genetic Markers ; Genetic Vectors/chemistry/metabolism ; NADH, NADPH Oxidoreductases/*genetics/metabolism ; Phosphites/*metabolism/pharmacology ; Phosphorus/*metabolism ; Pseudomonas stutzeri/chemistry/genetics ; Selection, Genetic ; Transformation, Genetic ; }, abstract = {Synthetic biology and genetic engineering in algae offer an unprecedented opportunity to develop species with traits that can help solve the problems associated with food and energy supply in the 21st century. In the green alga Chlamydomonas reinhardtii, foreign genes can be expressed from the chloroplast genome for molecular farming and metabolic engineering to obtain commodities and high-value molecules. To introduce these genes, selectable markers, which rely mostly on the use of antibiotics, are needed. This has risen social concern associated with the potential risk of horizontal gene transfer across life kingdoms, which has led to a quest for antibiotic-free selectable markers. Phosphorus (P) is a scarce nutrient element that most organisms can only assimilate in its most oxidized form as phosphate (Pi); however, some organisms are able to oxidize phosphite (Phi) to Pi prior to incorporation into the central metabolism of P. As an alternative to the use of the two positive selectable makers already available for chloroplast transformation in C. reinhardtii, the aadA and the aphA-6 genes, that require the use of antibiotics, we investigated if a phosphite-based selection method could be used for the direct recovery of chloroplast transformed lines in this alga. Here we show that following bombardment with a vector carrying the ptxD gene from Pseudomonas stutzeri WM88, only cells that integrate and express the gene proliferate and form colonies using Phi as the sole P source. Our results demonstrate that a selectable marker based on the assimilation of Phi can be used for chloroplasts transformation in a biotechnologically relevant organism. The portable selectable marker we have developed is, in more than 18 years, the latest addition to the markers available for selection of chloroplast transformed cells in C. reinhardtii. The ptxD gene will contribute to the repertoire of tools available for synthetic biology and genetic engineering in the chloroplast of C. reinhardtii.}, }
@article {pmid30997539, year = {2019}, author = {Cheng, M and Yan, X and He, J and Qiu, J and Chen, Q}, title = {Comparative genome analysis reveals the evolution of chloroacetanilide herbicide mineralization in Sphingomonas wittichii DC-6.}, journal = {Archives of microbiology}, volume = {201}, number = {7}, pages = {907-918}, doi = {10.1007/s00203-019-01660-w}, pmid = {30997539}, issn = {1432-072X}, support = {KJQN201940//Fundamental Research Funds for the Central Universities/ ; 31600080//National Natural Science Foundation of China/ ; 31800095//National Natural Science Foundation of China/ ; BK20180541//Natural Science Foundation of Jiangsu Province/ ; }, mesh = {Acetamides/*metabolism ; Base Sequence ; Biodegradation, Environmental ; Biological Evolution ; DNA, Ribosomal/genetics ; *Genome, Bacterial ; Phylogeny ; Sphingomonadaceae/classification ; Sphingomonas/*genetics/*metabolism ; }, abstract = {The environmental fate of the extensively used chloroacetanilide herbicides (CH) has been a cause of increasing concern in the past decade because of their carcinogenic properties. Although microbes play important roles in CH degradation, Sphingomonas wittichii DC-6 was the first reported CH-mineralizing bacterium. In this study, the complete genome of strain DC-6 was sequenced and comparative genomic analysis was performed using strain DC-6 and other three partial CH-degrading bacteria, Sphingobium quisquiliarum DC-2, Sphingobium baderi DE-13, and Sphingobium sp. MEA3-1. 16S rDNA phylogenetic analysis indicated that strain DC-2, MEA3-1, and DE-13 are closely related and DC-6 has relatively distant genetic relationship with the other three strains. The identified CH degradation genes responsible for the upstream and downstream pathway, including cndA, cmeH, meaXY, and meaAB, were all located in conserved DNA fragments (or genetic islands) in the vicinity of mobile element proteins. Protein BLAST in the NCBI database showed that cndA and cmeH were present in the genomes of other sequenced strains isolated from various habitats; however, the gene compositions in these host strains were completely different from those of other sphingomonads, and codon usage of genes for upstream pathway were also different from that of downstream pathway. These results showed that the upstream and downstream pathways of CH degradation in strain DC-6 have evolved by horizontal gene transfer and gene combination. In addition, the genes of the ring-cleavage pathway were not conserved and may have evolved directly from bacterial degradation of hydroxyquinol. The present study provides insights into the evolutionary strategy and microbial catabolic pathway of CH mineralization.}, }
@article {pmid30997305, year = {2019}, author = {Kanchan, S and Sharma, P and Chowdhury, S}, title = {Evolution of endonuclease IV protein family: an in silico analysis.}, journal = {3 Biotech}, volume = {9}, number = {5}, pages = {168}, pmid = {30997305}, issn = {2190-572X}, abstract = {DNA repair is one of the key cellular events which balances between evolvability and integrity of the genome. Endonuclease IV enzymes are class II AP endonucleases under base excision repair pathway which act on abasic site and break the phosphodiester bond at the 5' side. The role and activity of endonuclease IV proteins vary among different organisms; even it is absent in higher eukaryotes. The evolution of this protein family was studied by analyzing all homologs of the endonuclease IV protein family through different in silico techniques including phylogenetic tree generation and model building. The sequence analysis revealed four consensus sequence motifs within the AP2EC domain which are functionally important and conserved throughout the evolution process. It was also observed that the species and endonuclease IV gene evolution shape up differently in most of the organisms. Presence of the mitochondria-targeted signal peptides in fungal species Saccharomyces and Coccidioides suggest a possible endosymbiotic transfer of endonuclease IV genes to lower eukaryotes. Evolutionary changes among various clades in the protein-based phylogenetic tree have been investigated by comparison of homology models which suggests the conservation of overall fold of endonuclease IV proteins except for few alterations in loop orientation in few clades.}, }
@article {pmid30995570, year = {2019}, author = {Zhu, L and Zhao, Y and Yang, K and Chen, J and Zhou, H and Chen, X and Liu, Q and Wei, Z}, title = {Host bacterial community of MGEs determines the risk of horizontal gene transfer during composting of different animal manures.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {250}, number = {}, pages = {166-174}, doi = {10.1016/j.envpol.2019.04.037}, pmid = {30995570}, issn = {1873-6424}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/*genetics ; Cattle ; Chickens ; Composting ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/genetics ; Interspersed Repetitive Sequences/*genetics ; Manure/*microbiology ; }, abstract = {Mobile genetic elements (MGEs) play critical roles in transferring antibiotic resistance genes (ARGs) among different microorganisms in the environment. This study aimed to explore the fate of MGEs during chicken manure (CM) and bovine manure (BM) composting to assess horizontal transfer risks of ARGs. The results showed that the removal efficiency of MGEs during CM composting was significantly higher than that during BM composting, because the potential host bacteria of MGEs were eliminated largely during CM composting. Meanwhile, these potential host bacterial communities are significantly influenced by pH, NH4[+], NO3[-] and total N, which can be used to regulate host bacterial communities to remove MGEs during composting. Projection pursuit regression further confirmed that composting can effectively reduce the horizontal transfer risk of ARGs, especially for CM composting. These results identified the critical roles of host bacterial communities in MGEs removal during composting of different animal manures.}, }
@article {pmid30995539, year = {2019}, author = {Lejars, M and Kobayashi, A and Hajnsdorf, E}, title = {Physiological roles of antisense RNAs in prokaryotes.}, journal = {Biochimie}, volume = {164}, number = {}, pages = {3-16}, doi = {10.1016/j.biochi.2019.04.015}, pmid = {30995539}, issn = {1638-6183}, mesh = {*Archaea/genetics/pathogenicity/physiology ; *Bacteria/genetics/pathogenicity ; Bacterial Physiological Phenomena/*genetics ; Gene Expression Regulation, Archaeal ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal/*genetics ; *RNA, Antisense/genetics/physiology ; RNA, Archaeal/genetics/physiology ; RNA, Bacterial/genetics/physiology ; Virulence/*genetics ; }, abstract = {Prokaryotes encounter constant and often brutal modifications to their environment. In order to survive, they need to maintain fitness, which includes adapting their protein expression patterns. Many factors control gene expression but this review focuses on just one, namely antisense RNAs (asRNAs), a class of non-coding RNAs (ncRNAs) characterized by their location in cis and their perfect complementarity with their targets. asRNAs were considered for a long time to be trivial and only to be found on mobile genetic elements. However, recent advances in methodology have revealed that their abundance and potential activities have been underestimated. This review aims to illustrate the role of asRNA in various physiologically crucial functions in both archaea and bacteria, which can be regrouped in three categories: cell maintenance, horizontal gene transfer and virulence. A literature survey of asRNAs demonstrates the difficulties to characterize and assign a role to asRNAs. With the aim of facilitating this task, we describe recent technological advances that could be of interest to identify new asRNAs and to discover their function.}, }
@article {pmid30994094, year = {2019}, author = {Bartley, PS and Domitrovic, TN and Moretto, VT and Santos, CS and Ponce-Terashima, R and Reis, MG and Barbosa, LM and Blanton, RE and Bonomo, RA and Perez, F}, title = {Antibiotic Resistance in Enterobacteriaceae from Surface Waters in Urban Brazil Highlights the Risks of Poor Sanitation.}, journal = {The American journal of tropical medicine and hygiene}, volume = {100}, number = {6}, pages = {1369-1377}, pmid = {30994094}, issn = {1476-1645}, support = {R01 AI063517/AI/NIAID NIH HHS/United States ; R01 AI100560/AI/NIAID NIH HHS/United States ; R01 AI072219/AI/NIAID NIH HHS/United States ; R01 AI121330/AI/NIAID NIH HHS/United States ; R21 AI114508/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics/metabolism ; Brazil ; Drug Resistance, Multiple, Bacterial ; Enterobacteriaceae/*drug effects/genetics ; Gene Expression Regulation, Bacterial ; Humans ; Lakes ; Sanitation ; Urban Health ; *Water Microbiology ; }, abstract = {Surface waters are an unappreciated reservoir of antimicrobial resistance (AMR). Poor sanitation brings different species of environmental bacteria into contact, facilitating horizontal gene transfer. To investigate the role of surface waters as potential reservoirs of AMR, we studied the point prevalence of fecal contamination, AMR genes, and Enterobacteriaceae in an urban lake and rural river system in Northeast Brazil in comparison with a lake and sewer system in Northeast Ohio in the United States. Surface water samples were examined for evidence of human fecal contamination using microbial source tracking and screened for plasmid-mediated fluoroquinolone resistance and carbapenemase genes. Enterobacteriaceae were detected using selective agar followed by antimicrobial susceptibility testing and detection of AMR genes by microarray, and classified by repetitive sequence-based polymerase chain reaction and multilocus sequence typing. Concentrations of human fecal bacteria in the Brazilian urban lake and sewage in Northeast Ohio were similarly high. Filtered water samples from the Brazilian urban lake, however, showed the presence of bla OXA-48, bla KPC, bla VIM-2, qnrS, and aac(6')-lb-cr, whereas only bla VIM-2 was identified in raw sewage from Northeast Ohio. From the Brazilian urban lake, 85% of the Enterobacteriaceae (n = 40) cultured were resistant to at least one clinically important antibiotic, including ST131 Escherichia coli harboring the extended-spectrum beta-lactamase CTX-M. Although two isolates demonstrated polymyxin resistance, mcr-1/2 was not detected. Our findings indicate that surface waters in an urban Brazilian site can serve as an environmental reservoir of AMR and that improving wastewater treatment and sanitation generally may ameliorate AMR dissemination.}, }
@article {pmid30993329, year = {2019}, author = {Zheng, Z and Ye, L and Chan, EW and Chen, S}, title = {Identification and characterization of a conjugative blaVIM-1-bearing plasmid in Vibrio alginolyticus of food origin.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {74}, number = {7}, pages = {1842-1847}, doi = {10.1093/jac/dkz140}, pmid = {30993329}, issn = {1460-2091}, mesh = {Blotting, Southern ; Cephalosporin Resistance ; *Conjugation, Genetic ; Electrophoresis, Gel, Pulsed-Field ; *Food Microbiology ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Plasmids/*analysis ; Sequence Analysis, DNA ; Vibrio alginolyticus/drug effects/*enzymology/genetics/*isolation &amp; purification ; beta-Lactamases/*analysis/genetics ; }, abstract = {OBJECTIVES: To investigate the genetic features of the blaVIM-1 gene first detected in a cephalosporin-resistant Vibrio alginolyticus isolate, Vb1978.<br><br>METHODS: The MICs of V. alginolyticus strain Vb1978 were determined, and the &#x3b2;-lactamases produced were screened and analysed using conjugation, S1-PFGE and Southern blotting. The complete sequence of the blaVIM-1-encoding plasmid was also obtained using the Illumina and MinION sequencing platforms.<br><br>RESULTS: V. alginolyticus strain Vb1978, isolated from a retail shrimp sample, was resistant to cephalosporins and exhibited reduced susceptibility to carbapenems. A novel blaVIM-1-carrying conjugative plasmid, designated pVb1978, was identified in this strain. Plasmid pVb1978 had 50&#x2009;001&#x2009;bp and comprised 59 predicted coding sequences (CDSs). The plasmid backbone of pVb1978 was homologous to those of IncP-type plasmids, while its replication region was structurally similar to non-IncP plasmids. The blaVIM-1 gene was found to be carried by the class 1 integron In70 and associated with a defective Tn402-like transposon.<br><br>CONCLUSIONS: A novel blaVIM-1-carrying conjugative plasmid, pVb1978, was reported for the first time in V. alginolyticus, which warrants further investigation in view of its potential pathogenicity towards humans and widespread occurrence in the environment.}, }
@article {pmid30993325, year = {2019}, author = {Maertens, H and De Reu, K and Meyer, E and Van Weyenberg, S and Dewulf, J and Van Coillie, E}, title = {Exposure of ciprofloxacin-resistant Escherichia coli broiler isolates to subinhibitory concentrations of a quaternary ammonium compound does not increase antibiotic resistance gene transfer.}, journal = {Poultry science}, volume = {98}, number = {7}, pages = {2972-2976}, doi = {10.3382/ps/pez185}, pmid = {30993325}, issn = {1525-3171}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Benzalkonium Compounds/*pharmacology ; Chickens/microbiology ; Ciprofloxacin/pharmacology ; Disinfectants/*pharmacology ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/*drug effects/*genetics ; *Gene Transfer, Horizontal ; }, abstract = {Resistance to antibiotics threatens to become a worldwide health problem. An important attributing phenomenon in this context is that pathogens can acquire antibiotic resistance genes through conjugative transfer of plasmids. To prevent bacterial infections in agricultural settings, the use of veterinary hygiene products, such as disinfectants, has gained popularity and questions have been raised about their contribution to such spreading of antibiotic resistance. Therefore, this study investigated the effect of subinhibitory concentrations of benzalkoniumchloride (BKC), a quaternary ammonium compound (QAC), on the conjugative transfer of antibiotic resistance genes. Five Escherichia coli field strains originating from broiler chickens and with known transferable plasmid-mediated ciprofloxacin resistance were exposed to subinhibitory BKC concentrations: 1/3, 1/10 and 1/30 of the minimum bactericidal concentration. Antibiotic resistance transfer was assessed by liquid mating for 4 h at 25°C using E. coli K12 MG1655 as recipient strain. The transfer ratio was calculated as the number of transconjugants divided by the number of recipients. Without exposure to BKC, the strains showed a ciprofloxacin resistance transfer ratio ranging from 10-4 to 10-7. No significant effect of exposure to subinhibitory concentrations of BKC was observed on this transfer ratio.}, }
@article {pmid30993041, year = {2019}, author = {Loderer, C and Holmfeldt, K and Lundin, D}, title = {Non-host class II ribonucleotide reductase in Thermus viruses: sequence adaptation and host interaction.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6700}, pmid = {30993041}, issn = {2167-8359}, abstract = {Ribonucleotide reductases (RNR) are essential enzymes for all known life forms. Their current taxonomic distribution suggests extensive horizontal gene transfer e.g., by processes involving viruses. To improve our understanding of the underlying processes, we characterized a monomeric class II RNR (NrdJm) enzyme from a Thermus virus, a subclass not present in any sequenced Thermus spp. genome. Phylogenetic analysis revealed a distant origin of the nrdJm gene with the most closely related sequences found in mesophiles or moderate thermophiles from the Firmicutes phylum. GC-content, codon usage and the ratio of coding to non-coding substitutions (dN/dS) suggest extensive adaptation of the gene in the virus in terms of nucleotide composition and amino acid sequence. The NrdJm enzyme is a monomeric B12-dependent RNR with nucleoside triphosphate specificity. It exhibits a temperature optimum at 60-70 °C, which is in the range of the growth optimum of Thermus spp. Experiments in combination with the Thermus thermophilus thioredoxin system show that the enzyme is able to retrieve electrons from the host NADPH pool via host thioredoxin and thioredoxin reductases. This is different from other characterized viral RNRs such as T4 phage RNR, where a viral thioredoxin is present. We hence show that the monomeric class II RNR, present in Thermus viruses, was likely transferred from an organism phylogenetically distant from the one they were isolated from, and adapted to the new host in genetic signature and amino acids sequence.}, }
@article {pmid30991952, year = {2019}, author = {Dhaygude, K and Nair, A and Johansson, H and Wurm, Y and Sundström, L}, title = {The first draft genomes of the ant Formica exsecta, and its Wolbachia endosymbiont reveal extensive gene transfer from endosymbiont to host.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {301}, pmid = {30991952}, issn = {1471-2164}, support = {252411 and 284666 (Centre of Excellence in Biological Interactions)//Academy of Finland/ ; BB/K004204/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; NE/L00626X/1//Natural Environment Research Council/ ; }, mesh = {Animals ; Ants/*genetics/*microbiology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Insect/genetics ; *Genomics ; Symbiosis/*genetics ; Wolbachia/*genetics/*physiology ; }, abstract = {BACKGROUND: Adapting to changes in the environment is the foundation of species survival, and is usually thought to be a gradual process. However, transposable elements (TEs), epigenetic modifications, and/or genetic material acquired from other organisms by means of horizontal gene transfer (HGTs), can also lead to novel adaptive traits. Social insects form dense societies, which attract and maintain extra- and intracellular accessory inhabitants, which may facilitate gene transfer between species. The wood ant Formica exsecta (Formicidae; Hymenoptera), is a common ant species throughout the Palearctic region. The species is a well-established model for studies of ecological characteristics and evolutionary conflict.<br><br>RESULTS: In this study, we sequenced and assembled draft genomes for F. exsecta and its endosymbiont Wolbachia. The F. exsecta draft genome is 277.7&#x2009;Mb long; we identify 13,767 protein coding genes, for which we provide gene ontology and protein domain annotations. This is also the first report of a Wolbachia genome from ants, and provides insights into the phylogenetic position of this endosymbiont. We also identified multiple horizontal gene transfer events (HGTs) from Wolbachia to F. exsecta. Some of these HGTs have also occurred in parallel in multiple other insect genomes, highlighting the extent of HGTs in eukaryotes.<br><br>CONCLUSION: We present the first draft genome of ant F. exsecta, and its endosymbiont Wolbachia (wFex), and show considerable rates of gene transfer from the symbiont to the host. We expect that especially the F. exsecta genome will be valuable resource in further exploration of the molecular basis of the evolution of social organization.}, }
@article {pmid30991178, year = {2019}, author = {Zhang, Z and Li, B and Li, N and Sardar, MF and Song, T and Zhu, C and Lv, X and Li, H}, title = {Effects of UV disinfection on phenotypes and genotypes of antibiotic-resistant bacteria in secondary effluent from a municipal wastewater treatment plant.}, journal = {Water research}, volume = {157}, number = {}, pages = {546-554}, doi = {10.1016/j.watres.2019.03.079}, pmid = {30991178}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents ; Bacteria ; *Disinfection ; Genotype ; Phenotype ; *Wastewater ; }, abstract = {To elucidate the effects of UV disinfection on antibiotic resistance in biologically-treated wastewater, we investigated the antibiotic resistance profiles, species of cultivable heterotrophic bacteria, and antibiotic-resistance genes (ARGs) in antibiotic-resistant bacteria before and after treatment. UV disinfection greatly changed the bacterial community structure and the antibiotic resistance in wastewater. The antibiotic resistance in wastewater samples was strongly associated with the bacterial community. The proportions of Gram-positive bacteria gradually increased with increasing UV fluence. The proportions of bacteria resistant to cephalexin, penicillin, and vancomycin all greatly decreased after UV treatment in both sampling events (July 2018 and January 2019), and those for bacteria resistant to ofloxacin, ciprofloxacin, and sulfadiazine increased, resulting from the alternative antibiotic resistance profiles among different genera. UV disinfection induced the selection of multi-antibiotic resistant (MAR) bacteria. For example, the MAR indices of Aeromonas, the dominant genus during the treatments, were significantly increased after UV irradiation (P < 0.05). The MAR index was also markedly increased (P < 0.05) at a fluence of 5 mJ/cm[2] in both events. In UV10 treatment, the bacterial community structure was greatly changed. The genera with relatively low MAR indices replaced that with high MAR indices, and became the dominant genera. As a result, the MAR indices of treated samples showed a decreased trend after 10 mJ/cm[2] UV irradiation. The detection frequencies of ARGs located on the chromosome varied mainly due to the evolution of the microbial community. The occurrence of ARGs (tetA, tetC, tetM, tetW, tetX, and sul1) located on plasmid DNA decreased after UV disinfection, and the average detection frequencies of tet and sul genes decreased by 15% and 6%, respectively (P < 0.05). Generally speaking, the effect of UV disinfection on the enrichment of antibiotic resistance is limited in this study, and horizontal gene transfer via the plasmids in surviving bacteria might be impaired due to the decreased abundance of ARGs on the plasmids.}, }
@article {pmid30990401, year = {2019}, author = {Kaushik, M and Kumar, S and Kapoor, RK and Gulati, P}, title = {Integrons and antibiotic resistance genes in water-borne pathogens: threat detection and risk assessment.}, journal = {Journal of medical microbiology}, volume = {68}, number = {5}, pages = {679-692}, doi = {10.1099/jmm.0.000972}, pmid = {30990401}, issn = {1473-5644}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/pathogenicity ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal ; Humans ; Integrons/*genetics ; Microbial Sensitivity Tests ; Risk Assessment ; *Water Microbiology ; Waterborne Diseases/*microbiology ; }, abstract = {Antibiotic-resistant genes (ARGs) are regarded as emerging environmental pollutants and pose a serious health risk to the human population. Integrons are genetic elements that are involved in the spread of ARGs amongst bacterial species. They also act as reservoirs of these resistance traits, further contributing to the development of multi-drug resistance in several water-borne pathogens. Due to inter- and intra-species transfer, integrons are now commonly reported in important water-borne pathogens such as Vibrio, Campylobacter, Salmonella, Shigella, Escherichia coli and other opportunistic pathogens. These pathogens exhibit immense diversity in their resistance gene cassettes. The evolution of multiple novel and complex gene cassettes in integrons further suggests the selection and horizontal transfer of ARGs in multi-drug resistant bacteria. Thus, the detection and characterization of these integrons in water-borne pathogens, especially in epidemic and pandemic strains, is of the utmost importance. It will provide a framework in which health authorities can conduct improved surveillance of antibiotic resistance in our natural water bodies. Such a study will also be helpful in developing better strategies for the containment and cure of infections caused by these bacteria.}, }
@article {pmid30989200, year = {2019}, author = {Ye, L and Chan, EWC and Chen, S}, title = {Selective and suppressive effects of antibiotics on donor and recipient bacterial strains in gut microbiota determine transmission efficiency of blaNDM-1-bearing plasmids.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {74}, number = {7}, pages = {1867-1875}, doi = {10.1093/jac/dkz137}, pmid = {30989200}, issn = {1460-2091}, mesh = {Animals ; Anti-Bacterial Agents/*administration &amp; dosage ; Escherichia coli/*drug effects/genetics ; Gastrointestinal Microbiome/*drug effects ; Gene Transfer, Horizontal/*drug effects ; Klebsiella pneumoniae/*drug effects/genetics ; Male ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Rats, Sprague-Dawley ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: To test whether antibiotics of different functional categories exhibit differential potential in promoting transmission of MDR-encoding plasmids among members of the gut microbiome.<br><br>METHODS: Rats inoculated with blaNDM-1-bearing Klebsiella pneumoniae were subjected to treatment with different types of antibiotics. The structural changes in the gastrointestinal (GI) tract microbiome were determined by 16S rRNA sequencing and analysis. In addition, the efficiency of transmission of blaNDM-1-bearing plasmids to different subtypes of GI tract Escherichia coli was also confirmed in vitro.<br><br>RESULTS: We showed that drugs that are commonly used to treat Gram-negative bacterial infections, such as ampicillin and amoxicillin, could enrich both carbapenem-resistant Enterobacteriaceae (CRE) and antibiotic-susceptible E. coli in the GI tract, thereby promoting transmission of the blaNDM-1-bearing plasmid in the gut microbiome. In contrast, meropenem was found to minimize the population of CRE in the gut microbiome, hence treatment with this drug exhibited drastically lower potential to promote transmission of the blaNDM-1-bearing plasmid to the recipient strains. We further showed that an increased population size of Proteobacteria due to a suppressive effect on Firmicutes is a key factor in enhancing the efficiency of transmission of the blaNDM-1-bearing plasmid and hence dissemination of carbapenem-resistant strains.<br><br>CONCLUSIONS: This study depicted for the first time the effect of different antibiotics on the structure of the rat GI tract microbiome, which in turn determined the pattern and rate of transmission of the blaNDM-1-bearing plasmid. Such findings can help establish new guidelines for prudent antibiotic usage to minimize the chance of dissemination of mobile resistance elements among members of the GI tract microbiome.}, }
@article {pmid30989199, year = {2019}, author = {Ambrose, SJ and Hall, RM}, title = {Novel trimethoprim resistance gene, dfrA35, in IncC plasmids from Australia.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {74}, number = {7}, pages = {1863-1866}, doi = {10.1093/jac/dkz148}, pmid = {30989199}, issn = {1460-2091}, mesh = {Australia ; Conjugation, Genetic ; Cross Infection/*microbiology ; Escherichia coli/*enzymology/genetics/*isolation &amp; purification ; Escherichia coli Infections/*microbiology ; Gene Transfer, Horizontal ; Health Facilities ; Humans ; Plasmids/*analysis/classification ; Tetrahydrofolate Dehydrogenase/*genetics ; *Trimethoprim Resistance ; }, abstract = {BACKGROUND: In Gram-negative bacteria, over 30 different genes are known to encode a trimethoprim-insensitive dihydrofolate reductase that confers resistance to trimethoprim.<br><br>OBJECTIVES: To determine whether a gene encoding a putative dihydrofolate reductase found in type 2 IncC plasmids isolated between 2002 and 2013 in healthcare facilities in Melbourne, Australia, confers trimethoprim resistance.<br><br>METHODS: Conjugation was used to transfer plasmids into a laboratory Escherichia coli. A PCR-amplified fragment was cloned into pUC19 using Gibson Assembly and transformed into E. coli. The level of resistance to trimethoprim was determined using broth microdilution. MEGA (7.0.26) and Geneious Prime (7.0.9) were used to examine the relationship to known Dfr proteins.<br><br>RESULTS: The conjugative IncC plasmid pEc158 from a 2002 Melbourne clinical E. coli isolate was shown to transfer trimethoprim resistance. The putative DfrA protein encoded by a dfrA gene in pEc158 shares <40% amino acid identity with any previously identified DfrA protein. This gene was cloned and found to confer trimethoprim resistance. The gene and protein were named dfrA35/DfrA35. In pEc158 the dfrA35 gene is located near the ori end of a partial copy of the CR1 element, within a complex resistance island. It is found in the same location in further closely-related type 2 IncC plasmids from Klebsiella pneumoniae (Melbourne, 2013), which were not transfer proficient.<br><br>CONCLUSIONS: Resistance determinants continue to be found and will be missed using website-associated databases to infer phenotypes from genome sequences rather than direct phenotypic testing.}, }
@article {pmid30989197, year = {2019}, author = {Rooney, CM and Sheppard, AE and Clark, E and Davies, K and Hubbard, ATM and Sebra, R and Crook, DW and Walker, AS and Wilcox, MH and Chilton, CH}, title = {Dissemination of multiple carbapenem resistance genes in an in vitro gut model simulating the human colon.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {74}, number = {7}, pages = {1876-1883}, doi = {10.1093/jac/dkz106}, pmid = {30989197}, issn = {1460-2091}, mesh = {Bacterial Proteins/*genetics ; Carbapenem-Resistant Enterobacteriaceae/*enzymology/*genetics/growth &amp; development ; Colon/*microbiology ; *Gastrointestinal Microbiome ; *Gene Transfer, Horizontal ; Healthy Volunteers ; Humans ; *Microbiota ; Models, Biological ; beta-Lactamases/*genetics ; }, abstract = {BACKGROUND: Carbapenemase-producing Enterobacteriaceae (CPE) pose a major global health risk. Mobile genetic elements account for much of the increasing CPE burden.<br><br>OBJECTIVES: To investigate CPE colonization and the impact of antibiotic exposure on subsequent resistance gene dissemination within the gut microbiota using a model to simulate the human colon.<br><br>METHODS: Gut models seeded with CPE-negative human faeces [screened with BioM&#xe9;rieux chromID&#xae; CARBA-SMART (Carba-Smart), Cepheid Xpert&#xae; Carba-R assay (XCR)] were inoculated with distinct carbapenemase-producing Klebsiella pneumoniae strains (KPC, NDM) and challenged with imipenem or piperacillin/tazobactam then meropenem. Resistant populations were enumerated daily on selective agars (Carba-Smart); CPE genes were confirmed by PCR (XCR, Check-Direct CPE Screen for BD MAX&#x2122;). CPE gene dissemination was tracked using PacBio long-read sequencing.<br><br>RESULTS: CPE populations increased during inoculation, plateauing at &#x223c;105&#x2009;log10&#x2009;cfu/mL in both models and persisting throughout the experiments (>65&#x2009;days), with no evidence of CPE 'washout'. After antibiotic administration, there was evidence of interspecies plasmid transfer of blaKPC-2 (111742&#x2009;bp IncFII/IncR plasmid, 99% identity to pKpQIL-D2) and blaNDM-1 (&#x223c;170&#x2009;kb IncFIB/IncFII plasmid), and CPE populations rose from <0.01% to >45% of the total lactose-fermenting populations in the KPC model. Isolation of a blaNDM-1K. pneumoniae with one chromosomal single-nucleotide variant compared with the inoculated strain indicated clonal expansion within the model. Antibiotic administration exposed a previously undetected K. pneumoniae encoding blaOXA-232 (KPC model).<br><br>CONCLUSIONS: CPE exposure can lead to colonization, clonal expansion and resistance gene transfer within intact human colonic microbiota. Furthermore, under antibiotic selective pressure, new resistant populations emerge, emphasizing the need to control exposure to antimicrobials.}, }
@article {pmid30989181, year = {2019}, author = {Yan, S and Li, M and Luque-Sastre, L and Wang, W and Hu, Y and Peng, Z and Dong, Y and Gan, X and Nguyen, S and Anes, J and Bai, Y and Xu, J and Fanning, S and Li, F}, title = {Susceptibility (re)-testing of a large collection of Listeria monocytogenes from foods in China from 2012 to 2015 and WGS characterization of resistant isolates.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {74}, number = {7}, pages = {1786-1794}, doi = {10.1093/jac/dkz126}, pmid = {30989181}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/pharmacology ; China ; *Drug Resistance, Bacterial ; *Food Microbiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genotype ; Listeria monocytogenes/*classification/*drug effects/genetics ; Microbial Sensitivity Tests ; Molecular Typing ; Virulence Factors/genetics ; Whole Genome Sequencing ; }, abstract = {OBJECTIVES: Our aim was to determine the antimicrobial susceptibilities of 2862 Listeria monocytogenes cultured from various foods in China and to use WGS to characterize the antimicrobial resistance and virulence genotypes of those expressing a resistance phenotype.<br><br>METHODS: The susceptibilities of 2862&#x2009;L. monocytogenes were determined by broth microdilution. Twenty-eight L. monocytogenes were found to be resistant to one to four antibiotics. All 28 resistant isolates were subsequently sequenced using short-read high accuracy protocols. The corresponding genomes were assembled and further analysis was carried out using appropriate bioinformatics pipelines.<br><br>RESULTS: All 28 resistant L. monocytogenes were classified into five STs (ST3, ST8, ST9, ST155 and ST515). Both ST9 and ST155 were dominant and their genotypes correlated with their resistance phenotypes. All ST9 isolates were MDR and could be phylogenetically classified into two clusters. One was relatively close to clinical origins and one to food. Downstream analysis of the genetic contexts in which these resistance genotypes were found suggested that these may have been acquired from other bacteria by horizontal transfer or insertion into the chromosome. All isolates harboured Listeria pathogenicity island (LIPI)-1 and LIPI-2, and only two harboured LIPI-3.<br><br>CONCLUSIONS: This study reported on the antimicrobial susceptibilities of 2862 foodborne L. monocytogenes along with the genomic characterization of 28 resistant isolates, 11 of which expressed an MDR phenotype. These data showed that this bacterium can acquire resistance by horizontal gene transfer in and between species. This study may necessitate a re-evaluation of risk to public health, associated with this bacterial species.}, }
@article {pmid30988701, year = {2019}, author = {Palazzo, A and Lorusso, P and Miskey, C and Walisko, O and Gerbino, A and Marobbio, CMT and Ivics, Z and Marsano, RM}, title = {Transcriptionally promiscuous "blurry" promoters in Tc1/mariner transposons allow transcription in distantly related genomes.}, journal = {Mobile DNA}, volume = {10}, number = {}, pages = {13}, pmid = {30988701}, issn = {1759-8753}, abstract = {BACKGROUND: We have recently described a peculiar feature of the promoters in two Drosophila Tc1-like elements, Bari1 and Bari3. The AT-richness and the presence of weak core-promoter motifs make these promoters, that we have defined "blurry", able to activate transcription of a reporter gene in cellular systems as diverse as fly, human, yeast and bacteria. In order to clarify whether the blurry promoter is a specific feature of the Bari transposon family, we have extended this study to promoters isolated from three additional DNA transposon and from two additional LTR retrotransposons.<br><br>RESULTS: Here we show that the blurry promoter is also a feature of two vertebrate transposable elements, Sleeping Beauty and Hsmar1, belonging to the Tc1/mariner superfamily. In contrast, this feature is not shared by the promoter of the hobo transposon, which belongs to the hAT superfamily, nor by LTR retrotransposon-derived promoters, which, in general, do not activate transcription when introduced into non-related genomes.<br><br>CONCLUSIONS: Our results suggest that the blurry promoter could be a shared feature of the members of the Tc1/mariner superfamily with possible evolutionary and biotechnological implications.}, }
@article {pmid30988376, year = {2019}, author = {Pasari, N and Gupta, M and Eqbal, D and Yazdani, SS}, title = {Genome analysis of Paenibacillus polymyxa A18 gives insights into the features associated with its adaptation to the termite gut environment.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {6091}, pmid = {30988376}, issn = {2045-2322}, mesh = {Adaptation, Physiological/*genetics ; Animals ; Bacterial Proteins/genetics/metabolism ; Biofilms ; Cellulase/metabolism ; Enzymes/genetics/metabolism ; Gastrointestinal Microbiome/*physiology ; Genome, Bacterial/*genetics ; Genomics ; Glycoside Hydrolases/metabolism ; Isoptera/*microbiology ; Paenibacillus polymyxa/*physiology ; }, abstract = {Paenibacillus polymyxa A18 was isolated from termite gut and was identified as a potential cellulase and hemicellulase producer in our previous study. Considering that members belonging to genus Paenibacillus are mostly free-living in soil, we investigated here the essential genetic features that helped P. polymyxa A18 to survive in gut environment. Genome sequencing and analysis identified 4608 coding sequences along with several elements of horizontal gene transfer, insertion sequences, transposases and integrated phages, which add to its genetic diversity. Many genes coding for carbohydrate-active enzymes, including the enzymes responsible for woody biomass hydrolysis in termite gut, were identified in P. polymyxa A18 genome. Further, a series of proteins conferring resistance to 11 antibiotics and responsible for production of 4 antibiotics were also found to be encoded, indicating selective advantage for growth and colonization in the gut environment. To further identify genomic regions unique to this strain, a BLAST-based comparative analysis with the sequenced genomes of 47 members belonging to genus Paenibacillus was carried out. Unique regions coding for nucleic acid modifying enzymes like CRISPR/Cas and Type I Restriction-Modification enzymes were identified in P. polymyxa A18 genome suggesting the presence of defense mechanism to combat viral infections in the gut. In addition, genes responsible for the formation of biofilms, such as Type IV pili and adhesins, which might be assisting P. polymyxa A18 in colonizing the gut were also identified in its genome. In situ colonization experiment further confirmed the ability of P. polymyxa A18 to colonize the gut of termite.}, }
@article {pmid30986983, year = {2019}, author = {Kirsip, H and Abroi, A}, title = {Protein Structure-Guided Hidden Markov Models (HMMs) as A Powerful Method in the Detection of Ancestral Endogenous Viral Elements.}, journal = {Viruses}, volume = {11}, number = {4}, pages = {}, pmid = {30986983}, issn = {1999-4915}, mesh = {Algorithms ; Animals ; Databases, Protein ; Eukaryota/*genetics ; Gene Transfer, Horizontal ; Genome/genetics ; *Markov Chains ; Phylogeny ; Protein Domains ; Synteny ; Viral Proteins/*chemistry/*genetics ; Viruses/*genetics ; }, abstract = {It has been believed for a long time that the transfer and fixation of genetic material from RNA viruses to eukaryote genomes is very unlikely. However, during the last decade, there have been several cases in which "virus-to-host" gene transfer from various viral families into various eukaryotic phyla have been described. These transfers have been identified by sequence similarity, which may disappear very quickly, especially in the case of RNA viruses. However, compared to sequences, protein structure is known to be more conserved. Applying protein structure-guided protein domain-specific Hidden Markov Models, we detected homologues of the Virgaviridae capsid protein in Schizophora flies. Further data analysis supported "virus-to-host" transfer into Schizophora ancestors as a single transfer event. This transfer was not identifiable by BLAST or by other methods we applied. Our data show that structure-guided Hidden Markov Models should be used to detect ancestral virus-to-host transfers.}, }
@article {pmid30986243, year = {2019}, author = {Wyres, KL and Wick, RR and Judd, LM and Froumine, R and Tokolyi, A and Gorrie, CL and Lam, MMC and Duchêne, S and Jenney, A and Holt, KE}, title = {Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae.}, journal = {PLoS genetics}, volume = {15}, number = {4}, pages = {e1008114}, pmid = {30986243}, issn = {1553-7404}, mesh = {Bacterial Capsules/genetics/metabolism ; Bacteriophages/genetics ; Cross Infection/drug therapy/microbiology ; Drug Resistance, Bacterial/*genetics ; Drug Resistance, Multiple, Bacterial/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genetic Variation ; Genome, Bacterial ; Humans ; Klebsiella Infections/drug therapy/microbiology ; Klebsiella pneumoniae/drug effects/*genetics/pathogenicity ; Lipopolysaccharides/biosynthesis/genetics ; Models, Genetic ; Plasmids/genetics ; Virulence/*genetics ; }, abstract = {Klebsiella pneumoniae has emerged as an important cause of two distinct public health threats: multi-drug resistant (MDR) healthcare-associated infections and drug susceptible community-acquired invasive infections. These pathotypes are generally associated with two distinct subsets of K. pneumoniae lineages or 'clones' that are distinguished by the presence of acquired resistance genes and several key virulence loci. Genomic evolutionary analyses of the most notorious MDR and invasive community-associated ('hypervirulent') clones indicate differences in terms of chromosomal recombination dynamics and capsule polysaccharide diversity, but it remains unclear if these differences represent generalised trends. Here we leverage a collection of >2200 K. pneumoniae genomes to identify 28 common clones (n ≥ 10 genomes each), and perform the first genomic evolutionary comparison. Eight MDR and 6 hypervirulent clones were identified on the basis of acquired resistance and virulence gene prevalence. Chromosomal recombination, surface polysaccharide locus diversity, pan-genome, plasmid and phage dynamics were characterised and compared. The data showed that MDR clones were highly diverse, with frequent chromosomal recombination generating extensive surface polysaccharide locus diversity. Additional pan-genome diversity was driven by frequent acquisition/loss of both plasmids and phage. In contrast, chromosomal recombination was rare in the hypervirulent clones, which also showed a significant reduction in pan-genome diversity, largely driven by a reduction in plasmid diversity. Hence the data indicate that hypervirulent clones may be subject to some sort of constraint for horizontal gene transfer that does not apply to the MDR clones. Our findings are relevant for understanding the risk of emergence of individual K. pneumoniae strains carrying both virulence and acquired resistance genes, which have been increasingly reported and cause highly virulent infections that are extremely difficult to treat. Specifically, our data indicate that MDR clones pose the greatest risk, because they are more likely to acquire virulence genes than hypervirulent clones are to acquire resistance genes.}, }
@article {pmid30984480, year = {2019}, author = {Pestov, NB and Kalinovsky, DV and Larionova, TD and Zakirova, AZ and Modyanov, NN and Okkelman, IA and Korneenko, TV}, title = {Properties of a cryptic lysyl oxidase from haloarchaeon Haloterrigena turkmenica.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6691}, pmid = {30984480}, issn = {2167-8359}, abstract = {BACKGROUND: Lysyl oxidases (LOX) have been extensively studied in mammals, whereas properties and functions of recently found homologues in prokaryotic genomes remain enigmatic.<br><br>METHODS: LOX open reading frame was cloned from Haloterrigena turkmenica in an E. coli expression vector. Recombinant Haloterrigena turkmenica lysyl oxidase (HTU-LOX) proteins were purified using metal affinity chromatography under denaturing conditions followed by refolding. Amine oxidase activity has been measured fluorometrically as hydrogen peroxide release coupled with the oxidation of 10-acetyl-3,7-dihydroxyphenoxazine in the presence of horseradish peroxidase. Rabbit polyclonal antibodies were obtained and used in western blotting.<br><br>RESULTS: Cultured H. turkmenica has no detectable amine oxidase activity. HTU-LOX may be expressed in E. coli with a high protein yield. The full-length protein gives no catalytic activity. For this reason, we hypothesized that the hydrophobic N-terminal region may interfere with proper folding and its removal may be beneficial. Indeed, truncated His-tagged HTU-LOX lacking the N-terminal hydrophobic signal peptide purified under denaturing conditions can be successfully refolded into an active enzyme, and a larger N-terminal truncation further increases the amine oxidase activity. Refolding is optimal in the presence of Cu[2+] at pH 6.2 and is not sensitive to salt. HTU-LOX is sensitive to LOX inhibitor 3-aminopropionitrile. HTU-LOX deaminates usual substrates of mammalian LOX such as lysine-containing polypeptides and polymers. The major difference between HTU-LOX and mammalian LOX is a relaxed substrate specificity of the former. HTU-LOX readily oxidizes various primary amines including such compounds as taurine and glycine, benzylamine being a poor substrate. Of note, HTU-LOX is also active towards several aminoglycoside antibiotics and polymyxin. Western blotting indicates that epitopes for the anti-HTU-LOX polyclonal antibodies coincide with a high molecular weight protein in H. turkmenica cells.<br><br>CONCLUSION: H. turkmenica contains a lysyl oxidase gene that was heterologously expressed yielding an active recombinant enzyme with important biochemical features conserved between all known LOXes, for example, the sensitivity to 3-aminopropionitrile. However, the native function in the host appears to be cryptic.<br><br>SIGNIFICANCE: This is the first report on some properties of a lysyl oxidase from Archaea and an interesting example of evolution of enzymatic properties after hypothetical horizontal transfers between distant taxa.}, }
@article {pmid30984153, year = {2019}, author = {Buckley, A and MacGregor, B and Teske, A}, title = {Identification, Expression and Activity of Candidate Nitrite Reductases From Orange Beggiatoaceae, Guaymas Basin.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {644}, pmid = {30984153}, issn = {1664-302X}, abstract = {Orange filamentous Beggiatoaceae form massive microbial mats on hydrothermal sediments in Guaymas Basin; these bacteria are considered to oxidize sulfide with nitrate and nitrite as electron acceptors. From a previously analyzed genome of an orange Beggiatoaceae filament, three candidate genes for enzymes with nitrite-reducing function - an orange octaheme cytochrome, a nirS nitrite reductase, and a nitrite/tetrathionate-reducing octaheme cytochrome - were cloned and expressed in Escherichia coli. The expressed and purified orange cytochrome showed reduced nitrite-reducing activity compared to the multifunctional native protein obtained from microbial mats. The nirS gene product showed in vitro but no in-gel nitrite-reducing activity; and the nitrite/tetrathionate-reducing octaheme cytochrome was capable of reducing both nitrite and tetrathionate in vitro. Phylogenetic analysis shows that the orange Beggiatoaceae nirS, in contrast to the other candidate nitrite reductases, does not form monophyletic lineages with its counterparts in other large sulfur-oxidizing bacteria, and most likely represents a recent acquisition by lateral gene transfer. The nitrite/tetrathionate-reducing enzyme of the orange Beggiatoaceae is related to nitrite- and tetrathionate reductases harbored predominantly by Gammaproteobacteria, including obligate endosymbionts of hydrothermal vent tubeworms. Thus, the orange Guaymas Basin Beggiatoaceae have a repertoire of at least three different functional enzymes for nitrite reduction. By demonstrating the unusual diversity of enzymes with a potential role in nitrite reduction, we show that bacteria in highly dynamic, sulfide-rich hydrothermal vent habitats adapt to these conditions that usually prohibit nitrate and nitrite reduction. In the case of the orange Guaymas Beggiatoaceae, classical denitrification appears to be replaced by different multifunctional enzymes for nitrite and tetrathionate reduction; the resulting ecophysiological flexibility provides a new key to the dominance of these Beggiatoaceae in hydrothermal hot spots.}, }
@article {pmid30980894, year = {2019}, author = {Fraga, D and Stock, K and Aryal, M and Demoll, C and Fannin, L and Snider, MJ}, title = {Bacterial arginine kinases have a highly skewed distribution within the proteobacteria.}, journal = {Comparative biochemistry and physiology. Part B, Biochemistry &amp; molecular biology}, volume = {233}, number = {}, pages = {60-71}, doi = {10.1016/j.cbpb.2019.04.001}, pmid = {30980894}, issn = {1879-1107}, mesh = {Arginine Kinase/*genetics ; Bacterial Proteins/*genetics ; *Evolution, Molecular ; *Genome, Bacterial ; *Phylogeny ; Proteobacteria/enzymology/*genetics ; }, abstract = {Phosphagen kinases (PKs) are known to be distributed throughout the animal kingdom, but have recently been discovered in some protozoan and bacterial species. A recent search of the available bacterial genomes revealed 49 unique sequences that appear to code for an arginine kinase (AK). The distribution of sequences was highly skewed with thirty nine out the forty nine sequences being found in six Proteobacteria classes (α, β, δ, γ, ε, and ζ) which represented 46.6% of the 61,335 bacterial genomes available at JGI-IMG/M website. Moreover, twenty one of the unique and metagenome bAK sequences identified were from δ-Proteobacteria despite these representing only 0.88% of the total genomes available. Phylogenetic analyses revealed that the bacterial AK sequences were interpersed between basal species such as cnidarians, sponges and protozoa, displaying an unstable clustering that was dependent upon the parameters chosen for phylogenetic analysis. Three of these putative bacterial AK genes were cloned into the pET45 expression vector, expressed, and biochemically confirmed to be capable of phosphorylating arginine using ATP. Results of the kinetic analyses of the putative bAKs from Ahrensia, D. autotrophicum, and O. profundus show that the catalytic efficiencies with respect to arginine for each enzyme, measured at 10[4]-10[5] M[-1] s[-1], fall within the range expected for competent arginine kinases.}, }
@article {pmid30980672, year = {2019}, author = {Pratama, AA and van Elsas, JD}, title = {Gene mobility in microbiomes of the mycosphere and mycorrhizosphere -role of plasmids and bacteriophages.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {5}, pages = {}, doi = {10.1093/femsec/fiz053}, pmid = {30980672}, issn = {1574-6941}, mesh = {Bacteriophages/*genetics ; Burkholderiaceae/*genetics ; Fungi/*genetics ; Gene Transfer, Horizontal ; Microbiota ; Plasmids/*genetics ; Prophages/genetics ; *Soil Microbiology ; }, abstract = {Microbial activity in soil, including horizontal gene transfer (HGT), occurs in soil hot spots and at "hot moments". Given their capacities to explore soil for nutrients, soil fungi (associated or not with plant roots) can act as (1) selectors of myco(rrhizo)sphere-adapted organisms and (2) accelerators of HGT processes across the cell populations that are locally present. This minireview critically examines our current understanding of the drivers of gene mobility in the myco(rrhizo)sphere. We place a special focus on the role of two major groups of gene mobility agents, i.e. plasmids and bacteriophages. With respect to plasmids, there is mounting evidence that broad-host-range (IncP-1β and PromA group) plasmids are prominent drivers of gene mobility across mycosphere inhabitants. A role of IncP-1β plasmids in Fe uptake processes has been revealed. Moreover, a screening of typical mycosphere-inhabiting Paraburkholderia spp. revealed carriage of integrated plasmids, next to prophages, that presumably confer fitness enhancements. In particular, functions involved in biofilm formation and nutrient uptake were thus identified. The potential of the respective gene mobility agents to promote the movement of such genes is critically examined.}, }
@article {pmid30979072, year = {2019}, author = {Lerner, A and Shoenfeld, Y and Matthias, T}, title = {Probiotics: If It Does Not Help It Does Not Do Any Harm. Really?.}, journal = {Microorganisms}, volume = {7}, number = {4}, pages = {}, pmid = {30979072}, issn = {2076-2607}, abstract = {Probiotics per definition should have beneficial effects on human health, and their consumption has tremendously increased in the last decades. In parallel, the amount of published material and claims for their beneficial efficacy soared continuously. Recently, multiple systemic reviews, meta-analyses, and expert opinions expressed criticism on their claimed effects and safety. The present review describes the dark side of the probiotics, in terms of problematic research design, incomplete reporting, lack of transparency, and under-reported safety. Highlighted are the potential virulent factors and the mode of action in the intestinal lumen, risking the physiological microbiome equilibrium. Finally, regulatory topics are discussed to lighten the heterogeneous guidelines applied worldwide. The shift in the scientific world towards a better understanding of the human microbiome, before consumption of the probiotic cargo, is highly endorsed. It is hoped that better knowledge will extend the probiotic repertoire, re-confirm efficacy or safety, establish their efficacy and substantiate their beneficial effects.}, }
@article {pmid30978500, year = {2019}, author = {Snoeck, S and Pavlidi, N and Pipini, D and Vontas, J and Dermauw, W and Van Leeuwen, T}, title = {Substrate specificity and promiscuity of horizontally transferred UDP-glycosyltransferases in the generalist herbivore Tetranychus urticae.}, journal = {Insect biochemistry and molecular biology}, volume = {109}, number = {}, pages = {116-127}, doi = {10.1016/j.ibmb.2019.04.010}, pmid = {30978500}, issn = {1879-0240}, mesh = {Acaricides/*metabolism ; Animals ; Arthropod Proteins/chemistry/genetics ; Escherichia coli/genetics ; *Gene Expression ; Gene Transfer, Horizontal ; Glycosyltransferases/*chemistry/*genetics ; Herbivory ; Kinetics ; Metabolic Detoxication, Phase II ; Microorganisms, Genetically-Modified/genetics ; Phylogeny ; Substrate Specificity ; Tetranychidae/*chemistry/*genetics ; Uridine Diphosphate ; Xenobiotics/metabolism ; }, abstract = {Uridine diphosphate (UDP)-glycosyltransferases (UGTs) catalyze the addition of UDP-sugars to small hydrophobic molecules, turning them into more water-soluble metabolites. While their role in detoxification is well documented for vertebrates, arthropod UGTs have only recently been linked to the detoxification and sequestration of plant toxins and insecticides. The two-spotted spider mite Tetranychus urticae is a generalist herbivore notorious for rapidly developing resistance to insecticides and acaricides. We identified a set of eight UGT genes that were overexpressed in mites upon long-term acclimation or adaptation to a new host plant and/or in mite strains highly resistant to acaricides. Functional expression revealed that they were all catalytically active and that the majority preferred UDP-glucose as activated donor for glycosylation of model substrates. A high-throughput substrate screening of both plant secondary metabolites and pesticides revealed patterns of both substrate specificity and promiscuity. We further selected nine enzyme-substrate combinations for more comprehensive analysis and determined steady-state kinetic parameters. Among others, plant metabolites such as capsaicin and several flavonoids were shown to be glycosylated. The acaricide abamectin was also glycosylated by two UGTs and one of these was also overexpressed in an abamectin resistant strain. Our study corroborates the potential role of T. urticae UGTs in detoxification of both synthetic and natural xenobiotic compounds and paves the way for rapid substrate screening of arthropod UGTs.}, }
@article {pmid30976019, year = {2019}, author = {Jeong, H and Arif, B and Caetano-Anollés, G and Kim, KM and Nasir, A}, title = {Horizontal gene transfer in human-associated microorganisms inferred by phylogenetic reconstruction and reconciliation.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {5953}, pmid = {30976019}, issn = {2045-2322}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; Computational Biology/*methods ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genome, Bacterial ; Humans ; Models, Genetic ; *Phylogeny ; }, abstract = {Horizontal gene transfer (HGT) is widespread in the evolution of prokaryotes, especially those associated with the human body. Here, we implemented large-scale gene-species phylogenetic tree reconstructions and reconciliations to identify putative HGT-derived genes in the reference genomes of microbiota isolated from six major human body sites by the NIH Human Microbiome Project. Comparisons with a control group representing microbial genomes from diverse natural environments indicated that HGT activity increased significantly in the genomes of human microbiota, which is confirmatory of previous findings. Roughly, more than half of total genes in the genomes of human-associated microbiota were transferred (donated or received) by HGT. Up to 60% of the detected HGTs occurred either prior to the colonization of the human body or involved bacteria residing in different body sites. The latter could suggest 'genetic crosstalk' and movement of bacterial genes within the human body via hitherto poorly understood mechanisms. We also observed that HGT activity increased significantly among closely-related microorganisms and especially when they were united by physical proximity, suggesting that the 'phylogenetic effect' can significantly boost HGT activity. Finally, we identified several core and widespread genes least influenced by HGT that could become useful markers for building robust 'trees of life' and address several outstanding technical challenges to improve the phylogeny-based genome-wide HGT detection method for future applications.}, }
@article {pmid30975999, year = {2019}, author = {Xiong, L and Liu, S and Chen, S and Xiao, Y and Zhu, B and Gao, Y and Zhang, Y and Chen, B and Luo, J and Deng, Z and Chen, X and Wang, L and Chen, S}, title = {A new type of DNA phosphorothioation-based antiviral system in archaea.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1688}, pmid = {30975999}, issn = {2041-1723}, mesh = {Archaea/*physiology/virology ; Archaeal Proteins/genetics/immunology/*metabolism ; Archaeal Viruses/*genetics/pathogenicity ; DNA Replication/immunology ; DNA, Viral/*metabolism ; Gene Transfer, Horizontal/immunology ; Host Microbial Interactions/*genetics ; Immunity, Innate/genetics/immunology ; Phosphorothioate Oligonucleotides/metabolism ; RNA, Archaeal/genetics/isolation &amp; purification ; Sequence Analysis, DNA ; }, abstract = {Archaea and Bacteria have evolved different defence strategies that target virtually all steps of the viral life cycle. The diversified virion morphotypes and genome contents of archaeal viruses result in a highly complex array of archaea-virus interactions. However, our understanding of archaeal antiviral activities lags far behind our knowledges of those in bacteria. Here we report a new archaeal defence system that involves DndCDEA-specific DNA phosphorothioate (PT) modification and the PbeABCD-mediated halt of virus propagation via inhibition of DNA replication. In contrast to the breakage of invasive DNA by DndFGH in bacteria, DndCDEA-PbeABCD does not degrade or cleave viral DNA. The PbeABCD-mediated PT defence system is widespread and exhibits extensive interdomain and intradomain gene transfer events. Our results suggest that DndCDEA-PbeABCD is a new type of PT-based virus resistance system, expanding the known arsenal of defence systems as well as our understanding of host-virus interactions.}, }
@article {pmid30975079, year = {2019}, author = {Du, Y and Ma, J and Yin, Z and Liu, K and Yao, G and Xu, W and Fan, L and Du, B and Ding, Y and Wang, C}, title = {Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {283}, pmid = {30975079}, issn = {1471-2164}, support = {2017YFD0200804//the National Key Research and Development Program of China/ ; 31700094//National Natural Science Foundation of China/ ; 31770115//National Natural Science Foundation of China/ ; 31600090//National Natural Science Foundation of China/ ; 2014BAD16B02//the National Science and Technology Pillar Program of China/ ; SYL2017XTTD03//the funds of Shandong "Double Tops" Program/ ; }, mesh = {Adaptation, Physiological/genetics ; Bacillus/*genetics/metabolism/physiology ; *Evolution, Molecular ; *Genomics ; Multigene Family/genetics ; Phylogeny ; }, abstract = {BACKGROUND: Members of the genus Bacillus are important plant growth-promoting rhizobacteria that serve as biocontrol agents. Bacillus paralicheniformis MDJK30 is a PGPR isolated from the peony rhizosphere and can suppress plant-pathogenic bacteria and fungi. To further uncover the genetic mechanism of the plant growth-promoting traits of MDJK30 and its closely related strains, we used comparative genomics to provide insights into the genetic diversity and evolutionary relationship between B. paralicheniformis and B. licheniformis.<br><br>RESULTS: A comparative genomics analysis based on B. paralicheniformis MDJK30 and 55 other previously reported Bacillus strains was performed. The evolutionary position of MDJK30 and the evolutionary relationship between B. paralicheniformis and B. licheniformis were evaluated by studying the phylogeny of the core genomes, a population structure analysis and ANI results. Comparative genomic analysis revealed various features of B. paralicheniformis that contribute to its commensal lifestyle in the rhizosphere, including an opening pan genome, a diversity of transport and the metabolism of the carbohydrates and amino acids. There are notable differences in the numbers and locations of the insertion sequences, prophages, genomic islands and secondary metabolic synthase operons between B. paralicheniformis and B. licheniformis. In particular, we found most gene clusters of Fengycin, Bacitracin and Lantipeptide were only present in B. paralicheniformis and were obtained by horizontal gene transfer (HGT), and these clusters may be used as genetic markers for distinguishing B. paralicheniformis and B. licheniformis.<br><br>CONCLUSIONS: This study reveals that MDJK30 and the other strains of lineage paralicheniformis present plant growth-promoting traits at the genetic level and can be developed and commercially formulated in agriculture as PGPR. Core genome phylogenies and population structure analysis has proven to be a powerful tool for differentiating B. paralicheniformis and B. licheniformis. Comparative genomic analyses illustrate the genetic differences between the paralicheniformis-licheniformis group with respect to rhizosphere adaptation.}, }
@article {pmid30974905, year = {2019}, author = {Inoue, J and Nakashima, K and Satoh, N}, title = {ORTHOSCOPE Analysis Reveals the Presence of the Cellulose Synthase Gene in All Tunicate Genomes but Not in Other Animal Genomes.}, journal = {Genes}, volume = {10}, number = {4}, pages = {}, pmid = {30974905}, issn = {2073-4425}, mesh = {Animals ; Chromosome Mapping ; *Evolution, Molecular ; Genome/genetics ; Glucosyltransferases/*genetics ; *Phylogeny ; Plants/genetics ; Prokaryotic Cells/metabolism ; Urochordata/*genetics ; }, abstract = {Tunicates or urochordates-comprising ascidians, larvaceans, and salps-are the only metazoans that can synthesize cellulose, a biological function usually associated with bacteria and plants but not animals. Tunicate cellulose or tunicine is a major component of the outer acellular coverage (tunic) of the entire body of these organisms. Previous studies have suggested that the prokaryotic cellulose synthase gene (CesA) was horizontally transferred into the genome of a tunicate ancestor. However, no convenient tools have been devised to determine whether only tunicates harbor CesA. ORTHOSCOPE is a recently developed tool used to identify orthologous genes and to examine the phylogenic relationship of molecules within major metazoan taxa. The present analysis with this tool revealed the presence of CesA orthologs in all sequenced tunicate genomes but an absence in other metazoan genomes. This supports an evolutionary origin of animal cellulose and provides insights into the evolution of this animal taxon.}, }
@article {pmid30970170, year = {2019}, author = {Sojo, V}, title = {Why the Lipid Divide? Membrane Proteins as Drivers of the Split between the Lipids of the Three Domains of Life.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {41}, number = {5}, pages = {e1800251}, doi = {10.1002/bies.201800251}, pmid = {30970170}, issn = {1521-1878}, mesh = {Archaea/*chemistry/metabolism ; Bacteria/*chemistry/metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal ; Membrane Lipids/chemistry/*metabolism ; Membrane Proteins/chemistry/*metabolism ; Prokaryotic Cells/chemistry/metabolism ; }, abstract = {Recent results from engineered and natural samples show that the starkly different lipids of archaea and bacteria can form stable hybrid membranes. But if the two types can mix, why don't they? That is, why do most bacteria and all eukaryotes have only typically bacterial lipids, and archaea archaeal lipids? It is suggested here that the reason may lie on the other main component of cellular membranes: membrane proteins, and their close adaptation to the lipids. Archaeal lipids in modern bacteria could suggest that the last universal common ancestor (LUCA) had both lipid types. However, this would imply a rather elaborate evolutionary scenario, while negating simpler alternatives. In light of widespread horizontal gene transfer across the prokaryotic domains, hybrid membranes reveal that the lipid divide did not just occur once at the divergence of archaea and bacteria from LUCA. Instead, it continues to occur actively to this day.}, }
@article {pmid30968307, year = {2019}, author = {Garcia, LE and Zubko, MK and Zubko, EI and Sanchez-Puerta, MV}, title = {Elucidating genomic patterns and recombination events in plant cybrid mitochondria.}, journal = {Plant molecular biology}, volume = {100}, number = {4-5}, pages = {433-450}, pmid = {30968307}, issn = {1573-5028}, support = {M033//Universidad Nacional de Cuyo/ ; PICT1762//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; 1062432//National Science Foundation/ ; }, mesh = {DNA, Mitochondrial/chemistry ; *Genome, Mitochondrial ; Genome, Plant ; Homologous Recombination ; *Hybridization, Genetic ; Hyoscyamus/genetics ; Mitochondria/*genetics ; Nicotiana/genetics ; }, abstract = {Cybrid plant mitochondria undergo homologous recombination, mainly BIR, keep a single allele for each gene, and maintain exclusive sequences of each parent and a single copy of the homologous regions. The maintenance of a dynamic equilibrium between the mitochondrial and nuclear genomes requires continuous communication and a high level of compatibility between them, so that alterations in one genetic compartment need adjustments in the other. The co-evolution of nuclear and mitochondrial genomes has been poorly studied, even though the consequences and effects of this interaction are highly relevant for human health, as well as for crop improvement programs and for genetic engineering. The mitochondria of plants represent an excellent system to understand the mechanisms of genomic rearrangements, chimeric gene formation, incompatibility between nucleus and cytoplasm, and horizontal gene transfer. We carried out detailed analyses of the mtDNA of a repeated cybrid between the solanaceae Nicotiana tabacum and Hyoscyamus niger. The mtDNA of the cybrid was intermediate between the size of the parental mtDNAs and the sum of them. Noticeably, most of the homologous sequences inherited from both parents were lost. In contrast, the majority of the sequences exclusive of a single parent were maintained. The mitochondrial gene content included a majority of N. tabacum derived genes, but also chimeric, two-parent derived, and H. niger-derived genes in a tobacco nuclear background. Any of these alterations in the gene content could be the cause of CMS in the cybrid. The parental mtDNAs interacted through 28 homologous recombination events and a single case of illegitimate recombination. Three main homologous recombination mechanisms were recognized in the cybrid mitochondria. Break induced replication (BIR) pathway was the most frequent. We propose that BIR could be one of the mechanisms responsible for the loss of the majority of the repeated regions derived from H. niger.}, }
@article {pmid30967604, year = {2019}, author = {Mruk, I and Kaczorowski, T and Witczak, A}, title = {Natural tuning of restriction endonuclease synthesis by cluster of rare arginine codons.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {5808}, pmid = {30967604}, issn = {2045-2322}, mesh = {Arginine/*genetics ; Bacteriophage T7/genetics ; DNA Modification Methylases/*genetics ; DNA Restriction Enzymes/*genetics ; DNA Restriction-Modification Enzymes/*metabolism ; Escherichia coli K12/*genetics ; Gene Expression Regulation, Bacterial/genetics ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/genetics ; Plasmids/genetics ; }, abstract = {Restriction-modification (R-M) systems are highly widespread among bacteria and archaea, and they appear to play a pivotal role in modulating horizontal gene transfer, as well as in protecting the host organism against viruses and other invasive DNA particles. Type II R-M systems specify two independent enzymes: a restriction endonuclease (REase) and protective DNA methyltransferase (MTase). If the cell is to survive, the counteracting activities as toxin and antitoxin, must be finely balanced in vivo. The molecular basis of this regulatory process remains unclear and current searches for regulatory elements in R-M modules are focused mainly at the transcription step. In this report, we show new aspects of REase control that are linked to translation. We used the EcoVIII R-M system as a model. Both, the REase and MTase genes for this R-M system contain an unusually high number of rare arginine codons (AGA and AGG) when compared to the rest of the E. coli K-12 genome. Clusters of these codons near the N-terminus of the REase greatly affect the translational efficiency. Changing these to higher frequency codons for E. coli (CGC) improves the REase synthesis, making the R-M system more potent to defend its host against bacteriophages. However, this improved efficiency in synthesis reduces host fitness due to increased autorestriction. We hypothesize that expression of the endonuclease gene can be modulated depending on the host genetic context and we propose a novel post-transcriptional mode of R-M system regulation that alleviates the potential lethal action of the restriction enzyme.}, }
@article {pmid30967464, year = {2019}, author = {Giebel, AM and Hu, S and Rajaram, K and Finethy, R and Toh, E and Brothwell, JA and Morrison, SG and Suchland, RJ and Stein, BD and Coers, J and Morrison, RP and Nelson, DE}, title = {Genetic Screen in Chlamydia muridarum Reveals Role for an Interferon-Induced Host Cell Death Program in Antimicrobial Inclusion Rupture.}, journal = {mBio}, volume = {10}, number = {2}, pages = {}, pmid = {30967464}, issn = {2150-7511}, support = {P20 GM103625/GM/NIGMS NIH HHS/United States ; T32 AI007637/AI/NIAID NIH HHS/United States ; R56 AI099278/AI/NIAID NIH HHS/United States ; R01 AI099278/AI/NIAID NIH HHS/United States ; R37 AI103197/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Apoptosis ; Chlamydia Infections/microbiology/pathology ; Chlamydia muridarum/genetics/*immunology ; Disease Models, Animal ; Genetic Testing ; *Host-Pathogen Interactions ; *Immune Evasion ; *Immunity, Innate ; Inclusion Bodies/microbiology ; Interferon-gamma/*metabolism ; Mice ; }, abstract = {Interferon-regulated immune defenses protect mammals from pathogenically diverse obligate intracellular bacterial pathogens of the genus Chlamydia Interferon gamma (IFN-γ) is especially important in controlling the virulence of Chlamydia species and thus impacts the modeling of human chlamydial infection and disease in mice. How IFN-γ contributes to cell-autonomous defenses against Chlamydia species and how these pathogens evade IFN-γ-mediated immunity in their natural hosts are not well understood. We conducted a genetic screen which identified 31 IFN-γ-sensitive (Igs) mutants of the mouse model pathogen Chlamydia muridarum Genetic suppressor analysis and lateral gene transfer were used to map the phenotype of one of these mutants, Igs4, to a missense mutation in a putative chlamydial inclusion membrane protein, TC0574. We observed the lytic destruction of Igs4-occupied inclusions and accompanying host cell death in response to IFN-γ priming or various proapoptotic stimuli. However, Igs4 was insensitive to IFN-γ-regulated cell-autonomous defenses previously implicated in anti-Chlamydia trachomatis host defense in mice. Igs4 inclusion integrity was restored by caspase inhibitors, indicating that the IFN-γ-mediated destruction of Igs4 inclusions is dependent upon the function of caspases or related prodeath cysteine proteases. We further demonstrated that the Igs4 mutant is immune restricted in an IFN-γ-dependent manner in a mouse infection model, thereby implicating IFN-γ-mediated inclusion destruction and host cell death as potent in vivo host defense mechanisms to which wild-type C. muridarum is resistant. Overall, our results suggest that C. muridarum evolved resistance mechanisms to counter IFN-γ-elicited programmed cell death and the associated destruction of intravacuolar pathogens.IMPORTANCE Multiple obligatory intracellular bacteria in the genus Chlamydia are important pathogens. In humans, strains of C. trachomatis cause trachoma, chlamydia, and lymphogranuloma venereum. These diseases are all associated with extended courses of infection and reinfection that likely reflect the ability of chlamydiae to evade various aspects of host immune responses. Interferon-stimulated genes, driven in part by the cytokine interferon gamma, restrict the host range of various Chlamydia species, but how these pathogens evade interferon-stimulated genes in their definitive host is poorly understood. Various Chlamydia species can inhibit death of their host cells and may have evolved this strategy to evade prodeath signals elicited by host immune responses. We present evidence that chlamydia-induced programmed cell death resistance evolved to counter interferon- and immune-mediated killing of Chlamydia-infected cells.}, }
@article {pmid30965126, year = {2019}, author = {Crispim, JS and Dias, RS and Laguardia, CN and Araújo, LC and da Silva, JD and Vidigal, PMP and de Sousa, MP and da Silva, CC and Santana, MF and de Paula, SO}, title = {Desulfovibrio alaskensis prophages and their possible involvement in the horizontal transfer of genes by outer membrane vesicles.}, journal = {Gene}, volume = {703}, number = {}, pages = {50-57}, doi = {10.1016/j.gene.2019.04.016}, pmid = {30965126}, issn = {1879-0038}, mesh = {Desulfovibrio/growth &amp; development/*virology ; *Gene Transfer, Horizontal ; Mitomycin/pharmacology ; Prophages/*genetics ; Transcription, Genetic ; Transport Vesicles/*genetics ; Viral Proteins/genetics ; }, abstract = {Desulfovibrio alaskensis is a Gram-negative bacterial species that belongs to the group of Sulphate Reducing Bacteria (SRB) and presents prophages in genomes, a common characteristic of the genus Desulfovibrio. Genetic material can be transported by outer membrane vesicles, however, no data regarding the production of these vesicles has been reported for D. alaskensis. To verify the expression of D. alaskensis prophages and their involvement with outer membrane vesicles, the DSM16109 strain was used. The DSM16109 strain had three prophages and presented reduced growth after mitomycin C addition when compared to the control culture. This reduction was accompanied by the presence of virus-like particles (VLPs), indicating mitomycin C dependent prophage induction. The increase in the number of cap gene copies and transcriptions of the three prophages was verified in the control sample, however, without the formation of VLPs. Prophage genes were identified in outer membrane vesicles from cultures treated and not treated with mitomycin C. DSM16109 prophages are expressed spontaneously but only in the presence of mitomycin C was it possible to observe VLP formation. Due to the genetic material detection from the prophages within outer membrane vesicles, this property may be related to the horizontal transfer of viral genes.}, }
@article {pmid30963617, year = {2019}, author = {Vakirlis, N and Monerawela, C and McManus, G and Ribeiro, O and McLysaght, A and James, T and Bond, U}, title = {Evolutionary journey and characterisation of a novel pan-gene associated with beer strains of Saccharomyces cerevisiae.}, journal = {Yeast (Chichester, England)}, volume = {36}, number = {7}, pages = {425-437}, doi = {10.1002/yea.3391}, pmid = {30963617}, issn = {1097-0061}, support = {764364//European Commission, Marie Sk&#x142;odowska-Curie Innovative Training Network award/International ; 1592 award//Trinity College Dublin/International ; }, mesh = {Beer/*microbiology ; Cell Membrane/metabolism ; Chromosomes, Fungal/genetics ; Evolution, Molecular ; Fungal Proteins/*genetics/metabolism ; Gene Deletion ; Gene Expression ; Gene Transfer, Horizontal ; Genome, Fungal/genetics ; Open Reading Frames ; Saccharomyces/classification/genetics/growth &amp; development/isolation &amp; purification ; Saccharomyces cerevisiae/classification/*genetics/growth &amp; development/*isolation &amp; purification ; }, abstract = {The sequencing of over a thousand Saccharomyces cerevisiae genomes revealed a complex pangenome. Over one third of the discovered genes are not present in the S. cerevisiae core genome but instead are often restricted to a subset of yeast isolates and thus may be important for adaptation to specific environmental niches. We refer to these genes as "pan-genes," being part of the pangenome but not the core genome. Here, we describe the evolutionary journey and characterisation of a novel pan-gene, originally named hypothetical (HYPO) open-reading frame. Phylogenetic analysis reveals that HYPO has been predominantly retained in S. cerevisiae strains associated with brewing but has been repeatedly lost in most other fungal species during evolution. There is also evidence that HYPO was horizontally transferred at least once, from S. cerevisiae to Saccharomyces paradoxus. The phylogenetic analysis of HYPO exemplifies the complexity and intricacy of evolutionary trajectories of genes within the S. cerevisiae pangenome. To examine possible functions for Hypo, we overexpressed a HYPO-GFP fusion protein in both S. cerevisiae and Saccharomyces pastorianus. The protein localised to the plasma membrane where it accumulated initially in distinct foci. Time-lapse fluorescent imaging revealed that when cells are grown in wort, Hypo-gfp fluorescence spreads throughout the membrane during cell growth. The overexpression of Hypo-gfp in S. cerevisiae or S. pastorianus strains did not significantly alter cell growth in medium-containing glucose, maltose, maltotriose, or wort at different concentrations.}, }
@article {pmid30958259, year = {2019}, author = {Fineran, PC}, title = {Resistance is not futile: bacterial 'innate' and CRISPR-Cas 'adaptive' immune systems.}, journal = {Microbiology (Reading, England)}, volume = {165}, number = {8}, pages = {834-841}, doi = {10.1099/mic.0.000802}, pmid = {30958259}, issn = {1465-2080}, mesh = {Bacteria/*genetics/immunology ; Bacterial Proteins/genetics ; *Bacteriophages/pathogenicity ; *CRISPR-Cas Systems/physiology ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Gene Transfer, Horizontal/genetics ; Immunity ; }, abstract = {Bacteria are under a constant pressure from their viruses (phages) and other mobile genetic elements. They protect themselves through a range of defence strategies, which can be broadly classified as 'innate' and 'adaptive'. The bacterial innate immune systems include defences provided by restriction modification and abortive infection, among others. Bacterial adaptive immunity is elicited by a diverse range of CRISPR-Cas systems. Here, I discuss our research on both innate and adaptive phage resistance mechanisms and some of the evasion strategies employed by phages.}, }
@article {pmid30955795, year = {2019}, author = {Oikarainen, PE and Pohjola, LK and Pietola, ES and Heikinheimo, A}, title = {Direct vertical transmission of ESBL/pAmpC-producing Escherichia coli limited in poultry production pyramid.}, journal = {Veterinary microbiology}, volume = {231}, number = {}, pages = {100-106}, doi = {10.1016/j.vetmic.2019.03.001}, pmid = {30955795}, issn = {1873-2542}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/biosynthesis ; Chickens/*microbiology ; Cloaca/microbiology ; Escherichia coli/enzymology/*isolation &amp; purification ; Escherichia coli Infections/transmission/*veterinary ; Genome, Bacterial ; Infectious Disease Transmission, Vertical/*veterinary ; Ovum/microbiology ; Poultry/microbiology ; Poultry Diseases/microbiology/*transmission ; Whole Genome Sequencing ; beta-Lactamases/biosynthesis ; }, abstract = {Extended-spectrum beta-lactamase (ESBL) and plasmidic AmpC (pAmpC) producing Escherichia coli are found in the poultry production even without antibiotic use. The spread of these bacteria has been suggested to occur via imported parent birds, enabling transmission to production level broilers vertically via eggs. We studied transmission of ESBL/pAmpC-producing E. coli and E. coli without antibiotic selection by sampling imported parent birds (n = 450), egg surfaces prior to and after the incubation period (n = 300 and n = 428, respectively) and the laying house environment (n = 20). Samples were additionally taken from embryos (n = 422). To study the prevention of transmission, a competitive exclusion (CE) solution was added onto freshly laid eggs prior to incubation period (n = 150). Results showed carriage of ESBL/pAmpC-producing E. coli in parent birds (26.7%), the environment (5%) and egg surfaces before the incubation period (1.3%), but not from egg surfaces or embryos after the incubation period. Whole genome sequencing revealed ESBL/pAmpC-producing E. coli isolates belonging to clonal lineages ST429 and ST2040. However, the finding of E. coli cultured without antibiotic selection in two (2.2%) embryos strengthens the need to study E. coli transmission in poultry production in more depth. Since ESBL/pAmpC-producing E. coli seem not to persist on egg surfaces, there is no need to use CE solution ex ovo as a prevention method. The results indicate that other routes, such as for example transmission through fomites or horizontal gene transfer by other bacterial species, could be more important than vertical transmission in the spread of resistance in broiler production.}, }
@article {pmid30955771, year = {2019}, author = {Cotta, SR and Cadete, LL and van Elsas, JD and Andreote, FD and Dias, ACF}, title = {Exploring bacterial functionality in mangrove sediments and its capability to overcome anthropogenic activity.}, journal = {Marine pollution bulletin}, volume = {141}, number = {}, pages = {586-594}, doi = {10.1016/j.marpolbul.2019.03.001}, pmid = {30955771}, issn = {1879-3363}, mesh = {Bacteria/genetics/metabolism ; Biodiversity ; Brazil ; Carbon/metabolism ; Ecosystem ; Gene Transfer, Horizontal ; Geologic Sediments/*microbiology ; Metagenomics ; *Microbiota/genetics ; Sulfur/metabolism ; *Wetlands ; }, abstract = {Mangrove forests are highly productive yet vulnerable ecosystems that act as important carbon sinks ("blue carbon"). The objective of this work was to analyze the impact of anthropogenic activities on microbiome structure and functioning. The metagenomic analysis revealed that the taxonomic compositions were grossly similar across all mangrove microbiomes. Remarkably, these microbiomes, along the gradient of anthropogenic impact, showed fluctuations in the relative abundances of bacterial taxa predicted to be involved in sulfur cycling processes. Functions involved in sulfur metabolism, such as APS pathways (associated with sulfate reduction and sulfur oxidation processes) were prevalent across the microbiomes, being sox and dsrAB genes highly expressed on anthropogenically-impacted areas. Apparently, the oil-impacted microbiomes were more affected in taxonomic than in functional terms, as high functional redundancies were noted across them. The microbial gene diversity found was typical for a functional system, even following the previous disturbance.}, }
@article {pmid30953838, year = {2019}, author = {Gao, S and Gold, SE and Wisecaver, JH and Zhang, Y and Guo, L and Ma, LJ and Rokas, A and Glenn, AE}, title = {Genome-wide analysis of Fusarium verticillioides reveals inter-kingdom contribution of horizontal gene transfer to the expansion of metabolism.}, journal = {Fungal genetics and biology : FG &amp; B}, volume = {128}, number = {}, pages = {60-73}, doi = {10.1016/j.fgb.2019.04.002}, pmid = {30953838}, issn = {1096-0937}, mesh = {Fusarium/drug effects/*genetics/*metabolism ; *Gene Transfer, Horizontal ; *Genome, Fungal ; Host-Pathogen Interactions ; Multigene Family ; Nitric Oxide/pharmacology ; Phenotype ; *Phylogeny ; Secondary Metabolism ; Sequence Analysis, RNA ; }, abstract = {Horizontal gene transfer (HGT) is believed to shape genomes by facilitating the rapid acquisition of adaptive traits. We hypothesized that the economically important fungus Fusarium verticillioides is an excellent candidate for investigating the potential impact of HGT on the expansion of metabolic activities given its soilborne nature and versatile lifestyle as both a symptomless endophyte as well as a maize pathogen. To test this hypothesis, we used a phylogenomic pipeline followed by manual curation to perform a genome-wide identification of inter-kingdom derived HGT events. We found strong support for 36 genes in F. verticillioides putatively acquired from bacteria. Functional enrichment assessment of these 36 candidates suggested HGT potentially influenced several biochemical activities, including lysine, glycine and nitrogen metabolism. The expression of 25 candidate HGT genes was detected among RNA-Seq datasets from normal and various stress-related growth conditions, thus indicating potential functionality. FVEG_10494, one of the HGT candidates with homologs in only a few Fusarium species, was highly and specifically up-regulated under nitric oxide (NO) challenge. Functional analysis of FVEG_10494 suggests the gene moderately enhanced NO-triggered protective responses and suppressed expression of the F. verticillioides secondary metabolism gene cluster responsible for production of fusarin C. Overall, our global analysis of HGT events in F. verticillioides identified a well-supported set of transferred genes, providing further evidence that HGT offers a mechanism by which fungi can expand their metabolic capabilities, which in turn may enhance their adaptive strategies.}, }
@article {pmid30953568, year = {2019}, author = {Chen, W and Shakir, S and Bigham, M and Richter, A and Fei, Z and Jander, G}, title = {Genome sequence of the corn leaf aphid (Rhopalosiphum maidis Fitch).}, journal = {GigaScience}, volume = {8}, number = {4}, pages = {}, pmid = {30953568}, issn = {2047-217X}, mesh = {Animals ; Aphids/classification/drug effects/*genetics/metabolism ; Computational Biology/methods ; Gene Expression Profiling ; Gene Transfer, Horizontal ; *Genome ; *Genomics/methods ; Inactivation, Metabolic ; Insecticide Resistance ; Molecular Sequence Annotation ; Phylogeny ; Sequence Analysis, DNA ; Transcriptome ; }, abstract = {BACKGROUND: The corn leaf aphid (Rhopalosiphum maidis Fitch) is the most economically damaging aphid pest on maize (Zea mays), one of the world's most important grain crops. In addition to causing direct damage by removing photoassimilates, R. maidis transmits several destructive maize viruses, including maize yellow dwarf virus, barley yellow dwarf virus, sugarcane mosaic virus, and cucumber mosaic virus.<br><br>FINDINGS: The genome of a parthenogenetically reproducing R. maidis clone was assembled with a combination of Pacific Biosciences (207-fold coverage) and Illumina (83-fold coverage) sequencing. The 689 assembled contigs, which have an N50 size of 9.0 megabases (Mb) and a low level of heterozygosity, were clustered using Phase Genomics Hi-C interaction maps. Consistent with the commonly observed 2n = 8 karyotype of R. maidis, most of the contigs (473 spanning 321 Mb) were successfully oriented into 4 scaffolds. The genome assembly captured the full length of 95.8% of the core eukaryotic genes, indicating that it is highly complete. Repetitive sequences accounted for 21.2% of the assembly, and a total of 17,629 protein-coding genes were predicted with integrated evidence from ab initio and homology-based gene predictions and transcriptome sequences generated with both Pacific Biosciences and Illumina. An analysis of likely horizontally transferred genes identified 2 from bacteria, 7 from fungi, 2 from protozoa, and 9 from algae. Repeat elements, transposons, and genes encoding likely detoxification enzymes (cytochrome P450s, glutathione S-transferases, carboxylesterases, uridine diphosphate-glucosyltransferases, and ABC transporters) were identified in the genome sequence. Other than Buchnera aphidicola (642,929 base pairs, 602 genes), no endosymbiont bacteria were found in R. maidis.<br><br>CONCLUSIONS: A high-quality R. maidis genome was assembled at the chromosome level. This genome sequence will enable further research related to ecological interactions, virus transmission, pesticide resistance, and other aspects of R. maidis biology. It also serves as a valuable resource for comparative investigation of other aphid species.}, }
@article {pmid30953542, year = {2019}, author = {Raymond, F and Boissinot, M and Ouameur, AA and Déraspe, M and Plante, PL and Kpanou, SR and Bérubé, &#xc8; and Huletsky, A and Roy, PH and Ouellette, M and Bergeron, MG and Corbeil, J}, title = {Culture-enriched human gut microbiomes reveal core and accessory resistance genes.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {56}, pmid = {30953542}, issn = {2049-2618}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/*classification/drug effects/genetics/growth &amp; development ; Bacterial Proteins/genetics ; Bacteriological Techniques/*methods ; *Drug Resistance, Microbial ; Escherichia coli/genetics/growth &amp; development/isolation &amp; purification ; Feces/cytology/microbiology ; Gastrointestinal Microbiome ; Gene Transfer, Horizontal ; Humans ; Metagenomics ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: Low-abundance microorganisms of the gut microbiome are often referred to as a reservoir for antibiotic resistance genes. Unfortunately, these less-abundant bacteria can be overlooked by deep shotgun sequencing. In addition, it is a challenge to associate the presence of resistance genes with their risk of acquisition by pathogens. In this study, we used liquid culture enrichment of stools to assemble the genome of lower-abundance bacteria from fecal samples. We then investigated the gene content recovered from these culture-enriched and culture-independent metagenomes in relation with their taxonomic origin, specifically antibiotic resistance genes. We finally used a pangenome approach to associate resistance genes with the core or accessory genome of Enterobacteriaceae and inferred their propensity to horizontal gene transfer.<br><br>RESULTS: Using culture-enrichment approaches with stools allowed assembly of 187 bacterial species with an assembly size greater than 1 million nucleotides. Of these, 67 were found only in culture-enriched conditions, and 22 only in culture-independent microbiomes. These assembled metagenomes allowed the evaluation of the gene content of specific subcommunities of the gut microbiome. We observed that differentially distributed metabolic enzymes were associated with specific culture conditions and, for the most part, with specific taxa. Gene content differences between microbiomes, for example, antibiotic resistance, were for the most part not associated with metabolic enzymes, but with other functions. We used a pangenome approach to determine if the resistance genes found in Enterobacteriaceae, specifically E. cloacae or E. coli, were part of the core genome or of the accessory genome of this species. In our healthy volunteer cohort, we found that E. cloacae contigs harbored resistance genes that were part of the core genome of the species, while E. coli had a large accessory resistome proximal to mobile elements.<br><br>CONCLUSION: Liquid culture of stools contributed to an improved functional and comparative genomics study of less-abundant gut bacteria, specifically those associated with antibiotic resistance. Defining whether a gene is part of the core genome of a species helped in interpreting the genomes recovered from culture-independent or culture-enriched microbiomes.}, }
@article {pmid30952342, year = {2019}, author = {Zhou, R and Zeng, S and Hou, D and Liu, J and Weng, S and He, J and Huang, Z}, title = {Occurrence of human pathogenic bacteria carrying antibiotic resistance genes revealed by metagenomic approach: A case study from an aquatic environment.}, journal = {Journal of environmental sciences (China)}, volume = {80}, number = {}, pages = {248-256}, doi = {10.1016/j.jes.2019.01.001}, pmid = {30952342}, issn = {1001-0742}, mesh = {Drug Resistance, Microbial/*genetics ; Environmental Monitoring/*methods ; Metagenome/*physiology ; *Water Microbiology ; Water Pollution/*analysis/*statistics &amp; numerical data ; }, abstract = {Antibiotic resistance genes (ARGs), human pathogenic bacteria (HPB), and HPB carrying ARGs are public issues that pose a high risk to aquatic environments and public health. Their diversity and abundance in water, intestine, and sediments of shrimp culture pond were investigated using metagenomic approach. A total of 19 classes of ARGs, 52 HPB species, and 7 species of HPB carrying ARGs were found. Additionally, 157, 104, and 86 subtypes of ARGs were detected in shrimp intestine, pond water, and sediment samples, respectively. In all the samples, multidrug resistance genes were the highest abundant class of ARGs. The dominant HPB was Enterococcus faecalis in shrimp intestine, Vibrio parahaemolyticus in sediments, and Mycobacterium yongonense in water, respectively. Moreover, E. faecalis (contig Intestine_364647) and Enterococcus faecium (contig Intestine_80272) carrying efrA, efrB and ANT(6)-Ia were found in shrimp intestine, Desulfosaricina cetonica (contig Sediment_825143) and Escherichia coli (contig Sediment_188430) carrying mexB and APH(3')-IIa were found in sediments, and Laribacter hongkongensis (contig Water_478168 and Water_369477), Shigella sonnei (contig Water_880246), and Acinetobacter baumannii (contig Water_525520) carrying sul1, sul2, ereA, qacH, OXA-21, and mphD were found in pond water. Mobile genetic elements (MGEs) analysis indicated that horizontal gene transfer (HGT) of integrons, insertion sequences, and plasmids existed in shrimp intestine, sediment, and water samples, and the abundance of integrons was higher than that of other two MGEs. The results suggested that HPB carrying ARGs potentially existed in aquatic environments, and that these contributed to the environment and public health risk evaluation.}, }
@article {pmid30949677, year = {2019}, author = {Pillonel, T and Bertelli, C and Aeby, S and de Barsy, M and Jacquier, N and Kebbi-Beghdadi, C and Mueller, L and Vouga, M and Greub, G}, title = {Sequencing the Obligate Intracellular Rhabdochlamydia helvetica within Its Tick Host Ixodes ricinus to Investigate Their Symbiotic Relationship.}, journal = {Genome biology and evolution}, volume = {11}, number = {4}, pages = {1334-1344}, pmid = {30949677}, issn = {1759-6653}, mesh = {Animals ; Chlamydiales/*genetics/metabolism ; Female ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Host-Parasite Interactions ; Ixodes/*microbiology ; Symbiosis ; }, abstract = {The Rhabdochlamydiaceae family is one of the most widely distributed within the phylum Chlamydiae, but most of its members remain uncultivable. Rhabdochlamydia 16S rRNA was recently reported in more than 2% of 8,534 pools of ticks from Switzerland. Shotgun metagenomics was performed on a pool of five female Ixodes ricinus ticks presenting a high concentration of chlamydial DNA, allowing the assembly of a high-quality draft genome. About 60% of sequence reads originated from a single bacterial population that was named "Candidatus Rhabdochlamydia helvetica" whereas only few thousand reads mapped to the genome of "Candidatus Midichloria mitochondrii," a symbiont normally observed in all I. ricinus females. The 1.8 Mbp genome of R. helvetica is smaller than other Chlamydia-related bacteria. Comparative analyses with other chlamydial genomes identified transposases of the PD-(D/E)XK nuclease family that are unique to this new genome. These transposases show evidence of interphylum horizontal gene transfers between multiple arthropod endosymbionts, including Cardinium spp. (Bacteroidetes) and diverse proteobacteria such as Wolbachia, Rickettsia spp. (Rickettsiales), and Caedimonas varicaedens (Holosporales). Bacterial symbionts were previously suggested to provide B-vitamins to hematophagous hosts. However, incomplete metabolic capacities including for B-vitamin biosynthesis, high bacterial density and limited prevalence suggest that R. helvetica is parasitic rather than symbiotic to its host. The identification of novel Rhabdochlamydia strains in different hosts and their sequencing will help understanding if members of this genus have become highly specialized parasites with reduced genomes, like the Chlamydiaceae, or if they could be pathogenic to humans using ticks as a transmission vector.}, }
@article {pmid30949157, year = {2019}, author = {Galetti, R and Andrade, LN and Varani, AM and Darini, ALC}, title = {A Phage-Like Plasmid Carrying bla KPC-2 Gene in Carbapenem-Resistant Pseudomonas aeruginosa.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {572}, pmid = {30949157}, issn = {1664-302X}, abstract = {Background: Lateral gene transfer plays a central role in the dissemination of carbapenem resistance in bacterial pathogens associated with nosocomial infections, mainly Enterobacteriaceae and Pseudomonas aeruginosa. Despite their clinical significance, there is little information regarding the mobile genetic elements and mechanism of acquisition and propagation of lateral genes in P. aeruginosa, and they remain largely unknown. Objectives: The present study characterized the genetic context of bla KPC-2 in carbapenem-resistant P. aeruginosa strain BH9. Methods: Pseudomonas aeruginosa BH9 sequencing was performed using the long-read PacBio SMRT platform and the Ion Proton System. De novo assembly was carried out using the SMRT pipeline and Canu, and gene prediction and annotation were performed using Prokka and RAST. Results: Pseudomonas aeruginosa BH9 exhibited a 7.1 Mb circular chromosome. However, the bla KPC-2 gene is located in an additional contig composed by a small plasmid pBH6 from P. aeruginosa strain BH6 and several phage-related genes. Further analysis revealed that the beginning and end of the contig contain identical sequences, supporting a circular plasmid structure. This structure spans 41,087 bp, exhibiting all the Mu-like phage landmarks. In addition, 5-bp direct repeats (GGATG) flanking the pBH6 ends were found, strongly indicating integration of the Mu-like phage into the pBH6 plasmid. Mu phages are commonly found in P. aeruginosa. However, for the first time showing a potential impact in shaping the vehicles of the dissemination of antimicrobial (e.g., plasmid pBH6) resistance genes in the Pseudomonas genus. Conclusion: pBH6 captured the Mu-like Phage BH9, creating a co-integrate pBH6::Phage BH9, and this phage-plasmid complex may represent novel case of a phage-like plasmid.}, }
@article {pmid30948646, year = {2019}, author = {Zhang, Q and Chen, X and Xu, C and Zhao, H and Zhang, X and Zeng, G and Qian, Y and Liu, R and Guo, N and Mi, W and Meng, Y and Leger, RJS and Fang, W}, title = {Horizontal gene transfer allowed the emergence of broad host range entomopathogens.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {16}, pages = {7982-7989}, pmid = {30948646}, issn = {1091-6490}, mesh = {Animals ; Gene Transfer, Horizontal/*genetics ; Grasshoppers/microbiology ; Host Specificity/*genetics ; *Metarhizium/genetics/pathogenicity ; Virulence/*genetics ; }, abstract = {The emergence of new pathogenic fungi has profoundly impacted global biota, but the underlying mechanisms behind host shifts remain largely unknown. The endophytic insect pathogen Metarhizium robertsii evolved from fungi that were plant associates, and entomopathogenicity is a more recently acquired adaptation. Here we report that the broad host-range entomopathogen M. robertsii has 18 genes that are derived via horizontal gene transfer (HGT). The necessity of degrading insect cuticle served as a major selective pressure to retain these genes, as 12 are up-regulated during penetration; 6 were confirmed to have a role in penetration, and their collective actions are indispensable for infection. Two lipid-carrier genes are involved in utilizing epicuticular lipids, and a third (MrNPC2a) facilitates hemocoel colonization. Three proteases degraded the procuticular protein matrix, which facilitated up-regulation of other cuticle-degrading enzymes. The three lipid carriers and one of the proteases are present in all analyzed Metarhizium species and are essential for entomopathogenicity. Acquisition of another protease (MAA_01413) in an ancestor of broad host-range lineages contributed to their host-range expansion, as heterologous expression in the locust specialist Metarhizium acridum enabled it to kill caterpillars. Our work reveals that HGT was a key mechanism in the emergence of entomopathogenicity in Metarhizium from a plant-associated ancestor and in subsequent host-range expansion by some Metarhizium lineages.}, }
@article {pmid30946898, year = {2019}, author = {Sevillya, G and Snir, S}, title = {Synteny footprints provide clearer phylogenetic signal than sequence data for prokaryotic classification.}, journal = {Molecular phylogenetics and evolution}, volume = {136}, number = {}, pages = {128-137}, doi = {10.1016/j.ympev.2019.03.010}, pmid = {30946898}, issn = {1095-9513}, mesh = {Base Sequence ; Computer Simulation ; Databases, Genetic ; *Phylogeny ; Prokaryotic Cells/*classification ; Reproducibility of Results ; Synteny/*genetics ; }, abstract = {BACKGROUND: Extensive research efforts have been made to reconstruct the Tree of Life, aiming to explain the evolutionary history of life on earth. We expect the advent of next generation sequencing methods to bring us close to solving this challenge. Notwithstanding, with the accumulation of this mass of molecular data, it becomes evident that this solution is more complex and far from reach, especially among prokaryotes. One of the reasons for this is the ability of bacteria to perform horizontal gene transfer (HGT), creating substantial conflicts between different genes histories. Fortunately, evolution has equipped us with several markers with different levels of resolution, among which is synteny - the conservation of gene order along the chromosome.<br><br>RESULTS: We have performed a comprehensive phylogenomic study via synteny based footprints. We build on the synteny index (SI) concept, defined in a pilot work of ours, and extend it to a systematic phylogenetic method with well defined valid regions of operations. Applying it to the EggNOG repository, divides all species into 39 clusters, agreeing with the conventional taxonomy. We show analytically that the signal of the standard phylogenetic marker, the 16S, is too faint for reliable classification.<br><br>CONCLUSIONS: This work exhibits three separate yet related contributions. In terms of phylogenetics, it demonstrates quantitatively the advantage of the SI-based approach over the standard sequence based marker. Evolutionarily, the tree we produce is unique both in its specificity and broadness. Methodologically, the U-shape approach we developed, from synthetic realm, to real life and back to simulation, is novel and allow us to simulate the exact realistic conditions.}, }
@article {pmid30945693, year = {2019}, author = {Siddavattam, D and Yakkala, H and Samantarrai, D}, title = {Lateral transfer of organophosphate degradation (opd) genes among soil bacteria: mode of transfer and contributions to organismal fitness.}, journal = {Journal of genetics}, volume = {98}, number = {}, pages = {}, pmid = {30945693}, issn = {0973-7731}, mesh = {Bacteria/*enzymology/genetics ; Bacterial Proteins/*genetics/metabolism ; Base Sequence ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Organophosphates/*metabolism ; Phosphoric Triester Hydrolases/*genetics/metabolism ; Plasmids ; Sequence Homology ; Soil/*chemistry ; }, abstract = {Genes encoding structurally independent phosphotriesterases (PTEs) are identified in soil bacteria. These pte genes, often identified on mobilizable and self-transmissible plasmids are organized as mobile genetic elements. Their dissemination through lateral gene transfer is evident due to the detection of identical organophosphate degradation genes among soil bacteria with little orno taxonomic relationship. Convergent evolution of PTEs provided selective advantages to the bacterial strain as they convert toxic phosphotriesters (PTs) into a source of phosphate. The residues of organophosphate (OP) compounds that accumulate in a soil are proposed to contribute to the evolution of PTEs through substrate-assisted gain-of-function. This review provides comprehensive information on lateral transfer of pte genes and critically examines proposed hypotheses on their evolution in the light of the short half-life of OPs in the environment. The review also proposes alternate factors that have possibly contributed to the evolution and lateral mobility of PTEs by taking into account their biology and analyses of pte genes in genomic and metagenomic databases.}, }
@article {pmid30944881, year = {2019}, author = {Wu, Y and Liu, C and Li, WG and Xu, JL and Zhang, WZ and Dai, YF and Lu, JX}, title = {Independent Microevolution Mediated by Mobile Genetic Elements of Individual Clostridium difficile Isolates from Clade 4 Revealed by Whole-Genome Sequencing.}, journal = {mSystems}, volume = {4}, number = {2}, pages = {}, pmid = {30944881}, issn = {2379-5077}, abstract = {Horizontal gene transfer of mobile genetic elements (MGEs) accounts for the mosaic genome of Clostridium difficile, leading to acquisition of new phenotypes, including drug resistance and reconstruction of the genomes. MGEs were analyzed according to the whole-genome sequences of 37 C. difficile isolates with a variety of sequence types (STs) within clade 4 from China. Great diversity was found in each transposon even within isolates with the same ST. Two novel transposons were identified in isolates ZR9 and ZR18, of which approximately one third to half of the genes showed heterogenous origins compared with the usual intestinal bacterial genes. Most importantly, catD, known to be harbored by Tn4453a/b, was replaced by aac(6') aph(2'') in isolates 2, 7, and 28. This phenomenon illustrated the frequent occurrence of gene exchanges between C. difficile and other enterobacteria with individual heterogeneity. Numerous prophages and CRISPR arrays were identified in C. difficile isolates of clade 4. Approximately 20% of spacers were located in prophage-carried CRISPR arrays, providing a new method for typing and tracing the origins of closely related isolates, as well as in-depth studies of the mechanism underlying genome remodeling. The rates of drug resistance were obviously higher than those reported previously around the world, although all isolates retained high sensitivity to vancomycin and metronidazole. The increasing number of C. difficile isolates resistant to all antibiotics tested here suggests the ease with which resistance is acquired in vivo. This study gives insights into the genetic mechanism of microevolution within clade 4. IMPORTANCE Mobile genetic elements play a key role in the continuing evolution of Clostridium difficile, resulting in the emergence of new phenotypes for individual isolates. On the basis of whole-genome sequencing analysis, we comprehensively explored transposons, CRISPR, prophage, and genetic sites for drug resistance within clade 4 C. difficile isolates with different sequence types. Great diversity in MGEs and a high rate of multidrug resistance were found within this clade, including new transposons, Tn4453a/b with aac(6') aph(2'') instead of catD, and a relatively high rate of prophage-carried CRISPR arrays. These findings provide important new insights into the mechanism of genome remodeling within clade 4 and offer a new method for typing and tracing the origins of closely related isolates.}, }
@article {pmid30944871, year = {2019}, author = {Zwanzig, M and Harrison, E and Brockhurst, MA and Hall, JPJ and Berendonk, TU and Berger, U}, title = {Mobile Compensatory Mutations Promote Plasmid Survival.}, journal = {mSystems}, volume = {4}, number = {1}, pages = {}, pmid = {30944871}, issn = {2379-5077}, abstract = {The global dissemination of plasmids encoding antibiotic resistance represents an urgent issue for human health and society. While the fitness costs for host cells associated with plasmid acquisition are expected to limit plasmid dissemination in the absence of positive selection of plasmid traits, compensatory evolution can reduce this burden. Experimental data suggest that compensatory mutations can be located on either the chromosome or the plasmid, and these are likely to have contrasting effects on plasmid dynamics. Whereas chromosomal mutations are inherited vertically through bacterial fission, plasmid mutations can be inherited both vertically and horizontally and potentially reduce the initial cost of the plasmid in new host cells. Here we show using mathematical models and simulations that the dynamics of plasmids depends critically on the genomic location of the compensatory mutation. We demonstrate that plasmid-located compensatory evolution is better at enhancing plasmid persistence, even when its effects are smaller than those provided by chromosomal compensation. Moreover, either type of compensatory evolution facilitates the survival of resistance plasmids at low drug concentrations. These insights contribute to an improved understanding of the conditions and mechanisms driving the spread and the evolution of antibiotic resistance plasmids. IMPORTANCE Understanding the evolutionary forces that maintain antibiotic resistance genes in a population, especially when antibiotics are not used, is an important problem for human health and society. The most common platform for the dissemination of antibiotic resistance genes is conjugative plasmids. Experimental studies showed that mutations located on the plasmid or the bacterial chromosome can reduce the costs plasmids impose on their hosts, resulting in antibiotic resistance plasmids being maintained even in the absence of antibiotics. While chromosomal mutations are only vertically inherited by the daughter cells, plasmid mutations are also provided to bacteria that acquire the plasmid through conjugation. Here we demonstrate how the mode of inheritance of a compensatory mutation crucially influences the ability of plasmids to spread and persist in a bacterial population.}, }
@article {pmid30941540, year = {2019}, author = {Devanga Ragupathi, NK and Muthuirulandi Sethuvel, DP and Gajendran, R and Anandan, S and Walia, K and Veeraraghavan, B}, title = {Horizontal Transfer of Antimicrobial Resistance Determinants Among Enteric Pathogens Through Bacterial Conjugation.}, journal = {Current microbiology}, volume = {76}, number = {6}, pages = {666-672}, pmid = {30941540}, issn = {1432-0991}, support = {AMR/TF/55/13ECDII//Indian Council of Medical Research/ ; }, mesh = {Anti-Bacterial Agents/pharmacology ; *Conjugation, Genetic ; *Drug Resistance, Bacterial ; Escherichia coli/drug effects/*genetics/isolation &amp; purification ; Feces/microbiology ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Interspersed Repetitive Sequences ; Microbial Sensitivity Tests ; Plasmids/analysis ; Salmonella/drug effects/*genetics/isolation &amp; purification ; Shigella flexneri/drug effects/*genetics/isolation &amp; purification ; }, abstract = {Multi-drug resistance and transfer of mobile genetic elements among enteric pathogens is being reported to have increased rapidly. Commensal Escherichia coli was previously known to acquire mobile genetic elements from other genus/species. E. coli is also capable of disseminating these elements containing antimicrobial resistance determinants through horizontal transfer. Similarly, for Shigellae the antimicrobial resistance are on rise for fluoroquinolones and cephalosporins due to accumulation of mobile elements. Thus the study was hypothesized to investigate the role of transferable plasmids in commensal MDR E. coli vs Salmonella spp, and MDR Shigella flexneri vs Salmonella spp. pKP3-A plasmid containing qnrS1 was successfully transferred from E. coli to Salmonella spp. Similarly, a plasmid containing qnrS1 and blaCTX-M-15 was transferred from Shigella to Salmonella spp. However, blaCTX-M-15 was not transferred from E. coli as it was integrated into chromosome that was revealed by next-generation sequencing. This might be a reason that fluoroquinolone-resistant determinants are more frequently transferred than the cephalosporin resistant determinants. Findings from the study emphasize that mobile elements with AMR determinants are significant public health concern that has potential to rapidly disseminate.}, }
@article {pmid30939632, year = {2019}, author = {Hong, H and Lee, Y}, title = {Transfer of Antimicrobial-Resistant Escherichia coli and Resistance Genes in a Child Care Center.}, journal = {Journal of microbiology and biotechnology}, volume = {29}, number = {3}, pages = {465-472}, doi = {10.4014/jmb.1810.10068}, pmid = {30939632}, issn = {1738-8872}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Toxins/genetics ; *Child Care ; Child, Preschool ; Drug Resistance, Bacterial/*genetics ; Electrophoresis, Gel, Pulsed-Field/methods ; Escherichia coli/drug effects/enzymology/*genetics/isolation &amp; purification ; Escherichia coli Infections/microbiology ; Escherichia coli Proteins/genetics ; Feces/microbiology ; *Gene Transfer, Horizontal ; Humans ; Infant ; Microbial Sensitivity Tests ; Mutation ; Polymerase Chain Reaction/methods ; Quinolones/pharmacology ; Republic of Korea ; Virulence/genetics ; beta-Lactamases/genetics ; }, abstract = {Several reports describe antimicrobial-resistance transfer among children and the community in outbreak situations, but transfer between a child and a caregiver has not been examined in child care facilities under normal circumstances. We investigated the transfer of antimicrobialresistance genes, resistant bacteria, or both among healthy children and teachers. From 2007 to 2009, 104 Escherichia coli isolates were obtained from four teachers and 38 children in a child care center. Twenty-six cephem-resistant isolates were obtained from children in 2007 and 2008. In 2009, cephem-resistant isolates were detected in children as well as a teacher. Nalidixic acid-resistant isolates from the same teacher for 3 years showed low similarity (<50%) to each other. However, an isolate from a teacher in 2007 and another from a child in 2008 showed high similarity (87%). Pulsed-field gel electrophoresis revealed 100% similarity for four isolates in 2007 and one isolate in 2008, and also similarity among seven isolates carrying the virulence gene (CNF1). This study yielded the following findings: (1) a gene for extended-spectrum β-lactamase was transferred from a child to other children and a teacher; (2) a nalidixic acid-resistant isolate was transferred from a teacher to a child; and (3) a virulent bacterium was transferred between children.}, }
@article {pmid30939107, year = {2019}, author = {van Dorp, L and Wang, Q and Shaw, LP and Acman, M and Brynildsrud, OB and Eldholm, V and Wang, R and Gao, H and Yin, Y and Chen, H and Ding, C and Farrer, RA and Didelot, X and Balloux, F and Wang, H}, title = {Rapid phenotypic evolution in multidrug-resistant Klebsiella pneumoniae hospital outbreak strains.}, journal = {Microbial genomics}, volume = {5}, number = {4}, pages = {}, pmid = {30939107}, issn = {2057-5858}, support = {MR/N006364/1/MRC_/Medical Research Council/United Kingdom ; MR/N006364/2/MRC_/Medical Research Council/United Kingdom ; MR/P007597/1/MRC_/Medical Research Council/United Kingdom ; MR/R015600/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Carbapenem-Resistant Enterobacteriaceae/*genetics ; *Cross Infection/epidemiology/microbiology ; Disease Outbreaks ; Drug Resistance, Multiple, Bacterial/*genetics ; Genetic Variation ; Genome, Bacterial ; Humans ; *Klebsiella Infections/epidemiology/microbiology ; Klebsiella pneumoniae/*genetics ; Phylogeny ; Whole Genome Sequencing/methods ; }, abstract = {Carbapenem-resistant Klebsiella pneumoniae (CRKP) increasingly cause high-mortality outbreaks in hospital settings globally. Following a patient fatality at a hospital in Beijing due to a blaKPC-2-positive CRKP infection, close monitoring was put in place over the course of 14 months to characterize all blaKPC-2-positive CRKP in circulation in the hospital. Whole genome sequences were generated for 100 isolates from blaKPC-2-positive isolates from infected patients, carriers and the hospital environment. Phylogenetic analyses identified a closely related cluster of 82 sequence type 11 (ST11) isolates circulating in the hospital for at least a year prior to admission of the index patient. The majority of inferred transmissions for these isolates involved patients in intensive care units. Whilst the 82 ST11 isolates collected during the surveillance effort all had closely related chromosomes, we observed extensive diversity in their antimicrobial resistance (AMR) phenotypes. We were able to reconstruct the major genomic changes underpinning this variation in AMR profiles, including multiple gains and losses of entire plasmids and recombination events between plasmids, including transposition of blaKPC-2. We also identified specific cases where variation in plasmid copy number correlated with the level of phenotypic resistance to drugs, suggesting that the number of resistance elements carried by a strain may play a role in determining the level of AMR. Our findings highlight the epidemiological value of whole genome sequencing for investigating multi-drug-resistant hospital infections and illustrate that standard typing schemes cannot capture the extraordinarily fast genome evolution of CRKP isolates.}, }
@article {pmid30936095, year = {2019}, author = {Ma, F and Shen, C and Zheng, X and Liu, Y and Chen, H and Zhong, L and Liang, Y and Liao, K and Xia, Y and Tian, GB and Yang, Y}, title = {Identification of a Novel Plasmid Carrying mcr-4.3 in an Acinetobacter baumannii Strain in China.}, journal = {Antimicrobial agents and chemotherapy}, volume = {63}, number = {6}, pages = {}, pmid = {30936095}, issn = {1098-6596}, mesh = {Acinetobacter Infections/*microbiology ; Acinetobacter baumannii/drug effects/enzymology/*genetics/isolation &amp; purification ; Animals ; Anti-Bacterial Agents/*pharmacology ; China ; Colistin/*pharmacology ; Drug Resistance, Bacterial/*genetics ; Feces/microbiology ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Plasmids/genetics ; Swine ; Swine Diseases/*microbiology ; }, abstract = {Here, we identified mcr-4.3 in Acinetobacter baumannii, which had not been previously observed to carry an mcr gene. The mcr-4.3-harboring A. baumannii strain AB18PR065 was isolated from pig feces from a slaughterhouse in Guangdong Province of China. The mcr-4.3-carrying pAB18PR065 is 25,602 bp in size and could not be transferred in conjugation, transformation, and electroporation experiments, as we did not find any conjugation-related genes therein. pAB18PR065 harbors two copies of type II toxin-antitoxin systems, which are functional in plasmid stabilization and maintenance. pAB18PR065 shares similarity only with one recently identified plasmid, pAb-MCR4.3 (35,502 bp), from a clinical A. baumannii strain. It is likely that the emergence of pAb-MCR4.3 was due to the insertion of an 11,386-bp, ISAba19-based, composite transposon into pAB18PR065. These data indicate that mcr-4.3 was captured by an A. baumannii-original plasmid via horizontal gene transfer.}, }
@article {pmid30935921, year = {2019}, author = {Nguyen, TH and Barnes, CL and Agola, JP and Sherazi, S and Greene, LH and Lee, JW}, title = {Demonstration of horizontal gene transfer from genetically engineered Thermosynechococcus elongatus BP1 to wild-type E. coli DH5α.}, journal = {Gene}, volume = {704}, number = {}, pages = {49-58}, doi = {10.1016/j.gene.2019.03.014}, pmid = {30935921}, issn = {1879-0038}, mesh = {Cloning, Molecular ; Cyanobacteria/classification/*genetics ; DNA, Bacterial/genetics ; Escherichia coli/*genetics ; *Gene Transfer, Horizontal ; Genetic Engineering/methods ; Microbiological Techniques ; Organisms, Genetically Modified ; Synechococcus/genetics ; Synthetic Biology ; Transformation, Bacterial/genetics ; }, abstract = {Synthetic biology with genetically engineered (GE) cyanobacteria has the potential to produce valuable products such as biofuels. However, it is also essential to assess the potential risks of synthetic biology technology before it can be widely used. In order to address key concerns posed by the application of synthetic biology to microorganisms, studies were designed to monitor the horizontal transfer of engineered genes from GE cyanobacteria Thermosynechococcus elongatus BP1 to Escherichia coli through co-incubation. The results of these experiments demonstrated that the genetically engineered DNA construct containing alcohol producing genes and kanamycin resistance can be horizontally transferred from GE T. elongatus BP1 to wild-type E. coli following two days of liquid co-culturing. The rapid and facile transfer of foreign genes, which include antibiotic resistance, between bacterial communities signifies the need to continue to deepen our understanding of the process of horizontal gene transfer, chromosomal integration as well as further biosafety-oriented research efforts. In the era of synthetic biology, the natural microbial process for sharing genetic material will also significantly impact risk assessments, containment approaches and further policy development.}, }
@article {pmid30935422, year = {2019}, author = {Panfilio, KA and Vargas Jentzsch, IM and Benoit, JB and Erezyilmaz, D and Suzuki, Y and Colella, S and Robertson, HM and Poelchau, MF and Waterhouse, RM and Ioannidis, P and Weirauch, MT and Hughes, DST and Murali, SC and Werren, JH and Jacobs, CGC and Duncan, EJ and Armisén, D and Vreede, BMI and Baa-Puyoulet, P and Berger, CS and Chang, CC and Chao, H and Chen, MM and Chen, YT and Childers, CP and Chipman, AD and Cridge, AG and Crumière, AJJ and Dearden, PK and Didion, EM and Dinh, H and Doddapaneni, HV and Dolan, A and Dugan, S and Extavour, CG and Febvay, G and Friedrich, M and Ginzburg, N and Han, Y and Heger, P and Holmes, CJ and Horn, T and Hsiao, YM and Jennings, EC and Johnston, JS and Jones, TE and Jones, JW and Khila, A and Koelzer, S and Kovacova, V and Leask, M and Lee, SL and Lee, CY and Lovegrove, MR and Lu, HL and Lu, Y and Moore, PJ and Munoz-Torres, MC and Muzny, DM and Palli, SR and Parisot, N and Pick, L and Porter, ML and Qu, J and Refki, PN and Richter, R and Rivera-Pomar, R and Rosendale, AJ and Roth, S and Sachs, L and Santos, ME and Seibert, J and Sghaier, E and Shukla, JN and Stancliffe, RJ and Tidswell, O and Traverso, L and van der Zee, M and Viala, S and Worley, KC and Zdobnov, EM and Gibbs, RA and Richards, S}, title = {Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {64}, pmid = {30935422}, issn = {1474-760X}, support = {R01 GM080203/GM/NIGMS NIH HHS/United States ; R01 HG004483/HG/NHGRI NIH HHS/United States ; U54 HG003273/HG/NHGRI NIH HHS/United States ; R01 GM113230/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; CYS2-HIS2 Zinc Fingers ; *Evolution, Molecular ; Feeding Behavior ; Gene Dosage ; Gene Expression Profiling ; Gene Transfer, Horizontal ; Genes, Homeobox ; *Genome, Insect ; Hemiptera/*genetics/growth &amp; development/metabolism ; Pigmentation/genetics ; Smell ; Transcription Factors/genetics ; }, abstract = {BACKGROUND: The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae.<br><br>RESULTS: The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding.<br><br>CONCLUSIONS: With the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus's strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes.}, }
@article {pmid30930868, year = {2019}, author = {Timilsina, S and Pereira-Martin, JA and Minsavage, GV and Iruegas-Bocardo, F and Abrahamian, P and Potnis, N and Kolaczkowski, B and Vallad, GE and Goss, EM and Jones, JB}, title = {Multiple Recombination Events Drive the Current Genetic Structure of Xanthomonas perforans in Florida.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {448}, pmid = {30930868}, issn = {1664-302X}, abstract = {Prior to the identification of Xanthomonas perforans associated with bacterial spot of tomato in 1991, X. euvesicatoria was the only known species in Florida. Currently, X. perforans is the Xanthomonas sp. associated with tomato in Florida. Changes in pathogenic race and sequence alleles over time signify shifts in the dominant X. perforans genotype in Florida. We previously reported recombination of X. perforans strains with closely related Xanthomonas species as a potential driving factor for X. perforans evolution. However, the extent of recombination across the X. perforans genomes was unknown. We used a core genome multilocus sequence analysis approach to identify conserved genes and evaluated recombination-associated evolution of these genes in X. perforans. A total of 1,356 genes were determined to be "core" genes conserved among the 58 X. perforans genomes used in the study. Our approach identified three genetic groups of X. perforans in Florida based on the principal component analysis (PCA) using core genes. Nucleotide variation in 241 genes defined these groups, that are referred as Phylogenetic-group Defining (PgD) genes. Furthermore, alleles of many of these PgD genes showed 100% sequence identity with X. euvesicatoria, suggesting that variation likely has been introduced by recombination at multiple locations throughout the bacterial chromosome. Site-specific recombinase genes along with plasmid mobilization and phage associated genes were observed at different frequencies in the three phylogenetic groups and were associated with clusters of recombinant genes. Our analysis of core genes revealed the extent, source, and mechanisms of recombination events that shaped the current population and genomic structure of X. perforans in Florida.}, }
@article {pmid30930513, year = {2019}, author = {Koonin, EV}, title = {CRISPR: a new principle of genome engineering linked to conceptual shifts in evolutionary biology.}, journal = {Biology &amp; philosophy}, volume = {34}, number = {1}, pages = {9}, pmid = {30930513}, issn = {0169-3867}, abstract = {The CRISPR-Cas systems of bacterial and archaeal adaptive immunity have become a household name among biologists and even the general public thanks to the unprecedented success of the new generation of genome editing tools utilizing Cas proteins. However, the fundamental biological features of CRISPR-Cas are of no lesser interest and have major impacts on our understanding of the evolution of antivirus defense, host-parasite coevolution, self versus non-self discrimination and mechanisms of adaptation. CRISPR-Cas systems present the best known case in point for Lamarckian evolution, i.e. generation of heritable, adaptive genomic changes in response to encounters with external factors, in this case, foreign nucleic acids. CRISPR-Cas systems employ multiple mechanisms of self versus non-self discrimination but, as is the case with immune systems in general, are nevertheless costly because autoimmunity cannot be eliminated completely. In addition to the autoimmunity, the fitness cost of CRISPR-Cas systems appears to be determined by their inhibitory effect on horizontal gene transfer, curtailing evolutionary innovation. Hence the dynamic evolution of CRISPR-Cas loci that are frequently lost and (re)acquired by archaea and bacteria. Another fundamental biological feature of CRISPR-Cas is its intimate connection with programmed cell death and dormancy induction in microbes. In this and, possibly, other immune systems, active immune response appears to be coupled to a different form of defense, namely, "altruistic" shutdown of cellular functions resulting in protection of neighboring cells. Finally, analysis of the evolutionary connections of Cas proteins reveals multiple contributions of mobile genetic elements (MGE) to the origin of various components of CRISPR-Cas systems, furthermore, different biological systems that function by genome manipulation appear to have evolved convergently from unrelated MGE. The shared features of adaptive defense systems and MGE, namely the ability to recognize and cleave unique sites in genomes, make them ideal candidates for genome editing and engineering tools.}, }
@article {pmid30929798, year = {2019}, author = {Bedoya-Correa, CM and Rincón Rodríguez, RJ and Parada-Sanchez, MT}, title = {Genomic and phenotypic diversity of Streptococcus mutans.}, journal = {Journal of oral biosciences}, volume = {61}, number = {1}, pages = {22-31}, doi = {10.1016/j.job.2018.11.001}, pmid = {30929798}, issn = {1880-3865}, mesh = {Biofilms ; *Dental Caries ; Genomics ; Humans ; *Streptococcus mutans ; Virulence Factors ; }, abstract = {BACKGROUND: Streptococcus mutans (S. mutans) is a commensal microorganism found in the human oral cavity. However, due to environmental changes, selective pressures, and the presence of a variable genome, it adapts and may acquire new physiological and metabolic properties that alter dental biofilm homeostasis, promoting the development of dental caries. Although the plasticity and heterogeneity of S. mutans is widely recognized, very little is known about the mechanisms for the expression of pathogenic properties in specific genotypes.<br><br>HIGHLIGHT: The implementation of molecular biology techniques in the study of S. mutans has provided information on the genomic diversity of this species. This variability is generated by genome rearrangements, natural genetic transformation, and horizontal gene transfer, and continues to grow due to an open pan-genome. The main virulence factors associated with the cariogenic potential of S. mutans include adhesion, acid production (acidogenicity), and acid tolerance (aciduricity), and also show variability. These factors coordinate the modification of the physicochemical properties of the biofilm, which results in the accumulation of S. mutans and other acidogenic and aciduric species in the oral cavity.<br><br>CONCLUSION: We review the current literature on the main processes that generate S. mutans genomic diversity, as well as the phenotypic variability of its main virulence factors. S. mutans achieves its pathogenesis by sensing the intra- and extracellular environments and regulating gene transcription according to perceived environmental modifications. Consequently, this regulation gives rise to differential synthesis of proteins, allowing this species to potentially express virulence factors.}, }
@article {pmid30928844, year = {2019}, author = {Kim, DW and Thawng, CN and Lee, K and Wellington, EMH and Cha, CJ}, title = {A novel sulfonamide resistance mechanism by two-component flavin-dependent monooxygenase system in sulfonamide-degrading actinobacteria.}, journal = {Environment international}, volume = {127}, number = {}, pages = {206-215}, doi = {10.1016/j.envint.2019.03.046}, pmid = {30928844}, issn = {1873-6750}, mesh = {Actinobacteria/*drug effects/*enzymology ; *Drug Resistance, Bacterial ; Flavins/*metabolism ; Mixed Function Oxygenases/*metabolism ; Sulfonamides/*pharmacology ; }, abstract = {Sulfonamide-degrading bacteria have been discovered in various environments, suggesting the presence of novel resistance mechanisms via drug inactivation. In this study, Microbacterium sp. CJ77 capable of utilizing various sulfonamides as a sole carbon source was isolated from a composting facility. Genome and proteome analyses revealed that a gene cluster containing a flavin-dependent monooxygenase and a flavin reductase was highly up-regulated in response to sulfonamides. Biochemical analysis showed that the two-component monooxygenase system was key enzymes for the initial cleavage of sulfonamides. Co-expression of the two-component system in Escherichia coli conferred decreased susceptibility to sulfamethoxazole, indicating that the genes encoding drug-inactivating enzymes are potential resistance determinants. Comparative genomic analysis revealed that the gene cluster containing sulfonamide monooxygenase (renamed as sulX) and flavin reductase (sulR) was highly conserved in a genomic island shared among sulfonamide-degrading actinobacteria, all of which also contained sul1-carrying class 1 integrons. These results suggest that the sulfonamide metabolism may have evolved in sulfonamide-resistant bacteria which had already acquired the class 1 integron under sulfonamide selection pressures. Furthermore, the presence of multiple insertion sequence elements and putative composite transposon structures containing the sulX gene cluster indicated potential mobilization. This is the first study to report that sulX responsible for both sulfonamide degradation and resistance is prevalent in sulfonamide-degrading actinobacteria and its genetic signatures indicate horizontal gene transfer of the novel resistance gene.}, }
@article {pmid30928272, year = {2019}, author = {Coimbra-E-Souza, V and Rossi, CC and Jesus-de Freitas, LJ and Brito, MAVP and Laport, MS and Giambiagi-deMarval, M}, title = {Short communication: Diversity of species and transmission of antimicrobial resistance among Staphylococcus spp. isolated from goat milk.}, journal = {Journal of dairy science}, volume = {102}, number = {6}, pages = {5518-5524}, doi = {10.3168/jds.2018-15723}, pmid = {30928272}, issn = {1525-3198}, mesh = {Ampicillin/pharmacology ; Animals ; Anti-Bacterial Agents/*pharmacology ; Dairying ; Drug Resistance, Bacterial/*genetics ; Female ; Gene Transfer, Horizontal ; Goat Diseases/*microbiology ; Goats ; Milk/*microbiology ; Penicillin G/pharmacology ; Staphylococcal Infections/microbiology/*veterinary ; Staphylococcus/drug effects/*genetics ; Staphylococcus lugdunensis/drug effects/genetics ; }, abstract = {The increasing production of goat milk and its derivatives is affected by the occurrence of intramammary infections, which are highly associated with the presence of Staphylococcus species, including some with zoonotic potential. Staphylococci in general can exchange mobile genetic elements, a process that may be facilitated by the isolate's capacity of forming biofilms. In this study we identified, to the species level, Staphylococcus isolated from goat milk samples by MALDI-TOF and confirmed the identification by sequencing housekeeping genes (rrs and tuf). Eight species were identified, more than half being either Staphylococcus epidermidis or Staphylococcus lugdunensis. The isolates were shown by pulsed-field gel electrophoresis to be genetically diverse between the studied herds. Resistance to ampicillin and penicillin was widespread, and 2 Staph. epidermidis isolates contained the methicillin-resistance gene mecA. Most of the isolates that were resistant to at least 1 of the 13 antimicrobials tested harbored plasmids, one of which was demonstrated to be conjugative, being transferred from a Staph. epidermidis to a Staphylococcus aureus strain. Biofilm formation was observed in almost every isolate, which may contribute to their capacity of exchanging antimicrobial resistance genes in addition to acting as a physical barrier to the access of drugs. Our results showed that antimicrobial resistance among goat staphylococci may be emerging in a process facilitated by the exchange of mobile genetic elements between the bacteria and the establishment of biofilms, which calls for careful monitoring and more effective control therapies.}, }
@article {pmid30925042, year = {2019}, author = {Stark, JC and Huang, A and Hsu, KJ and Dubner, RS and Forbrook, J and Marshalla, S and Rodriguez, F and Washington, M and Rybnicky, GA and Nguyen, PQ and Hasselbacher, B and Jabri, R and Kamran, R and Koralewski, V and Wightkin, W and Martinez, T and Jewett, MC}, title = {BioBits Health: Classroom Activities Exploring Engineering, Biology, and Human Health with Fluorescent Readouts.}, journal = {ACS synthetic biology}, volume = {8}, number = {5}, pages = {1001-1009}, doi = {10.1021/acssynbio.8b00381}, pmid = {30925042}, issn = {2161-5063}, mesh = {CRISPR-Cas Systems/genetics ; Cell-Free System ; Drug Resistance, Microbial/genetics ; Gene Editing/methods ; Gene Transfer, Horizontal ; *Genetic Engineering ; Humans ; Optical Imaging ; Synthetic Biology/*education/methods ; }, abstract = {Recent advances in synthetic biology have resulted in biological technologies with the potential to reshape the way we understand and treat human disease. Educating students about the biology and ethics underpinning these technologies is critical to empower them to make informed future policy decisions regarding their use and to inspire the next generation of synthetic biologists. However, hands-on, educational activities that convey emerging synthetic biology topics can be difficult to implement due to the expensive equipment and expertise required to grow living cells. We present BioBits Health, an educational kit containing lab activities and supporting curricula for teaching antibiotic resistance mechanisms and CRISPR-Cas9 gene editing in high school classrooms. This kit links complex biological concepts to visual, fluorescent readouts in user-friendly freeze-dried cell-free reactions. BioBits Health represents a set of educational resources that promises to encourage teaching of cutting-edge, health-related synthetic biology topics in classrooms and other nonlaboratory settings.}, }
@article {pmid30923328, year = {2019}, author = {Bharathan, S and Sundaramoorthy, NS and Chandrasekaran, H and Rangappa, G and ArunKumar, G and Subramaniyan, SB and Veerappan, A and Nagarajan, S}, title = {Sub lethal levels of platinum nanoparticle cures plasmid and in combination with carbapenem, curtails carbapenem resistant Escherichia coli.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {5305}, pmid = {30923328}, issn = {2045-2322}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology/therapeutic use ; Biofilms/drug effects ; Ceftriaxone/pharmacology/therapeutic use ; Cell Membrane/drug effects ; DNA Cleavage/drug effects ; Disease Models, Animal ; Dose-Response Relationship, Drug ; Drug Resistance, Multiple, Bacterial/*drug effects/genetics ; Drug Therapy, Combination ; Escherichia coli/drug effects/genetics/physiology ; Escherichia coli Infections/*drug therapy/microbiology ; Gene Transfer, Horizontal ; Humans ; Meropenem/pharmacology/therapeutic use ; Metal Nanoparticles/*administration &amp; dosage ; Microbial Sensitivity Tests ; Plasmids/*drug effects/genetics ; Platinum/*administration &amp; dosage ; Zebrafish ; }, abstract = {Drug resistance traits are rapidly disseminated across bacteria by horizontal gene transfer, especially through plasmids. Plasmid curing agents that are active both in vitro and in vivo will resensitize Multi Drug Resistant (MDR) bacteria to antimicrobial agents. Pectin capped platinum nanoparticles (PtNPs) at sub MIC (20 µM) concentration was effective, in causing loss of Extended Spectrum Beta Lactamase (ESBL) harboring plasmid as evidenced by, absence of plasmid in agarose gel and by a concomitant (16-64 fold) drop in MIC for cell wall inhibitors ceftriaxone and meropenem, in carbapenem resistant Escherichia coli (CREC). Interestingly, the plasmid cured strain exhibited small colony morphology and displayed slower growth both in vitro and in vivo. Complementation of cured strain with plasmid from the wild type strain restored resistance towards meropenem and ceftriaxone. Relative to wild type, plasmid cured strain displayed 50% reduction in biofilm formation. Plasmid curing also occurred in vivo in infected zebrafish with curing efficiency of 17% for nanoparticle + meropenem treatment. PtNPs + meropenem reduced bioburden of CREC in infected zebrafish by 2.4 log CFU. Mechanistic studies revealed that nanoparticle interacted with cell surface and perturbed inner membrane integrity. PtNPs did not induce ROS, yet it caused plasmid DNA cleavage, as evidenced by gyrase inhibition assay. Our study for the first time reveals that PtNPs as plasmid curing agent can resensitize MDR bacteria to selective antimicrobial agents in vivo.}, }
@article {pmid30922803, year = {2019}, author = {Rahbar, MR and Zarei, M and Jahangiri, A and Khalili, S and Nezafat, N and Negahdaripour, M and Fattahian, Y and Ghasemi, Y}, title = {Trimeric autotransporter adhesins in Acinetobacter baumannii, coincidental evolution at work.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {71}, number = {}, pages = {116-127}, doi = {10.1016/j.meegid.2019.03.023}, pmid = {30922803}, issn = {1567-7257}, mesh = {Acinetobacter Infections ; Acinetobacter baumannii/*genetics ; Adhesins, Bacterial/genetics ; Computational Biology ; Cross Infection/microbiology ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Humans ; Type V Secretion Systems/*genetics ; Virulence Factors/genetics ; }, abstract = {Trimeric autotransporter (TAA), also known as type Vc secretion system, is expressed by many strains of Acinetobacter baumannii, an opportunistic pathogen, which is responsible for nosocomial infections worldwide. TAAs, are modular homotrimeric virulence factors, containing a signal peptide, complex stalk, and conserved membrane anchoring domain. The evolutionary mechanisms underlying the evolvement of these adhesins are not clear. Here, we showed that TAA genes were laterally acquired and underwent gene duplication and recombination. The heterogeneity of TAA nucleotide sequences, GC content, codon usage, and the probability of recombination and duplication events were assessed by MEGA7. Given the heterogeneity of sequences, we used all-against-all BLAST for clustering the TAAs. The pattern of distribution of TAAs are highly scattered; GC content and codon usage for these genes are variable. Multiple events of lateral gene transfer from the early history of Acinetobacter and the occurrence of gene duplication, gene loss, and recombination after acquiring the alien genes may explain the scattered pattern of distribution of TAAs. Additionally, this gene is not present in many clinical isolates of A. baumannii, thus is not a single virulence factor attributing to the infection. The advantage of harboring such genes might be adopting to different environments by developing the biofilm communities. We suggested that TAA genes were laterally acquired in the environmental context and incidentally provided some benefits at the infection site. Thus, coincidental evolution theory may be better suited for describing the evolution of TAA genes in A. baumannii genomes.}, }
@article {pmid30922221, year = {2019}, author = {Oppong, YEA and Phelan, J and Perdigão, J and Machado, D and Miranda, A and Portugal, I and Viveiros, M and Clark, TG and Hibberd, ML}, title = {Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {252}, pmid = {30922221}, issn = {1471-2164}, support = {MC_PC_15103/MRC_/Medical Research Council/United Kingdom ; UID/Multi/04413/2013//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; MR/R020973/1/MRC_/Medical Research Council/United Kingdom ; MR/M01360X/1/MRC_/Medical Research Council/United Kingdom ; MR/R025576/1/MRC_/Medical Research Council/United Kingdom ; MR/N010469/1/MRC_/Medical Research Council/United Kingdom ; BB/J014567/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/K000551/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Bacterial Proteins/genetics ; Drug Resistance, Multiple, Bacterial ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome-Wide Association Study/*methods ; Microbial Sensitivity Tests ; Mycobacterium tuberculosis/drug effects/*genetics ; *Polymorphism, Genetic ; *Tuberculosis, Multidrug-Resistant ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: Continuing evolution of the Mycobacterium tuberculosis (Mtb) complex genomes associated with resistance to anti-tuberculosis drugs is threatening tuberculosis disease control efforts. Both multi- and extensively drug resistant Mtb (MDR and XDR, respectively) are increasing in prevalence, but the full set of Mtb genes involved are not known. There is a need for increased sensitivity of genome-wide approaches in order to elucidate the genetic basis of anti-microbial drug resistance and gain a more detailed understanding of Mtb genome evolution in a context of widespread antimicrobial therapy. Population structure within the Mtb complex, due to clonal expansion, lack of lateral gene transfer and low levels of recombination between lineages, may be reducing statistical power to detect drug resistance associated variants.<br><br>RESULTS: To investigate the effect of lineage-specific effects on the identification of drug resistance associations, we applied genome-wide association study (GWAS) and convergence-based (PhyC) methods to multiple drug resistance phenotypes of a global dataset of Mtb lineages 2 and 4, using both lineage-wise and combined approaches. We identify both well-established drug resistance variants and novel associations; uniquely identifying associations for both lineage-specific and -combined GWAS analyses. We report 17 potential novel associations between antimicrobial resistance phenotypes and Mtb genomic variants.<br><br>CONCLUSIONS: For GWAS, both lineage-specific and -combined analyses are useful, whereas PhyC may perform better in contexts of greater diversity. Unique associations with XDR in lineage-specific analyses provide evidence of diverging evolutionary trajectories between lineages 2 and 4 in response to antimicrobial drug therapy.}, }
@article {pmid30919144, year = {2019}, author = {Godinho, O and Calisto, R and Øvreås, L and Quinteira, S and Lage, OM}, title = {Antibiotic susceptibility of marine Planctomycetes.}, journal = {Antonie van Leeuwenhoek}, volume = {112}, number = {8}, pages = {1273-1280}, doi = {10.1007/s10482-019-01259-7}, pmid = {30919144}, issn = {1572-9699}, support = {UID/Multi/04423/2013//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Aquatic Organisms/*drug effects ; Disk Diffusion Antimicrobial Tests ; Drug Resistance, Bacterial ; Planctomycetales/*drug effects ; }, abstract = {Antimicrobials are naturally produced by microbes and therefore have always been present in their environment, as well as accompanying resistance mechanisms. The antibiotic resistance profile of environmental species is particularly relevant since genetic determinants of resistance can spread through horizontal gene transfer and reach clinically important species. The phylum Planctomycetes comprises Gram-negative bacteria characterised by unusual features and appear to be ubiquitously distributed. Members of this group have recently been characterised as producers of bioactive compounds, namely antimicrobials, but their antibiotic susceptibility profile has been scarcely studied. In this study, the antibiotic susceptibility profile of six phylogenetically distinct strains of Planctomycetes was assessed. All strains showed resistance to beta-lactams, aminoglycosides and glycopeptides. Our results showed that antibiotics which target protein synthesis or DNA replication, with the exception of aminoglycosides, were the most effective against the tested strains. The highest efficacy was observed for chloramphenicol, clindamycin and ciprofloxacin. The highest level of antimicrobial resistance was observed in the uncharacterised novel taxon Planctomyces sp. strain FF15 which was only susceptible to erythromycin and ciprofloxacin.}, }
@article {pmid30918968, year = {2019}, author = {Smith, BA and Leligdon, C and Baltrus, DA}, title = {Just the Two of Us? A Family of Pseudomonas Megaplasmids Offers a Rare Glimpse into the Evolution of Large Mobile Elements.}, journal = {Genome biology and evolution}, volume = {11}, number = {4}, pages = {1192-1206}, pmid = {30918968}, issn = {1759-6653}, mesh = {*Evolution, Molecular ; Genes, Essential ; Multigene Family ; Plasmids/*genetics ; Pseudomonas putida/*genetics ; Pseudomonas syringae/*genetics ; RNA, Transfer/genetics ; }, abstract = {Pseudomonads are ubiquitous group of environmental proteobacteria, well known for their roles in biogeochemical cycling, in the breakdown of xenobiotic materials, as plant growth promoters, and as pathogens of a variety of host organisms. We have previously identified a large megaplasmid present within one isolate of the plant pathogen Pseudomonas syringae, and here we report that a second member of this megaplasmid family is found within an environmental Pseudomonad isolate most closely related to Pseudomonas putida. Many of the shared genes are involved in critical cellular processes like replication, transcription, translation, and DNA repair. We argue that presence of these shared pathways sheds new light on discussions about the types of genes that undergo horizontal gene transfer (i.e., the complexity hypothesis) as well as the evolution of pangenomes. Furthermore, although both megaplasmids display a high level of synteny, genes that are shared differ by over 50% on average at the amino acid level. This combination of conservation in gene order despite divergence in gene sequence suggests that this Pseudomonad megaplasmid family is relatively old, that gene order is under strong selection within this family, and that there are likely many more members of this megaplasmid family waiting to be found in nature.}, }
@article {pmid30917781, year = {2019}, author = {Shelyakin, PV and Bochkareva, OO and Karan, AA and Gelfand, MS}, title = {Micro-evolution of three Streptococcus species: selection, antigenic variation, and horizontal gene inflow.}, journal = {BMC evolutionary biology}, volume = {19}, number = {1}, pages = {83}, pmid = {30917781}, issn = {1471-2148}, mesh = {Animals ; Antigenic Variation/*genetics ; *Biological Evolution ; Conserved Sequence/genetics ; DNA, Intergenic ; Gene Flow ; Gene Ontology ; Gene Rearrangement/genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genome Size ; Humans ; Hydrolases/metabolism ; Nucleotides/genetics ; Phylogeny ; *Selection, Genetic ; Sequence Deletion ; Species Specificity ; Streptococcus/*genetics ; Streptococcus pneumoniae/genetics ; Virulence/genetics ; }, abstract = {BACKGROUND: The genus Streptococcus comprises pathogens that strongly influence the health of humans and animals. Genome sequencing of multiple Streptococcus strains demonstrated high variability in gene content and order even in closely related strains of the same species and created a newly emerged object for genomic analysis, the pan-genome. Here we analysed the genome evolution of 25 strains of Streptococcus suis, 50 strains of Streptococcus pyogenes and 28 strains of Streptococcus pneumoniae.<br><br>RESULTS: Fractions of the pan-genome, unique, periphery, and universal genes differ in size, functional composition, the level of nucleotide substitutions, and predisposition to horizontal gene transfer and genomic rearrangements. The density of substitutions in intergenic regions appears to be correlated with selection acting on adjacent genes, implying that more conserved genes tend to have more conserved regulatory regions. The total pan-genome of the genus is open, but only due to strain-specific genes, whereas other pan-genome fractions reach saturation. We have identified the set of genes with phylogenies inconsistent with species and non-conserved location in the chromosome; these genes are rare in at least one species and have likely experienced recent horizontal transfer between species. The strain-specific fraction is enriched with mobile elements and hypothetical proteins, but also contains a number of candidate virulence-related genes, so it may have a strong impact on adaptability and pathogenicity. Mapping the rearrangements to the phylogenetic tree revealed large parallel inversions in all species. A parallel inversion of length 15 kB with breakpoints formed by genes encoding surface antigen proteins PhtD and PhtB in S. pneumoniae leads to replacement of gene fragments that likely indicates the action of an antigen variation mechanism.<br><br>CONCLUSIONS: Members of genus Streptococcus have a highly dynamic, open pan-genome, that potentially confers them with the ability to adapt to changing environmental conditions, i.e. antibiotic resistance or transmission between different hosts. Hence, integrated analysis of all aspects of genome evolution is important for the identification of potential pathogens and design of drugs and vaccines.}, }
@article {pmid30913237, year = {2019}, author = {Vounba, P and Arsenault, J and Bada-Alambédji, R and Fairbrother, JM}, title = {Prevalence of antimicrobial resistance and potential pathogenicity, and possible spread of third generation cephalosporin resistance, in Escherichia coli isolated from healthy chicken farms in the region of Dakar, Senegal.}, journal = {PloS one}, volume = {14}, number = {3}, pages = {e0214304}, pmid = {30913237}, issn = {1932-6203}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics ; Cephalosporins/*pharmacology ; Chickens/*microbiology ; DNA Gyrase/genetics ; DNA Topoisomerase IV/genetics ; Drug Resistance, Multiple, Bacterial/*drug effects/genetics ; Escherichia coli/*isolation &amp; purification/metabolism/pathogenicity ; Farms ; Microbial Sensitivity Tests ; Mutation ; Poultry Diseases/diagnosis/epidemiology/microbiology ; Prevalence ; Risk Factors ; Senegal/epidemiology ; Virulence/genetics ; beta-Lactamases/genetics/metabolism ; }, abstract = {Escherichia coli is a normal inhabitant of the intestinal microbiota of chickens, a small proportion of which may be avian pathogenic E. coli (APEC) or potential extraintestinal pathogenic E. coli (ExPEC), capable of causing disease in humans. These E. coli may also be resistant to antimicrobials of critical importance in human or veterinary health. This study aims to 1) determine the prevalence of antimicrobial resistance (AMR) and resistance genes, multidrug resistance (MDR), chromosomal mechanisms of quinolone-resistance and virulence profiles of E. coli isolated from healthy chicken farms in the region of Dakar, Senegal, 2) investigate the spread of third-generation cephalosporins (3GC) resistance in E. coli isolated from healthy chicken farms with respect to virulence and resistance genes, serogroups, Pulsed-Field Gel Electrophoresis (PFGE), phylogenetic groups, plasmid types and transferability and 3) determine whether nonsusceptibility against 3GC on farms could be linked to risk factors. More than 68% of isolates from environmental faecal and drinking water samples, carcasses and carcass washes collected on 32 healthy chicken farms were multidrug resistant (MDR), resistance to antimicrobials critical in human health (3GC or ciprofloxacin) being found in all types of samples. Ciprofloxacin resistance was due to mutations in the gyrA and parC genes, 95% of tested farms harboring isolates carrying three mutations, in gyrA (Ser83Ile and Asp87Asn) and parC (Ser80Ile). Nine of the 32 farms (28.1%) demonstrated the presence of one or more 3GC-nonsusceptible indicator isolates but none of the potential risk factors were significantly associated with this presence on farms. Following ceftriaxone enrichment, presumptive extended-spectrum beta-lactamase/AmpC-beta-lactamase (ESBL/AmpC)-producer isolates were found in 17 of the 32 farms. 3GC resistance was mediated by blaCMY-2 or blaCTX-M genes, blaCTX-M being of genotypes blaCTX-M-1, blaCTX-M-8 and for the first time in chickens in Senegal, the genotype blaCTX-M-15. Clonally related ESBL/AmpC-producer isolates were found on different farms. In addition, blaCTX-M genes were identified on replicon plasmids I1 and K/B and blaCMY-2 on K/B, I1 and B/O. These plasmids were found in isolates of different clusters. In addition, 18 isolates, some of which were ESBL/AmpC-producers, were defined as potential human ExPEC. In conclusion, E. coli isolates potentially pathogenic for humans and demonstrating MDR, with resistance expressed against antimicrobials of critical importance in human health were found in healthy chickens in Senegal. Our results suggest that both clonal spreading and horizontal gene transfer play a role in the spread of 3GC-resistance and that chickens in Senegal could be a reservoir for AMR and ExPEC for humans. These results highlight the importance of raising awareness about compliance with biosecurity measures and prudent use of antimicrobials.}, }
@article {pmid30909880, year = {2019}, author = {Li, Z and Lu, X and Wang, D and Liang, WL and Zhang, J and Li, J and Xu, J and Pang, B and Kan, B}, title = {Genomic comparison of serogroups O159 and O170 with other Vibrio cholerae serogroups.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {241}, pmid = {30909880}, issn = {1471-2164}, support = {81601811//National Natural Science Foundation of China/ ; 81401715//National Natural Science Foundation of China/ ; 2016A104//the Young Scholars fund of the Chinese Center for Disease Control and Prevention/ ; H23-Shinkou- shitei-020//grant-in-aid of Ministry of Health, Labor and Welfare, the Government of Japan/ ; }, mesh = {Bacterial Proteins/*genetics ; Gene Regulatory Networks ; Gene Transfer, Horizontal ; Genomics/*methods ; O Antigens/*biosynthesis/immunology ; Phylogeny ; Selection, Genetic ; Sequence Analysis, DNA/methods ; Serogroup ; Vibrio cholerae/*genetics/immunology/metabolism ; Virulence Factors/genetics ; }, abstract = {BACKGROUND: Of the hundreds of Vibrio cholerae serogroups, O1 and O139 are the main epidemic-causing ones. Although non-O1/non-O139 serogroups rarely cause epidemics, the possibility exists for strains within them to have pathogenic potential.<br><br>RESULTS: We selected 25 representative strains within 16&#x2009;V. cholerae serogroups and examined their genomic and functional characteristics. We tentatively constructed a gene pool containing 405 homologous gene clusters, which is well organized and functions in O-antigen polysaccharide (O-PS) synthesis. Our network analysis indicate that great diversity exists in O-PS among the serogroups, and several serogroup pairs share a high number of homologous genes (e.g., O115 and O37; O170 and O139; O12 and O39). The phylogenetic analysis results suggest that a close relationship exists between serogroups O170, O89 and O144, based on neighbor-joining (NJ) and gene trees, although serogroup O159 showed an inconsistent phylogenetic relationship between the NJ tree and the gene tree, indicating that it may have undergone extensive recombination and horizontal gene transfer. Different phylogenetic structures were observed between the core genes, pan genes, and O-PS genes. The virulence gene analysis indicated that the virulence genes from all the representative strains may have their sources from four particular bacteria (Pseudomonas aeruginosa, V. vulnificus, Haemophilus somnus and H. influenzae), which suggests that V. cholerae may have exchanged virulence genes with other bacterial genera or species in certain environments. The mobile genetic element analysis indicated that O159 carries nearly complete VSP-II and partial VPI-1 and VPI-2, O170 carries partial VPI-1 and VPI-2, and several non-O1/non-O139 strains contain full or partial VPI-1 and VPI-2. Several genes showing evidence of positive selection are involved in chemotaxis, Na&#x2009;+&#x2009;resistance, or cell wall synthesis, suggestive of environmental adaptation.<br><br>CONCLUSIONS: This study reports on the newly sequenced O159 and O170 genomes and their comparisons with other V. cholerae serogroups. The complicated O-PS network of constituent genes highlights the detailed recombination mechanisms that have acted on the serogroups' genomes. The serogroups have different virulence-related gene profiles, and there is evidence of positive selection acting on other genes, possibly during adaptation to different environments and hosts.}, }
@article {pmid32547355, year = {2018}, author = {Yazdankhah, S and Skjerve, E and Wasteson, Y}, title = {Antimicrobial resistance due to the content of potentially toxic metals in soil and fertilizing products.}, journal = {Microbial ecology in health and disease}, volume = {29}, number = {1}, pages = {1548248}, pmid = {32547355}, issn = {0891-060X}, abstract = {Potentially toxic metals (PTM), along with PTM-resistant bacteria and PTM-resistance genes, may be introduced into soil and water through sewage systems, direct excretion, land application of biosolids (organic matter recycled from sewage, especially for use in agriculture) or animal manures as fertilizers, and irrigation with wastewater or treated effluents. In this review article, we have evaluated whether the content of arsenic (As), cadmium (Cd), chromium (CrIII + CrVI), copper (Cu), lead (Pb), mercury (Hg), nickel (Ni), and zinc (Zn) in soil and fertilizing products play a role in the development, spreading, and persistence of bacterial resistance to these elements, as well as cross- or co-resistance to antimicrobial agents. Several of the articles included in this review reported the development of resistance against PTM in both sewage and manure. Although PTM like As, Hg, Co, Cd, Pb, and Ni may be present in the fertilizing products, the concentration may be low since they occur due to pollution. In contrast, trace metals like Cu and Zn are actively added to animal feed in many countries. In several studies, several different bacterial species were shown to have a reduced susceptibility towards several PTM, simultaneously. However, neither the source of resistant bacteria nor the minimum co-selective concentration (MCC) for resistance induction are known. Co- or cross-resistance against highly important antimicrobials and critically important antimicrobials were identified in some of the bacterial isolates. This suggest that there is a genetic linkage or direct genetic causality between genetic determinants to these widely divergent antimicrobials, and metal resistance. Data regarding the routes and frequencies of transmission of AMR from bacteria of environmental origin to bacteria of animal and human origin were sparse. Due to the lack of such data, it is difficult to estimate the probability of development, transmission, and persistence of PTM resistance. Abbreviations: PTM: potentially toxic metals; AMR: antimicrobial resistance; ARG: antimicrobial resistance gene; MCC: minimum co-selective concentration; MDR: multidrug resistance; ARB: antimicrobial resistant bacteria; HGT: horizontal gene transfer; MIC: minimum inhibitory concentration.}, }
@article {pmid31828235, year = {2018}, author = {Ren, J and Bai, X and Lu, YY and Tang, K and Wang, Y and Reinert, G and Sun, F}, title = {Alignment-Free Sequence Analysis and Applications.}, journal = {Annual review of biomedical data science}, volume = {1}, number = {}, pages = {93-114}, pmid = {31828235}, issn = {2574-3414}, support = {R01 GM120624/GM/NIGMS NIH HHS/United States ; }, abstract = {Genome and metagenome comparisons based on large amounts of next generation sequencing (NGS) data pose significant challenges for alignment-based approaches due to the huge data size and the relatively short length of the reads. Alignment-free approaches based on the counts of word patterns in NGS data do not depend on the complete genome and are generally computationally efficient. Thus, they contribute significantly to genome and metagenome comparison. Recently, novel statistical approaches have been developed for the comparison of both long and shotgun sequences. These approaches have been applied to many problems including the comparison of gene regulatory regions, genome sequences, metagenomes, binning contigs in metagenomic data, identification of virus-host interactions, and detection of horizontal gene transfers. We provide an updated review of these applications and other related developments of word-count based approaches for alignment-free sequence analysis.}, }
@article {pmid31851631, year = {2018}, author = {Kanj, SS and Tayyar, R and Shehab, M and El-Hafi, B and Rasheed, SS and Kissoyan, KAB and Kanafani, ZA and Wakim, RH and Kara Zahreddine, N and Araj, GF and Dbaibo, G and Matar, GM}, title = {Increased blaOXA-23-like prevalence in Acinetobacter baumannii at a tertiary care center in Lebanon (2007-2013).}, journal = {Journal of infection in developing countries}, volume = {12}, number = {4}, pages = {228-234}, doi = {10.3855/jidc.9642}, pmid = {31851631}, issn = {1972-2680}, abstract = {INTRODUCTION: Acinetobacter baumannii has become one of the most feared organisms in hospital-acquired infections during the past decades. Their multi-drug resistant profiles have rendered many broad-spectrum antibiotics ineffective. The purpose of this retrospective study is to describe and compare molecular characteristics of A. baumannii isolated from patients at a tertiary care center in Lebanon from two outbreaks, the first in 2007-2008 as part of a case-controlled study involving Acinetobacter baumannii cases admitted to the ICU and the second in 2013.<br><br>METHODOLOGY: A total of 148 A. baumannii clinical isolates were collected from various clinical specimens during 2007-2008 and 2013. All A. baumannii isolates were subjected to PCR amplification of blaOXA-23-like and blaOXA-51-like genes of carbapenem resistance. Random amplification of polymorphic DNA (RAPD) was also performed to assess their genomic relatedness.<br><br>RESULTS: There was an increase in the prevalence of blaOXA-23-like and blaOXA-51-like between the two time periods; however, only with 22% genomic relatedness between 2007-2008 and 2013 isolates. Taking 80% as margin of compatibility, 31 distinct clusters containing 2 to 11 strains were observed in both time periods.<br><br>CONCLUSION: The presence of numerous clusters accompanied by a predominant increase in the prevalence of blaOXA-23-like gene between 2007 and 2013 suggests a horizontal transmission of the gene within various strains of the species, constituting a primary factor in the continued increase of carbapenem resistance over the years. As such, infection control measures ought to be taken with the highest priority and compliance among all involved healthcare workers is of utmost importance.}, }
@article {pmid31294189, year = {2017}, author = {Sugiura, C and Miyaue, S and Shibata, Y and Matsumoto, A and Maeda, S}, title = {Bacteriophage P1vir-induced cell-to-cell plasmid transformation in Escherichia coli.}, journal = {AIMS microbiology}, volume = {3}, number = {4}, pages = {784-797}, pmid = {31294189}, issn = {2471-1888}, abstract = {Bacteria undergo horizontal gene transfer via various mechanisms. We recently reported that cell-to-cell transfer of nonconjugative plasmids occurs between strains of Escherichia coli in co-cultures, and that a specific strain (CAG18439) causes frequent plasmid transfer involving a DNase-sensitive mechanism, which we termed "cell-to-cell transformation". Here we found that CAG18439 is a type of P1 bacteriophage lysogen that continuously releases phages. We tested the ability of P1vir bacteriophage to induce horizontal plasmid transfer and demonstrated that such a horizontal plasmid transfer was caused by adding culture supernatants of P1vir-infected cells harboring plasmids to other plasmid-free cells. This plasmid transfer system also reproduced the major features of plasmid transfer involving CAG18439, suggesting that P1vir-induced plasmid transfer is equivalent or very similar to plasmid transfer involving CAG18439. We further revealed that approximately two-thirds of the P1vir-induced plasmid transfer was DNase-sensitive, but that complete abolition of plasmid transfer was observed when proteins were denatured or removed, despite the presence or absence of DNase. Therefore, we concluded that P1vir-induced plasmid transfer is largely due to the occurrence of cell-to-cell transformation, which involves the assistance of some proteinaceous factor, and partly due to the occurrence of plasmid transduction, which is mediated by phage virions. This is the first demonstration of the P1-phage-induced cell-to-cell transformation.}, }
@article {pmid31967569, year = {2017}, author = {Mocaër, PY and Baudoux, AC}, title = {Les virus au service de l'écologie marine.}, journal = {Virologie (Montrouge, France)}, volume = {21}, number = {4}, pages = {160-172}, doi = {10.1684/vir.2017.0704}, pmid = {31967569}, issn = {1267-8694}, abstract = {In less than 50 years, marine viruses shifted from meaningless entities to major players of the oceanic ecosystems. These parasites numerically dominate marine microbial communities and mostly infect micro-organisms (bacteria, microalgae and other protists) that constitute the basis of trophic levels in the ocean. Viruses that replicate though a lysogenic cycle affect genetic expression of the host and promote horizontal gene transfer within the marine microbial communities. Viruses that replicate through a lytic cycle contribute to the control of host population and the release of a large amount of organic matter in the ocean. From the genetic manipulation of their hosts to the modification of the biogeochemical cycles, the marine viruses play a pivotal role for the structure and the functioning of their environment and cannot be excluded from ecological models anymore. This review presents the impact of viruses on the marine environment by focusing on three integration scales: the cell, the community and the ecosystem.}, }
@article {pmid32214476, year = {2017}, author = {Blinov, VM and Zverev, VV and Krasnov, GS and Filatov, FP and Shargunov, AV}, title = {Viral component of the human genome.}, journal = {Molecular biology}, volume = {51}, number = {2}, pages = {205-215}, pmid = {32214476}, issn = {0026-8933}, abstract = {Relationships between viruses and their human host are traditionally described from the point of view taking into consideration hosts as victims of viral aggression, which results in infectious diseases. However, these relations are in fact two-sided and involve modifications of both the virus and host genomes. Mutations that accumulate in the populations of viruses and hosts may provide them advantages such as the ability to overcome defense barriers of host cells or to create more efficient barriers to deal with the attack of the viral agent. One of the most common ways of reinforcing anti-viral barriers is the horizontal transfer of viral genes into the host genome. Within the host genome, these genes may be modified and extensively expressed to compete with viral copies and inhibit the synthesis of their products or modulate their functions in other ways. This review summarizes the available data on the horizontal gene transfer between viral and human genomes and discusses related problems.}, }
@article {pmid32131363, year = {2015}, author = {Nakabachi, A}, title = {Horizontal gene transfers in insects.}, journal = {Current opinion in insect science}, volume = {7}, number = {}, pages = {24-29}, doi = {10.1016/j.cois.2015.03.006}, pmid = {32131363}, issn = {2214-5753}, abstract = {Horizontal gene transfer is the transfer of genetic material across species boundaries. Although horizontal gene transfers are relatively rare in animals, the recent rapid accumulation of genomic data has identified increasing amounts of exogenous DNA inserts in insect genomes. Most of the horizontally acquired sequences appear to be non-functional; however, there is growing evidence that some genes are truly expressed and confer novel functions on the recipient insects. These include previously unavailable metabolic properties including digesting food, degrading toxins, providing resistance to pathogens, and facilitating an obligate mutualistic relationship with intracellular bacteria. A recent analysis revealed that an aphid gene of bacterial origin encodes a protein that is transported into the obligate symbiont, paralleling the evolution of endosymbiotic organelles.}, }
@article {pmid32218874, year = {2010}, author = {Cheng, WC and Liou, CY}, title = {Manifold construction based on local distance invariance.}, journal = {Memetic computing}, volume = {2}, number = {2}, pages = {149-160}, pmid = {32218874}, issn = {1865-9292}, abstract = {This paper presents a distance invariant manifold that preserves the neighborhood relations among data patterns. All patterns have their corresponding cells in the manifold space. The constellation of neighborhood cells closely resembles that of patterns. The manifold is invariant under the translation, rotation and scale of the pattern coordinates. The neighborhood relations among cells are adjusted and improved in each iteration according to the reduction of the distance preservation energy.}, }
@article {pmid30909861, year = {2019}, author = {Denancé, N and Briand, M and Gaborieau, R and Gaillard, S and Jacques, MA}, title = {Identification of genetic relationships and subspecies signatures in Xylella fastidiosa.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {239}, pmid = {30909861}, issn = {1471-2164}, support = {635646//RFI Objectif V&#xe9;g&#xe9;tal/ ; }, mesh = {DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Data Mining ; Gene Ontology ; Genomics/methods ; Phylogeny ; Polymorphism, Single Nucleotide ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; Xylella/*classification/genetics ; }, abstract = {BACKGROUND: The phytopathogenic bacterium Xylella fastidiosa was thought to be restricted to the Americas where it infects and kills numerous hosts. Its detection worldwide has been blooming since 2013 in Europe and Asia. Genetically diverse, this species is divided into six subspecies but genetic traits governing this classification are poorly understood.<br><br>RESULTS: SkIf (Specific k-mers Identification) was designed and exploited for comparative genomics on a dataset of 46 X. fastidiosa genomes, including seven newly sequenced individuals. It was helpful to quickly check the synonymy between strains from different collections. SkIf identified specific SNPs within 16S rRNA sequences that can be employed for predicting the distribution of Xylella through data mining. Applied to inter- and intra-subspecies analyses, it identified specific k-mers in genes affiliated to differential gene ontologies. Chemotaxis-related genes more prevalently possess specific k-mers in genomes from subspecies fastidiosa, morus and sandyi taken as a whole group. In the subspecies pauca increased abundance of specific k-mers was found in genes associated with the bacterial cell wall/envelope/plasma membrane. Most often, the k-mer specificity occurred in core genes with non-synonymous SNPs in their sequences in genomes of the other subspecies, suggesting putative impact in the protein functions. The presence of two integrative and conjugative elements (ICEs) was identified, one chromosomic and an entire plasmid in a single strain of X. fastidiosa subsp. pauca. Finally, a revised taxonomy of X. fastidiosa into three major clades defined by the subspecies pauca (clade I), multiplex (clade II) and the combination of fastidiosa, morus and sandyi (clade III) was strongly supported by k-mers specifically associated with these subspecies.<br><br>CONCLUSIONS: SkIf is a robust and rapid software, freely available, that can be dedicated to the comparison of sequence datasets and is applicable to any field of research. Applied to X. fastidiosa, an emerging pathogen in Europe, it provided an important resource to mine for identifying genetic markers of subspecies to optimize the strategies attempted to limit the pathogen dissemination in novel areas.}, }
@article {pmid30905895, year = {2019}, author = {Asakura, H and Sakata, J and Nakamura, H and Yamamoto, S and Murakami, S}, title = {Phylogenetic Diversity and Antimicrobial Resistance of Campylobacter coli from Humans and Animals in Japan.}, journal = {Microbes and environments}, volume = {34}, number = {2}, pages = {146-154}, pmid = {30905895}, issn = {1347-4405}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Campylobacter Infections/epidemiology/*microbiology ; Campylobacter coli/*classification/*drug effects/genetics/isolation &amp; purification ; Cattle ; DNA, Bacterial/genetics ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial/genetics ; *Genetic Variation ; Genotype ; Humans ; Japan/epidemiology ; Microbial Sensitivity Tests ; Multilocus Sequence Typing/veterinary ; *Phylogeny ; Poultry ; Sequence Analysis, DNA/veterinary ; Swine ; }, abstract = {The phylogenetic diversity and antimicrobial resistance (AMR) of Campylobacter coli from humans and animals in Japan between 2008 and 2014 were investigated. A total of 338 foodborne campylobacterioses were reported in Osaka, and C. coli was isolated from 38 cases (11.2%). In the present study, 119 C. coli strains (42 from humans, 25 each from poultry, cattle, and swine, and 2 from wild mallard) were examined by multilocus sequence typing (MLST). MLST assigned 36 sequence types (STs), including 14 novel STs; all human strains and 91% of animal strains (70/77) were assigned to the ST-828 clonal complex. The predominant human ST was ST-860 (18/42, 43%), followed by ST-1068 (8/42, 19%); these STs were also predominant in poultry (ST-860, 9/25, 36%) and cattle (ST-1068, 18/25, 72%). ST-1562 was only predominant in swine (11/25, 44.0%). Swine strains showed the greatest resistance to erythromycin (EM; 92.0%), while EM resistance was only found in 2 out of the 42 human strains examined (4.8%). All EM-resistant swine strains (n=15) exhibited a common point mutation in the 23S rRNA sequence (A2085G), and the tetO gene was detected in 22 out of the 23 TET-resistant swine strains. A whole genome sequencing analysis of four representative swine ST-1562 strains revealed abundant AMR-associated gene clusters in their genomes, suggesting horizontal gene transfer events during host adaptation. This is the first study to demonstrate the phylogenetic diversity and AMR profiles of C. coli in Japan. The present results suggest that poultry and cattle are major reservoirs, improving our knowledge on the epidemiological and ecological traits of this pathogen.}, }
@article {pmid30905287, year = {2019}, author = {Bernheim, A and Bikard, D and Touchon, M and Rocha, EPC}, title = {A matter of background: DNA repair pathways as a possible cause for the sparse distribution of CRISPR-Cas systems in bacteria.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {374}, number = {1772}, pages = {20180088}, pmid = {30905287}, issn = {1471-2970}, mesh = {Bacteria/*genetics ; CRISPR-Cas Systems/*genetics ; *DNA Repair ; DNA, Bacterial/*genetics ; *Gene Transfer, Horizontal ; }, abstract = {The absence of CRISPR-Cas systems in more than half of the sequenced bacterial genomes is intriguing, because their role in adaptive immunity and their frequent transfer between species should have made them almost ubiquitous, as is the case in Archaea. Here, we investigate the possibility that the success of CRISPR-Cas acquisition by horizontal gene transfer is affected by the interactions of these systems with the host genetic background and especially with components of double-strand break repair systems (DSB-RS). We first described the distribution of systems specialized in the repair of double-strand breaks in Bacteria: homologous recombination and non-homologous end joining. This allowed us to show that such systems are more often positively or negatively correlated with the frequency of CRISPR-Cas systems than random genes of similar frequency. The detailed analysis of these co-occurrence patterns shows that our method identifies previously known cases of mechanistic interactions between these systems. It also reveals other positive and negative patterns of co-occurrence between DSB-RS and CRISPR-Cas systems. Notably, it shows that the patterns of distribution of CRISPR-Cas systems in Proteobacteria are strongly dependent on the epistatic groups including RecBCD and AddAB. Our results suggest that the genetic background plays an important role in the success of adaptive immunity in different bacterial clades and provide insights to guide further experimental research on the interactions between CRISPR-Cas and DSB-RS. This article is part of a discussion meeting issue 'The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems'.}, }
@article {pmid30902858, year = {2019}, author = {Moller, AG and Lindsay, JA and Read, TD}, title = {Determinants of Phage Host Range in Staphylococcus Species.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {11}, pages = {}, pmid = {30902858}, issn = {1098-5336}, support = {MR/P028322/1/MRC_/Medical Research Council/United Kingdom ; R21 AI121860/AI/NIAID NIH HHS/United States ; }, mesh = {Clustered Regularly Interspaced Short Palindromic Repeats ; Gene Transfer, Horizontal ; Genomic Islands/genetics ; *Host Specificity ; Host-Pathogen Interactions ; Membrane Proteins ; Phage Therapy ; Staphylococcus/genetics/*virology ; Staphylococcus Phages/genetics/*physiology ; Teichoic Acids ; Virus Assembly ; }, abstract = {Bacteria in the genus Staphylococcus are important targets for phage therapy due to their prevalence as pathogens and increasing antibiotic resistance. Here we review Staphylococcus outer surface features and specific phage resistance mechanisms that define the host range, the set of strains that an individual phage can potentially infect. Phage infection goes through five distinct phases: attachment, uptake, biosynthesis, assembly, and lysis. Adsorption inhibition, encompassing outer surface teichoic acid receptor alteration, elimination, or occlusion, limits successful phage attachment and entry. Restriction-modification systems (in particular, type I and IV systems), which target phage DNA inside the cell, serve as the major barriers to biosynthesis as well as transduction and horizontal gene transfer between clonal complexes and species. Resistance to late stages of infection occurs through mechanisms such as assembly interference, in which staphylococcal pathogenicity islands siphon away superinfecting phage proteins to package their own DNA. While genes responsible for teichoic acid biosynthesis, capsule, and restriction-modification are found in most Staphylococcus strains, a variety of other host range determinants (e.g., clustered regularly interspaced short palindromic repeats, abortive infection, and superinfection immunity) are sporadic. The fitness costs of phage resistance through teichoic acid structure alteration could make staphylococcal phage therapies promising, but host range prediction is complex because of the large number of genes involved, and the roles of many of these are unknown. In addition, little is known about the genetic determinants that contribute to host range expansion in the phages themselves. Future research must identify host range determinants, characterize resistance development during infection and treatment, and examine population-wide genetic background effects on resistance selection.}, }
@article {pmid30902757, year = {2020}, author = {Banerjee, R and Shine, O and Rajachandran, V and Krishnadas, G and Minnick, MF and Paul, S and Chattopadhyay, S}, title = {Gene duplication and deletion, not horizontal transfer, drove intra-species mosaicism of Bartonella henselae.}, journal = {Genomics}, volume = {112}, number = {1}, pages = {467-471}, doi = {10.1016/j.ygeno.2019.03.009}, pmid = {30902757}, issn = {1089-8646}, mesh = {Bartonella henselae/*genetics ; *Evolution, Molecular ; *Gene Deletion ; *Gene Duplication ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; *Mosaicism ; }, abstract = {Bartonella henselae is a facultative intracellular pathogen that occurs worldwide and is responsible primarily for cat-scratch disease in young people and bacillary angiomatosis in immunocompromised patients. The principal source of genome-level diversity that contributes to B. henselae's host-adaptive features is thought to be horizontal gene transfer events. However, our analyses did not reveal the acquisition of horizontally-transferred islands in B. henselae after its divergence from other Bartonella. Rather, diversity in gene content and genome size was apparently acquired through two alternative mechanisms, including deletion and, more predominantly, duplication of genes. Interestingly, a majority of these events occurred in regions that were horizontally transferred long before B. henselae's divergence from other Bartonella species. Our study indicates the possibility that gene duplication, in response to positive selection pressures in specific clones of B. henselae, might be linked to the pathogen's adaptation to arthropod vectors, the cat reservoir, or humans as incidental host-species.}, }
@article {pmid30898140, year = {2019}, author = {Che, Y and Xia, Y and Liu, L and Li, AD and Yang, Y and Zhang, T}, title = {Mobile antibiotic resistome in wastewater treatment plants revealed by Nanopore metagenomic sequencing.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {44}, pmid = {30898140}, issn = {2049-2618}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; Bacterial Proteins/genetics ; *Drug Resistance, Microbial ; Gene Transfer, Horizontal ; High-Throughput Nucleotide Sequencing/instrumentation ; Lincosamides/pharmacology ; Macrolides/pharmacology ; Metagenomics/*instrumentation/methods ; Nanopores ; Phylogeny ; Sequence Analysis, DNA/*instrumentation/methods ; Sewage/microbiology ; Streptogramins/pharmacology ; Tetracycline/pharmacology ; Wastewater/*microbiology ; }, abstract = {BACKGROUND: Wastewater treatment plants (WWTPs) are recognized as hotspots for horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). Despite our understanding of the composition and distribution of ARGs in WWTPs, the genetic location, host, and fate of ARGs remain largely unknown.<br><br>RESULTS: In this study, we combined Oxford Nanopore and Illumina metagenomics sequencing to comprehensively uncover the resistome context of influent, activated sludge, and effluent of three WWTPs and simultaneously track the hosts of the ARGs. The results showed that most of the ARGs detected in all compartments of the WWTPs were carried by plasmids. Transposons and integrons also showed higher prevalence on plasmids than on the ARG-carrying chromosome. Notably, integrative and conjugative elements (ICEs) carrying five types of ARGs were detected, and they may play an important role in facilitating the transfer of ARGs, particularly for tetracycline and macrolide-lincosamide-streptogramin (MLS). A broad spectrum of ARGs carried by plasmids (29 subtypes) and ICEs (4 subtypes) was persistent across the WWTPs. Host tracking showed a variety of antibiotic-resistant bacteria in the effluent, suggesting the high potential for their dissemination into receiving environments. Importantly, phenotype-genotype analysis confirmed the significant role of conjugative plasmids in facilitating the survival and persistence of multidrug-resistant bacteria in the WWTPs. At last, the consistency in the quantitative results for major ARGs types revealed by Nanopore and Illumina sequencing platforms demonstrated the feasibility of Nanopore sequencing for resistome quantification.<br><br>CONCLUSION: Overall, these findings substantially expand our current knowledge of resistome in WWTPs, and help establish a baseline analysis framework to study ARGs in the environment.}, }
@article {pmid30897437, year = {2019}, author = {Sanganyado, E and Gwenzi, W}, title = {Antibiotic resistance in drinking water systems: Occurrence, removal, and human health risks.}, journal = {The Science of the total environment}, volume = {669}, number = {}, pages = {785-797}, doi = {10.1016/j.scitotenv.2019.03.162}, pmid = {30897437}, issn = {1879-1026}, mesh = {Disinfection ; Drinking Water/*microbiology ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Hydrogen Peroxide ; Oxidation-Reduction ; Ultraviolet Rays ; *Water Microbiology ; Water Purification/*methods/statistics &amp; numerical data ; }, abstract = {In recent years, there has been a growing interest on the occurrence of antibiotic-resistant bacteria (ARB) and antibiotic resistant genes (ARGs) in treated and untreated drinking water. ARB and ARGs pose a public health concern when they transfer antibiotic resistance (AR) to human pathogens. However, it is still unclear whether the presence of environmental ARB and ARGs in source water, drinking water treatment plants, and drinking water distribution systems has any significant impact on human exposure to pathogenic ARB. In this review, we critically examine the occurrence of AR in groundwater, surface water, and treated distributed water. This offered a new perspective on the human health threat posed by AR in drinking water and helped in crafting a strategy for monitoring AR effectively. Using existing data on removal of ARB and ARGs in drinking water treatment plants, presence and proliferation of AR in drinking water distribution systems, and mechanisms and pathways of AR transfer in drinking water treatment plants, we conclude that combining UV-irradiation with advanced oxidative processes (such as UV/chlorine, UV/H2O2, and H2O2/UV/TiO2) may enhance the removal of ARB and ARGs, while disinfection may promote horizontal gene transfer from environmental ARB to pathogens. The potential human health risks of AR were determined by examining human exposure to antibiotic resistant human pathogens and re-evaluating waterborne disease outbreaks and their links to environmental AR. We concluded that integrating disease outbreak analysis, human exposure modelling, and clinical data could provide critical information that can be used to estimate the dose-response relationships of pathogenic ARB in drinking water, which is required for accurate risk assessments.}, }
@article {pmid30894848, year = {2019}, author = {Kiss, J and Szabó, M and Hegyi, A and Douard, G and Praud, K and Nagy, I and Olasz, F and Cloeckaert, A and Doublet, B}, title = {Identification and Characterization of oriT and Two Mobilization Genes Required for Conjugative Transfer of Salmonella Genomic Island 1.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {457}, pmid = {30894848}, issn = {1664-302X}, abstract = {The integrative mobilizable elements of SGI1-family considerably contribute to the spread of resistance to critically important antibiotics among enteric bacteria. Even though many aspects of SGI1 mobilization by IncA and IncC plasmids have been explored, the basic transfer elements such as oriT and self-encoded mobilization proteins remain undiscovered. Here we describe the mobilization region of SGI1 that is well conserved throughout the family and carries the oriT SGI1 and two genes, mpsA and mpsB (originally annotated as S020 and S019, respectively) that are essential for the conjugative transfer of SGI1. OriT SGI1, which is located in the vicinity of the two mobilization genes proved to be a 125-bp GC-rich sequence with several important inverted repeat motifs. The mobilization proteins MpsA and MpsB are expressed from a bicistronic mRNA, although MpsB can be produced from its own mRNA as well. The protein structure predictions imply that MpsA belongs to the lambda tyrosine recombinase family, while MpsB resembles the N-terminal core DNA binding domains of these enzymes. The results suggest that MpsA may act as an atypical relaxase, which needs MpsB for SGI1 transfer. Although the helper plasmid-encoded relaxase proved not to be essential for SGI1 transfer, it appeared to be important to achieve the high transfer rate of the island observed with the IncA/IncC-SGI1 system.}, }
@article {pmid30893937, year = {2019}, author = {Fullmer, MS and Ouellette, M and Louyakis, AS and Papke, RT and Gogarten, JP}, title = {The Patchy Distribution of Restriction[-]Modification System Genes and the Conservation of Orphan Methyltransferases in Halobacteria.}, journal = {Genes}, volume = {10}, number = {3}, pages = {}, pmid = {30893937}, issn = {2073-4425}, mesh = {Archaeal Proteins/genetics ; DNA Methylation ; DNA Restriction-Modification Enzymes/*genetics ; Euryarchaeota/*enzymology/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Methyltransferases/*genetics ; Whole Genome Sequencing/methods ; }, abstract = {Restriction[-]modification (RM) systems in bacteria are implicated in multiple biological roles ranging from defense against parasitic genetic elements, to selfish addiction cassettes, and barriers to gene transfer and lineage homogenization. In bacteria, DNA-methylation without cognate restriction also plays important roles in DNA replication, mismatch repair, protein expression, and in biasing DNA uptake. Little is known about archaeal RM systems and DNA methylation. To elucidate further understanding for the role of RM systems and DNA methylation in Archaea, we undertook a survey of the presence of RM system genes and related genes, including orphan DNA methylases, in the halophilic archaeal class Halobacteria. Our results reveal that some orphan DNA methyltransferase genes were highly conserved among lineages indicating an important functional constraint, whereas RM systems demonstrated patchy patterns of presence and absence. This irregular distribution is due to frequent horizontal gene transfer and gene loss, a finding suggesting that the evolution and life cycle of RM systems may be best described as that of a selfish genetic element. A putative target motif (CTAG) of one of the orphan methylases was underrepresented in all of the analyzed genomes, whereas another motif (GATC) was overrepresented in most of the haloarchaeal genomes, particularly in those that encoded the cognate orphan methylase.}, }
@article {pmid30891598, year = {2019}, author = {Hao, W and Shan, X and Li, D and Schwarz, S and Zhang, SM and Li, XS and Du, XD}, title = {Analysis of a poxtA- and optrA-co-carrying conjugative multiresistance plasmid from Enterococcus faecalis.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {74}, number = {7}, pages = {1771-1775}, doi = {10.1093/jac/dkz109}, pmid = {30891598}, issn = {1460-2091}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Conjugation, Genetic ; *Drug Resistance, Bacterial ; Enterococcus faecalis/*genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Gram-Positive Bacterial Infections/microbiology/veterinary ; Microbial Sensitivity Tests ; Plasmids/*analysis ; Polymerase Chain Reaction ; Swine ; Transformation, Bacterial ; }, abstract = {OBJECTIVES: To investigate the presence and transferability of the poxtA gene and identify the genetic context of poxtA in two enterococcal plasmids from swine.<br><br>METHODS: MICs were determined by broth microdilution. A total of 114 porcine enterococci with florfenicol MICs of &#x2265;16&#x2009;mg/L were screened for the presence of the poxtA gene by PCR. Transferability of poxtA was investigated by conjugation and transformation. The poxtA-carrying plasmids were completely sequenced using the Illumina Miseq and PacBio RSII platform. The presence of circular intermediates was examined by inverse PCR.<br><br>RESULTS: The poxtA gene was present in 57.9% (66/114) of the florfenicol-resistant porcine enterococci. Two poxtA-carrying plasmids, pE035 and pE076, were identified. The conjugative 121524&#x2009;bp plasmid pE035 carried poxtA and optrA along with the resistance genes erm(A), erm(B), aac(A)-aph(D), lnu(G), fexB, dfrG and bcrABDR. Three mobile elements, comprising a mobile dfrG locus, a mobile bcrABDR locus and an unconventional circularizable structure containing aac(A)-aph(D), were located on this plasmid and all proved to be active by inverse PCR. The non-conjugative 19832&#x2009;bp plasmid pE076 only carried poxtA and fexB. After transfer, both the transconjugant and the transformant displayed elevated MICs of the respective antimicrobial agents.<br><br>CONCLUSIONS: To the best of our knowledge, this is the first report of the co-location of the oxazolidinone resistance genes poxtA and optrA on a conjugative multiresistance plasmid from a porcine enterococcal strain. In addition, the presence of three mobile elements in such a plasmid will aid in the persistence and dissemination of poxtA and optrA among enterococci.}, }
@article {pmid30891203, year = {2019}, author = {Ayala-Ruano, S and Santander-Gordón, D and Tejera, E and Perez-Castillo, Y and Armijos-Jaramillo, V}, title = {A putative antimicrobial peptide from Hymenoptera in the megaplasmid pSCL4 of Streptomyces clavuligerus ATCC 27064 reveals a singular case of horizontal gene transfer with potential applications.}, journal = {Ecology and evolution}, volume = {9}, number = {5}, pages = {2602-2614}, pmid = {30891203}, issn = {2045-7758}, abstract = {Streptomyces clavuligerus is a Gram-positive bacterium that is a high producer of secondary metabolites with industrial applications. The production of antibiotics such as clavulanic acid or cephamycin has been extensively studied in this species; nevertheless, other aspects, such as evolution or ecology, have received less attention. Furthermore, genes that arise from ancient events of lateral transfer have been demonstrated to be implicated in important functions of host species. This approximation discovered relevant genes that genomic analyses overlooked. Thus, we studied the impact of horizontal gene transfer in the S. clavuligerus genome. To perform this task, we applied whole-genome analysis to identify a laterally transferred sequence from different domains. The most relevant result was a putative antimicrobial peptide (AMP) with a clear origin in the Hymenoptera order of insects. Next, we determined that two copies of these genes were present in the megaplasmid pSCL4 but absent in the S. clavuligerus ATCC 27064 chromosome. Additionally, we found that these sequences were exclusive to the ATCC 27064 strain (and so were not present in any other bacteria) and we also verified the expression of the genes using RNAseq data. Next, we used several AMP predictors to validate the original annotation extracted from Hymenoptera sequences and explored the possibility that these proteins had post-translational modifications using peptidase cleavage prediction. We suggest that Hymenoptera AMP-like proteins of S. clavuligerus ATCC 27064 may be useful for both species adaptation and as an antimicrobial molecule with industrial applications.}, }
@article {pmid30890026, year = {2019}, author = {Cardona, T}, title = {Thinking twice about the evolution of photosynthesis.}, journal = {Open biology}, volume = {9}, number = {3}, pages = {180246}, pmid = {30890026}, issn = {2046-2441}, mesh = {Bacterial Proteins/metabolism ; *Biological Evolution ; Cyanobacteria/metabolism ; Earth, Planet ; *Origin of Life ; Oxygen/*metabolism ; Photosynthesis/*physiology ; Photosystem I Protein Complex/metabolism ; Photosystem II Protein Complex/metabolism ; }, abstract = {Sam Granick opened his seminal 1957 paper titled 'Speculations on the origins and evolution of photosynthesis' with the assertion that there is a constant urge in human beings to seek beginnings (I concur). This urge has led to an incessant stream of speculative ideas and debates on the evolution of photosynthesis that started in the first half of the twentieth century and shows no signs of abating. Some of these speculative ideas have become commonplace, are taken as fact, but find little support. Here, I review and scrutinize three widely accepted ideas that underpin the current study of the evolution of photosynthesis: first, that the photochemical reaction centres used in anoxygenic photosynthesis are more primitive than those in oxygenic photosynthesis; second, that the probability of acquiring photosynthesis via horizontal gene transfer is greater than the probability of losing photosynthesis; and third, and most important, that the origin of anoxygenic photosynthesis pre-dates the origin of oxygenic photosynthesis. I shall attempt to demonstrate that these three ideas are often grounded in incorrect assumptions built on more assumptions with no experimental or observational support. I hope that this brief review will not only serve as a cautionary tale but also that it will open new avenues of research aimed at disentangling the complex evolution of photosynthesis and its impact on the early history of life and the planet.}, }
@article {pmid30889807, year = {2019}, author = {Kim, BO and Kim, ES and Yoo, YJ and Bae, HW and Chung, IY and Cho, YH}, title = {Phage-Derived Antibacterials: Harnessing the Simplicity, Plasticity, and Diversity of Phages.}, journal = {Viruses}, volume = {11}, number = {3}, pages = {}, pmid = {30889807}, issn = {1999-4915}, mesh = {Animals ; Anti-Bacterial Agents/chemistry/*pharmacology ; Bacteria/*drug effects/virology ; Bacterial Infections/therapy ; Bacteriophages/*chemistry/genetics ; Drug Resistance, Multiple, Bacterial ; Genetic Engineering ; Genetic Variation ; Humans ; Mice ; Phage Therapy/adverse effects ; Synthetic Biology ; }, abstract = {Despite the successful use of antibacterials, the emergence of multidrug-resistant bacteria has become a serious threat to global healthcare. In this era of antibacterial crisis, bacteriophages (phages) are being explored as an antibacterial treatment option since they possess a number of advantages over conventional antibacterials, especially in terms of specificity and biosafety; phages specifically lyse target bacteria while not affecting normal and/or beneficial bacteria and display little or no toxicity in that they are mainly composed of proteins and nucleic acids, which consequently significantly reduces the time and cost involved in antibacterial development. However, these benefits also create potential issues regarding antibacterial spectra and host immunity; the antibacterial spectra being very narrow when compared to those of chemicals, with the phage materials making it possible to trigger host immune responses, which ultimately disarm antibacterial efficacy upon successive treatments. In addition, phages play a major role in horizontal gene transfer between bacterial populations, which poses serious concerns for the potential of disastrous consequences regarding antibiotic resistance. Fortunately, however, recent advancements in synthetic biology tools and the speedy development of phage genome resources have allowed for research on methods to circumvent the potentially disadvantageous aspects of phages. These novel developments empower research which goes far beyond traditional phage therapy approaches, opening up a new chapter for phage applications with new antibacterial platforms. Herein, we not only highlight the most recent synthetic phage engineering and phage product engineering studies, but also discuss a new proof-of-concept for phage-inspired antibacterial design based on the studies undertaken by our group.}, }
@article {pmid30887618, year = {2019}, author = {Anasontzis, GE and Lebrun, MH and Haon, M and Champion, C and Kohler, A and Lenfant, N and Martin, F and O'Connell, RJ and Riley, R and Grigoriev, IV and Henrissat, B and Berrin, JG and Rosso, MN}, title = {Broad-specificity GH131 β-glucanases are a hallmark of fungi and oomycetes that colonize plants.}, journal = {Environmental microbiology}, volume = {21}, number = {8}, pages = {2724-2739}, doi = {10.1111/1462-2920.14596}, pmid = {30887618}, issn = {1462-2920}, support = {ANR-11-IDEX-0001-02//French National Agency for Research/International ; ANR-13-BIME-0002//French National Agency for Research/International ; ANR-14-CE06-0020-01//French National Agency for Research/International ; DE-AC02-05CH11231//Office of Science of the U.S. Department of Energy/International ; FP7-26719//Seventh Framework Programme/International ; FP7-26719//EU's Seventh Framework Programme/International ; }, mesh = {Ascomycota/enzymology/genetics ; Cell Wall/metabolism ; Fungi/*enzymology/genetics ; Gene Transfer, Horizontal ; Glycoside Hydrolases/genetics/*metabolism ; Oomycetes/*enzymology/genetics ; Plants/*microbiology ; Symbiosis ; }, abstract = {Plant-tissue-colonizing fungi fine-tune the deconstruction of plant-cell walls (PCW) using different sets of enzymes according to their lifestyle. However, some of these enzymes are conserved among fungi with dissimilar lifestyles. We identified genes from Glycoside Hydrolase family GH131 as commonly expressed during plant-tissue colonization by saprobic, pathogenic and symbiotic fungi. By searching all the publicly available genomes, we found that GH131-coding genes were widely distributed in the Dikarya subkingdom, except in Taphrinomycotina and Saccharomycotina, and in phytopathogenic Oomycetes, but neither other eukaryotes nor prokaryotes. The presence of GH131 in a species was correlated with its association with plants as symbiont, pathogen or saprobe. We propose that GH131-family expansions and horizontal-gene transfers contributed to this adaptation. We analysed the biochemical activities of GH131 enzymes whose genes were upregulated during plant-tissue colonization in a saprobe (Pycnoporus sanguineus), a plant symbiont (Laccaria bicolor) and three hemibiotrophic-plant pathogens (Colletotrichum higginsianum, C. graminicola, Zymoseptoria tritici). These enzymes were all active on substrates with β-1,4, β-1,3 and mixed β-1,4/1,3 glucosidic linkages. Combined with a cellobiohydrolase, GH131 enzymes enhanced cellulose degradation. We propose that secreted GH131 enzymes unlock the PCW barrier and allow further deconstruction by other enzymes during plant tissue colonization by symbionts, pathogens and saprobes.}, }
@article {pmid30886355, year = {2019}, author = {Varble, A and Meaden, S and Barrangou, R and Westra, ER and Marraffini, LA}, title = {Recombination between phages and CRISPR-cas loci facilitates horizontal gene transfer in staphylococci.}, journal = {Nature microbiology}, volume = {4}, number = {6}, pages = {956-963}, pmid = {30886355}, issn = {2058-5276}, support = {DP1 GM128184/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Bacteriophages/*genetics ; CRISPR-Cas Systems ; Clustered Regularly Interspaced Short Palindromic Repeats/*genetics/immunology ; Endonucleases ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Genome, Viral ; Plasmids/genetics ; Pseudomonas aeruginosa/genetics ; Sequence Analysis, DNA ; Staphylococcus/*genetics ; Staphylococcus aureus/genetics ; Transduction, Genetic ; }, abstract = {CRISPR (clustered regularly interspaced short palindromic repeats) loci and their associated (cas) genes encode an adaptive immune system that protects prokaryotes from viral[1] and plasmid[2] invaders. Following viral (phage) infection, a small fraction of the prokaryotic cells are able to integrate a small sequence of the invader's genome into the CRISPR array[1]. These sequences, known as spacers, are transcribed and processed into small CRISPR RNA guides[3-5] that associate with Cas nucleases to specify a viral target for destruction[6-9]. Although CRISPR-cas loci are widely distributed throughout microbial genomes and often display hallmarks of horizontal gene transfer[10-12], the drivers of CRISPR dissemination remain unclear. Here, we show that spacers can recombine with phage target sequences to mediate a form of specialized transduction of CRISPR elements. Phage targets in phage 85, ΦNM1, ΦNM4 and Φ12 can recombine with spacers in either chromosomal or plasmid-borne CRISPR loci in Staphylococcus, leading to either the transfer of CRISPR-adjacent genes or the propagation of acquired immunity to other bacteria in the population, respectively. Our data demonstrate that spacer sequences not only specify the targets of Cas nucleases but also can promote horizontal gene transfer.}, }
@article {pmid30885806, year = {2019}, author = {Fu, P and Tang, Y and Li, G and Yu, L and Wang, Y and Jiang, X}, title = {Pandemic spread of blaKPC-2 among Klebsiella pneumoniae ST11 in China is associated with horizontal transfer mediated by IncFII-like plasmids.}, journal = {International journal of antimicrobial agents}, volume = {54}, number = {2}, pages = {117-124}, doi = {10.1016/j.ijantimicag.2019.03.014}, pmid = {30885806}, issn = {1872-7913}, mesh = {China/epidemiology ; Electrophoresis, Gel, Pulsed-Field ; *Gene Transfer, Horizontal ; Humans ; Interspersed Repetitive Sequences ; Klebsiella Infections/*epidemiology/*microbiology ; Klebsiella pneumoniae/classification/*drug effects/*genetics/isolation &amp; purification ; Multilocus Sequence Typing ; Pandemics ; Plasmids/*analysis/classification ; Polymerase Chain Reaction ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: The aim of this study was to investigate the spread of the blaKPC-2 gene among Klebsiella pneumoniae and to illustrate the mechanism of dissemination of K. pneumoniae carbapenemase-producing K. pneumoniae (KPC-Kp) ST11 in China.<br><br>METHODS: A total of 354 K. pneumoniae isolates were collected from four hospitals in China and were characterized by multilocus sequence typing (MLST). Mobile genetic elements (MGEs) and pulsed-field gel electrophoresis (PFGE) analysis were used to identify the subtypes of K. pneumoniae ST11. Polymerase chain reaction (PCR)-based amplification and sequencing were performed to analyse Tn1721 transposons and IncFII-like plasmids. Electroporation experiments and whole-genome sequencing (WGS) were used to reveal the genetic environment of the blaKPC-2 gene.<br><br>RESULTS: As the primary type (87.1%) of KPC-Kp, K. pneumoniae ST11 was not predominant in non-KPC-Kp (3.1%). ST11 KPC-Kp was clonally heterogeneous and could be further classified into 11 MGE types and 14 PFGE subtypes. Five Tn1721-blaKPC-2 variants were identified on IncFII-like plasmids. The detection rate of IncFII-like plasmids was much higher in ST11 KPC-Kp (100%) compared with non-ST11 KPC-Kp (16.0%) and the non-KPC-Kp group (7.5%). Moreover, the IncFII plasmid (with IIa replicon) was primarily detected on the MGE-F type (61.7%). The IncFIIk plasmid (with IIk replicon) was clustered into two subtypes: MGE-A (28.3%) and -F (41.5%). The detection of the IncFII and IncFIIk plasmids on MGE-A was 57.1% (20/35) and 42.9% (15/35), respectively.<br><br>CONCLUSIONS: A close correlation was shown between ST11 KPC-Kp and IncFII-like plasmids. Horizontal transfer mediated by IncFII-like plasmids plays an important role in the pandemic expansion of blaKPC-2 among K. pneumoniae ST11 in China.}, }
@article {pmid30884168, year = {2019}, author = {Pacheco-Sánchez, D and Rama-Garda, R and Marín, P and Martirani-Von Abercron, SM and Marqués, S}, title = {Occurrence and diversity of the oxidative hydroxyhydroquinone pathway for the anaerobic degradation of aromatic compounds in nitrate-reducing bacteria.}, journal = {Environmental microbiology reports}, volume = {11}, number = {4}, pages = {525-537}, doi = {10.1111/1758-2229.12752}, pmid = {30884168}, issn = {1758-2229}, support = {P08-CVI03591//Junta de Andaluc&#xed;a/International ; BIO2014-54361-R//Ministerio de Econom&#xed;a y Competitividad/International ; //European Regional Development Fund (FEDER)/International ; }, mesh = {Anaerobiosis ; Bacterial Proteins/genetics ; Betaproteobacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Environmental Microbiology ; Genetic Variation ; Genome, Bacterial/genetics ; Hydroquinones/*metabolism ; Hydroxybenzoates/metabolism ; Metabolic Networks and Pathways/*genetics ; Multigene Family ; Nitrates/*metabolism ; Oxidation-Reduction ; Phylogeny ; Resorcinols/metabolism ; }, abstract = {The nitrate-reducing betaproteobacteria Azoarcus anaerobius and Thauera aromatica AR-1 use an oxidative mechanism to anaerobically degrade resorcinol and 3,5-dihydroxybenzoate (3,5-DHB), respectively, rendering hydroxyhydroquinone as intermediate. The first pathway step is performed by a dimethylsulphoxide-reductase family hydroxylase. The gene cluster coding for the pathway is homologous in these strains. Only these two Rhodocyclales are known to follow this anaerobic pathway, and nothing is known about its distribution in prokaryotes. To determine the relevance and diversity of this strategy in nature, we enriched for bacteria able to oxidize resorcinol or 3,5-DHB under denitrifying conditions. Nitrate-reducing bacteria able to degrade these compounds were present in soil, aquifer and marine sediments. We were able to isolate a number of strains with this capacity from soil and aquifer samples. Amplicon libraries of rehL, the gene encoding the first step of this pathway, showed an overall low diversity, most sequences clustering with either pathway enzyme. Isolates belonging to the Beta- and Gammaproteobacteria able to grow on these substrates revealed rehL homologues only in strains belonging to Thauera and Azoarcus. Analysis of sequenced genomes in the databases detected the presence of highly similar clusters in two additional betaproteobacteria and in the gammaproteobacterium Sedimenticola selenatireducens, although anaerobic growth on a dihydroxyaromatic could only be confirmed in Thauera chlorobenzoica 3CB-1. The presence of mobile elements in the flanking sequences of some of the clusters suggested events of horizontal gene transfer, probably contributing to expand the pathway to a broader host range within the Proteobacteria.}, }
@article {pmid30881354, year = {2019}, author = {Liang, J and Huang, H and Wang, S}, title = {Distribution, Evolution, Catalytic Mechanism, and Physiological Functions of the Flavin-Based Electron-Bifurcating NADH-Dependent Reduced Ferredoxin: NADP[+] Oxidoreductase.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {373}, pmid = {30881354}, issn = {1664-302X}, abstract = {NADH-dependent reduced ferredoxin:NADP[+] oxidoreductase (Nfn) is an electron-bifurcating enzyme first discovered in the strict anaerobes Clostridium kluyveri and Moorella thermoacetica. In vivo, Nfn catalyzes the endergonic reduction of NADP[+] with NADH coupled to the exergonic reduction of NADP[+] with reduced ferredoxin. Most Nfn homologs consist of two subunits, although in certain species Nfn homologs are fused. In contrast to other electron-bifurcating enzymes, Nfn possess a simpler structure. Therefore, Nfn becomes a perfect model to determine the mechanism of flavin-based electron bifurcation, which is a novel energy coupling mode distributed among anaerobic bacteria and archaea. The crystal structures of Nfn from Thermotoga maritima and Pyrococcus furiosus are known, and studies have shown that the FAD molecule of the NfnB (b-FAD) is the site of electron bifurcation, and other cofactors, including a [2Fe2S] cluster, two [4Fe4S] clusters, and the FAD molecule on the NfnA subunit, contribute to electron transfer. Further, the short-lived anionic flavin semiquinone (ASQ) state of b-FAD is essential for electron bifurcation. Nfn homologs are widely distributed among microbes, including bacteria, archaea, and probably eukaryotes, most of which are anaerobes despite that certain species are facultative microbes and even aerobes. Moreover, potential evidence shows that lateral gene transfer may occur in the evolution of this enzyme. Nfn homologs present four different structural patterns, including the well-characterized NfnAB and three different kinds of fused Nfn homologs whose detailed properties have not been characterized. These findings indicate that gene fusion/fission and gene rearrangement may contribute to the evolution of this enzyme. Under physiological conditions, Nfn catalyzes the reduction of NADP[+] with NADH and reduced ferredoxin, which is then used in certain NADPH-dependent reactions. Deletion of nfn in several microbes causes low growth and redox unbalance and may influence the distribution of fermentation products. It's also noteworthy that different Nfn homologs perform different functions according to its circumstance. Physiological functions of Nfn indicate that it can be a potential tool in the metabolic engineering of industrial microorganisms, which can regulate the redox potential in vivo.}, }
@article {pmid30881351, year = {2019}, author = {Fan, XT and Li, H and Chen, QL and Zhang, YS and Ye, J and Zhu, YG and Su, JQ}, title = {Fate of Antibiotic Resistant Pseudomonas putida and Broad Host Range Plasmid in Natural Soil Microcosms.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {194}, pmid = {30881351}, issn = {1664-302X}, abstract = {Plasmid conjugation is one of the dominant mechanisms of horizontal gene transfer, playing a noticeable role in the rapid spread of antibiotic resistance genes (ARGs). Broad host range plasmids are known to transfer to diverse bacteria in extracted soil bacterial communities when evaluated by filter mating incubation. However, the persistence and dissemination of broad range plasmid in natural soil has not been well studied. In this study, Pseudomonas putida with a conjugative antibiotic resistance plasmid RP4 was inoculated into a soil microcosm, the fate and persistence of P. putida and RP4 were monitored by quantitative PCR. The concentrations of P. putida and RP4 both rapidly decreased within 15-day incubation. P. putida then decayed at a significantly lower rate during subsequent incubation, however, no further decay of RP4 was observed, resulting in an elevated RP4/P. putida ratio (up to 10) after 75-day incubation, which implied potential transfer of RP4 to soil microbiota. We further sorted RP4 recipient bacteria from the soil microcosms by fluorescence-activated cell sorting. Spread of RP4 increased during 75-day microcosm operation and was estimated at around 10[-4] transconjugants per recipient at the end of incubation. Analysis of 16S rRNA gene sequences of transconjugants showed that host bacteria of RP4 were affiliated to more than 15 phyla, with increased diversity and shift in the composition of host bacteria. Proteobacteria was the most dominant phylum in the transconjugant pools. Transient transfer of RP4 to some host bacteria was observed. These results emphasize the prolonged persistence of P. putida and RP4 in natural soil microcosms, and highlight the potential risks of increased spread potential of plasmid and broader range of host bacteria in disseminating ARGs in soil.}, }
@article {pmid30880586, year = {2019}, author = {Bamba, M and Aoki, S and Kajita, T and Setoguchi, H and Watano, Y and Sato, S and Tsuchimatsu, T}, title = {Exploring Genetic Diversity and Signatures of Horizontal Gene Transfer in Nodule Bacteria Associated with Lotus japonicus in Natural Environments.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {32}, number = {9}, pages = {1110-1120}, doi = {10.1094/MPMI-02-19-0039-R}, pmid = {30880586}, issn = {0894-0282}, mesh = {*Gene Transfer, Horizontal ; *Genetic Variation ; *Lotus/microbiology ; *Mesorhizobium/classification/genetics ; Phylogeny ; *Root Nodules, Plant/microbiology ; Symbiosis/genetics ; }, abstract = {To investigate the genetic diversity and understand the process of horizontal gene transfer (HGT) in nodule bacteria associated with Lotus japonicus, we analyzed sequences of three housekeeping and five symbiotic genes using samples from a geographically wide range in Japan. A phylogenetic analysis of the housekeeping genes indicated that L. japonicus in natural environments was associated with diverse lineages of Mesorhizobium spp., whereas the sequences of symbiotic genes were highly similar between strains, resulting in remarkably low nucleotide diversity at both synonymous and nonsynonymous sites. Guanine-cytosine content values were lower in symbiotic genes, and relative frequencies of recombination between symbiotic genes were also lower than those between housekeeping genes. An analysis of molecular variance showed significant genetic differentiation among populations in both symbiotic and housekeeping genes. These results confirm that the Mesorhizobium genes required for symbiosis with L. japonicus behave as a genomic island (i.e., a symbiosis island) and suggest that this island has spread into diverse genomic backgrounds of Mesorhizobium via HGT events in natural environments. Furthermore, our data compilation revealed that the genetic diversity of symbiotic genes in L. japonicus-associated symbionts was among the lowest compared with reports of other species, which may be related to the recent population expansion proposed in Japanese populations of L. japonicus.}, }
@article {pmid30879104, year = {2019}, author = {Ravindran, A and Sunderrajan, S and Pennathur, G}, title = {Phylogenetic Studies on the Prodigiosin Biosynthetic Operon.}, journal = {Current microbiology}, volume = {76}, number = {5}, pages = {597-606}, pmid = {30879104}, issn = {1432-0991}, support = {BT/PR5106/BRB/10/1073/2012//Department of Biotechnology, Ministry of Science and Technology/ ; 09/468/(0486)/2014-EMR-1//Council of Scientific and Industrial Research/ ; }, mesh = {Anti-Bacterial Agents/metabolism ; Bacterial Proteins/genetics ; Biosynthetic Pathways/*genetics ; *Evolution, Molecular ; Multigene Family ; *Operon ; *Phylogeny ; Prodigiosin/analogs &amp; derivatives/*biosynthesis ; Promoter Regions, Genetic ; Sequence Analysis, DNA ; Serratia/genetics ; Serratia marcescens/genetics ; Streptomyces/genetics ; }, abstract = {Prodigiosin and undecylprodigiosin are tripyrrolic red pigmented antibiotics produced by certain bacteria. Many strains of Serratia and certain other Gammaproteobacteria produce prodigiosin and undecylprodigiosin is produced by certain strains of Streptomyces. This is a multistage process which involves the synthesis of a bipyrrolic compound from L-proline and its subsequent condensation with a mono pyrrole synthesized from 2-octenal in the case of prodigiosin and malonyl-CoA in the case of undecylprodigiosin respectively. We have carried out sequence analysis of the genes involved in the pathway and identified the distribution of the prodigiosin producing genes amongst the various bacteria which have been fully sequenced. The presence of the operon was clearly seen in certain clustered branches suggesting inheritance from a common ancestor. This was further confirmed by the absence of traits observed in horizontally acquired genes like, GC content variation, codon bias or the presence of mobile elements. Multiple sequence alignment of the promoter of the prodigiosin operon in seven fully sequenced Serratia marcescens strains showed excellent homology. Putative regulatory elements in this region were identified by sequence analysis studies and many of them have been found to influence pigment production. The undecylprodigiosin gene cluster on the other hand, shows homology to other gene clusters involved in the production of other pyrrole-containing antibiotics of the genus Streptomyces. This coupled with the presence of ORFs with three different promoters could indicate lateral gene transfer. Hence the evolution of undecylprodigiosin operon could be an example of convergent evolution.}, }
@article {pmid30877310, year = {2019}, author = {Frank, AC}, title = {Molecular host mimicry and manipulation in bacterial symbionts.}, journal = {FEMS microbiology letters}, volume = {366}, number = {4}, pages = {}, doi = {10.1093/femsle/fnz038}, pmid = {30877310}, issn = {1574-6968}, mesh = {Bacteria/genetics ; *Biological Mimicry ; *Eukaryota ; *Symbiosis ; }, abstract = {It is common among intracellular bacterial pathogens to use eukaryotic-like proteins that mimic and manipulate host cellular processes to promote colonization and intracellular survival. Eukaryotic-like proteins are bacterial proteins with domains that are rare in bacteria, and known to function in the context of a eukaryotic cell. Such proteins can originate through horizontal gene transfer from eukaryotes or, in the case of simple repeat proteins, through convergent evolution. Recent studies of microbiomes associated with several eukaryotic hosts suggest that similar molecular strategies are deployed by cooperative bacteria that interact closely with eukaryotic cells. Some mimics, like ankyrin repeats, leucine rich repeats and tetratricopeptide repeats are shared across diverse symbiotic systems ranging from amoebae to plants, and may have originated early, or evolved independently in multiple systems. Others, like plant-mimicking domains in members of the plant microbiome are likely to be more recent innovations resulting from horizontal gene transfer from the host, or from microbial eukaryotes occupying the same host. Host protein mimics have only been described in a limited set of symbiotic systems, but are likely to be more widespread. Systematic searches for eukaryote-like proteins in symbiont genomes could lead to the discovery of novel mechanisms underlying host-symbiont interactions.}, }
@article {pmid30875553, year = {2019}, author = {Paul, D and Chakraborty, R and Mandal, SM}, title = {Biocides and health-care agents are more than just antibiotics: Inducing cross to co-resistance in microbes.}, journal = {Ecotoxicology and environmental safety}, volume = {174}, number = {}, pages = {601-610}, doi = {10.1016/j.ecoenv.2019.02.083}, pmid = {30875553}, issn = {1090-2414}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Disinfectants/*pharmacology ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Selection, Genetic ; Soil Microbiology ; }, abstract = {Health-care chemicals are used worldwide as important components of different industries as consumer products, food industry, animal husbandry and agribusiness. There are innumerable reports on the effect of these chemicals (biocides) impacting the development of cross to co-resistance in pathogenic bacteria. However, reports are limited on the concurrent use of agricides (pesticides, herbicides, fungicides and insecticides) which influence the microbial activities in soils and contribute to the increase in incidences of co-resistance. Undoubtedly, indiscriminate use of biocides and agricides has contaminated both water and soil environments. This review describes the onset of cross and co-resistance to biocides and antibiotics which is increasingly being exhibited by specific bacteria under a persistent selective pressure. It also re-examines the significance of mobile genetic platforms and horizontal gene transfer from one to another bacterial species, for understanding the kinetics and efficiency of genetic exchange in stressed environments leading to natural selection of tolerant strains over susceptible ones. The investigation is much warranted, particularly with respect to agricides that commonly occur in recalcitrant states in soil and water ecosystem, livestock, etc and is transmitted either directly or via the food-chain to human beings, facilitating the switch from cross to co-resistance.}, }
@article {pmid30874473, year = {2019}, author = {Joshi, PR and Thummeepak, R and Paudel, S and Acharya, M and Pradhan, S and Banjara, MR and Leungtongkam, U and Sitthisak, S}, title = {Molecular Characterization of Colistin-Resistant Escherichia coli Isolated from Chickens: First Report from Nepal.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {25}, number = {6}, pages = {846-854}, doi = {10.1089/mdr.2018.0326}, pmid = {30874473}, issn = {1931-8448}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Chickens/*microbiology ; Ciprofloxacin/pharmacology ; Colistin/*pharmacology ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/genetics/*isolation &amp; purification ; Escherichia coli Proteins/genetics ; Farms ; Gene Transfer, Horizontal/genetics ; Microbial Sensitivity Tests ; Nepal ; Phylogeny ; Plasmids/genetics ; Tetracycline/pharmacology ; Trimethoprim, Sulfamethoxazole Drug Combination/pharmacology ; beta-Lactamases/genetics ; }, abstract = {Dissemination of mcr-1 encoding colistin resistance in Gram-negative bacteria has created critical situation in poultry, livestock farming, and public health. In Nepal, for the first time, we initiated surveillance of colistin-resistant Escherichia coli in broilers from seven different chicken farms. A total of 324 cloacal swabs were collected and 118 E. coli were isolated, of which 27 (22.8%) were colistin resistance all harboring mcr-1 gene, but lacking ISApI1. Colistin-resistant isolates were characterized by antibiotic susceptibility testing, detecting antibiotic resistance genes, phylogenetic analysis, and plasmid replicon typing. These isolates belonged to the phylo-group A (70.37%) and phylo-group D (29.63%). In addition, most isolates (>80%) were resistant to ciprofloxacin, tetracycline, and sulfamethoxazole-trimethoprim. As much as 3 of the 27 mcr-1 encoding isolates were confirmed as extended-spectrum β-lactamase (ESBL) producer, all 3 isolates carrying blaCTX-M gene. We performed the conjugation experiment to check transferability of mcr-1, tet, and blaCTX-M genes, and only two donors were found to have transferred resistance to ticarcillin. The transfer of colistin and tetracycline resistance was not detected, which suggests the chromosomal location of mcr-1 and tet genes. The prevalence of Inc K/B and Inc I1 was 96.3% and 81.48%, respectively. This study shows the co-existence of mcr-1 with tet, sul, qnr, dfr, and blaCTX-M genes and dissemination of these resistant isolates in Nepalese chicken farms, which may pose huge threat to the livestock, especially chickens, and public health in Nepal.}, }
@article {pmid30867937, year = {2019}, author = {Kindle, P and Zurfluh, K and Nüesch-Inderbinen, M and von Ah, S and Sidler, X and Stephan, R and Kümmerlen, D}, title = {Phenotypic and genotypic characteristics of Escherichia coli with non-susceptibility to quinolones isolated from environmental samples on pig farms.}, journal = {Porcine health management}, volume = {5}, number = {}, pages = {9}, pmid = {30867937}, issn = {2055-5660}, abstract = {BACKGROUND: In the last decade, the growth of the pig-farming industry has led to an increase in antibiotic use, including several used in human medicine, e.g. (fluoro)quinolones. Data from several studies suggest that there is a link between the agricultural use of antibiotics and the prevalence of antibiotic-resistant bacteria in the pig farm environment, including (fluoro)quinolone resistance. This poses a threat to human and animal health. Our goal was to phenotypically and genotypically characterize 174 E. coli showing non-susceptibility to quinolones isolated from environmental samples from pig farms. Antimicrobial susceptibility testing (AST) was performed using the disk diffusion method. PCR and sequence analysis were performed to identify chromosomal mutations in the quinolone resistance-determining regions (QRDR) of gyrA and the isolates were screened for the presence of the plasmid-mediated quinolone resistance (PMQR) genes aac-(6')-Ib-cr, qepA, qnrA, qnrB, qnrC, qnrD and qnrS.Strain relatedness was assessed by phylogenetic classification and multilocus sequence typing (MLST).<br><br>RESULTS: Of 174 isolates, 81% (n&#x2009;=&#x2009;141) were resistant to nalidixic acid, and 19% (n&#x2009;=&#x2009;33) were intermediately resistant. Overall, 68.4% (n&#x2009;=&#x2009;119) were multidrug resistant. This study revealed a prevalence of 79.9% (n&#x2009;=&#x2009;139) for gyrA QRDR mutations, and detected 21.8% (n&#x2009;=&#x2009;38) isolates with at least one PMQR gene. The two most frequently detected PMQR genes were qnrB and qnrS (13.8% (n&#x2009;=&#x2009;24) and 9.8% (n&#x2009;=&#x2009;17, respectively). E. coli belonging to phylogenetic group A (48.3%/n&#x2009;=&#x2009;84) and group B1 (33.3% /n&#x2009;=&#x2009;58) were the most frequent. E. coli ST10 (n&#x2009;=&#x2009;20) and ST297 (n&#x2009;=&#x2009;20) were the most common STs.<br><br>CONCLUSIONS: E. coli with non-susceptibility to quinolones are widespread among the environment of Swiss pig farms and are often associated with an MDR phenotype. In several cases these isolates possess at least one PMQR gene, which could spread by horizontal gene transfer. E. coli from pig farms have diverse STs, some of which are associated with human and animal disease.}, }
@article {pmid30867571, year = {2019}, author = {Deniz, &#xd6; and Frost, JM and Branco, MR}, title = {Regulation of transposable elements by DNA modifications.}, journal = {Nature reviews. Genetics}, volume = {20}, number = {7}, pages = {417-431}, pmid = {30867571}, issn = {1471-0064}, mesh = {5-Methylcytosine/*metabolism ; Adenosine/analogs &amp; derivatives/metabolism ; Animals ; Biological Evolution ; DNA (Cytosine-5-)-Methyltransferases/genetics/*metabolism ; DNA Methylation ; *DNA Transposable Elements ; *Epigenesis, Genetic ; Gene Transfer, Horizontal ; Genetic Drift ; Humans ; Plants/genetics/metabolism ; RNA, Small Interfering/genetics/metabolism ; }, abstract = {Maintenance of genome stability requires control over the expression of transposable elements (TEs), whose activity can have substantial deleterious effects on the host. Chemical modification of DNA is a commonly used strategy to achieve this, and it has long been argued that the emergence of 5-methylcytosine (5mC) in many species was driven by the requirement to silence TEs. Potential roles in TE regulation have also been suggested for other DNA modifications, such as N6-methyladenine and oxidation derivatives of 5mC, although the underlying mechanistic relationships are poorly understood. Here, we discuss current evidence implicating DNA modifications and DNA-modifying enzymes in TE regulation across different species.}, }
@article {pmid30867296, year = {2019}, author = {Verma, J and Bag, S and Saha, B and Kumar, P and Ghosh, TS and Dayal, M and Senapati, T and Mehra, S and Dey, P and Desigamani, A and Kumar, D and Rana, P and Kumar, B and Maiti, TK and Sharma, NC and Bhadra, RK and Mutreja, A and Nair, GB and Ramamurthy, T and Das, B}, title = {Genomic plasticity associated with antimicrobial resistance in Vibrio cholerae.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {13}, pages = {6226-6231}, pmid = {30867296}, issn = {1091-6490}, mesh = {Anti-Bacterial Agents/pharmacology ; Cholera/*microbiology ; Conjugation, Genetic/genetics ; DNA Transposable Elements/genetics ; Diarrhea/microbiology ; Drug Resistance, Multiple, Bacterial/*genetics ; Evolution, Molecular ; Feces/microbiology ; *Gene Transfer, Horizontal ; Genetic Variation ; Genome, Bacterial/*genetics ; Genomic Islands/genetics ; Humans ; Imipenem/pharmacology ; India ; Interspersed Repetitive Sequences/genetics ; Phenotype ; Plasmids/genetics ; Prophages/genetics ; Proteome ; Vibrio cholerae/drug effects/*genetics/isolation &amp; purification/pathogenicity ; Vibrio cholerae O1/genetics/isolation &amp; purification/pathogenicity ; Whole Genome Sequencing ; }, abstract = {The Bay of Bengal is known as the epicenter for seeding several devastating cholera outbreaks across the globe. Vibrio cholerae, the etiological agent of cholera, has extraordinary competency to acquire exogenous DNA by horizontal gene transfer (HGT) and adapt them into its genome for structuring metabolic processes, developing drug resistance, and colonizing the human intestine. Antimicrobial resistance (AMR) in V. cholerae has become a global concern. However, little is known about the identity of the resistance traits, source of AMR genes, acquisition process, and stability of the genetic elements linked with resistance genes in V. cholerae Here we present details of AMR profiles of 443 V. cholerae strains isolated from the stool samples of diarrheal patients from two regions of India. We sequenced the whole genome of multidrug-resistant (MDR) and extensively drug-resistant (XDR) V. cholerae to identify AMR genes and genomic elements that harbor the resistance traits. Our genomic findings were further confirmed by proteome analysis. We also engineered the genome of V. cholerae to monitor the importance of the autonomously replicating plasmid and core genome in the resistance profile. Our findings provided insights into the genomes of recent cholera isolates and identified several acquired traits including plasmids, transposons, integrative conjugative elements (ICEs), pathogenicity islands (PIs), prophages, and gene cassettes that confer fitness to the pathogen. The knowledge generated from this study would help in better understanding of V. cholerae evolution and management of cholera disease by providing clinical guidance on preferred treatment regimens.}, }
@article {pmid30862050, year = {2019}, author = {Afify, SM and Seno, M}, title = {Conversion of Stem Cells to Cancer Stem Cells: Undercurrent of Cancer Initiation.}, journal = {Cancers}, volume = {11}, number = {3}, pages = {}, pmid = {30862050}, issn = {2072-6694}, abstract = {Cancer stem cells (CSCs) also known as cancer-initiating cells (CIC), are responsible for the sustained and uncontrolled growth of malignant tumors and are proposed to play significant roles in metastasis and recurrence. Several hypotheses have proposed that the events in either stem and/or differentiated cells, such as genomic instability, inflammatory microenvironment, cell fusion, and lateral gene transfer, should be considered as the possible origin of CSCs. However, until now, the exact origin of CSC has been obscure. The development of induced pluripotent stem cells (iPSCs) in 2007, by Yamanaka's group, has been met with much fervency and hailed as a breakthrough discovery by the scientific and research communities, especially in regeneration therapy. The studies on the development of CSC from iPSCs should also open a new page of cancer research, which will help in designing new therapies applicable to CSCs. Currently most reviews have focused on CSCs and CSC niches. However, the insight into the niche before the CSC niche should also be of keen interest. This review introduces the novel concept of cancer initiation introducing the conversion of iPSCs to CSCs and proposes a relationship between the inflammatory microenvironment and cancer initiation as the key concept of the cancer-inducing niche responsible for the development of CSC.}, }
@article {pmid30859257, year = {2019}, author = {Tran, PN and Yen, MR and Chiang, CY and Lin, HC and Chen, PY}, title = {Detecting and prioritizing biosynthetic gene clusters for bioactive compounds in bacteria and fungi.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {8}, pages = {3277-3287}, pmid = {30859257}, issn = {1432-0614}, support = {106-2311-B-001 -035 -MY3//Ministry of Science and Technology, Taiwan/ ; 106-2633-B-001 -001//Ministry of Science and Technology, Taiwan/ ; 106-2113-M-001-008-MY2//Ministry of Science and Technology, Taiwan/ ; 107-2320-B-001-025-MY3//Ministry of Science and Technology, Taiwan/ ; }, mesh = {Bacteria/chemistry/*genetics/metabolism ; Biological Products/metabolism ; *Computational Biology ; Drug Resistance, Microbial/genetics ; Fungi/chemistry/*genetics/metabolism ; Gene Duplication ; Gene Transfer, Horizontal ; Genome, Microbial/genetics ; Multigene Family/*genetics ; Secondary Metabolism/*genetics ; }, abstract = {Secondary metabolites (SM) produced by fungi and bacteria have long been of exceptional interest owing to their unique biomedical ramifications. The traditional discovery of new natural products that was mainly driven by bioactivity screening has now experienced a fresh new approach in the form of genome mining. Several bioinformatics tools have been continuously developed to detect potential biosynthetic gene clusters (BGCs) that are responsible for the production of SM. Although the principles underlying the computation of these tools have been discussed, the biological background is left underrated and ambiguous. In this review, we emphasize the biological hypotheses in BGC formation driven from the observations across genomes in bacteria and fungi, and provide a comprehensive list of updated algorithms/tools exclusively for BGC detection. Our review points to a direction that the biological hypotheses should be systematically incorporated into the BGC prediction and assist the prioritization of candidate BGC.}, }
@article {pmid30858294, year = {2019}, author = {Humbert, M and Huguet, KT and Coulombe, F and Burrus, V}, title = {Entry Exclusion of Conjugative Plasmids of the IncA, IncC, and Related Untyped Incompatibility Groups.}, journal = {Journal of bacteriology}, volume = {201}, number = {10}, pages = {}, pmid = {30858294}, issn = {1098-5530}, support = {PJT-153071//CIHR/Canada ; }, mesh = {Bacterial Proteins/genetics/metabolism ; *Conjugation, Genetic ; Gammaproteobacteria/genetics/*metabolism ; *Gene Transfer, Horizontal ; Plasmids/classification/*metabolism ; }, abstract = {Conjugative plasmids of incompatibility group C (IncC), formerly known as A/C2, disseminate antibiotic resistance genes globally in diverse pathogenic species of Gammaproteobacteria. Salmonella genomic island 1 (SGI1) can be mobilized by IncC plasmids and was recently shown to reshape the conjugative type IV secretion system (T4SS) encoded by these plasmids to evade entry exclusion. Entry exclusion blocks DNA translocation between cells containing identical or highly similar plasmids. Here, we report that the protein encoded by the entry exclusion gene of IncC plasmids (eexC) mediates entry exclusion in recipient cells through recognition of the IncC-encoded TraGC protein in donor cells. Phylogenetic analyses based on EexC and TraGC homologs predicted the existence of at least three different exclusion groups among IncC-related conjugative plasmids. Mating assays using Eex proteins encoded by representative IncC and IncA (former A/C1) and related untyped plasmids confirmed these predictions and showed that the IncC and IncA plasmids belong to the C exclusion group, thereby explaining their apparent incompatibility despite their compatible replicons. Representatives of the two other exclusion groups (D and E) are untyped conjugative plasmids found in Aeromonas sp. Finally, we determined through domain swapping that the carboxyl terminus of the EexC and EexE proteins controls the specificity of these exclusion groups. Together, these results unravel the role of entry exclusion in the apparent incompatibility between IncA and IncC plasmids while shedding light on the importance of the TraG subunit substitution used by SGI1 to evade entry exclusion.IMPORTANCE IncA and IncC conjugative plasmids drive antibiotic resistance dissemination among several pathogenic species of Gammaproteobacteria due to the diversity of drug resistance genes that they carry and their ability to mobilize antibiotic resistance-conferring genomic islands such as SGI1 of Salmonella enterica While historically grouped as "IncA/C," IncA and IncC replicons were recently confirmed to be compatible and to abolish each other's entry into the cell in which they reside during conjugative transfer. The significance of our study is in identifying an entry exclusion system that is shared by IncA and IncC plasmids. It impedes DNA transfer to recipient cells bearing a plasmid of either incompatibility group. The entry exclusion protein of this system is unrelated to any other known entry exclusion proteins.}, }
@article {pmid30856357, year = {2019}, author = {Le Rhun, A and Escalera-Maurer, A and Bratovič, M and Charpentier, E}, title = {CRISPR-Cas in Streptococcus pyogenes.}, journal = {RNA biology}, volume = {16}, number = {4}, pages = {380-389}, pmid = {30856357}, issn = {1555-8584}, mesh = {Adaptation, Physiological/genetics ; CRISPR-Cas Systems/*genetics ; Genetic Loci ; RNA/biosynthesis ; RNA Interference ; Streptococcus pyogenes/*genetics ; }, abstract = {The discovery and characterization of the prokaryotic CRISPR-Cas immune system has led to a revolution in genome editing and engineering technologies. Despite the fact that most applications emerged after the discovery of the type II-A CRISPR-Cas9 system of Streptococcus pyogenes, its biological importance in this organism has received little attention. Here, we provide a comprehensive overview of the current knowledge about CRISPR-Cas systems from S. pyogenes. We discuss how the interplay between CRISPR-mediated immunity and horizontal gene transfer might have modeled the evolution of this pathogen. We review the current literature about the CRISPR-Cas systems present in S. pyogenes (types I-C and II-A), and describe their distinctive biochemical and functional features. Finally, we summarize the main biotechnological applications that have arisen from the discovery of the CRISPR-Cas9 system in S. pyogenes.}, }
@article {pmid30851534, year = {2019}, author = {Guo, MT and Kong, C}, title = {Antibiotic resistant bacteria survived from UV disinfection: Safety concerns on genes dissemination.}, journal = {Chemosphere}, volume = {224}, number = {}, pages = {827-832}, doi = {10.1016/j.chemosphere.2019.03.004}, pmid = {30851534}, issn = {1879-1298}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/growth &amp; development/*radiation effects ; Conjugation, Genetic/*radiation effects ; Disinfection/methods ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal/*radiation effects ; *Ultraviolet Rays ; Wastewater/microbiology ; Water Purification ; }, abstract = {Antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are the emerging contaminants leading to a serious worldwide health problem. Although disinfection like ultraviolet (UV) irradiation could remove part of ARB and ARGs, there still are residual ARB and ARGs in the effluent of wastewater treatment plants. Conjugative transfer is main concern of the risk of ARGs and little is known about the effects of UV disinfection on the transfer ability of the non-inactivated ARB in the effluent which will enter the environment. Hence the influences of UV irradiation and reactivation on ARB conjugative transfer ability were studied under laboratory condition, focusing on the survival bacteria from UV irradiation and the reactivated bacteria, as well as their descendants. The experimental results imply that even 1 mJ/cm[2] UV disinfection can significantly decrease the conjugative transfer frequency of the survival bacteria. However, viable but not culturable state cells induced by UV can reactivate through both photoreactivation and dark repair and retain the same level of transfer ability as the untreated strains. This finding is essential for re-considering about the post safety of UV irradiated effluent and microbial safety control strategies were required.}, }
@article {pmid30849934, year = {2019}, author = {Lüli, Y and Cai, Q and Chen, ZH and Sun, H and Zhu, XT and Li, X and Yang, ZL and Luo, H}, title = {Genome of lethal Lepiota venenata and insights into the evolution of toxin-biosynthetic genes.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {198}, pmid = {30849934}, issn = {1471-2164}, support = {2017YFC0505200//National Key R &amp; D Program of China/ ; 31772377//Natural Science Foundation of China/ ; 31770588//Natural Science Foundation of China/ ; 151853KYSB20170026//International Partnership Program of Chinese Academy of Sciences/ ; }, mesh = {Agaricales/*genetics/*metabolism/physiology ; *Evolution, Molecular ; Genes, Fungal/*genetics ; Genomics ; Phylogeny ; Toxins, Biological/*biosynthesis ; }, abstract = {BACKGROUND: Genomes of lethal Amanita and Galerina mushrooms have gradually become available in the past ten years; in contrast the other known amanitin-producing genus, Lepiota, is still vacant in this aspect. A fatal mushroom poisoning case in China has led to acquisition of fresh L. venenata fruiting bodies, based on which a draft genome was obtained through PacBio and Illumina sequencing platforms. Toxin-biosynthetic MSDIN family and Porlyl oligopeptidase B (POPB) genes were mined from the genome and used for phylogenetic and statistical studies to gain insights into the evolution of the biosynthetic pathway.<br><br>RESULTS: The analysis of the genome data illustrated that only one MSDIN, named LvAMA1, exits in the genome, along with a POPB gene. No POPA homolog was identified by direct homology searching, however, one additional POP gene, named LvPOPC, was cloned and the gene structure determined. Similar to ApAMA1 in A. phalloides and GmAMA1 in G. marginata, LvAMA1 directly encodes &#x3b1;-amanitin. The two toxin genes were mapped to the draft genome, and the structures analyzed. Furthermore, phylogenetic and statistical analyses were conducted to study the evolution history of the POPB genes. Compared to our previous report, the phylogenetic trees unambiguously showed that a monophyletic POPB lineage clearly conflicted with the species phylogeny. In contrast, phylogeny of POPA genes resembled the species phylogeny. Topology and divergence tests showed that the POPB lineage was robust and these genes exhibited significantly shorter genetic distances than those of the house-keeping rbp2, a characteristic feature of genes with horizontal gene transfer (HGT) background. Consistently, same scenario applied to the only MSDIN, LvAMA1, in the genome.<br><br>CONCLUSIONS: To the best of our knowledge, this is the first reported genome of Lepiota. The analyses of the toxin genes indicate that the cyclic peptides are synthesized through a ribosomal mechanism. The toxin genes, LvAMA1 and LvPOPB, are not in the vicinity of each other. Phylogenetic and evolutionary studies suggest that HGT is the underlining cause for the occurrence of POPB and MSDIN in Amanita, Galerina and Lepiota, which are allocated in three distantly-related families.}, }
@article {pmid30849601, year = {2019}, author = {Liu, H and Sun, H and Zhang, M and Liu, Y}, title = {Dynamics of microbial community and tetracycline resistance genes in biological nutrient removal process.}, journal = {Journal of environmental management}, volume = {238}, number = {}, pages = {84-91}, doi = {10.1016/j.jenvman.2019.02.123}, pmid = {30849601}, issn = {1095-8630}, mesh = {Anti-Bacterial Agents ; *Microbiota ; Nutrients ; Tetracycline ; *Tetracycline Resistance ; Wastewater ; }, abstract = {The occurrence of antibiotics in wastewater has become a serious concern due to the possible development of antibiotic resistant bacteria in wastewater treatment process. In order to understand the dynamics of microbial community and tetracycline resistance genes in biological nutrient removal (BNR) process, three lab-scale sequencing batch reactors (SBRs) were operated under the stress of tetracycline. Results indicated that microbial community structure was altered, and tetracycline efflux pump genes were enhanced over 150-day operation in the presence of trace tetracycline of 20 and 50 μg L[-1], respectively. Furthermore, when the initial tetracycline concentrations were increased to 2 and 5 mg L[-1], substantial enhancement of tetracycline resistance was observed, accompanied with a sharp shift in microbial community structure. In this study, horizontal gene transfer was found to be the main mechanism for the development of tetracycline resistance genes under the long-terms stress of trace tetracycline. About 90.34% of the observed variations in tetracycline resistance genes could be explained by the dynamics of potential hosts of tetracycline resistance genes and class 1 integron. It should be noticed that the functional bacteria (e.g. Nitrospira, Dechloromonas, Rhodobacter and Candidatus_Accumulibacter) responsible for nutrient removal were positively correlated with tetracycline resistance, which might promote the prevalence of tetracycline resistance during biological wastewater treatment. Consequently, this study provided in-depth insights into the occurrence and prevalence of tetracycline resistance genes and their microbial hosts in BNR process.}, }
@article {pmid30849369, year = {2019}, author = {Lindsey, ARI and Newton, ILG}, title = {Some Like it HOT: Horizontal Operon Transfer.}, journal = {Cell}, volume = {176}, number = {6}, pages = {1243-1245}, doi = {10.1016/j.cell.2019.02.007}, pmid = {30849369}, issn = {1097-4172}, support = {R21 AI121849/AI/NIAID NIH HHS/United States ; R21 AI137918/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/genetics ; *Eukaryota ; Eukaryotic Cells ; Gene Transfer, Horizontal ; Operon ; }, abstract = {While horizontal gene transfer (HGT) is well documented in bacteria, the role and frequency of HGT across eukaryotes remains poorly understood. Kominek et al. identified a horizontal operon transfer (HOT) event, with clear evidence for selection to facilitate gene expression, that has allowed a group of yeasts to scavenge iron using bacterially derived genes.}, }
@article {pmid30848890, year = {2019}, author = {Vikesland, P and Garner, E and Gupta, S and Kang, S and Maile-Moskowitz, A and Zhu, N}, title = {Differential Drivers of Antimicrobial Resistance across the World.}, journal = {Accounts of chemical research}, volume = {52}, number = {4}, pages = {916-924}, doi = {10.1021/acs.accounts.8b00643}, pmid = {30848890}, issn = {1520-4898}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects ; *Drug Resistance, Bacterial/genetics ; Environmental Monitoring/*methods ; Food Microbiology ; Gene Transfer, Horizontal ; Humans ; Refuse Disposal ; Sanitation ; Soil Microbiology ; Water Microbiology ; }, abstract = {Antimicrobial resistance (AMR) is one of the greatest threats faced by humankind. The development of resistance in clinical and hospital settings has been well documented ever since the initial discovery of penicillin and the subsequent introduction of sulfonamides as clinical antibiotics. In contrast, the environmental (i.e., community-acquired) dimensions of resistance dissemination have been only more recently delineated. The global spread of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) between air, water, soil, and food is now well documented, while the factors that affect ARB and ARG dissemination (e.g., water and air quality, antibiotic fluxes, urbanization, sanitation practices) in these and other environmental matrices are just now beginning to be more fully appreciated. In this Account, we discuss how the global perpetuation of resistance is dictated by highly interconnected socioeconomic risk factors and illustrate that development status should be more fully considered when developing global strategies to address AMR. We first differentiate low to middle income countries (LMICs) and high-income countries (HICs), then we summarize the modes of action of commercially available antibiotics, and then discuss the four primary mechanisms by which bacteria develop resistance to those antibiotics. Resistance is disseminated via both vertical gene transfer (VGT; parent to offspring) as well as by horizontal gene transfer (HGT; cell to cell transference of genetic material). A key challenge hindering attempts to control resistance dissemination is the presence of native, environmental bacteria that can harbor ARGs. Such environmental "resistomes" have potential to transfer resistance to pathogens via HGT. Of particular concern is the development of resistance to antibiotics of last-resort such as the cephalosporins, carbapenems, and polymyxins. We then illustrate how antibiotic use differs in LMICs relative to HICs in terms of the volumes of antibiotics used and their fate within local environments. Antibiotic use in HICs has remained flat over the past 15 years, while in LMICs use over the same period has increased substantially as a result of economic improvements and changes in diet. These use and fate differences impact local citizens and thus the local dissemination of AMR. Various physical, social, and economic circumstances within LMICs potentially favor AMR dissemination. We focus on three physical factors: changing population density, sanitation infrastructure, and solid-waste disposal. We show that high population densities in cities within LMICs that suffer from poor sanitation and solid-waste disposal can potentially impact the dissemination of resistance. In the final section, we discuss potential monitoring approaches to quantify the spread of resistance both within LMICs as well as in HICs. We posit that culture-based approaches, molecular approaches, and cutting-edge nanotechnology-based methods for monitoring ARB and ARGs should be considered both within HICs and, as appropriate, within LMICs.}, }
@article {pmid30844419, year = {2019}, author = {LaBreck, PT and Li, Z and Gibbons, KP and Merrell, DS}, title = {Conjugative and replicative biology of the Staphylococcus aureus antimicrobial resistance plasmid, pC02.}, journal = {Plasmid}, volume = {102}, number = {}, pages = {71-82}, doi = {10.1016/j.plasmid.2019.02.006}, pmid = {30844419}, issn = {1095-9890}, mesh = {Base Sequence ; Cadmium/pharmacology ; *Conjugation, Genetic/drug effects ; DNA Replication/drug effects/*genetics ; Drug Resistance, Bacterial/drug effects/*genetics ; Erythromycin/pharmacology ; Gene Dosage ; Kinetics ; Plasmids/*genetics ; Staphylococcus aureus/drug effects/*genetics ; Time Factors ; }, abstract = {Genetic transfer among bacteria propels rapid resistance to antibiotics and decreased susceptibility to antiseptics. Staphylococcus aureus is a common culprit of hospital and community acquired infections, and S. aureus plasmids have been shown to carry a multitude of antimicrobial resistance genes. We previously identified a novel conjugative, multidrug resistance plasmid, pC02, from the clinical S. aureus isolate C02. This plasmid contained the chlorhexidine resistance gene qacA, and we were able to demonstrate that conjugative transfer of pC02 imparted decreased chlorhexidine susceptibility to recipient strains. In silico sequence analysis of pC02 suggested that the plasmid is part of the pWBG749-family of conjugative plasmids and that it contains three predicted origins of transfer (oriT), two of which we showed were functional and could mediate plasmid transfer. Furthermore, depending on which oriT was utilized, partial transfer of pC02 was consistently observed. To define the ability of the pC02 plasmid to utilize different oriT sequences, we examined the mobilization ability of nonconjugative plasmid variants that were engineered to contain a variety of oriT family inserts. The oriT-OTUNa family was transferred at the highest frequency; additional oriT families were also transferred but at lower frequencies. Plasmid stability was examined, and the copy number of pC02 was defined using droplet digital PCR (ddPCR). pC02 was stably maintained at approximately 4 copies per cell. Given the conjugative plasticity of pC02, we speculate that this plasmid could contribute to the spread of antimicrobial resistance across Staphylococcal strains and species.}, }
@article {pmid30842288, year = {2019}, author = {Milner, DS and Attah, V and Cook, E and Maguire, F and Savory, FR and Morrison, M and Müller, CA and Foster, PG and Talbot, NJ and Leonard, G and Richards, TA}, title = {Environment-dependent fitness gains can be driven by horizontal gene transfer of transporter-encoding genes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {12}, pages = {5613-5622}, pmid = {30842288}, issn = {1091-6490}, support = {//Wellcome Trust/United Kingdom ; BB/N016858/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; WT105618MA//Wellcome Trust/United Kingdom ; }, mesh = {Biological Evolution ; Evolution, Molecular ; Fungi/genetics ; Gene Transfer, Horizontal/*genetics ; Genetic Fitness/*genetics ; Genome ; Membrane Transport Proteins/genetics ; Phenotype ; Phylogeny ; Saccharomyces cerevisiae/*genetics ; Saccharomyces cerevisiae Proteins/genetics ; }, abstract = {Many microbes acquire metabolites in a "feeding" process where complex polymers are broken down in the environment to their subunits. The subsequent uptake of soluble metabolites by a cell, sometimes called osmotrophy, is facilitated by transporter proteins. As such, the diversification of osmotrophic microorganisms is closely tied to the diversification of transporter functions. Horizontal gene transfer (HGT) has been suggested to produce genetic variation that can lead to adaptation, allowing lineages to acquire traits and expand niche ranges. Transporter genes often encode single-gene phenotypes and tend to have low protein-protein interaction complexity and, as such, are potential candidates for HGT. Here we test the idea that HGT has underpinned the expansion of metabolic potential and substrate utilization via transfer of transporter-encoding genes. Using phylogenomics, we identify seven cases of transporter-gene HGT between fungal phyla, and investigate compatibility, localization, function, and fitness consequences when these genes are expressed in Saccharomyces cerevisiae Using this approach, we demonstrate that the transporters identified can alter how fungi utilize a range of metabolites, including peptides, polyols, and sugars. We then show, for one model gene, that transporter gene acquisition by HGT can significantly alter the fitness landscape of S. cerevisiae We therefore provide evidence that transporter HGT occurs between fungi, alters how fungi can acquire metabolites, and can drive gain in fitness. We propose a "transporter-gene acquisition ratchet," where transporter repertoires are continually augmented by duplication, HGT, and differential loss, collectively acting to overwrite, fine-tune, and diversify the complement of transporters present in a genome.}, }
@article {pmid30837979, year = {2019}, author = {Newberry, EA and Ebrahim, M and Timilsina, S and Zlatković, N and Obradović, A and Bull, CT and Goss, EM and Huguet-Tapia, JC and Paret, ML and Jones, JB and Potnis, N}, title = {Inference of Convergent Gene Acquisition Among Pseudomonas syringae Strains Isolated From Watermelon, Cantaloupe, and Squash.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {270}, pmid = {30837979}, issn = {1664-302X}, abstract = {Pseudomonas syringae sensu stricto (phylogroup 2; referred to as P. syringae) consists of an environmentally ubiquitous bacterial population associated with diseases of numerous plant species. Recent studies using multilocus sequence analysis have indicated the clonal expansion of several P. syringae lineages, located in phylogroups 2a and 2b, in association with outbreaks of bacterial spot disease of watermelon, cantaloupe, and squash in the United States. To investigate the evolutionary processes that led to the emergence of these epidemic lineages, we sequenced the genomes of six P. syringae strains that were isolated from cucurbits grown in the United States, Europe, and China over a period of more than a decade, as well as eight strains that were isolated from watermelon and squash grown in six different Florida counties during the 2013 and 2014 seasons. These data were subjected to comparative analyses along with 42 previously sequenced genomes of P. syringae stains collected from diverse plant species and environments available from GenBank. Maximum likelihood reconstruction of the P. syringae core genome revealed the presence of a hybrid phylogenetic group, comprised of cucurbit strains collected in Florida, Italy, Serbia, and France, which emerged through genome-wide homologous recombination between phylogroups 2a and 2b. Functional analysis of the recombinant core genome showed that pathways involved in the ATP-dependent transport and metabolism of amino acids, bacterial motility, and secretion systems were enriched for recombination. A survey of described virulence factors indicated the convergent acquisition of several accessory type 3 secreted effectors (T3SEs) among phylogenetically distinct lineages through integrative and conjugative element and plasmid loci. Finally, pathogenicity assays on watermelon and squash showed qualitative differences in virulence between strains of the same clonal lineage, which correlated with T3SEs acquired through various mechanisms of horizontal gene transfer (HGT). This study provides novel insights into the interplay of homologous recombination and HGT toward pathogen emergence and highlights the dynamic nature of P. syringae sensu lato genomes.}, }
@article {pmid30837965, year = {2019}, author = {Watanabe, M and Kojima, H and Umezawa, K and Fukui, M}, title = {Genomic Characteristics of Desulfonema ishimotonii Tokyo 01[T] Implying Horizontal Gene Transfer Among Phylogenetically Dispersed Filamentous Gliding Bacteria.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {227}, pmid = {30837965}, issn = {1664-302X}, abstract = {Desulfonema ishimotonii strain Tokyo 01[T] is a filamentous sulfate-reducing bacterium isolated from a marine sediment. In this study, the genome of this strain was sequenced and analyzed with a focus on gene transfer from phylogenetically distant organisms. While the strain belongs to the class Deltaproteobacteria, hundreds of proteins encoded in the genome showed the highest sequence similarities to those of organisms outside of the class Deltaproteobacteria, suggesting that more than 20% of the genome is putatively of foreign origins. Many of these proteins had the highest sequence identities with proteins encoded in the genomes of filamentous bacteria, including giant sulfur oxidizers of the orders Thiotrichales, cyanobacteria of various genera, and uncultured bacteria of the candidate phylum KSB3. As mobile genetic elements transferred from phylogenetically distant organisms, putative inteins were identified in the GyrB and DnaE proteins encoded in the genome of strain Tokyo 01[T]. Genes involved in DNA recombination and repair were enriched in comparison to the closest relatives in the same family. Some of these genes were also related to those of organisms outside of the class Deltaproteobacteria, suggesting that they were acquired by horizontal gene transfer from diverse bacteria. The genomic data suggested significant genetic transfer among filamentous gliding bacteria in phylogenetically dispersed lineages including filamentous sulfate reducers. This study provides insights into the genomic evolution of filamentous bacteria belonging to diverse lineages, characterized by various physiological functions and different ecological roles.}, }
@article {pmid30837332, year = {2019}, author = {Will, WR and Brzovic, P and Le Trong, I and Stenkamp, RE and Lawrenz, MB and Karlinsey, JE and Navarre, WW and Main-Hester, K and Miller, VL and Libby, SJ and Fang, FC}, title = {The Evolution of SlyA/RovA Transcription Factors from Repressors to Countersilencers in Enterobacteriaceae.}, journal = {mBio}, volume = {10}, number = {2}, pages = {}, pmid = {30837332}, issn = {2150-7511}, support = {R01 AI112640/AI/NIAID NIH HHS/United States ; R01 AI039557/AI/NIAID NIH HHS/United States ; R56 AI112640/AI/NIAID NIH HHS/United States ; R01 AI118962/AI/NIAID NIH HHS/United States ; R01 AI044486/AI/NIAID NIH HHS/United States ; R01 GM098503/GM/NIGMS NIH HHS/United States ; }, mesh = {Enterobacteriaceae/*genetics ; *Evolution, Molecular ; *Gene Expression Regulation, Bacterial ; *Gene Silencing ; Gene Transfer, Horizontal ; Transcription Factors/*genetics ; }, abstract = {Gene duplication and subsequent evolutionary divergence have allowed conserved proteins to develop unique roles. The MarR family of transcription factors (TFs) has undergone extensive duplication and diversification in bacteria, where they act as environmentally responsive repressors of genes encoding efflux pumps that confer resistance to xenobiotics, including many antimicrobial agents. We have performed structural, functional, and genetic analyses of representative members of the SlyA/RovA lineage of MarR TFs, which retain some ancestral functions, including repression of their own expression and that of divergently transcribed multidrug efflux pumps, as well as allosteric inhibition by aromatic carboxylate compounds. However, SlyA and RovA have acquired the ability to countersilence horizontally acquired genes, which has greatly facilitated the evolution of Enterobacteriaceae by horizontal gene transfer. SlyA/RovA TFs in different species have independently evolved novel regulatory circuits to provide the enhanced levels of expression required for their new role. Moreover, in contrast to MarR, SlyA is not responsive to copper. These observations demonstrate the ability of TFs to acquire new functions as a result of evolutionary divergence of both cis-regulatory sequences and in trans interactions with modulatory ligands.IMPORTANCE Bacteria primarily evolve via horizontal gene transfer, acquiring new traits such as virulence and antibiotic resistance in single transfer events. However, newly acquired genes must be integrated into existing regulatory networks to allow appropriate expression in new hosts. This is accommodated in part by the opposing mechanisms of xenogeneic silencing and countersilencing. An understanding of these mechanisms is necessary to understand the relationship between gene regulation and bacterial evolution. Here we examine the functional evolution of an important lineage of countersilencers belonging to the ancient MarR family of classical transcriptional repressors. We show that although members of the SlyA lineage retain some ancestral features associated with the MarR family, their cis-regulatory sequences have evolved significantly to support their new function. Understanding the mechanistic requirements for countersilencing is critical to understanding the pathoadaptation of emerging pathogens and also has practical applications in synthetic biology.}, }
@article {pmid30835731, year = {2019}, author = {Di Lelio, I and Illiano, A and Astarita, F and Gianfranceschi, L and Horner, D and Varricchio, P and Amoresano, A and Pucci, P and Pennacchio, F and Caccia, S}, title = {Evolution of an insect immune barrier through horizontal gene transfer mediated by a parasitic wasp.}, journal = {PLoS genetics}, volume = {15}, number = {3}, pages = {e1007998}, pmid = {30835731}, issn = {1553-7404}, mesh = {Animals ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Hemolymph/immunology/virology ; Larva/genetics/*immunology/virology ; Phylogeny ; Proteomics ; Symbiosis/genetics/immunology ; Wasps/genetics/*immunology/virology ; }, abstract = {Genome sequencing data have recently demonstrated that eukaryote evolution has been remarkably influenced by the acquisition of a large number of genes by horizontal gene transfer (HGT) across different kingdoms. However, in depth-studies on the physiological traits conferred by these accidental DNA acquisitions are largely lacking. Here we elucidate the functional role of Sl gasmin, a gene of a symbiotic virus of a parasitic wasp that has been transferred to an ancestor of the moth species Spodoptera littoralis and domesticated. This gene is highly expressed in circulating immune cells (haemocytes) of larval stages, where its transcription is rapidly boosted by injection of microorganisms into the body cavity. RNAi silencing of Sl gasmin generates a phenotype characterized by a precocious suppression of phagocytic activity by haemocytes, which is rescued when these immune cells are incubated in plasma samples of control larvae, containing high levels of the encoded protein. Proteomic analysis demonstrates that the protein Sl gasmin is released by haemocytes into the haemolymph, where it opsonizes the invading bacteria to promote their phagocytosis, both in vitro and in vivo. Our results show that important physiological traits do not necessarily originate from evolution of pre-existing genes, but can be acquired by HGT events, through unique pathways of symbiotic evolution. These findings indicate that insects can paradoxically acquire selective advantages with the help of their natural enemies.}, }
@article {pmid30834930, year = {2019}, author = {van Sluijs, L and van Houte, S and van der Oost, J and Brouns, SJ and Buckling, A and Westra, ER}, title = {Addiction systems antagonize bacterial adaptive immunity.}, journal = {FEMS microbiology letters}, volume = {366}, number = {5}, pages = {}, pmid = {30834930}, issn = {1574-6968}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Anti-Bacterial Agents/pharmacology ; CRISPR-Cas Systems/genetics/*physiology ; Drug Resistance, Bacterial/genetics ; Escherichia coli/drug effects/genetics/growth &amp; development/*physiology ; Gene Transfer, Horizontal ; Plasmids/genetics ; Toxin-Antitoxin Systems/genetics/*physiology ; }, abstract = {CRISPR-Cas systems provide adaptive immunity against mobile genetic elements, but employment of this resistance mechanism is often reported with a fitness cost for the host. Whether or not CRISPR-Cas systems are important barriers for the horizontal spread of conjugative plasmids, which play a crucial role in the spread of antibiotic resistance, will depend on the fitness costs of employing CRISPR-based defences and the benefits of resisting conjugative plasmids. To estimate these costs and benefits we measured bacterial fitness associated with plasmid immunity using Escherichia coli and the conjugative plasmid pOX38-Cm. We find that CRISPR-mediated immunity fails to confer a fitness benefit in the absence of antibiotics, despite the large fitness cost associated with carrying the plasmid in this context. Similar to many other conjugative plasmids, pOX38-Cm carries a CcdAB toxin-anti-toxin (TA) addiction system. These addiction systems encode long-lived toxins and short-lived anti-toxins, resulting in toxic effects following the loss of the TA genes from the bacterial host. Our data suggest that the lack of a fitness benefit associated with CRISPR-mediated defence is due to expression of the TA system before plasmid detection and degradation. As most antibiotic resistance plasmids encode TA systems this could have important consequences for the role of CRISPR-Cas systems in limiting the spread of antibiotic resistance.}, }
@article {pmid30834379, year = {2019}, author = {Campos, FS and Cerqueira, FB and Santos, GR and Pereira, EJG and Corrêia, RFT and Cangussu, ASR and Melo, FL and Ribeiro, BM and Aguiar, RWS}, title = {Complete Sequences of Two Plasmids Found in a Brazilian Bacillus thuringiensis Serovar israelensis Strain.}, journal = {Microbiology resource announcements}, volume = {8}, number = {9}, pages = {}, pmid = {30834379}, issn = {2576-098X}, abstract = {Plasmids play a crucial role in the evolution of bacterial genomes by mediating horizontal gene transfer. In this work, we sequenced two plasmids found in a Brazilian Bacillus thuringiensis serovar israelensis strain which showed 100% nucleotide identities with Bacillus thuringiensis serovar kurstaki plasmids.}, }
@article {pmid30832740, year = {2019}, author = {Song, W and Wemheuer, B and Zhang, S and Steensen, K and Thomas, T}, title = {MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {36}, pmid = {30832740}, issn = {2049-2618}, mesh = {Bacteria/classification/*genetics ; Computational Biology/*methods ; Databases, Genetic ; Drug Resistance, Bacterial ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Humans ; Metagenomics ; Phylogeny ; Soil Microbiology ; }, abstract = {BACKGROUND: Metagenomic datasets provide an opportunity to study horizontal gene transfer (HGT) on the level of a microbial community. However, current HGT detection methods cannot be applied to community-level datasets or require reference genomes. Here, we present MetaCHIP, a pipeline for reference-independent HGT identification at the community level.<br><br>RESULTS: Assessment of MetaCHIP's performance on simulated datasets revealed that it can predict HGTs with various degrees of genetic divergence from metagenomic datasets. The results also indicated that the detection of very recent gene transfers (i.e. those with low levels of genetic divergence) from metagenomics datasets is largely affected by the read assembly step. Comparison of MetaCHIP with a previous analysis on soil bacteria showed a high level of consistency for the prediction of recent HGTs and revealed a large number of additional non-recent gene transfers, which can provide new biological and ecological insight. Assessment of MetaCHIP's performance on real metagenomic datasets confirmed the role of HGT in the spread of genes related to antibiotic resistance in the human gut microbiome. Further testing also showed that functions related to energy production and conversion as well as carbohydrate transport and metabolism are frequently transferred among free-living microorganisms.<br><br>CONCLUSION: MetaCHIP provides an opportunity to study HGTs among members of a microbial community and therefore has several applications in the field of microbial ecology and evolution. MetaCHIP is implemented in Python and freely available at https://github.com/songweizhi/MetaCHIP .}, }
@article {pmid30832446, year = {2019}, author = {Patsilinakos, A and Artini, M and Papa, R and Sabatino, M and Božović, M and Garzoli, S and Vrenna, G and Buzzi, R and Manfredini, S and Selan, L and Ragno, R}, title = {Machine Learning Analyses on Data including Essential Oil Chemical Composition and In Vitro Experimental Antibiofilm Activities against Staphylococcus Species.}, journal = {Molecules (Basel, Switzerland)}, volume = {24}, number = {5}, pages = {}, pmid = {30832446}, issn = {1420-3049}, support = {FAR2018//Universit&#xe0; degli Studi di Ferrara/ ; }, mesh = {Anti-Bacterial Agents/chemistry/pharmacology ; Biofilms/*drug effects ; Humans ; Machine Learning ; Microbial Sensitivity Tests ; Oils, Volatile/*chemistry/pharmacology ; Staphylococcal Infections/*drug therapy/microbiology ; Staphylococcus/*drug effects/growth &amp; development/pathogenicity ; }, abstract = {Biofilm resistance to antimicrobials is a complex phenomenon, driven not only by genetic mutation induced resistance, but also by means of increased microbial cell density that supports horizontal gene transfer across cells. The prevention of biofilm formation and the treatment of existing biofilms is currently a difficult challenge; therefore, the discovery of new multi-targeted or combinatorial therapies is growing. The development of anti-biofilm agents is considered of major interest and represents a key strategy as non-biocidal molecules are highly valuable to avoid the rapid appearance of escape mutants. Among bacteria, staphylococci are predominant causes of biofilm-associated infections. Staphylococci, especially Staphylococcus aureus (S. aureus) is an extraordinarily versatile pathogen that can survive in hostile environmental conditions, colonize mucous membranes and skin, and can cause severe, non-purulent, toxin-mediated diseases or invasive pyogenic infections in humans. Staphylococcus epidermidis (S. epidermidis) has also emerged as an important opportunistic pathogen in infections associated with medical devices (such as urinary and intravascular catheters, orthopaedic implants, etc.), causing approximately from 30% to 43% of joint prosthesis infections. The scientific community is continuously looking for new agents endowed of anti-biofilm capabilities to fight S. aureus and S epidermidis infections. Interestingly, several reports indicated in vitro efficacy of non-biocidal essential oils (EOs) as promising treatment to reduce bacterial biofilm production and prevent the inducing of drug resistance. In this report were analyzed 89 EOs with the objective of investigating their ability to modulate bacterial biofilm production of different S. aureus and S. epidermidis strains. Results showed the assayed EOs to modulated the biofilm production with unpredictable results for each strain. In particular, many EOs acted mainly as biofilm inhibitors in the case of S. epidermidis strains, while for S. aureus strains, EOs induced either no effect or stimulate biofilm production. In order to elucidate the obtained experimental results, machine learning (ML) algorithms were applied to the EOs' chemical compositions and the determined associated anti-biofilm potencies. Statistically robust ML models were developed, and their analysis in term of feature importance and partial dependence plots led to indicating those chemical components mainly responsible for biofilm production, inhibition or stimulation for each studied strain, respectively.}, }
@article {pmid30829555, year = {2019}, author = {Liang, F and Lin, R and Yao, Y and Xiao, Y and Zhang, M and Shi, C and He, X and Zhou, B and Wang, B}, title = {Systematic Identification of Pathogenic Streptomyces sp. AMCC400023 That Causes Common Scab and Genomic Analysis of Its Pathogenicity Island.}, journal = {Phytopathology}, volume = {109}, number = {7}, pages = {1115-1128}, doi = {10.1094/PHYTO-07-18-0266-R}, pmid = {30829555}, issn = {0031-949X}, mesh = {China ; Genomic Islands/*genetics ; Genomics ; Phylogeny ; Plant Diseases/*microbiology ; *Solanum tuberosum/microbiology ; *Streptomyces/pathogenicity ; }, abstract = {Potato scab, a serious soilborne disease caused by Streptomyces spp., occurs in potato-growing areas worldwide and results in severe economic losses. In this paper, the pathogenicity of Streptomyces strain AMCC400023, isolated from potato scabs in Hebei Province, China, was verified systematically by the radish seedling test, the potato tuber slice assay, the potted back experiment, and the detection of phytotoxin thaxtomin A. Morphological, physiological, and biochemical characteristics were determined, and the 16S ribosomal RNA analyses of Streptomyces sp. AMCC400023 were carried out. To obtain the accurate taxonomic status of the pathogen strain, the whole genome was sequenced, and the phylogenetic tree among 31 Streptomyces genomes was formed. The average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) were analyzed, and at the same time, the toxicity-related genes between Streptomyces sp. AMCC400023 and Streptomyces scabiei were compared, all based on the whole-genome level. All of the data supported that, instead of a member of S. scabiei, test strain Streptomyces sp. AMCC400023 was a distinct phytopathogen of potato common scab, which had a relatively close relationship with S. scabiei while separating clearly from S. scabiei at least in the species level of taxonomic status. The complete pathogenicity island (PAI) composition of Streptomyces sp. AMCC400023 was identified, which contained a toxin region and a colonization region. It was conjectured that the PAI of Streptomyces sp. AMCC400023 might be directly or indirectly acquired from S. scabiei 87-22 by horizontal gene transfer, or at the very least, there was a very close homologous relationship between the two pathogens as indicated by a series of analyses, such as phylogenetic relationships among 31 Streptomyces species, ANI and isDDH analyses, PAI structure mapping, thaxtomin A synthetic gene cluster tree construction, and most important, the collinearity analysis at the genome level.}, }
@article {pmid30828325, year = {2019}, author = {Lambrechts, S and Willems, A and Tahon, G}, title = {Uncovering the Uncultivated Majority in Antarctic Soils: Toward a Synergistic Approach.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {242}, pmid = {30828325}, issn = {1664-302X}, abstract = {Although Antarctica was once believed to be a sterile environment, it is now clear that the microbial communities inhabiting the Antarctic continent are surprisingly diverse. Until the beginning of the new millennium, little was known about the most abundant inhabitants of the continent: prokaryotes. From then on, however, the rising use of deep sequencing techniques has led to a better understanding of the Antarctic prokaryote diversity and provided insights in the composition of prokaryotic communities in different Antarctic environments. Although these cultivation-independent approaches can produce millions of sequences, linking these data to organisms is hindered by several problems. The largest difficulty is the lack of biological information on large parts of the microbial tree of life, arising from the fact that most microbial diversity on Earth has never been characterized in laboratory cultures. These unknown prokaryotes, also known as microbial dark matter, have been dominantly detected in all major environments on our planet. Laboratory cultures provide access to the complete genome and the means to experimentally verify genomic predictions and metabolic functions and to provide evidence of horizontal gene transfer. Without such well-documented reference data, microbial dark matter will remain a major blind spot in deep sequencing studies. Here, we review our current understanding of prokaryotic communities in Antarctic ice-free soils based on cultivation-dependent and cultivation-independent approaches. We discuss advantages and disadvantages of both approaches and how these strategies may be combined synergistically to strengthen each other and allow a more profound understanding of prokaryotic life on the frozen continent.}, }
@article {pmid30827405, year = {2019}, author = {Wang, Z and Fu, Y and Schwarz, S and Yin, W and Walsh, TR and Zhou, Y and He, J and Jiang, H and Wang, Y and Wang, S}, title = {Genetic environment of colistin resistance genes mcr-1 and mcr-3 in Escherichia coli from one pig farm in China.}, journal = {Veterinary microbiology}, volume = {230}, number = {}, pages = {56-61}, doi = {10.1016/j.vetmic.2019.01.011}, pmid = {30827405}, issn = {1873-2542}, support = {G1100135/MRC_/Medical Research Council/United Kingdom ; MR/N028317/1/MRC_/Medical Research Council/United Kingdom ; MR/P007295/1/MRC_/Medical Research Council/United Kingdom ; MR/S013768/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; China ; Colistin/pharmacology ; Conjugation, Genetic ; Drug Resistance, Bacterial ; Escherichia coli/drug effects/*genetics ; Escherichia coli Infections/*veterinary ; Escherichia coli Proteins/*genetics ; Farms ; Feces/microbiology ; Gene Transfer, Horizontal ; Interspersed Repetitive Sequences ; Livestock/microbiology ; Microbial Sensitivity Tests ; Swine ; Transferases (Other Substituted Phosphate Groups)/*genetics ; Whole Genome Sequencing ; }, abstract = {The aim of this study was to assess the presence of mobile colistin resistance in bacteria isolated from the swine production environment and to analyze the genomic environment of the new colistin resistance gene mcr-3. Anal swabs and environmental samples were collected from a commercial pig farm. Direct sample testing (DST) for mcr genes and isolation of colistin-resistant isolates was performed. The mcr-3-positive isolates were subjected to whole genome sequencing (WGS). Transferability and genomic location analyses of mcr-3 gene were performed using conjugation and S1 nuclease-PFGE with Southern blotting assays, respectively. The antimicrobial susceptibility profiles of the mcr-carrying isolates were determined using the agar dilution method. A total of 65 samples were collected. The DST rates of mcr-1 (64.6%, 42/65) and mcr-3 (40.0%, 26/65) were considerably higher than the rates of mcr-1-positive E. coli (49.2%, 32/65) and mcr-3-positive E. coli (7.7%, 5/65) isolated from these samples, respectively. The five mcr-3-positive isolates were derived from different sources (pig, fly and soil) and four of the five isolates were also positive for mcr-1. The mcr-3 genes were located on IncP-1 plasmids in three isolates or IncHI2 plasmids in two isolates. Several mobile elements, including IS4321, ΔTnAs2 or ISKpn40, were identified in the flanking regions of mcr-3 in the E. coli isolates. In conclusion, the mobile colistin resistance genes mcr-1 and mcr-3 are prevalent in the monitored pig farm and its surrounding environment. Due to their location on broad-host range IncP-1 plasmids and their proximity to different IS sequences, mcr-3 gene might have excellent opportunities for transmission.}, }
@article {pmid30827384, year = {2019}, author = {Mourand, G and Andraud, M and Jouy, E and Chauvin, C and Le Devendec, L and Paboeuf, F and Kempf, I}, title = {Impact of colistin administered before or after inoculation on the transmission of a mcr-1 colistin-resistant Escherichia coli strain between pigs.}, journal = {Veterinary microbiology}, volume = {230}, number = {}, pages = {164-170}, doi = {10.1016/j.vetmic.2019.02.002}, pmid = {30827384}, issn = {1873-2542}, mesh = {Animals ; Anti-Bacterial Agents/administration &amp; dosage/pharmacology ; Colistin/*administration &amp; dosage/pharmacology ; *Drug Resistance, Multiple, Bacterial ; Escherichia coli/*drug effects ; Escherichia coli Infections/prevention &amp; control/transmission/*veterinary ; Escherichia coli Proteins/*genetics ; Farms ; Feces/microbiology ; Gene Transfer, Horizontal ; Livestock/microbiology ; Microbial Sensitivity Tests ; Plasmids/genetics ; Polymerase Chain Reaction ; Random Allocation ; Rifampin/pharmacology ; Swine ; }, abstract = {Colistin resistance associated with plasmidic resistance genes is a serious public health issue. We aimed at studying the transmission of an mcr-1 colistin- and rifampicin-resistant Escherichia coli strain between inoculated pigs and sentinels in different controlled conditions. Three groups of four pigs were bred in separated animal rooms and inoculated on Day 0 (D0). In each inoculated group, six contact pigs were introduced on D2. The first inoculated-and-contact group was left untreated. The ten pigs in the second inoculated-and-contact group received colistin (100 000 IU/kg) before inoculation or contact (D-7 to D-5), simulating prophylactic administration. Pigs in the third inoculated-and-contact group were treated just after inoculation or before transfer (D0 to D2), simulating metaphylactic administration. Faecal samples were regularly collected and segments of intestinal tracts were obtained at necropsy, on D20-D22. Samples were cultured on rifampicin-supplemented media, and PCR was used to detect the mcr-1 gene. The kinetics of infection, based on culture results, were analysed using an SIR model. The inoculated strain was detected in all inoculated and contact pigs. The SIR model showed that one infected pig could transmit the resistant bacteria to one susceptible individual in less than 3 h on average. Prophylactic administration significantly enhanced the transmission rate and resulted in more samples containing the mcr-1 resistance gene at necropsy. No effect of metaphylactic administration could be detected on the transmission rate, nor on the carriage of the resistant strain. Our study confirms that colistin should not be used in a prophylactic manner.}, }
@article {pmid30825306, year = {2019}, author = {Glushchenko, OE and Prianichnikov, NA and Olekhnovich, EI and Manolov, AI and Tyakht, AV and Starikova, EV and Odintsova, VE and Kostryukova, ES and Ilina, EI}, title = {VERA: agent-based modeling transmission of antibiotic resistance between human pathogens and gut microbiota.}, journal = {Bioinformatics (Oxford, England)}, volume = {35}, number = {19}, pages = {3803-3811}, doi = {10.1093/bioinformatics/btz154}, pmid = {30825306}, issn = {1367-4811}, mesh = {Anti-Bacterial Agents ; Drug Resistance, Microbial ; *Gastrointestinal Microbiome ; Gene Transfer, Horizontal ; Humans ; Systems Analysis ; }, abstract = {MOTIVATION: The resistance of bacterial pathogens to antibiotics is one of the most important issues of modern health care. The human microbiota can accumulate resistance determinants and transfer them to pathogenic microbiota by means of horizontal gene transfer. Thus, it is important to develop methods of prediction and monitoring of antibiotics resistance in human populations.<br><br>RESULTS: We present the agent-based VERA model, which allows simulation of the spread of pathogens, including the possible horizontal transfer of resistance determinants from a commensal microbiota community. The model considers the opportunity of residents to stay in the town or in a medical institution, have incorrect self-treatment, treatment with several antibiotics types and transfer and accumulation of resistance determinants from commensal microorganism to a pathogen. In this model, we have also created an assessment of optimum observation frequency of infection spread among the population. Investigating model behavior, we show a number of non-linear dependencies, including the exponential nature of the dependence of the total number of those infected on the average resistance of a pathogen. As the model infection, we chose infection with Shigella spp., though it could be applied to a wide range of other pathogens.<br><br>Source code and binaries VERA and VERA.viewer are freely available for download at github.com/lpenguin/microbiota-resistome. The code is written in Java, JavaScript and R for Linux platform.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid30824066, year = {2019}, author = {Forgione, I and Bonavita, S and Regina, TMR}, title = {Mitochondria of Cedrus atlantica and allied species: A new chapter in the horizontal gene transfer history.}, journal = {Plant science : an international journal of experimental plant biology}, volume = {281}, number = {}, pages = {93-101}, doi = {10.1016/j.plantsci.2019.01.013}, pmid = {30824066}, issn = {1873-2259}, mesh = {Cedrus/*genetics ; Gene Transfer, Horizontal/*genetics ; Genome, Mitochondrial/*genetics ; Ribosomal Proteins/*genetics ; }, abstract = {The extraordinary incidence of Horizontal Gene Transfer (HGT) mostly in mitochondrial genomes of flowering plants is well known. Here, we report another episode of HGT affecting a large mitochondrial gene region in the evergreen conifer Atlas cedar (Cedrus atlantica). Mitochondria of this Pinaceae species possess an rps3 gene that harbours two introns and shares the same genomic context with a downstream overlapping rpl16 gene, like in the major groups of gymnosperms and angiosperms analyzed so far. Interestingly, C. atlantica contains additional copies of the rps3 and rpl16 sequences that are more closely related to angiosperm counterparts than to those from gymnosperms, as also confirmed by phylogenetic analyses. This suggests that a lateral transfer from a flowering plant donor is the most likely mechanism for the origin of the Atlas cedar extra sequences. Quantitative PCR and reverse-transcription (RT)-PCR analyses demonstrate, respectively, mitochondrial location and lack of expression for the rps3 and rpl16 additional sequences in C. atlantica. Furthermore, our study provides evidence that a similar HGT event takes place in two other Cedrus species, which occurr in Cyprus and North Africa. Only the West Himalayan C. deodara lacks the transferred genes. The potential donor and the molecular mechanism underlying this lateral DNA transfer remain still unclear.}, }
@article {pmid30823887, year = {2019}, author = {Stairs, CW and Kokla, A and Ástvaldsson, &#xc1; and Jerlström-Hultqvist, J and Svärd, S and Ettema, TJG}, title = {Oxygen induces the expression of invasion and stress response genes in the anaerobic salmon parasite Spironucleus salmonicida.}, journal = {BMC biology}, volume = {17}, number = {1}, pages = {19}, pmid = {30823887}, issn = {1741-7007}, support = {310039/ERC_/European Research Council/International ; }, mesh = {Anaerobiosis/*genetics ; Animals ; Diplomonadida/drug effects/*genetics ; Gene Expression Regulation/drug effects ; Oxygen/*administration &amp; dosage ; Salmon/parasitology ; Stress, Physiological/*genetics ; }, abstract = {BACKGROUND: Spironucleus salmonicida is an anaerobic parasite that can cause systemic infections in Atlantic salmon. Unlike other diplomonad parasites, such as the human pathogen Giardia intestinalis, Spironucleus species can infiltrate the blood stream of their hosts eventually colonizing organs, skin and gills. How this presumed anaerobe can persist and invade oxygenated tissues, despite having a strictly anaerobic metabolism, remains elusive.<br><br>RESULTS: To investigate how S. salmonicida response to oxygen stress, we performed RNAseq transcriptomic analyses of cells grown in the presence of oxygen or antioxidant-free medium. We found that over 20% of the transcriptome is differentially regulated in oxygen (1705 genes) and antioxidant-depleted (2280 genes) conditions. These differentially regulated transcripts encode proteins related to anaerobic metabolism, cysteine and Fe-S cluster biosynthesis, as well as a large number of proteins of unknown function. S. salmonicida does not encode genes involved in the classical elements of oxygen metabolism (e.g., catalases, superoxide dismutase, glutathione biosynthesis, oxidative phosphorylation). Instead, we found that genes encoding bacterial-like oxidoreductases were upregulated in response to oxygen stress. Phylogenetic analysis revealed some of these oxygen-responsive genes (e.g., nadh oxidase, rubrerythrin, superoxide reductase) are rare in eukaryotes and likely derived from lateral gene transfer (LGT) events into diplomonads from prokaryotes. Unexpectedly, we observed that many host evasion- and invasion-related genes were also upregulated under oxidative stress suggesting that oxygen might be an important signal for pathogenesis.<br><br>CONCLUSION: While oxygen is toxic for related organisms, such as G. intestinalis, we find that oxygen is likely a gene induction signal for host invasion- and evasion-related pathways in S. salmonicida. These data provide the first molecular evidence for how S. salmonicida could tolerate oxic host environments and demonstrate how LGT can have a profound impact on the biology of anaerobic parasites.}, }
@article {pmid30822726, year = {2019}, author = {Fang, H and Huang, K and Yu, J and Ding, C and Wang, Z and Zhao, C and Yuan, H and Wang, Z and Wang, S and Hu, J and Cui, Y}, title = {Metagenomic analysis of bacterial communities and antibiotic resistance genes in the Eriocheir sinensis freshwater aquaculture environment.}, journal = {Chemosphere}, volume = {224}, number = {}, pages = {202-211}, doi = {10.1016/j.chemosphere.2019.02.068}, pmid = {30822726}, issn = {1879-1298}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; *Aquaculture ; Brachyura/*growth &amp; development ; China ; Drug Resistance, Microbial/drug effects/*genetics ; Fresh Water/*microbiology ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Metagenomics/*methods ; }, abstract = {Aquaculture has attracted significant attention as an environmental gateway to the development of antibiotic resistance. The industry of Chinese mitten crab Eriocheir sinensis contributes significantly to the freshwater aquaculture industry in China. However, the situation of antibiotic resistance in the E. sinensis aquaculture environment is not known. In this study, high-throughput sequencing based metagenomic approaches were used to comprehensively investigate the structure of bacterial communities, the abundance and diversity of antibiotic resistance genes (ARGs), as well as mobile genetic elements (MGEs) in three E. sinensis aquaculture ponds in Jiangsu Province, China. The dominant phyla were Proteobacteria, Actinobacteria, and Bacteroidetes in water samples and Proteobacteria, Chloroflexi, Verrucomicrobia, and Bacteroidetes in sediment samples. Bacitracin and multidrug were predominant ARG types in water and sediment samples, respectively. There was a significant correlation between MGEs and ARGs. In particular, plasmids were the most abundant MGEs and strongly correlated with ARGs. This is the first study of antibiotic resistome that uses metagenomic approaches in the E. sinensis aquaculture environment. The results indicate that the opportunistic pathogens may acquire ARGs via horizontal gene transfer, intensifying the potential risk to human health.}, }
@article {pmid30822689, year = {2019}, author = {Trasviña-Arenas, CH and David, SS and Delaye, L and Azuara-Liceaga, E and Brieba, LG}, title = {Evolution of Base Excision Repair in Entamoeba histolytica is shaped by gene loss, gene duplication, and lateral gene transfer.}, journal = {DNA repair}, volume = {76}, number = {}, pages = {76-88}, doi = {10.1016/j.dnarep.2019.02.009}, pmid = {30822689}, issn = {1568-7856}, mesh = {Amino Acid Sequence ; DNA Glycosylases/chemistry/genetics/metabolism ; DNA Repair/*genetics ; Entamoeba histolytica/enzymology/*genetics ; *Evolution, Molecular ; *Gene Duplication ; *Gene Transfer, Horizontal ; Genes, Protozoan/*genetics ; Humans ; Models, Molecular ; Protein Conformation ; }, abstract = {During its life cycle, the protist parasite Entamoeba histolytica encounters reactive oxygen and nitrogen species that alter its genome. Base excision repair (BER) is one of the most important pathways for the repair of DNA base lesions. Analysis of the E. histolytica genome revealed the presence of most of the BER components. Surprisingly, this included a gene encoding an apurinic/apyrimidinic (AP) endonuclease that previous studies had assumed was absent. Indeed, our analysis showed that the genome of E. histolytica harbors the necessary genes needed for both short and long-patch BER sub-pathways. These genes include DNA polymerases with predicted 5'-dRP lyase and strand-displacement activities and a sole DNA ligase. A distinct feature of the E. histolytica genome is the lack of several key damage-specific BER glycosylases, such as OGG1/MutM, MDB4, Mag1, MPG, SMUG, and TDG. Our evolutionary analysis indicates that several E. histolytica DNA glycosylases were acquired by lateral gene transfer (LGT). The genes that encode for MutY, AlkD, and UDG (Family VI) are included among these cases. Endonuclease III and UNG (family I) are the only DNA glycosylases with a eukaryotic origin in E. histolytica. A gene encoding a MutT 8-oxodGTPase was also identified that was acquired by LGT. The mixed composition of BER genes as a DNA metabolic pathway shaped by LGT in E. histolytica indicates that LGT plays a major role in the evolution of this eukaryote. Sequence and structural prediction of E. histolytica DNA glycosylases, as well as MutT, suggest that the E. histolytica DNA repair proteins evolved to harbor structural modifications that may confer unique biochemical features needed for the biology of this parasite.}, }
@article {pmid30814990, year = {2019}, author = {Carrasco, B and Serrano, E and Martín-González, A and Moreno-Herrero, F and Alonso, JC}, title = {Bacillus subtilis MutS Modulates RecA-Mediated DNA Strand Exchange Between Divergent DNA Sequences.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {237}, pmid = {30814990}, issn = {1664-302X}, abstract = {The efficiency of horizontal gene transfer, which contributes to acquisition and spread of antibiotic resistance and pathogenicity traits, depends on nucleotide sequence and different mismatch-repair (MMR) proteins participate in this process. To study how MutL and MutS MMR proteins regulate recombination across species boundaries, we have studied natural chromosomal transformation with DNA up to ∼23% sequence divergence. We show that Bacillus subtilis natural chromosomal transformation decreased logarithmically with increased sequence divergence up to 15% in wild type (wt) cells or in cells lacking MutS2 or mismatch repair proteins (MutL, MutS or both). Beyond 15% sequence divergence, the chromosomal transformation efficiency is ∼100-fold higher in ΔmutS and ΔmutSL than in ΔmutS2 or wt cells. In the first phase of the biphasic curve (up to 15% sequence divergence), RecA-catalyzed DNA strand exchange contributes to the delineation of species, and in the second phase, homology-facilitated illegitimate recombination might aid in the restoration of inactivated genes. To understand how MutS modulates the integration process, we monitored DNA strand exchange reactions using a circular single-stranded DNA and a linear double-stranded DNA substrate with an internal 77-bp region with ∼16% or ∼54% sequence divergence in an otherwise homologous substrate. The former substrate delayed, whereas the latter halted RecA-mediated strand exchange. Interestingly, MutS addition overcame the heterologous barrier. We propose that MutS assists DNA strand exchange by facilitating RecA disassembly, and indirectly re-engagement with the homologous 5'-end of the linear duplex. Our data supports the idea that MutS modulates bidirectional RecA-mediated integration of divergent sequences and this is important for speciation.}, }
@article {pmid30809245, year = {2019}, author = {Ramisetty, BCM and Sudhakari, PA}, title = {Bacterial 'Grounded' Prophages: Hotspots for Genetic Renovation and Innovation.}, journal = {Frontiers in genetics}, volume = {10}, number = {}, pages = {65}, pmid = {30809245}, issn = {1664-8021}, abstract = {Bacterial genomes are highly plastic allowing the generation of variants through mutations and acquisition of genetic information. The fittest variants are then selected by the econiche thereby allowing the bacterial adaptation and colonization of the habitat. Larger genomes, however, may impose metabolic burden and hence bacterial genomes are optimized by the loss of frivolous genetic information. The activity of temperate bacteriophages has acute consequences on the bacterial population as well as the bacterial genome through lytic and lysogenic cycles. Lysogeny is a selective advantage as the prophage provides immunity to the lysogen against secondary phage attack. Since the non-lysogens are eliminated by the lytic phages, lysogens multiply and colonize the habitat. Nevertheless, all lysogens have an imminent risk of lytic cycle activation and cell lysis. However, a mutation in the attachment sites or in the genes that encode the specific recombinase responsible for prophage excision could result in 'grounding' of the prophage. Since the lysogens with grounded prophage are immune to respective phage infection as well as dodge the induction of lytic cycle, we hypothesize that the selection of these mutant lysogens is favored relative to their normal lysogenic counterparts. These grounded prophages offer several advantages to the bacterial genome evolution through propensity for genetic variations including inversions, deletions, and insertions via horizontal gene transfer. We propose that the grounded prophages expedite bacterial genome evolution by acting as 'genetic buffer zones' thereby increasing the frequency as well as the diversity of variations on which natural selection favors the beneficial variants. The grounded prophages are also hotspots for horizontal gene transfer wherein several ecologically significant genes such as those involved in stress tolerance, antimicrobial resistance, and novel metabolic pathways, are integrated. Moreover, the high frequency of genetic changes within prophages also allows proportionate probability for the de novo genesis of genetic information. Through sequence analyses of well-characterized E. coli prophages we exemplify various roles of grounded prophages in E. coli ecology and evolution. Therefore, the temperate prophages are one of the most significant drivers of bacterial genome evolution and sites of biogenesis of genetic information.}, }
@article {pmid30805346, year = {2019}, author = {Piepenbrink, KH}, title = {DNA Uptake by Type IV Filaments.}, journal = {Frontiers in molecular biosciences}, volume = {6}, number = {}, pages = {1}, pmid = {30805346}, issn = {2296-889X}, support = {K22 AI123467/AI/NIAID NIH HHS/United States ; P20 GM113126/GM/NIGMS NIH HHS/United States ; }, abstract = {Bacterial uptake of DNA through type IV filaments is an essential component of natural competence in numerous gram-positive and gram-negative species. Recent advances in the field have broadened our understanding of the structures used to take up extracellular DNA. Here, we review seminal experiments in the literature describing DNA binding by type IV pili, competence pili and the flp pili of Micrococcus luteus; collectively referred to here as type IV filaments. We compare the current state of the field on mechanisms of DNA uptake for these three appendage systems and describe the current mechanistic understanding of both DNA-binding and DNA-uptake by these versatile molecular machines.}, }
@article {pmid30804909, year = {2019}, author = {Dick, JM and Yu, M and Tan, J and Lu, A}, title = {Changes in Carbon Oxidation State of Metagenomes Along Geochemical Redox Gradients.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {120}, pmid = {30804909}, issn = {1664-302X}, abstract = {There is widespread interest in how geochemistry affects the genomic makeup of microbial communities, but the possible impacts of oxidation-reduction (redox) conditions on the chemical composition of biomacromolecules remain largely unexplored. Here we document systematic changes in the carbon oxidation state, a metric derived from the chemical formulas of biomacromolecular sequences, using published metagenomic and metatranscriptomic datasets from 18 studies representing different marine and terrestrial environments. We find that the carbon oxidation states of DNA, as well as proteins inferred from coding sequences, follow geochemical redox gradients associated with mixing and cooling of hot spring fluids in Yellowstone National Park (USA) and submarine hydrothermal fluids. Thermodynamic calculations provide independent predictions for the environmental shaping of the gene and protein composition of microbial communities in these systems. On the other hand, the carbon oxidation state of DNA is negatively correlated with oxygen concentration in marine oxygen minimum zones. In this case, a thermodynamic model is not viable, but the low carbon oxidation state of DNA near the ocean surface reflects a low GC content, which can be attributed to genome reduction in organisms adapted to low-nutrient conditions. We also present evidence for a depth-dependent increase of oxidation state at the species level, which might be associated with alteration of DNA through horizontal gene transfer and/or selective degradation of relatively reduced (AT-rich) extracellular DNA by heterotrophic bacteria. Sediments exhibit even more complex behavior, where carbon oxidation state minimizes near the sulfate-methane transition zone and rises again at depth; markedly higher oxidation states are also associated with older freshwater-dominated sediments in the Baltic Sea that are enriched in iron oxides and have low organic carbon. This geobiochemical study of carbon oxidation state reveals a new aspect of environmental information in metagenomic sequences, and provides a reference frame for future studies that may use ancient DNA sequences as a paleoredox indicator.}, }
@article {pmid30804894, year = {2019}, author = {Flores-Ríos, R and Moya-Beltrán, A and Pareja-Barrueto, C and Arenas-Salinas, M and Valenzuela, S and Orellana, O and Quatrini, R}, title = {The Type IV Secretion System of ICEAfe1: Formation of a Conjugative Pilus in Acidithiobacillus ferrooxidans.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {30}, pmid = {30804894}, issn = {1664-302X}, abstract = {The dispersal of mobile genetic elements and their gene cargo relies on type IV secretion systems (T4SS). In this work the ICEAfe1 Tra-type T4SS nanomachine, encoded in the publicly available genome of Acidithiobacillus ferrooxidans ATCC 23270[TY], was characterized in terms of its organization, conservation, expression and mating bridge formation. Twenty-one conjugative genes grouped in four genetic clusters encode the ICEAfe1 T4SS, containing all the indispensable functions for the formation and stabilization of the pili and for DNA processing. The clusters' organization resembles that of other mobile genetic elements (such as plasmids and integrative and conjugative elements-ICEs). Sequence conservation, genetic organization and distribution of the tra system in the genomes of other sequenced Acidithiobacillus spp. suggests that the ICEAfe1 T4SS could mediate the lateral gene transfer between related bacteria. All ICEAfe1 T4SS genes are transcriptionally active and expressed from four independent operons. The transcriptional levels of selected marker genes increase in response to Mitomycin C treatment, a DNA damage elicitor that has acknowledged stimulatory effects on excision rates and gene expression of other ICEs, including ICEAfe1. Using a tailor-made pilin-antiserum against ICEAfe1 T4SS TraA pilin and epifluorescence microscopy, the presence of the conjugative pili on the cell surface of A. ferrooxidans could be demonstrated. Additionally, immunodetection assays, by immunogold, allowed the identification of pili-like extracellular structures. Together, the results obtained in this work demonstrate that the ICEAfe1 T4SS is phylogenetically conserved within the taxon, is expressed at mRNA and protein levels in vivo in the A. ferrooxidans type strain, and produces a pili-like structure of extracellular and intercellular localization in this model acidophile, supporting its functionality. Additional efforts will be required to prove conjugation of the ICEAfe1 or parts of this element through the cognate T4SS.}, }
@article {pmid30803810, year = {2019}, author = {Puozaa, DK and Jaiswal, SK and Dakora, FD}, title = {Phylogeny and distribution of Bradyrhizobium symbionts nodulating cowpea (Vigna unguiculata L. Walp) and their association with the physicochemical properties of acidic African soils.}, journal = {Systematic and applied microbiology}, volume = {42}, number = {3}, pages = {403-414}, pmid = {30803810}, issn = {1618-0984}, mesh = {Bradyrhizobium/*classification/genetics/*growth &amp; development/physiology ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Genes, Essential/genetics ; Genetic Variation ; Ghana ; Hydrogen-Ion Concentration ; *Phylogeny ; Polymorphism, Restriction Fragment Length ; Root Nodules, Plant/*microbiology ; Sequence Analysis, DNA ; Soil/*chemistry ; *Soil Microbiology ; South Africa ; *Symbiosis/genetics ; Vigna/*microbiology ; }, abstract = {In the N2-fixing symbiosis, the choice of a symbiotic partner is largely influenced by the host plant, the rhizobial symbiont, as well as soil factors. Understanding the soil environment conducive for the survival and multiplication of root-nodule bacteria is critical for microbial ecology. In this study, we collected cowpea-nodules from acidic soils in Ghana and South Africa, and nodule DNA isolates were characterized using 16S-23S rRNA-RFLP, phylogenetic analysis of housekeeping and symbiotic genes, and bradyrhizobial community structure through canonical correspondence analysis (CCA). The CCA ordination plot results showed that arrow of soil pH was overlapping on CCA2 axis and was the most important to the ordination. The test nodule DNA isolates from Ghana were positively influenced by soil Zn, Na and K while nodule DNA isolates from South Africa were influenced by P. The amplified 16S-23S rRNA region yielded single polymorphic bands of varying lengths (573-1298bp) that were grouped into 28 ITS types. The constructed ITS-dendrogram placed all the nodule DNA isolates in five major clusters at low cut-off of approx. 0.1 Jaccard's similarity coefficient. The phylogenetic analysis of 16S rRNA and housekeeping genes (glnII, gyrB, and atpD) formed distinct Bradyrhizobium groups in the phylogenetic trees. It revealed the presence of highly diverse bradyrhizobia (i.e. Bradyrhizobium vignae, Bradyrhizobium elkanii, Bradyrhizobium iriomotense, Bradyrhizobium pachyrhizi, and Bradyrhizobium yuanmingense) together with novel/unidentified bradyrhizobia in the acidic soils from Ghana and South Africa. Discrepancies noted in the phylogenies of some nodule DNA isolates could be attributed to horizontal gene transfer or recombination.}, }
@article {pmid30802650, year = {2019}, author = {Veloo, ACM and Baas, WH and Haan, FJ and Coco, J and Rossen, JW}, title = {Prevalence of antimicrobial resistance genes in Bacteroides spp. and Prevotella spp. Dutch clinical isolates.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {25}, number = {9}, pages = {1156.e9-1156.e13}, doi = {10.1016/j.cmi.2019.02.017}, pmid = {30802650}, issn = {1469-0691}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteroidaceae Infections/epidemiology/microbiology ; Bacteroides/drug effects/*genetics/isolation &amp; purification ; Drug Resistance, Bacterial/*genetics ; Genes, Bacterial/genetics ; Humans ; Microbial Sensitivity Tests ; Netherlands/epidemiology ; Prevalence ; Prevotella/drug effects/*genetics/isolation &amp; purification ; }, abstract = {OBJECTIVES: The prevalence of resistance genes in two important anaerobic genera, Bacteroides and Prevotella, was assessed by applying PCR specifically directed to genes of interest.<br><br>METHODS: A total of 101 Bacteroides spp. and 99 Prevotella spp. human clinical isolates were identified using MALDI-TOF MS. The presence of the resistance genes cfxA, cepA, cfiA, tetQ, ermF and nim, was assessed. Prevalence of resistance genes was compared with the phenotypic resistance against amoxicillin, clindamycin, meropenem and metronidazole.<br><br>RESULTS: Even though the majority of the Bacteroides isolates (95.0%) showed resistance towards amoxicillin, only 52/101 of the isolates harboured one of the resistance genes, accounting for this resistance. Within the genus Prevotella the presence of cfxA (50/99) almost perfectly matched the amoxicillin resistance (48/99). No difference in prevalence of the ermF gene (16/101 and 9/99) and clindamycin resistance (16/101 and 10/99) was observed within Bacteroides and Prevotella, respectively. Two isolates of Prevotella were resistant to metronidazole. One harboured the nim gene. One metronidazole-susceptible isolate of Bacteroides harboured a nim gene. Within the Bacteroides and Prevotella genera, 6/101 strains and 5/99 isolates harboured three different resistance genes, respectively, among them tetQ. TetQ is often located on a conjugative transposon, increasing the chance of horizontal gene transfer between isolates.<br><br>CONCLUSIONS: An unknown mechanism in Bacteroides non-fragilis isolates causes resistance to &#x3b2;-lactam antibiotics. The fact that the prevalence of the tetQ gene among Prevotella is increasing and the existence of isolates harbouring three resistance genes are worrisome developments.}, }
@article {pmid30801025, year = {2019}, author = {Entwistle, S and Li, X and Yin, Y}, title = {Orphan Genes Shared by Pathogenic Genomes Are More Associated with Bacterial Pathogenicity.}, journal = {mSystems}, volume = {4}, number = {1}, pages = {}, pmid = {30801025}, issn = {2379-5077}, support = {R15 GM114706/GM/NIGMS NIH HHS/United States ; }, abstract = {Orphan genes (also known as ORFans [i.e., orphan open reading frames]) are new genes that enable an organism to adapt to its specific living environment. Our focus in this study is to compare ORFans between pathogens (P) and nonpathogens (NP) of the same genus. Using the pangenome idea, we have identified 130,169 ORFans in nine bacterial genera (505 genomes) and classified these ORFans into four groups: (i) SS-ORFans (P), which are only found in a single pathogenic genome; (ii) SS-ORFans (NP), which are only found in a single nonpathogenic genome; (iii) PS-ORFans (P), which are found in multiple pathogenic genomes; and (iv) NS-ORFans (NP), which are found in multiple nonpathogenic genomes. Within the same genus, pathogens do not always have more genes, more ORFans, or more pathogenicity-related genes (PRGs)-including prophages, pathogenicity islands (PAIs), virulence factors (VFs), and horizontal gene transfers (HGTs)-than nonpathogens. Interestingly, in pathogens of the nine genera, the percentages of PS-ORFans are consistently higher than those of SS-ORFans, which is not true in nonpathogens. Similarly, in pathogens of the nine genera, the percentages of PS-ORFans matching the four types of PRGs are also always higher than those of SS-ORFans, but this is not true in nonpathogens. All of these findings suggest the greater importance of PS-ORFans for bacterial pathogenicity. IMPORTANCE Recent pangenome analyses of numerous bacterial species have suggested that each genome of a single species may have a significant fraction of its gene content unique or shared by a very few genomes (i.e., ORFans). We selected nine bacterial genera, each containing at least five pathogenic and five nonpathogenic genomes, to compare their ORFans in relation to pathogenicity-related genes. Pathogens in these genera are known to cause a number of common and devastating human diseases such as pneumonia, diphtheria, melioidosis, and tuberculosis. Thus, they are worthy of in-depth systems microbiology investigations, including the comparative study of ORFans between pathogens and nonpathogens. We provide direct evidence to suggest that ORFans shared by more pathogens are more associated with pathogenicity-related genes and thus are more important targets for development of new diagnostic markers or therapeutic drugs for bacterial infectious diseases.}, }
@article {pmid30799497, year = {2019}, author = {Shi-Kunne, X and van Kooten, M and Depotter, JRL and Thomma, BPHJ and Seidl, MF}, title = {The Genome of the Fungal Pathogen Verticillium dahliae Reveals Extensive Bacterial to Fungal Gene Transfer.}, journal = {Genome biology and evolution}, volume = {11}, number = {3}, pages = {855-868}, pmid = {30799497}, issn = {1759-6653}, mesh = {*Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genome, Fungal ; Verticillium/*genetics ; }, abstract = {Horizontal gene transfer (HGT) involves the transmission of genetic material between distinct evolutionary lineages and can be an important source of biological innovation. Reports of interkingdom HGT to eukaryotic microbial pathogens have accumulated over recent years. Verticillium dahliae is a notorious plant pathogen that causes vascular wilt disease on hundreds of plant species, resulting in high economic losses every year. Previously, the effector gene Ave1 and a glucosyltransferase-encoding gene were identified as virulence factor-encoding genes that were proposed to be horizontally acquired from a plant and a bacterial donor, respectively. However, to what extent HGT contributed to the overall genome composition of V. dahliae remained elusive. Here, we systematically searched for evidence of interkingdom HGT events in the genome of V. dahliae and provide evidence for extensive horizontal gene acquisition from bacterial origin.}, }
@article {pmid30799038, year = {2019}, author = {Kominek, J and Doering, DT and Opulente, DA and Shen, XX and Zhou, X and DeVirgilio, J and Hulfachor, AB and Groenewald, M and Mcgee, MA and Karlen, SD and Kurtzman, CP and Rokas, A and Hittinger, CT}, title = {Eukaryotic Acquisition of a Bacterial Operon.}, journal = {Cell}, volume = {176}, number = {6}, pages = {1356-1366.e10}, pmid = {30799038}, issn = {1097-4172}, support = {R21 AI105619/AI/NIAID NIH HHS/United States ; T32 HG002760/HG/NHGRI NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Escherichia coli/genetics ; Eukaryota/*genetics ; Eukaryotic Cells ; Evolution, Molecular ; Gene Expression Regulation, Bacterial/genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/genetics ; Genome, Bacterial/genetics ; Genome, Fungal/genetics ; Operon/*genetics ; Saccharomycetales/genetics ; Siderophores/genetics ; }, abstract = {Operons are a hallmark of bacterial genomes, where they allow concerted expression of functionally related genes as single polycistronic transcripts. They are rare in eukaryotes, where each gene usually drives expression of its own independent messenger RNAs. Here, we report the horizontal operon transfer of a siderophore biosynthesis pathway from relatives of Escherichia coli into a group of budding yeast taxa. We further show that the co-linearly arranged secondary metabolism genes are expressed, exhibit eukaryotic transcriptional features, and enable the sequestration and uptake of iron. After transfer, several genetic changes occurred during subsequent evolution, including the gain of new transcription start sites that were sometimes within protein-coding sequences, acquisition of polyadenylation sites, structural rearrangements, and integration of eukaryotic genes into the cluster. We conclude that the genes were likely acquired as a unit, modified for eukaryotic gene expression, and maintained by selection to adapt to the highly competitive, iron-limited environment.}, }
@article {pmid30798547, year = {2019}, author = {Fulsundar, S and Domingues, S and Nielsen, KM}, title = {Vesicle-Mediated Gene Transfer in Acinetobacter baumannii.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1946}, number = {}, pages = {87-94}, doi = {10.1007/978-1-4939-9118-1_9}, pmid = {30798547}, issn = {1940-6029}, mesh = {Acinetobacter Infections/*microbiology ; Acinetobacter baumannii/*genetics ; Biological Transport ; *Gene Transfer, Horizontal ; Humans ; Polymerase Chain Reaction ; *Transport Vesicles/genetics ; }, abstract = {The role of vesicle-mediated gene transfer in Acinetobacter baumannii populations has been investigated in the last decade. Importantly, outer membrane vesicles (OMVs) secreted from A. baumannii cells have proven to be efficient agents of transfer of antimicrobial resistance genes to other bacterial species. However, the measurement of vesicle-mediated transfer depends on many experimental parameters. Here, we describe an experimental method useful to study transfer of DNA via membrane vesicles of A. baumannii in various bacterial populations.}, }
@article {pmid30798546, year = {2019}, author = {Wilharm, G and Skiebe, E}, title = {Methods for Natural Transformation in Acinetobacter baumannii.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1946}, number = {}, pages = {75-85}, doi = {10.1007/978-1-4939-9118-1_8}, pmid = {30798546}, issn = {1940-6029}, mesh = {Acinetobacter Infections/microbiology ; Acinetobacter baumannii/drug effects/*physiology ; Anti-Bacterial Agents/pharmacology ; Cross Infection/microbiology ; Drug Resistance, Multiple, Bacterial ; Humans ; *Transformation, Bacterial ; }, abstract = {The genomes of Acinetobacter baumannii tell us stories about horizontal gene transfer (HGT) events that steadily drive the evolution of this nosocomial pathogen toward multidrug resistance. Natural transformation competence constitutes one of the several possible pathways that mediate HGT in A. baumannii. Here, we describe and discuss the methods for studying DNA uptake in A. baumannii via natural transformation.}, }
@article {pmid30798493, year = {2019}, author = {Brosius, J}, title = {Exaptation at the molecular genetic level.}, journal = {Science China. Life sciences}, volume = {62}, number = {4}, pages = {437-452}, doi = {10.1007/s11427-018-9447-8}, pmid = {30798493}, issn = {1869-1889}, mesh = {Adaptation, Biological/*genetics ; *Evolution, Molecular ; Exons ; Gene Duplication ; Gene Transfer, Horizontal ; Mutant Chimeric Proteins ; RNA, Untranslated ; Regulatory Elements, Transcriptional ; Retroelements ; Selection, Genetic ; }, abstract = {The realization that body parts of animals and plants can be recruited or coopted for novel functions dates back to, or even predates the observations of Darwin. S.J. Gould and E.S. Vrba recognized a mode of evolution of characters that differs from adaptation. The umbrella term aptation was supplemented with the concept of exaptation. Unlike adaptations, which are restricted to features built by selection for their current role, exaptations are features that currently enhance fitness, even though their present role was not a result of natural selection. Exaptations can also arise from nonaptations; these are characters which had previously been evolving neutrally. All nonaptations are potential exaptations. The concept of exaptation was expanded to the molecular genetic level which aided greatly in understanding the enormous potential of neutrally evolving repetitive DNA-including transposed elements, formerly considered junk DNA-for the evolution of genes and genomes. The distinction between adaptations and exaptations is outlined in this review and examples are given. Also elaborated on is the fact that such distinctions are sometimes more difficult to determine; this is a widespread phenomenon in biology, where continua abound and clear borders between states and definitions are rare.}, }
@article {pmid30797860, year = {2019}, author = {Vilchèze, C and Jacobs, WR}, title = {The Isoniazid Paradigm of Killing, Resistance, and Persistence in Mycobacterium tuberculosis.}, journal = {Journal of molecular biology}, volume = {431}, number = {18}, pages = {3450-3461}, pmid = {30797860}, issn = {1089-8638}, support = {U19 AI162598/AI/NIAID NIH HHS/United States ; R37 AI026170/AI/NIAID NIH HHS/United States ; R01 AI026170/AI/NIAID NIH HHS/United States ; U19 AI111276/AI/NIAID NIH HHS/United States ; R21 AI132940/AI/NIAID NIH HHS/United States ; }, mesh = {Acetylcysteine/metabolism ; Animals ; Ascorbic Acid/metabolism ; Bacterial Proteins/chemistry/drug effects/genetics ; Catalase/chemistry/genetics ; Drug Discovery ; Drug Resistance, Multiple, Bacterial/*drug effects/genetics/physiology ; Drug Therapy ; Gene Transfer, Horizontal/drug effects/genetics ; Humans ; Isoniazid/chemistry/*pharmacology ; Mycobacteriophages/genetics ; Mycobacterium tuberculosis/*drug effects/genetics/metabolism ; Oxidoreductases/chemistry/genetics ; Tuberculosis/microbiology ; }, abstract = {Isoniazid (INH) was the first synthesized drug that mediated bactericidal killing of the bacterium Mycobacterium tuberculosis, a major clinical breakthrough. To this day, INH remains a cornerstone of modern tuberculosis (TB) chemotherapy. This review describes the serendipitous discovery of INH, its effectiveness on TB patients, and early studies to discover its mechanisms of bacteriocidal activity. Forty years after its introduction as a TB drug, the development of gene transfer in mycobacteria enabled the discovery of the genes encoding INH resistance, namely, the activator (katG) and the target (inhA) of INH. Further biochemical and x-ray crystallography studies on KatG and InhA proteins and mutants provided comprehensive understanding of INH mode of action and resistance mechanisms. Bacterial cultures can harbor subpopulations that are genetically or phenotypically resistant cells, the latter known as persisters. Treatment of exponentially growing cultures of M. tuberculosis with INH reproducibly kills 99% to 99.9% of cells in 3 days. Importantly, the surviving cells are slowly replicating or non-replicating cells expressing a unique stress response signature: these are the persisters. These persisters can be visualized using dual-reporter mycobacteriophages and their formation prevented using reducing compounds, such as N-acetylcysteine or vitamin C, that enhance M. tuberculosis' respiration. Altogether, this review portrays a detailed molecular analysis of INH killing and resistance mechanisms including persistence. The phenomenon of persistence is clearly the single greatest impediment to TB control, and research aimed at understanding persistence will provide new strategies to improve TB chemotherapy.}, }
@article {pmid30796986, year = {2019}, author = {Pfeifer, E and Hünnefeld, M and Popa, O and Frunzke, J}, title = {Impact of Xenogeneic Silencing on Phage-Host Interactions.}, journal = {Journal of molecular biology}, volume = {431}, number = {23}, pages = {4670-4683}, pmid = {30796986}, issn = {1089-8638}, support = {757563/ERC_/European Research Council/International ; }, mesh = {Bacteria/*genetics/metabolism/*virology ; Bacteriophages/*physiology ; Binding Sites ; DNA-Binding Proteins/metabolism ; Gene Expression Regulation, Viral ; *Gene Silencing ; Gene Transfer, Horizontal ; Host-Pathogen Interactions/*genetics ; Plasmids/genetics ; }, abstract = {Phages, viruses that prey on bacteria, are the most abundant and diverse inhabitants of the Earth. Temperate bacteriophages can integrate into the host genome and, as so-called prophages, maintain a long-term association with their host. The close relationship between host and virus has significantly shaped microbial evolution and phage elements may benefit their host by providing new functions. Nevertheless, the strong activity of phage promoters and potentially toxic gene products may impose a severe fitness burden and must be tightly controlled. In this context, xenogeneic silencing (XS) proteins, which can recognize foreign DNA elements, play an important role in the acquisition of novel genetic information and facilitate the evolution of regulatory networks. Currently known XS proteins fall into four classes (H-NS, MvaT, Rok and Lsr2) and have been shown to follow a similar mode of action by binding to AT-rich DNA and forming an oligomeric nucleoprotein complex that silences gene expression. In this review, we focus on the role of XS proteins in phage-host interactions by highlighting the important function of XS proteins in maintaining the lysogenic state and by providing examples of how phages fight back by encoding inhibitory proteins that disrupt XS functions in the host. Sequence analysis of available phage genomes revealed the presence of genes encoding Lsr2-type proteins in the genomes of phages infecting Actinobacteria. These data provide an interesting perspective for future studies to elucidate the impact of phage-encoded XS homologs on the phage life cycle and phage-host interactions.}, }
@article {pmid30793504, year = {2019}, author = {Kwon, YM and Patra, AK and Chiura, HX and Kim, SJ}, title = {Production of extracellular vesicles with light-induced proton pump activity by proteorhodopsin-containing marine bacteria.}, journal = {MicrobiologyOpen}, volume = {8}, number = {8}, pages = {e00808}, pmid = {30793504}, issn = {2045-8827}, mesh = {Aquatic Organisms/*metabolism/radiation effects ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Extracellular Vesicles/*metabolism/ultrastructure ; Flavobacteriaceae/*metabolism/radiation effects ; Gene Expression Regulation, Bacterial/*radiation effects ; *Light ; Metabolic Networks and Pathways/genetics ; Microscopy, Electron, Transmission ; Phylogeny ; Proton Pumps/*metabolism ; RNA, Ribosomal, 16S/genetics ; Rhodopsins, Microbial/*metabolism ; Sequence Analysis, DNA ; }, abstract = {The production and release of extracellular vesicles (EVs) is a common process occurring in various types of bacteria. However, little is known regarding the functions of EVs derived from marine bacteria. We observed that during cell growth, Sediminicola sp. YIK13, a proteorhodopsin (PR)-containing marine flavobacterium, produces EVs (S13EVs). Transmission electron microscopy showed that Sediminicola sp. YIK13 released two spherical vesicle types, with mono- and/or bi-layered membranes, in the culture. Interestingly, the S13EVs have an orange pigment, indicating the presence of putative carotenoid and PR pigments ascribed to the parental cells. The S13EVs demonstrated the same PR-derived absorption peak spectrum and light-induced proton pump activity as the parental cells. Western blot (immunoblot) analysis of the S13EVs revealed the presence of PR. We confirmed the 16S rRNA gene, pro gene, and genes required for chromophore retinal synthesis, namely blh and crtI, in the DNA packaged into these vesicles. In addition, by metagenomic sequencing, we found microbial rhodopsin-related genes in vesicles derived from natural aquatic environments. Our results suggest that EVs as well potentially pursue horizontal gene transfer of diverse microbial rhodopsin genes in marine ecosystems.}, }
@article {pmid30793407, year = {2019}, author = {Bernardo, LP and Mombach, DM and Loreto, ELS}, title = {Characterization of Herves-like transposable elements (hATs) in Drosophila species and their evolutionary scenario.}, journal = {Insect molecular biology}, volume = {28}, number = {5}, pages = {616-627}, doi = {10.1111/imb.12577}, pmid = {30793407}, issn = {1365-2583}, mesh = {Animals ; DNA Copy Number Variations ; DNA Transposable Elements/*genetics ; Drosophila/classification/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Minisatellite Repeats/genetics ; Phylogeny ; }, abstract = {A monophyletic group of Drosophila hAT transposable elements, referred to as Herves-like, was characterized and found to be present in 46% of 57 screened Drosophila species. A remarkable characteristic of these elements is the presence of a long array of minisatellite repeats (MnRs) in both subterminal extremities of the elements. The copy number of these minisatellites was highly variable between and within populations. Twenty-three strains of Drosophila willistoni, covering its geographic distribution, were screened for polymorphism in the copy number of 5' MnRs, showing a variation from 7 to 20 repeat copies. These MnRs are well conserved among Drosophila species and probably function as transposase binding sequences, as provided by short subterminal repeats in other hAT elements. Miniature inverted repeat transposable elements were found in 27% of species carrying Herves-like elements. Phylogenetic analysis showed incongruences between transposable elements and species phylogenies, suggesting that at least four horizontal transfer events have occurred.}, }
@article {pmid30793159, year = {2019}, author = {Thynne, E and Mead, OL and Chooi, YH and McDonald, MC and Solomon, PS}, title = {Acquisition and Loss of Secondary Metabolites Shaped the Evolutionary Path of Three Emerging Phytopathogens of Wheat.}, journal = {Genome biology and evolution}, volume = {11}, number = {3}, pages = {890-905}, pmid = {30793159}, issn = {1759-6653}, mesh = {Ascomycota/*genetics/metabolism/pathogenicity ; *Biological Evolution ; Gene Duplication ; Gene Transfer, Horizontal ; Genome, Fungal ; Plant Diseases ; Polyketide Synthases/*genetics ; Secondary Metabolism ; Triticum/*microbiology ; }, abstract = {White grain disorder is a recently emerged wheat disease in Australia, caused by Eutiarosporella darliae, E. pseudodarliae, and E. tritici-australis. The disease cycle of these pathogens and the molecular basis of their interaction with wheat are poorly understood. To address this knowledge gap, we undertook a comparative genomics analysis focused on the secondary metabolite gene repertoire among these three species. This analysis revealed a diverse array of secondary metabolite gene clusters in these pathogens, including modular polyketide synthase genes. These genes have only been previously associated with bacteria and this is the first report of such genes in fungi. Subsequent phylogenetic analyses provided strong evidence that the modular PKS genes were horizontally acquired from a bacterial or a protist species. We also uncovered a secondary metabolite gene cluster with three polyketide/nonribosomal peptide synthase genes (Hybrid-1, -2, and -3) in E. darliae and E. pseudodarliae. In contrast, only remnant and partial genes homologous to this cluster were identified in E. tritici-australis, suggesting loss of this cluster. Homologues of Hybrid-2 in other fungi have been proposed to facilitate disease in woody plants, suggesting a possible alternative host range for E. darliae and E. pseudodarliae. Subsequent assays confirmed that E. darliae and E. pseudodarliae were both pathogenic on woody plants, but E. tritici-australis was not, implicating woody plants as potential host reservoirs for the fungi. Combined, these data have advanced our understanding of the lifestyle and potential host-range of these recently emerged wheat pathogens and shed new light on fungal secondary metabolism.}, }
@article {pmid30792518, year = {2019}, author = {Maeda, T and Horinouchi, T and Sakata, N and Sakai, A and Furusawa, C}, title = {High-throughput identification of the sensitivities of an Escherichia coli ΔrecA mutant strain to various chemical compounds.}, journal = {The Journal of antibiotics}, volume = {72}, number = {7}, pages = {566-573}, doi = {10.1038/s41429-019-0160-5}, pmid = {30792518}, issn = {1881-1469}, mesh = {Anti-Bacterial Agents/*pharmacology ; Chromates/toxicity ; DNA Damage ; DNA Replication/drug effects ; DNA-Binding Proteins/*drug effects/*genetics ; Escherichia coli/*drug effects/*genetics ; Escherichia coli Proteins/*drug effects/*genetics ; Gene Expression Regulation, Bacterial/drug effects ; Microarray Analysis ; Microbial Sensitivity Tests/*methods ; Mutation ; RNA, Bacterial/genetics ; Rec A Recombinases/*drug effects/*genetics ; SOS Response, Genetics/*drug effects ; }, abstract = {Antibiotic resistance is considered a global threat to public health. Adaptive resistance mutations and the acquisition of resistance genes by horizontal gene transfer are known to be facilitated by the RecA-dependent SOS response during antibiotic treatment, making RecA inhibitors promising agents for the prevention of antibiotic resistance. However, the impact of RecA inactivation on antibiotic sensitivities remains unclear. Therefore, in this study, we performed high-throughput screening to determine the minimum inhibitory concentrations (MICs) of 217 chemicals, including both antibiotics and toxic chemicals of unknown drug action, in the wild-type MDS42 and the ΔrecA mutant strains of Escherichia coli. The ΔrecA mutant showed increased sensitivity to DNA-damaging agents, DNA replication inhibitors, and chromate stress, as well as to other chemicals, such as S-(2-aminoethyl)-L-cysteine, L-histidine, ruthenium red, D-penicillamine, carbonyl cyanide 3-chlorophenylhydrazone (CCCP), cerulenin, and L-cysteine. Microarray analysis showed further that the ΔrecA mutant had lower expressions of glnK, nac, and glnLG, which encode nitrogen assimilation regulators, as well as amtB, which encodes an ammonium transporter, compared with the wild type. These findings suggest that the ΔrecA mutation affects not only the SOS response but also amino acid metabolism.}, }
@article {pmid30792076, year = {2019}, author = {Álvarez-Pérez, S and Lievens, B and Fukami, T}, title = {Yeast-Bacterium Interactions: The Next Frontier in Nectar Research.}, journal = {Trends in plant science}, volume = {24}, number = {5}, pages = {393-401}, doi = {10.1016/j.tplants.2019.01.012}, pmid = {30792076}, issn = {1878-4372}, mesh = {Bacteria ; *Flowers ; *Plant Nectar ; Pollination ; Yeasts ; }, abstract = {Beyond its role as a reward for pollinators, floral nectar also provides a habitat for specialized and opportunistic yeasts and bacteria. These microbes modify nectar chemistry, often altering mutualistic relationships between plants and pollinators in ways that we are only beginning to understand. Many studies on this multi-partite system have focused on either yeasts or bacteria without consideration of yeast-bacterium interactions, but recent evidence suggests that such interactions drive the assembly of nectar microbial communities and its consequences for pollination. Unexplored potential mechanisms of yeast-bacterium interactions include the formation of physical complexes, nutritional interactions, antibiosis, signaling-based interactions, and horizontal gene transfer. We argue that studying these mechanisms can elucidate how nectar microbial communities are established and affect plant fitness via pollinators.}, }
@article {pmid30791454, year = {2019}, author = {Lima, T and Domingues, S and Da Silva, GJ}, title = {Plasmid-Mediated Colistin Resistance in Salmonella enterica: A Review.}, journal = {Microorganisms}, volume = {7}, number = {2}, pages = {}, pmid = {30791454}, issn = {2076-2607}, abstract = {Colistin is widely used in food-animal production. Salmonella enterica is a zoonotic pathogen, which can pass from animal to human microbiota through the consumption of contaminated food, and cause disease, often severe, especially in young children, elderly and immunocompromised individuals. Recently, plasmid-mediated colistin resistance was recognised; mcr-like genes are being identified worldwide. Colistin is not an antibiotic used to treat Salmonella infections, but has been increasingly used as one of the last treatment options for carbapenem resistant Enterobacteria in human infections. The finding of mobilizable mcr-like genes became a global concern due to the possibility of horizontal transfer of the plasmid that often carry resistance determinants to beta-lactams and/or quinolones. An understanding of the origin and dissemination of mcr-like genes in zoonotic pathogens such as S. enterica will facilitate the management of colistin use and target interventions to prevent further spread. The main objective of this review was to collect epidemiological data about mobilized colistin resistance in S. enterica, describing the mcr variants, identified serovars, origin of the isolate, country and other resistance genes located in the same genetic platform.}, }
@article {pmid30789903, year = {2019}, author = {Ocaña-Pallarès, E and Najle, SR and Scazzocchio, C and Ruiz-Trillo, I}, title = {Reticulate evolution in eukaryotes: Origin and evolution of the nitrate assimilation pathway.}, journal = {PLoS genetics}, volume = {15}, number = {2}, pages = {e1007986}, pmid = {30789903}, issn = {1553-7404}, mesh = {Bacteria/genetics ; Computational Biology/methods ; Evolution, Molecular ; Fungi/*genetics/metabolism ; *Gene Transfer, Horizontal ; Metabolic Networks and Pathways ; Nitrates/*metabolism ; Oomycetes/*genetics/metabolism ; Phylogeny ; }, abstract = {Genes and genomes can evolve through interchanging genetic material, this leading to reticular evolutionary patterns. However, the importance of reticulate evolution in eukaryotes, and in particular of horizontal gene transfer (HGT), remains controversial. Given that metabolic pathways with taxonomically-patchy distributions can be indicative of HGT events, the eukaryotic nitrate assimilation pathway is an ideal object of investigation, as previous results revealed a patchy distribution and suggested that the nitrate assimilation cluster of dikaryotic fungi (Opisthokonta) could have been originated and transferred from a lineage leading to Oomycota (Stramenopiles). We studied the origin and evolution of this pathway through both multi-scale bioinformatic and experimental approaches. Our taxon-rich genomic screening shows that nitrate assimilation is present in more lineages than previously reported, although being restricted to autotrophs and osmotrophs. The phylogenies indicate a pervasive role of HGT, with three bacterial transfers contributing to the pathway origin, and at least seven well-supported transfers between eukaryotes. In particular, we propose a distinct and more complex HGT path between Opisthokonta and Stramenopiles than the one previously suggested, involving at least two transfers of a nitrate assimilation gene cluster. We also found that gene fusion played an essential role in this evolutionary history, underlying the origin of the canonical eukaryotic nitrate reductase, and of a chimeric nitrate reductase in Ichthyosporea (Opisthokonta). We show that the ichthyosporean pathway, including this novel nitrate reductase, is physiologically active and transcriptionally co-regulated, responding to different nitrogen sources; similarly to distant eukaryotes with independent HGT-acquisitions of the pathway. This indicates that this pattern of transcriptional control evolved convergently in eukaryotes, favoring the proper integration of the pathway in the metabolic landscape. Our results highlight the importance of reticulate evolution in eukaryotes, by showing the crucial contribution of HGT and gene fusion in the evolutionary history of the nitrate assimilation pathway.}, }
@article {pmid30787909, year = {2019}, author = {Alex, A and Antunes, A}, title = {Whole-Genome Comparisons Among the Genus Shewanella Reveal the Enrichment of Genes Encoding Ankyrin-Repeats Containing Proteins in Sponge-Associated Bacteria.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {5}, pmid = {30787909}, issn = {1664-302X}, abstract = {The bacterial members of the genus Shewanella are widely distributed and inhabit both freshwater and marine environments. Some members of Shewanella have gained considerable attention due to its ability to survive in redox-stratified environments. However, a gap of knowledge exists on the key genomic features of the sponge-associated Shewanella sp. involving the successful host-bacteria interaction, as sponge-symbiotic Shewanella are largely underrepresented in the public repositories. With the aim of identifying the genomic signatures of sponge-Shewanella association, we generated a high-quality genome data of a sponge-associated, Shewanella sp. OPT22, isolated from the intertidal marine sponge Ophlitaspongia papilla and performed comprehensive comparative analyses of 68 genome strains of the genus Shewanella including two previously reported genomes of sponge-associated bacteria, Shewanella spongiae KCTC 22492 and Shewanella sp. Alg231_23. The 16S rRNA-based phylogenetic reconstruction showed the well-supported affiliation of OPT22 and KCTC 22492 with previously reported sponge-associated bacteria, affirming the "sponge-specific" nature of these two bacterial strains isolated from different marine sponge species from the Atlantic and Pacific (East Sea) Oceans, respectively. The genome comparison of the 68 strains of Shewanella inhabiting different habitats revealed the unusual/previously unreported abundance of genes encoding for ankyrin-repeat containing proteins (ANKs) in the genomes of the two sponge-associated strains, OPT22 (ANKs; n = 45) and KCTC 22492 (ANKs; n = 52), which might be involved in sponge-Shewanella interactions. Focused analyses detected the syntenic organization of the gene cluster encoding major secretion system (type III/IV/VI) components and the presence of effector homologs in OPT22 and KCTC 22492 that seem to play a role in the virulence of the sponge bacteria. The genomic island (GI) of Shewanella sp. OPT22 was identified to localize a gene cluster encoding T4SS components and ANK (n = 1), whereas S. spongiae KCTC 22492 harbored a total of seven ANKs within multiple GIs. GIs may play a pivotal role in the dissemination of symbioses-related genes (ANKs) through the horizontal gene transfer, contributing to the diversification and adaptation of sponge-associated Shewanella. Overall, the genome analyses of Shewanella isolates from marine sponges revealed genomic repertoires that might be involved in establishing successful symbiotic relationships with the sponge hosts.}, }
@article {pmid30787193, year = {2019}, author = {Dunning, LT and Olofsson, JK and Parisod, C and Choudhury, RR and Moreno-Villena, JJ and Yang, Y and Dionora, J and Quick, WP and Park, M and Bennetzen, JL and Besnard, G and Nosil, P and Osborne, CP and Christin, PA}, title = {Lateral transfers of large DNA fragments spread functional genes among grasses.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {10}, pages = {4416-4425}, pmid = {30787193}, issn = {1091-6490}, support = {638333/ERC_/European Research Council/International ; MR/K001744/1/MRC_/Medical Research Council/United Kingdom ; BB/J004243/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Chromosomes, Plant ; DNA, Plant/*genetics ; *Gene Transfer, Horizontal ; *Genes, Plant ; Phylogeny ; Poaceae/classification/*genetics ; }, abstract = {A fundamental tenet of multicellular eukaryotic evolution is that vertical inheritance is paramount, with natural selection acting on genetic variants transferred from parents to offspring. This lineal process means that an organism's adaptive potential can be restricted by its evolutionary history, the amount of standing genetic variation, and its mutation rate. Lateral gene transfer (LGT) theoretically provides a mechanism to bypass many of these limitations, but the evolutionary importance and frequency of this process in multicellular eukaryotes, such as plants, remains debated. We address this issue by assembling a chromosome-level genome for the grass Alloteropsis semialata, a species surmised to exhibit two LGTs, and screen it for other grass-to-grass LGTs using genomic data from 146 other grass species. Through stringent phylogenomic analyses, we discovered 57 additional LGTs in the A. semialata nuclear genome, involving at least nine different donor species. The LGTs are clustered in 23 laterally acquired genomic fragments that are up to 170 kb long and have accumulated during the diversification of Alloteropsis. The majority of the 59 LGTs in A. semialata are expressed, and we show that they have added functions to the recipient genome. Functional LGTs were further detected in the genomes of five other grass species, demonstrating that this process is likely widespread in this globally important group of plants. LGT therefore appears to represent a potent evolutionary force capable of spreading functional genes among distantly related grass species.}, }
@article {pmid30782660, year = {2019}, author = {López-Pérez, M and Jayakumar, JM and Haro-Moreno, JM and Zaragoza-Solas, A and Reddi, G and Rodriguez-Valera, F and Shapiro, OH and Alam, M and Almagro-Moreno, S}, title = {Evolutionary Model of Cluster Divergence of the Emergent Marine Pathogen Vibrio vulnificus: From Genotype to Ecotype.}, journal = {mBio}, volume = {10}, number = {1}, pages = {}, pmid = {30782660}, issn = {2150-7511}, mesh = {Aquaculture ; Aquatic Organisms/microbiology ; Cluster Analysis ; Computational Biology ; *Ecotype ; Evolution, Molecular ; Gene Flow ; Gene Transfer, Horizontal ; *Genetic Variation ; Genome, Bacterial ; *Genotype ; Phenotype ; Recombination, Genetic ; Vibrio vulnificus/*classification/*genetics/isolation &amp; purification/physiology ; }, abstract = {Vibrio vulnificus, an opportunistic pathogen, is the causative agent of a life-threatening septicemia and a rising problem for aquaculture worldwide. The genetic factors that differentiate its clinical and environmental strains remain enigmatic. Furthermore, clinical strains have emerged from every clade of V. vulnificus In this work, we investigated the underlying genomic properties and population dynamics of the V. vulnificus species from an evolutionary and ecological point of view. Genome comparisons and bioinformatic analyses of 113 V. vulnificus isolates indicate that the population of V. vulnificus is made up of four different clusters. We found evidence that recombination and gene flow between the two largest clusters (cluster 1 [C1] and C2) have drastically decreased to the point where they are diverging independently. Pangenome and phenotypic analyses showed two markedly different lifestyles for these two clusters, indicating commensal (C2) and bloomer (C1) ecotypes, with differences in carbohydrate utilization, defense systems, and chemotaxis, among other characteristics. Nonetheless, we identified frequent intra- and interspecies exchange of mobile genetic elements (e.g., antibiotic resistance plasmids, novel "chromids," or two different and concurrent type VI secretion systems) that provide high levels of genetic diversity in the population. Surprisingly, we identified strains from both clusters in the mucosa of aquaculture species, indicating that manmade niches are bringing strains from the two clusters together. We propose an evolutionary model of V. vulnificus that could be broadly applicable to other pathogenic vibrios and facultative bacterial pathogens to pursue strategies to prevent their infections and emergence.IMPORTANCEVibrio vulnificus is an emergent marine pathogen and is the cause of a deadly septicemia. However, the genetic factors that differentiate its clinical and environmental strains and its several biotypes remain mostly enigmatic. In this work, we investigated the underlying genomic properties and population dynamics of the V. vulnificus species to elucidate the traits that make these strains emerge as a human pathogen. The acquisition of different ecological determinants could have allowed the development of highly divergent clusters with different lifestyles within the same environment. However, we identified strains from both clusters in the mucosa of aquaculture species, indicating that manmade niches are bringing strains from the two clusters together, posing a potential risk of recombination and of emergence of novel variants. We propose a new evolutionary model that provides a perspective that could be broadly applicable to other pathogenic vibrios and facultative bacterial pathogens to pursue strategies to prevent their infections.}, }
@article {pmid30782635, year = {2019}, author = {Magaziner, SJ and Zeng, Z and Chen, B and Salmond, GPC}, title = {The Prophages of Citrobacter rodentium Represent a Conserved Family of Horizontally Acquired Mobile Genetic Elements Associated with Enteric Evolution towards Pathogenicity.}, journal = {Journal of bacteriology}, volume = {201}, number = {9}, pages = {}, pmid = {30782635}, issn = {1098-5530}, support = {BB/G000298/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/H002677/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *Biological Evolution ; Citrobacter rodentium/*pathogenicity/*virology ; Computational Biology ; Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences ; Lipopolysaccharides/metabolism ; Mice ; Prophages/*genetics/growth &amp; development ; Virulence ; Virus Attachment ; }, abstract = {Prophage-mediated horizontal gene transfer (HGT) plays a key role in the evolution of bacteria, enabling access to new environmental niches, including pathogenicity. Citrobacter rodentium is a host-adapted intestinal mouse pathogen and important model organism for attaching and effacing (A/E) pathogens, including the clinically significant enterohaemorrhagic and enteropathogenic Escherichia coli (EHEC and EPEC, respectively). Even though C. rodentium contains 10 prophage genomic regions, including an active temperate phage, ΦNP, little was known regarding the nature of C. rodentium prophages in the bacterium's evolution toward pathogenicity. In this study, our characterization of ΦNP led to the discovery of a second, fully functional temperate phage, named ΦSM. We identify the bacterial host receptor for both phages as lipopolysaccharide (LPS). ΦNP and ΦSM are likely important mediators of HGT in C. rodentium Bioinformatic analysis of the 10 prophage regions reveals cargo genes encoding known virulence factors, including several type III secretion system (T3SS) effectors. C. rodentium prophages are conserved across a wide range of pathogenic enteric bacteria, including EPEC and EHEC as well as pathogenic strains of Salmonella enterica, Shigella boydii, and Klebsiella pneumoniae Phylogenetic analysis of core enteric backbone genes compared against prophage evolutionary models suggests that these prophages represent an important, conserved family of horizontally acquired enteric-bacterium-associated pathogenicity determinants. In addition to highlighting the transformative role of bacteriophage-mediated HGT in C. rodentium's evolution toward pathogenicity, these data suggest that the examination of conserved families of prophages in other pathogenic bacteria and disease outbreaks might provide deeper evolutionary and pathological insights otherwise obscured by more classical analysis.IMPORTANCE Bacteriophages are obligate intracellular parasites of bacteria. Some bacteriophages can confer novel bacterial phenotypes, including pathogenicity, through horizontal gene transfer (HGT). The pathogenic bacterium Citrobacter rodentium infects mice using mechanisms similar to those employed by human gastrointestinal pathogens, making it an important model organism. Here, we examined the 10 prophages of C. rodentium, investigating their roles in its evolution toward virulence. We characterized ΦNP and ΦSM, two endogenous active temperate bacteriophages likely important for HGT. We showed that the 10 prophages encode predicted virulence factors and are conserved within other intestinal pathogens. Phylogenetic analysis suggested that they represent a conserved family of horizontally acquired enteric-bacterium-associated pathogenic determinants. Consequently, similar analysis of prophage elements in other pathogens might further understanding of their evolution and pathology.}, }
@article {pmid30775784, year = {2019}, author = {Pathan, EK and Deshpande, MV}, title = {The puzzle of highly virulent Metarhizium anisopliae strains from Annona squamosa fields against Helicoverpa armigera.}, journal = {Journal of basic microbiology}, volume = {59}, number = {4}, pages = {392-401}, doi = {10.1002/jobm.201800631}, pmid = {30775784}, issn = {1521-4028}, support = {21(0962)/13/EMR2//Council of Scientific and Industrial Research Emeritus Scientist Scheme/ ; //Department of Biotechnology, Ministry of Science and Technology, Government of India (India)/ ; }, mesh = {Animals ; Annona/*microbiology ; Bacterial Proteins/genetics/metabolism ; Endophytes/isolation &amp; purification ; Gene Expression Profiling ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Genes, Plant/genetics ; Genomics ; Insecticides/metabolism ; Larva/microbiology ; Metarhizium/genetics/metabolism/*pathogenicity ; Moths/*microbiology ; *Pest Control, Biological ; Phylogeny ; Proteomics ; *Soil Microbiology ; }, abstract = {In our search for indigenous virulent strains of the entomopathogenic fungi, we observed that Metarhizium isolates from soils associated with Annona squamosa (custard apple) have higher virulence (>90% mortality of Helicoverpa armigera larvae at 1/10[th] spore concentration) than strains isolated from Solanum lycopersicum (tomato) fields. Proteomic analysis revealed two insecticidal cyclopeptides of A. squamosa origin in the M. anisopliae strains that led to higher virulence against H. armigera. Transcriptomic and genomic data indicated that M. anisopliae strains and A. squamosa had more than 20 genes in common, including those for cyclic hexapeptide synthase, non-ribosomal peptide synthetase, and plant cyclotide genes, which are involved in the biosynthesis of insecticidal cyclopeptides. These genes were absent in M. anisopliae strains isolated from the S. lycopersicum fields. Further, these strains can establish an endophytic relationship with A. squamosa suggesting that these rhizospheric strains originally could be endophytes, which were eventually released into the soil. Further, Metarhizium strains associated with Capsicum annuum (chili), Azadirachta indica (neem), and Carica papaya (papaya) - plants with insecticidal properties - also had higher virulence against H. armigera. Thus exploration of rhizospheres of plants producing insecticidal metabolites to isolate entomopathogenic fungi, per se, could be a viable strategy in agricultural for crop protection.}, }
@article {pmid30775458, year = {2019}, author = {Ono, R and Yasuhiko, Y and Aisaki, KI and Kitajima, S and Kanno, J and Hirabayashi, Y}, title = {Exosome-mediated horizontal gene transfer occurs in double-strand break repair during genome editing.}, journal = {Communications biology}, volume = {2}, number = {}, pages = {57}, pmid = {30775458}, issn = {2399-3642}, mesh = {Animals ; *CRISPR-Cas Systems ; Cattle ; DNA/*genetics/metabolism ; DNA Breaks, Double-Stranded ; *DNA Repair ; Embryo, Mammalian ; Escherichia coli/genetics/metabolism ; Exosomes/*genetics/metabolism ; Gene Editing/*ethics ; *Gene Transfer, Horizontal ; *Genome ; Goats ; High-Throughput Nucleotide Sequencing ; Humans ; Mice ; NIH 3T3 Cells ; Plasmids/chemistry/metabolism ; Retroelements ; Short Interspersed Nucleotide Elements ; }, abstract = {The CRISPR-Cas9 system has been successfully applied in many organisms as a powerful genome-editing tool. Undoubtedly, it will soon be applied to human genome editing, including gene therapy. We have previously reported that unintentional DNA sequences derived from retrotransposons, genomic DNA, mRNA and vectors are captured at double-strand breaks (DSBs) sites when DSBs are introduced by the CRISPR-Cas9 system. Therefore, it is possible that unintentional insertions associated with DSB repair represent a potential risk for human genome editing gene therapies. To address this possibility, comprehensive sequencing of DSB sites was performed. Here, we report that exosome-mediated horizontal gene transfer occurs in DSB repair during genome editing. Exosomes are present in all fluids from living animals, including seawater and breathing mammals, suggesting that exosome-mediated horizontal gene transfer is the driving force behind mammalian genome evolution. The findings of this study highlight an emerging new risk for this leading-edge technology.}, }
@article {pmid30773771, year = {2019}, author = {Liu, F and McDonald, M and Schwessinger, B and Joe, A and Pruitt, R and Erickson, T and Zhao, X and Stewart, V and Ronald, PC}, title = {Variation and inheritance of the Xanthomonas raxX-raxSTAB gene cluster required for activation of XA21-mediated immunity.}, journal = {Molecular plant pathology}, volume = {20}, number = {5}, pages = {656-672}, pmid = {30773771}, issn = {1364-3703}, support = {R01 GM055962/GM/NIGMS NIH HHS/United States ; R01 GM122968/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/genetics ; Conserved Sequence ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial ; Inheritance Patterns/*genetics ; *Multigene Family ; Mutation, Missense/genetics ; Oryza/*immunology/*microbiology ; Phylogeny ; Plant Immunity/*genetics ; Plant Proteins/*metabolism ; Plant Roots/growth &amp; development/microbiology ; Protein Serine-Threonine Kinases/*metabolism ; Recombination, Genetic/genetics ; Xanthomonas/*genetics ; }, abstract = {The rice XA21-mediated immune response is activated on recognition of the RaxX peptide produced by the bacterium Xanthomonas oryzae pv. oryzae (Xoo). The 60-residue RaxX precursor is post-translationally modified to form a sulfated tyrosine peptide that shares sequence and functional similarity with the plant sulfated tyrosine (PSY) peptide hormones. The 5-kb raxX-raxSTAB gene cluster of Xoo encodes RaxX, the RaxST tyrosylprotein sulfotransferase, and the RaxA and RaxB components of a predicted type I secretion system. To assess raxX-raxSTAB gene cluster evolution and to determine its phylogenetic distribution, we first identified rax gene homologues in other genomes. We detected the complete raxX-raxSTAB gene cluster only in Xanthomonas spp., in five distinct lineages in addition to X. oryzae. The phylogenetic distribution of the raxX-raxSTAB gene cluster is consistent with the occurrence of multiple lateral (horizontal) gene transfer events during Xanthomonas speciation. RaxX natural variants contain a restricted set of missense substitutions, as expected if selection acts to maintain peptide hormone-like function. Indeed, eight RaxX variants tested all failed to activate the XA21-mediated immune response, yet retained peptide hormone activity. Together, these observations support the hypothesis that the XA21 receptor evolved specifically to recognize Xoo RaxX.}, }
@article {pmid30773139, year = {2019}, author = {Sáenz, JS and Marques, TV and Barone, RSC and Cyrino, JEP and Kublik, S and Nesme, J and Schloter, M and Rath, S and Vestergaard, G}, title = {Oral administration of antibiotics increased the potential mobility of bacterial resistance genes in the gut of the fish Piaractus mesopotamicus.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {24}, pmid = {30773139}, issn = {2049-2618}, mesh = {Administration, Oral ; Animals ; Anti-Bacterial Agents/*administration &amp; dosage/adverse effects ; Aquaculture ; Bacteria/*classification/drug effects/genetics ; Bacterial Proteins/genetics ; Biodiversity ; Characiformes/*microbiology ; *Drug Resistance, Bacterial ; Gastrointestinal Microbiome ; Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences ; Phylogeny ; Thiamphenicol/administration &amp; dosage/adverse effects/*analogs &amp; derivatives ; }, abstract = {BACKGROUND: Aquaculture is on the rise worldwide, and the use of antibiotics is fostering higher production intensity. However, recent findings suggest that the use of antibiotics comes at the price of increased antibiotic resistance. Yet, the effect of the oral administration of antibiotics on the mobility of microbial resistance genes in the fish gut is not well understood. In the present study, Piaractus mesopotamicus was used as a model to evaluate the effect of the antimicrobial florfenicol on the diversity of the gut microbiome as well as antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) using a metagenomic approach.<br><br>RESULTS: The total relative abundance of ARGs and MGEs significantly increased during the antibiotic exposure. Additionally, phage integrases, transposases, and transposons flanking ARGs accumulated in the gut microbiome of P. mesopotamicus because of the antibiotic exposure. MGEs co-occurring with ARGs showed a significant positive correlation with the total ARGs found. Furthermore, shifts in the gut microbiome towards well-known putative pathogens such as Salmonella, Plesiomonas, and Citrobacter were observed following florfenicol treatment. Mainly Plesiomonas and Citrobacter harbored genes that code for multidrug and phenicol efflux pumps. Moreover, several genes related to RNA processing and modification, cell motility, SOS response, and extracellular structure were enriched due to the antibiotic application. The observed effects were visible during the complete application phase and disappeared at the post-exposure phase.<br><br>CONCLUSIONS: Our findings suggest that the oral administration of antibiotics increases the potential for MGE-mediated exchange of ARGs in the gut of fish and could contribute to the enrichment and dispersion of ARGs in aquaculture systems. Importantly, this increase in the potential for ARGs exchange could be an effect of changes in community structure and/or ARG mobilization.}, }
@article {pmid30772620, year = {2019}, author = {Chen, M and Cui, J}, title = {Discovery of endogenous retroviruses with mammalian envelopes in avian genomes uncovers long-term bird-mammal interaction.}, journal = {Virology}, volume = {530}, number = {}, pages = {27-31}, doi = {10.1016/j.virol.2019.02.005}, pmid = {30772620}, issn = {1096-0341}, mesh = {Animals ; *Birds ; Computational Biology ; Endogenous Retroviruses/*genetics/*isolation &amp; purification ; Evolution, Molecular ; Gene Products, env/*genetics ; Gene Transfer, Horizontal ; *Genome ; *Mammals ; *Phylogeny ; Sequence Homology, Nucleic Acid ; }, abstract = {Endogenous retroviruses (ERVs) arise from the infection and integration of past retroviruses into animal hosts. We performed large-scale genomic mining of 101 avian genomes for discovery of ERVs having none-avian origin and investigated the cross-species transmission events. Phylogenetic analysis of the reverse transcriptase (RT) of polymerase gene (pol) and the transmembrane subunit (TM) of the envelope gene (env) supported that avian ERVs with a mammalian env gene existed in at least 15 avian species and can be divided into two major groups: Group-1 were of recombinant ERVs with an alpha-like pol gene and a gamma-like env gene, and Group-2 included ERVs with both gamma-like pol and env genes. Group-1 represented the avian alpharetroviral/mammalian gammaretroviral recombinant while Group-2 documented viral jump from mammals to birds. Molecular dating analysis suggested that Group-1 ERVs had integrated into avian genomes continuously, until recent past. We have expanded the knowledge of ERVs with cross-order transmission.}, }
@article {pmid30769117, year = {2019}, author = {Socha, RD and Chen, J and Tokuriki, N}, title = {The Molecular Mechanisms Underlying Hidden Phenotypic Variation among Metallo-β-Lactamases.}, journal = {Journal of molecular biology}, volume = {431}, number = {6}, pages = {1172-1185}, doi = {10.1016/j.jmb.2019.01.041}, pmid = {30769117}, issn = {1089-8638}, support = {353714//CIHR/Canada ; }, mesh = {Bacteria/*genetics ; Bacterial Proteins/*genetics ; *Biological Variation, Population ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Klebsiella pneumoniae/genetics ; Models, Molecular ; Pseudomonas aeruginosa/genetics ; beta-Lactamases/*genetics ; }, abstract = {Genetic variation among orthologous genes has been largely formed through neutral genetic drift while maintaining the functional role of these genes. However, because the evolution of gene occurs in the context of each host organism, their sequence changes are also associated with adaptation to a specific environment. Thus, genetic variation can create critical phenotypic variation, particularly when genes are transferred to a new host by horizontal gene transfer. Unveiling "hidden phenotypic variation" is particularly important for genes that confer resistance to antibiotics. However, our understanding of the molecular mechanisms that underlie phenotypic variation remains limited. Here we sought to determine the extent of phenotypic variation in the B1 metallo-β-lactamase (MBL) family and its molecular basis by systematically characterizing eight MBL orthologs, including NDM-1 and VIM-2 and IMP-1. We found that these MBLs confer diverse levels of resistance. The phenotypic variation cannot be explained by variation in catalytic efficiency alone; rather, it is the combination of the catalytic efficiency and abundance of functional periplasmic enzyme that best predicts the observed variation in resistance. The level of functional periplasmic expression varied dramatically between MBL orthologs. This was the result of changes at multiple levels of each ortholog's: (1) quantity of mRNA, (2) amount of MBL expressed, and (3) efficacy of functional enzyme translocation to the periplasm. Overall, it is the interaction between each gene and the host's underlying cellular processes (transcription, translation, and translocation) that determines MBL genetic incompatibility through horizontal gene transfer. These host-specific processes may constrain the effective spread and deployment of MBLs to certain host species and could explain the current observed distribution bias.}, }
@article {pmid30767052, year = {2019}, author = {Hasić, D and Tannier, E}, title = {Gene tree species tree reconciliation with gene conversion.}, journal = {Journal of mathematical biology}, volume = {78}, number = {6}, pages = {1981-2014}, pmid = {30767052}, issn = {1432-1416}, mesh = {Algorithms ; Computer Simulation ; *Evolution, Molecular ; *Gene Conversion ; Gene Deletion ; Gene Duplication ; Gene Transfer, Horizontal ; *Models, Genetic ; *Phylogeny ; Probability ; }, abstract = {Gene tree/species tree reconciliation is a recent decisive progress in phylogenetic methods, accounting for the possible differences between gene histories and species histories. Reconciliation consists in explaining these differences by gene-scale events such as duplication, loss, transfer, which translates mathematically into a mapping between gene tree nodes and species tree nodes or branches. Gene conversion is a frequent and important evolutionary event, which results in the replacement of a gene by a copy of another from the same species and in the same gene tree. Including this event in reconciliation models has never been attempted because it introduces a dependency between lineages, and standard algorithms based on dynamic programming become ineffective. We propose here a novel mathematical framework including gene conversion as an evolutionary event in gene tree/species tree reconciliation. We describe a randomized algorithm that finds, in polynomial running time, a reconciliation minimizing the number of duplications, losses and conversions in the case when their weights are equal. We show that the space of optimal reconciliations includes an analog of the last common ancestor reconciliation, but is not limited to it. Our algorithm outputs any optimal reconciliation with a non-null probability. We argue that this study opens a research avenue on including gene conversion in reconciliation, and discuss its possible importance in biology.}, }
@article {pmid30763762, year = {2019}, author = {Shi, C and Chen, J and Xiao, B and Kang, X and Lao, X and Zheng, H}, title = {Discovery of NDM-1 inhibitors from natural products.}, journal = {Journal of global antimicrobial resistance}, volume = {18}, number = {}, pages = {80-87}, doi = {10.1016/j.jgar.2019.02.003}, pmid = {30763762}, issn = {2213-7173}, mesh = {Bacteria/drug effects/*enzymology ; Biological Products/chemistry/*pharmacology ; Computer Simulation ; Crystallography, X-Ray ; Hesperidin/chemistry/pharmacology ; Inhibitory Concentration 50 ; Models, Molecular ; Molecular Docking Simulation ; Molecular Structure ; Protein Conformation ; beta-Lactamase Inhibitors/chemistry/*pharmacology ; beta-Lactamases/*chemistry/metabolism ; }, abstract = {OBJECTIVES: Human health is seriously threatened by metallo-β-lactamase (MBL)-mediated bacterial antimicrobial resistance, among which New Delhi metallo-β-lactamase 1 (NDM-1) has received great attention due to its extensive substrate profile and high lateral gene transfer. Currently, there is no inhibitor of NDM-1 available in clinical therapy, thus making an urgent need for research and development of novel NDM-1 inhibitors.<br><br>METHODS: A natural compound library was screened to determine potential inhibitors of NDM-1 based on its crystal structure. Five known NDM-1 inhibitors were used as positive controls for the computer screening protocol. Based on the screening results, the half maximal inhibitory concentration (IC50) of several potential NDM-1 inhibitors was determined using purified NDM-1. The potential interaction between the inhibitor and NDM-1 was analysed using docking.<br><br>RESULTS: Five potential NDM-1 inhibitors were discovered with IC50 values ranging from 3.348&#xb1;1.35&#x3bc;M (hesperidin) to 214.1&#xb1;13.37&#x3bc;M (stevioside). The most active inhibitor, hesperidin, acts directly on key residues near the NDM-1 active site.<br><br>CONCLUSION: A series of NDM-1 inhibitors was discovered using virtual screening, which allows for improved screening efficiency and reduced costs. Considering the low toxicity of these compounds, they may be used as potential lead compounds for the development of NDM-1 inhibitors.}, }
@article {pmid30763382, year = {2019}, author = {Cooke, AC and Nello, AV and Ernst, RK and Schertzer, JW}, title = {Analysis of Pseudomonas aeruginosa biofilm membrane vesicles supports multiple mechanisms of biogenesis.}, journal = {PloS one}, volume = {14}, number = {2}, pages = {e0212275}, pmid = {30763382}, issn = {1932-6203}, support = {R15 GM135862/GM/NIGMS NIH HHS/United States ; R21 AI121848/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Outer Membrane Proteins/metabolism ; *Biofilms ; Humans ; Membrane Lipids/metabolism ; Pseudomonas Infections/microbiology ; Pseudomonas aeruginosa/cytology/*physiology ; Quinolones/metabolism ; Quorum Sensing ; }, abstract = {Outer Membrane Vesicles (OMVs) are ubiquitous in bacterial environments and enable interactions within and between species. OMVs are observed in lab-grown and environmental biofilms, but our understanding of their function comes primarily from planktonic studies. Planktonic OMVs assist in toxin delivery, cell-cell communication, horizontal gene transfer, small RNA trafficking, and immune system evasion. Previous studies reported differences in size and proteomic cargo between planktonic and agar plate biofilm OMVs, suggesting possible differences in function between OMV types. In Pseudomonas aeruginosa interstitial biofilms, extracellular vesicles were reported to arise through cell lysis, in contrast to planktonic OMV biogenesis that involves the Pseudomonas Quinolone Signal (PQS) without appreciable autolysis. Differences in biogenesis mechanism could provide a rationale for observed differences in OMV characteristics between systems. Using nanoparticle tracking, we found that P. aeruginosa PAO1 planktonic and biofilm OMVs had similar characteristics. However, P. aeruginosa PA14 OMVs were smaller, with planktonic OMVs also being smaller than their biofilm counterparts. Large differences in Staphylococcus killing ability were measured between OMVs from different strains, and a smaller within-strain difference was recorded between PA14 planktonic and biofilm OMVs. Across all conditions, the predatory ability of OMVs negatively correlated with their size. To address biogenesis mechanism, we analyzed vesicles from wild type and pqsA mutant biofilms. This showed that PQS is required for physiological-scale production of biofilm OMVs, and time-course analysis confirmed that PQS production precedes OMV production as it does in planktonic cultures. However, a small sub-population of vesicles was detected in pqsA mutant biofilms whose size distribution more resembled sonicated cell debris than wild type OMVs. These results support the idea that, while a small and unique population of vesicles in P. aeruginosa biofilms may result from cell lysis, the PQS-induced mechanism is required to generate the majority of OMVs produced by wild type communities.}, }
@article {pmid30761097, year = {2019}, author = {Sánchez-Baracaldo, P and Bianchini, G and Di Cesare, A and Callieri, C and Chrismas, NAM}, title = {Insights Into the Evolution of Picocyanobacteria and Phycoerythrin Genes (mpeBA and cpeBA).}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {45}, pmid = {30761097}, issn = {1664-302X}, abstract = {Marine picocyanobacteria, Prochlorococcus and Synechococcus, substantially contribute to marine primary production and have been the subject of extensive ecological and genomic studies. Little is known about their close relatives from freshwater and non-marine environments. Phylogenomic analyses (using 136 proteins) provide strong support for the monophyly of a clade of non-marine picocyanobacteria consisting of Cyanobium, Synechococcus and marine Sub-cluster 5.2; this clade itself is sister to marine Synechococcus and Prochlorococcus. The most basal lineage within the Syn/Pro clade, Sub-Cluster 5.3, includes marine and freshwater strains. Relaxed molecular clock (SSU, LSU) analyses show that while ancestors of the Syn/Pro clade date as far back as the end of the Pre-Cambrian, modern crown groups evolved during the Carboniferous and Triassic. Comparative genomic analyses reveal novel gene cluster arrangements involved in phycobilisome (PBS) metabolism in freshwater strains. Whilst PBS genes in marine Synechococcus are mostly found in one type of phycoerythrin (PE) rich gene cluster (Type III), strains from non-marine habitats, so far, appear to be more diverse both in terms of pigment content and gene arrangement, likely reflecting a wider range of habitats. Our phylogenetic analyses show that the PE genes (mpeBA) evolved via a duplication of the cpeBA genes in an ancestor of the marine and non-marine picocyanobacteria and of the symbiotic strains Synechococcus spongiarum. A 'primitive' Type III-like ancestor containing cpeBA and mpeBA had thus evolved prior to the divergence of the Syn/Pro clade and S. spongiarum. During the diversification of Synechococcus lineages, losses of mpeBA genes may explain the emergence of pigment cluster Types I, II, IIB, and III in both marine and non-marine habitats, with few lateral gene transfer events in specific taxa.}, }
@article {pmid30761094, year = {2019}, author = {Wu, X and Wu, X and Shen, L and Li, J and Yu, R and Liu, Y and Qiu, G and Zeng, W}, title = {Whole Genome Sequencing and Comparative Genomics Analyses of Pandoraea sp. XY-2, a New Species Capable of Biodegrade Tetracycline.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {33}, pmid = {30761094}, issn = {1664-302X}, abstract = {Few bacteria are resistant to tetracycline and can even biodegrade tetracycline in the environment. In this study, we isolated a bacterium Pandoraea sp. XY-2, which could biodegrade 74% tetracycline at pH 7.0 and 30°C within 6 days. Thereafter, we determined the whole genome sequence of Pandoraea sp. XY-2 genome is a single circular chromosome of 5.06 Mb in size. Genomic annotation showed that two AA6 family members-encoding genes and nine glutathione S-transferase (GSTs)-encoding genes could be relevant to tetracycline biodegradation. In addition, the average nucleotide identities (ANI) analysis between the genomes of Pandoraea sp. XY-2 and other Pandoraea spp. revealed that Pandoraea sp. XY-2 belongs to a new species. Moreover, comparative genome analysis of 36 Pandoraea strains identified the pan and specific genes, numerous single nucleotide polymorphisms (SNPs), insertions, and deletion variations (InDels) and different syntenial relationships in the genome of Pandoraea sp. XY-2. Finally, the evolution and the origin analysis of genes related to tetracycline resistance revealed that the six tetA(48) genes and two specificgenes tetG and tetR in Pandoraea sp. XY-2 were acquired by horizontal gene transfer (HGT) events from sources related to Paraburkholderia, Burkholderia, Caballeronia, Salmonella, Vibrio, Proteobacteria, Pseudomonas, Acinetobacter, Flavimaricola, and some unidentified sources. As a new species, Pandoraea sp. XY-2 will be an excellent resource for the bioremediation of tetracycline-contaminated environment.}, }
@article {pmid30753446, year = {2019}, author = {Bedhomme, S and Amorós-Moya, D and Valero, LM and Bonifaci, N and Pujana, M&#xc0; and Bravo, IG}, title = {Evolutionary Changes after Translational Challenges Imposed by Horizontal Gene Transfer.}, journal = {Genome biology and evolution}, volume = {11}, number = {3}, pages = {814-831}, pmid = {30753446}, issn = {1759-6653}, support = {647916/ERC_/European Research Council/International ; 682819/ERC_/European Research Council/International ; }, mesh = {Drug Resistance, Bacterial/genetics ; Escherichia coli ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Proteome ; }, abstract = {Genes acquired by horizontal gene transfer (HGT) may provide the recipient organism with potentially new functions, but proper expression level and integration of the transferred genes in the novel environment are not granted. Notably, transferred genes can differ from the receiving genome in codon usage preferences, leading to impaired translation and reduced functionality. Here, we characterize the genomic and proteomic changes undergone during experimental evolution of Escherichia coli after HGT of three synonymous versions, presenting very different codon usage preference, of an antibiotic resistance gene. The experimental evolution was conducted with and without the corresponding antibiotic and the mutational patterns and proteomic profiles after 1,000 generations largely depend on the experimental growth conditions (e.g., mutations in antibiotic off-target genes), and on the synonymous gene version transferred (e.g., mutations in genes responsive to translational stress). The transfer of an exogenous gene extensively modifies the whole proteome, and these proteomic changes are different for the different version of the transferred gene. Additionally, we identified conspicuous changes in global regulators and in intermediate metabolism, confirmed the evolutionary ratchet generated by mutations in DNA repair genes and highlighted the plasticity of bacterial genomes accumulating large and occasionally transient duplications. Our results support a central role of HGT in fuelling evolution as a powerful mechanism promoting rapid, often dramatic genotypic and phenotypic changes. The profound reshaping of the pre-existing geno/phenotype allows the recipient bacteria to explore new ways of functioning, far beyond the mere acquisition of a novel function.}, }
@article {pmid30753429, year = {2019}, author = {Coleman, GA and Pancost, RD and Williams, TA}, title = {Investigating the Origins of Membrane Phospholipid Biosynthesis Genes Using Outgroup-Free Rooting.}, journal = {Genome biology and evolution}, volume = {11}, number = {3}, pages = {883-898}, pmid = {30753429}, issn = {1759-6653}, mesh = {Archaea/enzymology/*genetics ; Bacteria/enzymology/*genetics ; *Biological Evolution ; *Gene Transfer, Horizontal ; Models, Genetic ; Phospholipids/biosynthesis/*genetics ; }, abstract = {One of the key differences between Bacteria and Archaea is their canonical membrane phospholipids, which are synthesized by distinct biosynthetic pathways with nonhomologous enzymes. This "lipid divide" has important implications for the early evolution of cells and the type of membrane phospholipids present in the last universal common ancestor. One of the main challenges in studies of membrane evolution is that the key biosynthetic genes are ancient and their evolutionary histories are poorly resolved. This poses major challenges for traditional rooting methods because the only available outgroups are distantly related. Here, we address this issue by using the best available substitution models for single-gene trees, by expanding our analyses to the diversity of uncultivated prokaryotes recently revealed by environmental genomics, and by using two complementary approaches to rooting that do not depend on outgroups. Consistent with some previous analyses, our rooted gene trees support extensive interdomain horizontal transfer of membrane phospholipid biosynthetic genes, primarily from Archaea to Bacteria. They also suggest that the capacity to make archaeal-type membrane phospholipids was already present in last universal common ancestor.}, }
@article {pmid30746801, year = {2019}, author = {Bertrand, C and Thibessard, A and Bruand, C and Lecointe, F and Leblond, P}, title = {Bacterial NHEJ: a never ending story.}, journal = {Molecular microbiology}, volume = {111}, number = {5}, pages = {1139-1151}, doi = {10.1111/mmi.14218}, pmid = {30746801}, issn = {1365-2958}, mesh = {Bacteria/*genetics ; *DNA Breaks, Double-Stranded ; *DNA End-Joining Repair ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genome, Bacterial ; Homologous Recombination ; }, abstract = {Double-strand breaks (DSBs) are the most detrimental DNA damage encountered by bacterial cells. DBSs can be repaired by homologous recombination thanks to the availability of an intact DNA template or by Non-Homologous End Joining (NHEJ) when no intact template is available. Bacterial NHEJ is performed by sets of proteins of growing complexity from Bacillus subtilis and Mycobacterium tuberculosis to Streptomyces and Sinorhizobium meliloti. Here, we discuss the contribution of these models to the understanding of the bacterial NHEJ repair mechanism as well as the involvement of NHEJ partners in other DNA repair pathways. The importance of NHEJ and of its complexity is discussed in the perspective of regulation through the biological cycle of the bacteria and in response to environmental stimuli. Finally, we consider the role of NHEJ in genome evolution, notably in horizontal gene transfer.}, }
@article {pmid30745391, year = {2019}, author = {Brolund, A and Rajer, F and Giske, CG and Melefors, &#xd6; and Titelman, E and Sandegren, L}, title = {Dynamics of Resistance Plasmids in Extended-Spectrum-β-Lactamase-Producing Enterobacteriaceae during Postinfection Colonization.}, journal = {Antimicrobial agents and chemotherapy}, volume = {63}, number = {4}, pages = {}, pmid = {30745391}, issn = {1098-6596}, mesh = {Bacterial Proteins/genetics ; Carrier State/microbiology ; Enterobacteriaceae/*genetics ; Enterobacteriaceae Infections/*microbiology ; Feces/microbiology ; Humans ; Plasmids/*genetics ; Urinary Tract Infections/microbiology ; beta-Lactamases/*genetics ; }, abstract = {Extended-spectrum β-lactamase-producing Enterobacteriaceae (EPE) are a major cause of bloodstream infections, and the colonization rate of EPE in the gut microbiota of individuals lacking prior hospitalization or comorbidities is increasing. In this study, we performed an in-depth investigation of the temporal dynamics of EPE and their plasmids during one year by collecting fecal samples from three patients initially seeking medical care for urinary tract infections. In two of the patients, the same strain that caused the urinary tract infection (UTI) was found at all consecutive samplings from the gut microbiota, and no other EPEs were detected, while in the third patient the UTI strain was only found in the initial UTI sample. Instead, this patient presented a complex situation where a mixed microbiota of different EPE strain types, including three different E. coli ST131 variants, as well as different bacterial species, was identified over the course of the study. Different plasmid dynamics were displayed in each of the patients, including the spread of plasmids between different strain types over time and the transposition of blaCTX-M-15 from the chromosome to a plasmid, followed by subsequent loss through homologous recombination. Small cryptic plasmids were found in all isolates from all patients, and they appear to move frequently between different strains in the microbiota. In conclusion, we could demonstrate an extensive variation of EPE strain types, plasmid composition, rearrangements, and horizontal gene transfer of genetic material illustrating the high dynamics nature and interactive environment of the gut microbiota during post-UTI carriage.}, }
@article {pmid30743970, year = {2019}, author = {Liao, H and Friman, VP and Geisen, S and Zhao, Q and Cui, P and Lu, X and Chen, Z and Yu, Z and Zhou, S}, title = {Horizontal gene transfer and shifts in linked bacterial community composition are associated with maintenance of antibiotic resistance genes during food waste composting.}, journal = {The Science of the total environment}, volume = {660}, number = {}, pages = {841-850}, doi = {10.1016/j.scitotenv.2018.12.353}, pmid = {30743970}, issn = {1879-1026}, support = {105624/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacteria/*genetics ; *Composting ; Drug Resistance, Microbial/*genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; }, abstract = {About 1.3 billion tons of food waste (FW) is annually produced at a global scale. A major fraction of FW is deposited into landfills thereby contributing to environmental pollution and emission of greenhouse gasses. While increasing amounts of FW are recycled more sustainably into fertilizers in industrial-scale composting, very little is known about the antibiotic resistance genes (ARGs) present in FW and how their abundance is affected by composting. To study this, we quantified the diversity and abundance of ARGs, mobile genetic elements (MGEs) and bacterial communities in the beginning, during and at the end of the FW composting. All targeted 27 ARGs and 5 MGEs were detected in every sample suggesting that composted FW remains a reservoir of ARGs and MGEs. While the composting drastically changed the abundance, composition and diversity of bacterial communities, an increase in total ARG and MGE abundances was observed. Changes in ARGs were linked with shifts in the composition of bacterial communities as revealed by a Procrustes analysis (P < 0.01). Crucially, even though the high composting temperatures reduced the abundance and diversity of initially ARG-associated bacterial taxa, ARG abundances were maintained in other associated bacterial taxa. This was likely driven by horizontal gene transfer and physicochemical composting properties as revealed by a clear positive correlation between ARGs, MGEs, pH, NO3[-] and moisture. Together our findings suggest that traditional composting is not efficient at removing ARGs and MGEs from FW. More effective composting strategies are thus needed to minimize ARG release from composted FW into agricultural environments.}, }
@article {pmid30738818, year = {2019}, author = {Xavier, BB and Renzi, G and Lammens, C and Cherkaoui, A and Goossens, H and Schrenzel, J and Harbarth, S and Malhotra-Kumar, S}, title = {Potential in vivo transfer of a blaCTX-M14-harbouring plasmid established by combining long- and short-read sequencing.}, journal = {Journal of microbiological methods}, volume = {159}, number = {}, pages = {1-4}, doi = {10.1016/j.mimet.2019.02.004}, pmid = {30738818}, issn = {1872-8359}, mesh = {Aged, 80 and over ; Bacterial Proteins/*genetics/metabolism ; Escherichia coli/*genetics/isolation &amp; purification/metabolism ; Escherichia coli Infections/microbiology ; Female ; *Gene Transfer, Horizontal ; Humans ; Klebsiella Infections/microbiology ; Klebsiella pneumoniae/*genetics/isolation &amp; purification/physiology ; Plasmids/*genetics ; Sequence Analysis, DNA ; beta-Lactamases/*genetics/metabolism ; }, abstract = {Horizontal transfer of plasmid-mediated antibiotic resistance has rarely been documented in vivo. Utilizing long-read (Oxford Nanopore) and short-read (Illumina) sequencing, we confirmed that a gut-colonizing Escherichia coli and a hypervirulent Klebsiella pneumoniae ST23, isolated from a surgical site culture of a patient receiving cefuroxime therapy, harboured a 100% identical blaCTX-M-14-harbouring plasmid, indicative of a potential transfer in vivo.}, }
@article {pmid30737914, year = {2019}, author = {Muschiol, S and Aschtgen, MS and Nannapaneni, P and Henriques-Normark, B}, title = {Gram-Positive Type IV Pili and Competence.}, journal = {Microbiology spectrum}, volume = {7}, number = {1}, pages = {}, pmid = {30737914}, issn = {2165-0497}, mesh = {Bacterial Adhesion/*genetics ; DNA Transformation Competence/genetics ; DNA, Bacterial/genetics/metabolism ; Fimbriae Proteins/*genetics ; Fimbriae, Bacterial/*genetics ; Gene Transfer, Horizontal/*genetics ; Streptococcus pneumoniae/*genetics/physiology ; }, abstract = {Type IV pili (T4P) are remarkable bacterial surface appendages that carry out a range of functions. Various types of T4P have been identified in bacteria and archaea, making them almost universal structures in prokaryotes. T4P are best characterized in Gram-negative bacteria, in which pilus biogenesis and T4P-mediated functions have been studied for decades. Recent advances in microbial whole-genome sequencing have provided ample evidence for the existence of T4P also in many Gram-positive species. However, comparatively little is known, and T4P in Gram-positive bacteria are just beginning to be dissected. So far, they have mainly been studied in Clostridium and Streptococcus spp. and are involved in diverse cellular processes such as adhesion, motility, and horizontal gene transfer. Here we summarize the current understanding of T4P in Gram-positive species and their functions, with particular focus on the type IV competence pilus produced by the human pathogen Streptococcus pneumoniae and its role in natural transformation.}, }
@article {pmid30737174, year = {2019}, author = {Uribe, RV and van der Helm, E and Misiakou, MA and Lee, SW and Kol, S and Sommer, MOA}, title = {Discovery and Characterization of Cas9 Inhibitors Disseminated across Seven Bacterial Phyla.}, journal = {Cell host &amp; microbe}, volume = {25}, number = {2}, pages = {233-241.e5}, doi = {10.1016/j.chom.2019.01.003}, pmid = {30737174}, issn = {1934-6069}, mesh = {CRISPR-Associated Protein 9/*antagonists &amp; inhibitors ; Enzyme Inhibitors/*isolation &amp; purification ; Gene Library ; Genetic Testing ; Metagenomics/*methods ; }, abstract = {CRISPR-Cas systems in bacteria and archaea provide immunity against bacteriophages and plasmids. To overcome CRISPR immunity, phages have acquired anti-CRISPR genes that reduce CRISPR-Cas activity. Using a synthetic genetic circuit, we developed a high-throughput approach to discover anti-CRISPR genes from metagenomic libraries based on their functional activity rather than sequence homology or genetic context. We identified 11 DNA fragments from soil, animal, and human metagenomes that circumvent Streptococcus pyogenes Cas9 activity in our selection strain. Further in vivo and in vitro characterization of a subset of these hits validated the activity of four anti-CRISPRs. Notably, homologs of some of these anti-CRISPRs were detected in seven different phyla, namely Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Cyanobacteria, Spirochaetes, and Balneolaeota, and have high sequence identity suggesting recent horizontal gene transfer. Thus, anti-CRISPRs against type II-A CRISPR-Cas systems are widely distributed across bacterial phyla, suggesting a more complex ecological role than previously appreciated.}, }
@article {pmid30735835, year = {2019}, author = {Mus, F and Colman, DR and Peters, JW and Boyd, ES}, title = {Geobiological feedbacks, oxygen, and the evolution of nitrogenase.}, journal = {Free radical biology &amp; medicine}, volume = {140}, number = {}, pages = {250-259}, doi = {10.1016/j.freeradbiomed.2019.01.050}, pmid = {30735835}, issn = {1873-4596}, mesh = {Bacteria, Aerobic/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Cyanobacteria/genetics/*metabolism ; Iron/metabolism ; Molybdenum/metabolism ; Nitrogen/metabolism ; Nitrogen Fixation/*genetics ; Nitrogenase/genetics/*metabolism ; Oxygen/*metabolism ; Photosynthesis/genetics ; }, abstract = {Biological nitrogen fixation via the activity of nitrogenase is one of the most important biological innovations, allowing for an increase in global productivity that eventually permitted the emergence of higher forms of life. The complex metalloenzyme termed nitrogenase contains complex iron-sulfur cofactors. Three versions of nitrogenase exist that differ mainly by the presence or absence of a heterometal at the active site metal cluster (either Mo or V). Mo-dependent nitrogenase is the most common while V-dependent or heterometal independent (Fe-only) versions are often termed alternative nitrogenases since they have apparent lower activities for N2 reduction and are expressed in the absence of Mo. Phylogenetic data indicates that biological nitrogen fixation emerged in an anaerobic, thermophilic ancestor of hydrogenotrophic methanogens and later diversified via lateral gene transfer into anaerobic bacteria, and eventually aerobic bacteria including Cyanobacteria. Isotopic evidence suggests that nitrogenase activity existed at 3.2 Ga, prior to the advent of oxygenic photosynthesis and rise of oxygen in the atmosphere, implying the presence of favorable environmental conditions for oxygen-sensitive nitrogenase to evolve. Following the proliferation of oxygenic phototrophs, diazotrophic organisms had to develop strategies to protect nitrogenase from oxygen inactivation and generate the right balance of low potential reducing equivalents and cellular energy for growth and nitrogen fixation activity. Here we review the fundamental advances in our understanding of biological nitrogen fixation in the context of the emergence, evolution, and taxonomic distribution of nitrogenase, with an emphasis placed on key events associated with its emergence and diversification from anoxic to oxic environments.}, }
@article {pmid30735528, year = {2019}, author = {Escasa, SR and Harrison, RL and Mowery, JD and Bauchan, GR and Cory, JS}, title = {The complete genome sequence of an alphabaculovirus from Spodoptera exempta, an agricultural pest of major economic significance in Africa.}, journal = {PloS one}, volume = {14}, number = {2}, pages = {e0209937}, pmid = {30735528}, issn = {1932-6203}, mesh = {Africa ; Animals ; Baculoviridae/*genetics ; Base Sequence ; Crops, Agricultural/parasitology ; DNA, Viral/genetics ; Genome, Viral ; Phylogeny ; Spodoptera/*virology ; Whole Genome Sequencing ; }, abstract = {Spodoptera exempta nucleopolyhedrovirus (SpexNPV) is a viral pathogen of the African armyworm, Spodoptera exempta (Lepidoptera: Noctuidae), a significant agricultural pest of cereal crops in Africa. SpexNPV has been evaluated as a potential insecticide for control of this pest and has served as the subject of research on baculovirus pathology and transmission. Occlusion bodies (OBs) of SpexNPV isolate 244.1 were examined, and the nucleotide sequence of the genome was determined and characterized. SpexNPV-244.1 OBs consisted of irregular polyhedra with a size and appearance typical for alphabaculoviruses. Virions within the polyhedra contained 1-8 nucleocapsids per unit envelope. The SpexNPV-244.1 genome was comprised of a 129,528 bp circular sequence, in which 139 ORFs were annotated. Five homologous regions (hrs) consisting of a variable number of 28-bp imperfect palindromes were identified in the genome. The genome sequence contained the 38 core genes of family Baculoviridae, as well as three ORFs unique to the SpexNPV sequence and one ORF that was apparently acquired by horizontal gene transfer with a betabaculovirus ancestor. Phylogenetic inference with core gene amino acid sequence alignments placed SpexNPV-244.1 in a lineage containing alphabaculoviruses of Spodoptera frugiperda and Spodopotera exigua which in turn is part of a larger group of alphabaculoviruses from the subfamily Noctuinae in the lepidopteran family Noctuidae. Kimura-2-parameter pairwise nucleotide distances indicated that SpexNPV-244.1 represented a different and previously unlisted species in the genus Alphabaculovirus. Gene parity plots indicated that the gene order of SpexNPV-244.l was extensively collinear with that of Spodoptera exigua NPV (SeMNPV). These plots also revealed a group of 17 core genes whose order was conserved in other alpha- and betabaculoviruses.}, }
@article {pmid30733176, year = {2019}, author = {Ghaith, DM and Mohamed, ZK and Farahat, MG and Aboulkasem Shahin, W and Mohamed, HO}, title = {Colonization of intestinal microbiota with carbapenemase-producing Enterobacteriaceae in paediatric intensive care units in Cairo, Egypt.}, journal = {Arab journal of gastroenterology : the official publication of the Pan-Arab Association of Gastroenterology}, volume = {20}, number = {1}, pages = {19-22}, doi = {10.1016/j.ajg.2019.01.002}, pmid = {30733176}, issn = {2090-2387}, mesh = {Bacterial Proteins/metabolism ; Carbapenem-Resistant Enterobacteriaceae/*enzymology/genetics/*isolation &amp; purification ; Carrier State/*microbiology ; Disk Diffusion Antimicrobial Tests ; Egypt ; Escherichia coli/enzymology/genetics/isolation &amp; purification ; Escherichia coli Proteins/genetics/metabolism ; Feces/microbiology ; Gastrointestinal Microbiome ; Genotype ; Humans ; Intensive Care Units, Pediatric ; Klebsiella oxytoca/enzymology/genetics/isolation &amp; purification ; Klebsiella pneumoniae/enzymology/genetics/isolation &amp; purification ; Phenotype ; Rectum/microbiology ; beta-Lactamases/genetics/metabolism ; }, abstract = {BACKGROUND AND STUDY AIMS: Colonized patients with carbapenamase producing Enterobacteriaceae (CPE) are vulnerable to invasive infections from their endogenous flora. We aimed to assess faecal colonization with (CPE) among children admitted to Cairo University paediatric intensive care units (ICUs). The phenotypic and genotypic characterizations of carbapenemase-producing Enterobacteriaceae were also studied.<br><br>PATIENTS AND METHODS: A total of 413 Enterobacteriaceae isolates have been isolated from cultured rectal swabs of 100 children. All swabs were inoculated on ChromID&#x2122; CARBA agar to screen for carbapenem resistant Enterobacteriaceae (CRE). Disk diffusion method, Modified Hodge test (MHT) and further genotypic detection of carbapenemases genes (blaOXA-48, blaKPC and blaNDM-1, blaVIM and blaIMP) by multiplex PCR were done.<br><br>RESULTS: Out of 413 Enterobacteriaceae isolates; 100 isolates were defined as CRE. BlaOXA-48 was detected in (33%); Escherichia coli (n&#x202f;=&#x202f;11), Klebsiella oxytoca (n&#x202f;=&#x202f;3) and Klebsiella pneumoniae (n&#x202f;=&#x202f;19), while (27%) carried blaNDM-1Escherichia coli (n&#x202f;=&#x202f;7), and Klebsiella pneumoniae (n&#x202f;=&#x202f;20).<br><br>CONCLUSION: Prevalence of carbapenem resistant Enterobacteriaceae was 24%, various genes of carbapenemases were detected in 80% of carbapenem resistant Enterobacteriaceae with dominance of blaOXA-48. Understanding the colonization status of our patients with strict infection control measures can reduce the risk of horizontal gene transfer of carbapenemases.}, }
@article {pmid30732613, year = {2019}, author = {Ebenezer, TE and Zoltner, M and Burrell, A and Nenarokova, A and Novák Vanclová, AMG and Prasad, B and Soukal, P and Santana-Molina, C and O'Neill, E and Nankissoor, NN and Vadakedath, N and Daiker, V and Obado, S and Silva-Pereira, S and Jackson, AP and Devos, DP and Lukeš, J and Lebert, M and Vaughan, S and Hampl, V and Carrington, M and Ginger, ML and Dacks, JB and Kelly, S and Field, MC}, title = {Transcriptome, proteome and draft genome of Euglena gracilis.}, journal = {BMC biology}, volume = {17}, number = {1}, pages = {11}, pmid = {30732613}, issn = {1741-7007}, support = {P009018/1//Medical Research Council/United Kingdom ; }, mesh = {Cell Nucleus ; Euglena gracilis/*genetics/metabolism ; *Genome ; Plastids ; *Proteome ; *Transcriptome ; }, abstract = {BACKGROUND: Photosynthetic euglenids are major contributors to fresh water ecosystems. Euglena gracilis in particular has noted metabolic flexibility, reflected by an ability to thrive in a range of harsh environments. E. gracilis has been a popular model organism and of considerable biotechnological interest, but the absence of a gene catalogue has hampered both basic research and translational efforts.<br><br>RESULTS: We report a detailed transcriptome and partial genome for E. gracilis Z1. The nuclear genome is estimated to be around 500&#x2009;Mb in size, and the transcriptome encodes over 36,000 proteins and the genome possesses less than 1% coding sequence. Annotation of coding sequences indicates a highly sophisticated endomembrane system, RNA processing mechanisms and nuclear genome contributions from several photosynthetic lineages. Multiple gene families, including likely signal transduction components, have been massively expanded. Alterations in protein abundance are controlled post-transcriptionally between light and dark conditions, surprisingly similar to trypanosomatids.<br><br>CONCLUSIONS: Our data provide evidence that a range of photosynthetic eukaryotes contributed to the Euglena nuclear genome, evidence in support of the 'shopping bag' hypothesis for plastid acquisition. We also suggest that euglenids possess unique regulatory mechanisms for achieving extreme adaptability, through mechanisms of paralog expansion and gene acquisition.}, }
@article {pmid30732586, year = {2019}, author = {Masonbrink, R and Maier, TR and Muppirala, U and Seetharam, AS and Lord, E and Juvale, PS and Schmutz, J and Johnson, NT and Korkin, D and Mitchum, MG and Mimee, B and den Akker, SE and Hudson, M and Severin, AJ and Baum, TJ}, title = {The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {119}, pmid = {30732586}, issn = {1471-2164}, support = {DE-AC02-05CH11231//U.S. Department of Energy/ ; DBI-1458267//U.S. National Science Foundation/ ; BB/R011311/1//Biotechnology and Biological Sciences Research Council (GB)/ ; ACI-1548562, ACI-1445606//National Foundation for Science and Technology Development (VN)/ ; None//Genome Canada/ ; None//G&#xe9;nome Qu&#xe9;bec/ ; }, mesh = {Animals ; *Evolution, Molecular ; *Gene Duplication ; *Genomics ; Genotype ; Host-Parasite Interactions ; Molecular Sequence Annotation ; Plant Diseases/parasitology ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Glycine max/*parasitology ; Tylenchoidea/*genetics/*physiology ; }, abstract = {BACKGROUND: Heterodera glycines, commonly referred to as the soybean cyst nematode (SCN), is an obligatory and sedentary plant parasite that causes over a billion-dollar yield loss to soybean production annually. Although there are genetic determinants that render soybean plants resistant to certain nematode genotypes, resistant soybean cultivars are increasingly ineffective because their multi-year usage has selected for virulent H. glycines populations. The parasitic success of H. glycines relies on the comprehensive re-engineering of an infection site into a syncytium, as well as the long-term suppression of host defense to ensure syncytial viability. At the forefront of these complex molecular interactions are effectors, the proteins secreted by H. glycines into host root tissues. The mechanisms of effector acquisition, diversification, and selection need to be understood before effective control strategies can be developed, but the lack of an annotated genome has been a major roadblock.<br><br>RESULTS: Here, we use PacBio long-read technology to assemble a H. glycines genome of 738 contigs into 123&#x2009;Mb with annotations for 29,769 genes. The genome contains significant numbers of repeats (34%), tandem duplicates (18.7&#x2009;Mb), and horizontal gene transfer events (151 genes). A large number of putative effectors (431 genes) were identified in the genome, many of which were found in transposons.<br><br>CONCLUSIONS: This advance provides a glimpse into the host and parasite interplay by revealing a diversity of mechanisms that give rise to virulence genes in the soybean cyst nematode, including: tandem duplications containing over a fifth of the total gene count, virulence genes hitchhiking in transposons, and 107 horizontal gene transfers not reported in other plant parasitic nematodes thus far. Through extensive characterization of the H. glycines genome, we provide new insights into H. glycines biology and shed light onto the mystery underlying complex host-parasite interactions. This genome sequence is an important prerequisite to enable work towards generating new resistance or control measures against H. glycines.}, }
@article {pmid30728359, year = {2019}, author = {Rosenkilde, CEH and Munck, C and Porse, A and Linkevicius, M and Andersson, DI and Sommer, MOA}, title = {Collateral sensitivity constrains resistance evolution of the CTX-M-15 β-lactamase.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {618}, pmid = {30728359}, issn = {2041-1723}, mesh = {Amdinocillin/pharmacology ; Animals ; Anti-Bacterial Agents/*pharmacology ; Cefotaxime/pharmacology ; Disease Models, Animal ; Drug Combinations ; Drug Resistance, Microbial/*genetics ; Escherichia coli/drug effects/genetics ; Female ; Gene Transfer, Horizontal/drug effects ; Mice ; Mice, Inbred BALB C ; Microbial Sensitivity Tests ; Mutation ; beta-Lactamases/*drug effects/genetics ; beta-Lactams ; }, abstract = {Antibiotic resistance is a major challenge to global public health. Discovery of new antibiotics is slow and to ensure proper treatment of bacterial infections new strategies are needed. One way to curb the development of antibiotic resistance is to design drug combinations where the development of resistance against one drug leads to collateral sensitivity to the other drug. Here we study collateral sensitivity patterns of the globally distributed extended-spectrum β-lactamase CTX-M-15, and find three non-synonymous mutations with increased resistance against mecillinam or piperacillin-tazobactam that simultaneously confer full susceptibility to several cephalosporin drugs. We show in vitro and in mice that a combination of mecillinam and cefotaxime eliminates both wild-type and resistant CTX-M-15. Our results indicate that mecillinam and cefotaxime in combination constrain resistance evolution of CTX-M-15, and illustrate how drug combinations can be rationally designed to limit the resistance evolution of horizontally transferred genes by exploiting collateral sensitivity patterns.}, }
@article {pmid30728258, year = {2019}, author = {Yoshikawa, G and Blanc-Mathieu, R and Song, C and Kayama, Y and Mochizuki, T and Murata, K and Ogata, H and Takemura, M}, title = {Medusavirus, a Novel Large DNA Virus Discovered from Hot Spring Water.}, journal = {Journal of virology}, volume = {93}, number = {8}, pages = {}, pmid = {30728258}, issn = {1098-5514}, mesh = {Acanthamoeba/virology ; *DNA Viruses/classification/genetics/isolation &amp; purification ; *Genome, Viral ; Hot Springs/*virology ; *Phylogeny ; Viral Proteins/*genetics ; *Water Microbiology ; }, abstract = {Recent discoveries of new large DNA viruses reveal high diversity in their morphologies, genetic repertoires, and replication strategies. Here, we report the novel features of medusavirus, a large DNA virus newly isolated from hot spring water in Japan. Medusavirus, with a diameter of 260 nm, shows a T=277 icosahedral capsid with unique spherical-headed spikes on its surface. It has a 381-kb genome encoding 461 putative proteins, 86 of which have their closest homologs in Acanthamoeba, whereas 279 (61%) are orphan genes. The virus lacks the genes encoding DNA topoisomerase II and RNA polymerase, showing that DNA replication takes place in the host nucleus, whereas the progeny virions are assembled in the cytoplasm. Furthermore, the medusavirus genome harbored genes for all five types of histones (H1, H2A, H2B, H3, and H4) and one DNA polymerase, which are phylogenetically placed at the root of the eukaryotic clades. In contrast, the host amoeba encoded many medusavirus homologs, including the major capsid protein. These facts strongly suggested that amoebae are indeed the most promising natural hosts of medusavirus, and that lateral gene transfers have taken place repeatedly and bidirectionally between the virus and its host since the early stage of their coevolution. Medusavirus reflects the traces of direct evolutionary interactions between the virus and eukaryotic hosts, which may be caused by sharing the DNA replication compartment and by evolutionarily long lasting virus-host relationships. Based on its unique morphological characteristics and phylogenomic relationships with other known large DNA viruses, we propose that medusavirus represents a new family, MedusaviridaeIMPORTANCE We have isolated a new nucleocytoplasmic large DNA virus (NCLDV) from hot spring water in Japan, named medusavirus. This new NCLDV is phylogenetically placed at the root of the eukaryotic clades based on the phylogenies of several key genes, including that encoding DNA polymerase, and its genome surprisingly encodes the full set of histone homologs. Furthermore, its laboratory host, Acanthamoeba castellanii, encodes many medusavirus homologs in its genome, including the major capsid protein, suggesting that the amoeba is the genuine natural host from ancient times of this newly described virus and that lateral gene transfers have repeatedly occurred between the virus and amoeba. These results suggest that medusavirus is a unique NCLDV preserving ancient footprints of evolutionary interactions with its hosts, thus providing clues to elucidate the evolution of NCLDVs, eukaryotes, and virus-host interaction. Based on the dissimilarities with other known NCLDVs, we propose that medusavirus represents a new viral family, Medusaviridae.}, }
@article {pmid30727958, year = {2019}, author = {Kampfraath, AA and Klasson, L and Anvar, SY and Vossen, RHAM and Roelofs, D and Kraaijeveld, K and Ellers, J}, title = {Genome expansion of an obligate parthenogenesis-associated Wolbachia poses an exception to the symbiont reduction model.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {106}, pmid = {30727958}, issn = {1471-2164}, support = {865.12.003//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 15494//Stichting voor de Technische Wetenschappen/ ; }, mesh = {Animals ; Arthropods/*microbiology/physiology ; DNA Repair ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; *Parthenogenesis ; Sequence Analysis, DNA ; *Symbiosis ; Wolbachia/*genetics/physiology ; }, abstract = {BACKGROUND: Theory predicts that dependency within host-endosymbiont interactions results in endosymbiont genome size reduction. Unexpectedly, the largest Wolbachia genome was found in the obligate, parthenogenesis-associated wFol. In this study, we investigate possible processes underlying this genome expansion by comparing a re-annotated wFol genome to other Wolbachia genomes. In addition, we also search for candidate genes related to parthenogenesis induction (PI).<br><br>RESULTS: Within wFol, we found five phage WO regions representing 25.4% of the complete genome, few pseudogenized genes, and an expansion of DNA-repair genes in comparison to other Wolbachia. These signs of genome conservation were mirrored in the wFol host, the springtail F. candida, which also had an expanded DNA-repair gene family and many horizontally transferred genes. Across all Wolbachia genomes, there was a strong correlation between gene numbers of Wolbachia strains and their hosts. In order to identify genes with a potential link to PI, we assembled the genome of an additional PI strain, wLcla. Comparisons between four PI Wolbachia, including wFol and wLcla, and fourteen non-PI Wolbachia yielded a small set of potential candidate genes for further investigation.<br><br>CONCLUSIONS: The strong similarities in genome content of wFol and its host, as well as the correlation between host and Wolbachia gene numbers suggest that there may be some form of convergent evolution between endosymbiont and host genomes. If such convergent evolution would be strong enough to overcome the evolutionary forces causing genome reduction, it would enable expanded genomes within long-term obligate endosymbionts.}, }
@article {pmid30723210, year = {2019}, author = {Fogg, PCM}, title = {Identification and characterization of a direct activator of a gene transfer agent.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {595}, pmid = {30723210}, issn = {2041-1723}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacterial Proteins/*genetics/metabolism ; Bacteriophages/genetics ; Base Sequence ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal/*genetics ; Models, Genetic ; Promoter Regions, Genetic/genetics ; Protein Binding ; Quorum Sensing/genetics ; Rhodobacter capsulatus/*genetics/metabolism ; Sequence Homology, Nucleic Acid ; Transcription Factors/*genetics/metabolism ; }, abstract = {Gene transfer agents (GTAs) are thought to be ancient bacteriophages that have been co-opted into serving their host and can now transfer any gene between bacteria. Production of GTAs is controlled by several global regulators through unclear mechanisms. In Rhodobacter capsulatus, gene rcc01865 encodes a putative regulatory protein that is essential for GTA production. Here, I show that rcc01865 (hereafter gafA) encodes a transcriptional regulator that binds to the GTA promoter to initiate production of structural and DNA packaging components. Expression of gafA is in turn controlled by the pleiotropic regulator protein CtrA and the quorum-sensing regulator GtaR. GafA and CtrA work together to promote GTA maturation and eventual release through cell lysis. Identification of GafA as a direct GTA regulator allows the first integrated regulatory model to be proposed and paves the way for discovery of GTAs in other species that possess gafA homologues.}, }
@article {pmid30720424, year = {2019}, author = {Rosenberg, E and Zilber-Rosenberg, I}, title = {The Hologenome Concept of Evolution: Medical Implications.}, journal = {Rambam Maimonides medical journal}, volume = {10}, number = {1}, pages = {}, pmid = {30720424}, issn = {2076-9172}, abstract = {All natural animals and plants are holobionts, consisting of the host and microbiome, which is composed of abundant and diverse microorganisms. Health and disease of holobionts depend as much on interactions between host and microbiome and within the microbiome, as on interactions between organs and body parts of the host. Recent evidence indicates that a significant fraction of the microbiome is transferred by a variety of mechanisms from parent to offspring for many generations. Genetic variation in holobionts can occur in the microbiome as well as in the host genome, and it occurs more rapidly and by more mechanisms in genomes of microbiomes than in host genomes (e.g. via acquisition of novel microbes and horizontal gene transfer of microbial genes into host chromosomes). Evidence discussed in this review supports the concept that holobionts with their hologenomes can be considered levels of selection in evolution. Though changes in the microbiome can lead to evolution of the holobiont, it can also lead to dysbiosis and diseases (e.g. obesity, diarrhea, inflammatory bowel disease, and autism). In practice, the possibility of manipulating microbiomes offers the potential to prevent and cure diseases.}, }
@article {pmid30719223, year = {2019}, author = {Lazebnik, Y}, title = {Gestational tumors as a model to probe reticulate evolution in human neoplasia.}, journal = {Oncotarget}, volume = {10}, number = {3}, pages = {259-262}, pmid = {30719223}, issn = {1949-2553}, abstract = {Reticulate evolution, which involves the transfer of genes and other inheritable information between organisms, is of interest to a cancer researcher if only because "pirating" a trait can help a cell and its progeny adapt, survive, or take over much faster than by accumulating random mutations. However, despite being observed repeatedly in experimental models of neoplasia, reticulate evolution is assumed to be negligible in human cancer primarily because detecting gene transfer between the cells of the same genetic background can be difficult or impossible. This commentary suggests that gestational tumors, which are genetically distinct from the women who carry them, provide an opportunity to test whether reticulate evolution affects the development of human neoplasia.}, }
@article {pmid30718644, year = {2019}, author = {Nisa, S and Bercker, C and Midwinter, AC and Bruce, I and Graham, CF and Venter, P and Bell, A and French, NP and Benschop, J and Bailey, KM and Wilkinson, DA}, title = {Combining MALDI-TOF and genomics in the study of methicillin resistant and multidrug resistant Staphylococcus pseudintermedius in New Zealand.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {1271}, pmid = {30718644}, issn = {2045-2322}, mesh = {Animals ; *Dog Diseases/genetics/metabolism/microbiology ; Dogs ; *Drug Resistance, Multiple, Bacterial ; *Genomics ; *Methicillin Resistance ; New Zealand ; *Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; *Staphylococcal Skin Infections/genetics/metabolism/veterinary ; *Staphylococcus/genetics/metabolism ; }, abstract = {Staphylococcus pseudintermedius is an opportunistic and emerging zoonotic pathogen that primarily colonises the skin of dogs. Many common variants are methicillin resistant (MRSP) or multidrug resistant (MDR), and drug resistance is increasingly reported across the globe. In New Zealand, MRSP isolation remains rare in clinics. To pre-emptively inform diagnostic and antimicrobial stewardship practices, we examine isolates of S. pseudintermedius, MRSP and MDR-MRSP from New Zealand dogs using a combination of methodologies. Genetic and genomic data combined with antimicrobial susceptibility screening identify common drug-resistance profiles and their genetic determinants. We demonstrate that sensitive and specific species-level identification of S. pseudintermedius can be achieved using Bruker MALDI-TOF MS and, further, that this technique can be used to identify some common subtype variants, providing a level of categorical precision that falls somewhere between single-locus and multi-locus sequence typing. Comparative genomics analysis of global S. pseudintermedius data shows that MRSP moves frequently across the globe, but that horizontal gene transfer events resulting in the acquisition of the SCCmec cassette (responsible for beta-lactam antibiotic resistance) are infrequent. This suggests that biosecurity and surveillance in addition to antibiotic stewardship should play important roles in mitigating the risk of MRSP, especially in countries such as New Zealand where MRSP is still rare.}, }
@article {pmid30718643, year = {2019}, author = {Solovev, YV and Prilepskii, AY and Krivoshapkina, EF and Fakhardo, AF and Bryushkova, EA and Kalikina, PA and Koshel, EI and Vinogradov, VV}, title = {Sol-gel derived boehmite nanostructures is a versatile nanoplatform for biomedical applications.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {1176}, pmid = {30718643}, issn = {2045-2322}, mesh = {A549 Cells ; Aluminum Hydroxide/*chemical synthesis ; Aluminum Oxide/*chemical synthesis ; Anti-Bacterial Agents/metabolism ; Antineoplastic Agents/metabolism ; Cell Survival/drug effects ; Drug Carriers/*chemical synthesis ; Escherichia coli/drug effects ; HeLa Cells ; Humans ; Hydrogen-Ion Concentration ; *Metal Nanoparticles ; *Phase Transition ; Protein Binding ; Proteins/metabolism ; }, abstract = {Alumina is one of the most promising carriers for drug delivery due to the long history of its usage as a vaccine adjuvant. Sol-gel synthesis provides excellent conditions for entrapment of biomolecules within an inorganic cage providing stabilization of proteins under the extremal conditions. In this paper, we show in vitro investigation of monodisperse alumina xerogel nanocontainers (AXNCs) using bovine serum albumin as a model protein entrapped in sol-gel alumina building blocks. Particularly, dose and cell-type dependent cytotoxicity in HeLa and A549 cancer cell lines were employed as well as investigation of antibacterial effect and stability of AXNCs in different biological media. It was shown, that the release of entrapped protein could be provided only in low pH buffer (as in cancer cell cytoplasm). This property could be applied for anticancer drug development. We also discovered boehmite nanoparticles effect on horizontal gene transfer and observed the appearance of antibiotic resistance by means of exchanging of the corresponding plasmid between two different E. coli strains. The present work may help to understand better the influence of AXNCs on various biological systems, such as prokaryotic and eukaryotic cells, and the activity of AXNCs in different biological media.}, }
@article {pmid30717668, year = {2019}, author = {McDonald, ND and Regmi, A and Morreale, DP and Borowski, JD and Boyd, EF}, title = {CRISPR-Cas systems are present predominantly on mobile genetic elements in Vibrio species.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {105}, pmid = {30717668}, issn = {1471-2164}, support = {T32 GM008550/GM/NIGMS NIH HHS/United States ; 5T32GM008550/NH/NIH HHS/United States ; P20 GM103446/GM/NIGMS NIH HHS/United States ; P20GM103446/NH/NIH HHS/United States ; IOS-1656688//National Science Foundation/ ; }, mesh = {Bacterial Proteins/genetics ; CRISPR-Associated Proteins/*genetics ; *DNA Transposable Elements ; *Gene Transfer, Horizontal ; *Genomic Islands ; Phylogeny ; *Plasmids ; Sequence Analysis, DNA ; Vibrio/*genetics/metabolism ; }, abstract = {BACKGROUND: Bacteria are prey for many viruses that hijack the bacterial cell in order to propagate, which can result in bacterial cell lysis and death. Bacteria have developed diverse strategies to counteract virus predation, one of which is the clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR associated (Cas) proteins immune defense system. Species within the bacterial family Vibrionaceae are marine organisms that encounter large numbers of phages. Our goal was to determine the significance of CRISPR-Cas systems as a mechanism of defense in this group by investigating their prevalence, phylogenetic distribution, and genome context.<br><br>RESULTS: Herein, we describe all the CRISPR-Cas system types and their distribution within the family Vibrionaceae. In Vibrio cholerae genomes, we identified multiple variant type I-F systems, which were also present in 41 additional species. In a large number of Vibrio species, we identified a mini type I-F system comprised of tniQcas5cas7cas6f, which was always associated with Tn7-like transposons. The Tn7-like elements, in addition to the CRISPR-Cas system, also contained additional cargo genes such as restriction modification systems and type three secretion systems. A putative hybrid CRISPR-Cas system was identified containing type III-B genes followed by a type I-F cas6f and a type I-F CRISPR that was associated with a prophage in V. cholerae and V. metoecus strains. Our analysis identified CRISPR-Cas types I-C, I-E, I-F, II-B, III-A, III-B, III-D, and the rare type IV systems as well as cas loci architectural variants among 70 species. All systems described contained a CRISPR array that ranged in size from 3 to 179 spacers. The systems identified were present predominantly within mobile genetic elements (MGEs) such as genomic islands, plasmids, and transposon-like elements. Phylogenetic analysis of Cas proteins indicated that the CRISPR-Cas systems were acquired by horizontal gene transfer.<br><br>CONCLUSIONS: Our data show that CRISPR-Cas systems are phylogenetically widespread but sporadic in occurrence, actively evolving, and present on MGEs within Vibrionaceae.}, }
@article {pmid30717270, year = {2019}, author = {Kampf, G}, title = {Antibiotic ResistanceCan Be Enhanced in Gram-Positive Species by Some Biocidal Agents Used for Disinfection.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {8}, number = {1}, pages = {}, pmid = {30717270}, issn = {2079-6382}, abstract = {Some biocidal agents used for disinfection have been described to enhance antibiotic resistance in Gram-negative species. The aim of this review was therefore to evaluate the effect of 13 biocidal agents at sublethal concentrations on antibiotic resistance in Gram-positive species. A MEDLINE search was performed for each biocidal agent on antibiotic tolerance, antibiotic resistance, horizontal gene transfer, and efflux pump. Most data were reported with food-associated bacterial species. In cells adapted to benzalkonium chloride, a new resistance was most frequently found to ampicillin (seven species), cefotaxime and sulfamethoxazole (six species each), and ceftazidime (five species), some of them with relevance for healthcare-associated infections such as Enterococcus faecium and Enterococcus faecalis. With chlorhexidine, a new resistance was often found to imipenem (ten species) as well as cefotaxime, ceftazidime, and tetracycline (seven species each). Cross-resistance was also found with triclosan and ceftazidime (eight species), whereas it was very uncommon for didecyldimethylammonium chloride or hydrogen peroxide. No cross-resistance to antibiotics has been described after low level exposure to glutaraldehyde, ethanol, propanol, peracetic acid, octenidine, povidone iodine, sodium hypochlorite, and polyhexanide. Preference should be given to disinfectant formulations based on biocidal agents with a low or no selection pressure potential.}, }
@article {pmid30716890, year = {2019}, author = {Thumu, SCR and Halami, PM}, title = {Conjugal transfer of erm(B) and multiple tet genes from Lactobacillus spp. to bacterial pathogens in animal gut, in vitro and during food fermentation.}, journal = {Food research international (Ottawa, Ont.)}, volume = {116}, number = {}, pages = {1066-1075}, doi = {10.1016/j.foodres.2018.09.046}, pmid = {30716890}, issn = {1873-7145}, mesh = {Animals ; Bacterial Proteins/*genetics ; *Conjugation, Genetic ; Enterococcus faecalis/*genetics ; Feces/microbiology ; Fermented Foods/*microbiology ; Food Microbiology ; *Gastrointestinal Microbiome ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Intestines/*microbiology ; Limosilactobacillus reuteri/*genetics ; Ligilactobacillus salivarius/*genetics ; Male ; Rats, Wistar ; Tetracycline Resistance/*genetics ; }, abstract = {Three strains of Lactobacillus comprising Lactobacillus salivarius (CHS-1E and CH7-1E) and Lactobacillus reuteri (CH2-2) previously isolated from chicken meat were analyzed for their transferability of antibiotic resistance (AR) genes to pathogenic strains under in vivo, in vitro, and during food fermentation. For in vivo model, Albino Wistar rats were inoculated with 10[10] CFU/g/ml of Enterococcus faecalis JH2-2 (recipient). After 7 days, either of two donors L. salivarius CH7-1E or L. reuteri [harbouring erythromycin and tetracycline resistance genes] were introduced at a concentration of 10[9] CFU/ml daily for 1 week. Two days after donor introduction, there was a stable increase in the number of transconjugants in the animal faeces from 10[2] to 10[3] CFU/g and presented erm(B), tet(M), tet(L) and tet(W) in their genome like donor strains. Similar observations were made with in vitro filter mating between CHS-1E, CH2-2 and CH7-1E and E. faecalis JH2-2 with transfer frequencies of 1 × 10[-4], 3.8 × 10[-3] and 2 × 10[-3] per donor cell respectively. With the results obtained in vivo and in vitro, the AR transferability of donor strains was estimated during food fermentation (chicken sausage, fermented milk or idli batter) with pathogenic recipient strains added as contaminants. At the end of mating period, phenotypic resistance to erythromycin and tetracycline in Listeria monocytogenes and Yersinia enterocolitica strains was observed. This study showed the ability of food borne Lactobacillus in diffusing their AR traits in diverse natural environments increasing their concern of AR dissemination in the food chain when used as food additives and/or probiotics.}, }
@article {pmid30715343, year = {2019}, author = {Parajuli, P and Deimel, LP and Verma, NK}, title = {Genome Analysis of Shigella flexneri Serotype 3b Strain SFL1520 Reveals Significant Horizontal Gene Acquisitions Including a Multidrug Resistance Cassette.}, journal = {Genome biology and evolution}, volume = {11}, number = {3}, pages = {776-785}, pmid = {30715343}, issn = {1759-6653}, mesh = {*Gene Transfer, Horizontal ; *Genes, MDR ; *Genome, Bacterial ; Genomic Islands ; Phylogeny ; Shigella flexneri/*genetics/pathogenicity ; }, abstract = {Shigella flexneri is a major etiological agent of shigellosis in developing countries, primarily occurring in children under 5 years of age. We have sequenced, for the first time, the complete genome of S. flexneri serotype 3b (strain SFL1520). We used a hybrid sequencing method--both long-read MinION Flow (Oxford Nanopore Technologies) and short-read MiSeq (Illumina) sequencing to generate a high-quality reference genome. The SFL1520 chromosome was found to be ∼4.58 Mb long, with 4,729 coding sequences. Despite sharing a substantial number of genes with other publicly available S. flexneri genomes (2,803), the SFL1520 strain contains 1,926 accessory genes. The phage-related genes accounted for 8% of the SFL1520 genome, including remnants of the Sf6 bacteriophage with an intact O-acetyltransferase gene specific to serotype 3b. The SFL1520 chromosome was also found to contain a multiple-antibiotic resistance cassette conferring resistance to ampicillin, chloramphenicol, streptomycin, and tetracycline, which was potentially acquired from a plasmid via transposases. The phylogenetic analysis based on core genes showed a high level of similarity of SFL1520 with other S. flexneri serotypes; however, there were marked differences in the accessory genes of SFL1520. In particular, a large number of unique genes were identified in SFL1520 suggesting significant horizontal gene acquisition in a relatively short time period. The major virulence traits of SFL1520 (such as serotype conversion and antimicrobial resistance) were associated with horizontal gene acquisitions highlighting the role of horizontal gene transfer in S. flexneri diversity and evolution.}, }
@article {pmid30715213, year = {2019}, author = {Kundu, S and Bansal, MS}, title = {SaGePhy: an improved phylogenetic simulation framework for gene and subgene evolution.}, journal = {Bioinformatics (Oxford, England)}, volume = {35}, number = {18}, pages = {3496-3498}, doi = {10.1093/bioinformatics/btz081}, pmid = {30715213}, issn = {1367-4811}, mesh = {*Algorithms ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Phylogeny ; *Software ; }, abstract = {SUMMARY: SaGePhy is a software package for improved phylogenetic simulation of gene and subgene evolution. SaGePhy can be used to generate species trees, gene trees and subgene or (protein) domain trees using a probabilistic birth-death process that allows for gene and subgene duplication, horizontal gene and subgene transfer and gene and subgene loss. SaGePhy implements a range of important features not found in other phylogenetic simulation frameworks/software. These include (i) simulation of subgene or domain level evolution inside one or more gene trees, (ii) simultaneous simulation of both additive and replacing horizontal gene/subgene transfers and (iii) probabilistic sampling of species tree and gene tree nodes, respectively, for gene- and domain-family birth. SaGePhy is open-source, platform independent and written in Java and Python.<br><br>Executables, source code (open-source under the revised BSD license) and a detailed manual are freely available from http://compbio.engr.uconn.edu/software/sagephy/.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid30714895, year = {2019}, author = {McCarthy, CGP and Fitzpatrick, DA}, title = {Pan-genome analyses of model fungal species.}, journal = {Microbial genomics}, volume = {5}, number = {2}, pages = {}, pmid = {30714895}, issn = {2057-5858}, mesh = {Evolution, Molecular ; Fungi/*classification/genetics ; *Genome, Fungal ; Genome-Wide Association Study ; Genomics ; Phylogeny ; }, abstract = {The concept of the species 'pan-genome', the union of 'core' conserved genes and all 'accessory' non-conserved genes across all strains of a species, was first proposed in prokaryotes to account for intraspecific variability. Species pan-genomes have been extensively studied in prokaryotes, but evidence of species pan-genomes has also been demonstrated in eukaryotes such as plants and fungi. Using a previously published methodology based on sequence homology and conserved microsynteny, in addition to bespoke pipelines, we have investigated the pan-genomes of four model fungal species: Saccharomyces cerevisiae, Candida albicans, Cryptococcus neoformans var. grubii and Aspergillus fumigatus. Between 80 and 90 % of gene models per strain in each of these species are core genes that are highly conserved across all strains of that species, many of which are involved in housekeeping and conserved survival processes. In many of these species, the remaining 'accessory' gene models are clustered within subterminal regions and may be involved in pathogenesis and antimicrobial resistance. Analysis of the ancestry of species core and accessory genomes suggests that fungal pan-genomes evolve by strain-level innovations such as gene duplication as opposed to wide-scale horizontal gene transfer. Our findings lend further supporting evidence to the existence of species pan-genomes in eukaryote taxa.}, }
@article {pmid30711653, year = {2019}, author = {Dong, P and Wang, H and Fang, T and Wang, Y and Ye, Q}, title = {Assessment of extracellular antibiotic resistance genes (eARGs) in typical environmental samples and the transforming ability of eARG.}, journal = {Environment international}, volume = {125}, number = {}, pages = {90-96}, doi = {10.1016/j.envint.2019.01.050}, pmid = {30711653}, issn = {1873-6750}, mesh = {Animals ; DNA/*analysis ; Drug Resistance, Microbial/*genetics ; Environmental Pollutants/*analysis ; Genes, Bacterial ; Hospitals ; Humans ; Manure/analysis ; Medical Waste/analysis ; Sewage/*chemistry ; Swine ; Transformation, Genetic ; Wastewater/*chemistry ; }, abstract = {The emergence and spread of antibiotic resistance has pose a huge threat to both human health and environmental ecosystem. However, little is known regarding the pool of ARGs in extracellular DNA (eDNA). In this study ten ARGs (sul1, sul2, tetW, tetX, ermA, ermB, blaTEM, ampC, cat and cmr) and class I integron (intI1) in the sludge from hospital, pharmaceutical industry, wastewater treatment plant (WWTP), and swine manure, and sediment in urban lake in the form of both eDNA and intracellular DNA (iDNA) were evaluated by quantitative polymerase chain reaction (qPCR). The results showed that every gram of sludge dry weight contained from 7.31 × 10[3] to 1.16 × 10[10] copies of extracellular ARGs (eARGs) and from 1.04 × 10[5] to 2.74 × 10[12] copies of intracellular ARGs (iARGs). The sludge from hospital with the highest ratio of eARGs to total ARGs (11.02-89.63%), followed by the sediment from urban lake, implying that most of the ARGs in these regions were contributed by eARGs. The relative abundance of eARGs were higher than iARGs in sludge from WWTP and pharmaceutical industry, moreover, 1/3 and 5/9 detected eARGs were higher than the ARGs in the iDNA extracted from sludge of hospital and sediment from urban lake, respectively. Furthermore, the transforming ability of eARGs suggesting that adsorbed eARG is more preferentially coupled to the competent cells than free eARG. These findings highlight the need to focus attention on the contribution of eARGs to the dissemination of antibiotic resistance into environment, and also future needs in mitigating the spread of eARGs in the environment.}, }
@article {pmid30710232, year = {2019}, author = {de Campos Moraes, I and de Campos Rume, G and Souza Sobrinho, F and Techio, VH}, title = {Characterization of aneuploidy in interspecific hybrid between Urochloa ruziziensis (R. Germ. &amp; Evrard) Crins and Urochloa decumbens (Stapf) R. D. Webster.}, journal = {Molecular biology reports}, volume = {46}, number = {2}, pages = {1931-1940}, pmid = {30710232}, issn = {1573-4978}, mesh = {Aneuploidy ; Chimera/*genetics ; Chromosomes, Plant/genetics ; Gene Transfer, Horizontal/genetics ; Genotype ; Karyotyping/methods ; Plants/genetics ; Poaceae/*genetics/metabolism ; Polyploidy ; Trisomy/genetics ; }, abstract = {The aim of the study was to characterize the type of aneuploidy present in the hybrid Urochloa ruziziensis × Urochloa decumbens and to confirm the origin of the additional chromosomes through comparative analysis of the hybrid and parental karyotypes. C and CMA banding techniques were used for chromosome differentiation. The parental genotypes showed 36 chromosomes. The hybrid presented plants with 36 + 2 chromosomes and plants with 36 + 1 chromosomes. Urochloa ruziziensis (4x) presented four chromosomes with CMA and C bands co-located in the terminal position. In U. decumbens, four chromosomes presented terminal CMA bands, eight chromosomes were distinguished by C banding with pericentromeric and terminal bands, one chromosome with terminal band at both ends and one chromosome presented one C terminal band. For the hybrid, CMA bands were found on five chromosomes and C bands on seven chromosomes, all in terminal position. Aneuploidy was identified in pairs 3' and 4' in the hybrid plants with 36 + 2 chromosomes, characterizing it as double trisomy. The karyotype of hybrid plants with 36 + 1 chromosomes indicated elimination of the additional chromosome identified in pair 4' and maintenance of trisomy on pair 3'. The comparative analysis of karyotypes indicates that the additional chromosomes that characterize the trisomy were inherited from U. ruziziensis (artificial tetraploid).}, }
@article {pmid30708172, year = {2019}, author = {Shaikevich, E and Bogacheva, A and Rakova, V and Ganushkina, L and Ilinsky, Y}, title = {Wolbachia symbionts in mosquitoes: Intra- and intersupergroup recombinations, horizontal transmission and evolution.}, journal = {Molecular phylogenetics and evolution}, volume = {134}, number = {}, pages = {24-34}, doi = {10.1016/j.ympev.2019.01.020}, pmid = {30708172}, issn = {1095-9513}, mesh = {Aedes/microbiology ; Alleles ; Animals ; Anopheles/genetics ; *Biological Evolution ; Culicidae/*microbiology ; Databases, Genetic ; *Gene Transfer, Horizontal ; Haplotypes/genetics ; Humans ; Mosquito Vectors/microbiology ; Multilocus Sequence Typing ; Phylogeny ; *Recombination, Genetic ; Species Specificity ; *Symbiosis ; Wolbachia/*genetics ; }, abstract = {Many mosquitoes harbour Wolbachia symbionts that could affect the biology of their host in different ways. Evolutionary relationships of mosquitoes' Wolbachia infection, geographical distribution and symbiont prevalence in many mosquito species are not yet clear. Here, we present the results of Wolbachia screening of 17 mosquito species of four genera-Aedes, Anopheles, Coquillettidia and Culex collected from five regions of Eastern Europe and the Caucasus in 2012-2016. Based on multilocus sequence typing (MLST) data previously published and generated in this study, we try to reveal genetic links between mosquitoes' and other hosts' Wolbachia. The Wolbachia symbionts are found in Culex pipiens, Aedes albopictus and Coquillettidia richiardii and for the first time in Aedes cinereus and Aedes cantans, which are important vectors of human pathogens. Phylogenetic analysis demonstrated multiple origins of infection in mosquitoes although the one-allele-criterion approach revealed links among B-supergroup mosquito Wolbachia with allele content of lepidopteran hosts. The MLST gene content of strain wAlbA from the A-supergroup is linked with different ant species. Several cases of intersupergroup recombinations were found. One of them occurred in the wAlbaB strain of Aedes albopictus, which contains the coxA allele of the A-supergroup, whereas other loci, including wsp, belong to supergroup B. Other cases are revealed for non-mosquito symbionts and they exemplified genetic exchanges of A, B and F supergroups. We conclude that modern Wolbachia diversity in mosquitoes and in many other insect taxa is a recent product of strain recombination and symbiont transfers.}, }
@article {pmid30708164, year = {2019}, author = {Tian, Z and Chi, Y and Yu, B and Yang, M and Zhang, Y}, title = {Thermophilic anaerobic digestion reduces ARGs in excess sludge even under high oxytetracycline concentrations.}, journal = {Chemosphere}, volume = {222}, number = {}, pages = {305-313}, doi = {10.1016/j.chemosphere.2019.01.139}, pmid = {30708164}, issn = {1879-1298}, mesh = {Anaerobiosis ; Anti-Bacterial Agents ; Drug Resistance, Microbial/*genetics ; Gene Transfer, Horizontal ; Oxytetracycline/*analysis ; Sewage/*chemistry/microbiology ; Tetracycline Resistance/genetics ; }, abstract = {The feasibility of thermophilic anaerobic digestion (AD) for the attenuation of antibiotic resistance genes (ARGs) in biomass wastes under high antibiotic concentrations remains unclear. In this study, a thermophilic completely stirred digester (55 °C) was fed with municipal excess sludge spiked with increasing concentrations of oxytetracycline (OTC) (0-1000 mg/L) over a period of 280 days. Results showed that thermophilic AD could maintain stable methane production (338.40 ± 26.26 mL/d/gVS) even at an OTC dose of 1000 mg/L with the sludge phase OTC concentration reaching around 24,000 mg/kg. More important, the abundance of resistome detected by high-throughput quantitative PCR in the substrate was reduced (p < 0.01) by 55.54%-86.27% by thermophilic AD over the whole period. Partial canonical correspondence and network analyses showed that the reduction of ARGs was achieved mainly through two ways: eliminating the original hosts of ARGs in the substrate (from 41.74% ± 2.60% in the substrate to 12.08% ± 1.02% in digested sludge), and blocking the horizontal proliferation of ARGs in the digested sludge by reducing the abundance of mobile genetic elements and restricting their horizontal exchange within a small number of thermophilic genera. This study showed that thermophilic AD is feasible for the attenuation of ARGs in biomass even containing high level of OTC.}, }
@article {pmid30707693, year = {2019}, author = {Reiss, D and Mialdea, G and Miele, V and de Vienne, DM and Peccoud, J and Gilbert, C and Duret, L and Charlat, S}, title = {Global survey of mobile DNA horizontal transfer in arthropods reveals Lepidoptera as a prime hotspot.}, journal = {PLoS genetics}, volume = {15}, number = {2}, pages = {e1007965}, pmid = {30707693}, issn = {1553-7404}, mesh = {Animals ; Arthropods/classification/*genetics ; Baculoviridae/genetics ; *DNA Transposable Elements ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; Genome, Insect ; Lepidoptera/classification/*genetics/virology ; Models, Genetic ; Phylogeny ; Polynesia ; }, abstract = {More than any other genome components, Transposable Elements (TEs) have the capacity to move across species barriers through Horizontal Transfer (HT), with substantial evolutionary consequences. Previous large-scale surveys, based on full-genomes comparisons, have revealed the transposition mode as an important predictor of HT rates variation across TE superfamilies. However, host biology could represent another major explanatory factor, one that needs to be investigated through extensive taxonomic sampling. Here we test this hypothesis using a field collection of 460 arthropod species from Tahiti and surrounding islands. Through targeted massive parallel sequencing, we uncover patterns of HT in three widely-distributed TE superfamilies with contrasted modes of transposition. In line with earlier findings, the DNA transposons under study (TC1-Mariner) were found to transfer horizontally at the highest frequency, closely followed by the LTR superfamily (Copia), in contrast with the non-LTR superfamily (Jockey), that mostly diversifies through vertical inheritance and persists longer within genomes. Strikingly, across all superfamilies, we observe a marked excess of HTs in Lepidoptera, an insect order that also commonly hosts baculoviruses, known for their ability to transport host TEs. These results turn the spotlight on baculoviruses as major potential vectors of TEs in arthropods, and further emphasize the importance of non-vertical TE inheritance in genome evolution.}, }
@article {pmid30705673, year = {2018}, author = {Inoue, M and Nakamoto, I and Omae, K and Oguro, T and Ogata, H and Yoshida, T and Sako, Y}, title = {Structural and Phylogenetic Diversity of Anaerobic Carbon-Monoxide Dehydrogenases.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3353}, pmid = {30705673}, issn = {1664-302X}, abstract = {Anaerobic Ni-containing carbon-monoxide dehydrogenases (Ni-CODHs) catalyze the reversible conversion between carbon monoxide and carbon dioxide as multi-enzyme complexes responsible for carbon fixation and energy conservation in anaerobic microbes. However, few biochemically characterized model enzymes exist, with most Ni-CODHs remaining functionally unknown. Here, we performed phylogenetic and structure-based Ni-CODH classification using an expanded dataset comprised of 1942 non-redundant Ni-CODHs from 1375 Ni-CODH-encoding genomes across 36 phyla. Ni-CODHs were divided into seven clades, including a novel clade. Further classification into 24 structural groups based on sequence analysis combined with structural prediction revealed diverse structural motifs for metal cluster formation and catalysis, including novel structural motifs potentially capable of forming metal clusters or binding metal ions, indicating Ni-CODH diversity and plasticity. Phylogenetic analysis illustrated that the metal clusters responsible for intermolecular electron transfer were drastically altered during evolution. Additionally, we identified novel putative Ni-CODH-associated proteins from genomic contexts other than the Wood-Ljungdahl pathway and energy converting hydrogenase system proteins. Network analysis among the structural groups of Ni-CODHs, their associated proteins and taxonomies revealed previously unrecognized gene clusters for Ni-CODHs, including uncharacterized structural groups with putative metal transporters, oxidoreductases, or transcription factors. These results suggested diversification of Ni-CODH structures adapting to their associated proteins across microbial genomes.}, }
@article {pmid30705162, year = {2019}, author = {Pennisi, E}, title = {Algae suggest eukaryotes get many gifts of bacteria DNA.}, journal = {Science (New York, N.Y.)}, volume = {363}, number = {6426}, pages = {439-440}, doi = {10.1126/science.363.6426.439-b}, pmid = {30705162}, issn = {1095-9203}, mesh = {Bacteria/genetics ; DNA, Bacterial/*genetics ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Rhodophyta/*genetics/microbiology ; }, }
@article {pmid30704394, year = {2019}, author = {Bastin, BR and Schneider, SQ}, title = {Taxon-specific expansion and loss of tektins inform metazoan ciliary diversity.}, journal = {BMC evolutionary biology}, volume = {19}, number = {1}, pages = {40}, pmid = {30704394}, issn = {1471-2148}, mesh = {Amino Acid Sequence ; Animals ; *Biodiversity ; Cilia/*metabolism ; Eukaryotic Cells/metabolism ; Evolution, Molecular ; Genome ; Microtubule Proteins/chemistry/*classification/genetics ; *Phylogeny ; }, abstract = {BACKGROUND: Cilia and flagella are complex cellular structures thought to have first evolved in a last ciliated eukaryotic ancestor due to the conserved 9 + 2 microtubule doublet structure of the axoneme and associated proteins. The Tektin family of coiled-coil domain containing proteins was previously identified in cilia of organisms as diverse as green algae and sea urchin. While studies have shown that some Tektins are necessary for ciliary function, there has been no comprehensive phylogenetic survey of tektin genes. To fill this gap, we sampled tektin sequences broadly among metazoan and unicellular lineages in order to determine how the tektin gene complements evolved in over 100 different extant species.<br><br>RESULTS: Using Bayesian and Maximum Likelihood analyses, we have ascertained with high confidence that all metazoan tektins arose from a single ancestral tektin gene in the last common ancestor of metazoans and choanoflagellates. Gene duplications gave rise to two tektin genes in the metazoan ancestor, and a subsequent expansion to three and four tektin genes in early bilaterian ancestors. While all four tektin genes remained highly conserved in most deuterostome and spiralian species surveyed, most tektin genes in ecdysozoans are highly derived with extensive gene loss in several lineages including nematodes and some crustaceans. In addition, while tektin-1, -&#x2009;2, and&#xa0;-&#x2009;4 have remained as single copy genes in most lineages, tektin-3/5 has been duplicated independently several times, notably at the base of the spiralian, vertebrate and hymenopteran (Ecdysozoa) clades.<br><br>CONCLUSIONS: We provide a solid description of tektin evolution supporting one, two, three, and four ancestral tektin genes in a holozoan, metazoan, bilaterian, and nephrozoan ancestor, respectively. The isolated presence of tektin in a cryptophyte and a chlorophyte branch invokes events of horizontal gene transfer, and that the last common ciliated eukaryotic ancestor lacked a tektin gene. Reconstructing the evolutionary history of the tektin complement in each extant metazoan species enabled us to pinpoint lineage specific expansions and losses. Our analysis will help to direct future studies on Tektin function, and how gain and loss of tektin genes might have contributed to the evolution of various types of cilia and flagella.}, }
@article {pmid30703035, year = {2020}, author = {Pons, JC and Scornavacca, C and Cardona, G}, title = {Generation of Level- k LGT Networks.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {17}, number = {1}, pages = {158-164}, doi = {10.1109/TCBB.2019.2895344}, pmid = {30703035}, issn = {1557-9964}, mesh = {Computational Biology/*methods ; Computer Simulation ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; *Models, Genetic ; *Phylogeny ; }, abstract = {Phylogenetic networks provide a mathematical model to represent the evolution of a set of species where, apart from speciation, reticulate evolutionary events have to be taken into account. Among these events, lateral gene transfers need special consideration due to the asymmetry in the roles of the species involved in such an event. To take into account this asymmetry, LGT networks were introduced. Contrarily to the case of phylogenetic trees, the combinatorial structure of phylogenetic networks is much less known and difficult to describe. One of the approaches in the literature is to classify them according to their level and find generators of the given level that can be used to recursively generate all networks. In this paper, we adapt the concept of generators to the case of LGT networks. We show how these generators, classified by their level, give rise to simple LGT networks of the specified level, and how any LGT network can be obtained from these simple networks, that act as building blocks of the generic structure. The stochastic models of evolution of phylogenetic networks are also much less studied than those for phylogenetic trees. In this setting, we introduce a novel two-parameter model that generates LGT networks. Finally, we present some computer simulations using this model in order to investigate the complexity of the generated networks, depending on the parameters of the model.}, }
@article {pmid30700430, year = {2019}, author = {García-Solache, M and Rice, LB}, title = {The Enterococcus: a Model of Adaptability to Its Environment.}, journal = {Clinical microbiology reviews}, volume = {32}, number = {2}, pages = {}, pmid = {30700430}, issn = {1098-6618}, mesh = {Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Multiple, Bacterial ; Enterococcus/drug effects/genetics/*growth &amp; development ; Gene Transfer, Horizontal ; Gram-Positive Bacterial Infections/drug therapy/*microbiology ; Humans ; Microbial Sensitivity Tests ; Mutation ; }, abstract = {The genus Enterococcus comprises a ubiquitous group of Gram-positive bacteria that are of great relevance to human health for their role as major causative agents of health care-associated infections. The enterococci are resilient and versatile species able to survive under harsh conditions, making them well adapted to the health care environment. Two species cause the majority of enterococcal infections: Enterococcus faecalis and Enterococcus faecium Both species demonstrate intrinsic resistance to common antibiotics, such as virtually all cephalosporins, aminoglycosides, clindamycin, and trimethoprim-sulfamethoxazole. Additionally, a remarkably plastic genome allows these two species to readily acquire resistance to further antibiotics, such as high-level aminoglycoside resistance, high-level ampicillin resistance, and vancomycin resistance, either through mutation or by horizontal transfer of genetic elements conferring resistance determinants.}, }
@article {pmid30697673, year = {2019}, author = {Wang, Q and Xu, FZ and An, LL and Xiang, HY and Zhang, WH and Liu, GS and Liu, HB}, title = {Molecular characterization of a new recombinant brassica yellows virus infecting tobacco in China.}, journal = {Virus genes}, volume = {55}, number = {2}, pages = {253-256}, pmid = {30697673}, issn = {1572-994X}, support = {2016B02//Science Foundation for Young Scholars of Tobacco Research Institute of Chinese Academy of Agricultural Sciences/ ; ZR2017QC003//Natural Science Foundation of Shandong Province (CN)/ ; 1610232016005//Fundamental Research Funds for China Agricultural Acadamy of Sciences/ ; }, mesh = {Brassica/virology ; Gene Transfer, Horizontal/genetics ; Genome, Viral ; Genotype ; Host Specificity/genetics ; Luteoviridae/*genetics/pathogenicity ; Luteovirus/genetics ; Open Reading Frames ; *Phylogeny ; Plant Diseases/*virology ; Raphanus/virology ; Nicotiana/genetics/*virology ; }, abstract = {Brassica yellows virus (BrYV), prevalently distributed throughout mainland China and South Korea while triggering serious diseases in cruciferous crops, is proposed to be a new species in the genus Polerovirus within the family Luteoviridae. There are three distinct genotypes (BrYV-A, BrYV-B and BrYV-C) reported in cabbage and radish. Here, we describe a new BrYV isolate infecting tobacco plants in the field, which was named BrYV-NtabQJ. The complete genome sequence of BrYV-NtabQJ is 5741 nt in length, and 89% of the sequence shares higher sequence identities (about 90%) with different BrYV isolates. However, it possesses a quite divergent region within ORF5, which is more close to Beet western yellows virus (BWYV), Beet mild yellowing virus (BMYV) and Beet chlorosis virus (BChV). A significant recombination event was then detected among BrYV-NtabQJ, BrYV-B Beijng isolate (BrYV-BBJ) and BWYV Leonurus sibiricus isolate (BWYV-LS). It is proposed that BrYV-NtabQJ might be an interspecific recombinant between BrYV-BBJ and BWYV-LS, and the recombination might result in the successful aphid transmission of BrYV from cruciferous crops to tobacco. And it also poses new challenges for BrYV diagnosis and the vegetable production.}, }
@article {pmid30694700, year = {2019}, author = {Wushke, S and Froese, A and Fristensky, B and Zhang, XL and Spicer, V and Krokhin, OV and Levin, DB and Sparling, R}, title = {Genomic comparison of facultatively anaerobic and obligatory aerobic Caldibacillus debilis strains GB1 and Tf helps explain physiological differences.}, journal = {Canadian journal of microbiology}, volume = {65}, number = {6}, pages = {421-428}, doi = {10.1139/cjm-2018-0464}, pmid = {30694700}, issn = {1480-3275}, mesh = {Bacillaceae/classification/*genetics/physiology ; *Genome, Bacterial ; Genomics ; Glycolysis ; Oxidation-Reduction ; Species Specificity ; }, abstract = {Caldibacillus debilis strains GB1 and Tf display distinct phenotypes. Caldibacillus debilis GB1 is capable of anaerobic growth and can synthesize ethanol while C. debilis Tf cannot. Comparison of the GB1 and Tf genome sequences revealed that the genomes were highly similar in gene content and showed a high level of synteny. At the genome scale, there were several large sections of DNA that appeared to be from lateral gene transfer into the GB1 genome. Tf did have unique genetic content but at a much smaller scale: 300 genes in Tf verses 857 genes in GB1 that matched at ≤90% sequence similarity. Gene complement and copy number of genes for the glycolysis, tricarboxylic acid cycle, and electron transport chain pathways were identical in both strains. While Tf is an obligate aerobe, it possesses the gene complement for an anaerobic lifestyle (ldh, ak, pta, adhE, pfl). As a species, other strains of C. debilis should be expected to have the potential for anaerobic growth. Assaying the whole cell lysate for alcohol dehydrogenase activity revealed an approximately 2-fold increase in the enzymatic activity in GB1 when compared with Tf.}, }
@article {pmid30694488, year = {2019}, author = {Hardy, L and Charpentier, X}, title = {Querying Legionella Genomes Using Transposition-Sequencing.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1921}, number = {}, pages = {107-122}, doi = {10.1007/978-1-4939-9048-1_7}, pmid = {30694488}, issn = {1940-6029}, mesh = {Computational Biology ; *DNA Transposable Elements ; Data Analysis ; Genes, Bacterial ; Genes, Essential ; *Genome, Bacterial ; Genomics/*methods ; High-Throughput Nucleotide Sequencing/methods ; Legionella/*genetics ; Mutagenesis, Insertional ; }, abstract = {Transposition-sequencing (Tn-seq) has recently emerged as a powerful technique to query bacterial genomes. Tn-seq can be used to query the bacterial genome with unprecedented resolution, allowing the identification of small genes (e.g., noncoding RNA) that may be missed in conventional screening approaches. Tn-seq can be used to predict genes essential for in vitro growth and to directly identify genetic requirements for survival under multiple conditions. For instance, Tn-seq can be applied to determine the genes, and cellular processes, required to resist an antibacterial treatment or to acquire new resistance genes, to adapt to intracellular life or to compete with other bacteria. Virtually any assay that involves a selection pressure can be used to identify the associated genetic determinants. So far, genome-wide Tn-seq has not been applied to Legionella species. Here, we provide a protocol covering all the different steps to conduct a Tn-seq analysis in L. pneumophila. This includes generating a high-density library of insertional mutants, setting up a selection screen, sequencing the libraries, mapping the insertion sites, and analyzing the data to obtain the list of genes involved in surviving the applied selection.}, }
@article {pmid30692976, year = {2018}, author = {Liang, Q and Jiang, X and Hu, L and Yin, Z and Gao, B and Zhao, Y and Yang, W and Yang, H and Tong, Y and Li, W and Jiang, L and Zhou, D}, title = {Sequencing and Genomic Diversity Analysis of IncHI5 Plasmids.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3318}, pmid = {30692976}, issn = {1664-302X}, abstract = {IncHI plasmids could be divided into five different subgroups IncHI1-5. In this study, the complete nucleotide sequences of seven bla IMP- or bla VIM-carrying IncHI5 plasmids from Klebsiella pneumoniae, K. quasipneumoniae, and K. variicola were determined and compared in detail with all the other four available sequenced IncHI5 plasmids. These plasmids carried conserved IncHI5 backbones composed of repHI5B and a repFIB-like gene (replication), parABC (partition), and tra1 (conjugal transfer). Integration of a number of accessory modules, through horizontal gene transfer, at various sites of IncHI5 backbones resulted in various deletions of surrounding backbone regions and thus considerable diversification of IncHI5 backbones. Among the accessory modules were three kinds of resistance accessory modules, namely Tn10 and two antibiotic resistance islands designated ARI-A and ARI-B. These two islands, inserted at two different fixed sites (one island was at one site and the other was at a different site) of IncHI5 backbones, were derived from the prototype Tn3-family transposons Tn1696 and Tn6535, respectively, and could be further discriminated as various intact transposons and transposon-like structures. The ARI-A or ARI-B islands from different IncHI5 plasmids carried distinct profiles of antimicrobial resistance markers and associated mobile elements, and complex events of transposition and homologous recombination accounted for assembly of these islands. The carbapenemase genes bla IMP-4, bla IMP-38 and bla VIM-1 were identified within various class 1 integrons from ARI-A or ARI-B of the seven plasmids sequenced in this study. Data presented here would provide a deeper insight into diversification and evolution history of IncHI5 plasmids.}, }
@article {pmid30692672, year = {2019}, author = {Devoto, AE and Santini, JM and Olm, MR and Anantharaman, K and Munk, P and Tung, J and Archie, EA and Turnbaugh, PJ and Seed, KD and Blekhman, R and Aarestrup, FM and Thomas, BC and Banfield, JF}, title = {Megaphages infect Prevotella and variants are widespread in gut microbiomes.}, journal = {Nature microbiology}, volume = {4}, number = {4}, pages = {693-700}, pmid = {30692672}, issn = {2058-5276}, support = {R01 AI092531/AI/NIAID NIH HHS/United States ; R21 AG055777/AG/NIA NIH HHS/United States ; }, mesh = {Adult ; Animals ; Bacteria/*virology ; Bacteriophages/classification/genetics/*isolation &amp; purification ; Female ; *Gastrointestinal Microbiome ; Genome, Viral ; Humans ; Male ; Metagenome ; *Microbiota ; Middle Aged ; Papio/*microbiology ; Phylogeny ; Prevotella/classification/genetics/*virology ; Swine/*microbiology ; }, abstract = {Bacteriophages (phages) dramatically shape microbial community composition, redistribute nutrients via host lysis and drive evolution through horizontal gene transfer. Despite their importance, much remains to be learned about phages in the human microbiome. We investigated the gut microbiomes of humans from Bangladesh and Tanzania, two African baboon social groups and Danish pigs; many of these microbiomes contain phages belonging to a clade with genomes >540 kilobases in length, the largest yet reported in the human microbiome and close to the maximum size ever reported for phages. We refer to these as Lak phages. CRISPR spacer targeting indicates that Lak phages infect bacteria of the genus Prevotella. We manually curated to completion 15 distinct Lak phage genomes recovered from metagenomes. The genomes display several interesting features, including use of an alternative genetic code, large intergenic regions that are highly expressed and up to 35 putative transfer RNAs, some of which contain enigmatic introns. Different individuals have distinct phage genotypes, and shifts in variant frequencies over consecutive sampling days reflect changes in the relative abundance of phage subpopulations. Recent homologous recombination has resulted in extensive genome admixture of nine baboon Lak phage populations. We infer that Lak phages are widespread in gut communities that contain the Prevotella species, and conclude that megaphages, with fascinating and underexplored biology, may be common but largely overlooked components of human and animal gut microbiomes.}, }
@article {pmid30691393, year = {2019}, author = {Gruen, DS and Wolfe, JM and Fournier, GP}, title = {Paleozoic diversification of terrestrial chitin-degrading bacterial lineages.}, journal = {BMC evolutionary biology}, volume = {19}, number = {1}, pages = {34}, pmid = {30691393}, issn = {1471-2148}, mesh = {Animals ; Bacteria/*classification ; Base Sequence ; Bayes Theorem ; Calibration ; Chitin/*metabolism ; Chitinases/genetics ; Fossils ; Fungi/classification ; Models, Biological ; Paleontology ; *Phylogeny ; Time Factors ; }, abstract = {BACKGROUND: Establishing the divergence times of groups of organisms is a major goal of evolutionary biology. This is especially challenging for microbial lineages due to the near-absence of preserved physical evidence (diagnostic body fossils or geochemical biomarkers). Horizontal gene transfer (HGT) can serve as a temporal scaffold between microbial groups and other fossil-calibrated clades, potentially improving these estimates. Specifically, HGT to or from organisms with fossil-calibrated age estimates can propagate these constraints to additional groups that lack fossils. While HGT is common between lineages, only a small subset of HGT events are potentially informative for dating microbial groups.<br><br>RESULTS: Constrained by published fossil-calibrated studies of fungal evolution, molecular clock analyses show that multiple clades of Bacteria likely acquired chitinase homologs via HGT during the very late Neoproterozoic into the early Paleozoic. These results also show that, following these HGT events, recipient terrestrial bacterial clades likely diversified ~&#x2009;300-500 million years ago, consistent with established timescales of arthropod and plant terrestrialization.<br><br>CONCLUSIONS: We conclude that these age estimates are broadly consistent with the dispersal of chitinase genes throughout the microbial world in direct response to the evolution and ecological expansion of detrital-chitin producing groups. The convergence of multiple lines of evidence demonstrates the utility of HGT-based dating methods in microbial evolution. The pattern of inheritance of chitinase genes in multiple terrestrial bacterial lineages via HGT processes suggests that these genes, and possibly other genes encoding substrate-specific enzymes, can serve as a "standard candle" for dating microbial lineages across the Tree of Life.}, }
@article {pmid30685797, year = {2019}, author = {Nedelcu, AM}, title = {Independent evolution of complex development in animals and plants: deep homology and lateral gene transfer.}, journal = {Development genes and evolution}, volume = {229}, number = {1}, pages = {25-34}, pmid = {30685797}, issn = {1432-041X}, mesh = {Animals ; Conserved Sequence ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Plant Proteins/chemistry/genetics ; Plants/genetics ; Protein Domains ; *Sequence Homology ; Transcription Factors/chemistry/genetics ; }, abstract = {The evolution of multicellularity is a premier example of phenotypic convergence: simple multicellularity evolved independently many times, and complex multicellular phenotypes are found in several distant groups. Furthermore, both animal and plant lineages have independently reached extreme levels of morphological, functional, and developmental complexity. This study explores the genetic basis for the parallel evolution of complex multicellularity and development in the animal and green plant (i.e., green algae and land plants) lineages. Specifically, the study (i) identifies the SAND domain-a DNA-binding domain with important roles in the regulation of cell proliferation and differentiation, as unique to animals, green algae, and land plants; and (ii) suggests that the parallel deployment of this ancestral domain in similar regulatory roles could have contributed to the independent evolution of complex development in these distant groups. Given the deep animal-green plant divergence, the limited distribution of the SAND domain is best explained by invoking a lateral gene transfer (LGT) event from a green alga to an early metazoan. The presence of a sequence motif specifically shared by a family of SAND-containing transcription factors involved in the evolution of complex multicellularity in volvocine algae and two types of SAND proteins that emerged early in the evolution of animals is consistent with this scenario. Overall, these findings imply that (i) in addition to be involved in the evolution of similar phenotypes, deep homologous sequences can also contribute to shaping parallel evolutionary trajectories in distant lineages, and (ii) LGT could provide an additional source of latent homologous sequences that can be deployed in analogous roles and affect the evolutionary potentials of distantly related groups.}, }
@article {pmid30685311, year = {2019}, author = {Kwapong, AA and Stapleton, P and Gibbons, S}, title = {Inhibiting plasmid mobility: The effect of isothiocyanates on bacterial conjugation.}, journal = {International journal of antimicrobial agents}, volume = {53}, number = {5}, pages = {629-636}, doi = {10.1016/j.ijantimicag.2019.01.011}, pmid = {30685311}, issn = {1872-7913}, mesh = {Conjugation, Genetic/*drug effects ; Escherichia coli/*drug effects/*genetics ; Gene Transfer, Horizontal/*drug effects ; Humans ; Isothiocyanates/*pharmacology ; Plasmids/*metabolism ; }, abstract = {Bacterial conjugation is the main mechanism for the transfer of multiple antimicrobial resistance genes among pathogenic micro-organisms. This process may be controlled by compounds that inhibit bacterial conjugation. In this study, the effects of allyl isothiocyanate, l-sulforaphane, benzyl isothiocyanate, phenylethyl isothiocyanate and 4-methoxyphenyl isothiocyanate on the conjugation of broad-host-range plasmids harbouring various antimicrobial resistance genes in Escherichia coli were investigated, namely plasmids pKM101 (IncN), TP114 (IncI2), pUB307 (IncP) and the low-copy-number plasmid R7K (IncW). Benzyl isothiocyanate (32 mg/L) significantly reduced conjugal transfer of pKM101, TP114 and pUB307 to 0.3 ± 0.6%, 10.7 ± 3.3% and 6.5 ± 1.0%, respectively. l-sulforaphane (16 mg/L; transfer frequency 21.5 ± 5.1%) and 4-methoxyphenyl isothiocyanate (100 mg/L; transfer frequency 5.2 ± 2.8%) were the only compounds showing anti-conjugal specificity by actively reducing the transfer of R7K and pUB307, respectively.}, }
@article {pmid30685310, year = {2019}, author = {Potron, A and Bour, M and Triponney, P and Muller, J and Koebel, C and A Bonnin, R and Plésiat, P}, title = {Sequential emergence of colistin and rifampicin resistance in an OXA-72- producing outbreak strain of Acinetobacter baumannii.}, journal = {International journal of antimicrobial agents}, volume = {53}, number = {5}, pages = {669-673}, doi = {10.1016/j.ijantimicag.2019.01.012}, pmid = {30685310}, issn = {1872-7913}, mesh = {Acinetobacter Infections/epidemiology/*microbiology ; Acinetobacter baumannii/classification/*drug effects/genetics/isolation &amp; purification ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics/*metabolism ; Colistin/*pharmacology ; Conjugation, Genetic ; Cross Infection/epidemiology/microbiology ; DNA-Directed RNA Polymerases/genetics ; Disease Outbreaks ; *Drug Resistance, Bacterial ; Female ; Gene Transfer, Horizontal ; Genotype ; Humans ; Male ; Molecular Typing ; Mutation ; Plasmids/analysis ; Rifampin/*pharmacology ; Sequence Analysis, DNA ; Transcription Factors/genetics ; beta-Lactamases/*metabolism ; }, abstract = {OBJECTIVES: This study reported a hospital outbreak due to an extensively drug-resistant (XDR) OXA-72-producing strain of Acinetobacter baumannii (A. baumannii).<br><br>METHODS AND RESULTS: The isolates were found to be genotypically indistinguishable by whole-genome multiple locus sequence typing, and to belong to the international clonal complex CC2. One of these isolates sequentially developed a high resistance to colistin and rifampicin under treatment, as a result of mutations in genes pmrB and rpoB, respectively. The blaOXA-72 gene was localised on a 10-kb transferable plasmid, named pAB-STR-1, whose sequence is nearly identical to that of another plasmid previously found in Lithuanian strains, pAB120.<br><br>CONCLUSION: This report highlighted the need to carefully monitor the emergence of colistin and rifampicin resistance in patients treated for infections with multidrug-resistant A. baumannii.}, }
@article {pmid30683745, year = {2019}, author = {Huang, X and Zheng, J and Tian, S and Liu, C and Liu, L and Wei, L and Fan, H and Zhang, T and Wang, L and Zhu, G and Xu, K}, title = {Higher Temperatures Do Not Always Achieve Better Antibiotic Resistance Gene Removal in Anaerobic Digestion of Swine Manure.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {7}, pages = {}, pmid = {30683745}, issn = {1098-5336}, mesh = {Anaerobiosis/genetics ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/*genetics/pathogenicity ; Body Weight ; DNA Transposable Elements/genetics ; Digestion/physiology ; Drug Resistance, Bacterial/drug effects/*genetics/physiology ; Drug Resistance, Microbial/*genetics ; Gene Transfer, Horizontal ; Manure/*microbiology ; Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Streptococcus/genetics ; Swine ; *Temperature ; }, abstract = {This study employed high-throughput quantitative PCR and 16S rRNA sequencing to evaluate the effect of temperature and residual antibiotics on the dynamics of antibiotic resistance genes (ARGs) and microbial communities during anaerobic digestion of swine manure. The abundances of total ARGs and 16S rRNA genes significantly decreased in all of four treatments (25°C, 37°C, and 37°C with 50 mg of wet weight antibiotics of body weight, and 55°C). The abundances of most ARG types were significantly correlated with those of the 16S rRNA gene and transposase gene (P < 0.01). However, the abundances of total ARGs at 55°C were much higher than those of other treatments. Meanwhile, the microbial communities at 55°C, where the Streptococcus pathogen remained at a relatively high abundance and cellulose degraders and hydrogen producers, such as Ethanoligenens and Coprococcus bacteria, increased, were markedly different from those of other treatments. Redundancy analysis indicates that temperature, pH, and the genus Streptococcus had the highest explanation for ARG variation among experimental factors, chemical properties, and representative genera, respectively. Network analysis further showed that the genus Streptococcus contributed greatly to the higher ARG abundance at 55°C. The moderate antibiotic residue only caused a slight and transitory inhibition for microbially diverse populations and promotion for ARG abundance, probably due to the degradation of antibiotics and microbial adaptability. Our results clarify the cooperativity of gene transfer-related items on ARG variation and intensively prove that higher temperature cannot always achieve better ARG removal in anaerobic digestion unless pathogens and gene transfer elements are more efficiently inhibited.IMPORTANCE Antibiotic resistance genes (ARGs) are frequently detected with high abundance in manure-applied soils. Anaerobic digestion is one of widely used processes for animal waste treatment. Thus, it is critical to understand the potential of anaerobic digestion to attenuate ARGs. Although some previous studies recommended thermophilic digestion for ARG removal, they did not get sufficient evidence to support this view. The antibiotics applied to animals are mostly excreted through feces and urine because of incomplete metabolism. It is indispensable to know whether residual antibiotics in manure will hinder ARG attenuation in anaerobic digesters. The significance of our research is in comprehensively understanding the evolution and mechanism of ARGs in anaerobic digestion of swine manure affected by temperature and residual antibiotics, which will allow the development of an ARG elimination strategy before their release into the environment.}, }
@article {pmid30682786, year = {2019}, author = {Domingues, S and Rosário, N and Cândido, &#xc2; and Neto, D and Nielsen, KM and Da Silva, GJ}, title = {Competence for Natural Transformation Is Common among Clinical Strains of Resistant Acinetobacter spp.}, journal = {Microorganisms}, volume = {7}, number = {2}, pages = {}, pmid = {30682786}, issn = {2076-2607}, support = {n.a.//Faculty of Pharmacy University of Coimbra/ ; UID/NEU/04539/2013//FEDER and FCT/ ; }, abstract = {Horizontal gene transfer events provide the basis for extensive dissemination of antimicrobial resistance traits between bacterial populations. Conjugation is considered to be the most frequent mechanism behind new resistance acquisitions in clinical pathogens but does not fully explain the resistance patterns seen in some bacterial genera. Gene transfer by natural transformation has been described for numerous clinical isolates, including some Acinetobacter species. The main aim of this study was to determine to what extent clinical, resistant Acinetobacter spp. isolates, express competence for natural transformation. Twenty-two clinical Acinetobacter spp. isolates collected over a 16-year time period, from five different geographical separated and/or distinct Portuguese Hospitals were tested for natural transformability. Fourteen isolates, including 11 A. baumannii, 2 A. nosocomialis and 1 Acinetobacter sp., were identified as competent on semisolid media facilitating surface-motility. Competent Acinetobacter isolates were found in all the hospitals tested. Furthermore, osmolarity was shown to influence the uptake of exogenous DNA by competent A. baumannii A118. Our study demonstrates that natural competence is common among clinical isolates of Acinetobacter spp., and hence likely an important trait for resistance acquisition.}, }
@article {pmid30682344, year = {2019}, author = {Sirot, LK}, title = {On the evolutionary origins of insect seminal fluid proteins.}, journal = {General and comparative endocrinology}, volume = {278}, number = {}, pages = {104-111}, doi = {10.1016/j.ygcen.2019.01.011}, pmid = {30682344}, issn = {1095-6840}, mesh = {Animals ; *Evolution, Molecular ; Gene Expression Regulation ; Insect Proteins/*genetics/metabolism ; Organ Specificity/genetics ; Semen/*metabolism ; }, abstract = {In most cases, proteins affect the phenotype of the individual in which they are produced. However, in some cases, proteins have evolved in such a way that they are able to influence the phenotype of another individual of the same or of a different species ("influential proteins"). Examples of interspecific influential proteins include venom proteins and proteins produced by parasites that influence their hosts' physiology or behavior. Examples of intraspecific influential proteins include those produced by both mothers and fetuses that mitigate maternal resource allocation and proteins transferred to females in the seminal fluid during mating that change female physiology and behavior. Although there has been much interest in the functions and evolutionary dynamics of these influential proteins, less is known about the origin of these proteins. Where does the DNA that encodes the proteins that can impact another individual's phenotype come from and how do the proteins acquire their influential abilities? In this mini-review, I use insect seminal fluid proteins as a case study to consider the origin of intraspecific influential proteins. The existing data suggest that influential insect seminal fluid proteins arise both through co-option of existing genes (both single copy genes and gene duplicates) and de novo evolution. Other mechanisms for the origin of new insect seminal fluid proteins (e.g., retrotransoposition and horizontal gene transfer) are plausible but have not yet been demonstrated. Additional gaps in our understanding of the origin of insect seminal fluid proteins include an understanding of the cis-regulatory elements that designate expression in the male reproductive tract and of the evolutionary steps by which individual proteins come to depend on other seminal fluid proteins for their activity within the mated female.}, }
@article {pmid30680880, year = {2019}, author = {Wang, Y and Zhang, SP and Zhang, MY and Kempher, ML and Guo, DD and Han, JT and Tao, X and Wu, Y and Zhang, LQ and He, YX}, title = {The antitoxin MqsA homologue in Pseudomonas fluorescens 2P24 has a rewired regulatory circuit through evolution.}, journal = {Environmental microbiology}, volume = {21}, number = {5}, pages = {1740-1756}, doi = {10.1111/1462-2920.14538}, pmid = {30680880}, issn = {1462-2920}, support = {lzujbky-2017-151//Fundamental Research Funds for the Central Universities from Lanzhou University/International ; 17JR5RA208//Lanzhou University/International ; 17JR5RA208//Natural Science Foundation of Gansu Province/International ; 31300616//National Natural Science Foundation of China/International ; 31770535//National Natural Science Foundation of China/International ; }, mesh = {Antitoxins/genetics/metabolism ; Bacterial Proteins/genetics/*metabolism ; DNA-Binding Proteins/genetics/metabolism ; Escherichia coli/genetics/metabolism ; Escherichia coli Proteins/genetics/metabolism ; Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Operon ; Pseudomonas fluorescens/genetics/*metabolism ; }, abstract = {The mqsRA operon encodes a toxin-antitoxin pair that was characterized to participate in biofilm and persister cell formation in Escherichia coli. Notably, the antitoxin MqsA possesses a C-terminal DNA-binding domain that recognizes the [5'-AACCT(N)2-4 AGGTT-3'] motif and acts as a transcriptional regulator controlling multiple genes including the general stress response regulator RpoS. However, it is unknown how the transcriptional circuits of MqsA homologues have changed in bacteria over evolutionary time. Here, we found mqsA in Pseudomonas fluorescens (PfmqsA) is acquired through horizontal gene transfer and binds to a slightly different motif [5'-TACCCT(N)3 AGGGTA-3'], which exists upstream of the PfmqsRA operon. Interestingly, an adjacent GntR-type transcriptional regulator, which was termed AgtR, is under negative control of PfMqsA. It was further demonstrated that PfMqsA reduces production of biofilm components through AgtR, which directly regulates the pga and fap operons involved in the synthesis of extracellular polymeric substances. Moreover, through quantitative proteomics analysis, we showed AgtR is a highly pleiotropic regulator that influences up to 252 genes related to diverse processes including chemotaxis, oxidative phosphorylation and carbon and nitrogen metabolism. Taken together, our findings suggest the rewired regulatory circuit of PfMqsA influences diverse physiological aspects of P. fluorescens 2P24 via the newly characterized AgtR.}, }
@article {pmid30675192, year = {2019}, author = {Daugavet, MA and Shabelnikov, S and Shumeev, A and Shaposhnikova, T and Adonin, LS and Podgornaya, O}, title = {Features of a novel protein, rusticalin, from the ascidian Styela rustica reveal ancestral horizontal gene transfer event.}, journal = {Mobile DNA}, volume = {10}, number = {}, pages = {4}, pmid = {30675192}, issn = {1759-8753}, abstract = {BACKGROUND: The transfer of genetic material from non-parent organisms is called horizontal gene transfer (HGT). One of the most conclusive cases of HGT in metazoans was previously described for the cellulose synthase gene in ascidians.<br><br>RESULTS: In this study we identified a new protein, rusticalin, from the ascidian Styela rustica and presented evidence for its likely origin by HGT. Discernible homologues of rusticalin were found in placozoans, coral, and basal Chordates. Rusticalin was predicted to consist of two distinct regions, an N-terminal domain and a C-terminal domain. The N-terminal domain comprises two cysteine-rich repeats and shows remote similarity to the tick carboxypeptidase inhibitor. The C-terminal domain shares significant sequence similarity with bacterial MD peptidases and bacteriophage A500 L-alanyl-D-glutamate peptidase. A possible transfer of the C-terminal domain by bacteriophage was confirmed by an analysis of noncoding sequences of C. intestinalis rusticalin-like gene, which was found to contain a sequence similar to the bacteriophage A500 recombination site. Moreover, a sequence similar to the bacteriophage recombination site was found to be adjacent to the cellulose synthase catalytic subunit gene in the genome of Streptomices sp., the donor of ascidian cellulose synthase.<br><br>CONCLUSIONS: The C-terminal domain of rusticalin and rusticalin-like proteins is likely to be horizontally transferred by the bacteriophage A500. A common mechanism involving bacteriophage mediated gene transfer can be proposed for at least two HGT events in ascidians.}, }
@article {pmid30671042, year = {2018}, author = {Kang, X and Liu, C and Shen, P and Hu, L and Lin, R and Ling, J and Xiong, X and Xie, B and Liu, D}, title = {Genomic Characterization Provides New Insights Into the Biosynthesis of the Secondary Metabolite Huperzine a in the Endophyte Colletotrichum gloeosporioides Cg01.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3237}, pmid = {30671042}, issn = {1664-302X}, abstract = {A reliable source of Huperzine A (HupA) meets an urgent need due to its wide use in Alzheimer's disease treatment. In this study, we sequenced and characterized the whole genomes of two HupA-producing endophytes, Penicillium polonicum hy4 and Colletotrichum gloeosporioides Cg01, to clarify the mechanism of HupA biosynthesis. The whole genomes of hy4 and Cg01 were 33.92 and 55.77 Mb, respectively. We compared the differentially expressed genes (DEGs) between the induced group (with added extracts of Huperzia serrata) and a control group. We focused on DEGs with similar expression patterns in hy4 and Cg01. The DEGs identified in GO (Gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways were primarily located in carbon and nitrogen metabolism and nucleolus, ribosome, and rRNA processing. Furthermore, we analyzed the gene expression for HupA biosynthesis genes proposed in plants, which include lysine decarboxylase (LDC), copper amine oxidase (CAO), polyketides synthases (PKS), etc. Two LDCs, one CAO, and three PKSs in Cg01 were selected as prime candidates for further validation. We found that single candidate biosynthesis-gene knock-out did not influence the HupA production, while both LDC gene knock-out led to increased HupA production. These results reveal that HupA biosynthesis in endophytes might differ from that proposed in plants, and imply that the HupA-biosynthesis genes in endophytic fungi might co-evolve with the plant machinery rather than being acquired through horizontal gene transfer (HGT). Moreover, we analyzed the function of the differentially expressed epigenetic modification genes. HupA production of the histone acetyltransferase (HAT) deletion mutant ΔCgSAS-2 was not changed, while that of the histone methyltransferase (HMT) and histone deacetylase (HDAC) deletion mutants ΔCgClr4, ΔCgClr3, and ΔCgSir2-6 was reduced. Recovery of HupA-biosynthetic ability can be achieved by retro-complementation, demonstrating that HMT and HDACs associated with histone modification are involved in the regulation of HupA biosynthesis in endophytic fungi. This is the first report on epigenetic modification in high value secondary metabolite- producing endophytes. These findings shed new light on HupA biosynthesis and regulation in HupA-producing endophytes and are crucial for industrial production of HupA from fungi.}, }
@article {pmid30670543, year = {2019}, author = {Tran, F and Boedicker, JQ}, title = {Plasmid Characteristics Modulate the Propensity of Gene Exchange in Bacterial Vesicles.}, journal = {Journal of bacteriology}, volume = {201}, number = {7}, pages = {}, pmid = {30670543}, issn = {1098-5530}, mesh = {DNA, Bacterial/*metabolism ; Escherichia coli/*genetics/*metabolism ; Extracellular Vesicles/*metabolism ; *Gene Transfer, Horizontal ; Plasmids/*metabolism ; }, abstract = {Horizontal gene transfer is responsible for the exchange of many types of genetic elements, including plasmids. Properties of the exchanged genetic element are known to influence the efficiency of transfer via the mechanisms of conjugation, transduction, and transformation. Recently, an alternative general pathway of horizontal gene transfer has been identified, namely, gene exchange by extracellular vesicles. Although extracellular vesicles have been shown to facilitate the exchange of several types of plasmids, the influence of plasmid characteristics on genetic exchange within vesicles is unclear. Here, a set of different plasmids was constructed to systematically test the impact of plasmid properties, specifically, plasmid copy number, size, and origin of replication, on gene transfer in vesicles. The influence of each property on the production, packaging, and uptake of vesicles containing bacterial plasmids was quantified, revealing how plasmid properties modulate vesicle-mediated horizontal gene transfer. The loading of plasmids into vesicles correlates with the plasmid copy number and is influenced by characteristics that help set the number of plasmids within a cell, including size and origin of replication. Plasmid origin also has a separate impact on both vesicle loading and uptake, demonstrating that the origin of replication is a major determinant of the propensity of specific plasmids to transfer within extracellular vesicles.IMPORTANCE Extracellular vesicle formation and exchange are common within bacterial populations. Vesicles package multiple types of biomolecules, including genetic material. The exchange of extracellular vesicles containing genetic material facilitates interspecies DNA transfer and may be a promiscuous mechanism of horizontal gene transfer. Unlike other mechanisms of horizontal gene transfer, it is unclear whether characteristics of the exchanged DNA impact the likelihood of transfer in vesicles. Here, we systematically examine the influence of plasmid copy number, size, and origin of replication on the loading of DNA into vesicles and the uptake of DNA containing vesicles by recipient cells. These results reveal how each plasmid characteristic impacts gene transfer in vesicles and contribute to a greater understanding of the importance of vesicle-mediated gene exchange in the landscape of horizontal gene transfer.}, }
@article {pmid30670542, year = {2019}, author = {Hibbins, MS and Hahn, MW}, title = {The Timing and Direction of Introgression Under the Multispecies Network Coalescent.}, journal = {Genetics}, volume = {211}, number = {3}, pages = {1059-1073}, pmid = {30670542}, issn = {1943-2631}, mesh = {*Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Fungal ; *Models, Genetic ; Mycobiome ; Saccharomyces/genetics ; }, abstract = {Introgression is a pervasive biological process, and many statistical methods have been developed to infer its presence from genomic data. However, many of the consequences and genomic signatures of introgression remain unexplored from a methodological standpoint. Here, we develop a model for the timing and direction of introgression based on the multispecies network coalescent, and from it suggest new approaches for testing introgression hypotheses. We suggest two new statistics, D1 and D2, which can be used in conjunction with other information to test hypotheses relating to the timing and direction of introgression, respectively. D1 may find use in evaluating cases of homoploid hybrid speciation (HHS), while D2 provides a four-taxon test for polarizing introgression. Although analytical expectations for our statistics require a number of assumptions to be met, we show how simulations can be used to test hypotheses about introgression when these assumptions are violated. We apply the D1 statistic to genomic data from the wild yeast Saccharomyces paradoxus-a proposed example of HHS-demonstrating its use as a test of this model. These methods provide new and powerful ways to address questions relating to the timing and direction of introgression.}, }
@article {pmid30670121, year = {2019}, author = {Yu, Y and Chang, D and Guo, Q and Wang, J and Liu, C}, title = {LCT-EF258 with S17I Mutation in DprA Exhibits Horizontal Gene Transfer Deficiency After Spaceflight.}, journal = {Aerospace medicine and human performance}, volume = {90}, number = {2}, pages = {116-122}, doi = {10.3357/AMHP.5120.2019}, pmid = {30670121}, issn = {2375-6314}, mesh = {Bacterial Proteins/*genetics ; Enterococcus faecium/*genetics ; Gene Transfer, Horizontal ; Humans ; Membrane Proteins/*genetics ; Mutation ; *Space Flight ; Vancomycin Resistance/*genetics ; Weightlessness ; }, abstract = {BACKGROUND: Space is a special environment in which microgravity and cosmic rays are the primary factors that induce gene mutations of microorganisms. In our previous studies, a single point mutation in the gene dprA was found in an Enterococcus faecium strain of LCT-EF258 after spaceflight. DNA processing protein A (DprA) plays a prominent role in the horizontal transfer of genes among bacteria (such as Streptococcus pneumoniae, Helicobacter pylori, Bacillus subtilis, and Rhodobacter capsulatus). However, the function of DprA in E. faecium remains unknown. Furthermore, E. faecium could acquire antibiotic resistance through the horizontal transfer of antibiotic resistance genes, but it is unclear whether dprA mutants could affect this process in E. faecium.METHODS: In this study, we constructed a plasmid containing the vancomycin resistance gene vanA and then transferred the gene vanA into the dprA-mutant strain LCT-EF258 and the control strain LCT-EF90 using the electroporation technique. We then used Discovery Studio[TM] software to construct the 3D protein structure.RESULTS: The results showed that the horizontal transfer efficiency of the vancomycin resistance gene vanA in the dprA-mutant E. faecium decreased. And the hydrophobic core of the mutant DprA became stable and the binding affinity between the mutant DprA and ssDNA reduced.DISCUSSION: This study is an exploration of bacterial gene mutation after spaceflight. The dprA mutant could affect the ability of E. faecium to acquire exogenous resistance gene vanA, which offered us an interesting path to block the dissemination of resistance genes between strains.Yu Y, Chang D, Guo Q, Wang J, Liu C. LCT-EF258 with S171 mutation in DprA exhibits horizontal gene transfer deficiency after spaceflight. Aerosp Med Hum Perform. 2019; 90(2):116-122.}, }
@article {pmid30669685, year = {2019}, author = {Blesa, A and Sánchez, M and Sacristán-Horcajada, E and González-de la Fuente, S and Peiró, R and Berenguer, J}, title = {Into the Thermus Mobilome: Presence, Diversity and Recent Activities of Insertion Sequences Across Thermus spp.}, journal = {Microorganisms}, volume = {7}, number = {1}, pages = {}, pmid = {30669685}, issn = {2076-2607}, support = {BIO2016-77031-R//Ministerio de Ciencia e Innovaci&#xf3;n/International ; 685474//Eropean Union/International ; Institutional//Fundaci&#xf3;n Ram&#xf3;n Areces/International ; }, abstract = {A high level of transposon-mediated genome rearrangement is a common trait among microorganisms isolated from thermal environments, probably contributing to the extraordinary genomic plasticity and horizontal gene transfer (HGT) observed in these habitats. In this work, active and inactive insertion sequences (ISs) spanning the sequenced members of the genus Thermus were characterized, with special emphasis on three T. thermophilus strains: HB27, HB8, and NAR1. A large number of full ISs and fragments derived from different IS families were found, concentrating within megaplasmids present in most isolates. Potentially active ISs were identified through analysis of transposase integrity, and domestication-related transposition events of ISTth7 were identified in laboratory-adapted HB27 derivatives. Many partial copies of ISs appeared throughout the genome, which may serve as specific targets for homologous recombination contributing to genome rearrangement. Moreover, recruitment of IS1000 32 bp segments as spacers for CRISPR sequence was identified, pointing to the adaptability of these elements in the biology of these thermophiles. Further knowledge about the activity and functional diversity of ISs in this genus may contribute to the generation of engineered transposons as new genetic tools, and enrich our understanding of the outstanding plasticity shown by these thermophiles.}, }
@article {pmid30668569, year = {2019}, author = {Faucher, M and Nouvel, LX and Dordet-Frisoni, E and Sagné, E and Baranowski, E and Hygonenq, MC and Marenda, MS and Tardy, F and Citti, C}, title = {Mycoplasmas under experimental antimicrobial selection: The unpredicted contribution of horizontal chromosomal transfer.}, journal = {PLoS genetics}, volume = {15}, number = {1}, pages = {e1007910}, pmid = {30668569}, issn = {1553-7404}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Enrofloxacin/pharmacology ; *Evolution, Molecular ; Fluoroquinolones/pharmacology ; Gene Transfer, Horizontal/drug effects/*genetics ; Genome/drug effects ; Genomics ; Mycoplasma agalactiae/drug effects/*genetics ; Selection, Genetic/drug effects/*genetics ; }, abstract = {Horizontal Gene Transfer was long thought to be marginal in Mycoplasma a large group of wall-less bacteria often portrayed as minimal cells because of their reduced genomes (ca. 0.5 to 2.0 Mb) and their limited metabolic pathways. This view was recently challenged by the discovery of conjugative exchanges of large chromosomal fragments that equally affected all parts of the chromosome via an unconventional mechanism, so that the whole mycoplasma genome is potentially mobile. By combining next generation sequencing to classical mating and evolutionary experiments, the current study further explored the contribution and impact of this phenomenon on mycoplasma evolution and adaptation using the fluoroquinolone enrofloxacin (Enro), for selective pressure and the ruminant pathogen Mycoplasma agalactiae, as a model organism. For this purpose, we generated isogenic lineages that displayed different combination of spontaneous mutations in Enro target genes (gyrA, gyrB, parC and parE) in association to gradual level of resistance to Enro. We then tested whether these mutations can be acquired by a susceptible population via conjugative chromosomal transfer knowing that, in our model organism, the 4 target genes are scattered in three distinct and distant loci. Our data show that under antibiotic selective pressure, the time scale of the mutational pathway leading to high-level of Enro resistance can be readily compressed into a single conjugative step, in which several EnroR alleles were transferred from resistant to susceptible mycoplasma cells. In addition to acting as an accelerator for antimicrobial dissemination, mycoplasma chromosomal transfer reshuffled genomes beyond expectations and created a mosaic of resistant sub-populations with unpredicted and unrelated features. Our findings provide insights into the process that may drive evolution and adaptability of several pathogenic Mycoplasma spp. via an unconventional conjugative mechanism.}, }
@article {pmid30661218, year = {2019}, author = {Boháčová, M and Pazlarová, J and Fuchsová, V and Švehláková, T and Demnerová, K}, title = {Quantitative evaluation of biofilm extracellular DNA by fluorescence-based techniques.}, journal = {Folia microbiologica}, volume = {64}, number = {4}, pages = {567-577}, doi = {10.1007/s12223-019-00681-8}, pmid = {30661218}, issn = {1874-9356}, support = {MSMT No 20-SVV/2016//Ministerstvo ?kolstv?, Ml?de?e a T?lov?chovy/ ; GA?R 17-15936S//Grantov? Agentura ?esk? Republiky/ ; }, mesh = {*Biofilms ; Biological Transport ; DNA, Bacterial/chemistry/genetics/metabolism ; Extracellular Space/*microbiology ; Humans ; Listeria monocytogenes/chemistry/*genetics/physiology ; Listeriosis/*microbiology ; Microscopy, Confocal ; Staphylococcal Infections/microbiology ; Staphylococcus aureus/chemistry/*genetics/physiology ; }, abstract = {The formation of a hardly removable biofilm in food processing and clinical settings calls for a deeper understanding of composition of the matrix that protects the biofilm cells, as the crucial matrix component is extracellular DNA (eDNA), participating in adhesion, aggregation and penetration reduction, yet serving as a horizontal gene transfer reservoir. Therefore, we evaluated eDNA release from the biofilm of two pathogens, Listeria monocytogenes and Staphylococcus aureus, with respect to their origin under different culturing condition. Primarily, the biofilms were observed by confocal laser scanning microscopy (CLSM) under conditions mimicking the food processing environment and human body. The eDNA was quantitatively characterised based on its area by IMARIS. Next, the eDNA content and biofilm formation were quantified by spectrophotometry. Data from both sets of experiments were statistically evaluated. The eDNA release varied between the microorganism, culturing conditions and the origin of strains. Independent of the method used, the clinical strains of S. aureus released more eDNA than the food related strains at 37 °C. eDNA content can be crucial discriminating matrix component between food related and clinical strains. Deeper understanding of the eDNA role in such a phenomenon could facilitate the design of effective strategy for biofilm disruption.}, }
@article {pmid30660368, year = {2019}, author = {Miles, JA and Machattou, P and Nevin-Jones, D and Webb, ME and Millard, A and Scanlan, DJ and Taylor, PC}, title = {Identification of a cyanobacterial aldehyde dehydrogenase that produces retinoic acid in vitro.}, journal = {Biochemical and biophysical research communications}, volume = {510}, number = {1}, pages = {27-34}, doi = {10.1016/j.bbrc.2018.12.171}, pmid = {30660368}, issn = {1090-2104}, mesh = {Aldehyde Dehydrogenase/*metabolism ; Cyanobacteria/*enzymology/metabolism ; Evolution, Molecular ; Phylogeny ; Tretinoin/*metabolism ; }, abstract = {Retinoic acid signalling is generally considered to be of animal origin. Recently, retinoic acid has been identified in cyanobacteria, yet no mechanism for its production has been identified. Here, we characterise for the first time a cyanobacterial aldehyde dehydrogenase that produces retinoic acid in vitro. Our computational studies suggest that the cyanobacterial aldehyde dehydrogenase resembles an ancestor of both eukaryotic aldehyde dehydrogenase 1 and aldehyde dehydrogenase 2. The Chlorogloeopsis fritschii aldehyde dehydrogenase described here may find applications in synthetic production of retinoic acid as well as contributing to our understanding of retinoid synthesis in cyanobacteria.}, }
@article {pmid30659146, year = {2019}, author = {Gomez-Valero, L and Rusniok, C and Carson, D and Mondino, S and Pérez-Cobas, AE and Rolando, M and Pasricha, S and Reuter, S and Demirtas, J and Crumbach, J and Descorps-Declere, S and Hartland, EL and Jarraud, S and Dougan, G and Schroeder, GN and Frankel, G and Buchrieser, C}, title = {More than 18,000 effectors in the Legionella genus genome provide multiple, independent combinations for replication in human cells.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {6}, pages = {2265-2273}, pmid = {30659146}, issn = {1091-6490}, support = {G1001729/MRC_/Medical Research Council/United Kingdom ; MR/L018225/1/MRC_/Medical Research Council/United Kingdom ; MR/P028225/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Bacterial Proteins/chemistry/genetics ; Bacterial Secretion Systems/genetics ; Computational Biology/methods ; Evolution, Molecular ; *Genome, Bacterial ; Genomics/methods ; Humans ; Intracellular Space/microbiology ; Legionella/classification/*physiology ; Legionellosis/*microbiology ; Phylogeny ; Protein Domains ; }, abstract = {The genus Legionella comprises 65 species, among which Legionella pneumophila is a human pathogen causing severe pneumonia. To understand the evolution of an environmental to an accidental human pathogen, we have functionally analyzed 80 Legionella genomes spanning 58 species. Uniquely, an immense repository of 18,000 secreted proteins encoding 137 different eukaryotic-like domains and over 200 eukaryotic-like proteins is paired with a highly conserved type IV secretion system (T4SS). Specifically, we show that eukaryotic Rho- and Rab-GTPase domains are found nearly exclusively in eukaryotes and Legionella Translocation assays for selected Rab-GTPase proteins revealed that they are indeed T4SS secreted substrates. Furthermore, F-box, U-box, and SET domains were present in >70% of all species, suggesting that manipulation of host signal transduction, protein turnover, and chromatin modification pathways are fundamental intracellular replication strategies for legionellae. In contrast, the Sec-7 domain was restricted to L. pneumophila and seven other species, indicating effector repertoire tailoring within different amoebae. Functional screening of 47 species revealed 60% were competent for intracellular replication in THP-1 cells, but interestingly, this phenotype was associated with diverse effector assemblages. These data, combined with evolutionary analysis, indicate that the capacity to infect eukaryotic cells has been acquired independently many times within the genus and that a highly conserved yet versatile T4SS secretes an exceptional number of different proteins shaped by interdomain gene transfer. Furthermore, we revealed the surprising extent to which legionellae have coopted genes and thus cellular functions from their eukaryotic hosts, providing an understanding of how dynamic reshuffling and gene acquisition have led to the emergence of major human pathogens.}, }
@article {pmid30657445, year = {2019}, author = {Wilson, K and Ely, B}, title = {Analyses of four new Caulobacter Phicbkviruses indicate independent lineages.}, journal = {The Journal of general virology}, volume = {100}, number = {2}, pages = {321-331}, pmid = {30657445}, issn = {1465-2099}, support = {R25 GM076277/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteriophages/*classification/genetics/*isolation &amp; purification ; Caulobacter/*virology ; Evolution, Molecular ; Gene Order ; Gene Transfer, Horizontal ; Genes, Viral ; *Genome, Viral ; Genomics ; Phylogeny ; Sequence Homology, Nucleic Acid ; }, abstract = {Bacteriophages with genomes larger than 200 kbp are considered giant phages, and the giant Phicbkviruses are the most frequently isolated Caulobacter crescentus phages. In this study, we compare six bacteriophage genomes that differ from the genomes of the majority of Phicbkviruses. Four of these genomes are much larger than those of the rest of the Phicbkviruses, with genome sizes that are more than 250 kbp. A comparison of 16 Phicbkvirus genomes identified a 'core genome' of 69 genes that is present in all of these Phicbkvirus genomes, as well as shared accessory genes and genes that are unique for each phage. Most of the core genes are clustered into the regions coding for structural proteins or those involved in DNA replication. A phylogenetic analysis indicated that these 16 CaulobacterPhicbkvirus genomes are related, but they represent four distinct branches of the Phicbkvirus genomic tree with distantly related branches sharing little nucleotide homology. In contrast, pairwise comparisons within each branch of the phylogenetic tree showed that more than 80 % of the entire genome is shared among phages within a group. This conservation of the genomes within each branch indicates that horizontal gene transfer events between the groups are rare. Therefore, the Phicbkvirus genus consists of at least four different phylogenetic branches that are evolving independently from one another. One of these branches contains a 27-gene inversion relative to the other three branches. Also, an analysis of the tRNA genes showed that they are relatively mobile within the Phicbkvirus genus.}, }
@article {pmid30654542, year = {2019}, author = {Woodman, M and Haeusler, IL and Grandjean, L}, title = {Tuberculosis Genetic Epidemiology: A Latin American Perspective.}, journal = {Genes}, volume = {10}, number = {1}, pages = {}, pmid = {30654542}, issn = {2073-4425}, support = {201470/Z/16/Z//Wellcome Trust/United Kingdom ; }, mesh = {Drug Resistance, Bacterial ; Humans ; Mycobacterium tuberculosis/drug effects/*genetics/pathogenicity ; South America ; Tuberculosis/*epidemiology/microbiology/transmission ; }, abstract = {There are an estimated 10 million new cases of tuberculosis worldwide annually, with 282,000 new or relapsed cases each year reported from the Americas. With improvements in genome sequencing technology, it is now possible to study the genetic diversity of tuberculosis with much greater resolution. Although tuberculosis bacteria do not engage in horizontal gene transfer, the genome is far more variable than previously thought. The study of genome-wide variation in tuberculosis has improved our understanding of the evolutionary origins of tuberculosis, the arrival of tuberculosis in Latin America, the genetic determinants of drug resistance, and lineage-specific associations with important clinical phenotypes. This article reviews what is known about the arrival of tuberculosis in Latin America, the genetic diversity of tuberculosis in Latin America, and the genotypic determinants of clinical phenotypes.}, }
@article {pmid30651609, year = {2019}, author = {Boyd, JA and Jungbluth, SP and Leu, AO and Evans, PN and Woodcroft, BJ and Chadwick, GL and Orphan, VJ and Amend, JP and Rappé, MS and Tyson, GW}, title = {Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi.}, journal = {The ISME journal}, volume = {13}, number = {5}, pages = {1269-1279}, pmid = {30651609}, issn = {1751-7370}, mesh = {Archaeal Proteins/*genetics/metabolism ; Butanes/metabolism ; Euryarchaeota/classification/*enzymology/*genetics/metabolism ; *Evolution, Molecular ; Metagenome ; Metagenomics ; Methane/metabolism ; Oxidation-Reduction ; Oxidoreductases/*genetics/metabolism ; Phylogeny ; Seawater/microbiology ; }, abstract = {The methyl-coenzyme M reductase (MCR) complex is a key enzyme in archaeal methane generation and has recently been proposed to also be involved in the oxidation of short-chain hydrocarbons including methane, butane, and potentially propane. The number of archaeal clades encoding the MCR continues to grow, suggesting that this complex was inherited from an ancient ancestor, or has undergone extensive horizontal gene transfer. Expanding the representation of MCR-encoding lineages through metagenomic approaches will help resolve the evolutionary history of this complex. Here, a near-complete Archaeoglobi metagenome-assembled genome (MAG; Ca. Polytropus marinifundus gen. nov. sp. nov.) was recovered from the deep subseafloor along the Juan de Fuca Ridge flank that encodes two divergent McrABG operons similar to those found in Ca. Bathyarchaeota and Ca. Syntrophoarchaeum MAGs. Ca. P. marinifundus is basal to members of the class Archaeoglobi, and encodes the genes for β-oxidation, potentially allowing an alkanotrophic metabolism similar to that proposed for Ca. Syntrophoarchaeum. Ca. P. marinifundus also encodes a respiratory electron transport chain that can potentially utilize nitrate, iron, and sulfur compounds as electron acceptors. Phylogenetic analysis suggests that the Ca. P. marinifundus MCR operons were horizontally transferred, changing our understanding of the evolution and distribution of this complex in the Archaea.}, }
@article {pmid30649343, year = {2019}, author = {Morroni, G and Brenciani, A and Litta-Mulondo, A and Vignaroli, C and Mangiaterra, G and Fioriti, S and Citterio, B and Cirioni, O and Giovanetti, E and Biavasco, F}, title = {Characterization of a new transferable MDR plasmid carrying the pbp5 gene from a clade B commensal Enterococcus faecium.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {74}, number = {4}, pages = {843-850}, doi = {10.1093/jac/dky549}, pmid = {30649343}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/pharmacology ; Blotting, Southern ; Chromosome Mapping ; Conjugation, Genetic ; *Drug Resistance, Multiple, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Enterococcus faecium/classification/*drug effects/*genetics/isolation &amp; purification ; *Gene Transfer, Horizontal ; Genes, Bacterial ; *Genotype ; Healthy Volunteers ; High-Throughput Nucleotide Sequencing ; Humans ; Listeria/genetics ; Methyltransferases/genetics ; Microbial Sensitivity Tests ; Penicillin-Binding Proteins/*genetics ; *Plasmids ; Real-Time Polymerase Chain Reaction ; }, abstract = {OBJECTIVES: To evaluate the transferability of antibiotic resistance from an MDR clade B Enterococcus faecium and to characterize the genetic elements involved.<br><br>METHODS: The erm(B)-positive strain E. faecium 37BA (donor) and strains E. faecium 64/3 and Listeria welshimeri 11857RF (recipients) were used in mating experiments. Donors and transconjugants were characterized using MIC assays, PFGE, Southern blotting and hybridization, quantitative RT-PCR (RT-qPCR), next-generation sequencing and PCR mapping.<br><br>RESULTS: One E. faecium and one L. welshimeri transconjugant were selected for in-depth investigation. Both acquired an &#x223c;40&#x2009;kb plasmid carrying erm(B). An additional plasmid of &#x223c;200&#x2009;kb, encoding the full conjugation machinery, was detected in the donor and in the E. faecium transconjugant. Next-generation sequencing revealed a new 40&#xa0;396&#x2009;bp plasmid that was designated pEf37BA; it contained 10 antibiotic resistance genes, tet(M), tet(L), erm(B), aadE, sat4, aphA, spw, lsa(E), lnu(B) and pbp5, resulting from the recombination of pM7M2 of E. faecium with an MDR chromosomal region of Erysipelothrix rhusiopathiae. A pbp5-carrying circular form was also detected. The PBP5 amino acid sequence differed from the C46 variant by two mutations (S39T and D644N). Its expression was documented in both transconjugants. pEf37BA persisted in the absence of selective pressure.<br><br>CONCLUSIONS: The MDR clade B E. faecium plasmid, deriving from the recombination of two different resistance regions, carried a pbp5 element and was transferable to different bacterial species. This finding further documents the dissemination of ampicillin resistance among community-associated E. faecium and the key role of commensal strains in the spread of antibiotic resistance.}, }
@article {pmid30647161, year = {2019}, author = {Apicella, MA}, title = {Commensal Bacteria: Not Just Innocent Bystanders.}, journal = {mBio}, volume = {10}, number = {1}, pages = {}, pmid = {30647161}, issn = {2150-7511}, support = {P30 DK054759/DK/NIDDK NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents ; *Anti-Infective Agents ; Bacterial Proteins/genetics ; Gene Expression Regulation, Bacterial ; *Neisseria gonorrhoeae ; Repressor Proteins/genetics ; }, abstract = {Neisseria gonorrhoeae is quickly becoming untreatable due to its acquisition of resistance to multiple antimicrobials. It is vital that we begin to understand the mechanisms by which this is occurring. The paper by C. E. Rouquette-Loughlin, J. L. Reimche, J. T. Balthazar, V. Dhulipala, et al. (mBio 9:e02281-18, https://doi.org/10.1128/mBio.02281-18) has shown that horizontal transfer of DNA from a nasopharyngeal commensal, Neisseria polysaccharea, has resulted in multiple sequence changes in the mtr locus that affect both regulatory and structural regions of the MtrCDE pump, resulting in low-level azithromycin resistance. Studies such as this are increasingly important in our understanding of the movement of resistance between species and for devising strategies to overcome such events.}, }
@article {pmid30645638, year = {2019}, author = {Agersø, Y and Bjerre, K and Brockmann, E and Johansen, E and Nielsen, B and Siezen, R and Stuer-Lauridsen, B and Wels, M and Zeidan, AA}, title = {Putative antibiotic resistance genes present in extant Bacillus licheniformis and Bacillus paralicheniformis strains are probably intrinsic and part of the ancient resistome.}, journal = {PloS one}, volume = {14}, number = {1}, pages = {e0210363}, pmid = {30645638}, issn = {1932-6203}, mesh = {Animals ; Bacillus/classification/*drug effects/*genetics ; Bacillus licheniformis/classification/*drug effects/*genetics ; Bacterial Proteins/genetics ; Chloramphenicol Resistance/genetics ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/*genetics ; Erythromycin/pharmacology ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genome, Bacterial ; Humans ; Microbial Sensitivity Tests ; Models, Genetic ; Multilocus Sequence Typing ; Phylogeny ; Streptomycin/pharmacology ; }, abstract = {Whole-genome sequencing and phenotypic testing of 104 strains of Bacillus licheniformis and Bacillus paralicheniformis from a variety of sources and time periods was used to characterize the genetic background and evolution of (putative) antimicrobial resistance mechanisms. Core proteins were identified in draft genomes and a phylogenetic analysis based on single amino acid polymorphisms allowed the species to be separated into two phylogenetically distinct clades with one outlier. Putative antimicrobial resistance genes were identified and mapped. A chromosomal ermD gene was found at the same location in all B. paralichenformis and in 27% of B. licheniformis genomes. Erythromycin resistance correlated very well with the presence of ermD. The putative streptomycin resistance genes, aph and aadK, were found in the chromosome of all strains as adjacent loci. Variations in amino acid sequence did not correlate with streptomycin susceptibility although the species were less susceptible than other Bacillus species. A putative chloramphenicol resistance gene (cat), encoding a novel chloramphenicol acetyltransferase protein was also found in the chromosome of all strains. Strains encoding a truncated CAT protein were sensitive to chloramphenicol. For all four resistance genes, the diversity and genetic context followed the overall phylogenetic relationship. No potentially mobile genetic elements were detected in their vicinity. Moreover, the genes were only distantly related to previously-described cat, aph, aad and erm genes present on mobile genetic elements or in other species. Thus, these genes are suggested to be intrinsic to B. licheniformis and B. paralicheniformis and part of their ancient resistomes. Since there is no evidence supporting horizontal transmission, these genes are not expected to add to the pool of antibiotic resistance elements considered to pose a risk to human or animal health. Whole-genome based phylogenetic and sequence analysis, combined with phenotypic testing, is proposed to be suitable for determining intrinsic resistance and evolutionary relationships.}, }
@article {pmid30643213, year = {2019}, author = {Ronda, C and Chen, SP and Cabral, V and Yaung, SJ and Wang, HH}, title = {Metagenomic engineering of the mammalian gut microbiome in situ.}, journal = {Nature methods}, volume = {16}, number = {2}, pages = {167-170}, pmid = {30643213}, issn = {1548-7105}, support = {DP5 OD009172/OD/NIH HHS/United States ; T32 GM007367/GM/NIGMS NIH HHS/United States ; R01 DK118044/DK/NIDDK NIH HHS/United States ; R01 AI132403/AI/NIAID NIH HHS/United States ; F30 DK111145/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Cell Separation ; Escherichia coli/genetics ; Female ; Flow Cytometry ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology/physiology ; Gene Transfer Techniques ; Genome ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; Mice ; Mice, Inbred C57BL ; Microbiota/*genetics ; Plasmids/genetics ; Protein Engineering/*methods ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Engineering of microbial communities in open environments remains challenging. Here we describe a platform used to identify and modify genetically tractable mammalian microbiota by engineering community-wide horizontal gene transfer events in situ. With this approach, we demonstrate that diverse taxa in the mouse gut microbiome can be modified directly with a desired genetic payload. In situ microbiome engineering in living animals allows novel capabilities to be introduced into established communities in their native milieu.}, }
@article {pmid30642585, year = {2019}, author = {Pan, Z and Liu, J and Zhang, Y and Chen, S and Ma, J and Dong, W and Wu, Z and Yao, H}, title = {A novel integrative conjugative element mediates transfer of multi-drug resistance between Streptococcus suis strains of different serotypes.}, journal = {Veterinary microbiology}, volume = {229}, number = {}, pages = {110-116}, doi = {10.1016/j.vetmic.2018.11.028}, pmid = {30642585}, issn = {1873-2542}, mesh = {*Conjugation, Genetic ; *Drug Resistance, Multiple, Bacterial ; Gene Transfer, Horizontal ; *Serogroup ; Streptococcus suis/*drug effects/genetics ; }, abstract = {Streptococcus suis represents a key antibiotic resistance gene reservoir and an important pathogen for humans and animals. Resistance can be spread through horizontal gene transfer of chromosome-borne mobile genetic elements; however, the exact mechanism by which this occurs remains poorly understood. In the present study, we identified and characterized a novel 82-kb integrative conjugative element (ICE) named ICESsuCZ130302 from the virulent S. suis strain CZ130302. It carries genes that provide resistance to multiple antibiotics, such as tetracycline, doxycycline, erythromycin, lincomycin, neomycin, and kanamycin. It also contains a nisin biosynthesis gene cluster, a toxin-antitoxin system, a type IV secretion system, and an integrase and excisase system. The mobile element can be excised from the chromosome, circulized, and transferred via conjugation from serotype Chz strain CZ130302 to serotype 2 strain P1/7, where it confers resistance to the aforementioned antimicrobial agents. The full length ICE, where multiple antimicrobial resistance genes accumulated, was further identified to be naturally transferred between different serotypes strains of S. suis. This finding illustrates how such elements represent a potential means by which antimicrobial resistance is introduced to a wide range of bacteria of veterinary and medical significance.}, }
@article {pmid30641258, year = {2019}, author = {Ding, J and Zhu, D and Hong, B and Wang, HT and Li, G and Ma, YB and Tang, YT and Chen, QL}, title = {Long-term application of organic fertilization causes the accumulation of antibiotic resistome in earthworm gut microbiota.}, journal = {Environment international}, volume = {124}, number = {}, pages = {145-152}, doi = {10.1016/j.envint.2019.01.017}, pmid = {30641258}, issn = {1873-6750}, mesh = {Animals ; Anti-Bacterial Agents/analysis/*pharmacology ; Bacteria/*drug effects ; Drug Resistance, Microbial/*drug effects/genetics ; Fertilizers/analysis/*toxicity ; Gastrointestinal Microbiome/*drug effects ; Genes, Bacterial ; Manure ; Oligochaeta/drug effects/*microbiology ; Real-Time Polymerase Chain Reaction ; Sewage ; Soil/chemistry ; Soil Pollutants/*toxicity ; }, abstract = {Antibiotic resistance genes (ARGs), prevalent across multiple environmental media, threaten human health worldwide and are considered emerging environmental contaminants. Earthworm gut, a niche for bacteria to survive, represents a potential reservoir for ARGs in soil. However, the compositions of ARGs in the earthworm gut microbiota remain elusive, especially under field conditions. In this study, we applied high-throughput quantitative PCR to profile the ARGs in the gut microbiota of earthworms after chronic exposure to fertilizers. To elucidate the factors that impact the ARGs composition, the bacterial community of gut microbiota, mobile genetic elements (MGEs), soil (nutrients, heavy metals, and antibiotics) and the properties of gut content (pH and nutrients) were analyzed. A total of 98 subtypes among 9 major types of ARGs, and 3 different MGEs were detected in the gut microbiota of earthworms. Organic fertilizer (sewage sludge and chicken manure) application significantly increased the diversity and abundance of ARGs. Of the 1123 identified operational taxonomic units (OTUs) at 97% similarity cutoff, most of them were assigned to Firmicutes (55.5%) and Proteobacteria (33.6%) in earthworm gut microbiota. Long-term organic fertilization slightly changed the microbiota composition, but did not impact the diversity. Partial redundancy analysis (pRDA) revealed that bacterial community, combined with environmental factors (soil and gut content properties) and MGEs, explained 72% of the variations of ARGs in the earthworm gut. Furthermore, the co-occurrence pattern between ARGs and MGEs indicated that horizontal gene transfer via MGEs may occur in the earthworm gut. These findings improve the current understanding of the dynamics of soil fauna-associated ARGs and the gut microbiota of earthworms may be an underappreciated hotspot for ARGs in the environment.}, }
@article {pmid30641219, year = {2019}, author = {Dubin, A and Chi, SI and Emblem, &#xc5; and Moum, T and Johansen, SD}, title = {Deep-water sea anemone with a two-chromosome mitochondrial genome.}, journal = {Gene}, volume = {692}, number = {}, pages = {195-200}, doi = {10.1016/j.gene.2018.12.074}, pmid = {30641219}, issn = {1879-0038}, mesh = {Animals ; Biological Evolution ; *Chromosomes ; Electron Transport Complex IV/genetics ; Gene Transfer, Horizontal ; *Genome, Mitochondrial ; Introns ; Oxidative Phosphorylation ; Phylogeny ; RNA, Ribosomal/genetics ; Sea Anemones/*genetics ; }, abstract = {Mitochondrial genome organization of sea anemones appears conserved among species and families, and is represented by a single circular DNA molecule of 17 to 21 kb. The mitochondrial gene content corresponds to the same 13 protein components of the oxidative phosphorylation (OxPhos) system as in vertebrates. Hallmarks, however, include a highly reduced tRNA gene repertoire and the presence of autocatalytic group I introns. Here we demonstrate that the mitochondrial genome of the deep-water sea anemone Protanthea simplex deviates significantly from that of other known sea anemones. The P. simplex mitochondrial genome contains a heavily scrambled order of genes that are coded on both DNA strands and organized along two circular mito-chromosomes, MCh-I and MCh-II. We found MCh-I to be representative of the prototypic sea anemone mitochondrial genome, encoding 12 OxPhos proteins, two ribosomal RNAs, two transfer RNAs, and a group I intron. In contrast, MCh-II was found to be a laterally transferred plasmid-like DNA carrying the conserved cytochrome oxidase II gene and a second allele of the small subunit ribosomal RNA gene.}, }
@article {pmid30638045, year = {2019}, author = {Srinivasan, K and Buys, EM}, title = {Insights into the role of bacteria in vitamin A biosynthesis: Future research opportunities.}, journal = {Critical reviews in food science and nutrition}, volume = {59}, number = {19}, pages = {3211-3226}, doi = {10.1080/10408398.2018.1546670}, pmid = {30638045}, issn = {1549-7852}, mesh = {Animals ; Bacteria/*metabolism ; Gastrointestinal Microbiome ; Humans ; Vitamin A/*biosynthesis ; Vitamin A Deficiency ; }, abstract = {Significant efforts have been made to address the hidden hunger challenges due to iron, zinc, iodine, and vitamin A since the beginning of the 21st century. Prioritizing the vitamin A deficiency (VAD) disorders, many countries are looking for viable alternative strategies such as biofortification. One of the leading causes of VAD is the poor bioconversion of β-carotene into retinoids. This review is focused on the opportunities of bacterial biosynthesis of retinoids, in particular, through the gut microbiota. The proposed hypothesis starts with the premise that an animal can able to store and timely convert carotenoids into retinoids in the liver and intestinal tissues. This theory is experimental with many scientific insights. The syntrophic metabolism, potential crosstalk of bile acids, lipocalins and lipopolysaccharides of gut microbiota are reported to contribute significantly to the retinoid biosynthesis. The gut bacteria respond to these kinds of factors by genetic restructuring driven mainly by events like horizontal gene transfer. A phylogenetic analysis of β-carotene 15, 15'-mono (di) oxygenase enzymes among a selected group of prokaryotes and eukaryotes was carried out to validate the hypotheses. Shedding light on the probiotic strategies through non-genetically modified organism such as gut bacteria capable of synthesizing vitamin A would address the VAD disorders.}, }
@article {pmid30635076, year = {2019}, author = {Koonin, EV and Yutin, N}, title = {Evolution of the Large Nucleocytoplasmic DNA Viruses of Eukaryotes and Convergent Origins of Viral Gigantism.}, journal = {Advances in virus research}, volume = {103}, number = {}, pages = {167-202}, doi = {10.1016/bs.aivir.2018.09.002}, pmid = {30635076}, issn = {1557-8399}, mesh = {*Biological Evolution ; DNA ; DNA Viruses/classification/*physiology ; Eukaryotic Cells/virology ; Genome Size ; Genome, Viral ; Giant Viruses/*physiology ; Phylogeny ; *Protein Biosynthesis ; Viral Proteins/genetics ; }, abstract = {The Nucleocytoplasmic Large DNA Viruses (NCLDV) of eukaryotes (proposed order "Megavirales") comprise an expansive group of eukaryotic viruses that consists of the families Poxviridae, Asfarviridae, Iridoviridae, Ascoviridae, Phycodnaviridae, Marseilleviridae, Pithoviridae, and Mimiviridae, as well as Pandoraviruses, Molliviruses, and Faustoviruses that so far remain unaccounted by the official virus taxonomy. All these viruses have double-stranded DNA genomes that range in size from about 100 kilobases (kb) to more than 2.5 megabases. The viruses with genomes larger than 500kb are informally considered "giant," and the largest giant viruses surpass numerous bacteria and archaea in both particle and genome size. The discovery of giant viruses has been highly unexpected and has changed the perception of viral size and complexity, and even, arguably, the entire concept of a virus. Given that giant viruses encode multiple proteins that are universal among cellular life forms and are components of the translation system, the quintessential cellular molecular machinery, attempts have been made to incorporate these viruses in the evolutionary tree of cellular life. Moreover, evolutionary scenarios of the origin of giant viruses from a fourth, supposedly extinct domain of cellular life have been proposed. However, despite all the differences in the genome size and gene repertoire, the NCLDV can be confidently defined as monophyletic group, on the strength of the presence of about 40 genes that can be traced back to their last common ancestor. Using several most strongly conserved genes from this ancestral set, a well-resolved phylogenetic tree of the NCLDV was built and employed as the scaffold to reconstruct the history of gene gain and loss throughout the course of the evolution of this group of viruses. This reconstruction reveals extremely dynamic evolution that involved extensive gene gain and loss in many groups of viruses and indicates that giant viruses emerged independently in several clades of the NCLDV. Thus, these giants of the virus world evolved repeatedly from smaller and simpler viruses, rather than from a fourth domain of cellular life, and captured numerous genes, including those for translation system components, from eukaryotes, along with some bacterial genes. Even deeper evolutionary reconstructions reveal apparent links between the NCLDV and smaller viruses of eukaryotes, such as adenoviruses, and ultimately, derive all these viruses from tailless bacteriophages.}, }
@article {pmid30634905, year = {2019}, author = {Kim, JI and Shin, H and Škaloud, P and Jung, J and Yoon, HS and Archibald, JM and Shin, W}, title = {Comparative plastid genomics of Synurophyceae: inverted repeat dynamics and gene content variation.}, journal = {BMC evolutionary biology}, volume = {19}, number = {1}, pages = {20}, pmid = {30634905}, issn = {1471-2148}, mesh = {Base Sequence ; DNA, Circular/genetics ; Evolution, Molecular ; Gene Dosage ; *Genetic Variation ; *Genome, Plastid ; *Genomics ; Inverted Repeat Sequences/*genetics ; Nucleic Acid Conformation ; Phylogeny ; RNA, Transfer/chemistry/genetics ; Stramenopiles/*genetics ; }, abstract = {BACKGROUND: The Synurophyceae is one of most important photosynthetic stramenopile algal lineages in freshwater ecosystems. They are characterized by siliceous scales covering the cell or colony surface and possess plastids of red-algal secondary or tertiary endosymbiotic origin. Despite their ecological and evolutionary significance, the relationships amongst extant Synurophyceae are unclear, as is their relationship to most other stramenopiles.<br><br>RESULTS: Here we report a comparative analysis of plastid genomes sequenced from five representative synurophycean algae. Most of these plastid genomes are highly conserved with respect to genome structure and coding capacity, with the exception of gene re-arrangements and partial duplications at the boundary of the inverted repeat and single-copy regions. Several lineage-specific gene loss/gain events and intron insertions were detected (e.g., cemA, dnaB, syfB, and trnL).<br><br>CONCLUSIONS: Unexpectedly, the cemA gene of Synurophyceae shows a strong relationship with sequences from members of the green-algal lineage, suggesting the occurrence of a lateral gene transfer event. Using a molecular clock approach based on silica fossil record data, we infer the timing of genome re-arrangement and gene gain/loss events in the plastid genomes of Synurophyceae.}, }
@article {pmid30631340, year = {2018}, author = {da Silva Filho, AC and Raittz, RT and Guizelini, D and De Pierri, CR and Augusto, DW and Dos Santos-Weiss, ICR and Marchaukoski, JN}, title = {Comparative Analysis of Genomic Island Prediction Tools.}, journal = {Frontiers in genetics}, volume = {9}, number = {}, pages = {619}, pmid = {30631340}, issn = {1664-8021}, abstract = {Tools for genomic island prediction use strategies for genomic comparison analysis and sequence composition analysis. The goal of comparative analysis is to identify unique regions in the genomes of related organisms, whereas sequence composition analysis evaluates and relates the composition of specific regions with other regions in the genome. The goal of this study was to qualitatively and quantitatively evaluate extant genomic island predictors. We chose tools reported to produce significant results using sequence composition prediction, comparative genomics, and hybrid genomics methods. To maintain diversity, the tools were applied to eight complete genomes of organisms with distinct characteristics and belonging to different families. Escherichia coli CFT073 was used as a control and considered as the gold standard because its islands were previously curated in vitro. The results of predictions with the gold standard were manually curated, and the content and characteristics of each predicted island were analyzed. For other organisms, we created GenBank (GBK) files using Artemis software for each predicted island. We copied only the amino acid sequences from the coding sequence and constructed a multi-FASTA file for each predictor. We used BLASTp to compare all results and generate hits to evaluate similarities and differences among the predictions. Comparison of the results with the gold standard revealed that GIPSy produced the best results, covering ~91% of the composition and regions of the islands, followed by Alien Hunter (81%), IslandViewer (47.8%), Predict Bias (31%), GI Hunter (17%), and Zisland Explorer (16%). The tools with the best results in the analyzes of the set of organisms were the same ones that presented better performance in the tests with the gold standard.}, }
@article {pmid30629162, year = {2019}, author = {Ševcíková, T and Yurchenko, T and Fawley, KP and Amaral, R and Strnad, H and Santos, LMA and Fawley, MW and Eliáš, M}, title = {Plastid Genomes and Proteins Illuminate the Evolution of Eustigmatophyte Algae and Their Bacterial Endosymbionts.}, journal = {Genome biology and evolution}, volume = {11}, number = {2}, pages = {362-379}, pmid = {30629162}, issn = {1759-6653}, support = {P20 GM103429/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; *Biological Evolution ; *Genome, Plastid ; *Operon ; Rickettsiaceae/*genetics ; Stramenopiles/*genetics/microbiology ; Symbiosis ; }, abstract = {Eustigmatophytes, a class of stramenopile algae (ochrophytes), include not only the extensively studied biotechnologically important genus Nannochloropsis but also a rapidly expanding diversity of lineages with much less well characterized biology. Recent discoveries have led to exciting additions to our knowledge about eustigmatophytes. Some proved to harbor bacterial endosymbionts representing a novel genus, Candidatus Phycorickettsia, and an operon of unclear function (ebo) obtained by horizontal gene transfer from the endosymbiont lineage was found in the plastid genomes of still other eustigmatophytes. To shed more light on the latter event, as well as to generally improve our understanding of the eustigmatophyte evolutionary history, we sequenced plastid genomes of seven phylogenetically diverse representatives (including new isolates representing undescribed taxa). A phylogenomic analysis of plastid genome-encoded proteins resolved the phylogenetic relationships among the main eustigmatophyte lineages and provided a framework for the interpretation of plastid gene gains and losses in the group. The ebo operon gain was inferred to have probably occurred within the order Eustigmatales, after the divergence of the two basalmost lineages (a newly discovered hitherto undescribed strain and the Pseudellipsoidion group). When looking for nuclear genes potentially compensating for plastid gene losses, we noticed a gene for a plastid-targeted acyl carrier protein that was apparently acquired by horizontal gene transfer from Phycorickettsia. The presence of this gene in all eustigmatophytes studied, including representatives of both principal clades (Eustigmatales and Goniochloridales), is a genetic footprint indicating that the eustigmatophyte-Phycorickettsia partnership started no later than in the last eustigmatophyte common ancestor.}, }
@article {pmid30627116, year = {2018}, author = {Pimentel, ZT and Zhang, Y}, title = {Evolution of the Natural Transformation Protein, ComEC, in Bacteria.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2980}, pmid = {30627116}, issn = {1664-302X}, abstract = {Natural transformation enables the incorporation of exogenous DNA into host genomes and plays a fundamental role in the evolution of microbial populations. At the center of the natural transformation machinery, the ComEC protein mediates DNA import and serves potential functions in DNA recognition and single strand degradation. Despite its importance, the evolution of ComEC is not fully understood. Here, we aim to fill this knowledge gap by surveying putative ComEC proteins across 5,574 bacteria that span diverse phyla. We first derived the presence of a universal, core Competence domain through the analysis of ComEC proteins from known naturally competent species. Then, we followed this observation to identify Competence domain containing proteins (CDCPs) from all bacteria and used CDCPs as putative ComEC proteins for evolutionary analysis. A near universal presence of CDCPs was revealed, with 89% of the proteomes and 96% of the genomes encoding a single CDCP or a CDCP-like fragment. Two domains, DUF4131 and Lactamase_B, were found to commonly co-occur with the Competence domain. Ancestral state reconstruction of CDCPs over the bacterial species phylogeny suggested an origin of a Competence-only domain profile, while multiple gains and losses of the DUF4131 and Lactamase_B domains were observed among diverse bacterial lineages.}, }
@article {pmid30626314, year = {2019}, author = {Xu, P and Lu, B and Liu, J and Chao, J and Donkersley, P and Holdbrook, R and Lu, Y}, title = {Duplication and expression of horizontally transferred polygalacturonase genes is associated with host range expansion of mirid bugs.}, journal = {BMC evolutionary biology}, volume = {19}, number = {1}, pages = {12}, pmid = {30626314}, issn = {1471-2148}, mesh = {Animals ; Evolution, Molecular ; *Gene Duplication ; Gene Expression Profiling ; *Gene Expression Regulation ; Gene Transfer, Horizontal/*genetics ; *Genes, Insect ; Heteroptera/*genetics ; Host Specificity/*genetics ; Phylogeny ; Polygalacturonase/*genetics ; Selection, Genetic ; Sequence Alignment ; Species Specificity ; }, abstract = {BACKGROUD: Horizontal gene transfer and gene duplication are two major mechanisms contributing to the evolutionary adaptation of organisms. Previously, polygalacturonase genes (PGs) were independently horizontally transferred and underwent multiple duplications in insects (e.g., mirid bugs and beetles). Here, we chose three phytozoophagous mirid bugs (Adelphocoris suturalis, A. fasciaticollis, A. lineolatus) and one zoophytophagous mirid bug (Nesidiocoris tenuis) to detect whether the duplication, molecular evolution, and expression levels of PGs were related to host range expansion in mirid bugs.<br><br>RESULTS: By RNA-seq, we reported 30, 20, 19 and 8 PGs in A. suturalis, A. fasciaticollis, A. lineolatus and N. tenuis, respectively. Interestingly, the number of PGs was significantly positive correlation to the number of host plants (P&#xa0;=&#x2009;0.0339) in mirid bugs. Most PGs (>&#x2009;17) were highly expressed in the three phytozoophagous mirid bugs, while only one PG was relatively highly expressed in the zoophytophagous mirid bug. Natural selection analysis clearly showed that a significant relaxation of selection pressure acted on the PGs in zoophytophagous mirid bugs (K&#x2009;=&#x2009;0.546, P&#xa0;=&#x2009;0.0158) rather than in phytozoophagous mirid bugs (K&#x2009;=&#x2009;1, P&#xa0;=&#x2009;0.92), suggesting a function constraint of PGs in phytozoophagous mirid bugs.<br><br>CONCLUSION: Taken together with gene duplication, molecular evolution, and expression levels, our results suggest that PGs are more strictly required by phytozoophagous than by zoophytophagous mirid bugs and that the duplication of PGs is associated with the expansion of host plant ranges in mirid bugs.}, }
@article {pmid30625669, year = {2019}, author = {Costeira, R and Doherty, R and Allen, CCR and Larkin, MJ and Kulakov, LA}, title = {Analysis of viral and bacterial communities in groundwater associated with contaminated land.}, journal = {The Science of the total environment}, volume = {656}, number = {}, pages = {1413-1426}, doi = {10.1016/j.scitotenv.2018.11.429}, pmid = {30625669}, issn = {1879-1026}, mesh = {Bacteria/classification/*genetics ; Groundwater/*microbiology/virology ; *Metagenome ; *Microbiota ; Northern Ireland ; Soil Pollutants/*analysis ; Viruses/classification/*genetics ; }, abstract = {This work aimed at the comprehensive analysis of total microbial communities inhabiting a typical hydrocarbon-polluted site, where chemical characteristics of the groundwater were readily available. To achieve this, a joint metagenomic characterization of bacteria and viruses surrounding a contaminant plume was performed over a one-year period. The results presented demonstrated that both potential hydrocarbon degraders and their bacteriophages were dominant around the plume, and that the viral and bacterial diversities found at the site were probably influenced by the pH of the groundwater. Niche-specific and dispersed associations between phages and bacteria were identified. The niche phage-host associations were found at the edge of the site and at the core of the plume where pH was the highest (9.52). The identified host populations included several classes of bacteria (e.g. Clostridia and Proteobacteria). Thirty-six viral generalists were also discovered, with BGW-G9 having the broadest host range across 23 taxa, including Pseudomonas, Polycyclovorans, Methylocaldum and Candidatus Magnetobacterium species. The phages with broad host ranges are presumed to have significant effects on prokaryotic production and horizontal gene transfer, and therefore impact the biodegradation processes conducted by various bacteria of the environment studied. This study for the first time characterized the phages and their bacterial hosts associated with a contaminant plume.}, }
@article {pmid30625112, year = {2019}, author = {Brooks, LE and Kaze, M and Sistrom, M}, title = {Where the plasmids roam: large-scale sequence analysis reveals plasmids with large host ranges.}, journal = {Microbial genomics}, volume = {5}, number = {1}, pages = {}, pmid = {30625112}, issn = {2057-5858}, mesh = {Corynebacterium/*genetics ; *Databases, Nucleic Acid ; Enterobacteriaceae/*genetics ; Plasmids/*genetics ; }, abstract = {Describing the role of plasmids and their contribution to the exchange of genetic material among bacteria is essential for understanding the fields of plasmid epidemiology, microbial ecology, and commercial and synthetic microbiology. Broad-host-range (BHR) plasmids are those that are found not only in a single bacterial species, but in members of different taxonomic groups and are of significant interest to researchers in many fields. We applied a novel approach to computationally identify new BHR plasmids, in which we searched for highly similar cognate plasmids within a comprehensive plasmid database. After identifying 125 plasmid groups with highly similar cognates found in multiple taxa, we closely examined BHR plasmids found in multiple families. The majority of our identified BHR plasmids are found in members of the Enterobacteriaceae and closely related taxa, while three BHR plasmids of potential commercial significance were found in two species of Cyanobacteria. One plasmid with an exceptionally broad host range was found in both Gram-positive and Gram-negative bacterial species. This analysis demonstrates the utility of this method in identifying new BHR plasmids while highlighting unknown ranges of previously documented plasmids.}, }
@article {pmid30624459, year = {2019}, author = {Morgado, SM and Vicente, ACP}, title = {Exploring tRNA gene cluster in archaea.}, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {114}, number = {}, pages = {e180348}, pmid = {30624459}, issn = {1678-8060}, mesh = {Archaea/*genetics ; Evolution, Molecular ; Genome, Archaeal/*genetics ; Multigene Family/*genetics ; Phylogeny ; RNA, Archaeal/*genetics ; RNA, Transfer/*genetics ; Sequence Alignment ; }, abstract = {BACKGROUND: Shared traits between prokaryotes and eukaryotes are helpful in the understanding of the tree of life evolution. In bacteria and eukaryotes, it has been shown a particular organisation of tRNA genes as clusters, but this trait has not been explored in the archaea domain.<br><br>OBJECTIVE: Explore the occurrence of tRNA gene clusters in archaea.<br><br>METHODS: In-silico analyses of complete and draft archaeal genomes based on tRNA gene isotype and synteny, tRNA gene cluster content and mobilome elements.<br><br>FINDINGS: We demonstrated the prevalence of tRNA gene clusters in archaea. tRNA gene clusters, composed of archaeal-type tRNAs, were identified in two Archaea class, Halobacteria and Methanobacteria from Euryarchaeota supergroup. Genomic analyses also revealed evidence of the association between tRNA gene clusters to mobile genetic elements and intra-domain horizontal gene transfer.<br><br>MAIN CONCLUSIONS: tRNA gene cluster occurs in the three domains of life, suggesting a role of this type of tRNA gene organisation in the biology of the living organisms.}, }
@article {pmid30622880, year = {2018}, author = {Luo, H and Cai, Q and Lüli, Y and Li, X and Sinha, R and Hallen-Adams, HE and Yang, ZL}, title = {The MSDIN family in amanitin-producing mushrooms and evolution of the prolyl oligopeptidase genes.}, journal = {IMA fungus}, volume = {9}, number = {}, pages = {225-242}, pmid = {30622880}, issn = {2210-6340}, abstract = {The biosynthetic pathway for amanitins and related cyclic peptides in deadly Amanita (Amanitaceae) mushrooms represents the first known ribosomal cyclic peptide pathway in the Fungi. Amanitins are found outside of the genus in distantly related agarics Galerina (Strophariaceae) and Lepiota (Agaricaceae). A long-standing question in the field persists: why is this pathway present in these phylogenetically disjunct agarics? Two deadly mushrooms, A. pallidorosea and A. subjunquillea, were deep sequenced, and sequences of biosynthetic genes encoding MSDINs (cyclic peptide precursor) and prolyl oligopeptidases (POPA and POPB) were obtained. The two Amanita species yielded 29 and 18 MSDINs, respectively. In addition, two MSDIN sequences were cloned from L. brunneoincarnata basidiomes. The toxin MSDIN genes encoding amatoxins or phallotoxins from the three genera were compared, and a phylogenetic tree constructed. Prolyl oligopeptidase B (POPB), a key enzyme in the biosynthetic pathway, was used in phylogenetic reconstruction to infer the evolutionary history of the genes. Phylogenies of POPB and POPA based on both coding and amino acid sequences showed very different results: while POPA genes clearly reflected the phylogeny of the host species, POPB did not; strikingly, it formed a well-supported monophyletic clade, despite that the species belong to different genera in disjunct families. POPA, a known house-keeping gene, was shown to be restricted in a branch containing only Amanita species and the phylogeny resembled that of those Amanita species. Phylogenetic analyses of MSDIN and POPB genes showed tight coordination and disjunct distribution. A POPB gene tree was compared with a corresponding species tree, and distances and substitution rates were compared. The result suggested POPB genes have significant smaller distances and rates than the house-keeping rpb2, discounting massive gene loss. Under this assumption, the incongruency between the gene tree and species tree was shown with strong support. Additionally, k-mer analyses consistently cluster Galerina and Amanita POPB genes, while Lepiota POPB is distinct. Our result suggests that horizontal gene transfer (HGT), at least between Amanita and Galerina, was involved in the acquisition of POPB genes, which may shed light on the evolution of the α-amanitin biosynthetic pathway.}, }
@article {pmid30619228, year = {2018}, author = {Bie, L and Fang, M and Li, Z and Wang, M and Xu, H}, title = {Identification and Characterization of New Resistance-Conferring SGI1s (Salmonella Genomic Island 1) in Proteus mirabilis.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3172}, pmid = {30619228}, issn = {1664-302X}, abstract = {Salmonella genomic island 1 (SGI1) is a resistance-conferring chromosomal genomic island that contains an antibiotic resistance gene cluster. The international spread of SGI1-containing strains drew attention to the role of genomic islands in the dissemination of antibiotic resistance genes in Salmonella and other Gram-negative bacteria. In this study, five SGI1 variants conferring multidrug and heavy metal resistance were identified and characterized in Proteus mirabilis strains: SGI1-PmCAU, SGI1-PmABB, SGI1-PmJN16, SGI1-PmJN40, and SGI1-PmJN48. The genetic structures of SGI1-PmCAU and SGI1-PmABB were identical to previously reported SGI1s, while structural analysis showed that SGI1-PmJN16, SGI1-PmJN40, and SGI1-PmJN48 are new SGI1 variants. SGI1-PmJN16 is derived from SGI1-Z with the MDR region containing a new gene cassette array dfrA12-orfF-aadA2-qacEΔ1-sul1-chrA-orf1. SGI1-PmJN40 has an unprecedented structure that contains two right direct repeat sequences separated by a transcriptional regulator-rich DNA fragment, and is predicted to form two different extrachromosomal mobilizable DNA circles for dissemination. SGI1-PmJN48 lacks a common ORF S044, and its right junction region exhibits a unique genetic organization due to the reverse integration of a P. mirabilis chromosomal gene cluster and the insertion of part of a P. mirabilis plasmid, making it the largest known SGI1 to date (189.1 kb). Further mobility functional analysis suggested that these SGIs can be excised from the chromosome for transfer between bacteria, which promotes the horizontal transfer of antibiotic and heavy metal resistance genes. The identification and characterization of the new SGI1 variants in this work suggested the diversity of SGI1 structures and their significant roles in the evolution of bacteria.}, }
@article {pmid30618567, year = {2018}, author = {Tucker, RP}, title = {Teneurins: Domain Architecture, Evolutionary Origins, and Patterns of Expression.}, journal = {Frontiers in neuroscience}, volume = {12}, number = {}, pages = {938}, pmid = {30618567}, issn = {1662-4548}, abstract = {Disruption of teneurin expression results in abnormal neural networks, but just how teneurins support the development of the central nervous system remains an area of active research. This review summarizes some of what we know about the functions of the various domains of teneurins, the possible evolution of teneurins from a bacterial toxin, and the intriguing patterns of teneurin expression. Teneurins are a family of type-2 transmembrane proteins. The N-terminal intracellular domain can be processed and localized to the nucleus, but the significance of this nuclear localization is unknown. The extracellular domain of teneurins is largely composed of tyrosine-aspartic acid repeats that fold into a hollow barrel, and the C-terminal domains of teneurins are stuffed, and least partly, into the barrel. A 6-bladed beta-propeller is found at the other end of the barrel. The same arrangement-6-bladed beta-propeller, tyrosine-aspartic acid repeat barrel, and the C-terminal domain inside the barrel-is seen in toxic proteins from bacteria, and there is evidence that teneurins may have evolved from a gene encoding a prokaryotic toxin via horizontal gene transfer into an ancestral choanoflagellate. Patterns of teneurin expression are often, but not always, complementary. In the central nervous system, where teneurins are best studied, interconnected populations of neurons often express the same teneurin. For example, in the chicken embryo neurons forming the tectofugal pathway express teneurin-1, whereas neurons forming the thalamofugal pathway express teneurin-2. In Drosophila melanogaster, Caenorhabditis elegans, zebrafish and mice, misexpression or knocking out teneurin expression leads to abnormal connections in the neural networks that normally express the relevant teneurin. Teneurins are also expressed in non-neuronal tissue during development, and in at least some regions the patterns of non-neuronal expression are also complementary. The function of teneurins outside the nervous system remains unclear.}, }
@article {pmid30611073, year = {2019}, author = {Ferreira, C and Bogas, D and Bikarolla, SK and Varela, AR and Frykholm, K and Linheiro, R and Nunes, OC and Westerlund, F and Manaia, CM}, title = {Genetic variation in the conjugative plasmidome of a hospital effluent multidrug resistant Escherichia coli strain.}, journal = {Chemosphere}, volume = {220}, number = {}, pages = {748-759}, doi = {10.1016/j.chemosphere.2018.12.130}, pmid = {30611073}, issn = {1879-1298}, mesh = {Drug Resistance, Microbial/genetics ; Drug Resistance, Multiple ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/*genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; *Genetic Variation ; Hospitals ; Metals/pharmacology ; Plasmids/genetics ; }, abstract = {Bacteria harboring conjugative plasmids have the potential for spreading antibiotic resistance through horizontal gene transfer. It is described that the selection and dissemination of antibiotic resistance is enhanced by stressors, like metals or antibiotics, which can occur as environmental contaminants. This study aimed at unveiling the composition of the conjugative plasmidome of a hospital effluent multidrug resistant Escherichia coli strain (H1FC54) under different mating conditions. To meet this objective, plasmid pulsed field gel electrophoresis, optical mapping analyses and DNA sequencing were used in combination with phenotype analysis. Strain H1FC54 was observed to harbor five plasmids, three of which were conjugative and two of these, pH1FC54_330 and pH1FC54_140, contained metal and antibiotic resistance genes. Transconjugants obtained in the absence or presence of tellurite (0.5 μM or 5 μM), arsenite (0.5 μM, 5 μM or 15 μM) or ceftazidime (10 mg/L) and selected in the presence of sodium azide (100 mg/L) and tetracycline (16 mg/L) presented distinct phenotypes, associated with the acquisition of different plasmid combinations, including two co-integrate plasmids, of 310 kbp and 517 kbp. The variable composition of the conjugative plasmidome, the formation of co-integrates during conjugation, as well as the transfer of non-transferable plasmids via co-integration, and the possible association between antibiotic, arsenite and tellurite tolerance was demonstrated. These evidences bring interesting insights into the comprehension of the molecular and physiological mechanisms that underlie antibiotic resistance propagation in the environment.}, }
@article {pmid30609821, year = {2019}, author = {Tang, J and Du, LM and Liang, YM and Daroch, M}, title = {Complete Genome Sequence and Comparative Analysis of Synechococcus sp. CS-601 (SynAce01), a Cold-Adapted Cyanobacterium from an Oligotrophic Antarctic Habitat.}, journal = {International journal of molecular sciences}, volume = {20}, number = {1}, pages = {}, pmid = {30609821}, issn = {1422-0067}, support = {2081917012//Chengdu University/ ; }, mesh = {Adaptation, Physiological ; Antarctic Regions ; Base Composition ; Cold Temperature ; Comparative Genomic Hybridization ; Ecosystem ; Gene Ontology ; *Genome, Bacterial ; Open Reading Frames/genetics ; Phylogeny ; RNA, Ribosomal, 16S/chemistry/classification/genetics ; Synechococcus/classification/*genetics ; }, abstract = {Marine picocyanobacteria belonging to Synechococcus are major contributors to the global carbon cycle, however the genomic information of its cold-adapted members has been lacking to date. To fill this void the genome of a cold-adapted planktonic cyanobacterium Synechococcus sp. CS-601 (SynAce01) has been sequenced. The genome of the strain contains a single chromosome of approximately 2.75 MBp and GC content of 63.92%. Gene prediction yielded 2984 protein coding sequences and 44 tRNA genes. The genome contained evidence of horizontal gene transfer events during its evolution. CS-601 appears as a transport generalist with some specific adaptation to an oligotrophic marine environment. It has a broad repertoire of transporters of both inorganic and organic nutrients to survive in inhospitable environments. The cold adaptation of the strain exhibited characteristics of a psychrotroph rather than psychrophile. Its salt adaptation strategy is likely to rely on the uptake and synthesis of osmolytes, like glycerol or glycine betaine. Overall, the genome reveals two distinct patterns of adaptation to the inhospitable environment of Antarctica. Adaptation to an oligotrophic marine environment is likely due to an abundance of genes, probably acquired horizontally, that are associated with increased transport of nutrients, osmolytes, and light harvesting. On the other hand, adaptations to low temperatures are likely due to prolonged evolutionary changes.}, }
@article {pmid30609386, year = {2019}, author = {van Hattem, JM and Cabal, A and Arcilla, MS and Alvarez, J and de Jong, MD and Melles, DC and Penders, J and ,  and Schmidt, CG and Schultsz, C}, title = {Risk of acquisition of human diarrhoeagenic Escherichia coli virulence genes in intercontinental travellers: A prospective, multi-centre study.}, journal = {Travel medicine and infectious disease}, volume = {31}, number = {}, pages = {101362}, doi = {10.1016/j.tmaid.2018.12.005}, pmid = {30609386}, issn = {1873-0442}, mesh = {Escherichia coli/*genetics/*pathogenicity ; Escherichia coli Infections/*microbiology ; Feces/microbiology ; Gene Transfer, Horizontal ; Humans ; Netherlands ; Prospective Studies ; Risk ; *Travel ; Virulence Factors/*genetics ; }, abstract = {BACKGROUND: We studied geographic distribution of diarrhoeagenic Escherichia coli virulence genes (DEC VGs) acquisition in travellers and investigated if they acquired highly virulent EAEC/STEC hybrid strains.<br><br>METHODS: From the prospective, multicentre COMBAT study among 2001 Dutch travellers, 491 travellers were selected based on travel destination to 7 subregions. Faecal samples taken directly before and after travel were screened for nine DEC VGs with real-time PCR. Incidence proportions and rates were calculated for each gene and subregion.<br><br>RESULTS: 479 travellers were analysed. 21.8% acquired aggR (EAEC), with highest acquisition rates in Northern and Western Africa and 15.3% acquired eae (STEC/EPEC) with highest rates in travellers to Western and Eastern Africa. ETEC (elt or est gene) was acquired by 4.2% of travellers and acquisition of est was associated with traveller's diarrhoea. Overall, the risk of acquiring DEC VGs was low in Southern Africa and South America. Although the combination of aggR (EAEC) and stx1/2 (STEC) was acquired by 3 travellers, these genes could not be detected together in a single E. coli strain.<br><br>CONCLUSIONS: The risk of acquisition of DEC VGs strongly depends on the travel destination, with those travelling to Africa - except Southern Africa - having a higher risk.}, }
@article {pmid30608550, year = {2019}, author = {diCenzo, GC and Mengoni, A and Perrin, E}, title = {Chromids Aid Genome Expansion and Functional Diversification in the Family Burkholderiaceae.}, journal = {Molecular biology and evolution}, volume = {36}, number = {3}, pages = {562-574}, doi = {10.1093/molbev/msy248}, pmid = {30608550}, issn = {1537-1719}, mesh = {Adaptation, Biological/genetics ; Burkholderiaceae/*genetics ; Gene Transfer, Horizontal ; Genome Size ; *Genome, Bacterial ; *Replicon ; Selection, Genetic ; }, abstract = {Multipartite genomes, containing at least two large replicons, are found in diverse bacteria; however, the advantage of this genome structure remains incompletely understood. Here, we perform comparative genomics of hundreds of finished β-proteobacterial genomes to gain insights into the role and emergence of multipartite genomes. Almost all essential secondary replicons (chromids) of the β-proteobacteria are found in the family Burkholderiaceae. These replicons arose from just two plasmid acquisition events, and they were likely stabilized early in their evolution by the presence of core genes. On average, Burkholderiaceae genera with multipartite genomes had a larger total genome size, but smaller chromosome, than genera without secondary replicons. Pangenome-level functional enrichment analyses suggested that interreplicon functional biases are partially driven by the enrichment of secondary replicons in the accessory pangenome fraction. Nevertheless, the small overlap in orthologous groups present in each replicon's pangenome indicated a clear functional separation of the replicons. Chromids appeared biased to environmental adaptation, as the functional categories enriched on chromids were also overrepresented on the chromosomes of the environmental genera (Paraburkholderia and Cupriavidus) compared with the pathogenic genera (Burkholderia and Ralstonia). Using ancestral state reconstruction, it was predicted that the rate of accumulation of modern-day genes by chromids was more rapid than the rate of gene accumulation by the chromosomes. Overall, the data are consistent with a model where the primary advantage of secondary replicons is in facilitating increased rates of gene acquisition through horizontal gene transfer, consequently resulting in replicons enriched in genes associated with adaptation to novel environments.}, }
@article {pmid30604012, year = {2019}, author = {Tyagi, A and Singh, B and Billekallu Thammegowda, NK and Singh, NK}, title = {Shotgun metagenomics offers novel insights into taxonomic compositions, metabolic pathways and antibiotic resistance genes in fish gut microbiome.}, journal = {Archives of microbiology}, volume = {201}, number = {3}, pages = {295-303}, doi = {10.1007/s00203-018-1615-y}, pmid = {30604012}, issn = {1432-072X}, support = {YSS/2014/000269//Science and Engineering Research Board/ ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Aquaculture ; *Bacteria/classification/drug effects/genetics ; Carps/*microbiology ; Drug Resistance, Multiple, Bacterial/*genetics ; Fishes ; Gastrointestinal Microbiome/*genetics ; Gene Transfer, Horizontal ; Metabolic Networks and Pathways ; Metagenomics/methods ; Probiotics ; }, abstract = {Gut microbiota of freshwater carp (Labeo rohita) was investigated by shotgun metagenomics to understand its taxonomic composition and functional capabilities. With the presence of 36 phyla, 326 families and 985 genera, the fish gut microbiota was found to be quite diverse in nature. However, at the phylum level, more than three-fourths of gut microbes belonged to Proteobacteria. Very low prevalence of commonly used probiotic bacteria (Bacillus, Lactobacillus, Streptococcus, and Lactococcus) in fish gut suggested the need to search for alternative probiotics for aquaculture use. Biosynthesis pathways were found to be the most dominant (51%) followed by degradation (39%), energy metabolism (4%) and fermentation (2%). In conformity with herbivorous feeding habit of L. rohita, gut microbiome also had pathways for the degradation of cellulose, hemicellulose, chitin, pectin, starch, and other complex carbohydrates. High prevalence of Actinobacteria and antibiotic biosynthesis pathways in the fish gut microbiome indicated its potential for bioprospecting of potentially novel natural antibiotics. Fifty-one different types of antibiotic resistance genes (ARGs) belonging to 15 antimicrobial resistance (AMR) gene families and conferring resistance against 24 antibiotic types were detected in fish gut. Some of the ARGs for multi-drug resistance were also found to be located on sequences of plasmid origin. The presence of pathogenic bacteria and ARGs on plasmid sequences suggested the potential risk due to horizontal gene transfer in the confined gut environment. The role of ARGs in fish gut microbiome needs further investigations.}, }
@article {pmid30603701, year = {2018}, author = {Nascimento, FX and Tavares, MJ and Rossi, MJ and Glick, BR}, title = {The modulation of leguminous plant ethylene levels by symbiotic rhizobia played a role in the evolution of the nodulation process.}, journal = {Heliyon}, volume = {4}, number = {12}, pages = {e01068}, pmid = {30603701}, issn = {2405-8440}, abstract = {Ethylene plays an important role in regulating the rhizobial nodulation process. Consequently, numerous strains of rhizobia possess the ability to decrease plant ethylene levels by the expression of the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase or via the production of rhizobitoxine, thus, leading to an increased ability to nodulate leguminous plants. Nevertheless, not much is understood about the prevalence of these ethylene modulation genes in different rhizobial groups nor their role in the evolution of the symbiotic process. In this work, we analyze the prevalence and evolution of the enzymes ACC deaminase (AcdS) and dihydrorhizobitoxine desaturase (RtxC) in 395 NodC[+] genomes from different rhizobial strains isolated from a wide range of locations and plant hosts, and discuss their importance in the evolution of the symbiotic process. The obtained results show that AcdS and RtxC are differentially prevalent in rhizobial groups, indicating the existence of several selection mechanisms governed by the rhizobial strain itself and its evolutionary origin, the environment, and, importantly, the leguminous plant host (co-evolution). Moreover, it was found that the prevalence of AcdS and RtxC is increased in Bradyrhizobium and Paraburkholderia, and lower in other groups. Data obtained from phylogenetic, evolutionary as well as gene localization analysis support the previous hypotheses regarding the ancient origin of the nodulation abilities in Bradyrhizobium and Paraburkholderia, and brings a new perspective for the importance of ethylene modulation genes in the development of the symbiotic process. The acquisition of AcdS by horizontal gene transfer and a positive selection in other rhizobial groups indicates that this enzyme plays an important role in the nodulation process of many rhizobia. On the other hand, RtxC is negatively selected in most symbioses. Understanding the evolution of ethylene modulation genes in rhizobia may be the key to the development of new strategies aiming for an increased nodulation and nitrogen fixation process.}, }
@article {pmid30602516, year = {2019}, author = {Shen, D and Ma, G and Li, C and Jia, X and Qin, C and Yang, T and Wang, L and Jiang, X and Ding, N and Zhang, X and Yue, L and Yin, Z and Zeng, L and Zhao, Y and Zhou, D and Chen, F}, title = {Emergence of a Multidrug-Resistant Hypervirulent Klebsiella pneumoniae Sequence Type 23 Strain with a Rare blaCTX-M-24-Harboring Virulence Plasmid.}, journal = {Antimicrobial agents and chemotherapy}, volume = {63}, number = {3}, pages = {}, pmid = {30602516}, issn = {1098-6596}, mesh = {Adult ; Animals ; Anti-Bacterial Agents/therapeutic use ; Bacterial Proteins/*genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Genome, Bacterial/genetics ; Humans ; Klebsiella Infections/drug therapy/microbiology ; Klebsiella pneumoniae/*drug effects/*genetics/isolation &amp; purification/pathogenicity ; Male ; Microbial Sensitivity Tests ; Moths/microbiology ; Plasmids/*genetics ; Virulence/genetics ; Virulence Factors/genetics ; beta-Lactamases/*genetics ; }, abstract = {Here, we report a multidrug-resistant hypervirulent Klebsiella pneumoniae (MDR-HvKP) strain of sequence type 23 (ST23) with a rare hybrid plasmid harboring virulence genes and blaCTX-M-24, and we analyze the genetic basis for relationship between genotypes and MDR-hypervirulence phenotypes. Further analysis indicates that the hybrid plasmid is formed by IS903D-mediated intermolecular transposition of the blaCTX-M-24 gene into the virulence plasmid. The emergence of MDR-HvKP strains, especially those carrying drug-resistant virulent plasmids, poses unprecedented threats/challenges to public health. This is a dangerous trend and should be closely monitored.}, }
@article {pmid30599142, year = {2019}, author = {Kneis, D and Hiltunen, T and Heß, S}, title = {A high-throughput approach to the culture-based estimation of plasmid transfer rates.}, journal = {Plasmid}, volume = {101}, number = {}, pages = {28-34}, doi = {10.1016/j.plasmid.2018.12.003}, pmid = {30599142}, issn = {1095-9890}, mesh = {Biological Evolution ; Conjugation, Genetic ; Escherichia coli/*genetics ; *Gene Transfer, Horizontal ; High-Throughput Screening Assays/statistics &amp; numerical data ; *Models, Statistical ; Plasmids/chemistry/*metabolism ; Serratia marcescens/*genetics ; Uncertainty ; }, abstract = {Horizontal gene transfer is an essential component of bacterial evolution. Quantitative information on transfer rates is particularly useful to better understand and possibly predict the spread of antimicrobial resistance. A variety of methods has been proposed to estimate the rates of plasmid-mediated gene transfer all of which require substantial labor input or financial resources. A cheap but reliable method with high-throughput capabilities is yet to be developed in order to better capture the variability of plasmid transfer rates, e.g. among strains or in response to environmental cues. We explored a new approach to the culture-based estimation of plasmid transfer rates in liquid media allowing for a large number of parallel experiments. It deviates from established approaches in the fact that it exploits data on the absence/presence of transconjugant cells in the wells of a well plate observed over time. Specifically, the binary observations are compared to the probability of transconjugant detection as predicted by a dynamic model. The bulk transfer rate is found as the best-fit value of a designated model parameter. The feasibility of the approach is demonstrated on mating experiments where the RP4 plasmid is transfered from Serratia marcescens to several Escherichia coli recipients. The method's uncertainty is explored via split sampling and virtual experiments.}, }
@article {pmid30594092, year = {2019}, author = {Garner, E and Inyang, M and Garvey, E and Parks, J and Glover, C and Grimaldi, A and Dickenson, E and Sutherland, J and Salveson, A and Edwards, MA and Pruden, A}, title = {Impact of blending for direct potable reuse on premise plumbing microbial ecology and regrowth of opportunistic pathogens and antibiotic resistant bacteria.}, journal = {Water research}, volume = {151}, number = {}, pages = {75-86}, doi = {10.1016/j.watres.2018.12.003}, pmid = {30594092}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents ; *Drinking Water ; *Legionella ; RNA, Ribosomal, 16S ; Sanitary Engineering ; Water Microbiology ; }, abstract = {Little is known about how introducing recycled water intended for direct potable reuse (DPR) into distribution systems and premise plumbing will affect water quality at the point of use, particularly with respect to effects on microbial communities and regrowth. The examination of potential growth of opportunistic pathogens (OPs) and spread of antibiotic resistance genes (ARGs), each representing serious and growing public health concerns, by introducing DPR water has not previously been evaluated. In this study, the impact of blending purified DPR water with traditional drinking water sources was investigated with respect to treatment techniques, blending location, and blending ratio. Water from four U.S. utility partners was treated in bench- and pilot-scale treatment trains to simulate DPR with blending. Water was incubated in simulated premise plumbing rigs made of PVC pipe containing brass coupons to measure regrowth of total bacteria (16S rRNA genes, heterotrophic plate count), OPs (Legionella spp., Mycobacterium spp., Pseudomonas aeruginosa), ARGs (qnrA, vanA), and an indicator of horizontal gene transfer and multi-drug resistance (intI1). The microbial community composition was profiled and the resistome (i.e., all ARGs present) was characterized in select samples using next generation sequencing. While regrowth of total bacteria (16S rRNA genes) from the start of the incubation through week eight consistently occurred across tested scenarios (Wilcoxon, p ≤ 0.0001), total bacteria were not more abundant in the water or biofilm of any DPR scenario than in the corresponding conventional potable condition (p ≥ 0.0748). Regrowth of OP marker genes, qnrA, vanA, and intI1 were not significantly greater in water or biofilm for any DPR blends treated with advanced oxidation compared to corresponding potable water (p ≥ 0.1047). This study of initial bacteria colonizing pipes after introduction of blended DPR water revealed little evidence (i.e., one target in one water type) of exacerbated regrowth of total bacteria, OPs, or ARGs in premise plumbing.}, }
@article {pmid30591014, year = {2018}, author = {Hoeksema, M and Jonker, MJ and Bel, K and Brul, S and Ter Kuile, BH}, title = {Genome rearrangements in Escherichia coli during de novo acquisition of resistance to a single antibiotic or two antibiotics successively.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {973}, pmid = {30591014}, issn = {1471-2164}, mesh = {Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Microbial/*genetics ; Escherichia coli/*drug effects/*genetics ; Gene Transfer, Horizontal ; Genome, Bacterial ; Whole Genome Sequencing/methods ; }, abstract = {BACKGROUND: The ability of bacteria to acquire resistance to antibiotics relies to a large extent on their capacity for genome modification. Prokaryotic genomes are highly plastic and can utilize horizontal gene transfer, point mutations, and gene deletions or amplifications to realize genome expansion and rearrangements. The contribution of point mutations to de novo acquisition of antibiotic resistance is well-established. In this study, the internal genome rearrangement of Escherichia coli during to de novo acquisition of antibiotic resistance was investigated using whole-genome sequencing.<br><br>RESULTS: Cells were made resistant to one of the four antibiotics and subsequently to one of the three remaining. This way the initial genetic rearrangements could be documented together with the effects of an altered genetic background on subsequent development of resistance. A DNA fragment including ampC was amplified by a factor sometimes exceeding 100 as a result of exposure to amoxicillin. Excision of prophage e14 was observed in many samples with a double exposure history, but not in cells exposed to a single antibiotic, indicating that the activation of the SOS stress response alone, normally the trigger for excision, was not sufficient to cause excision of prophage e14. Partial deletion of clpS and clpA occurred in strains exposed to enrofloxacin and tetracycline. Other deletions were observed in some strains, but not in replicates with the exact same exposure history. Various insertion sequence transpositions correlated with exposure to specific antibiotics.<br><br>CONCLUSIONS: Many of the genome rearrangements have not been reported before to occur during resistance development. The observed correlation between genome rearrangements and specific antibiotic pressure, as well as their presence in independent replicates indicates that these events do not occur randomly. Taken together, the observed genome rearrangements illustrate the plasticity of the E. coli genome when exposed to antibiotic stress.}, }
@article {pmid30590832, year = {2019}, author = {Rossoni, AW and Schï Nknecht, G and Lee, HJ and Rupp, RL and Flachbart, S and Mettler-Altmann, T and Weber, APM and Eisenhut, M}, title = {Cold Acclimation of the Thermoacidophilic Red Alga Galdieria sulphuraria: Changes in Gene Expression and Involvement of Horizontally Acquired Genes.}, journal = {Plant &amp; cell physiology}, volume = {60}, number = {3}, pages = {702-712}, doi = {10.1093/pcp/pcy240}, pmid = {30590832}, issn = {1471-9053}, mesh = {Adaptation, Physiological/genetics/physiology ; Algal Proteins/genetics/metabolism ; Cold Temperature ; Cold-Shock Response/genetics/physiology ; Gene Transfer, Horizontal/genetics/physiology ; Phylogeny ; Rhodophyta/genetics/*metabolism/physiology ; Systems Biology/methods ; }, abstract = {Galdieria sulphuraria is a unicellular red alga that lives in hot, acidic, toxic metal-rich, volcanic environments, where few other organisms survive. Its genome harbors up to 5% of genes that were most likely acquired through horizontal gene transfer. These genes probably contributed to G.sulphuraria's adaptation to its extreme habitats, resulting in today's polyextremophilic traits. Here, we applied RNA-sequencing to obtain insights into the acclimation of a thermophilic organism towards temperatures below its growth optimum and to study how horizontally acquired genes contribute to cold acclimation. A decrease in growth temperature from 42�C/46�C to 28�C resulted in an upregulation of ribosome biosynthesis, while excreted proteins, probably components of the cell wall, were downregulated. Photosynthesis was suppressed at cold temperatures, and transcript abundances indicated that C-metabolism switched from gluconeogenesis to glycogen degradation. Folate cycle and S-adenosylmethionine cycle (one-carbon metabolism) were transcriptionally upregulated, probably to drive the biosynthesis of betaine. All these cold-induced changes in gene expression were reversible upon return to optimal growth temperature. Numerous genes acquired by horizontal gene transfer displayed temperature-dependent expression changes, indicating that these genes contributed to adaptive evolution in G.sulphuraria.}, }
@article {pmid30590650, year = {2019}, author = {Will, SE and Henke, P and Boedeker, C and Huang, S and Brinkmann, H and Rohde, M and Jarek, M and Friedl, T and Seufert, S and Schumacher, M and Overmann, J and Neumann-Schaal, M and Petersen, J}, title = {Day and Night: Metabolic Profiles and Evolutionary Relationships of Six Axenic Non-Marine Cyanobacteria.}, journal = {Genome biology and evolution}, volume = {11}, number = {1}, pages = {270-294}, pmid = {30590650}, issn = {1759-6653}, mesh = {*Circadian Rhythm ; Cyanobacteria/genetics/*metabolism/ultrastructure ; Genome, Bacterial ; *Phylogeny ; }, abstract = {Cyanobacteria are dominant primary producers of various ecosystems and they colonize marine as well as freshwater and terrestrial habitats. On the basis of their oxygenic photosynthesis they are known to synthesize a high number of secondary metabolites, which makes them promising for biotechnological applications. State-of-the-art sequencing and analytical techniques and the availability of several axenic strains offer new opportunities for the understanding of the hidden metabolic potential of cyanobacteria beyond those of single model organisms. Here, we report comprehensive genomic and metabolic analyses of five non-marine cyanobacteria, that is, Nostoc sp. DSM 107007, Anabaena variabilis DSM 107003, Calothrix desertica DSM 106972, Chroococcidiopsis cubana DSM 107010, Chlorogloeopsis sp. PCC 6912, and the reference strain Synechocystis sp. PCC 6803. Five strains that are prevalently belonging to the order Nostocales represent the phylogenetic depth of clade B1, a morphologically highly diverse sister lineage of clade B2 that includes strain PCC 6803. Genome sequencing, light and scanning electron microscopy revealed the characteristics and axenicity of the analyzed strains. Phylogenetic comparisons showed the limits of the 16S rRNA gene for the classification of cyanobacteria, but documented the applicability of a multilocus sequence alignment analysis based on 43 conserved protein markers. The analysis of metabolites of the core carbon metabolism showed parts of highly conserved metabolic pathways as well as lineage specific pathways such as the glyoxylate shunt, which was acquired by cyanobacteria at least twice via horizontal gene transfer. Major metabolic changes were observed when we compared alterations between day and night samples. Furthermore, our results showed metabolic potential of cyanobacteria beyond Synechocystis sp. PCC 6803 as model organism and may encourage the cyanobacterial community to broaden their research to related organisms with higher metabolic activity in the desired pathways.}, }
@article {pmid30588403, year = {2018}, author = {Oliveira, ACP and Ferreira, RM and Ferro, MIT and Ferro, JA and Chandler, M and Varani, AM}, title = {Transposons and pathogenicity in Xanthomonas: acquisition of murein lytic transglycosylases by TnXax1 enhances Xanthomonas citri subsp. citri 306 virulence and fitness.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e6111}, pmid = {30588403}, issn = {2167-8359}, abstract = {Xanthomonas citri subsp. citri 306 (XccA) is the causal agent of type A citrus canker (CC), one of the most significant citriculture diseases. Murein lytic transglycosylases (LT), potentially involved in XccA pathogenicity, are enzymes responsible for peptidoglycan structure assembly, remodeling and degradation. They directly impact cell wall expansion during bacterial growth, septum division allowing cell separation, cell wall remodeling allowing flagellar assembly, bacterial conjugation, muropeptide recycling, and secretion system assembly, in particular the Type 3 Secretion System involved in bacterial virulence, which play a fundamental role in XccA pathogenicity. Information about the XccA LT arsenal is patchy: little is known about family diversity, their exact role or their connection to virulence in this bacterium. Among the LTs with possible involvement in virulence, two paralogue open reading frames (ORFs) (one on the chromosome and one in plasmid pXAC64) are passenger genes of the Tn3 family transposon TnXax1, known to play a significant role in the evolution and emergence of pathogenicity in Xanthomonadales and to carry a variety of virulence determinants. This study addresses LT diversity in the XccA genome and examines the role of plasmid and chromosomal TnXax1 LT passenger genes using site-directed deletion mutagenesis and functional characterization. We identified 13 XccA LTs: 12 belong to families 1A, 1B, 1C, 1D (two copies), 1F, 1G, 3A, 3B (two copies), 5A, 6A and one which is non-categorized. The non-categorized LT is exclusive to the Xanthomonas genus and related to the 3B family but contains an additional domain linked to carbohydrate metabolism. The categorized LTs are probably involved in cell wall remodeling to allow insertion of type 3, 4 and 6 secretion systems, flagellum assembly, division and recycling of cell wall and degradation and control of peptidoglycan production. The TnXax1 passenger LT genes (3B family) are not essential to XccA or for CC development but are implicated in peptidoglycan metabolism, directly impacting bacterial fitness and CC symptom enhancement in susceptible hosts (e.g., Citrus sinensis). This underlines the role of TnXax1 as a virulence and pathogenicity-propagating agent in XccA and suggests that LT acquisition by horizontal gene transfer mediated by TnXax1 may improve bacterial fitness, conferring adaptive advantages to the plant-pathogen interaction process.}, }
@article {pmid30588046, year = {2019}, author = {Xu, H and Huo, C and Sun, Y and Zhou, Y and Xiong, Y and Zhao, Z and Zhou, Q and Sha, L and Zhang, B and Chen, Y}, title = {Emergence and molecular characterization of multidrug-resistant Klebsiella pneumoniae isolates harboring bla CTX-M-15 extended-spectrum β-lactamases causing ventilator-associated pneumonia in China.}, journal = {Infection and drug resistance}, volume = {12}, number = {}, pages = {33-43}, pmid = {30588046}, issn = {1178-6973}, abstract = {BACKGROUND: Ventilator-associated pneumonia (VAP) is a common nosocomial infection associated with high morbidity due to multidrug-resistant (MDR) pathogens. The purpose of this study was to determine the occurrence of extended-spectrum β-lactamase (ESBL) genes, especially bla CTX-M-15, in Klebsiella pneumoniae (K. pneumoniae)-associated VAP and to investigate the antimicrobial resistance patterns and molecular epidemiological characteristics of K. pneumoniae strains.<br><br>MATERIALS AND METHODS: From January 2013 to December 2015, we retrospectively collected 89 VAP-causing K. pneumoniae isolates from tertiary-care hospitals in China, among which ESBL-producing strains were assessed for antimicrobial susceptibility. Several antibiotic resistance genes of clinical relevance in K. pneumonia isolates producing ESBL were investigated. Polymerase chain reaction (PCR) and DNA sequencing were employed to characterize the genetic contexts of bla CTX-M-15. Conjugative plasmids carrying bla CTX-M-15 were obtained by mating and further subjected to replicon typing. The genetic relatedness of isolates was assessed by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing.<br><br>RESULTS: All of the 30 ESBL-producing isolates identified displayed MDR phenotype, with bla SHV, bla CTX-M, bla OXA, and bla TEM detected in 21, 21, 1, and 20 isolates, respectively. bla CTX-M-15 was the most prevalent ESBL gene (19/30, 63.33%), and ISEcp1 was detected 48 bp upstream of 15 bla CTX-M-15 genes. Based on S1-PFGE analyses, 25 isolates exhibited different plasmid profiles, ranging from ~70 to 320 kb. The bla CTX-M-15 with bla TEM and qnr genes and the ISEcp1 element from eight isolates were co-transferrable to recipients via conjugation, with IncFIB, IncFIC, and IncFII being the most prevalent replicons. Twenty different PFGE patterns and 11 sequence types were identified, with ST304 being dominant.<br><br>CONCLUSION: This work reports the emergence of bla CTX-M-15 in K. pneumoniae-induced VAP in China. We showed that IncFIB, IncFIC, and/or IncFII plasmids carrying bla CTX-M-15 with bla TEM, qnr resistance genes, and the ISEcp1 element mediate the local prevalence in K. pneumoniae-associated VAP.}, }
@article {pmid30587229, year = {2018}, author = {Trinachartvanit, W and Maneewong, S and Kaenkan, W and Usananan, P and Baimai, V and Ahantarig, A}, title = {Coxiella-like bacteria in fowl ticks from Thailand.}, journal = {Parasites &amp; vectors}, volume = {11}, number = {1}, pages = {670}, pmid = {30587229}, issn = {1756-3305}, support = {BDC-PG2-160008//BDC PERDO/ ; }, mesh = {Animals ; Bird Diseases/*microbiology/parasitology/transmission ; Chickens ; Coxiella/classification/genetics/*isolation &amp; purification ; DNA, Bacterial/genetics ; Female ; Male ; Phylogeny ; Q Fever/microbiology/transmission/*veterinary ; RNA, Ribosomal, 16S/genetics ; Thailand ; Tick Infestations/parasitology/*veterinary ; Ticks/classification/*microbiology ; }, abstract = {BACKGROUND: Coxiella bacteria were identified from various tick species across the world. Q fever is a zoonotic disease caused by the bacteria Coxiella burnetii that most commonly infects a variety of mammals. Non-mammalian hosts, such as birds, have also been reported to be infected with the pathogenic form of "Candidatus Coxiella avium". This research increases the list of tick species that have been found with Coxiella-like bacteria in Thailand.<br><br>METHODS: A total of 69 ticks were collected from 27 domestic fowl (Gallus gallus domesticus), 2 jungle fowl (Gallus gallus) and 3 Siamese firebacks (Lophura diardi) at 10 locations (provinces) in Thailand. Ticks were identified and PCR was used to amplify Coxiella bacteria 16S rRNA, groEL and rpoB genes from the extracted tick DNA. MEGA6 was used to construct phylogenetic trees via a Maximum Likelihood method.<br><br>RESULTS: The phylogenetic analysis based on the 16S rRNA gene showed that the Coxiella sequences detected in this study grouped in the same clade with Coxiella sequences from the same tick genus (or species) reported previously. In contrast, rpoB gene of the Coxiella bacteria detected in this study did not cluster together with the same tick genus reported previously. Instead, they clustered by geographical distribution (Thai cluster and Malaysian cluster). In addition, phylogenetic analysis of the groEL gene (the chaperonin family) showed that all Coxiella bacteria found in this study were grouped in the same clade (three sister groups).<br><br>CONCLUSIONS: To our knowledge, we found for the first time rpoB genes of Coxiella-like bacteria in Haemaphysalis wellingtoni ticks forming two distinct clades by phylogenetic analysis. This may be indicative of a horizontal gene transfer event.}, }
@article {pmid30580043, year = {2019}, author = {Bell, NE and Ignatov, MS}, title = {Placing the regionally threatened moss Orthodontium gracile in the big picture - Phylogeny, genome incongruence and anthropogenic dispersal in the order Orthodontiales.}, journal = {Molecular phylogenetics and evolution}, volume = {134}, number = {}, pages = {186-199}, doi = {10.1016/j.ympev.2018.12.024}, pmid = {30580043}, issn = {1095-9513}, mesh = {Bayes Theorem ; Bryophyta/*classification/*genetics ; Evolution, Molecular ; *Genome, Plant ; Haplotypes/genetics ; Humans ; *Phylogeny ; Seed Dispersal/*genetics ; Time Factors ; }, abstract = {The Orthodontiaceae is a small family of predominantly Southern Hemisphere temperate and South East Asian mosses that has a key phylogenetic position for research into the evolution of pleurocarpy. In the United Kingdom it is represented by the rare conservation priority species Orthodontium gracile and the abundant exotic O. lineare, introduced from the Southern Hemisphere around a century ago. Although the two species are superficially very similar and difficult to tell apart in the field, very little is known about how closely they are related or about the phylogeny, biogeography and evolutionary history of the genus Orthodontium as a whole. Phylogenetic inference and divergence time estimation were used to explore relationships within the genus globally, date major lineage splits, detect reticulate evolutionary processes and test monophyly of taxa. It was shown that Orthodontium gracile belongs to a Holarctic and Asian clade that diverged from the exclusively southern temperate lineage of O. lineare approximately 53 Ma and that it is sister to the Himalayan and South Siberian bispecific genus Orthodontopsis, which we now recognise as a single species within Orthodontium, O. lignicola. Orthodontium lignicola is quite distinct from O. gracile morphologically but may have a closely overlapping centre of extant diversity in the Himalaya, in contrast to O. lineare which is morphologically similar but biogeographically dissimilar. The introduced European populations of Orthodontium lineare were shown to share plastid and nuclear haplotypes with four collections from Tasmania and Southern Chile, but to be distinct from other Chilean and South African haplotypes. Finally, well-supported incongruence between nuclear and plastid sequences in some Western North American populations of Orthodontium gracile strongly implies one or more chloroplast capture or horizontal genome transfer events involving this species and the regionally sympatric O. pellucens. An appeal is made for targeting phylogenetic research at the intersection points of practical conservation, taxonomic uncertainty and wider biological questions and for the factoring of historical evolutionary and phylogenetic diversity into conservation assessments.}, }
@article {pmid30580028, year = {2019}, author = {Nawaz, MA and Mesnage, R and Tsatsakis, AM and Golokhvast, KS and Yang, SH and Antoniou, MN and Chung, G}, title = {Addressing concerns over the fate of DNA derived from genetically modified food in the human body: A review.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {124}, number = {}, pages = {423-430}, doi = {10.1016/j.fct.2018.12.030}, pmid = {30580028}, issn = {1873-6351}, mesh = {Animals ; DNA, Plant/blood/*genetics ; Food, Genetically Modified/*adverse effects ; Gastrointestinal Tract/metabolism ; Gene Expression Regulation/genetics ; Gene Transfer, Horizontal/*genetics ; Humans ; MicroRNAs/genetics ; Plants, Genetically Modified/*genetics ; Transfection ; Transgenes/genetics ; }, abstract = {Global commercialization of GM food and feed has stimulated much debate over the fate of GM food-derived DNA in the body of the consumer and as to whether it poses any health risks. We reviewed the fate of DNA derived from GM food in the human body. During mechanical/chemical processing, integrity of DNA is compromised. Food-DNA can survive harsh processing and digestive conditions with fragments up to a few hundred bp detectable in the gastrointestinal tract. Compelling evidence supported the presence of food (also GM food) derived DNA in the blood and tissues of human/animal. There is limited evidence of food-born DNA integrating into the genome of the consumer and of horizontal transfer of GM crop DNA into gut-bacteria. We find no evidence that transgenes in GM crop-derived foods have a greater propensity for uptake and integration than the host DNA of the plant-food. We found no evidence of plant-food DNA function/expression following transfer to either the gut-bacteria or somatic cells. Strong evidence suggested that plant-food-miRNAs can survive digestion, enter the body and affect gene expression patterns. We envisage that this multi-dimensional review will address questions regarding the fate of GM food-derived DNA and gene-regulatory-RNA in the human body.}, }
@article {pmid30579929, year = {2019}, author = {Guo, M and Ye, J and Gao, D and Xu, N and Yang, J}, title = {Agrobacterium-mediated horizontal gene transfer: Mechanism, biotechnological application, potential risk and forestalling strategy.}, journal = {Biotechnology advances}, volume = {37}, number = {1}, pages = {259-270}, doi = {10.1016/j.biotechadv.2018.12.008}, pmid = {30579929}, issn = {1873-1899}, mesh = {Agrobacterium/*genetics ; Biotechnology/*trends ; Gene Transfer Techniques/*trends ; Plants, Genetically Modified/genetics ; Transformation, Genetic ; }, abstract = {The extraordinary capacity of Agrobacterium to transfer its genetic material to host cell makes it evolve from phytopathogen to a powerful transgenic vector. Agrobacterium-mediated stable transformation is widely used as the preferred method to create transgenic plants for molecular plant biology research and crop breeding. Recent years, both mechanism and application of Agrobacterium-mediated horizontal gene transfer have made significant progresses, especially Agrobacterium-mediated transient transformation was developed for plant biotechnology industry to produce recombinant proteins. Agrobacterium strains are almost used and saved not only by each of microbiology and molecular plant labs, but also by many of plant biotechnology manufacturers. Agrobacterium is able to transfer its genetic material to a broad range of hosts, including plant and non-plant hosts. As a consequence, the concern of environmental risk associated with the accidental release of genetically modified Agrobacterium arises. In this article, we outline the recent progress in the molecular mechanism of Agrobacterium-meditated gene transfer, focus on the application of Agrobacterium-mediated horizontal gene transfer, and review the potential risk associated with Agrobacterium-meditated gene transfer. Based on the comparison between the infecting process of Agrobacterium as a pathogen and the transgenic process of Agrobacterium as a transgenic vector, we realize that chemotaxis is the distinct difference between these two biological processes and thus discuss the possible role of chemotaxis in forestalling the potential risk of Agrobacterium-meditated horizontal gene transfer to non-target plant species.}, }
@article {pmid30578286, year = {2019}, author = {Daniels, CJ and Lai, LB and Chen, TH and Gopalan, V}, title = {Both kinds of RNase P in all domains of life: surprises galore.}, journal = {RNA (New York, N.Y.)}, volume = {25}, number = {3}, pages = {286-291}, pmid = {30578286}, issn = {1469-9001}, support = {R01 GM120582/GM/NIGMS NIH HHS/United States ; R21 NS096600/NS/NINDS NIH HHS/United States ; }, mesh = {Archaea/classification/genetics/metabolism ; Bacteria/classification/genetics/metabolism ; Biological Evolution ; Enzyme Activation ; Gene Transfer, Horizontal ; Ribonuclease P/*genetics/*metabolism ; Ribonucleoproteins/metabolism ; Species Specificity ; }, abstract = {RNase P, an essential housekeeping endonuclease needed for 5'-processing of tRNAs, exists in two distinct forms: one with an RNA- and the other with a protein-based active site. The notion that the protein form of RNase P exists only in eukaryotes has been upended by the recent discovery of a protein-only variant in Bacteria and Archaea. The use of these two divergent scaffolds, shaped by convergent evolution, in all three domains of life inspires questions relating to the ancestral form of RNase P, as well as their origins and function(s) in vivo. Results from our analysis of publicly available bacterial and archaeal genomes suggest that the widespread RNA-based ribonucleoprotein variant is likely the ancient form. We also discuss the possible genetic origins and function of RNase P, including how the simultaneous presence of its variants may contribute to the fitness of their host organisms.}, }
@article {pmid30576446, year = {2019}, author = {Ballinger, MJ and Gawryluk, RMR and Perlman, SJ}, title = {Toxin and Genome Evolution in a Drosophila Defensive Symbiosis.}, journal = {Genome biology and evolution}, volume = {11}, number = {1}, pages = {253-262}, pmid = {30576446}, issn = {1759-6653}, mesh = {Animals ; *Biological Evolution ; Drosophila/*microbiology ; Female ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Host-Parasite Interactions/*genetics ; Male ; Rhabditida ; Saporins/*genetics/metabolism ; Species Specificity ; Spiroplasma/*physiology ; Symbiosis ; Transcriptome ; }, abstract = {Defenses conferred by microbial symbionts play a vital role in the health and fitness of their animal hosts. An important outstanding question in the study of defensive symbiosis is what determines long term stability and effectiveness against diverse natural enemies. In this study, we combine genome and transcriptome sequencing, symbiont transfection and parasite protection experiments, and toxin activity assays to examine the evolution of the defensive symbiosis between Drosophila flies and their vertically transmitted Spiroplasma bacterial symbionts, focusing in particular on ribosome-inactivating proteins (RIPs), symbiont-encoded toxins that have been implicated in protection against both parasitic wasps and nematodes. Although many strains of Spiroplasma, including the male-killing symbiont (sMel) of Drosophila melanogaster, protect against parasitic wasps, only the strain (sNeo) that infects the mycophagous fly Drosophila neotestacea appears to protect against parasitic nematodes. We find that RIP repertoire is a major differentiating factor between strains that do and do not offer nematode protection, and that sMel RIPs do not show activity against nematode ribosomes in vivo. We also discovered a strain of Spiroplasma infecting a mycophagous phorid fly, Megaselia nigra. Although both the host and its Spiroplasma are distantly related to D. neotestacea and its symbiont, genome sequencing revealed that the M. nigra symbiont encodes abundant and diverse RIPs, including plasmid-encoded toxins that are closely related to the RIPs in sNeo. Our results suggest that distantly related Spiroplasma RIP toxins may perform specialized functions with regard to parasite specificity and suggest an important role for horizontal gene transfer in the emergence of novel defensive phenotypes.}, }
@article {pmid30576310, year = {2018}, author = {Rendueles, O and de Sousa, JAM and Bernheim, A and Touchon, M and Rocha, EPC}, title = {Genetic exchanges are more frequent in bacteria encoding capsules.}, journal = {PLoS genetics}, volume = {14}, number = {12}, pages = {e1007862}, pmid = {30576310}, issn = {1553-7404}, mesh = {Bacteria/classification/*genetics ; Bacterial Capsules/*genetics ; DNA Restriction-Modification Enzymes/genetics ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Homologous Recombination ; Interspersed Repetitive Sequences ; Phylogeny ; Species Specificity ; }, abstract = {Capsules allow bacteria to colonize novel environments, to withstand numerous stresses, and to resist antibiotics. Yet, even though genetic exchanges with other cells should be adaptive under such circumstances, it has been suggested that capsules lower the rates of homologous recombination and horizontal gene transfer. We analysed over one hundred pan-genomes and thousands of bacterial genomes for the evidence of an association between genetic exchanges (or lack thereof) and the presence of a capsule system. We found that bacteria encoding capsules have larger pan-genomes, higher rates of horizontal gene transfer, and higher rates of homologous recombination in their core genomes. Accordingly, genomes encoding capsules have more plasmids, conjugative elements, transposases, prophages, and integrons. Furthermore, capsular loci are frequent in plasmids, and can be found in prophages. These results are valid for Bacteria, independently of their ability to be naturally transformable. Since we have shown previously that capsules are commonly present in nosocomial pathogens, we analysed their co-occurrence with antibiotic resistance genes. Genomes encoding capsules have more antibiotic resistance genes, especially those encoding efflux pumps, and they constitute the majority of the most worrisome nosocomial bacteria. We conclude that bacteria with capsule systems are more genetically diverse and have fast-evolving gene repertoires, which may further contribute to their success in colonizing novel niches such as humans under antibiotic therapy.}, }
@article {pmid30574264, year = {2018}, author = {Armijos-Jaramillo, V and Santander-Gordón, D and Tejera, E and Perez-Castillo, Y}, title = {The dilemma of bacterial expansins evolution. The unusual case of Streptomyces acidiscabies and Kutzneria sp. 744.}, journal = {Communicative &amp; integrative biology}, volume = {11}, number = {5-6}, pages = {e1539612}, pmid = {30574264}, issn = {1942-0889}, abstract = {Expansins are a superfamily of proteins mainly present in plants that are also found in bacteria, fungi and amoebozoa. Expansin proteins bind the plant cells wall and relax the cellulose microfibrils without any enzymatic action. The evolution of this kind of proteins exposes a complex pattern of horizontal gene transferences that makes difficult to determine the precise origin of non-plant expansins. We performed a genome-wide search of inter-domain horizontal gene transfer events using Streptomyces species and found a plant-like expansin in the Streptomyces acidiscabies proteome. This finding leads us to study in deep the origin and the characteristics of this peculiar protein, also present in the species Kutzneria sp.744. Using phylogenetic analyses, we determine that indeed S. acidiscabies and Kutzneria sp.744 expansins are located inside the plants expansins A clade. Using secondary and tertiary structural information, we observed that the electrostatic potentials and the folding of expansins are similar, independently of the proteins' origin. Using all this information, we conclude that S. acidiscabies and Kutzneria sp.744 expansins have a plant origin but differ from plant and bacterial canonical expansins. This finding suggests that the experimental research around this kind of expansins can be promissory in the future.}, }
@article {pmid30574213, year = {2018}, author = {Botelho, J and Roberts, AP and León-Sampedro, R and Grosso, F and Peixe, L}, title = {Carbapenemases on the move: it's good to be on ICEs.}, journal = {Mobile DNA}, volume = {9}, number = {}, pages = {37}, pmid = {30574213}, issn = {1759-8753}, abstract = {BACKGROUND: The evolution and spread of antibiotic resistance is often mediated by mobile genetic elements. Integrative and conjugative elements (ICEs) are the most abundant conjugative elements among prokaryotes. However, the contribution of ICEs to horizontal gene transfer of antibiotic resistance has been largely unexplored.<br><br>RESULTS: Here we report that ICEs belonging to mating-pair formation (MPF) classes G and T are highly prevalent among the opportunistic pathogen Pseudomonas aeruginosa, contributing to the spread of carbapenemase-encoding genes (CEGs). Most CEGs of the MPFG class were encoded within class I integrons, which co-harbour genes conferring resistance to other antibiotics. The majority of the integrons were located within Tn3-like and composite transposons. Conserved attachment site could be predicted for the MPFG class ICEs. MPFT class ICEs carried the CEGs within composite transposons which were not associated with integrons.<br><br>CONCLUSIONS: The data presented here provides a global snapshot of the different CEG-harbouring ICEs and sheds light on the underappreciated contribution of these elements to the evolution and dissemination of antibiotic resistance on P. aeruginosa.}, }
@article {pmid30574133, year = {2018}, author = {Isidro, J and Menezes, J and Serrano, M and Borges, V and Paixão, P and Mimoso, M and Martins, F and Toscano, C and Santos, A and Henriques, AO and Oleastro, M}, title = {Genomic Study of a Clostridium difficile Multidrug Resistant Outbreak-Related Clone Reveals Novel Determinants of Resistance.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2994}, pmid = {30574133}, issn = {1664-302X}, abstract = {Background: Clostridium difficile infection (CDI) is prevalent in healthcare settings. The emergence of hypervirulent and antibiotic resistant strains has led to an increase in CDI incidence and frequent outbreaks. While the main virulence factors are the TcdA and TcdB toxins, antibiotic resistance is thought to play a key role in the infection by and dissemination of C. difficile. Methods: A CDI outbreak involving 12 patients was detected in a tertiary care hospital, in Lisbon, which extended from January to July, with a peak in February, in 2016. The C. difficile isolates, obtained from anaerobic culture of stool samples, were subjected to antimicrobial susceptibility testing with Etest[®]strips against 11 antibiotics, determination of toxin genes profile, PCR-ribotyping, multilocus variable-number tandem-repeat analysis (MLVA) and whole genome sequencing (WGS). Results: Of the 12 CDI cases detected, 11 isolates from 11 patients were characterized. All isolates were tcdA [-]/tcdB [+] and belonged to ribotype 017, and showed high level resistance to clindamycin, erythromycin, gentamicin, imipenem, moxifloxacin, rifampicin and tetracycline. The isolates belonged to four genetically related MLVA types, with six isolates forming a clonal cluster. Three outbreak isolates, each from a different MLVA type, were selected for WGS. Bioinformatics analysis showed the presence of several antibiotic resistance determinants, including the Thr82Ile substitution in gyrA, conferring moxifloxacin resistance, the substitutions His502Asn and Arg505Lys in rpoB for rifampicin resistance, the tetM gene, associated with tetracycline resistance, and two genes encoding putative aminoglycoside-modifying enzymes, aadE and aac(6')-aph(2″). Furthermore, a not previously described 61.3 kb putative mobile element was identified, presenting a mosaic structure and containing the genes ermG, mefA/msrD and vat, associated with macrolide, lincosamide and streptogramins resistance. A substitution found in a class B penicillin-binding protein, Cys721Ser, is thought to contribute to imipenem resistance. Conclusion: We describe an epidemic, tcdA [-]/tcdB [+], multidrug resistant clone of C. difficile from ribotype 017 associated with a hospital outbreak, providing further evidence that the lack of TcdA does not impair the infectious potential of these strains. We identified several determinants of antimicrobial resistance, including new ones located in mobile elements, highlighting the importance of horizontal gene transfer in the pathogenicity and epidemiological success of C. difficile.}, }
@article {pmid30567899, year = {2018}, author = {Sakuda, A and Suzuki-Minakuchi, C and Okada, K and Nojiri, H}, title = {Conjugative Selectivity of Plasmids Is Affected by Coexisting Recipient Candidates.}, journal = {mSphere}, volume = {3}, number = {6}, pages = {}, pmid = {30567899}, issn = {2379-5042}, mesh = {*Conjugation, Genetic ; Gene Transfer Techniques ; *Gene Transfer, Horizontal ; Plasmids/*metabolism ; Pseudomonas/*genetics ; }, abstract = {Understanding the mechanisms underlying plasmid behavior under conditions of various environments is important to predict the fate of plasmids in nature. Most previous studies on plasmid transfer employed two strains: one as a donor and the other as a recipient. However, in natural environments, there are usually different recipient cells available to which plasmid can be transferred. In this study, to reveal the underlying mechanisms, we assessed the transferability of plasmids from one donor strain to either of two recipient candidates as the most simplified model. We used Pseudomonas putida KT2440 and Pseudomonas resinovorans CA10dm4 as model hosts and pCAR1 (IncP-7), NAH7 (IncP-9), pB10 (IncP-1β), and R388 (IncW) as model plasmids. As expected, in most cases these plasmids were generally transferred more frequently to a recipient of the same species than to a recipient of a different one under conditions of liquid and filter mating, although NAH7 was transferred from P. resinovorans more frequently to P. putida than to P. resinovorans during filter mating. With the exception of pCAR1, which was less affected, the coexistence of other recipients enhanced the preferences of conjugative transfer to the same species. In particular, preferences corresponding to transfer from P. putida to a different recipient (P. resinovorans) were reduced by the presence of a coexisting same recipient (P. putida) during transfer of NAH7 in liquid and transfer of R388 in filter mating. We determined that large cell aggregates and substances secreted into culture supernatant were not responsible for this phenomenon. Overall, the results of this study suggest the existence of unknown factors determining optimal plasmid transfer to native recipients.IMPORTANCE Most previous studies on plasmid conjugal transfer employed experimental setups with two strains: one as a donor and the other as a recipient. However, the results obtained sometimes failed to agree with observations obtained under natural environmental conditions or in a model microcosm using natural soil and water samples. Therefore, we consider that there is a "gap" in our understanding of plasmid behavior in the context of bacterial consortia that exist under the actual environmental conditions. In this study, we clearly showed that the conjugation selectivity of a plasmid can be affected by the recipient candidates existing around the donor strain by the use of a simplified experimental setup with one strain as the donor and two strains as recipients. These phenomena could not be explained by factors known to affect plasmid transfer as suggested by previous studies. Therefore, we suggest the presence of novel elements regulating plasmid transfer within consortia.}, }
@article {pmid30564220, year = {2018}, author = {Nazarian, P and Tran, F and Boedicker, JQ}, title = {Modeling Multispecies Gene Flow Dynamics Reveals the Unique Roles of Different Horizontal Gene Transfer Mechanisms.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2978}, pmid = {30564220}, issn = {1664-302X}, abstract = {Horizontal gene transfer within diverse bacterial populations occurs through multiple mechanisms of exchange. The most established routes of gene transfer, transduction, transformation, and conjugation, have been characterized in detail, revealing the advantages and limitations of each mechanism. More recently, interspecies gene exchange via extracellular vesicles has been reported and characterized, making vesicle-mediated exchange a fourth, general mechanism of gene transfer. Despite an understanding of each individual pathway, how all of these mechanisms act in concert has not been explored. Here we develop a model of gene exchange in a multispecies bacterial community that takes into account the rates and limitations of all four gene transfer mechanisms. Our results reveal unique roles for each gene exchange mechanism, and highlight how multiple pathways working together are required for widespread gene exchange within diverse bacterial populations.}, }
@article {pmid30563906, year = {2018}, author = {Ryazansky, S and Kulbachinskiy, A and Aravin, AA}, title = {The Expanded Universe of Prokaryotic Argonaute Proteins.}, journal = {mBio}, volume = {9}, number = {6}, pages = {}, pmid = {30563906}, issn = {2150-7511}, mesh = {Archaea/*physiology ; Archaeal Proteins/physiology ; Argonaute Proteins/*physiology ; Bacteria/*metabolism ; Bacterial Proteins/physiology ; Eukaryota/genetics ; Gene Editing ; Gene Transfer, Horizontal ; *Genome ; Protein Binding ; RNA Interference ; }, abstract = {Members of the ancient family of Argonaute (Ago) proteins are present in all domains of life. The common feature of Ago proteins is the ability to bind small nucleic acid guides and use them for sequence-specific recognition-and sometimes cleavage-of complementary targets. While eukaryotic Ago (eAgo) proteins are key players in RNA interference and related pathways, the properties and functions of these proteins in archaeal and bacterial species have just started to emerge. We undertook comprehensive exploration of prokaryotic Ago (pAgo) proteins in sequenced genomes and revealed their striking diversity in comparison with eAgos. Many pAgos contain divergent variants of the conserved domains involved in interactions with nucleic acids, while having extra domains that are absent in eAgos, suggesting that they might have unusual specificities in the nucleic acid recognition and cleavage. Many pAgos are associated with putative nucleases, helicases, and DNA binding proteins in the same gene or operon, suggesting that they are involved in target processing. The great variability of pAgos revealed by our analysis opens new ways for exploration of their functions in host cells and for their use as potential tools in genome editing.IMPORTANCE The eukaryotic Ago proteins and the RNA interference pathways they are involved in are widely used as a powerful tool in research and as potential therapeutics. In contrast, the properties and functions of prokaryotic Ago (pAgo) proteins have remained poorly understood. Understanding the diversity and functions of pAgos holds a huge potential for discovery of new cellular pathways and novel tools for genome manipulations. Only few pAgos have been characterized by structural or biochemical approaches, while previous genomic studies discovered about 300 proteins in archaeal and eubacterial genomes. Since that time the number of bacterial strains with sequenced genomes has greatly expanded, and many previously sequenced genomes have been revised. We undertook comprehensive analysis of pAgo proteins in sequenced genomes and almost tripled the number of known genes of this family. Our research thus forms a foundation for further experimental characterization of pAgo functions that will be important for understanding of the basic biology of these proteins and their adoption as a potential tool for genome engineering in the future.}, }
@article {pmid30563853, year = {2019}, author = {Pang, TY and Lercher, MJ}, title = {Each of 3,323 metabolic innovations in the evolution of E. coli arose through the horizontal transfer of a single DNA segment.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {1}, pages = {187-192}, pmid = {30563853}, issn = {1091-6490}, mesh = {Adaptation, Physiological/genetics ; Biological Evolution ; DNA, Bacterial/*genetics ; Escherichia coli/*genetics/metabolism ; Gene Transfer, Horizontal/*genetics/physiology ; Genes, Bacterial/genetics ; Genetic Association Studies ; Phylogeny ; }, abstract = {Even closely related prokaryotes often show an astounding diversity in their ability to grow in different nutritional environments. It has been hypothesized that complex metabolic adaptations-those requiring the independent acquisition of multiple new genes-can evolve via selectively neutral intermediates. However, it is unclear whether this neutral exploration of phenotype space occurs in nature, or what fraction of metabolic adaptations is indeed complex. Here, we reconstruct metabolic models for the ancestors of a phylogeny of 53 Escherichia coli strains, linking genotypes to phenotypes on a genome-wide, macroevolutionary scale. Based on the ancestral and extant metabolic models, we identify 3,323 phenotypic innovations in the history of the E. coli clade that arose through changes in accessory genome content. Of these innovations, 1,998 allow growth in previously inaccessible environments, while 1,325 increase biomass yield. Strikingly, every observed innovation arose through the horizontal acquisition of a single DNA segment less than 30 kb long. Although we found no evidence for the contribution of selectively neutral processes, 10.6% of metabolic innovations were facilitated by horizontal gene transfers on earlier phylogenetic branches, consistent with a stepwise adaptation to successive environments. Ninety-eight percent of metabolic phenotypes accessible to the combined E. coli pangenome can be bestowed on any individual strain by transferring a single DNA segment from one of the extant strains. These results demonstrate an amazing ability of the E. coli lineage to adapt to novel environments through single horizontal gene transfers (followed by regulatory adaptations), an ability likely mirrored in other clades of generalist bacteria.}, }
@article {pmid30563447, year = {2018}, author = {Cordes, MHJ and Binford, GJ}, title = {Evolutionary dynamics of origin and loss in the deep history of phospholipase D toxin genes.}, journal = {BMC evolutionary biology}, volume = {18}, number = {1}, pages = {194}, pmid = {30563447}, issn = {1471-2148}, support = {R15 GM097676/GM/NIGMS NIH HHS/United States ; R15 GM097696/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Conserved Sequence ; *Evolution, Molecular ; Operon/genetics ; Phospholipase D/*genetics ; Phylogeny ; Protein Domains ; Sequence Homology, Amino Acid ; Toxins, Biological/*genetics ; }, abstract = {BACKGROUND: Venom-expressed sphingomyelinase D/phospholipase D (SMase D/PLD) enzymes evolved from the ubiquitous glycerophosphoryl diester phosphodiesterases (GDPD). Expression of GDPD-like SMaseD/PLD toxins in both arachnids and bacteria has inspired consideration of the relative contributions of lateral gene transfer and convergent recruitment in the evolutionary history of this lineage. Previous work recognized two distinct lineages, a SicTox-like (ST-like) clade including the arachnid toxins, and an Actinobacterial-toxin like (AT-like) clade including the bacterial toxins and numerous fungal homologs.<br><br>RESULTS: Here we expand taxon sampling by homology detection to discover new GDPD-like SMase D/PLD homologs. The ST-like clade now includes homologs in a wider variety of arthropods along with a sister group in Cnidaria; the AT-like clade now includes additional fungal phyla and proteobacterial homologs; and we report a third clade expressed in diverse aquatic metazoan taxa, a few single-celled eukaryotes, and a few aquatic proteobacteria. GDPD-like SMaseD/PLDs have an ancient presence in chelicerates within the ST-like family and ctenophores within the Aquatic family. A rooted phylogenetic tree shows that the three clades derived from a basal paraphyletic group of proteobacterial GDPD-like SMase D/PLDs, some of which are on mobile genetic elements. GDPD-like SMase D/PLDs share a signature C-terminal motif and a shortened &#x3b2;&#x3b1;1 loop, features that distinguish them from GDPDs. The three major clades also have active site loop signatures that distinguish them from GDPDs and from each other. Analysis of molecular phylogenies with respect to organismal relationships reveals a dynamic evolutionary history including both lateral gene transfer and gene duplication/loss.<br><br>CONCLUSIONS: The GDPD-like SMaseD/PLD enzymes derive from a single ancient ancestor, likely proteobacterial, and radiated into diverse organismal lineages at least in part through lateral gene transfer.}, }
@article {pmid30562602, year = {2019}, author = {Jain, M and Sharma, A and Sen, MK and Rani, V and Gaind, R and Suri, JC}, title = {Phenotypic and molecular characterization of Acinetobacter baumannii isolates causing lower respiratory infections among ICU patients.}, journal = {Microbial pathogenesis}, volume = {128}, number = {}, pages = {75-81}, doi = {10.1016/j.micpath.2018.12.023}, pmid = {30562602}, issn = {1096-1208}, mesh = {Acinetobacter Infections/epidemiology/*microbiology/transmission ; Acinetobacter baumannii/drug effects/*genetics/*isolation &amp; purification/pathogenicity ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Biofilms/drug effects/growth &amp; development ; Carbapenem-Resistant Enterobacteriaceae/genetics ; Carbapenems/pharmacology ; Colistin/pharmacology ; Cross Infection ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Genotype ; Hospitals ; Humans ; India ; *Intensive Care Units ; Microbial Sensitivity Tests ; Microbiological Techniques ; *Molecular Typing ; *Phenotype ; Prevalence ; Prospective Studies ; Respiratory Tract Infections/epidemiology/*microbiology/transmission ; Species Specificity ; Virulence ; beta-Lactamases/genetics ; }, abstract = {BACKGROUND: Multi-drug resistant Acinetobacter baumannii has emerged as important nosocomial pathogen associated with various infections including lower respiratory tract. Limited therapeutic options contribute to increased morbidity and mortality. Acinetobacter baumannii has the ability to persist in the environment for prolonged periods. Breach in infection control practices increases the chances of cross transmission between patients and inter/intraspecies transmission of resistance elements. The present prospective work was conducted among patients with lower respiratory tract infections (LRTI) in the intensive care unit (ICU) to study the etiology with special reference to Acinetobacter baumannii and the role of immediate patient environment in the ICU as possible source of infection. Acinetobacter baumannii were characterized for antimicrobial susceptibility, mechanism of carbapenem resistance and virulence determinants. Molecular typing of the clinical and environmental isolates was undertaken to study the probable modes of transmission.<br><br>MATERIALS AND METHODS: Appropriate respiratory samples from 107 patients with LRTI admitted to ICU during September 2016 to March 2017 were studied for likely bacterial pathogens. Environmental samples (n&#x202f;=&#x202f;71) were also screened. All the samples were processed using conventional microbiological methods. Consecutive Acinetobacter spp. isolated from clinical and environmental (health care workers and environment from ICU) samples were included in the study. Antimicrobial susceptibility was performed as per CLSI guidelines. Carbapenem resistance, mediated by carbapenemase genes (blaOXA-23-like,blaOXA-24-like,blaOXA-58-like and blaNDM-1) were studied by PCR. Biofilm forming ability was tested phenotypically using microtitre plate method. Pulse Field Gel Electrophoresis (PFGE) was used to study clonality of the clinical and environmental isolates.<br><br>RESULTS: The prevalence of Acinetobacter baumannii was 26.2% (28/107) and 11.26% (8/71) among patients with LRTI and environmental samples respectively. The carbapenem resistance was high, 96.42% (27/28) and 87.5% (7/8) in clinical and environmental isolates respectively. The most common carbapenemase associated with resistance was blaOXA-23-like gene followed by blaNDM-1 among both the clinical and environmental isolates. All isolates were sensitive to colistin (MIC&#x202f;&#x2264;&#x202f;1&#x202f;&#x3bc;g/ml). Biofilm production was observed among all clinical (n&#x202f;=&#x202f;28) and 87.5% (7/8) of the environmental isolates. Line listing of the cases suggests the occurrence of infections throughout the study period with no significant clustering. On PFGE, 12 clusters were observed and 16/36 isolates were present in one single cluster that included both clinical and environmental isolates which were either carbapenem resistant or sensitive.<br><br>DISCUSSION: Carbapenem resistant Acinetobacter baumannii (CRAB) is an important cause of LRTI in the ICU. PFGE suggests spread of carbapenem resistant isolates via cross transmission among patients and the environment. The detection of blaNDM-1 gene among Acinetobacter baumannii and existence of carbapenem resistant and sensitive isolates within the same clones suggests horizontal transmission of resistant genes among various bacterial species. The ability of Acinetobacter baumannii to form biofilms may contribute to its persistence in the environment. This along with breach in infection control practices are the likely factors contributing to this transmission. This information can be used to strengthen and monitor infection control (IC) and the hospital cleaning and disinfection practices to prevent spread of resistant organisms within the ICU. Colistin remains drug of choice for management of CRAB.}, }
@article {pmid30559406, year = {2019}, author = {Kintses, B and Méhi, O and Ari, E and Számel, M and Györkei, &#xc1; and Jangir, PK and Nagy, I and Pál, F and Fekete, G and Tengölics, R and Nyerges, &#xc1; and Likó, I and Bálint, A and Molnár, T and Bálint, B and Vásárhelyi, BM and Bustamante, M and Papp, B and Pál, C}, title = {Phylogenetic barriers to horizontal transfer of antimicrobial peptide resistance genes in the human gut microbiota.}, journal = {Nature microbiology}, volume = {4}, number = {3}, pages = {447-458}, pmid = {30559406}, issn = {2058-5276}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Antimicrobial Cationic Peptides/*genetics ; Bacteria/*genetics ; Escherichia coli/genetics ; Gastrointestinal Microbiome/*genetics ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Genome, Bacterial ; Humans ; Metagenomics ; *Phylogeny ; }, abstract = {The human gut microbiota has adapted to the presence of antimicrobial peptides (AMPs), which are ancient components of immune defence. Despite its medical importance, it has remained unclear whether AMP resistance genes in the gut microbiome are available for genetic exchange between bacterial species. Here, we show that AMP resistance and antibiotic resistance genes differ in their mobilization patterns and functional compatibilities with new bacterial hosts. First, whereas AMP resistance genes are widespread in the gut microbiome, their rate of horizontal transfer is lower than that of antibiotic resistance genes. Second, gut microbiota culturing and functional metagenomics have revealed that AMP resistance genes originating from phylogenetically distant bacteria have only a limited potential to confer resistance in Escherichia coli, an intrinsically susceptible species. Taken together, functional compatibility with the new bacterial host emerges as a key factor limiting the genetic exchange of AMP resistance genes. Finally, our results suggest that AMPs induce highly specific changes in the composition of the human microbiota, with implications for disease risks.}, }
@article {pmid30559200, year = {2018}, author = {Klemm, EJ and Wong, VK and Dougan, G}, title = {Emergence of dominant multidrug-resistant bacterial clades: Lessons from history and whole-genome sequencing.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {51}, pages = {12872-12877}, pmid = {30559200}, issn = {1091-6490}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/drug effects/*genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genotype ; *Whole Genome Sequencing ; }, abstract = {Antibiotic resistance in bacteria has emerged as a global challenge over the past 90 years, compromising our ability to effectively treat infections. There has been a dramatic increase in antibiotic resistance-associated determinants in bacterial populations, driven by the mobility and infectious nature of such determinants. Bacterial genome flexibility and antibiotic-driven selection are at the root of the problem. Genome evolution and the emergence of highly successful multidrug-resistant clades in different pathogens have made this a global challenge. Here, we describe some of the factors driving the origin, evolution, and spread of the antibiotic resistance genotype.}, }
@article {pmid30559176, year = {2018}, author = {Relman, DA and Lipsitch, M}, title = {Microbiome as a tool and a target in the effort to address antimicrobial resistance.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {51}, pages = {12902-12910}, pmid = {30559176}, issn = {1091-6490}, support = {R01 AI112401/AI/NIAID NIH HHS/United States ; R01 GM099534/GM/NIGMS NIH HHS/United States ; }, mesh = {Anti-Infective Agents/*pharmacology ; Communicable Disease Control/*methods ; Communicable Diseases/drug therapy ; Drug Resistance, Microbial/*drug effects/genetics ; Host Microbial Interactions/drug effects/genetics/immunology ; Humans ; Microbiota/*drug effects ; Vaccines/*therapeutic use ; }, abstract = {Reciprocal, intimate relationships between the human microbiome and the host immune system are shaped by past microbial encounters and prepare the host for future ones. Antibiotics and other antimicrobials leave their mark on both the microbiome and host immunity. Antimicrobials alter the structure of the microbiota, expand the host-specific pool of antimicrobial-resistance genes and organisms, degrade the protective effects of the microbiota against invasion by pathogens, and may impair vaccine efficacy. Through these effects on the microbiome they may affect immune responses. Vaccines that exert protective or therapeutic effects against pathogens may reduce the use of antimicrobials, the development and spread of antimicrobial resistance, and the harmful impacts of these drugs on the microbiome. Other strategies involving manipulation of the microbiome to deplete antibiotic-resistant organisms or to enhance immune responses to vaccines may prove valuable in addressing antimicrobial resistance as well. This article describes the intersections of immunity, microbiome and antimicrobial exposure, and the use of vaccines and other alternative strategies for the control and management of antimicrobial resistance.}, }
@article {pmid30559068, year = {2019}, author = {Garcia, BG and Castro, FS and Vieira, MAM and Girão, DM and Uenishi, LT and Cergole-Novella, MC and Dos Santos, LF and Piazza, RMF and Hernandes, RT and Gomes, TAT}, title = {Distribution of the pilS gene in Escherichia coli pathovars, its transfer ability and influence in the typical enteropathogenic E. coli adherence phenotype.}, journal = {International journal of medical microbiology : IJMM}, volume = {309}, number = {1}, pages = {66-72}, doi = {10.1016/j.ijmm.2018.12.001}, pmid = {30559068}, issn = {1618-0607}, mesh = {Alleles ; Bacterial Adhesion/*genetics ; Bacterial Proteins/*genetics ; Brazil ; Chile ; Conjugation, Genetic/genetics ; Enteropathogenic Escherichia coli/*genetics/isolation &amp; purification ; Escherichia coli Infections/*microbiology ; Escherichia coli Proteins/*genetics ; Fimbriae, Bacterial/genetics ; HeLa Cells ; Humans ; Operon ; Peru ; Plasmids ; Serogroup ; Transcription Factors/*genetics ; Virulence/genetics ; }, abstract = {Typical enteropathogenic Escherichia coli strains (tEPEC) cause attaching/effacing lesions in eukaryotic cells and produce the bundle-forming pilus (BFP), which interweaves and aggregates bacteria, resulting in the localized adherence (LA) pattern on eukaryotic cells. Previously, we identified tEPEC strains (serotype O119:H6) that exhibited LA simultaneously with an aggregative adherence (AA)-like pattern (LA/AA-like+). Remarkably, AA is characteristically produced by strains of enteroaggregative E. coli (EAEC), another diarrheagenic E. coli pathovar. In one LA/AA-like + strain (Ec404/03), we identified a conjugative plasmid containing the pil operon, which encodes the Pil fimbriae. Moreover, a pil operon associated with an AA pattern and plasmid transfer had been previously described in the EAEC C1096 strain. In this study, we investigated the occurrence of the two pilS alleles (pilSEc404 and pilSC1096) in tEPEC strains of different serotypes, origins and years of isolation. We also examined the potential relationship of pilS with the AA-like phenotype, its ability to be transferred by conjugation, and occurrence among strains of the other E. coli pathovars. The pilS alleles were found in 90 (55.2%) of 163 tEPEC strains, with pilSEc404 occurring more often (30.7%) than pilSC1096 (25.1%). About 21 tEPEC serotypes carried pilS. The pilS alleles were found in tEPEC strains from Chile, Peru and different Brazilian cities, with the oldest strain being isolated in 1966. No absolute correlation was found between the presence of pilS and the AA-like pattern. Conjugative pilS transfer was detected in 26.2% of pilSEc404+ strains and in 65.1% of pilSC1096+ strains, but only pilSEc404+ transconjugants were AA-like+, thus suggesting that the latter allele might need a different genetic background to express this phenotype. pilS was found in all other E. coli pathovars, where it was most prevalent in enterotoxigenic E. coli. More studies are needed to understand the mechanisms involved in the regulation of Pil expression and production.}, }
@article {pmid30558235, year = {2018}, author = {Kampf, G}, title = {Biocidal Agents Used for Disinfection Can Enhance Antibiotic Resistance in Gram-Negative Species.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {7}, number = {4}, pages = {}, pmid = {30558235}, issn = {2079-6382}, abstract = {Biocidal agents used for disinfection are usually not suspected to enhance cross-resistance to antibiotics. The aim of this review was therefore to evaluate the effect of 13 biocidal agents at sublethal concentrations on antibiotic resistance in Gram-negative species. A medline search was performed for each biocidal agent on antibiotic tolerance, antibiotic resistance, horizontal gene transfer, and efflux pump. In cells adapted to benzalkonium chloride a new resistance was most frequently found to ampicillin (eight species), cefotaxime (six species), and sulfamethoxazole (three species), some of them with relevance for healthcare-associated infections such as Enterobacter cloacae or Escherichia coli. With chlorhexidine a new resistance was often found to ceftazidime, sulfamethoxazole and imipenem (eight species each) as well as cefotaxime and tetracycline (seven species each). Cross-resistance to antibiotics was also found with triclosan, octenidine, sodium hypochlorite, and didecyldimethylammonium chloride. No cross-resistance to antibiotics has been described after low level exposure to ethanol, propanol, peracetic acid, polyhexanide, povidone iodine, glutaraldehyde, and hydrogen peroxide. Taking into account that some biocidal agents used in disinfectants have no health benefit (e.g., in alcohol-based hand rubs) but may cause antibiotic resistance it is obvious to prefer products without them.}, }
@article {pmid30557684, year = {2019}, author = {Tafaj, S and Gona, F and Kapisyzi, P and Cani, A and Hatibi, A and Bino, S and Fico, A and Koraqi, A and Kasmi, G and Cirillo, D}, title = {Isolation of the first New Delhi metallo-ß-lactamase-1 (NDM-1)-producing and colistin-resistant Klebsiella pneumoniae sequence type ST15 from a digestive carrier in Albania, May 2018.}, journal = {Journal of global antimicrobial resistance}, volume = {17}, number = {}, pages = {142-144}, doi = {10.1016/j.jgar.2018.12.002}, pmid = {30557684}, issn = {2213-7173}, mesh = {Aged ; Albania ; Anti-Bacterial Agents/*pharmacology ; Bacterial Typing Techniques ; Colistin/*pharmacology ; Drug Resistance, Multiple, Bacterial ; Gastrointestinal Tract/*microbiology ; Humans ; Klebsiella Infections/microbiology ; Klebsiella pneumoniae/classification/*drug effects/isolation &amp; purification ; Longitudinal Studies ; Male ; Microbial Sensitivity Tests ; Mouth/microbiology ; Multilocus Sequence Typing ; Plasmids/genetics ; Rectum/microbiology ; Sequence Analysis, DNA ; *beta-Lactamases ; }, abstract = {OBJECTIVES: Carbapenemases represent a public health threat, as they can spread through horizontal gene transfer and cause outbreaks. New Delhi metallo-ß-lactamase-1 (NDM-1) is a metallo-ß-lactamase that has spread rapidly in the last decade, causing worldwide alarm. This study aimed to describe the first isolate of NDM-1-producing and extensively drug resistant Klebsiella pneumoniae in Albania, its clinical context and genetic characterization.<br><br>METHODS: Strain was isolated from both oral and rectal intensive care unit admission screening swabs of a 70-year-old male patient with no history of international travel in the previous 6 months. Sequencing was performed by Illumina NextSeq500 platform, with a paired-end run of 2 by 150bp, after Nextera XT paired-end library preparation. Sequencing reads were assembled using SPAdes Genome (version 3.6.1) with accurate de novo settings. The assembled contigs were uploaded into the online tools: BIGSdb-Kp, ResFinder and PlasmidFinder.<br><br>RESULTS: Isolate was resistant to all tested antibiotics but tigecycline and trimethoprim-sulfamethoxazole. Sequencing revealed the presence of acquired resistance genes conferring resistance to &#x3b2;-lactams (blaNDM-1, blaCMY-6, blaCTX-M-15and blaSHV-28), aminoglycosides (rmtC, aac(6')-Ib3), fluoroquinolones (oqxA, oqxB, aac(6')-Ib-cr), fosfomycin (fosA) and sulfonamides (sul1). The blaNDM-1 gene was located on an IncA/C2 plasmid. Plasmid mediated mcr-1 to mcr-8 genes were absent in both isolates. Resistance to colistin was due to an amino acid substitution (Thr157Pro) in PmrB protein.<br><br>CONCLUSIONS: NDM-1-producing Enterobacteriaceae are spreading in the Balkans. Identification of NDM-1-producing and extensively drug resistant K. pneumoniae ST15 in Albania is a cause for serious concern. There should be a continuous national and Balkan multinational surveillance of blaNDM-1-carrying isolates.}, }
@article {pmid30555448, year = {2018}, author = {Peterson, E and Kaur, P}, title = {Antibiotic Resistance Mechanisms in Bacteria: Relationships Between Resistance Determinants of Antibiotic Producers, Environmental Bacteria, and Clinical Pathogens.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2928}, pmid = {30555448}, issn = {1664-302X}, abstract = {Emergence of antibiotic resistant pathogenic bacteria poses a serious public health challenge worldwide. However, antibiotic resistance genes are not confined to the clinic; instead they are widely prevalent in different bacterial populations in the environment. Therefore, to understand development of antibiotic resistance in pathogens, we need to consider important reservoirs of resistance genes, which may include determinants that confer self-resistance in antibiotic producing soil bacteria and genes encoding intrinsic resistance mechanisms present in all or most non-producer environmental bacteria. While the presence of resistance determinants in soil and environmental bacteria does not pose a threat to human health, their mobilization to new hosts and their expression under different contexts, for example their transfer to plasmids and integrons in pathogenic bacteria, can translate into a problem of huge proportions, as discussed in this review. Selective pressure brought about by human activities further results in enrichment of such determinants in bacterial populations. Thus, there is an urgent need to understand distribution of resistance determinants in bacterial populations, elucidate resistance mechanisms, and determine environmental factors that promote their dissemination. This comprehensive review describes the major known self-resistance mechanisms found in producer soil bacteria of the genus Streptomyces and explores the relationships between resistance determinants found in producer soil bacteria, non-producer environmental bacteria, and clinical isolates. Specific examples highlighting potential pathways by which pathogenic clinical isolates might acquire these resistance determinants from soil and environmental bacteria are also discussed. Overall, this article provides a conceptual framework for understanding the complexity of the problem of emergence of antibiotic resistance in the clinic. Availability of such knowledge will allow researchers to build models for dissemination of resistance genes and for developing interventions to prevent recruitment of additional or novel genes into pathogens.}, }
@article {pmid30552032, year = {2019}, author = {Liu, Y and Zhang, H and Zhang, X and Jiang, N and Zhang, Z and Zhang, J and Zhu, B and Wang, G and Zhao, K and Zhou, Y}, title = {Characterization of an NDM-19-producing Klebsiella pneumoniae strain harboring 2 resistance plasmids from China.}, journal = {Diagnostic microbiology and infectious disease}, volume = {93}, number = {4}, pages = {355-361}, doi = {10.1016/j.diagmicrobio.2018.11.007}, pmid = {30552032}, issn = {1879-0070}, mesh = {Carbapenem-Resistant Enterobacteriaceae/*enzymology/*genetics/isolation &amp; purification ; China ; Cities ; Conjugation, Genetic ; Gene Transfer, Horizontal ; Genes, Bacterial ; Hospitals ; Humans ; Interspersed Repetitive Sequences ; Klebsiella Infections/*microbiology ; Klebsiella pneumoniae/*enzymology/*genetics/isolation &amp; purification ; Plasmids/*analysis ; Polymerase Chain Reaction ; Respiratory Tract Infections/microbiology ; Sputum/microbiology ; Whole Genome Sequencing ; beta-Lactamases/*genetics ; }, abstract = {Carbapenem-resistant Klebsiella pneumoniae (CRKP) has become a major cause of nosocomial infections and posed challenges on clinical treatments. The main objective of this study was to determinate the genetic characteristics of the NDM-19-producing CRKP strain SCM96. From 2015 to 2017, 18 CRKP strains were recovered from sputum samples of patients in respiratory medicine in 6 hospitals from 5 provinces and cities in China. Polymerase chain reaction results for carbapenem resistance genes detection showed strain SCM96 carried blaNDM-19. Three types of transconjugants harboring different plasmids were selected by conjugation experiment. The Whole Genome Sequencing (WGS) was performed using the PacBio RS platform. The genome size of SCM96 was 5,579,775 bp and composed of chromosomal DNA (5,398,745 bp) and 2 plasmids, IncFII type plasmid pSCM96-1 (134,869 bp) and IncX3 type plasmid pSCM96-2 (46,161 bp). SCM96 belonged to ST15 and K28. In addition to the 4 antibiotic resistance genes located in the chromosome, pSCM96-1 carried a complex resistance region containing 17 resistance genes and several mobile genetic elements (MGEs) like △Tn6029, In4-like integron, and Tn3, and pSCM96-2 had only 1 blaNDM-19 gene. As far as we know, this was the first description of blaNDM-19 in K. pneumoniae. Up to 22 antibiotic resistance genes, several important MGEs, and transferable plasmids might increase the possibility of co-spreading of blaNDM-19 with other resistance genes.}, }
@article {pmid30548092, year = {2019}, author = {Arai, T and Fukami, D and Hoshino, T and Kondo, H and Tsuda, S}, title = {Ice-binding proteins from the fungus Antarctomyces psychrotrophicus possibly originate from two different bacteria through horizontal gene transfer.}, journal = {The FEBS journal}, volume = {286}, number = {5}, pages = {946-962}, doi = {10.1111/febs.14725}, pmid = {30548092}, issn = {1742-4658}, mesh = {Amino Acid Sequence ; Antifreeze Proteins/chemistry/genetics/*metabolism ; Ascomycota/*metabolism ; Bacteria/classification/*metabolism ; Bacterial Proteins/chemistry/genetics/metabolism ; Fungal Proteins/chemistry/genetics/*metabolism ; *Gene Transfer, Horizontal ; *Ice ; Sequence Homology, Amino Acid ; Species Specificity ; }, abstract = {Various microbes, including fungi and bacteria, that live in cold environments produce ice-binding proteins (IBPs) that protect them from freezing. Ascomycota and Basidiomycota are two major phyla of fungi, and Antarctomyces psychrotrophicus is currently designated as the sole ascomycete that produces IBP (AnpIBP). However, its complete amino acid sequence, ice-binding property, and evolutionary history have not yet been clarified. Here, we determined the peptide sequences of three new AnpIBP isoforms by total cDNA analysis and compared them with those of other microbial IBPs. The AnpIBP isoforms and ascomycete-putative IBPs were found to be phylogenetically close to the bacterial ones but far from the basidiomycete ones, which is supported by the higher sequence identities to bacterial IBPs than basidiomycete IBPs, although ascomycetes are phylogenetically distant from bacteria. In addition, two of the isoforms of AnpIBP share low sequence identity and are not close in the phylogenetic tree. It is hence presumable that these two AnpIBP isoforms were independently acquired from different bacteria through horizontal gene transfer (HGT), which implies that ascomycetes and bacteria frequently exchange their IBP genes. The non-colligative freezing-point depression ability of AnpIBP was not very high, whereas it exhibited significant abilities of ice recrystallization inhibition, ice shaping, and cryo-protection against freeze-thaw cycles even at submicromolar concentrations. These results suggest that HGT is crucial for the cold-adaptive evolution of ascomycetes, and their IBPs offer freeze resistance to organisms to enable them to inhabit the icy environments of Antarctica. DATABASES: Nucleotide sequence data are available in the DDBJ database under the accession numbers LC378707, LC378707, LC378707 for AnpIBP1a, AnpIBP1b, AnpIBP2, respectively.}, }
@article {pmid30547857, year = {2018}, author = {Firth, N and Jensen, SO and Kwong, SM and Skurray, RA and Ramsay, JP}, title = {Staphylococcal Plasmids, Transposable and Integrative Elements.}, journal = {Microbiology spectrum}, volume = {6}, number = {6}, pages = {}, pmid = {30547857}, issn = {2165-0497}, mesh = {Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; *DNA Transposable Elements ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/drug effects/*genetics ; Gene Expression Regulation, Bacterial ; Gene Rearrangement ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Plasmids/*genetics ; Staphylococcal Infections ; Staphylococcus/drug effects/*genetics ; Staphylococcus aureus/drug effects/*genetics ; }, abstract = {Strains of Staphylococcus aureus, and to a lesser extent other staphylococcal species, are a significant cause of morbidity and mortality. An important factor in the notoriety of these organisms stems from their frequent resistance to many antimicrobial agents used for chemotherapy. This review catalogues the variety of mobile genetic elements that have been identified in staphylococci, with a primary focus on those associated with the recruitment and spread of antimicrobial resistance genes. These include plasmids, transposable elements such as insertion sequences and transposons, and integrative elements including ICE and SCC elements. In concert, these diverse entities facilitate the intra- and inter-cellular gene mobility that enables horizontal genetic exchange, and have also been found to play additional roles in modulating gene expression and genome rearrangement.}, }
@article {pmid30547746, year = {2018}, author = {Fitzgerald, CB and Shkoporov, AN and Sutton, TDS and Chaplin, AV and Velayudhan, V and Ross, RP and Hill, C}, title = {Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {931}, pmid = {30547746}, issn = {1471-2164}, support = {SFI/12/RC/2273//Science Foundation Ireland/Ireland ; SFI/14/SP APC/B3032//Science Foundation Ireland (IE)/ ; NA//Janssen Biotech (US)/ ; }, mesh = {Cluster Analysis ; Comparative Genomic Hybridization ; Faecalibacterium prausnitzii/classification/*genetics/metabolism ; Feces/microbiology ; Gastrointestinal Microbiome ; *Genome, Bacterial ; Humans ; Phylogeny ; Principal Component Analysis ; Proteome ; RNA, Ribosomal, 16S/chemistry/isolation &amp; purification/metabolism ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {BACKGROUND: Faecalibacterium prausnitzii is a ubiquitous member of the human gut microbiome, constituting up to 15% of the total bacteria in the human gut. Substantial evidence connects decreased levels of F. prausnitzii with the onset and progression of certain forms of inflammatory bowel disease, which has been attributed to its anti-inflammatory potential. Two phylogroups of F. prausnitzii have been identified, with a decrease in phylogroup I being a more sensitive marker of intestinal inflammation. Much of the genomic and physiological data available to date was collected using phylogroup II strains. Little analysis of F. prausnitzii genomes has been performed so far and genetic differences between phylogroups I and II are poorly understood.<br><br>RESULTS: In this study we sequenced 11 additional F. prausnitzii genomes and performed comparative genomics to investigate intraspecies diversity, functional gene complement and the mobilome of 31 high-quality draft and complete genomes. We reveal a very low level of average nucleotide identity among F. prausnitzii genomes and a high level of genome plasticity. Two genomogroups can be separated based on differences in functional gene complement, albeit that this division does not fully agree with separation based on conserved gene phylogeny, highlighting the importance of horizontal gene transfer in shaping F. prausnitzii genomes. The difference between the two genomogroups is mainly in the complement of genes associated with catabolism of carbohydrates (such as a predicted sialidase gene in genomogroup I)&#xa0;and amino acids, as well as defense mechanisms.<br><br>CONCLUSIONS: Based on the combination of ANI of genomic sequences, phylogenetic analysis of core proteomes and functional differences we propose to separate the species F. prausnitzii into two new species level taxa: F. prausnitzii sensu stricto (neotype strain A2-165[T]&#x2009;=&#x2009;DSM 17677[T]&#x2009;=&#x2009;JCM 31915[T]) and F. moorei sp. nov. (type strain ATCC 27768[T]&#x2009;=&#x2009;NCIMB 13872[T]).}, }
@article {pmid30546353, year = {2018}, author = {Nagel, R and Bieber, JE and Schmidt-Dannert, MG and Nett, RS and Peters, RJ}, title = {A Third Class: Functional Gibberellin Biosynthetic Operon in Beta-Proteobacteria.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2916}, pmid = {30546353}, issn = {1664-302X}, support = {R01 GM109773/GM/NIGMS NIH HHS/United States ; R35 GM131885/GM/NIGMS NIH HHS/United States ; }, abstract = {The ability of plant-associated microbes to produce gibberellin A (GA) phytohormones was first described for the fungal rice pathogen Gibberella fujikuroi in the 1930s. Recently the capacity to produce GAs was shown for several bacteria, including symbiotic alpha-proteobacteria (α-rhizobia) and gamma-proteobacteria phytopathogens. All necessary enzymes for GA production are encoded by a conserved operon, which appears to have undergone horizontal transfer between and within these two phylogenetic classes of bacteria. Here the operon was shown to be present and functional in a third class, the beta-proteobacteria, where it is found in several symbionts (β-rhizobia). Conservation of function was examined by biochemical characterization of the enzymes encoded by the operon from Paraburkholderia mimosarum LMG 23256[T]. Despite the in-frame gene fusion between the short-chain alcohol dehydrogenase/reductase and ferredoxin, the encoded enzymes exhibited the expected activity. Intriguingly, together these can only produce GA9, the immediate precursor to the bioactive GA4, as the cytochrome P450 (CYP115) that catalyzes the final hydroxylation reaction is missing, similar to most α-rhizobia. However, phylogenetic analysis indicates that the operon from β-rhizobia is more closely related to examples from gamma-proteobacteria, which almost invariably have CYP115 and, hence, can produce bioactive GA4. This indicates not only that β-rhizobia acquired the operon by horizontal gene transfer from gamma-proteobacteria, rather than α-rhizobia, but also that they independently lost CYP115 in parallel to the α-rhizobia, further hinting at the possibility of detrimental effects for the production of bioactive GA4 by these symbionts.}, }
@article {pmid30546348, year = {2018}, author = {Guo, H and Xue, S and Nasir, M and Lv, J and Gu, J}, title = {Role of Bentonite on the Mobility of Antibiotic Resistance Genes, and Microbial Community in Oxytetracycline and Cadmium Contaminated Soil.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2722}, pmid = {30546348}, issn = {1664-302X}, abstract = {The effects of bentonite (BT), a commonly used heavy metal deactivator, on the ARGs and microbial communities in soils and lettuce systems contaminated by heavy metals and antibiotics are unclear. A study was conducted to investigate the effect of BT on the mobility of antibiotic resistance genes in oxytetracycline and cadmium contaminated soil. Results showed that the addition of BT reduced the accumulation of OTC and ARGs in the soil and lettuce roots, but increased the abundance of ARGs in lettuce leaves, and increase the risk of human pathogenic bacteria (HPB) transferring to lettuce leaves. Redundancy analysis showed that environmental factors (OTC, H2O, SOM, and pH) were the dominant factors that influence the distribution of ARGs and intI1. Network analysis showed that Proteobacteria and Bacteroidetes were the major host bacteria which caused changes in ARGs and intI1. There were significant positive correlations between ermX and ermQ, and a large number of HPB. The co-occurrence of intl1 with some ARGs (tetC, tetG, ermQ, sul1, and sul2), may threaten human health due to the dispersion of ARGs via horizontal gene transfer.}, }
@article {pmid30546254, year = {2018}, author = {Nakamura, Y}, title = {Prediction of Horizontally and Widely Transferred Genes in Prokaryotes.}, journal = {Evolutionary bioinformatics online}, volume = {14}, number = {}, pages = {1176934318810785}, pmid = {30546254}, issn = {1176-9343}, abstract = {Horizontal gene transfer (HGT) is the process whereby an organism acquires exogenous genes (horizontally transferred genes or HT genes) that are not inherited from the parent, but are derived from another organism. In prokaryotes, HGT has been considered as one of the important driving forces of evolution. Previously, genome-wide analyses have been conducted for estimating the proportion of HT genes in prokaryotic genomes, but the number of species examined at the time was limited, and gene annotation was relatively poor. Currently, tens of thousands of prokaryotic genomes have been published and gene annotation resources have improved. In the present study, HT gene prediction method was modified so that the estimate was robust to gene length, conducting a comprehensive search using 3017 representative prokaryotic genomes belonging to 1348 species. The result showed that an average of 13% (ranging from 0% to 30% across species) of protein-coding genes was predicted as being of horizontal origin. The proportion of the predicted HT genes per species was associated with the species' habitat, while a positive correlation between the proportion and genomic nucleotide frequency was also observed. Moreover, the functions of the predicted HT genes were inferred and compared according to two popular databases, the Clusters of Orthologous Groups and the Kyoto Encyclopedia of Genes and Genomes. As a result, both databases indicated that many of the widely transferred genes were involved in mobile genetic elements (transposons, phages, and plasmids) as expected. Notably, the present study predicted that six as-yet-uncharacterized genes were widely distributed HT genes, and therefore, will be interesting targets for evolutionary studies. Thus, this study demonstrates that a data-driven approach using massive sequence data may contribute to a broader understanding of HGT in prokaryotes.}, }
@article {pmid30546019, year = {2018}, author = {Catoni, M and Noris, E and Vaira, AM and Jonesman, T and Matić, S and Soleimani, R and Behjatnia, SAA and Vinals, N and Paszkowski, J and Accotto, GP}, title = {Virus-mediated export of chromosomal DNA in plants.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {5308}, pmid = {30546019}, issn = {2041-1723}, mesh = {Arabidopsis/virology ; Beta vulgaris/*genetics/*virology ; DNA, Circular/*genetics ; DNA, Plant/*genetics ; DNA, Single-Stranded/genetics ; DNA, Viral/*genetics ; Geminiviridae/*genetics ; Gene Transfer, Horizontal/*genetics ; Plant Diseases/virology ; Nicotiana/virology ; }, abstract = {The propensity of viruses to acquire genetic material from relatives and possibly from infected hosts makes them excellent candidates as vectors for horizontal gene transfer. However, virus-mediated acquisition of host genetic material, as deduced from historical events, appears to be rare. Here, we report spontaneous and surprisingly efficient generation of hybrid virus/host DNA molecules in the form of minicircles during infection of Beta vulgaris by Beet curly top Iran virus (BCTIV), a single-stranded DNA virus. The hybrid minicircles replicate, become encapsidated into viral particles, and spread systemically throughout infected plants in parallel with the viral infection. Importantly, when co-infected with BCTIV, B. vulgaris DNA captured in minicircles replicates and is transcribed in other plant species that are sensitive to BCTIV infection. Thus, we have likely documented in real time the initial steps of a possible path of virus-mediated horizontal transfer of chromosomal DNA between plant species.}, }
@article {pmid30544151, year = {2019}, author = {Jaffe, AL and Castelle, CJ and Dupont, CL and Banfield, JF}, title = {Lateral Gene Transfer Shapes the Distribution of RuBisCO among Candidate Phyla Radiation Bacteria and DPANN Archaea.}, journal = {Molecular biology and evolution}, volume = {36}, number = {3}, pages = {435-446}, pmid = {30544151}, issn = {1537-1719}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Bacteriophages/*genetics ; *Gene Transfer, Horizontal ; Metagenomics ; Phosphotransferases (Alcohol Group Acceptor)/genetics ; Phylogeny ; Ribulose-Bisphosphate Carboxylase/*genetics ; }, abstract = {Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is considered to be the most abundant enzyme on Earth. Despite this, its full diversity and distribution across the domains of life remain to be determined. Here, we leverage a large set of bacterial, archaeal, and viral genomes recovered from the environment to expand our understanding of existing RuBisCO diversity and the evolutionary processes responsible for its distribution. Specifically, we report a new type of RuBisCO present in Candidate Phyla Radiation (CPR) bacteria that is related to the archaeal Form III enzyme and contains the amino acid residues necessary for carboxylase activity. Genome-level metabolic analyses supported the inference that these RuBisCO function in a CO2-incorporating pathway that consumes nucleotides. Importantly, some Gottesmanbacteria (CPR) also encode a phosphoribulokinase that may augment carbon metabolism through a partial Calvin-Benson-Bassham cycle. Based on the scattered distribution of RuBisCO and its discordant evolutionary history, we conclude that this enzyme has been extensively laterally transferred across the CPR bacteria and DPANN archaea. We also report RuBisCO-like proteins in phage genomes from diverse environments. These sequences cluster with proteins in the Beckwithbacteria (CPR), implicating phage as a possible mechanism of RuBisCO transfer. Finally, we synthesize our metabolic and evolutionary analyses to suggest that lateral gene transfer of RuBisCO may have facilitated major shifts in carbon metabolism in several important bacterial and archaeal lineages.}, }
@article {pmid30524390, year = {2018}, author = {Gobet, A and Barbeyron, T and Matard-Mann, M and Magdelenat, G and Vallenet, D and Duchaud, E and Michel, G}, title = {Evolutionary Evidence of Algal Polysaccharide Degradation Acquisition by Pseudoalteromonas carrageenovora 9[T] to Adapt to Macroalgal Niches.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2740}, pmid = {30524390}, issn = {1664-302X}, abstract = {About half of seaweed biomass is composed of polysaccharides. Most of these complex polymers have a marked polyanionic character. For instance, the red algal cell wall is mainly composed of sulfated galactans, agars and carrageenans, while brown algae contain alginate and fucose-containing sulfated polysaccharides (FCSP) as cell wall polysaccharides. Some marine heterotrophic bacteria have developed abilities to grow on such macroalgal polysaccharides. This is the case of Pseudoalteromonas carrageenovora 9[T] (ATCC 43555[T]), a marine gammaproteobacterium isolated in 1955 and which was an early model organism for studying carrageenan catabolism. We present here the genomic analysis of P. carrageenovora. Its genome is composed of two chromosomes and of a large plasmid encompassing 109 protein-coding genes. P. carrageenovora possesses a diverse repertoire of carbohydrate-active enzymes (CAZymes), notably specific for the degradation of macroalgal polysaccharides (laminarin, alginate, FCSP, carrageenans). We confirm these predicted capacities by screening the growth of P. carrageenovora with a large collection of carbohydrates. Most of these CAZyme genes constitute clusters located either in the large chromosome or in the small one. Unexpectedly, all the carrageenan catabolism-related genes are found in the plasmid, suggesting that P. carrageenovora acquired its hallmark capacity for carrageenan degradation by horizontal gene transfer (HGT). Whereas P. carrageenovora is able to use lambda-carrageenan as a sole carbon source, genomic and physiological analyses demonstrate that its catabolic pathway for kappa- and iota-carrageenan is incomplete. This is due to the absence of the recently discovered 3,6-anhydro-D-galactosidase genes (GH127 and GH129 families). A genomic comparison with 52 Pseudoalteromonas strains confirms that carrageenan catabolism has been recently acquired only in a few species. Even though the loci for cellulose biosynthesis and alginate utilization are located on the chromosomes, they were also horizontally acquired. However, these HGTs occurred earlier in the evolution of the Pseudoalteromonas genus, the cellulose- and alginate-related loci being essentially present in one large, late-diverging clade (LDC). Altogether, the capacities to degrade cell wall polysaccharides from macroalgae are not ancestral in the Pseudoalteromonas genus. Such catabolism in P. carrageenovora resulted from a succession of HGTs, likely allowing an adaptation to the life on the macroalgal surface.}, }
@article {pmid30538181, year = {2018}, author = {Pinheiro, J and Biboy, J and Vollmer, W and Hirt, RP and Keown, JR and Artuyants, A and Black, MM and Goldstone, DC and Simoes-Barbosa, A}, title = {The Protozoan Trichomonas vaginalis Targets Bacteria with Laterally Acquired NlpC/P60 Peptidoglycan Hydrolases.}, journal = {mBio}, volume = {9}, number = {6}, pages = {}, pmid = {30538181}, issn = {2150-7511}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {*Antibiosis ; Bacteria/*drug effects ; Female ; Gene Expression Regulation ; Humans ; N-Acetylmuramoyl-L-alanine Amidase/genetics/*metabolism ; Peptidoglycan/*metabolism ; Trichomonas vaginalis/*enzymology/genetics/*physiology ; Vagina/microbiology/parasitology ; }, abstract = {The human eukaryotic pathogen Trichomonas vaginalis causes trichomoniasis, a prevalent sexually transmitted infection. This extracellular protozoan is intimately associated with the human vaginal mucosa and microbiota, but key aspects of the complex interactions between the parasite and the vaginal bacteria remain elusive. We report that T. vaginalis has acquired, by lateral gene transfer from bacteria, genes encoding peptidoglycan hydrolases of the NlpC/P60 family. Two of the T. vaginalis enzymes were active against bacterial peptidoglycan, retaining the active-site fold and specificity as dl-endopeptidases. The endogenous NlpC/P60 genes are transcriptionally upregulated in T. vaginalis in the presence of bacteria. The overexpression of an exogenous copy enables the parasite to outcompete bacteria from mixed cultures, consistent with the biochemical activity of the enzyme. Our study results highlight the relevance of the interactions of this eukaryotic pathogen with bacteria, a poorly understood aspect of the biology of this important human parasite.IMPORTANCETrichomonas vaginalis is a parasitic protozoan of the human urogenital tract that causes trichomoniasis, a very common sexually transmitted disease. Despite residing extracellularly and in close association with the vaginal bacteria (i.e., the microbiota), very little is known about the nature of the parasite-bacterium interactions. Our study showed that this parasite had acquired genes from bacteria which retained their original function. They produce active enzymes capable of degrading peptidoglycan, a unique polymer of the bacterial cell envelope, helping the parasite to outcompete bacteria in mixed cultures. This study was the first to show that a laterally acquired group of genes enables a eukaryotic mucosal pathogen to control bacterial population. We highlight the importance of understanding the interactions between pathogens and microbiota, as the outcomes of these interactions are increasingly understood to have important implications on health and disease.}, }
@article {pmid30538166, year = {2019}, author = {Wei, G and Jia, Q and Chen, X and Köllner, TG and Bhattacharya, D and Wong, GK and Gershenzon, J and Chen, F}, title = {Terpene Biosynthesis in Red Algae Is Catalyzed by Microbial Type But Not Typical Plant Terpene Synthases.}, journal = {Plant physiology}, volume = {179}, number = {2}, pages = {382-390}, pmid = {30538166}, issn = {1532-2548}, mesh = {Acetates/pharmacology ; Algal Proteins/genetics/*metabolism ; Alkyl and Aryl Transferases/genetics/*metabolism ; Bacterial Proteins/genetics/*metabolism ; Cyclopentanes/pharmacology ; Evolution, Molecular ; Gene Expression Regulation, Enzymologic/drug effects ; Oxylipins/pharmacology ; Phylogeny ; Porphyridium/drug effects/genetics/metabolism ; Rhodophyta/cytology/*genetics/metabolism ; Sesquiterpenes/analysis/metabolism ; Terpenes/*metabolism ; Tissue Culture Techniques ; Volatile Organic Compounds/analysis/metabolism ; }, abstract = {Red algae (Rhodophyta) and land plants belong to the monophyletic clade Archaeplastida, and taxa of both groups are rich producers of terpene secondary metabolites. The terpene carbon skeletons of land plants are made by two types of terpene synthases: typical plant terpene synthases and microbial-type terpene synthases (MTPSLs); however, terpene biosynthesis in red algae is poorly understood. By systematic sequence analysis of seven genomes and 34 transcriptomes of red algae, MTPSL homologs were identified within one genome and two transcriptomes, whereas no homolog of typical plant terpene synthase genes was found. Phylogenetic analysis showed that red algae MTPSLs group with bacterial terpene synthases. Analysis of the genome assembly and characterization of neighboring genes demonstrated red algal MTPSLs to be bona fide red algal genes and not microbial contaminants. MTPSL genes from Porphyridium purpureum and Erythrolobus australicus were characterized via heterologous expression in Escherichia coli and demonstrated to have sesquiterpene synthase activities. We detected a number of volatile sesquiterpenes in the headspace of P. purpureum and E. australicus cultures, most identical to the in vitro products of the respective MTPSLs. Expression of the MTPSL gene in P. purpureum was found to be induced by methyl jasmonate, suggesting a role for this gene in host defense. In summary, this study indicates that the formation of terpene carbon skeletons in red algae is carried out by MTPSLs that are phylogenetically unrelated to typical plant terpene synthases and most likely originated in Rhodophyta via horizontal gene transfer from bacteria.}, }
@article {pmid30537278, year = {2019}, author = {Wang, CF and Sun, W and Zhang, Z}, title = {Functional characterization of the horizontally transferred 4,5-DOPA extradiol dioxygenase gene in the domestic silkworm, Bombyx mori.}, journal = {Insect molecular biology}, volume = {28}, number = {3}, pages = {409-419}, doi = {10.1111/imb.12558}, pmid = {30537278}, issn = {1365-2583}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Bombyx/*genetics/growth &amp; development/metabolism ; Dihydroxyphenylalanine/*metabolism ; *Gene Transfer, Horizontal ; Insect Proteins/chemistry/*genetics/metabolism ; Larva/genetics/growth &amp; development/metabolism ; Oxygenases/chemistry/*genetics/metabolism ; Phylogeny ; Sequence Alignment ; *Transcription, Genetic ; }, abstract = {4,5-DOPA dioxygenase (DODA) is a crucial enzyme in the biosynthetic pathway of betalain. Previous studies have shown that DODA is present in plants, fungi and bacteria. Using updated data, here we show that DODA genes (BmDODA) in the domestic silkworm (Bombyx mori) and other lepidopteran insects are most likely to be horizontally transferred from fungi. A synteny analysis indicated that BmDODA1 is orthologous to other lepidopteran DODAs and that BmDODA2 is a paralogous gene. To explore the function of DODA in Lepidoptera, we first examined the expression patterns of BmDODA1. BmDODA1 showed high transcriptional and translational levels in the midgut and head. Then, we exogenously expressed the BmDODA1 gene, detected 4,5-DOPA ring-cleaving activity and calculated the kinetic parameters of the recombinant BmDODA1. We found that the transcription levels of BmDODA1 were significantly induced by the pathogens Bacillus bombyseptieus and Escherichia coli. Thus, the horizontal transfer of the BmDODA gene in the silkworm may be involved in dopa metabolism and contribute to antimicrobial activity in this species. Our results provide a documented example of functional horizontal gene transfer (HGT) between fungi and animals and expand our knowledge of HGT amongst eukaryotes.}, }
@article {pmid30533877, year = {2018}, author = {Federici, F and Manna, L and Rizzi, E and Galantini, E and Marini, U}, title = {Draft Genome Sequence of Lactobacillus kefiri SGL 13, a Potential Probiotic Strain Isolated from Kefir Grains.}, journal = {Microbiology resource announcements}, volume = {7}, number = {4}, pages = {}, pmid = {30533877}, issn = {2576-098X}, abstract = {In this report, we present the draft genome sequence of a newly discovered potential probiotic strain of Lactobacillus kefiri, SGL 13, isolated from kefir grains. Antibiotic resistance analysis did not reveal evidence of interspecific horizontal gene transfer since the identified bacitracin resistance gene does not have mobile genetic elements.}, }
@article {pmid30533761, year = {2018}, author = {Scott, DC and Scott, L and Wilson, K and Ross, K and Ingram, D and Lewter, T and Herring, J and Linton, L and Duncan, D and Aikins, A and Ely, B}, title = {Complete Genome Sequence of a Wild-Type Isolate of Caulobacter vibrioides Strain CB2.}, journal = {Microbiology resource announcements}, volume = {7}, number = {17}, pages = {}, pmid = {30533761}, issn = {2576-098X}, abstract = {The complete genome of Caulobacter vibrioides strain CB2 consists of a 4,123,726-bp chromosome, a GC content of 67.2%, and 3,896 coding DNA sequences. It has no rearrangements but numerous indels relative to the reference NA1000 genome. This will allow us to study the impact of horizontal gene transfer on caulobacter genomes.}, }
@article {pmid30530605, year = {2019}, author = {Pecora, N and Zhao, X and Nudel, K and Hoffmann, M and Li, N and Onderdonk, AB and Yokoe, D and Brown, E and Allard, M and Bry, L}, title = {Diverse Vectors and Mechanisms Spread New Delhi Metallo-β-Lactamases among Carbapenem-Resistant Enterobacteriaceae in the Greater Boston Area.}, journal = {Antimicrobial agents and chemotherapy}, volume = {63}, number = {2}, pages = {}, pmid = {30530605}, issn = {1098-6596}, support = {P30 DK034854/DK/NIDDK NIH HHS/United States ; T32 HL007627/HL/NHLBI NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Boston ; Carbapenem-Resistant Enterobacteriaceae/*genetics ; Carbapenems/*pharmacology ; Conjugation, Genetic/genetics ; Drug Resistance, Bacterial/genetics ; Enterobacter cloacae/*drug effects/genetics/isolation &amp; purification ; Escherichia coli/*drug effects/genetics/isolation &amp; purification ; Gene Transfer, Horizontal/genetics ; Humans ; Multilocus Sequence Typing ; Polymorphism, Single Nucleotide/genetics ; beta-Lactamases/*genetics ; }, abstract = {New Delhi metallo-beta-lactamases (NDMs) are an uncommon but emerging cause of carbapenem resistance in the United States. Genomic factors promoting their domestic spread remain poorly characterized. A prospective genomic surveillance program among Boston-area hospitals identified multiple new occurrences of NDM-carrying strains of Escherichia coli and Enterobacter cloacae complex in inpatient and outpatient settings, representing the first occurrences of NDM-mediated resistance since initiating genomic surveillance in 2011. Cases included domestic patients with no international exposures. PacBio sequencing of isolates identified strain characteristics, resistance genes, and the complement of mobile vectors mediating spread. Analyses revealed a common 3,114-bp region containing the blaNDM gene, with carriage of this conserved region among unique strains by diverse transposon and plasmid backbones. Functional studies revealed a broad capacity for blaNDM transmission by conjugation, transposition, and complex interplasmid recombination events. NDMs represent a rapidly spreading form of drug resistance that can occur in inpatient and outpatient settings and in patients without international exposures. In contrast to Tn4401-based spread of Klebsiella pneumoniae carbapenemases (KPCs), diverse transposable elements mobilize NDM enzymes, commonly with other resistance genes, enabling naive strains to acquire multi- and extensively drug-resistant profiles with single transposition or plasmid conjugation events. Genomic surveillance provides effective means to rapidly identify these gene-level drivers of resistance and mobilization in order to inform clinical decisions to prevent further spread.}, }
@article {pmid30529954, year = {2019}, author = {Zhao, Y and Cocerva, T and Cox, S and Tardif, S and Su, JQ and Zhu, YG and Brandt, KK}, title = {Evidence for co-selection of antibiotic resistance genes and mobile genetic elements in metal polluted urban soils.}, journal = {The Science of the total environment}, volume = {656}, number = {}, pages = {512-520}, doi = {10.1016/j.scitotenv.2018.11.372}, pmid = {30529954}, issn = {1879-1026}, mesh = {Cities ; Drug Resistance, Microbial/*genetics ; *Environmental Monitoring ; Interspersed Repetitive Sequences/*genetics ; Northern Ireland ; Selection, Genetic ; *Soil Microbiology ; Soil Pollutants/*adverse effects ; }, abstract = {Antibiotic resistance genes (ARGs) constitute emerging environmental pollutants and pose risks to public health. Toxic metals are known to select for metal-resistant bacteria in metal-contaminated soils, but there is growing concern that metal contaminants can also act as co-selective agents thereby causing environmental proliferation of antibiotic resistance. In this study, we quantified ARGs and selected mobile genetic elements (MGEs) known to constitute potential ARG hosts in 50 archived urban and suburban soils from the Belfast metropolitan area using a high-throughput qPCR ARG chip. ARG prevalence was linked to concentrations of individual metals and a soil metal toxicity index calculated based on the relative toxicity of different metals to soil microbial processes. A total of 164 ARGs were detected across the 50 soils analyzed with an average absolute abundance of 3.4 × 10[7] ARG gene copies per gram of soil. A significant correlation between abundance of ARGs and MGEs was observed, suggesting the importance of horizontal gene transfer for ARG dissemination. Network analysis revealed significant co-occurrence patterns between specific metals (As, Cd, Co, Cr, Cu. Hg, Ni and Zn) and associated ARGs. Path analysis further indicated that the soil metal toxicity index significantly affected the number of detected ARGs (λ = 0.32, P < 0.001) and the abundance of metal co-occurring ARGs (λ = 0.612, P < 0.001) via effects on MGEs. Collectively, our results indicate a role of soil metals in co-selection of ARGs and MGEs in urban and semi-urban soils and suggest a risk for environmental ARG dissemination via horizontal gene transfer.}, }
@article {pmid30529144, year = {2019}, author = {Schlachter, CR and Daneshian, L and Amaya, J and Klapper, V and Wybouw, N and Borowski, T and Van Leeuwen, T and Grbic, V and Grbic, M and Makris, TM and Chruszcz, M}, title = {Structural and functional characterization of an intradiol ring-cleavage dioxygenase from the polyphagous spider mite herbivore Tetranychus urticae Koch.}, journal = {Insect biochemistry and molecular biology}, volume = {107}, number = {}, pages = {19-30}, pmid = {30529144}, issn = {1879-0240}, support = {R01 AI077653/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Arthropod Proteins/*genetics/metabolism ; Dioxygenases/*genetics/metabolism ; *Gene Transfer, Horizontal ; Tetranychidae/*genetics/metabolism ; }, abstract = {Genome analyses of the polyphagous spider mite herbivore Tetranychus urticae (two-spotted spider mite) revealed the presence of a set of 17 genes that code for secreted proteins belonging to the "intradiol dioxygenase-like" subgroup. Phylogenetic analyses indicate that this novel enzyme family has been acquired by horizontal gene transfer. In order to better understand the role of these proteins in T. urticae, we have structurally and functionally characterized one paralog (tetur07g02040). It was demonstrated that this protein is indeed an intradiol ring-cleavage dioxygenase, as the enzyme is able to cleave catechol between two hydroxyl-groups using atmospheric dioxygen. The enzyme was characterized functionally and structurally. The active site of the T. urticae enzyme contains an Fe[3+] cofactor that is coordinated by two histidine and two tyrosine residues, an arrangement that is similar to those observed in bacterial homologs. However, the active site is significantly more solvent exposed than in bacterial proteins. Moreover, the mite enzyme is monomeric, while almost all structurally characterized bacterial homologs form oligomeric assemblies. Tetur07g02040 is not only the first spider mite dioxygenase that has been characterized at the molecular level, but is also the first structurally characterized intradiol ring-cleavage dioxygenase originating from a eukaryote.}, }
@article {pmid30528080, year = {2019}, author = {Sanchez-Puerta, MV and Edera, A and Gandini, CL and Williams, AV and Howell, KA and Nevill, PG and Small, I}, title = {Genome-scale transfer of mitochondrial DNA from legume hosts to the holoparasite Lophophytum mirabile (Balanophoraceae).}, journal = {Molecular phylogenetics and evolution}, volume = {132}, number = {}, pages = {243-250}, doi = {10.1016/j.ympev.2018.12.006}, pmid = {30528080}, issn = {1095-9513}, mesh = {Balanophoraceae/*genetics ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Fabaceae/genetics ; *Gene Transfer, Horizontal ; *Genome, Mitochondrial ; Likelihood Functions ; Sequence Alignment ; }, abstract = {Angiosperm mitochondrial horizontal gene transfer (HGT) has been widely reported during the past decades. With a few exceptions, foreign sequences are mitochondrial genes or intronic regions from other plants, indicating that HGT has played a major role in shaping mitochondrial genome evolution. Host-parasite relationships are a valuable system to study this phenomenon due to the high frequency of HGT. In particular, the interaction between mimosoid legumes and holoparasites of the genus Lophophytum represents an outstanding opportunity to discern HGT events. The mitochondrial genome of the holoparasite L. mirabile has remarkable properties, the most extraordinary of which is the presence of 34 out of 43 mitochondrial protein genes acquired from its legume host, with the stunning replacement of up to 26 native homologs. However, the origin of the intergenic sequences that represent the majority (>90%) of the L. mirabile mtDNA remains largely unknown. The lack of mitochondrial sequences available from the donor angiosperm lineage (mimosoid legumes) precluded a large-scale evolutionary study. We sequenced and assembled the mitochondrial genome of the mimosoid Acacia ligulata and performed genome wide comparisons with L. mirabile. The A. ligulata mitochondrial genome is almost 700 kb in size, encoding 60 genes. About 60% of the L. mirabile mtDNA had greatest affinity to members of the family Fabaceae (∼49% to mimosoids in particular) with an average sequence identity of ∼96%, including genes but mostly intergenic regions. These findings strengthen the mitochondrial fusion compatibility model for angiosperm mitochondrion-to-mitochondrion HGT.}, }
@article {pmid30527621, year = {2019}, author = {Lindblom, A and Kk, S and Müller, V and Öz, R and Sandström, H and Åhrén, C and Westerlund, F and Karami, N}, title = {Interspecies plasmid transfer appears rare in sequential infections with extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae.}, journal = {Diagnostic microbiology and infectious disease}, volume = {93}, number = {4}, pages = {380-385}, doi = {10.1016/j.diagmicrobio.2018.10.014}, pmid = {30527621}, issn = {1879-0070}, mesh = {Enterobacteriaceae/*enzymology/genetics/*isolation &amp; purification ; Enterobacteriaceae Infections/*microbiology ; *Gene Transfer, Horizontal ; Humans ; Plasmids/*analysis ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sweden ; Urine/*microbiology ; beta-Lactamases/*genetics ; }, abstract = {From a cohort of 1836 Swedish patients infected with ESBL-producing Enterobacteriaceae (EPE) during 2004-2014, 513 patients with recurrent EPE infection were identified. Only in 14 of the 513 patients was a change of species (ESBL-E. coli to ESBL-K. pneumoniae or vice versa) found between the index and subsequent infection. Eleven sequential urine isolates from 5 of the 14 patients were available for further analysis of possible transfer of ESBL-carrying plasmids. The plasmid content was studied using optical DNA mapping (ODM), PCR-based replicon typing, and ESBL gene sequencing. ODM allowed us to directly compare whole plasmids between isolates and found similar ESBL-carrying plasmids in 3 out of the 5 patients. The ODM results and the rarity in shift of species between ESBL-E. coli and ESBL-K. pneumoniae imply that in recurrent EPE infections interspecies plasmid transfer is uncommon.}, }
@article {pmid30521623, year = {2018}, author = {Leungtongkam, U and Thummeepak, R and Tasanapak, K and Sitthisak, S}, title = {Acquisition and transfer of antibiotic resistance genes in association with conjugative plasmid or class 1 integrons of Acinetobacter baumannii.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0208468}, pmid = {30521623}, issn = {1932-6203}, mesh = {Acinetobacter baumannii/*genetics/growth &amp; development ; Bacterial Proteins/genetics ; Conjugation, Genetic ; *Drug Resistance, Multiple, Bacterial ; *Integrons ; Kanamycin/pharmacology ; Microbial Sensitivity Tests ; Microbial Viability ; Plasmids/*genetics ; Sodium Azide/pharmacology ; Tetracycline/pharmacology ; Ticarcillin/pharmacology ; }, abstract = {Conjugation is a type of horizontal gene transfer (HGT) that serves as the primary mechanism responsible for accelerating the spread of antibiotic resistance genes in Gram-negative bacteria. The present study aimed to elucidate the mechanisms underlying the conjugation-mediated gene transfer from the extensively drug-resistant Acinetobacter baumannii (XDR-AB) and New Delhi Metallo-beta-lactamase-1-producing Acinetobacter baumannii (NDM-AB) to environmental isolates of Acinetobacter spp. Conjugation experiments demonstrated that resistance to ticarcillin and kanamycin could be transferred from four donors to two sodium azide-resistant A. baumannii strains, namely, NU013R and NU015R. No transconjugants were detected on Mueller-Hinton Agar (MHA) plates containing tetracycline. Plasmids obtained from donors as well as successful transconjugants were characterized by PCR-based replicon typing and S1-nuclease pulsed-field gel electrophoresis (S1-PFGE). Detection of antibiotic resistance genes and integrase genes (int) was performed using PCR. Results revealed that the donor AB364 strain can transfer the blaOXA-23 and blaPER-1 genes to both recipients in association with int1. A 240-kb plasmid was successfully transferred from the donor AB364 to recipients. In addition, the aphA6 and blaPER-1 genes were co-transferred with the int1 gene from the donor strains AB352 and AB405. The transfer of a 220-kb plasmid from the donors to recipient was detected. The GR6 plasmid containing the kanamycin resistance gene (aphA6) was successfully transferred from the donor strain AB140 to both recipient strains. However, the blaNDM-1 and tet(B) genes were not detected in all transconjugants. Our study is the first to demonstrate successful in vitro conjugation, which indicated that XDR-AB contained combination mechanisms of the co-transfer of antimicrobial resistance elements with integron cassettes or with the plasmid group GR6. Thus, conjugation could be responsible for the emergence of new types of antibiotic-resistant strains.}, }
@article {pmid30520969, year = {2019}, author = {Alva, V and Lupas, AN}, title = {Histones predate the split between bacteria and archaea.}, journal = {Bioinformatics (Oxford, England)}, volume = {35}, number = {14}, pages = {2349-2353}, doi = {10.1093/bioinformatics/bty1000}, pmid = {30520969}, issn = {1367-4811}, mesh = {*Archaea ; *Bacteria ; Histones ; Nucleosomes ; }, abstract = {MOTIVATION: Histones form octameric complexes called nucleosomes, which organize the genomic DNA of eukaryotes into chromatin. Each nucleosome comprises two copies each of the histones H2A, H2B, H3 and H4, which share a common ancestry. Although histones were initially thought to be a eukaryotic innovation, the subsequent identification of archaeal homologs led to the notion that histones emerged before the divergence of archaea and eukaryotes.<br><br>RESULTS: Here, we report the detection and classification of two new groups of histone homologs, which are present in both archaea and bacteria. Proteins in one group consist of two histone subunits welded into single-chain pseudodimers, whereas in the other they resemble eukaryotic core histone subunits and show sequence patterns characteristic of DNA binding. The sequences come from a broad spectrum of deeply-branching lineages, excluding their genesis by horizontal gene transfer. Our results extend the origin of histones to the last universal common ancestor.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid30519543, year = {2018}, author = {Crane, JK and Cheema, MB and Olyer, MA and Sutton, MD}, title = {Zinc Blockade of SOS Response Inhibits Horizontal Transfer of Antibiotic Resistance Genes in Enteric Bacteria.}, journal = {Frontiers in cellular and infection microbiology}, volume = {8}, number = {}, pages = {410}, pmid = {30519543}, issn = {2235-2988}, mesh = {Chloramphenicol/pharmacology ; Ciprofloxacin/pharmacology ; DNA Damage/drug effects ; DNA, Single-Stranded ; DNA-Binding Proteins/drug effects ; Drug Resistance, Bacterial/*genetics ; Electrophoretic Mobility Shift Assay/methods ; Enterobacter cloacae/drug effects/genetics ; Enterobacteriaceae/*drug effects/*genetics ; Escherichia coli/genetics ; Escherichia coli Proteins/drug effects/genetics ; *Gene Transfer, Horizontal ; Mutation/drug effects ; Organometallic Compounds/pharmacology ; Pyridines/pharmacology ; Rec A Recombinases/drug effects ; SOS Response, Genetics/*drug effects ; Zinc/*pharmacology ; beta-Lactamases/genetics ; }, abstract = {The SOS response is a conserved response to DNA damage that is found in Gram-negative and Gram-positive bacteria. When DNA damage is sustained and severe, activation of error-prone DNA polymerases can induce a higher mutation rate than is normally observed, which is called the SOS mutator phenotype or hypermutation. We previously showed that zinc blocked the hypermutation response induced by quinolone antibiotics and mitomycin C in Escherichia coli and Klebsiella pneumoniae. In this study, we demonstrate that zinc blocks the SOS-induced development of chloramphenicol resistance in Enterobacter cloacae. Zinc also blocked the transfer of an extended spectrum beta-lactamase (ESBL) gene from Enterobacter to a susceptible E. coli strain. A zinc ionophore, zinc pyrithione, was ~100-fold more potent than zinc salts in inhibition of ciprofloxacin-induced hypermutation in E. cloacae. Other divalent metals, such as iron and manganese, failed to inhibit these responses. Electrophoretic mobility shift assays (EMSAs) revealed that zinc, but not iron or manganese, blocked the ability of the E. coli RecA protein to bind to single-stranded DNA, an important early step in the recognition of DNA damage in enteric bacteria. This suggests a mechanism for zinc's inhibitory effects on bacterial SOS responses, including hypermutation.}, }
@article {pmid30507538, year = {2020}, author = {Yasui, N and Vogiatzis, C and Yoshida, R and Fukumizu, K}, title = {imPhy: Imputing Phylogenetic Trees with Missing Information Using Mathematical Programming.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {17}, number = {4}, pages = {1222-1230}, doi = {10.1109/TCBB.2018.2884459}, pmid = {30507538}, issn = {1557-9964}, mesh = {Algorithms ; Animals ; Computational Biology/*methods ; Databases, Genetic ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Models, Genetic ; Nonlinear Dynamics ; *Phylogeny ; *Software ; }, abstract = {Advances in modern genomics have allowed researchers to apply phylogenetic analyses on a genome-wide scale. While large volumes of genomic data can be generated cheaply and quickly, data missingness is a non-trivial and somewhat expected problem. Since the available information is often incomplete for a given set of genetic loci and individual organisms, a large proportion of trees that depict the evolutionary history of a single genetic locus, called gene trees, fail to contain all individuals. Data incompleteness causes difficulties in data collection, information extraction, and gene tree inference. Furthermore, identifying outlying gene trees, which can represent horizontal gene transfers, gene duplications, or hybridizations, is difficult when data is missing from the gene trees. The typical approach is to remove all individuals with missing data from the gene trees, and focus the analysis on individuals whose information is fully available - a huge loss of information. In this work, we propose and design an optimization-based imputation approach to infer the missing distances between leaves in a set of gene trees via a mixed integer non-linear programming model. We also present a new research pipeline, imPhy, that can (i) simulate a set of gene trees with leaves randomly missing in each tree, (ii) impute the missing pairwise distances in each gene tree, (iii) reconstruct the gene trees using the Neighbor Joining (NJ) and Unweighted Pair Group Method with Arithmetic Mean (UPGMA) methods, and (iv) analyze and report the efficiency of the reconstruction. To impute the missing leaves, we employ our newly proposed non-linear programming framework, and demonstrate its capability in reconstructing gene trees with incomplete information in both simulated and empirical datasets. In the empirical datasets apicomplexa and lungfish, our imputation has very small normalized mean square errors, even in the extreme case where 50 percent of the individuals in each gene tree are missing. Data, software, and user manuals can be found at https://github.com/yasuiniko/imPhy.}, }
@article {pmid30507057, year = {2019}, author = {Stal, LJ and Bolhuis, H and Cretoiu, MS}, title = {Phototrophic marine benthic microbiomes: the ecophysiology of these biological entities.}, journal = {Environmental microbiology}, volume = {21}, number = {5}, pages = {1529-1551}, doi = {10.1111/1462-2920.14494}, pmid = {30507057}, issn = {1462-2920}, mesh = {Bacteria/classification/genetics/*metabolism/*radiation effects ; Light ; *Microbiota ; Phototrophic Processes ; Seawater/*microbiology ; }, abstract = {Phototrophic biofilms are multispecies, self-sustaining and largely closed microbial ecosystems. They form macroscopic structures such as microbial mats and stromatolites. These sunlight-driven consortia consist of a number of functional groups of microorganisms that recycle the elements internally. Particularly, the sulfur cycle is discussed in more detail as this is fundamental to marine benthic microbial communities and because recently exciting new insights have been obtained. The cycling of elements demands a tight tuning of the various metabolic processes and require cooperation between the different groups of microorganisms. This is likely achieved through cell-to-cell communication and a biological clock. Biofilms may be considered as a macroscopic biological entity with its own physiology. We review the various components of some marine phototrophic biofilms and discuss their roles in the system. The importance of extracellular polymeric substances (EPS) as the matrix for biofilm metabolism and as substrate for biofilm microorganisms is discussed. We particularly assess the importance of extracellular DNA, horizontal gene transfer and viruses for the generation of genetic diversity and innovation, and for rendering resilience to external forcing to these biological entities.}, }
@article {pmid30504145, year = {2018}, author = {Tokuda, G and Mikaelyan, A and Fukui, C and Matsuura, Y and Watanabe, H and Fujishima, M and Brune, A}, title = {Fiber-associated spirochetes are major agents of hemicellulose degradation in the hindgut of wood-feeding higher termites.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {51}, pages = {E11996-E12004}, pmid = {30504145}, issn = {1091-6490}, mesh = {Animals ; Cellulases/genetics/metabolism ; Cellulose/metabolism ; Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract/microbiology ; Gene Expression Regulation, Bacterial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Glycoside Hydrolases/genetics/metabolism ; Isoptera/*microbiology ; Metagenome/genetics ; Metagenomics ; Phylogeny ; Polysaccharides/*metabolism ; Sequence Analysis, DNA ; Spirochaetales/*enzymology/*genetics/*metabolism ; Symbiosis ; Wood/*metabolism ; Xylans/metabolism ; Xylosidases/classification/genetics/metabolism ; }, abstract = {Symbiotic digestion of lignocellulose in wood-feeding higher termites (family Termitidae) is a two-step process that involves endogenous host cellulases secreted in the midgut and a dense bacterial community in the hindgut compartment. The genomes of the bacterial gut microbiota encode diverse cellulolytic and hemicellulolytic enzymes, but the contributions of host and bacterial symbionts to lignocellulose degradation remain ambiguous. Our previous studies of Nasutitermes spp. documented that the wood fibers in the hindgut paunch are consistently colonized not only by uncultured members of Fibrobacteres, which have been implicated in cellulose degradation, but also by unique lineages of Spirochaetes. Here, we demonstrate that the degradation of xylan, the major component of hemicellulose, is restricted to the hindgut compartment, where it is preferentially hydrolyzed over cellulose. Metatranscriptomic analysis documented that the majority of glycoside hydrolase (GH) transcripts expressed by the fiber-associated bacterial community belong to family GH11, which consists exclusively of xylanases. The substrate specificity was further confirmed by heterologous expression of the gene encoding the predominant homolog. Although the most abundant transcripts of GH11 in Nasutitermes takasagoensis were phylogenetically placed among their homologs of Firmicutes, immunofluorescence microscopy, compositional binning of metagenomics contigs, and the genomic context of the homologs indicated that they are encoded by Spirochaetes and were most likely obtained by horizontal gene transfer among the intestinal microbiota. The major role of spirochetes in xylan degradation is unprecedented and assigns the fiber-associated Treponema clades in the hindgut of wood-feeding higher termites a prominent part in the breakdown of hemicelluloses.}, }
@article {pmid30503569, year = {2019}, author = {Fišarová, L and Pantůček, R and Botka, T and Doškař, J}, title = {Variability of resistance plasmids in coagulase-negative staphylococci and their importance as a reservoir of antimicrobial resistance.}, journal = {Research in microbiology}, volume = {170}, number = {2}, pages = {105-111}, doi = {10.1016/j.resmic.2018.11.004}, pmid = {30503569}, issn = {1769-7123}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Coagulase ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; *Genetic Variation ; Humans ; Microbial Sensitivity Tests ; Plasmids/drug effects/*genetics ; Staphylococcal Infections ; Staphylococcus/drug effects/enzymology/*genetics ; Staphylococcus aureus/genetics ; }, abstract = {Coagulase-negative staphylococci (CoNS) are an important cause of human and animal diseases. Treatment of these diseases is complicated by their common antimicrobial resistance, caused by overuse of antibiotics in hospital and veterinary environment. Therefore, they are assumed to serve as a reservoir of resistance genes often located on plasmids. In this study, we analyzed plasmid content in 62 strains belonging to 10 CoNS species of human and veterinary origin. In 48 (77%) strains analyzed, 107 different plasmids were detected, and only some of them showed similarities with plasmids found previously. In total, seven different antimicrobial-resistance genes carried by plasmids were identified. Five of the CoNS staphylococci carried plasmids identical with either those of other CoNS species tested, or a well characterized Staphylococcus aureus strain COL, suggesting plasmid dissemination through horizontal transfer. To demonstrate the possibility of horizontal transfer, we performed electroporation of four resistance plasmids among Staphylococcus epidermidis, Staphylococcus petrasii, and coagulase-positive S. aureus strains. Plasmids were transferred unchanged, were stably maintained in recipient strains, and expressed resistance genes. Our work demonstrates a great variability of plasmids in human and veterinary staphylococcal strains and their ability to maintain and express resistance plasmids from other staphylococcal species.}, }
@article {pmid30517748, year = {2018}, author = {Rogers, RL and Zhou, L and Chu, C and Márquez, R and Corl, A and Linderoth, T and Freeborn, L and MacManes, MD and Xiong, Z and Zheng, J and Guo, C and Xun, X and Kronforst, MR and Summers, K and Wu, Y and Yang, H and Richards-Zawacki, CL and Zhang, G and Nielsen, R}, title = {Genomic Takeover by Transposable Elements in the Strawberry Poison Frog.}, journal = {Molecular biology and evolution}, volume = {35}, number = {12}, pages = {2913-2927}, pmid = {30517748}, issn = {1537-1719}, support = {R01 GM108626/GM/NIGMS NIH HHS/United States ; R35 GM128843/GM/NIGMS NIH HHS/United States ; 0701165//Nattional Science Foundation/International ; 1146370//National Science Foundation/International ; }, mesh = {Animals ; Anura/*genetics ; *DNA Transposable Elements ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Ion Channels/genetics ; RNA, Small Interfering ; Spliceosomes/genetics ; }, abstract = {We sequenced the genome of the strawberry poison frog, Oophaga pumilio, at a depth of 127.5× using variable insert size libraries. The total genome size is estimated to be 6.76 Gb, of which 4.76 Gb are from high copy number repetitive elements with low differentiation across copies. These repeats encompass DNA transposons, RNA transposons, and LTR retrotransposons, including at least 0.4 and 1.0 Gb of Mariner/Tc1 and Gypsy elements, respectively. Expression data indicate high levels of gypsy and Mariner/Tc1 expression in ova of O. pumilio compared with Xenopus laevis. We further observe phylogenetic evidence for horizontal transfer (HT) of Mariner elements, possibly between fish and frogs. The elements affected by HT are present in high copy number and are highly expressed, suggesting ongoing proliferation after HT. Our results suggest that the large amphibian genome sizes, at least partially, can be explained by a process of repeated invasion of new transposable elements that are not yet suppressed in the germline. We also find changes in the spliceosome that we hypothesize are related to permissiveness of O. pumilio to increases in intron length due to transposon proliferation. Finally, we identify the complement of ion channels in the first genomic sequenced poison frog and discuss its relation to the evolution of autoresistance to toxins sequestered in the skin.}, }
@article {pmid30517704, year = {2019}, author = {Dupuy, P and Sauviac, L and Bruand, C}, title = {Stress-inducible NHEJ in bacteria: function in DNA repair and acquisition of heterologous DNA.}, journal = {Nucleic acids research}, volume = {47}, number = {3}, pages = {1335-1349}, pmid = {30517704}, issn = {1362-4962}, mesh = {DNA Breaks, Double-Stranded ; DNA End-Joining Repair/*genetics ; DNA Helicases/genetics ; DNA Ligase ATP/*genetics ; Eukaryotic Cells/metabolism ; Ku Autoantigen/*genetics ; *Recombination, Genetic ; Sinorhizobium meliloti/genetics ; }, abstract = {DNA double-strand breaks (DSB) in bacteria can be repaired by non-homologous end-joining (NHEJ), a two-component system relying on Ku and LigD. While performing a genetic characterization of NHEJ in Sinorhizobium meliloti, a representative of bacterial species encoding several Ku and LigD orthologues, we found that at least two distinct functional NHEJ repair pathways co-exist: one is dependent on Ku2 and LigD2, while the other depends on Ku3, Ku4 and LigD4. Whereas Ku2 likely acts as canonical bacterial Ku homodimers, genetic evidences suggest that Ku3-Ku4 form eukaryotic-like heterodimers. Strikingly, we found that the efficiency of both NHEJ systems increases under stress conditions, including heat and nutrient starvation. We found that this stimulation results from the transcriptional up-regulation of the ku and/or ligD genes, and that some of these genes are controlled by the general stress response regulator RpoE2. Finally, we provided evidence that NHEJ not only repairs DSBs, but can also capture heterologous DNA fragments into genomic breaks. Our data therefore suggest that NHEJ could participate to horizontal gene transfer from distantly related species, bypassing the need of homology to integrate exogenous DNA. This supports the hypothesis that NHEJ contributes to evolution and adaptation of bacteria under adverse environmental conditions.}, }
@article {pmid30513413, year = {2019}, author = {Lin, H and Chapman, SJ and Freitag, TE and Kyle, C and Ma, J and Yang, Y and Zhang, Z}, title = {Fate of tetracycline and sulfonamide resistance genes in a grassland soil amended with different organic fertilizers.}, journal = {Ecotoxicology and environmental safety}, volume = {170}, number = {}, pages = {39-46}, doi = {10.1016/j.ecoenv.2018.11.059}, pmid = {30513413}, issn = {1090-2414}, mesh = {Anti-Bacterial Agents ; Composting ; DNA Fingerprinting ; DNA, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; *Fertilizers ; Gene Expression Regulation, Bacterial ; *Genes, Bacterial ; *Grassland ; Manure/microbiology ; Microbiota/drug effects/genetics ; Scotland ; Soil/*chemistry ; Soil Microbiology ; Sulfonamides ; Tetracycline ; }, abstract = {This study provided an assessment of the environmental fate of antibiotic resistance genes (ARGs) in a Scottish grassland field repeatedly treated with different organic fertilizers. The impacts of manure, biosolids and municipal food-derived compost on the relative abundances of tetracycline ARGs (tetA, tetB, tetC, tetG and tetW), sulfonamide ARGs (sul1 and sul2) and class 1 integron-integrase gene (IntI1) in soils were investigated, with inorganic fertilizer (NPK) as a comparison. The background soil with a history of low intensity farming showed a higher total relative abundance of tet ARGs over sul ARGs, with tetracycline efflux genes occurring in a higher frequency. In all treatments, the relative abundances of most ARGs detected in soils decreased over time, especially IntI1 and tet ARGs. This general attenuation of soil ARGs is a reflection of changes in the soil microbial community, which is supported by the result that almost all the soils at the end of the experiment had different bacterial communities from the untreated soil at the beginning of the experiment. Multiple applications of organic fertilizers to some extent counteracted the decreasing trend of soil ARGs relative abundances, which resulted in higher ARGs relative abundances in comparison to NPK, either by a lesser decrease of IntI1 and tet ARGs or an increase of sul ARGs. The enhancement of existing soil ARG prevalence by organic fertilizers was strongly dependent on the organic fertilizer type and the particular ARG. Compost contained the lowest relative abundance of inherent ARGs and had the least effect on the soil ARG decrease after application. The relative increase of tet ARGs caused by biosolids was larger than that of sul ARGs, while manure caused the opposite effect. Fertilization practices did not exert effective impacts on the soil bacterial community, although it caused significant changes in the profile of the ARG pool. Organic fertilization may thus accelerate the dissemination of ARGs in soil mainly through horizontal gene transfer (HGT), consistent with the enrichment of IntI1 in organic fertilized soils.}, }
@article {pmid30513101, year = {2018}, author = {Ramírez-Santos, E and Rendón, P and Bourtzis, K and Schetelig, MF and Cáceres, C and Targovska, A and Rehling, T and Guillén-Navarro, GK and Ruiz-Montoya, L and Toledo, J and Liedo, P}, title = {Evaluation of horizontal gene transfer risk between the Mediterranean fruit fly Ceratitis capitata (Tephritidae) and its parasitoid Fopius ceratitivorus (Braconidae).}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0207999}, pmid = {30513101}, issn = {1932-6203}, mesh = {Animals ; Animals, Genetically Modified/*genetics/parasitology ; Ceratitis capitata/*genetics/parasitology ; Female ; *Gene Transfer, Horizontal ; Host-Parasite Interactions/*genetics ; Hymenoptera/*genetics ; Male ; Pest Control, Biological/methods ; Transgenes/genetics ; }, abstract = {The transgenic strain of the Mediterranean fruit fly (medfly), Ceratitis capitata (Wied.) VIENNA 8 1260, developed from the classical genetic sexing strain VIENNA 8, has two molecular markers that exhibit red fluorescence in the body and green fluorescence in testicles and sperm. These traits offer a precise tool to discriminate between mass-reared sterile males and wild fertile males, and they could potentially increase the effectiveness of control programs for this pest. To assess the risk of horizontal transfer of the fluorescence transgenes in natural ecosystems, we used the VIENNA 8 1260 strain and the medfly parasitoid Fopius ceratitivorus. The fluorescence signal and the inheritance of the fluorescence gene markers were monitored for over 16 generations (about two years) in both species using fluorescence microscopy and a PCR-based assay. The PCR analysis was performed in four independent laboratories. Both fluorescence microscopy and PCR analysis indicated that no horizontal gene transfer of the DsRed transgene occurred during 16 generations of medfly parasitoid rearing under experimental conditions.}, }
@article {pmid30497396, year = {2018}, author = {Lindstedt, BA and Finton, MD and Porcellato, D and Brandal, LT}, title = {High frequency of hybrid Escherichia coli strains with combined Intestinal Pathogenic Escherichia coli (IPEC) and Extraintestinal Pathogenic Escherichia coli (ExPEC) virulence factors isolated from human faecal samples.}, journal = {BMC infectious diseases}, volume = {18}, number = {1}, pages = {544}, pmid = {30497396}, issn = {1471-2334}, mesh = {Animals ; Enteropathogenic Escherichia coli/genetics/*isolation &amp; purification ; Escherichia coli Infections/*epidemiology/*microbiology ; Escherichia coli Proteins/analysis/genetics/isolation &amp; purification ; Extraintestinal Pathogenic Escherichia coli/genetics/*isolation &amp; purification ; Feces/chemistry/*microbiology ; Humans ; Incidence ; Intestines/microbiology ; Meningitis, Escherichia coli/epidemiology/microbiology ; Norway/epidemiology ; Phylogeny ; Uropathogenic Escherichia coli/genetics/isolation &amp; purification ; Virulence/genetics ; Virulence Factors/*analysis/genetics/isolation &amp; purification ; }, abstract = {BACKGROUND: Classification of pathogenic Escherichia coli (E. coli) has traditionally relied on detecting specific virulence associated genes (VAGs) or combinations thereof. For E. coli isolated from faecal samples, the presence of specific genes associated with different intestinal pathogenic pathovars will determine their classification and further course of action. However, the E. coli genome is not a static entity, and hybrid strains are emerging that cross the pathovar definitions. Hybrid strains may show gene contents previously associated with several distinct pathovars making the correct diagnostic classification difficult. We extended the analysis of routinely submitted faecal isolates to include known virulence associated genes that are usually not examined in faecal isolates to detect the frequency of possible hybrid strains.<br><br>METHODS: From September 2012 to February 2013, 168 faecal isolates of E. coli routinely submitted to the Norwegian Institute of Public Health (NIPH) from clinical microbiological laboratories throughout Norway were analysed for 33 VAGs using multiplex-PCR, including factors associated with extraintestinal pathogenic E. coli (ExPEC) strains. The strains were further typed by Multiple Locus Variable-Number Tandem-Repeat Analysis (MLVA), and the phylogenetic grouping was determined. One isolate from the study was selected for whole genome sequencing (WGS) with a combination of Oxford Nanopore's MinION and Illumina's MiSeq.<br><br>RESULTS: The analysis showed a surprisingly high number of strains carrying ExPEC associated VAGs and strains carrying a combination of both intestinal pathogenic E. coli (IPEC) and ExPEC VAGs. In particular, 93.5% (101/108) of isolates classified as belonging to an IPEC pathovar additionally carried ExPEC VAGs. WGS analysis of a selected hybrid strain revealed that it could, with present classification criteria, be classified as belonging to all of the Enteropathogenic Escherichia coli (EPEC), Uropathogenic Escherichia coli (UPEC), Neonatal meningitis Escherichia coli (NMEC) and Avian pathogenic Escherichia coli (APEC) pathovars.<br><br>CONCLUSION: Hybrid ExPEC/IPEC E. coli strains were found at a very high frequency in faecal samples and were in fact the predominant species present. A sequenced hybrid isolate was confirmed to be a cross-pathovar strain possessing recognised hallmarks of several pathovars, and a genome heavily influenced by horizontal gene transfer.}, }
@article {pmid30496396, year = {2019}, author = {Freschi, L and Vincent, AT and Jeukens, J and Emond-Rheault, JG and Kukavica-Ibrulj, I and Dupont, MJ and Charette, SJ and Boyle, B and Levesque, RC}, title = {The Pseudomonas aeruginosa Pan-Genome Provides New Insights on Its Population Structure, Horizontal Gene Transfer, and Pathogenicity.}, journal = {Genome biology and evolution}, volume = {11}, number = {1}, pages = {109-120}, pmid = {30496396}, issn = {1759-6653}, support = {P30 DK089507/DK/NIDDK NIH HHS/United States ; }, mesh = {Drug Resistance, Bacterial/genetics ; *Gene Transfer, Horizontal ; *Genetic Variation ; *Phylogeny ; Pseudomonas aeruginosa/*genetics/pathogenicity ; Virulence/genetics ; }, abstract = {The huge increase in the availability of bacterial genomes led us to a point in which we can investigate and query pan-genomes, for example, the full set of genes of a given bacterial species or clade. Here, we used a data set of 1,311 high-quality genomes from the human pathogen Pseudomonas aeruginosa, 619 of which were newly sequenced, to show that a pan-genomic approach can greatly refine the population structure of bacterial species, provide new insights to define species boundaries, and generate hypotheses on the evolution of pathogenicity. The 665-gene P. aeruginosa core genome presented here, which constitutes only 1% of the entire pan-genome, is the first to be in the same order of magnitude as the minimal bacterial genome and represents a conservative estimate of the actual core genome. Moreover, the phylogeny based on this core genome provides strong evidence for a five-group population structure that includes two previously undescribed groups of isolates. Comparative genomics focusing on antimicrobial resistance and virulence genes showed that variation among isolates was partly linked to this population structure. Finally, we hypothesized that horizontal gene transfer had an important role in this respect, and found a total of 3,010 putative complete and fragmented plasmids, 5% and 12% of which contained resistance or virulence genes, respectively. This work provides data and strategies to study the evolutionary trajectories of resistance and virulence in P. aeruginosa.}, }
@article {pmid30488322, year = {2019}, author = {Gong, L and Yu, P and Zheng, H and Gu, W and He, W and Tang, Y and Wang, Y and Dong, Y and Peng, X and She, Q and Xie, L and Chen, L}, title = {Comparative genomics for non-O1/O139 Vibrio cholerae isolates recovered from the Yangtze River Estuary versus V. cholerae representative isolates from serogroup O1.}, journal = {Molecular genetics and genomics : MGG}, volume = {294}, number = {2}, pages = {417-430}, pmid = {30488322}, issn = {1617-4623}, support = {No.B-9500-10-0004//Shanghai Municipal Education Commission, Shanghai, China/ ; No.31271830//National Natural Science Foundation of China/ ; No.31671946//National Natural Science Foundation of China/ ; No.17050502200//Science and Technology Commission of Shanghai Municipality, China/ ; }, mesh = {Brazil ; China ; Cholera/*genetics/microbiology ; DNA Transposable Elements/genetics ; Estuaries ; Gene Transfer, Horizontal/genetics ; Genetic Variation ; Genome, Bacterial/*genetics ; Genomics ; Humans ; Molecular Sequence Annotation ; Phylogeny ; Rivers ; Serogroup ; Vibrio cholerae O1/*genetics/pathogenicity ; Vibrio cholerae non-O1/*genetics/pathogenicity ; Virulence/genetics ; }, abstract = {Vibriocholerae, which is autochthonous to estuaries worldwide, can cause human cholera that is still pandemic in developing countries. A number of V. cholerae isolates of clinical and environmental origin worldwide have been subjected to genome sequencing to address their phylogenesis and bacterial pathogenesis, however, little genome information is available for V. cholerae isolates derived from estuaries, particularly in China. In this study, we determined the complete genome sequence of V. cholerae CHN108B (non-O1/O139 serogroup) isolated from the Yangtze River Estuary, China and performed comparative genome analysis between CHN108B and other eight representative V. cholerae isolates. The 4,168,545-bp V. cholerae CHN108B genome (47.2% G+C) consists of two circular chromosomes with 3,691 predicted protein-encoding genes. It has 110 strain-specific genes, the highest number among the eight representative V. cholerae whole genomes from serogroup O1: there are seven clinical isolates linked to cholera pandemics (1937-2010) and one environmental isolate from Brazil. Various mobile genetic elements (such as insertion sequences, prophages, integrative and conjugative elements, and super-integrons) were identified in the nine V. cholerae genomes of clinical and environmental origin, indicating that the bacterium undergoes extensive genetic recombination via lateral gene transfer. Comparative genomics also revealed different virulence and antimicrobial resistance gene patterns among the V. cholerae isolates, suggesting some potential virulence factors and the rising development of resistance among pathogenic V. cholerae. Additionally, draft genome sequences of multiple V. cholerae isolates recovered from the Yangtze River Estuary were also determined, and comparative genomics revealed many genes involved in specific metabolism pathways, which are likely shaped by the unique estuary environment. These results provide additional evidence of V. cholerae genome plasticity and will facilitate better understanding of the genome evolution and pathogenesis of this severe water-borne pathogen worldwide.}, }
@article {pmid30487781, year = {2018}, author = {Panda, S and Singh, DV}, title = {Biofilm Formation by ica-Negative Ocular Isolates of Staphylococcus haemolyticus.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2687}, pmid = {30487781}, issn = {1664-302X}, abstract = {Staphylococcus haemolyticus is the second most frequently isolated CoNS from ocular infections and human blood cultures. In this study, we examined 18 ocular S. haemolyticus isolates for their capacity to form biofilm and conducted detachment assay to determine the composition of the biofilm matrix and involvement of various elements in cell lysis. PCR identified the presence of biofilm-associated genes, and ica operon and CLSM visualized the components of the biofilm matrix. We found that PIA-independent biofilm formation is the characteristic feature of S. haemolyticus isolates, irrespective of the sources of isolation, and protein or DNA or both are the major components of the biofilm matrix. Cell lysis enabling DNA release was an essential step for biofilm attachment during the initial stages of biofilm development. The srtA transcript expression study indicates its role in the early stages of biofilm development. We found the presence of antibiotic resistance genes in the eDNA and gDNA thus suggesting the possible role of biofilm in horizontal gene transfer of antibiotic resistance determinants. The overall study indicates that S. haemolyticus formed the biofilm comprising of protein or DNA or both and srtA play a role in the initial development of biofilm.}, }
@article {pmid30487573, year = {2018}, author = {Méric, G and Mageiros, L and Pensar, J and Laabei, M and Yahara, K and Pascoe, B and Kittiwan, N and Tadee, P and Post, V and Lamble, S and Bowden, R and Bray, JE and Morgenstern, M and Jolley, KA and Maiden, MCJ and Feil, EJ and Didelot, X and Miragaia, M and de Lencastre, H and Moriarty, TF and Rohde, H and Massey, R and Mack, D and Corander, J and Sheppard, SK}, title = {Disease-associated genotypes of the commensal skin bacterium Staphylococcus epidermidis.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {5034}, pmid = {30487573}, issn = {2041-1723}, support = {G0801929/MRC_/Medical Research Council/United Kingdom ; MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MR/M501608/1/MRC_/Medical Research Council/United Kingdom ; MR/R015600/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Genome, Bacterial/genetics ; Genome-Wide Association Study ; Genotype ; Humans ; Interleukin-8/metabolism ; Skin Diseases/*microbiology ; Staphylococcal Infections/*microbiology ; Staphylococcus epidermidis/*genetics/*pathogenicity ; }, abstract = {Some of the most common infectious diseases are caused by bacteria that naturally colonise humans asymptomatically. Combating these opportunistic pathogens requires an understanding of the traits that differentiate infecting strains from harmless relatives. Staphylococcus epidermidis is carried asymptomatically on the skin and mucous membranes of virtually all humans but is a major cause of nosocomial infection associated with invasive procedures. Here we address the underlying evolutionary mechanisms of opportunistic pathogenicity by combining pangenome-wide association studies and laboratory microbiology to compare S. epidermidis from bloodstream and wound infections and asymptomatic carriage. We identify 61 genes containing infection-associated genetic elements (k-mers) that correlate with in vitro variation in known pathogenicity traits (biofilm formation, cell toxicity, interleukin-8 production, methicillin resistance). Horizontal gene transfer spreads these elements, allowing divergent clones to cause infection. Finally, Random Forest model prediction of disease status (carriage vs. infection) identifies pathogenicity elements in 415 S. epidermidis isolates with 80% accuracy, demonstrating the potential for identifying risk genotypes pre-operatively.}, }
@article {pmid30487164, year = {2019}, author = {Gupta, A and Pande, A and Sabrin, A and Thapa, SS and Gioe, BW and Grove, A}, title = {MarR Family Transcription Factors from Burkholderia Species: Hidden Clues to Control of Virulence-Associated Genes.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {83}, number = {1}, pages = {}, pmid = {30487164}, issn = {1098-5557}, mesh = {Bacterial Proteins/chemistry/genetics/*physiology ; Burkholderia/*genetics/*pathogenicity ; Drug Resistance, Multiple, Bacterial ; *Gene Expression Regulation, Bacterial ; Gene Regulatory Networks ; Humans ; Plants/microbiology ; Protein Conformation ; Reactive Oxygen Species ; Transcription Factors/chemistry/genetics/*physiology ; Virulence/genetics ; }, abstract = {Species within the genus Burkholderia exhibit remarkable phenotypic diversity. Genomic plasticity, including genome reduction and horizontal gene transfer, has been correlated with virulence traits in several species. However, the conservation of virulence genes in species otherwise considered to have limited potential for infection suggests that phenotypic diversity may not be explained solely on the basis of genetic diversity. Instead, differential organization and control of gene regulatory networks may underlie many phenotypic differences. In this review, we evaluate how regulation of gene expression by members of the multiple antibiotic resistance regulator (MarR) family of transcription factors may contribute to shaping the physiological diversity of Burkholderia species, with a focus on the clinically relevant human pathogens. All Burkholderia species encode a relatively large number of MarR proteins, a feature common to bacteria that must respond to environmental changes such as those associated with host invasion. However, evolution of gene regulatory networks has likely resulted in orthologous transcription factors controlling disparate sets of genes. Adaptation to, and survival in, diverse habitats, including a human or plant host, is key to the success of Burkholderia species as (opportunistic) pathogens, and recent reports suggest that control of virulence-associated genes by MarR proteins features prominently among the survival strategies employed by these species. We suggest that identification of MarR regulons will contribute significantly to clarification of virulence determinants and phenotypic diversity.}, }
@article {pmid30486781, year = {2018}, author = {Hecox-Lea, BJ and Mark Welch, DB}, title = {Evolutionary diversity and novelty of DNA repair genes in asexual Bdelloid rotifers.}, journal = {BMC evolutionary biology}, volume = {18}, number = {1}, pages = {177}, pmid = {30486781}, issn = {1471-2148}, support = {R21 AG046899/AG/NIA NIH HHS/United States ; R21AG046899/AG/NIA NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Conserved Sequence/genetics ; DNA Repair/*genetics ; *Evolution, Molecular ; Gene Dosage ; Gene Transfer, Horizontal/genetics ; *Genetic Variation ; Phylogeny ; Proteins/chemistry/genetics ; Reproduction, Asexual/*genetics ; Rotifera/*genetics ; }, abstract = {BACKGROUND: Bdelloid rotifers are the oldest, most diverse and successful animal taxon for which males, hermaphrodites, and traditional meiosis are unknown. Their degenerate tetraploid genome, with 2-4 copies of most loci, includes thousands of genes acquired from all domains of life by horizontal transfer. Many bdelloid species thrive in ephemerally aquatic habitats by surviving desiccation at any life stage with no loss of fecundity or lifespan. Their unique genomic diversity and the intense selective pressure of desiccation provide an exceptional opportunity to study the evolution of diversity and novelty in genes involved in DNA repair.<br><br>RESULTS: We used genomic data and RNA-Seq of the desiccation process in the bdelloid Adineta vaga to characterize DNA damage reversal, translesion synthesis, and the major DNA repair pathways: base, nucleotide, and alternate excision repair, mismatch repair (MMR), and double strand break repair by homologous recombination (HR) and classical non-homologous end joining (NHEJ). We identify multiple horizontally transferred DNA damage response genes otherwise unknown in animals (AlkD, Fpg, LigK UVDE), and the presence of genes often considered vertebrate specific, particularly in the NHEJ complex and X family polymerases. While 75-100% of genes involved in MMR and HR are present in 0-2 copies, genes involved in NHEJ, which are present in only a single copy in nearly all other animals, are retained in 3-8 copies. We present structural predictions and expression evidence of neo- or sub-functionalization of multiple copy genes involved in NHEJ and other repair processes.<br><br>CONCLUSION: The horizontally-acquired genes and duplicated genes in BER and NHEJ suggest resilience to oxidative damage is conferred in part by increased DNA damage recognition and efficient end repair capabilities. The pattern of gene loss and retention in MMR and HR may facilitate recombination and gene conversion between divergent sequences, thus providing at least some of the benefits of sex. The unique retention and divergence of duplicates genes in NHEJ may be facilitated by the lack of efficient selection in the absence of meiotic recombination and independent assortment, and may contribute to the evolutionary success of bdelloids.}, }
@article {pmid30485808, year = {2018}, author = {Domenech, A and Slager, J and Veening, JW}, title = {Antibiotic-Induced Cell Chaining Triggers Pneumococcal Competence by Reshaping Quorum Sensing to Autocrine-Like Signaling.}, journal = {Cell reports}, volume = {25}, number = {9}, pages = {2390-2400.e3}, pmid = {30485808}, issn = {2211-1247}, mesh = {Anti-Bacterial Agents/*pharmacology ; *Autocrine Communication/drug effects ; Aztreonam/pharmacology ; Bacterial Proteins/metabolism ; Clavulanic Acid/pharmacology ; Gene Dosage ; Gene Transfer, Horizontal/genetics ; Models, Biological ; Peptides/metabolism ; Quorum Sensing/*drug effects ; *Signal Transduction/drug effects ; Streptococcus pneumoniae/drug effects/*physiology ; }, abstract = {Streptococcus pneumoniae can acquire antibiotic resistance by activation of competence and subsequent DNA uptake. Here, we demonstrate that aztreonam (ATM) and clavulanic acid (CLA) promote competence. We show that both compounds induce cell chain formation by targeting the d,d-carboxypeptidase PBP3. In support of the hypothesis that chain formation promotes competence, we demonstrate that an autolysin mutant (ΔlytB) is hypercompetent. Since competence is initiated by the binding of a small extracellular peptide (CSP) to a membrane-anchored receptor (ComD), we wondered whether chain formation alters CSP diffusion kinetics. Indeed, ATM or CLA presence affects competence synchronization by shifting from global to local quorum sensing, as CSP is primarily retained to chained cells, rather than shared in a common pool. Importantly, autocrine-like signaling prolongs the time window in which the population is able to take up DNA. Together, these insights demonstrate the versatility of quorum sensing and highlight the importance of an accurate antibiotic prescription.}, }
@article {pmid30483871, year = {2019}, author = {Ely, B and Wilson, K and Ross, K and Ingram, D and Lewter, T and Herring, J and Duncan, D and Aikins, A and Scott, D}, title = {Genome Comparisons of Wild Isolates of Caulobacter crescentus Reveal Rates of Inversion and Horizontal Gene Transfer.}, journal = {Current microbiology}, volume = {76}, number = {2}, pages = {159-167}, pmid = {30483871}, issn = {1432-0991}, support = {R25 GM076277/GM/NIGMS NIH HHS/United States ; P20GM103446//National Institute of General Medical Sciences/ ; P20 GM103446/GM/NIGMS NIH HHS/United States ; GM076277//National Institute of General Medical Sciences/ ; R25 GM066526/GM/NIGMS NIH HHS/United States ; }, mesh = {Caulobacter crescentus/*genetics/isolation &amp; purification ; *Chromosome Inversion ; Chromosome Mapping ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomics ; High-Throughput Nucleotide Sequencing ; INDEL Mutation ; Mutagenesis, Insertional ; Whole Genome Sequencing ; }, abstract = {Since previous interspecies comparisons of Caulobacter genomes have revealed extensive genome rearrangements, we decided to compare the nucleotide sequences of four C. crescentus genomes, NA1000, CB1, CB2, and CB13. To accomplish this goal, we used PacBio sequencing technology to determine the nucleotide sequence of the CB1, CB2, and CB13 genomes, and obtained each genome sequence as a single contig. To correct for possible sequencing errors, each genome was sequenced twice. The only differences we observed between the two sets of independently determined sequences were random omissions of a single base in a small percentage of the homopolymer regions where a single base is repeated multiple times. Comparisons of these four genomes indicated that horizontal gene transfer events that included small numbers of genes occurred at frequencies in the range of 10[-3] to 10[-4] insertions per generation. Large insertions were about 100 times less frequent. Also, in contrast to previous interspecies comparisons, we found no genome rearrangements when the closely related NA1000, CB1, and CB2 genomes were compared, and only eight inversions and one translocation when the more distantly related CB13 genome was compared to the other genomes. Thus, we estimate that inversions occur at a rate of one per 10 to 12 million generations in Caulobacter genomes. The inversions seem to be complex events that include the simultaneous creation of indels.}, }
@article {pmid30482699, year = {2019}, author = {Hara, N and Wajima, T and Seyama, S and Tanaka, E and Shirai, A and Shibata, M and Natsume, Y and Shiro, H and Noguchi, N}, title = {Isolation of multidrug-resistant Haemophilus influenzae harbouring multiple exogenous genes from a patient diagnosed with acute sinusitis.}, journal = {Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy}, volume = {25}, number = {5}, pages = {385-387}, doi = {10.1016/j.jiac.2018.09.015}, pmid = {30482699}, issn = {1437-7780}, mesh = {Acute Disease/therapy ; Anti-Bacterial Agents/*pharmacology/therapeutic use ; Child, Preschool ; Drug Resistance, Multiple, Bacterial/genetics ; Female ; Gene Transfer, Horizontal/*genetics ; Haemophilus Infections/drug therapy/*microbiology ; Haemophilus influenzae/*genetics/isolation &amp; purification ; Humans ; Microbial Interactions/genetics ; Microbial Sensitivity Tests ; Sinusitis/drug therapy/*microbiology ; Streptococcus pneumoniae/*genetics ; }, abstract = {In paediatric patients, β-lactams and macrolides are widely used to treat acute otitis media and sinusitis, which are often caused by either Streptococcus pneumoniae or Haemophilus influenzae. However, resistant isolates have emerged and are becoming more prevalent. H. influenzae generally acquires antimicrobial resistance by mutation or by expression of β-lactamase. In this study, we isolated H. influenzae from a paediatric patient diagnosed with acute sinusitis. This strain harboured multiple exogenous resistance genes: blaTEM-1, mef(A) and tet(M). DNA sequencing suggested that both mef(A) and tet(M) had been transferred from S. pneumoniae or another Streptococcus. This typical outpatient had not been exposed to excessive levels of antibiotics and had no underlying diseases, strongly suggesting that this type of resistant isolate could become more prevalent.}, }
@article {pmid30478289, year = {2019}, author = {Turgeman-Grott, I and Joseph, S and Marton, S and Eizenshtein, K and Naor, A and Soucy, SM and Stachler, AE and Shalev, Y and Zarkor, M and Reshef, L and Altman-Price, N and Marchfelder, A and Gophna, U}, title = {Pervasive acquisition of CRISPR memory driven by inter-species mating of archaea can limit gene transfer and influence speciation.}, journal = {Nature microbiology}, volume = {4}, number = {1}, pages = {177-186}, pmid = {30478289}, issn = {2058-5276}, mesh = {CRISPR-Cas Systems/*genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/*genetics ; DNA, Intergenic/*genetics ; Gene Transfer, Horizontal/*genetics ; Genetic Speciation ; Haloferax mediterranei/*genetics/growth &amp; development ; Haloferax volcanii/*genetics/growth &amp; development ; }, abstract = {CRISPR-Cas systems provide prokaryotes with sequence-specific immunity against viruses and plasmids based on DNA acquired from these invaders, known as spacers. Surprisingly, many archaea possess spacers that match chromosomal genes of related species, including those encoding core housekeeping genes. By sequencing genomes of environmental archaea isolated from a single site, we demonstrate that inter-species spacers are common. We show experimentally, by mating Haloferax volcanii and Haloferax mediterranei, that spacers are indeed acquired chromosome-wide, although a preference for integrated mobile elements and nearby regions of the chromosome exists. Inter-species mating induces increased spacer acquisition and may result in interactions between the acquisition machinery of the two species. Surprisingly, many of the spacers acquired following inter-species mating target self-replicons along with those originating from the mating partner, indicating that the acquisition machinery cannot distinguish self from non-self under these conditions. Engineering the chromosome of one species to be targeted by the other's CRISPR-Cas reduces gene exchange between them substantially. Thus, spacers acquired during inter-species mating could limit future gene transfer, resulting in a role for CRISPR-Cas systems in microbial speciation.}, }
@article {pmid30476045, year = {2019}, author = {Gill, S and Catchpole, R and Forterre, P}, title = {Extracellular membrane vesicles in the three domains of life and beyond.}, journal = {FEMS microbiology reviews}, volume = {43}, number = {3}, pages = {273-303}, pmid = {30476045}, issn = {1574-6976}, mesh = {*Archaea/cytology/virology ; *Bacteria/cytology/virology ; Cell Communication ; *Eukaryota/cytology/virology ; Extracellular Vesicles/*metabolism ; Virus Physiological Phenomena ; }, abstract = {Cells from all three domains of life, Archaea, Bacteria and Eukarya, produce extracellular vesicles (EVs) which are sometimes associated with filamentous structures known as nanopods or nanotubes. The mechanisms of EV biogenesis in the three domains remain poorly understood, although studies in Bacteria and Eukarya indicate that the regulation of lipid composition plays a major role in initiating membrane curvature. EVs are increasingly recognized as important mediators of intercellular communication via transfer of a wide variety of molecular cargoes. They have been implicated in many aspects of cell physiology such as stress response, intercellular competition, lateral gene transfer (via RNA or DNA), pathogenicity and detoxification. Their role in various human pathologies and aging has aroused much interest in recent years. EVs can be used as decoys against viral attack but virus-infected cells also produce EVs that boost viral infection. Here, we review current knowledge on EVs in the three domains of life and their interactions with the viral world.}, }
@article {pmid30474915, year = {2019}, author = {Zhao, Y and Qin, F and Zhang, R and Giovannoni, SJ and Zhang, Z and Sun, J and Du, S and Rensing, C}, title = {Pelagiphages in the Podoviridae family integrate into host genomes.}, journal = {Environmental microbiology}, volume = {21}, number = {6}, pages = {1989-2001}, doi = {10.1111/1462-2920.14487}, pmid = {30474915}, issn = {1462-2920}, support = {41706173//National Natural Science Foundation of China/International ; }, mesh = {Alphaproteobacteria/genetics/metabolism/*virology ; Bacteriophages/classification/genetics/isolation &amp; purification/*physiology ; Carbon/metabolism ; Genome, Bacterial ; Genome, Viral ; Lysogeny ; Phylogeny ; Podoviridae/classification/genetics/isolation &amp; purification/*physiology ; Prophages/classification/genetics/isolation &amp; purification/physiology ; *Virus Integration ; }, abstract = {The Pelagibacterales order (SAR11) in Alphaproteobacteria dominates marine surface bacterioplankton communities, where it plays a key role in carbon and nutrient cycling. SAR11 phages, known as pelagiphages, are among the most abundant phages in the ocean. Four pelagiphages that infect Pelagibacter HTCC1062 have been reported. Here, we report 11 new pelagiphages in the Podoviridae family. Comparative genomics classified these pelagiphages into the HTVC019Pvirus genus, which includes the previously reported pelagiphages HTVC011P and HTVC019P. Phylogenomic analysis clustered HTVC019Pvirus pelagiphages into three subgroups. Integrases were identified in all but one HTVC019Pvirus genome. Site-specific integration of HTVC019Pvirus pelagiphages into host tRNA genes was verified experimentally, demonstrating the capacity of these pelagiphages to propagate by both lytic and lysogenic infection. Evidence of pelagiphage integration was also retrieved from the Global Ocean Survey database, showing that prophages are found in natural SAR11 populations. HTVC019Pvirus pelagiphages could impact SAR11 populations by a variety of mechanisms, including mortality, genetic transduction and prophage-induced viral immunity. HTVC019Pvirus pelagiphages are a rare example of cultured lysogenic phage that can be implicated in ecological processes on broad scales. These pelagiphages have the potential to become a useful model for investigating strategies of host infection and phage-dependent horizontal gene transfer.}, }
@article {pmid30473684, year = {2018}, author = {Dorman, MJ and Dorman, CJ}, title = {Regulatory Hierarchies Controlling Virulence Gene Expression in Shigella flexneri and Vibrio cholerae.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2686}, pmid = {30473684}, issn = {1664-302X}, support = {//Wellcome Trust/United Kingdom ; }, abstract = {Gram-negative enteropathogenic bacteria use a variety of strategies to cause disease in the human host and gene regulation in some form is typically a part of the strategy. This article will compare the toxin-based infection strategy used by the non-invasive pathogen Vibrio cholerae, the etiological agent in human cholera, with the invasive approach used by Shigella flexneri, the cause of bacillary dysentery. Despite the differences in the mechanisms by which the two pathogens cause disease, they use environmentally-responsive regulatory hierarchies to control the expression of genes that have some features, and even some components, in common. The involvement of AraC-like transcription factors, the integration host factor, the Factor for inversion stimulation, small regulatory RNAs, the RNA chaperone Hfq, horizontal gene transfer, variable DNA topology and the need to overcome the pervasive silencing of transcription by H-NS of horizontally acquired genes are all shared features. A comparison of the regulatory hierarchies in these two pathogens illustrates some striking cross-species similarities and differences among mechanisms coordinating virulence gene expression. S. flexneri, with its low infectious dose, appears to use a strategy that is centered on the individual bacterial cell, whereas V. cholerae, with a community-based, quorum-dependent approach and an infectious dose that is several orders of magnitude higher, seems to rely more on the actions of a bacterial collective.}, }
@article {pmid30473355, year = {2018}, author = {Freitas-Silva, J and Inácio, &#xc2;S and Mourão, J and Antunes, P and Mendes, &#xc2; and de Carvalho, AP and Vasconcelos, V and Peixe, L and da Costa, PM}, title = {Occurrence of mcr-1 in Escherichia coli from rabbits of intensive farming.}, journal = {Veterinary microbiology}, volume = {227}, number = {}, pages = {78-81}, doi = {10.1016/j.vetmic.2018.10.020}, pmid = {30473355}, issn = {1873-2542}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Colistin/pharmacology ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/drug effects/*genetics ; Escherichia coli Infections/drug therapy/epidemiology/microbiology/*veterinary ; Escherichia coli Proteins/*genetics ; Farms ; Gene Transfer, Horizontal ; Livestock/microbiology ; Microbial Sensitivity Tests ; Plasmids/genetics ; Rabbits/*microbiology ; }, abstract = {The emergence of mobile colistin resistance genes (mcr) is yet another challenge in the fight against antimicrobial resistance, with reports proving the dissemination of these genes in different countries and different environments being of great concern. In the present study, we describe the recovery of three E. coli strains with mcr-1 gene in IncHI2 plasmids from intestinal content of necropsied meat rabbits reared in two intensive production systems in Portugal. Our findings are worrisome, given the high level of dependence on the usage of antibiotics in rabbit rearing and call for the development and implementation of an active surveillance system in this species.}, }
@article {pmid30471297, year = {2019}, author = {Vig-Milkovics, Z and Zachar, I and Kun, &#xc1; and Szilágyi, A and Szathmáry, E}, title = {Moderate sex between protocells can balance between a decrease in assortment load and an increase in parasite spread.}, journal = {Journal of theoretical biology}, volume = {462}, number = {}, pages = {304-310}, doi = {10.1016/j.jtbi.2018.11.020}, pmid = {30471297}, issn = {1095-8541}, mesh = {Artificial Cells/*cytology/parasitology ; Cell Fusion ; *Gene Transfer, Horizontal ; RNA, Catalytic ; }, abstract = {Sexual reproduction is widespread in nature despite the different kinds of cost that it entails. We do not know exactly when the first sexual process took place and especially why it was beneficial at first. It is clearer why sex is advantageous for the prokaryotes and eukaryotes but the benefit of sex for protocells with individually replicating ribozymes is not yet fully understood. In this context sex is the simple horizontal gene transfer among two protocells that undergo transient fusion. Many authors argue that horizontal gene transfer (HGT) was very common in the early stage of evolution. However, HGT is a risky mechanism considering both the disruption of optimal compositions and the spread of parasites among protocells. In order to test the effects of HGT on the fitness of a protocell population, we explored by numerical simulations those conditions under which fusion might have been beneficial. We investigated multiple conceivable types of fusion in the stochastic corrector model framework and we considered the spread of parasites in every case. Protocells contain up to five species of unlinked, essential ribozymes; if a protocell has the same amount of each, it reaches maximum fitness. Fusion is dangerous not only due to the spread of parasites but also because it can ruin the cells with balanced ribozyme composition. We show that fusion can restore the ribozyme composition of the protocells under certain circumstances (high gene count, intermediate split size and low rate of fusion) and thus it can decrease the effect of the genetic load. Fusion could have been a useful early mechanism in contributing to the reliable coexistence of the different ribozymes before the spread of the chromosomes.}, }
@article {pmid30465986, year = {2019}, author = {Chen, X and Yin, H and Li, G and Wang, W and Wong, PK and Zhao, H and An, T}, title = {Antibiotic-resistance gene transfer in antibiotic-resistance bacteria under different light irradiation: Implications from oxidative stress and gene expression.}, journal = {Water research}, volume = {149}, number = {}, pages = {282-291}, doi = {10.1016/j.watres.2018.11.019}, pmid = {30465986}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents ; Bacteria ; *Escherichia coli ; *Escherichia coli Proteins ; Gene Transfer, Horizontal ; Oxidative Stress ; }, abstract = {Due to the significant public health risks, there is substantial scientific interest in the increasing abundance of antibiotic-resistance bacteria (ARB) and the spread of antibiotic-resistance genes (ARGs) in aquatic environments. To clearly understand the mechanism of ARG transfer, this study examined the conjugative transfer of genes encoding resistance to cephalosporin (blaCTX) and polymyxin (mcr-1) from two antibiotic-resistant donor strains, namely E. coli DH5α (CTX) and E. coli DH5α (MCR), and to a streptomycin-resistant receptor strain (E. coli C600 (Sm)). Conjugative transfer was specifically studied under different light irradiation conditions including visible light (VL), simulated sunlight (SS) and ultraviolet light (UV254nm). Results show that the conjugative transfer frequency was not affected by VL irradiation, while it was slightly improved (2-10 fold) by SS irradiation and extremely accelerated (up to 100 fold) by UV irradiation. Furthermore, this study also explored the link between ARG transfer and stress conditions. This was done by studying physiological and biochemical changes; oxidative stress response; and functional gene expression of co-cultured AR-E. coli strains under stress conditions. When correlated with the transfer frequency results, we found that VL irradiation did not affect the physiological and biochemical characteristics of the bacteria, or induce oxidative stress and gene expression. For SS irradiation, oxidative stress occurred slowly, with a slight increase in the expression of target genes in the bacterial cells. In contrast, UV irradiation, rapidly inactivated the bacteria, the degree of oxidative stress was very severe and the expression of the target genes was markedly up-regulated. Our study could provide new insight into the underlying mechanisms and links between accelerated conjugative transfer and oxidative stress, as well as the altered expression of genes relevant to conjugation and other stress responses in bacterial cells.}, }
@article {pmid30465882, year = {2019}, author = {Lu, S and Faris, JD}, title = {Fusarium graminearum KP4-like proteins possess root growth-inhibiting activity against wheat and potentially contribute to fungal virulence in seedling rot.}, journal = {Fungal genetics and biology : FG &amp; B}, volume = {123}, number = {}, pages = {1-13}, doi = {10.1016/j.fgb.2018.11.002}, pmid = {30465882}, issn = {1096-0937}, mesh = {Aspergillus/genetics ; Fusarium/*genetics/pathogenicity ; Gene Transfer, Horizontal/genetics ; Genome, Fungal/genetics ; Host-Pathogen Interactions/genetics ; Humans ; Phylogeny ; Plant Diseases/*genetics ; Seedlings/genetics/growth &amp; development ; Triticum/*genetics/growth &amp; development/microbiology ; Viral Proteins/*genetics ; }, abstract = {The virally encoded KP4 killer toxin protein was first identified from Ustilago maydis (Um), and its homologues are present in diverse fungi and in one species of moss. No KP4-like (KP4L) proteins have been functionally characterized. Here, we report the identification and functional analysis of four KP4L proteins from Fusarium graminearum (Fg), the primary causal pathogen of Fusarium head blight (FHB), which is also known to associate with seedling rot of wheat. The four FgKP4L proteins (FgKP4L-1, -2, -3 and -4) are encoded by small open reading frames (378-825 bp) located on chromosome 1 with the FgKP4L-1, -2 and -3 genes clustering together. Sequence analysis indicated that FgKP4L proteins have conserved domains predicted to form a three-dimensional alpha/beta-sandwich structure as first reported for UmKP4, with FgKP4L-4 featuring double Kp4 domains. Further analyses revealed that the FgKP4L genes are expressed in vitro under certain stress conditions, and all up-regulated during FHB and/or seedling rot development, the recombinant FgKP4L-2 protein does not induce cell death in wheat leaves or spikelets, but inhibits root growth of young seedlings, and the elimination of the FgKP4L-1/-2/-3 gene cluster from the fungal genome results in reduced virulence in seedling rot but not in FHB. Database searches revealed KP4L proteins from ∼80 fungal species with more than half from human/animal pathogens. Phylogenetic analysis suggested that UmKP4 and the moss KP4L proteins are closely related to those from a zygromycete and Aspergillus, respectively, implying cross-kingdom horizontal gene transfer.}, }
@article {pmid30464559, year = {2018}, author = {Yin, M and Jiang, Y and Qian, C and Wu, F and Ying, Y and Wu, C and Li, P and Ying, J and Li, K and Xu, T and Bao, Q and Sun, C}, title = {Molecular characteristics and comparative genomics analysis of a clinical Enterococcus casseliflavus with a resistance plasmid.}, journal = {Infection and drug resistance}, volume = {11}, number = {}, pages = {2159-2167}, pmid = {30464559}, issn = {1178-6973}, abstract = {PURPOSE: The aim of this work was to investigate the molecular characterization of a clinical Enterococcus casseliflavus strain with a resistance plasmid.<br><br>MATERIALS AND METHODS: En. casseliflavus EC369 was isolated from a patient in a hospital in southern China. The minimum inhibitory concentration was found by means of the agar dilution method to determine the antimicrobial susceptibilities of the strains. Whole-genome sequencing and comparative genomics analysis were performed to analyze the mechanism of antibiotic resistance and the horizontal gene transfer of the resistance gene-related mobile genetic elements.<br><br>RESULTS: En. casseliflavus EC369 showed resistance to erythromycin, kanamycin, and streptomycin, but was susceptible to vancomycin, ampicillin, and streptothricin and other antimicrobials. There were six resistance genes (aph3', ant6, bla, sat4, and two ermBs) carried by a transposon identified on the plasmid pEC369 and a complete resistance gene cluster of vancomycin and a tet (M) gene encoded on the chromosome. This is the first complete plasmid sequence reported in clinically isolated En. casseliflavus. The plasmid with the greatest sequence identity with pEC369 was the plasmid of Enterococcus sp. FDAARGOS_375, followed by the plasmids of Enterococcus faecium strains F12085 and pRE25, whereas the sequence with the greatest identity to the resistance genes carrying a transposon of pEC369 was on the chromosome of Staphylococcus aureus strain GD1677.<br><br>CONCLUSION: The resistance profiles of En. casseliflavus EC369 might contribute to the resistance genes encoded on the plasmid. The fact that the most similar sequence to the transposon carrying resistance genes of pEC369 was encoded in the chromosome of a S. aureus strain provides insights into the mechanism of dissemination of multidrug resistance between bacteria of different species or genera through horizontal gene transfer.}, }
@article {pmid30463949, year = {2018}, author = {Mao, M and Yang, X and Bennett, GM}, title = {Evolution of host support for two ancient bacterial symbionts with differentially degraded genomes in a leafhopper host.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {50}, pages = {E11691-E11700}, pmid = {30463949}, issn = {1091-6490}, mesh = {Animals ; Bacteria/*genetics ; Bacterial Physiological Phenomena ; Bacteroidetes/genetics/physiology ; Betaproteobacteria/genetics/physiology ; *Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genome, Insect ; Hemiptera/cytology/genetics/*microbiology ; Host Microbial Interactions/*genetics/physiology ; Symbiosis/*genetics/physiology ; Transcriptome ; }, abstract = {Plant sap-feeding insects (Hemiptera) rely on bacterial symbionts for nutrition absent in their diets. These bacteria experience extreme genome reduction and require genetic resources from their hosts, particularly for basic cellular processes other than nutrition synthesis. The host-derived mechanisms that complete these processes have remained poorly understood. It is also unclear how hosts meet the distinct needs of multiple bacterial partners with differentially degraded genomes. To address these questions, we investigated the cell-specific gene-expression patterns in the symbiotic organs of the aster leafhopper (ALF), Macrosteles quadrilineatus (Cicadellidae). ALF harbors two intracellular symbionts that have two of the smallest known bacterial genomes: Nasuia (112 kb) and Sulcia (190 kb). Symbionts are segregated into distinct host cell types (bacteriocytes) and vary widely in their basic cellular capabilities. ALF differentially expresses thousands of genes between the bacteriocyte types to meet the functional needs of each symbiont, including the provisioning of metabolites and support of cellular processes. For example, the host highly expresses genes in the bacteriocytes that likely complement gene losses in nucleic acid synthesis, DNA repair mechanisms, transcription, and translation. Such genes are required to function in the bacterial cytosol. Many host genes comprising these support mechanisms are derived from the evolution of novel functional traits via horizontally transferred genes, reassigned mitochondrial support genes, and gene duplications with bacteriocyte-specific expression. Comparison across other hemipteran lineages reveals that hosts generally support the incomplete symbiont cellular processes, but the origins of these support mechanisms are generally specific to the host-symbiont system.}, }
@article {pmid30463550, year = {2018}, author = {Bardini, R and Di Carlo, S and Politano, G and Benso, A}, title = {Modeling antibiotic resistance in the microbiota using multi-level Petri Nets.}, journal = {BMC systems biology}, volume = {12}, number = {Suppl 6}, pages = {108}, pmid = {30463550}, issn = {1752-0509}, mesh = {Acinetobacter/drug effects ; Animals ; *Drug Resistance, Microbial ; Escherichia coli/drug effects ; Mice ; Microbiota/*drug effects ; *Models, Biological ; }, abstract = {BACKGROUND: The unregulated use of antibiotics not only in clinical practice but also in farm animals breeding is causing a unprecedented growth of antibiotic resistant bacterial strains. This problem can be analyzed at different levels, from the antibiotic resistance spreading dynamics at the host population level down to the molecular mechanisms at the bacteria level. In fact, antibiotic administration policies and practices affect the societal system where individuals developing resistance interact with each other and with the environment. Each individual can be seen as a meta-organism together with its associated microbiota, which proves to have a prominent role in the resistance spreading dynamics. Eventually, in each microbiota, bacterial population dynamics and vertical or horizontal gene transfer events activate cellular and molecular mechanisms for resistance spreading that can also be possible targets for its prevention.<br><br>RESULTS: In this work we show how to use the Nets-Within-Nets formalism to model the dynamics between different antibiotic administration protocols and antibiotic resistance, both at the individuals population and at the single microbiota level. Three application examples are presented to show the flexibility of this approach in integrating heterogeneous information in the same model, a fundamental property when creating computational models complex biological systems. Simulations allow to explicitly take into account timing and stochastic events.<br><br>CONCLUSIONS: This work demonstrates how the NWN formalism can be used to efficiently model antibiotic resistance population dynamics at different levels of detail. The proposed modeling approach not only provides a valuable tool for investigating causal, quantitative relations between different events and mechanisms, but can be also used as a valid support for decision making processes and protocol development.}, }
@article {pmid30459726, year = {2018}, author = {Brown, AMV and Wasala, SK and Howe, DK and Peetz, AB and Zasada, IA and Denver, DR}, title = {Comparative Genomics of Wolbachia-Cardinium Dual Endosymbiosis in a Plant-Parasitic Nematode.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2482}, pmid = {30459726}, issn = {1664-302X}, abstract = {Wolbachia and Cardinium are among the most important and widespread of all endosymbionts, occurring in nematodes and more than half of insect and arachnid species, sometimes as coinfections. These symbionts are of significant interest as potential biocontrol agents due to their abilities to cause major effects on host biology and reproduction through cytoplasmic incompatibility, sex ratio distortion, or obligate mutualism. The ecological and metabolic effects of coinfections are not well understood. This study examined a Wolbachia-Cardinium coinfection in the plant-parasitic nematode (PPN), Pratylenchus penetrans, producing the first detailed study of such a coinfection using fluorescence in situ hybridization (FISH), polymerase chain reaction (PCR), and comparative genomic analysis. Results from FISH and single-nematode PCR showed 123/127 individuals in a focal population carried Cardinium (denoted strain cPpe), and 48% were coinfected with Wolbachia strain wPpe. Both endosymbionts showed dispersed tissue distribution with highest densities in the anterior intestinal walls and gonads. Phylogenomic analyses confirmed an early place of cPpe and long distance from a sister strain in another PPN, Heterodera glycines, supporting a long history of both Cardinium and Wolbachia in PPNs. The genome of cPpe was 1.36 Mbp with 35.8% GC content, 1,131 predicted genes, 41% having no known function, and missing biotin and lipoate synthetic capacity and a plasmid present in other strains, despite having a slightly larger genome compared to other sequenced Cardinium. The larger genome revealed expansions of gene families likely involved in host-cellular interactions. More than 2% of the genes of cPpe and wPpe were identified as candidate horizontally transferred genes, with some of these from eukaryotes, including nematodes. A model of the possible Wolbachia-Cardinium interaction is proposed with possible complementation in function for pathways such as methionine and fatty acid biosynthesis and biotin transport.}, }
@article {pmid30458693, year = {2018}, author = {Doerfler, W and Weber, S and Naumann, A}, title = {Inheritable epigenetic response towards foreign DNA entry by mammalian host cells: a guardian of genomic stability.}, journal = {Epigenetics}, volume = {13}, number = {12}, pages = {1141-1153}, pmid = {30458693}, issn = {1559-2308}, mesh = {Animals ; DNA Methylation ; *Epigenesis, Genetic ; Gene Transfer, Horizontal ; Genomic Instability/*genetics ; Humans ; }, abstract = {Apart from its well-documented role in long-term promoter silencing, the genome-wide distribution patterns of ~ 28 million methylated or unmethylated CpG dinucleotides, e. g. in the human genome, is in search of genetic functions. We have set out to study changes in the cellular CpG methylation profile upon introducing foreign DNA into mammalian cells. As stress factors served the genomic integration of foreign (viral or bacterial plasmid) DNA, virus infections or the immortalization of cells with Epstein Barr Virus (EBV). In all instances investigated, alterations in cellular CpG methylation and transcription profiles were observed to different degrees. In the case of adenovirus DNA integration in adenovirus type 12 (Ad12)-transformed hamster cells, the extensive changes in cellular CpG methylation persisted even after the complete loss of all transgenomic Ad12 DNA. Hence, stress-induced alterations in CpG methylation can be inherited independent of the continued presence of the transgenome. Upon virus infections, changes in cellular CpG methylation appear early after infection. In EBV immortalized as compared to control cells, CpG hypermethylation in the far-upstream region of the human FMR1 promoter decreased four-fold. We conclude that in the wake of cellular stress due to foreign DNA entry, preexisting CpG methylation patterns were altered, possibly at specific CpG dinucleotides. Frequently, transcription patterns were also affected. As a working concept, we view CpG methylation profiles in mammalian genomes as a guarding sensor for genomic stability under epigenetic control. As a caveat towards manipulations of cells with foreign DNA, such cells can no longer be considered identical to their un-manipulated counterparts.}, }
@article {pmid30457889, year = {2019}, author = {Yohay, B and Snir, S}, title = {Extending the Evolvability Model to the Prokaryotic World: Simulations and Results on Real Data.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {26}, number = {8}, pages = {794-805}, doi = {10.1089/cmb.2018.0189}, pmid = {30457889}, issn = {1557-8666}, mesh = {*Computer Simulation ; Escherichia coli/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Models, Genetic ; *Prokaryotic Cells ; }, abstract = {In 2006, Valiant introduced a variation to his celebratedPAC (Probably Approximately Correct) model to biology, by which he wished to explain how, with two simple mechanisms-random variation and natural selection-complex life mechanisms evolved in such a short time. Subsequently, several works extended and specialized the evolvability framework to more specific processes. In this study, we extend the evolvability framework to accommodate horizontal gene transfer, the transfer of genetic material between unrelated organisms. While in a separate work, we focused on the theoretical aspects of this extension and its learnability power; here, the focus is on more practical and biological facets of this new model. Specifically, we focus on the evolutionary process of developing a trait and model it as theconjunctionfunction. We demonstrate the speedup in learning time for a variant of conjunction to which learning algorithms are known. We also confront the new model with the recombination model on real data ofEscherichia colistrains under the task of developing pathogenicity and obtain results adhering to current existing knowledge. Apart from the sheer extension to the understudied prokaryotic world, our work offers comparisons of three different models of evolution under the same conditions, which we believe is unique and of a separate interest.}, }
@article {pmid30456006, year = {2018}, author = {Li, J and Zhao, Z and Zhong, W and Zhong, C and Zong, G and Fu, J and Cao, G}, title = {Impacts of horizontal gene transfer on the compact genome of the clavulanic acid-producing Streptomyces strain F613-1.}, journal = {3 Biotech}, volume = {8}, number = {11}, pages = {472}, pmid = {30456006}, issn = {2190-572X}, abstract = {Mobile genetic elements involved in mediating horizontal transfer events contribute to bacterial evolution, and bacterial genomic plasticity and instability result in variation in functional genetic information in Streptomyces secondary metabolism. In a previous study, we reported the complete genome sequence of the industrial Streptomyces strain F613-1, which produces high yields of clavulanic acid. In this study, we used comparative genomics and bioinformatics to investigate the unique genomic features of this strain. Taken together, comparative genomics were used to systematically investigate secondary metabolism capabilities and indicated that frequent exchange of genetic materials between Streptomyces replicons may shape the remarkable diversities in their secondary metabolite repertoires. Moreover, a 136.9-kb giant region of plasticity (RGP) was found in the F613-1 chromosome, and the chromosome and plasmid pSCL4 are densely packed with an exceptionally large variety of potential secondary metabolic gene clusters, involving several determinants putatively accounting for antibiotic production. In addition, the differences in the architecture and size of plasmid pSCL4 between F613-1 and ATCC 27064 suggest that the pSCL4 plasmid could evolve from pSCL4-like and pSCL2-like extrachromosomal replicons. Furthermore, the genomic analyses revealed that strain F613-1 has developed specific genomic architectures and genetic patterns that are well suited to meet the requirements of industrial innovation processes.}, }
@article {pmid30455068, year = {2019}, author = {Music, MS and Samarzija, I and Hogenhout, SA and Haryono, M and Cho, ST and Kuo, CH}, title = {The genome of 'Candidatus Phytoplasma solani' strain SA-1 is highly dynamic and prone to adopting foreign sequences.}, journal = {Systematic and applied microbiology}, volume = {42}, number = {2}, pages = {117-127}, doi = {10.1016/j.syapm.2018.10.008}, pmid = {30455068}, issn = {1618-0984}, mesh = {Catharanthus/microbiology ; DNA, Bacterial ; *Gene Order ; *Genome, Bacterial ; Metagenomics ; Phylogeny ; Phytoplasma/*genetics ; }, abstract = {Bacteria of the genus 'Candidatus Phytoplasma' are uncultivated intracellular plant pathogens transmitted by phloem-feeding insects. They have small genomes lacking genes for essential metabolites, which they acquire from either plant or insect hosts. Nonetheless, some phytoplasmas, such as 'Ca. P. solani', have broad plant host range and are transmitted by several polyphagous insect species. To understand better how these obligate symbionts can colonize such a wide range of hosts, the genome of 'Ca. P. solani' strain SA-1 was sequenced from infected periwinkle via a metagenomics approach. The de novo assembly generated a draft genome with 19 contigs totalling 821,322bp, which corresponded to more than 80% of the estimated genome size. Further completion of the genome was challenging due to the high occurrence of repetitive sequences. The majority of repeats consisted of gene arrangements characteristic of phytoplasma potential mobile units (PMUs). These regions showed variation in gene orders intermixed with genes of unknown functions and lack of similarity to other phytoplasma genes, suggesting that they were prone to rearrangements and acquisition of new sequences via recombination. The availability of this high-quality draft genome also provided a foundation for genome-scale genotypic analysis (e.g., average nucleotide identity and average amino acid identity) and molecular phylogenetic analysis. Phylogenetic analyses provided evidence of horizontal transfer for PMU-like elements from various phytoplasmas, including distantly related ones. The 'Ca. P. solani' SA-1 genome also contained putative secreted protein/effector genes, including a homologue of SAP11, found in many other phytoplasma species.}, }
@article {pmid30453260, year = {2019}, author = {Zhao, X and Wang, J and Zhu, L and Wang, J}, title = {Field-based evidence for enrichment of antibiotic resistance genes and mobile genetic elements in manure-amended vegetable soils.}, journal = {The Science of the total environment}, volume = {654}, number = {}, pages = {906-913}, doi = {10.1016/j.scitotenv.2018.10.446}, pmid = {30453260}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/*drug effects/genetics ; China ; Copper/analysis ; Drug Resistance, Bacterial/*genetics ; Fertilizers/analysis ; Gene Transfer, Horizontal ; Genes, Bacterial/*drug effects ; Manure/analysis ; Polymerase Chain Reaction ; Soil/*chemistry ; Soil Pollutants/*analysis ; Sulfonamides/pharmacology ; Tetracyclines/pharmacology ; Zinc/analysis ; }, abstract = {The increasing prevalence of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) in the soil environment represents a serious threat to public health. In this study, the diversity and abundance of ARGs and mobile genetic elements (MGEs) in different years of manure-amended vegetable soils were investigated. A total of eight genes, including four tetracycline resistance genes: tetW, tetM, tetO and tetT; two sulfonamide resistance genes: sul1 and sul2; and two MGEs: intI1 and intI2; were quantified in ten vegetable soils. The relative abundance of ARGs in soils amended with manure was significantly higher than that in soils without manure application. The relative abundance of the intI1 and intI2 genes had significantly positive correlations with the relative abundance of the tetW, tetO, sul1 and sul2 genes. Under different concentrations of antibiotics, the resistant bacteria rates of manure-amended soil were much higher than the control soil. Bacillus and Chryseobacterium, more likely to be multi-drug-resistant bacteria, were detected in both two antibiotics. Moreover, the significant correlation was found between the concentrations of Cu and Zn and the ARGs. Our findings provide empirical evidence that the dissemination risk of ARGs and ARB in long-term manure-amended vegetable soils, which might promote to the development of effective strategies to reduce the spread of ARGs in agro-ecosystems.}, }
@article {pmid30451441, year = {2018}, author = {Zawistowska-Rojek, A and Tyski, S}, title = {Are Probiotic Really Safe for Humans?.}, journal = {Polish journal of microbiology}, volume = {67}, number = {3}, pages = {251-258}, pmid = {30451441}, issn = {1733-1331}, mesh = {Bacteremia/etiology ; Bifidobacterium ; *Consumer Product Safety ; Gene Transfer, Horizontal ; Humans ; Immunocompromised Host ; Lactobacillus ; Probiotics/*administration &amp; dosage/*adverse effects ; }, abstract = {Probiotic bacteria have been used as a health-promoting factor for a very long time. Nowadays, products containing probiotic bacteria are becoming more and more popular on the market. The term probiotics refers to the products belonging to the following groups: probiotic drugs (medicinal products - live biotherapeutic products for human use), medical devices, probiotic foods (e.g. foods, food ingredients, dietary supplements or food for special medical purposes), directly fed microorganisms (for animal use) and designer probiotics (genetically modified probiotics). Safety assessment of bacterial strains used as probiotics should be carefully studied. Even though probiotic bacteria have the generally recognized as safe (GRAS status), there are several reports about side effects triggered by the presence of these organisms. Microorganisms used as probiotics may cause systemic infections, stimulate the immune system, disturb metabolism and participate in horizontal gene transfer.}, }
@article {pmid30448253, year = {2019}, author = {Diop, A and Raoult, D and Fournier, PE}, title = {Paradoxical evolution of rickettsial genomes.}, journal = {Ticks and tick-borne diseases}, volume = {10}, number = {2}, pages = {462-469}, doi = {10.1016/j.ttbdis.2018.11.007}, pmid = {30448253}, issn = {1877-9603}, mesh = {*Evolution, Molecular ; *Genome, Bacterial ; Genomics ; Phylogeny ; RNA, Untranslated/genetics ; Repetitive Sequences, Nucleic Acid ; Rickettsia/*genetics ; Virulence ; }, abstract = {Rickettsia species are strictly intracellular bacteria that evolved approximately 150 million years ago from a presumably free-living common ancestor from the order Rickettsiales that followed a transition to an obligate intracellular lifestyle. Rickettsiae are best known as human pathogens vectored by various arthropods causing a range of mild to severe human diseases. As part of their obligate intracellular lifestyle, rickettsial genomes have undergone a convergent evolution that includes a strong genomic reduction resulting from progressive gene degradation, genomic rearrangements as well as a paradoxical expansion of various genetic elements, notably small RNAs and short palindromic elements whose role remains unknown. This reductive evolutionary process is not unique to members of the Rickettsia genus but is common to several human pathogenic bacteria. Gene loss, gene duplication, DNA repeat duplication and horizontal gene transfer all have shaped rickettsial genome evolution. Gene loss mostly involved amino-acid, ATP, LPS and cell wall component biosynthesis and transcriptional regulators, but with a high preservation of toxin-antitoxin (TA) modules, recombination and DNA repair proteins. Surprisingly the most virulent Rickettsia species were shown to have the most drastically reduced and degraded genomes compared to closely related species of milder pathogenesis. In contrast, the less pathogenic species harbored the greatest number of mobile genetic elements. Thus, this distinct evolutionary process observed in Rickettsia species may be correlated with the differences in virulence and pathogenicity observed in these obligate intracellular bacteria. However, future investigations are needed to provide novel insights into the evolution of genome sizes and content, for that a better understanding of the balance between proliferation and elimination of genetic material in these intracellular bacteria is required.}, }
@article {pmid30446709, year = {2018}, author = {Traglia, G and Chiem, K and Quinn, B and Fernandez, JS and Montaña, S and Almuzara, M and Mussi, MA and Tolmasky, ME and Iriarte, A and Centrón, D and Ramírez, MS}, title = {Genome sequence analysis of an extensively drug-resistant Acinetobacter baumannii indigo-pigmented strain depicts evidence of increase genome plasticity.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {16961}, pmid = {30446709}, issn = {2045-2322}, support = {SC3 GM125556/GM/NIGMS NIH HHS/United States ; T37 MD001368/MD/NIMHD NIH HHS/United States ; }, mesh = {Acinetobacter Infections/microbiology ; Acinetobacter baumannii/*genetics/metabolism/pathogenicity ; Anti-Bacterial Agents/classification/*pharmacology ; Cross Infection/microbiology ; DNA Transposable Elements/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Genes, Bacterial/*genetics ; Genome, Bacterial/*genetics ; Genomic Islands/*genetics ; Genomics/methods ; Humans ; Indigo Carmine/metabolism ; Microbial Sensitivity Tests ; Sequence Analysis, DNA ; Virulence/genetics ; }, abstract = {Acinetobacter baumannii is a multidrug resistant nosocomial pathogen that shows an outstanding ability to undergo genetic exchange, thereby acquiring different traits that contribute to its success. In this work, we identified genetic features of an indigo-pigmented A. baumannii strain (Ab33405) that belongs to the clonal complex CC113[B]/CC79[P]. Ab33405 possesses a high number of genes coding for antibiotic resistance and virulence factors that may contribute to its survival, not only in the human host, but also in the hospital environment. Thirteen genes conferring resistance to different antibiotic families (trimethoprim, florfenicol, β-lactams, aminoglycosides and sulfonamide) as well as the adeIJK genes and the capsule locus (KL) and outer core locus (OCL) were identified. Ab33405 includes 250 unique genes and a significant number of elements associated with Horizontal Gene Transfer, such as insertion sequences and transposons, genomic islands and prophage sequences. Also, the indigo-pigmented uncommon phenotype that could be associated with the monooxygenase or dioxygenase enzyme coded for by the iacA gene within the iac cluster was probably conferred by insertion of a 18-kb DNA fragment into the iacG gene belonging to this cluster. The Ab33405 genome includes all type VI secretion system genes and killing assays showed the ability of Ab33045 to kill Escherichia coli. In addition, Ab33405 can modulate susceptibility antibiotics when exposed to blue light.}, }
@article {pmid30445474, year = {2019}, author = {Fang, LX and Deng, GH and Jiang, Q and Cen, DJ and Yang, RS and Feng, YY and Xia, J and Sun, J and Liu, YH and Zhang, Q and Liao, XP}, title = {Clonal expansion and horizontal transmission of epidemic F2:A1:B1 plasmids involved in co-spread of rmtB with qepA and blaCTX-M-27 in extensively drug-resistant Salmonella enterica serovar Indiana isolates.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {74}, number = {2}, pages = {334-341}, doi = {10.1093/jac/dky441}, pmid = {30445474}, issn = {1460-2091}, mesh = {Animals ; Animals, Domestic/microbiology ; Anti-Bacterial Agents/pharmacology ; Chickens/microbiology ; China ; Drug Resistance, Multiple, Bacterial/*genetics ; Epidemics ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Methyltransferases/genetics ; Microbial Sensitivity Tests ; Plasmids/*genetics ; Salmonella Infections, Animal/epidemiology/microbiology ; Salmonella enterica/*drug effects/*genetics/pathogenicity ; Serogroup ; Virulence/genetics ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: To investigate the prevalence and transmission of 16S rRNA methylase genes among Salmonella isolates from food animals in China.<br><br>METHODS: A total of 310 Salmonella isolates collected from food animals in seven provinces of China during 2016-17 were screened for 16S RMTase genes. The clonal relationship of the 16S RMTase-producing isolates and their plasmid contents were also characterized.<br><br>RESULTS: rmtB and armA were respectively identified in 12 and 1 Salmonella enterica serovar Indiana (Salmonella Indiana) isolates from farmed ducks. These 13 isolates concurrently expressed high-level resistance to amikacin, cefotaxime and ciprofloxacin. They were assigned to seven distinct PFGE patterns and the high similarity among 10 of the 12 rmtB-carrying isolates suggests clonal expansion. The rmtB gene was co-transferred with blaCTX-M-27-qepA and qepA in eight and two of the isolates, respectively, and was located on F2:A1:B1 plasmids with sizes of 135 and 100&#x2009;kb, respectively. These 10 rmtB-bearing plasmids showed four restriction patterns with a high similarity. Four representative rmtB-bearing plasmids were fully sequenced and they exhibited remarkable similarity and possessed typical FII backbones. The primary differences were located in the region between blaTEM-1 and ycgA. Furthermore, a novel MDR region (13.5&#x2009;kb) was identified that contained qepA, rmtB and blaCTX-M-27.<br><br>CONCLUSIONS: This is the first report, to our knowledge, of the prevalence and complete sequences of plasmids simultaneously containing rmtB, qepA and blaCTX-M-27. These findings underscore a major public health threat posed by epidemic F2:A1:B1 plasmids bearing qepA-rmtB-blaCTX-M-27 that are circulating in XDR Salmonella Indiana clonal isolates from waterfowl husbandry.}, }
@article {pmid30445460, year = {2018}, author = {Dong, X and Chaisiri, K and Xia, D and Armstrong, SD and Fang, Y and Donnelly, MJ and Kadowaki, T and McGarry, JW and Darby, AC and Makepeace, BL}, title = {Genomes of trombidid mites reveal novel predicted allergens and laterally transferred genes associated with secondary metabolism.}, journal = {GigaScience}, volume = {7}, number = {12}, pages = {}, pmid = {30445460}, issn = {2047-217X}, mesh = {Alkyl and Aryl Transferases/classification/genetics ; Allergens/*genetics/immunology ; Animals ; Arthropod Proteins/analysis/classification/genetics/metabolism ; Bacteria/genetics ; Bacterial Proteins/classification/genetics ; Chromatography, High Pressure Liquid ; Fungal Proteins/classification/genetics ; Fungi/genetics ; Gene Transfer, Horizontal/*genetics ; *Genome ; Larva/genetics ; Mites/classification/*genetics/growth &amp; development ; Opsins/classification/genetics ; Phylogeny ; Salivary Proteins and Peptides/classification/genetics ; Secondary Metabolism/*genetics ; Tandem Mass Spectrometry ; Trombiculidae/classification/genetics ; }, abstract = {BACKGROUND: Trombidid mites have a unique life cycle in which only the larval stage is ectoparasitic. In the superfamily Trombiculoidea ("chiggers"), the larvae feed preferentially on vertebrates, including humans. Species in the genus Leptotrombidium are vectors of a potentially fatal bacterial infection, scrub typhus, that affects 1 million people annually. Moreover, chiggers can cause pruritic dermatitis (trombiculiasis) in humans and domesticated animals. In the Trombidioidea (velvet mites), the larvae feed on other arthropods and are potential biological control agents for agricultural pests. Here, we present the first trombidid mites genomes, obtained both for a chigger, Leptotrombidium deliense, and for a velvet mite, Dinothrombium tinctorium.<br><br>RESULTS: Sequencing was performed using Illumina technology. A 180 Mb draft assembly for D. tinctorium was generated from two paired-end and one mate-pair library using a single adult specimen. For L. deliense, a lower-coverage draft assembly (117 Mb) was obtained using pooled, engorged larvae with a single paired-end library. Remarkably, both genomes exhibited evidence of ancient lateral gene transfer from soil-derived bacteria or fungi. The transferred genes confer functions that are rare in animals, including terpene and carotenoid synthesis. Thirty-seven allergenic protein families were predicted in the L. deliense genome, of which nine were unique. Preliminary proteomic analyses identified several of these putative allergens in larvae.<br><br>CONCLUSIONS: Trombidid mite genomes appear to be more dynamic than those of other acariform mites. A priority for future research is to determine the biological function of terpene synthesis in this taxon and its potential for exploitation in disease control.}, }
@article {pmid30443861, year = {2018}, author = {Zhang, QY and Gui, JF}, title = {Diversity, evolutionary contribution and ecological roles of aquatic viruses.}, journal = {Science China. Life sciences}, volume = {61}, number = {12}, pages = {1486-1502}, doi = {10.1007/s11427-018-9414-7}, pmid = {30443861}, issn = {1869-1889}, mesh = {Animals ; Aquatic Organisms/virology ; *Biological Evolution ; *Ecosystem ; Gene Transfer, Horizontal ; *Genetic Variation ; Genome, Viral ; *Virus Physiological Phenomena ; Viruses/classification/*genetics ; *Water Microbiology ; }, abstract = {Aquatic viruses include infected viruses in aquatic animals, plants and microorganisms, and free-floating viruses (virioplankton) in water environments. In the last three decades, a huge number of aquatic viruses, especially diverse free-floating viruses, including cyanophages, phycoviruses, archaea viruses, giant viruses, and even virophages, have been identified by virological experiments and metagenomic analyses. Based on a comprehensive introduction of aquatic virus classification and their morphological and genetic diversity, here, we summarize and outline main virus species, their evolutionary contribution to aquatic communities through horizontal gene transfer, and their ecological roles for cyanobacterial bloom termination and global biogeochemical cycling in freshwater and marine ecosystems. Thereby, some novel insights of aquatic viruses and virus-host interactions, especially their evolutionary contribution and ecological rolesin diverse aquatic communities and ecosystems, are highlighted in this review.}, }
@article {pmid30441943, year = {2018}, author = {Bencko, V and Šíma, P}, title = {A horizontal transmission of genetic information and its importance for development of antibiotics resistance.}, journal = {Casopis lekaru ceskych}, volume = {157}, number = {3}, pages = {141-145}, pmid = {30441943}, issn = {0008-7335}, mesh = {*Anti-Bacterial Agents ; *Bacteria/drug effects/genetics ; *Gene Transfer, Horizontal ; }, abstract = {Genetic information is transmitted among organisms through two pathways - vertically from generation to generation (from parents to progeny) and horizontally (laterally) by direct exchange of genetic material across species barriers. These are primarily prokaryotes, in which the exchange of genes or whole gene segments by horizontal transmission is quite common. They can dynamically and in a relatively short time generate highly diverse genomes, which does not allow the vertical transmission. As a result, prokaryotes can rapidly acquire new properties such as virulence and pathogenicity as well as resistance to toxins, including antibiotics, by which they increase their adaptability. Therefore, reinfection-resistant microorganisms are always more difficult to treat than infections caused by non-resistant bacteria. Antibiotic resistance today is a global problem of health care service. Not only does the number of diseases caused by resistant pathogenic strains of bacteria increase, but also the cost of treatment increases disproportionately, the length of hospitalization is prolonged, and mortality is often rising. Therefore, when indicating antibiotic therapy, it is important to keep in mind that both overuse and abuse of antibiotics contribute to the spread of antibiotic resistance genes. This is equally true for antibiotic applications in veterinary medicine, agriculture, including aquacultures, or in the food industry. Keywords: horizontal transmission of genetic information, endosymbiosis, antibiotic resistance, risks of the emergence and spread of antibiotic resistance, prevention of antibiotic resistance.}, }
@article {pmid30431236, year = {2019}, author = {Lee, S and Lee, C}, title = {First detection of novel enterovirus G recombining a torovirus papain-like protease gene associated with diarrhoea in swine in South Korea.}, journal = {Transboundary and emerging diseases}, volume = {66}, number = {2}, pages = {1023-1028}, pmid = {30431236}, issn = {1865-1682}, support = {315021-04//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries/ ; //Ministry of Agriculture, Food and Rural Affairs/ ; }, mesh = {Amino Acid Sequence ; Animals ; Cysteine Proteases/*genetics ; Diarrhea/epidemiology/*veterinary/virology ; Enterovirus Infections/epidemiology/*veterinary/virology ; Enteroviruses, Porcine/*genetics/isolation &amp; purification ; Evolution, Molecular ; Feces/virology ; Genome, Viral ; Genotype ; Phylogeny ; Reassortant Viruses/*genetics ; *Recombination, Genetic ; Republic of Korea/epidemiology ; Sequence Homology ; Swine ; Swine Diseases ; Torovirus/*genetics ; }, abstract = {Enterovirus species G (EV-G) comprises a highly diversity of 20 genotypes that is prevalent in pig populations, with or without diarrhoea. In the present study, a novel EV-G strain (KOR/KNU-1811/2018) that resulted from cross-order recombination was discovered in diagnostic faecal samples from neonatal pigs with diarrhoea that were negative for swine enteric coronaviruses and rotavirus. The recombinant EV-G genome possessed an exogenous 594-nucleotide (198-amino acid) sequence, flanked by two viral 3C[pro] cleavage sites at the 5' and 3' ends in its 2C/3A junction region. This insertion encoded a predicted protease similar to the porcine torovirus papain-like cysteine protease (PLCP), which was recently found in the EV-G1, -G2, and -G17 genomes. The complete KNU-1811 genome shared 73.7% nucleotide identity with a prototype EV-G1 strain, but had 83.9%-86.7% sequence homology with the global EV-G1-PLCP strains. Genetic and phylogenetic analyses demonstrated that the Korean recombinant EV-G's own VP1 and inserted foreign PLCP genes are most closely related independently to contemporary chimeric G1-PLCP and G17-PLCP strains respectively. These results implied that the torovirus-derived PLCP gene might have undergone continuous nucleotide mutations in the respective EV-G genome following its independent acquisition through naturally occurring recombination. Our results advance the understanding of the genetic evolution of EV-G driven by infrequent viral recombination events, by which EV-G populations laterally gain an exotic gene encoding a virulence factor from heterogeneous virus families, thereby causing clinical disease in swine.}, }
@article {pmid30425695, year = {2018}, author = {Hiller, NL and Sá-Leão, R}, title = {Puzzling Over the Pneumococcal Pangenome.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2580}, pmid = {30425695}, issn = {1664-302X}, abstract = {The Gram positive bacterium Streptococcus pneumoniae (pneumococcus) is a major human pathogen. It is a common colonizer of the human host, and in the nasopharynx, sinus, and middle ear it survives as a biofilm. This mode of growth is optimal for multi-strain colonization and genetic exchange. Over the last decades, the far-reaching use of antibiotics and the widespread implementation of pneumococcal multivalent conjugate vaccines have posed considerable selective pressure on pneumococci. This scenario provides an exceptional opportunity to study the evolution of the pangenome of a clinically important bacterium, and has the potential to serve as a case study for other species. The goal of this review is to highlight key findings in the studies of pneumococcal genomic diversity and plasticity.}, }
@article {pmid30425415, year = {2018}, author = {Emri, T and Antal, K and Riley, R and Karányi, Z and Miskei, M and Orosz, E and Baker, SE and Wiebenga, A and de Vries, RP and Pócsi, I}, title = {Duplications and losses of genes encoding known elements of the stress defence system of the Aspergilli contribute to the evolution of these filamentous fungi but do not directly influence their environmental stress tolerance.}, journal = {Studies in mycology}, volume = {91}, number = {}, pages = {23-36}, pmid = {30425415}, issn = {0166-0616}, abstract = {The contribution of stress protein duplication and deletion events to the evolution of the Aspergilli was studied. We performed a large-scale homology analysis of stress proteins and generated and analysed three stress defence system models based on Saccharomyces cerevisiae, Schizosaccharomyces pombe and Aspergillus nidulans. Although both yeast-based and A. nidulans-based models were suitable to trace evolutionary changes, the A. nidulans-based model performed better in mapping stress protein radiations. The strong Mantel correlation found between the positions of species in the phylogenetic tree on the one hand and either in the A. nidulans-based or S. cerevisiae-based models on the other hand demonstrated that stress protein expansions and reductions contributed significantly to the evolution of the Aspergilli. Interestingly, stress tolerance attributes correlated well with the number of orthologs only for a few stress proteins. Notable examples are Ftr1 iron permease and Fet3 ferro-O2-oxidoreductase, elements of the reductive iron assimilation pathway, in the S. cerevisiae-based model, as well as MpkC, a HogA-like mitogen activated protein kinase in the A. nidulans-based model. In the case of the iron assimilation proteins, the number of orthologs showed a positive correlation with H2O2-induced stress tolerance while the number of MpkC orthologs correlated positively with Congo Red induced cell wall stress, sorbitol induced osmotic stress and H2O2 induced oxidative stress tolerances. For most stress proteins, changes in the number of orthologs did not correlate well with any stress tolerance attributes. As a consequence, stress tolerance patterns of the studied Aspergilli did not correlate with either the sets of stress response proteins in general or with the phylogeny of the species studied. These observations suggest that stress protein duplication and deletion events significantly contributed to the evolution of stress tolerance attributes of Aspergilli. In contrast, there are other processes, which may counterbalance the effects of stress gene duplications or deletions including (i) alterations in the structures of stress proteins leading to changes in their biological activities, (ii) varying biosynthesis of stress proteins, (iii) rewiring stress response regulatory networks or even (iv) acquiring new stress response genes by horizontal gene transfer. All these multilevel changes are indispensable for the successful adaptation of filamentous fungi to altering environmental conditions, especially when these organisms are entering new ecological niches.}, }
@article {pmid30422680, year = {2019}, author = {Avni, E and Snir, S}, title = {A New Quartet-Based Statistical Method for Comparing Sets of Gene Trees Is Developed Using a Generalized Hoeffding Inequality.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {26}, number = {1}, pages = {27-37}, doi = {10.1089/cmb.2018.0129}, pmid = {30422680}, issn = {1557-8666}, mesh = {Algorithms ; Animals ; Evolution, Molecular ; Gene Transfer, Horizontal ; Humans ; *Multigene Family ; Phylogeny ; }, abstract = {Extracting the strength of the tree signal that is encompassed by a collection of gene trees is an exceptionally challenging problem in phylogenomics. Often, this problem not only involves the construction of individual phylogenies based on different genes, which may be a difficult endeavor on its own, but is also exacerbated by many factors that create conflicts between the evolutionary histories of different gene families, such as duplications or losses of genes; hybridization events; incomplete lineage sorting; and horizontal gene transfer, the latter two play central roles in the evolution of eukaryotes and prokaryotes, respectively. In this work, we tackle the aforementioned problem by focusing on quartet trees, which are the most basic unit of information in the context of unrooted phylogenies. In the first part, we show how a theorem of Janson that generalizes the classical Hoeffding inequality can be used to develop a statistical test involving quartets. In the second part, we study real and simulated data using this theoretical advancement, thus demonstrating how the significance of the differences between sets of quartets can be assessed. Our results are particularly intriguing since they nonstandardly require the analysis of dependent random variables.}, }
@article {pmid30420840, year = {2018}, author = {Khadka, R and Clothier, L and Wang, L and Lim, CK and Klotz, MG and Dunfield, PF}, title = {Evolutionary History of Copper Membrane Monooxygenases.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2493}, pmid = {30420840}, issn = {1664-302X}, abstract = {Copper membrane monooxygenases (CuMMOs) oxidize ammonia, methane and some short-chain alkanes and alkenes. They are encoded by three genes, usually in an operon of xmoCAB. We aligned xmo operons from 66 microbial genomes, including members of the Alpha-, Beta-, and Gamma-proteobacteria, Verrucomicrobia, Actinobacteria, Thaumarchaeota and the candidate phylum NC10. Phylogenetic and compositional analyses were used to reconstruct the evolutionary history of the enzyme and detect potential lateral gene transfer (LGT) events. The phylogenetic analyses showed at least 10 clusters corresponding to a combination of substrate specificity and bacterial taxonomy, but with no overriding structure based on either function or taxonomy alone. Adaptation of the enzyme to preferentially oxidize either ammonia or methane has occurred more than once. Individual phylogenies of all three genes, xmoA, xmoB and xmoC, closely matched, indicating that this operon evolved or was consistently transferred as a unit, with the possible exception of the methane monooxygenase operons in Verrucomicrobia, where the pmoB gene has a distinct phylogeny from pmoA and pmoC. Compositional analyses indicated that some clusters of xmoCAB operons (for example, the pmoCAB in gammaproteobacterial methanotrophs and the amoCAB in betaproteobacterial nitrifiers) were compositionally very different from their genomes, possibly indicating recent lateral transfer of these operons. The combined phylogenetic and compositional analyses support the hypothesis that an ancestor of the nitrifying bacterium Nitrosococcus was the donor of methane monooxygenase (pMMO) to both the alphaproteobacterial and gammaproteobacterial methanotrophs, but that before this event the gammaproteobacterial methanotrophs originally possessed another CuMMO (Pxm), which has since been lost in many species.}, }
@article {pmid30420476, year = {2019}, author = {Walsh, SI and Peters, DS and Smith, PA and Craney, A and Dix, MM and Cravatt, BF and Romesberg, FE}, title = {Inhibition of Protein Secretion in Escherichia coli and Sub-MIC Effects of Arylomycin Antibiotics.}, journal = {Antimicrobial agents and chemotherapy}, volume = {63}, number = {2}, pages = {}, pmid = {30420476}, issn = {1098-6596}, support = {R21 AI081126/AI/NIAID NIH HHS/United States ; R35 CA231991/CA/NCI NIH HHS/United States ; R50 CA211526/CA/NCI NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics/*metabolism ; Drug Design ; Drug Resistance, Microbial/genetics ; Escherichia coli/*drug effects/*genetics ; Membrane Proteins/genetics/metabolism ; Microbial Sensitivity Tests ; Serine Endopeptidases/genetics/metabolism ; Virulence ; }, abstract = {At sufficient concentrations, antibiotics effectively eradicate many bacterial infections. However, during therapy, bacteria are unavoidably exposed to lower antibiotic concentrations, and sub-MIC exposure can result in a wide variety of other effects, including the induction of virulence, which can complicate therapy, or horizontal gene transfer (HGT), which can accelerate the spread of resistance genes. Bacterial type I signal peptidase (SPase) is an essential protein that acts at the final step of the general secretory pathway. This pathway is required for the secretion of many proteins, including many required for virulence, and the arylomycins are a class of natural product antibiotics that target SPase. Here, we investigated the consequences of exposing Escherichia coli cultures to sub-MIC levels of an arylomycin. Using multidimensional protein identification technology mass spectrometry, we found that arylomycin treatment inhibits the proper extracytoplasmic localization of many proteins, both those that appear to be SPase substrates and several that do not. The identified proteins are involved in a broad range of extracytoplasmic processes and include a number of virulence factors. The effects of arylomycin on several processes required for virulence were then individually examined, and we found that, at even sub-MIC levels, the arylomycins potently inhibit flagellation, motility, biofilm formation, and the dissemination of antibiotic resistance via HGT. Thus, we conclude that the arylomycins represent promising novel therapeutics with the potential to eradicate infections while simultaneously reducing virulence and the dissemination of resistance.}, }
@article {pmid30420211, year = {2019}, author = {Martinez, J and Liu, C and Rodman, N and Fernandez, JS and Barberis, C and Sieira, R and Perez, F and Bonomo, RA and Ramirez, MS}, title = {Human fluids alter DNA-acquisition in Acinetobacter baumannii.}, journal = {Diagnostic microbiology and infectious disease}, volume = {93}, number = {3}, pages = {183-187}, pmid = {30420211}, issn = {1879-0070}, support = {R01 AI100560/AI/NIAID NIH HHS/United States ; R21 AI114508/AI/NIAID NIH HHS/United States ; R01 AI072219/AI/NIAID NIH HHS/United States ; R01 AI063517/AI/NIAID NIH HHS/United States ; I01 BX001974/BX/BLRD VA/United States ; SC3 GM125556/GM/NIGMS NIH HHS/United States ; T37 MD001368/MD/NIMHD NIH HHS/United States ; }, mesh = {Acinetobacter Infections/microbiology ; Acinetobacter baumannii/*genetics ; Body Fluids/chemistry/microbiology/*physiology ; DNA/genetics ; DNA Transformation Competence/genetics ; Gene Expression ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/genetics ; Humans ; Serum Albumin, Human/analysis ; Transformation, Bacterial/*genetics ; }, abstract = {Transformation is one of the mechanisms of acquisition of foreign genetic material leading to the emergence of multidrug resistant (MDR) bacteria. Recently, human serum albumin (HSA) was shown to specifically increase transformation frequency in the nosocomial pathogen Acinetobacter baumannii. To further assess the relevance of HSA as a possible modulator of A. baumannii transformation in host-pathogen interactions, in this work we examined the effect of different human fluids. We observed a significant increase in transformation frequencies in the presence of pleural fluid, whole blood cells and liquid ascites, and to a lesser extent with urine. The observed effects correlate with both HSA and bacterial content found in the assayed patient fluids. Taken together, these results are in agreement with our previous findings that highlight HSA as a possible host signal with the ability to trigger natural transformation in A. baumannii.}, }
@article {pmid30420129, year = {2018}, author = {Zhou, ZC and Feng, WQ and Han, Y and Zheng, J and Chen, T and Wei, YY and Gillings, M and Zhu, YG and Chen, H}, title = {Prevalence and transmission of antibiotic resistance and microbiota between humans and water environments.}, journal = {Environment international}, volume = {121}, number = {Pt 2}, pages = {1155-1161}, doi = {10.1016/j.envint.2018.10.032}, pmid = {30420129}, issn = {1873-6750}, mesh = {Bacteria/drug effects ; Drug Resistance, Microbial/*genetics ; Feces/chemistry ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Microbiota/*genetics ; Prevalence ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Rivers ; Sewage/microbiology ; Wastewater/analysis ; *Water Microbiology ; }, abstract = {The transmission routes for antibiotic resistance genes (ARGs) and microbiota between humans and water environments is poorly characterized. Here, we used high-throughput qPCR analyses and 16S rRNA gene sequencing to examine the occurrence and abundance of antibiotic resistance genes and microbiota in both healthy humans and associated water environments from a Chinese village. Humans carried the most diverse assemblage of ARGs, with 234 different ARGs being detected. The total abundance of ARGs in feces, on skin, and in the effluent from domestic sewage treatment systems were approximately 23, 2, and 7 times higher than their abundance in river samples. In total, 53 ARGs and 28 bacteria genera that were present in human feces could also be found in the influent and effluent of rural sewage treatment systems, and also downstream of the effluent release point. We identified the bacterial taxa that showed a significant association with ARGs (P < 0.01, r > 0.8) by network analysis, supporting the idea that these bacteria could carry some ARGs and transfer between humans and the environment. Analysis of ARGs and microbiota in humans and in water environments helps to define the transmission routes and dynamics of antibiotic resistance within these environments. This study highlights human contribution to the load of ARGs into the environment and suggests means to prevent such dissemination.}, }
@article {pmid30419314, year = {2019}, author = {Nimmakayala, RK and Batra, SK and Ponnusamy, MP}, title = {Unraveling the journey of cancer stem cells from origin to metastasis.}, journal = {Biochimica et biophysica acta. Reviews on cancer}, volume = {1871}, number = {1}, pages = {50-63}, pmid = {30419314}, issn = {1879-2561}, support = {U01 CA200466/CA/NCI NIH HHS/United States ; U01 CA185148/CA/NCI NIH HHS/United States ; P50 CA127297/CA/NCI NIH HHS/United States ; U01 CA210240/CA/NCI NIH HHS/United States ; R01 CA183459/CA/NCI NIH HHS/United States ; R01 CA210637/CA/NCI NIH HHS/United States ; P01 CA217798/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Humans ; Neoplasm Invasiveness/*pathology ; Neoplasms/*pathology ; Neoplastic Stem Cells/*pathology ; }, abstract = {Cancer biology research over recent decades has given ample evidence for the existence of self-renewing and drug-resistant populations within heterogeneous tumors, widely recognized as cancer stem cells (CSCs). However, a lack of clear understanding about the origin, existence, maintenance, and metastatic roles of CSCs limit efforts towards the development of CSC-targeted therapy. In this review, we describe novel avenues of current CSC biology. In addition to cell fusion and horizontal gene transfer, CSCs are originated by mutations in somatic or differentiated cancer cells, resulting in de-differentiation and reprogramming. Recent studies also provided evidence for the existence of distinct or heterogeneous CSC populations within a single heterogeneous tumor. Our analysis of the literature also opens the doors for a novel hypothesis that CSC populations with specific phenotypes, metabolic profiles, and clonogenic potential metastasize to specific organs.}, }
@article {pmid30415838, year = {2018}, author = {Shen, XX and Opulente, DA and Kominek, J and Zhou, X and Steenwyk, JL and Buh, KV and Haase, MAB and Wisecaver, JH and Wang, M and Doering, DT and Boudouris, JT and Schneider, RM and Langdon, QK and Ohkuma, M and Endoh, R and Takashima, M and Manabe, RI and Čadež, N and Libkind, D and Rosa, CA and DeVirgilio, J and Hulfachor, AB and Groenewald, M and Kurtzman, CP and Hittinger, CT and Rokas, A}, title = {Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum.}, journal = {Cell}, volume = {175}, number = {6}, pages = {1533-1545.e20}, pmid = {30415838}, issn = {1097-4172}, support = {T32 GM007133/GM/NIGMS NIH HHS/United States ; T32 HG002760/HG/NHGRI NIH HHS/United States ; }, mesh = {*Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Fungal ; *Phylogeny ; Saccharomycetales/*classification/*genetics ; }, abstract = {Budding yeasts (subphylum Saccharomycotina) are found in every biome and are as genetically diverse as plants or animals. To understand budding yeast evolution, we analyzed the genomes of 332 yeast species, including 220 newly sequenced ones, which represent nearly one-third of all known budding yeast diversity. Here, we establish a robust genus-level phylogeny comprising 12 major clades, infer the timescale of diversification from the Devonian period to the present, quantify horizontal gene transfer (HGT), and reconstruct the evolution of 45 metabolic traits and the metabolic toolkit of the budding yeast common ancestor (BYCA). We infer that BYCA was metabolically complex and chronicle the tempo and mode of genomic and phenotypic evolution across the subphylum, which is characterized by very low HGT levels and widespread losses of traits and the genes that control them. More generally, our results argue that reductive evolution is a major mode of evolutionary diversification.}, }
@article {pmid30413888, year = {2018}, author = {Jha, V and Tikariha, H and Dafale, NA and Purohit, HJ}, title = {Exploring the rearrangement of sensory intelligence in proteobacteria: insight of Pho regulon.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {34}, number = {11}, pages = {172}, pmid = {30413888}, issn = {1573-0972}, mesh = {ATP-Binding Cassette Transporters/genetics ; Adenosine Triphosphatases/genetics ; Bacterial Proteins/genetics ; Base Sequence ; Binding Sites ; Carrier Proteins ; Gene Duplication ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genome, Bacterial/genetics ; Multigene Family ; Multilocus Sequence Typing ; Periplasmic Binding Proteins/genetics ; Phosphate-Binding Proteins/genetics ; Phosphates/metabolism ; Phylogeny ; Proteobacteria/classification/*genetics/*physiology ; RNA, Ribosomal, 16S/genetics ; Regulon/*genetics/*physiology ; }, abstract = {Pho regulon is a highly evolved and conserved mechanism across the microbes to fulfil their phosphate need. In this study, 52 proteobacteria genomes were analyzed for the presence of phosphorus acquisition genes, their pattern of arrangement and copy numbers. The diverse genetic architecture of the Pho regulon genes indicates the evolutionary challenge of nutrient limitation, particularly phosphorus, faced by bacteria in their environment. The incongruence between the Pho regulon proteins phylogeny and species phylogeny along with the presence of additional copies of pstS and pstB genes, having cross similarity with other genera, suggest the possibility of horizontal gene transfer event. The substitution rate analysis and multiple sequence alignment of the Pho regulon proteins were analyzed to gain additional insight into the evolution of the Pho regulon system. This comprehensive study confirms that genes perform the regulatory function (phoBR) were vertically inherited, whereas interestingly, genes whose product involved in direct interaction with the environment (pstS) acquired by horizontal gene transfer. The substantial amino acid substitutions in PstS most likely contribute to the successful adaptation of bacteria in different ecological condition dealing with different phosphorus availability. The findings decipher the intelligence of the bacteria which enable them to carry out the targeted alteration of genes to cope up with the environmental condition.}, }
@article {pmid30413471, year = {2019}, author = {Jang, J and Sakai, Y and Senoo, K and Ishii, S}, title = {Potentially Mobile Denitrification Genes Identified in Azospirillum sp. Strain TSH58.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {2}, pages = {}, pmid = {30413471}, issn = {1098-5336}, mesh = {Azospirillum/enzymology/genetics/*physiology ; DNA Transposable Elements/physiology ; DNA, Bacterial ; Denitrification/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial/*physiology ; Interspersed Repetitive Sequences/*physiology ; Nitrite Reductases/*genetics/metabolism ; Phylogeny ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; }, abstract = {Denitrification ability is sporadically distributed among diverse bacteria, archaea, and fungi. In addition, disagreement has been found between denitrification gene phylogenies and the 16S rRNA gene phylogeny. These facts have suggested potential occurrences of horizontal gene transfer (HGT) for the denitrification genes. However, evidence of HGT has not been clearly presented thus far. In this study, we identified the sequences and the localization of the nitrite reductase genes in the genomes of 41 denitrifying Azospirillum sp. strains and searched for mobile genetic elements that contain denitrification genes. All Azospirillum sp. strains examined in this study possessed multiple replicons (4 to 11 replicons), with their sizes ranging from 7 to 1,031 kbp. Among those, the nitrite reductase gene nirK was located on large replicons (549 to 941 kbp). Genome sequencing showed that Azospirillum strains that had similar nirK sequences also shared similar nir-nor gene arrangements, especially between the TSH58, Sp7[T], and Sp245 strains. In addition to the high similarity between nir-nor gene clusters among the three Azospirillum strains, a composite transposon structure was identified in the genome of strain TSH58, which contains the nir-nor gene cluster and the novel IS6 family insertion sequences (ISAz581 and ISAz582). The nirK gene within the composite transposon system was actively transcribed under denitrification-inducing conditions. Although not experimentally verified in this study, the composite transposon system containing the nir-nor gene cluster could be transferred to other cells if it is moved to a prophage region and the phage becomes activated and released outside the cells. Taken together, strain TSH58 most likely acquired its denitrification ability by HGT from closely related Azospirillum sp. denitrifiers.IMPORTANCE The evolutionary history of denitrification is complex. While the occurrence of horizontal gene transfer has been suggested for denitrification genes, most studies report circumstantial evidences, such as disagreement between denitrification gene phylogenies and the 16S rRNA gene phylogeny. Based on the comparative genome analyses of Azospirillum sp. denitrifiers, we identified denitrification genes, including nirK and norCBQD, located on a mobile genetic element in the genome of Azospirillum sp. strain TSH58. The nirK was actively transcribed under denitrification-inducing conditions. Since this gene was the sole nitrite reductase gene in strain TSH58, this strain most likely benefitted by acquiring denitrification genes via horizontal gene transfer. This finding will significantly advance our scientific knowledge regarding the ecology and evolution of denitrification.}, }
@article {pmid30411512, year = {2019}, author = {Nanayakkara, BS and O'Brien, CL and Gordon, DM}, title = {Diversity and distribution of Klebsiella capsules in Escherichia coli.}, journal = {Environmental microbiology reports}, volume = {11}, number = {2}, pages = {107-117}, doi = {10.1111/1758-2229.12710}, pmid = {30411512}, issn = {1758-2229}, mesh = {Australia ; Bacterial Capsules/*genetics ; DNA, Bacterial/genetics ; Escherichia coli/*classification/*cytology/genetics/growth &amp; development ; Fresh Water/microbiology ; Genetic Variation ; Genome, Bacterial/genetics ; Klebsiella/*cytology/genetics ; O Antigens/genetics ; *Phylogeny ; Sequence Alignment ; Serogroup ; }, abstract = {E. coli strains responsible for elevated counts (blooms) in freshwater reservoirs in Australia carry a capsule originating from Klebsiella. The occurrence of Klebsiella capsules in E. coli was about 7% overall and 23 different capsule types were detected. Capsules were observed in strains from phylogroups A, B1 and C, but were absent from phylogroup B2, D, E and F strains. In general, few A, B1 or C lineages were capsule-positive, but when a lineage was encapsulated multiple different capsule types were present. All Klebsiella capsule-positive strains were of serogroups O8, O9 and O89. Regardless of the phylogroup, O9 strains were more likely to be capsule-positive than O8 strains. Given the sequence similarity, it appears that both the capsule region and the O-antigen gene region are transferred to E. coli from Klebsiella as a single block via horizontal gene transfer events. Pan genome analysis indicated that there were only modest differences between encapsulated and non-encapsulated strains belonging to phylogroup A. The possession of a Klebsiella capsule, but not the type of capsule, is likely a key determinant of the bloom status of a strain.}, }
@article {pmid30410748, year = {2018}, author = {Lu, J and Zhang, J and Xu, L and Liu, Y and Li, P and Zhu, T and Cheng, C and Lu, S and Xu, T and Yi, H and Li, K and Zhou, W and Li, P and Ni, L and Bao, Q}, title = {Spread of the florfenicol resistance floR gene among clinical Klebsiella pneumoniae isolates in China.}, journal = {Antimicrobial resistance and infection control}, volume = {7}, number = {}, pages = {127}, pmid = {30410748}, issn = {2047-2994}, mesh = {Anti-Bacterial Agents/*pharmacology/therapeutic use ; China/epidemiology ; Conjugation, Genetic ; *Drug Resistance, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; *Genes, Bacterial ; Genome, Bacterial ; Genomics/methods ; Humans ; Klebsiella Infections/drug therapy/*epidemiology/*microbiology/transmission ; Klebsiella pneumoniae/classification/*drug effects/*genetics ; Microbial Sensitivity Tests ; Phylogeny ; Sequence Analysis, DNA ; Thiamphenicol/*analogs &amp; derivatives/pharmacology/therapeutic use ; }, abstract = {BACKGROUND: Florfenicol is a derivative of chloramphenicol that is used only for the treatment of animal diseases. A key resistance gene for florfenicol, floR, can spread among bacteria of the same and different species or genera through horizontal gene transfer. To analyze the potential transmission of resistance genes between animal and human pathogens, we investigated floR in Klebsiella pneumoniae isolates from patient samples. floR in human pathogens may originate from animal pathogens and would reflect the risk to human health of using antimicrobial agents in animals.<br><br>METHODS: PCR was used to identify floR-positive strains. The floR genes were cloned, and the minimum inhibitory concentrations (MICs) were determined to assess the relative resistance levels of the genes and strains. Sequencing and comparative genomics methods were used to analyze floR gene-related sequence structure as well as the molecular mechanism of resistance dissemination.<br><br>RESULTS: Of the strains evaluated, 20.42% (67/328) were resistant to florfenicol, and 86.96% (20/23) of the floR-positive strains demonstrated high resistance to florfenicol with MICs &#x2265;512&#xa0;&#x3bc;g/mL. Conjugation experiments showed that transferrable plasmids carried the floR gene in three isolates. Sequencing analysis of a plasmid approximately 125&#xa0;kb in size (pKP18-125) indicated that the floR gene was flanked by multiple copies of mobile genetic elements. Comparative genomics analysis of a 9-kb transposon-like fragment of pKP18-125 showed that an approximately 2-kb sequence encoding lysR-floR-virD2 was conserved in the majority (79.01%, 83/105) of floR sequences collected from NCBI nucleotide database. Interestingly, the most similar sequence was a 7-kb fragment of plasmid pEC012 from an Escherichia coli strain isolated from a chicken.<br><br>CONCLUSIONS: Identified on a transferable plasmid in the human pathogen K. pneumoniae, the floR gene may be disseminated through horizontal gene transfer from animal pathogens. Studies on the molecular mechanism of resistance gene dissemination in different bacterial species of animal origin could provide useful information for preventing or controlling the spread of resistance between animal and human pathogens.}, }
@article {pmid30410473, year = {2018}, author = {Redfield, RJ and Soucy, SM}, title = {Evolution of Bacterial Gene Transfer Agents.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2527}, pmid = {30410473}, issn = {1664-302X}, abstract = {Bacterial gene transfer agents (GTAs) are small virus-like particles that package DNA fragments and inject them into cells. They are encoded by gene clusters resembling defective prophages, with genes for capsid head and tail components. These gene clusters are usually assumed to be maintained by selection for the benefits of GTA-mediated recombination, but this has never been tested. We rigorously examined the potential benefits of GTA-mediated recombination, considering separately transmission of GTA-encoding genes and recombination of all chromosomal genes. In principle GTA genes could be directly maintained if GTA particles spread them to GTA[-] cells often enough to compensate for the loss of GTA-producing cells. However, careful bookkeeping showed that losses inevitably exceed gains for two reasons. First, cells must lyse to release particles to the environment. Second, GTA genes are not preferentially replicated before DNA is packaged. A simulation model was then used to search for conditions where recombination of chromosomal genes makes GTA[+] populations fitter than GTA[-] populations. Although the model showed that both synergistic epistasis and some modes of regulation could generate fitness benefits large enough to overcome the cost of lysis, these benefits neither allowed GTA[+] cells to invade GTA[-] populations, nor allowed GTA[+] populations to resist invasion by GTA[-] cells. Importantly, the benefits depended on highly improbable assumptions about the efficiencies of GTA production and recombination. Thus, the selective benefits that maintain GTA gene clusters over many millions of years must arise from consequences other than transfer of GTA genes or recombination of chromosomal genes.}, }
@article {pmid30409991, year = {2018}, author = {Liu, G and Fu, W and Zhang, Z and He, Y and Yu, H and Wang, Y and Wang, X and Zhao, YL and Deng, Z and Wu, G and He, X}, title = {Structural basis for the recognition of sulfur in phosphorothioated DNA.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {4689}, pmid = {30409991}, issn = {2041-1723}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry ; Base Sequence ; DNA/*chemistry/genetics ; Gene Transfer, Horizontal/genetics ; Phosphorothioate Oligonucleotides/*chemistry ; Phylogeny ; Protein Binding ; Protein Domains ; Protein Structure, Secondary ; Streptococcus/metabolism ; Sulfur/*chemistry ; }, abstract = {There have been very few reports on protein domains that specifically recognize sulfur. Here we present the crystal structure of the sulfur-binding domain (SBD) from the DNA phosphorothioation (PT)-dependent restriction endonuclease ScoMcrA. SBD contains a hydrophobic surface cavity that is formed by the aromatic ring of Y164, the pyrolidine ring of P165, and the non-polar side chains of four other residues that serve as lid, base, and wall of the cavity. The SBD and PT-DNA undergo conformational changes upon binding. The S[187]RGRR[191] loop inserts into the DNA major groove to make contacts with the bases of the GPSGCC core sequence. Mutating key residues of SBD impairs PT-DNA association. More than 1000 sequenced microbial species from fourteen phyla contain SBD homologs. We show that three of these homologs bind PT-DNA in vitro and restrict PT-DNA gene transfer in vivo. These results show that SBD-like PT-DNA readers exist widely in prokaryotes.}, }
@article {pmid30409983, year = {2018}, author = {Mashburn-Warren, L and Goodman, SD and Federle, MJ and Prehna, G}, title = {The conserved mosaic prophage protein paratox inhibits the natural competence regulator ComR in Streptococcus.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {16535}, pmid = {30409983}, issn = {2045-2322}, support = {R01 AI091779/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/chemistry/*genetics/*metabolism ; Crystallography, X-Ray ; DNA Transformation Competence ; Evolution, Molecular ; Gene Transfer, Horizontal ; Models, Molecular ; Mutation ; Protein Domains ; Protein Folding ; Quorum Sensing ; Streptococcus/chemistry/genetics/*metabolism ; Transcriptional Activation ; }, abstract = {Horizontal gene transfer is an important means of bacterial evolution. This includes natural genetic transformation, where bacterial cells become "competent" and DNA is acquired from the extracellular environment. Natural competence in many species of Streptococcus, is regulated by quorum sensing via the ComRS receptor-signal pair. The ComR-XIP (mature ComS peptide) complex induces expression of the alternative sigma factor SigX, which targets RNA polymerase to CIN-box promoters to activate genes involved in DNA uptake and recombination. In addition, the widely distributed Streptococcus prophage gene paratox (prx) also contains a CIN-box, and here we demonstrate it to be transcriptionally activated by XIP. In vitro experiments demonstrate that Prx binds ComR directly and prevents the ComR-XIP complex from interacting with DNA. Mutations of prx in vivo caused increased expression of the late competence gene ssb when induced with XIP as compared to wild-type, and Prx orthologues are able to inhibit ComR activation by XIP in a reporter strain which lacks an endogenous prx. Additionally, an X-ray crystal structure of Prx reveals a unique fold that implies a novel molecular mechanism to inhibit ComR. Overall, our results suggest Prx functions to inhibit the acquisition of new DNA by Streptococcus.}, }
@article {pmid30407540, year = {2018}, author = {Kado, T and Innan, H}, title = {Horizontal Gene Transfer in Five Parasite Plant Species in Orobanchaceae.}, journal = {Genome biology and evolution}, volume = {10}, number = {12}, pages = {3196-3210}, pmid = {30407540}, issn = {1759-6653}, mesh = {Chromosome Mapping ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Plant ; Orobanche/*genetics ; Pedicularis/*genetics ; Sequence Analysis, DNA ; }, abstract = {We sequenced genomes of five parasite species in family Orobanchaceae to explore the evolutionary role of horizontal gene transfer in plants. Orobanche minor and Aeginetia indica are obligate parasites with no photosynthetic activity, whereas the other three (Pedicularis keiskei, Phtheirospermum japonicum, and Melampyrum roseum) are facultative parasites. By using reference genome sequences and/or transcriptomes of 14 species from Fabaceae and Poaceae, their major host families, we detected 106 horizontally transferred genes (HGT genes), only in the genomes of the two obligate parasites (22 and 84 for Oro. minor and Ae. indica, respectively), whereas none in the three facultative parasites. The HGT genes, respectively, account for roughly 0.1% and 0.2% of the coding genes in the two species. We found that almost all HGT genes retained introns at the same locations as their homologs in potential host species, indicating a crucial role of DNA-mediated gene transfer, rather than mRNA mediated retro transfer. Furthermore, some of the HGT genes might have transferred simultaneously because they located very closely in the host reference genome, indicating that the length of transferred DNA could exceed 100 kb. We confirmed that almost all introns are spliced in the current genome of the parasite species, and that about half HGT genes do not have any missense mutations or frameshift-causing indels, suggesting that some HGT genes may be still functional. Evolutionary analyses revealed that the nonsynonymous-synonymous substitution ratio is on average elevated on the lineage leading to HGT genes, due to either relaxation of selection or positive selection.}, }
@article {pmid30405200, year = {2018}, author = {Kim, HT and Kim, KJ}, title = {Evolution of six novel ORFs in the plastome of Mankyua chejuense and phylogeny of eusporangiate ferns.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {16466}, pmid = {30405200}, issn = {2045-2322}, mesh = {Computational Biology/methods ; DNA, Chloroplast ; Ferns/*classification/*genetics ; Genomics/methods ; High-Throughput Nucleotide Sequencing ; Models, Biological ; *Open Reading Frames ; Phylogeny ; }, abstract = {In this paper, three plastomes of Mankyua chejuense, Helminthostachys zeylanica, and Botrychium ternatum in Ophioglossaceae were completely sequenced in order to investigate the plastome evolution and phylogeny of eusporangiate ferns. They were similar to each other in terms of length and the gene orders; however, six unknown open reading frames (ORFs) were found between rps4 and trnL-UAA genes in M. chejuense. Similar sequence regions of six ORFs of M. chejuense were found at the plastomes of Ophioglossum californicum and H. zeylanica, as well as the mitochondrial genome (mitogenome) of H. zeylanica, but not in B. ternatum. Interestingly, the translated amino acid sequences of three ORFs were more similar to the proteins of distantly related taxa such as algae and bacteria than they were to proteins in land plants. It is likely that the six ORFs region arose from endosymbiotic gene transfer (EGT) or horizontal gene transfer (HGT), but further study is needed to verify this. Phylogenetic analyses suggested that Mankyua was resolved as the earliest diverging lineage and that Ophioglossum was subsequently diverged in Ophioglossaceae. This result supports why the plastome of M. chejuense have contained the most ancestral six ORFs in the family.}, }
@article {pmid30404935, year = {2018}, author = {Sivertsen, A and Janice, J and Pedersen, T and Wagner, TM and Hegstad, J and Hegstad, K}, title = {The Enterococcus Cassette Chromosome, a Genomic Variation Enabler in Enterococci.}, journal = {mSphere}, volume = {3}, number = {6}, pages = {}, pmid = {30404935}, issn = {2379-5042}, mesh = {*Chromosomes, Bacterial ; Conjugation, Genetic ; DNA Transposable Elements ; Enterococcus faecium/*genetics ; *Gene Transfer, Horizontal ; *Genomic Islands ; Plasmids ; *Recombination, Genetic ; Sequence Analysis, DNA ; }, abstract = {Enterococcus faecium has a highly variable genome prone to recombination and horizontal gene transfer. Here, we have identified a novel genetic island with an insertion locus and mobilization genes similar to those of staphylococcus cassette chromosome elements SCCmec This novel element termed the enterococcus cassette chromosome (ECC) element was located in the 3' region of rlmH and encoded large serine recombinases ccrAB similar to SCCmec Horizontal transfer of an ECC element termed ECC::cat containing a knock-in cat chloramphenicol resistance determinant occurred in the presence of a conjugative reppLG1 plasmid. We determined the ECC::cat insertion site in the 3' region of rlmH in the E. faecium recipient by long-read sequencing. ECC::cat also mobilized by homologous recombination through sequence identity between flanking insertion sequence (IS) elements in ECC::cat and the conjugative plasmid. The ccrABEnt genes were found in 69 of 516 E. faecium genomes in GenBank. Full-length ECC elements were retrieved from 32 of these genomes. ECCs were flanked by attR and attL sites of approximately 50 bp. The attECC sequences were found by PCR and sequencing of circularized ECCs in three strains. The genes in ECCs contained an amalgam of common and rare E. faecium genes. Taken together, our data imply that ECC elements act as hot spots for genetic exchange and contribute to the large variation of accessory genes found in E. faeciumIMPORTANCEEnterococcus faecium is a bacterium found in a great variety of environments, ranging from the clinic as a nosocomial pathogen to natural habitats such as mammalian intestines, water, and soil. They are known to exchange genetic material through horizontal gene transfer and recombination, leading to great variability of accessory genes and aiding environmental adaptation. Identifying mobile genetic elements causing sequence variation is important to understand how genetic content variation occurs. Here, a novel genetic island, the enterococcus cassette chromosome, is shown to contain a wealth of genes, which may aid E. faecium in adapting to new environments. The transmission mechanism involves the only two conserved genes within ECC, ccrABEnt, large serine recombinases that insert ECC into the host genome similarly to SCC elements found in staphylococci.}, }
@article {pmid30401990, year = {2019}, author = {Pomahacova, R and Zamboryova, J and Paterova, P and Krepelova, A and Subrt, I and Jaklova, R and Vohradska, P and Hrdonkova, E and Sykora, J}, title = {Late diagnosis of complete androgen insensitivity syndrome and transmission/carriers of the condition in a family with mutation c.2495G&gt; T p.(Arg832Leu) in exon 7 of the androgen receptor gene: genetic, clinical and ethical aspects.}, journal = {Biomedical papers of the Medical Faculty of the University Palacky, Olomouc, Czechoslovakia}, volume = {163}, number = {4}, pages = {379-382}, doi = {10.5507/bp.2018.067}, pmid = {30401990}, issn = {1804-7521}, mesh = {Androgen-Insensitivity Syndrome/*diagnosis/*genetics/physiopathology ; Disorders of Sex Development/*diagnosis/*genetics/physiopathology ; Female ; Fetal Development/*genetics ; *Gene Transfer, Horizontal ; Genetic Predisposition to Disease ; Humans ; Male ; Mutation ; Receptors, Androgen/*genetics ; }, abstract = {BACKGROUND: The complete androgen insensitivity syndrome (CAIS) is a rare genetic disorder causing insensitivity to androgens in a person with female phenotype and 46,XY karyotype due to a mutation in the androgen receptor gene located on chromosome X. These children are born with female external genitalia, and females are transmitters.<br><br>CASE REPORT: We illustrate an unexpected diagnosis of CAIS in two siblings during examination for short stature, and describe transmission/carriers in the family along with ethical aspects.<br><br>CONCLUSION: A genetic examination could have earlier revealed the transmission of c.2495G>Tp.(Arg832Leu) mutation in exon 7. Our experience highlights the possibility of prenatal testing for the management of pregnancy in a family with a history of CAIS. The implications of prenatal testing in relation to CAIS with clearer explication of ethical and clinical issues warrant further investigation.}, }
@article {pmid30401812, year = {2018}, author = {Lutfullahoğlu-Bal, G and Seferoğlu, AB and Keskin, A and Akdoğan, E and Dunn, CD}, title = {A bacteria-derived tail anchor localizes to peroxisomes in yeast and mammalian cells.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {16374}, pmid = {30401812}, issn = {2045-2322}, support = {637649/ERC_/European Research Council/International ; }, mesh = {Amino Acid Sequence ; Escherichia coli/genetics/metabolism ; Escherichia coli Proteins/chemistry/*metabolism ; Gene Transfer, Horizontal ; HEK293 Cells ; Humans ; Mixed Function Oxygenases/chemistry/*metabolism ; Peroxisomes/*metabolism ; Protein Transport ; Saccharomyces cerevisiae/*cytology/metabolism ; }, abstract = {Prokaryotes can provide new genetic information to eukaryotes by horizontal gene transfer (HGT), and such transfers are likely to have been particularly consequential in the era of eukaryogenesis. Since eukaryotes are highly compartmentalized, it is worthwhile to consider the mechanisms by which newly transferred proteins might reach diverse organellar destinations. Toward this goal, we have focused our attention upon the behavior of bacteria-derived tail anchors (TAs) expressed in the eukaryote Saccharomyces cerevisiae. In this study, we report that a predicted membrane-associated domain of the Escherichia coli YgiM protein is specifically trafficked to peroxisomes in budding yeast, can be found at a pre-peroxisomal compartment (PPC) upon disruption of peroxisomal biogenesis, and can functionally replace an endogenous, peroxisome-directed TA. Furthermore, the YgiM(TA) can localize to peroxisomes in mammalian cells. Since the YgiM(TA) plays no endogenous role in peroxisomal function or assembly, this domain is likely to serve as an excellent tool allowing further illumination of the mechanisms by which TAs can travel to peroxisomes. Moreover, our findings emphasize the ease with which bacteria-derived sequences might target to organelles in eukaryotic cells following HGT, and we discuss the importance of flexible recognition of organelle targeting information during and after eukaryogenesis.}, }
@article {pmid30401772, year = {2018}, author = {Blau, K and Bettermann, A and Jechalke, S and Fornefeld, E and Vanrobaeys, Y and Stalder, T and Top, EM and Smalla, K}, title = {The Transferable Resistome of Produce.}, journal = {mBio}, volume = {9}, number = {6}, pages = {}, pmid = {30401772}, issn = {2150-7511}, mesh = {Coriandrum/microbiology ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/drug effects/*genetics ; Gene Transfer, Horizontal ; Germany ; Integrons/genetics ; Microbial Sensitivity Tests ; Plasmids/*genetics ; Polymerase Chain Reaction ; Raw Foods/microbiology ; Tetracycline/pharmacology ; Vegetables/*microbiology ; }, abstract = {Produce is increasingly recognized as a reservoir of human pathogens and transferable antibiotic resistance genes. This study aimed to explore methods to characterize the transferable resistome of bacteria associated with produce. Mixed salad, arugula, and cilantro purchased from supermarkets in Germany were analyzed by means of cultivation- and DNA-based methods. Before and after a nonselective enrichment step, tetracycline (TET)-resistant Escherichia coli were isolated and plasmids conferring TET resistance were captured by exogenous plasmid isolation. TET-resistant E. coli isolates, transconjugants, and total community DNA (TC-DNA) from the microbial fraction detached from leaves or after enrichment were analyzed for the presence of resistance genes, class 1 integrons, and various plasmids by real-time PCR and PCR-Southern blot hybridization. Real-time PCR primers were developed for IncI and IncF plasmids. TET-resistant E. coli isolated from arugula and cilantro carried IncF, IncI1, IncN, IncHI1, IncU, and IncX1 plasmids. Three isolates from cilantro were positive for IncN plasmids and blaCTX-M-1 From mixed salad and cilantro, IncF, IncI1, and IncP-1β plasmids were captured exogenously. Importantly, whereas direct detection of IncI and IncF plasmids in TC-DNA failed, these plasmids became detectable in DNA extracted from enrichment cultures. This confirms that cultivation-independent DNA-based methods are not always sufficiently sensitive to detect the transferable resistome in the rare microbiome. In summary, this study showed that an impressive diversity of self-transmissible multiple resistance plasmids was detected in bacteria associated with produce that is consumed raw, and exogenous capturing into E. coli suggests that they could transfer to gut bacteria as well.IMPORTANCE Produce is one of the most popular food commodities. Unfortunately, leafy greens can be a reservoir of transferable antibiotic resistance genes. We found that IncF and IncI plasmids were the most prevalent plasmid types in E. coli isolates from produce. This study highlights the importance of the rare microbiome associated with produce as a source of antibiotic resistance genes that might escape cultivation-independent detection, yet may be transferred to human pathogens or commensals.}, }
@article {pmid30392576, year = {2018}, author = {Gehring, T and Heydeck, D and Niewienda, A and Janek, K and Kuhn, H}, title = {Do lipoxygenases occur in viruses?: Expression and characterization of a viral lipoxygenase-like protein did not provide evidence for the existence of functional viral lipoxygenases.}, journal = {Prostaglandins, leukotrienes, and essential fatty acids}, volume = {138}, number = {}, pages = {14-23}, doi = {10.1016/j.plefa.2018.10.002}, pmid = {30392576}, issn = {1532-2823}, mesh = {Acanthamoeba/virology ; *Gene Expression ; *Lipoxygenase/chemistry/genetics/isolation &amp; purification ; *Mimiviridae/enzymology/genetics ; Oxidation-Reduction ; Recombinant Proteins/chemistry/genetics/isolation &amp; purification ; *Viral Proteins/chemistry/genetics/isolation &amp; purification ; }, abstract = {Lipoxygenases are lipid peroxidizing enzymes, which frequently occur in higher plants and animals. In bacteria, these enzymes are rare and have been introduced via horizontal gene transfer. Since viruses function as horizontal gene transfer vectors and since lipoxygenases may be helpful for releasing assembled virus particles from host cells we explored whether these enzymes may actually occur in viruses. For this purpose we developed a four-step in silico screening strategy and searching the publically available viral genomes for lipoxygenase-like sequences we detected a single functional gene in the genome of a mimivirus infecting Acantamoeba polyphaga. The primary structure of this protein involved two putative metal ligand clusters but the recombinant enzyme did neither contain iron nor manganese. Most importantly, it did not exhibit lipoxygenase activity. These data suggests that this viral lipoxygenase-like sequence does not encode a functional lipoxygenase and that these enzymes do not occur in viruses.}, }
@article {pmid30392330, year = {2018}, author = {Wang, W and Li, FQ}, title = {[Overview of Staphylococcus aureus mobile genetic elements and horizontal gene transfer of antimicrobial resistance genes].}, journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]}, volume = {52}, number = {10}, pages = {1067-1071}, doi = {10.3760/cma.j.issn.0253-9624.2018.10.020}, pmid = {30392330}, issn = {0253-9624}, support = {2016YFD0401102//National Key R&amp;D Program of China/ ; 2018 Talent Training Program//Senior Talent Competency Development Program/ ; }, mesh = {Animals ; Drug Resistance, Bacterial/*genetics ; *Gene Transfer, Horizontal ; Humans ; *Interspersed Repetitive Sequences ; Staphylococcus aureus/*genetics ; }, abstract = {The mechanism of antimicrobial resistance transmission mediated by mobile genetic elements (MGEs) in Staphylococcus aureus is highly complicated, leading a significant challenge for controlling the spread of the resistant Staphylococcus aureus strains. Based on the latest literature acquired in this work, we have overviewed the transmission mechanism of antimicrobial resistance encoding MGEs. It is notably that there are a number of MGEs, which may encode different antimicrobial resistance determinants and possess specific transmission mechanism. In spite of this specificity of the strains to their host (human or animal), some Staphylococcus aureus strains can be transmitted from animals to humans or vice versa. This ability of cross staphylococci transfer is an additional means to acquire new genetic material encoded by MGE. It was suggested in this review that study on transmission mechanism of MGEs mediated antimicrobial resistance genes could provide important biological information of their spreading and effectively help prevent and control of the resistant strains and/or resistance genes among human, animals and ecologies.}, }
@article {pmid30391842, year = {2019}, author = {Tong, J and Tang, A and Wang, H and Liu, X and Huang, Z and Wang, Z and Zhang, J and Wei, Y and Su, Y and Zhang, Y}, title = {Microbial community evolution and fate of antibiotic resistance genes along six different full-scale municipal wastewater treatment processes.}, journal = {Bioresource technology}, volume = {272}, number = {}, pages = {489-500}, doi = {10.1016/j.biortech.2018.10.079}, pmid = {30391842}, issn = {1873-2976}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bioreactors ; *Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Microbiota/*drug effects ; Sewage/microbiology ; Wastewater/*microbiology ; }, abstract = {The evolution of microbial community and the fate of ARGs along different full-scale wastewater treatment processes (i.e., Anaerobic-Anoxic-Oxic, Oxidation Ditch, and Cyclic Activated Sludge System) were investigated in this study. We found that the sludges of bioreactors treating similar influent showed the similar microbial communities, independent of the treatment technologies. The horizontal gene transfer (HGT) mainly occurred in aeration tank rather that anaerobic/anoxic tank. More co-occurrence of potential pathogens and ARGs was found in wastewater than in sludge. Microbial biomass was the key driver for the fate of ARGs in wastewater, while mobile genetic elements (MGEs) was the key factor for the fate of ARGs in sludge. Combination of wastewater characteristics, microbial diversity, microbial biomass, and MGEs contributed to the variation of ARGs. Finally, it was found that enhanced nutrients removal process and tertiary treatment would benefit ARGs removal.}, }
@article {pmid30389769, year = {2019}, author = {Li, L and Liu, Z and Meng, D and Liu, X and Li, X and Zhang, M and Tao, J and Gu, Y and Zhong, S and Yin, H}, title = {Comparative Genomic Analysis Reveals the Distribution, Organization, and Evolution of Metal Resistance Genes in the Genus Acidithiobacillus.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {2}, pages = {}, pmid = {30389769}, issn = {1098-5336}, mesh = {Acidithiobacillus/*genetics ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/*drug effects ; *Genome, Bacterial ; Genomics ; Metals, Heavy/*pharmacology ; Phylogeny ; }, abstract = {Members of the genus Acidithiobacillus, which can adapt to extremely high concentrations of heavy metals, are universally found at acid mine drainage (AMD) sites. Here, we performed a comparative genomic analysis of 37 strains within the genus Acidithiobacillus to answer the untouched questions as to the mechanisms and the evolutionary history of metal resistance genes in Acidithiobacillus spp. The results showed that the evolutionary history of metal resistance genes in Acidithiobacillus spp. involved a combination of gene gains and losses, horizontal gene transfer (HGT), and gene duplication. Phylogenetic analyses revealed that metal resistance genes in Acidithiobacillus spp. were acquired by early HGT events from species that shared habitats with Acidithiobacillus spp., such as Acidihalobacter, Thiobacillus, Acidiferrobacter, and Thiomonas species. Multicopper oxidase genes involved in copper detoxification were lost in iron-oxidizing Acidithiobacillus ferridurans, Acidithiobacillus ferrivorans, and Acidithiobacillus ferrooxidans and were replaced by rusticyanin genes during evolution. In addition, widespread purifying selection and the predicted high expression levels emphasized the indispensable roles of metal resistance genes in the ability of Acidithiobacillus spp. to adapt to harsh environments. Altogether, the results suggested that Acidithiobacillus spp. recruited and consolidated additional novel functionalities during the adaption to challenging environments via HGT, gene duplication, and purifying selection. This study sheds light on the distribution, organization, functionality, and complex evolutionary history of metal resistance genes in Acidithiobacillus spp.IMPORTANCE Horizontal gene transfer (HGT), natural selection, and gene duplication are three main engines that drive the adaptive evolution of microbial genomes. Previous studies indicated that HGT was a main adaptive mechanism in acidophiles to cope with heavy-metal-rich environments. However, evidences of HGT in Acidithiobacillus species in response to challenging metal-rich environments and the mechanisms addressing how metal resistance genes originated and evolved in Acidithiobacillus are still lacking. The findings of this study revealed a fascinating phenomenon of putative cross-phylum HGT, suggesting that Acidithiobacillus spp. recruited and consolidated additional novel functionalities during the adaption to challenging environments via HGT, gene duplication, and purifying selection. Altogether, the insights gained in this study have improved our understanding of the metal resistance strategies of Acidithiobacillus spp.}, }
@article {pmid30389763, year = {2019}, author = {Huo, W and Adams, HM and Trejo, C and Badia, R and Palmer, KL}, title = {A Type I Restriction-Modification System Associated with Enterococcus faecium Subspecies Separation.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {2}, pages = {}, pmid = {30389763}, issn = {1098-5336}, support = {K22 AI099088/AI/NIAID NIH HHS/United States ; R01 AI116610/AI/NIAID NIH HHS/United States ; }, mesh = {Computational Biology ; Deoxyribonucleases, Type I Site-Specific/*genetics/metabolism ; Enterococcus faecium/*genetics/metabolism ; *Evolution, Molecular ; Genome, Bacterial/*genetics ; Gram-Positive Bacterial Infections/microbiology ; High-Throughput Nucleotide Sequencing ; Hospitals ; }, abstract = {The gastrointestinal colonizer Enterococcus faecium is a leading cause of hospital-acquired infections. Multidrug-resistant (MDR) E. faecium isolates are particularly concerning for infection treatment. Previous comparative genomic studies revealed that subspecies referred to as clade A and clade B exist within E. faecium MDR E. faecium isolates belong to clade A, while clade B consists of drug-susceptible fecal commensal E. faecium isolates. Isolates from clade A are further grouped into two subclades, clades A1 and A2. In general, clade A1 isolates are hospital-epidemic isolates, whereas clade A2 isolates are isolates from animals and sporadic human infections. Such phylogenetic separation indicates that reduced gene exchange occurs between the clades. We hypothesize that endogenous barriers to gene exchange exist between E. faecium clades. Restriction-modification (R-M) systems are such barriers in other microbes. We utilized a bioinformatics analysis coupled with second-generation and third-generation deep-sequencing platforms to characterize the methylomes of two representative E. faecium strains, one from clade A1 and one from clade B. We identified a type I R-M system that is clade A1 specific, is active for DNA methylation, and significantly reduces the transformability of clade A1 E. faecium Based on our results, we conclude that R-M systems act as barriers to horizontal gene exchange in E. faecium and propose that R-M systems contribute to E. faecium subspecies separation.IMPORTANCEEnterococcus faecium is a leading cause of hospital-acquired infections around the world. Rising antibiotic resistance in certain E. faecium lineages leaves fewer treatment options. The overarching aim of this work was to determine whether restriction-modification (R-M) systems contribute to the structure of the E. faecium species, wherein hospital-epidemic and non-hospital-epidemic isolates have distinct evolutionary histories and highly resolved clade structures. R-M provides bacteria with a type of innate immunity to horizontal gene transfer (HGT). We identified a type I R-M system that is enriched in the hospital-epidemic clade and determined that it is active for DNA modification activity and significantly impacts HGT. Overall, this work is important because it provides a mechanism for the observed clade structure of E. faecium as well as a mechanism for facilitated gene exchange among hospital-epidemic E. faecium isolates.}, }
@article {pmid30389380, year = {2018}, author = {Lu, J and Wang, Y and Li, J and Mao, L and Nguyen, SH and Duarte, T and Coin, L and Bond, P and Yuan, Z and Guo, J}, title = {Triclosan at environmentally relevant concentrations promotes horizontal transfer of multidrug resistance genes within and across bacterial genera.}, journal = {Environment international}, volume = {121}, number = {Pt 2}, pages = {1217-1226}, doi = {10.1016/j.envint.2018.10.040}, pmid = {30389380}, issn = {1873-6750}, mesh = {Anti-Bacterial Agents/*pharmacology ; Conjugation, Genetic ; Drug Resistance, Bacterial/*genetics ; Environmental Pollutants/*pharmacology ; Escherichia coli K12/*drug effects/genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; *Genes, MDR ; Humans ; Plasmids ; Pseudomonas putida/drug effects/genetics ; Triclosan/*pharmacology ; }, abstract = {BACKGROUND: Antibiotic resistance poses an increasing threat to public health. Horizontal gene transfer (HGT) promoted by antibiotics is recognized as a significant pathway to disseminate antibiotic resistance genes (ARGs). However, it is unclear whether non-antibiotic, anti-microbial (NAAM) chemicals can directly promote HGT of ARGs in the environment.<br><br>OBJECTIVES: We aimed to investigate whether triclosan (TCS), a widely-used NAAM chemical in personal care products, is able to stimulate the conjugative transfer of antibiotic multi-resistance genes carried by plasmid within and across bacterial genera.<br><br>METHODS: We established two model mating systems, to investigate intra-genera transfer and inter-genera transfer. Escherichia coli K-12 LE392 carrying IncP-&#x3b1; plasmid RP4 was used as the donor, and E. coli K-12 MG1655 or Pseudomonas putida KT2440 were the intra- and inter-genera recipients, respectively. The mechanisms of the HGT promoted by TCS were unveiled by detecting oxidative stress and cell membrane permeability, in combination with Nanopore sequencing, genome-wide RNA sequencing and proteomic analyses.<br><br>RESULTS: Exposure of the bacteria to environmentally relevant concentrations of TCS (from 0.02&#x202f;&#x3bc;g/L to 20&#x202f;&#x3bc;g/L) significantly stimulated the conjugative transfer of plasmid-encoded multi-resistance genes within and across genera. The TCS exposure promoted ROS generation and damaged bacterial membrane, and caused increased expression of the SOS response regulatory genes umuC, dinB and dinD in the donor. In addition, higher expression levels of ATP synthesis encoding genes in E. coli and P. putida were found with increased TCS dosage.<br><br>CONCLUSIONS: TCS could enhance the conjugative ARGs transfer between bacteria by triggering ROS overproduction at environmentally relevant concentrations. These findings improve our awareness of the hidden risks of NAAM chemicals on the spread of antibiotic resistance.}, }
@article {pmid30386310, year = {2018}, author = {Wüthrich, D and Irmler, S and Berthoud, H and Guggenbühl, B and Eugster, E and Bruggmann, R}, title = {Conversion of Methionine to Cysteine in Lactobacillus paracasei Depends on the Highly Mobile cysK-ctl-cysE Gene Cluster.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2415}, pmid = {30386310}, issn = {1664-302X}, abstract = {Milk and dairy products are rich in nutrients and are therefore habitats for various microbiomes. However, the composition of nutrients can be quite diverse, in particular among the sulfur containing amino acids. In milk, methionine is present in a 25-fold higher abundance than cysteine. Interestingly, a fraction of strains of the species L. paracasei - a flavor-enhancing adjunct culture species - can grow in medium with methionine as the sole sulfur source. In this study, we focus on genomic and evolutionary aspects of sulfur dependence in L. paracasei strains. From 24 selected L. paracasei strains, 16 strains can grow in medium with methionine as sole sulfur source. We sequenced these strains to perform gene-trait matching. We found that one gene cluster - consisting of a cysteine synthase, a cystathionine lyase, and a serine acetyltransferase - is present in all strains that grow in medium with methionine as sole sulfur source. In contrast, strains that depend on other sulfur sources do not have this gene cluster. We expanded the study and searched for this gene cluster in other species and detected it in the genomes of many bacteria species used in the food production. The comparison to these species showed that two different versions of the gene cluster exist in L. paracasei which were likely gained in two distinct events of horizontal gene transfer. Additionally, the comparison of 62 L. paracasei genomes and the two versions of the gene cluster revealed that this gene cluster is mobile within the species.}, }
@article {pmid30383852, year = {2018}, author = {Avni, E and Montoya, D and Lopez, D and Modlin, R and Pellegrini, M and Snir, S}, title = {A phylogenomic study quantifies competing mechanisms for pseudogenization in prokaryotes-The Mycobacterium leprae case.}, journal = {PloS one}, volume = {13}, number = {11}, pages = {e0204322}, pmid = {30383852}, issn = {1932-6203}, support = {R01 AI022553/AI/NIAID NIH HHS/United States ; }, mesh = {Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial ; Genomics/*methods ; Humans ; Leprosy/*microbiology ; Mycobacterium leprae/*genetics ; *Phylogeny ; *Pseudogenes ; }, abstract = {BACKGROUND: Pseudogenes are non-functional sequences in the genome with homologous sequences that are functional (i.e. genes). They are abundant in eukaryotes where they have been extensively investigated, while in prokaryotes they are significantly scarcer and less well studied. Here we conduct a comprehensive analysis of the evolution of orthologs of Mycobacterium leprae pseudogenes in prokaryotes. The leprosy pathogen M. leprae is of particular interest since it contains an unusually large number of pseudogenes, comprising approximately 40% of its entire genome. The analysis is conducted in both broad and narrow phylogenetic ranges.<br><br>RESULTS: We have developed an informatics-based approach to characterize the evolution of pseudogenes. This approach combines tools from phylogenomics, genomics, and transcriptomics. The results we obtain are used to assess the contributions of two mechanisms for pseudogene formation: failed horizontal gene transfer events and disruption of native genes.<br><br>CONCLUSIONS: We conclude that, although it was reported that in most bacteria the former is most likely responsible for the majority of pseudogenization events, in mycobacteria, and in particular in M. leprae with its exceptionally high pseudogene numbers, the latter predominates. We believe that our study sheds new light on the evolution of pseudogenes in bacteria, by utilizing new methodologies that are applied to the unusually abundant M. leprae pseudogenes and their orthologs.}, }
@article {pmid30383524, year = {2018}, author = {Arredondo-Alonso, S and Rogers, MRC and Braat, JC and Verschuuren, TD and Top, J and Corander, J and Willems, RJL and Schürch, AC}, title = {mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species.}, journal = {Microbial genomics}, volume = {4}, number = {11}, pages = {}, pmid = {30383524}, issn = {2057-5858}, mesh = {*Chromosomes, Bacterial ; Drug Resistance, Bacterial/genetics ; Enterococcus faecium/genetics ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Klebsiella pneumoniae/genetics ; Machine Learning ; Plasmids/*genetics ; *Software ; Support Vector Machine ; Whole Genome Sequencing ; }, abstract = {Assembly of bacterial short-read whole-genome sequencing data frequently results in hundreds of contigs for which the origin, plasmid or chromosome, is unclear. Complete genomes resolved by long-read sequencing can be used to generate and label short-read contigs. These were used to train several popular machine learning methods to classify the origin of contigs from Enterococcus faecium, Klebsiella pneumoniae and Escherichia coli using pentamer frequencies. We selected support-vector machine (SVM) models as the best classifier for all three bacterial species (F1-score E. faecium=0.92, F1-score K. pneumoniae=0.90, F1-score E. coli=0.76), which outperformed other existing plasmid prediction tools using a benchmarking set of isolates. We demonstrated the scalability of our models by accurately predicting the plasmidome of a large collection of 1644 E. faecium isolates and illustrate its applicability by predicting the location of antibiotic-resistance genes in all three species. The SVM classifiers are publicly available as an R package and graphical-user interface called 'mlplasmids'. We anticipate that this tool may significantly facilitate research on the dissemination of plasmids encoding antibiotic resistance and/or contributing to host adaptation.}, }
@article {pmid30383521, year = {2018}, author = {Fleshman, A and Mullins, K and Sahl, J and Hepp, C and Nieto, N and Wiggins, K and Hornstra, H and Kelly, D and Chan, TC and Phetsouvanh, R and Dittrich, S and Panyanivong, P and Paris, D and Newton, P and Richards, A and Pearson, T}, title = {Corrigendum: Comparative pan-genomic analyses of Orientia tsutsugamushi reveal an exceptional model of bacterial evolution driving genomic diversity.}, journal = {Microbial genomics}, volume = {4}, number = {10}, pages = {}, doi = {10.1099/mgen.0.000230}, pmid = {30383521}, issn = {2057-5858}, }
@article {pmid30380474, year = {2019}, author = {Cerqueira, F and Matamoros, V and Bayona, J and Piña, B}, title = {Antibiotic resistance genes distribution in microbiomes from the soil-plant-fruit continuum in commercial Lycopersicon esculentum fields under different agricultural practices.}, journal = {The Science of the total environment}, volume = {652}, number = {}, pages = {660-670}, doi = {10.1016/j.scitotenv.2018.10.268}, pmid = {30380474}, issn = {1879-1026}, mesh = {Agriculture/*methods ; Drug Resistance, Microbial/*genetics ; *Environmental Monitoring ; Fruit/microbiology ; *Genes, Bacterial ; Solanum lycopersicum/*microbiology ; Microbiota ; Soil ; *Soil Microbiology ; }, abstract = {While the presence of antibiotic resistance genes (ARGs) in agricultural soils and products has been firmly established, their distribution among the different plant parts and the contribution of agricultural practices, including irrigation with reclaimed water, have not been adequately addressed yet. To this end, we analyzed the levels of seven ARGs (sul1, blaTEM, blaCTX-M-32, mecA, qnrS1, tetM, blaOXA-58), plus the integrase gene intl1, in soils, roots, leaves, and fruits from two commercial tomato fields irrigated with either unpolluted groundwater or from a channel impacted by treated wastewater, using culture-independent, quantitative real-time PCR methods. ARGs and intl1 sequences were found in leaves and fruits at levels representing from 1 to 10% of those found in roots or soil. The relative abundance of intl1 sequences correlated with tetM, blaTEM, and sul1 levels, suggesting a high horizontal mobility potential for these ARGs. High-throughput 16S rDNA sequencing revealed microbiome differences both between sample types (soil plus roots versus leaves plus fruits) and sampling zones, and a correlation between the prevalence of Pseudomonadaceae and the levels of different ARGs, particularly in fruits and leaves. We concluded that both microbiome composition and ARGs levels in plants parts, including fruits, were likely influenced by agricultural practices.}, }
@article {pmid30380104, year = {2018}, author = {Val-Calvo, J and Luque-Ortega, JR and Crespo, I and Miguel-Arribas, A and Abia, D and Sánchez-Hevia, DL and Serrano, E and Gago-Córdoba, C and Ares, S and Alfonso, C and Rojo, F and Wu, LJ and Boer, DR and Meijer, WJJ}, title = {Novel regulatory mechanism of establishment genes of conjugative plasmids.}, journal = {Nucleic acids research}, volume = {46}, number = {22}, pages = {11910-11926}, pmid = {30380104}, issn = {1362-4962}, mesh = {Bacillus pumilus/*genetics/metabolism ; Bacterial Proteins/*chemistry/genetics/metabolism ; Base Sequence ; Binding Sites ; Cloning, Molecular ; Conjugation, Genetic ; DNA/*chemistry/genetics/metabolism ; Drug Resistance, Multiple, Bacterial/genetics ; Escherichia coli/genetics/metabolism ; Gene Expression ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Genetic Vectors/chemistry/metabolism ; Nucleic Acid Conformation ; Plasmids/*chemistry/metabolism ; Promoter Regions, Genetic ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; Recombinant Proteins/chemistry/genetics/metabolism ; Repressor Proteins/*chemistry/genetics/metabolism ; Shigella flexneri/genetics/metabolism ; }, abstract = {The principal route for dissemination of antibiotic resistance genes is conjugation by which a conjugative DNA element is transferred from a donor to a recipient cell. Conjugative elements contain genes that are important for their establishment in the new host, for instance by counteracting the host defense mechanisms acting against incoming foreign DNA. Little is known about these establishment genes and how they are regulated. Here, we deciphered the regulation mechanism of possible establishment genes of plasmid p576 from the Gram-positive bacterium Bacillus pumilus. Unlike the ssDNA promoters described for some conjugative plasmids, the four promoters of these p576 genes are repressed by a repressor protein, which we named Reg576. Reg576 also regulates its own expression. After transfer of the DNA, these genes are de-repressed for a period of time until sufficient Reg576 is synthesized to repress the promoters again. Complementary in vivo and in vitro analyses showed that different operator configurations in the promoter regions of these genes lead to different responses to Reg576. Each operator is bound with extreme cooperativity by two Reg576-dimers. The X-ray structure revealed that Reg576 has a Ribbon-Helix-Helix core and provided important insights into the high cooperativity of DNA recognition.}, }
@article {pmid30380051, year = {2019}, author = {Srivastava, A and Mohan, S and Mauchline, TH and Davies, KG}, title = {Evidence for diversifying selection of genetic regions of encoding putative collagen-like host-adhesive fibers in Pasteuria penetrans.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {1}, pages = {}, pmid = {30380051}, issn = {1574-6941}, mesh = {Adhesives/*metabolism ; Amino Acid Sequence ; Bacterial Proteins/chemistry/*genetics/metabolism ; Collagen/chemistry/*genetics/metabolism ; Pasteuria/chemistry/classification/*genetics/metabolism ; Phylogeny ; Sequence Alignment ; Spores, Bacterial/chemistry/genetics/metabolism ; }, abstract = {Pasteuria spp. belong to a group of genetically diverse endospore-forming bacteria (phylum: Firmicutes) that are known to parasitize plant-parasitic nematodes and water fleas (Daphnia spp.). Collagen-like fibres form the nap on the surface of endospores and the genes encoding these sequences have been hypothesised to be involved in the adhesion of the endospores of Pasteuria spp. to their hosts. We report a group of 17 unique collagen-like genes putatively encoded by Pasteuria penetrans (strain: Res148) that formed five different phylogenetic clusters and suggest that collagen-like proteins are an important source of genetic diversity in animal pathogenic Firmicutes including Pasteuria. Additionally, and unexpectedly, we identified a putative collagen-like sequence which had a very different sequence structure to the other collagen-like proteins but was similar to the protein sequences in Megaviruses that are involved in host-parasite interactions. We, therefore, suggest that these diverse endospore surface proteins in Pasteuria are involved in biological functions, such as cellular adhesion; however, they are not of monophyletic origin and were possibly obtained de novo by mutation or possibly through selection acting upon several historic horizontal gene transfer events.}, }
@article {pmid30377851, year = {2018}, author = {Klein, S and Pipes, S and Lovell, CR}, title = {Occurrence and significance of pathogenicity and fitness islands in environmental vibrios.}, journal = {AMB Express}, volume = {8}, number = {1}, pages = {177}, pmid = {30377851}, issn = {2191-0855}, support = {1//Office of the Vice President for Research, University of South Carolina (US), South Carolina Floods Research Initiative/ ; }, abstract = {Pathogenicity islands (PAIs) are large genomic regions that contain virulence genes, which aid pathogens in establishing infections. While PAIs in clinical strains (strains isolated from a human infection) are well-studied, less is known about the occurrence of PAIs in strains isolated from the environment. In this study we describe three PAIs found in environmental Vibrio vulnificus and Vibrio parahaemolyticus strains, as well as a genomic fitness island found in a Vibrio diabolicus strain. All four islands had markedly different GC profiles than the rest of the genome, indicating that all of these islands were acquired via lateral gene transfer. Genes on the PAIs and fitness island were characterized. The PAI found in V. parahaemolyticus contained the tdh gene, a collagenase gene, and genes involved in the type 3 secretion system II (T3SS2). A V. vulnificus environmental strain contained two PAIs, a small 25 kbp PAI and a larger 143 kbp PAI. Both PAIs contained virulence genes. Toxin-antitoxin (TA) genes were found in all three species: on the V. diabolicus fitness island, and on the V. parahaemolyticus and V. vulnificus PAIs.}, }
@article {pmid30376113, year = {2019}, author = {Nadimpalli, M and Fabre, L and Yith, V and Sem, N and Gouali, M and Delarocque-Astagneau, E and Sreng, N and Le Hello, S and , }, title = {CTX-M-55-type ESBL-producing Salmonella enterica are emerging among retail meats in Phnom Penh, Cambodia.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {74}, number = {2}, pages = {342-348}, doi = {10.1093/jac/dky451}, pmid = {30376113}, issn = {1460-2091}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics ; Cambodia/epidemiology ; Chickens ; Drug Resistance, Multiple, Bacterial ; Fishes/microbiology ; Food Microbiology ; Gene Transfer, Horizontal ; Genome, Bacterial ; Meat/*microbiology ; Plasmids/*genetics ; Poultry/microbiology ; Prevalence ; Salmonella Infections, Animal/epidemiology/microbiology ; Salmonella enterica/enzymology/*genetics ; beta-Lactamases/*genetics ; }, abstract = {BACKGROUND: Salmonella enterica is a leading cause of human gastroenteritis. S. enterica strains that produce ESBLs (ESBL-Salm) remain rare in Europe and North America, but less is known about their prevalence among animal-derived foods in countries with weaker food safety practices and unregulated veterinary antibiotic use.<br><br>OBJECTIVES: To examine the prevalence and characteristics of ESBL-Salm from retail meats in Phnom Penh, Cambodia.<br><br>METHODS: We tested fish, pork and chicken from two markets for ESBL- and carbapenemase-producing Salmonella from September-December 2016, using cefotaxime- and ertapenem-supplemented media, respectively. ESBL-Salm were sequenced and their genomes characterized. We performed plasmid conjugation experiments to assess the co-transferability of ESBL-encoding genes and MDR phenotypes.<br><br>RESULTS: Twenty-six of 150 fish and meat samples (17%) were positive for ESBL-Salm, including 10/60 fish (17%), 15/60 pork (25%) and 1/30 chicken (3%). Carbapenemase-producing Salmonella strains were not detected. Pork-origin ESBL-Salm were primarily serotypes Rissen (10/15) or a monophasic variant of Typhimurium 4,5,12:i:- (3/15), whereas Saintpaul (3/10) and Newport (4/10) were more common among fish. Most ESBL enzymes were encoded by blaCTX-M-55 genes (24/26) harboured on conjugative IncA/C2 (n&#x2009;=&#x2009;14) or IncHI2 (n&#x2009;=&#x2009;10) plasmids. Resistance to up to six additional drug classes was co-transferred by each plasmid type. ESBL-Salm were resistant to almost every antibiotic recommended for severe salmonellosis treatment.<br><br>CONCLUSIONS: CTX-M-55-type S. enterica are highly prevalent among pork and fish from Phnom Penh markets and their spread appears to be mediated by MDR IncA/C2 and IncHI2 plasmids. Food safety must be improved and veterinary antibiotic use should be regulated to protect public health.}, }
@article {pmid30375330, year = {2018}, author = {Ma, NJ and Hemez, CF and Barber, KW and Rinehart, J and Isaacs, FJ}, title = {Organisms with alternative genetic codes resolve unassigned codons via mistranslation and ribosomal rescue.}, journal = {eLife}, volume = {7}, number = {}, pages = {}, pmid = {30375330}, issn = {2050-084X}, support = {R01 GM125951/GM/NIGMS NIH HHS/United States ; T32 GM007223/GM/NIGMS NIH HHS/United States ; Beckman Scholar Award//Arnold and Mabel Beckman Foundation/International ; HR0011-15-C-0091//Defense Advanced Research Projects Agency/International ; Graduate Research Fellowship DGE-1122492//National Science Foundation/International ; Graduate Research Fellowship//Gruber Foundation/International ; R01 GM117230/GM/NIGMS NIH HHS/United States ; Graduate Training Grants T32GM007499,T32GM007223/NH/NIH HHS/United States ; N66001-12-C-4211//Defense Advanced Research Projects Agency/International ; R01GM117230/NH/NIH HHS/United States ; 152339.5055249.100//U.S. Department of Energy/International ; Young Investigator Award//Arnold and Mabel Beckman Foundation/International ; T32 GM007499/GM/NIGMS NIH HHS/United States ; R01GM125951/NH/NIH HHS/United States ; Young Professor Award//DuPont/International ; }, mesh = {Codon, Terminator/*genetics ; Escherichia coli/genetics ; Escherichia coli Proteins/*genetics ; Frameshifting, Ribosomal/genetics ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal/*genetics ; Genetic Code/*genetics ; Genome, Bacterial/genetics ; Plasmids/genetics ; RNA, Bacterial/genetics ; RNA-Binding Proteins/*genetics ; Viruses/genetics ; }, abstract = {Organisms possessing genetic codes with unassigned codons raise the question of how cellular machinery resolves such codons and how this could impact horizontal gene transfer. Here, we use a genomically recoded Escherichia coli to examine how organisms address translation at unassigned UAG codons, which obstruct propagation of UAG-containing viruses and plasmids. Using mass spectrometry, we show that recoded organisms resolve translation at unassigned UAG codons via near-cognate suppression, dramatic frameshifting from at least -3 to +19 nucleotides, and rescue by ssrA-encoded tmRNA, ArfA, and ArfB. We then demonstrate that deleting tmRNA restores expression of UAG-ending proteins and propagation of UAG-containing viruses and plasmids in the recoded strain, indicating that tmRNA rescue and nascent peptide degradation is the cause of impaired virus and plasmid propagation. The ubiquity of tmRNA homologs suggests that genomic recoding is a promising path for impairing horizontal gene transfer and conferring genetic isolation in diverse organisms.}, }
@article {pmid30374192, year = {2018}, author = {Estes, AM and Hearn, DJ and Agrawal, S and Pierson, EA and Dunning Hotopp, JC}, title = {Comparative genomics of the Erwinia and Enterobacter olive fly endosymbionts.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {15936}, pmid = {30374192}, issn = {2045-2322}, mesh = {Base Composition ; Enterobacter/*genetics ; Erwinia/*genetics ; *Genome, Bacterial ; Genomics/*methods ; Nitrogen/metabolism ; Olea/microbiology ; RNA, Ribosomal, 16S/chemistry/genetics/metabolism ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {The pestivorous tephritid olive fly has long been known as a frequent host of the obligately host-associated bacterial endosymbiont, Erwinia dacicola, as well as other facultative endosymbionts. The genomes of Erwinia dacicola and Enterobacter sp. OLF, isolated from a California olive fly, encode the ability to supplement amino acids and vitamins missing from the olive fruit on which the larvae feed. The Enterobacter sp. OLF genome encodes both uricase and ureases, and the Er. dacicola genome encodes an allantoate transport pathway, suggesting that bird feces or recycling the fly's waste products may be important sources of nitrogen. No homologs to known nitrogenases were identified in either bacterial genome, despite suggestions of their presence from experiments with antibiotic-treated flies. Comparisons between the olive fly endosymbionts and their free-living relatives revealed similar GC composition and genome size. The Er. dacicola genome has fewer genes for amino acid metabolism, cell motility, and carbohydrate transport and metabolism than free-living Erwinia spp. while having more genes for cell division, nucleotide metabolism and replication as well as mobile elements. A 6,696 bp potential lateral gene transfer composed primarily of amino acid synthesis and transport genes was identified that is also observed in Pseudomonas savastanoii pv savastanoii, the causative agent of olive knot disease.}, }
@article {pmid30373756, year = {2019}, author = {Peck, RF and Graham, SM and Gregory, AM}, title = {Species Widely Distributed in Halophilic Archaea Exhibit Opsin-Mediated Inhibition of Bacterioruberin Biosynthesis.}, journal = {Journal of bacteriology}, volume = {201}, number = {2}, pages = {}, pmid = {30373756}, issn = {1098-5530}, support = {P20 GM103423/GM/NIGMS NIH HHS/United States ; }, mesh = {Actinobacteria/chemistry ; Aerobiosis ; Anaerobiosis ; Carotenoids/*biosynthesis ; Enzyme Inhibitors/isolation &amp; purification/metabolism ; Gene Expression Regulation, Archaeal ; Halobacteriales/*drug effects/*metabolism ; Opsins/isolation &amp; purification/*metabolism ; }, abstract = {Halophilic Archaea are a distinctive pink color due to a carotenoid pigment called bacterioruberin. To sense or utilize light, many halophilic Archaea also produce rhodopsins, complexes of opsin proteins with a retinal prosthetic group. Both bacterioruberin and retinal are synthesized from isoprenoid precursors, with lycopene as the last shared intermediate. We previously described a regulatory mechanism by which Halobacterium salinarum bacterioopsin and Haloarcula vallismortis cruxopsin inhibit bacterioruberin synthesis catalyzed by lycopene elongase. In this work, we found that opsins in all three major Halobacteria clades inhibit bacterioruberin synthesis, suggesting that this regulatory mechanism existed in the common Halobacteria ancestor. Halophilic Archaea, which are generally heterotrophic and aerobic, likely evolved from an autotrophic, anaerobic methanogenic ancestor by acquiring many genes from Bacteria via lateral gene transfer. These bacterial "imports" include genes encoding opsins and lycopene elongases. To determine if opsins from Bacteria inhibit bacterioruberin synthesis, we tested bacterial opsins and found that an opsin from Curtobacterium, in the Actinobacteria phylum, inhibits bacterioruberin synthesis catalyzed by its own lycopene elongase, as well as that catalyzed by several archaeal enzymes. We also determined that the lycopene elongase from Halococcus salifodinae, a species from a family of Halobacteria lacking opsin homologs, retained the capacity to be inhibited by opsins. Together, our results indicate that opsin-mediated inhibition of bacterioruberin biosynthesis is a widely distributed mechanism found in both Archaea and Bacteria, possibly predating the divergence of the two domains. Further analysis may provide insight into the acquisition and evolution of the genes and their host species.IMPORTANCE All organisms use a variety of mechanisms to allocate limited resources to match their needs in their current environment. Here, we explore how halophilic microbes use a novel mechanism to allow efficient production of rhodopsin, a complex of an opsin protein and a retinal prosthetic group. We previously demonstrated that Halobacterium salinarum bacterioopsin directs available resources toward retinal by inhibiting synthesis of bacterioruberin, a molecule that shares precursors with retinal. In this work, we show that this mechanism can be carried out by proteins from halophilic Archaea that are not closely related to H. salinarum and those in at least one species of Bacteria Therefore, opsin-mediated inhibition of bacterioruberin synthesis may be a highly conserved, ancient regulatory mechanism.}, }
@article {pmid30373513, year = {2018}, author = {Zhang, J and Hu, J and Shen, H and Zhang, Y and Sun, D and Pu, X and Yang, Q and Fan, Q and Lin, B}, title = {Genomic analysis of the Phalaenopsis pathogen Dickeya sp. PA1, representing the emerging species Dickeya fangzhongdai.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {782}, pmid = {30373513}, issn = {1471-2164}, support = {2015A030312002//Natural Science Foundation of Guangdong Province/ ; 31300118//National Natural Science Foundation of China/ ; }, mesh = {Bacterial Secretion Systems/genetics ; Base Composition ; Clustered Regularly Interspaced Short Palindromic Repeats ; Computational Biology/methods ; Conserved Sequence ; Enterobacteriaceae/*classification/*genetics/metabolism ; Evolution, Molecular ; Gene Order ; Genes, Bacterial ; *Genome, Bacterial ; *Genomics/methods ; Molecular Sequence Annotation ; Open Reading Frames ; Orchidaceae/*microbiology ; Phylogeny ; Plant Diseases/microbiology ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: Dickeya sp. strain PA1 is the causal agent of bacterial soft rot in Phalaenopsis, an important indoor orchid in China. PA1 and a few other strains were grouped into a novel species, Dickeya fangzhongdai, and only the orchid-associated strains have been shown to cause soft rot symptoms.<br><br>METHODS: We constructed the complete PA1 genome sequence and used comparative genomics to explore the differences in genomic features between D. fangzhongdai and other Dickeya species.<br><br>RESULTS: PA1 has a 4,979,223-bp circular genome with 4269 predicted protein-coding genes. D. fangzhongdai was phylogenetically similar to Dickeya solani and Dickeya dadantii. The type I to type VI secretion systems (T1SS-T6SS), except for the stt-type T2SS, were identified in D. fangzhongdai. The three phylogenetically similar species varied significantly in terms of their T5SSs and T6SSs, as did the different D. fangzhongdai strains. Genomic island (GI) prediction and synteny analysis (compared to D. fangzhongdai strains) of PA1 also indicated the presence of T5SSs and T6SSs in strain-specific regions. Two typical CRISPR arrays were identified in D. fangzhongdai and in most other Dickeya species, except for D. solani. CRISPR-1 was present in all of these Dickeya species, while the presence of CRISPR-2 varied due to species differentiation. A large polyketide/nonribosomal peptide (PK/NRP) cluster, similar to the zeamine biosynthetic gene cluster in Dickeya zeae rice strains, was discovered in D. fangzhongdai and D. solani. The D. fangzhongdai and D. solani strains might recently have acquired this gene cluster by horizontal gene transfer (HGT).<br><br>CONCLUSIONS: Orchid-associated strains are the typical members of D. fangzhongdai. Genomic analysis of PA1 suggested that this strain presents the genomic characteristics of this novel species. Considering the absence of the stt-type T2SS, the presence of CRISPR loci and the zeamine biosynthetic gene cluster, D. fangzhongdai is likely a transitional form between D. dadantii and D. solani. This is supported by the later acquisition of the zeamine cluster and the loss of CRISPR arrays by D. solani. Comparisons of phylogenetic positions and virulence determinants could be helpful for the effective quarantine and control of this emerging species.}, }
@article {pmid30373071, year = {2019}, author = {Bondarczuk, K and Piotrowska-Seget, Z}, title = {Microbial diversity and antibiotic resistance in a final effluent-receiving lake.}, journal = {The Science of the total environment}, volume = {650}, number = {Pt 2}, pages = {2951-2961}, doi = {10.1016/j.scitotenv.2018.10.050}, pmid = {30373071}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Physiological Phenomena/*drug effects ; *Drug Resistance, Bacterial ; Lakes/*microbiology ; Microbiota/drug effects ; Poland ; Waste Disposal, Fluid ; Wastewater/*microbiology ; beta-Lactams/pharmacology ; }, abstract = {Wastewater treatment plants have been recognised as hotspots for antibiotic resistance genes and antibiotic-resistant bacteria which enter the environment. However, the persistence of these genes and bacteria in receiving ecosystems remains poorly understood. The aim of the study was to evaluate the effect of final effluent release on microbial diversity and the antibiotic resistance gene pool in a final effluent-receiving lake. The numbers of total culturable heterotrophs and unculturable bacteria (represented as the 16S rRNA gene copy number) were significantly reduced during the treatment process. The number of ampicillin-resistant bacteria was higher in the sediment than in water samples, suggesting accumulation of ampicillin-resistant bacteria in freshwater sediments. Using an exogenous method, we captured 56 resistance plasmids which were further characterised. Next-generation sequencing revealed that the microbial phyla represented in the studied metagenomes were typical of corresponding environments. The highest relative abundance of antibiotic resistance genes was observed in the final effluent, suggesting that a considerable number of genes were released from the wastewater treatment plant. However, the lowest relative abundance and lowest diversity of the genes in the lake water, compared to the other studied metagenomes, suggest a negligible effect of treated sewage release on antibiotic resistance within water microbial communities of the lake. Furthermore, uncontrolled sewage dumping into this reservoir in the past as well as lower quality of the water upstream of the lake indicated that the wastewater treatment plant protected the studied ecosystem.}, }
@article {pmid30370317, year = {2018}, author = {Cooper, R and Tsimring, L and Hasty, J}, title = {Microfluidics-Based Analysis of Contact-dependent Bacterial Interactions.}, journal = {Bio-protocol}, volume = {8}, number = {16}, pages = {}, pmid = {30370317}, issn = {2331-8325}, support = {P50 GM085764/GM/NIGMS NIH HHS/United States ; }, abstract = {Bacteria in nature live in complex communities with multiple cell types and spatially-dependent interactions. Studying cells in well-mixed environments such as shaking culture tubes or flasks cannot capture these spatial dynamics, but cells growing in full-fledged biofilms are difficult to observe in real time. We present here a protocol for observing time-resolved, multi-species interactions at single-cell resolution. The protocol involves growing bacterial cells in a near monolayer in a microfluidic device. As a demonstration, we describe in particular observing the dynamic interactions between E. coli and Acinetobacter baylyi. In this case, the protocol is capable of observing both contact-dependent lysis of E. coli by A. baylyi via the Type VI Secretion System (T6SS) and subsequent functional horizontal gene transfer (HGT) of genes from E. coli to A. baylyi.}, }
@article {pmid30368956, year = {2018}, author = {Grum-Grzhimaylo, AA and Falkoski, DL and van den Heuvel, J and Valero-Jiménez, CA and Min, B and Choi, IG and Lipzen, A and Daum, CG and Aanen, DK and Tsang, A and Henrissat, B and Bilanenko, EN and de Vries, RP and van Kan, JAL and Grigoriev, IV and Debets, AJM}, title = {The obligate alkalophilic soda-lake fungus Sodiomyces alkalinus has shifted to a protein diet.}, journal = {Molecular ecology}, volume = {27}, number = {23}, pages = {4808-4819}, doi = {10.1111/mec.14912}, pmid = {30368956}, issn = {1365-294X}, mesh = {*Alkalies ; Ascomycota/*classification/enzymology ; Gene Transfer, Horizontal ; *Genome, Fungal ; Hydrogen-Ion Concentration ; Lakes/*microbiology ; Phylogeny ; Plants ; }, abstract = {Sodiomyces alkalinus is one of the very few alkalophilic fungi, adapted to grow optimally at high pH. It is widely distributed at the plant-deprived edges of extremely alkaline lakes and locally abundant. We sequenced the genome of S. alkalinus and reconstructed evolution of catabolic enzymes, using a phylogenomic comparison. We found that the genome of S. alkalinus is larger, but its predicted proteome is smaller and heavily depleted of both plant-degrading enzymes and proteinases, when compared to its closest plant-pathogenic relatives. Interestingly, despite overall losses, S. alkalinus has retained many proteinases families and acquired bacterial cell wall-degrading enzymes, some of them via horizontal gene transfer from bacteria. This fungus has very potent proteolytic activity at high pH values, but slowly induced low activity of cellulases and hemicellulases. Our experimental and in silico data suggest that plant biomass, a common food source for most fungi, is not a preferred substrate for S. alkalinus in its natural environment. We conclude that the fungus has abandoned the ancestral plant-based diet and has become specialized in a more protein-rich food, abundantly available in soda lakes in the form of prokaryotes and small crustaceans.}, }
@article {pmid30368822, year = {2019}, author = {Sun, X and Chen, W and Ivanov, S and MacLean, AM and Wight, H and Ramaraj, T and Mudge, J and Harrison, MJ and Fei, Z}, title = {Genome and evolution of the arbuscular mycorrhizal fungus Diversispora epigaea (formerly Glomus versiforme) and its bacterial endosymbionts.}, journal = {The New phytologist}, volume = {221}, number = {3}, pages = {1556-1573}, doi = {10.1111/nph.15472}, pmid = {30368822}, issn = {1469-8137}, support = {1237993//US National Science Foundation, Plant Genome Research program/International ; DE-SC0012460//Office of Science, Office of Biological and Environmental Research/International ; 2014-67013-21571//National Institute of Food and Agriculture/International ; }, mesh = {*Biological Evolution ; Gene Duplication ; Gene Transfer, Horizontal/genetics ; Genes, Fungal ; *Genome, Fungal ; Glomeromycota/*genetics/metabolism ; Multigene Family ; Mycoplasma/*physiology ; Mycorrhizae/*genetics ; Phylogeny ; Spores, Fungal/physiology ; Symbiosis/*genetics ; Tenericutes/*physiology ; }, abstract = {Arbuscular mycorrhizal (AM) fungi form endosymbioses with most plants, and they themselves are hosts for Mollicutes/Mycoplasma-related endobacteria (MRE). Despite their significance, genomic information for AM fungi and their MRE are relatively sparse, which hinders our understanding of their biology and evolution. We assembled the genomes of the AM fungus Diversispora epigaea (formerly Glomus versiforme) and its MRE and performed comparative genomics and evolutionary analyses. The D. epigaea genome showed a pattern of substantial gene duplication and differential evolution of gene families, including glycosyltransferase family 25, whose activities are exclusively lipopolysaccharide biosynthesis. Genes acquired by horizontal transfer from bacteria possibly function in defense against foreign DNA or viruses. The MRE population was diverse, with multiple genomes displaying characteristics of differential evolution and encoding many MRE-specific genes as well as genes of AM fungal origin. Gene family expansion in D. epigaea may enhance adaptation to both external and internal environments, such as expansion of kinases for signal transduction upon external stimuli and expansion of nucleoside salvage pathway genes potentially for competition with MRE, whose genomes lack purine and pyrimidine biosynthetic pathways. Collectively, this metagenome provides high-quality references and begins to reveal the diversity within AM fungi and their MRE.}, }
@article {pmid30367593, year = {2018}, author = {Kundu, S and Bansal, MS}, title = {On the impact of uncertain gene tree rooting on duplication-transfer-loss reconciliation.}, journal = {BMC bioinformatics}, volume = {19}, number = {Suppl 9}, pages = {290}, pmid = {30367593}, issn = {1471-2105}, mesh = {*Algorithms ; *Evolution, Molecular ; *Gene Duplication ; *Gene Transfer, Horizontal ; Genomics/*methods ; *Multigene Family ; *Phylogeny ; Software ; Uncertainty ; }, abstract = {BACKGROUND: Duplication-Transfer-Loss (DTL) reconciliation is a powerful and increasingly popular technique for studying the evolution of microbial gene families. DTL reconciliation requires the use of rooted gene trees to perform the reconciliation with the species tree, and the standard technique for rooting gene trees is to assign a root that results in the minimum reconciliation cost across all rootings of that gene tree. However, even though it is well understood that many gene trees have multiple optimal roots, only a single optimal root is randomly chosen to create the rooted gene tree and perform the reconciliation. This remains an important overlooked and unaddressed problem in DTL reconciliation, leading to incorrect evolutionary inferences. In this work, we perform an in-depth analysis of the impact of uncertain gene tree rooting on the computed DTL reconciliation and provide the first computational tools to quantify and negate the impact of gene tree rooting uncertainty on DTL reconciliation.<br><br>RESULTS: Our analysis of a large data set of over 4500 gene families from 100 species shows that a large fraction of gene trees have multiple optimal rootings, that these multiple roots often, but not always, appear closely clustered together in the same region of the gene tree, that many aspects of the reconciliation remain conserved across the multiple rootings, that gene tree error has a profound impact on the prevalence and structure of multiple optimal rootings, and that there are specific interesting patterns in the reconciliation of those gene trees that have multiple optimal roots.<br><br>CONCLUSIONS: Our results show that unrooted gene trees can be meaningfully reconciled and high-quality evolutionary information can be obtained from them even after accounting for multiple optimal rootings. In addition, the techniques and tools introduced in this paper make it possible to systematically avoid incorrect evolutionary inferences caused by incorrect or uncertain gene tree rooting. These tools have been implemented in the phylogenetic reconciliation software package RANGER-DTL 2.0, freely available from http://compbio.engr.uconn.edu/software/RANGER-DTL/ .}, }
@article {pmid30367577, year = {2018}, author = {Avni, E and Snir, S}, title = {Reconstruction of real and simulated phylogenies based on quartet plurality inference.}, journal = {BMC genomics}, volume = {19}, number = {Suppl 6}, pages = {570}, pmid = {30367577}, issn = {1471-2164}, mesh = {Computer Simulation ; Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; *Phylogeny ; }, abstract = {BACKGROUND: Deciphering the history of life on Earth has long been regarded as one of the most central tasks in biology. In past years, widespread discordance between the evolutionary histories of different groups of orthologous genes of prokaryotes have been revealed, primarily due to horizontal gene transfers (HGTs). Nonetheless, evidence that support a strong tree-like signal of evolution have been uncovered, despite the presence of HGT events. Therefore, a challenging task is to distill this tree-like signal from the noise induced by all sources of non-tree-like events.<br><br>RESULTS: In this work we tackle this question, using real and simulated data. We first tighten a recent related theoretical result in this field. In a simulation study, we infer individual quartet topologies, and then use the inferred quartets to reconstruct simulated species trees. We demonstrate that accurate tree reconstruction is feasible despite surprisingly high rates of HGT. In a real data study, we construct phylogenies of two sets of prokaryotes, and show that our tree reconstruction scheme is comparable with (and complementary better than) other commonly used methods.<br><br>CONCLUSIONS: Using a blend of theoretical and empirical investigations, our study proves the feasibility of accurate quartet-based phylogenetic reconstruction, the vast impact of HGT events notwithstanding.}, }
@article {pmid30361635, year = {2019}, author = {Kudo, H and Usui, M and Nagafuji, W and Oka, K and Takahashi, M and Yamaguchi, H and Tamura, Y}, title = {Inhibition effect of flavophospholipol on conjugative transfer of the extended-spectrum β-lactamase and vanA genes.}, journal = {The Journal of antibiotics}, volume = {72}, number = {2}, pages = {79-85}, pmid = {30361635}, issn = {1881-1469}, mesh = {Animal Feed ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics ; Bambermycins/*pharmacology ; Carbon-Oxygen Ligases/genetics ; Conjugation, Genetic/*drug effects ; Drug Resistance, Multiple, Bacterial/genetics ; Enterococcus faecalis/*growth &amp; development ; Escherichia coli/*growth &amp; development ; Escherichia coli Infections/prevention &amp; control ; Food Additives/*pharmacology ; Gene Transfer, Horizontal/*drug effects ; Gram-Positive Bacterial Infections/prevention &amp; control ; Microbial Sensitivity Tests ; Plasmids/genetics/physiology ; Vancomycin-Resistant Enterococci/*growth &amp; development ; beta-Lactamases/genetics ; }, abstract = {Flavophospholipol (FPL) is an antimicrobial feed additive that has been approved for use in livestock animals and has the potential to decrease horizontal dissemination of antimicrobial resistance genes. Since previous studies showed that FPL has an inhibitory effect on plasmid transfer, in vitro experiments have proven the efficacy of FPL in reducing the conjugative transfer of plasmids encoding the extended-spectrum β-lactamase (ESBL) and vanA genes. These are among the most important antimicrobial resistance loci known. ESBL-producing Escherichia coli and vancomycin-resistant Enterococcus faecalis (VRE) were exposed to several concentrations of FPL, and transfer frequency and plasmid curing activity were determined. FPL inhibited the conjugative transfer of plasmids harboring ESBL and vanA genes in a concentration-dependent manner in all strains. Further transfer experiments revealed that FPL could decrease or increase transfer frequency depending on plasmid type when transfer frequency was at low levels. The plasmid curing activity of FPL was also observed in ESBL-producing E. coli in a concentration-dependent manner, suggesting that they partially contribute to the inhibition of conjugative transfer. These results suggest that the use of FPL as a feed additive might decrease the dissemination of ESBL and vanA genes among livestock animals.}, }
@article {pmid30359954, year = {2019}, author = {Imran, M and Das, KR and Naik, MM}, title = {Co-selection of multi-antibiotic resistance in bacterial pathogens in metal and microplastic contaminated environments: An emerging health threat.}, journal = {Chemosphere}, volume = {215}, number = {}, pages = {846-857}, doi = {10.1016/j.chemosphere.2018.10.114}, pmid = {30359954}, issn = {1879-1298}, mesh = {Anti-Bacterial Agents/*toxicity ; Bacteria/drug effects/genetics/*pathogenicity ; *Drug Resistance, Multiple, Bacterial ; Environmental Pollution/*analysis ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Metals/*toxicity ; Plastics/*toxicity ; }, abstract = {Misuse/over use of antibiotics increases the threats to human health since this is a main reason behind evolution of antibiotic resistant bacterial pathogens. However, metals such as mercury, lead, zinc, copper and cadmium are accumulating to critical concentration in the environment and triggering co-selection of antibiotic resistance in bacteria. The co-selection of metal driven antibiotic resistance in bacteria is achieved through co-resistance or cross resistance. Metal driven antibiotic resistant determinants evolved in bacteria and present on same mobile genetic elements are horizontally transferred to distantly related bacterial human pathogens. Additionally, in marine environment persistent pollutants like microplastics is recognized as a vector for the proliferation of metal/antibiotics and human pathogens. Recently published research confirmed that horizontal gene transfer between phylogenetically distinct microbes present on microplastics is much faster than free living microbes. Therefore, microplastics act as an emerging hotspot for metal driven co-selection of multidrug resistant human pathogens and pose serious threat to humans which do recreational activities in marine environment and ingest marine derived foods. Therefore, marine environment co-polluted with metal, antibiotics, human pathogens and microplastics pose an emerging health threat globally.}, }
@article {pmid30358122, year = {2019}, author = {Ben-Hur, S and Biton, M and Regev-Rudzki, N}, title = {Extracellular Vesicles: A Prevalent Tool for Microbial Gene Delivery?.}, journal = {Proteomics}, volume = {19}, number = {1-2}, pages = {e1800170}, doi = {10.1002/pmic.201800170}, pmid = {30358122}, issn = {1615-9861}, mesh = {Evolution, Molecular ; Extracellular Vesicles/*metabolism ; Gene Transfer, Horizontal/genetics/*physiology ; }, abstract = {Genetic plasticity of prokaryotic microbial communities is largely dependent on the ongoing exchange of genetic determinants by Horizontal Gene Transfer (HGT). HGT events allow beneficial genetic transitions to occur throughout microbial life, thus promoting adaptation to changing environmental conditions. Here, the significance of secreted vesicles in mediating HGT between microorganisms is discussed, while focusing on the benefits gained by vesicle-mediated gene delivery and its occurrence under different environmental cues. The potential use of secreted DNA-harboring vesicles as a mechanism of currently unresolved HGT events in eukaryotic microbes is further discussed.}, }
@article {pmid30357893, year = {2018}, author = {Matsushita, M and Okubo, T and Hasegawa, T and Matsuo, J and Watanabe, T and Iwasaki, S and Fukumoto, T and Hayasaka, K and Akizawa, K and Shimizu, C and Yamaguchi, H}, title = {Tetrahymena promotes interactive transfer of carbapenemase gene encoded in plasmid between fecal Escherichia coli and environmental Aeromonas caviae.}, journal = {Microbiology and immunology}, volume = {62}, number = {11}, pages = {720-728}, doi = {10.1111/1348-0421.12656}, pmid = {30357893}, issn = {1348-0421}, support = {16K15270//Japan Society for the Promotion of Science, KAKENHI/ ; }, mesh = {Aeromonas caviae/drug effects/*genetics ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; Environmental Microbiology ; Escherichia coli/genetics ; Feces/*microbiology ; *Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Microbial Sensitivity Tests ; Plasmids/*genetics ; Tetrahymena/*microbiology/physiology ; beta-Lactamases/*genetics ; }, abstract = {Tetrahymena can facilitate plasmid transfer among Escherichia coli or from E. coli to Salmonella Enteritidis via vesicle accumulation. In this study, whether ciliates promote the interactive transfer of plasmids encoding blaIMP-1 between fecal E. coli and environmental Aeromonas caviae was investigated. Both bacteria were mixed with or without ciliates and incubated overnight at 30°C. The frequency of plasmid-acquired bacteria was estimated by colony counts using an agar plate containing ceftazidim (CAZ) followed by determination of the minimum inhibitory concentration (MIC). Cultures containing ciliates interactively transferred the plasmid between E. coli and Aeromonas with a frequency of 10[-4] to 10[-5] . All plasmid-acquired bacteria showed a MIC against CAZ of >128 μg/mL and the plasmid transfer was confirmed by PCR amplification of the blaIMP-1 gene. Fluorescent observation showed that both bacteria accumulated in the same vesicle and that transwell sequestering significantly decreased the transfer frequency. Although ciliates preferentially ingested E. coli rather than A. caviae, both bacteria were co-localized into the same vesicles of ciliates, indicating that their meeting is associated with the gene transfer. Thus, ciliates interactively promote plasmid transfer between E. coli and A. caviae. The results of this study will facilitate control of the spread of multiple-antibiotic resistant bacteria.}, }
@article {pmid30352726, year = {2019}, author = {Palmer, M and Venter, SN and Coetzee, MPA and Steenkamp, ET}, title = {Prokaryotic species are sui generis evolutionary units.}, journal = {Systematic and applied microbiology}, volume = {42}, number = {2}, pages = {145-158}, doi = {10.1016/j.syapm.2018.10.002}, pmid = {30352726}, issn = {1618-0984}, mesh = {Bacteria/*classification/genetics ; *Biological Evolution ; *Gene Transfer, Horizontal ; Genetic Variation ; *Models, Genetic ; }, abstract = {Many gene flow barriers associated with genetic isolation during eukaryotic species divergence, are lacking in prokaryotes. In these organisms the processes associated with horizontal gene transfer (HGT) may provide both the homogenizing force needed for genetic cohesion and the genetic variation essential to speciation. This is because HGT events can broadly be grouped into genetic conversions (where endogenous genetic material are replaced with homologs acquired from external sources) and genetic introductions (where novel genetic material is acquired from external sources). HGT-based genetic conversions therefore causes homogenization, while genetic introductions drive divergence of populations upon fixation of genetic variants. The impact of HGT in different prokaryotic species may vary substantially and can range from very low levels to rampant HGT, producing chimeric groups of isolates. Combined with other evolutionary processes, these varying levels of HGT causes diversity space to be occupied by unique groups that are mostly incomparable in terms of genetic similarity, genomic cohesion and evolutionary age. As a result, the conventional, cut-off based metrics for species delineation are not adequate. Rather, a pluralistic approach to prokaryotic species recognition is required to accommodate the unique evolutionary ages and tendencies, population dynamics, and evolutionary fates of individual prokaryotic species. Following this approach, all prokaryotic species may be regarded as unique and each of their own kind (sui generis). Taxonomic decisions thus require evolutionary information that integrates vertical inheritances with all possible sources of genetic heterogeneity to ultimately produce robust and biologically meaningful classifications.}, }
@article {pmid30348665, year = {2019}, author = {Soliman, AM and Shimamoto, T and Nariya, H and Shimamoto, T}, title = {Emergence of Salmonella Genomic Island 1 Variant SGI1-W in a Clinical Isolate of Providencia stuartii from Egypt.}, journal = {Antimicrobial agents and chemotherapy}, volume = {63}, number = {1}, pages = {}, pmid = {30348665}, issn = {1098-6596}, mesh = {Anti-Bacterial Agents/pharmacology ; Cephalosporins/pharmacology ; Chloramphenicol/pharmacology ; Chromosome Mapping ; Chromosomes, Bacterial/*chemistry ; Ciprofloxacin/pharmacology ; Drug Resistance, Multiple, Bacterial/*genetics ; Enterobacteriaceae Infections/diagnosis/drug therapy/*microbiology ; *Gene Transfer, Horizontal ; *Genomic Islands ; Humans ; Integrons ; Male ; Morganella morganii/genetics ; Proteus Infections/genetics ; Providencia/drug effects/*genetics/growth &amp; development/isolation &amp; purification ; Salmonella typhimurium/genetics ; Thiamphenicol/analogs &amp; derivatives/pharmacology ; }, }
@article {pmid30348081, year = {2018}, author = {Langhanki, L and Berger, P and Treffon, J and Catania, F and Kahl, BC and Mellmann, A}, title = {In vivo competition and horizontal gene transfer among distinct Staphylococcus aureus lineages as major drivers for adaptational changes during long-term persistence in humans.}, journal = {BMC microbiology}, volume = {18}, number = {1}, pages = {152}, pmid = {30348081}, issn = {1471-2180}, mesh = {Adaptation, Physiological/*genetics ; Cystic Fibrosis/*microbiology ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Humans ; Interspersed Repetitive Sequences ; Microbial Interactions ; Phenotype ; Respiratory System/microbiology ; Staphylococcal Infections/microbiology ; Staphylococcus aureus/*genetics/growth &amp; development ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: The airways of the majority of adolescent cystic fibrosis (CF) patients are persistently colonized or infected by Staphylococcus aureus. Using whole genome sequencing, we studied the evolutionary traits within a S. aureus population in the airways of a CF patient hypothesizing that horizontal gene transfer (HGT) and inter-bacterial interaction play a major role in adaptation during long-term persistence.<br><br>RESULTS: Whole genome sequencing of 21&#xa0;S. aureus isolates spanning 13&#xa0;years resulted in seven lineages defined by the spa types t012, t021, t331, t338, t364, t056, and t2351. Of these, the successfully persisting lineages t012 and t021 were closely related suggesting the evolution of t021 from t012, which was further corroborated by a nearly identical, syntenic set of mobile genetic elements. During transformation from t012 to t021, an increase of genomic changes including HGT from other S. aureus lineages was detected.<br><br>CONCLUSIONS: In summary, our in vivo data enabled us to conceptualize an evolutionary model showing the impact of HGT and inter-bacterial interaction on bacterial long-term adaptation to the human host during CF.}, }
@article {pmid30346688, year = {2018}, author = {Reimer, JM and Harb, I and Ovchinnikova, OG and Jiang, J and Whitfield, C and Schmeing, TM}, title = {Structural Insight into a Novel Formyltransferase and Evolution to a Nonribosomal Peptide Synthetase Tailoring Domain.}, journal = {ACS chemical biology}, volume = {13}, number = {11}, pages = {3161-3172}, doi = {10.1021/acschembio.8b00739}, pmid = {30346688}, issn = {1554-8937}, support = {FDN-148472//Canadian Institutes of Health Research/International ; }, mesh = {Anoxybacillus/enzymology ; Crystallography, X-Ray ; Gene Transfer, Horizontal ; Hydro-Lyases/chemistry/genetics ; Hydroxymethyl and Formyl Transferases/*chemistry/genetics ; Ligands ; Multigene Family ; Peptide Synthases/*chemistry/genetics ; Protein Domains ; Transaminases/chemistry/genetics ; }, abstract = {Nonribosomal peptide synthetases (NRPSs) increase the chemical diversity of their products by acquiring tailoring domains. Linear gramicidin synthetase starts with a tailoring formylation (F) domain, which likely originated from a sugar formyltransferase (FT) gene. Here, we present studies on an Anoxybacillus kamchatkensis sugar FT representative of the prehorizontal gene transfer FT. Gene cluster analysis reveals that this FT acts on a UDP-sugar in a novel pathway for synthesis of a 7-formamido derivative of CMP-pseudaminic acid. We recapitulate the pathway up to and including the formylation step in vitro, experimentally demonstrating the role of the FT. We also present X-ray crystal structures of the FT alone and with ligands, which unveil contrasts with other structurally characterized sugar FTs and show close structural similarity with the F domain. The structures reveal insights into the adaptations that were needed to co-opt and evolve a sugar FT into a functional and useful NRPS domain.}, }
@article {pmid30346514, year = {2018}, author = {Bansal, K and Kumar, S and Patil, PB}, title = {Complete Genome Sequence Reveals Evolutionary Dynamics of an Emerging and Variant Pathovar of Xanthomonas euvesicatoria.}, journal = {Genome biology and evolution}, volume = {10}, number = {11}, pages = {3104-3109}, pmid = {30346514}, issn = {1759-6653}, mesh = {*Biological Evolution ; *Genome, Bacterial ; Lipopolysaccharides/biosynthesis ; Multigene Family ; Plant Diseases/microbiology ; Whole Genome Sequencing ; Xanthomonas/*genetics/metabolism ; }, abstract = {Xanthomonas, a complex group of pathogens, infects more than 400 plants, which is expanding to new hosts causing serious diseases. Genome-based studies are transforming our understanding on diversity and relationship of host-specific members, known as pathovars. In this study, we report complete genome sequence of a novel pathovar Xanthomonas axonopodis pv. commiphorae (Xcom) from India. It causes gumming disease of Commiphora wightii, a medicinally important plant. Genome-based phylogenetic and taxonomic investigation revealed that the pathovar belongs to Xanthomonas euvesicatoria and not X. axonopodis as reported earlier. Interestingly, it is a novel host and novel geographic origin for a X. euvesicatoria pathovar. A core-genome-based phylogenetic analysis resolved the pathovar complex of this species on the basis of their hosts. Interestingly, this pathovar harbors a unique 35-kb plasmid encoding type III effectors and toxin-antitoxin gene that is absent in other X. euvesicatoria pathovars and infects tomato, pepper, rose, onion, philodendron, alfalfa, and citrus plants. The pathovar contains two TAL (transcription activator-like) genes, one on plasmid and another on genomic region with an additional pseudo TAL gene flanked by IS elements in the plasmid. Further, Xcom has acquired a novel set of lipopolysaccharide biosynthesis genes after its divergence from the closely related pathovar that infects rose and supports the role of horizontal gene transfer in hypervariation at this locus in the species. Complete genome sequence of this variant pathovar has provided novel insights into evolution of an emerging pathovar in Xanthomonas and will be valuable resource in pathogenomics of X. euvesicatoria.}, }
@article {pmid30345180, year = {2018}, author = {Kurenbach, B and Hill, AM and Godsoe, W and van Hamelsveld, S and Heinemann, JA}, title = {Agrichemicals and antibiotics in combination increase antibiotic resistance evolution.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e5801}, pmid = {30345180}, issn = {2167-8359}, abstract = {Antibiotic resistance in our pathogens is medicine's climate change: caused by human activity, and resulting in more extreme outcomes. Resistance emerges in microbial populations when antibiotics act on phenotypic variance within the population. This can arise from either genotypic diversity (resulting from a mutation or horizontal gene transfer), or from differences in gene expression due to environmental variation, referred to as adaptive resistance. Adaptive changes can increase fitness allowing bacteria to survive at higher concentrations of antibiotics. They can also decrease fitness, potentially leading to selection for antibiotic resistance at lower concentrations. There are opportunities for other environmental stressors to promote antibiotic resistance in ways that are hard to predict using conventional assays. Exploiting our previous observation that commonly used herbicides can increase or decrease the minimum inhibitory concentration (MIC) of different antibiotics, we provide the first comprehensive test of the hypothesis that the rate of antibiotic resistance evolution under specified conditions can increase, regardless of whether a herbicide increases or decreases the antibiotic MIC. Short term evolution experiments were used for various herbicide and antibiotic combinations. We found conditions where acquired resistance arises more frequently regardless of whether the exogenous non-antibiotic agent increased or decreased antibiotic effectiveness. This is attributed to the effect of the herbicide on either MIC or the minimum selective concentration (MSC) of a paired antibiotic. The MSC is the lowest concentration of antibiotic at which the fitness of individuals varies because of the antibiotic, and is lower than MIC. Our results suggest that additional environmental factors influencing competition between bacteria could enhance the ability of antibiotics to select antibiotic resistance. Our work demonstrates that bacteria may acquire antibiotic resistance in the environment at rates substantially faster than predicted from laboratory conditions.}, }
@article {pmid30343487, year = {2019}, author = {Graf, FE and Palm, M and Warringer, J and Farewell, A}, title = {Inhibiting conjugation as a tool in the fight against antibiotic resistance.}, journal = {Drug development research}, volume = {80}, number = {1}, pages = {19-23}, doi = {10.1002/ddr.21457}, pmid = {30343487}, issn = {1098-2299}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Conjugation, Genetic/drug effects/*physiology ; Drug Resistance, Microbial/drug effects/*physiology ; Humans ; Plasmids/genetics/metabolism ; }, abstract = {Antibiotic resistance, especially in gram-negative bacteria, is spreading globally and rapidly. Development of new antibiotics lags behind; therefore, novel approaches to the problem of antibiotic resistance are sorely needed and this commentary highlights one relatively unexplored target for drug development: conjugation. Conjugation is a common mechanism of horizontal gene transfer in bacteria that is instrumental in the spread of antibiotic resistance among bacteria. Most resistance genes are found on mobile genetic elements and primarily spread by conjugation. Furthermore, conjugative elements can act as a reservoir to maintain antibiotic resistance in the bacterial population even in the absence of antibiotic selection. Thus, conjugation can spread antibiotic resistance quickly between bacteria of the microbiome and pathogens when selective pressure (antibiotics) is introduced. Potential drug targets include the plasmid-encoded conjugation system and the host-encoded proteins important for conjugation. Ideally, a conjugation inhibitor will be used alongside antibiotics to prevent the spread of resistance to or within pathogens while not acting as a growth inhibitor itself. Inhibiting conjugation will be an important addition to our arsenal of strategies to combat the antibiotic resistance crisis, allowing us to extend the usefulness of antibiotics.}, }
@article {pmid30342621, year = {2018}, author = {Kusch, S and Frantzeskakis, L and Thieron, H and Panstruga, R}, title = {Small RNAs from cereal powdery mildew pathogens may target host plant genes.}, journal = {Fungal biology}, volume = {122}, number = {11}, pages = {1050-1063}, doi = {10.1016/j.funbio.2018.08.008}, pmid = {30342621}, issn = {1878-6146}, mesh = {Ascomycota/genetics/*metabolism ; DNA Transposable Elements ; Gene Transfer, Horizontal ; Hordeum/genetics/*microbiology ; Host-Pathogen Interactions ; Phylogeny ; Plant Diseases/*microbiology ; RNA, Fungal/genetics/*metabolism ; RNA, Small Untranslated/genetics/*metabolism ; Triticum/genetics/*microbiology ; }, abstract = {Small RNAs (sRNAs) play a key role in eukaryotic gene regulation, for example by gene silencing via RNA interference (RNAi). The biogenesis of sRNAs depends on proteins that are generally conserved in all eukaryotic lineages, yet some species that lack part or all the components of the mechanism exist. Here we explored the presence of the RNAi machinery and its expression as well as the occurrence of sRNA candidates and their putative endogenous as well as host targets in phytopathogenic powdery mildew fungi. We focused on the species Blumeria graminis, which occurs in various specialized forms (formae speciales) that each have a strictly limited host range. B. graminis f. sp. hordei and B. graminis f. sp. tritici, colonizing barley and wheat, respectively, have genomes that are characterized by extensive gene loss. Nonetheless, we find that the RNAi machinery appears to be largely complete and expressed during infection. sRNA sequencing data enabled the identification of putative sRNAs in both pathogens. While a considerable part of the sRNA candidates have predicted target sites in endogenous genes and transposable elements, a small proportion appears to have targets in planta, suggesting potential cross-kingdom RNA transfer between powdery mildew fungi and their respective plant hosts.}, }
@article {pmid30341165, year = {2018}, author = {Dorival, J and Ruppert, S and Gunnoo, M and Orłowski, A and Chapelais-Baron, M and Dabin, J and Labourel, A and Thompson, D and Michel, G and Czjzek, M and Genicot, S}, title = {The laterally acquired GH5 ZgEngAGH5_4 from the marine bacterium Zobellia galactanivorans is dedicated to hemicellulose hydrolysis.}, journal = {The Biochemical journal}, volume = {475}, number = {22}, pages = {3609-3628}, doi = {10.1042/BCJ20180486}, pmid = {30341165}, issn = {1470-8728}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/genetics/*metabolism ; Flavobacteriaceae/*enzymology/genetics ; Gene Transfer, Horizontal ; Glycoside Hydrolases/classification/genetics/*metabolism ; Hydrolysis ; Models, Molecular ; Molecular Dynamics Simulation ; Mutation ; Phylogeny ; Polysaccharides/*metabolism ; Protein Conformation ; Seawater/microbiology ; Sequence Homology, Amino Acid ; Substrate Specificity ; }, abstract = {Cell walls of marine macroalgae are composed of diverse polysaccharides that provide abundant carbon sources for marine heterotrophic bacteria. Among them, Zobellia galactanivorans is considered as a model for studying algae-bacteria interactions. The degradation of typical algal polysaccharides, such as agars or alginate, has been intensively studied in this model bacterium, but the catabolism of plant-like polysaccharides is essentially uncharacterized. Here, we identify a polysaccharide utilization locus in the genome of Z. galactanivorans, induced by laminarin (β-1,3-glucans), and containing a putative GH5 subfamily 4 (GH5_4) enzyme, currently annotated as a endoglucanase (ZgEngAGH5_4). A phylogenetic analysis indicates that ZgEngAGH5_4 was laterally acquired from an ancestral Actinobacteria We performed the biochemical and structural characterization of ZgEngAGH5_4 and demonstrated that this GH5 is, in fact, an endo-β-glucanase, most active on mixed-linked glucan (MLG). Although ZgEngAGH5_4 and GH16 lichenases both hydrolyze MLG, these two types of enzymes release different series of oligosaccharides. Structural analyses of ZgEngAGH5_4 reveal that all the amino acid residues involved in the catalytic triad and in the negative glucose-binding subsites are conserved, when compared with the closest relative, the cellulase EngD from Clostridium cellulovorans, and some other GH5s. In contrast, the positive glucose-binding subsites of ZgEngAGH5_4 are different and this could explain the preference for MLG, with respect to cellulose or laminarin. Molecular dynamics computer simulations using different hexaoses reveal that the specificity for MLG occurs through the +1 and +2 subsites of the binding pocket that display the most important differences when compared with the structures of other GH5_4 enzymes.}, }
@article {pmid30337917, year = {2018}, author = {Hasegawa, H and Suzuki, E and Maeda, S}, title = {Horizontal Plasmid Transfer by Transformation in Escherichia coli: Environmental Factors and Possible Mechanisms.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2365}, pmid = {30337917}, issn = {1664-302X}, abstract = {Transformation is one mode of horizontal gene transfer (HGT) in bacteria, wherein extracellular naked DNA is taken up by cells that have developed genetic competence. Sensitivity to DNase, which degrades naked DNA, is the key to distinguishing transformation from the DNase-resistant HGT mechanisms. In general, Escherichia coli is not believed to be naturally transformable; it develops high competence only under artificial conditions, including exposure to high Ca[2+] concentrations. However, E. coli can reportedly express modest competence under certain conditions that are feasible in natural environments outside laboratory. In addition, recent data suggest that environmental factors influence multiple routes of transformation. In this mini review, we (1) summarize our studies on transformation-based HGT using E. coli experimental systems and (2) discuss the possible occurrence of transformation via multiple mechanisms in the environment and its possible impact on the spread of antibiotic resistance genes.}, }
@article {pmid30326830, year = {2018}, author = {Matteoli, FP and Passarelli-Araujo, H and Reis, RJA and da Rocha, LO and de Souza, EM and Aravind, L and Olivares, FL and Venancio, TM}, title = {Genome sequencing and assessment of plant growth-promoting properties of a Serratia marcescens strain isolated from vermicompost.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {750}, pmid = {30326830}, issn = {1471-2164}, support = {E-26/111.827/2013//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; 449904/2014-8//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; PhD fellowship//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; }, mesh = {Biofilms ; Biological Transport/genetics ; Biomass ; *Composting ; Fusarium/growth &amp; development ; Gene Transfer, Horizontal ; Genome, Bacterial/*genetics ; Manure/microbiology ; Pest Control, Biological ; Phenols/metabolism ; Phosphorus/chemistry/metabolism ; Serratia marcescens/*genetics/isolation &amp; purification/metabolism/*physiology ; Solubility ; Spermidine/biosynthesis ; Zea mays/*growth &amp; development/*microbiology ; Zinc/chemistry/metabolism ; }, abstract = {BACKGROUND: Plant-bacteria associations have been extensively studied for their potential in increasing crop productivity in a sustainable manner. Serratia marcescens is a species of Enterobacteriaceae found in a wide range of environments, including soil.<br><br>RESULTS: Here we describe the genome sequencing and assessment of plant growth-promoting abilities of S. marcescens UENF-22GI, a strain isolated from mature cattle manure vermicompost. In vitro, S. marcescens UENF-22GI is able to solubilize P and Zn, to produce indole compounds (likely IAA), to colonize hyphae and counter the growth of two phytopathogenic fungi. Inoculation of maize with this strain remarkably increased seedling growth and biomass under greenhouse conditions. The S. marcescens UENF-22GI genome has 5&#xa0;Mb, assembled in 17 scaffolds comprising 4662 genes (4528 are protein-coding). No plasmids were identified. S. marcescens UENF-22GI is phylogenetically placed within a clade comprised almost exclusively of non-clinical strains. We identified genes and operons that are likely responsible for the interesting plant-growth promoting features that were experimentally described. The S. marcescens UENF-22GI genome harbors a horizontally-transferred genomic island involved in antibiotic production, antibiotic resistance, and anti-phage defense via a novel ADP-ribosyltransferase-like protein and possible modification of DNA by a deazapurine base, which likely contributes to its competitiveness against other bacteria.<br><br>CONCLUSIONS: Collectively, our results suggest that S. marcescens UENF-22GI is a strong candidate to be used in the enrichment of substrates for plant growth promotion or as part of bioinoculants for agriculture.}, }
@article {pmid30326137, year = {2018}, author = {Salisbury, AM and Woo, K and Sarkar, S and Schultz, G and Malone, M and Mayer, DO and Percival, SL}, title = {Tolerance of Biofilms to Antimicrobials and Significance to Antibiotic Resistance in Wounds.}, journal = {Surgical technology international}, volume = {33}, number = {}, pages = {59-66}, pmid = {30326137}, issn = {1090-3941}, mesh = {Anti-Infective Agents/*pharmacology ; Biofilms/*drug effects ; *Drug Resistance, Bacterial ; Humans ; Wound Healing/*drug effects ; Wounds and Injuries/microbiology ; }, abstract = {A biofilm is a community of microorganisms that adhere to each other and to surfaces and secrete extracellular polymeric substances (EPS) encasing themselves in a matrix. Biofilms are a major healthcare concern, as they can form on medical devices leading to infection. Additionally, there is growing evidence to show their ability to form in chronic wounds, which leads to delayed wound healing and inflammation. Due to a number of reasons, such as formation of the EPS resulting in sub-inhibitory concentrations of antimicrobials reaching the bacterial cells, slow growth rate of bacterial cells rendering some antibiotics ineffective, and the presence of persister cells, biofilms show increased tolerance to many antimicrobials and antibiotics. Additionally, studies have started to emerge showing a link between resistance to antimicrobials and antibiotics. Cross-resistance can be attributed to a number of factors, for example, increased expression of multidrug efflux pumps that efflux a wide range of substrates and horizontal gene transfer of genetic material encoding multiple resistance genes between different species within the polymicrobial biofilm. Antimicrobial resistance is an increasing threat caused by multiple factors including cross-resistance, and it is a global health concern. This review focuses on current research on antimicrobial and antibiotic resistance and cross-resistance found between antimicrobials and antibiotics commonly used in woundcare to evaluate the significance of this acquired antibiotic resistance. Furthermore, the review discusses the significance of antimicrobial tolerance and the role biofilms play in enhancing antibiotic resistance.}, }
@article {pmid30323263, year = {2019}, author = {Rinke, C and Rubino, F and Messer, LF and Youssef, N and Parks, DH and Chuvochina, M and Brown, M and Jeffries, T and Tyson, GW and Seymour, JR and Hugenholtz, P}, title = {A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.).}, journal = {The ISME journal}, volume = {13}, number = {3}, pages = {663-675}, pmid = {30323263}, issn = {1751-7370}, mesh = {Adaptation, Physiological ; Archaea/*genetics/isolation &amp; purification ; Biological Evolution ; Ecology ; *Gene Transfer, Horizontal ; Genome, Archaeal/*genetics ; *Metagenome ; Oceans and Seas ; Phylogeny ; Plankton/*genetics/isolation &amp; purification ; Rhodopsins, Microbial/*genetics ; Seawater ; }, abstract = {Marine Group II (MGII) archaea represent the most abundant planktonic archaeal group in ocean surface waters, but our understanding of the group has been limited by a lack of cultured representatives and few sequenced genomes. Here, we conducted a comparative phylogenomic analysis of 270 recently available MGII metagenome-assembled genomes (MAGs) to investigate their evolution and ecology. Based on a rank-normalised genome phylogeny, we propose that MGII is an order-level lineage for which we propose the name Candidatus Poseidoniales (after Gr. n. Poseidon, God of the sea), comprising the families Candidatus Poseidonaceae fam. nov. (formerly subgroup MGIIa) and Candidatus Thalassarchaeaceae fam. nov. (formerly subgroup MGIIb). Within these families, 21 genera could be resolved, many of which had distinct biogeographic ranges and inferred nutrient preferences. Phylogenetic analyses of key metabolic functions suggest that the ancestor of Ca. Poseidoniales was a surface water-dwelling photoheterotroph that evolved to occupy multiple related ecological niches based primarily on spectral tuning of proteorhodopsin genes. Interestingly, this adaptation appears to involve an overwrite mechanism whereby an existing single copy of the proteorhodopsin gene is replaced by a horizontally transferred copy, which in many instances should allow an abrupt change in light absorption capacity. Phototrophy was lost entirely from five Ca. Poseidoniales genera coinciding with their adaptation to deeper aphotic waters. We also report the first instances of nitrate reductase in two genera acquired via horizontal gene transfer (HGT), which was a potential adaptation to oxygen limitation. Additional metabolic traits differentiating families and genera include flagellar-based adhesion, transporters, and sugar, amino acid, and peptide degradation. Our results suggest that HGT has shaped the evolution of Ca. Poseidoniales to occupy a variety of ecological niches and to become the most successful archaeal lineage in ocean surface waters.}, }
@article {pmid30323231, year = {2018}, author = {Cenci, U and Qiu, H and Pillonel, T and Cardol, P and Remacle, C and Colleoni, C and Kadouche, D and Chabi, M and Greub, G and Bhattacharya, D and Ball, SG}, title = {Host-pathogen biotic interactions shaped vitamin K metabolism in Archaeplastida.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {15243}, pmid = {30323231}, issn = {2045-2322}, mesh = {Archaea/genetics/metabolism ; Cyanobacteria/classification/*genetics/*metabolism ; Eukaryotic Cells/metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Plastid ; Host-Pathogen Interactions/*genetics ; Metabolic Networks and Pathways/genetics ; Phylogeny ; Plastids/*genetics ; Rhodophyta/genetics/metabolism ; Symbiosis/physiology ; Vitamin K/*metabolism ; }, abstract = {Menaquinone (vitamin K2) shuttles electrons between membrane-bound respiratory complexes under microaerophilic conditions. In photosynthetic eukaryotes and cyanobacteria, phylloquinone (vitamin K1) participates in photosystem I function. Here we elucidate the evolutionary history of vitamin K metabolism in algae and plants. We show that Chlamydiales intracellular pathogens made major genetic contributions to the synthesis of the naphthoyl ring core and the isoprenoid side-chain of these quinones. Production of the core in extremophilic red algae is under control of a menaquinone (Men) gene cluster consisting of 7 genes that putatively originated via lateral gene transfer (LGT) from a chlamydial donor to the plastid genome. In other green and red algae, functionally related nuclear genes also originated via LGT from a non-cyanobacterial, albeit unidentified source. In addition, we show that 3-4 of the 9 required steps for synthesis of the isoprenoid side chains are under control of genes of chlamydial origin. These results are discussed in the light of the hypoxic response experienced by the cyanobacterial endosymbiont when it gained access to the eukaryotic cytosol.}, }
@article {pmid30322533, year = {2018}, author = {Tong, H and Liu, J and Yao, X and Jia, H and Wei, J and Shao, D and Liu, K and Qiu, Y and Ma, Z and Li, B}, title = {High carriage rate of mcr-1 and antimicrobial resistance profiles of mcr-1-positive Escherichia coli isolates in swine faecal samples collected from eighteen provinces in China.}, journal = {Veterinary microbiology}, volume = {225}, number = {}, pages = {53-57}, doi = {10.1016/j.vetmic.2018.09.018}, pmid = {30322533}, issn = {1873-2542}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Carbapenems/pharmacology ; China/epidemiology ; *Drug Resistance, Multiple, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/*drug effects/*genetics/isolation &amp; purification ; Escherichia coli Infections/epidemiology/microbiology/*veterinary ; Escherichia coli Proteins/*genetics/isolation &amp; purification ; Farms ; Feces/*microbiology ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Plasmids/genetics ; Polymerase Chain Reaction ; Swine/microbiology ; Swine Diseases/epidemiology/*virology ; Tigecycline/pharmacology ; }, abstract = {The mcr-1 gene is a plasmid-borne and globally distributed colistin-resistance gene, which threatens the last-line role of colistin in treatment of infections caused by multi-drug resistant(MDR) Gram-negative bacteria in humans. The aim of this study was to obtain a comprehensive understanding of mcr-1 prevalence in the pig industry in China. A total of 600 faecal samples were collected from 60 swine farms in 18 provinces of China. Faecal DNA was extracted and subjected to PCR screening to detect the presence of mcr-1. Positive samples were randomly selected for isolation of colistin-resistant bacteria. A total of 152 mcr-1-positive isolates collected from different provinces were characterized by antimicrobial susceptibility testing and pulsed-field gel electrophoresis (PFGE) typing. Extremely high rate of faecal carriage of mcr-1(457/600, 76.2%) was observed, with positive rates ranging from 45.0%-100% among the provinces. All colistin-resistant colonies were identified as Escherichia coli and mcr-1-positive. The 152 representative mcr-1-positive E. coli isolates showed high level resistance to ampicillin (79.60%), tetracycline(94.74%), doxycycline(93.42%), florfenicol(78.29%), enrofloxacin(44.08%), and ciprofloxacin(38.82%) and low level resistance to ceftiofur(26.32%), cefoxitin(0.66%), and amikacin(0.66%). No resistant isolates were detected for gentamicin, meropenem, and tigecycline. The mcr-1-positive E. coli strains exhibited highly diverse PFGE patterns, which suggested that horizontal transfer through plasmids or other mobile elements was the main mechanism for the wide dissemination of mcr-1 in pig farms. Similar studies are warranted to continuously monitor colistin resistance and mcr-1 prevalence in food-animal production.}, }
@article {pmid30321713, year = {2019}, author = {Xin, R and Zhang, K and Wu, N and Zhang, Y and Niu, Z}, title = {The pollution level of the blaOXA-58 carbapenemase gene in coastal water and its host bacteria characteristics.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {244}, number = {}, pages = {66-71}, doi = {10.1016/j.envpol.2018.10.023}, pmid = {30321713}, issn = {1873-6424}, mesh = {Bacteria/*genetics/growth &amp; development/isolation &amp; purification ; Bacterial Proteins/*genetics ; Bays ; *Carbapenems/pharmacology ; Drug Resistance, Microbial/*genetics ; *Environmental Monitoring ; *Estuaries ; Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; Polymerase Chain Reaction ; Sequence Homology, Nucleic Acid ; Water Microbiology ; *Water Pollution ; beta-Lactamases/*genetics ; }, abstract = {This paper investigated 10 carbapenemase genes and selected the hosts of these genes in the estuary of Bohai Bay. The results showed that the OXA-58 producer accounted for a large percentage of carbapenem resistant bacteria in the sampling points, whereas the VIM, KPC, NDM, IMP, GES, OXA-23, OXA-24, OXA-48 and OXA-51 producers were not detected in the study. In addition, 9 bacterial genera with 100% identical blaOXA-58 sequences, including Pseudomonas, Rheinheimera, Stenotrophomonas, Shewanella, Raoultella, Vibrio, Pseudoalteromonas, Algoriphagus, Bowmanella and Thalassospira, were isolated from seawater. It is suggested that the host of blaOXA-58 gene were varied and many kinds of them could survive in the seawater. Moreover, we preformed the quantitative RT-PCR and the result shown the abundance of blaOXA-58 fluctuated between 2.8×10[-6] copies/16S and 2.46×10[-4] copies/16S, which was of the same order of magnitude as some common antibiotic resistance genes in environment. Furthermore, the variation trend of blaOXA-58 gene suggested that pollution discharge and horizontal gene transfer could contribute to the increase of the gene in coastal area.}, }
@article {pmid30319685, year = {2018}, author = {Jiang, S and Lin, T and Xie, Q and Wang, L}, title = {Network Analysis of RAD51 Proteins in Metazoa and the Evolutionary Relationships With Their Archaeal Homologs.}, journal = {Frontiers in genetics}, volume = {9}, number = {}, pages = {383}, pmid = {30319685}, issn = {1664-8021}, abstract = {The RAD51 (DNA repair protein RAD51) recombinases are essential for homologous recombination, DNA repair, and genome stability. Overexpression of RAD51 proteins has been observed in many cancer cells, such as thyroid carcinoma, breast cancer, pancreatic cancer, and others. In Metazoa, there are multiple members of RAD51 (RAD51, RAD51B, RAD51C, RAD51D, DMC1) (DNA meiotic recombinase 1), XRCC2 (X-ray repair cross-complementing 2), and XRCC3. In this study, we used a protein sequence similarity network (SSN) to analyze the evolutionary relationship within this protein family. The SSN based on the RAD51 proteins from Metazoa indicated that there are several proteins that have yet to be functionally defined. The SSN based on the distribution of the proteins supports the hypothesis that horizontal gene transfer plays an important role in the evolution of RAD51 proteins. Multiple sequence alignments with structural information revealed that the amino acid residues for ATP and Mg[2+] are highly conserved. The seven RAD51 proteins in humans are under different selective pressure: RAD51 and DMC1 are under stringent negative selection, while other proteins are subject to relatively relaxed negative selection. Furthermore, the expression levels of the seven genes in different tissues showed that the genes in the same cluster in the phylogenetic tree showed similar expression profiles. Finally, the SSN based on the RAD51 proteins from both eukaryotes and prokaryotes suggested that the eukaryotic RAD51 recombinases share a common ancestor with the archaeal homologs, but XRCC2 may have a different origin. These findings expand the understanding of the evolution and diversity of RAD51 recombinases in Metazoa.}, }
@article {pmid30319562, year = {2018}, author = {Sand, KK and Jelavić, S}, title = {Mineral Facilitated Horizontal Gene Transfer: A New Principle for Evolution of Life?.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2217}, pmid = {30319562}, issn = {1664-302X}, abstract = {A number of studies have highlighted that adsorption to minerals increases DNA longevity in the environment. Such DNA-mineral associations can essentially serve as pools of genes that can be stored across time. Importantly, this DNA is available for incorporation into alien organisms through the process of horizontal gene transfer (HGT). Here we argue that minerals hold an unrecognized potential for successfully transferring genetic material across environments and timescales to distant organisms and hypothesize that this process has significantly influenced the evolution of life. Our hypothesis is illustrated in the context of the evolution of early microbial life and the oxygenation of the Earth's atmosphere and offers an explanation for observed outbursts of evolutionary events caused by HGT.}, }
@article {pmid30317145, year = {2019}, author = {Bron, PA and Marcelli, B and Mulder, J and van der Els, S and Morawska, LP and Kuipers, OP and Kok, J and Kleerebezem, M}, title = {Renaissance of traditional DNA transfer strategies for improvement of industrial lactic acid bacteria.}, journal = {Current opinion in biotechnology}, volume = {56}, number = {}, pages = {61-68}, doi = {10.1016/j.copbio.2018.09.004}, pmid = {30317145}, issn = {1879-0429}, mesh = {CRISPR-Cas Systems ; Clustered Regularly Interspaced Short Palindromic Repeats ; Food Microbiology ; Gene Editing/*methods ; Gene Transfer, Horizontal ; Lactobacillales/*genetics ; Transduction, Genetic ; }, abstract = {The ever-expanding genomic insight in natural diversity of lactic acid bacteria (LAB) has revived the industrial interest in traditional and natural genetic mobilization methodologies. Here, we review recent advances in horizontal gene transfer processes in LAB, including natural competence, conjugation, and phage transduction. In addition, we envision the possibilities for industrial strain improvement arising from the recent discoveries of molecular exchanges between bacteria through nanotubes and extracellular vesicles, as well as the constantly expanding genome editing possibilities using the CRISPR-Cas technology.}, }
@article {pmid30316087, year = {2019}, author = {Murray, R and Tien, YC and Scott, A and Topp, E}, title = {The impact of municipal sewage sludge stabilization processes on the abundance, field persistence, and transmission of antibiotic resistant bacteria and antibiotic resistance genes to vegetables at harvest.}, journal = {The Science of the total environment}, volume = {651}, number = {Pt 2}, pages = {1680-1687}, doi = {10.1016/j.scitotenv.2018.10.030}, pmid = {30316087}, issn = {1879-1026}, mesh = {Bacteria/*drug effects/genetics ; Crops, Agricultural/growth &amp; development ; Drug Resistance, Microbial/*genetics ; *Environmental Monitoring ; Fertilizers/analysis ; Ontario ; Sewage/*analysis ; *Soil Microbiology ; Soil Pollutants/*analysis ; Waste Disposal, Fluid/*methods ; }, abstract = {Biosolids were obtained from four Ontario municipalities that vary in how the sewage sludge is treated. These included a Class B biosolids that was anaerobically digested, a Class A biosolids that were heat treated and pelletized (Propell), and two Class A biosolids that were stabilized using either the N-Viro (N-Rich) or Lystek (LysteGro) processes. Viable enteric indicator or pathogenic bacteria in the biosolids were enumerated by plate count, gene targets associated with antibiotic resistance or horizontal gene transfer were detected by PCR, and a subset of these gene targets were quantified by qPCR. Following application at commercial rates to field plots, the persistence of enteric bacteria and gene targets in soil was followed during the growing season. Carrots, radishes and lettuce were sown into the amended and unamended control plots, and the diversity and abundance of gene targets they carried at harvest determined. All three Class A biosolids carried fewer and less abundant antibiotic resistance genes than did the Class B biosolids, in particular the very alkaline N-Viro product (N-Rich). Following application, some gene targets (e.g. int1, sul1, strA/B, aadA) that are typically associated with mobile gene cassettes remained detectable throughout the growing season, whereas others (e.g. ermB, ermF, blaOXA20) that are not associated with cassettes became undetectable within three weeks or less. At harvest a larger number of gene targets were detected on the carrots and radishes than in the lettuce. Overall, land application of Class A biosolids will entrain fewer viable bacteria and genes associated with antibiotic resistance into crop ground than will amendment with Class B biosolids.}, }
@article {pmid30315317, year = {2019}, author = {Kunath, BJ and Delogu, F and Naas, AE and Arntzen, M&#xd8; and Eijsink, VGH and Henrissat, B and Hvidsten, TR and Pope, PB}, title = {From proteins to polysaccharides: lifestyle and genetic evolution of Coprothermobacter proteolyticus.}, journal = {The ISME journal}, volume = {13}, number = {3}, pages = {603-617}, pmid = {30315317}, issn = {1751-7370}, mesh = {Bacteria/*genetics/metabolism ; *Bacterial Physiological Phenomena ; Bacterial Proteins/genetics/*metabolism ; Cellulose/metabolism ; *Evolution, Molecular ; Hydrolysis ; Lignin/metabolism ; *Metagenome ; Metagenomics ; Polysaccharides/*metabolism ; }, abstract = {Microbial communities that degrade lignocellulosic biomass are typified by high levels of species- and strain-level complexity, as well as synergistic interactions between both cellulolytic and non-cellulolytic microorganisms. Coprothermobacter proteolyticus frequently dominates thermophilic, lignocellulose-degrading communities with wide geographical distribution, which is in contrast to reports that it ferments proteinaceous substrates and is incapable of polysaccharide hydrolysis. Here we deconvolute a highly efficient cellulose-degrading consortium (SEM1b) that is co-dominated by Clostridium (Ruminiclostridium) thermocellum and multiple heterogenic strains affiliated to C. proteolyticus. Metagenomic analysis of SEM1b recovered metagenome-assembled genomes (MAGs) for each constituent population, whereas in parallel two novel strains of C. proteolyticus were successfully isolated and sequenced. Annotation of all C. proteolyticus genotypes (two strains and one MAG) revealed their genetic acquisition of carbohydrate-active enzymes (CAZymes), presumably derived from horizontal gene transfer (HGT) events involving polysaccharide-degrading Firmicutes or Thermotogae-affiliated populations that are historically co-located. HGT material included a saccharolytic operon, from which a CAZyme was biochemically characterized and demonstrated hydrolysis of multiple hemicellulose polysaccharides. Finally, temporal genome-resolved metatranscriptomic analysis of SEM1b revealed expression of C. proteolyticus CAZymes at different SEM1b life stages as well as co-expression of CAZymes from multiple SEM1b populations, inferring deeper microbial interactions that are dedicated toward community degradation of cellulose and hemicellulose. We show that C. proteolyticus, a ubiquitous population, consists of closely related strains that have adapted via HGT to presumably degrade both oligo- and longer polysaccharides present in decaying plants and microbial cell walls, thus explaining its dominance in thermophilic anaerobic digesters on a global scale.}, }
@article {pmid30315316, year = {2019}, author = {Ahlgren, NA and Fuchsman, CA and Rocap, G and Fuhrman, JA}, title = {Discovery of several novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode amoC nitrification genes.}, journal = {The ISME journal}, volume = {13}, number = {3}, pages = {618-631}, pmid = {30315316}, issn = {1751-7370}, support = {R01 GM120624/GM/NIGMS NIH HHS/United States ; }, mesh = {Ammonia/metabolism ; Archaea/*virology ; Carbon Cycle ; Gene Transfer, Horizontal ; Marine Biology ; *Metagenome ; Metagenomics ; Nitrification ; Nitrogen Cycle ; Oceans and Seas ; Oxidoreductases/*genetics ; Phylogeny ; Viral Proteins/genetics ; Viruses/enzymology/*genetics/isolation &amp; purification ; }, abstract = {Much of the diversity of prokaryotic viruses has yet to be described. In particular, there are no viral isolates that infect abundant, globally significant marine archaea including the phylum Thaumarchaeota. This phylum oxidizes ammonia, fixes inorganic carbon, and thus contributes to globally significant nitrogen and carbon cycles in the oceans. Metagenomics provides an alternative to culture-dependent means for identifying and characterizing viral diversity. Some viruses carry auxiliary metabolic genes (AMGs) that are acquired via horizontal gene transfer from their host(s), allowing inference of what host a virus infects. Here we present the discovery of 15 new genomically and ecologically distinct Thaumarchaeota virus populations, identified as contigs that encode viral capsid and thaumarchaeal ammonia monooxygenase genes (amoC). These viruses exhibit depth and latitude partitioning and are distributed globally in various marine habitats including pelagic waters, estuarine habitats, and hydrothermal plume water and sediments. We found evidence of viral amoC expression and that viral amoC AMGs sometimes comprise up to half of total amoC DNA copies in cellular fraction metagenomes, highlighting the potential impact of these viruses on N cycling in the oceans. Phylogenetics suggest they are potentially tailed viruses and share a common ancestor with related marine Euryarchaeota viruses. This work significantly expands our view of viruses of globally important marine Thaumarchaeota.}, }
@article {pmid30312149, year = {2018}, author = {David, S and Mentasti, M and Lai, S and Vaghji, L and Ready, D and Chalker, VJ and Parkhill, J}, title = {Spatial structuring of a Legionella pneumophila population within the water system of a large occupational building.}, journal = {Microbial genomics}, volume = {4}, number = {10}, pages = {}, pmid = {30312149}, issn = {2057-5858}, support = {//Wellcome Trust/United Kingdom ; 098051//Wellcome Trust/United Kingdom ; }, mesh = {*Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomics ; Humans ; Legionella pneumophila/*genetics/isolation &amp; purification/pathogenicity ; Legionnaires' Disease/genetics/microbiology/transmission ; *Phylogeny ; Plasmids/*genetics ; *Water Microbiology ; }, abstract = {The diversity of Legionella pneumophila populations within single water systems is not well understood, particularly in those unassociated with cases of Legionnaires' disease. Here, we performed genomic analysis of 235 L. pneumophila isolates obtained from 28 water samples in 13 locations within a large occupational building. Despite regular treatment, the water system of this building is thought to have been colonized by L. pneumophila for at least 30 years without evidence of association with Legionnaires' disease cases. All isolates belonged to one of three sequence types (STs), ST27 (n=81), ST68 (n=122) and ST87 (n=32), all three of which have been recovered from Legionnaires' disease patients previously. Pairwise single nucleotide polymorphism differences amongst isolates of the same ST were low, ranging from 0 to 19 in ST27, from 0 to 30 in ST68 and from 0 to 7 in ST87, and no homologous recombination was observed in any lineage. However, there was evidence of horizontal transfer of a plasmid, which was found in all ST87 isolates and only one ST68 isolate. A single ST was found in 10/13 sampled locations, and isolates of each ST were also more similar to those from the same location compared with those from different locations, demonstrating spatial structuring of the population within the water system. These findings provide the first insights into the diversity and genomic evolution of a L. pneumophila population within a complex water system not associated with disease.}, }
@article {pmid30310966, year = {2018}, author = {Suzuki, H}, title = {Peculiarities and biotechnological potential of environmental adaptation by Geobacillus species.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {24}, pages = {10425-10437}, doi = {10.1007/s00253-018-9422-6}, pmid = {30310966}, issn = {1432-0614}, support = {25450105//Japan Society for the Promotion of Science/ ; 17K06925//Japan Society for the Promotion of Science/ ; }, mesh = {Adaptation, Biological/*genetics ; Biotechnology/*methods ; Directed Molecular Evolution/*methods ; Enzyme Stability ; Genetic Engineering ; Genetic Variation ; Geobacillus/*physiology ; Phylogeny ; }, abstract = {The genus Geobacillus comprises thermophilic bacilli capable of endospore formation. The members of this genus provide thermostable proteins and can be used in whole cell applications at elevated temperatures; therefore, these organisms are of biotechnological importance. While these applications have been described in previous reviews, the present paper highlights the environmental adaptations and genome diversifications of Geobacillus spp. and their applications in evolutionary-protein engineering. Despite their obligate thermophilic properties, Geobacillus spp. are widely distributed in nature. Because several isolates demonstrate remarkable properties for cell reproduction in their respective niches, they seem to exist not only as endospores but also as vegetative cells in diverse environments. This suggests their excellence in environmental adaptation via genome diversification; in fact, evidence suggests that Geobacillus spp. were derived from Bacillus spp. while diversifying their genomes via horizontal gene transfer. Moreover, when subjected to an environmental stressor, Geobacillus spp. diversify their genomes using inductive mutations and transposable elements to produce derivative cells that are adaptive to the stressor. Notably, inductive mutations in Geobacillus spp. occur more rapidly and frequently than the stress-induced mutagenesis observed in other microorganisms. Owing to this, Geobacillus spp. can efficiently generate mutant genes coding for thermostable enzyme variants from the thermolabile enzyme genes under appropriate selection pressures. This phenomenon provides a new approach to generate thermostable enzymes, termed as thermoadaptation-directed enzyme evolution, thereby expanding the biotechnological potentials of Geobacillus spp. In this review, we have discussed this approach using successful examples and major challenges yet to be addressed.}, }
@article {pmid30308860, year = {2019}, author = {Karmakar, R and Bindiya, S and Hariprasad, P}, title = {Convergent evolution in bacteria from multiple origins under antibiotic and heavy metal stress, and endophytic conditions of host plant.}, journal = {The Science of the total environment}, volume = {650}, number = {Pt 1}, pages = {858-867}, doi = {10.1016/j.scitotenv.2018.09.078}, pmid = {30308860}, issn = {1879-1026}, mesh = {Adaptation, Physiological/physiology ; Anti-Bacterial Agents/*toxicity ; Bacteria/*genetics ; *Biological Evolution ; Endophytes ; Integrons ; Metals, Heavy/*toxicity ; Plants/*microbiology ; Soil Pollutants/*toxicity ; }, abstract = {The focus of this work is to study the convergent evolution in bacteria from multiple origins under antibiotic and heavy metal stress, and endophytic conditions of host plant cultivated on the Yamuna river bank. Forty-one endophytic bacteria (EB) were isolated from green leafy vegetables (GLV's) and were found to be resistant to a wide range of antibiotics (AB) and heavy metals (HM) tested. Further, they showed susceptibility to Quinolones group of antibiotics, and the HM, Cadmium, Chromium, and Mercury. Twenty-seven percent of these bacteria endowed with Class I integron. The probability of co-existence of HM resistance with β‑lactams was higher, whereas quinolones group of AB recorded lesser values. These EB owned a wide array of beneficial traits, through which they improved the plant health under HM and salt stress conditions. Bacterial identity revealed the association of both plant beneficial and human pathogenic bacteria as an endophyte with GLV's. Principal component analysis showed a pattern of convergent evolution irrespective of their origin. In conclusion, under the selection pressure of AB and HM, the susceptible EB population may reduce with time and the resistant native/introduced bacteria might survive. The vertical and horizontal gene transfer between introduced and native bacteria is the crucial factor in enhancing their fitness along with the host plant to survive under abiotic stress conditions.}, }
@article {pmid30305318, year = {2018}, author = {Shima, K and Wanker, M and Skilton, RJ and Cutcliffe, LT and Schnee, C and Kohl, TA and Niemann, S and Geijo, J and Klinger, M and Timms, P and Rattei, T and Sachse, K and Clarke, IN and Rupp, J}, title = {The Genetic Transformation of Chlamydia pneumoniae.}, journal = {mSphere}, volume = {3}, number = {5}, pages = {}, pmid = {30305318}, issn = {2379-5042}, mesh = {Animals ; Chlamydia/*genetics ; Chlamydophila pneumoniae/*genetics/isolation &amp; purification ; Chloramphenicol O-Acetyltransferase/genetics ; Gene Transfer, Horizontal ; *Genetic Vectors ; Genome-Wide Association Study ; Green Fluorescent Proteins/genetics ; Humans ; Plasmids/*genetics ; Transformation, Bacterial/*genetics ; }, abstract = {We demonstrate the genetic transformation of Chlamydia pneumoniae using a plasmid shuttle vector system which generates stable transformants. The equine C. pneumoniae N16 isolate harbors the 7.5-kb plasmid pCpnE1. We constructed the plasmid vector pRSGFPCAT-Cpn containing a pCpnE1 backbone, plus the red-shifted green fluorescent protein (RSGFP), as well as the chloramphenicol acetyltransferase (CAT) gene used for the selection of plasmid shuttle vector-bearing C. pneumoniae transformants. Using the pRSGFPCAT-Cpn plasmid construct, expression of RSGFP in koala isolate C. pneumoniae LPCoLN was demonstrated. Furthermore, we discovered that the human cardiovascular isolate C. pneumoniae CV-6 and the human community-acquired pneumonia-associated C. pneumoniae IOL-207 could also be transformed with pRSGFPCAT-Cpn. In previous studies, it was shown that Chlamydia spp. cannot be transformed when the plasmid shuttle vector is constructed from a different plasmid backbone to the homologous species. Accordingly, we confirmed that pRSGFPCAT-Cpn could not cross the species barrier in plasmid-bearing and plasmid-free C. trachomatis, C. muridarum, C. caviae, C. pecorum, and C. abortus However, contrary to our expectation, pRSGFPCAT-Cpn did transform C. felis Furthermore, pRSGFPCAT-Cpn did not recombine with the wild-type plasmid of C. felis Taken together, we provide for the first time an easy-to-handle transformation protocol for C. pneumoniae that results in stable transformants. In addition, the vector can cross the species barrier to C. felis, indicating the potential of horizontal pathogenic gene transfer via a plasmid.IMPORTANCE The absence of tools for the genetic manipulation of C. pneumoniae has hampered research into all aspects of its biology. In this study, we established a novel reproducible method for C. pneumoniae transformation based on a plasmid shuttle vector system. We constructed a C. pneumoniae plasmid backbone shuttle vector, pRSGFPCAT-Cpn. The construct expresses the red-shifted green fluorescent protein (RSGFP) fused to chloramphenicol acetyltransferase in C. pneumoniaeC. pneumoniae transformants stably retained pRSGFPCAT-Cpn and expressed RSGFP in epithelial cells, even in the absence of chloramphenicol. The successful transformation in C. pneumoniae using pRSGFPCAT-Cpn will advance the field of chlamydial genetics and is a promising new approach to investigate gene functions in C. pneumoniae biology. In addition, we demonstrated that pRSGFPCAT-Cpn overcame the plasmid species barrier without the need for recombination with an endogenous plasmid, indicating the potential probability of horizontal chlamydial pathogenic gene transfer by plasmids between chlamydial species.}, }
@article {pmid30304703, year = {2019}, author = {Wang, H and Abassi, S and Ki, JS}, title = {Origin and roles of a novel copper-zinc superoxide dismutase (CuZnSOD) gene from the harmful dinoflagellate Prorocentrum minimum.}, journal = {Gene}, volume = {683}, number = {}, pages = {113-122}, doi = {10.1016/j.gene.2018.10.013}, pmid = {30304703}, issn = {1879-0038}, mesh = {Cell Nucleus/genetics ; Chloroplasts/metabolism ; Cloning, Molecular/*methods ; Dinoflagellida/*enzymology ; Gene Transfer, Horizontal ; Open Reading Frames ; Oxidative Stress ; Phylogeny ; Protozoan Proteins/genetics/metabolism ; Sequence Analysis, DNA/*methods ; Superoxide Dismutase-1/*genetics/metabolism ; }, abstract = {Superoxide dismutase (SOD) acts as the first line of defence against reactive oxygen species (ROS) within cells. In this study, we characterized a novel SOD gene (PmCuZnSOD) from the dinoflagellate Prorocentrum minimum, and examined its structural features, putative origin and gene expression. The SOD cDNA is 895 bp in length, containing dinoflagellate splice-leader (dinoSL) sequence, 714-bp ORF (237 aa), and poly (A) tail. In addition, PmCuZnSOD is coded on the dinoflagellate nuclear genome without introns and in a non-tandem repeat manner; however, the encoded protein is probably localized in chloroplasts. Phylogenetic analysis indicated that it might be acquired from cyanobacteria via horizontal gene transfer (HGT) and then the gene possibly relocated from the chloroplast to the nuclear genome. Excess copper dramatically increased the PmCuZnSOD transcripts and SOD activity in cells, caused by ROS generation and decrease of photosynthetic efficiency in the treated cells. These suggest that CuZnSOD may function to defend against oxidative stress for the survival of the dinoflagellate.}, }
@article {pmid30304394, year = {2018}, author = {Lee, CC and Wang, J}, title = {Rapid Expansion of a Highly Germline-Expressed Mariner Element Acquired by Horizontal Transfer in the Fire Ant Genome.}, journal = {Genome biology and evolution}, volume = {10}, number = {12}, pages = {3262-3278}, pmid = {30304394}, issn = {1759-6653}, mesh = {Animals ; Ants/*genetics/metabolism ; *DNA Transposable Elements ; DNA-Binding Proteins ; Female ; *Gene Transfer, Horizontal ; *Genome, Insect ; Germ Cells/*metabolism ; Male ; Polymorphism, Genetic ; Selection, Genetic ; Silent Mutation ; Transposases ; }, abstract = {Transposable elements (TEs) are present in almost all organisms and affect the host in various ways. TE activity can increase genomic variation and thereby affect host evolution. Currently active TEs are particularly interesting because they are likely generating new genomic diversity. These active TEs have been poorly studied outside of model organisms. In this study, we aimed to identify currently active TEs of a notorious invasive species, the red imported fire ant Solenopsis invicta. Using RNA profiling of male and female germline tissues, we found that the majority of TE-containing transcripts in the fire ant germline belong to the IS630-Tc1-Mariner superfamily. Subsequent genomic characterization of fire ant mariner content, molecular evolution analysis, and population comparisons revealed a highly expressed and highly polymorphic mariner element that is rapidly expanding in the fire ant genome. Additionally, using comparative genomics of multiple insect species we showed that this mariner has undergone several recent horizontal transfer events (<5.1 My). Our results document a rare case of a currently active TE originating from horizontal transfer.}, }
@article {pmid30303480, year = {2019}, author = {Reid, CJ and DeMaere, MZ and Djordjevic, SP}, title = {Australian porcine clonal complex 10 (CC10) Escherichia coli belong to multiple sublineages of a highly diverse global CC10 phylogeny.}, journal = {Microbial genomics}, volume = {5}, number = {3}, pages = {}, pmid = {30303480}, issn = {2057-5858}, mesh = {Animals ; Australia ; Bacterial Typing Techniques ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; Escherichia coli/*classification/*genetics/isolation &amp; purification ; Escherichia coli Infections/microbiology/veterinary ; Escherichia coli Proteins/genetics ; Feces ; Food Microbiology ; Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; Molecular Epidemiology ; *Phylogeny ; Plasmids ; Swine/*microbiology ; Swine Diseases/microbiology ; Virulence/genetics ; Whole Genome Sequencing ; }, abstract = {We recently identified clonal complex 10 (CC10) Escherichia coli as the predominant clonal group in two populations of healthy Australian food-production pigs. CC10 are highly successful, colonizing humans, food-production animals, fresh produce and environmental niches. Furthermore, E. coli within CC10 are frequently drug resistant and increasingly reported as human and animal extra-intestinal pathogens. In order to develop a high-resolution global phylogeny and determine the repertoire of antimicrobial-resistance genes, virulence-associated genes and plasmid types within this clonal group, we downloaded 228 publicly available CC10 short-read genome sequences for comparison with 20 porcine CC10 we have previously described. Core genome single nucleotide polymorphism phylogeny revealed a highly diverse global phylogeny consisting of multiple lineages that did not cluster by geography or source of the isolates. Australian porcine strains belonged to several of these divergent lineages, indicative that CC10 is present in these animals due to multiple colonization events. Differences in resistance gene and plasmid carriage between porcine strains and the global collection highlighted the role of lateral gene transfer in the evolution of CC10 strains. Virulence profiles typical of extra-intestinal pathogenic E. coli were present in both Australian porcine strains and the broader collection. As both the core phylogeny and accessory gene characteristics appeared unrelated to the geography or source of the isolates, it is likely that the global expansion of CC10 is not a recent event and may be associated with faecal carriage in humans.}, }
@article {pmid30301851, year = {2018}, author = {Best, A and Abu Kwaik, Y}, title = {Evolution of the Arsenal of Legionella pneumophila Effectors To Modulate Protist Hosts.}, journal = {mBio}, volume = {9}, number = {5}, pages = {}, pmid = {30301851}, issn = {2150-7511}, support = {R01 AI120244/AI/NIAID NIH HHS/United States ; }, mesh = {Amoebozoa/microbiology ; *Biological Coevolution ; Ciliophora/microbiology ; Cytoplasm/microbiology ; *Genome, Bacterial ; Host-Pathogen Interactions/*genetics ; Humans ; Legionella pneumophila/*genetics/pathogenicity ; Macrophages/microbiology ; }, abstract = {Within the human host, Legionella pneumophila replicates within alveolar macrophages, leading to pneumonia. However, L. pneumophila is an aquatic generalist pathogen that replicates within a wide variety of protist hosts, including amoebozoa, percolozoa, and ciliophora. The intracellular lifestyles of L. pneumophila within the two evolutionarily distant hosts macrophages and protists are remarkably similar. Coevolution with numerous protist hosts has shaped plasticity of the genome of L. pneumophila, which harbors numerous proteins encoded by genes acquired from primitive eukaryotic hosts through interkingdom horizontal gene transfer. The Dot/Icm type IVb translocation system translocates ∼6,000 effectors among Legionella species and >320 effector proteins in L. pneumophila into host cells to modulate a plethora of cellular processes to create proliferative niches. Since many of the effectors have likely evolved to modulate cellular processes of primitive eukaryotic hosts, it is not surprising that most of the effectors do not contribute to intracellular growth within human macrophages. Some of the effectors may modulate highly conserved eukaryotic processes, while others may target protist-specific processes that are absent in mammals. The lack of studies to determine the role of the effectors in adaptation of L. pneumophila to various protists has hampered the progress to determine the function of most of these effectors, which are routinely studied in mouse or human macrophages. Since many protists restrict L. pneumophila, utilization of such hosts can also be instrumental in deciphering the mechanisms of failure of L. pneumophila to overcome restriction of certain protist hosts. Here, we review the interaction of L. pneumophila with its permissive and restrictive protist environmental hosts and outline the accomplishments as well as gaps in our knowledge of L. pneumophila-protist host interaction and L. pneumophila's evolution to become a human pathogen.}, }
@article {pmid30301483, year = {2019}, author = {Zarlenga, DS and Mitreva, M and Thompson, P and Tyagi, R and Tuo, W and Hoberg, EP}, title = {A tale of three kingdoms: members of the Phylum Nematoda independently acquired the detoxifying enzyme cyanase through horizontal gene transfer from plants and bacteria.}, journal = {Parasitology}, volume = {146}, number = {4}, pages = {445-452}, pmid = {30301483}, issn = {1469-8161}, support = {R01 AI081803/AI/NIAID NIH HHS/United States ; R01 GM097435/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics ; *Biological Evolution ; Carbon-Nitrogen Lyases/*analysis ; *Gene Transfer, Horizontal ; Helminth Proteins/*analysis ; Nematoda/*genetics ; Plants/genetics ; }, abstract = {Horizontal gene transfer (HGT) has played an important role in the evolution of nematodes. Among candidate genes, cyanase, which is typically found only in plants, bacteria and fungi, is present in more than 35 members of the Phylum Nematoda, but absent from free-living and clade V organisms. Phylogenetic analyses showed that the cyanases of clade I organisms Trichinella spp., Trichuris spp. and Soboliphyme baturini (Subclass: Dorylaimia) represent a well-supported monophyletic clade with plant cyanases. In contrast, all cyanases found within the Subclass Chromadoria which encompasses filarioids, ascaridoids and strongyloids are homologous to those of bacteria. Western blots exhibited typical multimeric forms of the native molecule in protein extracts of Trichinella spiralis muscle larvae, where immunohistochemical staining localized the protein to the worm hypodermis and underlying muscle. Recombinant Trichinella cyanase was bioactive where gene transcription profiles support functional activity in vivo. Results suggest that: (1) independent HGT in parasitic nematodes originated from different Kingdoms; (2) cyanase acquired an active role in the biology of extant Trichinella; (3) acquisition occurred more than 400 million years ago (MYA), prior to the divergence of the Trichinellida and Dioctophymatida, and (4) early, free-living ancestors of the genus Trichinella had an association with terrestrial plants.}, }
@article {pmid30298054, year = {2018}, author = {Sultan, I and Rahman, S and Jan, AT and Siddiqui, MT and Mondal, AH and Haq, QMR}, title = {Antibiotics, Resistome and Resistance Mechanisms: A Bacterial Perspective.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2066}, pmid = {30298054}, issn = {1664-302X}, abstract = {History of mankind is regarded as struggle against infectious diseases. Rather than observing the withering away of bacterial diseases, antibiotic resistance has emerged as a serious global health concern. Medium of antibiotic resistance in bacteria varies greatly and comprises of target protection, target substitution, antibiotic detoxification and block of intracellular antibiotic accumulation. Further aggravation to prevailing situation arose on observing bacteria gradually becoming resistant to different classes of antibiotics through acquisition of resistance genes from same and different genera of bacteria. Attributing bacteria with feature of better adaptability, dispersal of antibiotic resistance genes to minimize effects of antibiotics by various means including horizontal gene transfer (conjugation, transformation, and transduction), Mobile genetic elements (plasmids, transposons, insertion sequences, integrons, and integrative-conjugative elements) and bacterial toxin-antitoxin system led to speedy bloom of antibiotic resistance amongst bacteria. Proficiency of bacteria to obtain resistance genes generated an unpleasant situation; a grave, but a lot unacknowledged, feature of resistance gene transfer.}, }
@article {pmid30295814, year = {2019}, author = {Marsh, JW and Pacey, MP and Ezeonwuka, C and Ohm, SL and Snyder, D and Cooper, VS and Harrison, LH and Doi, Y and Mustapha, MM}, title = {Clostridioides difficile: a potential source of NpmA in the clinical environment.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {74}, number = {2}, pages = {521-523}, pmid = {30295814}, issn = {1460-2091}, support = {R01 AI127472/AI/NIAID NIH HHS/United States ; }, mesh = {Aminoglycosides/pharmacology ; Animals ; Anti-Bacterial Agents/pharmacology ; Cattle/microbiology ; Clostridioides difficile/drug effects/enzymology/*genetics ; Clostridium Infections/microbiology ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli Proteins/genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; Methyltransferases/*genetics ; Swine/microbiology ; }, }
@article {pmid30291330, year = {2019}, author = {Wang, Y and Lu, J and Mao, L and Li, J and Yuan, Z and Bond, PL and Guo, J}, title = {Antiepileptic drug carbamazepine promotes horizontal transfer of plasmid-borne multi-antibiotic resistance genes within and across bacterial genera.}, journal = {The ISME journal}, volume = {13}, number = {2}, pages = {509-522}, pmid = {30291330}, issn = {1751-7370}, mesh = {Anticonvulsants/pharmacology ; Bacteria/*drug effects/genetics ; Carbamazepine/*pharmacology ; Drug Resistance, Bacterial/*drug effects/*genetics ; Drug Resistance, Microbial/genetics ; Escherichia coli/genetics ; Gene Transfer, Horizontal/*drug effects ; Microbial Sensitivity Tests ; Plasmids ; Proteomics ; }, abstract = {Antibiotic resistance is a severe global threat for public health, causing around 700,000 deaths per year. Horizontal gene transfer (HGT) is one of the most significant pathways to disseminate antibiotic resistance. It is commonly acknowledged that sub-minimum inhibition concentrations of antibiotics are major contributors in promoting antibiotic resistance through HGT. Pharmaceuticals are occurring in our environments at increased levels, yet little is known whether non-antibiotic pharmaceuticals cause or accelerate the dissemination of antibiotic resistance. Here, we report for the first time that the antiepileptic drug, carbamazepine, promotes conjugative transfer of antibiotic resistance genes. It was seen that environmentally relevant concentrations of carbamazepine (e.g., 0.05 mg/L) significantly enhanced the conjugative transfer of multiresistance genes carried by plasmid within and across bacterial genera. The underlying mechanisms of the enhanced HGT were revealed by detecting oxidative stress and cell membrane permeability, in combination with MinION DNA sequencing, genome-wide RNA sequencing, and proteomic analysis. Carbamazepine induced a series of acute responses, including increased levels of reactive oxygen species, the SOS response; increased cell membrane permeability, and pilus generation. Expressional levels of genes related to these processes were significantly upregulated during carbamazepine exposure. Given that HGT occurs widely among different species in various environments, these findings are an early warning for a wide assessment of the roles of non-antibiotic pharmaceuticals in the spread of antibiotic resistance.}, }
@article {pmid30290202, year = {2019}, author = {Chen, S and Liu, H and Liang, W and Hong, L and Zhang, B and Huang, L and Guo, X and Duan, G}, title = {Insertion sequences in the CRISPR-Cas system regulate horizontal antimicrobial resistance gene transfer in Shigella strains.}, journal = {International journal of antimicrobial agents}, volume = {53}, number = {2}, pages = {109-115}, doi = {10.1016/j.ijantimicag.2018.09.020}, pmid = {30290202}, issn = {1872-7913}, mesh = {Anti-Bacterial Agents/pharmacology ; CRISPR-Cas Systems/*genetics ; Chloramphenicol/pharmacology ; Chloramphenicol Resistance/genetics ; DNA Transposable Elements/genetics ; DNA, Intergenic/*genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal/*genetics ; Humans ; Microbial Sensitivity Tests ; Shigella/drug effects/*genetics/isolation &amp; purification ; }, abstract = {Multidrug-resistant (MDR) Shigella strains are an enormous threat to public health. Antimicrobial resistance genes are frequently located on plasmids, phages and integrons, which enter bacterial cells by horizontal gene transfer (HGT). CRISPR-Cas systems are adaptive prokaryotic immune systems in bacteria that confer resistance to foreign genetic material such as phages and other mobile genetic elements. However, this may come at a cost of inhibiting the acquisition of other beneficial genes through HGT. This study investigated how Shigella strains regulate the activity of the CRISPR-Cas system spontaneously when they require an exogenous gene necessary for survival. Insertion sequence (IS) elements were identified in cas genes, such as IS600 in cse2, ISSfl2 in cas6e and IS629 in cse1-cas3. The number of spacers in CRISPR-Cas arrays in strains containing an IS was less than that for strains with no IS. Interestingly, fewer spacers were also found in MDR Shigella isolates. Furthermore, an antimicrobial-resistant strain was constructed by electrotransformation of a resistance plasmid in order to detect changes in the CRISPR-Cas system. It was found that the cse2 gene had a new IS (IS600) in the antimicrobial-resistant strain. Bioinformatics analyses showed that the IS600 insertion hotspot was TGC-GGC in the cse2 gene, and the tertiary structure of the Cse2 protein was different with IS600. IS600 caused a five-order of magnitude decrease in relative expression of the cse2 gene. This study sheds mechanistic light on CRISPR-Cas-mediated HGT of antimicrobial resistance genes in Shigella spp. isolates.}, }
@article {pmid30289455, year = {2019}, author = {Wang, L and Jiang, S and Deng, Z and Dedon, PC and Chen, S}, title = {DNA phosphorothioate modification-a new multi-functional epigenetic system in bacteria.}, journal = {FEMS microbiology reviews}, volume = {43}, number = {2}, pages = {109-122}, pmid = {30289455}, issn = {1574-6976}, support = {P30 ES002109/ES/NIEHS NIH HHS/United States ; }, mesh = {Bacteria/enzymology/*genetics ; Bacterial Proteins/genetics ; DNA, Bacterial/*metabolism ; Epigenesis, Genetic/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial/genetics ; Phosphates/*metabolism ; }, abstract = {Synthetic phosphorothioate (PT) internucleotide linkages, in which a nonbridging oxygen is replaced by a sulphur atom, share similar physical and chemical properties with phosphodiesters but confer enhanced nuclease tolerance on DNA/RNA, making PTs a valuable biochemical and pharmacological tool. Interestingly, PT modification was recently found to occur naturally in bacteria in a sequence-selective and RP configuration-specific manner. This oxygen-sulphur swap is catalysed by the gene products of dndABCDE, which constitute a defence barrier with DndFGH in some bacterial strains that can distinguish and attack non-PT-modified foreign DNA, resembling DNA methylation-based restriction-modification (R-M) systems. Despite their similar defensive mechanisms, PT- and methylation-based R-M systems have evolved to target different consensus contexts in the host cell because when they share the same recognition sequences, the protective function of each can be impeded. The redox and nucleophilic properties of PT sulphur render PT modification a versatile player in the maintenance of cellular redox homeostasis, epigenetic regulation and environmental fitness. The widespread presence of dnd systems is considered a consequence of extensive horizontal gene transfer, whereas the lability of PT during oxidative stress and the susceptibility of PT to PT-dependent endonucleases provide possible explanations for the ubiquitous but sporadic distribution of PT modification in the bacterial world.}, }
@article {pmid30288745, year = {2019}, author = {Shao, Z and Thomas, Y and Hembach, L and Xing, X and Duan, D and Moerschbacher, BM and Bulone, V and Tirichine, L and Bowler, C}, title = {Comparative characterization of putative chitin deacetylases from Phaeodactylum tricornutum and Thalassiosira pseudonana highlights the potential for distinct chitin-based metabolic processes in diatoms.}, journal = {The New phytologist}, volume = {221}, number = {4}, pages = {1890-1905}, doi = {10.1111/nph.15510}, pmid = {30288745}, issn = {1469-8137}, support = {No. 41806175//National Natural Science Foundation of China/International ; ANR-1253 11-IDEX-0001-02//Paris Sciences et Lettres/International ; //European Research Council Advanced Award 'Diatomite'/International ; ANR-10-LABX-54//French Government 'Investissements d'Avenir' programmes MEMO LIFE/International ; }, mesh = {Amidohydrolases/chemistry/*genetics/*metabolism ; Cell Wall/chemistry/metabolism ; Chitin/metabolism ; Chitosan/metabolism ; Diatoms/*genetics/growth &amp; development/*metabolism ; Evolution, Molecular ; Green Fluorescent Proteins/genetics/metabolism ; Organisms, Genetically Modified ; Phylogeny ; Polysaccharides/chemistry/genetics ; Recombinant Fusion Proteins/genetics/metabolism ; }, abstract = {Chitin is generally considered to be present in centric diatoms but not in pennate species. Many aspects of chitin biosynthetic pathways have not been explored in diatoms. We retrieved chitin metabolic genes from pennate (Phaeodactylum tricornutum) and centric (Thalassiosira pseudonana) diatom genomes. Chitin deacetylase (CDA) genes from each genome (PtCDA and TpCDA) were overexpressed in P. tricornutum. We performed comparative analysis of their sequence structure, phylogeny, transcriptional profiles, localization and enzymatic activities. The chitin relevant proteins show complex subcellular compartmentation. PtCDA was likely acquired by horizontal gene transfer from prokaryotes, whereas TpCDA has closer relationships with sequences in Opisthokonta. Using transgenic P. tricornutum lines expressing CDA-green fluorescent protein (GFP) fusion proteins, PtCDA predominantly localizes to Golgi apparatus whereas TpCDA localizes to endoplasmic reticulum/chloroplast endoplasmic reticulum membrane. CDA-GFP overexpression upregulated the transcription of chitin synthases and potentially enhanced the ability of chitin synthesis. Although both CDAs are active on GlcNAc5 , TpCDA is more active on the highly acetylated chitin polymer DA60. We have addressed the ambiguous characters of CDAs from P. tricornutum and T. pseudonana. Differences in localization, evolution, expression and activities provide explanations underlying the greater potential of centric diatoms for chitin biosynthesis. This study paves the way for in vitro applications of novel CDAs.}, }
@article {pmid30288581, year = {2019}, author = {Silar, P and Dauget, JM and Gautier, V and Grognet, P and Chablat, M and Hermann-Le Denmat, S and Couloux, A and Wincker, P and Debuchy, R}, title = {A gene graveyard in the genome of the fungus Podospora comata.}, journal = {Molecular genetics and genomics : MGG}, volume = {294}, number = {1}, pages = {177-190}, pmid = {30288581}, issn = {1617-4623}, mesh = {Base Sequence ; Chromosome Mapping ; Evolution, Molecular ; Fungal Proteins/*genetics ; Gene Deletion ; Gene Expression Regulation, Fungal ; Genetic Speciation ; Podospora/classification/*genetics ; Pseudogenes ; Sequence Analysis, DNA/*methods ; Sequence Analysis, RNA ; }, abstract = {Mechanisms involved in fine adaptation of fungi to their environment include differential gene regulation associated with single nucleotide polymorphisms and indels (including transposons), horizontal gene transfer, gene copy amplification, as well as pseudogenization and gene loss. The two Podospora genome sequences examined here emphasize the role of pseudogenization and gene loss, which have rarely been documented in fungi. Podospora comata is a species closely related to Podospora anserina, a fungus used as model in several laboratories. Comparison of the genome of P. comata with that of P. anserina, whose genome is available for over 10 years, should yield interesting data related to the modalities of genome evolution between these two closely related fungal species that thrive in the same types of biotopes, i.e., herbivore dung. Here, we present the genome sequence of the mat + isolate of the P. comata reference strain T. Comparison with the genome of the mat + isolate of P. anserina strain S confirms that P. anserina and P. comata are likely two different species that rarely interbreed in nature. Despite having a 94-99% of nucleotide identity in the syntenic regions of their genomes, the two species differ by nearly 10% of their gene contents. Comparison of the species-specific gene sets uncovered genes that could be responsible for the known physiological differences between the two species. Finally, we identified 428 and 811 pseudogenes (3.8 and 7.2% of the genes) in P. anserina and P. comata, respectively. Presence of high numbers of pseudogenes supports the notion that difference in gene contents is due to gene loss rather than horizontal gene transfers. We propose that the high frequency of pseudogenization leading to gene loss in P. anserina and P. comata accompanies specialization of these two fungi. Gene loss may be more prevalent during the evolution of other fungi than usually thought.}, }
@article {pmid30287860, year = {2018}, author = {Panda, A and Drancourt, M and Tuller, T and Pontarotti, P}, title = {Genome-wide analysis of horizontally acquired genes in the genus Mycobacterium.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {14817}, pmid = {30287860}, issn = {2045-2322}, mesh = {Bacterial Proteins/genetics ; Computational Biology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genome, Bacterial ; Mycobacterium/*genetics ; Phylogeny ; Sequence Homology ; }, abstract = {Horizontal gene transfer (HGT) was attributed as a major driving force for the innovation and evolution of prokaryotic genomes. Previously, multiple research endeavors were undertaken to decipher HGT in different bacterial lineages. The genus Mycobacterium houses some of the most deadly human pathogens; however, the impact of HGT in Mycobacterium has never been addressed in a systematic way. Previous initiatives to explore the genomic imprints of HGTs in Mycobacterium were focused on few selected species, specifically among the members of Mycobacterium tuberculosis complex. Considering the recent availability of a large number of genomes, the current study was initiated to decipher the probable events of HGTs among 109 completely sequenced Mycobacterium species. Our comprehensive phylogenetic analysis with more than 9,000 families of Mycobacterium proteins allowed us to list several instances of gene transfers spread across the Mycobacterium phylogeny. Moreover, by examining the topology of gene phylogenies here, we identified the species most likely to donate and receive these genes and provided a detailed overview of the putative functions these genes may be involved in. Our study suggested that horizontally acquired foreign genes had played an enduring role in the evolution of Mycobacterium genomes and have contributed to their metabolic versatility and pathogenicity.}, }
@article {pmid30287653, year = {2018}, author = {Reeves, RG and Voeneky, S and Caetano-Anollés, D and Beck, F and Boëte, C}, title = {Agricultural research, or a new bioweapon system?.}, journal = {Science (New York, N.Y.)}, volume = {362}, number = {6410}, pages = {35-37}, doi = {10.1126/science.aat7664}, pmid = {30287653}, issn = {1095-9203}, mesh = {Agriculture/*standards ; Animals ; *Biological Warfare ; *Gene Editing ; *Gene Transfer, Horizontal ; Insecta/genetics/*virology ; Solanum lycopersicum ; *Social Control, Formal ; Viruses/*genetics ; Zea mays ; }, }
@article {pmid30285631, year = {2018}, author = {Oney-Birol, S and Fitz-Gibbon, S and Chen, JM and Gugger, PF and Sork, VL}, title = {Assessment of shared alleles in drought-associated candidate genes among southern California white oak species (Quercus sect. Quercus).}, journal = {BMC genetics}, volume = {19}, number = {1}, pages = {88}, pmid = {30285631}, issn = {1471-2156}, mesh = {*Droughts ; Evolution, Molecular ; Gene Expression Profiling ; *Gene Transfer, Horizontal ; *Genes, Plant ; *Polymorphism, Genetic ; Quercus/*genetics/physiology ; Sequence Analysis, RNA ; Species Specificity ; *Stress, Physiological ; }, abstract = {BACKGROUND: Hybridization and introgression are common phenomena among oak species. These processes can be beneficial by introducing favorable genetic variants across species (adaptive introgression). Given that drought is an important stress, impacting physiological and morphological variation and limiting distributions, our goal was to identify drought-related genes that might exhibit patterns of introgression influenced by natural selection. Using RNAseq, we sequenced whole transcriptomes of 24 individuals from three oaks in southern California: (Quercus engelmannii, Quercus berberidifolia, Quercus cornelius-mulleri) and identified genetic variants to estimate admixture rates of all variants and those in drought genes.<br><br>RESULTS: We found 398,042 variants across all loci and 4352 variants in 139 drought candidate genes. STRUCTURE analysis of all variants revealed the majority of our samples were assignable to a single species, but with several highly admixed individuals. When using drought-associated variants, the same individuals exhibited less admixture and their allele frequencies were more polarized between Engelmann and scrub oaks than when using the total gene set. These findings are consistent with the hypothesis that selection may act differently on functional genes, such as drought-associated genes, and point to candidate genes that are suggestive of divergent selection among species maintaining adaptive differences. For example, the drought genes that showed the strongest bias against engelmannii-fixed oak variants in scrub oaks were related to sugar transporter, coumarate-coA ligases, glutathione S-conjugation, and stress response.<br><br>CONCLUSION: This pilot study illustrates that whole transcriptomes of individuals will provide useful data for identifying functional genes that contribute to adaptive divergence among hybridizing species.}, }
@article {pmid30285620, year = {2018}, author = {Wright, ES and Baum, DA}, title = {Exclusivity offers a sound yet practical species criterion for bacteria despite abundant gene flow.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {724}, pmid = {30285620}, issn = {1471-2164}, mesh = {*Gene Flow ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Phylogeny ; Streptomycetaceae/*classification/*genetics ; }, abstract = {BACKGROUND: The question of whether bacterial species objectively exist has long divided microbiologists. A major source of contention stems from the fact that bacteria regularly engage in horizontal gene transfer (HGT), making it difficult to ascertain relatedness and draw boundaries between taxa. A natural way to define taxa is based on exclusivity of relatedness, which applies when members of a taxon are more closely related to each other than they are to any outsider. It is largely unknown whether exclusive bacterial taxa exist when averaging over the genome or are rare due to rampant hybridization.<br><br>RESULTS: Here, we analyze a collection of 701 genomes representing a wide variety of environmental isolates from the family Streptomycetaceae, whose members are competent at HGT. We find that the presence/absence of auxiliary genes in the pan-genome displays a hierarchical (tree-like) structure that correlates significantly with the genealogy of the core-genome. Moreover, we identified the existence of many exclusive taxa,&#xa0;although individual genes often contradict these taxa. These conclusions were supported by repeating the analysis on 1,586 genomes belonging to the genus Bacillus. However, despite confirming the existence of exclusive groups (taxa), we were unable to identify an objective threshold at which to assign the rank of species.<br><br>CONCLUSIONS: The existence of bacterial taxa is justified by considering average relatedness across the entire genome, as captured by exclusivity, but is rejected if one requires unanimous agreement of all parts of the genome. We propose using exclusivity to delimit taxa and conventional genome similarity thresholds to assign bacterial taxa to the species rank. This approach recognizes species that are phylogenetically meaningful, while also establishing some degree of comparability across species-ranked taxa in different bacterial clades.}, }
@article {pmid30283985, year = {2019}, author = {Pons, JC and Semple, C and Steel, M}, title = {Tree-based networks: characterisations, metrics, and support trees.}, journal = {Journal of mathematical biology}, volume = {78}, number = {4}, pages = {899-918}, pmid = {30283985}, issn = {1432-1416}, mesh = {Animals ; *Biological Evolution ; Computational Biology ; Mathematical Concepts ; Models, Genetic ; *Phylogeny ; }, abstract = {Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer. One way to obtain such a network is by starting with a (rooted) phylogenetic tree T, called a base tree, and adding arcs between arcs of T. The class of phylogenetic networks that can be obtained in this way is called tree-based networks and includes the prominent classes of tree-child and reticulation-visible networks. Initially defined for binary phylogenetic networks, tree-based networks naturally extend to arbitrary phylogenetic networks. In this paper, we generalise recent tree-based characterisations and associated proximity measures for binary phylogenetic networks to arbitrary phylogenetic networks. These characterisations are in terms of matchings in bipartite graphs, path partitions, and antichains. Some of the generalisations are straightforward to establish using the original approach, while others require a very different approach. Furthermore, for an arbitrary tree-based network N, we characterise the support trees of N, that is, the tree-based embeddings of N. We use this characterisation to give an explicit formula for the number of support trees of N when N is binary. This formula is written in terms of the components of a bipartite graph.}, }
@article {pmid30283667, year = {2018}, author = {Reynolds, HT and Vijayakumar, V and Gluck-Thaler, E and Korotkin, HB and Matheny, PB and Slot, JC}, title = {Horizontal gene cluster transfer increased hallucinogenic mushroom diversity.}, journal = {Evolution letters}, volume = {2}, number = {2}, pages = {88-101}, pmid = {30283667}, issn = {2056-3744}, abstract = {Secondary metabolites are a heterogeneous class of chemicals that often mediate interactions between species. The tryptophan-derived secondary metabolite, psilocin, is a serotonin receptor agonist that induces altered states of consciousness. A phylogenetically disjunct group of mushroom-forming fungi in the Agaricales produce the psilocin prodrug, psilocybin. Spotty phylogenetic distributions of fungal compounds are sometimes explained by horizontal transfer of metabolic gene clusters among unrelated fungi with overlapping niches. We report the discovery of a psilocybin gene cluster in three hallucinogenic mushroom genomes, and evidence for its horizontal transfer between fungal lineages. Patterns of gene distribution and transmission suggest that synthesis of psilocybin may have provided a fitness advantage in the dung and late wood-decay fungal niches, which may serve as reservoirs of fungal indole-based metabolites that alter behavior of mycophagous and wood-eating invertebrates. These hallucinogenic mushroom genomes will serve as models in neurochemical ecology, advancing the (bio)prospecting and synthetic biology of novel neuropharmaceuticals.}, }
@article {pmid30283411, year = {2018}, author = {Terceti, MS and Vences, A and Matanza, XM and Dalsgaard, I and Pedersen, K and Osorio, CR}, title = {Molecular Epidemiology of Photobacterium damselae subsp. damselae Outbreaks in Marine Rainbow Trout Farms Reveals Extensive Horizontal Gene Transfer and High Genetic Diversity.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2155}, pmid = {30283411}, issn = {1664-302X}, abstract = {The marine bacterium Photobacterium damselae subsp. damselae is a pathogen for a variety of marine animals, as well as for humans, and is nowadays considered an emerging pathogen for fish of importance in marine aquaculture. Recent studies have suggested that outbreaks in fish farms are caused by multiclonal populations of this subspecies that exist in the environment. Here, we report the study of a collection of 31 strains isolated during the course of disease outbreaks in marine rainbow trout farms in Denmark in 1994, 1995, and 2006, respectively. A phylogenetic analysis based on the toxR gene sequence, and the screening of virulence-related genes uncovered a high genetic heterogeneity, even among strains isolated from the same fish farm at the same time. Moreover, comparative analysis of the whole genome sequences of four selected strains revealed a large number of differentially occurring genes, which included virulence genes, pPHDD1 plasmid, polysaccharide synthesis gene clusters, CRISPR-Cas systems and putative new mobile genetic elements. This study provides sound evidence that P. damselae subsp. damselae outbreaks in Danish rainbow trout farms were caused by multiclonal populations and that horizontal gene transfer constitutes a strong driving force in the generation of intraspecific diversity in this pathogen.}, }
@article {pmid30279346, year = {2018}, author = {Vicente, CM and Thibessard, A and Lorenzi, JN and Benhadj, M and Hôtel, L and Gacemi-Kirane, D and Lespinet, O and Leblond, P and Aigle, B}, title = {Comparative Genomics among Closely Related Streptomyces Strains Revealed Specialized Metabolite Biosynthetic Gene Cluster Diversity.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {7}, number = {4}, pages = {}, pmid = {30279346}, issn = {2079-6382}, support = {ANR Streptoflux ANR-07-BLAN-0096//French National Research Agency/ ; ANR MiGenIs ANR-13-BSV6-0006//French National Research Agency/ ; ANR-11-LABX-0002-01//R&#xe9;gion Lorraine and the Laboratory Excellence ARBRE/ ; FP7-609398.0000//R&#xe9;gion Grand Est, French National Institute for Agricultural Research (INRA) and AgreenSkillsPlus Program/ ; }, abstract = {Specialized metabolites are of great interest due to their possible industrial and clinical applications. The increasing number of antimicrobial resistant infectious agents is a major health threat and therefore, the discovery of chemical diversity and new antimicrobials is crucial. Extensive genomic data from Streptomyces spp. confirm their production potential and great importance. Genome sequencing of the same species strains indicates that specialized metabolite biosynthetic gene cluster (SMBGC) diversity is not exhausted, and instead, a pool of novel specialized metabolites still exists. Here, we analyze the genome sequence data from six phylogenetically close Streptomyces strains. The results reveal that the closer strains are phylogenetically, the number of shared gene clusters is higher. Eight specialized metabolites comprise the core metabolome, although some strains have only six core gene clusters. The number of conserved gene clusters common between the isolated strains and their closest phylogenetic counterparts varies from nine to 23 SMBGCs. However, the analysis of these phylogenetic relationships is not affected by the acquisition of gene clusters, probably by horizontal gene transfer events, as each strain also harbors strain-specific SMBGCs. Between one and 15 strain-specific gene clusters were identified, of which up to six gene clusters in a single strain are unknown and have no identifiable orthologs in other species, attesting to the existing SMBGC novelty at the strain level.}, }
@article {pmid30277517, year = {2018}, author = {Smalla, K and Cook, K and Djordjevic, SP and Klümper, U and Gillings, M}, title = {Environmental dimensions of antibiotic resistance: assessment of basic science gaps.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {12}, pages = {}, doi = {10.1093/femsec/fiy195}, pmid = {30277517}, issn = {1574-6941}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/*genetics ; Biological Evolution ; Drug Resistance, Bacterial/*genetics ; Ecology ; Gene Transfer, Horizontal/genetics ; Humans ; Interspersed Repetitive Sequences/*genetics ; }, abstract = {Antibiotic resistance is one of the major problems facing medical practice in the 21st century. Historical approaches to managing antibiotic resistance have often focused on individual patients, specific pathogens and particular resistance phenotypes. However, it is increasingly recognized that antibiotic resistance is a complex ecological and evolutionary problem. As such, understanding the dynamics of antibiotic resistance requires integration of data on the diverse mobile genetic elements often associated with antibiotic resistance genes, and their dissemination by various mechanisms of horizontal gene transfer between bacterial cells and environments. Most important is understanding the fate and effects of antibiotics at sub-inhibitory concentrations, and co-selection. This opinion paper identifies key knowledge gaps in our understanding of resistance phenomena, and outlines research needs that should be addressed to help us manage resistance into the future.}, }
@article {pmid30272802, year = {2018}, author = {Taggar, G and Rehman, MA and Yin, X and Lepp, D and Ziebell, K and Handyside, P and Boerlin, P and Diarra, MS}, title = {Antimicrobial-Resistant E. coli from Surface Waters in Southwest Ontario Dairy Farms.}, journal = {Journal of environmental quality}, volume = {47}, number = {5}, pages = {1068-1078}, doi = {10.2134/jeq2018.04.0139}, pmid = {30272802}, issn = {0047-2425}, mesh = {Animals ; *Anti-Infective Agents ; Cattle ; *Escherichia coli O157 ; Farms ; Female ; Humans ; Microbial Sensitivity Tests ; Ontario ; Phylogeny ; }, abstract = {Untreated surface waters can be contaminated with a variety of bacteria, including , some of which can be pathogenic for both humans and animals. Therefore, such waters need to be treated before their use in dairy operations to mitigate risks to dairy cow health and milk safety. To understand the molecular ecology of , this study aimed to assess antimicrobial resistance (AMR) in recovered from untreated surface water sources of dairy farms. Untreated surface water samples (= 240) from 15 dairy farms were collected and processed to isolate . A total of 234 isolates were obtained and further characterized for their serotypes and antimicrobial susceptibility. Of the 234 isolates, 71.4% were pan-susceptible, 23.5% were resistant to one or two antimicrobial classes, and 5.1% were resistant to three or more antimicrobial classes. Whole genome sequence analysis of 11 selected multidrug-resistant isolates revealed AMR genes including and that confer resistance to the critically important extended-spectrum cephalosporins, as well as a variety of plasmids (mainly of the replicon type) and class 1 integrons. Phylogenetic and comparative genome analysis revealed a genetic relationship between some of the sequenced and Shiga toxin-producing O157:H7 (STEC), which warrants further investigation. This study shows that untreated surface water sources contain antimicrobial-resistant which may serve as a reservoir of AMR that could be disseminated through horizontal gene transfer. This is another reason why effective water treatment before usage should be routinely done on dairy farm operations.}, }
@article {pmid30272794, year = {2018}, author = {Son, DI and Aleta, P and Park, M and Yoon, H and Cho, KH and Kim, YM and Kim, S}, title = {Seasonal Changes in Antibiotic Resistance Genes in Rivers and Reservoirs in South Korea.}, journal = {Journal of environmental quality}, volume = {47}, number = {5}, pages = {1079-1085}, doi = {10.2134/jeq2017.12.0493}, pmid = {30272794}, issn = {0047-2425}, mesh = {*Anti-Bacterial Agents ; Cities ; Drug Resistance, Microbial ; Genes, Bacterial ; Republic of Korea ; *Rivers ; Seasons ; Wastewater ; }, abstract = {The fate of antibiotic resistance genes (ARGs) in aquatic environments, especially in rivers and reservoirs, is receiving growing attention in South Korea because reservoirs are an important source of drinking water in this country. Seasonal changes in the abundance of 11 ARGs and a mobile genetic element () in two reservoirs in South Korea, located near drinking water treatment plants in Cheonan and Cheongju cities, were monitored for 6 mo. In these drinking water sources, total ARG concentrations reached 2.5 × 10 copies mL, which is one order of magnitude higher than in influents of some wastewater treatment plants in South Korea. During the sampling periods in August, October, and November 2016 and January 2017, sulfonamides (), β-lactam antibiotics (), and tetracycline () resistance genes were the most abundant genes at the two sites. The ARG abundance consistently increased in January relative to 16S ribosomal ribonucleic acid (rRNA) counts. General stress responses to oxidative stress and other environmental factors associated with the cold season could be significant drivers of ARG horizontal gene transfer in the environment. Accordingly, removal of ARGs as a key step in water treatment warrants more attention.}, }
@article {pmid30272774, year = {2018}, author = {McConnell, MM and Hansen, LT and Neudorf, KD and Hayward, JL and Jamieson, RC and Yost, CK and Tong, A}, title = {Sources of Antibiotic Resistance Genes in a Rural River System.}, journal = {Journal of environmental quality}, volume = {47}, number = {5}, pages = {997-1005}, doi = {10.2134/jeq2017.12.0477}, pmid = {30272774}, issn = {0047-2425}, mesh = {*Anti-Bacterial Agents ; Canada ; Drug Resistance, Microbial ; *Genes, Bacterial ; Humans ; Rivers ; }, abstract = {The increasing prevalence of antibiotic resistance genes (ARGs) in the environment is problematic due to the risk of horizontal gene transfer and development of antibiotic resistant pathogenic bacteria. Using a suite of monitoring tools, this study aimed to investigate the sources of ARGs in a rural river system in Nova Scotia, Canada. The monitoring program specifically focused on the relative contribution of ARGs from a single tertiary-level wastewater treatment plant (WWTP) in comparison to contributions from the upgradient rural, sparsely developed, watershed. The overall gene concentration significantly (< 0.05) increased downstream from the WWTP, suggesting that tertiary-level treatment still contributes ARGs to the environment. As a general trend, ARG concentrations upstream were found to decrease as proximity to human-impacted areas decreased; however, many ARGs remained above detection limits in headwater river samples, which suggested their ubiquitous presence in this watershed in the absence of obvious pollution sources. Significant correlations with ARGs were found for human fecal marker, and some antibiotics, suggesting that these markers may be useful for prediction and understanding of ARG levels and sources in rural rivers.}, }
@article {pmid30271939, year = {2018}, author = {Ding, Y and Teo, JWP and Drautz-Moses, DI and Schuster, SC and Givskov, M and Yang, L}, title = {Acquisition of resistance to carbapenem and macrolide-mediated quorum sensing inhibition by Pseudomonas aeruginosa via ICETn4371 6385.}, journal = {Communications biology}, volume = {1}, number = {}, pages = {57}, pmid = {30271939}, issn = {2399-3642}, abstract = {Pseudomonas aeruginosa can cause life-threatening infections in immunocompromised patients. The first-line agents to treat P. aeruginosa infections are carbapenems. However, the emergence of carbapenem-resistant P. aeruginosa strains greatly compromised the effectiveness of carbapenem treatment, which makes the surveillance on their spreading and transmission important. Here we characterized the full-length genomes of two carbapenem-resistant P. aeruginosa clinical isolates that are capable of producing New Delhi metallo-β-lactamase-1 (NDM-1). We show that bla NDM-1 is carried by a novel integrative and conjugative element (ICE) ICETn4371 6385, which also carries the macrolide resistance gene msr(E) and the florfenicol resistance gene floR. By exogenously expressing msr(E) in P. aeruginosa laboratory strains, we show that Msr(E) can abolish azithromycin-mediated quorum sensing inhibition in vitro and anti-Pseudomonas effect in vivo. We conclude that ICEs are important in transmitting carbapenem resistance, and that anti-virulence treatment of P. aeruginosa infections using sub-inhibitory concentrations of macrolides can be challenged by horizontal gene transfer.}, }
@article {pmid30267758, year = {2019}, author = {Dong, H and Xiang, H and Mu, D and Wang, D and Wang, T}, title = {Exploiting a conjugative CRISPR/Cas9 system to eliminate plasmid harbouring the mcr-1 gene from Escherichia coli.}, journal = {International journal of antimicrobial agents}, volume = {53}, number = {1}, pages = {1-8}, doi = {10.1016/j.ijantimicag.2018.09.017}, pmid = {30267758}, issn = {1872-7913}, mesh = {CRISPR-Associated Protein 9/genetics/metabolism ; *CRISPR-Cas Systems ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/classification/drug effects/*genetics ; Escherichia coli Proteins/*genetics ; Gene Expression Regulation, Bacterial ; Genetic Engineering ; Plasmids/*genetics ; RNA, Bacterial/genetics/metabolism ; }, abstract = {The transfer of multi-drug-resistance plasmids by bacterial conjugation is largely responsible for the development of drug resistance in bacteria, and causes serious problems in the treatment of infectious diseases. Since the first discovery of plasmid-borne colistin resistance gene mcr-1 was reported in late 2016, this gene has been found in a great number of Escherichia coli and other Gram-negative pathogens separated from different types of sources worldwide. The elimination of plasmids carrying mcr-1 and restoration of polymyxin sensitivity has very important clinical significance because polymyxins are frequently used as last-resort antibiotics to treat extensively drug-resistant Gram-negative bacterial infections. A host-independent conjugative plasmid was constructed in this study, and an engineered CRISPR/Cas9 system was used to remove plasmid harbouring mcr-1 from bacteria. This study found that this conjugative plasmid can not only be used as a new tool to remove resistance plasmids and sensitize the recipient bacteria to antibiotics, but can also make the recipient cell acquire immunity against mcr-1. This strategy provides a novel method to counteract the ever-worsening spread of mcr-1 among bacterial pathogens.}, }
@article {pmid30266092, year = {2018}, author = {Pers, D and Lynch, JA}, title = {Ankyrin domain encoding genes from an ancient horizontal transfer are functionally integrated into Nasonia developmental gene regulatory networks.}, journal = {Genome biology}, volume = {19}, number = {1}, pages = {148}, pmid = {30266092}, issn = {1474-760X}, support = {R03 HD078578/HD/NICHD NIH HHS/United States ; R03 HD087476/HD/NICHD NIH HHS/United States ; 1R03HD087476/NH/NIH HHS/United States ; 1R03HD078578/NH/NIH HHS/United States ; }, mesh = {Animals ; *Ankyrin Repeat ; Body Patterning ; *Gene Expression Regulation, Developmental ; *Gene Regulatory Networks ; Gene Transfer, Horizontal ; Genes, Insect ; Insect Proteins/chemistry/*genetics/metabolism ; Wasps/embryology/*genetics ; }, abstract = {BACKGROUND: How regulatory networks incorporate additional components and how novel genes are functionally integrated into well-established developmental processes are two important and intertwined questions whose answers have major implications for understanding the evolution of development. We recently discovered a set of lineage-restricted genes with strong and specific expression patterns along the dorsal-ventral (DV) axis of the embryo of the wasp Nasonia that may serve as a powerful system for addressing these questions. We sought to both understand the evolutionary history of these genes and to determine their functions in the Nasonia DV patterning system.<br><br>RESULTS: We have found that the novel DV genes are part of a large family of rapidly duplicating and diverging ankyrin domain-encoding genes that originated most likely by horizontal transfer from a prokaryote in a common ancestor of the wasp superfamily Chalcidoidea. We tested the function of those ankyrin-encoding genes expressed along the DV axis and found that they participate in early embryonic DV patterning. We also developed a new wasp model system (Melittobia) and found that some functional integration of ankyrin genes have been preserved for over 90 million years.<br><br>CONCLUSIONS: Our results indicate that regulatory networks can incorporate novel genes that then become necessary for stable and repeatable outputs. Even a modest role in developmental networks may be enough to allow novel or duplicate genes to be maintained in the genome and become fully integrated network components.}, }
@article {pmid30265303, year = {2018}, author = {Ward, AC and Allenby, NE}, title = {Genome mining for the search and discovery of bioactive compounds: the Streptomyces paradigm.}, journal = {FEMS microbiology letters}, volume = {365}, number = {24}, pages = {}, doi = {10.1093/femsle/fny240}, pmid = {30265303}, issn = {1574-6968}, mesh = {Anti-Bacterial Agents/*biosynthesis/chemistry ; Bacterial Proteins/genetics/metabolism ; *Drug Discovery ; *Genome, Bacterial ; Multigene Family ; Phylogeny ; Streptomyces/classification/genetics/isolation &amp; purification/*metabolism ; }, abstract = {The need for new antimicrobials is indisputable. The flight from natural products in drug discovery was unfortunate; however, the revolution that is genome mining, enabled by the explosion in sequencing technology, is a cause for hope. Nevertheless, renewed search and discovery is still a challenge. We explore novel metabolite diversity and the challenges in Streptomyces. Estimating the extent of novel bioactive metabolites remaining to be discovered is an important driver for future investment. Frequent re-discovery of known natural products was a major factor in big pharma exiting search and discovery, and remains a reality. We explore whether this is due to exhaustive isolation and frequent lateral gene transfer. Analysing all biosynthetic gene clusters across all genomes is challenging. Therefore, representative examples of the patterns of secondary metabolite diversity suggest that re-discovery is linked to frequent expression in frequently isolated (and frequently misidentified) strains. Lateral gene transfer of complete biosynthetic clusters is less frequent than might be perceived but frequent gene exchange implies a massive combinatorial biosynthesis experiment. Genome sequencing emphasises rare expression of many secondary metabolite gene clusters and diversification at the finest levels of phylogenetic discrimination. In addition, we are only just beginning to unravel the impact of ecology. The hidden diversity suggests that cluster cloning and heterologous expression in microbial cell factories will explore this diversity more effectively.}, }
@article {pmid30264928, year = {2019}, author = {González-Rivera, C and Khara, P and Awad, D and Patel, R and Li, YG and Bogisch, M and Christie, PJ}, title = {Two pKM101-encoded proteins, the pilus-tip protein TraC and Pep, assemble on the Escherichia coli cell surface as adhesins required for efficient conjugative DNA transfer.}, journal = {Molecular microbiology}, volume = {111}, number = {1}, pages = {96-117}, pmid = {30264928}, issn = {1365-2958}, support = {F32 AI114182/AI/NIAID NIH HHS/United States ; R01 GM048746/GM/NIGMS NIH HHS/United States ; R01GM48476/NH/NIH HHS/United States ; }, mesh = {Adhesins, Bacterial/*metabolism ; Bacteriophage PRD1/physiology ; *Conjugation, Genetic ; DNA, Bacterial/genetics/metabolism ; Escherichia coli/*genetics ; Fimbriae Proteins/*metabolism ; *Gene Transfer, Horizontal ; *Plasmids ; Protein Multimerization ; Protein Transport ; Type IV Secretion Systems/metabolism ; Type VI Secretion Systems/metabolism ; Virus Attachment ; }, abstract = {Mobile genetic elements (MGEs) encode type IV secretion systems (T4SSs) known as conjugation machines for their transmission between bacterial cells. Conjugation machines are composed of an envelope-spanning translocation channel, and those functioning in Gram-negative species additionally elaborate an extracellular pilus to initiate donor-recipient cell contacts. We report that pKM101, a self-transmissible MGE functioning in the Enterobacteriaceae, has evolved a second target cell attachment mechanism. Two pKM101-encoded proteins, the pilus-tip adhesin TraC and a protein termed Pep, are exported to the cell surface where they interact and also form higher order complexes appearing as distinct foci or patches around the cell envelope. Surface-displayed TraC and Pep are required for an efficient conjugative transfer, 'extracellular complementation' potentially involving intercellular protein transfer, and activation of a Pseudomonas aeruginosa type VI secretion system. Both proteins are also required for bacteriophage PRD1 infection. TraC and Pep are exported across the outer membrane by a mechanism potentially involving the β-barrel assembly machinery. The pKM101 T4SS, thus, deploys alternative routing pathways for the delivery of TraC to the pilus tip or both TraC and Pep to the cell surface. We propose that T4SS-encoded, pilus-independent attachment mechanisms maximize the probability of MGE propagation and might be widespread among this translocation superfamily.}, }
@article {pmid30263930, year = {2018}, author = {Berridge, MV and Crasso, C and Neuzil, J}, title = {Mitochondrial Genome Transfer to Tumor Cells Breaks The Rules and Establishes a New Precedent in Cancer Biology.}, journal = {Molecular &amp; cellular oncology}, volume = {5}, number = {5}, pages = {e1023929}, pmid = {30263930}, issn = {2372-3556}, abstract = {Horizontal gene transfer is known to occur in bacteria and archaea whereas higher organisms including mammals undergo vertical transfer. Our recent results demonstrate horizontal transfer of mitochondrial DNA (mtDNA) from normal host cells to tumor cells lacking mitochondrial DNA (mtDNA). This mtDNA migration results in recovery of respiration, restored tumor initiation, and metastasis.}, }
@article {pmid30261266, year = {2019}, author = {Perdigão, J and Portugal, I}, title = {Genetics and roadblocks of drug resistant tuberculosis.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {72}, number = {}, pages = {113-130}, doi = {10.1016/j.meegid.2018.09.023}, pmid = {30261266}, issn = {1567-7257}, mesh = {Antitubercular Agents/*pharmacology/therapeutic use ; Diarylquinolines/pharmacology/therapeutic use ; *Drug Resistance, Multiple, Bacterial/genetics ; Epistasis, Genetic ; Humans ; Mutation ; Mycobacterium tuberculosis/drug effects/*genetics ; Nitroimidazoles/pharmacology/therapeutic use ; Oxazoles/pharmacology/therapeutic use ; Phylogeny ; *Tuberculosis, Multidrug-Resistant/drug therapy/epidemiology/microbiology ; }, abstract = {Considering the extensive evolutionary history of Mycobacterium tuberculosis, anti-Tuberculosis (TB) drug therapy exerts a recent selective pressure. However, in a microorganism devoid of horizontal gene transfer and with a strictly clonal populational structure such as M. tuberculosis the usual, but not sole, path to overcome drug susceptibility is through de novo mutations on a relatively strict set of genes. The possible allelic diversity that can be associated with drug resistance through several mechanisms such as target alteration or target overexpression, will dictate how these genes can become associated with drug resistance. The success demonstrated by this pathogenic microbe in this latter process and its ability to spread is currently one of the major obstacles to an effective TB elimination. This article reviews the action mechanism of the more important anti-TB drugs, including bedaquiline and delamanid, along with new findings on specific resistance mechanisms. With the development, validation and endorsement of new in vitro molecular tests for drug resistance, knowledge on these resistance mechanisms and microevolutionary dynamics leading to the emergence and fixation of drug resistance mutations within the host is highly important. Additionally, the fitness toll imposed by resistance development is also herein discussed together with known compensatory mechanisms. By elucidating the possible mechanisms that enable one strain to reacquire the original fitness levels, it will be theoretically possible to make more informed decisions and develop novel strategies that can force M. tuberculosis microevolutionary trajectory down through a path of decreasing fitness levels.}, }
@article {pmid30258425, year = {2018}, author = {Day, A and Ahn, J and Salmond, GPC}, title = {Jumbo Bacteriophages Are Represented Within an Increasing Diversity of Environmental Viruses Infecting the Emerging Phytopathogen, Dickeya solani.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2169}, pmid = {30258425}, issn = {1664-302X}, support = {BB/G000298/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/H002677/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {Dickeya species are economically important phytopathogens widespread in mainland Europe that can reduce crop yields by 25%. There are no effective environmentally-acceptable chemical systems available for diseases caused by Dickeya. Bacteriophages have been suggested for use in biocontrol of these pathogens in the field, and limited field trials have been conducted. To date the majority of bacteriophages capable of infecting Dickeya solani, one of the more aggressive species, are from the same family, the Ackermannviridae, many representatives of which have been shown to be unsuitable for use in the field due to their capacity for generalized transduction. Members of this family are also only capable of forming individual plaques on D. solani. Here we describe novel bacteriophages from environmental sources isolated on D. solani, including members of two other viral families; Myoviridae and Podoviridae, most of which are capable of forming plaques on multiple Dickeya species. Full genomic sequencing revealed that the Myoviridae family members form two novel clusters of jumbo bacteriophages with genomes over 250 kbp, with one cluster containing phages of another phytopathogen Erwinia amylovora. Transduction experiments showed that the majority of the new environmental bacteriophages are also capable of facilitating efficient horizontal gene transfer, however the single Podoviridae family member is not. This particular phage therefore has potential for use as a biocontrol agent against multiple species of Dickeya.}, }
@article {pmid30258041, year = {2018}, author = {Lécuyer, F and Bourassa, JS and Gélinas, M and Charron-Lamoureux, V and Burrus, V and Beauregard, PB}, title = {Biofilm Formation Drives Transfer of the Conjugative Element ICEBs1 in Bacillus subtilis.}, journal = {mSphere}, volume = {3}, number = {5}, pages = {}, pmid = {30258041}, issn = {2379-5042}, mesh = {Bacillus subtilis/genetics/*physiology ; Biofilms/*growth &amp; development ; *Conjugation, Genetic ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial ; Extracellular Matrix/genetics ; *Gene Transfer, Horizontal ; }, abstract = {Horizontal gene transfer by integrative and conjugative elements (ICEs) is a very important mechanism for spreading antibiotic resistance in various bacterial species. In environmental and clinical settings, most bacteria form biofilms as a way to protect themselves against extracellular stress. However, much remains to be known about ICE transfer in biofilms. Using ICEBs1 from Bacillus subtilis, we show that the natural conjugation efficiency of this ICE is greatly affected by the ability of the donor and recipient to form a biofilm. ICEBs1 transfer considerably increases in biofilm, even at low donor/recipient ratios. Also, while there is a clear temporal correlation between biofilm formation and ICEBs1 transfer, biofilms do not alter the level of ICEBs1 excision in donor cells. Conjugative transfer appears to be favored by the biophysical context of biofilms. Indeed, extracellular matrix production, particularly from the recipient cells, is essential for biofilms to promote ICEBs1 transfer. Our study provides basic new knowledge on the high rate of conjugative transfer of ICEs in biofilms, a widely preponderant bacterial lifestyle in the environment, which could have a major impact on our understanding of horizontal gene transfer in natural and clinical environments.IMPORTANCE Transfer of mobile genetic elements from one bacterium to another is the principal cause of the spread of antibiotic resistance. However, the dissemination of these elements in environmental contexts is poorly understood. In clinical and environmental settings, bacteria are often found living in multicellular communities encased in a matrix, a structure known as a biofilm. In this study, we examined how forming a biofilm influences the transmission of an integrative and conjugative element (ICE). Using the model Gram-positive bacterium B. subtilis, we observed that biofilm formation highly favors ICE transfer. This increase in conjugative transfer is due to the production of extracellular matrix, which creates an ideal biophysical context. Our study provides important insights into the role of the biofilm structure in driving conjugative transfer, which is of major importance since biofilm is a widely preponderant bacterial lifestyle for clinically relevant bacterial strains.}, }
@article {pmid30258003, year = {2018}, author = {Odon, V and Georgana, I and Holley, J and Morata, J and Maluquer de Motes, C}, title = {Novel Class of Viral Ankyrin Proteins Targeting the Host E3 Ubiquitin Ligase Cullin-2.}, journal = {Journal of virology}, volume = {92}, number = {23}, pages = {}, pmid = {30258003}, issn = {1098-5514}, support = {BB/M003647/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Ankyrins/*metabolism ; Cullin Proteins/*metabolism ; HEK293 Cells ; Humans ; Immunity, Innate ; Poxviridae/*physiology ; Poxviridae Infections/immunology/*metabolism/virology ; Proteome/*analysis ; Sequence Homology ; Viral Proteins/*metabolism ; }, abstract = {Ankyrin repeat (ANK) domains are among the most abundant motifs in eukaryotic proteins. ANK proteins are rare amongst viruses, with the exception of poxviruses, which presumably acquired them from the host via horizontal gene transfer. The architecture of poxvirus ANK proteins is, however, different from that of their cellular counterparts, and this precludes a direct acquisition event. Here we combine bioinformatics analysis and quantitative proteomics to discover a new class of viral ANK proteins with a domain organization that relates to cellular ANK proteins. These noncanonical viral ANK proteins, termed ANK/BC, interact with host Cullin-2 via a C-terminal BC box resembling that of cellular Cullin-2 substrate adaptors such as the von Hippel-Lindau protein. Mutagenesis of the BC box-like sequence abrogates binding to Cullin-2, whereas fusion of this motif to an ANK-only protein confers Cullin-2 association. We demonstrated that these viral ANK/BC proteins are potent immunomodulatory proteins suppressing the activation of the proinflammatory transcription factors NF-κB and interferon (IFN)-responsive factor 3 (IRF-3) and the production of cytokines and chemokines, including interferon, and that association with Cullin-2 is required for optimal inhibitory activity. ANK/BC proteins exist in several orthopoxviruses and cluster into 2 closely related orthologue groups in a phylogenetic lineage that is separate from that of canonical ANK/F-box proteins. Given the existence of cellular proteins with similar architecture, viral ANK/BC proteins may be closely related to the original ANK gene acquired by an ancestral orthopoxvirus. These findings uncover a novel viral strategy to antagonize innate immunity and shed light on the origin of the poxviral ANK protein family.IMPORTANCE Viruses encode multiple proteins aimed at modulating cellular homeostasis and antagonizing the host antiviral response. Most of these genes were originally acquired from the host and subsequently adapted to benefit the virus. ANK proteins are common in eukaryotes but are unusual amongst viruses, with the exception of poxviruses, where they represent one of the largest protein families. We report here the existence of a new class of viral ANK proteins, termed ANK/BC, that provide new insights into the origin of poxvirus ANK proteins. ANK/BC proteins target the host E3 ubiquitin ligase Cullin-2 via a C-terminal BC box domain and are potent suppressors of the production of inflammatory cytokines, including interferon. The existence of cellular ANK proteins whose architecture is similar suggests the acquisition of a host ANK/BC gene by an ancestral orthopoxvirus and its subsequent duplication and adaptation to widen the repertoire of immune evasion strategies.}, }
@article {pmid30254617, year = {2018}, author = {Headd, B and Bradford, SA}, title = {Physicochemical Factors That Favor Conjugation of an Antibiotic Resistant Plasmid in Non-growing Bacterial Cultures in the Absence and Presence of Antibiotics.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2122}, pmid = {30254617}, issn = {1664-302X}, abstract = {Horizontal gene transfer (HGT) of antibiotic resistance genes has received increased scrutiny from the scientific community in recent years owing to the public health threat associated with antibiotic resistant bacteria. Most studies have examined HGT in growing cultures. We examined conjugation in growing and non-growing cultures of E. coli using a conjugative multi antibiotic and metal resistant plasmid to determine physiochemical parameters that favor horizontal gene transfer. The conjugation frequency in growing and non-growing cultures was generally greater under shaken than non-shaken conditions, presumably due to increased frequency of cell collisions. Non-growing cultures in 9.1 mM NaCl had a similar conjugation frequency to that of growing cultures in Luria-Bertaini broth, whereas those in 1 mM or 90.1 mM NaCl were much lower. This salinity effect on conjugation was attributed to differences in cell-cell interactions and conformational changes in cell surface macromolecules. In the presence of antibiotics, the conjugation frequencies of growing cultures did not increase, but in non-growing cultures of 9.1 mM NaCl supplemented with Cefotaxime the conjugation frequency was as much as nine times greater than that of growing cultures. The mechanism responsible for the increased conjugation in non-growing bacteria was attributed to the likely lack of penicillin-binding protein 3 (the target of Cefotaxime), in non-growing cells that enabled Cefotaxime to interact with the plasmid and induce conjugation. Our results suggests that more attention may be owed to HGT in non-growing bacteria as most bacteria in the environment are likely not growing and the proposed mechanism for increased conjugation may not be unique to the bacteria/plasmid system we studied.}, }
@article {pmid30253038, year = {2018}, author = {De Simone, G and Polticelli, F and Aime, S and Ascenzi, P}, title = {Lanthanides-based catalysis in eukaryotes.}, journal = {IUBMB life}, volume = {70}, number = {11}, pages = {1067-1075}, doi = {10.1002/iub.1933}, pmid = {30253038}, issn = {1521-6551}, mesh = {Alcohol Oxidoreductases/genetics/*metabolism ; Amino Acid Sequence ; Calcium/*metabolism ; Catalysis ; Cerium/*metabolism ; Eukaryota/*metabolism ; Lanthanoid Series Elements/*metabolism ; Methanol/metabolism ; Phylogeny ; Prokaryotic Cells/*metabolism ; Sequence Homology ; }, abstract = {Rare earth elements play a pivotal role in high-technology devices, are used as contrast agents for magnetic resonance imaging in clinical settings, are explored as drug carriers for tumor photodynamic therapy, and are used as fertilizers. From the biochemical viewpoint, they act not only as antagonists of Ca[2+] but have been proposed as alternative to Ca[2+] in metallo-enzymes, in particular in Ce[3+] -based methanol dehydrogenases (MDHs). Up to now, the analysis of protein sequence databases identified Ce[3+] -based MHDs only in Archea and Bacteria. Here, we report evidence that Ce[3+] -based MDHs are also present in higher organisms. These enzymes, identified in the parasite Plasmodium yoelii yoelii, in the spider Nephila clavipes, in the Tibetan antelope Pantholops hodgsonii, and in Homo sapiens, are encoded by intronless genes, thus representing a case of multiple, independent lateral gene transfer from Prokaryotes to Eukaryotes. The conservation of residues involved in the Ce[3+] coordination, pyrroquinoline quinone cofactor recognition and in the structure stabilization suggests that these enzymes belong to the Ce[3+] -dependent MDH family, hitherto considered as exclusive of Prokaryotes. © 2018 IUBMB Life, 70(11):1067-1075, 2018.}, }
@article {pmid30252837, year = {2018}, author = {García-Pastor, L and Sánchez-Romero, MA and Gutiérrez, G and Puerta-Fernández, E and Casadesús, J}, title = {Formation of phenotypic lineages in Salmonella enterica by a pleiotropic fimbrial switch.}, journal = {PLoS genetics}, volume = {14}, number = {9}, pages = {e1007677}, pmid = {30252837}, issn = {1553-7404}, mesh = {DNA-Binding Proteins/metabolism ; Fimbriae Proteins/*genetics/metabolism ; Fimbriae, Bacterial/*genetics/metabolism ; Flow Cytometry ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Operon/*genetics ; Phenotype ; Salmonella enterica/*genetics ; Single-Cell Analysis ; }, abstract = {The std locus of Salmonella enterica, an operon acquired by horizontal transfer, encodes fimbriae that permit adhesion to epithelial cells in the large intestine. Expression of the std operon is bistable, yielding a major subpopulation of StdOFF cells (99.7%) and a minor subpopulation of StdON cells (0.3%). In addition to fimbrial proteins, the std operon encodes two proteins, StdE and StdF, that have DNA binding capacity and control transcription of loci involved in flagellar synthesis, chemotaxis, virulence, conjugal transfer, biofilm formation, and other cellular functions. As a consequence of StdEF pleiotropic transcriptional control, StdON and StdOFF subpopulations may differ not only in the presence or absence of Std fimbriae but also in additional phenotypic traits. Separation of StdOFF and StdON lineages by cell sorting confirms the occurrence of lineage-specific features. Formation of StdOFF and StdON lineages may thus be viewed as a rudimentary bacterial differentiation program.}, }
@article {pmid30252102, year = {2018}, author = {Duan, B and Ding, P and Hughes, TR and Navarre, WW and Liu, J and Xia, B}, title = {How bacterial xenogeneic silencer rok distinguishes foreign from self DNA in its resident genome.}, journal = {Nucleic acids research}, volume = {46}, number = {19}, pages = {10514-10529}, pmid = {30252102}, issn = {1362-4962}, support = {MOP-15107//CIHR/Canada ; PJT-156261//CIHR/Canada ; MOP-86683//CIHR/Canada ; }, mesh = {Bacillus subtilis/*genetics ; Bacterial Proteins/metabolism/*physiology ; Base Composition/physiology ; Base Sequence ; *Gene Expression Regulation, Bacterial ; Gene Silencing ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial ; Mutant Proteins/genetics/metabolism ; Protein Domains ; Repetitive Sequences, Nucleic Acid ; Repressor Proteins/chemistry/metabolism/*physiology ; }, abstract = {Bacterial xenogeneic silencers play important roles in bacterial evolution by recognizing and inhibiting expression from foreign genes acquired through horizontal gene transfer, thereby buffering against potential fitness consequences of their misregulated expression. Here, the detailed DNA binding properties of Rok, a xenogeneic silencer in Bacillus subtilis, was studied using protein binding microarray, and the solution structure of its C-terminal DNA binding domain was determined in complex with DNA. The C-terminal domain of Rok adopts a typical winged helix fold, with a novel DNA recognition mechanism different from other winged helix proteins or xenogeneic silencers. Rok binds the DNA minor groove by forming hydrogen bonds to bases through N154, T156 at the N-terminal of α3 helix and R174 of wing W1, assisted by four lysine residues interacting electrostatically with DNA backbone phosphate groups. These structural features endow Rok with preference towards DNA sequences harboring AACTA, TACTA, and flexible multiple TpA steps, while rigid A-tracts are disfavored. Correspondingly, the Bacillus genomes containing Rok are rich in A-tracts and show a dramatic underrepresentation of AACTA and TACTA, which are significantly enriched in Rok binding regions. These observations suggest that the xenogeneic silencing protein and its resident genome may have evolved cooperatively.}, }
@article {pmid30252055, year = {2019}, author = {Gauthier, L and Dortet, L and Jousset, AB and Mihaila, L and Golse, N and Naas, T and Bonnin, RA}, title = {Molecular characterization of plasmid-encoded Tripoli MBL 1 (TMB-1) in Enterobacteriaceae.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {74}, number = {1}, pages = {42-47}, doi = {10.1093/jac/dky372}, pmid = {30252055}, issn = {1460-2091}, mesh = {Bile/microbiology ; Carbapenem-Resistant Enterobacteriaceae/genetics/*isolation &amp; purification ; Carbapenems/pharmacology ; Cephalosporins/pharmacology ; Citrobacter freundii/enzymology/genetics/*isolation &amp; purification ; Conjugation, Genetic ; Enterobacter/enzymology/genetics/*isolation &amp; purification ; Enterobacteriaceae Infections/*microbiology ; Escherichia coli/drug effects/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Plasmids/analysis ; Rectum/microbiology ; Whole Genome Sequencing ; beta-Lactam Resistance ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: Available commercial tools (molecular methods or immunochromatographic assays) usually allow the detection of the five most prevalent carbapenemases (KPC, NDM, VIM, IMP and OXA-48-like), but miss minor carbapenemases. Here, we characterize two enterobacterial isolates with reduced susceptibility to carbapenems and negative for the most commonly encountered carbapenemase genes.<br><br>METHODS: Enterobacter hormaechei and Citrobacter freundii isolates were recovered from a bile sample and rectal screening, respectively. Both isolates were investigated by WGS. Resistance genes were detected using ResFinder. The blaTMB-1-harbouring plasmid was reconstructed using CLC genomic workbench 10.0 and was annotated using the RAST tool. Transfer frequency was determined by conjugation experiments using the laboratory strain Escherichia coli J53.<br><br>RESULTS: The two isolates were resistant to broad-spectrum cephalosporins and carbapenems. WGS revealed the presence of blaTMB-1, which has previously only been described in non-fermenters. blaTMB-1 was located within an ISKpn19-based composite class 1 transposon. Comparative genomics revealed that this structure was carried on a conjugative IncN-type plasmid within an integration hotspot. Conjugation experiments revealed high transfer frequencies of &#x223c;1&#x205f;&#xd7;&#x205f;10-3.<br><br>CONCLUSIONS: To the best of our knowledge, this study corresponds to the first report of Tripoli MBL 1-producing Enterobacteriaceae. Despite always being described as likely to be chromosomally located in non-fermenters, the blaTMB-1 gene is now found to be carried by a conjugative plasmid among Enterobacteriaceae, raising concern about the possible dissemination of this carbapenemase. The blaTMB-1 gene should now be suspected when PCRs targeting the main carbapenemases remain negative.}, }
@article {pmid30250458, year = {2018}, author = {Radford, D and Strange, P and Lepp, D and Hernandez, M and Rehman, MA and Diarra, MS and Balamurugan, S}, title = {Genomic and Proteomic Analyses of Salmonella enterica Serovar Enteritidis Identifying Mechanisms of Induced de novo Tolerance to Ceftiofur.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2123}, pmid = {30250458}, issn = {1664-302X}, abstract = {With the alarming proliferation of antibiotic resistance, it is important to understand the de novo development of bacterial adaptation to antibiotics in formerly susceptible lineages, in the absence of external genetic input from existing resistance pools. A strain of ceftiofur susceptible Salmonella enterica serovar Enteritidis ABB07-SB3071 (MIC = 1.0 μg/ml) was successively exposed to sub-MIC of ceftiofur to allow its adaptation for tolerance to a concentration of 2.0 μg/ml of this antibiotic. Genomic and proteomic comparative analyses of the parental strain and induced tolerant derived lineages were performed to characterize underlying mechanisms of de novo adaptation (tolerance). Expression and localization of specific drug-, heme-, sugar-, amino acid-, and sulfate-transporters were altered, as was the localization of the cell membrane stabilizing protein OsmY in the tolerant strains adapted to 2.0 μg/ml compared to the parental isolate lines. This redistribution of existing transporters acts to minimize the concentrations of ceftiofur in the periplasm, by decreasing facilitated import and increasing active efflux and cytosolic sequestration as determined by high performance liquid chromatography quantification of residual total and extracellular ceftiofur after growth. Genetic, subcellular localization, and abundance changes of specific regulators of transcription, translation, and post-translational dynamics in the derived ceftiofur tolerant lineages decrease metabolic strain on cell walls and enhance periplasmic envelop stability against stress. This produces slower growing, more tolerant populations, which deplete free ceftiofur concentrations significantly more than susceptible parental populations (P < 0.05), as measured by recoverable levels of ceftiofur from cultures of equivalent cellular density incubated with equal ceftiofur concentrations. Genetic and abundance changes to specific carbon and nitrogen metabolism enzymes, not traditionally associated with beta-lactam metabolism, establish an enzymatic framework with the potential to detoxify/degrade ceftiofur, while mutations and changes in subcellular localization in specific cell surface factors enhance the stability of the Gram-negative cell envelop despite the compromising effect of ceftiofur. The observed changes highlight generalizable mechanisms of de novo tolerance without horizontal gene transfer, and thus can inform policies to combat antibiotic tolerance and minimize induction of de novo tolerance.}, }
@article {pmid30250154, year = {2018}, author = {Roger, AJ and Susko, E}, title = {Molecular clocks provide little information to date methanogenic Archaea.}, journal = {Nature ecology &amp; evolution}, volume = {2}, number = {11}, pages = {1676-1677}, pmid = {30250154}, issn = {2397-334X}, mesh = {Archaea/*genetics ; *Gene Transfer, Horizontal ; Phylogeny ; Soil Microbiology ; }, }
@article {pmid30250051, year = {2019}, author = {Ju, F and Beck, K and Yin, X and Maccagnan, A and McArdell, CS and Singer, HP and Johnson, DR and Zhang, T and Bürgmann, H}, title = {Wastewater treatment plant resistomes are shaped by bacterial composition, genetic exchange, and upregulated expression in the effluent microbiomes.}, journal = {The ISME journal}, volume = {13}, number = {2}, pages = {346-360}, pmid = {30250051}, issn = {1751-7370}, mesh = {Anti-Bacterial Agents/analysis ; Bacteria/drug effects/genetics/metabolism ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Metagenome ; Metagenomics ; *Microbiota ; Transcriptome ; Up-Regulation ; Waste Disposal, Fluid ; Wastewater/chemistry/*microbiology ; }, abstract = {Wastewater treatment plants (WWTPs) are implicated as hotspots for the dissemination of antibacterial resistance into the environment. However, the in situ processes governing removal, persistence, and evolution of resistance genes during wastewater treatment remain poorly understood. Here, we used quantitative metagenomic and metatranscriptomic approaches to achieve a broad-spectrum view of the flow and expression of genes related to antibacterial resistance to over 20 classes of antibiotics, 65 biocides, and 22 metals. All compartments of 12 WWTPs share persistent resistance genes with detectable transcriptional activities that were comparatively higher in the secondary effluent, where mobility genes also show higher relative abundance and expression ratios. The richness and abundance of resistance genes vary greatly across metagenomes from different treatment compartments, and their relative and absolute abundances correlate with bacterial community composition and biomass concentration. No strong drivers of resistome composition could be identified among the chemical stressors analyzed, although the sub-inhibitory concentration (hundreds of ng/L) of macrolide antibiotics in wastewater correlates with macrolide and vancomycin resistance genes. Contig-based analysis shows considerable co-localization between resistance and mobility genes and implies a history of substantial horizontal resistance transfer involving human bacterial pathogens. Based on these findings, we propose future inclusion of mobility incidence (M%) and host pathogenicity of antibiotic resistance genes in their quantitative health risk ranking models with an ultimate goal to assess the biological significance of wastewater resistomes with regard to disease control in humans or domestic livestock.}, }
@article {pmid30249706, year = {2018}, author = {Afonina, I and Lim, XN and Tan, R and Kline, KA}, title = {Planktonic Interference and Biofilm Alliance between Aggregation Substance and Endocarditis- and Biofilm-Associated Pili in Enterococcus faecalis.}, journal = {Journal of bacteriology}, volume = {200}, number = {24}, pages = {}, pmid = {30249706}, issn = {1098-5530}, mesh = {Adhesins, Bacterial/*genetics/*metabolism ; Bacterial Adhesion ; Bacterial Proteins/genetics/metabolism ; Bacteriological Techniques ; Biofilms/growth &amp; development ; Endocarditis, Bacterial/microbiology ; Enterococcus faecalis/growth &amp; development/metabolism/*physiology ; Gene Transfer, Horizontal ; Humans ; Pheromones/pharmacology ; }, abstract = {Like many bacteria, Enterococcus faecalis encodes a number of adhesins involved in colonization or infection of different niches. Two well-studied E. faecalis adhesins, aggregation substance (AS) and endocarditis- and biofilm-associated pili (Ebp), both contribute to biofilm formation on abiotic surfaces and in endocarditis, suggesting that they may be expressed at the same time. Because different regulatory pathways have been reported for AS and Ebp, here, we examined if they are coexpressed on the same cells and what is the functional impact of coexpression on individual cells and within a population. We found that while Ebp are only expressed on a subset of cells, when Ebp and AS are expressed on the same cells, pili interfere with AS-mediated clumping and impede AS-mediated conjugative plasmid transfer during planktonic growth. However, when the population density increases, horizontal gene transfer rates normalize and are no longer affected by pilus expression. Instead, at higher cell densities during biofilm formation, Ebp and AS differentially contribute to biofilm development and structure, synergizing to promote maximal biofilm formation.IMPORTANCE Most bacteria express multiple adhesins that contribute to surface attachment and colonization. However, the network and relationships between the various adhesins of a single bacterial species are less well understood. Here, we examined two well-characterized adhesins in Enterococcus faecalis, aggregation substance and endocarditis- and biofilm-associated pili, and found that they exhibit distinct functional contributions depending on the growth stage of the bacterial community. Pili interfere with aggregation substance-mediated clumping and plasmid transfer under planktonic conditions, whereas the two adhesins structurally complement one another during biofilm development. This study advances our understanding of how E. faecalis, a ubiquitous member of the human gut microbiome and an opportunistic pathogen, uses multiple surface structures to evolve and thrive.}, }
@article {pmid30249685, year = {2018}, author = {Decraene, V and Phan, HTT and George, R and Wyllie, DH and Akinremi, O and Aiken, Z and Cleary, P and Dodgson, A and Pankhurst, L and Crook, DW and Lenney, C and Walker, AS and Woodford, N and Sebra, R and Fath-Ordoubadi, F and Mathers, AJ and Seale, AC and Guiver, M and McEwan, A and Watts, V and Welfare, W and Stoesser, N and Cawthorne, J and , }, title = {A Large, Refractory Nosocomial Outbreak of Klebsiella pneumoniae Carbapenemase-Producing Escherichia coli Demonstrates Carbapenemase Gene Outbreaks Involving Sink Sites Require Novel Approaches to Infection Control.}, journal = {Antimicrobial agents and chemotherapy}, volume = {62}, number = {12}, pages = {}, pmid = {30249685}, issn = {1098-6596}, support = {HPRU-2012-10041//Department of Health/United Kingdom ; }, mesh = {Cross Infection/drug therapy/*epidemiology/microbiology/transmission ; DNA, Bacterial/genetics ; *Disease Outbreaks ; Disease Reservoirs/microbiology ; Escherichia coli/drug effects/*genetics/isolation &amp; purification/pathogenicity ; Escherichia coli Infections/drug therapy/*epidemiology/microbiology/transmission ; Gene Expression ; Gene Transfer, Horizontal ; Genotype ; Hospitals, University ; Humans ; Infection Control/methods ; Klebsiella pneumoniae/*genetics/pathogenicity ; Medical Waste ; Phylogeny ; Prevalence ; United Kingdom/epidemiology ; Wastewater/microbiology ; beta-Lactamases/*genetics ; }, abstract = {Carbapenem-resistant Enterobacteriaceae (CRE) represent a health threat, but effective control interventions remain unclear. Hospital wastewater sites are increasingly being highlighted as important potential reservoirs. We investigated a large Klebsiella pneumoniae carbapenemase (KPC)-producing Escherichia coli outbreak and wider CRE incidence trends in the Central Manchester University Hospital NHS Foundation Trust (CMFT) (United Kingdom) over 8 years, to determine the impact of infection prevention and control measures. Bacteriology and patient administration data (2009 to 2017) were linked, and a subset of CMFT or regional hospital KPC-producing E. coli isolates (n = 268) were sequenced. Control interventions followed international guidelines and included cohorting, rectal screening (n = 184,539 screens), environmental sampling, enhanced cleaning, and ward closure and plumbing replacement. Segmented regression of time trends for CRE detections was used to evaluate the impact of interventions on CRE incidence. Genomic analysis (n = 268 isolates) identified the spread of a KPC-producing E. coli outbreak clone (strain A, sequence type 216 [ST216]; n = 125) among patients and in the environment, particularly on 2 cardiac wards (wards 3 and 4), despite control measures. ST216 strain A had caused an antecedent outbreak and shared its KPC plasmids with other E. coli lineages and Enterobacteriaceae species. CRE acquisition incidence declined after closure of wards 3 and 4 and plumbing replacement, suggesting an environmental contribution. However, ward 3/ward 4 wastewater sites were rapidly recolonized with CRE and patient CRE acquisitions recurred, albeit at lower rates. Patient relocation and plumbing replacement were associated with control of a clonal KPC-producing E. coli outbreak; however, environmental contamination with CRE and patient CRE acquisitions recurred rapidly following this intervention. The large numbers of cases and the persistence of blaKPC in E. coli, including pathogenic lineages, are of concern.}, }
@article {pmid30249179, year = {2018}, author = {Stocchi, N and Revuelta, MV and Castronuovo, PAL and Vera, DMA and Ten Have, A}, title = {Molecular dynamics and structure function analysis show that substrate binding and specificity are major forces in the functional diversification of Eqolisins.}, journal = {BMC bioinformatics}, volume = {19}, number = {1}, pages = {338}, pmid = {30249179}, issn = {1471-2105}, support = {PICT2013-2296//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; }, mesh = {Amino Acid Sequence ; Amino Acid Substitution/genetics ; Aspartic Acid Endopeptidases/*chemistry/genetics/*metabolism ; Bayes Theorem ; Binding Sites ; Conserved Sequence ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Glycine/chemistry ; Models, Molecular ; *Molecular Dynamics Simulation ; Mutation/genetics ; Phylogeny ; Protein Structure, Secondary ; Sequence Homology, Amino Acid ; Structure-Activity Relationship ; Substrate Specificity ; Thermodynamics ; }, abstract = {BACKGROUND: Eqolisins are rare acid proteases found in archaea, bacteria and fungi. Certain fungi secrete acids as part of their lifestyle and interestingly these also have many eqolisin paralogs, up to nine paralogs have been recorded. This suggests a process of functional redundancy and diversification has occurred, which was the subject of the research we performed and describe here.<br><br>RESULTS: We identified eqolisin homologs by means of iterative HMMER analysis of the NR database. The identified sequences were scrutinized for which new hallmarks were identified by molecular dynamics simulations of mutants in highly conserved positions, using the structure of an eqolisin that was crystallized in the presence of a transition state inhibitor. Four conserved glycines were shown to be important for functionality. A substitution of W67F is shown to be accompanied by the L105W substitution. Molecular dynamics shows that the W67 binds to the substrate via a &#x3c0;-&#x3c0; stacking and a salt bridge, the latter being stronger in a virtual W67F/L105W double mutant of the resolved structure of Scytalido-carboxyl peptidase-B (PDB ID: 2IFW). Additional problematic mutations are discussed. Upon sequence scrutiny we obtained a set of 233 sequences that was used to reconstruct a Bayesian phylogenetic tree. We identified 14 putative specificity determining positions (SDPs) of which four are explained by mere structural explanations and nine seem to correspond to functional diversification related with substrate binding and specificity. A first sub-network of SDPs is related to substrate specificity whereas the second sub-network seems to affect the dynamics of three loops that are involved in substrate binding.<br><br>CONCLUSION: The eqolisins form a small superfamily of acid proteases with nevertheless many paralogs in acidic fungi. Functional redundancy has resulted in diversification related to substrate specificity and substrate binding.}, }
@article {pmid30248271, year = {2019}, author = {Lerminiaux, NA and Cameron, ADS}, title = {Horizontal transfer of antibiotic resistance genes in clinical environments.}, journal = {Canadian journal of microbiology}, volume = {65}, number = {1}, pages = {34-44}, doi = {10.1139/cjm-2018-0275}, pmid = {30248271}, issn = {1480-3275}, mesh = {Conjugation, Genetic ; Drug Resistance, Microbial/*genetics ; *Gene Transfer, Horizontal ; Humans ; Plasmids ; Transduction, Genetic ; Transformation, Genetic ; }, abstract = {A global medical crisis is unfolding as antibiotics lose effectiveness against a growing number of bacterial pathogens. Horizontal gene transfer (HGT) contributes significantly to the rapid spread of resistance, yet the transmission dynamics of genes that confer antibiotic resistance are poorly understood. Multiple mechanisms of HGT liberate genes from normal vertical inheritance. Conjugation by plasmids, transduction by bacteriophages, and natural transformation by extracellular DNA each allow genetic material to jump between strains and species. Thus, HGT adds an important dimension to infectious disease whereby an antibiotic resistance gene (ARG) can be the agent of an outbreak by transferring resistance to multiple unrelated pathogens. Here, we review the small number of cases where HGT has been detected in clinical environments. We discuss differences and synergies between the spread of plasmid-borne and chromosomal ARGs, with a special consideration of the difficulties of detecting transduction and transformation by routine genetic diagnostics. We highlight how 11 of the top 12 priority antibiotic-resistant pathogens are known or predicted to be naturally transformable, raising the possibility that this mechanism of HGT makes significant contributions to the spread of ARGs. HGT drives the evolution of untreatable "superbugs" by concentrating ARGs together in the same cell, thus HGT must be included in strategies to prevent the emergence of resistant organisms in hospitals and other clinical settings.}, }
@article {pmid30245567, year = {2018}, author = {Kalesinskas, L and Cudone, E and Fofanov, Y and Putonti, C}, title = {S-plot2: Rapid Visual and Statistical Analysis of Genomic Sequences.}, journal = {Evolutionary bioinformatics online}, volume = {14}, number = {}, pages = {1176934318797354}, pmid = {30245567}, issn = {1176-9343}, abstract = {With the daily release of data from whole genome sequencing projects, tools to facilitate comparative studies are hard-pressed to keep pace. Graphical software solutions can readily recognize synteny by measuring similarities between sequences. Nevertheless, regions of dissimilarity can prove to be equally informative; these regions may harbor genes acquired via lateral gene transfer (LGT), signify gene loss or gain, or include coding regions under strong selection. Previously, we developed the software S-plot. This tool employed an alignment-free approach for comparing bacterial genomes and generated a heatmap representing the genomes' similarities and dissimilarities in nucleotide usage. In prior studies, this tool proved valuable in identifying genome rearrangements as well as exogenous sequences acquired via LGT in several bacterial species. Herein, we present the next generation of this tool, S-plot2. Similar to its predecessor, S-plot2 creates an interactive, 2-dimensional heatmap capturing the similarities and dissimilarities in nucleotide usage between genomic sequences (partial or complete). This new version, however, includes additional metrics for analysis, new reporting options, and integrated BLAST query functionality for the user to interrogate regions of interest. Furthermore, S-plot2 can evaluate larger sequences, including whole eukaryotic chromosomes. To illustrate some of the applications of the tool, 2 case studies are presented. The first examines strain-specific variation across the Pseudomonas aeruginosa genome and strain-specific LGT events. In the second case study, corresponding human, chimpanzee, and rhesus macaque autosomes were studied and lineage specific contributions to divergence were estimated. S-plot2 provides a means to both visually and quantitatively compare nucleotide sequences, from microbial genomes to eukaryotic chromosomes. The case studies presented illustrate just 2 potential applications of the tool, highlighting its capability to identify and investigate the variation in molecular divergence rates across sequences. S-plot2 is freely available through https://bitbucket.org/lkalesinskas/splot and is supported on the Linux and MS Windows operating systems.}, }
@article {pmid30243983, year = {2018}, author = {Dolejska, M and Papagiannitsis, CC}, title = {Plasmid-mediated resistance is going wild.}, journal = {Plasmid}, volume = {99}, number = {}, pages = {99-111}, doi = {10.1016/j.plasmid.2018.09.010}, pmid = {30243983}, issn = {1095-9890}, mesh = {Animals ; Anti-Bacterial Agents/therapeutic use ; Bacterial Proteins/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal/*genetics ; Gram-Negative Bacteria/drug effects/*genetics/pathogenicity ; Humans ; Plasmids/*genetics ; beta-Lactamases/genetics ; beta-Lactams/therapeutic use ; }, abstract = {Multidrug resistant (MDR) Gram-negative bacteria have been increasingly reported in humans, companion animals and farm animals. The growing trend of plasmid-mediated resistance to antimicrobial classes of critical importance is attributed to the emergence of epidemic plasmids, rapidly disseminating resistance genes among the members of Enterobacteriaceae family. The use of antibiotics to treat humans and animals has had a significant impact on the environment and on wild animals living and feeding in human-influenced habitats. Wildlife can acquire MDR bacteria selected in hospitals, community or livestock from diverse sources, including wastewater, sewage systems, landfills, farm facilities or agriculture fields. Therefore, wild animals are considered indicators of environmental pollution by antibiotic resistant bacteria, but they can also act as reservoirs and vectors spreading antibiotic resistance across the globe. The level of resistance and reported plasmid-mediated resistance mechanisms observed in bacteria of wildlife origin seem to correlate well with the situation described in humans and domestic animals. Additionaly, the identification of epidemic plasmids in samples from different human, animal and wildlife sources underlines the role of horizontal gene transfer in the dissemination of resistance genes. The present review focuses on reports of plasmid-mediated resistance to critically important antimicrobial classes such as broad-spectrum beta-lactams and colistin in Enterobacteriaceae isolates from samples of wildlife origin. The role of plasmids in the dissemination of ESBL-, AmpC- and carbapenemase-encoding genes as well as plasmid-mediated colistin resistance determinants in wildlife are discussed, and their similarities to plasmids previously identified in samples of human clinical or livestock origin are highlighted. Furthermore, we present features of completely sequenced plasmids reported from wildlife Enterobacteriaceae isolates, with special focus on genes that could be associated with the plasticity and stable maintenance of these molecules in antibiotic-free environments.}, }
@article {pmid30243595, year = {2019}, author = {Brusch, GA and DeNardo, DF}, title = {Egg desiccation leads to dehydration and enhanced innate immunity in python embryos.}, journal = {Developmental and comparative immunology}, volume = {90}, number = {}, pages = {147-151}, doi = {10.1016/j.dci.2018.09.013}, pmid = {30243595}, issn = {1879-0089}, mesh = {Animals ; Animals, Newborn ; Boidae/*immunology ; Dehydration ; Desiccation ; Embryo, Nonmammalian ; Energy Metabolism ; Female ; Gene Expression Regulation, Developmental ; Gene Transfer, Horizontal ; Immunity, Innate ; Immunomodulation ; Life Cycle Stages ; *Organism Hydration Status ; Ovum/*physiology ; }, abstract = {The immune system is essential for survival and its performance can vary depending on the physiological state of the organism. Much of the current research into immune function dynamics has examined newborn to adult life stages, despite previous studies documenting physiological responses in embryos to environmental stimuli. While energy balance has been the predominant focus as the driver of changes in immune function, recent research has found a positive relationship between dehydration and innate immune performance in adult reptiles. We expanded the understanding of this relationship by examining trans-generational immune effects of female dehydration as well as the effects of egg desiccation on embryonic hydration state and innate immunity using Children's pythons, Antaresia childreni. We used a 2 × 2 experiment with hydrated or dehydrated mothers and eggs either incubated under continuous optimal conditions or experiencing desiccating conditions for 24 h. Our results demonstrate that, similar to adults, embryos enhance some metrics of innate immunity when they are dehydrated.}, }
@article {pmid30243525, year = {2019}, author = {Gagetti, P and Bonofiglio, L and García Gabarrot, G and Kaufman, S and Mollerach, M and Vigliarolo, L and von Specht, M and Toresani, I and Lopardo, HA}, title = {Resistance to β-lactams in enterococci.}, journal = {Revista Argentina de microbiologia}, volume = {51}, number = {2}, pages = {179-183}, doi = {10.1016/j.ram.2018.01.007}, pmid = {30243525}, issn = {0325-7541}, mesh = {Drug Resistance, Bacterial ; Enterococcus/*drug effects ; Gram-Positive Bacterial Infections/drug therapy ; Humans ; Lactobacillales ; Microbial Sensitivity Tests ; beta-Lactams/*pharmacology/therapeutic use ; }, abstract = {Enterococci are intrinsically resistant to several antimicrobial classes and show a great ability to acquire new mechanisms of resistance. Resistance to β-lactam antibiotics is a major concern because these drugs either alone or in combination are commonly used for the treatment of enterococcal infections. Ampicillin resistance, which is rare in Enterococcus faecalis, occurs in most of the hospital-associated Enterococcus faecium isolates. High-level resistance to ampicillin in E. faecium is mainly due to the enhanced production of PBP5 and/or by polymorphisms in the beta subunit of this protein. The dissemination of high-level ampicillin resistance can be the result of both clonal spread of strains with mutated pbp5 genes and horizontal gene transfer.}, }
@article {pmid30242003, year = {2018}, author = {Zeng, X and Wu, Z and Zhang, Q and Lin, J}, title = {A Cotransformation Method To Identify a Restriction-Modification Enzyme That Reduces Conjugation Efficiency in Campylobacter jejuni.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {23}, pages = {}, pmid = {30242003}, issn = {1098-5336}, support = {R21 AI119462/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/*metabolism ; Campylobacter jejuni/*enzymology/*genetics/metabolism ; *Conjugation, Genetic ; DNA Restriction-Modification Enzymes/genetics/*metabolism ; DNA, Bacterial/genetics ; Endonucleases/genetics/*metabolism ; Transformation, Bacterial ; }, abstract = {Conjugation is an important mechanism for horizontal gene transfer in Campylobacter jejuni, the leading cause of human bacterial gastroenteritis in developed countries. However, to date, the factors that significantly influence conjugation efficiency in Campylobacter spp. are still largely unknown. Given that multiple recombinant loci could independently occur within one recipient cell during natural transformation, the genetic materials from a high-frequency conjugation (HFC) C. jejuni strain may be cotransformed with a selection marker into a low-frequency conjugation (LFC) recipient strain, creating new HFC transformants suitable for the identification of conjugation factors using a comparative genomics approach. To test this, an erythromycin resistance selection marker was created in an HFC C. jejuni strain; subsequently, the DNA of this strain was naturally transformed into NCTC 11168, an LFC C. jejuni strain, leading to the isolation of NCTC 11168-derived HFC transformants. Whole-genome sequencing analysis and subsequent site-directed mutagenesis identified Cj1051c, a putative restriction-modification enzyme (aka CjeI) that could drastically reduce the conjugation efficiency of NCTC 11168 (>5,000-fold). Chromosomal complementation of three diverse HFC C. jejuni strains with CjeI also led to a dramatic reduction in conjugation efficiency (∼1,000-fold). The purified recombinant CjeI could effectively digest the Escherichia coli-derived shuttle vector pRY107. The endonuclease activity of CjeI was abolished upon short heat shock treatment at 50°C, which is consistent with our previous observation that heat shock enhanced conjugation efficiency in C. jejuni Together, in this study, we successfully developed and utilized a unique cotransformation strategy to identify a restriction-modification enzyme that significantly influences conjugation efficiency in C. jejuniIMPORTANCE Conjugation is an important horizontal gene transfer mechanism contributing to the evolution of bacterial pathogenesis and antimicrobial resistance. Campylobacter jejuni, the leading foodborne bacterial organism, displays significant strain diversity due to horizontal gene transfer; however, the molecular components influencing conjugation efficiency in C. jejuni are still largely unknown. In this study, we developed a cotransformation strategy for comparative genomics analysis and successfully identified a restriction-modification enzyme that significantly influences conjugation efficiency in C. jejuni The new cotransformation strategy developed in this study is also expected to be broadly applied in other naturally competent bacteria for functional comparative genomics research.}, }
@article {pmid30240700, year = {2018}, author = {Gama, JA and Zilhão, R and Dionisio, F}, title = {Impact of plasmid interactions with the chromosome and other plasmids on the spread of antibiotic resistance.}, journal = {Plasmid}, volume = {99}, number = {}, pages = {82-88}, doi = {10.1016/j.plasmid.2018.09.009}, pmid = {30240700}, issn = {1095-9890}, mesh = {Bacteria/drug effects/genetics/pathogenicity ; Chromosomes, Bacterial/*genetics ; Conjugation, Genetic ; Drug Resistance, Bacterial/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Humans ; Plasmids/*genetics ; }, abstract = {Naturally occurring plasmids have medical importance given that they frequently code for virulence or antibiotic resistance. In many cases, plasmids impose a fitness cost to their hosts, meaning that the growth rate of plasmid-bearing cells is lower than that of plasmid-free cells. However, this does not fit with the fact that plasmids are ubiquitous in nature nor that plasmids and their hosts adapt to each other very fast - as has been shown in laboratory evolutionary assays. Even when plasmids are costly, they seem to largely interact in such a way that the cost of two plasmids is lower than the cost of one of them alone. Moreover, it has been argued that transfer rates are too low to compensate for plasmid costs and segregation. Several mechanisms involving interactions between plasmids and other replicons could overcome this limitation, hence contributing to the maintenance of plasmids in bacterial populations. We examine the importance of these mechanisms from a clinical point of view, particularly the spread of antibiotic resistance genes.}, }
@article {pmid30239714, year = {2018}, author = {Goryanin, II and Kudryavtseva, AA and Balabanov, VP and Biryukova, VS and Manukhov, IV and Zavilgelsky, GB}, title = {Antirestriction activities of KlcA (RP4) and ArdB (R64) proteins.}, journal = {FEMS microbiology letters}, volume = {365}, number = {23}, pages = {}, doi = {10.1093/femsle/fny227}, pmid = {30239714}, issn = {1574-6968}, mesh = {Amino Acid Sequence ; Bacterial Proteins/*antagonists &amp; inhibitors/genetics ; Conserved Sequence ; DNA Restriction Enzymes/*antagonists &amp; inhibitors ; Enzyme Inhibitors/*metabolism ; Escherichia coli/enzymology/genetics ; *Gene Transfer, Horizontal ; Klebsiella pneumoniae/enzymology/genetics ; *Plasmids ; Sequence Homology, Amino Acid ; }, abstract = {Antirestriction proteins of the ArdB group (ArdB, KlcA) specifically inhibit restriction (endonuclease) activity of restriction-modification (RM) type I systems. Antirestriction activity of KlcA and ArdB, encoded in transmissible plasmids RP4 (IncPα) and R64 (IncI1), respectively, has been determined. We show that the protein KlcA (RP4), an amino acid sequence identical to that of the protein KlcA (RK2), inhibits the activity of EcoKI when the klcA gene is located on the plasmid under the control of strong promoter. It was demonstrated that proteins KlcA (RP4) and ArdB (R64) are characterized by approximately equal antirestriction activity. Analysis of amino acid sequences of ArdB homologs revealed four groups of conserved amino acids located on the surface of the protein globule: (1) R16, E32, W51; (2) Y46, G48; (3) S84, D86, E132 and (4) N77, L140, D141. It was shown that substitution of polar amino acids to hydrophobic A and L leads to a significant decrease in the ArdB antirestriction activity level (approximately 100-fold). A conserved region forming a 'ring belt' on the globule surface consisting of E32, S84, E132, and both N77 and D141 as the 'key section' of ArdB/KlcA was identified.}, }
@article {pmid30239713, year = {2018}, author = {Haverkamp, THA and Geslin, C and Lossouarn, J and Podosokorskaya, OA and Kublanov, I and Nesbø, CL}, title = {Thermosipho spp. Immune System Differences Affect Variation in Genome Size and Geographical Distributions.}, journal = {Genome biology and evolution}, volume = {10}, number = {11}, pages = {2853-2866}, pmid = {30239713}, issn = {1759-6653}, mesh = {Bacteria/*genetics/immunology ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Hydrothermal Vents/*microbiology ; Oil and Gas Fields/*microbiology ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Thermosipho species inhabit thermal environments such as marine hydrothermal vents, petroleum reservoirs, and terrestrial hot springs. A 16S rRNA phylogeny of available Thermosipho spp. sequences suggested habitat specialists adapted to living in hydrothermal vents only, and habitat generalists inhabiting oil reservoirs, hydrothermal vents, and hotsprings. Comparative genomics of 15 Thermosipho genomes separated them into three distinct species with different habitat distributions: The widely distributed T. africanus and the more specialized, T. melanesiensis and T. affectus. Moreover, the species can be differentiated on the basis of genome size (GS), genome content, and immune system composition. For instance, the T. africanus genomes are largest and contained the most carbohydrate metabolism genes, which could explain why these isolates were obtained from ecologically more divergent habitats. Nonetheless, all the Thermosipho genomes, like other Thermotogae genomes, show evidence of genome streamlining. GS differences between the species could further be correlated to differences in defense capacities against foreign DNA, which influence recombination via HGT. The smallest genomes are found in T. affectus that contain both CRISPR-cas Type I and III systems, but no RM system genes. We suggest that this has caused these genomes to be almost devoid of mobile elements, contrasting the two other species genomes that contain a higher abundance of mobile elements combined with different immune system configurations. Taken together, the comparative genomic analyses of Thermosipho spp. revealed genetic variation allowing habitat differentiation within the genus as well as differentiation with respect to invading mobile DNA.}, }
@article {pmid30237794, year = {2018}, author = {Sun, D}, title = {Pull in and Push Out: Mechanisms of Horizontal Gene Transfer in Bacteria.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2154}, pmid = {30237794}, issn = {1664-302X}, abstract = {Horizontal gene transfer (HGT) plays an important role in bacterial evolution. It is well accepted that DNA is pulled/pushed into recipient cells by conserved membrane-associated DNA transport systems, which allow the entry of only single-stranded DNA (ssDNA). However, recent studies have uncovered a new type of natural bacterial transformation in which double-stranded DNA (dsDNA) is taken up into the cytoplasm, thus complementing the existing methods of DNA transfer among bacteria. Regulated by the stationary-phase regulators RpoS and cAMP receptor protein (CRP), Escherichia coli establishes competence for natural transformation with dsDNA, which occurs in agar plates. To pass across the outer membrane, a putative channel, which may compete for the substrate with the porin OmpA, may mediate the transfer of exogenous dsDNA into the cell. To pass across the inner membrane, dsDNA may be bound to the periplasmic protein YdcS, which delivers it into the inner membrane channel formed by YdcV. The discovery of cell-to-cell contact-dependent plasmid transformation implies the presence of additional mechanism(s) of transformation. This review will summarize the current knowledge about mechanisms of HGT with an emphasis on recent progresses regarding non-canonical mechanisms of natural transformation. Fully understanding the mechanisms of HGT will provide a foundation for monitoring and controlling multidrug resistance.}, }
@article {pmid30237791, year = {2018}, author = {Chelkha, N and Levasseur, A and Pontarotti, P and Raoult, D and Scola, B and Colson, P}, title = {A Phylogenomic Study of Acanthamoeba polyphaga Draft Genome Sequences Suggests Genetic Exchanges With Giant Viruses.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2098}, pmid = {30237791}, issn = {1664-302X}, abstract = {Acanthamoeba are ubiquitous phagocytes predominant in soil and water which can ingest many microbes. Giant viruses of amoebae are listed among the Acanthamoeba-resisting microorganisms. Their sympatric lifestyle within amoebae is suspected to promote lateral nucleotide sequence transfers. Some Acanthamoeba species have shown differences in their susceptibility to giant viruses. Until recently, only the genome of a single Acanthamoeba castellanii Neff was available. We analyzed the draft genome sequences of Acanthamoeba polyphaga through several approaches, including comparative genomics, phylogeny, and sequence networks, with the aim of detecting putative nucleotide sequence exchanges with giant viruses. We identified a putative sequence trafficking between this Acanthamoeba species and giant viruses, with 366 genes best matching with viral genes. Among viruses, Pandoraviruses provided the greatest number of best hits with 117 (32%) for A. polyphaga. Then, genes from mimiviruses, Mollivirus sibericum, marseilleviruses, and Pithovirus sibericum were best hits in 67 (18%), 35 (9%), 24 (7%), and 2 (0.5%) cases, respectively. Phylogenetic reconstructions showed in a few cases that the most parsimonious evolutionary scenarios were a transfer of gene sequences from giant viruses to A. polyphaga. Nevertheless, in most cases, phylogenies were inconclusive regarding the sense of the sequence flow. The number and nature of putative nucleotide sequence transfers between A. polyphaga, and A. castellanii ATCC 50370 on the one hand, and pandoraviruses, mimiviruses and marseilleviruses on the other hand were analyzed. The results showed a lower number of differences within the same giant viral family compared to between different giant virus families. The evolution of 10 scaffolds that were identified among the 14 Acanthamoeba sp. draft genome sequences and that harbored ≥ 3 genes best matching with viruses showed a conservation of these scaffolds and their 46 viral genes in A. polyphaga, A. castellanii ATCC 50370 and A. pearcei. In contrast, the number of conserved genes decreased for other Acanthamoeba species, and none of these 46 genes were present in three of them. Overall, this work opens up several potential avenues for future studies on the interactions between Acanthamoeba species and giant viruses.}, }
@article {pmid30236952, year = {2018}, author = {Bender, JK and Fleige, C and Lange, D and Klare, I and Werner, G}, title = {Rapid emergence of highly variable and transferable oxazolidinone and phenicol resistance gene optrA in German Enterococcus spp. clinical isolates.}, journal = {International journal of antimicrobial agents}, volume = {52}, number = {6}, pages = {819-827}, doi = {10.1016/j.ijantimicag.2018.09.009}, pmid = {30236952}, issn = {1872-7913}, mesh = {Anti-Infective Agents/*pharmacology ; Chloramphenicol/pharmacology ; Conjugation, Genetic ; *Drug Resistance, Bacterial ; Enterococcus faecalis/classification/*drug effects/genetics/isolation &amp; purification ; Enterococcus faecium/classification/*drug effects/genetics/isolation &amp; purification ; Gene Order ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genetic Variation ; Germany ; Gram-Positive Bacterial Infections/*microbiology ; Humans ; Interspersed Repetitive Sequences ; Oxazolidinones/*pharmacology ; Polymerase Chain Reaction ; Retrospective Studies ; Whole Genome Sequencing ; }, abstract = {The number of linezolid-resistant Enterococcus spp. isolates received by the National Reference Centre for Staphylococci and Enterococci in Germany has been increasing since 2011. Although the majority are E. faecium, clinical linezolid-resistant E. faecalis have also been isolated. With respect to the newly discovered linezolid resistance protein OptrA, the authors conducted a retrospective polymerase chain reaction screening of 698 linezolid-resistant enterococcus clinical isolates. That yielded 43 optrA-positive strains, of which a subset was analysed by whole-genome sequencing in order to infer linezolid resistance-associated mechanisms and phylogenetic relatedness, and to disclose optrA genetic environments. Multiple optrA variants were detected. The originally described variant from China (optrAWT) was the only variant shared between the two Enterococcus spp.; however, distinct optrAWT loci were detected for E. faecium and E. faecalis. Generally, optrA localized to a plethora of genetic backgrounds that differed even for identical optrA variants. This suggests transmission of a mobile genetic element harbouring the resistance locus. Additionally, identical optrA variants detected on presumably identical plasmids, that were present in unrelated strains, indicates dissemination of the entire optrA-containing plasmid. In accordance, in vitro conjugation experiments verified transfer of optrA plasmids between enterococci of the same and of different species. In conclusion, multiple optrA variants located on distinct plasmids and mobile genetic elements with the potential for conjugative transfer are supposedly causative for the emergence of optrA-positive enterococci. Hence, rapid dissemination of the resistance determinant under selective pressure imposed by extensive use of last-resort antibiotics in clinical settings could be expected.}, }
@article {pmid30232602, year = {2018}, author = {Jenkins, C}, title = {Enteroaggregative Escherichia coli.}, journal = {Current topics in microbiology and immunology}, volume = {416}, number = {}, pages = {27-50}, doi = {10.1007/82_2018_105}, pmid = {30232602}, issn = {0070-217X}, mesh = {Bacterial Adhesion ; Diarrhea/*microbiology ; Escherichia coli/genetics/*pathogenicity ; Escherichia coli Infections/*microbiology ; Humans ; Virulence Factors/genetics/metabolism ; }, abstract = {Enteroaggregative Escherichia coli (EAEC, formerly known as "EAggEC") cause acute or persistent watery diarrhoea (with or without mucus) in children, predominantly in low-income countries, and are associated with travellers' diarrhoea in children and adults in middle and high income countries. The diverse nature of EAEC is such that not all strains cause disease. Conversely, certain strains of EAEC possess additional virulence determinants associated with the ability to cause severe diarrhoea and other symptoms, which might be life-threatening in vulnerable patients. The EAEC virulence factors described to date are either encoded on the large virulence plasmid of EAEC (plasmid of aggregative adherence) or on pathogenicity islands on the chromosome. Testing of food and faecal samples involves the detection of EAEC-associated traits in the matrix followed by isolation of the organism and confirmation of the presence of EAEC-associated genes using PCR. The variability of the plasmid structure and virulence gene sequences and the possibility that this mobile genetic element may be lost has necessitated the inclusion of chromosomal markers in the molecular screening assays. There is evidence in the literature of foodborne transmission of EAEC, but currently no evidence of a zoonotic reservoir. Fimbriae-mediated adhesion and biofilm formation are likely to be involved in both clinical manifestations of infection and attachment to foodstuffs. Multidrug resistance appears to be common in EAEC and geographically widespread. Whole-genome sequencing has revealed the mosaic genomic structure of EAEC and provided evidence that horizontal gene transfer and recombination are the driving force for acquisition of novel genome features and potentially novel pathogenic mechanisms. This has significant public health implications in terms of the diversity and pathogenesis of EAEC and its ability to colonise and cause disease in the human host.}, }
@article {pmid30232155, year = {2018}, author = {Schneider, AC and Chun, H and Stefanović, S and Baldwin, BG}, title = {Punctuated plastome reduction and host-parasite horizontal gene transfer in the holoparasitic plant genus Aphyllon.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1887}, pages = {}, pmid = {30232155}, issn = {1471-2954}, mesh = {Biological Evolution ; Galium/genetics/*parasitology ; *Gene Transfer, Horizontal ; Genes, Plant ; Genome, Chloroplast/*genetics ; Genome, Mitochondrial ; Orobanchaceae/*genetics ; Phylogeny ; Selection, Genetic ; }, abstract = {Foundational studies of chloroplast genome (plastome) evolution in parasitic plants have focused on broad trends across large clades, particularly among the Orobanchaceae, a species-rich and ecologically diverse family of root parasites. However, the extent to which such patterns and processes of plastome evolution, such as stepwise gene loss following the complete loss of photosynthesis (shift to holoparasitism), are detectable at shallow evolutionary time scale is largely unknown. We used genome skimming to assemble eight chloroplast genomes representing complete taxonomic sampling of Aphyllon sect. Aphyllon, a small clade within the Orobanchaceae that evolved approximately 6 Ma, long after the origin of holoparasitism. We show substantial plastome reduction occurred in the stem lineage, but subsequent change in plastome size, gene content, and structure has been relatively minimal, albeit detectable. This lends additional fine-grained support to existing models of stepwise plastome reduction in holoparasitic plants. Additionally, we report phylogenetic evidence based on an rbcL gene tree and assembled 60+ kb fragments of the Aphyllon epigalium mitochondrial genome indicating host-to-parasite horizontal gene transfers (hpHGT) of several genes originating from the plastome of an ancient Galium host into the mitochondrial genome of a recent common ancestor of A. epigalium Ecologically, this evidence of hpHGT suggests that the host-parasite associations between Galium and A. epigalium have been stable at least since its subspecies diverged hundreds of thousands of years ago.}, }
@article {pmid30231876, year = {2018}, author = {Peng, T and Xu, Y and Zhang, Y}, title = {Comparative genomics of molybdenum utilization in prokaryotes and eukaryotes.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {691}, pmid = {30231876}, issn = {1471-2164}, support = {31771407//National Natural Science Foundation of China/ ; 2015A030313555//Natural Science Foundation of Guangdong Province/ ; }, mesh = {Biological Evolution ; Eukaryota/*genetics/metabolism ; Genomics/*methods ; Metalloproteins/*genetics/metabolism ; Molybdenum/*metabolism ; Phylogeny ; Prokaryotic Cells/*metabolism ; Proteome/*metabolism ; }, abstract = {BACKGROUND: Molybdenum (Mo) is an essential micronutrient for almost all biological systems, which holds key positions in several enzymes involved in carbon, nitrogen and sulfur metabolism. In general, this transition metal needs to be coordinated to a unique pterin, thus forming a prosthetic group named molybdenum cofactor (Moco) at the catalytic sites of molybdoenzymes. The biochemical functions of many molybdoenzymes have been characterized; however, comprehensive analyses of the evolution of Mo metabolism and molybdoproteomes are quite limited.<br><br>RESULTS: In this study, we analyzed almost 5900 sequenced organisms to examine the occurrence of the Mo utilization trait at the levels of Mo transport system, Moco biosynthetic pathway and molybdoproteins in all three domains of life. A global map of Moco biosynthesis and molybdoproteins has been generated, which shows the most detailed understanding of Mo utilization in prokaryotes and eukaryotes so far. Our results revealed that most prokaryotes and all higher eukaryotes utilize Mo whereas many unicellular eukaryotes such as parasites and most yeasts lost the ability to use this metal. By characterizing the molybdoproteomes of all organisms, we found many new molybdoprotein-rich species, especially in bacteria. A variety of new domain fusions were detected for different molybdoprotein families, suggesting the presence of novel proteins that are functionally linked to molybdoproteins or Moco biosynthesis. Moreover, horizontal gene transfer event involving both the Moco biosynthetic pathway and molybdoproteins was identified. Finally, analysis of the relationship between environmental factors and Mo utilization showed new evolutionary trends of the Mo utilization trait.<br><br>CONCLUSIONS: Our data provide new insights into the evolutionary history of Mo utilization in nature.}, }
@article {pmid30225854, year = {2018}, author = {Barth, C and Weiss, MC and Roettger, M and Martin, WF and Unden, G}, title = {Origin and phylogenetic relationships of [4Fe-4S]-containing O2 sensors of bacteria.}, journal = {Environmental microbiology}, volume = {20}, number = {12}, pages = {4567-4586}, doi = {10.1111/1462-2920.14411}, pmid = {30225854}, issn = {1462-2920}, support = {93046//Volkswagen Foundation/International ; 666053//European Research Council/International ; UN 49/18-1//Deutsche Forschungsgemeinschaft/International ; }, mesh = {Bacteria/*metabolism ; *Biological Evolution ; Escherichia coli/metabolism ; Iron-Sulfur Proteins/*metabolism ; Mycobacterium tuberculosis/metabolism ; Oxygen/*metabolism ; Phylogeny ; }, abstract = {The advent of environmental O2 about 2.5 billion years ago forced microbes to metabolically adapt and to develop mechanisms for O2 sensing. Sensing of O2 by [4Fe-4S][2+] to [2Fe-2S][2+] cluster conversion represents an ancient mechanism that is used by FNREc (Escherichia coli), FNRBs (Bacillus subtilis), NreBSa (Staphylococcus aureus) and WhiB3Mt (Mycobacterium tuberculosis). The phylogenetic relationship of these sensors was investigated. FNREc homologues are restricted to the proteobacteria and a few representatives from other phyla. Homologues of FNRBs and NreBSa are located within the bacilli, of WhiB3 within the actinobacteria. Archaea contain no homologues. The data reveal no similarity between the FNREc , FNRBs , NreBSa and WhiB3 sensor families on the sequence and structural levels. These O2 sensor families arose independently in phyla that were already present at the time O2 appeared, their members were subsequently distributed by lateral gene transfer. The chemistry of [4Fe-4S] and [2Fe-2S] cluster formation and interconversion appears to be shared by the sensor protein families. The type of signal output is, however, family specific. The homologues of FNREc and NreBSa vary with regard to the number of Cys residues that coordinate the cluster. It is suggested that the variants derive from lateral gene transfer and gained other functions.}, }
@article {pmid30223892, year = {2018}, author = {Sitaraman, R}, title = {Prokaryotic horizontal gene transfer within the human holobiont: ecological-evolutionary inferences, implications and possibilities.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {163}, pmid = {30223892}, issn = {2049-2618}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; Bacterial Physiological Phenomena ; *Biological Evolution ; *Gene Transfer, Horizontal ; Humans ; *Microbiota ; *Symbiosis ; }, abstract = {The ubiquity of horizontal gene transfer in the living world, especially among prokaryotes, raises interesting and important scientific questions regarding its effects on the human holobiont i.e., the human and its resident bacterial communities considered together as a unit of selection. Specifically, it would be interesting to determine how particular gene transfer events have influenced holobiont phenotypes in particular ecological niches and, conversely, how specific holobiont phenotypes have influenced gene transfer events. In this synthetic review, we list some notable and recent discoveries of horizontal gene transfer among the prokaryotic component of the human microbiota, and analyze their potential impact on the holobiont from an ecological-evolutionary viewpoint. Finally, the human-Helicobacter pylori association is presented as an illustration of these considerations, followed by a delineation of unresolved questions and avenues for future research.}, }
@article {pmid30220504, year = {2018}, author = {De Clerck, O and Kao, SM and Bogaert, KA and Blomme, J and Foflonker, F and Kwantes, M and Vancaester, E and Vanderstraeten, L and Aydogdu, E and Boesger, J and Califano, G and Charrier, B and Clewes, R and Del Cortona, A and D'Hondt, S and Fernandez-Pozo, N and Gachon, CM and Hanikenne, M and Lattermann, L and Leliaert, F and Liu, X and Maggs, CA and Popper, ZA and Raven, JA and Van Bel, M and Wilhelmsson, PKI and Bhattacharya, D and Coates, JC and Rensing, SA and Van Der Straeten, D and Vardi, A and Sterck, L and Vandepoele, K and Van de Peer, Y and Wichard, T and Bothwell, JH}, title = {Insights into the Evolution of Multicellularity from the Sea Lettuce Genome.}, journal = {Current biology : CB}, volume = {28}, number = {18}, pages = {2921-2933.e5}, doi = {10.1016/j.cub.2018.08.015}, pmid = {30220504}, issn = {1879-0445}, mesh = {*Biological Evolution ; Chromosome Mapping ; *Genome ; *Life History Traits ; Multigene Family ; Ulva/*genetics/growth &amp; development ; }, abstract = {We report here the 98.5 Mbp haploid genome (12,924 protein coding genes) of Ulva mutabilis, a ubiquitous and iconic representative of the Ulvophyceae or green seaweeds. Ulva's rapid and abundant growth makes it a key contributor to coastal biogeochemical cycles; its role in marine sulfur cycles is particularly important because it produces high levels of dimethylsulfoniopropionate (DMSP), the main precursor of volatile dimethyl sulfide (DMS). Rapid growth makes Ulva attractive biomass feedstock but also increasingly a driver of nuisance "green tides." Ulvophytes are key to understanding the evolution of multicellularity in the green lineage, and Ulva morphogenesis is dependent on bacterial signals, making it an important species with which to study cross-kingdom communication. Our sequenced genome informs these aspects of ulvophyte cell biology, physiology, and ecology. Gene family expansions associated with multicellularity are distinct from those of freshwater algae. Candidate genes, including some that arose following horizontal gene transfer from chromalveolates, are present for the transport and metabolism of DMSP. The Ulva genome offers, therefore, new opportunities to understand coastal and marine ecosystems and the fundamental evolution of the green lineage.}, }
@article {pmid30219855, year = {2018}, author = {Zhou, X and Chlebowicz, MA and Bathoorn, E and Rosema, S and Couto, N and Lokate, M and Arends, JP and Friedrich, AW and Rossen, JWA}, title = {Elucidating vancomycin-resistant Enterococcus faecium outbreaks: the role of clonal spread and movement of mobile genetic elements.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {73}, number = {12}, pages = {3259-3267}, doi = {10.1093/jac/dky349}, pmid = {30219855}, issn = {1460-2091}, mesh = {Bacterial Typing Techniques ; Cross Infection/epidemiology/microbiology ; DNA Transposable Elements ; *Disease Outbreaks ; Enterococcus faecium/classification/drug effects/*genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Genotype ; Gram-Positive Bacterial Infections/*transmission ; Humans ; *Interspersed Repetitive Sequences ; Multilocus Sequence Typing ; Phylogeny ; Retrospective Studies ; Sequence Analysis, DNA ; Vancomycin-Resistant Enterococci/*genetics ; }, abstract = {BACKGROUND: Vancomycin-resistant Enterococcus faecium (VREfm) has emerged as a nosocomial pathogen worldwide. The dissemination of VREfm is due to both clonal spread and spread of mobile genetic elements (MGEs) such as transposons.<br><br>OBJECTIVES: We aimed to combine vanB-carrying transposon data with core-genome MLST (cgMLST) typing and epidemiological data to understand the pathways of transmission in nosocomial outbreaks.<br><br>METHODS: Retrospectively, 36 VREfm isolates obtained from 34 patients from seven VREfm outbreak investigations in 2014 were analysed. Isolates were sequenced on a MiSeq and a MinION instrument. De novo assembly was performed in CLC Genomics Workbench and the hybrid assemblies were obtained through Unicycler v0.4.1. Ridom SeqSphere+ was used to extract MLST and cgMLST data. Detailed analysis of each transposon and their integration points was performed using the Artemis Comparison Tool (ACT) and multiple blast analyses.<br><br>RESULTS: Four different vanB transposons were found among the isolates. cgMLST divided ST80 isolates into three cluster types (CTs); CT16, CT104 and CT106. ST117 isolates were divided into CT24, CT103 and CT105. Within VREfm isolates belonging to CT103, two different vanB transposons were found. In contrast, VREfm isolates belonging to CT104 and CT106 harboured an identical vanB transposon.<br><br>CONCLUSIONS: cgMLST provides a high discriminatory power for the epidemiological analysis of VREfm. However, additional transposon analysis is needed to detect horizontal gene transfer. Combining these two methods allows investigation of both clonal spread as well as the spread of MGEs. This leads to new insights and thereby better understanding of the complex transmission routes in VREfm outbreaks.}, }
@article {pmid30219829, year = {2018}, author = {van Hoek, AHAM and Veenman, C and Florijn, A and Huijbers, PMC and Graat, EAM and de Greeff, S and Dierikx, CM and van Duijkeren, E}, title = {Longitudinal study of ESBL Escherichia coli carriage on an organic broiler farm.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {73}, number = {12}, pages = {3298-3304}, doi = {10.1093/jac/dky362}, pmid = {30219829}, issn = {1460-2091}, mesh = {Animals ; Bacterial Typing Techniques ; Carrier State/microbiology/*veterinary ; Chickens/microbiology ; Drug Resistance, Bacterial/genetics ; Escherichia coli/enzymology/*isolation &amp; purification ; Escherichia coli Infections/transmission/*veterinary ; *Gene Transfer, Horizontal ; Longitudinal Studies ; Multilocus Sequence Typing ; Organic Agriculture ; Plasmids/classification/genetics ; Poultry Diseases/*microbiology ; beta-Lactamases/metabolism ; }, abstract = {OBJECTIVES: To determine the molecular characteristics of ESBL-producing Escherichia coli (ESBL-E) collected during a longitudinal study on an organic broiler farm in order to investigate clonal expansion and horizontal gene transfer.<br><br>METHODS: Isolates were obtained from a longitudinal study performed previously on an organic broiler fattening farm. Samples from individually followed-up broilers, the broiler house, the transport van and persons that took the samples, taken at several timepoints (days 1, 3, 4, 7, 10, 42 and 70) within a production round and during the consecutive one (days 1, 2, 3 and 70), had been investigated for the occurrence of ESBL-E. In the current study, ESBL genes and MLST STs of these ESBL-E were determined. Plasmids were characterized and subtyped.<br><br>RESULTS: On arrival in round_1, ESBL-E of ST88 predominated, while on days 3, 4, 7 and 10 ST10 was most often found and at slaughter age ST155 and ST1551 prevailed. A shift in STs was also observed in round_2. None of the 35 individually selected broilers followed up in round_1 was positive for the same ESBL-E ST at all sampling times. All isolates carried CTX-M-1 group genes, confirmed as blaCTX-M-1 in 158 isolates. Further analysis of 36 isolates of different STs showed blaCTX-M-1 on IncI1/ST3 plasmids.<br><br>CONCLUSIONS: The rapid dissemination of ESBL-E on this broiler farm was not due to the spread of one specific E. coli clone, but most likely the result of horizontal transfer of an IncI1/ST3 plasmid carrying blaCTX-M-1 resulting in a shift in the predominant ESBL-E population in broilers.}, }
@article {pmid30217838, year = {2018}, author = {Berg, JA and Merrill, BD and Breakwell, DP and Hope, S and Grose, JH}, title = {A PCR-Based Method for Distinguishing between Two Common Beehive Bacteria, Paenibacillus larvae and Brevibacillus laterosporus.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {22}, pages = {}, pmid = {30217838}, issn = {1098-5336}, mesh = {Animals ; Bacterial Typing Techniques/*methods ; Bees/microbiology ; Brevibacillus/classification/genetics/*isolation &amp; purification ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Paenibacillus larvae/classification/genetics/*isolation &amp; purification ; Phylogeny ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S ; }, abstract = {Paenibacillus larvae and Brevibacillus laterosporus are two bacteria that are members of the Paenibacillaceae family. Both are commonly found in beehives and have historically been difficult to distinguish from each other due to related genetic and phenotypic characteristics and a shared ecological niche. Here, we discuss the likely mischaracterization of three 16S rRNA sequences previously published as P. larvae and provide the phylogenetic evidence that supported the GenBank reassignment of the sequences as B. laterosporus We explore the issues that arise by using only 16S rRNA or other single-gene analyses to distinguish between these bacteria. We also present three sets of molecular markers, two sets that distinguish P. larvae from B. laterosporus and other closely related species within the Paenibacillus genus and a third set that distinguishes B. laterosporus from P. larvae and other closely related species within the Brevibacillus genus. These molecular markers provide a tool for proper identification of these oft-mistaken species.IMPORTANCE 16S rRNA gene sequencing in bacteria has long been held as the gold standard for typing bacteria and, for the most part, is an excellent method of taxonomically identifying different bacterial species. However, the high level of 16S rRNA sequence similarity of some published strains of P. larvae and B. laterosporus, as well as possible horizontal gene transfer events within their shared ecological niche, complicates the use of 16S rRNA sequence as an effective molecular marker for differentiating these two species. Additionally, shared characteristics of these bacteria limit the effectiveness of using traditional phenotypic identification assays, such as the catalase test. The results from this study provide PCR methods to quickly differentiate between these two genera and will be useful when studying Brevibacillus, Paenibacillus, and other disease-relevant bacteria commonly found in beehives.}, }
@article {pmid30210140, year = {2018}, author = {Mazurek, J and Bok, E and Baldy-Chudzik, K}, title = {Complexity of Antibiotic Resistance in Commensal Escherichia coli Derived from Pigs from an Intensive-Production Farm.}, journal = {Microbes and environments}, volume = {33}, number = {3}, pages = {242-248}, pmid = {30210140}, issn = {1347-4405}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Cluster Analysis ; DNA Transposable Elements ; Drug Resistance, Multiple, Bacterial/drug effects/*genetics ; Escherichia coli/*drug effects/genetics/*isolation &amp; purification ; Escherichia coli Infections/microbiology/*veterinary ; Escherichia coli Proteins/genetics ; Farms ; Feces/microbiology ; Female ; Gene Transfer, Horizontal ; Genes, Bacterial ; Microbial Sensitivity Tests/veterinary ; Microbial Viability/drug effects ; Plasmids ; Poland ; Swine/*microbiology ; Weaning ; }, abstract = {Antibiotics in animal husbandry are used to maintain welfare, but lead to the generation of resistant strains. We analyzed commensal multidrug-resistant Escherichia coli from pigs at the beginning and end of the production cycle in a farm with a farrow-to-finish system in order to investigate whether clonal spread or horizontal gene transfer constitutes the main factor responsible for the prevalence of resistance in this environment. Among 380 isolates, 56 multidrug-resistant E. coli with a similar resistant phenotype were selected for more detailed investigations including a genomic similarity analysis and the detection of mobile elements. Isolates carried blaTEM-1, aadA1, strA/B, tetA, tetB, tetC, dfrA1, dfrA5, dfrA7, dfrA12, sul1, sul2, sul3, and qnrS resistance genes, with the common co-occurrence of genes encoding the same resistance phenotype. A pulse-field gel electrophoresis analysis of the genomic similarity of multidrug-resistant E. coli showed ≤65% similarity of most of the tested strains and did not reveal a dominant clone responsible for the prevalence of resistance. Class 1 and 2 integrons and transposons 7 and 21 were detected among mobile elements; however, some were truncated. Plasmids were represented by 11 different incompatibility groups (K, FIB, I1, FIIA, FIC, FIA, Y, P, HI1, B/O, and T). Genetic resistance traits were unevenly spread in the clonal groups and suggested the major rearrangement of genetic material by horizontal gene transfer. The present results revealed that in commensal E. coli from pigs in a homogeneous farm environment, there was no dominant clone responsible for the spread of resistance and persistence in the population.}, }
@article {pmid30209344, year = {2019}, author = {Bottery, MJ and Wood, AJ and Brockhurst, MA}, title = {Temporal dynamics of bacteria-plasmid coevolution under antibiotic selection.}, journal = {The ISME journal}, volume = {13}, number = {2}, pages = {559-562}, pmid = {30209344}, issn = {1751-7370}, support = {//Wellcome Trust/United Kingdom ; 102295//Wellcome Trust/United Kingdom ; BB/R006253/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; WT095024MA//Wellcome Trust/United Kingdom ; }, mesh = {Adaptation, Physiological/drug effects/genetics ; *Biological Coevolution ; Escherichia coli/*drug effects/*genetics ; Gene Transfer, Horizontal ; Plasmids/*genetics ; Replicon ; Selection, Genetic ; Tetracycline/*pharmacology ; Tetracycline Resistance/*genetics ; }, abstract = {Horizontally acquired genes can be costly to express even if they encode useful traits, such as antibiotic resistance. We previously showed that when selected with tetracycline, Escherichia coli carrying the tetracycline-resistance plasmid RK2 evolved mutations on both replicons that together provided increased tetracycline resistance at reduced cost. Here we investigate the temporal dynamics of this intragenomic coevolution. Using genome sequencing we show that the order of adaptive mutations was highly repeatable across three independently evolving populations. Each population first gained a chromosomal mutation in ompF which shortened lag phase and increased tetracycline resistance. This was followed by mutations impairing the plasmid-encoded tetracycline efflux pump, and finally, additional resistance-associated chromosomal mutations. Thus, reducing the cost of the horizontally acquired tetracycline resistance was contingent on first evolving a degree of chromosomally encoded resistance. We conclude therefore that the trajectory of bacteria-plasmid coevolution was constrained to a single repeatable path.}, }
@article {pmid30207005, year = {2019}, author = {Kean, KM and Karplus, PA}, title = {Structure and role for active site lid of lactate monooxygenase from Mycobacterium smegmatis.}, journal = {Protein science : a publication of the Protein Society}, volume = {28}, number = {1}, pages = {135-149}, pmid = {30207005}, issn = {1469-896X}, support = {R01 GM119227/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R01GM119227/NH/NIH HHS/United States ; }, mesh = {Bacterial Proteins/*chemistry ; Catalytic Domain ; Crystallography, X-Ray ; Flavin Mononucleotide/*chemistry ; Mixed Function Oxygenases/*chemistry ; Mycobacterium smegmatis/*enzymology ; }, abstract = {Lactate monooxygenase (LMO) catalyzes the FMN-dependent "coupled" oxidation of lactate and O2 to acetate, carbon dioxide, and water, involving pyruvate and hydrogen peroxide as enzyme-bound intermediates. Other α-hydroxy acid oxidase family members follow an "uncoupled pathway," wherein the α-keto acid product quickly dissociates before the reduced flavin reacts with oxygen. Here, we report the structures of Mycobacterium smegmatis wild-type LMO and a wild-type-like C203A variant at 2.1 Å and 1.7 Å resolution, respectively. The overall LMO fold and active site organization, including a bound sulfate mimicking substrate, resemble those of other α-hydroxy acid oxidases. Based on structural similarity, LMO is similarly distant from lactate oxidase, glycolate oxidase, mandelate dehydrogenase, and flavocytochrome b2 and is the first representative enzyme of its type. Comparisons with other α-hydroxy acid oxidases reveal that LMO has a longer and more compact folded active site loop (Loop 4), which is known in related flavoenzymes to undergo order/disorder transitions to allow substrate/product binding and release. We propose that LMO's Loop 4 has an enhanced stability that is responsible for the slow product release requisite for the coupled pathway. We also note electrostatic features of the LMO active site that promote substrate binding. Whereas the physiological role of LMO remains unknown, we document what can currently be assessed of LMO's distribution in nature, including its unexpected occurrence, presumably through horizontal gene transfer, in halophilic archaea and in a limited group of fungi of the genus Beauveria. BROAD STATEMENT OF IMPACT: This first crystal structure of the FMN-dependent α-hydroxy acid oxidase family member lactate monooxygenase (LMO) reveals it has a uniquely large active site lid that we hypothesize is stable enough to explain the slow dissociation of pyruvate that leads to its "coupled" oxidation of lactate and O2 to produce acetate, carbon dioxide, and water. Also, the relatively widespread distribution of putative LMOs supports their importance and provides new motivation for their further study.}, }
@article {pmid30200850, year = {2018}, author = {Blázquez, J and Rodríguez-Beltrán, J and Matic, I}, title = {Antibiotic-Induced Genetic Variation: How It Arises and How It Can Be Prevented.}, journal = {Annual review of microbiology}, volume = {72}, number = {}, pages = {209-230}, doi = {10.1146/annurev-micro-090817-062139}, pmid = {30200850}, issn = {1545-3251}, mesh = {Adaptation, Biological ; Anti-Bacterial Agents/*adverse effects ; Bacteria/*drug effects/genetics ; Genetic Variation/*drug effects ; Genomic Instability/drug effects ; Mutation ; Reactive Oxygen Species/metabolism ; Recombination, Genetic ; Selection, Genetic/drug effects ; Stress, Physiological ; }, abstract = {By targeting essential cellular processes, antibiotics provoke metabolic perturbations and induce stress responses and genetic variation in bacteria. Here we review current knowledge of the mechanisms by which these molecules generate genetic instability. They include production of reactive oxygen species, as well as induction of the stress response regulons, which lead to enhancement of mutation and recombination rates and modulation of horizontal gene transfer. All these phenomena influence the evolution and spread of antibiotic resistance. The use of strategies to stop or decrease the generation of resistant variants is also discussed.}, }
@article {pmid30194973, year = {2018}, author = {Zhang, JM and Wang, Q and Han, TY and Liu, JH and Hu, XX and Qiao, F and Yang, XY and Li, CR and You, XF}, title = {Structure analysis of transposons carrying the aac(6')-aph(2″) gene in Enterococcus faecalis isolated in Beijing, China, and comparison of their transfer efficiency.}, journal = {International journal of antimicrobial agents}, volume = {52}, number = {6}, pages = {799-804}, doi = {10.1016/j.ijantimicag.2018.08.025}, pmid = {30194973}, issn = {1872-7913}, mesh = {Acetyltransferases/*genetics ; Anti-Bacterial Agents/pharmacology ; Beijing ; Chromosome Mapping ; Conjugation, Genetic ; *DNA Transposable Elements ; *Drug Resistance, Bacterial ; Enterococcus faecalis/classification/drug effects/*genetics/isolation &amp; purification ; *Gene Transfer, Horizontal ; Genetic Variation ; Gentamicins/pharmacology ; Gram-Positive Bacterial Infections/*microbiology ; Humans ; Phosphotransferases (Alcohol Group Acceptor)/*genetics ; Plasmids/analysis ; Polymerase Chain Reaction ; }, abstract = {Transfer of aac(6')-aph(2″) transposons mediating high-level gentamicin resistance (HLGR) in Enterococcus faecalis is a serious problem in the clinic. However, factors affecting the transfer of aac(6')-aph(2″) have not yet been elucidated. The current study aimed to examine the genetic and molecular basis of HLGR in E. faecalis strains isolated in Beijing (China) and to clarify the relationship between transfer efficiency of aac(6')-aph(2″) transposons and the transposon structure/location. A total of five transposon structures were identified by PCR mapping of the corresponding transposon regions, including a Tn5281-like non-truncated transposon and four truncated transposons. A plasmid location study of aac(6')-aph(2″) by Southern blot following S1-PFGE and filter mating conjugation experiments demonstrated that plasmid location rates correlated with conjugation-positive rates. Chromosome walking to identify the sequence upstream of a representative type III truncated transposon found a truncated aph(2″)-Ia region, and further PCR analysis of this region among strains from different groups revealed similar a positive rate trend as the transposon plasmid location rate and conjugation-positive rate. In conclusion, aac(6')-aph(2″) transposons were of different structures in E. faecalis strains from Beijing, with two new transposon structures that have not been reported elsewhere. Presence of the truncated aph(2″)-Ia region upstream of some truncated transposons suggests recombination between aminoglycoside-modifying enzyme genes. Possible links exist among plasmid location, conjugation and the presence of truncated aph(2″)-Ia upstream of the transposon.}, }
@article {pmid30193985, year = {2019}, author = {Faure, G and Makarova, KS and Koonin, EV}, title = {CRISPR-Cas: Complex Functional Networks and Multiple Roles beyond Adaptive Immunity.}, journal = {Journal of molecular biology}, volume = {431}, number = {1}, pages = {3-20}, doi = {10.1016/j.jmb.2018.08.030}, pmid = {30193985}, issn = {1089-8638}, mesh = {Adaptive Immunity/genetics ; Archaea/*genetics ; Bacteria/*genetics ; CRISPR-Cas Systems/*genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/*genetics ; DNA Repair/genetics ; DNA Transposable Elements/*genetics ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal/genetics ; Plasmids/genetics ; Signal Transduction/genetics ; }, abstract = {CRISPR-Cas is a prokaryotic adaptive immune system that functions by incorporating fragments of foreign DNA into CRISPR arrays. The arrays containing spacers derived from foreign DNA are transcribed, and the transcripts are processed to generate spacer-containing mature CRISPR-RNAs that are employed as guides to specifically recognize and cleave the DNA or RNA of the cognate parasitic genetic elements. The CRISPR-Cas systems show remarkable complexity and diversity of molecular organization and appear to be involved in various cellular functions that are distinct from, even if connected to, adaptive immunity. In this review, we discuss some of such functional links of CRISPR-Cas systems including their effect on horizontal gene transfer that can be either inhibitory or stimulatory, connections between CRISPR-Cas and DNA repair systems as well as programmed cell death and signal transduction mechanisms, and potential role of CRISPR-Cas in transposon integration and plasmid maintenance. The interplay between the primary function of CRISPR-Cas as an adaptive immunity mechanism and these other roles defines the richness of the biological effects of these systems and affects their spread among bacteria and archaea.}, }
@article {pmid30191942, year = {2018}, author = {Roy, R and Samanta, S and Patra, S and Mahato, NK and Saha, RP}, title = {In silico identification and characterization of sensory motifs in the transcriptional regulators of the ArsR-SmtB family.}, journal = {Metallomics : integrated biometal science}, volume = {10}, number = {10}, pages = {1476-1500}, doi = {10.1039/c8mt00082d}, pmid = {30191942}, issn = {1756-591X}, mesh = {*Amino Acid Motifs ; Amino Acid Sequence ; Archaea/genetics/*metabolism ; Archaeal Proteins/chemistry/genetics/*metabolism ; Bacteria/genetics/*metabolism ; Bacterial Proteins/chemistry/genetics/*metabolism ; Binding Sites ; *Computer Simulation ; Gene Expression Regulation, Archaeal ; Gene Expression Regulation, Bacterial ; Gene Regulatory Networks ; Metals/*metabolism ; Models, Molecular ; Multigene Family ; Protein Binding ; Protein Conformation ; *Transcription, Genetic ; }, abstract = {The ArsR-SmtB family of proteins displays the greatest diversity among the bacterial metal-binding transcriptional regulators with regard to the variety of metal ions that they can sense. In the presence of increased levels of toxic heavy metals, these proteins dissociate from their cognate DNA upon the direct binding of metal ions to the appropriate sites, designated motifs on the proteins, either at the interface of the dimers or at the intra-subunit locations. In addition to the metal-mediated regulation, some proteins were also found to control transcription via redox reactions. In the present work, we have identified several new sequence motifs and expanded the knowledge base of metal binding sites in the ArsR-SmtB family of transcriptional repressors, and characterized them in terms of the ligands to the metal, distribution among different phyla of bacteria and archaea, amino acid propensities, protein length distributions and evolutionary interrelationships. We built structural models of the motifs to show the importance of specific residues in an individual motif. The wide abundance of these motifs in sequences of bacteria and archaea indicates the importance of these regulators in combating metal-toxicity within and outside of the hosts. We also show that by using residue composition, one can distinguish the ArsR-SmtB proteins from other metalloregulatory families. In addition, we show the importance of horizontal gene transfer in microorganisms, residing in similar habitats, on the evolution of the structural motifs in the family. Knowledge of the diverse metalloregulatory systems in microorganisms could enable us to manipulate specific genes that may result in a toxic metal-free environment.}, }
@article {pmid30191802, year = {2018}, author = {Bessen, DE and Smeesters, PR and Beall, BW}, title = {Molecular Epidemiology, Ecology, and Evolution of Group A Streptococci.}, journal = {Microbiology spectrum}, volume = {6}, number = {5}, pages = {}, pmid = {30191802}, issn = {2165-0497}, support = {R01 AI065572/AI/NIAID NIH HHS/United States ; R21 AI117088/AI/NIAID NIH HHS/United States ; }, mesh = {Ecology ; Evolution, Molecular ; Gene Transfer, Horizontal ; Host-Pathogen Interactions ; Humans ; Molecular Epidemiology ; Streptococcal Infections/*epidemiology/*microbiology ; Streptococcus pyogenes/*genetics/*pathogenicity ; Virulence ; }, abstract = {The clinico-epidemiological features of diseases caused by group A streptococci (GAS) is presented through the lens of the ecology, population genetics, and evolution of the organism. The serological targets of three typing schemes (M, T, SOF) are themselves GAS cell surface proteins that have a myriad of virulence functions and a diverse array of structural forms. Horizontal gene transfer expands the GAS antigenic cell surface repertoire by generating numerous combinations of M, T, and SOF antigens. However, horizontal gene transfer of the serotype determinant genes is not unconstrained, and therein lies a genetic organization that may signify adaptations to a narrow ecological niche, such as the primary tissue reservoirs of the human host. Adaptations may be further shaped by selection pressures such as herd immunity. Understanding the molecular evolution of GAS on multiple levels-short, intermediate, and long term-sheds insight on mechanisms of host-pathogen interactions, the emergence and spread of new clones, rational vaccine design, and public health interventions.}, }
@article {pmid30189014, year = {2018}, author = {Lee, RS and Gonçalves da Silva, A and Baines, SL and Strachan, J and Ballard, S and Carter, GP and Kwong, JC and Schultz, MB and Bulach, DM and Seemann, T and Stinear, TP and Howden, BP}, title = {The changing landscape of vancomycin-resistant Enterococcus faecium in Australia: a population-level genomic study.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {73}, number = {12}, pages = {3268-3278}, doi = {10.1093/jac/dky331}, pmid = {30189014}, issn = {1460-2091}, support = {152448//CIHR/Canada ; }, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Australia/epidemiology ; Bacteremia/epidemiology ; Cross-Sectional Studies ; DNA, Bacterial/genetics ; Enterococcus faecium/*drug effects/*genetics ; Female ; Gene Transfer, Horizontal ; Genotype ; Gram-Positive Bacterial Infections/*epidemiology ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Microbial Sensitivity Tests ; Middle Aged ; Phylogeny ; Plasmids/genetics ; Public Health Surveillance ; Vancomycin-Resistant Enterococci/classification/*genetics ; Young Adult ; }, abstract = {BACKGROUND: Vancomycin-resistant Enterococcus faecium (VREfm) represent a major source of nosocomial infection worldwide. In Australia, there has been a recent concerning increase in bacteraemia associated with the vanA genotype, prompting investigation into the genomic epidemiology of VREfm.<br><br>METHODS: A population-level study of VREfm (10 November-9 December 2015) was conducted. A total of 321 VREfm isolates (from 286 patients) across Victoria State were collected and sequenced with Illumina NextSeq. SNPs were used to assess relatedness. STs and genes associated with resistance and virulence were identified. The vanA-harbouring plasmid from an isolate from each ST was assembled using long-read data. Illumina reads from remaining isolates were then mapped to these assemblies to identify their probable vanA-harbouring plasmid.<br><br>RESULTS: vanA-VREfm comprised 17.8% of isolates. ST203, ST80 and a pstS(-) clade, ST1421, predominated (30.5%, 30.5% and 37.2%, respectively). Most vanB-VREfm were ST796 (77.7%). vanA-VREfm were more closely related within hospitals versus between them [core SNPs 10 (IQR 1-357) versus 356 (179-416), respectively], suggesting discrete introductions of vanA-VREfm, with subsequent intra-hospital transmission. In contrast, vanB-VREfm had similar core SNP distributions within versus between hospitals, due to widespread dissemination of ST796. Different vanA-harbouring plasmids were found across STs. With the exception of ST78 and ST796, Tn1546 transposons also varied. Phylogenetic analysis revealed Australian strains were often interspersed with those from other countries, suggesting ongoing cross-continental transmission.<br><br>CONCLUSIONS: Emerging vanA-VREfm in Australia is polyclonal, indicating repeat introductions of vanA-VREfm into hospitals and subsequent dissemination. The close relationship to global strains reinforces the need for ongoing screening and control of VREfm in Australia and abroad.}, }
@article {pmid30188064, year = {2018}, author = {Hu, YR and Jiang, L and Zhang, TY and Lei, DD and Jiang, WW and Zhang, D and Lin, KF and Cui, CZ}, title = {[Distribution Characteristics of Sulfonamide Antibiotic Resistance Genes in a Drinking Water Source in East China].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {39}, number = {9}, pages = {4222-4228}, doi = {10.13227/j.hjkx.201712106}, pmid = {30188064}, issn = {0250-3301}, mesh = {Anti-Bacterial Agents ; China ; Drinking Water/*analysis ; Drug Resistance, Microbial/*genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Sulfonamides ; }, abstract = {Antibiotic resistance genes (ARGs) in drinking water sources have attracted widespread attention due to the threat they pose to water security and human health. This study mainly focused on the distribution of sulfonamide ARGs (sul 1, sul 2) and one integrase gene (intI 1) in water and sediment using qualitative and fluorescent quantitative PCR, based on previous work on the characteristics of 13 kinds of sulfonamides in a drinking water source in East China. Results showed that the three target genes were all detected in water and sediment. The sul 1 gene was the sulfonamide ARG with highest concentration, with 1.5×10[4]-6.4×10[5] copies·mL[-1] in source water and maximum concentration of 1.6×10[8] copies·g[-1] in sediment. Concentration of sul 1 was 0.6-2.2, 0.5-1.9 order of magnitudes higher than sul 2 and intI 1 genes, respectively. There was no significant difference between the absolute concentrations of sul 1, sul 2, and intI 1 in inflow and outflow. However, in the case of sediment, absolute abundances of sul 1, sul 2, and intI 1 in outflow were higher than those in inflow. The maximum concentration of sul 1 was detected in outflow in summer (6.4×10[5] copies·mL[-1]). The concentration of intI 1 was higher in winter compared to other seasons. There was a positive correlation between sul 1 and 13 sulfonamides (r=0.69, P<0.05), and the relative concentration of sul 1 and amount of sulfamethoxazole were significantly positively related (r=0.79, P<0.01). There were also positive correlations between the relative concentrations of intI 1 and sul 1, sul 2 (r:0.80 and 0.73, P<0.05), respectively, suggesting that intI 1 played an important role in horizontal gene transfer of sulfonamide ARGs in this drinking water source. This study provides basic data for monitoring pollution of ARGs, as well as a basis for controlling ARG pollution in the drinking water environment and making management decisions.}, }
@article {pmid30184126, year = {2018}, author = {Foflonker, F and Mollegard, D and Ong, M and Yoon, HS and Bhattacharya, D}, title = {Genomic Analysis of Picochlorum Species Reveals How Microalgae May Adapt to Variable Environments.}, journal = {Molecular biology and evolution}, volume = {35}, number = {11}, pages = {2702-2711}, doi = {10.1093/molbev/msy167}, pmid = {30184126}, issn = {1537-1719}, mesh = {*Adaptation, Biological ; Chlorophyta/*genetics/metabolism ; Environment ; *Gene Transfer, Horizontal ; Genetic Variation ; Genome, Chloroplast ; Genomics ; Microalgae/*genetics/metabolism ; Phylogeny ; Salt Stress ; Synteny ; Transcriptome ; }, abstract = {Understanding how microalgae adapt to rapidly changing environments is not only important to science but can help clarify the potential impact of climate change on the biology of primary producers. We sequenced and analyzed the nuclear genome of multiple Picochlorum isolates (Chlorophyta) to elucidate strategies of environmental adaptation. It was previously found that coordinated gene regulation is involved in adaptation to salinity stress, and here we show that gene gain and loss also play key roles in adaptation. We determined the extent of horizontal gene transfer (HGT) from prokaryotes and their role in the origin of novel functions in the Picochlorum clade. HGT is an ongoing and dynamic process in this algal clade with adaptation being driven by transfer, divergence, and loss. One HGT candidate that is differentially expressed under salinity stress is indolepyruvate decarboxylase that is involved in the production of a plant auxin that mediates bacteria-diatom symbiotic interactions. Large differences in levels of heterozygosity were found in diploid haplotypes among Picochlorum isolates. Biallelic divergence was pronounced in P. oklahomensis (salt plains environment) when compared with its closely related sister taxon Picochlorum SENEW3 (brackish water environment), suggesting a role of diverged alleles in response to environmental stress. Our results elucidate how microbial eukaryotes with limited gene inventories expand habitat range from mesophilic to halophilic through allelic diversity, and with minor but important contributions made by HGT. We also explore how the nature and quality of genome data may impact inference of nuclear ploidy.}, }
@article {pmid30183405, year = {2018}, author = {Nützmann, HW and Scazzocchio, C and Osbourn, A}, title = {Metabolic Gene Clusters in Eukaryotes.}, journal = {Annual review of genetics}, volume = {52}, number = {}, pages = {159-183}, doi = {10.1146/annurev-genet-120417-031237}, pmid = {30183405}, issn = {1545-2948}, support = {BBS/E/J/00000614/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/J/000PR9790/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P012523/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/L014130/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Eukaryota/genetics/metabolism ; Fungi/*genetics/metabolism ; Gene Transfer, Horizontal ; Genome/genetics ; Metabolic Networks and Pathways/*genetics ; Multigene Family/*genetics ; Operon/genetics ; Plants/*genetics/metabolism ; }, abstract = {In bacteria, more than half of the genes in the genome are organized in operons. In contrast, in eukaryotes, functionally related genes are usually dispersed across the genome. There are, however, numerous examples of functional clusters of nonhomologous genes for metabolic pathways in fungi and plants. Despite superficial similarities with operons (physical clustering, coordinate regulation), these clusters have not usually originated by horizontal gene transfer from bacteria, and (unlike operons) the genes are typically transcribed separately rather than as a single polycistronic message. This clustering phenomenon raises intriguing questions about the origins of clustered metabolic pathways in eukaryotes and the significance of clustering for pathway function. Here we review metabolic gene clusters from fungi and plants, highlight commonalities and differences, and consider how these clusters form and are regulated. We also identify opportunities for future research in the areas of large-scale genomics, synthetic biology, and experimental evolution.}, }
@article {pmid30181870, year = {2018}, author = {Szymanek-Majchrzak, K and Mlynarczyk, A and Mlynarczyk, G}, title = {Characteristics of glycopeptide-resistant Staphylococcus aureus strains isolated from inpatients of three teaching hospitals in Warsaw, Poland.}, journal = {Antimicrobial resistance and infection control}, volume = {7}, number = {}, pages = {105}, pmid = {30181870}, issn = {2047-2994}, mesh = {Anti-Bacterial Agents/pharmacology ; *Cross Infection ; Genes, Bacterial ; Genotype ; *Hospitals, Teaching ; Humans ; *Inpatients ; Methicillin-Resistant Staphylococcus aureus/classification/genetics/*isolation &amp; purification ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Phenotype ; Poland/epidemiology ; Staphylococcal Infections/*epidemiology/*microbiology ; Vancomycin/pharmacology ; }, abstract = {BACKGROUND: Vancomycin is still one of the most commonly used drug for treatment of severe methicillin-resistant Staphylococcus aureus (MRSA) infections. Vancomycin-resistant S. aureus (VRSA) strains are a serious danger for public health. This study aimed to characterize healthcare-associated MRSA (HA-MRSA) strains, resistant to at least one of glycopeptide antibiotics: vancomycin (VRSA) and/or teicoplanin (TRSA), isolated at three Warsaw hospitals over a period of 17-years (1991-2007).<br><br>METHODS: Among 600 HA-MRSA strains, isolated from patients with symptomatic infections, 47 were subjected to detailed analysis. In the study, mechanisms behind VRSA phenotypes were determined (E-tests, GRD-test, agar-dilution method and vanA/B detection). Characteristics of selected isolates on molecular level: i) by detection of resistance genes ermA/ermB/ermC, msrA/msrB, linA/linA', aacA-aphD, aadD, aph(3")-IIIa; ii) SCCmec-typing and iii) MLST-typing was done.<br><br>RESULTS: In general population of studied strains, 11/47 (23.4%) were VRSA and 36/47 (76.6%) were resistant only to teicoplanin. All isolates exhibited van-independent mechanisms of resistance. Over 80% of isolates belonged to clonal complex CC8, with the following predominant sequence types (STs)/clones: ST247-IA/Iberian, ST241-III/Finland-UK, and ST239-III/Brazilian. Most of the isolated strains harboured ermA and aacA-aphD genes, encoding additional resistance to macrolides, lincosamides, streptogramin B, and majority of aminoglycosides. They occurred also in Polish VRSA/TRSA population over the period, which was subjected for analysis: an increase in MIC values for glycopeptides, evolution in terms of the level and extent of resistance, and genetic re-assortment in epidemic clones.<br><br>CONCLUSIONS: VRSA strains isolated from patients hospitalized at three Warsaw teaching hospitals in Poland, over a period of 17-years do not pose a threat as potential donors of van genes in horizontal-gene transfer processes, but are constantly evolving and represent international epidemic clones.}, }
@article {pmid30181252, year = {2018}, author = {Capone, DG}, title = {Discovery of New Nitrite-Oxidizing Bacteria Increases Phylogenetic and Metabolic Diversity within This Niche.}, journal = {mBio}, volume = {9}, number = {5}, pages = {}, pmid = {30181252}, issn = {2150-7511}, mesh = {Bacteria ; *Nitrites ; Oxidation-Reduction ; *Phylogeny ; }, abstract = {K. Kitzinger et al. (mBio 9:e01186-18, 2018, https://doi.org/10.1128/mBio.01186-18) report the first isolation of a novel nitrite-oxidizing bacterium, "Candidatus Nitrotoga," and provide the first detailed information on the physiology, phylogeny, and characterization of the nitrite-oxidizing system of this genus. The isolate was derived from a wastewater treatment system and exhibits adaptation and tolerance to relatively high levels of nitrite. The origin of its nitrite oxidoreductase is distinct from other known nitrite oxidoreductase (NXR) systems, having arisen either in this organism or by horizontal gene transfer. In contrast to many earlier-characterized nitrite oxidizers, it displays substantial metabolic plasticity in its mode of energetic metabolism with capabilities to use both hydrogen and sulfite as electron donors.}, }
@article {pmid30180347, year = {2019}, author = {Urra, J and Alkorta, I and Mijangos, I and Epelde, L and Garbisu, C}, title = {Application of sewage sludge to agricultural soil increases the abundance of antibiotic resistance genes without altering the composition of prokaryotic communities.}, journal = {The Science of the total environment}, volume = {647}, number = {}, pages = {1410-1420}, doi = {10.1016/j.scitotenv.2018.08.092}, pmid = {30180347}, issn = {1879-1026}, mesh = {Agriculture/*methods ; Anti-Bacterial Agents ; Drug Resistance, Microbial/*genetics ; Humans ; Metals, Heavy ; Sewage ; Soil ; *Soil Microbiology ; Soil Pollutants ; Waste Disposal, Fluid/*methods ; }, abstract = {The application of sewage sludge as soil amendment is a common agricultural practice. However, wastewater treatment plants, sewage sludge and sewage sludge-amended soils have been reported as hotspots for the appearance and dissemination of antibiotic resistance, driven, among other factors, by selection pressure exerted by co-exposure to antibiotics and heavy metals. To address this threat to environmental and human health, soil samples from a long-term (24 years) field experiment, carried out to study the impact of thermally dried and anaerobically digested sewage sludge (at different doses and frequencies of application) on agricultural soil quality, were investigated for the presence of genes encoding antibiotic resistance (ARGs) and mobile genetic elements (MGEs). Sewage sludge-induced changes in specific soil physicochemical and microbial properties, as indicators of soil quality, were also investigated. The application of sewage sludge increased the total concentration of copper and zinc in amended soils, but without affecting the bioavailability of these metals, possibly due to the high values of soil pH and organic matter content. Soil microbal quality, as reflected by the value of the Soil Quality Index, was higher in sewage sludge-amended soils. Similarly, the application of sewage sludge increased soil microbial activity and biomass, as well as the abundance of ARGs and MGE genes, posing a risk of dissemination of antibiotic resistance. In contrast, the composition of soil prokaryotic communities was not significantly altered by the application of sewage sludge. We found correlation between soil Cu and Zn concentrations and the abundance of ARGs and MGE genes. It was concluded that sewage sludge-derived amendments must be properly treated and managed if they are to be applied to agricultural soil.}, }
@article {pmid30179497, year = {2018}, author = {Li, B and Qiu, Y and Zhang, J and Huang, X and Shi, H and Yin, H}, title = {Real-Time Study of Rapid Spread of Antibiotic Resistance Plasmid in Biofilm Using Microfluidics.}, journal = {Environmental science &amp; technology}, volume = {52}, number = {19}, pages = {11132-11141}, doi = {10.1021/acs.est.8b03281}, pmid = {30179497}, issn = {1520-5851}, mesh = {*Biofilms ; Conjugation, Genetic ; Drug Resistance, Microbial ; Gene Transfer, Horizontal ; Humans ; *Microfluidics ; Plasmids ; Time and Motion Studies ; }, abstract = {Gene transfer in biofilms is known to play an important role in antibiotic resistance dissemination. However, the process remains poorly understood. In this study, microfluidics with time-lapse imaging was used for real-time monitoring of plasmid-mediated horizontal gene transfer (HGT) in biofilms. Pseudomonas putida KT2440 harboring an antibiotic resistance plasmid RP4 was chosen as the donor while Escherichia coli and activated sludge bacteria were used as the recipient cells. Dynamic features of the transfer process, including the transfer rate, cell growth rate and kinetic changes of the transfer frequency, were determined. It was found that the routes for gene transfer strongly depend on the structure and composition of a biofilm. While intraspecies HGT is essential to initiate a transfer event, the secondary retransfer from transconjugants to the same species is more efficient and can cause cascading gene spread in single-strain biofilms. For the activated sludge biofilm, only small and scattered colonies formed and vertical gene transfer appears to be the dominant route after initial intraspecies transfer. Furthermore, more than 46% of genera in the activated sludge were permissive to plasmid RP4, many of which are associated with human pathogens. These phenomena imply early prevention and interruptions to biofilm structure could provide an effect way to inhibit rapid antibiotic resistance gene spread and reduce the likelihood of catastrophic events associated with antibiotic resistance.}, }
@article {pmid30176752, year = {2018}, author = {Davies, PL and Graham, LA}, title = {Protein evolution revisited.}, journal = {Systems biology in reproductive medicine}, volume = {64}, number = {6}, pages = {403-416}, doi = {10.1080/19396368.2018.1511764}, pmid = {30176752}, issn = {1939-6376}, mesh = {Animals ; Antifreeze Proteins/*physiology ; Cryopreservation ; DNA Copy Number Variations ; *Evolution, Molecular ; Fishes/*physiology ; Gene Amplification ; Gene Expression Regulation ; Ice ; Oxo-Acid-Lyases/genetics ; Spermatogenesis ; }, abstract = {Antifreeze proteins (AFPs) protect marine fishes from freezing in icy seawater. They evolved relatively recently, most likely in response to the formation of sea ice and Cenozoic glaciations that occurred less than 50 million years ago, following a greenhouse Earth event. Based on their diversity, AFPs have independently evolved on many occasions to serve the same function, with some remarkable examples of convergent evolution at the structural level, and even instances of lateral gene transfer. For some AFPs, the progenitor gene is recognizable. The intense selection pressure exerted by icy seawater, which can rapidly kill unprotected fish, has led to massive AFP gene amplification, as well as some partial gene duplications that have increased the size and activity of the antifreeze. The many protein evolutionary processes described in Gordon H. Dixon's Essays in Biochemistry article will be illustrated here by examples from studies on AFPs. Abbreviations: AFGP: antifreeze glycoproteins; AFP: antifreeze proteins; GHD: Gordon H. Dixon; SAS: sialic acid synthase; TH: thermal hysteresis.}, }
@article {pmid30174653, year = {2018}, author = {Tagini, F and Pillonel, T and Croxatto, A and Bertelli, C and Koutsokera, A and Lovis, A and Greub, G}, title = {Distinct Genomic Features Characterize Two Clades of Corynebacterium diphtheriae: Proposal of Corynebacterium diphtheriae Subsp. diphtheriae Subsp. nov. and Corynebacterium diphtheriae Subsp. lausannense Subsp. nov.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1743}, pmid = {30174653}, issn = {1664-302X}, abstract = {Corynebacterium diphtheriae is the etiological agent of diphtheria, a disease caused by the presence of the diphtheria toxin. However, an increasing number of records report non-toxigenic C. diphtheriae infections. Here, a C. diphtheriae strain was recovered from a patient with a past history of bronchiectasis who developed a severe tracheo-bronchitis with multiple whitish lesions of the distal trachea and the mainstem bronchi. Whole-genome sequencing (WGS), performed in parallel with PCR targeting the toxin gene and the Elek test, provided clinically relevant results in a short turnaround time, showing that the isolate was non-toxigenic. A comparative genomic analysis of the new strain (CHUV2995) with 56 other publicly available genomes of C. diphtheriae revealed that the strains CHUV2995, CCUG 5865 and CMCNS703 share a lower average nucleotide identity (ANI) (95.24 to 95.39%) with the C. diphtheriae NCTC 11397[T] reference genome than all other C. diphtheriae genomes (>98.15%). Core genome phylogeny confirmed the presence of two monophyletic clades. Based on these findings, we propose here two new C. diphtheriae subspecies to replace the lineage denomination used in previous multilocus sequence typing studies: C. diphtheriae subsp. lausannense subsp. nov. (instead of lineage-2), regrouping strains CHUV2995, CCUG 5865, and CMCNS703, and C. diphtheriae subsp. diphtheriae subsp. nov, regrouping all other C. diphtheriae in the dataset (instead of lineage-1). Interestingly, members of subspecies lausannense displayed a larger genome size than subspecies diphtheriae and were enriched in COG categories related to transport and metabolism of lipids (I) and inorganic ion (P). Conversely, they lacked all genes involved in the synthesis of pili (SpaA-type, SpaD-type and SpaH-type), molybdenum cofactor and of the nitrate reductase. Finally, the CHUV2995 genome is particularly enriched in mobility genes and harbors several prophages. The genome encodes a type II-C CRISPR-Cas locus with 2 spacers that lacks csn2 or cas4, which could hamper the acquisition of new spacers and render strain CHUV2995 more susceptible to bacteriophage infections and gene acquisition through various mechanisms of horizontal gene transfer.}, }
@article {pmid30172904, year = {2018}, author = {Alizadeh, N and Seyyed Mousavi, MN and Hajibonabi, F and Memar, MY and Mehramuz, B and Aziziyan, K and Shiralizadeh, S and Yousefi, M and Kafil, HS}, title = {Microbes involving in carcinogenesis; growing state of the art.}, journal = {Microbial pathogenesis}, volume = {125}, number = {}, pages = {1-6}, doi = {10.1016/j.micpath.2018.08.061}, pmid = {30172904}, issn = {1096-1208}, mesh = {Animals ; Bacteria/genetics/pathogenicity ; *Carcinogenesis ; Cell Proliferation ; Communicable Diseases/*complications ; Gene Transfer, Horizontal ; Humans ; Neoplasms/*microbiology/*physiopathology ; Viruses/genetics/pathogenicity ; }, abstract = {Lateral gene transfer (LGT) has been demonstrated as a transfer process of novel genes between different species. LGT proceedings are occurring between microbes and plants, as well as between microbes and animals. New evidence demonstrates that bacterial insertional mutagenesis may occur in cancer cells. Due to the important role of genetic changes in the increase of cell proliferation and cancer development, we reviewed the effects of microbial-animal LGT in human oncogenesis. In addition, viral DNA can induce cancer development by random insertion into cancer-related genes or by inducing translocations. In conclusion, growing evidence shows the contribution of the microbial genome in cancer and autoimmune disease.}, }
@article {pmid30166338, year = {2018}, author = {Rozman Grinberg, I and Lundin, D and Sahlin, M and Crona, M and Berggren, G and Hofer, A and Sjöberg, BM}, title = {A glutaredoxin domain fused to the radical-generating subunit of ribonucleotide reductase (RNR) functions as an efficient RNR reductant.}, journal = {The Journal of biological chemistry}, volume = {293}, number = {41}, pages = {15889-15900}, pmid = {30166338}, issn = {1083-351X}, mesh = {Aerococcaceae/chemistry ; Catalysis ; Deoxyadenine Nucleotides/metabolism ; Flavobacteriaceae/chemistry ; Gene Transfer, Horizontal ; Glutaredoxins/chemistry/genetics/*metabolism ; Oxidation-Reduction ; Protein Binding ; Protein Domains ; Protein Multimerization/drug effects ; Ribonucleotide Reductases/genetics/*metabolism ; }, abstract = {Class I ribonucleotide reductase (RNR) consists of a catalytic subunit (NrdA) and a radical-generating subunit (NrdB) that together catalyze reduction of ribonucleotides to their corresponding deoxyribonucleotides. NrdB from the firmicute Facklamia ignava is a unique fusion protein with N-terminal add-ons of a glutaredoxin (Grx) domain followed by an ATP-binding domain, the ATP cone. Grx, usually encoded separately from the RNR operon, is a known RNR reductant. We show that the fused Grx domain functions as an efficient reductant of the F. ignava class I RNR via the common dithiol mechanism and, interestingly, also via a monothiol mechanism, although less efficiently. To our knowledge, a Grx that uses both of these two reaction mechanisms has not previously been observed with a native substrate. The ATP cone is in most RNRs an N-terminal domain of the catalytic subunit. It is an allosteric on/off switch promoting ribonucleotide reduction in the presence of ATP and inhibiting RNR activity in the presence of dATP. We found that dATP bound to the ATP cone of F. ignava NrdB promotes formation of tetramers that cannot form active complexes with NrdA. The ATP cone bound two dATP molecules but only one ATP molecule. F. ignava NrdB contains the recently identified radical-generating cofactor Mn[III]/Mn[IV] We show that NrdA from F. ignava can form a catalytically competent RNR with the Mn[III]/Mn[IV]-containing NrdB from the flavobacterium Leeuwenhoekiella blandensis In conclusion, F. ignava NrdB is fused with a Grx functioning as an RNR reductant and an ATP cone serving as an on/off switch.}, }
@article {pmid30165560, year = {2018}, author = {Thorpe, P and Escudero-Martinez, CM and Cock, PJA and Eves-van den Akker, S and Bos, JIB}, title = {Shared Transcriptional Control and Disparate Gain and Loss of Aphid Parasitism Genes.}, journal = {Genome biology and evolution}, volume = {10}, number = {10}, pages = {2716-2733}, pmid = {30165560}, issn = {1759-6653}, support = {BB/M014207/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Aphids/*genetics ; Biological Evolution ; Gene Duplication ; *Gene Expression Regulation ; Gene Transfer, Horizontal ; *Genome, Insect ; Herbivory/*genetics ; }, abstract = {Aphids are a diverse group of taxa that contain agronomically important species, which vary in their host range and ability to infest crop plants. The genome evolution underlying agriculturally important aphid traits is not well understood. We generated draft genome assemblies for two aphid species: Myzus cerasi (black cherry aphid) and the cereal specialist Rhopalosiphum padi. Using a de novo gene prediction pipeline on both these, and three additional aphid genome assemblies (Acyrthosiphon pisum, Diuraphis noxia, and Myzus persicae), we show that aphid genomes consistently encode similar gene numbers. We compare gene content, gene duplication, synteny, and putative effector repertoires between these five species to understand the genome evolution of globally important plant parasites. Aphid genomes show signs of relatively distant gene duplication, and substantial, relatively recent, gene birth. Putative effector repertoires, originating from duplicated and other loci, have an unusual genomic organization and evolutionary history. We identify a highly conserved effector pair that is tightly physically linked in the genomes of all aphid species tested. In R. padi, this effector pair is tightly transcriptionally linked and shares an unknown transcriptional control mechanism with a subset of ∼50 other putative effectors and secretory proteins. This study extends our current knowledge on the evolution of aphid genomes and reveals evidence for an as-of-yet unknown shared control mechanism, which underlies effector expression, and ultimately plant parasitism.}, }
@article {pmid30165545, year = {2018}, author = {Simão, MC and Haudry, A and Granzotto, A and de Setta, N and Carareto, CMA}, title = {Helena and BS: Two Travellers between the Genera Drosophila and Zaprionus.}, journal = {Genome biology and evolution}, volume = {10}, number = {10}, pages = {2671-2685}, pmid = {30165545}, issn = {1759-6653}, mesh = {Animals ; *DNA Transposable Elements ; Drosophila/*genetics ; *Gene Transfer, Horizontal ; *Genome, Insect ; Phylogeny ; }, abstract = {The frequency of horizontal transfers of transposable elements (HTTs) varies among the types of elements according to the transposition mode and the geographical and temporal overlap of the species involved in the transfer. The drosophilid species of the genus Zaprionus and those of the melanogaster, obscura, repleta, and virilis groups of the genus Drosophila investigated in this study shared space and time at some point in their evolutionary history. This is particularly true of the subgenus Zaprionus and the melanogaster subgroup, which overlapped both geographically and temporally in Tropical Africa during their period of origin and diversification. Here, we tested the hypothesis that this overlap may have facilitated the transfer of retrotransposons without long terminal repeats (non-LTRs) between these species. We estimated the HTT frequency of the non-LTRs BS and Helena at the genome-wide scale by using a phylogenetic framework and a vertical and horizontal inheritance consistence analysis (VHICA). An excessively low synonymous divergence among distantly related species and incongruities between the transposable element and species phylogenies allowed us to propose at least four relatively recent HTT events of Helena and BS involving ancestors of the subgroup melanogaster and ancestors of the subgenus Zaprionus during their concomitant diversification in Tropical Africa, along with older possible events between species of the subgenera Drosophila and Sophophora. This study provides the first evidence for HTT of non-LTRs retrotransposons between Drosophila and Zaprionus, including an in-depth reconstruction of the time frame and geography of these events.}, }
@article {pmid30160044, year = {2019}, author = {Zhan, Y and Chen, F}, title = {The smallest ssDNA phage infecting a marine bacterium.}, journal = {Environmental microbiology}, volume = {21}, number = {6}, pages = {1916-1928}, doi = {10.1111/1462-2920.14394}, pmid = {30160044}, issn = {1462-2920}, mesh = {Bacteriophages/classification/genetics/*isolation &amp; purification/physiology ; Genome, Viral ; Metagenome ; Microviridae/classification/genetics/isolation &amp; purification/*physiology ; Open Reading Frames ; Phylogeny ; Rhodobacteraceae/genetics/isolation &amp; purification/*virology ; Seawater/microbiology ; Sequence Analysis, DNA ; }, abstract = {In the marine environment, only a few lytic single-stranded DNA (ssDNA) phages have been isolated and characterized, despite the fact that diverse ssDNA bacteriophages have been discovered via metagenomic studies. In this study, we isolated and characterized a new ssDNA phage, vB_RpoMi-Mini, which infects a marine bacterium Ruegeria pomeroyi DSS-3. With a genome size of 4248 bp and only four putative open reading frames (ORF), vB_RpoMi-Mini becomes the smallest ssDNA phage among the known ssDNA phage isolates and represents the DNA bacteriophage with the least number of ORFs. Genome-wide analysis reveals that bacteriophage Mini is distantly related to the known ssDNA phages and belongs to an unclassified ssDNA phage within the Microviridae family. The presence of peptidase in vB_RpoMi-Mini genome further implies that horizontal gene transfer could be an important driving force in the evolution of ssDNA phages. Bacteriophage Mini seems to have lost the spike protein commonly seen in ssDNA phages, suggesting that ssDNA phage can be more diverse than previously thought. Metagenomic analysis indicates that Mini-like phages are widely distributed in the environments. The discovery of vB_RpoMi-Mini expands our understanding of ssDNA phages in nature, and also indicates our dearth of knowledge regarding of ssDNA phages.}, }
@article {pmid30158920, year = {2018}, author = {Li, P and Shen, K and Zhang, Y and Ying, J and Zhu, T and Liu, Y and Xu, L and Lin, C and Zhang, K and Li, P and Lu, J and Li, K and Yi, H and Bao, Q and Xu, T}, title = {Characterization of a Novel blaKLUC Variant With Reduced β-Lactam Resistance From an IncA/C Group Plasmid in a Clinical Klebsiella pneumoniae Isolate.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1908}, pmid = {30158920}, issn = {1664-302X}, abstract = {Similar to other CTX-M family enzymes, KLUC is a recently identified and emerging determinant of cefotaxime resistance that has been recovered from at least three Enterobacteriaceae species, including Kluyvera cryocrescens, Escherichia coli, and Enterobacter cloacae. Whether this extended-spectrum β-lactamase (ESBL) has been disseminated among commonly isolated Enterobacteriaceae is worthy of further investigation. In this study, we screened 739 nosocomial Enterobacteriaceae isolates (240 Klebsiella pneumoniae and 499 E. coli strains) and found that one K. pneumoniae and four E. coli isolates harbored the blaKLUC gene. Three blaKLUC determinants isolated from E. coli were entirely identical to a blaKLUC-3 gene previously recovered in the same hospital. PFGE of four blaKLUC-harboring E. coli strains showed that prevalence of these determinants was most likely mediated by horizontal gene transfer but not clonal dissemination. However, the variant isolated from K. pneumoniae belonged to a novel member of the KLUC enzyme group. This newly identified enzyme (KLUC-5) has an amino acid substitution compared with previously identified KLUC-1 (G18S) and KLUC-3 (G240D). Antimicrobial susceptibility tests showed that KLUC-5 significantly reduced resistance activity to almost all the selected antimicrobials compared to previously identified KLUC-3. Site-directed mutagenesis showed that blaKLUC-5-D240G and blaKLUC-5-S18G significantly enhanced the MIC against its best substrate. Conjugation and S1-PFGE indicated that blaKLUC-5 was located on a transferable plasmid, which was further decoded by single-molecule, real-time sequencing. Comparative genome analysis showed that its backbone exhibited genetic homology to the IncA/C incompatibility group plasmids. A transposable element, ISEcp1, was detected 256-bp upstream of the blaKLUC-5 gene; this location was inconsistent with the previously identified blaKLUC-1 but congruent with the variants recovered from E. coli in the same hospital. These data provide evidence of the increasingly emerging KLUC group of ESBLs in China.}, }
@article {pmid30154804, year = {2018}, author = {Matveeva, T and Provorov, N and Valkonen, JPT}, title = {Editorial: Cooperative Adaptation and Evolution in Plant-Microbe Systems.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {1090}, doi = {10.3389/fpls.2018.01090}, pmid = {30154804}, issn = {1664-462X}, }
@article {pmid30152215, year = {2018}, author = {Ning, N and Wang, H}, title = {[Mechanism and influencing factors of natural transformation in bacteria].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {34}, number = {8}, pages = {1297-1305}, doi = {10.13345/j.cjb.180005}, pmid = {30152215}, issn = {1872-2075}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/*genetics ; Bacteriophages ; Drug Resistance, Bacterial/*genetics ; *Gene Transfer, Horizontal ; }, abstract = {Horizontal gene transfer contributes to the spread of antibiotic-resistance cassettes, the distribution of toxin-encoding phages and the transfer of pathogenicity islands. Natural transformation, which is the process of competent cells to uptake free DNA from environment and to recombine this DNA into the chromosome, is a mode of horizontal gene transfer. Natural transformation promotes the spread of antibiotic-resistance cassettes among different bacteria, resulting in the emergence of antibiotic resistant bacteria. The emergence of antibiotic resistant pathogens poses an enormous threat to the treatment of infections. Natural transformation could occur in many bacteria, but the mechanism many be different in different bacteria. Also, the inducer and efficiency of natural transformation in different bacteria are influenced by various factors. This review focuses on the mechanism and influencing factors of natural transformation in bacteria.}, }
@article {pmid30152208, year = {2018}, author = {Wang, Y and Hu, Y and Zhu, B and Jiao, X and Gao, GF}, title = {[Antibiotic resistome in farm animals and their related environments: a review].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {34}, number = {8}, pages = {1226-1233}, doi = {10.13345/j.cjb.180163}, pmid = {30152208}, issn = {1872-2075}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/*genetics ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Livestock/*microbiology ; }, abstract = {Overuse of antibiotics in livestock farming has enriched antibiotic-resistant genes as well as resistant bacteria in farm animals and their related environments. These antibiotic-resistant genes can spread to the natural environments by horizontal gene transfer and even to the food chain, posing a serious threat to the ecological environment, food safety and human health. With the development of genomic technology, the diversity and ecological distribution of antibiotic-resistant genes in farm animals and their related environments have been recently revealed. Here we summarized the research progress on antibiotic resistance genes in related fields, potential influence on human health, and future research needs.}, }
@article {pmid30150628, year = {2018}, author = {Li, Z and Bock, R}, title = {Replication of bacterial plasmids in the nucleus of the red alga Porphyridium purpureum.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {3451}, pmid = {30150628}, issn = {2041-1723}, support = {ERC-ADG-2014; grant agreement 669982//EC | European Research Council (ERC)/International ; }, mesh = {Cell Nucleus/*metabolism ; Gene Transfer, Horizontal/genetics ; Genome, Plant/genetics ; Plasmids/*genetics ; Porphyridium/*genetics/*microbiology ; Rhodophyta/*genetics/*microbiology ; }, abstract = {Rhodophytes (red algae) are a diverse group of algae with great ecological and economic importance. However, tools for post-genomic research on red algae are still largely lacking. Here, we report the development of an efficient genetic transformation system for the model rhodophyte Porphyridium purpureum. We show that transgenes can be expressed to unprecedented levels of up to 5% of the total soluble protein. Surprisingly, the transgenic DNA is maintained episomally, as extrachromosomal high-copy number plasmid. The bacterial replication origin confers replication in the algal nucleus, thus providing an intriguing example of a prokaryotic replication origin functioning in a eukaryotic system. The extended presence of bacterial episomal elements may provide an evolutionary explanation for the frequent natural occurrence of extrachromosomal plasmids in red algae, and may also have contributed to the high rate of horizontal gene transfer from bacteria to the nuclear genome of Porphyridium purpureum and other rhodophytes.}, }
@article {pmid30149667, year = {2018}, author = {Greiner, T and Moroni, A and Van Etten, JL and Thiel, G}, title = {Genes for Membrane Transport Proteins: Not So Rare in Viruses.}, journal = {Viruses}, volume = {10}, number = {9}, pages = {}, pmid = {30149667}, issn = {1999-4915}, support = {695078/ERC_/European Research Council/International ; }, mesh = {Animals ; Databases, Nucleic Acid ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genome, Viral ; HEK293 Cells ; Host-Pathogen Interactions/genetics ; Humans ; Membrane Transport Proteins/chemistry/*genetics ; Patch-Clamp Techniques ; Phylogeny ; Potassium Channels/genetics ; Sequence Homology, Amino Acid ; Viral Proteins/chemistry/*genetics ; Viruses/*genetics ; }, abstract = {Some viruses have genes encoding proteins with membrane transport functions. It is unknown if these types of proteins are rare or are common in viruses. In particular, the evolutionary origin of some of the viral genes is obscure, where other viral proteins have homologs in prokaryotic and eukaryotic organisms. We searched virus genomes in databases looking for transmembrane proteins with possible transport function. This effort led to the detection of 18 different types of putative membrane transport proteins indicating that they are not a rarity in viral genomes. The most abundant proteins are K[+] channels. Their predicted structures vary between different viruses. With a few exceptions, the viral proteins differed significantly from homologs in their current hosts. In some cases the data provide evidence for a recent gene transfer between host and virus, but in other cases the evidence indicates a more complex evolutionary history.}, }
@article {pmid30149053, year = {2018}, author = {Osborne, CD and Haritos, VS}, title = {Horizontal gene transfer of three co-inherited methane monooxygenase systems gave rise to methanotrophy in the Proteobacteria.}, journal = {Molecular phylogenetics and evolution}, volume = {129}, number = {}, pages = {171-181}, doi = {10.1016/j.ympev.2018.08.010}, pmid = {30149053}, issn = {1095-9513}, mesh = {Bayes Theorem ; *Gene Transfer, Horizontal ; Methane/metabolism ; Oxidation-Reduction ; Oxygenases/*genetics/*metabolism ; Phylogeny ; Proteobacteria/*enzymology/*genetics ; RNA, Ribosomal, 16S/genetics ; Solubility ; }, abstract = {The critical role that bacterial methanotrophs have in regulating the environmental concentrations of the potent greenhouse gas, methane, under aerobic conditions is dependent on monooxygenase enzymes which oxidise the substrate as both a carbon and energy source. Despite the importance of these organisms, the evolutionary origins of aerobic methane oxidation capability and its relationship to proteobacterial evolution is not well understood. Here we investigated the phylogenetic relationship of proteobacterial methanotrophs with related, non-methanotrophic bacteria using 16S rRNA and the evolution of two forms of methane monooxygenase: membrane bound (pMMO and pXMO) and cytoplasmic (sMMO). Through analysis we have concluded that extant proteobacterial methanotrophs evolved from up to five ancestral species, and that all three methane monooxygenase systems, pMMO, pXMO and sMMO, were likely present in the ancestral species (although pXMO and sMMO are not present in most of the present day methanotrophs). Here we propose that the three monooxygenase systems entered the ancestral species by horizontal gene transfer, with these likely to have pre-existing physiological and metabolic attributes that supported conversion to methanotrophy. Further, we suggest that prior to these enzyme systems developing methane oxidation capabilities, the membrane-bound and cytoplasmic monooxygenases were already both functionally and phylogenetically associated. These results not only suggest that sMMO and pXMO have a far greater role in methanotrophic evolution than previously understood but also implies that the co-inheritance of membrane bound and cytoplasmic monooxygenases have roles additional to that of supporting methanotrophy.}, }
@article {pmid30137422, year = {2018}, author = {Kovar, L and Nageswara-Rao, M and Ortega-Rodriguez, S and Dugas, DV and Straub, S and Cronn, R and Strickler, SR and Hughes, CE and Hanley, KA and Rodriguez, DN and Langhorst, BW and Dimalanta, ET and Bailey, CD}, title = {PacBio-Based Mitochondrial Genome Assembly of Leucaena trichandra (Leguminosae) and an Intrageneric Assessment of Mitochondrial RNA Editing.}, journal = {Genome biology and evolution}, volume = {10}, number = {9}, pages = {2501-2517}, pmid = {30137422}, issn = {1759-6653}, support = {52008103/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Fabaceae/*genetics ; Gene Transfer, Horizontal ; *Genome, Mitochondrial ; *RNA Editing ; RNA, Mitochondrial/*genetics ; RNA, Plant/*genetics ; Repetitive Sequences, Nucleic Acid ; Tandem Repeat Sequences ; Tetraploidy ; }, abstract = {Reconstructions of vascular plant mitochondrial genomes (mt-genomes) are notoriously complicated by rampant recombination that has resulted in comparatively few plant mt-genomes being available. The dearth of plant mitochondrial resources has limited our understanding of mt-genome structural diversity, complex patterns of RNA editing, and the origins of novel mt-genome elements. Here, we use an efficient long read (PacBio) iterative assembly pipeline to generate mt-genome assemblies for Leucaena trichandra (Leguminosae: Caesalpinioideae: mimosoid clade), providing the first assessment of non-papilionoid legume mt-genome content and structure to date. The efficiency of the assembly approach facilitated the exploration of alternative structures that are common place among plant mitochondrial genomes. A compact version (729 kbp) of the recovered assemblies was used to investigate sources of mt-genome size variation among legumes and mt-genome sequence similarity to the legume associated root holoparasite Lophophytum. The genome and an associated suite of transcriptome data from select species of Leucaena permitted an in-depth exploration of RNA editing in a diverse clade of closely related species that includes hybrid lineages. RNA editing in the allotetraploid, Leucaena leucocephala, is consistent with co-option of nearly equal maternal and paternal C-to-U edit components, generating novel combinations of RNA edited sites. A preliminary investigation of L. leucocephala C-to-U edit frequencies identified the potential for a hybrid to generate unique pools of alleles from parental variation through edit frequencies shared with one parental lineage, those intermediate between parents, and transgressive patterns.}, }
@article {pmid30137329, year = {2018}, author = {Liu, C and Wright, B and Allen-Vercoe, E and Gu, H and Beiko, R}, title = {Phylogenetic Clustering of Genes Reveals Shared Evolutionary Trajectories and Putative Gene Functions.}, journal = {Genome biology and evolution}, volume = {10}, number = {9}, pages = {2255-2265}, pmid = {30137329}, issn = {1759-6653}, support = {U54 HG004969/HG/NHGRI NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics ; Biological Coevolution ; Clostridiales/*genetics ; Cluster Analysis ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Markov Chains ; Multigene Family ; *Phylogeny ; }, abstract = {Homologous genes in prokaryotes can be described using phylogenetic profiles which summarize their patterns of presence or absence across a set of genomes. Phylogenetic profiles have been used for nearly twenty years to cluster genes based on measures such as the Euclidean distance between profile vectors. However, most approaches do not take into account the phylogenetic relationships amongst the profiled genomes, and overrepresentation of certain taxonomic groups (i.e., pathogenic species with many sequenced representatives) can skew the interpretation of profiles. We propose a new approach that uses a coevolutionary method defined by Pagel to account for the phylogenetic relationships amongst target organisms, and a hierarchical-clustering approach to define sets of genes with common distributions across the organisms. The clusters we obtain using our method show greater evidence of phylogenetic and functional clustering than a recently published approach based on hidden Markov models. Our clustering method identifies sets of amino-acid biosynthesis genes that constitute cohesive pathways, and motility/chemotaxis genes with common histories of descent and lateral gene transfer.}, }
@article {pmid30126366, year = {2018}, author = {Argemi, X and Matelska, D and Ginalski, K and Riegel, P and Hansmann, Y and Bloom, J and Pestel-Caron, M and Dahyot, S and Lebeurre, J and Prévost, G}, title = {Comparative genomic analysis of Staphylococcus lugdunensis shows a closed pan-genome and multiple barriers to horizontal gene transfer.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {621}, pmid = {30126366}, issn = {1471-2164}, support = {2014/15/B/NZ1/03357//Polish National Science Centre/ ; }, mesh = {CRISPR-Cas Systems/genetics ; Gene Transfer, Horizontal/*genetics ; *Genome, Bacterial ; Humans ; Phylogeny ; Sequence Analysis, DNA ; Staphylococcal Infections/microbiology ; Staphylococcus lugdunensis/*genetics ; Virulence ; Virulence Factors/genetics ; }, abstract = {BACKGROUND: Coagulase negative staphylococci (CoNS) are commensal bacteria on human skin. Staphylococcus lugdunensis is a unique CoNS which produces various virulence factors and may, like S. aureus, cause severe infections, particularly in hospital settings. Unlike other staphylococci, it remains highly susceptible to antimicrobials, and genome-based phylogenetic studies have evidenced a highly conserved genome that distinguishes it from all other staphylococci.<br><br>RESULTS: We demonstrate that S. lugdunensis possesses a closed pan-genome with a very limited number of new genes, in contrast to other staphylococci that have an open pan-genome. Whole-genome nucleotide and amino acid identity levels are also higher than in other staphylococci. We identified numerous genetic barriers to horizontal gene transfer that might explain this result. The S. lugdunensis genome has multiple operons encoding for restriction-modification, CRISPR/Cas and toxin/antitoxin systems. We also identified a new PIN-like domain-associated protein that might belong to a larger operon, comprising a metalloprotease, that could function as a new toxin/antitoxin or detoxification system.<br><br>CONCLUSION: We show that S. lugdunensis has a unique genome profile within staphylococci, with a closed pan-genome and several systems to prevent horizontal gene transfer. Its virulence in clinical settings does not rely on its ability to acquire and exchange antibiotic resistance genes or other virulence factors as shown for other staphylococci.}, }
@article {pmid30125679, year = {2018}, author = {Magistrali, CF and Curcio, L and Luppi, A and Pezzotti, G and Orsini, S and Tofani, S and Feudi, C and Carattoli, A and Villa, L}, title = {Mobile colistin resistance genes in Escherichia coli from pigs affected by colibacillosis.}, journal = {International journal of antimicrobial agents}, volume = {52}, number = {5}, pages = {744-746}, doi = {10.1016/j.ijantimicag.2018.08.008}, pmid = {30125679}, issn = {1872-7913}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Colistin/*pharmacology ; *Drug Resistance, Bacterial ; Enterotoxigenic Escherichia coli/classification/*drug effects/genetics/isolation &amp; purification ; Escherichia coli Infections/microbiology/*veterinary ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genotype ; Interspersed Repetitive Sequences ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Plasmids/analysis ; Shiga-Toxigenic Escherichia coli/classification/*drug effects/genetics/isolation &amp; purification ; Swine ; Swine Diseases/*microbiology ; Virulence Factors/genetics ; }, }
@article {pmid30125655, year = {2018}, author = {Chu, H and Jo, Y and Choi, H and Lee, BC and Cho, WK}, title = {Identification of viral domains integrated into Arabidopsis proteome.}, journal = {Molecular phylogenetics and evolution}, volume = {128}, number = {}, pages = {246-257}, doi = {10.1016/j.ympev.2018.08.009}, pmid = {30125655}, issn = {1095-9513}, mesh = {Amino Acid Sequence ; Arabidopsis/genetics/*virology ; Base Sequence ; Chromosomes, Plant/genetics ; Gene Ontology ; Genes, Plant ; Genome, Viral ; Phylogeny ; Plant Viruses/*genetics ; Protein Interaction Maps ; Proteome/*metabolism ; Viral Proteins/genetics ; }, abstract = {Horizontal gene transfer (HGT) contributes to the genome evolution of living organisms. In particular, several recent studies provide convincing data on the integration of viral sequences into diverse organisms. Here, we identified 101 viral domains integrated into the model plant Arabidopsis proteome. Functional analysis based on gene ontology (GO) terms indicates that viral domains in the Arabidopsis proteome were involved in various stress responses with binding functions. Protein interaction networks support the strong protein interactions of viral domains with other Arabidopsis proteins. A proteome-wide analysis gave a comprehensive evolutionary view of viral domains integrated into 41 plant proteomes, revealing the specific and conserved integration of viral domains into plant proteomes. Phylogenetic analyses revealed the possible HGT between viral domains and plant proteomes. Our results provide an overview of the integration of viral domains into plant proteomes and their possible functional roles associated with plant defense mechanisms.}, }
@article {pmid30123321, year = {2018}, author = {Whitford, CM and Dymek, S and Kerkhoff, D and März, C and Schmidt, O and Edich, M and Droste, J and Pucker, B and Rückert, C and Kalinowski, J}, title = {Auxotrophy to Xeno-DNA: an exploration of combinatorial mechanisms for a high-fidelity biosafety system for synthetic biology applications.}, journal = {Journal of biological engineering}, volume = {12}, number = {}, pages = {13}, pmid = {30123321}, issn = {1754-1611}, abstract = {BACKGROUND: Biosafety is a key aspect in the international Genetically Engineered Machine (iGEM) competition, which offers student teams an amazing opportunity to pursue their own research projects in the field of Synthetic Biology. iGEM projects often involve the creation of genetically engineered bacterial strains. To minimize the risks associated with bacterial release, a variety of biosafety systems were constructed, either to prevent survival of bacteria outside the lab or to hinder horizontal or vertical gene transfer.<br><br>MAIN BODY: Physical containment methods such as bioreactors or microencapsulation are considered the first safety level. Additionally, various systems involving auxotrophies for both natural and synthetic compounds have been utilized by iGEM teams in recent years. Combinatorial systems comprising multiple auxotrophies have been shown to reduced escape frequencies below the detection limit. Furthermore, a number of natural toxin-antitoxin systems can be deployed to kill cells under certain conditions. Additionally, parts of naturally occurring toxin-antitoxin systems can be used for the construction of 'kill switches' controlled by synthetic regulatory modules, allowing control of cell survival. Kill switches prevent cell survival but do not completely degrade nucleic acids. To avoid horizontal gene transfer, multiple mechanisms to cleave nucleic acids can be employed, resulting in 'self-destruction' of cells. Changes in light or temperature conditions are powerful regulators of gene expression and could serve as triggers for kill switches or self-destruction systems. Xenobiology-based containment uses applications of Xeno-DNA, recoded codons and non-canonical amino acids to nullify the genetic information of constructed cells for wild type organisms. A 'minimal genome' approach brings the opportunity to reduce the genome of a cell to only genes necessary for survival under lab conditions. Such cells are unlikely to survive in the natural environment and are thus considered safe hosts. If suitable for the desired application, a shift to cell-free systems based on Xeno-DNA may represent the ultimate biosafety system.<br><br>CONCLUSION: Here we describe different containment approaches in synthetic biology, ranging from auxotrophies to minimal genomes, which can be combined to significantly improve reliability. Since the iGEM competition greatly increases the number of people involved in synthetic biology, we will focus especially on biosafety systems developed and applied in the context of the iGEM competition.}, }
@article {pmid30122496, year = {2018}, author = {Prosdocimi, F and Jheeta, S and Torres de Farias, S}, title = {Conceptual challenges for the emergence of the biological system: Cell theory and self-replication.}, journal = {Medical hypotheses}, volume = {119}, number = {}, pages = {79-83}, doi = {10.1016/j.mehy.2018.07.029}, pmid = {30122496}, issn = {1532-2777}, mesh = {Archaea ; Bacteria ; Bacterial Physiological Phenomena ; *Biological Evolution ; DNA/analysis ; DNA Replication ; *Evolution, Molecular ; Models, Biological ; *Origin of Life ; Phylogeny ; RNA/chemistry ; Viruses ; }, abstract = {We re-evaluate research relating to the current theories of the emergence of biological systems. The challenge being that research programmes concerning the emergence of these systems are viewed as the same as those relating to the origin of cells. Cells are strikingly important biological entities, hard wired into the entire field of biology. The development of biological systems took place much earlier than the origin of cells and even before the existence of the Last Universal Common Ancestor (LUCA); a period which could be construed as being preLUCA and which would have taken place during in a ribonucleoprotein world. This latter entity was named FUCA (First Universal Common Ancestor) and could be viewed as a "great-grandmother" to LUCA, from which the three domains of life, namely Archaea, Bacteria, and Eukarya (emerging as a chimera of the two) evolved. RNA-world theories are the focus of mainstream research programmes for the origin of life stricto sensu. In the RNA-world view, self-replication of nucleic acids is seen as one of the most relevant events in the pre-biotic world. Without denying the relevance of self-replication, we argue here that the most germane event which occurred in the pre-biotic world was the crosstalk between nucleic acids and peptides. When these two macromolecules started to interact, the singularity that aggregated the complexity required to produce life began to emerge. Thus, comprehension of the early origins of the translation machinery and the assembly of the genetic code is key. Therefore, the relevance of cell theory and self-replication should be re-evaluated as well as the concept of life itself.}, }
@article {pmid30122234, year = {2018}, author = {Liu, Y}, title = {Darwin's Pangenesis and Graft Hybridization.}, journal = {Advances in genetics}, volume = {102}, number = {}, pages = {27-66}, doi = {10.1016/bs.adgen.2018.05.007}, pmid = {30122234}, issn = {0065-2660}, mesh = {*Biological Evolution ; *Hybridization, Genetic ; Plants/*genetics ; }, abstract = {Although there were many records of graft-induced variations in ancient China, it was Darwin who coined the term "graft hybridization", the formation of hybrids between distinct species or varieties, through plant grafting, without the intervention of the sexual organs. He described many cases of the so-called "graft hybrids", in which shoots produced from grafted plants exhibited a combination of characters of both rootstock and scion, and explained their formation by his Pangenesis. Michurin invented "mentor-grafting" and "preliminary vegetative approximation" methods, which greatly increased the production of graft hybrids, thus providing a solution to Darwin's puzzle. Over the past decides, the existence of graft hybrids has been extensively documented, and graft hybridization is considered to be a simple and efficient means of plant breeding, and would be especially significant in the improvement of fruit trees. Graft hybridization is now explained by horizontal gene transfer and DNA transformation. In addition, the long-distance transport of mRNA and small RNAs is also considered to be involved in the formation of graft hybrids.}, }
@article {pmid30121762, year = {2018}, author = {Kang, W and Zhang, YJ and Shi, X and He, JZ and Hu, HW}, title = {Short-term copper exposure as a selection pressure for antibiotic resistance and metal resistance in an agricultural soil.}, journal = {Environmental science and pollution research international}, volume = {25}, number = {29}, pages = {29314-29324}, pmid = {30121762}, issn = {1614-7499}, support = {DP170103628//Australian Research Council/ ; ACSRF48165//Australian-China Joint Research Centre/ ; }, mesh = {Agriculture ; Anti-Bacterial Agents/pharmacology ; Bacteria/*genetics ; Copper/*adverse effects ; Drug Resistance, Microbial/*genetics ; Genes, Bacterial ; Metals, Heavy/*adverse effects ; Real-Time Polymerase Chain Reaction ; *Selection, Genetic ; *Soil Microbiology ; Soil Pollutants/*adverse effects ; }, abstract = {Owing to the similar mechanisms of antibiotic and metal resistance, there is a growing concern that metal contamination may select for antibiotic resistance genes (ARGs) in the environment. Here, we constructed short-term laboratory microcosms to investigate the dynamics of a wide range of ARGs and two copper (Cu) resistance genes in an agricultural soil amended with a gradient of Cu concentrations (0~1000 mg kg[-1]). Mobile genetic elements (MGEs) were also quantified as a proxy for the horizontal gene transfer potential of ARGs. We detected 126 unique ARGs across all the soil samples using the high-capacity quantitative PCR array, and multidrug and β-lactam resistance were the most abundant ARG categories. The copper amendments significantly enhanced the absolute and relative abundances of ARGs and MGEs, which gradually increased along the gradient of increasing Cu concentrations. The two Cu resistance genes (copA and pcoR) were highly enriched in low-level Cu treatment (50 and 100 mg kg[-1]), and their abundances decreased with the increasing Cu concentrations. The level of metal and antibiotic resistance gradually declined over time in all Cu-amended treatments but was still considerably higher in contaminated soils than untreated soils after 56 days' incubation. Significant associations among ARGs and MGEs were revealed by the network analysis, suggesting the mobility potential of antibiotic resistance in Cu-amended soils. No significant positive correlations were found between ARGs and copper resistance genes, suggesting that these genes are not located in the same bacterial hosts. Taken together, our results provide empirical evidence that short-term copper stress can cause evolution of high-level antibiotic and metal resistance and significantly change the diversity, abundance, and horizontal transfer potential of soil ARGs.}, }
@article {pmid30120119, year = {2018}, author = {Wang, Z and Li, P and Luo, L and Simpson, DJ and Gänzle, MG}, title = {Daqu Fermentation Selects for Heat-Resistant Enterobacteriaceae and Bacilli.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {21}, pages = {}, pmid = {30120119}, issn = {1098-5336}, mesh = {Bacillus/*chemistry/genetics/isolation &amp; purification/*metabolism ; Enterobacteriaceae/*chemistry/genetics/isolation &amp; purification/*metabolism ; Fermentation ; Food Microbiology ; Genomic Islands ; Hot Temperature ; Operon ; Spores, Bacterial/classification/genetics/metabolism ; Wine/analysis/*microbiology ; }, abstract = {Daqu is a spontaneous solid-state cereal fermentation used as saccharification and starter culture in Chinese vinegar and liquor production. The evolution of microbiota in this spontaneous fermentation is controlled by the temperature profile, which reaches temperatures from 50 to 65°C for several days. Despite these high temperatures, mesophilic Enterobacteriaceae (including Cronobacter) and bacilli are present throughout Daqu fermentation. This study aimed to determine whether Daqu spontaneous solid-state fermentation selects for heat-resistant variants of these organisms. Heat resistance in Enterobacteriaceae is mediated by the locus of heat resistance (LHR). One LHR-positive strain of Kosakonia cowanii was identified in Daqu, and it exhibited higher heat resistance than the LHR-negative K. cowanii isolated from malted oats. Heat resistance in Bacillus endospores is mediated by the spoVA[2mob] operon. Out of 10 Daqu isolates of the species Bacillus licheniformis, Brevibacillus parabrevis, Bacillus subtilis, Bacillus amyloliquefaciens, and Bacillus velezensis, 5 did not contain spoVA[2mob], 3 contained one copy, and 2 contained two copies. The presence and copy number of the spoVA[2mob] operon increased the resistance of spores to treatment with 110°C. To confirm the selection of LHR- and spoVA[2mob]-positive strains during Daqu fermentation, the copy numbers of these genetic elements in Daqu samples were quantified by quantitative PCR (qPCR). The abundance of LHR and the spoVA[2mob] operon in community DNA relative to that of total bacterial 16S rRNA genes increased 3-fold and 5-fold, respectively, during processing. In conclusion, culture-dependent and culture-independent analyses suggest that Daqu fermentation selects for heat-resistant Enterobacteriaceae and bacilli.IMPORTANCE Daqu fermentations select for mobile genetic elements conferring heat resistance in Enterobacteriaceae and bacilli. The locus of heat resistance (LHR), a genomic island conferring heat resistance in Enterobacteriaceae, and the spoVA[2mob] operon, conferring heat resistance on bacterial endospores, were enriched 3- to 5-fold during Daqu fermentation and maturation. It is therefore remarkable that the LHR and the spoVA[2mob] operon are accumulated in the same food fermentation. The presence of heat-resistant Kosakonia spp. and Bacillus spp. in Daqu is not of concern for food safety; however, both genomic islands are mobile and transferable to pathogenic bacteria or toxin-producing bacteria by horizontal gene transfer. The identification of the LHR and the spoVA[2mob] operon as indicators of fitness of Enterobacteriaceae and bacilli in Daqu fermentation provides insights into environmental sources of heat-resistant organisms that may contaminate the food supply.}, }
@article {pmid30114187, year = {2018}, author = {Weiss, MC and Preiner, M and Xavier, JC and Zimorski, V and Martin, WF}, title = {The last universal common ancestor between ancient Earth chemistry and the onset of genetics.}, journal = {PLoS genetics}, volume = {14}, number = {8}, pages = {e1007518}, pmid = {30114187}, issn = {1553-7404}, mesh = {Archaea/genetics ; Bacteria/genetics ; Eukaryota/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Code ; Genome ; Mitochondria/genetics ; Nucleic Acid Conformation ; Origin of Life ; *Phylogeny ; Prokaryotic Cells ; }, abstract = {All known life forms trace back to a last universal common ancestor (LUCA) that witnessed the onset of Darwinian evolution. One can ask questions about LUCA in various ways, the most common way being to look for traits that are common to all cells, like ribosomes or the genetic code. With the availability of genomes, we can, however, also ask what genes are ancient by virtue of their phylogeny rather than by virtue of being universal. That approach, undertaken recently, leads to a different view of LUCA than we have had in the past, one that fits well with the harsh geochemical setting of early Earth and resembles the biology of prokaryotes that today inhabit the Earth's crust.}, }
@article {pmid30113623, year = {2018}, author = {Krasovec, M and Vancaester, E and Rombauts, S and Bucchini, F and Yau, S and Hemon, C and Lebredonchel, H and Grimsley, N and Moreau, H and Sanchez-Brosseau, S and Vandepoele, K and Piganeau, G}, title = {Genome Analyses of the Microalga Picochlorum Provide Insights into the Evolution of Thermotolerance in the Green Lineage.}, journal = {Genome biology and evolution}, volume = {10}, number = {9}, pages = {2347-2365}, pmid = {30113623}, issn = {1759-6653}, mesh = {Acclimatization ; Chlorophyta/*genetics/physiology ; *Evolution, Molecular ; Gene Expression Regulation, Plant ; Gene Transfer, Horizontal ; Genome, Plant ; *Heat-Shock Response ; Microalgae/*genetics/physiology ; Phylogeny ; Thermotolerance ; Transcriptome ; }, abstract = {While the molecular events involved in cell responses to heat stress have been extensively studied, our understanding of the genetic basis of basal thermotolerance, and particularly its evolution within the green lineage, remains limited. Here, we present the 13.3-Mb haploid genome and transcriptomes of a halotolerant and thermotolerant unicellular green alga, Picochlorum costavermella (Trebouxiophyceae) to investigate the evolution of the genomic basis of thermotolerance. Differential gene expression at high and standard temperatures revealed that more of the gene families containing up-regulated genes at high temperature were recently evolved, and less originated at the ancestor of green plants. Inversely, there was an excess of ancient gene families containing transcriptionally repressed genes. Interestingly, there is a striking overlap between the thermotolerance and halotolerance transcriptional rewiring, as more than one-third of the gene families up-regulated at 35 °C were also up-regulated under variable salt concentrations in Picochlorum SE3. Moreover, phylogenetic analysis of the 9,304 protein coding genes revealed 26 genes of horizontally transferred origin in P. costavermella, of which five were differentially expressed at higher temperature. Altogether, these results provide new insights about how the genomic basis of adaptation to halo- and thermotolerance evolved in the green lineage.}, }
@article {pmid30107780, year = {2018}, author = {Dong, S and Zhao, C and Chen, F and Liu, Y and Zhang, S and Wu, H and Zhang, L and Liu, Y}, title = {The complete mitochondrial genome of the early flowering plant Nymphaea colorata is highly repetitive with low recombination.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {614}, pmid = {30107780}, issn = {1471-2164}, support = {31470314//National Natural Science Foundation of China/ ; 31600171//National Natural Science Foundation of China/ ; FLSF2017-03//National Natural Science Foundation of China/ ; 201520//Shenzhen Urban Management Bureau Fund/ ; DEB-1240045//National Science Foundation/ ; JCYJ20150529150409546//Shenzhen Municipal Government of China/ ; }, mesh = {*Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/methods ; Mitochondria/*genetics ; Nymphaea/*genetics/growth &amp; development ; *Recombination, Genetic ; Repetitive Sequences, Nucleic Acid ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Mitochondrial genomes of flowering plants (angiosperms) are highly dynamic in genome structure. The mitogenome of the earliest angiosperm Amborella is remarkable in carrying rampant foreign DNAs, in contrast to Liriodendron, the other only known early angiosperm mitogenome that is described as 'fossilized'. The distinctive features observed in the two early flowering plant mitogenomes add to the current confusions of what early flowering plants look like. Expanded sampling would provide more details in understanding the mitogenomic evolution of early angiosperms. Here we report the complete mitochondrial genome of water lily Nymphaea colorata from Nymphaeales, one of the three orders of the earliest angiosperms.<br><br>RESULTS: Assembly of data from Pac-Bio long-read sequencing yielded a circular mitochondria chromosome of 617,195&#xa0;bp with an average depth of 601&#xd7;. The genome encoded 41 protein coding genes, 20 tRNA and three rRNA genes with 25 group II introns disrupting 10 protein coding genes. Nearly half of the genome is composed of repeated sequences, which contributed substantially to the intron size expansion, making the gross intron length of the Nymphaea mitochondrial genome one of the longest among angiosperms, including an 11.4-Kb intron in cox2, which is the longest organellar intron reported to date in plants. Nevertheless, repeat mediated homologous recombination is unexpectedly low in Nymphaea evidenced by 74 recombined reads detected from ten recombinationally active repeat pairs among 886,982 repeat pairs examined. Extensive gene order changes were detected in the three early angiosperm mitogenomes, i.e. 38 or 44 events of inversions and translocations are needed to reconcile the mitogenome of Nymphaea with Amborella or Liriodendron, respectively. In contrast to Amborella with six genome equivalents of foreign mitochondrial DNA, not a single horizontal gene transfer event was observed in the Nymphaea mitogenome.<br><br>CONCLUSIONS: The Nymphaea mitogenome resembles the other available early angiosperm mitogenomes by a similarly rich 64-coding gene set, and many conserved gene clusters, whereas stands out by its highly repetitive nature and resultant remarkable intron expansions. The low recombination level in Nymphaea provides evidence for the predominant master conformation in vivo with a highly substoichiometric set of rearranged molecules.}, }
@article {pmid30103675, year = {2018}, author = {Chen, NWG and Serres-Giardi, L and Ruh, M and Briand, M and Bonneau, S and Darrasse, A and Barbe, V and Gagnevin, L and Koebnik, R and Jacques, MA}, title = {Horizontal gene transfer plays a major role in the pathological convergence of Xanthomonas lineages on common bean.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {606}, pmid = {30103675}, issn = {1471-2164}, support = {ANR-2010-GENM-013-02//Agence Nationale de la Recherche/ ; ANR-10-INBS-0009//Agence Nationale de la Recherche/ ; 154/AP2006-2007//Genoscope/ ; 18/AP2009-2010//Genoscope/ ; }, mesh = {Bacterial Proteins/genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial ; *Host-Pathogen Interactions ; Phaseolus/genetics/growth &amp; development/*microbiology ; Phylogeny ; Plant Diseases/*genetics/microbiology ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Virulence ; Whole Genome Sequencing ; Xanthomonas/classification/*pathogenicity ; }, abstract = {BACKGROUND: Host specialization is a hallmark of numerous plant pathogens including bacteria, fungi, oomycetes and viruses. Yet, the molecular and evolutionary bases of host specificity are poorly understood. In some cases, pathological convergence is observed for individuals belonging to distant phylogenetic clades. This is the case for Xanthomonas strains responsible for common bacterial blight of bean, spread across four genetic lineages. All the strains from these four lineages converged for pathogenicity on common bean, implying possible gene convergences and/or sharing of a common arsenal of genes conferring the ability to infect common bean.<br><br>RESULTS: To search for genes involved in common bean specificity, we used a combination of whole-genome analyses without a priori, including a genome scan based on k-mer search. Analysis of 72 genomes from a collection of Xanthomonas pathovars unveiled 115 genes bearing DNA sequences specific to strains responsible for common bacterial blight, including 20 genes located on a plasmid. Of these 115 genes, 88 were involved in successive events of horizontal gene transfers among the four genetic lineages, and 44 contained nonsynonymous polymorphisms unique to the causal agents of common bacterial blight.<br><br>CONCLUSIONS: Our study revealed that host specificity of common bacterial blight agents is associated with a combination of horizontal transfers of genes, and highlights the role of plasmids in these horizontal transfers.}, }
@article {pmid30102350, year = {2018}, author = {Lo, WS and Gasparich, GE and Kuo, CH}, title = {Convergent Evolution among Ruminant-Pathogenic Mycoplasma Involved Extensive Gene Content Changes.}, journal = {Genome biology and evolution}, volume = {10}, number = {8}, pages = {2130-2139}, pmid = {30102350}, issn = {1759-6653}, mesh = {Biological Evolution ; Genes, Bacterial ; Gram-Negative Bacteria/classification/genetics ; Mycoplasma/*classification/*genetics ; Phylogeny ; Synteny ; }, abstract = {Convergent evolution, a process by which organisms evolved independently to have similar traits, provides opportunities to understand adaptation. The bacterial genus Mycoplasma contains multiple species that evolved independently to become ruminant pathogens, which represents an interesting study system for investigating the process. In this work, we determined the genome sequences of 11 Entomoplasma/Mesoplasma species. This new data set, together with the other available Mollicutes genomes, provided comprehensive taxon sampling for inferring the gene content evolution that led to the emergence of Mycoplasma Mycoides cluster. Our results indicated that the most recent common ancestor (MRCA) of the Mycoides-Entomoplasmataceae clade lost ∼15% of the core genes when it diverged from the Spiroplasma Apis clade. After this initial wave of genome reduction, relatively few gene gains or losses were inferred until the emergence of the Mycoides cluster. Compared with those Entomoplasmataceae lineages that maintained the association with insects, the MRCA of the Mycoides cluster experienced a second wave of gene losses, as well as acquiring >100 novel genes through horizontal gene transfer. These gene acquisitions involved many with the Mycoplasma Hominis/Pneumoniae lineages as the putative donors, suggesting that gene exchanges among these vertebrate symbionts with distinct phylogenetic affiliations may be important in the emergence of the Mycoides cluster. These findings demonstrated that the gene content of bacterial genomes could be exceedingly dynamic, even for those symbionts with highly reduced genomes. Moreover, the emergence of novel pathogens may involve extensive remodeling of gene content, rather than acquisition of few virulence genes.}, }
@article {pmid30099057, year = {2018}, author = {Carroll, LM and Zurfluh, K and Jang, H and Gopinath, G and Nüesch-Inderbinen, M and Poirel, L and Nordmann, P and Stephan, R and Guldimann, C}, title = {First report of an mcr-1-harboring Salmonella enterica subsp. enterica serotype 4,5,12:i:- strain isolated from blood of a patient in Switzerland.}, journal = {International journal of antimicrobial agents}, volume = {52}, number = {5}, pages = {740-741}, doi = {10.1016/j.ijantimicag.2018.08.003}, pmid = {30099057}, issn = {1872-7913}, mesh = {Aged ; Anti-Bacterial Agents/*pharmacology ; Bacteremia/*diagnosis/microbiology/pathology ; Colistin/*pharmacology ; Conjugation, Genetic ; *Drug Resistance, Bacterial ; Escherichia coli Proteins/*genetics ; Gene Transfer, Horizontal ; Humans ; Male ; Microbial Sensitivity Tests ; Polymerase Chain Reaction ; Salmonella Infections/*diagnosis/microbiology/pathology ; Salmonella enterica/drug effects/*genetics/isolation &amp; purification ; Sequence Analysis, DNA ; Serogroup ; Switzerland ; }, }
@article {pmid30097663, year = {2018}, author = {San Millan, A and Toll-Riera, M and Qi, Q and Betts, A and Hopkinson, RJ and McCullagh, J and MacLean, RC}, title = {Integrative analysis of fitness and metabolic effects of plasmids in Pseudomonas aeruginosa PAO1.}, journal = {The ISME journal}, volume = {12}, number = {12}, pages = {3014-3024}, pmid = {30097663}, issn = {1751-7370}, support = {WT106918AIA/WT_/Wellcome Trust/United Kingdom ; G0900747 91070/MRC_/Medical Research Council/United Kingdom ; G0900747/MRC_/Medical Research Council/United Kingdom ; 281591/ERC_/European Research Council/International ; /WT_/Wellcome Trust/United Kingdom ; 090532/Z/09/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*DNA Replication ; DNA, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genetic Fitness ; Plasmids/*genetics ; Pseudomonas aeruginosa/*genetics/physiology ; }, abstract = {Horizontal gene transfer (HGT) mediated by the spread of plasmids fuels evolution in prokaryotes. Although plasmids provide bacteria with new adaptive genes, they also produce physiological alterations that often translate into a reduction in bacterial fitness. The fitness costs associated with plasmids represent an important limit to plasmid maintenance in bacterial communities, but their molecular origins remain largely unknown. In this work, we combine phenomics, transcriptomics and metabolomics to study the fitness effects produced by a collection of diverse plasmids in the opportunistic pathogen Pseudomonas aeruginosa PAO1. Using this approach, we scan the physiological changes imposed by plasmids and test the generality of some main mechanisms that have been proposed to explain the cost of HGT, including increased biosynthetic burden, reduced translational efficiency, and impaired chromosomal replication. Our results suggest that the fitness effects of plasmids have a complex origin, since none of these mechanisms could individually provide a general explanation for the cost of plasmid carriage. Interestingly, our results also showed that plasmids alter the expression of a common set of metabolic genes in PAO1, and produce convergent changes in host cell metabolism. These surprising results suggest that there is a common metabolic response to plasmids in P. aeruginosa PAO1.}, }
@article {pmid30096674, year = {2019}, author = {Cheng, JH and Tang, XY and Cui, JF}, title = {Effect of long-term manure slurry application on the occurrence of antibiotic resistance genes in arable purple soil (entisol).}, journal = {The Science of the total environment}, volume = {647}, number = {}, pages = {853-861}, doi = {10.1016/j.scitotenv.2018.08.028}, pmid = {30096674}, issn = {1879-1026}, mesh = {Agriculture ; Animals ; Anti-Bacterial Agents ; Drug Resistance, Microbial/*genetics ; Environmental Monitoring ; *Genes, Bacterial ; Manure ; Soil/chemistry ; *Soil Microbiology ; Swine ; Waste Disposal, Fluid ; }, abstract = {The application of animal manure is a highly recommended traditional agricultural practice for soils of relatively low fertility. However, for the farmland purple soils that are widely distributed in the upper Yangtze River region, little knowledge has been established in previous studies about the changes in the antibiotic resistome upon manure amendment. In the present study, the impact of long-term pig manure slurry application on the occurrence of antibiotic resistance genes (ARGs) and bacterial community was assessed in arable calcareous purple soil using high-throughput quantitative polymerase chain reaction and Illumina sequencing. Four treatments, including a non-fertilization control (CK) and pig manure (OM), OM plus mineral N fertilizer (OMN) and OM plus mineral NPK fertilizer (OMNPK) treatments were investigated. Across all the soil samples receiving different treatments, a total of 139 unique ARGs and 6 mobile genetic element genes were detected, with multidrug and beta-lactam the two most dominant types of ARGs. The results of the principal coordinate analysis (PCoA) suggest that the profiles of soil ARGs in the two treatments of OM combined with mineral fertilizer(s) (i.e., OMN and OMNPK) were similar to those in the control treatment, while the soil receiving only pig manure application had a different pattern of ARGs from the soils in the other three treatments. A clear reduction of soil ARGs was observed in the OM treatment. Significant and positive relationships were found not only among ARGs but also between mobile genetic elements (MGEs) and ARGs. However, no significant relationships were detected between ARG patterns and bacterial community composition. These results imply that the long-term application of pig manure slurry to purple soil does not lead to the prevalence of ARGs; however, the potential for the horizontal transfer of ARGs in calcareous purple soil should not be ignored.}, }
@article {pmid30086339, year = {2018}, author = {Pinilla-Redondo, R and Cyriaque, V and Jacquiod, S and Sørensen, SJ and Riber, L}, title = {Monitoring plasmid-mediated horizontal gene transfer in microbiomes: recent advances and future perspectives.}, journal = {Plasmid}, volume = {99}, number = {}, pages = {56-67}, doi = {10.1016/j.plasmid.2018.08.002}, pmid = {30086339}, issn = {1095-9890}, mesh = {Anti-Bacterial Agents/adverse effects/therapeutic use ; Bacteria/drug effects/*genetics/pathogenicity ; Conjugation, Genetic ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal/*genetics ; Humans ; Microbiota/genetics ; Plasmids/*genetics ; }, abstract = {The emergence of antimicrobial resistant bacteria constitutes an increasing global health concern. Although it is well recognized that the cornerstone underlying this phenomenon is the dissemination of antimicrobial resistance via plasmids and other mobile genetic elements, the antimicrobial resistance transfer routes remain largely uncharted. In this review, we describe different methods for assessing the transfer frequency and host ranges of plasmids within complex microbiomes. The discussion is centered around the critical evaluation of recent advances for monitoring the fate of fluorescently tagged plasmids in bacterial communities through the coupling of fluorescence activated cell sorting and next generation sequencing techniques. We argue that this approach constitutes an exceptional tool for obtaining quantitative data regarding the extent of plasmid transfer, key disseminating taxa, and possible propagation routes. The integration of this information will provide valuable insights on how to develop alternative avenues for fighting the rise of antimicrobial resistant pathogens, as well as the means for constructing more comprehensive risk assessment models.}, }
@article {pmid30085064, year = {2018}, author = {Grüll, MP and Mulligan, ME and Lang, AS}, title = {Small extracellular particles with big potential for horizontal gene transfer: membrane vesicles and gene transfer agents.}, journal = {FEMS microbiology letters}, volume = {365}, number = {19}, pages = {}, doi = {10.1093/femsle/fny192}, pmid = {30085064}, issn = {1574-6968}, mesh = {Bacteria/*genetics ; *Cytoplasmic Vesicles ; DNA, Bacterial ; *Gene Transfer, Horizontal ; Intracellular Membranes ; }, abstract = {Bacteria are known to release different types of particles that serve various purposes such as the processing of metabolites, communication, and the transfer of genetic material. One of the most interesting aspects of the production of such particles is the biogenesis and trafficking of complex particles that can carry DNA, RNA, proteins or toxins into the surrounding environment to aid in bacterial survival or lead to gene transfer. Two important bacterial extracellular complexes are membrane vesicles and gene transfer agents. In this review, we will discuss the production, contents and functions of these two types of particles as related to their abilities to facilitate horizontal gene transfer.}, }
@article {pmid30085063, year = {2018}, author = {Buckner, MMC and Ciusa, ML and Piddock, LJV}, title = {Strategies to combat antimicrobial resistance: anti-plasmid and plasmid curing.}, journal = {FEMS microbiology reviews}, volume = {42}, number = {6}, pages = {781-804}, pmid = {30085063}, issn = {1574-6976}, support = {/WT_/Wellcome Trust/United Kingdom ; MR/N012933/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics ; Drug Resistance, Bacterial/*genetics ; Environmental Microbiology ; Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Humans ; Plasmids/*genetics ; }, abstract = {Antimicrobial resistance (AMR) is a global problem hindering treatment of bacterial infections, rendering many aspects of modern medicine less effective. AMR genes (ARGs) are frequently located on plasmids, which are self-replicating elements of DNA. They are often transmissible between bacteria, and some have spread globally. Novel strategies to combat AMR are needed, and plasmid curing and anti-plasmid approaches could reduce ARG prevalence, and sensitise bacteria to antibiotics. We discuss the use of curing agents as laboratory tools including chemicals (e.g. detergents and intercalating agents), drugs used in medicine including ascorbic acid, psychotropic drugs (e.g. chlorpromazine), antibiotics (e.g. aminocoumarins, quinolones and rifampicin) and plant-derived compounds. Novel strategies are examined; these include conjugation inhibitors (e.g. TraE inhibitors, linoleic, oleic, 2-hexadecynoic and tanzawaic acids), systems designed around plasmid incompatibility, phages and CRISPR/Cas-based approaches. Currently, there is a general lack of in vivo curing options. This review highlights this important shortfall, which if filled could provide a promising mechanism to reduce ARG prevalence in humans and animals. Plasmid curing mechanisms which are not suitable for in vivo use could still prove important for reducing the global burden of AMR, as high levels of ARGs exist in the environment.}, }
@article {pmid30085054, year = {2018}, author = {Pindling, S and Azulai, D and Zheng, B and Dahan, D and Perron, GG}, title = {Dysbiosis and early mortality in zebrafish larvae exposed to subclinical concentrations of streptomycin.}, journal = {FEMS microbiology letters}, volume = {365}, number = {18}, pages = {}, pmid = {30085054}, issn = {1574-6968}, mesh = {Animals ; Anti-Bacterial Agents/*administration &amp; dosage ; Drug Resistance, Bacterial ; Dysbiosis/*chemically induced ; Gastrointestinal Microbiome/*drug effects ; Gene Transfer, Horizontal ; Interspersed Repetitive Sequences ; Larva/*drug effects/microbiology/physiology ; Selection, Genetic ; Streptomycin/*administration &amp; dosage ; Survival Analysis ; Zebrafish/*embryology/microbiology ; }, abstract = {Exposure to low concentrations of antibiotics found in aquatic environments can increase susceptibility to infection in adult fish due to microbiome disruption. However, little is known regarding the effect of antibiotic pollution on fish larvae. Here, we show that exposure to streptomycin, a common antibiotic used in medicine and aquaculture, disrupts the normal composition of zebrafish larvae microbiomes, significantly reducing the microbial diversity found in the fish. Exposure to streptomycin also significantly increased early mortality among fish larvae, causing full mortality within a few days of exposure at 10 μg/mL. Finally, we found that subclinical concentrations of streptomycin also increased the abundance of class 1 integrons, an integrase-dependent genetic system associated to the horizontal transfer of antibiotic resistance genes, in the larvae microbiomes. These results suggest that even low concentrations of streptomycin associated with environmental pollution could impact fish populations and lead to the creation of antibiotic resistance reservoirs.}, }
@article {pmid30084143, year = {2019}, author = {Roossinck, MJ}, title = {Evolutionary and ecological links between plant and fungal viruses.}, journal = {The New phytologist}, volume = {221}, number = {1}, pages = {86-92}, doi = {10.1111/nph.15364}, pmid = {30084143}, issn = {1469-8137}, support = {//Huck Institute of Life Sciences and the College of Agricultural Science/International ; //Penn State University/International ; }, mesh = {*Biological Evolution ; Ecosystem ; Fungal Viruses/genetics/*physiology ; Fungi/virology ; Metagenomics/methods ; Phylogeny ; Plant Viruses/genetics/*physiology ; Plants/virology ; }, abstract = {Contents Summary 86 I. Introduction 86 II. Lineages shared by plant and fungal viruses 87 III. Virus transmission between plants and fungi 90 IV. Additional plant virus families identified in fungi by metagenomics 91 Acknowledgements 91 References 91 SUMMARY: Plants and microorganisms have been interacting in both positive and negative ways for millions of years. They are also frequently infected with viruses that can have positive or negative impacts. A majority of virus families with members that infect fungi have counterparts that infect plants, and in some cases the phylogenetic analyses of these virus families indicate transmission between the plant and fungal kingdoms. These similarities reflect the host relationships; fungi are evolutionarily more closely related to animals than to plants but share very few viral signatures with animal viruses. The details of several of these interactions are described, and the evolutionary implications of viral cross-kingdom interactions and horizontal gene transfer are proposed.}, }
@article {pmid30084090, year = {2018}, author = {Velimirov, B and Ranftler, C}, title = {Unexpected aspects in the dynamics of horizontal gene transfer of prokaryotes: the impact of outer membrane vesicles.}, journal = {Wiener medizinische Wochenschrift (1946)}, volume = {168}, number = {11-12}, pages = {307-313}, pmid = {30084090}, issn = {1563-258X}, mesh = {*Escherichia coli/genetics ; *Gene Transfer, Horizontal/genetics ; Genomics/*methods ; }, abstract = {Horizontal gene transfer (HGT) was observed by incubation of an amino acid-deficient strain of Escherichia coli (AB1157) with particles gained from an oligotrophic environment, when all deficiencies were restored with frequencies up to 1.94 × 10[-5] and no preference for a single marker. Hence, the DNA transfer to the revertant cells was carried out by generalized transduction. Those particles display structural features of outer membrane vesicles (OMVs) but contain high amounts of DNA. Due to a process called serial transduction, the revertant's particles were likewise transferring genetic information to deficient E. coli AB1157 cells. These results indicate a new way of HGT, in which mobilized DNA is transferred in particles from the donor to the recipient. Extracted OMV-associated DNA of known alpha-, and gamma-proteobacterials, Ahrensia kielensis and Pseudoalteromonas marina, respectively, was larger than 30 kbp with all sequences in single copy and identified as prokaryotic sequences. Inserted viral sequences were not found.}, }
@article {pmid30083465, year = {2018}, author = {Matsuo, E and Inagaki, Y}, title = {Patterns in evolutionary origins of heme, chlorophyll a and isopentenyl diphosphate biosynthetic pathways suggest non-photosynthetic periods prior to plastid replacements in dinoflagellates.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e5345}, pmid = {30083465}, issn = {2167-8359}, abstract = {BACKGROUND: The ancestral dinoflagellate most likely established a peridinin-containing plastid, which have been inherited in the extant photosynthetic descendants. However, kareniacean dinoflagellates and Lepidodinium species were known to bear "non-canonical" plastids lacking peridinin, which were established through haptophyte and green algal endosymbioses, respectively. For plastid function and maintenance, the aforementioned dinoflagellates were known to use nucleus-encoded proteins vertically inherited from the ancestral dinoflagellates (vertically inherited- or VI-type), and those acquired from non-dinoflagellate organisms (including the endosymbiont). These observations indicated that the proteomes of the non-canonical plastids derived from a haptophyte and a green alga were modified by "exogenous" genes acquired from non-dinoflagellate organisms. However, there was no systematic evaluation addressing how "exogenous" genes reshaped individual metabolic pathways localized in a non-canonical plastid.<br><br>RESULTS: In this study, we surveyed transcriptomic data from two kareniacean species (Karenia brevis and Karlodinium veneficum) and Lepidodinium chlorophorum, and identified proteins involved in three plastid metabolic pathways synthesizing chlorophyll a (Chl a), heme and isoprene. The origins of the individual proteins of our interest were investigated, and we assessed how the three pathways were modified before and after the algal endosymbioses, which gave rise to the current non-canonical plastids. We observed a clear difference in the contribution of VI-type proteins across the three pathways. In both Karenia/Karlodinium and Lepidodinium, we observed a substantial contribution of VI-type proteins to the isoprene and heme biosynthesises. In sharp contrast, VI-type protein was barely detected in the Chl a biosynthesis in the three dinoflagellates.<br><br>DISCUSSION: Pioneering works hypothesized that the ancestral kareniacean species had lost the photosynthetic activity prior to haptophyte endosymbiosis. The absence of VI-type proteins in the Chl a biosynthetic pathway in Karenia or Karlodinium is in good agreement with the putative non-photosynthetic nature proposed for their ancestor. The dominance of proteins with haptophyte origin in the Karenia/Karlodinium pathway suggests that their ancestor rebuilt the particular pathway by genes acquired from the endosymbiont. Likewise, we here propose that the ancestral Lepidodinium likely experienced a non-photosynthetic period and discarded the entire Chl a biosynthetic pathway prior to the green algal endosymbiosis. Nevertheless, Lepidodinium rebuilt the pathway by genes transferred from phylogenetically diverse organisms, rather than the green algal endosymbiont. We explore the reasons why green algal genes were barely utilized to reconstruct the Lepidodinium pathway.}, }
@article {pmid30081098, year = {2018}, author = {Stasyk, OG and Denega, IO and Padhorny, D and Dmytruk, KV and Kozakov, D and Abbas, C and Stasyk, OV}, title = {Glucose regulation in the methylotrophic yeast Hansenula (Ogataea) polymorpha is mediated by a putative transceptor Gcr1.}, journal = {The international journal of biochemistry &amp; cell biology}, volume = {103}, number = {}, pages = {25-34}, doi = {10.1016/j.biocel.2018.08.002}, pmid = {30081098}, issn = {1878-5875}, mesh = {*Fungal Proteins/genetics/metabolism ; *Gene Expression Regulation, Fungal ; Glucose/*metabolism ; *Pichia/genetics/metabolism ; *Receptors, G-Protein-Coupled/genetics/metabolism ; }, abstract = {The HpGcr1, a hexose transporter homologue from the methylotrophic yeast Hansenula (Ogataea) polymorpha, was previously identified as being involved in glucose repression. Intriguingly, potential HpGcr1 orthologues are found only in the genomes of a few yeasts phylogenetically closely related to H. polymorpha, but are absent in all other yeasts. The other closest HpGcr1 homologues are fungal high-affinity glucose symporters or putative transceptors suggesting a possible HpGcr1 origin due to a specific archaic gene retention or via horizontal gene transfer from Eurotiales fungi. Herein we report that, similarly to other yeast non-transporting glucose sensors, the substitution of the conserved arginine residue converts HpGcr1[R165K] into a constitutively signaling form. Synthesis of HpGcr1[R165K] in gcr1Δ did not restore glucose transport or repression but instead profoundly impaired growth independent of carbon source used. Simultaneously, gcr1Δ was impaired in transcriptional induction of repressible peroxisomal alcohol oxidase and in growth on methanol. Overexpression of the functional transporter HpHxt1 in gcr1Δ partially restored growth on glucose and glucose repression but did not rescue impaired growth on methanol. Heterologous expression of HpGcr1 in a Saccharomyces cerevisiae hxt-null strain did not restore glucose uptake due to protein mislocalization. However, HpGcr1 overexpression in H. polymorpha led to increased sensitivity to extracellular 2-deoxyglucose, suggesting HpGcr1 is a functional glucose carrier. The combined data suggest that HpGcr1 represents a novel type of yeast glucose transceptor functioning also in the absence of glucose.}, }
@article {pmid30080276, year = {2018}, author = {Gieseler, F and Plattfaut, C and Quecke, T and Freund, A and Ungefroren, H and Ender, F}, title = {Heterogeneity of microvesicles from cancer cell lines under inflammatory stimulation with TNF-α.}, journal = {Cell biology international}, volume = {42}, number = {11}, pages = {1533-1544}, doi = {10.1002/cbin.11040}, pmid = {30080276}, issn = {1095-8355}, support = {AAS1612//Annelise-Asmussen Stiftung, Luebeck, Germany/ ; //LEO Pharma GmbH, Frankfurt, Germany/ ; }, mesh = {Biological Assay ; Caspase 3/metabolism ; Cell Count ; Cell Line, Tumor ; Cell Movement ; Extracellular Vesicles/drug effects/*metabolism/ultrastructure ; Humans ; Inflammation/*pathology ; Oligopeptides/pharmacology ; Phosphatidylserines/metabolism ; Receptor, PAR-2/antagonists &amp; inhibitors/metabolism ; Signal Transduction/drug effects ; Thromboplastin/metabolism ; Tumor Necrosis Factor-alpha/*adverse effects ; }, abstract = {Microvesicles (MVs) represent a subgroup of extracellular vesicles (EVs) emerging from various cells by blebbing of their outer membrane. Therefore, they share features such as membrane composition and antigenicity with their parental cells. Released by many immune and tumor cells, MVs act as intercellular messengers, account for horizontal gene transfer and can activate the coagulation system. With the aim to investigate their relevance for tumor cell biology, we characterized MVs released by human tumor cell lines of various origins in the absence or presence of TNF-α. After stimulation, we used the combination of low and high-speed centrifugation to enrich MVs from cell culture supernatants. We analyzed the presentation of phosphatidylserine (PS) and tissue factor (TF) activity on the cell surface and investigated their potency to induce tumor cell migration. In all tumor cell lines, TNF-α stimulation enhanced the release of MVs. While the expression of PS was universally increased, an elevated activity of procoagulant TF could be detected on MVs from lung, pancreatic, and colon carcinoma, but not from breast and ovarian cancer cell lines. Functionally, TNF-α stimulation significantly increased the potency of MVs to induce tumor cell migration. In conclusion, inflammatory conditions promote the release of MVs with increased procoagulant activity from tumor cell lines in vitro. PS-containing and TF-expressing MVs may account for systemic activation of the coagulation system as seen in cancer patients and, since they induce tumor cell migration, they may serve as biomarkers for tumor progression.}, }
@article {pmid30076977, year = {2019}, author = {De Backer, S and Xavier, BB and Vanjari, L and Coppens, J and Lammens, C and Vemu, L and Carevic, B and Hryniewicz, W and Jorens, P and Kumar-Singh, S and Lee, A and Harbarth, S and Schrenzel, J and Tacconelli, E and Goossens, H and Malhotra-Kumar, S}, title = {Remarkable geographical variations between India and Europe in carriage of the staphylococcal surface protein-encoding sasX/sesI and in the population structure of methicillin-resistant Staphylococcus aureus belonging to clonal complex 8.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {25}, number = {5}, pages = {628.e1-628.e7}, doi = {10.1016/j.cmi.2018.07.024}, pmid = {30076977}, issn = {1469-0691}, mesh = {Bacterial Proteins/*genetics ; Carrier State/*epidemiology/microbiology ; Europe/epidemiology ; *Genotype ; Humans ; India/epidemiology ; Membrane Proteins/*genetics ; Methicillin-Resistant Staphylococcus aureus/*genetics/isolation &amp; purification ; Molecular Epidemiology ; Multilocus Sequence Typing ; Polymerase Chain Reaction ; Staphylococcal Infections/*epidemiology/microbiology ; Tertiary Care Centers ; Whole Genome Sequencing ; }, abstract = {OBJECTIVES: sasX is a colonization-virulence factor that potentially underlies the success of methicillin-resistant Staphylococcus aureus (MRSA) sequence type (ST) 239 in Asia. We aimed to study the spread of sasX and the population structure of MRSA in two geographically distinct regions, Europe and India.<br><br>METHODS: MRSA (n&#xa0;=&#xa0;128) from screening and clinical samples from tertiary care patients in 12 European countries (n&#xa0;=&#xa0;119), and from India (n&#xa0;=&#xa0;9) were multilocus-sequence-typed and screened for sasX and its carrier &#x3c6;SP&#x3b2;-like prophage by PCR. Whole genome sequencing was performed on sasX-harbouring strains from India (n&#xa0;=&#xa0;5) and Europe (n&#xa0;=&#xa0;2) and on a selection non-harbouring sasX (n&#xa0;=&#xa0;36) (2&#xa0;&#xd7;&#xa0;150 bp, Miseq, Illumina). Reads were mapped to the ST239 reference strain, TW20.<br><br>RESULTS: sasX and sesI, a sasX homologue native to Staphylococcus epidermidis, were detected in five of the nine Indian MRSA belonging to ST239 and to other sequence types of CC8. In contrast, sasX was restricted to two ST239 strains in Europe. The intact sasX and sesI carrier &#x3c6;SP&#x3b2;-like prophages were &#x223c;80 kb and &#x223c;118 kb, and integrated in the yeeE gene. We identified 'novel' ST239 clades in India and Serbia that showed significant differences in base substitution frequencies (0.130 and 0.007, respectively, Tamura-Nei model) (p <0.05).<br><br>CONCLUSIONS: Our data highlight dissemination of sasX to non-ST239 sequence types of CC8. Detection of the S.&#xa0;epidermidis-associated sesI in MRSA provided unquestionable evidence of transfer between the two species. Stark differences in evolutionary rates between the novel Indian and Serbian ST239 clades identified here might be due to inherent clade characteristics or influenced by other environmental differences such as antibiotic use.}, }
@article {pmid30076785, year = {2018}, author = {Stewart, L and D M Edgar, J and Blakely, G and Patrick, S}, title = {Antigenic mimicry of ubiquitin by the gut bacterium Bacteroides fragilis: a potential link with autoimmune disease.}, journal = {Clinical and experimental immunology}, volume = {194}, number = {2}, pages = {153-165}, pmid = {30076785}, issn = {1365-2249}, mesh = {Adult ; Antibody Specificity/genetics/*immunology ; Antigens, Bacterial/chemistry/genetics/*immunology ; Autoantibodies/blood ; Autoimmune Diseases/*immunology/microbiology ; Autoimmunity ; Bacteroides fragilis/*immunology ; Cross Reactions ; Gastrointestinal Microbiome/*immunology ; Gene Transfer, Horizontal ; Humans ; Middle Aged ; Models, Molecular ; Molecular Conformation ; Molecular Mimicry ; Structure-Activity Relationship ; Ubiquitin/chemistry/genetics/*immunology ; }, abstract = {Ubiquitin is highly conserved across eukaryotes and is essential for normal eukaryotic cell function. The bacterium Bacteroides fragilis is a member of the normal human gut microbiota, and the only bacterium known to encode a homologue of eukaryotic ubiquitin. The B. fragilis gene sequence indicates a past horizontal gene transfer event from a eukaryotic source. It encodes a protein (BfUbb) with 63% identity to human ubiquitin which is exported from the bacterial cell. The aim of this study was (i) to determine if there was antigenic cross-reactivity between B. fragilis ubiquitin and human ubiquitin and (ii) to determine if humans produced antibodies to BfUbb. Molecular model comparisons of BfUbb and human ubiquitin predicted a high level (99·8% confidence) of structural similarity. Linear epitope mapping identified epitopes in BfUbb and human ubiquitin that cross-react. BfUbb also has epitope(s) that do not cross-react with human ubiquitin. The reaction of human serum (n = 474) to BfUbb and human ubiquitin from the following four groups of subjects was compared by enzyme-linked immunosorbent assay (ELISA): (1) newly autoantibody-positive patients, (2) allergen-specific immunoglobulin (Ig)E-negative patients, (3) ulcerative colitis patients and (4) healthy volunteers. We show that the immune system of some individuals has been exposed to BfUbb which has resulted in the generation of IgG antibodies. Serum from patients referred for first-time testing to an immunology laboratory for autoimmune disease are more likely to have a high level of antibodies to BfUbb than healthy volunteers. Molecular mimicry of human ubiquitin by BfUbb could be a trigger for autoimmune disease.}, }
@article {pmid30076773, year = {2019}, author = {Meline, V and Delage, W and Brin, C and Li-Marchetti, C and Sochard, D and Arlat, M and Rousseau, C and Darrasse, A and Briand, M and Lebreton, G and Portier, P and Fischer-Le Saux, M and Durand, K and Jacques, MA and Belin, E and Boureau, T}, title = {Role of the acquisition of a type 3 secretion system in the emergence of novel pathogenic strains of Xanthomonas.}, journal = {Molecular plant pathology}, volume = {20}, number = {1}, pages = {33-50}, pmid = {30076773}, issn = {1364-3703}, mesh = {Mutagenesis, Insertional/genetics ; Necrosis ; Phylogeny ; Plasmids/genetics ; Seeds/microbiology ; Nicotiana/microbiology ; Type III Secretion Systems/*metabolism ; Xanthomonas/isolation &amp; purification/*metabolism/*pathogenicity ; }, abstract = {Cases of emergence of novel plant-pathogenic strains are regularly reported that reduce the yields of crops and trees. However, the molecular mechanisms underlying such emergence are still poorly understood. The acquisition by environmental non-pathogenic strains of novel virulence genes by horizontal gene transfer has been suggested as a driver for the emergence of novel pathogenic strains. In this study, we tested such an hypothesis by transferring a plasmid encoding the type 3 secretion system (T3SS) and four associated type 3 secreted proteins (T3SPs) to the non-pathogenic strains of Xanthomonas CFBP 7698 and CFBP 7700, which lack genes encoding T3SS and any previously known T3SPs. The resulting strains were phenotyped on Nicotiana benthamiana using chlorophyll fluorescence imaging and image analysis. Wild-type, non-pathogenic strains induced a hypersensitive response (HR)-like necrosis, whereas strains complemented with T3SS and T3SPs suppressed this response. Such suppression depends on a functional T3SS. Amongst the T3SPs encoded on the plasmid, Hpa2, Hpa1 and, to a lesser extent, XopF1 collectively participate in suppression. Monitoring of the population sizes in planta showed that the sole acquisition of a functional T3SS by non-pathogenic strains impairs growth inside leaf tissues. These results provide functional evidence that the acquisition via horizontal gene transfer of a T3SS and four T3SPs by environmental non-pathogenic strains is not sufficient to make strains pathogenic. In the absence of a canonical effector, the sole acquisition of a T3SS seems to be counter-selective, and further acquisition of type 3 effectors is probably needed to allow the emergence of novel pathogenic strains.}, }
@article {pmid30075254, year = {2018}, author = {Fogolari, M and Mavian, C and Angeletti, S and Salemi, M and Lampel, KA and Maurelli, AT}, title = {Distribution and characterization of Shiga toxin converting temperate phages carried by Shigella flexneri in Hispaniola.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {65}, number = {}, pages = {321-328}, pmid = {30075254}, issn = {1567-7257}, support = {R01 AI024656/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteriophages/*genetics/*physiology ; Dominican Republic/epidemiology ; Dysentery, Bacillary/epidemiology/microbiology ; Gene Transfer, Horizontal ; Genetic Variation ; Haiti/epidemiology ; Humans ; Phylogeography ; Polymorphism, Single Nucleotide ; Shiga Toxin/*metabolism ; Shigella flexneri/*metabolism/*virology ; }, abstract = {Shigella infections account for a considerable burden of acute diarrheal diseases worldwide and remain a major cause of childhood mortality in developing countries. Although, all four species of Shigella (S. dysenteriae, S. flexneri, S. boydii, and S. sonnei) cause bacillary dysentery, historically only S. dysenteriae type 1 has been recognized as carrying the genes for Shiga toxin (stx). Recent epidemiological data, however, have suggested that the emergence of stx carrying S. flexneri strains may have originated from bacteriophage-mediated inter-species horizontal gene transfer in one specific geographical area, Hispaniola. To test this hypothesis, we analyzed whole genome sequences of stx-encoding phages carried by S. flexneri strains isolated in Haiti and S. flexneri S. boydii and S. dysenteriae strains isolated from international travelers who likely acquired the infection in Haiti or the Dominican Republic. Phylogenetic analysis showed that phage sequences encoded in the Shigella strains from Hispaniola were bacteriophage φPOC-J13 and they were all closely related to a phage isolated from a USA isolate, E. coli 2009C-3133 serotype O119:H4. In addition, despite the low genetic heterogeneity of phages from different Shigella spp. circulating in the Caribbean island between 2001 and 2014, two distinct clusters emerged in Haiti and the Dominican Republic. Each cluster possibly originated from phages isolated from S. flexneri 2a, and within each cluster several instances of horizontal phage transfer from S. flexneri 2a to other species were detected. The implications of the emergence of stx-producing non-S. dysenteriae type 1 Shigella species, such as S. flexneri, spans not only the basic science behind horizontal phage spread, but also extends to medical treatment of patients infected with this pathogen.}, }
@article {pmid30072959, year = {2018}, author = {González-Torres, P and Gabaldón, T}, title = {Genome Variation in the Model Halophilic Bacterium Salinibacter ruber.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1499}, pmid = {30072959}, issn = {1664-302X}, abstract = {The halophilic bacterium Salinibacter ruber is an abundant and ecologically important member of halophilic communities worldwide. Given its broad distribution and high intraspecific genetic diversity, S. ruber is considered one of the main models for ecological and evolutionary studies of bacterial adaptation to hypersaline environments. However, current insights on the genomic diversity of this species is limited to the comparison of the genomes of two co-isolated strains. Here, we present a comparative genomic analysis of eight S. ruber strains isolated at two different time points in each of two different Mediterranean solar salterns. Our results show an open pangenome with contrasting evolutionary patterns in the core and accessory genomes. We found that the core genome is shaped by extensive homologous recombination (HR), which results in limited sequence variation within population clusters. In contrast, the accessory genome is modulated by horizontal gene transfer (HGT), with genomic islands and plasmids acting as gateways to the rest of the genome. In addition, both types of genetic exchange are modulated by restriction and modification (RM) or CRISPR-Cas systems. Finally, genes differentially impacted by such processes reveal functional processes potentially relevant for environmental interactions and adaptation to extremophilic conditions. Altogether, our results support scenarios that conciliate "Neutral" and "Constant Diversity" models of bacterial evolution.}, }
@article {pmid30071355, year = {2018}, author = {Djenadi, K and Zhang, L and Murray, AK and Gaze, WH}, title = {Carbapenem resistance in bacteria isolated from soil and water environments in Algeria.}, journal = {Journal of global antimicrobial resistance}, volume = {15}, number = {}, pages = {262-267}, doi = {10.1016/j.jgar.2018.07.013}, pmid = {30071355}, issn = {2213-7173}, mesh = {Algeria ; Anti-Bacterial Agents/*pharmacology ; Carbapenems/*pharmacology ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Gram-Negative Bacteria/classification/*drug effects/genetics/*isolation &amp; purification ; Mass Spectrometry ; Microbial Sensitivity Tests ; *Soil Microbiology ; *Water Microbiology ; }, abstract = {OBJECTIVES: Recent research has demonstrated that natural populations of bacteria carry large numbers of mobile genetic elements that may harbour antibiotic resistance determinants. This study aimed to investigate carbapenem resistance in Gram-negative bacteria isolated from natural environments in Béjaïa (Algeria) and to determine the horizontal gene transfer potential of a subset of these antibiotic resistance genes (ARGs).<br><br>METHODS: Antibiotic-resistant bacteria were isolated and the host was identified using MALDI-TOF/MS and 16S rRNA sequencing. ARG carriage was investigated by the double-disk synergy test, metallo-&#x3b2;-lactamase (MBL) production test and PCR screening for carbapenemase genes. Conjugation experiments were performed to determine potential ARG mobility. To identify ARGs, genomic libraries were constructed and functionally screened and inserts were sequenced.<br><br>RESULTS: A total of 62 antibiotic-resistant strains isolated from soil and water samples were classified as belonging to the Enterobacteriaceae, Pseudomonadaceae, Xanthomonadaceae and Aeromonadaceae families. Four highly imipenem-resistant (MIC>64&#x3bc;g/mL) and cefotaxime-resistant (MIC>8&#x3bc;g/mL) clinically-relevant strains were selected for further characterisation. All four strains produced extended-spectrum &#x3b2;-lactamases, but MBL production was not confirmed. Imipenem and cefotaxime resistance was transferable to Escherichia coli but was not conferred by blaAmpC, blaIMP, blaNDM, blaKPC, blaOXA-48 or blaGES genes. Novel putative resistance mechanisms were identified, including a novel DHA &#x3b2;-lactamase conferring clinical resistance to cefotaxime.<br><br>CONCLUSIONS: The environment is a reservoir of carbapenem-resistant bacteria. Further investigation of the evolution and dissemination of antibiotic resistance in environmental bacteria is required in order to understand and prevent the emergence of resistance in the clinical environment.}, }
@article {pmid30070649, year = {2019}, author = {Schierstaedt, J and Bziuk, N and Kuzmanović, N and Blau, K and Smalla, K and Jechalke, S}, title = {Role of Plasmids in Plant-Bacteria Interactions.}, journal = {Current issues in molecular biology}, volume = {30}, number = {}, pages = {17-38}, doi = {10.21775/cimb.030.017}, pmid = {30070649}, issn = {1467-3045}, mesh = {*Bacterial Physiological Phenomena ; Endophytes ; Gene Transfer, Horizontal ; Host-Pathogen Interactions ; Microbiota ; Plant Diseases/microbiology ; *Plant Physiological Phenomena ; Plasmids/*genetics ; Rhizosphere ; *Symbiosis ; }, abstract = {Plants are colonized by diverse microorganisms, which may positively or negatively influence the plant fitness. The positive impact includes nutrient acquisition, enhancement of resistance to biotic and abiotic stresses, both important factors for plant growth and survival, while plant pathogenic bacteria can cause diseases. Plant pathogens are adapted to negate or evade plant defense mechanisms, e.g. by the injection of effector proteins into the host cells or by avoiding the recognition by the host. Plasmids play an important role in the rapid bacterial adaptation to stresses and changing environmental conditions. In the plant environment, plasmids can further provide a selective advantage for the host bacteria, e.g. by carrying genes encoding metabolic pathways, metal and antibiotic resistances, or pathogenicity-related genes. However, we are only beginning to understand the role of mobile genetic elements and horizontal gene transfer for plant-associated bacteria. In this review, we aim to provide a short update on what is known about plasmids and horizontal gene transfer of plant associated bacteria and their role in plant-bacteria interactions. Furthermore, we discuss tools available to study the plant-associated mobilome, its transferability, and its bacterial hosts.}, }
@article {pmid30068738, year = {2018}, author = {Partridge, SR and Kwong, SM and Firth, N and Jensen, SO}, title = {Mobile Genetic Elements Associated with Antimicrobial Resistance.}, journal = {Clinical microbiology reviews}, volume = {31}, number = {4}, pages = {}, pmid = {30068738}, issn = {1098-6618}, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria/drug effects/*genetics ; Bacterial Infections/drug therapy ; Biological Evolution ; *DNA Transposable Elements ; Drug Resistance, Bacterial/*genetics ; *Gene Transfer, Horizontal ; }, abstract = {Strains of bacteria resistant to antibiotics, particularly those that are multiresistant, are an increasing major health care problem around the world. It is now abundantly clear that both Gram-negative and Gram-positive bacteria are able to meet the evolutionary challenge of combating antimicrobial chemotherapy, often by acquiring preexisting resistance determinants from the bacterial gene pool. This is achieved through the concerted activities of mobile genetic elements able to move within or between DNA molecules, which include insertion sequences, transposons, and gene cassettes/integrons, and those that are able to transfer between bacterial cells, such as plasmids and integrative conjugative elements. Together these elements play a central role in facilitating horizontal genetic exchange and therefore promote the acquisition and spread of resistance genes. This review aims to outline the characteristics of the major types of mobile genetic elements involved in acquisition and spread of antibiotic resistance in both Gram-negative and Gram-positive bacteria, focusing on the so-called ESKAPEE group of organisms (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli), which have become the most problematic hospital pathogens.}, }
@article {pmid30064034, year = {2018}, author = {Lu, C and Gu, J and Wang, X and Liu, J and Zhang, K and Zhang, X and Zhang, R}, title = {Effects of coal gasification slag on antibiotic resistance genes and the bacterial community during swine manure composting.}, journal = {Bioresource technology}, volume = {268}, number = {}, pages = {20-27}, doi = {10.1016/j.biortech.2018.07.086}, pmid = {30064034}, issn = {1873-2976}, mesh = {Animals ; Anti-Bacterial Agents ; *Coal ; *Composting ; Drug Resistance, Microbial/*genetics ; *Genes, Bacterial ; Manure/*microbiology ; Swine ; }, abstract = {This study investigated the effects of the addition of coal gasification slag (CGS) at three levels (0%, 5%, and 10% w/w) on antibiotic resistance genes (ARGs) and the bacterial community during composting. The addition of CGS effectively facilitated the removal of ARGs and mobile genetic elements (MGEs), where it significantly reduced the relative abundances of 5/11 ARGs and three MGEs in the swine manure composting product. In addition, the enrichment of ARGs and intI1 was lower under the addition of 10% CGS compared with 0% CGS. The bacterial community was distributed according to the composting time under different treatments. Redundancy analysis showed that bacterial community succession and MGE-mediated horizontal gene transfer played important roles in the variations in ARGs. Network analysis indicated the co-occurrence of ARGs and MGEs with specific microorganisms. Thus, 10% CGS may be a suitable additive for reducing the risks of ARGs in compost products.}, }
@article {pmid30063910, year = {2018}, author = {Hernández-Ramírez, KC and Reyes-Gallegos, RI and Chávez-Jacobo, VM and Díaz-Magaña, A and Meza-Carmen, V and Ramírez-Díaz, MI}, title = {A plasmid-encoded mobile genetic element from Pseudomonas aeruginosa that confers heavy metal resistance and virulence.}, journal = {Plasmid}, volume = {98}, number = {}, pages = {15-21}, doi = {10.1016/j.plasmid.2018.07.003}, pmid = {30063910}, issn = {1095-9890}, mesh = {Animals ; Caenorhabditis elegans/growth &amp; development/*microbiology ; DNA, Bacterial ; *Drug Resistance, Bacterial ; Humans ; *Interspersed Repetitive Sequences ; Metals, Heavy/*toxicity ; Plasmids/*genetics ; Pseudomonas Infections/drug therapy/genetics/*microbiology ; Pseudomonas aeruginosa/*genetics/pathogenicity ; Virulence Factors/genetics ; }, abstract = {Mobile plasmid-encoded elements are DNA segments that are transferred for horizontal gene transfer and that confer adaptive proprieties, as well as virulence and antibiotic and heavy metal resistance to bacteria. The conjugative plasmid pUM505, isolated from a clinical strain of Pseudomonas aeruginosa, possesses a putative 31.292 kb mobile element (denominated Mpe: Mobile plasmid- encoded element) that, in addition to possessing chr genes that confer chromate resistance to Pseudomonas, contains two putative mer operons that could confer mercury resistance. Moreover, the Mpe contains genes related previously with the virulence of both P. aeruginosa and Escherichia coli strains. In this work, we determined that Mpe from pUM505 was able to independently move to another DNA molecule, conferring chromate and mercury resistance to P. aeruginosa PAO1 and mercury resistance to E. coli JM101, suggesting that its transference might be beneficial to bacteria under certain environmental conditions. Additionally, the transference of Mpe increased the virulence of P. aeruginosa PAO1 against the nematode Caenorhabditis elegans, suggesting its contribution to the pathogenicity of P. aeruginosa. In this work, we describe a new mobile plasmid-encoded element that possesses the potential to be transferred by horizontal gene transference, which could provide bacteria with a wide variety of adaptive traits such as heavy metal resistance and virulence, which can be selective factors for the distribution and prevalence of this plasmid in diverse environments, including hospitals and heavy metal contaminated soils.}, }
@article {pmid30062554, year = {2018}, author = {Kutralam-Muniasamy, G and Marsch, R and Pérez-Guevara, F}, title = {Investigation on the Evolutionary Relation of Diverse Polyhydroxyalkanoate Gene Clusters in Betaproteobacteria.}, journal = {Journal of molecular evolution}, volume = {86}, number = {7}, pages = {470-483}, pmid = {30062554}, issn = {1432-1432}, support = {CB-2014-01; 236285 and Fronteras de la Ciencia 2015-1: 016//CONACyT/International ; }, mesh = {Amino Acid Sequence/genetics ; Bacterial Proteins/genetics ; Betaproteobacteria/*genetics/metabolism ; Biological Evolution ; Computational Biology/methods ; Evolution, Molecular ; Gene Expression Regulation, Bacterial/genetics ; Gene Transfer, Horizontal/genetics ; Multigene Family/genetics ; Phylogeny ; Polyhydroxyalkanoates/*genetics/metabolism ; }, abstract = {Products of numerous genes (phaC, phaA, phaB, phaP, phaR, and phaZ) are involved in the synthesis and degradation processes of the ubiquitous prokaryotic polyhydroxyalkanoate (PHA) intracellular reserve storage system. In this study, we performed a bioinformatics analysis to identify PHA-related genes and proteins in the genome of 66 selected organisms (class: Betaproteobacteria) that occur in various habitats; besides, evolutionary trajectories of the PHA system are reported here. The identified PHA-related genes were organized into clusters, and the gene arrangement was highly diverse. The occurrence and distribution of PHA-related clusters revealed that a single cluster was primarily segmented into small gene groups among various genomes, which were further reorganized as novel clusters based on various functional genes. The individual phylogenies of gene and protein sequences supported that the clusters were assembled through the relocation of native orthologous genes that underwent insertion, deletion, and elongation events. Furthermore, the neighboring genes provided valuable evolutionary and functional cues regarding the conservation and maintenance of PHA-related genes in the genome. Overall, the aforementioned results strongly indicate the influence of horizontal gene transfer on the organization of PHA-related gene clusters. Therefore, our results reveal new insights into the organization, evolutionary history, and cluster conservation of the PHA-related gene inventories among Betaproteobacterial organisms.}, }
@article {pmid30061870, year = {2018}, author = {Dantur, KI and Chalfoun, NR and Claps, MP and Tórtora, ML and Silva, C and Jure, &#xc1; and Porcel, N and Bianco, MI and Vojnov, A and Castagnaro, AP and Welin, B}, title = {The Endophytic Strain Klebsiella michiganensis Kd70 Lacks Pathogenic Island-Like Regions in Its Genome and Is Incapable of Infecting the Urinary Tract in Mice.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1548}, pmid = {30061870}, issn = {1664-302X}, abstract = {Klebsiella spp. have been isolated from many different environmental habitats but have mainly been associated with nosocomial acquired diseases in humans. Although there are many recently published sequenced genomes of members of this genus, there are very few studies on whole genome comparisons between clinical and non-clinical isolates, and it is therefore still an open question if a strain found in nature is capable of infecting humans/animals. Klebsiella michiganensis Kd70 was isolated from the intestine of larvae of Diatraea saccharalis but genome analysis revealed multiple genes associated with colonization and growth promotion in plants suggesting an endophytic lifestyle. Kd70 cells labeled with gfp confirmed capability of root colonization and soil application of Kd70 promoted growth in greenhouse grown sugarcane. Further genomic analysis showed that the Kd70 genome harbored fewer mammalian virulence factors and no pathogen island-like regions when compared to clinical isolates of this species, suggesting attenuated animal/human pathogenicity. This postulation was corroborated by in vivo experiments in which it was demonstrated that Kd70 was unable to infect the mouse urinary tract. This is to the best of our knowledge the first experimental example of a member of a pathogenic Klebsiella spp. unable to infect a mammalian organism. A proteomic comparison deduced from the genomic sequence between Kd70 and several other K. michiganensis strains showed a high similarity with isolates from many different environments including clinical strains, and demonstrated the existence of conserved genetic lineages within this species harboring members from different ecological niches and geographical locations. Furthermore, most genetic differences were found to be associated with genomic islands of clinical isolates, suggesting that evolutionary adaptation of animal pathogenicity to a large extent has depended on horizontal gene transfer. In conclusion our results demonstrate the importance of conducting thorough in vivo pathogenicity studies before presupposing animal/human virulence of non-clinical bacterial isolates.}, }
@article {pmid30059325, year = {2018}, author = {Hamici, Z}, title = {Towards Genetic Cryptography for Biomedical Wireless Sensor Networks Gateways.}, journal = {IEEE journal of biomedical and health informatics}, volume = {22}, number = {6}, pages = {1814-1823}, doi = {10.1109/JBHI.2018.2860980}, pmid = {30059325}, issn = {2168-2208}, mesh = {*Algorithms ; Computer Communication Networks ; *Computer Security ; Medical Informatics/*methods ; Models, Genetic ; *Wireless Technology ; }, abstract = {The integration of wireless sensor networks into Internet of things, led to a new generation of sensor nodes, directly connected to remote servers, for signal processing and decision making. The migration of data processing from the local node, achieved by decoupling the node hardware from the required processing capabilities, is only possible through implementation of network virtualization. The virtualization which brings new services that are executed remotely has led to security challenges, yet to be resolved, due to the increasing amount of data being continually exchanged between the sensor node hub and remote servers. In this regard, we introduce a novel genetic algorithm for data security with a powerful security architecture that performs one-time key, single block enciphering instead of a block chaining or weak stream enciphering. The algorithm architecture produces variable (stealthy) keys and data that adopt the white noise statistical behavior, therefore, having high immunity to cryptanalysis. The algorithm combines gene fusion and horizontal gene transfer inspired from the spread of antibiotic resistance in bacteria. A salt extracted from the data block hash value adds the stealthy-key feature to the cipher. In fact, the avalanche effect for a block of encrypted sensors data of 16 × 16 B achieves an average of 98% with a single bit flipped in the data. An application in biomedical WSN/IoT with simulation and experimental results is presented.}, }
@article {pmid30059025, year = {2018}, author = {Yoshida, Y and Konno, S and Nishino, R and Murai, Y and Tomita, M and Arakawa, K}, title = {Ultralow Input Genome Sequencing Library Preparation from a Single Tardigrade Specimen.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {137}, pages = {}, pmid = {30059025}, issn = {1940-087X}, mesh = {Animals ; Base Sequence/*genetics ; Chromosome Mapping/*methods ; *Gene Library ; Tardigrada/*chemistry ; }, abstract = {Tardigrades are microscopic animals that enter an ametabolic state called anhydrobiosis when facing desiccation and can return to their original state when water is supplied. The genomic sequencing of microscopic animals such as tardigrades risks bacterial contamination that sometimes leads to erroneous interpretations, for example, regarding the extent of horizontal gene transfer in these animals. Here, we provide an ultralow input method to sequence the genome of the tardigrade, Hypsibius dujardini, from a single specimen. By employing rigorous washing and contaminant exclusion along with an efficient extraction of the 50 ~ 200 pg genomic DNA from a single individual, we constructed a library sequenced with a DNA sequencing instrument. These libraries were highly reproducible and unbiased, and an informatics analysis of the sequenced reads with other H. dujardini genomes showed a minimal amount of contamination. This method can be applied to unculturable tardigrades that could not be sequenced using previous methods.}, }
@article {pmid30058084, year = {2018}, author = {Mansfield, MJ and Sugiman-Marangos, SN and Melnyk, RA and Doxey, AC}, title = {Identification of a diphtheria toxin-like gene family beyond the Corynebacterium genus.}, journal = {FEBS letters}, volume = {592}, number = {16}, pages = {2693-2705}, doi = {10.1002/1873-3468.13208}, pmid = {30058084}, issn = {1873-3468}, mesh = {Actinobacteria/genetics/metabolism ; Bacterial Toxins/*chemistry/*genetics/metabolism ; Catalytic Domain ; Cloning, Molecular ; Corynebacterium/genetics/metabolism ; Diphtheria Toxin/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Models, Molecular ; Multigene Family ; Phylogeny ; Protein Conformation ; Streptomyces/genetics/*metabolism ; }, abstract = {Diphtheria toxin (DT), produced by Corynebacterium diphtheria, is the causative agent of diphtheria and one of the most potent protein toxins known; however, it has an unclear evolutionary history. Here, we report the discovery of a DT-like gene family in several bacterial lineages outside of Corynebacterium, including Austwickia and Streptomyces. These DT-like genes form sister lineages in the DT phylogeny and conserve key DT features including catalytic and translocation motifs, but possess divergent receptor-binding domains. DT-like genes are not associated with corynephage, but have undergone lateral transfer through a separate mechanism. The discovery of the first non-Corynebacterium homologs of DT sheds light on its evolutionary origin and highlights novelties that may have resulted in the emergence of DT targeting humans.}, }
@article {pmid30055976, year = {2018}, author = {Berger, M and Berger, P and Denamur, E and Mellmann, A and Dobrindt, U}, title = {Core elements of the vegetative replication control of the Inc1 plasmid pO104_90 of Escherichia coli O104:H4 also regulate its transfer frequency.}, journal = {International journal of medical microbiology : IJMM}, volume = {308}, number = {7}, pages = {962-968}, doi = {10.1016/j.ijmm.2018.07.003}, pmid = {30055976}, issn = {1618-0607}, mesh = {Bacteriocins/metabolism ; Conjugation, Genetic/genetics ; Disease Outbreaks ; Escherichia coli Infections/epidemiology ; Escherichia coli O104/*genetics ; Gene Transfer, Horizontal/*genetics ; Germany/epidemiology ; Hemolytic-Uremic Syndrome/epidemiology/microbiology ; Host Specificity/*genetics ; Humans ; Plasmids/*genetics ; Salmonella typhimurium/*genetics ; Sequence Analysis, DNA ; Shigella flexneri/*genetics ; beta-Lactamases/genetics ; }, abstract = {The highly virulent Escherichia coli O104:H4 isolate that caused a large outbreak in 2011 carries three plasmids. Out of these, only one, the IncI plasmid pO104_90 that encodes two extended spectrum beta-lactamases, can transfer itself by conjugation. Considering its potential contribution to the emergence and virulence of the outbreak strain, we aimed to get a closer insight into pO104_90 transfer efficiency and control. We tested the host spectrum of the plasmid and observed transmission into Enterobactericeae including clinically relevant enterobacterial pathogens like Salmonella typhimurium and Shigella flexneri. However, we found that this plasmid did not transfer into E. coli strains that kill the donor strain due to bacteriocin production, e.g. the probiotic E. coli Nissle 1917. Under the same conditions, the highly transmittable control plasmid RP4 was efficiently transferred into all these recipients. Therefore we hypothesized that the failure of transfer of pO104_90 was simply due to the generally much lower transmission rates of this IncI plasmid and we decided to screen for factors that negatively affect the transfer of the plasmid by an in vivo deletion analysis. Our attempts to delete larger regions of the plasmid resulted in cells containing both a truncated plasmid (Δ50 kb and Δ75 kb) and a wild type copy of pO104_90. When used as donors in conjugation experiments, these cells transferred the wild type plasmid at dramatically increased rates. This indicated that the relatively limited region shared by both plasmids contained an activator of transfer. We therefore analyzed its transcriptional organization, dissected the candidate region by subcloning and showed that additional copies of repY/INC were sufficient to increase the transfer frequency of pO104_90 to the observed level. To our knowledge, this is the first evidence for a direct regulatory cross talk between core control elements of the vegetative replication and the transfer functions of an IncI1 plasmid.}, }
@article {pmid30054764, year = {2018}, author = {Venturini, C and Ginn, AN and Wilson, BE and Tsafnat, G and Paulsen, I and Partridge, SR and Iredell, JR}, title = {Ecological effects of cefepime use during antibiotic cycling on the Gram-negative enteric flora of ICU patients.}, journal = {Intensive care medicine experimental}, volume = {6}, number = {1}, pages = {19}, pmid = {30054764}, issn = {2197-425X}, support = {NHMRC_1001020//National Health and Medical Research Council/ ; NHMRC_1046889//National Health and Medical Research Council/ ; }, abstract = {This study examines the impact of cefepime and APP-β (antipseudomonal penicillin/ β-lactamase inhibitor combinations) on Gram-negative bacterial colonization and resistance in two Australian ICUs. While resistance did not cumulatively increase, cefepime (but not APP-β treatment) was associated with acquisition of antibiotic resistant Enterobacteriaceae, consistent with an ecological effect. Analysis of the resident gut E. coli population in a subset of patients showed an increase in markers of horizontal gene transfer after cefepime exposure that helps explain the increase in APP-β resistance and reminds us that unmeasured impacts on the microbiome are key outcome determinants that need to be fully explored.}, }
@article {pmid30054462, year = {2018}, author = {Janečka, JE and Davis, BW and Ghosh, S and Paria, N and Das, PJ and Orlando, L and Schubert, M and Nielsen, MK and Stout, TAE and Brashear, W and Li, G and Johnson, CD and Metz, RP and Zadjali, AMA and Love, CC and Varner, DD and Bellott, DW and Murphy, WJ and Chowdhary, BP and Raudsepp, T}, title = {Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {2945}, pmid = {30054462}, issn = {2041-1723}, support = {DNRF94//Danmarks Grundforskningsfond (Danish National Research Foundation)/International ; DNRF94//Danmarks Grundforskningsfond (Danish National Research Foundation)/International ; ERC-CoG-2015-681605//EC | European Research Council (ERC)/International ; ERC-CoG-2015-681605//EC | European Research Council (ERC)/International ; 2012-67015-19632//USDA | National Institute of Food and Agriculture (NIFA)/International ; 2012-67015-19632//USDA | National Institute of Food and Agriculture (NIFA)/International ; 2012-67015-19632//USDA | National Institute of Food and Agriculture (NIFA)/International ; 2012-67015-19632//USDA | National Institute of Food and Agriculture (NIFA)/International ; }, mesh = {Animals ; Ascaridoidea/genetics ; Equidae/genetics ; *Evolution, Molecular ; Fertility/*genetics ; Gene Dosage/genetics ; Gene Transfer, Horizontal ; Horses/*genetics ; Hybridization, Genetic ; Male ; Phylogeny ; Testis/metabolism ; X Chromosome/genetics ; Y Chromosome/*genetics ; }, abstract = {Dynamic evolutionary processes and complex structure make the Y chromosome among the most diverse and least understood regions in mammalian genomes. Here, we present an annotated assembly of the male specific region of the horse Y chromosome (eMSY), representing the first comprehensive Y assembly in odd-toed ungulates. The eMSY comprises single-copy, equine specific multi-copy, PAR transposed, and novel ampliconic sequence classes. The eMSY gene density approaches that of autosomes with the highest number of retained X-Y gametologs recorded in eutherians, in addition to novel Y-born and transposed genes. Horse, donkey and mule testis RNAseq reveals several candidate genes for stallion fertility. A novel testis-expressed XY ampliconic sequence class, ETSTY7, is shared with the parasite Parascaris genome, providing evidence for eukaryotic horizontal transfer and inter-chromosomal mobility. Our study highlights the dynamic nature of the Y and provides a reference sequence for improved understanding of equine male development and fertility.}, }
@article {pmid30054356, year = {2018}, author = {Peng, M and Salaheen, S and Buchanan, RL and Biswas, D}, title = {Alterations of Salmonella enterica Serovar Typhimurium Antibiotic Resistance under Environmental Pressure.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {19}, pages = {}, pmid = {30054356}, issn = {1098-5336}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Genome, Bacterial ; Microbial Sensitivity Tests ; Phylogeny ; Plasmids/genetics/metabolism ; Salmonella Infections, Animal/microbiology ; Salmonella typhimurium/classification/*drug effects/*genetics/isolation &amp; purification ; Selection, Genetic ; Soil Microbiology ; Tetracycline/pharmacology ; }, abstract = {Microbial horizontal gene transfer is a continuous process that shapes bacterial genomic adaptation to the environment and the composition of concurrent microbial ecology. This includes the potential impact of synthetic antibiotic utilization in farm animal production on overall antibiotic resistance issues; however, the mechanisms behind the evolution of microbial communities are not fully understood. We explored potential mechanisms by experimentally examining the relatedness of phylogenetic inference between multidrug-resistant Salmonella enterica serovar Typhimurium isolates and pathogenic Salmonella Typhimurium strains based on genome-wide single-nucleotide polymorphism (SNP) comparisons. Antibiotic-resistant S Typhimurium isolates in a simulated farm environment barely lost their resistance, whereas sensitive S Typhimurium isolates in soils gradually acquired higher tetracycline resistance under antibiotic pressure and manipulated differential expression of antibiotic-resistant genes. The expeditious development of antibiotic resistance and the ensuing genetic alterations in antimicrobial resistance genes in S Typhimurium warrant effective actions to control the dissemination of Salmonella antibiotic resistance.IMPORTANCE Antibiotic resistance is attributed to the misuse or overuse of antibiotics in agriculture, and antibiotic resistance genes can also be transferred to bacteria under environmental stress. In this study, we report a unidirectional alteration in antibiotic resistance from susceptibility to increased resistance. Highly sensitive Salmonella enterica serovar Typhimurium isolates from organic farm systems quickly acquired tetracycline resistance under antibiotic pressure in simulated farm soil environments within 2 weeks, with expression of antibiotic resistance-related genes that was significantly upregulated. Conversely, originally resistant S Typhimurium isolates from conventional farm systems lost little of their resistance when transferred to environments without antibiotic pressure. Additionally, multidrug-resistant S Typhimurium isolates genetically shared relevancy with pathogenic S Typhimurium isolates, whereas susceptible isolates clustered with nonpathogenic strains. These results provide detailed discussion and explanation about the genetic alterations and simultaneous acquisition of antibiotic resistance in S Typhimurium in agricultural environments.}, }
@article {pmid30053416, year = {2018}, author = {Liu, B and Zhou, Y and Li, K and Hu, X and Wang, C and Cao, G and Xue, R and Gong, C}, title = {The complete genome of Cyprinid herpesvirus 2, a new strain isolated from Allogynogenetic crucian carp.}, journal = {Virus research}, volume = {256}, number = {}, pages = {6-10}, doi = {10.1016/j.virusres.2018.07.016}, pmid = {30053416}, issn = {1872-7492}, mesh = {Animals ; Carps/*virology ; China ; Evolution, Molecular ; Fish Diseases/*virology ; Gene Transfer, Horizontal ; Genetic Variation ; *Genome, Viral ; Herpesviridae/*genetics/isolation &amp; purification ; Herpesviridae Infections/*veterinary/virology ; MicroRNAs/genetics ; Mutation ; Open Reading Frames ; Promoter Regions, Genetic ; RNA, Viral/genetics ; *Sequence Analysis, DNA ; Terminal Repeat Sequences ; }, abstract = {The haemorrhagic disease of the gill is caused by Cyprinid herpesvirus 2 (CyHV2) infection, which often results in the severe economic losses in the farm of Allogynogenetic crucian carp (ACC). In this study, the genome of CyHV2 strain CyHV2-SY (SY) collected from Sheyang County, Jiangsu Province, China was sequenced. The complete genome of SY is at length of 290,455 bp with 154 potential open reading frames (ORFs) and a terminal direct repeat (TR) of 15,353 bp. Many variations were found by comparison the sequenced CyHV2 genomes. The ORF10, ORF107, ORF156 of SY genome have insertions or deletions of repeat sequences compared with ST-J1 and SY-C1, which may be used as the marks of SY strains. Besides, the promoter sequence analysis showed that 13 of the 150 ORFs have TATA-box elements and 119 of the 150 ORFs have SP1 cis-acting elements in the promoter region (350 bp upstream sequence of the initiation codon ATG). Twenty-eight viral miRNAs candidates were predicted in the CyHV2 genome and expression of 24 virogenes may be regulated by viral miRNAs. Horizontal transfer analysis indicated that 16 and 2 genes in the CyHV2 genome may transfer from the host and bacteria, respectively. By the genome sequencing and sequence mining, our results provided more new clues to further understand CyHV2 genome.}, }
@article {pmid30052167, year = {2019}, author = {Tellis, MB and Gujar, NN and Joshi, RS}, title = {Evolutionary and structure-function analysis elucidates diversification of prokaryotic and eukaryotic trehalases.}, journal = {Journal of biomolecular structure &amp; dynamics}, volume = {37}, number = {11}, pages = {2926-2937}, doi = {10.1080/07391102.2018.1497542}, pmid = {30052167}, issn = {1538-0254}, mesh = {*Biological Evolution ; Eukaryota/*enzymology ; Gene Duplication ; Gene Rearrangement ; Phylogeny ; Prokaryotic Cells/*enzymology ; Protein Conformation ; Species Specificity ; Trehalase/*chemistry/classification/genetics/*metabolism ; Trehalose/chemistry/*metabolism ; }, abstract = {Trehalase catalyses the breakdown of trehalose into two glucose moieties and is ubiquitous in all organisms. Here, we provide insights into the enigmatic origin and evolution of trehalase in major species. Study of taxonomic distribution, orthology, phylogeny and functional domains indicated that trehalase possibly originates from bacteria and was transmitted to other taxa through horizontal gene transfer. Domain analysis showed that glycosyl hydrolase family 37 is present in most of the sequences and represents dominant activity during evolution, and also, illustrating that cytosolic trehalase is primitive than its transmembrane form. Furthermore, it was observed that trehalase went through domain rearrangement to facilitate its activity in adverse environmental conditions like acidic pH. Gene context analysis depicts that trehalase neighbourhood consists of sugar transport and lipid metabolism genes. This highlights their relatedness in metabolic activity and similarity in gene regulation, respectively. Evolutionary and selection pressure analysis demonstrated that trehalase genes were duplicated and evolved under purifying selection, following horizontal gene transfer. Moreover, site-specific rate of evolution emphasized conservation of functionally important residues. In comparison with acid trehalase, neutral trehalase has an extra N-terminal extension. This study serves as an instigation to understand evolution and functionality of trehalase across diverse species. Communicated by Ramaswamy H. Sarma.}, }
@article {pmid30050509, year = {2018}, author = {Serrano, E and Carrasco, B and Gilmore, JL and Takeyasu, K and Alonso, JC}, title = {RecA Regulation by RecU and DprA During Bacillus subtilis Natural Plasmid Transformation.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1514}, pmid = {30050509}, issn = {1664-302X}, abstract = {Natural plasmid transformation plays an important role in the dissemination of antibiotic resistance genes in bacteria. During this process, Bacillus subtilis RecA physically interacts with RecU, RecX, and DprA. These three proteins are required for plasmid transformation, but RecA is not. In vitro, DprA recruits RecA onto SsbA-coated single-stranded (ss) DNA, whereas RecX inhibits RecA filament formation, leading to net filament disassembly. We show that a null recA (ΔrecA) mutation suppresses the plasmid transformation defect of competent ΔrecU cells, and that RecU is essential for both chromosomal and plasmid transformation in the ΔrecX context. RecU inhibits RecA filament growth and facilitates RecA disassembly from preformed filaments. Increasing SsbA concentrations additively contributes to RecU-mediated inhibition of RecA filament extension. DprA is necessary and sufficient to counteract the negative effect of both RecU and SsbA on RecA filament growth onto ssDNA. DprA-SsbA activates RecA to catalyze DNA strand exchange in the presence of RecU, but this effect was not observed if RecU was added prior to RecA. We propose that DprA contributes to RecA filament growth onto any internalized SsbA-coated ssDNA. When the ssDNA is homologous to the recipient, DprA antagonizes the inhibitory effect of RecU on RecA filament growth and helps RecA to catalyze chromosomal transformation. On the contrary, RecU promotes RecA filament disassembly from a heterologous (plasmid) ssDNA, overcoming an unsuccessful homology search and favoring plasmid transformation. The DprA-DprA interaction may promote strand annealing upon binding to the complementary plasmid strands and facilitating thereby plasmid transformation rather than through a mediation of RecA filament growth.}, }
@article {pmid30049587, year = {2018}, author = {San Millan, A}, title = {Evolution of Plasmid-Mediated Antibiotic Resistance in the Clinical Context.}, journal = {Trends in microbiology}, volume = {26}, number = {12}, pages = {978-985}, doi = {10.1016/j.tim.2018.06.007}, pmid = {30049587}, issn = {1878-4380}, mesh = {Adaptation, Physiological ; Anti-Bacterial Agents/pharmacology ; Bacteria/*genetics ; Drug Resistance, Microbial/*genetics ; *Evolution, Molecular ; Gastrointestinal Microbiome/genetics ; Gene Transfer, Horizontal ; Humans ; Mutation ; Plasmids/*genetics ; }, abstract = {Antibiotic-resistant infections are an urgent problem in clinical settings because they sharply increase mortality risk in critically ill patients. The horizontal spread of antibiotic resistance genes among bacteria is driven by bacterial plasmids, promoting the evolution of resistance. Crucially, particular associations exist between resistance plasmids and bacterial clones that become especially successful in clinical settings. However, the factors underlying the success of these associations remain unknown. Recent in vitro evidence reveals (i) that plasmids produce fitness costs in bacteria, and (ii) that these costs are alleviated over time through compensatory mutations. I argue that plasmid-imposed costs and subsequent compensatory adaptation may determine the success of associations between plasmids and bacteria in clinical settings, shaping the in vivo evolution of antibiotic resistance.}, }
@article {pmid30047163, year = {2019}, author = {Chajęcka-Wierzchowska, W and Zadernowska, A and Zarzecka, U and Zakrzewski, A and Gajewska, J}, title = {Enterococci from ready-to-eat food - horizontal gene transfer of antibiotic resistance genes and genotypic characterization by PCR melting profile.}, journal = {Journal of the science of food and agriculture}, volume = {99}, number = {3}, pages = {1172-1179}, doi = {10.1002/jsfa.9285}, pmid = {30047163}, issn = {1097-0010}, support = {DEC-2013/09/N/NZ9/01630//National Science Centre/ ; }, mesh = {Aminoglycosides/pharmacology ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics/metabolism ; Drug Resistance, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Enterococcus/*drug effects/*genetics/isolation &amp; purification ; Fast Foods/*microbiology ; Food Contamination/analysis ; Gene Transfer, Horizontal ; Genotype ; Humans ; Poland ; Polymerase Chain Reaction ; }, abstract = {BACKGROUND: The aim of this study was to evaluate the possibility of the horizontal transfer of genes encoding resistance to aminoglycosides (aac(6')-Ie-aph(2″)-Ia, aph(2″)-Ib, aph(2″)-Ic, aph(2″)-Id, ant(4')-Ia and ant(6')-Ia), tetracyclines (tetM, tetL, tetK, tetO and tetW), and macrolides (ermA, ermB, ermC, msrC, mefAB) in Enterococcus strains isolated from ready-to-eat dishes purchased in bars and restaurants in Olsztyn, Poland.<br><br>RESULTS: It was found that 74% of tested strains were able to conjugal transfer at least one of the antibiotic resistance genes. Transfer of resistance to tetracyclines in strains was observed with a frequency ranging from 1.3 &#xd7; 10[-6] to 8.7 &#xd7; 10[-7] transconjugants/donor. The int gene and the tetM gene were transferred simultaneously, which indicated that a transposon of the Tn916/Tn1545 also participated in the conjugation process. The frequency of transferring genes of resistance to macrolides ranged from 3.2 &#xd7; 10[-6] to 2.4 &#xd7; 10[-8] transconjugants/donor. The ermB gene was transferred the most frequently. The frequency of acquisition of genes encoding aminoglycosides in strains isolated from food ranged from 1.7 &#xd7; 10[-6] to 3,2 &#xd7; 10[-8] transconjugants/donor. Transfer of the aac(6')-Ie-aph(2&#x2033;) gene was the most frequent. In all reactions, the clonal character of transconjugants and recipients was confirmed by the polymerase chain reaction melting profile (PCR MP) method, which is an alternative to the pulsed field gel electrophoresis (PFGE) method.<br><br>CONCLUSION: The findings of this study indicate that Enterococcus isolated from ready-to-eat food is able to horizontally transfer genes encoding various antibiotic resistance mechanisms. &#xa9; 2018 Society of Chemical Industry.}, }
@article {pmid30043533, year = {2018}, author = {Monteil, CL and Perrière, G and Menguy, N and Ginet, N and Alonso, B and Waisbord, N and Cruveiller, S and Pignol, D and Lefèvre, CT}, title = {Genomic study of a novel magnetotactic Alphaproteobacteria uncovers the multiple ancestry of magnetotaxis.}, journal = {Environmental microbiology}, volume = {20}, number = {12}, pages = {4415-4430}, doi = {10.1111/1462-2920.14364}, pmid = {30043533}, issn = {1462-2920}, support = {//European Regional Development Fund/International ; ANR-14-CE35-0018//DFG-ANR project/International ; DJ/ST/IP/2013/D-112//Appel &#xe0; Projets en G&#xe9;nomique Environnementale - CNRS/International ; ANR-16-TERC-0025-01//French National Research Agency/International ; }, mesh = {Alphaproteobacteria/*genetics ; *Evolution, Molecular ; France ; Gene Transfer, Horizontal ; Genome, Bacterial ; Magnetics ; Magnetosomes/*genetics ; Mediterranean Sea ; Water Microbiology ; }, abstract = {Ecological and evolutionary processes involved in magnetotactic bacteria (MTB) adaptation to their environment have been a matter of debate for many years. Ongoing efforts for their characterization are progressively contributing to understand these processes, including the genetic and molecular mechanisms responsible for biomineralization. Despite numerous culture-independent MTB characterizations, essentially within the Proteobacteria phylum, only few species have been isolated in culture because of their complex growth conditions. Here, we report a newly cultivated magnetotactic, microaerophilic and chemoorganoheterotrophic bacterium isolated from the Mediterranean Sea in Marseille, France: Candidatus Terasakiella magnetica strain PR-1 that belongs to an Alphaproteobacteria genus with no magnetotactic relative. By comparing the morphology and the whole genome shotgun sequence of this MTB with those of closer relatives, we brought further evidence that the apparent vertical ancestry of magnetosome genes suggested by previous studies within Alphaproteobacteria hides a more complex evolutionary history involving horizontal gene transfers and/or duplication events before and after the emergence of Magnetospirillum, Magnetovibrio and Magnetospira genera. A genome-scale comparative genomics analysis identified several additional candidate functions and genes that could be specifically associated to MTB lifestyle in this class of bacteria.}, }
@article {pmid30038484, year = {2018}, author = {Watanabe, T and Yamazaki, S and Maita, C and Matushita, M and Matsuo, J and Okubo, T and Yamaguchi, H}, title = {Lateral Gene Transfer Between Protozoa-Related Giant Viruses of Family Mimiviridae and Chlamydiae.}, journal = {Evolutionary bioinformatics online}, volume = {14}, number = {}, pages = {1176934318788337}, pmid = {30038484}, issn = {1176-9343}, abstract = {Obligate intracellular chlamydiae diverged into pathogenic and environmental chlamydiae 0.7-1.4 billion years ago. While pathogenic chlamydiae have adapted to a wide range of vertebrates, environmental chlamydiae inhabit unicellular amoebae, the free-living Acanthamoeba. However, how and why this divergence occurred remains unclear. Meanwhile, giant viruses consisting of protozoa-related and protozoa-unrelated viruses have been discovered, with the former group being suggested to have more influenced environmental chlamydiae during their evolution while cohabiting host amoebae. Against this background, we attempted to visualize genes of giant viruses in chlamydial genomes by bioinformatic analysis mainly with comparative genome and phylogenic analysis, seeking genes present in chlamydiae that are specifically shared with protozoa-related giant viruses. As a result, in contrast to protozoa-unrelated giant viruses, the genes of protozoa-related giant viruses were significantly shared in both the chlamydia genomes depending on the giant virus type. In particular, the prevalence of Mimiviridae genes among the protozoa-related giant virus genes in chlamydial genomes was significantly high. Meanwhile, the prevalence of protozoa-related giant virus genes in pathogenic chlamydia genomes was consistently higher than those of environmental chlamydiae; the actual number of sequences similar to giant virus was also significantly predominant compared with those in the environmental chlamydial genomes. Among them, the most prevalent of giant virus was in the case of chlamydiae with Megavirus chiliensis; total of 1338 genes of the chlamydiae were found to be shared with the virus (444 genes specific to environmental chlamydiae, 892 genes shared between both chlamydiae, only two genes in the pathogenic chlamydiae). Phylogenic analysis with most prevalent sets (Megavirus chiliensis and Protochlamydia EI2 or Chlamydia trachomatis L2 434Bu) showed the presence of orthologs between these with several clustered. In addition, Pearson's single regression analysis revealed that almost the prevalence of the genes from the giant viruses in chlamydial genomes was negatively and specifically correlated with the number of chlamydial open reading frames (ORFs). Thus, these results indicated the trace of lateral gene transfer between protozoa-related giant viruses of family Mimiviridae and chlamydiae. This is the first demonstration of a putative linkage between chlamydiae and the giant viruses, providing us with a hint to understand chlamydial evolution.}, }
@article {pmid30038246, year = {2018}, author = {Richardson, EJ and Bacigalupe, R and Harrison, EM and Weinert, LA and Lycett, S and Vrieling, M and Robb, K and Hoskisson, PA and Holden, MTG and Feil, EJ and Paterson, GK and Tong, SYC and Shittu, A and van Wamel, W and Aanensen, DM and Parkhill, J and Peacock, SJ and Corander, J and Holmes, M and Fitzgerald, JR}, title = {Gene exchange drives the ecological success of a multi-host bacterial pathogen.}, journal = {Nature ecology &amp; evolution}, volume = {2}, number = {9}, pages = {1468-1478}, pmid = {30038246}, issn = {2397-334X}, support = {BB/I013873/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; G1001787/MRC_/Medical Research Council/United Kingdom ; 109385//Wellcome Trust/United Kingdom ; 201531//Wellcome Trust/United Kingdom ; MR/S00291X/1/MRC_/Medical Research Council/United Kingdom ; 098600//Wellcome Trust/United Kingdom ; MR/N02995X/1/MRC_/Medical Research Council/United Kingdom ; MR/P007201/1/MRC_/Medical Research Council/United Kingdom ; G1000803/MRC_/Medical Research Council/United Kingdom ; //Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Cattle ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Genome-Wide Association Study ; *Host-Pathogen Interactions ; Humans ; Livestock ; Phylogeny ; Pseudogenes ; Staphylococcal Infections/veterinary ; Staphylococcus aureus/*physiology ; }, abstract = {The capacity for some pathogens to jump into different host-species populations is a major threat to public health and food security. Staphylococcus aureus is a multi-host bacterial pathogen responsible for important human and livestock diseases. Here, using a population-genomic approach, we identify humans as a major hub for ancient and recent S. aureus host-switching events linked to the emergence of endemic livestock strains, and cows as the main animal reservoir for the emergence of human epidemic clones. Such host-species transitions are associated with horizontal acquisition of genetic elements from host-specific gene pools conferring traits required for survival in the new host-niche. Importantly, genes associated with antimicrobial resistance are unevenly distributed among human and animal hosts, reflecting distinct antibiotic usage practices in medicine and agriculture. In addition to gene acquisition, genetic diversification has occurred in pathways associated with nutrient acquisition, implying metabolic remodelling after a host switch in response to distinct nutrient availability. For example, S. aureus from dairy cattle exhibit enhanced utilization of lactose-a major source of carbohydrate in bovine milk. Overall, our findings highlight the influence of human activities on the multi-host ecology of a major bacterial pathogen, underpinned by horizontal gene transfer and core genome diversification.}, }
@article {pmid30037391, year = {2018}, author = {Liu, Y}, title = {Darwin's Pangenesis and the Lamarckian Inheritance of Acquired Characters.}, journal = {Advances in genetics}, volume = {101}, number = {}, pages = {115-144}, doi = {10.1016/bs.adgen.2018.05.005}, pmid = {30037391}, issn = {0065-2660}, mesh = {Animals ; *Biological Evolution ; Databases, Genetic ; *Ecosystem ; Gene Transfer, Horizontal ; Humans ; Selection, Genetic ; }, abstract = {Since the earliest days of evolutionary thought, the problem of the inheritance of acquired characters has been a central debate. Darwin accepted the inheritance of acquired characters as an established fact and gave many instances. His Pangenesis was more than anything else an attempt to provide a theory for its explanation. Over the past several decades, there has been increasing evidence for the inheritance of acquired habit and immunity, and for heritable changes induced by food and fertilizer, stress, chemicals, temperature, light and other environmental factors. Many studies also suggest that parental age has certain influences on the characters of offspring. The current explanations include environmentally induced DNA changes (mainly DNA rearrangements and DNA methylation), RNA-mediated inheritance, and horizontal gene transfer. These mechanistic explanations are consistent with Darwin's Pangenesis.}, }
@article {pmid30035711, year = {2018}, author = {Fleshman, A and Mullins, K and Sahl, J and Hepp, C and Nieto, N and Wiggins, K and Hornstra, H and Kelly, D and Chan, TC and Phetsouvanh, R and Dittrich, S and Panyanivong, P and Paris, D and Newton, P and Richards, A and Pearson, T}, title = {Comparative pan-genomic analyses of Orientia tsutsugamushi reveal an exceptional model of bacterial evolution driving genomic diversity.}, journal = {Microbial genomics}, volume = {4}, number = {9}, pages = {}, pmid = {30035711}, issn = {2057-5858}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {*Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; *Genetic Variation ; *Genome, Bacterial ; Genomics ; Models, Genetic ; Orientia tsutsugamushi/classification/*genetics ; Phylogeny ; Polymorphism, Single Nucleotide ; Recombination, Genetic ; }, abstract = {Orientia tsutsugamushi, formerly Rickettsia tsutsugamushi, is an obligate intracellular pathogen that causes scrub typhus, an underdiagnosed acute febrile disease with high morbidity. Scrub typhus is transmitted by the larval stage (chigger) of Leptotrombidium mites and is irregularly distributed across endemic regions of Asia, Australia and islands of the western Pacific Ocean. Previous work to understand population genetics in O. tsutsugamushi has been based on sub-genomic sampling methods and whole-genome characterization of two genomes. In this study, we compared 40 genomes from geographically dispersed areas and confirmed patterns of extensive homologous recombination likely driven by transposons, conjugative elements and repetitive sequences. High rates of lateral gene transfer (LGT) among O. tsutsugamushi genomes appear to have effectively eliminated a detectable clonal frame, but not our ability to infer evolutionary relationships and phylogeographical clustering. Pan-genomic comparisons using 31 082 high-quality bacterial genomes from 253 species suggests that genomic duplication in O. tsutsugamushi is almost unparalleled. Unlike other highly recombinant species where the uptake of exogenous DNA largely drives genomic diversity, the pan-genome of O. tsutsugamushi is driven by duplication and divergence. Extensive gene innovation by duplication is most commonly attributed to plants and animals and, in contrast with LGT, is thought to be only a minor evolutionary mechanism for bacteria. The near unprecedented evolutionary characteristics of O. tsutsugamushi, coupled with extensive intra-specific LGT, expand our present understanding of rapid bacterial evolutionary adaptive mechanisms.}, }
@article {pmid30034183, year = {2018}, author = {Lalruatdiki, A and Dutta, TK and Roychoudhury, P and Subudhi, PK}, title = {Extended-spectrum β-lactamases producing multidrug resistance Escherichia coli, Salmonella and Klebsiella pneumoniae in pig population of Assam and Meghalaya, India.}, journal = {Veterinary world}, volume = {11}, number = {6}, pages = {868-873}, pmid = {30034183}, issn = {0972-8988}, abstract = {AIM: The present study was conducted to record the prevalence of extended spectrum β-lactamases (ESBLs) producing Escherichia coli, Salmonella spp., and Klebsiella pneumoniae from pig population of Assam and Meghalaya and to record the ability of the resistant bacteria to transfer the resistance genes horizontally.<br><br>MATERIALS AND METHODS: Fecal samples (n=228), collected from pigs of Assam (n=99) and Meghalaya (n=129), were processed for isolation and identification of E. coli and Salmonella spp. All the isolates were tested for ESBLs production by double disc synergy test (DDST) followed by screening for ESBLs producing genes (blaTEM, blaSHV, blaCTX-M, and blaCMY) by polymerase chain reaction (PCR). Possible transfer of resistance encoding genes between enteric bacterial species was carried out by in vitro and in vivo horizontal gene transfer (HGT) method.<br><br>RESULTS: A total of 897 enteric bacteria (867 E. coli and 30 Salmonella) were isolated and identified. Altogether 25.41% isolates were confirmed as ESBL producers by DDST method. Majority of the isolates were E. coli followed by Salmonella. By PCR, 9.03% isolates were found positive for at least one of the target resistance genes. blaSHV was absent in all the isolates. blaCMY was the most prevalent gene. All the E. coli isolates from Assam were negative for blaTEM. A total of 2.76% isolates were positive for blaTEM + blaCMY. On the other hand, 0.67% isolates were positive for blaCTX-M + blaCMY genes. Only 0.33% isolates carried all the three genes. Altogether, 4.68% bacteria carried the resistance encoding genes in their plasmids. blaTEM gene could be successfully transferred from Salmonella (donor) to E. coli (recipient) by in vitro (5.5-5.7&#xd7;10[-5]) and in vivo (6.5&#xd7;10[-5] to 8.8&#xd7;10[-4]) methods. In vivo method was more effective than in vitro in the transfer of resistance genes.<br><br>CONCLUSION: The pig population of Assam and Meghalaya are carrying multidrug resistance and ESBLs producing E. coli and Salmonella. The isolates are also capable to transfer their resistance trait to other bacterial species by HGT. The present finding could be considered as a serious public health concern as similar trait can also be transmitted to the human commensal bacteria as well as pathogens.}, }
@article {pmid30031590, year = {2019}, author = {Foster, TJ}, title = {Can β-Lactam Antibiotics Be Resurrected to Combat MRSA?.}, journal = {Trends in microbiology}, volume = {27}, number = {1}, pages = {26-38}, doi = {10.1016/j.tim.2018.06.005}, pmid = {30031590}, issn = {1878-4380}, mesh = {Anti-Bacterial Agents/pharmacology/*therapeutic use ; Daptomycin/pharmacology/therapeutic use ; *Drug Synergism ; Drug Therapy, Combination/methods ; Humans ; Hydroxymethylglutaryl-CoA Reductase Inhibitors/pharmacology/therapeutic use ; Methicillin-Resistant Staphylococcus aureus/*drug effects ; Staphylococcal Infections/*drug therapy/*microbiology ; Vancomycin/pharmacology/therapeutic use ; beta-Lactams/pharmacology/*therapeutic use ; }, abstract = {The use of β-lactam antibiotics to treat infections caused by Staphylococcus aureus has been severely compromised by the acquisition by horizontal gene transfer of a gene that encodes the β-lactam-insensitive penicillin-binding protein PBP2a. This allows methicillin-resistant S. aureus (MRSA) to proliferate in the presence of β-lactam antibiotics. Paradoxically the dependence on PBP2a for the essential transpeptidase activity in cell wall peptidoglycan biosynthesis is the 'Achilles heel' of MRSA. Compounds that disrupt the divisome, wall teichoic acid, and functional membrane microdomains act synergistically with β-lactams against MRSA. These include drugs such as statins that are widely used in human medicine. The antibiotics vancomycin and daptomycin are also synergistic with β-lactams, and combinations have been employed to treat persistent MRSA infections. An additional benefit of exposing MRSA to β-lactams could be a reduction in virulence mediated by interfering with the global regulator Agr. The mechanistic basis of synergy is discussed, and the possibility that β-lactams can be resurrected to combat MRSA infections is explored.}, }
@article {pmid30031405, year = {2018}, author = {Zhang, AN and Li, LG and Ma, L and Gillings, MR and Tiedje, JM and Zhang, T}, title = {Conserved phylogenetic distribution and limited antibiotic resistance of class 1 integrons revealed by assessing the bacterial genome and plasmid collection.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {130}, pmid = {30031405}, issn = {2049-2618}, mesh = {*Drug Resistance, Bacterial ; Evolution, Molecular ; Gammaproteobacteria/drug effects/*genetics ; Gene Transfer, Horizontal ; Genome, Bacterial ; *Integrons ; Phylogeny ; Plasmids/*genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Integrons, especially the class 1 integrons, are major contributors to the acquisition and dissemination of antibiotic resistance genes (ARGs). However, comprehensive knowledge of the types, content, and distribution of integrons in bacterial taxa is lacking to evaluate their contribution.<br><br>RESULTS: We have constructed a new integrase database and developed a pipeline that provides comprehensive recovery of class 1 integrons. Previous PCR-based techniques might only detect one fourth of the integron-integrases and integrons recovered in this study. By exploring the class 1 integrons in over 73,000 currently available complete and draft bacterial genomes, the contribution of class 1 integrons in spreading and acquiring ARGs was evaluated. Firstly, the host species of class 1 integrons are highly conserved within (96%) in class Gammaproteobacteria, dominated by four pathogenic species of "ESKAPE." Secondly, more than half of class 1 integrons are embedded in chromosomes with less potential for horizontal gene transfer. Finally, ARGs that have been acquired by these integrons only cover 11% of all the ARG genotypes detected in bacterial genomes.<br><br>CONCLUSIONS: The above observations indicated that there are both biological and ecological limitations to class 1 integrons in acquiring and spreading ARGs across different classes of the domain Bacteria.}, }
@article {pmid30030013, year = {2018}, author = {Anjum, M and Madsen, JS and Espinosa-Gongora, C and Jana, B and Wiese, M and Nielsen, DS and Sørensen, SJ and Moodley, A and Bortolaia, V and Guardabassi, L}, title = {A culture-independent method for studying transfer of IncI1 plasmids from wild-type Escherichia coli in complex microbial communities.}, journal = {Journal of microbiological methods}, volume = {152}, number = {}, pages = {18-26}, doi = {10.1016/j.mimet.2018.07.009}, pmid = {30030013}, issn = {1872-8359}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Conjugation, Genetic ; Culture Techniques/*methods ; Escherichia coli/*genetics ; Escherichia coli Proteins/genetics ; Gene Expression Regulation, Bacterial ; *Gene Transfer Techniques ; Genetic Engineering/methods ; Green Fluorescent Proteins/genetics ; Microbiota/*genetics ; Plasmids/*genetics ; beta-Lactam Resistance/genetics ; beta-Lactamases/genetics ; }, abstract = {IncI1 plasmids play a central role in the transfer of antimicrobial resistance genes among Enterobacteriaceae in animals and humans. Knowledge on the dynamics of IncI1 plasmid transfer is limited, mainly due to lack of culture-independent methods that can quantify donor strain survival and plasmid transfer in complex microbial communities. The aim of this study was to develop a culture-independent method to study the dynamics of IncI1 plasmids transfer by fluorescence-activated cell sorting. We genetically modified three wild-type Escherichia coli of animal (n = 2) and human (n = 1) origin carrying blaCMY-2 or blaCTX-M-1 on two epidemic IncI1 plasmids (pST12 and pST7). Non-coding regions on the chromosome and on the IncI1 plasmid of each strain were tagged with mCherry (red) and GFPmut3 (green) fluorescent proteins, respectively, using lambda recombineering. A gene cassette expressing mCherry and lacI[q] was inserted into the chromosome, whereas the plasmid was marked with a GFPmut3 cassette with LacI[q] repressible promoter. Therefore, gfpmut3 was repressed in donor strains but expressed in recipient strains acquiring the plasmids. We demonstrated that genetic engineering of the strains did not affect the growth rate and plasmid transfer-ability in filter and broth matings. A proof-of-concept experiment using the CoMiniGut, an in vitro model of the colon, proved the validity of our method for studying the survival of wild-type E. coli and horizontal transfer of IncI1 plasmids under different pH and oxygen conditions. The dual-labeling method by fluorescent proteins is useful to determine persistence of exogenous E. coli and transfer dynamics of IncI1 plasmids in microbial communities.}, }
@article {pmid30027301, year = {2018}, author = {Soutar, CD and Stavrinides, J}, title = {The evolution of three siderophore biosynthetic clusters in environmental and host-associating strains of Pantoea.}, journal = {Molecular genetics and genomics : MGG}, volume = {293}, number = {6}, pages = {1453-1467}, pmid = {30027301}, issn = {1617-4623}, support = {2015-06417//Natural Sciences and Engineering Research Council of Canada/ ; 28591//Canada Foundation for Innovation (CA)/ ; }, mesh = {Animals ; Biosynthetic Pathways/genetics ; Deferoxamine/metabolism ; Enterobacteriaceae Infections/*genetics/microbiology ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Gene-Environment Interaction ; Host Specificity/genetics ; Host-Pathogen Interactions/*genetics ; Humans ; Multigene Family ; Pantoea/*genetics ; Phylogeny ; Siderophores/*biosynthesis/*genetics ; Virulence ; }, abstract = {For many pathogenic members of the Enterobacterales, siderophores play an important role in virulence, yet the siderophores of the host-associating members of the genus Pantoea remain unexplored. We conducted a genome-wide survey of environmental and host-associating strains of Pantoea to identify known and candidate siderophore biosynthetic clusters. Our analysis identified three clusters homologous to those of enterobactin, desferrioxamine, and aerobactin that were prevalent among Pantoea species. Using both phylogenetic and comparative genomic approaches, we demonstrate that the enterobactin-like cluster was present in the common ancestor of all Pantoea, with evidence for three independent losses of the cluster in P. eucalypti, P. eucrina, and the P. ananatis-P. stewartii lineage. The desferrioxamine biosynthetic cluster, previously described and characterized in Pantoea, was horizontally acquired from its close relative Erwinia, with phylogenetic evidence that these transfer events were ancient and occurred between ancestral lineages. The aerobactin cluster was identified in three host-associating species groups, P. septica, P. ananatis, and P. stewartii, with strong evidence for horizontal acquisition from human-pathogenic members of the Enterobacterales. Our work identifies and describes the key siderophore clusters in Pantoea, shows three distinct evolutionary processes driving their diversification, and provides a foundation for exploring the roles that these siderophores may play in human opportunistic infections.}, }
@article {pmid30026808, year = {2018}, author = {Zhong, C and Han, M and Yu, S and Yang, P and Li, H and Ning, K}, title = {Pan-genome analyses of 24 Shewanella strains re-emphasize the diversification of their functions yet evolutionary dynamics of metal-reducing pathway.}, journal = {Biotechnology for biofuels}, volume = {11}, number = {}, pages = {193}, pmid = {30026808}, issn = {1754-6834}, support = {R34 AA021502/AA/NIAAA NIH HHS/United States ; }, abstract = {BACKGROUND: Shewanella strains are important dissimilatory metal-reducing bacteria which are widely distributed in diverse habitats. Despite efforts to genomically characterize Shewanella, knowledge of the molecular components, functional information and evolutionary patterns remain lacking, especially for their compatibility in the metal-reducing pathway. The increasing number of genome sequences of Shewanella strains offers a basis for pan-genome studies.<br><br>RESULTS: A comparative pan-genome analysis was conducted to study genomic diversity and evolutionary relationships among 24 Shewanella strains. Results revealed an open pan-genome of 13,406 non-redundant genes and a core-genome of 1878 non-redundant genes. Selective pressure acted on the invariant members of core genome, in which purifying selection drove evolution in the housekeeping mechanisms. Shewanella strains exhibited extensive genome variability, with high levels of gene gain and loss during the evolution, which affected variable gene sets and facilitated the rapid evolution. Additionally, genes related to metal reduction were diversely distributed in Shewanella strains and evolved under purifying selection, which highlighted the basic conserved functionality and specificity of respiratory systems.<br><br>CONCLUSIONS: The diversity of genes present in the accessory and specific genomes of Shewanella strains indicates that each strain uses different strategies to adapt to diverse environments. Horizontal gene transfer is an important evolutionary force in shaping Shewanella genomes. Purifying selection plays an important role in the stability of the core-genome and also drives evolution in mtr-omc cluster of different Shewanella strains.}, }
@article {pmid30026612, year = {2018}, author = {Poulter, RTM and Ho, J and Handley, T and Taiaroa, G and Butler, MI}, title = {Comparison between complete genomes of an isolate of Pseudomonas syringae pv. actinidiae from Japan and a New Zealand isolate of the pandemic lineage.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {10915}, pmid = {30026612}, issn = {2045-2322}, support = {UORG 2017 113005//University of Otago (Te Whare W&#x0101;nanga o Ot&#x0101;go)/International ; }, mesh = {Actinidia/microbiology ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing/*methods ; Japan ; Methylation ; New Zealand ; Pandemics ; Plant Diseases/microbiology ; Pseudomonas syringae/genetics/*pathogenicity ; RNA, Transfer/genetics ; Virulence Factors/*genetics ; }, abstract = {The modern pandemic of the bacterial kiwifruit pathogen Pseudomonas syringae pv actinidiae (Psa) is caused by a particular Psa lineage. To better understand the genetic basis of the virulence of this lineage, we compare the completely assembled genome of a pandemic New Zealand strain with that of the Psa type strain first isolated in Japan in 1983. Aligning the two genomes shows numerous translocations, constrained so as to retain the appropriate orientation of the Architecture Imparting Sequences (AIMs). There are several large horizontally acquired regions, some of which include Type I, Type II or Type III restriction systems. The activity of these systems is reflected in the methylation patterns of the two strains. The pandemic strain carries an Integrative Conjugative Element (ICE) located at a tRNA-Lys site. Two other complex elements are also present at tRNA-Lys sites in the genome. These elements are derived from ICE but have now acquired some alternative secretion function. There are numerous types of mobile element in the two genomes. Analysis of these elements reveals no evidence of recombination between the two Psa lineages.}, }
@article {pmid30026532, year = {2018}, author = {Hua, ZS and Qu, YN and Zhu, Q and Zhou, EM and Qi, YL and Yin, YR and Rao, YZ and Tian, Y and Li, YX and Liu, L and Castelle, CJ and Hedlund, BP and Shu, WS and Knight, R and Li, WJ}, title = {Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {2832}, pmid = {30026532}, issn = {2041-1723}, support = {31600298//National Natural Science Foundation of China (National Science Foundation of China)/International ; }, mesh = {Anaerobiosis/*genetics ; Archaea/classification/*genetics ; Bayes Theorem ; *Biological Evolution ; Carbon Monoxide/metabolism ; Chemoautotrophic Growth/*genetics ; China ; Gene Transfer, Horizontal ; *Genome, Archaeal ; Genomics ; Hot Springs/microbiology ; Hot Temperature ; Metabolic Networks and Pathways/*genetics ; Oxidation-Reduction ; Phylogeny ; Sulfides/metabolism ; }, abstract = {Microbes of the phylum Aigarchaeota are widely distributed in geothermal environments, but their physiological and ecological roles are poorly understood. Here we analyze six Aigarchaeota metagenomic bins from two circumneutral hot springs in Tengchong, China, to reveal that they are either strict or facultative anaerobes, and most are chemolithotrophs that can perform sulfide oxidation. Applying comparative genomics to the Thaumarchaeota and Aigarchaeota, we find that they both originated from thermal habitats, sharing 1154 genes with their common ancestor. Horizontal gene transfer played a crucial role in shaping genetic diversity of Aigarchaeota and led to functional partitioning and ecological divergence among sympatric microbes, as several key functional innovations were endowed by Bacteria, including dissimilatory sulfite reduction and possibly carbon monoxide oxidation. Our study expands our knowledge of the possible ecological roles of the Aigarchaeota and clarifies their evolutionary relationship to their sister lineage Thaumarchaeota.}, }
@article {pmid30024971, year = {2018}, author = {Matsuo, M and Katahata, A and Satoh, S and Matsuzaki, M and Nomura, M and Ishida, KI and Inagaki, Y and Obokata, J}, title = {Characterization of spliced leader trans-splicing in a photosynthetic rhizarian amoeba, Paulinella micropora, and its possible role in functional gene transfer.}, journal = {PloS one}, volume = {13}, number = {7}, pages = {e0200961}, pmid = {30024971}, issn = {1932-6203}, mesh = {Biodiversity ; Cercozoa/classification/*genetics/growth &amp; development ; Chromatophores/metabolism ; DNA, Protozoan/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Protozoan ; *Photosynthesis ; Phylogeny ; RNA, Spliced Leader/*genetics ; Symbiosis ; *Trans-Splicing ; }, abstract = {Paulinella micropora is a rhizarian thecate amoeba, belonging to a photosynthetic Paulinella species group that has a unique organelle termed chromatophore, whose cyanobacterial origin is distinct from that of plant and algal chloroplasts. Because acquisition of the chromatophore was quite a recent event compared with that of the chloroplast ancestor, the Paulinella species are thought to be model organisms for studying the early process of primary endosymbiosis. To obtain insight into how endosymbiotically transferred genes acquire expression competence in the host nucleus, here we analyzed the 5' end sequences of the mRNAs of P. micropora MYN1 strain with the aid of a cap-trapper cDNA library. As a result, we found that mRNAs of 27 genes, including endosymbiotically transferred genes, possessed the common 5' end sequence of 28-33 bases that were posttranscriptionally added by spliced leader (SL) trans-splicing. We also found two subtypes of SL RNA genes encoded by the P. micropora MYN1 genome. Differing from the other SL trans-splicing organisms that usually possess poly(A)-less SL RNAs, this amoeba has polyadenylated SL RNAs. In this study, we characterize the SL trans-splicing of this unique organism and discuss the putative merits of SL trans-splicing in functional gene transfer and genome evolution.}, }
@article {pmid30024366, year = {2018}, author = {Sproston, EL and Wimalarathna, HML and Sheppard, SK}, title = {Trends in fluoroquinolone resistance in Campylobacter.}, journal = {Microbial genomics}, volume = {4}, number = {8}, pages = {}, pmid = {30024366}, issn = {2057-5858}, support = {/WT_/Wellcome Trust/United Kingdom ; G0801929/MRC_/Medical Research Council/United Kingdom ; MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; BB/I02464X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Campylobacter/classification/*genetics/growth &amp; development/isolation &amp; purification ; *Ciprofloxacin ; Drug Resistance, Bacterial/*genetics ; *Gene Transfer, Horizontal ; Humans ; }, abstract = {Members of the genus Campylobacter remain a leading cause of bacterial gastroenteritis worldwide. Infection is usually self-limiting but in severe cases may require antibiotic treatment. In a recent statement by the World Health Organization (WHO) Campylobacter was named as one of the 12 bacteria that pose the greatest threat to human health because they are resistant to antibiotics. In this mini review we describe recent trends in fluoroquinolone (FQ) (particularly ciprofloxacin) resistance in strains of members of the genus Campylobacter isolated from livestock and clinical samples from several countries. Using evidence from phenotyping surveys and putative resistance prediction from DNA sequence data, we discuss the acquisition and spread of FQ resistance and the role of horizontal gene transfer and describe trends in FQ-resistance in samples from livestock and clinical cases. This review emphasises that FQ resistance remains common among isolates of members of the genus Campylobacter from various sources.}, }
@article {pmid30022808, year = {2018}, author = {Lang, SA and Shain, DH}, title = {Atypical Evolution of the F1Fo Adenosine Triphosphate Synthase Regulatory ATP6 subunit in Glacier Ice Worms (Annelida: Clitellata: Mesenchytraeus).}, journal = {Evolutionary bioinformatics online}, volume = {14}, number = {}, pages = {1176934318788076}, pmid = {30022808}, issn = {1176-9343}, support = {R15 GM093685/GM/NIGMS NIH HHS/United States ; }, abstract = {The glacier ice worm, Mesenchytraeus solifugus, is among a few animals that reside permanently in glacier ice. Their adaptation to cold temperature has been linked to relatively high intracellular adenosine triphosphate (ATP) levels, which compensate for reductions in molecular motion at low physiological temperatures. Here, we show that ATP6-the critical regulatory subunit of the F1Fo-ATP synthase and primary target of mitochondrial disease-acquired an unprecedented histidine-rich, 18-amino acid carboxy-terminal extension, which counters the strong evolutionary trend of mitochondrial genome compaction. Furthermore, sequence analysis suggests that this insertion is not of metazoan origin, but rather is a product of horizontal gene transfer from a microbial dietary source, and may act as a proton shuttle to accelerate the rate of ATP synthesis.}, }
@article {pmid30022749, year = {2018}, author = {Koraimann, G}, title = {Spread and Persistence of Virulence and Antibiotic Resistance Genes: A Ride on the F Plasmid Conjugation Module.}, journal = {EcoSal Plus}, volume = {8}, number = {1}, pages = {}, pmid = {30022749}, issn = {2324-6200}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Outer Membrane Proteins/genetics ; Conjugation, Genetic/*genetics ; DNA Transposable Elements/genetics ; DNA, Bacterial/genetics ; Drug Resistance, Microbial/*genetics ; Escherichia coli/genetics ; F Factor/*genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Integrons/genetics ; Sequence Analysis, DNA ; Type IV Secretion Systems/genetics ; Virulence ; Virulence Factors/genetics ; }, abstract = {The F plasmid or F-factor is a large, 100-kbp, circular conjugative plasmid of Escherichia coli and was originally described as a vector for horizontal gene transfer and gene recombination in the late 1940s. Since then, F and related F-like plasmids have served as role models for bacterial conjugation. At present, more than 200 different F-like plasmids with highly related DNA transfer genes, including those for the assembly of a type IV secretion apparatus, are completely sequenced. They belong to the phylogenetically related MOBF12A group. F-like plasmids are present in enterobacterial hosts isolated from clinical as well as environmental samples all over the world. As conjugative plasmids, F-like plasmids carry genetic modules enabling plasmid replication, stable maintenance, and DNA transfer. In this plasmid backbone of approximately 60 kbp, the DNA transfer genes occupy the largest and mostly conserved part. Subgroups of MOBF12A plasmids can be defined based on the similarity of TraJ, a protein required for DNA transfer gene expression. In addition, F-like plasmids harbor accessory cargo genes, frequently embedded within transposons and/or integrons, which harness their host bacteria with antibiotic resistance and virulence genes, causing increasingly severe problems for the treatment of infectious diseases. Here, I focus on key genetic elements and their encoded proteins present on the F-factor and other typical F-like plasmids belonging to the MOBF12A group of conjugative plasmids.}, }
@article {pmid30021873, year = {2018}, author = {Wang, J and Zeng, ZL and Huang, XY and Ma, ZB and Guo, ZW and Lv, LC and Xia, YB and Zeng, L and Song, QH and Liu, JH}, title = {Evolution and Comparative Genomics of F33:A-:B- Plasmids Carrying blaCTX-M-55 or blaCTX-M-65 in Escherichia coli and Klebsiella pneumoniae Isolated from Animals, Food Products, and Humans in China.}, journal = {mSphere}, volume = {3}, number = {4}, pages = {}, pmid = {30021873}, issn = {2379-5042}, mesh = {Animals ; Conjugation, Genetic ; Enterobacteriaceae Infections/*microbiology/*veterinary ; Escherichia coli/*enzymology/genetics/isolation &amp; purification ; Evolution, Molecular ; *Food Microbiology ; Gene Transfer, Horizontal ; Genetic Variation ; Hong Kong ; Humans ; Integrons ; Klebsiella pneumoniae/*enzymology/genetics/isolation &amp; purification ; Plasmids/*analysis/classification ; Recombination, Genetic ; beta-Lactamases/*genetics ; }, abstract = {To understand the underlying evolution process of F33:A-:B- plasmids among Enterobacteriaceae isolates of various origins in China, the complete sequences of 17 blaCTX-M-harboring F33:A-:B- plasmids obtained from Escherichia coli and Klebsiella pneumoniae isolates from different sources (animals, animal-derived food, and human clinics) in China were determined. F33:A-:B- plasmids shared similar plasmid backbones comprising replication, leading, and conjugative transfer regions and differed by the numbers of repeats in yddA and traD and by the presence of group II intron, except that pHNAH9 lacked a large segment of the leading and transfer regions. The variable regions of F33:A-B- plasmids were distinct and were inserted downstream of the addiction system pemI/pemK, identified as the integration hot spot among F33:A-B- plasmids. The variable region contained resistance genes and mobile elements or contained segments from other types of plasmids, such as IncI1, IncN1, and IncX1. Three plasmids encoding CTX-M-65 were very similar to our previously described pHN7A8 plasmid. Four CTX-M-55-producing plasmids contained multidrug resistance regions related to that of F2:A-B- plasmid pHK23a from Hong Kong. Five plasmids with IncN and/or IncX replication regions and IncI1-backbone fragments had variable regions related to those of pE80 and p42-2. The remaining five plasmids with IncN replicons and an IncI1 segment also possessed closely related variable regions. The diversity in variable regions was presumably associated with rearrangements, insertions, and/or deletions mediated by mobile elements, such as IS26 and IS1294IMPORTANCE Worldwide spread of antibiotic resistance genes among Enterobacteriaceae isolates is of great concern. F33:A-:B- plasmids are important vectors of resistance genes, such as blaCTX-M-55/-65, blaNDM-1, fosA3, and rmtB, among E. coli isolates from various sources in China. We determined and compared the complete sequences of 17 F33:A-:B- plasmids from various sources. These plasmids appear to have evolved from the same ancestor by mobile element-mediated rearrangement, acquisition, and/or loss of resistance modules and similar IncN1, IncI1, and/or IncX1 plasmid backbone segments. Our findings highlight the evolutionary potential of F33:A-:B- plasmids as efficient vectors to capture and diffuse clinically relevant resistance genes.}, }
@article {pmid30018876, year = {2018}, author = {Lücking, R and Hawksworth, DL}, title = {Formal description of sequence-based voucherless Fungi: promises and pitfalls, and how to resolve them.}, journal = {IMA fungus}, volume = {9}, number = {1}, pages = {143-166}, pmid = {30018876}, issn = {2210-6340}, abstract = {There is urgent need for a formal nomenclature of sequence-based, voucherless Fungi, given that environmental sequencing has accumulated more than one billion fungal ITS reads in the Sequence Read Archive, about 1,000 times as many as fungal ITS sequences in GenBank. These unnamed Fungi could help to bridge the gap between 115,000 to 140,000 currently accepted and 2.2 to 3.8 million predicted species, a gap that cannot realistically be filled using specimen or culture-based inventories. The Code never aimed at placing restrictions on the nature of characters chosen for taxonomy, and the requirement for physical types is now becoming a constraint on the advancement of science. We elaborate on the promises and pitfalls of sequence-based nomenclature and provide potential solutions to major concerns of the mycological community. Types of sequence-based taxa, which by default lack a physical specimen or culture, could be designated in four alternative ways: (1) the underlying sample ('bag' type), (2) the DNA extract, (3) fluorescent in situ hybridization (FISH), or (4) the type sequence itself. Only (4) would require changes to the Code and the latter would be the most straightforward approach, complying with three of the five principal functions of types better than physical specimens. A fifth way, representation of the sequence in an illustration, has been ruled as unacceptable in the Code. Potential flaws in sequence data are analogous to flaws in physical types, and artifacts are manageable if a stringent analytical approach is applied. Conceptual errors such as homoplasy, intragenomic variation, gene duplication, hybridization, and horizontal gene transfer, apply to all molecular approaches and cannot be used as a specific argument against sequence-based nomenclature. The potential impact of these phenomena is manageable, as phylogenetic species delimitation has worked satisfactorily in Fungi. The most serious shortcoming of sequence-based nomenclature is the likelihood of parallel classifications, either by describing taxa that already have names based on physical types, or by using different markers to delimit species within the same lineage. The probability of inadvertently establishing sequence-based species that have names available is between 20.4 % and 1.5 % depending on the number of globally predicted fungal species. This compares favourably to a historical error rate of about 30 % based on physical types, and this rate could be reduced to practically zero by adding specific provisions to this approach in the Code. To avoid parallel classifications based on different markers, sequence-based nomenclature should be limited to a single marker, preferably the fungal ITS barcoding marker; this is possible since sequence-based nomenclature does not aim at accurate species delimitation but at naming lineages to generate a reference database, independent of whether these lineages represent species, closely related species complexes, or infraspecies. We argue that clustering methods are inappropriate for sequence-based nomenclature; this approach must instead use phylogenetic methods based on multiple alignments, combined with quantitative species recognition methods. We outline strategies to obtain higher-level phylogenies for ITS-based, voucherless species, including phylogenetic binning, 'hijacking' species delimitation methods, and temporal banding. We conclude that voucherless, sequence-based nomenclature is not a threat to specimen and culture-based fungal taxonomy, but a complementary approach capable of substantially closing the gap between known and predicted fungal diversity, an approach that requires careful work and high skill levels.}, }
@article {pmid30018870, year = {2018}, author = {Van Wyk, S and Wingfield, BD and De Vos, L and Santana, QC and Van der Merwe, NA and Steenkamp, ET}, title = {Multiple independent origins for a subtelomeric locus associated with growth rate in Fusarium circinatum.}, journal = {IMA fungus}, volume = {9}, number = {1}, pages = {27-36}, pmid = {30018870}, issn = {2210-6340}, abstract = {Fusarium is a diverse assemblage that includes a large number of species of considerable medical and agricultural importance. Not surprisingly, whole genome sequences for many Fusarium species have been published or are in the process of being determined, the availability of which is invaluable for deciphering the genetic basis of key phenotypic traits. Here we investigated the distribution, genic composition, and evolutionary history of a locus potentially determining growth rate in the pitch canker pathogen F. circinatum. We found that the genomic region underlying this locus is highly conserved amongst F. circinatum and its close relatives, except for the presence of a 12 000 base pair insertion in all of the examined isolates of F. circinatum. This insertion encodes for five genes and our phylogenetic analyses revealed that each was most likely acquired through horizontal gene transfer from polyphyletic origins. Our data further showed that this region is located in a region low in G+C content and enriched for repetitive sequences and transposable elements, which is situated near the telomere of Chromosome 3 of F. circinatum. As have been shown for other fungi, these findings thus suggest that the emergence of the unique 12 000 bp region in F. circinatum is linked to the dynamic evolutionary processes associated with subtelomeres that, in turn, have been implicated in the ecological adaptation of fungal pathogens.}, }
@article {pmid30017563, year = {2018}, author = {Mir-Sanchis, I and Pigli, YZ and Rice, PA}, title = {Crystal Structure of an Unusual Single-Stranded DNA-Binding Protein Encoded by Staphylococcal Cassette Chromosome Elements.}, journal = {Structure (London, England : 1993)}, volume = {26}, number = {8}, pages = {1144-1150.e3}, pmid = {30017563}, issn = {1878-4186}, support = {R01 GM121655/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacterial Proteins/*chemistry/genetics/metabolism ; Binding Sites ; Cloning, Molecular ; Conserved Sequence ; Crystallography, X-Ray ; DNA Replication ; DNA, Bacterial/*chemistry/genetics/metabolism ; DNA, Single-Stranded/*chemistry/genetics/metabolism ; DNA-Binding Proteins/*chemistry/genetics/metabolism ; Escherichia coli/genetics/metabolism ; Gene Expression ; Genetic Vectors/chemistry/metabolism ; Hydrophobic and Hydrophilic Interactions ; Methicillin Resistance/genetics ; Methicillin-Resistant Staphylococcus aureus/*chemistry/genetics/metabolism ; Models, Molecular ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; Recombinant Proteins/chemistry/genetics/metabolism ; Sequence Alignment ; Substrate Specificity ; }, abstract = {Methicillin-resistant Staphylococcus aureus is a global public health threat. Methicillin resistance is carried on mobile genetic elements belonging to the staphylococcal cassette chromosome (SCC) family. The molecular mechanisms that SCC elements exploit for stable maintenance and for horizontal transfer are poorly understood. Previously, we identified several conserved SCC genes with putative functions in DNA replication, including lp1413, which we found encodes a single-stranded DNA (ssDNA)-binding protein. We report here the 2.18 Å crystal structure of LP1413, which shows that it adopts a winged helix-turn-helix fold rather than the OB-fold normally seen in replication-related ssDNA-binding proteins. However, conserved residues form a hydrophobic pocket not normally found in winged helix-turn-helix domains. LP1413 also has a conserved but disordered C-terminal tail. As deletion of the tail does not significantly affect cooperative binding to ssDNA, we propose that it mediates interactions with other proteins. LP1413 could play several different roles in vivo.}, }
@article {pmid30017483, year = {2018}, author = {Wilson, CG and Nowell, RW and Barraclough, TG}, title = {Cross-Contamination Explains "Inter and Intraspecific Horizontal Genetic Transfers" between Asexual Bdelloid Rotifers.}, journal = {Current biology : CB}, volume = {28}, number = {15}, pages = {2436-2444.e14}, doi = {10.1016/j.cub.2018.05.070}, pmid = {30017483}, issn = {1879-0445}, mesh = {Animals ; Biological Evolution ; *Gene Transfer, Horizontal ; Genome ; Genomics ; Rotifera/*genetics ; }, abstract = {A few metazoan lineages are thought to have persisted for millions of years without sexual reproduction. If so, they would offer important clues to the evolutionary paradox of sex itself [1, 2]. Most "ancient asexuals" are subject to ongoing doubt because extant populations continue to invest in males [3-9]. However, males are famously unknown in bdelloid rotifers, a class of microscopic invertebrates comprising hundreds of species [10-12]. Bdelloid genomes have acquired an unusually high proportion of genes from non-metazoans via horizontal transfer [13-17]. This well-substantiated finding has invited speculation [13] that homologous horizontal transfer between bdelloid individuals also may occur, perhaps even "replacing" sex [14]. In 2016, Current Biology published an article claiming to supply evidence for this idea. Debortoli et al. [18] sampled rotifers from natural populations and sequenced one mitochondrial and four nuclear loci. Species assignments were incongruent among loci for several samples, which was interpreted as evidence of "interspecific horizontal genetic transfers." Here, we use sequencing chromatograms supplied by the authors to demonstrate that samples treated as individuals actually contained two or more highly divergent mitochondrial and ribosomal sequences, revealing cross-contamination with DNA from multiple animals of different species. Other chromatograms indicate contamination with DNA from conspecific animals, explaining genetic and genomic evidence for "intraspecific horizontal exchanges" reported in the same study. Given the clear evidence of contamination, the data and findings of Debortoli et al. [18] provide no reliable support for their conclusions that DNA is transferred horizontally between or within bdelloid species.}, }
@article {pmid30016933, year = {2018}, author = {Baheti, S and Tang, X and O'Brien, DR and Chia, N and Roberts, LR and Nelson, H and Boughey, JC and Wang, L and Goetz, MP and Kocher, JA and Kalari, KR}, title = {HGT-ID: an efficient and sensitive workflow to detect human-viral insertion sites using next-generation sequencing data.}, journal = {BMC bioinformatics}, volume = {19}, number = {1}, pages = {271}, pmid = {30016933}, issn = {1471-2105}, support = {P50 CA116201/CA/NCI NIH HHS/United States ; U54 GM114838/GM/NIGMS NIH HHS/United States ; P50CA116201//Mayo Clinic Breast Specialized Program of Research Excellence/International ; U54GM114838/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Base Sequence ; Breast Neoplasms/virology ; Cell Line, Tumor ; Computer Simulation ; Female ; Gene Transfer, Horizontal/*genetics ; *Genome, Human ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; ROC Curve ; Software ; Virus Integration/*genetics ; Whole Genome Sequencing ; Workflow ; }, abstract = {BACKGROUND: Transfer of genetic material from microbes or viruses into the host genome is known as horizontal gene transfer (HGT). The integration of viruses into the human genome is associated with multiple cancers, and these can now be detected using next-generation sequencing methods such as whole genome sequencing and RNA-sequencing.<br><br>RESULTS: We designed a novel computational workflow, HGT-ID, to identify the integration of viruses into the human genome using the sequencing data. The HGT-ID workflow primarily follows a four-step procedure: i) pre-processing of unaligned reads, ii) virus detection using subtraction approach, iii) identification of virus integration site using discordant and soft-clipped reads and iv) HGT candidates prioritization through a scoring function. Annotation and visualization of the events, as well as primer design for experimental validation, are also provided in the final report. We evaluated the tool performance with the well-understood cervical cancer samples. The HGT-ID workflow accurately detected known human papillomavirus (HPV) integration sites with high sensitivity and specificity compared to previous HGT methods. We applied HGT-ID to The Cancer Genome Atlas (TCGA) whole-genome sequencing data (WGS) from liver tumor-normal pairs. Multiple hepatitis B virus (HBV) integration sites were identified in TCGA liver samples and confirmed by HGT-ID using the RNA-Seq data from the matched liver pairs. This shows the applicability of the method in both the data types and cross-validation of the HGT events in liver samples. We also processed 220 breast tumor WGS data through the workflow; however, there were no HGT events detected in those samples.<br><br>CONCLUSIONS: HGT-ID is a novel computational workflow to detect the integration of viruses in the human genome using the sequencing data. It is fast and accurate with functions such as prioritization, annotation, visualization and primer design for future validation of HGTs. The HGT-ID workflow is released under the MIT License and available at http://kalarikrlab.org/Software/HGT-ID.html .}, }
@article {pmid30014616, year = {2018}, author = {Rands, CM and Starikova, EV and Brüssow, H and Kriventseva, EV and Govorun, VM and Zdobnov, EM}, title = {ACI-1 beta-lactamase is widespread across human gut microbiomes in Negativicutes due to transposons harboured by tailed prophages.}, journal = {Environmental microbiology}, volume = {20}, number = {6}, pages = {2288-2300}, doi = {10.1111/1462-2920.14276}, pmid = {30014616}, issn = {1462-2920}, support = {IZLRZ3_163863 16-54-21012//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/International ; //Russian Foundation for Basic Research/International ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/classification/drug effects/genetics/*metabolism ; China ; Drug Resistance, Bacterial/*genetics ; Europe ; Firmicutes/genetics ; *Gastrointestinal Microbiome ; Gene Transfer, Horizontal ; Humans ; Metagenome ; Phylogeny ; Prophages/*genetics ; United States ; beta-Lactamases/genetics/*metabolism ; }, abstract = {Antibiotic resistance is increasing among pathogens, and the human microbiome contains a reservoir of antibiotic resistance genes. Acidaminococcus intestini is the first Negativicute bacterium (Gram-negative Firmicute) shown to be resistant to beta-lactam antibiotics. Resistance is conferred by the aci1 gene, but its evolutionary history and prevalence remain obscure. We discovered that ACI-1 proteins are phylogenetically distinct from beta-lactamases of Gram-positive Firmicutes and that aci1 occurs in bacteria scattered across the Negativicute clade, suggesting lateral gene transfer. In the reference A. intestini RyC-MR95 genome, we found transposons residing within a tailed prophage context are likely vehicles for aci1's mobility. We found aci1 in 56 (4.4%) of 1,267 human gut metagenomes, mostly hosted within A. intestini, and, where could be determined, mostly within a consistent mobile element constellation. These samples are from Europe, China and the USA, showing that aci1 is distributed globally. We found that for most Negativicute assemblies with aci1, the prophage observed in A. instestini is absent, but in all cases aci1 is flanked by varying transposons. The chimeric mobile elements we identify here likely have a complex evolutionary history and potentially provide multiple complementary mechanisms for antibiotic resistance gene transfer both within and between cells.}, }
@article {pmid30013540, year = {2018}, author = {De la Cruz Barrón, M and Merlin, C and Guilloteau, H and Montargès-Pelletier, E and Bellanger, X}, title = {Suspended Materials in River Waters Differentially Enrich Class 1 Integron- and IncP-1 Plasmid-Carrying Bacteria in Sediments.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1443}, pmid = {30013540}, issn = {1664-302X}, abstract = {Aquatic ecosystems are frequently considered as the final receiving environments of anthropogenic pollutants such as pharmaceutical residues or antibiotic resistant bacteria, and as a consequence tend to form reservoirs of antibiotic resistance genes. Considering the global threat posed by the antibiotic resistance, the mechanisms involved in both the formation of such reservoirs and their remobilization are a concern of prime importance. Antibiotic resistance genes are strongly associated with mobile genetic elements that are directly involved in their dissemination. Most mobile genetic element-mediated gene transfers involve replicative mechanisms and, as such, localized gene transfers should participate in the local increase in resistance gene abundance. Additionally, the carriage of conjugative mobile elements encoding cell appendages acting as adhesins has already been demonstrated to increase biofilm-forming capability of bacteria and, therefore, should also contribute to their selective enrichment on surfaces. In the present study, we investigated the occurrence of two families of mobile genetic elements, IncP-1 plasmids and class 1 integrons, in the water column and bank sediments of the Orne River, in France. We show that these mobile elements, especially IncP-1 plasmids, are enriched in the bacteria attached on the suspended matters in the river waters, and that a similar abundance is found in freshly deposited sediments. Using the IncP-1 plasmid pB10 as a model, in vitro experiments demonstrated that local enrichment of plasmid-bearing bacteria on artificial surfaces mainly resulted from an increase in bacterial adhesion properties conferred by the plasmid rather than an improved dissemination frequency of the plasmid between surface-attached bacteria. We propose plasmid-mediated adhesion to particles to be one of the main contributors in the formation of mobile genetic element-reservoirs in sediments, with adhesion to suspended matter working as a selective enrichment process of antibiotic resistant genes and bacteria.}, }
@article {pmid30012729, year = {2018}, author = {Godeux, AS and Lupo, A and Haenni, M and Guette-Marquet, S and Wilharm, G and Laaberki, MH and Charpentier, X}, title = {Fluorescence-Based Detection of Natural Transformation in Drug-Resistant Acinetobacter baumannii.}, journal = {Journal of bacteriology}, volume = {200}, number = {19}, pages = {}, pmid = {30012729}, issn = {1098-5530}, mesh = {Acinetobacter Infections/microbiology ; Acinetobacter baumannii/drug effects/*genetics ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics ; Carbapenems/pharmacology ; DNA-Binding Proteins/genetics ; *Drug Resistance, Multiple, Bacterial ; Flow Cytometry ; *Gene Transfer, Horizontal ; Green Fluorescent Proteins/genetics ; Microbial Sensitivity Tests ; Microscopy, Fluorescence ; *Transformation, Bacterial ; }, abstract = {Acinetobacter baumannii is a nosocomial agent with a high propensity for developing resistance to antibiotics. This ability relies on horizontal gene transfer mechanisms occurring in the Acinetobacter genus, including natural transformation. To study natural transformation in bacteria, the most prevalent method uses selection for the acquisition of an antibiotic resistance marker in a target chromosomal locus by the recipient cell. Most clinical isolates of A. baumannii are resistant to multiple antibiotics, limiting the use of such selection-based methods. Here, we report the development of a phenotypic and selection-free method based on flow cytometry to detect transformation events in multidrug-resistant (MDR) clinical A. baumannii isolates. To this end, we engineered a translational fusion between the abundant and conserved A. baumannii nucleoprotein (HU) and the superfolder green fluorescent protein (sfGFP). The new method was benchmarked against the conventional antibiotic selection-based method. Using this new method, we investigated several parameters affecting transformation efficiencies and identified conditions of transformability one hundred times higher than those previously reported. Using optimized transformation conditions, we probed natural transformation in a set of MDR clinical and nonclinical animal A. baumannii isolates. Regardless of their origin, the majority of the isolates displayed natural transformability, indicative of a conserved trait in the species. Overall, this new method and optimized protocol will greatly facilitate the study of natural transformation in the opportunistic pathogen A. baumanniiIMPORTANCE Antibiotic resistance is a pressing global health concern with the rise of multiple and panresistant pathogens. The rapid and unfailing resistance to multiple antibiotics of the nosocomial agent Acinetobacter baumannii, notably to carbapenems, prompt to understand the mechanisms behind acquisition of new antibiotic resistance genes. Natural transformation, one of the horizontal gene transfer mechanisms in bacteria, was only recently described in A. baumannii and could explain its ability to acquire resistance genes. We developed a reliable method to probe and study natural transformation mechanism in A. baumannii More broadly, this new method based on flow cytometry will allow experimental detection and quantification of horizontal gene transfer events in multidrug-resistant A. baumannii.}, }
@article {pmid30012442, year = {2018}, author = {Santona, A and Taviani, E and Hoang, HM and Fiamma, M and Deligios, M and Ngo, TVQ and Van Le, A and Cappuccinelli, P and Rubino, S and Paglietti, B}, title = {Emergence of unusual vanA/vanB2 genotype in a highly mutated vanB2-vancomycin-resistant hospital-associated E. faecium background in Vietnam.}, journal = {International journal of antimicrobial agents}, volume = {52}, number = {5}, pages = {586-592}, doi = {10.1016/j.ijantimicag.2018.07.006}, pmid = {30012442}, issn = {1872-7913}, mesh = {Bacterial Proteins/*genetics ; Carbon-Oxygen Ligases/*genetics ; Chromosomes, Bacterial ; Cross Infection/epidemiology/microbiology/transmission ; DNA Transposable Elements ; Disease Transmission, Infectious ; Drug Resistance, Bacterial ; Enterococcus faecium/genetics/*isolation &amp; purification ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genotype ; Gram-Positive Bacterial Infections/epidemiology/microbiology/transmission ; Hospitals ; Humans ; Molecular Epidemiology ; Molecular Typing ; Mutation ; Operon ; Plasmids ; Polymorphism, Single Nucleotide ; Teicoplanin/pharmacology ; Vancomycin/pharmacology ; Vancomycin-Resistant Enterococci/classification/genetics/*isolation &amp; purification ; Vietnam/epidemiology ; Whole Genome Sequencing ; }, abstract = {Enterococcus faecium has become a globally disseminated nosocomial pathogen mainly because of acquisition and diffusion of virulence factors and multidrug resistance determinants, including glycopeptides, which are some of the last resort antimicrobials used to treat more serious infections common in high-risk patients. In this study we investigated and characterized hospital-associated (HA) E. faecium isolates collected at Hue Central Hospital, Vietnam. Our results highlighted the spread among hospital wards of a surprisingly heterogeneous multidrug-resistant E. faecium population comprising five different CC17-related sequence types (STs), of which 46% VREf carry the vanB gene. Whole genome sequencing of selected E. faecium isolates showed that VREf from different STs carried the same chromosomal integrated Tn1549-like transposon, with a highly mutated vanB2-operon, showing an increased level of vancomycin resistance (VanB phenotype) and able, in one isolate, to confer resistance to teicoplanin (VanA incongruent phenotype). Two unusual vanA/vanB2-type strains were detected within the vanB2-type ST17 population, harbouring a Tn1546-vanA-like transposon in pJEG40-like plasmids. Wg-SNPs-based analysis showed the genetic relatedness of VSEf/VREf of the same STs and indicated lateral exchange of the Tn1549-like element among isolates followed by clonal expansion. Microevolution among ST17 isolates, including the vanA/vanB2-type strains, and inter-wards VREf transmission, were highlighted. The use of teicoplanin is strongly discouraged in the study hospital because of the spreading of Tn1549-vanB2 associated to teicoplanin resistance. A rational use of glycopeptides and effective surveillance measures are required to reduce nosocomial VSEF/VREf spread and to avoid the rise of unusual and misleading VREf genotypes.}, }
@article {pmid30009332, year = {2019}, author = {Bag, S and Ghosh, TS and Banerjee, S and Mehta, O and Verma, J and Dayal, M and Desigamani, A and Kumar, P and Saha, B and Kedia, S and Ahuja, V and Ramamurthy, T and Das, B}, title = {Molecular Insights into Antimicrobial Resistance Traits of Commensal Human Gut Microbiota.}, journal = {Microbial ecology}, volume = {77}, number = {2}, pages = {546-557}, pmid = {30009332}, issn = {1432-184X}, support = {BT/MB/THSTI/HMC-SFC/2011//Department of Biotechnology , Ministry of Science and Technology/ ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics/isolation &amp; purification ; DNA Transposable Elements/genetics ; Drug Resistance, Bacterial/*genetics ; Feces/microbiology ; Gastrointestinal Microbiome/drug effects/*genetics ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/*genetics ; Genome, Bacterial ; Genotype ; Humans ; Interspersed Repetitive Sequences/genetics ; Metagenome/genetics ; Microbial Sensitivity Tests ; *Phenotype ; *Symbiosis ; Transformation, Genetic/genetics ; Vibrio cholerae/genetics ; Whole Genome Sequencing ; }, abstract = {Antimicrobial resistance (AMR) among bacterial species that resides in complex ecosystems is a natural phenomenon. Indiscriminate use of antimicrobials in healthcare, livestock, and agriculture provides an evolutionary advantage to the resistant variants to dominate the ecosystem. Ascendency of resistant variants threatens the efficacy of most, if not all, of the antimicrobial drugs commonly used to prevent and/or cure microbial infections. Resistant phenotype is very common in enteric bacteria. The most common mechanisms of AMR are enzymatic modifications to the antimicrobials or their target molecules. In enteric bacteria, most of the resistance traits are acquired by horizontal gene transfer from closely or distantly related bacterial population. AMR traits are generally linked with mobile genetic elements (MGEs) and could rapidly disseminate to the bacterial species through horizontal gene transfer (HGT) from a pool of resistance genes. Although prevalence of AMR genes among pathogenic bacteria is widely studied in the interest of infectious disease management, the resistance profile and the genetic traits that encode resistance to the commensal microbiota residing in the gut of healthy humans are not well-studied. In the present study, we have characterized AMR phenotypes and genotypes of five dominant commensal enteric bacteria isolated from the gut of healthy Indians. Our study revealed that like pathogenic bacteria, enteric commensals are also multidrug-resistant. The genes encoding antibiotic resistance are physically linked with MGEs and could disseminate vertically to the progeny and laterally to the distantly related microbial species. Consequently, the AMR genes present in the chromosome of commensal gut bacteria could be a potential source of resistance functions for other enteric pathogens.}, }
@article {pmid30006589, year = {2018}, author = {Lam, MMC and Wyres, KL and Duchêne, S and Wick, RR and Judd, LM and Gan, YH and Hoh, CH and Archuleta, S and Molton, JS and Kalimuddin, S and Koh, TH and Passet, V and Brisse, S and Holt, KE}, title = {Population genomics of hypervirulent Klebsiella pneumoniae clonal-group 23 reveals early emergence and rapid global dissemination.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {2703}, pmid = {30006589}, issn = {2041-1723}, support = {OPP1175797//Bill and Melinda Gates Foundation/International ; 1061409//Department of Health | National Health and Medical Research Council (NHMRC)/International ; }, mesh = {Americas/epidemiology ; Animals ; Asia/epidemiology ; Bacterial Translocation ; Europe/epidemiology ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; Klebsiella pneumoniae/classification/*genetics/isolation &amp; purification/*pathogenicity ; Liver/microbiology/pathology ; Liver Abscess, Pyogenic/*epidemiology/microbiology/pathology ; Lung/microbiology/pathology ; Mice ; Mice, Inbred C57BL ; Peptides/genetics/metabolism ; Phenols/metabolism ; *Phylogeny ; Phylogeography ; Polyketides/metabolism ; Spleen/microbiology/pathology ; Thiazoles/metabolism ; Virulence ; Virulence Factors/biosynthesis/*genetics ; Whole Genome Sequencing ; }, abstract = {Severe liver abscess infections caused by hypervirulent clonal-group CG23 Klebsiella pneumoniae have been increasingly reported since the mid-1980s. Strains typically possess several virulence factors including an integrative, conjugative element ICEKp encoding the siderophore yersiniabactin and genotoxin colibactin. Here we investigate CG23's evolutionary history, showing several deep-branching sublineages associated with distinct ICEKp acquisitions. Over 80% of liver abscess isolates belong to sublineage CG23-I, which emerged in ~1928 following acquisition of ICEKp10 (encoding yersiniabactin and colibactin), and then disseminated globally within the human population. CG23-I's distinguishing feature is the colibactin synthesis locus, which reportedly promotes gut colonisation and metastatic infection in murine models. These data show circulation of CG23 K. pneumoniae decades before the liver abscess epidemic was first recognised, and provide a framework for future epidemiological and experimental studies of hypervirulent K. pneumoniae. To support such studies we present an open access, completely sequenced CG23-I human liver abscess isolate, SGH10.}, }
@article {pmid30005599, year = {2018}, author = {Natarajan, M and Kumar, D and Mandal, J and Biswal, N and Stephen, S}, title = {A study of virulence and antimicrobial resistance pattern in diarrhoeagenic Escherichia coli isolated from diarrhoeal stool specimens from children and adults in a tertiary hospital, Puducherry, India.}, journal = {Journal of health, population, and nutrition}, volume = {37}, number = {1}, pages = {17}, pmid = {30005599}, issn = {2072-1315}, mesh = {Adult ; Aged ; Anti-Bacterial Agents/*pharmacology ; Biological Evolution ; Child, Preschool ; Diarrhea/etiology/*microbiology ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/genetics/*pathogenicity ; Escherichia coli Infections/*complications/microbiology ; Feces/microbiology ; Female ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; India ; Infant ; Male ; Microbial Sensitivity Tests ; Middle Aged ; Polymerase Chain Reaction ; Sulfonamides/pharmacology ; Tertiary Care Centers ; Virulence/*genetics ; Young Adult ; }, abstract = {BACKGROUND: Emergence of atypical enteropathogenic Escherichia coli (EPEC) and hybrid E. coli (harboring genes of more than one DEC pathotypes) strains have complicated the issue of growing antibiotic resistance in diarrhoeagenic Escherichia coli (DEC). This ongoing evolution occurs in nature predominantly via horizontal gene transfers involving the mobile genetic elements like integrons notably class 1 integron. This study was undertaken to determine the virulence pattern and antibiotic resistance among the circulating DEC strains in a tertiary care center in south of India.<br><br>METHODS: Diarrhoeal stool specimens were obtained from 120 children (<&#x2009;5&#xa0;years) and 100 adults (>&#x2009;18&#xa0;years), subjected to culture and isolation of diarrhoeal pathogens. Conventional PCR was performed to detect 10 virulence and 27 antimicrobial resistance (AMR) genes among the E. coli isolated.<br><br>RESULTS: DEC infection was observed in 45 (37.5%) children and 18 (18%) adults, among which [18 (40%), 10 (10%)] atypical EPEC was most commonly detected followed by [6 (13.3%), 4 (4%)] ETEC, [5 (11.1%) 2 (2%)] EAEC, [(3 (6.6%), 0 (0%)] EIEC, [3 (6.6%), 0 (0%] typical EPEC, and [4 (8.8%), 1 (1%)] STEC, and no NTEC and CDEC was detected. DEC co-infection in 3 (6.6%) children, and 1(1%) adult and sole hybrid DEC infection in 3 (6.6%) children was detected. The distribution of sulphonamide resistance genes (sulI, sulII, and sulIII were 83.3 and 21%, 60.41 and 42.1%, and 12.5 and 26.3%, respectively) and class 1 integron (int1) genes (41.6 and 26.31%) was higher in DEC strains isolated from children and adults, respectively. Other AMR genes detected were qnrS, qnrB, aac(6')Ib-cr, dhfr1, aadB, aac(3)-IV, tetA, tetB, tetD, catI, blaCTX, blaSHV, and blaTEM. None harbored qnrA, qnrC, qepA, tetE, tetC, tetY, ermA, mcr1, int2, and int3 genes.<br><br>CONCLUSIONS: Atypical EPEC was a primary etiological agent of diarrhea in children and adults among the DEC pathotypes. Detection of high numbers of AMR genes and class 1 integron genes indicate the importance of mobile genetic elements in spreading of multidrug resistance genes among these strains.}, }
@article {pmid30003866, year = {2018}, author = {Poirel, L and Madec, JY and Lupo, A and Schink, AK and Kieffer, N and Nordmann, P and Schwarz, S}, title = {Antimicrobial Resistance in Escherichia coli.}, journal = {Microbiology spectrum}, volume = {6}, number = {4}, pages = {}, pmid = {30003866}, issn = {2165-0497}, mesh = {Animals ; Anti-Bacterial Agents/classification/*pharmacology ; Bacterial Proteins/genetics ; Drug Resistance, Bacterial/*drug effects/*genetics ; Drug Resistance, Multiple, Bacterial/drug effects/genetics ; Escherichia coli/*drug effects/*genetics ; Escherichia coli Infections/drug therapy/microbiology/veterinary ; Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Humans ; Integrons/genetics ; Plasmids/genetics ; }, abstract = {Multidrug resistance in Escherichia coli has become a worrying issue that is increasingly observed in human but also in veterinary medicine worldwide. E. coli is intrinsically susceptible to almost all clinically relevant antimicrobial agents, but this bacterial species has a great capacity to accumulate resistance genes, mostly through horizontal gene transfer. The most problematic mechanisms in E. coli correspond to the acquisition of genes coding for extended-spectrum β-lactamases (conferring resistance to broad-spectrum cephalosporins), carbapenemases (conferring resistance to carbapenems), 16S rRNA methylases (conferring pan-resistance to aminoglycosides), plasmid-mediated quinolone resistance (PMQR) genes (conferring resistance to [fluoro]quinolones), and mcr genes (conferring resistance to polymyxins). Although the spread of carbapenemase genes has been mainly recognized in the human sector but poorly recognized in animals, colistin resistance in E. coli seems rather to be related to the use of colistin in veterinary medicine on a global scale. For the other resistance traits, their cross-transfer between the human and animal sectors still remains controversial even though genomic investigations indicate that extended-spectrum β-lactamase producers encountered in animals are distinct from those affecting humans. In addition, E. coli of animal origin often also show resistances to other-mostly older-antimicrobial agents, including tetracyclines, phenicols, sulfonamides, trimethoprim, and fosfomycin. Plasmids, especially multiresistance plasmids, but also other mobile genetic elements, such as transposons and gene cassettes in class 1 and class 2 integrons, seem to play a major role in the dissemination of resistance genes. Of note, coselection and persistence of resistances to critically important antimicrobial agents in human medicine also occurs through the massive use of antimicrobial agents in veterinary medicine, such as tetracyclines or sulfonamides, as long as all those determinants are located on the same genetic elements.}, }
@article {pmid30001586, year = {2018}, author = {Zhang, L and Gu, J and Wang, X and Zhang, R and Tuo, X and Guo, A and Qiu, L}, title = {Fate of antibiotic resistance genes and mobile genetic elements during anaerobic co-digestion of Chinese medicinal herbal residues and swine manure.}, journal = {Bioresource technology}, volume = {250}, number = {}, pages = {799-805}, doi = {10.1016/j.biortech.2017.10.100}, pmid = {30001586}, issn = {1873-2976}, mesh = {Animals ; Anti-Bacterial Agents ; Drug Resistance, Microbial/*genetics ; Drugs, Chinese Herbal/*chemistry ; Genes, Bacterial ; Interspersed Repetitive Sequences ; *Manure ; Swine ; }, abstract = {Swine manure is an important reservoir for antibiotic resistance genes (ARGs) but anaerobic co-digestion (AcoD) can potentially reduce the abundance of these ARGs. However, few studies have considered the effects of Chinese medicinal herbal residues (CMHRs) on the variations in ARGs and mobile genetic elements (MGEs) during AcoD. Thus, this study explored the fate of ARGs and MGEs during the AcoD of CMHRs and swine manure. The results showed that CMHRs effectively reduced the abundances of the main ARGs (excluding ermF, qnrA, and tetW) and four MGEs (by 36.7-96.5%) after AcoD. Redundancy analysis showed that changes in the bacterial community mainly affected the fate of ARGs rather than horizontal gene transfer by MGEs. Network analysis indicated that 17 bacterial genera were possible hosts of ARGs. The results of this study suggest that AcoD with CMHRs could be employed to remove some ARGs and MGEs from swine manure.}, }
@article {pmid29998422, year = {2018}, author = {Thompson, MA and Onyeziri, MC and Fuqua, C}, title = {Function and Regulation of Agrobacterium tumefaciens Cell Surface Structures that Promote Attachment.}, journal = {Current topics in microbiology and immunology}, volume = {418}, number = {}, pages = {143-184}, pmid = {29998422}, issn = {0070-217X}, support = {R01 GM120337/GM/NIGMS NIH HHS/United States ; R13 GM082170/GM/NIGMS NIH HHS/United States ; }, mesh = {Agrobacterium tumefaciens/*cytology/*metabolism/pathogenicity ; *Bacterial Adhesion ; Bacterial Proteins/metabolism ; Fimbriae, Bacterial/metabolism ; Flagella/metabolism ; Virulence ; }, abstract = {Agrobacterium tumefaciens attaches stably to plant host tissues and abiotic surfaces. During pathogenesis, physical attachment to the site of infection is a prerequisite to infection and horizontal gene transfer to the plant. Virulent and avirulent strains may also attach to plant tissue in more benign plant associations, and as with other soil microbes, to soil surfaces in the terrestrial environment. Although most A. tumefaciens virulence functions are encoded on the tumor-inducing plasmid, genes that direct general surface attachment are chromosomally encoded, and thus this process is not obligatorily tied to virulence, but is a more fundamental capacity. Several different cellular structures are known or suspected to contribute to the attachment process. The flagella influence surface attachment primarily via their propulsive activity, but control of their rotation during the transition to the attached state may be quite complex. A. tumefaciens produces several pili, including the Tad-type Ctp pili, and several plasmid-borne conjugal pili encoded by the Ti and At plasmids, as well as the so-called T-pilus, involved in interkingdom horizontal gene transfer. The Ctp pili promote reversible interactions with surfaces, whereas the conjugal and T-pili drive horizontal gene transfer (HGT) interactions with other cells and tissues. The T-pilus is likely to contribute to physical association with plant tissues during DNA transfer to plants. A. tumefaciens can synthesize a variety of polysaccharides including cellulose, curdlan (β-1,3 glucan), β-1,2 glucan (cyclic and linear), succinoglycan, and a localized polysaccharide(s) that is confined to a single cellular pole and is called the unipolar polysaccharide (UPP). Lipopolysaccharides are also in the outer leaflet of the outer membrane. Cellulose and curdlan production can influence attachment under certain conditions. The UPP is required for stable attachment under a range of conditions and on abiotic and biotic surfaces. Other factors that have been reported to play a role in attachment include the elusive protein called rhicadhesin. The process of surface attachment is under extensive regulatory control and can be modulated by environmental conditions, as well as by direct responses to surface contact. Complex transcriptional and post-transcriptional control circuitry underlies much of the production and deployment of these attachment functions.}, }
@article {pmid29996470, year = {2018}, author = {Wang, W and Liu, D and Zhang, X and Chen, D and Cheng, Y and Shen, F}, title = {Plant MicroRNAs in Cross-Kingdom Regulation of Gene Expression.}, journal = {International journal of molecular sciences}, volume = {19}, number = {7}, pages = {}, pmid = {29996470}, issn = {1422-0067}, mesh = {Evolution, Molecular ; Gene Expression Regulation, Plant ; Gene Transfer, Horizontal ; Host-Pathogen Interactions ; MicroRNAs/*genetics ; Plants/*classification/*genetics ; RNA, Plant/genetics ; }, abstract = {MicroRNAs (miRNAs) are a class of noncoding small RNAs, which play a crucial role in post-transcriptional gene regulation. Recently, various reports revealed that miRNAs could be transmitted between species to mediate cross-kingdom regulation by integrating into a specific target gene-mediated regulatory pathway to exert relevant biological functions. Some scholars and researchers have observed this as an attractive hypothesis that may provide a foundation for novel approaches in the diagnosis, prognosis, and treatment of disease. Meanwhile, others deem the mentioned results were obtained from a “false positive effect” of performed experiments. Here, we focus on several current studies concerning plant miRNA-mediated cross-kingdom regulation (from both fronts) and discuss the existing issues that need further consideration. We also discuss possible miRNA horizontal transfer mechanisms from one species to another and analyze the relationship between miRNA-mediated cross-kingdom regulation and coevolution during a long-term specific host[-]pathogen interaction.}, }
@article {pmid29995987, year = {2018}, author = {Johnston, C and Mortier-Barriere, I and Khemici, V and Polard, P}, title = {Fine-tuning cellular levels of DprA ensures transformant fitness in the human pathogen Streptococcus pneumoniae.}, journal = {Molecular microbiology}, volume = {109}, number = {5}, pages = {663-675}, doi = {10.1111/mmi.14068}, pmid = {29995987}, issn = {1365-2958}, mesh = {Adaptation, Physiological ; Bacterial Proteins/genetics/*metabolism ; DNA Primers/genetics/metabolism ; DNA Transformation Competence/drug effects/*physiology ; DNA, Single-Stranded/genetics/metabolism ; Homologous Recombination ; Humans ; Isopropyl Thiogalactoside/pharmacology ; Membrane Proteins/genetics/*metabolism ; Rec A Recombinases/genetics/metabolism ; Streptococcus pneumoniae/drug effects/genetics/*pathogenicity/*physiology ; Transformation, Bacterial/drug effects/*physiology ; }, abstract = {Natural genetic transformation is a widespread mechanism of horizontal gene transfer. It involves the internalization of exogenous DNA as single strands and chromosomal integration via homologous recombination, promoting acquisition of new genetic traits. Transformation occurs during a distinct physiological state called competence. In Streptococcus pneumoniae, competence is controlled by ComDE, a two-component system induced by an exported peptide pheromone. DprA is universal among transformable species, strongly induced during pneumococcal competence, and crucial for pneumococcal transformation. Pneumococcal DprA plays three crucial roles in transformation and competence. Firstly, DprA protects internalized DNA from degradation. Secondly, DprA loads the homologous recombinase RecA onto transforming DNA to promote transformation. Finally, DprA interacts with the response regulator ComE to shut-off competence. Here, we explored the effect of altering the cellular levels of DprA on these three roles. High cellular levels of DprA were not required for the primary role of DprA as a transformation-dedicated recombinase loader or for protection of transforming DNA. In contrast, full expression of dprA was required for optimal competence shut-off and transformant fitness. High cellular levels of DprA thus ensure the fitness of pneumococcal transformants by mediating competence shut-off. This promotes survival and propagation of transformants, maximizing pneumococcal adaptive potential.}, }
@article {pmid29992898, year = {2018}, author = {Schwarz, S and Feßler, AT and Loncaric, I and Wu, C and Kadlec, K and Wang, Y and Shen, J}, title = {Antimicrobial Resistance among Staphylococci of Animal Origin.}, journal = {Microbiology spectrum}, volume = {6}, number = {4}, pages = {}, pmid = {29992898}, issn = {2165-0497}, mesh = {Animals ; Anti-Bacterial Agents/classification/*pharmacology ; Drug Resistance, Bacterial/*drug effects/*genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Gram-Positive Bacteria/genetics ; Humans ; Plasmids ; Staphylococcal Infections ; Staphylococcus/*drug effects/*genetics ; }, abstract = {Antimicrobial resistance among staphylococci of animal origin is based on a wide variety of resistance genes. These genes mediate resistance to many classes of antimicrobial agents approved for use in animals, such as penicillins, cephalosporins, tetracyclines, macrolides, lincosamides, phenicols, aminoglycosides, aminocyclitols, pleuromutilins, and diaminopyrimidines. In addition, numerous mutations have been identified that confer resistance to specific antimicrobial agents, such as ansamycins and fluoroquinolones. The gene products of some of these resistance genes confer resistance to only specific members of a class of antimicrobial agents, whereas others confer resistance to the entire class or even to members of different classes of antimicrobial agents, including agents approved solely for human use. The resistance genes code for all three major resistance mechanisms: enzymatic inactivation, active efflux, and protection/modification/replacement of the cellular target sites of the antimicrobial agents. Mobile genetic elements, in particular plasmids and transposons, play a major role as carriers of antimicrobial resistance genes in animal staphylococci. They facilitate not only the exchange of resistance genes among members of the same and/or different staphylococcal species, but also between staphylococci and other Gram-positive bacteria. The observation that plasmids of staphylococci often harbor more than one resistance gene points toward coselection and persistence of resistance genes even without direct selective pressure by a specific antimicrobial agent. This chapter provides an overview of the resistance genes and resistance-mediating mutations known to occur in staphylococci of animal origin.}, }
@article {pmid29992359, year = {2018}, author = {Singer, K}, title = {The Mechanism of T-DNA Integration: Some Major Unresolved Questions.}, journal = {Current topics in microbiology and immunology}, volume = {418}, number = {}, pages = {287-317}, doi = {10.1007/82_2018_98}, pmid = {29992359}, issn = {0070-217X}, mesh = {Agrobacterium/*genetics ; DNA, Bacterial/*genetics ; Gene Targeting ; Genome, Plant/*genetics ; *Recombination, Genetic ; Transformation, Genetic/genetics ; *Uncertainty ; }, abstract = {The mechanism of T-DNA integration into plant genomes during Agrobacterium-mediated genetic transformation is still not understood. As genetic transformation of plants via Agrobacterium has become a routine practice among plant biologists, understanding T-DNA integration remains important for several reasons. First, T-DNA is the final step in one of the unique cases of inter-kingdom horizontal gene transfer in nature. Second, understanding T-DNA integration is important for biotechnological applications. For example, better knowledge of this process may help develop methods to transform species that are currently not susceptible to Agrobacterium-mediated transformation. In addition, regulatory agencies usually require "clean" and "precise" transgenic insertion events, whereas transgenic insertions are commonly complex unpredictable structures. Furthermore, whereas T-DNA integration under natural conditions occurs randomly, technology to direct T-DNA to specific sites in the genome is highly desired. A better understanding of T-DNA integration may help develop methods to achieve more desirable results. Finally, gene targeting methods that require a foreign DNA template for precise DNA modifications in plants often utilize Agrobacterium to deliver the DNA template. Better understanding of the fate of T-DNA in the plant nucleus may help utilize T-DNA for more efficient gene targeting. For introducing gene targeting reagents, efficient delivery of T-DNA without ectopic integration would be useful. The following review summarizes current knowledge related to T-DNA integration. Five major open questions related to T-DNA integration are being presented. Finally, different models for T-DNA integration are being discussed, and a revised model is proposed.}, }
@article {pmid29991765, year = {2018}, author = {Chaignaud, P and Morawe, M and Besaury, L and Kröber, E and Vuilleumier, S and Bringel, F and Kolb, S}, title = {Methanol consumption drives the bacterial chloromethane sink in a forest soil.}, journal = {The ISME journal}, volume = {12}, number = {11}, pages = {2681-2693}, pmid = {29991765}, issn = {1751-7370}, mesh = {Actinobacteria/genetics/*metabolism ; Alphaproteobacteria/genetics/*metabolism ; Forests ; Methanol/*metabolism ; Methyl Chloride/*metabolism ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Halogenated volatile organic compounds (VOCs) emitted by terrestrial ecosystems, such as chloromethane (CH3Cl), have pronounced effects on troposphere and stratosphere chemistry and climate. The magnitude of the global CH3Cl sink is uncertain since it involves a largely uncharacterized microbial sink. CH3Cl represents a growth substrate for some specialized methylotrophs, while methanol (CH3OH), formed in much larger amounts in terrestrial environments, may be more widely used by such microorganisms. Direct measurements of CH3Cl degradation rates in two field campaigns and in microcosms allowed the identification of top soil horizons (i.e., organic plus mineral A horizon) as the major biotic sink in a deciduous forest. Metabolically active members of Alphaproteobacteria and Actinobacteria were identified by taxonomic and functional gene biomarkers following stable isotope labeling (SIP) of microcosms with CH3Cl and CH3OH, added alone or together as the [[13]C]-isotopologue. Well-studied reference CH3Cl degraders, such as Methylobacterium extorquens CM4, were not involved in the sink activity of the studied soil. Nonetheless, only sequences of the cmuA chloromethane dehalogenase gene highly similar to those of known strains were detected, suggesting the relevance of horizontal gene transfer for CH3Cl degradation in forest soil. Further, CH3Cl consumption rate increased in the presence of CH3OH. Members of Alphaproteobacteria and Actinobacteria were also [13]C-labeled upon [[13]C]-CH3OH amendment. These findings suggest that key bacterial CH3Cl degraders in forest soil benefit from CH3OH as an alternative substrate. For soil CH3Cl-utilizing methylotrophs, utilization of several one-carbon compounds may represent a competitive advantage over heterotrophs that cannot utilize one-carbon compounds.}, }
@article {pmid29990821, year = {2018}, author = {Zhang, R and Gu, J and Wang, X and Li, Y and Zhang, K and Yin, Y and Zhang, X}, title = {Contributions of the microbial community and environmental variables to antibiotic resistance genes during co-composting with swine manure and cotton stalks.}, journal = {Journal of hazardous materials}, volume = {358}, number = {}, pages = {82-91}, doi = {10.1016/j.jhazmat.2018.06.052}, pmid = {29990821}, issn = {1873-3336}, mesh = {Animals ; Composting/*methods ; Drug Resistance, Microbial/*genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial/drug effects ; Gossypium/*chemistry ; Integrons/genetics ; Manure/analysis/*microbiology ; Microbiota/*genetics ; Swine ; Tylosin/analysis/toxicity ; Veterinary Drugs/analysis/toxicity ; }, abstract = {Understanding the main drivers that affect the spread of antibiotic resistance genes (ARGs) during the composting process is important for the removal of ARGs. In this study, three levels of tylosin (25, 50, and 75 mg kg[-1] on a dry weight basis) were added to swine manure plus a control, which was composted with cotton stalks. Each treatment was repeated in triplicate and the ARG profiles were determined with different levels of tylosin. The top 35 genera and ARGs profiles were clustered together based on the composting time. Combined composting parameters (temperature, pH, NH4[+]-N, NO3-N, and moisture content) accounted for 78.4% of the total variation in the changes in the potential host bacteria. In addition, the selected five composting parameters and six phyla (including 25 potential host bacterial genera) explained 46.9% and 30.7% of the variation in the ARG profiles according to redundancy analysis, respectively. The variations in ARGs during the composting process were mainly affected by the dynamics of potential host bacteria rather than integrons and the selective pressure due to bio-Cu and bio-Zn.}, }
@article {pmid29987711, year = {2018}, author = {Maréchal, E}, title = {Primary Endosymbiosis: Emergence of the Primary Chloroplast and the Chromatophore, Two Independent Events.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1829}, number = {}, pages = {3-16}, doi = {10.1007/978-1-4939-8654-5_1}, pmid = {29987711}, issn = {1940-6029}, mesh = {Alphaproteobacteria/genetics ; Cell Membrane/metabolism ; Chlamydia/genetics/metabolism ; Chloroplasts/*pathology ; Chromatophores/*physiology ; Cyanobacteria/metabolism ; Eukaryota/physiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Glaucophyta/genetics/metabolism ; Inheritance Patterns ; Mitochondria/genetics/metabolism ; Rhizaria ; *Symbiosis ; }, abstract = {The emergence of semiautonomous organelles, such as the mitochondrion, the chloroplast, and more recently, the chromatophore, are critical steps in the evolution of eukaryotes. They resulted from primary endosymbiotic events that seem to share general features, i.e., an acquisition of a bacterium/cyanobacteria likely via a phagocytic membrane, a genome reduction coinciding with an escape of genes from the organelle to the nucleus, and finally the appearance of an active system translocating nuclear-encoded proteins back to the organelles. An intense mobilization of foreign genes of bacterial origin, via horizontal gene transfers, plays a critical role. Some third partners, like Chlamydia, might have facilitated the transition from cyanobacteria to the early chloroplast. This chapter describes our current understanding of primary endosymbiosis, with a specific focus on primary chloroplasts considered to have emerged more than one billion years ago, and on the chromatophore, having emerged about one hundred million years ago.}, }
@article {pmid29986941, year = {2018}, author = {Dmowski, M and Gołębiewski, M and Kern-Zdanowicz, I}, title = {Characteristics of the Conjugative Transfer System of the IncM Plasmid pCTX-M3 and Identification of Its Putative Regulators.}, journal = {Journal of bacteriology}, volume = {200}, number = {18}, pages = {}, pmid = {29986941}, issn = {1098-5530}, mesh = {*Conjugation, Genetic ; DNA, Bacterial/genetics ; Enterobacteriaceae/*genetics ; Escherichia coli/genetics ; Gene Deletion ; *Gene Expression Regulation, Bacterial ; *Genes, Bacterial ; Genome, Bacterial ; Plasmids/*genetics ; Pseudomonas putida/genetics ; Type IV Secretion Systems/genetics ; }, abstract = {Plasmid conjugative transfer systems comprise type IV secretion systems (T4SS) coupled to DNA processing and replication. The T4SSs are divided into two phylogenetic subfamilies, namely, IVA and IVB, or on the basis of the phylogeny of the VirB4 ATPase, into eight groups. The conjugation system of the IncM group plasmid pCTX-M3, from Citrobacter freundii, is classified in the IVB subfamily and in the MPFI group, as are the conjugation systems of IncI1 group plasmids. Although the majority of the conjugative genes of the IncM and IncI1 plasmids display conserved synteny, there are several differences. Here, we present a deletion analysis of 27 genes in the conjugative transfer regions of pCTX-M3. Notably, the deletion of either of two genes dispensable for conjugative transfer, namely, orf35 and orf36, resulted in an increased plasmid mobilization efficiency. Transcriptional analysis of the orf35 and orf36 deletion mutants suggested an involvement of these genes in regulating the expression of conjugative transfer genes. We also revised the host range of the pCTX-M3 replicon by finding that this replicon is unable to support replication in Agrobacterium tumefaciens, Ralstonia eutropha, and Pseudomonas putida, though its conjugation system is capable of introducing plasmids bearing oriTpCTX-M3 into these bacteria, which are representatives of Alpha-, Beta-, and Gammaproteobacteria, respectively. Thus, the conjugative transfer system of pCTX-M3 has a much broader host range than its replicon.IMPORTANCE Horizontal gene transfer is responsible for rapid changes in bacterial genomes, and the conjugative transfer of plasmids has a great impact on the plasticity of bacteria. Here, we present a deletion analysis of the conjugative transfer system genes of the pCTX-M3 plasmid of the IncM group, which is responsible for the dissemination of antibiotic resistance genes in Enterobacteriaceae We found that the deletion of either of the orf35 and orf36 genes, which are dispensable for conjugative transfer, increased the plasmid mobilization efficiency. Real-time quantitative PCR (RT-qPCR) analysis suggested the involvement of orf35 and orf36 in regulating the expression of transfer genes. We also revised the host range of pCTX-M3 by showing that its conjugative transfer system has a much broader host range than its replicon.}, }
@article {pmid29984669, year = {2018}, author = {Alam, M and Imran, M}, title = {Screening and Potential of the Incidence of Resistance Transfer Among the Multidrug and Heavy Metal Resistant Gram-Negative Isolates from Hospital Effluents of Northern India.}, journal = {Recent patents on anti-infective drug discovery}, volume = {13}, number = {2}, pages = {164-179}, doi = {10.2174/1574891X13666180702111330}, pmid = {29984669}, issn = {2212-4071}, mesh = {Anti-Bacterial Agents/*pharmacology/therapeutic use ; Drug Resistance, Multiple, Bacterial/drug effects/*genetics ; Gene Flow ; Gene Transfer, Horizontal ; Gram-Negative Bacteria/drug effects/isolation &amp; purification/*physiology ; Gram-Negative Bacterial Infections/drug therapy/microbiology ; Hospitals ; Humans ; India ; Medical Waste Disposal ; Metals, Heavy/*pharmacology/therapeutic use ; Microbial Sensitivity Tests ; Patents as Topic ; Plasmids/genetics ; Wastewater/*microbiology ; }, abstract = {BACKGROUND: Hospital wastewater has a high amount of both organic and inorganic matter, as well as high densities of living organisms, including pathogenic, and environmental bacteria. It has been suggested that genes encoding resistance to an antibiotic can be located together with heavy metals resistance genes on either the same genetic structure (plasmid) or different genetic structures within the same bacterial strain. Resistance transfer is mainly attributed to conjugation since many antimicrobial resistance genes are situated on mobile elements, such as plasmids and conjugative transposons, whereas renovation and transduction are usually more limited. Our study confirmed the flow of resistance genes between indigenous and foreign organisms and indicated the possibility of resistance transfer from environmental reservoirs to pathogenic strains, which should be underlined in the future. The recent patents on drug resistance (US20030130169, WO/2001/060387, WO/2016/151092) and gene transfer (JP2003189855, JP2010094090), helped in this study.<br><br>METHODS: Water samples were collected from three different sites of hospital wastewater. Isolation of Gram-negative bacteria from hospital wastewater samples was done using the standard microbial procedure. The heavy metal resistance was determined by the minimum inhibitory concentration (MIC) against the test bacterial strain by spot plate method. The antibiotic resistance was determined by a standard disc diffusion technique. The bacterial resistance transfer studies were determined between donor and recipient strain in nutrient as well as wastewater. The antibiogram and MIC of the donors and transconjugants were studied by above-described methods.<br><br>RESULTS: A high number of Gram-Negative Bacterial Isolates (GNB) exhibited antibiotic and metal resistance transfer into E. coli K-12 and similar GNB isolates in nutrient broth as compared to wastewater. The microbial conjugation experiments showed that a high percentage of multi-resistant GNB (75% and 66%) was able to transfer their single or multidrug resistance patterns to E. coli K-12 among antibiotic while 58%, 66% of the multiresistant isolates were able to transfer their single or multi-metal resistance patterns to E. coli K-12 among metal in nutrient medium and wastewater, respectively. In the present conjugation study, 97.5% and 70% of the total tested GNB isolates were able to transfer an antibiotic-resistant marker to recipient GNB in both the medium (nutrient medium and wastewater), whereas 92.5% and72.5% of the isolates were able to transfer metal resistant marker to recipient GNB in nutrient medium and wastewater from all the site tested. The higher (6.8x10-1 and 5.9x10-1) frequency of transfer was observed among antibiotic and metal while the lower frequency of transfer was (7.0x10-3 and 2.0x10-3) exhibited against antibiotic and metal in both the medium from the entire site tested, respectively.<br><br>CONCLUSION: We can recommend that the hospital water is heavily polluted with several types of antibiotics, toxic metals as well as the potentially hazardous bacterial flora because of their capacity to resist one or the other well known antibiotic and chemotherapeutic agents. These studies provide evidence that a wide variety of clinically important antibiotic and metal resistance genes is mobile within aquatic bacterial communities one step ahead of the above, we can envisage the alarming situation prevailing in our system and surrounding in the light of transmissible nature of R-plasmids.}, }
@article {pmid29983116, year = {2018}, author = {Ivancevic, AM and Kortschak, RD and Bertozzi, T and Adelson, DL}, title = {Horizontal transfer of BovB and L1 retrotransposons in eukaryotes.}, journal = {Genome biology}, volume = {19}, number = {1}, pages = {85}, pmid = {29983116}, issn = {1474-760X}, mesh = {Animals ; DNA Transposable Elements/*genetics ; Eukaryota/*genetics ; Gene Transfer, Horizontal/*genetics ; Genomics/methods ; Insect Vectors/genetics ; Long Interspersed Nucleotide Elements/*genetics ; Mammals/genetics ; Phylogeny ; Retroelements/*genetics ; }, abstract = {BACKGROUND: Transposable elements (TEs) are mobile DNA sequences, colloquially known as jumping genes because of their ability to replicate to new genomic locations. TEs can jump between organisms or species when given a vector of transfer, such as a tick or virus, in a process known as horizontal transfer. Here, we propose that LINE-1 (L1) and Bovine-B (BovB), the two most abundant TE families in mammals, were initially introduced as foreign DNA via ancient horizontal transfer events.<br><br>RESULTS: Using analyses of 759 plant, fungal and animal genomes, we identify multiple possible L1 horizontal transfer events in eukaryotic species, primarily involving Tx-like L1s in marine eukaryotes. We also extend the BovB paradigm by increasing the number of estimated transfer events compared to previous studies, finding new parasite vectors of transfer such as bed bug, leech and locust, and BovB occurrences in new lineages such as bat and frog. Given that these transposable elements have colonised more than half of the genome sequence in today's mammals, our results support a role for horizontal transfer in causing long-term genomic change in new host organisms.<br><br>CONCLUSIONS: We describe extensive horizontal transfer of BovB retrotransposons and provide the first evidence that L1 elements can also undergo horizontal transfer. With the advancement of genome sequencing technologies and bioinformatics tools, we anticipate our study to be a valuable resource for inferring horizontal transfer from large-scale genomic data.}, }
@article {pmid29982676, year = {2018}, author = {Veloo, ACM and Chlebowicz, M and Winter, HLJ and Bathoorn, D and Rossen, JWA}, title = {Three metronidazole-resistant Prevotella bivia strains harbour a mobile element, encoding a novel nim gene, nimK, and an efflux small MDR transporter.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {73}, number = {10}, pages = {2687-2690}, pmid = {29982676}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteroidaceae Infections/microbiology ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/*genetics ; Genes, Bacterial ; Genome, Bacterial ; Humans ; *Interspersed Repetitive Sequences ; Male ; Membrane Transport Proteins/*genetics ; Metronidazole/*pharmacology ; Microbial Sensitivity Tests ; Prevotella/*drug effects/*genetics ; Whole Genome Sequencing ; }, abstract = {OBJECTIVES: In this study we assess the antibiotic resistance genes in three metronidazole-resistant Prevotella bivia clinical isolates.<br><br>METHODS: Strains were whole-genome sequenced. De novo assembly was performed and genes were annotated in RAST. Manual adjustments were made, when required, to the annotation and length of the genes.<br><br>RESULTS: In all three strains a novel nim gene, nimK, was encountered located on a mobile genetic element (MGE). The nimK gene was associated with an IS1380 family transposase. On the same MGE, genes encoding an efflux small MDR (SMR) transporter were present and were associated with a crp/fnr regulator.<br><br>CONCLUSIONS: This is the first description of the presence of a novel nim gene in metronidazole-resistant P. bivia clinical isolates. This gene is co-located with an efflux SMR transporter on an MGE, which has been named Tn6456 (MG827401). The identification of these resistance genes on an MGE is worrisome, since this indicates the horizontal gene transfer of antibiotic and/or biocide resistance from one strain to the other.}, }
@article {pmid29982428, year = {2018}, author = {Heß, S and Berendonk, TU and Kneis, D}, title = {Antibiotic resistant bacteria and resistance genes in the bottom sediment of a small stream and the potential impact of remobilization.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {9}, pages = {}, doi = {10.1093/femsec/fiy128}, pmid = {29982428}, issn = {1574-6941}, mesh = {Anti-Bacterial Agents/*pharmacology ; Biofilms/growth &amp; development ; Drug Resistance, Bacterial/*genetics ; Environmental Monitoring ; Escherichia coli/*drug effects/genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Geologic Sediments/*microbiology ; Rivers/*microbiology ; }, abstract = {River sediments are regarded as hot spots of bacterial density and activity. Moreover, high bacterial densities and biofilm formation are known to promote horizontal gene transfer, the latter playing a vital role in the spread of antimicrobial resistance. It can thus be hypothesized that sediments act as a reservoir of antibiotic resistant bacteria (ARB) and resistance genes (ARGs), particularly in rivers receiving microbes and drug residues from treated sewage. We analyzed the phenotypic susceptibility of 782 Escherichia coli isolates against 24 antimicrobials and we measured the relative abundances of five ARGs in water and sediment extracts of a small stream. We did not find evidence for a general increase in the proportion of resistant E. coli isolated from sediments as compared to those found in stream water. For most antimicrobials, the likelihood of detecting a resistant isolate was similar in water and sediment or it was even lower in the latter compartment. The mean relative abundance of ARGs was moderately increased in sediment-borne samples. Generally, absolute abundances of resistant cells and resistance genes in the sediment exceeded the pelagic level owing to higher bacterial densities. The river bottom thus represents a reservoir of ARB and ARGs that can be mobilized by resuspension.}, }
@article {pmid29980701, year = {2018}, author = {Piña-Iturbe, A and Ulloa-Allendes, D and Pardo-Roa, C and Coronado-Arrázola, I and Salazar-Echegarai, FJ and Sclavi, B and González, PA and Bueno, SM}, title = {Comparative and phylogenetic analysis of a novel family of Enterobacteriaceae-associated genomic islands that share a conserved excision/integration module.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {10292}, pmid = {29980701}, issn = {2045-2322}, mesh = {Bacterial Proteins/*genetics ; Base Sequence ; Chromosomes, Bacterial/*genetics ; DNA, Bacterial/genetics ; Enterobacteriaceae/*genetics/isolation &amp; purification ; Enterobacteriaceae Infections/*genetics/microbiology ; *Genome, Bacterial ; *Genomic Islands ; *Phylogeny ; Virulence ; Virulence Factors ; }, abstract = {Genomic Islands (GIs) are DNA regions acquired through horizontal gene transfer that encode advantageous traits for bacteria. Many GIs harbor genes that encode the molecular machinery required for their excision from the bacterial chromosome. Notably, the excision/integration dynamics of GIs may modulate the virulence of some pathogens. Here, we report a novel family of GIs found in plant and animal Enterobacteriaceae pathogens that share genes with those found in ROD21, a pathogenicity island whose excision is involved in the virulence of Salmonella enterica serovar Enteritidis. In these GIs we identified a conserved set of genes that includes an excision/integration module, suggesting that they are excisable. Indeed, we found that GIs within carbapenem-resistant Klebsiella pneumoniae ST258 KP35 and enteropathogenic Escherichia coli O127:H6 E2348/69 are excised from the bacterial genome. In addition to putative virulence factors, these GIs encode conjugative transfer-related proteins and short and full-length homologues of the global transcriptional regulator H-NS. Phylogenetic analyses suggest that the identified GIs likely originated in phytopathogenic bacteria. Taken together, our findings indicate that these GIs are excisable and may play a role in bacterial interactions with their hosts.}, }
@article {pmid29975637, year = {2018}, author = {Orosz, F}, title = {Does apicortin, a characteristic protein of apicomplexan parasites and placozoa, occur in Eumetazoa?.}, journal = {Acta parasitologica}, volume = {63}, number = {3}, pages = {617-633}, doi = {10.1515/ap-2018-0071}, pmid = {29975637}, issn = {1896-1851}, mesh = {Amino Acid Sequence ; Animals ; Apicomplexa/*genetics ; Gene Transfer, Horizontal ; Invertebrates/*genetics ; Phylogeny ; Protozoan Proteins/*genetics ; Sequence Alignment ; }, abstract = {Apicortin is a characteristic protein of apicomplexan parasites which has recently been identified in their free-living cousins, chromerids as well. The placozoan Trichoplax adhaerens is the only animal possessing this protein and apicortin is one of its most abundant proteins. The recently published transcriptome of the cnidarian Porites astreoides contains an apicortin-like sequence. Other cnidarians do not have it, thus it is its first occurrence not only in this phylum but also in Eumetazoa. However, its translated amino acid sequence is more similar to apicomplexan apicortins than to that of T. adhaerens, the GC ratio is much higher than either the genome-wide GC ratio of P. astreoides or that of the placozoan apicortin gene, and phylogenetic analyses suggest that this apicortin has an apicomplexan origin. Although these data might be indicative for a horizontal gene transfer event, we should be cautious to state it; it is more probable that it is a contamination from a gregarine, a marine Apicomplexa. Thus T. adhaerens remains the only animal where the presence of apicortin is proved.}, }
@article {pmid29973926, year = {2018}, author = {Chen, YX and Zou, L and Penttinen, P and Chen, Q and Li, QQ and Wang, CQ and Xu, KW}, title = {Faba Bean (Vicia faba L.) Nodulating Rhizobia in Panxi, China, Are Diverse at Species, Plant Growth Promoting Ability, and Symbiosis Related Gene Levels.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1338}, pmid = {29973926}, issn = {1664-302X}, abstract = {We isolated 65 rhizobial strains from faba bean (Vicia faba L.) from Panxi, China, studied their plant growth promoting ability with nitrogen free hydroponics, genetic diversity with clustered analysis of combined ARDRA and IGS-RFLP, and phylogeny by sequence analyses of 16S rRNA gene, three housekeeping genes and symbiosis related genes. Eleven strains improved the plant shoot dry mass significantly comparing to that of not inoculated plants. According to the clustered analysis of combined ARDRA and IGS-RFLP the isolates were genetically diverse. Forty-one of 65 isolates represented Rhizobium anhuiense, and the others belonged to R. fabae, Rhizobium vallis, Rhizobium sophorae, Agrobacterium radiobacter, and four species related to Rhizobium and Agrobacterium. The isolates carried four and five genotypes of nifH and nodC, respectively, in six different nifH-nodC combinations. When looking at the species-nifH-nodC combinations it is noteworthy that all but two of the six R. anhuiense isolates were different. Our results suggested that faba bean rhizobia in Panxi are diverse at species, plant growth promoting ability and symbiosis related gene levels.}, }
@article {pmid29973916, year = {2018}, author = {Piechocki, M and Giska, F and Koczyk, G and Grynberg, M and Krzymowska, M}, title = {An Engineered Distant Homolog of Pseudomonas syringae TTSS Effector From Physcomitrella patens Can Act as a Bacterial Virulence Factor.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1060}, pmid = {29973916}, issn = {1664-302X}, abstract = {Pseudomonas syringae pv. phaseolicola is the causative agent of halo blight in common bean (Phaseolus vulgaris). Similar to other pathogenic gram-negative bacteria, it secrets a set of type III effectors into host cells to subvert defense mechanisms. HopQ1 (for Hrp outer protein Q) is one of these type III effectors contributing to virulence of bacteria. Upon delivery into a plant cell, HopQ1 undergoes phosphorylation, binds host 14-3-3 proteins and suppresses defense-related signaling. Some plants however, evolved systems to recognize HopQ1 and respond to its presence and thus to prevent infection. HopQ1 shows homology to Nucleoside Hydrolases (NHs), but it contains a modified calcium binding motif not found in the canonical enzymes. CLuster ANalysis of Sequences (CLANS) revealed that HopQ1 and alike proteins make a distinct group of putative NHs located distantly from the classical enzymes. The HopQ1 - like protein (HLP) group comprises sequences from plant pathogenic bacteria, fungi, and lower plants. Our data suggest that the evolution of HopQ1 homologs in bacteria, fungi, and algae was independent. The location of moss HopQ1 homologs inside the fungal clade indicates a possibility of horizontal gene transfer (HGT) between those taxa. We identified a HLP in the moss Physcomitrella patens. Our experiments show that this protein (referred to as PpHLP) extended by a TTSS signal of HopQ1 promoted P. syringae growth in bean and was recognized by Nicotiana benthamiana immune system. Thus, despite the low sequence similarity to HopQ1 the engineered PpHLP acted as a bacterial virulence factor and displayed similar to HopQ1 virulence properties.}, }
@article {pmid29971903, year = {2019}, author = {Hawkins, NJ and Bass, C and Dixon, A and Neve, P}, title = {The evolutionary origins of pesticide resistance.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {94}, number = {1}, pages = {135-155}, pmid = {29971903}, issn = {1469-185X}, support = {646625//European Research Council (ERC)/ ; //Strategic Longer and Larger (LoLa)/ ; BB/L001489/1BBS/OS/CP/000001/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {Durable crop protection is an essential component of current and future food security. However, the effectiveness of pesticides is threatened by the evolution of resistant pathogens, weeds and insect pests. Pesticides are mostly novel synthetic compounds, and yet target species are often able to evolve resistance soon after a new compound is introduced. Therefore, pesticide resistance provides an interesting case of rapid evolution under strong selective pressures, which can be used to address fundamental questions concerning the evolutionary origins of adaptations to novel conditions. We ask: (i) whether this adaptive potential originates mainly from de novo mutations or from standing variation; (ii) which pre-existing traits could form the basis of resistance adaptations; and (iii) whether recurrence of resistance mechanisms among species results from interbreeding and horizontal gene transfer or from independent parallel evolution. We compare and contrast the three major pesticide groups: insecticides, herbicides and fungicides. Whilst resistance to these three agrochemical classes is to some extent united by the common evolutionary forces at play, there are also important differences. Fungicide resistance appears to evolve, in most cases, by de novo point mutations in the target-site encoding genes; herbicide resistance often evolves through selection of polygenic metabolic resistance from standing variation; and insecticide resistance evolves through a combination of standing variation and de novo mutations in the target site or major metabolic resistance genes. This has practical implications for resistance risk assessment and management, and lessons learnt from pesticide resistance should be applied in the deployment of novel, non-chemical pest-control methods.}, }
@article {pmid29970465, year = {2018}, author = {Shen, Y and Wu, Z and Wang, Y and Zhang, R and Zhou, HW and Wang, S and Lei, L and Li, M and Cai, J and Tyrrell, J and Tian, GB and Wu, C and Zhang, Q and Shen, J and Walsh, TR and Shen, Z}, title = {Heterogeneous and Flexible Transmission of mcr-1 in Hospital-Associated Escherichia coli.}, journal = {mBio}, volume = {9}, number = {4}, pages = {}, pmid = {29970465}, issn = {2150-7511}, support = {MR/N028317/1/MRC_/Medical Research Council/United Kingdom ; MR/P007295/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; China ; Colistin/*pharmacology ; *Drug Resistance, Bacterial ; Escherichia coli/classification/*genetics/isolation &amp; purification ; Escherichia coli Infections/microbiology ; Escherichia coli Proteins/*genetics ; Feces/microbiology ; *Gene Transfer, Horizontal ; Genetic Variation ; Hospitals ; Humans ; Molecular Typing ; Plasmids/*analysis ; }, abstract = {The recent emergence of a transferable colistin resistance mechanism, MCR-1, has gained global attention because of its threat to clinical treatment of infections caused by multidrug-resistant Gram-negative bacteria. However, the possible transmission route of mcr-1 among Enterobacteriaceae species in clinical settings is largely unknown. Here, we present a comprehensive genomic analysis of Escherichia coli isolates collected in a hospital in Hangzhou, China. We found that mcr-1-carrying isolates from clinical infections and feces of inpatients and healthy volunteers were genetically diverse and were not closely related phylogenetically, suggesting that clonal expansion is not involved in the spread of mcr-1 The mcr-1 gene was found on either chromosomes or plasmids, but in most of the E. coli isolates, mcr-1 was carried on plasmids. The genetic context of the plasmids showed considerable diversity as evidenced by the different functional insertion sequence (IS) elements, toxin-antitoxin (TA) systems, heavy metal resistance determinants, and Rep proteins of broad-host-range plasmids. Additionally, the genomic analysis revealed nosocomial transmission of mcr-1 and the coexistence of mcr-1 with other genes encoding β-lactamases and fluoroquinolone resistance in the E. coli isolates. These findings indicate that mcr-1 is heterogeneously disseminated in both commensal and pathogenic strains of E. coli, suggest the high flexibility of this gene in its association with diverse genetic backgrounds of the hosts, and provide new insights into the genome epidemiology of mcr-1 among hospital-associated E. coli strains.IMPORTANCE Colistin represents one of the very few available drugs for treating infections caused by extensively multidrug-resistant Gram-negative bacteria. The recently emergent mcr-1 colistin resistance gene threatens the clinical utility of colistin and has gained global attention. How mcr-1 spreads in hospital settings remains unknown and was investigated by whole-genome sequencing of mcr-1-carrying Escherichia coli in this study. The findings revealed extraordinary flexibility of mcr-1 in its spread among genetically diverse E. coli hosts and plasmids, nosocomial transmission of mcr-1-carrying E. coli, and the continuous emergence of novel Inc types of plasmids carrying mcr-1 and new mcr-1 variants. Additionally, mcr-1 was found to be frequently associated with other genes encoding β-lactams and fluoroquinolone resistance. These findings provide important information on the transmission and epidemiology of mcr-1 and are of significant public health importance as the information is expected to facilitate the control of this significant antibiotic resistance threat.}, }
@article {pmid29970462, year = {2018}, author = {Baranowski, E and Dordet-Frisoni, E and Sagné, E and Hygonenq, MC and Pretre, G and Claverol, S and Fernandez, L and Nouvel, LX and Citti, C}, title = {The Integrative Conjugative Element (ICE) of Mycoplasma agalactiae: Key Elements Involved in Horizontal Dissemination and Influence of Coresident ICEs.}, journal = {mBio}, volume = {9}, number = {4}, pages = {}, pmid = {29970462}, issn = {2150-7511}, mesh = {Conjugation, Genetic ; Gene Knockout Techniques ; *Gene Transfer, Horizontal ; Genetic Complementation Test ; *Interspersed Repetitive Sequences ; Lipoproteins/genetics/metabolism ; Membrane Proteins/genetics/metabolism ; Mycoplasma agalactiae/*genetics ; }, abstract = {The discovery of integrative conjugative elements (ICEs) in wall-less mycoplasmas and the demonstration of their role in massive gene flows within and across species have shed new light on the evolution of these minimal bacteria. Of these, the ICE of the ruminant pathogen Mycoplasma agalactiae (ICEA) represents a prototype and belongs to a new clade of the Mutator-like superfamily that has no preferential insertion site and often occurs as multiple chromosomal copies. Here, functional genomics and mating experiments were combined to address ICEA functions and define the minimal ICEA chassis conferring conjugative properties to M. agalactiae Data further indicated a complex interaction among coresident ICEAs, since the minimal ICEA structure was influenced by the occurrence of additional ICEA copies that can trans-complement conjugation-deficient ICEAs. However, this cooperative behavior was limited to the CDS14 surface lipoprotein, which is constitutively expressed by coresident ICEAs, and did not extend to other ICEA proteins, including the cis-acting DDE recombinase and components of the mating channel whose expression was detected only sporadically. Remarkably, conjugation-deficient mutants containing a single ICEA copy knocked out in cds14 can be complemented by neighboring cells expressing CDS14. This result, together with those revealing the conservation of CDS14 functions in closely related species, may suggest a way for mycoplasma ICEs to extend their interaction outside their chromosomal environment. Overall, this report provides a first model of conjugative transfer in mycoplasmas and offers valuable insights into understanding horizontal gene transfer in this highly adaptive and diverse group of minimal bacteria.IMPORTANCE Integrative conjugative elements (ICEs) are self-transmissible mobile genetic elements that are key mediators of horizontal gene flow in bacteria. Recently, a new category of ICEs was identified that confer conjugative properties to mycoplasmas, a highly adaptive and diverse group of wall-less bacteria with reduced genomes. Unlike classical ICEs, these mobile elements have no preferential insertion specificity, and multiple mycoplasma ICE copies can be found randomly integrated into the host chromosome. Here, the prototype ICE of Mycoplasma agalactiae was used to define the minimal conjugative machinery and to propose the first model of ICE transfer in mycoplasmas. This model unveils the complex interactions taking place among coresident ICEs and suggests a way for these elements to extend their influence outside their chromosomal environment. These data pave the way for future studies aiming at deciphering chromosomal transfer, an unconventional mechanism of DNA swapping that has been recently associated with mycoplasma ICEs.}, }
@article {pmid29967517, year = {2018}, author = {Li, FW and Brouwer, P and Carretero-Paulet, L and Cheng, S and de Vries, J and Delaux, PM and Eily, A and Koppers, N and Kuo, LY and Li, Z and Simenc, M and Small, I and Wafula, E and Angarita, S and Barker, MS and Bräutigam, A and dePamphilis, C and Gould, S and Hosmani, PS and Huang, YM and Huettel, B and Kato, Y and Liu, X and Maere, S and McDowell, R and Mueller, LA and Nierop, KGJ and Rensing, SA and Robison, T and Rothfels, CJ and Sigel, EM and Song, Y and Timilsena, PR and Van de Peer, Y and Wang, H and Wilhelmsson, PKI and Wolf, PG and Xu, X and Der, JP and Schluepmann, H and Wong, GK and Pryer, KM}, title = {Fern genomes elucidate land plant evolution and cyanobacterial symbioses.}, journal = {Nature plants}, volume = {4}, number = {7}, pages = {460-472}, pmid = {29967517}, issn = {2055-0278}, mesh = {*Biological Evolution ; *Cyanobacteria ; Ferns/*genetics/microbiology ; Gene Duplication/genetics ; Genes, Plant/genetics ; Genome, Plant/*genetics ; Phylogeny ; *Symbiosis/genetics ; }, abstract = {Ferns are the closest sister group to all seed plants, yet little is known about their genomes other than that they are generally colossal. Here, we report on the genomes of Azolla filiculoides and Salvinia cucullata (Salviniales) and present evidence for episodic whole-genome duplication in ferns-one at the base of 'core leptosporangiates' and one specific to Azolla. One fern-specific gene that we identified, recently shown to confer high insect resistance, seems to have been derived from bacteria through horizontal gene transfer. Azolla coexists in a unique symbiosis with N2-fixing cyanobacteria, and we demonstrate a clear pattern of cospeciation between the two partners. Furthermore, the Azolla genome lacks genes that are common to arbuscular mycorrhizal and root nodule symbioses, and we identify several putative transporter genes specific to Azolla-cyanobacterial symbiosis. These genomic resources will help in exploring the biotechnological potential of Azolla and address fundamental questions in the evolution of plant life.}, }
@article {pmid29967018, year = {2018}, author = {Lei, CW and Chen, YP and Kang, ZZ and Kong, LH and Wang, HN}, title = {Characterization of a Novel SXT/R391 Integrative and Conjugative Element Carrying cfr, blaCTX-M-65, fosA3, and aac(6')-Ib-cr in Proteus mirabilis.}, journal = {Antimicrobial agents and chemotherapy}, volume = {62}, number = {9}, pages = {}, pmid = {29967018}, issn = {1098-6596}, mesh = {Animals ; China ; Conjugation, Genetic/*genetics ; DNA Transposable Elements/*genetics ; DNA, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/genetics ; Fluoroquinolones/pharmacology ; Fosfomycin/pharmacology ; Gene Transfer, Horizontal/*genetics ; Methyltransferases/genetics ; Microbial Sensitivity Tests ; Phosphotransferases (Alcohol Group Acceptor)/genetics ; Proteus mirabilis/*drug effects/*genetics/isolation &amp; purification ; Swine ; beta-Lactamases/genetics ; }, abstract = {A novel 139,487-bp SXT/R391 integrative and conjugative element, ICEPmiChnBCP11, was characterized in Proteus mirabilis of swine origin in China. ICEPmiChnBCP11 harbors 20 different antimicrobial resistance genes, including the clinically important rRNA methyltransferase gene cfr, the extended-spectrum β-lactamase gene blaCTX-M-65, fosfomycin resistance gene fosA3, and fluoroquinolone resistance gene aac(6')-Ib-cr An ISPpu12-mediated composite transposon containing various resistance genes and 10 copies of IS26 is inserted in hot spot 4. ICEPmiChnBCP11 was successfully transferred to Escherichia coli.}, }
@article {pmid29965001, year = {2018}, author = {Yang, F and Xu, WL and Qian, YJ and Liu, ZH and Xue, G and Gao, P}, title = {[Effect of Zero Valent Iron on the Horizontal Gene Transfer of Tetracycline Resistance Genes During Anaerobic Sludge Digestion Process].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {39}, number = {4}, pages = {1748-1755}, doi = {10.13227/j.hjkx.201708054}, pmid = {29965001}, issn = {0250-3301}, mesh = {Anti-Bacterial Agents ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Iron/*chemistry ; Sewage/*microbiology ; Tetracycline Resistance/*genetics ; }, abstract = {The problem of bacterial resistance has become an important issue in the area of global ecological safety and human health. Waste sludge is an important reservoir and discharge source for antibiotic resistance genes (ARGs). In this study, the quantities of seven tetracycline resistance genes (TC-ARGs), including tetA, tetC, tetG, tetM, tetO, tetW, and tetX, as well as those of class 1 integron (intI1) genes, during anaerobic sludge digestion process were comprehensively quantified by quantitative PCR (qPCR). The effects of different doses of zero valent iron (Fe[0]) on the decrease and increase in the quantities of TC-ARGs and intI1 genes were investigated. The influence of plasmid conjugation on the horizontal gene transfer (HGT) of the target TC-ARGs was preliminarily analyzed. The correlations between the quantities of TC-ARGs and intI1 gene have been discussed. The results showed that the quantities of TC-ARGs and intI1 genes decreased in different degrees during anaerobic sludge digestion, and the abundance of tetX gene was reduced by 2.4 orders of magnitude. When Fe[0] was added, no significant reduction in the quantities of TC-ARGs and intI1 genes was observed. However, as the addition of Fe[0] increased, the quantities of TC-ARGs and intI1 genes increased correspondingly, as compared to those in the control group. The results obtained from the quantities of TC-ARGs carried by plasmid DNA showed that plasmid conjugation probably promoted the HGT of TC-ARGs. A positive significant correlation was found between the quantities of tetG and intI1 genes, indicating that intI1 might play an important role in the evolution of tetG during sludge anaerobic digestion process.}, }
@article {pmid29958091, year = {2018}, author = {Hou, F and Ma, B and Xin, Y and Kuang, L and He, N}, title = {Horizontal transfers of LTR retrotransposons in seven species of Rosales.}, journal = {Genome}, volume = {61}, number = {8}, pages = {587-594}, doi = {10.1139/gen-2017-0208}, pmid = {29958091}, issn = {1480-3321}, mesh = {Computational Biology ; Conserved Sequence/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome, Plant/genetics ; Phylogeny ; Retroelements/*genetics ; Rosales/*genetics ; Terminal Repeat Sequences/genetics ; }, abstract = {Horizontal transposable element transfer (HTT) events have occurred among a large number of species and play important roles in the composition and evolution of eukaryotic genomes. HTTs are also regarded as effective forces in promoting genomic variation and biological innovation. In the present study, HTT events were identified and analyzed in seven sequenced species of Rosales using bioinformatics methods by comparing sequence conservation and Ka/Ks value of reverse transcriptase (RT) with 20 conserved genes, estimating the dating of HTTs, and analyzing the phylogenetic relationships. Seven HTT events involving long terminal repeat (LTR) retrotransposons, two HTTs between Morus notabilis and Ziziphus jujuba, and five between Malus domestica and Pyrus bretschneideri were identified. Further analysis revealed that these LTR retrotransposons had functional structures, and the copy insertion times were lower than the dating of HTTs, particularly in Mn.Zj.1 and Md.Pb.3. Altogether, the results demonstrate that LTR retrotransposons still have potential transposition activity in host genomes. These results indicate that HTT events are another strategy for exchanging genetic material among species and are important for the evolution of genomes.}, }
@article {pmid29958076, year = {2018}, author = {Koskella, B and Taylor, TB}, title = {Multifaceted Impacts of Bacteriophages in the Plant Microbiome.}, journal = {Annual review of phytopathology}, volume = {56}, number = {}, pages = {361-380}, doi = {10.1146/annurev-phyto-080417-045858}, pmid = {29958076}, issn = {1545-2107}, mesh = {Bacteria/*virology ; Bacteriophages/*physiology ; Biological Evolution ; *Microbiota ; Plants/*microbiology/virology ; }, abstract = {Plant-associated bacteria face multiple selection pressures within their environments and have evolved countless adaptations that both depend on and shape bacterial phenotype and their interaction with plant hosts. Explaining bacterial adaptation and evolution therefore requires considering each of these forces independently as well as their interactions. In this review, we examine how bacteriophage viruses (phages) can alter the ecology and evolution of plant-associated bacterial populations and communities. This includes influencing a bacterial population's response to both abiotic and biotic selection pressures and altering ecological interactions within the microbiome and between the bacteria and host plant. We outline specific ways in which phages can alter bacterial phenotype and discuss when and how this might impact plant-microbe interactions, including for plant pathogens. Finally, we highlight key open questions in phage-bacteria-plant research and offer suggestions for future study.}, }
@article {pmid29955043, year = {2018}, author = {Vogel, A and Schwacke, R and Denton, AK and Usadel, B and Hollmann, J and Fischer, K and Bolger, A and Schmidt, MH and Bolger, ME and Gundlach, H and Mayer, KFX and Weiss-Schneeweiss, H and Temsch, EM and Krause, K}, title = {Footprints of parasitism in the genome of the parasitic flowering plant Cuscuta campestris.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {2515}, pmid = {29955043}, issn = {2041-1723}, mesh = {Carrier Proteins/genetics/metabolism ; Cuscuta/classification/*genetics ; Gene Deletion ; *Gene Duplication ; *Gene Expression Regulation, Plant ; Gene Ontology ; *Genome, Plant ; *Host-Parasite Interactions ; Karyotype ; Metabolic Networks and Pathways/genetics ; Molecular Sequence Annotation ; Pelargonium/parasitology ; Photosynthesis/genetics ; Phylogeny ; Plant Proteins/*genetics/metabolism ; }, abstract = {A parasitic lifestyle, where plants procure some or all of their nutrients from other living plants, has evolved independently in many dicotyledonous plant families and is a major threat for agriculture globally. Nevertheless, no genome sequence of a parasitic plant has been reported to date. Here we describe the genome sequence of the parasitic field dodder, Cuscuta campestris. The genome contains signatures of a fairly recent whole-genome duplication and lacks genes for pathways superfluous to a parasitic lifestyle. Specifically, genes needed for high photosynthetic activity are lost, explaining the low photosynthesis rates displayed by the parasite. Moreover, several genes involved in nutrient uptake processes from the soil are lost. On the other hand, evidence for horizontal gene transfer by way of genomic DNA integration from the parasite's hosts is found. We conclude that the parasitic lifestyle has left characteristic footprints in the C. campestris genome.}, }
@article {pmid29954915, year = {2018}, author = {Morcrette, H and Morgan, MS and Farbos, A and O'Neill, P and Moore, K and Titball, RW and Studholme, DJ}, title = {Genome Sequence of Staphylococcus aureus Ex1, Isolated from a Patient with Spinal Osteomyelitis.}, journal = {Genome announcements}, volume = {6}, number = {26}, pages = {}, pmid = {29954915}, issn = {2169-8287}, abstract = {Here, we present the genome sequence of Staphylococcus aureus Ex1, isolated in 2015 from a patient with spinal osteomyelitis at the Royal Devon and Exeter Hospital in the United Kingdom. The availability of the Ex1 genome sequence provides a resource for studying the basis for spinal infection and horizontal gene transfer in S. aureus.}, }
@article {pmid29954903, year = {2018}, author = {Osieka, V and Grobbel, M and Schmoger, S and Szentiks, CA and Irrgang, A and Käsbohrer, A and Tenhagen, BA and Hammerl, JA}, title = {Complete Draft Genome Sequence of an Extended-Spectrum β-Lactamase-Producing Citrobacter freundii Strain Recovered from the Intestine of a House Sparrow (Passer domesticus) in Germany, 2017.}, journal = {Genome announcements}, volume = {6}, number = {26}, pages = {}, pmid = {29954903}, issn = {2169-8287}, abstract = {Here, we announce the genome of an extended-spectrum β-lactamase-producing Citrobacter freundii strain isolated from the cecum of a house sparrow that was found dead in Berlin-Lichtenberg, Germany, in 2017. This isolate exhibits increased MICs for several antimicrobials and a comprehensive set of acquired resistance determinants potentially involved in horizontal gene transfer.}, }
@article {pmid29954653, year = {2018}, author = {Tanner, JR and Kingsley, RA}, title = {Evolution of Salmonella within Hosts.}, journal = {Trends in microbiology}, volume = {26}, number = {12}, pages = {986-998}, pmid = {29954653}, issn = {1878-4380}, support = {BB/R012504/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/N007964/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M025489/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Adaptation, Physiological ; Animals ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; Genome, Bacterial ; Host Specificity ; Host-Pathogen Interactions/*genetics/physiology ; Humans ; Phenotype ; Point Mutation ; Salmonella/*genetics/*pathogenicity ; Typhoid Fever ; }, abstract = {Within-host evolution has resulted in thousands of variants of Salmonella that exhibit remarkable diversity in host range and disease outcome, from broad host range to exquisite host restriction, causing gastroenteritis to disseminated disease such as typhoid fever. Within-host evolution is a continuing process driven by genomic variation that occurs during each infection, potentiating adaptation to a new niche resulting from changes in animal husbandry, the use of antimicrobials, and emergence of immune compromised populations. We discuss key advances in our understanding of the evolution of Salmonella within the host, inferred from (i) the process of host adaptation of Salmonella pathovars in the past, and (ii) direct observation of the generation of variation and selection of beneficial traits during single infections.}, }
@article {pmid29954096, year = {2018}, author = {Andrews, M and De Meyer, S and James, EK and Stępkowski, T and Hodge, S and Simon, MF and Young, JPW}, title = {Horizontal Transfer of Symbiosis Genes within and Between Rhizobial Genera: Occurrence and Importance.}, journal = {Genes}, volume = {9}, number = {7}, pages = {}, pmid = {29954096}, issn = {2073-4425}, abstract = {Rhizobial symbiosis genes are often carried on symbiotic islands or plasmids that can be transferred (horizontal transfer) between different bacterial species. Symbiosis genes involved in horizontal transfer have different phylogenies with respect to the core genome of their ‘host’. Here, the literature on legume[-]rhizobium symbioses in field soils was reviewed, and cases of phylogenetic incongruence between rhizobium core and symbiosis genes were collated. The occurrence and importance of horizontal transfer of rhizobial symbiosis genes within and between bacterial genera were assessed. Horizontal transfer of symbiosis genes between rhizobial strains is of common occurrence, is widespread geographically, is not restricted to specific rhizobial genera, and occurs within and between rhizobial genera. The transfer of symbiosis genes to bacteria adapted to local soil conditions can allow these bacteria to become rhizobial symbionts of previously incompatible legumes growing in these soils. This, in turn, will have consequences for the growth, life history, and biogeography of the legume species involved, which provides a critical ecological link connecting the horizontal transfer of symbiosis genes between rhizobial bacteria in the soil to the above-ground floral biodiversity and vegetation community structure.}, }
@article {pmid29951855, year = {2018}, author = {Geiß, M and Anders, J and Stadler, PF and Wieseke, N and Hellmuth, M}, title = {Reconstructing gene trees from Fitch's xenology relation.}, journal = {Journal of mathematical biology}, volume = {77}, number = {5}, pages = {1459-1491}, pmid = {29951855}, issn = {1432-1416}, support = {278966//Deutscher Akademischer Austauschdienst/International ; 031A538A//Bundesministerium f&#xfc;r Bildung und Forschung/International ; }, mesh = {Algorithms ; Computer Simulation ; Gene Duplication ; *Gene Transfer, Horizontal ; Genetic Speciation ; Heuristics ; Mathematical Concepts ; *Models, Genetic ; *Multigene Family ; *Phylogeny ; }, abstract = {Two genes are xenologs in the sense of Fitch if they are separated by at least one horizontal gene transfer event. Horizonal gene transfer is asymmetric in the sense that the transferred copy is distinguished from the one that remains within the ancestral lineage. Hence xenology is more precisely thought of as a non-symmetric relation: y is xenologous to x if y has been horizontally transferred at least once since it diverged from the least common ancestor of x and y. We show that xenology relations are characterized by a small set of forbidden induced subgraphs on three vertices. Furthermore, each xenology relation can be derived from a unique least-resolved edge-labeled phylogenetic tree. We provide a linear-time algorithm for the recognition of xenology relations and for the construction of its least-resolved edge-labeled phylogenetic tree. The fact that being a xenology relation is a heritable graph property, finally has far-reaching consequences on approximation problems associated with xenology relations.}, }
@article {pmid29951040, year = {2018}, author = {Mašlaňová, I and Wertheimer, Z and Sedláček, I and Švec, P and Indráková, A and Kovařovic, V and Schumann, P and Spröer, C and Králová, S and Šedo, O and Krištofová, L and Vrbovská, V and Füzik, T and Petráš, P and Zdráhal, Z and Ružičková, V and Doškař, J and Pantuček, R}, title = {Description and Comparative Genomics of Macrococcus caseolyticus subsp. hominis subsp. nov., Macrococcus goetzii sp. nov., Macrococcus epidermidis sp. nov., and Macrococcus bohemicus sp. nov., Novel Macrococci From Human Clinical Material With Virulence Potential and Suspected Uptake of Foreign DNA by Natural Transformation.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1178}, pmid = {29951040}, issn = {1664-302X}, abstract = {The genus Macrococcus is a close relative of the genus Staphylococcus. Whilst staphylococci are widespread as human pathogens, macrococci have not yet been reported from human clinical specimens. Here we investigated Gram-positive and catalase-positive cocci recovered from human clinical material and identified as Macrococcus sp. by a polyphasic taxonomic approach and by comparative genomics. Relevant phenotypic, genotypic and chemotaxonomic methods divided the analyzed strains into two separate clusters within the genus Macrococcus. Comparative genomics of four representative strains revealed enormous genome structural plasticity among the studied isolates. We hypothesize that high genomic variability is due to the presence of a com operon, which plays a key role in the natural transformation of bacilli and streptococci. The possible uptake of exogenous DNA by macrococci can contribute to a different mechanism of evolution from staphylococci, where phage-mediated horizontal gene transfer predominates. The described macrococcal genomes harbor novel plasmids, genomic islands and islets, as well as prophages. Capsule gene clusters, intracellular protease, and a fibronectin-binding protein enabling opportunistic pathogenesis were found in all four strains. Furthermore, the presence of a CRISPR-Cas system with 90 spacers in one of the sequenced genomes corresponds with the need to limit the burden of foreign DNA. The highly dynamic genomes could serve as a platform for the exchange of virulence and resistance factors, as was described for the methicillin resistance gene, which was found on the novel composite SCCmec-like element containing a unique mec gene complex that is considered to be one of the missing links in SCC evolution. The phenotypic, genotypic, chemotaxonomic and genomic results demonstrated that the analyzed strains represent one novel subspecies and three novel species of the genus Macrococcus, for which the names Macrococcus caseolyticus subsp. hominis subsp. nov. (type strain CCM 7927[T] = DSM 103682[T]), Macrococcus goetzii sp. nov. (type strain CCM 4927[T] = DSM 103683[T]), Macrococcus epidermidis sp. nov. (type strain CCM 7099[T] = DSM 103681[T]), and Macrococcus bohemicus sp. nov. (type strain CCM 7100[T] = DSM 103680[T]) are proposed. Moreover, a formal description of Macrococcus caseolyticus subsp. caseolyticus subsp. nov. and an emended description of the genus Macrococcus are provided.}, }
@article {pmid29947776, year = {2018}, author = {Li, W and Liu, B and Yang, Y and Ren, Y and Wang, S and Liu, C and Zhang, N and Qu, Z and Yang, W and Zhang, Y and Yan, H and Jiang, F and Li, L and Li, S and Jia, W and Yin, H and Cai, X and Liu, T and McManus, DP and Fan, W and Fu, B}, title = {The genome of tapeworm Taenia multiceps sheds light on understanding parasitic mechanism and control of coenurosis disease.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {25}, number = {5}, pages = {499-510}, pmid = {29947776}, issn = {1756-1663}, mesh = {Animals ; Cestoda/drug effects/*genetics ; Cestode Infections/*veterinary ; Computational Biology/methods ; DNA Transposable Elements ; Dog Diseases/*parasitology ; Dogs ; Environment ; Evolution, Molecular ; Gene Expression Regulation ; Gene Transfer, Horizontal ; *Genome, Helminth ; Genomics/methods ; Host-Pathogen Interactions ; Molecular Sequence Annotation ; Phylogeny ; }, abstract = {Coenurosis, caused by the larval coenurus of the tapeworm Taenia multiceps, is a fatal central nervous system disease in both sheep and humans. Though treatment and prevention options are available, the control of coenurosis still faces presents great challenges. Here, we present a high-quality genome sequence of T. multiceps in which 240 Mb (96%) of the genome has been successfully assembled using Pacbio single-molecule real-time (SMRT) and Hi-C data with a N50 length of 44.8 Mb. In total, 49.5 Mb (20.6%) repeat sequences and 13, 013 gene models were identified. We found that Taenia spp. have an expansion of transposable elements and recent small-scale gene duplications following the divergence of Taenia from Echinococcus, but not in Echinococcus genomes, and the genes underlying environmental adaptability and dosage effect tend to be over-retained in the T. multiceps genome. Moreover, we identified several genes encoding proteins involved in proglottid formation and interactions with the host central nervous system, which may contribute to the adaption of T. multiceps to its parasitic life style. Our study not only provides insights into the biology and evolution of T. multiceps, but also identifies a set of species-specific gene targets for developing novel treatment and control tools for coenurosis.}, }
@article {pmid29946103, year = {2018}, author = {Flórez, LV and Scherlach, K and Miller, IJ and Rodrigues, A and Kwan, JC and Hertweck, C and Kaltenpoth, M}, title = {An antifungal polyketide associated with horizontally acquired genes supports symbiont-mediated defense in Lagria villosa beetles.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {2478}, pmid = {29946103}, issn = {2041-1723}, mesh = {Animals ; Antifungal Agents/chemistry/*metabolism ; Burkholderia/*genetics/*metabolism ; Coleoptera/metabolism/*microbiology ; Ecosystem ; Female ; Gene Transfer, Horizontal ; Genes, Bacterial ; Multigene Family ; Ovum/microbiology ; Polyketides/chemistry/*metabolism ; Soil Microbiology ; Symbiosis/*genetics ; }, abstract = {Microbial symbionts are often a source of chemical novelty and can contribute to host defense against antagonists. However, the ecological relevance of chemical mediators remains unclear for most systems. Lagria beetles live in symbiosis with multiple strains of Burkholderia bacteria that protect their offspring against pathogens. Here, we describe the antifungal polyketide lagriamide, and provide evidence supporting that it is produced by an uncultured symbiont, Burkholderia gladioli Lv-StB, which is dominant in field-collected Lagria villosa. Interestingly, lagriamide is structurally similar to bistramides, defensive compounds found in marine tunicates. We identify a gene cluster that is probably involved in lagriamide biosynthesis, provide evidence for horizontal acquisition of these genes, and show that the naturally occurring symbiont strains on the egg are protective in the soil environment. Our findings highlight the potential of microbial symbionts and horizontal gene transfer as influential sources of ecological innovation.}, }
@article {pmid29946090, year = {2018}, author = {Reardon, S}, title = {Genetically modified bacteria enlisted in fight against disease.}, journal = {Nature}, volume = {558}, number = {7711}, pages = {497-498}, pmid = {29946090}, issn = {1476-4687}, mesh = {Animals ; Bacteria/*genetics/*metabolism ; Bacteroides/genetics/metabolism ; Biological Therapy/adverse effects/*methods ; Clinical Trials as Topic ; Colitis/microbiology/therapy ; Escherichia coli/genetics/metabolism ; Gene Transfer, Horizontal/ethics ; HIV Infections/microbiology/prevention &amp; control ; Humans ; Lactobacillus/genetics/metabolism ; Lactococcus lactis/genetics/metabolism ; Mice ; Phenylalanine/metabolism ; Phenylketonurias/microbiology/therapy ; }, }
@article {pmid29944192, year = {2018}, author = {Staley, JT and Caetano-Anollés, G}, title = {Archaea-First and the Co-Evolutionary Diversification of Domains of Life.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {40}, number = {8}, pages = {e1800036}, doi = {10.1002/bies.201800036}, pmid = {29944192}, issn = {1521-1878}, mesh = {Archaea/genetics/*physiology ; Archaeal Proteins/chemistry/genetics/metabolism ; Bacteria/cytology/genetics ; *Biological Evolution ; Cell Membrane/metabolism ; Cell Wall/chemistry/metabolism ; Eukaryota/cytology/genetics/*physiology ; Gene Transfer, Horizontal ; Genomics ; Methane/metabolism ; Phospholipids/metabolism ; Phylogeny ; Proteome ; }, abstract = {The origins and evolution of the Archaea, Bacteria, and Eukarya remain controversial. Phylogenomic-wide studies of molecular features that are evolutionarily conserved, such as protein structural domains, suggest Archaea is the first domain of life to diversify from a stem line of descent. This line embodies the last universal common ancestor of cellular life. Here, we propose that ancestors of Euryarchaeota co-evolved with those of Bacteria prior to the diversification of Eukarya. This co-evolutionary scenario is supported by comparative genomic and phylogenomic analyses of the distributions of fold families of domains in the proteomes of free-living organisms, which show horizontal gene recruitments and informational process homologies. It also benefits from the molecular study of cell physiologies responsible for membrane phospholipids, methanogenesis, methane oxidation, cell division, gas vesicles, and the cell wall. Our theory however challenges popular cell fusion and two-domain of life scenarios derived from sequence analysis, demanding phylogenetic reconciliation. Also see the video abstract here: https://youtu.be/9yVWn_Q9faY.}, }
@article {pmid29942828, year = {2018}, author = {Conghui, L and Bo, L and Yan, Z and Fan, J and Yuwei, R and Shuqu, L and Hengchao, W and Wei, F}, title = {Data on horizontally transferred genes in California two-spot octopus, Octopus bimaculoides.}, journal = {Data in brief}, volume = {19}, number = {}, pages = {1274-1286}, pmid = {29942828}, issn = {2352-3409}, abstract = {Horizontal gene transfer (HGT), a mechanism that shares genetic material between the host and donor from separated offspring branches, has been described as a means of producing novel and beneficial phenotypes for the host organisms. In the present study, 12 HGT genes were identified from California two-spot octopus Octopus bimaculoides based on a similarity search, phylogenetic construction, gene composition analysis and PCR (Polymerase Chain Reaction) validation. The data collected from the HGT genes from octopus, indicating the phylogenetic incongruences, CodonW analysis, PCR products, detailed motifs and organisms used in screening. In phylogenetic screening, those genes were nested within bacteria homologs and identified as HGT genes transferred from the bacteria to the octopus. The motifs were similar in proteins of the horizontally acquired Zn-metalloproteinases, but differed to endogenous proteins. CodonW was employed to investigate the codon usage bias between HGT genes and other genes in the octopus genome. In PCR validation, all the HGT genes could be produced as amplified fragments. The results collectively indicated the existence of HGT in molluscs and its potential l contribution to the evolution of octopus with regards to functional innovation and adaptability.}, }
@article {pmid29942291, year = {2018}, author = {Kazou, M and Alexandraki, V and Blom, J and Pot, B and Tsakalidou, E and Papadimitriou, K}, title = {Comparative Genomics of Lactobacillus acidipiscis ACA-DC 1533 Isolated From Traditional Greek Kopanisti Cheese Against Species Within the Lactobacillus salivarius Clade.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1244}, pmid = {29942291}, issn = {1664-302X}, abstract = {Lactobacillus acidipiscis belongs to the Lactobacillus salivarius clade and it is found in a variety of fermented foods. Strain ACA-DC 1533 was isolated from traditional Greek Kopanisti cheese and among the available L. acidipiscis genomes it is the only one with a fully sequenced chromosome. L. acidipiscis strains exhibited a high degree of conservation at the genome level. Investigation of the distribution of prophages and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) among the three strains suggests the potential existence of lineages within the species. Based on the presence/absence patterns of these genomic traits, strain ACA-DC 1533 seems to be more related to strain JCM 10692[T] than strain KCTC 13900. Interestingly, strains ACA-DC 1533 and JCM 10692[T] which lack CRISPRs, carry two similar prophages. In contrast, strain KCTC 13900 seems to have acquired immunity to these prophages according to the sequences of spacers in its CRISPRs. Nonetheless, strain KCTC 13900 has a prophage that is absent from strains ACA-DC 1533 and JCM 10692[T]. Furthermore, comparative genomic analysis was performed among L. acidipiscis ACA-DC 1533, L. salivarius UCC118 and Lactobacillus ruminis ATCC 27782. The chromosomes of the three species lack long-range synteny. Important differences were also determined in the number of glycobiome related proteins, proteolytic enzymes, transporters, insertion sequences and regulatory proteins. Moreover, no obvious genomic traits supporting a probiotic potential of L. acidipiscis ACA-DC 1533 were detected when compared to the probiotic L. salivarius UCC118. However, the existence of more than one glycine-betaine transporter within the genome of ACA-DC 1533 may explain the ability of L. acidipiscis to grow in fermented foods containing high salt concentrations. Finally, in silico analysis of the L. acidipiscis ACA-DC 1533 genome revealed pathways that could underpin the production of major volatile compounds during the catabolism of amino acids that may contribute to the typical piquant flavors of Kopanisti cheese.}, }
@article {pmid29941641, year = {2018}, author = {Hong, E and Deghmane, AE and Taha, MK}, title = {Acquisition of Beta-Lactamase by Neisseria meningitidis through Possible Horizontal Gene Transfer.}, journal = {Antimicrobial agents and chemotherapy}, volume = {62}, number = {9}, pages = {}, pmid = {29941641}, issn = {1098-6596}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Adult ; Female ; France ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial/genetics ; Haemophilus influenzae/drug effects/*genetics ; Humans ; Meningococcal Infections/drug therapy/microbiology ; Microbial Sensitivity Tests ; Neisseria meningitidis/*drug effects/*genetics/isolation &amp; purification ; Whole Genome Sequencing ; Young Adult ; beta-Lactamases/*genetics ; beta-Lactams/pharmacology ; }, abstract = {We report the detection in France of a beta-lactamase-producing invasive meningococcal isolate. Whole-genome sequencing of the isolate revealed a ROB-1-type beta-lactamase gene that is frequently encountered in Haemophilus influenzae, suggesting horizontal transfer between isolates of these bacterial species. Beta-lactamases are exceptional in meningococci, with no reports for more than 2 decades. This report is worrying, as the expansion of such isolates may jeopardize the effective treatment against invasive meningococcal disease.}, }
@article {pmid29941591, year = {2018}, author = {Boutanaev, AM and Osbourn, AE}, title = {Multigenome analysis implicates miniature inverted-repeat transposable elements (MITEs) in metabolic diversification in eudicots.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {28}, pages = {E6650-E6658}, pmid = {29941591}, issn = {1091-6490}, support = {BBS/E/J/00000614/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/J/000PR9790/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P012523/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Aquilegia/*genetics ; *Genome, Plant ; *Inverted Repeat Sequences ; Kalanchoe/*genetics ; *Multigene Family ; }, abstract = {Plants produce a plethora of natural products, including many drugs. It has recently emerged that the genes encoding different natural product pathways may be organized as biosynthetic gene clusters in plant genomes, with >30 examples reported so far. Despite superficial similarities with microbes, these clusters have not arisen by horizontal gene transfer, but rather by gene duplication, neofunctionalization, and relocation via unknown mechanisms. Previously we reported that two Arabidopsis thaliana biosynthetic gene clusters are located in regions of the genome that are significantly enriched in transposable elements (TEs). Other plant biosynthetic gene clusters also harbor abundant TEs. TEs can mediate genomic rearrangement by providing homologous sequences that enable illegitimate recombination and gene relocation. Thus, TE-mediated recombination may contribute to plant biosynthetic gene cluster formation. TEs may also facilitate establishment of regulons. However, a systematic analysis of the TEs associated with plant biosynthetic gene clusters has not been carried out. Here we investigate the TEs associated with clustered terpene biosynthetic genes in multiple plant genomes and find evidence to suggest a role for miniature inverted-repeat transposable elements in cluster formation in eudicots. Through investigation of the newly sequenced Amborella trichopoda, Aquilegia coerulea, and Kalanchoe fedtschenkoi genomes, we further show that the "block" mechanism of founding of biosynthetic gene clusters through duplication and diversification of pairs of terpene synthase and cytochrome P450 genes that is prevalent in the eudicots arose around 90-130 million years ago, after the appearance of the basal eudicots and before the emergence of the superrosid clade.}, }
@article {pmid29941421, year = {2018}, author = {Zhang, X and Jin, T and Deng, L and Wang, C and Zhang, Y and Chen, X}, title = {Stress-Induced, Highly Efficient, Donor Cell-Dependent Cell-to-Cell Natural Transformation in Bacillus subtilis.}, journal = {Journal of bacteriology}, volume = {200}, number = {17}, pages = {}, pmid = {29941421}, issn = {1098-5530}, mesh = {Bacillus subtilis/*genetics ; Bacterial Proteins/genetics/metabolism ; DNA ; Plasmids ; *Stress, Physiological ; Transcription Factors/genetics ; *Transformation, Bacterial ; }, abstract = {Horizontal gene transfer (HGT) is a driving force for bacterial evolution that occurs via conjugation, transduction, and transformation. Whereas conjugation and transduction depend on nonbacterial vehicles, transformation is considered a naturally occurring process in which naked DNA molecules are taken up by a competent recipient cell. Here, we report that HGT occurred between two Bacillus subtilis strains cocultured on a minimum medium agar plate for 10 h. This process was almost completely resistant to DNase treatment and appeared to require close proximity between cells. The deletion of comK in the recipient completely abolished gene transfer, indicating that the process involved transformation. This process was also highly efficient, reaching 1.75 × 10[6] transformants/μg DNA compared to 5.3 × 10[3] and 1.86 × 10[5] transformants/μg DNA for DNA-to-cell transformation by the same agar method and the standard two-step procedure, respectively. Interestingly, when three distantly localized chromosomal markers were selected simultaneously, the efficiency of cell-to-cell transformation still reached 6.26 × 10[4] transformants/μg DNA, whereas no transformants were obtained when free DNA was used as the donor. Stresses, such as starvation and exposure to antibiotics, further enhanced transformation efficiency by affecting the donor cells, suggesting that stress served as an important signal for promoting this type of HGT. Taken together, our results defined a bona fide process of cell-to-cell natural transformation (CTCNT) in B. subtilis and related species. This finding reveals the previously unrecognized role of donor cells in bacterial natural transformation and improves our understanding of how HGT drives bacterial evolution at a mechanistic level.IMPORTANCE Because DNA is easily prepared, studies of bacterial natural genetic transformation traditionally focus on recipient cells. However, such laboratory artifacts cannot explain how this process occurs in nature. In most cases, competence is only transient and involves approximately 20 to 50 genes, and it is unreasonable for bacteria to spend so many genetic resources on unpredictable and uncertain environmental DNA. Here, we characterized a donor cell-dependent CTCNT process in B. subtilis and related species that was almost completely resistant to DNase treatment and was more efficient than classical natural transformation using naked DNA as a donor, i.e., DNA-to-cell transformation, suggesting that DNA donor cells were also important in the transformation process in natural environments.}, }
@article {pmid29940436, year = {2018}, author = {Díaz-Quiroz, CA and Francisco Hernández-Chávez, J and Ulloa-Mercado, G and Gortáres-Moroyoqui, P and Martínez-Macías, R and Meza-Escalante, E and Serrano-Palacios, D}, title = {Simultaneous quantification of antibiotics in wastewater from pig farms by capillary electrophoresis.}, journal = {Journal of chromatography. B, Analytical technologies in the biomedical and life sciences}, volume = {1092}, number = {}, pages = {386-393}, doi = {10.1016/j.jchromb.2018.06.017}, pmid = {29940436}, issn = {1873-376X}, mesh = {Animals ; Anti-Bacterial Agents/*analysis ; Electrophoresis, Capillary/*methods ; *Farms ; Limit of Detection ; Linear Models ; Reproducibility of Results ; Swine ; Wastewater/*chemistry ; Water Pollutants, Chemical/*analysis ; }, abstract = {Pig farming is an important activity in the economic development of Mexico with millions of tons of meat produced annually. Antibiotics are used in therapeutic dose to prevent diseases, and sometimes as growth promoters. These compounds are not completely metabolized; they are carried into the environment in its active form at concentrations that could induce antibiotic resistance in bacteria, which could be transferred to human pathogens by horizontal gene transfer. The objective of this work was to develop methods of analysis for simultaneous quantification of the antibiotics Oxytetracycline (OXT), Chlortetracycline (CLT), Enrofloxacin (ENRO) and Ciprofloxacin (CIPRO) by field-amplified sampling injection in capillary zone electrophoresis (FASI-CZE). The method was validated by parameters of (1) linearity, obtaining a lineal range of 0.05 at 1 μg mL[-1] for ENRO and CIPRO, and from 0.1 to 1 μg mL[-1] for OXT and CLT; (2) precision, obtaining values <5% of standard deviation for CIPRO and ENRO and <10% of standard deviation for OXT and CLT; (3) accuracy, with recovery values from 93 to 115%; (4) selectivity, with values of resolution >2 for the all antibiotics tested. To prove the method, a sample of wastewater from a local pig farm was analyzed, detecting a concentration of 0.140 ± 0.009 for OXT. This concentration was higher than the minimal selective concentration, indicating the point in which resistance to a determined antibiotic could develop. The methods were validated with precision and sensitivity comparable to chromatographic methods, which can be used to analyze wastewater from pig farms directly.}, }
@article {pmid29937760, year = {2018}, author = {Espejo, RT and Plaza, N}, title = {Multiple Ribosomal RNA Operons in Bacteria; Their Concerted Evolution and Potential Consequences on the Rate of Evolution of Their 16S rRNA.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1232}, pmid = {29937760}, issn = {1664-302X}, abstract = {Bacterial species differ greatly in the number and location of the rRNA operons which may be present in the bacterial chromosomes and plasmids. Most bacterial species contain more than one ribosomal RNA operon copy in their genomes, with some species containing up to 15 such copies. We review the number and location of the rRNA operons and discuss evolution of 16S rRNA (rrs) genes -which are considered as ultimate chronometers for phylogenetic classification- in bacteria with multiple copies of these genes. In these bacterial species, the rrs genes must evolve in concert and sequence changes generated by mutation or horizontal gene transfer must be either erased or spread to every gene copy to avoid divergence, as it occurs when they are present in different species. Analysis of polymorphic sites in intra-genomic rrs copies identifies putative conversion events and demonstrates that sequence conversion is patchy and occurs in small conversion tracts. Sequence conversion probably arises by a non-reciprocal transfer between two or more copies where one copy contributes only a small contiguous segment of DNA, whereas the other copy contributes the rest of the genome in a fairly well understood molecular process. Because concerted evolution implies that a mutation in any of the rrs copies is either eliminated or transferred to every rrs gene in the genome, this process should slow their evolution rate relative to that of single copy genes. However, available data on the rrs genes in bacterial genomes do not show a clear relationship between their evolution rates and the number of their copies in the genome.}, }
@article {pmid29930334, year = {2018}, author = {Beye, M and Hasni, I and Seng, P and Michelle, C and La Scola, B and Raoult, D and Fournier, PE}, title = {Genomic analysis of a Raoultella ornithinolytica strain causing prosthetic joint infection in an immunocompetent patient.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {9462}, pmid = {29930334}, issn = {2045-2322}, mesh = {Aged ; Enterobacteriaceae/classification/*genetics/isolation &amp; purification/pathogenicity ; Enterobacteriaceae Infections/*microbiology ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomic Islands ; Humans ; Joint Prosthesis/microbiology ; Male ; Phylogeny ; Prosthesis-Related Infections/*microbiology ; }, abstract = {We sequenced the genome of Raoultella ornithinolytica strain Marseille-P1025 that caused a rare case of prosthetic joint infection in a 67-year-old immunocompetent male. The 6.7-Mb genome exhibited a genomic island (RoGI) that was unique among R. ornithinolytica strains. RoGI was likely acquired by lateral gene transfer from a member of the Pectobacterium genus and coded for a type IVa secretion system found in other pathogenic bacteria and that may have conferred strain Marseille-P1025 an increased virulence. Strain Marseille-P1025 was also able to infect, multiply within, and kill Acanthamoaeba castellanii amoebae.}, }
@article {pmid29928943, year = {2018}, author = {Shi, H and Zhou, X and Zou, W and Wang, Y and Lei, C and Xiang, R and Zhou, L and Liu, B and Zhang, A and Wang, H}, title = {Co-occurrence of biofilm formation and quinolone resistance in Salmonella enterica serotype typhimurium carrying an IncHI2-type oqxAB-positive plasmid.}, journal = {Microbial pathogenesis}, volume = {123}, number = {}, pages = {68-73}, doi = {10.1016/j.micpath.2018.06.006}, pmid = {29928943}, issn = {1096-1208}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Biofilms/*drug effects/growth &amp; development ; Chickens/microbiology ; Conjugation, Genetic/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal/genetics ; Microbial Sensitivity Tests ; Plasmids/*genetics ; Poultry Diseases/microbiology ; Quinolones/*pharmacology ; Salmonella typhimurium/*drug effects/isolation &amp; purification ; }, abstract = {The objective of this study was to investigate the co-occurrence of biofilms and quinolone resistance in Salmonella enterica serotype Typhimurium mediated by IncHI2-type oqxAB-positive plasmids. Among the 40 Salmonella strains, we found that 27 isolates formed biofilms and displayed identical multidrug-resistance profiles to ciprofloxacin, doxycycline, sulfamethoxazole-trimethoprim, ampicillin and streptomycin, based on biofilm formation assays and antimicrobial susceptibility testing. In particular, a single S. Typhimurium isolate named SC523 produced the thickest biofilms and exhibited the highest-level resistance (MIC = 8 μg/mL) to ciprofloxacin compared to those of the other isolates. The detection of known plasmid-mediated quinolone resistance (PMQR) genes and point mutations in the quinolone resistance-determining region (QRDR) by PCR assay showed that oqxAB genes were present in 27 biofilm-positive isolates. Conjugation experiments, S1-pulse-field gel electrophoresis and biofilm formation assays demonstrated that the conjugative plasmid that encoded biofilms and quinolone resistance in Salmonella SC523 could be transferred to a recipient with a frequency of 4.7 × 10[-3] per recipient cell. The results of PCR-based replicon typing (PBRT) showed that the IncHI2-type plasmids accounted for 100% of the biofilm-oqxAB-positive isolates and transconjugants. The sequence analysis of Salmonella SC523 confirmed that the oqxAB cassette and fourteen DNA transfer genes in the IncHI2-type oqxAB-positive conjugative plasmid were genetically responsible for the phenotypic quinolone resistance and biofilm formation. The conclusion is that the IncHI2-type plasmid in S. Typhimurium isolate from chicken farm was identified and sequenced, which contained oqxAB and tra/trh and encoded quinolone resistance and biofilms, and could be transferred to recipients through conjugation. Notably, the prevalence of IncHI2-type biofilm-oqxAB-positive plasmids in animal-origin Salmonella poses a threat to public health, as these Salmonella from poultry farms show a decreased susceptibility to quinolones and could spread to humans.}, }
@article {pmid29928825, year = {2018}, author = {Jiang, S and Zeng, J and Zhou, X and Li, Y}, title = {Drug Resistance and Gene Transfer Mechanisms in Respiratory/Oral Bacteria.}, journal = {Journal of dental research}, volume = {97}, number = {10}, pages = {1092-1099}, doi = {10.1177/0022034518782659}, pmid = {29928825}, issn = {1544-0591}, mesh = {Anti-Bacterial Agents/*therapeutic use ; Drug Resistance, Bacterial/*genetics ; *Gene Transfer, Horizontal/genetics ; Humans ; Microbiota/*drug effects/genetics ; Mouth/*microbiology ; Respiratory System/*microbiology ; }, abstract = {Growing evidence suggests the existence of new antibiotic resistance mechanisms. Recent studies have revealed that quorum-quenching enzymes, such as MacQ, are involved in both antibiotic resistance and cell-cell communication. Furthermore, some small bacterial regulatory RNAs, classified into RNA attenuators and small RNAs, modulate the expression of resistance genes. For example, small RNA sprX, can shape bacterial resistance to glycopeptide antibiotics via specific downregulation of protein SpoVG. Moreover, some bacterial lipocalins capture antibiotics in the extracellular space, contributing to severe multidrug resistance. But this defense mechanism may be influenced by Agr-regulated toxins and liposoluble vitamins. Outer membrane porin proteins and efflux pumps can influence intracellular concentrations of antibiotics. Alterations in target enzymes or antibiotics prevent binding to targets, which act to confer high levels of resistance in respiratory/oral bacteria. As described recently, horizontal gene transfer, including conjugation, transduction and transformation, is common in respiratory/oral microflora. Many conjugative transposons and plasmids discovered to date encode antibiotic resistance proteins and can be transferred from donor bacteria to transient recipient bacteria. New classes of mobile genetic elements are also being identified. For example, nucleic acids that circulate in the bloodstream (circulating nucleic acids) can integrate into the host cell genome by up-regulation of DNA damage and repair pathways. With multidrug resistant bacteria on the rise, new drugs have been developed to combate bacterial antibiotic resistance, such as innate defense regulators, reactive oxygen species and microbial volatile compounds. This review summaries various aspects and mechanisms of antibiotic resistance in the respiratory/oral microbiota. A better understanding of these mechanisms will facilitate minimization of the emergence of antibiotic resistance.}, }
@article {pmid29927707, year = {2018}, author = {Feurtey, A and Stukenbrock, EH}, title = {Interspecific Gene Exchange as a Driver of Adaptive Evolution in Fungi.}, journal = {Annual review of microbiology}, volume = {72}, number = {}, pages = {377-398}, doi = {10.1146/annurev-micro-090817-062753}, pmid = {29927707}, issn = {1545-3251}, mesh = {*Adaptation, Biological ; *Evolution, Molecular ; Fungi/*genetics ; *Gene Transfer, Horizontal ; *Recombination, Genetic ; }, abstract = {Throughout evolutionary history in the kingdom Fungi, taxa have exchanged genetic information among species, as revealed in particular by analyses of genome sequences. In fungi, hybridization can occur by sexual mating or by fusion of vegetative structures giving rise to new species or leaving traces of introgression in the genome. Furthermore, gene exchange can occur by horizontal gene transfer between species and can even include organisms outside the kingdom Fungi. In several cases, interspecific gene exchange has been instrumental in rapid adaptive evolution of fungal species and has notably played a role in the emergence of new pathogens. Here we summarize mechanisms and examples of gene exchange in fungi with a particular focus on the genomic context. We emphasize the need for and potential of applying population genetic approaches to better understand the processes and the impact of interspecific gene exchange in rapid adaptive evolution and species diversification. The broad occurrence of gene exchange among fungal species challenges our species concepts in the kingdom Fungi.}, }
@article {pmid29925310, year = {2018}, author = {Chang, WH and Lai, AG}, title = {Mixed evolutionary origins of endogenous biomass-depolymerizing enzymes in animals.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {483}, pmid = {29925310}, issn = {1471-2164}, support = {LT0241/2014-L//Human Frontier Science Program/ ; ALTF 1154-2013//European Molecular Biology Organization/ ; }, mesh = {Animals ; Biofuels ; Gene Transfer, Horizontal/genetics ; Genomics/*methods ; Glycoside Hydrolases/*genetics ; Transcriptome/*genetics ; }, abstract = {BACKGROUND: Animals are thought to achieve lignocellulose digestion via symbiotic associations with gut microbes; this view leads to significant focus on bacteria and fungi for lignocellulolytic systems. The presence of biomass conversion systems hardwired into animal genomes has not yet been unequivocally demonstrated.<br><br>RESULTS: We perform an exhaustive search for glycoside hydrolase (GH) genes from 21 genomes representing major bilaterian (Ecdysozoa, Spiralia, Echinodermata and Chordata) and basal metazoan (Porifera and Cnidaria) lineages. We also assessed the genome of a unicellular relative of Metazoa, Capsaspora owczarzaki and together with comparative analyses on 126 crustacean transcriptomes, we found that animals are living bioreactors at a microscale as they encode enzymatic suites for biomass decomposition. We identified a total of 16,723 GH homologs (2373 genes from animal genomes and 14,350 genes from crustacean transcriptomes) that are further classified into 60 GH families. Strikingly, through phylogenetic analyses, we observed that animal lignocellulosic enzymes have multiple origins, either inherited vertically over millions of years from a common ancestor or acquired more recently from non-animal organisms.<br><br>CONCLUSION: We have conducted a systematic and comprehensive survey of GH genes across major animal lineages. The ability of biomass decay appears to be determined by animals' dietary strategies. Detritivores have genes that accomplish broad enzymatic functions while the number of GH families is reduced in animals that have evolved specialized diets. Animal GH candidates identified in this study will not only facilitate future functional genomics research but also provide an analysis platform to identify enzyme candidates with industrial potential.}, }
@article {pmid29924338, year = {2018}, author = {Gong, Z and Han, GZ}, title = {Insect Retroelements Provide Novel Insights into the Origin of Hepatitis B Viruses.}, journal = {Molecular biology and evolution}, volume = {35}, number = {9}, pages = {2254-2259}, doi = {10.1093/molbev/msy129}, pmid = {29924338}, issn = {1537-1719}, mesh = {Animals ; *Gene Transfer, Horizontal ; *Genome, Insect ; Hepatitis B virus/*genetics ; *Host-Pathogen Interactions ; Phylogeny ; *Retroelements ; }, abstract = {The origin of hepadnaviruses (Hepadnaviridae), a group of reverse-transcribing DNA viruses that infect vertebrates, remains mysterious. All the known retrotransposons are only distantly related to hepadnaviruses. Here, we report the discovery of two novel lineages of retroelements, which we designate hepadnavirus-like retroelement (HEART1 and HEART2), within the insect genomes through screening 1, 095 eukaryotic genomes. Both phylogenetic and similarity analyses suggest that the HEART retroelements represent the closest nonviral relatives of hepadnaviruses so far. The discovery of HEART retroelements narrows down the evolutionary gap between hepadnaviruses and retrotransposons and might thus provide unique insights into the origin and evolution of hepadnaviruses.}, }
@article {pmid29923454, year = {2019}, author = {Yair, Y and Gophna, U}, title = {Repeat modularity as a beneficial property of multiple CRISPR-Cas systems.}, journal = {RNA biology}, volume = {16}, number = {4}, pages = {585-587}, pmid = {29923454}, issn = {1555-8584}, mesh = {Base Sequence ; CRISPR-Cas Systems/*genetics ; Conserved Sequence/genetics ; Immunologic Memory/genetics ; Phylogeny ; RNA/genetics ; Repetitive Sequences, Nucleic Acid/*genetics ; }, abstract = {CRISPR-Cas systems are a highly effective immune mechanism for prokaryotes, providing defense against invading foreign DNA. By definition, all CRISPR-Cas systems have short repeats interspersing their spacers. These repeats play a key role in preventing cleavage of self DNA and in the integration of new spacers. Here we focus on the phenomenon of repeat modularity, namely the unexpectedly high degree of repeat conservation across different systems within a genome or between different species. We hypothesize that modularity can be beneficial for CRISPR-Cas containing organisms, because it facilitates horizontal acquisition of 'pre-immunized' CRISPR arrays and allows the utilization of spacers acquired by one system for use by other systems within the same cell.}, }
@article {pmid29922518, year = {2018}, author = {Hernandez, AM and Ryan, JF}, title = {Horizontally transferred genes in the ctenophore Mnemiopsis leidyi.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e5067}, pmid = {29922518}, issn = {2167-8359}, abstract = {Horizontal gene transfer (HGT) has had major impacts on the biology of a wide range of organisms from antibiotic resistance in bacteria to adaptations to herbivory in arthropods. A growing body of literature shows that HGT between non-animals and animals is more commonplace than previously thought. In this study, we present a thorough investigation of HGT in the ctenophore Mnemiopsis leidyi. We applied tests of phylogenetic incongruence to identify nine genes that were likely transferred horizontally early in ctenophore evolution from bacteria and non-metazoan eukaryotes. All but one of these HGTs (an uncharacterized protein) are homologous to characterized enzymes, supporting previous observations that genes encoding enzymes are more likely to be retained after HGT events. We found that the majority of these nine horizontally transferred genes were expressed during development, suggesting that they are active and play a role in the biology of M. leidyi. This is the first report of HGT in ctenophores, and contributes to an ever-growing literature on the prevalence of genetic information flowing between non-animals and animals.}, }
@article {pmid29920267, year = {2018}, author = {Lukeš, J and Husník, F}, title = {Microsporidia: A Single Horizontal Gene Transfer Drives a Great Leap Forward.}, journal = {Current biology : CB}, volume = {28}, number = {12}, pages = {R712-R715}, doi = {10.1016/j.cub.2018.05.031}, pmid = {29920267}, issn = {1879-0445}, mesh = {Animals ; Eukaryotic Cells ; Gene Transfer, Horizontal ; *Membrane Transport Proteins ; *Microsporidia ; *Parasites ; }, abstract = {Horizontal gene transfer from bacteria to eukaryotes is the subject of much debate. A recent study reveals the instrumental role that the acquisition of bacterial nucleotide transporters played in the evolution of the ubiquitous, intracellular eukaryotic parasites, the microsporidia.}, }
@article {pmid29916797, year = {2018}, author = {Beghain, J and Bridier-Nahmias, A and Le Nagard, H and Denamur, E and Clermont, O}, title = {ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping.}, journal = {Microbial genomics}, volume = {4}, number = {7}, pages = {}, pmid = {29916797}, issn = {2057-5858}, mesh = {Base Sequence ; Computer Simulation ; DNA Primers ; Enterobacteriaceae Infections/*microbiology ; Escherichia/*classification/genetics ; Gene Transfer, Horizontal ; Genome, Bacterial ; Molecular Typing/*methods ; Multiplex Polymerase Chain Reaction/*methods ; Mutation ; Phylogeny ; Polymorphism, Single Nucleotide ; Whole Genome Sequencing ; }, abstract = {The genus Escherichia is composed of Escherichia albertii, E. fergusonii, five cryptic Escherichia clades and E. coli sensu stricto. Furthermore, the E. coli species can be divided into seven main phylogroups termed A, B1, B2, C, D, E and F. As specific lifestyles and/or hosts can be attributed to these species/phylogroups, their identification is meaningful for epidemiological studies. Classical phenotypic tests fail to identify non-sensu stricto E. coli as well as phylogroups. Clermont and colleagues have developed PCR assays that allow the identification of most of these species/phylogroups, the triplex/quadruplex PCR for E. coli phylogroup determination being the most popular. With the growing availability of whole genome sequences, we have developed the ClermonTyping method and its associated web-interface, the ClermonTyper, that allows a given strain sequence to be assigned to E. albertii, E. fergusonii, Escherichia clades I-V, E. coli sensu stricto as well as to the seven main E. coli phylogroups. The ClermonTyping is based on the concept of in vitro PCR assays and maintains the principles of ease of use and speed that prevailed during the development of the in vitro assays. This in silico approach shows 99.4 % concordance with the in vitro PCR assays and 98.8 % with the Mash genome-clustering tool. The very few discrepancies result from various errors occurring mainly from horizontal gene transfers or SNPs in the primers. We propose the ClermonTyper as a freely available resource to the scientific community at: http://clermontyping.iame-research.center/.}, }
@article {pmid29915048, year = {2018}, author = {Hosseini, SR and Wagner, A}, title = {Genomic organization underlying deletional robustness in bacterial metabolic systems.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {27}, pages = {7075-7080}, pmid = {29915048}, issn = {1091-6490}, mesh = {Bacteria/*genetics/*metabolism ; *Evolution, Molecular ; *Gene Deletion ; *Genome, Bacterial ; *Multigene Family ; }, abstract = {Large-scale DNA deletions and gene loss are pervasive in bacterial genomes. This observation raises the possibility that evolutionary adaptation has altered bacterial genome organization to increase its robustness to large-scale tandem gene deletions. To find out, we systematically analyzed 55 bacterial genome-scale metabolisms and showed that metabolic gene ordering renders an organism's viability in multiple nutrient environments significantly more robust against tandem multigene deletions than expected by chance. This excess robustness is caused by multiple factors, which include the clustering of essential metabolic genes, a greater-than-expected distance of synthetically lethal metabolic gene pairs, and the clustering of nonessential metabolic genes. By computationally creating minimal genomes, we show that a nonadaptive origin of such clustering could in principle arise as a passive byproduct of bacterial genome growth. However, because genome randomization forces such as translocation and inversion would eventually erode such clustering, adaptive processes are necessary to sustain it. We provide evidence suggesting that this organization might result from adaptation to ongoing gene deletions, and from selective advantages associated with coregulating functionally related genes. Horizontal gene transfer in the presence of gene deletions contributes to sustaining the clustering of essential genes. In sum, our observations suggest that the genome organization of bacteria is driven by adaptive processes that provide phenotypic robustness in response to large-scale gene deletions. This robustness may be especially important for bacterial populations that take advantage of gene loss to adapt to new environments.}, }
@article {pmid29914658, year = {2018}, author = {Nesse, LL and Simm, R}, title = {Biofilm: A Hotspot for Emerging Bacterial Genotypes.}, journal = {Advances in applied microbiology}, volume = {103}, number = {}, pages = {223-246}, doi = {10.1016/bs.aambs.2018.01.003}, pmid = {29914658}, issn = {0065-2164}, mesh = {Bacteria/*genetics/*growth &amp; development ; Biofilms/*growth &amp; development ; Drug Resistance, Bacterial ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genetic Variation ; *Genotype ; *Recombination, Genetic ; }, abstract = {Bacteria have the ability to adapt to changing environments through rapid evolution mediated by modification of existing genetic information, as well as by horizontal gene transfer (HGT). This makes bacteria a highly successful life form when it comes to survival. Unfortunately, this genetic plasticity may result in emergence and dissemination of antimicrobial resistance and virulence genes, and even the creation of multiresistant "superbugs" which may pose serious threats to public health. As bacteria commonly reside in biofilms, there has been an increased interest in studying these phenomena within biofilms in recent years. This review summarizes the present knowledge within this important area of research. Studies on bacterial evolution in biofilms have shown that mature biofilms develop into diverse communities over time. There is growing evidence that the biofilm lifestyle may be more mutagenic than planktonic growth. Furthermore, all three main mechanisms for HGT have been observed in biofilms. This has been shown to occur both within and between bacterial species, and higher transfer rates in biofilms than in planktonic cultures were detected. Of special concern are the observations that mutants with increased antibiotic resistance occur at higher frequency in biofilms than in planktonic cultures even in the absence of antibiotic exposure. Likewise, efficient dissemination of antimicrobial resistance genes, as well as virulence genes, has been observed within the biofilm environment. This new knowledge emphasizes the importance of biofilm awareness and control.}, }
@article {pmid29914363, year = {2018}, author = {Dunning Hotopp, JC}, title = {Grafting or pruning in the animal tree: lateral gene transfer and gene loss?.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {470}, pmid = {29914363}, issn = {1471-2164}, support = {R01 CA206188/CA/NCI NIH HHS/United States ; ABI-1457957//National Science Foundation/ ; 1-R01-CA206188//National Cancer Institute/ ; }, mesh = {Animals ; Bacteria/*genetics ; Eukaryota/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome ; Humans ; Phylogeny ; Prokaryotic Cells/*metabolism ; }, abstract = {BACKGROUND: Lateral gene transfer (LGT), also known as horizontal gene transfer, into multicellular eukaryotes with differentiated tissues, particularly gonads, continues to be met with skepticism by many prominent evolutionary and genomic biologists. A detailed examination of 26 animal genomes identified putative LGTs in invertebrate and vertebrate genomes, concluding that there are fewer predicted LGTs in vertebrates/chordates than invertebrates, but there is still evidence of LGT into chordates, including humans. More recently, a reanalysis of a subset of these putative LGTs into vertebrates concluded that there is not horizontal gene transfer in the human genome. One of the genes in dispute is an N-acyl-aromatic-L-amino acid amidohydrolase (ENSG00000132744), which encodes ACY3. This gene was initially identified as a putative bacteria-chordate LGT but was later debunked as it has a significant BLAST match to a more recently deposited genome of Saccoglossus kowalevskii, a flatworm, Metazoan, and hemichordate.<br><br>RESULTS: Using BLAST searches, HMM searches, and phylogenetics to assess the evidence for LGT, gene loss, and rate variation in ACY3/ASPA homologues, the most parsimonious explanation for the distribution of ACY3/ASPA genes in eukaryotes involves both gene loss and bacteria-animal LGT, albeit LGT that occurred hundreds of millions of years ago prior to the divergence of gnathostomes.<br><br>CONCLUSIONS: ACY3/ASPA is most likely a bacteria-animal LGT. LGTs at these time scales in the ancestors of humans are not unexpected given the many known, well-characterized, and adaptive LGTs from bacteria to insects and nematodes.}, }
@article {pmid29912320, year = {2018}, author = {Kumar, V and Thakur, V and Ambika,  and Kumar, S and Singh, D}, title = {Bioplastic reservoir of diverse bacterial communities revealed along altitude gradient of Pangi-Chamba trans-Himalayan region.}, journal = {FEMS microbiology letters}, volume = {365}, number = {14}, pages = {}, doi = {10.1093/femsle/fny144}, pmid = {29912320}, issn = {1574-6968}, mesh = {Acyltransferases/genetics ; Adaptation, Physiological ; *Altitude ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics ; *Biodiversity ; Environmental Microbiology ; Gene Transfer, Horizontal ; India ; Phylogeny ; Polyhydroxyalkanoates/analysis/*biosynthesis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Himalaya hosts a unique environment for microbial ecology. The present study aimed to explore the bioplastic producing bacterial communities along altitude gradient of Pangi-Chamba trans-Himalayan region. A total of 411 bacteria were isolated and 70 characterized at the molecular level for potential polyhydroxyalkanoates (PHA) producers. The most abundant phylum for PHA synthesis was Proteobacteria (73%), followed by Actinobacteria (11%), Firmicutes (10%) and Bacteroidetes (6%). However, at the genus level, Pseudomonas and Janthinobacterium were dominantly reported. Also, the ability to synthesize PHA was reported for the first time for few genera such as Collimonas, Pseudarthrobacter and Paenarthrobacter. Phylogenetic analysis of partial 16S rDNA and phaC genes revealed conservation in phaC and possibility of horizontal gene transfer among distant taxa. Furthermore, GC-MS also confirmed the ability of potential bacterial isolates to synthesize PHA. In fact, we found that PHA-positive bacteria are dominant in the high altitude of Himalaya, suggesting the vital role of PHA in bacterial adaptation and survival. Together, these findings had revealed the rich bacterial diversity and genetic machinery for PHA synthesis which does have potential for further utilization in the commercial applications.}, }
@article {pmid29910775, year = {2018}, author = {Martínez-Carranza, E and Barajas, H and Alcaraz, LD and Servín-González, L and Ponce-Soto, GY and Soberón-Chávez, G}, title = {Variability of Bacterial Essential Genes Among Closely Related Bacteria: The Case of Escherichia coli.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1059}, pmid = {29910775}, issn = {1664-302X}, abstract = {The definition of bacterial essential genes has been widely pursued using different approaches. Their study has impacted several fields of research such as synthetic biology, the construction of bacteria with minimal chromosomes, the search for new antibiotic targets, or the design of strains with biotechnological applications. Bacterial genomes are mosaics that only share a small subset of gene-sequences (core genome) even among members of the same species. It has been reported that the presence of essential genes is highly variable between closely related bacteria and even among members of the same species, due to the phenomenon known as "non-orthologous gene displacement" that refers to the coding for an essential function by genes with no sequence homology due to horizontal gene transfer (HGT). The existence of dormant forms among bacteria and the high incidence of HGT have been proposed to be driving forces of bacterial evolution, and they might have a role in the low level of conservation of essential genes among related bacteria by non-orthologous gene displacement, but this correlation has not been recognized. The aim of this mini-review is to give a brief overview of the approaches that have been taken to define and study essential genes, and the implications of non-orthologous gene displacement in bacterial evolution, focusing mainly in the case of Escherichia coli. To this end, we reviewed the available literature, and we searched for the presence of the essential genes defined by mutagenesis in the genomes of the 63 best-sequenced E. coli genomes that are available in NCBI database. We could not document specific cases of non-orthologous gene displacement among the E. coli strains analyzed, but we found that the quality of the genome-sequences in the database is not enough to make accurate predictions about the conservation of essential-genes among members of this bacterial species.}, }
@article {pmid29909525, year = {2018}, author = {Sanchez, DG and de Melo, FM and Savazzi, EA and Stehling, EG}, title = {Detection of different β-lactamases encoding genes, including blaNDM, and plasmid-mediated quinolone resistance genes in different water sources from Brazil.}, journal = {Environmental monitoring and assessment}, volume = {190}, number = {7}, pages = {407}, pmid = {29909525}, issn = {1573-2959}, support = {2015/18990-2//FAPESP/ ; }, mesh = {Brazil ; Drug Resistance, Microbial/*genetics ; *Environmental Monitoring ; Fluoroquinolones ; *Genes, Bacterial ; Humans ; Microbial Sensitivity Tests ; Plasmids ; Quinolones ; Water ; Water Microbiology ; Water Pollution/*analysis/statistics &amp; numerical data ; beta-Lactamases/*genetics ; }, abstract = {Bacterial resistance occurs by spontaneous mutations or horizontal gene transfer mediated by mobile genetic elements, which represents a great concern. Resistance to β-lactam antibiotics is mainly due to the production of β-lactamases, and an important mechanism of fluoroquinolone resistance is the acquisition plasmid determinants. The aim of this study was to verify the presence of β-lactamase-encoding genes and plasmid-mediated quinolone resistance genes in different water samples obtained from São Paulo state, Brazil. A high level of these resistance genes was detected, being the blaSHV, blaGES, and qnr the most prevalent. Besides that, the blaNDM gene, which codify an important and hazardous metallo-β-lactamase, was detected.}, }
@article {pmid29909361, year = {2018}, author = {Zhang, J and Yang, M and Zhong, H and Liu, M and Sui, Q and Zheng, L and Tong, J and Wei, Y}, title = {Deciphering the factors influencing the discrepant fate of antibiotic resistance genes in sludge and water phases during municipal wastewater treatment.}, journal = {Bioresource technology}, volume = {265}, number = {}, pages = {310-319}, doi = {10.1016/j.biortech.2018.06.021}, pmid = {29909361}, issn = {1873-2976}, mesh = {Anti-Bacterial Agents ; *Drug Resistance, Microbial ; *Genes, Bacterial ; Sewage/*microbiology ; *Wastewater ; Water ; }, abstract = {The discrepant fate of antibiotic resistance genes (ARGs) in sludge and water phases was investigated in a municipal wastewater treatment plant, and a lab-scale A[2]O-MBR was operated to provide background value of ARGs. The influencing factors of ARGs including microbial community, co-selection from heavy metals, biomass and horizontal gene transfer were concerned. Results showed that iA[2]O (inversed A[2]O) showed better ARGs reduction, and longer SRT (sludge retention time) increased ARGs relative abundance while reduced the gene copies of ARGs in the effluent, but significantly increased the ARGs in sludge phase. Compared to background value, the most enriched ARG was tetX in water phase, while it was intI1 in sludge phase. There existed higher abundance of multi-resistant bacteria in sludge phase, and microbial community determined the fate of ARGs in both water and sludge phase, while the direct effects from horizontal gene transfer should not be overlooked especially in water phase.}, }
@article {pmid29909325, year = {2018}, author = {Qiu, Y and Zhang, J and Li, B and Wen, X and Liang, P and Huang, X}, title = {A novel microfluidic system enables visualization and analysis of antibiotic resistance gene transfer to activated sludge bacteria in biofilm.}, journal = {The Science of the total environment}, volume = {642}, number = {}, pages = {582-590}, doi = {10.1016/j.scitotenv.2018.06.012}, pmid = {29909325}, issn = {1879-1026}, mesh = {*Biofilms ; Drug Resistance, Microbial/*genetics ; Gene Transfer, Horizontal ; *Microfluidics ; Plasmids ; Sewage/*microbiology ; }, abstract = {Antibiotic resistance genes (ARGs) in environment have become a growing public concern, due to their potential to be obtained by pathogens and their duplication along cell division. Horizontal gene transfer (HGT) was reported to be responsible for ARGs dissemination in microbes, but the HGT feature in environmental biofilm was still unclear due to insufficient assay tools. To address this challenge, we applied a novel microfluidic system to cultivate thin biofilm by continuous supply of nutrients and close contact between cells. Resembling the living state of biofilm in open environment, this chip visualized the transfer of ARG-encoded plasmids RP4 and pKJK5 to the receptors, e.g., activated sludge bacteria. The average plasmid transfer frequency per receptor (T/R) from RP4-hosted Pseudomonas putida KT2440 to activated sludge bacteria was quantified to be 2.5 × 10[-3] via flow cytometry, and T/R for pKJK5-hosted Escherichia coli MG1655 was 8.9 × 10[-3], while the corresponding average frequencies per donor (T/D) were diverse for the two host strains as 4.3 × 10[-3] and 1.4 × 10[-1] respectively. The difference between T/R and T/D was explained by the plasmid transfer kinetics, implying specific purposes of the two calculations. Finally, we collected the transconjugants by fluorescent activated cell sorting and further sequenced their 16S rDNA. Bacteria from phyla Proteobacteria and Firmicutes were found more susceptible to be transconjugants than those from Bacteroidetes. Our work demonstrated that microfluidic system was advantageous in biofilm HGT study, which can provide more insights into environmental ARG control.}, }
@article {pmid29909172, year = {2018}, author = {Dziri, O and Alonso, CA and Dziri, R and Gharsa, H and Maraoub, A and Torres, C and Chouchani, C}, title = {Metallo-β-lactamases and class D carbapenemases in south-east Tunisia: Implication of mobile genetic elements in their dissemination.}, journal = {International journal of antimicrobial agents}, volume = {52}, number = {6}, pages = {871-877}, doi = {10.1016/j.ijantimicag.2018.06.002}, pmid = {29909172}, issn = {1872-7913}, mesh = {Bacterial Proteins/*genetics ; Conjugation, Genetic ; Electrophoresis, Gel, Pulsed-Field ; Gene Transfer, Horizontal ; Genotype ; Gram-Negative Bacteria/classification/*enzymology/genetics/isolation &amp; purification ; Gram-Negative Bacterial Infections/epidemiology/*microbiology/transmission ; Humans ; *Interspersed Repetitive Sequences ; Molecular Epidemiology ; Multilocus Sequence Typing ; Plasmids/analysis/classification ; Polymerase Chain Reaction ; Tunisia/epidemiology ; beta-Lactamases/*genetics ; }, abstract = {Carbapenem resistance in Gram-negative bacteria constitutes a major clinical problem. We characterized molecular features among carbapenem-resistant Gram-negative clinical isolates collected from Southeastern Tunisian Island Hospital. Eighteen carbapenem-resistant clinical isolates (13 Klebsiella pneumoniae, 1 Proteus mirabilis, 1 Enterobacter cloacae, 3 Acinetobacter baumannii) were recovered during April 2015-August 2016. Molecular characterization of antimicrobial resistance was performed using polymerase chain reaction (PCR) and sequencing. Molecular typing of carbapenemase-producing K. pneumoniae was performed by pulsed-field gel electrophoresis (PFGE) after XbaI digestion and multilocus sequence typing (MLST). Conjugation experiments were conducted and type/number/size of plasmids were characterized by PCR-Based-Replicon-Typing and PFGE after S1 digestion. Carbapenemase genes were detected in K. pneumoniae [blaNDM-1(8), blaNDM-1+blaOXA-48(1), blaOXA-48(4)], P. mirabilis [blaOXA-48(1)], E. cloacae [blaVIM-2(1)] and A. baumannii [blaOXA-23(3)]. K. pneumoniae isolates were typed as ST15, ST1412 and ST147 and showed seven different pulsotypes. The genetic structure surrounding blaNDM-1 was composed of ISAba125 and ble. The blaVIM-2 carried by E. cloacae was located within the variable region of a class1 integron and blaOXA-48 gene was inserted into Tn1999.2. IncA/C and IncFIIA replicons were implicated in dissemination of blaNDM-1 and a non-typeable 48.5 kb plasmid in the propagation of blaOXA-48. The emergence of carbapenemase-producing Gram-negative species in a Tunisian hospital shows the need for preventive strategies and hygiene measures to minimize their spread. Although conjugative plasmids play an important role in rapid carbapenemase genes dissemination, other mobile genetic elements, such as insertion sequences, transposons and integrons, are involved in acquisition of these resistances.}, }
@article {pmid29907766, year = {2018}, author = {Usman, WM and Pham, TC and Kwok, YY and Vu, LT and Ma, V and Peng, B and Chan, YS and Wei, L and Chin, SM and Azad, A and He, AB and Leung, AYH and Yang, M and Shyh-Chang, N and Cho, WC and Shi, J and Le, MTN}, title = {Efficient RNA drug delivery using red blood cell extracellular vesicles.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {2359}, pmid = {29907766}, issn = {2041-1723}, support = {81770099//National Natural Science Foundation of China (National Science Foundation of China)/International ; 81602514, 81773246//National Natural Science Foundation of China (National Science Foundation of China)/International ; 9211101//Food and Health Bureau of the Government of the Hong Kong Special Administrative Region | Health and Medical Research Fund (HMRF)/International ; 21106616//Research Grants Council, University Grants Committee (RGC, UGC)/International ; 9610343, 9667133, 7200475//City University of Hong Kong (CityU)/International ; }, mesh = {Animals ; Breast Neoplasms/genetics/metabolism ; CRISPR-Cas Systems ; Cell Line, Tumor ; *Drug Delivery Systems ; Erythrocytes/*metabolism ; *Extracellular Vesicles ; Female ; Humans ; Mice ; Mice, Nude ; Mice, SCID ; MicroRNAs/genetics ; Neoplasm Transplantation ; Oligonucleotides, Antisense/genetics ; RNA/*analysis ; *RNA, Guide, CRISPR-Cas Systems ; }, abstract = {Most of the current methods for programmable RNA drug therapies are unsuitable for the clinic due to low uptake efficiency and high cytotoxicity. Extracellular vesicles (EVs) could solve these problems because they represent a natural mode of intercellular communication. However, current cellular sources for EV production are limited in availability and safety in terms of horizontal gene transfer. One potentially ideal source could be human red blood cells (RBCs). Group O-RBCs can be used as universal donors for large-scale EV production since they are readily available in blood banks and they are devoid of DNA. Here, we describe and validate a new strategy to generate large-scale amounts of RBC-derived EVs for the delivery of RNA drugs, including antisense oligonucleotides, Cas9 mRNA, and guide RNAs. RNA drug delivery with RBCEVs shows highly robust microRNA inhibition and CRISPR-Cas9 genome editing in both human cells and xenograft mouse models, with no observable cytotoxicity.}, }
@article {pmid29905872, year = {2018}, author = {Cury, J and Oliveira, PH and de la Cruz, F and Rocha, EPC}, title = {Host Range and Genetic Plasticity Explain the Coexistence of Integrative and Extrachromosomal Mobile Genetic Elements.}, journal = {Molecular biology and evolution}, volume = {35}, number = {9}, pages = {2230-2239}, pmid = {29905872}, issn = {1537-1719}, support = {281605/ERC_/European Research Council/International ; }, mesh = {*Conjugation, Genetic ; *Interspersed Repetitive Sequences ; *Plasmids ; Proteobacteria/*genetics ; }, abstract = {Self-transmissible mobile genetic elements drive horizontal gene transfer between prokaryotes. Some of these elements integrate in the chromosome, whereas others replicate autonomously as plasmids. Recent works showed the existence of few differences, and occasional interconversion, between the two types of elements. Here, we enquired on why evolutionary processes have maintained the two types of mobile genetic elements by comparing integrative and conjugative elements (ICE) with extrachromosomal ones (conjugative plasmids) of the highly abundant MPFT conjugative type. We observed that plasmids encode more replicases, partition systems, and antibiotic resistance genes, whereas ICEs encode more integrases and metabolism-associated genes. ICEs and plasmids have similar average sizes, but plasmids are much more variable, have more DNA repeats, and exchange genes more frequently. On the other hand, we found that ICEs are more frequently transferred between distant taxa. We propose a model where the different genetic plasticity and amplitude of host range between elements explain the co-occurrence of integrative and extrachromosomal elements in microbial populations. In particular, the conversion from ICE to plasmid allows ICE to be more plastic, while the conversion from plasmid to ICE allows the expansion of the element's host range.}, }
@article {pmid29905149, year = {2018}, author = {Qu, G and Piazza, CL and Smith, D and Belfort, M}, title = {Group II intron inhibits conjugative relaxase expression in bacteria by mRNA targeting.}, journal = {eLife}, volume = {7}, number = {}, pages = {}, pmid = {29905149}, issn = {2050-084X}, support = {GM39422/NH/NIH HHS/United States ; R37 GM039422/GM/NIGMS NIH HHS/United States ; GM44844/NH/NIH HHS/United States ; R01 GM039422/GM/NIGMS NIH HHS/United States ; R01 GM044844/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/metabolism ; *Conjugation, Genetic ; DNA Transposable Elements/genetics ; Escherichia coli/genetics/metabolism ; Exons ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Interspersed Repetitive Sequences ; Introns ; Lactococcus lactis/*genetics/metabolism ; Plasmids/*chemistry/metabolism ; *RNA Splicing ; RNA, Messenger/*genetics/metabolism ; Spliceosomes/genetics/metabolism ; }, abstract = {Group II introns are mobile ribozymes that are rare in bacterial genomes, often cohabiting with various mobile elements, and seldom interrupting housekeeping genes. What accounts for this distribution has not been well understood. Here, we demonstrate that Ll.LtrB, the group II intron residing in a relaxase gene on a conjugative plasmid from Lactococcus lactis, inhibits its host gene expression and restrains the naturally cohabiting mobile element from conjugative horizontal transfer. We show that reduction in gene expression is mainly at the mRNA level, and results from the interaction between exon-binding sequences (EBSs) in the intron and intron-binding sequences (IBSs) in the mRNA. The spliced intron targets the relaxase mRNA and reopens ligated exons, causing major mRNA loss. Taken together, this study provides an explanation for the distribution and paucity of group II introns in bacteria, and suggests a potential force for those introns to evolve into spliceosomal introns.}, }
@article {pmid29904377, year = {2018}, author = {Peng, S and Dolfing, J and Feng, Y and Wang, Y and Lin, X}, title = {Enrichment of the Antibiotic Resistance Gene tet(L) in an Alkaline Soil Fertilized With Plant Derived Organic Manure.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1140}, pmid = {29904377}, issn = {1664-302X}, abstract = {Fifteen antibiotic resistance genes (ARGs) and intI1, a gene involved in horizontal gene transfer (HGT) of ARGs, were quantified in three different soil samples from a 22 year old field experiment that had received inorganic fertilizer (NPK), organic manure (OM; a mixture of wheat straw, soybean oil cake and cotton cake), and control fields that had received no fertilizer and manure (CK). Tet(L) was the most abundant ARG in OM, which also contained considerable levels of intI1. Molecular analysis of yearly collected archived soils over the past 22 years showed that tet(L) and intI1 were higher in OM soils than in NPK soils. The relative abundance of tet(L) was essentially constant during these years, while the level of intI1 in OM soils decreased over time. The main genotype of tet(L) was the same in archived and in fresh soil, OM, and irrigation water. Phylogenetic analysis of the 16S rRNA genes of tetracycline-resistant bacteria (TRB) isolates indicated that the Firmucutes carrying tet(L) in OM were similar to those in the OM soil, suggesting that OM transferred TRB into the OM soils where they survived. Almost all of the TRB isolated from OM carried tet(L) and belonged to the Firmicutes. Survival of bacteria from the organic manure that carried tet(L) may be the cause of the increased level of tet(L) in OM soil.}, }
@article {pmid29901262, year = {2018}, author = {Pettis, GS}, title = {Spreading the news about the novel conjugation mechanism in Streptomyces bacteria.}, journal = {Environmental microbiology reports}, volume = {10}, number = {5}, pages = {503-510}, doi = {10.1111/1758-2229.12659}, pmid = {29901262}, issn = {1758-2229}, mesh = {Bacterial Proteins/metabolism ; Biological Transport ; Chromosomes, Bacterial/genetics/metabolism ; *Conjugation, Genetic ; DNA/metabolism ; DNA, Bacterial/genetics/*metabolism ; Gene Transfer, Horizontal ; Mycelium ; Plasmids/genetics/metabolism ; Streptomyces/*genetics/*metabolism ; }, abstract = {The hallmark of mycelial spore-forming bacteria of the genus Streptomyces is their prolific production of antibiotics and other bioactive secondary metabolites as part of a complex morphological and physiological developmental program. They are further distinguished by a conjugation mechanism that differs substantially from the single-strand mode of DNA transfer via Type IV secretion, which is exhibited by numerous unicellular Gram-negative and Gram-positive bacteria. At the crux of the novel intermycelial transfer event in Streptomyces spp. is a membrane pore composed of a single plasmid protein (TraB), which also functions as an FtsK-like DNA pump driven by the energy of ATP hydrolysis. TraB binds to specific 8-mer repeats within the non-coding clt plasmid transfer locus and the DNA is then translocated intercellularly in double-strand form. TraB also translocates chromosomal DNA most likely by binding to 8-mer clc sequences (clt-like chromosomal sequences) distributed throughout streptomycete chromosomes. In the recipient, plasmids are dispersed through septal crosswalls apparently by a multiprotein complex comprising TraB and plasmid Spd proteins. Continued rounds of such intramycelial spreading distribute plasmids well beyond the initial entrance point during the time prior to cell differentiation and sporulation.}, }
@article {pmid29899518, year = {2018}, author = {Madsen, JS and Hylling, O and Jacquiod, S and Pécastaings, S and Hansen, LH and Riber, L and Vestergaard, G and Sørensen, SJ}, title = {An intriguing relationship between the cyclic diguanylate signaling system and horizontal gene transfer.}, journal = {The ISME journal}, volume = {12}, number = {9}, pages = {2330-2334}, pmid = {29899518}, issn = {1751-7370}, mesh = {Bacteria/enzymology/*genetics/metabolism/pathogenicity ; Bacterial Physiological Phenomena ; Biofilms/growth &amp; development ; Cyclic GMP/*analogs &amp; derivatives/metabolism ; *Gene Transfer, Horizontal ; Plasmids/genetics ; Signal Transduction ; Virulence ; }, abstract = {The second messenger cyclic diguanylate (c-di-GMP) is ubiquitously used by bacteria to modulate and shift between different phenotypes including motility, biofilm formation and virulence. Here we show that c-di-GMP-associated genes are widespread on plasmids and that enzymes that synthesize or degrade c-di-GMP are preferentially encoded on transmissible plasmids. Additionally, expression of enzymes that synthesize c-di-GMP was found to increase both biofilm formation and, interestingly, conjugative plasmid transfer rates.}, }
@article {pmid29897833, year = {2018}, author = {Le Roux, F and Blokesch, M}, title = {Eco-evolutionary Dynamics Linked to Horizontal Gene Transfer in Vibrios.}, journal = {Annual review of microbiology}, volume = {72}, number = {}, pages = {89-110}, doi = {10.1146/annurev-micro-090817-062148}, pmid = {29897833}, issn = {1545-3251}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Adaptation, Biological ; Ecosystem ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Genetics, Population ; Host-Pathogen Interactions ; Interspersed Repetitive Sequences ; Symbiosis ; Vibrio/*genetics/*growth &amp; development ; Virulence Factors/genetics ; }, abstract = {Vibrio is a genus of ubiquitous heterotrophic bacteria found in aquatic environments. Although they are a small percentage of the bacteria in these environments, vibrios can predominate during blooms. Vibrios also play important roles in the degradation of polymeric substances, such as chitin, and in other biogeochemical processes. Vibrios can be found as free-living bacteria, attached to particles, or associated with other organisms in a mutualistic, commensal, or pathogenic relationship. This review focuses on vibrio ecology and genome plasticity, which confers an ability to adapt to new niches and is driven, at least in part, by horizontal gene transfer (HGT). The extent of HGT and its role in pathogen emergence are discussed based on genomic studies of environmental and pathogenic vibrios, mobile genetically encoded virulence factors, and mechanistic studies on the different modes of HGT.}, }
@article {pmid29896176, year = {2018}, author = {Elbehery, AHA and Feichtmayer, J and Singh, D and Griebler, C and Deng, L}, title = {The Human Virome Protein Cluster Database (HVPC): A Human Viral Metagenomic Database for Diversity and Function Annotation.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1110}, pmid = {29896176}, issn = {1664-302X}, abstract = {Human virome, including those of bacteria (bacteriophages) have received an increasing attention recently, owing to the rapid developments in human microbiome research and the awareness of the far-reaching influence of microbiomes on health and disease. Nevertheless, human viromes are still underrepresented in literature making viruses a virtually untapped resource of diversity, functional and physiological information. Here we present the human virome protein cluster database as an effort to improve functional annotation and characterization of human viromes. The database was built out of hundreds of virome datasets from six different body sites. We also show the utility of this database through its use for the characterization of three bronchoalveolar lavage (BAL) viromes from one healthy control in addition to one moderate and one severe chronic obstructive pulmonary disease (COPD) patients. The use of the database allowed for a better functional annotation, which were otherwise poorly characterized when limited to annotation using sequences from full-length viral genomes. In addition, our BAL samples gave a first insight into viral communities of COPD patients and confirm a state of dysbiosis for viruses that increases with disease progression. Moreover, they shed light on the potential role of phages in the horizontal gene transfer of bacterial virulence factors, a phenomenon that highlights a possible contribution of phages to etiopathology.}, }
@article {pmid29895787, year = {2018}, author = {Dhawde, R and Macaden, R and Saranath, D and Nilgiriwala, K and Ghadge, A and Birdi, T}, title = {Antibiotic Resistance Characterization of Environmental E. coli Isolated from River Mula-Mutha, Pune District, India.}, journal = {International journal of environmental research and public health}, volume = {15}, number = {6}, pages = {}, pmid = {29895787}, issn = {1660-4601}, mesh = {Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/*drug effects/genetics/isolation &amp; purification ; Escherichia coli Proteins/genetics ; Genetic Markers ; India ; Microbial Sensitivity Tests ; Rivers/*microbiology ; *Water Microbiology ; }, abstract = {In the current study, ceftazidime- and ciprofloxacin-resistant&amp;mdash;or dual drug-resistant (DDR)&amp;mdash;E. coli were isolated from river Mula-Mutha, which flows through rural Pune district and Pune city. The DDR E. coli were further examined for antibiotic resistance to six additional antibiotics. The study also included detection of genes responsible for ceftazidime and ciprofloxacin resistance and vectors for horizontal gene transfer. Twenty-eight percent of the identified DDR E. coli were resistant to more than six antibiotics, with 12% being resistant to all eight antibiotics tested. Quinolone resistance was determined through the detection of qnrA, qnrB, qnrS and oqxA genes, whereas cephalosporin resistance was confirmed through detection of TEM, CTX-M-15, CTX-M-27 and SHV genes. Out of 219 DDR E. coli, 8.2% were qnrS positive and 0.4% were qnrB positive. Percentage of isolates positive for the TEM, CTX-M-15 and CTX-M-27 genes were 32%, 46% and 0.9%, respectively. None of the DDR E. coli tested carried the qnrA, SHV and oqxA genes. Percentage of DDR E. coli carrying Class 1 and 2 integrons (mobile genetic elements) were 47% and 8%, respectively. The results showed that antibiotic resistance genes (ARGs) and integrons were present in the E. coli isolated from the river at points adjoining and downstream of Pune city.}, }
@article {pmid29892948, year = {2018}, author = {Subhadra, B and Kim, DH and Kim, J and Woo, K and Sohn, KM and Kim, HJ and Han, K and Oh, MH and Choi, CH}, title = {Complete genome sequence of uropathogenic Escherichia coli isolate UPEC 26-1.}, journal = {Genes &amp; genomics}, volume = {40}, number = {6}, pages = {643-655}, pmid = {29892948}, issn = {2092-9293}, mesh = {Base Composition/genetics ; Base Sequence/genetics ; Chromosome Mapping ; DNA, Bacterial/genetics ; Escherichia coli/genetics ; Escherichia coli Infections/genetics ; Escherichia coli Proteins/genetics ; Genome, Bacterial/genetics ; Genomic Islands ; Phylogeny ; Urinary Tract Infections/genetics ; Uropathogenic Escherichia coli/*genetics/*pathogenicity ; Virulence ; Virulence Factors/genetics ; Whole Genome Sequencing/methods ; }, abstract = {Urinary tract infections (UTIs) are among the most common infections in humans, predominantly caused by uropathogenic Escherichia coli (UPEC). The diverse genomes of UPEC strains mostly impede disease prevention and control measures. In this study, we comparatively analyzed the whole genome sequence of a highly virulent UPEC strain, namely UPEC 26-1, which was isolated from urine sample of a patient suffering from UTI in Korea. Whole genome analysis showed that the genome consists of one circular chromosome of 5,329,753 bp, comprising 5064 protein-coding genes, 122 RNA genes (94 tRNA, 22 rRNA and 6 ncRNA genes), and 100 pseudogenes, with an average G+C content of 50.56%. In addition, we identified 8 prophage regions comprising 5 intact, 2 incomplete and 1 questionable ones and 63 genomic islands, suggesting the possibility of horizontal gene transfer in this strain. Comparative genome analysis of UPEC 26-1 with the UPEC strain CFT073 revealed an average nucleotide identity of 99.7%. The genome comparison with CFT073 provides major differences in the genome of UPEC 26-1 that would explain its increased virulence and biofilm formation. Nineteen of the total GIs were unique to UPEC 26-1 compared to CFT073 and nine of them harbored unique genes that are involved in virulence, multidrug resistance, biofilm formation and bacterial pathogenesis. The data from this study will assist in future studies of UPEC strains to develop effective control measures.}, }
@article {pmid29891864, year = {2018}, author = {Ellison, CK and Dalia, TN and Vidal Ceballos, A and Wang, JC and Biais, N and Brun, YV and Dalia, AB}, title = {Retraction of DNA-bound type IV competence pili initiates DNA uptake during natural transformation in Vibrio cholerae.}, journal = {Nature microbiology}, volume = {3}, number = {7}, pages = {773-780}, pmid = {29891864}, issn = {2058-5276}, support = {K22 AI118863/AI/NIAID NIH HHS/United States ; R35 GM122556/GM/NIGMS NIH HHS/United States ; R35 GM128674/GM/NIGMS NIH HHS/United States ; SC2 AI116566/AI/NIAID NIH HHS/United States ; }, abstract = {Natural transformation is a broadly conserved mechanism of horizontal gene transfer in bacterial species that can shape evolution and foster the spread of antibiotic resistance determinants, promote antigenic variation and lead to the acquisition of novel virulence factors. Surface appendages called competence pili promote DNA uptake during the first step of natural transformation [1] ; however, their mechanism of action has remained unclear owing to an absence of methods to visualize these structures in live cells. Here, using the model naturally transformable species Vibrio cholerae and a pilus-labelling method, we define the mechanism for type IV competence pilus-mediated DNA uptake during natural transformation. First, we show that type IV competence pili bind to extracellular double-stranded DNA via their tip and demonstrate that this binding is critical for DNA uptake. Next, we show that type IV competence pili are dynamic structures and that pilus retraction brings tip-bound DNA to the cell surface. Finally, we show that pilus retraction is spatiotemporally coupled to DNA internalization and that sterically obstructing pilus retraction prevents DNA uptake. Together, these results indicate that type IV competence pili directly bind to DNA via their tip and mediate DNA internalization through retraction during this conserved mechanism of horizontal gene transfer.}, }
@article {pmid29891839, year = {2018}, author = {Legendre, M and Fabre, E and Poirot, O and Jeudy, S and Lartigue, A and Alempic, JM and Beucher, L and Philippe, N and Bertaux, L and Christo-Foroux, E and Labadie, K and Couté, Y and Abergel, C and Claverie, JM}, title = {Diversity and evolution of the emerging Pandoraviridae family.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {2285}, pmid = {29891839}, issn = {2041-1723}, mesh = {Acanthamoeba/*virology ; DNA Viruses/*classification/*genetics/physiology ; DNA, Viral/genetics ; Environmental Microbiology ; Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; Genetic Variation ; Genome, Viral ; Molecular Sequence Annotation ; Phylogeny ; Proteomics ; Sequence Analysis, DNA ; Virion/ultrastructure ; Virus Replication ; }, abstract = {With DNA genomes reaching 2.5 Mb packed in particles of bacterium-like shape and dimension, the first two Acanthamoeba-infecting pandoraviruses remained up to now the most complex viruses since their discovery in 2013. Our isolation of three new strains from distant locations and environments is now used to perform the first comparative genomics analysis of the emerging worldwide-distributed Pandoraviridae family. Thorough annotation of the genomes combining transcriptomic, proteomic, and bioinformatic analyses reveals many non-coding transcripts and significantly reduces the former set of predicted protein-coding genes. Here we show that the pandoraviruses exhibit an open pan-genome, the enormous size of which is not adequately explained by gene duplications or horizontal transfers. As most of the strain-specific genes have no extant homolog and exhibit statistical features comparable to intergenic regions, we suggest that de novo gene creation could contribute to the evolution of the giant pandoravirus genomes.}, }
@article {pmid29891837, year = {2018}, author = {Clerissi, C and Touchon, M and Capela, D and Tang, M and Cruveiller, S and Genthon, C and Lopez-Roques, C and Parker, MA and Moulin, L and Masson-Boivin, C and Rocha, EPC}, title = {Parallels between experimental and natural evolution of legume symbionts.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {2264}, pmid = {29891837}, issn = {2041-1723}, support = {ANR-12-ADAP-0014-01//Agence Nationale de la Recherche (French National Research Agency)/International ; ANR-16-CE20-0011-01//Agence Nationale de la Recherche (French National Research Agency)/International ; ANR-10-INBS-09//Agence Nationale de la Recherche (French National Research Agency)/International ; ANR-10-LABX-41//Agence Nationale de la Recherche (French National Research Agency)/International ; }, mesh = {Adaptation, Physiological/genetics ; Cupriavidus/genetics/physiology ; *Directed Molecular Evolution ; *Evolution, Molecular ; Fabaceae/*microbiology ; Gene Regulatory Networks ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Variation ; Mimosa/microbiology ; Mutation ; Plasmids/genetics ; Ralstonia solanacearum/genetics/physiology ; Symbiosis/*genetics/physiology ; }, abstract = {The emergence of symbiotic interactions has been studied using population genomics in nature and experimental evolution in the laboratory, but the parallels between these processes remain unknown. Here we compare the emergence of rhizobia after the horizontal transfer of a symbiotic plasmid in natural populations of Cupriavidus taiwanensis, over 10 MY ago, with the experimental evolution of symbiotic Ralstonia solanacearum for a few hundred generations. In spite of major differences in terms of time span, environment, genetic background, and phenotypic achievement, both processes resulted in rapid genetic diversification dominated by purifying selection. We observe no adaptation in the plasmid carrying the genes responsible for the ecological transition. Instead, adaptation was associated with positive selection in a set of genes that led to the co-option of the same quorum-sensing system in both processes. Our results provide evidence for similarities in experimental and natural evolutionary transitions and highlight the potential of comparisons between both processes to understand symbiogenesis.}, }
@article {pmid29887874, year = {2018}, author = {Li, M and Zhao, J and Tang, N and Sun, H and Huang, J}, title = {Horizontal Gene Transfer From Bacteria and Plants to the Arbuscular Mycorrhizal Fungus Rhizophagus irregularis.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {701}, pmid = {29887874}, issn = {1664-462X}, abstract = {Arbuscular mycorrhizal fungi (AMF) belong to Glomeromycotina, and are mutualistic symbionts of many land plants. Associated bacteria accompany AMF during their lifecycle to establish a robust tripartite association consisting of fungi, plants and bacteria. Physical association among this trinity provides possibilities for the exchange of genetic materials. However, very few horizontal gene transfer (HGT) from bacteria or plants to AMF has been reported yet. In this study, we complement existing algorithms by developing a new pipeline, Blast2hgt, to efficiently screen for putative horizontally derived genes from a whole genome. Genome analyses of the glomeromycete Rhizophagus irregularis identified 19 fungal genes that had been transferred between fungi and bacteria/plants, of which seven were obtained from bacteria. Another 18 R. irregularis genes were found to be recently acquired from either plants or bacteria. In the R. irregularis genome, gene duplication has contributed to the expansion of three foreign genes. Importantly, more than half of the R. irregularis foreign genes were expressed in various transcriptomic experiments, suggesting that these genes are functional in R. irregularis. Functional annotation and available evidence showed that these acquired genes may participate in diverse but fundamental biological processes such as regulation of gene expression, mitosis and signal transduction. Our study suggests that horizontal gene influx through endosymbiosis is a source of new functions for R. irregularis, and HGT might have played a role in the evolution and symbiotic adaptation of this arbuscular mycorrhizal fungus.}, }
@article {pmid29885781, year = {2018}, author = {Ghaly, TM and Gillings, MR}, title = {Mobile DNAs as Ecologically and Evolutionarily Independent Units of Life.}, journal = {Trends in microbiology}, volume = {26}, number = {11}, pages = {904-912}, doi = {10.1016/j.tim.2018.05.008}, pmid = {29885781}, issn = {1878-4380}, mesh = {Adaptation, Biological ; Anti-Bacterial Agents ; Bacteria/*genetics/pathogenicity ; Conjugation, Genetic/genetics ; DNA Transposable Elements/*genetics ; Drug Resistance, Bacterial/*genetics ; *Ecology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; Host-Parasite Interactions/genetics ; Selection, Genetic ; Virulence/genetics ; }, abstract = {Mobile DNAs drive the spread of virulence and antibiotic-resistance determinants across diverse bacterial lineages. However, they have been largely overlooked as therapeutic targets, limiting our ability to prevent the spread of their clinically relevant cargo genes. Mobile DNAs adopt various behavioural, evolutionary, and ecological strategies to enhance their diversification, transmission, and replicative fitness. They can do this even at the expense of their host bacterium. Here, we explore evidence that mobile DNAs are inherently selfish, and resemble endoparasites. Viewing them as such helps us to better understand their dynamics, and ultimately, could identify ways to limit their role in the spread of resistance. Shifting our therapeutic focus towards targeting the transmission of mobile DNAs could help us to manage the resistance crisis.}, }
@article {pmid29884344, year = {2018}, author = {Saravana Kumar, P and Yuvaraj, P and Gabrial Paulraj, M and Ignacimuthu, S and Abdullah Al-Dhabi, N}, title = {Bio-prospecting of soil Streptomyces and its bioassay-guided isolation of microbial derived auxin with antifungal properties.}, journal = {Journal de mycologie medicale}, volume = {28}, number = {3}, pages = {462-468}, doi = {10.1016/j.mycmed.2018.05.009}, pmid = {29884344}, issn = {1773-0449}, mesh = {Antifungal Agents/*metabolism/pharmacology ; Biological Assay/methods ; Indoleacetic Acids/*metabolism/pharmacology ; Microbial Sensitivity Tests ; Mycological Typing Techniques ; RNA, Fungal/analysis/isolation &amp; purification ; RNA, Ribosomal, 16S/analysis ; *Soil Microbiology ; *Streptomyces/classification/genetics/isolation &amp; purification/metabolism ; }, abstract = {The present study was aimed to isolate bioactive actinomycetes with antifungal properties. Twenty-seven distinct soil derived actinomycetes were investigated for their antifungal activities. Among these, one isolate exhibited significant antifungal activity. Phenotypic and 16s rRNA gene sequence analysis strongly suggested that the active isolate BG4 belonged to the genus Streptomyces. Further, the chemical investigation of the active extract resulted in the isolation of a major compound and it was structurally elucidated as phenyl acetic acid (PAA). PAA exhibited promising antifungal activity with 100% inhibition, ranging from 31.25 to 25μg/mL. It is to be noted that PAA is naturally occurring and biologically active auxin. In addition, it has also been hypothesized that phytohormone endorsing the source of soil-symbionts has similar pathways for synthesizing compounds and its congeners of host due to horizontal gene transfer. These findings demonstrate that microbially derived phytohormone can be used to treat fungal infections.}, }
@article {pmid29881445, year = {2018}, author = {Ciach, MA and Muszewska, A and Górecki, P}, title = {Locus-aware decomposition of gene trees with respect to polytomous species trees.}, journal = {Algorithms for molecular biology : AMB}, volume = {13}, number = {}, pages = {11}, pmid = {29881445}, issn = {1748-7188}, abstract = {BACKGROUND: Horizontal gene transfer (HGT), a process of acquisition and fixation of foreign genetic material, is an important biological phenomenon. Several approaches to HGT inference have been proposed. However, most of them either rely on approximate, non-phylogenetic methods or on the tree reconciliation, which is computationally intensive and sensitive to parameter values.<br><br>RESULTS: We investigate the locus tree inference problem as a possible alternative that combines the advantages of both approaches. We present several algorithms to solve the problem in the parsimony framework. We introduce a novel tree mapping, which allows us to obtain a heuristic solution to the problems of locus tree inference and duplication classification.<br><br>CONCLUSIONS: Our approach allows for faster comparisons of gene and species trees and improves known algorithms for duplication inference in the presence of polytomies in the species trees. We have implemented our algorithms in a software tool available at https://github.com/mciach/LocusTreeInference.}, }
@article {pmid29880910, year = {2018}, author = {Yurchenko, T and Ševčíková, T and Přibyl, P and El Karkouri, K and Klimeš, V and Amaral, R and Zbránková, V and Kim, E and Raoult, D and Santos, LMA and Eliáš, M}, title = {A gene transfer event suggests a long-term partnership between eustigmatophyte algae and a novel lineage of endosymbiotic bacteria.}, journal = {The ISME journal}, volume = {12}, number = {9}, pages = {2163-2175}, pmid = {29880910}, issn = {1751-7370}, mesh = {*Gene Transfer, Horizontal ; Genomics ; Operon ; Rickettsiaceae/*genetics ; Stramenopiles/*microbiology ; Symbiosis ; }, abstract = {Rickettsiales are obligate intracellular bacteria originally found in metazoans, but more recently recognized as widespread endosymbionts of various protists. One genus was detected also in several green algae, but reports on rickettsialean endosymbionts in other algal groups are lacking. Here we show that several distantly related eustigmatophytes (coccoid algae belonging to Ochrophyta, Stramenopiles) are infected by Candidatus Phycorickettsia gen. nov., a new member of the family Rickettsiaceae. The genome sequence of Ca. Phycorickettsia trachydisci sp. nov., an endosymbiont of Trachydiscus minutus CCALA 838, revealed genomic features (size, GC content, number of genes) typical for other Rickettsiales, but some unusual aspects of the gene content were noted. Specifically, Phycorickettsia lacks genes for several components of the respiration chain, haem biosynthesis pathway, or c-di-GMP-based signalling. On the other hand, it uniquely harbours a six-gene operon of enigmatic function that we recently reported from plastid genomes of two distantly related eustigmatophytes and from various non-rickettsialean bacteria. Strikingly, the eustigmatophyte operon is closely related to the one from Phycorickettsia, suggesting a gene transfer event between the endosymbiont and host lineages in early eustigmatophyte evolution. We hypothesize an important role of the operon in the physiology of Phycorickettsia infection and a long-term eustigmatophyte-Phycorickettsia coexistence.}, }
@article {pmid29880023, year = {2018}, author = {Méheust, R and Watson, AK and Lapointe, FJ and Papke, RT and Lopez, P and Bapteste, E}, title = {Hundreds of novel composite genes and chimeric genes with bacterial origins contributed to haloarchaeal evolution.}, journal = {Genome biology}, volume = {19}, number = {1}, pages = {75}, pmid = {29880023}, issn = {1474-760X}, support = {#615274//FP7 Ideas: European Research Council/International ; 1716046//National Science Foundation/International ; NNX15AM09G/NASA/NASA/United States ; OGP249644//Natural Sciences and Engineering Research Council of Canada/International ; }, mesh = {Amino Acids/genetics ; Archaea/*genetics ; Archaeal Proteins/genetics ; Bacteria/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genes, Archaeal/*genetics ; Genes, Bacterial/*genetics ; Genome, Archaeal/genetics ; Genome, Bacterial/genetics ; }, abstract = {BACKGROUND: Haloarchaea, a major group of archaea, are able to metabolize sugars and to live in oxygenated salty environments. Their physiology and lifestyle strongly contrast with that of their archaeal ancestors. Amino acid optimizations, which lowered the isoelectric point of haloarchaeal proteins, and abundant lateral gene transfers from bacteria have been invoked to explain this deep evolutionary transition. We use network analyses to show that the evolution of novel genes exclusive to Haloarchaea also contributed to the evolution of this group.<br><br>RESULTS: We report the creation of 320 novel composite genes, both early in the evolution of Haloarchaea during haloarchaeal genesis and later in diverged haloarchaeal groups. One hundred and twenty-six of these novel composite genes derived from genetic material from bacterial genomes. These latter genes, largely involved in metabolic functions but also in oxygenic lifestyle, constitute a different gene pool from the laterally acquired bacterial genes formerly identified. These novel composite genes were likely advantageous for their hosts, since they show significant residence times in haloarchaeal genomes-consistent with a long phylogenetic history involving vertical descent and lateral gene transfer-and encode proteins with optimized isoelectric points.<br><br>CONCLUSIONS: Overall, our work encourages a systematic search for composite genes across all archaeal major groups, in order to better understand the origins of novel prokaryotic genes, and in order to test to what extent archaea might have adjusted their lifestyles by incorporating and recycling laterally acquired bacterial genetic fragments into new archaeal genes.}, }
@article {pmid29879198, year = {2018}, author = {Nonaka, L and Yamamoto, T and Maruyama, F and Hirose, Y and Onishi, Y and Kobayashi, T and Suzuki, S and Nomura, N and Masuda, M and Yano, H}, title = {Interplay of a non-conjugative integrative element and a conjugative plasmid in the spread of antibiotic resistance via suicidal plasmid transfer from an aquaculture Vibrio isolate.}, journal = {PloS one}, volume = {13}, number = {6}, pages = {e0198613}, pmid = {29879198}, issn = {1932-6203}, mesh = {Aquaculture ; Aquatic Organisms/drug effects/genetics/*physiology ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/drug effects/genetics/*physiology ; Gene Transfer, Horizontal ; R Factors/*genetics ; Vibrio/drug effects/genetics/*physiology ; Whole Genome Sequencing ; }, abstract = {The capture of antimicrobial resistance genes (ARGs) by mobile genetic elements (MGEs) plays a critical role in resistance acquisition for human-associated bacteria. Although aquaculture environments are recognized as important reservoirs of ARGs, intra- and intercellular mobility of MGEs discovered in marine organisms is poorly characterized. Here, we show a new pattern of interspecies ARGs transfer involving a 'non-conjugative' integrative element. To identify active MGEs in a Vibrio ponticus isolate, we conducted whole-genome sequencing of a transconjugant obtained by mating between Escherichia coli and Vibrio ponticus. This revealed integration of a plasmid (designated pSEA1) into the chromosome, consisting of a self-transmissible plasmid backbone of the MOBH group, ARGs, and a 13.8-kb integrative element Tn6283. Molecular genetics analysis suggested a two-step gene transfer model. First, Tn6283 integrates into the recipient chromosome during suicidal plasmid transfer, followed by homologous recombination between the Tn6283 copy in the chromosome and that in the newly transferred pSEA1. Tn6283 is unusual among integrative elements in that it apparently does not encode transfer function and its excision barely generates unoccupied donor sites. Thus, its movement is analogous to the transposition of insertion sequences rather than to that of canonical integrative and conjugative elements. Overall, this study reveals the presence of a previously unrecognized type of MGE in a marine organism, highlighting diversity in the mode of interspecies gene transfer.}, }
@article {pmid29876934, year = {2019}, author = {Mortimer, TD and Grad, YH}, title = {Applications of genomics to slow the spread of multidrug-resistant Neisseria gonorrhoeae.}, journal = {Annals of the New York Academy of Sciences}, volume = {1435}, number = {1}, pages = {93-109}, pmid = {29876934}, issn = {1749-6632}, support = {R01 AI132606/AI/NIAID NIH HHS/United States ; //Smith Family Foundation/International ; }, mesh = {Anti-Bacterial Agents/therapeutic use ; Drug Resistance, Bacterial ; *Genomics ; Gonorrhea/drug therapy/*epidemiology/*genetics ; Humans ; Molecular Epidemiology ; *Neisseria gonorrhoeae/genetics/pathogenicity ; *Whole Genome Sequencing ; }, abstract = {Infections with Neisseria gonorrhoeae, a sexually transmitted pathogen that causes urethritis, cervicitis, and more severe complications, are increasing. Gonorrhea is typically treated with antibiotics; however, N. gonorrhoeae has rapidly acquired resistance to many antibiotic classes, and lineages with reduced susceptibility to the currently recommended therapies are emerging worldwide. In this review, we discuss the contributions of whole genome sequencing (WGS) to our understanding of resistant N. gonorrhoeae. Genomics has illuminated the evolutionary origins and population structure of N. gonorrhoeae and the magnitude of horizontal gene transfer within and between Neisseria species. WGS can be used to predict the susceptibility of N. gonorrhoeae based on known resistance determinants, track the spread of these determinants throughout the N. gonorrhoeae population, and identify novel loci contributing to resistance. WGS has also allowed more detailed epidemiological analysis of transmission of N. gonorrhoeae between individuals and populations than previously used typing methods. Ongoing N. gonorrhoeae genomics will complement other laboratory techniques to understand the biology and evolution of the pathogen, improve diagnostics and treatment in the clinic, and inform public health policies to limit the impact of antibiotic resistance.}, }
@article {pmid29875435, year = {2018}, author = {Fillol-Salom, A and Martínez-Rubio, R and Abdulrahman, RF and Chen, J and Davies, R and Penadés, JR}, title = {Phage-inducible chromosomal islands are ubiquitous within the bacterial universe.}, journal = {The ISME journal}, volume = {12}, number = {9}, pages = {2114-2128}, pmid = {29875435}, issn = {1751-7370}, support = {/WT_/Wellcome Trust/United Kingdom ; MR/M003876/1/MRC_/Medical Research Council/United Kingdom ; BB/N002873/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 201531/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacteriophages/*physiology ; Chromosomes, Bacterial ; Gene Transfer, Horizontal ; *Genomic Islands ; Gram-Negative Bacteria/*genetics ; }, abstract = {Phage-inducible chromosomal islands (PICIs) are a recently discovered family of pathogenicity islands that contribute substantively to horizontal gene transfer, host adaptation and virulence in Gram-positive cocci. Here we report that similar elements also occur widely in Gram-negative bacteria. As with the PICIs from Gram-positive cocci, their uniqueness is defined by a constellation of features: unique and specific attachment sites, exclusive PICI genes, a phage-dependent mechanism of induction, conserved replication origin organization, convergent mechanisms of phage interference, and specific packaging of PICI DNA into phage-like infectious particles, resulting in very high transfer frequencies. We suggest that the PICIs represent two or more distinct lineages, have spread widely throughout the bacterial world, and have diverged much more slowly than their host organisms or their prophage cousins. Overall, these findings represent the discovery of a universal class of mobile genetic elements.}, }
@article {pmid29868925, year = {2018}, author = {Cole, MJ and Ison, C and Woodford, N}, title = {Transfer of a gonococcal β-lactamase plasmid into Neisseria gonorrhoeae belonging to the globally distributed ST1407 lineage.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {73}, number = {9}, pages = {2576-2577}, doi = {10.1093/jac/dky194}, pmid = {29868925}, issn = {1460-2091}, mesh = {Cefixime/pharmacology ; Ceftriaxone/pharmacology ; Ciprofloxacin/pharmacology ; *Gene Transfer, Horizontal ; Genotype ; Humans ; Microbial Sensitivity Tests ; Neisseria gonorrhoeae/classification/*enzymology/*genetics ; *Plasmids ; beta-Lactamases/*genetics ; }, }
@article {pmid29868902, year = {2019}, author = {Bertelli, C and Tilley, KE and Brinkman, FSL}, title = {Microbial genomic island discovery, visualization and analysis.}, journal = {Briefings in bioinformatics}, volume = {20}, number = {5}, pages = {1685-1698}, pmid = {29868902}, issn = {1477-4054}, mesh = {Databases, Genetic ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Machine Learning ; }, abstract = {Horizontal gene transfer (also called lateral gene transfer) is a major mechanism for microbial genome evolution, enabling rapid adaptation and survival in specific niches. Genomic islands (GIs), commonly defined as clusters of bacterial or archaeal genes of probable horizontal origin, are of particular medical, environmental and/or industrial interest, as they disproportionately encode virulence factors and some antimicrobial resistance genes and may harbor entire metabolic pathways that confer a specific adaptation (solvent resistance, symbiosis properties, etc). As large-scale analyses of microbial genomes increases, such as for genomic epidemiology investigations of infectious disease outbreaks in public health, there is increased appreciation of the need to accurately predict and track GIs. Over the past decade, numerous computational tools have been developed to tackle the challenges inherent in accurate GI prediction. We review here the main types of GI prediction methods and discuss their advantages and limitations for a routine analysis of microbial genomes in this era of rapid whole-genome sequencing. An assessment is provided of 20 GI prediction software methods that use sequence-composition bias to identify the GIs, using a reference GI data set from 104 genomes obtained using an independent comparative genomics approach. Finally, we present guidelines to assist researchers in effectively identifying these key genomic regions.}, }
@article {pmid29868511, year = {2018}, author = {Yang, Y and Zhou, M and Hardwidge, PR and Cui, H and Zhu, G}, title = {Isolation and Characterization of N-acyl Homoserine Lactone-Producing Bacteria From Cattle Rumen and Swine Intestines.}, journal = {Frontiers in cellular and infection microbiology}, volume = {8}, number = {}, pages = {155}, pmid = {29868511}, issn = {2235-2988}, mesh = {Acyl-Butyrolactones/*isolation &amp; purification/*metabolism ; Aeromonas hydrophila/isolation &amp; purification/metabolism ; Animals ; Bacteria/*classification/*isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics ; Cattle ; DNA, Ribosomal/genetics ; Escherichia coli/genetics ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Intestines/*microbiology ; Phylogeny ; Pseudomonas aeruginosa/isolation &amp; purification/metabolism ; Quorum Sensing/genetics ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Swine ; Transcription Factors/genetics ; }, abstract = {Quorum sensing systems regulate gene expression in response to bacterial population density. Acyl-homoserine lactones are a class of quorum sensing molecules found in cattle rumen that are thought to regulate the gene expression of enterohemorrhagic Escherichia coli and thus help this pathogen survive in animal gastrointestinal tracts. However, the specific bacteria that produce these signaling molecules in bovine and porcine gastrointestinal tracts are unknown. Here we developed methods to concentrate gastrointestinal fluids and screen the bacteria that produce acyl-homoserine lactones. We isolated a Pseudomonas aeruginosa strain YZ1 from cattle rumen, and an Aeromonas hydrophila strain YZ2 from pig intestine. Mass spectrometry analysis of culture supernatants indicated at least three specific classes of acyl-homoserine lactones produced by YZ1, and a C4-acyl-homoserine lactone produced by YZ2. Transformation of E. coli with P. aeruginosa or A. hydrophila luxI homologs,which can produce short- or long-chain acyl-homoserine lactones conferred upon E. coli the ability to synthesize acyl-homoserine lactones and affected gene expression, motility, and acid tolerance of E. coli. This is the first study reporting the isolation and characterization of acyl-homoserine lactone synthase-positive bacteria from cattle rumen and swine intestines.}, }
@article {pmid29867913, year = {2018}, author = {Morgado, SM and Vicente, ACP}, title = {Beyond the Limits: tRNA Array Units in Mycobacterium Genomes.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1042}, pmid = {29867913}, issn = {1664-302X}, abstract = {tRNA array unit, a genomic region presenting an intriguing high tRNA gene number and density, was supposed to occur only in few bacteria phyla, particularly Firmicutes. Here, we identified and characterized an abundance and diversity of tRNA array units in Mycobacterium associated genomes. These genomes comprised chromosome, bacteriophages and plasmids from mycobacteria. Firstly, we had identified 32 tRNA genes organized in an array unit within a mycobacteria plasmid genome and therefore, we hypothesized the presence of such structures in Mycobacterium genus. However, at the time, bioinformatics tools only predict tRNA genes, not characterizing their arrangement as arrays. In order to test our hypothesis, we developed and applied an in-house Perl script that identified tRNA genes organization as an array unit. This survey included a total of 7,670 complete and drafts genomes of Mycobacterium genus, 4312 mycobacteriophage genomes and 40 mycobacteria plasmids. We showed that tRNA array units are abundant in genomes associated to the Mycobacterium genus, mainly in Mycobacterium abscessus complex species, being spread in chromosome, prophage, and plasmid genomes. Moreover, other non-coding RNA species (tmRNA and structured RNA) were also identified in these regions. Our results revealed that tRNA array units are not restrict, as previously assumed, to few bacteria phyla and genomes being present in one of the most diverse bacteria genus. We also provide a bioinformatics tool that allows further exploration of this issue in huge genomic databases. The presence of tRNA array units in plasmids and bacteriophages, associated with horizontal gene transfer, and in a bacteria genus that explores diverse niches, are indicatives that tRNA array units have impact in the bacteria biology.}, }
@article {pmid29867876, year = {2018}, author = {Li, X and Tong, W and Wang, L and Rahman, SU and Wei, G and Tao, S}, title = {A Novel Strategy for Detecting Recent Horizontal Gene Transfer and Its Application to Rhizobium Strains.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {973}, pmid = {29867876}, issn = {1664-302X}, abstract = {Recent horizontal gene transfer (HGT) is crucial for enabling microbes to rapidly adapt to their novel environments without relying upon rare beneficial mutations that arise spontaneously. For several years now, computational approaches have been developed to detect HGT, but they typically lack the sensitivity and ability to detect recent HGT events. Here we introduce a novel strategy, named RecentHGT. The number of genes undergoing recent HGT between two bacterial genomes was estimated by a new algorithm derived from the expectation-maximization algorithm and is based on the theoretical sequence-similarity distribution of orthologous genes. We tested the proposed strategy by applying it to a set of 10 Rhizobium genomes, and detected several large-scale recent HGT events. We also found that our strategy was more sensitive than other available HGT detection methods. These HGT events were mainly mediated by symbiotic plasmids. Our new strategy can provide clear evidence of recent HGT events and thus it brings us closer to the goal of detecting these potentially adaptive evolution processes in rhizobia as well as pathogens.}, }
@article {pmid29867787, year = {2018}, author = {Sandner-Miranda, L and Vinuesa, P and Cravioto, A and Morales-Espinosa, R}, title = {The Genomic Basis of Intrinsic and Acquired Antibiotic Resistance in the Genus Serratia.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {828}, pmid = {29867787}, issn = {1664-302X}, abstract = {Serratia marcescens, a member of the Enterobacteriaceae family, was long thought to be a non-pathogenic bacterium prevalent in environmental habitats. Together with other members of this genus, it has emerged in recent years as an opportunistic nosocomial pathogen causing various types of infections. One important feature of pathogens belonging to this genus is their intrinsic and acquired resistance to a variety of antibiotic families, including β-lactam, aminoglycosides, quinolones and polypeptide antibiotics. The aim of this study was to elucidate which genes participate in the intrinsic and acquired antibiotic resistance of this genus in order to determine the Serratia genus resistome. We performed phylogenomic and comparative genomic analyses using 32 Serratia spp. genomes deposited in the NCBI GenBank from strains isolated from different ecological niches and different lifestyles. S. marcescens strain SmUNAM836, which was previously isolated from a Mexican adult with obstructive pulmonary disease, was included in this study. The results show that most of the antibiotic resistance genes (ARGs) were found on the chromosome, and to a lesser degree, on plasmids and transposons acquired through horizontal gene transfer. Four strains contained the gyrA point mutation in codon Ser83 that confers quinolone resistance. Pathogenic and environmental isolates presented a high number of ARGs, especially genes associated with efflux systems. Pathogenic strains, specifically nosocomial strains, presented more acquired resistance genes than environmental isolates. We may conclude that the environment provides a natural reservoir for antibiotic resistance, which has been underestimated in the medical field.}, }
@article {pmid29867096, year = {2018}, author = {Breitbart, M and Bonnain, C and Malki, K and Sawaya, NA}, title = {Phage puppet masters of the marine microbial realm.}, journal = {Nature microbiology}, volume = {3}, number = {7}, pages = {754-766}, pmid = {29867096}, issn = {2058-5276}, mesh = {Bacteria/*growth &amp; development/virology ; Bacteriophages/*physiology ; Ecological and Environmental Phenomena ; Gene Transfer, Horizontal ; Host-Pathogen Interactions ; Seawater/*microbiology ; }, abstract = {Viruses numerically dominate our oceans; however, we have only just begun to document the diversity, host range and infection dynamics of marine viruses, as well as the subsequent effects of infection on both host cell metabolism and oceanic biogeochemistry. Bacteriophages (that is, phages: viruses that infect bacteria) are highly abundant and are known to play critical roles in bacterial mortality, biogeochemical cycling and horizontal gene transfer. This Review Article summarizes current knowledge of marine viral ecology and highlights the importance of phage particles to the dissolved organic matter pool, as well as the complex interactions between phages and their bacterial hosts. We emphasize the newly recognized roles of phages as puppet masters of their bacterial hosts, where phages are capable of altering the metabolism of infected bacteria through the expression of auxiliary metabolic genes and the redirection of host gene expression patterns. Finally, we propose the 'royal family model' as a hypothesis to describe successional patterns of bacteria and phages over time in marine systems, where despite high richness and significant seasonal differences, only a small number of phages appear to continually dominate a given marine ecosystem. Although further testing is required, this model provides a framework for assessing the specificity and ecological consequences of phage-host dynamics.}, }
@article {pmid29866828, year = {2018}, author = {Wang, CY and Patel, N and Wholey, WY and Dawid, S}, title = {ABC transporter content diversity in Streptococcus pneumoniae impacts competence regulation and bacteriocin production.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {25}, pages = {E5776-E5785}, pmid = {29866828}, issn = {1091-6490}, support = {R01 AI101285/AI/NIAID NIH HHS/United States ; R56 AI101285/AI/NIAID NIH HHS/United States ; T32 AI007528/AI/NIAID NIH HHS/United States ; T32 GM007863/GM/NIGMS NIH HHS/United States ; }, mesh = {ATP-Binding Cassette Transporters/*metabolism ; Animals ; Bacterial Proteins/*metabolism ; Bacteriocins/*metabolism ; Female ; Gene Expression Regulation, Bacterial/physiology ; Membrane Transport Proteins/metabolism ; Mice ; Mice, Inbred BALB C ; Nasopharynx/metabolism/microbiology ; Pheromones/metabolism ; Streptococcus pneumoniae/*metabolism ; }, abstract = {The opportunistic pathogen Streptococcus pneumoniae (pneumococcus) uses natural genetic competence to increase its adaptability through horizontal gene transfer. One method of acquiring DNA is through predation of neighboring strains with antimicrobial peptides called "bacteriocins." Competence and production of the major family of pneumococcal bacteriocins, pneumocins, are regulated by the quorum-sensing systems com and blp, respectively. In the classical paradigm, the ABC transporters ComAB and BlpAB each secretes its own system's signaling pheromone and in the case of BlpAB also secretes the pneumocins. While ComAB is found in all pneumococci, only 25% of strains encode an intact version of BlpAB [BlpAB(+)] while the rest do not [BlpAB(-)]. Contrary to the classical paradigm, it was previously shown that BlpAB(-) strains can activate blp through ComAB-mediated secretion of the blp pheromone during brief periods of competence. To better understand the full extent of com-blp crosstalk, we examined the contribution of each transporter to competence development and pneumocin secretion. We found that BlpAB(+) strains have a greater capacity for competence activation through BlpAB-mediated secretion of the com pheromone. Similarly, we show that ComAB and BlpAB are promiscuous and both can secrete pneumocins. Consequently, differences in pneumocin secretion between BlpAB(+) and BlpAB(-) strains derive from the regulation and kinetics of transporter expression rather than substrate specificity. We speculate that BlpAB(-) strains (opportunists) use pneumocins mainly in a narrowly tailored role for DNA acquisition and defense during competence while BlpAB(+) strains (aggressors) expand their use for the general inhibition of rival strains.}, }
@article {pmid29866485, year = {2018}, author = {Garin-Fernandez, A and Pereira-Flores, E and Glöckner, FO and Wichels, A}, title = {The North Sea goes viral: Occurrence and distribution of North Sea bacteriophages.}, journal = {Marine genomics}, volume = {41}, number = {}, pages = {31-41}, doi = {10.1016/j.margen.2018.05.004}, pmid = {29866485}, issn = {1876-7478}, mesh = {Bacteriophages/classification/*physiology ; *Biodiversity ; Metagenomics ; North Sea ; Water Movements ; }, abstract = {Marine viruses are dominated by phages and have an enormous influence on microbial population dynamics, due to lysis and horizontal gene transfer. The aim of this study is to analyze the occurrence and diversity of phages in the North Sea, considering the virus-host interactions and biogeographic factors. The virus community of four sampling stations were described using virus metagenomics (viromes). The results show that the virus community was not evenly distributed throughout the North Sea. The dominant phage members were identified as unclassified phage group, followed by Caudovirales order. Myoviridae was the dominant phage family in the North Sea, which occurrence decreased from the coast to the open sea. In contrast, the occurrence of Podoviridae increased and the occurrence of Siphoviridae was low throughout the North Sea. The occurrence of other groups such as Phycodnaviridae decreased from the coast to the open sea. The coastal virus community was genetically more diverse than the open sea community. The influence of riverine inflow and currents, for instance the English Channel flow affects the genetic virus diversity with the community carrying genes from a variety of metabolic pathways and other functions. The present study offers the first insights in the virus community in the North Sea using viromes and shows the variation in virus diversity and the genetic information moved from coastal to open sea areas.}, }
@article {pmid29862249, year = {2018}, author = {Xu, L and Yin, M and Zhu, T and Liu, Y and Ying, Y and Lu, J and Lin, C and Ying, J and Xu, T and Ni, L and Bao, Q and Lu, S}, title = {Comparative Genomics Analysis of Plasmid pPV989-94 from a Clinical Isolate of Pantoea vagans PV989.}, journal = {International journal of genomics}, volume = {2018}, number = {}, pages = {1242819}, pmid = {29862249}, issn = {2314-436X}, abstract = {Pantoea vagans, a gram-negative bacterium from the genus Pantoea and family Enterobacteriaceae, is present in various natural environments and considered to be plant endophytes. We isolated the Pantoea vagans PV989 strain from the clinic and sequenced its whole genome. Besides a chromosome DNA molecule, it also harboured three large plasmids. A comparative genomics analysis was performed for the smallest plasmid, pPV989-94. It can be divided into four regions, including three conservative regions related to replication (R1), transfer conjugation (R2), and transfer leading (R3), and one variable region (R4). Further analysis showed that pPV989-94 is most similar to plasmids LA637P2 and pEA68 of Erwinia amylovora strains isolated from fruit trees. These three plasmids share three conservative regions (R1, R2, and R3). Interestingly, a fragment (R4') in R4, mediated by phage integrase and phage integrase family site-specific recombinase and encoding 9 genes related to glycometabolism, resistance, and DNA repair, was unique in pPV989-94. Homologues of R4' were found in other plasmids or chromosomes, suggesting that horizontal gene transfer (HGT) occurred among different bacteria of various species or genera. The acquired functional genes may play important roles in the adaptation of bacteria to different hosts or environmental conditions.}, }
@article {pmid29860283, year = {2018}, author = {Tsai, YM and Chang, A and Kuo, CH}, title = {Horizontal Gene Acquisitions Contributed to Genome Expansion in Insect-Symbiotic Spiroplasma clarkii.}, journal = {Genome biology and evolution}, volume = {10}, number = {6}, pages = {1526-1532}, pmid = {29860283}, issn = {1759-6653}, mesh = {Animals ; Carbohydrates/genetics ; DNA, Bacterial/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome Size/genetics ; Genome, Bacterial/*genetics ; Insecta/*microbiology ; Phylogeny ; Spiroplasma/*growth &amp; development ; Symbiosis/*genetics ; }, abstract = {Genome reduction is a recurring theme of symbiont evolution. The genus Spiroplasma contains species that are mostly facultative insect symbionts. The typical genome sizes of those species within the Apis clade were estimated to be ∼1.0-1.4 Mb. Intriguingly, Spiroplasma clarkii was found to have a genome size that is >30% larger than the median of other species within the same clade. To investigate the molecular evolution events that led to the genome expansion of this bacterium, we determined its complete genome sequence and inferred the evolutionary origin of each protein-coding gene based on the phylogenetic distribution of homologs. Among the 1,346 annotated protein-coding genes, 641 were originated from within the Apis clade while 233 were putatively acquired from outside of the clade (including 91 high-confidence candidates). Additionally, 472 were specific to S. clarkii without homologs in the current database (i.e., the origins remained unknown). The acquisition of protein-coding genes, rather than mobile genetic elements, appeared to be a major contributing factor of genome expansion. Notably, >50% of the high-confidence acquired genes are related to carbohydrate transport and metabolism, suggesting that these acquired genes contributed to the expansion of both genome size and metabolic capability. The findings of this work provided an interesting case against the general evolutionary trend observed among symbiotic bacteria and further demonstrated the flexibility of Spiroplasma genomes. For future studies, investigation on the functional integration of these acquired genes, as well as the inference of their contribution to fitness could improve our knowledge of symbiont evolution.}, }
@article {pmid29859211, year = {2018}, author = {Fan, Y and Xiao, Y and Momeni, B and Liu, YY}, title = {Horizontal gene transfer can help maintain the equilibrium of microbial communities.}, journal = {Journal of theoretical biology}, volume = {454}, number = {}, pages = {53-59}, doi = {10.1016/j.jtbi.2018.05.036}, pmid = {29859211}, issn = {1095-8541}, mesh = {Ecosystem ; Gene Transfer, Horizontal/*physiology ; Genotype ; Homeostasis/genetics ; Microbial Interactions/*genetics ; Microbiota/genetics/*physiology ; *Models, Biological ; Models, Genetic ; Population Dynamics ; }, abstract = {Horizontal gene transfer and species coexistence are two focal points in the study of microbial communities. Yet, the evolutionary advantage of horizontal gene transfer has not been well understood and is constantly being debated. Here we propose a simple population dynamics model based on frequency-dependent genotype interactions to evaluate the influence of horizontal gene transfer on microbial communities. In particular, we examine the structural stability of coexistence (i.e., the capability of the system to maintain species coexistence in response to small changes in parameters), as well as the robustness (defined as the maximal degree of perturbation the system can sustain around a stable coexistence steady state) of microbial communities. We find that both structural stability of coexistence and robustness of the microbial community are strongly affected by the gene transfer rate and direction. An optimal gene flux can stabilize the ecosystem, helping it recover from disturbance and maintain the species coexistence.}, }
@article {pmid29859036, year = {2018}, author = {Adamek, M and Alanjary, M and Sales-Ortells, H and Goodfellow, M and Bull, AT and Winkler, A and Wibberg, D and Kalinowski, J and Ziemert, N}, title = {Comparative genomics reveals phylogenetic distribution patterns of secondary metabolites in Amycolatopsis species.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {426}, pmid = {29859036}, issn = {1471-2164}, support = {TTU 9.704//Deutsches Zentrum f&#xfc;r Infektionsforschung/ ; 031A533//Bielefeld-Gie&#xdf;en Center for Microbial Bioinformatics/ ; Emeritus Fellowship//Leverhulme Trust/ ; }, mesh = {Actinomycetales/*genetics/*metabolism ; Genome, Bacterial/genetics ; *Genomics ; Multigene Family/genetics ; *Phylogeny ; Secondary Metabolism/*genetics ; }, abstract = {BACKGROUND: Genome mining tools have enabled us to predict biosynthetic gene clusters that might encode compounds with valuable functions for industrial and medical applications. With the continuously increasing number of genomes sequenced, we are confronted with an overwhelming number of predicted clusters. In order to guide the effective prioritization of biosynthetic gene clusters towards finding the most promising compounds, knowledge about diversity, phylogenetic relationships and distribution patterns of biosynthetic gene clusters is necessary.<br><br>RESULTS: Here, we provide a comprehensive analysis of the model actinobacterial genus Amycolatopsis and its potential for the production of secondary metabolites. A phylogenetic characterization, together with a pan-genome analysis showed that within this highly diverse genus, four major lineages could be distinguished which differed in their potential to produce secondary metabolites. Furthermore, we were able to distinguish gene cluster families whose distribution correlated with phylogeny, indicating that vertical gene transfer plays a major role in the evolution of secondary metabolite gene clusters. Still, the vast majority of the diverse biosynthetic gene clusters were derived from clusters unique to the genus, and also unique in comparison to a database of known compounds. Our study on the locations of biosynthetic gene clusters in the genomes of Amycolatopsis' strains showed that clusters acquired by horizontal gene transfer tend to be incorporated into non-conserved regions of the genome thereby allowing us to distinguish core and hypervariable regions in Amycolatopsis genomes.<br><br>CONCLUSIONS: Using a comparative genomics approach, it was possible to determine the potential of the genus Amycolatopsis to produce a huge diversity of secondary metabolites. Furthermore, the analysis demonstrates that horizontal and vertical gene transfer play an important role in the acquisition and maintenance of valuable secondary metabolites. Our results cast light on the interconnections between secondary metabolite gene clusters and provide a way to prioritize biosynthetic pathways in the search and discovery of novel compounds.}, }
@article {pmid29857552, year = {2018}, author = {Roszniowski, B and McClean, S and Drulis-Kawa, Z}, title = {Burkholderia cenocepacia Prophages-Prevalence, Chromosome Location and Major Genes Involved.}, journal = {Viruses}, volume = {10}, number = {6}, pages = {}, pmid = {29857552}, issn = {1999-4915}, mesh = {Burkholderia cenocepacia/*genetics/virology ; Burkholderia cepacia complex/genetics/virology ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; *Genome, Bacterial ; *Genome, Viral ; Humans ; Lysogeny ; Prevalence ; Prophages/*genetics ; Sequence Analysis, DNA ; Toxin-Antitoxin Systems/genetics ; Virulence Factors/genetics ; }, abstract = {Burkholderia cenocepacia, is a Gram-negative opportunistic pathogen that belongs to Burkholderia cepacia complex (BCC) group. BCC representatives carry various pathogenicity factors and can infect humans and plants. Phages as bacterial viruses play a significant role in biodiversity and ecological balance in the environment. Specifically, horizontal gene transfer (HGT) and lysogenic conversion (temperate phages) influence microbial diversification and fitness. In this study, we describe the prevalence and gene content of prophages in 16 fully sequenced B. cenocepacia genomes stored in NCBI database. The analysis was conducted in silico by manual and automatic approaches. Sixty-three potential prophage regions were found and classified as intact, incomplete, questionable, and artifacts. The regions were investigated for the presence of known virulence factors, resulting in the location of sixteen potential pathogenicity mechanisms, including toxin[-]antitoxin systems (TA), Major Facilitator Superfamily (MFS) transporters and responsible for drug resistance. Investigation of the region's closest neighborhood highlighted three groups of genes with the highest occurrence-tRNA-Arg, dehydrogenase family proteins, and ABC transporter substrate-binding proteins. Searches for antiphage systems such as BacteRiophage EXclusion (BREX) and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) in the analyzed strains suggested 10 sequence sets of CRISPR elements. Our results suggest that intact B. cenocepacia prophages may provide an evolutionary advantage to the bacterium, while domesticated prophages may help to maintain important genes.}, }
@article {pmid29856934, year = {2018}, author = {Sundin, GW and Wang, N}, title = {Antibiotic Resistance in Plant-Pathogenic Bacteria.}, journal = {Annual review of phytopathology}, volume = {56}, number = {}, pages = {161-180}, doi = {10.1146/annurev-phyto-080417-045946}, pmid = {29856934}, issn = {1545-2107}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects ; Biological Evolution ; *Drug Resistance, Microbial ; *Microbiota ; Plant Diseases/*microbiology ; }, abstract = {Antibiotics have been used for the management of relatively few bacterial plant diseases and are largely restricted to high-value fruit crops because of the expense involved. Antibiotic resistance in plant-pathogenic bacteria has become a problem in pathosystems where these antibiotics have been used for many years. Where the genetic basis for resistance has been examined, antibiotic resistance in plant pathogens has most often evolved through the acquisition of a resistance determinant via horizontal gene transfer. For example, the strAB streptomycin-resistance genes occur in Erwinia amylovora, Pseudomonas syringae, and Xanthomonas campestris, and these genes have presumably been acquired from nonpathogenic epiphytic bacteria colocated on plant hosts under antibiotic selection. We currently lack knowledge of the effect of the microbiome of commensal organisms on the potential of plant pathogens to evolve antibiotic resistance. Such knowledge is critical to the development of robust resistance management strategies to ensure the safe and effective continued use of antibiotics in the management of critically important diseases.}, }
@article {pmid29855603, year = {2018}, author = {González-Tortuero, E and Rodríguez-Beltrán, J and Radek, R and Blázquez, J and Rodríguez-Rojas, A}, title = {Clay-induced DNA breaks as a path for genetic diversity, antibiotic resistance, and asbestos carcinogenesis.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {8504}, pmid = {29855603}, issn = {2045-2322}, mesh = {Animal Husbandry ; Animals ; Asbestos/*adverse effects ; Carcinogenesis/*chemically induced ; Clay/chemistry ; *DNA Breaks, Double-Stranded/drug effects ; *Drug Resistance, Microbial ; Escherichia coli/drug effects/*genetics ; Gene Transfer, Horizontal ; Magnesium Silicates/*adverse effects/chemistry ; Mutagenesis/drug effects ; }, abstract = {Natural clays and synthetic nanofibres can have a severe impact on human health. After several decades of research, the molecular mechanism of how asbestos induces cancer is not well understood. Different fibres, including asbestos, can penetrate cell membranes and introduce foreign DNA in bacterial and eukaryotic cells. Incubating Escherichia coli under friction forces with sepiolite, a clayey material, or with asbestos, causes double-strand DNA breaks. Antibiotics and clays are used together in animal husbandry, the mutagenic effect of these fibres could be a pathway to antibiotic resistance due to the friction provided by peristalsis of the gut from farm animals in addition to horizontal gene transfer. Moreover, we raise the possibility that the same mechanism could generate bacteria diversity in natural scenarios, playing a role in the evolution of species. Finally, we provide a new model on how asbestos may promote mutagenesis and cancer based on the observed mechanical genotoxicity.}, }
@article {pmid29855598, year = {2018}, author = {Bulagonda, EP and Manivannan, B and Mahalingam, N and Lama, M and Chanakya, PP and Khamari, B and Jadhao, S and Vasudevan, M and Nagaraja, V}, title = {Comparative genomic analysis of a naturally competent Elizabethkingia anophelis isolated from an eye infection.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {8447}, pmid = {29855598}, issn = {2045-2322}, mesh = {Aged ; Anti-Bacterial Agents/pharmacology ; Comparative Genomic Hybridization ; Drug Resistance, Bacterial/drug effects/genetics ; Endophthalmitis/*microbiology/pathology ; Flavobacteriaceae/classification/*genetics/metabolism/pathogenicity ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; Phylogeny ; Virulence/genetics ; }, abstract = {Elizabethkingia anophelis has now emerged as an opportunistic human pathogen. However, its mechanisms of transmission remain unexplained. Comparative genomic (CG) analysis of E. anopheles endophthalmitis strain surprisingly found from an eye infection patient with twenty-five other E. anophelis genomes revealed its potential to participate in horizontal gene transfer. CG analysis revealed that the study isolate has an open pan genome and has undergone extensive gene rearrangements. We demonstrate that the strain is naturally competent, hitherto not reported in any members of Elizabethkingia. Presence of competence related genes, mobile genetic elements, Type IV, VI secretory systems and a unique virulence factor arylsulfatase suggests a different lineage of the strain. Deciphering the genome of E. anophelis having a reservoir of antibiotic resistance genes and virulence factors associated with diverse human infections may open up avenues to deal with the myriad of its human infections and devise strategies to combat the pathogen.}, }
@article {pmid29853205, year = {2018}, author = {Gyogluu, C and Jaiswal, SK and Kyei-Boahen, S and Dakora, FD}, title = {Identification and distribution of microsymbionts associated with soybean nodulation in Mozambican soils.}, journal = {Systematic and applied microbiology}, volume = {41}, number = {5}, pages = {506-515}, pmid = {29853205}, issn = {1618-0984}, mesh = {Bradyrhizobium/*classification/genetics/*isolation &amp; purification ; DNA, Bacterial/genetics ; Genes, Bacterial/genetics ; Genes, Essential/genetics ; Genetic Variation ; Genome, Bacterial/genetics ; Mozambique ; Nitrogen Fixation/genetics ; *Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Root Nodules, Plant/*microbiology ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; Glycine max/*microbiology ; Symbiosis/genetics/*physiology ; }, abstract = {Indigenous soybean rhizobial strains were isolated from root nodules sampled from farmers' fields in Mozambique to determine their identity, distribution and symbiotic relationships. Plant infection assays revealed variable nodulation and symbiotic effectiveness among the 43 bacterial isolates tested. Strains from Ruace generally promoted greater whole-plant growth than the others. 16S rRNA-RFLP analysis of genomic DNA extracted from the rhizobial isolates produced different banding patterns, a clear indication of high bacterial diversity. However, the multilocus sequence analysis (MLSA) data showed alignment of the isolates with B. elkanii species. The 16S rRNA sequences of representative soybean isolates selected from each 16S rRNA-RFLP cluster showed their relatedness to B. elkanii, as well as to other Bradyrhizobium species. But a concatenated phylogeny of two housekeeping genes (glnII and gyrB) identified the soybean nodulating isolates as Bradyrhizobium, with very close relatedness to B. elkanii. The nifH and nodC sequences also showed that the majority of the test soybean isolates were closely related to B. elkanii, albeit the inconsistency with some isolates. Taken together, these findings suggest that the B. elkanii group are the preferred dominant microsymbiont of soybean grown in Mozambican soils. Furthermore, the distribution of soybean rhizobia in the agricultural soils of Mozambique was found to be markedly influenced by soil pH, followed by the concentrations of plant-available P and Mn. This study suggested that the identified isolates TUTMJM5, TUTMIITA5A and TUTLBC2B can be used as inoculants for increased soybean production in Mozambique.}, }
@article {pmid29851413, year = {2018}, author = {Coertze, RD and Bezuidenhout, CC}, title = {The prevalence and diversity of AmpC β-lactamase genes in plasmids from aquatic systems.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {2017}, number = {2}, pages = {603-611}, doi = {10.2166/wst.2018.188}, pmid = {29851413}, issn = {0273-1223}, mesh = {Bacteria/*classification/genetics ; Bacterial Proteins/*analysis ; Plasmids/*analysis ; Rivers/*microbiology ; South Africa ; beta-Lactamases/*analysis ; }, abstract = {This study aimed to investigate the presence and diversity of AmpC β-lactamase and integrase genes among DNA (genomic and plasmid) from bacterial populations in selected aquatic systems. Following an enrichment step, DNA was isolated and subjected to polymerase chain reaction (PCR) and digital droplet PCR. The intI1 gene and AmpC β-lactamase genes were present in genomic and plasmid DNA from all sites in the Mooi, Crocodile and Marico Rivers, with the exception of intI1 in the Marico River. Digital droplet PCR demonstrated that copy numbers varied considerably (0.0 to 29.38 copies per picogram of DNA). Some samples in which ampC was not detected, intI1 was present. Amplicons of ampC genes were subjected to restriction digest using HindIII. Samples where the restriction markers were absent were purified by cloning followed by plasmid extraction, PCR amplification, and sequencing of individual AmpC gene fragments. Phylogenetic analysis identified all positive AmpC genes as Class C β-lactamases, comprising of ampC, CMY- and ACT-families. Detecting AmpC and intl1 genes on plasmids suggests a high risk of horizontal gene transfer and potential dissemination of these and other antibiotic resistance genes surrounding immediate aquatic environments. Consequences of β-lactamase diversity in aquatic ecosystems are relatively unexplored in South African aquatic ecosystems.}, }
@article {pmid29850825, year = {2018}, author = {Gallagher, AL and Miller, SR}, title = {Expression of Novel Gene Content Drives Adaptation to Low Iron in the Cyanobacterium Acaryochloris.}, journal = {Genome biology and evolution}, volume = {10}, number = {6}, pages = {1484-1492}, pmid = {29850825}, issn = {1759-6653}, mesh = {Adaptation, Physiological/*genetics ; Cyanobacteria/*genetics ; DNA, Bacterial/genetics ; Evolution, Molecular ; Gene Dosage/genetics ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/*genetics ; Genes, Duplicate/genetics ; Genome, Bacterial/*genetics ; Iron/*metabolism ; }, abstract = {Variation in genome content is a potent mechanism of microbial adaptation. The genomes of members of the cyanobacterial genus Acaryochloris vary greatly in gene content as a consequence of the idiosyncratic retention of both recent gene duplicates and plasmid-encoded genes acquired by horizontal transfer. For example, the genome of Acaryochloris strain MBIC11017, which was isolated from an iron-limited environment, is enriched in duplicated and novel genes involved in iron assimilation. Here, we took an integrative approach to characterize the adaptation of Acaryochloris MBIC11017 to low environmental iron availability and the relative contributions of the expression of duplicated versus novel genes. We observed that Acaryochloris MBIC11017 grew faster and to a higher yield in the presence of nanomolar concentrations of iron than did a closely related strain. These differences were associated with both a higher rate of iron assimilation and a greater abundance of iron assimilation transcripts. However, recently duplicated genes contributed little to increased transcript dosage; rather, the maintenance of these duplicates in the MBIC11017 genome is likely due to the sharing of ancestral dosage by expression reduction. Instead, novel, horizontally transferred genes are responsible for the differences in transcript abundance. The study provides insights on the mechanisms of adaptive genome evolution and gene expression in Acaryochloris.}, }
@article {pmid29850801, year = {2018}, author = {Nishiyama, E and Ohshima, K}, title = {Cross-Kingdom Commonality of a Novel Insertion Signature of RTE-Related Short Retroposons.}, journal = {Genome biology and evolution}, volume = {10}, number = {6}, pages = {1471-1483}, pmid = {29850801}, issn = {1759-6653}, mesh = {Animals ; DNA Transposable Elements/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome, Plant/genetics ; Lizards/genetics ; Long Interspersed Nucleotide Elements/genetics ; Magnoliopsida/genetics ; Mammals/genetics ; Microsatellite Repeats/genetics ; Mutagenesis, Insertional/methods ; Phylogeny ; Retroelements/*genetics ; Reverse Transcription/genetics ; Short Interspersed Nucleotide Elements/genetics ; }, abstract = {In multicellular organisms, such as vertebrates and flowering plants, horizontal transfer (HT) of genetic information is thought to be a rare event. However, recent findings unveiled unexpectedly frequent HT of RTE-clade LINEs. To elucidate the molecular footprints of the genomic integration machinery of RTE-related retroposons, the sequence patterns surrounding the insertion sites of plant Au-like SINE families were analyzed in the genomes of a wide variety of flowering plants. A novel and remarkable finding regarding target site duplications (TSDs) for SINEs was they start with thymine approximately one helical pitch (ten nucleotides) downstream of a thymine stretch. This TSD pattern was found in RTE-clade LINEs, which share the 3'-end sequence of these SINEs, in the genome of leguminous plants. These results demonstrably show that Au-like SINEs were mobilized by the enzymatic machinery of RTE-clade LINEs. Further, we discovered the same TSD pattern in animal SINEs from lizard and mammals, in which the RTE-clade LINEs sharing the 3'-end sequence with these animal SINEs showed a distinct TSD pattern. Moreover, a significant correlation was observed between the first nucleotide of TSDs and microsatellite-like sequences found at the 3'-ends of SINEs and LINEs. We propose that RTE-encoded protein could preferentially bind to a DNA region that contains a thymine stretch to cleave a phosphodiester bond downstream of the stretch. Further, determination of cleavage sites and/or efficiency of primer sites for reverse transcription may depend on microsatellite-like repeats in the RNA template. Such a unique mechanism may have enabled retroposons to successfully expand in frontier genomes after HT.}, }
@article {pmid29850800, year = {2018}, author = {Guillory, WX and Onyshchenko, A and Ruck, EC and Parks, M and Nakov, T and Wickett, NJ and Alverson, AJ}, title = {Recurrent Loss, Horizontal Transfer, and the Obscure Origins of Mitochondrial Introns in Diatoms (Bacillariophyta).}, journal = {Genome biology and evolution}, volume = {10}, number = {6}, pages = {1504-1515}, pmid = {29850800}, issn = {1759-6653}, mesh = {DNA, Mitochondrial/genetics ; Diatoms/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome, Mitochondrial/*genetics ; Introns/*genetics ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {We sequenced mitochondrial genomes from five diverse diatoms (Toxarium undulatum, Psammoneis japonica, Eunotia naegelii, Cylindrotheca closterium, and Nitzschia sp.), chosen to fill important phylogenetic gaps and help us characterize broadscale patterns of mitochondrial genome evolution in diatoms. Although gene content was strongly conserved, intron content varied widely across species. The vast majority of introns were of group II type and were located in the cox1 or rnl genes. Although recurrent intron loss appears to be the principal underlying cause of the sporadic distributions of mitochondrial introns across diatoms, phylogenetic analyses showed that intron distributions superficially consistent with a recurrent-loss model were sometimes more complicated, implicating horizontal transfer as a likely mechanism of intron acquisition as well. It was not clear, however, whether diatoms were the donors or recipients of horizontally transferred introns, highlighting a general challenge in resolving the evolutionary histories of many diatom mitochondrial introns. Although some of these histories may become clearer as more genomes are sampled, high rates of intron loss suggest that the origins of many diatom mitochondrial introns are likely to remain unclear.}, }
@article {pmid29850463, year = {2018}, author = {García-Martínez, J and Maldonado, RD and Guzmán, NM and Mojica, FJM}, title = {The CRISPR conundrum: evolve and maybe die, or survive and risk stagnation.}, journal = {Microbial cell (Graz, Austria)}, volume = {5}, number = {6}, pages = {262-268}, pmid = {29850463}, issn = {2311-2638}, abstract = {CRISPR-Cas represents a prokaryotic defense mechanism against invading genetic elements. Although there is a diversity of CRISPR-Cas systems, they all share similar, essential traits. In general, a CRISPR-Cas system consists of one or more groups of DNA repeats named CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats), regularly separated by unique sequences referred to as spacers, and a set of functionally associated cas (CRISPR associated) genes typically located next to one of the repeat arrays. The origin of spacers is in many cases unknown but, when ascertained, they usually match foreign genetic molecules. The proteins encoded by some of the cas genes are in charge of the incorporation of new spacers upon entry of a genetic element. Other Cas proteins participate in generating CRISPR-spacer RNAs and perform the task of destroying nucleic acid molecules carrying sequences similar to the spacer. In this way, CRISPR-Cas provides protection against genetic intruders that could substantially affect the cell viability, thus acting as an adaptive immune system. However, this defensive action also hampers the acquisition of potentially beneficial, horizontally transferred genes, undermining evolution. Here we cover how the model bacterium Escherichia coli deals with CRISPR-Cas to tackle this major dilemma, evolution versus survival.}, }
@article {pmid29848774, year = {2018}, author = {Corvec, S}, title = {Clinical and Biological Features of Cutibacterium (Formerly Propionibacterium) avidum, an Underrecognized Microorganism.}, journal = {Clinical microbiology reviews}, volume = {31}, number = {3}, pages = {}, pmid = {29848774}, issn = {1098-6618}, mesh = {Actinomycetales Infections/diagnosis/drug therapy/*microbiology/*pathology ; Anti-Bacterial Agents/therapeutic use ; Humans ; Phylogeny ; Propionibacterium/*classification/*physiology ; }, abstract = {The recent description of the genus Cutibacterium has altered the taxonomy of Propionibacterium species. These organisms still belong to the genera of the skin coryneform group, and the most-studied species remains Cutibacterium acnes. Cutibacterium avidum is also a known skin commensal. This underrecognized microorganism can, however, act as a pathogen after bacterial seeding and can be considered opportunistic, causing either superficial or deep/invasive infections. It can cause numerous infections, including but not limited to breast infections, skin abscesses, infective endocarditis, and device-related infections. The ecological niche of C. avidum is clearly different from that of other members of the genus: it is found in the axillary region or at wet sites rather than in dry, exposed areas, and the number of microorganisms increases during puberty. Historically, it has been used for its ability to modulate the immune response and for its antitumor properties. Conventional microbial culture methods and identification processes allow for its accurate identification and characterization. Thanks to the modern omics tools used for phylogenomic approaches, understanding C. avidum pathogenesis (including host-bacterium interactions and virulence factor characterization) is becoming easier, allowing for more thorough molecular characterization. These analyses have revealed that C. avidum causes diverse diseases mediated by multiple virulence factors. The recent genome approach has revealed specific genomic regions within this species that are involved in adherence and biofilm formation as well as fitness, survival, and defense functions. Numerous regions show the presence of phages and horizontal gene transfer. C. avidum remains highly sensitive to a broad spectrum of antibiotics, such as β-lactams, fluoroquinolones, macrolides, and rifampin, although erythromycin and clindamycin resistance has been described. A long-term treatment regimen with a combination of antibiotics is required to successfully eliminate the remaining adherent bacteria, particularly in the case of deep infections after debridement surgery.}, }
@article {pmid29846396, year = {2018}, author = {Silveira, MC and Catanho, M and Miranda, AB}, title = {Genomic analysis of bifunctional Class C-Class D β-lactamases in environmental bacteria.}, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {113}, number = {8}, pages = {e180098}, pmid = {29846396}, issn = {1678-8060}, mesh = {Catalytic Domain/*genetics ; *Environmental Microbiology ; *Genomics ; Gram-Negative Bacteria/*enzymology/isolation &amp; purification ; beta-Lactamases/*genetics ; }, abstract = {β-lactamases, which are found in several bacterial species and environments, are the main cause of resistance to β-lactams in Gram-negative bacteria. In 2009, a protein (LRA-13) with two β-lactamase domains (one class C domain and one class D domain) was experimentally characterised, and an extended action spectrum against β-lactams consistent with two functional domains was found. Here, we present the results of searches in the non-redundant NCBI protein database that revealed the existence of a group of homologous bifunctional β-lactamases in the genomes of environmental bacteria. These findings suggest that bifunctional β-lactamases are widespread in nature; these findings also raise concern that bifunctional β-lactamases may be transferred to bacteria of clinical importance through lateral gene transfer mechanisms.}, }
@article {pmid29844490, year = {2018}, author = {Best, A and Jones, S and Abu Kwaik, Y}, title = {Mammalian Solute Carrier (SLC)-like transporters of Legionella pneumophila.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {8352}, pmid = {29844490}, issn = {2045-2322}, support = {R01 AI120244/AI/NIAID NIH HHS/United States ; }, mesh = {Acanthamoeba/genetics/metabolism ; Animals ; Bacterial Proteins/genetics ; Eukaryota/metabolism ; Humans ; Legionella pneumophila/genetics/metabolism/*physiology ; Macrophages/metabolism ; Mammals/metabolism ; Membrane Transport Proteins/*genetics/*metabolism ; }, abstract = {Acquisition of nutrients during intra-vacuolar growth of L. pneumophila within macrophages or amoebae is poorly understood. Since many genes of L. pneumophila are acquired by inter-kingdom horizontal gene transfer from eukaryotic hosts, we examined the presence of human solute carrier (SLC)-like transporters in the L. pneumophila genome using I-TASSER to assess structural alignments. We identified 11 SLC-like putative transporters in L. pneumophila that are structurally similar to SLCs, eight of which are amino acid transporters, and one is a tricarboxylate transporter. The two other transporters, LstA and LstB, are structurally similar to the human glucose transporter, SLC2a1/Glut1. Single mutants of lstA or lstB have decreased ability to import, while the lstA/lstB double mutant is severely defective for uptake of glucose. While lstA or lstB single mutants are not defective in intracellular proliferation within Acanthamoeba polyphaga and human monocyte-derived macrophages, the lstA/lstB double mutant is severely defective in both host cells. The two phenotypic defects of the lstA/lstB double mutant in uptake of glucose and intracellular replication are both restored upon complementation of either lstA or lstB. Our data show that the two glucose transporters, LstA and LstB, are redundant and are required for intracellular replication within human macrophages and amoebae.}, }
@article {pmid29813058, year = {2018}, author = {Hendrickson, HL and Barbeau, D and Ceschin, R and Lawrence, JG}, title = {Chromosome architecture constrains horizontal gene transfer in bacteria.}, journal = {PLoS genetics}, volume = {14}, number = {5}, pages = {e1007421}, pmid = {29813058}, issn = {1553-7404}, support = {R01-GM7809204/NH/NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; Chromosome Inversion ; Chromosomes/*genetics ; DNA Replication ; Gene Rearrangement/*genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Phylogeny ; *Selection, Genetic ; }, abstract = {Despite significant frequencies of lateral gene transfer between species, higher taxonomic groups of bacteria show ecological and phenotypic cohesion. This suggests that barriers prevent panmictic dissemination of genes via lateral gene transfer. We have proposed that most bacterial genomes have a functional architecture imposed by Architecture IMparting Sequences (AIMS). AIMS are defined as 8 base pair sequences preferentially abundant on leading strands, whose abundance and strand-bias are positively correlated with proximity to the replication terminus. We determined that inversions whose endpoints lie within a single chromosome arm, which would reverse the polarity of AIMS in the inverted region, are both shorter and less frequent near the replication terminus. This distribution is consistent with the increased selection on AIMS function in this region, thus constraining DNA rearrangement. To test the hypothesis that AIMS also constrain DNA transfer between genomes, AIMS were identified in genomes while ignoring atypical, potentially laterally-transferred genes. The strand-bias of AIMS within recently acquired genes was negatively correlated with the distance of those genes from their genome's replication terminus. This suggests that selection for AIMS function prevents the acquisition of genes whose AIMS are not found predominantly in the permissive orientation. This constraint has led to the loss of at least 18% of genes acquired by transfer in the terminus-proximal region. We used completely sequenced genomes to produce a predictive road map of paths of expected horizontal gene transfer between species based on AIMS compatibility between donor and recipient genomes. These results support a model whereby organisms retain introgressed genes only if the benefits conferred by their encoded functions outweigh the detriments incurred by the presence of foreign DNA lacking genome-wide architectural information.}, }
@article {pmid29807455, year = {2018}, author = {Shao, S and Hu, Y and Cheng, J and Chen, Y}, title = {Research progress on distribution, migration, transformation of antibiotics and antibiotic resistance genes (ARGs) in aquatic environment.}, journal = {Critical reviews in biotechnology}, volume = {38}, number = {8}, pages = {1195-1208}, doi = {10.1080/07388551.2018.1471038}, pmid = {29807455}, issn = {1549-7801}, mesh = {Animals ; Anti-Bacterial Agents/*analysis ; Bacteria/genetics ; Drug Resistance, Microbial/*genetics ; *Genes, Bacterial ; Humans ; Water Microbiology ; Water Pollutants/*analysis ; }, abstract = {Antimicrobial and antibiotics resistance caused by misuse or overuse of antibiotics exposure is a growing and significant threat to global public health. The spread and horizontal transfer of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) by the selective pressure of antibiotics in an aquatic environment is a major public health issue. To develop a better understanding of potential ecological risks die to antibiotics and ARGs, this study mainly summarizes research progress about: (i) the occurrence, concentration, fate, and potential ecological effects of antibiotics and ARGs in various aquatic environments, (ii) the threat, spread, and horizontal gene transfer (HGT) of ARGs, and (iii) the relationship between antibiotics, ARGs, and ARB. Finally, this review also proposes future research direction on antibiotics and ARGs.}, }
@article {pmid29807140, year = {2018}, author = {Grgic, M and Williamson, A and Kjæreng Bjerga, GE and Altermark, B and Leiros, I}, title = {Biochemical characterization of ParI, an orphan C5-DNA methyltransferase from Psychrobacter arcticus 273-4.}, journal = {Protein expression and purification}, volume = {150}, number = {}, pages = {100-108}, doi = {10.1016/j.pep.2018.05.012}, pmid = {29807140}, issn = {1096-0279}, mesh = {*Bacterial Proteins/biosynthesis/chemistry/genetics/isolation &amp; purification ; *DNA (Cytosine-5-)-Methyltransferases/biosynthesis/chemistry/genetics/isolation &amp; purification ; Enzyme Stability ; Hot Temperature ; Psychrobacter/*enzymology/genetics ; Recombinant Proteins/biosynthesis/chemistry/genetics/isolation &amp; purification ; }, abstract = {Cytosine-specific DNA methyltransferases are important enzymes in most living organisms. In prokaryotes, most DNA methyltransferases are members of the type II restriction-modification system where they methylate host DNA, thereby protecting it from digestion by the accompanying restriction endonucleases. DNA methyltransferases can also act as solitary enzymes having important roles in controlling gene expression, DNA replication, cell cycle and DNA post-replicative mismatch repair. They have potential applications in biotechnology, such as in labeling of biopolymers, DNA mapping or epigenetic analysis, as well as for general DNA-protein interaction studies. The parI gene from the psychrophilic bacterium Psychrobacter arcticus 273-4 encodes a cytosine-specific DNA methyltransferase. In this work, recombinant ParI was expressed and purified in fusion to either an N-terminal hexahistidine affinity tag, or a maltose binding protein following the hexahistidine affinity tag, for solubility improvement. After removal of the fusion partners, recombinant ParI was found to be monomeric by size exclusion chromatography, with its molecular mass estimated to be 54 kDa. The apparent melting temperature of the protein was 53 °C with no detectable secondary structures above 65 °C. Both recombinant and native ParI showed methyltransferase activity in vivo. In addition, MBP- and His-tagged ParI also demonstrated in vitro activity. Although the overall structure of ParI exhibits high thermal stability, the loss of in vitro activity upon removal of solubility tags or purification from the cellular milieu indicates that the catalytically active form is more labile. Horizontal gene transfer may explain the acquisition of a protein-encoding gene that does not display common cold-adapted features.}, }
@article {pmid29803035, year = {2018}, author = {Wang, Q and Zeng, X and Yang, Q and Yang, C}, title = {Identification of a bacteriophage from an environmental multidrug-resistant E. coli isolate and its function in horizontal transfer of ARGs.}, journal = {The Science of the total environment}, volume = {639}, number = {}, pages = {617-623}, doi = {10.1016/j.scitotenv.2018.05.213}, pmid = {29803035}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents ; Bacteria ; Bacteriophages/*growth &amp; development ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/isolation &amp; purification/*virology ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Wastewater/microbiology/virology ; }, abstract = {Horizontal transfer of ARGs was generally considered to be mediated by three methods - transformation, conjugation and transduction through phages - during which the contribution of bacteriophages to gene transfer in the environment is unclear or even questioned. In this study, a multiple-antibiotic-resistant Escherichia coli strain and its phage (YZ1) were isolated from a municipal wastewater treatment system. The results of the morphological and genomic analyses of phage YZ1 showed that it is a member of the T7 viral genus in the subfamily Autographivirinae. Its genome is similar to that of the E. coli phage K1F in both organization and sequence and does not encode ARGs. However, 28 paired reads in the raw sequencing data aligned to ARGs, including those promoting β-lactam, aminoglycoside, and fluoroquinolone resistance, among others. Quantitative PCR showed that ARGs were present in bacteriophage DNA (approximately 10[3] copies/mL) and were also detected in the bacterial host DNA. The results suggested that while infrequent, some ARG-carrying transducing phages were presumably generated by erroneous packaging during infection of antibiotic-resistant bacteria, which may create the possibility of horizontal transfer of ARGs.}, }
@article {pmid29802996, year = {2018}, author = {Hurtado, R and Carhuaricra, D and Soares, S and Viana, MVC and Azevedo, V and Maturrano, L and Aburjaile, F}, title = {Pan-genomic approach shows insight of genetic divergence and pathogenic-adaptation of Pasteurella multocida.}, journal = {Gene}, volume = {670}, number = {}, pages = {193-206}, doi = {10.1016/j.gene.2018.05.084}, pmid = {29802996}, issn = {1879-0038}, mesh = {Animals ; Gene Transfer, Horizontal ; Genetic Drift ; Genome, Bacterial ; Genomics/*methods ; Pasteurella Infections/*microbiology ; Pasteurella multocida/*classification/genetics/isolation &amp; purification/pathogenicity ; Phylogeny ; }, abstract = {Pasteurella multocida is a gram-negative, non-motile bacterial pathogen, which is associated with chronic and acute infections as snuffles, pneumonia, atrophic rhinitis, fowl cholera and hemorrhagic septicemia. These diseases affect a wide range of domestic animals, leading to significant morbidity and mortality and causing significant economic losses worldwide. Due to the interest in deciphering the genetic diversity and process adaptive between P. multocida strains, this work aimed was to perform a pan-genome analysis to evidence horizontal gene transfer and positive selection among 23 P. multocida strains isolated from distinct diseases and hosts. The results revealed an open pan-genome containing 3585 genes and an accessory genome presenting 1200 genes. The phylogenomic analysis based on the presence/absence of genes and islands exhibit high levels of plasticity, which reflects a high intraspecific diversity and a possible adaptive mechanism responsible for the specific disease manifestation between the established groups (pneumonia, fowl cholera, hemorrhagic septicemia and snuffles). Additionally, we identified differences in accessory genes among groups, which are involved in sugar metabolism and transport systems, virulence-related genes and a high concentration of hypothetical proteins. However, there was no specific indispensable functional mechanism to decisively correlate the presence of genes and their adaptation to a specific host/disease. Also, positive selection was found only for two genes from sub-group hemorrhagic septicemia, serotype B. This comprehensive comparative genome analysis will provide new insights of horizontal gene transfers that play an essential role in the diversification and adaptation mechanism into P. multocida species to a specific disease.}, }
@article {pmid29802609, year = {2018}, author = {Xiong, W and Sun, Y and Zeng, Z}, title = {Antimicrobial use and antimicrobial resistance in food animals.}, journal = {Environmental science and pollution research international}, volume = {25}, number = {19}, pages = {18377-18384}, pmid = {29802609}, issn = {1614-7499}, support = {31702290//the National Natural Science Foundation of China/ ; 31672608//the National Natural Science Foundation of China/ ; 2016A030311029//the Natural Science Foundation of Guangdong Province/ ; }, mesh = {Animal Husbandry/*methods ; Animals ; Animals, Domestic/*microbiology ; Anti-Infective Agents/*administration &amp; dosage ; *Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Humans ; }, abstract = {Antimicrobials have been widely used in food animals for growth promotion since the 1950s. Antimicrobial resistance emerges in animal production settings and frequently spreads to humans through the food chain and direct contact. There have been international efforts to restrict or ban antimicrobials used for both humans and animals. Denmark has taken positive strides in the development of a comprehensive database DANMAP to track antimicrobial usage and resistance. Although food animals are sources of antimicrobial resistance, there is little evidence that antimicrobial resistance originates from food animals. This review comprehensively introduces the history and trends of antimicrobial use, the emergence and spread of antimicrobial resistance in food animals provides suggestions to tackle the problems of the spread of antimicrobial resistance.}, }
@article {pmid29802195, year = {2018}, author = {Mertens, J and Aliyu, H and Cowan, DA}, title = {LEA Proteins and the Evolution of the WHy Domain.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {15}, pages = {}, pmid = {29802195}, issn = {1098-5336}, mesh = {Bacteria/chemistry/classification/genetics/*metabolism ; Bacterial Proteins/*chemistry/genetics/metabolism ; *Evolution, Molecular ; Phylogeny ; Plant Proteins/chemistry/genetics/*metabolism ; Plants/chemistry/classification/genetics/*metabolism ; Protein Domains ; }, abstract = {The late embryogenesis abundant (LEA) family is composed of a diverse collection of multidomain and multifunctional proteins found in all three domains of the tree of life, but they are particularly common in plants. Most members of the family are known to play an important role in abiotic stress response and stress tolerance in plants but are also part of the plant hypersensitive response to pathogen infection. The mechanistic basis for LEA protein functionality is still poorly understood. The group of LEA 2 proteins harbor one or more copies of a unique domain, the water stress and hypersensitive response (WHy) domain. This domain sequence has recently been identified as a unique open reading frame (ORF) in some bacterial genomes (mostly in the phylum Firmicutes), and the recombinant bacterial WHy protein has been shown to exhibit a stress tolerance phenotype in Escherichia coli and an in vitro protein denaturation protective function. Multidomain phylogenetic analyses suggest that the WHy protein gene sequence may have ancestral origins in the domain Archaea, with subsequent acquisition in Bacteria and eukaryotes via endosymbiont or horizontal gene transfer mechanisms. Here, we review the structure, function, and nomenclature of LEA proteins, with a focus on the WHy domain as an integral component of the LEA constructs and as an independent protein.}, }
@article {pmid29802189, year = {2018}, author = {Zolfaghari Emameh, R and Barker, HR and Hytönen, VP and Parkkila, S}, title = {Involvement of β-Carbonic Anhydrase Genes in Bacterial Genomic Islands and Their Horizontal Transfer to Protists.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {15}, pages = {}, pmid = {29802189}, issn = {1098-5336}, mesh = {Amino Acid Sequence ; Bacteria/chemistry/classification/*enzymology/*genetics ; Bacterial Proteins/chemistry/*genetics/metabolism ; Carbonic Anhydrases/chemistry/*genetics/metabolism ; Chromosomes, Bacterial/genetics/metabolism ; Eukaryota/classification/enzymology/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genomic Islands ; Phylogeny ; Plasmids/genetics/metabolism ; Sequence Alignment ; }, abstract = {Genomic islands (GIs) are a type of mobile genetic element (MGE) that are present in bacterial chromosomes. They consist of a cluster of genes that produce proteins that contribute to a variety of functions, including, but not limited to, the regulation of cell metabolism, antimicrobial resistance, pathogenicity, virulence, and resistance to heavy metals. The genes carried in MGEs can be used as a trait reservoir in times of adversity. Transfer of genes using MGEs, occurring outside reproduction, is called horizontal gene transfer (HGT). Previous data have shown that numerous HGT events have occurred through endosymbiosis between prokaryotes and eukaryotes. β-Carbonic anhydrase (β-CA) enzymes play a critical role in the biochemical pathways of many prokaryotes and eukaryotes. We previously suggested the horizontal transfer of β-CA genes from plasmids of some prokaryotic endosymbionts to their protozoan hosts. In this study, we set out to identify β-CA genes that might have been transferred between prokaryotic and protist species through HGT in GIs. Therefore, we investigated prokaryotic chromosomes containing β-CA-encoding GIs and utilized multiple bioinformatics tools to reveal the distinct movements of β-CA genes among a wide variety of organisms. Our results identify the presence of β-CA genes in GIs of several medically and industrially relevant bacterial species, and phylogenetic analyses reveal multiple cases of likely horizontal transfer of β-CA genes from GIs of ancestral prokaryotes to protists.IMPORTANCE The evolutionary process is mediated by mobile genetic elements (MGEs), such as genomic islands (GIs). A gene or set of genes in the GIs is exchanged between and within various species through horizontal gene transfer (HGT). Based on the crucial role that GIs can play in bacterial survival and proliferation, they were introduced as environment- and pathogen-associated factors. Carbonic anhydrases (CAs) are involved in many critical biochemical pathways, such as the regulation of pH homeostasis and electrolyte transfer. Among the six evolutionary families of CAs, β-CA gene sequences are present in many bacterial species, which can be horizontally transferred to protists during evolution. This study shows the involvement of bacterial β-CA gene sequences in the GIs and suggests their horizontal transfer to protists during evolution.}, }
@article {pmid29795276, year = {2018}, author = {Brinkmann, H and Göker, M and Koblížek, M and Wagner-Döbler, I and Petersen, J}, title = {Horizontal operon transfer, plasmids, and the evolution of photosynthesis in Rhodobacteraceae.}, journal = {The ISME journal}, volume = {12}, number = {8}, pages = {1994-2010}, pmid = {29795276}, issn = {1751-7370}, mesh = {DNA Replication ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Multigene Family ; Operon ; *Photosynthesis ; Phototrophic Processes ; Phylogeny ; Plasmids/*genetics/metabolism ; Rhodobacteraceae/classification/*genetics/metabolism ; }, abstract = {The capacity for anoxygenic photosynthesis is scattered throughout the phylogeny of the Proteobacteria. Their photosynthesis genes are typically located in a so-called photosynthesis gene cluster (PGC). It is unclear (i) whether phototrophy is an ancestral trait that was frequently lost or (ii) whether it was acquired later by horizontal gene transfer. We investigated the evolution of phototrophy in 105 genome-sequenced Rhodobacteraceae and provide the first unequivocal evidence for the horizontal transfer of the PGC. The 33 concatenated core genes of the PGC formed a robust phylogenetic tree and the comparison with single-gene trees demonstrated the dominance of joint evolution. The PGC tree is, however, largely incongruent with the species tree and at least seven transfers of the PGC are required to reconcile both phylogenies. The origin of a derived branch containing the PGC of the model organism Rhodobacter capsulatus correlates with a diagnostic gene replacement of pufC by pufX. The PGC is located on plasmids in six of the analyzed genomes and its DnaA-like replication module was discovered at a conserved central position of the PGC. A scenario of plasmid-borne horizontal transfer of the PGC and its reintegration into the chromosome could explain the current distribution of phototrophy in Rhodobacteraceae.}, }
@article {pmid29794045, year = {2018}, author = {Harrison, E and Hall, JPJ and Brockhurst, MA}, title = {Migration promotes plasmid stability under spatially heterogeneous positive selection.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1879}, pages = {}, pmid = {29794045}, issn = {1471-2954}, mesh = {Environment ; *Gene Transfer, Horizontal ; Mercury ; Plasmids/*genetics ; Pseudomonas fluorescens/*genetics ; Selection, Genetic ; *Symbiosis ; }, abstract = {Bacteria-plasmid associations can be mutualistic or antagonistic depending on the strength of positive selection for plasmid-encoded genes, with contrasting outcomes for plasmid stability. In mutualistic environments, plasmids are swept to high frequency by positive selection, increasing the likelihood of compensatory evolution to ameliorate the plasmid cost, which promotes long-term stability. In antagonistic environments, plasmids are purged by negative selection, reducing the probability of compensatory evolution and driving their extinction. Here we show, using experimental evolution of Pseudomonas fluorescens and the mercury-resistance plasmid, pQBR103, that migration promotes plasmid stability in spatially heterogeneous selection environments. Specifically, migration from mutualistic environments, by increasing both the frequency of the plasmid and the supply of compensatory mutations, stabilized plasmids in antagonistic environments where, without migration, they approached extinction. These data suggest that spatially heterogeneous positive selection, which is common in natural environments, coupled with migration helps to explain the stability of plasmids and the ecologically important genes that they encode.}, }
@article {pmid29793114, year = {2018}, author = {Zhang, J and Sui, Q and Tong, J and Zhong, H and Wang, Y and Chen, M and Wei, Y}, title = {Soil types influence the fate of antibiotic-resistant bacteria and antibiotic resistance genes following the land application of sludge composts.}, journal = {Environment international}, volume = {118}, number = {}, pages = {34-43}, doi = {10.1016/j.envint.2018.05.029}, pmid = {29793114}, issn = {1873-6750}, mesh = {Agriculture ; Anti-Bacterial Agents/pharmacology ; *Bacteria/drug effects/genetics ; Drug Resistance, Bacterial/*genetics ; Fertilizers/*microbiology ; Genes, Bacterial/*genetics ; Sewage/*microbiology ; Soil/classification ; *Soil Microbiology ; }, abstract = {Sewage sludge was generally considered a significant reservoir of antibiotic resistance genes (ARGs) and could enter agricultural systems as fertilizer after composting. Soil types and the discrepancy of sludge composts could have influenced the fate of antibiotic-resistant bacteria (ARB) following the land application of sludge composts, which deserved to be clarified. Thus, the fate of ARB and ARGs following the land application of three types of sludge composts (A, B, and C) to three different soils (red soil, loess, and black soil) was investigated. The results showed that tetX, which was enriched the most during composting, did not affect the soil resistome, whereas tetG did. Soil types influenced the dynamics of ARB and ARGs significantly, whereas no significant difference was observed among compost types. The advantage of reducing ARGs during the composting process in compost B did not extend to land application. Land application of composts influenced the microbial community significantly at the early stage, but the microbial community returned to the control pattern gradually. Changes in the microbial community contributed more to the dynamics of ARGs in red and black soil compared with other factors, including co-selection from heavy metals, horizontal gene transfer, biomass and environmental factors, whereas horizontal gene transfer, reflected by intI1 levels, contributed the most in loess.}, }
@article {pmid29792566, year = {2018}, author = {Condon, BJ and Elliott, C and González, JB and Yun, SH and Akagi, Y and Wiesner-Hanks, T and Kodama, M and Turgeon, BG}, title = {Clues to an Evolutionary Mystery: The Genes for T-Toxin, Enabler of the Devastating 1970 Southern Corn Leaf Blight Epidemic, Are Present in Ancestral Species, Suggesting an Ancient Origin.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {31}, number = {11}, pages = {1154-1165}, doi = {10.1094/MPMI-03-18-0070-R}, pmid = {29792566}, issn = {0894-0282}, mesh = {Ascomycota/*genetics/metabolism ; Biological Evolution ; Fungal Proteins/*genetics/metabolism ; Multigene Family ; Mutation ; Mycotoxins/genetics/*metabolism ; Phylogeny ; Plant Diseases/*microbiology ; Plant Leaves/microbiology ; Zea mays/*microbiology ; }, abstract = {The Southern corn leaf blight (SCLB) epidemic of 1970 devastated fields of T-cytoplasm corn planted in monoculture throughout the eastern United States. The epidemic was driven by race T, a previously unseen race of Cochliobolus heterostrophus. A second fungus, Phyllosticta zeae-maydis, with the same biological specificity, appeared coincidentally. Race T produces T-toxin, while Phyllosticta zeae-maydis produces PM-toxin, both host-selective polyketide toxins necessary for supervirulence. The present abundance of genome sequences offers an opportunity to tackle the evolutionary origins of T- and PM- toxin biosynthetic genes, previously thought unique to these species. Using the C. heterostrophus genes as probes, we identified orthologs in six additional Dothideomycete and three Eurotiomycete species. In stark contrast to the genetically fragmented race T Tox1 locus that encodes these genes, all newly found Tox1-like genes in other species reside at a single collinear locus. This compact arrangement, phylogenetic analyses, comparisons of Tox1 protein tree topology to a species tree, and Tox1 gene characteristics suggest that the locus is ancient and that some species, including C. heterostrophus, gained Tox1 by horizontal gene transfer. C. heterostrophus and Phyllosticta zeae-maydis did not exchange Tox1 DNA at the time of the SCLB epidemic, but how they acquired Tox1 remains uncertain. The presence of additional genes in Tox1-like clusters of other species, although not in C. heterostrophus and Phyllosticta zeae-maydis, suggests that the metabolites produced differ from T- and PM-toxin.}, }
@article {pmid29788909, year = {2018}, author = {Lacey, JA and Allnutt, TR and Vezina, B and Van, TTH and Stent, T and Han, X and Rood, JI and Wade, B and Keyburn, AL and Seemann, T and Chen, H and Haring, V and Johanesen, PA and Lyras, D and Moore, RJ}, title = {Whole genome analysis reveals the diversity and evolutionary relationships between necrotic enteritis-causing strains of Clostridium perfringens.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {379}, pmid = {29788909}, issn = {1471-2164}, support = {1.1.2//Poultry Cooperative Research Centre/ ; }, mesh = {Animals ; Chickens/microbiology ; Chromosomes/genetics ; Clostridium perfringens/*genetics/*physiology ; Enteritis/complications/*microbiology ; *Evolution, Molecular ; *Genetic Variation ; Necrosis/complications ; Plasmids/genetics ; }, abstract = {BACKGROUND: Clostridium perfringens causes a range of diseases in animals and humans including necrotic enteritis in chickens and food poisoning and gas gangrene in humans. Necrotic enteritis is of concern in commercial chicken production due to the cost of the implementation of infection control measures and to productivity losses. This study has focused on the genomic analysis of a range of chicken-derived C. perfringens isolates, from around the world and from different years. The genomes were sequenced and compared with 20 genomes available from public databases, which were from a diverse collection of isolates from chickens, other animals, and humans. We used a distance based phylogeny that was constructed based on gene content rather than sequence identity. Similarity between strains was defined as the number of genes that they have in common divided by their total number of genes. In this type of phylogenetic analysis, evolutionary distance can be interpreted in terms of evolutionary events such as acquisition and loss of genes, whereas the underlying properties (the gene content) can be interpreted in terms of function. We also compared these methods to the sequence-based phylogeny of the core genome.<br><br>RESULTS: Distinct pathogenic clades of necrotic enteritis-causing C. perfringens were identified. They were characterised by variable regions encoded on the chromosome, with predicted roles in capsule production, adhesion, inhibition of related strains, phage integration, and metabolism. Some strains have almost identical genomes, even though they were isolated from different geographic regions at various times, while other highly distant genomes appear to result in similar outcomes with regard to virulence and pathogenesis.<br><br>CONCLUSIONS: The high level of diversity in chicken isolates suggests there is no reliable factor that defines a chicken strain of C. perfringens, however, disease-causing strains can be defined by the presence of netB-encoding plasmids. This study reveals that horizontal gene transfer appears to play a significant role in genetic variation of the C. perfringens chromosome as well as the plasmid content within strains.}, }
@article {pmid29786161, year = {2018}, author = {Simbaqueba, J and Catanzariti, AM and González, C and Jones, DA}, title = {Evidence for horizontal gene transfer and separation of effector recognition from effector function revealed by analysis of effector genes shared between cape gooseberry- and tomato-infecting formae speciales of Fusarium oxysporum.}, journal = {Molecular plant pathology}, volume = {19}, number = {10}, pages = {2302-2318}, pmid = {29786161}, issn = {1364-3703}, mesh = {Fungal Proteins/genetics ; Fusarium/genetics/*pathogenicity ; Gene Transfer, Horizontal/*genetics ; Solanum lycopersicum/*microbiology ; Physalis/*microbiology ; Plant Diseases/*microbiology ; }, abstract = {RNA sequencing (RNAseq) reads from cape gooseberry plants (Physalis peruviana) infected with Fusarium oxysporumf. sp. physali (Foph) were mapped against the lineage-specific transcriptome of Fusarium oxysporumf. sp. lycopersici (Fol) to look for putative effector genes. Homologues of Fol SIX1(designated SIX1a and SIX1b), SIX7, SIX10, SIX12, SIX15 and Ave1were identified. The near identity of the Foph and Fol SIX7, SIX10 and SIX12genes and their intergenic regions suggest that this gene cluster may have undergone recent lateral transfer. Foph SIX1a and SIX1bwere tested for their ability to complement a SIX1 knockout mutant of Fol. This mutant shows reduced pathogenicity on susceptible tomato plants, but is able to infect otherwise resistant tomato plants carrying the I-3 gene for Fusarium wilt resistance (SIX1 corresponds to Avr3). Neither SIX1a nor SIX1b could restore full pathogenicity on susceptible tomato plants, suggesting that any role they may play in pathogenicity is likely to be specific to cape gooseberry. SIX1b, but not SIX1a, was able to restore avirulence on tomato plants carrying I-3.These findings separate the recognition of SIX1 from its role as an effector and suggest direct recognition by I-3. A hypervariable region of SIX1undergoing diversifying selection within the F. oxysporum species complex is likely to play an important role in SIX1 recognition. These findings also indicate that I-3could potentially be deployed as a transgene in cape gooseberry to protect this emerging crop from Foph.Alternatively, cape gooseberry germplasm could be explored for I-3homologues capable of providing resistance to Foph.}, }
@article {pmid29784978, year = {2018}, author = {Otto, TD and Gilabert, A and Crellen, T and Böhme, U and Arnathau, C and Sanders, M and Oyola, SO and Okouga, AP and Boundenga, L and Willaume, E and Ngoubangoye, B and Moukodoum, ND and Paupy, C and Durand, P and Rougeron, V and Ollomo, B and Renaud, F and Newbold, C and Berriman, M and Prugnolle, F}, title = {Genomes of all known members of a Plasmodium subgenus reveal paths to virulent human malaria.}, journal = {Nature microbiology}, volume = {3}, number = {6}, pages = {687-697}, pmid = {29784978}, issn = {2058-5276}, support = {/WT_/Wellcome Trust/United Kingdom ; 098051/WT_/Wellcome Trust/United Kingdom ; 104792/WT_/Wellcome Trust/United Kingdom ; 206194/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Speciation ; *Genome, Protozoan ; Host Specificity ; Humans ; Malaria/*parasitology ; Multigene Family ; Phylogeny ; Plasmodium/genetics/*pathogenicity ; Plasmodium falciparum/genetics/pathogenicity ; Sequence Analysis, DNA/*methods ; Virulence ; }, abstract = {Plasmodium falciparum, the most virulent agent of human malaria, shares a recent common ancestor with the gorilla parasite Plasmodium praefalciparum. Little is known about the other gorilla- and chimpanzee-infecting species in the same (Laverania) subgenus as P. falciparum, but none of them are capable of establishing repeated infection and transmission in humans. To elucidate underlying mechanisms and the evolutionary history of this subgenus, we have generated multiple genomes from all known Laverania species. The completeness of our dataset allows us to conclude that interspecific gene transfers, as well as convergent evolution, were important in the evolution of these species. Striking copy number and structural variations were observed within gene families and one, stevor, shows a host-specific sequence pattern. The complete genome sequence of the closest ancestor of P. falciparum enables us to estimate the timing of the beginning of speciation to be 40,000-60,000 years ago followed by a population bottleneck around 4,000-6,000 years ago. Our data allow us also to search in detail for the features of P. falciparum that made it the only member of the Laverania able to infect and spread in humans.}, }
@article {pmid29778228, year = {2018}, author = {Zhao, L and Song, Y and Li, L and Gan, N and Brand, JJ and Song, L}, title = {The highly heterogeneous methylated genomes and diverse restriction-modification systems of bloom-forming Microcystis.}, journal = {Harmful algae}, volume = {75}, number = {}, pages = {87-93}, doi = {10.1016/j.hal.2018.04.005}, pmid = {29778228}, issn = {1878-1470}, mesh = {Bacterial Proteins/*genetics ; DNA Methylation/*genetics ; DNA Restriction-Modification Enzymes/*genetics ; Eutrophication ; *Genome, Bacterial ; Microcystis ; }, abstract = {The occurrence of harmful Microcystis blooms is increasing in frequency in a myriad of freshwater ecosystems. Despite considerable research pertaining to the cause and nature of these blooms, the molecular mechanisms behind the cosmopolitan distribution and phenotypic diversity in Microcystis are still unclear. We compared the patterns and extent of DNA methylation in three strains of Microcystis, PCC 7806SL, NIES-2549 and FACHB-1757, using Single Molecule Real-Time (SMRT) sequencing technology. Intact restriction-modification (R-M) systems were identified from the genomes of these strains, and from two previously sequenced strains of Microcystis, NIES-843 and TAIHU98. A large number of methylation motifs and R-M genes were identified in these strains, which differ substantially among different strains. Of the 35 motifs identified, eighteen had not previously been reported. Strain NIES-843 contains a larger number of total putative methyltransferase genes than have been reported previously from any bacterial genome. Genomic comparisons reveal that methyltransferases (some partial) may have been acquired from the environment through horizontal gene transfer.}, }
@article {pmid29778206, year = {2018}, author = {Freitag, C and Michael, GB and Li, J and Kadlec, K and Wang, Y and Hassel, M and Schwarz, S}, title = {Occurrence and characterisation of ESBL-encoding plasmids among Escherichia coli isolates from fresh vegetables.}, journal = {Veterinary microbiology}, volume = {219}, number = {}, pages = {63-69}, doi = {10.1016/j.vetmic.2018.03.028}, pmid = {29778206}, issn = {1873-2542}, mesh = {Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Escherichia coli/drug effects/enzymology/genetics/*isolation &amp; purification ; Fosfomycin/pharmacology ; Gene Transfer, Horizontal ; Germany ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Plasmids/genetics/*isolation &amp; purification ; Replicon ; Vegetables/*microbiology ; beta-Lactamases/biosynthesis/*genetics ; }, abstract = {Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolates have been increasingly reported in different reservoirs. The aims of this study were to investigate the presence of ESBL-producing E. coli in fresh vegetables and to characterise their ESBL gene-carrying plasmids. Among the 245 samples from vegetables investigated during 2011-2013, seven putative ESBL-producing E. coli (salad n = 2, sprouts n = 5) were found. They were subjected to ESBL phenotypic confirmatory tests, detection/sequencing of ESBL genes, antimicrobial susceptibility testing (AST), phylotyping, XbaI-macrorestriction analysis, multilocus sequence typing and transformation. Transformants were characterised by AST, S1-nuclease PFGE, replicon typing, conjugation and investigated for co-located antimicrobial resistance genes. Two ESBL gene-carrying plasmids were sequenced using a HiSeq 2500 system. The seven isolates were confirmed as ESBL producers, displayed unrelated XbaI-patterns and unique sequence types (STs) and belonged to the phylogroups A, B1 or D. The ESBL genes were located on plasmids. Two plasmids carrying blaCTX-M-14 genes (incompatibility group IncK or IncHI2) were seen in isolates from salad (ST973) and sprout (ST527). Two blaCTX-M-15- (IncFIB; non-typeable) and the IncN blaCTX-M-65- and IncHI2 blaCTX-M-125-carrying plasmids were found in isolates from sprouts (ST410, ST847, ST10, ST542). All plasmids were conjugative, except for the IncFIA-FIB blaCTX-M-2-carrying plasmid. Sequence analysis of two plasmids identified the ESBL genes in close location to other resistance genes: sulfonamide resistance gene sul2, streptomycin resistance genes strA and strB, the plasmid-mediated quinolone resistance gene qnrS1 and blaTEM-1 (sul2-strA-strB-IS66-blaTEM-1-tnpR-ΔtnpA-ISEcp1-blaCTX-M-15-Δorf477-ΔtnpA-qnrS1) or the fosfomycin resistance gene fosA3 (ΔISEcp1-blaCTX-M-125-ΔIS903B-fosA3). These observations underline the importance of vegetables as reservoirs for multidrug resistant ESBL-producing E. coli.}, }
@article {pmid29778183, year = {2018}, author = {Sadikalay, S and Reynaud, Y and Guyomard-Rabenirina, S and Falord, M and Ducat, C and Fabre, L and Le Hello, S and Talarmin, A and Ferdinand, S}, title = {High genetic diversity of extended-spectrum β-lactamases producing Escherichia coli in feces of horses.}, journal = {Veterinary microbiology}, volume = {219}, number = {}, pages = {117-122}, doi = {10.1016/j.vetmic.2018.04.016}, pmid = {29778183}, issn = {1873-2542}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Escherichia coli/classification/drug effects/enzymology/*genetics ; Escherichia coli Infections/microbiology/*veterinary ; Escherichia coli Proteins/*biosynthesis/drug effects/genetics ; Feces/*microbiology ; Gastrointestinal Microbiome ; Gene Transfer, Horizontal ; *Genetic Variation ; Horses/microbiology ; Microbial Sensitivity Tests ; Phylogeny ; Plasmids ; Whole Genome Sequencing ; beta-Lactamases/*biosynthesis/drug effects/genetics ; }, abstract = {Extended-spectrum beta-lactamases (ESBLs), especially those of the CTX-M type, represent a major public health problem throughout the world. Although the carriage of ESBL-producing Enterobacteriaceae (EPE) in feces of horses is now well recognized, little is known about the diversity of EPE after treatment of horses with antibiotics. We undertook this study to assess and follow the diversity of EP Escherichia coli isolated from horses after antibiotic treatment for an infection. Fecal samples from two horses treated and two that were untreated were tested for the presence of EPE on different days. All isolated E. coli strains were evaluated for antimicrobial resistance (AMR) and by whole-genome sequencing. Multi locus sequence typing, phylogrouping, resistance genes and plasmid content were extracted from genomic data. A phylogenetic analysis based on single nucleotide polymorphism (SNP) divergence was also performed on the core genome. We isolated 35 strains belonging to the A, B1 and C phylo-groups. All but one expressed SHV-12 enzymes and one expressed CTX-M-1. Intra- and inter-horse genetic diversity of E. coli strains was identified in the genome analysis and 10 AMR profiles. Two distinct EP E. coli-resistant populations (phylo-group B1: ST4164-AMR3 and ST155-AMR2) were found in one horse, and five other resistant populations were found in the second horse (phylo-group A: ST1250-AMR1; phylo-group B1: ST1250-AMR1, ST6981-AMR1 and phylo-group C: ST10-AMR4). Some persistent EP E. coli strains were detected at least 1 month after treatment. These results indicate that EP E. coli strains isolated from horse feces show intra- and inter-host genetic diversity, even in a region with low ESBL prevalence and in horses that are rarely treated with third-generation cephalosporins. These results also suggest that horizontal gene transfer and/or selection of resistance genes probably occurs in vivo within the horse gut microbiome. Follow-up of EP E. coli resistance profiles for at least 1 month after treatment is warranted to prevent persistence of EP E. coli.}, }
@article {pmid29775685, year = {2018}, author = {Courtois, N and Caspar, Y and Maurin, M}, title = {Phenotypic and genetic resistance traits of Pseudomonas aeruginosa strains infecting cystic fibrosis patients: A French cohort study.}, journal = {International journal of antimicrobial agents}, volume = {52}, number = {3}, pages = {358-364}, doi = {10.1016/j.ijantimicag.2018.05.008}, pmid = {29775685}, issn = {1872-7913}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics ; Ceftazidime/pharmacology ; Cephalosporinase/*genetics/metabolism ; Cloxacillin/pharmacology ; Cystic Fibrosis/microbiology ; Drug Resistance, Multiple, Bacterial/*genetics ; France ; Humans ; Imipenem/pharmacology ; Microbial Sensitivity Tests ; Porins/*genetics ; Pseudomonas Infections/complications/microbiology ; Pseudomonas aeruginosa/*drug effects/*genetics/isolation &amp; purification ; beta-Lactam Resistance/genetics ; beta-Lactamases/*genetics ; }, abstract = {Pseudomonas aeruginosa is responsible for chronic respiratory tract colonisation and acute exacerbations in cystic fibrosis (CF) patients. This Gram-negative bacterium often develops multidrug resistance, which represents a therapeutic challenge. The objective of this study was to characterise the phenotypic and genetic β-lactam resistance traits of P. aeruginosa strains isolated from CF patients at Grenoble Alpes University Hospital (Grenoble, France). The susceptibility to β-lactam compounds of 123 P. aeruginosa strains collected from the lower respiratory tract of 45 CF patients between 2010-2014 was evaluated. Genetic analyses focused on characterisation of the presence of carbapenemase- and extended-spectrum β-lactamases (ESBL)-encoding genes as well as alterations in the oprD gene encoding the OprD porin. Among the 123 P. aeruginosa strains evaluated, 25 were susceptible to both ceftazidime (CAZ) and imipenem (IPM), 9 only to IPM and 36 only to CAZ; 53 strains were resistant to both drugs. CAZ resistance could be reverted by cloxacillin in 29 strains, indicating overproduction of cephalosporinase. Genetic analyses performed for 79 P. aeruginosa strains revealed no ESBL- or carbapenemases-encoding genes. Among the 74 IPM-resistant strains, 42 (56.8%) displayed major alterations in the OprD protein sequence. This study shows that in this CF patient cohort, cephalosporinase overproduction and OprD alterations were the main resistance mechanisms of P. aeruginosa to CAZ and IPM, respectively. No genes coding for ESBLs or carbapenemases were detected, but monitoring of the emergence of such resistance genes in CF patients is warranted owing to their ability to rapidly spread by horizontal gene transfer.}, }
@article {pmid29775460, year = {2018}, author = {Alex, A and Antunes, A}, title = {Genus-wide comparison of Pseudovibrio bacterial genomes reveal diverse adaptations to different marine invertebrate hosts.}, journal = {PloS one}, volume = {13}, number = {5}, pages = {e0194368}, pmid = {29775460}, issn = {1932-6203}, mesh = {*Adaptation, Physiological ; Animals ; Aquatic Organisms/*microbiology ; DNA, Bacterial ; *Genome, Bacterial ; Invertebrates/*microbiology ; Phylogeny ; Seawater/*microbiology ; Symbiosis ; Vibrionaceae/*genetics/isolation &amp; purification ; }, abstract = {Bacteria belonging to the genus Pseudovibrio have been frequently found in association with a wide variety of marine eukaryotic invertebrate hosts, indicative of their versatile and symbiotic lifestyle. A recent comparison of the sponge-associated Pseudovibrio genomes has shed light on the mechanisms influencing a successful symbiotic association with sponges. In contrast, the genomic architecture of Pseudovibrio bacteria associated with other marine hosts has received less attention. Here, we performed genus-wide comparative analyses of 18 Pseudovibrio isolated from sponges, coral, tunicates, flatworm, and seawater. The analyses revealed a certain degree of commonality among the majority of sponge- and coral-associated bacteria. Isolates from other marine invertebrate host, tunicates, exhibited a genetic repertoire for cold adaptation and specific metabolic abilities including mucin degradation in the Antarctic tunicate-associated bacterium Pseudovibrio sp. Tun.PHSC04_5.I4. Reductive genome evolution was simultaneously detected in the flatworm-associated bacteria and the sponge-associated bacterium P. axinellae AD2, through the loss of major secretion systems (type III/VI) and virulence/symbioses factors such as proteins involved in adhesion and attachment to the host. Our study also unraveled the presence of a CRISPR-Cas system in P. stylochi UST20140214-052 a flatworm-associated bacterium possibly suggesting the role of CRISPR-based adaptive immune system against the invading virus particles. Detection of mobile elements and genomic islands (GIs) in all bacterial members highlighted the role of horizontal gene transfer for the acquisition of novel genetic features, likely enhancing the bacterial ecological fitness. These findings are insightful to understand the role of genome diversity in Pseudovibrio as an evolutionary strategy to increase their colonizing success across a wide range of marine eukaryotic hosts.}, }
@article {pmid29773850, year = {2018}, author = {Salto, IP and Torres Tejerizo, G and Wibberg, D and Pühler, A and Schlüter, A and Pistorio, M}, title = {Comparative genomic analysis of Acinetobacter spp. plasmids originating from clinical settings and environmental habitats.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {7783}, pmid = {29773850}, issn = {2045-2322}, mesh = {Acinetobacter/*genetics ; Argentina ; DNA Replication ; Gene Transfer, Horizontal ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Plasmids/*genetics ; Sequence Analysis, DNA ; }, abstract = {Bacteria belonging to the genus Acinetobacter have become of clinical importance over the last decade due to the development of a multi-resistant phenotype and their ability to survive under multiple environmental conditions. The development of these traits among Acinetobacter strains occurs frequently as a result of plasmid-mediated horizontal gene transfer. In this work, plasmids from nosocomial and environmental Acinetobacter spp. collections were separately sequenced and characterized. Assembly of the sequenced data resulted in 19 complete replicons in the nosocomial collection and 77 plasmid contigs in the environmental collection. Comparative genomic analysis showed that many of them had conserved backbones. Plasmid coding sequences corresponding to plasmid specific functions were bioinformatically and functionally analyzed. Replication initiation protein analysis revealed the predominance of the Rep_3 superfamily. The phylogenetic tree constructed from all Acinetobacter Rep_3 superfamily plasmids showed 16 intermingled clades originating from nosocomial and environmental habitats. Phylogenetic analysis of relaxase proteins revealed the presence of a new sub-clade named MOBQAci, composed exclusively of Acinetobacter relaxases. Functional analysis of proteins belonging to this group showed that they behaved differently when mobilized using helper plasmids belonging to different incompatibility groups.}, }
@article {pmid29772393, year = {2018}, author = {Croughs, PD and Klaassen, CHW and van Rosmalen, J and Maghdid, DM and Boers, SA and Hays, JP and Goessens, WHF and , }, title = {Unexpected mechanisms of resistance in Dutch Pseudomonas aeruginosa isolates collected during 14 years of surveillance.}, journal = {International journal of antimicrobial agents}, volume = {52}, number = {3}, pages = {407-410}, doi = {10.1016/j.ijantimicag.2018.05.009}, pmid = {29772393}, issn = {1872-7913}, mesh = {Anti-Bacterial Agents/pharmacology ; Ceftazidime/pharmacology ; Cross Infection/microbiology ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal ; Humans ; Imipenem/pharmacology ; Intensive Care Units ; Meropenem/pharmacology ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Netherlands/epidemiology ; Pseudomonas Infections/drug therapy/*epidemiology ; Pseudomonas aeruginosa/*drug effects/genetics/*isolation &amp; purification ; beta-Lactamases/*genetics ; }, abstract = {Pseudomonas aeruginosa is one of the most important causes of infection in intensive care units (ICUs). It is intrinsically resistant to many antimicrobials and easily acquires additional resistance genes via horizontal gene transfer of mobile genetic elements. In this study, 1528 P. aeruginosa isolates obtained from a Dutch national surveillance programme between the years 1998-2011 were analysed for the presence of extended-spectrum β-lactamase (ESBL) genes (blaCTX-M, blaSHV, blaTEM, blaBEL, blaPER, blaVEB and blaOXA-10) and metallo-β-lactamase (MBL) genes (blaIMP, blaVIM and blaNDM). Of the ceftazidime-resistant isolates, 6.2% tested phenotypically positive for ESBL. Moreover, a Verona integron-encoded MBL (VIM) gene was found in 3.1% of isolates that were phenotypically resistant to imipenem and/or meropenem. Multilocus sequence typing (MLST) of ESBL-positive isolates indicated ST1216, ST111 and ST622, with all blaVIM-positive isolates belonging to the ST111 clone. Although the prevalence of ESBL and MBL phenotypes in this Dutch national surveillance collection of >1500 ICU P. aeruginosa isolates was very low, all VIM-producing isolates belonged to the high risk-associated, international, clonal complex CC111, and most ESBL-producing isolates belonged to clonal complexes known for their successful spread, e.g. CC111 and CC235. These data indicate that high-risk clones of P. aeruginosa were present in the Netherlands between 1998-2011 and probably spread unnoticed throughout Dutch hospitals.}, }
@article {pmid29769737, year = {2018}, author = {Lee, JW and Chan, CTY and Slomovic, S and Collins, JJ}, title = {Next-generation biocontainment systems for engineered organisms.}, journal = {Nature chemical biology}, volume = {14}, number = {6}, pages = {530-537}, pmid = {29769737}, issn = {1552-4469}, mesh = {Codon, Terminator ; *Containment of Biohazards ; Escherichia coli/metabolism ; Gene Editing ; Gene Expression Regulation ; Gene Transfer, Horizontal ; Genetic Engineering/*adverse effects/*methods ; Genome ; Humans ; Lactobacillus ; Mutagenesis ; Organisms, Genetically Modified ; Synthetic Biology/methods ; Transgenes ; }, abstract = {The increasing use of engineered organisms for industrial, clinical, and environmental applications poses a growing risk of spreading hazardous biological entities into the environment. To address this biosafety issue, significant effort has been invested in creating ways to confine these organisms and transgenic materials. Emerging technologies in synthetic biology involving genetic circuit engineering, genome editing, and gene expression regulation have led to the development of novel biocontainment systems. In this perspective, we highlight recent advances in biocontainment and suggest a number of approaches for future development, which may be applied to overcome remaining challenges in safeguard implementation.}, }
@article {pmid29769695, year = {2018}, author = {Liakopoulos, A and van der Goot, J and Bossers, A and Betts, J and Brouwer, MSM and Kant, A and Smith, H and Ceccarelli, D and Mevius, D}, title = {Genomic and functional characterisation of IncX3 plasmids encoding blaSHV-12 in Escherichia coli from human and animal origin.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {7674}, pmid = {29769695}, issn = {2045-2322}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Escherichia coli/drug effects/enzymology/*genetics/isolation &amp; purification ; Escherichia coli Infections/drug therapy/epidemiology/transmission/*veterinary ; Escherichia coli Proteins/*genetics/metabolism ; Genomics ; Humans ; Plasmids/*genetics/metabolism ; Poultry/microbiology ; Poultry Diseases/drug therapy/*epidemiology/microbiology/transmission ; beta-Lactamases/*genetics/metabolism ; beta-Lactams/pharmacology ; }, abstract = {The blaSHV-12 β-lactamase gene is one of the most prevalent genes conferring resistance to extended-spectrum β-lactams in Enterobacteriaceae disseminating within and between reservoirs, mostly via plasmid-mediated horizontal gene transfer. Yet, studies regarding the biology of plasmids encoding blaSHV-12 are very limited. In this study, we revealed the emergence of IncX3 plasmids alongside IncI1α/γ in blaSHV-12 in animal-related Escherichia coli isolates. Four representative blaSHV-12-encoding IncX3 plasmids were selected for genome sequencing and further genetic and functional characterization. We report here the first complete sequences of IncX3 plasmids of animal origin and show that IncX3 plasmids exhibit remarkable synteny in their backbone, while the major differences lie in their blaSHV-12-flanking region. Our findings indicate that plasmids of this subgroup are conjugative and highly stable, while they exert no fitness cost on their bacterial host. These favourable features might have contributed to the emergence of IncX3 amongst SHV-12-producing E. coli in the Netherlands, highlighting the epidemic potential of these plasmids.}, }
@article {pmid29765367, year = {2018}, author = {Brown-Jaque, M and Rodriguez Oyarzun, L and Cornejo-Sánchez, T and Martín-Gómez, MT and Gartner, S and de Gracia, J and Rovira, S and Alvarez, A and Jofre, J and González-López, JJ and Muniesa, M}, title = {Detection of Bacteriophage Particles Containing Antibiotic Resistance Genes in the Sputum of Cystic Fibrosis Patients.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {856}, pmid = {29765367}, issn = {1664-302X}, abstract = {Cystic fibrosis (CF) is a chronic disease in which the bacterial colonization of the lung is linked to an excessive inflammatory response that leads to respiratory failure. The microbiology of CF is complex. Staphylococcus aureus is the first bacterium to colonize the lungs in 30% of pediatric CF patients, and 80% of adult patients develop a chronic Pseudomonas aeruginosa infection, but other microorganisms can also be found. The use of antibiotics is essential to treat the disease, but antibiotic performance is compromised by resistance mechanisms. Among various mechanisms of transfer of antibiotic resistance genes (ARGs), the recently been reported bacteriophages are the least explored in clinical settings. To determine the role of phages in CF as mobile genetic elements (MGEs) carrying ARGs, we evaluated their presence in 71 CF patients. 71 sputum samples taken from these patients were screened for eight ARGs (blaTEM, blaCTX-M-1-group, blaCTX-M-9-group, blaOXA-48, blaVIM, mecA, qnrA, and qnrS) in the bacteriophage DNA fraction. The phages found were also purified and observed by electron microscopy. 32.4% of CF patients harbored ARGs in phage DNA. β-lactamase genes, particularly blaVIM and blaTEM, were the most prevalent and abundant, whereas mecA, qnrA, and qnrS were very rare. Siphoviridae phage particles capable of infecting P. aeruginosa and Klebsiella pneumoniae were detected in CF sputum. Phage particles harboring ARGs were found to be abundant in the lungs of both CF patients and healthy individuals and could contribute to the colonization of multiresistant strains.}, }
@article {pmid29764363, year = {2018}, author = {Noutahi, E and El-Mabrouk, N}, title = {GATC: a genetic algorithm for gene tree construction under the Duplication-Transfer-Loss model of evolution.}, journal = {BMC genomics}, volume = {19}, number = {Suppl 2}, pages = {102}, pmid = {29764363}, issn = {1471-2164}, mesh = {Algorithms ; Cyanobacteria/*genetics ; Evolution, Molecular ; Gene Duplication ; *Genes, Bacterial ; Genomics/*methods ; Internet ; Models, Genetic ; Multigene Family ; Phylogeny ; }, abstract = {BACKGROUND: Several methods have been developed for the accurate reconstruction of gene trees. Some of them use reconciliation with a species tree to correct, a posteriori, errors in gene trees inferred from multiple sequence alignments. Unfortunately the best fit to sequence information can be lost during this process.<br><br>RESULTS: We describe GATC, a new algorithm for reconstructing a binary gene tree with branch length. GATC returns optimal solutions according to a measure combining both tree likelihood (according to sequence evolution) and a reconciliation score under the Duplication-Transfer-Loss (DTL) model. It can either be used to construct a gene tree from scratch or to correct trees infered by existing reconstruction method, making it highly flexible to various input data types. The method is based on a genetic algorithm acting on a population of trees at each step. It substantially increases the efficiency of the phylogeny space exploration, reducing the risk of falling into local minima, at a reasonable computational time. We have applied GATC to a dataset of simulated cyanobacterial phylogenies, as well as to an empirical dataset of three reference gene families, and showed that it is able to improve gene tree reconstructions compared with current state-of-the-art algorithms.<br><br>CONCLUSION: The proposed algorithm is able to accurately reconstruct gene trees and is highly suitable for the construction of reference trees. Our results also highlight the efficiency of multi-objective optimization algorithms for the gene tree reconstruction problem. GATC is available on Github at: https://github.com/UdeM-LBIT/GATC .}, }
@article {pmid29760209, year = {2018}, author = {Chodur, DM and Rowe-Magnus, DA}, title = {Complex Control of a Genomic Island Governing Biofilm and Rugose Colony Development in Vibrio vulnificus.}, journal = {Journal of bacteriology}, volume = {200}, number = {16}, pages = {}, pmid = {29760209}, issn = {1098-5530}, mesh = {Bacterial Proteins/genetics ; Biofilms/*growth &amp; development ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genome, Bacterial ; *Genomic Islands ; Operon ; Phenotype ; Promoter Regions, Genetic ; Signal Transduction ; Vibrio vulnificus/*genetics/*physiology ; }, abstract = {Vibrio vulnificus is a potent opportunistic human pathogen that contaminates the human food chain by asymptomatically colonizing seafood. The expression of the 9-gene brp exopolysaccharide locus mediates surface adherence and is controlled by the secondary signaling molecule c-di-GMP and the regulator BrpT. Here, we show that c-di-GMP and BrpT also regulate the expression of an adjacent 5-gene cluster that includes the cabABC operon, brpT, and another VpsT-like transcriptional regulator gene, brpS The expression of the 14 genes spanning the region increased with elevated intracellular c-di-GMP levels in a BrpT-dependent manner, save for brpS, which was positively regulated by c-di-GMP and repressed by BrpT. BrpS repressed brpA expression and was required for rugose colony development. The mutation of its consensus WFSA c-di-GMP binding motif blocked these activities, suggesting that BrpS function is dependent on binding c-di-GMP. BrpT specifically bound the cabA, brpT, and brpS promoters, and binding sites homologous to the Vibrio cholerae VpsT binding site were identified upstream of brpA and brpT Transcription was initiated distal to brpA, and a conserved RfaH-recruiting ops element and a potential Rho utilization (rut) terminator site were identified within the 100-bp leader region, suggesting the integration of early termination and operon polarity suppression into the regulation of brp transcription. The GC content and codon usage of the 16-kb brp region was 5.5% lower relative to that of the flanking DNA, suggesting its recent assimilation via horizontal transfer. Thus, architecturally, the brp region can be considered an acquired biofilm and rugosity island that is subject to complex regulation.IMPORTANCE Biofilm and rugose colony formation are developmental programs that underpin the evolution of Vibrio vulnificus as a potent opportunistic human pathogen and successful environmental organism. A better understanding of the regulatory pathways governing theses phenotypes promotes the development and implementation of strategies to mitigate food chain contamination by this pathogen. c-di-GMP signaling is central to both pathways. We show that the molecule orchestrates the expression of 14 genes clustered in a 16-kb segment of the genome that governs biofilm and rugose colony development. This region exhibits the hallmarks of horizontal transfer, suggesting complex regulatory control of a recently assimilated genetic island governing the colonization response of V. vulnificus.}, }
@article {pmid29760148, year = {2018}, author = {Muller, M}, title = {Bacterial Silver Resistance Gained by Cooperative Interspecies Redox Behavior.}, journal = {Antimicrobial agents and chemotherapy}, volume = {62}, number = {8}, pages = {}, pmid = {29760148}, issn = {1098-6596}, mesh = {Anti-Bacterial Agents/pharmacology ; Escherichia coli/*drug effects/genetics ; Oxidation-Reduction/drug effects ; Pseudomonas aeruginosa/*drug effects/genetics ; Pyocyanine/*pharmacology ; Silver/chemistry/*pharmacology ; Staphylococcus aureus/*drug effects/genetics ; }, abstract = {Silver has emerged as an important therapeutic option for wound infections in recent years due to its broad-spectrum antimicrobial activity. The silver cation (Ag[+]), but not the bulk metal (Ag[0]), is highly toxic for most microorganisms, although resistance due to genetic modification or horizontal gene transfer does occur. Pseudomonas aeruginosa, however, achieves silver resistance by producing the redox-active metabolite pyocyanin that reduces Ag[+] to nontoxic Ag[0] Pyocyanin also possesses broad-spectrum antimicrobial activity. Many microbial species reduce pyocyanin, which reduces molecular oxygen to antimicrobial hydrogen peroxide. In this study, it was hypothesized that both Ag[+] and oxygen would act as competing terminal electron acceptors for pyocyanin, thus acting as a universal microbial protectant from Ag[+] while avoiding hydrogen peroxide formation. Escherichia coli and Staphylococcus aureus efficiently reduced pyocyanin and generated hydrogen peroxide, while Ag[+] markedly reduced the amount of hydrogen peroxide produced. Although unable to reduce directly Ag[+] to Ag[0] on their own, E. coli and S. aureus did so when pyocyanin was present, resulting in increased survival when exposed to Ag[+] Coincubation experiments with either E. coli or S. aureus with P. aeruginosa demonstrated increased survival for those species to Ag[+], but only if pyocyanin was present. These data demonstrate that microorganisms that display no intrinsic silver resistance may survive and proliferate under potentially toxic conditions, provided their environment contains a suitable redox-active metabolite-producing bacterium. Chronic wounds are often polymicrobial in nature, with pyocyanin-producing P. aeruginosa bacteria frequently being present; therefore, redox-based silver resistance may compromise treatment efforts.}, }
@article {pmid29753892, year = {2018}, author = {Shrestha, N and Weber, PH and Burke, SV and Wysocki, WP and Duvall, MR and Bujarski, JJ}, title = {Next generation sequencing reveals packaging of host RNAs by brome mosaic virus.}, journal = {Virus research}, volume = {252}, number = {}, pages = {82-90}, doi = {10.1016/j.virusres.2018.05.011}, pmid = {29753892}, issn = {1872-7492}, mesh = {Bromovirus/*genetics ; Capsid Proteins/genetics ; DNA Transposable Elements/genetics ; Gene Transfer, Horizontal ; *High-Throughput Nucleotide Sequencing ; Hordeum/virology ; Host-Pathogen Interactions/genetics ; RNA, Messenger/genetics ; RNA, Viral/*genetics ; Nicotiana/virology ; Virion/genetics ; Virus Assembly/*genetics ; }, abstract = {Although RNA viruses evolved the mechanisms of specific encapsidation, miss-packaging of cellular RNAs has been reported in such RNA virus systems as flock house virus or cucumber necrosis virus. To find out if brome mosaic virus (BMV), a tripartite RNA virus, can package cellular RNAs, BMV was propagated in barley and in Nicotiana benthamiana hosts, purified by cesium chloride (CsCl) gradient ultracentrifugation followed by nuclease treatment to remove any contaminating cellular (host) RNAs. The extracted virion RNA was then sequenced by using next-generation sequencing (NGS RNA-Seq) with the Illumina protocol. Bioinformatic analysis revealed the content of host RNAs ranging from 0.07% for BMV extracted from barley to 0.10% for the virus extracted from N. benthamiana. The viruses from two sources appeared to co-encapsidate different patterns of host-RNAs, including ribosomal RNAs (rRNAs), messenger RNAs (mRNAs) but also mitochondrial and plastid RNAs and, interestingly, transposable elements, both transposons and retrotransposons. Our data reveal that BMV virions can carry host RNAs, having a potential to mediate horizontal gene transfer (HGT) in plants.}, }
@article {pmid29752561, year = {2018}, author = {Santos, AS and Ramos, RT and Silva, A and Hirata, R and Mattos-Guaraldi, AL and Meyer, R and Azevedo, V and Felicori, L and Pacheco, LGC}, title = {Searching whole genome sequences for biochemical identification features of emerging and reemerging pathogenic Corynebacterium species.}, journal = {Functional &amp; integrative genomics}, volume = {18}, number = {5}, pages = {593-610}, pmid = {29752561}, issn = {1438-7948}, support = {JCB0031/2013//FAPESB/ ; PROCAD 071/2013//CAPES/ ; }, mesh = {ATP-Binding Cassette Transporters/genetics ; Bacterial Proteins/*genetics ; Bacterial Typing Techniques/*methods ; Corynebacterium/classification/*genetics/metabolism ; Fructokinases/genetics ; *Genome, Bacterial ; Phosphoenolpyruvate Sugar Phosphotransferase System/genetics ; Phosphoglucomutase/genetics ; Phylogeny ; Polymorphism, Genetic ; }, abstract = {Biochemical tests are traditionally used for bacterial identification at the species level in clinical microbiology laboratories. While biochemical profiles are generally efficient for the identification of the most important corynebacterial pathogen Corynebacterium diphtheriae, their ability to differentiate between biovars of this bacterium is still controversial. Besides, the unambiguous identification of emerging human pathogenic species of the genus Corynebacterium may be hampered by highly variable biochemical profiles commonly reported for these species, including Corynebacterium striatum, Corynebacterium amycolatum, Corynebacterium minutissimum, and Corynebacterium xerosis. In order to identify the genomic basis contributing for the biochemical variabilities observed in phenotypic identification methods of these bacteria, we combined a comprehensive literature review with a bioinformatics approach based on reconstruction of six specific biochemical reactions/pathways in 33 recently released whole genome sequences. We used data retrieved from curated databases (MetaCyc, PathoSystems Resource Integration Center (PATRIC), The SEED, TransportDB, UniProtKB) associated with homology searches by BLAST and profile Hidden Markov Models (HMMs) to detect enzymes participating in the various pathways and performed ab initio protein structure modeling and molecular docking to confirm specific results. We found a differential distribution among the various strains of genes that code for some important enzymes, such as beta-phosphoglucomutase and fructokinase, and also for individual components of carbohydrate transport systems, including the fructose-specific phosphoenolpyruvate-dependent sugar phosphotransferase (PTS) and the ribose-specific ATP-binging cassette (ABC) transporter. Horizontal gene transfer plays a role in the biochemical variability of the isolates, as some genes needed for sucrose fermentation were seen to be present in genomic islands. Noteworthy, using profile HMMs, we identified an enzyme with putative alpha-1,6-glycosidase activity only in some specific strains of C. diphtheriae and this may aid to understanding of the differential abilities to utilize glycogen and starch between the biovars.}, }
@article {pmid29751164, year = {2018}, author = {An, XL and Su, JQ and Li, B and Ouyang, WY and Zhao, Y and Chen, QL and Cui, L and Chen, H and Gillings, MR and Zhang, T and Zhu, YG}, title = {Tracking antibiotic resistome during wastewater treatment using high throughput quantitative PCR.}, journal = {Environment international}, volume = {117}, number = {}, pages = {146-153}, doi = {10.1016/j.envint.2018.05.011}, pmid = {29751164}, issn = {1873-6750}, mesh = {Anti-Bacterial Agents/*pharmacology ; *Bacteria/drug effects/genetics ; Drug Resistance, Bacterial/*genetics ; Genome, Bacterial/*genetics ; Real-Time Polymerase Chain Reaction/*methods ; Wastewater/*microbiology ; }, abstract = {Wastewater treatment plants (WWTPs) contain diverse antibiotic resistance genes (ARGs), and thus are considered as a major pathway for the dissemination of these genes into the environments. However, comprehensive evaluations of ARGs dynamic during wastewater treatment process lack extensive investigations on a broad spectrum of ARGs. Here, we investigated the dynamics of ARGs and bacterial community structures in 114 samples from eleven Chinese WWTPs using high-throughput quantitative PCR and 16S rRNA-based Illumina sequencing analysis. Significant shift of ARGs profiles was observed and wastewater treatment process could significantly reduce the abundance and diversity of ARGs, with the removal of ARGs concentration by 1-2 orders of magnitude. Whereas, a considerable number of ARGs were detected and enriched in effluents compared with influents. In particular, seven ARGs mainly conferring resistance to beta-lactams and aminoglycosides and three mobile genetic elements persisted in all WWTPs samples after wastewater treatment. ARGs profiles varied with wastewater treatment processes, seasons and regions. This study tracked the footprint of ARGs during wastewater treatment process, which would support the assessment on the spread of ARGs from WWTPs and provide data for identifying management options to improve ARG mitigation in WWTPs.}, }
@article {pmid29751066, year = {2018}, author = {Gupta, S and Lemenze, A and Donnelly, RJ and Connell, ND and Kadouri, DE}, title = {Keeping it together: absence of genetic variation and DNA incorporation by the predatory bacteria Micavibrio aeruginosavorus and Bdellovibrio bacteriovorus during predation.}, journal = {Research in microbiology}, volume = {169}, number = {4-5}, pages = {237-243}, doi = {10.1016/j.resmic.2018.03.002}, pmid = {29751066}, issn = {1769-7123}, mesh = {Alphaproteobacteria/*genetics/isolation &amp; purification ; Antibiosis/genetics ; Bdellovibrio bacteriovorus/*genetics/isolation &amp; purification ; Biological Control Agents ; Coculture Techniques ; DNA, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genetic Variation/*genetics ; Gram-Negative Bacterial Infections/therapy ; Humans ; Klebsiella pneumoniae/genetics ; }, abstract = {The use of predatory bacteria as a potential live therapeutic to control human infection is gaining increased attention. Earlier work with Micavibrio spp. and Bdellovibrio spp. has demonstrated the ability of these predators to control drug-resistant Gram-negative pathogens, Tier-1 select agents and biofilms. Additional studies also confirmed that introducing high doses of the predators into animals does not negatively impact animal well-being and might assist in reducing bacterial burden in vivo. The survival of predators requires extreme proximity to the prey cell, which might bring about horizontal transfer of genetic material, such as genes encoding for pathogenic genetic islands that would indirectly facilitate the spread of genetic material to other organisms. In this study, we examined the genetic makeup of several lab isolates of the predators Bdellovibriobacteriovorus and Micavibrioaeruginosavorus that were cultured repeatedly and stored over a course of 13 years. We also conducted controlled experiments in which the predators were sequentially co-cultured on Klebsiella pneumoniae followed by genetic analysis of the predator. In both cases, we saw little genetic variation and no evidence of horizontally transferred chromosomal DNA from the prey during predator-prey interaction. Culturing the predators repeatedly did not cause any change in predation efficacy.}, }
@article {pmid29746697, year = {2018}, author = {Legras, JL and Galeote, V and Bigey, F and Camarasa, C and Marsit, S and Nidelet, T and Sanchez, I and Couloux, A and Guy, J and Franco-Duarte, R and Marcet-Houben, M and Gabaldon, T and Schuller, D and Sampaio, JP and Dequin, S}, title = {Adaptation of S. cerevisiae to Fermented Food Environments Reveals Remarkable Genome Plasticity and the Footprints of Domestication.}, journal = {Molecular biology and evolution}, volume = {35}, number = {7}, pages = {1712-1727}, pmid = {29746697}, issn = {1537-1719}, mesh = {*Adaptation, Biological ; *Biological Evolution ; DNA Copy Number Variations ; *Domestication ; Fermentation ; Fermented Foods/*microbiology ; Gene Transfer, Horizontal ; Genome, Fungal ; Saccharomyces cerevisiae/*genetics ; Selection, Genetic ; }, abstract = {The budding yeast Saccharomyces cerevisiae can be found in the wild and is also frequently associated with human activities. Despite recent insights into the phylogeny of this species, much is still unknown about how evolutionary processes related to anthropogenic niches have shaped the genomes and phenotypes of S. cerevisiae. To address this question, we performed population-level sequencing of 82 S. cerevisiae strains from wine, flor, rum, dairy products, bakeries, and the natural environment (oak trees). These genomic data enabled us to delineate specific genetic groups corresponding to the different ecological niches and revealed high genome content variation across the groups. Most of these strains, compared with the reference genome, possessed additional genetic elements acquired by introgression or horizontal transfer, several of which were population-specific. In addition, several genomic regions in each population showed evidence of nonneutral evolution, as shown by high differentiation, or of selective sweeps including genes with key functions in these environments (e.g., amino acid transport for wine yeast). Linking genetics to lifestyle differences and metabolite traits has enabled us to elucidate the genetic basis of several niche-specific population traits, such as growth on galactose for cheese strains. These data indicate that yeast has been subjected to various divergent selective pressures depending on its niche, requiring the development of customized genomes for better survival in these environments. These striking genome dynamics associated with local adaptation and domestication reveal the remarkable plasticity of the S. cerevisiae genome, revealing this species to be an amazing complex of specialized populations.}, }
@article {pmid29745854, year = {2018}, author = {Nute, M and Chou, J and Molloy, EK and Warnow, T}, title = {The performance of coalescent-based species tree estimation methods under models of missing data.}, journal = {BMC genomics}, volume = {19}, number = {Suppl 5}, pages = {286}, pmid = {29745854}, issn = {1471-2164}, mesh = {Algorithms ; Classification/*methods ; Computer Simulation ; Genes ; *Genetic Speciation ; Genomics ; *Models, Genetic ; *Phylogeny ; Species Specificity ; }, abstract = {BACKGROUND: Estimation of species trees from multiple genes is complicated by processes such as incomplete lineage sorting, gene duplication and loss, and horizontal gene transfer, that result in gene trees that differ from each other and from the species phylogeny. Methods to estimate species trees in the presence of gene tree discord due to incomplete lineage sorting have been developed and proved to be statistically consistent when gene tree discord is due only to incomplete lineage sorting and every gene tree includes the full set of species.<br><br>RESULTS: We establish statistical consistency of certain coalescent-based species tree estimation methods under some models of taxon deletion from genes. We also evaluate the impact of missing data on four species tree estimation methods (ASTRAL-II, ASTRID, MP-EST, and SVDquartets) using simulated datasets with varying levels of incomplete lineage sorting, gene tree estimation error, and degrees/patterns of missing data.<br><br>CONCLUSIONS: All the species tree estimation methods improved in accuracy as the number of genes increased and often produced highly accurate species trees even when the amount of missing data was large. These results together indicate that accurate species tree estimation is possible under a variety of conditions, even when there are substantial amounts of missing data.}, }
@article {pmid29743625, year = {2018}, author = {Ahlstrom, CA and Bonnedahl, J and Woksepp, H and Hernandez, J and Olsen, B and Ramey, AM}, title = {Acquisition and dissemination of cephalosporin-resistant E. coli in migratory birds sampled at an Alaska landfill as inferred through genomic analysis.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {7361}, pmid = {29743625}, issn = {2045-2322}, mesh = {Alaska ; Animals ; Birds/*microbiology ; Cephalosporins/*pharmacology ; *Drug Resistance, Bacterial/genetics ; Escherichia coli/classification/drug effects/genetics/*isolation &amp; purification ; Feces/microbiology ; *Genomics ; *Models, Animal ; Phenotype ; Phylogeny ; *Waste Disposal Facilities ; Whole Genome Sequencing ; }, abstract = {Antimicrobial resistance (AMR) in bacterial pathogens threatens global health, though the spread of AMR bacteria and AMR genes between humans, animals, and the environment is still largely unknown. Here, we investigated the role of wild birds in the epidemiology of AMR Escherichia coli. Using next-generation sequencing, we characterized cephalosporin-resistant E. coli cultured from sympatric gulls and bald eagles inhabiting a landfill habitat in Alaska to identify genetic determinants conferring AMR, explore potential transmission pathways of AMR bacteria and genes at this site, and investigate how their genetic diversity compares to isolates reported in other taxa. We found genetically diverse E. coli isolates with sequence types previously associated with human infections and resistance genes of clinical importance, including blaCTX-M and blaCMY. Identical resistance profiles were observed in genetically unrelated E. coli isolates from both gulls and bald eagles. Conversely, isolates with indistinguishable core-genomes were found to have different resistance profiles. Our findings support complex epidemiological interactions including bacterial strain sharing between gulls and bald eagles and horizontal gene transfer among E. coli harboured by birds. Results suggest that landfills may serve as a source for AMR acquisition and/or maintenance, including bacterial sequence types and AMR genes relevant to human health.}, }
@article {pmid29743566, year = {2018}, author = {Willemsen, A and Carrasco, JL and Elena, SF and Zwart, MP}, title = {Going, going, gone: predicting the fate of genomic insertions in plant RNA viruses.}, journal = {Heredity}, volume = {121}, number = {5}, pages = {499-509}, pmid = {29743566}, issn = {1365-2540}, mesh = {DNA Transposable Elements/*genetics ; Gene Transfer, Horizontal ; *Genome, Viral ; Mutagenesis ; Potyvirus/*genetics ; RNA Viruses/*genetics ; Recombination, Genetic ; Sequence Deletion ; }, abstract = {Horizontal gene transfer is common among viruses, while they also have highly compact genomes and tend to lose artificial genomic insertions rapidly. Understanding the stability of genomic insertions in viral genomes is therefore relevant for explaining and predicting their evolutionary patterns. Here, we revisit a large body of experimental research on a plant RNA virus, tobacco etch potyvirus (TEV), to identify the patterns underlying the stability of a range of homologous and heterologous insertions in the viral genome. We obtained a wide range of estimates for the recombination rate-the rate at which deletions removing the insertion occur-and these appeared to be independent of the type of insertion and its location. Of the factors we considered, recombination rate was the best predictor of insertion stability, although we could not identify the specific sequence characteristics that would help predict insertion instability. We also considered experimentally the possibility that functional insertions lead to higher mutational robustness through increased redundancy. However, our observations suggest that both functional and non-functional increases in genome size decreased the mutational robustness. Our results therefore demonstrate the importance of recombination rates for predicting the long-term stability and evolution of viral RNA genomes and suggest that there are unexpected drawbacks to increases in genome size for mutational robustness.}, }
@article {pmid29741366, year = {2018}, author = {Garner, E and Chen, C and Xia, K and Bowers, J and Engelthaler, DM and McLain, J and Edwards, MA and Pruden, A}, title = {Metagenomic Characterization of Antibiotic Resistance Genes in Full-Scale Reclaimed Water Distribution Systems and Corresponding Potable Systems.}, journal = {Environmental science &amp; technology}, volume = {52}, number = {11}, pages = {6113-6125}, doi = {10.1021/acs.est.7b05419}, pmid = {29741366}, issn = {1520-5851}, mesh = {*Anti-Bacterial Agents ; Drug Resistance, Microbial ; Genes, Bacterial ; RNA, Ribosomal, 16S ; Wastewater ; *Water ; }, abstract = {Water reclamation provides a valuable resource for meeting nonpotable water demands. However, little is known about the potential for wastewater reuse to disseminate antibiotic resistance genes (ARGs). Here, samples were collected seasonally in 2014-2015 from four U.S. utilities' reclaimed and potable water distribution systems before treatment, after treatment, and at five points of use (POU). Shotgun metagenomic sequencing was used to profile the resistome (i.e., full contingent of ARGs) of a subset (n = 38) of samples. Four ARGs (qnrA, blaTEM, vanA, sul1) were quantified by quantitative polymerase chain reaction. Bacterial community composition (via 16S rRNA gene amplicon sequencing), horizontal gene transfer (via quantification of intI1 integrase and plasmid genes), and selection pressure (via detection of metals and antibiotics) were investigated as potential factors governing the presence of ARGs. Certain ARGs were elevated in all (sul1; p ≤ 0.0011) or some (blaTEM, qnrA; p ≤ 0.0145) reclaimed POU samples compared to corresponding potable samples. Bacterial community composition was weakly correlated with ARGs (Adonis, R[2] = 0.1424-0.1734) and associations were noted between 193 ARGs and plasmid-associated genes. This study establishes that reclaimed water could convey greater abundances of certain ARGs than potable waters and provides observations regarding factors that likely control ARG occurrence in reclaimed water systems.}, }
@article {pmid29739310, year = {2018}, author = {Gu, Y and Wang, Y and Sun, Y and Zhao, K and Xiang, Q and Yu, X and Zhang, X and Chen, Q}, title = {Genetic diversity and characterization of arsenic-resistant endophytic bacteria isolated from Pteris vittata, an arsenic hyperaccumulator.}, journal = {BMC microbiology}, volume = {18}, number = {1}, pages = {42}, pmid = {29739310}, issn = {1471-2180}, mesh = {Agrobacterium/growth &amp; development/*isolation &amp; purification ; Arsenic/pharmacology ; Bacillus/growth &amp; development/*isolation &amp; purification ; Bacteria/*classification/genetics/metabolism ; Bacterial Proteins/genetics ; DNA, Ribosomal/genetics ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Genetic Variation ; Indoleacetic Acids/metabolism ; Lead ; Mining ; Phylogeny ; Pteris/*microbiology ; RNA, Ribosomal, 16S/*genetics ; Zinc ; }, abstract = {BACKGROUND: Alleviating arsenic (As) contamination is a high-priority environmental issue. Hyperaccumulator plants may harbor endophytic bacteria able to detoxify As. Therefore, we investigated the distribution, diversity, As (III) resistance levels, and resistance-related functional genes of arsenite-resistant bacterial endophytes in Pteris vittata L. growing in a lead-zinc mining area with different As contamination levels.<br><br>RESULTS: A total of 116 arsenite-resistant bacteria were isolated from roots of P. vittata with different As concentrations. Based on the 16S rRNA gene sequence analysis of representative isolates, the isolates belonged to Proteobacteria, Actinobacteria, and Firmicutes. Major genera found were Agrobacterium, Stenotrophomonas, Pseudomonas, Rhodococcus, and Bacillus. The most highly arsenite-resistant bacteria (minimum inhibitory concentration&#x2009;>&#x2009;45&#xa0;mM) were isolated from P. vittata with high As concentrations and belonged to the genera Agrobacterium and Bacillus. The strains with high As tolerance also showed high levels of indole-3-acetic acid (IAA) production and carried arsB/ACR3(2) genes. The arsB and ACR3(2) were most likely horizontally transferred among the strains.<br><br>CONCLUSION: The results of this study suggest that P. vittata plants with high As concentrations may select diverse arsenite-resistant bacteria; this diversity might, at least partly, be a result of horizontal gene transfer. These diverse endophytic bacteria are potential candidates to enhance phytoremediation techniques.}, }
@article {pmid29738840, year = {2018}, author = {Liu, C and Liu, B and Zhang, Y and Jiang, F and Ren, Y and Li, S and Wang, H and Fan, W}, title = {Ancient horizontally transferred genes in the genome of California two-spot octopus, Octopus bimaculoides.}, journal = {Gene}, volume = {667}, number = {}, pages = {34-44}, doi = {10.1016/j.gene.2018.05.013}, pmid = {29738840}, issn = {1879-0038}, mesh = {Animals ; Evolution, Molecular ; Gene Ontology ; *Gene Transfer, Horizontal ; Octopodiformes/classification/*genetics ; Phylogeny ; Proteins/*genetics/metabolism ; Tissue Distribution ; }, abstract = {Horizontal gene transfer (HGT), a mechanism that shares genetic material between the host and donor from separated offspring branches, has been described as a means of producing novel and beneficial phenotypes for the host organisms. However, in molluscs, the second most diverse group, the existence of HGT is still controversial. In the present study, 12 HGT genes were identified from California two-spot octopus Octopus bimaculoides based on a similarity search, phylogenetic construction, gene composition analysis and PCR (Polymerase Chain Reaction) validation. Based on the phylogenetic topologies, ten HGT genes were identified to have been transferred into the possible molluscan ancestor, possibly before its radiation. Furthermore, most of the donor organisms were predicted to be familiar bacteria in marine environments. These horizontally transferred genes were under a strong negative selection and could be transcribed in octopus functionally. The predicted biochemical functions of these genes include metabolism, neurotransmission, immune defense and tissue integrity. Seven Zn-metalloproteinases were validated as the main type of HGT genes in octopus with divergent motif composition, intron presence and phylogenetic relationship to the endogenous ones. Furthermore, the functions of Zn-metalloproteinase were predicted to be responsible for immune defense and tissue remolding. Three HGT genes were distributed mainly in the nervous system and were predicted to regulate the neurotransmission through glia-neuronal interactions. The results collectively indicated the existence of HGT in molluscs and its potential contribution to the evolution of octopus with regards to functional innovation and adaptability.}, }
@article {pmid29738837, year = {2018}, author = {Kamlárová, A and Chovanová, K and Zámocký, M}, title = {Peculiar genes for thermostable bifunctional catalase-peroxidases in Chaetomium thermophilum and their molecular evolution.}, journal = {Gene}, volume = {666}, number = {}, pages = {83-91}, doi = {10.1016/j.gene.2018.05.007}, pmid = {29738837}, issn = {1879-0038}, mesh = {Amino Acid Sequence ; Catalase/chemistry/*genetics/metabolism ; Catalytic Domain ; Chaetomium/enzymology/*genetics/growth &amp; development ; Conserved Sequence ; Enzyme Stability ; Evolution, Molecular ; Fungal Proteins/chemistry/*genetics/metabolism ; Gene Expression ; Hot Temperature ; Models, Molecular ; Peroxidase/chemistry/*genetics/metabolism ; Phylogeny ; Protein Conformation, alpha-Helical ; }, abstract = {Catalase-peroxidases represent one important subfamily of ancestral antioxidant enzymes originally evolved in bacteria for the protection against various forms of oxidative stress. KatG genes coding for these bifunctional catalase-peroxidases were during their peculiar evolution transferred from Bacteroidetes to the fungal phylum Ascomycota via a horizontal gene transfer event. Here we analyse a newly discovered fungal katG gene without introns coding for a thermostable catalase-peroxidase from Chaetomium thermophilum var. dissitum and compare it with closely related thermophilic and mesophilic katGs and their translation products. We show that CthediskatG gene resembling its bacterial counterparts has a typical eukaryotic transcription start site and also contains a conserved eukaryotic polyadenylation signal behind its 3' terminus. Moreover, we have detected polyA tails in corresponding transcripts of katG from two different mRNA libraries of C. thermophilum var. disstum. Although otherwise highly conserved, only in katG genes of two C. thermophilum variants a unique 60 bp long deletion leading in the translated product with high probability to a modified loop and thus access to the prosthetic heme group was observed. We also present an updated molecular phylogeny revealing the evolutionary position of fungal thermostable catalase-peroxidases within a robust phylogenetic tree of the whole KatG subfamily.}, }
@article {pmid29738815, year = {2018}, author = {Orji, FA and Ugbogu, OC and Ugbogu, EA and Barbabosa-Pliego, A and Monroy, JC and Elghandour, MMMY and Salem, AZM}, title = {Pathogenic flora composition and overview of the trends used for bacterial pathogenicity identifications.}, journal = {Microbial pathogenesis}, volume = {121}, number = {}, pages = {139-146}, doi = {10.1016/j.micpath.2018.05.006}, pmid = {29738815}, issn = {1096-1208}, mesh = {Animals ; Bacteria/genetics/*isolation &amp; purification ; Biofilms ; Gene Transfer, Horizontal ; *Genomic Islands ; Host-Pathogen Interactions/genetics ; Humans ; Immunity, Innate ; Phylogeny ; Proteomics ; Quorum Sensing ; Virulence Factors ; }, abstract = {Over 250 species of resident flora in the class of bacteria are known to be associated with humans. These conventional flora compositions is often determined by factors which may not be limited to genetics, age, sex, stress and nutrition of humans. Man is constantly in contact with bacteria through media such as air, water, soil and food. This paper reviews the concept of bacterial pathogenesis from the sequential point of colonization to tissue injury. The paper in addition to examination of the factors which enhance virulence in bacterial pathogens also x-rayed the concept of pathogenicity islands and the next generation approaches or rather current trends/methods used in the bacterial pathogenicity investigations. In terms of pathogenicity which of course is the capacity to cause disease in animals, requires that the attacking bacterial strain is virulent, and has ability to bypass the host immune defensive mechanisms. In order to achieve or exhibit pathogenicity, the virulence factors required by microorganisms include capsule, pigments, enzymes, iron acquisition through siderophores. Bacterial Pathogenicity Islands as a distinct concept in bacterial pathogenesis are just loci on the chromosome or extra chromosomal units which are acquired by horizontal gene transfer within pathogens in a microbial community or biofilm. In the area of laboratory investigations, bacterial pathogenesis was initially carried out using culture dependent approaches, which can only detect about 1% of human and veterinary-important pathogens. However, in the recent paradigms shift, the use of proteomics, metagenomics, phylogenetic tree analyses, spooligotyping, and finger printing etc. have made it possible that 100% of the bacterial pathogens in nature can be extensively studied.}, }
@article {pmid29735763, year = {2018}, author = {Banerjee, SK and Rutley, R and Bussey, J}, title = {Diversity and Dynamics of the Canadian Coastal Vibrio Community: an Emerging Trend Detected in the Temperate Regions.}, journal = {Journal of bacteriology}, volume = {200}, number = {15}, pages = {}, pmid = {29735763}, issn = {1098-5530}, mesh = {Animals ; Atlantic Ocean ; Biodiversity ; Canada ; Estuaries ; Mollusca/*microbiology ; Pacific Ocean ; Time Factors ; Vibrio/*classification/genetics/*isolation &amp; purification ; *Water Microbiology ; }, abstract = {Vibrio species are indigenous to the marine and estuarine environments around the world and are the leading cause of water- and seafood-borne illnesses due to conditions favoring the transmission and growth of the species. Horizontal gene transfer, recombination, and mutation enable Vibrio spp. to adapt rapidly to environmental challenges from biotic and abiotic parameters, including temperature, salinity, and nutrient status of the coastal waters. This surveillance study provides evidence of Vibrio cholerae emerging in the temperate estuaries of Canada, thereby redefining the diversity and dynamics of its coastal Vibrio population. The presence of the pathogenic context in Vibrio parahaemolyticus was also detected with an increasing trend during the study period.IMPORTANCE Proliferation and abundance of the harmful biotypes of Vibrio spp. in the estuaries of Canada indicate the possibility of producing contaminated seafood for human consumption. The findings of this surveillance study may lead to awareness which may help efforts to reduce the occurrence of illnesses or outbreaks caused by Vibrio spp. in seafood.}, }
@article {pmid29735685, year = {2018}, author = {Brynildsrud, OB and Eldholm, V and Bohlin, J and Uadiale, K and Obaro, S and Caugant, DA}, title = {Acquisition of virulence genes by a carrier strain gave rise to the ongoing epidemics of meningococcal disease in West Africa.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {21}, pages = {5510-5515}, pmid = {29735685}, issn = {1091-6490}, mesh = {Africa, Western/epidemiology ; Antigens, Bacterial/genetics/immunology ; *Epidemics ; Gene Expression Profiling ; Humans ; Meningitis, Meningococcal/*epidemiology/microbiology/prevention &amp; control ; Meningococcal Vaccines/*administration &amp; dosage/immunology ; Neisseria meningitidis/classification/genetics/immunology/*isolation &amp; purification ; Population Surveillance ; Spatio-Temporal Analysis ; Viral Proteins/*genetics ; Virulence/*genetics ; }, abstract = {In the African meningitis belt, a region of sub-Saharan Africa comprising 22 countries from Senegal in the west to Ethiopia in the east, large epidemics of serogroup A meningococcal meningitis have occurred periodically. After gradual introduction from 2010 of mass vaccination with a monovalent meningococcal A conjugate vaccine, serogroup A epidemics have been eliminated. Starting in 2013, the northwestern part of Nigeria has been affected by yearly outbreaks of meningitis caused by a novel strain of serogroup C Neisseria meningitidis (NmC). In 2015, the strain spread to the neighboring country Niger, where it caused a severe epidemic. Following a relative calm in 2016, the largest ever recorded epidemic of NmC broke out in Nigeria in 2017. Here, we describe the recent evolution of this new outbreak strain and show how the acquisition of capsule genes and virulence factors by a strain previously circulating asymptomatically in the African population led to the emergence of a virulent pathogen. This study illustrates the power of long-read whole-genome sequencing, combined with Illumina sequencing, for high-resolution epidemiological investigations.}, }
@article {pmid29733586, year = {2018}, author = {Jiang, L and Luo, C and Zhang, D and Song, M and Sun, Y and Zhang, G}, title = {Biphenyl-Metabolizing Microbial Community and a Functional Operon Revealed in E-Waste-Contaminated Soil.}, journal = {Environmental science &amp; technology}, volume = {52}, number = {15}, pages = {8558-8567}, doi = {10.1021/acs.est.7b06647}, pmid = {29733586}, issn = {1520-5851}, mesh = {Biphenyl Compounds ; *Electronic Waste ; *Microbiota ; Operon ; *Polychlorinated Biphenyls ; Soil ; Soil Microbiology ; *Soil Pollutants ; }, abstract = {Primitive electronic waste (e-waste) recycling activities release massive amounts of persistent organic pollutants (POPs) and heavy metals into surrounding soils, posing a major threat to the ecosystem and human health. Microbes capable of metabolizing POPs play important roles in POPs remediation in soils, but their phylotypes and functions remain unclear. Polychlorinated biphenyls (PCBs), one of the main pollutants in e-waste contaminated soils, have drawn increasing attention due to their high persistence, toxicity, and bioaccumulation. In the present study, we employed the culture-independent method of DNA stable-isotope probing to identify active biphenyl and PCB degraders in e-waste-contaminated soil. A total of 19 rare operational taxonomic units and three dominant bacterial genera (Ralstonia, Cupriavidus, and uncultured bacterium DA101) were enriched in the [13]C heavy DNA fraction, confirming their functions in PCBs metabolism. Additionally, a 13.8 kb bph operon was amplified, containing a bphA gene labeled by [13]C that was concentrated in the heavy DNA fraction. The tetranucleotide signature characteristics of the bph operon suggest that it originated from Ralstonia. The bph operon may be shared by horizontal gene transfer because it contains a transposon gene and is found in various bacterial species. This study gives us a deeper understanding of PCB-degrading mechanisms and provides a potential resource for the bioremediation of PCBs-contaminated soils.}, }
@article {pmid29732410, year = {2018}, author = {Kabeya, N and Fonseca, MM and Ferrier, DEK and Navarro, JC and Bay, LK and Francis, DS and Tocher, DR and Castro, LFC and Monroig, &#xd3;}, title = {Genes for de novo biosynthesis of omega-3 polyunsaturated fatty acids are widespread in animals.}, journal = {Science advances}, volume = {4}, number = {5}, pages = {eaar6849}, pmid = {29732410}, issn = {2375-2548}, mesh = {Animals ; Biosynthetic Pathways/*genetics ; Enzyme Activation ; Fatty Acid Desaturases/genetics ; Fatty Acids, Omega-3/*biosynthesis ; *Gene Expression Regulation, Enzymologic ; Genome ; Genomics/methods ; Mutation ; Phylogeny ; }, abstract = {Marine ecosystems are responsible for virtually all production of omega-3 (ω3) long-chain polyunsaturated fatty acids (PUFA), which are essential nutrients for vertebrates. Current consensus is that marine microbes account for this production, given their possession of key enzymes including methyl-end (or "ωx") desaturases. ωx desaturases have also been described in a small number of invertebrate animals, but their precise distribution has not been systematically explored. This study identifies 121 ωx desaturase sequences from 80 species within the Cnidaria, Rotifera, Mollusca, Annelida, and Arthropoda. Horizontal gene transfer has contributed to this hitherto unknown widespread distribution. Functional characterization of animal ωx desaturases provides evidence that multiple invertebrates have the ability to produce ω3 PUFA de novo and further biosynthesize ω3 long-chain PUFA. This finding represents a fundamental revision in our understanding of ω3 long-chain PUFA production in global food webs, by revealing that numerous widespread and abundant invertebrates have the endogenous capacity to make significant contributions beyond that coming from marine microbes.}, }
@article {pmid29731740, year = {2018}, author = {Wu, J and Huang, Y and Rao, D and Zhang, Y and Yang, K}, title = {Evidence for Environmental Dissemination of Antibiotic Resistance Mediated by Wild Birds.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {745}, pmid = {29731740}, issn = {1664-302X}, abstract = {The aquatic bird, egret, could carry antibiotic resistance (AR) from a contaminated waterway (Jin River, Chengdu, China) into the surrounding environment (Wangjianglou Park). A systematic study was carried out on the unique environmental dissemination mode of AR mediated by birds. The minimum inhibitory concentrations of various antibiotics against the environmental Escherichia coli isolates were used to evaluate the bacterial AR at the environmental locations where these isolates were recovered, i.e., the Jin River water, the egret feces, the park soil, and the campus soil. The level of AR in the park soil was significantly higher than that in the campus soil that was seldom affected by the egrets, which suggested that the egrets mediated the transportation of AR from the polluted waterway to the park. Genotyping of the resistant E. coli isolates via repetitive-element PCR gave no strong correlation between the genotypes and the AR patterns of the bacteria. So, the transfer of resistant strains should not be the main mode of AR transportation in this process. The results of real-time PCR revealed that the abundance of antibiotic resistance genes (ARGs) and mobile genetic element (MGE) sequences (transposase and integrase genes) declined along the putative transportation route. The transportation of ARGs could be due to their linkage with MGE sequences, and horizontal gene transfer should have contributed to the process. The movable colistin-resistance gene mcr-1 was detected among the colistin-resistant E. coli strains isolated from the river water and the egret feces, which indicated the possibility of the environmental dissemination of this gene. Birds, especially the migratory birds, for the role they played on the dissemination of environmental AR, should be considered when studying the ecology of AR.}, }
@article {pmid29728072, year = {2018}, author = {Gambetta, GA and Matthews, MA and Syvanen, M}, title = {The Xylella fastidosa RTX operons: evidence for the evolution of protein mosaics through novel genetic exchanges.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {329}, pmid = {29728072}, issn = {1471-2164}, support = {01-0712//California Department of Food and Agriculture (US)/ ; 2005-34442-15841//USDA/ ; }, mesh = {Amino Acid Sequence ; Bacterial Proteins/classification/genetics ; Base Sequence ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Hemolysin Proteins/classification/*genetics ; Operon/*genetics ; Phylogeny ; Plant Diseases/microbiology ; Plant Leaves/genetics/metabolism/microbiology ; Sequence Alignment ; Vitis/genetics/metabolism/microbiology ; Xylella/*genetics ; }, abstract = {BACKGROUND: Xylella fastidiosa (Xf) is a gram negative bacterium inhabiting the plant vascular system. In most species this bacterium lives as a benign symbiote, but in several agriculturally important plants (e.g. coffee, citrus, grapevine) Xf is pathogenic. Xf has four loci encoding homologues to hemolysin RTX proteins, virulence factors involved in a wide range of plant pathogen interactions.<br><br>RESULTS: We show that all four genes are expressed during pathogenesis in grapevine. The sequences from these four genes have a complex repetitive structure. At the C-termini, sequence diversity between strains is what would be expected from orthologous genes. However, within strains there is no N-terminal homology, indicating these loci encode RTXs of different functions and/or specificities. More striking is that many of the orthologous loci between strains share this extreme variation at the N-termini. Thus these RTX orthologues are most easily visualized as fusions between the orthologous C-termini and different N-termini. Further, the four genes are found in operons having a peculiar structure with an extensively duplicated module encoding a small protein with homology to the N-terminal region of the full length RTX. Surprisingly, some of these small peptides are most similar not to their corresponding full length RTX, but to the N-termini of RTXs from other Xf strains, and even other remotely related species.<br><br>CONCLUSIONS: These results demonstrate that these genes are expressed in planta during pathogenesis. Their structure suggests extensive evolutionary restructuring through horizontal gene transfers and heterologous recombination mechanisms. The sum of the evidence suggests these repetitive modules are a novel kind of mobile genetic element.}, }
@article {pmid29726587, year = {2018}, author = {Hulin, MT and Armitage, AD and Vicente, JG and Holub, EB and Baxter, L and Bates, HJ and Mansfield, JW and Jackson, RW and Harrison, RJ}, title = {Comparative genomics of Pseudomonas syringae reveals convergent gene gain and loss associated with specialization onto cherry (Prunus avium).}, journal = {The New phytologist}, volume = {219}, number = {2}, pages = {672-696}, doi = {10.1111/nph.15182}, pmid = {29726587}, issn = {1469-8137}, support = {BB/P006272/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Alleles ; Bacterial Secretion Systems ; Gene Transfer, Horizontal/genetics ; *Genes, Bacterial ; *Genomics ; Models, Biological ; Phylogeny ; Plant Diseases/microbiology ; Prunus avium/*microbiology ; Pseudomonas syringae/classification/*genetics/pathogenicity ; Sequence Analysis, DNA ; Virulence/genetics ; Virulence Factors/metabolism ; }, abstract = {Genome-wide analyses of the effector- and toxin-encoding genes were used to examine the phylogenetics and evolution of pathogenicity amongst diverse strains of Pseudomonas syringae causing bacterial canker of cherry (Prunus avium), including pathovars P. syringae pv morsprunorum (Psm) races 1 and 2, P. syringae pv syringae (Pss) and P. syringae pv avii. Phylogenetic analyses revealed Psm races and P. syringae pv avii clades were distinct and were each monophyletic, whereas cherry-pathogenic strains of Pss were interspersed amongst strains from other host species. A maximum likelihood approach was used to predict effectors associated with pathogenicity on cherry. Pss possesses a smaller repertoire of type III effectors but has more toxin biosynthesis clusters than Psm and P. syringae pv avii. Evolution of cherry pathogenicity was correlated with gain of genes such as hopAR1 and hopBB1 through putative phage transfer and horizontal transfer respectively. By contrast, loss of the avrPto/hopAB redundant effector group was observed in cherry-pathogenic clades. Ectopic expression of hopAB and hopC1 triggered the hypersensitive reaction in cherry leaves, confirming computational predictions. Cherry canker provides a fascinating example of convergent evolution of pathogenicity that is explained by the mix of effector and toxin repertoires acting on a common host.}, }
@article {pmid29724163, year = {2018}, author = {Clasen, FJ and Pierneef, RE and Slippers, B and Reva, O}, title = {EuGI: a novel resource for studying genomic islands to facilitate horizontal gene transfer detection in eukaryotes.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {323}, pmid = {29724163}, issn = {1471-2164}, support = {93134//National Research Foundation (ZA)/ ; 93664//National Research Foundation (ZA)/ ; 102973//National Research Foundation (ZA)/ ; }, mesh = {Aspergillus fumigatus/genetics ; Comparative Genomic Hybridization ; Databases, Genetic ; Eukaryota/*genetics ; *Gene Transfer, Horizontal ; Genome, Fungal ; Genomic Islands ; Internet ; *User-Computer Interface ; }, abstract = {BACKGROUND: Genomic islands (GIs) are inserts of foreign DNA that have potentially arisen through horizontal gene transfer (HGT). There are evidences that GIs can contribute significantly to the evolution of prokaryotes. The acquisition of GIs through HGT in eukaryotes has, however, been largely unexplored. In this study, the previously developed GI prediction tool, SeqWord Gene Island Sniffer (SWGIS), is modified to predict GIs in eukaryotic chromosomes. Artificial simulations are used to estimate ratios of predicting false positive and false negative GIs by inserting GIs into different test chromosomes and performing the SWGIS v2.0 algorithm. Using SWGIS v2.0, GIs are then identified in 36 fungal, 22 protozoan and 8 invertebrate genomes.<br><br>RESULTS: SWGIS v2.0 predicts GIs in large eukaryotic chromosomes based on the atypical nucleotide composition of these regions. Averages for predicting false negative and false positive GIs were 20.1% and 11.01% respectively. A total of 10,550 GIs were identified in 66 eukaryotic species with 5299 of these GIs coding for at least one functional protein. The EuGI web-resource, freely accessible at http://eugi.bi.up.ac.za , was developed that allows browsing the database created from identified GIs and genes within GIs through an interactive and visual interface.<br><br>CONCLUSIONS: SWGIS v2.0 along with the EuGI database, which houses GIs identified in 66 different eukaryotic species, and the EuGI web-resource, provide the first comprehensive resource for studying HGT in eukaryotes.}, }
@article {pmid29723434, year = {2018}, author = {Schmitt, A and Jiang, K and Camacho, MI and Jonna, VR and Hofer, A and Westerlund, F and Christie, PJ and Berntsson, RP}, title = {PrgB promotes aggregation, biofilm formation, and conjugation through DNA binding and compaction.}, journal = {Molecular microbiology}, volume = {109}, number = {3}, pages = {291-305}, pmid = {29723434}, issn = {1365-2958}, support = {R01 GM048746/GM/NIGMS NIH HHS/United States ; R21 AI105454/AI/NIAID NIH HHS/United States ; }, mesh = {Adherens Junctions/*physiology ; Adhesins, Bacterial/*chemistry/genetics/*metabolism ; Biofilms/*growth &amp; development ; Cell Line ; *Conjugation, Genetic ; DNA-Binding Proteins/chemistry/genetics/metabolism ; Enterococcus faecalis/genetics/*physiology ; Gene Transfer, Horizontal ; Lipopolysaccharides/chemistry/metabolism ; Plasmids/chemistry/genetics/metabolism ; Protein Binding ; Protein Conformation ; Teichoic Acids/chemistry/metabolism ; Type IV Secretion Systems ; }, abstract = {Gram-positive bacteria deploy type IV secretion systems (T4SSs) to facilitate horizontal gene transfer. The T4SSs of Gram-positive bacteria rely on surface adhesins as opposed to conjugative pili to facilitate mating. Enterococcus faecalis PrgB is a surface adhesin that promotes mating pair formation and robust biofilm development in an extracellular DNA (eDNA) dependent manner. Here, we report the structure of the adhesin domain of PrgB. The adhesin domain binds and compacts DNA in vitro. In vivo PrgB deleted of its adhesin domain does not support cellular aggregation, biofilm development and conjugative DNA transfer. PrgB also binds lipoteichoic acid (LTA), which competes with DNA binding. We propose that PrgB binding and compaction of eDNA facilitates cell aggregation and plays an important role in establishment of early biofilms in mono- or polyspecies settings. Within these biofilms, PrgB mediates formation and stabilization of direct cell-cell contacts through alternative binding of cell-bound LTA, which in turn promotes establishment of productive mating junctions and efficient intra- or inter-species T4SS-mediated gene transfer.}, }
@article {pmid29722872, year = {2018}, author = {Nero, TM and Dalia, TN and Wang, JC and Kysela, DT and Bochman, ML and Dalia, AB}, title = {ComM is a hexameric helicase that promotes branch migration during natural transformation in diverse Gram-negative species.}, journal = {Nucleic acids research}, volume = {46}, number = {12}, pages = {6099-6111}, pmid = {29722872}, issn = {1362-4962}, support = {K22 AI118863/AI/NIAID NIH HHS/United States ; R01 GM113121/GM/NIGMS NIH HHS/United States ; R35 GM122556/GM/NIGMS NIH HHS/United States ; R35 GM128674/GM/NIGMS NIH HHS/United States ; }, mesh = {Acinetobacter/enzymology/*genetics ; Adenosine Triphosphate/metabolism ; Bacterial Proteins/physiology ; DNA/metabolism ; DNA Helicases/*metabolism/physiology ; DNA Repair ; DNA, Bacterial/metabolism ; DNA, Single-Stranded/metabolism ; DNA-Binding Proteins/physiology ; Gene Transfer, Horizontal ; Gram-Negative Bacteria/enzymology/genetics ; Protein Multimerization ; *Transformation, Genetic ; Vibrio cholerae/enzymology/*genetics ; }, abstract = {Acquisition of foreign DNA by natural transformation is an important mechanism of adaptation and evolution in diverse microbial species. Here, we characterize the mechanism of ComM, a broadly conserved AAA+ protein previously implicated in homologous recombination of transforming DNA (tDNA) in naturally competent Gram-negative bacterial species. In vivo, we found that ComM was required for efficient comigration of linked genetic markers in Vibrio cholerae and Acinetobacter baylyi, which is consistent with a role in branch migration. Also, ComM was particularly important for integration of tDNA with increased sequence heterology, suggesting that its activity promotes the acquisition of novel DNA sequences. In vitro, we showed that purified ComM binds ssDNA, oligomerizes into a hexameric ring, and has bidirectional helicase and branch migration activity. Based on these data, we propose a model for tDNA integration during natural transformation. This study provides mechanistic insight into the enigmatic steps involved in tDNA integration and uncovers the function of a protein required for this conserved mechanism of horizontal gene transfer.}, }
@article {pmid29718236, year = {2018}, author = {Goz, E and Zafrir, Z and Tuller, T}, title = {Universal evolutionary selection for high dimensional silent patterns of information hidden in the redundancy of viral genetic code.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {19}, pages = {3241-3248}, pmid = {29718236}, issn = {1367-4811}, mesh = {Codon ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Code ; *Genome, Viral ; *Genomics ; Open Reading Frames ; Selection, Genetic ; Viruses/*genetics ; }, abstract = {MOTIVATION: Understanding how viruses co-evolve with their hosts and adapt various genomic level strategies in order to ensure their fitness may have essential implications in unveiling the secrets of viral evolution, and in developing new vaccines and therapeutic approaches. Here, based on a novel genomic analysis of 2625 different viruses and 439 corresponding host organisms, we provide evidence of universal evolutionary selection for high dimensional 'silent' patterns of information hidden in the redundancy of viral genetic code.<br><br>RESULTS: Our model suggests that long substrings of nucleotides in the coding regions of viruses from all classes, often also repeat in the corresponding viral hosts from all domains of life. Selection for these substrings cannot be explained only by such phenomena as codon usage bias, horizontal gene transfer and the encoded proteins. Genes encoding structural proteins responsible for building the core of the viral particles were found to include more host-repeating substrings, and these substrings tend to appear in the middle parts of the viral coding regions. In addition, in human viruses these substrings tend to be enriched with motives related to transcription factors and RNA binding proteins. The host-repeating substrings are possibly related to the evolutionary pressure on the viruses to effectively interact with host's intracellular factors and to efficiently escape from the host's immune system.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid29718211, year = {2018}, author = {Kapust, N and Nelson-Sathi, S and Schönfeld, B and Hazkani-Covo, E and Bryant, D and Lockhart, PJ and Röttger, M and Xavier, JC and Martin, WF}, title = {Failure to Recover Major Events of Gene Flux in Real Biological Data Due to Method Misapplication.}, journal = {Genome biology and evolution}, volume = {10}, number = {5}, pages = {1198-1209}, pmid = {29718211}, issn = {1759-6653}, mesh = {Archaea/genetics ; Chloroplast Proteins/genetics ; Computational Biology/*standards ; Eukaryota/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Plastid ; Genomics ; Models, Genetic ; *Phylogeny ; Plastids/*classification/*genetics ; Software ; Symbiosis/genetics ; Validation Studies as Topic ; }, abstract = {In prokaryotes, known mechanisms of lateral gene transfer (transformation, transduction, conjugation, and gene transfer agents) generate new combinations of genes among chromosomes during evolution. In eukaryotes, whose host lineage is descended from archaea, lateral gene transfer from organelles to the nucleus occurs at endosymbiotic events. Recent genome analyses studying gene distributions have uncovered evidence for sporadic, discontinuous events of gene transfer from bacteria to archaea during evolution. Other studies have used traditional models designed to investigate gene family size evolution (Count) to support claims that gene transfer to archaea was continuous during evolution, rather than involving occasional periodic mass gene influx events. Here, we show that the methodology used in analyses favoring continuous gene transfers to archaea was misapplied in other studies and does not recover known events of single simultaneous origin for many genes followed by differential loss in real data: plastid genomes. Using the same software and the same settings, we reanalyzed presence/absence pattern data for proteins encoded in plastid genomes and for eukaryotic protein families acquired from plastids. Contrary to expectations under a plastid origin model, we found that the methodology employed inferred that gene acquisitions occurred uniformly across the plant tree. Sometimes as many as nine different acquisitions by plastid DNA were inferred for the same protein family. That is, the methodology that recovered gradual and continuous lateral gene transfer among lineages for archaea obtains the same result for plastids, even though it is known that massive gains followed by gradual differential loss is the true evolutionary process that generated plastid gene distribution data. Our findings caution against the use of models designed to study gene family size evolution for investigating gene transfer processes, especially when transfers involving more than one gene per event are possible.}, }
@article {pmid29717025, year = {2018}, author = {Sukmana, A and Yang, Z}, title = {The type IV pilus assembly motor PilB is a robust hexameric ATPase with complex kinetics.}, journal = {The Biochemical journal}, volume = {475}, number = {11}, pages = {1979-1993}, doi = {10.1042/BCJ20180167}, pmid = {29717025}, issn = {1470-8728}, mesh = {Acidobacteria/chemistry/genetics/*metabolism ; Adenosine Triphosphatases/chemistry/genetics/*metabolism ; Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Bacterial Proteins/chemistry/genetics/*metabolism ; Fimbriae, Bacterial/chemistry/*enzymology/genetics ; Kinetics ; Models, Molecular ; Oxidoreductases/chemistry/genetics/*metabolism ; Sequence Alignment ; }, abstract = {The bacterial type IV pilus (T4P) is a versatile nanomachine that functions in pathogenesis, biofilm formation, motility, and horizontal gene transfer. T4P assembly is powered by the motor ATPase PilB which is proposed to hydrolyze ATP by a symmetrical rotary mechanism. This mechanism, which is deduced from the structure of PilB, is untested. Here, we report the first kinetic studies of the PilB ATPase, supporting co-ordination among the protomers of this hexameric enzyme. Analysis of the genome sequence of Chloracidobacterium thermophilum identified a pilB gene whose protein we then heterologously expressed. This PilB formed a hexamer in solution and exhibited highly robust ATPase activity. It displays complex steady-state kinetics with an incline followed by a decline over an ATP concentration range of physiological relevance. The incline is multiphasic and the decline signifies substrate inhibition. These observations suggest that variations in intracellular ATP concentrations may regulate T4P assembly and T4P-mediated functions in vivo in accordance with the physiological state of bacteria with unanticipated complexity. We also identified a mutant pilB gene in the genomic DNA of C. thermophilum from an enrichment culture. The mutant PilB variant, which is significantly less active, exhibited similar inhibition of its ATPase activity by high concentrations of ATP. Our findings here with the PilB ATPase from C. thermophilum provide the first line of biochemical evidence for the co-ordination among PilB protomers consistent with the symmetrical rotary model of catalysis based on structural studies.}, }
@article {pmid29717009, year = {2018}, author = {Hullahalli, K and Rodrigues, M and Nguyen, UT and Palmer, K}, title = {An Attenuated CRISPR-Cas System in Enterococcus faecalis Permits DNA Acquisition.}, journal = {mBio}, volume = {9}, number = {3}, pages = {}, pmid = {29717009}, issn = {2150-7511}, support = {R01 AI116610/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/metabolism ; *CRISPR-Cas Systems ; Clustered Regularly Interspaced Short Palindromic Repeats ; DNA Replication ; DNA, Bacterial/*genetics/metabolism ; Enterococcus faecalis/*genetics/metabolism ; }, abstract = {Antibiotic-resistant bacteria are critical public health concerns. Among the prime causative factors for the spread of antibiotic resistance is horizontal gene transfer (HGT). A useful model organism for investigating the relationship between HGT and antibiotic resistance is the opportunistic pathogen Enterococcus faecalis, since the species possesses highly conjugative plasmids that readily disseminate antibiotic resistance genes and virulence factors in nature. Unlike many commensal E. faecalis strains, the genomes of multidrug-resistant (MDR) E. faecalis clinical isolates are enriched for mobile genetic elements (MGEs) and lack clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein (Cas) genome defense systems. CRISPR-Cas systems cleave foreign DNA in a programmable, sequence-specific manner and are disadvantageous for MGE-derived genome expansion. An unexplored facet of CRISPR biology in E. faecalis is that MGEs that are targeted by native CRISPR-Cas systems can be maintained transiently. Here, we investigate the basis for this "CRISPR tolerance." We observe that E. faecalis can maintain self-targeting constructs that direct Cas9 to cleave the chromosome, but at a fitness cost. Interestingly, DNA repair genes were not upregulated during self-targeting, but integrated prophages were strongly induced. We determined that low cas9 expression contributes to this transient nonlethality and used this knowledge to develop a robust CRISPR-assisted genome-editing scheme. Our results suggest that E. faecalis has maximized the potential for DNA acquisition by attenuating its CRISPR machinery, thereby facilitating the acquisition of potentially beneficial MGEs that may otherwise be restricted by genome defense.IMPORTANCE CRISPR-Cas has provided a powerful toolkit to manipulate bacteria, resulting in improved genetic manipulations and novel antimicrobials. These powerful applications rely on the premise that CRISPR-Cas chromosome targeting, which leads to double-stranded DNA breaks, is lethal. In this study, we show that chromosomal CRISPR targeting in Enterococcus faecalis is transiently nonlethal. We uncover novel phenotypes associated with this "CRISPR tolerance" and, after determining its genetic basis, develop a genome-editing platform in E. faecalis with negligible off-target effects. Our findings reveal a novel strategy exploited by a bacterial pathogen to cope with CRISPR-induced conflicts to more readily accept DNA, and our robust CRISPR editing platform will help simplify genetic modifications in this organism.}, }
@article {pmid29713466, year = {2018}, author = {Li, X and Fu, Y and Shen, M and Huang, D and Du, X and Hu, Q and Zhou, Y and Wang, D and Yu, Y}, title = {Dissemination of blaNDM-5 gene via an IncX3-type plasmid among non-clonal Escherichia coli in China.}, journal = {Antimicrobial resistance and infection control}, volume = {7}, number = {}, pages = {59}, pmid = {29713466}, issn = {2047-2994}, mesh = {Anti-Bacterial Agents/therapeutic use ; Carbapenems/therapeutic use ; China/epidemiology ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/drug effects/*genetics/isolation &amp; purification ; Escherichia coli Infections/epidemiology ; Gene Transfer, Horizontal/*genetics ; Humans ; Microbial Sensitivity Tests ; Plasmids/*genetics ; beta-Lactamases/*genetics ; }, abstract = {BACKGROUND: The emergence and spread of New Delhi metallo-β-lactamase-producing Enterobacteriaceae has been a serious challenge to manage in the clinic due to its rapid dissemination of multi-drug resistance worldwide. As one main type of carbapenemases, New Delhi metallo-β-lactamase (NDM)is able to confer resistance to almost all β-lactams, including carbapenems, in Enterobacteriaceae. Recently, New Delhi metallo-β-lactamase-5 attracted extensive attention because of increased resistance to carbapenems and widespread dissemination. However, the dissemination mechanism of blaNDM-5 gene remains unclear.<br><br>METHODS: A total of 224 carbapenem-resistant Enterobacteriaceae isolates (CRE) were collected from different hospitals in Zhejiang province. NDM-5-positive isolates were identified and subjected to genotyping, susceptibility testing, and clinical data analysis. We established the genetic location of blaNDM-5 with southern blot hybridisation, and analysed plasmids containing blaNDM-5 with filter mating and DNA sequencing.<br><br>RESULTS: Eleven New Delhi metallo-&#x3b2;-lactamase-5 (NDM-5)-producing strains were identified, including 9 Escherichia coli strains, 1 Klebsiella pneumoniae strain, and 1 Citrobacter freundii strain. No epidemiological links for E. coli isolates were identified by multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). S1-PFGE and southern blot suggested that the blaNDM-5 gene was located on a 46-kb IncX3-type plasmid in all isolates. Nine of the 11 isolates (81.8%) tested could successfully transfer their carbapenem-resistant phenotype to E. coli strain C600. Moreover, sequence analysis further showed that this plasmid possessed high sequence similarity to most of previously reported blaNDM-5-habouring plasmids in China.<br><br>CONCLUSION: The present data in this study showed the IncX3 type plasmid played an important role in the dissemination of blaNDM-5 in Enterobacteriaceae. In addition, to the best of our knowledge, this report is the first to isolate both E. coli and C. freundii strains carrying blaNDM-5 from one single patient, which further indicated the possibility of blaNDM-5 transmission among diverse species. Close surveillance is urgently needed to monitor the further dissemination of NDM-5-producing isolates.}, }
@article {pmid29713314, year = {2018}, author = {Tang, K and Lu, YY and Sun, F}, title = {Background Adjusted Alignment-Free Dissimilarity Measures Improve the Detection of Horizontal Gene Transfer.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {711}, pmid = {29713314}, issn = {1664-302X}, support = {R01 GM120624/GM/NIGMS NIH HHS/United States ; }, abstract = {Horizontal gene transfer (HGT) plays an important role in the evolution of microbial organisms including bacteria. Alignment-free methods based on single genome compositional information have been used to detect HGT. Currently, Manhattan and Euclidean distances based on tetranucleotide frequencies are the most commonly used alignment-free dissimilarity measures to detect HGT. By testing on simulated bacterial sequences and real data sets with known horizontal transferred genomic regions, we found that more advanced alignment-free dissimilarity measures such as CVTree and [Formula: see text] that take into account the background Markov sequences can solve HGT detection problems with significantly improved performance. We also studied the influence of different factors such as evolutionary distance between host and donor sequences, size of sliding window, and host genome composition on the performances of alignment-free methods to detect HGT. Our study showed that alignment-free methods can predict HGT accurately when host and donor genomes are in different order levels. Among all methods, CVTree with word length of 3, [Formula: see text] with word length 3, Markov order 1 and [Formula: see text] with word length 4, Markov order 1 outperform others in terms of their highest F1-score and their robustness under the influence of different factors.}, }
@article {pmid29710372, year = {2018}, author = {Knowles, LL and Huang, H and Sukumaran, J and Smith, SA}, title = {A matter of phylogenetic scale: Distinguishing incomplete lineage sorting from lateral gene transfer as the cause of gene tree discord in recent versus deep diversification histories.}, journal = {American journal of botany}, volume = {105}, number = {3}, pages = {376-384}, doi = {10.1002/ajb2.1064}, pmid = {29710372}, issn = {1537-2197}, mesh = {Computer Simulation ; *Gene Transfer, Horizontal ; *Genetic Loci ; *Genetic Speciation ; Genome ; Magnoliopsida/genetics ; *Models, Genetic ; Mutation ; *Phylogeny ; }, abstract = {PREMISE OF THE STUDY: Discordant gene trees are commonly encountered when sequences from thousands of loci are applied to estimate phylogenetic relationships. Several processes contribute to this discord. Yet, we have no methods that jointly model different sources of conflict when estimating phylogenies. An alternative to analyzing entire genomes or all the sequenced loci is to identify a subset of loci for phylogenetic analysis. If we can identify data partitions that are most likely to reflect descent from a common ancestor (i.e., discordant loci that indeed reflect incomplete lineage sorting [ILS], as opposed to some other process, such as lateral gene transfer [LGT]), we can analyze this subset using powerful coalescent-based species-tree approaches.<br><br>METHODS: Test data sets were simulated where discord among loci could arise from ILS and LGT. Data sets where analyzed using the newly developed program CLASSIPHY (Huang et&#xa0;al.,) to assess whether our ability to distinguish the cause of discord among loci varied when ILS and LGT occurred in the recent versus deep past and whether the accuracy of these inferences were affected by the mutational process.<br><br>KEY RESULTS: We show that accuracy of probabilistic classification of individual loci by the cause of discord differed when ILS and LGT events occurred more recently compared with the distant past and that the signal-to-noise ratio arising from the mutational process contributes to difficulties in inferring LGT data partitions.<br><br>CONCLUSIONS: We discuss our findings in terms of the promise and limitations of identifying subsets of loci for species-tree inference that will not violate the underlying coalescent model (i.e., data partitions in which ILS, and not LGT, contributes to discord). We also discuss the empirical implications of our work given the many recalcitrant nodes in the tree of life (e.g., origins of angiosperms, amniotes, or Neoaves), and recent arguments for concatenating loci.}, }
@article {pmid29705204, year = {2018}, author = {Godde, JS and Baichoo, S and Mungloo-Dilmohamud, Z and Jaufeerally-Fakim, Y}, title = {Comparison of genomic islands in cyanobacteria: Evidence of bacteriophage-mediated horizontal gene transfer from eukaryotes.}, journal = {Microbiological research}, volume = {211}, number = {}, pages = {31-46}, doi = {10.1016/j.micres.2018.03.005}, pmid = {29705204}, issn = {1618-0623}, mesh = {Bacteriophages/*genetics ; Base Composition ; Chlorophyta/genetics ; Cyanobacteria/*genetics ; Eukaryota/*genetics ; *Evolution, Molecular ; Fructose-Bisphosphate Aldolase/genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; *Genomic Islands ; Genomics ; Microsatellite Repeats ; Phylogeny ; Prochlorococcus/genetics ; Rhodophyta/genetics ; Sequence Analysis, Protein ; Sulfate Adenylyltransferase/classification/genetics ; }, abstract = {A number of examples of putative eukaryote-to-prokaryote horizontal gene transfer (HGT) have been proposed in the past using phylogenetic analysis in support of these claims but none have attempted to map these gene transfers to the presence of genomic islands (GIs) in the host. Two of these cases have been examined in detail, including an ATP sulfurylase (ATPS) gene and a class I fructose bisphosphate aldolase (FBA I) gene that were putatively transferred to cyanobacteria of the genus Prochlorococcus from either green or red algae, respectively. Unlike previous investigations of HGT, parametric methods were initially used to detect genomic islands, then more traditional phylogenomic and phylogenetic methods were used to confirm or deny the HGT status of these genes. The combination of these three methods of analysis- detection of GIs, the determination of genomic neighborhoods, as well as traditional phylogeny, lends strong support to the claim that trans-domain HGT has occurred in only one of these cases and further suggests a new insight into the method of transmission of FBA I, namely that cyanophage-mediated transfer may have been responsible for the HGT event in question. The described methods were then applied to a range of prochlorococcal genomes in order to characterize a candidate for eukaryote-to-prokaryote HGT that had not been previously studied by others. Application of the same methodology used to confirm or deny HGT for ATPS and FBA I identified a ⊗12 fatty acid desaturase (FAD) gene that was likely transferred to Prochlorococcus from either green or red algae.}, }
@article {pmid29703975, year = {2018}, author = {Dean, P and Sendra, KM and Williams, TA and Watson, AK and Major, P and Nakjang, S and Kozhevnikova, E and Goldberg, AV and Kunji, ERS and Hirt, RP and Embley, TM}, title = {Transporter gene acquisition and innovation in the evolution of Microsporidia intracellular parasites.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {1709}, pmid = {29703975}, issn = {2041-1723}, support = {/WT_/Wellcome Trust/United Kingdom ; MC_U105663139/MRC_/Medical Research Council/United Kingdom ; MC_UU_00015/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Cell Line ; *Evolution, Molecular ; Gene Duplication ; *Gene Transfer, Horizontal ; Genome, Fungal/genetics ; Host-Pathogen Interactions/*genetics ; Metabolic Networks and Pathways/genetics ; Microsporidia/*genetics/metabolism ; Nucleotide Transport Proteins/*genetics/metabolism ; Nucleotides/metabolism ; Phylogeny ; Rabbits ; }, abstract = {The acquisition of genes by horizontal transfer can impart entirely new biological functions and provide an important route to major evolutionary innovation. Here we have used ancient gene reconstruction and functional assays to investigate the impact of a single horizontally transferred nucleotide transporter into the common ancestor of the Microsporidia, a major radiation of intracellular parasites of animals and humans. We show that this transporter provided early microsporidians with the ability to steal host ATP and to become energy parasites. Gene duplication enabled the diversification of nucleotide transporter function to transport new substrates, including GTP and NAD[+], and to evolve the proton-energized net import of nucleotides for nucleic acid biosynthesis, growth and replication. These innovations have allowed the loss of pathways for mitochondrial and cytosolic energy generation and nucleotide biosynthesis that are otherwise essential for free-living eukaryotes, resulting in the highly unusual and reduced cells and genomes of contemporary Microsporidia.}, }
@article {pmid29701821, year = {2018}, author = {Bastide, P and Solís-Lemus, C and Kriebel, R and William Sparks, K and Ané, C}, title = {Phylogenetic Comparative Methods on Phylogenetic Networks with Reticulations.}, journal = {Systematic biology}, volume = {67}, number = {5}, pages = {800-820}, doi = {10.1093/sysbio/syy033}, pmid = {29701821}, issn = {1076-836X}, mesh = {Algorithms ; Animals ; Cyprinodontiformes/classification/*genetics ; *Evolution, Molecular ; *Gene Flow ; *Gene Transfer, Horizontal ; *Hybridization, Genetic ; Models, Genetic ; Phenotype ; *Phylogeny ; }, abstract = {The goal of phylogenetic comparative methods (PCMs) is to study the distribution of quantitative traits among related species. The observed traits are often seen as the result of a Brownian Motion (BM) along the branches of a phylogenetic tree. Reticulation events such as hybridization, gene flow or horizontal gene transfer, can substantially affect a species' traits, but are not modeled by a tree. Phylogenetic networks have been designed to represent reticulate evolution. As they become available for downstream analyses, new models of trait evolution are needed, applicable to networks. We develop here an efficient recursive algorithm to compute the phylogenetic variance matrix of a trait on a network, in only one preorder traversal of the network. We then extend the standard PCM tools to this new framework, including phylogenetic regression with covariates (or phylogenetic ANOVA), ancestral trait reconstruction, and Pagel's $\lambda$ test of phylogenetic signal. The trait of a hybrid is sometimes outside of the range of its two parents, for instance because of hybrid vigor or hybrid depression. These two phenomena are rather commonly observed in present-day hybrids. Transgressive evolution can be modeled as a shift in the trait value following a reticulation point. We develop a general framework to handle such shifts and take advantage of the phylogenetic regression view of the problem to design statistical tests for ancestral transgressive evolution in the evolutionary history of a group of species. We study the power of these tests in several scenarios and show that recent events have indeed the strongest impact on the trait distribution of present-day taxa. We apply those methods to a data set of Xiphophorus fishes, to confirm and complete previous analysis in this group. All the methods developed here are available in the Julia package PhyloNetworks.}, }
@article {pmid29701800, year = {2018}, author = {Savory, FR and Milner, DS and Miles, DC and Richards, TA}, title = {Ancestral Function and Diversification of a Horizontally Acquired Oomycete Carboxylic Acid Transporter.}, journal = {Molecular biology and evolution}, volume = {35}, number = {8}, pages = {1887-1900}, pmid = {29701800}, issn = {1537-1719}, mesh = {Dicarboxylic Acid Transporters/*genetics/*metabolism ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Multigene Family ; Oomycetes/*genetics ; Saccharomyces cerevisiae ; }, abstract = {Horizontal gene transfer (HGT) can equip organisms with novel genes, expanding the repertoire of genetic material available for evolutionary innovation and allowing recipient lineages to colonize new environments. However, few studies have characterized the functions of HGT genes experimentally or examined postacquisition functional divergence. Here, we report the use of ancestral sequence reconstruction and heterologous expression in Saccharomyces cerevisiae to examine the evolutionary history of an oomycete transporter gene family that was horizontally acquired from fungi. We demonstrate that the inferred ancestral oomycete HGT transporter proteins and their extant descendants transport dicarboxylic acids which are intermediates of the tricarboxylic acid cycle. The substrate specificity profile of the most ancestral protein has largely been retained throughout the radiation of oomycetes, including in both plant and animal pathogens and in a free-living saprotroph, indicating that the ancestral HGT transporter function has been maintained by selection across a range of different lifestyles. No evidence of neofunctionalization in terms of substrate specificity was detected for different HGT transporter paralogues which have different patterns of temporal expression. However, a striking expansion of substrate range was observed for one plant pathogenic oomycete, with a HGT derived paralogue from Pythium aphanidermatum encoding a protein that enables tricarboxylic acid uptake in addition to dicarboxylic acid uptake. This demonstrates that HGT acquisitions can provide functional additions to the recipient proteome as well as the foundation material for the evolution of expanded protein functions.}, }
@article {pmid29697049, year = {2018}, author = {Stairs, CW and Eme, L and Muñoz-Gómez, SA and Cohen, A and Dellaire, G and Shepherd, JN and Fawcett, JP and Roger, AJ}, title = {Microbial eukaryotes have adapted to hypoxia by horizontal acquisitions of a gene involved in rhodoquinone biosynthesis.}, journal = {eLife}, volume = {7}, number = {}, pages = {}, pmid = {29697049}, issn = {2050-084X}, support = {MOP 341174//CIHR/Canada ; MOP 142349//CIHR/Canada ; R15 GM096398/GM/NIGMS NIH HHS/United States ; 1R15GM096398-01/NH/NIH HHS/United States ; }, mesh = {*Adaptation, Biological ; *Anaerobiosis ; Bacteria/genetics ; Electron Transport Complex II/*genetics/metabolism ; Eukaryota/*genetics/*physiology ; Fumarates/metabolism ; *Gene Transfer, Horizontal ; Genetic Variation ; Oxidation-Reduction ; Phylogeny ; Ubiquinone/*analogs &amp; derivatives/biosynthesis ; }, abstract = {Under hypoxic conditions, some organisms use an electron transport chain consisting of only complex I and II (CII) to generate the proton gradient essential for ATP production. In these cases, CII functions as a fumarate reductase that accepts electrons from a low electron potential quinol, rhodoquinol (RQ). To clarify the origins of RQ-mediated fumarate reduction in eukaryotes, we investigated the origin and function of rquA, a gene encoding an RQ biosynthetic enzyme. RquA is very patchily distributed across eukaryotes and bacteria adapted to hypoxia. Phylogenetic analyses suggest lateral gene transfer (LGT) of rquA from bacteria to eukaryotes occurred at least twice and the gene was transferred multiple times amongst protists. We demonstrate that RquA functions in the mitochondrion-related organelles of the anaerobic protist Pygsuia and is correlated with the presence of RQ. These analyses reveal the role of gene transfer in the evolutionary remodeling of mitochondria in adaptation to hypoxia.}, }
@article {pmid29696375, year = {2018}, author = {Schwab, S and Terra, LA and Baldani, JI}, title = {Genomic characterization of Nitrospirillum amazonense strain CBAmC, a nitrogen-fixing bacterium isolated from surface-sterilized sugarcane stems.}, journal = {Molecular genetics and genomics : MGG}, volume = {293}, number = {4}, pages = {997-1016}, pmid = {29696375}, issn = {1617-4623}, support = {573.828/2008-3//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 476254/2013-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 304750/2013//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; E-26/102.312/2013//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; E-26/110.235/2011//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; }, mesh = {*Genome, Bacterial ; *Nitrogen Fixation ; Plant Stems/*microbiology ; Rhodospirillaceae/*genetics/isolation &amp; purification ; Saccharum/*microbiology ; }, abstract = {Nitrospirillum amazonense is a nitrogen-fixing bacterium that shows potential to promote plant growth when inoculated into sugarcane and rice plants. This microorganism has been the subject of biochemical and genetic characterization to elucidate important functions related to host plant interaction and growth promotion, including the determination of draft genome sequences of two strains, Y2 and CBAmC, the second of which is the aim of the present study. CBAmC has been isolated from sugarcane (Saccharum spp.), and is currently used in a sugarcane consortium inoculant with four other nitrogen-fixing bacterial strains. The present paper describes a significant improvement in the genome sequence and assembly for the N. amazonense strain CBAmC, and determination for the first time of a complete genome sequence for this bacterial species, using PacBio technology. The analysis of the genomic data obtained allowed the discovery of genes coding for metabolic pathways and cellular structures that may be determinant for the success of the bacterial establishment and colonization into the host sugarcane plant, besides conferring important characteristics to the inoculant. These include genes for the use of sucrose and N-glycans, biosynthesis of autoinducer molecules, siderophore production and acquisition, auxin and polyamine biosynthesis, flagellum, σ-fimbriae, a variety of secretion systems, and a complete denitrification system. Concerning genes for nitrogenase and auxiliary proteins, it was possible to corroborate literature data that in N. amazonense these probably had originated from horizontal gene transfer, from bacteria of the Rhizobiales order. The complete genomic sequence of the CBAmC strain of N. amazonense revealed that the bacterium harbors four replicons, including three chromosomes and one chromid, a profile that coincides with that of other two strains, according to literature data, suggesting that as a replicon pattern for the species. Finally, results of phylogenomic analyses in this work support the recent reclassification of the species, separating it from the Azospirillum genus. More importantly, results of the present work shall guide subsequent studies on strain CBAmC as well as the development of a sugarcane inoculant.}, }
@article {pmid29695294, year = {2018}, author = {Rosenberg, E and Zilber-Rosenberg, I}, title = {The hologenome concept of evolution after 10 years.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {78}, pmid = {29695294}, issn = {2049-2618}, mesh = {Animals ; *Biological Evolution ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; Genome/genetics ; Humans ; Microbiota/*genetics ; Plants ; Symbiosis/*physiology ; }, abstract = {The holobiont (host with its endocellular and extracellular microbiome) can function as a distinct biological entity, an additional organismal level to the ones previously considered, on which natural selection operates. The holobiont can function as a whole: anatomically, metabolically, immunologically, developmentally, and during evolution. Consideration of the holobiont with its hologenome as an independent level of selection in evolution has led to a better understanding of underappreciated modes of genetic variation and evolution. The hologenome is comprised of two complimentary parts: host and microbiome genomes. Changes in either genome can result in variations that can be selected for or against. The host genome is highly conserved, and genetic changes within it occur slowly, whereas the microbiome genome is dynamic and can change rapidly in response to the environment by increasing or reducing particular microbes, by acquisition of novel microbes, by horizontal gene transfer, and by mutation. Recent experiments showing that microbiota can play an initial role in speciation have been suggested as an additional mode of enhancing evolution. Some of the genetic variations can be transferred to offspring by a variety of mechanisms. Strain-specific DNA analysis has shown that at least some of the microbiota can be maintained across hundreds of thousands of host generations, implying the existence of a microbial core. We argue that rapid changes in the microbiome genome could allow holobionts to adapt and survive under changing environmental conditions thus providing the time necessary for the host genome to adapt and evolve. As Darwin wrote, "It is not the strongest of the species that survives but the most adaptable".}, }
@article {pmid29692961, year = {2018}, author = {Song, L and Wang, X and Zhang, W and Ye, L and Feng, X}, title = {Low-intensity ultrasound promotes the horizontal transfer of resistance genes mediated by plasmids in E. coli.}, journal = {3 Biotech}, volume = {8}, number = {5}, pages = {224}, pmid = {29692961}, issn = {2190-572X}, abstract = {Widespread of pathogenic bacteria resistant to antibiotics has become a worldwide public health concern. Conjugative transfer between bacteria is an important mechanism for the horizontal transfer of antibiotic resistance genes. Ultrasound has been widely applied in many fields, but the effect of ultrasound on horizontal transfer of antibiotic-resistant genes is still not clear. We discovered that low-intensity (≤ 0.05 W/cm[2]) ultrasound had no effect on bacterial growth and survival rates, but increased the permeability of cell membrane, and consequentially elevated the transfer rates of plasmid. Low-intensity ultrasound enhanced conjugation between bacteria, induced expression of conjugation genes TrpBp and TrfAp, and inhibited expression of global regulatory genes KorA, KorB, TrbA, and TrbK. In conclusion, low-intensity ultrasound promoted horizontal transfer of antibiotic-resistant genes by enhancing conjugation and regulating expression of horizontal transfer-related genes.}, }
@article {pmid29690879, year = {2018}, author = {Inglin, RC and Meile, L and Stevens, MJA}, title = {Clustering of Pan- and Core-genome of Lactobacillus provides Novel Evolutionary Insights for Differentiation.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {284}, pmid = {29690879}, issn = {1471-2164}, support = {145214//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; }, mesh = {Algorithms ; Cluster Analysis ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomics ; Lactobacillus/*genetics ; }, abstract = {BACKGROUND: Bacterial taxonomy aims to classify bacteria based on true evolutionary events and relies on a polyphasic approach that includes phenotypic, genotypic and chemotaxonomic analyses. Until now, complete genomes are largely ignored in taxonomy. The genus Lactobacillus consists of 173 species and many genomes are available to study taxonomy and evolutionary events.<br><br>RESULTS: We analyzed and clustered 98 completely sequenced genomes of the genus Lactobacillus and 234 draft genomes of 5 different Lactobacillus species, i.e. L. reuteri, L. delbrueckii, L. plantarum, L. rhamnosus and L. helveticus. The core-genome of the genus Lactobacillus contains 266 genes and the pan-genome 20'800 genes. Clustering of the Lactobacillus pan- and core-genome resulted in two highly similar trees. This shows that evolutionary history is traceable in the core-genome and that clustering of the core-genome is sufficient to explore relationships. Clustering of core- and pan-genomes at species' level resulted in similar trees as well. Detailed analyses of the core-genomes showed that the functional class "genetic information processing" is conserved in the core-genome but that "signaling and cellular processes" is not. The latter class encodes functions that are involved in environmental interactions. Evolution of lactobacilli seems therefore directed by the environment. The type species L. delbrueckii was analyzed in detail and its pan-genome based tree contained two major clades whose members contained different genes yet identical functions. In addition, evidence for horizontal gene transfer between strains of L. delbrueckii, L. plantarum, and L. rhamnosus, and between species of the genus Lactobacillus is presented. Our data provide evidence for evolution of some lactobacilli according to a parapatric-like model for species differentiation.<br><br>CONCLUSIONS: Core-genome trees are useful to detect evolutionary relationships in lactobacilli and might be useful in taxonomic analyses. Lactobacillus' evolution is directed by the environment and HGT.}, }
@article {pmid29689213, year = {2018}, author = {Forsberg, KJ and Malik, HS}, title = {Microbial Genomics: The Expanding Universe of Bacterial Defense Systems.}, journal = {Current biology : CB}, volume = {28}, number = {8}, pages = {R361-R364}, doi = {10.1016/j.cub.2018.02.053}, pmid = {29689213}, issn = {1879-0445}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Bacteria/*genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomic Islands ; Genomics ; }, abstract = {Bacteria protect themselves against infection using multiple defensive systems that move by horizontal gene transfer and accumulate in genomic 'defense islands'. A recent study exploited these features to uncover ten novel defense systems, substantially expanding the catalog of bacterial defense systems and predicting the discovery of many more.}, }
@article {pmid29689046, year = {2018}, author = {Nguyen, TA and Greig, J and Khan, A and Goh, C and Jedd, G}, title = {Evolutionary novelty in gravity sensing through horizontal gene transfer and high-order protein assembly.}, journal = {PLoS biology}, volume = {16}, number = {4}, pages = {e2004920}, pmid = {29689046}, issn = {1545-7885}, mesh = {Bacterial Proteins/*genetics/metabolism ; *Biological Evolution ; Cloning, Molecular ; Escherichia coli/classification/*genetics/metabolism ; Gene Expression ; *Gene Transfer, Horizontal ; Genes, Reporter ; Genetic Vectors/chemistry/metabolism ; *Gravitation ; Green Fluorescent Proteins/genetics/metabolism ; HeLa Cells ; Humans ; Luminescent Proteins/genetics/metabolism ; Mucorales/classification/*genetics/metabolism ; Periplasm/metabolism ; Phylogeny ; Protein Multimerization ; Recombinant Proteins/chemistry/genetics/metabolism ; Vacuoles/metabolism ; Red Fluorescent Protein ; }, abstract = {Horizontal gene transfer (HGT) can promote evolutionary adaptation by transforming a species' relationship to the environment. In most well-understood cases of HGT, acquired and donor functions appear to remain closely related. Thus, the degree to which HGT can lead to evolutionary novelties remains unclear. Mucorales fungi sense gravity through the sedimentation of vacuolar protein crystals. Here, we identify the octahedral crystal matrix protein (OCTIN). Phylogenetic analysis strongly supports acquisition of octin by HGT from bacteria. A bacterial OCTIN forms high-order periplasmic oligomers, and inter-molecular disulphide bonds are formed by both fungal and bacterial OCTINs, suggesting that they share elements of a conserved assembly mechanism. However, estimated sedimentation velocities preclude a gravity-sensing function for the bacterial structures. Together, our data suggest that HGT from bacteria into the Mucorales allowed a dramatic increase in assembly scale and emergence of the gravity-sensing function. We conclude that HGT can lead to evolutionary novelties that emerge depending on the physiological and cellular context of protein assembly.}, }
@article {pmid29689044, year = {2018}, author = {Nowell, RW and Almeida, P and Wilson, CG and Smith, TP and Fontaneto, D and Crisp, A and Micklem, G and Tunnacliffe, A and Boschetti, C and Barraclough, TG}, title = {Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species.}, journal = {PLoS biology}, volume = {16}, number = {4}, pages = {e2004830}, pmid = {29689044}, issn = {1545-7885}, support = {BB/F020562/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/F020856/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Adaptation, Physiological/*genetics ; Animals ; Desiccation ; Ecosystem ; Fresh Water ; Gene Transfer, Horizontal ; *Genetic Speciation ; *Genome, Helminth ; Genomics/methods ; Phylogeny ; Rotifera/classification/*genetics ; *Synteny ; Tetraploidy ; Whole Genome Sequencing ; }, abstract = {Bdelloid rotifers are a class of microscopic invertebrates that have existed for millions of years apparently without sex or meiosis. They inhabit a variety of temporary and permanent freshwater habitats globally, and many species are remarkably tolerant of desiccation. Bdelloids offer an opportunity to better understand the evolution of sex and recombination, but previous work has emphasised desiccation as the cause of several unusual genomic features in this group. Here, we present high-quality whole-genome sequences of 3 bdelloid species: Rotaria macrura and R. magnacalcarata, which are both desiccation intolerant, and Adineta ricciae, which is desiccation tolerant. In combination with the published assembly of A. vaga, which is also desiccation tolerant, we apply a comparative genomics approach to evaluate the potential effects of desiccation tolerance and asexuality on genome evolution in bdelloids. We find that ancestral tetraploidy is conserved among all 4 bdelloid species, but homologous divergence in obligately aquatic Rotaria genomes is unexpectedly low. This finding is contrary to current models regarding the role of desiccation in shaping bdelloid genomes. In addition, we find that homologous regions in A. ricciae are largely collinear and do not form palindromic repeats as observed in the published A. vaga assembly. Consequently, several features interpreted as genomic evidence for long-term ameiotic evolution are not general to all bdelloid species, even within the same genus. Finally, we substantiate previous findings of high levels of horizontally transferred nonmetazoan genes in both desiccating and nondesiccating bdelloid species and show that this unusual feature is not shared by other animal phyla, even those with desiccation-tolerant representatives. These comparisons call into question the proposed role of desiccation in mediating horizontal genetic transfer.}, }
@article {pmid29685100, year = {2018}, author = {Moolhuijzen, P and See, PT and Hane, JK and Shi, G and Liu, Z and Oliver, RP and Moffat, CS}, title = {Comparative genomics of the wheat fungal pathogen Pyrenophora tritici-repentis reveals chromosomal variations and genome plasticity.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {279}, pmid = {29685100}, issn = {1471-2164}, support = {COR00023//Grains Research and Development Corporation/ ; }, mesh = {Ascomycota/*genetics/*physiology ; Chromosomes, Fungal/*genetics ; Gene Transfer, Horizontal ; *Genetic Variation ; Genome, Fungal/*genetics ; Genome, Mitochondrial/genetics ; *Genomics ; Molecular Sequence Annotation ; Phylogeny ; Sequence Homology, Nucleic Acid ; Triticum/*microbiology ; }, abstract = {BACKGROUND: Pyrenophora tritici-repentis (Ptr) is a necrotrophic fungal pathogen that causes the major wheat disease, tan spot. We set out to provide essential genomics-based resources in order to better understand the pathogenicity mechanisms of this important pathogen.<br><br>RESULTS: Here, we present eight new Ptr isolate genomes, assembled and annotated; representing races 1, 2 and 5, and a new race. We report a high quality Ptr reference genome, sequenced by PacBio technology with Illumina paired-end data support and optical mapping. An estimated 98% of the genome coverage was mapped to 10 chromosomal groups, using a two-enzyme hybrid approach. The final reference genome was 40.9&#xa0;Mb and contained a total of 13,797 annotated genes, supported by transcriptomic and proteogenomics data sets.<br><br>CONCLUSIONS: Whole genome comparative analysis revealed major chromosomal segmental rearrangements and fusions, highlighting intraspecific genome plasticity in this species. Furthermore, the Ptr race classification was not supported at the whole genome level, as phylogenetic analysis did not cluster the ToxA producing isolates. This expansion of available Ptr genomics resources will directly facilitate research aimed at controlling tan spot disease.}, }
@article {pmid29684487, year = {2018}, author = {Chauhan, S and Rahman, H and Mastan, SG and Pamidimarri, DVNS and Reddy, MP}, title = {Isolation and sequence characterization of DNA-A genome of a new begomovirus strain associated with severe leaf curling symptoms of Jatropha curcas L.}, journal = {Gene}, volume = {664}, number = {}, pages = {37-43}, doi = {10.1016/j.gene.2018.04.062}, pmid = {29684487}, issn = {1879-0038}, mesh = {Begomovirus/*genetics/pathogenicity ; Biological Evolution ; DNA, Viral/*isolation &amp; purification ; Euphorbia/virology ; Gene Transfer, Horizontal/genetics ; *Genome, Viral ; Jatropha/*virology ; Mosaic Viruses/genetics ; Phylogeny ; Plant Diseases/*virology ; Plant Leaves/virology ; Viral Proteins/genetics ; }, abstract = {Begomoviruses belong to the family Geminiviridae are associated with several disease symptoms, such as mosaic and leaf curling in Jatropha curcas. The molecular characterization of these viral strains will help in developing management strategies to control the disease. In this study, J. curcas that was infected with begomovirus and showed acute leaf curling symptoms were identified. DNA-A segment from pathogenic viral strain was isolated and sequenced. The sequenced genome was assembled and characterized in detail. The full-length DNA-A sequence was covered by primer walking. The genome sequence showed the general organization of DNA-A from begomovirus by the distribution of ORFs in both viral and anti-viral strands. The genome size ranged from 2844 bp-2852 bp. Three strains with minor nucleotide variations were identified, and a phylogenetic analysis was performed by comparing the DNA-A segments from other reported begomovirus isolates. The maximum sequence similarity was observed with Euphorbia yellow mosaic virus (FN435995). In the phylogenetic tree, no clustering was observed with previously reported begomovirus strains isolated from J. curcas host. The strains isolated in this study belong to new begomoviral strain that elicits symptoms of leaf curling in J. curcas. The results indicate that the probable origin of the strains is from Jatropha mosaic virus infecting J. gassypifolia. The strains isolated in this study are referred as Jatropha curcas leaf curl India virus (JCLCIV) based on the major symptoms exhibited by host J. curcas.}, }
@article {pmid29684127, year = {2018}, author = {Yamaguchi, T and Kawahara, R and Harada, K and Teruya, S and Nakayama, T and Motooka, D and Nakamura, S and Nguyen, PD and Kumeda, Y and Van Dang, C and Hirata, K and Yamamoto, Y}, title = {The presence of colistin resistance gene mcr-1 and -3 in ESBL producing Escherichia coli isolated from food in Ho Chi Minh City, Vietnam.}, journal = {FEMS microbiology letters}, volume = {365}, number = {11}, pages = {}, doi = {10.1093/femsle/fny100}, pmid = {29684127}, issn = {1574-6968}, mesh = {Anti-Bacterial Agents/*pharmacology ; Cities ; Colistin/*pharmacology ; *Drug Resistance, Bacterial ; Escherichia coli/drug effects/*isolation &amp; purification ; Escherichia coli Proteins/*genetics ; *Food Microbiology ; Gene Transfer, Horizontal ; Plasmids/analysis/classification ; Prevalence ; Transferases (Other Substituted Phosphate Groups)/*genetics ; Vietnam ; beta-Lactamases/metabolism ; }, abstract = {Colistin is indicated for the treatment of multidrug-resistant gram-negative bacterial infections. However, the spread of colistin-resistant bacteria harbouring an mcr gene has become a serious concern. This study investigated local foods in Vietnam for contamination with colistin-resistant bacteria. A total of 261 extended-spectrum β-lactamase (ESBL)- and AmpC-producing Escherichia coli isolates from 330 meat and seafood products were analysed for colistin susceptibility and the presence of mcr genes. Approximately, 24% (62/261) of ESBL- or AmpC-producing E. coli isolates showed colistin resistance; 97% (60/62) of colistin-resistant isolates harboured mcr-1, whereas 3% (2/62) harboured mcr-3. As the result of plasmid analysis of two strains, both plasmids harbouring mcr-3 revealed that plasmid replicon type was IncFII. Sequencing analysis indicated that an insertion sequence was present near mcr-3, suggesting that IncFII plasmids harbouring mcr-3 could be transferred to other bacterial species by horizontal transfer of the plasmid or transfer with some insertion sequence. In conclusion, ESBL-producing E. coli and AmpC-producing E. coli have acquired colistin resistance because 24% of such isolates show colistin resistance and 3% of the colistin-resistant strains harbour mcr-3. We reported the present of the mcr-3-carrying ESBL-producing E. coli isolated from pork in Vietnam.}, }
@article {pmid29683780, year = {2018}, author = {Xie, Y and Tian, L and Li, G and Qu, H and Sun, J and Liang, W and Li, X and Wang, X and Deng, Z and Liu, J and Ou, HY}, title = {Emergence of the third-generation cephalosporin-resistant hypervirulent Klebsiella pneumoniae due to the acquisition of a self-transferable blaDHA-1-carrying plasmid by an ST23 strain.}, journal = {Virulence}, volume = {9}, number = {1}, pages = {838-844}, pmid = {29683780}, issn = {2150-5608}, mesh = {Animal Structures ; Animals ; Anti-Bacterial Agents/*pharmacology ; Bacterial Load ; Cephalosporins/*pharmacology ; Disease Models, Animal ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Humans ; Klebsiella Infections/microbiology ; Klebsiella pneumoniae/drug effects/*genetics/pathogenicity ; Lepidoptera ; Microbial Sensitivity Tests ; Plasmids/*analysis ; Survival Analysis ; Virulence ; *beta-Lactam Resistance ; beta-Lactamases/*genetics ; }, }
@article {pmid29681895, year = {2018}, author = {Papadopoulou, ES and Perruchon, C and Vasileiadis, S and Rousidou, C and Tanou, G and Samiotaki, M and Molassiotis, A and Karpouzas, DG}, title = {Metabolic and Evolutionary Insights in the Transformation of Diphenylamine by a Pseudomonas putida Strain Unravelled by Genomic, Proteomic, and Transcription Analysis.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {676}, pmid = {29681895}, issn = {1664-302X}, abstract = {Diphenylamine (DPA) is a common soil and water contaminant. A Pseudomonas putida strain, recently isolated from a wastewater disposal site, was efficient in degrading DPA. Thorough knowledge of the metabolic capacity, genetic stability and physiology of bacteria during biodegradation of pollutants is essential for their future industrial exploitation. We employed genomic, proteomic, transcription analyses and plasmid curing to (i) identify the genetic network of P. putida driving the microbial transformation of DPA and explore its evolution and origin and (ii) investigate the physiological response of bacterial cells during degradation of DPA. Genomic analysis identified (i) two operons encoding a biphenyl (bph) and an aniline (tdn) dioxygenase, both flanked by transposases and (ii) two operons and several scattered genes encoding the ortho-cleavage of catechol. Proteomics identified 11 putative catabolic proteins, all but BphA1 up-regulated in DPA- and aniline-growing cells, and showed that the bacterium mobilized cellular mechanisms to cope with oxidative stress, probably induced by DPA and its derivatives. Transcription analysis verified the role of the selected genes/operons in the metabolic pathway: DPA was initially transformed to aniline and catechol by a biphenyl dioxygenase (DPA-dioxygenase); aniline was then transformed to catechol which was further metabolized via the ortho-cleavage pathway. Plasmid curing of P. putida resulted in loss of the DPA and aniline dioxygenase genes and the corresponding degradation capacities. Overall our findings provide novel insights into the evolution of the DPA degradation pathway and suggests that the degradation capacity of P. putida was acquired through recruitment of the bph and tdn operons via horizontal gene transfer.}, }
@article {pmid29678917, year = {2018}, author = {Jibrin, MO and Potnis, N and Timilsina, S and Minsavage, GV and Vallad, GE and Roberts, PD and Jones, JB and Goss, EM}, title = {Genomic Inference of Recombination-Mediated Evolution in Xanthomonas euvesicatoria and X. perforans.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {13}, pages = {}, pmid = {29678917}, issn = {1098-5336}, mesh = {Bacterial Proteins/genetics ; Base Sequence ; Breeding ; *Evolution, Molecular ; Florida ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genomics ; Homologous Recombination ; Host-Pathogen Interactions ; India ; Italy ; Solanum lycopersicum/microbiology ; Nigeria ; Phylogeny ; Piper/microbiology ; Plant Diseases/microbiology ; *Recombination, Genetic ; Type III Secretion Systems/genetics ; Virulence Factors/genetics ; Xanthomonas/classification/*genetics/pathogenicity ; }, abstract = {Recombination is a major driver of evolution in bacterial populations, because it can spread and combine independently evolved beneficial mutations. Recombinant lineages of bacterial pathogens of plants are typically associated with the colonization of novel hosts and the emergence of new diseases. Here we show that recombination between evolutionarily and phenotypically distinct plant-pathogenic lineages generated recombinant lineages with unique combinations of pathogenicity and virulence factors. Xanthomonas euvesicatoria and Xanthomonas perforans are two closely related lineages causing bacterial spot disease on tomato and pepper worldwide. We sequenced the genomes of atypical strains collected from tomato in Nigeria and observed recombination in the type III secretion system and effector genes, which showed alleles from both X. euvesicatoria and X. perforans Wider horizontal gene transfer was indicated by the fact that the lipopolysaccharide cluster of one strain was most similar to that of a distantly related Xanthomonas pathogen of barley. This strain and others have experienced extensive genomewide homologous recombination, and both species exhibited dynamic open pangenomes. Variation in effector gene repertoires within and between species must be taken into consideration when one is breeding tomatoes for disease resistance. Resistance breeding strategies that target specific effectors must consider possibly dramatic variation in bacterial spot populations across global production regions, as illustrated by the recombinant strains observed here.IMPORTANCE The pathogens that cause bacterial spot of tomato and pepper are extensively studied models of plant-microbe interactions and cause problematic disease worldwide. Atypical bacterial spot strains collected from tomato in Nigeria, and other strains from Italy, India, and Florida, showed evidence of genomewide recombination that generated genetically distinct pathogenic lineages. The strains from Nigeria and Italy were found to have a mix of type III secretion system genes from X. perforans and X. euvesicatoria, as well as effectors from Xanthomonas gardneri These genes and effectors are important in the establishment of disease, and effectors are common targets of resistance breeding. Our findings point to global diversity in the genomes of bacterial spot pathogens, which is likely to affect the host-pathogen interaction and influence management decisions.}, }
@article {pmid29678911, year = {2018}, author = {Andreevskaya, M and Jääskeläinen, E and Johansson, P and Ylinen, A and Paulin, L and Björkroth, J and Auvinen, P}, title = {Food Spoilage-Associated Leuconostoc, Lactococcus, and Lactobacillus Species Display Different Survival Strategies in Response to Competition.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {13}, pages = {}, pmid = {29678911}, issn = {1098-5336}, mesh = {Bacteriocins ; Colony Count, Microbial ; Fatty Acids/biosynthesis ; Fermentation ; *Food Microbiology ; Food Packaging ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Genes, Essential/genetics ; Lactobacillales/genetics/growth &amp; development/metabolism ; Lactobacillus/genetics/*growth &amp; development/metabolism ; Lactococcus/genetics/*growth &amp; development/metabolism ; Leuconostoc/genetics/*growth &amp; development/metabolism ; Meat Products/*microbiology ; Microbial Interactions/physiology ; Microbiota ; Sequence Analysis, RNA ; Transcriptome ; }, abstract = {Psychrotrophic lactic acid bacteria (LAB) are the prevailing spoilage organisms in packaged cold-stored meat products. Species composition and metabolic activities of such LAB spoilage communities are determined by the nature of the meat product, storage conditions, and interspecies interactions. Our knowledge of system level responses of LAB during such interactions is very limited. To expand it, we studied interactions between three common psychrotrophic spoilage LAB (Leuconostoc gelidum, Lactococcus piscium, and Lactobacillus oligofermentans) by comparing their time course transcriptome profiles obtained during their growth in individual, pairwise, and triple cultures. The study revealed how these LAB employed different strategies to cope with the consequences of interspecies competition. The fastest-growing bacterium, Le. gelidum, attempted to enhance its nutrient-scavenging and growth capabilities in the presence of other LAB through upregulation of carbohydrate catabolic pathways, pyruvate fermentation enzymes, and ribosomal proteins, whereas the slower-growing Lc. piscium and Lb. oligofermentans downregulated these functions. These findings may explain the competitive success and predominance of Le. gelidum in a variety of spoiled foods. Peculiarly, interspecies interactions induced overexpression of prophage genes and restriction modification systems (mechanisms of DNA exchange and protection against it) in Lc. piscium and Lb. oligofermentans but not in Le. gelidum Cocultivation induced also overexpression of the numerous putative adhesins in Lb. oligofermentans These adhesins might contribute to the survival of this slowly growing bacterium in actively growing meat spoilage communities.IMPORTANCE Despite the apparent relevance of LAB for biotechnology and human health, interactions between members of LAB communities are not well known. Knowledge of such interactions is crucial for understanding how these communities function and, consequently, whether there is any possibility to develop new strategies to interfere with their growth and to postpone spoilage of packaged and refrigerated foods. With the help of controlled experiments, detailed regulation events can be observed. This study gives an insight into the system level interactions and the different competition-induced survival strategies related to enhanced uptake and catabolism of carbon sources, overexpression of adhesins and putative bacteriocins, and the induction of exchange of genetic material. Even though this experiment dealt with only three LAB strains in vitro, these findings agreed well with the relative abundance patterns typically reported for these species in natural food microbial communities.}, }
@article {pmid29678218, year = {2018}, author = {Williamson, CHD and Wagner, DM and Keim, P and Sahl, JW}, title = {Developing Inclusivity and Exclusivity Panels for Testing Diagnostic and Detection Tools Targeting Burkholderia pseudomallei, the Causative Agent of Melioidosis.}, journal = {Journal of AOAC International}, volume = {101}, number = {6}, pages = {1920-1926}, doi = {10.5740/jaoacint.18-0014}, pmid = {29678218}, issn = {1944-7922}, mesh = {Bacterial Typing Techniques/*methods/standards ; Burkholderia mallei/genetics/isolation &amp; purification ; Burkholderia pseudomallei/genetics/*isolation &amp; purification ; Genotyping Techniques/*methods/standards ; Glanders/diagnosis/microbiology ; Humans ; Limit of Detection ; Melioidosis/*diagnosis/microbiology ; }, abstract = {Background: Diagnostic tools designed to target Burkholderia pseudomallei, the causative agent of melioidosis that was classified as a Tier 1 Select Agent by the U.S. Centers for Disease Control and Prevention, have typically suffered from false-positive and false-negative results because of a lack of understanding of the genomic diversity of B. pseudomallei and its genetic near neighbors. Objective: In this review, we discuss a strategy for using comparative genomics to guide the design of inclusivity and exclusivity panels for the validation of assays as defined by the Standard Method Performance Requirement (SMPR). Methods: Based upon a literature review, comparative genomic analyses, and hands-on experience with diagnostic development and testing, we describe important factors to consider when developing inclusivity and exclusivity panels for testing diagnostic and/or detection tools. Results: The genomic diversity of B. pseudomallei is substantial, with the genome characterized by horizontal gene transfer, including the acquisition of genomic islands from near-neighbor species. This genomic diversity, core genome reduction, and signal erosion can complicate molecular diagnostic tool development and validation. Conclusions: Accurate diagnostic and/or detection tools targeting B. pseudomallei, an important pathogen from a public health and biodefense perspective, are needed for many applications. Utilizing whole genome sequencing data and comparative genomic techniques can guide the development and validation of such tools. Amplicon sequencing assays and assay redundancy can provide improved assay performance. Highlights: When developing and validating diagnostic and/or detection tools targeting B. pseudomallei, it is important to consider genomic diversity, genome reduction, and signal erosion to reduce the effects of typical diagnostic errors.}, }
@article {pmid29675935, year = {2019}, author = {Aijaz, I and Koudelka, GB}, title = {Cheating, facilitation and cooperation regulate the effectiveness of phage-encoded exotoxins as antipredator molecules.}, journal = {MicrobiologyOpen}, volume = {8}, number = {2}, pages = {e00636}, pmid = {29675935}, issn = {2045-8827}, mesh = {*Antibiosis ; Coliphages/*genetics ; Escherichia coli/*growth &amp; development/*virology ; Microbial Interactions ; Shiga Toxins/genetics/metabolism/*toxicity ; Tetrahymena thermophila/*drug effects/*growth &amp; development ; }, abstract = {Temperate phage encoded Shiga toxin (Stx) kills the bacterivorous predator, Tetrahymena thermophila, providing Stx[+] Escherichia coli with a survival advantage over Stx[-] cells. Although bacterial death accompanies Stx release, since bacteria grow clonally the fitness benefits of predator killing accrue to the kin of the sacrificed organism, meaning Stx-mediated protist killing is a form of self-destructive cooperation. We show here that the fitness benefits of Stx production are not restricted to the kin of the phage-encoding bacteria. Instead, nearby "free loading" bacteria, irrespective of their genotype, also reap the benefit of Stx-mediated predator killing. This finding indicates that the phage-borne Stx exotoxin behaves as a public good. Stx is encoded by a mobile phage. We find that Stx-encoding phage can use susceptible bacteria in the population as surrogates to enhance toxin and phage production. Moreover, our findings also demonstrate that engulfment and concentration of Stx-encoding and susceptible Stx[-] bacteria in the Tetrahymena phagosome enhances the transfer of Stx-encoding temperate phage from the host to the susceptible bacteria. This transfer increases the population of cooperating bacteria within the community. Since these bacteria now encode Stx, the predation-stimulated increase in phage transfer increases the population of toxin encoding bacteria in the environment.}, }
@article {pmid29675838, year = {2018}, author = {Mohan Raj, JR and Vittal, R and Huilgol, P and Bhat, U and Karunasagar, I}, title = {T4-like Escherichia coli phages from the environment carry blaCTX-M.}, journal = {Letters in applied microbiology}, volume = {67}, number = {1}, pages = {9-14}, doi = {10.1111/lam.12994}, pmid = {29675838}, issn = {1472-765X}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteriophage T4/classification/*genetics/isolation &amp; purification ; Disk Diffusion Antimicrobial Tests ; Escherichia coli/drug effects/*genetics/isolation &amp; purification ; Escherichia coli Infections/microbiology ; Escherichia coli Proteins/*genetics ; Gene Transfer, Horizontal/*genetics ; Humans ; India ; Plasmids/genetics ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Soil Microbiology ; Water Microbiology ; beta-Lactamases/*genetics ; beta-Lactams/*pharmacology ; }, abstract = {UNLABELLED: The resistance determinant blaCTX-M has many variants and has been the most commonly reported gene in clinical isolates of extended spectrum beta-lactamase producing Escherichia coli. Phages have been speculated as potential reservoirs of resistance genes and efficient vehicles for horizontal gene transfer. The objective of the study was to determine the prevalence and characterize bacteriophages that harbour the resistance determinant blaCTX-M . Escherichia coli specific bacteriophages were isolated from 15 samples including soil and water across Mangaluru, India using bacterial hosts that were sensitive to β-lactams. Phenotypic and genotypic characterization based on plaque morphology, host range, restriction fragment length polymorphism (RFLP), presence of blaCTX-M and electron microscopy was performed. Of 36 phages isolated, seven were positive for Group 1 of blaCTX-M . Based on host range and RFLP pattern, the seven phages were classified into four distinct groups, each harbouring a variant of blaCTX-M . Five phages were T4-like Myoviridae by electron microscopy which was further confirmed by polymerase chain reaction (PCR) for T4 specific gp14. Generalized transduction of the CTX-M gene from these phages was also observed. The high prevalence (20%) of this gene blaCTX-M in the phage pool confirms the significant role of Myoviridae members, specifically T4-like phages in the dissemination of this resistance gene.<br><br>The CTX-M gene that confers resistance to Beta-lactam class of drugs is widespread and diverse. Understanding mechanisms of antimicrobial resistance transfer is a key to devise methods for controlling it. Few studies indicate that bacteriophages are involved in the transfer of this gene but the type of phages involved and the degree of involvement remains to be explored. Our work has been able to identify the class of phages and the magnitude of involvement in the dissemination of this gene.}, }
@article {pmid29673327, year = {2018}, author = {Chu, HY and Sprouffske, K and Wagner, A}, title = {Assessing the benefits of horizontal gene transfer by laboratory evolution and genome sequencing.}, journal = {BMC evolutionary biology}, volume = {18}, number = {1}, pages = {54}, pmid = {29673327}, issn = {1471-2148}, support = {739874//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/International ; EpiphysX RTD//SystemsX.ch/International ; }, mesh = {Adaptation, Physiological/genetics ; Base Sequence ; Butyric Acid/metabolism ; *Directed Molecular Evolution ; Escherichia coli/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; *Genome, Bacterial ; Mutation/genetics ; Open Reading Frames/genetics ; Operon/genetics ; Phenotype ; Phenylacetates/metabolism ; *Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Recombination is widespread across the tree of life, because it helps purge deleterious mutations and creates novel adaptive traits. In prokaryotes, it often takes the form of horizontal gene transfer from a donor to a recipient bacterium. While such transfer is widespread in natural communities, its immediate fitness benefits are usually unknown. We asked whether any such benefits depend on the environment, and on the identity of donor and recipient strains. To this end, we adapted Escherichia coli to two novel carbon sources over several hundred generations of laboratory evolution, exposing evolving populations to various DNA donors.<br><br>RESULTS: At the end of these experiments, we measured fitness and sequenced the genomes of 65 clones from 34 replicate populations to study the genetic changes associated with adaptive evolution. Furthermore, we identified candidate de novo beneficial mutations. During adaptive evolution on the first carbon source, 4-Hydroxyphenylacetic acid (HPA), recombining populations adapted better, which was likely mediated by acquiring the hpa operon from the donor. In contrast, recombining populations did not adapt better to the second carbon source, butyric acid, even though they suffered fewer extinctions than non-recombining populations. The amount of DNA transferred, but not its benefit, strongly depended on the donor-recipient strain combination.<br><br>CONCLUSIONS: To our knowledge, our study is the first to investigate the genomic consequences of prokaryotic recombination and horizontal gene transfer during laboratory evolution. It shows that the benefits of recombination strongly depend on the environment and the foreign DNA donor.}, }
@article {pmid29671722, year = {2018}, author = {Nelson, M and Guhlin, J and Epstein, B and Tiffin, P and Sadowsky, MJ}, title = {The complete replicons of 16 Ensifer meliloti strains offer insights into intra- and inter-replicon gene transfer, transposon-associated loci, and repeat elements.}, journal = {Microbial genomics}, volume = {4}, number = {5}, pages = {}, pmid = {29671722}, issn = {2057-5858}, mesh = {Animals ; Bacterial Proteins/genetics ; Base Composition ; Chromosomes, Bacterial ; DNA Transposable Elements/*genetics ; Evolution, Molecular ; Fabaceae/microbiology ; Gene Transfer, Horizontal ; *Genetic Loci ; *Genome, Bacterial ; Genomics ; Nitrogen Fixation/genetics ; Plant Root Nodulation/genetics ; Plasmids ; *Replicon ; Rhizobium/genetics/metabolism ; Sequence Analysis, DNA ; Sinorhizobium meliloti/*genetics/metabolism ; }, abstract = {Ensifer meliloti (formerly Rhizobium meliloti and Sinorhizobium meliloti) is a model bacterium for understanding legume-rhizobial symbioses. The tripartite genome of E. meliloti consists of a chromosome, pSymA and pSymB, and in some instances strain-specific accessory plasmids. The majority of previous sequencing studies have relied on the use of assemblies generated from short read sequencing, which leads to gaps and assembly errors. Here we used PacBio-based, long-read assemblies and were able to assemble, de novo, complete circular replicons. In this study, we sequenced, de novo-assembled and analysed 10 E. meliloti strains. Sequence comparisons were also done with data from six previously published genomes. We identified genome differences between the replicons, including mol% G+C and gene content, nucleotide repeats, and transposon-associated loci. Additionally, genomic rearrangements both within and between replicons were identified, providing insight into evolutionary processes at the structural level. There were few cases of inter-replicon gene transfer of core genes between the main replicons. Accessory plasmids were more similar to pSymA than to either pSymB or the chromosome, with respect to gene content, transposon content and G+C content. In our population, the accessory plasmids appeared to share an open genome with pSymA, which contains many nodulation- and nitrogen fixation-related genes. This may explain previous observations that horizontal gene transfer has a greater effect on the content of pSymA than pSymB, or the chromosome, and why some rhizobia show unstable nodulation phenotypes on legume hosts.}, }
@article {pmid29670105, year = {2018}, author = {Irwin, NAT and Martin, BJE and Young, BP and Browne, MJG and Flaus, A and Loewen, CJR and Keeling, PJ and Howe, LJ}, title = {Viral proteins as a potential driver of histone depletion in dinoflagellates.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {1535}, pmid = {29670105}, issn = {2041-1723}, mesh = {Cell Nucleus/metabolism ; Chromatin/metabolism ; Chromatin Immunoprecipitation ; Computational Biology ; DNA/chemistry ; Dinoflagellida/*metabolism/*virology ; Genome ; Histones/*metabolism ; Microscopy, Fluorescence ; Nucleosomes/*metabolism ; Phenotype ; Saccharomyces cerevisiae/metabolism ; Transcription, Genetic ; Viral Proteins/genetics/*metabolism ; }, abstract = {Within canonical eukaryotic nuclei, DNA is packaged with highly conserved histone proteins into nucleosomes, which facilitate DNA condensation and contribute to genomic regulation. Yet the dinoflagellates, a group of unicellular algae, are a striking exception to this otherwise universal feature as they have largely abandoned histones and acquired apparently viral-derived substitutes termed DVNPs (dinoflagellate-viral-nucleoproteins). Despite the magnitude of this transition, its evolutionary drivers remain unknown. Here, using Saccharomyces cerevisiae as a model, we show that DVNP impairs growth and antagonizes chromatin by localizing to histone binding sites, displacing nucleosomes, and impairing transcription. Furthermore, DVNP toxicity can be relieved through histone depletion and cells diminish their histones in response to DVNP expression suggesting that histone reduction could have been an adaptive response to these viral proteins. These findings provide insights into eukaryotic chromatin evolution and highlight the potential for horizontal gene transfer to drive the divergence of cellular systems.}, }
@article {pmid29669918, year = {2018}, author = {Metzger, MJ and Paynter, AN and Siddall, ME and Goff, SP}, title = {Horizontal transfer of retrotransposons between bivalves and other aquatic species of multiple phyla.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {18}, pages = {E4227-E4235}, pmid = {29669918}, issn = {1091-6490}, support = {T32 CA009503/CA/NCI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Bivalvia/*genetics ; *Gene Transfer, Horizontal ; *Genome ; *Retroelements ; }, abstract = {The LTR retrotransposon Steamer is a selfish endogenous element in the soft-shell clam genome that was first detected because of its dramatic amplification in bivalve transmissible neoplasia afflicting the species. We amplified and sequenced related retrotransposons from the genomic DNA of many other bivalve species, finding evidence of horizontal transfer of retrotransposons from the genome of one species to another. First, the phylogenetic tree of the Steamer-like elements from 19 bivalve species is markedly discordant with host phylogeny, suggesting frequent cross-species transfer throughout bivalve evolution. Second, sequences nearly identical to Steamer were identified in the genomes of Atlantic razor clams and Baltic clams, indicating recent transfer. Finally, a search of the National Center for Biotechnology Information sequence database revealed that Steamer-like elements are present in the genomes of completely unrelated organisms, including zebrafish, sea urchin, acorn worms, and coral. Phylogenetic incongruity, a patchy distribution, and a higher similarity than would be expected by vertical inheritance all provide evidence for multiple long-distance cross-phyla horizontal transfer events. These data suggest that over both short- and long-term evolutionary timescales, Steamer-like retrotransposons, much like retroviruses, can move between organisms and integrate new copies into new host genomes.}, }
@article {pmid29669186, year = {2018}, author = {Gray, TA and Derbyshire, KM}, title = {Blending genomes: distributive conjugal transfer in mycobacteria, a sexier form of HGT.}, journal = {Molecular microbiology}, volume = {108}, number = {6}, pages = {601-613}, pmid = {29669186}, issn = {1365-2958}, support = {F32 GM018306/GM/NIGMS NIH HHS/United States ; R01 AI097191/AI/NIAID NIH HHS/United States ; R21 AI107258/AI/NIAID NIH HHS/United States ; }, mesh = {*Conjugation, Genetic ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; Mycobacterium/*genetics ; Mycobacterium Infections/microbiology ; Plasmids/genetics ; }, abstract = {This review discusses a novel form of horizontal gene transfer (HGT) found in mycobacteria called Distributive Conjugal Transfer (DCT). While satisfying the criteria for conjugation, DCT occurs by a mechanism so distinct from oriT-mediated conjugation that it could be considered a fourth category of HGT. DCT involves the transfer of chromosomal DNA between mycobacteria and, most significantly, generates transconjugants with mosaic genomes of the parental strains. Multiple segments of donor chromosomal DNA can be co-transferred regardless of their location or the genetic selection and, as a result, the transconjugant genome contains many donor-derived segments; hence the name DCT. This distinguishing feature of DCT separates it from the other known mechanisms of HGT, which generally result in the introduction of a single, defined segment of DNA into the recipient chromosome (Fig.). Moreover, these mosaic progeny are generated from a single conjugal event, which provides enormous capacity for rapid adaptation and evolution, again distinguishing it from the three classical modes of HGT. Unsurprisingly, the unusual mosaic products of DCT are generated by a conjugal mechanism that is also unusual. Here, we will describe the unique features of DCT and contrast those to other mechanisms of HGT, both from a mechanistic and an evolutionary perspective. Our focus will be on transfer of chromosomal DNA, as opposed to plasmid mobilization, because DCT mediates transfer of chromosomal DNA and is a chromosomally encoded process.}, }
@article {pmid29665886, year = {2017}, author = {Lin, J}, title = {Antimicrobial resistance: from basic science to translational innovation.}, journal = {Animal health research reviews}, volume = {18}, number = {2}, pages = {85-86}, doi = {10.1017/S1466252317000172}, pmid = {29665886}, issn = {1475-2654}, mesh = {Animals ; *Drug Resistance, Bacterial ; Food Safety ; Humans ; }, abstract = {The rise in antimicrobial resistance (AMR) poses a major threat to animal agriculture and human health. To summarize and update current and emerging AMR issues that are significant for animal health and food safety, this issue presents a virtual AMR symposium consisting of seven review papers. These reviews cover a newly described AMR mechanism in Campylobacter, effects of AMR and microbiome on Campylobacter infection, plasmid-mediated colistin resistance in food-producing animals, the impact of point source or antibiotic residues on the environmental resistome, and potential factors influencing horizontal gene transfer in the intestines of food animals. These papers also identify significant knowledge gaps in AMR research and provide new directions for the development of innovative and effective strategies to mitigate AMR in the animal production system.}, }
@article {pmid29665884, year = {2017}, author = {Zeng, X and Lin, J}, title = {Factors influencing horizontal gene transfer in the intestine.}, journal = {Animal health research reviews}, volume = {18}, number = {2}, pages = {153-159}, doi = {10.1017/S1466252317000159}, pmid = {29665884}, issn = {1475-2654}, support = {R21 AI119462/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics ; Drug Resistance, Microbial/genetics ; *Gene Transfer, Horizontal ; Intestines/*microbiology ; Microbiota ; }, abstract = {Antibiotic resistance (AR) is ancient. Use of antibiotics is a selective driving force that enriches AR genes and promotes the emergence of resistant pathogens. It also has been widely accepted that horizontal gene transfer (HGT) occurs everywhere and plays a critical role in the transmission of AR genes among bacteria. However, our understanding of HGT processes primarily build on extensive in vitro studies; to date, there is still a significant knowledge gap regarding in situ HGT events as well as the factors that influence HGT in different ecological niches. This review is focused on the HGT process in the intestinal tract, a 'melting pot' for gene exchange. Several factors that potentially influence in vivo HGT efficiency in the intestine are identified and summarized, which include SOS-inducing agents, stress hormones, microbiota and microbiota-derived factors. We highlight recent discoveries demonstrating that certain antibiotics, which are widely used in animal industry, can enhance HGT in the intestine by serving as DNA-damaging, SOS-inducing agents. Despite recent progress, research on in vivo HGT events is still in its infancy. A better understanding of the factors influencing HGT in the intestine is highly warranted for developing effective strategies to mitigate AR in animal production as well as in future agricultural ecosystems.}, }
@article {pmid29664687, year = {2018}, author = {Lifshitz, Z and Sturlesi, N and Parizade, M and Blum, SE and Gordon, M and Taran, D and Adler, A}, title = {Distinctiveness and Similarities Between Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolated from Cattle and the Community in Israel.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {24}, number = {6}, pages = {868-875}, doi = {10.1089/mdr.2017.0407}, pmid = {29664687}, issn = {1931-8448}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Cattle ; Community-Acquired Infections/drug therapy/*microbiology ; Cross-Sectional Studies/methods ; Escherichia coli/*genetics/*isolation &amp; purification ; Escherichia coli Infections/drug therapy/*microbiology/veterinary ; Humans ; Israel ; Microbial Sensitivity Tests/methods ; Multilocus Sequence Typing/methods ; Phylogeny ; beta-Lactamases/*genetics ; }, abstract = {The goal of this study was to compare the molecular features of bovine- and human community-acquired extended-spectrum β-lactamase (ESBL)-producing Escherichia coli in Israel. Bovine ESBL-producing E. coli were isolated during a point-prevalence study from the main farming locations throughout Israel. Human ESBL-producing E. coli isolates were collected from community-acquired urinary tract infection cases. Molecular typing was done initially by repetitive extragenic palindromic-PCR. Representative isolates were subjected to next-generation sequencing (NGS) and analyzed for multilocus sequence typing (MLST), core genome MLST (cgMLST), blaCTX-M gene allele, and mobile genetic elements (MGEs) surrounding it. Out of the 287 bovine- and 104 community-derived ESBL-producing E. coli isolates, 44 and 26 isolates were subjected to NGS, respectively. Both populations exhibited a diverse but distinct clonal structure with predominance of several sequence types (STs); two clones, ST-10/167 (n = 13) and ST-38 (n = 8), were present. cgMLST analysis of these clones revealed that the majority of isolates exhibited phylogenetic distance (PD) of >178 gene difference from their closest isolate, with the exception of five isolates that exhibited PD of <24 gene difference, including two bovine- to three community-derived isolates. Hence, clonal transmission of ESBL-producing E. coli between cattle and the community, although uncommon, is likely to have occurred. The blaCTX-M-15 gene was identified in 52/70 (74%) isolates from both cattle and the community and was surrounded by MGEs that were composed mostly of either the Tn3 or IS1380 families. Thus, MGEs are likely to play an important role in the exchange of resistance genes.}, }
@article {pmid29661139, year = {2018}, author = {Di Cesare, A and Cabello-Yeves, PJ and Chrismas, NAM and Sánchez-Baracaldo, P and Salcher, MM and Callieri, C}, title = {Genome analysis of the freshwater planktonic Vulcanococcus limneticus sp. nov. reveals horizontal transfer of nitrogenase operon and alternative pathways of nitrogen utilization.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {259}, pmid = {29661139}, issn = {1471-2164}, mesh = {Cyanobacteria/classification/*genetics/isolation &amp; purification/metabolism ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Lakes/microbiology ; Nitrogen/*metabolism ; Nitrogenase/*genetics ; *Operon ; Phenotype ; Phylogeny ; Plankton/genetics/isolation &amp; purification ; }, abstract = {BACKGROUND: Many cyanobacteria are capable of fixing atmospheric nitrogen, playing a crucial role in biogeochemical cycling. Little is known about freshwater unicellular cyanobacteria Synechococcus spp. at the genomic level, despite being recognised of considerable ecological importance in aquatic ecosystems. So far, it has not been shown whether these unicellular picocyanobacteria have the potential for nitrogen fixation. Here, we present the draft-genome of the new pink-pigmented Synechococcus-like strain Vulcanococcus limneticus. sp. nov., isolated from the volcanic Lake Albano (Central Italy).<br><br>RESULTS: The novel species Vulcanococcus limneticus sp. nov. falls inside the sub-cluster 5.2, close to the estuarine/marine strains in a maximum-likelihood phylogenetic tree generated with 259 marker genes with representatives from marine, brackish, euryhaline and freshwater habitats. V.limneticus sp. nov. possesses a complete nitrogenase and nif operon. In an experimental setup under nitrogen limiting and non-limiting conditions, growth was observed in both cases. However, the nitrogenase genes (nifHDK) were not transcribed, i.e., V.limneticus sp. nov. did not fix nitrogen, but instead degraded the phycobilisomes to produce sufficient amounts of ammonia. Moreover, the strain encoded many other pathways to incorporate ammonia, nitrate and sulphate, which are energetically less expensive for the cell than fixing nitrogen. The association of the nif operon to a genomic island, the relatively high amount of mobile genetic elements (52 transposases) and the lower observed GC content of V.limneticus sp. nov. nif operon (60.54%) compared to the average of the strain (68.35%) support the theory that this planktonic strain may have obtained, at some point of its evolution, the nif operon by horizontal gene transfer (HGT) from a filamentous or heterocystous cyanobacterium.<br><br>CONCLUSIONS: In this study, we describe the novel species Vulcanococcus limneticus sp. nov., which possesses a complete nif operon for nitrogen fixation. The finding that in our experimental conditions V.limneticus sp. nov. did not express the nifHDK genes led us to reconsider the actual ecological meaning of these accessory genes located in genomic island that have possibly been acquired via HGT.}, }
@article {pmid29660617, year = {2018}, author = {Zhu, Y and Zhang, Q and Xu, J and Qu, Q and Lu, T and Du, B and Ke, M and Zhang, M and Qian, H}, title = {Changes in bacterial community structure and antibiotic resistance genes in soil in the vicinity of a pharmaceutical factory.}, journal = {Ecotoxicology and environmental safety}, volume = {158}, number = {}, pages = {87-93}, doi = {10.1016/j.ecoenv.2018.04.016}, pmid = {29660617}, issn = {1090-2414}, mesh = {Bacteria/genetics/*isolation &amp; purification ; China ; *Drug Industry ; Drug Resistance, Microbial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Pharmaceutical Preparations/analysis ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/analysis ; }, abstract = {China is the largest global producer of antibiotics. With the demand for antibiotics increasing every year, it is necessary to assess potential environmental risks and the spread of antibiotic resistance genes (ARGs) associated with antibiotic production. Here, we investigated the occurrence and distribution of ARGs in soil in the vicinity of a pharmaceutical factory. The results showed that antibiotic concentrations were under the detection limit; however, ARGs were present in soil and tended to be enriched near the factory. A significant correlation between the relative abundance of intI-1 and tetracycline ARGs implied that horizontal gene transfer might play an important role in the spread of ARGs. The occurrence of these ARGs could be the results of previous antibiotic contamination. However, the soil bacterial community structure seemed to be more affected by nutrients or other factors than by antibiotics. Overall, this study supports the viewpoint that long-term pharmaceutical activity might have a negative effect on environmental health, thus, underscoring the need to regulate antibiotic production and management.}, }
@article {pmid29659855, year = {2018}, author = {Ma, S and Sun, C and Hulth, A and Li, J and Nilsson, LE and Zhou, Y and Börjesson, S and Bi, Z and Bi, Z and Sun, Q and Wang, Y}, title = {Mobile colistin resistance gene mcr-5 in porcine Aeromonas hydrophila.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {73}, number = {7}, pages = {1777-1780}, pmid = {29659855}, issn = {1460-2091}, mesh = {Aeromonas hydrophila/*drug effects/*genetics ; Animals ; Anti-Bacterial Agents/*pharmacology ; China ; Drug Resistance, Bacterial/*genetics ; Farms ; Feces/microbiology ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genome, Bacterial ; Gram-Negative Bacterial Infections/microbiology/veterinary ; Interspersed Repetitive Sequences ; Microbial Sensitivity Tests ; Plasmids/genetics ; Polymerase Chain Reaction ; Swine/microbiology ; Whole Genome Sequencing ; }, abstract = {OBJECTIVES: To characterize the mobile colistin resistance gene mcr-5 in Aeromonas hydrophila from backyard pigs in rural areas of China.<br><br>METHODS: Pig faecal samples from 194 households were directly tested for the presence of mcr-5 by PCR assay and the phenotypic antimicrobial susceptibility profiles of the mcr-5-positive isolates were determined using the broth dilution method. The genomic location and transferability of mcr-5 were analysed by S1-PFGE with Southern blotting and DNA hybridization, and natural transformation, respectively. One strain isolated from an mcr-5-positive sample was subjected to WGS and the stability of the mcr-5-harbouring plasmid over successive generations was examined by subculturing.<br><br>RESULTS: One mcr-5-positive A. hydrophila isolate showing resistance, with a colistin MIC of 4&#x2009;mg/L, was isolated from a backyard pig faecal sample. mcr-5 was located on a 7915&#x2009;bp plasmid designated pI064-2, which could naturally transform into a colistin-susceptible A. hydrophila strain of porcine origin and mediated colistin resistance in both the original isolate and its transformants. The plasmid backbone (3790&#x2009;bp) of pI064-2 showed 81% nucleotide sequence identity to the corresponding region of the ColE2-type plasmid pAsa1 from Aeromonas salmonicida, while similar replication primases are widely distributed among aeromonads, Enterobacteriaceae and Pseudomonas species.<br><br>CONCLUSIONS: To the best of our knowledge, this is the first identification of the novel colistin resistance gene mcr-5 in an A. hydrophila isolate from the faeces of a backyard pig. mcr-5 is expected to be able to disseminate among different bacterial species and genera.}, }
@article {pmid29659762, year = {2018}, author = {Torres-Puig, S and Martínez-Torró, C and Granero-Moya, I and Querol, E and Piñol, J and Pich, OQ}, title = {Activation of σ20-dependent recombination and horizontal gene transfer in Mycoplasma genitalium.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {25}, number = {4}, pages = {383-393}, pmid = {29659762}, issn = {1756-1663}, mesh = {Bacterial Proteins ; DNA, Bacterial/metabolism ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Variation ; *Homologous Recombination ; Mycoplasma genitalium/*genetics/metabolism ; Rec A Recombinases/metabolism ; Sigma Factor/genetics/*metabolism ; }, abstract = {In the human pathogen Mycoplasma genitalium, homologous recombination is under the control of σ20, an alternative sigma factor that boosts the generation of genetic and antigenic diversity in the population. Under laboratory growth conditions, σ20 activation is rare and the factors governing its intermittent activity are unknown. Two σ20-regulated genes, rrlA and rrlB, showed to be important for recombination of homologous DNA sequences in this bacterium. Herein, we demonstrate that rrlA and rrlB code for two small proteins that participate in a feed-forward loop essential for σ20 function. In addition, we identify novel genes regulated by σ20 and show that several non-coding regions, which function as a reservoir for the generation of antigenic diversity, are also activated by this alternative sigma factor. Finally, we reveal that M. genitalium cells can transfer DNA horizontally by a novel mechanism that requires RecA and is facilitated by σ20 over-expression. This DNA transfer system is arguably fundamental for persistence of M. genitalium within the host since it could facilitate a rapid dissemination of successful antigenic variants within the population. Overall, these findings impose a novel conception of genome evolution, genetic variation and survival of M. genitalium within the host.}, }
@article {pmid29658073, year = {2018}, author = {Afonyushkin, VN and Kozlova, YN and Tromenshleger, IN and Filipenko, ML and Novikova, OB}, title = {Comparative Characteristics of Discrimination of S. enterica Isolates by Phagotyping Test and Dienes Test.}, journal = {Bulletin of experimental biology and medicine}, volume = {164}, number = {6}, pages = {790-793}, doi = {10.1007/s10517-018-4081-2}, pmid = {29658073}, issn = {1573-8221}, mesh = {Antibiosis ; *Bacterial Typing Techniques ; Cluster Analysis ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genetic Heterogeneity ; Salmonella Phages/*classification/physiology ; Salmonella enterica/*classification/genetics/virology ; }, abstract = {We propose an original methodological approach to discrimination of newly isolated Salmonella enterica strains with the use of Dienes test. Dienes test is used for identification of P. vulgaris and P. mirabilis strains. It consists in growth suppression by mobile bacterial strain cultures and the formation of a demarcation line (Dienes line) between the strains growing towards each other. Similarities and differences between salmonella phagotyping method and Dienes test-based discrimination of the strains are detected. The studied sample of salmonellas was divided into 12 phagotypes. Cluster analysis has shown that most of the salmonella strains could not be clusterized by both methods. Discrimination by different methods has shown that the largest clusters contain the same strains. Clusterization of salmonella strains by different methods shows moderate congruency. Rand index used for comparison of the results of the sample clusterization by different methods is 0.88. High heterogeneity of salmonella strains is presumably explained by heterogeneity of antagonism factors within the S. enterica species. Intraspecies antagonism is essential for limitation of the horizontal gene transfer in closely related strains and for increase of the genetic heterogeneity of salmonella population in the host.}, }
@article {pmid29654279, year = {2018}, author = {Baker, KS and Dallman, TJ and Field, N and Childs, T and Mitchell, H and Day, M and Weill, FX and Lefèvre, S and Tourdjman, M and Hughes, G and Jenkins, C and Thomson, N}, title = {Horizontal antimicrobial resistance transfer drives epidemics of multiple Shigella species.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {1462}, pmid = {29654279}, issn = {2041-1723}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Adolescent ; Adult ; Anti-Bacterial Agents/*pharmacology ; Azithromycin/pharmacology ; Drug Resistance, Bacterial/*genetics ; Dysentery, Bacillary/*microbiology ; *Gene Transfer, Horizontal ; Genome-Wide Association Study ; Homosexuality, Male ; Humans ; Male ; Microbial Sensitivity Tests ; Middle Aged ; Phenotype ; Phylogeny ; Plasmids/metabolism ; Shigella/*genetics ; Time Factors ; Young Adult ; }, abstract = {Horizontal gene transfer has played a role in developing the global public health crisis of antimicrobial resistance (AMR). However, the dynamics of AMR transfer through bacterial populations and its direct impact on human disease is poorly elucidated. Here, we study parallel epidemic emergences of multiple Shigella species, a priority AMR organism, in men who have sex with men to gain insight into AMR emergence and spread. Using genomic epidemiology, we show that repeated horizontal transfer of a single AMR plasmid among Shigella enhanced existing and facilitated new epidemics. These epidemic patterns contrasted with slighter, slower increases in disease caused by organisms with vertically inherited (chromosomally encoded) AMR. This demonstrates that horizontal transfer of AMR directly affects epidemiological outcomes of globally important AMR pathogens and highlights the need for integration of genomic analyses into all areas of AMR research, surveillance and management.}, }
@article {pmid29651978, year = {2018}, author = {Vigliotti, C and Bicep, C and Bapteste, E and Lopez, P and Corel, E}, title = {Tracking the Rules of Transmission and Introgression with Networks.}, journal = {Microbiology spectrum}, volume = {6}, number = {2}, pages = {}, pmid = {29651978}, issn = {2165-0497}, mesh = {Animals ; Bacteria/genetics ; Evolution, Molecular ; Gastrointestinal Microbiome/*genetics/physiology ; Gastrointestinal Tract/*microbiology ; *Gene Regulatory Networks ; Gene Transfer, Horizontal ; Genetic Variation ; Humans ; Interspersed Repetitive Sequences ; Metagenome/genetics ; Microbiota/*genetics/physiology ; Plasmids/genetics ; *Recombination, Genetic ; Sequence Homology ; Viruses/genetics ; }, abstract = {Understanding how an animal organism and its gut microbes form an integrated biological organization, known as a holobiont, is becoming a central issue in biological studies. Such an organization inevitably involves a complex web of transmission processes that occur on different scales in time and space, across microbes and hosts. Network-based models are introduced in this chapter to tackle aspects of this complexity and to better take into account vertical and horizontal dimensions of transmission. Two types of network-based models are presented, sequence similarity networks and bipartite graphs. One interest of these networks is that they can consider a rich diversity of important players in microbial evolution that are usually excluded from evolutionary studies, like plasmids and viruses. These methods bring forward the notion of "gene externalization," which is defined as the presence of redundant copies of prokaryotic genes on mobile genetic elements (MGEs), and therefore emphasizes a related although distinct process from lateral gene transfer between microbial cells. This chapter introduces guidelines to the construction of these networks, reviews their analysis, and illustrates their possible biological interpretations and uses. The application to human gut microbiomes shows that sequences present in a higher diversity of MGEs have both biased functions and a broader microbial and human host range. These results suggest that an "externalized gut metagenome" is partly common to humans and benefits the gut microbial community. We conclude that testing relationships between microbial genes, microbes, and their animal hosts, using network-based methods, could help to unravel additional mechanisms of transmission in holobionts.}, }
@article {pmid29651977, year = {2018}, author = {Vanrompay, D and Nguyen, TLA and Cutler, SJ and Butaye, P}, title = {Antimicrobial Resistance in Chlamydiales, Rickettsia, Coxiella, and Other Intracellular Pathogens.}, journal = {Microbiology spectrum}, volume = {6}, number = {2}, pages = {}, pmid = {29651977}, issn = {2165-0497}, mesh = {Animal Diseases/microbiology ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacteriological Techniques/methods ; Cell Culture Techniques/methods ; Chlamydiales/drug effects/pathogenicity/*physiology ; Coxiella/drug effects/pathogenicity/*physiology ; Cytoplasm/microbiology ; Drug Resistance, Bacterial/*physiology ; Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests/methods ; Rickettsia/drug effects/pathogenicity/*physiology ; Zoonoses/microbiology ; }, abstract = {This article will provide current insights into antimicrobial susceptibilities and resistance of an important group of bacterial pathogens that are not phylogenetically related but share lifestyle similarities in that they are generally considered to be obligate intracellular microbes. As such, there are shared challenges regarding methods for their detection and subsequent clinical management. Similarly, from the laboratory perspective, susceptibility testing is rarely undertaken, though molecular approaches might provide new insights. One should also bear in mind that the highly specialized microbial lifestyle restricts the opportunity for lateral gene transfer and, consequently, acquisition of resistance.}, }
@article {pmid29651277, year = {2018}, author = {Yoon, EJ and Kang, DY and Yang, JW and Kim, D and Lee, H and Lee, KJ and Jeong, SH}, title = {New Delhi Metallo-Beta-Lactamase-Producing Enterobacteriaceae in South Korea Between 2010 and 2015.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {571}, pmid = {29651277}, issn = {1664-302X}, abstract = {This study was carried out to investigate the epidemiological time-course of New Delhi metallo-beta-lactamase- (NDM-) mediated carbapenem resistance in Enterobacteriaceae in South Korea. A total of 146 non-duplicate NDM-producing Enterobacteriaceae recovered between 2010 and 2015 were voluntarily collected from 33 general hospitals and confirmed by PCR. The species were identified by sequences of the 16S rDNA. Antimicrobial susceptibility was determined either by the disk diffusion method or by broth microdilution, and the carbapenem MICs were determined by agar dilution. Then, multilocus sequence typing and PCR-based replicon typing was carried out. Co-carried genes for drug resistance were identified by PCR and sequencing. The entire genomes of eight random selected NDM producers were sequenced. A total of 69 Klebsiella pneumoniae of 12 sequence types (STs), 34 Escherichia coli of 15 STs, 28 Enterobacter spp. (including one Enterobacter aerogenes), nine Citrobacter freundii, four Raoultella spp., and two Klebsiella oxytoca isolates produced either NDM-1 (n = 126), NDM-5 (n = 18), or NDM-7 (n = 2). The isolates co-produced CTX-M-type ESBL (52.1%), AmpCs (27.4%), additional carbapenemases (7.1%), and/or 16S rRNA methyltransferases (4.8%), resulting in multidrug-resistance (47.9%) or extensively drug-resistance (52.1%). Among plasmids harboring blaNDM, IncX3 was predominant (77.4%), followed by the IncFII type (5.8%). Genome analysis revealed inter-species and inter-strain horizontal gene transfer of the plasmid. Both clonal dissemination and plasmid transfer contributed to the wide dissemination of NDM producers in South Korea.}, }
@article {pmid29651164, year = {2018}, author = {Zhang, N and Cai, G and Price, DC and Crouch, JA and Gladieux, P and Hillman, B and Khang, CH and LeBrun, MH and Lee, YH and Luo, J and Qiu, H and Veltri, D and Wisecaver, JH and Zhu, J and Bhattacharya, D}, title = {Genome wide analysis of the transition to pathogenic lifestyles in Magnaporthales fungi.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {5862}, pmid = {29651164}, issn = {2045-2322}, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genome, Fungal/genetics ; Host-Pathogen Interactions/genetics ; Magnaporthe/*genetics/pathogenicity ; Oryza/genetics/microbiology ; Phylogeny ; Plant Diseases/*genetics/microbiology ; Selection, Genetic/*genetics ; }, abstract = {The rice blast fungus Pyricularia oryzae (syn. Magnaporthe oryzae, Magnaporthe grisea), a member of the order Magnaporthales in the class Sordariomycetes, is an important plant pathogen and a model species for studying pathogen infection and plant-fungal interaction. In this study, we generated genome sequence data from five additional Magnaporthales fungi including non-pathogenic species, and performed comparative genome analysis of a total of 13 fungal species in the class Sordariomycetes to understand the evolutionary history of the Magnaporthales and of fungal pathogenesis. Our results suggest that the Magnaporthales diverged ca. 31 millon years ago from other Sordariomycetes, with the phytopathogenic blast clade diverging ca. 21 million years ago. Little evidence of inter-phylum horizontal gene transfer (HGT) was detected in Magnaporthales. In contrast, many genes underwent positive selection in this order and the majority of these sequences are clade-specific. The blast clade genomes contain more secretome and avirulence effector genes, which likely play key roles in the interaction between Pyricularia species and their plant hosts. Finally, analysis of transposable elements (TE) showed differing proportions of TE classes among Magnaporthales genomes, suggesting that species-specific patterns may hold clues to the history of host/environmental adaptation in these fungi.}, }
@article {pmid29650391, year = {2018}, author = {Dietel, AK and Kaltenpoth, M and Kost, C}, title = {Convergent Evolution in Intracellular Elements: Plasmids as Model Endosymbionts.}, journal = {Trends in microbiology}, volume = {26}, number = {9}, pages = {755-768}, doi = {10.1016/j.tim.2018.03.004}, pmid = {29650391}, issn = {1878-4380}, mesh = {*Bacteria/genetics/metabolism ; Chromosome Segregation ; Cytoplasm ; DNA Transposable Elements ; Eukaryota ; Evolution, Molecular ; Gene Transfer, Horizontal ; Host Microbial Interactions/genetics/physiology ; Mutation ; *Plasmids/genetics/metabolism ; *Symbiosis/genetics/physiology ; }, abstract = {Endosymbionts are organisms that live inside the cells of other species. This lifestyle is ubiquitous across the tree of life and is featured by unicellular eukaryotes, prokaryotes, and by extrachromosomal genetic elements such as plasmids. Given that all of these elements dwell in the cytoplasm of their host cell, they should be subject to similar selection pressures. Here we show that strikingly similar features have evolved in both bacterial endosymbionts and plasmids. Since host and endosymbiont are often metabolically tightly intertwined, they are difficult to disentangle experimentally. We propose that using plasmids as tractable model systems can help to solve this problem, thus allowing fundamental questions to be experimentally addressed about the ecology and evolution of endosymbiotic interactions.}, }
@article {pmid29648541, year = {2018}, author = {Citti, C and Dordet-Frisoni, E and Nouvel, LX and Kuo, CH and Baranowski, E}, title = {Horizontal Gene Transfers in Mycoplasmas (Mollicutes).}, journal = {Current issues in molecular biology}, volume = {29}, number = {}, pages = {3-22}, doi = {10.21775/cimb.029.003}, pmid = {29648541}, issn = {1467-3045}, mesh = {Chromosomes, Bacterial ; Conjugation, Genetic ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Mycoplasma/classification/*physiology ; Response Elements ; Tenericutes/classification/*physiology ; }, abstract = {The class Mollicutes (trivial name "mycoplasma") is composed of wall-less bacteria with reduced genomes whose evolution was long thought to be only driven by gene losses. Recent evidences of massive horizontal gene transfer (HGT) within and across species provided a new frame to understand the successful adaptation of these minimal bacteria to a broad range of hosts. Mobile genetic elements are being identified in a growing number of mycoplasma species, but integrative and conjugative elements (ICEs) are emerging as pivotal in HGT. While sharing common traits with other bacterial ICEs, such as their chromosomal integration and the use of a type IV secretion system to mediate horizontal dissemination, mycoplasma ICEs (MICEs) revealed unique features: their chromosomal integration is totally random and driven by a DDE recombinase related to the Mutator-like superfamily. Mycoplasma conjugation is not restricted to ICE transmission, but also involves the transfer of large chromosomal fragments that generates progenies with mosaic genomes, nearly every position of chromosome being mobile. Mycoplasmas have thus developed efficient ways to gain access to a considerable reservoir of genetic resources distributed among a vast number of species expanding the concept of minimal cell to the broader context of flowing information.}, }
@article {pmid29648540, year = {2018}, author = {Roberts, AP}, title = {Editorial: ICE and Small.}, journal = {Current issues in molecular biology}, volume = {29}, number = {}, pages = {1-2}, doi = {10.21775/cimb.029.001}, pmid = {29648540}, issn = {1467-3045}, mesh = {*Conjugation, Genetic ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genomics/methods ; }, abstract = {Bacterial genomes vary considerably in terms of size and gene content. The proportion of a genome composed of horizontally acquired DNA or mobile genetic elements also varies, but follows an ecological pattern with more mobile genetic element genes being found in facultative intracellular bacteria than those considered extracellular and both containing more than obligately intracellular bacteria.}, }
@article {pmid29648539, year = {2018}, author = {Blesa, A and Averhoff, B and Berenguer, J}, title = {Horizontal Gene Transfer in Thermus spp.}, journal = {Current issues in molecular biology}, volume = {29}, number = {}, pages = {23-36}, doi = {10.21775/cimb.029.023}, pmid = {29648539}, issn = {1467-3045}, mesh = {Adaptive Immunity ; Bacterial Proteins/genetics/metabolism ; Conjugation, Genetic ; DNA, Bacterial ; *Gene Transfer, Horizontal ; Gram-Negative Bacterial Infections/immunology/microbiology ; Host-Pathogen Interactions ; Immunity, Innate ; Models, Biological ; Thermus/*physiology ; Transduction, Genetic ; }, abstract = {The small amount of genetic content in thermophiles generally limits their adaptability to environmental changes. In Thermus spp., very active horizontal gene transfer (HGT) mechanisms allow the rapid spread of strain-specific adaptive gene modules among the entire population. Constitutive expression of a rather particular and highly efficient DNA transport apparatus (DTA) is at the center of this HGT-mediated enhanced adaptability. The function of the DTA is dependent on the integrity and longevity of the extracellular DNA (eDNA) being transformed, which can be improved by the production of extracellular vesicles (EV) through lysis of a fraction of the population. The DTA must also contend with the recipient cell's defensive barriers, namely restriction enzymes, a panoply of CRISPR-Cas systems, and the argonaute-like protein TtAgo, which may be bypassed by transjugation, a new class of bidirectional transformation-dependent conjugation. Efficient transjugation depends on the presence of the ICETh1, an integrative and conjugative element which promotes simultaneous, generalized DNA transfer from several points in the genome. Transjugation shows preference for genes located within a megaplasmid replicon, where the main strain-specific adaptive modules are located. Contribution of transformation, vesicle-mediated eDNAs, and transjugation to HGT in this genus is discussed.}, }
@article {pmid29648535, year = {2018}, author = {Gonçalves, C and Wisecaver, JH and Kominek, J and Oom, MS and Leandro, MJ and Shen, XX and Opulente, DA and Zhou, X and Peris, D and Kurtzman, CP and Hittinger, CT and Rokas, A and Gonçalves, P}, title = {Evidence for loss and reacquisition of alcoholic fermentation in a fructophilic yeast lineage.}, journal = {eLife}, volume = {7}, number = {}, pages = {}, pmid = {29648535}, issn = {2050-084X}, support = {747775//Marie Curie/United Kingdom ; }, mesh = {Bacterial Proteins/genetics/*metabolism ; *Biological Evolution ; Ethanol/*metabolism ; *Fermentation ; Fructose/*metabolism ; Fungal Proteins/genetics/*metabolism ; *Gene Transfer, Horizontal ; Genome, Fungal ; Glucose ; Phylogeny ; Saccharomycetales/genetics/growth &amp; development/*metabolism ; }, abstract = {Fructophily is a rare trait that consists of the preference for fructose over other carbon sources. Here, we show that in a yeast lineage (the Wickerhamiella/Starmerella, W/S clade) comprised of fructophilic species thriving in the high-sugar floral niche, the acquisition of fructophily is concurrent with a wider remodeling of central carbon metabolism. Coupling comparative genomics with biochemical and genetic approaches, we gathered ample evidence for the loss of alcoholic fermentation in an ancestor of the W/S clade and subsequent reinstatement through either horizontal acquisition of homologous bacterial genes or modification of a pre-existing yeast gene. An enzyme required for sucrose assimilation was also acquired from bacteria, suggesting that the genetic novelties identified in the W/S clade may be related to adaptation to the high-sugar environment. This work shows how even central carbon metabolism can be remodeled by a surge of HGT events.}, }
@article {pmid29642965, year = {2018}, author = {Husnik, F}, title = {Host-symbiont-pathogen interactions in blood-feeding parasites: nutrition, immune cross-talk and gene exchange.}, journal = {Parasitology}, volume = {145}, number = {10}, pages = {1294-1303}, doi = {10.1017/S0031182018000574}, pmid = {29642965}, issn = {1469-8161}, mesh = {Animals ; Arthropods/*genetics/microbiology ; Blood ; Feeding Behavior ; Gene Transfer, Horizontal ; Host-Pathogen Interactions/genetics/*immunology ; Microbiota ; Nematoda/genetics/microbiology ; Parasites/*genetics/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Symbiosis ; }, abstract = {Animals are common hosts of mutualistic, commensal and pathogenic microorganisms. Blood-feeding parasites feed on a diet that is nutritionally unbalanced and thus often rely on symbionts to supplement essential nutrients. However, they are also of medical importance as they can be infected by pathogens such as bacteria, protists or viruses that take advantage of the blood-feeding nutritional strategy for own transmission. Since blood-feeding evolved multiple times independently in diverse animals, it showcases a gradient of host-microbe interactions. While some parasitic lineages are possibly asymbiotic and manage to supplement their diet from other food sources, other lineages are either loosely associated with extracellular gut symbionts or harbour intracellular obligate symbionts that are essential for the host development and reproduction. What is perhaps even more diverse are the pathogenic lineages that infect blood-feeding parasites. This microbial diversity not only puts the host into a complicated situation - distinguishing between microorganisms that can greatly decrease or increase its fitness - but also increases opportunity for horizontal gene transfer to occur in this environment. In this review, I first introduce this diversity of mutualistic and pathogenic microorganisms associated with blood-feeding animals and then focus on patterns in their interactions, particularly nutrition, immune cross-talk and gene exchange.}, }
@article {pmid29642605, year = {2018}, author = {Wang, X and Gu, J and Gao, H and Qian, X and Li, H}, title = {Abundances of Clinically Relevant Antibiotic Resistance Genes and Bacterial Community Diversity in the Weihe River, China.}, journal = {International journal of environmental research and public health}, volume = {15}, number = {4}, pages = {}, pmid = {29642605}, issn = {1660-4601}, mesh = {Anti-Bacterial Agents/*isolation &amp; purification ; Bacteria/*genetics ; China ; Drug Resistance, Microbial/*genetics ; *Genes, Bacterial ; RNA, Ribosomal, 16S/*genetics ; Rivers/*chemistry/*microbiology ; }, abstract = {The spread of antibiotic resistance genes in river systems is an emerging environmental issue due to their potential threat to aquatic ecosystems and public health. In this study, we used droplet digital polymerase chain reaction (ddPCR) to evaluate pollution with clinically relevant antibiotic resistance genes (ARGs) at 13 monitoring sites along the main stream of the Weihe River in China. Six clinically relevant ARGs and a class I integron-integrase (intI1) gene were analyzed using ddPCR, and the bacterial community was evaluated based on the bacterial 16S rRNA V3-V4 regions using MiSeq sequencing. The results indicated Proteobacteria, Actinobacteria, Cyanobacteria, and Bacteroidetes as the dominant phyla in the water samples from the Weihe River. Higher abundances of blaTEM, strB, aadA, and intI1 genes (10[3] to 10[5] copies/mL) were detected in the surface water samples compared with the relatively low abundances of strA, mecA, and vanA genes (0-1.94 copies/mL). Eight bacterial genera were identified as possible hosts of the intI1 gene and three ARGs (strA, strB, and aadA) based on network analysis. The results suggested that the bacterial community structure and horizontal gene transfer were associated with the variations in ARGs.}, }
@article {pmid29642473, year = {2018}, author = {Fernández, J and Guerra, B and Rodicio, MR}, title = {Resistance to Carbapenems in Non-Typhoidal Salmonella enterica Serovars from Humans, Animals and Food.}, journal = {Veterinary sciences}, volume = {5}, number = {2}, pages = {}, pmid = {29642473}, issn = {2306-7381}, abstract = {Non-typhoidal serovars of Salmonella enterica (NTS) are a leading cause of food-borne disease in animals and humans worldwide. Like other zoonotic bacteria, NTS have the potential to act as reservoirs and vehicles for the transmission of antimicrobial drug resistance in different settings. Of particular concern is the resistance to critical "last resort" antimicrobials, such as carbapenems. In contrast to other Enterobacteriaceae (e.g., Klebsiella pneumoniae, Escherichia coli, and Enterobacter, which are major nosocomial pathogens affecting debilitated and immunocompromised patients), carbapenem resistance is still very rare in NTS. Nevertheless, it has already been detected in isolates recovered from humans, companion animals, livestock, wild animals, and food. Five carbapenemases with major clinical importance-namely KPC (Klebsiella pneumoniae carbapenemase) (class A), IMP (imipenemase), NDM (New Delhi metallo-β-lactamase), VIM (Verona integron-encoded metallo-β-lactamase) (class B), and OXA-48 (oxacillinase, class D)-have been reported in NTS. Carbapenem resistance due to the production of extended spectrum- or AmpC β-lactamases combined with porin loss has also been detected in NTS. Horizontal gene transfer of carbapenemase-encoding genes (which are frequently located on self-transferable plasmids), together with co- and cross-selective adaptations, could have been involved in the development of carbapenem resistance by NTS. Once acquired by a zoonotic bacterium, resistance can be transmitted from humans to animals and from animals to humans through the food chain. Continuous surveillance of resistance to these "last resort" antibiotics is required to establish possible links between reservoirs and to limit the bidirectional transfer of the encoding genes between S. enterica and other commensal or pathogenic bacteria.}, }
@article {pmid29636744, year = {2018}, author = {Zhang, X and Liu, X and Yang, F and Chen, L}, title = {Pan-Genome Analysis Links the Hereditary Variation of Leptospirillum ferriphilum With Its Evolutionary Adaptation.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {577}, pmid = {29636744}, issn = {1664-302X}, abstract = {Niche adaptation has long been recognized to drive intra-species differentiation and speciation, yet knowledge about its relatedness with hereditary variation of microbial genomes is relatively limited. Using Leptospirillum ferriphilum species as a case study, we present a detailed analysis of genomic features of five recognized strains. Genome-to-genome distance calculation preliminarily determined the roles of spatial distance and environmental heterogeneity that potentially contribute to intra-species variation within L. ferriphilum species at the genome level. Mathematical models were further constructed to extrapolate the expansion of L. ferriphilum genomes (an 'open' pan-genome), indicating the emergence of novel genes with new sequenced genomes. The identification of diverse mobile genetic elements (MGEs) (such as transposases, integrases, and phage-associated genes) revealed the prevalence of horizontal gene transfer events, which is an important evolutionary mechanism that provides avenues for the recruitment of novel functionalities and further for the genetic divergence of microbial genomes. Comprehensive analysis also demonstrated that the genome reduction by gene loss in a broad sense might contribute to the observed diversification. We thus inferred a plausible explanation to address this observation: the community-dependent adaptation that potentially economizes the limiting resources of the entire community. Now that the introduction of new genes is accompanied by a parallel abandonment of some other ones, our results provide snapshots on the biological fitness cost of environmental adaptation within the L. ferriphilum genomes. In short, our genome-wide analyses bridge the relation between genetic variation of L. ferriphilum with its evolutionary adaptation.}, }
@article {pmid29635848, year = {2019}, author = {Wetzel, ME and Asenstorfer, RE and Tate, ME and Farrand, SK}, title = {Quorum-dependent transfer of the opine-catabolic plasmid pAoF64/95 is regulated by a novel mechanism involving inhibition of the TraR antiactivator TraM.}, journal = {MicrobiologyOpen}, volume = {8}, number = {1}, pages = {e00625}, pmid = {29635848}, issn = {2045-8827}, support = {R01 GM052465/GM/NIGMS NIH HHS/United States ; }, mesh = {Agrobacterium tumefaciens/drug effects/*genetics/physiology ; *Conjugation, Genetic ; Gene Expression Regulation, Bacterial/*drug effects ; *Gene Transfer, Horizontal ; Mannitol/*analogs &amp; derivatives/metabolism ; *Plasmids ; Protein Interaction Mapping ; *Quorum Sensing ; }, abstract = {We previously described a plasmid of Agrobacterium spp., pAoF64/95, in which the quorum-sensing system that controls conjugative transfer is induced by the opine mannopine. We also showed that the quorum-sensing regulators TraR, TraM, and TraI function similarly to their counterparts in other repABC plasmids. However, traR, unlike its counterpart on Ti plasmids, is monocistronic and not located in an operon that is inducible by the conjugative opine. Here, we report that both traR and traM are expressed constitutively and not regulated by growth with mannopine. We report two additional regulatory genes, mrtR and tmsP, that are involved in a novel mechanism of control of TraR activity. Both genes are located in the distantly linked region of pAoF64/95 encoding mannopine utilization. MrtR, in the absence of mannopine, represses the four-gene mocC operon as well as tmsP, which is the distal gene of the eight-gene motA operon. As judged by a bacterial two-hybrid analysis, TmsP, which shows amino acid sequence relatedness with the TraM-binding domain of TraR, interacts with the antiactivator. We propose a model in which mannopine, acting through the repressor MrtR, induces expression of TmsP which then titrates the levels of TraM thereby freeing TraR to activate the tra regulon.}, }
@article {pmid29633936, year = {2018}, author = {Chourashi, R and Das, S and Dhar, D and Okamoto, K and Mukhopadhyay, AK and Chatterjee, NS}, title = {Chitin-induced T6SS in Vibrio cholerae is dependent on ChiS activation.}, journal = {Microbiology (Reading, England)}, volume = {164}, number = {5}, pages = {751-763}, doi = {10.1099/mic.0.000656}, pmid = {29633936}, issn = {1465-2080}, mesh = {Bacterial Proteins/genetics/*metabolism ; Chitin/*metabolism ; Chitinases/metabolism ; Coculture Techniques ; Gene Deletion ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal/genetics ; Histidine Kinase/genetics/*metabolism ; Microbial Viability ; Transcriptional Activation ; Type VI Secretion Systems/*genetics/metabolism ; Vibrio cholerae/genetics/growth &amp; development/metabolism/*physiology ; }, abstract = {Vibrio cholerae regularly colonizes the chitinous exoskeleton of crustacean shells in the aquatic region. The type 6 secretion system (T6SS) in V. cholerae is an interbacterial killing device. This system is thought to provide a competitive advantage to V. cholerae in a polymicrobial community of the aquatic region under nutrient-poor conditions. V. cholerae chitin sensing is known to be initiated by the activation of a two-component sensor histidine kinase ChiS in the presence of GlcNAc2 (N,N'-diacetylchitobiose) residues generated by the action of chitinases on chitin. It is known that T6SS in V. cholerae is generally induced by chitin. However, the effect of ChiS activation on T6SS is unknown. Here, we found that ChiS inactivation resulted in impaired bacterial killing and reduced expression of T6SS genes. Active ChiS positively affected T6SS-mediated natural transformation in V. cholerae. ChiS depletion or inactivation also resulted in reduced colonization on insoluble chitin surfaces. Therefore, we have shown that V. cholerae colonization on chitinous surfaces activates ChiS, which promotes T6SS-dependent bacterial killing and horizontal gene transfer. We also highlight the importance of chitinases in T6SS upregulation.}, }
@article {pmid29633037, year = {2018}, author = {Westphal-Settele, K and Konradi, S and Balzer, F and Schönfeld, J and Schmithausen, R}, title = {[The environment as a reservoir for antimicrobial resistance : A growing problem for public health?].}, journal = {Bundesgesundheitsblatt, Gesundheitsforschung, Gesundheitsschutz}, volume = {61}, number = {5}, pages = {533-542}, doi = {10.1007/s00103-018-2729-8}, pmid = {29633037}, issn = {1437-1588}, mesh = {Animal Husbandry/trends ; Animals ; Anti-Bacterial Agents/therapeutic use ; Antimicrobial Stewardship ; Disinfectants/adverse effects ; Drug Resistance, Microbial/drug effects/*genetics ; Forecasting ; Gene Transfer, Horizontal/drug effects/*genetics ; Germany ; Humans ; Metals, Heavy/adverse effects ; Public Health/*trends ; }, abstract = {Antimicrobial resistance (AMR) is a threat to public and animal health on the global scale. The origin of the genes associated with resistance has long been unknown. Recently, there is a growing body of evidence demonstrating that environmental bacteria are resistant to a multitude of antibiotic substances and that this environmental reservoir of AMR is still growing. The analysis of the genomes of bacterial pathogens indicates that they have acquired their resistance profiles by incorporating different genetic elements through horizontal gene transfer. The ancestors of pathogenic bacteria, as well as the origin of resistance determinants, lay most likely in the environmental microbiota. Indeed, there is some evidence that at least some clinically relevant resistance genes have originated in environmental bacterial species. Thus, feasible measures are required to reduce the risks posed by AMR genes and resistant bacteria that occur in the environment. It has been shown that a concurrence of factors, such as high concentrations of antibiotics or heavy metals used as biocides and high bacterial densities, promote development and spread of antimicrobial resistance. For this purpose, it is essential to restrict the use of antibiotics for the treatment of livestock and humans to medical necessity, as well as to reduce the application of biocides and heavy metals in animal husbandry. Moreover, it is important to further develop sanitary measures at the interface between the environment and clinical settings or livestock farming.}, }
@article {pmid29632094, year = {2018}, author = {Corzett, CH and Elsherbini, J and Chien, DM and Hehemann, JH and Henschel, A and Preheim, SP and Yu, X and Alm, EJ and Polz, MF}, title = {Evolution of a Vegetarian Vibrio: Metabolic Specialization of Vibrio breoganii to Macroalgal Substrates.}, journal = {Journal of bacteriology}, volume = {200}, number = {15}, pages = {}, pmid = {29632094}, issn = {1098-5530}, mesh = {*Adaptation, Physiological ; Carbohydrate Metabolism/physiology ; Carbohydrates/classification ; Gene Expression Regulation, Bacterial ; Genomics ; Host Microbial Interactions ; Seaweed/*microbiology ; Transcriptome ; Vibrio/*physiology ; }, abstract = {While most Vibrionaceae are considered generalists that thrive on diverse substrates, including animal-derived material, we show that Vibrio breoganii has specialized for the consumption of marine macroalga-derived substrates. Genomic and physiological comparisons of V. breoganii with other Vibrionaceae isolates revealed the ability to degrade alginate, laminarin, and additional glycans present in algal cell walls. Moreover, the widely conserved ability to hydrolyze animal-derived polymers, including chitin and glycogen, was lost, along with the ability to efficiently grow on a variety of amino acids. Ecological data showing associations with particulate algal material but not zooplankton further support this shift in niche preference, and the loss of motility appears to reflect a sessile macroalga-associated lifestyle. Together, these findings indicate that algal polysaccharides have become a major source of carbon and energy in V. breoganii, and these ecophysiological adaptations may facilitate transient commensal associations with marine invertebrates that feed on algae.IMPORTANCE Vibrios are often considered animal specialists or generalists. Here, we show that Vibrio breoganii has undergone massive genomic changes to become specialized on algal carbohydrates. Accompanying genomic changes include massive gene import and loss. These vibrios may help us better understand how algal biomass is degraded in the environment and may serve as a blueprint on how to optimize the conversion of algae to biofuels.}, }
@article {pmid29631053, year = {2018}, author = {Chen, Y and Hammer, EE and Richards, VP}, title = {Phylogenetic signature of lateral exchange of genes for antibiotic production and resistance among bacteria highlights a pattern of global transmission of pathogens between humans and livestock.}, journal = {Molecular phylogenetics and evolution}, volume = {125}, number = {}, pages = {255-264}, doi = {10.1016/j.ympev.2018.03.034}, pmid = {29631053}, issn = {1095-9513}, mesh = {Animals ; Anti-Bacterial Agents/*biosynthesis ; Bacteria/*classification/genetics ; Cattle ; DNA Transposable Elements/genetics ; Drug Resistance, Bacterial/*genetics ; Gene Order ; Gene Transfer, Horizontal/*genetics ; *Genes, Bacterial ; Haplotypes/genetics ; Humans ; Likelihood Functions ; *Livestock ; Operon/genetics ; *Phylogeny ; Species Specificity ; Swine ; Virulence Factors ; Zoonoses/*microbiology/*transmission ; }, abstract = {The exchange of bacterial virulence factors driven by lateral gene transfer (LGT) can help indicate possible bacterial transmission among different hosts. Specifically, overlaying the phylogenetic signal of LGT among bacteria onto the distribution of respective isolation sources (hosts) can indicate patterns of transmission among these hosts. Here, we apply this approach towards a better understanding of patterns of bacterial transmission between humans and livestock. We utilize comparative genomics to trace patterns of LGT for an 11-gene operon responsible for the production of the antibiotic nisin and infer transmission of bacteria among respective host species. A total of 147 bacterial genomes obtained from NCBI were determined to contain the complete operon. Isolated from human, porcine and bovine hosts, these genomes represented six Streptococcus and one Staphylococcus species. Phylogenetic analyses of the operon sequences revealed a signature of frequent and recent lateral gene transfer that indicated extensive bacterial transmission between humans and pigs. For 11 isolates, we detected a Tn916-like transposon inserted into the operon. The transposon contained the tetM gene (tetracycline resistance) and additional phylogenetic analyses indicated transmission among human and animal hosts. The bacteria possessing the nisin operon and transposon were isolated from hosts distributed globally. These findings possibly reflect both the globalization of the food industry and an increasingly mobile and expanding human population. In addition to concerns regarding zoonosis, these findings also highlight the potential threat to livestock worldwide due to reverse zoonosis.}, }
@article {pmid29630596, year = {2018}, author = {Druzhinina, IS and Chenthamara, K and Zhang, J and Atanasova, L and Yang, D and Miao, Y and Rahimi, MJ and Grujic, M and Cai, F and Pourmehdi, S and Salim, KA and Pretzer, C and Kopchinskiy, AG and Henrissat, B and Kuo, A and Hundley, H and Wang, M and Aerts, A and Salamov, A and Lipzen, A and LaButti, K and Barry, K and Grigoriev, IV and Shen, Q and Kubicek, CP}, title = {Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts.}, journal = {PLoS genetics}, volume = {14}, number = {4}, pages = {e1007322}, pmid = {29630596}, issn = {1553-7404}, mesh = {Basidiomycota/classification/enzymology/genetics ; Cell Wall/*metabolism/microbiology ; Fungal Proteins/*genetics/metabolism ; *Gene Transfer, Horizontal ; Glycoside Hydrolases/genetics/metabolism ; Host-Pathogen Interactions ; Hyphae/enzymology/genetics/ultrastructure ; Hypocreales/classification/enzymology/genetics ; Microscopy, Electron, Scanning ; Phylogeny ; Plants/*metabolism/microbiology ; Trichoderma/enzymology/*genetics/physiology ; }, abstract = {Unlike most other fungi, molds of the genus Trichoderma (Hypocreales, Ascomycota) are aggressive parasites of other fungi and efficient decomposers of plant biomass. Although nutritional shifts are common among hypocrealean fungi, there are no examples of such broad substrate versatility as that observed in Trichoderma. A phylogenomic analysis of 23 hypocrealean fungi (including nine Trichoderma spp. and the related Escovopsis weberi) revealed that the genus Trichoderma has evolved from an ancestor with limited cellulolytic capability that fed on either fungi or arthropods. The evolutionary analysis of Trichoderma genes encoding plant cell wall-degrading carbohydrate-active enzymes and auxiliary proteins (pcwdCAZome, 122 gene families) based on a gene tree / species tree reconciliation demonstrated that the formation of the genus was accompanied by an unprecedented extent of lateral gene transfer (LGT). Nearly one-half of the genes in Trichoderma pcwdCAZome (41%) were obtained via LGT from plant-associated filamentous fungi belonging to different classes of Ascomycota, while no LGT was observed from other potential donors. In addition to the ability to feed on unrelated fungi (such as Basidiomycota), we also showed that Trichoderma is capable of endoparasitism on a broad range of Ascomycota, including extant LGT donors. This phenomenon was not observed in E. weberi and rarely in other mycoparasitic hypocrealean fungi. Thus, our study suggests that LGT is linked to the ability of Trichoderma to parasitize taxonomically related fungi (up to adelphoparasitism in strict sense). This may have allowed primarily mycotrophic Trichoderma fungi to evolve into decomposers of plant biomass.}, }
@article {pmid29628918, year = {2018}, author = {Shen, Y and Cai, J and Davies, MR and Zhang, C and Gao, K and Qiao, D and Jiang, H and Yao, W and Li, Y and Zeng, M and Chen, M}, title = {Identification and Characterization of Fluoroquinolone Non-susceptible Streptococcus pyogenes Clones Harboring Tetracycline and Macrolide Resistance in Shanghai, China.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {542}, pmid = {29628918}, issn = {1664-302X}, abstract = {Streptococcus pyogenes, also known as group A Streptococcus (GAS), is one of the top 10 infectious causes of death worldwide. Macrolide and tetracycline resistant GAS has emerged as a major health concern in China coinciding with an ongoing scarlet fever epidemic. Furthermore, increasing rates of fluoroquinolone (FQ) non-susceptibility within GAS from geographical regions outside of China has also been reported. Fluoroquinolones are the third most commonly prescribed antibiotic in China and is an therapeutic alternative for multi-drug resistant GAS. The purpose of this study was to investigate the epidemiological and molecular features of GAS fluoroquinolone (FQ) non-susceptibility in Shanghai, China. GAS (n = 2,258) recovered between 2011 and 2016 from children and adults were tested for FQ-non-susceptibility. Efflux phenotype and mutations in parC, parE, gyrA, and gyrB were investigated and genetic relationships were determined by emm typing, pulsed-field gel electrophoresis and phylogenetic analysis. The frequency of GAS FQ-non-susceptibility was 1.3% (30/2,258), with the phenotype more prevalent in GAS isolated from adults (14.3%) than from children (1.2%). Eighty percent (24/30) of FQ-non-susceptible isolates were also resistant to both macrolides (ermB) and tetracycline (tetM) including the GAS sequence types emm12, emm6, emm11, and emm1. Genomic fingerprinting analysis of the 30 isolates revealed that non-susceptibility may arise in various genetic backgrounds even within a single emm type. No efflux phenotype was observed in FQ non-susceptible isolates, and molecular analysis of the quinolone resistance-determining regions (QRDRs) identified several sequence polymorphisms in ParC and ParE, and none in GyrA and GyrB. Expansion of this analysis to 152 publically available GAS whole genome sequences from Hong Kong predicted 7.9% (12/152) of Hong Kong isolates harbored a S79F ParC mutation, of which 66.7% (8/12) were macrolide and tetracycline resistant. Phylogenetic analysis of the parC QRDR sequences suggested the possibility that FQ resistance may be acquired through inter-species lateral gene transfer. This study reports the emergence of macrolide, tetracycline, and fluoroquinolone multidrug-resistant clones across several GAS emm types including emm1 and emm12, warranting continual surveillance given the extensive use of fluoroquinolones in clinical use.}, }
@article {pmid29626635, year = {2018}, author = {Gygli, G and de Vries, RP and van Berkel, WJH}, title = {On the origin of vanillyl alcohol oxidases.}, journal = {Fungal genetics and biology : FG &amp; B}, volume = {116}, number = {}, pages = {24-32}, doi = {10.1016/j.fgb.2018.04.003}, pmid = {29626635}, issn = {1096-0937}, mesh = {Alcohol Oxidoreductases/*analysis/chemistry/genetics ; Amino Acid Motifs ; Ascomycota/enzymology ; Bacteria/enzymology ; Conserved Sequence ; Databases, Genetic ; *Evolution, Molecular ; Fungal Proteins/analysis/chemistry/genetics ; Fungi/*enzymology ; Genome, Fungal ; Phylogeny ; Species Specificity ; }, abstract = {Vanillyl alcohol oxidase (VAO) is a fungal flavoenzyme that converts a wide range of para-substituted phenols. The products of these conversions, e.g. vanillin, coniferyl alcohol and chiral aryl alcohols, are of interest for several industries. VAO is the only known fungal member of the 4-phenol oxidising (4PO) subgroup of the VAO/PCMH flavoprotein family. While the enzyme has been biochemically characterised in great detail, little is known about its physiological role and distribution in fungi. We have identified and analysed novel, fungal candidate VAOs and found them to be mostly present in Pezizomycotina and Agaricomycotina. The VAOs group into three clades, of which two clades do not have any characterised member. Interestingly, bacterial relatives of VAO do not form a single outgroup, but rather split up into two separate clades. We have analysed the distribution of candidate VAOs in fungi, as well as their genomic environment. VAOs are present in low frequency in species of varying degrees of relatedness and in regions of low synteny. These findings suggest that fungal VAOs may have originated from bacterial ancestors, obtained by fungi through horizontal gene transfer. Because the overall conservation of fungal VAOs varies between 60 and 30% sequence identity, we argue for a more reliable functional prediction using critical amino acid residues. We have defined a sequence motif P-x-x-x-x-S-x-G-[RK]-N-x-G-Y-G-[GS] that specifically recognizes 4PO enzymes of the VAO/PCMH family, as well as additional motifs that can help to further narrow down putative functions. We also provide an overview of fingerprint residues that are specific to VAOs.}, }
@article {pmid29625982, year = {2018}, author = {Westbye, AB and Kater, L and Wiesmann, C and Ding, H and Yip, CK and Beatty, JT}, title = {The Protease ClpXP and the PAS Domain Protein DivL Regulate CtrA and Gene Transfer Agent Production in Rhodobacter capsulatus.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {11}, pages = {}, pmid = {29625982}, issn = {1098-5336}, support = {93779//CIHR/Canada ; }, mesh = {Bacterial Proteins/*genetics ; Endopeptidase Clp/*genetics/metabolism ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Phosphorylation ; Protein Domains ; Rhodobacter capsulatus/*enzymology/*genetics ; }, abstract = {Several members of the Rhodobacterales (Alphaproteobacteria) produce a conserved horizontal gene transfer vector, called the gene transfer agent (GTA), that appears to have evolved from a bacteriophage. The model system used to study GTA biology is the Rhodobacter capsulatus GTA (RcGTA), a small, tailed bacteriophage-like particle produced by a subset of the cells in a culture. The response regulator CtrA is conserved in the Alphaproteobacteria and is an essential regulator of RcGTA production: it controls the production and maturation of the RcGTA particle and RcGTA release from cells. CtrA also controls the natural transformation-like system required for cells to receive RcGTA-donated DNA. Here, we report that dysregulation of the CckA-ChpT-CtrA phosphorelay either by the loss of the PAS domain protein DivL or by substitution of the autophosphorylation residue of the hybrid histidine kinase CckA decreased CtrA phosphorylation and greatly increased RcGTA protein production in R. capsulatus We show that the loss of the ClpXP protease or the three C-terminal residues of CtrA results in increased CtrA levels in R. capsulatus and identify ClpX(P) to be essential for the maturation of RcGTA particles. Furthermore, we show that CtrA phosphorylation is important for head spike production. Our results provide novel insight into the regulation of CtrA and GTAs in the RhodobacteralesIMPORTANCE Members of the Rhodobacterales are abundant in ocean and freshwater environments. The conserved GTA produced by many Rhodobacterales may have an important role in horizontal gene transfer (HGT) in aquatic environments and provide a significant contribution to their adaptation. GTA production is controlled by bacterial regulatory systems, including the conserved CckA-ChpT-CtrA phosphorelay; however, several questions about GTA regulation remain. Our identification that a short DivL homologue and ClpXP regulate CtrA in R. capsulatus extends the model of CtrA regulation from Caulobacter crescentus to a member of the Rhodobacterales We found that the magnitude of RcGTA production greatly depends on DivL and CckA kinase activity, adding yet another layer of regulatory complexity to RcGTA. RcGTA is known to undergo CckA-dependent maturation, and we extend the understanding of this process by showing that the ClpX chaperone is required for formation of tailed, DNA-containing particles.}, }
@article {pmid29625976, year = {2018}, author = {Flynn, CM and Schmidt-Dannert, C}, title = {Sesquiterpene Synthase-3-Hydroxy-3-Methylglutaryl Coenzyme A Synthase Fusion Protein Responsible for Hirsutene Biosynthesis in Stereum hirsutum.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {11}, pages = {}, pmid = {29625976}, issn = {1098-5336}, support = {R01 GM080299/GM/NIGMS NIH HHS/United States ; }, mesh = {Acyl Coenzyme A/*genetics ; Alkyl and Aryl Transferases/*genetics ; Basidiomycota/*enzymology/*genetics ; Cloning, Molecular ; Gene Expression Regulation, Enzymologic ; Genome, Fungal ; Multigene Family ; Phylogeny ; Polycyclic Sesquiterpenes ; Recombinant Fusion Proteins/metabolism ; Sesquiterpenes/*metabolism ; }, abstract = {The wood-rotting mushroom Stereum hirsutum is a known producer of a large number of namesake hirsutenoids, many with important bioactivities. Hirsutenoids form a structurally diverse and distinct class of sesquiterpenoids. No genes involved in hirsutenoid biosynthesis have yet been identified or their enzymes characterized. Here, we describe the cloning and functional characterization of a hirsutene synthase as an unexpected fusion protein of a sesquiterpene synthase (STS) with a C-terminal 3-hydroxy-3-methylglutaryl-coenzyme A (3-hydroxy-3-methylglutaryl-CoA) synthase (HMGS) domain. Both the full-length fusion protein and truncated STS domain are highly product-specific 1,11-cyclizing STS enzymes with kinetic properties typical of STSs. Complementation studies in Saccharomyces cerevisiae confirmed that the HMGS domain is also functional in vivo Phylogenetic analysis shows that the hirsutene synthase domain does not form a clade with other previously characterized sesquiterpene synthases from Basidiomycota. Comparative gene structure analysis of this hirsutene synthase with characterized fungal enzymes reveals a significantly higher intron density, suggesting that this enzyme may be acquired by horizontal gene transfer. In contrast, the HMGS domain is clearly related to other fungal homologs. This STS-HMGS fusion protein is part of a biosynthetic gene cluster that includes P450s and oxidases that are expressed and could be cloned from cDNA. Finally, this unusual fusion of a terpene synthase to an HMGS domain, which is not generally recognized as a key regulatory enzyme of the mevalonate isoprenoid precursor pathway, led to the identification of additional HMGS duplications in many fungal genomes, including the localization of HMGSs in other predicted sesquiterpenoid biosynthetic gene clusters.IMPORTANCE Hirsutenoids represent a structurally diverse class of bioactive sesquiterpenoids isolated from fungi. Identification of their biosynthetic pathways will provide access to this chemodiversity for the discovery and synthesis of molecules with new bioactivities. The identification and successful cloning of the previously elusive hirsutene synthase from the S. hirsutum provide important insights and strategies for biosynthetic gene discovery in Basidiomycota. The finding of a terpene synthase-HMGS fusion, the discovery of other sesquiterpenoid biosynthetic gene clusters with dedicated HMGS genes, and HMGS gene duplications in fungal genomes give new importance to the role of HMGS as a key regulatory enzyme in isoprenoid and sterol biosynthesis that should be exploited for metabolic engineering.}, }
@article {pmid29623873, year = {2018}, author = {Shen, Z and Wang, Y and Zhang, Q and Shen, J}, title = {Antimicrobial Resistance in Campylobacter spp.}, journal = {Microbiology spectrum}, volume = {6}, number = {2}, pages = {}, pmid = {29623873}, issn = {2165-0497}, support = {R01 AI118283/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/classification/*pharmacology ; Bacterial Proteins/genetics ; Campylobacter/*drug effects/genetics ; Drug Resistance, Bacterial/genetics/*physiology ; Drug Resistance, Multiple, Bacterial/genetics/physiology ; Gene Transfer, Horizontal ; Genomic Islands ; Humans ; Membrane Transport Proteins ; Mutation ; }, abstract = {Campylobacter is a major foodborne pathogen and has become increasingly resistant to clinically important antimicrobials. To cope with the selection pressure from antimicrobial use in both veterinary and human medicine, Campylobacter has developed multiple mechanisms for antibiotic resistance, including modification or mutation of antimicrobial targets, modification or inactivation of antibiotics, and reduced drug accumulation by drug efflux pumps. Some of these mechanisms confer resistance to a specific class of antimicrobials, while others give rise to multidrug resistance. Notably, new antibiotic resistance mechanisms continuously emerge in Campylobacter, and some examples include the recently discovered multidrug resistance genomic islands harboring multiple genes involved in the resistance to aminoglycosides and macrolides, a novel Cfr(C) conferring resistance to phenicols and other drugs, and a potent multidrug efflux pump CmeABC variant (RE-CmeABC) that shows a significantly enhanced function in multidrug resistance and is associated with exceedingly high-level resistance to fluoroquinolones. These newly emerged resistance mechanisms are horizontally transferable and greatly facilitate the adaptation of Campylobacter in the food-producing environments where antibiotics are frequently used. In this article, we will discuss how Campylobacter resists the action of various classes of antimicrobials, with an emphasis on newly discovered mechanisms.}, }
@article {pmid29623872, year = {2018}, author = {Dutcher, HA and Raghavan, R}, title = {Origin, Evolution, and Loss of Bacterial Small RNAs.}, journal = {Microbiology spectrum}, volume = {6}, number = {2}, pages = {}, pmid = {29623872}, issn = {2165-0497}, support = {R03 AI123464/AI/NIAID NIH HHS/United States ; R03 AI133023/AI/NIAID NIH HHS/United States ; R15 AI126385/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/genetics/metabolism ; Binding Sites ; *Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/genetics ; MicroRNAs/genetics/physiology ; Molecular Sequence Annotation ; Mutation ; Phylogeny ; Protein Binding ; RNA, Bacterial/*genetics/*physiology ; RNA, Small Untranslated/*genetics/*physiology ; Sigma Factor ; }, abstract = {Despite the central role of bacterial noncoding small RNAs (sRNAs) in posttranscriptional regulation, little is understood about their evolution. Here we compile what has been studied to date and trace a life cycle of sRNAs-from their mechanisms of emergence, through processes of change and frequent neofunctionalization, to their loss from bacterial lineages. Because they possess relatively unrestrictive structural requirements, we find that sRNA origins are varied, and include de novo emergence as well as formation from preexisting genetic elements via duplication events and horizontal gene transfer. The need for only partial complementarity to their mRNA targets facilitates apparent rapid change, which also contributes to significant challenges in tracing sRNAs across broad evolutionary distances. We document that recently emerged sRNAs in particular evolve quickly, mirroring dynamics observed in microRNAs, their functional analogs in eukaryotes. Mutations in mRNA-binding regions, transcriptional regulator or sigma factor binding sites, and protein-binding regions are all likely sources of shifting regulatory roles of sRNAs. Finally, using examples from the few evolutionary studies available, we examine cases of sRNA loss and describe how these may be the result of adaptive in addition to neutral processes. We highlight the need for more-comprehensive analyses of sRNA evolutionary patterns as a means to improve novel sRNA detection, enhance genome annotation, and deepen our understanding of regulatory networks in bacteria.}, }
@article {pmid29621975, year = {2018}, author = {Tahiri, N and Willems, M and Makarenkov, V}, title = {A new fast method for inferring multiple consensus trees using k-medoids.}, journal = {BMC evolutionary biology}, volume = {18}, number = {1}, pages = {48}, pmid = {29621975}, issn = {1471-2148}, mesh = {*Algorithms ; Archaea/metabolism ; Cluster Analysis ; Computer Simulation ; Gene Transfer, Horizontal/genetics ; Genomics/*methods ; *Phylogeny ; Ribosomal Proteins/metabolism ; Species Specificity ; }, abstract = {BACKGROUND: Gene trees carry important information about specific evolutionary patterns which characterize the evolution of the corresponding gene families. However, a reliable species consensus tree cannot be inferred from a multiple sequence alignment of a single gene family or from the concatenation of alignments corresponding to gene families having different evolutionary histories. These evolutionary histories can be quite different due to horizontal transfer events or to ancient gene duplications which cause the emergence of paralogs within a genome. Many methods have been proposed to infer a single consensus tree from a collection of gene trees. Still, the application of these tree merging methods can lead to the loss of specific evolutionary patterns which characterize some gene families or some groups of gene families. Thus, the problem of inferring multiple consensus trees from a given set of gene trees becomes relevant.<br><br>RESULTS: We describe a new fast method for inferring multiple consensus trees from a given set of phylogenetic trees (i.e. additive trees or X-trees) defined on the same set of species (i.e. objects or taxa). The traditional consensus approach yields a single consensus tree. We use the popular k-medoids partitioning algorithm to divide a given set of trees into several clusters of trees. We propose novel versions of the well-known Silhouette and Cali&#x144;ski-Harabasz cluster validity indices that are adapted for tree clustering with k-medoids. The efficiency of the new method was assessed using both synthetic and real data, such as a well-known phylogenetic dataset consisting of 47 gene trees inferred for 14 archaeal organisms.<br><br>CONCLUSIONS: The method described here allows inference of multiple consensus trees from a given set of gene trees. It can be used to identify groups of gene trees having similar intragroup and different intergroup evolutionary histories. The main advantage of our method is that it is much faster than the existing tree clustering approaches, while providing similar or better clustering results in most cases. This makes it particularly well suited for the analysis of large genomic and phylogenetic datasets.}, }
@article {pmid29621708, year = {2018}, author = {Lv, B and Cui, Y and Tian, W and Li, J and Xie, B and Yin, F}, title = {Abundances and profiles of antibiotic resistance genes as well as co-occurrences with human bacterial pathogens in ship ballast tank sediments from a shipyard in Jiangsu Province, China.}, journal = {Ecotoxicology and environmental safety}, volume = {157}, number = {}, pages = {169-175}, doi = {10.1016/j.ecoenv.2018.03.053}, pmid = {29621708}, issn = {1090-2414}, mesh = {Bacteria/genetics/isolation &amp; purification ; China ; Drug Resistance, Microbial/*genetics ; *Genes, Bacterial ; Geologic Sediments/microbiology ; *Ships ; }, abstract = {Ship ballasting operations may transfer harmful aquatic organisms across global ocean. This study aims to reveal the occurrences and abundances of antibiotic resistance genes (ARGs) and human bacterial pathogens (HBPs) in ballast tank sediments. Nine samples were collected and respectively analyzed by real-time quantitative PCR and high-throughput sequencing technologies. Ten ARGs (aadA1, blaCTX-M, blaTEM, ermB, mefA, strB, sul1, sul2, tetM, and tetQ) and the Class-I integron gene (intI1) were highly prevalent (10[5]-10[9] gene copies/g) in ballast tank sediments. The sul1 was the most abundant ARG with the concentration of 10[8]-10[9] copies/g and intI1 was much more abundant than the ARGs in ballast tank sediments. The strong positive correlations between intI1 and ARGs (blaCTX-M, sul1, sul2 and tetM) indicated the potential spread of ARGs via horizontal gene transfer. In ballast tank sediments, 44 bacterial species were identified as HBPs and accounted for 0.13-21.46% of the total bacterial population although the three indicator pathogenic microbes (Vibrio cholerae, Escherichia coli, and Enterococci) proposed by the International Maritime Organization were not detected. Pseudomonas pseudoalcaligenes, Enterococcus hirae, Shigella sonnei and Bacillus anthracis were the dominant pathogens in ballast tank sediments. Zn and P in sediments had positive effects on the ARGs. Network analysis results indicated that sul1 and sul2 genes existed in several bacterial pathogens. Ballast tank sediments could be regarded as a carrier for the migration of ARGs. It is important to manage ballast tank sediments reasonably in order to prevent the dissemination of ARGs and bacterial pathogens.}, }
@article {pmid29621277, year = {2018}, author = {Kim, H and Kwak, W and Yoon, SH and Kang, DK and Kim, H}, title = {Horizontal gene transfer of Chlamydia: Novel insights from tree reconciliation.}, journal = {PloS one}, volume = {13}, number = {4}, pages = {e0195139}, pmid = {29621277}, issn = {1932-6203}, mesh = {Chlamydia/classification/*physiology ; Computational Biology/methods ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Virulence/genetics ; Whole Genome Sequencing ; }, abstract = {Recent comparative genomics studies have suggested that horizontal gene transfer (HGT) is one of the major processes in bacterial evolution. In this study, HGT events of 64 Chlamydia strains were investigated based on the pipeline employed in HGTree database constructed in our recent study. Tree reconciliation method was applied in order to calculate feasible HGT events. Following initial detection and an evaluation procedure, evidence of the HGT was identified in 548 gene families including 42 gene families transferred from outside of Chlamydiae phylum with high reliability. The donor species of inter-phylum HGT consists of 12 different bacterial and archaeal phyla, suggesting that Chlamydia might have even more various host range than in previous reports. In addition, each species of Chlamydia showed varying preference towards HGT, and genes engaged in HGT within Chlamydia and between other species showed different functional distribution. Also, examination of individual gene flows of niche-specific genes suggested that many of such genes are transferred mainly within Chlamydia genus. Our results uncovered novel features of HGT acting on Chlamydia genome evolution, and it would be also strong evidence that HGT is an ongoing process for intracellular pathogens. We expect that the results provide more insight into lineage- and niche-specific adaptations regarding their infectivity and pathogenicity.}, }
@article {pmid29617810, year = {2018}, author = {Murillo, T and Ramírez-Vargas, G and Riedel, T and Overmann, J and Andersen, JM and Guzmán-Verri, C and Chaves-Olarte, E and Rodríguez, C}, title = {Two Groups of Cocirculating, Epidemic Clostridiodes difficile Strains Microdiversify through Different Mechanisms.}, journal = {Genome biology and evolution}, volume = {10}, number = {3}, pages = {982-998}, pmid = {29617810}, issn = {1759-6653}, mesh = {Clostridioides difficile/*genetics ; Clostridium Infections/*genetics/microbiology ; Disease Outbreaks ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal/*genetics ; *Genetic Variation ; Genome, Bacterial ; Genotype ; Humans ; Mutation ; Virulence/genetics ; }, abstract = {Clostridiodes difficile strains from the NAPCR1/ST54 and NAP1/ST01 types have caused outbreaks despite of their notable differences in genome diversity. By comparing whole genome sequences of 32 NAPCR1/ST54 isolates and 17 NAP1/ST01 recovered from patients infected with C. difficile we assessed whether mutation, homologous recombination (r) or nonhomologous recombination (NHR) through lateral gene transfer (LGT) have differentially shaped the microdiversification of these strains. The average number of single nucleotide polymorphisms (SNPs) in coding sequences (NAPCR1/ST54 = 24; NAP1/ST01 = 19) and SNP densities (NAPCR1/ST54 = 0.54/kb; NAP1/ST01 = 0.46/kb) in the NAPCR1/ST54 and NAP1/ST01 isolates was comparable. However, the NAP1/ST01 isolates showed 3× higher average dN/dS rates (8.35) that the NAPCR1/ST54 isolates (2.62). Regarding r, whereas 31 of the NAPCR1/ST54 isolates showed 1 recombination block (3,301-8,226 bp), the NAP1/ST01 isolates showed no bases in recombination. As to NHR, the pangenome of the NAPCR1/ST54 isolates was larger (4,802 gene clusters, 26% noncore genes) and more heterogeneous (644 ± 33 gene content changes) than that of the NAP1/ST01 isolates (3,829 gene clusters, ca. 6% noncore genes, 129 ± 37 gene content changes). Nearly 55% of the gene content changes seen among the NAPCR1/ST54 isolates (355 ± 31) were traced back to MGEs with putative genes for antimicrobial resistance and virulence factors that were only detected in single isolates or isolate clusters. Congruently, the LGT/SNP rate calculated for the NAPCR1/ST54 isolates (26.8 ± 2.8) was 4× higher than the one obtained for the NAP1/ST1 isolates (6.8 ± 2.0). We conclude that NHR-LGT has had a greater role in the microdiversification of the NAPCR1/ST54 strains, opposite to the NAP1/ST01 strains, where mutation is known to play a more prominent role.}, }
@article {pmid29614372, year = {2018}, author = {Basu, S and Mukherjee, M}, title = {Incidence and risk of co-transmission of plasmid-mediated quinolone resistance and extended-spectrum β-lactamase genes in fluoroquinolone-resistant uropathogenic Escherichia coli: a first study from Kolkata, India.}, journal = {Journal of global antimicrobial resistance}, volume = {14}, number = {}, pages = {217-223}, doi = {10.1016/j.jgar.2018.03.009}, pmid = {29614372}, issn = {2213-7173}, mesh = {Bacterial Proteins/*genetics ; Disk Diffusion Antimicrobial Tests ; *Drug Resistance, Multiple, Bacterial ; Escherichia coli Infections/*urine ; Fluoroquinolones/pharmacology ; Gene Transfer, Horizontal ; Humans ; Incidence ; India/epidemiology ; Molecular Typing ; Plasmids/*genetics ; Quinolones/pharmacology ; Replicon ; Uropathogenic Escherichia coli/*classification/drug effects/genetics/isolation &amp; purification ; beta-Lactam Resistance ; }, abstract = {OBJECTIVES: Co-resistance to fluoroquinolones and β-lactams results in treatment complications for uropathogenic Escherichia coli (UPEC) infections. This study aimed to detect the coexistence and co-transmission of plasmid-mediated quinolone resistance (PMQR) and extended-spectrum β-lactamase (ESBL) genes in UPEC from Kolkata, India.<br><br>METHODS: Escherichia coli was detected biochemically from culture-positive urine samples. Antimicrobial resistance and ESBL production were confirmed by disk diffusion assay. Transfer of PMQR and ESBL genes was performed using azide-resistant E. coli J53 as recipient. PCR was conducted to identify PMQR and ESBL genes, plasmid incompatibility types, insertion sequences, integrons and ERIC-PCR patterns.<br><br>RESULTS: PMQR determinants were detected in 50.0% (35/70) of ciprofloxacin-resistant isolates, with ESBL production in 42.9% (15/35) and a &#x3b2;-lactamase inhibitor-resistant phenotype in 51.4% (18/35). The highest co-occurrence (37.1%; 13/35) and co-transmission of aac(6')-Ib-cr with blaTEM, blaCTX-M and blaOXA was observed. Among the conjugal plasmids, replicon types FrepB/FrepB+F1B were predominant, with rare incidences of A/C, N, X, I1, FIIS, L/M and H1. Distribution of integrons and ISEcp1 and IS26, either alone or in combination, irrespective of PMQR and ESBL gene types was observed. Discrete ERIC-PCR profiles indicated that acquisition of PMQR and ESBLs and their dissemination may be attributed to horizontal gene transfer.<br><br>CONCLUSION: This study demonstrates for the first time the risk of co-transmission of fluoroquinolone and &#x3b2;-lactam resistance amongst UPEC from Kolkata, posing a major public-health threat and limiting treatment options. Monitoring at the molecular level is necessary to design appropriate prescription policies to combat the alarming rise in drug resistance amongst these uropathogens.}, }
@article {pmid29610471, year = {2018}, author = {Davín, AA and Tannier, E and Williams, TA and Boussau, B and Daubin, V and Szöllősi, GJ}, title = {Gene transfers can date the tree of life.}, journal = {Nature ecology &amp; evolution}, volume = {2}, number = {5}, pages = {904-909}, pmid = {29610471}, issn = {2397-334X}, support = {714774/ERC_/European Research Council/International ; }, mesh = {Cyanobacteria/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Archaeal ; *Genome, Bacterial ; *Genome, Fungal ; *Phylogeny ; }, abstract = {Biodiversity has always been predominantly microbial, and the scarcity of fossils from bacteria, archaea and microbial eukaryotes has prevented a comprehensive dating of the tree of life. Here, we show that patterns of lateral gene transfer deduced from an analysis of modern genomes encode a novel and abundant source of information about the temporal coexistence of lineages throughout the history of life. We use state-of-the-art species tree-aware phylogenetic methods to reconstruct the history of thousands of gene families and demonstrate that dates implied by gene transfers are consistent with estimates from relaxed molecular clocks in Bacteria, Archaea and Eukarya. We present the order of speciations according to lateral gene transfer data calibrated to geological time for three datasets comprising 40 genomes for Cyanobacteria, 60 genomes for Archaea and 60 genomes for Fungi. An inspection of discrepancies between transfers and clocks and a comparison with mammalian fossils show that gene transfer in microbes is potentially as informative for dating the tree of life as the geological record in macroorganisms.}, }
@article {pmid29610470, year = {2018}, author = {Dos Reis, M}, title = {Fossil-free dating.}, journal = {Nature ecology &amp; evolution}, volume = {2}, number = {5}, pages = {771-772}, doi = {10.1038/s41559-018-0532-4}, pmid = {29610470}, issn = {2397-334X}, mesh = {*Fossils ; *Gene Transfer, Horizontal ; Phylogeny ; }, }
@article {pmid29610466, year = {2018}, author = {Wolfe, JM and Fournier, GP}, title = {Horizontal gene transfer constrains the timing of methanogen evolution.}, journal = {Nature ecology &amp; evolution}, volume = {2}, number = {5}, pages = {897-903}, doi = {10.1038/s41559-018-0513-7}, pmid = {29610466}, issn = {2397-334X}, mesh = {*Biological Evolution ; Cyanobacteria/*genetics/metabolism ; Euryarchaeota/*genetics/metabolism ; Evolution, Planetary ; *Gene Transfer, Horizontal ; Methane/*metabolism ; Phylogeny ; Temperature ; }, abstract = {Microbial methanogenesis may have been a major component of Earth's carbon cycle during the Archaean eon, generating a methane greenhouse that increased global temperatures enough for a liquid hydrosphere, despite the Sun's lower luminosity at the time. Evaluation of potential solutions to the 'faint young Sun' hypothesis by determining the age of microbial methanogenesis has been limited by ambiguous geochemical evidence and the absence of a diagnostic fossil record. To overcome these challenges, we use a temporal constraint: a horizontal gene transfer event from within archaeal methanogens to the ancestor of Cyanobacteria, one of the few microbial clades with recognized crown-group fossils. Results of molecular clock analyses calibrated by this horizontal-gene-transfer-propagated constraint show methanogens diverging within Euryarchaeota no later than 3.51 billion years ago, with methanogenesis itself probably evolving earlier. This timing provides independent support for scenarios wherein microbial methane production was important in maintaining temperatures on the early Earth.}, }
@article {pmid29602365, year = {2018}, author = {McKenna, DD}, title = {Beetle genomes in the 21st century: prospects, progress and priorities.}, journal = {Current opinion in insect science}, volume = {25}, number = {}, pages = {76-82}, doi = {10.1016/j.cois.2017.12.002}, pmid = {29602365}, issn = {2214-5753}, mesh = {Animals ; Biodiversity ; Coleoptera/classification/*genetics ; Female ; *Genome, Insect ; Male ; Phylogeny ; }, abstract = {The order Coleoptera (beetles) is arguably the most species-rich lineage of animals. Beetles exhibit an extraordinary variety of life histories and occupy most terrestrial environments. Whole genome sequences are available for 11 beetle species, only six of which have been published. Studies of beetle genomes have revealed remarkable new insights into the genomic basis and evolution of beetle life histories and other aspects of beetle biodiversity, including the genes underlying chemoperception, detoxification, and specialized plant feeding, as well as the role of horizontal gene transfer in elaboration of the beetle trophic repertoire. Nonetheless, such studies are in their infancy. The study of beetle genomes has the potential to further revolutionize our understanding of beetle biodiversity, but genomic studies of beetles remain seriously limited in scope and resolution by the very few genomes that are currently available for study.}, }
@article {pmid29600772, year = {2018}, author = {Haenni, M and Lupo, A and Madec, JY}, title = {Antimicrobial Resistance in Streptococcus spp.}, journal = {Microbiology spectrum}, volume = {6}, number = {2}, pages = {}, pmid = {29600772}, issn = {2165-0497}, mesh = {Animals ; Anti-Bacterial Agents/*classification/*pharmacology/therapeutic use ; Cattle ; Drug Combinations ; Drug Resistance, Bacterial/*drug effects/genetics ; Evolution, Molecular ; Female ; Gene Transfer, Horizontal ; Humans ; Mastitis, Bovine/drug therapy/microbiology ; Molecular Epidemiology ; Prevalence ; Streptococcal Infections/drug therapy/*veterinary ; Streptococcus/*classification/drug effects/genetics/*pathogenicity ; Zoonoses/microbiology ; beta-Lactam Resistance ; }, abstract = {The genus Streptococcus includes Gram-positive organisms shaped in cocci and organized in chains. They are commensals, pathogens, and opportunistic pathogens for humans and animals. Most Streptococcus species of veterinary relevance have a specific ecological niche, such as S. uberis, which is almost exclusively an environmental pathogen causing bovine mastitis. In contrast, S. suis can be considered as a true zoonotic pathogen, causing specific diseases in humans after contact with infected animals or derived food products. Finally, Streptococcus species such as S. agalactiae can be sporadically zoonotic, even though they are pathogens of both humans and animals independently. For clarification, a short taxonomical overview will be given here to highlight the diversity of streptococci that infect animals. Several families of antibiotics are used to treat animals for streptococcal infections. First-line treatments are penicillins (alone or in combination with aminoglycosides), macrolides and lincosamides, fluoroquinolones, and tetracyclines. Because of the selecting role of antibiotics, resistance phenotypes have been reported in streptococci isolated from animals worldwide. Globally, the dynamic of resistance acquisition in streptococci is slower than what is experienced in Enterobacteriaceae, probably due to the much more limited horizontal spread of resistance genes. Nonetheless, transposons or integrative and conjugative elements can disseminate resistance determinants among streptococci. Besides providing key elements on the prevalence of resistance in streptococci from animals, this article will also largely consider the mechanisms and molecular epidemiology of the major types of resistance to antimicrobials encountered in the most important streptococcal species in veterinary medicine.}, }
@article {pmid29596346, year = {2018}, author = {Huber, I and Potapova, K and Kuhn, A and Schmidt, H and Hinrichs, J and Rohde, C and Beyer, W}, title = {1st German Phage Symposium-Conference Report.}, journal = {Viruses}, volume = {10}, number = {4}, pages = {}, pmid = {29596346}, issn = {1999-4915}, mesh = {Animals ; Bacteria/*virology ; Bacteriophages/*physiology ; Biotechnology ; Drug Resistance, Microbial ; Evolution, Molecular ; Gene Transfer, Horizontal ; Germany ; Host-Pathogen Interactions ; Humans ; Phage Therapy ; }, abstract = {In Germany, phage research and application can be traced back to the beginning of the 20th century. However, with the triumphal march of antibiotics around the world, the significance of bacteriophages faded in most countries, and respective research mainly focused on fundamental questions and niche applications. After a century, we pay tribute to the overuse of antibiotics that led to multidrug resistance and calls for new strategies to combat pathogenic microbes. Against this background, bacteriophages came into the spotlight of researchers and practitioners again resulting in a fast growing "phage community". In October 2017, part of this community met at the 1st German Phage Symposium to share their knowledge and experiences. The participants discussed open questions and challenges related to phage therapy and the application of phages in general. This report summarizes the presentations given, highlights the main points of the round table discussion and concludes with an outlook for the different aspects of phage application.}, }
@article {pmid29588379, year = {2018}, author = {Brand, P and Lin, W and Johnson, BR}, title = {The Draft Genome of the Invasive Walking Stick, Medauroidea extradendata, Reveals Extensive Lineage-Specific Gene Family Expansions of Cell Wall Degrading Enzymes in Phasmatodea.}, journal = {G3 (Bethesda, Md.)}, volume = {8}, number = {5}, pages = {1403-1408}, pmid = {29588379}, issn = {2160-1836}, mesh = {Animals ; Cell Wall/*enzymology ; DNA Transposable Elements ; Genome Size ; *Genome, Insect ; Insecta/*genetics ; *Introduced Species ; Molecular Sequence Annotation ; *Multigene Family ; *Phylogeny ; }, abstract = {Plant cell wall components are the most abundant macromolecules on Earth. The study of the breakdown of these molecules is thus a central question in biology. Surprisingly, plant cell wall breakdown by herbivores is relatively poorly understood, as nearly all early work focused on the mechanisms used by symbiotic microbes to breakdown plant cell walls in insects such as termites. Recently, however, it has been shown that many organisms make endogenous cellulases. Insects, and other arthropods, in particular have been shown to express a variety of plant cell wall degrading enzymes in many gene families with the ability to break down all the major components of the plant cell wall. Here we report the genome of a walking stick, Medauroidea extradentata, an obligate herbivore that makes uses of endogenously produced plant cell wall degrading enzymes. We present a draft of the 3.3Gbp genome along with an official gene set that contains a diversity of plant cell wall degrading enzymes. We show that at least one of the major families of plant cell wall degrading enzymes, the pectinases, have undergone a striking lineage-specific gene family expansion in the Phasmatodea. This genome will be a useful resource for comparative evolutionary studies with herbivores in many other clades and will help elucidate the mechanisms by which metazoans breakdown plant cell wall components.}, }
@article {pmid29580513, year = {2018}, author = {Haubert, L and Cunha, CEPD and Lopes, GV and Silva, WPD}, title = {Food isolate Listeria monocytogenes harboring tetM gene plasmid-mediated exchangeable to Enterococcus faecalis on the surface of processed cheese.}, journal = {Food research international (Ottawa, Ont.)}, volume = {107}, number = {}, pages = {503-508}, doi = {10.1016/j.foodres.2018.02.062}, pmid = {29580513}, issn = {1873-7145}, mesh = {Cheese/*microbiology ; Conjugation, Genetic/genetics ; Enterococcus faecalis/*drug effects/*genetics ; Food Handling ; Food Microbiology/methods ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/drug effects/genetics ; Listeria monocytogenes/*drug effects/*genetics ; Microbial Sensitivity Tests ; Plasmids/genetics ; Polymerase Chain Reaction ; Tetracycline Resistance/*genetics ; }, abstract = {The genetic basis of tetracycline resistance in a food isolate Listeria monocytogenes (Lm16) was evaluated. Resistance to tetracycline was associated with the presence of the tetM gene in plasmid DNA. The sequence of tetM showed 100% of similarity with the Enterococcus faecalis sequences found in the EMBL database, suggesting that Lm16 received this gene from E. faecalis. Various size bands were detected in the DNA plasmid analysis, the largest being approximately 54.38 kb. Transferability of the tetM gene was achieved in vitro by agar matings between Lm16 and E. faecalis JH2-2, proving the potential for the spread of tetM by horizontal gene transfer. Furthermore, the conjugation experiments were performed on the surface of processed cheese, confirming the transferability in a food matrix. PCR assays were used to confirm the identity of E. faecalis and to detect the tetM gene in transconjugant bacteria. Additionally, the minimal inhibitory concentration for tetracycline and rifampicin and plasmid profiling were performed. This is the first report of a food isolate L. monocytogenes carrying the tetM gene in plasmid DNA, and it highlights the potential risk of spreading antimicrobial resistance genes between different bacteria.}, }
@article {pmid29575366, year = {2018}, author = {Ivanov, V and Lee, KM and Mutanen, M}, title = {Mitonuclear discordance in wolf spiders: Genomic evidence for species integrity and introgression.}, journal = {Molecular ecology}, volume = {27}, number = {7}, pages = {1681-1695}, doi = {10.1111/mec.14564}, pmid = {29575366}, issn = {1365-294X}, mesh = {Animals ; Cell Nucleus/*genetics ; Electron Transport Complex IV/genetics ; Genetic Loci ; *Genome, Mitochondrial ; *Genomics ; Likelihood Functions ; Mitochondria/genetics ; Phylogeny ; Species Specificity ; Spiders/*genetics ; }, abstract = {Systematists and taxonomists have benefited greatly from the emergence of molecular methods. Species identification has become straightforward through DNA barcoding and the rapid build-up of massive DNA barcode reference libraries. In animals, mitonuclear discordance can significantly complicate the process of species identification and delimitation. The causes of mitonuclear discordance are either biological (e.g., introgression, incomplete lineage sorting, horizontal gene transfer androgenesis) or induced by operational factors (e.g., human error with specimen misidentification or incorrect species delimitation). Moreover, endosymbionts may play an important role in promoting fixation of mitochondrial genomes. Here, we study the mitonuclear discordance of wolf spiders species (Lycosidae) (independent cases from Alopecosa aculeata and Pardosa pullata groups) that share identical COI DNA barcodes. We approached the case utilizing double-digest restriction site-associated DNA sequencing (ddRADseq) to obtain and analyse genomic-scale data. Our results suggest that the observed cases of mitonuclear discordance are not due to operational reasons but result from biological processes. Further analysis indicated introgression and that incomplete lineage sorting is unlikely to have been responsible for the observed discrepancy. Additional survey of endosymbionts provided ideas on further research and their role in shaping mitochondrial DNA distribution patterns. Thus, ddRADseq grants an efficient way to study the taxonomy of problematic groups with insight into underlying evolutionary processes.}, }
@article {pmid29572211, year = {2018}, author = {Sun, Y and Luo, H}, title = {Homologous Recombination in Core Genomes Facilitates Marine Bacterial Adaptation.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {11}, pages = {}, pmid = {29572211}, issn = {1098-5336}, mesh = {Adaptation, Physiological/*genetics ; Alleles ; Aquatic Organisms/*genetics ; Bacteria/*genetics/metabolism ; Ecosystem ; Ecotype ; Evolution, Molecular ; Genetic Loci ; *Genome, Bacterial ; Genomics ; *Homologous Recombination ; Phylogeny ; Prochlorococcus/genetics ; Seawater/microbiology ; }, abstract = {Acquisition of ecologically relevant genes is common among ocean bacteria, but whether it has a major impact on genome evolution in marine environments remains unknown. Here, we analyzed the core genomes of 16 phylogenetically diverse and ecologically relevant bacterioplankton lineages, each consisting of up to five genomes varying at the strain level. Statistical approaches identified from each lineage up to ∼50 loci showing anomalously high divergence at synonymous sites, which is best explained by recombination with distantly related organisms. The enriched gene categories in these outlier loci match well with the characteristics previously identified as the key phenotypes of these lineages. Examples are antibiotic synthesis and detoxification in Phaeobacter inhibens, exopolysaccharide production in Alteromonas macleodii, hydrocarbon degradation in Marinobacter hydrocarbonoclasticus, and cold adaptation in Pseudoalteromonas haloplanktis Intriguingly, the outlier loci feature polysaccharide catabolism in Cellulophaga baltica but not in Cellulophaga lytica, consistent with their primary habitat preferences in macroalgae and beach sands, respectively. Likewise, analysis of Prochlorococcus showed that photosynthesis-related genes listed in the outlier loci are found only in the high-light-adapted ecotype and not in the low-light adapted ecotype. These observations strongly suggest that recombination with distant relatives is a key mechanism driving the ecological diversification among marine bacterial lineages.IMPORTANCE Acquisition of new metabolic genes has been known as an important mechanism driving bacterial evolution and adaptation in the ocean, but acquisition of novel alleles of existing genes and its potential ecological role have not been examined. Guided by population genetic theories, our genomic analysis showed that divergent allele acquisition is prevalent in phylogenetically diverse marine bacterial lineages and that the affected loci often encode metabolic functions that underlie the known ecological roles of the lineages under study.}, }
@article {pmid29572210, year = {2018}, author = {Watt, AE and Browning, GF and Legione, AR and Bushell, RN and Stent, A and Cutler, RS and Young, ND and Marenda, MS}, title = {A Novel Glaesserella sp. Isolated from Pigs with Severe Respiratory Infections Has a Mosaic Genome with Virulence Factors Putatively Acquired by Horizontal Transfer.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {11}, pages = {}, pmid = {29572210}, issn = {1098-5336}, mesh = {Animals ; Australia ; Bacterial Proteins/genetics ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Haemophilus Infections/microbiology/*veterinary ; Haemophilus parasuis/*genetics/isolation &amp; purification/pathogenicity ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Respiratory Tract Infections/microbiology/*veterinary ; Swine/microbiology ; Swine Diseases/microbiology ; Virulence ; Virulence Factors/*genetics ; }, abstract = {An unknown member of the family Pasteurellaceae was repeatedly isolated from 20- to 24-week-old pigs with severe pulmonary lesions reared on the same farm in Victoria, Australia. The etiological diagnosis of the disease was inconclusive. The complete genome sequence analysis of one strain, 15-184, revealed some phylogenic proximity to Glaesserella (Haemophilus) parasuis, the cause of Glasser's disease. However, the sequences of the 16S rRNA and housekeeping genes, as well as the average nucleotide identity scores, differed from those of all other known species in the family Pasteurellaceae The protein content of 15-184 was composite, with 60% of coding sequences matching known G. parasuis products, while more than 20% had a closer relative in the genera Actinobacillus, Mannheimia, Pasteurella, and Bibersteinia Several putative virulence genes absent from G. parasuis but present in other Pasteurellaceae were also found, including the apxIII RTX toxin gene from Actinobacillus pleuropneumoniae, ABC transporters from Actinobacillus minor, and iron transporters from various species. Three prophages and one integrative conjugative element were present in the isolate. Horizontal gene transfers might explain the mosaic genomic structure and atypical metabolic and virulence characteristics of 15-184. This organism has not been assigned a taxonomic position in the family, but this study underlines the need for a large-scale epidemiological and clinical characterization of this novel pathogen in swine populations, as a genomic analysis suggests it could have a severe impact on pig health.IMPORTANCE Several species of Pasteurellaceae cause a range of significant diseases in pigs. A novel member of this family was recently isolated from Australian pigs suffering from severe respiratory infections. Comparative whole-genome analyses suggest that this bacterium represents a new species, which possesses a number of virulence genes horizontally acquired from a diverse range of other Pasteurellaceae While the possible contribution of other coinfecting noncultivable agents to the disease has not been ruled out in this study, the repertoire of virulence genes found in this organism may nevertheless explain some aspects of the associated pathology observed on the farm. The prevalence of this novel pathogen within pig populations is currently unknown. This finding is of particular importance for the pig industry, as this organism can have a serious impact on the health of these animals.}, }
@article {pmid29567094, year = {2018}, author = {Santos, L and Ramos, F}, title = {Antimicrobial resistance in aquaculture: Current knowledge and alternatives to tackle the problem.}, journal = {International journal of antimicrobial agents}, volume = {52}, number = {2}, pages = {135-143}, doi = {10.1016/j.ijantimicag.2018.03.010}, pmid = {29567094}, issn = {1872-7913}, mesh = {Animal Feed ; Animal Husbandry/ethics/*methods ; Animals ; Anti-Bacterial Agents/pharmacology ; Aquaculture/methods ; Bacteria/drug effects ; Bacterial Infections/drug therapy/immunology/microbiology/*prevention &amp; control ; Bacterial Vaccines/*administration &amp; dosage ; Diet/methods ; Disease Resistance/*drug effects ; Drug Resistance, Bacterial/*drug effects ; Fisheries/organization &amp; administration ; Gene Transfer, Horizontal ; Humans ; Immunity, Innate/drug effects ; Probiotics/*pharmacology ; }, abstract = {Aquaculture is a rapidly growing industry that currently accounts for almost half of the fish used for human consumption worldwide. Intensive and semi-intensive practices are used to produce large stocks of fish, but frequent disease outbreaks occur, and the use of antimicrobials has become a customary practice to control them. The selective pressure exerted by these drugs, which are usually present at sub-therapeutic levels for prolonged periods in the water and the sediments, provides ideal conditions for the emergence and selection of resistant bacterial strains and stimulates horizontal gene transfer. It is now widely recognized that the passage of antimicrobial resistance genes and resistant bacteria from aquatic to terrestrial animal husbandry and to the human environment and vice versa can have detrimental effects on both human and animal health and on aquatic ecosystems. A global effort must be made to cease antimicrobial overuse in aquaculture and encourage stakeholders to adopt other disease-prevention measures. Shaping a new path is crucial to containing the increasing threat of antimicrobial resistance.}, }
@article {pmid29567068, year = {2018}, author = {Górska, A and Peter, S and Willmann, M and Autenrieth, I and Schlaberg, R and Huson, DH}, title = {Dynamics of the human gut phageome during antibiotic treatment.}, journal = {Computational biology and chemistry}, volume = {74}, number = {}, pages = {420-427}, doi = {10.1016/j.compbiolchem.2018.03.011}, pmid = {29567068}, issn = {1476-928X}, mesh = {Anti-Bacterial Agents/administration &amp; dosage/*pharmacology ; Ciprofloxacin/administration &amp; dosage/*pharmacology ; Gastrointestinal Microbiome/*drug effects/genetics ; Gastrointestinal Tract/*drug effects/microbiology ; Healthy Volunteers ; Humans ; Metagenomics ; }, abstract = {Bacterial viruses contribute to the dynamics of the microbiome communities, as they are involved in the horizontal gene transfer. Previously we studied changes in the gut microbiome of the two healthy individuals over the course of a 6-days antibiotics treatment and subsequent 28 days recovery time (Willmann et al., 2015). Now, from the same samples, the virus-like particles were isolated and sequenced. As the phage sequences are currently poorly represented in reference databases, the reads had to be assembled, annotated and their abundance had to be evaluated via reads mapping. We analyzed and compared patterns of changes in abundance of the phage scaffolds and scaffolds with antibiotics resistant genes, in both phage and whole-genome metagenomic sets. We observed an increase in abundance of scaffolds carrying antibiotic-resistant genes in response to the treatment.}, }
@article {pmid29566638, year = {2018}, author = {Lu, B and Leong, HW}, title = {GI-Cluster: Detecting genomic islands via consensus clustering on multiple features.}, journal = {Journal of bioinformatics and computational biology}, volume = {16}, number = {3}, pages = {1840010}, doi = {10.1142/S0219720018400103}, pmid = {29566638}, issn = {1757-6334}, mesh = {*Cluster Analysis ; Computational Biology/*methods ; Databases, Genetic ; Gene Transfer, Horizontal ; Genome ; *Genomic Islands ; Genomics/*methods ; Salmonella typhi/genetics ; Vibrio cholerae/genetics ; }, abstract = {The accurate detection of genomic islands (GIs) in microbial genomes is important for both evolutionary study and medical research, because GIs may promote genome evolution and contain genes involved in pathogenesis. Various computational methods have been developed to predict GIs over the years. However, most of them cannot make full use of GI-associated features to achieve desirable performance. Additionally, many methods cannot be directly applied to newly sequenced genomes. We develop a new method called GI-Cluster, which provides an effective way to integrate multiple GI-related features via consensus clustering. GI-Cluster does not require training datasets or existing genome annotations, but it can still achieve comparable or better performance than supervised learning methods in comprehensive evaluations. Moreover, GI-Cluster is widely applicable, either to complete and incomplete genomes or to initial GI predictions from other programs. GI-Cluster also provides plots to visualize the distribution of predicted GIs and related features. GI-Cluster is available at https://github.com/icelu/GI_Cluster.}, }
@article {pmid29565971, year = {2018}, author = {Haskett, TL and Terpolilli, JJ and Ramachandran, VK and Verdonk, CJ and Poole, PS and O'Hara, GW and Ramsay, JP}, title = {Sequential induction of three recombination directionality factors directs assembly of tripartite integrative and conjugative elements.}, journal = {PLoS genetics}, volume = {14}, number = {3}, pages = {e1007292}, pmid = {29565971}, issn = {1553-7404}, mesh = {Amino Acid Sequence ; Chromosomes, Bacterial ; DNA Nucleotidyltransferases/metabolism ; Gene Transfer, Horizontal ; Genes, Bacterial ; High-Throughput Nucleotide Sequencing ; Mesorhizobium/*genetics ; Quorum Sensing ; RNA, Bacterial/genetics ; Real-Time Polymerase Chain Reaction ; *Recombination, Genetic ; Viral Proteins/metabolism ; }, abstract = {Tripartite integrative and conjugative elements (ICE3) are a novel form of ICE that exist as three separate DNA regions integrated within the genomes of Mesorhizobium spp. Prior to conjugative transfer the three ICE3 regions of M. ciceri WSM1271 ICEMcSym1271 combine and excise to form a single circular element. This assembly requires three coordinated recombination events involving three site-specific recombinases IntS, IntG and IntM. Here, we demonstrate that three excisionases-or recombination directionality factors-RdfS, RdfG and RdfM are required for ICE3 excision. Transcriptome sequencing revealed that expression of ICE3 transfer and conjugation genes was induced by quorum sensing. Quorum sensing activated expression of rdfS, and in turn RdfS stimulated transcription of both rdfG and rdfM. Therefore, RdfS acts as a "master controller" of ICE3 assembly and excision. The dependence of all three excisive reactions on RdfS ensures that ICE3 excision occurs via a stepwise sequence of recombination events that avoids splitting the chromosome into a non-viable configuration. These discoveries expose a surprisingly simple control system guiding molecular assembly of these novel and complex mobile genetic elements and highlight the diverse and critical functions of excisionase proteins in control of horizontal gene transfer.}, }
@article {pmid29563901, year = {2018}, author = {Singh, NS and Singhal, N and Virdi, JS}, title = {Genetic Environment of blaTEM-1, blaCTX-M-15, blaCMY-42 and Characterization of Integrons of Escherichia coli Isolated From an Indian Urban Aquatic Environment.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {382}, pmid = {29563901}, issn = {1664-302X}, abstract = {The presence of antibiotic resistance genes (ARGs) including those expressing ESBLs and AmpC-β-lactamases in Escherichia coli inhabiting the aquatic environments is a serious health problem. The situation is further complicated by the fact that ARGs can be easily transferred among bacterial species with the help of mobile genetic elements - plasmids, integrons, insertion sequences (IS), and transposons. Therefore, the analysis of genetic environment and mobile genetic elements associated with ARGs is important as these provide useful information about the epidemiology of these genes. In our previous study, we had reported presence of various β-lactam resistance genes present in E. coli strains inhabiting the river Yamuna traversing the National Capital Territory of Delhi (India). In the present study, we have analyzed the genetic environment of three ARGs blaTEM-1, blaCTX-M-15, and blaCMY -42 of those E. coli strains. The structure of class 1 integrons and their gene cassettes was also analyzed. Insertion sequence IS26 was present upstream of blaTEM-1, ISEcp1 was present upstream of blaCTXM-15 gene and orf477 was present downstream of blaCTXM-15. ISEcp1 was also present upstream of blaCMY -42 and, blc and sugE genes were present in the downstream region of this gene. Thus, the overall genetic environment surrounding these genes was similar to that reported from E. coli strains isolated globally. Conjugation assays, isolation and analysis of plasmid DNA of the transconjugants indicated that blaTEM-1, blaCTX-M-15, blaCMY -42 and class 1 integron were plasmid-mediated and possibly transmit between genera through horizontal gene transfer (HGT). This might lead to dissemination of antimicrobial resistance genes in aquatic environment. The work embodied in this paper is the first describing the genetic environment of bla and integrons in aquatic E. coli isolated from India.}, }
@article {pmid29563494, year = {2018}, author = {Wang, R and van Dorp, L and Shaw, LP and Bradley, P and Wang, Q and Wang, X and Jin, L and Zhang, Q and Liu, Y and Rieux, A and Dorai-Schneiders, T and Weinert, LA and Iqbal, Z and Didelot, X and Wang, H and Balloux, F}, title = {The global distribution and spread of the mobilized colistin resistance gene mcr-1.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {1179}, pmid = {29563494}, issn = {2041-1723}, support = {//Wellcome Trust/United Kingdom ; MR/P007597/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Americas/epidemiology ; Anti-Bacterial Agents/pharmacology ; Asia/epidemiology ; Carbapenems/pharmacology ; Colistin/*pharmacology ; *DNA Transposable Elements ; Drug Resistance, Multiple, Bacterial/*genetics ; Enterobacteriaceae/classification/drug effects/*genetics/isolation &amp; purification ; Enterobacteriaceae Infections/*epidemiology/microbiology/transmission ; Escherichia coli Proteins/*genetics/metabolism ; Europe/epidemiology ; Evolution, Molecular ; Gene Expression ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; Plasmids/chemistry/metabolism ; Population Dynamics ; }, abstract = {Colistin represents one of the few available drugs for treating infections caused by carbapenem-resistant Enterobacteriaceae. As such, the recent plasmid-mediated spread of the colistin resistance gene mcr-1 poses a significant public health threat, requiring global monitoring and surveillance. Here, we characterize the global distribution of mcr-1 using a data set of 457 mcr-1-positive sequenced isolates. We find mcr-1 in various plasmid types but identify an immediate background common to all mcr-1 sequences. Our analyses establish that all mcr-1 elements in circulation descend from the same initial mobilization of mcr-1 by an ISApl1 transposon in the mid 2000s (2002-2008; 95% highest posterior density), followed by a marked demographic expansion, which led to its current global distribution. Our results provide the first systematic phylogenetic analysis of the origin and spread of mcr-1, and emphasize the importance of understanding the movement of antibiotic resistance genes across multiple levels of genomic organization.}, }
@article {pmid29563186, year = {2018}, author = {diCenzo, GC and Wellappili, D and Golding, GB and Finan, TM}, title = {Inter-replicon Gene Flow Contributes to Transcriptional Integration in the Sinorhizobium meliloti Multipartite Genome.}, journal = {G3 (Bethesda, Md.)}, volume = {8}, number = {5}, pages = {1711-1720}, pmid = {29563186}, issn = {2160-1836}, mesh = {3-Hydroxybutyric Acid/metabolism ; Bacterial Proteins/genetics/metabolism ; Chromosomes, Bacterial/genetics ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; *Gene Flow ; Gene Knockout Techniques ; Genes, Reporter ; *Genome, Bacterial ; Replicon/*genetics ; Sinorhizobium meliloti/*genetics ; *Transcription, Genetic ; Up-Regulation/genetics ; }, abstract = {Integration of newly acquired genes into existing regulatory networks is necessary for successful horizontal gene transfer (HGT). Ten percent of bacterial species contain at least two DNA replicons over 300 kilobases in size, with the secondary replicons derived predominately through HGT. The Sinorhizobium meliloti genome is split between a 3.7 Mb chromosome, a 1.7 Mb chromid consisting largely of genes acquired through ancient HGT, and a 1.4 Mb megaplasmid consisting primarily of recently acquired genes. Here, RNA-sequencing is used to examine the transcriptional consequences of massive, synthetic genome reduction produced through the removal of the megaplasmid and/or the chromid. Removal of the pSymA megaplasmid influenced the transcription of only six genes. In contrast, removal of the chromid influenced expression of ∼8% of chromosomal genes and ∼4% of megaplasmid genes. This was mediated in part by the loss of the ETR DNA region whose presence on pSymB is due to a translocation from the chromosome. No obvious functional bias among the up-regulated genes was detected, although genes with putative homologs on the chromid were enriched. Down-regulated genes were enriched in motility and sensory transduction pathways. Four transcripts were examined further, and in each case the transcriptional change could be traced to loss of specific pSymB regions. In particularly, a chromosomal transporter was induced due to deletion of bdhA likely mediated through 3-hydroxybutyrate accumulation. These data provide new insights into the evolution of the multipartite bacterial genome, and more generally into the integration of horizontally acquired genes into the transcriptome.}, }
@article {pmid29558455, year = {2018}, author = {Shalev, Y and Soucy, SM and Papke, RT and Gogarten, JP and Eichler, J and Gophna, U}, title = {Comparative Analysis of Surface Layer Glycoproteins and Genes Involved in Protein Glycosylation in the Genus Haloferax.}, journal = {Genes}, volume = {9}, number = {3}, pages = {}, pmid = {29558455}, issn = {2073-4425}, abstract = {Within the Haloferax genus, both the surface (S)-layer protein, and the glycans that can decorate it, vary between species, which can potentially result in many different surface types, analogous to bacterial serotypes. This variation may mediate phenotypes, such as sensitivity to different viruses and mating preferences. Here, we describe S-layer glycoproteins found in multiple Haloferax strains and perform comparative genomics analyses of major and alternative glycosylation clusters of isolates from two coastal sites. We analyze the phylogeny of individual glycosylation genes and demonstrate that while the major glycosylation cluster tends to be conserved among closely related strains, the alternative cluster is highly variable. Thus, geographically- and genetically-related strains may exhibit diverse surface structures to such an extent that no two isolates present an identical surface profile.}, }
@article {pmid29556740, year = {2018}, author = {Paquola, ACM and Asif, H and Pereira, CAB and Feltes, BC and Bonatto, D and Lima, WC and Menck, CFM}, title = {Horizontal Gene Transfer Building Prokaryote Genomes: Genes Related to Exchange Between Cell and Environment are Frequently Transferred.}, journal = {Journal of molecular evolution}, volume = {86}, number = {3-4}, pages = {190-203}, pmid = {29556740}, issn = {1432-1432}, mesh = {Bacteria/genetics ; Escherichia coli/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Phylogeny ; *Prokaryotic Cells ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Horizontal gene transfer (HGT) has a major impact on the evolution of prokaryotic genomes, as it allows genes evolved in different contexts to be combined in a single genome, greatly enhancing the ways evolving organisms can explore the gene content space and adapt to the environment. A systematic analysis of HGT in a large number of genomes is of key importance in understanding the impact of HGT in the evolution of prokaryotes. We developed a method for the detection of genes that potentially originated by HGT based on the comparison of BLAST scores between homologous genes to 16S rRNA-based phylogenetic distances between the involved organisms. The approach was applied to 697 prokaryote genomes and estimated that in average approximately 15% of the genes in prokaryote genomes originated by HGT, with a clear correlation between the proportion of predicted HGT genes and the size of the genome. The methodology was strongly supported by evolutionary relationships, as tested by the direct phylogenetic reconstruction of many of the HGT candidates. Studies performed with Escherichia coli W3110 genome clearly show that HGT proteins have fewer interactions when compared to those predicted as vertical inherited, an indication that the number of protein partners imposes limitations to horizontal transfer. A detailed functional classification confirms that genes related to protein translation are vertically inherited, whereas interestingly, transport and binding proteins are strongly enriched among HGT genes. Because these genes are related to the cell exchange with their environment, their transfer most likely contributed to successful adaptation throughout evolution.}, }
@article {pmid29555638, year = {2018}, author = {Ferralli, J and Tucker, RP and Chiquet-Ehrismann, R}, title = {The teneurin C-terminal domain possesses nuclease activity and is apoptogenic.}, journal = {Biology open}, volume = {7}, number = {3}, pages = {}, pmid = {29555638}, issn = {2046-6390}, abstract = {Teneurins are type 2 transmembrane proteins expressed by developing neurons during periods of synaptogenesis and apoptosis. Neurons expressing teneurin-1 synapse with other teneurin-1-expressing neurons, and neurons expressing teneurin-2 synapse with other teneurin-2-expressing neurons. Knockdowns and mutations of teneurins lead to abnormal neuronal connections, but the mechanisms underlying teneurin action remain unknown. Teneurins appear to have evolved via horizontal gene transfer from prokaryotic proteins involved in bacterial self-recognition. The bacterial teneurin-like proteins contain a cytotoxic C-terminal domain that is encapsulated in a tyrosine-aspartic acid repeat barrel. Teneurins are likely to be organized in the same way, but it is unclear if the C-terminal domains of teneurins have cytotoxic properties. Here we show that expression of teneurin C-terminal domains or the addition of purified teneurin C-terminal domains leads to an increase in apoptosis in vitro The C-terminal domains of teneurins are most similar to bacterial nucleases, and purified C-terminal domains of teneurins linearize pcDNA3 and hydrolyze mitochondrial DNA. We hypothesize that yet to be identified stimuli lead to the release of the encapsulated teneurin C-terminal domain into the intersynaptic region, resulting in programmed cell death or the disruption of mitochondrial DNA and the subsequent pruning of inappropriate contacts.}, }
@article {pmid29554291, year = {2018}, author = {Warshan, D and Liaimer, A and Pederson, E and Kim, SY and Shapiro, N and Woyke, T and Altermark, B and Pawlowski, K and Weyman, PD and Dupont, CL and Rasmussen, U}, title = {Genomic Changes Associated with the Evolutionary Transitions of Nostoc to a Plant Symbiont.}, journal = {Molecular biology and evolution}, volume = {35}, number = {5}, pages = {1160-1175}, pmid = {29554291}, issn = {1537-1719}, mesh = {Amino Acid Sequence ; Benzaldehydes/metabolism ; *Biological Evolution ; Bryophyta/*microbiology ; Chemotaxis ; Endophytes/genetics/metabolism ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Magnoliopsida/*microbiology ; Nostoc/*genetics/metabolism ; Phototaxis ; Polysaccharides/metabolism ; Selection, Genetic ; Sulfur/metabolism ; Symbiosis ; }, abstract = {Cyanobacteria belonging to the genus Nostoc comprise free-living strains and also facultative plant symbionts. Symbiotic strains can enter into symbiosis with taxonomically diverse range of host plants. Little is known about genomic changes associated with evolutionary transition of Nostoc from free-living to plant symbiont. Here, we compared the genomes derived from 11 symbiotic Nostoc strains isolated from different host plants and infer phylogenetic relationships between strains. Phylogenetic reconstructions of 89 Nostocales showed that symbiotic Nostoc strains with a broad host range, entering epiphytic and intracellular or extracellular endophytic interactions, form a monophyletic clade indicating a common evolutionary history. A polyphyletic origin was found for Nostoc strains which enter only extracellular symbioses, and inference of transfer events implied that this trait was likely acquired several times in the evolution of the Nostocales. Symbiotic Nostoc strains showed enriched functions in transport and metabolism of organic sulfur, chemotaxis and motility, as well as the uptake of phosphate, branched-chain amino acids, and ammonium. The genomes of the intracellular clade differ from that of other Nostoc strains, with a gain/enrichment of genes encoding proteins to generate l-methionine from sulfite and pathways for the degradation of the plant metabolites vanillin and vanillate, and of the macromolecule xylan present in plant cell walls. These compounds could function as C-sources for members of the intracellular clade. Molecular clock analysis indicated that the intracellular clade emerged ca. 600 Ma, suggesting that intracellular Nostoc symbioses predate the origin of land plants and the emergence of their extant hosts.}, }
@article {pmid29553064, year = {2018}, author = {Nakajima, Y and Tsukamoto, T and Kumagai, Y and Ogura, Y and Hayashi, T and Song, J and Kikukawa, T and Demura, M and Kogure, K and Sudo, Y and Yoshizawa, S}, title = {Presence of a Haloarchaeal Halorhodopsin-Like Cl[-] Pump in Marine Bacteria.}, journal = {Microbes and environments}, volume = {33}, number = {1}, pages = {89-97}, pmid = {29553064}, issn = {1347-4405}, mesh = {Archaea ; Chlorides/*metabolism ; Cyanobacteria/classification/*genetics/metabolism ; Escherichia coli/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial ; Halorhodopsins/*genetics/metabolism ; Ion Pumps/*genetics/metabolism ; Light ; Phylogeny ; Rhodopsin/genetics ; Seawater/*microbiology ; }, abstract = {Light-driven ion-pumping rhodopsins are widely distributed among bacteria, archaea, and eukaryotes in the euphotic zone of the aquatic environment. H[+]-pumping rhodopsin (proteorhodopsin: PR), Na[+]-pumping rhodopsin (NaR), and Cl[-]-pumping rhodopsin (ClR) have been found in marine bacteria, which suggests that these genes evolved independently in the ocean. Putative microbial rhodopsin genes were identified in the genome sequences of marine Cytophagia. In the present study, one of these genes was heterologously expressed in Escherichia coli cells and the rhodopsin protein named Rubricoccus marinus halorhodopsin (RmHR) was identified as a light-driven inward Cl[-] pump. Spectroscopic assays showed that the estimated dissociation constant (Kd,int.) of this rhodopsin was similar to that of haloarchaeal halorhodopsin (HR), while the Cl[-]-transporting photoreaction mechanism of this rhodopsin was similar to that of HR, but different to that of the already-known marine bacterial ClR. This amino acid sequence similarity also suggested that this rhodopsin is similar to haloarchaeal HR and cyanobacterial HRs (e.g., SyHR and MrHR). Additionally, a phylogenetic analysis revealed that retinal biosynthesis pathway genes (blh and crtY) belong to a phylogenetic lineage of haloarchaea, indicating that these marine Cytophagia acquired rhodopsin-related genes from haloarchaea by lateral gene transfer. Based on these results, we concluded that inward Cl[-]-pumping rhodopsin is present in genera of the class Cytophagia and may have the same evolutionary origins as haloarchaeal HR.}, }
@article {pmid29549790, year = {2018}, author = {Han, J and Pendleton, SJ and Deck, J and Singh, R and Gilbert, J and Johnson, TJ and Sanad, YM and Nayak, R and Foley, SL}, title = {Impact of co-carriage of IncA/C plasmids with additional plasmids on the transfer of antimicrobial resistance in Salmonella enterica isolates.}, journal = {International journal of food microbiology}, volume = {271}, number = {}, pages = {77-84}, doi = {10.1016/j.ijfoodmicro.2018.01.018}, pmid = {29549790}, issn = {1879-3460}, mesh = {Anti-Bacterial Agents/*pharmacology ; Conjugation, Genetic/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal/*genetics ; Humans ; Microbial Sensitivity Tests ; Plasmids/*genetics ; Polymerase Chain Reaction ; Replicon/genetics ; Salmonella enterica/*drug effects/*genetics/isolation &amp; purification ; }, abstract = {BACKGROUND: Antimicrobial resistance in Salmonella enterica is often plasmid encoded. A key resistance plasmid group is the incompatibility group (Inc) A/C plasmids that often carry multiple resistance determinants. Previous studies showed that IncA/C plasmids were often co-located with other plasmids. The current study was undertaken to evaluate the impact of plasmid co-carriage on antimicrobial resistance and plasmid transfer.<br><br>METHODS: A total of 1267 Salmonella isolates, representing multiple serotypes and sources were previously subjected to susceptibility testing and 251 isolates with resistance to at least 5 antimicrobial agents were identified for further study. Each isolate was subjected to PCR-based replicon typing, and those with IncA/C plasmids were selected for plasmid isolation, PCR-based mapping of IncA/C plasmid backbone genes, and conjugation assays to evaluate resistance plasmid transferability.<br><br>RESULTS: Of the 87 identified IncA/C positive isolates, approximately 75% carried a plasmid with another identified replicon type, with the most common being I1 (39%), FIA, FIIA, FIB and HI2 (each 15%). PCR-based mapping indicated significant diversity in IncA/C backbone content, especially in regions encoding transfer-associated and hypothetical proteins. Conjugation experiments showed that nearly 68% of the isolates transferred resistance plasmids, with 90% containing additional identified plasmids or larger (>50&#x202f;kb) non-typeable plasmids.<br><br>CONCLUSIONS: The majority of IncA/C-positive strains were able to conjugally transfer antimicrobial resistance to the recipient, encoded by IncA/C and/or co-carried plasmids. These findings highlight the importance of co-located plasmids for resistance dissemination either by directly transferring resistance genes or by potentially providing the needed conjugation machinery for IncA/C plasmid transfer.}, }
@article {pmid29546438, year = {2018}, author = {Rua, CPJ and de Oliveira, LS and Froes, A and Tschoeke, DA and Soares, AC and Leomil, L and Gregoracci, GB and Coutinho, R and Hajdu, E and Thompson, CC and Berlinck, RGS and Thompson, FL}, title = {Microbial and Functional Biodiversity Patterns in Sponges that Accumulate Bromopyrrole Alkaloids Suggest Horizontal Gene Transfer of Halogenase Genes.}, journal = {Microbial ecology}, volume = {76}, number = {3}, pages = {825-838}, pmid = {29546438}, issn = {1432-184X}, support = {CNE E-26/110.735/2013//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; CIMAR 1986/2014//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; BIOTA/BIOprospecTA grant 2013/50228-8//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2014/17616- 7//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; }, mesh = {Alkaloids/*metabolism ; Animals ; Bacteria/*enzymology/genetics/isolation &amp; purification/metabolism ; Bacterial Proteins/*genetics/metabolism ; *Biodiversity ; Bromine/metabolism ; Gene Transfer, Horizontal ; Hydrolases/*genetics/metabolism ; Phylogeny ; Porifera/chemistry/*microbiology ; Secondary Metabolism ; }, abstract = {Marine sponge holobionts harbor complex microbial communities whose members may be the true producers of secondary metabolites accumulated by sponges. Bromopyrrole alkaloids constitute a typical class of secondary metabolites isolated from sponges that very often display biological activities. Bromine incorporation into secondary metabolites can be catalyzed by either halogenases or haloperoxidases. The diversity of the metagenomes of sponge holobiont species containing bromopyrrole alkaloids (Agelas spp. and Tedania brasiliensis) as well as holobionts devoid of bromopyrrole alkaloids spanning in a vast biogeographic region (approx. Seven thousand km) was studied. The origin and specificity of the detected halogenases was also investigated. The holobionts Agelas spp. and T. brasiliensis did not share microbial halogenases, suggesting a species-specific pattern. Bacteria of diverse phylogenetic origins encoding halogenase genes were found to be more abundant in bromopyrrole-containing sponges. The sponge holobionts (e.g., Agelas spp.) with the greatest number of sequences related to clustered, interspaced, short, palindromic repeats (CRISPRs) exhibited the fewest phage halogenases, suggesting a possible mechanism of protection from phage infection by the sponge host. This study highlights the potential of phages to transport halogenases horizontally across host sponges, particularly in more permissive holobiont hosts, such as Tedania spp.}, }
@article {pmid29543982, year = {2018}, author = {Leger, MM and Eme, L and Stairs, CW and Roger, AJ}, title = {Demystifying Eukaryote Lateral Gene Transfer (Response to Martin 2017 DOI: 10.1002/bies.201700115).}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {40}, number = {5}, pages = {e1700242}, doi = {10.1002/bies.201700242}, pmid = {29543982}, issn = {1521-1878}, support = {MOP&#x2010;142349//CIHR/Canada ; }, mesh = {*Eukaryota ; Eukaryotic Cells ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Phylogeny ; }, abstract = {In a recent BioEssays paper [W. F. Martin, BioEssays 2017, 39, 1700115], William Martin sharply criticizes evolutionary interpretations that involve lateral gene transfer (LGT) into eukaryotic genomes. Most published examples of LGTs in eukaryotes, he suggests, are in fact contaminants, ancestral genes that have been lost from other extant lineages, or the result of artefactual phylogenetic inferences. Martin argues that, except for transfers that occurred from endosymbiotic organelles, eukaryote LGT is insignificant. Here, in reviewing this field, we seek to correct some of the misconceptions presented therein with regard to the evidence for LGT in eukaryotes.}, }
@article {pmid29543191, year = {2018}, author = {Bonomo, ME and Deem, MW}, title = {The physicist's guide to one of biotechnology's hottest new topics: CRISPR-Cas.}, journal = {Physical biology}, volume = {15}, number = {4}, pages = {041002}, doi = {10.1088/1478-3975/aab6d6}, pmid = {29543191}, issn = {1478-3975}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Biological Evolution ; CRISPR-Cas Systems/*genetics ; *Gene Transfer, Horizontal ; Population Dynamics ; *Selection, Genetic ; }, abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) constitute a multi-functional, constantly evolving immune system in bacteria and archaea cells. A heritable, molecular memory is generated of phage, plasmids, or other mobile genetic elements that attempt to attack the cell. This memory is used to recognize and interfere with subsequent invasions from the same genetic elements. This versatile prokaryotic tool has also been used to advance applications in biotechnology. Here we review a large body of CRISPR-Cas research to explore themes of evolution and selection, population dynamics, horizontal gene transfer, specific and cross-reactive interactions, cost and regulation, non-immunological CRISPR functions that boost host cell robustness, as well as applicable mechanisms for efficient and specific genetic engineering. We offer future directions that can be addressed by the physics community. Physical understanding of the CRISPR-Cas system will advance uses in biotechnology, such as developing cell lines and animal models, cell labeling and information storage, combatting antibiotic resistance, and human therapeutics.}, }
@article {pmid29540701, year = {2018}, author = {Jackson, VA and Meijer, DH and Carrasquero, M and van Bezouwen, LS and Lowe, ED and Kleanthous, C and Janssen, BJC and Seiradake, E}, title = {Structures of Teneurin adhesion receptors reveal an ancient fold for cell-cell interaction.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {1079}, pmid = {29540701}, issn = {2041-1723}, support = {/WT_/Wellcome Trust/United Kingdom ; MR/L018039/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Alternative Splicing/genetics/physiology ; Cell Communication/physiology ; Cryoelectron Microscopy ; Crystallography, X-Ray ; Membrane Glycoproteins/chemistry/metabolism ; Platelet Glycoprotein GPIb-IX Complex/*chemistry/genetics/*metabolism ; Protein Structure, Secondary ; Tenascin/chemistry/genetics/metabolism ; }, abstract = {Teneurins are ancient cell-cell adhesion receptors that are vital for brain development and synapse organisation. They originated in early metazoan evolution through a horizontal gene transfer event when a bacterial YD-repeat toxin fused to a eukaryotic receptor. We present X-ray crystallography and cryo-EM structures of two Teneurins, revealing a ~200 kDa extracellular super-fold in which eight sub-domains form an intricate structure centred on a spiralling YD-repeat shell. An alternatively spliced loop, which is implicated in homophilic Teneurin interaction and specificity, is exposed and thus poised for interaction. The N-terminal side of the shell is 'plugged' via a fibronectin-plug domain combination, which defines a new class of YD proteins. Unexpectedly, we find that these proteins are widespread amongst modern bacteria, suggesting early metazoan receptor evolution from a distinct class of proteins, which today includes both bacterial proteins and eukaryotic Teneurins.}, }
@article {pmid29539595, year = {2018}, author = {An, XL and Chen, QL and Zhu, D and Su, JQ}, title = {Distinct effects of struvite and biochar amendment on the class 1 integron antibiotic resistance gene cassettes in phyllosphere and rhizosphere.}, journal = {The Science of the total environment}, volume = {631-632}, number = {}, pages = {668-676}, doi = {10.1016/j.scitotenv.2018.03.034}, pmid = {29539595}, issn = {1879-1026}, mesh = {Charcoal/*chemistry ; Drug Resistance, Microbial/*genetics ; Environmental Restoration and Remediation/*methods ; *Rhizosphere ; Struvite/*chemistry ; }, abstract = {Struvite recovered from wastewater is promising for recycling phosphorus into soil as fertilizers. However, struvite application may prompt the proliferation of antibiotic resistance in soil and plant. This study examined the impacts of struvite application and biochar amendment on integrons abundance and gene cassette contexts in rhizosphere soil and phyllosphere using quantitative PCR and clone library analysis. Microcosm experiments revealed that class 1 integron was the most prevalent in all samples, with higher concentration and higher relative abundance in rhizosphere than those in phyllosphere. The majority of resistance gene cassettes were associated with genes encoding resistance to aminoglycosides, beta-lactams and chloramphenicols. Struvite application significantly increased the genetic diversity of antibiotic resistance gene cassettes in both rhizosphere and phyllosphere. However, biochar amendment attenuated the increasing effect of struvite application exerting on the class 1 integron antibiotic resistance gene cassette pool in phyllosphere. These findings highlighted human activities to be the source of integron gene cassette pool and raised the possibility of using biochar amendment as an alternative mean for mitigating antibiotic resistance in environments.}, }
@article {pmid29536871, year = {2018}, author = {Huang, K and Xia, H and Wu, Y and Chen, J and Cui, G and Li, F and Chen, Y and Wu, N}, title = {Effects of earthworms on the fate of tetracycline and fluoroquinolone resistance genes of sewage sludge during vermicomposting.}, journal = {Bioresource technology}, volume = {259}, number = {}, pages = {32-39}, doi = {10.1016/j.biortech.2018.03.021}, pmid = {29536871}, issn = {1873-2976}, mesh = {Animals ; Anti-Bacterial Agents ; Drug Resistance, Microbial ; *Fluoroquinolones ; Genes, Bacterial ; *Oligochaeta ; *Sewage ; Tetracycline ; }, abstract = {Diverse antibiotic resistance genes (ARGs) present in sewage sludge are difficult to be eliminated using conventional sludge treatment processes. To date, little remains known on the fate of the ARGs during vermicomposting of sludge. This study aimed to investigate the effect of earthworms on the fate of tetracycline and fluoroquinolone resistance genes, and integrons during vermicomposting of sewage sludge through contrasting two systems of sludge stabilization with and without earthworms. Compared to the control without earthworms, vermicomposting significantly (p < 0.05) decreased the abundances of tetracycline and fluoroquinolone resistance genes and int1, with complete removal for parC. Variations in ARGs were associated with environmental factors, horizontal gene transfer, bacterial community composition, and earthworms during vermicomposting. In addition, earthworms strongly affected the possible host bacteria encoding ARGs and Int1, abating the pathogenic bacteria in vermicomposting product. These results imply that vermicomposting could effectively reduce tetracycline and fluoroquinolone resistance genes in the sludge.}, }
@article {pmid29535449, year = {2018}, author = {Martin, WF}, title = {Eukaryote lateral gene transfer is Lamarckian.}, journal = {Nature ecology &amp; evolution}, volume = {2}, number = {5}, pages = {754}, doi = {10.1038/s41559-018-0521-7}, pmid = {29535449}, issn = {2397-334X}, mesh = {Eukaryota/*genetics ; Eukaryotic Cells ; *Gene Transfer, Horizontal ; Phylogeny ; }, }
@article {pmid29535448, year = {2018}, author = {Roger, AJ}, title = {Reply to 'Eukaryote lateral gene transfer is Lamarckian'.}, journal = {Nature ecology &amp; evolution}, volume = {2}, number = {5}, pages = {755}, doi = {10.1038/s41559-018-0522-6}, pmid = {29535448}, issn = {2397-334X}, mesh = {Eukaryota/*genetics ; Eukaryotic Cells ; Gene Transfer, Horizontal ; Phylogeny ; }, }
@article {pmid29535201, year = {2018}, author = {Cross, KL and Chirania, P and Xiong, W and Beall, CJ and Elkins, JG and Giannone, RJ and Griffen, AL and Guss, AM and Hettich, RL and Joshi, SS and Mokrzan, EM and Martin, RK and Zhulin, IB and Leys, EJ and Podar, M}, title = {Insights into the Evolution of Host Association through the Isolation and Characterization of a Novel Human Periodontal Pathobiont, Desulfobulbus oralis.}, journal = {mBio}, volume = {9}, number = {2}, pages = {}, pmid = {29535201}, issn = {2150-7511}, support = {R01 DE024463/DE/NIDCR NIH HHS/United States ; }, mesh = {*Adaptation, Biological ; Deltaproteobacteria/*genetics/*isolation &amp; purification ; *Evolution, Molecular ; Gene Expression Profiling ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Gingiva/*microbiology ; Humans ; Ohio ; Periodontitis/microbiology ; Phylogeny ; Proteome/analysis ; }, abstract = {The human oral microbiota encompasses representatives of many bacterial lineages that have not yet been cultured. Here we describe the isolation and characterization of previously uncultured Desulfobulbus oralis, the first human-associated representative of its genus. As mammalian-associated microbes rarely have free-living close relatives, D. oralis provides opportunities to study how bacteria adapt and evolve within a host. This sulfate-reducing deltaproteobacterium has adapted to the human oral subgingival niche by curtailing its physiological repertoire, losing some biosynthetic abilities and metabolic independence, and by dramatically reducing environmental sensing and signaling capabilities. The genes that enable free-living Desulfobulbus to synthesize the potent neurotoxin methylmercury were also lost by D. oralis, a notably positive outcome of host association. However, horizontal gene acquisitions from other members of the microbiota provided novel mechanisms of interaction with the human host, including toxins like leukotoxin and hemolysins. Proteomic and transcriptomic analysis revealed that most of those factors are actively expressed, including in the subgingival environment, and some are secreted. Similar to other known oral pathobionts, D. oralis can trigger a proinflammatory response in oral epithelial cells, suggesting a direct role in the development of periodontal disease.IMPORTANCE Animal-associated microbiota likely assembled as a result of numerous independent colonization events by free-living microbes followed by coevolution with their host and other microbes. Through specific adaptation to various body sites and physiological niches, microbes have a wide range of contributions, from beneficial to disease causing. Desulfobulbus oralis provides insights into genomic and physiological transformations associated with transition from an open environment to a host-dependent lifestyle and the emergence of pathogenicity. Through a multifaceted mechanism triggering a proinflammatory response, D. oralis is a novel periodontal pathobiont. Even though culture-independent approaches can provide insights into the potential role of the human microbiome "dark matter," cultivation and experimental characterization remain important to studying the roles of individual organisms in health and disease.}, }
@article {pmid29524923, year = {2018}, author = {Zhang, Y and Gu, AZ and Cen, T and Li, X and Li, D and Chen, J}, title = {Petrol and diesel exhaust particles accelerate the horizontal transfer of plasmid-mediated antimicrobial resistance genes.}, journal = {Environment international}, volume = {114}, number = {}, pages = {280-287}, doi = {10.1016/j.envint.2018.02.038}, pmid = {29524923}, issn = {1873-6750}, support = {P50 ES026049/ES/NIEHS NIH HHS/United States ; }, mesh = {Drug Resistance, Bacterial/*drug effects ; Escherichia coli/drug effects/genetics ; Gasoline/*toxicity ; *Gene Transfer, Horizontal/drug effects/genetics ; Plasmids/genetics ; *Vehicle Emissions ; }, abstract = {Particles exhausted from petrol and diesel consumptions are major components of urban air pollution that can be exposed to human via direct inhalation or other routes due to atmospheric deposition into water and soil. Antimicrobial resistance is one of the most serious threats to modern health care. However, how the petrol and diesel exhaust particles affect the development and spread of antimicrobial resistance genes (ARGs) in various environments remain largely unknown. This study investigated the effects and potential mechanisms of four representative petrol and diesel exhaust particles, namely 97 octane petrol, 93 octane petrol, light diesel oil, and marine heavy diesel oil, on the horizontal transfer of ARGs between two opportunistic Escherichia coli (E. coli) strains, E. coli S17-1 (donor) and E. coli K12 (recipient). The results demonstrated that these four representative types of nano-scale particles induced concentration-dependent increases in conjugative transfer rates compared with the controls. The underlying mechanisms involved in the accelerated transfer of ARGs were also identified, including the generation of intracellular reactive oxygen species (ROS) and the consequent induction of oxidative stress, SOS response, changes in cell morphology, and the altered mRNA expression of membrane protein genes and those involved in the promotion of conjugative transfer. The findings provide new evidences and mechanistic insights into the antimicrobial resistance risks posed by petrol and diesel exhaust particles, and highlight the implications and need for stringent strategies on alternative fuels to mitigate air pollution and health risks.}, }
@article {pmid29524814, year = {2018}, author = {Liu, X and Lv, Y and Xu, K and Xiao, X and Xi, B and Lu, S}, title = {Response of ginger growth to a tetracycline-contaminated environment and residues of antibiotic and antibiotic resistance genes.}, journal = {Chemosphere}, volume = {201}, number = {}, pages = {137-143}, doi = {10.1016/j.chemosphere.2018.02.178}, pmid = {29524814}, issn = {1879-1298}, mesh = {Anti-Bacterial Agents/metabolism/*toxicity ; Drug Resistance, Microbial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Zingiber officinale/drug effects/genetics/growth &amp; development ; Rhizome/genetics ; Soil/chemistry ; Soil Pollutants/metabolism/*toxicity ; Tetracycline/metabolism/*toxicity ; }, abstract = {The presence of antibiotic residues in vegetables has been highlighted as a risk to human health; antibiotics not only cause toxic effects to plants but can also induce antibiotic resistance gene (ARG) expression. Using a soil-free approach, this study aimed to explore the response of ginger growth to tetracycline (TC) pollution and to assess the levels of antibiotic residues in different plant organs and the presence of ARGs in the rhizome. Ginger growth in a highly TC-contaminated environment was remarkably inhibited. Photosynthetic parameters, fluorescence parameters, and some physiological indicators (oxidative substances, photosynthetic pigments, enzyme activity, etc.) were negatively influenced by TC contamination. Although the superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activity levels significantly increased, their effects appear to be limited. The accumulation of TC in the rhizome (28.1 mg kg[-1]) was greater than that in the roots, stem, or leaves. All tested antibiotic resistance genes except for tetL were detectable in the rhizome, and their relative abundance was in the order integron1>tetG > tetA > tetC > tetB > tetM. The level of TC in ginger rhizomes was much higher than the maximum residue limits. The potential dose of TC acquired from the consumption of ginger grown in a highly TC-contaminated environment poses no obvious risk to adults but may be a threat to children.}, }
@article {pmid29522743, year = {2018}, author = {Ferreiro, A and Crook, N and Gasparrini, AJ and Dantas, G}, title = {Multiscale Evolutionary Dynamics of Host-Associated Microbiomes.}, journal = {Cell}, volume = {172}, number = {6}, pages = {1216-1227}, pmid = {29522743}, issn = {1097-4172}, support = {R01 GM099538/GM/NIGMS NIH HHS/United States ; T32 DK077653/DK/NIDDK NIH HHS/United States ; R01 AI123394/AI/NIAID NIH HHS/United States ; R01 HD092414/HD/NICHD NIH HHS/United States ; U01 AI123394/AI/NIAID NIH HHS/United States ; T32 GM007067/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Ecosystem ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Variation ; Host Specificity ; Humans ; Metagenome/*genetics ; Microbiota/*genetics ; }, abstract = {The composite members of the microbiota face a range of selective pressures and must adapt to persist in the host. We highlight recent work characterizing the evolution and transfer of genetic information across nested scales of host-associated microbiota, which enable resilience to biotic and abiotic perturbations. At the strain level, we consider the preservation and diversification of adaptive information in progeny lineages. At the community level, we consider genetic exchange between distinct microbes in the ecosystem. Finally, we frame microbiomes as open systems subject to acquisition of novel information from foreign ecosystems through invasion by outsider microbes.}, }
@article {pmid29521452, year = {2018}, author = {Scott, KM and Williams, J and Porter, CMB and Russel, S and Harmer, TL and Paul, JH and Antonen, KM and Bridges, MK and Camper, GJ and Campla, CK and Casella, LG and Chase, E and Conrad, JW and Cruz, MC and Dunlap, DS and Duran, L and Fahsbender, EM and Goldsmith, DB and Keeley, RF and Kondoff, MR and Kussy, BI and Lane, MK and Lawler, S and Leigh, BA and Lewis, C and Lostal, LM and Marking, D and Mancera, PA and McClenthan, EC and McIntyre, EA and Mine, JA and Modi, S and Moore, BD and Morgan, WA and Nelson, KM and Nguyen, KN and Ogburn, N and Parrino, DG and Pedapudi, AD and Pelham, RP and Preece, AM and Rampersad, EA and Richardson, JC and Rodgers, CM and Schaffer, BL and Sheridan, NE and Solone, MR and Staley, ZR and Tabuchi, M and Waide, RJ and Wanjugi, PW and Young, S and Clum, A and Daum, C and Huntemann, M and Ivanova, N and Kyrpides, N and Mikhailova, N and Palaniappan, K and Pillay, M and Reddy, TBK and Shapiro, N and Stamatis, D and Varghese, N and Woyke, T and Boden, R and Freyermuth, SK and Kerfeld, CA}, title = {Genomes of ubiquitous marine and hypersaline Hydrogenovibrio, Thiomicrorhabdus and Thiomicrospira spp. encode a diversity of mechanisms to sustain chemolithoautotrophy in heterogeneous environments.}, journal = {Environmental microbiology}, volume = {20}, number = {8}, pages = {2686-2708}, doi = {10.1111/1462-2920.14090}, pmid = {29521452}, issn = {1462-2920}, support = {MOE-2008-02036//USDA Higher Education Challenge Grant/International ; NSF-IOS-1257532//USDA Higher Education Challenge Grant/International ; DE-AC02-05CH11231//Office of Science of the U.S. Department of Energy/International ; }, mesh = {*Chemoautotrophic Growth ; Ecosystem ; *Genome, Bacterial ; Hydrogenase/genetics ; Phylogeny ; Piscirickettsiaceae/classification/enzymology/*genetics/metabolism ; Sulfur/metabolism ; }, abstract = {Chemolithoautotrophic bacteria from the genera Hydrogenovibrio, Thiomicrorhabdus and Thiomicrospira are common, sometimes dominant, isolates from sulfidic habitats including hydrothermal vents, soda and salt lakes and marine sediments. Their genome sequences confirm their membership in a deeply branching clade of the Gammaproteobacteria. Several adaptations to heterogeneous habitats are apparent. Their genomes include large numbers of genes for sensing and responding to their environment (EAL- and GGDEF-domain proteins and methyl-accepting chemotaxis proteins) despite their small sizes (2.1-3.1 Mbp). An array of sulfur-oxidizing complexes are encoded, likely to facilitate these organisms' use of multiple forms of reduced sulfur as electron donors. Hydrogenase genes are present in some taxa, including group 1d and 2b hydrogenases in Hydrogenovibrio marinus and H. thermophilus MA2-6, acquired via horizontal gene transfer. In addition to high-affinity cbb3 cytochrome c oxidase, some also encode cytochrome bd-type quinol oxidase or ba3 -type cytochrome c oxidase, which could facilitate growth under different oxygen tensions, or maintain redox balance. Carboxysome operons are present in most, with genes downstream encoding transporters from four evolutionarily distinct families, which may act with the carboxysomes to form CO2 concentrating mechanisms. These adaptations to habitat variability likely contribute to the cosmopolitan distribution of these organisms.}, }
@article {pmid29521441, year = {2018}, author = {Purves, J and Thomas, J and Riboldi, GP and Zapotoczna, M and Tarrant, E and Andrew, PW and Londoño, A and Planet, PJ and Geoghegan, JA and Waldron, KJ and Morrissey, JA}, title = {A horizontally gene transferred copper resistance locus confers hyper-resistance to antibacterial copper toxicity and enables survival of community acquired methicillin resistant Staphylococcus aureus USA300 in macrophages.}, journal = {Environmental microbiology}, volume = {20}, number = {4}, pages = {1576-1589}, pmid = {29521441}, issn = {1462-2920}, support = {//Wellcome Trust/United Kingdom ; HHSN272200700055C/AI/NIAID NIH HHS/United States ; 098375/Z/12/Z//Wellcome Trust/United Kingdom ; }, mesh = {Anti-Bacterial Agents/*toxicity ; Copper/*toxicity ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal/genetics ; Humans ; Immunity, Innate/immunology ; Macrophages/*microbiology ; Membrane Transport Proteins/*genetics ; *Methicillin-Resistant Staphylococcus aureus/drug effects/genetics/growth &amp; development ; Operon ; Staphylococcal Infections/microbiology ; }, abstract = {Excess copper is highly toxic and forms part of the host innate immune system's antibacterial arsenal, accumulating at sites of infection and acting within macrophages to kill engulfed pathogens. We show for the first time that a novel, horizontally gene transferred copper resistance locus (copXL), uniquely associated with the SCCmec elements of the highly virulent, epidemic, community acquired methicillin resistant Staphylococcus aureus (CA-MRSA) USA300, confers copper hyper-resistance. These genes are additional to existing core genome copper resistance mechanisms, and are not found in typical S. aureus lineages, but are increasingly identified in emerging pathogenic isolates. Our data show that CopX, a putative P1B-3 -ATPase efflux transporter, and CopL, a novel lipoprotein, confer copper hyper-resistance compared to typical S. aureus strains. The copXL genes form an operon that is tightly repressed in low copper environments by the copper regulator CsoR. Significantly, CopX and CopL are important for S. aureus USA300 intracellular survival within macrophages. Therefore, the emergence of new S. aureus clones with the copXL locus has significant implications for public health because these genes confer increased resistance to antibacterial copper toxicity, enhancing bacterial fitness by altering S. aureus interaction with innate immunity.}, }
@article {pmid29519532, year = {2018}, author = {Niero, G and Bortolaia, V and Vanni, M and Intorre, L and Guardabassi, L and Piccirillo, A}, title = {High diversity of genes and plasmids encoding resistance to third-generation cephalosporins and quinolones in clinical Escherichia coli from commercial poultry flocks in Italy.}, journal = {Veterinary microbiology}, volume = {216}, number = {}, pages = {93-98}, doi = {10.1016/j.vetmic.2018.02.012}, pmid = {29519532}, issn = {1873-2542}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Cephalosporins/*pharmacology ; Chickens ; *Drug Resistance, Multiple, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/*drug effects/genetics ; Escherichia coli Infections/epidemiology/microbiology/*veterinary ; Gene Transfer, Horizontal ; Genes, Bacterial ; Italy/epidemiology ; Multilocus Sequence Typing ; Plasmids/*drug effects/isolation &amp; purification ; Poultry/microbiology ; Poultry Diseases/epidemiology/microbiology ; Quinolones/*pharmacology ; Turkeys/microbiology ; beta-Lactamases/biosynthesis/genetics ; }, abstract = {The aim was to investigate occurrence and diversity of plasmid-mediated resistance to third-generation cephalosporins (3GC) and quinolones in clinical Escherichia coli from 200 industrial poultry farms across Italy. E. coli was isolated from colibacillosis lesions in turkeys (n = 109), broilers (n = 98) and layers (n = 22) between 2008 and 2012. 3GC-resistant isolates were screened for extended-spectrum and AmpC β-lactamase (ESBL/AmpC), while all isolates were tested for plasmid-mediated quinolone resistance (PMQR) genes. ESBL/AmpC- and PMQR-positive isolates were typed by pulsed-field gel electrophoresis and antimicrobial susceptibility testing, and their plasmids were characterised by replicon typing, multilocus sequence typing, restriction fragment length polymorphism and conjugation. EBSL/AmpC genes (blaCTX-M-1, blaCTX-M-14, blaCTX-M-2, blaSHV-12 and blaCMY-2) were detected in 7%, 9% and 4% of isolates from turkeys, broilers and layers, respectively. We identified seven ESBL/AmpC-encoding plasmid types, usually conjugative (78%), with a marked prevalence of IncI1/pST3 plasmids carrying blaCTX-M-1. PMQR occurred less frequently among isolates from turkeys (0.9%) compared to those from broilers (5%) and layers (4%). The PMQR genes qnrS, qnrB19 and oqxA/B were located on three plasmid types and two non-typeable plasmids, mostly (85%) conjugative. ESBL/AmpC- and PMQR-positive isolates were genetically unrelated and 64% of them were additionally resistant to aminoglycosides, sulfonamides and tetracyclines. Our data show that 3GC- and quinolone-resistant clinical E. coli in Italian poultry production represent a highly diverse population often resistant to most antimicrobials available for poultry. These findings underline the crucial need to develop new strategies for prevention and control of colibacillosis.}, }
@article {pmid29518208, year = {2018}, author = {Carter, GP and Harjani, JR and Li, L and Pitcher, NP and Nong, Y and Riley, TV and Williamson, DA and Stinear, TP and Baell, JB and Howden, BP}, title = {1,2,4-Oxadiazole antimicrobials act synergistically with daptomycin and display rapid kill kinetics against MDR Enterococcus faecium.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {73}, number = {6}, pages = {1562-1569}, doi = {10.1093/jac/dky064}, pmid = {29518208}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/*pharmacology ; Daptomycin/*pharmacology ; Drug Resistance, Multiple, Bacterial ; Drug Synergism ; Enterococcus faecalis/drug effects ; Enterococcus faecium/*drug effects ; Erythrocytes/drug effects ; Gram-Positive Bacterial Infections/drug therapy/microbiology ; Hemolysis ; Humans ; Kinetics ; Microbial Sensitivity Tests ; Oxadiazoles/chemistry/*pharmacology ; Staphylococcus aureus/drug effects ; Vancomycin/pharmacology ; Vancomycin-Resistant Enterococci/*drug effects ; }, abstract = {BACKGROUND: Enterococcus faecium is an important nosocomial pathogen. It has a high propensity for horizontal gene transfer, which has resulted in the emergence of MDR strains that are difficult to treat. The most notorious of these, vancomycin-resistant E. faecium, are usually treated with linezolid or daptomycin. Resistance has, however, been reported, meaning that new therapeutics are urgently needed. The 1,2,4-oxadiazoles are a recently discovered family of antimicrobials that are active against Gram-positive pathogens and therefore have therapeutic potential for treating E. faecium. However, only limited data are available on the activity of these antimicrobials against E. faecium.<br><br>OBJECTIVES: To determine whether the 1,2,4-oxadiazole antimicrobials are active against MDR and daptomycin-non-susceptible E. faecium.<br><br>METHODS: The activity of the 1,2,4-oxadiazole antimicrobials against vancomycin-susceptible, vancomycin-resistant and daptomycin-non-susceptible E. faecium was determined using susceptibility testing, time-kill assays and synergy assays. Toxicity was also evaluated against human cells by XTT and haemolysis assays.<br><br>RESULTS: The 1,2,4-oxadiazoles are active against a range of MDR E. faecium, including isolates that display non-susceptibility to vancomycin and daptomycin. This class of antimicrobial displays rapid bactericidal activity and demonstrates superior killing of E. faecium compared with daptomycin. Finally, the 1,2,4-oxadiazoles act synergistically with daptomycin against E. faecium, with subinhibitory concentrations reducing the MIC of daptomycin for non-susceptible isolates to a level below the clinical breakpoint.<br><br>CONCLUSIONS: The 1,2,4-oxadiazoles are active against MDR and daptomycin-non-susceptible E. faecium and hold great promise as future therapeutics for treating infections caused by these difficult-to-treat isolates.}, }
@article {pmid29515543, year = {2018}, author = {Ward, LM and Hemp, J and Shih, PM and McGlynn, SE and Fischer, WW}, title = {Evolution of Phototrophy in the Chloroflexi Phylum Driven by Horizontal Gene Transfer.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {260}, pmid = {29515543}, issn = {1664-302X}, abstract = {The evolutionary mechanisms behind the extant distribution of photosynthesis is a point of substantial contention. Hypotheses range from the presence of phototrophy in the last universal common ancestor and massive gene loss in most lineages, to a later origin in Cyanobacteria followed by extensive horizontal gene transfer into the extant phototrophic clades, with intermediate scenarios that incorporate aspects of both end-members. Here, we report draft genomes of 11 Chloroflexi: the phototrophic Chloroflexia isolate Kouleothrix aurantiaca as well as 10 genome bins recovered from metagenomic sequencing of microbial mats found in Japanese hot springs. Two of these metagenome bins encode photrophic reaction centers and several of these bins form a metabolically diverse, monophyletic clade sister to the Anaerolineae class that we term Candidatus Thermofonsia. Comparisons of organismal (based on conserved ribosomal) and phototrophy (reaction center and bacteriochlorophyll synthesis) protein phylogenies throughout the Chloroflexi demonstrate that two new lineages acquired phototrophy independently via horizontal gene transfer (HGT) from different ancestral donors within the classically phototrophic Chloroflexia class. These results illustrate a complex history of phototrophy within this group, with metabolic innovation tied to HGT. These observations do not support simple hypotheses for the evolution of photosynthesis that require massive character loss from many clades; rather, HGT appears to be the defining mechanic for the distribution of phototrophy in many of the extant clades in which it appears.}, }
@article {pmid29514229, year = {2018}, author = {Hultman, J and Tamminen, M and Pärnänen, K and Cairns, J and Karkman, A and Virta, M}, title = {Host range of antibiotic resistance genes in wastewater treatment plant influent and effluent.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {4}, pages = {}, pmid = {29514229}, issn = {1574-6941}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/*drug effects/*genetics ; Drug Resistance, Microbial/*genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/genetics ; Host Specificity ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Wastewater/*microbiology ; Water Purification ; }, abstract = {Wastewater treatment plants (WWTPs) collect wastewater from various sources for a multi-step treatment process. By mixing a large variety of bacteria and promoting their proximity, WWTPs constitute potential hotspots for the emergence of antibiotic resistant bacteria. Concerns have been expressed regarding the potential of WWTPs to spread antibiotic resistance genes (ARGs) from environmental reservoirs to human pathogens. We utilized epicPCR (Emulsion, Paired Isolation and Concatenation PCR) to detect the bacterial hosts of ARGs in two WWTPs. We identified the host distribution of four resistance-associated genes (tetM, int1, qacEΔ1and blaOXA-58) in influent and effluent. The bacterial hosts of these resistance genes varied between the WWTP influent and effluent, with a generally decreasing host range in the effluent. Through 16S rRNA gene sequencing, it was determined that the resistance gene carrying bacteria include both abundant and rare taxa. Our results suggest that the studied WWTPs mostly succeed in decreasing the host range of the resistance genes during the treatment process. Still, there were instances where effluent contained resistance genes in bacterial groups not carrying these genes in the influent. By permitting exhaustive profiling of resistance-associated gene hosts in WWTP bacterial communities, the application of epicPCR provides a new level of precision to our resistance gene risk estimates.}, }
@article {pmid29505963, year = {2018}, author = {Gilbert, C and Feschotte, C}, title = {Horizontal acquisition of transposable elements and viral sequences: patterns and consequences.}, journal = {Current opinion in genetics &amp; development}, volume = {49}, number = {}, pages = {15-24}, pmid = {29505963}, issn = {1879-0380}, support = {R01 GM059290/GM/NIGMS NIH HHS/United States ; R01 GM077582/GM/NIGMS NIH HHS/United States ; R01 GM112972/GM/NIGMS NIH HHS/United States ; R35 GM122550/GM/NIGMS NIH HHS/United States ; }, mesh = {DNA Transposable Elements/*genetics ; Eukaryota/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome/genetics ; Viruses/*genetics ; }, abstract = {It is becoming clear that most eukaryotic transposable elements (TEs) owe their evolutionary success in part to horizontal transfer events, which enable them to invade new species. Recent large-scale studies are beginning to unravel the mechanisms and ecological factors underlying this mode of transmission. Viruses are increasingly recognized as vectors in the process but also as a direct source of genetic material horizontally acquired by eukaryotic organisms. Because TEs and endogenous viruses are major catalysts of variation and innovation in genomes, we argue that horizontal inheritance has had a more profound impact in eukaryotic evolution than is commonly appreciated. To support this proposal, we compile a list of examples, including some previously unrecognized, whereby new host functions and phenotypes can be directly attributed to horizontally acquired TE or viral sequences. We predict that the number of examples will rapidly grow in the future as the prevalence of horizontal transfer in the life cycle of TEs becomes even more apparent, firmly establishing this form of non-Mendelian inheritance as a consequential facet of eukaryotic evolution.}, }
@article {pmid29501917, year = {2018}, author = {Papagiannitsis, CC and Sarrou, S and Tsilipounidaki, K and Malli, E and Medvecky, M and Hrabak, J and Fthenakis, GC and Petinaki, E}, title = {Characterisation of a ST100 Staphylococcus epidermidis producing an LnuB nucleotidyltransferase: Evidence for interspecies spread of an lnuB-carrying transposon.}, journal = {Journal of global antimicrobial resistance}, volume = {13}, number = {}, pages = {9-10}, doi = {10.1016/j.jgar.2018.02.017}, pmid = {29501917}, issn = {2213-7173}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *DNA Transposable Elements ; Gene Order ; *Gene Transfer, Horizontal ; Greece ; Mastitis/microbiology/veterinary ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Nucleotidyltransferases/*genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sheep ; Sheep Diseases/*microbiology ; Staphylococcal Infections/microbiology/*veterinary ; Staphylococcus epidermidis/drug effects/*enzymology/genetics/*isolation &amp; purification ; }, }
@article {pmid29500561, year = {2018}, author = {Lacroix, B and Citovsky, V}, title = {Beyond Agrobacterium-Mediated Transformation: Horizontal Gene Transfer from Bacteria to Eukaryotes.}, journal = {Current topics in microbiology and immunology}, volume = {418}, number = {}, pages = {443-462}, pmid = {29500561}, issn = {0070-217X}, support = {R01 GM050224/GM/NIGMS NIH HHS/United States ; }, mesh = {Agrobacterium/*genetics/*pathogenicity ; Animals ; Eukaryota/*classification/*genetics ; *Gene Transfer, Horizontal ; Plants/genetics/microbiology ; *Transformation, Genetic ; }, abstract = {Besides the massive gene transfer from organelles to the nuclear genomes, which occurred during the early evolution of eukaryote lineages, the importance of horizontal gene transfer (HGT) in eukaryotes remains controversial. Yet, increasing amounts of genomic data reveal many cases of bacterium-to-eukaryote HGT that likely represent a significant force in adaptive evolution of eukaryotic species. However, DNA transfer involved in genetic transformation of plants by Agrobacterium species has traditionally been considered as the unique example of natural DNA transfer and integration into eukaryotic genomes. Recent discoveries indicate that the repertoire of donor bacterial species and of recipient eukaryotic hosts potentially are much wider than previously thought, including donor bacterial species, such as plant symbiotic nitrogen-fixing bacteria (e.g., Rhizobium etli) and animal bacterial pathogens (e.g., Bartonella henselae, Helicobacter pylori), and recipient species from virtually all eukaryotic clades. Here, we review the molecular pathways and potential mechanisms of these trans-kingdom HGT events and discuss their utilization in biotechnology and research.}, }
@article {pmid29500262, year = {2018}, author = {Martínez, N and Luque, R and Milani, C and Ventura, M and Bañuelos, O and Margolles, A}, title = {A Gene Homologous to rRNA Methylase Genes Confers Erythromycin and Clindamycin Resistance in Bifidobacterium breve.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {10}, pages = {}, pmid = {29500262}, issn = {1098-5336}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics/*metabolism ; Bifidobacterium breve/*drug effects/*enzymology/genetics ; Clindamycin/*pharmacology ; Drug Resistance, Bacterial ; Erythromycin/*pharmacology ; Gastrointestinal Microbiome ; Gene Transfer, Horizontal ; Humans ; Intestines/microbiology ; Methyltransferases/genetics/*metabolism ; Phylogeny ; }, abstract = {Bifidobacteria are mutualistic intestinal bacteria, and their presence in the human gut has been associated with health-promoting activities. The presence of antibiotic resistance genes in this genus is controversial, since, although bifidobacteria are nonpathogenic microorganisms, they could serve as reservoirs of resistance determinants for intestinal pathogens. However, until now, few antibiotic resistance determinants have been functionally characterized in this genus. In this work, we show that Bifidobacterium breve CECT7263 displays atypical resistance to erythromycin and clindamycin. In order to delimit the genomic region responsible for the observed resistance phenotype, a library of genomic DNA was constructed and a fragment of 5.8 kb containing a gene homologous to rRNA methylase genes was able to confer erythromycin resistance in Escherichia coli This genomic region seems to be very uncommon, and homologs of the gene have been detected in only one strain of Bifidobacterium longum and two other strains of B. breve In this context, analysis of shotgun metagenomics data sets revealed that the gene is also uncommon in the microbiomes of adults and infants. The structural gene and its upstream region were cloned into a B. breve-sensitive strain, which became resistant after acquiring the genetic material. In vitro conjugation experiments did not allow us to detect gene transfer to other recipients. Nevertheless, prediction of genes potentially acquired through horizontal gene transfer events revealed that the gene is located in a putative genomic island.IMPORTANCEBifidobacterium breve is a very common human intestinal bacterium. Often described as a pioneer microorganism in the establishment of early-life intestinal microbiota, its presence has been associated with several beneficial effects for the host, including immune stimulation and protection against infections. Therefore, some strains of this species are considered probiotics. In relation to this, because probiotic bacteria are used for human and animal consumption, one of the safety concerns over these bacteria is the presence of antibiotic resistance genes, since the human gut is a densely populated habitat that could favor the transfer of genetic material to potential pathogens. In this study, we analyzed the genetic basis responsible for the erythromycin and clindamycin resistance phenotype of B. breve CECT7263. We were able to identify and characterize a novel gene homologous to rRNA methylase genes which confers erythromycin and clindamycin resistance. This gene seems to be very uncommon in other bifidobacteria and in the gut microbiomes of both adults and infants. Even though conjugation experiments showed the absence of transferability under in vitro conditions, it has been predicted to be located in a putative genomic island recently acquired by specific bifidobacterial strains.}, }
@article {pmid29500259, year = {2018}, author = {Vior, NM and Lacret, R and Chandra, G and Dorai-Raj, S and Trick, M and Truman, AW}, title = {Discovery and Biosynthesis of the Antibiotic Bicyclomycin in Distantly Related Bacterial Classes.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {9}, pages = {}, pmid = {29500259}, issn = {1098-5336}, support = {BBS/E/J/000PR9790/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P012523/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004561/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/P007570/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Alphaproteobacteria/metabolism ; Anti-Bacterial Agents/*biosynthesis ; Bacteria/classification/*metabolism ; Betaproteobacteria/metabolism ; Bridged Bicyclo Compounds, Heterocyclic/metabolism ; Gammaproteobacteria/metabolism ; Multigene Family/*genetics ; }, abstract = {Bicyclomycin (BCM) is a clinically promising antibiotic that is biosynthesized by Streptomyces cinnamoneus DSM 41675. BCM is structurally characterized by a core cyclo(l-Ile-l-Leu) 2,5-diketopiperazine (DKP) that is extensively oxidized. Here, we identify the BCM biosynthetic gene cluster, which shows that the core of BCM is biosynthesized by a cyclodipeptide synthase, and the oxidative modifications are introduced by five 2-oxoglutarate-dependent dioxygenases and one cytochrome P450 monooxygenase. The discovery of the gene cluster enabled the identification of BCM pathways encoded by the genomes of hundreds of Pseudomonas aeruginosa isolates distributed globally, and heterologous expression of the pathway from P. aeruginosa SCV20265 demonstrated that the product is chemically identical to BCM produced by S. cinnamoneus Overall, putative BCM gene clusters have been found in at least seven genera spanning Actinobacteria and Proteobacteria (Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria). This represents a rare example of horizontal gene transfer of an intact biosynthetic gene cluster across such distantly related bacteria, and we show that these gene clusters are almost always associated with mobile genetic elements.IMPORTANCE Bicyclomycin is the only natural product antibiotic that selectively inhibits the transcription termination factor Rho. This mechanism of action, combined with its proven biological safety and its activity against clinically relevant Gram-negative bacterial pathogens, makes it a very promising antibiotic candidate. Here, we report the identification of the bicyclomycin biosynthetic gene cluster in the known bicyclomycin-producing organism Streptomyces cinnamoneus, which will enable the engineered production of new bicyclomycin derivatives. The identification of this gene cluster also led to the discovery of hundreds of bicyclomycin pathways encoded in highly diverse bacteria, including in the opportunistic pathogen Pseudomonas aeruginosa This wide distribution of a complex biosynthetic pathway is very unusual and provides an insight into how a pathway for an antibiotic can be transferred between diverse bacteria.}, }
@article {pmid29498209, year = {2018}, author = {Vance, TDR and Graham, LA and Davies, PL}, title = {An ice-binding and tandem beta-sandwich domain-containing protein in Shewanella frigidimarina is a potential new type of ice adhesin.}, journal = {The FEBS journal}, volume = {285}, number = {8}, pages = {1511-1527}, doi = {10.1111/febs.14424}, pmid = {29498209}, issn = {1742-4658}, support = {353755//CIHR/Canada ; }, mesh = {Adhesins, Bacterial/chemistry/genetics/*metabolism ; Amino Acid Sequence ; Antarctic Regions ; Bacterial Adhesion ; Bacterial Proteins/chemistry/genetics/*metabolism ; Crystallography, X-Ray ; *Ice ; Models, Molecular ; Protein Domains ; Sequence Homology, Amino Acid ; Shewanella/genetics/*metabolism ; }, abstract = {UNLABELLED: Out of the dozen different ice-binding protein (IBP) structures known, the DUF3494 domain is the most widespread, having been passed many times between prokaryotic and eukaryotic microorganisms by horizontal gene transfer. This ~25-kDa β-solenoid domain with an adjacent parallel α-helix is most commonly associated with an N-terminal secretory signal peptide. However, examples of the DUF3494 domain preceded by tandem Bacterial Immunoglobulin-like (BIg) domains are sometimes found, though uncharacterized. Here, we present one such protein (SfIBP_1) from the Antarctic bacterium Shewanella frigidimarina. We have confirmed and characterized the ice-binding activity of its ice-binding domain using thermal hysteresis measurements, fluorescent ice plane affinity analysis, and ice recrystallization inhibition assays. X-ray crystallography was used to solve the structure of the SfIBP_1 ice-binding domain, to further characterize its ice-binding surface and unique method of stabilizing or 'capping' the ends of the solenoid structure. The latter is formed from the interaction of two loops mediated by a combination of tandem prolines and electrostatic interactions. Furthermore, given their domain architecture and membrane association, we propose that these BIg-containing DUF3494 IBPs serve as ice-binding adhesion proteins that are capable of adsorbing their host bacterium onto ice.<br><br>DATABASE: Submitted new structure to the Protein Data Bank (PDB: 6BG8).}, }
@article {pmid29496860, year = {2018}, author = {Leslie, M}, title = {Nature's strategies: Stealing genes to survive.}, journal = {Science (New York, N.Y.)}, volume = {359}, number = {6379}, pages = {979}, doi = {10.1126/science.359.6379.979}, pmid = {29496860}, issn = {1095-9203}, mesh = {Adaptation, Physiological ; Drug Resistance, Bacterial/*genetics ; *Gene Transfer, Horizontal ; Humans ; Klebsiella Infections/microbiology/mortality ; Klebsiella pneumoniae/*genetics/*physiology ; }, }
@article {pmid29496843, year = {2018}, author = {Diop, A and Diop, K and Tomei, E and Raoult, D and Fenollar, F and Fournier, PE}, title = {Draft Genome Sequence of Ezakiella peruensis Strain M6.X2, a Human Gut Gram-Positive Anaerobic Coccus.}, journal = {Genome announcements}, volume = {6}, number = {9}, pages = {}, pmid = {29496843}, issn = {2169-8287}, abstract = {We report here the draft genome sequence of Ezakiella peruensis strain M6.X2[T] The draft genome is 1,672,788 bp long and harbors 1,589 predicted protein-encoding genes, including 26 antibiotic resistance genes with 1 gene encoding vancomycin resistance. The genome also exhibits 1 clustered regularly interspaced short palindromic repeat region and 333 genes acquired by horizontal gene transfer.}, }
@article {pmid29496594, year = {2018}, author = {Potter, RF and Wallace, MA and McMullen, AR and Prusa, J and Stallings, CL and Burnham, CAD and Dantas, G}, title = {blaIMP-27 on transferable plasmids in Proteus mirabilis and Providencia rettgeri.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {24}, number = {9}, pages = {1019.e5-1019.e8}, pmid = {29496594}, issn = {1469-0691}, support = {R01 GM099538/GM/NIGMS NIH HHS/United States ; T32 GM007067/GM/NIGMS NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics ; Disk Diffusion Antimicrobial Tests ; *Gene Transfer, Horizontal ; High-Throughput Nucleotide Sequencing ; Humans ; Imipenem/pharmacology ; Meropenem ; Plasmids/*genetics/metabolism ; Proteus mirabilis/drug effects/*genetics ; Providencia/drug effects/*genetics ; Sequence Analysis, DNA ; Thienamycins/pharmacology ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: A carbapenem-resistant Providencia rettgeri (PR1) isolate was recovered from a wound infection in Missouri, USA. This isolate possessed an EDTA-inhibitable carbapenemase that was unidentified using the Xpert CARBA-R assay. Our objective was to elucidate the molecular determinant of carbapenem resistance in this isolate. We then sought to test the transmissibility of blaIMP-27 loci in clinical P. rettgeri and Proteus mirabilis isolates.<br><br>METHODS: In October 2016 the novel ambler Class B carbapenemase blaIMP-27, was reported in two different Proteus mirabilis (PM185 and PM187) isolates. Broth mating assays for transfer of carbapenemase activity were performed for the three clinical isolates with recipient sodium azide-resistant Escherichia coli J53. Antibiotic susceptibility testing and phenotypic carbapenemase activity testing were performed on the clinical isolates, J53 and transconjugants using the Kirby-Bauer disc diffusion method according to CLSI guidelines. Plasmid DNA from PM187, PR1 and their transconjugants were used as input for Nextera Illumina sequencing libraries and sequenced on a NextSeq platform.<br><br>RESULTS: PR1 was resistant to both imipenem and meropenem. PM187 and PR1 could transfer resistance to E.&#xa0;coli through plasmid conjugation (pPM187 and pPR1). pPM187 had a virB/virD4 type IV secretion system whereas pPR1 had a traB/traD type IV secretion system.<br><br>CONCLUSION: Two of three blaIMP-27-bearing clinical isolates tested could conjugate resistance into E.&#xa0;coli. The resulting transconjugants became positive for phenotypic carbapenemase production but did not pass clinical resistance breakpoints. blaIMP-27 can be transmitted on different plasmid replicon types that rely on distinct classes of type IV secretion system for horizontal transfer.}, }
@article {pmid29494919, year = {2018}, author = {Arias-Andres, M and Klümper, U and Rojas-Jimenez, K and Grossart, HP}, title = {Microplastic pollution increases gene exchange in aquatic ecosystems.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {237}, number = {}, pages = {253-261}, doi = {10.1016/j.envpol.2018.02.058}, pmid = {29494919}, issn = {1873-6424}, support = {MR/N007174/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Bacteria/genetics ; Biofilms ; Drug Resistance, Microbial/genetics ; *Ecosystem ; Environmental Monitoring ; Environmental Pollution ; Escherichia coli/genetics ; Gene Transfer, Horizontal/*drug effects ; Plasmids ; Plastics/*toxicity ; Water Pollutants, Chemical/*toxicity ; }, abstract = {Pollution by microplastics in aquatic ecosystems is accumulating at an unprecedented scale, emerging as a new surface for biofilm formation and gene exchange. In this study, we determined the permissiveness of aquatic bacteria towards a model antibiotic resistance plasmid, comparing communities that form biofilms on microplastics vs. those that are free-living. We used an exogenous and red-fluorescent E. coli donor strain to introduce the green-fluorescent broad-host-range plasmid pKJK5 which encodes for trimethoprim resistance. We demonstrate an increased frequency of plasmid transfer in bacteria associated with microplastics compared to bacteria that are free-living or in natural aggregates. Moreover, comparison of communities grown on polycarbonate filters showed that increased gene exchange occurs in a broad range of phylogenetically-diverse bacteria. Our results indicate horizontal gene transfer in this habitat could distinctly affect the ecology of aquatic microbial communities on a global scale. The spread of antibiotic resistance through microplastics could also have profound consequences for the evolution of aquatic bacteria and poses a neglected hazard for human health.}, }
@article {pmid29487592, year = {2018}, author = {Muraille, E}, title = {Diversity Generator Mechanisms Are Essential Components of Biological Systems: The Two Queen Hypothesis.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {223}, pmid = {29487592}, issn = {1664-302X}, abstract = {Diversity is widely known to fuel adaptation and evolutionary processes and increase robustness at the population, species and ecosystem levels. The Neo-Darwinian paradigm proposes that the diversity of biological entities is the consequence of genetic changes arising spontaneously and randomly, without regard for their usefulness. However, a growing body of evidence demonstrates that the evolutionary process has shaped mechanisms, such as horizontal gene transfer mechanisms, meiosis and the adaptive immune system, which has resulted in the regulated generation of diversity among populations. Though their origins are unrelated, these diversity generator (DG) mechanisms share common functional properties. They (i) contribute to the great unpredictability of the composition and/or behavior of biological systems, (ii) favor robustness and collectivism among populations and (iii) operate mainly by manipulating the systems that control the interaction of living beings with their environment. The definition proposed here for DGs is based on these properties and can be used to identify them according to function. Interestingly, prokaryotic DGs appear to be mainly reactive, as they generate diversity in response to environmental stress. They are involved in the widely described Red Queen/arms race/Cairnsian dynamic. The emergence of multicellular organisms harboring K selection traits (longer reproductive life cycle and smaller population size) has led to the acquisition of a new class of DGs that act anticipatively to stress pressures and generate a distinct dynamic called the "White Queen" here. The existence of DGs leads to the view of evolution as a more "intelligent" and Lamarckian-like process. Their repeated selection during evolution could be a neglected example of convergent evolution and suggests that some parts of the evolutionary process are tightly constrained by ecological factors, such as the population size, the generation time and the intensity of selective pressure. The ubiquity of DGs also suggests that regulated auto-generation of diversity is a fundamental property of life.}, }
@article {pmid29487238, year = {2018}, author = {Gladieux, P and Condon, B and Ravel, S and Soanes, D and Maciel, JLN and Nhani, A and Chen, L and Terauchi, R and Lebrun, MH and Tharreau, D and Mitchell, T and Pedley, KF and Valent, B and Talbot, NJ and Farman, M and Fournier, E}, title = {Gene Flow between Divergent Cereal- and Grass-Specific Lineages of the Rice Blast Fungus Magnaporthe oryzae.}, journal = {mBio}, volume = {9}, number = {1}, pages = {}, pmid = {29487238}, issn = {2150-7511}, mesh = {Bangladesh ; Biota ; Edible Grain/microbiology ; *Gene Flow ; Gene Transfer, Horizontal ; Genetic Variation ; Magnaporthe/classification/*genetics/isolation &amp; purification ; Poaceae/microbiology ; Sequence Analysis, DNA ; South America ; Whole Genome Sequencing ; }, abstract = {Delineating species and epidemic lineages in fungal plant pathogens is critical to our understanding of disease emergence and the structure of fungal biodiversity and also informs international regulatory decisions. Pyricularia oryzae (syn. Magnaporthe oryzae) is a multihost pathogen that infects multiple grasses and cereals, is responsible for the most damaging rice disease (rice blast), and is of growing concern due to the recent introduction of wheat blast to Bangladesh from South America. However, the genetic structure and evolutionary history of M. oryzae, including the possible existence of cryptic phylogenetic species, remain poorly defined. Here, we use whole-genome sequence information for 76 M. oryzae isolates sampled from 12 grass and cereal genera to infer the population structure of M. oryzae and to reassess the species status of wheat-infecting populations of the fungus. Species recognition based on genealogical concordance, using published data or extracting previously used loci from genome assemblies, failed to confirm a prior assignment of wheat blast isolates to a new species (Pyricularia graminis-tritici). Inference of population subdivisions revealed multiple divergent lineages within M. oryzae, each preferentially associated with one host genus, suggesting incipient speciation following host shift or host range expansion. Analyses of gene flow, taking into account the possibility of incomplete lineage sorting, revealed that genetic exchanges have contributed to the makeup of multiple lineages within M. oryzae These findings provide greater understanding of the ecoevolutionary factors that underlie the diversification of M. oryzae and highlight the practicality of genomic data for epidemiological surveillance in this important multihost pathogen.IMPORTANCE Infection of novel hosts is a major route for disease emergence by pathogenic microorganisms. Understanding the evolutionary history of multihost pathogens is therefore important to better predict the likely spread and emergence of new diseases. Magnaporthe oryzae is a multihost fungus that causes serious cereal diseases, including the devastating rice blast disease and wheat blast, a cause of growing concern due to its recent spread from South America to Asia. Using whole-genome analysis of 76 fungal strains from different hosts, we have documented the divergence of M. oryzae into numerous lineages, each infecting a limited number of host species. Our analyses provide evidence that interlineage gene flow has contributed to the genetic makeup of multiple M. oryzae lineages within the same species. Plant health surveillance is therefore warranted to safeguard against disease emergence in regions where multiple lineages of the fungus are in contact with one another.}, }
@article {pmid29487186, year = {2018}, author = {Toenshoff, ER and Fields, PD and Bourgeois, YX and Ebert, D}, title = {The End of a 60-year Riddle: Identification and Genomic Characterization of an Iridovirus, the Causative Agent of White Fat Cell Disease in Zooplankton.}, journal = {G3 (Bethesda, Md.)}, volume = {8}, number = {4}, pages = {1259-1272}, pmid = {29487186}, issn = {2160-1836}, mesh = {Animals ; Base Composition/genetics ; Conserved Sequence ; Cytoplasm/virology ; Daphnia/*virology ; Genes, Viral ; Genome Size ; *Genome, Viral ; Genotype ; Iridovirus/*genetics/ultrastructure ; Open Reading Frames/genetics ; Phylogeny ; RNA Caps/genetics ; Sequence Homology, Nucleic Acid ; Viral Proteins/genetics ; Virion/ultrastructure ; Zooplankton/*virology ; }, abstract = {The planktonic freshwater crustacean of the genus Daphnia are a model system for biomedical research and, in particular, invertebrate-parasite interactions. Up until now, no virus has been characterized for this system. Here we report the discovery of an iridovirus as the causative agent of White Fat Cell Disease (WFCD) in Daphnia WFCD is a highly virulent disease of Daphnia that can easily be cultured under laboratory conditions. Although it has been studied from sites across Eurasia for more than 60 years, its causative agent had not been described, nor had an iridovirus been connected to WFCD before now. Here we find that an iridovirus-the Daphnia iridescent virus 1 (DIV-1)-is the causative agent of WFCD. DIV-1 has a genome sequence of about 288 kbp, with 39% G+C content and encodes 367 predicted open reading frames. DIV-1 clusters together with other invertebrate iridoviruses but has by far the largest genome among all sequenced iridoviruses. Comparative genomics reveal that DIV-1 has apparently recently lost a substantial number of unique genes but has also gained genes by horizontal gene transfer from its crustacean host. DIV-1 represents the first invertebrate iridovirus that encodes proteins to purportedly cap RNA, and it contains unique genes for a DnaJ-like protein, a membrane glycoprotein and protein of the immunoglobulin superfamily, which may mediate host-pathogen interactions and pathogenicity. Our findings end a 60-year search for the causative agent of WFCD and add to our knowledge of iridovirus genomics and invertebrate-virus interactions.}, }
@article {pmid29483121, year = {2018}, author = {Dolejska, M and Papagiannitsis, CC and Medvecky, M and Davidova-Gerzova, L and Valcek, A}, title = {Characterization of the Complete Nucleotide Sequences of IMP-4-Encoding Plasmids, Belonging to Diverse Inc Families, Recovered from Enterobacteriaceae Isolates of Wildlife Origin.}, journal = {Antimicrobial agents and chemotherapy}, volume = {62}, number = {5}, pages = {}, pmid = {29483121}, issn = {1098-6596}, mesh = {Anti-Bacterial Agents/pharmacology ; Enterobacteriaceae/*genetics/pathogenicity ; Enterobacteriaceae Infections/microbiology ; Gene Transfer, Horizontal/genetics ; Plasmids/*genetics ; }, abstract = {The complete nucleotide sequences of six IMP-4-encoding plasmids recovered from Enterobacteriaceae isolates of wildlife origin were characterized. Sequencing data showed that plasmids of different incompatibility groups (IncM, IncI1, IncF, and nontypeable [including an IncX5_2 and two pPrY2001-like]) carried the blaIMP-4-carrying integrons In809 or In1460. Most of the plasmids carried an mph(A) region, and chrA-like, aac(3)-IId, and blaTEM-1b genes. Finally, plasmid analysis revealed the involvement of two different IS26- and Tn1696-associated mechanisms in the mobilization of IMP-4-encoding integrons.}, }
@article {pmid29479648, year = {2018}, author = {Matsui, K and Endo, G}, title = {Mercury bioremediation by mercury resistance transposon-mediated in situ molecular breeding.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {7}, pages = {3037-3048}, doi = {10.1007/s00253-018-8847-2}, pmid = {29479648}, issn = {1432-0614}, mesh = {Bacteria/*genetics/*metabolism ; *Biodegradation, Environmental ; DNA Shuffling ; DNA Transposable Elements/*genetics ; Drug Resistance, Bacterial/genetics ; Mercury/*metabolism ; Operon/genetics ; }, abstract = {Mercury-resistant (Hg[R]) bacteria occur in various bacterial species from a wide variety of environmental sources. Resistance is conferred by a set of operon genes termed the mer operon. Many Hg[R] bacteria have been isolated from diverse environments and clinical samples, and it is recognized that mer operons are often localized on transposons. Previous research reports have suggested that Hg[R] transposons participate in the horizontal gene transfer of mer operons among bacteria. This was confirmed by a study that found that mer operons were distributed worldwide in Bacilli with dissemination of TnMERI1-like transposons. In this mini review, possible strategies for transposon-mediated in situ molecular breeding (ISMoB) of Hg[R] bacteria in their natural habitat are discussed. In ISMoB, the target microorganisms for breeding are indigenous bacteria that are not Hg[R] but that are dominant and robust in their respective environments. Additionally, we propose a new concept of bioremediation technology for environmental mercury pollution by applying transposon-mediated ISMoB for environmental mercury pollution control.}, }
@article {pmid29478272, year = {2018}, author = {Kamikawa, R and Yazaki, E and Tahara, M and Sakura, T and Matsuo, E and Nagamune, K and Hashimoto, T and Inagaki, Y}, title = {Fates of Evolutionarily Distinct, Plastid-type Glyceraldehyde 3-phosphate Dehydrogenase Genes in Kareniacean Dinoflagellates.}, journal = {The Journal of eukaryotic microbiology}, volume = {65}, number = {5}, pages = {669-678}, doi = {10.1111/jeu.12512}, pmid = {29478272}, issn = {1550-7408}, mesh = {Dinoflagellida/classification/enzymology/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Glyceraldehyde-3-Phosphate Dehydrogenases/*genetics ; Phylogeny ; Plastids/*enzymology/genetics ; Protozoan Proteins/*genetics ; }, abstract = {The ancestral kareniacean dinoflagellate has undergone tertiary endosymbiosis, in which the original plastid is replaced by a haptophyte endosymbiont. During this plastid replacement, the endosymbiont genes were most likely flowed into the host dinoflagellate genome (endosymbiotic gene transfer or EGT). Such EGT may have generated the redundancy of functionally homologous genes in the host genome-one has resided in the host genome prior to the haptophyte endosymbiosis, while the other transferred from the endosymbiont genome. However, it remains to be well understood how evolutionarily distinct but functionally homologous genes were dealt in the dinoflagellate genomes bearing haptophyte-derived plastids. To model the gene evolution after EGT in plastid replacement, we here compared the characteristics of the two evolutionally distinct genes encoding plastid-type glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in Karenia brevis and K. mikimotoi bearing haptophyte-derived tertiary plastids: "gapC1h" acquired from the haptophyte endosymbiont and "gapC1p" inherited from the ancestral dinoflagellate. Our experiments consistently and clearly demonstrated that, in the two species examined, the principal plastid-type GAPDH is encoded by gapC1h rather than gapC1p. We here propose an evolutionary scheme resolving the EGT-derived redundancy of genes involved in plastid function and maintenance in the nuclear genomes of dinoflagellates that have undergone plastid replacements. Although K. brevis and K. mikimotoi are closely related to each other, the statuses of the two evolutionarily distinct gapC1 genes in the two Karenia species correspond to different steps in the proposed scheme.}, }
@article {pmid29477666, year = {2018}, author = {Le Devendec, L and Jouy, E and Kempf, I}, title = {Evaluation of resistance gene transfer from heat-treated Escherichia coli.}, journal = {International journal of food microbiology}, volume = {270}, number = {}, pages = {39-43}, doi = {10.1016/j.ijfoodmicro.2018.02.019}, pmid = {29477666}, issn = {1879-3460}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Cephalosporins/pharmacology ; Conjugation, Genetic/*physiology ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/*genetics ; Gene Transfer, Horizontal/*genetics ; Hot Temperature/adverse effects ; Microbial Sensitivity Tests ; Plasmids/genetics/metabolism ; Sulfonamides/pharmacology ; Tetracycline/pharmacology ; Transformation, Bacterial/*physiology ; }, abstract = {Antimicrobial-resistant Escherichia coli may be present in various foods. The aim of this study was to evaluate the impact of heat treatment, simulating food preparation, on the possibility of antimicrobial resistance genes being transferred from E. coli cells. The study was performed on antimicrobial-resistant E. coli cells in suspension in a sterile saline solution. The stability of resistance genes and the possibility of their transfer by transformation or conjugation were analyzed. Results showed that antimicrobial-resistant E. coli cells managing to survive after a few minutes at 60 °C retained their antimicrobial resistance. No plasmid could be transferred by conjugation from antimicrobial-resistant E. coli cells heated to 60 °C for ten or more minutes. Twelve electroporation experiments were performed using a bacterial suspension heated to 70 °C for 30 min. Genes coding for resistance to extended-spectrum cephalosporins, tetracycline or sulfonamides were transferred to an E. coli DH5α recipient on two occasions. In conclusion we showed that heat-treated E. coli may occasionally transfer resistance genes.}, }
@article {pmid29477117, year = {2018}, author = {Zhang, Y and Gu, AZ and Cen, T and Li, X and He, M and Li, D and Chen, J}, title = {Sub-inhibitory concentrations of heavy metals facilitate the horizontal transfer of plasmid-mediated antibiotic resistance genes in water environment.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {237}, number = {}, pages = {74-82}, doi = {10.1016/j.envpol.2018.01.032}, pmid = {29477117}, issn = {1873-6424}, mesh = {Anti-Bacterial Agents ; Drug Resistance, Microbial/*genetics ; Escherichia coli/drug effects ; *Gene Transfer, Horizontal ; Genes, Bacterial/drug effects ; Metals, Heavy/*toxicity ; Microbial Sensitivity Tests ; Plasmids ; Water Pollutants, Chemical/*toxicity ; }, abstract = {Although widespread antibiotic resistance has been mostly attributed to the selective pressure generated by overuse and misuse of antibiotics, recent growing evidence suggests that chemicals other than antibiotics, such as certain metals, can also select and stimulate antibiotic resistance via both co-resistance and cross-resistance mechanisms. For instance, tetL, merE, and oprD genes are resistant to both antibiotics and metals. However, the potential de novo resistance induced by heavy metals at environmentally-relevant low concentrations (much below theminimum inhibitory concentrations [MICs], also referred as sub-inhibitory) has hardly been explored. This study investigated and revealed that heavy metals, namely Cu(II), Ag(I), Cr(VI), and Zn(II), at environmentally-relevant and sub-inhibitory concentrations, promoted conjugative transfer of antibiotic resistance genes (ARGs) between E. coli strains. The mechanisms of this phenomenon were further explored, which involved intracellular reactive oxygen species (ROS) formation, SOS response, increased cell membrane permeability, and altered expression of conjugation-relevant genes. These findings suggest that sub-inhibitory levels of heavy metals that widely present in various environments contribute to the resistance phenomena via facilitating horizontal transfer of ARGs. This study provides evidence from multiple aspects implicating the ecological effect of low levels of heavy metals on antibiotic resistance dissemination and highlights the urgency of strengthening efficacious policy and technology to control metal pollutants in the environments.}, }
@article {pmid29476343, year = {2018}, author = {Stritzler, M and Soto, G and Ayub, N}, title = {Plant Growth-Promoting Genes can Switch to be Virulence Factors via Horizontal Gene Transfer.}, journal = {Microbial ecology}, volume = {76}, number = {3}, pages = {579-583}, pmid = {29476343}, issn = {1432-184X}, support = {PICT-2014-3659//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; }, mesh = {Bacterial Proteins/*genetics/metabolism ; *Gene Transfer, Horizontal ; Medicago sativa/growth &amp; development/*microbiology ; Pectobacterium carotovorum/*genetics/metabolism ; Phylogeny ; Plant Diseases/*microbiology ; Pseudomonas fluorescens/*genetics/metabolism ; Virulence Factors/*genetics/metabolism ; }, abstract = {There are increasing evidences that horizontal gene transfer (HGT) is a critical mechanism of bacterial evolution, while its complete impact remains unclear. A main constraint of HGT effects on microbial evolution seems to be the conservation of the function of the horizontally transferred genes. From this perspective, inflexible nomenclature and functionality criteria have been established for some mobile genetic elements such as pathogenic and symbiotic islands. Adhesion is a universal prerequisite for both beneficial and pathogenic plant-microbe interactions, and thus, adhesion systems (e.g., the Lap cluster) are candidates to have a dual function depending on the genomic background. In this study, we showed that the virulent factor Lap of the phytopathogen Erwinia carotovora SCRI1043, which is located within a genomic island, was acquired by HGT and probably derived from Pseudomonas. The transformation of the phytopathogen Erwinia pyrifoliae Ep1/96 with the beneficial factor Lap from the plant growth-promoting bacterium Pseudomonas fluorescens Pf-5 significantly increased its natural virulence, experimentally recapitulating the beneficial-to-virulence functional switch of the Lap cluster via HGT. To our knowledge, this is the first report of a functional switch of an individual gene or a cluster of genes mediated by HGT.}, }
@article {pmid29476089, year = {2018}, author = {Froese, T and Campos, JI and Fujishima, K and Kiga, D and Virgo, N}, title = {Horizontal transfer of code fragments between protocells can explain the origins of the genetic code without vertical descent.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {3532}, pmid = {29476089}, issn = {2045-2322}, mesh = {Amino Acyl-tRNA Synthetases/genetics/metabolism ; Aminoacylation ; Codon ; Computer Simulation ; *Evolution, Molecular ; Extinction, Biological ; *Gene Transfer, Horizontal ; *Genetic Code ; *Models, Genetic ; Origin of Life ; *Protein Biosynthesis ; RNA, Catalytic/genetics/metabolism ; RNA, Transfer/genetics/metabolism ; }, abstract = {Theories of the origin of the genetic code typically appeal to natural selection and/or mutation of hereditable traits to explain its regularities and error robustness, yet the present translation system presupposes high-fidelity replication. Woese's solution to this bootstrapping problem was to assume that code optimization had played a key role in reducing the effect of errors caused by the early translation system. He further conjectured that initially evolution was dominated by horizontal exchange of cellular components among loosely organized protocells ("progenotes"), rather than by vertical transmission of genes. Here we simulated such communal evolution based on horizontal transfer of code fragments, possibly involving pairs of tRNAs and their cognate aminoacyl tRNA synthetases or a precursor tRNA ribozyme capable of catalysing its own aminoacylation, by using an iterated learning model. This is the first model to confirm Woese's conjecture that regularity, optimality, and (near) universality could have emerged via horizontal interactions alone.}, }
@article {pmid29475871, year = {2018}, author = {Heine, T and Zimmerling, J and Ballmann, A and Kleeberg, SB and Rückert, C and Busche, T and Winkler, A and Kalinowski, J and Poetsch, A and Scholtissek, A and Oelschlägel, M and Schmidt, G and Tischler, D}, title = {On the Enigma of Glutathione-Dependent Styrene Degradation in Gordonia rubripertincta CWB2.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {9}, pages = {}, pmid = {29475871}, issn = {1098-5336}, mesh = {Biodegradation, Environmental ; Butadienes/*metabolism ; Glutathione/*metabolism ; Gordonia Bacterium/*metabolism ; Hemiterpenes/*metabolism ; Plasmids/isolation &amp; purification ; Styrene/*metabolism ; }, abstract = {Among bacteria, only a single styrene-specific degradation pathway has been reported so far. It comprises the activity of styrene monooxygenase, styrene oxide isomerase, and phenylacetaldehyde dehydrogenase, yielding phenylacetic acid as the central metabolite. The alternative route comprises ring-hydroxylating enzymes and yields vinyl catechol as central metabolite, which undergoes meta-cleavage. This was reported to be unspecific and also allows the degradation of benzene derivatives. However, some bacteria had been described to degrade styrene but do not employ one of those routes or only parts of them. Here, we describe a novel "hybrid" degradation pathway for styrene located on a plasmid of foreign origin. As putatively also unspecific, it allows metabolizing chemically analogous compounds (e.g., halogenated and/or alkylated styrene derivatives). Gordonia rubripertincta CWB2 was isolated with styrene as the sole source of carbon and energy. It employs an assembled route of the styrene side-chain degradation and isoprene degradation pathways that also funnels into phenylacetic acid as the central metabolite. Metabolites, enzyme activity, genome, transcriptome, and proteome data reinforce this observation and allow us to understand this biotechnologically relevant pathway, which can be used for the production of ibuprofen.IMPORTANCE The degradation of xenobiotics by bacteria is not only important for bioremediation but also because the involved enzymes are potential catalysts in biotechnological applications. This study reveals a novel degradation pathway for the hazardous organic compound styrene in Gordonia rubripertincta CWB2. This study provides an impressive illustration of horizontal gene transfer, which enables novel metabolic capabilities. This study presents glutathione-dependent styrene metabolization in an (actino-)bacterium. Further, the genomic background of the ability of strain CWB2 to produce ibuprofen is demonstrated.}, }
@article {pmid29475864, year = {2018}, author = {An, XL and Chen, QL and Zhu, D and Zhu, YG and Gillings, MR and Su, JQ}, title = {Impact of Wastewater Treatment on the Prevalence of Integrons and the Genetic Diversity of Integron Gene Cassettes.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {9}, pages = {}, pmid = {29475864}, issn = {1098-5336}, mesh = {Bacteria/drug effects/*genetics ; China ; Cities ; Drug Resistance, Bacterial/genetics ; *Genetic Variation ; Integrons/*genetics ; Interspersed Repetitive Sequences/*genetics ; Waste Disposal, Fluid ; Wastewater/*microbiology ; }, abstract = {The integron platform allows the acquisition, expression, and dissemination of antibiotic resistance genes within gene cassettes. Wastewater treatment plants (WWTPs) contain abundant resistance genes; however, knowledge about the impacts of wastewater treatment on integrons and their gene cassettes is limited. In this study, by using clone library analysis and high-throughput sequencing, we investigated the abundance of class 1, 2, and 3 integrons and their corresponding gene cassettes in three urban WWTPs. Our results showed that class 1 integrons were most abundant in WWTPs and that wastewater treatment significantly reduced the abundance of all integrons. The WWTP influents harbored the highest diversity of class 1 integron gene cassettes, whereas class 3 integron gene cassettes exhibited highest diversity in activated sludge. Most of the gene cassette arrays detected in class 1 integrons were novel. Aminoglycoside, beta-lactam, and trimethoprim resistance genes were highly prevalent in class 1 integron gene cassettes, while class 3 integrons mainly carried beta-lactam resistance gene cassettes. A core class 1 integron resistance gene cassette pool persisted during wastewater treatment, implying that these resistance genes could have high potential to spread into environments through WWTPs. These data provide new insights into the impact of wastewater treatment on integron pools and highlight the need for surveillance of resistance genes within both class 1 and 3 integrons.IMPORTANCE Wastewater treatment plants represent a significant sink and transport medium for antibiotic resistance bacteria and genes spreading into environments. Integrons are important genetic elements involved in the evolution of antibiotic resistance. To better understand the impact of wastewater treatment on integrons and their gene cassette contexts, we conducted clone library construction and high-throughput sequencing to analyze gene cassette contexts for class 1 and class 3 integrons during the wastewater treatment process. This study comprehensively profiled the distribution of integrons and their gene cassettes (especially class 3 integrons) in influents, activated sludge, and effluents of conventional municipal wastewater treatment plants. We further demonstrated that while wastewater treatment significantly reduced the abundance of integrons and the diversity of associated gene cassettes, a large fraction of integrons persisted in wastewater effluents and were consequentially discharged into downstream natural environments.}, }
@article {pmid29473528, year = {2018}, author = {Kumar, A and Bag, S and Das, B}, title = {Novel Genetic Tool to Study the Stability of Genomic Islands.}, journal = {Recent patents on biotechnology}, volume = {12}, number = {3}, pages = {200-207}, doi = {10.2174/1872208312666180223113618}, pmid = {29473528}, issn = {2212-4012}, mesh = {Chloramphenicol O-Acetyltransferase/genetics ; Gene Targeting/*methods ; *Genetic Vectors ; *Genomic Instability ; Genomic Islands/*genetics ; Hexosyltransferases/genetics ; Patents as Topic ; Vibrio cholerae/genetics ; Virulence/genetics ; }, abstract = {BACKGROUND: Genomic islands (GIs) are discrete segments of mobile DNA with defined boundaries according to recent patents, acquired in the bacterial genome from another organism by horizontal gene transfer during the course of evolution. GIs contribute significantly to virulence, disease development, antimicrobial resistance and metabolic process.<br><br>OBJECTIVE: The present study focuses on the development of a vector based genetic tool carrying selectable and counter-selectable markers, in order to flag the GIs in the bacterial chromosome and monitor their stability under in vitro and in vivo conditions.<br><br>METHOD: We engineered suicide vectors, pSB40 and pSB41, carrying single or tandem copies of chloramphenicol acetyltransferase (cat) and levansucrase (sacB) alleles, respectively. The sacB-cat allele in both the vectors is flanked by several restriction sites. To test the suitability of sacB-cat allele for monitoring GI loss, we introduced the allele in the Vibrio Pathogenicity Island-1 (VPI-1) in Vibrio cholerae genome.<br><br>RESULTS: The V. cholerae strain carrying sacB-cat allele in VPI-1 element showed resistance to chloramphenicol and sensitivity to sucrose at optimal growth conditions. Loss of VPI-1 element from the V. cholerae genome was simply monitored by growing the cells on selection agar plates supplemented with sucrose. Our results showed that the genetic tool we developed is suitable for monitoring GI stability in the bacterial genome.<br><br>CONCLUSION: The present study indicates that pSB40 and pSB41are efficient and sensitive genetic tool that can be used for reverse genetics experiments and monitoring stability of mobile genetic elements in the bacterial genome.}, }
@article {pmid29471872, year = {2018}, author = {Van Goethem, MW and Pierneef, R and Bezuidt, OKI and Van De Peer, Y and Cowan, DA and Makhalanyane, TP}, title = {A reservoir of 'historical' antibiotic resistance genes in remote pristine Antarctic soils.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {40}, pmid = {29471872}, issn = {2049-2618}, support = {93074//National Research Foundation of South Africa/International ; 97891//National Research Foundation of South Africa/International ; 99320//National Research Foundation of South Africa/International ; 110717//National Research Foundation/International ; }, mesh = {Antarctic Regions ; Anti-Bacterial Agents/*metabolism ; Bacteria/*classification/*drug effects ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/genetics ; Membrane Transport Proteins/genetics ; Metagenomics/methods ; Soil Microbiology ; }, abstract = {BACKGROUND: Soil bacteria naturally produce antibiotics as a competitive mechanism, with a concomitant evolution, and exchange by horizontal gene transfer, of a range of antibiotic resistance mechanisms. Surveys of bacterial resistance elements in edaphic systems have originated primarily from human-impacted environments, with relatively little information from remote and pristine environments, where the resistome may comprise the ancestral gene diversity.<br><br>METHODS: We used shotgun metagenomics to assess antibiotic resistance gene (ARG) distribution in 17 pristine and remote Antarctic surface soils within the undisturbed Mackay Glacier region. We also interrogated the phylogenetic placement of ARGs compared to environmental ARG sequences and tested for the presence of horizontal gene transfer elements flanking ARGs.<br><br>RESULTS: In total, 177 naturally occurring ARGs were identified, most of which encoded single or multi-drug efflux pumps. Resistance mechanisms for the inactivation of aminoglycosides, chloramphenicol and &#x3b2;-lactam antibiotics were also common. Gram-negative bacteria harboured most ARGs (71%), with fewer genes from Gram-positive Actinobacteria and Bacilli (Firmicutes) (9%), reflecting the taxonomic composition of the soils. Strikingly, the abundance of ARGs per sample had a strong, negative correlation with species richness (r&#x2009;=&#x2009;-&#x2009;0.49, P&#x2009;<&#x2009;0.05). This result, coupled with a lack of mobile genetic elements flanking ARGs, suggests that these genes are ancient acquisitions of horizontal transfer events.<br><br>CONCLUSIONS: ARGs in these remote and uncontaminated soils most likely represent functional efficient historical genes that have since been vertically inherited over generations. The historical ARGs in these pristine environments carry a strong phylogenetic signal and form a monophyletic group relative to ARGs from other similar environments.}, }
@article {pmid29463604, year = {2018}, author = {Kobayashi, H}, title = {Regeneration of Escherichia coli from Minicells through Lateral Gene Transfer.}, journal = {Journal of bacteriology}, volume = {200}, number = {9}, pages = {}, pmid = {29463604}, issn = {1098-5530}, mesh = {*Conjugation, Genetic ; DNA, Bacterial/genetics ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/*cytology/*genetics ; *Gene Transfer Techniques ; *Genome, Bacterial ; Mutation ; Plasmids/genetics ; }, abstract = {Recently, artificial life has been created with artificial materials and methods. Life can be created when genomic DNA molecules are integrated in liposomes containing biochemical reactions for biogenic needs. However, it is not yet known whether the integration of these parts will be able to occur in nature and constitute a living system. I planned to regenerate bacteria from biologically active liposomes by inserting genomic DNA using only natural materials and methods. Minicells of Escherichia coli, containing plasmids and activated SOS proteins, act as protocells. Four new E. coli strains were regenerated from minicells by inserting the genomes by using the system for conjugation between F[-] and Hfr strains. Cells of the four regenerated strains showed the same genetic markers as the two genome donors. Pulse-field gel electrophoresis of their genomes showed admixing of those of both donors. In addition, the genomes of the four regenerated strains had chimeric genome of the two donors. These results show that synthesis of life can occur in nature without artificial arrangement.IMPORTANCE What is the difference between inanimate objects and organisms? Organisms always have genomic DNA. When organisms lose their genomes, they can neither grow nor reproduce. As the result, organisms turn into inanimate objects without their genomes. In this study, I regenerated microbes from cells that had lost their genomes (cell corpses) by inserting another genome. All steps of regeneration used the natural behavior of microbes. The same regeneration of microbes could happen in nature. These primitive lives have plasticity, which accelerates evolution and provides various kinds of life in the world.}, }
@article {pmid29463055, year = {2018}, author = {de Paula, ACL and Medeiros, JD and de Azevedo, AC and de Assis Chagas, JM and da Silva, VL and Diniz, CG}, title = {Antibiotic Resistance Genetic Markers and Integrons in White Soft Cheese: Aspects of Clinical Resistome and Potentiality of Horizontal Gene Transfer.}, journal = {Genes}, volume = {9}, number = {2}, pages = {}, pmid = {29463055}, issn = {2073-4425}, abstract = {Antibiotic resistance poses an important threat to global public health and has become a challenge to modern medicine. The occurrence of antibiotic-resistant bacteria in a broad range of foods has led to a growing concern about the impact that food may have as a reservoir of antibiotic resistance genes. Considering Minas Frescal Cheese (MFC)-a typical Brazilian white soft cheese-and its economic and cultural values, in this study, medically relevant antimicrobial-resistance genetic markers (AR genes) were screened, and the occurrence of integrons were evaluated in manufactured MFC using culture-independent approaches. Through a fingerprinting analysis, the tested MFCs were brand-clustered, indicating reproducibility along the production chain. A common core of resistance markers in all brands evaluated and related antimicrobials such as β-lactams, tetracyclines, quinolones, and sulfonamide was detected. Several other markers, including efflux pumps and aminoglycosides-resistance were distributed among brands. Class 1 and 2 integrons were observed, respectively, in 77% and 97% of the samples. The presence of AR genes is of special interest due to their clinical relevance. Taken together, the data may suggest that the production chain of MFC might contribute to the spread of putative drug-resistant bacteria, which could greatly impact human health. Furthermore, detection of class 1 and class 2 integrons in MFC has led to discussions about resistance gene spread in this traditional cheese, providing evidence of potential horizontal transfer of AR genes to human gut microbiota.}, }
@article {pmid29458521, year = {2018}, author = {Mikoulinskaia, GV and Chernyshov, SV and Shavrina, MS and Molochkov, NV and Lysanskaya, VY and Zimin, AA}, title = {Two novel thermally resistant endolysins encoded by pseudo T-even bacteriophages RB43 and RB49.}, journal = {The Journal of general virology}, volume = {99}, number = {3}, pages = {402-415}, doi = {10.1099/jgv.0.001014}, pmid = {29458521}, issn = {1465-2099}, abstract = {Identification and cloning of genes as well as biochemical characterization of the gene products were carried out for two novel endolysins of pseudo T-even lytic bacteriophages RB43 and RB49, which represent different myovirus groups of the subfamily Tevenvirinae. Genes RB43ORF159c and RB49р102 were cloned in E. coli cells, and their products were purified to electrophoretic homogeneity with an up to 80 % yield of total activity. In respect to substrate specificity, both enzymes were found to be lytic l-alanoyl-d-glutamate peptidases belonging to the M15 family. The pH optimum functioning of both endolysins was within the range 7.0-9.0, whereas the optimal values of ionic strength were different for the two proteins (25 mM vs 100 mM for the RB43 and RB49 endolysins respectively). Both peptidases were thermally resistant, with the RB43 endolysin being more stable (it restored 81 % of enzyme activity and 96 % of secondary structure after a 10 min heating at 90 °C) than its RB49 counterpart (27 and 77% respectively). The possible origin of genes of lytic l-alanoyl-d-glutamate peptidases of myoviruses as a result of horizontal transfer in the variable parts of genomes between unrelated phages having a common host is discussed.}, }
@article {pmid29456528, year = {2018}, author = {Poidevin, M and Sato, M and Altinoglu, I and Delaplace, M and Sato, C and Yamaichi, Y}, title = {Mutation in ESBL Plasmid from Escherichia coli O104:H4 Leads Autoagglutination and Enhanced Plasmid Dissemination.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {130}, pmid = {29456528}, issn = {1664-302X}, abstract = {Conjugative plasmids are one of the main driving force of wide-spreading of multidrug resistance (MDR) bacteria. They are self-transmittable via conjugation as carrying the required set of genes and cis-acting DNA locus for direct cell-to-cell transfer. IncI incompatibility plasmids are nowadays often associated with extended-spectrum beta-lactamases producing Enterobacteria in clinic and environment. pESBL-EA11 was isolated from Escherichia coli O104:H4 outbreak strain in Germany in 2011. During the previous study identifying transfer genes of pESBL-EA11, it was shown that transposon insertion at certain DNA region of the plasmid, referred to as Hft, resulted in great enhancement of transfer ability. This suggested that genetic modifications can enhance dissemination of MDR plasmids. Such 'superspreader' mutations have attracted little attention so far despite their high potential to worsen MDR spreading. Present study aimed to gain our understanding on regulatory elements that involved pESBL transfer. While previous studies of IncI plasmids indicated that immediate downstream gene of Hft, traA, is not essential for conjugative transfer, here we showed that overexpression of TraA in host cell elevated transfer rate of pESBL-EA11. Transposon insertion or certain nucleotide substitutions in Hft led strong TraA overexpression which resulted in activation of essential regulator TraB and likely overexpression of conjugative pili. Atmospheric Scanning Electron Microscopy observation suggested that IncI pili are distinct from other types of conjugative pili (such as long filamentous F-type pili) and rather expressed throughout the cell surface. High transfer efficiency in the mutant pESBL-EA11 was involved with hyperpiliation which facilitates cell-to-cell adhesion, including autoagglutination. The capability of plasmids to evolve to highly transmissible mutant is alarming, particularly it might also have adverse effect on host pathogenicity.}, }
@article {pmid29453715, year = {2018}, author = {Gorovtsov, AV and Sazykin, IS and Sazykina, MA}, title = {The influence of heavy metals, polyaromatic hydrocarbons, and polychlorinated biphenyls pollution on the development of antibiotic resistance in soils.}, journal = {Environmental science and pollution research international}, volume = {25}, number = {10}, pages = {9283-9292}, pmid = {29453715}, issn = {1614-7499}, support = {6.2379.2017/PCh//Ministry of Education and Science of the Russian Federation/ ; 17-04-00787 A//Russian Foundation for Basic Research/ ; NSh-3464.2018.11//President of Russian Federation/ ; }, mesh = {Agriculture ; Anti-Bacterial Agents/*analysis ; Bacteria/*chemistry/genetics ; Drug Resistance, Microbial/*genetics ; Environmental Pollution/*analysis ; Gene Transfer, Horizontal ; Genome, Bacterial ; Manure/*analysis ; Metals, Heavy/*analysis/chemistry ; Microbiota/*genetics ; Polychlorinated Biphenyls/*analysis/chemistry ; Soil/*chemistry ; }, abstract = {The minireview is devoted to the analysis of the influence of soil pollution with heavy metals, polyaromatic hydrocarbons (PAHs), and the polychlorinated biphenyls (PCBs) on the distribution of antibiotics resistance genes (ARGs) in soil microbiomes. It is shown that the best understanding of ARGs distribution process requires studying the influence of pollutants on this process in natural microbiocenoses. Heavy metals promote co-selection of genes determining resistance to them together with ARGs in the same mobile elements of a bacterial genome, but the majority of studies focus on agricultural soils enriched with ARGs originating from manure. Studying nonagricultural soils would clear mechanisms of ARGs transfer in natural and anthropogenically transformed environments and highlight the role of antibiotic-producing bacteria. PAHs make a considerable shift in soil microbiomes leading to an increase in the number of Actinobacteria which are the source of antibiotics formation and bear multiple ARGs. The soils polluted with PAHs can be a selective medium for bacteria resistant to antibiotics, and the level of ARGs expression is much higher. PCBs are accumulated in soils and significantly alter the specific structure of soil microbiocenoses. In such soils, representatives of the genera Acinetobacter, Pseudomonas, and Alcanivorax dominate, and the ability to degrade PCBs is connected to horizontal gene transfer (HGT) and high level of genomic plasticity. The attention is also focused on the need to study the properties of the soil having an impact on the bioavailability of pollutants and, as a result, on resistome of soil microorganisms.}, }
@article {pmid29452198, year = {2018}, author = {Wen, S and Feng, D and Lu, Z and Liu, J and Peters, BM and Tang, H and Su, D and Lin, YP and Yang, L and Xu, Z and Shirtliff, ME and Chen, D}, title = {Microbial infection pattern, pathogenic features and resistance mechanism of carbapenem-resistant Gram negative bacilli during long-term hospitalization.}, journal = {Microbial pathogenesis}, volume = {117}, number = {}, pages = {356-360}, doi = {10.1016/j.micpath.2018.02.025}, pmid = {29452198}, issn = {1096-1208}, mesh = {Aged ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics/isolation &amp; purification ; Carbapenem-Resistant Enterobacteriaceae/enzymology/*genetics/*pathogenicity ; China/epidemiology ; Citrobacter freundii/genetics ; Cross Infection/microbiology ; DNA, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli ; Gene Transfer, Horizontal ; Gene-Environment Interaction ; Gram-Negative Bacteria/enzymology/*genetics ; *Hospitalization ; Hospitals ; Humans ; Klebsiella pneumoniae/genetics ; Male ; Microbial Sensitivity Tests ; *Molecular Epidemiology ; Molecular Typing ; Multilocus Sequence Typing ; Plasmids/genetics ; Pseudomonas aeruginosa/genetics ; Virulence Factors/genetics ; beta-Lactamases/*genetics/isolation &amp; purification ; }, abstract = {BACKGROUND: Carbapenem-resistant Gram-negative bacilli (GNB) have become an important cause of nosocomial infections of hospitalized patients.<br><br>METHODS: To investigate the microbial infection patterns and molecular epidemiology characteristics of the carbapenem-resistant GNB isolates from a long-term hospitalized patient, antimicrobial susceptibility testing, phenotypic screening test for carbapenemase production, PCR screening and DNA sequencing of carbapenemase genes, repetitive extragenic palindromic sequence-based PCR (REP-PCR), multilocus sequencing typing (MLST) and genetic environment analysis were performed.<br><br>RESULTS: Twelve strains with carbapenemase genes were detected from 63 carbapenem-resistant isolates, including two blaIMP-25-carrying Pseudomonas aeruginosa, one blaNDM-1-carrying Citrobacter freundii, three blaNDM-1-carrying Klebsiella pneumoniae and six blaKPC-2-carrying K. pneumoniae. Only the blaNDM-1 genes were successfully transferred from three K. pneumoniae strains to Escherichia coli C600 by conjugation. Genetic environment of blaIMP-25, blaNDM-1 and blaKPC-2 genes in our study were consistent with previous reports. Molecular typing of K. pneumoniae performed by MLST revealed that most of the isolates belonged to ST11. blaNDM-1-carrying K. pneumoniae sequencing type 1416 was first reported in our study.<br><br>CONCLUSIONS: Carbapenem-resistant GNB are common pathogens during long-term hospitalization, and ST11 blaKPC-2-carrying K. pneumoniae is the dominant bacterium in our study. Colonization and horizontal transmission of resistance by plasmids of carbapenem-resistant GNB have increased the risks of persistent infection and mortality of long-term hospitalized patients.}, }
@article {pmid29449580, year = {2018}, author = {Nawrocki, EM and Bradshaw, M and Johnson, EA}, title = {Botulinum neurotoxin-encoding plasmids can be conjugatively transferred to diverse clostridial strains.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {3100}, pmid = {29449580}, issn = {2045-2322}, support = {T32 GM007215/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Botulinum Toxins/*genetics/metabolism ; Chromosomes ; Clostridiales/genetics ; Clostridium/genetics ; Clostridium botulinum/*genetics/*metabolism ; DNA Transposable Elements/genetics ; Humans ; Mice ; Phylogeny ; Plasmids/genetics ; }, abstract = {Most Group I Clostridium botulinum strains harbor botulinum neurotoxin (bont) genes on their chromosome, while some carry these genes (including bont/a, bont/b, and bont/f) on large plasmids. Prior work in our laboratory demonstrated that Group I BoNT plasmids were mobilized to C. botulinum recipient strains containing the Tn916 transposon. Here, we show that Tn916 is nonessential for plasmid transfer. Relying on an auxotrophic donor phenotype and a plasmid-borne selectable marker, we observed the transfer of pCLJ, a 270 kb plasmid harboring two bont genes, from its host strain to various clostridia. Transfer frequency was greatest to other Group I C. botulinum strains, but the plasmid was also transferred into traditionally nontoxigenic species, namely C. sporogenes and C. butyricum. Expression and toxicity of BoNT/A4 was confirmed in transconjugants by immunoblot and mouse bioassay. These data indicate that conjugation within the genus Clostridium can occur across physiological Groups of C. botulinum, supporting horizontal gene transfer via bont-bearing plasmids. The transfer of plasmids possessing bont genes to resistant Clostridium spp. such as C. sporogenes could impact biological safety for animals and humans. These plasmids may play an environmental role in initiating death in vertebrates, leading to decomposition and nutrient recycling of animal biomass.}, }
@article {pmid29448332, year = {2018}, author = {Saakian, DB}, title = {Looking for the optimal rate of recombination for evolutionary dynamics.}, journal = {Physical review. E}, volume = {97}, number = {1-1}, pages = {012409}, doi = {10.1103/PhysRevE.97.012409}, pmid = {29448332}, issn = {2470-0053}, mesh = {*Evolution, Molecular ; Genetic Fitness ; *Models, Genetic ; Mutation ; *Recombination, Genetic/physiology ; }, abstract = {We consider many-site mutation-recombination models of evolution with selection. We are looking for situations where the recombination increases the mean fitness of the population, and there is an optimal recombination rate. We found two fitness landscapes supporting such nonmonotonic behavior of the mean fitness versus the recombination rate. The first case is related to the evolution near the error threshold on a neutral-network-like fitness landscape, for moderate genome lengths and large population. The more realistic case is the second one, in which we consider the evolutionary dynamics of a finite population on a rugged fitness landscape (the smooth fitness landscape plus some random contributions to the fitness). We also give the solution to the horizontal gene transfer model in the case of asymmetric mutations. To obtain nonmonotonic behavior for both mutation and recombination, we need a specially designed (ideal) fitness landscape.}, }
@article {pmid29445231, year = {2018}, author = {Eymard-Vernain, E and Luche, S and Rabilloud, T and Lelong, C}, title = {Impact of nanoparticles on the Bacillus subtilis (3610) competence.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {2978}, pmid = {29445231}, issn = {2045-2322}, mesh = {ATP-Binding Cassette Transporters/genetics/metabolism ; Adaptation, Physiological ; Anti-Bacterial Agents/pharmacology ; Bacillus subtilis/*physiology ; Bacterial Proteins/genetics/metabolism ; Biofilms/growth &amp; development ; *DNA Transformation Competence ; Drug Resistance, Microbial/genetics ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Nanoparticles/chemistry/*metabolism ; Titanium/chemistry ; Transformation, Bacterial ; Zinc Oxide/chemistry ; }, abstract = {Due to the physicochemical properties of nanoparticles, the use of nanomaterials increases every year in industrial and medical processes. At the same time, the increasing number of bacteria becoming resistant to many antibiotics, mostly by a horizontal gene transfer process, is a major public health concern. We herein report, for the first time, the role of nanoparticles in the physiological induction of horizontal gene transfer in bacteria. Besides the most well-known impacts of nanoparticles on bacteria, i.e. death or oxidative stress, two nanoparticles, n-ZnO and n-TiO2, significantly and oppositely impact the transformation efficiency of Bacillus subtilis in biofilm growth conditions, by modification of the physiological processes involved in the induction of competence, the first step of transformation. This effect is the consequence of a physiological adaptation rather than a physical cell injury: two oligopeptide ABC transporters, OppABCDF and AppDFABC, are differentially expressed in response to nanoparticles. Interestingly, a third tested nanoparticle, n-Ag, has no significant effect on competence in our experimental conditions. Overall, these results show that nanoparticles, by altering bacterial physiology and especially competence, may have profound influences in unsuspected areas, such as the dissemination of antibiotic resistance in bacteria.}, }
@article {pmid29442448, year = {2018}, author = {Wackett, LP}, title = {Horizontal gene transfer (HGT) in biodegradation: An annotated selection of world wide web sites relevant to the topics in environmental microbiology.}, journal = {Environmental microbiology}, volume = {20}, number = {2}, pages = {920-921}, doi = {10.1111/1462-2920.14052}, pmid = {29442448}, issn = {1462-2920}, }
@article {pmid29441122, year = {2018}, author = {Nøjgaard, N and Geiß, M and Merkle, D and Stadler, PF and Wieseke, N and Hellmuth, M}, title = {Time-consistent reconciliation maps and forbidden time travel.}, journal = {Algorithms for molecular biology : AMB}, volume = {13}, number = {}, pages = {2}, pmid = {29441122}, issn = {1748-7188}, abstract = {BACKGROUND: In the absence of horizontal gene transfer it is possible to reconstruct the history of gene families from empirically determined orthology relations, which are equivalent to event-labeled gene trees. Knowledge of the event labels considerably simplifies the problem of reconciling a gene tree T with a species trees S, relative to the reconciliation problem without prior knowledge of the event types. It is well-known that optimal reconciliations in the unlabeled case may violate time-consistency and thus are not biologically feasible. Here we investigate the mathematical structure of the event labeled reconciliation problem with horizontal transfer.<br><br>RESULTS: We investigate the issue of time-consistency for the event-labeled version of the reconciliation problem, provide a convenient axiomatic framework, and derive a complete characterization of time-consistent reconciliations. This characterization depends on certain weak conditions on the event-labeled gene trees that reflect conditions under which evolutionary events are observable at least in principle. We give an [Formula: see text]-time algorithm to decide whether a time-consistent reconciliation map exists. It does not require the construction of explicit timing maps, but relies entirely on the comparably easy task of checking whether a small auxiliary graph is acyclic. The algorithms are implemented in C++ using the boost graph library and are freely available at https://github.com/Nojgaard/tc-recon.<br><br>SIGNIFICANCE: The combinatorial characterization of time consistency and thus biologically feasible reconciliation is an important step towards the inference of gene family histories with horizontal transfer from orthology data, i.e., without presupposed gene and species trees. The fast algorithm to decide time consistency is useful in a broader context because it constitutes an attractive component for all tools that address tree reconciliation problems.}, }
@article {pmid29440578, year = {2018}, author = {Watson, BNJ and Staals, RHJ and Fineran, PC}, title = {CRISPR-Cas-Mediated Phage Resistance Enhances Horizontal Gene Transfer by Transduction.}, journal = {mBio}, volume = {9}, number = {1}, pages = {}, pmid = {29440578}, issn = {2150-7511}, mesh = {Bacteriolysis ; Bacteriophages/*genetics/growth &amp; development ; *CRISPR-Cas Systems ; Gene Transfer, Horizontal ; Pectobacterium/*genetics/*virology ; *Transduction, Genetic ; }, abstract = {A powerful contributor to prokaryotic evolution is horizontal gene transfer (HGT) through transformation, conjugation, and transduction, which can be advantageous, neutral, or detrimental to fitness. Bacteria and archaea control HGT and phage infection through CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) adaptive immunity. Although the benefits of resisting phage infection are evident, this can come at a cost of inhibiting the acquisition of other beneficial genes through HGT. Despite the ability of CRISPR-Cas to limit HGT through conjugation and transformation, its role in transduction is largely overlooked. Transduction is the phage-mediated transfer of bacterial DNA between cells and arguably has the greatest impact on HGT. We demonstrate that in Pectobacterium atrosepticum, CRISPR-Cas can inhibit the transduction of plasmids and chromosomal loci. In addition, we detected phage-mediated transfer of a large plant pathogenicity genomic island and show that CRISPR-Cas can inhibit its transduction. Despite these inhibitory effects of CRISPR-Cas on transduction, its more common role in phage resistance promotes rather than diminishes HGT via transduction by protecting bacteria from phage infection. This protective effect can also increase transduction of phage-sensitive members of mixed populations. CRISPR-Cas systems themselves display evidence of HGT, but little is known about their lateral dissemination between bacteria and whether transduction can contribute. We show that, through transduction, bacteria can acquire an entire chromosomal CRISPR-Cas system, including cas genes and phage-targeting spacers. We propose that the positive effect of CRISPR-Cas phage immunity on enhancing transduction surpasses the rarer cases where gene flow by transduction is restricted.IMPORTANCE The generation of genetic diversity through acquisition of DNA is a powerful contributor to microbial evolution and occurs through transformation, conjugation, and transduction. Of these, transduction, the phage-mediated transfer of bacterial DNA, is arguably the major route for genetic exchange. CRISPR-Cas adaptive immune systems control gene transfer by conjugation and transformation, but transduction has been mostly overlooked. Our results indicate that CRISPR-Cas can impede, but typically enhances the transduction of plasmids, chromosomal genes, and pathogenicity islands. By limiting wild-type phage replication, CRISPR-Cas immunity increases transduction in both phage-resistant and -sensitive members of mixed populations. Furthermore, we demonstrate mobilization of a chromosomal CRISPR-Cas system containing phage-targeting spacers by generalized transduction, which might partly account for the uneven distribution of these systems in nature. Overall, the ability of CRISPR-Cas to promote transduction reveals an unexpected impact of adaptive immunity on horizontal gene transfer, with broader implications for microbial evolution.}, }
@article {pmid29440568, year = {2018}, author = {Hirt, H and Greenwood-Quaintance, KE and Karau, MJ and Till, LM and Kashyap, PC and Patel, R and Dunny, GM}, title = {Enterococcus faecalis Sex Pheromone cCF10 Enhances Conjugative Plasmid Transfer In Vivo.}, journal = {mBio}, volume = {9}, number = {1}, pages = {}, pmid = {29440568}, issn = {2150-7511}, support = {R01 DK114007/DK/NIDDK NIH HHS/United States ; R35 GM118079/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Carrier State/microbiology ; Conjugation, Genetic/*drug effects ; Enterococcus faecalis/*drug effects/*genetics ; Gene Transfer, Horizontal/*drug effects ; Germ-Free Life ; Gram-Positive Bacterial Infections/microbiology ; Intestines/microbiology ; Mice ; Models, Animal ; Oligopeptides/*metabolism ; Pheromones/deficiency/*metabolism ; *Plasmids ; }, abstract = {Cell-cell communication mediated by peptide pheromones (cCF10 [CF]) is essential for high-frequency plasmid transfer in vitro in Enterococcus faecalis To examine the role of pheromone signaling in vivo, we established either a CF-producing (CF+) recipient or a recipient producing a biologically inactive variant of CF (CF- recipient) in a germfree mouse model 3 days before donor inoculation and determined transfer frequencies of the pheromone-inducible plasmid pCF10. Plasmid transfer was detected in the upper and middle sections of the intestinal tract 5 h after donor inoculation and was highly efficient in the absence of antibiotic selection. The transconjugant/donor ratio reached a maximum level approaching 1 on day 4 in the upper intestinal tract. Plasmid transfer was significantly lower with the CF- recipient. While rescue of the CF- mating defect by coculture with CF+ recipients is easily accomplished in vitro, no extracellular complementation occurred in vivo This suggests that most pheromone signaling in the gut occurs between recipient and donor cells in very close proximity. Plasmid-bearing cells (donors plus transconjugants) steadily increased in the population from 0.1% after donor inoculation to about 10% at the conclusion of the experiments. This suggests a selective advantage of pCF10 carriage distinct from antibiotic resistance or bacteriocin production. Our results demonstrate that pheromone signaling is required for efficient pCF10 transfer in vivo In the absence of CF+ recipients, a low level of transfer to CF- recipients occurred in the gut. This may result from low-level host-mediated induction of the donors in the gastrointestinal (GI) tract, similar to that previously observed in serum.IMPORTANCE Horizontal gene transfer is a major factor in the biology of Enterococcus faecalis, an important nosocomial pathogen. Previous studies showing efficient conjugative plasmid transfer in the gastrointestinal (GI) tracts of experimental animals did not examine how the enterococcal sex pheromone response impacts the efficiency of transfer. Our study demonstrates for the first time pheromone-enhanced, high-frequency plasmid transfer of E. faecalis plasmid pCF10 in a mouse model in the absence of antibiotic or bacteriocin selection. Pheromone production by recipients dramatically increased plasmid transfer in germfree mice colonized initially with recipients, followed by donors. The presence of a coresident community of common gut microbes did not significantly reduce in vivo plasmid transfer between enterococcal donors and recipients. In mice colonized with enterococcal recipients, we detected plasmid transfer in the intestinal tract within 5 h of addition of donors, before transconjugants could be cultured from feces. Surprisingly, pCF10 carriage provided a competitive fitness advantage unrelated to antibiotic resistance or bacteriocin production.}, }
@article {pmid29439501, year = {2018}, author = {Zhao, N and Wang, Y and Hua, J}, title = {The Roles of Mitochondrion in Intergenomic Gene Transfer in Plants: A Source and a Pool.}, journal = {International journal of molecular sciences}, volume = {19}, number = {2}, pages = {}, pmid = {29439501}, issn = {1422-0067}, mesh = {Evolution, Molecular ; *Gene Pool ; *Gene Transfer, Horizontal ; *Genome, Mitochondrial ; *Genome, Plant ; Plants/genetics ; }, abstract = {Intergenomic gene transfer (IGT) is continuous in the evolutionary history of plants. In this field, most studies concentrate on a few related species. Here, we look at IGT from a broader evolutionary perspective, using 24 plants. We discover many IGT events by assessing the data from nuclear, mitochondrial and chloroplast genomes. Thus, we summarize the two roles of the mitochondrion: a source and a pool. That is, the mitochondrion gives massive sequences and integrates nuclear transposons and chloroplast tRNA genes. Though the directions are opposite, lots of likenesses emerge. First, mitochondrial gene transfer is pervasive in all 24 plants. Second, gene transfer is a single event of certain shared ancestors during evolutionary divergence. Third, sequence features of homologies vary for different purposes in the donor and recipient genomes. Finally, small repeats (or micro-homologies) contribute to gene transfer by mediating recombination in the recipient genome.}, }
@article {pmid29438383, year = {2018}, author = {Schwarz, D and Adato, O and Horovitz, A and Unger, R}, title = {Comparative genomic analysis of mollicutes with and without a chaperonin system.}, journal = {PloS one}, volume = {13}, number = {2}, pages = {e0192619}, pmid = {29438383}, issn = {1932-6203}, mesh = {Chaperonins/*metabolism ; Codon ; Escherichia coli/*genetics ; Escherichia coli Proteins/*genetics ; *Genome, Bacterial ; Heat-Shock Proteins/*genetics ; Phylogeny ; Tenericutes/*genetics ; }, abstract = {The GroE chaperonin system, which comprises GroEL and GroES, assists protein folding in vivo and in vitro. It is conserved in all prokaryotes except in most, but not all, members of the class of mollicutes. In Escherichia coli, about 60 proteins were found to be obligatory clients of the GroE system. Here, we describe the properties of the homologs of these GroE clients in mollicutes and the evolution of chaperonins in this class of bacteria. Comparing the properties of these homologs in mollicutes with and without chaperonins enabled us to search for features correlated with the presence of GroE. Interestingly, no sequence-based features of proteins such as average length, amino acid composition and predicted folding/disorder propensity were found to be affected by the absence of GroE. Other properties such as genome size and number of proteins were also found to not differ between mollicute species with and without GroE. Our data suggest that two clades of mollicutes re-acquired the GroE system, thereby supporting the view that gaining the system occurred polyphyletically and not monophyletically, as previously debated. Our data also suggest that there might have been three isolated cases of lateral gene transfer from specific bacterial sources. Taken together, our data indicate that loss of GroE does not involve crossing a high evolutionary barrier and can be compensated for by a small number of changes within the few dozen client proteins.}, }
@article {pmid29437921, year = {2018}, author = {Schniete, JK and Cruz-Morales, P and Selem-Mojica, N and Fernández-Martínez, LT and Hunter, IS and Barona-Gómez, F and Hoskisson, PA}, title = {Expanding Primary Metabolism Helps Generate the Metabolic Robustness To Facilitate Antibiotic Biosynthesis in Streptomyces.}, journal = {mBio}, volume = {9}, number = {1}, pages = {}, pmid = {29437921}, issn = {2150-7511}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Anti-Bacterial Agents/*biosynthesis ; Gene Duplication ; Gene Expression ; Kinetics ; Metabolic Networks and Pathways/*genetics ; Multigene Family ; Pyruvate Kinase/genetics/metabolism ; Streptomyces coelicolor/*genetics/*metabolism ; }, abstract = {The expansion of the genetic repertoire of an organism by gene duplication or horizontal gene transfer (HGT) can aid adaptation. Streptomyces bacteria are prolific producers of bioactive specialized metabolites that have adaptive functions in nature and have found extensive utility in human medicine. While the biosynthesis of these specialized metabolites is directed by dedicated biosynthetic gene clusters, little attention has been focused on how these organisms have evolved robustness in their genomes to facilitate the metabolic plasticity required to provide chemical precursors for biosynthesis during the complex metabolic transitions from vegetative growth to specialized metabolite production and sporulation. Here, we examine genetic redundancy in actinobacteria and show that specialized metabolite-producing bacterial families exhibit gene family expansion in primary metabolism. Focusing on a gene duplication event, we show that the two pyruvate kinases in the genome of Streptomyces coelicolor arose by an ancient duplication event and that each has evolved altered enzymatic kinetics, with Pyk1 having a 20-fold-higher kcat than Pyk2 (4,703 s[-1] compared to 215 s[-1], respectively), and yet both are constitutively expressed. The pyruvate kinase mutants were also found to be compromised in terms of fitness compared to wild-type Streptomyces These data suggest that expanding gene families can help maintain cell functionality during metabolic perturbation such as nutrient limitation and/or specialized metabolite production.IMPORTANCE The rise of antimicrobial-resistant infections has prompted a resurgence in interest in understanding the production of specialized metabolites, such as antibiotics, by Streptomyces The presence of multiple genes encoding the same enzymatic function is an aspect of Streptomyces biology that has received little attention; however, understanding how the metabolic expansion influences these organisms can help enhance production of clinically useful molecules. Here, we show that expanding the number of pyruvate kinases enables metabolic adaptation, increases strain fitness, and represents an excellent target for metabolic engineering of industrial specialized metabolite-producing bacteria and the activation of cryptic specialized metabolites.}, }
@article {pmid29437851, year = {2018}, author = {Breuer, RJ and Hirt, H and Dunny, GM}, title = {Mechanistic Features of the Enterococcal pCF10 Sex Pheromone Response and the Biology of Enterococcus faecalis in Its Natural Habitat.}, journal = {Journal of bacteriology}, volume = {200}, number = {14}, pages = {}, pmid = {29437851}, issn = {1098-5530}, support = {R01 AI122742/AI/NIAID NIH HHS/United States ; R35 GM118079/GM/NIGMS NIH HHS/United States ; T32 GM008347/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/*metabolism ; Conjugation, Genetic/*physiology ; Enterococcus faecalis/genetics/*metabolism ; Gene Expression Regulation, Bacterial/physiology ; Gene Transfer, Horizontal/*genetics ; Plasmids ; }, abstract = {Conjugative transfer of plasmids in enterococci is promoted by intercellular communication using peptide pheromones. The regulatory mechanisms that control transfer have been extensively studied in vitro However, the complicated systems that regulate the spread of these plasmids did not evolve in the laboratory test tube, and remarkably little is known about this form of signaling in the intestinal tract, the primary niche of these organisms. Because the evolution of Enterococcus faecalis strains and their coresident pheromone-inducible plasmids, such as pCF10, have occurred in the gastrointestinal (GI) tract, it is important to consider the functions controlled by pheromones in light of this ecology. This review summarizes our current understanding of the pCF10-encoded pheromone response. We consider how selective pressures in the natural environment may have selected for the complex and very tightly regulated systems controlling conjugation, and we pay special attention to the ecology of enterococci and the pCF10 plasmid as a gut commensal. We summarize the results of recent studies of the pheromone response at the single-cell level, as well as those of the first experiments demonstrating a role for pheromone signaling in plasmid transfer and in GI tract competitive fitness. These results will serve as a foundation for further in vivo studies that could lead to novel interventions to reduce opportunistic infections and the spread of antibiotic resistance.}, }
@article {pmid29435265, year = {2018}, author = {Liu, B and Wu, H and Zhai, Y and He, Z and Sun, H and Cai, T and He, D and Liu, J and Wang, S and Pan, Y and Yuan, L and Hu, G}, title = {Prevalence and molecular characterization of oqxAB in clinical Escherichia coli isolates from companion animals and humans in Henan Province, China.}, journal = {Antimicrobial resistance and infection control}, volume = {7}, number = {}, pages = {18}, pmid = {29435265}, issn = {2047-2994}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Cats ; China/epidemiology ; Ciprofloxacin/pharmacology ; Conjugation, Genetic ; Dogs ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/drug effects/*genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; Genes, MDR/*genetics ; Humans ; Microbial Sensitivity Tests ; *Molecular Epidemiology ; Multilocus Sequence Typing ; Pets/*microbiology ; Phylogeny ; Plasmids ; Prevalence ; }, abstract = {BACKGROUND: The plasmid-encoded multidrug efflux pump oqxAB confers bacterial resistance primarily to olaquindox, quinolones, and chloramphenicol. The aims of this study were to investigate the prevalence of oqxAB among Escherichia coli isolates from dogs, cats, and humans in Henan, China and the susceptibilities of E. coli isolates to common antibiotics.<br><br>METHODS: From 2012 to 2014, a total of 600 samples which included 400 rectal samples and 200 clinical human specimens were tested for the presence of E. coli. All isolates were screened for oqxAB genes by PCR and sequencing. The MICs of 11 antimicrobial agents were determined by the broth microdilution method. A total of 30 representative oqxAB-positive isolates were subjected to ERIC-PCR and MLST. Additionally, conjugation experiments and southern hybridizations were performed.<br><br>RESULTS: Of 270 isolates, 58.5% (62/106) of the isolates from dogs, 56.25% (36/64) of the isolates from cats, and 42.0% (42/100) of the isolates from humans were positive for the oqxAB. Olaquindox resistance was found for 85.7%-100% of oqxAB-positive isolates. Of oqxAB-positive isolates from dogs, cats, and humans, ciprofloxacin resistance was inspected for 85.8%, 59.1%, and 93.8%, respectively. Several oqxAB-positive isolates were demonstrated by ERIC-PCR and MLST, and have high similarity. Phylogenetic analysis showed that oqxAB-positive isolates could be divided into 7 major clusters. OqxAB-positive conjugants were obtained, southern hybridization verified that the oqxAB gene complex was primarily located on plasmids.<br><br>CONCLUSION: In conclusion, oqxAB-positive isolates were widespread in animals and humans in Henan, China. Carriage of oqxAB on plasmids of E. coli isolates may facilitate the emergence of multidrug resistant and its transmission via horizontal transfer, and might pose a potential threat to public health.}, }
@article {pmid29433445, year = {2018}, author = {Lin, H and Yu, M and Wang, X and Zhang, XH}, title = {Comparative genomic analysis reveals the evolution and environmental adaptation strategies of vibrios.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {135}, pmid = {29433445}, issn = {1471-2164}, support = {41730530//National Natural Science Foundation of China/International ; 41476112//National Natural Science Foundation of China/International ; 41521064//National Natural Science Foundation of China/International ; 41506154//National Natural Science Foundation of China/International ; }, mesh = {Adaptation, Physiological/*genetics ; *Evolution, Molecular ; Genetic Variation ; Genome, Bacterial/*genetics ; Genomics/*methods ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Seawater/microbiology ; Species Specificity ; Vibrio/classification/*genetics ; }, abstract = {BACKGROUND: Vibrios are among the most diverse and ecologically important marine bacteria, which have evolved many characteristics and lifestyles to occupy various niches. The relationship between genome features and environmental adaptation strategies is an essential part for understanding the ecological functions of vibrios in the marine system. The advent of complete genome sequencing technology has provided an important method of examining the genetic characteristics of vibrios on the genomic level.<br><br>RESULTS: Two Vibrio genomes were sequenced and found to occupy many unique orthologues families which absent from the previously genes pool of the complete genomes of vibrios. Comparative genomics analysis found vibrios encompass a steady core-genome and tremendous pan-genome with substantial gene gain and horizontal gene transfer events in the evolutionary history. Evolutionary analysis based on the core-genome tree suggested that V. fischeri emerged ~&#x2009;385 million years ago, along with the occurrence of cephalopods and the flourish of fish. The relatively large genomes, the high number of 16S rRNA gene copies, and the presence of R-M systems and CRISPR system help vibrios live in various marine environments. Chitin-degrading related genes are carried in nearly all the Vibrio genomes. The number of chitinase genes in vibrios has been extremely expanded compared to which in the most recent ancestor of the genus. The chitinase A genes were estimated to have evolved along with the genus, and have undergone significant purifying selective force to conserve the ancestral state.<br><br>CONCLUSIONS: Vibrios have experienced extremely genome expansion events during their evolutionary history, allowing them to develop various functions to spread globally. Despite their close phylogenetic relationships, vibrios were found to have a tremendous pan-genome with a steady core-genome, which indicates the highly plastic genome of the genus. Additionally, the existence of various chitin-degrading related genes and the expansion of chitinase A in the genus demonstrate the importance of the chitin utilization for vibrios. Defensive systems in the Vibrio genomes may protect them from the invasion of external DNA. These genomic features investigated here provide a better knowledge of how the evolutionary process has forged Vibrio genomes to occupy various niches.}, }
@article {pmid29428509, year = {2018}, author = {Sahoo, RK and Lohman, DJ and Wahlberg, N and Müller, CJ and Brattström, O and Collins, SC and Peggie, D and Aduse-Poku, K and Kodandaramaiah, U}, title = {Evolution of Hypolimnas butterflies (Nymphalidae): Out-of-Africa origin and Wolbachia-mediated introgression.}, journal = {Molecular phylogenetics and evolution}, volume = {123}, number = {}, pages = {50-58}, doi = {10.1016/j.ympev.2018.02.001}, pmid = {29428509}, issn = {1095-9513}, mesh = {Africa ; Animals ; Base Sequence ; Bayes Theorem ; Biodiversity ; *Biological Evolution ; Butterflies/*genetics/*microbiology ; DNA, Mitochondrial/genetics ; Haplotypes/genetics ; Larva/physiology ; Likelihood Functions ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; Wolbachia/*physiology ; }, abstract = {Hypolimnas butterflies (Nymphalidae), commonly known as eggflies, are a popular model system for studying a wide range of ecological questions including mimicry, polymorphism, wing pattern evolution, and Wolbachia-host interactions. The lack of a time-calibrated phylogeny for this group has precluded understanding its evolutionary history. We reconstruct a species-level phylogeny using a nine gene dataset and estimate species divergence times. Based on the resulting tree, we investigate the taxon's historical biogeography, examine the evolution of host plant preferences, and test the hypothesis that the endosymbiotic bacterium Wolbachia mediates gene transfer between species. Our analyses indicate that the species are grouped within three strongly supported, deeply divergent clades. However, relationships among these three clades are uncertain. In addition, many Hypolimnas species are not monophyletic or monophyletic with weak support, suggesting widespread incomplete lineage sorting and/or introgression. Biogeographic analysis strongly indicates that the genus diverged from its ancestor in Africa and subsequently dispersed to Asia; the strength of this result is not affected by topological uncertainties. While the larvae of African species feed almost exclusively on Urticaceae, larvae of species found further east often feed on several additional families. Interestingly, we found an identical mitochondrial haplotype in two Hypolimnas species, H. bolina and H. alimena, and a strong association between this mitotype and the Wolbachia strain wBol1a. Future investigations should explore the plausibility of Wolbachia-mediated introgression between species.}, }
@article {pmid29428457, year = {2018}, author = {Alonso, CA and Cortés-Cortés, G and Maamar, E and Massó, M and Rocha-Gracia, RDC and Torres, C and Centrón, D and Quiroga, MP}, title = {Molecular diversity and conjugal transferability of class 2 integrons among Escherichia coli isolates from food, animal and human sources.}, journal = {International journal of antimicrobial agents}, volume = {51}, number = {6}, pages = {905-911}, doi = {10.1016/j.ijantimicag.2018.02.001}, pmid = {29428457}, issn = {1872-7913}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Base Sequence ; Conjugation, Genetic/*genetics ; DNA, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/*genetics/isolation &amp; purification ; Gene Transfer, Horizontal/*genetics ; Humans ; Integrons/*genetics ; Multilocus Sequence Typing ; Red Meat/microbiology ; }, abstract = {Integrons are genetic platforms able to excise, integrate and express antibiotic resistance gene cassettes (GCs). Here we investigated the complete genetic organisation, genetic environment, location and conjugative transferability of a collection of class 2 integrons carried by Escherichia coli strains from different sources (poultry/pork meat, animals and humans). PCR cartography was conducted to determine the genetic arrangement of the integrons, their physical linkage to Tn7 and chromosomal insertion at the attTn7 site. Clonal relatedness of specific isolates was determined by MLST and DO-PCR. Transferability of class 2 integrons was tested by conjugation. The resulting transconjugants were characterised by antimicrobial resistance genotyping, S1-PFGE and replicon typing. Although a limited diversity of GCs was shown, a high percentage of novel structures was identified owing to the integration of insertion sequence (IS) elements at different sites (IS3/IS4/IS5/IS21 families). Insertion of IS10 in the attI2 site of a class 2 integron, between Pc2B and Pc2C promoters, was likely mediated by a site-specific transposition event. Chromosomal insertion of integrons at attTn7 was confirmed in 80% of the isolates. Conjugation experiments demonstrated that 29% of class 2 integrons could be mobilised to E. coli CHS26, demonstrating that they can be located in conjugative/mobilisable elements at a low frequency. Reported structures evidence how class 2 integrons have evolved by the activity of integron integrases and the invasion of ISs. Since most of them are chromosomally located, dispersion is predominantly vertical, although conjugation events also contribute to the spread of class 2 integrons among bacterial communities.}, }
@article {pmid29428427, year = {2018}, author = {Poey, ME and Laviña, M}, title = {Horizontal transfer of class 1 integrons from uropathogenic Escherichia coli to E. coli K12.}, journal = {Microbial pathogenesis}, volume = {117}, number = {}, pages = {16-22}, doi = {10.1016/j.micpath.2018.02.006}, pmid = {29428427}, issn = {1096-1208}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Carrier Proteins/genetics ; Conjugation, Genetic ; Dihydropteroate Synthase/genetics ; Drug Resistance, Bacterial/genetics ; Escherichia coli K12/*genetics ; Escherichia coli Proteins/genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Integrons/*genetics ; Microbial Sensitivity Tests ; Transduction, Genetic ; Uropathogenic Escherichia coli/*genetics ; }, abstract = {Class 1 integrons are genetic elements that carry a variable set of antibiotic resistance genes, being frequently found in clinical Gram-negative isolates. It is generally assumed that they easily spread horizontally among bacteria, thus contributing to the appearance of multidrug resistant clones. However, there are few experimental studies on the lateral transfer of these elements performed with bacterial collections that had been gathered following an epidemiological design. In this work, a collection with these characteristics, comprising uropathogenic Escherichia coli (UPEC) isolates bearing class 1 integrons, was employed to study the horizontal transfer of the integron to an E. coli K12 strain by means of conjugation and transduction experiments. Donor and resultant strains were characterized for their antibiotic resistances, presence of sul1, sul2 and sul3 genes, integron cassette arrays, plasmid replicons and tra region. Conjugation assays were carried out using 45 UPEC isolates as integron donors and transconjugants were obtained in 18 cases (40%). P1-transduction experiments only added the integron transfer from a single donor isolate. Thus, a collection of E. coli K12 strains carrying the class 1 integron from 19 UPEC isolates was generated. In all cases, the integron was co-transferred with at least one low-copy-number plasmid, generally of the F replicon type. Several variables were searched for that could be related to the ability to horizontally transfer the integron. Although no strict correlation was observed, the phylogenetic background of the donor strain and the presence of the sul2 gene appeared as candidates to influence the process. Therefore, there appears that besides being carried by mobile genetic elements, class 1 integrons may be influenced by other factors to accomplish their horizontal transfer, a topic that requires further studies.}, }
@article {pmid29416569, year = {2018}, author = {Delahay, RM and Croxall, NJ and Stephens, AD}, title = {Phylogeographic diversity and mosaicism of the Helicobacter pylori tfs integrative and conjugative elements.}, journal = {Mobile DNA}, volume = {9}, number = {}, pages = {5}, pmid = {29416569}, issn = {1759-8753}, support = {G0901104/MRC_/Medical Research Council/United Kingdom ; }, abstract = {BACKGROUND: The genome of the gastric pathogen Helicobacter pylori is characterised by considerable variation of both gene sequence and content, much of which is contained within three large genomic islands comprising the cag pathogenicity island (cagPAI) and two mobile integrative and conjugative elements (ICEs) termed tfs3 and tfs4. All three islands are implicated as virulence factors, although whereas the cagPAI is well characterised, understanding of how the tfs elements influence H. pylori interactions with different human hosts is significantly confounded by limited definition of their distribution, diversity and structural representation in the global H. pylori population.<br><br>RESULTS: To gain a global perspective of tfs ICE population dynamics we established a bioinformatics workflow to extract and precisely define the full tfs pan-gene content contained within a global collection of 221 draft and complete H. pylori genome sequences. Complete (ca. 35-55kbp) and remnant tfs ICE clusters were reconstructed from a dataset comprising >&#x2009;12,000 genes, from which orthologous gene complements and distinct alleles descriptive of different tfs ICE types were defined and classified in comparative analyses. The genetic variation within defined ICE modular segments was subsequently used to provide a complete description of tfs ICE diversity and a comprehensive assessment of their phylogeographic context. Our further examination of the apparent ICE modular types identified an ancient and complex history of ICE residence, mobility and interaction within particular H. pylori phylogeographic lineages and further, provided evidence of both contemporary inter-lineage and inter-species ICE transfer and displacement.<br><br>CONCLUSIONS: Our collective results establish a clear view of tfs ICE diversity and phylogeographic representation in the global H. pylori population, and provide a robust contextual framework for elucidating the functional role of the tfs ICEs particularly as it relates to the risk of gastric disease associated with different tfs ICE genotypes.}, }
@article {pmid29411913, year = {2018}, author = {Hogg, DW and Chen, Y and D'Aquila, AL and Xu, M and Husić, M and Tan, LA and Bull, C and Lovejoy, DA}, title = {A novel role of the corticotrophin-releasing hormone regulating peptide, teneurin C-terminal associated peptide 1, on glucose uptake into the brain.}, journal = {Journal of neuroendocrinology}, volume = {30}, number = {4}, pages = {e12579}, doi = {10.1111/jne.12579}, pmid = {29411913}, issn = {1365-2826}, mesh = {Animals ; Biological Transport/drug effects ; Blood Glucose ; Brain/diagnostic imaging/*drug effects/metabolism ; Cell Line ; Functional Neuroimaging ; Glucagon/blood ; Glucose/*metabolism ; Hypothalamus/cytology/drug effects/metabolism ; Insulin/blood ; Neurons/cytology/*drug effects/metabolism ; Peptides/*pharmacology ; Phosphorylation/drug effects ; Positron-Emission Tomography ; Rats ; Rats, Wistar ; Signal Transduction/drug effects ; }, abstract = {Teneurin C-terminal associated peptide (TCAP) is an ancient paracrine signalling agent that evolved via lateral gene transfer from prokaryotes into an early metazoan ancestor. Although it bears structural similarity to corticotrophin-releasing hormone (CRH), it inhibits the in vivo actions of CRH. The TCAPs are highly expressed in neurones, where they induce rapid cytoskeletal rearrangement and are neuroprotective. Because these processes are highly energy-dependent, this suggests that TCAP has the potential to regulate glucose uptake because glucose is the primary energy substrate in brain, and neurones require a steady supply to meet the high metabolic demands of neuronal communication. Therefore, the objective of the present study was to assess the effect of TCAP-mediated glucose uptake in the brain and in neuronal cell models. TCAP-mediated [18] F-deoxyglucose (FDG) uptake into brain tissue was assessed in male wild-type Wistar rats by functional positron emission tomography. TCAP-1 increased FDG uptake by over 40% into cortical regions of the brain, demonstrating that TCAP-1 can significantly enhance glucose supply. Importantly, a single nanomolar injection of TCAP-1 increased brain glucose after 3 days and decreased blood glucose after 1 week. This is corroborated by a decreased serum concentration of insulin and an increased serum concentration of glucagon. In immortalised hypothalamic neurones, TCAP-1 increased ATP production and enhanced glucose uptake by increasing glucose transporter recruitment to the plasma membrane likely via AKT and mitogen-activated protein kinase/ERK phosphorylation events. Taken together, these data demonstrate that TCAP-1 increases glucose metabolism in neurones, and may represent a peptide signalling agent that regulated glucose uptake before insulin and related peptides.}, }
@article {pmid29411500, year = {2018}, author = {Arjona-Lopez, JM and Telengech, P and Jamal, A and Hisano, S and Kondo, H and Yelin, MD and Arjona-Girona, I and Kanematsu, S and Lopez-Herrera, CJ and Suzuki, N}, title = {Novel, diverse RNA viruses from Mediterranean isolates of the phytopathogenic fungus, Rosellinia necatrix: insights into evolutionary biology of fungal viruses.}, journal = {Environmental microbiology}, volume = {20}, number = {4}, pages = {1464-1483}, doi = {10.1111/1462-2920.14065}, pmid = {29411500}, issn = {1462-2920}, mesh = {Base Sequence ; Biological Evolution ; Fungal Viruses/*genetics ; Gene Transfer, Horizontal/genetics ; Mediterranean Region ; RNA Viruses/*genetics ; RNA, Double-Stranded ; Sequence Analysis, RNA ; Xylariales/*virology ; }, abstract = {To reveal mycovirus diversity, we conducted a search of as-yet-unexplored Mediterranean isolates of the phytopathogenic ascomycete Rosellinia necatrix for virus infections. Of seventy-nine, eleven fungal isolates tested RNA virus-positive, with many showing coinfections, indicating a virus incidence of 14%, which is slightly lower than that (approximately 20%) previously reported for extensive surveys of over 1000 Japanese R. necatrix isolates. All viral sequences were fully or partially characterized by Sanger and next-generation sequencing. These sequences appear to represent isolates of various new species spanning at least 6 established or previously proposed families such as Partiti-, Hypo-, Megabirna-, Yado-kari-, Fusagra- and Fusarividae, as well as a newly proposed family, Megatotiviridae. This observation greatly expands the diversity of R. necatrix viruses, because no hypo-, fusagra- or megatotiviruses were previously reported from R. necatrix. The sequence analyses showed a rare horizontal gene transfer event of the 2A-like protease domain between a dsRNA (phlegivirus) and a positive-sense, single-stranded RNA virus (hypovirus). Moreover, many of the newly detected viruses showed the closest relation to viruses reported from fungi other than R. necatrix, such as Fusarium spp., which are sympatric to R. necatrix. These combined results imply horizontal virus transfer between these soil-inhabitant fungi.}, }
@article {pmid29410400, year = {2018}, author = {Porse, A and Schou, TS and Munck, C and Ellabaan, MMH and Sommer, MOA}, title = {Biochemical mechanisms determine the functional compatibility of heterologous genes.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {522}, pmid = {29410400}, issn = {2041-1723}, mesh = {Bacterial Proteins/*genetics/metabolism ; Databases, Genetic ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Open Reading Frames ; *Phylogeny ; }, abstract = {Elucidating the factors governing the functional compatibility of horizontally transferred genes is important to understand bacterial evolution, including the emergence and spread of antibiotic resistance, and to successfully engineer biological systems. In silico efforts and work using single-gene libraries have suggested that sequence composition is a strong barrier for the successful integration of heterologous genes. Here we sample 200 diverse genes, representing >80% of sequenced antibiotic resistance genes, to interrogate the factors governing genetic compatibility in new hosts. In contrast to previous work, we find that GC content, codon usage, and mRNA-folding energy are of minor importance for the compatibility of mechanistically diverse gene products at moderate expression. Instead, we identify the phylogenetic origin, and the dependence of a resistance mechanism on host physiology, as major factors governing the functionality and fitness of antibiotic resistance genes. These findings emphasize the importance of biochemical mechanism for heterologous gene compatibility, and suggest physiological constraints as a pivotal feature orienting the evolution of antibiotic resistance.}, }
@article {pmid29408405, year = {2018}, author = {Wang, H and Park, BS and Lim, WA and Ki, JS}, title = {CpMCA, a novel metacaspase gene from the harmful dinoflagellate Cochlodinium polykrikoides and its expression during cell death.}, journal = {Gene}, volume = {651}, number = {}, pages = {70-78}, doi = {10.1016/j.gene.2018.02.002}, pmid = {29408405}, issn = {1879-0038}, mesh = {Caspases/*genetics ; Cell Death/drug effects/genetics ; DNA, Complementary ; DNA, Protozoan ; Dinoflagellida/drug effects/enzymology/*genetics ; Gene Expression ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genes, Protozoan ; Herbicides/pharmacology ; Phylogeny ; Sequence Analysis, DNA ; Transcription, Genetic/drug effects ; }, abstract = {Metacaspases (MCAs) are cysteine proteases that share sequence homology with caspases, and may play roles in programmed cell death (PCD). In the present study, we identified a novel MCA gene (CpMCA) from the red tide dinoflagellate Cochlodinium polykrikoides, and examined its molecular characteristics and gene expression in response to algicide-induced cell death. CpMCA cDNA is 1164 bp in length, containing a dinoflagellate spliced leader sequence (dinoSL), an 879-bp open reading frame (ORF), which codes for a 293-aa protein, and a poly (A) tail. Multi-sequence comparison indicated that CpMCA belongs to type I MCA, but it has a different structure at the N-terminal. Phylogenetic analysis showed that C. polykrikoides may have acquired the MCA gene from bacteria by means of horizontal gene transfer (HGT). In addition, expressions of CpMCA significantly increased following exposure to the common algicides copper sulfate and oxidizing chlorine, which trigger cell death in dinoflagellates, suggesting that CpMCA may be involved in cell death.}, }
@article {pmid29407274, year = {2018}, author = {Lin, YT and Hung, WC and Tsai, JC and Leong, KH and Chen, HJ and Hsueh, PR and Teng, LJ}, title = {Wide dissemination of SCCfusC in fusidic acid-resistant coagulase-negative staphylococci and implication for its spread to methicillin-resistant staphylococcus aureus in Taiwan.}, journal = {International journal of antimicrobial agents}, volume = {51}, number = {6}, pages = {875-880}, doi = {10.1016/j.ijantimicag.2018.01.020}, pmid = {29407274}, issn = {1872-7913}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics ; Drug Resistance, Bacterial/*genetics ; Fusidic Acid/*pharmacology ; Gene Transfer, Horizontal/*genetics ; Humans ; Methicillin-Resistant Staphylococcus aureus/*drug effects/*genetics/isolation &amp; purification ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Staphylococcus capitis/drug effects/genetics/isolation &amp; purification ; Staphylococcus epidermidis/drug effects/genetics/isolation &amp; purification ; Staphylococcus haemolyticus/drug effects/genetics/isolation &amp; purification ; Staphylococcus hominis/drug effects/*genetics/isolation &amp; purification ; Taiwan ; }, abstract = {The fusidic acid (FUS) resistance determinants fusB, fusC, fusD and fusF in coagulase-negative staphylococci (CoNS) clinical isolates were examined. Among 208 FUS-resistant isolates, the fusB gene was the most common resistance determinant in each species, except in Staphylococcus hominis subsp. hominis or in species carrying intrinsic fusD or fusF. In S. hominis subsp. hominis, the fusC gene was the major determinant responsible for FUS resistance. To understand the genetic context of fusC in S. hominis subsp. hominis, 31 fusC-positive S. hominis subsp. hominis isolates were examined. Among these isolates, 14 carried SCCfusC, 3 carried an SCC476-like element and 7 carried a new SCC structure (SCC3390). As shown by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) analyses, the S. hominis subsp. hominis clinical isolates showed limited clonality. Taken together, SCCfusC has been found in S. hominis subsp. hominis, Staphylococcus epidermidis, Staphylococcus haemolyticus, Staphylococcus capitis subsp. ureolyticus and Staphylococcus aureus, suggesting its wide distribution and spread among different species of staphylococci.}, }
@article {pmid29406971, year = {2018}, author = {Medernach, RL and Logan, LK}, title = {The Growing Threat of Antibiotic Resistance in Children.}, journal = {Infectious disease clinics of North America}, volume = {32}, number = {1}, pages = {1-17}, pmid = {29406971}, issn = {1557-9824}, support = {K08 AI112506/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/enzymology/genetics ; Child ; Child, Preschool ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal ; Gram-Positive Bacteria/drug effects/genetics ; Humans ; Infant ; Public Health ; beta-Lactamases/biosynthesis/drug effects/genetics/isolation &amp; purification ; }, abstract = {Antimicrobial resistance is a global public health threat and a danger that continues to escalate. These menacing bacteria are having an impact on all populations; however, until recently, the increasing trend in drug-resistant infections in infants and children has gone relatively unrecognized. This article highlights the current clinical and molecular data regarding infection with antibiotic-resistant bacteria in children, with an emphasis on transmissible resistance and spread via horizontal gene transfer.}, }
@article {pmid29405325, year = {2018}, author = {Boto, L}, title = {Are There Really Too Many Eukaryote LGTs? A Reply To William Martin.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {40}, number = {3}, pages = {}, doi = {10.1002/bies.201800001}, pmid = {29405325}, issn = {1521-1878}, mesh = {*Eukaryota ; *Eukaryotic Cells ; Gene Transfer, Horizontal ; }, }
@article {pmid29404424, year = {2018}, author = {Mortimer, TD and Weber, AM and Pepperell, CS}, title = {Signatures of Selection at Drug Resistance Loci in Mycobacterium tuberculosis.}, journal = {mSystems}, volume = {3}, number = {1}, pages = {}, pmid = {29404424}, issn = {2379-5077}, support = {R01 AI113287/AI/NIAID NIH HHS/United States ; T32 GM007215/GM/NIGMS NIH HHS/United States ; T32 HG000040/HG/NHGRI NIH HHS/United States ; }, abstract = {Tuberculosis (TB) is the leading cause of death by an infectious disease, and global TB control efforts are increasingly threatened by drug resistance in Mycobacterium tuberculosis. Unlike most bacteria, where lateral gene transfer is an important mechanism of resistance acquisition, resistant M. tuberculosis arises solely by de novo chromosomal mutation. Using whole-genome sequencing data from two natural populations of M. tuberculosis, we characterized the population genetics of known drug resistance loci using measures of diversity, population differentiation, and convergent evolution. We found resistant subpopulations to be less diverse than susceptible subpopulations, consistent with ongoing transmission of resistant M. tuberculosis. A subset of resistance genes ("sloppy targets") were characterized by high diversity and multiple rare variants; we posit that a large genetic target for resistance and relaxation of purifying selection contribute to high diversity at these loci. For "tight targets" of selection, the path to resistance appeared narrower, evidenced by single favored mutations that arose numerous times in the phylogeny and segregated at markedly different frequencies in resistant and susceptible subpopulations. These results suggest that diverse genetic architectures underlie drug resistance in M. tuberculosis and that combined approaches are needed to identify causal mutations. Extrapolating from patterns observed for well-characterized genes, we identified novel candidate variants involved in resistance. The approach outlined here can be extended to identify resistance variants for new drugs, to investigate the genetic architecture of resistance, and when phenotypic data are available, to find candidate genetic loci underlying other positively selected traits in clonal bacteria. IMPORTANCEMycobacterium tuberculosis, the causative agent of tuberculosis (TB), is a significant burden on global health. Antibiotic treatment imposes strong selective pressure on M. tuberculosis populations. Identifying the mutations that cause drug resistance in M. tuberculosis is important for guiding TB treatment and halting the spread of drug resistance. Whole-genome sequencing (WGS) of M. tuberculosis isolates can be used to identify novel mutations mediating drug resistance and to predict resistance patterns faster than traditional methods of drug susceptibility testing. We have used WGS from natural populations of drug-resistant M. tuberculosis to characterize effects of selection for advantageous mutations on patterns of diversity at genes involved in drug resistance. The methods developed here can be used to identify novel advantageous mutations, including new resistance loci, in M. tuberculosis and other clonal pathogens.}, }
@article {pmid29403454, year = {2017}, author = {Oberbeckmann, S and Kreikemeyer, B and Labrenz, M}, title = {Environmental Factors Support the Formation of Specific Bacterial Assemblages on Microplastics.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2709}, pmid = {29403454}, issn = {1664-302X}, abstract = {While the global distribution of microplastics (MP) in the marine environment is currently being critically evaluated, the potential role of MP as a vector for distinct microbial assemblages or even pathogenic bacteria is hardly understood. To gain a deeper understanding, we investigated how different in situ conditions contribute to the composition and specificity of MP-associated bacterial communities in relation to communities on natural particles. Polystyrene (PS), polyethylene (PE), and wooden pellets were incubated for 2 weeks along an environmental gradient, ranging from marine (coastal Baltic Sea) to freshwater (waste water treatment plant, WWTP) conditions. The associated assemblages as well as the water communities were investigated applying high-throughput 16S rRNA gene sequencing. Our setup allowed for the first time to determine MP-dependent and -independent assemblage factors as subject to different environmental conditions in one system. Most importantly, plastic-specific assemblages were found to develop solely under certain conditions, such as lower nutrient concentration and higher salinity, while the bacterial genus Erythrobacter, known for the ability to utilize polycyclic aromatic hydrocarbons (PAH), was found specifically on MP across a broader section of the gradient. We discovered no enrichment of potential pathogens on PE or PS; however, the abundant colonization of MP in a WWTP by certain bacteria commonly associated with antibiotic resistance suggests MP as a possible hotspot for horizontal gene transfer. Taken together, our study clarifies that the surrounding environment prevailingly shapes the biofilm communities, but that MP-specific assemblage factors exist. These findings point to the ecological significance of specific MP-promoted bacterial populations in aquatic environments and particularly in plastic accumulation zones.}, }
@article {pmid29403020, year = {2018}, author = {Wilkinson, DA and O'Donnell, AJ and Akhter, RN and Fayaz, A and Mack, HJ and Rogers, LE and Biggs, PJ and French, NP and Midwinter, AC}, title = {Updating the genomic taxonomy and epidemiology of Campylobacter hyointestinalis.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {2393}, pmid = {29403020}, issn = {2045-2322}, mesh = {Animals ; Campylobacter Infections/epidemiology/microbiology/*veterinary ; Campylobacter hyointestinalis/*classification/*genetics/isolation &amp; purification ; Cattle ; Cattle Diseases/epidemiology/microbiology ; Deer ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Variation ; Genome, Bacterial ; Genomics ; New Zealand/epidemiology ; *Phylogeny ; Sheep ; Sheep Diseases/epidemiology/microbiology ; Zoonoses/*epidemiology/*microbiology ; }, abstract = {Campylobacter hyointestinalis is a member of an emerging group of zoonotic Campylobacter spp. that are increasingly identified in both gastric and non-gastric disease in humans. Here, we discovered C. hyointestinalis in three separate classes of New Zealand ruminant livestock; cattle, sheep and deer. To investigate the relevance of these findings we performed a systematic literature review on global C. hyointestinalis epidemiology and used comparative genomics to better understand and classify members of the species. We found that C. hyointestinalis subspecies hyointestinalis has an open pangenome, with accessory gene contents involved in many essential processes such as metabolism, virulence and defence. We observed that horizontal gene transfer is likely to have played an overwhelming role in species diversification, favouring a public-goods-like mechanism of gene 'acquisition and resampling' over a tree-of-life-like vertical inheritance model of evolution. As a result, simplistic gene-based inferences of taxonomy by similarity are likely to be misleading. Such genomic plasticity will also mean that local evolutionary histories likely influence key species characteristics, such as host-association and virulence. This may help explain geographical differences in reported C. hyointestinalis epidemiology and limits what characteristics may be generalised, requiring further genomic studies of C. hyointestinalis in areas where it causes disease.}, }
@article {pmid29401285, year = {2018}, author = {Dunivin, TK and Shade, A}, title = {Community structure explains antibiotic resistance gene dynamics over a temperature gradient in soil.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {3}, pages = {}, pmid = {29401285}, issn = {1574-6941}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/drug effects/*genetics/isolation &amp; purification/metabolism ; Bacterial Proteins/*genetics ; *Drug Resistance, Bacterial ; Fires ; Gene Transfer, Horizontal ; Genes, Bacterial ; Soil/*chemistry ; *Soil Microbiology ; Temperature ; }, abstract = {Soils are reservoirs of antibiotic resistance genes (ARGs), but environmental dynamics of ARGs are largely unknown. Long-term disturbances offer opportunities to examine microbiome responses at scales relevant for both ecological and evolutionary processes and can be insightful for studying ARGs. We examined ARGs in soils overlying the underground coal seam fire in Centralia, PA, which has been burning since 1962. As the fire progresses, previously hot soils can recover to ambient temperatures, which creates a gradient of fire impact. We examined metagenomes from surface soils along this gradient to examine ARGs using a gene-targeted assembler. We targeted 35 clinically relevant ARGs and two horizontal gene transfer-related genes (intI and repA). We detected 17 ARGs in Centralia: AAC6-Ia, adeB, bla_A, bla_B, bla_C, cmlA, dfra12, intI, sul2, tetA, tetW, tetX, tolC, vanA, vanH, vanX and vanZ. The diversity and abundance of bla_A, bla_B, dfra12 and tolC decreased with soil temperature, and changes in ARGs were largely explained by changes in community structure. We observed sequence-specific biogeography along the temperature gradient and observed compositional shifts in bla_A, dfra12 and intI. These results suggest that increased temperatures can reduce soil ARGs but that this is largely due to a concomitant reduction in community-level diversity.}, }
@article {pmid29398650, year = {2018}, author = {Fu, Y and Ho, BT and Mekalanos, JJ}, title = {Tracking Vibrio cholerae Cell-Cell Interactions during Infection Reveals Bacterial Population Dynamics within Intestinal Microenvironments.}, journal = {Cell host &amp; microbe}, volume = {23}, number = {2}, pages = {274-281.e2}, pmid = {29398650}, issn = {1934-6069}, support = {R01 AI018045/AI/NIAID NIH HHS/United States ; R37 AI018045/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Cholera/microbiology/*pathology ; Conjugation, Genetic/physiology ; Host-Pathogen Interactions/*physiology ; Intestines/*microbiology/pathology ; Plasmids/genetics ; Rabbits ; Type VI Secretion Systems/*physiology ; *Vibrio cholerae/genetics/growth &amp; development/pathogenicity ; }, abstract = {Vibrio cholerae is the causative agent of the diarrheal disease cholera. Although many V. cholerae virulence factors have been studied, the role of interbacterial interactions within the host gut and their influence on colonization are poorly understood. Here, we utilized the conjugative properties of a Vibrio-specific plasmid to serve as a quantifiable genetic marker for direct contact among V. cholerae cells in the infant rabbit model for cholera. In conjunction, we also quantified contact-dependent type 6 secretion system (T6SS)-mediated killing of co-infecting V. cholerae strains. Tracking these interbacterial interactions revealed that most contact-dependent cell-cell interactions among V. cholerae occur in specific intestinal microenvironments, notably the distal small intestine and cecum, and that the T6SS confers a competitive advantage within the middle small intestine. These results support a model for V. cholerae gut colonization, which includes microenvironments where critical microbial-host and bacterial-bacterial interactions occur to facilitate colonization by this pathogen.}, }
@article {pmid29397687, year = {2018}, author = {Feng, Y}, title = {Transferability of MCR-1/2 Polymyxin Resistance: Complex Dissemination and Genetic Mechanism.}, journal = {ACS infectious diseases}, volume = {4}, number = {3}, pages = {291-300}, doi = {10.1021/acsinfecdis.7b00201}, pmid = {29397687}, issn = {2373-8227}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics ; *Drug Resistance, Bacterial ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; *Plasmids ; Polymyxins/*pharmacology ; }, abstract = {Polymyxins, a group of cationic antimicrobial polypeptides, act as a last-resort defense against lethal infections by carbapenem-resistant Gram-negative pathogens. Recent emergence and fast spread of mobilized colistin resistance determinant mcr-1 argue the renewed interest of colistin in clinical therapies, threatening global public health and agriculture production. This mini-review aims to present an updated overview of mcr-1, covering its global dissemination, the diversity of its hosts/plasmid reservoirs, the complexity in the genetic environment adjacent to mcr-1, the appearance of new mcr-like genes, and the molecular mechanisms for mobilized colistin resistance determinant 1/2 (MCR-1/2).}, }
@article {pmid29396989, year = {2018}, author = {Chen, K and Dorlhac de Borne, F and Sierro, N and Ivanov, NV and Alouia, M and Koechler, S and Otten, L}, title = {Organization of the TC and TE cellular T-DNA regions in Nicotiana otophora and functional analysis of three diverged TE-6b genes.}, journal = {The Plant journal : for cell and molecular biology}, volume = {94}, number = {2}, pages = {274-287}, doi = {10.1111/tpj.13853}, pmid = {29396989}, issn = {1365-313X}, mesh = {Agrobacterium/genetics ; Chromosome Mapping ; DNA, Bacterial/*genetics ; DNA, Plant/genetics ; Evolution, Molecular ; Flowers/growth &amp; development ; Gene Expression Regulation, Plant ; Genes, Plant/*genetics/physiology ; Seeds/growth &amp; development ; Nicotiana/anatomy &amp; histology/*genetics/growth &amp; development ; }, abstract = {Nicotiana otophora contains Agrobacterium-derived T-DNA sequences introduced by horizontal gene transfer (Chen et al., 2014). Sixty-nine contigs were assembled into four different cellular T-DNAs (cT-DNAs) totalling 83 kb. TC and TE result from two successive transformation events, each followed by duplication, yielding two TC and two TE inserts. TC is also found in other Nicotiana species, whereas TE is unique to N. otophora. Both cT-DNA regions are partially duplicated inverted repeats. Analysis of the cT-DNA divergence patterns allowed reconstruction of the evolution of the TC and TE regions. TC and TE carry 10 intact open reading frames. Three of these are TE-6b genes, derived from a single 6b gene carried by the Agrobacterium strain which inserted TE in the N. otophora ancestor. 6b genes have so far only been found in Agrobacterium tumefaciens or Agrobacterium vitis T-DNAs and strongly modify plant growth (Chen and Otten, 2016). The TE-6b genes were expressed in Nicotiana tabacum under the constitutive 2 × 35S promoter. TE-1-6b-R and TE-2-6b led to shorter plants, dark-green leaves, a strong increase in leaf vein development and modified petiole wings. TE-1-6b-L expression led to a similar phenotype, but in addition leaves show outgrowths at the margins, flowers were modified and plants became viviparous, i.e. embryos germinated in the capsules at an early stage of their development. Embryos could be rescued by culture in vitro. The TE-6b phenotypes are very different from the earlier described 6b phenotypes and could provide new insight into the mode of action of the 6b genes.}, }
@article {pmid29394244, year = {2018}, author = {Czech, L and Bremer, E}, title = {With a pinch of extra salt-Did predatory protists steal genes from their food?.}, journal = {PLoS biology}, volume = {16}, number = {2}, pages = {e2005163}, pmid = {29394244}, issn = {1545-7885}, mesh = {Amino Acids, Diamino/metabolism ; Archaea/genetics/metabolism/*physiology ; Bacteria/*genetics/metabolism ; *Bacterial Physiological Phenomena ; Betaine/metabolism ; Biological Transport ; *Genes, Archaeal ; *Genes, Bacterial ; Inositol/metabolism ; Introns ; Models, Biological ; Osmotic Pressure ; Phylogeny ; *Salinity ; Salt Stress/*genetics ; Transcription, Genetic ; }, abstract = {The cellular adjustment of Bacteria and Archaea to high-salinity habitats is well studied and has generally been classified into one of two strategies. These are to accumulate high levels either of ions (the "salt-in" strategy) or of physiologically compliant organic osmolytes, the compatible solutes (the "salt-out" strategy). Halophilic protists are ecophysiological important inhabitants of salt-stressed ecosystems because they are not only very abundant but also represent the majority of eukaryotic lineages in nature. However, their cellular osmostress responses have been largely neglected. Recent reports have now shed new light on this issue using the geographically widely distributed halophilic heterotrophic protists Halocafeteria seosinensis, Pharyngomonas kirbyi, and Schmidingerothrix salinarum as model systems. Different approaches led to the joint conclusion that these unicellular Eukarya use the salt-out strategy to cope successfully with the persistent high salinity in their habitat. They accumulate various compatible solutes, e.g., glycine betaine, myo-inositol, and ectoines. The finding of intron-containing biosynthetic genes for ectoine and hydroxyectoine, their salt stress-responsive transcription in H. seosinensis, and the production of ectoine and its import by S. salinarum come as a considerable surprise because ectoines have thus far been considered exclusive prokaryotic compatible solutes. Phylogenetic considerations of the ectoine/hydroxyectoine biosynthetic genes of H. seosinensis suggest that they have been acquired via lateral gene transfer by these bacterivorous Eukarya from ectoine/hydroxyectoine-producing food bacteria that populate the same habitat.}, }
@article {pmid29385126, year = {2018}, author = {Maddamsetti, R and Lenski, RE}, title = {Analysis of bacterial genomes from an evolution experiment with horizontal gene transfer shows that recombination can sometimes overwhelm selection.}, journal = {PLoS genetics}, volume = {14}, number = {1}, pages = {e1007199}, pmid = {29385126}, issn = {1553-7404}, mesh = {Base Sequence ; Conjugation, Genetic/physiology ; Directed Molecular Evolution/methods ; Escherichia coli K12/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*physiology ; Genetic Variation/physiology ; Genome, Bacterial/*genetics ; Recombination, Genetic/*physiology ; Selection, Genetic/*genetics ; Sequence Analysis, DNA ; }, abstract = {Few experimental studies have examined the role that sexual recombination plays in bacterial evolution, including the effects of horizontal gene transfer on genome structure. To address this limitation, we analyzed genomes from an experiment in which Escherichia coli K-12 Hfr (high frequency recombination) donors were periodically introduced into 12 evolving populations of E. coli B and allowed to conjugate repeatedly over the course of 1000 generations. Previous analyses of the evolved strains from this experiment showed that recombination did not accelerate adaptation, despite increasing genetic variation relative to asexual controls. However, the resolution in that previous work was limited to only a few genetic markers. We sought to clarify and understand these puzzling results by sequencing complete genomes from each population. The effects of recombination were highly variable: one lineage was mostly derived from the donors, while another acquired almost no donor DNA. In most lineages, some regions showed repeated introgression and others almost none. Regions with high introgression tended to be near the donors' origin of transfer sites. To determine whether introgressed alleles imposed a genetic load, we extended the experiment for 200 generations without recombination and sequenced whole-population samples. Beneficial alleles in the recipient populations were occasionally driven extinct by maladaptive donor-derived alleles. On balance, our analyses indicate that the plasmid-mediated recombination was sufficiently frequent to drive donor alleles to fixation without providing much, if any, selective advantage.}, }
@article {pmid29384268, year = {2018}, author = {Magnabosco, C and Moore, KR and Wolfe, JM and Fournier, GP}, title = {Dating phototrophic microbial lineages with reticulate gene histories.}, journal = {Geobiology}, volume = {16}, number = {2}, pages = {179-189}, pmid = {29384268}, issn = {1472-4669}, mesh = {Chlorobi/genetics ; Chloroflexi/*genetics ; Cyanobacteria/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Metabolic Networks and Pathways/*genetics ; *Phototrophic Processes ; }, abstract = {Phototrophic bacteria are among the most biogeochemically significant organisms on Earth and are physiologically related through the use of reaction centers to collect photons for energy metabolism. However, the major phototrophic lineages are not closely related to one another in bacterial phylogeny, and the origins of their respective photosynthetic machinery remain obscured by time and low sequence similarity. To better understand the co-evolution of Cyanobacteria and other ancient anoxygenic phototrophic lineages with respect to geologic time, we designed and implemented a variety of molecular clocks that use horizontal gene transfer (HGT) as additional, relative constraints. These HGT constraints improve the precision of phototroph divergence date estimates and indicate that stem green non-sulfur bacteria are likely the oldest phototrophic lineage. Concurrently, crown Cyanobacteria age estimates ranged from 2.2 Ga to 2.7 Ga, with stem Cyanobacteria diverging ~2.8 Ga. These estimates provide a several hundred Ma window for oxygenic photosynthesis to evolve prior to the Great Oxidation Event (GOE) ~2.3 Ga. In all models, crown green sulfur bacteria diversify after the loss of the banded iron formations from the sedimentary record (~1.8 Ga) and may indicate the expansion of the lineage into a new ecological niche following the GOE. Our date estimates also provide a timeline to investigate the temporal feasibility of different photosystem HGT events between phototrophic lineages. Using this approach, we infer that stem Cyanobacteria are unlikely to be the recipient of an HGT of photosystem I proteins from green sulfur bacteria but could still have been either the HGT donor or the recipient of photosystem II proteins with green non-sulfur bacteria, prior to the GOE. Together, these results indicate that HGT-constrained molecular clocks are useful tools for the evaluation of various geological and evolutionary hypotheses, using the evolutionary histories of both genes and organismal lineages.}, }
@article {pmid29379098, year = {2018}, author = {Zrimec, J and Lapanje, A}, title = {DNA structure at the plasmid origin-of-transfer indicates its potential transfer range.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {1820}, pmid = {29379098}, issn = {2045-2322}, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics ; Base Sequence ; Conjugation, Genetic/genetics ; DNA, Bacterial/*genetics ; Gene Transfer, Horizontal/*genetics ; Plasmids/*genetics ; Replication Origin/genetics ; }, abstract = {Horizontal gene transfer via plasmid conjugation enables antimicrobial resistance (AMR) to spread among bacteria and is a major health concern. The range of potential transfer hosts of a particular conjugative plasmid is characterised by its mobility (MOB) group, which is currently determined based on the amino acid sequence of the plasmid-encoded relaxase. To facilitate prediction of plasmid MOB groups, we have developed a bioinformatic procedure based on analysis of the origin-of-transfer (oriT), a merely 230 bp long non-coding plasmid DNA region that is the enzymatic substrate for the relaxase. By computationally interpreting conformational and physicochemical properties of the oriT region, which facilitate relaxase-oriT recognition and initiation of nicking, MOB groups can be resolved with over 99% accuracy. We have shown that oriT structural properties are highly conserved and can be used to discriminate among MOB groups more efficiently than the oriT nucleotide sequence. The procedure for prediction of MOB groups and potential transfer range of plasmids was implemented using published data and is available at http://dnatools.eu/MOB/plasmid.html .}, }
@article {pmid29379078, year = {2018}, author = {Peyraud, R and Cottret, L and Marmiesse, L and Genin, S}, title = {Control of primary metabolism by a virulence regulatory network promotes robustness in a plant pathogen.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {418}, pmid = {29379078}, issn = {2041-1723}, mesh = {Computer Simulation ; Gene Regulatory Networks/*genetics ; High-Throughput Screening Assays ; Metabolic Networks and Pathways/*genetics ; Ralstonia solanacearum/*genetics/metabolism ; Virulence/*genetics ; Virulence Factors/*genetics/metabolism ; }, abstract = {Robustness is a key system-level property of living organisms to maintain their functions while tolerating perturbations. We investigate here how a regulatory network controlling multiple virulence factors impacts phenotypic robustness of a bacterial plant pathogen. We reconstruct a cell-scale model of Ralstonia solanacearum connecting a genome-scale metabolic network, a virulence macromolecule network, and a virulence regulatory network, which includes 63 regulatory components. We develop in silico methods to quantify phenotypic robustness under a broad set of conditions in high-throughput simulation analyses. This approach reveals that the virulence regulatory network exerts a control of the primary metabolism to promote robustness upon infection. The virulence regulatory network plugs into the primary metabolism mainly through the control of genes likely acquired via horizontal gene transfer, which results in a functional overlay with ancestral genes. These results support the view that robustness may be a selected trait that promotes pathogenic fitness upon infection.}, }
@article {pmid29377385, year = {2018}, author = {Wybouw, N and Van Leeuwen, T and Dermauw, W}, title = {A massive incorporation of microbial genes into the genome of Tetranychus urticae, a polyphagous arthropod herbivore.}, journal = {Insect molecular biology}, volume = {27}, number = {3}, pages = {333-351}, doi = {10.1111/imb.12374}, pmid = {29377385}, issn = {1365-2583}, mesh = {Animals ; Female ; *Gene Transfer, Horizontal ; *Genes, Microbial ; Genome ; Phylogeny ; Tetranychidae/*genetics ; *Transcriptome ; }, abstract = {A number of horizontal gene transfers (HGTs) have been identified in the spider mite Tetranychus urticae, a chelicerate herbivore. However, the genome of this mite species has at present not been thoroughly mined for the presence of HGT genes. Here, we performed a systematic screen for HGT genes in the T. urticae genome using the h-index metric. Our results not only validated previously identified HGT genes but also uncovered 25 novel HGT genes. In addition to HGT genes with a predicted biochemical function in carbohydrate, lipid and folate metabolism, we also identified the horizontal transfer of a ketopantoate hydroxymethyltransferase and a pantoate β-alanine ligase gene. In plants and bacteria, both genes are essential for vitamin B5 biosynthesis and their presence in the mite genome strongly suggests that spider mites, similar to Bemisia tabaci and nematodes, can synthesize their own vitamin B5. We further show that HGT genes were physically embedded within the mite genome and were expressed in different life stages. By screening chelicerate genomes and transcriptomes, we were able to estimate the evolutionary histories of these HGTs during chelicerate evolution. Our study suggests that HGT has made a significant and underestimated impact on the metabolic repertoire of plant-feeding spider mites.}, }
@article {pmid29374269, year = {2018}, author = {Amos, GCA and Ploumakis, S and Zhang, L and Hawkey, PM and Gaze, WH and Wellington, EMH}, title = {The widespread dissemination of integrons throughout bacterial communities in a riverine system.}, journal = {The ISME journal}, volume = {12}, number = {3}, pages = {681-691}, pmid = {29374269}, issn = {1751-7370}, support = {BB/L027801/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/classification/drug effects/*genetics/isolation &amp; purification ; Bacterial Proteins/genetics/metabolism ; Drug Resistance, Bacterial ; Escherichia coli/drug effects/genetics ; *Gene Transfer, Horizontal ; Humans ; *Integrons ; Quaternary Ammonium Compounds/metabolism ; Wastewater/*microbiology ; }, abstract = {Anthropogenic inputs increase levels of antimicrobial resistance (AMR) in the environment, however, it is unknown how these inputs create this observed increase, and if anthropogenic sources impact AMR in environmental bacteria. The aim of this study was to characterise the role of waste water treatment plants (WWTPs) in the dissemination of class 1 integrons (CL1s) in the riverine environment. Using sample sites from upstream and downstream of a WWTP, we demonstrate through isolation and culture-independent analysis that WWTP effluent significantly increases both CL1 abundance and antibiotic resistance in the riverine environment. Characterisation of CL1-bearing isolates revealed that CL1s were distributed across a diverse range of bacteria, with identical complex genetic resistance determinants isolated from both human-associated and common environmental bacteria across connected sites. Over half of sequenced CL1s lacked the 3'-conserved sequence ('atypical' CL1s); surprisingly, bacteria carrying atypical CL1s were on average resistant to more antibiotics than bacteria carrying 3'-CS CL1s. Quaternary ammonium compound (QAC) resistance genes were observed across 75% of sequenced CL1 gene cassette arrays. Chemical data analysis indicated high levels of boron (a detergent marker) downstream of the WWTP. Subsequent phenotypic screening of CL1-bearing isolates demonstrated that ~90% were resistant to QAC detergents, with in vitro experiments demonstrating that QACs could solely select for the transfer of clinical antibiotic resistance genes to a naive Escherichia coli recipient. In conclusion, this study highlights the significant impact of WWTPs on environmental AMR, and demonstrates the widespread carriage of clinically important resistance determinants by environmentally associated bacteria.}, }
@article {pmid29373594, year = {2018}, author = {Grimm, I and Dumke, J and Dreier, J and Knabbe, C and Vollmer, T}, title = {Biofilm formation and transcriptome analysis of Streptococcus gallolyticus subsp. gallolyticus in response to lysozyme.}, journal = {PloS one}, volume = {13}, number = {1}, pages = {e0191705}, pmid = {29373594}, issn = {1932-6203}, mesh = {*Biofilms ; Muramidase/*metabolism ; Streptococcus gallolyticus subspecies gallolyticus/genetics/*metabolism ; *Transcriptome ; }, abstract = {Streptococcus gallolyticus subsp. gallolyticus is a commensal bacterium of the human gastrointestinal tract, and a pathogen causing infective endocarditis and other biofilm-associated infections via exposed collagen. This study focuses on the characterization of the biofilm formation and collagen adhesion of S. gallolyticus subsp. gallolyticus under different conditions. In this study, it has been observed that the isolate UCN 34 is resistant to 20 mg/ml lysozyme in BHI medium, whereas the strain BAA-2069 builds more biofilm in the presence of lysozyme compared to in a control of BHI without lysozyme. A transcriptome analysis with whole genome microarrays of these two isolates in BHI medium with lysozyme compared to control without lysozyme revealed changes in gene expression levels. In the isolate BAA-2069, 67 genes showed increased expression in the presence of lysozyme, while in the isolate UCN 34, 165 genes showed increased expression and 30 genes showed decreased expression through lysozyme treatment. Products of genes which were higher expressed are in involved in transcription and translation, in cell-wall modification, in hydrogen peroxide resistance and in bacterial immunity. Furthermore, the adhesion ability of different strains of S. gallolyticus subsp. gallolyticus to collagen type I and IV was analyzed. Thereby, we compared the adhesion of 46 human isolates with 23 isolates from animals. It was shown that the adhesion ability depends significantly on whether the isolate was isolated from human or animal. For example, high adhesion ability was observed for strain UCN 34 isolated from an infective endocarditis patient, whereas strain DSM 16831 isolated from koala feces adhered only marginally to collagen. Full genome microarray analysis of these two strains revealed strain-dependent gene expression due to adhesion. The expression of 25 genes of a transposon and 15 genes of a phage region in strain DSM 16831 were increased, which corresponds to horizontal gene transfer. Adherence to collagen in strain UCN 34 led to higher expression of 27 genes and lower expression of 31 genes. This was suggestive of a change in nutrient uptake.}, }
@article {pmid29370371, year = {2018}, author = {Rozwandowicz, M and Brouwer, MSM and Fischer, J and Wagenaar, JA and Gonzalez-Zorn, B and Guerra, B and Mevius, DJ and Hordijk, J}, title = {Plasmids carrying antimicrobial resistance genes in Enterobacteriaceae.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {73}, number = {5}, pages = {1121-1137}, doi = {10.1093/jac/dkx488}, pmid = {29370371}, issn = {1460-2091}, mesh = {*Drug Resistance, Bacterial ; Enterobacteriaceae/classification/*drug effects/*genetics ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Genotype ; Humans ; Plasmids/*analysis/*classification ; }, abstract = {Bacterial antimicrobial resistance (AMR) is constantly evolving and horizontal gene transfer through plasmids plays a major role. The identification of plasmid characteristics and their association with different bacterial hosts provides crucial knowledge that is essential to understand the contribution of plasmids to the transmission of AMR determinants. Molecular identification of plasmid and strain genotypes elicits a distinction between spread of AMR genes by plasmids and dissemination of these genes by spread of bacterial clones. For this reason several methods are used to type the plasmids, e.g. PCR-based replicon typing (PBRT) or relaxase typing. Currently, there are 28 known plasmid types in Enterobacteriaceae distinguished by PBRT. Frequently reported plasmids [IncF, IncI, IncA/C, IncL (previously designated IncL/M), IncN and IncH] are the ones that bear the greatest variety of resistance genes. The purpose of this review is to provide an overview of all known AMR-related plasmid families in Enterobacteriaceae, the resistance genes they carry and their geographical distribution.}, }
@article {pmid29370270, year = {2018}, author = {Dunivin, TK and Miller, J and Shade, A}, title = {Taxonomically-linked growth phenotypes during arsenic stress among arsenic resistant bacteria isolated from soils overlying the Centralia coal seam fire.}, journal = {PloS one}, volume = {13}, number = {1}, pages = {e0191893}, pmid = {29370270}, issn = {1932-6203}, mesh = {Arsenic/pharmacokinetics/*toxicity ; Bacteria, Aerobic/classification/drug effects/genetics ; Biodegradation, Environmental ; Biotransformation ; *Coal ; Drug Resistance, Bacterial/genetics ; *Fires ; Gene Transfer, Horizontal ; Genes, Bacterial ; Pennsylvania ; Phylogeny ; *Soil Microbiology ; Soil Pollutants/pharmacokinetics/*toxicity ; Stress, Physiological ; }, abstract = {Arsenic (As), a toxic element, has impacted life since early Earth. Thus, microorganisms have evolved many As resistance and tolerance mechanisms to improve their survival outcomes given As exposure. We isolated As resistant bacteria from Centralia, PA, the site of an underground coal seam fire that has been burning since 1962. From a 57.4°C soil collected from a vent above the fire, we isolated 25 unique aerobic As resistant bacterial strains spanning seven genera. We examined their diversity, resistance gene content, transformation abilities, inhibitory concentrations, and growth phenotypes. Although As concentrations were low at the time of soil collection (2.58 ppm), isolates had high minimum inhibitory concentrations (MICs) of arsenate and arsenite (>300 mM and 20 mM respectively), and most isolates were capable of arsenate reduction. We screened isolates (PCR and sequencing) using 12 published primer sets for six As resistance genes (AsRGs). Genes encoding arsenate reductase (arsC) and arsenite efflux pumps (arsB, ACR3(2)) were present, and phylogenetic incongruence between 16S rRNA genes and AsRGs provided evidence for horizontal gene transfer. A detailed investigation of differences in isolate growth phenotypes across As concentrations (lag time to exponential growth, maximum growth rate, and maximum OD590) showed a relationship with taxonomy, providing information that could help to predict an isolate's performance given As exposure in situ. Our results suggest that microbiological management and remediation of environmental As could be informed by taxonomically-linked As tolerance, potential for resistance gene transferability, and the rare biosphere.}, }
@article {pmid29367050, year = {2018}, author = {Guo, N and Wang, Y and Tong, T and Wang, S}, title = {The fate of antibiotic resistance genes and their potential hosts during bio-electrochemical treatment of high-salinity pharmaceutical wastewater.}, journal = {Water research}, volume = {133}, number = {}, pages = {79-86}, doi = {10.1016/j.watres.2018.01.020}, pmid = {29367050}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents/chemistry ; Chloramphenicol/chemistry ; Drug Resistance, Microbial/*genetics ; Electrochemical Techniques ; *Genes, Bacterial ; Salinity ; Waste Disposal, Fluid/*methods ; Wastewater/analysis ; Water Pollutants, Chemical/chemistry ; }, abstract = {Pharmaceutical wastewaters containing antibiotics and high salinity can damage traditional biological treatment and result in the proliferation of antibiotic resistance genes (ARGs). Bioelectrochemical system (BES) is a promising approach for treating pharmaceutical wastewater. However, the fate of ARGs in BES and their correlations with microbial communities and horizontal genes transfer are unknown. In this study, we investigated the response of ARGs to bio-electrochemical treatment of chloramphenicol wastewater and their potential hosts under different salinities. Three ARGs encoding efflux pump (cmlA, floR and tetC), one class 1 integron integrase encoding gene (intI1), and sul1 gene (associate with intI1) were analyzed. Correlation analysis between microbial community and ARGs revealed that the abundances of potential hosts of ARGs were strongly affected by salinity, which further determined the alteration in ARGs abundances under different salinities. There were no significant correlations between ARGs and intI1, indicating that horizontal gene transfer was not related to the important changes in ARGs. Moreover, the chloramphenicol removal efficiency was enhanced under a moderate salinity, attributed to the altered microbial community driven by salinity. Therefore, microbial community shift is the major factor for the changes of ARGs and chloramphenicol removal efficiency in BES under different salinities. This study provides new insights on the mechanisms underlying the alteration of ARGs in BES treating high-salinity pharmaceutical wastewater.}, }
@article {pmid29363431, year = {2018}, author = {Zhao, Y and Sun, C and Zhao, D and Zhang, Y and You, Y and Jia, X and Yang, J and Wang, L and Wang, J and Fu, H and Kang, Y and Chen, F and Yu, J and Wu, J and Xiao, J}, title = {PGAP-X: extension on pan-genome analysis pipeline.}, journal = {BMC genomics}, volume = {19}, number = {Suppl 1}, pages = {36}, pmid = {29363431}, issn = {1471-2164}, mesh = {Chlamydia trachomatis/classification/*genetics ; Computer Graphics ; *Evolution, Molecular ; *Genetic Variation ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; *Software ; Streptococcus pneumoniae/classification/*genetics ; }, abstract = {BACKGROUND: Since PGAP (pan-genome analysis pipeline) was published in 2012, it has been widely employed in bacterial genomics research. Though PGAP has integrated several modules for pan-genomics analysis, how to properly and effectively interpret and visualize the results data is still a challenge.<br><br>RESULT: To well present bacterial genomic characteristics, a novel cross-platform software was developed, named PGAP-X. Four kinds of data analysis modules were developed and integrated: whole genome sequences alignment, orthologous genes clustering, pan-genome profile analysis, and genetic variants analysis. The results from these analyses can be directly visualized in PGAP-X. The modules for data visualization in PGAP-X include: comparison of genome structure, gene distribution by conservation, pan-genome profile curve and variation on genic and genomic region. Meanwhile, result data produced by other programs with similar function can be imported to be further analyzed and visualized in PGAP-X. To test the performance of PGAP-X, we comprehensively analyzed 14&#xa0;Streptococcus pneumonia strains and 14 Chlamydia trachomatis. The results show that, S. pneumonia strains have higher diversity on genome structure and gene contents than C. trachomatis strains. In addition, S. pneumonia strains might have suffered many evolutionary events, such genomic rearrangements, frequent horizontal gene transfer, homologous recombination, and other evolutionary process.<br><br>CONCLUSION: Briefly, PGAP-X directly presents the characteristics of bacterial genomic diversity with different visualization methods, which could help us to intuitively understand dynamics and evolution in bacterial genomes. The source code and the pre-complied executable programs are freely available from http://pgapx.ybzhao.com .}, }
@article {pmid29359184, year = {2018}, author = {Enos, BG and Anthony, MK and DeGiorgis, JA and Williams, LE}, title = {Prey Range and Genome Evolution of Halobacteriovorax marinus Predatory Bacteria from an Estuary.}, journal = {mSphere}, volume = {3}, number = {1}, pages = {}, pmid = {29359184}, issn = {2379-5042}, support = {P20 GM103430/GM/NIGMS NIH HHS/United States ; }, abstract = {Halobacteriovorax strains are saltwater-adapted predatory bacteria that attack Gram-negative bacteria and may play an important role in shaping microbial communities. To understand how Halobacteriovorax strains impact ecosystems and develop them as biocontrol agents, it is important to characterize variation in predation phenotypes and investigate Halobacteriovorax genome evolution. We isolated Halobacteriovorax marinus BE01 from an estuary in Rhode Island using Vibrio from the same site as prey. Small, fast-moving, attack-phase BE01 cells attach to and invade prey cells, consistent with the intraperiplasmic predation strategy of the H. marinus type strain, SJ. BE01 is a prey generalist, forming plaques on Vibrio strains from the estuary, Pseudomonas from soil, and Escherichia coli. Genome analysis revealed extremely high conservation of gene order and amino acid sequences between BE01 and SJ, suggesting strong selective pressure to maintain the genome in this H. marinus lineage. Despite this, we identified two regions of gene content difference that likely resulted from horizontal gene transfer. Analysis of modal codon usage frequencies supports the hypothesis that these regions were acquired from bacteria with different codon usage biases than H. marinus. In one of these regions, BE01 and SJ carry different genes associated with mobile genetic elements. Acquired functions in BE01 include the dnd operon, which encodes a pathway for DNA modification, and a suite of genes involved in membrane synthesis and regulation of gene expression that was likely acquired from another Halobacteriovorax lineage. This analysis provides further evidence that horizontal gene transfer plays an important role in genome evolution in predatory bacteria. IMPORTANCE Predatory bacteria attack and digest other bacteria and therefore may play a role in shaping microbial communities. To investigate phenotypic and genotypic variation in saltwater-adapted predatory bacteria, we isolated Halobacteriovorax marinus BE01 from an estuary in Rhode Island, assayed whether it could attack different prey bacteria, and sequenced and analyzed its genome. We found that BE01 is a prey generalist, attacking bacteria from different phylogenetic groups and environments. Gene order and amino acid sequences are highly conserved between BE01 and the H. marinus type strain, SJ. By comparative genomics, we detected two regions of gene content difference that likely occurred via horizontal gene transfer events. Acquired genes encode functions such as modification of DNA, membrane synthesis and regulation of gene expression. Understanding genome evolution and variation in predation phenotypes among predatory bacteria will inform their development as biocontrol agents and clarify how they impact microbial communities.}, }
@article {pmid29358726, year = {2018}, author = {Akita, T and Takuno, S and Innan, H}, title = {Coalescent framework for prokaryotes undergoing interspecific homologous recombination.}, journal = {Heredity}, volume = {120}, number = {5}, pages = {474-484}, pmid = {29358726}, issn = {1365-2540}, mesh = {Gene Transfer, Horizontal/*genetics ; Homologous Recombination/genetics ; Models, Theoretical ; Mutation ; Polymorphism, Single Nucleotide/*genetics ; *Prokaryotic Cells ; }, abstract = {Coalescent process for prokaryote species is theoretically considered. Prokaryotes undergo homologous recombination with individuals of the same species (intraspecific recombination) and with individuals of other species (interspecific recombination). This work particularly focuses on interspecific recombination because intraspecific recombination has been well incorporated in coalescent framework. We present a simulation framework for generating SNP (single-nucleotide polymorphism) patterns that allows external DNA integration into host genome from other species. Using this simulation tool, msPro, we observed that the joint processes of intra- and interspecific recombination generate complex SNP patterns. The direct effect of interspecific recombination includes increased polymorphism. Because interspecific recombination is very rare in nature, it generates regions with exceptionally high polymorphism. Following interspecific recombination, intraspecific recombination cuts the integrated external DNA into small fragments, generating a complex SNP pattern that appears as if external DNA was integrated multiple times. The insight gained from our work using the msPro simulator will be useful for understanding and evaluating the relative contributions of intra- and interspecific recombination events in generating complex SNP patters in prokaryotes.}, }
@article {pmid29358710, year = {2018}, author = {Seeleuthner, Y and Mondy, S and Lombard, V and Carradec, Q and Pelletier, E and Wessner, M and Leconte, J and Mangot, JF and Poulain, J and Labadie, K and Logares, R and Sunagawa, S and de Berardinis, V and Salanoubat, M and Dimier, C and Kandels-Lewis, S and Picheral, M and Searson, S and ,  and Pesant, S and Poulton, N and Stepanauskas, R and Bork, P and Bowler, C and Hingamp, P and Sullivan, MB and Iudicone, D and Massana, R and Aury, JM and Henrissat, B and Karsenti, E and Jaillon, O and Sieracki, M and de Vargas, C and Wincker, P}, title = {Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {310}, pmid = {29358710}, issn = {2041-1723}, support = {294823/ERC_/European Research Council/International ; }, abstract = {Single-celled eukaryotes (protists) are critical players in global biogeochemical cycling of nutrients and energy in the oceans. While their roles as primary producers and grazers are well appreciated, other aspects of their life histories remain obscure due to challenges in culturing and sequencing their natural diversity. Here, we exploit single-cell genomics and metagenomics data from the circumglobal Tara Oceans expedition to analyze the genome content and apparent oceanic distribution of seven prevalent lineages of uncultured heterotrophic stramenopiles. Based on the available data, each sequenced genome or genotype appears to have a specific oceanic distribution, principally correlated with water temperature and depth. The genome content provides hypotheses for specialization in terms of cell motility, food spectra, and trophic stages, including the potential impact on their lifestyles of horizontal gene transfer from prokaryotes. Our results support the idea that prominent heterotrophic marine protists perform diverse functions in ocean ecology.}, }
@article {pmid29357812, year = {2018}, author = {Xie, W and Yang, X and Chen, C and Yang, Z and Guo, L and Wang, D and Huang, J and Zhang, H and Wen, Y and Zhao, J and Wu, Q and Wang, S and Coates, BS and Zhou, X and Zhang, Y}, title = {The invasive MED/Q Bemisia tabaci genome: a tale of gene loss and gene gain.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {68}, pmid = {29357812}, issn = {1471-2164}, mesh = {Animals ; Crops, Agricultural/parasitology ; Cytochrome P-450 Enzyme System/genetics ; *Genome, Insect ; Glucuronosyltransferase/genetics ; Hemiptera/*classification/*genetics ; Host Specificity ; Insect Proteins/*genetics ; *Insecticide Resistance ; Multigene Family ; Phylogeny ; Symbiosis ; Transcriptome ; }, abstract = {BACKGROUND: Sweetpotato whitefly, Bemisia tabaci MED/Q and MEAM1/B, are two economically important invasive species that cause considerable damages to agriculture crops through direct feeding and indirect vectoring of plant pathogens. Recently, a draft genome of B. tabaci MED/Q has been assembled. In this study, we focus on the genomic comparison between MED/Q and MEAM1/B, with a special interest in MED/Q's genomic signatures that may contribute to the highly invasive nature of this emerging insect pest.<br><br>RESULTS: The genomes of both species share similarity in syntenic blocks, but have significant divergence in the gene coding sequence. Expansion of cytochrome P450 monooxygenases and UDP glycosyltransferases in MED/Q and MEAM1/B genome is functionally validated for mediating insecticide resistance in MED/Q using in vivo RNAi. The amino acid biosynthesis pathways in MED/Q genome are partitioned among the host and endosymbiont genomes in a manner distinct from other hemipterans. Evidence of horizontal gene transfer to the host genome may explain their obligate relationship. Putative loss-of-function in the immune deficiency-signaling pathway due to the gene loss is a shared ancestral trait among hemipteran insects.<br><br>CONCLUSIONS: The expansion of detoxification genes families, such as P450s, may contribute to the development of insecticide resistance traits and a broad host range in MED/Q and MEAM1/B, and facilitate species' invasions into intensively managed cropping systems. Numerical and compositional changes in multiple gene families (gene loss and gene gain) in the MED/Q genome sets a foundation for future hypothesis testing that will advance our understanding of adaptation, viral transmission, symbiosis, and plant-insect-pathogen tritrophic interactions.}, }
@article {pmid29350317, year = {2018}, author = {Zhang, Y and Ma, Q and Su, B and Chen, R and Lin, J and Lin, Z and Wang, D and Yu, Y}, title = {A study on the role that quorum sensing play in antibiotic-resistant plasmid conjugative transfer in Escherichia coli.}, journal = {Ecotoxicology (London, England)}, volume = {27}, number = {2}, pages = {209-216}, pmid = {29350317}, issn = {1573-3017}, support = {PCRRK16007//Foundation of the State Key Laboratory of Pollution Control and Resource Reuse Foundation/ ; 21377096, 21577105, 21777123//the National Natural Science Foundation of China/ ; 14DZ2261100, 17DZ1200103//the 111 Project, Science and Technology Commission of Shanghai Municipality/ ; 2016M600332//China Postdoctoral Science Foundation/ ; KF2016-11//State Key Laboratory of Environmental Chemistry and Ecotoxicology/ ; }, mesh = {Anti-Bacterial Agents ; Drug Resistance, Microbial/*genetics ; Escherichia coli/drug effects/*genetics ; Genes, Bacterial ; Plasmids ; Quorum Sensing ; }, abstract = {Horizontal genes transfer (HGT) plays an important role in the dissemination of antibiotic resistance genes (ARGs) in the environment. However, the mechanisms of HGT of ARGs under the influence of antibiotics in sub-MIC remain rarely explored. Moreover, given its collective nature, HGT was considered to be relative to quorum sensing (QS) system. To investigate whether QS has any impact on horizontal gene transfer of ARGs, experiments were conducted to determine the conjugative efficiency of plasmid RP4 on Escherichia coli (E.coli) under the influences of tetracyclines (TCs), quorum sensing autoinducers (AIs) and quorum sensing inhibitors (QSIs). The results indicated that the sub-MIC TCs could facilitate the conjugative transfer of RP4, a process which could be enhanced by AIs but inhibited by QSIs. This study demonstrated the roles that QS played in the dissemination of ARGs, and provided theoretical insights into the mechanism of HGT of ARGs in the environment.}, }
@article {pmid29350135, year = {2018}, author = {Becker, K and van Alen, S and Idelevich, EA and Schleimer, N and Seggewiß, J and Mellmann, A and Kaspar, U and Peters, G}, title = {Plasmid-Encoded Transferable mecB-Mediated Methicillin Resistance in Staphylococcus aureus.}, journal = {Emerging infectious diseases}, volume = {24}, number = {2}, pages = {242-248}, pmid = {29350135}, issn = {1080-6059}, mesh = {Aged ; Bacterial Proteins/*genetics ; Gene Transfer, Horizontal ; Humans ; Male ; Methicillin Resistance/*genetics ; Methicillin-Resistant Staphylococcus aureus/*genetics ; Plasmids/*genetics ; }, abstract = {During cefoxitin-based nasal screening, phenotypically categorized methicillin-resistant Staphylococcus aureus (MRSA) was isolated and tested negative for the presence of the mecA and mecC genes as well as for the SCCmec-orfX junction region. The isolate was found to carry a mecB gene previously described for Macrococcus caseolyticus but not for staphylococcal species. The gene is flanked by β-lactam regulatory genes similar to mecR, mecI, and blaZ and is part of an 84.6-kb multidrug-resistance plasmid that harbors genes encoding additional resistances to aminoglycosides (aacA-aphD, aphA, and aadK) as well as macrolides (ermB) and tetracyclines (tetS). This further plasmidborne β-lactam resistance mechanism harbors the putative risk of acceleration or reacceleration of MRSA spread, resulting in broad ineffectiveness of β-lactams as a main therapeutic application against staphylococcal infections.}, }
@article {pmid29350130, year = {2018}, author = {Martínez, JL}, title = {Ecology and Evolution of Chromosomal Gene Transfer between Environmental Microorganisms and Pathogens.}, journal = {Microbiology spectrum}, volume = {6}, number = {1}, pages = {}, pmid = {29350130}, issn = {2165-0497}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/*drug effects/*genetics/pathogenicity ; Bacterial Infections/drug therapy/pathology ; Drug Resistance, Multiple, Bacterial/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genetic Speciation ; Genome, Bacterial/*genetics ; Interspersed Repetitive Sequences/genetics ; Virulence/genetics ; }, abstract = {Inspection of the genomes of bacterial pathogens indicates that their pathogenic potential relies, at least in part, on the activity of different elements that have been acquired by horizontal gene transfer from other (usually unknown) microorganisms. Similarly, in the case of resistance to antibiotics, besides mutation-driven resistance, the incorporation of novel resistance genes is a widespread evolutionary procedure for the acquisition of this phenotype. Current information in the field supports the idea that most (if not all) genes acquired by horizontal gene transfer by bacterial pathogens and contributing to their virulence potential or to antibiotic resistance originate in environmental, not human-pathogenic, microorganisms. Herein I discuss the potential functions that the genes that are dubbed virulence or antibiotic resistance genes may have in their original hosts in nonclinical, natural ecosystems. In addition, I discuss the potential bottlenecks modulating the transfer of virulence and antibiotic resistance determinants and the consequences in terms of speciation of acquiring one or another of both categories of genes. Finally, I propose that exaptation, a process by which a change of function is achieved by a change of habitat and not by changes in the element with the new functionality, is the basis of the evolution of virulence determinants and of antibiotic resistance genes.}, }
@article {pmid29348510, year = {2018}, author = {Lin, R and Qin, F and Shen, B and Shi, Q and Liu, C and Zhang, X and Jiao, Y and Lu, J and Gao, Y and Suarez-Fernandez, M and Lopez-Moya, F and Lopez-Llorca, LV and Wang, G and Mao, Z and Ling, J and Yang, Y and Cheng, X and Xie, B}, title = {Genome and secretome analysis of Pochonia chlamydosporia provide new insight into egg-parasitic mechanisms.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {1123}, pmid = {29348510}, issn = {2045-2322}, mesh = {Chromosomes, Fungal ; Computational Biology/methods ; Gene Duplication ; Gene Transfer, Horizontal ; Genomics/methods ; High-Throughput Nucleotide Sequencing ; Host-Parasite Interactions ; Host-Pathogen Interactions ; Hypocreales/*genetics/*metabolism ; *Metabolome ; Phylogeny ; Plants/microbiology/parasitology ; *Proteome ; Selection, Genetic ; *Transcriptome ; }, abstract = {Pochonia chlamydosporia infects eggs and females of economically important plant-parasitic nematodes. The fungal isolates parasitizing different nematodes are genetically distinct. To understand their intraspecific genetic differentiation, parasitic mechanisms, and adaptive evolution, we assembled seven putative chromosomes of P. chlamydosporia strain 170 isolated from root-knot nematode eggs (~44 Mb, including 7.19% of transposable elements) and compared them with the genome of the strain 123 (~41 Mb) isolated from cereal cyst nematode. We focus on secretomes of the fungus, which play important roles in pathogenicity and fungus-host/environment interactions, and identified 1,750 secreted proteins, with a high proportion of carboxypeptidases, subtilisins, and chitinases. We analyzed the phylogenies of these genes and predicted new pathogenic molecules. By comparative transcriptome analysis, we found that secreted proteins involved in responses to nutrient stress are mainly comprised of proteases and glycoside hydrolases. Moreover, 32 secreted proteins undergoing positive selection and 71 duplicated gene pairs encoding secreted proteins are identified. Two duplicated pairs encoding secreted glycosyl hydrolases (GH30), which may be related to fungal endophytic process and lost in many insect-pathogenic fungi but exist in nematophagous fungi, are putatively acquired from bacteria by horizontal gene transfer. The results help understanding genetic origins and evolution of parasitism-related genes.}, }
@article {pmid29346651, year = {2018}, author = {Corel, E and Méheust, R and Watson, AK and McInerney, JO and Lopez, P and Bapteste, E}, title = {Bipartite Network Analysis of Gene Sharings in the Microbial World.}, journal = {Molecular biology and evolution}, volume = {35}, number = {4}, pages = {899-913}, pmid = {29346651}, issn = {1537-1719}, mesh = {Gene Flow ; *Gene Transfer, Horizontal ; *Genes, Microbial ; Plasmids/genetics ; Viruses/genetics ; }, abstract = {Extensive microbial gene flows affect how we understand virology, microbiology, medical sciences, genetic modification, and evolutionary biology. Phylogenies only provide a narrow view of these gene flows: plasmids and viruses, lacking core genes, cannot be attached to cellular life on phylogenetic trees. Yet viruses and plasmids have a major impact on cellular evolution, affecting both the gene content and the dynamics of microbial communities. Using bipartite graphs that connect up to 149,000 clusters of homologous genes with 8,217 related and unrelated genomes, we can in particular show patterns of gene sharing that do not map neatly with the organismal phylogeny. Homologous genes are recycled by lateral gene transfer, and multiple copies of homologous genes are carried by otherwise completely unrelated (and possibly nested) genomes, that is, viruses, plasmids and prokaryotes. When a homologous gene is present on at least one plasmid or virus and at least one chromosome, a process of "gene externalization," affected by a postprocessed selected functional bias, takes place, especially in Bacteria. Bipartite graphs give us a view of vertical and horizontal gene flow beyond classic taxonomy on a single very large, analytically tractable, graph that goes beyond the cellular Web of Life.}, }
@article {pmid29346643, year = {2018}, author = {Sassi, M and Guérin, F and Lesec, L and Isnard, C and Fines-Guyon, M and Cattoir, V and Giard, JC}, title = {Genetic characterization of a VanG-type vancomycin-resistant Enterococcus faecium clinical isolate.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {73}, number = {4}, pages = {852-855}, doi = {10.1093/jac/dkx510}, pmid = {29346643}, issn = {1460-2091}, mesh = {Adult ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/*genetics ; Drug Resistance, Microbial/*genetics ; Enterococcus faecium/*drug effects/*genetics/isolation &amp; purification ; Female ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; Gene Transfer Techniques ; Gene Transfer, Horizontal ; Genotype ; Gram-Positive Bacterial Infections/*microbiology ; Humans ; Interspersed Repetitive Sequences ; Microbial Sensitivity Tests ; Operon ; Phenotype ; Real-Time Polymerase Chain Reaction ; Reverse Transcriptase Polymerase Chain Reaction ; Teicoplanin/pharmacology ; Vancomycin/*pharmacology ; *Vancomycin Resistance ; Whole Genome Sequencing ; }, abstract = {OBJECTIVES: To characterize, phenotypically and genotypically, the first Enterococcus faecium clinical isolate harbouring a vanG operon.<br><br>METHODS: The antibiotic resistance profile of E. faecium 16-346 was determined and its whole genome sequenced using PacBio technology. Attempts to transfer vancomycin resistance by filter mating were performed and the inducibility of expression of the vanG operon was studied by reverse-transcription quantitative PCR (RT-qPCR) in the presence or absence of subinhibitory concentrations of vancomycin.<br><br>RESULTS: E. faecium 16-346 was resistant to rifampicin (MIC >4&#x2009;mg/L), erythromycin (MIC >4&#x2009;mg/L), tetracycline (MIC >16&#x2009;mg/L) and vancomycin (MIC 8&#x2009;mg/L), but susceptible to teicoplanin (MIC 0.5&#x2009;mg/L). The strain harboured the vanG operon in its chromosome, integrated in a 45.5&#x2009;kb putative mobile genetic element, similar to that of Enterococcus faecalis BM4518. We were unable to transfer vancomycin resistance from E. faecium 16-346 to E. faecium BM4107 and E. faecalis JH2-2. Lastly, transcription of the vanG gene was inducible by vancomycin.<br><br>CONCLUSIONS: This is, to the best of our knowledge, the first report of a VanG-type vancomycin-resistant strain of E. faecium. Despite the alarm pulled because of the therapeutic problems caused by VRE, our work shows that new resistant loci can still be found in E. faecium.}, }
@article {pmid29343426, year = {2018}, author = {Shoulah, SA and Oschmann, AM and Selim, A and Semmler, T and Schwarz, C and Kamal, E and Hamouda, F and Galila, E and Bitter, W and Lewin, A}, title = {Environmental Mycobacterium avium subsp. hominissuis have a higher probability to act as a recipient in conjugation than clinical strains.}, journal = {Plasmid}, volume = {95}, number = {}, pages = {28-35}, doi = {10.1016/j.plasmid.2018.01.003}, pmid = {29343426}, issn = {1095-9890}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Base Sequence ; *Conjugation, Genetic ; Drug Resistance, Multiple, Bacterial/genetics ; Gene Transfer, Horizontal ; Genetic Variation ; *Genome, Bacterial ; Genomic Islands ; Humans ; Microbial Sensitivity Tests ; Mycobacterium avium/drug effects/*genetics/isolation &amp; purification ; Opportunistic Infections/microbiology ; Plasmids/*chemistry/metabolism ; Sequence Alignment ; *Soil Microbiology ; Tuberculosis/microbiology ; *Water Microbiology ; }, abstract = {Mycobacterium avium subsp. hominissuis (MAH) is a widespread opportunistic pathogen that can be isolated from environment (dust, soil and water) and patients with lung or lymphnode infection. In our previous research we revealed the pronounced genetic diversity in MAH by identifying eight different types of a newly described genomic island. In order to identify mechanisms of such horizontal gene transfer we now analyzed the ability of 47 MAH isolates to inherit the conjugative plasmid pRAW from M. marinum. A higher percentage of environmental isolates (22.7%) compared to clinical isolates (8%) had the capacity to function as recipient in conjugal plasmid transfer. Genetic analysis showed additionally that environmental isolates contained more genes homologous to genes present on conjugative mycobacterial plasmids than clinical isolates. Comparative analysis of the genomes of the isolates pointed to a possible association between the ability to act as recipient in conjugation and the structure of a genomic region containing the radC gene and a type I restriction/modification system. Finally we found that uptake of pRAW decreased the resistance against various antibiotics.}, }
@article {pmid29339424, year = {2018}, author = {Vidor, CJ and Watts, TD and Adams, V and Bulach, D and Couchman, E and Rood, JI and Fairweather, NF and Awad, M and Lyras, D}, title = {Clostridium sordellii Pathogenicity Locus Plasmid pCS1-1 Encodes a Novel Clostridial Conjugation Locus.}, journal = {mBio}, volume = {9}, number = {1}, pages = {}, pmid = {29339424}, issn = {2150-7511}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Clostridium sordellii/*genetics ; Computational Biology ; *Conjugation, Genetic ; *Gene Transfer, Horizontal ; Genes, Bacterial ; *Genetic Loci ; Multigene Family ; *Plasmids ; }, abstract = {A major virulence factor in Clostridium sordellii-mediated infection is the toxin TcsL, which is encoded within a region of the genome called the pathogenicity locus (PaLoc). C. sordellii isolates carry the PaLoc on the pCS1 family of plasmids, of which there are four characterized members. Here, we determined the potential mobility of pCS1 plasmids and characterized a fifth unique pCS1 member. Using a derivative of the pCS1-1 plasmid from strain ATCC 9714 which had been marked with the ermB erythromycin resistance gene, conjugative transfer into a recipient C. sordellii isolate, R28058, was demonstrated. Bioinformatic analysis of pCS1-1 identified a novel conjugation gene cluster defined as the C. sordellii transfer (cst) locus. Interruption of genes within the cst locus resulted in loss of pCS1-1 transfer, which was restored upon complementation in trans These studies provided clear evidence that genes within the cst locus are essential for the conjugative transfer of pCS1-1. The cst locus is present on all pCS1 subtypes, and homologous loci were identified on toxin-encoding plasmids from Clostridium perfringens and Clostridium botulinum and also carried within genomes of Clostridium difficile isolates, indicating that it is a widespread clostridial conjugation locus. The results of this study have broad implications for the dissemination of toxin genes and, potentially, antibiotic resistance genes among members of a diverse range of clostridial pathogens, providing these microorganisms with a survival advantage within the infected host.IMPORTANCEC. sordellii is a bacterial pathogen that causes severe infections in humans and animals, with high mortality rates. While the pathogenesis of C. sordellii infections is not well understood, it is known that the toxin TcsL is an important virulence factor. Here, we have shown the ability of a plasmid carrying the tcsL gene to undergo conjugative transfer between distantly related strains of C. sordellii, which has far-reaching implications for the ability of C. sordellii to acquire the capacity to cause disease. Plasmids that carry tcsL encode a previously uncharacterized conjugation locus, and individual genes within this locus were shown to be required for conjugative transfer. Furthermore, homologues on toxin plasmids from other clostridial species were identified, indicating that this region represents a novel clostridial conjugation locus. The results of this study have broad implications for the dissemination of virulence genes among members of a diverse range of clostridial pathogens.}, }
@article {pmid29339296, year = {2018}, author = {Zhou, K and Luo, Q and Wang, Q and Huang, C and Lu, H and Rossen, JWA and Xiao, Y and Li, L}, title = {Silent transmission of an IS1294b-deactivated mcr-1 gene with inducible colistin resistance.}, journal = {International journal of antimicrobial agents}, volume = {51}, number = {6}, pages = {822-828}, doi = {10.1016/j.ijantimicag.2018.01.004}, pmid = {29339296}, issn = {1872-7913}, mesh = {Aged ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics ; Colistin/*pharmacology ; Conjugation, Genetic/genetics ; DNA Transposable Elements/*genetics ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/*drug effects/*genetics/isolation &amp; purification ; Escherichia coli Proteins/*genetics ; Female ; Gene Transfer, Horizontal/genetics ; Humans ; }, abstract = {Global dissemination of the mobile colistin resistance mcr-1 is of particular concern as colistin is one of the last-resort antibiotics for the treatment of severe infections caused by carbapenem-resistant Gram-negative bacteria. In this study, an inactive form of mcr-1 in a fluoroquinolone-resistant and colistin-susceptible uropathogenic Escherichia coli isolate (ECO3347) was characterised. The mcr-1 gene was deactivated by insertion of a 1.7-kb IS1294b element flanked by two tetramers (GTTC) and located on a 62-kb pHNSHP45-like plasmid (p3347-mcr-1). Single-step and multistep selections were used to induce colistin resistance in vitro in ECO3347. ECO3347 acquired colistin resistance (MIC = 16-32 mg/L) only after a serial passage selection with increasing concentrations of colistin (2-8 mg/L). Deactivated mcr-1 was re-activated by loss of IS1294b without any remnants in most colistin-resistant mutants. In addition, a novel amino acid variant (Leu105Pro) in the CheY homologous receiver domain of PmrA was detected in one colistin-resistant mutant. Plasmid p3347-mcr-1[+] carrying the re-activated mcr-1 gene is transferrable to E. coli J53 recipient with a high conjugation rate (ca. 10[-1] cells per recipient cell). Transconjugants showed an identical growth status to J53, suggesting lack of a fitness cost after acquiring p3347-mcr-1[+]. These results highlight that the disrupted mcr-1 gene has the potential for wide silent dissemination with the help of pHNSHP45-like epidemic plasmids. Inducible colistin resistance may likely compromise the success of clinical treatment and infection control. Continuous monitoring of mcr-1 is imperative for understanding and tackling its dissemination in different forms.}, }
@article {pmid29333587, year = {2018}, author = {Zhang, K and Di, YN and Qi, L and Sui, Y and Wang, TY and Fan, L and Lv, ZM and Wu, XC and Wang, PM and Zheng, DQ}, title = {Genetic characterization and modification of a bioethanol-producing yeast strain.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {5}, pages = {2213-2223}, doi = {10.1007/s00253-017-8727-1}, pmid = {29333587}, issn = {1432-0614}, support = {31401058//National Natural Science Foundation of China/ ; 31370132//National Natural Science Foundation of China/ ; LY18C060002//Natural Science Foundation of Zhejiang Province/ ; }, mesh = {Diploidy ; Ethanol/*metabolism ; Fermentation ; Genome, Fungal ; Molecular Sequence Annotation ; Phenotype ; Phylogeny ; Saccharomyces cerevisiae/classification/*genetics/isolation &amp; purification/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; }, abstract = {Yeast Saccharomyces cerevisiae strains isolated from different sources generally show extensive genetic and phenotypic diversity. Understanding how genomic variations influence phenotypes is important for developing strategies with improved economic traits. The diploid S. cerevisiae strain NY1308 is used for cellulosic bioethanol production. Whole genome sequencing identified an extensive amount of single nucleotide variations and small insertions/deletions in the genome of NY1308 compared with the S288c genome. Gene annotation of the assembled NY1308 genome showed that 43 unique genes are absent in the S288c genome. Phylogenetic analysis suggested most of the unique genes were obtained through horizontal gene transfer from other species. RNA-Seq revealed that some unique genes were not functional in NY1308 due to unidentified intron sequences. During bioethanol fermentation, NY1308 tends to flocculate when certain inhibitors (derived from the pretreatment of cellulosic feedstock) are present in the fermentation medium. qRT-PCR and genetic manipulation confirmed that the novel gene, NYn43, contributed to the flocculation ability of NY1308. Deletion of NYn43 resulted in a faster fermentation rate for NY1308. This work disclosed the genetic characterization of a bioethanol-producing S. cerevisiae strain and provided a useful paradigm showing how the genetic diversity of the yeast population would facilitate the personalized development of desirable traits.}, }
@article {pmid29330182, year = {2018}, author = {Pinilla-Redondo, R and Riber, L and Sørensen, SJ}, title = {Fluorescence Recovery Allows the Implementation of a Fluorescence Reporter Gene Platform Applicable for the Detection and Quantification of Horizontal Gene Transfer in Anoxic Environments.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {6}, pages = {}, pmid = {29330182}, issn = {1098-5336}, mesh = {Anaerobiosis ; Bacteria/*genetics ; *Environment ; Fluorescence ; *Gene Transfer, Horizontal ; *Genes, Reporter ; Staining and Labeling/instrumentation/*methods ; }, abstract = {The study of horizontal gene transfer (HGT) in microbial communities has been revolutionized by significant advances in cultivation-independent methods based on fluorescence reporter gene technologies. Recently, the combination of these novel approaches with flow cytometry has presented itself as one of the most powerful tools to study the spread of mobile genetic elements (MGEs) in the environment. However, the use of fluorescent markers, like green fluorescent protein (GFP) and mCherry, is limited by environmental constraints, such as oxygen availability and pH levels, that affect the correct maturation of their fluorophores. Few studies have characterized the effects of such environmental conditions in a systematic way, and the sheer amount of distinct protein variants requires each system to be examined in an individual fashion. The lack of efficient and reliable markers to monitor HGT in anaerobic environments, coupled to the abundance of ecologically and clinically relevant oxygen-deprived niches in which bacteria thrive, calls for the urgent development of suitable tools that permit its study. In an attempt to devise a process that allows the implementation of the mentioned dual-labeling system to anoxic milieus, the aerobic fluorescence recovery of mCherry and GFPmut3, as well as the effect of pH on their fluorescence intensities, was studied. The findings present a solution to an intrinsic problem that has long hampered the utilization of this system, highlight its pH limitations, and provide experimental tools that will help broaden its horizon of application to other fields.IMPORTANCE Many anaerobic environments, like the gastrointestinal tract, anaerobic digesters, and the interiors of dense biofilms, have been shown to be hotspots for horizontal gene transfer (HGT). Despite the increasing wealth of reports warning about the alarming spread of antibiotic resistance determinants, to date, HGT studies mainly rely on cultivation-based methods. Unfortunately, the relevance of these studies is often questionable, as only a minor fraction of bacteria can be cultivated. A recently developed approach to monitoring the fate of plasmids in microbial communities is based on a fluorescence dual-labeling system and allows the bypassing of cultivation. However, the fluorescent proteins on which it is founded are constrained by pH levels and by their strict dependence on oxygen for the maturation of their fluorophores. This study focused on the development and validation of an appropriate aerobic fluorescence recovery (AFR) method for this platform, as this embodies the missing technical link impeding its implementation in anoxic environments.}, }
@article {pmid29329601, year = {2018}, author = {Khafizova, G and Dobrynin, P and Polev, D and Matveeva, T}, title = {Nicotiana glauca whole-genome investigation for cT-DNA study.}, journal = {BMC research notes}, volume = {11}, number = {1}, pages = {18}, pmid = {29329601}, issn = {1756-0500}, support = {16-16-10010//Russian Science Foundation/ ; 1.52.1647.2016//Saint Petersburg State University/ ; }, mesh = {DNA, Bacterial/*genetics ; Gene Transfer, Horizontal/*genetics ; Genome, Plant/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; Sequence Analysis, DNA/*methods ; Nicotiana/*genetics ; }, abstract = {OBJECTIVE: Nicotiana glauca (tree tobacco) is a naturally transgenic plant, containing sequences acquired from Agrobacterium rhizogenes by horizontal gene transfer. Besides, N. glauca contains a wide profile of alkaloids of medical interest.<br><br>DATA DESCRIPTION: We report a high-depth sequencing and de novo assembly of N. glauca full genome and analysis of genome elements with bacterial origin. The draft genome assembly is 3.2&#xa0;Gb, with N50 size of 31.1&#xa0;kbp. Comparative analysis confirmed the presence of single, previously described gT insertion. No evidence was acquired to support idea of multiple T-DNA insertions in the N. glauca genome. Our data is the first comprehensive de novo assembly of tree tobacco and provide valuable information for researches in pharmacological and in phylogenetic fields.}, }
@article {pmid29329439, year = {2018}, author = {Lee, SJ and Kong, M and Harrison, P and Hijri, M}, title = {Conserved Proteins of the RNA Interference System in the Arbuscular Mycorrhizal Fungus Rhizoglomus irregulare Provide New Insight into the Evolutionary History of Glomeromycota.}, journal = {Genome biology and evolution}, volume = {10}, number = {1}, pages = {328-343}, pmid = {29329439}, issn = {1759-6653}, mesh = {Amino Acid Sequence ; Cyanobacteria/chemistry/genetics ; *Evolution, Molecular ; Fungal Proteins/chemistry/genetics ; Gene Transfer, Horizontal ; Genes, Fungal ; Glomeromycota/chemistry/*genetics ; Mycorrhizae/chemistry/*genetics ; *Phylogeny ; RNA Interference ; Ribonuclease III/chemistry/genetics ; Sequence Alignment ; Symbiosis ; Transcriptome ; }, abstract = {Horizontal gene transfer (HGT) is an important mechanism in the evolution of many living organisms particularly in Prokaryotes where genes are frequently dispersed between taxa. Although, HGT has been reported in Eukaryotes, its accumulative effect and its frequency has been questioned. Arbuscular mycorrhizal fungi (AMF) are an early diverged fungal lineage belonging to phylum Glomeromycota, whose phylogenetic position is still under debate. The history of AMF and land plant symbiosis dates back to at least 460 Ma. However, Glomeromycota are estimated to have emerged much earlier than land plants. In this study, we surveyed genomic and transcriptomic data of the model arbuscular mycorrhizal fungus Rhizoglomus irregulare (synonym Rhizophagus irregularis) and its relatives to search for evidence of HGT that occurred during AMF evolution. Surprisingly, we found a signature of putative HGT of class I ribonuclease III protein-coding genes that occurred from autotrophic cyanobacteria genomes to R. irregulare. At least one of two HGTs was conserved among AMF species with high levels of sequence similarity. Previously, an example of intimate symbiosis between AM fungus and cyanobacteria was reported in the literature. Ribonuclease III family enzymes are important in small RNA regulation in Fungi together with two additional core proteins (Argonaute/piwi and RdRP). The eukaryotic RNA interference system found in AMF was conserved and showed homology with high sequence similarity in Mucoromycotina, a group of fungi closely related to Glomeromycota. Prior to this analysis, class I ribonuclease III has not been identified in any eukaryotes. Our results indicate that a unique acquisition of class I ribonuclease III in AMF is due to a HGT event that occurred from cyanobacteria to Glomeromycota, at the latest before the divergence of the two Glomeromycota orders Diversisporales and Glomerales.}, }
@article {pmid29327679, year = {2018}, author = {Getino, M and de la Cruz, F}, title = {Natural and Artificial Strategies To Control the Conjugative Transmission of Plasmids.}, journal = {Microbiology spectrum}, volume = {6}, number = {1}, pages = {}, pmid = {29327679}, issn = {2165-0497}, mesh = {Anti-Bacterial Agents/pharmacology ; Antibodies, Monoclonal/immunology ; Bacterial Proteins/immunology ; Conjugation, Genetic/genetics/*physiology ; Drug Resistance, Multiple, Bacterial/*genetics ; Endodeoxyribonucleases/immunology ; Escherichia coli/*genetics/*metabolism ; Fatty Acids, Unsaturated/chemistry ; Gene Transfer, Horizontal/*physiology ; Pili, Sex/immunology/physiology ; Plasmids/genetics/*physiology ; }, abstract = {Conjugative plasmids are the main carriers of transmissible antibiotic resistance (AbR) genes. For that reason, strategies to control plasmid transmission have been proposed as potential solutions to prevent AbR dissemination. Natural mechanisms that bacteria employ as defense barriers against invading genomes, such as restriction-modification or CRISPR-Cas systems, could be exploited to control conjugation. Besides, conjugative plasmids themselves display mechanisms to minimize their associated burden or to compete with related or unrelated plasmids. Thus, FinOP systems, composed of FinO repressor protein and FinP antisense RNA, aid plasmids to regulate their own transfer; exclusion systems avoid conjugative transfer of related plasmids to the same recipient bacteria; and fertility inhibition systems block transmission of unrelated plasmids from the same donor cell. Artificial strategies have also been designed to control bacterial conjugation. For instance, intrabodies against R388 relaxase expressed in recipient cells inhibit plasmid R388 conjugative transfer; pIII protein of bacteriophage M13 inhibits plasmid F transmission by obstructing conjugative pili; and unsaturated fatty acids prevent transfer of clinically relevant plasmids in different hosts, promoting plasmid extinction in bacterial populations. Overall, a number of exogenous and endogenous factors have an effect on the sophisticated process of bacterial conjugation. This review puts them together in an effort to offer a wide picture and inform research to control plasmid transmission, focusing on Gram-negative bacteria.}, }
@article {pmid29326683, year = {2017}, author = {Kim, BJ and Kim, BR and Kook, YH and Kim, BJ}, title = {Role of the DNA Mismatch Repair Gene MutS4 in Driving the Evolution of Mycobacterium yongonense Type I via Homologous Recombination.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2578}, pmid = {29326683}, issn = {1664-302X}, abstract = {We recently showed that Mycobacterium yongonense could be divided into two genotypes: Type I, in which the rpoB gene has been transferred from Mycobacterium parascrofulaceum, and Type II, in which the rpoB gene has not been transferred. Comparative genome analysis of three M. yongonense Type I, two M. yongonense Type II and M. parascrofulaceum type strains were performed in this study to gain insight into gene transfer from M. parascrofulaceum into M. yongonense Type I strains. We found two genome regions transferred from M. parascrofulaceum: one contained 3 consecutive genes, including the rpoBC operon, and the other contained 57 consecutive genes that had been transferred into M. yongonense Type I genomes via homologous recombination. Further comparison between the M. yongonense Type I and II genomes revealed that Type I, but not Type II has a distinct DNA mismatch repair gene (MutS4 subfamily) that was possibly transferred via non-homologous recombination from other actinomycetes. We hypothesized that it could facilitate homologous recombination from the M. parascrofulaceum to the M. yongonense Type I genomes. We therefore generated recombinant Mycobacterium smegmatis containing a MutS4 operon of M. yongonense. We found that the M. tuberculosis rpoB fragment with a rifampin resistance-conferring mutation was more frequently inserted into recombinant M. smegmatis than the wild type, suggesting that MutS4 is a driving force in the gene transfer from M. parascrofulaceum to M. yongonense Type I strains via homologous recombination. In conclusion, our data indicated that MutS4 in M. yongonense Type I genomes may drive gene transfer from M. parascrofulaceum via homologous recombination, resulting in division of M. yongonense into two genotypes, Type I and II.}, }
@article {pmid29325123, year = {2018}, author = {Tomasch, J and Wang, H and Hall, ATK and Patzelt, D and Preusse, M and Petersen, J and Brinkmann, H and Bunk, B and Bhuju, S and Jarek, M and Geffers, R and Lang, AS and Wagner-Döbler, I}, title = {Packaging of Dinoroseobacter shibae DNA into Gene Transfer Agent Particles Is Not Random.}, journal = {Genome biology and evolution}, volume = {10}, number = {1}, pages = {359-369}, pmid = {29325123}, issn = {1759-6653}, mesh = {Bacterial Proteins/genetics ; Base Composition ; DNA, Bacterial/*genetics ; *Gene Transfer, Horizontal ; Multigene Family ; Oceans and Seas ; Rhodobacteraceae/*genetics ; }, abstract = {Gene transfer agents (GTAs) are phage-like particles which contain a fragment of genomic DNA of the bacterial or archaeal producer and deliver this to a recipient cell. GTA gene clusters are present in the genomes of almost all marine Rhodobacteraceae (Roseobacters) and might be important contributors to horizontal gene transfer in the world's oceans. For all organisms studied so far, no obvious evidence of sequence specificity or other nonrandom process responsible for packaging genomic DNA into GTAs has been found. Here, we show that knock-out of an autoinducer synthase gene of Dinoroseobacter shibae resulted in overproduction and release of functional GTA particles (DsGTA). Next-generation sequencing of the 4.2-kb DNA fragments isolated from DsGTAs revealed that packaging was not random. DNA from low-GC conjugative plasmids but not from high-GC chromids was excluded from packaging. Seven chromosomal regions were strongly overrepresented in DNA isolated from DsGTA. These packaging peaks lacked identifiable conserved sequence motifs that might represent recognition sites for the GTA terminase complex. Low-GC regions of the chromosome, including the origin and terminus of replication, were underrepresented in DNA isolated from DsGTAs. DNA methylation reduced packaging frequency while the level of gene expression had no influence. Chromosomal regions found to be over- and underrepresented in DsGTA-DNA were regularly spaced. We propose that a "headful" type of packaging is initiated at the sites of coverage peaks and, after linearization of the chromosomal DNA, proceeds in both directions from the initiation site. GC-content, DNA-modifications, and chromatin structure might influence at which sides GTA packaging can be initiated.}, }
@article {pmid29322462, year = {2018}, author = {Huseby, DL and Hughes, D}, title = {Methods to Determine Mutational Trajectories After Experimental Evolution of Antibiotic Resistance.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1736}, number = {}, pages = {95-103}, doi = {10.1007/978-1-4939-7638-6_9}, pmid = {29322462}, issn = {1940-6029}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/*genetics ; *DNA Mutational Analysis/methods ; *Drug Resistance, Bacterial ; Genome, Bacterial ; *Microbial Sensitivity Tests ; *Mutation ; Whole Genome Sequencing ; }, abstract = {The evolution of bacterial resistance to antibiotics by mutation within the genome (as distinct from horizontal gene transfer of new material into a genome) could occur in a single step but is usually a multistep process. Resistance evolution can be studied in laboratory environments by serial passage of bacteria in liquid culture or on agar, with selection at constant, or varying, concentrations of drug. Whole genome sequencing can be used to make an initial analysis of the evolved mutants. The trajectory of evolution can be determined by sequence analysis of strains from intermediate steps in the evolution, complemented by phenotypic analysis of genetically reconstructed isogenic strains that recapitulate the intermediate steps in the evolution.}, }
@article {pmid29321570, year = {2018}, author = {Knudsen, PK and Gammelsrud, KW and Alfsnes, K and Steinbakk, M and Abrahamsen, TG and Müller, F and Bohlin, J}, title = {Transfer of a bla CTX-M-1-carrying plasmid between different Escherichia coli strains within the human gut explored by whole genome sequencing analyses.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {280}, pmid = {29321570}, issn = {2045-2322}, mesh = {Escherichia coli/classification/drug effects/*genetics ; Escherichia coli Infections/*microbiology ; Gastrointestinal Tract/*microbiology ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; Multilocus Sequence Typing ; Phylogeny ; Plasmids/*genetics ; Polymorphism, Single Nucleotide ; Whole Genome Sequencing ; beta-Lactam Resistance ; beta-Lactamases/*genetics ; }, abstract = {Horizontal transfer of antibiotic resistance determinants contributes to dissemination of antibiotic resistance. Such transfer of resistance genes within the human gut has been documented in some in vivo studies. The present study investigated seven bla CTX-M-1-carrying Escherichia coli isolates from three consecutive faecal samples collected from one cystic fibrosis patient in a nine-months period, by analysing whole genome sequencing data. The analyses showed that the seven E. coli isolates represented three genetically diverse strains. All isolates contained bla CTX-M-1-carrying Incl1 plasmids that shared a common 101 kb backbone differing by only four SNPs. The plasmids harboured by the three different E. coli strains varied within limited regions suggestive of recombination events, according to the phylogenetic topology of the genomes of the isolates harbouring them. The findings strongly suggest that horizontal transfer of a bla CTX-M-1-carrying plasmid had occurred within the patient´s gut. The study illustrates the within-host diversity of faecally carried resistant E. coli isolates and highlights the value of collecting multiple bacterial colonies from longitudinally collected samples to assess faecal carriage of resistant enterobacteria. The clustering of the plasmids with the corresponding E. coli strains carrying them indicates that the plasmids appear to have adapted to their respective E. coli hosts.}, }
@article {pmid29321301, year = {2018}, author = {Stevenson, C and Hall, JPJ and Brockhurst, MA and Harrison, E}, title = {Plasmid stability is enhanced by higher-frequency pulses of positive selection.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1870}, pages = {}, pmid = {29321301}, issn = {1471-2954}, mesh = {Adaptation, Physiological ; Analysis of Variance ; Conjugation, Genetic ; DNA Transposable Elements ; Environment ; Gene Transfer, Horizontal ; Mercury/toxicity ; Operon ; Phenotype ; Plasmids/drug effects/*genetics ; Pseudomonas fluorescens/drug effects/*genetics ; *Selection, Genetic ; }, abstract = {Plasmids accelerate bacterial adaptation by sharing ecologically important traits between lineages. However, explaining plasmid stability in bacterial populations is challenging owing to their associated costs. Previous theoretical and experimental studies suggest that pulsed positive selection may explain plasmid stability by favouring gene mobility and promoting compensatory evolution to ameliorate plasmid cost. Here we test how the frequency of pulsed positive selection affected the dynamics of a mercury-resistance plasmid, pQBR103, in experimental populations of Pseudomonas fluorescens SBW25. Plasmid dynamics varied according to the frequency of Hg[2+] positive selection: in the absence of Hg[2+] plasmids declined to low frequency, whereas pulses of Hg[2+] selection allowed plasmids to sweep to high prevalence. Compensatory evolution to ameliorate the cost of plasmid carriage was widespread across the entire range of Hg[2+] selection regimes, including both constant and pulsed Hg[2+] selection. Consistent with theoretical predictions, gene mobility via conjugation appeared to play a greater role in promoting plasmid stability under low-frequency pulses of Hg[2+] selection. However, upon removal of Hg[2+] selection, plasmids which had evolved under low-frequency pulse selective regimes declined over time. Our findings suggest that temporally variable selection environments, such as those created during antibiotic treatments, may help to explain the stability of mobile plasmid-encoded resistance.}, }
@article {pmid29320853, year = {2018}, author = {Clark, RL and Gordon, GC and Bennett, NR and Lyu, H and Root, TW and Pfleger, BF}, title = {High-CO2 Requirement as a Mechanism for the Containment of Genetically Modified Cyanobacteria.}, journal = {ACS synthetic biology}, volume = {7}, number = {2}, pages = {384-391}, pmid = {29320853}, issn = {2161-5063}, support = {T32 GM008349/GM/NIGMS NIH HHS/United States ; }, mesh = {Carbon Dioxide/*metabolism ; *Gene Deletion ; *Gene Transfer, Horizontal ; *Microorganisms, Genetically-Modified/genetics/growth &amp; development ; *Synechococcus/genetics/growth &amp; development ; }, abstract = {As researchers engineer cyanobacteria for biotechnological applications, we must consider potential environmental release of these organisms. Previous theoretical work has considered cyanobacterial containment through elimination of the CO2-concentrating mechanism (CCM) to impose a high-CO2 requirement (HCR), which could be provided in the cultivation environment but not in the surroundings. In this work, we experimentally implemented an HCR containment mechanism in Synechococcus sp. strain PCC7002 (PCC7002) through deletion of carboxysome shell proteins and showed that this mechanism contained cyanobacteria in a 5% CO2 environment. We considered escape through horizontal gene transfer (HGT) and reduced the risk of HGT escape by deleting competence genes. We showed that the HCR containment mechanism did not negatively impact the performance of a strain of PCC7002 engineered for L-lactate production. We showed through coculture experiments of HCR strains with ccm-containing strains that this HCR mechanism reduced the frequency of escape below the NIH recommended limit for recombinant organisms of one escape event in 10[8] CFU.}, }
@article {pmid29316517, year = {2018}, author = {Marathe, NP and Janzon, A and Kotsakis, SD and Flach, CF and Razavi, M and Berglund, F and Kristiansson, E and Larsson, DGJ}, title = {Functional metagenomics reveals a novel carbapenem-hydrolyzing mobile beta-lactamase from Indian river sediments contaminated with antibiotic production waste.}, journal = {Environment international}, volume = {112}, number = {}, pages = {279-286}, doi = {10.1016/j.envint.2017.12.036}, pmid = {29316517}, issn = {1873-6750}, mesh = {Anti-Bacterial Agents/pharmacology ; Carbapenems/*metabolism ; Drug Industry ; Geologic Sediments/*microbiology ; Industrial Waste/adverse effects ; *Metagenome/drug effects/genetics ; Metagenomics ; Rivers/microbiology ; Water Pollutants, Chemical/*analysis ; *beta-Lactam Resistance/drug effects/genetics ; beta-Lactamases/*genetics ; }, abstract = {Evolution has provided environmental bacteria with a plethora of genes that give resistance to antibiotic compounds. Under anthropogenic selection pressures, some of these genes are believed to be recruited over time into pathogens by horizontal gene transfer. River sediment polluted with fluoroquinolones and other drugs discharged from bulk drug production in India constitute an environment with unprecedented, long-term antibiotic selection pressures. It is therefore plausible that previously unknown resistance genes have evolved and/or are promoted here. In order to search for novel resistance genes, we therefore analyzed such river sediments by a functional metagenomics approach. DNA fragments providing resistance to different antibiotics in E. coli were sequenced using Sanger and PacBio RSII platforms. We recaptured the majority of known antibiotic resistance genes previously identified by open shot-gun metagenomics sequencing of the same samples. In addition, seven novel resistance gene candidates (six beta-lactamases and one amikacin resistance gene) were identified. Two class A beta-lactamases, blaRSA1 and blaRSA2, were phylogenetically close to clinically important ESBLs like blaGES, blaBEL and blaL2, and were further characterized for their substrate spectra. The blaRSA1 protein, encoded as an integron gene cassette, efficiently hydrolysed penicillins, first generation cephalosporins and cefotaxime, while blaRSA2 was an inducible class A beta-lactamase, capable of hydrolyzing carbapenems albeit with limited efficiency, similar to the L2 beta-lactamase from Stenotrophomonas maltophilia. All detected novel genes were associated with plasmid mobilization proteins, integrons, and/or other resistance genes, suggesting a potential for mobility. This study provides insight into a resistome shaped by an exceptionally strong and long-term antibiotic selection pressure. An improved knowledge of mobilized resistance factors in the external environment may make us better prepared for the resistance challenges that we may face in clinics in the future.}, }
@article {pmid29315358, year = {2018}, author = {Dotto, BR and Carvalho, EL and da Silva, AF and Dezordi, FZ and Pinto, PM and Campos, TL and Rezende, AM and Wallau, GDL}, title = {HTT-DB: new features and updates.}, journal = {Database : the journal of biological databases and curation}, volume = {2018}, number = {}, pages = {}, pmid = {29315358}, issn = {1758-0463}, mesh = {*DNA Transposable Elements ; *Databases, Genetic ; *Eukaryota ; *Gene Transfer, Horizontal ; *Internet ; *Transduction, Genetic ; }, abstract = {Horizontal Transfer (HT) of genetic material between species is a common phenomenon among Bacteria and Archaea species and several databases are available for information retrieval and data mining. However, little attention has been given to this phenomenon among eukaryotic species mainly due to the lower proportion of these events. In the last years, a vertiginous amount of new HT events involving eukaryotic species was reported in the literature, highlighting the need of a common repository to keep the scientific community up to date and describe overall trends. Recently, we published the first HT database focused on HT of transposable elements among eukaryotes: the Horizontal Transposon Transfer DataBase (http://lpa.saogabriel.unipampa.edu.br: 8080/httdatabase/). Here, we present new features and updates of this unique database: (i) its expansion to include virus-host exchange of genetic material, which we called Horizontal Virus Transfer (HVT) and (ii) the availability of a web server for HT detection, where we implemented the online version of vertical and horizontal inheritance consistence analysis (VHICA), an R package developed for HT detection. These improvements will help researchers to navigate through known HVT cases, take data-informed decision and export figures based on keywords searches. Moreover, the availability of the VHICA as an online tool will make this software easily reachable even for researchers with no or little computation knowledge as well as foster our capability to detect new HT events in a wide variety of taxa. (Database URL: http://lpa.saogabriel.unipampa.edu.br:8080/httdatabase/).}, }
@article {pmid29314736, year = {2018}, author = {De Puysseleyr, K and Kieckens, E and De Puysseleyr, L and Van den Wyngaert, H and Ahmed, B and Van Lent, S and Creasy, HH and Myers, GSA and Vanrompay, D}, title = {Development of a Chlamydia suis-specific antibody enzyme-linked immunosorbent assay based on the use of a B-cell epitope of the polymorphic membrane protein C.}, journal = {Transboundary and emerging diseases}, volume = {65}, number = {2}, pages = {e457-e469}, doi = {10.1111/tbed.12783}, pmid = {29314736}, issn = {1865-1682}, mesh = {Animals ; Antibodies, Bacterial/*blood ; Bacterial Outer Membrane Proteins/*immunology ; Chlamydia/*immunology ; Chlamydia Infections/immunology/*veterinary ; Complement Fixation Tests ; Enzyme-Linked Immunosorbent Assay/*veterinary ; Epitopes, B-Lymphocyte/*immunology ; Female ; Membrane Proteins ; Protein C ; Recombinant Proteins/immunology ; Red Meat ; Serologic Tests ; Swine ; Swine Diseases/*immunology ; }, abstract = {Chlamydia suis infections lead to economic loss in the pork industry. Chlamydia suis infections could be successfully treated with tetracyclines until the appearance of a tetracycline resistant phenotype, which was acquired via horizontal gene transfer of the tet(C) gene. Given the importance of C. suis as a swine pathogen and as a recently emerged tetracycline resistant pathogen with zoonotic potential, our aim was to develop a sensitive C. suis-specific antibody ELISA based on the polymorphic membrane proteins (Pmps). Chlamydia Pmps are important virulence factors and candidate antigens for serodiagnosis. We identified nine Pmps (PmpA to I) in C. suis strain MD56 using a recently developed Hidden-Markov model. PmpC was the most promising candidate for the development of a C. suis-specific antibody ELISA as the protein was absent in C. abortus, C. pecorum and C. psittaci which also infect pigs and as the protein contained C. suis-specific amino acid regions, absent in C. trachomatis PmpC. We identified an immunodominant B-cell epitope in C. suis PmpC using experimental porcine sera. The sensitivity and specificity of the PmpC ELISA was compared to the complement fixation test (CFT) and to a recombinant MOMP ELISA using experimental sera. The PmpC ELISA detected all positive control sera and was in contrast to CFT and the rMOMP ELISA 100% C. suis specific as positive control sera against other Chlamydia species did not react in the PmpC ELISA. The test was successfully validated using slaughterhouse sera and sera from clinically affected pigs. The PmpC ELISA could assist in diminishing the spread of C. suis infections in the pork industry.}, }
@article {pmid29312823, year = {2018}, author = {Madueño, L and Paul, C and Junier, T and Bayrychenko, Z and Filippidou, S and Beck, K and Greub, G and Bürgmann, H and Junier, P}, title = {A historical legacy of antibiotic utilization on bacterial seed banks in sediments.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e4197}, pmid = {29312823}, issn = {2167-8359}, abstract = {The introduction of antibiotics for both medical and non-medical purposes has had a positive effect on human welfare and agricultural output in the past century. However, there is also an important ecological legacy regarding the use of antibiotics and the consequences of increased levels of these compounds in the environment as a consequence of their use and disposal. This legacy was investigated by quantifying two antibiotic resistance genes (ARG) conferring resistance to tetracycline (tet(W)) and sulfonamide (sul1) in bacterial seed bank DNA in sediments. The industrial introduction of antibiotics caused an abrupt increase in the total abundance of tet(W) and a steady increase in sul1. The abrupt change in tet(W) corresponded to an increase in relative abundance from ca. 1960 that peaked around 1976. This pattern of accumulation was highly correlated with the abundance of specific members of the seed bank community belonging to the phylum Firmicutes. In contrast, the relative abundance of sul1 increased after 1976. This correlated with a taxonomically broad spectrum of bacteria, reflecting sul1 dissemination through horizontal gene transfer. The accumulation patterns of both ARGs correspond broadly to the temporal scale of medical antibiotic use. Our results show that the bacterial seed bank can be used to look back at the historical usage of antibiotics and resistance prevalence.}, }
@article {pmid29312272, year = {2017}, author = {Flórez, AB and Mayo, B}, title = {Antibiotic Resistance-Susceptibility Profiles of Streptococcus thermophilus Isolated from Raw Milk and Genome Analysis of the Genetic Basis of Acquired Resistances.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2608}, pmid = {29312272}, issn = {1664-302X}, abstract = {The food chain is thought to play an important role in the transmission of antibiotic resistances from commensal and beneficial bacteria to pathogens. Streptococcus thermophilus is a lactic acid bacterium of major importance as a starter for the dairy industry. This study reports the minimum inhibitory concentration (MIC) of 16 representative antimicrobial agents to 41 isolates of S. thermophilus derived from raw milk. Strains showing resistance to tetracycline (seven), erythromycin and clindamycin (two), and streptomycin and neomycin (one) were found. PCR amplification identified tet(S) in all the tetracycline-resistant strains, and ermB in the two erythromycin/clindamycin-resistant strains. Hybridisation experiments suggested each resistance gene to be located in the chromosome with a similar genetic organization. Five antibiotic-resistant strains -two resistant to tetracycline (St-2 and St-9), two resistant to erythromycin/clindamycin (St-5 and St-6), and one resistant to streptomycin/neomycin (St-10)- were subjected to genome sequencing and analysis. The tet(S) gene was identified in small contigs of 3.2 and 3.7 kbp in St-2 and St-9, respectively, flanked by truncated copies of insertion sequence (IS) elements. Similarly, ermB in St-6 and St-5 was found in contigs of 1.6 and 28.1 kbp, respectively. Sequence analysis and comparison of the largest contig showed it to contain three segments (21.9, 3.7, and 1.4 kbp long) highly homologous to non-collinear sequences of pRE25 from Enterococcus faecalis. These segments contained the ermB gene, a transference module with an origin of transfer (oriT) plus 15 open reading frames encoding proteins involved in conjugation, and modules for plasmid replication and segregation. Homologous stretches were separated by short, IS-related sequences, resembling the genetic organization of the integrative and conjugative elements (ICEs) found in Streptococcus species. No gene known to provide aminoglycoside resistance was seen in St-10. Four strain-specific amino acid substitutions in the RsmG methyltransferase were scored in this strain; these might be associated to its streptomycin/neomycin resistance. Under yogurt manufacturing and storage conditions, no transfer of either tet(S) or ermB from S. thermophilus to L. delbrueckii was detected. The present results contribute toward characterisation of the antibiotic resistance profiles in S. thermophilus, provide evidence for the genetic basis of acquired resistances and deepen on their transference capability.}, }
@article {pmid29312194, year = {2017}, author = {Kiu, R and Caim, S and Alexander, S and Pachori, P and Hall, LJ}, title = {Probing Genomic Aspects of the Multi-Host Pathogen Clostridium perfringens Reveals Significant Pangenome Diversity, and a Diverse Array of Virulence Factors.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2485}, pmid = {29312194}, issn = {1664-302X}, support = {/WT_/Wellcome Trust/United Kingdom ; BB/J004529/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/00044409/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {Clostridium perfringens is an important cause of animal and human infections, however information about the genetic makeup of this pathogenic bacterium is currently limited. In this study, we sought to understand and characterise the genomic variation, pangenomic diversity, and key virulence traits of 56 C. perfringens strains which included 51 public, and 5 newly sequenced and annotated genomes using Whole Genome Sequencing. Our investigation revealed that C. perfringens has an "open" pangenome comprising 11667 genes and 12.6% of core genes, identified as the most divergent single-species Gram-positive bacterial pangenome currently reported. Our computational analyses also defined C. perfringens phylogeny (16S rRNA gene) in relation to some 25 Clostridium species, with C. baratii and C. sardiniense determined to be the closest relatives. Profiling virulence-associated factors confirmed presence of well-characterised C. perfringens-associated exotoxins genes including α-toxin (plc), enterotoxin (cpe), and Perfringolysin O (pfo or pfoA), although interestingly there did not appear to be a close correlation with encoded toxin type and disease phenotype. Furthermore, genomic analysis indicated significant horizontal gene transfer events as defined by presence of prophage genomes, and notably absence of CRISPR defence systems in >70% (40/56) of the strains. In relation to antimicrobial resistance mechanisms, tetracycline resistance genes (tet) and anti-defensins genes (mprF) were consistently detected in silico (tet: 75%; mprF: 100%). However, pre-antibiotic era strain genomes did not encode for tet, thus implying antimicrobial selective pressures in C. perfringens evolutionary history over the past 80 years. This study provides new genomic understanding of this genetically divergent multi-host bacterium, and further expands our knowledge on this medically and veterinary important pathogen.}, }
@article {pmid29312186, year = {2017}, author = {Mohsin, M and Raza, S and Schaufler, K and Roschanski, N and Sarwar, F and Semmler, T and Schierack, P and Guenther, S}, title = {High Prevalence of CTX-M-15-Type ESBL-Producing E. coli from Migratory Avian Species in Pakistan.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2476}, pmid = {29312186}, issn = {1664-302X}, abstract = {The increased presence of clinically relevant multidrug resistant bacteria in natural environments is an emerging challenge for global health care. Little is known regarding the occurrence of extended-spectrum beta-lactamase producing Escherichia coli (ESBL-E. coli) from environmental sentinels in Pakistan. The goal of the current study was to gain insights into the prevalence and phylogenetic relationships of ESBL-E. coli recovered from wild birds in Pakistan during winter migration. After initial screening of fecal samples on selective chromogenic agar, ESBL-E.coli were analyzed phenotypically using the Vitek-2 automated system. Genotypic characterization was performed using whole genome sequencing (WGS) followed by an in-depth in silico analysis. Of 150 birds screened, 26 (17.3%) were fecal carriers of ESBL-E. coli. Of these, 88.4% isolates exhibited multidrug resistance (MDR) phenotypes. Resistance to cefotaxime, ceftazidime, ampicillin, doxycycline, tetracycline and sulfamethoxazole/trimethoprim (CTX-CAZ-AM-DC-TE-SXT) represented the most common pattern of MDR (76.9%). WGS data analysis found blaCTX-M-15 as the predominant ESBL genotype (92.3%). Other genes encoding resistance to sulfonamides (sul1/sul2/sul3), aminoglycosides (strA, strB, aadA1, aadA2, aadA5, aac(3)-IId-like, aac(3)-IVa-like and aph(4)-Ia), trimethoprim (dfrA14 or dfrA17), tetracyclines [tet(A)/tet(B)], and fluoroquinolones (qnrS1) were detected commonly, often encoded on IncF-type plasmids (76.9%). ESBL-E. coli were assigned to 17 different sequence types (STs) of which ST10 and ST7097 (4 isolates each) were the most abundant followed by ST4720, ST93, and ST1139 (2 isolates each). Core-genome phylogeny of the isolates found low numbers (0-29) of single nucleotide polymorphisms (SNPs) in isolates belonged to ST7097 originated from two different locations (Chashma barrage and Rasul barrage). Similar trends were found among isolates belong to ST1139. In addition, WGS-based plasmid typing and S1-digestion found plasmids of the same pMLST type (IncF[F-:A-:B53]) and similar sizes in different bacterial and avian hosts suggesting horizontal gene transfer as another possibility for the spread of ESBL-E. coli in avian wildlife in Pakistan.}, }
@article {pmid29311273, year = {2018}, author = {Trokter, M and Waksman, G}, title = {Translocation through the Conjugative Type IV Secretion System Requires Unfolding of Its Protein Substrate.}, journal = {Journal of bacteriology}, volume = {200}, number = {6}, pages = {}, pmid = {29311273}, issn = {1098-5530}, support = {098302/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacterial Proteins/chemistry/*metabolism ; Conjugation, Genetic/*physiology ; Escherichia coli ; Plasmids ; *Protein Unfolding ; Tetrahydrofolate Dehydrogenase/metabolism ; Type IV Secretion Systems/*physiology ; }, abstract = {Bacterial conjugation, a mechanism of horizontal gene transfer, is the major means by which antibiotic resistance spreads among bacteria (1, 2). Conjugative plasmids are transferred from one bacterium to another through a type IV secretion system (T4SS) in the form of single-stranded DNA covalently attached to a protein called relaxase. The relaxase is fully functional both in a donor cell (prior to conjugation) and recipient cell (after conjugation). Here, we demonstrate that the protein substrate has to unfold for efficient translocation through the conjugative T4SS. Furthermore, we present various relaxase modifications that preserve the function of the relaxase but block substrate translocation. This study brings us a step closer to deciphering the complete mechanism of T4SS substrate translocation, which is vital for the development of new therapies against multidrug-resistant pathogenic bacteria.IMPORTANCE Conjugation is the principal means by which antibiotic resistance genes spread from one bacterium to another (1, 2). During conjugation, a covalent complex of single-stranded DNA and a protein termed relaxase is transported by a type IV secretion system. To date, it is not known whether the relaxase requires unfolding prior to transport. In this report, we use functional assays to monitor the transport of wild-type relaxase and variants containing unfolding-resistant domains and show that these domains reduce conjugation and protein transport dramatically. Mutations that lower the free energy of unfolding in these domains do not block translocation and can even promote it. We thus conclude that the unfolding of the protein substrate is required during transport.}, }
@article {pmid29311079, year = {2018}, author = {Igawa, G and Yamagishi, Y and Lee, KI and Dorin, M and Shimuta, K and Suematsu, H and Nakayama, SI and Mikamo, H and Unemo, M and Ohnishi, M}, title = {Neisseria cinerea with High Ceftriaxone MIC Is a Source of Ceftriaxone and Cefixime Resistance-Mediating penA Sequences in Neisseria gonorrhoeae.}, journal = {Antimicrobial agents and chemotherapy}, volume = {62}, number = {3}, pages = {}, pmid = {29311079}, issn = {1098-6596}, mesh = {Alleles ; Bacteremia/diagnosis/drug therapy/*microbiology ; Base Sequence ; Carrier Proteins/*genetics/metabolism ; Cephalosporin Resistance/*genetics ; Gene Expression ; *Gene Transfer, Horizontal ; Gonorrhea/diagnosis/drug therapy/*microbiology ; Humans ; Microbial Sensitivity Tests ; Mutation ; Neisseria cinerea/drug effects/*genetics/metabolism ; Neisseria gonorrhoeae/drug effects/*genetics/metabolism ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Serine-Type D-Ala-D-Ala Carboxypeptidase ; }, abstract = {Mosaic penA alleles have caused most of the cephalosporin resistance in Neisseria gonorrhoeae, but their evolution is mostly unknown. The penA gene from Neisseria cinerea strain AM1601 (ceftriaxone MIC, 1.0 μg/ml) caused ceftriaxone resistance (MIC, 1 μg/ml) in a ceftriaxone-susceptible gonococcal strain. The 3'-terminal half of AM1601 penA was almost identical to that of the ceftriaxone-resistant gonococcal GU140106 and FC428 strains. N. cinerea can serve as a reservoir of ceftriaxone resistance-mediating penA sequences that can be transferred to gonococci.}, }
@article {pmid29311060, year = {2018}, author = {Mancini, S and Poirel, L and Kieffer, N and Nordmann, P}, title = {Transposition of Tn1213 Encoding the PER-1 Extended-Spectrum β-Lactamase.}, journal = {Antimicrobial agents and chemotherapy}, volume = {62}, number = {3}, pages = {}, pmid = {29311060}, issn = {1098-6596}, mesh = {Anti-Bacterial Agents/pharmacology ; Base Sequence ; Chloramphenicol/pharmacology ; *DNA Transposable Elements ; Drug Resistance, Multiple, Bacterial/genetics ; Escherichia coli/drug effects/enzymology/*genetics/growth &amp; development ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Plasmids/*chemistry/metabolism ; beta-Lactamases/*genetics/metabolism ; }, abstract = {PER-1 is an extended-spectrum β-lactamase that is encoded by a gene located in composite transposon Tn1213 made by two distinct insertion sequences, namely, ISPa12 and ISPa13. In vitro mobilization performed in Escherichia coli shows that Tn1213 is functional and is able to mobilize the blaPER-1 gene, although at a very low frequency (ca. 1 × 10[-9]).}, }
@article {pmid29307571, year = {2018}, author = {Bibbal, D and Um, MM and Diallo, AA and Kérourédan, M and Dupouy, V and Toutain, PL and Bousquet-Mélou, A and Oswald, E and Brugère, H}, title = {Mixing of Shiga toxin-producing and enteropathogenic Escherichia coli in a wastewater treatment plant receiving city and slaughterhouse wastewater.}, journal = {International journal of hygiene and environmental health}, volume = {221}, number = {2}, pages = {355-363}, doi = {10.1016/j.ijheh.2017.12.009}, pmid = {29307571}, issn = {1618-131X}, mesh = {*Abattoirs ; Drug Resistance, Bacterial ; Enteropathogenic Escherichia coli/genetics/*isolation &amp; purification ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Phylogeny ; Shiga-Toxigenic Escherichia coli/genetics/*isolation &amp; purification ; Virulence Factors/genetics ; Wastewater/*microbiology ; Water Purification ; }, abstract = {Wastewater of human and animal may contain Shiga toxin-producing (STEC) and enteropathogenic (EPEC) Escherichia coli. We evaluated the prevalence of such strains in a wastewater treatment plant (WWTP) receiving both city and slaughterhouse wastewater. PCR screenings were performed on 12,248 E. coli isolates. The prevalence of STEC in city wastewater, slaughterhouse wastewater and treated effluent was 0.22%, 0.07% and 0.22%, respectively. The prevalence of EPEC at the same sampling sites was 0.63%, 0.90% and 0.55%. No significant difference was observed between the sampling points. Treatment had no impact on these prevalences. Enterohemorrhagic E. coli (EHEC) O157:H7 and O111:H8 were isolated from the treated effluent rejected into the river. The characteristics of STEC and EPEC differed according to their origin. City wastewater contained STEC with various stx subtypes associated with serious human disease, whereas slaughterhouse wastewater contained exclusively STEC with stx2e subtype. All the EPEC strains were classified as atypical and were screened for the ε, γ1 and β1 subtypes, known to be associated with the EHEC mainly involved in human infections in France. In city wastewater, eae subtypes remained largely unidentified; whereas eae-β1 was the most frequent subtype in slaughterhouse wastewater. Moreover, the EPEC isolated from slaughterhouse wastewater were positive for other EHEC-associated virulence markers, including top five serotypes, the ehxA gene, putative adherence genes and OI-122 associated genes. The possibility that city wastewater could contain a pool of stx genes associated with human disease and that slaughterhouse wastewater could contain a pool of EPEC sharing similar virulence genes with EHEC, was highlighted. Mixing of such strains in WWTP could lead to the emergence of EHEC by horizontal gene transfer.}, }
@article {pmid29306353, year = {2017}, author = {Levade, I and Terrat, Y and Leducq, JB and Weil, AA and Mayo-Smith, LM and Chowdhury, F and Khan, AI and Boncy, J and Buteau, J and Ivers, LC and Ryan, ET and Charles, RC and Calderwood, SB and Qadri, F and Harris, JB and LaRocque, RC and Shapiro, BJ}, title = {Vibrio cholerae genomic diversity within and between patients.}, journal = {Microbial genomics}, volume = {3}, number = {12}, pages = {}, pmid = {29306353}, issn = {2057-5858}, support = {T32 AI007061/AI/NIAID NIH HHS/United States ; K08 AI089721/AI/NIAID NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; //CIHR/Canada ; R01 AI099243/AI/NIAID NIH HHS/United States ; K08 AI123494/AI/NIAID NIH HHS/United States ; R01 AI106878/AI/NIAID NIH HHS/United States ; U01 AI058935/AI/NIAID NIH HHS/United States ; R01 AI103055/AI/NIAID NIH HHS/United States ; R56 AI106878/AI/NIAID NIH HHS/United States ; R37 AI106878/AI/NIAID NIH HHS/United States ; }, mesh = {Bangladesh/epidemiology ; Cholera/*epidemiology/*microbiology ; Evolution, Molecular ; Gain of Function Mutation ; Gene Transfer, Horizontal ; *Genetic Variation ; Genomics ; Haiti/epidemiology ; Humans ; Loss of Function Mutation ; Plasmids/genetics ; Point Mutation ; Vibrio cholerae/classification/*genetics ; Whole Genome Sequencing ; }, abstract = {Cholera is a severe, water-borne diarrhoeal disease caused by toxin-producing strains of the bacterium Vibrio cholerae. Comparative genomics has revealed 'waves' of cholera transmission and evolution, in which clones are successively replaced over decades and centuries. However, the extent of V. cholerae genetic diversity within an epidemic or even within an individual patient is poorly understood. Here, we characterized V. cholerae genomic diversity at a micro-epidemiological level within and between individual patients from Bangladesh and Haiti. To capture within-patient diversity, we isolated multiple (8 to 20) V. cholerae colonies from each of eight patients, sequenced their genomes and identified point mutations and gene gain/loss events. We found limited but detectable diversity at the level of point mutations within hosts (zero to three single nucleotide variants within each patient), and comparatively higher gene content variation within hosts (at least one gain/loss event per patient, and up to 103 events in one patient). Much of the gene content variation appeared to be due to gain and loss of phage and plasmids within the V. cholerae population, with occasional exchanges between V. cholerae and other members of the gut microbiota. We also show that certain intra-host variants have phenotypic consequences. For example, the acquisition of a Bacteroides plasmid and non-synonymous mutations in a sensor histidine kinase gene both reduced biofilm formation, an important trait for environmental survival. Together, our results show that V. cholerae is measurably evolving within patients, with possible implications for disease outcomes and transmission dynamics.}, }
@article {pmid29306352, year = {2017}, author = {Reid, CJ and Wyrsch, ER and Roy Chowdhury, P and Zingali, T and Liu, M and Darling, AE and Chapman, TA and Djordjevic, SP}, title = {Porcine commensal Escherichia coli: a reservoir for class 1 integrons associated with IS26.}, journal = {Microbial genomics}, volume = {3}, number = {12}, pages = {}, pmid = {29306352}, issn = {2057-5858}, mesh = {Animals ; Australia ; Drug Resistance, Multiple, Bacterial/*genetics ; Environmental Pollutants ; Escherichia coli/*classification/*genetics/isolation &amp; purification/pathogenicity ; Feces/*microbiology ; *Food Microbiology ; Gene Transfer, Horizontal ; Genetic Variation ; Humans ; Integrons/*genetics ; Mutagenesis, Insertional ; Swine/*microbiology ; Symbiosis ; Virulence/genetics ; Whole Genome Sequencing ; Zoonoses/microbiology ; }, abstract = {Porcine faecal waste is a serious environmental pollutant. Carriage of antimicrobial-resistance genes (ARGs) and virulence-associated genes (VAGs), and the zoonotic potential of commensal Escherichia coli from swine are largely unknown. Furthermore, little is known about the role of commensal E. coli as contributors to the mobilization of ARGs between food animals and the environment. Here, we report whole-genome sequence analysis of 103 class 1 integron-positive E. coli from the faeces of healthy pigs from two commercial production facilities in New South Wales, Australia. Most strains belonged to phylogroups A and B1, and carried VAGs linked with extraintestinal infection in humans. The 103 strains belonged to 37 multilocus sequence types and clonal complex 10 featured prominently. Seventeen ARGs were detected and 97 % (100/103) of strains carried three or more ARGs. Heavy-metal-resistance genes merA, cusA and terA were also common. IS26 was observed in 98 % (101/103) of strains and was often physically associated with structurally diverse class 1 integrons that carried unique genetic features, which may be tracked. This study provides, to our knowledge, the first detailed genomic analysis and point of reference for commensal E. coli of porcine origin in Australia, facilitating tracking of specific lineages and the mobile resistance genes they carry.}, }
@article {pmid29306009, year = {2018}, author = {Li, Y and Yang, L and Fu, J and Yan, M and Chen, D and Zhang, L}, title = {Genotyping and high flux sequencing of the bacterial pathogenic elements - integrons.}, journal = {Microbial pathogenesis}, volume = {116}, number = {}, pages = {22-25}, doi = {10.1016/j.micpath.2017.12.073}, pmid = {29306009}, issn = {1096-1208}, mesh = {Bacterial Infections/microbiology ; China ; Drug Resistance, Bacterial ; Enterococcus/*genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; Genotyping Techniques/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; *Integrons ; *Interspersed Repetitive Sequences ; Pseudomonas/*genetics/isolation &amp; purification ; Staphylococcus/*genetics/isolation &amp; purification ; Virulence ; }, abstract = {Regarded as a common genetic element responsible for horizontal gene transfer and wide spread of antimicrobial resistance among a large variety of bacteria, integrons are commonly distributed and considered as a determinant in the acquisition and evolution of virulence and antibiotic resistance. To date, the surveillances of integrons have been widely conducted in clinic, community even husbandry. For exact and accurate integron screening, as well as resistant cassettes, reliable monitoring methods is need. Current methods applied on integron screening are mainly conducted by the screening of integrases, followed by the detection of various gene cassettes inserted into integrons. PCR and PCR-related methods (such as RFLP) are mainly employed under such circumstances. Matured LAMP and Sequencing technology have lowered cost and dramatically increased throughput in integron screening and possessed the advantages in similarity analysis of mutated resistant cassettes. This review focused on the classification and characterization of integrons, antimicrobial resistance of integron and genotyping methods for integrons. In methodology, PCR, LAMP and Sequencing technology were mainly introduced for the screening of various classes' integrons and the detection of resistant gene cassettes. Staphylococcus, Pseudomonas and Enterococcus were selected as typical integron-positive clinical and environmental pathogens screened with three methods mentioned above. With the surveillance of the occurrence of integron and resistance gene cassettes conducted in South China, the review also summarized the occurrence, pathogenicity and virulence mediated by integrons.}, }
@article {pmid29305957, year = {2018}, author = {Liu, J and Yang, Y and Li, Y and Liu, D and Tuo, H and Wang, H and Call, DR and Davis, M and Zhang, A}, title = {Isolation of an IncP-1 plasmid harbouring mcr-1 from a chicken isolate of Citrobacter braakii in China.}, journal = {International journal of antimicrobial agents}, volume = {51}, number = {6}, pages = {936-940}, doi = {10.1016/j.ijantimicag.2017.12.030}, pmid = {29305957}, issn = {1872-7913}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Chickens ; Citrobacter/*drug effects/*genetics/isolation &amp; purification ; Colistin/*pharmacology ; DNA Transposable Elements/*genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Ethanolaminephosphotransferase/*genetics ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/genetics ; Humans ; Microbial Sensitivity Tests ; Plasmids/*genetics ; Whole Genome Sequencing ; }, abstract = {The plasmid-mediated colistin resistance gene mcr-1 has been found worldwide, but the diversity of organisms harbouring this gene is unknown. In this study, 12 colistin-resistant Citrobacter spp. isolates were obtained from diseased or dead chickens in China, and PCR analysis indicated that five were positive for mcr-1. One Citrobacter braakii strain (SCC4) with a multidrug-resistant phenotype was chosen for further analysis. SCC4 was resistant or intermediate-resistant to ten of the tested antibiotics, and the colistin minimum inhibitory concentration (MIC) was >4 µg/mL. A conjugation assay demonstrated successful transfer of colistin resistance to Escherichia coli strain J53 at a frequency of 10[-7] cells per recipient cell. Whole-genome sequencing revealed that SCC4 contained 13 antibiotic resistance genes in its genome, and the mcr-1 gene resided on a 44-kb self-transmissible IncP-type plasmid of a recently discovered IncP-1 clade. In addition, the mcr-1 gene was part of an insertion element (ISApl1-mcr-1-orf-ISApl1) that was excised from the plasmid as a circular intermediate form. This is the first report of mcr-1-posiitve C. braakii of animal origin and these findings highlight the fact that the mcr-1 gene can be found in normal enteric flora as part of broad-host-range plasmids.}, }
@article {pmid29301977, year = {2018}, author = {Dunning Hotopp, JC and Klasson, L}, title = {The Complexities and Nuances of Analyzing the Genome of Drosophila ananassae and Its Wolbachia Endosymbiont.}, journal = {G3 (Bethesda, Md.)}, volume = {8}, number = {1}, pages = {373-374}, pmid = {29301977}, issn = {2160-1836}, support = {R01 CA206188/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Drosophila/genetics ; Drosophila melanogaster ; Genome ; Retroelements ; Wolbachia/*genetics ; }, abstract = {In "Retrotransposons Are the Major Contributors to the Expansion of the Drosophila ananassae Muller F Element," Leung et al. (2017) improved contigs attributed to the Muller F element from the original CAF1 assembly, and used them to conclude that most of the sequence expansion of the fourth chromosome of D. ananassae is due to a higher transposon load than previously thought, but is not due to Wolbachia DNA integrations. While we do not disagree with the first conclusion, the authors base their second conclusion on the lack of homology detected between their improved CAF1 genome assembly attributed to D. ananassae and reference Wolbachia genomes. While the consensus CAF1 genome assembly lacks any sequence similarity to the reference genome of the Wolbachia endosymbiont of Drosophila melanogaster (wMel), numerous studies from multiple laboratories provide experimental support for a large lateral/horizontal gene transfer (LGT) of a Wolbachia genome into this D. ananassae line. As such, we strongly suspect that the original whole genome assembly was either constructed after the removal of all Wolbachia reads, or that Wolbachia sequences were directly removed from the contigs in the CAF1 assembly. Hence, Leung et al. (2017) could not have identified the Wolbachia LGT using the CAF1 assembly. This manuscript by Leung et al. (2017) highlights that an assembly of the Wolbachia sequence reads and their mate pairs was erroneously attributed solely to the Wolbachia endosymbiont, albeit before we understood the extent of LGT in D. ananassae As such, we recommend that the sequences deposited at the National Center for Biotechnology Information (NCBI) under PRJNA13365 should not be attributed to Wolbachia endosymbiont of D. ananassae, but should have their taxonomy reclassified by NCBI as "Unclassified sequences." As our knowledge about genome biology improves, we need to reconsider and reanalyze earlier genomes removing the prejudice introduced from now defunct paradigms.}, }
@article {pmid29300936, year = {2018}, author = {Martini, MC and Quiroga, MP and Pistorio, M and Lagares, A and Centrón, D and Del Papa, MF}, title = {Novel environmental class 1 integrons and cassette arrays recovered from an on-farm bio-purification plant.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {3}, pages = {}, doi = {10.1093/femsec/fix190}, pmid = {29300936}, issn = {1574-6941}, mesh = {Animals ; Bacteria/classification/enzymology/*genetics/isolation &amp; purification ; Bacterial Proteins/genetics/metabolism ; Farms ; Integrases/genetics/metabolism ; *Integrons ; Livestock ; Manure/microbiology ; Plasmids/genetics ; *Soil Microbiology ; }, abstract = {Rapid dissemination and emergence of novel antibiotic resistance genes among bacteria are rising problems worldwide. Since their discovery in clinical isolates in the late 1980s, class 1 integrons have been found in a wide range of bacterial genera and have been extensively studied as contributors to dissemination of antibiotic resistance. The present study aimed to investigate the presence and structure of class 1 integrons in plasmid-carrying bacterial isolates obtained from a biopurification system used for decontamination of pesticide-contaminated water as well as their possible role as reservoir of antimicrobial resistance gene cassettes. A total of 35 representative isolates were screened for the presence of class 1 integron integrase encoded by intI1. PCR and DNA sequencing revealed the presence of six class 1 integrons with four variable regions: 5΄CS-aadA1b-3΄CS, 5΄CS-aadA2-3΄CS, 5΄CS-aadA11cΔ-3΄CS and 5΄CS-dfrB3-aadA1di-catB2-aadA6k-3΄CS, the last two being unseen arrays of antimicrobial resistance gene cassettes associated with novel environmental alleles of intI1. These four class 1 integrons were identified as being present in four different genera, including Ochrobactrum, and Variovorax, where class 1 integrons have not been previously reported. The results provide evidence of the biopurification systems as a tank of class 1 integron carrying strains and novel environmental class 1 integron integrases associated with antimicrobial resistance gene cassette arrays.}, }
@article {pmid29294118, year = {2018}, author = {Wiktor, J and van der Does, M and Büller, L and Sherratt, DJ and Dekker, C}, title = {Direct observation of end resection by RecBCD during double-stranded DNA break repair in vivo.}, journal = {Nucleic acids research}, volume = {46}, number = {4}, pages = {1821-1833}, pmid = {29294118}, issn = {1362-4962}, support = {200782/Z/16/Z//Wellcome Trust/United Kingdom ; 247072/ERC_/European Research Council/International ; BB/I004785/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*DNA Breaks, Double-Stranded ; *DNA Repair ; DNA, Bacterial/metabolism ; Deoxyribonucleases, Type II Site-Specific ; Escherichia coli/genetics ; Escherichia coli Proteins/genetics/*metabolism ; Exodeoxyribonuclease V/genetics/*metabolism ; Gene Deletion ; Gene Transfer, Horizontal ; Luminescent Proteins ; Microscopy, Fluorescence ; Real-Time Polymerase Chain Reaction ; Saccharomyces cerevisiae Proteins ; }, abstract = {The formation of 3' single-stranded DNA overhangs is a first and essential step during homology-directed repair of double-stranded breaks (DSB) of DNA, a task that in Escherichia coli is performed by RecBCD. While this protein complex has been well characterized through in vitro single-molecule studies, it has remained elusive how end resection proceeds in the crowded and complex environment in live cells. Here, we develop a two-color fluorescent reporter to directly observe the resection of individual inducible DSB sites within live E. coli cells. Real-time imaging shows that RecBCD during end resection degrades DNA with remarkably high speed (∼1.6 kb/s) and high processivity (>∼100 kb). The results show a pronounced asymmetry in the processing of the two DNA ends of a DSB, where much longer stretches of DNA are degraded in the direction of terminus. The microscopy observations are confirmed using quantitative polymerase chain reaction measurements of the DNA degradation. Deletion of the recD gene drastically decreased the length of resection, allowing for recombination with short ectopic plasmid homologies and significantly increasing the efficiency of horizontal gene transfer between strains. We thus visualized and quantified DNA end resection by the RecBCD complex in live cells, recorded DNA-degradation linked to end resection and uncovered a general relationship between the length of end resection and the choice of the homologous recombination template.}, }
@article {pmid29294107, year = {2018}, author = {Bottacini, F and Morrissey, R and Roberts, RJ and James, K and van Breen, J and Egan, M and Lambert, J and van Limpt, K and Knol, J and Motherway, MO and van Sinderen, D}, title = {Comparative genome and methylome analysis reveals restriction/modification system diversity in the gut commensal Bifidobacterium breve.}, journal = {Nucleic acids research}, volume = {46}, number = {4}, pages = {1860-1877}, pmid = {29294107}, issn = {1362-4962}, mesh = {Bifidobacterium breve/classification/enzymology/*genetics ; *DNA Methylation ; DNA Modification Methylases/*genetics ; DNA Restriction Enzymes/genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomics ; Nucleotide Motifs ; Phylogeny ; }, abstract = {Bifidobacterium breve represents one of the most abundant bifidobacterial species in the gastro-intestinal tract of breast-fed infants, where their presence is believed to exert beneficial effects. In the present study whole genome sequencing, employing the PacBio Single Molecule, Real-Time (SMRT) sequencing platform, combined with comparative genome analysis allowed the most extensive genetic investigation of this taxon. Our findings demonstrate that genes encoding Restriction/Modification (R/M) systems constitute a substantial part of the B. breve variable gene content (or variome). Using the methylome data generated by SMRT sequencing, combined with targeted Illumina bisulfite sequencing (BS-seq) and comparative genome analysis, we were able to detect methylation recognition motifs and assign these to identified B. breve R/M systems, where in several cases such assignments were confirmed by restriction analysis. Furthermore, we show that R/M systems typically impose a very significant barrier to genetic accessibility of B. breve strains, and that cloning of a methyltransferase-encoding gene may overcome such a barrier, thus allowing future functional investigations of members of this species.}, }
@article {pmid29293812, year = {2017}, author = {Rabah, SO and Lee, C and Hajrah, NH and Makki, RM and Alharby, HF and Alhebshi, AM and Sabir, JSM and Jansen, RK and Ruhlman, TA}, title = {Plastome Sequencing of Ten Nonmodel Crop Species Uncovers a Large Insertion of Mitochondrial DNA in Cashew.}, journal = {The plant genome}, volume = {10}, number = {3}, pages = {}, doi = {10.3835/plantgenome2017.03.0020}, pmid = {29293812}, issn = {1940-3372}, mesh = {Anacardium/*genetics ; Crops, Agricultural/classification/*genetics ; DNA, Mitochondrial/*genetics ; *Genome, Plastid ; Introns ; Inverted Repeat Sequences ; *Mutagenesis, Insertional ; Phylogeny ; Species Specificity ; }, abstract = {In plant evolution, intracellular gene transfer (IGT) is a prevalent, ongoing process. While nuclear and mitochondrial genomes are known to integrate foreign DNA via IGT and horizontal gene transfer (HGT), plastid genomes (plastomes) have resisted foreign DNA incorporation and only recently has IGT been uncovered in the plastomes of a few land plants. In this study, we completed plastome sequences for l0 crop species and describe a number of structural features including variation in gene and intron content, inversions, and expansion and contraction of the inverted repeat (IR). We identified a putative in cinnamon (J. Presl) and other sequenced Lauraceae and an apparent functional transfer of to the nucleus of quinoa (Willd.). In the orchard tree cashew (L.), we report the insertion of an ∼6.7-kb fragment of mitochondrial DNA into the plastome IR. BLASTn analyses returned high identity hits to mitogenome sequences including an intact open reading frame. Using three plastome markers for five species of , we generated a phylogeny to investigate the distribution and timing of the insertion. Four species share the insertion, suggesting that this event occurred <20 million yr ago in a single clade in the genus. Our study extends the observation of mitochondrial to plastome IGT to include long-lived tree species. While previous studies have suggested possible mechanisms facilitating IGT to the plastome, more examples of this phenomenon, along with more complete mitogenome sequences, will be required before a common, or variable, mechanism can be elucidated.}, }
@article {pmid29292172, year = {2019}, author = {Killeen, PR}, title = {The non-Darwinian evolution of behavers and behaviors.}, journal = {Behavioural processes}, volume = {161}, number = {}, pages = {45-53}, doi = {10.1016/j.beproc.2017.12.024}, pmid = {29292172}, issn = {1872-8308}, mesh = {Animals ; *Behavior ; *Behavior, Animal ; *Biological Evolution ; *Cultural Evolution ; Culture ; Ecosystem ; Humans ; Selection, Genetic ; }, abstract = {Many readers of this journal have been schooled in both Darwinian evolution and Skinnerian psychology, which have in common the vision of powerful control of their subjects by their sequalae. Individuals of species that generate more successful offspring come to dominate their habitat; responses of those individuals that generate more reinforcers come to dominate the repertoire of the individual in that context. This is unarguable. What is questionable is how large a role these forces of selection play in the larger landscape of existing organisms and the repertoires of their individuals. Here it is argued that non-Darwinian and non-Skinnerian selection play much larger roles in both than the reader may appreciate. The argument is based on the history of, and recent advances in, microbiology. Lessons from that history re-illuminate the three putative domains of selection by consequences: The evolution of species, response repertoires, and cultures. It is argued that before, beneath, and after the cosmically brief but crucial epoch of Darwinian evolution that shaped creatures such as ourselves, non-Darwinian forces pervade all three domains.}, }
@article {pmid29291715, year = {2018}, author = {Groß, U and Brzuszkiewicz, E and Gunka, K and Starke, J and Riedel, T and Bunk, B and Spröer, C and Wetzel, D and Poehlein, A and Chibani, C and Bohne, W and Overmann, J and Zimmermann, O and Daniel, R and Liesegang, H}, title = {Comparative genome and phenotypic analysis of three Clostridioides difficile strains isolated from a single patient provide insight into multiple infection of C. difficile.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {1}, pmid = {29291715}, issn = {1471-2164}, support = {VWZN2889/3215//Nieders&#xe4;chsisches Vorab/International ; }, mesh = {Clostridiales/classification/cytology/*genetics/isolation &amp; purification ; Flagella/genetics/ultrastructure ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomics ; Gram-Positive Bacterial Infections/*microbiology ; Humans ; Phenotype ; Phylogeny ; }, abstract = {BACKGROUND: Clostridioides difficile infections (CDI) have emerged over the past decade causing symptoms that range from mild, antibiotic-associated diarrhea (AAD) to life-threatening toxic megacolon. In this study, we describe a multiple and isochronal (mixed) CDI caused by the isolates DSM 27638, DSM 27639 and DSM 27640 that already initially showed different morphotypes on solid media.<br><br>RESULTS: The three isolates belonging to the ribotypes (RT) 012 (DSM 27639) and 027 (DSM 27638 and DSM 27640) were phenotypically characterized and high quality closed genome sequences were generated. The genomes were compared with seven reference strains including three strains of the RT 027, two of the RT 017, and one of the RT 078 as well as a multi-resistant RT 012 strain. The analysis of horizontal gene transfer events revealed gene acquisition incidents that sort the strains within the time line of the spread of their RTs within Germany. We could show as well that horizontal gene transfer between the members of different RTs occurred within this multiple infection. In addition, acquisition and exchange of virulence-related features including antibiotic resistance genes were observed. Analysis of the two genomes assigned to RT 027 revealed three single nucleotide polymorphisms (SNPs) and apparently a regional genome modification within the flagellar switch that regulates the fli operon.<br><br>CONCLUSION: Our findings show that (i) evolutionary events based on horizontal gene transfer occur within an ongoing CDI and contribute to the adaptation of the species by the introduction of new genes into the genomes, (ii) within a multiple infection of a single patient the exchange of genetic material was responsible for a much higher genome variation than the observed SNPs.}, }
@article {pmid29283188, year = {2018}, author = {Peccoud, J and Cordaux, R and Gilbert, C}, title = {Analyzing Horizontal Transfer of Transposable Elements on a Large Scale: Challenges and Prospects.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {40}, number = {2}, pages = {}, doi = {10.1002/bies.201700177}, pmid = {29283188}, issn = {1521-1878}, mesh = {Animals ; DNA Transposable Elements/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome ; Sequence Analysis/methods ; }, abstract = {Whoever compares the genomes of distantly related species might find aberrantly high sequence similarity at certain loci. Such anomaly can only be explained by genetic material being transferred through other means than reproduction, that is, a horizontal transfer (HT). Between multicellular organisms, the transferred material will likely turn out to be a transposable element (TE). Because TEs can move between loci and invade chromosomes by replicating themselves, HT of TEs (HTT) profoundly impacts genome evolution. Yet, very few studies have quantified HTT at large taxonomic scales. Indeed, this task currently faces difficulties that range from the variable quality of available genome sequences to limitations of analytical procedures, some of which have been overlooked. Here we review the many challenges that an extensive analysis of HTT must overcome, we expose biases and limits of current methods, suggest solutions or workarounds, and reflect upon approaches that could be developed to better quantify this phenomenon.}, }
@article {pmid29281838, year = {2017}, author = {Ringel, PD and Hu, D and Basler, M}, title = {The Role of Type VI Secretion System Effectors in Target Cell Lysis and Subsequent Horizontal Gene Transfer.}, journal = {Cell reports}, volume = {21}, number = {13}, pages = {3927-3940}, doi = {10.1016/j.celrep.2017.12.020}, pmid = {29281838}, issn = {2211-1247}, mesh = {Acinetobacter/genetics ; Anti-Bacterial Agents/metabolism ; Bacterial Proteins/metabolism ; Gene Transfer, Horizontal/*genetics ; Immunity ; *Microbial Viability ; Peptidoglycan/metabolism ; Phenotype ; Pseudomonas aeruginosa/metabolism ; Type VI Secretion Systems/*genetics ; }, abstract = {Bacteria use type VI secretion systems (T6SSs) to manipulate host cells during pathogenesis or to kill competing bacteria, which, in some cases, increases horizontal gene transfer. These functions largely depend on T6SS regulation, dynamics, and the set of effectors that the system delivers into the target cells. Here, we show that Acinetobacter baylyi ADP1 assembles a highly dynamic T6SS capable of killing and lysing bacterial cells. T6SS function depends on conserved T6SS components as well as Acinetobacter-specific genes of unknown function. Five different effectors, encoded next to VgrG or PAAR proteins and their cognate immunity proteins, cause distinct changes in the prey cells, resulting in various degrees of their lysis. Prey lysis correlates with the rate of DNA transfer from prey to predator, suggesting that lytic effectors are required for efficient T6SS-dependent horizontal gene transfer in naturally competent bacteria.}, }
@article {pmid29277876, year = {2018}, author = {Rödelsperger, C}, title = {Comparative Genomics of Gene Loss and Gain in Caenorhabditis and Other Nematodes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1704}, number = {}, pages = {419-432}, doi = {10.1007/978-1-4939-7463-4_16}, pmid = {29277876}, issn = {1940-6029}, mesh = {Animals ; Biological Evolution ; Caenorhabditis/*genetics ; *Evolution, Molecular ; *Gene Duplication ; Gene Expression Regulation ; *Genes, Helminth ; Genome, Helminth ; Genomics/methods ; Nematoda/*genetics ; Phylogeny ; Species Specificity ; }, abstract = {Nematodes, such as Caenorhabditis elegans, form one of the most species-rich animal phyla. By now more than 30 nematode genomes have been published allowing for comparative genomic analyses at various different time-scales. The majority of a nematode's gene repertoire is represented by either duplicated or so-called orphan genes of unknown origin. This indicates the importance of mechanisms that generate new genes during the course of evolution. While it is certain that nematodes have acquired genes by horizontal gene transfer from various donors, this process only explains a small portion of the nematode gene content. As evolutionary genomic analyses strongly support that most orphan genes are indeed protein-coding, future studies will have to decide, whether they are result from extreme divergence or evolved de novo from previously noncoding sequences. In this contribution, I summarize several studies investigating gene loss and gain in nematodes and discuss the strengths and weaknesses of individual approaches and datasets. These approaches can be used to ask nematode-specific questions such as associated with the evolution of parasitism or with switches in mating systems, but also can complement studies in other animal phyla like vertebrates and insects to broaden our general view on genome evolution.}, }
@article {pmid29272410, year = {2018}, author = {Brito, PH and Chevreux, B and Serra, CR and Schyns, G and Henriques, AO and Pereira-Leal, JB}, title = {Genetic Competence Drives Genome Diversity in Bacillus subtilis.}, journal = {Genome biology and evolution}, volume = {10}, number = {1}, pages = {108-124}, pmid = {29272410}, issn = {1759-6653}, mesh = {Bacillus subtilis/*genetics ; Bacterial Proteins/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genetic Variation ; Genome, Bacterial ; Phylogeny ; }, abstract = {Prokaryote genomes are the result of a dynamic flux of genes, with increases achieved via horizontal gene transfer and reductions occurring through gene loss. The ecological and selective forces that drive this genomic flexibility vary across species. Bacillus subtilis is a naturally competent bacterium that occupies various environments, including plant-associated, soil, and marine niches, and the gut of both invertebrates and vertebrates. Here, we quantify the genomic diversity of B. subtilis and infer the genome dynamics that explain the high genetic and phenotypic diversity observed. Phylogenomic and comparative genomic analyses of 42 B. subtilis genomes uncover a remarkable genome diversity that translates into a core genome of 1,659 genes and an asymptotic pangenome growth rate of 57 new genes per new genome added. This diversity is due to a large proportion of low-frequency genes that are acquired from closely related species. We find no gene-loss bias among wild isolates, which explains why the cloud genome, 43% of the species pangenome, represents only a small proportion of each genome. We show that B. subtilis can acquire xenologous copies of core genes that propagate laterally among strains within a niche. While not excluding the contributions of other mechanisms, our results strongly suggest a process of gene acquisition that is largely driven by competence, where the long-term maintenance of acquired genes depends on local and global fitness effects. This competence-driven genomic diversity provides B. subtilis with its generalist character, enabling it to occupy a wide range of ecological niches and cycle through them.}, }
@article {pmid29269503, year = {2018}, author = {Chu, BTT and Petrovich, ML and Chaudhary, A and Wright, D and Murphy, B and Wells, G and Poretsky, R}, title = {Metagenomics Reveals the Impact of Wastewater Treatment Plants on the Dispersal of Microorganisms and Genes in Aquatic Sediments.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {5}, pages = {}, pmid = {29269503}, issn = {1098-5336}, mesh = {Bacteria/genetics/*isolation &amp; purification ; Genes, Bacterial ; Geologic Sediments/*microbiology ; Lakes/*microbiology ; *Metagenome ; *Microbiota ; Wastewater/*microbiology ; Wisconsin ; }, abstract = {Wastewater treatment plants (WWTPs) release treated effluent containing mobile genetic elements (MGEs), antibiotic resistance genes (ARGs), and microorganisms into the environment, yet little is known about their influence on nearby microbial communities and the retention of these factors in receiving water bodies. Our research aimed to characterize the genes and organisms from two different WWTPs that discharge into Lake Michigan, as well as from surrounding lake sediments to determine the dispersal and fate of these factors with respect to distance from the effluent outfall. Shotgun metagenomics coupled to distance-decay analyses showed a higher abundance of genes identical to those in WWTP effluent genes in sediments closer to outfall sites than in sediments farther away, indicating their possible WWTP origin. We also found genes attributed to organisms, such as those belonging to Helicobacteraceae, Legionellaceae, Moraxellaceae, and Neisseriaceae, in effluent from both WWTPs and decreasing in abundance in lake sediments with increased distance from WWTPs. Moreover, our results showed that the WWTPs likely influence the ARG composition in lake sediments close to the effluent discharge. Many of these ARGs were located on MGEs in both the effluent and sediment samples, indicating a relatively broad propensity for horizontal gene transfer (HGT). Our approach allowed us to specifically link genes to organisms and their genetic context, providing insight into WWTP impacts on natural microbial communities. Overall, our results suggest a substantial influence of wastewater effluent on gene content and microbial community structure in the sediments of receiving water bodies.IMPORTANCE Wastewater treatment plants (WWTPs) release their effluent into aquatic environments. Although treated, effluent retains many genes and microorganisms that have the potential to influence the receiving water in ways that are poorly understood. Here, we tracked the genetic footprint, including genes specific to antibiotic resistance and mobile genetic elements and their associated organisms, from WWTPs to lake sediments. Our work is novel in that we used metagenomic data sets to comprehensively evaluate total gene content and the genetic and taxonomic context of specific genes in environmental samples putatively impacted by WWTP inputs. Based on two different WWTPs with different treatment processes, our findings point to an influence of WWTPs on the presence, abundance, and composition of these factors in the environment.}, }
@article {pmid29267255, year = {2017}, author = {McDowell, A}, title = {Over a Decade of recA and tly Gene Sequence Typing of the Skin Bacterium Propionibacterium acnes: What Have We Learnt?.}, journal = {Microorganisms}, volume = {6}, number = {1}, pages = {}, pmid = {29267255}, issn = {2076-2607}, abstract = {The Gram-positive, anaerobic bacterium Propionibacterium acnes forms part of the normal microbiota on human skin and mucosal surfaces. While normally associated with skin health, P. acnes is also an opportunistic pathogen linked with a range of human infections and clinical conditions. Over the last decade, our knowledge of the intraspecies phylogenetics and taxonomy of this bacterium has increased tremendously due to the introduction of DNA typing schemes based on single and multiple gene loci, as well as whole genomes. Furthermore, this work has led to the identification of specific lineages associated with skin health and human disease. In this review we will look back at the introduction of DNA sequence typing of P. acnes based on recA and tly loci, and then describe how these methods provided a basic understanding of the population genetic structure of the bacterium, and even helped characterize the grapevine-associated lineage of P. acnes, known as P. acnes type Zappe, which appears to have undergone a host switch from humans-to-plants. Particular limitations of recA and tly sequence typing will also be presented, as well as a detailed discussion of more recent, higher resolution, DNA-based methods to type P. acnes and investigate its evolutionary history in greater detail.}, }
@article {pmid29265877, year = {2018}, author = {Kaldhone, PR and Han, J and Deck, J and Khajanchi, B and Nayak, R and Foley, SL and Ricke, SC}, title = {Evaluation of the Genetics and Functionality of Plasmids in Incompatibility Group I1-Positive Salmonella enterica.}, journal = {Foodborne pathogens and disease}, volume = {15}, number = {3}, pages = {168-176}, doi = {10.1089/fpd.2017.2332}, pmid = {29265877}, issn = {1556-7125}, mesh = {Animals ; Anti-Infective Agents/*pharmacology ; Drug Resistance, Microbial/*genetics ; Escherichia coli/*growth &amp; development ; Gene Transfer, Horizontal ; Genotype ; Humans ; Phenotype ; Plasmids/*genetics ; Polymerase Chain Reaction ; Salmonella enterica/*genetics/immunology/pathogenicity ; *Virulence ; }, abstract = {Salmonella is a predominant foodborne pathogen in the United States and other countries. Mobile genetic elements such as plasmids allow Salmonella to adapt to external stress factors such as nutrient deprivation and host factors. Incompatibility group I1 (IncI1) plasmid-carrying Salmonella enterica strains were examined to determine the presence of plasmid-associated genes and their influence on phenotypic characteristics. The objective of this study was to understand the genetic determinants on IncI1 plasmids and their impact on antimicrobial susceptibility, competitive growth inhibition of Escherichia coli, and plasmid transfer. Primers were designed for genes that play a role in virulence, antimicrobial resistance, and plasmid transfer based on previously sequenced IncI1 plasmids. Polymerase chain reaction assays were conducted on 92 incompatibility group I1 (IncI1)-positive S. enterica strains. Phenotypic characterization included conjugation assays, antimicrobial susceptibility testing, and bacteriocin production based on the inhibition of growth of colicin-negative E. coli J53. The antimicrobial resistance genes aadA1, tetA, sul1, and blaCMY were detected in 88%, 87%, 80%, and 48% of the strains, respectively. Over half of the strains were resistant or intermediately resistant to streptomycin (85%), sulfonamides (76%), tetracycline (74%), and ampicillin (68%) and 57% of the strains inhibited growth of E. coli J53 strain. Among putative virulence genes, colicin-associated colI and cib were detected in 23% and 35% of strains and imm and ccdA were present in 58% and 54% of strains, respectively. Approximately 61% of strains contained plasmids that conjugally transferred antimicrobial resistance, including 83% where the recipient received IncI1 plasmids. Most of the strains carried an assortment of transfer associated (pil and tra) genes with between 63% and 99% of strains being positive for individual genes. Taken together the study affirms that IncI1 plasmids likely play roles in the dissemination of antimicrobial resistance and virulence-associated factors among enteric organisms.}, }
@article {pmid29264970, year = {2018}, author = {Hafner, LM and Timms, P}, title = {Development of a Chlamydia trachomatis vaccine for urogenital infections: novel tools and new strategies point to bright future prospects.}, journal = {Expert review of vaccines}, volume = {17}, number = {1}, pages = {57-69}, doi = {10.1080/14760584.2018.1417044}, pmid = {29264970}, issn = {1744-8395}, mesh = {Adolescent ; Adult ; Animals ; Bacterial Vaccines/*administration &amp; dosage/immunology ; Child ; Chlamydia Infections/complications/*prevention &amp; control/transmission ; Chlamydia trachomatis/immunology ; Drug Design ; Female ; Humans ; Pregnancy ; Sexually Transmitted Diseases/complications/microbiology/*prevention &amp; control ; }, abstract = {INTRODUCTION: The "cloaked" bacterial pathogen that is Chlamydia trachomatis continues to cause sexually transmitted infections (STIs) that adversely affect the health and well-being of children, adolescents and adults globally. The reproductive disease sequelae follow unresolved or untreated chronic or recurrent asymptomatic C.trachomatis infections of the lower female genital tract (FGT) and can include pelvic pain, pelvic inflammatory disease (PID) and ectopic pregnancy. Tubal Factor Infertility (TFI) can also occur since protective and long-term natural immunity to chlamydial infection is incomplete, allowing for ascension of the organism to the upper FGT. Developing countries including the WHO African (8.3 million cases) and South-East Asian regions (7.2 million cases) bear the highest burden of chlamydial STIs.<br><br>AREAS COVERED: Genetic advances for Chlamydia have provided tools for transformation (including dendrimer-enabled transformation), lateral gene transfer and chemical mutagenesis. Recent progress in these areas is reviewed with a focus on vaccine development for Chlamydia infections of the female genital tract.<br><br>EXPERT COMMENTARY: A vaccine that can elicit immuno-protective responses whilst avoiding adverse immuno-pathologic host responses is required. The current technological advances in chlamydial genetics and proteomics, as well as novel and improved adjuvants and delivery systems, provide new hope that the elusive chlamydial vaccine is an imminent and realistic goal.}, }
@article {pmid29263683, year = {2017}, author = {Sonnevend, &#xc1; and Yahfoufi, N and Ghazawi, A and Jamal, W and Rotimi, V and Pál, T}, title = {Contribution of horizontal gene transfer to the emergence of VIM-4 carbapenemase producer Enterobacteriaceae in Kuwait.}, journal = {Infection and drug resistance}, volume = {10}, number = {}, pages = {469-478}, pmid = {29263683}, issn = {1178-6973}, abstract = {Carbapenem-resistant Enterobacteriaceae encountered in countries of the Arabian Peninsula usually produce OXA-48-like and New Delhi metallo-beta-lactamases (NDM) carbapenemases. However, a temporary increase in VIM-4-producing, clonally unrelated Enterobacteriaceae strains was described earlier in a Kuwaiti hospital. We investigated the genetic support of blaVIM-4 in six Klebsiella pneumoniae strains, one Escherichia coli, and one Enterobacter cloacae strain and compared it to that of VIM-4-producing isolates from other countries of the region. Five K. pneumoniae strains and the E. coli strain from Kuwait carried an ~165 kb IncA/C-type plasmid indistinguishable by restriction fragment length polymorphism. The complete sequence of one of them (pKKp4-VIM) was established. pKKp4-VIM exhibited extensive similarities to episomes pKP-Gr642 carrying blaVIM-19 encountered in Greece and to the partially sequenced pCC416 harboring blaVIM-4 detected in Italy. In other countries of the region, the only similar plasmid was the one detected in the isolate from the UAE. In all Kuwaiti strains, irrespective of the species and their VIM plasmids, the blaVIM-4 gene was located within the same integron structure (In416), different from those of other countries of the region. Our data show that the spread of this IncA/C plasmid and particularly that of the In416 integron caused a considerable, albeit temporary, increase in the rate of mostly clonally unrelated VIM-producing Enterobacteriaceae strains of multiple species. Monitoring of such events is of high importance as the interference with the spread of mobile genetic elements may represent a formidable challenge to infection control.}, }
@article {pmid29263245, year = {2017}, author = {Jani, M and Sengupta, S and Hu, K and Azad, RK}, title = {Deciphering pathogenicity and antibiotic resistance islands in methicillin-resistant Staphylococcus aureus genomes.}, journal = {Open biology}, volume = {7}, number = {12}, pages = {}, pmid = {29263245}, issn = {2046-2441}, mesh = {Bacterial Proteins/genetics ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Methicillin-Resistant Staphylococcus aureus/drug effects/*genetics/pathogenicity ; Penicillin-Binding Proteins/genetics ; Virulence/genetics ; }, abstract = {Staphylococcus aureus is a versatile pathogen that is capable of causing infections in both humans and animals. It can cause furuncles, septicaemia, pneumonia and endocarditis. Adaptation of S. aureus to the modern hospital environment has been facilitated, in part, by the horizontal acquisition of drug resistance genes, such as mecA gene that imparts resistance to methicillin. Horizontal acquisitions of islands of genes harbouring virulence and antibiotic resistance genes have made S. aureus resistant to commonly used antibiotics. To decipher genomic islands (GIs) in 22 hospital- and 9 community-associated methicillin-resistant S. aureus strains and classify a subset of GIs carrying virulence and resistance genes as pathogenicity and resistance islands respectively, we applied a host of methods for localizing genomic islands in prokaryotic genomes. Surprisingly, none of the frequently used GI prediction methods could perform well in delineating the resistance islands in the S. aureus genomes. Rather, a gene clustering procedure exploiting biases in codon usage for identifying horizontally transferred genes outperformed the current methods for GI detection, in particular in identifying the known islands in S. aureus including the SCCmec island that harbours the mecA resistance gene. The gene clustering approach also identified novel, as yet unreported islands, with many of these found to harbour virulence and/or resistance genes. These as yet unexplored islands may provide valuable information on the evolution of drug resistance in S. aureus.}, }
@article {pmid29263094, year = {2018}, author = {Lee, C and Franke, KB and Kamal, SM and Kim, H and Lünsdorf, H and Jäger, J and Nimtz, M and Trček, J and Jänsch, L and Bukau, B and Mogk, A and Römling, U}, title = {Stand-alone ClpG disaggregase confers superior heat tolerance to bacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {2}, pages = {E273-E282}, pmid = {29263094}, issn = {1091-6490}, mesh = {*Adaptation, Physiological ; Bacterial Proteins/genetics/*metabolism ; Gene Expression Regulation, Bacterial ; Gene Expression Regulation, Enzymologic ; Gene Transfer, Horizontal ; *Hot Temperature ; Phylogeny ; Pseudomonas aeruginosa/*enzymology/genetics/metabolism ; }, abstract = {AAA+ disaggregases solubilize aggregated proteins and confer heat tolerance to cells. Their disaggregation activities crucially depend on partner proteins, which target the AAA+ disaggregases to protein aggregates while concurrently stimulating their ATPase activities. Here, we report on two potent ClpG disaggregase homologs acquired through horizontal gene transfer by the species Pseudomonas aeruginosa and subsequently abundant P. aeruginosa clone C. ClpG exhibits high, stand-alone disaggregation potential without involving any partner cooperation. Specific molecular features, including high basal ATPase activity, a unique aggregate binding domain, and almost exclusive expression in stationary phase distinguish ClpG from other AAA+ disaggregases. Consequently, ClpG largely contributes to heat tolerance of P. aeruginosa primarily in stationary phase and boosts heat resistance 100-fold when expressed in Escherichia coli This qualifies ClpG as a potential persistence and virulence factor in P. aeruginosa.}, }
@article {pmid29260747, year = {2017}, author = {Belaia, OF and Yudina, YV and Volchkova, EV and Payevskaya, OA and Belaya, YA and Gyulazyan, NM and Zuyevskaya, SN}, title = {[Identification of Shiga toxin in patients with acute intestinal infections in the presence of mono- and mixed-O-antigens of pathogens].}, journal = {Terapevticheskii arkhiv}, volume = {89}, number = {11}, pages = {55-59}, doi = {10.17116/terarkh2017891155-59}, pmid = {29260747}, issn = {0040-3660}, mesh = {Acute Disease ; Adolescent ; Adult ; Bacteriological Techniques/*methods/standards ; Coinfection/epidemiology/*immunology ; Comorbidity ; Enterobacteriaceae Infections/epidemiology/*immunology ; Female ; Humans ; Intestinal Diseases/epidemiology/*immunology ; Male ; Middle Aged ; O Antigens/*immunology ; Shiga Toxin/*immunology ; Young Adult ; }, abstract = {AIM: To investigate the time course of changes in the detection rates and levels of Shiga toxin antigen (STA) in their stool and middle-molecule circulating immune complexes (CICs) containing IgG (IgG CIC) in patients with acute intestinal infections (AIIs) in the presence of the body's circulation of mono- and mixed-LPS/O-antigens of intestinal pathogens.<br><br>SUBJECTS AND METHODS: A total of 147 patients aged 15 to 55 years who had been hospitalized with AIIs were examined. The diagnosis was bacteriologically verified in 19% of the patients; in the others, it was confirmed by the detection of LPS/O-antigens of Shigella, Salmonella, Yersinia, and Campylobacter in their stool by means of the reaction of coagglutination (RCA) on glass slides. Plates for RCA displayed STA in the fecal and IgG CIC samples.<br><br>RESULTS: Mono- and mixed infections were detected in 32 and 68%, respectively. The RCA plates exhibited STA in 25.2% of the fecal samples and in 90.5% of the IgG CIC ones from patients with AIIs and did not in those from donors. In monoinfection, the detection rates and levels of STA in the feces became lower in the course of the disease and remained unchanged in IgG CIC and the levels of STA also decreased in the feces, but increased in IgG CIC in mixed infection.<br><br>CONCLUSION: In 25.2% of the patients with early AIIs, their stools show free STA; its detection rate and levels are significantly higher in mixed infections than those in monoinfection. The level of STA in serum IgG CIC was significantly higher in mixed infection, suggesting an active immune response to the pathogen. Given that the Shiga toxin-producing strains are present in patients with AIIs, caution should be exercised in the choice of an antibacterial drug to prevent horizontal gene transfer and to enhance toxin production and the body's intoxication. One of the advantages of RCA is the possibility of rapidly changing the spectrum of test systems, depending on the region of their application and the epidemiological situation.}, }
@article {pmid29260580, year = {2018}, author = {Xu, S and Yang, J and Yin, C and Zhao, X}, title = {The dominance of bacterial genotypes leads to susceptibility variations under sublethal antibiotic pressure.}, journal = {Future microbiology}, volume = {13}, number = {}, pages = {165-185}, doi = {10.2217/fmb-2017-0070}, pmid = {29260580}, issn = {1746-0921}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/*genetics ; Bacterial Physiological Phenomena ; Drug Resistance, Bacterial/*drug effects/*genetics ; Gene Transfer, Horizontal/drug effects ; Genetic Variation ; Genome, Bacterial/genetics ; Genotype ; Models, Biological ; Plasmids/genetics ; Selection, Genetic ; }, abstract = {AIM: To investigate the collective resistance of the bacteria population with resistant horizontal gene transfer under sublethal bactericide pressure.<br><br>MATERIALS &amp; METHODS: By employing qualitative analysis of ordinary differential equations, particularly bifurcation theory and several numerical simulations, a modified 4D ordinary differential equation model describing antibiotic susceptibility variations induced by sublethal antibiotic pressure is analyzed in detail.<br><br>RESULTS: The long-term behaviors and collective resistance of different bacterial genotype populations in different sublethal bactericide concentration subintervals exhibit high levels of heterogeneity and are determined by the protection provided by resistant genes on chromosome or plasmid, their fitness costs, plasmid segregation rate and sublethal bactericide pressure.<br><br>CONCLUSION: First, the possible mechanism of antibiotic susceptibility variations is the dominance of different bacterial genotypes under sublethal bactericide pressure, rather than persistence, tolerance or resistance. Additionally, the combination of vertical genetic transfer, horizontal genetic transfer and plasmid segregation can lead to unique switch between two states of different bacterial genotypes.}, }
@article {pmid29259590, year = {2017}, author = {Pasqua, M and Michelacci, V and Di Martino, ML and Tozzoli, R and Grossi, M and Colonna, B and Morabito, S and Prosseda, G}, title = {The Intriguing Evolutionary Journey of Enteroinvasive E. coli (EIEC) toward Pathogenicity.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2390}, pmid = {29259590}, issn = {1664-302X}, abstract = {Among the intestinal pathogenic Escherichia coli, enteroinvasive E. coli (EIEC) are a group of intracellular pathogens able to enter epithelial cells of colon, multiplicate within them, and move between adjacent cells with a mechanism similar to Shigella, the ethiological agent of bacillary dysentery. Despite EIEC belong to the same pathotype of Shigella, they neither have the full set of traits that define Shigella nor have undergone the extensive gene decay observed in Shigella. Molecular analysis confirms that EIEC are widely distributed among E. coli phylogenetic groups and correspond to bioserotypes found in many E. coli serogroups. Like Shigella, also in EIEC the critical event toward a pathogenic life-style consisted in the acquisition by horizontal gene transfer of a large F-type plasmid (pINV) containing the genes required for invasion, intracellular survival, and spreading through the intestinal mucosa. In Shigella, the ample gain in virulence determinants has been counteracted by a substantial loss of functions that, although important for the survival in the environment, are redundant or deleterious for the life inside the host. The pathoadaptation process that has led Shigella to modify its metabolic profile and increase its pathogenic potential is still in infancy in EIEC, although maintenance of some features typical of E. coli might favor their emerging relevance as intestinal pathogens worldwide, as documented by recent outbreaks in industrialized countries. In this review, we will discuss the evolution of EIEC toward Shigella-like invasive forms going through the epidemiology, including the emergence of new virulent strains, their genome organization, and the complex interactions they establish with the host.}, }
@article {pmid29254962, year = {2018}, author = {Raven, JA}, title = {Evolution and palaeophysiology of the vascular system and other means of long-distance transport.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {373}, number = {1739}, pages = {}, pmid = {29254962}, issn = {1471-2970}, mesh = {Biological Transport ; Embryophyta/*physiology ; *Fossils ; Paleontology ; Plant Vascular Bundle/*physiology ; Scotland ; }, abstract = {Photolithotrophic growth on land using atmospheric CO2 inevitably involves H2O vapour loss. Embryophytes greater than or equal to 100 mm tall are homoiohydric and endohydric with mass flow of aqueous solution through the xylem in tracheophytes. Structural details in Rhynie sporophytes enable modelling of the hydraulics of H2O supply to the transpiring surface, and the potential for gas exchange with the Devonian atmosphere. Xylem carrying H2O under tension involves programmed cell death, rigid cell walls and embolism repair; fossils provide little evidence on these functions other than the presence of lignin. The phenylalanine ammonia lyase essential for lignin synthesis came from horizontal gene transfer. Rhynie plants lack endodermes, limiting regulation of the supply of soil nutrients to shoots. The transfer of organic solutes from photosynthetic sites to growing and storage tissues involves mass flow through phloem in extant tracheophytes. Rhynie plants show little evidence of phloem; possible alternatives for transport of organic solutes are discussed. Extant examples of the arbuscular mycorrhizas found in Rhynie plants exchange soil-derived nutrients (especially P) for plant-derived organic matter, involving bidirectional mass flow along the hyphae. The aquatic cyanobacteria and the charalean Palaeonitella at Rhynie also have long-distance (relative to the size of the organism) transport.This article is part of a discussion meeting issue 'The Rhynie cherts: our earliest terrestrial ecosystem revisited'.}, }
@article {pmid29253871, year = {2017}, author = {Dachev, M and Bína, D and Sobotka, R and Moravcová, L and Gardian, Z and Kaftan, D and Šlouf, V and Fuciman, M and Polívka, T and Koblížek, M}, title = {Unique double concentric ring organization of light harvesting complexes in Gemmatimonas phototrophica.}, journal = {PLoS biology}, volume = {15}, number = {12}, pages = {e2003943}, pmid = {29253871}, issn = {1545-7885}, mesh = {Bacteria/classification/metabolism ; Bacterial Physiological Phenomena ; Bacterial Proteins/*chemistry ; Gene Transfer, Horizontal ; Light-Harvesting Protein Complexes/*chemistry ; Photosynthesis/*physiology ; Phylogeny ; }, abstract = {The majority of life on Earth depends directly or indirectly on the sun as a source of energy. The initial step of photosynthesis is facilitated by light-harvesting complexes, which capture and transfer light energy into the reaction centers (RCs). Here, we analyzed the organization of photosynthetic (PS) complexes in the bacterium G. phototrophica, which so far is the only phototrophic representative of the bacterial phylum Gemmatimonadetes. The isolated complex has a molecular weight of about 800 ± 100 kDa, which is approximately 2 times larger than the core complex of Rhodospirillum rubrum. The complex contains 62.4 ± 4.7 bacteriochlorophyll (BChl) a molecules absorbing in 2 distinct infrared absorption bands with maxima at 816 and 868 nm. Using femtosecond transient absorption spectroscopy, we determined the energy transfer time between these spectral bands as 2 ps. Single particle analyses of the purified complexes showed that they were circular structures with an outer diameter of approximately 18 nm and a thickness of 7 nm. Based on the obtained, we propose that the light-harvesting complexes in G. phototrophica form 2 concentric rings surrounding the type 2 RC. The inner ring (corresponding to the B868 absorption band) is composed of 15 subunits and is analogous to the inner light-harvesting complex 1 (LH1) in purple bacteria. The outer ring is composed of 15 more distant BChl dimers with no or slow energy transfer between them, resulting in the B816 absorption band. This completely unique and elegant organization offers good structural stability, as well as high efficiency of light harvesting. Our results reveal that while the PS apparatus of Gemmatimonadetes was acquired via horizontal gene transfer from purple bacteria, it later evolved along its own pathway, devising a new arrangement of its light harvesting complexes.}, }
@article {pmid29250433, year = {2017}, author = {Shakya, M and Soucy, SM and Zhaxybayeva, O}, title = {Insights into origin and evolution of α-proteobacterial gene transfer agents.}, journal = {Virus evolution}, volume = {3}, number = {2}, pages = {vex036}, pmid = {29250433}, issn = {2057-1577}, abstract = {Several bacterial and archaeal lineages produce nanostructures that morphologically resemble small tailed viruses, but, unlike most viruses, contain apparently random pieces of the host genome. Since these elements can deliver the packaged DNA to other cells, they were dubbed gene transfer agents (GTAs). Because many genes involved in GTA production have viral homologs, it has been hypothesized that the GTA ancestor was a virus. Whether GTAs represent an atypical virus, a defective virus, or a virus co-opted by the prokaryotes for some function, remains to be elucidated. To evaluate these possibilities, we examined the distribution and evolutionary histories of genes that encode a GTA in the α-proteobacterium Rhodobacter capsulatus (RcGTA). We report that although homologs of many individual RcGTA genes are abundant across bacteria and their viruses, RcGTA-like genomes are mainly found in one subclade of α-proteobacteria. When compared with the viral homologs, genes of the RcGTA-like genomes evolve significantly slower, and do not have higher %A+T nucleotides than their host chromosomes. Moreover, they appear to reside in stable regions of the bacterial chromosomes that are generally conserved across taxonomic orders. These findings argue against RcGTA being an atypical or a defective virus. Our phylogenetic analyses suggest that RcGTA ancestor likely originated in the lineage that gave rise to contemporary α-proteobacterial orders Rhizobiales, Rhodobacterales, Caulobacterales, Parvularculales, and Sphingomonadales, and since that time the RcGTA-like element has co-evolved with its host chromosomes. Such evolutionary history is compatible with maintenance of these elements by bacteria due to some selective advantage. As for many other prokaryotic traits, horizontal gene transfer played a substantial role in the evolution of RcGTA-like elements, not only in shaping its genome components within the orders, but also in occasional dissemination of RcGTA-like regions across the orders and even to different bacterial phyla.}, }
@article {pmid29250047, year = {2017}, author = {Wawrzyniak, P and Płucienniczak, G and Bartosik, D}, title = {The Different Faces of Rolling-Circle Replication and Its Multifunctional Initiator Proteins.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2353}, pmid = {29250047}, issn = {1664-302X}, abstract = {Horizontal gene transfer (HGT) contributes greatly to the plasticity and evolution of prokaryotic and eukaryotic genomes. The main carriers of foreign DNA in HGT are mobile genetic elements (MGEs) that have extremely diverse genetic structures and properties. Various strategies are used for the maintenance and spread of MGEs, including (i) vegetative replication, (ii) transposition (and other types of recombination), and (iii) conjugal transfer. In many MGEs, all of these processes are dependent on rolling-circle replication (RCR). RCR is one of the most well characterized models of DNA replication. Although many studies have focused on describing its mechanism, the role of replication initiator proteins has only recently been subject to in-depth analysis, which indicates their involvement in multiple biological process associated with RCR. In this review, we present a general overview of RCR and its impact in HGT. We focus on the molecular characteristics of RCR initiator proteins belonging to the HUH and Rep_trans protein families. Despite analogous mechanisms of action these are distinct groups of proteins with different catalytic domain structures. This is the first review describing the multifunctional character of various types of RCR initiator proteins, including the latest discoveries in the field. Recent reports provide evidence that (i) proteins initiating vegetative replication (Rep) or mobilization for conjugal transfer (Mob) may also have integrase (Int) activity, (ii) some Mob proteins are capable of initiating vegetative replication (Rep activity), and (iii) some Rep proteins can act like Mob proteins to mobilize plasmid DNA for conjugal transfer. These findings have significant consequences for our understanding of the role of RCR, not only in DNA metabolism but also in the biology of many MGEs.}, }
@article {pmid29248513, year = {2018}, author = {Khodadadian, R and Rahdar, HA and Javadi, A and Safari, M and Khorshidi, A}, title = {Detection of VIM-1 and IMP-1 genes in Klebsiella pneumoniae and relationship with biofilm formation.}, journal = {Microbial pathogenesis}, volume = {115}, number = {}, pages = {25-30}, doi = {10.1016/j.micpath.2017.12.036}, pmid = {29248513}, issn = {1096-1208}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Biofilms/*growth &amp; development ; Child ; Child, Preschool ; Cross-Sectional Studies ; Disk Diffusion Antimicrobial Tests ; Drug Resistance, Multiple, Bacterial/genetics ; Female ; Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Hospitals ; Humans ; Infant ; Klebsiella Infections/microbiology ; Klebsiella pneumoniae/*genetics/isolation &amp; purification/*physiology ; Male ; Middle Aged ; Molecular Epidemiology ; Phenotype ; Urinary Tract Infections/microbiology ; Urine/microbiology ; Young Adult ; beta-Lactamases/*genetics ; }, abstract = {Klebsiella pneumoniae is an important human pathogen that is considered in recent years due to nosocomial infections resistant to treatment as well as the ability to form biofilms particularly in patients with urinary tract infection in ICU or hospital. The aim of this study was to evaluate the prevalence of VIM1, IMP1 genes and their ability to form biofilm in K. pneumoniae strains isolated from patients with urinary tract infection. In the study, using culture and biochemical methods, 1807 K. pneumoniae samples were isolated from patients with urinary tract infection hospitalized or referred to hospitals in Qom in 2013-2014. For isolation of MBL producing isolates, Double Disk Synergy Test (DDST) was used. Then MBL positive isolates were examined for the presence of VIM1, IMP1 genes using PCR method. Furthermore, all strains were investigated for biofilm formation by phenotypic microplate method. From 3165 urine samples cultured, 1807 isolates of K. pneumoniae were isolated and 109 strains (93.2%) were positive for MBL enzymes production. PCR results showed that the prevalence of VIM1 and IMP1 genes are 15.6 and 6.4%, respectively. The Phenotypic method indicated that 91.2% of isolates formed biofilm. Biofilm formation in K. pneumoniae isolates is high and there is a significant relationship between strong biofilm formation and prevalence of VIM1 and IMP1 genes. Also due to the presence of MBL genes in K. pneumoniae and horizontal transfer of genes to other bacteria, and to control the indiscriminate use of antibiotics, the hospital infection control methods must be considered.}, }
@article {pmid29247061, year = {2018}, author = {Dahmane, N and Robert, E and Deschamps, J and Meylheuc, T and Delorme, C and Briandet, R and Leblond-Bourget, N and Guédon, E and Payot, S}, title = {Impact of Cell Surface Molecules on Conjugative Transfer of the Integrative and Conjugative Element ICESt3 of Streptococcus thermophilus.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {5}, pages = {}, pmid = {29247061}, issn = {1098-5336}, mesh = {*Conjugation, Genetic ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Streptococcus thermophilus/*genetics ; }, abstract = {Integrative conjugative elements (ICEs) are chromosomal elements that are widely distributed in bacterial genomes, hence contributing to genome plasticity, adaptation, and evolution of bacteria. Conjugation requires a contact between both the donor and the recipient cells and thus likely depends on the composition of the cell surface envelope. In this work, we investigated the impact of different cell surface molecules, including cell surface proteins, wall teichoic acids, lipoteichoic acids, and exopolysaccharides, on the transfer and acquisition of ICESt3 from Streptococcus thermophilus The transfer of ICESt3 from wild-type (WT) donor cells to mutated recipient cells increased 5- to 400-fold when recipient cells were affected in lipoproteins, teichoic acids, or exopolysaccharides compared to when the recipient cells were WT. These mutants displayed an increased biofilm-forming ability compared to the WT, suggesting better cell interactions that could contribute to the increase of ICESt3 acquisition. Microscopic observations of S. thermophilus cell surface mutants showed different phenotypes (aggregation in particular) that can also have an impact on conjugation. In contrast, the same mutations did not have the same impact when the donor cells, instead of recipient cells, were mutated. In that case, the transfer frequency of ICESt3 decreased compared to that with the WT. The same observation was made when both donor and recipient cells were mutated. The dominant effect of mutations in donor cells suggests that modifications of the cell envelope could impair the establishment or activity of the conjugation machinery required for DNA transport.IMPORTANCE ICEs contribute to horizontal gene transfer of adaptive traits (for example, virulence, antibiotic resistance, or biofilm formation) and play a considerable role in bacterial genome evolution, thus underlining the need of a better understanding of their conjugative mechanism of transfer. While most studies focus on the different functions encoded by ICEs, little is known about the effect of host factors on their conjugative transfer. Using ICESt3 of S. thermophilus as a model, we demonstrated the impact of lipoproteins, teichoic acids, and exopolysaccharides on ICE transfer and acquisition. This opens up new avenues to control gene transfer mediated by ICEs.}, }
@article {pmid29244123, year = {2018}, author = {Wu, HK and Chen, JH and Yang, L and Li, AR and Su, DH and Lin, YP and Chen, DQ}, title = {Emergence and genomic analysis of MDR Laribacter hongkongensis strain HLGZ1 from Guangzhou, China.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {73}, number = {3}, pages = {643-647}, doi = {10.1093/jac/dkx470}, pmid = {29244123}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Typing Techniques ; China/epidemiology ; DNA, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Feces/microbiology ; Gastroenteritis/microbiology ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomic Islands ; Genomics ; Gram-Negative Bacterial Infections/epidemiology ; Humans ; Integrons ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Neisseriaceae/drug effects/*genetics/isolation &amp; purification ; Salmonella enterica/genetics ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: Laribacter hongkongensis is a facultative anaerobic, non-fermentative, Gram-negative bacillus associated with community-acquired gastroenteritis and traveller's diarrhoea. No clinical MDR L. hongkongensis isolate has been reported yet.<br><br>METHODS: We performed WGS (PacBio and Illumina) on a clinical L. hongkongensis strain HLGZ1 with an MDR phenotype.<br><br>RESULTS: HLGZ1 was resistant to eight classes of commonly used antibiotics. Its complete genome was a single circular chromosome of 3&#x202f;424&#x202f;272&#x2009;bp with a G&#x2009;+&#x2009;C content of 62.29%. In comparison with the reference strain HLHK9, HLGZ1 had a higher abundance of genes associated with DNA metabolism and recombination. Several inserts including two acquired resistance gene clusters (RC1 and RC2) were also identified. RC1 carried two resistance gene cassette arrays, aac(6')-Ib-cr-aadA2-&#x394;qac-&#x394;sul1-floR-tetR-tetG and arr-3-dfrA32-ereA2-&#x394;qac-sul1, which shared significant nucleotide sequence identities with the MDR region of Salmonella Genomic Island 1 from Salmonella enterica serovar Typhimurium DT104. There was also an integron-like structure, intl1-arr3-dfrA27-&#x394;qac-sul1-aph(3')-Ic, and a tetR-tetA operon located on RC2. MLST analysis identified HLGZ1 as ST167, a novel ST clustered with two strains previously isolated from frogs.<br><br>CONCLUSIONS: This study provides insight into the genomic characteristics of MDR L. hongkongensis and highlights the possibilities of horizontal resistance gene transfer in this bacterium with other pathogens.}, }
@article {pmid29243150, year = {2018}, author = {Naik, OA and Shashidhar, R and Rath, D and Bandekar, JR and Rath, A}, title = {Characterization of multiple antibiotic resistance of culturable microorganisms and metagenomic analysis of total microbial diversity of marine fish sold in retail shops in Mumbai, India.}, journal = {Environmental science and pollution research international}, volume = {25}, number = {7}, pages = {6228-6239}, pmid = {29243150}, issn = {1614-7499}, support = {2012/37B/50/BRNS//Board of Research in Nuclear Sciences/ ; }, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Bacteria/*classification/genetics ; Biodiversity ; Drug Resistance, Multiple, Bacterial/*genetics ; Fishes/*microbiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; India ; Integrons/genetics ; *Metagenomics ; Microbial Sensitivity Tests ; Plasmids/genetics ; }, abstract = {Marine fish species were analyzed for culturable and total metagenomic microbial diversity, antibiotic resistance (AR) pattern, and horizontal gene transfer in culturable microorganisms. We observed a high AR microbial load of 3 to 4 log CFU g[-1]. Many fish pathogens like Providencia, Staphylococcus, Klebsiella pneumoniae, Enterobacter, Vagococcus, and Aeromonas veronii were isolated. Photobacterium and Vibrio were two major fish and human pathogens which were identified in the fish metagenome. Other pathogens that were identified were Shewanella, Acinetobacter, Psychrobacter, and Flavobacterium. Most of these pathogens were resistant to multiple antibiotics such as erythromycin, kanamycin, neomycin, streptomycin, penicillin, cefotaxime, bacitracin, rifampicin, trimethoprim, ciprofloxacin, and doxycycline with a high multiple antibiotic resistance index of 0.54-0.77. The fish microflora showed high prevalence of AR genes like bla TEM, Class I integron, tetA, aph(3')-IIIa, ermB, aadA, and sul1. Nineteen of 26 AR isolates harbored Class I integrons showing high co-resistance to trimethoprim, kanamycin, doxycycline, and cefotaxime. Mobile R-plasmids from 6 of the 12 AR pathogens were transferred to recipient E. coli after conjugation. The transconjugants harbored the same R-plasmid carrying bla CTX-M, dfr1, tetA, bla TEM, and cat genes. This study confirms that fish is a potential carrier of AR pathogens which can enter the human gut via food chain. To the best of our knowledge, this is the first study in the Indian subcontinent reporting a direct evidence of spread of AR pathogens to humans from specific marine fish consumption.}, }
@article {pmid29240843, year = {2017}, author = {Dan, H and Ikeda, N and Fujikami, M and Nakabachi, A}, title = {Behavior of bacteriome symbionts during transovarial transmission and development of the Asian citrus psyllid.}, journal = {PloS one}, volume = {12}, number = {12}, pages = {e0189779}, pmid = {29240843}, issn = {1932-6203}, mesh = {Alphaproteobacteria/*pathogenicity ; Animals ; Bacterial Infections/*microbiology ; Citrus/*parasitology ; Female ; Hemiptera/*microbiology/physiology ; Host-Parasite Interactions ; Host-Pathogen Interactions ; *Insect Vectors ; Ovary/*microbiology ; Plant Diseases/*microbiology ; }, abstract = {The Asian citrus psyllid Diaphorina citri Kuwayama (Hemiptera: Liviidae) is a serious pest worldwide, transmitting Candidatus Liberibacter spp. (Alphaproteobacteria), the causative agents of a devastating citrus disease known as huanglongbing or greening disease. In a symbiotic organ called the bacteriome, D. citri possesses an organelle-like defensive symbiont, Candidatus Profftella armatura (Betaproteobacteria), and a nutritional symbiont, Ca. Carsonella ruddii (Gammaproteobacteria). Drastically reduced symbiont genomes and metabolic complementarity among the symbionts and D. citri indicate their mutually indispensable association. Moreover, horizontal gene transfer between the Profftella and Liberibacter lineages suggests ecological and evolutionary interactions between the bacteriome symbiont and the HLB pathogen. Using fluorescence in situ hybridization, we examined the behavior of Profftella and Carsonella during transovarial transmission and the development of D. citri. In the bacteriomes of sexually-mature female adults, symbionts transformed from an extremely elongated tubular form into spherical or short-rod forms, which migrated toward the ovary. The symbionts then formed mosaic masses, which entered at the posterior pole of the vitellogenic oocytes. After anatrepsis, Carsonella and Profftella migrated to the central and peripheral parts of the mass, respectively. Following the appearance of host nuclei, the mass cellularized, segregating Carsonella and Profftella in the central syncytium and peripheral uninucleate bacteriocytes, respectively. Subsequently, the uninucleate bacteriocytes harboring Profftella assembled at the posterior pole, while the syncytium, containing Carsonella, sat on the anterior side facing the germ band initiating katatrepsis. During dorsal closure, the syncytium was divided into uninuclear bacteriocytes, which surrounded the mass of bacteriocytes containing Profftella. Once fully surrounded, the bacteriocyte mass containing Profftella was fused into a syncytium. Prior to hatching, a pair of wing-like protrusions arose from both lateral sides of the bacteriome, which continued to grow throughout the nymphal stages. These findings provide a foundation for better understanding the intricate relationship between D. citri and its microbiota.}, }
@article {pmid29239371, year = {2017}, author = {Rappuoli, R and Bloom, DE and Black, S}, title = {Deploy vaccines to fight superbugs.}, journal = {Nature}, volume = {552}, number = {7684}, pages = {165-167}, doi = {10.1038/d41586-017-08323-0}, pmid = {29239371}, issn = {1476-4687}, mesh = {Adjuvants, Immunologic ; Anti-Bacterial Agents/administration &amp; dosage/pharmacology/therapeutic use ; Bacterial Vaccines/*administration &amp; dosage/economics/*immunology ; Clinical Trials as Topic ; *Drug Resistance, Bacterial/drug effects/genetics ; Gene Transfer, Horizontal/genetics ; Health Policy/*trends ; Humans ; Plasmids/genetics ; Policy Making ; Stakeholder Participation ; }, }
@article {pmid29238909, year = {2018}, author = {Francis, A and Huber, KT and Moulton, V}, title = {Tree-Based Unrooted Phylogenetic Networks.}, journal = {Bulletin of mathematical biology}, volume = {80}, number = {2}, pages = {404-416}, pmid = {29238909}, issn = {1522-9602}, mesh = {Bacteria/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Hybridization, Genetic ; Mathematical Concepts ; *Models, Genetic ; *Phylogeny ; Plants/genetics ; }, abstract = {Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An unrooted phylogenetic network on a non-empty, finite set X of taxa, or network, is a connected, simple graph in which every vertex has degree 1 or 3 and whose leaf set is X. It is called a phylogenetic tree if the underlying graph is a tree. In this paper we consider properties of tree-based networks, that is, networks that can be constructed by adding edges into a phylogenetic tree. We show that although they have some properties in common with their rooted analogues which have recently drawn much attention in the literature, they have some striking differences in terms of both their structural and computational properties. We expect that our results could eventually have applications to, for example, detecting horizontal gene transfer or hybridization which are important factors in the evolution of many organisms.}, }
@article {pmid29238335, year = {2017}, author = {Møller, TSB and Liu, G and Boysen, A and Thomsen, LE and Lüthje, FL and Mortensen, S and Møller-Jensen, J and Olsen, JE}, title = {Treatment with Cefotaxime Affects Expression of Conjugation Associated Proteins and Conjugation Transfer Frequency of an IncI1 Plasmid in Escherichia coli.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2365}, pmid = {29238335}, issn = {1664-302X}, abstract = {Horizontal gene transfer (HGT) is the major mechanism responsible for spread of antibiotic resistance. Antibiotic treatment has been suggested to promote HGT, either by directly affecting the conjugation process itself or by selecting for conjugations subsequent to DNA transfer. However, recent research suggests that the effect of antibiotic treatment on plasmid conjugation frequencies, and hence the spread of resistance plasmids, may have been overestimated. We addressed the question by quantifying transfer proteins and conjugation frequencies of a blaCTX-M-1 encoding IncI1 resistance plasmid in Escherichia coli MG1655 in the presence and absence of therapeutically relevant concentrations of cefotaxime (CTX). Analysis of the proteome by iTRAQ labeling and liquid chromatography tandem mass spectrometry revealed that Tra proteins were significantly up-regulated in the presence of CTX. The up-regulation of the transfer machinery was confirmed at the transcriptional level for five selected genes. The CTX treatment did not cause induction of the SOS-response as revealed by absence of significantly regulated SOS associated proteins in the proteome and no significant up-regulation of recA and sfiA genes. The frequency of plasmid conjugation, measured in an antibiotic free environment, increased significantly when the donor was pre-grown in broth containing CTX compared to growth without this drug, regardless of whether blaCTX-M-1 was located on the plasmid or in trans on the chromosome. The results shows that antibiotic treatment can affect expression of a plasmid conjugation machinery and subsequent DNA transfer.}, }
@article {pmid29237003, year = {2018}, author = {Phan, HTT and Stoesser, N and Maciuca, IE and Toma, F and Szekely, E and Flonta, M and Hubbard, ATM and Pankhurst, L and Do, T and Peto, TEA and Walker, AS and Crook, DW and Timofte, D}, title = {Illumina short-read and MinION long-read WGS to characterize the molecular epidemiology of an NDM-1 Serratia marcescens outbreak in Romania.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {73}, number = {3}, pages = {672-679}, pmid = {29237003}, issn = {1460-2091}, support = {//Wellcome Trust/United Kingdom ; WT098615/Z/12/Z//Wellcome Trust/United Kingdom ; HICF-T5-358//Department of Health/United Kingdom ; }, mesh = {DNA, Bacterial/genetics ; Disease Outbreaks ; Enterobacteriaceae/genetics ; Enterobacteriaceae Infections/epidemiology ; Feces/microbiology ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Hospitals ; Humans ; Klebsiella Infections/epidemiology ; Klebsiella pneumoniae/genetics ; Plasmids/genetics ; Romania/epidemiology ; Sequence Analysis, DNA ; Serratia Infections/*epidemiology ; Serratia marcescens/enzymology/*genetics ; Whole Genome Sequencing/methods ; beta-Lactamases/biosynthesis/*genetics ; }, abstract = {BACKGROUND AND OBJECTIVES: Serratia marcescens is an emerging nosocomial pathogen, and the carbapenemase blaNDM has been reported in several surveys in Romania. We aimed to investigate the molecular epidemiology of S. marcescens in two Romanian hospitals over 2010-15, including a neonatal NDM-1 S. marcescens outbreak.<br><br>METHODS: Isolates were sequenced using Illumina technology together with carbapenem-non-susceptible NDM-1-positive and NDM-1-negative Klebsiella pneumoniae and Enterobacter cloacae to provide genomic context. A subset was sequenced with MinION to fully resolve NDM-1 plasmid structures. Resistance genes, plasmid replicons and ISs were identified in silico for all isolates; an annotated phylogeny was reconstructed for S. marcescens. Fully resolved study NDM-1 plasmid sequences were compared with the most closely related publicly available NDM-1 plasmid reference.<br><br>RESULTS: 44/45 isolates were successfully sequenced (S. marcescens, n&#x2009;=&#x2009;33; K. pneumoniae, n&#x2009;=&#x2009;7; E. cloacae, n&#x2009;=&#x2009;4); 10 with MinION. The S. marcescens phylogeny demonstrated several discrete clusters of NDM-1-positive and -negative isolates. All NDM-1-positive isolates across species harboured a pKOX_NDM1-like plasmid; more detailed comparisons of the plasmid structures demonstrated a number of differences, but highlighted the largely conserved plasmid backbones across species and hospital sites.<br><br>CONCLUSIONS: The molecular epidemiology is most consistent with the importation of a pKOX_NDM1-like plasmid into Romania and its dissemination amongst K. pneumoniae/E. cloacae and subsequently S. marcescens across hospitals. The data suggested multiple acquisitions of this plasmid by S. marcescens in the two hospitals studied; transmission events within centres, including a large outbreak on the Targu Mures neonatal unit; and sharing of the pKOX_NDM1-like plasmid between species within outbreaks.}, }
@article {pmid29233893, year = {2017}, author = {Steele, MI and Kwong, WK and Whiteley, M and Moran, NA}, title = {Diversification of Type VI Secretion System Toxins Reveals Ancient Antagonism among Bee Gut Microbes.}, journal = {mBio}, volume = {8}, number = {6}, pages = {}, pmid = {29233893}, issn = {2150-7511}, support = {R01 GM108477/GM/NIGMS NIH HHS/United States ; R01 GM116547/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Antibiosis ; Bacterial Toxins/*genetics/isolation &amp; purification/pharmacology ; Bees/*microbiology ; Escherichia coli/genetics ; Evolution, Molecular ; Gammaproteobacteria/classification/genetics/isolation &amp; purification ; Gastrointestinal Microbiome/drug effects/genetics/*physiology ; Gene Expression Profiling ; High-Throughput Nucleotide Sequencing ; Multigene Family ; Mutagenesis ; Neisseriaceae/classification/genetics/physiology ; Symbiosis ; Type VI Secretion Systems/classification/*genetics/metabolism/toxicity ; Up-Regulation ; }, abstract = {Microbial communities are shaped by interactions among their constituent members. Some Gram-negative bacteria employ type VI secretion systems (T6SSs) to inject protein toxins into neighboring cells. These interactions have been theorized to affect the composition of host-associated microbiomes, but the role of T6SSs in the evolution of gut communities is not well understood. We report the discovery of two T6SSs and numerous T6SS-associated Rhs toxins within the gut bacteria of honey bees and bumble bees. We sequenced the genomes of 28 strains of Snodgrassella alvi, a characteristic bee gut microbe, and found tremendous variability in their Rhs toxin complements: altogether, these strains appear to encode hundreds of unique toxins. Some toxins are shared with Gilliamella apicola, a coresident gut symbiont, implicating horizontal gene transfer as a source of toxin diversity in the bee gut. We use data from a transposon mutagenesis screen to identify toxins with antibacterial function in the bee gut and validate the function and specificity of a subset of these toxin and immunity genes in Escherichia coli Using transcriptome sequencing, we demonstrate that S. alvi T6SSs and associated toxins are upregulated in the gut environment. We find that S. alvi Rhs loci have a conserved architecture, consistent with the C-terminal displacement model of toxin diversification, with Rhs toxins, toxin fragments, and cognate immunity genes that are expressed and confer strong fitness effects in vivo Our findings of T6SS activity and Rhs toxin diversity suggest that T6SS-mediated competition may be an important driver of coevolution within the bee gut microbiota.IMPORTANCE The structure and composition of host-associated bacterial communities are of broad interest, because these communities affect host health. Bees have a simple, conserved gut microbiota, which provides an opportunity to explore interactions between species that have coevolved within their host over millions of years. This study examined the role of type VI secretion systems (T6SSs)-protein complexes used to deliver toxic proteins into bacterial competitors-within the bee gut microbiota. We identified two T6SSs and diverse T6SS-associated toxins in bacterial strains from bees. Expression of these genes is increased in bacteria in the bee gut, and toxin and immunity genes demonstrate antibacterial and protective functions, respectively, when expressed in Escherichia coli Our results suggest that coevolution among bacterial species in the bee gut has favored toxin diversification and maintenance of T6SS machinery, and demonstrate the importance of antagonistic interactions within host-associated microbial communities.}, }
@article {pmid29231817, year = {2017}, author = {Melnyk, RA and Haney, CH}, title = {Plasmid-powered evolutionary transitions.}, journal = {eLife}, volume = {6}, number = {}, pages = {}, pmid = {29231817}, issn = {2050-084X}, mesh = {Bacterial Proteins/genetics ; *Biological Evolution ; Plant Diseases/*microbiology ; Plasmids/*genetics ; Rhodococcus/genetics/*pathogenicity ; Virulence ; }, abstract = {The acquisition of a virulence plasmid is sufficient to turn a beneficial strain of Rhodococcus bacteria into a pathogen.}, }
@article {pmid29231813, year = {2017}, author = {Savory, EA and Fuller, SL and Weisberg, AJ and Thomas, WJ and Gordon, MI and Stevens, DM and Creason, AL and Belcher, MS and Serdani, M and Wiseman, MS and Grünwald, NJ and Putnam, ML and Chang, JH}, title = {Evolutionary transitions between beneficial and phytopathogenic Rhodococcus challenge disease management.}, journal = {eLife}, volume = {6}, number = {}, pages = {}, pmid = {29231813}, issn = {2050-084X}, mesh = {Disease Management ; *Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Phylogeny ; Pistacia/growth &amp; development/*microbiology ; Plant Diseases/*microbiology ; Plasmids ; Rhodococcus/*genetics/growth &amp; development/*pathogenicity ; Virulence ; }, abstract = {Understanding how bacteria affect plant health is crucial for developing sustainable crop production systems. We coupled ecological sampling and genome sequencing to characterize the population genetic history of Rhodococcus and the distribution patterns of virulence plasmids in isolates from nurseries. Analysis of chromosome sequences shows that plants host multiple lineages of Rhodococcus, and suggested that these bacteria are transmitted due to independent introductions, reservoir populations, and point source outbreaks. We demonstrate that isolates lacking virulence genes promote beneficial plant growth, and that the acquisition of a virulence plasmid is sufficient to transition beneficial symbionts to phytopathogens. This evolutionary transition, along with the distribution patterns of plasmids, reveals the impact of horizontal gene transfer in rapidly generating new pathogenic lineages and provides an alternative explanation for pathogen transmission patterns. Results also uncovered a misdiagnosed epidemic that implicated beneficial Rhodococcus bacteria as pathogens of pistachio. The misdiagnosis perpetuated the unnecessary removal of trees and exacerbated economic losses.}, }
@article {pmid29230215, year = {2017}, author = {Lerner, A and Matthias, T and Aminov, R}, title = {Potential Effects of Horizontal Gene Exchange in the Human Gut.}, journal = {Frontiers in immunology}, volume = {8}, number = {}, pages = {1630}, pmid = {29230215}, issn = {1664-3224}, abstract = {Many essential functions of the human body are dependent on the symbiotic microbiota, which is present at especially high numbers and diversity in the gut. This intricate host-microbe relationship is a result of the long-term coevolution between the two. While the inheritance of mutational changes in the host evolution is almost exclusively vertical, the main mechanism of bacterial evolution is horizontal gene exchange. The gut conditions, with stable temperature, continuous food supply, constant physicochemical conditions, extremely high concentration of microbial cells and phages, and plenty of opportunities for conjugation on the surfaces of food particles and host tissues, represent one of the most favorable ecological niches for horizontal gene exchange. Thus, the gut microbial system genetically is very dynamic and capable of rapid response, at the genetic level, to selection, for example, by antibiotics. There are many other factors to which the microbiota may dynamically respond including lifestyle, therapy, diet, refined food, food additives, consumption of pre- and probiotics, and many others. The impact of the changing selective pressures on gut microbiota, however, is poorly understood. Presumably, the gut microbiome responds to these changes by genetic restructuring of gut populations, driven mainly via horizontal gene exchange. Thus, our main goal is to reveal the role played by horizontal gene exchange in the changing landscape of the gastrointestinal microbiome and potential effect of these changes on human health in general and autoimmune diseases in particular.}, }
@article {pmid29228300, year = {2018}, author = {Kaneko, S and Fukushima, H and Nakahama, M and Asano, S and Miyazaki, Y and Aizawa, Y and Itaya, M}, title = {DNA synthesis by fragment assembly using extra-cellular DNA delivered by artificial controlled horizontal transfer.}, journal = {Journal of biochemistry}, volume = {163}, number = {4}, pages = {305-312}, doi = {10.1093/jb/mvx085}, pmid = {29228300}, issn = {1756-2651}, mesh = {Animals ; Bacillus subtilis/*genetics/*metabolism ; DNA/*biosynthesis/chemistry ; Escherichia coli/cytology/*metabolism ; *Gene Transfer Techniques ; Mice ; Mitochondria/*metabolism ; Plasmids ; }, abstract = {DNA synthesis in the Bacillus subtilis cells has become possible using extra-cellular DNA. Generally, purified DNAs in a test tube have been required to introduce into the host cells for molecular cloning technology in the laboratory. We have developed a cell lysis technique for natural transformation using stable extra-cellular plasmid DNAs, in which the extra-cellular plasmid DNAs are released from lysed Escherichia coli cells. DNA synthesis then proceeds by fragment assembly using the stable extracellular DNAs, without biochemical purification. DNA synthesis of the mouse mitochondrial genome in B. subtilis genome was illustrated using four E. coli strains with plasmid DNAs carrying contiguous DNA fragments. In the natural environment, unpurified extra-cellular DNAs contribute to the gene delivery during horizontal gene transfer (HGT). The technology introduced in the present study mimics HGT and should have a wide range of applications.}, }
@article {pmid29228229, year = {2018}, author = {Kottara, A and Hall, JPJ and Harrison, E and Brockhurst, MA}, title = {Variable plasmid fitness effects and mobile genetic element dynamics across Pseudomonas species.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {1}, pages = {}, pmid = {29228229}, issn = {1574-6941}, support = {311490/ERC_/European Research Council/International ; }, mesh = {Conjugation, Genetic ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Interspersed Repetitive Sequences/genetics ; Mercury/*pharmacology ; Plasmids/*genetics ; Pseudomonas aeruginosa/*drug effects/*genetics ; Pseudomonas fluorescens/*drug effects/*genetics ; Pseudomonas putida/*drug effects/*genetics ; }, abstract = {Mobile genetic elements (MGE) such as plasmids and transposons mobilise genes within and between species, playing a crucial role in bacterial evolution via horizontal gene transfer (HGT). Currently, we lack data on variation in MGE dynamics across bacterial host species. We tracked the dynamics of a large conjugative plasmid, pQBR103, and its Tn5042 mercury resistance transposon, in five diverse Pseudomonas species in environments with and without mercury selection. Plasmid fitness effects and stability varied extensively between host species and environments, as did the propensity for chromosomal capture of the Tn5042 mercury resistance transposon associated with loss of the plasmid. Whereas Pseudomonas fluorescens and Pseudomonas savastanoi stably maintained the plasmid in both environments, the plasmid was highly unstable in Pseudomonas aeruginosa and Pseudomonas putida, where plasmid-free genotypes with Tn5042 captured to the chromosome invaded to higher frequency under mercury selection. These data confirm that plasmid stability is dependent upon the specific genetic interaction of the plasmid and host chromosome rather than being a property of plasmids alone, and moreover imply that MGE dynamics in diverse natural communities are likely to be complex and driven by a subset of species capable of stably maintaining plasmids that would then act as hubs of HGT.}, }
@article {pmid29225610, year = {2017}, author = {Quispe-Huamanquispe, DG and Gheysen, G and Kreuze, JF}, title = {Horizontal Gene Transfer Contributes to Plant Evolution: The Case of Agrobacterium T-DNAs.}, journal = {Frontiers in plant science}, volume = {8}, number = {}, pages = {2015}, pmid = {29225610}, issn = {1664-462X}, abstract = {Horizontal gene transfer (HGT) can be defined as the acquisition of genetic material from another organism without being its offspring. HGT is common in the microbial world including archaea and bacteria, where HGT mechanisms are widely understood and recognized as an important force in evolution. In eukaryotes, HGT now appears to occur more frequently than originally thought. Many studies are currently detecting novel HGT events among distinct lineages using next-generation sequencing. Most examples to date include gene transfers from bacterial donors to recipient organisms including fungi, plants, and animals. In plants, one well-studied example of HGT is the transfer of the tumor-inducing genes (T-DNAs) from some Agrobacterium species into their host plant genomes. Evidence of T-DNAs from Agrobacterium spp. into plant genomes, and their subsequent maintenance in the germline, has been reported in Nicotiana, Linaria and, more recently, in Ipomoea species. The transferred genes do not produce the usual disease phenotype, and appear to have a role in evolution of these plants. In this paper, we review previous reported cases of HGT from Agrobacterium, including the transfer of T-DNA regions from Agrobacterium spp. to the sweetpotato [Ipomoea batatas (L.) Lam.] genome which is, to date, the sole documented example of a naturally-occurring incidence of HGT from Agrobacterium to a domesticated crop plant. We also discuss the possible evolutionary impact of T-DNA acquisition on plants.}, }
@article {pmid29223450, year = {2018}, author = {Rangasamy, K and Athiappan, M and Devarajan, N and Samykannu, G and Parray, JA and Aruljothi, KN and Shameem, N and Alqarawi, AA and Hashem, A and Abd Allah, EF}, title = {Pesticide degrading natural multidrug resistance bacterial flora.}, journal = {Microbial pathogenesis}, volume = {114}, number = {}, pages = {304-310}, doi = {10.1016/j.micpath.2017.12.013}, pmid = {29223450}, issn = {1096-1208}, mesh = {Anti-Bacterial Agents/metabolism/pharmacology ; Bacteria/drug effects/enzymology/*genetics/*metabolism ; Bacterial Physiological Phenomena ; Bacterial Proteins/genetics ; Biodegradation, Environmental ; Crops, Agricultural/microbiology ; DNA Transposable Elements ; Drug Resistance, Multiple, Bacterial/*genetics/*physiology ; Environmental Microbiology ; Environmental Pollution ; *Gene Transfer, Horizontal ; Ligands ; Pesticides/*metabolism/pharmacology ; Plasmids/genetics ; Selection, Genetic ; }, abstract = {Multidrug-resistant (MDR) bacteria are a growing threat to humans across the world. Antibiotic resistance is a global problem that has developed through continuous antibiotic use, combinatorial antibiotic use, pesticide-antibiotic cross-resistance, and horizontal gene transfer, as well as various other modes. Pesticide-antibiotic cross-resistance and the subsequent expansion of drug-resistant bacteria are critically documented in this review, the primary focus of which is to assess the impact of indiscriminate pesticide use on the development of microbial communities with parallel pesticide and multidrug resistance. The consumption of pesticide-contaminated food products and the use of broad-spectrum antibiotics by humans and in livestock animals have favored the development of both antibiotic and pesticide-resistant bacterial flora via natural selection. Pesticide resistance mainly develops through defensive bacterial adaptations such as biofilm formation, induced mutations, and horizontal/vertical gene transfer through plasmids or transposons, as well as through the increased expression of certain hydrolytic enzymes. Pesticide resistance genes are always transferred as gene clusters, and they may also carry genes essential for antibiotic resistance. Moreover, for some induced mutations, the mutated active site of the affected enzyme may allow degradation of both pesticides and antibiotics, resulting in cross-resistance. A few studies have shown that the sub-lethal exposure of wild-type strains to herbicides induces antibiotic resistance. This review concludes that xenobiotic exposure leads to cross-resistance in wild microbial flora, which requires further study to develop therapeutic approaches to overcome the threats of MDR bacteria and superbugs.}, }
@article {pmid29222754, year = {2018}, author = {Vignolini, T and Mengoni, A and Fondi, M}, title = {Template-Assisted Metabolic Reconstruction and Assembly of Hybrid Bacterial Models.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1716}, number = {}, pages = {177-196}, doi = {10.1007/978-1-4939-7528-0_8}, pmid = {29222754}, issn = {1940-6029}, mesh = {Bacteria/*genetics ; Computational Biology/*methods ; Computer Simulation ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial ; Internet ; Metabolic Engineering ; *Metabolic Networks and Pathways ; *Models, Biological ; }, abstract = {Intraspecific genomic exchanges happen frequently between bacteria living in the same natural environment and can also be performed artificially in the laboratory for basic research or genetic/metabolic engineering purposes. In silico metabolic reconstruction and simulation of the metabolism of the hybrid strains that result from these processes can be used to predict the phenotypic outcome of such genomic rearrangements; this can be especially helpful as a designing tool in the purview of synthetic biology. However, reconstructing the metabolism of a bacterium with a hybrid genome through in silico approaches is not a trivial task, as it requires taking into account the complex relationships existing between metabolic genes and how they change (or remain unchanged) when new genes are placed in a different genomic context. Furthermore, in order to "mix" the metabolic models of different bacterial strains one needs at least two different metabolic models to begin with, and reconstructing a genome-scale model from the ground up is a challenging task itself, requiring an intensive manual effort and a great deal of information. In this chapter, we propose two general protocols to address the aforementioned issues of: (1) quickly generating strain-specific metabolic models, given the relevant genomic sequence and an already existing, high-quality metabolic model of a different strain belonging to the same species, and (2) reconstructing the metabolic model of a hybrid strain containing genomic elements from two different parental strains.}, }
@article {pmid29220785, year = {2018}, author = {Lekunberri, I and Balcázar, JL and Borrego, CM}, title = {Metagenomic exploration reveals a marked change in the river resistome and mobilome after treated wastewater discharges.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {234}, number = {}, pages = {538-542}, doi = {10.1016/j.envpol.2017.12.001}, pmid = {29220785}, issn = {1873-6424}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/*drug effects/*genetics/isolation &amp; purification/metabolism ; Bacterial Proteins/genetics/metabolism ; Drug Resistance, Bacterial ; Drug Resistance, Microbial/genetics ; Humans ; Metagenomics ; Rivers/*microbiology ; Wastewater/*chemistry/microbiology ; }, abstract = {Mobile genetic elements (MGEs) are key agents in the spread of antibiotic resistance genes (ARGs) across environments. Here we used metagenomics to compare the river resistome (collection of all ARGs) and mobilome (e.g., integrases, transposases, integron integrases and insertion sequence common region "ISCR" elements) between samples collected upstream (n = 6) and downstream (n = 6) of an urban wastewater treatment plant (UWWTP). In comparison to upstream metagenomes, downstream metagenomes showed a drastic increase in the abundance of ARGs, as well as markers of MGEs, particularly integron integrases and ISCR elements. These changes were accompanied by a concomitant prevalence of 16S rRNA gene signatures of bacteria affiliated to families encompassing well-known human and animal pathogens. Our results confirm that chronic discharges of treated wastewater severely impact the river resistome affecting not only the abundance and diversity of ARGs but also their potential spread by enriching the river mobilome in a wide variety of MGEs.}, }
@article {pmid29220487, year = {2017}, author = {Lassalle, F and Planel, R and Penel, S and Chapulliot, D and Barbe, V and Dubost, A and Calteau, A and Vallenet, D and Mornico, D and Bigot, T and Guéguen, L and Vial, L and Muller, D and Daubin, V and Nesme, X}, title = {Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium.}, journal = {Genome biology and evolution}, volume = {9}, number = {12}, pages = {3413-3431}, pmid = {29220487}, issn = {1759-6653}, mesh = {Agrobacterium/*cytology/*genetics ; *Biological Evolution ; Computational Biology ; *Ecology ; *Genetic Variation ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Software ; }, abstract = {Horizontal gene transfer (HGT) is considered as a major source of innovation in bacteria, and as such is expected to drive adaptation to new ecological niches. However, among the many genes acquired through HGT along the diversification history of genomes, only a fraction may have actively contributed to sustained ecological adaptation. We used a phylogenetic approach accounting for the transfer of genes (or groups of genes) to estimate the history of genomes in Agrobacterium biovar 1, a diverse group of soil and plant-dwelling bacterial species. We identified clade-specific blocks of cotransferred genes encoding coherent biochemical pathways that may have contributed to the evolutionary success of key Agrobacterium clades. This pattern of gene coevolution rejects a neutral model of transfer, in which neighboring genes would be transferred independently of their function and rather suggests purifying selection on collectively coded acquired pathways. The acquisition of these synapomorphic blocks of cofunctioning genes probably drove the ecological diversification of Agrobacterium and defined features of ancestral ecological niches, which consistently hint at a strong selective role of host plant rhizospheres.}, }
@article {pmid29218031, year = {2017}, author = {Tajkarimi, M and Wexler, HM}, title = {CRISPR-Cas Systems in Bacteroides fragilis, an Important Pathobiont in the Human Gut Microbiome.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2234}, pmid = {29218031}, issn = {1664-302X}, support = {I01 BX000563/BX/BLRD VA/United States ; R21 AI109545/AI/NIAID NIH HHS/United States ; }, abstract = {Background: While CRISPR-Cas systems have been identified in bacteria from a wide variety of ecological niches, there are no studies to describe CRISPR-Cas elements in Bacteroides species, the most prevalent anaerobic bacteria in the lower intestinal tract. Microbes of the genus Bacteroides make up ~25% of the total gut microbiome. Bacteroides fragilis comprises only 2% of the total Bacteroides in the gut, yet causes of >70% of Bacteroides infections. The factors causing it to transition from benign resident of the gut microbiome to virulent pathogen are not well understood, but a combination of horizontal gene transfer (HGT) of virulence genes and differential transcription of endogenous genes are clearly involved. The CRISPR-Cas system is a multi-functional system described in prokaryotes that may be involved in control both of HGT and of gene regulation. Results: Clustered regularly interspaced short palindromic repeats (CRISPR) elements in all strains of B. fragilis (n = 109) with publically available genomes were identified. Three different CRISPR-Cas types, corresponding most closely to Type IB, Type IIIB, and Type IIC, were identified. Thirty-five strains had two CRISPR-Cas types, and three strains included all three CRISPR-Cas types in their respective genomes. The cas1 gene in the Type IIIB system encoded a reverse-transcriptase/Cas1 fusion protein rarely found in prokaryotes. We identified a short CRISPR (3 DR) with no associated cas genes present in most of the isolates; these CRISPRs were found immediately upstream of a hipA/hipB operon and we speculate that this element may be involved in regulation of this operon related to formation of persister cells during antimicrobial exposure. Also, blood isolates of B. fragilis did not have Type IIC CRISPR-Cas systems and had atypical Type IIIB CRISPR-Cas systems that were lacking adjacent cas genes. Conclusions: This is the first systematic report of CRISPR-Cas systems in a wide range of B. fragilis strains from a variety of sources. There are four apparent CRISPR-Cas systems in B. fragilis-three systems have adjacent cas genes. Understanding CRISPR/Cas function in B. fragilis will elucidate their role in gene expression, DNA repair and ability to survive exposure to antibiotics. Also, based on their unique CRISPR-Cas arrays, their phylogenetic clustering and their virulence potential, we are proposing that blood isolates of B. fragilis be viewed a separate subgroup.}, }
@article {pmid29217794, year = {2017}, author = {Federici, F and Manna, L and Rizzi, E and Galantini, E and Marini, U}, title = {Draft Genome Sequence of Lactobacillus salivarius SGL 03, a Novel Potential Probiotic Strain.}, journal = {Genome announcements}, volume = {5}, number = {49}, pages = {}, pmid = {29217794}, issn = {2169-8287}, abstract = {In this work, we report the draft genome sequence of Lactobacillus salivarius SGL 03, a novel potential probiotic strain isolated from healthy infant stools. Antibiotic resistance analysis revealed the presence of a tetracycline resistance gene without elements potentially responsible for interspecific horizontal gene transfer.}, }
@article {pmid29216827, year = {2017}, author = {Pham, NP and Layec, S and Dugat-Bony, E and Vidal, M and Irlinger, F and Monnet, C}, title = {Comparative genomic analysis of Brevibacterium strains: insights into key genetic determinants involved in adaptation to the cheese habitat.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {955}, pmid = {29216827}, issn = {1471-2164}, support = {ANR-10-INBS-09//Agence Nationale de la Recherche/ ; }, mesh = {Bacteriocins/biosynthesis ; Brevibacterium/classification/*genetics/isolation &amp; purification/metabolism ; Cheese/*microbiology ; Genomics ; Glycerol/metabolism ; Iron/metabolism ; Lipid Metabolism/genetics ; Osmotic Pressure ; Phenazines/metabolism ; Phylogeny ; }, abstract = {BACKGROUND: Brevibacterium strains are widely used for the manufacturing of surface-ripened cheeses, contributing to the breakdown of lipids and proteins and producing volatile sulfur compounds and red-orange pigments. The objective of the present study was to perform comparative genomic analyses in order to better understand the mechanisms involved in their ability to grow on the cheese surface and the differences between the strains.<br><br>RESULTS: The genomes of 23 Brevibacterium strains, including twelve strains isolated from cheeses, were compared for their gene repertoire involved in salt tolerance, iron acquisition, bacteriocin production and the ability to use the energy compounds present in cheeses. All or almost all the genomes encode the enzymes involved in ethanol, acetate, lactate, 4-aminobutyrate and glycerol catabolism, and in the synthesis of the osmoprotectants ectoine, glycine-betaine and trehalose. Most of the genomes contain two contiguous genes encoding extracellular proteases, one of which was previously characterized for its activity on caseins. Genes encoding a secreted triacylglycerol lipase or involved in the catabolism of galactose and D-galactonate or in the synthesis of a hydroxamate-type siderophore are present in part of the genomes. Numerous Fe[3+]/siderophore ABC transport components are present, part of them resulting from horizontal gene transfers. Two cheese-associated strains have also acquired catecholate-type siderophore biosynthesis gene clusters by horizontal gene transfer. Predicted bacteriocin biosynthesis genes are present in most of the strains, and one of the corresponding gene clusters is located in a probable conjugative transposon that was only found in cheese-associated strains.<br><br>CONCLUSIONS: Brevibacterium strains show differences in their gene repertoire potentially involved in the ability to grow on the cheese surface. Part of these differences can be explained by different phylogenetic positions or by horizontal gene transfer events. Some of the distinguishing features concern biotic interactions with other strains such as the secretion of proteases and triacylglycerol lipases, and competition for iron or bacteriocin production. In the future, it would be interesting to take the properties deduced from genomic analyses into account in order to improve the screening and selection of Brevibacterium strains, and their association with other ripening culture components.}, }
@article {pmid29211859, year = {2018}, author = {Apagyi, KJ and Fraser, C and Croucher, NJ}, title = {Transformation Asymmetry and the Evolution of the Bacterial Accessory Genome.}, journal = {Molecular biology and evolution}, volume = {35}, number = {3}, pages = {575-581}, pmid = {29211859}, issn = {1537-1719}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {Bacterial transformation can insert or delete genomic islands (GIs), depending on the donor and recipient genotypes, if an homologous recombination spans the GI's integration site and includes sufficiently long flanking homologous arms. Combining mathematical models of recombination with experiments using pneumococci found GI insertion rates declined geometrically with the GI's size. The decrease in acquisition frequency with length (1.08×10-3 bp-1) was higher than a previous estimate of the analogous rate at which core genome recombinations terminated. Although most efficient for shorter GIs, transformation-mediated deletion frequencies did not vary consistently with GI length, with removal of 10-kb GIs ∼50% as efficient as acquisition of base substitutions. Fragments of 2 kb, typical of transformation event sizes, could drive all these deletions independent of island length. The strong asymmetry of transformation, and its capacity to efficiently remove GIs, suggests nonmobile accessory loci will decline in frequency without preservation by selection.}, }
@article {pmid29208130, year = {2017}, author = {Husain, F and Tang, K and Veeranagouda, Y and Boente, R and Patrick, S and Blakely, G and Wexler, HM}, title = {Novel large-scale chromosomal transfer in Bacteroides fragilis contributes to its pan-genome and rapid environmental adaptation.}, journal = {Microbial genomics}, volume = {3}, number = {11}, pages = {}, pmid = {29208130}, issn = {2057-5858}, support = {R21 AI109545/AI/NIAID NIH HHS/United States ; }, mesh = {Adaptation, Biological/*genetics ; Antigenic Variation/*genetics ; Bacteroides Infections/*microbiology ; Bacteroides fragilis/*genetics/pathogenicity/physiology ; Chromosomes, Bacterial/*genetics ; DNA Transposable Elements ; Gastrointestinal Microbiome/*genetics ; Gene Transfer, Horizontal/*genetics ; Humans ; Polysaccharides, Bacterial/biosynthesis/genetics ; Recombination, Genetic ; }, abstract = {Bacteroides fragilis, an important component of the human gastrointestinal microbiota, can cause lethal extra-intestinal infection upon escape from the gastrointestinal tract. We demonstrated transfer and recombination of large chromosomal segments from B. fragilis HMW615, a multidrug resistant clinical isolate, to B. fragilis 638R. In one example, the transfer of a segment of ~435 Kb/356 genes replaced ~413 Kb/326 genes of the B. fragilis 638R chromosome. In addition to transfer of antibiotic resistance genes, these transfers (1) replaced complete divergent polysaccharide biosynthesis loci; (2) replaced DNA inversion-controlled intergenic shufflons (that control expression of genes encoding starch utilization system outer membrane proteins) with more complex, divergent shufflons; and (3) introduced additional intergenic shufflons encoding divergent Type 1 restriction/modification systems. Conjugative transposon-like genes within a transferred segment and within a putative integrative conjugative element (ICE5) ~45 kb downstream from the transferred segment both encode proteins that may be involved in the observed transfer. These data indicate that chromosomal transfer is a driver of antigenic diversity and nutrient adaptation in Bacteroides that (1) contributes to the dissemination of the extensive B. fragilis pan-genome, (2) allows rapid adaptation to a changing environment and (3) can confer pathogenic characteristics to host symbionts.}, }
@article {pmid29207350, year = {2018}, author = {Garbisu, C and Garaiyurrebaso, O and Lanzén, A and Álvarez-Rodríguez, I and Arana, L and Blanco, F and Smalla, K and Grohmann, E and Alkorta, I}, title = {Mobile genetic elements and antibiotic resistance in mine soil amended with organic wastes.}, journal = {The Science of the total environment}, volume = {621}, number = {}, pages = {725-733}, doi = {10.1016/j.scitotenv.2017.11.221}, pmid = {29207350}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents ; Codon, Nonsense ; Conjugation, Genetic ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/genetics ; *Integrons ; *Mining ; *Plasmids ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Metal resistance has been associated with antibiotic resistance due to co- or cross-resistance mechanisms. Here, metal contaminated mine soil treated with organic wastes was screened for the presence of mobile genetic elements (MGEs). The occurrence of conjugative IncP-1 and mobilizable IncQ plasmids, as well as of class 1 integrons, was confirmed by PCR and Southern blot hybridization, suggesting that bacteria from these soils have gene-mobilizing capacity with implications for the dissemination of resistance factors. Moreover, exogenous isolation of MGEs from the soil bacterial community was attempted under antibiotic selection pressure by using Escherichia coli as recipient. Seventeen putative transconjugants were identified based on increased antibiotic resistance. Metabolic traits and metal resistance of putative transconjugants were investigated, and whole genome sequencing was carried out for two of them. Most putative transconjugants displayed a multi-resistant phenotype for a broad spectrum of antibiotics. They also displayed changes regarding the ability to metabolise different carbon sources, RNA: DNA ratio, growth rate and biofilm formation. Genome sequencing of putative transconjugants failed to detect genes acquired by horizontal gene transfer, but instead revealed a number of nonsense mutations, including in ubiH, whose inactivation was linked to the observed resistance to aminoglycosides. Our results confirm that mine soils contain MGEs encoding antibiotic resistance. Moreover, they point out the role of spontaneous mutations in achieving low-level antibiotic resistance in a short time, which was associated with a trade-off in the capability to metabolise specific carbon sources.}, }
@article {pmid29206153, year = {2017}, author = {Rodríguez-Rubio, L and Jofre, J and Muniesa, M}, title = {Is Genetic Mobilization Considered When Using Bacteriophages in Antimicrobial Therapy?.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {6}, number = {4}, pages = {}, pmid = {29206153}, issn = {2079-6382}, abstract = {The emergence of multi-drug resistant bacteria has undermined our capacity to control bacterial infectious diseases. Measures needed to tackle this problem include controlling the spread of antibiotic resistance, designing new antibiotics, and encouraging the use of alternative therapies. Phage therapy seems to be a feasible alternative to antibiotics, although there are still some concerns and legal issues to overcome before it can be implemented on a large scale. Here we highlight some of those concerns, especially those related to the ability of bacteriophages to transport bacterial DNA and, in particular, antibiotic resistance genes.}, }
@article {pmid29205228, year = {2017}, author = {Krishnamurthi, R and Ghosh, S and Khedkar, S and Seshasayee, ASN}, title = {Repression of YdaS Toxin Is Mediated by Transcriptional Repressor RacR in the Cryptic rac Prophage of Escherichia coli K-12.}, journal = {mSphere}, volume = {2}, number = {6}, pages = {}, pmid = {29205228}, issn = {2379-5042}, support = {IA/I/16/2/502711/WTDBT_/DBT-Wellcome Trust India Alliance/India ; }, abstract = {Horizontal gene transfer is a major driving force behind the genomic diversity seen in prokaryotes. The cryptic rac prophage in Escherichia coli K-12 carries the gene for a putative transcription factor RacR, whose deletion is lethal. We have shown that the essentiality of racR in E. coli K-12 is attributed to its role in transcriptionally repressing toxin gene(s) called ydaS and ydaT, which are adjacent to and coded divergently to racR. IMPORTANCE Transcription factors in the bacterium E. coli are rarely essential, and when they are essential, they are largely toxin-antitoxin systems. While studying transcription factors encoded in horizontally acquired regions in E. coli, we realized that the protein RacR, a putative transcription factor encoded by a gene on the rac prophage, is an essential protein. Here, using genetics, biochemistry, and bioinformatics, we show that its essentiality derives from its role as a transcriptional repressor of the ydaS and ydaT genes, whose products are toxic to the cell. Unlike type II toxin-antitoxin systems in which transcriptional regulation involves complexes of the toxin and antitoxin, repression by RacR is sufficient to keep ydaS transcriptionally silent.}, }
@article {pmid29202688, year = {2017}, author = {Abrahamian, M and Kagda, M and Ah-Fong, AMV and Judelson, HS}, title = {Rethinking the evolution of eukaryotic metabolism: novel cellular partitioning of enzymes in stramenopiles links serine biosynthesis to glycolysis in mitochondria.}, journal = {BMC evolutionary biology}, volume = {17}, number = {1}, pages = {241}, pmid = {29202688}, issn = {1471-2148}, mesh = {Animals ; *Biological Evolution ; Cytosol ; Eukaryotic Cells/*metabolism ; Genes ; *Glycolysis ; Mitochondria/genetics/*metabolism ; Oomycetes/metabolism ; Phosphorylation ; Phylogeny ; Phytophthora infestans/metabolism ; Serine/*biosynthesis ; Stramenopiles/*enzymology/*metabolism ; }, abstract = {BACKGROUND: An important feature of eukaryotic evolution is metabolic compartmentalization, in which certain pathways are restricted to the cytosol or specific organelles. Glycolysis in eukaryotes is described as a cytosolic process. The universality of this canon has been challenged by recent genome data that suggest that some glycolytic enzymes made by stramenopiles bear mitochondrial targeting peptides.<br><br>RESULTS: Mining of oomycete, diatom, and brown algal genomes indicates that stramenopiles encode two forms of enzymes for the second half of glycolysis, one with and the other without mitochondrial targeting peptides. The predicted mitochondrial targeting was confirmed by using fluorescent tags to localize phosphoglycerate kinase, phosphoglycerate mutase, and pyruvate kinase in Phytophthora infestans, the oomycete that causes potato blight. A genome-wide search for other enzymes with atypical mitochondrial locations identified phosphoglycerate dehydrogenase, phosphoserine aminotransferase, and phosphoserine phosphatase, which form a pathway for generating serine from the glycolytic intermediate 3-phosphoglycerate. Fluorescent tags confirmed the delivery of these serine biosynthetic enzymes to P. infestans mitochondria. A cytosolic form of this serine biosynthetic pathway, which occurs in most eukaryotes, is missing from oomycetes and most other stramenopiles. The glycolysis and serine metabolism pathways of oomycetes appear to be mosaics of enzymes with different ancestries. While some of the noncanonical oomycete mitochondrial enzymes have the closest affinity in phylogenetic analyses with proteins from other stramenopiles, others cluster with bacterial, plant, or animal proteins. The genes encoding the mitochondrial phosphoglycerate kinase and serine-forming enzymes are physically linked on oomycete chromosomes, which suggests a shared origin.<br><br>CONCLUSIONS: Stramenopile metabolism appears to have been shaped through the acquisition of genes by descent and lateral or endosymbiotic gene transfer, along with the targeting of the proteins to locations that are novel compared to other eukaryotes. Colocalization of the glycolytic and serine biosynthesis enzymes in mitochondria is apparently necessary since they share a common intermediate. The results indicate that descriptions of metabolism in textbooks do not cover the full diversity of eukaryotic biology.}, }
@article {pmid29198740, year = {2018}, author = {Tran-Dien, A and Le Hello, S and Bouchier, C and Weill, FX}, title = {Early transmissible ampicillin resistance in zoonotic Salmonella enterica serotype Typhimurium in the late 1950s: a retrospective, whole-genome sequencing study.}, journal = {The Lancet. Infectious diseases}, volume = {18}, number = {2}, pages = {207-214}, doi = {10.1016/S1473-3099(17)30705-3}, pmid = {29198740}, issn = {1474-4457}, mesh = {Ampicillin/therapeutic use ; *Ampicillin Resistance ; Animals ; Anti-Bacterial Agents/therapeutic use ; Disk Diffusion Antimicrobial Tests ; *Food Microbiology ; France ; Gene Transfer Techniques ; *Gene Transfer, Horizontal ; Global Health ; History, 20th Century ; Humans ; *Plasmids ; Retrospective Studies ; Salmonella Infections/history/*microbiology ; Salmonella Infections, Animal/history/*microbiology ; Salmonella typhimurium/classification/*drug effects/genetics/isolation &amp; purification ; Tunisia ; United Kingdom ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: Ampicillin, the first semi-synthetic penicillin active against Enterobacteriaceae, was released onto the market in 1961. The first outbreaks of disease caused by ampicillin-resistant strains of Salmonella enterica serotype Typhimurium were identified in the UK in 1962 and 1964. We aimed to date the emergence of this resistance in historical isolates of S enterica serotype Typhimurium.<br><br>METHODS: In this retrospective, whole-genome sequencing study, we analysed 288 S enterica serotype Typhimurium isolates collected between 1911 and 1969 from 31 countries on four continents and from various sources including human beings, animals, feed, and food. All isolates were tested for antimicrobial drug susceptibility with the disc diffusion method, and isolates shown to be resistant to ampicillin underwent resistance-transfer experiments. To provide insights into population structure and mechanisms of ampicillin resistance, we did whole-genome sequencing on a subset of 225 isolates, selected to maximise source, spatiotemporal, and genetic diversity.<br><br>FINDINGS: 11 (4%) of 288 isolates were resistant to ampicillin because of acquisition of various &#x3b2; lactamase genes, including blaTEM-1, carried by various plasmids, including the virulence plasmid of S enterica serotype Typhimurium. These 11 isolates were from three phylogenomic groups. One isolate producing TEM-1 &#x3b2; lactamase was isolated in France in 1959 and two isolates producing TEM-1 &#x3b2; lactamase were isolated in Tunisia in 1960, before ampicillin went on sale. The vectors for ampicillin resistance were different from those reported in the strains responsible for the outbreaks in the UK in the 1960s.<br><br>INTERPRETATION: The association between antibiotic use and selection of resistance determinants is not as direct as often presumed. Our results suggest that the non-clinical use of narrow-spectrum penicillins (eg, benzylpenicillin) might have favoured the diffusion of plasmids carrying the blaTEM-1 gene in S enterica serotype Typhimurium in the late 1950s.<br><br>FUNDING: Institut Pasteur, Sant&#xe9; publique France, the French Government's Investissement d'Avenir programme, the Fondation Le Roch-Les Mousquetaires.}, }
@article {pmid29194520, year = {2017}, author = {Freese, HM and Sikorski, J and Bunk, B and Scheuner, C and Meier-Kolthoff, JP and Spröer, C and Gram, L and Overmann, J}, title = {Trajectories and Drivers of Genome Evolution in Surface-Associated Marine Phaeobacter.}, journal = {Genome biology and evolution}, volume = {9}, number = {12}, pages = {3297-3311}, pmid = {29194520}, issn = {1759-6653}, mesh = {Adaptation, Physiological ; *Chromosomes, Bacterial ; DNA, Bacterial ; *Evolution, Molecular ; *Genome, Bacterial ; Genomics/*methods ; Phylogeny ; Rhodobacteraceae/classification/*genetics/physiology ; Synteny ; }, abstract = {The extent of genome divergence and the evolutionary events leading to speciation of marine bacteria have mostly been studied for (locally) abundant, free-living groups. The genus Phaeobacter is found on different marine surfaces, seems to occupy geographically disjunct habitats, and is involved in different biotic interactions, and was therefore targeted in the present study. The analysis of the chromosomes of 32 closely related but geographically spread Phaeobacter strains revealed an exceptionally large, highly syntenic core genome. The flexible gene pool is constantly but slightly expanding across all Phaeobacter lineages. The horizontally transferred genes mostly originated from bacteria of the Roseobacter group and horizontal transfer most likely was mediated by gene transfer agents. No evidence for geographic isolation and habitat specificity of the different phylogenomic Phaeobacter clades was detected based on the sources of isolation. In contrast, the functional gene repertoire and physiological traits of different phylogenomic Phaeobacter clades were sufficiently distinct to suggest an adaptation to an associated lifestyle with algae, to additional nutrient sources, or toxic heavy metals. Our study reveals that the evolutionary trajectories of surface-associated marine bacteria can differ significantly from free-living marine bacteria or marine generalists.}, }
@article {pmid29193598, year = {2018}, author = {Csuka, P and Juhász, V and Kohári, S and Filip, A and Varga, A and Sátorhelyi, P and Bencze, LC and Barton, H and Paizs, C and Poppe, L}, title = {Pseudomonas fluorescens Strain R124 Encodes Three Different MIO Enzymes.}, journal = {Chembiochem : a European journal of chemical biology}, volume = {19}, number = {4}, pages = {411-418}, doi = {10.1002/cbic.201700530}, pmid = {29193598}, issn = {1439-7633}, mesh = {Ammonia-Lyases/chemistry/genetics/*metabolism ; Biocatalysis ; Histidine Ammonia-Lyase/chemistry/genetics/*metabolism ; Imidazoles/chemistry ; Intramolecular Transferases/chemistry/genetics/*metabolism ; Molecular Structure ; Phenylalanine Ammonia-Lyase/chemistry/genetics/*metabolism ; Pseudomonas fluorescens/*enzymology/genetics/isolation &amp; purification ; }, abstract = {A number of class I lyase-like enzymes, including aromatic ammonia-lyases and aromatic 2,3-aminomutases, contain the electrophilic 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO) catalytic moiety. This study reveals that Pseudomonas fluorescens R124 strain isolated from a nutrient-limited cave encodes a histidine ammonia-lyase, a tyrosine/phenylalanine/histidine ammonia-lyase (XAL), and a phenylalanine 2,3-aminomutase (PAM), and demonstrates that an organism under nitrogen-limited conditions can develop novel nitrogen fixation and transformation pathways to enrich the possibility of nitrogen metabolism by gaining a PAM through horizontal gene transfer. The novel MIO enzymes are potential biocatalysts in the synthesis of enantiopure unnatural amino acids. The broad substrate acceptance and high thermal stability of PfXAL indicate that this enzyme is highly suitable for biocatalysis.}, }
@article {pmid29191398, year = {2018}, author = {Bell, G and MacLean, C}, title = {The Search for 'Evolution-Proof' Antibiotics.}, journal = {Trends in microbiology}, volume = {26}, number = {6}, pages = {471-483}, doi = {10.1016/j.tim.2017.11.005}, pmid = {29191398}, issn = {1878-4380}, support = {106918/Z/15/Z//Wellcome Trust/United Kingdom ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/drug effects/*genetics ; Depsipeptides/pharmacology ; Drug Discovery ; Drug Resistance, Bacterial/*genetics ; *Evolution, Molecular ; Metagenomics ; Mutation ; }, abstract = {The effectiveness of antibiotics has been widely compromised by the evolution of resistance among pathogenic bacteria. It would be restored by the development of antibiotics to which bacteria cannot evolve resistance. We first discuss two kinds of 'evolution-proof' antibiotic. The first comprises literally evolution-proof antibiotics to which bacteria cannot become resistant by mutation or horizontal gene transfer. The second category comprises agents to which resistance may arise, but so rarely that it does not become epidemic. The likelihood that resistance to a novel agent will spread is evaluated here by a simple model that includes biological and therapeutic parameters governing the evolution of resistance within hosts and the transmission of resistant strains between hosts. This model leads to the conclusion that epidemic spread is unlikely if the frequency of mutations that confer resistance falls below a defined minimum value, and it identifies potential targets for intervention to prevent the evolution of resistance. Whether or not evolution-proof antibiotics are ever found, searching for them is likely to improve the deployment of new and existing agents by advancing our understanding of how resistance evolves.}, }
@article {pmid29186777, year = {2017}, author = {Martin, JF and Álvarez-Álvarez, R and Liras, P}, title = {Clavine Alkaloids Gene Clusters of Penicillium and Related Fungi: Evolutionary Combination of Prenyltransferases, Monooxygenases and Dioxygenases.}, journal = {Genes}, volume = {8}, number = {12}, pages = {}, pmid = {29186777}, issn = {2073-4425}, abstract = {The clavine alkaloids produced by the fungi of the Aspergillaceae and Arthrodermatacea families differ from the ergot alkaloids produced by Claviceps and Neotyphodium. The clavine alkaloids lack the extensive peptide chain modifications that occur in lysergic acid derived ergot alkaloids. Both clavine and ergot alkaloids arise from the condensation of tryptophan and dimethylallylpyrophosphate by the action of the dimethylallyltryptophan synthase. The first five steps of the biosynthetic pathway that convert tryptophan and dimethylallyl-pyrophosphate (DMA-PP) in chanoclavine-1-aldehyde are common to both clavine and ergot alkaloids. The biosynthesis of ergot alkaloids has been extensively studied and is not considered in this article. We focus this review on recent advances in the gene clusters for clavine alkaloids in the species of Penicillium, Aspergillus (Neosartorya), Arthroderma and Trychophyton and the enzymes encoded by them. The final products of the clavine alkaloids pathways derive from the tetracyclic ergoline ring, which is modified by late enzymes, including a reverse type prenyltransferase, P450 monooxygenases and acetyltransferases. In Aspergillus japonicus, a α-ketoglutarate and Fe[2+]-dependent dioxygenase is involved in the cyclization of a festuclavine-like unknown type intermediate into cycloclavine. Related dioxygenases occur in the biosynthetic gene clusters of ergot alkaloids in Claviceps purpurea and also in the clavine clusters in Penicillium species. The final products of the clavine alkaloid pathway in these fungi differ from each other depending on the late biosynthetic enzymes involved. An important difference between clavine and ergot alkaloid pathways is that clavine producers lack the enzyme CloA, a P450 monooxygenase, involved in one of the steps of the conversion of chanoclavine-1-aldehyde into lysergic acid. Bioinformatic analysis of the sequenced genomes of the Aspergillaceae and Arthrodermataceae fungi showed the presence of clavine gene clusters in Arthroderma species, Penicillium roqueforti, Penicillium commune, Penicillium camemberti, Penicillium expansum, Penicillium steckii and Penicillium griseofulvum. Analysis of the gene clusters in several clavine alkaloid producers indicates that there are gene gains, gene losses and gene rearrangements. These findings may be explained by a divergent evolution of the gene clusters of ergot and clavine alkaloids from a common ancestral progenitor six genes cluster although horizontal gene transfer of some specific genes may have occurred more recently.}, }
@article {pmid29185915, year = {2018}, author = {Do, TT and Tamames, J and Stedtfeld, RD and Guo, X and Murphy, S and Tiedje, JM and Walsh, F}, title = {Antibiotic Resistance Gene Detection in the Microbiome Context.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {24}, number = {5}, pages = {542-546}, doi = {10.1089/mdr.2017.0199}, pmid = {29185915}, issn = {1931-8448}, mesh = {Anti-Bacterial Agents/*therapeutic use ; Bacteria/drug effects/*genetics ; Drug Resistance, Microbial/*genetics ; Feces/microbiology ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/*genetics ; Humans ; Microbiota/drug effects/*genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Within the past decade, microbiologists have moved from detecting single antibiotic resistance genes (ARGs) to detecting all known resistance genes within a sample due to advances in next generation sequencing. This has provided a wealth of data on the variation and relative abundances of ARGs present in a total bacterial population. However, to use these data in terms of therapy or risk to patients, they must be analyzed in the context of the background microbiome. Using a quantitative PCR ARG chip and 16S rRNA amplicon sequencing, we have sought to identify the ARGs and bacteria present in a fecal sample of a healthy adult using genomic tools. Of the 42 ARGs detected, 12 fitted into the ResCon1 category of ARGs: cfxA, cphA, bacA, sul3, aadE, blaTEM, aphA1, aphA3, aph(2')-Id, aacA/aphd, catA1, and vanC. Therefore, we describe these 12 genes as the core resistome of this person's fecal microbiome and the remaining 30 ARGs as descriptors of the microbial population within the fecal microbiome. The dominant phyla and genera agree with those previously detected in the greatest abundances in fecal samples of healthy humans. The majority of the ARGs detected were associated with the presence of specific bacterial taxa, which were confirmed using microbiome analysis. We acknowledge the limitations of the data in the context of the limited sample set. However, the principle of combining qPCR and microbiome analysis was shown to be helpful to identify the association of the ARGs with specific taxa.}, }
@article {pmid29183407, year = {2017}, author = {Tamang, MD and Sunwoo, H and Jeon, B}, title = {Phage-mediated dissemination of virulence factors in pathogenic bacteria facilitated by antibiotic growth promoters in animals: a perspective.}, journal = {Animal health research reviews}, volume = {18}, number = {2}, pages = {160-166}, doi = {10.1017/S1466252317000147}, pmid = {29183407}, issn = {1475-2654}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/*drug effects/*pathogenicity ; Bacteriophages/*metabolism ; Drug Resistance, Microbial ; Growth Substances/pharmacology ; *Virulence Factors ; }, abstract = {Addition of sub-therapeutic antibiotics to the feed of food-producing animals for growth promotion and disease prevention has become a common agricultural practice in many countries. The emergence of antibiotic-resistant pathogens is a looming concern associated with the use of antibiotic growth promoters (AGPs) around the world. In addition, some studies have shown that AGPs may not only affect antibiotic resistance but may also stimulate the dissemination of virulence factors via bacteriophages. Although only a few studies are currently available in the literature regarding this topic, in this article we endeavor to provide a perspective about how AGPs would impact the transmission of virulence factors by horizontal gene transfer via phages in a few pathogenic bacterial species significant to livestock production.}, }
@article {pmid29180992, year = {2017}, author = {Sato, M and Miyazaki, K}, title = {Phylogenetic Network Analysis Revealed the Occurrence of Horizontal Gene Transfer of 16S rRNA in the Genus Enterobacter.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2225}, pmid = {29180992}, issn = {1664-302X}, abstract = {Horizontal gene transfer (HGT) is a ubiquitous genetic event in bacterial evolution, but it seldom occurs for genes involved in highly complex supramolecules (or biosystems), which consist of many gene products. The ribosome is one such supramolecule, but several bacteria harbor dissimilar and/or chimeric 16S rRNAs in their genomes, suggesting the occurrence of HGT of this gene. However, we know little about whether the genes actually experience HGT and, if so, the frequency of such a transfer. This is primarily because the methods currently employed for phylogenetic analysis (e.g., neighbor-joining, maximum likelihood, and maximum parsimony) of 16S rRNA genes assume point mutation-driven tree-shape evolution as an evolutionary model, which is intrinsically inappropriate to decipher the evolutionary history for genes driven by recombination. To address this issue, we applied a phylogenetic network analysis, which has been used previously for detection of genetic recombination in homologous alleles, to the 16S rRNA gene. We focused on the genus Enterobacter, whose phylogenetic relationships inferred by multi-locus sequence alignment analysis and 16S rRNA sequences are incompatible. All 10 complete genomic sequences were retrieved from the NCBI database, in which 71 16S rRNA genes were included. Neighbor-joining analysis demonstrated that the genes residing in the same genomes clustered, indicating the occurrence of intragenomic recombination. However, as suggested by the low bootstrap values, evolutionary relationships between the clusters were uncertain. We then applied phylogenetic network analysis to representative sequences from each cluster. We found three ancestral 16S rRNA groups; the others were likely created through recursive recombination between the ancestors and chimeric descendants. Despite the large sequence changes caused by the recombination events, the RNA secondary structures were conserved. Successive intergenomic and intragenomic recombination thus shaped the evolution of 16S rRNA genes in the genus Enterobacter.}, }
@article {pmid29180282, year = {2018}, author = {Brown-Jaque, M and Calero-Cáceres, W and Espinal, P and Rodríguez-Navarro, J and Miró, E and González-López, JJ and Cornejo, T and Hurtado, JC and Navarro, F and Muniesa, M}, title = {Antibiotic resistance genes in phage particles isolated from human faeces and induced from clinical bacterial isolates.}, journal = {International journal of antimicrobial agents}, volume = {51}, number = {3}, pages = {434-442}, doi = {10.1016/j.ijantimicag.2017.11.014}, pmid = {29180282}, issn = {1872-7913}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Bacteriophages/*genetics/isolation &amp; purification ; Child ; Child, Preschool ; DNA, Viral/*genetics ; *Drug Resistance, Bacterial ; Escherichia coli/isolation &amp; purification/*virology ; Feces/*microbiology ; Female ; *Genes, Bacterial ; Healthy Volunteers ; Humans ; Klebsiella pneumoniae/isolation &amp; purification/*virology ; Male ; Middle Aged ; Real-Time Polymerase Chain Reaction ; Young Adult ; }, abstract = {Phage particles have emerged as elements with the potential to mobilise antibiotic resistance genes (ARGs) in different environments, including the intestinal habitat. This study aimed to determine the occurrence of ARGs in phage particles present in faecal matter and induced from strains isolated from faeces. Nine ARGs (blaTEM, blaCTX-M-1 group, blaCTX-M-9 group, blaOXA-48, qnrA, qnrS, mecA, sul1 and armA) were quantified by qPCR in the phage DNA fractions of 150 faecal samples obtained from healthy individuals who had not received antibiotic treatment or travelled abroad in the 3 months prior to sample collection. On the suspicion that the detected particles originated from bacterial flora, 82 Escherichia coli and Klebsiella pneumoniae isolates possessing at least one identified ARG (blaTEM, blaCTX-M-1 group, blaCTX-M-9 group, armA, qnrA, qnrS and sul1) were isolated and their capacity to produce phage particles carrying these ARGs following induction was evaluated. Of 150 samples, 72.7% were positive for at least one ARG, with blaTEM and blaCTX-M-9 group being the most prevalent and abundant. Of the 82 isolates, 51 (62%) showed an increase in the number of copies of the respective ARG in the phage fraction following induction, with blaTEM, blaCTX-M-1 group, blaCTX-M-9 group and sul1 being the most abundant. Phages induced from the isolates were further purified and visualised using microscopy and their DNA showed ARG levels of up to 10[10] gene copies/mL. This study highlights the abundance of phage particles harbouring ARGs and indicates that bacterial strains in the intestinal habitat could be source of these particles.}, }
@article {pmid29180279, year = {2018}, author = {Tietgen, M and Semmler, T and Riedel-Christ, S and Kempf, VAJ and Molinaro, A and Ewers, C and Göttig, S}, title = {Impact of the colistin resistance gene mcr-1 on bacterial fitness.}, journal = {International journal of antimicrobial agents}, volume = {51}, number = {4}, pages = {554-561}, doi = {10.1016/j.ijantimicag.2017.11.011}, pmid = {29180279}, issn = {1872-7913}, mesh = {A549 Cells ; Animals ; Anti-Bacterial Agents/pharmacology ; Cell Line ; Colistin/pharmacology ; Drug Resistance, Bacterial/genetics ; Escherichia coli/drug effects/*genetics/*growth &amp; development ; Escherichia coli Proteins/*genetics ; Genome, Bacterial/genetics ; Humans ; Klebsiella pneumoniae/drug effects/*genetics/*growth &amp; development ; L-Lactate Dehydrogenase/metabolism ; Microbial Sensitivity Tests ; Moths/microbiology ; Plasmids/genetics ; }, abstract = {A Klebsiella pneumoniae isolate harbouring a 217 kb IncHI2-type plasmid (pKP2442) encoding the colistin resistance gene mcr-1 was isolated from a leukaemia patient. pKP2442 was mobilised by intragenus and intergenus transconjugation from the clinical isolate to Escherichia coli J53 (transconjugation frequency 6.86 × 10[-8] ± 5.57 × 10[-8]) and K. pneumoniae PRZ (transconjugation frequency 4.04 × 10[-8] ± 3.03 × 10[-8]), respectively. Since acquisition of resistance determinants often results in a loss of fitness, the impact of mcr-1 on the fitness of E. coli and K. pneumoniae was investigated. Escherichia coli J53 and K. pneumoniae PRZ transformants harbouring the TOPO expression vector encoding mcr-1 displayed significantly decreased growth rates compared with isogenic parental strains and controls. In contrast, competitive growth experiments revealed equal growth rates between E. coli J53 pKP2442 transconjugants (TcpKP2442) and the parental strain, whereas K. pneumoniae PRZ TcpKP2442 showed significantly reduced growth rates compared with their parental strain (selection rate constant -1.62 ± 0.49), indicating a decrease in fitness. Infection of A549 human lung epithelial cells with TcpKP2442 or mcr-1 transformants and controls revealed equal lactate dehydrogenase activities, indicating no significant impact of mcr-1 on cytotoxicity. Likewise, survival of Galleria mellonella larvae infected with mcr-1-expressing strains and isogenic controls was similar. These data indicate that expression of mcr-1 is able to cause a fitness cost when encoded on expression vectors and that acquisition of natural plasmid-borne mcr-1 does not impair fitness in E. coli J53 but negatively influences growth rates in K. pneumoniae PRZ.}, }
@article {pmid29179769, year = {2017}, author = {Ma, L and Li, B and Jiang, XT and Wang, YL and Xia, Y and Li, AD and Zhang, T}, title = {Catalogue of antibiotic resistome and host-tracking in drinking water deciphered by a large scale survey.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {154}, pmid = {29179769}, issn = {2049-2618}, support = {172057/15E//Hong Kong General Research Fund/ ; JCYJ20150831192847649//Shenzhen Knowledge Innovation Program-Basic Research Project/ ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/classification/drug effects/genetics/*isolation &amp; purification ; China ; Drinking Water/*analysis/*microbiology ; Drug Resistance, Microbial/*genetics ; Drug Resistance, Multiple/genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Hong Kong ; Humans ; Metagenomics/methods ; Microbial Consortia/drug effects/genetics ; Public Health ; Surveys and Questionnaires ; United States ; Water Purification ; }, abstract = {BACKGROUND: Excesses of antibiotic resistance genes (ARGs), which are regarded as emerging environmental pollutants, have been observed in various environments. The incidence of ARGs in drinking water causes potential risks to human health and receives more attention from the public. However, ARGs harbored in drinking water remain largely unexplored. In this study, we aimed at establishing an antibiotic resistome catalogue in drinking water samples from a wide range of regions and to explore the potential hosts of ARGs.<br><br>RESULTS: A catalogue of antibiotic resistome in drinking water was established, and the host-tracking of ARGs was conducted through a large-scale survey using metagenomic approach. The drinking water samples were collected at the point of use in 25 cities in mainland China, Hong Kong, Macau, Taiwan, South Africa, Singapore and the USA. In total, 181 ARG subtypes belonging to 16 ARG types were detected with an abundance range of 2.8&#x2009;&#xd7;&#x2009;10[-2] to 4.2&#x2009;&#xd7;&#x2009;10[-1] copies of ARG per cell. The highest abundance was found in northern China (Henan Province). Bacitracin, multidrug, aminoglycoside, sulfonamide, and beta-lactam resistance genes were dominant in drinking water. Of the drinking water samples tested, 84% had a higher ARG abundance than typical environmental ecosystems of sediment and soil. Metagenomic assembly-based host-tracking analysis identified Acidovorax, Acinetobacter, Aeromonas, Methylobacterium, Methyloversatilis, Mycobacterium, Polaromonas, and Pseudomonas as the hosts of ARGs. Moreover, potential horizontal transfer of ARGs in drinking water systems was proposed by network and Procrustes analyses.<br><br>CONCLUSIONS: The antibiotic resistome catalogue compiled using a large-scale survey provides a useful reference for future studies on the global surveillance and risk management of ARGs in drinking water. .}, }
@article {pmid29179671, year = {2017}, author = {Hudaiberdiev, S and Shmakov, S and Wolf, YI and Terns, MP and Makarova, KS and Koonin, EV}, title = {Phylogenomics of Cas4 family nucleases.}, journal = {BMC evolutionary biology}, volume = {17}, number = {1}, pages = {232}, pmid = {29179671}, issn = {1471-2148}, support = {R35 GM118160/GM/NIGMS NIH HHS/United States ; Intramural Funds//U.S. Department of Health and Human Services/International ; R35 GM118160/NH/NIH HHS/United States ; }, mesh = {Archaea/enzymology/genetics ; Bacteria/enzymology/genetics ; Base Sequence ; CRISPR-Cas Systems/*genetics ; DNA Transposable Elements/genetics ; Endonucleases/*genetics ; Gene Transfer, Horizontal/genetics ; Genetic Loci ; Genome, Archaeal ; Genome, Bacterial ; *Genomics ; *Multigene Family ; Phylogeny ; Selection, Genetic ; }, abstract = {BACKGROUND: The Cas4 family endonuclease is a component of the adaptation module in many variants of CRISPR-Cas adaptive immunity systems. Unlike most of the other Cas proteins, Cas4 is often encoded outside CRISPR-cas loci (solo-Cas4) and is also found in mobile genetic elements (MGE-Cas4).<br><br>RESULTS: As part of our ongoing investigation of CRISPR-Cas evolution, we explored the phylogenomics of the Cas4 family. About 90% of the archaeal genomes encode Cas4 compared to only about 20% of the bacterial genomes. Many archaea encode both the CRISPR-associated form (CAS-Cas4) and solo-Cas4, whereas in bacteria, this combination is extremely rare. The solo-cas4 genes are over-represented in environmental bacteria and archaea with small genomes that typically lack CRISPR-Cas, suggesting that Cas4 could perform uncharacterized defense or repair functions in these microbes. Phylogenomic analysis indicates that both the CRISPR-associated cas4 genes are often transferred horizontally but almost exclusively, as part of the adaptation module. The evolutionary integrity of the adaptation module sharply contrasts the rampant shuffling of CRISPR-cas modules whereby a given variant of the adaptation module can combine with virtually any effector module. The solo-cas4 genes evolve primarily via vertical inheritance and are subject only to occasional horizontal transfer. The selection pressure on cas4 genes does not substantially differ between CAS-Cas4 and solo-cas4, and is close to the genomic median. Thus, cas4 genes, similarly to cas1 and cas2, evolve similarly to 'regular' microbial genes involved in various cellular functions, showing no evidence of direct involvement in virus-host arms races. A notable feature of the Cas4 family evolution is the frequent recruitment of cas4 genes by various mobile genetic elements (MGE), particularly, archaeal viruses. The functions of Cas4 in these elements are unknown and potentially might involve anti-defense roles.<br><br>CONCLUSIONS: Unlike most of the other Cas proteins, Cas4 family members are as often encoded by stand-alone genes as they are incorporated in CRISPR-Cas systems. In addition, cas4 genes were repeatedly recruited by MGE, perhaps, for anti-defense functions. Experimental characterization of the solo and MGE-encoded Cas4 nucleases is expected to reveal currently uncharacterized defense and anti-defense systems and their interactions with CRISPR-Cas systems.}, }
@article {pmid30677354, year = {2017}, author = {Henry, PM and Kirkpatrick, SC and Islas, CM and Pastrana, AM and Yoshisato, JA and Koike, ST and Daugovish, O and Gordon, TR}, title = {The Population of Fusarium oxysporum f. sp. fragariae, Cause of Fusarium Wilt of Strawberry, in California.}, journal = {Plant disease}, volume = {101}, number = {4}, pages = {550-556}, doi = {10.1094/PDIS-07-16-1058-RE}, pmid = {30677354}, issn = {0191-2917}, abstract = {The objectives of this study were to investigate the structure of the population of Fusarium oxysporum f. sp. fragariae in California and to evaluate methods for its detection. Fifty-nine isolates of F. oxysporum f. sp. fragariae were obtained from diseased strawberry plants and their identity was confirmed by pathogenicity testing. The full nuclear ribosomal intergenic spacer (IGS) and elongation factor 1-α gene (EF-1α) were amplified by polymerase chain reaction (PCR) and sequenced to elucidate phylogenetic relationships among isolates. IGS and EF-1α sequences revealed three main lineages, which corresponded to three somatic compatibility groups. Primers designed to detect F. oxysporum f. sp. fragariae in Japan amplified a 239-bp product from 55 of 59 California isolates of F. oxysporum f. sp. fragariae and from no nonpathogenic isolates of F. oxysporum. The sequence of this PCR product was identical to the sequence obtained from F. oxysporum f. sp. fragariae isolates in Japan. Intensive sampling at two locations in California showed results of tests based on PCR and somatic compatibility to be in agreement for 97% (257 of 264) of isolates tested. Our findings revealed considerable diversity in the California population of F. oxysporum f. sp. fragariae, and indications that horizontal gene transfer may have occurred.}, }
@article {pmid29964528, year = {2017}, author = {Wei, X and Xue, SL and Yang, F and Li, X and Liu, ZH and Xue, G and Gao, P}, title = {[Effect of Zero Valent Iron on the Decline of Tetracycline Resistance Genes and Class 1 Integrons During Thermophilic Anaerobic Digestion of Sludge].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {38}, number = {2}, pages = {697-702}, doi = {10.13227/j.hjkx.201607235}, pmid = {29964528}, issn = {0250-3301}, mesh = {Drug Resistance, Bacterial ; *Genes, Bacterial ; *Integrons ; Iron/*chemistry ; Sewage/*microbiology ; Tetracycline Resistance/*genetics ; }, abstract = {To investigate the effects of zero valent iron (Fe[0]) on the decline of antibiotic resistance genes during thermophilic anaerobic digestion of sludge, the abundances of seven tetracycline resistance genes (TC-ARGs, including tetA, tetC, tetG, tetM, tetO, tetW, and tetX) and class 1 integron gene (intI1) were quantified by quantitative PCR (qPCR). Also, the concentrations of volatile fatty acids (VFAs) were determined. The correlations between the abundances of TC-ARGs and intI1 gene and the concentrations of VFAs were discussed. The results showed that appropriate dose of Fe[0] such as 0.10 g·g[-1] VSS could enhance the anaerobic digestion process of sludge, and the production of total VFAs and acetic acid increased significantly. The decrease in the abundances of TC-ARGs and intI1 gene was also enhanced. However, excessive Fe[0] such as 1.17 g·g[-1] VSS could not further improve the reduction in the abundances of TC-ARGs and intI1 gene, probably resulted from the occurrence of horizontal gene transfer. The abundances of TC-ARGs except tetO gene, as well as intI1 gene exhibited significant negative correlation with the concentration of acetic acid, indicating that acetic acid probably had an enhanced effect on the decline of TC-ARGs and intI1 gene during thermophilic anaerobic digestion of sludge.}, }
@article {pmid30207147, year = {2017}, author = {Agafonova, NV and Doronina, NV and Kaparullina, EN and Fedorov, DN and Gafarov, AB and Sazonova, OI and Sokolov, SL and Trotsenko, YA}, title = {[A novel Delftia plant symbiont capable of autotrophic methylotrophy].}, journal = {Mikrobiologiia}, volume = {86}, number = {1}, pages = {88-98}, pmid = {30207147}, issn = {0026-3656}, mesh = {Autotrophic Processes/*physiology ; *Delftia/classification/genetics/isolation &amp; purification/metabolism ; Lupinus/*microbiology ; Root Nodules, Plant/*microbiology ; Symbiosis/*physiology ; }, abstract = {A facultative methylotrophic bacterium, strain Lp-1, which was isolated from root nodules of lupine (Lupinus polyphyllus L.) on the medium with methanol as a carbon and energy source, exhibited high similarity of the 16S rRNA gene sequences to Delftia strains (94‒99.9%). The cells of Delftia sp. Lp-1 were motile gram-negative rods dividing by binary fission. Predominant fatty acids were C16:0 (34.2%), C16:1ω9 (14.5%), and C18:1ω7c (17.3%). Phosphatidylethanolamine, phosphatidylcholine, and phosphatidylglycerol were the dominant phospholipids. Q8 was the major ubiquinone. Optimal growth occurred at 24‒26°C and pH 7.1‒7.3; growth was inhibited by 1% NaCl. The organism oxidized methanol with the classical methanol dehydrogenase and used the ribulose bisphosphate pathway of C1 metabolism. Analysis of translated amino acid sequence of the large subunit of the MxaF methanol dehydrogenase revealed 85.5‒94% similarity to the sequences of such autotrophic methylotrophs of the class Alphaproteobacteria as Angulomicrobium, Starkeya, and Ancylobacter, indicating the possible acquisition of the mxaF gene via horizontal gene transfer. Delftia sp. Lp-1 (VKM B-3039, DSM 24446), the first methylotrophic member of the genus Delftia, was shown to be a plant symbiont, stimulating plant growth and morphogenesis, increasing the level of photosynthetic pigments and specific leaf weight. It possesses the nifH gene of nitrogen fixation, is capable of phosphate solubilization, synthesis of auxins and siderophores, and is antagonistic to plant pathogenic fungi and bacilli.}, }
@article {pmid29956652, year = {2017}, author = {Bernheim, A}, title = {[Why so rare if so essentiel: the determinants of the sparse distribution of CRISPR-Cas systems in bacterial genomes].}, journal = {Biologie aujourd'hui}, volume = {211}, number = {4}, pages = {255-264}, doi = {10.1051/jbio/2018005}, pmid = {29956652}, issn = {2105-0686}, mesh = {Archaea/genetics ; Bacteria/genetics ; CRISPR-Cas Systems/genetics/physiology ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics/*physiology ; *Evolution, Molecular ; *Gene Dosage ; Gene Transfer, Horizontal/physiology ; Genes, Essential/*physiology ; Genetic Variation ; Genome, Bacterial/*genetics ; }, abstract = {CRISPR-Cas (Cluster of Regularly Interspaced Short Palindromic Repeats) systems confer bacteria and archaea an adaptative immunity against phages and other invading genetic elements playing an important role in bacterial evolution. However, despite the protection they generate and high rate of horizontal transfer, less than 50% of bacterial genomes harbor a CRISPR-Cas system. As a comparison, 90% of archaea encode a CRISPR-Cas system and a bacterial genome codes for two restriction modification systems on average. This review describes CRISPR-Cas systems distribution in bacterial genomes and then details the different hypotheses put forward to explain the relative scarcity of CRISPR-Cas systems. More specifically, phage escape mechanisms, ecological factors such as phage diversity and abundance and intrinsic costs, such as maintenance or autoimmunity, are discussed. Overall, a better understanding of the downsides of encoding CRISPR-Cas systems is essential to explain their evolutionary dynamics and their relative success in different environments and clades.}, }
@article {pmid29536355, year = {2017}, author = {Stingl, K and Koraimann, G}, title = {Prokaryotic Information Games: How and When to Take up and Secrete DNA.}, journal = {Current topics in microbiology and immunology}, volume = {413}, number = {}, pages = {61-92}, doi = {10.1007/978-3-319-75241-9_3}, pmid = {29536355}, issn = {0070-217X}, mesh = {Anti-Bacterial Agents ; DNA, Bacterial/*metabolism ; Gene Transfer, Horizontal ; *Gram-Negative Bacteria ; Gram-Positive Bacteria ; Plasmids ; Prokaryotic Cells ; }, abstract = {Besides transduction via bacteriophages natural transformation and bacterial conjugation are the most important mechanisms driving bacterial evolution and horizontal gene spread. Conjugation systems have evolved in eubacteria and archaea. In Gram-positive and Gram-negative bacteria, cell-to-cell DNA transport is typically facilitated by a type IV secretion system (T4SS). T4SSs also mediate uptake of free DNA in Helicobacter pylori, while most transformable bacteria use a type II secretion/type IV pilus system. In this chapter, we focus on how and when bacteria "decide" that such a DNA transport apparatus is to be expressed and assembled in a cell that becomes competent. Development of DNA uptake competence and DNA transfer competence is driven by a variety of stimuli and often involves intricate regulatory networks leading to dramatic changes in gene expression patterns and bacterial physiology. In both cases, genetically homogeneous populations generate a distinct subpopulation that is competent for DNA uptake or DNA transfer or might uniformly switch into competent state. Phenotypic conversion from one state to the other can rely on bistable genetic networks that are activated stochastically with the integration of external signaling molecules. In addition, we discuss principles of DNA uptake processes in naturally transformable bacteria and intend to understand the exceptional use of a T4SS for DNA import in the gastric pathogen H. pylori. Realizing the events that trigger developmental transformation into competence within a bacterial population will eventually help to create novel and effective therapies against the transmission of antibiotic resistances among pathogens.}, }
@article {pmid29492276, year = {2016}, author = {Quaiser, A and Krupovic, M and Dufresne, A and Francez, AJ and Roux, S}, title = {Diversity and comparative genomics of chimeric viruses in Sphagnum-dominated peatlands.}, journal = {Virus evolution}, volume = {2}, number = {2}, pages = {vew025}, pmid = {29492276}, issn = {2057-1577}, abstract = {A new group of viruses carrying naturally chimeric single-stranded (ss) DNA genomes that encompass genes derived from eukaryotic ssRNA and ssDNA viruses has been recently identified by metagenomic studies. The host range, genomic diversity, and abundance of these chimeric viruses, referred to as cruciviruses, remain largely unknown. In this article, we assembled and analyzed thirty-seven new crucivirus genomes from twelve peat viromes, representing twenty-four distinct genome organizations, and nearly tripling the number of available genomes for this group. All genomes possess the two characteristic genes encoding for the conserved capsid protein (CP) and a replication protein. Additional ORFs were conserved only in nearly identical genomes with no detectable similarity to known genes. Two cruciviruses possess putative introns in their replication-associated genes. Sequence and phylogenetic analyses of the replication proteins revealed intra-gene chimerism in at least eight chimeric genomes. This highlights the large extent of horizontal gene transfer and recombination events in the evolution of ssDNA viruses, as previously suggested. Read mapping analysis revealed that members of the 'Cruciviridae' group are particularly prevalent in peat viromes. Sequences matching the CP ranged from 0.6 up to 10.9 percent in the twelve peat viromes. In contrast, from sixty-nine available viromes derived from other environments, only twenty-four contained cruciviruses, which on average accounted for merely 0.2 percent of sequences. Overall, this study provides new genome information and insights into the diversity of chimeric viruses, a necessary first step in progressing toward an accurate quantification and host range identification of these new viruses.}, }
@article {pmid29368868, year = {2016}, author = {Zakharov, IA}, title = {[Horizontal gene transfer into the genomes of insects].}, journal = {Genetika}, volume = {52}, number = {7}, pages = {804-809}, pmid = {29368868}, issn = {0016-6758}, mesh = {Animals ; *Evolution, Molecular ; Gene Transfer, Horizontal/*physiology ; Insecta/*genetics ; }, abstract = {Horizontal gene transfer (HGT) is widespread in the world of prokaryotes, but the examples of this phenomenon among multicellular animals, particularly insects, are few. This review examines the transfer of genetic material to the nuclear genomes of insects from the mitochondrial genome (intracellular HGT), as well as from the genomes of viruses, bacteria, fungi, and unrelated insects. In most cases, the mechanisms of this transfer are unknown. Many pro- and eukaryotic genes that moved through the HGT are expressed in the insect genome and in some cases can provide the evolutionary innovations that are considered as aromorphoses.}, }
@article {pmid30159459, year = {2016}, author = {Sun, T and Xu, Y and Zhang, D and Zhuang, H and Wu, J and Sun, G}, title = {An acyltransferase gene that putatively functions in anthocyanin modification was horizontally transferred from Fabaceae into the genus Cuscuta.}, journal = {Plant diversity}, volume = {38}, number = {3}, pages = {149-155}, pmid = {30159459}, issn = {2468-2659}, abstract = {Horizontal gene transfer (HGT) refers to the flow of genetic materials to non-offspring, and occasionally HGT in plants can improve the adaptation of organisms in new niches due to expanded metabolic capability. Anthocyanins are an important group of water-soluble red, purple, or blue secondary metabolites, whose diversity results from modification after the main skeleton biosynthesis. Cuscuta is a stem holoparasitic genus, whose members form direct connection with hosts to withdraw water, nutrients, and macromolecules. Such intimate association is thought to increase the frequency of HGT. By transcriptome screening for foreign genes in Cuscuta australis, we discovered that one gene encoding a putative anthocyanin acyltransferase gene of the BAHD family, which is likely to be involved in anthocyanin modification, was acquired by C. australis from Fabaceae through HGT. The anthocyanin acyltransferase-like (AT-like) gene was confirmed to be present in the genome assembly of C. australis and the transcriptomes of Cuscuta pentagona. The higher transcriptional level in old stems is consistent with its putative function in secondary metabolism by stabilizing anthocyanin at neutral pH and thus HGT of this AT-like gene may have improved biotic and abiotic resistance of Cuscuta.}, }
@article {pmid29616532, year = {2016}, author = {Luncã, C and Iancu, LS and Vremerã, T and Tuchiluş, CG and Dorneanu, O}, title = {Characterization of MRSA strains by phenotypic and OCR-based methods.}, journal = {Roumanian archives of microbiology and immunology}, volume = {75}, number = {1-2}, pages = {37-43}, pmid = {29616532}, issn = {1222-3891}, mesh = {Bacterial Proteins/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Methicillin-Resistant Staphylococcus aureus/*classification/genetics/isolation &amp; purification ; Multiplex Polymerase Chain Reaction/*methods ; Penicillin-Binding Proteins/genetics ; Phenotype ; R Factors/*genetics ; Romania/epidemiology ; Staphylococcal Infections/epidemiology/microbiology ; }, abstract = {With the emergence and spread of new methicilin resistant Staphylococcus aureus (MRSA) strains, control of dissemination, both in hospitals and in the community, requires the molecular characterization of the circulating strains in order to establish their dynamics and identify the sources of infection. During this study we analyzed the MRSA isolates by means of PCR-based methods in order to improve epidemiological surveillance and early application of prevention measures. The presence of mecA, nuc, lukF-PV and lukS-PV genes, as well as SCCmec types was assessed in relation to clinical characteristics and multidrug resistance (MDR) for 86 MRSA isolates and showed that 51% of MDR strains were carriers of mobile genetic elements SCCmec IV and the majority of non-MDR SCCmec type IV strains were PVL-positive (81.8%). Comparison of diagnostic methods showed that PBP2 detection represents an extremely useful alternative to PCR for the rapid screening of MRSA isolates, in laboratories that lack facilities necessary for molecular diagnosis, such as PFGE (Pulse Field Gel Electrophoresis), spa-typing and/or MLST (Multilocus Sequence Typing).}, }
@article {pmid30743331, year = {2011}, author = {Liu, R and Zhang, P and Pu, X and Xing, X and Chen, J and Deng, X}, title = {Analysis of a Prophage Gene Frequency Revealed Population Variation of 'Candidatus Liberibacter asiaticus' from Two Citrus-Growing Provinces in China.}, journal = {Plant disease}, volume = {95}, number = {4}, pages = {431-435}, doi = {10.1094/PDIS-04-10-0300}, pmid = {30743331}, issn = {0191-2917}, abstract = {Prophages are important genetic elements of bacterial genomes and are involved in lateral gene transfer, pathogenicity, environmental adaptations, and interstrain genetic variability. In this study, the sequence of a prophage terminase gene of 'Candidatus Liberibacter asiaticus', a bacterium associated with citrus Huanglongbing (HLB), was selected as a molecular marker to assess the genetic variation in two 'Ca. L. asiaticus' populations from geographically distinct provinces (Guangdong and Yunnan) in China. The frequency of the prophage terminase gene was 15.8% (19/120) in Guangdong (altitude <500 m) and 97.4% (38/39) in Yunnan (altitude >2,000 m). The difference was highly significant (P < 0.0001) based on χ[2] analysis. However, the partial prophage terminase gene sequences obtained from 10 Guangdong strains and 6 Yunnan strains were identical or highly similar, suggesting that at least some bacterial strains in the two locations shared a common recent origin. This is the first report on population variation of 'Ca. L. asiaticus' in China, where HLB was first described. The population variation of 'Ca. L. asiaticus' in the two geographical regions and the related HLB epidemiology were discussed.}, }
@article {pmid30786616, year = {2006}, author = {Putnam, ML and Miller, M}, title = {Pathogenic Isolates of Rhodococcus fascians from New Hosts in the United States.}, journal = {Plant disease}, volume = {90}, number = {4}, pages = {526}, doi = {10.1094/PD-90-0526C}, pmid = {30786616}, issn = {0191-2917}, abstract = {Rhodococcus fascians is important to the nursery industry due to its broad host range (68 genera) (2) and potential for horizontal gene transfer of plasmid-borne virulence genes. Since 2001, many herbaceous ornamental plants with symptoms of leafy galls or basal or axillary shoot proliferation suggestive of infection by R. fascians have been submitted to the Oregon State University Plant Clinic for diagnosis. R. fascians was isolated from symptomatic plants by placing affected tissues into saline or liquid D2 medium (1) for 30 to 120 min and then dilution plating onto D2 agar. Orange colonies were purified by dilution streaking and identified as R. fascians by substrate utilization (Biolog, Hayward, CA) and fatty acid analysis (L. Barnes, Texas A &amp; M University, College Station, TX). Pathogenicity was confirmed by inoculation of 10 newly germinated Pisum sativum 'Laxton Progress' and 'Sugar Pod' seedlings with bacteria from 2-day-old cultures (10[7] CFU/ml) or water (controls). Our isolates produced shoot proliferations typical of R. fascians infection of peas, confirming pathogenicity. Control plants remained healthy. Pathogenic R. fascians isolates were associated with and isolated from eight species not previously reported as hosts: Acanthus mollis, Campanula sarastro, Heliopsis helianthoides 'Loraine Sunshine', Nemesia × 'Natalie', Hosta × 'Blue Umbrella', Verbascum 'Sierra Sunset', Veronica spicata 'Minuet' and Viola × 'Purple Showers'. References: (1) N. W. Schaad et al. Laboratory Guide to Plant Pathogenic Bacteria. The American Phytopathological Society, 2001. (2) D. Vereecke et al. Mol. Plant-Microbe Interact. 6:53, 2003.}, }
@article {pmid29539054, year = {2005}, author = {Chen, W and Wang, Y and Chen, C}, title = {Identification of a Genomic Island of Actinobacillus actinomycetemcomitans.}, journal = {Journal of periodontology}, volume = {76 Suppl 11S}, number = {}, pages = {2052-2060}, doi = {10.1902/jop.2005.76.11-S.2052}, pmid = {29539054}, issn = {1943-3670}, support = {R01 DE012212/DE/NIDCR NIH HHS/United States ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT) is a process by which bacteria acquire genes from organisms of distant taxa. HGT is now recognized as a major driving force in the evolution of bacterial pathogens. Through this process, bacteria may accumulate blocks of DNA such as genomic islands (GEIs) that encode fitness or virulence factors. The periodontal pathogen A. actinomycetemcomitans has been known to exhibit variable virulence potential. It is postulated that GEIs may play a role in modifying the virulence potential of A. actinomycetemcomitans. This study was initiated to identify and determine the distribution of GEIs in A. actinomycetemcomitans.<br><br>METHODS: Forty-seven A. actinomycetemcomitans strains of serotypes a through f were examined. Strain-specific variant DNA in the genomes of A. actinomycetemcomitans was identified by polymerase chain reaction (PCR) genomic mapping and sequenced to identify GEIs. The distribution of the GEIs among test strains of A. actinomycetemcomitans was determined by PCR analysis and Southern hybridization assays.<br><br>RESULTS: An &#x223c;22 kb GEI of A. actinomycetemcomitans, designated AAI-1, was identified in five serotype b strains. The AAI-1 exhibits low %G+C and encodes proteins of phage, restriction modification systems, mobile elements, and other hypothetical proteins of unknown functions. The insertion of AAI-1 was found to cause truncation of A. actinomycetemcomitans genes at the insertion site.<br><br>CONCLUSIONS: Some A. actinomycetemcomitans strains may harbor GEIs, which were acquired via HGT by the bacteria. The GEIs may increase the gene repertoire of A. actinomycetemcomitans. However, the insertion of the GEIs in A. actinomycetemcomitans may also cause truncation and inactivation of resident genes at the insertion sites. The virulence significance of such gain and loss of genes in A. actinomycetemcomitans remains to be determined.}, }
@article {pmid29177480, year = {2017}, author = {Wang, Z and Wu, M}, title = {Comparative Genomic Analysis of Acanthamoeba Endosymbionts Highlights the Role of Amoebae as a "Melting Pot" Shaping the Rickettsiales Evolution.}, journal = {Genome biology and evolution}, volume = {9}, number = {11}, pages = {3214-3224}, pmid = {29177480}, issn = {1759-6653}, mesh = {Acanthamoeba/*microbiology/physiology ; Alphaproteobacteria/classification/*genetics/physiology ; Biological Evolution ; Gene Transfer, Horizontal ; Phylogeny ; Symbiosis ; }, abstract = {Amoebae have been considered as a genetic "melting pot" for its symbionts, facilitating genetic exchanges of the bacteria that co-inhabit the same host. To test the "melting pot" hypothesis, we analyzed six genomes of amoeba endosymbionts within Rickettsiales, four of which belong to Holosporaceae family and two to Candidatus Midichloriaceae. For the first time, we identified plasmids in obligate amoeba endosymbionts, which suggests conjugation as a potential mechanism for lateral gene transfers (LGTs) that underpin the "melting pot" hypothesis. We found strong evidence of recent LGTs between the Rickettsiales amoeba endosymbionts, suggesting that the LGTs are continuous and ongoing. In addition, comparative genomic and phylogenomic analyses revealed pervasive and recurrent LGTs between Rickettsiales and distantly related amoeba-associated bacteria throughout the Rickettsiales evolution. Many of these exchanged genes are important for amoeba-symbiont interactions, including genes in transport system, antibiotic resistance, stress response, and bacterial virulence, suggesting that LGTs have played important roles in the adaptation of endosymbionts to their intracellular habitats. Surprisingly, we found little evidence of LGTs between amoebae and their bacterial endosymbionts. Our study strongly supports the "melting pot" hypothesis and highlights the role of amoebae in shaping the Rickettsiales evolution.}, }
@article {pmid29177479, year = {2017}, author = {Lo, WS and Kuo, CH}, title = {Horizontal Acquisition and Transcriptional Integration of Novel Genes in Mosquito-Associated Spiroplasma.}, journal = {Genome biology and evolution}, volume = {9}, number = {12}, pages = {3246-3259}, pmid = {29177479}, issn = {1759-6653}, mesh = {Animals ; Culicidae/*microbiology ; DNA, Bacterial ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Genome, Bacterial ; Phylogeny ; Spiroplasma/classification/*genetics ; *Symbiosis ; Transcriptome ; Virulence Factors/*genetics ; }, abstract = {Genetic differentiation among symbiotic bacteria is important in shaping biodiversity. The genus Spiroplasma contains species occupying diverse niches and is a model system for symbiont evolution. Previous studies have established that two mosquito-associated species have diverged extensively in their carbohydrate metabolism genes despite having a close phylogenetic relationship. Notably, although the commensal Spiroplasma diminutum lacks identifiable pathogenicity factors, the pathogenic Spiroplasma taiwanense was found to have acquired a virulence factor glpO and its associated genes through horizontal transfer. However, it is unclear if these acquired genes have been integrated into the regulatory network. In this study, we inferred the gene content evolution in these bacteria, as well as examined their transcriptomes in response to glucose availability. The results indicated that both species have many more gene acquisitions from the Mycoides-Entomoplasmataceae clade, which contains several important pathogens of ruminants, than previously thought. Moreover, several acquired genes have higher expression levels than the vertically inherited homologs, indicating possible functional replacement. Finally, the virulence factor and its functionally linked genes in S. taiwanense were up-regulated in response to glucose starvation, suggesting that these acquired genes are under expression regulation and the pathogenicity may be a stress response. In summary, although differential gene losses are a major process for symbiont divergence, gene gains are critical in counteracting genome degradation and driving diversification among facultative symbionts.}, }
@article {pmid29177446, year = {2018}, author = {Martin, WF and Bryant, DA and Beatty, JT}, title = {A physiological perspective on the origin and evolution of photosynthesis.}, journal = {FEMS microbiology reviews}, volume = {42}, number = {2}, pages = {205-231}, pmid = {29177446}, issn = {1574-6976}, mesh = {Archaea/physiology ; *Biological Evolution ; Cyanobacteria/physiology ; Photosynthesis/*physiology ; Pigments, Biological/metabolism ; }, abstract = {The origin and early evolution of photosynthesis are reviewed from an ecophysiological perspective. Earth's first ecosystems were chemotrophic, fueled by geological H2 at hydrothermal vents and, required flavin-based electron bifurcation to reduce ferredoxin for CO2 fixation. Chlorophyll-based phototrophy (chlorophototrophy) allowed autotrophs to generate reduced ferredoxin without electron bifurcation, providing them access to reductants other than H2. Because high-intensity, short-wavelength electromagnetic radiation at Earth's surface would have been damaging for the first chlorophyll (Chl)-containing cells, photosynthesis probably arose at hydrothermal vents under low-intensity, long-wavelength geothermal light. The first photochemically active pigments were possibly Zn-tetrapyrroles. We suggest that (i) after the evolution of red-absorbing Chl-like pigments, the first light-driven electron transport chains reduced ferredoxin via a type-1 reaction center (RC) progenitor with electrons from H2S; (ii) photothioautotrophy, first with one RC and then with two, was the bridge between H2-dependent chemolithoautotrophy and water-splitting photosynthesis; (iii) photothiotrophy sustained primary production in the photic zone of Archean oceans; (iv) photosynthesis arose in an anoxygenic cyanobacterial progenitor; (v) Chl a is the ancestral Chl; and (vi), anoxygenic chlorophototrophic lineages characterized so far acquired, by horizontal gene transfer, RCs and Chl biosynthesis with or without autotrophy, from the architects of chlorophototrophy-the cyanobacterial lineage.}, }
@article {pmid29177088, year = {2017}, author = {Petitjean, M and Martak, D and Silvant, A and Bertrand, X and Valot, B and Hocquet, D}, title = {Genomic characterization of a local epidemic Pseudomonas aeruginosa reveals specific features of the widespread clone ST395.}, journal = {Microbial genomics}, volume = {3}, number = {10}, pages = {e000129}, pmid = {29177088}, issn = {2057-5858}, mesh = {CRISPR-Cas Systems ; Copper/adverse effects ; Disease Outbreaks ; Disease Transmission, Infectious ; Drug Resistance, Microbial/*genetics ; Gene Transfer, Horizontal ; Genome, Bacterial ; Genomic Islands ; Humans ; Mutation ; Pseudomonas Infections/*epidemiology/*microbiology ; *Pseudomonas aeruginosa/genetics/isolation &amp; purification/pathogenicity ; Virulence Factors/*genetics ; }, abstract = {Pseudomonas aeruginosa is a ubiquitous opportunistic pathogen with several clones being frequently associated with outbreaks in hospital settings. ST395 is among these so-called 'international' clones. We aimed here to define the biological features that could have helped the implantation and spread of the clone ST395 in hospital settings. The complete genome of a multidrug resistant index isolate (DHS01) of a large hospital outbreak was analysed. We identified DHS01-specific genetic elements, among which were identified those shared with a panel of six independent ST395 isolates responsible for outbreaks in other hospitals. DHS01 has the fifth largest chromosome of the species (7.1 Mbp), with most of its 1555 accessory genes borne by either genomic islands (GIs, n=48) or integrative and conjugative elements (ICEs, n=5). DHS01 is multidrug resistant mostly due to chromosomal mutations. It displayed signatures of adaptation to chronic infection in part due to the loss of a 131 kbp chromosomal fragment. Four GIs were specific to the clone ST395 and contained genes involved in metabolism (GI-4), in virulence (GI-6) and in resistance to copper (GI-7). GI-7 harboured an array of six copper transporters and was shared with non-pathogenic Pseudomonas sp. retrieved from copper-contaminated environments. Copper resistance was confirmed phenotypically in all other ST395 isolates and possibly accounted for the spreading capability of the clone in hospital outbreaks, where water networks have been incriminated. This suggests that genes transferred from copper-polluted environments may have favoured the implantation and spread of the international clone P. aeruginosa ST395 in hospital settings.}, }
@article {pmid29176894, year = {2017}, author = {Levillain, F and Poquet, Y and Mallet, L and Mazères, S and Marceau, M and Brosch, R and Bange, FC and Supply, P and Magalon, A and Neyrolles, O}, title = {Horizontal acquisition of a hypoxia-responsive molybdenum cofactor biosynthesis pathway contributed to Mycobacterium tuberculosis pathoadaptation.}, journal = {PLoS pathogens}, volume = {13}, number = {11}, pages = {e1006752}, pmid = {29176894}, issn = {1553-7374}, mesh = {Animals ; Bacterial Proteins/genetics/metabolism ; Coenzymes/*biosynthesis ; Female ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Humans ; Hypoxia/metabolism/microbiology ; Metalloproteins/*biosynthesis ; Mice ; Mice, Inbred C57BL ; Molybdenum Cofactors ; Mycobacterium/genetics/metabolism ; Mycobacterium tuberculosis/*genetics/*metabolism ; Nitrates/metabolism ; Oxygen/*metabolism ; Pteridines ; Tuberculosis/metabolism/*microbiology ; }, abstract = {The unique ability of the tuberculosis (TB) bacillus, Mycobacterium tuberculosis, to persist for long periods of time in lung hypoxic lesions chiefly contributes to the global burden of latent TB. We and others previously reported that the M. tuberculosis ancestor underwent massive episodes of horizontal gene transfer (HGT), mostly from environmental species. Here, we sought to explore whether such ancient HGT played a part in M. tuberculosis evolution towards pathogenicity. We were interested by a HGT-acquired M. tuberculosis-specific gene set, namely moaA1-D1, which is involved in the biosynthesis of the molybdenum cofactor. Horizontal acquisition of this gene set was striking because homologues of these moa genes are present all across the Mycobacterium genus, including in M. tuberculosis. Here, we discovered that, unlike their paralogues, the moaA1-D1 genes are strongly induced under hypoxia. In vitro, a M. tuberculosis moaA1-D1-null mutant has an impaired ability to respire nitrate, to enter dormancy and to survive in oxygen-limiting conditions. Conversely, heterologous expression of moaA1-D1 in the phylogenetically closest non-TB mycobacterium, Mycobacterium kansasii, which lacks these genes, improves its capacity to respire nitrate and grants it with a marked ability to survive oxygen depletion. In vivo, the M. tuberculosis moaA1-D1-null mutant shows impaired survival in hypoxic granulomas in C3HeB/FeJ mice, but not in normoxic lesions in C57BL/6 animals. Collectively, our results identify a novel pathway required for M. tuberculosis resistance to host-imposed stress, namely hypoxia, and provide evidence that ancient HGT bolstered M. tuberculosis evolution from an environmental species towards a pervasive human-adapted pathogen.}, }
@article {pmid29176581, year = {2018}, author = {Husnik, F and McCutcheon, JP}, title = {Functional horizontal gene transfer from bacteria to eukaryotes.}, journal = {Nature reviews. Microbiology}, volume = {16}, number = {2}, pages = {67-79}, pmid = {29176581}, issn = {1740-1534}, mesh = {Adaptation, Physiological/*genetics ; Bacteria/*genetics ; Biological Evolution ; Eukaryota/*genetics ; Gene Expression Regulation ; Gene Transfer, Horizontal/*physiology ; }, abstract = {Bacteria influence eukaryotic biology as parasitic, commensal or beneficial symbionts. Aside from these organismal interactions, bacteria have also been important sources of new genetic sequences through horizontal gene transfer (HGT) for eukaryotes. In this Review, we focus on gene transfers from bacteria to eukaryotes, discuss how horizontally transferred genes become functional and explore what functions are endowed upon a broad diversity of eukaryotes by genes derived from bacteria. We classify HGT events into two broad types: those that maintain pre-existing functions and those that provide the recipient with new functionality, including altered host nutrition, protection and adaptation to extreme environments.}, }
@article {pmid29174700, year = {2018}, author = {Shun-Mei, E and Zeng, JM and Yuan, H and Lu, Y and Cai, RX and Chen, C}, title = {Sub-inhibitory concentrations of fluoroquinolones increase conjugation frequency.}, journal = {Microbial pathogenesis}, volume = {114}, number = {}, pages = {57-62}, doi = {10.1016/j.micpath.2017.11.036}, pmid = {29174700}, issn = {1096-1208}, mesh = {Anti-Bacterial Agents/pharmacology ; Anti-Infective Agents/*pharmacology ; Ciprofloxacin/pharmacology ; Conjugation, Genetic/*genetics ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/drug effects/genetics/growth &amp; development ; Fluoroquinolones/*antagonists &amp; inhibitors ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal/drug effects/physiology ; Levofloxacin/pharmacology ; Microbial Sensitivity Tests ; Plasmids/genetics ; Pseudomonas aeruginosa/drug effects/genetics ; SOS Response, Genetics/genetics ; Transcriptome ; Virulence Factors/genetics ; Exome Sequencing ; }, abstract = {Bacteria are subjected to sub-minimal inhibitory concentrations (sub-MIC) of antibiotics in various niches where the low-dosage treatment plays a key role in antibiotic resistance selection. However, the mechanism of sub-MIC of antibiotics on the resistant gene transfer is largely unknown. Here, we used Escherichia coli SM10λpir in which the RP4 plasmid was chromosomally-integrated as the donor strain, to investigate the effects of sub-MIC of Ciprofloxacin(Cip) or Levofloxacin(Lev) on conjugational transfer of mobilisable plasmid-pUCP24T from SM10λpir to Pseudomonas aeruginosa. The results showed that the transfer frequency was significantly increased by treating E. coli with sub-MIC of Cip or Lev. To investigate the molecular mechanisms, complete transcriptome sequencing was performed. We found that the sub-MIC of Cip or Lev enhanced the expression of several genes on the RP4 plasmid, which was consistent with the conjugation efficiency. Moreover, the expression of genes associated with SOS response in donor SM10λpir was increased, but had no correlation with conjugation efficiency. These findings suggested that sub-MIC of Cip or Lev may promote conjugational transfer by up-regulating the expression of conjugation associated genes via an SOS-independent mechanism.}, }
@article {pmid29173837, year = {2017}, author = {Lang, A and Thomas Beatty, J and Rice, PA}, title = {Guest editorial: Mobile genetic elements and horizontal gene transfer in prokaryotes.}, journal = {Current opinion in microbiology}, volume = {38}, number = {}, pages = {v-vii}, doi = {10.1016/j.mib.2017.09.018}, pmid = {29173837}, issn = {1879-0364}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; DNA Transposable Elements ; *Gene Transfer, Horizontal ; Genes, Archaeal/genetics ; Genes, Bacterial/genetics ; Genomic Islands ; Interspersed Repetitive Sequences/*genetics ; Plasmids ; }, }
@article {pmid29170246, year = {2017}, author = {Schneider, AC and Moore, AJ}, title = {Parallel Pleistocene amphitropical disjunctions of a parasitic plant and its host.}, journal = {American journal of botany}, volume = {104}, number = {11}, pages = {1745-1755}, doi = {10.3732/ajb.1700181}, pmid = {29170246}, issn = {1537-2197}, mesh = {Ecology ; Evolution, Molecular ; Fossils ; Grindelia/*parasitology ; North America ; Orobanchaceae/genetics/*physiology ; Phylogeny ; Plant Diseases/*parasitology ; *Plant Dispersal ; South America ; }, abstract = {PREMISE OF THE STUDY: Aphyllon is a clade of holoparasites that includes closely related North American and South American species parasitic on Grindelia. Both Aphyllon (Orobanchaceae) and Grindelia (Asteraceae) have amphitropical disjunctions between North America and South America; however, the timing of these patterns and the processes to explain them are unknown.<br><br>METHODS: Chronograms for the Orobanchaceae and Grindelia and their relatives were constructed using fossil and secondary calibration points, one of which was based on the inferred timing of horizontal gene transfer from a papilionoid legume into the common ancestor of Orobanche and Phelipanche. Elevated rates of molecular evolution in the Orobanchaceae have hindered efforts to determine reliable divergence time estimates in the absence of a fossil record. However, using a horizontal gene transfer event as a secondary calibration overcomes this limitation. These chronograms were used to reconstruct the biogeography of Aphyllon, Grindelia, and relatives using a DEC+J model implemented in RevBayes.<br><br>KEY RESULTS: Aphyllon had two amphitropical dispersals from North America to South America, while Grindelia had a single dispersal. The dispersal of the Aphyllon lineage that is parasitic on Grindelia (0.40 Ma) took place somewhat after Grindelia began to diversify in South America (0.93 Ma). Using a secondary calibration based on horizontal gene transfer, we infer more recent divergence dates of holoparasitic Orobancheae than previous studies.<br><br>CONCLUSIONS: Parallel host-parasite amphitropical disjunctions in Grindelia and Aphyllon illustrate one means by which ecological specialization may result in nonindependent patterns of diversity in distantly related lineages. Although Grindelia and Aphyllon both dispersed to South America recently, Grindelia appears to have diversified more extensively following colonization. More broadly, recent Pleistocene glaciations probably have also contributed to patterns of diversity and biogeography of temperate northern hemisphere Orobancheae. We also demonstrate the utility of using horizontal gene transfer events from well-dated clades to calibrate parasite phylogenies in the absence of a fossil record.}, }
@article {pmid29169219, year = {2018}, author = {Kim, J and Park, W}, title = {Genome Analysis of Naphthalene-Degrading Pseudomonas sp. AS1 Harboring the Megaplasmid pAS1.}, journal = {Journal of microbiology and biotechnology}, volume = {28}, number = {2}, pages = {330-337}, doi = {10.4014/jmb.1709.09002}, pmid = {29169219}, issn = {1738-8872}, mesh = {Base Sequence ; Biodegradation, Environmental ; Carbon/metabolism ; Chromosomes, Bacterial ; Dioxygenases/genetics ; Environmental Pollutants/metabolism ; Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Multigene Family ; Naphthalenes/*metabolism ; Plasmids/genetics ; Pseudomonas/enzymology/*genetics/isolation &amp; purification/*metabolism ; Pseudomonas putida/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Soil Microbiology ; }, abstract = {Polycyclic aromatic hydrocarbons (PAHs), including naphthalene, are widely distributed in nature. Naphthalene has been regarded as a model PAH compound for investigating the mechanisms of bacterial PAH biodegradation. Pseudomonas sp. AS1 isolated from an arsenic-contaminated site is capable of growing on various aromatic compounds such as naphthalene, salicylate, and catechol, but not on gentisate. The genome of strain AS1 consists of a 6,126,864 bp circular chromosome and the 81,841 bp circular plasmid pAS1. Pseudomonas sp. AS1 has multiple dioxygenases and related enzymes involved in the degradation of aromatic compounds, which might contribute to the metabolic versatility of this isolate. The pAS1 plasmid exhibits extremely high similarity in size and sequences to the well-known naphthalene-degrading plasmid pDTG1 in Pseudomonas putida strain NCIB 9816-4. Two gene clusters involved in the naphthalene degradation pathway were identified on pAS1. The expression of several nah genes on the plasmid was upregulated by more than 2-fold when naphthalene was used as a sole carbon source. Strains have been isolated at different times and places with different characteristics, but similar genes involved in the degradation of aromatic compounds have been identified on their plasmids, which suggests that the transmissibility of the plasmids might play an important role in the adaptation of the microorganisms to mineralize the compounds.}, }
@article {pmid29168417, year = {2018}, author = {Castillo, A and Tello, M and Ringwald, K and Acuña, LG and Quatrini, R and Orellana, O}, title = {A DNA segment encoding the anticodon stem/loop of tRNA determines the specific recombination of integrative-conjugative elements in Acidithiobacillus species.}, journal = {RNA biology}, volume = {15}, number = {4-5}, pages = {492-499}, pmid = {29168417}, issn = {1555-8584}, mesh = {Acidithiobacillus/*genetics/metabolism ; Anticodon/chemistry/metabolism ; Attachment Sites, Microbiological ; Base Sequence ; Chromosome Mapping ; Chromosomes, Bacterial/chemistry/metabolism ; DNA Damage ; *DNA Transposable Elements ; DNA, Bacterial/*genetics/metabolism ; Escherichia coli/genetics/metabolism ; *Gene Transfer, Horizontal ; Integrases/genetics/metabolism ; Mutagenesis, Site-Directed ; Nucleic Acid Conformation ; RNA, Transfer, Ala/*genetics/metabolism ; Recombination, Genetic ; Synteny ; }, abstract = {Horizontal gene transfer is crucial for the adaptation of microorganisms to environmental cues. The acidophilic, bioleaching bacterium Acidithiobacillus ferrooxidans encodes an integrative-conjugative genetic element (ICEAfe1) inserted in the gene encoding a tRNA[Ala]. This genetic element is actively excised from the chromosome upon induction of DNA damage. A similar genetic element (ICEAcaTY.2) is also found in an equivalent position in the genome of Acidithiobacillus caldus. The local genomic context of both mobile genetic elements is highly syntenous and the cognate integrases are well conserved. By means of site directed mutagenesis, target site deletions and in vivo integrations assays in the heterologous model Escherichia coli, we assessed the target sequence requirements for site-specific recombination to be catalyzed by these integrases. We determined that each enzyme recognizes a specific small DNA segment encoding the anticodon stem/loop of the tRNA as target site and that specific positions in these regions are well conserved in the target attB sites of orthologous integrases. Also, we demonstrate that the local genetic context of the target sequence is not relevant for the integration to take place. These findings shed new light on the mechanism of site-specific integration of integrative-conjugative elements in members of Acidithiobacillus genus.}, }
@article {pmid29164671, year = {2018}, author = {Gasmi, L and Jakubowska, AK and Ferré, J and Ogliastro, M and Herrero, S}, title = {Characterization of two groups of Spodoptera exigua Hübner (Lepidoptera: Noctuidae) C-type lectins and insights into their role in defense against the densovirus JcDV.}, journal = {Archives of insect biochemistry and physiology}, volume = {97}, number = {1}, pages = {}, doi = {10.1002/arch.21432}, pmid = {29164671}, issn = {1520-6327}, mesh = {Animals ; Densovirinae/*physiology ; Insect Proteins/*genetics/metabolism ; Larva/genetics/growth &amp; development/immunology/virology ; Lectins, C-Type/*genetics/metabolism ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Spodoptera/*genetics/growth &amp; development/*immunology/virology ; }, abstract = {Insect innate immunity relies on numerous soluble and membrane-bound receptors, named pattern recognition proteins (PRPs), which enable the insect to recognize pathogen-associated molecular patterns. C-type lectins are among the best-studied PRPs and constitute the most diverse family of animal lectins. Here we have characterized two groups of Spodoptera exigua C-type lectins that differ in their phylogeny, domain architecture, and expression pattern. One group includes C-type lectins with similar characteristics to other lepidopteran lectins, and a second group includes bracoviral-related lectins (bracovirus-like lectins, Se-BLLs) recently acquired by horizontal gene transfer. Subsequently, we have investigated the potential role of some selected lectins in the susceptibility to Junonia coenia densovirus (JcDV). For this purpose, three of the bracoviral-related lectins were expressed, purified, and their effect on the densovirus infection to two different Spodoptera species was assessed. The results showed that Se-BLL3 specifically reduce the mortality of Spodoptera frugiperda larvae caused by JcDV. In contrast, no such effect was observed with S. exigua larvae. In a previous work, we have also shown that Se-BLL2 increased the tolerance of S. exigua larvae to baculovirus infection. Taken together, these results confirm the implication of two different C-type lectins in antiviral response and reflect the biological relevance of the acquisition of bracoviral genes in Spodoptera spp.}, }
@article {pmid29163424, year = {2017}, author = {Miguel-Arribas, A and Hao, JA and Luque-Ortega, JR and Ramachandran, G and Val-Calvo, J and Gago-Córdoba, C and González-Álvarez, D and Abia, D and Alfonso, C and Wu, LJ and Meijer, WJJ}, title = {The Bacillus subtilis Conjugative Plasmid pLS20 Encodes Two Ribbon-Helix-Helix Type Auxiliary Relaxosome Proteins That Are Essential for Conjugation.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2138}, pmid = {29163424}, issn = {1664-302X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {Bacterial conjugation is the process by which a conjugative element (CE) is transferred horizontally from a donor to a recipient cell via a connecting pore. One of the first steps in the conjugation process is the formation of a nucleoprotein complex at the origin of transfer (oriT), where one of the components of the nucleoprotein complex, the relaxase, introduces a site- and strand specific nick to initiate the transfer of a single DNA strand into the recipient cell. In most cases, the nucleoprotein complex involves, besides the relaxase, one or more additional proteins, named auxiliary proteins, which are encoded by the CE and/or the host. The conjugative plasmid pLS20 replicates in the Gram-positive Firmicute bacterium Bacillus subtilis. We have recently identified the relaxase gene and the oriT of pLS20, which are separated by a region of almost 1 kb. Here we show that this region contains two auxiliary genes that we name aux1LS20 and aux2LS20 , and which we show are essential for conjugation. Both Aux1LS20 and Aux2LS20 are predicted to contain a Ribbon-Helix-Helix DNA binding motif near their N-terminus. Analyses of the purified proteins show that Aux1LS20 and Aux2LS20 form tetramers and hexamers in solution, respectively, and that they both bind preferentially to oriTLS20 , although with different characteristics and specificities. In silico analyses revealed that genes encoding homologs of Aux1LS20 and/or Aux2LS20 are located upstream of almost 400 relaxase genes of the RelLS20 family (MOBL) of relaxases. Thus, Aux1LS20 and Aux2LS20 of pLS20 constitute the founding member of the first two families of auxiliary proteins described for CEs of Gram-positive origin.}, }
@article {pmid29163422, year = {2017}, author = {Esposito, EP and Gaiarsa, S and Del Franco, M and Crivaro, V and Bernardo, M and Cuccurullo, S and Pennino, F and Triassi, M and Marone, P and Sassera, D and Zarrilli, R}, title = {A Novel IncA/C1 Group Conjugative Plasmid, Encoding VIM-1 Metallo-Beta-Lactamase, Mediates the Acquisition of Carbapenem Resistance in ST104 Klebsiella pneumoniae Isolates from Neonates in the Intensive Care Unit of V. Monaldi Hospital in Naples.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2135}, pmid = {29163422}, issn = {1664-302X}, abstract = {The emergence of carbapenemase producing Enterobacteriaceae has raised major public health concern. The aim of this study was to investigate the molecular epidemiology and the mechanism of carbapenem resistance acquisition of multidrug-resistant Klebsiella pneumoniae isolates from 20 neonates in the neonatal intensive care unit (NICU) of the V. Monaldi Hospital in Naples, Italy, from April 2015 to March 2016. Genotype analysis by pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST) identified PFGE type A and subtypes A1 and A2 in 17, 2, and 1 isolates, respectively, and assigned all isolates to sequence type (ST) 104. K. pneumoniae isolates were resistant to all classes of β-lactams including carbapenems, fosfomycin, gentamicin, and trimethoprim-sulfamethoxazole, but susceptible to quinolones, amikacin, and colistin. Conjugation experiments demonstrated that resistance to third-generation cephems and imipenem could be transferred along with an IncA/C plasmid containing the extended spectrum β-lactamase blaSHV -12 and carbapenem-hydrolyzing metallo-β-lactamase blaV IM-1 genes. The plasmid that we called pIncAC_KP4898 was 156,252 bp in size and included a typical IncA/C backbone, which was assigned to ST12 and core genome (cg) ST12.1 using the IncA/C plasmid MLST (PMLST) scheme. pIncAC_KP4898 showed a mosaic structure with blaV IM-1 into a class I integron, blaSHV -12 flanked by IS6 elements, a mercury resistance and a macrolide 2'-phosphotransferase clusters, ant(3″), aph(3″), aacA4, qnrA1, sul1, and dfrA14 conferring resistance to aminoglycosides, quinolones, sulfonamides, and trimethoprim, respectively, several genes predicted to encode transfer functions and proteins involved in DNA transposition. The acquisition of pIncAC_KP4898 carrying blaV IM-1 and blaSHV -12 contributed to the spread of ST104 K. pneumoniae in the NICU of V. Monaldi Hospital in Naples.}, }
@article {pmid29163404, year = {2017}, author = {Malik, SS and Azem-E-Zahra, S and Kim, KM and Caetano-Anollés, G and Nasir, A}, title = {Do Viruses Exchange Genes across Superkingdoms of Life?.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2110}, pmid = {29163404}, issn = {1664-302X}, abstract = {Viruses can be classified into archaeoviruses, bacterioviruses, and eukaryoviruses according to the taxonomy of the infected host. The host-constrained perception of viruses implies preference of genetic exchange between viruses and cellular organisms of their host superkingdoms and viral origins from host cells either via escape or reduction. However, viruses frequently establish non-lytic interactions with organisms and endogenize into the genomes of bacterial endosymbionts that reside in eukaryotic cells. Such interactions create opportunities for genetic exchange between viruses and organisms of non-host superkingdoms. Here, we take an atypical approach to revisit virus-cell interactions by first identifying protein fold structures in the proteomes of archaeoviruses, bacterioviruses, and eukaryoviruses and second by tracing their spread in the proteomes of superkingdoms Archaea, Bacteria, and Eukarya. The exercise quantified protein structural homologies between viruses and organisms of their host and non-host superkingdoms and revealed likely candidates for virus-to-cell and cell-to-virus gene transfers. Unexpected lifestyle-driven genetic affiliations between bacterioviruses and Eukarya and eukaryoviruses and Bacteria were also predicted in addition to a large cohort of protein folds that were universally shared by viral and cellular proteomes and virus-specific protein folds not detected in cellular proteomes. These protein folds provide unique insights into viral origins and evolution that are generally difficult to recover with traditional sequence alignment-dependent evolutionary analyses owing to the fast mutation rates of viral gene sequences.}, }
@article {pmid29162798, year = {2017}, author = {Lopatkin, AJ and Meredith, HR and Srimani, JK and Pfeiffer, C and Durrett, R and You, L}, title = {Persistence and reversal of plasmid-mediated antibiotic resistance.}, journal = {Nature communications}, volume = {8}, number = {1}, pages = {1689}, pmid = {29162798}, issn = {2041-1723}, support = {R01 AI125604/AI/NIAID NIH HHS/United States ; R01 GM098642/GM/NIGMS NIH HHS/United States ; R01 GM110494/GM/NIGMS NIH HHS/United States ; }, mesh = {Conjugation, Genetic ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/drug effects/genetics ; Genetic Engineering ; Genetic Techniques ; Microbial Consortia/drug effects/genetics ; Models, Genetic ; Plasmids/*genetics ; Synthetic Biology ; }, abstract = {In the absence of antibiotic-mediated selection, sensitive bacteria are expected to displace their resistant counterparts if resistance genes are costly. However, many resistance genes persist for long periods in the absence of antibiotics. Horizontal gene transfer (primarily conjugation) could explain this persistence, but it has been suggested that very high conjugation rates would be required. Here, we show that common conjugal plasmids, even when costly, are indeed transferred at sufficiently high rates to be maintained in the absence of antibiotics in Escherichia coli. The notion is applicable to nine plasmids from six major incompatibility groups and mixed populations carrying multiple plasmids. These results suggest that reducing antibiotic use alone is likely insufficient for reversing resistance. Therefore, combining conjugation inhibition and promoting plasmid loss would be an effective strategy to limit conjugation-assisted persistence of antibiotic resistance.}, }
@article {pmid29162202, year = {2017}, author = {Petzold, M and Prior, K and Moran-Gilad, J and Harmsen, D and Lück, C}, title = {Epidemiological information is key when interpreting whole genome sequence data - lessons learned from a large Legionella pneumophila outbreak in Warstein, Germany, 2013.}, journal = {Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin}, volume = {22}, number = {45}, pages = {}, pmid = {29162202}, issn = {1560-7917}, mesh = {Base Sequence ; *Disease Outbreaks ; Germany/epidemiology ; Humans ; Legionella pneumophila/*isolation &amp; purification ; Legionnaires' Disease/diagnosis/*epidemiology ; Molecular Epidemiology/methods ; Multilocus Sequence Typing/methods ; Retrospective Studies ; *Whole Genome Sequencing ; }, abstract = {IntroductionWhole genome sequencing (WGS) is increasingly used in Legionnaires' disease (LD) outbreak investigations, owing to its higher resolution than sequence-based typing, the gold standard typing method for Legionella pneumophila, in the analysis of endemic strains. Recently, a gene-by-gene typing approach based on 1,521 core genes called core genome multilocus sequence typing (cgMLST) was described that enables a robust and standardised typing of L. pneumophila. Methods: We applied this cgMLST scheme to isolates obtained during the largest outbreak of LD reported so far in Germany. In this outbreak, the epidemic clone ST345 had been isolated from patients and four different environmental sources. In total 42 clinical and environmental isolates were retrospectively typed. Results: Epidemiologically unrelated ST345 isolates were clearly distinguishable from the epidemic clone. Remarkably, epidemic isolates split up into two distinct clusters, ST345-A and ST345-B, each respectively containing a mix of clinical and epidemiologically-related environmental samples. Discussion/conclusion: The outbreak was therefore likely caused by both variants of the single sequence type, which pre-existed in the environmental reservoirs. The two clusters differed by 40 alleles located in two neighbouring genomic regions of ca 42 and 26 kb. Additional analysis supported horizontal gene transfer of the two regions as responsible for the difference between the variants. Both regions comprise virulence genes and have previously been reported to be involved in recombination events. This corroborates the notion that genomic outbreak investigations should always take epidemiological information into consideration when making inferences. Overall, cgMLST proved helpful in disentangling the complex genomic epidemiology of the outbreak.}, }
@article {pmid29161442, year = {2018}, author = {Tamarit, D and Neuvonen, MM and Engel, P and Guy, L and Andersson, SGE}, title = {Origin and Evolution of the Bartonella Gene Transfer Agent.}, journal = {Molecular biology and evolution}, volume = {35}, number = {2}, pages = {451-464}, doi = {10.1093/molbev/msx299}, pmid = {29161442}, issn = {1537-1719}, mesh = {Bartonella/genetics/*virology ; *Biological Evolution ; Gene Amplification ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Inheritance Patterns ; Lysogeny ; *Models, Genetic ; Prophages/*physiology ; Virus Replication ; }, abstract = {Gene transfer agents (GTAs) are domesticated bacteriophages that have evolved into molecular machines for the transfer of bacterial DNA. Despite their widespread nature and their biological implications, the mechanisms and selective forces that drive the emergence of GTAs are still poorly understood. Two GTAs have been identified in the Alphaproteobacteria: the RcGTA, which is widely distributed in a broad range of species; and the BaGTA, which has a restricted host range that includes vector-borne intracellular bacteria of the genus Bartonella. The RcGTA packages chromosomal DNA randomly, whereas the BaGTA particles contain a relatively higher fraction of genes for host interaction factors that are amplified from a nearby phage-derived origin of replication. In this study, we compare the BaGTA genes with homologous bacteriophage genes identified in the genomes of Bartonella species and close relatives. Unlike the BaGTA, the prophage genes are neither present in all species, nor inserted into homologous genomic sites. Phylogenetic inferences and substitution frequency analyses confirm codivergence of the BaGTA with the host genome, as opposed to multiple integration and recombination events in the prophages. Furthermore, the organization of segments flanking the BaGTA differs from that of the prophages by a few rearrangement events, which have abolished the normal coordination between phage genome replication and phage gene expression. Based on the results of our comparative analysis, we propose a model for how a prophage may be transformed into a GTA that transfers amplified bacterial DNA segments.}, }
@article {pmid29161377, year = {2018}, author = {Ravi, A and Valdés-Varela, L and Gueimonde, M and Rudi, K}, title = {Transmission and persistence of IncF conjugative plasmids in the gut microbiota of full-term infants.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {1}, pages = {}, doi = {10.1093/femsec/fix158}, pmid = {29161377}, issn = {1574-6941}, mesh = {Actinobacteria/*genetics/isolation &amp; purification ; Enterobacteriaceae/*genetics/isolation &amp; purification ; Feces/microbiology ; Gammaproteobacteria/*genetics/isolation &amp; purification ; Gastrointestinal Microbiome/*genetics ; Gene Transfer, Horizontal/*genetics ; Humans ; Infant ; Infant, Newborn ; Longitudinal Studies ; Plasmids/*genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; Replicon/genetics ; Term Birth ; }, abstract = {Conjugative plasmids represent major reservoirs for horizontal transmission of antibiotic resistance and virulence genes. Our knowledge about the ecology and persistence of these plasmids in the gut microbiota remains limited. The IncF plasmids are the most widespread in clinical samples and in healthy humans and the main aim of this work was to study their ecology and association with the developing gut microbiota. Using a longitudinal (2, 10, 30 and 90 days) cohort of full-term infants, we investigated the transmission and persistence of IncFIA and IncFIB plasmids. The prevalence of IncFIB plasmids was higher than IncFIA in the cohort, while IncFIA always co-occurred with IncFIB. However, the relative gene abundance of IncFIA was significantly higher than IncFIB for all time points, indicating that IncFIA may be a higher copy-number plasmid. Through linear discriminant analysis effect size and operational taxonomic unit-level associations, we observed major differences in the abundance of Enterobacteriaceae in samples positive and negative for IncFIB. This association was significant at 2, 10 and 30 days and showed an association with vaginal delivery. From shot-gun analyses, we assembled de novo multi-replicon shared (IncFIA/IncFIB) and integrated (IncFIA/IB) plasmids that were persistent through the dataset. Overall, the study demonstrates the nature of IncF plasmids in complex microbial communities.}, }
@article {pmid29158994, year = {2017}, author = {Dittami, SM and Corre, E}, title = {Detection of bacterial contaminants and hybrid sequences in the genome of the kelp Saccharina japonica using Taxoblast.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e4073}, pmid = {29158994}, issn = {2167-8359}, abstract = {Modern genome sequencing strategies are highly sensitive to contamination making the detection of foreign DNA sequences an important part of analysis pipelines. Here we use Taxoblast, a simple pipeline with a graphical user interface, for the post-assembly detection of contaminating sequences in the published genome of the kelp Saccharina japonica. Analyses were based on multiple blastn searches with short sequence fragments. They revealed a number of probable bacterial contaminations as well as hybrid scaffolds that contain both bacterial and algal sequences. This or similar types of analysis, in combination with manual curation, may thus constitute a useful complement to standard bioinformatics analyses prior to submission of genomic data to public repositories. Our analysis pipeline is open-source and freely available at http://sdittami.altervista.org/taxoblast and via SourceForge (https://sourceforge.net/projects/taxoblast).}, }
@article {pmid29158279, year = {2018}, author = {Brunel, R and Descours, G and Durieux, I and Doublet, P and Jarraud, S and Charpentier, X}, title = {KKL-35 Exhibits Potent Antibiotic Activity against Legionella Species Independently of trans-Translation Inhibition.}, journal = {Antimicrobial agents and chemotherapy}, volume = {62}, number = {2}, pages = {}, pmid = {29158279}, issn = {1098-6596}, mesh = {Anti-Bacterial Agents/*pharmacology ; Benzamides/*pharmacology ; Cell Line ; Drug Resistance, Bacterial/*drug effects ; Humans ; Legionella/*drug effects/growth &amp; development ; Legionella pneumophila/*drug effects/growth &amp; development ; Legionnaires' Disease ; Macrolides/pharmacology ; Macrophages/drug effects/microbiology ; Microbial Sensitivity Tests ; Oxadiazoles/*pharmacology ; Protein Biosynthesis ; }, abstract = {trans-Translation is a ribosome-rescue system that is ubiquitous in bacteria. Small molecules defining a new family of oxadiazole compounds that inhibit trans-translation have been found to have broad-spectrum antibiotic activity. We sought to determine the activity of KKL-35, a potent member of the oxadiazole family, against the human pathogen Legionella pneumophila and other related species that can also cause Legionnaires' disease (LD). Consistent with the essential nature of trans-translation in L. pneumophila, KKL-35 inhibited the growth of all tested strains at submicromolar concentrations. KKL-35 was also active against other LD-causing Legionella species. KKL-35 remained equally active against L. pneumophila mutants that have evolved resistance to macrolides. KKL-35 inhibited the multiplication of L. pneumophila in human macrophages at several stages of infection. No resistant mutants could be obtained, even during extended and chronic exposure. Surprisingly, KKL-35 was not synergistic with other ribosome-targeting antibiotics and did not induce the filamentation phenotype observed in cells defective for trans-translation. Importantly, KKL-35 remained active against L. pneumophila mutants expressing an alternate ribosome-rescue system and lacking transfer-messenger RNA, the essential component of trans-translation. These results indicate that the antibiotic activity of KKL-35 is not related to the specific inhibition of trans-translation and its mode of action remains to be identified. In conclusion, KKL-35 is an effective antibacterial agent against the intracellular pathogen L. pneumophila with no detectable resistance development. However, further studies are needed to better understand its mechanism of action and to assess further the potential of oxadiazoles in treatment.}, }
@article {pmid29156585, year = {2017}, author = {Dassa, B and Borovok, I and Lombard, V and Henrissat, B and Lamed, R and Bayer, EA and Moraïs, S}, title = {Pan-Cellulosomics of Mesophilic Clostridia: Variations on a Theme.}, journal = {Microorganisms}, volume = {5}, number = {4}, pages = {}, pmid = {29156585}, issn = {2076-2607}, abstract = {The bacterial cellulosome is an extracellular, multi-enzyme machinery, which efficiently depolymerizes plant biomass by degrading plant cell wall polysaccharides. Several cellulolytic bacteria have evolved various elaborate modular architectures of active cellulosomes. We present here a genome-wide analysis of a dozen mesophilic clostridia species, including both well-studied and yet-undescribed cellulosome-producing bacteria. We first report here, the presence of cellulosomal elements, thus expanding our knowledge regarding the prevalence of the cellulosomal paradigm in nature. We explored the genomic organization of key cellulosome components by comparing the cellulosomal gene clusters in each bacterial species, and the conserved sequence features of the specific cellulosomal modules (cohesins and dockerins), on the background of their phylogenetic relationship. Additionally, we performed comparative analyses of the species-specific repertoire of carbohydrate-degrading enzymes for each of the clostridial species, and classified each cellulosomal enzyme into a specific CAZy family, thus indicating their putative enzymatic activity (e.g., cellulases, hemicellulases, and pectinases). Our work provides, for this large group of bacteria, a broad overview of the blueprints of their multi-component cellulosomal complexes. The high similarity of their scaffoldin clusters and dockerin-based recognition residues suggests a common ancestor, and/or extensive horizontal gene transfer, and potential cross-species recognition. In addition, the sporadic spatial organization of the numerous dockerin-containing genes in several of the genomes, suggests the importance of the cellulosome paradigm in the given bacterial species. The information gained in this work may be utilized directly or developed further by genetically engineering and optimizing designer cellulosome systems for enhanced biotechnological biomass deconstruction and biofuel production.}, }
@article {pmid29153400, year = {2017}, author = {Zhang, Y and Ma, LJ}, title = {Deciphering Pathogenicity of Fusarium oxysporum From a Phylogenomics Perspective.}, journal = {Advances in genetics}, volume = {100}, number = {}, pages = {179-209}, doi = {10.1016/bs.adgen.2017.09.010}, pmid = {29153400}, issn = {0065-2660}, mesh = {Agriculture ; *Chromosomes, Fungal ; Disease Management ; Fusariosis/*microbiology ; Fusarium/classification/*genetics/*pathogenicity ; Gene Transfer, Horizontal ; *Genome, Fungal ; Genomics ; Host Specificity ; Humans ; *Phylogeny ; Plant Diseases/*microbiology ; Virulence/genetics ; }, abstract = {Fusarium oxysporum is a large species complex of both plant and human pathogens that attack a diverse array of species in a host-specific manner. Comparative genomic studies have revealed that the host-specific pathogenicity of the F. oxysporum species complex (FOSC) was determined by distinct sets of supernumerary (SP) chromosomes. In contrast to common vertical transfer, where genetic materials are transmitted via cell division, SP chromosomes can be transmitted horizontally between phylogenetic lineages, explaining the polyphyletic nature of the host-specific pathogenicity of the FOSC. The existence of a diverse array of SP chromosomes determines the broad host range of this species complex, while the conserved core genome maintains essential house-keeping functions. Recognition of these SP chromosomes enables the functional and structural compartmentalization of F. oxysporum genomes. In this review, we examine the impact of this group of cross-kingdom pathogens on agricultural productivity and human health. Focusing on the pathogenicity of F. oxysporum in the phylogenomic framework of the genus Fusarium, we elucidate the evolution of pathogenicity within the FOSC. We conclude that a population genomics approach within a clearly defined phylogenomic framework is essential not only for understanding the evolution of the pathogenicity mechanism but also for identifying informative candidates associated with pathogenicity that can be developed as targets in disease management programs.}, }
@article {pmid29153399, year = {2017}, author = {Slot, JC}, title = {Fungal Gene Cluster Diversity and Evolution.}, journal = {Advances in genetics}, volume = {100}, number = {}, pages = {141-178}, doi = {10.1016/bs.adgen.2017.09.005}, pmid = {29153399}, issn = {0065-2660}, mesh = {*Evolution, Molecular ; Fungi/enzymology/*genetics/*metabolism ; Gene Transfer, Horizontal ; *Genes, Fungal ; *Genetic Variation ; Genome, Fungal ; Metabolic Networks and Pathways/genetics ; *Multigene Family ; Phylogeny ; }, abstract = {Metabolic gene clusters (MGCs) have provided some of the earliest glimpses at the biochemical machinery of yeast and filamentous fungi. MGCs encode diverse genetic mechanisms for nutrient acquisition and the synthesis/degradation of essential and adaptive metabolites. Beyond encoding the enzymes performing these discrete anabolic or catabolic processes, MGCs may encode a range of mechanisms that enable their persistence as genetic consortia; these include enzymatic mechanisms to protect their host fungi from their inherent toxicities, and integrated regulatory machinery. This modular, self-contained nature of MGCs contributes to the metabolic and ecological adaptability of fungi. The phylogenetic and ecological patterns of MGC distribution reflect the broad diversity of fungal life cycles and nutritional modes. While the origins of most gene clusters are enigmatic, MGCs are thought to be born into a genome through gene duplication, relocation, or horizontal transfer, and analyzing the death and decay of gene clusters provides clues about the mechanisms selecting for their assembly. Gene clustering may provide inherent fitness advantages through metabolic efficiency and specialization, but experimental evidence for this is currently limited. The identification and characterization of gene clusters will continue to be powerful tools for elucidating fungal metabolism as well as understanding the physiology and ecology of fungi.}, }
@article {pmid29152584, year = {2017}, author = {Grubbs, KJ and Bleich, RM and Santa Maria, KC and Allen, SE and Farag, S and ,  and Shank, EA and Bowers, AA}, title = {Large-Scale Bioinformatics Analysis of Bacillus Genomes Uncovers Conserved Roles of Natural Products in Bacterial Physiology.}, journal = {mSystems}, volume = {2}, number = {6}, pages = {}, pmid = {29152584}, issn = {2379-5077}, support = {R01 GM112981/GM/NIGMS NIH HHS/United States ; }, abstract = {Bacteria possess an amazing capacity to synthesize a diverse range of structurally complex, bioactive natural products known as specialized (or secondary) metabolites. Many of these specialized metabolites are used as clinical therapeutics, while others have important ecological roles in microbial communities. The biosynthetic gene clusters (BGCs) that generate these metabolites can be identified in bacterial genome sequences using their highly conserved genetic features. We analyzed an unprecedented 1,566 bacterial genomes from Bacillus species and identified nearly 20,000 BGCs. By comparing these BGCs to one another as well as a curated set of known specialized metabolite BGCs, we discovered that the majority of Bacillus natural products are comprised of a small set of highly conserved, well-distributed, known natural product compounds. Most of these metabolites have important roles influencing the physiology and development of Bacillus species. We identified, in addition to these characterized compounds, many unique, weakly conserved BGCs scattered across the genus that are predicted to encode unknown natural products. Many of these "singleton" BGCs appear to have been acquired via horizontal gene transfer. Based on this large-scale characterization of metabolite production in the Bacilli, we go on to connect the alkylpyrones, natural products that are highly conserved but previously biologically uncharacterized, to a role in Bacillus physiology: inhibiting spore development. IMPORTANCEBacilli are capable of producing a diverse array of specialized metabolites, many of which have gained attention for their roles as signals that affect bacterial physiology and development. Up to this point, however, the Bacillus genus's metabolic capacity has been underexplored. We undertook a deep genomic analysis of 1,566 Bacillus genomes to understand the full spectrum of metabolites that this bacterial group can make. We discovered that the majority of the specialized metabolites produced by Bacillus species are highly conserved, known compounds with important signaling roles in the physiology and development of this bacterium. Additionally, there is significant unique biosynthetic machinery distributed across the genus that might lead to new, unknown metabolites with diverse biological functions. Inspired by the findings of our genomic analysis, we speculate that the highly conserved alkylpyrones might have an important biological activity within this genus. We go on to validate this prediction by demonstrating that these natural products are developmental signals in Bacillus and act by inhibiting sporulation.}, }
@article {pmid29151601, year = {2018}, author = {Du Toit, A}, title = {Antimicrobials: Daylight robbery by Acinetobacter.}, journal = {Nature reviews. Microbiology}, volume = {16}, number = {1}, pages = {2-3}, pmid = {29151601}, issn = {1740-1534}, mesh = {*Acinetobacter ; *Anti-Infective Agents ; Drug Resistance, Microbial ; Gene Transfer, Horizontal ; Population Dynamics ; }, }
@article {pmid29150506, year = {2018}, author = {Humisto, A and Jokela, J and Liu, L and Wahlsten, M and Wang, H and Permi, P and Machado, JP and Antunes, A and Fewer, DP and Sivonen, K}, title = {The Swinholide Biosynthesis Gene Cluster from a Terrestrial Cyanobacterium, Nostoc sp. Strain UHCC 0450.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {3}, pages = {}, pmid = {29150506}, issn = {1098-5336}, mesh = {Bacterial Proteins/*genetics/metabolism ; Marine Toxins/*biosynthesis/genetics ; *Multigene Family ; Nostoc/*genetics/metabolism ; Phylogeny ; Polyketide Synthases/*genetics/metabolism ; Sequence Analysis, DNA ; }, abstract = {Swinholides are 42-carbon ring polyketides with a 2-fold axis of symmetry. They are potent cytotoxins that disrupt the actin cytoskeleton. Swinholides were discovered from the marine sponge Theonella sp. and were long suspected to be produced by symbiotic bacteria. Misakinolide, a structural variant of swinholide, was recently demonstrated to be the product of a symbiotic heterotrophic proteobacterium. Here, we report the production of swinholide A by an axenic strain of the terrestrial cyanobacterium Nostoc sp. strain UHCC 0450. We located the 85-kb trans-AT polyketide synthase (PKS) swinholide biosynthesis gene cluster from a draft genome of Nostoc sp. UHCC 0450. The swinholide and misakinolide biosynthesis gene clusters share an almost identical order of catalytic domains, with 85% nucleotide sequence identity, and they group together in phylogenetic analysis. Our results resolve speculation around the true producer of swinholides and demonstrate that bacteria belonging to two distantly related phyla both produce structural variants of the same natural product. In addition, we described a biosynthesis cluster from Anabaena sp. strain UHCC 0451 for the synthesis of the cytotoxic and antifungal scytophycin. All of these biosynthesis gene clusters were closely related to each other and created a group of cytotoxic macrolide compounds produced by trans-AT PKSs of cyanobacteria and proteobacteria.IMPORTANCE Many of the drugs in use today originate from natural products. New candidate compounds for drug development are needed due to increased drug resistance. An increased knowledge of the biosynthesis of bioactive compounds can be used to aid chemical synthesis to produce novel drugs. Here, we show that a terrestrial axenic culture of Nostoc cyanobacterium produces swinholides, which have been previously found only from marine sponge or samples related to them. Swinholides are polyketides with a 2-fold axis of symmetry, and they are potent cytotoxins that disrupt the actin cytoskeleton. We describe the biosynthesis gene clusters of swinholide from Nostoc cyanobacteria, as well as the related cytotoxic and antifungal scytophycin from Anabaena cyanobacteria, and we study the evolution of their trans-AT polyketide synthases. Interestingly, swinholide is closely related to misakinolide produced by a symbiotic heterotrophic proteobacterium, demonstrating that bacteria belonging to two distantly related phyla and different habitats can produce similar natural products.}, }
@article {pmid29149337, year = {2018}, author = {Fraile-Ribot, PA and Cabot, G and Mulet, X and Periañez, L and Martín-Pena, ML and Juan, C and Pérez, JL and Oliver, A}, title = {Mechanisms leading to in vivo ceftolozane/tazobactam resistance development during the treatment of infections caused by MDR Pseudomonas aeruginosa.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {73}, number = {3}, pages = {658-663}, doi = {10.1093/jac/dkx424}, pmid = {29149337}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics ; Bacterial Typing Techniques ; Cephalosporins/*pharmacology ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Pseudomonas Infections/*drug therapy ; Pseudomonas aeruginosa/*drug effects/genetics ; Tazobactam/*pharmacology ; beta-Lactamases/genetics ; }, abstract = {OBJECTIVES: Characterization of the mechanisms driving ceftolozane/tazobactam resistance development in 5 of 47 (10.6%) patients treated for MDR Pseudomonas aeruginosa infections in a Spanish hospital.<br><br>METHODS: Five pairs of ceftolozane/tazobactam-susceptible/resistant P. aeruginosa isolates were studied. MICs were determined by broth microdilution, clonal relatedness was assessed by MLST and resistance mechanisms were investigated by phenotypic and genotypic methods, including WGS. ampC variants were cloned to assess their impact on resistance.<br><br>RESULTS: In all five cases, the same clone was detected for the susceptible/resistant pairs; the widespread ST175 high-risk clone in four of the cases and ST179 in the remaining case. Genomic analysis of the four initial ST175 isolates revealed the characteristic OprD mutation (Q142X) responsible for carbapenem resistance and the AmpR mutation (G154R) responsible for AmpC overexpression and &#x3b2;-lactam resistance. The final isolates had developed ceftolozane/tazobactam and ceftazidime/avibactam resistance, and each additionally showed a mutation in AmpC: E247K in one of the isolates, T96I in two isolates and a deletion of 19 amino acids (G229-E247) in the remaining isolate. The cloned AmpC variants showed greatly increased ceftolozane/tazobactam and ceftazidime/avibactam MICs compared with WT AmpC, but, in contrast, yielded lower MICs of imipenem, cefepime and particularly piperacillin/tazobactam. On the other hand, ceftolozane/tazobactam resistance development in ST179 was shown to be driven by the emergence of the extended-spectrum OXA &#x3b2;-lactamase OXA-14, through the selection of an N146S mutation from OXA-10.<br><br>CONCLUSIONS: Modification of intrinsic (AmpC) and horizontally acquired &#x3b2;-lactamases appears to be the main mechanism leading to ceftolozane/tazobactam resistance in MDR P. aeruginosa.}, }
@article {pmid29149178, year = {2017}, author = {Lind, AL and Wisecaver, JH and Lameiras, C and Wiemann, P and Palmer, JM and Keller, NP and Rodrigues, F and Goldman, GH and Rokas, A}, title = {Drivers of genetic diversity in secondary metabolic gene clusters within a fungal species.}, journal = {PLoS biology}, volume = {15}, number = {11}, pages = {e2003583}, pmid = {29149178}, issn = {1545-7885}, support = {R01 AI065728/AI/NIAID NIH HHS/United States ; T15 LM007450/LM/NLM NIH HHS/United States ; }, mesh = {Alleles ; Aspergillus fumigatus/*genetics/metabolism ; Biological Evolution ; Fungal Proteins/metabolism ; Fungi/genetics ; Genetic Variation/genetics ; Genome, Fungal/genetics ; Genomics/methods ; Metabolic Networks and Pathways/*genetics ; Multigene Family/genetics ; Mutation/genetics ; Polymorphism, Genetic/genetics ; Secondary Metabolism/*genetics ; }, abstract = {Filamentous fungi produce a diverse array of secondary metabolites (SMs) critical for defense, virulence, and communication. The metabolic pathways that produce SMs are found in contiguous gene clusters in fungal genomes, an atypical arrangement for metabolic pathways in other eukaryotes. Comparative studies of filamentous fungal species have shown that SM gene clusters are often either highly divergent or uniquely present in one or a handful of species, hampering efforts to determine the genetic basis and evolutionary drivers of SM gene cluster divergence. Here, we examined SM variation in 66 cosmopolitan strains of a single species, the opportunistic human pathogen Aspergillus fumigatus. Investigation of genome-wide within-species variation revealed 5 general types of variation in SM gene clusters: nonfunctional gene polymorphisms; gene gain and loss polymorphisms; whole cluster gain and loss polymorphisms; allelic polymorphisms, in which different alleles corresponded to distinct, nonhomologous clusters; and location polymorphisms, in which a cluster was found to differ in its genomic location across strains. These polymorphisms affect the function of representative A. fumigatus SM gene clusters, such as those involved in the production of gliotoxin, fumigaclavine, and helvolic acid as well as the function of clusters with undefined products. In addition to enabling the identification of polymorphisms, the detection of which requires extensive genome-wide synteny conservation (e.g., mobile gene clusters and nonhomologous cluster alleles), our approach also implicated multiple underlying genetic drivers, including point mutations, recombination, and genomic deletion and insertion events as well as horizontal gene transfer from distant fungi. Finally, most of the variants that we uncover within A. fumigatus have been previously hypothesized to contribute to SM gene cluster diversity across entire fungal classes and phyla. We suggest that the drivers of genetic diversity operating within a fungal species shown here are sufficient to explain SM cluster macroevolutionary patterns.}, }
@article {pmid29148975, year = {2017}, author = {Kirkup, B}, title = {Learning from losers.}, journal = {eLife}, volume = {6}, number = {}, pages = {}, pmid = {29148975}, issn = {2050-084X}, mesh = {*Acinetobacter ; Bacteria ; Drug Resistance, Microbial ; *Gene Transfer, Horizontal ; Population Dynamics ; }, abstract = {Bacteria can overcome environmental challenges by killing nearby bacteria and incorporating their DNA.}, }
@article {pmid29148380, year = {2017}, author = {Kieffer, N and Aires-de-Sousa, M and Nordmann, P and Poirel, L}, title = {High Rate of MCR-1-Producing Escherichia coli and Klebsiella pneumoniae among Pigs, Portugal.}, journal = {Emerging infectious diseases}, volume = {23}, number = {12}, pages = {2023-2029}, pmid = {29148380}, issn = {1080-6059}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Colistin/pharmacology ; Conjugation, Genetic ; Escherichia coli/drug effects/*genetics/isolation &amp; purification/metabolism ; Escherichia coli Infections/*epidemiology/microbiology/prevention &amp; control/transmission ; Escherichia coli Proteins/*genetics/metabolism ; Farms ; Gene Dosage ; Gene Expression ; *Gene Transfer, Horizontal ; Klebsiella Infections/*epidemiology/microbiology/prevention &amp; control/transmission ; Klebsiella pneumoniae/drug effects/*genetics/isolation &amp; purification/metabolism ; Membrane Proteins/*genetics/metabolism ; Plasmids/chemistry/metabolism ; Portugal/epidemiology ; Swine ; }, abstract = {The mcr-1 (mobile colistin resistance 1) gene, which encodes phosphoethanolamine transferase, has been recently identified as a source of acquired resistance to polymyxins in Escherichia coli. Using the SuperPolymyxin selective medium, we prospectively screened 100 pigs at 2 farms in Portugal for polymyxin-resistant Enterobacteriaceae and recovered 98 plasmid-mediated MCR-1-producing isolates. Most isolates corresponded to nonclonally related E. coli belonging to many sequence types; we also found 2 Klebsiella pneumoniae sequence types. The mcr-1 gene was carried on IncHI2 or IncP plasmid backbones. Our finding of a high rate of MCR-1 producers on 2 pig farms in Portugal highlights the diffusion of that colistin-resistance determinant at the farm level. The fact that the pigs received colistin as metaphylaxis in their feed during the 6 weeks before sampling suggests selective pressure.}, }
@article {pmid29146383, year = {2018}, author = {Papanicolas, LE and Gordon, DL and Wesselingh, SL and Rogers, GB}, title = {Not Just Antibiotics: Is Cancer Chemotherapy Driving Antimicrobial Resistance?.}, journal = {Trends in microbiology}, volume = {26}, number = {5}, pages = {393-400}, doi = {10.1016/j.tim.2017.10.009}, pmid = {29146383}, issn = {1878-4380}, mesh = {Anti-Bacterial Agents/*pharmacology ; Antineoplastic Agents/*pharmacology ; Bacteria/drug effects/genetics ; DNA Damage ; Drug Combinations ; Drug Resistance, Bacterial/*drug effects/genetics ; Dysbiosis/microbiology ; Gastrointestinal Microbiome/drug effects ; Gene Transfer, Horizontal ; Humans ; Mutagenesis ; Neoplasms/complications/drug therapy ; Sepsis/microbiology ; Symbiosis/drug effects ; }, abstract = {The global spread of antibiotic-resistant pathogens threatens to increase the mortality of cancer patients significantly. We propose that chemotherapy contributes to the emergence of antibiotic-resistant bacteria within the gut and, in combination with antibiotics, drives pathogen overgrowth and translocation into the bloodstream. In our model, these processes are mediated by the effects of chemotherapy on bacterial mutagenesis and horizontal gene transfer, the disruption of commensal gut microbiology, and alterations to host physiology. Clinically, this model manifests as a cycle of recurrent sepsis, with each episode involving ever more resistant organisms and requiring increasingly broad-spectrum antimicrobial therapy. Therapies that restore the gut microbiota following chemotherapy or antibiotics could provide a means to break this cycle of infection and treatment failure.}, }
@article {pmid29142104, year = {2017}, author = {Stubenrauch, CJ and Dougan, G and Lithgow, T and Heinz, E}, title = {Constraints on lateral gene transfer in promoting fimbrial usher protein diversity and function.}, journal = {Open biology}, volume = {7}, number = {11}, pages = {}, pmid = {29142104}, issn = {2046-2441}, support = {/WT_/Wellcome Trust/United Kingdom ; 206194/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Enteropathogenic Escherichia coli/*genetics ; Escherichia coli Proteins/chemistry/*genetics ; *Gene Transfer, Horizontal ; Genetic Variation ; Molecular Chaperones/chemistry/*genetics ; Protein Folding ; }, abstract = {Fimbriae are long, adhesive structures widespread throughout members of the family Enterobacteriaceae. They are multimeric extrusions, which are moved out of the bacterial cell through an integral outer membrane protein called usher. The complex folding mechanics of the usher protein were recently revealed to be catalysed by the membrane-embedded translocation and assembly module (TAM). Here, we examine the diversity of usher proteins across a wide range of extraintestinal (ExPEC) and enteropathogenic (EPEC) Escherichia coli, and further focus on a so far undescribed chaperone-usher system, with this usher referred to as UshC. The fimbrial system containing UshC is distributed across a discrete set of EPEC types, including model strains like E2348/67, as well as ExPEC ST131, currently the most prominent multi-drug-resistant uropathogenic E. coli strain worldwide. Deletion of the TAM from a naive strain of E. coli results in a drastic time delay in folding of UshC, which can be observed for a protein from EPEC as well as for two introduced proteins from related organisms, Yersinia and Enterobacter We suggest that this models why the TAM machinery is essential for efficient folding of proteins acquired via lateral gene transfer.}, }
@article {pmid29137267, year = {2017}, author = {Zhang, Y and Zhou, N and Yu, X and Zhang, X and Li, S and Lei, Z and Hu, R and Li, H and Mao, Y and Wang, X and Zhang, J and Li, Y and Guo, H and Irwin, DM and Niu, G and Tan, H}, title = {Tumacrophage: macrophages transformed into tumor stem-like cells by virulent genetic material from tumor cells.}, journal = {Oncotarget}, volume = {8}, number = {47}, pages = {82326-82343}, pmid = {29137267}, issn = {1949-2553}, abstract = {Tumor-associated macrophages are regarded as tumor-enhancers as they have key roles in the subversion of adaptive immunity and in inflammatory circuits that promote tumor progression. Here, we show that cancer cells can subvert macrophages yielding cells that have gained pro-tumor functions. When macrophages isolated from mice or humans are co-cultured with dead cancer cell line cells, induced to undergo apoptosis to mimic chemotherapy, up-regulation of pro-tumor gene expression was identified. Phagocytosis of apoptotic cancer cells by macrophages resulted in their transformation into tumor stem (initiating)-like cells, as indicated by the expression of epithelial markers (e.g., cytokeratin) and stem cell markers (e.g., Oct4) and their capability to differentiate in vitro and self-renew in serum-free media. Moreover, we identified a subset of monocytes/macrophages cells in the blood of cancer (breast, ovarian and colorectal) patients undergoing chemotherapy that harbor tumor transcripts. Our findings uncover a new role for macrophages in tumor development, where they can be transformed into tumor-like cells, potentially by horizontal gene transfer of tumor-derived genes, thus, by taking advantage of chemotherapy, these transformed macrophages promote tumor metastasis by escaping immune surveillance.}, }
@article {pmid29134153, year = {2017}, author = {Song, W and Steensen, K and Thomas, T}, title = {HgtSIM: a simulator for horizontal gene transfer (HGT) in microbial communities.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e4015}, pmid = {29134153}, issn = {2167-8359}, abstract = {The development and application of metagenomic approaches have provided an opportunity to study and define horizontal gene transfer (HGT) on the level of microbial communities. However, no current metagenomic data simulation tools offers the option to introduce defined HGT within a microbial community. Here, we present HgtSIM, a pipeline to simulate HGT event among microbial community members with user-defined mutation levels. It was developed for testing and benchmarking pipelines for recovering HGTs from complex microbial datasets. HgtSIM is implemented in Python3 and is freely available at: https://github.com/songweizhi/HgtSIM.}, }
@article {pmid29133838, year = {2017}, author = {Nazir, R and Shen, JP and Wang, JT and Hu, HW and He, JZ}, title = {Fungal networks serve as novel ecological routes for enrichment and dissemination of antibiotic resistance genes as exhibited by microcosm experiments.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {15457}, pmid = {29133838}, issn = {2045-2322}, mesh = {Animal Husbandry ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/*genetics ; Drug Resistance, Bacterial/*genetics ; Fungi/*genetics ; *Gene Transfer, Horizontal ; Humans ; Manure/microbiology ; Microbial Consortia/genetics ; Microbial Interactions/genetics ; *Soil Microbiology ; Sus scrofa/microbiology ; Transposases/genetics ; Wastewater/microbiology ; }, abstract = {Antibiotic resistance genes (ARGs) in the environment and their subsequent acquisition by clinically important microorganisms are a serious concern. However, the spread of environmental ARGs remain largely unknown. We report, for the first time, the involvement of soil fungi in the distribution of bacteria with ARGs via soil microcosms. qPCR assay detected unique ARGs specifically found in the mycosphere of different fungi. Interestingly, the taxonomically and ecologically different fungi exerted different selection pressures on ARGs originating from the same source. Test fungi supported different antibiotic resistance bacteria enriched in the mycosphere and even transported to distant places. The relative abundance of the tnpA gene decreased, for manure, along mycelial networks of all fungi. While the fungal strain NFC-5 enriched the intI1 gene more, opposite to two other fungi at the migration front compared with the inoculation point for both sources. Such data indicate the differential effect of different fungi to facilitate horizontal gene transfer potential under fungal selection pressure. Our study provides the evidence that fungi can contribute ARGs, host bacterial diversity and abundance, and such interactive microbial consortia have the potential to disseminate the resistance determinants from one place to another, thus increasing the ARGs exposure risk to humans.}, }
@article {pmid29133441, year = {2017}, author = {Goldenfeld, N and Biancalani, T and Jafarpour, F}, title = {Universal biology and the statistical mechanics of early life.}, journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences}, volume = {375}, number = {2109}, pages = {}, pmid = {29133441}, issn = {1471-2962}, mesh = {Biological Evolution ; *Biology ; Exobiology ; Gene Transfer, Horizontal ; *Origin of Life ; }, abstract = {All known life on the Earth exhibits at least two non-trivial common features: the canonical genetic code and biological homochirality, both of which emerged prior to the Last Universal Common Ancestor state. This article describes recent efforts to provide a narrative of this epoch using tools from statistical mechanics. During the emergence of self-replicating life far from equilibrium in a period of chemical evolution, minimal models of autocatalysis show that homochirality would have necessarily co-evolved along with the efficiency of early-life self-replicators. Dynamical system models of the evolution of the genetic code must explain its universality and its highly refined error-minimization properties. These have both been accounted for in a scenario where life arose from a collective, networked phase where there was no notion of species and perhaps even individuality itself. We show how this phase ultimately terminated during an event sometimes known as the Darwinian transition, leading to the present epoch of tree-like vertical descent of organismal lineages. These examples illustrate concrete examples of universal biology: the quest for a fundamental understanding of the basic properties of living systems, independent of precise instantiation in chemistry or other media.This article is part of the themed issue 'Reconceptualizing the origins of life'.}, }
@article {pmid29133277, year = {2017}, author = {Jahangiri-Tazehkand, S and Wong, L and Eslahchi, C}, title = {OrthoGNC: A Software for Accurate Identification of Orthologs Based on Gene Neighborhood Conservation.}, journal = {Genomics, proteomics &amp; bioinformatics}, volume = {15}, number = {6}, pages = {361-370}, pmid = {29133277}, issn = {2210-3244}, mesh = {Algorithms ; Computer Simulation ; *Conserved Sequence ; *Genes ; Genomics/*methods ; Mycobacterium/genetics/metabolism ; Phylogeny ; Proteome/metabolism ; *Sequence Homology, Nucleic Acid ; *Software ; Time Factors ; }, abstract = {Orthology relations can be used to transfer annotations from one gene (or protein) to another. Hence, detecting orthology relations has become an important task in the post-genomic era. Various genomic events, such as duplication and horizontal gene transfer, can cause erroneous assignment of orthology relations. In closely-related species, gene neighborhood information can be used to resolve many ambiguities in orthology inference. Here we present OrthoGNC, a software for accurately predicting pairwise orthology relations based on gene neighborhood conservation. Analyses on simulated and real data reveal the high accuracy of OrthoGNC. In addition to orthology detection, OrthoGNC can be employed to investigate the conservation of genomic context among potential orthologs detected by other methods. OrthoGNC is freely available online at http://bs.ipm.ir/softwares/orthognc and http://tinyurl.com/orthoGNC.}, }
@article {pmid29129284, year = {2017}, author = {Douglas, AE}, title = {The B vitamin nutrition of insects: the contributions of diet, microbiome and horizontally acquired genes.}, journal = {Current opinion in insect science}, volume = {23}, number = {}, pages = {65-69}, doi = {10.1016/j.cois.2017.07.012}, pmid = {29129284}, issn = {2214-5753}, mesh = {Animals ; Diet ; Gene Transfer, Horizontal ; Genes, Bacterial ; Insecta/genetics/metabolism/*physiology ; Microbiota/*physiology ; Vitamin B Complex/biosynthesis/*metabolism ; Vitamin B Deficiency ; }, abstract = {Insects generally cannot synthesize eight B vitamins that function as co-enzymes in various required enzymatic reactions. Most insects derive their B vitamin requirements from the diet, microbial symbionts, or a combination of these complementary sources. Exceptionally, the genomes of a few insects bear genes in vitamin B5 (pantothenate) and B7 (biotin) synthesis, horizontally acquired from bacteria. Biomarkers of B vitamin deficiency (e.g. vitamin titers, activity of vitamin-dependent enzymes) offer routes to investigate the incidence and the physiological and fitness consequences of B vitamin deficiency in laboratory and field populations of insects.}, }
@article {pmid29127343, year = {2017}, author = {Matamoros, S and van Hattem, JM and Arcilla, MS and Willemse, N and Melles, DC and Penders, J and Vinh, TN and Thi Hoa, N and Bootsma, MCJ and van Genderen, PJ and Goorhuis, A and Grobusch, M and Molhoek, N and Oude Lashof, AML and Stobberingh, EE and Verbrugh, HA and de Jong, MD and Schultsz, C}, title = {Global phylogenetic analysis of Escherichia coli and plasmids carrying the mcr-1 gene indicates bacterial diversity but plasmid restriction.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {15364}, pmid = {29127343}, issn = {2045-2322}, support = {MR/R002762/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Escherichia coli/classification/*growth &amp; development/isolation &amp; purification ; Escherichia coli Proteins/*genetics ; Europe ; *Gene Transfer, Horizontal ; Humans ; *Phylogeny ; Plasmids/*genetics ; }, abstract = {To understand the dynamics behind the worldwide spread of the mcr-1 gene, we determined the population structure of Escherichia coli and of mobile genetic elements (MGEs) carrying the mcr-1 gene. After a systematic review of the literature we included 65 E. coli whole genome sequences (WGS), adding 6 recently sequenced travel related isolates, and 312 MLST profiles. We included 219 MGEs described in 7 Enterobacteriaceae species isolated from human, animal and environmental samples. Despite a high overall diversity, 2 lineages were observed in the E. coli population that may function as reservoirs of the mcr-1 gene, the largest of which was linked to ST10, a sequence type known for its ubiquity in human faecal samples and in food samples. No genotypic clustering by geographical origin or isolation source was observed. Amongst a total of 13 plasmid incompatibility types, the IncI2, IncX4 and IncHI2 plasmids accounted for more than 90% of MGEs carrying the mcr-1 gene. We observed significant geographical clustering with regional spread of IncHI2 plasmids in Europe and IncI2 in Asia. These findings point towards promiscuous spread of the mcr-1 gene by efficient horizontal gene transfer dominated by a limited number of plasmid incompatibility types.}, }
@article {pmid29126393, year = {2017}, author = {Peter, S and Oberhettinger, P and Schuele, L and Dinkelacker, A and Vogel, W and Dörfel, D and Bezdan, D and Ossowski, S and Marschal, M and Liese, J and Willmann, M}, title = {Genomic characterisation of clinical and environmental Pseudomonas putida group strains and determination of their role in the transfer of antimicrobial resistance genes to Pseudomonas aeruginosa.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {859}, pmid = {29126393}, issn = {1471-2164}, mesh = {Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Bacterial/*genetics ; *Environment ; *Gene Transfer, Horizontal ; *Genomics ; Humans ; Phylogeny ; Pseudomonas aeruginosa/*genetics ; Pseudomonas putida/drug effects/*genetics/physiology ; }, abstract = {BACKGROUND: Pseudomonas putida is a Gram-negative, non-fermenting bacterium frequently encountered in various environmental niches. P. putida rarely causes disease in humans, though serious infections and outbreaks have been reported from time to time. Some have suggested that P. putida functions as an exchange platform for antibiotic resistance genes (ARG), and thus represents a serious concern in the spread of ARGs to more pathogenic organisms within a hospital. Though poorly understood, the frequency of ARG exchange between P. putida and the more virulent Pseudomonas aeruginosa and its clinical relevance are particularly important for designing efficient infection control strategies, such as deciding whether high-risk patients colonized with a multidrug resistant but typically low pathogenic P. putida strain should be contact isolated or not.<br><br>RESULTS: In this study, 21,373 screening samples (stool, rectal and throat swab) were examined to determine the presence of P. putida in a high-risk group of haemato-oncology patients during a 28-month period. A total of 89 P. putida group strains were isolated from 85 patients, with 41 of 89 (46.1%) strains harbouring the metallo-beta-lactamase gene bla VIM. These 41 clinical isolates, plus 18 bla VIM positive environmental P. putida isolates, and 17 bla VIM positive P. aeruginosa isolates, were characterized by whole genome sequencing (WGS). We constructed a maximum-likelihood tree to separate the 59 bla VIM positive P. putida group strains into eight distinct phylogenetic clusters. Bla VIM-1 was present in 6 clusters while bla VIM-2 was detected in 4 clusters. Five P. putida group strains contained both, bla VIM-1 and bla VIM-2 genes. In contrast, all P. aeruginosa strains belonged to a single genetic cluster and contained the same ARGs. Apart from bla VIM-2 and sul genes, no other ARGs were shared between P. aeruginosa and P. putida. Furthermore, the bla VIM-2 gene in P. aeruginosa was predicted to be only chromosomally located.<br><br>CONCLUSION: These data provide evidence that no exchange of comprehensive ARG harbouring mobile genetic elements had occurred between P. aeruginosa and P. putida group strains during the study period, thus eliminating the need to implement enhanced infection control measures for high-risk patients colonized with a bla VIM positiv P. putida group strains in our clinical setting.}, }
@article {pmid29126189, year = {2017}, author = {Xu, C and Zhang, R and Sun, G and Gleason, ML}, title = {Comparative Genome Analysis Reveals Adaptation to the Ectophytic Lifestyle of Sooty Blotch and Flyspeck Fungi.}, journal = {Genome biology and evolution}, volume = {9}, number = {11}, pages = {3137-3151}, pmid = {29126189}, issn = {1759-6653}, mesh = {Adaptation, Biological ; Amino Acid Sequence ; Ascomycota/*classification/*genetics/physiology ; Evolution, Molecular ; Fungal Proteins/chemistry/genetics ; Gene Transfer, Horizontal ; Genome, Fungal ; Host-Pathogen Interactions ; Molecular Sequence Annotation ; Phylogeny ; Plant Diseases/microbiology ; Sequence Alignment ; }, abstract = {Sooty blotch and flyspeck (SBFS) fungi are a distinctive group of plant pathogens which, although phylogenetically diverse, occupy an exclusively surface-dwelling niche. They cause economic losses by superficially blemishing the fruit of several tree crops, principally apple, in moist temperate regions worldwide. In this study, we performed genome-wide comparative analyses separately within three pairs of species of ascomycete pathogens; each pair contained an SBFS species as well as a closely related but plant-penetrating parasite (PPP) species. Our results showed that all three of the SBFS pathogens had significantly smaller genome sizes, gene numbers and repeat ratios than their counterpart PPPs. The pathogenicity-related genes encoding MFS transporters, secreted proteins (mainly effectors and peptidases), plant cell wall degrading enzymes, and secondary metabolism enzymes were also drastically reduced in the SBFS fungi compared with their PPP relatives. We hypothesize that the above differences in genome composition are due largely to different levels of acquisition, loss, expansion, and contraction of gene families and emergence of orphan genes. Furthermore, results suggested that horizontal gene transfer may have played a role, although limited, in the divergent evolutionary paths of SBFS pathogens and PPPs; repeat-induced point mutation could have inhibited the propagation of transposable elements and expansion of gene families in the SBFS group, given that this mechanism is stronger in the SBFS fungi than in their PPP relatives. These results substantially broaden understanding of evolutionary mechanisms of adaptation of fungi to the epicuticular niche of plants.}, }
@article {pmid29125597, year = {2018}, author = {Simmons, EL and Drescher, K and Nadell, CD and Bucci, V}, title = {Phage mobility is a core determinant of phage-bacteria coexistence in biofilms.}, journal = {The ISME journal}, volume = {12}, number = {2}, pages = {531-543}, pmid = {29125597}, issn = {1751-7370}, support = {P20 GM113132/GM/NIGMS NIH HHS/United States ; R15 AI112985/AI/NIAID NIH HHS/United States ; }, mesh = {*Bacterial Physiological Phenomena ; Bacteriophages/*physiology ; *Biofilms/growth &amp; development ; Computer Simulation ; Diffusion ; *Microbial Interactions ; }, abstract = {Many bacteria are adapted for attaching to surfaces and for building complex communities, termed biofilms. The biofilm mode of life is predominant in bacterial ecology. So too is the exposure of bacteria to ubiquitous viral pathogens, termed bacteriophages. Although biofilm-phage encounters are likely to be common in nature, little is known about how phages might interact with biofilm-dwelling bacteria. It is also unclear how the ecological dynamics of phages and their hosts depend on the biological and physical properties of the biofilm environment. To make headway in this area, we develop a biofilm simulation framework that captures key mechanistic features of biofilm growth and phage infection. Using these simulations, we find that the equilibrium state of interaction between biofilms and phages is governed largely by nutrient availability to biofilms, infection likelihood per host encounter and the ability of phages to diffuse through biofilm populations. Interactions between the biofilm matrix and phage particles are thus likely to be of fundamental importance, controlling the extent to which bacteria and phages can coexist in natural contexts. Our results open avenues to new questions of host-parasite coevolution and horizontal gene transfer in spatially structured biofilm contexts.}, }
@article {pmid29123229, year = {2017}, author = {}, title = {A flourishing field: going back to the roots of the Archaea.}, journal = {Nature reviews. Microbiology}, volume = {15}, number = {12}, pages = {705}, pmid = {29123229}, issn = {1740-1534}, mesh = {Adaptation, Biological/*genetics ; Archaea/classification/*genetics/physiology/virology ; Bacteria/genetics ; *Biodiversity ; Ecology ; Eukaryota/genetics ; Gene Transfer, Horizontal ; *Genetic Speciation ; Genome, Archaeal/*genetics ; }, }
@article {pmid29122644, year = {2018}, author = {Hisano, S and Zhang, R and Faruk, MI and Kondo, H and Suzuki, N}, title = {A neo-virus lifestyle exhibited by a (+)ssRNA virus hosted in an unrelated dsRNA virus: Taxonomic and evolutionary considerations.}, journal = {Virus research}, volume = {244}, number = {}, pages = {75-83}, doi = {10.1016/j.virusres.2017.11.006}, pmid = {29122644}, issn = {1872-7492}, mesh = {Amino Acid Sequence ; Capsid Proteins/genetics/metabolism ; Evolution, Molecular ; Fungal Viruses/classification/*genetics/isolation &amp; purification/metabolism ; Fungi/*virology ; Gene Transfer, Horizontal ; Microbial Interactions ; *Phylogeny ; RNA Viruses/classification/*genetics/isolation &amp; purification/metabolism ; RNA, Double-Stranded/genetics/metabolism ; RNA, Viral/*genetics/metabolism ; RNA-Dependent RNA Polymerase/genetics/metabolism ; Satellite Viruses/classification/*genetics/isolation &amp; purification/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Virus Replication ; }, abstract = {Recent studies illustrate that fungi as virus hosts provides a unique platform for hunting viruses and exploring virus/virus and virus/host interactions. Such studies have revealed a number of as-yet-unreported viruses and virus/virus interactions. Among them is a unique intimate relationship between a (+)ssRNA virus, yado-kari virus (YkV1) and an unrelated dsRNA virus, yado-nushi virus (YnV1). YkV1 dsRNA, a replicated form of YkV1, and RNA-dependent RNA polymerase, are trans-encapsidated by the capsid protein of YnV1. While YnV1 can complete its replication cycle, YkV1 relies on YnV1 for its viability. We previously proposed a model in which YkV1 diverts YnV1 capsids as the replication sites. YkV1 is neither satellite virus nor satellite RNA, because YkV1 appears to encode functional RdRp and enhances YnV1 accumulation. This represents a unique mutualistic virus/virus interplay and similar relations in other virus/host fungus systems are detectable. We propose to establish the family Yadokariviridae that accommodates YkV1 and recently discovered viruses phylogenetically related to YkV1. This article overviews what is known and unknown about the YkV1/YnV1 interactions. Also discussed are the YnV1 Phytoreo_S7 and YkV1 2A-like domains that may have been captured via horizontal transfer during the course of evolution and are conserved across extant diverse RNA viruses. Lastly, evolutionary scenarios are envisioned for YkV1 and YnV1.}, }
@article {pmid29122240, year = {2017}, author = {Cai, F and Yu, G and Zhang, K and Chen, Y and Li, Q and Yang, Y and Xie, J and Wang, Y and Li, R}, title = {Geosmin production and polyphasic characterization of Oscillatoria limosa Agardh ex Gomont isolated from the open canal of a large drinking water system in Tianjin City, China.}, journal = {Harmful algae}, volume = {69}, number = {}, pages = {28-37}, doi = {10.1016/j.hal.2017.09.006}, pmid = {29122240}, issn = {1878-1470}, mesh = {Base Sequence ; China ; Cities ; DNA, Ribosomal/genetics ; Drinking Water/*microbiology ; Geography ; Light ; Naphthols/*metabolism ; Oscillatoria/chemistry/genetics/growth &amp; development/*isolation &amp; purification ; Phylogeny ; Rivers/chemistry ; Temperature ; Volatile Organic Compounds/analysis ; }, abstract = {Taste and odor (T &amp; O) episodes always cause strong effects on drinking water supply system. Luanhe River diversion into Tianjin City in China is an important drinking water resource. Massive growth of a benthic filamentous cyanobacterium with geosmin production in the open canal caused a strong earthy odor episode in Tianjin. On the basis of the morphological and molecular identification of this cyanobacterium as Oscillatoria limosa Agardh ex Gomont, the genetic basis for geosmin biosynthesis and factors influencing growth and geosmin production of O. limosa CHAB 7000 were studied in this work. A 2268-bp open reading frame, encoding 755 amino acids, was amplified and characterized as the geosmin synthase gene (geo), followed by a cyclic nucleotide-binding protein gene (cnb). Phylogenetic analysis implied that the evolution of the geosmin genes in O. limosa CHAB 7000 might involve a horizontal gene transfer event. Examination on the growth and geosmin production of O. limosa CHAB 7000 at different light intensities showed that the maximum geosmin production was observed at 10μmol photons m[-2]s[-1], while the optimum growth was at 60μmol photons m[-2]s[-1]. Under three temperature conditions (15°C, 25°C, and 35°C), the maximum growth and geosmin production were observed at 25°C. Most amounts of geosmin were retained in cells during the growth phase, but high temperature and low light intensity increased the release of geosmin into the medium, implying that O. limosa CHAB 7000 had a high potential harm for the release of geosmin from its cells at these adverse conditions.}, }
@article {pmid29120392, year = {2017}, author = {Drezen, JM and Josse, T and Bézier, A and Gauthier, J and Huguet, E and Herniou, EA}, title = {Impact of Lateral Transfers on the Genomes of Lepidoptera.}, journal = {Genes}, volume = {8}, number = {11}, pages = {}, pmid = {29120392}, issn = {2073-4425}, abstract = {Transfer of DNA sequences between species regardless of their evolutionary distance is very common in bacteria, but evidence that horizontal gene transfer (HGT) also occurs in multicellular organisms has been accumulating in the past few years. The actual extent of this phenomenon is underestimated due to frequent sequence filtering of "alien" DNA before genome assembly. However, recent studies based on genome sequencing have revealed, and experimentally verified, the presence of foreign DNA sequences in the genetic material of several species of Lepidoptera. Large DNA viruses, such as baculoviruses and the symbiotic viruses of parasitic wasps (bracoviruses), have the potential to mediate these transfers in Lepidoptera. In particular, using ultra-deep sequencing, newly integrated transposons have been identified within baculovirus genomes. Bacterial genes have also been acquired by genomes of Lepidoptera, as in other insects and nematodes. In addition, insertions of bracovirus sequences were present in the genomes of certain moth and butterfly lineages, that were likely corresponding to rearrangements of ancient integrations. The viral genes present in these sequences, sometimes of hymenopteran origin, have been co-opted by lepidopteran species to confer some protection against pathogens.}, }
@article {pmid29120256, year = {2018}, author = {Ellis, MJ and Carfrae, LA and Macnair, CR and Trussler, RS and Brown, ED and Haniford, DB}, title = {Silent but deadly: IS200 promotes pathogenicity in Salmonella Typhimurium.}, journal = {RNA biology}, volume = {15}, number = {2}, pages = {176-181}, pmid = {29120256}, issn = {1555-8584}, mesh = {5' Untranslated Regions ; Animals ; Bacterial Proteins/genetics ; *DNA Transposable Elements ; Down-Regulation ; Gastrointestinal Tract/microbiology ; Gene Expression Regulation, Bacterial ; Mice ; RNA, Small Untranslated/*genetics ; Salmonella Infections, Animal/genetics/*microbiology ; Salmonella typhimurium/genetics/*pathogenicity ; Transposases/*genetics ; Virulence ; }, abstract = {Bacterial transposons were long thought of as selfish mobile genetic elements that propagate at the expense of 'host' bacterium fitness. However, limited transposition can benefit the host organism by promoting DNA rearrangements and facilitating horizontal gene transfer. Here we discuss and provide context for our recently published work which reported the surprising finding that an otherwise dormant transposon, IS200, encodes a regulatory RNA in Salmonella Typhimurium. This previous work identified a trans-acting sRNA that is encoded in the 5'UTR of IS200 transposase mRNA (tnpA). This sRNA represses expression of genes encoded within Salmonella Pathogenicity Island 1 (SPI-1), and accordingly limits invasion into non-phagocytic cells in vitro. We present new data here that shows IS200 elements are important for colonization of the mouse gastrointestinal tract. We discuss our previous and current findings in the context of transposon biology and suggest that otherwise 'silent' transposons may in fact play an important role in controlling host gene expression.}, }
@article {pmid29117270, year = {2017}, author = {Mavrici, D and Yambao, JC and Lee, BG and Quiñones, B and He, X}, title = {Screening for the presence of mcr-1/mcr-2 genes in Shiga toxin-producing Escherichia coli recovered from a major produce-production region in California.}, journal = {PloS one}, volume = {12}, number = {11}, pages = {e0187827}, pmid = {29117270}, issn = {1932-6203}, mesh = {Animals ; California/epidemiology ; DNA, Bacterial/*genetics ; Epidemiological Monitoring ; Escherichia coli Infections/epidemiology/microbiology/prevention &amp; control ; Escherichia coli Proteins/*genetics ; *Food Microbiology ; Gene Transfer, Horizontal ; Humans ; Livestock/microbiology ; Plasmids/*chemistry/isolation &amp; purification ; Polymerase Chain Reaction ; Protein Isoforms/genetics ; Shiga Toxins/*genetics/isolation &amp; purification ; Shiga-Toxigenic Escherichia coli/*genetics/isolation &amp; purification ; Vegetables/microbiology ; }, abstract = {The rapid spreading of polymyxin E (colistin) resistance among bacterial strains through the horizontally transmissible mcr-1 and mcr-2 plasmids has become a serious concern. The emergence of these genes in Shiga toxin-producing Escherichia coli (STEC), a group of human pathogenic bacteria was even more worrisome, urging us to investigate the prevalence of mcr genes among STEC isolates. A total of 1000 STEC isolates, recovered from livestock, wildlife, produce and other environmental sources in a major production region for leafy vegetables in California during 2006-2014, were screened by PCR for the presence of plasmid-borne mcr-1 and mcr-2. All isolates tested yielded negative results, indicating if any, the occurrence rate of mcr-1/mcr-2 among STEC was very low in this agricultural region. This study provides valuable information such as sample size needed and methodologies for future surveillance programs of antimicrobial resistance.}, }
@article {pmid29116639, year = {2017}, author = {Warner, DF and Rock, JM and Fortune, SM and Mizrahi, V}, title = {DNA Replication Fidelity in the Mycobacterium tuberculosis Complex.}, journal = {Advances in experimental medicine and biology}, volume = {1019}, number = {}, pages = {247-262}, doi = {10.1007/978-3-319-64371-7_13}, pmid = {29116639}, issn = {0065-2598}, support = {U01HD085531-02//US National Institute of Child Health and Human Development/International ; 1DP20D001378/NH/NIH HHS/United States ; U19 AI107774-0/AI/NIAID NIH HHS/United States ; }, mesh = {Antitubercular Agents/therapeutic use ; Bacterial Proteins/classification/*genetics/metabolism ; Biological Evolution ; *DNA Replication ; DNA, Bacterial/*genetics/metabolism ; DNA-Directed DNA Polymerase/classification/*genetics/metabolism ; Drug Resistance, Multiple, Bacterial/genetics ; Genetic Variation ; *Genome, Bacterial ; Humans ; Mutation Rate ; Mycobacterium tuberculosis/drug effects/enzymology/*genetics/growth &amp; development ; Protein Domains ; Tuberculosis, Multidrug-Resistant/diagnosis/drug therapy/transmission ; Tuberculosis, Pulmonary/diagnosis/drug therapy/transmission ; }, abstract = {Mycobacterium tuberculosis is genetically isolated, with no evidence for horizontal gene transfer or the acquisition of episomal genetic information in the modern evolution of strains of the Mycobacterium tuberculosis complex. When considered in the context of the specific features of the disease M. tuberculosis causes (e.g., transmission via cough aerosol, replication within professional phagocytes, subclinical persistence, and stimulation of a destructive immune pathology), this implies that to understand the mechanisms ensuring preservation of genomic integrity in infecting mycobacterial populations is to understand the source of genetic variation, including the emergence of microdiverse sub-populations that may be linked to the acquisition of drug resistance. In this chapter, we focus on mechanisms involved in maintaining DNA replication fidelity in M. tuberculosis, and consider the potential to target components of the DNA replication machinery as part of novel therapeutic regimens designed to curb the emerging threat of drug-resistance.}, }
@article {pmid29112874, year = {2017}, author = {Roger, AJ and Muñoz-Gómez, SA and Kamikawa, R}, title = {The Origin and Diversification of Mitochondria.}, journal = {Current biology : CB}, volume = {27}, number = {21}, pages = {R1177-R1192}, doi = {10.1016/j.cub.2017.09.015}, pmid = {29112874}, issn = {1879-0445}, mesh = {Adenosine Triphosphate/biosynthesis/metabolism ; Alphaproteobacteria/*genetics/growth &amp; development ; *Biological Evolution ; Eukaryotic Cells/*metabolism ; Genome, Mitochondrial/genetics ; Membrane Transport Proteins/genetics ; *Mitochondria/genetics/metabolism/physiology ; Protein Transport/genetics/physiology ; Symbiosis/genetics/physiology ; }, abstract = {Mitochondria are best known for their role in the generation of ATP by aerobic respiration. Yet, research in the past half century has shown that they perform a much larger suite of functions and that these functions can vary substantially among diverse eukaryotic lineages. Despite this diversity, all mitochondria derive from a common ancestral organelle that originated from the integration of an endosymbiotic alphaproteobacterium into a host cell related to Asgard Archaea. The transition from endosymbiotic bacterium to permanent organelle entailed a massive number of evolutionary changes including the origins of hundreds of new genes and a protein import system, insertion of membrane transporters, integration of metabolism and reproduction, genome reduction, endosymbiotic gene transfer, lateral gene transfer and the retargeting of proteins. These changes occurred incrementally as the endosymbiont and the host became integrated. Although many insights into this transition have been gained, controversy persists regarding the nature of the original endosymbiont, its initial interactions with the host and the timing of its integration relative to the origin of other features of eukaryote cells. Since the establishment of the organelle, proteins have been gained, lost, transferred and retargeted as mitochondria have specialized into the spectrum of functional types seen across the eukaryotic tree of life.}, }
@article {pmid29112840, year = {2018}, author = {Jutkina, J and Marathe, NP and Flach, CF and Larsson, DGJ}, title = {Antibiotics and common antibacterial biocides stimulate horizontal transfer of resistance at low concentrations.}, journal = {The Science of the total environment}, volume = {616-617}, number = {}, pages = {172-178}, doi = {10.1016/j.scitotenv.2017.10.312}, pmid = {29112840}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents/*pharmacology ; Chlorhexidine/pharmacology ; Disinfectants/*pharmacology ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/drug effects/*genetics ; *Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Triclosan/pharmacology ; }, abstract = {There is a rising concern that antibiotics, and possibly other antimicrobial agents, can promote horizontal transfer of antibiotic resistance genes. For most types of antimicrobials their ability to induce conjugation below minimal inhibitory concentrations (MICs) is still unknown. Our aim was therefore to explore the potential of commonly used antibiotics and antibacterial biocides to induce horizontal transfer of antibiotic resistance. Effects of a wide range of sub-MIC concentrations of the antibiotics cefotaxime, ciprofloxacin, gentamicin, erythromycin, sulfamethoxazole, trimethoprim and the antibacterial biocides chlorhexidine digluconate, hexadecyltrimethylammoniumchloride and triclosan were investigated using a previously optimized culture-based assay with a complex bacterial community as a donor of mobile resistance elements and a traceable Escherichia coli strain as a recipient. Chlorhexidine (24.4μg/L), triclosan (0.1mg/L), gentamicin (0.1mg/L) and sulfamethoxazole (1mg/L) significantly increased the frequencies of transfer of antibiotic resistance whereas similar effects were not observed for any other tested antimicrobial compounds. This corresponds to 200 times below the MIC of the recipient for chlorhexidine, 1/20 of the MIC for triclosan, 1/16 of the MIC for sulfamethoxazole and right below the MIC for gentamicin. To our best knowledge, this is the first study showing that triclosan and chlorhexidine could stimulate the horizontal transfer of antibiotic resistance. Together with recent research showing that tetracycline is a potent inducer of conjugation, our results indicate that several antimicrobials including both common antibiotics and antibacterial biocides at low concentrations could contribute to antibiotic resistance development by facilitating the spread of antibiotic resistance between bacteria.}, }
@article {pmid29112720, year = {2018}, author = {Zhu, C and Mahlich, Y and Miller, M and Bromberg, Y}, title = {fusionDB: assessing microbial diversity and environmental preferences via functional similarity networks.}, journal = {Nucleic acids research}, volume = {46}, number = {D1}, pages = {D535-D541}, pmid = {29112720}, issn = {1362-4962}, mesh = {Bacteria/classification/genetics ; Bacterial Physiological Phenomena ; Bacterial Proteins/genetics/physiology ; Biodiversity ; *Databases, Factual ; Databases, Genetic ; Environmental Microbiology ; Gene Transfer, Horizontal ; Humans ; Internet ; Metadata ; Metagenomics ; Microbiota/*physiology ; Phylogeny ; Synechococcus/classification/genetics/physiology ; User-Computer Interface ; }, abstract = {Microbial functional diversification is driven by environmental factors, i.e. microorganisms inhabiting the same environmental niche tend to be more functionally similar than those from different environments. In some cases, even closely phylogenetically related microbes differ more across environments than across taxa. While microbial similarities are often reported in terms of taxonomic relationships, no existing databases directly link microbial functions to the environment. We previously developed a method for comparing microbial functional similarities on the basis of proteins translated from their sequenced genomes. Here, we describe fusionDB, a novel database that uses our functional data to represent 1374 taxonomically distinct bacteria annotated with available metadata: habitat/niche, preferred temperature, and oxygen use. Each microbe is encoded as a set of functions represented by its proteome and individual microbes are connected via common functions. Users can search fusionDB via combinations of organism names and metadata. Moreover, the web interface allows mapping new microbial genomes to the functional spectrum of reference bacteria, rendering interactive similarity networks that highlight shared functionality. fusionDB provides a fast means of comparing microbes, identifying potential horizontal gene transfer events, and highlighting key environment-specific functionality.}, }
@article {pmid29112165, year = {2017}, author = {Oliveira, GP and Rodrigues, RAL and Lima, MT and Drumond, BP and Abrahão, JS}, title = {Poxvirus Host Range Genes and Virus-Host Spectrum: A Critical Review.}, journal = {Viruses}, volume = {9}, number = {11}, pages = {}, pmid = {29112165}, issn = {1999-4915}, mesh = {Animals ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Viral ; Host Specificity/*genetics ; Humans ; Phylogeny ; Poxviridae/*genetics/*physiology ; Viral Proteins/*genetics ; Virus Replication ; }, abstract = {The Poxviridae family is comprised of double-stranded DNA viruses belonging to nucleocytoplasmic large DNA viruses (NCLDV). Among the NCLDV, poxviruses exhibit the widest known host range, which is likely observed because this viral family has been more heavily investigated. However, relative to each member of the Poxviridae family, the spectrum of the host is variable, where certain viruses can infect a large range of hosts, while others are restricted to only one host species. It has been suggested that the variability in host spectrum among poxviruses is linked with the presence or absence of some host range genes. Would it be possible to extrapolate the restriction of viral replication in a specific cell lineage to an animal, a far more complex organism? In this study, we compare and discuss the relationship between the host range of poxvirus species and the abundance/diversity of host range genes. We analyzed the sequences of 38 previously identified and putative homologs of poxvirus host range genes, and updated these data with deposited sequences of new poxvirus genomes. Overall, the term host range genes might not be the most appropriate for these genes, since no correlation between them and the viruses' host spectrum was observed, and a change in nomenclature should be considered. Finally, we analyzed the evolutionary history of these genes, and reaffirmed the occurrence of horizontal gene transfer (HGT) for certain elements, as previously suggested. Considering the data presented in this study, it is not possible to associate the diversity of host range factors with the amount of hosts of known poxviruses, and this traditional nomenclature creates misunderstandings.}, }
@article {pmid29109702, year = {2017}, author = {Fernandes, GR and Barbosa, AEAD and Almeida, RN and Castro, FFDS and da Ponte, MCP and Faria-Junior, C and Müller, FMP and Viana, AAB and Grattapaglia, D and Franco, OL and Alencar, SA and Dias, SC}, title = {Genomic Comparison among Lethal Invasive Strains of Streptococcus pyogenes Serotype M1.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1993}, pmid = {29109702}, issn = {1664-302X}, abstract = {Streptococcus pyogenes, also known as group A Streptococcus (GAS), is a human pathogen that causes diverse human diseases including streptococcal toxic shock syndrome (STSS). A GAS outbreak occurred in Brasilia, Brazil, during the second half of the year 2011, causing 26 deaths. Whole genome sequencing was performed using Illumina platform. The sequences were assembled and genes were predicted for comparative analysis with emm type 1 strains: MGAS5005 and M1 GAS. Genomics comparison revealed one of the invasive strains that differ from others isolates and from emm 1 reference genomes. Also, the new invasive strain showed differences in the content of virulence factors compared to other isolated in the same outbreak. The evolution of contemporary GAS strains is strongly associated with horizontal gene transfer. This is the first genomic study of a Streptococcal emm 1 outbreak in Brazil, and revealed the rapid bacterial evolution leading to new clones. The emergence of new invasive strains can be a consequence of the injudicious use of antibiotics in Brazil during the past decades.}, }
@article {pmid29107607, year = {2018}, author = {Liang, WJ and Liu, HY and Duan, GC and Zhao, YX and Chen, SY and Yang, HY and Xi, YL}, title = {Emergence and mechanism of carbapenem-resistant Escherichia coli in Henan, China, 2014.}, journal = {Journal of infection and public health}, volume = {11}, number = {3}, pages = {347-351}, doi = {10.1016/j.jiph.2017.09.020}, pmid = {29107607}, issn = {1876-035X}, mesh = {Aged ; Aged, 80 and over ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/biosynthesis/*drug effects ; Carbapenems/*pharmacology ; China/epidemiology ; Conjugation, Genetic/genetics ; Enterobacteriaceae Infections/*drug therapy/epidemiology ; Escherichia coli/*drug effects/enzymology/genetics/isolation &amp; purification ; Female ; Gene Transfer, Horizontal ; High-Throughput Nucleotide Sequencing ; Hospitals ; Humans ; Imipenem/pharmacology ; Klebsiella pneumoniae ; Male ; Meropenem ; Microbial Sensitivity Tests ; Middle Aged ; Multilocus Sequence Typing ; Prevalence ; Thienamycins/pharmacology ; beta-Lactamases/biosynthesis/*drug effects/genetics ; }, abstract = {The emergence and dissemination of carbapenem-resistant Escherichia coli (E. coli) strains is a main risk for global public health, but little is known of carbapenemase producing E. coli in Henan, China. The study was undertaken to investigate the prevalence and mechanism of carbapenem-resistant E. coli strains in a hospital in Xinxiang, Henan, China, 2014. A total of 5 carbapenemase-producing E. coli strains were screened from 1014 isolates. We found that they were all resistant to meropenem and imipenem. Amikacin showed the best sensitivity, with gentamicin coming up next. The positive rate of blaNDM was 80% (4/5). The sequencing results showed that two isolates belonged to blaNDM-1 whereas other 2 isolates carried the blaNDM-5. Other carbapenemase genes including blaIMP,blaVIM, blaKPC and blaOXA-48 were not detected. The blaCTX-M-15,blaTEM-1,sul2, aad, and aac(6")-Ib-cr were also detected. MLST analysis showed that NDM-producing E. coli were sporadic. Conjugation test indicated blaNDM could be transferred. In conclusion, the blaNDM was the principal resistance mechanism of carbapenem-resistant E. coli in the hospital, Henan, China.}, }
@article {pmid29105256, year = {2018}, author = {Kazan, K and Gardiner, DM}, title = {Fusarium crown rot caused by Fusarium pseudograminearum in cereal crops: recent progress and future prospects.}, journal = {Molecular plant pathology}, volume = {19}, number = {7}, pages = {1547-1562}, pmid = {29105256}, issn = {1364-3703}, mesh = {Avena/microbiology ; Edible Grain/microbiology ; Fusarium/*pathogenicity ; Hordeum/microbiology ; Plant Diseases/*microbiology ; Triticum/microbiology ; }, abstract = {Diseases caused by Fusarium pathogens inflict major yield and quality losses on many economically important plant species worldwide, including cereals. Fusarium crown rot (FCR), caused by Fusarium pseudograminearum, is a cereal disease that occurs in many arid and semi-arid cropping regions of the world. In recent years, this disease has become more prevalent, in part as a result of the adoption of moisture-preserving cultural practices, such as minimum tillage and stubble retention. In this pathogen profile, we present a brief overview of recent research efforts that have not only advanced our understanding of the interactions between F. pseudograminearum and cereal hosts, but have also provided new disease management options. For instance, significant progress has been made in the genetic characterization of pathogen populations, the development of new tools for disease prediction, and the identification and pyramiding of loci that confer quantitative resistance to FCR in wheat and barley. In addition, transcriptome analyses have revealed new insights into the processes involved in host defence. Significant progress has also been made in understanding the mechanistic details of the F. pseudograminearum infection process. The sequencing and comparative analyses of the F. pseudograminearum genome have revealed novel virulence factors, possibly acquired through horizontal gene transfer. In addition, a conserved pathogen gene cluster involved in the degradation of wheat defence compounds has been identified, and a role for the trichothecene toxin deoxynivalenol (DON) in pathogen virulence has been reported. Overall, a better understanding of cereal host-F. pseudograminearum interactions will lead to the development of new control options for this increasingly important disease problem. Taxonomy: Fusarium pseudograminearum O'Donnell &amp; Aoki; Kingdom Fungi; Phylum Ascomycota; Subphylum Pezizomycotina; Class Sordariomycetes; Subclass Hypocreomycetidae; Order Hypocreales; Family Nectriaceae; Genus Fusarium. Disease symptoms: Fusarium crown rot caused by F. pseudograminearum is also known as crown rot, foot rot and root rot. Infected seedlings can die before or after emergence. If infected seedlings survive, typical disease symptoms are browning of the coleoptile, subcrown internode, lower leaf sheaths and adjacent stems and nodal tissues; this browning can become evident within a few weeks after planting or throughout plant development. Infected plants may develop white heads with no or shrivelled grains. Disease symptoms are exacerbated under water limitation. Identification and detection: Fusarium pseudograminearum macroconidia usually contain three to five septa (22-60.5 × 2.5-5.5 μm). On potato dextrose agar (PDA), aerial mycelia appear floccose and reddish white, with red or reddish-brown reverse pigmentation. Diagnostic polymerase chain reaction (PCR) tests based on the amplification of the gene encoding translation elongation factor-1a (TEF-1a) have been developed for molecular identification. Host range: All major winter cereals can be colonized by F. pseudograminearum. However, the main impact of this pathogen is on bread (Triticum aestivum L.) and durum (Triticum turgidum L. spp. durum (Dest.)) wheat and barley (Hordeum vulgare L.). Oats (Avena sativa L.) can be infected, but show little or no disease symptoms. In addition, the pathogen has been isolated from various other grass genera, such as Phalaris, Agropyron and Bromus, which may occur as common weeds. Useful websites: https://nt.ars-grin.gov/fungaldatabases/; http://plantpath.psu.edu/facilities/fusarium-research-center; https://nt.ars-grin.gov/fungaldatabases/; http://www.speciesfungorum.org/Names/Names.asp.}, }
@article {pmid29101189, year = {2018}, author = {Chidebe, IN and Jaiswal, SK and Dakora, FD}, title = {Distribution and Phylogeny of Microsymbionts Associated with Cowpea (Vigna unguiculata) Nodulation in Three Agroecological Regions of Mozambique.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {2}, pages = {}, pmid = {29101189}, issn = {1098-5336}, mesh = {Bradyrhizobium/*genetics/isolation &amp; purification/metabolism ; DNA, Bacterial/genetics ; DNA, Ribosomal Spacer/genetics ; Gene Transfer, Horizontal ; Genetic Variation ; Geography ; Mozambique ; Nitrogen Fixation ; *Phylogeny ; Plant Root Nodulation ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Rhizobium/*genetics/isolation &amp; purification/metabolism ; Root Nodules, Plant/microbiology ; Symbiosis/genetics ; Vigna/*microbiology ; }, abstract = {Cowpea derives most of its N nutrition from biological nitrogen fixation (BNF) via symbiotic bacteroids in root nodules. In Sub-Saharan Africa, the diversity and biogeographic distribution of bacterial microsymbionts nodulating cowpea and other indigenous legumes are not well understood, though needed for increased legume production. The aim of this study was to describe the distribution and phylogenies of rhizobia at different agroecological regions of Mozambique using PCR of the BOX element (BOX-PCR), restriction fragment length polymorphism of the internal transcribed spacer (ITS-RFLP), and sequence analysis of ribosomal, symbiotic, and housekeeping genes. A total of 122 microsymbionts isolated from two cowpea varieties (IT-1263 and IT-18) grouped into 17 clades within the BOX-PCR dendrogram. The PCR-ITS analysis yielded 17 ITS types for the bacterial isolates, while ITS-RFLP analysis placed all test isolates in six distinct clusters (I to VI). BLASTn sequence analysis of 16S rRNA and four housekeeping genes (glnII, gyrB, recA, and rpoB) showed their alignment with Rhizobium and Bradyrhizobium species. The results revealed a group of highly diverse and adapted cowpea-nodulating microsymbionts which included Bradyrhizobium pachyrhizi, Bradyrhizobium arachidis, Bradyrhizobium yuanmingense, and a novel Bradyrhizobium sp., as well as Rhizobium tropici, Rhizobium pusense, and Neorhizobium galegae in Mozambican soils. Discordances observed in single-gene phylogenies could be attributed to horizontal gene transfer and/or subsequent recombinations of the genes. Natural deletion of 60 bp of the gyrB region was observed in isolate TUTVU7; however, this deletion effect on DNA gyrase function still needs to be confirmed. The inconsistency of nifH with core gene phylogenies suggested differences in the evolutionary history of both chromosomal and symbiotic genes.IMPORTANCE A diverse group of both Bradyrhizobium and Rhizobium species responsible for cowpea nodulation in Mozambique was found in this study. Future studies could prove useful in evaluating these bacterial isolates for symbiotic efficiency and strain competitiveness in Mozambican soils.}, }
@article {pmid29101082, year = {2018}, author = {Bi, R and Qin, T and Fan, W and Ma, P and Gu, B}, title = {The emerging problem of linezolid-resistant enterococci.}, journal = {Journal of global antimicrobial resistance}, volume = {13}, number = {}, pages = {11-19}, doi = {10.1016/j.jgar.2017.10.018}, pmid = {29101082}, issn = {2213-7173}, mesh = {Anti-Bacterial Agents/*pharmacology ; Communicable Diseases, Emerging/*epidemiology/microbiology ; Cross Infection/epidemiology/microbiology ; *Drug Resistance, Bacterial ; Enterococcus faecalis/drug effects/*isolation &amp; purification ; Enterococcus faecium/drug effects/*isolation &amp; purification ; Gene Transfer, Horizontal ; Genes, Bacterial ; Gram-Positive Bacterial Infections/*epidemiology/microbiology ; Humans ; Linezolid/*pharmacology ; Mutation ; Prevalence ; }, abstract = {Enterococcus is a significant pathogen in numerous infections, particularly in nosocomial infections, and is thus a great challenge to clinicians. Linezolid (LNZ), an oxazolidinone antibiotic, is an important therapeutic option for infections caused by Gram-positive bacterial pathogens, especially vancomycin-resistant enterococci. A systematic review was performed of the available literature on LNZ-resistant enterococci (LRE) to characterise these infections with respect to epidemiological, microbiological and clinical features. The results validated the potency of LNZ against enterococcal infections, with a sustained susceptibility rate of 99.8% in ZAAPS and 99.2% in LEADER surveillance programmes. Patients with LRE had been predominantly exposed to LNZ prior to isolation of LRE, with a mean treatment duration of 29.8±48.8days for Enterococcus faecalis and 23.1±21.4days for Enterococcus faecium. Paradoxically, LRE could also develop in patients without prior LNZ exposure. LNZ resistance was attributed to 23S rRNA (G2576T) mutations (51.2% of E. faecalis and 80.5% of E. faecium) as well as presence of the cfr gene (4.7% and 4.8%, respectively), which could transfer horizontally among the strains. In addition to the cfr gene, 32 cases of optrA-positive LRE were identified. Further study is required to determine the prevalence of novel resistance genes. The emergence of LRE thus hampers the treatment of such infections, which warrants worldwide surveillance.}, }
@article {pmid29100762, year = {2017}, author = {Novick, RP and Ram, G}, title = {Staphylococcal pathogenicity islands-movers and shakers in the genomic firmament.}, journal = {Current opinion in microbiology}, volume = {38}, number = {}, pages = {197-204}, pmid = {29100762}, issn = {1879-0364}, support = {R01 AI022159/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteriophages/genetics/physiology ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genomic Islands ; *Interspersed Repetitive Sequences ; Staphylococcus/*genetics/*pathogenicity ; Transduction, Genetic ; Virulence Factors/*genetics/*metabolism ; }, abstract = {The staphylococcal pathogenicity islands (SaPIs) are highly mobile 15kb genomic islands that carry superantigen genes and other virulence factors and are mobilized by helper phages. Helper phages counteract the SaPI repressor to induce the SaPI replication cycle, resulting in encapsidation in phage like particles, enabling high frequency transfer. The SaPIs split from a protophage lineage in the distant past, have evolved a variety of novel and salient features, and have become an invaluable component of the staphylococcal genome. This review focuses on recent studies describing three different mechanisms of SaPI interference with helper phage reproduction and other studies demonstrating that helper phage mutations to resistance against this interference impact phage evolution. Also described are recent results showing that SaPIs contribute in a major way to lateral transfer of host genes as well as enabling their own transfer. SaPI-like elements, readily identifiable in the bacterial genome, are widespread throughout the Gram-positive cocci, though functionality has thus far been demonstrated for only a single one of these.}, }
@article {pmid29099338, year = {2018}, author = {Van Melderen, L and Jurenas, D and Garcia-Pino, A}, title = {Messing up translation from the start: How AtaT inhibits translation initiation in E. coli.}, journal = {RNA biology}, volume = {15}, number = {3}, pages = {303-307}, pmid = {29099338}, issn = {1555-8584}, mesh = {Acetylation ; Acyltransferases/genetics/*metabolism ; Escherichia coli/genetics/*metabolism ; Escherichia coli Proteins/chemistry/genetics/metabolism ; Methionine/chemistry ; Models, Molecular ; *Peptide Chain Initiation, Translational ; Prokaryotic Initiation Factor-2/metabolism ; RNA, Transfer, Met/*chemistry ; }, abstract = {Toxin-antitoxin systems (TA) are widespread in bacteria and archea. They are commonly found in chromosomes and mobile genetic elements. These systems move from different genomic locations and bacterial hosts through horizontal gene transfer, using mobile elements as vehicles. Their potential roles in bacterial physiology are still a matter of debate in the field. The mechanisms of action of different toxin families have been deciphered at the molecular level. Intriguingly, the vast majority of these toxins target protein synthesis. They use a variety of molecular mechanisms and inhibit nearly every step of the translation process. Recently, we have identified a novel toxin, AtaT, presenting acetyltransferase activity. [1] Our work uncovered the molecular activity of AtaT: it specifically acetylates the methionine moiety on the initiator Met-tRNAfMet. This modification drastically impairs recognition by initiation factor 2 (IF2), thereby inhibiting the initiation step of translation.}, }
@article {pmid29098760, year = {2017}, author = {Herbold, CW and Lehtovirta-Morley, LE and Jung, MY and Jehmlich, N and Hausmann, B and Han, P and Loy, A and Pester, M and Sayavedra-Soto, LA and Rhee, SK and Prosser, JI and Nicol, GW and Wagner, M and Gubry-Rangin, C}, title = {Ammonia-oxidising archaea living at low pH: Insights from comparative genomics.}, journal = {Environmental microbiology}, volume = {19}, number = {12}, pages = {4939-4952}, pmid = {29098760}, issn = {1462-2920}, support = {294343/ERC_/European Research Council/International ; P 23117/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Ammonia/*metabolism ; Base Sequence ; Biological Evolution ; DNA, Archaeal/genetics ; Euryarchaeota/*genetics/*metabolism ; Gene Transfer, Horizontal ; Genome, Archaeal/*genetics ; Genomics ; Nitrification/*physiology ; Oxidation-Reduction ; Phylogeny ; Proteomics ; Sequence Analysis, DNA ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Obligate acidophilic members of the thaumarchaeotal genus Candidatus Nitrosotalea play an important role in nitrification in acidic soils, but their evolutionary and physiological adaptations to acidic environments are still poorly understood, with only a single member of this genus (Ca. N. devanaterra) having its genome sequenced. In this study, we sequenced the genomes of two additional cultured Ca. Nitrosotalea strains, extracted an almost complete Ca. Nitrosotalea metagenome-assembled genome from an acidic fen, and performed comparative genomics of the four Ca. Nitrosotalea genomes with 19 other archaeal ammonia oxidiser genomes. Average nucleotide and amino acid identities revealed that the four Ca. Nitrosotalea strains represent separate species within the genus. The four Ca. Nitrosotalea genomes contained a core set of 103 orthologous gene families absent from all other ammonia-oxidizing archaea and, for most of these gene families, expression could be demonstrated in laboratory culture or the environment via proteomic or metatranscriptomic analyses respectively. Phylogenetic analyses indicated that four of these core gene families were acquired by the Ca. Nitrosotalea common ancestor via horizontal gene transfer from acidophilic representatives of Euryarchaeota. We hypothesize that gene exchange with these acidophiles contributed to the competitive success of the Ca. Nitrosotalea lineage in acidic environments.}, }
@article {pmid29096001, year = {2017}, author = {Schmickl, R and Marburger, S and Bray, S and Yant, L}, title = {Hybrids and horizontal transfer: introgression allows adaptive allele discovery.}, journal = {Journal of experimental botany}, volume = {68}, number = {20}, pages = {5453-5470}, doi = {10.1093/jxb/erx297}, pmid = {29096001}, issn = {1460-2431}, support = {BBS/E/J/000PR9773/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Adaptation, Biological ; *Alleles ; Gene Flow/*genetics ; Gene Transfer, Horizontal/genetics ; Hybridization, Genetic/*genetics ; Plants/*genetics ; }, abstract = {Evolution has devised countless remarkable solutions to diverse challenges. Understanding the mechanistic basis of these solutions provides insights into how biological systems can be subtly tweaked without maladaptive consequences. The knowledge gained from illuminating these mechanisms is equally important to our understanding of fundamental evolutionary mechanisms as it is to our hopes of developing truly rational plant breeding and synthetic biology. In particular, modern population genomic approaches are proving very powerful in the detection of candidate alleles for mediating consequential adaptations that can be tested functionally. Especially striking are signals gained from contexts involving genetic transfers between populations, closely related species, or indeed between kingdoms. Here we discuss two major classes of these scenarios, adaptive introgression and horizontal gene flow, illustrating discoveries made across kingdoms.}, }
@article {pmid29095687, year = {2017}, author = {Hage, E and Dhingra, A and Liebert, UG and Bergs, S and Ganzenmueller, T and Heim, A}, title = {Three novel, multiple recombinant types of species of human mastadenovirus D (HAdV-D 73, 74 &amp; 75) isolated from diarrhoeal faeces of immunocompromised patients.}, journal = {The Journal of general virology}, volume = {98}, number = {12}, pages = {3037-3045}, doi = {10.1099/jgv.0.000968}, pmid = {29095687}, issn = {1465-2099}, abstract = {Species D is the largest of the seven species of human mastadenoviruses (HAdV), but few of its multiple types are associated with asevere disease, e.g. epidemic keratoconjunctivitis. Many other types are hardly ever associated with significant diseases in immunocompetent patients, but have been isolated from the diarrhoeal faeces of terminal AIDS patients suggesting their role as opportunistic pathogens. Three novel HAdV-D strains were isolated from the faeces of three immunocompromised adult patients (clinical diagnoses: lymphoma, myelodysplastic syndrome and AIDS CDC3B, respectively). These strains were not typeable by imputed serology of the hexon and fibre gene and therefore complete genomic sequences were generated by next-generation sequencing (NGS). All three strains were multiple recombinants and fulfilled the criteria for designation as types 73, 74 and 75 with the penton/hexon/fibre genotype codes P67H45F27, P70H74F51 and P75H26F29, respectively. A novel genomic backbone and also a novel hexon neutralization epitope sequence were discovered in type 74, and a novel penton sequence in type 75. At the complete genome level, types 73, 74 and 75 were closely related neither to each other nor to type 70, which was previously isolated in the same region. However, these four HAdV-D types were closely related to each other in single genes and gene regions, e.g. penton, E1 and E4 due to recombination events in their phylogeny. In conclusion, regional co-circulation of opportunistic HAdV-D types facilitated co- and super-infections, which are essential for homologous recombination, and thus resulted in the evolution of novel genotypes by lateral gene transfer.}, }
@article {pmid29091227, year = {2017}, author = {AbuOun, M and Stubberfield, EJ and Duggett, NA and Kirchner, M and Dormer, L and Nunez-Garcia, J and Randall, LP and Lemma, F and Crook, DW and Teale, C and Smith, RP and Anjum, MF}, title = {mcr-1 and mcr-2 variant genes identified in Moraxella species isolated from pigs in Great Britain from 2014 to 2015.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {72}, number = {10}, pages = {2745-2749}, pmid = {29091227}, issn = {1460-2091}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Colistin/pharmacology ; DNA Transposable Elements/genetics ; Drug Resistance, Bacterial/genetics ; Escherichia coli/drug effects ; Escherichia coli Proteins/genetics ; Farms ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genetic Variation/*genetics ; Humans ; Membrane Proteins/genetics ; Microbial Sensitivity Tests ; Moraxella/classification/drug effects/*genetics/*isolation &amp; purification ; Moraxellaceae Infections/epidemiology/microbiology/transmission/veterinary ; Phylogeny ; Sus scrofa/microbiology ; Swine ; Swine Diseases/microbiology ; United Kingdom/epidemiology ; beta-Lactamases/genetics ; }, abstract = {OBJECTIVES: To determine the occurrence of mcr-1 and mcr-2 genes in Gram-negative bacteria isolated from healthy pigs in Great Britain.<br><br>METHODS: Gram-negative bacteria (n&#x2009;=&#x2009;657) isolated from pigs between 2014 and 2015 were examined by WGS.<br><br>RESULTS: Variants of mcr-1 and mcr-2 were identified in Moraxella spp. isolated from pooled caecal contents of healthy pigs at slaughter collected from six farms in Great Britain. Other bacteria, including Escherichia coli from the same farms, were not detected harbouring mcr-1 or mcr-2. A Moraxella porci-like isolate, MSG13-C03, harboured MCR-1.10 with 98.7% identity to MCR-1, and a Moraxella pluranimalium-like isolate, MSG47-C17, harboured an MCR-2.2 variant with 87.9% identity to MCR-2, from E. coli; the isolates had colistin MICs of 1-2&#x2009;mg/L. No intact insertion elements were identified in either MSG13-C03 or MSG47-C17, although MSG13-C03 harboured the conserved nucleotides abutting the ISApl1 composite transposon found in E. coli plasmids and the intervening &#x223c;2.6&#x2009;kb fragment showed 97% identity. Six Moraxella osloensis isolates were positive for phosphoethanolamine transferase (EptA). They shared 62%-64.5% identity to MCR-1 and MCR-2, with colistin MICs from 2 to 4&#x2009;mg/L. Phylogenetic analysis indicated that MCR and EptA have evolved from a common ancestor. In addition to mcr, the &#x3b2;-lactamase gene, blaBRO-1, was found in both isolates, whilst the tetracycline resistance gene, tetL, was found in MSG47-C17.<br><br>CONCLUSIONS: Our results add further evidence for the mobilization of the mcr-pap2 unit from Moraxella via composite transposons leading to its global dissemination. The presence of mcr-pap2 from recent Moraxella isolates indicates they may comprise a reservoir for mcr.}, }
@article {pmid29091031, year = {2017}, author = {Cooper, RM and Tsimring, L and Hasty, J}, title = {Inter-species population dynamics enhance microbial horizontal gene transfer and spread of antibiotic resistance.}, journal = {eLife}, volume = {6}, number = {}, pages = {}, pmid = {29091031}, issn = {2050-084X}, support = {P50 GM085764/GM/NIGMS NIH HHS/United States ; R01 GM069811/GM/NIGMS NIH HHS/United States ; }, mesh = {Acinetobacter/genetics/*physiology ; *Antibiosis ; *Bacteriolysis ; *Drug Resistance, Bacterial ; Escherichia coli/genetics/*physiology ; *Gene Transfer, Horizontal ; Population Dynamics ; }, abstract = {Horizontal gene transfer (HGT) plays a major role in the spread of antibiotic resistance. Of particular concern are Acinetobacter baumannii bacteria, which recently emerged as global pathogens, with nosocomial mortality rates reaching 19-54% (Centers for Disease Control and Prevention, 2013; Joly Guillou, 2005; Talbot et al., 2006). Acinetobacter gains antibiotic resistance remarkably rapidly (Antunes et al., 2014; Joly Guillou, 2005), with multi drug-resistance (MDR) rates exceeding 60% (Antunes et al., 2014; Centers for Disease Control and Prevention, 2013). Despite growing concern (Centers for Disease Control and Prevention, 2013; Talbot et al., 2006), the mechanisms underlying this extensive HGT remain poorly understood (Adams et al., 2008; Fournier et al., 2006; Imperi et al., 2011; Ramirez et al., 2010; Wilharm et al., 2013). Here, we show bacterial predation by Acinetobacter baylyi increases cross-species HGT by orders of magnitude, and we observe predator cells functionally acquiring adaptive resistance genes from adjacent prey. We then develop a population-dynamic model quantifying killing and HGT on solid surfaces. We show DNA released via cell lysis is readily available for HGT and may be partially protected from the environment, describe the effects of cell density, and evaluate potential environmental inhibitors. These findings establish a framework for understanding, quantifying, and combating HGT within the microbiome and the emergence of MDR super-bugs.}, }
@article {pmid29090447, year = {2018}, author = {Arsène-Ploetze, F and Chiboub, O and Lièvremont, D and Farasin, J and Freel, KC and Fouteau, S and Barbe, V}, title = {Adaptation in toxic environments: comparative genomics of loci carrying antibiotic resistance genes derived from acid mine drainage waters.}, journal = {Environmental science and pollution research international}, volume = {25}, number = {2}, pages = {1470-1483}, pmid = {29090447}, issn = {1614-7499}, support = {ANR-12-ADAP-0013//Agence Nationale de la Recherche/ ; ANR-12-ADAP-0013//Agence Nationale de la Recherche/ ; }, mesh = {Acids/pharmacology ; Adaptation, Biological/*genetics ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics ; Databases, Genetic ; Drug Resistance, Microbial/drug effects/*genetics ; *Genomics ; Metals, Heavy/pharmacology ; *Mining ; Wastewater/*microbiology ; }, abstract = {Several studies have suggested the existence of a close relationship between antibiotic-resistant phenotypes and resistance to other toxic compounds such as heavy metals, which involve co-resistance or cross-resistance mechanisms. A metagenomic library was previously constructed in Escherichia coli with DNA extracted from the bacterial community inhabiting an acid mine drainage (AMD) site highly contaminated with heavy metals. Here, we conducted a search for genes involved in antibiotic resistance using this previously constructed library. In particular, resistance to antibiotics was observed among five clones carrying four different loci originating from CARN5 and CARN2, two genomes reconstructed from the metagenomic data. Among the three CARN2 loci, two carry genes homologous to those previously proposed to be involved in antibiotic resistance. The third CARN2 locus carries a gene encoding a membrane transporter with an unknown function and was found to confer bacterial resistance to rifampicin, gentamycin, and kanamycin. The genome of Thiomonas delicata DSM 16361 and Thiomonas sp. X19 were sequenced in this study. Homologs of genes carried on these three CARN2 loci were found in these genomes, two of these loci were found in genomic islands. Together, these findings confirm that AMD environments contaminated with several toxic metals also constitute habitats for bacteria that function as reservoirs for antibiotic resistance genes.}, }
@article {pmid29090367, year = {2018}, author = {Brothwell, JA and Muramatsu, MK and Zhong, G and Nelson, DE}, title = {Advances and Obstacles in the Genetic Dissection of Chlamydial Virulence.}, journal = {Current topics in microbiology and immunology}, volume = {412}, number = {}, pages = {133-158}, pmid = {29090367}, issn = {0070-217X}, support = {R01 AI121989/AI/NIAID NIH HHS/United States ; R21 AI105712/AI/NIAID NIH HHS/United States ; R01 AI116706/AI/NIAID NIH HHS/United States ; R56 AI099278/AI/NIAID NIH HHS/United States ; R01 AI047997/AI/NIAID NIH HHS/United States ; R01 AI099278/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Chlamydia/*genetics/*pathogenicity ; Gene Transfer, Horizontal ; Genome, Bacterial/genetics ; Genomics ; Virulence ; Virulence Factors/genetics/metabolism ; }, abstract = {Obligate intracellular pathogens in the family Chlamydiaceae infect taxonomically diverse eukaryotes ranging from amoebae to mammals. However, many fundamental aspects of chlamydial cell biology and pathogenesis remain poorly understood. Genetic dissection of chlamydial biology has historically been hampered by a lack of genetic tools. Exploitation of the ability of chlamydia to recombine genomic material by lateral gene transfer (LGT) ushered in a new era in chlamydia research. With methods to map mutations in place, genetic screens were able to assign functions and phenotypes to specific chlamydial genes. Development of an approach for stable transformation of chlamydia also provided a mechanism for gene delivery and platforms for disrupting chromosomal genes. Here, we explore how these and other tools have been used to test hypotheses concerning the functions of known chlamydial virulence factors and discover the functions of completely uncharacterized genes. Refinement and extension of the existing genetic tools to additional Chlamydia spp. will substantially advance understanding of the biology and pathogenesis of this important group of pathogens.}, }
@article {pmid29089611, year = {2017}, author = {Kumar, P and Bag, S and Ghosh, TS and Dey, P and Dayal, M and Saha, B and Verma, J and Pant, A and Saxena, S and Desigamani, A and Rana, P and Kumar, D and Sharma, NC and Hanpude, P and Maiti, TK and Mukhopadhyay, AK and Bhadra, RK and Nair, GB and Ramamurthy, T and Das, B}, title = {Molecular Insights into Antimicrobial Resistance Traits of Multidrug Resistant Enteric Pathogens isolated from India.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {14468}, pmid = {29089611}, issn = {2045-2322}, support = {001/WHO_/World Health Organization/International ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Bacterial Infections/drug therapy ; Drug Resistance, Bacterial/*drug effects ; Drug Resistance, Multiple/*genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Gastrointestinal Microbiome/drug effects/*genetics ; Gram-Negative Bacteria/drug effects ; Humans ; India ; Microbial Sensitivity Tests ; Phenotype ; Whole Genome Sequencing ; }, abstract = {Emergence of antimicrobial resistant Gram-negative bacteria has created a serious global health crisis and threatens the effectiveness of most, if not all, antibiotics commonly used to prevent and treat bacterial infections. There is a dearth of detailed studies on the prevalence of antimicrobial resistance (AMR) patterns in India. Here, we have isolated and examined AMR patterns of 654 enteric pathogens and investigated complete genome sequences of isolates from six representative genera, which in aggregate encode resistance against 22 antibiotics representing nine distinct drug classes. This study revealed that ~97% isolates are resistant against ≥2 antibiotics, ~24% isolates are resistant against ≥10 antibiotics and ~3% isolates are resistant against ≥15 antibiotics. Analyses of whole genome sequences of six extensive drug resistant enteric pathogens revealed presence of multiple mobile genetic elements, which are physically linked with resistance traits. These elements are therefore appearing to be responsible for disseminating drug resistance among bacteria through horizontal gene transfer. The present study provides insights into the linkages between the resistance patterns to certain antibiotics and their usage in India. The findings would be useful to understand the genetics of resistance traits and severity of and difficulty in tackling AMR enteric pathogens.}, }
@article {pmid29087008, year = {2017}, author = {Ludvigsen, J and Porcellato, D and L'Abée-Lund, TM and Amdam, GV and Rudi, K}, title = {Geographically widespread honeybee-gut symbiont subgroups show locally distinct antibiotic-resistant patterns.}, journal = {Molecular ecology}, volume = {26}, number = {23}, pages = {6590-6607}, doi = {10.1111/mec.14392}, pmid = {29087008}, issn = {1365-294X}, mesh = {Animals ; Arizona ; Base Composition ; Bees/*microbiology ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/*genetics ; Gammaproteobacteria/*genetics ; Gastrointestinal Tract/microbiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome Size ; Geography ; Microbiota ; Neisseriaceae/*genetics ; Norway ; Phylogeny ; Symbiosis ; }, abstract = {How long-term antibiotic treatment affects host bacterial associations is still largely unknown. The honeybee-gut microbiota has a simple composition, so we used this gut community to investigate how long-term antibiotic treatment affects host-associated microbiota. We investigated the phylogenetic relatedness, genomic content (GC percentage, genome size, number of genes and CRISPR) and antibiotic-resistant genes (ARG) for strains from two abundant members of the honeybee core gut microbiota (Gilliamella apicola and Snodgrassella alvi). Domesticated honeybees are subjected to geographically different management policies, so we used two research apiaries, representing different antibiotic treatment regimens in their apiculture: low antibiotic usage (Norway) and high antibiotic usage (Arizona, USA). We applied whole-genome shotgun sequencing on 48 G. apicola and 22 S. alvi. We identified three predominating subgroups of G. apicola in honeybees from both Norway and Arizona. For G. apicola, genetic content substantially varied between subgroups and distance similarity calculations showed similarity discrepancy between subgroups. Functional differences between subgroups, such as pectin-degrading enzymes (G. apicola), were also identified. In addition, we identified horizontal gene transfer (HGT) of transposon (Tn10)-associated tetracycline resistance (Tet B) across the G. apicola subgroups in the Arizonan honeybees, using interspace polymorphisms in the Tet B determinant. Our results support that honeybee-gut symbiont subgroups can resist long-term antibiotic treatment and maintain functionality through acquisition of geographically distinct antibiotic-resistant genes by HGT.}, }
@article {pmid29085912, year = {2017}, author = {Antic, I and Brothers, KM and Stolzer, M and Lai, H and Powell, E and Eutsey, R and Cuevas, RA and Miao, X and Kowalski, RP and Shanks, RMQ and Durand, D and Hiller, NL}, title = {Gene Acquisition by a Distinct Phyletic Group within Streptococcus pneumoniae Promotes Adhesion to the Ocular Epithelium.}, journal = {mSphere}, volume = {2}, number = {5}, pages = {}, pmid = {29085912}, issn = {2379-5042}, support = {F32 EY024785/EY/NEI NIH HHS/United States ; F32 GM066658/GM/NIGMS NIH HHS/United States ; R01 EY027331/EY/NEI NIH HHS/United States ; }, abstract = {Streptococcus pneumoniae (pneumococcus) displays broad tissue tropism and infects multiple body sites in the human host. However, infections of the conjunctiva are limited to strains within a distinct phyletic group with multilocus sequence types ST448, ST344, ST1186, ST1270, and ST2315. In this study, we sequenced the genomes of six pneumococcal strains isolated from eye infections. The conjunctivitis isolates are grouped in a distinct phyletic group together with a subset of nasopharyngeal isolates. The keratitis (infection of the cornea) and endophthalmitis (infection of the vitreous body) isolates are grouped with the remainder of pneumococcal strains. Phenotypic characterization is consistent with morphological differences associated with the distinct phyletic group. Specifically, isolates from the distinct phyletic group form aggregates in planktonic cultures and chain-like structures in biofilms grown on abiotic surfaces. To begin to investigate the association between genotype and epidemiology, we focused on a predicted surface-exposed adhesin (SspB) encoded exclusively by this distinct phyletic group. Phylogenetic analysis of the gene encoding SspB in the context of a streptococcal species tree suggests that sspB was acquired by lateral gene transfer from Streptococcus suis. Furthermore, an sspB deletion mutant displays decreased adherence to cultured cells from the ocular epithelium compared to the isogenic wild-type and complemented strains. Together these findings suggest that acquisition of genes from outside the species has contributed to pneumococcal tissue tropism by enhancing the ability of a subset of strains to infect the ocular epithelium causing conjunctivitis. IMPORTANCE Changes in the gene content of pathogens can modify their ability to colonize and/or survive in different body sites in the human host. In this study, we investigate a gene acquisition event and its role in the pathogenesis of Streptococccus pneumoniae (pneumococcus). Our findings suggest that the gene encoding the predicted surface protein SspB has been transferred from Streptococcus suis (a distantly related streptococcal species) into a distinct set of pneumococcal strains. This group of strains distinguishes itself from the remainder of pneumococcal strains by extensive differences in genomic composition and by the ability to cause conjunctivitis. We find that the presence of sspB increases adherence of pneumococcus to the ocular epithelium. Thus, our data support the hypothesis that a subset of pneumococcal strains has gained genes from neighboring species that enhance their ability to colonize the epithelium of the eye, thus expanding into a new niche.}, }
@article {pmid29085354, year = {2017}, author = {Águila-Arcos, S and Álvarez-Rodríguez, I and Garaiyurrebaso, O and Garbisu, C and Grohmann, E and Alkorta, I}, title = {Biofilm-Forming Clinical Staphylococcus Isolates Harbor Horizontal Transfer and Antibiotic Resistance Genes.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2018}, pmid = {29085354}, issn = {1664-302X}, abstract = {Infections caused by staphylococci represent a medical concern, especially when related to biofilms located in implanted medical devices, such as prostheses and catheters. Unfortunately, their frequent resistance to high doses of antibiotics makes the treatment of these infections a difficult task. Moreover, biofilms represent a hot spot for horizontal gene transfer (HGT) by bacterial conjugation. In this work, 25 biofilm-forming clinical staphylococcal isolates were studied. We found that Staphylococcus epidermidis isolates showed a higher biofilm-forming capacity than Staphylococcus aureus isolates. Additionally, horizontal transfer and relaxase genes of two common staphylococcal plasmids, pSK41 and pT181, were detected in all isolates. In terms of antibiotic resistance genes, aac6-aph2a, ermC, and tetK genes, which confer resistance to gentamicin, erythromycin, and tetracycline, respectively, were the most prevalent. The horizontal transfer and antibiotic resistance genes harbored on these staphylococcal clinical strains isolated from biofilms located in implanted medical devices points to the potential risk of the development and dissemination of multiresistant bacteria.}, }
@article {pmid29084346, year = {2018}, author = {Chen, JY and Liu, C and Gui, YJ and Si, KW and Zhang, DD and Wang, J and Short, DPG and Huang, JQ and Li, NY and Liang, Y and Zhang, WQ and Yang, L and Ma, XF and Li, TG and Zhou, L and Wang, BL and Bao, YM and Subbarao, KV and Zhang, GY and Dai, XF}, title = {Comparative genomics reveals cotton-specific virulence factors in flexible genomic regions in Verticillium dahliae and evidence of horizontal gene transfer from Fusarium.}, journal = {The New phytologist}, volume = {217}, number = {2}, pages = {756-770}, pmid = {29084346}, issn = {1469-8137}, mesh = {Base Sequence ; Evolution, Molecular ; Fusarium/*genetics ; *Gene Transfer, Horizontal ; *Genome, Fungal ; *Genomics ; Gossypium/*microbiology ; Host-Pathogen Interactions/genetics ; Lactuca/microbiology ; Solanum lycopersicum/microbiology ; Multigene Family ; Phylogeny ; Species Specificity ; Synteny/genetics ; Verticillium/*genetics/*pathogenicity ; Virulence/genetics ; Virulence Factors/*metabolism ; }, abstract = {Verticillium dahliae isolates are most virulent on the host from which they were originally isolated. Mechanisms underlying these dominant host adaptations are currently unknown. We sequenced the genome of V. dahliae Vd991, which is highly virulent on its original host, cotton, and performed comparisons with the reference genomes of JR2 (from tomato) and VdLs.17 (from lettuce). Pathogenicity-related factor prediction, orthology and multigene family classification, transcriptome analyses, phylogenetic analyses, and pathogenicity experiments were performed. The Vd991 genome harbored several exclusive, lineage-specific (LS) genes within LS regions (LSRs). Deletion mutants of the seven genes within one LSR (G-LSR2) in Vd991 were less virulent only on cotton. Integration of G-LSR2 genes individually into JR2 and VdLs.17 resulted in significantly enhanced virulence on cotton but did not affect virulence on tomato or lettuce. Transcription levels of the seven LS genes in Vd991 were higher during the early stages of cotton infection, as compared with other hosts. Phylogenetic analyses suggested that G-LSR2 was acquired from Fusarium oxysporum f. sp. vasinfectum through horizontal gene transfer. Our results provide evidence that horizontal gene transfer from Fusarium to Vd991 contributed significantly to its adaptation to cotton and may represent a significant mechanism in the evolution of an asexual plant pathogen.}, }
@article {pmid29084254, year = {2017}, author = {Liu, H and Zhang, L and Meng, A and Zhang, J and Xie, M and Qin, Y and Faulk, DC and Zhang, B and Yang, S and Qiu, L}, title = {Isolation and molecular identification of endophytic diazotrophs from seeds and stems of three cereal crops.}, journal = {PloS one}, volume = {12}, number = {10}, pages = {e0187383}, pmid = {29084254}, issn = {1932-6203}, mesh = {Crops, Agricultural/*microbiology ; Edible Grain/*microbiology ; Endophytes/genetics/*isolation &amp; purification ; Genes, Plant ; Phylogeny ; Plant Stems/*microbiology ; RNA, Ribosomal, 16S/genetics ; Random Amplified Polymorphic DNA Technique ; Seeds/*microbiology ; }, abstract = {Ten strains of endophytic diazotroph were isolated and identified from the plants collected from three different agricultural crop species, wheat, rice and maize, using the nitrogen-free selective isolation conditions. The nitrogen-fixing ability of endophytic diazotroph was verified by the nifH-PCR assay that showed positive nitrogen fixation ability. These identified strains were classified by 879F-RAPD and 16S rRNA sequence analysis. RAPD analyses revealed that the 10 strains were clustered into seven 879F-RAPD groups, suggesting a clonal origin. 16S rRNA sequencing analyses allowed the assignment of the 10 strains to known groups of nitrogen-fixing bacteria, including organisms from the genera Paenibacillus, Enterobacter, Klebsiella and Pantoea. These representative genus are not endophytic diazotrophs in the conventional sense. They may have obtained nitrogen fixation ability through lateral gene transfer, however, the evolutionary forces of lateral gene transfer are not well known. Molecular identification results from 16S rRNA analyses were also confirmed by morphological and biochemical data. The test strains SH6A and MZB showed positive effect on the growth of plants.}, }
@article {pmid29081464, year = {2017}, author = {Shin, E and Mduma, S and Keyyu, J and Fyumagwa, R and Lee, Y}, title = {An Investigation of Enterococcus Species Isolated from the African Buffalo (Syncerus caffer) in Serengeti National Park, Tanzania.}, journal = {Microbes and environments}, volume = {32}, number = {4}, pages = {402-406}, pmid = {29081464}, issn = {1347-4405}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Buffaloes/*microbiology ; Drug Resistance, Bacterial/genetics ; Enterococcus/*classification/*drug effects/genetics/isolation &amp; purification ; Gene Transfer, Horizontal/genetics ; Humans ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Parks, Recreational ; RNA, Ribosomal, 16S/genetics ; Tanzania ; }, abstract = {We isolated Enterococcus species that colonized in the African buffalo (Syncerus caffer) in order to investigate their genetic relatedness and antimicrobial susceptibility. A total of 219 isolates were obtained and a 16S rRNA gene sequence analysis showed they were classified into Enterococcus avium, E. casseliflavus, E. faecalis, E. faecium, E. hirae, or E. mundtii. Multilocus sequence typing of E. faecalis and E. faecium isolates indicated that some of the isolates showed an evolutionary distance that was far from the primary founders. The antimicrobial susceptibility of the enterococcal isolates suggested that the significant transmission of antimicrobial resistance via human intervention had not yet occurred.}, }
@article {pmid29080779, year = {2018}, author = {Steel, M and Kauffman, S}, title = {A note on random catalytic branching processes.}, journal = {Journal of theoretical biology}, volume = {437}, number = {}, pages = {222-224}, doi = {10.1016/j.jtbi.2017.10.024}, pmid = {29080779}, issn = {1095-8541}, mesh = {*Algorithms ; Artificial Cells/*metabolism ; Computer Simulation ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Bacterial/genetics ; Markov Chains ; *Models, Genetic ; Origin of Life ; Prokaryotic Cells/*metabolism ; }, abstract = {A variety of evolutionary processes in biology can be viewed as settings where organisms 'catalyse' the formation of new types of organisms. One example, relevant to the origin of life, is where transient biological colonies (e.g. prokaryotes or protocells) give rise to new colonies via lateral gene transfer. In this short note, we describe and analyse a simple random process which models such settings. By applying theory from general birth-death processes, we describe how the survival of a population under catalytic diversification depends on interplay of the catalysis rate and the initial population size. We also note how such process can also be viewed within the framework of 'self-sustaining autocatalytic networks'.}, }
@article {pmid29079617, year = {2018}, author = {Pantůček, R and Sedláček, I and Indráková, A and Vrbovská, V and Mašlaňová, I and Kovařovic, V and Švec, P and Králová, S and Krištofová, L and Kekláková, J and Petráš, P and Doškař, J}, title = {Staphylococcus edaphicus sp. nov., Isolated in Antarctica, Harbors the mecC Gene and Genomic Islands with a Suspected Role in Adaptation to Extreme Environments.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {2}, pages = {}, pmid = {29079617}, issn = {1098-5336}, mesh = {Adaptation, Biological/*genetics ; Antarctic Regions ; *Extreme Cold ; *Extreme Environments ; Genes, Bacterial/*physiology ; Genomic Islands/*physiology ; Staphylococcus/*classification/genetics/physiology ; }, abstract = {Two Gram-stain-positive, coagulase-negative staphylococcal strains were isolated from abiotic sources comprising stone fragments and sandy soil in James Ross Island, Antarctica. Here, we describe properties of a novel species of the genus Staphylococcus that has a 16S rRNA gene sequence nearly identical to that of Staphylococcus saprophyticus However, compared to S. saprophyticus and the next closest relatives, the new species demonstrates considerable phylogenetic distance at the whole-genome level, with an average nucleotide identity of <85% and inferred DNA-DNA hybridization of <30%. It forms a separate branch in the S. saprophyticus phylogenetic clade as confirmed by multilocus sequence analysis of six housekeeping genes, rpoB, hsp60, tuf, dnaJ, gap, and sod Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and key biochemical characteristics allowed these bacteria to be distinguished from their nearest phylogenetic neighbors. In contrast to S. saprophyticus subsp. saprophyticus, the novel strains are pyrrolidonyl arylamidase and β-glucuronidase positive and β-galactosidase negative, nitrate is reduced, and acid produced aerobically from d-mannose. Whole-genome sequencing of the 2.69-Mb large chromosome revealed the presence of a number of mobile genetic elements, including the 27-kb pseudo-staphylococcus cassette chromosome mec of strain P5085[T] (ψSCCmecP5085), harboring the mecC gene, two composite phage-inducible chromosomal islands probably essential to adaptation to extreme environments, and one complete and one defective prophage. Both strains are resistant to penicillin G, ampicillin, ceftazidime, methicillin, cefoxitin, and fosfomycin. We hypothesize that antibiotic resistance might represent an evolutionary advantage against beta-lactam producers, which are common in a polar environment. Based on these results, a novel species of the genus Staphylococcus is described and named Staphylococcus edaphicus sp. nov. The type strain is P5085[T] (= CCM 8730[T] = DSM 104441[T]).IMPORTANCE The description of Staphylococcus edaphicus sp. nov. enables the comparison of multidrug-resistant staphylococci from human and veterinary sources evolved in the globalized world to their geographically distant relative from the extreme Antarctic environment. Although this new species was not exposed to the pressure of antibiotic treatment in human or veterinary practice, mobile genetic elements carrying antimicrobial resistance genes were found in the genome. The genomic characteristics presented here elucidate the evolutionary relationships in the Staphylococcus genus with a special focus on antimicrobial resistance, pathogenicity, and survival traits. Genes encoded on mobile genetic elements were arranged in unique combinations but retained conserved locations for the integration of mobile genetic elements. These findings point to enormous plasticity of the staphylococcal pangenome, shaped by horizontal gene transfer. Thus, S. edaphicus can act not only as a reservoir of antibiotic resistance in a natural environment but also as a mediator for the spread and evolution of resistance genes.}, }
@article {pmid29073157, year = {2017}, author = {Johansen, JR and Mareš, J and Pietrasiak, N and Bohunická, M and Zima, J and Štenclová, L and Hauer, T}, title = {Highly divergent 16S rRNA sequences in ribosomal operons of Scytonema hyalinum (Cyanobacteria).}, journal = {PloS one}, volume = {12}, number = {10}, pages = {e0186393}, pmid = {29073157}, issn = {1932-6203}, mesh = {Cyanobacteria/classification/*genetics ; DNA, Bacterial/genetics/isolation &amp; purification ; Nucleic Acid Conformation ; *Operon ; Phylogeny ; Promoter Regions, Genetic ; RNA, Bacterial/chemistry/*genetics ; RNA, Ribosomal, 16S/chemistry/*genetics ; Ribosomes/*metabolism ; }, abstract = {A highly divergent 16S rRNA gene was found in one of the five ribosomal operons present in a species complex currently circumscribed as Scytonema hyalinum (Nostocales, Cyanobacteria) using clone libraries. If 16S rRNA sequence macroheterogeneity among ribosomal operons due to insertions, deletions or truncation is excluded, the sequence heterogeneity observed in S. hyalinum was the highest observed in any prokaryotic species thus far (7.3-9.0%). The secondary structure of the 16S rRNA molecules encoded by the two divergent operons was nearly identical, indicating possible functionality. The 23S rRNA gene was examined for a few strains in this complex, and it was also found to be highly divergent from the gene in Type 2 operons (8.7%), and likewise had nearly identical secondary structure between the Type 1 and Type 2 operons. Furthermore, the 16S-23S ITS showed marked differences consistent between operons among numerous strains. Both operons have promoter sequences that satisfy consensus requirements for functional prokaryotic transcription initiation. Horizontal gene transfer from another unknown heterocytous cyanobacterium is considered the most likely explanation for the origin of this molecule, but does not explain the ultimate origin of this sequence, which is very divergent from all 16S rRNA sequences found thus far in cyanobacteria. The divergent sequence is highly conserved among numerous strains of S. hyalinum, suggesting adaptive advantage and selective constraint of the divergent sequence.}, }
@article {pmid29073103, year = {2017}, author = {Sansone, P and Savini, C and Kurelac, I and Chang, Q and Amato, LB and Strillacci, A and Stepanova, A and Iommarini, L and Mastroleo, C and Daly, L and Galkin, A and Thakur, BK and Soplop, N and Uryu, K and Hoshino, A and Norton, L and Bonafé, M and Cricca, M and Gasparre, G and Lyden, D and Bromberg, J}, title = {Packaging and transfer of mitochondrial DNA via exosomes regulate escape from dormancy in hormonal therapy-resistant breast cancer.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {43}, pages = {E9066-E9075}, pmid = {29073103}, issn = {1091-6490}, support = {MR/L007339/1/MRC_/Medical Research Council/United Kingdom ; P30 CA008748/CA/NCI NIH HHS/United States ; U01 CA169538/CA/NCI NIH HHS/United States ; }, mesh = {Breast Neoplasms/*drug therapy/*metabolism/pathology ; Cell Line, Tumor ; DNA, Mitochondrial/genetics/*metabolism ; Drug Resistance, Neoplasm/*genetics ; Exosomes/*genetics ; Female ; Fibroblasts/pathology ; Gene Transfer, Horizontal ; Genome, Mitochondrial/genetics ; Humans ; MCF-7 Cells ; NADH Dehydrogenase/genetics ; Oxidative Phosphorylation ; Receptors, Estrogen/metabolism ; Xenograft Model Antitumor Assays ; }, abstract = {The horizontal transfer of mtDNA and its role in mediating resistance to therapy and an exit from dormancy have never been investigated. Here we identified the full mitochondrial genome in circulating extracellular vesicles (EVs) from patients with hormonal therapy-resistant (HTR) metastatic breast cancer. We generated xenograft models of HTR metastatic disease characterized by EVs in the peripheral circulation containing mtDNA. Moreover, these human HTR cells had acquired host-derived (murine) mtDNA promoting estrogen receptor-independent oxidative phosphorylation (OXPHOS). Functional studies identified cancer-associated fibroblast (CAF)-derived EVs (from patients and xenograft models) laden with whole genomic mtDNA as a mediator of this phenotype. Specifically, the treatment of hormone therapy (HT)-naive cells or HT-treated metabolically dormant populations with CAF-derived mtDNA[hi] EVs promoted an escape from metabolic quiescence and HTR disease both in vitro and in vivo. Moreover, this phenotype was associated with the acquisition of EV mtDNA, especially in cancer stem-like cells, expression of EV mtRNA, and restoration of OXPHOS. In summary, we have demonstrated that the horizontal transfer of mtDNA from EVs acts as an oncogenic signal promoting an exit from dormancy of therapy-induced cancer stem-like cells and leading to endocrine therapy resistance in OXPHOS-dependent breast cancer.}, }
@article {pmid29073018, year = {2017}, author = {Nickel, AI and Wäber, NB and Gößringer, M and Lechner, M and Linne, U and Toth, U and Rossmanith, W and Hartmann, RK}, title = {Minimal and RNA-free RNase P in Aquifex aeolicus.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {42}, pages = {11121-11126}, pmid = {29073018}, issn = {1091-6490}, mesh = {Archaea/*enzymology/genetics ; Bacteria/*enzymology/genetics ; Gene Transfer, Horizontal ; Phylogeny ; Ribonuclease P/genetics/isolation &amp; purification/*metabolism ; }, abstract = {RNase P is an essential tRNA-processing enzyme in all domains of life. We identified an unknown type of protein-only RNase P in the hyperthermophilic bacterium Aquifex aeolicus: Without an RNA subunit and the smallest of its kind, the 23-kDa polypeptide comprises a metallonuclease domain only. The protein has RNase P activity in vitro and rescued the growth of Escherichia coli and Saccharomyces cerevisiae strains with inactivations of their more complex and larger endogenous ribonucleoprotein RNase P. Homologs of Aquifex RNase P (HARP) were identified in many Archaea and some Bacteria, of which all Archaea and most Bacteria also encode an RNA-based RNase P; activity of both RNase P forms from the same bacterium or archaeon could be verified in two selected cases. Bioinformatic analyses suggest that A. aeolicus and related Aquificaceae likely acquired HARP by horizontal gene transfer from an archaeon.}, }
@article {pmid29069493, year = {2018}, author = {Gao, D and Chu, Y and Xia, H and Xu, C and Heyduk, K and Abernathy, B and Ozias-Akins, P and Leebens-Mack, JH and Jackson, SA}, title = {Horizontal Transfer of Non-LTR Retrotransposons from Arthropods to Flowering Plants.}, journal = {Molecular biology and evolution}, volume = {35}, number = {2}, pages = {354-364}, pmid = {29069493}, issn = {1537-1719}, mesh = {Animals ; Arachis/*genetics ; Arthropods/*genetics ; Base Sequence ; *Gene Transfer, Horizontal ; Genome, Plant ; Phylogeny ; *Retroelements ; Sequence Homology, Nucleic Acid ; }, abstract = {Even though lateral movements of transposons across families and even phyla within multicellular eukaryotic kingdoms have been found, little is known about transposon transfer between the kingdoms Animalia and Plantae. We discovered a novel non-LTR retrotransposon, AdLINE3, in a wild peanut species. Sequence comparisons and phylogenetic analyses indicated that AdLINE3 is a member of the RTE clade, originally identified in a nematode and rarely reported in plants. We identified RTE elements in 82 plants, spanning angiosperms to algae, including recently active elements in some flowering plants. RTE elements in flowering plants were likely derived from a single family we refer to as An-RTE. Interestingly, An-RTEs show significant DNA sequence identity with non-LTR retroelements from 42 animals belonging to four phyla. Moreover, the sequence identity of RTEs between two arthropods and two plants was higher than that of homologous genes. Phylogenetic and evolutionary analyses of RTEs from both animals and plants suggest that the An-RTE family was likely transferred horizontally into angiosperms from an ancient aphid(s) or ancestral arthropod(s). Notably, some An-RTEs were recruited as coding sequences of functional genes participating in metabolic or other biochemical processes in plants. This is the first potential example of horizontal transfer of transposons between animals and flowering plants. Our findings help to understand exchanges of genetic material between the kingdom Animalia and Plantae and suggest arthropods likely impacted on plant genome evolution.}, }
@article {pmid29069382, year = {2018}, author = {Bengtsson-Palme, J and Kristiansson, E and Larsson, DGJ}, title = {Environmental factors influencing the development and spread of antibiotic resistance.}, journal = {FEMS microbiology reviews}, volume = {42}, number = {1}, pages = {}, pmid = {29069382}, issn = {1574-6976}, mesh = {Bacterial Physiological Phenomena/*genetics ; Drug Resistance, Microbial/*genetics ; *Environment ; *Evolution, Molecular ; }, abstract = {Antibiotic resistance and its wider implications present us with a growing healthcare crisis. Recent research points to the environment as an important component for the transmission of resistant bacteria and in the emergence of resistant pathogens. However, a deeper understanding of the evolutionary and ecological processes that lead to clinical appearance of resistance genes is still lacking, as is knowledge of environmental dispersal barriers. This calls for better models of how resistance genes evolve, are mobilized, transferred and disseminated in the environment. Here, we attempt to define the ecological and evolutionary environmental factors that contribute to resistance development and transmission. Although mobilization of resistance genes likely occurs continuously, the great majority of such genetic events do not lead to the establishment of novel resistance factors in bacterial populations, unless there is a selection pressure for maintaining them or their fitness costs are negligible. To enable preventative measures it is therefore critical to investigate under what conditions and to what extent environmental selection for resistance takes place. In addition, understanding dispersal barriers is not only key to evaluate risks, but also to prevent resistant pathogens, as well as novel resistance genes, from reaching humans.}, }
@article {pmid29069366, year = {2018}, author = {Silva, L and Mourão, J and Grosso, F and Peixe, L}, title = {Uncommon carbapenemase-encoding plasmids in the clinically emergent Acinetobacter pittii.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {73}, number = {1}, pages = {52-56}, doi = {10.1093/jac/dkx364}, pmid = {29069366}, issn = {1460-2091}, mesh = {*Acinetobacter/drug effects/genetics/isolation &amp; purification ; Acinetobacter Infections/*drug therapy/microbiology ; Anti-Bacterial Agents/*therapeutic use ; Bacterial Proteins/*genetics ; Base Sequence ; Carbapenems/*therapeutic use ; Gene Transfer, Horizontal/genetics ; Humans ; Microbial Sensitivity Tests ; Plasmids/*genetics ; Portugal ; Sequence Analysis, DNA ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: Two carbapenemase-carrying plasmids, pLS488 (blaOXA-23) and pLS535 (blaOXA-58) from Acinetobacter pittii clinical isolates, were characterized in this study, including their ability to be transferred to Acinetobacter baumannii.<br><br>METHODS: The clinical isolates were obtained from drainage fluid of a patient with biliary tract cancer and from an exudate of a patient with a hip infection (Portuguese University Hospital, 2012). Isolate characterization included antimicrobial susceptibility tests, carbapenemase production by Blue-Carba, carbapenem-hydrolysing class D &#x3b2;-lactamase (CHDL) gene search by PCR sequencing, ApaI-PFGE, CHDL genetic location and plasmid size by hybridization and WGS. Plasmid transfer was performed by conjugation or electroporation.<br><br>RESULTS: pLS488 constitutes the first conjugative plasmid reported to carry a carbapenem resistance gene in A. pittii and is part of a potential new incompatibility group that might also account for the dissemination of OXA-23 in A. baumannii. pLS535 belongs to the Acinetobacter GR7 incompatibility group and presents a new scaffold for OXA-58. This plasmid lacked the machinery for conjugation, but was transferable by electroporation to A. baumannii. Both isolates, which displayed the same PFGE pattern, represent the first report of CHDL-carrying A. pittii in Portuguese hospitals.<br><br>CONCLUSIONS: Altogether, these results emphasize the importance of A. pittii, or particular A. pittii clones, as a source of resistance genes, facilitating their dissemination among different bacterial species.}, }
@article {pmid29069349, year = {2017}, author = {Ríhová, J and Nováková, E and Husník, F and Hypša, V}, title = {Legionella Becoming a Mutualist: Adaptive Processes Shaping the Genome of Symbiont in the Louse Polyplax serrata.}, journal = {Genome biology and evolution}, volume = {9}, number = {11}, pages = {2946-2957}, pmid = {29069349}, issn = {1759-6653}, mesh = {Adaptation, Physiological ; Animals ; Anoplura/genetics/*microbiology ; Biological Coevolution ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial/*genetics ; Legionella/*classification/*genetics/physiology ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {Legionellaceae are intracellular bacteria known as important human pathogens. In the environment, they are mainly found in biofilms associated with amoebas. In contrast to the gammaproteobacterial family Enterobacteriaceae, which established a broad spectrum of symbioses with many insect taxa, the only instance of legionella-like symbiont has been reported from lice of the genus Polyplax. Here, we sequenced the complete genome of this symbiont and compared its main characteristics to other Legionella species and insect symbionts. Based on rigorous multigene phylogenetic analyses, we confirm this bacterium as a member of the genus Legionella and propose the name Candidatus Legionella polyplacis, sp.n. We show that the genome of Ca. Legionella polyplacis underwent massive degeneration, including considerable size reduction (529.746 bp, 484 protein coding genes) and a severe decrease in GC content (23%). We identify several possible constraints underlying the evolution of this bacterium. On one hand, Ca. Legionella polyplacis and the louse symbionts Riesia and Puchtella experienced convergent evolution, perhaps due to adaptation to similar hosts. On the other hand, some metabolic differences are likely to reflect different phylogenetic positions of the symbionts and hence availability of particular metabolic function in the ancestor. This is exemplified by different arrangements of thiamine metabolism in Ca. Legionella polyplacis and Riesia. Finally, horizontal gene transfer is shown to play a significant role in the adaptive and diversification process. Particularly, we show that Ca. L. polyplacis horizontally acquired a complete biotin operon (bioADCHFB) that likely assisted this bacterium when becoming an obligate mutualist.}, }
@article {pmid29068466, year = {2017}, author = {Martin, WF}, title = {Too Much Eukaryote LGT.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {39}, number = {12}, pages = {}, doi = {10.1002/bies.201700115}, pmid = {29068466}, issn = {1521-1878}, mesh = {Animals ; Eukaryota/classification/*genetics ; Eukaryotic Cells/cytology/metabolism ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome ; Mitochondria/genetics ; Phylogeny ; Plants/classification/genetics ; Plastids/genetics ; Prokaryotic Cells/cytology/metabolism ; Symbiosis/*genetics ; }, abstract = {The realization that prokaryotes naturally and frequently disperse genes across steep taxonomic boundaries via lateral gene transfer (LGT) gave wings to the idea that eukaryotes might do the same. Eukaryotes do acquire genes from mitochondria and plastids and they do transfer genes during the process of secondary endosymbiosis, the spread of plastids via eukaryotic algal endosymbionts. From those observations it, however, does not follow that eukaryotes transfer genes either in the same ways as prokaryotes do, or to a quantitatively similar degree. An important illustration of the difference is that eukaryotes do not exhibit pangenomes, though prokaryotes do. Eukaryotes reveal no detectable cumulative effects of LGT, though prokaryotes do. A critical analysis suggests that something is deeply amiss with eukaryote LGT theories.}, }
@article {pmid29067010, year = {2017}, author = {Santana, MM and Gonzalez, JM and Cruz, C}, title = {Nitric Oxide Accumulation: The Evolutionary Trigger for Phytopathogenesis.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1947}, pmid = {29067010}, issn = {1664-302X}, abstract = {Many publications highlight the importance of nitric oxide (NO) in plant-bacteria interactions, either in the promotion of health and plant growth or in pathogenesis. However, the role of NO in the signaling between bacteria and plants and in the fate of their interaction, as well as the reconstruction of their interactive evolution, remains largely unknown. Despite the complexity of the evolution of life on Earth, we explore the hypothesis that denitrification and aerobic respiration were responsible for local NO accumulation, which triggered primordial antagonistic biotic interactions, namely the first phytopathogenic interactions. N-oxides, including NO, could globally accumulate via lightning synthesis in the early anoxic ocean and constitute pools for the evolution of denitrification, considered an early step of the biological nitrogen cycle. Interestingly, a common evolution may be proposed for components of denitrification and aerobic respiration pathways, namely for NO and oxygen reductases, a theory compatible with the presence of low amounts of oxygen before the great oxygenation event (GOE), which was generated by Cyanobacteria. During GOE, the increase in oxygen caused the decrease of Earth's temperature and the consequent increase of oxygen dissolution and availability, making aerobic respiration an increasingly dominant trait of the expanding mesophilic lifestyle. Horizontal gene transfer was certainly important in the joint expansion of mesophily and aerobic respiration. First denitrification steps lead to NO formation through nitrite reductase activity, and NO may further accumulate when oxygen binds NO reductase, resulting in denitrification blockage. The consequent transient NO surplus in an oxic niche could have been a key factor for a successful outcome of an early denitrifying prokaryote able to scavenge oxygen by NO/oxygen reductase or by an independent heterotrophic aerobic respiration pathway. In fact, NO surplus could result in toxicity causing "the first disease" in oxygen-producing Cyanobacteria. We inspected in bacteria the presence of sequences similar to the NO-producing nitrite reductase nirS gene of Thermus thermophilus, an extreme thermophilic aerobe of the Thermus/Deinococcus group, which constitutes an ancient lineage related to Cyanobacteria. In silico analysis revealed the relationship between the presence of nirS genes and phytopathogenicity in Gram-negative bacteria.}, }
@article {pmid29067005, year = {2017}, author = {Botts, RT and Apffel, BA and Walters, CJ and Davidson, KE and Echols, RS and Geiger, MR and Guzman, VL and Haase, VS and Montana, MA and La Chat, CA and Mielke, JA and Mullen, KL and Virtue, CC and Brown, CJ and Top, EM and Cummings, DE}, title = {Characterization of Four Multidrug Resistance Plasmids Captured from the Sediments of an Urban Coastal Wetland.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1922}, pmid = {29067005}, issn = {1664-302X}, support = {R15 GM102995/GM/NIGMS NIH HHS/United States ; }, abstract = {Self-transmissible and mobilizable plasmids contribute to the emergence and spread of multidrug-resistant bacteria by enabling the horizontal transfer of acquired antibiotic resistance. The objective of this study was to capture and characterize self-transmissible and mobilizable resistance plasmids from a coastal wetland impacted by urban stormwater runoff and human wastewater during the rainy season. Four plasmids were captured, two self-transmissible and two mobilizable, using both mating and enrichment approaches. Plasmid genomes, sequenced with either Illumina or PacBio platforms, revealed representatives of incompatibility groups IncP-6, IncR, IncN3, and IncF. The plasmids ranged in size from 36 to 144 kb and encoded known resistance genes for most of the major classes of antibiotics used to treat Gram-negative infections (tetracyclines, sulfonamides, β-lactams, fluoroquinolones, aminoglycosides, and amphenicols). The mobilizable IncP-6 plasmid pLNU-11 was discovered in a strain of Citrobacter freundii enriched from the wetland sediments with tetracycline and nalidixic acid, and encodes a novel AmpC-like β-lactamase (blaWDC-1), which shares less than 62% amino acid sequence identity with the PDC class of β-lactamases found in Pseudomonas aeruginosa. Although the IncR plasmid pTRE-1611 was captured by mating wetland bacteria with P. putida KT2440 as recipient, it was found to be mobilizable rather than self-transmissible. Two self-transmissible multidrug-resistance plasmids were also captured: the small (48 kb) IncN3 plasmid pTRE-131 was captured by mating wetland bacteria with Escherichia coli HY842 where it is seemed to be maintained at nearly 240 copies per cell, while the large (144 kb) IncF plasmid pTRE-2011, which was isolated from a cefotaxime-resistant environmental strain of E. coli ST744, exists at just a single copy per cell. Furthermore, pTRE-2011 bears the globally epidemic blaCTX-M-55 extended-spectrum β-lactamase downstream of ISEcp1. Our results indicate that urban coastal wetlands are reservoirs of diverse self-transmissible and mobilizable plasmids of relevance to human health.}, }
@article {pmid29066402, year = {2018}, author = {Balcázar, JL}, title = {How do bacteriophages promote antibiotic resistance in the environment?.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {24}, number = {5}, pages = {447-449}, doi = {10.1016/j.cmi.2017.10.010}, pmid = {29066402}, issn = {1469-0691}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteriophages/*drug effects/genetics ; Drug Resistance, Bacterial/*genetics ; *Environmental Microbiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Interspersed Repetitive Sequences ; Transduction, Genetic ; }, }
@article {pmid29066043, year = {2018}, author = {Jia, Q and Köllner, TG and Gershenzon, J and Chen, F}, title = {MTPSLs: New Terpene Synthases in Nonseed Plants.}, journal = {Trends in plant science}, volume = {23}, number = {2}, pages = {121-128}, doi = {10.1016/j.tplants.2017.09.014}, pmid = {29066043}, issn = {1878-4372}, mesh = {Alkyl and Aryl Transferases/*genetics/*metabolism ; Bacterial Proteins/genetics/metabolism ; Chlorophyta/enzymology ; *Evolution, Molecular ; Fungal Proteins/genetics/metabolism ; Gene Transfer, Horizontal ; Phylogeny ; Plant Proteins/genetics/*metabolism ; Plants/genetics/*metabolism ; Secondary Metabolism ; Seeds ; Terpenes/metabolism ; }, abstract = {Terpenes constitute a large class of plant secondary metabolites. It was once presumed that these compounds are biosynthesized by typical plant terpene synthases in all land plants. This view has changed with the identification of a new group of terpene synthase genes called MTPSLs for microbial terpene synthase-like genes. MTPSLs are structurally and phylogenetically more related to bacterial and fungal terpene synthases than to typical plant terpene synthases. They are widely distributed in nonseed plants but absent in seed plants and green algae. Much of the terpene diversity in nonseed plants is presumed to be determined by MTPSLs. Phylogenetic analysis suggests that ancestral MTPSL genes were acquired by early land plants from bacteria and fungi through horizontal gene transfer.}, }
@article {pmid29065523, year = {2017}, author = {Danchin, EGJ and Perfus-Barbeoch, L and Rancurel, C and Thorpe, P and Da Rocha, M and Bajew, S and Neilson, R and Guzeeva, ES and Da Silva, C and Guy, J and Labadie, K and Esmenjaud, D and Helder, J and Jones, JT and den Akker, SE}, title = {The Transcriptomes of Xiphinema index and Longidorus elongatus Suggest Independent Acquisition of Some Plant Parasitism Genes by Horizontal Gene Transfer in Early-Branching Nematodes.}, journal = {Genes}, volume = {8}, number = {10}, pages = {}, pmid = {29065523}, issn = {2073-4425}, abstract = {Nematodes have evolved the ability to parasitize plants on at least four independent occasions, with plant parasites present in Clades 1, 2, 10 and 12 of the phylum. In the case of Clades 10 and 12, horizontal gene transfer of plant cell wall degrading enzymes from bacteria and fungi has been implicated in the evolution of plant parasitism. We have used ribonucleic acid sequencing (RNAseq) to generate reference transcriptomes for two economically important nematode species, Xiphinema index and Longidorus elongatus, representative of two genera within the early-branching Clade 2 of the phylum Nematoda. We used a transcriptome-wide analysis to identify putative horizontal gene transfer events. This represents the first in-depth transcriptome analysis from any plant-parasitic nematode of this clade. For each species, we assembled ~30 million Illumina reads into a reference transcriptome. We identified 62 and 104 transcripts, from X. index and L. elongatus, respectively, that were putatively acquired via horizontal gene transfer. By cross-referencing horizontal gene transfer prediction with a phylum-wide analysis of Pfam domains, we identified Clade 2-specific events. Of these, a GH12 cellulase from X. index was analysed phylogenetically and biochemically, revealing a likely bacterial origin and canonical enzymatic function. Horizontal gene transfer was previously shown to be a phenomenon that has contributed to the evolution of plant parasitism among nematodes. Our findings underline the importance and the extensiveness of this phenomenon in the evolution of plant-parasitic life styles in this speciose and widespread animal phylum.}, }
@article {pmid29062941, year = {2016}, author = {Tang, B and Xie, F and Zhao, W and Wang, J and Dai, S and Zheng, H and Ding, X and Cen, X and Liu, H and Yu, Y and Zhou, H and Zhou, Y and Zhang, L and Goodfellow, M and Zhao, GP}, title = {A systematic study of the whole genome sequence of Amycolatopsis methanolica strain 239[T] provides an insight into its physiological and taxonomic properties which correlate with its position in the genus.}, journal = {Synthetic and systems biotechnology}, volume = {1}, number = {3}, pages = {169-186}, pmid = {29062941}, issn = {2405-805X}, abstract = {The complete genome of methanol-utilizing Amycolatopsis methanolica strain 239[T] was generated, revealing a single 7,237,391 nucleotide circular chromosome with 7074 annotated protein-coding sequences (CDSs). Comparative analyses against the complete genome sequences of Amycolatopsis japonica strain MG417-CF17[T], Amycolatopsis mediterranei strain U32 and Amycolatopsis orientalis strain HCCB10007 revealed a broad spectrum of genomic structures, including various genome sizes, core/quasi-core/non-core configurations and different kinds of episomes. Although polyketide synthase gene clusters were absent from the A. methanolica genome, 12 gene clusters related to the biosynthesis of other specialized (secondary) metabolites were identified. Complete pathways attributable to the facultative methylotrophic physiology of A. methanolica strain 239[T], including both the mdo/mscR encoded methanol oxidation and the hps/hpi encoded formaldehyde assimilation via the ribulose monophosphate cycle, were identified together with evidence that the latter might be the result of horizontal gene transfer. Phylogenetic analyses based on 16S rDNA or orthologues of AMETH_3452, a novel actinobacterial class-specific conserved gene against 62 or 18 Amycolatopsis type strains, respectively, revealed three major phyletic lineages, namely the mesophilic or moderately thermophilic A. orientalis subclade (AOS), the mesophilic Amycolatopsis taiwanensis subclade (ATS) and the thermophilic A. methanolica subclade (AMS). The distinct growth temperatures of members of the subclades correlated with corresponding genetic variations in their encoded compatible solutes. This study shows the value of integrating conventional taxonomic with whole genome sequence data.}, }
@article {pmid29062312, year = {2017}, author = {Garbisu, C and Garaiyurrebaso, O and Epelde, L and Grohmann, E and Alkorta, I}, title = {Plasmid-Mediated Bioaugmentation for the Bioremediation of Contaminated Soils.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1966}, pmid = {29062312}, issn = {1664-302X}, abstract = {Bioaugmentation, or the inoculation of microorganisms (e.g., bacteria harboring the required catabolic genes) into soil to enhance the rate of contaminant degradation, has great potential for the bioremediation of soils contaminated with organic compounds. Regrettably, cell bioaugmentation frequently turns into an unsuccessful initiative, owing to the rapid decrease of bacterial viability and abundance after inoculation, as well as the limited dispersal of the inoculated bacteria in the soil matrix. Genes that encode the degradation of organic compounds are often located on plasmids and, consequently, they can be spread by horizontal gene transfer into well-established, ecologically competitive, indigenous bacterial populations. Plasmid-mediated bioaugmentation aims to stimulate the spread of contaminant degradation genes among indigenous soil bacteria by the introduction of plasmids, located in donor cells, harboring such genes. But the acquisition of plasmids by recipient cells can affect the host's fitness, a crucial aspect for the success of plasmid-mediated bioaugmentation. Besides, environmental factors (e.g., soil moisture, temperature, organic matter content) can play important roles for the transfer efficiency of catabolic plasmids, the expression of horizontally acquired genes and, finally, the contaminant degradation activity. For plasmid-mediated bioaugmentation to be reproducible, much more research is needed for a better selection of donor bacterial strains and accompanying plasmids, together with an in-depth understanding of indigenous soil bacterial populations and the environmental conditions that affect plasmid acquisition and the expression and functioning of the catabolic genes of interest.}, }
@article {pmid29062071, year = {2018}, author = {Pawluk, A and Davidson, AR and Maxwell, KL}, title = {Anti-CRISPR: discovery, mechanism and function.}, journal = {Nature reviews. Microbiology}, volume = {16}, number = {1}, pages = {12-17}, pmid = {29062071}, issn = {1740-1534}, mesh = {Bacteria/*virology ; *Bacterial Physiological Phenomena ; Bacteriophages/*physiology ; Biological Evolution ; Biotechnology ; *CRISPR-Cas Systems ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Evolution, Molecular ; Host-Pathogen Interactions/*genetics/immunology ; Protein Binding ; Viral Proteins/genetics/metabolism ; }, abstract = {CRISPR-Cas adaptive immune systems are widespread among bacteria and archaea. Recent studies have shown that these systems have minimal long-term evolutionary effects in limiting horizontal gene transfer. This suggests that the ability to evade CRISPR-Cas immunity must also be widespread in phages and other mobile genetic elements. In this Progress article, we discuss recent discoveries that highlight how phages inactivate CRISPR-Cas systems by using anti-CRISPR proteins, and we outline evolutionary and biotechnological implications of their activity.}, }
@article {pmid29061896, year = {2017}, author = {Hall, JPJ and Brockhurst, MA and Harrison, E}, title = {Sampling the mobile gene pool: innovation via horizontal gene transfer in bacteria.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {372}, number = {1735}, pages = {}, pmid = {29061896}, issn = {1471-2970}, support = {311490/ERC_/European Research Council/International ; }, mesh = {Bacteria/*genetics ; *Biological Evolution ; *Gene Transfer, Horizontal ; }, abstract = {In biological systems, evolutionary innovations can spread not only from parent to offspring (i.e. vertical transmission), but also 'horizontally' between individuals, who may or may not be related. Nowhere is this more apparent than in bacteria, where novel ecological traits can spread rapidly within and between species through horizontal gene transfer (HGT). This important evolutionary process is predominantly a by-product of the infectious spread of mobile genetic elements (MGEs). We will discuss the ecological conditions that favour the spread of traits by HGT, the evolutionary and social consequences of sharing traits, and how HGT is shaped by inherent conflicts between bacteria and MGEs.This article is part of the themed issue 'Process and pattern in innovations from cells to societies'.}, }
@article {pmid29058514, year = {2018}, author = {Suhartono, S and Savin, MC and Gbur, EE}, title = {Transmissible Plasmids and Integrons Shift Escherichia coli Population Toward Larger Multiple Drug Resistance Numbers.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {24}, number = {3}, pages = {244-252}, doi = {10.1089/mdr.2016.0329}, pmid = {29058514}, issn = {1931-8448}, mesh = {Anti-Bacterial Agents/pharmacology ; Arkansas ; Bacterial Proteins/genetics/metabolism ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/drug effects/*genetics/isolation &amp; purification ; Escherichia coli Proteins/genetics/metabolism ; Fresh Water/microbiology ; Gene Dosage ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Humans ; *Integrons ; Microbial Sensitivity Tests ; Plasmids/*chemistry/metabolism ; Wastewater/microbiology ; Water Microbiology ; }, abstract = {Transmissible plasmids and integrons may play important roles in the persistence and spread of antibiotic-resistant bacteria throughout aquatic environment by accumulating antibiotic resistance genes (ARG). Class 1 and class 2 integron (intI), mobilization (mob), sulfamethoxazole resistance (sul), and trimethoprim resistance (dfr) genes were PCR-amplified and confirmed through DNA sequencing following plasmid extraction from 139 antibiotic-resistant Escherichia coli. E. coli had previously been recovered from wastewater treatment plant effluent and receiving stream water in Northwest Arkansas and isolates had expressed resistance to one to six antibiotics. Almost half of the total isolates (47%) carried putatively transmissible plasmids with mobF12 gene as the most frequently detected mobilization gene. When two or three mob genes were detected per isolate, there was a significant shift in the population toward larger multiple drug resistance (MDR) number. Class 1 and/or 2 integrons were prevalent (46%), and the presence of integron significantly shifted the isolate population toward larger MDR number. More isolates carried single or coexistence of two or three sul genes (99.3%), and single or a combination up to five dfr genes (89.3%) than had exhibited in vitro resistance to the respective antibiotics. These findings indicate not only the role of the wastewater treatment effluent and the stream environment in coaccumulation of ARG with transmissible plasmids and integrons in multiple antibiotic-resistant E. coli populations but also suggest that density of sul and dfr resistance genes within an isolate may serve as a biomarker for mobile MDR in general.}, }
@article {pmid29055834, year = {2018}, author = {Jacquiod, S and Cyriaque, V and Riber, L and Al-Soud, WA and Gillan, DC and Wattiez, R and Sørensen, SJ}, title = {Long-term industrial metal contamination unexpectedly shaped diversity and activity response of sediment microbiome.}, journal = {Journal of hazardous materials}, volume = {344}, number = {}, pages = {299-307}, doi = {10.1016/j.jhazmat.2017.09.046}, pmid = {29055834}, issn = {1873-3336}, mesh = {Biodiversity ; DNA, Bacterial/genetics ; Geologic Sediments/chemistry/*microbiology ; Industrial Waste ; *Metals ; Microbiota ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Rivers ; *Water Microbiology ; *Water Pollutants, Chemical ; }, abstract = {Metal contamination poses serious biotoxicity and bioaccumulation issues, affecting both abiotic conditions and biological activity in ecosystem trophic levels, especially sediments. The MetalEurop foundry released metals directly into the French river "la Deûle" during a century, contaminating sediments with a 30-fold increase compared to upstream unpolluted areas (Férin, Sensée canal). Previous metaproteogenomic work revealed phylogenetically analogous, but functionally different microbial communities between the two locations. However, their potential activity status in situ remains unknown. The present study respectively compares the structures of both total and active fractions of sediment prokaryotic microbiomes by coupling DNA and RNA-based sequencing approaches at the polluted MetalEurop site and its upstream control. We applied the innovative ecological concept of Functional Response Groups (FRGs) to decipher the adaptive tolerance range of the communities through characterization of microbial lifestyles and strategists. The complementing use of DNA and RNA sequencing revealed indications that metals selected for mechanisms such as microbial facilitation via "public-good" providing bacteria, Horizontal Gene Transfer (HGT) and community coalescence, overall resulting in an unexpected higher microbial diversity at the polluted site.}, }
@article {pmid29055778, year = {2017}, author = {Iwaï, H and Mikula, KM and Oeemig, JS and Zhou, D and Li, M and Wlodawer, A}, title = {Structural Basis for the Persistence of Homing Endonucleases in Transcription Factor IIB Inteins.}, journal = {Journal of molecular biology}, volume = {429}, number = {24}, pages = {3942-3956}, pmid = {29055778}, issn = {1089-8638}, support = {HHSN261200800001C/CA/NCI NIH HHS/United States ; HHSN261200800001E/CA/NCI NIH HHS/United States ; ZIA BC010348-17/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Crystallography, X-Ray ; Endonucleases/*chemistry/genetics/metabolism ; *Inteins ; Methanococcus/*enzymology/genetics ; Models, Molecular ; Protein Conformation ; Protein Splicing ; Sequence Homology ; Transcription Factor TFIIB/*chemistry/genetics/metabolism ; }, abstract = {Inteins are mobile genetic elements that are spliced out of proteins after translation. Some inteins contain a homing endonuclease (HEN) responsible for their propagation. Hedgehog/INTein (HINT) domains catalyzing protein splicing and their nested HEN domains are thought to be functionally independent because of the existence of functional mini-inteins without HEN domains. Despite the lack of obvious mutualism between HEN and HINT domains, HEN domains are persistently found at one specific site in inteins, indicating their potential functional role in protein splicing. Here we report crystal structures of inactive and active mini-inteins derived from inteins residing in the transcription factor IIB of Methanococcus jannaschii and Methanocaldococcus vulcanius, revealing a novel modified HINT fold that might provide new insights into the mutualism between the HEN and HINT domains. We propose an evolutionary model of inteins and a functional role of HEN domains in inteins.}, }
@article {pmid29052138, year = {2017}, author = {Zhu, C and Wang, Y and Cai, C and Cai, Q}, title = {Bacterial Infection and Associated Cancers.}, journal = {Advances in experimental medicine and biology}, volume = {1018}, number = {}, pages = {181-191}, doi = {10.1007/978-981-10-5765-6_11}, pmid = {29052138}, issn = {0065-2598}, mesh = {Bacterial Infections/complications/epidemiology/*microbiology ; Biofilms/growth &amp; development ; Carcinogenesis/*genetics ; Gene Transfer, Horizontal/ethics ; Helicobacter pylori/genetics/*pathogenicity ; Humans ; Microbiota/genetics ; Neoplasms/complications/epidemiology/*microbiology ; }, abstract = {Bacterial infections were traditionally not considered as major causes of cancer. However, increasing evidence in the past decades has suggested that several cancers are highly associated with bacterial infection. The bacterial infections have evolved some unique strategies including lateral gene transfer, biofilm and microbiome to induce genome instability and chronic inflammation, as well as escape of immune surveillance for carcinogenesis. Here we summarize and highlight the recent progress on understanding of how bacterial infection plays a role in tumor formation and malignancy.}, }
@article {pmid29051988, year = {2018}, author = {Hegedüs, B and Kós, PB and Bende, G and Bounedjoum, N and Maróti, G and Laczi, K and Szuhaj, M and Perei, K and Rákhely, G}, title = {Starvation- and xenobiotic-related transcriptomic responses of the sulfanilic acid-degrading bacterium, Novosphingobium resinovorum SA1.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {1}, pages = {305-318}, doi = {10.1007/s00253-017-8553-5}, pmid = {29051988}, issn = {1432-0614}, support = {HU09-0044-A1-2013//Norway Grant/ ; EFOP-3.6.2-16-2017-00010//European Union Agency for Network and Information Security (GR)/ ; }, mesh = {Biodegradation, Environmental ; Gene Expression Profiling ; Genomics ; Sphingomonadaceae/*genetics/metabolism ; Sulfanilic Acids/*metabolism ; *Transcriptome ; *Xenobiotics ; }, abstract = {Novosphingobium resinovorum SA1 was the first single isolate capable of degrading sulfanilic acid, a widely used representative of sulfonated aromatic compounds. The genome of the strain was recently sequenced, and here, we present whole-cell transcriptome analyses of cells exposed to sulfanilic acid as compared to cells grown on glucose. The comparison of the transcript profiles suggested that the primary impact of sulfanilic acid on the cell transcriptome was a starvation-like effect. The genes of the peripheral, central, and common pathways of sulfanilic acid biodegradation had distinct transcript profiles. The peripheral genes located on a plasmid had very high basal expressions which were hardly upregulated by sulfanilic acid. The genomic context and the codon usage preference of these genes suggested that they were acquired by horizontal gene transfer. The genes of the central pathways were remarkably inducible by sulfanilic acid indicating the presence of a substrate-specific regulatory system in the cells. Surprisingly, the genes of the common part of the metabolic pathway had low and sulfanilic acid-independent transcript levels. The approach applied resulted in the identification of the genes of proteins involved in auxiliary processes such as electron transfer, substrate and iron transports, sulfite oxidases, and sulfite transporters. The whole transcriptome analysis revealed that the cells exposed to xenobiotics had multiple responses including general starvation-like, substrate-specific, and substrate-related effects. From the results, we propose that the genes of the peripheral, central, and common parts of the pathway have been evolved independently.}, }
@article {pmid29048529, year = {2017}, author = {Levasseur, A and Merhej, V and Baptiste, E and Sharma, V and Pontarotti, P and Raoult, D}, title = {The Rhizome of Lokiarchaeota Illustrates the Mosaicity of Archaeal Genomes.}, journal = {Genome biology and evolution}, volume = {9}, number = {10}, pages = {2635-2639}, pmid = {29048529}, issn = {1759-6653}, mesh = {Archaea/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genes, Viral ; *Genome, Archaeal ; *Mosaicism ; }, abstract = {Genome remodeling and exchange of sequences are widespread in the prokaryotic world and mosaic genomes challenge the classification of prokaryotes, which cannot be properly achieved in terms of a single gene or group of genes. Here, we studied individually the gene collection of the archaic microorganism Lokiarchaeum sp., suggested as an archaeal host close to the emergence of the eukaryotes. The network or rhizome of all Lokiarchaeum sp. genes revealed that the genomic repertoire is mainly composed of genes from archaeal (∼36%) and bacterial origin (∼28%), distantly followed by components of eukaryotic origin (∼2%). Thirty-three percent of genes were unique to this species (ORFans). The mosaicity of archaea was also supported by studying Methanomassiliicoccus luminyensis, an archaea from the gut, in which 67% of the genomic repertoire arised from archaea and 22% from bacteria. Our results illustrate the intricate evolutionary relationships of the archaeal genome repertoire and highlight the rhizome-like processes of evolution in archaea, their mosaicity, and chimeric origin composed of different domains of life, questioning the reality of a tree of life.}, }
@article {pmid29047329, year = {2017}, author = {Guo, X and Li, S and Zhang, J and Wu, F and Li, X and Wu, D and Zhang, M and Ou, Z and Jie, Z and Yan, Q and Li, P and Yi, J and Peng, Y}, title = {Genome sequencing of 39 Akkermansia muciniphila isolates reveals its population structure, genomic and functional diverisity, and global distribution in mammalian gut microbiotas.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {800}, pmid = {29047329}, issn = {1471-2164}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Evolution, Molecular ; Gastrointestinal Microbiome/*genetics ; Humans ; Mammals/*microbiology ; Mice ; Molecular Sequence Annotation ; Verrucomicrobia/drug effects/*genetics/*physiology ; *Whole Genome Sequencing ; }, abstract = {BACKGROUND: Akkermansia muciniphila is one of the most dominant bacteria that resides on the mucus layer of intestinal tract and plays key role in human health, however, little is known about its genomic content.<br><br>RESULTS: Herein, we for the first time characterized the genomic architecture of A. muciniphila based on whole-genome sequencing, assembling, and annotating of 39 isolates derived from human and mouse feces. We revealed a flexible open pangenome of A. muciniphila currently consisting of 5644 unique proteins. Phylogenetic analysis identified three species-level A. muciniphila phylogroups exhibiting distinct metabolic and functional features. Based on the comprehensive genome catalogue, we reconstructed 106 newly A. muciniphila metagenome assembled genomes (MAGs) from available metagenomic datasets of human, mouse and pig gut microbiomes, revealing a transcontinental distribution of A. muciniphila phylogroups across mammalian gut microbiotas. Accurate quantitative analysis of A. muciniphila phylogroups in human subjects further demonstrated its strong correlation with body mass index and anti-diabetic drug usage. Furthermore, we found that, during their mammalian gut evolution history, A. muciniphila acquired extra genes, especially antibiotic resistance genes, from symbiotic microbes via recent lateral gene transfer.<br><br>CONCLUSIONS: The genome repertoire of A. muciniphila provided insights into population structure, evolutionary and functional specificity of this significant bacterium.}, }
@article {pmid29046741, year = {2017}, author = {Xu, Z and Puranik, R and Hu, J and Xu, H and Han, D}, title = {Complete genome sequence of Thermotoga sp. strain RQ7.}, journal = {Standards in genomic sciences}, volume = {12}, number = {}, pages = {62}, pmid = {29046741}, issn = {1944-3277}, abstract = {Thermotoga sp. strain RQ7 is a member of the family Thermotogaceae in the order Thermotogales. It is a Gram negative, hyperthermophilic, and strictly anaerobic bacterium. It grows on diverse simple and complex carbohydrates and can use protons as the final electron acceptor. Its complete genome is composed of a chromosome of 1,851,618 bp and a plasmid of 846 bp. The chromosome contains 1906 putative genes, including 1853 protein coding genes and 53 RNA genes. The genetic features pertaining to various lateral gene transfer mechanisms are analyzed. The genome carries a complete set of putative competence genes, 8 loci of CRISPRs, and a deletion of a well-conserved Type II R-M system.}, }
@article {pmid29046540, year = {2017}, author = {Loftie-Eaton, W and Bashford, K and Quinn, H and Dong, K and Millstein, J and Hunter, S and Thomason, MK and Merrikh, H and Ponciano, JM and Top, EM}, title = {Compensatory mutations improve general permissiveness to antibiotic resistance plasmids.}, journal = {Nature ecology &amp; evolution}, volume = {1}, number = {9}, pages = {1354-1363}, pmid = {29046540}, issn = {2397-334X}, support = {P20 GM103408/GM/NIGMS NIH HHS/United States ; P30 GM103324/GM/NIGMS NIH HHS/United States ; R01 AI084918/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/metabolism ; DNA Helicases/genetics/metabolism ; DNA-Directed RNA Polymerases/genetics/metabolism ; Drug Resistance, Microbial/*genetics ; *Gene Transfer, Horizontal ; *Mutation ; Plasmids/*drug effects/genetics ; Pseudomonas/*drug effects/genetics ; }, abstract = {Horizontal gene transfer mediated by broad-host-range plasmids is an important mechanism of antibiotic resistance spread. While not all bacteria maintain plasmids equally well, plasmid persistence can improve over time, yet no general evolutionary mechanisms have emerged. Our goal was to identify these mechanisms and to assess if adaptation to one plasmid affects the permissiveness to others. We experimentally evolved Pseudomonas sp. H2 containing multidrug resistance plasmid RP4, determined plasmid persistence and cost using a joint experimental-modelling approach, resequenced evolved clones, and reconstructed key mutations. Plasmid persistence improved in fewer than 600 generations because the fitness cost turned into a benefit. Improved retention of naive plasmids indicated that the host evolved towards increased plasmid permissiveness. Key chromosomal mutations affected two accessory helicases and the RNA polymerase β-subunit. Our and other findings suggest that poor plasmid persistence can be caused by a high cost involving helicase-plasmid interactions that can be rapidly ameliorated.}, }
@article {pmid29042411, year = {2017}, author = {Heringer, P and Dias, GB and Kuhn, GCS}, title = {A Horizontally Transferred Autonomous Helitron Became a Full Polydnavirus Segment in Cotesia vestalis.}, journal = {G3 (Bethesda, Md.)}, volume = {7}, number = {12}, pages = {3925-3935}, pmid = {29042411}, issn = {2160-1836}, mesh = {Animals ; Bombyx/genetics/parasitology ; DNA Helicases/genetics ; DNA Transposable Elements/genetics ; Drosophila/genetics/parasitology ; Gene Transfer, Horizontal/*genetics ; Genome, Viral/genetics ; Hymenoptera/*genetics/virology ; Insect Vectors/*genetics/virology ; Polydnaviridae/*genetics ; }, abstract = {Bracoviruses associate symbiotically with thousands of parasitoid wasp species in the family Braconidae, working as virulence gene vectors, and allowing the development of wasp larvae within hosts. These viruses are composed of multiple DNA circles that are packaged into infective particles, and injected together with wasp's eggs during parasitization. One of the viral segments of Cotesia vestalis bracovirus contains a gene that has been previously described as a helicase of unknown origin. Here, we demonstrate that this gene is a Rep/Helicase from an intact Helitron transposable element that covers the viral segment almost entirely. We also provide evidence that this element underwent at least two horizontal transfers, which appear to have occurred consecutively: first from a Drosophila host ancestor to the genome of the parasitoid wasp C. vestalis and its bracovirus, and then from C. vestalis to a lepidopteran host (Bombyx mori). Our results reinforce the idea of parasitoid wasps as frequent agents of horizontal transfers in eukaryotes. Additionally, this Helitron-bracovirus segment is the first example of a transposable element that effectively became a whole viral circle.}, }
@article {pmid29041914, year = {2017}, author = {Wu, C and Jordan, MD and Newcomb, RD and Gemmell, NJ and Bank, S and Meusemann, K and Dearden, PK and Duncan, EJ and Grosser, S and Rutherford, K and Gardner, PP and Crowhurst, RN and Steinwender, B and Tooman, LK and Stevens, MI and Buckley, TR}, title = {Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {795}, pmid = {29041914}, issn = {1471-2164}, mesh = {Animals ; Arthropods/*genetics/growth &amp; development/metabolism ; Chitinases/genetics ; DNA Methylation ; *Evolution, Molecular ; Gene Expression Profiling ; Gene Transfer, Horizontal ; *Genomics ; Molecular Sequence Annotation ; Phylogeny ; Sex Determination Processes/genetics ; }, abstract = {BACKGROUND: The New Zealand collembolan genus Holacanthella contains the largest species of springtails (Collembola) in the world. Using Illumina technology we have sequenced and assembled a draft genome and transcriptome from Holacanthella duospinosa (Salmon). We have used this annotated assembly to investigate the genetic basis of a range of traits critical to the evolution of the Hexapoda, the phylogenetic position of H. duospinosa and potential horizontal gene transfer events.<br><br>RESULTS: Our genome assembly was ~375 Mbp in size with a scaffold N50 of ~230 Kbp and sequencing coverage of ~180&#xd7;. DNA elements, LTRs and simple repeats and LINEs formed the largest components and SINEs were very rare. Phylogenomics (370,877 amino acids) placed H. duospinosa within the Neanuridae. We recovered orthologs of the conserved sex determination genes thought to play a role in sex determination. Analysis of CpG content suggested the absence of DNA methylation, and consistent with this we were unable to detect orthologs of the DNA methyltransferase enzymes. The small subunit rRNA gene contained a possible retrotransposon. The Hox gene complex was broken over two scaffolds. For chemosensory ability, at least 15 and 18 ionotropic glutamate and gustatory receptors were identified, respectively. However, we were unable to identify any odorant receptors or their obligate co-receptor Orco. Twenty-three chitinase-like genes were identified from the assembly. Members of this multigene family may play roles in the digestion of fungal cell walls, a common food source for these saproxylic organisms. We also detected 59 and 96 genes that blasted to bacteria and fungi, respectively, but were located on scaffolds that otherwise contained arthropod genes.<br><br>CONCLUSIONS: The genome of H. duospinosa contains some unusual features including a Hox complex broken over two scaffolds, in a different manner to other arthropod species, a lack of odorant receptor genes and an apparent lack of environmentally responsive DNA methylation, unlike many other arthropods. Our detection of candidate horizontal gene transfer candidates confirms that this phenomenon is occurring across Collembola. These findings allow us to narrow down the regions of the arthropod phylogeny where key innovations have occurred that have facilitated the evolutionary success of Hexapoda.}, }
@article {pmid29038487, year = {2017}, author = {Koskella, B and Hall, LJ and Metcalf, CJE}, title = {The microbiome beyond the horizon of ecological and evolutionary theory.}, journal = {Nature ecology &amp; evolution}, volume = {1}, number = {11}, pages = {1606-1615}, doi = {10.1038/s41559-017-0340-2}, pmid = {29038487}, issn = {2397-334X}, support = {BBS/E/F/00044409/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Biological Evolution ; *Ecology ; *Eukaryota ; *Microbiota ; Models, Theoretical ; }, abstract = {The ecological and evolutionary study of community formation, diversity, and stability is rooted in general theory and reinforced by decades of system-specific empirical work. Deploying these ideas to study the assembly, complexity, and dynamics of microbial communities living in and on eukaryotes has proved seductive, but challenging. The success of this research endeavour depends on our capacity to observe and characterize the distributions, abundances, and functional traits of microbiota, representing an array of technical and analytical challenges. Furthermore, a number of unique characteristics of microbial species, such as horizontal gene transfer, the production of public goods, toxin and antibiotic production, rapid evolution, and feedbacks between the microbiome and its host, are not easily accommodated by current ecological and evolutionary theory. Here we highlight potential pitfalls in the application of existing theoretical tools without careful consideration of the unique complexities of the microbiome, focusing particularly on the issue of human health, and anchoring our discussion in existing empirical evidence.}, }
@article {pmid29036591, year = {2017}, author = {Vielva, L and de Toro, M and Lanza, VF and de la Cruz, F}, title = {PLACNETw: a web-based tool for plasmid reconstruction from bacterial genomes.}, journal = {Bioinformatics (Oxford, England)}, volume = {33}, number = {23}, pages = {3796-3798}, doi = {10.1093/bioinformatics/btx462}, pmid = {29036591}, issn = {1367-4811}, mesh = {Bacteria/*genetics ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomics/methods ; Internet ; *Plasmids ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {SUMMARY: PLACNET is a graph-based tool for reconstruction of plasmids from next generation sequence pair-end datasets. PLACNET graphs contain two types of nodes (assembled contigs and reference genomes) and two types of edges (scaffold links and homology to references). Manual pruning of the graphs is a necessary requirement in PLACNET, but this is difficult for users without solid bioinformatic background. PLACNETw, a webtool based on PLACNET, provides an interactive graphic interface, automates BLAST searches, and extracts the relevant information for decision making. It allows a user with domain expertise to visualize the scaffold graphs and related information of contigs as well as reference sequences, so that the pruning operations can be done interactively from a personal computer without the need for additional tools. After successful pruning, each plasmid becomes a separate connected component subgraph. The resulting data are automatically downloaded by the user.<br><br>PLACNETw is freely available at https://castillo.dicom.unican.es/upload/.<br><br>CONTACT: delacruz@unican.es.<br><br>SUPPLEMENTARY INFORMATION: A tutorial video and several solved examples are available at https://castillo.dicom.unican.es/placnetw_video/ and https://castillo.dicom.unican.es/examples/.}, }
@article {pmid29034217, year = {2017}, author = {Ilyas, B and Tsai, CN and Coombes, BK}, title = {Evolution of Salmonella-Host Cell Interactions through a Dynamic Bacterial Genome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {7}, number = {}, pages = {428}, pmid = {29034217}, issn = {2235-2988}, support = {//CIHR/Canada ; }, mesh = {Adaptation, Physiological ; Animals ; Bacterial Proteins/*genetics/metabolism ; DNA, Bacterial ; Epithelial Cells/microbiology ; *Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomic Islands/genetics ; Host-Pathogen Interactions/*genetics/immunology ; Humans ; Membrane Proteins/genetics ; Salmonella Infections/genetics ; Salmonella typhimurium/*genetics/*pathogenicity ; Transcription Factors/metabolism ; Virulence/genetics ; Virulence Factors/genetics ; }, abstract = {Salmonella Typhimurium has a broad arsenal of genes that are tightly regulated and coordinated to facilitate adaptation to the various host environments it colonizes. The genome of Salmonella Typhimurium has undergone multiple gene acquisition events and has accrued changes in non-coding DNA that have undergone selection by regulatory evolution. Together, at least 17 horizontally acquired pathogenicity islands (SPIs), prophage-associated genes, and changes in core genome regulation contribute to the virulence program of Salmonella. Here, we review the latest understanding of these elements and their contributions to pathogenesis, emphasizing the regulatory circuitry that controls niche-specific gene expression. In addition to an overview of the importance of SPI-1 and SPI-2 to host invasion and colonization, we describe the recently characterized contributions of other SPIs, including the antibacterial activity of SPI-6 and adhesion and invasion mediated by SPI-4. We further discuss how these fitness traits have been integrated into the regulatory circuitry of the bacterial cell through cis-regulatory evolution and by a careful balance of silencing and counter-silencing by regulatory proteins. Detailed understanding of regulatory evolution within Salmonella is uncovering novel aspects of infection biology that relate to host-pathogen interactions and evasion of host immunity.}, }
@article {pmid29033338, year = {2018}, author = {Karkman, A and Do, TT and Walsh, F and Virta, MPJ}, title = {Antibiotic-Resistance Genes in Waste Water.}, journal = {Trends in microbiology}, volume = {26}, number = {3}, pages = {220-228}, doi = {10.1016/j.tim.2017.09.005}, pmid = {29033338}, issn = {1878-4380}, mesh = {Anti-Bacterial Agents/pharmacology ; Disinfectants/pharmacology ; Drug Resistance, Microbial/*genetics ; *Gene Transfer, Horizontal ; Metagenomics/methods ; Metals ; Polymerase Chain Reaction/methods ; Sewage/microbiology ; Wastewater/*microbiology ; }, abstract = {Waste water and waste water treatment plants can act as reservoirs and environmental suppliers of antibiotic resistance. They have also been proposed to be hotspots for horizontal gene transfer, enabling the spread of antibiotic resistance genes between different bacterial species. Waste water contains antibiotics, disinfectants, and metals which can form a selection pressure for antibiotic resistance, even in low concentrations. Our knowledge of antibiotic resistance in waste water has increased tremendously in the past few years with advances in the molecular methods available. However, there are still some gaps in our knowledge on the subject, such as how active is horizontal gene transfer in waste water and what is the role of the waste water treatment plant in the environmental resistome? The purpose of this review is to briefly describe some of the main methods for studying antibiotic resistance in waste waters and the latest research and main knowledge gaps on the issue. In addition, some future research directions are proposed.}, }
@article {pmid29032652, year = {2017}, author = {Sung, JY and Kim, S and Kwon, G and Koo, SH}, title = {Molecular Characterization of Salmonella Genomic Island 1 in Proteus mirabilis Isolates from Chungcheong Province, Korea.}, journal = {Journal of microbiology and biotechnology}, volume = {27}, number = {11}, pages = {2052-2059}, doi = {10.4014/jmb.1708.08040}, pmid = {29032652}, issn = {1738-8872}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Chickens ; Chromosome Mapping ; Chromosomes, Bacterial/genetics ; DNA, Bacterial/genetics ; Disk Diffusion Antimicrobial Tests ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Genomic Islands/*genetics ; Gentamicins/pharmacology ; Humans ; Molecular Typing/*methods ; Polymerase Chain Reaction ; Proteus mirabilis/*genetics/*isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Salmonella/*genetics ; Salmonella enterica/genetics ; Spectinomycin/pharmacology ; Streptomycin/pharmacology ; }, abstract = {The emergence and dissemination of Salmonella genomic island 1 (SGI1) are strongly associated with the occurrence of multidrug-resistant (MDR) enterobacteria in humans and animals. Diverse SGI1s have been reported among Salmonella enterica and Proteus mirabilis in several countries. We aimed to characterize SGI1 in P. mirabilis isolates from humans and chickens in Chungcheong Province, Korea. A total of 44 P. mirabilis isolates were recovered from humans (n = 20) and chickens (n = 24). Antimicrobial susceptibility was determined by disk diffusion assay. To detect and characterize SGI1s, PCR amplification and PCR mapping experiments were performed. Repetitive extragenic palindromic-PCR (REP-PCR) was performed to assess the clonality of the isolates. The four P. mirabilis strains (16.7%) from chicken harbored a SGI1, whereas none of the isolates from clinical specimens contained SGI1. The SGI1s detected in our study were all confirmed as SGI1-PmABB harboring aminoglycoside-resistant genes (aacCA5 and aadA7). In P. mirabilis isolates, the presence of SGI1-PmABB was significantly correlated with high resistance rates of the isolates to antimicrobial agents, such as gentamicin, streptomycin, and spectinomycin. Moreover, the four SGI1-bearing isolates showed the same REP-PCR patterns and that suggested both horizontal and clonal spread of the isolates. This study is the first attempt to determine SGI1s in P. mirabilis isolates in Korea. We confirmed that P. mirabilis isolates carrying SGI1-PmABB were distributed at poultry farms in Korea. The present study emphasizes the need for continuous monitoring of SGI1s to prevent spreading of the MDR genomic islands among P. mirabilis isolates from humans and animals.}, }
@article {pmid29032346, year = {2018}, author = {Finet, JE and Wan, X and Donahue, JK}, title = {Fusion of Anthopleurin-B to AAV2 increases specificity of cardiac gene transfer.}, journal = {Virology}, volume = {513}, number = {}, pages = {43-51}, pmid = {29032346}, issn = {1096-0341}, support = {R01 EB002846/EB/NIBIB NIH HHS/United States ; R01 HL093486/HL/NHLBI NIH HHS/United States ; R01 HL134185/HL/NHLBI NIH HHS/United States ; R01 HL067148/HL/NHLBI NIH HHS/United States ; R21 AG042701/AG/NIA NIH HHS/United States ; R01 HL130376/HL/NHLBI NIH HHS/United States ; }, mesh = {Capsid Proteins/genetics/metabolism ; Cell Line ; Dependovirus ; *Gene Transfer, Horizontal ; Genetic Therapy/methods ; *Genetic Vectors ; Humans ; Intercellular Signaling Peptides and Proteins ; Myocytes, Cardiac/virology ; NAV1.5 Voltage-Gated Sodium Channel/metabolism ; Parvovirinae/*genetics/physiology ; Peptides/genetics/*metabolism ; Recombinant Fusion Proteins/genetics/metabolism ; *Transduction, Genetic ; *Viral Tropism ; Virus Attachment ; }, abstract = {AAV-mediated gene therapy has become a promising therapeutic strategy for chronic diseases. Its clinical utilization, however, is limited by the potential risk of off-target effects. In this work we attempt to overcome this challenge, hypothesizing that cardiac ion channel-specific ligands could be fused onto the AAV capsid, and narrow its tropism to cardiac myocytes. We successfully fused the cardiac sodium channel (Nav1.5)-binding toxin Anthopleurin-B onto the AAV2 capsid without compromising virus integrity, and demonstrated increased specificity of cardiomyocyte attachment. Although virus attachment to Nav1.5 did not supersede the natural heparan-mediated virus binding, heparan-binding ablated vectors carrying Anthopleurin-B eliminated hepatic and other extracardiac gene transfer, while preserving cardiac myocyte gene transfer. Virus binding to the cardiac sodium channel transiently decreased sodium current density, but did not cause any arrhythmias. Our findings expand the knowledge of attachment, infectivity, and intracellular processing of AAV vectors, and present an alternative strategy for vector retargeting.}, }
@article {pmid29030446, year = {2018}, author = {van Dam, P and de Sain, M and Ter Horst, A and van der Gragt, M and Rep, M}, title = {Use of Comparative Genomics-Based Markers for Discrimination of Host Specificity in Fusarium oxysporum.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {1}, pages = {}, pmid = {29030446}, issn = {1098-5336}, mesh = {Cucurbitaceae/*microbiology ; Fusarium/*classification/*genetics/isolation &amp; purification ; *Genome, Fungal ; *Host Specificity ; Phylogeny ; Plant Diseases/classification/*microbiology ; *Whole Genome Sequencing ; }, abstract = {The polyphyletic nature of many formae speciales of Fusarium oxysporum prevents molecular identification of newly encountered strains based on conserved, vertically inherited genes. Alternative molecular detection methods that could replace labor- and time-intensive disease assays are therefore highly desired. Effectors are functional elements in the pathogen-host interaction and have been found to show very limited sequence diversity between strains of the same forma specialis, which makes them potential markers for host-specific pathogenicity. We therefore compared candidate effector genes extracted from 60 existing and 22 newly generated genome assemblies, specifically targeting strains affecting cucurbit plant species. Based on these candidate effector genes, a total of 18 PCR primer pairs were designed to discriminate between each of the seven Cucurbitaceae-affecting formae speciales When tested on a collection of strains encompassing different clonal lineages of these formae speciales, nonpathogenic strains, and strains of other formae speciales, they allowed clear recognition of the host range of each evaluated strain. Within Fusarium oxysporum f. sp. melonis more genetic variability exists than anticipated, resulting in three F. oxysporum f. sp. melonis marker patterns that partially overlapped with the cucurbit-infecting Fusarium oxysporum f. sp. cucumerinum, Fusarium oxysporum f. sp. niveum, Fusarium oxysporum f. sp. momordicae, and/or Fusarium oxysporum f. sp. lagenariae For F. oxysporum f. sp. niveum, a multiplex TaqMan assay was evaluated and was shown to allow quantitative and specific detection of template DNA quantities as low as 2.5 pg. These results provide ready-to-use marker sequences for the mentioned F. oxysporum pathogens. Additionally, the method can be applied to find markers distinguishing other host-specific forms of F. oxysporumIMPORTANCE Pathogenic strains of Fusarium oxysporum are differentiated into formae speciales based on their host range, which is normally restricted to only one or a few plant species. However, horizontal gene transfer between strains in the species complex has resulted in a polyphyletic origin of host specificity in many of these formae speciales This hinders accurate and rapid pathogen detection through molecular methods. In our research, we compared the genomes of 88 strains of F. oxysporum with each other, specifically targeting virulence-related genes that are typically highly similar within each forma specialis Using this approach, we identified marker sequences that allow the discrimination of F. oxysporum strains affecting various cucurbit plant species through different PCR-based methods.}, }
@article {pmid29030439, year = {2017}, author = {Lacey, JA and Keyburn, AL and Ford, ME and Portela, RW and Johanesen, PA and Lyras, D and Moore, RJ}, title = {Conjugation-Mediated Horizontal Gene Transfer of Clostridium perfringens Plasmids in the Chicken Gastrointestinal Tract Results in the Formation of New Virulent Strains.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {24}, pages = {}, pmid = {29030439}, issn = {1098-5336}, mesh = {Animals ; *Chickens ; Clostridium Infections/microbiology/*veterinary ; Clostridium perfringens/*genetics/pathogenicity ; *Conjugation, Genetic ; Gastrointestinal Tract/microbiology ; *Gene Transfer, Horizontal ; Plasmids/genetics ; Poultry Diseases/*microbiology ; Virulence ; }, abstract = {Clostridium perfringens is a gastrointestinal pathogen capable of causing disease in a variety of hosts. Necrotic enteritis in chickens is caused by C. perfringens strains that produce the pore-forming toxin NetB, the major virulence factor for this disease. Like many other C. perfringens toxins and antibiotic resistance genes, NetB is encoded on a conjugative plasmid. Conjugative transfer of the netB-containing plasmid pJIR3535 has been demonstrated in vitro with a netB-null mutant. This study has investigated the effect of plasmid transfer on disease pathogenesis, with two genetically distinct transconjugants constructed under in vitro conditions, within the intestinal tract of chickens. This study also demonstrates that plasmid transfer can occur naturally in the host gut environment without the need for antibiotic selective pressure to be applied. The demonstration of plasmid transfer within the chicken host may have implications for the progression and pathogenesis of C. perfringens-mediated disease. Such horizontal gene transfer events are likely to be common in the clostridia and may be a key factor in strain evolution, both within animals and in the wider environment.IMPORTANCEClostridium perfringens is a major gastrointestinal pathogen of poultry. C. perfringens strains that express the NetB pore-forming toxin, which is encoded on a conjugative plasmid, cause necrotic enteritis. This study demonstrated that the conjugative transfer of the netB-containing plasmid to two different nonpathogenic strains converted them into disease-causing strains with disease-causing capability similar to that of the donor strain. Plasmid transfer of netB and antibiotic resistance was also demonstrated to occur within the gastrointestinal tract of chickens, with approximately 14% of the isolates recovered comprising three distinct, in vivo-derived, transconjugant types. The demonstration of in vivo plasmid transfer indicates the potential importance of strain plasticity and the contribution of plasmids to strain virulence.}, }
@article {pmid29030023, year = {2018}, author = {Kubyshkin, V and Acevedo-Rocha, CG and Budisa, N}, title = {On universal coding events in protein biogenesis.}, journal = {Bio Systems}, volume = {164}, number = {}, pages = {16-25}, doi = {10.1016/j.biosystems.2017.10.004}, pmid = {29030023}, issn = {1872-8324}, mesh = {Animals ; Codon/*biosynthesis/genetics ; Genetic Code/*physiology ; Humans ; Protein Biosynthesis/*physiology ; Protein Folding ; RNA, Transfer/genetics/metabolism ; Ribosomes/genetics/*metabolism ; }, abstract = {The complete ribosomal protein synthesis cycle and codon-amino acids associations are universally preserved in all life taxa on Earth. This process is accompanied by a set of hierarchically organized recognition and controlling events at different complexity levels. It starts with amino acid activation by aminoacyl tRNA synthetases (aaRS) followed by matching with the acceptor units of their cognate tRNAs ("operational RNA code") and ribosomal codon-anticodon pairing of messenger RNA ("triplet code"). However, this codon-anticodon matching is possible only when protein translation machinery (translation factors, ribosome) accepts an esterified amino acid. This capacity ("charge code") correlates mainly with the amino acid nature and the identity elements in the tRNA 3D structure. A fourth potential "folding code" (also referred as "stereochemical code") between the translation dynamics, sequence composition and folding of the resulting protein can also be defined in the frame of the 'Anfinsen dogma' followed by post-translational modifications. All these coding events as well as the basic chemistry of life are deemed invariant across biological taxa due to the horizontal gene transfer (HGT) making the 'universal genetic code' the 'lingua franca' of life of earth. When cells (or organelles) are prevented from transmitting genetic information (i.e., HGT) the deviations in the above-mentioned coding events become inevitable. A better understanding of these codes, in particular the mechanisms of their conservation in the context of HGT could provide a guide for the experimental engineering[1] of the ribosomal protein biosynthesis machinery. This is highly relevant, among others, in attempts to create synthetic life forms in genetic isolation by using tailored "minimal genomes" and may explain the necessity for multiple coding evens in nature.}, }
@article {pmid29029703, year = {2017}, author = {Zaccaron, AZ and Woloshuk, CP and Bluhm, BH}, title = {Comparative genomics of maize ear rot pathogens reveals expansion of carbohydrate-active enzymes and secondary metabolism backbone genes in Stenocarpella maydis.}, journal = {Fungal biology}, volume = {121}, number = {11}, pages = {966-983}, doi = {10.1016/j.funbio.2017.08.006}, pmid = {29029703}, issn = {1878-6146}, mesh = {Amylases/*genetics ; Ascomycota/genetics/*metabolism ; Aspergillus flavus/genetics ; *Carbohydrate Metabolism ; Cellulose/metabolism ; Computational Biology ; Fusarium/genetics ; Genome, Fungal ; Genomics ; Metabolic Networks and Pathways/*genetics ; Multigene Family ; Plant Diseases/*microbiology ; Polysaccharides/metabolism ; *Secondary Metabolism ; Sequence Analysis, DNA ; Zea mays/*microbiology ; }, abstract = {Stenocarpella maydis is a plant pathogenic fungus that causes Diplodia ear rot, one of the most destructive diseases of maize. To date, little information is available regarding the molecular basis of pathogenesis in this organism, in part due to limited genomic resources. In this study, a 54.8 Mb draft genome assembly of S. maydis was obtained with Illumina and PacBio sequencing technologies, and analyzed. Comparative genomic analyses with the predominant maize ear rot pathogens Aspergillus flavus, Fusarium verticillioides, and Fusarium graminearum revealed an expanded set of carbohydrate-active enzymes for cellulose and hemicellulose degradation in S. maydis. Analyses of predicted genes involved in starch degradation revealed six putative α-amylases, four extracellular and two intracellular, and two putative γ-amylases, one of which appears to have been acquired from bacteria via horizontal transfer. Additionally, 87 backbone genes involved in secondary metabolism were identified, which represents one of the largest known assemblages among Pezizomycotina species. Numerous secondary metabolite gene clusters were identified, including two clusters likely involved in the biosynthesis of diplodiatoxin and chaetoglobosins. The draft genome of S. maydis presented here will serve as a useful resource for molecular genetics, functional genomics, and analyses of population diversity in this organism.}, }
@article {pmid29029255, year = {2017}, author = {Khodadoost, L and Hussain, H and Mullany, P}, title = {Plasmids can transfer to Clostridium difficile CD37 and 630Δerm both by a DNase resistant conjugation-like mechanism and a DNase sensitive mechanism.}, journal = {FEMS microbiology letters}, volume = {364}, number = {21}, pages = {}, doi = {10.1093/femsle/fnx208}, pmid = {29029255}, issn = {1574-6968}, mesh = {Clostridioides difficile/*genetics ; *Conjugation, Genetic ; DNA/metabolism ; DNA Transposable Elements ; Deoxyribonucleases/*metabolism ; Escherichia coli/*genetics ; Gene Transfer, Horizontal ; Plasmids/*genetics ; }, abstract = {Broad host range conjugative plasmids that replicate in Escherichia coli have been widely used to mobilise smaller replicons, bearing their cognate origin of transfer (oriT) into a variety of organisms that are less tractable genetically, such as Clostridium (Clostridioides) difficile. In this work we demonstrated that the oriT region of pMTL9301 (derived from RK2) is not required for transfer between E. coli and C. difficile strains 630Δerm and CD37 and that this oriT-independent transfer is abolished in the presence of DNase when CD37 is the recipient. Transfer to the 630Δerm strain is DNase resistant even without an obvious oriT, when E. coli CA434 is used as a donor and is sensitive to DNase when E. coli HB101 is the donor.}, }
@article {pmid29029188, year = {2017}, author = {Rojas, LJ and Weinstock, GM and De La Cadena, E and Diaz, L and Rios, R and Hanson, BM and Brown, JS and Vats, P and Phillips, DS and Nguyen, H and Hujer, KM and Correa, A and Adams, MD and Perez, F and Sodergren, E and Narechania, A and Planet, PJ and Villegas, MV and Bonomo, RA and Arias, CA}, title = {An Analysis of the Epidemic of Klebsiella pneumoniae Carbapenemase-Producing K. pneumoniae: Convergence of Two Evolutionary Mechanisms Creates the "Perfect Storm".}, journal = {The Journal of infectious diseases}, volume = {217}, number = {1}, pages = {82-92}, pmid = {29029188}, issn = {1537-6613}, support = {K24 AI121296/AI/NIAID NIH HHS/United States ; R01 AI072219/AI/NIAID NIH HHS/United States ; R21 AI143229/AI/NIAID NIH HHS/United States ; }, mesh = {Carbapenem-Resistant Enterobacteriaceae/*genetics/isolation &amp; purification ; Cities/epidemiology ; Colombia/epidemiology ; DNA, Bacterial/chemistry/genetics ; Disease Transmission, Infectious ; *Epidemics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Humans ; Interspersed Repetitive Sequences ; Klebsiella Infections/*epidemiology/*microbiology ; Klebsiella pneumoniae/classification/*genetics/isolation &amp; purification ; Molecular Epidemiology ; Phylogeny ; Sequence Analysis, DNA ; Tertiary Care Centers ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: Carbapenem resistance is a critical healthcare challenge worldwide. Particularly concerning is the widespread dissemination of Klebsiella pneumoniae carbapenemase (KPC). Klebsiella pneumoniae harboring blaKPC (KPC-Kpn) is endemic in many areas including the United States, where the epidemic was primarily mediated by the clonal dissemination of Kpn ST258. We postulated that the spread of blaKPC in other regions occurs by different and more complex mechanisms. To test this, we investigated the evolution and dynamics of spread of KPC-Kpn in Colombia, where KPC became rapidly endemic after emerging in 2005.<br><br>METHODS: We sequenced the genomes of 133 clinical isolates recovered from 24 tertiary care hospitals located in 10 cities throughout Colombia, between 2002 (before the emergence of KPC-Kpn) and 2014. Phylogenetic reconstructions and evolutionary mapping were performed to determine temporal and genetic associations between the isolates.<br><br>RESULTS: Our results indicate that the start of the epidemic was driven by horizontal dissemination of mobile genetic elements carrying blaKPC-2, followed by the introduction and subsequent spread of clonal group 258 (CG258) isolates containing blaKPC-3.<br><br>CONCLUSIONS: The combination of 2 evolutionary mechanisms of KPC-Kpn within a challenged health system of a developing country created the "perfect storm" for sustained endemicity of these multidrug-resistant organisms in Colombia.}, }
@article {pmid29029065, year = {2018}, author = {Wang, J and Yao, X and Luo, J and Lv, L and Zeng, Z and Liu, JH}, title = {Emergence of Escherichia coli co-producing NDM-1 and KPC-2 carbapenemases from a retail vegetable, China.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {73}, number = {1}, pages = {252-254}, doi = {10.1093/jac/dkx335}, pmid = {29029065}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/pharmacology ; China ; Conjugation, Genetic ; Escherichia coli/*enzymology/*isolation &amp; purification ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Transformation, Bacterial ; Vegetables/*microbiology ; beta-Lactamases/*analysis/genetics ; }, }
@article {pmid29028004, year = {2018}, author = {Colman, DR and Poudel, S and Hamilton, TL and Havig, JR and Selensky, MJ and Shock, EL and Boyd, ES}, title = {Geobiological feedbacks and the evolution of thermoacidophiles.}, journal = {The ISME journal}, volume = {12}, number = {1}, pages = {225-236}, pmid = {29028004}, issn = {1751-7370}, mesh = {Archaea/classification/genetics/isolation &amp; purification/*physiology ; *Biological Evolution ; Ecosystem ; Gene Transfer, Horizontal ; Genome, Archaeal ; Hot Springs/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Wyoming ; }, abstract = {Oxygen-dependent microbial oxidation of sulfur compounds leads to the acidification of natural waters. How acidophiles and their acidic habitats evolved, however, is largely unknown. Using 16S rRNA gene abundance and composition data from 72 hot springs in Yellowstone National Park, Wyoming, we show that hyperacidic (pH<3.0) hydrothermal ecosystems are dominated by a limited number of archaeal lineages with an inferred ability to respire O2. Phylogenomic analyses of 584 existing archaeal genomes revealed that hyperacidophiles evolved independently multiple times within the Archaea, each coincident with the emergence of the ability to respire O2, and that these events likely occurred in the recent evolutionary past. Comparative genomic analyses indicated that archaeal thermoacidophiles from independent lineages are enriched in similar protein-coding genes, consistent with convergent evolution aided by horizontal gene transfer. Because the generation of acidic environments and their successful habitation characteristically require O2, these results suggest that thermoacidophilic Archaea and the acidity of their habitats co-evolved after the evolution of oxygenic photosynthesis. Moreover, it is likely that dissolved O2 concentrations in thermal waters likely did not reach levels capable of sustaining aerobic thermoacidophiles and their acidifying activity until ~0.8 Ga, when present day atmospheric levels were reached, a time period that is supported by our estimation of divergence times for archaeal thermoacidophilic clades.}, }
@article {pmid29027482, year = {2017}, author = {Zhao, Y and Wang, L and Zhang, Z and Feng, J and Kang, H and Fang, L and Jiang, X and Zhang, D and Zhan, Z and Zhou, D and Tong, Y}, title = {Structural genomics of pNDM-BTR harboring In191 and Tn6360, and other bla NDM-carrying IncN1 plasmids.}, journal = {Future microbiology}, volume = {12}, number = {}, pages = {1271-1281}, doi = {10.2217/fmb-2017-0067}, pmid = {29027482}, issn = {1746-0921}, mesh = {Aged, 80 and over ; DNA Transposable Elements ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/drug effects/*genetics/isolation &amp; purification ; Female ; Gene Transfer, Horizontal ; Genome, Bacterial/genetics ; Genomics ; Humans ; Plasmids/genetics ; beta-Lactamases/*genetics ; }, abstract = {AIM: To characterize a conjugative bla NDM-1-carrying plasmid pNDM-BTR from a clinical Escherichia coli isolate.<br><br>MATERIALS &amp; METHODS: The complete nucleotide sequence of pNDM-BTR was determined using next-generation sequencing technology. Comparative genomic analysis of bla NDM-carrying IncN1 plasmids, including pNDM-BTR, was performed, and the antimicrobial resistance phenotypes were determined.<br><br>RESULTS: pNDM-BTR contained three accessory modules, namely IS26, a novel Tn3-family transposon Tn6360 and the dfrA14 region composed of In191, ecoRII-ecoRIImet and &#x394;IS1X2. The relatively small IncN1 backbones could integrate massive accessory modules, most of which were integrated at two 'hotspots'. These IncN1 plasmids contained distinct profiles of accessory modules, which included those carrying various resistance genes.<br><br>CONCLUSION: This study provides a deeper insight into horizontal transfer of resistance genes among IncN1 plasmids.}, }
@article {pmid29026795, year = {2017}, author = {Ranjbar, R and Farahani, O}, title = {The Prevalence of Plasmid-mediated Quinolone Resistance Genes in Escherichia coli Isolated from Hospital Wastewater Sources in Tehran, Iran.}, journal = {Iranian journal of public health}, volume = {46}, number = {9}, pages = {1285-1291}, pmid = {29026795}, issn = {2251-6085}, abstract = {BACKGROUND: Considering the importance of hospital wastewaters as potential reservoirs for the dissemination of bacterial pathogens such as Escherichia coli and antibiotic resistance genes in the environment, the need for such information becomes imperative.<br><br>METHODS: E. coli strains were isolated from hospital wastewater sources in Tehran, Iran, over a 24-month sampling period (Jun 2014- Jun 2016) and identified using standard bacteriological methods. Quinolone resistance among the strains was determined using Kirby-Bauer method and the frequency of plasmid-mediated quinolone resistance genes (qnrA, qnrB, qnrS) was investigated by PCR.<br><br>RESULTS: In total, 80 E. coli strains were isolated during the study period, of which 51 (63.8%) isolates were resistant to tested antibiotics. Of note, 13 isolates were resistant to all the antibiotics employed. The highest rates of antibiotic resistance were obtained for nalidixic acid (60%), followed by norfloxacin (30%), and ciprofloxacin (25%). Of the 51 quinolone-resistant strains, 24 (47.1%) isolates harbored qnr genes. None of the isolates harboured the qnrA gene, while 11 (45.8%) and 7 (29.2%) isolates contained qnrB and qnrS, respectively.<br><br>CONCLUSION: Our findings showed high rates of quinolone resistance (63.8%) and qnr genes, underlining the importance of hospital wastewaters as reservoirs for dissemination of potentially pathogenic E. coli and horizontal gene transfer between other waterborne bacterial species. Other possible mechanisms of resistance should also be investigated for better characterization of quinolone-resistant E. coli isolates.}, }
@article {pmid29026659, year = {2017}, author = {Lamelas, A and Hauser, J and Dangy, JP and Hamid, AM and Röltgen, K and Abdul Sater, MR and Hodgson, A and Sie, A and Junghanss, T and Harris, SR and Parkhill, J and Bentley, SD and Pluschke, G}, title = {Emergence and genomic diversification of a virulent serogroup W:ST-2881(CC175) Neisseria meningitidis clone in the African meningitis belt.}, journal = {Microbial genomics}, volume = {3}, number = {8}, pages = {e000120}, pmid = {29026659}, issn = {2057-5858}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Burkina Faso/epidemiology ; Disease Outbreaks ; Gene Transfer, Horizontal ; Ghana/epidemiology ; Humans ; Meningitis, Meningococcal/epidemiology/*microbiology ; Neisseria meningitidis/*genetics/pathogenicity ; Virulence ; }, abstract = {Countries of the African 'meningitis belt' are susceptible to meningococcal meningitis outbreaks. While in the past major epidemics have been primarily caused by serogroup A meningococci, W strains are currently responsible for most of the cases. After an epidemic in Mecca in 2000, W:ST-11 strains have caused many outbreaks worldwide. An unrelated W:ST-2881 clone was described for the first time in 2002, with the first meningitis cases caused by these bacteria reported in 2003. Here we describe results of a comparative whole-genome analysis of 74 W:ST-2881 strains isolated within the framework of two longitudinal colonization and disease studies conducted in Ghana and Burkina Faso. Genomic data indicate that the W:ST-2881 clone has emerged from Y:ST-175(CC175) bacteria by capsule switching. The circulating W:ST-2881 populations were composed of a variety of closely related but distinct genomic variants with no systematic differences between colonization and disease isolates. Two distinct and geographically clustered phylogenetic clonal variants were identified in Burkina Faso and a third in Ghana. On the basis of the presence or absence of 17 recombination fragments, the Ghanaian variant could be differentiated into five clusters. All 25 Ghanaian disease isolates clustered together with 23 out of 40 Ghanaian isolates associated with carriage within one cluster, indicating that W:ST-2881 clusters differ in virulence. More than half of the genes affected by horizontal gene transfer encoded proteins of the 'cell envelope' and the 'transport/binding protein' categories, which indicates that exchange of non-capsular antigens plays an important role in immune evasion.}, }
@article {pmid29026655, year = {2017}, author = {Ludden, C and Reuter, S and Judge, K and Gouliouris, T and Blane, B and Coll, F and Naydenova, P and Hunt, M and Tracey, A and Hopkins, KL and Brown, NM and Woodford, N and Parkhill, J and Peacock, SJ}, title = {Sharing of carbapenemase-encoding plasmids between Enterobacteriaceae in UK sewage uncovered by MinION sequencing.}, journal = {Microbial genomics}, volume = {3}, number = {7}, pages = {e000114}, pmid = {29026655}, issn = {2057-5858}, support = {WT098600/WT_/Wellcome Trust/United Kingdom ; /DH_/Department of Health/United Kingdom ; 103387/Z/13/Z/WT_/Wellcome Trust/United Kingdom ; 201344/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 110243/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacterial Proteins ; *Carbapenem-Resistant Enterobacteriaceae/classification/genetics ; DNA, Bacterial/*genetics ; England ; *Gene Transfer, Horizontal ; Plasmids/*genetics ; Sequence Analysis, DNA ; Sewage/*microbiology ; beta-Lactamases ; }, abstract = {Dissemination of carbapenem resistance among pathogenic Gram-negative bacteria is a looming medical emergency. Efficient spread of resistance within and between bacterial species is facilitated by mobile genetic elements. We hypothesized that wastewater contributes to the dissemination of carbapenemase-producing Enterobacteriaceae (CPE), and studied this through a cross-sectional observational study of wastewater in the East of England. We isolated clinically relevant species of CPE in untreated and treated wastewater, confirming that waste treatment does not prevent release of CPE into the environment. We observed that CPE-positive plants were restricted to those in direct receipt of hospital waste, suggesting that hospital effluent may play a role in disseminating carbapenem resistance. We postulated that plasmids carrying carbapenemase genes were exchanged between bacterial hosts in sewage, and used short-read (Illumina) and long-read (MinION) technologies to characterize plasmids encoding resistance to antimicrobials and heavy metals. We demonstrated that different CPE species (Enterobacter kobei and Raoultella ornithinolytica) isolated from wastewater from the same treatment plant shared two plasmids of 63 and 280 kb. The former plasmid conferred resistance to carbapenems (blaOXA-48), and the latter to numerous drug classes and heavy metals. We also report the complete genome sequence for Enterobacter kobei. Small, portable sequencing instruments such as the MinION have the potential to improve the quality of information gathered on antimicrobial resistance in the environment.}, }
@article {pmid29023575, year = {2017}, author = {Nakazawa, S and Haramiishi, A and Fukuda, K and Kanayama, Y and Watanabe, T and Yuki, M and Ohkuma, M and Takeda, K and Kimbara, K and Shintani, M}, title = {Different transferability of incompatibility (Inc) P-7 plasmid pCAR1 and IncP-1 plasmid pBP136 in stirring liquid conditions.}, journal = {PloS one}, volume = {12}, number = {10}, pages = {e0186248}, pmid = {29023575}, issn = {1932-6203}, mesh = {Conjugation, Genetic ; Gene Transfer, Horizontal ; Pili, Sex/physiology ; Plasmids/*genetics ; Pseudomonas putida/genetics ; }, abstract = {Self-transmissible plasmids are classified into two types based on their sex pili: short and rigid pili, and long and flexible pili. The transferability of two plasmids with different types of sex pili, pBP136 and pCAR1, was compared in stirring liquid conditions with different cell density. The most probable number method to count transconjugants could detect differences in the transfer frequency with higher resolution in comparison with the conventional CFU counting method. Both plasmids showed higher transfer frequency in high stirring rates than static liquid conditions when the donor and recipient density was 106-107 CFU mL-1. The probability of donor-initiated plasmid transfer was investigated by a single-cell-level analysis using a cell sorter. The probability was >36-fold higher for pBP136 than for pCAR1; thus, the simulated transfer frequency of pBP136 was much higher than that of pCAR1 in stirring liquid conditions. Nevertheless, the transfer frequency of pCAR1 was as high as that of pBP136 when the donor and recipient cell density was 106 CFU mL-1. This fact indicates that the lower probability of the donor pCAR1 to initiate transfer could be overcome by its high tolerance to the shearing force between donor and recipient cells under higher stirring liquid conditions. Our findings can explain the different survival strategies of these two types of plasmids based on their preferences of transfer conditions.}, }
@article {pmid29018426, year = {2017}, author = {Gumpert, H and Kubicek-Sutherland, JZ and Porse, A and Karami, N and Munck, C and Linkevicius, M and Adlerberth, I and Wold, AE and Andersson, DI and Sommer, MOA}, title = {Transfer and Persistence of a Multi-Drug Resistance Plasmid in situ of the Infant Gut Microbiota in the Absence of Antibiotic Treatment.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1852}, pmid = {29018426}, issn = {1664-302X}, abstract = {The microbial ecosystem residing in the human gut is believed to play an important role in horizontal exchange of virulence and antibiotic resistance genes that threatens human health. While the diversity of gut-microorganisms and their genetic content has been studied extensively, high-resolution insight into the plasticity, and selective forces shaping individual genomes is scarce. In a longitudinal study, we followed the dynamics of co-existing Escherichia coli lineages in an infant not receiving antibiotics. Using whole genome sequencing, we observed large genomic deletions, bacteriophage infections, as well as the loss and acquisition of plasmids in these lineages during their colonization of the human gut. In particular, we captured the exchange of multidrug resistance genes, and identified a clinically relevant conjugative plasmid mediating the transfer. This resistant transconjugant lineage was maintained for months, demonstrating that antibiotic resistance genes can disseminate and persist in the gut microbiome; even in absence of antibiotic selection. Furthermore, through in vivo competition assays, we suggest that the resistant transconjugant can persist through a fitness advantage in the mouse gut in spite of a fitness cost in vitro. Our findings highlight the dynamic nature of the human gut microbiota and provide the first genomic description of antibiotic resistance gene transfer between bacteria in the unperturbed human gut. These results exemplify that conjugative plasmids, harboring resistance determinants, can transfer and persists in the gut in the absence of antibiotic treatment.}, }
@article {pmid29018417, year = {2017}, author = {Valero-Rello, A and López-Sanz, M and Quevedo-Olmos, A and Sorokin, A and Ayora, S}, title = {Molecular Mechanisms That Contribute to Horizontal Transfer of Plasmids by the Bacteriophage SPP1.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1816}, pmid = {29018417}, issn = {1664-302X}, abstract = {Natural transformation and viral-mediated transduction are the main avenues of horizontal gene transfer in Firmicutes. Bacillus subtilis SPP1 is a generalized transducing bacteriophage. Using this lytic phage as a model, we have analyzed how viral replication and recombination systems contribute to the transfer of plasmid-borne antibiotic resistances. Phage SPP1 DNA replication relies on essential phage-encoded replisome organizer (G38P), helicase loader (G39P), hexameric replicative helicase (G40P), recombinase (G35P) and in less extent on the partially dispensable 5'→3' exonuclease (G34.1P), the single-stranded DNA binding protein (G36P) and the Holliday junction resolvase (G44P). Correspondingly, the accumulation of linear concatemeric plasmid DNA, and the formation of transducing particles were blocked in the absence of G35P, G38P, G39P, and G40P, greatly reduced in the G34.1P, G36P mutants, and slightly reduced in G44P mutants. In contrast, establishment of injected linear plasmid DNA in the recipient host was independent of viral-encoded functions. DNA homology between SPP1 and the plasmid, rather than a viral packaging signal, enhanced the accumulation of packagable plasmid DNA. The transfer efficiency was also dependent on plasmid copy number, and rolling-circle plasmids were encapsidated at higher frequencies than theta-type replicating plasmids.}, }
@article {pmid29018197, year = {2017}, author = {Oliveira, PH and Touchon, M and Cury, J and Rocha, EPC}, title = {The chromosomal organization of horizontal gene transfer in bacteria.}, journal = {Nature communications}, volume = {8}, number = {1}, pages = {841}, pmid = {29018197}, issn = {2041-1723}, support = {281605/ERC_/European Research Council/International ; }, mesh = {Bacteria/*genetics ; *Chromosomes, Bacterial ; *Gene Transfer, Horizontal ; Genetic Variation ; *Genome, Bacterial ; Homologous Recombination ; }, abstract = {Bacterial adaptation is accelerated by the acquisition of novel traits through horizontal gene transfer, but the integration of these genes affects genome organization. We found that transferred genes are concentrated in only ~1% of the chromosomal regions (hotspots) in 80 bacterial species. This concentration increases with genome size and with the rate of transfer. Hotspots diversify by rapid gene turnover; their chromosomal distribution depends on local contexts (neighboring core genes), and content in mobile genetic elements. Hotspots concentrate most changes in gene repertoires, reduce the trade-off between genome diversification and organization, and should be treasure troves of strain-specific adaptive genes. Most mobile genetic elements and antibiotic resistance genes are in hotspots, but many hotspots lack recognizable mobile genetic elements and exhibit frequent homologous recombination at flanking core genes. Overrepresentation of hotspots with fewer mobile genetic elements in naturally transformable bacteria suggests that homologous recombination and horizontal gene transfer are tightly linked in genome evolution.Horizontal gene transfer (HGT) is an important mechanism for genome evolution and adaptation in bacteria. Here, Oliveira and colleagues find HGT hotspots comprising ~ 1% of the chromosomal regions in 80 bacterial species.}, }
@article {pmid28993659, year = {2017}, author = {Xing, Z and Geng, W and Li, C and Sun, Y and Wang, Y}, title = {Comparative genomics of Lactobacillus kefiranofaciens ZW3 and related members of Lactobacillus. spp reveal adaptations to dairy and gut environments.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {12827}, pmid = {28993659}, issn = {2045-2322}, mesh = {Adaptation, Physiological/*genetics ; Animals ; Biosynthetic Pathways ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; CpG Islands/genetics ; DNA Restriction-Modification Enzymes/metabolism ; DNA, Circular/genetics ; Dairy Products/*microbiology ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/microbiology ; Gene Expression Regulation, Bacterial ; Genes, Bacterial ; *Genomics ; Hydrophobic and Hydrophilic Interactions ; Lactobacillus/*genetics ; Microbial Viability/genetics ; Milk/microbiology ; Phylogeny ; Polysaccharides, Bacterial/metabolism ; Sequence Homology, Nucleic Acid ; }, abstract = {It is important for probiotics that are currently utilized in the dairy industry to have clear genetic backgrounds. In this study, the genetic characteristics of Lactobacillus kefiranofaciens ZW3 were studied by undertaking a comparative genomics study, and key genes for adaptation to different environments were investigated and validated in vitro. Evidence for horizontal gene transfer resulting in strong self-defense mechanisms was detected in the ZW3 genome. We identified a series of genes relevant for dairy environments and the intestinal tract, particularly for extracellular polysaccharide (EPS) production. Reverse transcription-qPCR (RT-qPCR) revealed significant increases in the relative expression of pgm, ugp, and uge during the mid-logarithmic phase, whereas the expression of pgi was higher at the beginning of the stationary phase. The enzymes encoded by these four genes concertedly regulated carbon flux, which in turn modulated the production of EPS precursors. Moreover, ZW3 tolerated pH 3.5 and 3% bile salt and retained cell surface hydrophobicity and auto-aggregation. In conclusion, we explored the potential of ZW3 for utilization in both the dairy industry and in probiotic applications. Additionally, we elucidated the regulation of the relevant genes involved in EPS production.}, }
@article {pmid28993333, year = {2017}, author = {Lu, Y and Zeng, J and Wang, L and Lan, K and E, S and Wang, L and Xiao, Q and Luo, Q and Huang, X and Huang, B and Chen, C}, title = {Antibiotics Promote Escherichia coli-Pseudomonas aeruginosa Conjugation through Inhibiting Quorum Sensing.}, journal = {Antimicrobial agents and chemotherapy}, volume = {61}, number = {12}, pages = {}, pmid = {28993333}, issn = {1098-6596}, mesh = {Anti-Bacterial Agents/*pharmacology ; Azithromycin/pharmacology ; Bacterial Proteins/genetics ; Chloramphenicol/pharmacology ; Conjugation, Genetic/*drug effects ; DNA Helicases/genetics ; Escherichia coli/drug effects/*metabolism ; Gene Transfer, Horizontal/*drug effects ; Gentamicins/pharmacology ; Ligases/genetics ; Plasmids/genetics/metabolism ; Pseudomonas aeruginosa/drug effects/*metabolism ; Quorum Sensing/*drug effects ; Trans-Activators/genetics ; Transcription Factors/genetics ; }, abstract = {The effect of antibiotics on horizontal gene transfer (HGT) is controversial, and the underlying mechanism remains poorly understood. Here, using Escherichia coli SM10λπ as the donor strain, which carries a chromosomally integrated RP4 plasmid, we investigated the effect of antibiotics on conjugational transfer of a mobilizable gentamicin (Gm) resistance plasmid. The results showed that an exposure to gentamicin that restricted the survival of recipient cells significantly enhanced SM10λπ-Pseudomonas aeruginosa PAO1 conjugation, which was attenuated by a deficiency of lasI-rhlI, genes associated with the generation of the quorum sensing signals N-acyl homoserine lactones (AHLs) in PAO1, or the deletion of the AHL receptor SdiA in SM10λπ. Subsequent mechanistic investigations revealed that a treatment with Gm repressed the mRNA expression of lasI and rhlI in PAO1 and upregulated traI expression in SM10λπ. Moreover, PAO1 treated with other quorum sensing (QS)-inhibiting antibiotics such as azithromycin or chloramphenicol also showed a conjugation-promoting ability. On the other hand, when using non-AHL-producing E. coli strain EC600 as the recipient cells, the promoting effect of Gm on conjugation could not be observed. These data suggest that AHL-SdiA contributes to the effectiveness of antibiotics on plasmid conjugation. Collectively, our findings highlight the HGT-promoting effect of antibiotics and suggest quorum sensing as a promising target for controlling antibiotic resistance dissemination. These findings have implications for assessing the risks of antibiotic use and developing advisable antibiotic treatment protocols.}, }
@article {pmid28992304, year = {2017}, author = {Miller, EL and Evans, BA and Cornejo, OE and Roberts, IS and Rozen, DE}, title = {Pherotype Polymorphism in Streptococcus pneumoniae Has No Obvious Effects on Population Structure and Recombination.}, journal = {Genome biology and evolution}, volume = {9}, number = {10}, pages = {2546-2559}, pmid = {28992304}, issn = {1759-6653}, support = {//Wellcome Trust/United Kingdom ; BB/J006009/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; 105610/Z/14/Z//Wellcome Trust/United Kingdom ; }, mesh = {Bacterial Proteins/*genetics ; *Genome, Bacterial ; Polymorphism, Genetic ; *Recombination, Genetic ; Streptococcus pneumoniae/*genetics ; }, abstract = {Natural transformation in the Gram-positive pathogen Streptococcus pneumoniae occurs when cells become "competent," a state that is induced in response to high extracellular concentrations of a secreted peptide signal called competence stimulating peptide (CSP) encoded by the comC locus. Two main CSP signal types (pherotypes) are known to dominate the pherotype diversity across strains. Using 4,089 fully sequenced pneumococcal genomes, we confirm that pneumococcal populations are highly genetically structured and that there is significant variation among diverged populations in pherotype frequencies; most carry only a single pherotype. Moreover, we find that the relative frequencies of the two dominant pherotypes significantly vary within a small range across geographical sites. It has been variously proposed that pherotypes either promote genetic exchange among cells expressing the same pherotype, or conversely that they promote recombination between strains bearing different pherotypes. We attempt to distinguish these hypotheses using a bioinformatics approach by estimating recombination frequencies within and between pherotypes across 4,089 full genomes. Despite underlying population structure, we observe extensive recombination between populations; additionally, we found significantly higher (although marginal) rates of genetic exchange between strains expressing different pherotypes than among isolates carrying the same pherotype. Our results indicate that pherotypes do not restrict, and may even slightly facilitate, recombination between strains; however, these marginal effects suggest the more likely possibility that the cause of CSP polymorphism lies outside of its effects on transformation. Our results suggest that the CSP balanced polymorphism does not causally underlie population differentiation. Therefore, when strains carrying different pherotypes encounter one another during cocolonization, genetic exchange can occur without restriction.}, }
@article {pmid28985292, year = {2017}, author = {Petitjean, C and Makarova, KS and Wolf, YI and Koonin, EV}, title = {Extreme Deviations from Expected Evolutionary Rates in Archaeal Protein Families.}, journal = {Genome biology and evolution}, volume = {9}, number = {10}, pages = {2791-2811}, pmid = {28985292}, issn = {1759-6653}, mesh = {Archaea/*classification/*genetics ; Archaeal Proteins/*genetics ; Cluster Analysis ; Computational Biology ; *Evolution, Molecular ; Gene Duplication ; Genes, Archaeal/genetics ; Genes, Essential/genetics ; Genetic Speciation ; Genetic Variation ; Genome, Archaeal/*genetics ; Models, Genetic ; *Phylogeny ; }, abstract = {Origin of new biological functions is a complex phenomenon ranging from single-nucleotide substitutions to the gain of new genes via horizontal gene transfer or duplication. Neofunctionalization and subfunctionalization of proteins is often attributed to the emergence of paralogs that are subject to relaxed purifying selection or positive selection and thus evolve at accelerated rates. Such phenomena potentially could be detected as anomalies in the phylogenies of the respective gene families. We developed a computational pipeline to search for such anomalies in 1,834 orthologous clusters of archaeal genes, focusing on lineage-specific subfamilies that significantly deviate from the expected rate of evolution. Multiple potential cases of neofunctionalization and subfunctionalization were identified, including some ancient, house-keeping gene families, such as ribosomal protein S10, general transcription factor TFIIB and chaperone Hsp20. As expected, many cases of apparent acceleration of evolution are associated with lineage-specific gene duplication. On other occasions, long branches in phylogenetic trees correspond to horizontal gene transfer across long evolutionary distances. Significant deceleration of evolution is less common than acceleration, and the underlying causes are not well understood; functional shifts accompanied by increased constraints could be involved. Many gene families appear to be "highly evolvable," that is, include both long and short branches. Even in the absence of precise functional predictions, this approach allows one to select targets for experimentation in search of new biology.}, }
@article {pmid28983932, year = {2017}, author = {Harrison, E and Brockhurst, MA}, title = {Ecological and Evolutionary Benefits of Temperate Phage: What Does or Doesn't Kill You Makes You Stronger.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {39}, number = {12}, pages = {}, doi = {10.1002/bies.201700112}, pmid = {28983932}, issn = {1521-1878}, support = {311490/ERC_/European Research Council/International ; }, mesh = {Bacteria/genetics/growth &amp; development/*virology ; Bacteriophages/*genetics/growth &amp; development ; *Biological Coevolution ; Chromosomes, Bacterial/chemistry ; Ecosystem ; Gene Transfer, Horizontal ; Genetic Variation ; Mutagenesis, Insertional ; Symbiosis/*genetics ; }, abstract = {Infection by a temperate phage can lead to death of the bacterial cell, but sometimes these phages integrate into the bacterial chromosome, offering the potential for a more long-lasting relationship to be established. Here we define three major ecological and evolutionary benefits of temperate phage for bacteria: as agents of horizontal gene transfer (HGT), as sources of genetic variation for evolutionary innovation, and as weapons of bacterial competition. We suggest that a coevolutionary perspective is required to understand the roles of temperate phages in bacterial populations.}, }
@article {pmid28983469, year = {2017}, author = {Zhang, Y and Zhen, M and Zhan, Y and Song, Y and Zhang, Q and Wang, J}, title = {Population-Genomic Insights into Variation in Prevotella intermedia and Prevotella nigrescens Isolates and Its Association with Periodontal Disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {7}, number = {}, pages = {409}, pmid = {28983469}, issn = {2235-2988}, mesh = {Adult ; Bacteroidaceae Infections/*microbiology ; Base Sequence ; Cohort Studies ; Female ; Gene Transfer, Horizontal ; Genetic Variation ; Genome, Bacterial ; Gingiva/microbiology/pathology ; Humans ; Male ; Middle Aged ; Periodontitis/*microbiology ; Prevotella intermedia/*genetics/isolation &amp; purification ; Prevotella nigrescens/*genetics/isolation &amp; purification ; Virulence Factors/genetics ; }, abstract = {High-throughput sequencing has helped to reveal the close relationship between Prevotella and periodontal disease, but the roles of subspecies diversity and genomic variation within this genus in periodontal diseases still need to be investigated. We performed a comparative genome analysis of 48 Prevotella intermedia and Prevotella nigrescens isolates that from the same cohort of subjects to identify the main drivers of their pathogenicity and adaptation to different environments. The comparisons were done between two species and between disease and health based on pooled sequences. The results showed that both P. intermedia and P. nigrescens have highly dynamic genomes and can take up various exogenous factors through horizontal gene transfer. The major differences between disease-derived and health-derived samples of P. intermedia and P. nigrescens were factors related to genome modification and recombination, indicating that the Prevotella isolates from disease sites may be more capable of genomic reconstruction. We also identified genetic elements specific to each sample, and found that disease groups had more unique virulence factors related to capsule and lipopolysaccharide synthesis, secretion systems, proteinases, and toxins, suggesting that strains from disease sites may have more specific virulence, particularly for P. intermedia. The differentially represented pathways between samples from disease and health were related to energy metabolism, carbohydrate and lipid metabolism, and amino acid metabolism, consistent with data from the whole subgingival microbiome in periodontal disease and health. Disease-derived samples had gained or lost several metabolic genes compared to healthy-derived samples, which could be linked with the difference in virulence performance between diseased and healthy sample groups. Our findings suggest that P. intermedia and P. nigrescens may serve as "crucial substances" in subgingival plaque, which may reflect changes in microbial and environmental dynamics in subgingival microbial ecosystems. This provides insight into the potential of P. intermedia and P. nigrescens as new predictive biomarkers and targets for effective interventions in periodontal disease.}, }
@article {pmid28983283, year = {2017}, author = {Bartling, P and Brinkmann, H and Bunk, B and Overmann, J and Göker, M and Petersen, J}, title = {The Composite 259-kb Plasmid of Martelella mediterranea DSM 17316[T]-A Natural Replicon with Functional RepABC Modules from Rhodobacteraceae and Rhizobiaceae.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1787}, pmid = {28983283}, issn = {1664-302X}, abstract = {A multipartite genome organization with a chromosome and many extrachromosomal replicons (ECRs) is characteristic for Alphaproteobacteria. The best investigated ECRs of terrestrial rhizobia are the symbiotic plasmids for legume root nodulation and the tumor-inducing (Ti) plasmid of Agrobacterium tumefaciens. RepABC plasmids represent the most abundant alphaproteobacterial replicon type. The currently known homologous replication modules of rhizobia and Rhodobacteraceae are phylogenetically distinct. In this study, we surveyed type-strain genomes from the One Thousand Microbial Genomes (KMG-I) project and identified a roseobacter-specific RepABC-type operon in the draft genome of the marine rhizobium Martelella mediterranea DSM 17316[T]. PacBio genome sequencing demonstrated the presence of three circular ECRs with sizes of 593, 259, and 170-kb. The rhodobacteral RepABC module is located together with a rhizobial equivalent on the intermediate sized plasmid pMM259, which likely originated in the fusion of a pre-existing rhizobial ECR with a conjugated roseobacter plasmid. Further evidence for horizontal gene transfer (HGT) is given by the presence of a roseobacter-specific type IV secretion system on the 259-kb plasmid and the rhodobacteracean origin of 62% of the genes on this plasmid. Functionality tests documented that the genuine rhizobial RepABC module from the Martelella 259-kb plasmid is only maintained in A. tumefaciens C58 (Rhizobiaceae) but not in Phaeobacter inhibens DSM 17395 (Rhodobacteraceae). Unexpectedly, the roseobacter-like replication system is functional and stably maintained in both host strains, thus providing evidence for a broader host range than previously proposed. In conclusion, pMM259 is the first example of a natural plasmid that likely mediates genetic exchange between roseobacters and rhizobia.}, }
@article {pmid28980328, year = {2017}, author = {McTavish, EJ and Drew, BT and Redelings, B and Cranston, KA}, title = {How and Why to Build a Unified Tree of Life.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {39}, number = {11}, pages = {}, doi = {10.1002/bies.201700114}, pmid = {28980328}, issn = {1521-1878}, mesh = {Archaea/genetics ; Bacteria/genetics ; *Biological Evolution ; Eukaryota/genetics ; Gene Transfer, Horizontal ; Genomics/*methods ; *Phylogeny ; }, abstract = {Phylogenetic trees are a crucial backbone for a wide breadth of biological research spanning systematics, organismal biology, ecology, and medicine. In 2015, the Open Tree of Life project published a first draft of a comprehensive tree of life, summarizing digitally available taxonomic and phylogenetic knowledge. This paper reviews, investigates, and addresses the following questions as a follow-up to that paper, from the perspective of researchers involved in building this summary of the tree of life: Is there a tree of life and should we reconstruct it? Is available data sufficient to reconstruct the tree of life? Do we have access to phylogenetic inferences in usable form? Can we combine different phylogenetic estimates across the tree of life? And finally, what is the future of understanding the tree of life?}, }
@article {pmid28977764, year = {2017}, author = {Bergsveinson, J and Ziola, B}, title = {Comparative genomic and plasmid analysis of beer-spoiling and non-beer-spoiling Lactobacillus brevis isolates.}, journal = {Canadian journal of microbiology}, volume = {63}, number = {12}, pages = {970-983}, doi = {10.1139/cjm-2017-0405}, pmid = {28977764}, issn = {1480-3275}, mesh = {Beer/microbiology ; *Food Microbiology ; Genetic Variation ; Genome, Bacterial/*genetics ; Levilactobacillus brevis/*genetics/isolation &amp; purification ; Plasmids/*genetics ; }, abstract = {Beer-spoilage-related lactic acid bacteria (BSR LAB) belong to multiple genera and species; however, beer-spoilage capacity is isolate-specific and partially acquired via horizontal gene transfer within the brewing environment. Thus, the extent to which genus-, species-, or environment- (i.e., brewery-) level genetic variability influences beer-spoilage phenotype is unknown. Publicly available Lactobacillus brevis genomes were analyzed via BlAst Diagnostic Gene findEr (BADGE) for BSR genes and assessed for pangenomic relationships. Also analyzed were functional coding capacities of plasmids of LAB inhabiting extreme niche environments. Considerable genetic variation was observed in L. brevis isolated from clinical samples, whereas 16 candidate genes distinguish BSR and non-BSR L. brevis genomes. These genes are related to nutrient scavenging of gluconate or pentoses, mannose, and metabolism of pectin. BSR L. brevis isolates also have higher average nucleotide identity and stronger pangenome association with one another, though isolation source (i.e., specific brewery) also appears to influence the plasmid coding capacity of BSR LAB. Finally, it is shown that niche-specific adaptation and phenotype are plasmid-encoded for both BSR and non-BSR LAB. The ultimate combination of plasmid-encoded genes dictates the ability of L. brevis to survive in the most extreme beer environment, namely, gassed (i.e., pressurized) beer.}, }
@article {pmid28975058, year = {2017}, author = {Fuchsman, CA and Collins, RE and Rocap, G and Brazelton, WJ}, title = {Effect of the environment on horizontal gene transfer between bacteria and archaea.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e3865}, pmid = {28975058}, issn = {2167-8359}, abstract = {BACKGROUND: Horizontal gene transfer, the transfer and incorporation of genetic material between different species of organisms, has an important but poorly quantified role in the adaptation of microbes to their environment. Previous work has shown that genome size and the number of horizontally transferred genes are strongly correlated. Here we consider how genome size confuses the quantification of horizontal gene transfer because the number of genes an organism accumulates over time depends on its evolutionary history and ecological context (e.g., the nutrient regime for which it is adapted).<br><br>RESULTS: We investigated horizontal gene transfer between archaea and bacteria by first counting reciprocal BLAST hits among 448 bacterial and 57 archaeal genomes to find shared genes. Then we used the DarkHorse algorithm, a probability-based, lineage-weighted method (Podell &amp; Gaasterland, 2007), to identify potential horizontally transferred genes among these shared genes. By removing the effect of genome size in the bacteria, we have identified bacteria with unusually large numbers of shared genes with archaea for their genome size. Interestingly, archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share unusually large numbers of genes. However, high salt was not found to significantly affect the numbers of shared genes. Numbers of shared (genome size-corrected, reciprocal BLAST hits) and transferred genes (identified by DarkHorse) were strongly correlated. Thus archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share horizontally transferred genes. These horizontally transferred genes are over-represented by genes involved in energy conversion as well as the transport and metabolism of inorganic ions and amino acids.<br><br>CONCLUSIONS: Anaerobic and thermophilic bacteria share unusually large numbers of genes with archaea. This is mainly due to horizontal gene transfer of genes from the archaea to the bacteria. In general, these transfers are from archaea that live in similar oxygen and temperature conditions as the bacteria that receive the genes. Potential hotspots of horizontal gene transfer between archaea and bacteria include hot springs, marine sediments, and oil wells. Cold spots for horizontal transfer included dilute, aerobic, mesophilic environments such as marine and freshwater surface waters.}, }
@article {pmid28975015, year = {2017}, author = {Osman, WAM and van Berkum, P and León-Barrios, M and Velázquez, E and Elia, P and Tian, R and Ardley, J and Gollagher, M and Seshadri, R and Reddy, TBK and Ivanova, N and Woyke, T and Pati, A and Markowitz, V and Baeshen, MN and Baeshen, NN and Kyrpides, N and Reeve, W}, title = {High-quality draft genome sequence of Ensifer meliloti Mlalz-1, a microsymbiont of Medicago laciniata (L.) miller collected in Lanzarote, Canary Islands, Spain.}, journal = {Standards in genomic sciences}, volume = {12}, number = {}, pages = {58}, pmid = {28975015}, issn = {1944-3277}, abstract = {10.1601/nm.1335 Mlalz-1 (INSDC = ATZD00000000) is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing nodule of Medicago laciniata (L.) Miller from a soil sample collected near the town of Guatiza on the island of Lanzarote, the Canary Islands, Spain. This strain nodulates and forms an effective symbiosis with the highly specific host M. laciniata. This rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) sequencing project. Here the features of 10.1601/nm.1335 Mlalz-1 are described, together with high-quality permanent draft genome sequence information and annotation. The 6,664,116 bp high-quality draft genome is arranged in 99 scaffolds of 100 contigs, containing 6314 protein-coding genes and 74 RNA-only encoding genes. Strain Mlalz-1 is closely related to 10.1601/nm.1335 10.1601/strainfinder?urlappend=%3Fid%3DIAM+12611 [T], 10.1601/nm.1334 A 321[T] and 10.1601/nm.17831 10.1601/strainfinder?urlappend=%3Fid%3DORS+1407 [T], based on 16S rRNA gene sequences. gANI values of ≥98.1% support the classification of strain Mlalz-1 as 10.1601/nm.1335. Nodulation of M. laciniata requires a specific nodC allele, and the nodC gene of strain Mlalz-1 shares ≥98% sequence identity with nodC of M. laciniata-nodulating 10.1601/nm.1328 strains, but ≤93% with nodC of 10.1601/nm.1328 strains that nodulate other Medicago species. Strain Mlalz-1 is unique among sequenced 10.1601/nm.1335 strains in possessing genes encoding components of a T2SS and in having two versions of the adaptive acid tolerance response lpiA-acvB operon. In 10.1601/nm.1334 strain 10.1601/strainfinder?urlappend=%3Fid%3DWSM+419, lpiA is essential for enhancing survival in lethal acid conditions. The second copy of the lpiA-acvB operon of strain Mlalz-1 has highest sequence identity (> 96%) with that of 10.1601/nm.1334 strains, which suggests genetic recombination between strain Mlalz-1 and 10.1601/nm.1334 and the horizontal gene transfer of lpiA-acvB.}, }
@article {pmid28972415, year = {2017}, author = {Aslam, B and Nisar, MA and Khurshid, M and Farooq Salamat, MK}, title = {Immune escape strategies of Borrelia burgdorferi.}, journal = {Future microbiology}, volume = {12}, number = {}, pages = {1219-1237}, doi = {10.2217/fmb-2017-0013}, pmid = {28972415}, issn = {1746-0921}, mesh = {Antigen-Antibody Complex ; Antigenic Variation ; Antigens, Bacterial ; Bacterial Proteins/metabolism ; Borrelia burgdorferi/genetics/*immunology/pathogenicity/physiology ; Cytokines ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Host-Pathogen Interactions/*immunology ; *Immune Evasion ; Lyme Disease/*immunology ; Recombination, Genetic ; Spirochaetales/immunology ; }, abstract = {The borrelial resurge demonstrates that Borrelia burgdorferi is a persistent health problem. This spirochete is responsible for a global public health concern called Lyme disease. B. burgdorferi faces diverse environmental conditions of its vector and host during its life cycle. To circumvent the host immune system is a prominent feature of B. burgdorferi. To date, numerous studies have reported on the various mechanisms used by this pathogen to evade the host defense mechanisms. This current review attempts to consolidate this information to describe the immunological and molecular methods used by B. burgdorferi for its survival.}, }
@article {pmid28967569, year = {2017}, author = {Wang, M and Shen, W and Yan, L and Wang, XH and Xu, H}, title = {Stepwise impact of urban wastewater treatment on the bacterial community structure, antibiotic contents, and prevalence of antimicrobial resistance.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {231}, number = {Pt 2}, pages = {1578-1585}, doi = {10.1016/j.envpol.2017.09.055}, pmid = {28967569}, issn = {1873-6424}, mesh = {Anti-Bacterial Agents/analysis/*toxicity ; Disinfection/methods ; Drug Resistance, Bacterial/*drug effects/genetics ; Gram-Negative Bacteria/drug effects/genetics ; Gram-Positive Bacteria/drug effects/genetics ; Integrons/drug effects/genetics ; *Wastewater/chemistry/microbiology ; Water Pollutants, Chemical/analysis/*toxicity ; Water Purification/*methods ; }, abstract = {Bacteria, antibiotics, and antibiotic resistance determinants are key biological pollutants in aquatic systems, which may lead to bacterial infections or prevent the cure of bacterial infections. In this study, we investigated how the wastewater treatment processes in wastewater treatment plants (WWTPs) affect these pollutants. We found that the addition of oxygen, polyaluminum chloride (PAC), and polyacrylamide (PAM), as well as ultraviolet (UV) disinfection could significantly alter the bacterial communities in the water samples. An overall shift from Gram-negative bacteria to Gram-positive bacteria was observed throughout the wastewater treatment steps, but the overall bacterial biomass was not reduced in the WWTP samples. The antibiotic contents were reduced by the WWTP, but the size of the reduction and the step when antibiotic degradation occurred differed among antibiotics. Ciprofloxacin, sulfamethoxazole and erythromycin could be removed completely by the WWTP, whereas cephalexin could not. The removal of ciprofloxacin, cephalexin, and erythromycin occurred in the anaerobic digester, whereas the removal of sulfamethoxazole occurred after the addition of PAC and PAM, and UV disinfection. Antimicrobial resistance determinants were highly prevalent in all of the samples analyzed, except for those targeting vancomycin and colistin. However, wastewater treatment was ineffective at removing antimicrobial resistance determinants from wastewater. There were strong correlations between intI1, floR, sul1, and ermB, thereby suggesting the importance of integrons for the spread of these antimicrobial resistance genes. In general, this study comprised a stepwise analysis of the impact of WWTPs on three biological pollutants: bacteria, antibiotics, and antimicrobial resistance determinants, where our results suggest that the design of WWTPs needs to be improved to address the threats due to these pollutants.}, }
@article {pmid28967207, year = {2018}, author = {Graf, L and Wu, K and Wilson, JW}, title = {Transfer and analysis of Salmonella pdu genes in a range of Gram-negative bacteria demonstrate exogenous microcompartment expression across a variety of species.}, journal = {Microbial biotechnology}, volume = {11}, number = {1}, pages = {199-210}, pmid = {28967207}, issn = {1751-7915}, mesh = {Bacterial Proteins/*genetics ; Colicins/metabolism ; *Gene Expression ; *Gene Transfer, Horizontal ; Gram-Negative Bacteria/*genetics ; Macromolecular Substances/isolation &amp; purification/*metabolism ; Metabolic Engineering/*methods ; Propylene Glycols/metabolism ; }, abstract = {Bacterial microcompartments (MCPs) are protein organelles that typically house toxic or volatile reaction intermediates involved in metabolic pathways. Engineering bacteria to express exogenous MCPs will allow these cells to gain useful functions involving molecule compartmentalization. We cloned a 38 kb region from the Salmonella enterica serovar Typhimurium genome containing the pdu 1,2 propanediol (1,2 PD) utilization and cob/cbi genes using the FRT-Capture strategy to clone and transfer large genomic segments. We transferred this clone to a range of Gram-negative bacteria and found the clone to be functional for 1,2 PD metabolism in a variety of species including S. Typhimurium Δpdu, Escherichia coli, Salmonella bongori, Klebsiella pneumoniae, Cronobacter sakazakii, Serratia marcescens, and different Pseudomonas species. We successfully isolated MCPs expressed from the clone from several, but not all, of these strains, and we observed this utilizing a range of different media and in the absence of protease inhibitor. We also present a mini-prep protocol that allows rapid, small-scale screening of strains for MCP production. To date, this is the first analysis of cloned, exogenous microcompartment expression across several different Gram-negative backgrounds and provides a foundation for MCP use in a variety of bacterial species using a full, intact clone.}, }
@article {pmid28961793, year = {2017}, author = {Martin, J and Phan, HTT and Findlay, J and Stoesser, N and Pankhurst, L and Navickaite, I and De Maio, N and Eyre, DW and Toogood, G and Orsi, NM and Kirby, A and Young, N and Turton, JF and Hill, RLR and Hopkins, KL and Woodford, N and Peto, TEA and Walker, AS and Crook, DW and Wilcox, MH}, title = {Covert dissemination of carbapenemase-producing Klebsiella pneumoniae (KPC) in a successfully controlled outbreak: long- and short-read whole-genome sequencing demonstrate multiple genetic modes of transmission.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {72}, number = {11}, pages = {3025-3034}, pmid = {28961793}, issn = {1460-2091}, mesh = {Adult ; Aged ; Bacterial Proteins/*biosynthesis/genetics ; Cross Infection/epidemiology ; DNA, Bacterial/genetics ; *Disease Outbreaks/prevention &amp; control ; Enterobacteriaceae/genetics/isolation &amp; purification ; Female ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; Klebsiella Infections/*epidemiology/*microbiology ; Klebsiella pneumoniae/*enzymology/*genetics ; Male ; Middle Aged ; Multilocus Sequence Typing ; Phylogeny ; Plasmids ; Sequence Analysis, DNA ; United Kingdom/epidemiology ; Whole Genome Sequencing/methods ; beta-Lactamases/*biosynthesis/genetics ; }, abstract = {BACKGROUND: Carbapenemase-producing Enterobacteriaceae (CPE), including KPC-producing Klebsiella pneumoniae (KPC-Kpn), are an increasing threat to patient safety.<br><br>OBJECTIVES: To use WGS to investigate the extent and complexity of carbapenemase gene dissemination in a controlled KPC outbreak.<br><br>MATERIALS AND METHODS: Enterobacteriaceae with reduced ertapenem susceptibility recovered from rectal screening swabs/clinical samples, during a 3&#x2009;month KPC outbreak (2013-14), were investigated for carbapenemase production, antimicrobial susceptibility, variable-number-tandem-repeat profile and WGS [short-read (Illumina), long-read (MinION)]. Short-read sequences were used for MLST and plasmid/Tn4401 fingerprinting, and long-read sequence assemblies for plasmid identification. Phylogenetic analysis used IQTree followed by ClonalFrameML, and outbreak transmission dynamics were inferred using SCOTTI.<br><br>RESULTS: Twenty patients harboured KPC-positive isolates (6 infected, 14 colonized), and 23 distinct KPC-producing Enterobacteriaceae were identified. Four distinct KPC plasmids were characterized but of 20 KPC-Kpn (from six STs), 17 isolates shared a single pKpQIL-D2 KPC plasmid. All isolates had an identical transposon (Tn4401a), except one KPC-Kpn (ST661) with a single nucleotide variant. A sporadic case of KPC-Kpn (ST491) with Tn4401a-carrying pKpQIL-D2 plasmid was identified 10&#x2009;months before the outbreak. This plasmid was later seen in two other species and other KPC-Kpn (ST14,ST661) including clonal spread of KPC-Kpn (ST661) from a symptomatic case to nine ward contacts.<br><br>CONCLUSIONS: WGS of outbreak KPC isolates demonstrated blaKPC dissemination via horizontal transposition (Tn4401a), plasmid spread (pKpQIL-D2) and clonal spread (K. pneumoniae ST661). Despite rapid outbreak control, considerable dissemination of blaKPC still occurred among K. pneumoniae and other Enterobacteriaceae, emphasizing its high transmission potential and the need for enhanced control efforts.}, }
@article {pmid28961704, year = {2017}, author = {Abou Zaki, N and Salloum, T and Osman, M and Rafei, R and Hamze, M and Tokajian, S}, title = {Typing and comparative genome analysis of Brucella melitensis isolated from Lebanon.}, journal = {FEMS microbiology letters}, volume = {364}, number = {19}, pages = {}, doi = {10.1093/femsle/fnx199}, pmid = {28961704}, issn = {1574-6968}, mesh = {Bacterial Proteins/genetics/metabolism ; Bacterial Typing Techniques ; Brucella melitensis/classification/genetics/*isolation &amp; purification ; Brucellosis/*microbiology ; DNA, Bacterial ; Genetic Variation ; *Genome, Bacterial ; Genomics ; Genotype ; Humans ; Lebanon ; Multiplex Polymerase Chain Reaction ; Phylogeny ; Polymorphism, Single Nucleotide ; }, abstract = {Brucella melitensis is the main causative agent of the zoonotic disease brucellosis. This study aimed at typing and characterizing genetic variation in 33 Brucella isolates recovered from patients in Lebanon. Bruce-ladder multiplex PCR and PCR-RFLP of omp31, omp2a and omp2b were performed. Sixteen representative isolates were chosen for draft-genome sequencing and analyzed to determine variations in virulence, resistance, genomic islands, prophages and insertion sequences. Comparative whole-genome single nucleotide polymorphism analysis was also performed. The isolates were confirmed to be B. melitensis. Genome analysis revealed multiple virulence determinants and efflux pumps. Genome comparisons and single nucleotide polymorphisms divided the isolates based on geographical distribution but revealed high levels of similarity between the strains. Sequence divergence in B. melitensis was mainly due to lateral gene transfer of mobile elements. This is the first report of an in-depth genomic characterization of B. melitensis in Lebanon.}, }
@article {pmid28961409, year = {2017}, author = {Williamson, KE and Fuhrmann, JJ and Wommack, KE and Radosevich, M}, title = {Viruses in Soil Ecosystems: An Unknown Quantity Within an Unexplored Territory.}, journal = {Annual review of virology}, volume = {4}, number = {1}, pages = {201-219}, doi = {10.1146/annurev-virology-101416-041639}, pmid = {28961409}, issn = {2327-0578}, mesh = {*Biodiversity ; DNA, Single-Stranded/isolation &amp; purification ; *Ecosystem ; Food Chain ; Gene Transfer, Horizontal ; Genome, Viral ; Humans ; Metagenomics ; *Soil Microbiology ; Virus Physiological Phenomena ; Viruses/*genetics ; }, abstract = {Viral abundance in soils can range from below detection limits in hot deserts to over 1 billion per gram in wetlands. Abundance appears to be strongly influenced by water availability and temperature, but a lack of informational standards creates difficulties for cross-study analysis. Soil viral diversity is severely underestimated and undersampled, although current measures of viral richness are higher for soils than for aquatic ecosystems. Both morphometric and metagenomic analyses have raised questions about the prevalence of nontailed, ssDNA viruses in soils. Soil is complex and critically important to terrestrial biodiversity and human civilization, but impacts of viral activities on soil ecosystem services are poorly understood. While information from aquatic systems and medical microbiology suggests the potential for viral influences on nutrient cycles, food web interactions, gene transfer, and other key processes in soils, very few empirical data are available. To understand the soil virome, much work remains.}, }
@article {pmid28961181, year = {2017}, author = {Rancurel, C and Legrand, L and Danchin, EGJ}, title = {Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life.}, journal = {Genes}, volume = {8}, number = {10}, pages = {}, pmid = {28961181}, issn = {2073-4425}, abstract = {Horizontal gene transfer (HGT) is the transmission of genes between organisms by other means than parental to offspring inheritance. While it is prevalent in prokaryotes, HGT is less frequent in eukaryotes and particularly in Metazoa. Here, we propose Alienness, a taxonomy-aware web application available at http://alienness.sophia.inra.fr. Alienness parses BLAST results against public libraries to rapidly identify candidate HGT in any genome of interest. Alienness takes as input the result of a BLAST of a whole proteome of interest against any National Center for Biotechnology Information (NCBI) protein library. The user defines recipient (e.g., Metazoa) and donor (e.g., bacteria, fungi) branches of interest in the NCBI taxonomy. Based on the best BLAST E-values of candidate donor and recipient taxa, Alienness calculates an Alien Index (AI) for each query protein. An AI > 0 indicates a better hit to candidate donor than recipient taxa and a possible HGT. Higher AI represent higher gap of E-values between candidate donor and recipient and a more likely HGT. We confirmed the accuracy of Alienness on phylogenetically confirmed HGT of non-metazoan origin in plant-parasitic nematodes. Alienness scans whole proteomes to rapidly identify possible HGT in any species of interest and thus fosters exploration of HGT more easily and largely across the tree of life.}, }
@article {pmid28961177, year = {2017}, author = {López-Madrigal, S and Gil, R}, title = {Et tu, Brute? Not Even Intracellular Mutualistic Symbionts Escape Horizontal Gene Transfer.}, journal = {Genes}, volume = {8}, number = {10}, pages = {}, pmid = {28961177}, issn = {2073-4425}, abstract = {Many insect species maintain mutualistic relationships with endosymbiotic bacteria. In contrast to their free-living relatives, horizontal gene transfer (HGT) has traditionally been considered rare in long-term endosymbionts. Nevertheless, meta-omics exploration of certain symbiotic models has unveiled an increasing number of bacteria-bacteria and bacteria-host genetic transfers. The abundance and function of transferred loci suggest that HGT might play a major role in the evolution of the corresponding consortia, enhancing their adaptive value or buffering detrimental effects derived from the reductive evolution of endosymbionts' genomes. Here, we comprehensively review the HGT cases recorded to date in insect-bacteria mutualistic consortia, and discuss their impact on the evolutionary success of these associations.}, }
@article {pmid28957508, year = {2017}, author = {Déraspe, M and Raymond, F and Boisvert, S and Culley, A and Roy, PH and Laviolette, F and Corbeil, J}, title = {Phenetic Comparison of Prokaryotic Genomes Using k-mers.}, journal = {Molecular biology and evolution}, volume = {34}, number = {10}, pages = {2716-2729}, pmid = {28957508}, issn = {1537-1719}, mesh = {Bacteria/genetics ; Biological Evolution ; Cluster Analysis ; Computational Biology/*methods ; Computer Simulation ; Evolution, Molecular ; Genome, Bacterial/*genetics ; Genomics/methods ; Metagenomics ; Phylogeny ; Prokaryotic Cells ; Sequence Analysis, DNA/*methods ; Software ; }, abstract = {Bacterial genomics studies are getting more extensive and complex, requiring new ways to envision analyses. Using the Ray Surveyor software, we demonstrate that comparison of genomes based on their k-mer content allows reconstruction of phenetic trees without the need of prior data curation, such as core genome alignment of a species. We validated the methodology using simulated genomes and previously published phylogenomic studies of Streptococcus pneumoniae and Pseudomonas aeruginosa. We also investigated the relationship of specific genetic determinants with bacterial population structures. By comparing clusters from the complete genomic content of a genome population with clusters from specific functional categories of genes, we can determine how the population structures are correlated. Indeed, the strain clustering based on a subset of k-mers allows determination of its similarity with the whole genome clusters. We also applied this methodology on 42 species of bacteria to determine the correlational significance of five important bacterial genomic characteristics. For example, intrinsic resistance is more important in P. aeruginosa than in S. pneumoniae, and the former has increased correlation of its population structure with antibiotic resistance genes. The global view of the pangenome of bacteria also demonstrated the taxa-dependent interaction of population structure with antibiotic resistance, bacteriophage, plasmid, and mobile element k-mer data sets.}, }
@article {pmid28956196, year = {2017}, author = {Li, J and Zhang, D and Song, M and Jiang, L and Wang, Y and Luo, C and Zhang, G}, title = {Novel bacteria capable of degrading phenanthrene in activated sludge revealed by stable-isotope probing coupled with high-throughput sequencing.}, journal = {Biodegradation}, volume = {28}, number = {5-6}, pages = {423-436}, doi = {10.1007/s10532-017-9806-9}, pmid = {28956196}, issn = {1572-9729}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Carbon Isotopes/chemistry/metabolism ; Phenanthrenes/metabolism ; RNA, Ribosomal, 16S/genetics ; Sewage/chemistry/*microbiology ; }, abstract = {The indigenous microorganisms responsible for degrading phenanthrene (PHE) in activated biosludge were identified using DNA-based stable isotope probing. Besides the well-known PHE degraders Burkholderia, Ralstonia, Sinobacteraceae and Arthrobacter, we for the first time linked the taxa Paraburkholderia and Kaistobacter with in situ PHE biodegradation. Analysis of PAH-RHDα gene detected in the heavy DNA fraction of [13]C-PHE treatment suggested the mechanisms of horizontal gene transfer or inter-species hybridisation in PAH-RHD gene spread within the microbial community. Additionally, three cultivable PHE degraders, Microbacterium sp. PHE-1, Rhodanobacter sp. PHE-2 and Rhodococcus sp. PHE-3, were isolated from the same activated biosludge. Among them, Rhodanobacter sp. PHE-2 is the first identified strain in its genus with PHE-degrading ability. However, the involvement of these strains in PHE degradation in situ was questionable, due to their limited enrichment in the heavy DNA fraction of [13]C-PHE treatment and lack of PAH-RHDα gene found in these isolates. Collectively, our findings provide a deeper understanding of the diversity and functions of indigenous microbes in PHE degradation.}, }
@article {pmid28950916, year = {2017}, author = {Cheng, WH and Huang, KY and Huang, PJ and Lee, CC and Yeh, YM and Ku, FM and Lin, R and Cheng, ML and Chiu, CH and Tang, P}, title = {γ-Carboxymuconolactone decarboxylase: a novel cell cycle-related basal body protein in the early branching eukaryote Trichomonas vaginalis.}, journal = {Parasites &amp; vectors}, volume = {10}, number = {1}, pages = {443}, pmid = {28950916}, issn = {1756-3305}, mesh = {Basal Bodies/*enzymology ; Benzoates/metabolism ; Carboxy-Lyases/genetics/*metabolism ; *Cell Cycle ; Iron/metabolism ; Protozoan Proteins/genetics/*metabolism ; Trichomonas vaginalis/cytology/*enzymology/genetics ; }, abstract = {BACKGROUND: γ-Carboxymuconolactone decarboxylase (CMD) participates in the β-ketoadipate pathway, which catalyzes aromatic compounds to produce acetyl- or succinyl-CoA, in prokaryotes and yeast. Our previous study demonstrated that expression of a CMD homologue that contains two signatures (dualCMD) is negatively regulated by iron in Trichomonas vaginalis. However, we were not able to identify the components of the β-ketoadipate pathway in the parasite's genome. These observations prompted us to investigate the biological functions of this novel CMD homologue in T. vaginalis.<br><br>METHODS: The specific anti-TvCMD1 antibody was generated, and the expression of TvCMD1 in T. vaginalis cultured under iron-rich and iron-deficient were evaluated. Phylogenetic, metabolomic and substrate induction (protocatechuate and benzoate) analysis were conducted to clarify the function of dualCMD in trichomonad cells. Subcellular localization of TvCMD1 was observed by confocal microscopy. The cell cycle-related role of TvCMD1 was assessed by treating cells with G2/M inhibitor nocodazole.<br><br>RESULTS: We confirmed that T. vaginalis is not able to catabolize the aromatic compounds benzoate and protocatechuate, which are known substrates of the &#x3b2;-ketoadipate pathway. Using immunofluorescence microscopy, we found that TvCMD1 is spatially associated with the basal body, a part of the cytoskeletal organizing center in T. vaginalis. TvCMD1 accumulated upon treatment with the G2/M inhibitor nocodazole. Additionally, TvCMD1 was expressed and transported to/from the basal body during cytokinesis, suggesting that TvCMD1 plays a role in cell division.<br><br>CONCLUSION: We demonstrated that TvCMD1 is unlikely to participate in the &#x3b2;-ketoadipate pathway and demonstrated that it is a novel basal body-localizing (associated) protein. This model sheds light on the importance of genes that are acquired laterally in the coevolution of ancient protists, which surprisingly functions in cell cycle regulation of T. vaginalis.}, }
@article {pmid28949044, year = {2017}, author = {Dautermann, O and Lohr, M}, title = {A functional zeaxanthin epoxidase from red algae shedding light on the evolution of light-harvesting carotenoids and the xanthophyll cycle in photosynthetic eukaryotes.}, journal = {The Plant journal : for cell and molecular biology}, volume = {92}, number = {5}, pages = {879-891}, doi = {10.1111/tpj.13725}, pmid = {28949044}, issn = {1365-313X}, mesh = {Biological Evolution ; Genes, Plant ; Metabolic Networks and Pathways ; Oxidoreductases/genetics/*metabolism ; Photosynthesis ; Phylogeny ; Rhodophyta/genetics/*metabolism ; Xanthophylls/*metabolism ; }, abstract = {The epoxy-xanthophylls antheraxanthin and violaxanthin are key precursors of light-harvesting carotenoids and participate in the photoprotective xanthophyll cycle. Thus, the invention of zeaxanthin epoxidase (ZEP) catalyzing their formation from zeaxanthin has been a fundamental step in the evolution of photosynthetic eukaryotes. ZEP genes have only been found in Viridiplantae and chromalveolate algae with secondary plastids of red algal ancestry, suggesting that ZEP evolved in the Viridiplantae and spread to chromalveolates by lateral gene transfer. By searching publicly available sequence data from 11 red algae covering all currently recognized red algal classes we identified ZEP candidates in three species. Phylogenetic analyses showed that the red algal ZEP is most closely related to ZEP proteins from photosynthetic chromalveolates possessing secondary plastids of red algal origin. Its enzymatic activity was assessed by high performance liquid chromatography (HPLC) analyses of red algal pigment extracts and by cloning and functional expression of the ZEP gene from Madagascaria erythrocladioides in leaves of the ZEP-deficient aba2 mutant of Nicotiana plumbaginifolia. Unlike other ZEP enzymes examined so far, the red algal ZEP introduces only a single epoxy group into zeaxanthin, yielding antheraxanthin instead of violaxanthin. The results indicate that ZEP evolved before the split of Rhodophyta and Viridiplantae and that chromalveolates acquired ZEP from the red algal endosymbiont and not by lateral gene transfer. Moreover, the red algal ZEP enables engineering of transgenic plants incorporating antheraxanthin instead of violaxanthin in their photosynthetic machinery.}, }
@article {pmid28945783, year = {2017}, author = {Puozaa, DK and Jaiswal, SK and Dakora, FD}, title = {African origin of Bradyrhizobium populations nodulating Bambara groundnut (Vigna subterranea L. Verdc) in Ghanaian and South African soils.}, journal = {PloS one}, volume = {12}, number = {9}, pages = {e0184943}, pmid = {28945783}, issn = {1932-6203}, mesh = {*Bradyrhizobium/genetics/physiology ; Ghana ; Phylogeny ; Polymorphism, Restriction Fragment Length/genetics ; RNA, Ribosomal, 16S/genetics ; Root Nodules, Plant/*microbiology ; Sequence Analysis, DNA ; *Soil Microbiology ; South Africa ; Vigna/*microbiology ; }, abstract = {Flavonoids secreted by legumes play a major role as signal molecules for attracting compatible rhizobia. The aim of this study was to assess and understand the diversity of microsymbionts nodulating Bambara groundnut (Vigna subterranea L. Verdc.) landraces of different seedcoat colours using restriction fragment length polymorphism and phylogenetic analysis. Seedcoat pigmentation of landraces had effect on the diversity of microsymbionts of Bambara groundnut. Even when planted together in one hole, nodulating bradyrhizobia clustered differently. For example, 16S rDNA-RFLP typing of rhizobial samples TUTVSBLM.I, TUTVSCRM.I and TUTVSRDM.I originating respectively from Black, Cream and Red landraces that were co-planted in the same hole at Manga in the Sudano-sahelian savanna, as well as TUTVSCRK.I and TUTVSRDK.I respectively from Cream and Red landraces co-planted at Kpalisogu in the Guinea savanna, revealed different 16S rDNA- RFLP types. Phylogenetic analysis of 16S rDNA, glnII, recA and atpD sequences showed that Vigna subterranea was nodulated specifically by a diverse group of Bradyrhizobium species (e.g. Bradyrhizobium vignae, and a novel group of Bradyrhizobium spp.) in soils from Ghana and South Africa. The recA gene phylogeny showed incongruency with the other housekeeping genes, indicating the possibility of lateral gene transfer and/or recombination events. The grouping of isolates according to symbiotic gene (nifH and nodD) phylogenies revealed inter- and intra-specific symbiotic plasmid transfer and different evolutionary history. The results also showed that a cropping history and physico-chemical environment of soils increased bradyrhizobial diversity in Ghana and South Africa.}, }
@article {pmid28944751, year = {2017}, author = {San Millan, A and MacLean, RC}, title = {Fitness Costs of Plasmids: a Limit to Plasmid Transmission.}, journal = {Microbiology spectrum}, volume = {5}, number = {5}, pages = {}, pmid = {28944751}, issn = {2165-0497}, mesh = {Adaptation, Physiological ; Bacteria/classification/*genetics ; Bacterial Physiological Phenomena ; Biological Evolution ; Gene Transfer, Horizontal ; Plasmids/*genetics/metabolism ; }, abstract = {Plasmids mediate the horizontal transmission of genetic information between bacteria, facilitating their adaptation to multiple environmental conditions. An especially important example of the ability of plasmids to catalyze bacterial adaptation and evolution is their instrumental role in the global spread of antibiotic resistance, which constitutes a major threat to public health. Plasmids provide bacteria with new adaptive tools, but they also entail a metabolic burden that, in the absence of selection for plasmid-encoded traits, reduces the competitiveness of the plasmid-carrying clone. Although this fitness reduction can be alleviated over time through compensatory evolution, the initial cost associated with plasmid carriage is the main constraint on the vertical and horizontal replication of these genetic elements. The fitness effects of plasmids therefore have a crucial influence on their ability to associate with new bacterial hosts and consequently on the evolution of plasmid-mediated antibiotic resistance. However, the molecular mechanisms underlying plasmid fitness cost remain poorly understood. Here, we analyze the literature in the field and examine the potential fitness effects produced by plasmids throughout their life cycle in the host bacterium. We also explore the various mechanisms evolved by plasmids and bacteria to minimize the cost entailed by these mobile genetic elements. Finally, we discuss potential future research directions in the field.}, }
@article {pmid28943084, year = {2017}, author = {Lu, Y and Stegemann, S and Agrawal, S and Karcher, D and Ruf, S and Bock, R}, title = {Horizontal Transfer of a Synthetic Metabolic Pathway between Plant Species.}, journal = {Current biology : CB}, volume = {27}, number = {19}, pages = {3034-3041.e3}, doi = {10.1016/j.cub.2017.08.044}, pmid = {28943084}, issn = {1879-0445}, mesh = {*Gene Transfer Techniques ; *Genes, Plant ; *Genome, Chloroplast ; Plastids ; Nicotiana/*genetics ; *Transgenes ; Xanthophylls/genetics ; }, abstract = {Transgene expression from the plastid (chloroplast) genome provides unique advantages, including high levels of foreign protein accumulation, convenient transgene stacking in operons, and increased biosafety due to exclusion of plastids from pollen transmission [1, 2]. However, applications in biotechnology and synthetic biology are severely restricted by the very small number of plant species whose plastid genomes currently can be transformed [3, 4]. Here we report a simple method for the introduction of useful plastid transgenes into non-transformable species. The transgenes tested comprised a synthetic operon encoding three components of a biosynthetic pathway for producing the high-value ketocarotenoid astaxanthin in the plastids of the cigarette tobacco, Nicotiana tabacum. Transplastomic N. tabacum plants accumulated astaxanthin to up to 1% of the plants' dry weight. We then used grafting, a procedure recently shown to facilitate horizontal genome transfer between plants [5-7], to let the transgenic chloroplast genome move across the graft junction from N. tabacum plants into plants of the nicotine-free tree species Nicotiana glauca. Transplastomic N. glauca trees expressing the synthetic pathway were recovered at high frequency, thus providing a straightforward method for extension of the transplastomic technology to new species.}, }
@article {pmid28942850, year = {2017}, author = {Marcotte, H and Krogh Andersen, K and Lin, Y and Zuo, F and Zeng, Z and Larsson, PG and Brandsborg, E and Brønstad, G and Hammarström, L}, title = {Characterization and complete genome sequences of L. rhamnosus DSM 14870 and L. gasseri DSM 14869 contained in the EcoVag[®] probiotic vaginal capsules.}, journal = {Microbiological research}, volume = {205}, number = {}, pages = {88-98}, doi = {10.1016/j.micres.2017.08.003}, pmid = {28942850}, issn = {1618-0623}, mesh = {Anti-Bacterial Agents ; Antibiosis ; Bacterial Adhesion/genetics ; Bacterial Proteins/genetics ; Caco-2 Cells ; Capsules/*therapeutic use ; Chromosomes, Bacterial ; DNA Transposable Elements ; DNA, Bacterial ; Drug Resistance, Bacterial/genetics ; Female ; Fimbriae, Bacterial/genetics ; Gardnerella vaginalis/growth &amp; development ; Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Humans ; Lactobacillus gasseri/cytology/*genetics/growth &amp; development ; Lacticaseibacillus rhamnosus/cytology/*genetics/growth &amp; development ; Membrane Proteins/genetics ; Multigene Family ; Probiotics/*therapeutic use ; Vagina/*microbiology ; Vaginosis, Bacterial/*drug therapy ; *Whole Genome Sequencing ; }, abstract = {Lactobacillus rhamnosus DSM 14870 and Lactobacillus gasseri DSM 14869 were previously isolated from the vaginal epithelial cells (VEC) of healthy women and selected for the development of the vaginal EcoVag[®] probiotic capsules. EcoVag[®] was subsequently shown to provide long-term cure and reduce relapse of bacterial vaginosis (BV) as an adjunct to antibiotic therapy. To identify genes potentially involved in probiotic activity, we performed genome sequencing and characterization of the two strains. The complete genome analysis of both strains revealed the presence of genes encoding functions related to adhesion, exopolysaccharide (EPS) biosynthesis, antimicrobial activity, and CRISPR adaptive immunity but absence of antibiotic resistance genes. Interesting features of L. rhamnosus DSM 14870 genome include the presence of the spaCBA-srtC gene encoding spaCBA pili and interruption of the gene cluster encoding long galactose-rich EPS by integrases. Unique to L. gasseri DSM 14869 genome was the presence of a gene encoding a putative (1456 amino acid) new adhesin containing two rib/alpha-like repeats. L. rhamnosus DSM 14870 and L. gasseri DSM 14869 showed acidification of the culture medium (to pH 3.8) and a strong adhesion capability to the Caco-2 cell line and VEC. L. gasseri DSM 14869 could produce a thick (40nm) EPS layer and hydrogen peroxide. L. rhamnosus DSM 14870 was shown to produce SpaCBA pili and a 20nm EPS layer, and could inhibit the growth of Gardnerella vaginalis, a bacterium commonly associated with BV. The genome sequences provide a basis for further elucidation of the molecular basis for their probiotic functions.}, }
@article {pmid28942844, year = {2017}, author = {Lee, JY and Han, GG and Kim, EB and Choi, YJ}, title = {Comparative genomics of Lactobacillus salivarius strains focusing on their host adaptation.}, journal = {Microbiological research}, volume = {205}, number = {}, pages = {48-58}, doi = {10.1016/j.micres.2017.08.008}, pmid = {28942844}, issn = {1618-0623}, mesh = {Acclimatization/*genetics ; Animals ; Bacterial Outer Membrane Proteins/genetics ; Base Sequence ; Carbohydrate Metabolism ; Cell Wall/chemistry/genetics ; Chickens ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; Feces/microbiology ; Gastrointestinal Tract/microbiology ; Gene Order ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics/physiology ; Genetic Structures ; *Genome, Bacterial ; Genomics ; Humans ; Ligilactobacillus salivarius/classification/*genetics/isolation &amp; purification/*physiology ; Phylogeny ; Probiotics ; Species Specificity ; Swine ; Symbiosis/genetics/physiology ; }, abstract = {Lactobacillus salivarius is an important member of the animal gut microflora and is a promising probiotic bacterium. However, there is a lack of research on the genomic diversity of L. salivarius species. In this study, we generated 21 L. salivarius draft genomes, and investigated the pan-genome of L. salivarius strains isolated from humans, pigs and chickens using all available genomes, focusing on host adaptation. Phylogenetic clustering showed a distinct categorization of L. salivarius strains depending on their hosts. In the pan-genome, 15 host-specific genes and 16 dual-host-shared genes that only one host isolate did not possess were identified. Comparison of 56 extracellular protein encoding genes and 124 orthologs related to exopolysaccharide production in the pan-genome revealed that extracellular components of the assayed bacteria have been globally acquired and mutated under the selection pressure for host adaptation. We also found the three host-specific genes that are responsible for energy production in L. salivarius. These results showed that L. salivarius has evolved to adapt to host habitats in two ways, by gaining the abilities for niche adhesion and efficient utilization of nutrients. Our study offers a deeper understanding of the probiotic species L. salivarius, and provides a basis for future studies on L. salivarius and other mutualistic bacteria.}, }
@article {pmid28941941, year = {2017}, author = {Jurėnas, D and Garcia-Pino, A and Van Melderen, L}, title = {Novel toxins from type II toxin-antitoxin systems with acetyltransferase activity.}, journal = {Plasmid}, volume = {93}, number = {}, pages = {30-35}, doi = {10.1016/j.plasmid.2017.08.005}, pmid = {28941941}, issn = {1095-9890}, mesh = {Acetyltransferases/*genetics ; Antitoxins/genetics ; Bacteria/genetics ; Bacterial Proteins/genetics ; Bacterial Toxins/genetics ; Genome, Bacterial/genetics ; Toxin-Antitoxin Systems/*genetics ; }, abstract = {Type II toxin-antitoxin (TA) systems are widespread in bacterial and archeal genomes. These modules are very dynamic and participate in bacterial genome evolution through horizontal gene transfer. TA systems are commonly composed of a labile antitoxin and a stable toxin. Toxins appear to preferentially inhibit the protein synthesis process. Toxins use a variety of molecular mechanisms and target nearly every step of translation to achieve their inhibitory function. This review focuses on a recently identified TA family that includes acetyltransferase toxins. The AtaT and TacT toxins are the best-characterized to date in this family. AtaT and TacT both inhibit translation by acetylating the amino acid charged on tRNAs. However, the specificities of these 2 toxins are different as AtaT inhibits translation initiation by acetylation of the initiator tRNA whereas TacT acetylates elongator tRNAs. The molecular mechanisms of these toxins are discussed, as well as the functions and possible evolutionary origins of this diverse toxin family.}, }
@article {pmid28936945, year = {2017}, author = {Taylor, JW and Branco, S and Gao, C and Hann-Soden, C and Montoya, L and Sylvain, I and Gladieux, P}, title = {Sources of Fungal Genetic Variation and Associating It with Phenotypic Diversity.}, journal = {Microbiology spectrum}, volume = {5}, number = {5}, pages = {}, pmid = {28936945}, issn = {2165-0497}, mesh = {Fungi/classification/*genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; *Genetic Variation ; Genome, Fungal ; Phenotype ; }, abstract = {The first eukaryotic genome to be sequenced was fungal, and there continue to be more sequenced genomes in the kingdom Fungi than in any other eukaryotic kingdom. Comparison of these genomes reveals many sources of genetic variation, from single nucleotide polymorphisms to horizontal gene transfer and on to changes in the arrangement and number of chromosomes, not to mention endofungal bacteria and viruses. Population genomics shows that all sources generate variation all the time and implicate natural selection as the force maintaining genome stability. Variation in wild populations is a rich resource for associating genetic variation with phenotypic variation, whether through quantitative trait locus mapping, genome-wide association studies, or reverse ecology. Subjects of studies associating genetic and phenotypic variation include model fungi, e.g., Saccharomyces and Neurospora, but pioneering studies have also been made with fungi pathogenic to plants, e.g., Pyricularia (= Magnaporthe), Zymoseptoria, and Fusarium, and to humans, e.g., Coccidioides, Cryptococcus, and Candida.}, }
@article {pmid28932624, year = {2017}, author = {Sansevere, EA and Robinson, DA}, title = {Staphylococci on ICE: Overlooked agents of horizontal gene transfer.}, journal = {Mobile genetic elements}, volume = {7}, number = {4}, pages = {1-10}, pmid = {28932624}, issn = {2159-2543}, support = {R01 GM080602/GM/NIGMS NIH HHS/United States ; }, abstract = {Horizontal gene transfer plays a significant role in spreading antimicrobial resistance and virulence genes throughout the genus Staphylococcus, which includes species of clinical relevance to humans and animals. While phages and plasmids are the most well-studied agents of horizontal gene transfer in staphylococci, the contribution of integrative conjugative elements (ICEs) has been mostly overlooked. Experimental work demonstrating the activity of ICEs in staphylococci remained frozen for years after initial work in the 1980s that showed Tn916 was capable of transfer from Enterococcus to Staphylococcus. However, recent work has begun to thaw this field. To date, 2 families of ICEs have been identified among staphylococci - Tn916 that includes the Tn5801 subfamily, and ICE6013 that includes at least 7 subfamilies. Both Tn5801 and ICE6013 commonly occur in clinical strains of S. aureus. Tn5801 is the most studied of the Tn916 family elements in staphylococci and encodes tetracycline resistance and a protein that, when expressed in Escherichia coli, inhibits restriction barriers to incoming DNA. ICE6013 is among the shortest known ICEs, but it still includes many uncharacterized open reading frames. This element uses an IS30-like transposase as its recombinase, providing some versatility in integration sites. ICE6013 also conjugatively transfers among receptive S. aureus strains at relatively higher frequency than Tn5801. Continued study of these mobile genetic elements may reveal the full extent to which ICEs impact horizontal gene transfer and the evolution of staphylococci.}, }
@article {pmid28932232, year = {2017}, author = {Wang, Q and Sun, H and Huang, J}, title = {Re-analyses of "Algal" Genes Suggest a Complex Evolutionary History of Oomycetes.}, journal = {Frontiers in plant science}, volume = {8}, number = {}, pages = {1540}, pmid = {28932232}, issn = {1664-462X}, abstract = {The spread of photosynthesis is one of the most important but constantly debated topics in eukaryotic evolution. Various hypotheses have been proposed to explain the plastid distribution in extant eukaryotes. Notably, the chromalveolate hypothesis suggested that multiple eukaryotic lineages were derived from a photosynthetic ancestor that had a red algal endosymbiont. As such, genes of plastid/algal origin in aplastidic chromalveolates, such as oomycetes, were considered to be important supporting evidence. Although the chromalveolate hypothesis has been seriously challenged, some of its supporting evidence has not been carefully investigated. In this study, we re-evaluate the "algal" genes from oomycetes with a larger sampling and careful phylogenetic analyses. Our data provide no conclusive support for a common photosynthetic ancestry of stramenopiles, but show that the initial estimate of "algal" genes in oomycetes was drastically inflated due to limited genome data available then for certain eukaryotic lineages. These findings also suggest that the evolutionary histories of these "algal" genes might be attributed to complex scenarios such as differential gene loss, serial endosymbioses, or horizontal gene transfer.}, }
@article {pmid28929967, year = {2017}, author = {Sarı, AN and Süzük, S and Karatuna, O and Öğünç, D and Karakoç, AE and Çizmeci, Z and Alışkan, HE and Cömert, F and Bakıcı, MZ and Akpolat, N and Çilli, FF and Zer, Y and Karataş, A and Akgün Karapınar, B and Bayramoğlu, G and Özdamar, M and Kalem, F and Delialioğlu, N and Aktaş, E and Yılmaz, N and Gürcan, &#x15e; and Gülay, Z}, title = {[Results of a multicenter study investigating plasmid mediated colistin resistance genes (mcr-1 and mcr-2) in clinical Enterobacteriaceae ısolates from Turkey].}, journal = {Mikrobiyoloji bulteni}, volume = {51}, number = {3}, pages = {299-303}, doi = {10.5578/mb.57515}, pmid = {28929967}, issn = {0374-9096}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/*genetics ; Colistin/*pharmacology ; Drug Resistance, Bacterial/*genetics ; Enterobacteriaceae/drug effects/*genetics/isolation &amp; purification ; Humans ; *R Factors ; Turkey ; }, abstract = {Colistin is a polymyxin antibiotic which is considered as one of the last line agents against infections due to multidrug resistant or carbapenem resistant gram-negative pathogens. Colistin resistance is associated with chromosomal alterations which can usually cause mutations in genes coding specific two component regulator systems. The first plasmid-mediated colistin resistance gene, mcr-1 was described in Escherichia coli and Klebsiella pneumoniae isolates in December 2015 and followed by another plasmid-mediated colistin resistance gene mcr-2 in 2016. The rapid and interspecies dissemination of plasmid-mediated resistance mechanisms through horizontal gene transfer, have made these genes considerably threatening. After the first reports, although mcr-1/mcr-2 producing Enterobacteriaceae isolates have been reported from many countries, there have been no reports from Turkey. Thus, the aim of this study was to investigate the presence of mcr-1/mcr-2 in clinical Enterobacteriaceae isolates from different parts of our country. A total of 329 Enterobacteriaceae isolates from 22 laboratories were collected which were isolated between March, 2015 and February, 2016. mcr-1/mcr-2 were investigated by polymerase chain reaction during February-March, 2016. Two hundred and seventeen of Klebsiella pneumoniae (66%), 75 of Salmonella spp. (22.8%), 31 of Esherichia coli (9.4%), 3 of Enterobacter cloacae (0.9%), 2 of Klebsiella oxytoca (0.6%) and 1 of Enterobacter aerogenes (0.3%) isolates were included to the study. Agarose gel electrophoresis results of PCR studies have shown expected band sizes for positive control isolates as 309 bp for mcr-1 and 567 bp for mcr-2. However, the presence of mcr-1/mcr-2 genes was not detected among the tested study isolates of Enterobacteriaceae. Although mcr-1/mcr-2 were not detected in our study isolates, it is highly important to understand the mechanism of resistance dissemination and determine the resistant isolates by considering that colistin is a last-line antibiotic against infections of multidrug or carbapenem resistant gram-negative bacteria. Thus, it is suggested that these mechanisms should be followed-up in both clinical and non-clinical (e.g. isolates from food animals, raw meats and environment) isolates of special populations.}, }
@article {pmid28923961, year = {2017}, author = {Shih, PM and Ward, LM and Fischer, WW}, title = {Evolution of the 3-hydroxypropionate bicycle and recent transfer of anoxygenic photosynthesis into the Chloroflexi.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {40}, pages = {10749-10754}, pmid = {28923961}, issn = {1091-6490}, mesh = {Bacterial Proteins/genetics/*metabolism ; *Biological Evolution ; Chloroflexi/genetics/growth &amp; development/*metabolism ; Genome, Bacterial ; Genomics ; Lactic Acid/*analogs &amp; derivatives/metabolism ; Oxidation-Reduction ; Oxygen/*metabolism ; *Photosynthesis ; Phylogeny ; }, abstract = {Various lines of evidence from both comparative biology and the geologic record make it clear that the biochemical machinery for anoxygenic photosynthesis was present on early Earth and provided the evolutionary stock from which oxygenic photosynthesis evolved ca. 2.3 billion years ago. However, the taxonomic identity of these early anoxygenic phototrophs is uncertain, including whether or not they remain extant. Several phototrophic bacterial clades are thought to have evolved before oxygenic photosynthesis emerged, including the Chloroflexi, a phylum common across a wide range of modern environments. Although Chloroflexi have traditionally been thought to be an ancient phototrophic lineage, genomics has revealed a much greater metabolic diversity than previously appreciated. Here, using a combination of comparative genomics and molecular clock analyses, we show that phototrophic members of the Chloroflexi phylum are not particularly ancient, having evolved well after the rise of oxygen (ca. 867 million years ago), and thus cannot be progenitors of oxygenic photosynthesis. Similarly, results show that the carbon fixation pathway that defines this clade-the 3-hydroxypropionate bicycle-evolved late in Earth history as a result of a series of horizontal gene transfer events, explaining the lack of geological evidence for this pathway based on the carbon isotope record. These results demonstrate the role of horizontal gene transfer in the recent metabolic innovations expressed within this phylum, including its importance in the development of a novel carbon fixation pathway.}, }
@article {pmid28923605, year = {2017}, author = {Li, Y and Yang, L and Fu, J and Yan, M and Chen, D and Zhang, L}, title = {Microbial pathogenicity and virulence mediated by integrons on Gram-positive microorganisms.}, journal = {Microbial pathogenesis}, volume = {111}, number = {}, pages = {481-486}, doi = {10.1016/j.micpath.2017.09.035}, pmid = {28923605}, issn = {1096-1208}, mesh = {Animals ; Gene Transfer, Horizontal ; Gram-Positive Bacteria/*genetics/metabolism/*pathogenicity ; Gram-Positive Bacterial Infections/*microbiology ; Humans ; *Integrons ; Virulence ; }, abstract = {Gram-positive microorganisms are one of leading pathogenic microorganisms in public health, including several typical "Super Bugs" as methicillin-resistant Staphylococcus aureus, Klebsiella pneumoniae carbapenemase and vancomycin-resistant enterococci, which caused a increasement of infections, clinical failures and expenses. Regarded as a common genetic element responsible for horizontal gene transfer, integrons are widely distributed in various pathogens considered as a determinant in the acquisition and evolution of antibiotic resistance. Current investigations mainly focus on the distribution of integrons in Gram-negative microorganisms, while the role of integron in antibiotic resistance among Gram-positive microorganisms remains unclear and need investigation. To date, the surveillances of integrons in Gram-positive microorganism have been widely conducted in clinic, community even husbandry. China remains one of the worst country in antibiotics abuse worldwide and considered as a potential area for the prevalence of antimicrobial microorganisms and the occurrence of various 'Super Bugs'. Recently, the surveillance of the occurrence of integron and resistance gene cassettes was conducted in South China during the first 10 years of the 21st century. Referred to the surveillance in South China and other investigation in Asian countries, this review aims to summarize the occurrence, pathogenicity and virulence mediated by integrons in typical Gram-positive microorganisms (Staphylococcus, Enterococcus, Corynebacterium and Streptococcus) and the role of integrons in antibiotic resistance.}, }
@article {pmid28923604, year = {2017}, author = {Lin, Q and Xu, P and Li, J and Huang, J and Chen, Y and Deng, S}, title = {Study on the excision and integration mediated by class 1 integron in Streptococcus pneumoniae.}, journal = {Microbial pathogenesis}, volume = {111}, number = {}, pages = {446-449}, doi = {10.1016/j.micpath.2017.09.031}, pmid = {28923604}, issn = {1096-1208}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; *Integrons ; Plasmids/genetics/metabolism ; Streptococcus pneumoniae/drug effects/*genetics/metabolism ; }, abstract = {As a novel antibiotic resistance mobile element, integron was recognized as a primary source of antibiotic genes among Gram-positive organisms for its excision and integration of exogenous genes. In this study, Streptococcus pneumoniae was subjected to investigate the excision and integration of class 1 integron with eight different plasmids. As the results indicated, excision in both att site and gene cassettes were successfully observed, which was further confirmed by integration assays and PCR amplification. The observation of class 1 integron mediated excision and integration of various exogenous antibiotics resistance genes may raise the attention of integrons as novel antibiotic resistance determinant in Gram-positive bacteria, especially in Streptococcus.}, }
@article {pmid28923487, year = {2017}, author = {Oakley, TH}, title = {Furcation and fusion: The phylogenetics of evolutionary novelty.}, journal = {Developmental biology}, volume = {431}, number = {1}, pages = {69-76}, doi = {10.1016/j.ydbio.2017.09.015}, pmid = {28923487}, issn = {1095-564X}, mesh = {Animals ; *Biological Evolution ; Evolution, Molecular ; Gene Expression Regulation, Developmental ; Gene Regulatory Networks ; Growth and Development/genetics ; Models, Genetic ; *Phylogeny ; }, abstract = {Novelty and innovation are fundamental yet relatively understudied concepts in evolution. We may study the history and provenance of novelty using phylogenetics, where key questions include when evolution occurs by tree-like branching and when it occurs by movement of distantly related parts in processes akin to horizontal transfer. Perfectly vertical inheritance, often an assumption of evolutionary trees, requires simultaneous co-duplication of the parts of a duplicating or speciating (processes I collectively call 'furcating') biological feature. However, simultaneous co-duplication of many parts usually requires variational processes that are rare. Therefore, instead of always being perfectly tree-like, evolution often involves events that incorporate or fuse more distantly related parts into new units during evolution, which herein I call 'fusion'. Exon shuffling, horizontal gene transfer, introgression, and co-option are such fusion processes at different levels of organization. The ubiquity of processes that fuse distantly related parts has wide ranging implications for the study of macroevolution. For one, the central metaphor of a tree of life will often be incomplete, to the point where we may consider a different metaphor, such as economic public goods, or a 'web of life'. Secondly, we often may need to expand commonly used phylogenetic models and methods, highlighting a need for an expansive toolkit for studying evolutionary history. Even though furcation - the splitting and individuation of biological features - does happen, fusion of distant parts may often be just as critical for the evolution of novelties, and must formally be incorporated into the metaphors, models, and visualization of evolutionary history. This will allow us to understand the timing, order of appearance, and diversification rates of developmental systems, including cell types, organs, behavior, and language, which very commonly evolve through co-option.}, }
@article {pmid28920507, year = {2018}, author = {Sharma, A and Rani, S and Goel, M}, title = {Navigating the structure-function-evolutionary relationship of CsaA chaperone in archaea.}, journal = {Critical reviews in microbiology}, volume = {44}, number = {3}, pages = {274-289}, doi = {10.1080/1040841X.2017.1357535}, pmid = {28920507}, issn = {1549-7828}, mesh = {Archaea/chemistry/classification/genetics/*metabolism ; Archaeal Proteins/*chemistry/genetics/*metabolism ; *Evolution, Molecular ; Molecular Chaperones/*chemistry/genetics/*metabolism ; Phylogeny ; }, abstract = {CsaA is a protein involved in the post-translational translocation of proteins across the cytoplasmic membrane. It is considered to be a functional homolog of SecB which participates in the Sec-dependent translocation pathway in an analogous manner. CsaA has also been reported to act as a molecular chaperone, preventing aggregation of unfolded proteins. It is essentially a prokaryotic protein which is absent in eukaryotes, but found extensively in bacteria and earlier thought to be widely present in archaea. The study of phylogenetic distribution of CsaA among prokaryotes suggests that it is present only in few archaeal organisms, mainly species of Thermoplasmatales and Halobacteriales. Interestingly, the CsaA protein from these two archaeal orders cluster separately on the phylogenetic tree with CsaA from Gram-positive and Gram-negative bacteria. It, thus, appears that this protein might have been acquired in these archaeal organisms through independent horizontal gene transfer (HGT) events from different bacteria. In this review, we summarize the earlier biochemical, structural, and functional characterization studies of CsaA. We draw new insights into the evolutionary history of this protein through phylogenetic and structural comparison of bacterial CsaA with modelled archaeal CsaA from Picrophilus torridus and Natrialba magadii.}, }
@article {pmid28916329, year = {2017}, author = {Nakajima, T}, title = {Ecological extension of the theory of evolution by natural selection from a perspective of Western and Eastern holistic philosophy.}, journal = {Progress in biophysics and molecular biology}, volume = {131}, number = {}, pages = {298-311}, doi = {10.1016/j.pbiomolbio.2017.09.005}, pmid = {28916329}, issn = {1873-1732}, mesh = {Adaptation, Physiological ; *Biological Evolution ; *Philosophy ; *Selection, Genetic ; *Western World ; }, abstract = {Evolution by natural selection requires the following conditions: (1) a particular selective environment; (2) variation of traits in the population; (3) differential survival/reproduction among the types of organisms; and (4) heritable traits. However, the traditional (standard) model does not clearly explain how and why these conditions are generated or determined. What generates a selective environment? What generates new types? How does a certain type replace, or coexist with, others? In this paper, based on the holistic philosophy of Western and Eastern traditions, I focus on the ecosystem as a higher-level system and generator of conditions that induce the evolution of component populations; I also aim to identify the ecosystem processes that generate those conditions. In particular, I employ what I call the scientific principle of dependent-arising (SDA), which is tailored for scientific use and is based on Buddhism principle called "pratītya-samutpāda" in Sanskrit. The SDA principle asserts that there exists a higher-level system, or entity, which includes a focal process of a system as a part within it; this determines or generates the conditions required for the focal process to work in a particular way. I conclude that the ecosystem generates (1) selective environments for component species through ecosystem dynamics; (2) new genetic types through lateral gene transfer, hybridization, and symbiogenesis among the component species of the ecosystem; (3) mechanistic processes of replacement of an old type with a new one. The results of this study indicate that the ecological extension of the theoretical model of adaptive evolution is required for better understanding of adaptive evolution.}, }
@article {pmid28915794, year = {2017}, author = {Wang, B and Liang, X and Gleason, ML and Zhang, R and Sun, G}, title = {Genome sequence of the ectophytic fungus Ramichloridium luteum reveals unique evolutionary adaptations to plant surface niche.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {729}, pmid = {28915794}, issn = {1471-2164}, mesh = {Adaptation, Physiological/*genetics ; Ascomycota/*genetics/*physiology ; *Evolution, Molecular ; Genome, Fungal/genetics ; *Genomics ; Phylogeny ; Plants/*microbiology ; Stress, Physiological/genetics ; }, abstract = {BACKGROUND: Ectophytic fungi occupy the waxy plant surface, an extreme environment characterized by prolonged desiccation, nutrient limitation, and exposure to solar radiation. The nature of mechanisms that facilitate adaptation to this environment remains unclear. In this study, we sequenced the complete genome of an ectophytic fungus, Ramichloridium luteum, which colonizes the surface of apple fruit, and carried out comparative genomic and transcriptome analysis.<br><br>RESULTS: The R. luteum genome was 28.18&#xa0;Mb and encoded 9466 genes containing 1.85% repetitive elements. Compared with cell-penetrating pathogens, genes encoding plant cell wall degrading enzymes (PCWDEs), PTH11-like G protein-coupled receptors (GPCRs) and effectors were drastically reduced. In contrast, genes encoding cutinases and secretory lipases were strikingly expanded, and four of nine secretory lipases were probably acquired by horizontal gene transfer from Basidiomycota. Transcriptomic analysis revealed elevated expression of genes involved in cuticle degradation (cutinase, secretory lipase) and stress responses (melanin biosynthesis, aquaporins, lysozymes and HOG pathway).<br><br>CONCLUSIONS: Taken together, our results highlight genomic features associated with evolution of surface niche adaptation by the ectophytic fungus R. luteum, namely the contraction of PCWDEs, PTH11-like GPCRs and effectors, and the expansion of cuticle degradation and stress tolerance.}, }
@article {pmid28914880, year = {2018}, author = {Gil, R and Vargas-Chavez, C and López-Madrigal, S and Santos-García, D and Latorre, A and Moya, A}, title = {Tremblaya phenacola PPER: an evolutionary beta-gammaproteobacterium collage.}, journal = {The ISME journal}, volume = {12}, number = {1}, pages = {124-135}, pmid = {28914880}, issn = {1751-7370}, mesh = {Animals ; Bacterial Proteins/genetics/metabolism ; Betaproteobacteria/classification/*genetics/isolation &amp; purification/physiology ; Biological Evolution ; Gene Transfer, Horizontal ; Genome, Bacterial ; Hemiptera/*microbiology/physiology ; Phylogeny ; Symbiosis ; }, abstract = {Many insects rely on bacterial endosymbionts to obtain nutrients that are scarce in their highly specialized diets. The most surprising example corresponds to the endosymbiotic system found in mealybugs from subfamily Pseudococcinae in which two bacteria, the betaproteobacterium 'Candidatus Tremblaya princeps' and a gammaproteobacterium, maintain a nested endosymbiotic consortium. In the sister subfamily Phenacoccinae, however, a single beta-endosymbiont, 'Candidatus Tremblaya phenacola', has been described. In a previous study, we detected a trpB gene of gammaproteobacterial origin in 'Ca. Tremblaya phenacola' from two Phenacoccus species, apparently indicating an unusual case of horizontal gene transfer (HGT) in a bacterial endosymbiont. What we found by sequencing the genome of 'Ca. Tremblaya phenacola' PPER, single endosymbiont of Phenacoccus peruvianus, goes beyond a HGT phenomenon. It rather represents a genome fusion between a beta and a gammaproteobacterium, followed by massive rearrangements and loss of redundant genes, leading to an unprecedented evolutionary collage. Mediated by the presence of several repeated sequences, there are many possible genome arrangements, and different subgenomic sequences might coexist within the same population.}, }
@article {pmid28912766, year = {2017}, author = {Day, A and Ahn, J and Fang, X and Salmond, GPC}, title = {Environmental Bacteriophages of the Emerging Enterobacterial Phytopathogen, Dickeya solani, Show Genomic Conservation and Capacity for Horizontal Gene Transfer between Their Bacterial Hosts.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1654}, pmid = {28912766}, issn = {1664-302X}, support = {BB/G000298/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/H002677/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {Dickeya solani is an economically important phytopathogen widespread in mainland Europe that can reduce potato crop yields by 25%. There are no effective environmentally-acceptable chemical systems available for diseases caused by Dickeya. Bacteriophages have been suggested for use in biocontrol of this pathogen in the field, and limited field trials have been conducted. To date only a small number of bacteriophages capable of infecting D. solani have been isolated and characterized, and so there is a need to expand the repertoire of phages that may have potential utility in phage therapy strategies. Here we describe 67 bacteriophages from environmental sources, the majority of which are members of the viral family Myoviridae. Full genomic sequencing of two isolates revealed a high degree of DNA identity with D. solani bacteriophages isolated in Europe in the past 5 years, suggesting a wide ecological distribution of this phage family. Transduction experiments showed that the majority of the new environmental bacteriophages are capable of facilitating efficient horizontal gene transfer. The possible risk of unintentional transfer of virulence or antibiotic resistance genes between hosts susceptible to transducing phages cautions against their environmental use for biocontrol, until specific phages are fully tested for transduction capabilities.}, }
@article {pmid28911112, year = {2017}, author = {Cury, J and Touchon, M and Rocha, EPC}, title = {Integrative and conjugative elements and their hosts: composition, distribution and organization.}, journal = {Nucleic acids research}, volume = {45}, number = {15}, pages = {8943-8956}, pmid = {28911112}, issn = {1362-4962}, support = {281605/ERC_/European Research Council/International ; }, mesh = {Actinobacteria/classification/genetics/metabolism ; Archaea/classification/genetics/metabolism ; *Conjugation, Genetic ; DNA Replication ; *DNA Transposable Elements ; DNA, Bacterial/*genetics/metabolism ; Evolution, Molecular ; Firmicutes/classification/genetics/metabolism ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Integrases/genetics/metabolism ; Lysogeny ; *Phylogeny ; Plasmids/*chemistry/metabolism ; Proteobacteria/classification/genetics/metabolism ; Recombinases/genetics/metabolism ; }, abstract = {Conjugation of single-stranded DNA drives horizontal gene transfer between bacteria and was widely studied in conjugative plasmids. The organization and function of integrative and conjugative elements (ICE), even if they are more abundant, was only studied in a few model systems. Comparative genomics of ICE has been precluded by the difficulty in finding and delimiting these elements. Here, we present the results of a method that circumvents these problems by requiring only the identification of the conjugation genes and the species' pan-genome. We delimited 200 ICEs and this allowed the first large-scale characterization of these elements. We quantified the presence in ICEs of a wide set of functions associated with the biology of mobile genetic elements, including some that are typically associated with plasmids, such as partition and replication. Protein sequence similarity networks and phylogenetic analyses revealed that ICEs are structured in functional modules. Integrases and conjugation systems have different evolutionary histories, even if the gene repertoires of ICEs can be grouped in function of conjugation types. Our characterization of the composition and organization of ICEs paves the way for future functional and evolutionary analyses of their cargo genes, composed of a majority of unknown function genes.}, }
@article {pmid28904857, year = {2017}, author = {Tang, VH and Stewart, GA and Chang, BJ}, title = {Dermatophagoides pteronyssinus lytFM encoding an NlpC/P60 endopeptidase is also present in mite-associated bacteria that express LytFM variants.}, journal = {FEBS open bio}, volume = {7}, number = {9}, pages = {1267-1280}, pmid = {28904857}, issn = {2211-5463}, abstract = {The bodies and faecal pellets of the house dust mite (HDM), Dermatophagoides pteronyssinus, are the source of many allergenic and nonallergenic proteins. One of these, the 14-kDa bacteriolytic enzyme LytFM, originally isolated from the spent HDM growth medium, may contribute to bacteriolytic activity previously detected by zymography at 14 kDa in the culture supernatants of some bacterial species isolated from surface-sterilised HDM. Based on previously reported findings of lateral gene transfer between microbes and their eukaryotic hosts, we investigated the presence of lytFM in the genomes of nine Gram-positive bacteria from surface-sterilised HDM, and the expression by these isolates of LytFM and its variants LytFM1/LytFM2. The lytFM gene was detected by PCR in the genomes of three of the isolates: Bacillus licheniformis strain 1, B. licheniformis strain 2 and Staphylococcus aureus. Expression of the variant LytFM1 was detected in culture supernatants of these bacteria by mass spectrometry (MS) and ELISA, and the bacterial LytFM proteins were shown by zymography to be able to hydrolyse peptidoglycan. Our previous reports of LytFM homologues in other mite species and their phylogenetic analysis had suggested that they originated from a common mite ancestor. The phylogenetic analysis reported herein and the detection of other D. pteronyssinus proteins by MS in the culture supernatants of the three isolates that secreted LytFM1 further support the hypothesis of lateral gene transfer to the bacterial endosymbionts from their HDM host. The complete sequence homology observed between the genes amplified from the microbes and those in their eukaryotic host indicated that the lateral gene transfer was an event that occurred recently.}, }
@article {pmid28900256, year = {2017}, author = {Blasi, B and Tafer, H and Kustor, C and Poyntner, C and Lopandic, K and Sterflinger, K}, title = {Genomic and transcriptomic analysis of the toluene degrading black yeast Cladophialophora immunda.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {11436}, pmid = {28900256}, issn = {2045-2322}, support = {P 25119/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Ascomycota/classification/*genetics/*metabolism ; Computational Biology/methods ; Evolution, Molecular ; *Gene Expression Profiling/methods ; Gene Transfer, Horizontal ; Genes, Fungal ; Genome, Fungal ; *Genomics/methods ; Metabolic Networks and Pathways ; Molecular Sequence Annotation ; Phylogeny ; Secondary Metabolism/genetics ; Toluene/*metabolism ; }, abstract = {Cladophialophora immunda is an ascomycotal species belonging to the group of the black yeasts. These fungi have a thick and melanized cell wall and other physiological adaptations that allows them to cope with several extreme physical and chemical conditions. Member of the group can colonize some of the most extremophilic environments on Earth. Cladophialophora immunda together with a few other species of the order Chaetothyriales show a special association with hydrocarbon polluted environments. The finding that the fungus is able to completely mineralize toluene makes it an interesting candidate for bioremediation purposes. The present study is the first transcriptomic investigation of a fungus grown in presence of toluene as sole carbon and energy source. We could observe the activation of genes involved in toluene degradatation and several stress response mechanisms which allowed the fungus to survive the toluene exposure. The thorough comparative genomics analysis allowed us to identify several events of horizontal gene transfer between bacteria and Cladophialophora immunda and unveil toluene degradation steps that were previously reported in bacteria. The work presented here aims to give new insights into the ecology of Cladophialophora immunda and its adaptation strategies to hydrocarbon polluted environments.}, }
@article {pmid28899756, year = {2017}, author = {Toman, J and Flegr, J}, title = {Stability-based sorting: The forgotten process behind (not only) biological evolution.}, journal = {Journal of theoretical biology}, volume = {435}, number = {}, pages = {29-41}, doi = {10.1016/j.jtbi.2017.09.004}, pmid = {28899756}, issn = {1095-8541}, mesh = {*Biological Evolution ; Biota ; Models, Genetic ; Reproduction ; *Selection, Genetic ; }, abstract = {Natural selection is considered to be the main process that drives biological evolution. It requires selected entities to originate dependent upon one another by the means of reproduction or copying, and for the progeny to inherit the qualities of their ancestors. However, natural selection is a manifestation of a more general persistence principle, whose temporal consequences we propose to name "stability-based sorting" (SBS). Sorting based on static stability, i.e., SBS in its strict sense and usual conception, favours characters that increase the persistence of their holders and act on all material and immaterial entities. Sorted entities could originate independently from each other, are not required to propagate and need not exhibit heredity. Natural selection is a specific form of SBS-sorting based on dynamic stability. It requires some form of heredity and is based on competition for the largest difference between the speed of generating its own copies and their expiration. SBS in its strict sense and selection thus have markedly different evolutionary consequences that are stressed in this paper. In contrast to selection, which is opportunistic, SBS is able to accumulate even momentarily detrimental characters that are advantageous for the long-term persistence of sorted entities. However, it lacks the amplification effect based on the preferential propagation of holders of advantageous characters. Thus, it works slower than selection and normally is unable to create complex adaptations. From a long-term perspective, SBS is a decisive force in evolution-especially macroevolution. SBS offers a new explanation for numerous evolutionary phenomena, including broad distribution and persistence of sexuality, altruistic behaviour, horizontal gene transfer, patterns of evolutionary stasis, planetary homeostasis, increasing ecosystem resistance to disturbances, and the universal decline of disparity in the evolution of metazoan lineages. SBS acts on all levels in all biotic and abiotic systems. It could be the only truly universal evolutionary process, and an explanatory framework based on SBS could provide new insight into the evolution of complex abiotic and biotic systems.}, }
@article {pmid28898777, year = {2017}, author = {Liu, P and Jia, S and He, X and Zhang, X and Ye, L}, title = {Different impacts of manure and chemical fertilizers on bacterial community structure and antibiotic resistance genes in arable soils.}, journal = {Chemosphere}, volume = {188}, number = {}, pages = {455-464}, doi = {10.1016/j.chemosphere.2017.08.162}, pmid = {28898777}, issn = {1879-1298}, mesh = {Agriculture/methods ; China ; Drug Resistance, Microbial/*genetics ; *Fertilizers ; Genes, Bacterial ; High-Throughput Screening Assays ; *Manure ; Metagenomics ; Microbiota/*drug effects/genetics ; Soil/*chemistry ; Soil Microbiology/*standards ; }, abstract = {Both manure and chemical fertilizers are widely used in modern agriculture. However, the impacts of different fertilizers on bacterial community structure and antibiotic resistance genes (ARGs) in arable soils still remain unclear. In this study, high-throughput sequencing and quantitative PCR were employed to investigate the bacterial community structure, ARGs and mobile genetic elements (MGEs) influenced by the application of different fertilizers, including chemical fertilizers, piggery manure and straw ash. The results showed that the application of fertilizers could significantly change the soil bacterial community and the abundance of Gaiella under phylum Actinobacteria was significantly reduced from 12.9% in unfertilized soil to 4.1%-7.4% in fertilized soil (P < 0.05). It was also found that the application of manure could cause a transient effect on soil resistome composition and the relative abundance of ARGs increased from 7.37 ppm to 32.10 ppm. The abundance of aminoglycoside, sulfonamide and tetracycline resistance genes greatly increased after manure fertilization and then gradually returned to normal levels with the decay of some intestinal bacteria carrying ARGs. In contrast, the application of chemical fertilizers and straw ash significantly changed the bacterial community structure but exerted little effect on soil resistome. Overall, the results of this study illustrated the different effects of different fertilizers on the soil resistome and revealed that the changes of soil resistome induced by manure application mainly resulted from alteration of bacteria community rather than the horizontal gene transfer.}, }
@article {pmid28894932, year = {2017}, author = {Pollo, SMJ and Adebusuyi, AA and Straub, TJ and Foght, JM and Zhaxybayeva, O and Nesbø, CL}, title = {Genomic insights into temperature-dependent transcriptional responses of Kosmotoga olearia, a deep-biosphere bacterium that can grow from 20 to 79 °C.}, journal = {Extremophiles : life under extreme conditions}, volume = {21}, number = {6}, pages = {963-979}, pmid = {28894932}, issn = {1433-4909}, mesh = {Acclimatization ; Gene Expression Regulation, Bacterial ; *Genome, Bacterial ; Gram-Negative Anaerobic Straight, Curved, and Helical Rods/*genetics/metabolism ; *Heat-Shock Response ; *Transcriptome ; }, abstract = {Temperature is one of the defining parameters of an ecological niche. Most organisms thrive within a temperature range that rarely exceeds ~30 °C, but the deep subsurface bacterium Kosmotoga olearia can grow over a temperature range of 59 °C (20-79 °C). To identify genes correlated with this flexible phenotype, we compared transcriptomes of K. olearia cultures grown at its optimal 65 °C to those at 30, 40, and 77 °C. The temperature treatments affected expression of 573 of 2224 K. olearia genes. Notably, this transcriptional response elicits re-modeling of the cellular membrane and changes in metabolism, with increased expression of genes involved in energy and carbohydrate metabolism at high temperatures and up-regulation of amino acid metabolism at lower temperatures. At sub-optimal temperatures, many transcriptional changes were similar to those observed in mesophilic bacteria at physiologically low temperatures, including up-regulation of typical cold stress genes and ribosomal proteins. Comparative genomic analysis of additional Thermotogae genomes indicates that one of K. olearia's strategies for low-temperature growth is increased copy number of some typical cold response genes through duplication and/or lateral acquisition. At 77 °C one-third of the up-regulated genes are of hypothetical function, indicating that many features of high-temperature growth are unknown.}, }
@article {pmid28894459, year = {2017}, author = {Jeong, H and Nasir, A}, title = {A Preliminary List of Horizontally Transferred Genes in Prokaryotes Determined by Tree Reconstruction and Reconciliation.}, journal = {Frontiers in genetics}, volume = {8}, number = {}, pages = {112}, pmid = {28894459}, issn = {1664-8021}, abstract = {Genome-wide global detection of genes involved in horizontal gene transfer (HGT) remains an active area of research in medical microbiology and evolutionary genomics. Utilizing the explicit evolutionary method of comparing topologies of a total of 154,805 orthologous gene trees against corresponding 16S rRNA "reference" trees, we previously detected a total of 660,894 candidate HGT events in 2,472 completely-sequenced prokaryotic genomes. Here, we report an HGT-index for each individual gene-reference tree pair reconciliation, representing the total number of detected HGT events on the gene tree divided by the total number of genomes (taxa) member of that tree. HGT-index is thus a simple measure indicating the sensitivity of prokaryotic genes to participate (or not participate) in HGT. Our preliminary list provides HGT-indices for a total of 69,365 genes (detected in >10 and <50% available prokaryotic genomes) that are involved in a wide range of biological processes such as metabolism, information, and bacterial response to environment. Identification of horizontally-derived genes is important to combat antibiotic resistance and is a step forward toward reconstructions of improved phylogenies describing the history of life. Our effort is thus expected to benefit ongoing research in the fields of clinical microbiology and evolutionary biology.}, }
@article {pmid28894204, year = {2017}, author = {Suhadolnik, MLS and Salgado, APC and Scholte, LLS and Bleicher, L and Costa, PS and Reis, MP and Dias, MF and Ávila, MP and Barbosa, FAR and Chartone-Souza, E and Nascimento, AMA}, title = {Novel arsenic-transforming bacteria and the diversity of their arsenic-related genes and enzymes arising from arsenic-polluted freshwater sediment.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {11231}, pmid = {28894204}, issn = {2045-2322}, mesh = {Anaerobiosis ; Arsenic/*metabolism ; Bacteria/*classification/genetics/isolation &amp; purification ; Biotransformation ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Enzymes/genetics ; Fresh Water/*microbiology ; *Genetic Variation ; Geologic Sediments/*microbiology ; Metabolic Networks and Pathways/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Bacteria are essential in arsenic cycling. However, few studies have addressed 16S rRNA and arsenic-related functional gene diversity in long-term arsenic-contaminated tropical sediment. Here, using culture-based, metagenomic and computational approaches, we describe the diversity of bacteria, genes and enzymes involved in AsIII and AsV transformation in freshwater sediment and in anaerobic AsIII- and AsV-enrichment cultures (ECs). The taxonomic profile reveals significant differences among the communities. Arcobacter, Dechloromonas, Sedimentibacter and Clostridium thermopalmarium were exclusively found in ECs, whereas Anaerobacillus was restricted to AsV-EC. Novel taxa that are both AsV-reducers and AsIII-oxidizers were identified: Dechloromonas, Acidovorax facilis, A. delafieldii, Aquabacterium, Shewanella, C. thermopalmarium and Macellibacteroides fermentans. Phylogenic discrepancies were revealed among the aioA, arsC and arrA genes and those of other species, indicating horizontal gene transfer. ArsC and AioA have sets of amino acids that can be used to assess their functional and structural integrity and familial subgroups. The positions required for AsV reduction are conserved, suggesting strong selective pressure for maintaining the functionality of ArsC. Altogether, these findings highlight the role of freshwater sediment bacteria in arsenic mobility, and the untapped diversity of dissimilatory arsenate-reducing and arsenate-resistant bacteria, which might contribute to arsenic toxicity in aquatic environments.}, }
@article {pmid28893987, year = {2017}, author = {Hirooka, S and Hirose, Y and Kanesaki, Y and Higuchi, S and Fujiwara, T and Onuma, R and Era, A and Ohbayashi, R and Uzuka, A and Nozaki, H and Yoshikawa, H and Miyagishima, SY}, title = {Acidophilic green algal genome provides insights into adaptation to an acidic environment.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {39}, pages = {E8304-E8313}, pmid = {28893987}, issn = {1091-6490}, mesh = {Adaptation, Physiological/*genetics ; Chlamydomonas reinhardtii/*genetics/metabolism ; *Genome, Plant ; Hydrogen-Ion Concentration ; Plant Proteins/*genetics/metabolism ; }, abstract = {Some microalgae are adapted to extremely acidic environments in which toxic metals are present at high levels. However, little is known about how acidophilic algae evolved from their respective neutrophilic ancestors by adapting to particular acidic environments. To gain insights into this issue, we determined the draft genome sequence of the acidophilic green alga Chlamydomonas eustigma and performed comparative genome and transcriptome analyses between Ceustigma and its neutrophilic relative Chlamydomonas reinhardtii The results revealed the following features in Ceustigma that probably contributed to the adaptation to an acidic environment. Genes encoding heat-shock proteins and plasma membrane H[+]-ATPase are highly expressed in Ceustigma This species has also lost fermentation pathways that acidify the cytosol and has acquired an energy shuttle and buffering system and arsenic detoxification genes through horizontal gene transfer. Moreover, the arsenic detoxification genes have been multiplied in the genome. These features have also been found in other acidophilic green and red algae, suggesting the existence of common mechanisms in the adaptation to acidic environments.}, }
@article {pmid28893837, year = {2017}, author = {Burmistrz, M and Rodriguez Martinez, JI and Krochmal, D and Staniec, D and Pyrc, K}, title = {Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) RNAs in the Porphyromonas gingivalis CRISPR-Cas I-C System.}, journal = {Journal of bacteriology}, volume = {199}, number = {23}, pages = {}, pmid = {28893837}, issn = {1098-5530}, mesh = {CRISPR-Associated Proteins/genetics ; CRISPR-Cas Systems/*genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/*genetics ; Gene Transfer, Horizontal/genetics ; Porphyromonas gingivalis/*genetics ; RNA/*genetics ; }, abstract = {The CRISPR-Cas (clustered regularly interspaced short palindromic repeat-CRISPR-associated protein) system is unique to prokaryotes and provides the majority of bacteria and archaea with immunity against nucleic acids of foreign origin. CRISPR RNAs (crRNAs) are the key element of this system, since they are responsible for its selectivity and effectiveness. Typical crRNAs consist of a spacer sequence flanked with 5' and 3' handles originating from repeat sequences that are important for recognition of these small RNAs by the Cas machinery. In this investigation, we studied the type I-C CRISPR-Cas system in Porphyromonas gingivalis, a human pathogen associated with periodontitis, rheumatoid arthritis, cardiovascular disease, and aspiration pneumonia. We demonstrated the importance of the 5' handle for crRNA recognition by the effector complex and consequently activity, as well as secondary trimming of the 3' handle, which was not affected by modifications of the repeat sequence.IMPORTANCEPorphyromonas gingivalis, a clinically relevant Gram-negative, anaerobic bacterium, is one of the major etiologic agents of periodontitis and has been linked with the development of other clinical conditions, including rheumatoid arthritis, cardiovascular disease, and aspiration pneumonia. The presented results on the biogenesis and functions of crRNAs expand our understanding of CRISPR-Cas cellular defenses in P. gingivalis and of horizontal gene transfer in bacteria.}, }
@article {pmid28890711, year = {2017}, author = {Bolotin, E and Hershberg, R}, title = {Horizontally Acquired Genes Are Often Shared between Closely Related Bacterial Species.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1536}, pmid = {28890711}, issn = {1664-302X}, abstract = {Horizontal gene transfer (HGT) serves as an important source of innovation for bacterial species. We used a pangenome-based approach to identify genes that were horizontally acquired by four closely related bacterial species, belonging to the Enterobacteriaceae family. This enabled us to examine the extent to which such closely related species tend to share horizontally acquired genes. We find that a high percent of horizontally acquired genes are shared among these closely related species. Furthermore, we demonstrate that the extent of sharing of horizontally acquired genes among these four closely related species is predictive of the extent to which these genes will be found in additional bacterial species. Finally, we show that acquired genes shared by more species tend to be better optimized for expression within the genomes of their new hosts. Combined, our results demonstrate the existence of a large pool of frequently horizontally acquired genes that have distinct characteristics from horizontally acquired genes that are less frequently shared between species.}, }
@article {pmid28889978, year = {2017}, author = {Singer, A and Poschmann, G and Mühlich, C and Valadez-Cano, C and Hänsch, S and Hüren, V and Rensing, SA and Stühler, K and Nowack, ECM}, title = {Massive Protein Import into the Early-Evolutionary-Stage Photosynthetic Organelle of the Amoeba Paulinella chromatophora.}, journal = {Current biology : CB}, volume = {27}, number = {18}, pages = {2763-2773.e5}, doi = {10.1016/j.cub.2017.08.010}, pmid = {28889978}, issn = {1879-0445}, mesh = {Cercozoa/*physiology ; Chromatophores/*physiology ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Mass Spectrometry ; Metabolic Networks and Pathways ; Proteome/*analysis ; Protozoan Proteins/*analysis ; Sequence Analysis, Protein ; Symbiosis ; }, abstract = {The endosymbiotic acquisition of mitochondria and plastids more than 1 Ga ago profoundly impacted eukaryote evolution. At the heart of understanding organelle evolution is the re-arrangement of the endosymbiont proteome into a host-controlled organellar proteome. However, early stages in this process as well as the timing of events that underlie organelle integration remain poorly understood. The amoeba Paulinella chromatophora contains cyanobacterium-derived photosynthetic organelles, termed "chromatophores," that were acquired more recently (around 100 Ma ago). To explore the re-arrangement of an organellar proteome during its integration into a eukaryotic host cell, here we characterized the chromatophore proteome by protein mass spectrometry. Apparently, genetic control over the chromatophore has shifted substantially to the nucleus. Two classes of nuclear-encoded proteins-which differ in protein length-are imported into the chromatophore, most likely through independent pathways. Long imported proteins carry a putative, conserved N-terminal targeting signal, and many specifically fill gaps in chromatophore-encoded metabolic pathways or processes. Surprisingly, upon heterologous expression in a plant cell, the putative chromatophore targeting signal conferred chloroplast localization. This finding suggests common features in the protein import pathways of chromatophores and plastids, two organelles that evolved independently and more than 1 Ga apart from each other. By combining experimental data with in silico predictions, we provide a comprehensive catalog of almost 450 nuclear-encoded, chromatophore-targeted proteins. Interestingly, most imported proteins seem to derive from ancestral host genes, suggesting that the re-targeting of nuclear-encoded proteins that resulted from endosymbiotic gene transfers plays only a minor role at the onset of chromatophore integration.}, }
@article {pmid28889973, year = {2017}, author = {Guan, Z and Cai, T and Liu, Z and Dou, Y and Hu, X and Zhang, P and Sun, X and Li, H and Kuang, Y and Zhai, Q and Ruan, H and Li, X and Li, Z and Zhu, Q and Mai, J and Wang, Q and Lai, L and Ji, J and Liu, H and Xia, B and Jiang, T and Luo, SJ and Wang, HW and Xie, C}, title = {Origin of the Reflectin Gene and Hierarchical Assembly of Its Protein.}, journal = {Current biology : CB}, volume = {27}, number = {18}, pages = {2833-2842.e6}, doi = {10.1016/j.cub.2017.07.061}, pmid = {28889973}, issn = {1879-0445}, mesh = {Aliivibrio fischeri/*physiology ; Animals ; Cephalopoda/genetics/*physiology ; Color ; DNA Transposable Elements/*genetics ; Proteins/*analysis ; Skin Physiological Phenomena ; *Symbiosis ; }, abstract = {Cephalopods, the group of animals including octopus, squid, and cuttlefish, have remarkable ability to instantly modulate body coloration and patterns so as to blend into surrounding environments [1, 2] or send warning signals to other animals [3]. Reflectin is expressed exclusively in cephalopods, filling the lamellae of intracellular Bragg reflectors that exhibit dynamic iridescence and structural color change [4]. Here, we trace the possible origin of the reflectin gene back to a transposon from the symbiotic bioluminescent bacterium Vibrio fischeri and report the hierarchical structural architecture of reflectin protein. Intrinsic self-assembly, and higher-order assembly tightly modulated by aromatic compounds, provide insights into the formation of multilayer reflectors in iridophores and spherical microparticles in leucophores and may form the basis of structural color change in cephalopods. Self-assembly and higher-order assembly in reflectin originated from a core repeating octapeptide (here named protopeptide), which may be from the same symbiotic bacteria. The origin of the reflectin gene and assembly features of reflectin protein are of considerable biological interest. The hierarchical structural architecture of reflectin and its domain and protopeptide not only provide insights for bioinspired photonic materials but also serve as unique "assembly tags" and feasible molecular platforms in biotechnology.}, }
@article {pmid28888816, year = {2018}, author = {Wrobel, A and Ottoni, C and Leo, JC and Gulla, S and Linke, D}, title = {The repeat structure of two paralogous genes, Yersinia ruckeri invasin (yrInv) and a "Y. ruckeri invasin-like molecule", (yrIlm) sheds light on the evolution of adhesive capacities of a fish pathogen.}, journal = {Journal of structural biology}, volume = {201}, number = {2}, pages = {171-183}, doi = {10.1016/j.jsb.2017.08.008}, pmid = {28888816}, issn = {1095-8657}, mesh = {Adhesins, Bacterial/*chemistry/*genetics/metabolism ; Animals ; Culture Media ; Evolution, Molecular ; Fish Diseases/microbiology ; Gene Expression Regulation, Bacterial ; Genome, Bacterial ; Iron/pharmacokinetics ; Oxygen ; Polymerase Chain Reaction ; Temperature ; Yersinia ruckeri/*genetics/isolation &amp; purification/pathogenicity ; }, abstract = {Inverse autotransporters comprise the recently identified type Ve secretion system and are exemplified by intimin from enterohaemorrhagic Escherichia coli and invasin from enteropathogenic Yersiniae. These proteins share a common domain architecture and promote bacterial adhesion to host cells. Here, we identified and characterized two putative inverse autotransporter genes in the fish pathogen Yersinia ruckeri NVH_3758, namely yrInv (for Y. ruckeri invasin) and yrIlm (for Y. ruckeri invasin-like molecule). When trying to clone the highly repetitive genes for structural and functional studies, we experienced problems in obtaining PCR products. PCR failures and the highly repetitive nature of inverse autotransporters prompted us to sequence the genome of Y. ruckeri NVH_3758 using PacBio sequencing, which produces some of the longest average read lengths available in the industry at this moment. According to our sequencing data, YrIlm is composed of 2603 amino acids (7812bp) and has a molecular mass of 256.4kDa. Based on the new genome information, we performed PCR analysis on four non-sequenced Y. ruckeri strains as well as the sequenced. Y. ruckeri type strain. We found that the genes are variably present in the strains, and that the length of yrIlm, when present, also varies. In addition, the length of the gene product for all strains, including the type strain, was much longer than expected based on deposited sequences. The internal repeats of the yrInv gene product are highly diverged, but represent the same bacterial immunoglobulin-like domains as in yrIlm. Using qRT-PCR, we found that yrIlm and yrInv are differentially expressed under conditions relevant for pathogenesis. In addition, we compared the genomic context of both genes in the newly sequenced Y. ruckeri strain to all available PacBio-sequenced Y. ruckeri genomes, and found indications of recent events of horizontal gene transfer. Taken together, this study demonstrates and highlights the power of Single Molecule Real-Time technology for sequencing highly repetitive proteins, and sheds light on the genetic events that gave rise to these highly repetitive genes in a commercially important fish pathogen.}, }
@article {pmid28886881, year = {2017}, author = {Wang, J and Wang, J and Zhao, Z and Chen, J and Lu, H and Liu, G and Zhou, J and Guan, X}, title = {PAHs accelerate the propagation of antibiotic resistance genes in coastal water microbial community.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {231}, number = {Pt 1}, pages = {1145-1152}, doi = {10.1016/j.envpol.2017.07.067}, pmid = {28886881}, issn = {1873-6424}, mesh = {China ; Drug Resistance, Microbial/*drug effects/genetics ; Environmental Monitoring ; Gene Transfer, Horizontal/drug effects ; *Genes, Bacterial/drug effects ; Integrons/genetics ; Microbial Consortia/*genetics ; Polycyclic Aromatic Hydrocarbons/*toxicity ; Seawater/*chemistry ; Water Pollutants, Chemical/*toxicity ; }, abstract = {Antibiotic resistance genes (ARGs) have been regarded as emerging contaminants and have attracted growing attention owing to their widespread presence in the environment. In addition to the well-documented selective pressure of antibiotics, ARGs have also become prevalent because of anthropogenic impacts. Coastal habitats are located between terrestrial and marine ecosystems, which are a hotspot for anthropogenic impacts. Excessive accumulation of polycyclic aromatic hydrocarbons (PAHs) has posed a serious threat to coastal habitats, but no information is available on the effect of PAHs on antibiotic resistance in the microbial community of coastal environments. In this study, the effect of two typical PAHs, naphthalene and phenanthrene, on antibiotic resistance propagation was investigated in a coastal microbial community. The results indicated that the presence of 100 mg/L of naphthalene or 10 mg/L of phenanthrene significantly enhanced the abundance of class I integrase gene (intI1), sulfanilamide resistance gene (sulI), and aminoglycosides resistance gene (aadA2) in the microbial community. Horizontal gene transfer experiment demonstrated that increased abundance of ARGs was primarily a result of conjugative transfer mediated by class I integrons. These findings provided direct evidence that coastal microbial community exposed to PAHs might have resulted in the dissemination of ARGs and implied that a more comprehensive risk assessment of PAHs to natural ecosystems and public health is necessary.}, }
@article {pmid28886679, year = {2017}, author = {Cosgrove, DJ}, title = {Microbial Expansins.}, journal = {Annual review of microbiology}, volume = {71}, number = {}, pages = {479-497}, doi = {10.1146/annurev-micro-090816-093315}, pmid = {28886679}, issn = {1545-3251}, mesh = {Actinobacteria/*enzymology/genetics ; Bacillus/*enzymology/genetics ; Bacterial Proteins/genetics/*metabolism ; Cellulose/*metabolism ; Gene Transfer, Horizontal ; Plants/*microbiology ; Trichoderma/*enzymology/genetics ; }, abstract = {Expansins are small proteins that loosen plant cell walls and cellulosic materials without lytic activity. First discovered in plants, expansin genes are found in the genomes of numerous bacteria and fungi that interact with plants in pathogenic and mutualistic patterns, as well as in microbes that feed on plant debris. Horizontal gene transfer from plants to microbes and between microbes accounts for expansins' irregular taxonomic distribution. Expansins facilitate plant colonization by Bacillus, Clavibacter, and Trichoderma species, a list likely to grow as knowledge of microbial expansin function deepens. Studies have documented a synergistic action of expansins for cellulose digestion by cellulases, but only rarely to an extent that is commercially relevant. Expansins' biophysical actions remain enigmatic because of limited understanding of cell wall structure. Deeper understanding of microbial expansins may lead to novel approaches for biomass deconstruction and biocontrol of plant diseases.}, }
@article {pmid28885139, year = {2017}, author = {Huang, L and Hu, YY and Zhang, R}, title = {Prevalence of fosfomycin resistance and plasmid-mediated fosfomycin-modifying enzymes among carbapenem-resistant Enterobacteriaceae in Zhejiang, China.}, journal = {Journal of medical microbiology}, volume = {66}, number = {9}, pages = {1332-1334}, doi = {10.1099/jmm.0.000578}, pmid = {28885139}, issn = {1473-5644}, mesh = {Carbapenems/*pharmacology ; China ; Drug Resistance, Multiple, Bacterial/*genetics ; Enterobacter cloacae/*drug effects/genetics/isolation &amp; purification ; Enterobacteriaceae Infections/drug therapy/microbiology ; Escherichia coli/*drug effects/genetics/isolation &amp; purification ; Escherichia coli Proteins/genetics ; Fosfomycin/*pharmacology ; Gene Transfer, Horizontal/genetics ; Humans ; Klebsiella pneumoniae/*drug effects/genetics/isolation &amp; purification ; Microbial Sensitivity Tests ; Plasmids/*genetics ; }, abstract = {Two hundred and thirty-three nonduplicated clinical isolates of carbapenem-resistant Enterobacteriaceae were collected from four hospitals in Zhejiang, China. 45.1 % (105/233) strains were resistant to fosfomycin, among which plasmid-mediated fosfomycin-modifying enzymes fosA, fosA2, fosA3 and fosA5 were positive, and the other fos genes were negative. 80 % (12/15) Enterobacter cloacae isolates were positive for fosA. 100 % (73/73) Klebsiella pneumoniae isolates were positive for fosA5. A conjugation experiment indicated that fosfomycin resistance could be transferred to an Escherichia coli recipient strain successfully. Fosfomycin still exhibits partial activity in carbapenem-resistant Enterobacteriaceae, especially carbapenem-resistant Escherichia coli. To our knowledge, plasmid-mediated fosfomycin-modifying enzymes account for the dominance in the carbapenem-resistant Enterobacteriaceae. Therefore, we need to pay attention to the plasmid-mediated fosfomycin-modifying enzymes fosA and fosA5 in Enterobacter cloacae and K. pneumoniae to prevent clonal dissemination in China.}, }
@article {pmid28884488, year = {2017}, author = {Mi-Ichi, F and Miyamoto, T and Yoshida, H}, title = {Uniqueness of Entamoeba sulfur metabolism: sulfolipid metabolism that plays pleiotropic roles in the parasitic life cycle.}, journal = {Molecular microbiology}, volume = {106}, number = {3}, pages = {479-491}, doi = {10.1111/mmi.13827}, pmid = {28884488}, issn = {1365-2958}, mesh = {Amino Acids/metabolism ; Entamoeba/metabolism ; Entamoeba histolytica/*metabolism ; Genetic Pleiotropy/genetics ; Lipid Metabolism ; Lipids/*biosynthesis/physiology ; Protozoan Proteins/metabolism ; Sulfur/*metabolism ; }, abstract = {Sulfur metabolism is ubiquitous and terminally synthesizes various biomolecules that are crucial for organisms, such as sulfur-containing amino acids and co-factors, sulfolipids and sulfated saccharides. Entamoeba histolytica, a protozoan parasite responsible for amoebiasis, possesses the unique sulfur metabolism features of atypical localization and its terminal product being limited to sulfolipids. Here, we present an overall scheme of E. histolytica sulfur metabolism by relating all sulfotransferases and sulfatases to their substrates and products. Furthermore, a novel sulfur metabolite, fatty alcohol disulfates, was identified and shown to play an important role in trophozoite proliferation. Cholesteryl sulfate, another synthesized sulfolipid, was previously demonstrated to play an important role in encystation, a differentiation process from proliferative trophozoite to dormant cyst. Entamoeba survives by alternating between these two distinct forms; therefore, Entamoeba sulfur metabolism contributes to the parasitic life cycle via its terminal products. Interestingly, this unique feature of sulfur metabolism is not conserved in the nonparasitic close relative of Entamoeba, Mastigamoeba, because lateral gene transfer-mediated acquisition of sulfatases and sulfotransferases, critical enzymes conferring this feature, has only occurred in the Entamoeba lineage. Hence, our findings suggest that sulfolipid metabolism has a causal relationship with parasitism.}, }
@article {pmid28878752, year = {2017}, author = {Livingstone, PG and Morphew, RM and Whitworth, DE}, title = {Myxobacteria Are Able to Prey Broadly upon Clinically-Relevant Pathogens, Exhibiting a Prey Range Which Cannot Be Explained by Phylogeny.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1593}, pmid = {28878752}, issn = {1664-302X}, abstract = {Myxobacteria are natural predators of microorganisms and the subjects of concerted efforts to identify novel antimicrobial compounds. Myxobacterial predatory activity seems to require more than just the possession of specific antimicrobial metabolites. Thus a holistic approach to studying predation promises novel insights into antimicrobial action. Here, we report the isolation of 113 myxobacteria from samples of soil taken from a range of habitats in mid Wales. Predatory activity of each isolate was quantified against a panel of clinically important prey organisms, including Klebsiella pneumoniae, Proteus mirabilis, Candida albicans, Enterococcus faecalis, and three species of Staphylococcus. Myxobacterial isolates exhibited a wide range of predation activity profiles against the panel of prey. Efficient predation of all prey by isolates within the collection was observed, with K. pneumoniae and C. albicans proving particularly susceptible to myxobacterial predation. Notably efficient predators tended to be proficient at predating multiple prey organisms, suggesting they possess gene(s) encoding a broad range killing activity. However, predatory activity was not congruent with phylogeny, suggesting prey range is subject to relatively rapid specialization, potentially involving lateral gene transfer. The broad but patchy prey ranges observed for natural myxobacterial isolates also implies multiple (potentially overlapping) genetic determinants are responsible for dictating predatory activity.}, }
@article {pmid28875307, year = {2018}, author = {Dias, ACF and Cotta, SR and Andreote, FD and van Elsas, JD}, title = {The parA Region of Broad-Host-Range PromA Plasmids Is a Carrier of Mobile Genes.}, journal = {Microbial ecology}, volume = {75}, number = {2}, pages = {479-486}, pmid = {28875307}, issn = {1432-184X}, support = {2015/01290-8//FAPESP/ ; 443815/2014-3//CNPq/ ; }, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; Ecosystem ; *Gene Transfer, Horizontal ; Plasmids/*genetics/metabolism ; Polymerase Chain Reaction/*methods ; Soil/chemistry ; Species Specificity ; }, abstract = {The ecological competences in microbiomes are driven by the adaptive capabilities present within microbiome members. Horizontal gene transfer (HGT) promoted by plasmids provides a rapid adaptive strategy to microbiomes, an interesting feature considering the constantly changing conditions in most environments. This study examined the parA locus, found in the highly promiscuous PromA class of plasmids, as the insertion site for incoming genes. A novel PCR system was designed that enabled examining insertions into this locus. Microbiomes of mangrove sediments, salt marsh, mycosphere, and bulk soil revealed habitat-specific sets of insertions in this plasmid region. Furthermore, such habitats could be differentiated based on patterns of parA-inserted genes, and the genes carried by these plasmids. Thus, a suite of dioxygenase-related genes and transposase elements were found in oil-affected mangroves, whereas genes involved in nitrogen and carbon cycling were detected in salt marsh and soils. All genes detected could be associated with capabilities of members of the microbiome to adapt to and survive in each habitat. The methodology developed in this work was effective, sensitive, and practical, allowing detection of mobilized genes between microorganisms.}, }
@article {pmid28875260, year = {2018}, author = {Pepori, AL and Bettini, PP and Comparini, C and Sarrocco, S and Bonini, A and Frascella, A and Ghelardini, L and Scala, A and Vannacci, G and Santini, A}, title = {Geosmithia-Ophiostoma: a New Fungus-Fungus Association.}, journal = {Microbial ecology}, volume = {75}, number = {3}, pages = {632-646}, pmid = {28875260}, issn = {1432-184X}, support = {2009RZ94KA_003//MIUR/ ; }, mesh = {Animals ; Ascomycota/genetics/growth &amp; development/physiology ; Biological Control Agents ; Coleoptera/microbiology ; DNA, Fungal/genetics ; Fungal Proteins/genetics ; Gene Transfer, Horizontal ; Genes, Fungal/genetics ; Hyphae ; Hypocreales/genetics/growth &amp; development/*physiology ; Microbial Interactions/genetics/*physiology ; Ophiostoma/genetics/growth &amp; development/pathogenicity/*physiology ; Plant Diseases/microbiology ; Ulmus/*microbiology ; }, abstract = {In Europe as in North America, elms are devastated by Dutch elm disease (DED), caused by the alien ascomycete Ophiostoma novo-ulmi. Pathogen dispersal and transmission are ensured by local species of bark beetles, which established a novel association with the fungus. Elm bark beetles also transport the Geosmithia fungi genus that is found in scolytids' galleries colonized by O. novo-ulmi. Widespread horizontal gene transfer between O. novo-ulmi and Geosmithia was recently observed. In order to define the relation between these two fungi in the DED pathosystem, O. novo-ulmi and Geosmithia species from elm, including a GFP-tagged strain, were grown in dual culture and mycelial interactions were observed by light and fluorescence microscopy. Growth and sporulation of O. novo-ulmi in the absence or presence of Geosmithia were compared. The impact of Geosmithia on DED severity was tested in vivo by co-inoculating Geosmithia and O. novo-ulmi in elms. A close and stable relation was observed between the two fungi, which may be classified as mycoparasitism by Geosmithia on O. novo-ulmi. These results prove the existence of a new component in the complex of organisms involved in DED, which might be capable of reducing the disease impact.}, }
@article {pmid28871175, year = {2017}, author = {Amlinger, L and Hoekzema, M and Wagner, EGH and Koskiniemi, S and Lundgren, M}, title = {Fluorescent CRISPR Adaptation Reporter for rapid quantification of spacer acquisition.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {10392}, pmid = {28871175}, issn = {2045-2322}, mesh = {Adaptation, Physiological ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Escherichia coli/genetics/*growth &amp; development ; Fluorescence ; Gene Transfer, Horizontal ; Genes, Reporter ; }, abstract = {CRISPR-Cas systems are adaptive prokaryotic immune systems protecting against horizontally transferred DNA or RNA such as viruses and other mobile genetic elements. Memory of past invaders is stored as spacers in CRISPR loci in a process called adaptation. Here we developed a novel assay where spacer integration results in fluorescence, enabling detection of memory formation in single cells and quantification of as few as 0.05% cells with expanded CRISPR arrays in a bacterial population. Using this fluorescent CRISPR Adaptation Reporter (f-CAR), we quantified adaptation of the two CRISPR arrays of the type I-E CRISPR-Cas system in Escherichia coli, and confirmed that more integration events are targeted to CRISPR-II than to CRISPR-I. The f-CAR conveniently analyzes and compares many samples, allowing new insights into adaptation. For instance, we show that in an E. coli culture the majority of acquisition events occur in late exponential phase.}, }
@article {pmid28870171, year = {2017}, author = {Jamrozy, D and Coll, F and Mather, AE and Harris, SR and Harrison, EM and MacGowan, A and Karas, A and Elston, T and Estée Török, M and Parkhill, J and Peacock, SJ}, title = {Evolution of mobile genetic element composition in an epidemic methicillin-resistant Staphylococcus aureus: temporal changes correlated with frequent loss and gain events.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {684}, pmid = {28870171}, issn = {1471-2164}, support = {/WT_/Wellcome Trust/United Kingdom ; 201344/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; G1000803/MRC_/Medical Research Council/United Kingdom ; MR/N029399/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Epidemics ; *Evolution, Molecular ; Humans ; Interspersed Repetitive Sequences/*genetics ; Methicillin-Resistant Staphylococcus aureus/*genetics/physiology ; Phylogeny ; }, abstract = {BACKGROUND: Horizontal transfer of mobile genetic elements (MGEs) that carry virulence and antimicrobial resistance genes mediates the evolution of methicillin-resistant Staphylococcus aureus, and the emergence of new MRSA clones. Most MRSA lineages show an association with specific MGEs and the evolution of MGE composition following clonal expansion has not been widely studied.<br><br>RESULTS: We investigated the genomes of 1193&#xa0;S. aureus bloodstream isolates, 1169 of which were MRSA, collected in the UK and the Republic of Ireland between 2001 and 2010. The majority of isolates belonged to clonal complex (CC)22 (n&#xa0;=&#xa0;923), which contained diverse MGEs including elements that were found in other MRSA lineages. Several MGEs showed variable distribution across the CC22 phylogeny, including two antimicrobial resistance plasmids (pWBG751-like and SAP078A-like, carrying erythromycin and heavy metal resistance genes, respectively), a pathogenicity island carrying the enterotoxin C gene and two phage types Sa1int and Sa6int. Multiple gains and losses of these five MGEs were identified in the CC22 phylogeny using ancestral state reconstruction. Analysis of the temporal distribution of the five MGEs between 2001 and 2010 revealed an unexpected reduction in prevalence of the two plasmids and the pathogenicity island, and an increase in the two phage types. This occurred across the lineage and was not correlated with changes in the relative prevalence of CC22, or of any sub-lineages within in.<br><br>CONCLUSIONS: Ancestral state reconstruction coupled with temporal trend analysis demonstrated that epidemic MRSA CC22 has an evolving MGE composition, and indicates that this important MRSA lineage has continued to adapt to changing selective pressure since its emergence.}, }
@article {pmid28870170, year = {2017}, author = {Li, S and Darwish, O and Alkharouf, NW and Musungu, B and Matthews, BF}, title = {Analysis of the genome sequence of Phomopsis longicolla: a fungal pathogen causing Phomopsis seed decay in soybean.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {688}, pmid = {28870170}, issn = {1471-2164}, mesh = {Ascomycota/*genetics/*physiology ; Cell Wall/enzymology ; Gene Transfer, Horizontal ; *Genomics ; Molecular Sequence Annotation ; Plant Diseases/*microbiology ; Repetitive Sequences, Nucleic Acid/genetics ; Seeds/*microbiology ; Glycine max/*microbiology ; Transposases/genetics ; }, abstract = {BACKGROUND: Phomopsis longicolla T. W. Hobbs (syn. Diaporthe longicolla) is a seed-borne fungus causing Phomopsis seed decay in soybean. This disease is one of the most devastating diseases reducing soybean seed quality worldwide. To facilitate investigation of the genomic basis of pathogenicity and to understand the mechanism of the disease development, the genome of an isolate, MSPL10-6, from Mississippi, USA was sequenced, de novo assembled, and analyzed.<br><br>RESULTS: The genome of MSPL 10-6 was estimated to be approximately 62&#xa0;Mb in size with an overall G&#xa0;+&#xa0;C content of 48.6%. Of 16,597 predicted genes, 9866 genes (59.45%) had significant matches to genes in the NCBI nr database, while 18.01% of them did not link to any gene ontology classification, and 9.64% of genes did not significantly match any known genes. Analysis of the 1221 putative genes that encoded carbohydrate-activated enzymes (CAZys) indicated that 715 genes belong to three classes of CAZy that have a direct role in degrading plant cell walls. A novel fungal ulvan lyase (PL24; EC 4.2.2.-) was identified. Approximately 12.7% of the P. longicolla genome consists of repetitive elements. A total of 510 potentially horizontally transferred genes were identified. They appeared to originate from 22 other fungi, 26 eubacteria and 5 archaebacteria.<br><br>CONCLUSIONS: The genome of the P. longicolla isolate MSPL10-6 represented the first reported genome sequence in the fungal Diaporthe-Phomopsis complex causing soybean diseases. The genome contained a number of Pfams not described previously. Information obtained from this study enhances our knowledge about this seed-borne pathogen and will facilitate further research on the genomic basis and pathogenicity mechanism of P. longicolla and aids in development of improved strategies for efficient management of Phomopsis seed decay in soybean.}, }
@article {pmid28870165, year = {2017}, author = {Kollmar, M and Mühlhausen, S}, title = {Myosin repertoire expansion coincides with eukaryotic diversification in the Mesoproterozoic era.}, journal = {BMC evolutionary biology}, volume = {17}, number = {1}, pages = {211}, pmid = {28870165}, issn = {1471-2148}, mesh = {Eukaryota/*classification/*genetics ; Eukaryotic Cells ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Speciation ; Genome ; Introns ; Myosins/chemistry/*genetics ; Phylogeny ; Spliceosomes ; }, abstract = {BACKGROUND: The last eukaryotic common ancestor already had an amazingly complex cell possessing genomic and cellular features such as spliceosomal introns, mitochondria, cilia-dependent motility, and a cytoskeleton together with several intracellular transport systems. In contrast to the microtubule-based dyneins and kinesins, the actin-filament associated myosins are considerably divergent in extant eukaryotes and a unifying picture of their evolution has not yet emerged.<br><br>RESULTS: Here, we manually assembled and annotated 7852 myosins from 929 eukaryotes providing an unprecedented dense sequence and taxonomic sampling. For classification we complemented phylogenetic analyses with gene structure comparisons resulting in 79 distinct myosin classes. The intron pattern analysis and the taxonomic distribution of the classes suggest two myosins in the last eukaryotic common ancestor, a class-1 prototype and another myosin, which is most likely the ancestor of all other myosin classes. The sparse distribution of class-2 and class-4 myosins outside their major lineages contradicts their presence in the last eukaryotic common ancestor but instead strongly suggests early eukaryote-eukaryote horizontal gene transfer.<br><br>CONCLUSIONS: By correlating the evolution of myosin diversity with the history of Earth we found that myosin innovation occurred in independent major "burst" events in the major eukaryotic lineages. Most myosin inventions happened in the Mesoproterozoic era. In the late Neoproterozoic era, a process of extensive independent myosin loss began simultaneously with further eukaryotic diversification. Since the Cambrian explosion, myosin repertoire expansion is driven by lineage- and species-specific gene and genome duplications leading to subfunctionalization and fine-tuning of myosin functions.}, }
@article {pmid28869687, year = {2017}, author = {Merda, D and Briand, M and Bosis, E and Rousseau, C and Portier, P and Barret, M and Jacques, MA and Fischer-Le Saux, M}, title = {Ancestral acquisitions, gene flow and multiple evolutionary trajectories of the type three secretion system and effectors in Xanthomonas plant pathogens.}, journal = {Molecular ecology}, volume = {26}, number = {21}, pages = {5939-5952}, pmid = {28869687}, issn = {1365-294X}, mesh = {*Evolution, Molecular ; *Gene Flow ; Gene Transfer, Horizontal ; Genes, Bacterial ; Homologous Recombination ; Phylogeny ; Type III Secretion Systems/*genetics ; Virulence Factors/genetics ; Xanthomonas/*genetics ; }, abstract = {Deciphering the evolutionary history and transmission patterns of virulence determinants is necessary to understand the emergence of novel pathogens. The main virulence determinant of most pathogenic proteobacteria is the type three secretion system (T3SS). The Xanthomonas genus includes bacteria responsible for numerous epidemics in agroecosystems worldwide and represents a major threat to plant health. The main virulence factor of Xanthomonas is the Hrp2 family T3SS; however, this system is not conserved in all strains and it has not been previously determined whether the distribution of T3SS in this bacterial genus has resulted from losses or independent acquisitions. Based on comparative genomics of 82 genome sequences representing the diversity of the genus, we have inferred three ancestral acquisitions of the Hrp2 cluster during Xanthomonas evolution followed by subsequent losses in some commensal strains and re-acquisition in some species. While mutation was the main force driving polymorphism at the gene level, interspecies homologous recombination of large fragments expanding through several genes shaped Hrp2 cluster polymorphism. Horizontal gene transfer of the entire Hrp2 cluster also occurred. A reduced core effectome composed of xopF1, xopM, avrBs2 and xopR was identified that may allow commensal strains overcoming plant basal immunity. In contrast, stepwise accumulation of numerous type 3 effector genes was shown in successful pathogens responsible for epidemics. Our data suggest that capacity to intimately interact with plants through T3SS would be an ancestral trait of xanthomonads. Since its acquisition, T3SS has experienced a highly dynamic evolutionary history characterized by intense gene flux between species that may reflect its role in host adaptation.}, }
@article {pmid28869409, year = {2017}, author = {Westbye, AB and O'Neill, Z and Schellenberg-Beaver, T and Beatty, JT}, title = {The Rhodobacter capsulatus gene transfer agent is induced by nutrient depletion and the RNAP omega subunit.}, journal = {Microbiology (Reading, England)}, volume = {163}, number = {9}, pages = {1355-1363}, doi = {10.1099/mic.0.000519}, pmid = {28869409}, issn = {1465-2080}, support = {93779//CIHR/Canada ; }, mesh = {Amino Acids/metabolism ; Bacterial Proteins/genetics/metabolism ; Carbon/metabolism ; DNA-Directed RNA Polymerases/*genetics/*metabolism ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Mutation ; Plasmids/genetics ; Promoter Regions, Genetic ; Rhodobacter capsulatus/*physiology ; }, abstract = {Small bacteriophage-like particles called gene transfer agents (GTAs) that mediate DNA transfer between cells are produced by a variety of prokaryotes. The model GTA, produced by the alphaproteobacterium Rhodobacter capsulatus (RcGTA), is controlled by several cellular regulators, and production is induced upon entry into the stationary phase. We report that RcGTA production and gene transfer are stimulated by nutrient depletion. Cells depleted of organic carbon or blocked for amino acid biosynthesis increased RcGTA production and release from cells. Furthermore, cells lacking the sole RelA-SpoT homologue produced decreased levels of RcGTA, and the RNA polymerase omega (ω) subunit was required for appreciable production of RcGTA.}, }
@article {pmid28869059, year = {2017}, author = {Bromfield, ESP and Cloutier, S and Tambong, JT and Tran Thi, TV}, title = {Soybeans inoculated with root zone soils of Canadian native legumes harbour diverse and novel Bradyrhizobium spp. that possess agricultural potential.}, journal = {Systematic and applied microbiology}, volume = {40}, number = {7}, pages = {440-447}, doi = {10.1016/j.syapm.2017.07.007}, pmid = {28869059}, issn = {1618-0984}, mesh = {Bacterial Proteins/genetics ; Base Sequence ; Bradyrhizobium/*classification/*genetics/isolation &amp; purification ; Canada ; DNA, Bacterial/genetics ; Fabaceae/*microbiology ; N-Acetylglucosaminyltransferases/genetics ; Nitrogen Fixation/genetics/physiology ; Oxidoreductases/genetics ; Phylogeny ; Plant Roots/*microbiology ; RNA, Ribosomal, 16S/genetics ; Rec A Recombinases/genetics ; Root Nodules, Plant/*microbiology ; Sequence Analysis, DNA ; Soil Microbiology ; Glycine max/*microbiology ; Symbiosis/genetics ; }, abstract = {An assessment was made of the evolutionary relationships of soybean nodulating bacteria associated with legumes native to eastern Canada to identify potential new sources of soybean inoculant strains. Short season soybeans were used to selectively trap bacteria from root zone soils of four native legume species. Screening of more than 800 bacterial isolates from soybean root nodules by analysis of recA gene sequences followed by analyses of selected genotypes using six core and two symbiosis (nodC and nifH) gene sequences permitted identification of diverse taxa that included eight novel and four named Bradyrhizobium species as well as lineages attributed to the genera Afipia and Tardiphaga. Plant tests showed that symbionts related to four named species as well as a novel Bradyrhizobium lineage were highly efficient with regard to nitrogen fixation on soybeans relative to an inoculant strain. A new symbiovar (sv. septentrionalis) is proposed based on a group of four novel Bradyrhizobium spp. that possess distinctive nodC and nifH gene sequences and symbiotic characteristics. Evidence is provided for horizontal transfer of sv. septentrionalis symbiosis genes between novel Bradyrhizobium spp., a process that rendered recipient bacteria ineffective on soybeans. Diverse lineages of non-symbiotic and symbiotic Bradyrhizobium spp. co-occured within monophyletic clusters in a phylogenetic tree of concatenated core genes, suggesting that loss and/or gain of symbiosis genes has occurred in the evolutionary history of the bacterial genus. Our data suggest that symbiont populations associated with legumes native to eastern Canada harbour elite strains of Bradyrhizobium for soybean inoculation.}, }
@article {pmid28868644, year = {2018}, author = {Tancos, MA and Lowe-Power, TM and Peritore-Galve, FC and Tran, TM and Allen, C and Smart, CD}, title = {Plant-like bacterial expansins play contrasting roles in two tomato vascular pathogens.}, journal = {Molecular plant pathology}, volume = {19}, number = {5}, pages = {1210-1221}, pmid = {28868644}, issn = {1364-3703}, support = {T32 GM007215/GM/NIGMS NIH HHS/United States ; }, mesh = {Actinobacteria/*metabolism/pathogenicity ; Bacterial Proteins/genetics/*metabolism ; Fruit/microbiology ; Genes, Bacterial ; Likelihood Functions ; Solanum lycopersicum/*microbiology ; Mutation/genetics ; Phenotype ; Phylogeny ; Plant Diseases/microbiology ; Plant Proteins/*metabolism ; Plant Roots/microbiology ; Plant Vascular Bundle/*microbiology ; Ralstonia solanacearum/genetics/*metabolism/pathogenicity ; Seedlings/microbiology ; Virulence ; }, abstract = {Expansin proteins, which loosen plant cell walls, play critical roles in normal plant growth and development. The horizontal acquisition of functional plant-like expansin genes in numerous xylem-colonizing phytopathogenic bacteria suggests that bacterial expansins may also contribute to virulence. To investigate the role of bacterial expansins in plant diseases, we mutated the non-chimeric expansin genes (CmEXLX2 and RsEXLX) of two xylem-inhabiting bacterial pathogens, the Actinobacterium Clavibacter michiganensis ssp. michiganensis (Cmm) and the β-proteobacterium Ralstonia solanacearum (Rs), respectively. The Cmm ΔCmEXLX2 mutant caused increased symptom development on tomato, which was characterized by more rapid wilting, greater vascular necrosis and abundant atypical lesions on distant petioles. This increased disease severity correlated with larger in planta populations of the ΔCmEXLX2 mutant, even though the strains grew as well as the wild-type in vitro. Similarly, when inoculated onto tomato fruit, ΔCmEXLX2 caused significantly larger lesions with larger necrotic centres. In contrast, the Rs ΔRsEXLX mutant showed reduced virulence on tomato following root inoculation, but not following direct petiole inoculation, suggesting that the RsEXLX expansin contributes to early virulence at the root infection stage. Consistent with this finding, ΔRsEXLX attached to tomato seedling roots better than the wild-type Rs, which may prevent mutants from invading the plant's vasculature. These contrasting results demonstrate the diverse roles of non-chimeric bacterial expansins and highlight their importance in plant-bacterial interactions.}, }
@article {pmid28867496, year = {2017}, author = {Kim, HJ and Jang, S}, title = {Draft genome sequence of multidrug-resistant Staphylococcus haemolyticus IPK_TSA25 harbouring a Staphylococcus aureus plasmid, pS0385-1.}, journal = {Journal of global antimicrobial resistance}, volume = {11}, number = {}, pages = {8-9}, doi = {10.1016/j.jgar.2017.08.010}, pmid = {28867496}, issn = {2213-7173}, mesh = {Anti-Bacterial Agents/pharmacology ; DNA, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/drug effects/*genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial/genetics ; Humans ; Microbial Sensitivity Tests ; Plasmids/*genetics ; Republic of Korea ; Sequence Analysis, DNA ; Staphylococcal Infections/*microbiology ; Staphylococcus aureus/drug effects/*genetics ; Staphylococcus haemolyticus/drug effects/*genetics/pathogenicity ; }, abstract = {OBJECTIVES: Staphylococcus haemolyticus is the second most frequently isolated coagulase-negative staphylococci from blood cultures. Moreover, multidrug resistance associated with the genome flexibility of S. haemolyticus has been increasingly reported worldwide. Here we report the draft genome sequence of multidrug-resistant S. haemolyticus IPK_TSA25 isolated from a building surface in South Korea.<br><br>METHODS: Genomic DNA of S. haemolyticus IPK_TSA25 was sequenced using the PacBio RS II sequencing platform. Generated reads were assembled using PacBio SMRT Analysis 2.3.0. The draft genome was annotated and antibiotic resistance genes were identified.<br><br>RESULTS: The genome of 2517398bp contains various antibiotic resistance genes associated with resistance to &#x3b2;-lactams, aminoglycosides and macrolides. Genome analysis also revealed chromosomal integration of the full-length Staphylococcus aureus plasmid pS0385-1 containing a tetracycline resistance gene.<br><br>CONCLUSIONS: The genome sequence reported in this study will provide valuable information to understand the flexibility of the S. haemolyticus genome, which facilitates acquisition of antibiotic resistance genes and contributes to the dissemination of antibiotic resistance by this emerging pathogen.}, }
@article {pmid28865446, year = {2017}, author = {Boulund, F and Berglund, F and Flach, CF and Bengtsson-Palme, J and Marathe, NP and Larsson, DGJ and Kristiansson, E}, title = {Computational discovery and functional validation of novel fluoroquinolone resistance genes in public metagenomic data sets.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {682}, pmid = {28865446}, issn = {1471-2164}, mesh = {*Databases, Genetic ; Drug Resistance, Bacterial/*genetics ; Fluoroquinolones/*pharmacology ; Humans ; *Metagenomics ; }, abstract = {BACKGROUND: Fluoroquinolones are broad-spectrum antibiotics used to prevent and treat a wide range of bacterial infections. Plasmid-mediated qnr genes provide resistance to fluoroquinolones in many bacterial species and are increasingly encountered in clinical settings. Over the last decade, several families of qnr genes have been discovered and characterized, but their true prevalence and diversity still remain unclear. In particular, environmental and host-associated bacterial communities have been hypothesized to maintain a large and unknown collection of qnr genes that could be mobilized into pathogens.<br><br>RESULTS: In this study we used computational methods to screen genomes and metagenomes for novel qnr genes. In contrast to previous studies, we analyzed an almost 20-fold larger dataset comprising almost 13 terabases of sequence data. In total, 362,843 potential qnr gene fragments were identified, from which 611 putative qnr genes were reconstructed. These gene sequences included all previously described plasmid-mediated qnr gene families. Fifty-two of the 611 identified qnr genes were reconstructed from metagenomes, and 20 of these were previously undescribed. All of the novel qnr genes were assembled from metagenomes associated with aquatic environments. Nine of the novel genes were selected for validation, and six of the tested genes conferred consistently decreased susceptibility to ciprofloxacin when expressed in Escherichia coli.<br><br>CONCLUSIONS: The results presented in this study provide additional evidence for the ubiquitous presence of qnr genes in environmental microbial communities, expand the number of known qnr gene variants and further elucidate the diversity of this class of resistance genes. This study also strengthens the hypothesis that environmental bacterial communities act as sources of previously uncharacterized qnr genes.}, }
@article {pmid28865225, year = {2017}, author = {Tu, J and Qi, K and Song, X and Xue, T and Ji, H and Shao, Y and Liu, H and Zhou, X and Zhu, L}, title = {Horizontal transfer and functional evaluation of high pathogenicity islands in Avian Escherichia coli.}, journal = {Polish journal of veterinary sciences}, volume = {20}, number = {2}, pages = {395-402}, doi = {10.1515/pjvs-2017-0048}, pmid = {28865225}, issn = {1505-1773}, mesh = {Animals ; Chickens ; Escherichia coli/genetics/*metabolism/pathogenicity ; Escherichia coli Infections/*microbiology ; Gene Transfer, Horizontal/*physiology ; Genomic Islands/*genetics ; Iron/metabolism ; Poultry Diseases/*microbiology ; Virulence ; }, abstract = {High pathogenicity islands (HPIs) in Escherichia coli encode genes that are primarily involved in iron uptake and regulation, and confer virulence and pathogenicity. The aim of this study was to investigate the transfer of HPIs in avian E. coli and identify the function of HPI in the acceptor strain. The HPI transfer strain was obtained under conditions of low temperature and low iron abundance, and the donor and acceptor strains were confirmed. E. coli HPIs are transferred by horizontal gene transfer events, which are likely mediated primarily by homologous recombination in HPI-adjacent sequences. Assays for biological activity and pathogenicity changes in the acceptor strain indicated that HPIs might not be involved in pathogenesis in avian E. coli, and thus the main function of HPIs in this strain of bacteria may be to regulate iron nutrition.}, }
@article {pmid28864953, year = {2017}, author = {Wichmann, F and Wyrsch, I and Frank, J and Müller, M and Bertschi, N and Brodmann, P and Bagutti, C}, title = {Monitoring of genetically modified Escherichia coli in laboratory wastewater.}, journal = {Environmental science and pollution research international}, volume = {24}, number = {30}, pages = {23725-23734}, pmid = {28864953}, issn = {1614-7499}, mesh = {Ampicillin/*chemistry/pharmacology ; Ampicillin Resistance/*genetics ; Escherichia coli/chemistry/*genetics ; Gene Transfer, Horizontal ; Plasmids ; RNA, Ribosomal, 16S/*chemistry/genetics ; Wastewater ; }, abstract = {Containment of genetically modified (GM) microorganisms such as Escherichia coli is a legal requirement to protect the environment from an unintended release and to avoid horizontal gene transfer (HGT) of recombinant DNA to native bacteria. In this study, we sampled the laboratory wastewater (LWW) at a large Swiss university from three sources over 2 years and cultured ampicillin-resistant, presumptive GM E. coli. From a total of 285 samples, 127 contained presumptive GM E. coli (45%) at a mean concentration of 2.8 × 10[2] CFU/ml. Plasmid DNA of 11 unique clones was partially or entirely sequenced. All consisted of cloning vectors harboring research-specific inserts. To estimate the chance of HGT between GM E. coli and native bacteria in LWW, we identified taxa representative for the bacterial community in LWW using 16S rRNA amplicon sequencing and measured conjugation frequencies of E. coli with five LWW isolates. At optimal conjugation conditions, frequencies were between 3.4 × 10[-3] and 2.4 × 10[-5]. Given the absence of transferable broad-host range plasmids and suboptimal conjugation conditions in the LWW system, we conclude that the chance of HGT is relatively low. Still, this study shows that the implementation of robust containment measures is key to avoid the escape of GM microorganisms.}, }
@article {pmid28861118, year = {2017}, author = {Hellmuth, M}, title = {Biologically feasible gene trees, reconciliation maps and informative triples.}, journal = {Algorithms for molecular biology : AMB}, volume = {12}, number = {}, pages = {23}, pmid = {28861118}, issn = {1748-7188}, abstract = {BACKGROUND: The history of gene families-which are equivalent to event-labeled gene trees-can be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes. The question then arises as whether inferred event-labeled gene trees are biologically feasible, that is, if there is a possible true history that would explain a given gene tree. In practice, this problem is boiled down to finding a reconciliation map-also known as DTL-scenario-between the event-labeled gene trees and a (possibly unknown) species tree.<br><br>RESULTS: In this contribution, we first characterize whether there is a valid reconciliation map for binary event-labeled gene trees T that contain speciation, duplication and horizontal gene transfer events and some unknown species tree S in terms of "informative" triples that are displayed in T and provide information of the topology of S. These informative triples are used to infer the unknown species tree S for T. We obtain a similar result for non-binary gene trees. To this end, however, the reconciliation map needs to be further restricted. We provide a polynomial-time algorithm to decide whether there is a species tree for a given event-labeled gene tree, and in the positive case, to construct the species tree and the respective (restricted) reconciliation map. However, informative triples as well as DTL-scenarios have their limitations when they are used to explain the biological feasibility of gene trees. While reconciliation maps imply biological feasibility, we show that the converse is not true in general. Moreover, we show that informative triples neither provide enough information to characterize "relaxed" DTL-scenarios nor non-restricted reconciliation maps for non-binary biologically feasible gene trees.}, }
@article {pmid28861068, year = {2017}, author = {Brito, AF and Pinney, JW}, title = {Protein-Protein Interactions in Virus-Host Systems.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1557}, pmid = {28861068}, issn = {1664-302X}, abstract = {To study virus-host protein interactions, knowledge about viral and host protein architectures and repertoires, their particular evolutionary mechanisms, and information on relevant sources of biological data is essential. The purpose of this review article is to provide a thorough overview about these aspects. Protein domains are basic units defining protein interactions, and the uniqueness of viral domain repertoires, their mode of evolution, and their roles during viral infection make viruses interesting models of study. Mutations at protein interfaces can reduce or increase their binding affinities by changing protein electrostatics and structural properties. During the course of a viral infection, both pathogen and cellular proteins are constantly competing for binding partners. Endogenous interfaces mediating intraspecific interactions-viral-viral or host-host interactions-are constantly targeted and inhibited by exogenous interfaces mediating viral-host interactions. From a biomedical perspective, blocking such interactions is the main mechanism underlying antiviral therapies. Some proteins are able to bind multiple partners, and their modes of interaction define how fast these "hub proteins" evolve. "Party hubs" have multiple interfaces; they establish simultaneous/stable (domain-domain) interactions, and tend to evolve slowly. On the other hand, "date hubs" have few interfaces; they establish transient/weak (domain-motif) interactions by means of short linear peptides (15 or fewer residues), and can evolve faster. Viral infections are mediated by several protein-protein interactions (PPIs), which can be represented as networks (protein interaction networks, PINs), with proteins being depicted as nodes, and their interactions as edges. It has been suggested that viral proteins tend to establish interactions with more central and highly connected host proteins. In an evolutionary arms race, viral and host proteins are constantly changing their interface residues, either to evade or to optimize their binding capabilities. Apart from gaining and losing interactions via rewiring mechanisms, virus-host PINs also evolve via gene duplication (paralogy); conservation (orthology); horizontal gene transfer (HGT) (xenology); and molecular mimicry (convergence). The last sections of this review focus on PPI experimental approaches and their limitations, and provide an overview of sources of biomolecular data for studying virus-host protein interactions.}, }
@article {pmid28861060, year = {2017}, author = {Rossi, CC and Souza-Silva, T and Araújo-Alves, AV and Giambiagi-deMarval, M}, title = {CRISPR-Cas Systems Features and the Gene-Reservoir Role of Coagulase-Negative Staphylococci.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1545}, pmid = {28861060}, issn = {1664-302X}, abstract = {The claimed role of gene reservoir of coagulase-negative staphylococci (CoNS) could be contradicted by estimates that CRISPR/Cas systems are found in the genomes of 40-50% of bacteria, as these systems interfere with plasmid uptake in staphylococci. To further correlate this role with presence of CRISPR, we analyzed, by computational methods, 122 genomes from 15 species of CoNS. Only 15% of them harbored CRISPR/Cas systems, and this proportion was much lower for S. epidermidis and S. haemolyticus, the CoNS most frequently associated with opportunistic infections in humans. These systems are of type II or III, and at least two of them are located within SCCmec, a mobile genetic element of Staphylococcus bacterial species. An analysis of the spacers of these CRISPRs, which come from exogenous origin, allowed us to track the transference of the SCCmec, which was exchanged between different strains, species and hosts. Some of the spacers are derived from plasmids described in Staphylococcus species that are different from those in which the CRISPR are found, evidencing the attempt (and failure) of plasmid transference between them. Based on the polymorphisms of the cas1 gene in CRISPRs of types II and III, we developed a multiplex polymerase chain reaction (PCR) suitable to screen and type CRISPR systems in CoNS. The PCR was tested in 59 S. haemolyticus strains, of which only two contained a type III cas1. This gene was shown to be expressed in the exponential growth, stationary phase and during biofilm formation. The low abundance of CRISPRs in CoNS is in accordance with their role as gene reservoirs, but when present, their spacers sequence evidence and give an insight on the dynamics of horizontal genetic transfer among staphylococci.}, }
@article {pmid28860320, year = {2017}, author = {Bernardini, F and Galizi, R and Wunderlich, M and Taxiarchi, C and Kranjc, N and Kyrou, K and Hammond, A and Nolan, T and Lawniczak, MNK and Papathanos, PA and Crisanti, A and Windbichler, N}, title = {Cross-Species Y Chromosome Function Between Malaria Vectors of the Anopheles gambiae Species Complex.}, journal = {Genetics}, volume = {207}, number = {2}, pages = {729-740}, pmid = {28860320}, issn = {1943-2631}, support = {//Wellcome Trust/United Kingdom ; 335724/ERC_/European Research Council/International ; G1100339//Medical Research Council/United Kingdom ; 098051//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Anopheles/*genetics ; Chromosomes, Insect/*genetics ; *Evolution, Molecular ; Gene Flow ; Gene Transfer, Horizontal ; Genetic Background ; Genetic Fitness ; *Hybridization, Genetic ; Infertility, Male/genetics ; Male ; Mosquito Vectors/*genetics ; Y Chromosome/*genetics ; }, abstract = {Y chromosome function, structure and evolution is poorly understood in many species, including the Anopheles genus of mosquitoes-an emerging model system for studying speciation that also represents the major vectors of malaria. While the Anopheline Y had previously been implicated in male mating behavior, recent data from the Anopheles gambiae complex suggests that, apart from the putative primary sex-determiner, no other genes are conserved on the Y. Studying the functional basis of the evolutionary divergence of the Y chromosome in the gambiae complex is complicated by complete F1 male hybrid sterility. Here, we used an F1 × F0 crossing scheme to overcome a severe bottleneck of male hybrid incompatibilities that enabled us to experimentally purify a genetically labeled A. gambiae Y chromosome in an A. arabiensis background. Whole genome sequencing (WGS) confirmed that the A. gambiae Y retained its original sequence content in the A. arabiensis genomic background. In contrast to comparable experiments in Drosophila, we find that the presence of a heterospecific Y chromosome has no significant effect on the expression of A. arabiensis genes, and transcriptional differences can be explained almost exclusively as a direct consequence of transcripts arising from sequence elements present on the A. gambiae Y chromosome itself. We find that Y hybrids show no obvious fertility defects, and no substantial reduction in male competitiveness. Our results demonstrate that, despite their radically different structure, Y chromosomes of these two species of the gambiae complex that diverged an estimated 1.85 MYA function interchangeably, thus indicating that the Y chromosome does not harbor loci contributing to hybrid incompatibility. Therefore, Y chromosome gene flow between members of the gambiae complex is possible even at their current level of divergence. Importantly, this also suggests that malaria control interventions based on sex-distorting Y drive would be transferable, whether intentionally or contingent, between the major malaria vector species.}, }
@article {pmid28859885, year = {2018}, author = {de Santis, B and Stockhofe, N and Wal, JM and Weesendorp, E and Lallès, JP and van Dijk, J and Kok, E and De Giacomo, M and Einspanier, R and Onori, R and Brera, C and Bikker, P and van der Meulen, J and Kleter, G}, title = {Case studies on genetically modified organisms (GMOs): Potential risk scenarios and associated health indicators.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {117}, number = {}, pages = {36-65}, doi = {10.1016/j.fct.2017.08.033}, pmid = {28859885}, issn = {1873-6351}, mesh = {Animal Feed/*adverse effects ; Animals ; DNA, Plant/genetics ; European Union ; Food Hypersensitivity/etiology/*veterinary ; *Gene Transfer, Horizontal ; Humans ; Livestock/*physiology ; Mycotoxins/*toxicity ; Nutritive Value ; Plants, Genetically Modified/*adverse effects/genetics ; Product Surveillance, Postmarketing ; Risk Assessment ; }, abstract = {Within the frame of the EU-funded MARLON project, background data were reviewed to explore the possibility of measuring health indicators during post-market monitoring for potential effects of feeds, particularly genetically modified (GM) feeds, on livestock animal health, if applicable. Four case studies (CSs) of potential health effects on livestock were framed and the current knowledge of a possible effect of GM feed was reviewed. Concerning allergenicity (CS-1), there are no case-reports of allergic reactions or immunotoxic effects resulting from GM feed consumption as compared with non-GM feed. The likelihood of horizontal gene transfer (HGT; CS-2) of GMO-related DNA to different species is not different from that for other DNA and is unlikely to raise health concerns. Concerning mycotoxins (CS-3), insect-resistant GM maize may reduce fumonisins contamination as a health benefit, yet other Fusarium toxins and aflatoxins show inconclusive results. For nutritionally altered crops (CS-4), the genetic modifications applied lead to compositional changes which require special considerations of their nutritional impacts. No health indicators were thus identified except for possible beneficial impacts of reduced mycotoxins and nutritional enhancement. More generally, veterinary health data should ideally be linked with animal exposure information so as to be able to establish cause-effect relationships.}, }
@article {pmid28857443, year = {2017}, author = {Park, C and Shin, B and Jung, J and Lee, Y and Park, W}, title = {Metabolic and stress responses of Acinetobacter oleivorans DR1 during long-chain alkane degradation.}, journal = {Microbial biotechnology}, volume = {10}, number = {6}, pages = {1809-1823}, pmid = {28857443}, issn = {1751-7915}, mesh = {Acinetobacter/classification/enzymology/genetics/*metabolism ; Alkanes/chemistry/*metabolism ; Bacteria/classification/enzymology/genetics ; Bacterial Proteins/genetics/metabolism ; Biodegradation, Environmental ; Cytochrome P-450 CYP4A/genetics/metabolism ; Phylogeny ; Siderophores/metabolism ; Trehalose/metabolism ; }, abstract = {Acinetobacter oleivorans DR1 can utilize C12 -C30 alkanes as a sole carbon source but not short-chain alkanes (C6 , C10). Two copies of each alkB-, almA- and ladA-type alkane hydroxylase (AH) are present in the genome of DR1 cells. Expression and mutational analyses of AHs showed that alkB1 and alkB2 are the major AH-encoding genes under C12 -C30 , and the roles of other almA- and ladA genes are negligible. Our data suggested that AlkB1 is responsible for long-chain alkane utilization (C24 -C26), and AlkB2 is important for medium-chain alkane (C12 -C16) metabolism. Phylogenetic analyses revealed large incongruities between phylogenies of 16S rRNA and each AH gene, which implies that A. oleivorans DR1 has acquired multiple alkane hydroxylases through horizontal gene transfer. Transcriptomic and qRT-PCR analyses suggested that genes participating in the synthesis of siderophore, trehalose and poly 3-hydroxybutyrate (PHB) were expressed at much higher levels when cells used C30 than when used succinate as a carbon source. The following biochemical assays supported our gene expression analyses: (i) quantification of siderophore, (ii) measurement of trehalose and (iii) observation of PHB storage. Interestingly, highly induced both ackA gene encoding an acetate kinase A and pta gene encoding a phosphotransacetylase suggested unusual ATP synthesis during C30 alkane degradation, which was demonstrated by ATP measurement using the ΔackA mutant. Impaired growth of the ΔaceA mutant indicated that the glyoxylate shunt pathway is important when C30 alkane is utilized. Our data provide insight into long-chain alkane degradation in soil microorganisms.}, }
@article {pmid28856785, year = {2017}, author = {Czarnecki, J and Dziewit, L and Puzyna, M and Prochwicz, E and Tudek, A and Wibberg, D and Schlüter, A and Pühler, A and Bartosik, D}, title = {Lifestyle-determining extrachromosomal replicon pAMV1 and its contribution to the carbon metabolism of the methylotrophic bacterium Paracoccus aminovorans JCM 7685.}, journal = {Environmental microbiology}, volume = {19}, number = {11}, pages = {4536-4550}, doi = {10.1111/1462-2920.13901}, pmid = {28856785}, issn = {1462-2920}, mesh = {Carbon/*metabolism ; Gene Expression Regulation, Bacterial/genetics ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/genetics ; Paracoccus/*genetics/*metabolism ; Plasmids/*genetics ; Replicon/*genetics ; }, abstract = {Plasmids play an important role in the adaptation of bacteria to changeable environmental conditions. As the main vectors of horizontal gene transfer, they can spread genetic information among bacteria, sometimes even across taxonomic boundaries. Some plasmids carry genes involved in the utilization of particular carbon compounds, which can provide a competitive advantage to their hosts in particular ecological niches. Analysis of the multireplicon genome of the soil bacterium P. aminovorans JCM 7685 revealed the presence of an extrachromosomal replicon pAMV1 (185 kb) with a unique structure and properties. This lifestyle-determining plasmid carries genes facilitating the metabolism of many different carbon compounds including sugars, short-chain organic acids and C1 compounds. Plasmid pAMV1 contains a large methylotrophy island (MEI) that is essential not only for the utilization of particular C1 compounds but also for the central methylotrophic metabolism required for the assimilation of C1 units (serine cycle). We demonstrate that the expression of the main serine cycle genes is induced in the presence of C1 compounds by the transcriptional regulator ScyR. The extrachromosomal localization of the MEI and the distribution of related genes in Paracoccus spp. indicate that it could have been acquired by HGT by an ancestor of P. aminovorans.}, }
@article {pmid28855596, year = {2017}, author = {Tsukuda, M and Kitahara, K and Miyazaki, K}, title = {Comparative RNA function analysis reveals high functional similarity between distantly related bacterial 16 S rRNAs.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {9993}, pmid = {28855596}, issn = {2045-2322}, mesh = {Acidobacteria/genetics/*growth &amp; development ; Escherichia coli/genetics/*growth &amp; development ; Nucleic Acid Conformation ; Protein Conformation ; RNA, Bacterial/*genetics/*metabolism ; RNA, Ribosomal, 16S/*genetics/*metabolism ; Ribosomal Proteins/chemistry/metabolism ; }, abstract = {The 16 S rRNA sequence has long been used uncritically as a molecular clock to infer phylogenetic relationships among prokaryotes without fully elucidating the evolutionary changes that this molecule undergoes. In this study, we investigated the functional evolvability of 16 S rRNA, using comparative RNA function analyses between the 16 S rRNAs of Escherichia coli (Proteobacteria) and Acidobacteria (78% identity, 334 nucleotide differences) in the common genetic background of E. coli. While the growth phenotype of an E. coli mutant harboring the acidobacterial gene was disrupted significantly, it was restored almost completely following introduction of a 16 S rRNA sequence with a single base-pair variation in helix 44; the remaining 332 nucleotides were thus functionally similar to those of E. coli. Our results suggest that 16 S rRNAs share an inflexible cradle structure formed by ribosomal proteins and have evolved by accumulating species-specific yet functionally similar mutations. While this experimental evidence suggests the neutral evolvability of 16 S rRNA genes and hence satisfies the necessary requirements to use the sequence as a molecular clock, it also implies the promiscuous nature of the 16 S rRNA gene, i.e., the occurrence of horizontal gene transfer among bacteria.}, }
@article {pmid28854875, year = {2017}, author = {Ruh, M and Briand, M and Bonneau, S and Jacques, MA and Chen, NWG}, title = {Xanthomonas adaptation to common bean is associated with horizontal transfers of genes encoding TAL effectors.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {670}, pmid = {28854875}, issn = {1471-2164}, mesh = {*Adaptation, Physiological ; DNA Transposable Elements/genetics ; Evolution, Molecular ; Gene Duplication ; *Gene Transfer, Horizontal ; Genomics ; Host-Pathogen Interactions/genetics ; Phaseolus/*microbiology ; Phylogeny ; Transcription Activator-Like Effectors/*genetics ; Xanthomonas/*genetics/metabolism/*physiology ; }, abstract = {BACKGROUND: Common bacterial blight is a devastating bacterial disease of common bean (Phaseolus vulgaris) caused by Xanthomonas citri pv. fuscans and Xanthomonas phaseoli pv. phaseoli. These phylogenetically distant strains are able to cause similar symptoms on common bean, suggesting that they have acquired common genetic determinants of adaptation to common bean. Transcription Activator-Like (TAL) effectors are bacterial type III effectors that are able to induce the expression of host genes to promote infection or resistance. Their capacity to bind to a specific host DNA sequence suggests that they are potential candidates for host adaption.<br><br>RESULTS: To study the diversity of tal genes from Xanthomonas strains responsible for common bacterial blight of bean, whole genome sequences of 17 strains representing the diversity of X. citri pv. fuscans and X. phaseoli pv. phaseoli were obtained by single molecule real time sequencing. Analysis of these genomes revealed the existence of four tal genes named tal23A, tal20F, tal18G and tal18H, respectively. While tal20F and tal18G were chromosomic, tal23A and tal18H were carried on plasmids and shared between phylogenetically distant strains, therefore suggesting recent horizontal transfers of these genes between X. citri pv. fuscans and X. phaseoli pv. phaseoli strains. Strikingly, tal23A was present in all strains studied, suggesting that it played an important role in adaptation to common bean. In silico predictions of TAL effectors targets in the common bean genome suggested that TAL effectors shared by X. citri pv. fuscans and X. phaseoli pv. phaseoli strains target the promoters of genes of similar functions. This could be a trace of convergent evolution among TAL effectors from different phylogenetic groups, and comforts the hypothesis that TAL effectors have been implied in the adaptation to common bean.<br><br>CONCLUSIONS: Altogether, our results favour a model where plasmidic TAL effectors are able to contribute to host adaptation by being horizontally transferred between distant lineages.}, }
@article {pmid28854671, year = {2017}, author = {Sabir, DK and Grosjean, N and Rylott, EL and Bruce, NC}, title = {Investigating differences in the ability of XplA/B-containing bacteria to degrade the explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX).}, journal = {FEMS microbiology letters}, volume = {364}, number = {14}, pages = {}, doi = {10.1093/femsle/fnx144}, pmid = {28854671}, issn = {1574-6968}, mesh = {Actinomycetales/genetics/*metabolism ; Biodegradation, Environmental ; Cytochrome P-450 Enzyme System/*genetics/metabolism ; DNA, Bacterial/genetics ; Explosive Agents/chemistry/*metabolism ; Gene Transfer, Horizontal ; Glutamate-Ammonia Ligase/genetics ; Gordonia Bacterium/genetics/metabolism ; NADH, NADPH Oxidoreductases/*genetics/metabolism ; Nitrogen/metabolism ; Rhodococcus/genetics/metabolism ; Sequence Analysis, DNA ; Soil Pollutants/metabolism ; Triazines/*metabolism ; }, abstract = {The xenobiotic hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is a toxic explosive and environmental pollutant. This study examines three bacterial species that degrade RDX, using it as a sole source of nitrogen for growth. Although isolated from diverse geographical locations, the species contain near identical copies of genes encoding the RDX-metabolising cytochrome P450, XplA and accompanying reductase, XplB. Sequence analysis indicates a single evolutionary origin for xplA and xplB as part of a genomic island, which has been distributed around the world via horizontal gene transfer. Despite the fact that xplA and xplB are highly conserved between species, Gordonia sp. KTR9 and Microbacterium sp. MA1 degrade RDX more slowly than Rhodococcus rhodochrous 11Y. Both Gordonia sp. KTR9 and Microbacterium sp. MA1 were found to contain single base-pair mutations in xplB which, following expression and purification, were found to encode inactive XplB protein. Additionally, the Gordonia sp. KTR9 XplB was fused to glutamine synthetase, which would be likely to sterically inhibit XplB activity. Although the glutamine synthetase is fused to XplB and truncated by 71 residues, it was found to be active. Glutamine synthetase has been implicated in the regulation of nitrogen levels; controlling nitrogen availability will be important for effective bioremediation of RDX.}, }
@article {pmid28854630, year = {2017}, author = {Palazzo, A and Caizzi, R and Viggiano, L and Marsano, RM}, title = {Does the Promoter Constitute a Barrier in the Horizontal Transposon Transfer Process? Insight from Bari Transposons.}, journal = {Genome biology and evolution}, volume = {9}, number = {6}, pages = {1637-1645}, pmid = {28854630}, issn = {1759-6653}, mesh = {Animals ; Bacteria/*genetics ; *DNA Transposable Elements ; Diptera/*genetics ; *Gene Transfer, Horizontal ; Genes, Reporter ; Genome, Human ; Humans ; *Promoter Regions, Genetic ; Yeasts/*genetics ; }, abstract = {The contribution of the transposons' promoter in the horizontal transfer process is quite overlooked in the scientific literature. To shed light on this aspect we have mimicked the horizontal transfer process in laboratory and assayed in a wide range of hosts (fly, human, yeast and bacteria) the promoter activity of the 5' terminal sequences in Bari1 and Bari3, two Drosophila transposons belonging to the Tc1-mariner superfamily. These sequences are able to drive the transcription of a reporter gene even in distantly related organisms at least at the episomal level. By combining bioinformatics and experimental approaches, we define two distinct promoter sequences for each terminal sequence analyzed, which allow transcriptional activity in prokaryotes and eukaryotes, respectively. We propose that the Bari family of transposons, and possibly other members of the Tc1-mariner superfamily, might have evolved "blurry promoters," which have facilitated their diffusion in many living organisms through horizontal transfer.}, }
@article {pmid28854597, year = {2017}, author = {Kim, JI and Moore, CE and Archibald, JM and Bhattacharya, D and Yi, G and Yoon, HS and Shin, W}, title = {Evolutionary Dynamics of Cryptophyte Plastid Genomes.}, journal = {Genome biology and evolution}, volume = {9}, number = {7}, pages = {1859-1872}, pmid = {28854597}, issn = {1759-6653}, mesh = {Cryptophyta/*genetics/physiology ; *Evolution, Molecular ; *Genome, Plastid ; Phylogeny ; Plastids/*genetics ; Sequence Analysis, DNA/methods ; *Symbiosis ; }, abstract = {Cryptophytes are an ecologically important group of largely photosynthetic unicellular eukaryotes. This lineage is of great interest to evolutionary biologists because their plastids are of red algal secondary endosymbiotic origin and the host cell retains four different genomes (host nuclear, mitochondrial, plastid, and red algal nucleomorph). Here, we report a comparative analysis of plastid genomes from six representative cryptophyte genera. Four newly sequenced cryptophyte plastid genomes of Chroomonas mesostigmatica, Ch. placoidea, Cryptomonas curvata, and Storeatula sp. CCMP1868 share a number of features including synteny and gene content with the previously sequenced genomes of Cryptomonas paramecium, Rhodomonas salina, Teleaulax amphioxeia, and Guillardia theta. Our analysis of these plastid genomes reveals examples of gene loss and intron insertion. In particular, the chlB/chlL/chlN genes, which encode light-independent (dark active) protochlorophyllide oxidoreductase (LIPOR) proteins have undergone recent gene loss and pseudogenization in cryptophytes. Comparison of phylogenetic trees based on plastid and nuclear genome data sets show the introduction, via secondary endosymbiosis, of a red algal derived plastid in a lineage of chlorophyll-c containing algae. This event was followed by additional rounds of eukaryotic endosymbioses that spread the red lineage plastid to diverse groups such as haptophytes and stramenopiles.}, }
@article {pmid28853922, year = {2017}, author = {Koonin, EV and Novozhilov, AS}, title = {Origin and Evolution of the Universal Genetic Code.}, journal = {Annual review of genetics}, volume = {51}, number = {}, pages = {45-62}, doi = {10.1146/annurev-genet-120116-024713}, pmid = {28853922}, issn = {1545-2948}, mesh = {Amino Acids/genetics/metabolism ; Amino Acyl-tRNA Synthetases/genetics/metabolism ; Anticodon/chemistry/metabolism ; Biota/*genetics ; Codon/chemistry/metabolism ; *Evolution, Molecular ; Extinction, Biological ; Gene Transfer, Horizontal ; *Genetic Code ; *Genome ; *Models, Genetic ; Phylogeny ; *Protein Biosynthesis ; RNA, Transfer/genetics/metabolism ; }, abstract = {The standard genetic code (SGC) is virtually universal among extant life forms. Although many deviations from the universal code exist, particularly in organelles and prokaryotes with small genomes, they are limited in scope and obviously secondary. The universality of the code likely results from the combination of a frozen accident, i.e., the deleterious effect of codon reassignment in the SGC, and the inhibitory effect of changes in the code on horizontal gene transfer. The structure of the SGC is nonrandom and ensures high robustness of the code to mutational and translational errors. However, this error minimization is most likely a by-product of the primordial code expansion driven by the diversification of the repertoire of protein amino acids, rather than a direct result of selection. Phylogenetic analysis of translation system components, in particular aminoacyl-tRNA synthetases, shows that, at a stage of evolution when the translation system had already attained high fidelity, the correspondence between amino acids and cognate codons was determined by recognition of amino acids by RNA molecules, i.e., proto-tRNAs. We propose an experimentally testable scenario for the evolution of the code that combines recognition of amino acids by unique sites on proto-tRNAs (distinct from the anticodons), expansion of the code via proto-tRNA duplication, and frozen accident.}, }
@article {pmid28851932, year = {2017}, author = {Woodcock, DJ and Krusche, P and Strachan, NJC and Forbes, KJ and Cohan, FM and Méric, G and Sheppard, SK}, title = {Genomic plasticity and rapid host switching can promote the evolution of generalism: a case study in the zoonotic pathogen Campylobacter.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {9650}, pmid = {28851932}, issn = {2045-2322}, support = {BB/I02464X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MR/M501608/1/MRC_/Medical Research Council/United Kingdom ; 088786/C/09/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Adaptation, Biological ; *Adaptation, Physiological ; *Biological Evolution ; Campylobacter/*genetics/*physiology ; Gene Transfer, Horizontal ; *Models, Genetic ; Recombination, Genetic ; Selection, Genetic ; }, abstract = {Horizontal gene transfer accelerates bacterial adaptation to novel environments, allowing selection to act on genes that have evolved in multiple genetic backgrounds. This can lead to ecological specialization. However, little is known about how zoonotic bacteria maintain the ability to colonize multiple hosts whilst competing with specialists in the same niche. Here we develop a stochastic evolutionary model and show how genetic transfer of host segregating alleles, distributed as predicted for niche specifying genes, and the opportunity for host transition could interact to promote the emergence of host generalist lineages of the zoonotic bacterium Campylobacter. Using a modelling approach we show that increasing levels of homologous recombination enhance the efficiency with which selection can fix combinations of beneficial alleles, speeding adaptation. We then show how these predictions change in a multi-host system, with low levels of recombination, consistent with real r/m estimates, increasing the standing variation in the population, allowing a more effective response to changes in the selective landscape. Our analysis explains how observed gradients of host specialism and generalism can evolve in a multihost system through the transfer of ecologically important loci among coexisting strains.}, }
@article {pmid28851849, year = {2017}, author = {Kacar, B and Garmendia, E and Tuncbag, N and Andersson, DI and Hughes, D}, title = {Functional Constraints on Replacing an Essential Gene with Its Ancient and Modern Homologs.}, journal = {mBio}, volume = {8}, number = {4}, pages = {}, pmid = {28851849}, issn = {2150-7511}, mesh = {Bacterial Proteins ; *DNA, Ancient ; Escherichia coli/*genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genes, Essential ; Genetic Fitness ; Genome, Bacterial ; Peptide Elongation Factor Tu/*genetics/metabolism ; Phylogeny ; *Protein Biosynthesis ; Proteobacteria/genetics ; }, abstract = {Genes encoding proteins that carry out essential informational tasks in the cell, in particular where multiple interaction partners are involved, are less likely to be transferable to a foreign organism. Here, we investigated the constraints on transfer of a gene encoding a highly conserved informational protein, translation elongation factor Tu (EF-Tu), by systematically replacing the endogenous tufA gene in the Escherichia coli genome with its extant and ancestral homologs. The extant homologs represented tuf variants from both near and distant homologous organisms. The ancestral homologs represented phylogenetically resurrected tuf sequences dating from 0.7 to 3.6 billion years ago (bya). Our results demonstrate that all of the foreign tuf genes are transferable to the E. coli genome, provided that an additional copy of the EF-Tu gene, tufB, remains present in the E. coli genome. However, when the tufB gene was removed, only the variants obtained from the gammaproteobacterial family (extant and ancestral) supported growth which demonstrates the limited functional interchangeability of E. coli tuf with its homologs. Relative bacterial fitness correlated with the evolutionary distance of the extant tuf homologs inserted into the E. coli genome. This reduced fitness was associated with reduced levels of EF-Tu and reduced rates of protein synthesis. Increasing the expression of tuf partially ameliorated these fitness costs. In summary, our analysis suggests that the functional conservation of protein activity, the amount of protein expressed, and its network connectivity act to constrain the successful transfer of this essential gene into foreign bacteria.IMPORTANCE Horizontal gene transfer (HGT) is a fundamental driving force in bacterial evolution. However, whether essential genes can be acquired by HGT and whether they can be acquired from distant organisms are very poorly understood. By systematically replacing tuf with ancestral homologs and homologs from distantly related organisms, we investigated the constraints on HGT of a highly conserved gene with multiple interaction partners. The ancestral homologs represented phylogenetically resurrected tuf sequences dating from 0.7 to 3.6 bya. Only variants obtained from the gammaproteobacterial family (extant and ancestral) supported growth, demonstrating the limited functional interchangeability of E. coli tuf with its homologs. Our analysis suggests that the functional conservation of protein activity, the amount of protein expressed, and its network connectivity act to constrain the successful transfer of this essential gene into foreign bacteria.}, }
@article {pmid28846900, year = {2018}, author = {Zheng, J and Chen, T and Chen, H}, title = {Antibiotic resistome promotion in drinking water during biological activated carbon treatment: Is it influenced by quorum sensing?.}, journal = {The Science of the total environment}, volume = {612}, number = {}, pages = {1-8}, doi = {10.1016/j.scitotenv.2017.08.072}, pmid = {28846900}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents ; Bacteria/classification ; Biofilms ; Drinking Water/*analysis ; *Drug Resistance, Bacterial ; *Genes, Bacterial ; *Quorum Sensing ; Water Purification ; }, abstract = {The contamination of antibiotic resistance genes (ARGs) in drinking water may pose a direct threat to human health. This study applied high-throughput qPCR and sequencing to investigate the dynamics of ARGs and bacterial communities during the advanced treatment of drinking water using biological activated carbon. The promotion of ARGs was observed, and the normalized copy number of ARGs increased significantly after BAC treatment, raising the number of detected ARGs from 84 to 159. Twenty-nine ARGs were identified as biofilm-influencing sources in the BAC, and they persisted after chlorination. The shift of bacterial communities primarily had effects on the changes in resistome. Firmicutes, Cyanobacteria were related to persistent ARGs mostly in the BAC biofilm. Meanwhile, the Acyl-Homoserine Lactones (AHLs), quorum sensing molecules, and bacteria that produced AHLs were identified to understand the promotion of ARGs. The isolated AHL-producing bacteria belonged to the Proteobacteria, Firmicutes and Bacteroidetes phyla. Six detectable AHLs had an influence on plasmid-based horizontal gene transfer in the intragenus mating systems, indicating that the dynamics of ARGs were strongly affected by quorum sensing between specific bacteria in the biofilm. These results provide new insight into the mechanism of antibiotic resistome promotion in BAC biofilms.}, }
@article {pmid28846455, year = {2017}, author = {Bock, R}, title = {Witnessing Genome Evolution: Experimental Reconstruction of Endosymbiotic and Horizontal Gene Transfer.}, journal = {Annual review of genetics}, volume = {51}, number = {}, pages = {1-22}, doi = {10.1146/annurev-genet-120215-035329}, pmid = {28846455}, issn = {1545-2948}, mesh = {Cell Nucleus/genetics/metabolism ; Chloroplasts/genetics/metabolism ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genetic Speciation ; *Genome, Plant ; Genomics/methods ; Mitochondria/genetics/metabolism ; Plant Cells/metabolism ; Plants/*genetics ; Symbiosis/*genetics ; }, abstract = {Present day mitochondria and plastids (chloroplasts) evolved from formerly free-living bacteria that were acquired through endosymbiosis more than a billion years ago. Conversion of the bacterial endosymbionts into cell organelles involved the massive translocation of genetic material from the organellar genomes to the nucleus. The development of transformation technologies for organellar genomes has made it possible to reconstruct this endosymbiotic gene transfer in laboratory experiments and study the mechanisms involved. Recently, the horizontal transfer of genetic information between organisms has also become amenable to experimental investigation. It led to the discovery of horizontal genome transfer as an asexual process generating new species and new combinations of nuclear and organellar genomes. This review describes experimental approaches towards studying endosymbiotic and horizontal gene transfer processes, discusses the new knowledge gained from these approaches about both the evolutionary significance of gene transfer and the underlying molecular mechanisms, and highlights exciting possibilities to exploit gene and genome transfer in biotechnology and synthetic biology.}, }
@article {pmid28842650, year = {2017}, author = {Ye, Q and Tian, H and Chen, B and Shao, J and Qin, Y and Wen, J}, title = {Giardia's primitive GPL biosynthesis pathways with parasitic adaptation 'patches': implications for Giardia's evolutionary history and for finding targets against Giardiasis.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {9507}, pmid = {28842650}, issn = {2045-2322}, mesh = {Antiprotozoal Agents/pharmacology ; Biological Evolution ; *Biosynthetic Pathways ; Drug Discovery ; Gene Expression Regulation ; Gene Expression Regulation, Enzymologic ; Giardia/classification/drug effects/genetics/*metabolism ; Giardiasis/*parasitology ; Glycerophospholipids/*metabolism ; Phylogeny ; Protozoan Proteins/metabolism ; }, abstract = {Giardia is a worldwide spread protozoan parasite colonizing in small intestines of vertebrates, causing Giardiasis. The controversy about whether it is an extremely primitive eukaryote or just a highly evolved parasite has become a fetter to its uses as a model for both evolutionary and parasitological studies for years. Glycerophospholipid (GPL) synthesis is a conserved essential cellular process, and thus may retain some original features reflecting its evolutionary position, and this process should also have undergone parasitic adaptation to suit Giardia's dietary lipid-rich environment. Thus, GPL synthesis pathways may be a perfect object to examine the controversy over Giardia. Here, we first clarified Giardia's previously confusing GPL synthesis by re-identifying a reliable set of GPL synthesis genes/enzymes. Then using phylogenetic and comparative genomic analyses, we revealed that these pathways turn out to be evolutionarily primitive ones, but with many secondary parasitic adaptation 'patches' including gene loss, rapid evolution, product relocation, and horizontal gene transfer. Therefore, modern Giardia should be a mosaic of 'primary primitivity' and 'secondary parasitic adaptability', and to make a distinction between the two categories of features would restart the studies of eukaryotic evolution and parasitic adaptation using Giardia as a model system.}, }
@article {pmid28842276, year = {2017}, author = {Avni, E and Snir, S}, title = {Toxic genes present a unique phylogenetic signature.}, journal = {Molecular phylogenetics and evolution}, volume = {116}, number = {}, pages = {141-148}, doi = {10.1016/j.ympev.2017.08.007}, pmid = {28842276}, issn = {1095-9513}, mesh = {Archaea/genetics ; Computer Simulation ; Escherichia coli ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; Toxins, Biological/*genetics ; }, abstract = {Horizontal gene transfer (HGT) is a major part of the evolution of Archaea and Bacteria, to the extent that the validity of the Tree of Life concept for prokaryotes has been seriously questioned. The patterns and routes of HGT remain a subject of intense study and debate. It was discovered that while several genes exhibit rampant HGT across the whole prokaryotic tree of life, others are lethal to certain organisms and therefore cannot be successfully transferred to them. We distinguish between these two classes of genes and show analytically that genes found to be toxic to a specific species (E. coli) also resist HGT in general. Several tools we employ show evidence to support that claim. One of those tools is the quartet plurality distribution (QPD), a mathematical tool that measures tendency to HGT over a large set of genes and species. When aggregated over a collection of genes, it can reveal important properties of this collection. We conclude that evidence of toxicity of certain genes to a wide variety of prokaryotes are revealed using the new tool of quartet plurality distribution.}, }
@article {pmid28842132, year = {2017}, author = {Gama, JA and Zilhão, R and Dionisio, F}, title = {Conjugation efficiency depends on intra and intercellular interactions between distinct plasmids: Plasmids promote the immigration of other plasmids but repress co-colonizing plasmids.}, journal = {Plasmid}, volume = {93}, number = {}, pages = {6-16}, doi = {10.1016/j.plasmid.2017.08.003}, pmid = {28842132}, issn = {1095-9890}, mesh = {Conjugation, Genetic/*genetics ; Drug Resistance, Microbial/*genetics ; Gene Transfer, Horizontal/genetics ; Plasmids/*genetics ; }, abstract = {Conjugative plasmids encode the genes responsible for the synthesis of conjugative pili and plasmid transfer. Expression of the conjugative machinery (including conjugative pili) may be costly to bacteria, not only due to the energetic/metabolic cost associated with their expression but also because they serve as receptors for certain viruses. Consequently, the presence of two plasmids in the same cell may be disadvantageous to each plasmid, because they may impose a higher fitness cost on the host. Therefore, plasmids may encode mechanisms to cope with co-resident plasmids. Moreover, it is possible that the transfer rate of a plasmid is affected by the presence of a distinct plasmid in the recipient cell. In this work, we measured transfer rates of twelve natural plasmids belonging to seven incompatibility groups in three situations, namely when: (i) donor cells contain a plasmid and recipient cells are plasmid-free; (ii) donor cells contain two unrelated plasmids and recipient cells are plasmid-free; and (iii) half of the cells contain a given plasmid and the other half contain another, unrelated, plasmid. In the third situation, recipient cells of a plasmid are the donor cells of the other plasmid. We show that there are more negative interactions (reduction of a plasmid's conjugative efficiency) between plasmids if they reside in the same cell than if they reside in different cells. However, if plasmids interacted intercellularly, the transfer rate of one of the plasmids was often higher (when the unrelated conjugative plasmid was present in the recipient cell) than if the recipient cell was plasmid-free - a positive effect. Experimental data retrieved from the study of mutant plasmids not expressing conjugative pili on the cell surface suggest that positive effects result from a higher efficiency of mating pair formation. Overall, our results suggest that negative interactions are significantly more frequent when plasmids occupy the same cell. Such interactions may determine how antibiotic resistance disseminates in bacterial populations.}, }
@article {pmid28842131, year = {2017}, author = {Gama, JA and Zilhão, R and Dionisio, F}, title = {Co-resident plasmids travel together.}, journal = {Plasmid}, volume = {93}, number = {}, pages = {24-29}, doi = {10.1016/j.plasmid.2017.08.004}, pmid = {28842131}, issn = {1095-9890}, mesh = {Conjugation, Genetic/genetics ; Escherichia coli/genetics ; Gene Transfer, Horizontal/genetics ; Plasmids/*genetics ; }, abstract = {Conjugative plasmids encode genes that enable them to transfer, by conjugation, from a given host cell to another cell. Conjugative transfer, despite being an important feature of conjugative plasmids, is not constitutive for most plasmids, the reason being that genes involved in horizontal transfer are mostly repressed. Only upon their transient de-repression are plasmids able to transfer horizontally. If host cells harbour multiple plasmids, their simultaneous transfer depends on simultaneous transient de-repression of all plasmids. If de-repression of different plasmids was random and independent events, simultaneous de-repression should be a rare event because the probability of simultaneous de-repression would be the product of the probabilities of de-repression of each plasmid. Some previous observations support this hypothesis, while others show that co-transfer of plasmids is more frequent than this reasoning indicates. Here, we show that co-transfer of multiple plasmids mainly results from non-independent events: the probability that all plasmids within a cell become de-repressed is much higher than if de-repression of plasmids genes were independent. We found a simple model for the probability of co-transfer: the plasmid having the lowest conjugation rates is the one who limits co-transfer. In this sense, cells receiving the plasmid with the lower transfer rate also receive the other plasmid. If de-repression happens simultaneously on co-resident plasmids, common cues may stimulate de-repression of distinct plasmids.}, }
@article {pmid28839126, year = {2017}, author = {Fang, H and Huangfu, L and Chen, R and Li, P and Xu, S and Zhang, E and Cao, W and Liu, L and Yao, Y and Liang, G and Xu, C and Zhou, Y and Yang, Z}, title = {Ancestor of land plants acquired the DNA-3-methyladenine glycosylase (MAG) gene from bacteria through horizontal gene transfer.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {9324}, pmid = {28839126}, issn = {2045-2322}, mesh = {Bacteria/*enzymology/*genetics ; DNA Glycosylases/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Sequence Homology ; Streptophyta/*enzymology/*genetics ; }, abstract = {The origin and evolution of land plants was an important event in the history of life and initiated the establishment of modern terrestrial ecosystems. From water to terrestrial environments, plants needed to overcome the enhanced ultraviolet (UV) radiation and many other DNA-damaging agents. Evolving new genes with the function of DNA repair is critical for the origin and radiation of land plants. In bacteria, the DNA-3-methyladenine glycosylase (MAG) recognizes of a variety of base lesions and initiates the process of the base excision repair for damaged DNA. The homologs of MAG gene are present in all major lineages of streptophytes, and both the phylogenic and sequence similarity analyses revealed that green plant MAG gene originated through an ancient horizontal gene transfer (HGT) event from bacteria. Experimental evidence demonstrated that the expression of the maize ZmMAG gene was induced by UV and zeocin, both of which are known as DNA-damaging agents. Further investigation revealed that Streptophyta MAG genes had undergone positive selection during the initial evolutionary period in the ancestor of land plants. Our findings demonstrated that the ancient HGT of MAG to the ancestor of land plants probably played an important role in preadaptation to DNA-damaging agents in terrestrial environments.}, }
@article {pmid28831055, year = {2017}, author = {Shinozuka, H and Hettiarachchige, IK and Shinozuka, M and Cogan, NOI and Spangenberg, GC and Cocks, BG and Forster, JW and Sawbridge, TI}, title = {Horizontal transfer of a ß-1,6-glucanase gene from an ancestral species of fungal endophyte to a cool-season grass host.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {9024}, pmid = {28831055}, issn = {2045-2322}, mesh = {Adaptation, Biological ; Endophytes/enzymology/genetics ; Evolution, Molecular ; Fungal Proteins/genetics ; Fungi/*enzymology/genetics ; Gene Transfer, Horizontal ; Glycoside Hydrolases/*genetics ; Lolium/*enzymology/genetics/microbiology ; Phylogeny ; Plant Proteins/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Molecular characterisation has convincingly demonstrated some types of horizontal gene transfer in eukaryotes, but nuclear gene transfer between distantly related eukaryotic groups appears to have been rare. For angiosperms (flowering plants), nuclear gene transfer events identified to date have been confined to genes originating from prokaryotes or other plant species. In this report, evidence for ancient horizontal transfer of a fungal nuclear gene, encoding a ß-1,6-glucanase enzyme for fungal cell wall degradation, into an angiosperm lineage is presented for the first time. The gene was identified from de novo sequencing and assembly of the genome and transcriptome of perennial ryegrass, a cool-season grass species. Molecular analysis confirmed the presence of the complete gene in the genome of perennial ryegrass. No corresponding sequence was found in other plant species, apart from members of the Poeae sub-tribes Loliinae and Dactylidinae. Evidence suggests that a common ancestor of the two sub-tribes acquired the gene from a species ancestral to contemporary grass-associated fungal endophytes around 9-13 million years ago. This first report of horizontal transfer of a nuclear gene from a taxonomically distant eukaryote to modern flowering plants provides evidence for a novel adaptation mechanism in angiosperms.}, }
@article {pmid28830554, year = {2017}, author = {Chen, XP and Li, WG and Zheng, H and Du, HY and Zhang, L and Zhang, L and Che, J and Wu, Y and Liu, SM and Lu, JX}, title = {Extreme diversity and multiple SCCmec elements in coagulase-negative Staphylococcus found in the Clinic and Community in Beijing, China.}, journal = {Annals of clinical microbiology and antimicrobials}, volume = {16}, number = {1}, pages = {57}, pmid = {28830554}, issn = {1476-0711}, mesh = {Bacterial Proteins/genetics ; Bacterial Typing Techniques ; Beijing ; China ; Chromosomes, Bacterial/*genetics ; Coagulase/*analysis ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Methicillin Resistance/*genetics ; Microbial Sensitivity Tests ; Oxacillin/pharmacology ; Penicillin-Binding Proteins/genetics ; Phylogeny ; Polymerase Chain Reaction ; RNA, Messenger/analysis ; Recombinases/*genetics ; Staphylococcal Infections/microbiology ; Staphylococcus aureus/drug effects/*genetics/growth &amp; development/isolation &amp; purification ; }, abstract = {BACKGROUND: Coagulase-negative staphylococci (CoNS) are recognized as a large reservoir of staphylococcal cassette chromosome mec (SCCmec) harboured by Staphylococcus aureus. However, data of SCCmec in CoNS are relatively absent particularly in China.<br><br>METHODS: Seventy-eight CoNS clinical and 47 community isolates were collected in Beijing. PCR was performed to classify SCCmec types. Under oxacillin treatment, quantitative real-time reverse transcription PCR (qRT-PCR) was performed to compare mecA mRNA levels and mRNA half-life between isolates with single SCCmec element and those with multiple one. Their growth curves were analysed. Their bacterial cell wall integrity was also compared by performing a Gram stain. All ccr complex segments were sequenced and obtained ccr segments were analysed by phylogenetic analyses.<br><br>RESULTS: All 78 clinical isolates had mecA segments compared with 38% in community isolates (total 47). Only 29% clinical isolates and 33% community isolates (among mecA positive isolates) harboured a single previously identified SCCmec type; notably, 17% clinical isolates and 28% community isolates had multiple SCCmec types. Further studies indicated that isolates with multiple SCCmec elements had more stable mecA mRNA expression compared with isolates with single SCCmec elements. CoNS with multiple SCCmec elements demonstrated superior cell wall integrity. Interestingly, phylogenetic analyses of obtained 70&#xa0;ccr segments indicated that horizontal gene transfer of the ccr complex might exist among various species of clinical CoNS, community CoNS and S. aureus.<br><br>CONCLUSIONS: CoNS recovered from patients carried extremely diverse but distinctive SCCmec elements compared with isolates from the community. More attention should be given to CoNS with multiple SCCmec not only because they had superior cell wall integrity, but also because CoNS and S. aureus might acquire multiple SCCmec through the ccr complex.}, }
@article {pmid28830351, year = {2017}, author = {Lorenz, SC and Gonzalez-Escalona, N and Kotewicz, ML and Fischer, M and Kase, JA}, title = {Genome sequencing and comparative genomics of enterohemorrhagic Escherichia coli O145:H25 and O145:H28 reveal distinct evolutionary paths and marked variations in traits associated with virulence &amp; colonization.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {183}, pmid = {28830351}, issn = {1471-2180}, mesh = {Adhesins, Bacterial/genetics ; Base Sequence ; *Biological Evolution ; Enterohemorrhagic Escherichia coli/*classification/*genetics/virology ; Escherichia coli/classification/genetics/virology ; Escherichia coli O157/classification/genetics/virology ; Escherichia coli Proteins/genetics ; Evolution, Molecular ; Fimbriae, Bacterial/genetics ; Genetic Variation ; *Genome, Bacterial ; Genomic Islands/genetics ; Genomics ; Humans ; Multigene Family ; Phenotype ; Phylogeny ; Prophages/genetics ; *Serogroup ; Virulence/*genetics ; }, abstract = {BACKGROUND: Enterohemorrhagic Escherichia coli (EHEC) O145 are among the top non-O157 serogroups associated with severe human disease worldwide. Two serotypes, O145:H25 and O145:H28 have been isolated from human patients but little information is available regarding the virulence repertoire, origin and evolutionary relatedness of O145:H25. Hence, we sequenced the complete genome of two O145:H25 strains associated with hemolytic uremic syndrome (HUS) and compared the genomes with those of previously sequenced O145:H28 and other EHEC strains.<br><br>RESULTS: The genomes of the two O145:H25 strains were 5.3 Mbp in size; slightly smaller than those of O145:H28 and other EHEC strains. Both strains contained three nearly identical plasmids and several prophages and integrative elements, many of which differed significantly in size, gene content and organization as compared to those present in O145:H28 and other EHECs. Furthermore, notable variations were observed in several fimbrial gene cluster and intimin types possessed by O145:H25 and O145:H28 indicating potential adaptation to distinct areas of host colonization. Comparative genomics further revealed that O145:H25 are genetically more similar to other non-O157 EHEC strains than to O145:H28.<br><br>CONCLUSION: Phylogenetic analysis accompanied by comparative genomics revealed that O145:H25 and O145:H28 evolved from two separate clonal lineages and that horizontal gene transfer and gene loss played a major role in the divergence of these EHEC serotypes. The data provide further evidence that ruminants might be a possible reservoir for O145:H25 but that they might be impaired in their ability to establish a persistent colonization as compared to other EHEC strains.}, }
@article {pmid28829895, year = {2017}, author = {Chen, FF and Ma, CY and Yan, LP and Zhang, H and Wang, W and Zhang, Y and Ma, LB}, title = {Isolation and characterization of polymorphic microsatellite markers for the chub mackerel (Scomber japonicus) and cross-species amplification in the blue mackerel (S. australasicus).}, journal = {Genetics and molecular research : GMR}, volume = {16}, number = {3}, pages = {}, doi = {10.4238/gmr16039712}, pmid = {28829895}, issn = {1676-5680}, mesh = {Animals ; *Gene Amplification ; Gene Flow ; Gene Transfer, Horizontal ; Linkage Disequilibrium ; *Microsatellite Repeats ; Perciformes/classification/*genetics ; *Polymorphism, Genetic ; }, abstract = {In this study, 10 polymorphic microsatellite markers were developed in Scomber japonicus and were examined on 30 individuals collected from the North Pacific. The number of alleles per locus ranged from 4 to 17. The observed and expected heterozygosities per locus ranged from 0.2759 to 0.8621 and from 0.43071 to 0.9177, respectively. The polymorphism information content (PIC) was from 0.3931 to 0.8939. One locus showed moderate polymorphism (0.25 < PIC < 0.5), while the rest were highly polymorphic (PIC > 0.5). Two loci showed significant deviation from Hardy-Weinberg equilibrium after Bonferroni corrections (P < 0.005). No linkage disequilibrium was detected among the loci. Results of cross-species amplification showed that 10 microsatellite markers were successfully amplified in 29 individuals of S. australasicus and 9 indicated polymorphisms. These markers will be useful for investigating the genetic structure, gene flow, and species identification of S. japonicus and S. australasicus, its closely related species.}, }
@article {pmid28828268, year = {2017}, author = {Morozov, SY and Lazareva, EA and Solovyev, AG}, title = {RNA helicase domains of viral origin in proteins of insect retrotransposons: possible source for evolutionary advantages.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e3673}, pmid = {28828268}, issn = {2167-8359}, abstract = {Recently, a novel phenomenon of horizontal gene transfer of helicase-encoding sequence from positive-stranded RNA viruses to LINE transposons in insect genomes was described. TRAS family transposons encoding an ORF2 protein, which comprised all typical functional domains and an additional helicase domain, were found to be preserved in many families during the evolution of the order Lepidoptera. In the present paper, in species of orders Hemiptera and Orthoptera, we found helicase domain-encoding sequences integrated into ORF1 of retrotransposons of the Jockey family. RNA helicases encoded by transposons of TRAS and Jockey families represented separate brunches in a phylogenetic tree of helicase domains and thus could be considered as independently originated in the evolution of insect transposons. Transcriptome database analyses revealed that both TRAS and Jockey transposons encoding the helicase domain represented transcribed genome sequences. Moreover, the transposon-encoded helicases were found to contain the full set of conserved motifs essential for their enzymatic activities. Taking into account the previously reported ability of RNA helicase encoded by TRAS ORF2 to suppress post-transcriptional RNA silencing, we propose possible scenarios of evolutionary fixation of actively expressed functional helicases of viral origin in insect retrotransposons as genetic elements advantageous for both transposons and their insect hosts.}, }
@article {pmid28827361, year = {2017}, author = {Monier, A and Chambouvet, A and Milner, DS and Attah, V and Terrado, R and Lovejoy, C and Moreau, H and Santoro, AE and Derelle, &#xc9; and Richards, TA}, title = {Host-derived viral transporter protein for nitrogen uptake in infected marine phytoplankton.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {36}, pages = {E7489-E7498}, pmid = {28827361}, issn = {1091-6490}, support = {//Wellcome Trust/United Kingdom ; WT105618MA//Wellcome Trust/United Kingdom ; }, mesh = {Cell Membrane/virology ; Chlorophyta/virology ; Gene Transfer, Horizontal/*genetics ; Genes, Viral/genetics ; Genome, Viral/genetics ; Host-Pathogen Interactions/*genetics ; Nitrogen/*metabolism ; Phytoplankton/*virology ; Viral Proteins/*metabolism ; }, abstract = {Phytoplankton community structure is shaped by both bottom-up factors, such as nutrient availability, and top-down processes, such as predation. Here we show that marine viruses can blur these distinctions, being able to amend how host cells acquire nutrients from their environment while also predating and lysing their algal hosts. Viral genomes often encode genes derived from their host. These genes may allow the virus to manipulate host metabolism to improve viral fitness. We identify in the genome of a phytoplankton virus, which infects the small green alga Ostreococcus tauri, a host-derived ammonium transporter. This gene is transcribed during infection and when expressed in yeast mutants the viral protein is located to the plasma membrane and rescues growth when cultured with ammonium as the sole nitrogen source. We also show that viral infection alters the nature of nitrogen compound uptake of host cells, by both increasing substrate affinity and allowing the host to access diverse nitrogen sources. This is important because the availability of nitrogen often limits phytoplankton growth. Collectively, these data show that a virus can acquire genes encoding nutrient transporters from a host genome and that expression of the viral gene can alter the nutrient uptake behavior of host cells. These results have implications for understanding how viruses manipulate the physiology and ecology of phytoplankton, influence marine nutrient cycles, and act as vectors for horizontal gene transfer.}, }
@article {pmid28826484, year = {2017}, author = {Silas, S and Lucas-Elio, P and Jackson, SA and Aroca-Crevillén, A and Hansen, LL and Fineran, PC and Fire, AZ and Sánchez-Amat, A}, title = {Type III CRISPR-Cas systems can provide redundancy to counteract viral escape from type I systems.}, journal = {eLife}, volume = {6}, number = {}, pages = {}, pmid = {28826484}, issn = {2050-084X}, support = {R01 GM037706/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Bacteriophages/genetics/growth &amp; development/metabolism ; Base Sequence ; CRISPR-Cas Systems/*immunology ; Clustered Regularly Interspaced Short Palindromic Repeats/*immunology ; DNA, Viral/genetics/metabolism ; Gene Transfer, Horizontal ; Marinomonas/*genetics/immunology/virology ; Plasmids/chemistry/immunology/metabolism ; RNA, Viral/genetics/metabolism ; Type I Secretion Systems/*genetics/immunology ; Type III Secretion Systems/*genetics/immunology ; }, abstract = {CRISPR-Cas-mediated defense utilizes information stored as spacers in CRISPR arrays to defend against genetic invaders. We define the mode of target interference and role in antiviral defense for two CRISPR-Cas systems in Marinomonas mediterranea. One system (type I-F) targets DNA. A second system (type III-B) is broadly capable of acquiring spacers in either orientation from RNA and DNA, and exhibits transcription-dependent DNA interference. Examining resistance to phages isolated from Mediterranean seagrass meadows, we found that the type III-B machinery co-opts type I-F CRISPR-RNAs. Sequencing and infectivity assessments of related bacterial and phage strains suggests an 'arms race' in which phage escape from the type I-F system can be overcome through use of type I-F spacers by a horizontally-acquired type III-B system. We propose that the phage-host arms race can drive selection for horizontal uptake and maintenance of promiscuous type III interference modules that supplement existing host type I CRISPR-Cas systems.}, }
@article {pmid28826473, year = {2017}, author = {Bowring, J and Neamah, MM and Donderis, J and Mir-Sanchis, I and Alite, C and Ciges-Tomas, JR and Maiques, E and Medmedov, I and Marina, A and Penadés, JR}, title = {Pirating conserved phage mechanisms promotes promiscuous staphylococcal pathogenicity island transfer.}, journal = {eLife}, volume = {6}, number = {}, pages = {}, pmid = {28826473}, issn = {2050-084X}, support = {/WT_/Wellcome Trust/United Kingdom ; MR/M003876/1/MRC_/Medical Research Council/United Kingdom ; BB/N002873/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 201531/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; *Genomic Islands ; Host-Parasite Interactions ; *Interspersed Repetitive Sequences ; Repressor Proteins/metabolism ; Staphylococcus Phages ; Staphylococcus aureus/*genetics/*virology ; *Transduction, Genetic ; Viral Proteins/metabolism ; }, abstract = {Targeting conserved and essential processes is a successful strategy to combat enemies. Remarkably, the clinically important Staphylococcus aureus pathogenicity islands (SaPIs) use this tactic to spread in nature. SaPIs reside passively in the host chromosome, under the control of the SaPI-encoded master repressor, Stl. It has been assumed that SaPI de-repression is effected by specific phage proteins that bind to Stl, initiating the SaPI cycle. Different SaPIs encode different Stl repressors, so each targets a specific phage protein for its de-repression. Broadening this narrow vision, we report here that SaPIs ensure their promiscuous transfer by targeting conserved phage mechanisms. This is accomplished because the SaPI Stl repressors have acquired different domains to interact with unrelated proteins, encoded by different phages, but in all cases performing the same conserved function. This elegant strategy allows intra- and inter-generic SaPI transfer, highlighting these elements as one of nature's most fascinating subcellular parasites.}, }
@article {pmid28825126, year = {2018}, author = {Chi, S and Liu, T and Wang, X and Wang, R and Wang, S and Wang, G and Shan, G and Liu, C}, title = {Functional genomics analysis reveals the biosynthesis pathways of important cellular components (alginate and fucoidan) of Saccharina.}, journal = {Current genetics}, volume = {64}, number = {1}, pages = {259-273}, pmid = {28825126}, issn = {1432-0983}, support = {41376143//National Natural Science Foundation of China/ ; 14-2-4-104-jch//Qingdao applied basic research project/ ; }, mesh = {Alginates/*metabolism ; *Biosynthetic Pathways/genetics ; Computational Biology/methods ; Evolution, Molecular ; Gene Expression Profiling ; Gene Expression Regulation ; Gene Transfer, Horizontal ; *Genome ; *Genomics/methods ; Glucuronic Acid/metabolism ; Hexuronic Acids/metabolism ; High-Throughput Nucleotide Sequencing ; Phaeophyceae/classification/*genetics/*metabolism ; Phylogeny ; Polysaccharides/*metabolism ; Symbiosis/genetics ; Transcriptome ; }, abstract = {Although alginate and fucoidan are unique cellular components and have important biological significance in brown algae, and many possible involved genes are present in brown algal genomes, their functions and regulatory mechanisms have not been fully revealed. Both polysaccharides may play important roles in the evolution of multicellular brown algae, but specific and in-depth studies are still limited. In this study, a functional genomics analysis of alginate and fucoidan biosynthesis routes was conducted in Saccharina, and the key events in these pathways in brown algae were identified. First, genes from different sources, including eukaryotic hosts via endosymbiotic gene transfer and bacteria via horizontal gene transfer, were combined to build a complete pathway framework. Then, a critical event occurred to drive these pathways to have real function: one of the mannose-6-phosphate isomerase homologs that arose by gene duplication subsequently adopted the function of the mannose-1-phosphate guanylyltransferase (MGP) gene, which was absent in algal genomes. Further, downstream pathway genes proceeded with gene expansions and complex transcriptional mechanisms, which may be conducive to the synthesis of alginate and fucoidan with diverse structures and contents depending on the developmental stage, tissue structure, and environmental conditions. This study revealed the alginate and fucoidan synthesis pathways and all included genes from separate phylogenetic sources in brown algae. Enzyme assays confirmed the function of key genes and led to the determination of a substitute for the missing MPG. All gene families had constitutively expressed member(s) to maintain the basic synthesis; and the gene function differentiation, enzyme characterization and gene expression regulation differences separated brown algae from other algae lineages and were considered to be the major driving forces for sophisticated system evolution of brown algae.}, }
@article {pmid28821711, year = {2017}, author = {Tran, F and Boedicker, JQ}, title = {Genetic cargo and bacterial species set the rate of vesicle-mediated horizontal gene transfer.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {8813}, pmid = {28821711}, issn = {2045-2322}, mesh = {Bacteria/classification/*genetics/*metabolism ; *Bacterial Physiological Phenomena ; Extracellular Vesicles/*metabolism ; *Gene Transfer, Horizontal ; Plasmids/genetics ; RNA, Ribosomal, 16S ; Species Specificity ; }, abstract = {Most bacteria release extracellular vesicles (EVs). Recent studies have found these vesicles are capable of gene delivery, however the consequences of vesicle-mediated transfer on the patterns and rates of gene flow within microbial communities remains unclear. Previous studies have not determined the impact of both the genetic cargo and the donor and recipient species on the rate of vesicle-mediated gene exchange. This report examines the potential for EVs as a mechanism of gene transfer within heterogeneous microbial populations. EVs were harvested from three species of Gram-negative microbes carrying different plasmids. The dynamics of gene transfer into recipient species was measured. This study demonstrates that vesicles enable gene exchange between five species of Gram-negative bacteria, and that the identity of the genetic cargo, donor strain, and recipient strain all influence gene transfer rates. Each species released and acquired vesicles containing genetic material to a variable degree, and the transfer rate did not correlate with the relatedness of the donor and recipient species. The results suggest that EVs may be a general mechanism to exchange non-specialized genetic cargo between bacterial species.}, }
@article {pmid28818623, year = {2017}, author = {Caimi, K and Repetto, SA and Varni, V and Ruybal, P}, title = {Leptospira species molecular epidemiology in the genomic era.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {54}, number = {}, pages = {478-485}, doi = {10.1016/j.meegid.2017.08.013}, pmid = {28818623}, issn = {1567-7257}, mesh = {Bayes Theorem ; Evolution, Molecular ; Genome, Bacterial ; Leptospira/*classification/*genetics ; Multilocus Sequence Typing/*methods ; Phylogeny ; Whole Genome Sequencing ; }, abstract = {Leptospirosis is a zoonotic disease which global burden is increasing often related to climatic change. Hundreds of whole genome sequences from worldwide isolates of Leptospira spp. are available nowadays, together with online tools that permit to assign MLST sequence types (STs) directly from raw sequence data. In this work we have applied R7L-MLST to near 500 genomes and strains collection globally distributed. All 10 pathogenic species as well as intermediate were typed using this MLST scheme. The correlation observed between STs and serogroups in our previous work, is still satisfied with this higher dataset sustaining the implementation of MLST to assist serological classification as a complementary approach. Bayesian phylogenetic analysis of concatenated sequences from R7-MLST loci allowed us to resolve taxonomic inconsistencies but also showed that events such as recombination, gene conversion or lateral gene transfer played an important role in the evolution of Leptospira genus. Whole genome sequencing allows us to contribute with suitable epidemiologic information useful to apply in the design of control strategies and also in diagnostic methods for this illness.}, }
@article {pmid28812563, year = {2016}, author = {San Millan, A and Escudero, JA and Gifford, DR and Mazel, D and MacLean, RC}, title = {Multicopy plasmids potentiate the evolution of antibiotic resistance in bacteria.}, journal = {Nature ecology &amp; evolution}, volume = {1}, number = {1}, pages = {10}, doi = {10.1038/s41559-016-0010}, pmid = {28812563}, issn = {2397-334X}, abstract = {Plasmids are thought to play a key role in bacterial evolution by acting as vehicles for horizontal gene transfer, but the role of plasmids as catalysts of gene evolution remains unexplored. We challenged populations of Escherichia coli carrying the blaTEM-1 β-lactamase gene on either the chromosome or a multicopy plasmid (19 copies per cell) with increasing concentrations of ceftazidime. The plasmid accelerated resistance evolution by increasing the rate of appearance of novel TEM-1 mutations, thereby conferring resistance to ceftazidime, and then by amplifying the effect of TEM-1 mutations due to the increased gene dosage. Crucially, this dual effect was necessary and sufficient for the evolution of clinically relevant levels of resistance. Subsequent evolution occurred by mutations in a regulatory RNA that increased the plasmid copy number, resulting in marginal gains in ceftazidime resistance. These results uncover a role for multicopy plasmids as catalysts for the evolution of antibiotic resistance in bacteria.}, }
@article {pmid28810712, year = {2017}, author = {Kopejtka, K and Tomasch, J and Zeng, Y and Tichý, M and Sorokin, DY and Koblížek, M}, title = {Genomic Analysis of the Evolution of Phototrophy among Haloalkaliphilic Rhodobacterales.}, journal = {Genome biology and evolution}, volume = {9}, number = {7}, pages = {1950-1962}, pmid = {28810712}, issn = {1759-6653}, mesh = {Aerobiosis ; Bacterial Proteins/*genetics ; *Evolution, Molecular ; Genomics ; Light ; Photosynthesis ; *Phototrophic Processes ; Phylogeny ; Rhodobacter/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {A characteristic feature of the order Rhodobacterales is the presence of a large number of photoautotrophic and photoheterotrophic species containing bacteriochlorophyll. Interestingly, these phototrophic species are phylogenetically mixed with chemotrophs. To better understand the origin of such variability, we sequenced the genomes of three closely related haloalkaliphilic species, differing in their phototrophic capacity and oxygen preference: the photoheterotrophic and facultatively anaerobic bacterium Rhodobaca barguzinensis, aerobic photoheterotroph Roseinatronobacter thiooxidans, and aerobic heterotrophic bacterium Natronohydrobacter thiooxidans. These three haloalcaliphilic species are phylogenetically related and share many common characteristics with the Rhodobacter species, forming together the Rhodobacter-Rhodobaca (RR) group. A comparative genomic analysis showed close homology of photosynthetic proteins and similarity in photosynthesis gene organization among the investigated phototrophic RR species. On the other hand, Rhodobaca barguzinensis and Roseinatronobacter thiooxidans lack an inorganic carbon fixation pathway and outer light-harvesting genes. This documents the reduction of their photosynthetic machinery towards a mostly photoheterotrophic lifestyle. Moreover, both phototrophic species contain 5-aminolevulinate synthase (encoded by the hemA gene) incorporated into their photosynthesis gene clusters, which seems to be a common feature of all aerobic anoxygenic phototrophic Alphaproteobacteria. Interestingly, the chrR-rpoE (sigma24) operon, which is part of singlet oxygen defense in phototrophic species, was found in the heterotrophic strain Natronohydrobacter thiooxidans. This suggests that this organism evolved from a photoheterotrophic ancestor through the loss of its photosynthesis genes. The overall evolution of phototrophy among the haloalkaliphilic members of the RR group is discussed.}, }
@article {pmid28808128, year = {2017}, author = {Burbank, LP and Van Horn, CR}, title = {Conjugative Plasmid Transfer in Xylella fastidiosa Is Dependent on tra and trb Operon Functions.}, journal = {Journal of bacteriology}, volume = {199}, number = {21}, pages = {}, pmid = {28808128}, issn = {1098-5530}, mesh = {*Conjugation, Genetic ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; *Operon ; *Plasmids ; Type IV Secretion Systems/genetics ; Xylella/*genetics ; }, abstract = {The insect-transmitted plant pathogen Xylella fastidiosa is capable of efficient horizontal gene transfer (HGT) and recombination. Natural transformation occurs at high rates in X. fastidiosa, but there also is evidence that certain strains of X. fastidiosa carry native plasmids equipped with transfer and mobilization genes, suggesting conjugation as an additional mechanism of HGT in some instances. Two operons, tra and trb, putatively encoding a conjugative type IV secretion system, are found in some but not all X. fastidiosa isolates, often on native plasmids. X. fastidiosa strains that carry the conjugative transfer genes can belong to different subspecies and frequently differ in host ranges. Using X. fastidiosa strain M23 (X. fastidiosa subsp. fastidiosa) or Dixon (X. fastidiosa subsp. multiplex) as the donor strain and Temecula (X. fastidiosa subsp. fastidiosa) as the recipient strain, plasmid transfer was characterized using the mobilizable broad-host-range vector pBBR5pemIK. Transfer of plasmid pBBR5pemIK was observed under in vitro conditions with both donor strains and was dependent on both tra and trb operon functions. A conjugative mechanism likely contributes to gene transfer between diverse strains of X. fastidiosa, possibly facilitating adaptation to new environments or different hosts.IMPORTANCEXylella fastidiosa is an important plant pathogen worldwide, infecting a wide range of different plant species. The emergence of new diseases caused by X. fastidiosa, or host switching of existing strains, is thought to be primarily due to the high frequency of HGT and recombination in this pathogen. Transfer of plasmids by a conjugative mechanism enables movement of larger amounts of genetic material at one time, compared with other routes of gene transfer such as natural transformation. Establishing the prevalence and functionality of this mechanism in X. fastidiosa contributes to a better understanding of HGT, adaptation, and disease emergence in this diverse pathogen.}, }
@article {pmid28803933, year = {2017}, author = {Gunathilaka, GU and Tahlan, V and Mafiz, A and Polur, M and Zhang, Y}, title = {Phages in urban wastewater have the potential to disseminate antibiotic resistance.}, journal = {International journal of antimicrobial agents}, volume = {50}, number = {5}, pages = {678-683}, doi = {10.1016/j.ijantimicag.2017.08.013}, pmid = {28803933}, issn = {1872-7913}, mesh = {Cities ; Coliphages/*genetics/*isolation &amp; purification/physiology/ultrastructure ; DNA, Viral/genetics ; *Drug Resistance, Bacterial ; Escherichia coli/*virology ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Host Specificity ; Microscopy, Electron, Transmission ; Polymerase Chain Reaction ; *Transduction, Genetic ; Wastewater/*virology ; }, abstract = {A total of 29 Escherichia coli phages were isolated from wastewater samples collected from an urban wastewater treatment plant and were characterised by host range determination, transmission electron microscopy, antibiotic resistance gene identification and phage transduction. β-Lactam resistance genes (blaCMY, blaTEM, blaSHV, blaCTX-M and blaOXA) were amplified on phage DNA by PCR. Of nine host range patterns observed, six were able to multiply in three or more indicator strains, including Shiga toxin-producing E. coli (STEC). Twelve E. coli phages were able to grow in all four E. coli O157 strains tested. The blaTEM gene was detected in 15 phages, of which 6 were able to transduce blaTEM into E. coli ATCC 13706. These data suggest that phages with broad host range are prevalent in the urban environment and can serve as a natural reservoir of antibiotic resistance genes. These phages can also transfer antibiotic resistance genes via phage transduction and may contribute to the dissemination of antibiotic resistance in the environment.}, }
@article {pmid28802584, year = {2017}, author = {Romaniuk, K and Krucon, T and Decewicz, P and Gorecki, A and Dziewit, L}, title = {Molecular characterization of the pA3J1 plasmid from the psychrotolerant Antarctic bacterium Pseudomonas sp. ANT_J3.}, journal = {Plasmid}, volume = {92}, number = {}, pages = {49-56}, doi = {10.1016/j.plasmid.2017.08.001}, pmid = {28802584}, issn = {1095-9890}, mesh = {Amino Acid Sequence ; Antarctic Regions ; Bacterial Proteins/chemistry/genetics ; DNA Replication/genetics ; Environmental Microbiology ; Gene Transfer, Horizontal ; Open Reading Frames ; Phylogeny ; Plasmids/*genetics ; Pseudomonas/*genetics ; Replicon ; Sequence Analysis, DNA ; }, abstract = {The knowledge on plasmids of cold-active bacteria is highly limited. In this study, the molecular characterization of the pA3J1 plasmid of Antarctic psychrotolerant bacterium Pseudomonas sp. ANT_J3 was performed. Within this plasmid, thirteen putative open reading frames were identified. Nine of them encoded proteins involved in replication, partitioning, postsegregational elimination of plasmid-less cells (via a toxin-antitoxin system activity), multimer resolution and mobilization by conjugal transfer. These genes constitute the plasmid backbone. The functional analysis of the pA3J1 maintenance region revealed that it is a narrow host range replicon, stably maintained in the host cells by the combined activities of the partitioning and relBE-type toxin-antitoxin systems. It was also suggested that the replication system of the pA3J1 plasmid may be temperature-sensitive. Comparative analyses revealed the presence of 16 Pseudomonas plasmids encoding homologous replication proteins and 5 plasmids carrying mobA genes homologous to the corresponding gene of pA3J1. The relaxase (MobA) of the pA3J1 plasmid was classified into MOBQ family, and the phylogenetic analysis suggested that this may be a representative of a novel group (or subgroup) within this family. The structural and comparative analyses revealed that the arrangement of genetic modules in the pA3J1 plasmid is unique.}, }
@article {pmid28802274, year = {2017}, author = {Pornsukarom, S and Thakur, S}, title = {Horizontal Dissemination of Antimicrobial Resistance Determinants in Multiple Salmonella Serotypes following Isolation from the Commercial Swine Operation Environment after Manure Application.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {20}, pages = {}, pmid = {28802274}, issn = {1098-5336}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Conjugation, Genetic ; *Drug Resistance, Bacterial ; *Gene Transfer, Horizontal ; Integrons ; Manure/*microbiology ; Microbial Sensitivity Tests ; Phylogeny ; Plasmids/genetics/metabolism ; Salmonella Infections, Animal/*microbiology ; Salmonella enterica/drug effects/*genetics/isolation &amp; purification/metabolism ; Serogroup ; Swine ; Swine Diseases/*microbiology ; }, abstract = {The aim of this study was to characterize the plasmids carrying antimicrobial resistance (AMR) determinants in multiple Salmonella serotypes recovered from the commercial swine farm environment after manure application on land. Manure and soil samples were collected on day 0 before and after manure application on six farms in North Carolina, and sequential soil samples were recollected on days 7, 14, and 21 from the same plots. All environmental samples were processed for Salmonella, and their plasmid contents were further characterized. A total of 14 isolates including Salmonella enterica serotypes Johannesburg (n = 2), Ohio (n = 2), Rissen (n = 1), Typhimurium var5- (n = 5), Worthington (n = 3), and 4,12:i:- (n = 1), representing different farms, were selected for plasmid analysis. Antimicrobial susceptibility testing was done by broth microdilution against a panel of 14 antimicrobials on the 14 confirmed transconjugants after conjugation assays. The plasmids were isolated by modified alkaline lysis, and PCRs were performed on purified plasmid DNA to identify the AMR determinants and the plasmid replicon types. The plasmids were sequenced for further analysis and to compare profiles and create phylogenetic trees. A class 1 integron with an ANT(2″)-Ia-aadA2 cassette was detected in the 50-kb IncN plasmids identified in S Worthington isolates. We identified 100-kb and 90-kb IncI1 plasmids in S Johannesburg and S Rissen isolates carrying the blaCMY-2 and tet(A) genes, respectively. An identical 95-kb IncF plasmid was widely disseminated among the different serotypes and across different farms. Our study provides evidence on the importance of horizontal dissemination of resistance determinants through plasmids of multiple Salmonella serotypes distributed across commercial swine farms after manure application.IMPORTANCE The horizontal gene transfer of antimicrobial resistance (AMR) determinants located on plasmids is considered to be the main reason for the rapid proliferation and spread of drug resistance. The deposition of manure generated in swine production systems into the environment is identified as a potential source of AMR dissemination. In this study, AMR gene-carrying plasmids were detected in multiple Salmonella serotypes across different commercial swine farms in North Carolina. The plasmid profiles were characterized based on Salmonella serotype donors and incompatibility (Inc) groups. We found that different Inc plasmids showed evidence of AMR gene transfer in multiple Salmonella serotypes. We detected an identical 95-kb plasmid that was widely distributed across swine farms in North Carolina. These conjugable resistance plasmids were able to persist on land after swine manure application. Our study provides strong evidence of AMR determinant dissemination present in plasmids of multiple Salmonella serotypes in the environment after manure application.}, }
@article {pmid28802203, year = {2017}, author = {Campbell, S and Aswad, A and Katzourakis, A}, title = {Disentangling the origins of virophages and polintons.}, journal = {Current opinion in virology}, volume = {25}, number = {}, pages = {59-65}, doi = {10.1016/j.coviro.2017.07.011}, pmid = {28802203}, issn = {1879-6265}, mesh = {DNA Transposable Elements/*genetics ; DNA, Viral/genetics ; Eukaryota/*virology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Viral ; Giant Viruses/*genetics/physiology ; Phylogeny ; Virophages/*genetics ; Virus Diseases/genetics/transmission ; }, abstract = {Virophages and polintons are part of a complex system that also involves eukaryotes, giant viruses, as well as other viruses and transposable elements. Virophages are cosmopolitan, being found in environments ranging from the Amazon River to Antarctic hypersaline lakes, while polintons are found in many single celled and multicellular eukaryotes. Virophages and polintons have a shared ancestry, but their exact origins are unknown and obscured by antiquity and extensive horizontal gene transfer (HGT). Paleovirology can help disentangle the complicated gene flow between these two, as well as their giant viral and eukaryotic hosts. We outline the evidence and theoretical support for polintons being descended from viruses and not vice versa. In order to disentangle the natural history of polintons and virophages, we suggest that there is much to be gained by embracing rigorous metagenomics and evolutionary analyses. Methods from paleovirology will play a pivotal role in unravelling ancient relationships, HGT and patterns of cross-species transmission.}, }
@article {pmid28802020, year = {2018}, author = {Czislowski, E and Fraser-Smith, S and Zander, M and O'Neill, WT and Meldrum, RA and Tran-Nguyen, LTT and Batley, J and Aitken, EAB}, title = {Investigation of the diversity of effector genes in the banana pathogen, Fusarium oxysporum f. sp. cubense, reveals evidence of horizontal gene transfer.}, journal = {Molecular plant pathology}, volume = {19}, number = {5}, pages = {1155-1171}, pmid = {28802020}, issn = {1364-3703}, mesh = {Base Sequence ; Evolution, Molecular ; Fusarium/*genetics ; *Gene Transfer, Horizontal ; Genes, Essential ; *Genes, Fungal ; *Genetic Variation ; Inheritance Patterns/genetics ; Likelihood Functions ; Musa/*microbiology ; Phylogeny ; Species Specificity ; }, abstract = {It is hypothesized that the virulence of phytopathogenic fungi is mediated through the secretion of small effector proteins that interfere with the defence responses of the host plant. In Fusarium oxysporum, one family of effectors, the Secreted In Xylem (SIX) genes, has been identified. We sought to characterize the diversity and evolution of the SIX genes in the banana-infecting lineages of F. oxysporum f. sp. cubense (Foc). Whole-genome sequencing data were generated for the 23 genetic lineages of Foc, which were subsequently queried for the 14 known SIX genes (SIX1-SIX14). The sequences of the identified SIX genes were confirmed in a larger collection of Foc isolates. Genealogies were generated for each of the SIX genes identified in Foc to further investigate the evolution of the SIX genes in Foc. Within Foc, variation of the SIX gene profile, including the presence of specific SIX homologues, correlated with the pathogenic race structure of Foc. Furthermore, the topologies of the SIX gene trees were discordant with the topology of an infraspecies phylogeny inferred from EF-1α/RPB1/RPB2 (translation elongation factor-1α/RNA polymerase II subunit I/RNA polymerase II subunit II). A series of topological constraint models provided strong evidence for the horizontal transmission of SIX genes in Foc. The horizontal inheritance of pathogenicity genes in Foc counters previous assumptions that convergent evolution has driven the polyphyletic phylogeny of Foc. This work has significant implications for the management of Foc, including the improvement of diagnostics and breeding programmes.}, }
@article {pmid28801276, year = {2017}, author = {Poole, TL and Callaway, TR and Norman, KN and Scott, HM and Loneragan, GH and Ison, SA and Beier, RC and Harhay, DM and Norby, B and Nisbet, DJ}, title = {Transferability of antimicrobial resistance from multidrug-resistant Escherichia coli isolated from cattle in the USA to E. coli and Salmonella Newport recipients.}, journal = {Journal of global antimicrobial resistance}, volume = {11}, number = {}, pages = {123-132}, doi = {10.1016/j.jgar.2017.08.001}, pmid = {28801276}, issn = {2213-7173}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Cattle ; Cattle Diseases/*microbiology ; Conjugation, Genetic ; *Drug Resistance, Multiple, Bacterial ; Escherichia coli/classification/genetics/*isolation &amp; purification ; Escherichia coli Infections/*microbiology ; Escherichia coli Proteins/genetics ; *Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Phenotype ; Plasmids/genetics ; Salmonella enterica/*genetics ; Whole Genome Sequencing ; }, abstract = {OBJECTIVES: This study aimed to evaluate conjugative transfer of cephalosporin resistance among 100 strains of multidrug-resistant Escherichia coli (MDRE) to Salmonella enterica serotype Newport and E. coli DH5α recipients.<br><br>METHODS: Phenotypic and genotypic profiles were determined for MDRE as well as for Salmonella Newport (trSN) and E. coli DH5&#x3b1; (trDH) transconjugants.<br><br>RESULTS: Of 95 MDRE donor isolates, 26 (27%) and 27 (28%) transferred resistance to trSN and trDH recipients, respectively. A total of 27 MDRE (27%) were confirmed as extended-spectrum &#x3b2;-lactamase (ESBL)-producers based on the double-disk synergy assay and whole-genome sequencing (WGS). WGS was performed on 25 of the ESBL-producing isolates, showing that 2 isolates carried blaCTX-M-6, 22 possessed blaCTX-M-32 and 1 was negative for blaCTX-M genes. Fourteen of the ESBLs sequenced were qnrB19. Differential transfer of IncA/C and IncN from MDRE32 was observed between trSN32 and trDH32. IncN-positive trDH32 displayed an ESBL phenotype, whereas IncA/C-positive trSN32 displayed an AmpC phenotype. The rate of ESBL transfer to trSN and trDH recipients was 11% and 96%, respectively.<br><br>CONCLUSIONS: Twenty-seven MDRE were phenotypically identified as ESBL-producers. WGS of 25 MDRE revealed that 2 and 22 isolates carried blaCTX-M-6 and blaCTX-M-32, respectively. One multidrug-resistant isolate exhibited conversion from an AmpC phenotype to an ESBL phenotype with the transfer of only the IncN plasmid. The rate of resistance transfer to Salmonella or E. coli recipients was nearly identical. However, the ESBL phenotype was transferred with significantly greater prevalence to E. coli compared with Salmonella Newport (96% and 11%, respectively).}, }
@article {pmid28801222, year = {2017}, author = {Chan, YB and Ranwez, V and Scornavacca, C}, title = {Inferring incomplete lineage sorting, duplications, transfers and losses with reconciliations.}, journal = {Journal of theoretical biology}, volume = {432}, number = {}, pages = {1-13}, doi = {10.1016/j.jtbi.2017.08.008}, pmid = {28801222}, issn = {1095-8541}, mesh = {Algorithms ; *Gene Duplication ; *Gene Transfer, Horizontal ; Haploidy ; Models, Genetic ; *Phylogeny ; }, abstract = {Gene trees and species trees can be discordant due to several processes. Standard models of reconciliations consider macro-evolutionary events at the gene level: duplications, losses and transfers of genes. However, another common source of gene tree-species tree discordance is incomplete lineage sorting (ILS), whereby gene divergences corresponding to speciations occur "out of order". However, ILS is seldom considered in reconciliation models. In this paper, we devise a unified formal IDTL reconciliation model which includes all the above mentioned processes. We show how to properly cost ILS under this model, and then give a fixed-parameter tractable (FPT) algorithm which calculates the most parsimonious IDTL reconciliation, with guaranteed time-consistency of transfer events. Provided that the number of branches in contiguous regions of the species tree in which ILS is allowed is bounded by a constant, this algorithm is linear in the number of genes and quadratic in the number of species. This provides a formal foundation to the inference of ILS in a reconciliation framework.}, }
@article {pmid28800729, year = {2017}, author = {Hong, CP and Park, J and Lee, Y and Lee, M and Park, SG and Uhm, Y and Lee, J and Kim, CK}, title = {accD nuclear transfer of Platycodon grandiflorum and the plastid of early Campanulaceae.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {607}, pmid = {28800729}, issn = {1471-2164}, mesh = {Acetyl-CoA Carboxylase/*genetics ; Base Sequence ; Cell Nucleus/*genetics ; Evolution, Molecular ; Gene Rearrangement ; *Gene Transfer, Horizontal ; Genome, Chloroplast/genetics ; Phylogeny ; Plastids/*genetics ; Platycodon/cytology/*enzymology/*genetics ; RNA Editing ; }, abstract = {BACKGROUND: Campanulaceae species are known to have highly rearranged plastid genomes lacking the acetyl-CoA carboxylase (ACC) subunit D gene (accD), and instead have a nuclear (nr)-accD. Plastid genome information has been thought to depend on studies concerning Trachelium caeruleum and genome announcements for Adenophora remotiflora, Campanula takesimana, and Hanabusaya asiatica. RNA editing information for plastid genes is currently unavailable for Campanulaceae. To understand plastid genome evolution in Campanulaceae, we have sequenced and characterized the chloroplast (cp) genome and nr-accD of Platycodon grandiflorum, a basal member of Campanulaceae.<br><br>RESULTS: We sequenced the 171,818&#xa0;bp cp genome containing a 79,061&#xa0;bp large single-copy (LSC) region, a 42,433&#xa0;bp inverted repeat (IR) and a 7840&#xa0;bp small single-copy (SSC) region, which represents the cp genome with the largest IR among species of Campanulaceae. The genome contains 110 genes and 18 introns, comprising 77 protein-coding genes, four RNA genes, 29 tRNA genes, 17 group II introns, and one group I intron. RNA editing of genes was detected in 18 sites of 14 protein-coding genes. Platycodon has an IR containing a 3' rps12 operon, which occurs in the middle of the LSC region in four other species of Campanulaceae (T. caeruleum, A. remotiflora, C. takesimana, and H. asiatica), but lacks accD, clpP, infA, and rpl23, as has been found in these four species. Platycodon nr-accD contains about 3.2&#xa0;kb intron between nr-accD.e1 and nr-accD.e2 at the same insertion point as in other Campanulaceae. The phylogenies of the plastid genomes and accD show that Platycodon is basal in the Campanulaceae clade, indicating that IR disruption in Campanulaceae occurred after the loss of accD, clpP, infA, and rpl23 in the cp genome, which occurred during plastid evolution in Campanulaceae.<br><br>CONCLUSIONS: The plastid genome of P. grandiflorum lacks the rearrangement of the IR found in T. caeruleum, A. remotiflora, C. takesimana, and H. asiatica. The absence of accD, clpP, infA, and rpl23 in the plastid genome is a synapomorphic characteristic of Campanulaceae. The chloroplast genome phylogeny supports the hypothesis that chloroplast genomic arrangement occurred after accD nuclear transfer and loss of the four genes in the plastid of early Campanulaceae as a lineage of asterids.}, }
@article {pmid28799681, year = {2017}, author = {Fresia, P and Jara, R and Sierra, R and Ferrés, I and Greif, G and Iraola, G and Collado, L}, title = {Genomic and clinical evidence uncovers the enterohepatic species Helicobacter valdiviensis as a potential human intestinal pathogen.}, journal = {Helicobacter}, volume = {22}, number = {5}, pages = {}, doi = {10.1111/hel.12425}, pmid = {28799681}, issn = {1523-5378}, mesh = {Adult ; Base Composition ; Case-Control Studies ; Child, Preschool ; Computational Biology ; Feces/*microbiology ; Female ; Gastrointestinal Diseases/epidemiology/*microbiology/*pathology ; Helicobacter/*classification/genetics/*isolation &amp; purification/pathogenicity ; Helicobacter Infections/epidemiology/*microbiology/*pathology ; Humans ; Incidence ; Infant ; Male ; Mass Screening/methods ; Middle Aged ; Phylogeny ; Polymerase Chain Reaction ; Retrospective Studies ; Sequence Analysis, DNA ; Virulence Factors/genetics ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: Helicobacter valdiviensis is a recently described enterohepatic species isolated from wild bird's fecal samples. Currently, its pathogenic potential and clinical significance are unknown mainly due to the lack of whole-genome sequences to compare with other helicobacters and the absence of specific screenings to determine its prevalence in humans.<br><br>MATERIALS AND METHODS: The species type strain (WBE14[T]) was whole-genome-sequenced, and comparative analyses were carried out including the genomes from other Helicobacter species to determine the exact phylogenetic position of H.&#xa0;valdiviensis and to study the presence and evolution of virulence determinants. In parallel, stools from diarrheic patients and healthy individuals were screened by PCR to assess the clinical incidence of H.&#xa0;valdiviensis.<br><br>RESULTS: Helicobacter valdiviensis belongs to a monophyletic clade conformed by H.&#xa0;canadensis, H.&#xa0;pullorum, H.&#xa0;winghamensis, H.&#xa0;rodentium, and H.&#xa0;apodemus. Its predicted genome size is 2&#xa0;176&#xa0;246&#xa0;bp., with 30% of G+C content and 2064 annotated protein-coding genes. The patterns of virulence factors in H.&#xa0;valdiviensis were similar to other enterohepatic species, but evidence of horizontal gene transfer from Campylobacter species was detected for key genes like those coding for the CDT subunits. Positive PCR results confirmed the presence of H.&#xa0;valdiviensis in 2 of 254 (0.78%) stools of patients with acute diarrhea while not a single sample was positive in healthy individuals.<br><br>CONCLUSIONS: Horizontal gene transfer has contributed to shape the gene repertory of H.&#xa0;valdiviensis, which codes for virulence factors conserved in other pathogens that are well-known human pathogens. Additionally, the detection of H.&#xa0;valdiviensisDNA in diarrheic patients supports its role as a potential emergent intestinal pathogen. Further, sampling efforts are needed to uncover the clinical relevance of this species, which should be accomplished by the isolation of H.&#xa0;valdiviensis from ill humans and the obtention of whole genomes from clinical isolates.}, }
@article {pmid28799224, year = {2017}, author = {Peng, Z and Li, M and Wang, W and Liu, H and Fanning, S and Hu, Y and Zhang, J and Li, F}, title = {Genomic insights into the pathogenicity and environmental adaptability of Enterococcus hirae R17 isolated from pork offered for retail sale.}, journal = {MicrobiologyOpen}, volume = {6}, number = {6}, pages = {}, pmid = {28799224}, issn = {2045-8827}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics/metabolism ; China ; Ciprofloxacin/pharmacology ; Drug Resistance, Bacterial ; Enterococcus hirae/drug effects/*genetics/isolation &amp; purification/*pathogenicity ; Erythromycin/pharmacology ; Food Contamination/analysis ; Genomics ; Microbial Sensitivity Tests ; Red Meat/*microbiology ; Swine ; Virulence ; Virulence Factors/genetics/metabolism ; }, abstract = {Genetic information about Enterococcus hirae is limited, a feature that has compromised our understanding of these clinically challenging bacteria. In this study, comparative analysis was performed of E. hirae R17, a daptomycin-resistant strain isolated from pork purchased from a retail market in Beijing, China, and three other enterococcal genomes (Enterococcus faecium DO, Enterococcus faecalis V583, and E. hirae ATCC[™] 9790). Some 1,412 genes were identified that represented the core genome together with an additional 139 genes that were specific to E. hirae R17. The functions of these R17 strain-specific coding sequences relate to the COGs categories of carbohydrate transport and metabolism and transcription, a finding that suggests the carbohydrate utilization capacity of E. hirae R17 may be more extensive when compared with the other three bacterial species (spp.). Analysis of genomic islands and virulence genes highlighted the potential that horizontal gene transfer played as a contributor of variations in pathogenicity in this isolate. Drug-resistance gene prediction and antibiotic susceptibility testing indicated E. hirae R17 was resistant to several antimicrobial compounds, including bacitracin, ciprofloxacin, daptomycin, erythromycin, and tetracycline, thereby limiting chemotherapeutic treatment options. Further, tolerance to biocides and metals may confer a phenotype that facilitates the survival and adaptation of this isolate against food preservatives, disinfectants, and antibacterial coatings. The genomic plasticity, mediated by IS elements, transposases, and tandem repeats, identified in the E. hirae R17 genome may support adaptation to new environmental niches, such as those that are found in hospitalized patients. A predicted transmissible plasmid, pRZ1, was found to carry several antimicrobial determinants, along with some predicted pathogenic genes. These data supported the previously determined phenotype confirming that the foodborne E. hirae R17 is a multidrug-resistant pathogenic bacterium with evident genome plasticity and environmental adaptability.}, }
@article {pmid28798731, year = {2017}, author = {Ibáñez de Aldecoa, AL and Zafra, O and González-Pastor, JE}, title = {Mechanisms and Regulation of Extracellular DNA Release and Its Biological Roles in Microbial Communities.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1390}, pmid = {28798731}, issn = {1664-302X}, abstract = {The capacity to release genetic material into the extracellular medium has been reported in cultures of numerous species of bacteria, archaea, and fungi, and also in the context of multicellular microbial communities such as biofilms. Moreover, extracellular DNA (eDNA) of microbial origin is widespread in natural aquatic and terrestrial environments. Different specific mechanisms are involved in eDNA release, such as autolysis and active secretion, as well as through its association with membrane vesicles. It is noteworthy that in microorganisms, in which DNA release has been studied in detail, the production of eDNA is coordinated by the population when it reaches a certain cell density, and is induced in a subpopulation in response to the accumulation of quorum sensing signals. Interestingly, in several bacteria there is also a relationship between eDNA release and the development of natural competence (the ability to take up DNA from the environment), which is also controlled by quorum sensing. Then, what is the biological function of eDNA? A common biological role has not been proposed, since different functions have been reported depending on the microorganism. However, it seems to be important in biofilm formation, can be used as a nutrient source, and could be involved in DNA damage repair and gene transfer. This review covers several aspects of eDNA research: (i) its occurrence and distribution in natural environments, (ii) the mechanisms and regulation of its release in cultured microorganisms, and (iii) its biological roles. In addition, we propose that eDNA release could be considered a social behavior, based on its quorum sensing-dependent regulation and on the described functions of eDNA in the context of microbial communities.}, }
@article {pmid28798375, year = {2017}, author = {Chen, SC and Sun, GX and Rosen, BP and Zhang, SY and Deng, Y and Zhu, BK and Rensing, C and Zhu, YG}, title = {Recurrent horizontal transfer of arsenite methyltransferase genes facilitated adaptation of life to arsenic.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {7741}, pmid = {28798375}, issn = {2045-2322}, support = {R01 ES023779/ES/NIEHS NIH HHS/United States ; R01 GM055425/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Biological/*drug effects/*genetics ; Animals ; Archaea/drug effects/genetics ; Arsenic/metabolism/*toxicity ; Bacteria/drug effects/genetics ; Eukaryota/drug effects/genetics ; Fungi/drug effects/genetics ; *Gene Transfer, Horizontal ; Methylation ; Methyltransferases/*genetics/metabolism ; Models, Biological ; Phylogeny ; }, abstract = {The toxic metalloid arsenic has been environmentally ubiquitous since life first arose nearly four billion years ago and presents a challenge for the survival of all living organisms. Its bioavailability has varied dramatically over the history of life on Earth. As life spread, biogeochemical and climate changes cyclically increased and decreased bioavailable arsenic. To elucidate the history of arsenic adaptation across the tree of life, we reconstructed the phylogeny of the arsM gene that encodes the As(III) S-adenosylmethionine (SAM) methyltransferase. Our results suggest that life successfully moved into arsenic-rich environments in the late Archean Eon and Proterozoic Eon, respectively, by the spread of arsM genes. The arsM genes of bacterial origin have been transferred to other kingdoms of life on at least six occasions, and the resulting domesticated arsM genes promoted adaptation to environmental arsenic. These results allow us to peer into the history of arsenic adaptation of life on our planet and imply that dissemination of genes encoding diverse adaptive functions to toxic chemicals permit adaptation to changes in concentrations of environmental toxins over evolutionary history.}, }
@article {pmid28798101, year = {2017}, author = {Spang, A and Caceres, EF and Ettema, TJG}, title = {Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life.}, journal = {Science (New York, N.Y.)}, volume = {357}, number = {6351}, pages = {}, doi = {10.1126/science.aaf3883}, pmid = {28798101}, issn = {1095-9203}, support = {//European Research Council/International ; }, mesh = {Archaea/*classification/*genetics/metabolism ; Carbon Cycle/genetics ; Eukaryota/classification/genetics ; Gene Transfer, Horizontal ; *Genetic Variation ; Genome, Archaeal ; Genomics ; Metagenomics ; Nitrogen Cycle/genetics ; Oxidoreductases/classification/genetics ; Phylogeny ; RNA, Ribosomal, 16S/classification/genetics ; }, abstract = {About 40 years ago, Archaea were recognized as a major prokaryotic domain of life besides Bacteria. Recently, cultivation-independent sequencing methods have produced a wealth of genomic data for previously unidentified archaeal lineages, several of which appear to represent newly revealed branches in the tree of life. Analyses of some recently obtained genomes have uncovered previously unknown metabolic traits and provided insights into the evolution of archaea and their relationship to eukaryotes. On the basis of our current understanding, much archaeal diversity still defies genomic exploration. Efforts to obtain and study genomes and enrichment cultures of uncultivated microbial lineages will likely further expand our knowledge about archaeal phylogenetic and metabolic diversity and their cell biology and ecological function.}, }
@article {pmid28794030, year = {2017}, author = {Oliveira, GP and Lima, MT and Arantes, TS and Assis, FL and Rodrigues, RAL and da Fonseca, FG and Bonjardim, CA and Kroon, EG and Colson, P and La Scola, B and Abrahão, JS}, title = {The Investigation of Promoter Sequences of Marseilleviruses Highlights a Remarkable Abundance of the AAATATTT Motif in Intergenic Regions.}, journal = {Journal of virology}, volume = {91}, number = {21}, pages = {}, pmid = {28794030}, issn = {1098-5514}, mesh = {Acanthamoeba/*virology ; Base Sequence ; Computational Biology ; DNA Viruses/*genetics/pathogenicity ; *DNA, Intergenic ; DNA, Viral ; *Genome, Viral ; Genomics ; *Nucleotide Motifs ; Phylogeny ; Promoter Regions, Genetic/*genetics ; }, abstract = {Viruses display a wide range of genomic profiles and, consequently, a variety of gene expression strategies. Specific sequences associated with transcriptional processes have been described in viruses, and putative promoter motifs have been elucidated for some nucleocytoplasmic large DNA viruses (NCLDV). Among NCLDV, the Marseilleviridae is a well-recognized family because of its genomic mosaicism. The marseilleviruses have an ability to incorporate foreign genes, especially from sympatric organisms inhabiting Acanthamoeba, its main known host. Here, we identified for the first time an eight-nucleotide A/T-rich promoter sequence (AAATATTT) associated with 55% of marseillevirus genes that is conserved in all marseilleviruses lineages, a higher level of conservation than that of any giant virus described to date. We instigated our prediction about the promoter motif by biological assays and by evaluating how single mutations in this octamer can impact gene expression. The investigation of sequences that regulate the expression of genes relative to lateral transfer revealed that the promoter motifs do not appear to be incorporated by marseilleviruses from donor organisms. Indeed, analyses of the intergenic regions that regulate lateral gene transfer-related genes have revealed an independent origin of the marseillevirus intergenic regions that does not match gene-donor organisms. About 50% of AAATATTT motifs spread throughout intergenic regions of the marseilleviruses are present as multiple copies. We believe that such multiple motifs are associated with increased expression of a given gene or are related to incorporation of foreign genes into the mosaic genome of marseilleviruses.IMPORTANCE The marseilleviruses draw attention because of the peculiar features of their genomes; however, little is known about their gene expression patterns or the factors that regulate those expression patterns. The limited published research on the expression patterns of the marseilleviruses and their unique genomes has led us to study the promoter motif sequences in the intergenic regions of the marseilleviruses. This work is the first to analyze promoter sequences in the genomes of the marseilleviruses. We also suggest a strong capacity to acquire foreign genes and to express those genes mediated by multiple copies of the promoter motifs available in intergenic regions. These findings contribute to an understanding of genomic expansion and plasticity observed in these giant viruses.}, }
@article {pmid28793862, year = {2017}, author = {Raghuram, GV and Gupta, D and Subramaniam, S and Gaikwad, A and Khare, NK and Nobre, M and Nair, NK and Mittra, I}, title = {Physical shearing imparts biological activity to DNA and ability to transmit itself horizontally across species and kingdom boundaries.}, journal = {BMC molecular biology}, volume = {18}, number = {1}, pages = {21}, pmid = {28793862}, issn = {1471-2199}, mesh = {Animals ; Cell Line ; Cell-Free Nucleic Acids/chemistry/genetics ; Chromosomes/chemistry/genetics/metabolism ; DNA/chemistry/*genetics/metabolism ; Fluorescent Antibody Technique ; *Gene Transfer, Horizontal ; Histones/metabolism ; Humans ; Mice ; Microscopy, Fluorescence ; Molecular Weight ; NF-kappa B/metabolism ; Species Specificity ; }, abstract = {BACKGROUND: We have recently reported that cell-free DNA (cfDNA) fragments derived from dying cells that circulate in blood are biologically active molecules and can readily enter into healthy cells to activate DNA damage and apoptotic responses in the recipients. However, DNA is not conventionally known to spontaneously enter into cells or to have any intrinsic biological activity. We hypothesized that cellular entry and acquisition of biological properties are functions of the size of DNA.<br><br>RESULTS: To test this hypothesis, we generated small DNA fragments by sonicating high molecular weight DNA (HMW DNA) to mimic circulating cfDNA. Sonication of HMW DNA isolated from cancerous and non-cancerous human cells, bacteria and plant generated fragments 300-3000&#xa0;bp in size which are similar to that reported for circulating cfDNA. We show here that while HMW DNAs were incapable of entering into cells, sonicated DNA (sDNA) from different sources could do so indiscriminately without heed to species or kingdom boundaries. Thus, sDNA from human cells and those from bacteria and plant could enter into nuclei of mouse cells and sDNA from human, bacterial and plant sources could spontaneously enter into bacteria. The intracellular sDNA associated themselves with host cell chromosomes and integrated into their genomes. Furthermore, sDNA, but not HMW DNA, from all four sources could phosphorylate H2AX and activate the pro-inflammatory transcription factor NF&#x3ba;B in mouse cells, indicating that sDNAs had acquired biological activities.<br><br>CONCLUSIONS: Our results show that small fragments of DNA from different sources can indiscriminately enter into other cells across species and kingdom boundaries to integrate into their genomes and activate biological processes. This raises the possibility that fragmented DNA that are generated following organismal cell-death may have evolutionary implications by acting as mobile genetic elements that are involved in horizontal gene transfer.}, }
@article {pmid28790994, year = {2017}, author = {Espejo, RT and García, K and Plaza, N}, title = {Insight Into the Origin and Evolution of the Vibrio parahaemolyticus Pandemic Strain.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1397}, pmid = {28790994}, issn = {1664-302X}, abstract = {A strain of Vibrio parahaemolyticus that emerged in 1995 caused the first known pandemic involving this species. This strain comprises clonal autochthonous ocean-dwelling bacteria whose evolution has occurred in the ocean environment. The low sequence diversity in this population enabled the discovery of information on its origin and evolution that has been hidden in bacterial clones that have evolved over a long period. Multilocus sequencing and microarray analysis, together with phylogenetic analysis, of pandemic and pre-pandemic isolates has suggested that the founder clone was an O3:K6 non-pathogenic strain that initially acquired a toxRS/new region and subsequently acquired at least seven novel genomic islands. Sequencing and comparison of whole genomes later confirmed these early observations, and it confirmed that most of the genetic changes occurred via gene conversion involving horizontally transmitted DNA. The highly clonal population rapidly diversified, especially in terms of antigenicity, and 27 serotypes have already been reported. Comparisons of the core genomes derived from the founder clone indicate that there are only a few hundred single-nucleotide variations between isolates. However, when the whole genome is considered (the core plus non-core genome and from any clonal frame), the amount of DNA with a different clonal frame can reach up to 4.2% and the number of single-nucleotide variations can reach several hundred thousand. Altogether, these and previous observations based on multilocus sequence typing, microarray analysis, and whole-genome sequencing indicate the large contribution made by DNA with different clonal genealogy to genome diversification. The evidence also indicates that horizontal gene transfer (HGT) caused the emergence of new pathogens. Furthermore, the extent of HGT seems to depend on the vicissitudes of the life of each bacterium, as exemplified by differences in thousands of base pairs acquired by HGT among almost identical genetic isolates.}, }
@article {pmid28787798, year = {2017}, author = {Zhao, Q and Yue, S and Bilal, M and Hu, H and Wang, W and Zhang, X}, title = {Comparative genomic analysis of 26 Sphingomonas and Sphingobium strains: Dissemination of bioremediation capabilities, biodegradation potential and horizontal gene transfer.}, journal = {The Science of the total environment}, volume = {609}, number = {}, pages = {1238-1247}, doi = {10.1016/j.scitotenv.2017.07.249}, pmid = {28787798}, issn = {1879-1026}, mesh = {*Biodegradation, Environmental ; *Gene Transfer, Horizontal ; Sphingomonadaceae/*genetics/metabolism ; Sphingomonas ; }, abstract = {Bacteria belonging to the genera Sphingomonas and Sphingobium are known for their ability to catabolize aromatic compounds. In this study, we analyzed the whole genome sequences of 26 strains in the genera Sphingomonas and Sphingobium to gain insight into dissemination of bioremediation capabilities, biodegradation potential, central pathways and genome plasticity. Phylogenetic analysis revealed that both Sphingomonas sp. strain BHC-A and Sphingomonas paucimobilis EPA505 should be placed in the genus Sphingobium. The bph and xyl gene cluster was found in 6 polycyclic aromatic hydrocarbons-degrading strains. Transposase and IS coding genes were found in the 6 gene clusters, suggesting the mobility of bph and xyl gene clusters. β-ketoadipate and homogentisate pathways were the main central pathways in Sphingomonas and Sphingobium strains. A large number of oxygenase coding genes were predicted in the 26 genomes, indicating a huge biodegradation potential of the Sphingomonas and Sphingobium strains. Horizontal gene transfer related genes and prophages were predicted in the analyzed strains, suggesting the ongoing evolution and shaping of the genomes. Analysis of the 26 genomes in this work contributes to the understanding of dispersion of bioremediation capabilities, bioremediation potential and genome plasticity in strains belonging to the genera Sphingomonas and Sphingobium.}, }
@article {pmid28785421, year = {2017}, author = {Villa, L and Feudi, C and Fortini, D and Brisse, S and Passet, V and Bonura, C and Endimiani, A and Mammina, C and Ocampo, AM and Jimenez, JN and Doumith, M and Woodford, N and Hopkins, K and Carattoli, A}, title = {Diversity, virulence, and antimicrobial resistance of the KPC-producing Klebsiella pneumoniae ST307 clone.}, journal = {Microbial genomics}, volume = {3}, number = {4}, pages = {e000110}, pmid = {28785421}, issn = {2057-5858}, mesh = {Bacterial Proteins/*genetics ; *Carbapenem-Resistant Enterobacteriaceae/drug effects/genetics/pathogenicity ; Colombia/epidemiology ; Cross Infection/epidemiology/*microbiology ; Drug Resistance, Microbial/*genetics ; England/epidemiology ; Gene Transfer, Horizontal ; Genetic Variation ; Genome, Bacterial ; Humans ; Italy/epidemiology ; Klebsiella Infections/epidemiology/*microbiology ; *Klebsiella pneumoniae/drug effects/genetics/pathogenicity ; Molecular Epidemiology ; Multilocus Sequence Typing ; Virulence/genetics ; Virulence Factors/*genetics ; Whole Genome Sequencing ; beta-Lactamases/*genetics ; }, abstract = {The global spread of Klebsiella pneumoniae producing Klebsiella pneumoniae carbapenemase (KPC) has been mainly associated with the dissemination of high-risk clones. In the last decade, hospital outbreaks involving KPC-producing K. pneumoniae have been predominantly attributed to isolates belonging to clonal group (CG) 258. However, results of recent epidemiological analysis indicate that KPC-producing sequence type (ST) 307, is emerging in different parts of the world and is a candidate to become a prevalent high-risk clone in the near future. Here we show that the ST307 genome encodes genetic features that may provide an advantage in adaptation to the hospital environment and the human host. Sequence analysis revealed novel plasmid-located virulence factors, including a cluster for glycogen synthesis. Glycogen production is considered to be one of the possible adaptive responses to long-term survival and growth in environments outside the host. Chromosomally-encoded virulence traits in the clone comprised fimbriae, an integrative conjugative element carrying the yersiniabactin siderophore, and two different capsular loci. Compared with the ST258 clone, capsulated ST307 isolates showed higher resistance to complement-mediated killing. The acquired genetic features identified in the genome of this new emerging clone may contribute to increased persistence of ST307 in the hospital environment and shed light on its potential epidemiological success.}, }
@article {pmid28784816, year = {2017}, author = {Peck, RF and Pleşa, AM and Graham, SM and Angelini, DR and Shaw, EL}, title = {Opsin-Mediated Inhibition of Bacterioruberin Synthesis in Halophilic Archaea.}, journal = {Journal of bacteriology}, volume = {199}, number = {21}, pages = {}, pmid = {28784816}, issn = {1098-5530}, support = {P20 GM103423/GM/NIGMS NIH HHS/United States ; R15 GM094735/GM/NIGMS NIH HHS/United States ; }, mesh = {Archaea/*metabolism ; Bacteriorhodopsins/genetics/*metabolism ; Carotenoids/*biosynthesis ; Cloning, Molecular ; Colorimetry ; Gene Expression ; Haloarcula/enzymology/genetics ; Haloferax volcanii/genetics/*metabolism ; Recombinant Proteins/genetics/metabolism ; Retinaldehyde/metabolism ; }, abstract = {Halophilic archaea often inhabit environments with limited oxygen, and many produce ion-pumping rhodopsin complexes that allow them to maintain electrochemical gradients when aerobic respiration is inhibited. Rhodopsins require a protein, an opsin, and an organic cofactor, retinal. We previously demonstrated that in Halobacterium salinarum, bacterioopsin (BO), when not bound by retinal, inhibits the production of bacterioruberin, a biochemical pathway that shares intermediates with retinal biosynthesis. In this work, we used heterologous expression in a related halophilic archaeon, Haloferax volcanii, to demonstrate that BO is sufficient to inhibit bacterioruberin synthesis catalyzed by the H. salinarum lycopene elongase (Lye) enzyme. This inhibition was observed both in liquid culture and in a novel colorimetric assay to quantify bacterioruberin abundance based on the colony color. Addition of retinal to convert BO to the bacteriorhodopsin complex resulted in a partial rescue of bacterioruberin production. To explore if this regulatory mechanism occurs in other organisms, we expressed a Lye homolog and an opsin from Haloarcula vallismortis in H. volcaniiH. vallismortis cruxopsin-3 expression inhibited bacterioruberin synthesis catalyzed by H. vallismortis Lye but had no effect when bacterioruberin synthesis was catalyzed by H. salinarum or H. volcanii Lye. Conversely, H. salinarum BO did not inhibit H. vallismortis Lye activity. Together, our data suggest that opsin-mediated inhibition of Lye is potentially widespread and represents an elegant regulatory mechanism that allows organisms to efficiently utilize ion-pumping rhodopsins obtained through lateral gene transfer.IMPORTANCE Many enzymes are complexes of proteins and nonprotein organic molecules called cofactors. To ensure efficient formation of functional complexes, organisms must regulate the production of proteins and cofactors. To study this regulation, we used bacteriorhodopsin from the archaeon Halobacterium salinarum Bacteriorhodopsin consists of the bacterioopsin protein and a retinal cofactor. In this article, we further characterize a novel regulatory mechanism in which bacterioopsin promotes retinal production by inhibiting a reaction that consumes lycopene, a retinal precursor. By expressing H. salinarum genes in a different organism, Haloferax volcanii, we demonstrated that bacterioopsin alone is sufficient for this inhibition. We also found that an opsin from Haloarcula vallismortis has inhibitory activity, suggesting that this regulatory mechanism might be found in other organisms.}, }
@article {pmid28784044, year = {2017}, author = {Lang, AS and Westbye, AB and Beatty, JT}, title = {The Distribution, Evolution, and Roles of Gene Transfer Agents in Prokaryotic Genetic Exchange.}, journal = {Annual review of virology}, volume = {4}, number = {1}, pages = {87-104}, doi = {10.1146/annurev-virology-101416-041624}, pmid = {28784044}, issn = {2327-0578}, support = {//CIHR/Canada ; }, mesh = {Bacteria/*genetics ; Bacteriophages/*genetics/isolation &amp; purification/physiology ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Viral ; Homologous Recombination ; Phylogeny ; Rhodobacter capsulatus/genetics ; }, abstract = {Diverse prokaryotes produce gene transfer agents (GTAs), which are bacteriophage-like particles that exclusively package pieces of the producing cell's genome and transfer them to other cells. There are clear evolutionary connections between GTAs and phages, but GTAs have properties that lead us to suggest they are more than simply defective phages and instead provide a selective advantage for the producing organisms. The five types of currently known GTAs are genetically distinct, indicating multiple instances of convergent evolution. GTA production can be regulated by the producing organism and coordinated to coincide with development of the capability to receive DNA from GTAs. Recent discoveries of the genetic basis of GTA production in the bacterium Rhodobacter capsulatus and characterization of novel phages that possess homologs of this GTA's structural and regulatory genes have provided important new connections among these elements and highlight the tangled evolutionary relationships within the phageome.}, }
@article {pmid28783104, year = {2017}, author = {Guenat, D and Hermetet, F and Prétet, JL and Mougin, C}, title = {Exosomes and Other Extracellular Vesicles in HPV Transmission and Carcinogenesis.}, journal = {Viruses}, volume = {9}, number = {8}, pages = {}, pmid = {28783104}, issn = {1999-4915}, mesh = {Animals ; Biomarkers ; *Carcinogenesis ; *Cell Communication ; Exosomes/*physiology ; Extracellular Vesicles/*physiology ; Gene Transfer, Horizontal ; Humans ; Mice ; MicroRNAs ; Neoplasms/physiopathology/virology ; Oncogenes ; Papillomaviridae/genetics/*physiology ; RNA, Messenger ; }, abstract = {Extracellular vesicles (EVs), including exosomes (Exos), microvesicles (MVs) and apoptotic bodies (ABs) are released in biofluids by virtually all living cells. Tumor-derived Exos and MVs are garnering increasing attention because of their ability to participate in cellular communication or transfer of bioactive molecules (mRNAs, microRNAs, DNA and proteins) between neighboring cancerous or normal cells, and to contribute to human cancer progression. Malignant traits can also be transferred from apoptotic cancer cells to phagocytizing cells, either professional or non-professional. In this review, we focus on Exos and ABs and their relationship with human papillomavirus (HPV)-associated tumor development. The potential implication of EVs as theranostic biomarkers is also addressed.}, }
@article {pmid28782269, year = {2017}, author = {Liu, Y and Li, Y and Wang, X}, title = {Molecular evolution of acetohydroxyacid synthase in bacteria.}, journal = {MicrobiologyOpen}, volume = {6}, number = {6}, pages = {}, pmid = {28782269}, issn = {2045-8827}, mesh = {Acetolactate Synthase/chemistry/*genetics/metabolism ; Amino Acid Sequence ; Bacteria/classification/*enzymology/*genetics ; Bacterial Proteins/chemistry/*genetics/metabolism ; *Evolution, Molecular ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; }, abstract = {Acetohydroxyacid synthase (AHAS) is the key enzyme in the biosynthetic pathways of branched chain amino acids in bacteria. Since it does not exist in animal and plant cells, AHAS is an attractive target for developing antimicrobials and herbicides. In some bacteria, there is a single copy of AHAS, while in others there are multiple copies. Therefore, it is necessary to investigate the origin and evolutionary pathway of various AHASs in bacteria. In this study, all the available protein sequences of AHAS in bacteria were investigated, and an evolutionary model of AHAS in bacteria is proposed, according to gene structure, organization and phylogeny. Multiple copies of AHAS in some bacteria might be evolved from the single copy of AHAS, the ancestor. Gene duplication, domain deletion and horizontal gene transfer might occur during the evolution of this enzyme. The results show the biological significance of AHAS, help to understand the functions of various AHASs in bacteria, and would be useful for developing industrial production strains of branched chain amino acids or novel antimicrobials.}, }
@article {pmid28781345, year = {2017}, author = {Lupan, I and Carpa, R and Oltean, A and Kelemen, BS and Popescu, O}, title = {Release of Antibiotic Resistant Bacteria by a Waste Treatment Plant from Romania.}, journal = {Microbes and environments}, volume = {32}, number = {3}, pages = {219-225}, pmid = {28781345}, issn = {1347-4405}, mesh = {Bacteria/*drug effects ; *Drug Resistance, Bacterial ; Genes, Bacterial ; Rivers/microbiology ; Romania ; Tetracycline ; *Waste Disposal Facilities ; Wastewater/*microbiology ; }, abstract = {The occurrence and spread of bacterial antibiotic resistance are subjects of great interest, and the role of wastewater treatment plants has been attracting particular interest. These stations are a reservoir of bacteria, have a large range of organic and inorganic substances, and the amount of bacteria released into the environment is very high. The main purpose of the present study was to assess the removal degree of bacteria with resistance to antibiotics and identify the contribution of a wastewater treatment plant to the microbiota of Someşul Mic river water in Cluj county. The resistance to sulfamethoxazole and tetracycline and some of their representative resistance genes: sul1, tet(O), and tet(W) were assessed in this study. The results obtained showed that bacteria resistant to sulphonamides were more abundant than those resistant to tetracycline. The concentration of bacteria with antibiotic resistance changed after the treatment, namely, bacteria resistant to sulfamethoxazole. The removal of all bacteria and antibiotic-resistant bacteria was 98-99% and the degree of removal of bacteria resistant to tetracycline was higher than the bacteria resistant to sulfamethoxazole compared to total bacteria. The wastewater treatment plant not only contributed to elevating ARG concentrations, it also enhanced the possibility of horizontal gene transfer (HGT) by increasing the abundance of the intI1 gene. Even though the treatment process reduced the concentration of bacteria by two orders of magnitude, the wastewater treatment plant in Cluj-Napoca contributed to an increase in antibiotic-resistant bacteria concentrations up to 10 km downstream of its discharge in Someşul Mic river.}, }
@article {pmid28780691, year = {2018}, author = {Gothwal, R and Thatikonda, S}, title = {Mathematical model for the transport of fluoroquinolone and its resistant bacteria in aquatic environment.}, journal = {Environmental science and pollution research international}, volume = {25}, number = {21}, pages = {20439-20452}, pmid = {28780691}, issn = {1614-7499}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics ; Drug Industry ; Drug Resistance, Microbial/*genetics ; Fluoroquinolones/*pharmacology ; *Gene Transfer, Horizontal ; Metals, Heavy ; Models, Theoretical ; Plasmids ; Rivers/*microbiology ; Water Microbiology ; Water Pollutants, Chemical/*pharmacology ; }, abstract = {Development of antibiotic resistance in environmental bacteria is a direct threat to public health. Therefore, it becomes necessary to understand the fate and transport of antibiotic and its resistant bacteria. This paper presents a mathematical model for spatial and temporal transport of fluoroquinolone and its resistant bacteria in the aquatic environment of the river. The model includes state variables for organic matter, fluoroquinolone, heavy metals, and susceptible and resistant bacteria in the water column and sediment bed. Resistant gene is the factor which makes bacteria resistant to a particular antibiotic and is majorly carried on plasmids. Plasmid-mediated resistance genes are transferable between different bacterial species through conjugation (horizontal resistance transfer). This model includes plasmid dynamics between susceptible and resistant bacteria by considering the rate of horizontal resistance gene transfer among bacteria and the rate of losing resistance (segregation). The model describes processes which comprise of advection, dispersion, degradation, adsorption, diffusion, settling, resuspension, microbial growth, segregation, and transfer of resistance genes. The mathematical equations were solved by using numerical methods (implicit-explicit scheme) with appropriate boundary conditions. The development of the present model was motivated by the fact that the Musi River is heavily impacted by antibiotic pollution which led to the development of antibiotic resistance in its aquatic environment. The model was simulated for hypothetical pollution scenarios to predict the future conditions under various pollution management alternatives. The simulation results of the model for different cases show that the concentration of antibiotic, the concentration of organic matter, segregation rate, and horizontal transfer rate are the governing factors in the variation of population density of resistant bacteria. The treatment of effluents for antibiotics might be costly for the bulk drug manufacturing industries, but the guidelines can be made to reduce the organic matter which can limit the growth rate of microbes and reduce the total microbial population in the river. The reduction in antibiotic concentration can reduce the selection pressure on bacteria and can limit the population of resistant culture and its influence zone in the river stretch; however, complete removal of antibiotics may not result in complete elimination of antibiotic-resistant bacteria.}, }
@article {pmid28780258, year = {2017}, author = {Zhang, L and Gu, J and Wang, X and Sun, W and Yin, Y and Sun, Y and Guo, A and Tuo, X}, title = {Behavior of antibiotic resistance genes during co-composting of swine manure with Chinese medicinal herbal residues.}, journal = {Bioresource technology}, volume = {244}, number = {Pt 1}, pages = {252-260}, doi = {10.1016/j.biortech.2017.07.035}, pmid = {28780258}, issn = {1873-2976}, mesh = {Animals ; Anti-Bacterial Agents ; *Drug Resistance, Microbial ; Genes, Bacterial ; *Manure ; Refuse Disposal ; Soil ; Swine ; }, abstract = {Swine manure is considered to be a reservoir for antibiotic resistance genes (ARGs) but little is known about the variations in ARGs during the co-composting of swine manure with Chinese medicinal herbal residues (CMHRs). Thus, this study explored the effects of CMHRs on the variations in ARGs during co-composting with swine manure. The results showed that CMHRs could reduce effectively most of the targeted ARGs (0.18-2.82logs) and mobile genetic elements (MGEs) (0.47-3.34logs). The correlations indicated that CMHRs might decrease the spread of ARGs via horizontal gene transfer. Redundancy analysis showed that the bacterial communities had more important effects on the variations in ARGs compared with environmental factors and MGEs. The results of this study demonstrate that CMHRs can decrease the abundances of ARGs and MGEs, as well as reducing the risk of ARGs spreading during the application of compost products to farmland.}, }
@article {pmid28777924, year = {2017}, author = {Mehrabi, R and Mirzadi Gohari, A and Kema, GHJ}, title = {Karyotype Variability in Plant-Pathogenic Fungi.}, journal = {Annual review of phytopathology}, volume = {55}, number = {}, pages = {483-503}, doi = {10.1146/annurev-phyto-080615-095928}, pmid = {28777924}, issn = {1545-2107}, mesh = {Chromosomes, Fungal/*genetics ; Evolution, Molecular ; Fungi/*genetics/*pathogenicity ; Gene Rearrangement ; Genome, Fungal ; *Karyotype ; Plant Diseases/*microbiology ; Plants/*microbiology ; }, abstract = {Recent advances in genetic and molecular technologies gradually paved the way for the transition from traditional fungal karyotyping to more comprehensive chromosome biology studies. Extensive chromosomal polymorphisms largely resulting from chromosomal rearrangements (CRs) are widely documented in fungal genomes. These extraordinary CRs in fungi generate substantial genome plasticity compared to other eukaryotic organisms. Here, we review the most recent findings on fungal CRs and their underlying mechanisms and discuss the functional consequences of CRs for adaptation, fungal evolution, host range, and pathogenicity of fungal plant pathogens in the context of chromosome biology. In addition to a complement of permanent chromosomes called core chromosomes, the genomes of many fungal pathogens comprise distinct unstable chromosomes called dispensable chromosomes (DCs) that also contribute to chromosome polymorphisms. Compared to the core chromosomes, the structural features of DCs usually differ for gene density, GC content, housekeeping genes, and recombination frequency. Despite their dispensability for normal growth and development, DCs have important biological roles with respect to pathogenicity in some fungi but not in others. Therefore, their evolutionary origin is also reviewed in relation to overall fungal physiology and pathogenicity.}, }
@article {pmid28774859, year = {2017}, author = {Jaimee, G and Halami, PM}, title = {Conjugal transfer of aac(6')Ie-aph(2″)Ia gene from native species and mechanism of regulation and cross resistance in Enterococcus faecalis MCC3063 by real time-PCR.}, journal = {Microbial pathogenesis}, volume = {110}, number = {}, pages = {546-553}, doi = {10.1016/j.micpath.2017.07.049}, pmid = {28774859}, issn = {1096-1208}, mesh = {Acetyltransferases/*genetics ; Aminoglycosides/pharmacology ; Animals ; Anti-Bacterial Agents/pharmacology ; Blotting, Southern ; *Conjugation, Genetic ; DNA, Bacterial/genetics ; *Drug Resistance, Bacterial ; Enterococcus/*drug effects/enzymology/genetics ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Kanamycin Kinase/*genetics ; Lactobacillus plantarum/drug effects/genetics ; Pediococcus/drug effects/genetics ; Plasmids/analysis ; Real-Time Polymerase Chain Reaction ; }, abstract = {High level aminoglycoside resistance (HLAR) in the lactic acid bacteria (LAB) derived from food animals is detrimental. The aim of this study was to investigate the localization and conjugal transfer of aminoglycoside resistance genes, aac(6')Ie-aph(2″)Ia and aph(3')IIIa in different Enterococcus species. The cross resistance patterns in Enterococcus faecalis MCC3063 to clinically important aminoglycosides by real time PCR were also studied. Southern hybridization experiments revealed the presence of aac(6')Ie-aph(2[″])Ia and aph(3')IIIa genes conferring HLAR in high molecular weight plasmids except in Lactobacillus plantarum. The plasmid encoded bifunctional aac(6')Ie-aph(2″)Ia gene was transferable from Enterococcus avium (n = 2), E. cecorum (n = 1), E. faecalis (n = 1) and Pediococcus lolii (n = 1) species into the recipient strain; E. faecalis JH2-2 by filter mating experiments thus indicating the possible risks of gene transfer into pathogenic strains. Molecular analysis of cross resistance patterns in native isolate of E. faecalis MCC3063 carrying aac(6')Ie-aph(2″)Ia and aph(3')IIIa gene was displayed by quantification of the mRNA levels in this study. For this, the culture was induced with increasing concentrations of gentamicin, kanamycin and streptomycin (2048, 4096, 8192, 16384 μg/mL) individually. The increasing concentrations of gentamicin and kanamycin induced the expression of the aac(6')Ie-aph(2″)Ia and aph(3')IIIa resistance genes, respectively. Interestingly, it was observed that induction with streptomycin triggered a significant fold increase in the expression of the aph(3')IIIa gene which otherwise was not known to modify the aminoglycoside. This is noteworthy as streptomycin was found to confer cross resistance to structurally unrelated kanamycin. Also, expression of the aph(3')IIIa gene when induced with streptomycin, revealed that bacteria harbouring this gene will be able to overcome streptomycin bactericidal action at specific concentrations. HLAR in E. faecalis MCC3063 may be due to the combined expression of both the aac(6')Ie-aph(2″)Ia and aph(3')IIIa genes which could be therapeutically challenging. A combined expression of both the genes in E. faecalis MCC3063 may yield HLAR which could be therapeutically challenging. The study highlights the significant alterations in the mRNA expression levels of aac(6')Ie-aph(2″)Ia and aph(3')IIIa in resistant pathogens, upon exposure to clinically vital aminoglycosides.}, }
@article {pmid28769910, year = {2017}, author = {Petersen, J and Wagner-Döbler, I}, title = {Plasmid Transfer in the Ocean - A Case Study from the Roseobacter Group.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1350}, pmid = {28769910}, issn = {1664-302X}, abstract = {Plasmid mediated horizontal gene transfer (HGT) has been speculated to be one of the prime mechanisms for the adaptation of roseobacters (Rhodobacteraceae) to their ecological niches in the marine habitat. Their plasmids contain ecologically crucial functional modules of up to ∼40-kb in size, e.g., for aerobic anoxygenic photosynthesis, flagellar formation and the biosynthesis of the antibiotic tropodithietic acid. Furthermore, the widely present type four secretion system (T4SS) of roseobacters has been shown to mediate conjugation across genus barriers, albeit in the laboratory. Here we discovered that Confluentimicrobium naphthalenivorans NS6[T], a tidal flat bacterium isolated in Korea, carries a 185-kb plasmid, which exhibits a long-range synteny with the conjugative 126-kb plasmid of Dinoroseobacter shibae DFL12[T]. Both replicons are stably maintained by RepABC operons of the same compatibility group (-2) and they harbor a homologous T4SS. Principal component analysis of the codon usage shows a large similarity between the two plasmids, while the chromosomes are very distinct, showing that neither of the two bacterial species represents the original host of those RepABC-2 type plasmids. The two species do not share a common habitat today and they are phylogenetically only distantly related. Our finding demonstrates the first clear-cut evidence for conjugational plasmid transfer across biogeographical and phylogenetic barriers in Rhodobacteraceae and documents the importance of conjugative HGT in the ocean.}, }
@article {pmid28769116, year = {2017}, author = {Toro, N and Martínez-Abarca, F and González-Delgado, A}, title = {The Reverse Transcriptases Associated with CRISPR-Cas Systems.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {7089}, pmid = {28769116}, issn = {2045-2322}, mesh = {Archaea/genetics ; Bacteria/genetics ; *CRISPR-Cas Systems ; Genetic Loci ; Genome ; Phylogeny ; Protein Domains/genetics ; RNA-Directed DNA Polymerase/chemistry/*genetics ; }, abstract = {CRISPR (clustered regularly interspaced short palindromic repeats) and associated proteins (Cas) act as adaptive immune systems in bacteria and archaea. Some CRISPR-Cas systems have been found to be associated with putative reverse transcriptases (RT), and an RT-Cas1 fusion associated with a type III-B system has been shown to acquire RNA spacers in vivo. Nevertheless, the origin and evolutionary relationships of these RTs and associated CRISPR-Cas systems remain largely unknown. We performed a comprehensive phylogenetic analysis of these RTs and associated Cas1 proteins, and classified their CRISPR-Cas modules. These systems were found predominantly in bacteria, and their presence in archaea may be due to a horizontal gene transfer event. These RTs cluster into 12 major clades essentially restricted to particular phyla, suggesting host-dependent functioning. The RTs and associated Cas1 proteins may have largely coevolved. They are, therefore, subject to the same selection pressures, which may have led to coadaptation within particular protein complexes. Furthermore, our results indicate that the association of an RT with a CRISPR-Cas system has occurred on multiple occasions during evolution.}, }
@article {pmid28765541, year = {2017}, author = {Rajput, A and Kumar, M}, title = {In silico analyses of conservational, functional and phylogenetic distribution of the LuxI and LuxR homologs in Gram-positive bacteria.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {6969}, pmid = {28765541}, issn = {2045-2322}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/*genetics/metabolism ; Computer Simulation ; Conserved Sequence ; Databases, Protein ; *Gene Transfer, Horizontal ; Gram-Positive Bacteria/genetics/metabolism/*physiology ; Phylogeny ; Protein Domains ; Quorum Sensing ; RNA, Ribosomal, 16S/genetics ; Repressor Proteins/chemistry/*genetics/metabolism ; Trans-Activators/chemistry/*genetics/metabolism ; Transcription Factors/chemistry/*genetics/metabolism ; }, abstract = {LuxI and LuxR are key factors that drive quorum sensing (QS) in bacteria through secretion and perception of the signaling molecules e.g. N-Acyl homoserine lactones (AHLs). The role of these proteins is well established in Gram-negative bacteria for intercellular communication but remain under-explored in Gram-positive bacteria where QS peptides are majorly responsible for cell-to-cell communication. Therefore, in the present study, we explored conservation, potential function, topological arrangements and evolutionarily aspects of these proteins in Gram-positive bacteria. Putative LuxI/LuxR containing proteins were retrieved using the domain-based strategy from InterPro v62.0 meta-database. Conservational analyses via multiple sequence alignment and domain showed that these are well conserved in Gram-positive bacteria and possess relatedness with Gram-negative bacteria. Further, Gene ontology and ligand-based functional annotation explain their active involvement in signal transduction mechanism via QS signaling molecules. Moreover, Phylogenetic analyses (LuxI, LuxR, LuxI + LuxR and 16s rRNA) revealed horizontal gene transfer events with significant statistical support among Gram-positive and Gram-negative bacteria. This in-silico study offers a detailed overview of potential LuxI/LuxR distribution in Gram-positive bacteria (mainly Firmicutes and Actinobacteria) and their functional role in QS. It would further help in understanding the extent of interspecies communications between Gram-positive and Gram-negative bacteria through QS signaling molecules.}, }
@article {pmid28763439, year = {2017}, author = {Gambette, P and van Iersel, L and Jones, M and Lafond, M and Pardi, F and Scornavacca, C}, title = {Rearrangement moves on rooted phylogenetic networks.}, journal = {PLoS computational biology}, volume = {13}, number = {8}, pages = {e1005611}, pmid = {28763439}, issn = {1553-7358}, mesh = {Animals ; Computational Biology/*methods ; Gene Rearrangement/*genetics ; Hominidae/genetics ; Humans ; *Models, Genetic ; *Phylogeny ; }, abstract = {Phylogenetic tree reconstruction is usually done by local search heuristics that explore the space of the possible tree topologies via simple rearrangements of their structure. Tree rearrangement heuristics have been used in combination with practically all optimization criteria in use, from maximum likelihood and parsimony to distance-based principles, and in a Bayesian context. Their basic components are rearrangement moves that specify all possible ways of generating alternative phylogenies from a given one, and whose fundamental property is to be able to transform, by repeated application, any phylogeny into any other phylogeny. Despite their long tradition in tree-based phylogenetics, very little research has gone into studying similar rearrangement operations for phylogenetic network-that is, phylogenies explicitly representing scenarios that include reticulate events such as hybridization, horizontal gene transfer, population admixture, and recombination. To fill this gap, we propose "horizontal" moves that ensure that every network of a certain complexity can be reached from any other network of the same complexity, and "vertical" moves that ensure reachability between networks of different complexities. When applied to phylogenetic trees, our horizontal moves-named rNNI and rSPR-reduce to the best-known moves on rooted phylogenetic trees, nearest-neighbor interchange and rooted subtree pruning and regrafting. Besides a number of reachability results-separating the contributions of horizontal and vertical moves-we prove that rNNI moves are local versions of rSPR moves, and provide bounds on the sizes of the rNNI neighborhoods. The paper focuses on the most biologically meaningful versions of phylogenetic networks, where edges are oriented and reticulation events clearly identified. Moreover, our rearrangement moves are robust to the fact that networks with higher complexity usually allow a better fit with the data. Our goal is to provide a solid basis for practical phylogenetic network reconstruction.}, }
@article {pmid28761786, year = {2017}, author = {McCuaig, B and Liboiron, F and Dufour, SC}, title = {The bivalve Thyasira cf. gouldi hosts chemoautotrophic symbiont populations with strain level diversity.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e3597}, pmid = {28761786}, issn = {2167-8359}, abstract = {Invertebrates from various marine habitats form nutritional symbioses with chemosynthetic bacteria. In chemosynthetic symbioses, both the mode of symbiont transmission and the site of bacterial housing can affect the composition of the symbiont population. Vertically transmitted symbionts, as well as those hosted intracellularly, are more likely to form clonal populations within their host. Conversely, symbiont populations that are environmentally acquired and extracellular may be more likely to be heterogeneous/mixed within host individuals, as observed in some mytilid bivalves. The symbionts of thyasirid bivalves are also extracellular, but limited 16S rRNA sequencing data suggest that thyasirid individuals contain uniform symbiont populations. In a recent study, Thyasira cf. gouldi individuals from Bonne Bay, Newfoundland, Canada were found to host one of three 16S rRNA phylotypes of sulfur-oxidizing gammaproteobacteria, suggesting environmental acquisition of symbionts and some degree of site-specificity. Here, we use Sanger sequencing of both 16S RNA and the more variable ribulose-1,5-bisphosphate carboxylase (RuBisCO) PCR products to further examine Thyasira cf. gouldi symbiont diversity at the scale of host individuals, as well as to elucidate any temporal or spatial patterns in symbiont diversity within Bonne Bay, and relationships with host OTU or size. We obtained symbiont 16S rRNA and RuBisCO Form II sequences from 54 and 50 host individuals, respectively, during nine sampling trips to three locations over four years. Analyses uncovered the same three closely related 16S rRNA phylotypes obtained previously, as well as three divergent RuBisCO phylotypes; these were found in various pair combinations within host individuals, suggesting incidents of horizontal gene transfer during symbiont evolution. While we found no temporal patterns in phylotype distribution or relationships with host OTU or size, some spatial effects were noted, with some phylotypes only found within particular sampling sites. The sequencing also revealed symbiont populations within individual hosts that appeared to be a mixture of different phylotypes, based on multiple base callings at divergent sites. This work provides further evidence that Thyasira cf. gouldi acquires its symbionts from the environment, and supports the theory that hosts can harbour symbiont populations consisting of multiple, closely related bacterial phylotypes.}, }
@article {pmid28761011, year = {2017}, author = {Borges, RM}, title = {Co-niche construction between hosts and symbionts: ideas and evidence.}, journal = {Journal of genetics}, volume = {96}, number = {3}, pages = {483-489}, pmid = {28761011}, issn = {0973-7731}, mesh = {Animals ; Biological Evolution ; *Ecosystem ; Gene Transfer, Horizontal ; Genome/genetics ; Host Specificity/*genetics ; *Inheritance Patterns ; Phenotype ; Symbiosis/*genetics ; }, abstract = {Symbiosis is a process that can generate evolutionary novelties and can extend the phenotypic niche space of organisms. Symbionts can act together with their hosts to co-construct host organs, within which symbionts are housed. Once established within hosts, symbionts can also influence various aspects of host phenotype, such as resource acquisition, protection from predation by acquisition of toxicity, as well as behaviour. Once symbiosis is established, its fidelity between generations must be ensured. Hosts evolve various mechanisms to screen unwanted symbionts and to facilitate faithful transmission of mutualistic partners between generations. Microbes are the most important symbionts that have influenced plant and animal phenotypes; multicellular organisms engage in developmental symbioses with microbes at many stages in ontogeny. The co-construction of niches may result in composite organisms that are physically nested within each other. While it has been advocated that these composite organisms need new evolutionary theories and perspectives to describe their properties and evolutionary trajectories, it appears that standard evolutionary theories are adequate to explore selection pressures on their composite or individual traits. Recent advances in our understanding of composite organisms open up many important questions regarding the stability and transmission of these units.}, }
@article {pmid28760680, year = {2017}, author = {Almuzara, M and Montaña, S and Lazzaro, T and Uong, S and Parmeciano Di Noto, G and Traglia, G and Bakai, R and Centrón, D and Iriarte, A and Quiroga, C and Ramirez, MS}, title = {Genetic analysis of a PER-2-producing Shewanella sp. strain harbouring a variety of mobile genetic elements and antibiotic resistance determinants.}, journal = {Journal of global antimicrobial resistance}, volume = {11}, number = {}, pages = {81-86}, doi = {10.1016/j.jgar.2017.06.005}, pmid = {28760680}, issn = {2213-7173}, mesh = {Aged ; Anti-Bacterial Agents/pharmacology ; DNA Transposable Elements/*genetics ; DNA, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Genome, Bacterial ; Gram-Negative Bacterial Infections/microbiology ; Humans ; Integrons ; Male ; Microbial Sensitivity Tests ; Open Reading Frames ; Phylogeny ; Plasmids/genetics ; R Factors/genetics ; RNA, Untranslated ; Sequence Analysis, DNA ; Shewanella/drug effects/*enzymology/*genetics/isolation &amp; purification ; Whole Genome Sequencing ; beta-Lactamases/*genetics ; }, abstract = {The objective of this study was to investigate the molecular mechanisms explaining the multidrug-resistant (MDR) phenotype found in a novel clinical Shewanella sp. strain (Shew256) recovered from a diabetic patient. Whole-genome shotgun sequencing was performed using Illumina MiSeq-I and Nextera XT DNA library. De novo assembly was performed with SPAdes. RAST Server was used to predict the open-reading frames and the predictions were confirmed using BLAST. Further genomic analysis was carried out using average nucleotide identity (ANI), ACT (Artemis), OrthoMCL, ARG-ANNOT, ISfinder, PHAST, tRNAscan-SE, plasmidSPAdes, PlasmidFinder and MAUVE. PCR and plasmid extraction were also performed. Genomic analysis revealed a total of 456 predicted genes unique to Shew256 compared with other Shewanella genomes. Moreover, the presence of different resistance genes, including blaPER-2, was found. A complex class 1 integron containing the ISCR1 gene, disrupted by two putative transposase genes, was identified. Furthermore, other resistance genes, a transposon containing aph(3'), insertion sequences, phages and non-coding RNAs were also found. In conclusion, evidence of acquisition of resistance genes and mobile elements that could explain the MDR phenotype were observed. This Shewanella sp. represents a prime example of how antibiotic resistance determinants can be acquired by uncommon pathogens.}, }
@article {pmid28757648, year = {2017}, author = {Sommer, MOA and Munck, C and Toft-Kehler, RV and Andersson, DI}, title = {Prediction of antibiotic resistance: time for a new preclinical paradigm?.}, journal = {Nature reviews. Microbiology}, volume = {15}, number = {11}, pages = {689-696}, pmid = {28757648}, issn = {1740-1534}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics ; Drug Evaluation, Preclinical ; Drug Resistance, Multiple, Bacterial/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Host-Pathogen Interactions ; Humans ; }, abstract = {Predicting the future is difficult, especially for evolutionary processes that are influenced by numerous unknown factors. Still, this is what is required of drug developers when they assess the risk of resistance arising against a new antibiotic candidate during preclinical development. In this Opinion article, we argue that the traditional procedures that are used for the prediction of antibiotic resistance today could be markedly improved by including a broader analysis of bacterial fitness, infection dynamics, horizontal gene transfer and other factors. This will lead to more informed preclinical decisions for continuing or discontinuing the development of drug candidates.}, }
@article {pmid28754709, year = {2017}, author = {Milani, C and Mangifesta, M and Mancabelli, L and Lugli, GA and Mancino, W and Viappiani, A and Faccini, A and van Sinderen, D and Ventura, M and Turroni, F}, title = {The Sortase-Dependent Fimbriome of the Genus Bifidobacterium: Extracellular Structures with Potential To Modulate Microbe-Host Dialogue.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {19}, pages = {}, pmid = {28754709}, issn = {1098-5336}, mesh = {Bacterial Adhesion ; Bifidobacterium/classification/*enzymology/genetics/physiology ; Cysteine Endopeptidases/genetics/*metabolism ; Evolution, Molecular ; Extracellular Matrix/*microbiology ; Fimbriae, Bacterial/*enzymology/genetics ; Gastrointestinal Tract/microbiology ; Genome, Bacterial ; Humans ; Phylogeny ; }, abstract = {Bifidobacteria are important gut commensals of mammals, including humans, of any age. However, the molecular mechanisms by which these microorganisms establish themselves in the mammalian gut and persist in this environment are largely unknown. Here, we analyzed the genetic diversity of the predicted arsenal of sortase-dependent pili of known and sequenced members of the Bifidobacterium genus and constructed a bifidobacterial sortase-dependent fimbriome database. Our analyses revealed considerable genetic variability of the sortase-dependent fimbriome among bifidobacterial (sub)species, which appears to have been due to horizontal gene transfer events and for which we were able to perform evolutionary mapping. Functional assessment by transcriptome analysis and binding assays involving different substrates demonstrates how bifidobacterial pili are pivotal in promoting various abilities for adhesion to glycans and extracellular matrix proteins, thereby supporting the ecological success of bifidobacteria in the mammalian gut.IMPORTANCE Adhesion of bifidobacterial cells to the mucosa of the large intestine is considered a hallmark for the persistence and colonization of these bacteria in the human gut. In this context, we analyzed the genetic diversity of the predicted arsenal of sortase-dependent pili of known and sequenced members of the Bifidobacterium genus, and constructed a bifidobacterial sortase-dependent fimbriome database. Our analyses revealed considerable genetic variability of the sortase-dependent fimbriome among bifidobacterial (sub)species, which appears to have been due to horizontal gene transfer events. In addition, functional assessment by transcriptome analysis and binding assays involving different substrates demonstrates how bifidobacterial pili are crucial in promoting various abilities for adhesion to glycans and extracellular matrix proteins, thereby supporting the ecological success of bifidobacteria in the mammalian gut. This study represents a complete genomic study regarding the presence of fimbriae in the genus Bifidobacterium.}, }
@article {pmid28754703, year = {2017}, author = {Bown, L and Li, Y and Berrué, F and Verhoeven, JTP and Dufour, SC and Bignell, DRD}, title = {Coronafacoyl Phytotoxin Biosynthesis and Evolution in the Common Scab Pathogen Streptomyces scabiei.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {19}, pages = {}, pmid = {28754703}, issn = {1098-5336}, abstract = {Coronafacoyl phytotoxins are an important family of plant toxins that are produced by several different phytopathogenic bacteria, including the gammaproteobacterium Pseudomonas syringae and the actinobacterium Streptomyces scabiei (formerly Streptomyces scabies). The phytotoxins consist of coronafacic acid (CFA) linked via an amide bond to different amino acids or amino acid derivatives. Previous work suggested that S. scabiei and P. syringae use distinct biosynthetic pathways for producing CFA, which is subsequently linked to its amino acid partner to form the complete phytotoxin. Here, we provide further evidence that the S. scabiei CFA biosynthetic pathway is novel by characterizing the role of CYP107AK1, a predicted cytochrome P450 that has no homologue in P. syringae Deletion of the CYP107AK1 gene abolished production of coronafacoyl-isoleucine (CFA-Ile), the primary coronafacoyl phytotoxin produced by S. scabiei Structural elucidation of accumulated biosynthetic intermediates in the ΔCYP107AK1 mutant indicated that CYP107AK1 is required for introducing the oxygen atom that ultimately forms the carbonyl group in the CFA backbone. The CYP107AK1 gene along with two additional genes involved in CFA-Ile biosynthesis in S. scabiei were found to be associated with putative CFA biosynthetic genes in other actinobacteria but not in other organisms. Analysis of the overall genetic content and organization of known and putative CFA biosynthetic gene clusters, together with phylogenetic analysis of the core biosynthetic genes, indicates that horizontal gene transfer has played an important role in the dissemination of the gene cluster and that rearrangement, insertion, and/or deletion events have likely contributed to the divergent biosynthetic evolution of coronafacoyl phytotoxins in bacteria.IMPORTANCE The ability of plants to defend themselves against invading pathogens relies on complex signaling pathways that are controlled by key phytohormones such as jasmonic acid (JA). Some phytopathogenic bacteria have evolved the ability to manipulate JA signaling in order to overcome host defenses by producing coronatine (COR), which functions as a potent JA mimic. COR and COR-like molecules, collectively referred to as coronafacoyl phytotoxins, are produced by several different plant-pathogenic bacteria, and this study provides supporting evidence that different biosynthetic pathways are utilized by different bacteria for production of these phytotoxins. In addition, our study provides a greater understanding of how coronafacoyl phytotoxin biosynthesis may have evolved in phylogenetically distinct bacteria, and we demonstrate that production of these compounds may be more widespread than previously recognized and that their role for the producing organism may not be limited to host-pathogen interactions.}, }
@article {pmid28753988, year = {2017}, author = {Cordaux, R and Gilbert, C}, title = {Evolutionary Significance of Wolbachia-to-Animal Horizontal Gene Transfer: Female Sex Determination and the f Element in the Isopod Armadillidium vulgare.}, journal = {Genes}, volume = {8}, number = {7}, pages = {}, pmid = {28753988}, issn = {2073-4425}, abstract = {An increasing number of horizontal gene transfer (HGT) events from bacteria to animals have been reported in the past years, many of which involve Wolbachia bacterial endosymbionts and their invertebrate hosts. Most transferred Wolbachia genes are neutrally-evolving fossils embedded in host genomes. A remarkable case of Wolbachia HGT for which a clear evolutionary significance has been demonstrated is the "f element", a nuclear Wolbachia insert involved in female sex determination in the terrestrial isopod Armadillidium vulgare. The f element represents an instance of bacteria-to-animal HGT that has occurred so recently that it was possible to infer the donor (feminizing Wolbachia closely related to the wVulC Wolbachia strain of A. vulgare) and the mechanism of integration (a nearly complete genome inserted by micro-homology-mediated recombination). In this review, we summarize our current knowledge of the f element and discuss arising perspectives regarding female sex determination, unstable inheritance, population dynamics and the molecular evolution of the f element. Overall, the f element unifies three major areas in evolutionary biology: symbiosis, HGT and sex determination. Its characterization highlights the tremendous impact sex ratio distorters can have on the evolution of sex determination mechanisms and sex chromosomes in animals and plants.}, }
@article {pmid28752817, year = {2017}, author = {Andersson, DI and Hughes, D}, title = {Selection and Transmission of Antibiotic-Resistant Bacteria.}, journal = {Microbiology spectrum}, volume = {5}, number = {4}, pages = {}, pmid = {28752817}, issn = {2165-0497}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics ; Bacterial Infections/*microbiology/transmission ; Bacterial Physiological Phenomena ; *Drug Resistance, Bacterial ; Humans ; }, abstract = {Ever since antibiotics were introduced into human and veterinary medicine to treat and prevent bacterial infections there has been a steady selection and increase in the frequency of antibiotic resistant bacteria. To be able to reduce the rate of resistance evolution, we need to understand how various biotic and abiotic factors interact to drive the complex processes of resistance emergence and transmission. We describe several of the fundamental factors that underlay resistance evolution, including rates and niches of emergence and persistence of resistant bacteria, time- and space-gradients of various selective agents, and rates and routes of transmission of resistant bacteria between humans, animals and other environments. Furthermore, we discuss the options available to reduce the rate of resistance evolution and/ or transmission and their advantages and disadvantages.}, }
@article {pmid28752517, year = {2017}, author = {Kameya, M and Kanbe, H and Igarashi, Y and Arai, H and Ishii, M}, title = {Nitrate reductases in Hydrogenobacter thermophilus with evolutionarily ancient features: distinctive localization and electron transfer.}, journal = {Molecular microbiology}, volume = {106}, number = {1}, pages = {129-141}, doi = {10.1111/mmi.13756}, pmid = {28752517}, issn = {1365-2958}, mesh = {Archaea/metabolism ; Bacteria/genetics ; Bacterial Proteins/metabolism ; Biological Evolution ; Chemoautotrophic Growth/*genetics ; Electron Transport ; Electrons ; Evolution, Molecular ; Ferredoxins/metabolism ; Nitrate Reductase/*metabolism ; Nitrates/metabolism ; Nitrogen/metabolism ; Periplasm/metabolism ; Phylogeny ; }, abstract = {Dissimilatory nitrate reductase (NAR) and assimilatory nitrate reductase (NAS) serve as key enzymes for nitrogen catabolism and anabolism in many organisms. We purified NAR and NAS from H. thermophilus, a hydrogen-oxidizing chemolithoautotroph belonging to the phylogenetically deepest branch in the Bacteria domain. Physiological contribution of these enzymes to nitrate respiration and assimilation was clarified by transcriptomic analysis and gene disruption experiments. These enzymes showed several features unreported in bacteria, such as the periplasmic orientation of NAR anchored with a putative transmembrane subunit and the specific electron transfer from a [4Fe-4S]-type ferredoxin to NAS. While some of their enzymatic properties are shared with NARs from archaea and with NASs from phototrophs, phylogenetic analysis indicated that H. thermophilus NAR and NAS have deep evolutionary origins that cannot be explained by a recent horizontal gene transfer event from archaea and phototrophs. These findings revealed the diversity of NAR and NAS in nonphotosynthetic bacteria, and they also implied that the outward orientation of NAR and the ferredoxin-dependent electron transfer of NAS are evolutionarily ancient features preserved in H. thermophilus.}, }
@article {pmid28752109, year = {2017}, author = {Walker, FC and Hatoum-Aslan, A}, title = {Conjugation Assay for Testing CRISPR-Cas Anti-plasmid Immunity in Staphylococci.}, journal = {Bio-protocol}, volume = {7}, number = {9}, pages = {}, pmid = {28752109}, issn = {2331-8325}, support = {K22 AI113106/AI/NIAID NIH HHS/United States ; }, abstract = {CRISPR-Cas is a prokaryotic adaptive immune system that prevents uptake of mobile genetic elements such as bacteriophages and plasmids. Plasmid transfer between bacteria is of particular clinical concern due to increasing amounts of antibiotic resistant pathogens found in humans as a result of transfer of resistance plasmids within and between species. Testing the ability of CRISPR-Cas systems to block plasmid transfer in various conditions or with CRISPR-Cas mutants provides key insights into the functionality and mechanisms of CRISPR-Cas as well as how antibiotic resistance spreads within bacterial communities. Here, we describe a method for quantifying the impact of CRISPR-Cas on the efficiency of plasmid transfer by conjugation. While this method is presented in Staphylococcus species, it could be more broadly used for any conjugative prokaryote.}, }
@article {pmid28751420, year = {2017}, author = {Dixit, PD and Pang, TY and Maslov, S}, title = {Recombination-Driven Genome Evolution and Stability of Bacterial Species.}, journal = {Genetics}, volume = {207}, number = {1}, pages = {281-295}, pmid = {28751420}, issn = {1943-2631}, mesh = {Bacteria/*genetics ; *Evolution, Molecular ; Gene Frequency ; Genetic Drift ; Genome, Bacterial ; *Genomic Instability ; *Models, Genetic ; *Recombination, Genetic ; Reproductive Isolation ; }, abstract = {While bacteria divide clonally, horizontal gene transfer followed by homologous recombination is now recognized as an important contributor to their evolution. However, the details of how the competition between clonality and recombination shapes genome diversity remains poorly understood. Using a computational model, we find two principal regimes in bacterial evolution and identify two composite parameters that dictate the evolutionary fate of bacterial species. In the divergent regime, characterized by either a low recombination frequency or strict barriers to recombination, cohesion due to recombination is not sufficient to overcome the mutational drift. As a consequence, the divergence between pairs of genomes in the population steadily increases in the course of their evolution. The species lacks genetic coherence with sexually isolated clonal subpopulations continuously formed and dissolved. In contrast, in the metastable regime, characterized by a high recombination frequency combined with low barriers to recombination, genomes continuously recombine with the rest of the population. The population remains genetically cohesive and temporally stable. Notably, the transition between these two regimes can be affected by relatively small changes in evolutionary parameters. Using the Multi Locus Sequence Typing (MLST) data, we classify a number of bacterial species to be either the divergent or the metastable type. Generalizations of our framework to include selection, ecologically structured populations, and horizontal gene transfer of nonhomologous regions are discussed as well.}, }
@article {pmid28751120, year = {2017}, author = {van de Guchte, M}, title = {Horizontal Gene Transfer and Ecosystem Function Dynamics.}, journal = {Trends in microbiology}, volume = {25}, number = {9}, pages = {699-700}, doi = {10.1016/j.tim.2017.07.002}, pmid = {28751120}, issn = {1878-4380}, mesh = {Bacteria/*genetics ; DNA, Bacterial ; *Ecosystem ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Models, Genetic ; *Molecular Dynamics Simulation ; }, abstract = {Horizontal gene transfer can provide bacteria with new functions that confer an important competitive advantage, and is therefore likely to affect the dynamics of bacterial ecosystems. Two studies by Wolfe et al. and Bonham et al. prepare the way to study this hypothesis in a model ecosystem with reproducible properties.}, }
@article {pmid28749982, year = {2017}, author = {Yoshida, Y and Koutsovoulos, G and Laetsch, DR and Stevens, L and Kumar, S and Horikawa, DD and Ishino, K and Komine, S and Kunieda, T and Tomita, M and Blaxter, M and Arakawa, K}, title = {Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus.}, journal = {PLoS biology}, volume = {15}, number = {7}, pages = {e2002266}, pmid = {28749982}, issn = {1545-7885}, mesh = {Animals ; Base Sequence ; Chromosome Mapping/veterinary ; DNA/chemistry/metabolism ; Desiccation ; Extremophiles/*genetics/growth &amp; development/physiology ; Gene Expression Profiling/veterinary ; *Gene Expression Regulation ; Gene Transfer, Horizontal ; Genetic Linkage ; Genome Size ; Genome-Wide Association Study/veterinary ; Genomic Library ; High-Throughput Nucleotide Sequencing/veterinary ; Multigene Family ; Phylogeny ; Proteome/genetics/*metabolism ; Reproducibility of Results ; Species Specificity ; Tardigrada/*genetics/growth &amp; development/physiology ; }, abstract = {Tardigrada, a phylum of meiofaunal organisms, have been at the center of discussions of the evolution of Metazoa, the biology of survival in extreme environments, and the role of horizontal gene transfer in animal evolution. Tardigrada are placed as sisters to Arthropoda and Onychophora (velvet worms) in the superphylum Panarthropoda by morphological analyses, but many molecular phylogenies fail to recover this relationship. This tension between molecular and morphological understanding may be very revealing of the mode and patterns of evolution of major groups. Limnoterrestrial tardigrades display extreme cryptobiotic abilities, including anhydrobiosis and cryobiosis, as do bdelloid rotifers, nematodes, and other animals of the water film. These extremophile behaviors challenge understanding of normal, aqueous physiology: how does a multicellular organism avoid lethal cellular collapse in the absence of liquid water? Meiofaunal species have been reported to have elevated levels of horizontal gene transfer (HGT) events, but how important this is in evolution, and particularly in the evolution of extremophile physiology, is unclear. To address these questions, we resequenced and reassembled the genome of H. dujardini, a limnoterrestrial tardigrade that can undergo anhydrobiosis only after extensive pre-exposure to drying conditions, and compared it to the genome of R. varieornatus, a related species with tolerance to rapid desiccation. The 2 species had contrasting gene expression responses to anhydrobiosis, with major transcriptional change in H. dujardini but limited regulation in R. varieornatus. We identified few horizontally transferred genes, but some of these were shown to be involved in entry into anhydrobiosis. Whole-genome molecular phylogenies supported a Tardigrada+Nematoda relationship over Tardigrada+Arthropoda, but rare genomic changes tended to support Tardigrada+Arthropoda.}, }
@article {pmid28748289, year = {2017}, author = {Gratia, JP}, title = {Genetic recombinational events in prokaryotes and their viruses: insight into the study of evolution and biodiversity.}, journal = {Antonie van Leeuwenhoek}, volume = {110}, number = {12}, pages = {1493-1514}, doi = {10.1007/s10482-017-0916-5}, pmid = {28748289}, issn = {1572-9699}, mesh = {Archaea/genetics ; Bacteria/genetics/virology ; Bacteriophages/genetics ; Biodiversity ; Biological Evolution ; Evolution, Molecular ; Gene Transfer, Horizontal ; Host-Pathogen Interactions/*genetics ; Mutagenesis, Insertional ; Mutation ; Prokaryotic Cells/*metabolism/*virology ; *Recombination, Genetic ; Sequence Deletion ; Viruses/*genetics ; }, abstract = {The exact meaning of sexual reproduction and the precise evolutionary period at which recombination first took place remains the subject of intense debates. Despite some unity in biochemical organisation of genetic recombination, a plethora of mechanisms are found to exist in microbes and their viruses. Some routes used by viruses bypass barriers to genetic heterology and provide bacteria with genes conferring a selective advantage, and some contribute to genome enlargement. The present review aims at highlighting the diversity of such mechanisms with a particular focus on spontaneous zygogenesis (or Z-mating). The latter mode of genetic recombination, which was recently discovered in Escherichia coli, resembles gamete fusion in eukaryotes in that it involves complete genetic mixing. Vertical and horizontal evolution through mutations and homo- or heterospecific Z-mating can be monitored to some extent, providing a mean to interrogate the mechanisms of evolution in a way similar to introgression and symbiogenesis. The question arises as to whether Z-mating might represent a remainder of what happened in the very first organisms appearing on earth, as well as recombination events among viruses.}, }
@article {pmid28744785, year = {2017}, author = {van Dam, P and Rep, M}, title = {The Distribution of Miniature Impala Elements and SIX Genes in the Fusarium Genus is Suggestive of Horizontal Gene Transfer.}, journal = {Journal of molecular evolution}, volume = {85}, number = {1-2}, pages = {14-25}, pmid = {28744785}, issn = {1432-1432}, support = {93512007//Netherlands Genomics Initiative/ ; }, mesh = {*DNA Transposable Elements ; Fusarium/*genetics/pathogenicity ; *Gene Transfer, Horizontal ; *Genes, Fungal ; Genomics ; Phylogeny ; Sequence Analysis, DNA ; Virulence ; }, abstract = {The mimp family of miniature inverted-repeat transposable elements was previously found only in genomes of Fusarium oxysporum and is contextually associated with virulence genes in this species. Through extensive comparative analysis of 83 F. oxysporum and 52 other Fusarium genomes, we uncovered the distribution of different mimp families throughout the genus. We show that (i) mimps are not exclusive to F. oxysporum; (ii) pathogenic isolates generally possess more mimps than non-pathogenic strains and (iii) two isolates of F. hostae and one F. proliferatum isolate display evidence for horizontal transfer of genetic material to or from F. oxysporum. Multiple instances of mimp elements identical to F. oxysporum mimps were encountered in the genomes of these isolates. Moreover, homologs of effector genes (SIX1, 2, 6, 7, 11 and FomAVR2) were discovered here, several with very high (97-100%) pairwise nucleotide sequence identity scores. These three strains were isolated from infected flower bulbs (Hyacinthus and Lilium spp.). Their ancestors may thus have lived in close proximity to pathogenic strains of F. oxysporum f. sp. hyacinthi and f. sp. lilii. The Fo f. sp. lycopersici SIX2 effector gene was found to be widely distributed (15/18 isolates) throughout the F. fujikuroi species complex, exhibiting a predominantly vertical inheritance pattern. These findings shed light on the potential evolutionary mechanism underlying plant-pathogenicity in Fusarium and show that interspecies horizontal gene transfer may have occurred.}, }
@article {pmid28744270, year = {2017}, author = {Hembach, N and Schmid, F and Alexander, J and Hiller, C and Rogall, ET and Schwartz, T}, title = {Occurrence of the mcr-1 Colistin Resistance Gene and other Clinically Relevant Antibiotic Resistance Genes in Microbial Populations at Different Municipal Wastewater Treatment Plants in Germany.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1282}, pmid = {28744270}, issn = {1664-302X}, abstract = {Seven wastewater treatment plants (WWTPs) with different population equivalents and catchment areas were screened for the prevalence of the colistin resistance gene mcr-1 mediating resistance against last resort antibiotic polymyxin E. The abundance of the plasmid-associated mcr-1 gene in total microbial populations during water treatment processes was quantitatively analyzed by qPCR analyses. The presence of the colistin resistance gene was documented for all of the influent wastewater samples of the seven WWTPs. In some cases the mcr-1 resistance gene was also detected in effluent samples of the WWTPs after conventional treatment reaching the aquatic environment. In addition to the occurrence of mcr-1 gene, CTX-M-32, blaTEM, CTX-M, tetM, CMY-2, and ermB genes coding for clinically relevant antibiotic resistances were quantified in higher abundances in all WWTPs effluents. In parallel, the abundances of Acinetobacter baumannii, Klebsiella pneumoniae, and Escherichia coli were quantified via qPCR using specific taxonomic gene markers which were detected in all influent and effluent wastewaters in significant densities. Hence, opportunistic pathogens and clinically relevant antibiotic resistance genes in wastewaters of the analyzed WWTPs bear a risk of dissemination to the aquatic environment. Since many of the antibiotic resistance gene are associated with mobile genetic elements horizontal gene transfer during wastewater treatment can't be excluded.}, }
@article {pmid28743812, year = {2017}, author = {Thomas, J and Watve, SS and Ratcliff, WC and Hammer, BK}, title = {Horizontal Gene Transfer of Functional Type VI Killing Genes by Natural Transformation.}, journal = {mBio}, volume = {8}, number = {4}, pages = {}, pmid = {28743812}, issn = {2150-7511}, support = {NNX15AR33G//NASA/United States ; }, mesh = {Alleles ; *Antibiosis ; Bacterial Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Mutation ; Operon ; *Transformation, Bacterial ; Type VI Secretion Systems/*genetics ; Vibrio cholerae/*genetics/*physiology ; }, abstract = {Horizontal gene transfer (HGT) can have profound effects on bacterial evolution by allowing individuals to rapidly acquire adaptive traits that shape their strategies for competition. One strategy for intermicrobial antagonism often used by Proteobacteria is the genetically encoded contact-dependent type VI secretion system (T6SS), a weapon used to kill heteroclonal neighbors by direct injection of toxic effectors. Here, we experimentally demonstrate that Vibrio cholerae can acquire new T6SS effector genes via horizontal transfer and utilize them to kill neighboring cells. Replacement of one or more parental alleles with novel effectors allows the recombinant strain to dramatically outcompete its parent. Using spatially explicit modeling, we examine how this process could affect the ecology and evolution of surface-attached microbial populations. HGT of T6SS effector-immunity pairs is risky: transformation brings a cell into conflict with its former clone mates but can be adaptive when superior T6SS alleles are acquired. More generally, we find that these costs and benefits are not symmetric and that high rates of HGT can act as a hedge against competitors with unpredictable T6SS efficacy. We conclude that antagonism and horizontal transfer drive successive rounds of weapon optimization and selective sweeps, dynamically shaping the composition of microbial communities.IMPORTANCE The contact-dependent type VI secretion system (T6SS) is frequently used by Proteobacteria to kill adjacent competitors. While DNA released by T6 killing can be horizontally acquired, it remains untested whether T6 genes themselves can be horizontally acquired and then utilized to compete with neighboring cells. Using naturally transformable Vibrio cholerae, we provide the first direct empirical support for the hypothesis that T6 genes are exchanged horizontally (e.g., from dead competitors) and functionally deployed to compete with neighboring cells. Using computational simulations, we also demonstrate that high rates of HGT can be adaptive, allowing V. cholerae to improve upon existing T6 weaponry and survive direct encounters with otherwise superior competitors. We anticipate that our evolutionary results are of broad microbiological relevance, applying to many bacteria capable of HGT that utilize the T6SS or similar antagonistic systems, and highlight the profound impact of HGT in shaping microbial community structure.}, }
@article {pmid28743462, year = {2017}, author = {Bakhshinejad, B and Ghiasvand, S}, title = {Bacteriophages in the human gut: Our fellow travelers throughout life and potential biomarkers of heath or disease.}, journal = {Virus research}, volume = {240}, number = {}, pages = {47-55}, doi = {10.1016/j.virusres.2017.07.013}, pmid = {28743462}, issn = {1872-7492}, mesh = {Animals ; Bacteriophages/classification/genetics/*isolation &amp; purification/physiology ; Biomarkers/analysis/metabolism ; Gastrointestinal Tract/*virology ; Health ; Humans ; }, abstract = {The gastrointestinal (GI) tract is populated by a huge variety of viruses. Bacterial viruses (bacteriophages) constitute the largest and the most unrecognized part of virome. The total bacteriophage community of the human gut is called phageome. Phages colonize the gut from the earliest moments of life and become our fellow travelers throughout life. Phageome seems to be unique to each individual and shows a high degree of interpersonal variation. In the healthy gut, a vast majority of phages have a lysogenic lifestyle. These prophages serve as a major respository of mobile genetic elements in the gut and play key roles in the exchange of genetic material between bacterial species via horizontal gene transfer (HGT). But, imbalance in the gut microbial community during dysbiosis, caused by diseases or environmental stresses such as antibiotics, is accompanied by induction of prophages leading to a decreased ratio of symbionts to pathobionts. Based on this, a diseased gut is transformed from an environment predominantly occupied by prophages to an ecosystem mostly inhabited by lytic phages. A growing body of evidence has provided support for the notion that phageome structure and composition change dependent on the physiological or pathological status of the body. This has been demonstrated by pronounced quantitative and qualitative differences between the phageome of healthy individuals and patients. Although many aspects of the contribution made by phages to human biology remain to be understood, recent findings favor the suggestion that phageome might represent potential to serve as a biomarker of health or disease.}, }
@article {pmid28742284, year = {2017}, author = {Fu, J and Yang, D and Jin, M and Liu, W and Zhao, X and Li, C and Zhao, T and Wang, J and Gao, Z and Shen, Z and Qiu, Z and Li, JW}, title = {Aquatic animals promote antibiotic resistance gene dissemination in water via conjugation: Role of different regions within the zebra fish intestinal tract, and impact on fish intestinal microbiota.}, journal = {Molecular ecology}, volume = {26}, number = {19}, pages = {5318-5333}, doi = {10.1111/mec.14255}, pmid = {28742284}, issn = {1365-294X}, mesh = {Animals ; Bacteria/*classification ; Conjugation, Genetic ; Drug Resistance, Bacterial/*genetics ; Feces/microbiology ; *Gastrointestinal Microbiome ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Intestines/microbiology ; Plasmids/genetics ; RNA, Ribosomal, 16S/genetics ; Water ; Zebrafish/*microbiology ; }, abstract = {The aqueous environment is one of many reservoirs of antibiotic resistance genes (ARGs). Fish, as important aquatic animals which possess ideal intestinal niches for bacteria to grow and multiply, may ingest antibiotic resistance bacteria from aqueous environment. The fish gut would be a suitable environment for conjugal gene transfer including those encoding antibiotic resistance. However, little is known in relation to the impact of ingested ARGs or antibiotic resistance bacteria (ARB) on gut microbiota. Here, we applied the cultivation method, qPCR, nuclear molecular genetic marker and 16S rDNA amplicon sequencing technologies to develop a plasmid-mediated ARG transfer model of zebrafish. Furthermore, we aimed to investigate the dissemination of ARGs in microbial communities of zebrafish guts after donors carrying self-transferring plasmids that encode ARGs were introduced in aquaria. On average, 15% of faecal bacteria obtained ARGs through RP4-mediated conjugal transfer. The hindgut was the most important intestinal region supporting ARG dissemination, with concentrations of donor and transconjugant cells almost 25 times higher than those of other intestinal segments. Furthermore, in the hindgut where conjugal transfer occurred most actively, there was remarkable upregulation of the mRNA expression of the RP4 plasmid regulatory genes, trbBp and trfAp. Exogenous bacteria seem to alter bacterial communities by increasing Escherichia and Bacteroides species, while decreasing Aeromonas compared with control groups. We identified the composition of transconjugants and abundance of both cultivable and uncultivable bacteria (the latter accounted for 90.4%-97.2% of total transconjugants). Our study suggests that aquatic animal guts contribute to the spread of ARGs in water environments.}, }
@article {pmid28739894, year = {2017}, author = {Pluta, R and Boer, DR and Lorenzo-Díaz, F and Russi, S and Gómez, H and Fernández-López, C and Pérez-Luque, R and Orozco, M and Espinosa, M and Coll, M}, title = {Structural basis of a histidine-DNA nicking/joining mechanism for gene transfer and promiscuous spread of antibiotic resistance.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {32}, pages = {E6526-E6535}, pmid = {28739894}, issn = {1091-6490}, mesh = {Bacterial Proteins/*chemistry/genetics/metabolism ; *DNA Breaks, Single-Stranded ; DNA, Bacterial/*chemistry/genetics/metabolism ; Endodeoxyribonucleases/*chemistry/genetics/metabolism ; Histidine/chemistry/genetics/metabolism ; *Models, Molecular ; Plasmids/*chemistry/genetics/metabolism ; Staphylococcus aureus/*enzymology/genetics ; }, abstract = {Relaxases are metal-dependent nucleases that break and join DNA for the initiation and completion of conjugative bacterial gene transfer. Conjugation is the main process through which antibiotic resistance spreads among bacteria, with multidrug-resistant staphylococci and streptococci infections posing major threats to human health. The MOBV family of relaxases accounts for approximately 85% of all relaxases found in Staphylococcus aureus isolates. Here, we present six structures of the MOBV relaxase MobM from the promiscuous plasmid pMV158 in complex with several origin of transfer DNA fragments. A combined structural, biochemical, and computational approach reveals that MobM follows a previously uncharacterized histidine/metal-dependent DNA processing mechanism, which involves the formation of a covalent phosphoramidate histidine-DNA adduct for cell-to-cell transfer. We discuss how the chemical features of the high-energy phosphorus-nitrogen bond shape the dominant position of MOBV histidine relaxases among small promiscuous plasmids and their preference toward Gram-positive bacteria.}, }
@article {pmid28738827, year = {2017}, author = {Lutfullahoğlu-Bal, G and Keskin, A and Seferoğlu, AB and Dunn, CD}, title = {Bacterial tail anchors can target to the mitochondrial outer membrane.}, journal = {Biology direct}, volume = {12}, number = {1}, pages = {16}, pmid = {28738827}, issn = {1745-6150}, support = {637649/ERC_/European Research Council/International ; }, mesh = {Escherichia coli Proteins/chemistry/*metabolism ; Eukaryotic Cells/metabolism/ultrastructure ; Mitochondria/metabolism ; Mitochondrial Membranes/*metabolism ; Organelle Biogenesis ; Protein Sorting Signals/physiology ; Protein Transport ; Saccharomyces cerevisiae/*metabolism/ultrastructure ; }, abstract = {BACKGROUND: During the generation and evolution of the eukaryotic cell, a proteobacterial endosymbiont was re-fashioned into the mitochondrion, an organelle that appears to have been present in the ancestor of all present-day eukaryotes. Mitochondria harbor proteomes derived from coding information located both inside and outside the organelle, and the rate-limiting step toward the formation of eukaryotic cells may have been development of an import apparatus allowing protein entry to mitochondria. Currently, a widely conserved translocon allows proteins to pass from the cytosol into mitochondria, but how proteins encoded outside of mitochondria were first directed to these organelles at the dawn of eukaryogenesis is not clear. Because several proteins targeted by a carboxyl-terminal tail anchor (TA) appear to have the ability to insert spontaneously into the mitochondrial outer membrane (OM), it is possible that self-inserting, tail-anchored polypeptides obtained from bacteria might have formed the first gate allowing proteins to access mitochondria from the cytosol.<br><br>RESULTS: Here, we tested whether bacterial TAs are capable of targeting to mitochondria. In a survey of proteins encoded by the proteobacterium Escherichia coli, predicted TA sequences were directed to specific subcellular locations within the yeast Saccharomyces cerevisiae. Importantly, TAs obtained from DUF883 family members ElaB and YqjD were abundantly localized to and inserted at the mitochondrial OM.<br><br>CONCLUSIONS: Our results support the notion that eukaryotic cells are able to utilize membrane-targeting signals present in bacterial proteins obtained by lateral gene transfer, and our findings make plausible a model in which mitochondrial protein translocation was first driven by tail-anchored proteins.<br><br>REVIEWERS: This article was reviewed by Michael Ryan and Thomas Simmen.}, }
@article {pmid28738194, year = {2017}, author = {Jiang, X and Xu, Y and Li, Y and Zhang, K and Liu, L and Wang, H and Tian, J and Ying, H and Shi, L and Yu, T}, title = {Characterization and horizontal transfer of qacH-associated class 1 integrons in Escherichia coli isolated from retail meats.}, journal = {International journal of food microbiology}, volume = {258}, number = {}, pages = {12-17}, doi = {10.1016/j.ijfoodmicro.2017.07.009}, pmid = {28738194}, issn = {1879-3460}, mesh = {Anti-Bacterial Agents/*pharmacology ; Benzalkonium Compounds/*pharmacology ; Disinfectants/*pharmacology ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/*drug effects/*genetics/isolation &amp; purification ; Food Contamination ; Gene Transfer, Horizontal/*genetics ; Integrons/genetics ; Meat/microbiology ; Microbial Sensitivity Tests ; Plasmids/genetics ; Polymerase Chain Reaction ; }, abstract = {The aim of this study was to examine the presence of genes responsible for resistance to quaternary ammonium compounds (QACs) and the association of qac genes with class 1 integrons in Escherichia coli isolated from retail meats. Among the 179 E. coli isolates tested, the minimum inhibitory concentrations (MICs) of benzalkonium chloride (BC) ranged from 4 to 64μg/mL. PCR assays indicated that QAC-resistance genes sugE(c), ydgE/ydgF, mdfA, emrE and qacEΔ1 were commonly present (40.2%-88.3%) in these isolates, but qacE, qacF, qacH and sugE(p) were less prevalent (2.2%-28.5%). Seven different gene cassette arrangements were identified in 31 intI1-positive isolates. Three types of qacH-sul3-associated non-classic integrons were observed in four isolates: dfrA12-orfF-aadA2-cmlA1-aadA1-qacH-IS440-sul3, aadA2-cmlA1-aadA1-qacH-IS440-sul3 and dfrA1-aadA1-qacH-IS440-sul3. Non-classic class 1 integrons were located on plasmids of 100-150kb in these four isolates. Our results demonstrated that the qacH-associated integrons located on 100 kb plasmids in two isolates could be transferred to an E. coli recipient, indicating the co-existence and co-dissemination of disinfectant and antimicrobial resistance genes among bacterial species.}, }
@article {pmid28732786, year = {2017}, author = {Safari Sinegani, AA and Younessi, N}, title = {Antibiotic resistance of bacteria isolated from heavy metal-polluted soils with different land uses.}, journal = {Journal of global antimicrobial resistance}, volume = {10}, number = {}, pages = {247-255}, doi = {10.1016/j.jgar.2017.05.012}, pmid = {28732786}, issn = {2213-7173}, mesh = {Amoxicillin/pharmacology ; Ampicillin/pharmacology ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*classification/drug effects/genetics/isolation &amp; purification ; *Drug Resistance, Multiple, Bacterial ; Environmental Monitoring ; Gene Transfer, Horizontal ; Industrial Waste/analysis ; Manure/microbiology ; Metals, Heavy/*pharmacology ; Mining ; Phylogeny ; Prevalence ; Soil/*chemistry ; Soil Microbiology ; Solid Waste/adverse effects ; }, abstract = {OBJECTIVES: The main objective of this study was to determine the relationship between the antibiotic and heavy metal tolerance of culturable bacteria isolated from mining waste, pasture, and agricultural soils containing different levels of heavy metals.<br><br>MATERIALS AND METHODS: The populations of total culturable bacteria, and heavy metal- and antibiotic-tolerant bacteria in the soils were enumerated on nutrient agar, nutrient agar amended with metals, and Mueller-Hinton agar amended with antibiotics, respectively. The multiple antibiotic resistance index, and patterns of antibiotic resistance and heavy metal-antibiotic co-resistance were determined for 237 isolates.<br><br>RESULTS: Among all the samples, those of the tailings of mines with higher levels of heavy metals had the lowest number of bacteria, but a relatively higher abundance of heavy metal- and antibiotic-resistant bacteria. A high degree of resistance was observed for ampicillin and amoxicillin in the isolates from all soils. The agricultural soil isolates had a high prevalence of resistance towards vancomycin, tetracycline, and streptomycin. Among all the tested antibiotics, gentamicin was the most potent. The most frequent pattern of multiple antibiotic resistance in the isolates from agricultural soils was amoxicillin, ampicillin, streptomycin, vancomycin, tetracycline, and doxycycline. The percentage of isolates with multiple antibiotic resistance was considerably higher in the agricultural soils than in the mining waste soils. A high rate of co-resistance towards Hg and antibiotics was observed among the gram-negative isolates, and towards Zn, Ni, Hg, and the beta-lactam antibiotics among the gram-positive isolates.<br><br>CONCLUSIONS: The higher percentage of isolates with multiple antibiotic resistance in the agricultural soils that in the mining waste soils may be related to (1) the level of soil heavy metals, (2) the population and diversity of soil bacteria, (3) the application of manures, and (4) other factors affecting gene transfer between bacteria.}, }
@article {pmid28732043, year = {2017}, author = {Messerer, M and Fischer, W and Schubert, S}, title = {Investigation of horizontal gene transfer of pathogenicity islands in Escherichia coli using next-generation sequencing.}, journal = {PloS one}, volume = {12}, number = {7}, pages = {e0179880}, pmid = {28732043}, issn = {1932-6203}, mesh = {Escherichia coli/*genetics/*pathogenicity ; *Gene Transfer, Horizontal ; *Genomic Islands ; High-Throughput Nucleotide Sequencing ; Phylogeny ; }, abstract = {Horizontal gene transfer (HGT) contributes to the evolution of bacteria. All extraintestinal pathogenic Escherichia coli (ExPEC) harbour pathogenicity islands (PAIs), however relatively little is known about the acquisition of these PAIs. Due to these islands, ExPEC have properties to colonize and invade its hosts efficiently. Even though these PAIs are known to be acquired by HGT, only very few PAIs do carry mobilization and transfer genes required for the transmission by HGT. In this study, we apply for the first time next-generation sequencing (NGS) and in silico analyses in combination with in vitro experiments to decipher the mechanisms of PAI acquisition in ExPEC. For this, we investigated three neighbouring E. coli PAIs, namely the high-pathogenicity island (HPI), the pks and the serU island. As these PAIs contain no mobilization and transfer genes, they are immobile and dependent on transfer vehicles. By whole genome sequencing of the entire E. coli reference (ECOR) collection and by applying a phylogenetic approach we could unambiguously demonstrate that these PAIs are transmitted not only vertically, but also horizontally. Furthermore, we could prove in silico that distinct groups of PAIs were transferred "en bloc" in conjunction with the neighbouring chromosomal backbone. We traced this PAI transfer in vitro using an F' plasmid. Different lengths of transferred DNA were exactly detectable in the sequenced transconjugants indicating NGS as a powerful tool for determination of PAI transfer.}, }
@article {pmid28731472, year = {2017}, author = {Vigil-Stenman, T and Ininbergs, K and Bergman, B and Ekman, M}, title = {High abundance and expression of transposases in bacteria from the Baltic Sea.}, journal = {The ISME journal}, volume = {11}, number = {11}, pages = {2611-2623}, pmid = {28731472}, issn = {1751-7370}, mesh = {Bacteria/classification/*enzymology/genetics/isolation &amp; purification ; Bacterial Proteins/*genetics/metabolism ; Baltic States ; Gene Transfer, Horizontal ; Genome, Bacterial ; Metagenome ; Phylogeny ; Seawater/*microbiology ; Transposases/*genetics/metabolism ; }, abstract = {Transposases are mobile genetic elements suggested to have an important role in bacterial genome plasticity and host adaptation but their transcriptional activity in natural bacterial communities is largely unexplored. Here we analyzed metagenomes and -transcriptomes of size fractionated (0.1-0.8, 0.8-3.0 and 3.0-200 μm) bacterial communities from the brackish Baltic Sea, and adjacent marine waters. The Baltic Sea transposase levels, up to 1.7% of bacterial genes and 2% of bacterial transcripts, were considerably higher than in marine waters and similar to levels reported for extreme environments. Large variations in expression were found between transposase families and groups of bacteria, with a two-fold higher transcription in Cyanobacteria than in any other phylum. The community-level results were corroborated at the genus level by Synechococcus transposases reaching up to 5.2% of genes and 6.9% of transcripts, which is in contrast to marine Synechococcus that largely lack these genes. Levels peaked in Synechococcus from the largest size fraction, suggesting high frequencies of lateral gene transfer and high genome plasticity in colony-forming picocyanobacteria. Together, the results support an elevated rate of transposition-based genome change and adaptation in bacterial populations of the Baltic Sea, and possibly also of other highly dynamic estuarine waters.}, }
@article {pmid28728564, year = {2017}, author = {McGill, SE and Barker, D}, title = {Comparison of the protein-coding genomes of three deep-sea, sulfur-oxidising bacteria: "Candidatus Ruthia magnifica", "Candidatus Vesicomyosocius okutanii" and Thiomicrospira crunogena.}, journal = {BMC research notes}, volume = {10}, number = {1}, pages = {296}, pmid = {28728564}, issn = {1756-0500}, mesh = {Bacterial Proteins/*genetics ; DNA, Bacterial/*genetics ; Seawater/*microbiology ; Sulfur-Reducing Bacteria/*genetics ; *Water Microbiology ; }, abstract = {OBJECTIVE: " Candidatus Ruthia magnifica", "Candidatus Vesicomyosocius okutanii" and Thiomicrospira crunogena are all sulfur-oxidising bacteria found in deep-sea vent environments. Recent research suggests that the two symbiotic organisms, "Candidatus R. magnifica" and "Candidatus V. okutanii", may share common ancestry with the autonomously living species T. crunogena. We used comparative genomics to examine the genome-wide protein-coding content of all three species to explore their similarities. In particular, we used the OrthoMCL algorithm to sort proteins into groups of putative orthologs on the basis of sequence similarity.<br><br>RESULTS: The OrthoMCL inflation parameter was tuned using biological criteria. Using the tuned value, OrthoMCL delimited 1070 protein groups. 63.5% of these groups contained one protein from each species. Two groups contained duplicate protein copies from all three species. 123 groups were unique to T. crunogena and ten groups included multiple copies of T. crunogena proteins but only single copies from the other species. "Candidatus R. magnifica" had one unique group, and had multiple copies in one group where the other species had a single copy. There were no groups unique to "Candidatus V. okutanii", and no groups in which there were multiple "Candidatus V. okutanii" proteins but only single proteins from the other species. Results align with previous suggestions that all three species share a common ancestor. However this is not definitive evidence to make taxonomic conclusions and the possibility of horizontal gene transfer was not investigated. Methodologically, the tuning of the OrthoMCL inflation parameter using biological criteria provides further methods to refine the OrthoMCL procedure.}, }
@article {pmid28727895, year = {2018}, author = {Sitkiewicz, I}, title = {How to become a killer, or is it all accidental? Virulence strategies in oral streptococci.}, journal = {Molecular oral microbiology}, volume = {33}, number = {1}, pages = {1-12}, doi = {10.1111/omi.12192}, pmid = {28727895}, issn = {2041-1014}, mesh = {Adaptation, Psychological ; Carbohydrate Metabolism ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Humans ; Microbiota ; Mouth/*microbiology ; Mouth Diseases/microbiology ; Streptococcal Infections/microbiology ; Streptococcus/*genetics/metabolism/*pathogenicity ; Streptococcus anginosus/genetics/pathogenicity ; Streptococcus mitis/genetics/pathogenicity ; Streptococcus pyogenes/genetics/pathogenicity ; Virulence/genetics ; Virulence Factors/*genetics ; }, abstract = {Streptococci are a diverse group of Gram-positive microorganisms sharing common virulence traits and similar strategies to escape the oral niche and establish an infection in other parts of the host organism. Invasive infection with oral streptococci is "a perfect storm" that requires the concerted action of multiple biotic and abiotic factors. Our understanding of streptococcal pathogenicity and infectivity should probably be less mechanistic and driven not only by the identification of novel virulence factors. The observed diversity of the genus, including the range of virulence and pathogenicity mechanisms, is most likely the result of interspecies interactions, a massive horizontal gene transfer between streptococci within a shared oral niche, recombination events, selection of specialized clones, and modification of regulatory circuits. Selective pressure by the host and bacterial communities is a driving force for the selection of virulence traits and shaping the streptococcal genome. Global regulatory events driving niche adaptation and interactions with bacterial communities and the host steer research interests towards attempts to define the oral interactome on the transcriptional level and define signal cross-feeding and co-expression and co-regulation of virulence genes.}, }
@article {pmid28725221, year = {2017}, author = {Shalev, Y and Turgeman-Grott, I and Tamir, A and Eichler, J and Gophna, U}, title = {Cell Surface Glycosylation Is Required for Efficient Mating of Haloferax volcanii.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1253}, pmid = {28725221}, issn = {1664-302X}, abstract = {Halophilic archaea use a fusion-based mating system for lateral gene transfer across cells, yet the molecular mechanisms involved remain unknown. Previous work implied that cell fusion involves cell-cell recognition since fusion occurs more efficiently between cells from the same species. Long believed to be restricted only to Eukarya, it is now known that cells of all three domains of life perform N-glycosylation, the covalent attachment of glycans to select target asparagine residues in proteins, and that this post-translational modification is common for archaeal cell surface proteins. Here, we show that differences in glycosylation of the Haloferax volcanii surface-layer glycoprotein, brought about either by changing medium salinity or by knocking out key glycosylation genes, reduced mating success. Thus, different glycosylation patterns are likely to underlie mating preference in halophilic archaea, contributing to speciation processes.}, }
@article {pmid28720902, year = {2017}, author = {Xu, H and Qin, S and Lan, Y and Liu, M and Cao, X and Qiao, D and Cao, Y and Cao, Y}, title = {Comparative genomic analysis of Paenibacillus sp. SSG-1 and its closely related strains reveals the effect of glycometabolism on environmental adaptation.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {5720}, pmid = {28720902}, issn = {2045-2322}, mesh = {*Adaptation, Biological ; Agar/metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genomics ; Hydrolysis ; Metabolic Networks and Pathways/*genetics ; Paenibacillus/*genetics/*metabolism ; Polysaccharides/*metabolism ; }, abstract = {The extensive environmental adaptability of the genus Paenibacillus is related to the enormous diversity of its gene repertoires. Paenibacillus sp. SSG-1 has previously been reported, and its agar-degradation trait has attracted our attention. Here, the genome sequence of Paenibacillus sp. SSG-1, together with 76 previously sequenced strains, was comparatively studied. The results show that the pan-genome of Paenibacillus is open and indicate that the current taxonomy of this genus is incorrect. The incessant flux of gene repertoires resulting from the processes of gain and loss largely contributed to the difference in genomic content and genome size in Paenibacillus. Furthermore, a large number of genes gained are associated with carbohydrate transport and metabolism. It indicates that the evolution of glycometabolism is a key factor for the environmental adaptability of Paenibacillus species. Interestingly, through horizontal gene transfer, Paenibacillus sp. SSG-1 acquired an approximately 150 kb DNA fragment and shows an agar-degrading characteristic distinct from most other non-marine bacteria. This region may be transported in bacteria as a complete unit responsible for agar degradation. Taken together, these results provide insights into the evolutionary pattern of Paenibacillus and have implications for studies on the taxonomy and functional genomics of this genus.}, }
@article {pmid28720731, year = {2017}, author = {Card, RM and Cawthraw, SA and Nunez-Garcia, J and Ellis, RJ and Kay, G and Pallen, MJ and Woodward, MJ and Anjum, MF}, title = {An In Vitro Chicken Gut Model Demonstrates Transfer of a Multidrug Resistance Plasmid from Salmonella to Commensal Escherichia coli.}, journal = {mBio}, volume = {8}, number = {4}, pages = {}, pmid = {28720731}, issn = {2150-7511}, support = {MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Cecum/*microbiology ; Cefotaxime/pharmacology ; Chickens ; *Drug Resistance, Multiple, Bacterial ; Escherichia coli/drug effects/*genetics ; Gastrointestinal Microbiome/drug effects ; *Gene Transfer, Horizontal ; *Models, Theoretical ; *Plasmids ; Salmonella/drug effects/*genetics ; }, abstract = {The chicken gastrointestinal tract is richly populated by commensal bacteria that fulfill various beneficial roles for the host, including helping to resist colonization by pathogens. It can also facilitate the conjugative transfer of multidrug resistance (MDR) plasmids between commensal and pathogenic bacteria which is a significant public and animal health concern as it may affect our ability to treat bacterial infections. We used an in vitro chemostat system to approximate the chicken cecal microbiota, simulate colonization by an MDR Salmonella pathogen, and examine the dynamics of transfer of its MDR plasmid harboring several genes, including the extended-spectrum beta-lactamase blaCTX-M1 We also evaluated the impact of cefotaxime administration on plasmid transfer and microbial diversity. Bacterial community profiles obtained by culture-independent methods showed that Salmonella inoculation resulted in no significant changes to bacterial community alpha diversity and beta diversity, whereas administration of cefotaxime caused significant alterations to both measures of diversity, which largely recovered. MDR plasmid transfer from Salmonella to commensal Escherichia coli was demonstrated by PCR and whole-genome sequencing of isolates purified from agar plates containing cefotaxime. Transfer occurred to seven E. coli sequence types at high rates, even in the absence of cefotaxime, with resistant strains isolated within 3 days. Our chemostat system provides a good representation of bacterial interactions, including antibiotic resistance transfer in vivo It can be used as an ethical and relatively inexpensive approach to model dissemination of antibiotic resistance within the gut of any animal or human and refine interventions that mitigate its spread before employing in vivo studies.IMPORTANCE The spread of antimicrobial resistance presents a grave threat to public health and animal health and is affecting our ability to respond to bacterial infections. Transfer of antimicrobial resistance via plasmid exchange is of particular concern as it enables unrelated bacteria to acquire resistance. The gastrointestinal tract is replete with bacteria and provides an environment for plasmid transfer between commensals and pathogens. Here we use the chicken gut microbiota as an exemplar to model the effects of bacterial infection, antibiotic administration, and plasmid transfer. We show that transfer of a multidrug-resistant plasmid from the zoonotic pathogen Salmonella to commensal Escherichia coli occurs at a high rate, even in the absence of antibiotic administration. Our work demonstrates that the in vitro gut model provides a powerful screening tool that can be used to assess and refine interventions that mitigate the spread of antibiotic resistance in the gut before undertaking animal studies.}, }
@article {pmid28720494, year = {2017}, author = {Waddell, GL and Gilmer, CR and Taylor, NG and Reveral, JRS and Forconi, M and Fox, JL}, title = {The eukaryotic enzyme Bds1 is an alkyl but not an aryl sulfohydrolase.}, journal = {Biochemical and biophysical research communications}, volume = {491}, number = {2}, pages = {382-387}, pmid = {28720494}, issn = {1090-2104}, support = {P20 GM103499/GM/NIGMS NIH HHS/United States ; P20 RR016461/RR/NCRR NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Amino Acid Sequence ; Biocatalysis ; Cloning, Molecular ; Escherichia coli/*enzymology/genetics ; Gene Expression ; Gene Transfer, Horizontal ; Kinetics ; Recombinant Proteins/genetics/metabolism ; Saccharomyces cerevisiae/*enzymology/genetics ; Saccharomyces cerevisiae Proteins/genetics/*metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Substrate Specificity ; Sulfatases/genetics/*metabolism ; Sulfuric Acid Esters/*metabolism ; beta-Lactamases/genetics/*metabolism ; }, abstract = {The eukaryotic enzyme Bds1 in Saccharomyces cerevisiae is a metallo-β-lactamase-related enzyme evolutionarily originating from bacterial horizontal gene transfer that serves an unknown biological role. Previously, Bds1 was reported to be an alkyl and aryl sulfatase. However, we demonstrate here that Bds1 acts on primary alkyl sulfates (of 6-12 carbon atoms) but not the aryl sulfates p-nitrophenyl sulfate and p-nitrocatechol sulfate. The apparent catalytic rate constant for hydrolysis of the substrate 1-hexyl sulfate by Bds1 is over 100 times lower than that of the reaction catalyzed by its bacterial homolog SdsA1. We show that Bds1 shares a catalytic mechanism with SdsA1 in which the carbon atom of the sulfate ester is the subject of nucleophilic attack, rather than the sulfur atom, resulting in C-O bond lysis. In contrast to SdsA1 and another bacterial homolog with selectivity for secondary alkyl sulfates named Pisa1, Bds1 does not show any substantial activity towards secondary alkyl sulfates. Neither Bds1 nor SdsA1 have any significant activity towards a branched primary alkyl sulfate, primary and secondary steroid sulfates, or phosphate diesters. Therefore, the enzymes homologous to SdsA1 that have been identified and characterized thus far vary in their selectivity towards primary and secondary alkyl sulfates but do not exhibit aryl sulfatase activity.}, }
@article {pmid28716960, year = {2017}, author = {Díaz-Celis, C and Risca, VI and Hurtado, F and Polka, JK and Hansen, SD and Maturana, D and Lagos, R and Mullins, RD and Monasterio, O}, title = {Bacterial Tubulins A and B Exhibit Polarized Growth, Mixed-Polarity Bundling, and Destabilization by GTP Hydrolysis.}, journal = {Journal of bacteriology}, volume = {199}, number = {19}, pages = {}, pmid = {28716960}, issn = {1098-5530}, support = {R35 GM118119/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*metabolism ; Bacterial Proteins/physiology ; Cytoskeletal Proteins/*physiology ; Cytoskeleton/physiology ; Gene Transfer, Horizontal ; Guanosine Triphosphate/*metabolism ; Hydrolysis ; Kinetics ; Microscopy ; Microtubules/chemistry/metabolism ; Models, Molecular ; Polymerization ; Tubulin/chemistry/*physiology ; }, abstract = {Bacteria of the genus Prosthecobacter express homologs of eukaryotic α- and β-tubulin, called BtubA and BtubB (BtubA/B), that have been observed to assemble into filaments in the presence of GTP. BtubA/B polymers are proposed to be composed in vitro by two to six protofilaments in contrast to that in vivo, where they have been reported to form 5-protofilament tubes named bacterial microtubules (bMTs). The btubAB genes likely entered the Prosthecobacter lineage via horizontal gene transfer and may be derived from an early ancestor of the modern eukaryotic microtubule (MT). Previous biochemical studies revealed that BtubA/B polymerization is reversible and that BtubA/B folding does not require chaperones. To better understand BtubA/B filament behavior and gain insight into the evolution of microtubule dynamics, we characterized in vitro BtubA/B assembly using a combination of polymerization kinetics assays and microscopy. Like eukaryotic microtubules, BtubA/B filaments exhibit polarized growth with different assembly rates at each end. GTP hydrolysis stimulated by BtubA/B polymerization drives a stochastic mechanism of filament disassembly that occurs via polymer breakage and/or fast continuous depolymerization. We also observed treadmilling (continuous addition and loss of subunits at opposite ends) of BtubA/B filament fragments. Unlike MTs, polymerization of BtubA/B requires KCl, which reduces the critical concentration for BtubA/B assembly and induces it to form stable mixed-orientation bundles in the absence of any additional BtubA/B-binding proteins. The complex dynamics that we observe in stabilized and unstabilized BtubA/B filaments may reflect common properties of an ancestral eukaryotic tubulin polymer.IMPORTANCE Microtubules are polymers within all eukaryotic cells that perform critical functions; they segregate chromosomes, organize intracellular transport, and support the flagella. These functions rely on the remarkable range of tunable dynamic behaviors of microtubules. Bacterial tubulin A and B (BtubA/B) are evolutionarily related proteins that form polymers. They are proposed to be evolved from the ancestral eukaryotic tubulin, a missing link in microtubule evolution. Using microscopy and biochemical approaches to characterize BtubA/B assembly in vitro, we observed that they exhibit complex and structurally polarized dynamic behavior like eukaryotic microtubules but differ in how they self-associate into bundles and how this bundling affects their stability. Our results demonstrate the diversity of mechanisms through which tubulin homologs promote filament dynamics and monomer turnover.}, }
@article {pmid27703668, year = {2016}, author = {Koehorst, JJ and Saccenti, E and Schaap, PJ and Martins Dos Santos, VAP and Suarez-Diez, M}, title = {Protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics.}, journal = {F1000Research}, volume = {5}, number = {}, pages = {1987}, pmid = {27703668}, issn = {2046-1402}, abstract = {A functional comparative genome analysis is essential to understand the mechanisms underlying bacterial evolution and adaptation. Detection of functional orthologs using standard global sequence similarity methods faces several problems; the need for defining arbitrary acceptance thresholds for similarity and alignment length, lateral gene acquisition and the high computational cost for finding bi-directional best matches at a large scale. We investigated the use of protein domain architectures for large scale functional comparative analysis as an alternative method. The performance of both approaches was assessed through functional comparison of 446 bacterial genomes sampled at different taxonomic levels. We show that protein domain architectures provide a fast and efficient alternative to methods based on sequence similarity to identify groups of functionally equivalent proteins within and across taxonomic boundaries, and it is suitable for large scale comparative analysis. Running both methods in parallel pinpoints potential functional adaptations that may add to bacterial fitness.}, }
@article {pmid28708455, year = {2018}, author = {Alamos, P and Tello, M and Bustamante, P and Gutiérrez, F and Shmaryahu, A and Maldonado, J and Levicán, G and Orellana, O}, title = {Functionality of tRNAs encoded in a mobile genetic element from an acidophilic bacterium.}, journal = {RNA biology}, volume = {15}, number = {4-5}, pages = {518-527}, pmid = {28708455}, issn = {1555-8584}, mesh = {Acidithiobacillus/classification/*genetics/metabolism ; Aminoacylation ; Conjugation, Genetic ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genome, Bacterial ; *Interspersed Repetitive Sequences ; Mutation ; Nucleic Acid Conformation ; Phylogeny ; Protein Biosynthesis ; RNA, Transfer/*genetics/metabolism ; }, abstract = {The genome of the acidophilic, bioleaching bacterium Acidithiobacillus ferrooxidans, strain ATCC 23270, contains 95 predicted tRNA genes. Thirty-six of these genes (all 20 species) are clustered within an actively excising integrative-conjugative element (ICEAfe1). We speculated that these tRNA genes might have a role in adapting the bacterial tRNA pool to the codon usage of ICEAfe1 genes. To answer this question, we performed theoretical calculations of the global tRNA adaptation index to the entire A. ferrooxidans genome with and without the ICEAfe1 encoded tRNA genes. Based on these calculations, we observed that tRNAs encoded in ICEAfe1 negatively contribute to adapt the tRNA pool to the codon use in A. ferrooxidans. Although some of the tRNAs encoded in ICEAfe1 are functional in aminoacylation or protein synthesis, we found that they are expressed at low levels. These findings, along with the identification of a tRNA-like RNA encoded in the same cluster, led us to speculate that tRNA genes encoded in the mobile genetic element ICEAfe1 might have acquired mutations that would result in either inactivation or the acquisition of new functions.}, }
@article {pmid28706512, year = {2017}, author = {Machado, H and Gram, L}, title = {Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1204}, pmid = {28706512}, issn = {1664-302X}, abstract = {Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur, amino-acid usage, ANI), which allowed us to identify two misidentified strains. Genome analyses also revealed occurrence of higher and lower GC content clades, correlating with phylogenetic clusters. Pan- and core-genome analysis revealed the conservation of 25% of the genome throughout the genus, with a large and open pan-genome. The major source of genomic diversity could be traced to the smaller chromosome and plasmids. Several of the physiological traits studied in the genus did not correlate with phylogenetic data. Since horizontal gene transfer (HGT) is often suggested as a source of genetic diversity and a potential driver of genomic evolution in bacterial species, we looked into evidence of such in Photobacterium genomes. Genomic islands were the source of genomic differences between strains of the same species. Also, we found transposase genes and CRISPR arrays that suggest multiple encounters with foreign DNA. Presence of genomic exchange traits was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms.}, }
@article {pmid28705769, year = {2017}, author = {Tseng, SP and Wang, SF and Ma, L and Wang, TY and Yang, TY and Siu, LK and Chuang, YC and Lee, PS and Wang, JT and Wu, TL and Lin, JC and Lu, PL}, title = {The plasmid-mediated fosfomycin resistance determinants and synergy of fosfomycin and meropenem in carbapenem-resistant Klebsiella pneumoniae isolates in Taiwan.}, journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi}, volume = {50}, number = {5}, pages = {653-661}, doi = {10.1016/j.jmii.2017.03.003}, pmid = {28705769}, issn = {1995-9133}, mesh = {Bacterial Proteins/genetics ; Carbapenem-Resistant Enterobacteriaceae/*genetics/isolation &amp; purification ; DNA Transposable Elements/genetics ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/drug effects/*genetics ; Drug Synergism ; Fosfomycin/*pharmacology ; Genes, Bacterial/genetics ; Genotype ; Hospitals ; Humans ; Klebsiella Infections/epidemiology/microbiology ; Klebsiella pneumoniae/drug effects/*genetics ; Meropenem ; Microbial Sensitivity Tests ; Molecular Epidemiology ; Multilocus Sequence Typing ; Plasmids/*genetics ; Taiwan/epidemiology ; Thienamycins/*pharmacology ; beta-Lactamases/genetics ; }, abstract = {BACKGROUND: Epidemiology of fosfomycin susceptibility and the plasmid-mediated fosfomycinase genes of carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates in Taiwan remain unclear.<br><br>METHODS: 642 CRKP clinical isolates were collected from a nation-wide surveillance study (16 hospitals) in Taiwan in 2012-2013. Antimicrobial susceptibilities were determined. PFGE and MLST determined the clonal relatedness. Carbapenemases and fosfomycinases genes were detected by PCR, and their flanking regions were determined by PCR and sequencing. Synergistic activity of meropenem with fosfomycin was examined by the checkerboard method.<br><br>RESULTS: In total, 36.4% (234/642) of CRKP isolates in Taiwan were resistant to fosfomycin. Among 234 fosfomycin-resistant CRKP isolates, PFGE analysis revealed 81 pulsotypes. Pulsotype XXIII (n&#xa0;=&#xa0;63) was predominant and belonged to ST11. 71 had carbapnemases (65&#xa0;blaKPC-2-positive, 1 blaVIM-1-positive and 5 blaIMP-8-positive) and 62 had fosfomycinases (35 fosA3-positive and 27 foskp96-positive). Only 18.5% (5/27) of foskp96-positive isolates carried&#xa0;foskp96 and blaKPC-2, while 71.4% (25/35) of fosA3-positive isolates contained fosA3 and blaKPC-2. There were five types of flanking sequences for fosA3, and 85.7% (30/35) of fosA3 genes were flanked by IS26, suggesting possible horizontal gene transfer. Synergistic effect of&#xa0;fosfomycin and meropenem was observed in all 25 randomly selected pulsotype XXIII strains&#xa0;(100%; 25/25), even those containing fosfomycinase (48%, 12/25) or carbapnemase (96%, 24/25).<br><br>CONCLUSIONS: A clone (pulsotype XXIII, ST11) has been found to be prevailing among fosfomycin-resistant CRKP in Taiwan. According to the in&#xa0;vitro data, the combination of fosfomycin and meropenem is a potentially alternative choice.}, }
@article {pmid28705673, year = {2017}, author = {Xue, H and Wu, Z and Qiao, D and Tong, C and Zhao, X}, title = {Global acquisition of genetic material from different bacteria into the staphylococcal cassette chromosome elements of a Staphylococcus epidermidis isolate.}, journal = {International journal of antimicrobial agents}, volume = {50}, number = {4}, pages = {581-587}, doi = {10.1016/j.ijantimicag.2017.06.015}, pmid = {28705673}, issn = {1872-7913}, mesh = {Animals ; Bacterial Proteins/*genetics ; Cattle ; Clustered Regularly Interspaced Short Palindromic Repeats/*genetics ; DNA Restriction-Modification Enzymes/*genetics ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial/genetics ; Humans ; Metals, Heavy/pharmacology ; Methicillin Resistance/*genetics ; Methicillin-Resistant Staphylococcus aureus/genetics ; Microbial Sensitivity Tests ; Milk/microbiology ; Polyamines/pharmacology ; Sorbitol/metabolism ; Staphylococcus epidermidis/*genetics/isolation &amp; purification/pathogenicity ; Streptococcus/genetics ; Virulence/genetics ; beta-Lactams/pharmacology ; }, abstract = {Staphylococcus epidermidis has been suggested as a main reservoir of methicillin resistance and virulence genes facilitating the evolution of Staphylococcus aureus as a successful pathogen. However, it remains a mystery where and how S. epidermidis obtains these numerous genes to serve as the reservoir. In this study, methicillin-resistant S. epidermidis isolate NW32 from a mastitic milk sample was sequenced and its staphylococcal cassette chromosome (SCC) elements were characterised. The SCC composite island covered 3.5% of the genome and consisted of three intact SCC elements carrying resistance genes against β-lactam antibiotics, several heavy metals and polyamines as well as genes for utilisation of sorbitol as a carbon source. Analysis of the postulated evolutionary route suggested that the three SCC elements were assembled from genetic material from various bacterial species (staphylococci, streptococci, salinicocci and Lysinibacillus) from three habitats (human, soil and cow) in different countries (Asia, North America, South America and Europe). We propose that the hsdS restriction-modification profile and the lack of CRISPR (clustered regularly interspaced short palindromic repeat) sequences in this bacterium may facilitate the genetic exchange of SCC elements among different staphylococcal species.}, }
@article {pmid28704543, year = {2017}, author = {Pérez-Morales, D and Banda, MM and Chau, NYE and Salgado, H and Martínez-Flores, I and Ibarra, JA and Ilyas, B and Coombes, BK and Bustamante, VH}, title = {The transcriptional regulator SsrB is involved in a molecular switch controlling virulence lifestyles of Salmonella.}, journal = {PLoS pathogens}, volume = {13}, number = {7}, pages = {e1006497}, pmid = {28704543}, issn = {1553-7374}, mesh = {Animals ; Bacterial Proteins/genetics/*metabolism ; *Gene Expression Regulation, Bacterial ; Genomic Islands ; Humans ; Mice ; Salmonella typhimurium/genetics/*metabolism/*pathogenicity ; Transcription Factors/genetics/*metabolism ; Virulence ; }, abstract = {The evolution of bacterial pathogenicity, heavily influenced by horizontal gene transfer, provides new virulence factors and regulatory connections that alter bacterial phenotypes. Salmonella pathogenicity islands 1 and 2 (SPI-1 and SPI-2) are chromosomal regions that were acquired at different evolutionary times and are essential for Salmonella virulence. In the intestine of mammalian hosts, Salmonella expresses the SPI-1 genes that mediate its invasion to the gut epithelium. Once inside the cells, Salmonella down-regulates the SPI-1 genes and induces the expression of the SPI-2 genes, which favor its intracellular replication. The mechanism by which the invasion machinery is deactivated following successful invasion of host cells is not known. Here, we show that the SPI-2 encoded transcriptional regulator SsrB, which positively controls SPI-2, acts as a dual regulator that represses expression of SPI-1 during intracellular stages of infection. The mechanism of this SPI-1 repression by SsrB was direct and acts upon the hilD and hilA regulatory genes. The phenotypic effect of this molecular switch activity was a significant reduction in invasion ability of S. enterica serovar Typhimurium while promoting the expression of genes required for intracellular survival. During mouse infections, Salmonella mutants lacking SsrB had high levels of hilA (SPI-1) transcriptional activity whereas introducing a constitutively active SsrB led to significant hilA repression. Thus, our results reveal a novel SsrB-mediated mechanism of transcriptional crosstalk between SPI-1 and SPI-2 that helps Salmonella transition to the intracellular lifestyle.}, }
@article {pmid28698278, year = {2017}, author = {Silas, S and Makarova, KS and Shmakov, S and Páez-Espino, D and Mohr, G and Liu, Y and Davison, M and Roux, S and Krishnamurthy, SR and Fu, BXH and Hansen, LL and Wang, D and Sullivan, MB and Millard, A and Clokie, MR and Bhaya, D and Lambowitz, AM and Kyrpides, NC and Koonin, EV and Fire, AZ}, title = {On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires.}, journal = {mBio}, volume = {8}, number = {4}, pages = {}, pmid = {28698278}, issn = {2150-7511}, support = {R01 GM037706/GM/NIGMS NIH HHS/United States ; R01 GM037949/GM/NIGMS NIH HHS/United States ; T32 GM007790/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {CRISPR-Associated Proteins/genetics ; *CRISPR-Cas Systems ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Gene Transfer, Horizontal ; Genes, Bacterial ; Phylogeny ; RNA ; RNA-Directed DNA Polymerase/*genetics ; Spirulina/*genetics ; }, abstract = {Cas1 integrase is the key enzyme of the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas adaptation module that mediates acquisition of spacers derived from foreign DNA by CRISPR arrays. In diverse bacteria, the cas1 gene is fused (or adjacent) to a gene encoding a reverse transcriptase (RT) related to group II intron RTs. An RT-Cas1 fusion protein has been recently shown to enable acquisition of CRISPR spacers from RNA. Phylogenetic analysis of the CRISPR-associated RTs demonstrates monophyly of the RT-Cas1 fusion, and coevolution of the RT and Cas1 domains. Nearly all such RTs are present within type III CRISPR-Cas loci, but their phylogeny does not parallel the CRISPR-Cas type classification, indicating that RT-Cas1 is an autonomous functional module that is disseminated by horizontal gene transfer and can function with diverse type III systems. To compare the sequence pools sampled by RT-Cas1-associated and RT-lacking CRISPR-Cas systems, we obtained samples of a commercially grown cyanobacterium-Arthrospira platensis Sequencing of the CRISPR arrays uncovered a highly diverse population of spacers. Spacer diversity was particularly striking for the RT-Cas1-containing type III-B system, where no saturation was evident even with millions of sequences analyzed. In contrast, analysis of the RT-lacking type III-D system yielded a highly diverse pool but reached a point where fewer novel spacers were recovered as sequencing depth was increased. Matches could be identified for a small fraction of the non-RT-Cas1-associated spacers, and for only a single RT-Cas1-associated spacer. Thus, the principal source(s) of the spacers, particularly the hypervariable spacer repertoire of the RT-associated arrays, remains unknown.IMPORTANCE While the majority of CRISPR-Cas immune systems adapt to foreign genetic elements by capturing segments of invasive DNA, some systems carry reverse transcriptases (RTs) that enable adaptation to RNA molecules. From analysis of available bacterial sequence data, we find evidence that RT-based RNA adaptation machinery has been able to join with CRISPR-Cas immune systems in many, diverse bacterial species. To investigate whether the abilities to adapt to DNA and RNA molecules are utilized for defense against distinct classes of invaders in nature, we sequenced CRISPR arrays from samples of commercial-scale open-air cultures of Arthrospira platensis, a cyanobacterium that contains both RT-lacking and RT-containing CRISPR-Cas systems. We uncovered a diverse pool of naturally occurring immune memories, with the RT-lacking locus acquiring a number of segments matching known viral or bacterial genes, while the RT-containing locus has acquired spacers from a distinct sequence pool for which the source remains enigmatic.}, }
@article {pmid28696425, year = {2017}, author = {Mackelprang, R and Burkert, A and Haw, M and Mahendrarajah, T and Conaway, CH and Douglas, TA and Waldrop, MP}, title = {Microbial survival strategies in ancient permafrost: insights from metagenomics.}, journal = {The ISME journal}, volume = {11}, number = {10}, pages = {2305-2318}, pmid = {28696425}, issn = {1751-7370}, mesh = {Bacteria/classification/*genetics/*growth &amp; development/isolation &amp; purification ; Freezing ; Metagenomics ; Microbial Viability ; Permafrost/chemistry/*microbiology ; Phylogeny ; Salinity ; Temperature ; }, abstract = {In permafrost (perennially frozen ground) microbes survive oligotrophic conditions, sub-zero temperatures, low water availability and high salinity over millennia. Viable life exists in permafrost tens of thousands of years old but we know little about the metabolic and physiological adaptations to the challenges presented by life in frozen ground over geologic time. In this study we asked whether increasing age and the associated stressors drive adaptive changes in community composition and function. We conducted deep metagenomic and 16 S rRNA gene sequencing across a Pleistocene permafrost chronosequence from 19 000 to 33 000 years before present (kyr). We found that age markedly affected community composition and reduced diversity. Reconstruction of paleovegetation from metagenomic sequence suggests vegetation differences in the paleo record are not responsible for shifts in community composition and function. Rather, we observed shifts consistent with long-term survival strategies in extreme cryogenic environments. These include increased reliance on scavenging detrital biomass, horizontal gene transfer, chemotaxis, dormancy, environmental sensing and stress response. Our results identify traits that may enable survival in ancient cryoenvironments with no influx of energy or new materials.}, }
@article {pmid28693085, year = {2017}, author = {Bai, L and Pan, Z and Xu, J and Li, FQ}, title = {[Molecular characterization genetic diversity of extended-spectrum β-lactamases-harboring conjugative plasmids identified in multi-drug resistant Escherichia coli isolated from food in China].}, journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]}, volume = {51}, number = {7}, pages = {610-614}, doi = {10.3760/cma.j.issn.0253-9624.2017.07.007}, pmid = {28693085}, issn = {0253-9624}, mesh = {Bacterial Typing Techniques ; Cefotaxime ; China ; Drug Resistance, Multiple, Bacterial/genetics ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/classification/*genetics ; Escherichia coli Infections/*epidemiology ; Escherichia coli Proteins ; Genes, Bacterial ; Genetic Variation ; Microbial Sensitivity Tests ; *Plasmids ; Polymerase Chain Reaction ; beta-Lactamases/*genetics ; }, abstract = {Objective: The purpose of this study was to investigate the molecular characteristics of ESBL-encoding conjugative plasmid identified in muti-drug resistant Escherichia coli isolated from food. Methods: 465 Escherichia coli isolates were collected from national foodborne disease surveillance net from 2013 to 2014 (salad, n=159; meat, n=102; processed meat, n=95; cakes/rice, n=46; cooked dish, n=63). ESBLs strain was detected by Mueller-Hinton agar plate, and then its drug resistance was tested by agar dilution method. Polymerase chain reaction (PCR) and DNA sequencing were performed to identify the corresponding ESBL genes. Plasmids were typed by PCR-based replicon typing and their characteristics were determined by S1-nuclease pulsed-field gel electrophoresis method. Broth mating assays were carried out for all isolates to determine whether the ESBL marker could be transferred by conjugation. Results: 12 E. coli were found to be resistant to cefotaxime, and all of which were confirmed as ESBLs. The 12 isolates all carried different types of CTX-M genes resistant to drug, and 7 of which carried TEM type as well. All 12 isolates contained at least one plasmid and some had four plasmids, with size ranging from 47-to 220-kb by S1-PFGE anaylsis. Seven isolates demonstrated the ability to transfer their cefotaxime resistance marker to the recotper strain J53 by only one plasmid. Conclusion: This study highlights the diversity of the multi-drug resistant E. coli and also the diversity of ESBL genes in China. Plasmids carrying these genes poses a serious threat to food safety in China.}, }
@article {pmid28692019, year = {2017}, author = {Mavrich, TN and Hatfull, GF}, title = {Bacteriophage evolution differs by host, lifestyle and genome.}, journal = {Nature microbiology}, volume = {2}, number = {}, pages = {17112}, pmid = {28692019}, issn = {2058-5276}, support = {R01 GM116884/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteriophages/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Variation ; Genome, Viral ; Humans ; Phylogeny ; }, abstract = {Bacteriophages play key roles in microbial evolution[1,2], marine nutrient cycling[3] and human disease[4]. Phages are genetically diverse, and their genome architectures are characteristically mosaic, driven by horizontal gene transfer with other phages and host genomes[5]. As a consequence, phage evolution is complex and their genomes are composed of genes with distinct and varied evolutionary histories[6,7]. However, there are conflicting perspectives on the roles of mosaicism and the extent to which it generates a spectrum of genome diversity[8] or genetically discrete populations[9,10]. Here, we show that bacteriophages evolve within two general evolutionary modes that differ in the extent of horizontal gene transfer by an order of magnitude. Temperate phages distribute into high and low gene flux modes, whereas lytic phages share only the lower gene flux mode. The evolutionary modes are also a function of the bacterial host and different proportions of temperate and lytic phages are distributed in either mode depending on the host phylum. Groups of genetically related phages fall into either the high or low gene flux modes, suggesting there are genetic as well as ecological drivers of horizontal gene transfer rates. Consequently, genome mosaicism varies depending on the host, lifestyle and genetic constitution of phages.}, }
@article {pmid28690319, year = {2017}, author = {Veening, JW and Blokesch, M}, title = {Interbacterial predation as a strategy for DNA acquisition in naturally competent bacteria.}, journal = {Nature reviews. Microbiology}, volume = {15}, number = {10}, pages = {621-629}, pmid = {28690319}, issn = {1740-1534}, support = {309064/ERC_/European Research Council/International ; }, mesh = {Biological Transport ; DNA Transformation Competence/*genetics ; DNA, Bacterial/*genetics ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal/*genetics ; Streptococcus pneumoniae/*genetics ; Transformation, Bacterial/*genetics ; Type VI Secretion Systems/genetics ; Vibrio cholerae/*genetics ; }, abstract = {Natural competence enables bacteria to take up exogenous DNA. The evolutionary function of natural competence remains controversial, as imported DNA can act as a source of substrates or can be integrated into the genome. Exogenous homologous DNA can also be used for genome repair. In this Opinion article, we propose that predation of non-related neighbouring bacteria coupled with competence regulation might function as an active strategy for DNA acquisition. Competence-dependent kin-discriminated killing has been observed in the unrelated bacteria Vibrio cholerae and Streptococcus pneumoniae. Importantly, both the regulatory networks and the mode of action of neighbour predation differ between these organisms, with V. cholerae using a type VI secretion system and S. pneumoniae secreting bacteriocins. We argue that the forced release of DNA from killed bacteria and the transfer of non-clonal genetic material have important roles in bacterial evolution.}, }
@article {pmid28689895, year = {2017}, author = {Kim, JS and Kim, S and Park, J and Shin, E and Yun, YS and Lee, DY and Kwak, HS and Seong, WK and Chung, GT and Kim, J}, title = {Plasmid-mediated transfer of CTX-M-55 extended-spectrum beta-lactamase among different strains of Salmonella and Shigella spp. in the Republic of Korea.}, journal = {Diagnostic microbiology and infectious disease}, volume = {89}, number = {1}, pages = {86-88}, doi = {10.1016/j.diagmicrobio.2017.03.014}, pmid = {28689895}, issn = {1879-0070}, mesh = {Animals ; *Gene Transfer, Horizontal ; Humans ; Plasmids/*analysis/classification ; Republic of Korea ; Salmonella/*enzymology/*genetics/isolation &amp; purification ; Shigella/*enzymology/*genetics/isolation &amp; purification ; beta-Lactamases/*genetics ; }, abstract = {We screened 10 CTX-M-55-producing Shigella and Salmonella isolates from a national surveillance in Korea. The blaCTX-M-55 was located on the IncI1 (n=5), IncA/C (n=4) and IncZ (n=1) plasmids, downstream of ISEcp1, IS26-ISEcp1 and ISEcp1-IS5 sequences, respectively. These results indicate that CTX-M-55 has disseminated to other bacteria by lateral plasmid transfer.}, }
@article {pmid28684751, year = {2017}, author = {Huang, H and Yu, W and Wang, R and Li, H and Xie, H and Wang, S}, title = {Genomic and transcriptomic analyses of Agrobacterium tumefaciens S33 reveal the molecular mechanism of a novel hybrid nicotine-degrading pathway.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {4813}, pmid = {28684751}, issn = {2045-2322}, mesh = {Agrobacterium tumefaciens/*genetics/metabolism ; Biodegradation, Environmental ; Gene Expression Profiling ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Metabolic Networks and Pathways/*genetics ; Multigene Family ; Nicotine/*metabolism ; Ochrobactrum/genetics/metabolism ; Plasmids/chemistry/metabolism ; Pyridines/metabolism ; Pyrrolidines/metabolism ; Nicotiana/metabolism ; *Transcriptome ; }, abstract = {Agrobacterium tumefaciens S33 is able to degrade nicotine via a novel hybrid of the pyridine and pyrrolidine pathways. It can be utilized to remove nicotine from tobacco wastes and transform nicotine into important functionalized pyridine precursors for some valuable drugs and insecticides. However, the molecular mechanism of the hybrid pathway is still not completely clear. Here we report the genome analysis of strain S33 and its transcriptomes grown in glucose-ammonium medium and nicotine medium. The complete gene cluster involved in nicotine catabolism was found to be located on a genomic island composed of genes functionally similar but not in sequences to those of the pyridine and pyrrolidine pathways, as well as genes encoding plasmid partitioning and replication initiation proteins, conjugal transfer proteins and transposases. This suggests that the evolution of this hybrid pathway is not a simple fusion of the genes involved in the two pathways, but the result of a complicated lateral gene transfer. In addition, other genes potentially involved in the hybrid pathway could include those responsible for substrate sensing and transport, transcription regulation and electron transfer during nicotine degradation. This study provides new insights into the molecular mechanism of the novel hybrid pathway for nicotine degradation.}, }
@article {pmid28684374, year = {2017}, author = {Negahdaripour, M and Nezafat, N and Hajighahramani, N and Rahmatabadi, SS and Ghasemi, Y}, title = {Investigating CRISPR-Cas systems in Clostridium botulinum via bioinformatics tools.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {54}, number = {}, pages = {355-373}, doi = {10.1016/j.meegid.2017.06.027}, pmid = {28684374}, issn = {1567-7257}, mesh = {Botulinum Toxins/genetics ; *CRISPR-Cas Systems ; Clostridium botulinum/chemistry/*genetics ; Computational Biology/*methods ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial ; Phylogeny ; RNA, Bacterial/chemistry ; }, abstract = {The Clustered regularly interspaced short palindromic repeats (CRISPR) systems are a type of innate immunity found in some prokaryotes, which protect them against alien genetic elements by targeting foreign nucleic acids. Some other functions are also attributed to these systems. Clostridium botulinum bacteria produce botulinum neurotoxins (BoNT), one of the deadliest known toxins for humans and some animals. Food poisoning due to these bacteria is still a challenge in food industries. On the other hand, BoNT has been widely investigated for therapeutic applications including different muscle disorders. Bont genes may be located on bacterial chromosomes, plasmids, or even prophages. Generally, the genomes of Cl. botulinum show a high level of plasticity. In order to investigate the presence and characteristics of CRISPRs in these anaerobe bacteria, an in silico study on 113 CRISPR arrays identified in 38 Cl. botulinum strains was performed. A high occurrence of CRISPR arrays (80%) were found, with a remarkable frequency on plasmids. Several (CRISPR-associated) Cas proteins from different types were recognized in the studied strains, which were mostly Cas6. The CRISPR-Cas systems were identified as type I or III, but no type II. The spacers showed more homology with bacterial plasmids than phages. Active CRISPR-Cas systems can prevent the transfer of foreign genes, which may also include bont genes. This study provides the first insight into the probable roles of CRISPR-Cas systems in Cl. botulinum strains such as toxigenicity.}, }
@article {pmid28683122, year = {2017}, author = {Klancher, CA and Hayes, CA and Dalia, AB}, title = {The nucleoid occlusion protein SlmA is a direct transcriptional activator of chitobiose utilization in Vibrio cholerae.}, journal = {PLoS genetics}, volume = {13}, number = {7}, pages = {e1006877}, pmid = {28683122}, issn = {1553-7404}, support = {K22 AI118863/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/*genetics ; Binding Sites ; Chitin/metabolism ; Cholera/*genetics/microbiology ; DNA-Binding Proteins/genetics ; Disaccharides/biosynthesis/*genetics ; Escherichia coli/genetics ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal/genetics ; Humans ; Operon/*genetics ; Point Mutation ; Promoter Regions, Genetic ; Transcriptional Activation/*genetics ; Vibrio cholerae/*genetics/pathogenicity ; }, abstract = {Chitin utilization by the cholera pathogen Vibrio cholerae is required for its persistence and evolution via horizontal gene transfer in the marine environment. Genes involved in the uptake and catabolism of the chitin disaccharide chitobiose are encoded by the chb operon. The orphan sensor kinase ChiS is critical for regulation of this locus, however, the mechanisms downstream of ChiS activation that result in expression of the chb operon are poorly understood. Using an unbiased transposon mutant screen, we uncover that the nucleoid occlusion protein SlmA is a regulator of the chb operon. SlmA has not previously been implicated in gene regulation. Also, SlmA is a member of the TetR family of proteins, which are generally transcriptional repressors. In vitro, we find that SlmA binds directly to the chb operon promoter, and in vivo, we show that this interaction is required for transcriptional activation of this locus and for chitobiose utilization. Using point mutations that disrupt distinct functions of SlmA, we find that DNA-binding, but not nucleoid occlusion, is critical for transcriptional activation. This study identifies a novel role for SlmA as a transcriptional regulator in V. cholerae in addition to its established role as a cell division licensing factor.}, }
@article {pmid28682556, year = {2017}, author = {Keke, Z and Xuedong, Z and Xin, X}, title = {[The origin of hydrogen peroxide in oral cavity and its role in oral microecology balance].}, journal = {Hua xi kou qiang yi xue za zhi = Huaxi kouqiang yixue zazhi = West China journal of stomatology}, volume = {35}, number = {2}, pages = {215-220}, pmid = {28682556}, issn = {1000-1182}, mesh = {Biofilms ; *Hydrogen Peroxide ; *Mouth ; Streptococcus ; }, abstract = {Hydrogen peroxide, an important antimicrobial agent in oral cavity, plays a significant role in the balance of oral microecology. At the early stage of biofilm formation, about 80% of the detected initial colonizers belong to the genus Streptococcus. These oral streptococci use different oxidase to produce hydrogen peroxide. Recent studies showed that the produced hydrogen peroxide plays a critical role in modulating oral microecology. Hydrogen peroxide modulates biofilm development attributed to its growth inhibitory nature. Hydrogen peroxide production is closely associated with extracellular DNA(eDNA) release from microbe and the development of its competent cell which are critical for biofilm development and also serves as source for horizontal gene transfer. Microbe also can reduce the damage to themselves through several detoxification mechanisms. Moreover, hydrogen peroxide is also involved in the regulation of interactions between oral microorganisms and host. Taken together, hydrogen peroxide is an imperative ecological factor that contributes to the microbial equilibrium in the oral cavity. Here we will give a brief review of both the origin and the function in the oral microecology balance of hydrogen peroxide.}, }
@article {pmid28679522, year = {2017}, author = {Weterings, V and Bosch, T and Witteveen, S and Landman, F and Schouls, L and Kluytmans, J}, title = {Next-Generation Sequence Analysis Reveals Transfer of Methicillin Resistance to a Methicillin-Susceptible Staphylococcus aureus Strain That Subsequently Caused a Methicillin-Resistant Staphylococcus aureus Outbreak: a Descriptive Study.}, journal = {Journal of clinical microbiology}, volume = {55}, number = {9}, pages = {2808-2816}, pmid = {28679522}, issn = {1098-660X}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics ; DNA, Bacterial/genetics ; Disease Outbreaks ; Drug Resistance, Multiple, Bacterial/*genetics ; Female ; Fusidic Acid/pharmacology ; Gene Transfer, Horizontal/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Interspersed Repetitive Sequences/genetics ; Male ; Methicillin/pharmacology ; Methicillin Resistance/*genetics ; Methicillin-Resistant Staphylococcus aureus/drug effects/*genetics ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Netherlands ; Penicillin-Binding Proteins/*genetics ; Polymorphism, Single Nucleotide/genetics ; Sequence Analysis, DNA ; Staphylococcal Infections/microbiology/*transmission ; }, abstract = {Resistance to methicillin in Staphylococcus aureus is caused primarily by the mecA gene, which is carried on a mobile genetic element, the staphylococcal cassette chromosome mec (SCCmec). Horizontal transfer of this element is supposed to be an important factor in the emergence of new clones of methicillin-resistant Staphylococcus aureus (MRSA) but has been rarely observed in real time. In 2012, an outbreak occurred involving a health care worker (HCW) and three patients, all carrying a fusidic acid-resistant MRSA strain. The husband of the HCW was screened for MRSA carriage, but only a methicillin-susceptible S. aureus (MSSA) strain, which was also resistant to fusidic acid, was detected. Multiple-locus variable-number tandem-repeat analysis (MLVA) typing showed that both the MSSA and MRSA isolates were MT4053-MC0005. This finding led to the hypothesis that the MSSA strain acquired the SCCmec and subsequently caused an outbreak. To support this hypothesis, next-generation sequencing of the MSSA and MRSA isolates was performed. This study showed that the MSSA isolate clustered closely with the outbreak isolates based on whole-genome multilocus sequence typing and single-nucleotide polymorphism (SNP) analysis, with a genetic distance of 17 genes and 44 SNPs, respectively. Remarkably, there were relatively large differences in the mobile genetic elements in strains within and between individuals. The limited genetic distance between the MSSA and MRSA isolates in combination with a clear epidemiologic link supports the hypothesis that the MSSA isolate acquired a SCCmec and that the resulting MRSA strain caused an outbreak.}, }
@article {pmid28676809, year = {2017}, author = {Huang, Y and Wang, J and Yang, Y and Fan, C and Chen, J}, title = {Phylogenomic Analysis and Dynamic Evolution of Chloroplast Genomes in Salicaceae.}, journal = {Frontiers in plant science}, volume = {8}, number = {}, pages = {1050}, pmid = {28676809}, issn = {1664-462X}, abstract = {Chloroplast genomes of plants are highly conserved in both gene order and gene content. Analysis of the whole chloroplast genome is known to provide much more informative DNA sites and thus generates high resolution for plant phylogenies. Here, we report the complete chloroplast genomes of three Salix species in family Salicaceae. Phylogeny of Salicaceae inferred from complete chloroplast genomes is generally consistent with previous studies but resolved with higher statistical support. Incongruences of phylogeny, however, are observed in genus Populus, which most likely results from homoplasy. By comparing three Salix chloroplast genomes with the published chloroplast genomes of other Salicaceae species, we demonstrate that the synteny and length of chloroplast genomes in Salicaceae are highly conserved but experienced dynamic evolution among species. We identify seven positively selected chloroplast genes in Salicaceae, which might be related to the adaptive evolution of Salicaceae species. Comparative chloroplast genome analysis within the family also indicates that some chloroplast genes are lost or became pseudogenes, infer that the chloroplast genes horizontally transferred to the nucleus genome. Based on the complete nucleus genome sequences from two Salicaceae species, we remarkably identify that the entire chloroplast genome is indeed transferred and integrated to the nucleus genome in the individual of the reference genome of P. trichocarpa at least once. This observation, along with presence of the large nuclear plastid DNA (NUPTs) and NUPTs-containing multiple chloroplast genes in their original order in the chloroplast genome, favors the DNA-mediated hypothesis of organelle to nucleus DNA transfer. Overall, the phylogenomic analysis using chloroplast complete genomes clearly elucidates the phylogeny of Salicaceae. The identification of positively selected chloroplast genes and dynamic chloroplast-to-nucleus gene transfers in Salicaceae provide resources to better understand the successful adaptation of Salicaceae species.}, }
@article {pmid28676794, year = {2017}, author = {Colavecchio, A and Cadieux, B and Lo, A and Goodridge, LD}, title = {Bacteriophages Contribute to the Spread of Antibiotic Resistance Genes among Foodborne Pathogens of the Enterobacteriaceae Family - A Review.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1108}, pmid = {28676794}, issn = {1664-302X}, abstract = {Foodborne illnesses continue to have an economic impact on global health care systems. There is a growing concern regarding the increasing frequency of antibiotic resistance in foodborne bacterial pathogens and how such resistance may affect treatment outcomes. In an effort to better understand how to reduce the spread of resistance, many research studies have been conducted regarding the methods by which antibiotic resistance genes are mobilized and spread between bacteria. Transduction by bacteriophages (phages) is one of many horizontal gene transfer mechanisms, and recent findings have shown phage-mediated transduction to be a significant contributor to dissemination of antibiotic resistance genes. Here, we review the viability of transduction as a contributing factor to the dissemination of antibiotic resistance genes in foodborne pathogens of the Enterobacteriaceae family, including non-typhoidal Salmonella and Shiga toxin-producing Escherichia coli, as well as environmental factors that increase transduction of antibiotic resistance genes.}, }
@article {pmid28674017, year = {2017}, author = {Bryon, A and Kurlovs, AH and Dermauw, W and Greenhalgh, R and Riga, M and Grbić, M and Tirry, L and Osakabe, M and Vontas, J and Clark, RM and Van Leeuwen, T}, title = {Disruption of a horizontally transferred phytoene desaturase abolishes carotenoid accumulation and diapause in Tetranychus urticae.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {29}, pages = {E5871-E5880}, pmid = {28674017}, issn = {1091-6490}, support = {T32 GM007464/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Arthropod Proteins/*genetics/metabolism ; Carotenoids/genetics/*metabolism ; Diapause/genetics/*physiology ; Female ; Gene Transfer, Horizontal ; Genetic Complementation Test ; Male ; Mutation ; Oxidoreductases/*genetics/metabolism ; Pigmentation/genetics ; Tetranychidae/genetics/metabolism/*physiology ; }, abstract = {Carotenoids underlie many of the vibrant yellow, orange, and red colors in animals, and are involved in processes ranging from vision to protection from stresses. Most animals acquire carotenoids from their diets because de novo synthesis of carotenoids is primarily limited to plants and some bacteria and fungi. Recently, sequencing projects in aphids and adelgids, spider mites, and gall midges identified genes with homology to fungal sequences encoding de novo carotenoid biosynthetic proteins like phytoene desaturase. The finding of horizontal gene transfers of carotenoid biosynthetic genes to three arthropod lineages was unprecedented; however, the relevance of the transfers for the arthropods that acquired them has remained largely speculative, which is especially true for spider mites that feed on plant cell contents, a known source of carotenoids. Pigmentation in spider mites results solely from carotenoids. Using a combination of genetic approaches, we show that mutations in a single horizontally transferred phytoene desaturase result in complete albinism in the two-spotted spider mite, Tetranychus urticae, as well as in the citrus red mite, Panonychus citri Further, we show that phytoene desaturase activity is essential for photoperiodic induction of diapause in an overwintering strain of T. urticae, consistent with a role for this enzyme in provisioning provitamin A carotenoids required for light perception. Carotenoid biosynthetic genes of fungal origin have therefore enabled some mites to forgo dietary carotenoids, with endogenous synthesis underlying their intense pigmentation and ability to enter diapause, a key to the global distribution of major spider mite pests of agriculture.}, }
@article {pmid28672159, year = {2017}, author = {Gilbert, C and Cordaux, R}, title = {Viruses as vectors of horizontal transfer of genetic material in eukaryotes.}, journal = {Current opinion in virology}, volume = {25}, number = {}, pages = {16-22}, doi = {10.1016/j.coviro.2017.06.005}, pmid = {28672159}, issn = {1879-6265}, mesh = {Animals ; *DNA Transposable Elements ; Eukaryota/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genetic Vectors ; Host-Pathogen Interactions/genetics ; Mice ; Phylogeny ; Viruses/*genetics ; }, abstract = {Horizontal transfer (HT) of genetic material, mainly transposable elements, is increasingly recognized as an important factor shaping eukaryote genomes. Yet our understanding of the mechanisms and vectors underpinning these transfers is still limited. It has been proposed that such transfers may be facilitated by viruses, because they typically inject their genomes into host cells to replicate and they can be horizontally transmitted between their hosts. Recent evidence from high throughput sequencing of viral populations and paleovirology shows that both virus-to-host and host-to-virus gene flow can be common in a variety of eukaryote lineages. We argue that such studies reinforce the hypothesis of viruses as major vectors of HT in eukaryotes.}, }
@article {pmid28671948, year = {2017}, author = {Breuer, RJ and Bandyopadhyay, A and O'Brien, SA and Barnes, AMT and Hunter, RC and Hu, WS and Dunny, GM}, title = {Stochasticity in the enterococcal sex pheromone response revealed by quantitative analysis of transcription in single cells.}, journal = {PLoS genetics}, volume = {13}, number = {7}, pages = {e1006878}, pmid = {28671948}, issn = {1553-7404}, support = {R35 GM118079/GM/NIGMS NIH HHS/United States ; T32 GM008347/GM/NIGMS NIH HHS/United States ; R01 GM081388/GM/NIGMS NIH HHS/United States ; R01 GM049530/GM/NIGMS NIH HHS/United States ; T32 HL007741/HL/NHLBI NIH HHS/United States ; }, mesh = {Drug Resistance, Bacterial/genetics ; Enterococcus faecalis/drug effects/*genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; In Situ Hybridization, Fluorescence ; Pheromones/*genetics ; Plasmids/genetics ; Sex Attractants/*genetics ; Single-Cell Analysis ; }, abstract = {In Enterococcus faecalis, sex pheromone-mediated transfer of antibiotic resistance plasmids can occur under unfavorable conditions, for example, when inducing pheromone concentrations are low and inhibiting pheromone concentrations are high. To better understand this paradox, we adapted fluorescence in situ hybridization chain reaction (HCR) methodology for simultaneous quantification of multiple E. faecalis transcripts at the single cell level. We present direct evidence for variability in the minimum period, maximum response level, and duration of response of individual cells to a specific inducing condition. Tracking of induction patterns of single cells temporally using a fluorescent reporter supported HCR findings. It also revealed subpopulations of rapid responders, even under low inducing pheromone concentrations where the overall response of the entire population was slow. The strong, rapid induction of small numbers of cells in cultures exposed to low pheromone concentrations is in agreement with predictions of a stochastic model of the enterococcal pheromone response. The previously documented complex regulatory circuitry controlling the pheromone response likely contributes to stochastic variation in this system. In addition to increasing our basic understanding of the biology of a horizontal gene transfer system regulated by cell-cell signaling, demonstration of the stochastic nature of the pheromone response also impacts any future efforts to develop therapeutic agents targeting the system. Quantitative single cell analysis using HCR also has great potential to elucidate important bacterial regulatory mechanisms not previously amenable to study at the single cell level, and to accelerate the pace of functional genomic studies.}, }
@article {pmid28669811, year = {2017}, author = {Haskett, TL and Ramsay, JP and Bekuma, AA and Sullivan, JT and O'Hara, GW and Terpolilli, JJ}, title = {Evolutionary persistence of tripartite integrative and conjugative elements.}, journal = {Plasmid}, volume = {92}, number = {}, pages = {30-36}, doi = {10.1016/j.plasmid.2017.06.001}, pmid = {28669811}, issn = {1095-9890}, mesh = {Base Sequence ; *Conjugation, Genetic ; *DNA Transposable Elements ; *Evolution, Molecular ; Genomic Islands ; Mesorhizobium/genetics ; Plants/microbiology ; Recombination, Genetic ; Symbiosis ; }, abstract = {Integrative and conjugative elements (ICEs) are generally regarded as regions of contiguous DNA integrated within a bacterial genome that are capable of excision and horizontal transfer via conjugation. We recently characterized a unique group of ICEs present in Mesorhizobium spp., which exist as three entirely separate but inextricably linked chromosomal regions termed α, β and γ. These regions occupy three different recombinase attachment (att) sites; however, they do not excise independently. Rather, they recombine the host chromosome to form a single contiguous region prior to excision and conjugative transfer. Like the single-part ICE carried by M. loti R7A (ICEMlSym[R7A]), these "tripartite" ICEs (ICE[3]s) are widespread throughout the Mesorhizobium genus and enable strains to form nitrogen-fixing symbioses with a variety of legumes. ICE[3]s have likely evolved following recombination between three separate ancestral integrative elements, however, the persistence of ICE[3] structure in diverse mesorhizobia is perplexing due to its seemingly unnecessary complexity. In this study, examination of ICE[3]s revealed that most symbiosis genes are carried on the large α fragment. Some ICE[3]-β and γ regions also carry genes that potentially contribute to the symbiosis, or to persistence in the soil environment, but these regions have been frequently subjected to recombination events including deletions, insertions and recombination with genes located on other integrative elements. Examination of a new ICE[3] in M. ciceri Ca181 revealed it has jettisoned the genetic cargo from its β region and recruited a serine recombinase gene within its γ region, resulting in replacement of one of the three ICE[3] integration sites. Overall the recombination loci appear to be the only conserved features of the β and γ regions, suggesting that the tripartite structure itself provides a selective benefit to the element. We propose the ICE[3] structure provides enhanced host range, host stability and resistance to destabilization by tandem insertion of competing integrative elements. Furthermore, we suspect the ICE[3] tripartite structure increases the likelihood of gene capture from integrative elements sharing the same attachment sites.}, }
@article {pmid28668691, year = {2017}, author = {Hu, YY and Wang, YL and Sun, QL and Huang, ZX and Wang, HY and Zhang, R and Chen, GX}, title = {Colistin resistance gene mcr-1 in gut flora of children.}, journal = {International journal of antimicrobial agents}, volume = {50}, number = {4}, pages = {593-597}, doi = {10.1016/j.ijantimicag.2017.06.011}, pmid = {28668691}, issn = {1872-7913}, mesh = {Anti-Bacterial Agents/*pharmacology ; Child ; Citrobacter freundii/drug effects/*genetics/isolation &amp; purification ; Colistin/*pharmacology ; Drug Resistance, Bacterial/genetics ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/drug effects/*genetics/isolation &amp; purification ; Escherichia coli Proteins/*genetics ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects/genetics ; Gene Transfer, Horizontal/genetics ; Humans ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Plasmids/genetics ; Polymyxins/pharmacology ; Quinolones/pharmacology ; beta-Lactamases/genetics ; }, abstract = {The aim of this study was to determine the prevalence and transmission mechanism(s) of mcr-1 in the gut flora of children. Faecal samples (n = 173) were obtained from non-diarrhoea patients at the Children's Hospital of Zhejiang University (Hangzhou, China). PCR-based analysis indicated that 17 isolates from 9.8% of the samples were positive for mcr-1, comprising 16 Escherichia coli and 1 Citrobacter freundii. Nine mcr-1-bearing isolates co-expressed extended-spectrum β-lactamase (ESBL) genes, but plasmid-mediated quinolone resistance (PMQR) genes were not detected. Transconjugation followed by Southern hybridisation analysis revealed that 14 of the E. coli isolates were able to transfer their colistin-resistant phenotype to E. coli EC600. All 14 of these E. coli strains contained a major mcr-1-containing conjugative plasmid with a size of ca. 33 kb or 55 kb. All but two of the E. coli isolates presented distinct pulsed-field gel electrophoresis (PFGE) patterns. Multilocus sequence typing (MLST) analysis revealed 11 sequence types (STs) among the E. coli 16 isolates, with ST117 being the most common. The finding of a high prevalence of mcr-1 in the intestinal flora of children, with the majority of mcr-1-positive isolates being E. coli, highlights the need for more rational use of polymyxins to prevent polymyxin resistance from becoming disseminated among different microbial pathogens. Given the high detection rate of mcr-1 in children, we recommend that polymyxin is no longer used as a last-resort antimicrobial agent and that alternative strategies are developed to treat infections caused by such pathogens.}, }
@article {pmid28668675, year = {2018}, author = {Peeters, LEJ and Croubels, S and Rasschaert, G and Imberechts, H and Daeseleire, E and Dewulf, J and Heyndrickx, M and Butaye, P and Haesebrouck, F and Smet, A}, title = {Effect of residual doxycycline concentrations on resistance selection and transfer in porcine commensal Escherichia coli.}, journal = {International journal of antimicrobial agents}, volume = {51}, number = {1}, pages = {123-127}, doi = {10.1016/j.ijantimicag.2017.04.018}, pmid = {28668675}, issn = {1872-7913}, mesh = {Animal Feed/*analysis ; Animals ; Anti-Bacterial Agents/*administration &amp; dosage/pharmacology ; Antiporters/genetics ; Bacterial Proteins/genetics ; Chlortetracycline/*analysis/pharmacology ; Doxycycline/*analysis/pharmacology ; Drug Combinations ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/*drug effects/*genetics/isolation &amp; purification ; Feces/microbiology ; Gene Transfer, Horizontal/genetics ; Intestines/microbiology ; Plasmids/genetics ; Sulfadiazine/*analysis/pharmacology ; Swine ; Trimethoprim/*analysis/pharmacology ; }, abstract = {Pig feed may contain various levels of antimicrobial residues due to cross-contamination. A previous study showed that a 3% carry-over level of doxycycline (DOX) in the feed results in porcine faecal concentrations of approximately 4 mg/L. The aim of this study was to determine the effect of residual DOX concentrations (1 and 4 mg/L) in vitro on selection of DOX-resistant porcine commensal Escherichia coli and transfer of their resistance plasmids. Three different DOX-resistant porcine commensal E. coli strains and their plasmids were characterised. These strains were each brought in competition with a susceptible strain in a medium containing 0, 1 and 4 mg/L DOX. Resistant bacteria, susceptible bacteria and transconjugants were enumerated after 24 h and 48 h. The tet(A)-carrying plasmids showed genetic backbones that are also present among human E. coli isolates. Ratios of resistant to susceptible bacteria were significantly higher at 1 and 4 mg/L DOX compared with the blank control, but there was no significant difference between 1 and 4 mg/L. Plasmid transfer frequencies were affected by 1 or 4 mg/L DOX in the medium for only one of the resistance plasmids. In conclusion, DOX concentrations of 1 and 4 mg/L can select for resistant E. coli in vitro. Further research is needed to determine the effect of these concentrations in the complex environment of the porcine intestinal microbiota.}, }
@article {pmid28666753, year = {2017}, author = {Pulss, S and Semmler, T and Prenger-Berninghoff, E and Bauerfeind, R and Ewers, C}, title = {First report of an Escherichia coli strain from swine carrying an OXA-181 carbapenemase and the colistin resistance determinant MCR-1.}, journal = {International journal of antimicrobial agents}, volume = {50}, number = {2}, pages = {232-236}, doi = {10.1016/j.ijantimicag.2017.03.014}, pmid = {28666753}, issn = {1872-7913}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Carbapenems/pharmacology ; Colistin/pharmacology ; Conjugation, Genetic ; Drug Resistance, Bacterial ; Escherichia coli/classification/*genetics/*isolation &amp; purification ; Escherichia coli Infections/microbiology/*veterinary ; Escherichia coli Proteins/*genetics ; Farms ; Gene Transfer, Horizontal ; Italy ; Multilocus Sequence Typing ; Plasmids/analysis ; Swine ; beta-Lactamases/*genetics ; }, abstract = {Plasmid-mediated resistance to carbapenems and colistin in Enterobacteriaceae represents an emerging public health threat. Although animals have been identified as a relevant source of multidrug-resistant (MDR) bacteria, there are only a few reports on the presence of carbapenemases in animal isolates. In this study, 7850 faecal Escherichia coli isolates obtained from 2160 pigs were screened for carbapenem non-susceptibility using Mueller-Hinton agar supplemented with meropenem. Eleven isolates showed growth on meropenem-containing agar but only two proved positive by PCR for a carbapenemase gene, namely blaOXA-48-like. The two isolates were obtained from different pigs housed at the same farm in Italy and were not genetically related by multilocus sequence typing (MLST), comprising ST359 and ST641. Whole-genome sequencing revealed the presence of blaOXA-181 in both isolates; in addition, the colistin resistance gene mcr-1 and aminoglycoside resistance gene armA were found in one isolate. The blaOXA-181 resistance gene was located on a 51.5-kb non-conjugative plasmid of replicon type IncX3 and the mcr-1 gene on a 33.3-kb transferable IncX4 plasmid. The high nucleotide similarity (>99%) of plasmids pEcIHIT31346-OXA-181 and pEcIHIT31346-MCR-1 to published plasmids from various human and animal sources suggests that specific antibiotic resistance plasmids are circulating among E. coli strains worldwide and across vertebrate species barriers. Although carbapenems are not licensed for use in livestock and the overall prevalence of carbapenemases in porcine E. coli appears to be low, the current findings indicate that even pigs can host MDR strains with accumulated plasmid-mediated resistance against several last-line antibiotics.}, }
@article {pmid28666750, year = {2017}, author = {Wang, N and Hang, X and Zhang, M and Peng, X and Yang, H}, title = {New genetic environments of the macrolide-lincosamide-streptogramin resistance determinant erm(X) and their influence on potential horizontal transferability in bifidobacteria.}, journal = {International journal of antimicrobial agents}, volume = {50}, number = {4}, pages = {572-580}, doi = {10.1016/j.ijantimicag.2017.04.007}, pmid = {28666750}, issn = {1872-7913}, mesh = {Adult ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/*genetics ; Bifidobacterium/*drug effects/*genetics/isolation &amp; purification ; Child, Preschool ; Conjugation, Genetic/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Feces/microbiology ; Gastrointestinal Microbiome/genetics ; Gene Transfer, Horizontal/*genetics ; Humans ; Lincosamides/*pharmacology ; Macrolides/*pharmacology ; Microbial Sensitivity Tests ; Promoter Regions, Genetic/genetics ; Streptogramins/*pharmacology ; }, abstract = {With the abuse of macrolide, lincosamide, and streptogramin (MLS), the traditionally safe bifidobacterial strains in the human intestine could serve as a reservoir of MLS resistance genes. In this study, the erm(X) gene was detected in 29 MLS-resistant strains and one MLS-susceptible strain among 92 bifidobacterial strains of human origin. This study is the first to report erm(X)-mediated MLS resistance in Bifidobacterium pseudocatenulatum, Bifidobacterium breve and Bifidobacterium bifidum. The insertion sequences (ISs) flanking antibiotic resistance (AR) genes (i.e., the genetic environment of AR genes) could contribute to the horizontal spreading of AR. However, the potential transferability of erm(X) in bifidobacteria has not been previously verified. Here, we retrieved four genetic environments (I-IV) of erm(X) from 30 erm(X)-positive bifidobacterial strains. This study is the first to identify the erm(X) gene in three new genetic environments (II, III and IV) in bifidobacteria. The erm(X) gene was individually flanked by IS1249 or IS3 in genetic environments I, II and IV and was simultaneously flanked by IS1249 and IS3 elements in genetic environment III. Only the transfer of erm(X) from genetic environment III simultaneously flanked by IS1249 and IS3 elements was successfully observed in filter mating experiments. These findings indicate a synergic effect of IS1249 and IS3 elements in the transfer of erm(X) in bifidobacteria, and further reveal that the various genetic environments of erm(X) result in significant differences in the transferability of erm(X) in bifidobacteria.}, }
@article {pmid28666748, year = {2018}, author = {Tacão, M and Araújo, S and Vendas, M and Alves, A and Henriques, I}, title = {Shewanella species as the origin of blaOXA-48 genes: insights into gene diversity, associated phenotypes and possible transfer mechanisms.}, journal = {International journal of antimicrobial agents}, volume = {51}, number = {3}, pages = {340-348}, doi = {10.1016/j.ijantimicag.2017.05.014}, pmid = {28666748}, issn = {1872-7913}, mesh = {*Biological Variation, Population ; Cluster Analysis ; DNA Gyrase/genetics ; DNA Transposable Elements ; *Gene Transfer, Horizontal ; *Genetic Variation ; Genotype ; Humans ; Integrons ; Microbial Sensitivity Tests ; Nucleic Acid Hybridization ; Plasmids ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sequence Homology ; Shewanella/*drug effects/*genetics ; *beta-Lactam Resistance ; beta-Lactamases/classification/*genetics ; }, abstract = {Chromosome-encoded beta-lactamases of Shewanella spp. have been indicated as probable progenitors of blaOXA-48-like genes. However, these have been detected in few Shewanella spp. and dissemination mechanisms are unclear. Thus, our main objective was to confirm the role of Shewanella species as progenitors of blaOXA-48-like genes. In silico analysis of Shewanella genomes was performed to detect blaOXA-48-like genes and context, and 43 environmental Shewanella spp. were characterised. Clonal relatedness was determined by BOX-PCR. Phylogenetic affiliation was assessed by 16S rDNA and gyrB sequencing. Antibiotic susceptibility phenotypes were determined. The blaOXA-48-like genes and genetic context were inspected by PCR, hybridisation and sequence analysis. Gene variants were cloned in Escherichia coli and MICs were determined. Shewanella isolates were screened for integrons, plasmids and insertion sequences. Analysis of Shewanella spp. genomes showed that putative blaOXA-48-like is present in the majority and in an identical context. Isolates presenting unique BOX profiles affiliated with 11 Shewanella spp. blaOXA-48-like genes were detected in 22 isolates from 6 species. Genes encoded enzymes identical to OXA-48, OXA-204, OXA-181, and 7 new variants differing from OXA-48 from 2 to 82 amino acids. IS1999 was detected in 24 isolates, although not in the vicinity of blaOXA-48 genes. Recombinant E. coli strains presented altered MICs. The presence/absence of blaOXA-48-like genes was species-related. Gene variants encoded enzymes with hydrolytic spectra similar to OXA-48-like from non-shewanellae. From the mobile elements previously described in association with blaOXA-48-like genes, only the IS1999 was found in Shewanella, which indicates its relevance in blaOXA-48-like genes transfer to other hosts.}, }
@article {pmid28665176, year = {2018}, author = {Adler, A and Glick, R and Lifshitz, Z and Carmeli, Y}, title = {Does Acinetobacter baumannii Serve as a Source for blaNDM Dissemination into Enterobacteriaceae in Hospitalized Patients?.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {24}, number = {2}, pages = {150-153}, doi = {10.1089/mdr.2016.0330}, pmid = {28665176}, issn = {1931-8448}, mesh = {Acinetobacter Infections/drug therapy/*epidemiology/microbiology ; Acinetobacter baumannii/classification/drug effects/*genetics/isolation &amp; purification ; Anti-Bacterial Agents/pharmacology ; Cross Infection/drug therapy/*epidemiology/microbiology ; DNA Transposable Elements ; Electrophoresis, Gel, Pulsed-Field ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Hospitalization ; Humans ; Isoenzymes/genetics/metabolism ; Israel/epidemiology ; Klebsiella Infections/drug therapy/*epidemiology/microbiology ; Klebsiella pneumoniae/classification/drug effects/*genetics/isolation &amp; purification ; Microbial Sensitivity Tests ; Plasmids/chemistry/metabolism ; Prospective Studies ; beta-Lactamases/*genetics/metabolism ; beta-Lactams/pharmacology ; }, abstract = {The goal was to study the possibility that Acinetobacter baumannii serve as an epidemiologically significant source for transmission of the blaNDM gene to Enterobacteriaceae by horizontal gene transfer (HGT) in hospitalized patients. The study was done at the Tel-Aviv Sourasky Medical Center from December 2014 until August 2015. Clinical and surveillance rectal cultures were collected as per hospital policies and were analyzed for the presence of New Delhi metallo-beta-lactamase-producing Enterobacteriaceae (NDME) and A. baumannii (NDMAb). Isolates were typed by pulsed-field gel electrophoresis (PFGE). The location of the blaNDM gene within the Tn125 transposon was studied by sequencing. A transmission event (TE) was determined if patients shared the same PFGE type of either NDME or NDMAb and were simultaneous in the same ward. HGT-related TE was considered if the two isolates shared identical blaNDM gene allele and transposon. There were 16 NDMAb- (clinical, 10; surveillance, 4; both, 2) and 13 NDME- (clinical, 3; surveillance, 8; both, 2) infected/colonized patients. All NDMAb isolates except two harbored the blaNDM-1 allele that was located within a Tn125 transposon and was plasmid borne. The majority of patients (n = 10/16) were infected by one PFGE type of NDMAb, and five clonal TEs were identified. NDME were either Escherichia coli (n = 4) or Klebsiella pneumoniae (n = 9) of different PFGE types with only one NDME TE. The blaNDM gene was within a Tn125 in three K. pneumoniae isolates. Although one HGT-related TE between NDMAb and K. pneumoniae was epidemiologically suspected, the low similarity between the Tn125 transposons (75.7%) excluded that possibility. In conclusion, whereas NDMAb appears to disseminate by clonal spread, we did not find evidence for HGT-mediated transmission in NDME in hospitalized patients.}, }
@article {pmid28659871, year = {2017}, author = {Tran, TTT and Mangenot, S and Magdelenat, G and Payen, E and Rouy, Z and Belahbib, H and Grail, BM and Johnson, DB and Bonnefoy, V and Talla, E}, title = {Comparative Genome Analysis Provides Insights into Both the Lifestyle of Acidithiobacillus ferrivorans Strain CF27 and the Chimeric Nature of the Iron-Oxidizing Acidithiobacilli Genomes.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1009}, pmid = {28659871}, issn = {1664-302X}, abstract = {The iron-oxidizing species Acidithiobacillus ferrivorans is one of few acidophiles able to oxidize ferrous iron and reduced inorganic sulfur compounds at low temperatures (<10°C). To complete the genome of At. ferrivorans strain CF27, new sequences were generated, and an update assembly and functional annotation were undertaken, followed by a comparative analysis with other Acidithiobacillus species whose genomes are publically available. The At. ferrivorans CF27 genome comprises a 3,409,655 bp chromosome and a 46,453 bp plasmid. At. ferrivorans CF27 possesses genes allowing its adaptation to cold, metal(loid)-rich environments, as well as others that enable it to sense environmental changes, allowing At. ferrivorans CF27 to escape hostile conditions and to move toward favorable locations. Interestingly, the genome of At. ferrivorans CF27 exhibits a large number of genomic islands (mostly containing genes of unknown function), suggesting that a large number of genes has been acquired by horizontal gene transfer over time. Furthermore, several genes specific to At. ferrivorans CF27 have been identified that could be responsible for the phenotypic differences of this strain compared to other Acidithiobacillus species. Most genes located inside At. ferrivorans CF27-specific gene clusters which have been analyzed were expressed by both ferrous iron-grown and sulfur-attached cells, indicating that they are not pseudogenes and may play a role in both situations. Analysis of the taxonomic composition of genomes of the Acidithiobacillia infers that they are chimeric in nature, supporting the premise that they belong to a particular taxonomic class, distinct to other proteobacterial subgroups.}, }
@article {pmid28659339, year = {2017}, author = {Muschiol, S and Erlendsson, S and Aschtgen, MS and Oliveira, V and Schmieder, P and de Lichtenberg, C and Teilum, K and Boesen, T and Akbey, U and Henriques-Normark, B}, title = {Structure of the competence pilus major pilin ComGC in Streptococcus pneumoniae.}, journal = {The Journal of biological chemistry}, volume = {292}, number = {34}, pages = {14134-14146}, pmid = {28659339}, issn = {1083-351X}, mesh = {Bacterial Proteins/genetics/metabolism ; Cryoelectron Microscopy ; Dimerization ; Fimbriae Proteins/*chemistry/genetics/metabolism ; Fimbriae, Bacterial/metabolism/*ultrastructure ; Gene Deletion ; Hydrophobic and Hydrophilic Interactions ; Kinetics ; Lipid Bilayers/chemistry/metabolism ; Microscopy, Electron, Transmission ; *Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; Operon ; Peptide Fragments/chemistry/genetics/metabolism ; Protein Conformation ; Protein Conformation, alpha-Helical ; Recombinant Fusion Proteins ; Solubility ; Streptococcus pneumoniae/*physiology/ultrastructure ; Trans-Activators/genetics/metabolism ; Virulence Factors/*chemistry/genetics/metabolism ; }, abstract = {Type IV pili are important virulence factors on the surface of many pathogenic bacteria and have been implicated in a wide range of diverse functions, including attachment, twitching motility, biofilm formation, and horizontal gene transfer. The respiratory pathogen Streptococcus pneumoniae deploys type IV pili to take up DNA during transformation. These "competence pili" are composed of the major pilin protein ComGC and exclusively assembled during bacterial competence, but their biogenesis remains unclear. Here, we report the high resolution NMR structure of N-terminal truncated ComGC revealing a highly flexible and structurally divergent type IV pilin. It consists of only three α-helical segments forming a well-defined electronegative cavity and confined electronegative and hydrophobic patches. The structure is particularly flexible between the first and second α-helix with the first helical part exhibiting slightly slower dynamics than the rest of the pilin, suggesting that the first helix is involved in forming the pilus structure core and that parts of helices two and three are primarily surface-exposed. Taken together, our results provide the first structure of a type IV pilin protein involved in the formation of competence-induced pili in Gram-positive bacteria and corroborate the remarkable structural diversity among type IV pilin proteins.}, }
@article {pmid28659179, year = {2017}, author = {Faddeeva-Vakhrusheva, A and Kraaijeveld, K and Derks, MFL and Anvar, SY and Agamennone, V and Suring, W and Kampfraath, AA and Ellers, J and Le Ngoc, G and van Gestel, CAM and Mariën, J and Smit, S and van Straalen, NM and Roelofs, D}, title = {Coping with living in the soil: the genome of the parthenogenetic springtail Folsomia candida.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {493}, pmid = {28659179}, issn = {1471-2164}, mesh = {Animals ; Anti-Bacterial Agents/biosynthesis ; Arthropods/*genetics/metabolism/*physiology ; Gene Rearrangement ; Gene Transfer, Horizontal ; *Genomics ; Multigene Family/genetics ; Phylogeny ; *Soil ; }, abstract = {BACKGROUND: Folsomia candida is a model in soil biology, belonging to the family of Isotomidae, subclass Collembola. It reproduces parthenogenetically in the presence of Wolbachia, and exhibits remarkable physiological adaptations to stress. To better understand these features and adaptations to life in the soil, we studied its genome in the context of its parthenogenetic lifestyle.<br><br>RESULTS: We applied Pacific Bioscience sequencing and assembly to generate a reference genome for F. candida of 221.7 Mbp, comprising only 162 scaffolds. The complete genome of its endosymbiont Wolbachia, was also assembled and turned out to be the largest strain identified so far. Substantial gene family expansions and lineage-specific gene clusters were linked to stress response. A large number of genes (809) were acquired by horizontal gene transfer. A substantial fraction of these genes are involved in lignocellulose degradation. Also, the presence of genes involved in antibiotic biosynthesis was confirmed. Intra-genomic rearrangements of collinear gene clusters were observed, of which 11 were organized as palindromes. The Hox gene cluster of F. candida showed major rearrangements compared to arthropod consensus cluster, resulting in a disorganized cluster.<br><br>CONCLUSIONS: The expansion of stress response gene families suggests that stress defense was important to facilitate colonization of soils. The large number of HGT genes related to lignocellulose degradation could be beneficial to unlock carbohydrate sources in soil, especially those contained in decaying plant and fungal organic matter. Intra- as well as inter-scaffold duplications of gene clusters may be a consequence of its parthenogenetic lifestyle. This high quality genome will be instrumental for evolutionary biologists investigating deep phylogenetic lineages among arthropods and will provide the basis for a more mechanistic understanding in soil ecology and ecotoxicology.}, }
@article {pmid28655863, year = {2017}, author = {Michael, AJ}, title = {Evolution of biosynthetic diversity.}, journal = {The Biochemical journal}, volume = {474}, number = {14}, pages = {2277-2299}, doi = {10.1042/BCJ20160823}, pmid = {28655863}, issn = {1470-8728}, mesh = {Animals ; Biocatalysis ; *Biodiversity ; Ecological and Environmental Phenomena ; Enzymes/chemistry/genetics/*metabolism ; *Evolution, Molecular ; Gene Deletion ; Gene Duplication ; Gene Fusion ; Gene Transfer, Horizontal ; Humans ; *Models, Molecular ; Polyamines/metabolism ; *Protein Biosynthesis ; Protein Folding ; Structural Homology, Protein ; Symbiosis ; }, abstract = {Since the emergence of the last common ancestor from which all extant life evolved, the metabolite repertoire of cells has increased and diversified. Not only has the metabolite cosmos expanded, but the ways in which the same metabolites are made have diversified. Enzymes catalyzing the same reaction have evolved independently from different protein folds; the same protein fold can produce enzymes recognizing different substrates, and enzymes performing different chemistries. Genes encoding useful enzymes can be transferred between organisms and even between the major domains of life. Organisms that live in metabolite-rich environments sometimes lose the pathways that produce those same metabolites. Fusion of different protein domains results in enzymes with novel properties. This review will consider the major evolutionary mechanisms that generate biosynthetic diversity: gene duplication (and gene loss), horizontal and endosymbiotic gene transfer, and gene fusion. It will also discuss mechanisms that lead to convergence as well as divergence. To illustrate these mechanisms, one of the original metabolisms present in the last universal common ancestor will be employed: polyamine metabolism, which is essential for the growth and cell proliferation of archaea and eukaryotes, and many bacteria.}, }
@article {pmid28655818, year = {2017}, author = {Yin, W and Li, H and Shen, Y and Liu, Z and Wang, S and Shen, Z and Zhang, R and Walsh, TR and Shen, J and Wang, Y}, title = {Novel Plasmid-Mediated Colistin Resistance Gene mcr-3 in Escherichia coli.}, journal = {mBio}, volume = {8}, number = {3}, pages = {}, pmid = {28655818}, issn = {2150-7511}, support = {MR/P007295/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Colistin/*pharmacology ; Conjugation, Genetic ; *Drug Resistance, Bacterial ; Escherichia coli/*drug effects/*genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Plasmids/*analysis ; Sequence Analysis, DNA ; Sequence Homology ; Swine ; }, abstract = {The mobile colistin resistance gene mcr-1 has attracted global attention, as it heralds the breach of polymyxins, one of the last-resort antibiotics for the treatment of severe clinical infections caused by multidrug-resistant Gram-negative bacteria. To date, six slightly different variants of mcr-1, and a second mobile colistin resistance gene, mcr-2, have been reported or annotated in the GenBank database. Here, we characterized a third mobile colistin resistance gene, mcr-3 The gene coexisted with 18 additional resistance determinants in the 261-kb IncHI2-type plasmid pWJ1 from porcine Escherichia colimcr-3 showed 45.0% and 47.0% nucleotide sequence identity to mcr-1 and mcr-2, respectively, while the deduced amino acid sequence of MCR-3 showed 99.8 to 100% and 75.6 to 94.8% identity to phosphoethanolamine transferases found in other Enterobacteriaceae species and in 10 Aeromonas species, respectively. pWJ1 was mobilized to an E. coli recipient by conjugation and contained a plasmid backbone similar to those of other mcr-1-carrying plasmids, such as pHNSHP45-2 from the original mcr-1-harboring E. coli strain. Moreover, a truncated transposon element, TnAs2, which was characterized only in Aeromonas salmonicida, was located upstream of mcr-3 in pWJ1. This ΔTnAs2-mcr-3 element was also identified in a shotgun genome sequence of a porcine E. coli isolate from Malaysia, a human Klebsiella pneumoniae isolate from Thailand, and a human Salmonella enterica serovar Typhimurium isolate from the United States. These results suggest the likelihood of a wide dissemination of the novel mobile colistin resistance gene mcr-3 among Enterobacteriaceae and aeromonads; the latter may act as a potential reservoir for mcr-3IMPORTANCE The emergence of the plasmid-mediated colistin resistance gene mcr-1 has attracted substantial attention worldwide. Here, we examined a colistin-resistant Escherichia coli isolate that was negative for both mcr-1 and mcr-2 and discovered a novel mobile colistin resistance gene, mcr-3 The amino acid sequence of MCR-3 aligned closely with phosphoethanolamine transferases from Enterobacteriaceae and Aeromonas species originating from both clinical infections and environmental samples collected in 12 countries on four continents. Due to the ubiquitous profile of aeromonads in the environment and the potential transfer of mcr-3 between Enterobacteriaceae and Aeromonas species, the wide spread of mcr-3 may be largely underestimated. As colistin has been and still is widely used in veterinary medicine and used at increasing frequencies in human medicine, the continuous monitoring of mobile colistin resistance determinants in colistin-resistant Gram-negative bacteria is imperative for understanding and tackling the dissemination of mcr genes in both the agricultural and health care sectors.}, }
@article {pmid28652353, year = {2017}, author = {Iranzo, J and Cuesta, JA and Manrubia, S and Katsnelson, MI and Koonin, EV}, title = {Disentangling the effects of selection and loss bias on gene dynamics.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {28}, pages = {E5616-E5624}, pmid = {28652353}, issn = {1091-6490}, mesh = {Computational Biology ; Computer Simulation ; DNA Transposable Elements ; Evolution, Molecular ; Gene Dosage ; *Gene Expression Regulation ; *Gene Transfer, Horizontal ; Genome, Archaeal ; Genome, Bacterial ; Genomics ; Host-Parasite Interactions ; Models, Theoretical ; Mutation ; Parasitic Diseases/microbiology ; *Selection, Genetic ; }, abstract = {We combine mathematical modeling of genome evolution with comparative analysis of prokaryotic genomes to estimate the relative contributions of selection and intrinsic loss bias to the evolution of different functional classes of genes and mobile genetic elements (MGE). An exact solution for the dynamics of gene family size was obtained under a linear duplication-transfer-loss model with selection. With the exception of genes involved in information processing, particularly translation, which are maintained by strong selection, the average selection coefficient for most nonparasitic genes is low albeit positive, compatible with observed positive correlation between genome size and effective population size. Free-living microbes evolve under stronger selection for gene retention than parasites. Different classes of MGE show a broad range of fitness effects, from the nearly neutral transposons to prophages, which are actively eliminated by selection. Genes involved in antiparasite defense, on average, incur a fitness cost to the host that is at least as high as the cost of plasmids. This cost is probably due to the adverse effects of autoimmunity and curtailment of horizontal gene transfer caused by the defense systems and selfish behavior of some of these systems, such as toxin-antitoxin and restriction modification modules. Transposons follow a biphasic dynamics, with bursts of gene proliferation followed by decay in the copy number that is quantitatively captured by the model. The horizontal gene transfer to loss ratio, but not duplication to loss ratio, correlates with genome size, potentially explaining increased abundance of neutral and costly elements in larger genomes.}, }
@article {pmid28651991, year = {2017}, author = {Lapadula, WJ and Ayub, MJ}, title = {Ribosome Inactivating Proteins from an evolutionary perspective.}, journal = {Toxicon : official journal of the International Society on Toxinology}, volume = {136}, number = {}, pages = {6-14}, doi = {10.1016/j.toxicon.2017.06.012}, pmid = {28651991}, issn = {1879-3150}, mesh = {Animals ; Bacteria ; *Evolution, Molecular ; Fungi ; Gene Duplication ; Gene Transfer, Horizontal ; Phylogeny ; Plants ; Ribosome Inactivating Proteins/*genetics ; }, abstract = {Ribosome Inactivating Proteins (RIPs) are rRNA N-glycosidases that inhibit protein synthesis through the elimination of a single adenine residue from 28S rRNA. Many of these toxins have been characterized in depth from a biochemical and molecular point of view. In addition, their potential use in medicine as highly selective toxins is being explored. In contrast, the evolutionary history of RIP encoding genes has remained traditionally underexplored. In recent years, accumulation of large genomic data has fueled research on this issue and revealed unexpected information about the origin and evolution of RIP toxins. In this review we summarize the current evidence available on the occurrence of different evolutionary mechanisms (gene duplication and losses, horizontal gene transfer, synthesis de novo and domain combination) involved in the evolution of the RIP gene family. Finally, we propose a revised nomenclature for RIP genes based on their evolutionary history.}, }
@article {pmid28648290, year = {2017}, author = {Bartoszewicz, M and Marjańska, PS}, title = {Milk-originated Bacillus cereus sensu lato strains harbouring Bacillus anthracis-like plasmids are genetically and phenotypically diverse.}, journal = {Food microbiology}, volume = {67}, number = {}, pages = {23-30}, doi = {10.1016/j.fm.2017.05.009}, pmid = {28648290}, issn = {1095-9998}, mesh = {Animals ; Bacillus anthracis/classification/*genetics/isolation &amp; purification ; Bacillus cereus/classification/genetics/*isolation &amp; purification ; Cattle ; Gene Transfer, Horizontal ; Milk/chemistry/*microbiology ; Multilocus Sequence Typing ; Phenotype ; Phylogeny ; Plasmids/*genetics ; Recombination, Genetic ; }, abstract = {Bacillus cereus sensu lato is widely distributed in food products, including raw and processed milk. Plasmids often determine bacterial virulence and toxicity, but their role in the evolution of B. cereus sensu lato is only partly known. Here, we observed that nearly 8% of B. cereus sensu lato isolates were positive for pXO1-like plasmids and 12% for pXO2-like plasmids in raw and ultra-heat-treated (UHT) milk from one dairy plant. However, pXO1-like plasmids were significantly more frequent in raw milk, while pXO2-like plasmids were more frequent in processed milk. Strains from raw and UHT milk were enterotoxigenic, with up to one-fifth of the isolates being psychrotolerant. Phylogenetic assessment using multi-locus sequence typing revealed a polyphyletic structure for these bacilli, with distinct groups of cold-adapted isolates and pathogenic strains (including emetic B. cereus). Populations corresponding to both sampling sites exhibited significant linkage disequilibrium and the presence of purifying selection. The far-from-clonal population structure indicated the presence of sequence types or ecotypes adapted to specific conditions in the dairy industry. A high recombination-to-mutation ratio suggested an important role for horizontal gene transfer among B. cereus sensu lato isolates in milk.}, }
@article {pmid28646115, year = {2017}, author = {Zheng, H and Dietrich, C and Brune, A}, title = {Genome Analysis of Endomicrobium proavitum Suggests Loss and Gain of Relevant Functions during the Evolution of Intracellular Symbionts.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {17}, pages = {}, pmid = {28646115}, issn = {1098-5336}, mesh = {Animals ; Bacteria/classification/*genetics/isolation &amp; purification ; Bacterial Physiological Phenomena ; Eukaryota/physiology ; Evolution, Molecular ; *Genome, Bacterial ; Genomics ; Isoptera/microbiology ; Phylogeny ; *Symbiosis ; }, abstract = {Bacterial endosymbionts of eukaryotes show progressive genome erosion, but detailed investigations of the evolutionary processes involved in the transition to an intracellular lifestyle are generally hampered by the lack of extant free-living lineages. Here, we characterize the genome of the recently isolated, free-living Endomicrobium proavitum, the second member of the Elusimicrobia phylum brought into pure culture, and compare it to the closely related "Candidatus Endomicrobium trichonymphae" strain Rs-D17, a previously described but uncultured endosymbiont of termite gut flagellates. A reconstruction of the metabolic pathways of Endomicrobium proavitum matched the fermentation products formed in pure culture and underscored its restriction to glucose as the substrate. However, several pathways present in the free-living strain, e.g., for the uptake and activation of glucose and its subsequent fermentation, ammonium assimilation, and outer membrane biogenesis, were absent or disrupted in the endosymbiont, probably lost during the massive genome rearrangements that occurred during symbiogenesis. While the majority of the genes in strain Rs-D17 have orthologs in Endomicrobium proavitum, the endosymbiont also possesses a number of functions that are absent from the free-living strain and may represent adaptations to the intracellular lifestyle. Phylogenetic analysis revealed that the genes encoding glucose 6-phosphate and amino acid transporters, acetaldehyde/alcohol dehydrogenase, and the pathways of glucuronic acid catabolism and thiamine pyrophosphate biosynthesis were either acquired by horizontal gene transfer or may represent ancestral traits that were lost in the free-living strain. The polyphyletic origin of Endomicrobia in different flagellate hosts makes them excellent models for future studies of convergent and parallel evolution during symbiogenesis.IMPORTANCE The isolation of a free-living relative of intracellular symbionts provides the rare opportunity to identify the evolutionary processes that occur in the course of symbiogenesis. Our study documents that the genome of "Candidatus Endomicrobium trichonymphae," which represents a clade of endosymbionts that have coevolved with termite gut flagellates for more than 40 million years, is not simply a subset of the genes present in Endomicrobium proavitum, a member of the ancestral, free-living lineage. Rather, comparative genomics revealed that the endosymbionts possess several relevant functions that were either prerequisites for colonization of the intracellular habitat or might have served to compensate for genes losses that occurred during genome erosion. Some gene sets found only in the endosymbiont were apparently acquired by horizontal transfer from other gut bacteria, which suggests that the intracellular bacteria of flagellates are not entirely cut off from gene flow.}, }
@article {pmid28645486, year = {2017}, author = {Arnold, ML and Kunte, K}, title = {Adaptive Genetic Exchange: A Tangled History of Admixture and Evolutionary Innovation.}, journal = {Trends in ecology &amp; evolution}, volume = {32}, number = {8}, pages = {601-611}, doi = {10.1016/j.tree.2017.05.007}, pmid = {28645486}, issn = {1872-8383}, mesh = {*Biological Evolution ; Eukaryota ; Eukaryotic Cells ; *Gene Flow ; Hybridization, Genetic ; Phylogeny ; }, abstract = {Genetic exchange between divergent evolutionary lineages, from introgressive hybridization between locally adapted populations to insertion of retroviral sequences into eukaryotic genomes, has now been documented. The detection of frequent divergence-with-gene-flow contrasts the neo-Darwinian paradigm of largely allopatric diversification. Nevertheless, of even greater significance is the growing wealth of data suggesting that the recipients of the transferred genomic material gain adaptive phenotypes from the donor lineages. This adaptive enrichment is reflected by changes in pathogenicity in viruses and bacteria, the transformation of ecological amplitude in eukaryotes, and adaptive radiations in extremely diverse lineages. Although genetic exchange may produce maladaptive consequences, most of the recently reported examples suggest increases in fitness, and many such adaptive trait transfers have been identified in our own species.}, }
@article {pmid28645177, year = {2017}, author = {Cehovin, A and Lewis, SB}, title = {Mobile genetic elements in Neisseria gonorrhoeae: movement for change.}, journal = {Pathogens and disease}, volume = {75}, number = {6}, pages = {}, doi = {10.1093/femspd/ftx071}, pmid = {28645177}, issn = {2049-632X}, mesh = {Anti-Bacterial Agents/therapeutic use ; Bacteriophages/genetics ; *Conjugation, Genetic ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Gonorrhea/drug therapy/microbiology/pathology ; Humans ; *Interspersed Repetitive Sequences ; Neisseria gonorrhoeae/drug effects/*genetics/growth &amp; development/pathogenicity ; Plasmids/chemistry/metabolism ; Recombination, Genetic ; }, abstract = {Neisseria gonorrhoeae, the causative agent of the sexually transmitted disease gonorrhoeae, possesses several mobile genetic elements (MGEs). The MGEs such as transposable elements mediate intrachromosomal rearrangements, while plasmids and the gonococcal genetic island are involved in interchromosomal gene transfer. Additionally, gonococcal MGEs serve as hotspots for recombination and integration of other genetic elements such as bacteriophages, contribute to gene regulation or spread genes through gonococcal populations by horizontal gene transfer. In this review, we summarise the literature on the structure and biology of MGEs and discuss how these genetic elements may play a role in the pathogenesis and spread of antimicrobial resistance in N. gonorrhoeae. Although an abundance of information about gonococcal MGEs exists (mainly from whole genome sequencing and bioinformatic analysis), there are still many open questions on how MGEs influence the biology of N. gonorrhoeae.}, }
@article {pmid28644126, year = {2017}, author = {Bonham, KS and Wolfe, BE and Dutton, RJ}, title = {Extensive horizontal gene transfer in cheese-associated bacteria.}, journal = {eLife}, volume = {6}, number = {}, pages = {}, pmid = {28644126}, issn = {2050-084X}, support = {P50 GM068763/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; Cheese/*microbiology ; *Gene Transfer, Horizontal ; *Microbiota ; }, abstract = {Acquisition of genes through horizontal gene transfer (HGT) allows microbes to rapidly gain new capabilities and adapt to new or changing environments. Identifying widespread HGT regions within multispecies microbiomes can pinpoint the molecular mechanisms that play key roles in microbiome assembly. We sought to identify horizontally transferred genes within a model microbiome, the cheese rind. Comparing 31 newly sequenced and 134 previously sequenced bacterial isolates from cheese rinds, we identified over 200 putative horizontally transferred genomic regions containing 4733 protein coding genes. The largest of these regions are enriched for genes involved in siderophore acquisition, and are widely distributed in cheese rinds in both Europe and the US. These results suggest that HGT is prevalent in cheese rind microbiomes, and that identification of genes that are frequently transferred in a particular environment may provide insight into the selective forces shaping microbial communities.}, }
@article {pmid28644125, year = {2017}, author = {Hullahalli, K and Rodrigues, M and Palmer, KL}, title = {Exploiting CRISPR-Cas to manipulate Enterococcus faecalis populations.}, journal = {eLife}, volume = {6}, number = {}, pages = {}, pmid = {28644125}, issn = {2050-084X}, support = {R01 AI116610/AI/NIAID NIH HHS/United States ; }, mesh = {*CRISPR-Cas Systems ; Drug Resistance, Multiple, Bacterial ; Enterococcus faecalis/*genetics ; *Evolution, Molecular ; Genetic Fitness ; Selection, Genetic ; }, abstract = {CRISPR-Cas provides a barrier to horizontal gene transfer in prokaryotes. It was previously observed that functional CRISPR-Cas systems are absent from multidrug-resistant (MDR) Enterococcus faecalis, which only possess an orphan CRISPR locus, termed CRISPR2, lacking cas genes. Here, we investigate how the interplay between CRISPR-Cas genome defense and antibiotic selection for mobile genetic elements shapes in vitro E. faecalis populations. We demonstrate that CRISPR2 can be reactivated for genome defense in MDR strains. Interestingly, we observe that E. faecalis transiently maintains CRISPR targets despite active CRISPR-Cas systems. Subsequently, if selection for the CRISPR target is present, toxic CRISPR spacers are lost over time, while in the absence of selection, CRISPR targets are lost over time. We find that forced maintenance of CRISPR targets induces a fitness cost that can be exploited to alter heterogeneous E. faecalis populations.}, }
@article {pmid28642992, year = {2018}, author = {Tomova, A and Ivanova, L and Buschmann, AH and Godfrey, HP and Cabello, FC}, title = {Plasmid-Mediated Quinolone Resistance (PMQR) Genes and Class 1 Integrons in Quinolone-Resistant Marine Bacteria and Clinical Isolates of Escherichia coli from an Aquacultural Area.}, journal = {Microbial ecology}, volume = {75}, number = {1}, pages = {104-112}, pmid = {28642992}, issn = {1432-184X}, support = {FB001//Lenfest Ocean Program/Pew Charitable Trusts/ ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Aquaculture ; *Drug Resistance, Bacterial ; Escherichia coli Infections/*microbiology ; Escherichia coli Proteins/genetics/metabolism ; Fishes/growth &amp; development/microbiology ; Gene Transfer, Horizontal ; Humans ; *Integrons ; Microbial Sensitivity Tests ; Plasmids/*genetics/metabolism ; Quinolones/*pharmacology ; Seawater/*microbiology ; Uropathogenic Escherichia coli/classification/*drug effects/genetics/isolation &amp; purification ; }, abstract = {Antimicrobial usage in aquaculture selects for antimicrobial-resistant microorganisms in the marine environment. The relevance of this selection to terrestrial animal and human health is unclear. Quinolone-resistance genes qnrA, qnrB, and qnrS were chromosomally located in four randomly chosen quinolone-resistant marine bacteria isolated from an aquacultural area with heavy quinolone usage. In quinolone-resistant uropathogenic clinical isolates of Escherichia coli from a coastal area bordering the same aquacultural region, qnrA was chromosomally located in two E. coli isolates, while qnrB and qnrS were located in small molecular weight plasmids in two other E. coli isolates. Three quinolone-resistant marine bacteria and three quinolone-resistant E. coli contained class 1 integrons but without physical association with PMQR genes. In both marine bacteria and uropathogenic E. coli, class 1 integrons had similar co-linear structures, identical gene cassettes, and similarities in their flanking regions. In a Marinobacter sp. marine isolate and in one E. coli clinical isolate, sequences immediately upstream of the qnrS gene were homologous to comparable sequences of numerous plasmid-located qnrS genes while downstream sequences were different. The observed commonality of quinolone resistance genes and integrons suggests that aquacultural use of antimicrobials might facilitate horizontal gene transfer between bacteria in diverse ecological locations.}, }
@article {pmid28634029, year = {2017}, author = {Qiu, H and Zelzion, E and Putnam, HM and Gates, RD and Wagner, NE and Adams, DK and Bhattacharya, D}, title = {Discovery of SCORs: Anciently derived, highly conserved gene-associated repeats in stony corals.}, journal = {Genomics}, volume = {109}, number = {5-6}, pages = {383-390}, doi = {10.1016/j.ygeno.2017.06.003}, pmid = {28634029}, issn = {1089-8646}, mesh = {Animals ; Anthozoa/classification/*genetics ; Conserved Sequence ; DNA/chemistry ; Evolution, Molecular ; Gene Expression Profiling/*methods ; Gene Expression Regulation ; Gene Transfer, Horizontal ; Multigene Family ; Nucleic Acid Conformation ; Phylogeny ; Sequence Analysis, DNA/*methods ; Sequence Analysis, RNA/*methods ; }, abstract = {Stony coral (Scleractinia) genomes are still poorly explored and many questions remain about their evolution and contribution to the success and longevity of reefs. We analyzed transcriptome and genome data from Montipora capitata, Acropora digitifera, and transcriptome data from 20 other coral species. To our surprise, we found highly conserved, anciently derived, Scleractinia COral-specific Repeat families (SCORs) that are abundant in all the studied lineages. SCORs form complex secondary structures and are located in untranslated regions and introns, but most abundant in intergenic DNA. These repeat families have undergone frequent duplication and degradation, suggesting a 'boom and bust' cycle of invasion and loss. We speculate that due to their surprisingly high sequence identities across deeply diverged corals, physical association with genes, and dynamic evolution, SCORs might have adaptive functions in corals that need to be explored using population genomic and function-based approaches.}, }
@article {pmid28630398, year = {2017}, author = {Tachibana, A and Hamajima, R and Tomizaki, M and Kondo, T and Nanba, Y and Kobayashi, M and Yamada, H and Ikeda, M}, title = {HCF-1 encoded by baculovirus AcMNPV is required for productive nucleopolyhedrovirus infection of non-permissive Tn368 cells.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {3807}, pmid = {28630398}, issn = {2045-2322}, mesh = {Animals ; Cell Line ; *Nuclear Proteins/genetics/metabolism ; *Nucleopolyhedroviruses/genetics/metabolism ; Spodoptera ; *Viral Proteins/genetics/metabolism ; }, abstract = {Baculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV) replicates in both Spodoptera frugiperda Sf21 and Trichoplusia ni Tn368 cells, whereas AcMNPV defective in hcf-1 (host cell-factor 1) gene productively infects only Sf21 cells, indicating that HCF-1 is indispensable for the AcMNPV productive infection of Tn368 cells. Here, we demonstrated that HCF-1 protein transiently expressed in Tn368 cells promotes the DNA synthesis of Hyphantria cunea MNPV (HycuMNPV), Orygia pseudotsugata MNPV and Bombyx mori NPV, which are normally unable to replicate in Tn368 cells. We also demonstrated that a recombinant HycuMNPV harboring the hcf-1 gene successfully replicates in Tn368 cells, generating substantial yields of progeny viruses and polyhedra. These results indicate that HCF-1 encoded by AcMNPV is an essential viral factor for productive NPV infection of Tn368 cells. Taken together with the previous findings on HRF-1 (host range factor 1), the present results provide strong evidence that viral genes acquired through horizontal gene transfer play an important role in baculovirus evolution, serving to expand the host range of baculoviruses.}, }
@article {pmid28627648, year = {2017}, author = {Huang, J and Deng, S and Ren, J and Tu, J and Ye, M and Wang, M}, title = {Characterization of a blaNDM‑1‑harboring plasmid from a Salmonella enterica clinical isolate in China.}, journal = {Molecular medicine reports}, volume = {16}, number = {2}, pages = {1087-1092}, pmid = {28627648}, issn = {1791-3004}, mesh = {China ; DNA, Circular/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial ; Phenotype ; Plasmids/*genetics ; Salmonella enterica/*enzymology/*isolation &amp; purification ; Sequence Analysis, DNA ; beta-Lactamases/*metabolism ; }, abstract = {The plasmid-mediated transmission of antibiotic resistance genes has been reported to be involved in the development of antibiotic resistance in bacteria, and poses a serious threat for the success of bacterial infection treatment and human health worldwide. The present study used a 454 GS‑FLX pyrosequencing system to determine the ~140 kb nucleotide sequence of plasmid pHS36‑NDM, which was identified in a Salmonella Stanley isolate from the stool sample of an 11‑month‑old girl at Lishui Central Hospital, China, and which contains a New Delhi metallo‑β‑lactamase‑1 (NDM‑1) carbapenem resistance gene (blaNDM‑1). The 181 open reading frames encode proteins with functions including replication, stable inheritance, antibiotic resistance and mobile genetic elements. Both horizontal transfer and passage stability‑related genes were identified in pHS36‑NDM, including a conserved type 4 secretion system and stbA (stable plasmid inheritance protein A). Two multidrug resistance gene islands were identified: The ISEcp1‑blaCMY transposition unit which contains a CMY‑6 β‑lactamase gene (blaCMY‑6) and a quaternary ammonium compound resistance gene (sugE); and the intI1‑ISCR27 accessory region, which contained a trimethoprim resistance gene (dfrA12), two aminoglycoside resistance genes (aadA2 and rmtC), a truncated quaternary ammonium compound resistance gene (qacE∆1), a sulfonamide resistance gene (sul1), the blaNDM‑1 carbapenemase and a bleomycin resistance gene (bleMBL). pHS36‑NDM shared high homology with other blaNDM‑1‑containing plasmids reported in Sweden, Italy and Japan. However, no previous international travel history was documented for the patient and her family, even to neighboring cities. Furthermore, pHS36‑NDM is of a different incompatibility group to other published blaNDM‑1‑carrying plasmids reported in China, with low homology in the surrounding structure of blaNDM‑1. The present study will facilitate the understanding of the underlying resistance and dispersal mechanism of pHS36‑NDM, and will deepen our recognition of the ongoing spread of the blaNDM‑1‑containing plasmids.}, }
@article {pmid28624614, year = {2017}, author = {Québatte, M and Christen, M and Harms, A and Körner, J and Christen, B and Dehio, C}, title = {Gene Transfer Agent Promotes Evolvability within the Fittest Subpopulation of a Bacterial Pathogen.}, journal = {Cell systems}, volume = {4}, number = {6}, pages = {611-621.e6}, pmid = {28624614}, issn = {2405-4712}, mesh = {Bacterial Proteins/genetics ; Bacteriophages/genetics ; Bartonella/*genetics ; Cell Division/genetics ; Gene Transfer, Horizontal/*genetics ; Genetics ; Guanosine Tetraphosphate/genetics ; }, abstract = {The Bartonella gene transfer agent (BaGTA) is an archetypical example for domestication of a phage-derived element to permit high-frequency genetic exchange in bacterial populations. Here we used multiplexed transposon sequencing (TnSeq) and single-cell reporters to globally define the core components and transfer dynamics of BaGTA. Our systems-level analysis has identified inner- and outer-circle components of the BaGTA system, including 55 regulatory components, as well as an additional 74 and 107 components mediating donor transfer and recipient uptake functions. We show that the stringent response signal guanosine-tetraphosphate (ppGpp) restricts BaGTA induction to a subset of fast-growing cells, whereas BaGTA particle uptake depends on a functional Tol-Pal trans-envelope complex that mediates outer-membrane invagination upon cell division. Our findings suggest that Bartonella evolved an efficient strategy to promote genetic exchange within the fittest subpopulation while disfavoring exchange of deleterious genetic information, thereby facilitating genome integrity and rapid host adaptation.}, }
@article {pmid28622673, year = {2019}, author = {Kordi, M and Bansal, MS}, title = {Exact Algorithms for Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {16}, number = {4}, pages = {1077-1090}, doi = {10.1109/TCBB.2017.2710342}, pmid = {28622673}, issn = {1557-9964}, mesh = {Algorithms ; Bacteria/*genetics ; Computational Biology/*methods ; Evolution, Molecular ; *Gene Duplication ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genomics/methods ; Models, Genetic ; Multigene Family ; Phylogeny ; Software ; Uncertainty ; }, abstract = {Duplication-Transfer-Loss (DTL) reconciliation is a powerful method for studying gene family evolution in the presence of horizontal gene transfer. DTL reconciliation seeks to reconcile gene trees with species trees by postulating speciation, duplication, transfer, and loss events. Efficient algorithms exist for finding optimal DTL reconciliations when the gene tree is binary. In practice, however, gene trees are often non-binary due to uncertainty in the gene tree topologies, and DTL reconciliation with non-binary gene trees is known to be NP-hard. In this paper, we present the first exact algorithms for DTL reconciliation with non-binary gene trees. Specifically, we (i) show that the DTL reconciliation problem for non-binary gene trees is fixed-parameter tractable in the maximum degree of the gene tree, (ii) present an exponential-time, but in-practice efficient, algorithm to track and enumerate all optimal binary resolutions of a non-binary input gene tree, and (iii) apply our algorithms to a large empirical data set of over 4,700 gene trees from 100 species to study the impact of gene tree uncertainty on DTL-reconciliation and to demonstrate the applicability and utility of our algorithms. The new techniques and algorithms introduced in this paper will help biologists avoid incorrect evolutionary inferences caused by gene tree uncertainty.}, }
@article {pmid28621762, year = {2017}, author = {Jheeta, S}, title = {The Landscape of the Emergence of Life.}, journal = {Life (Basel, Switzerland)}, volume = {7}, number = {2}, pages = {}, pmid = {28621762}, issn = {2075-1729}, abstract = {This paper reports on the various nuances of the origins of life on Earth and highlights the latest findings in that arena as reported at the Network of Researchers on Horizontal Gene Transfer and the Last Universal Common Ancestor (NoR HGT and LUCA) which was held from the 3-4th November 2016 at the Open University, UK. Although the answers to the question of the origin of life on Earth will not be fathomable anytime soon, a wide variety of subject matter was able to be covered, ranging from examining what constitutes a LUCA, looking at viral connections and "from RNA to DNA", i.e., could DNA have been formed simultaneously with RNA, rather than RNA first and then describing the emergence of DNA from RNA. Also discussed are proteins and the origins of genomes as well as various ideas that purport to explain the origin of life here on Earth and potentially further afield elsewhere on other planets.}, }
@article {pmid28620358, year = {2017}, author = {Soberón-Chávez, G and Alcaraz, LD and Morales, E and Ponce-Soto, GY and Servín-González, L}, title = {The Transcriptional Regulators of the CRP Family Regulate Different Essential Bacterial Functions and Can Be Inherited Vertically and Horizontally.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {959}, pmid = {28620358}, issn = {1664-302X}, abstract = {One of the best-studied transcriptional regulatory proteins in bacteria is the Escherichia coli catabolite repressor protein (CRP) that when complexed with 3'-5'-cyclic AMP (cAMP) changes its conformation and interacts with specific DNA-sequences. CRP DNA-binding can result in positive or negative regulation of gene expression depending on the position of its interaction with respect to RNA polymerase binding site. The aim of this work is to review the biological role and phylogenetic relations that some members of the CRP family of transcriptional regulators (also known as cAMP receptor protein family) have in different bacterial species. This work is not intended to give an exhaustive revision of bacterial CRP-orthologs, but to provide examples of the role that these proteins play in the expression of genes that are fundamental for the life style of some bacterial species. We highlight the conservation of their structural characteristics and of their binding to conserved-DNA sequences, in contrast to their very diverse repertoire of gene activation. CRP activates a wide variety of fundamental genes for the biological characteristic of each bacterial species, which in several instances form part of their core-genome (defined as the gene sequences present in all members of a bacterial species). We present evidence that support the fact that some of the transcriptional regulators that belong to the CRP family in different bacterial species, and some of the genes that are regulated by them, can be inherited by horizontal gene transfer. These data are discussed in the framework of bacterial evolution models.}, }
@article {pmid28619611, year = {2017}, author = {Dasgupta, N and Paul, D and Dhar Chanda, D and Ingti, B and Bhattacharjee, D and Chakravarty, A and Bhattacharjee, A}, title = {An insight into selection specificity of quinolone resistance determinants within Enterobacteriaceae family.}, journal = {Journal of global antimicrobial resistance}, volume = {10}, number = {}, pages = {40-46}, doi = {10.1016/j.jgar.2017.03.010}, pmid = {28619611}, issn = {2213-7173}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/*genetics ; Bacterial Typing Techniques/methods/*veterinary ; Biomarkers ; Community Health Centers ; Drug Resistance, Bacterial/*genetics ; Enterobacteriaceae/*drug effects/*genetics/isolation &amp; purification ; Enterobacteriaceae Infections/microbiology ; Escherichia coli/genetics ; Escherichia coli Proteins/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Hospitals ; Humans ; India ; Microbial Sensitivity Tests ; Molecular Epidemiology ; Multiplex Polymerase Chain Reaction ; Plasmids/genetics ; Prevalence ; Quinolones/*pharmacology/therapeutic use ; R Factors/*genetics ; }, abstract = {OBJECTIVES: Quinolone antimicrobials are frequently misused due to self-medication and suboptimal dose administration, leading to the development of resistance as well as treatment failure. The present study aimed to characterise plasmid-mediated quinolone resistance (PMQR) determinants and their genetic selection in the presence of quinolone stress within members of the Enterobacteriaceae.<br><br>METHODS: A total of 209 non-duplicate Enterobacteriaceae isolates were collected from hospital and community health centres over the period July 2013-June 2014. Molecular characterisation of phenotypically screened quinolone-resistant isolates was done by multiplex PCR. Plasmids bearing the qnr and aac(6')-Ib-cr genes were transformed into Escherichia coli DH5&#x3b1; and were selected on Muller-Hinton agar plates containing 0.25&#x3bc;g/mL and 0.5&#x3bc;g/mL ciprofloxacin, norfloxacin, ofloxacin, levofloxacin and moxifloxacin. Conjugation experiments were performed to determine whether the aac(6')-Ib-cr- and qnr-carrying plasmids were self-transferable.<br><br>RESULTS: The transformation assay revealed that transformants carrying qnrA could be selected in media containing norfloxacin, ciprofloxacin and levofloxacin, whereas qnrB and aac(6')-Ib-cr were selected on media containing norfloxacin and ciprofloxacin. Transformed qnrD could be selected in media containing norfloxacin and ofloxacin, and qnrS was selected only in the presence of levofloxacin.<br><br>CONCLUSIONS: The presence of qnr genes has been associated with an increase in quinolone minimum inhibitory concentrations (MICs) and therefore leads to treatment failure when quinolones are used as selective therapeutic drugs. Since PMQR determinants have a high prevalence, effective measures should be taken and surveillance should be performed in order to avoid treatment failures using this group of antimicrobials.}, }
@article {pmid28616744, year = {2017}, author = {Medrano, EG and Bell, AA}, title = {Demonstration that a Klebsiella pneumoniae subsp. pneumoniae isolated from an insect (Nezara viridula) harbors a plasmid-borne type IV secretion system.}, journal = {Current microbiology}, volume = {74}, number = {9}, pages = {1033-1042}, pmid = {28616744}, issn = {1432-0991}, mesh = {Animals ; Conjugation, Genetic ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Heteroptera/*microbiology ; Klebsiella pneumoniae/*enzymology/*genetics/isolation &amp; purification ; Molecular Sequence Annotation ; *Plasmids ; Sequence Homology, Nucleic Acid ; Type IV Secretion Systems/*genetics ; }, abstract = {Previously, we reported the isolation of Klebsiella pneumoniae subspecies pneumoniae strain Kp 5-1 from a southern green stink bug (Nezara viridula) that is a significant pest of numerous economically important crops. We subsequently sequenced the strains whole genome. Here, we report the presence of a functional plasmid-borne type IV secretion (TFSS) system that was identified using genomic mining of the annotated genome. Comparison of the Kp 5-1 resident 186 kb plasmid (pKp 5-1) with nine other Klebsiella with plasmids of comparable size from clinical and environmental strains revealed putative TFSS with identities ranging from 70 to 99%. A primer set was designed at the pKp 5-1 region that shared homology with traC of the conjugation capable F-plasmid. The 2.4 kb amplified PCR product was cloned, sequenced, and used in hybridization experiments verify that the predicted gene was extra-chromosomally located. Based on biparental mating experimental results, a K. pneumoniae Kp 5-1 derivative transformed with the non-self-transmissible pMMB207αβ (an IncQ RSF1010 derivative) mobilized the vector into the parental strain with transfer frequencies of 10[-3] transconjugants/donor. Identification of a TFSS in strain Kp 5-1 is significant since in other systems the mobilization capacity is involved in dissemination of plasmids that may confer antibiotic resistance and/or the delivery of virulence proteins into host cells, and thus may have an important role in the fitness of this strain as well. This is the first report that both compared and demonstrated functionality of a plasmid-harbored TFSS in a K. pneumoniae isolated from a N. viridula.}, }
@article {pmid28616070, year = {2017}, author = {Ridenhour, BJ and Metzger, GA and France, M and Gliniewicz, K and Millstein, J and Forney, LJ and Top, EM}, title = {Persistence of antibiotic resistance plasmids in bacterial biofilms.}, journal = {Evolutionary applications}, volume = {10}, number = {6}, pages = {640-647}, pmid = {28616070}, issn = {1752-4571}, abstract = {The emergence and spread of antibiotic resistance is a crisis in health care today. Antibiotic resistance is often horizontally transferred to susceptible bacteria by means of multidrug resistance plasmids that may or may not persist in the absence of antibiotics. Because bacterial pathogens often grow as biofilms, there is a need to better understand the evolution of plasmid persistence in these environments. Here we compared the evolution of plasmid persistence in the pathogen Acinetobacter baumannii when grown under antibiotic selection in biofilms versus well-mixed liquid cultures. After 4 weeks, clones in which the plasmid was more stably maintained in the absence of antibiotic selection were present in both populations. On average plasmid persistence increased more in liquid batch cultures, but variation in the degree of persistence was greater among biofilm-derived clones. The results of this study show for the first time that the persistence of MDR plasmids improves in biofilms.}, }
@article {pmid28613863, year = {2017}, author = {Schlachter, CR and Klapper, V and Wybouw, N and Radford, T and Van Leeuwen, T and Grbic, M and Chruszcz, M}, title = {Structural Characterization of a Eukaryotic Cyanase from Tetranychus urticae.}, journal = {Journal of agricultural and food chemistry}, volume = {65}, number = {27}, pages = {5453-5462}, doi = {10.1021/acs.jafc.7b01333}, pmid = {28613863}, issn = {1520-5118}, mesh = {Amino Acid Sequence ; Animals ; Arthropod Proteins/*chemistry/genetics/metabolism ; Carbon-Nitrogen Lyases/*chemistry/genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; Protein Conformation ; Sequence Alignment ; Tetranychidae/chemistry/*enzymology/genetics ; }, abstract = {The two-spotted spider mite Tetranychus urticae is a polyphagous agricultural pest and poses a high risk to global crop production as it is rapidly developing pesticide resistance. Genomic and transcriptomic analysis has revealed the presence of a remarkable cyanase gene in T. urticae and related mite species within the Acariformes lineage. Cyanase catalyzes the detoxification of cyanate and is potentially an attractive protein target for the development of new acaricides. Phylogenetic analysis indicates that within the Acariformes, the cyanase gene originates from a single horizontal gene transfer event, which precedes subsequent speciation. Our structural studies presented here compare and contrast prokaryotic cyanases to T. urticae cyanase, which all form homodecamers and have conserved active site residues, but display different surface areas between homodimers in the overall decameric structure.}, }
@article {pmid28611826, year = {2017}, author = {Bobay, LM and Ochman, H}, title = {The Evolution of Bacterial Genome Architecture.}, journal = {Frontiers in genetics}, volume = {8}, number = {}, pages = {72}, pmid = {28611826}, issn = {1664-8021}, support = {R35 GM118038/GM/NIGMS NIH HHS/United States ; }, abstract = {The genome architecture of bacteria and eukaryotes evolves in opposite directions when subject to genetic drift, a difference that can be ascribed to the fact that bacteria exhibit a mutational bias that deletes superfluous sequences, whereas eukaryotes are biased toward large insertions. Expansion of eukaryotic genomes occurs through the addition of non-functional sequences, such as repetitive sequences and transposable elements, whereas variation in bacterial genome size is largely due to the acquisition and loss of functional accessory genes. These properties create the situation in which eukaryotes with very similar numbers of genes can have vastly different genome sizes, while in bacteria, gene number scales linearly with genome size. Some bacterial genomes, however, particularly those of species that undergo bottlenecks due to recent association with hosts, accumulate pseudogenes and mobile elements, conferring them a low gene content relative to their genome size. These non-functional sequences are gradually eroded and eliminated after long-term association with hosts, with the result that obligate symbionts have the smallest genomes of any cellular organism. The architecture of bacterial genomes is shaped by complex and diverse processes, but for most bacterial species, genome size is governed by a non-adaptive process, i.e., genetic drift coupled with a mutational bias toward deletions. Thus, bacteria with small effective population sizes typically have the smallest genomes. Some marine bacteria counter this near-universal trend: despite having immense population sizes, selection, not drift, acts to reduce genome size in response to metabolic constraints in their nutrient-limited environment.}, }
@article {pmid28611746, year = {2017}, author = {Harding, T and Roger, AJ and Simpson, AGB}, title = {Adaptations to High Salt in a Halophilic Protist: Differential Expression and Gene Acquisitions through Duplications and Gene Transfers.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {944}, pmid = {28611746}, issn = {1664-302X}, abstract = {The capacity of halophiles to thrive in extreme hypersaline habitats derives partly from the tight regulation of ion homeostasis, the salt-dependent adjustment of plasma membrane fluidity, and the increased capability to manage oxidative stress. Halophilic bacteria, and archaea have been intensively studied, and substantial research has been conducted on halophilic fungi, and the green alga Dunaliella. By contrast, there have been very few investigations of halophiles that are phagotrophic protists, i.e., protozoa. To gather fundamental knowledge about salt adaptation in these organisms, we studied the transcriptome-level response of Halocafeteria seosinensis (Stramenopiles) grown under contrasting salinities. We provided further evolutionary context to our analysis by identifying genes that underwent recent duplications. Genes that were highly responsive to salinity variations were involved in stress response (e.g., chaperones), ion homeostasis (e.g., Na[+]/H[+] transporter), metabolism and transport of lipids (e.g., sterol biosynthetic genes), carbohydrate metabolism (e.g., glycosidases), and signal transduction pathways (e.g., transcription factors). A significantly high proportion (43%) of duplicated genes were also differentially expressed, accentuating the importance of gene expansion in adaptation by H. seosinensis to high salt environments. Furthermore, we found two genes that were lateral acquisitions from bacteria, and were also highly up-regulated and highly expressed at high salt, suggesting that this evolutionary mechanism could also have facilitated adaptation to high salt. We propose that a transition toward high-salt adaptation in the ancestors of H. seosinensis required the acquisition of new genes via duplication, and some lateral gene transfers (LGTs), as well as the alteration of transcriptional programs, leading to increased stress resistance, proper establishment of ion gradients, and modification of cell structure properties like membrane fluidity.}, }
@article {pmid28611742, year = {2017}, author = {Uhrynowski, W and Decewicz, P and Dziewit, L and Radlinska, M and Krawczyk, PS and Lipinski, L and Adamska, D and Drewniak, L}, title = {Analysis of the Genome and Mobilome of a Dissimilatory Arsenate Reducing Aeromonas sp. O23A Reveals Multiple Mechanisms for Heavy Metal Resistance and Metabolism.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {936}, pmid = {28611742}, issn = {1664-302X}, abstract = {Aeromonas spp. are among the most ubiquitous microorganisms, as they have been isolated from different environmental niches including waters, soil, as well as wounds and digestive tracts of poikilothermic animals and humans. Although much attention has been paid to the pathogenicity of Aeromonads, the role of these bacteria in environmentally important processes, such as transformation of heavy metals, remains to be discovered. Therefore, the aim of this study was a detailed genomic characterization of Aeromonas sp. O23A, the first representative of this genus capable of dissimilatory arsenate reduction. The strain was isolated from microbial mats from the Zloty Stok mine (SW Poland), an environment strongly contaminated with arsenic. Previous physiological studies indicated that O23A may be involved in both mobilization and immobilization of this metalloid in the environment. To discover the molecular basis of the mechanisms behind the observed abilities, the genome of O23A (∼5.0 Mbp) was sequenced and annotated, and genes for arsenic respiration, heavy metal resistance (hmr) and other phenotypic traits, including siderophore production, were identified. The functionality of the indicated gene modules was assessed in a series of minimal inhibitory concentration analyses for various metals and metalloids, as well as mineral dissolution experiments. Interestingly, comparative analyses revealed that O23A is related to a fish pathogen Aeromonas salmonicida subsp. salmonicida A449 which, however, does not carry genes for arsenic respiration. This indicates that the dissimilatory arsenate reduction ability may have been lost during genome reduction in pathogenic strains, or acquired through horizontal gene transfer. Therefore, particular emphasis was placed upon the mobilome of O23A, consisting of four plasmids, a phage, and numerous transposable elements, which may play a role in the dissemination of hmr and arsenic metabolism genes in the environment. The obtained results indicate that Aeromonas sp. O23A is well-adapted to the extreme environmental conditions occurring in the Zloty Stok mine. The analysis of genome encoded traits allowed for a better understanding of the mechanisms of adaptation of the strain, also with respect to its presumable role in colonization and remediation of arsenic-contaminated waters, which may never have been discovered based on physiological analyses alone.}, }
@article {pmid28611213, year = {2017}, author = {Fagerlund, RD and Wilkinson, ME and Klykov, O and Barendregt, A and Pearce, FG and Kieper, SN and Maxwell, HWR and Capolupo, A and Heck, AJR and Krause, KL and Bostina, M and Scheltema, RA and Staals, RHJ and Fineran, PC}, title = {Spacer capture and integration by a type I-F Cas1-Cas2-3 CRISPR adaptation complex.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {26}, pages = {E5122-E5128}, pmid = {28611213}, issn = {1091-6490}, mesh = {Bacterial Proteins/genetics/*metabolism ; CRISPR-Cas Systems/*physiology ; Endonucleases/genetics/*metabolism ; Multienzyme Complexes/genetics/*metabolism ; Pectobacterium/*enzymology/genetics ; }, abstract = {CRISPR-Cas adaptive immune systems capture DNA fragments from invading bacteriophages and plasmids and integrate them as spacers into bacterial CRISPR arrays. In type I-E and II-A CRISPR-Cas systems, this adaptation process is driven by Cas1-Cas2 complexes. Type I-F systems, however, contain a unique fusion of Cas2, with the type I effector helicase and nuclease for invader destruction, Cas3. By using biochemical, structural, and biophysical methods, we present a structural model of the 400-kDa Cas14-Cas2-32 complex from Pectobacterium atrosepticum with bound protospacer substrate DNA. Two Cas1 dimers assemble on a Cas2 domain dimeric core, which is flanked by two Cas3 domains forming a groove where the protospacer binds to Cas1-Cas2. We developed a sensitive in vitro assay and demonstrated that Cas1-Cas2-3 catalyzed spacer integration into CRISPR arrays. The integrase domain of Cas1 was necessary, whereas integration was independent of the helicase or nuclease activities of Cas3. Integration required at least partially duplex protospacers with free 3'-OH groups, and leader-proximal integration was stimulated by integration host factor. In a coupled capture and integration assay, Cas1-Cas2-3 processed and integrated protospacers independent of Cas3 activity. These results provide insight into the structure of protospacer-bound type I Cas1-Cas2-3 adaptation complexes and their integration mechanism.}, }
@article {pmid28610890, year = {2017}, author = {Brodie, J and Chan, CX and De Clerck, O and Cock, JM and Coelho, SM and Gachon, C and Grossman, AR and Mock, T and Raven, JA and Smith, AG and Yoon, HS and Bhattacharya, D}, title = {The Algal Revolution.}, journal = {Trends in plant science}, volume = {22}, number = {8}, pages = {726-738}, doi = {10.1016/j.tplants.2017.05.005}, pmid = {28610890}, issn = {1878-4372}, support = {BB/L014130/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Biodiversity ; Biological Evolution ; Biotechnology ; Ecology ; Gene Transfer, Horizontal ; *Photosynthesis ; Stramenopiles/*genetics/physiology ; Symbiosis ; }, abstract = {Algae are (mostly) photosynthetic eukaryotes that occupy multiple branches of the tree of life, and are vital for planet function and health. In this review, we highlight a transformative period in studies of the evolution and functioning of this extraordinary group of organisms and their potential for novel applications, wrought by high-throughput 'omic' and reverse genetic methods. We cover the origin and diversification of algal groups, explore advances in understanding the link between phenotype and genotype, consider algal sex determination, and review progress in understanding the roots of algal multicellularity. Experimental evolution studies to determine how algae evolve in changing environments are highlighted, as is their potential as production platforms for compounds of commercial interest, such as biofuel precursors, nutraceuticals, or therapeutics.}, }
@article {pmid28607039, year = {2017}, author = {Wang, S and Chen, Y}, title = {Origin of magnetotaxis: Vertical inheritance or horizontal transfer?.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {26}, pages = {E5016-E5018}, pmid = {28607039}, issn = {1091-6490}, mesh = {Databases, Genetic ; *Gene Transfer, Horizontal ; Humans ; *Transfer, Psychology ; }, }
@article {pmid28604829, year = {2017}, author = {Kim, BJ and Kim, GN and Kim, BR and Shim, TS and Kook, YH and Kim, BJ}, title = {Phylogenetic analysis of Mycobacterium massiliense strains having recombinant rpoB gene laterally transferred from Mycobacterium abscessus.}, journal = {PloS one}, volume = {12}, number = {6}, pages = {e0179237}, pmid = {28604829}, issn = {1932-6203}, mesh = {Bacterial Proteins/*genetics ; DNA-Directed RNA Polymerases/*genetics ; *Gene Transfer, Horizontal ; Humans ; Multilocus Sequence Typing ; Mycobacterium/*classification/*genetics ; *Phylogeny ; *Recombination, Genetic ; Sequence Analysis, DNA ; }, abstract = {Recent multi locus sequence typing (MLST) and genome based studies indicate that lateral gene transfer (LGT) events in the rpoB gene are prevalent between Mycobacterium abscessus complex strains. To check the prevalence of the M. massiliense strains subject to rpoB LGT (Rec-mas), we applied rpoB typing (711 bp) to 106 Korean strains of M. massiliense infection that had already been identified by hsp65 sequence analysis (603 bp). The analysis indicated 6 smooth strains in M. massiliense Type I (10.0%, 6/60) genotypes but no strains in M. massiliense Type II genotypes (0%, 0/46), showing a discrepancy between the 2 typing methods. Further MLST analysis based on the partial sequencing of seven housekeeping genes, argH, cya, glpK, gnd, murC, pta and purH, as well as erm(41) PCR proved that these 6 Rec-mas strains consisted of two distinct genotypes belonging to M. massiliense and not M. abscessus. The complete rpoB sequencing analysis showed that these 6 Rec-mas strains have an identical hybrid rpoB gene, of which a 478 bp partial rpoB fragment may be laterally transferred from M. abscessus. Notably, five of the 6 Rec-mas strains showed complete identical sequences in a total of nine genes, including the seven MLST genes, hsp65, and rpoB, suggesting their clonal propagation in South Korea. In conclusion, we identified 6 M. massiliense smooth strains of 2 phylogenetically distinct genotypes with a specific hybrid rpoB gene laterally transferred from M. abscessus from Korean patients. Their clinical relevance and bacteriological traits remain to be elucidated.}, }
@article {pmid28602701, year = {2017}, author = {Bie, L and Wu, H and Wang, XH and Wang, M and Xu, H}, title = {Identification and characterization of new members of the SXT/R391 family of integrative and conjugative elements (ICEs) in Proteus mirabilis.}, journal = {International journal of antimicrobial agents}, volume = {50}, number = {2}, pages = {242-246}, doi = {10.1016/j.ijantimicag.2017.01.045}, pmid = {28602701}, issn = {1872-7913}, mesh = {Anti-Bacterial Agents/metabolism ; China ; Conjugation, Genetic ; *Drug Resistance, Multiple, Bacterial ; Evolution, Molecular ; Gene Order ; Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences ; Microbial Sensitivity Tests ; Phylogeny ; Proteus mirabilis/*drug effects/*genetics ; Trimethoprim, Sulfamethoxazole Drug Combination/metabolism ; }, abstract = {Integrative and conjugative elements (ICEs) are self-transmissible chromosomal mobile elements that play significant roles in the dissemination of antimicrobial resistance genes. Identification of the structures and functions of ICEs, particularly those in pathogens, improves understanding of the dissemination of antimicrobial resistance. This study identified new members of the sulfamethoxazole-trimethoprim (SXT)/R391 family of ICEs that could confer multi-drug resistance in the opportunistic pathogen Proteus mirabilis, characterized their genetic structures, and explored their evolutionary connection with other members of this family of ICEs. Three new members of the SXT/R391 family of ICEs were detected in six of 77 P. mirabilis strains isolated in China: ICEPmiChn2 (one strain), ICEPmiChn3 (one strain) and ICEPmiChn4 (three strains). All three new ICEs harbour antimicrobial resistance genes from diverse origins, suggesting their capability in acquiring foreign genes and serving as important carriers for antimicrobial resistance genes. Structural analysis showed that ICEPmiChn3 is a particularly interesting and unique ICE that has lost core genes involved in conjugation, and could not transfer to other cells via conjugation. This finding confirmed the key roles of these missing genes in conjugation. Further phylogenetic analysis suggested that ICEs in geographically close strains are also connected evolutionarily, and ICEPmiChn3 lost its conjugation cassette from a former mobile ICE. The identification and characterization of the three new members of the SXT/R391 family of ICEs in this work leads to suggestions of core ICE genes essential for conjugation, and extends understanding on the structures of ICEs, evolutionary relationships between ICEs, and the antimicrobial resistance mechanisms of P. mirabilis.}, }
@article {pmid28600959, year = {2017}, author = {García-Aljaro, C and Ballesté, E and Muniesa, M}, title = {Beyond the canonical strategies of horizontal gene transfer in prokaryotes.}, journal = {Current opinion in microbiology}, volume = {38}, number = {}, pages = {95-105}, doi = {10.1016/j.mib.2017.04.011}, pmid = {28600959}, issn = {1879-0364}, mesh = {Bacteria/*genetics ; *Gene Transfer, Horizontal ; Interspersed Repetitive Sequences ; *Prokaryotic Cells ; }, abstract = {Efforts to identify and characterize strategies for horizontal gene transfer (HGT) in prokaryotes could have overlooked some mechanisms that do not entirely fit in with the canonical ones most often described (conjugation of plasmids, phage transduction and transformation). The difficulty in distinguishing the different HGT strategies could have contributed to underestimate their real extent. Here we review non classical HGT strategies: some that require mobile genetic elements (MGEs) and others independent of MGE. Among those strategies that require MGEs, there is a range of newly reported, hybrid and intermediate MGEs mobilizing only their own DNA, others that mobilize preferentially bacterial DNA, or both. Considering HGT strategies independent of MGE, a few are even not restricted to DNA transfer, but can also mobilize other molecules. This review considers those HGT strategies that are less commonly dealt with in the literature. The real impact of these elements could, in some conditions, be more relevant than previously thought.}, }
@article {pmid28600539, year = {2017}, author = {Guo, Y and Lin, WK and Chen, Q and Vallejo, VA and Warner, RM}, title = {Genetic Determinants of Crop Timing and Quality Traits in Two Interspecific Petunia Recombinant Inbred Line Populations.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {3200}, pmid = {28600539}, issn = {2045-2322}, mesh = {Crops, Agricultural/*genetics/growth &amp; development ; Flowers/genetics/growth &amp; development ; Gene Transfer, Horizontal/*genetics ; Genetic Linkage ; Petunia/*genetics/growth &amp; development ; Phenotype ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci/genetics ; }, abstract = {The rate at which plants develop new nodes (development rate) is a major determinant of crop production time, yet the genetic control of this process, including genetic interactions with crop quality parameters, is poorly understood. We employed a modified genotyping-by-sequencing approach and generated genetic linkage maps with 6,291 and 3,297 single nucleotide polymorphisms (SNPs) for the interspecific Petunia recombinant inbred line (RIL) population - P. axillaris × P. exserta (AE) and P. integrifolia × P. axillaris (IA), respectively. Comparative mapping between the populations revealed perfect collinearity of marker order but different recombination frequency at the corresponding linkage groups (LGs). Quantitative trait loci (QTL) mapping conducted for development traits and other important quality traits indicated QTL clustered on chromosome 1, 2, 4 and 6 for the AE population and chromosome 1, 2, 5 and 6 for the IA population. Additionally, 209 differentially expressed unique transcripts were identified in shoot apex tissue between fast- and slow-developing RILs, 13 of which mapped to within 1 cM of a development rate QTL. These results will facilitate the identification of novel genes controlling crop timing and quality traits in Petunia and highlight the power of using multiple interspecific populations to elucidate genetic determinants of natural variation.}, }
@article {pmid28599143, year = {2017}, author = {Westbye, AB and Beatty, JT and Lang, AS}, title = {Guaranteeing a captive audience: coordinated regulation of gene transfer agent (GTA) production and recipient capability by cellular regulators.}, journal = {Current opinion in microbiology}, volume = {38}, number = {}, pages = {122-129}, doi = {10.1016/j.mib.2017.05.003}, pmid = {28599143}, issn = {1879-0364}, mesh = {Biological Factors/genetics/*metabolism ; *DNA Transformation Competence ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Rhodobacter capsulatus/*genetics ; Transduction, Genetic ; Transformation, Bacterial ; }, abstract = {Gene transfer agents (GTAs) are bacteriophage-like particles produced by many prokaryotes. Several members of the Alphaproteobacteria produce a class of genetically-related GTAs that is best studied in Rhodobacter capsulatus. DNA transfer by the R. capsulatus GTA (RcGTA) combines aspects of both transduction and natural transformation, as recipient cells require a natural transformation-like system to incorporate donated DNA. The genes involved in RcGTA production and recipient capability are located at multiple loci in the bacterial genome; however, a conserved phosphorelay containing the response regulator CtrA and a quorum sensing system regulate both RcGTA production and recipient capability. This review highlights recent discoveries in RcGTA biology, and focuses on the co-regulation of genes involved in RcGTA production and recipient capability.}, }
@article {pmid28598078, year = {2016}, author = {Wu, LJ and Wang, TT and He, QY and Zhao, D and Tang, SS and Kang, M and He, C and Xie, Y}, title = {[The Transmission of KPC-2 Gene in Klebsiella Species].}, journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition}, volume = {47}, number = {5}, pages = {674-678}, pmid = {28598078}, issn = {1672-173X}, mesh = {Anti-Bacterial Agents ; Bacterial Proteins ; Carbapenems ; China ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Klebsiella Infections ; Klebsiella pneumoniae/drug effects/*genetics ; Microbial Sensitivity Tests ; Plasmids/genetics ; Random Amplified Polymorphic DNA Technique ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: To explore the mechanisms of imipenem resistance inKlebsiella spp. and the transmission of Klebsiella pneumoniae Carbapenemase-2(KPC-2) gene in Klebsiella species.<br><br>METHODS: The imipenem resistant Klebsiella pneumoniae and Klebsiella oxytoca were isolated in the West China Hospital of Sichuan University in 2009/2010 and 2012/2013. Their minimal inhibitory concentration (MIC) was determined by agar dilution method. CARB ChromID plate and improved Hodge test were undertaken to detect carbapenemases resistant phenotype. PCR method was used for detecting KPC-2 gene. Plasmid transmission was detected by plasmid conjugation tests. The homology of the plasmids and the strains was analyzed using random amplified polymorphic DNA (RAPD) and enterobacterial repetitive intergenic consensus PCR(ERIC-PCR) methods.<br><br>RESULTS: Three strains of Klebsiella oxytoca collected in 2009/2010 and 7 Klebsiella pneumoniae collected in 2012/2013 developed carbapenemases resistance, all of which carried KPC-2 gene. The 3 KPC-2 positive plasmids isolated from Klebsiella oxytoca transited to recipient organisms and showed homology with the 7 KPC-2 gene positive plasmids isolated from Klebsiella pneumoniae. The ERIC-PCR showed homology of the 7 KPC positive Klebsiella pneumoniae.<br><br>CONCLUSIONS: Carbapenemases inKlebsiella spp with expressed KPC-2 gene contribute to the development of resistance in this hospital. The transmission of KPC-2 plasmid in Klebsiella oxytoca may cause imipenem resistance in Klebsiella pneumonia. The horizontal transmission may be the main mechanism in the spread of imipenem resistance inKlebsiella spp.}, }
@article {pmid28596991, year = {2017}, author = {Rieger, M and Mauch, H and Hakenbeck, R}, title = {Long Persistence of a Streptococcus pneumoniae 23F Clone in a Cystic Fibrosis Patient.}, journal = {mSphere}, volume = {2}, number = {3}, pages = {}, pmid = {28596991}, issn = {2379-5042}, abstract = {Streptococcus pneumoniae isolates of serotype 23F with intermediate penicillin resistance were recovered on seven occasions over a period of 37 months from a cystic fibrosis patient in Berlin. All isolates expressed the same multilocus sequence type (ST), ST10523. The genome sequences of the first and last isolates, D122 and D141, revealed the absence of two phage-related gene clusters compared to the genome of another ST10523 strain, D219, isolated earlier at a different place in Germany. Genomes of all three strains carried the same novel mosaic penicillin-binding protein (PBP) genes, pbp2x, pbp2b, and pbp1a; these genes were distinct from those of other penicillin-resistant S. pneumoniae strains except for pbp1a of a Romanian S. pneumoniae isolate. All PBPs contained mutations that have been associated with the penicillin resistance phenotype. Most interestingly, a mosaic block identical to an internal pbp2x sequence of ST10523 was present in pbp2x of Streptococcus mitis strain B93-4, which was isolated from the same patient. This suggests interspecies gene transfer from S. pneumoniae to S. mitis within the host. Nearly all genes expressing surface proteins, which represent major virulence factors of S. pneumoniae and are typical for this species, were present in the genome of ST10523. One exception was the hyaluronidase gene hlyA, which contained a 12-nucleotide deletion within the promoter region and an internal stop codon. The lack of a functional hyaluronidase might contribute to the ability to persist in the host for an unusually long period of time. IMPORTANCEStreptococcus pneumoniae is a common resident in the human nasopharynx. However, carriage can result in severe diseases due to a unique repertoire of pathogenicity factors that are rare in closely related commensal streptococci. We investigated a penicillin-resistant S. pneumoniae clone of serotype 23F isolated from a cystic fibrosis patient on multiple occasions over an unusually long period of over 3 years that was present without causing disease. Genome comparisons revealed an apparent nonfunctional pneumococcus-specific gene encoding a hyaluronidase, supporting the view that this enzyme adds to the virulence potential of the bacterium. The 23F clone harbored unique mosaic genes encoding penicillin resistance determinants, the product of horizontal gene transfer involving the commensal S. mitis as donor species. Sequences identical to one such mosaic gene were identified in an S. mitis strain from the same patient, suggesting that in this case S. pneumoniae played the role of donor.}, }
@article {pmid28593799, year = {2017}, author = {Jalasvuori, M and Penttinen, R}, title = {What can evolutionary rescue tell us about the emergence of new resistant bacteria?.}, journal = {Future microbiology}, volume = {12}, number = {}, pages = {731-733}, doi = {10.2217/fmb-2017-0079}, pmid = {28593799}, issn = {1746-0921}, mesh = {Anti-Bacterial Agents/*administration &amp; dosage ; Bacteria/*drug effects/*genetics ; Bacterial Infections/*drug therapy ; *Drug Resistance, Bacterial ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Humans ; Mutation ; Selection, Genetic ; }, }
@article {pmid28592505, year = {2017}, author = {Dujon, BA and Louis, EJ}, title = {Genome Diversity and Evolution in the Budding Yeasts (Saccharomycotina).}, journal = {Genetics}, volume = {206}, number = {2}, pages = {717-750}, pmid = {28592505}, issn = {1943-2631}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Biological Evolution ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Variation ; Genetics, Population ; *Genome, Fungal ; Genotype ; Phenotype ; Saccharomyces cerevisiae/*genetics ; }, abstract = {Considerable progress in our understanding of yeast genomes and their evolution has been made over the last decade with the sequencing, analysis, and comparisons of numerous species, strains, or isolates of diverse origins. The role played by yeasts in natural environments as well as in artificial manufactures, combined with the importance of some species as model experimental systems sustained this effort. At the same time, their enormous evolutionary diversity (there are yeast species in every subphylum of Dikarya) sparked curiosity but necessitated further efforts to obtain appropriate reference genomes. Today, yeast genomes have been very informative about basic mechanisms of evolution, speciation, hybridization, domestication, as well as about the molecular machineries underlying them. They are also irreplaceable to investigate in detail the complex relationship between genotypes and phenotypes with both theoretical and practical implications. This review examines these questions at two distinct levels offered by the broad evolutionary range of yeasts: inside the best-studied Saccharomyces species complex, and across the entire and diversified subphylum of Saccharomycotina. While obviously revealing evolutionary histories at different scales, data converge to a remarkably coherent picture in which one can estimate the relative importance of intrinsic genome dynamics, including gene birth and loss, vs. horizontal genetic accidents in the making of populations. The facility with which novel yeast genomes can now be studied, combined with the already numerous available reference genomes, offer privileged perspectives to further examine these fundamental biological questions using yeasts both as eukaryotic models and as fungi of practical importance.}, }
@article {pmid28591314, year = {2017}, author = {Morgado, SM and Marín, MA and Freitas, FS and Fonseca, EL and Vicente, ACP}, title = {Complete plasmid sequence carrying type IV-like and type VII secretion systems from an atypical mycobacteria strain.}, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {112}, number = {7}, pages = {514-516}, pmid = {28591314}, issn = {1678-8060}, mesh = {DNA, Bacterial/*genetics ; Humans ; Molecular Sequence Data ; Nontuberculous Mycobacteria/*genetics ; Plasmids/genetics ; Sequence Analysis, DNA ; Type IV Secretion Systems/*genetics ; Type VII Secretion Systems/*genetics ; }, abstract = {The genus Mycobacterium is highly diverse and ubiquitous in nature, comprehending fast- and slow-growing species with distinct impact in public health. The plasmid-mediated horizontal gene transfer represents one of the major events in bacteria evolution. Here, we report the complete sequence of a 160,489 bp circular plasmid (pCBMA213_2) from an atypical and fast-growing environmental mycobacteria. This is a unique plasmid, in comparison with the characterised mycobacteria plasmids, harboring a type IV-like and ESX-P2 type VII secretion systems. pCBMA213_2 can be further explored for evolutionary and conjugation studies as well as a tool to manipulate DNA within this bacteria genus.}, }
@article {pmid28590877, year = {2017}, author = {Kikuchi, T and Eves-van den Akker, S and Jones, JT}, title = {Genome Evolution of Plant-Parasitic Nematodes.}, journal = {Annual review of phytopathology}, volume = {55}, number = {}, pages = {333-354}, doi = {10.1146/annurev-phyto-080516-035434}, pmid = {28590877}, issn = {1545-2107}, support = {BB/M014207/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Helminth ; Multigene Family ; Nematoda/*genetics ; Plant Diseases/*parasitology ; Plants/*parasitology ; }, abstract = {Plant parasitism has evolved independently on at least four separate occasions in the phylum Nematoda. The application of next-generation sequencing (NGS) to plant-parasitic nematodes has allowed a wide range of genome- or transcriptome-level comparisons, and these have identified genome adaptations that enable parasitism of plants. Current genome data suggest that horizontal gene transfer, gene family expansions, evolution of new genes that mediate interactions with the host, and parasitism-specific gene regulation are important adaptations that allow nematodes to parasitize plants. Sequencing of a larger number of nematode genomes, including plant parasites that show different modes of parasitism or that have evolved in currently unsampled clades, and using free-living taxa as comparators would allow more detailed analysis and a better understanding of the organization of key genes within the genomes. This would facilitate a more complete understanding of the way in which parasitism has shaped the genomes of plant-parasitic nematodes.}, }
@article {pmid28589945, year = {2017}, author = {Jiang, X and Ellabaan, MMH and Charusanti, P and Munck, C and Blin, K and Tong, Y and Weber, T and Sommer, MOA and Lee, SY}, title = {Dissemination of antibiotic resistance genes from antibiotic producers to pathogens.}, journal = {Nature communications}, volume = {8}, number = {}, pages = {15784}, pmid = {28589945}, issn = {2041-1723}, mesh = {Acinetobacter/drug effects/genetics ; Actinobacteria/drug effects/genetics ; Anti-Bacterial Agents/metabolism/pharmacology ; Bacterial Proteins/*genetics ; DNA Transposable Elements ; Drug Resistance, Microbial/*genetics ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Phylogeny ; Proteobacteria/*drug effects/*genetics/pathogenicity ; Streptomyces/drug effects/*genetics ; }, abstract = {It has been hypothesized that some antibiotic resistance genes (ARGs) found in pathogenic bacteria derive from antibiotic-producing actinobacteria. Here we provide bioinformatic and experimental evidence supporting this hypothesis. We identify genes in proteobacteria, including some pathogens, that appear to be closely related to actinobacterial ARGs known to confer resistance against clinically important antibiotics. Furthermore, we identify two potential examples of recent horizontal transfer of actinobacterial ARGs to proteobacterial pathogens. Based on this bioinformatic evidence, we propose and experimentally test a 'carry-back' mechanism for the transfer, involving conjugative transfer of a carrier sequence from proteobacteria to actinobacteria, recombination of the carrier sequence with the actinobacterial ARG, followed by natural transformation of proteobacteria with the carrier-sandwiched ARG. Our results support the existence of ancient and, possibly, recent transfers of ARGs from antibiotic-producing actinobacteria to proteobacteria, and provide evidence for a defined mechanism.}, }
@article {pmid28588130, year = {2017}, author = {McDonald, BR and Currie, CR}, title = {Lateral Gene Transfer Dynamics in the Ancient Bacterial Genus Streptomyces.}, journal = {mBio}, volume = {8}, number = {3}, pages = {}, pmid = {28588130}, issn = {2150-7511}, support = {T32 GM007215/GM/NIGMS NIH HHS/United States ; U19 AI109673/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/biosynthesis ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Phylogeny ; Point Mutation ; Streptomyces/*genetics/metabolism ; }, abstract = {Lateral gene transfer (LGT) profoundly shapes the evolution of bacterial lineages. LGT across disparate phylogenetic groups and genome content diversity between related organisms suggest a model of bacterial evolution that views LGT as rampant and promiscuous. It has even driven the argument that species concepts and tree-based phylogenetics cannot be applied to bacteria. Here, we show that acquisition and retention of genes through LGT are surprisingly rare in the ubiquitous and biomedically important bacterial genus Streptomyces Using a molecular clock, we estimate that the Streptomyces bacteria are ~380 million years old, indicating that this bacterial genus is as ancient as land vertebrates. Calibrating LGT rate to this geologic time span, we find that on average only 10 genes per million years were acquired and subsequently maintained. Over that same time span, Streptomyces accumulated thousands of point mutations. By explicitly incorporating evolutionary timescale into our analyses, we provide a dramatically different view on the dynamics of LGT and its impact on bacterial evolution.IMPORTANCE Tree-based phylogenetics and the use of species as units of diversity lie at the foundation of modern biology. In bacteria, these pillars of evolutionary theory have been called into question due to the observation of thousands of lateral gene transfer (LGT) events within and between lineages. Here, we show that acquisition and retention of genes through LGT are exceedingly rare in the bacterial genus Streptomyces, with merely one gene acquired in Streptomyces lineages every 100,000 years. These findings stand in contrast to the current assumption of rampant genetic exchange, which has become the dominant hypothesis used to explain bacterial diversity. Our results support a more nuanced understanding of genetic exchange, with LGT impacting evolution over short timescales but playing a significant role over long timescales. Deeper understanding of LGT provides new insight into the evolutionary history of life on Earth, as the vast majority of this history is microbial.}, }
@article {pmid28587172, year = {2017}, author = {Watts, JEM and Schreier, HJ and Lanska, L and Hale, MS}, title = {The Rising Tide of Antimicrobial Resistance in Aquaculture: Sources, Sinks and Solutions.}, journal = {Marine drugs}, volume = {15}, number = {6}, pages = {}, pmid = {28587172}, issn = {1660-3397}, mesh = {Animals ; Anti-Infective Agents/pharmacology ; Aquaculture/methods ; Bacteria/drug effects ; Drug Resistance, Microbial/*genetics ; Gene Transfer, Horizontal/genetics ; Humans ; Probiotics/pharmacology ; }, abstract = {As the human population increases there is an increasing reliance on aquaculture to supply a safe, reliable, and economic supply of food. Although food production is essential for a healthy population, an increasing threat to global human health is antimicrobial resistance. Extensive antibiotic resistant strains are now being detected; the spread of these strains could greatly reduce medical treatment options available and increase deaths from previously curable infections. Antibiotic resistance is widespread due in part to clinical overuse and misuse; however, the natural processes of horizontal gene transfer and mutation events that allow genetic exchange within microbial populations have been ongoing since ancient times. By their nature, aquaculture systems contain high numbers of diverse bacteria, which exist in combination with the current and past use of antibiotics, probiotics, prebiotics, and other treatment regimens-singularly or in combination. These systems have been designated as "genetic hotspots" for gene transfer. As our reliance on aquaculture grows, it is essential that we identify the sources and sinks of antimicrobial resistance, and monitor and analyse the transfer of antimicrobial resistance between the microbial community, the environment, and the farmed product, in order to better understand the implications to human and environmental health.}, }
@article {pmid28586714, year = {2017}, author = {Fernandez-Lopez, R and Redondo, S and Garcillan-Barcia, MP and de la Cruz, F}, title = {Towards a taxonomy of conjugative plasmids.}, journal = {Current opinion in microbiology}, volume = {38}, number = {}, pages = {106-113}, doi = {10.1016/j.mib.2017.05.005}, pmid = {28586714}, issn = {1879-0364}, mesh = {*Conjugation, Genetic ; Gene Transfer, Horizontal ; Plasmids/analysis/*classification ; }, abstract = {Conjugative plasmids are the keystone of horizontal gene transfer. Metagenomic research and clinical understanding of plasmid transmission beg for a taxonomical approach to conjugative plasmid classification. Up to now, a meaningful classification was difficult to achieve for lack of appropriate analytical tools. The advent of the genomic era revolutionized the landscape, offering a plethora of plasmid sequences as well as bioinformatic analytical tools. Given the need and the opportunity, in view of the available evidence, a taxonomy of conjugative plasmids is proposed in the hope that it will leverage plasmid studies.}, }
@article {pmid28578314, year = {2017}, author = {Mina, JG and Thye, JK and Alqaisi, AQI and Bird, LE and Dods, RH and Grøftehauge, MK and Mosely, JA and Pratt, S and Shams-Eldin, H and Schwarz, RT and Pohl, E and Denny, PW}, title = {Functional and phylogenetic evidence of a bacterial origin for the first enzyme in sphingolipid biosynthesis in a phylum of eukaryotic protozoan parasites.}, journal = {The Journal of biological chemistry}, volume = {292}, number = {29}, pages = {12208-12219}, pmid = {28578314}, issn = {1083-351X}, support = {MR/K018779/1/MRC_/Medical Research Council/United Kingdom ; BB/M024156/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/D52396X/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Catalytic Domain ; Computational Biology ; Conserved Sequence ; Dimerization ; Endoplasmic Reticulum/*enzymology ; Gene Deletion ; Gene Duplication ; Gene Transfer, Horizontal ; Isoenzymes/chemistry/genetics/isolation &amp; purification/metabolism ; *Models, Molecular ; Peptide Fragments/chemistry/genetics/metabolism ; *Phylogeny ; Protein Conformation ; Protein Interaction Domains and Motifs ; Protein Transport ; Protozoan Proteins/chemistry/genetics/isolation &amp; purification/*metabolism ; Recombinant Fusion Proteins/chemistry/metabolism ; Sequence Alignment ; Serine C-Palmitoyltransferase/chemistry/genetics/isolation &amp; purification/*metabolism ; Structural Homology, Protein ; Toxoplasma/*enzymology ; }, abstract = {Toxoplasma gondii is an obligate, intracellular eukaryotic apicomplexan protozoan parasite that can cause fetal damage and abortion in both animals and humans. Sphingolipids are essential and ubiquitous components of eukaryotic membranes that are both synthesized and scavenged by the Apicomplexa. Here we report the identification, isolation, and analyses of the Toxoplasma serine palmitoyltransferase, an enzyme catalyzing the first and rate-limiting step in sphingolipid biosynthesis: the condensation of serine and palmitoyl-CoA. In all eukaryotes analyzed to date, serine palmitoyltransferase is a highly conserved heterodimeric enzyme complex. However, biochemical and structural analyses demonstrated the apicomplexan orthologue to be a functional, homodimeric serine palmitoyltransferase localized to the endoplasmic reticulum. Furthermore, phylogenetic studies indicated that it was evolutionarily related to the prokaryotic serine palmitoyltransferase, identified in the Sphingomonadaceae as a soluble homodimeric enzyme. Therefore this enzyme, conserved throughout the Apicomplexa, is likely to have been obtained via lateral gene transfer from a prokaryote.}, }
@article {pmid28578196, year = {2017}, author = {Jiao, YN and Chen, H and Gao, RX and Zhu, YG and Rensing, C}, title = {Organic compounds stimulate horizontal transfer of antibiotic resistance genes in mixed wastewater treatment systems.}, journal = {Chemosphere}, volume = {184}, number = {}, pages = {53-61}, doi = {10.1016/j.chemosphere.2017.05.149}, pmid = {28578196}, issn = {1879-1298}, mesh = {Anti-Bacterial Agents/analysis ; Drug Resistance, Microbial/*genetics ; Environmental Monitoring ; Escherichia coli/drug effects ; Genes, Bacterial/drug effects ; *Genes, Microbial ; *Humic Substances ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Sewage ; *Waste Disposal, Fluid ; Wastewater/chemistry/*microbiology ; }, abstract = {Domestic wastewater treatment plants as a reservoir of antibiotic resistance genes (ARGs) have received much attention, but the effect of dyes on the propagation of ARGs has rarely been investigated. In this study, we investigated the differences in distributions of ARGs and microbial communities using high-throughput qPCR and 16S rRNA gene sequencing, respectively, between mixed (dyeing and domestic) wastewater and domestic sewage. The relative abundance of ARGs in inflows of mixed wastewater (IW2 and IW3) was higher than that of domestic wastewater (IW1). The relative abundance of mobile genetic elements in the inflow of textile dyeing wastewater (IDW3) was 3- to 13-fold higher than that in other samples. Moreover, in IDW3, some distinct high abundance ARGs, particularly operons encoding efflux pumps (such as acrR-01, acrB-01 and acrF), were significantly correlated with Streptococcus of the Firmicutes. To explore why the abundance of ARGs was relatively high in mixed wastewater, six representative types of organic compounds in textile dyeing wastewater were used to test the effect on plasmid-based conjugative transfer from E. coli HB101 to E. coli NK5449. These six compounds all facilitated the transfer of resistance-carrying RP4 plasmid, and the highest transfer frequency (approximately 10[-5]-10[-3]) was over 4- to 200-fold higher than that in the control group (approximately 10[-6]-10[-5]). These results illustrated that the six common residual compounds, particularly low-dose substances in IDW3, could facilitate the dissemination of ARGs in aquatic environments. More importantly, this study revealed for the first time that dyeing contaminants influenced horizontal gene transfer (HGT) of ARGs.}, }
@article {pmid28575409, year = {2017}, author = {Arkhipova, IR and Yushenova, IA and Rodriguez, F}, title = {Giant Reverse Transcriptase-Encoding Transposable Elements at Telomeres.}, journal = {Molecular biology and evolution}, volume = {34}, number = {9}, pages = {2245-2257}, pmid = {28575409}, issn = {1537-1719}, support = {R01 GM111917/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; DNA Transposable Elements/genetics ; Eukaryotic Cells/metabolism ; Gene Transfer, Horizontal/genetics ; Open Reading Frames ; Phylogeny ; RNA ; RNA, Catalytic/genetics ; RNA-Directed DNA Polymerase/genetics ; Retroelements/genetics ; Rotifera/genetics ; Sequence Homology, Amino Acid ; Telomere/*genetics/metabolism ; }, abstract = {Transposable elements are omnipresent in eukaryotic genomes and have a profound impact on chromosome structure, function and evolution. Their structural and functional diversity is thought to be reasonably well-understood, especially in retroelements, which transpose via an RNA intermediate copied into cDNA by the element-encoded reverse transcriptase, and are characterized by a compact structure. Here, we report a novel type of expandable eukaryotic retroelements, which we call Terminons. These elements can attach to G-rich telomeric repeat overhangs at the chromosome ends, in a process apparently facilitated by complementary C-rich repeats at the 3'-end of the RNA template immediately adjacent to a hammerhead ribozyme motif. Terminon units, which can exceed 40 kb in length, display an unusually complex and diverse structure, and can form very long chains, with host genes often captured between units. As the principal polymerizing component, Terminons contain Athena reverse transcriptases previously described in bdelloid rotifers and belonging to the enigmatic group of Penelope-like elements, but can additionally accumulate multiple cooriented ORFs, including DEDDy 3'-exonucleases, GDSL esterases/lipases, GIY-YIG-like endonucleases, rolling-circle replication initiator (Rep) proteins, and putatively structural ORFs with coiled-coil motifs and transmembrane domains. The extraordinary length and complexity of Terminons and the high degree of interfamily variability in their ORF content challenge the current views on the structural organization of eukaryotic retroelements, and highlight their possible connections with the viral world and the implications for the elevated frequency of gene transfer.}, }
@article {pmid28574575, year = {2019}, author = {Jeukens, J and Freschi, L and Kukavica-Ibrulj, I and Emond-Rheault, JG and Tucker, NP and Levesque, RC}, title = {Genomics of antibiotic-resistance prediction in Pseudomonas aeruginosa.}, journal = {Annals of the New York Academy of Sciences}, volume = {1435}, number = {1}, pages = {5-17}, pmid = {28574575}, issn = {1749-6632}, support = {2610//Cystic Fibrosis Canada/International ; }, mesh = {Animals ; *Computer Simulation ; Drug Resistance, Multiple, Bacterial/*genetics ; Humans ; Pseudomonas Infections/*genetics ; Pseudomonas aeruginosa/*genetics ; }, abstract = {Antibiotic resistance is a worldwide health issue spreading quickly among human and animal pathogens, as well as environmental bacteria. Misuse of antibiotics has an impact on the selection of resistant bacteria, thus contributing to an increase in the occurrence of resistant genotypes that emerge via spontaneous mutation or are acquired by horizontal gene transfer. There is a specific and urgent need not only to detect antimicrobial resistance but also to predict antibiotic resistance in silico. We now have the capability to sequence hundreds of bacterial genomes per week, including assembly and annotation. Novel and forthcoming bioinformatics tools can predict the resistome and the mobilome with a level of sophistication not previously possible. Coupled with bacterial strain collections and databases containing strain metadata, prediction of antibiotic resistance and the potential for virulence are moving rapidly toward a novel approach in molecular epidemiology. Here, we present a model system in antibiotic-resistance prediction, along with its promises and limitations. As it is commonly multidrug resistant, Pseudomonas aeruginosa causes infections that are often difficult to eradicate. We review novel approaches for genotype prediction of antibiotic resistance. We discuss the generation of microbial sequence data for real-time patient management and the prediction of antimicrobial resistance.}, }
@article {pmid28570771, year = {2017}, author = {Gavelis, GS and Keeling, PJ and Leander, BS}, title = {How exaptations facilitated photosensory evolution: Seeing the light by accident.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {39}, number = {7}, pages = {}, doi = {10.1002/bies.201600266}, pmid = {28570771}, issn = {1521-1878}, mesh = {Adaptation, Physiological/physiology ; Animals ; Eukaryota/physiology ; Evolution, Molecular ; Gene Transfer, Horizontal/physiology ; Humans ; Light ; Organelles/physiology ; Photoreceptor Cells/*physiology ; Symbiosis/physiology ; Vision, Ocular/*physiology ; }, abstract = {Exaptations are adaptations that have undergone a major change in function. By recruiting genes from sources originally unrelated to vision, exaptation has allowed for sudden and critical photosensory innovations, such as lenses, photopigments, and photoreceptors. Here we review new or neglected findings, with an emphasis on unicellular eukaryotes (protists), to illustrate how exaptation has shaped photoreception across the tree of life. Protist phylogeny attests to multiple origins of photoreception, as well as the extreme creativity of evolution. By appropriating genes and even entire organelles from foreign organisms via lateral gene transfer and endosymbiosis, protists have cobbled photoreceptors and eyespots from a diverse set of ingredients. While refinement through natural selection is paramount, exaptation helps illustrate how novelties arise in the first place, and is now shedding light on the origins of photoreception itself.}, }
@article {pmid28567486, year = {2018}, author = {Schmidt, M and Pei, L and Budisa, N}, title = {Xenobiology: State-of-the-Art, Ethics, and Philosophy of New-to-Nature Organisms.}, journal = {Advances in biochemical engineering/biotechnology}, volume = {162}, number = {}, pages = {301-315}, doi = {10.1007/10_2016_14}, pmid = {28567486}, issn = {0724-6145}, mesh = {*Bioethical Issues ; Genetic Engineering/*ethics ; *Organisms, Genetically Modified ; Systems Biology/*ethics ; }, abstract = {The basic chemical constitution of all living organisms in the context of carbon-based chemistry consists of a limited number of small molecules and polymers. Until the twenty-first century, biology was mainly an analytical science and has now reached a point where it merges with engineering science, paving the way for synthetic biology. One of the objectives of synthetic biology is to try to change the chemical compositions of living cells, that is, to create an artificial biological diversity, which in turn fosters a new sub-field of synthetic biology, xenobiology. In particular, the genetic code in living systems is based on highly standardized chemistry composed of the same "letters" or nucleotides as informational polymers (DNA, RNA) and the 20 amino acids which serve as basic building blocks for proteins. The universality of the genetic code enables not only vertical gene transfer within the same species but also horizontal gene transfer across biological taxa, which require a high degree of standardization and interconnectivity. Although some minor alterations of the standard genetic code are found in nature (e.g., proteins containing non-conical amino acids exist in nature, and some organisms use alternated coding systems), all structurally deep chemistry changes within living systems are generally lethal, making the creation of artificial biological system an extremely difficult challenge.In this context, one of the great challenges for bioscience is the development of a strategy for expanding the standard basic chemical repertoire of living cells. Attempts to alter the meaning of the genetic information stored in DNA as an informational polymer by changing the chemistry of the polymer (i.e., xeno-nucleic acids) or by changes in the genetic code have already yielded successful results. In the future this should enable the partial or full redirection of the biological information flow to generate "new" version(s) of the genetic code derived from the "old" biological world.In addition to the scientific challenges, the attempt to increase biochemical diversity also raises important ethical and philosophical issues. Although promotors of this branch of synthetic biology highlight the many potential applications to come (e.g., novel tools for diagnostics and fighting infection diseases), such developments could also bring risks affecting social, political, and other structures of nearly all societies.}, }
@article {pmid28566541, year = {2017}, author = {Parker, BJ and McLean, AHC and Hrček, J and Gerardo, NM and Godfray, HCJ}, title = {Establishment and maintenance of aphid endosymbionts after horizontal transfer is dependent on host genotype.}, journal = {Biology letters}, volume = {13}, number = {5}, pages = {}, pmid = {28566541}, issn = {1744-957X}, mesh = {Animals ; Aphids ; Gene Transfer, Horizontal ; Genotype ; *Symbiosis ; }, abstract = {Animal-associated microbial communities have important effects on host phenotypes. Individuals within and among species differ in the strains and species of microbes that they harbour, but how natural selection shapes the distribution and abundance of symbionts in natural populations is not well understood. Symbionts can be beneficial in certain environments but also impose costs on their hosts. Consequently, individuals that can or cannot associate with symbionts will be favoured under different ecological circumstances. As a result, we predict that individuals within a species vary in terms of how well they accept and maintain symbionts. In pea aphids, the frequency of endosymbionts varies among host-plant-associated populations ('biotypes'). We show that aphid genotypes from different biotypes vary in how well they accept and maintain symbionts after horizontal transfer. We find that aphids from biotypes that frequently harbour symbionts are better able to associate with novel symbionts than those from biotypes that less frequently harbour symbionts. Intraspecific variation in the ability of hosts to interact with symbionts is an understudied factor explaining patterns of host-symbiont association.}, }
@article {pmid28559885, year = {2017}, author = {Piotrowska, M and Przygodzińska, D and Matyjewicz, K and Popowska, M}, title = {Occurrence and Variety of β-Lactamase Genes among Aeromonas spp. Isolated from Urban Wastewater Treatment Plant.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {863}, pmid = {28559885}, issn = {1664-302X}, abstract = {Members of the genus Aeromonas that commonly occur in various aquatic ecosystems are taken into account as vectors spreading antibiotic resistance genes (ARGs) in the environment. In our study strains of Aeromonas spp. (n = 104) not susceptible to ampicillin were isolated from municipal sewage of different levels of purification - raw sewage, activated sludge and treated wastewater. The crucial step of the study was the identification of β-lactamase resistance genes. The identified genes encode β-lactamases from 14 families - blaTEM, blaOXA, blaSHV, blaCTX-M, blaMOX, blaACC, blaFOX, blaGES, blaPER, blaV EB, blaKPC, cphA, imiH, and cepH. There were no significant differences in number of identified ARGs between isolation points. BlaOXA, blaFOX variants and, characteristic for Aeromonas genus, metallo-β-lactamase cphA-related genes were the most commonly identified types of β-lactam resistance determinants. Moreover, we found four extended-spectrum β-lactamases (blaSHV -11, blaCTX-M-27, blaCTX-M-98, and blaPER-4) - and seven AmpC (blaACC, blaFOX-2-like, blaFOX-3, blaFOX-4-like, blaFOX-9, blaFOX-10-like, and blaFOX-13-like) types and variants of genes that had never been found among Aeromonas spp. before. Five of the β-lactamases families (blaTEM, blaOXA, blaFOX, blaV EB, and cphA) were identified in all three isolation sites, which supports the hypothesis that wastewater treatment plants (WWTPs) are hot spots of ARGs dissemination. The obtained ARGs sequences share high identity with previously described β-lactamases, but new variants of those genes have to be considered as well. Characterization of antibiotic susceptibility was performed using disk the diffusion method with 12 different antibiotics according to CLSI guidelines. Over 60% of the strains are unsusceptible to cefepime and chloramphenicol and the majority of the strains have a multidrug resistance phenotype (68%). Finally, analysis of plasmid profiles among the resistant strains showed that 62% of the isolates from all three points of the WWTP carry plasmids of different sizes. Among some of the isolated plasmids blaFOX-4-like and blaGES genes have been found. To sum up, the results strongly suggest that Aeromonas spp. can be considered as agents of antibiotic resistance dissemination from wastewater to the natural environment.}, }
@article {pmid28559293, year = {2017}, author = {Chilton, SS and Falbel, TG and Hromada, S and Burton, BM}, title = {A Conserved Metal Binding Motif in the Bacillus subtilis Competence Protein ComFA Enhances Transformation.}, journal = {Journal of bacteriology}, volume = {199}, number = {15}, pages = {}, pmid = {28559293}, issn = {1098-5530}, support = {T32 GM008349/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Amino Acid Substitution ; Bacillus subtilis/*genetics ; Bacterial Proteins/*genetics/*metabolism ; Conserved Sequence ; Cysteine/genetics/metabolism ; DNA Mutational Analysis ; *DNA Transformation Competence ; DNA-Binding Proteins/*genetics/*metabolism ; Metals/*metabolism ; Protein Binding ; *Transformation, Bacterial ; *Zinc Fingers ; }, abstract = {Genetic competence is a process in which cells are able to take up DNA from their environment, resulting in horizontal gene transfer, a major mechanism for generating diversity in bacteria. Many bacteria carry homologs of the central DNA uptake machinery that has been well characterized in Bacillus subtilis It has been postulated that the B. subtilis competence helicase ComFA belongs to the DEAD box family of helicases/translocases. Here, we made a series of mutants to analyze conserved amino acid motifs in several regions of B. subtilis ComFA. First, we confirmed that ComFA activity requires amino acid residues conserved among the DEAD box helicases, and second, we show that a zinc finger-like motif consisting of four cysteines is required for efficient transformation. Each cysteine in the motif is important, and mutation of at least two of the cysteines dramatically reduces transformation efficiency. Further, combining multiple cysteine mutations with the helicase mutations shows an additive phenotype. Our results suggest that the helicase and metal binding functions are two distinct activities important for ComFA function during transformation.IMPORTANCE ComFA is a highly conserved protein that has a role in DNA uptake during natural competence, a mechanism for horizontal gene transfer observed in many bacteria. Investigation of the details of the DNA uptake mechanism is important for understanding the ways in which bacteria gain new traits from their environment, such as drug resistance. To dissect the role of ComFA in the DNA uptake machinery, we introduced point mutations into several motifs in the protein sequence. We demonstrate that several amino acid motifs conserved among ComFA proteins are important for efficient transformation. This report is the first to demonstrate the functional requirement of an amino-terminal cysteine motif in ComFA.}, }
@article {pmid28559213, year = {2017}, author = {Cid, NG and Sanchez Granel, ML and Montes, MG and Elguero, ME and Nudel, CB and Nusblat, AD}, title = {Phylogenomic analysis of integral diiron membrane histidine motif-containing enzymes in ciliates provides insights into their function and evolutionary relationships.}, journal = {Molecular phylogenetics and evolution}, volume = {114}, number = {}, pages = {1-13}, doi = {10.1016/j.ympev.2017.05.023}, pmid = {28559213}, issn = {1095-9513}, mesh = {Amino Acid Motifs ; Base Sequence ; Ciliophora/*classification/enzymology/genetics ; *Evolution, Molecular ; Fatty Acid Desaturases/*classification/genetics ; Fatty Acids/analysis ; Gas Chromatography-Mass Spectrometry ; Genomics ; Histidine/chemistry ; Oxidoreductases/classification/genetics ; Phylogeny ; Stearoyl-CoA Desaturase/classification/genetics ; }, abstract = {The Integral Membrane Histidine Motif-containing Enzymes (IMHME) are a class of binuclear non-heme iron proteins widely distributed among prokaryotes and eukaryotes. They are characterized by a conserved tripartite motif consisting of eight to ten histidine residues. Their known function is the activation of the dioxygen moiety to serve as efficient catalysts for reactions of hydroxylation, desaturation or reduction. To date most studies on IMHME were carried out in metazoan, phototrophic or parasitic organisms, whereas genome-wide analysis in heterotrophic free living protozoa, such as the Ciliophora phylum, has not been undertaken. In the seven fully sequenced genomes available we retrieved 118 putative sequences of the IMHME type, albeit with large differences in number among the ciliates: 11 sequences in Euplotes octocarinatus, 7 in Ichthyophthirius multifiliis, 13 in Oxytricha trifallax, 18 in Stylonychia lemnae, 25 in Tetrahymena thermophila, 31 in Paramecium tetraurelia and 13 in Pseudocohnilembus persalinus. The pool of putative sequences was classified in 16 orthologous groups from which 11 were related to fatty acid desaturase (FAD) and 5 to the fatty acid hydroxylase (FAH) superfamilies. Noteworthy, a large diversity on the number and type of FAD / FAH proteins were found among the ciliates, a feature that, in principle, may be attributed to peculiarities of the evolutionary process, such as gene expansion and reduction, but also to horizontal gene transfer, as we demonstrate in this work. We identified twelve putative enzymatic activities, from which four were newly assigned activities: sphingolipid Δ4-desaturase, ω3/Δ15 fatty acid desaturase, a large group of alkane 1-monooxygenases, and acylamide-delta-3(E)-desaturase, although unequivocal allocation would require additional experiments. We also combined the phylogenetics analysis with lipids analysis, thereby allowing the detection of two enzymatic activities not previously reported: a C-5 sterol desaturase in P. tetraurelia and a delta-9 fatty acid desaturase in Cohnilembus reniformis. The analysis revealed a significant lower number of FAD's sequences in the spirotrichea ciliates than in the oligohymenophorea, emphasizing the importance of fatty acids trophic transfer among aquatic organisms as a source of variation in metabolic activity, individual and population growth rates, and reproduction.}, }
@article {pmid28555641, year = {2017}, author = {Haitjema, CH and Gilmore, SP and Henske, JK and Solomon, KV and de Groot, R and Kuo, A and Mondo, SJ and Salamov, AA and LaButti, K and Zhao, Z and Chiniquy, J and Barry, K and Brewer, HM and Purvine, SO and Wright, AT and Hainaut, M and Boxma, B and van Alen, T and Hackstein, JHP and Henrissat, B and Baker, SE and Grigoriev, IV and O'Malley, MA}, title = {A parts list for fungal cellulosomes revealed by comparative genomics.}, journal = {Nature microbiology}, volume = {2}, number = {}, pages = {17087}, pmid = {28555641}, issn = {2058-5276}, mesh = {Cellulosomes/*genetics ; Fungal Proteins/*genetics ; *Genomics ; Neocallimastigales/*enzymology/*genetics ; Protein Binding ; Protein Multimerization ; Proteomics ; }, abstract = {Cellulosomes are large, multiprotein complexes that tether plant biomass-degrading enzymes together for improved hydrolysis[1]. These complexes were first described in anaerobic bacteria, where species-specific dockerin domains mediate the assembly of enzymes onto cohesin motifs interspersed within protein scaffolds[1]. The versatile protein assembly mechanism conferred by the bacterial cohesin-dockerin interaction is now a standard design principle for synthetic biology[2,3]. For decades, analogous structures have been reported in anaerobic fungi, which are known to assemble by sequence-divergent non-catalytic dockerin domains (NCDDs)[4]. However, the components, modular assembly mechanism and functional role of fungal cellulosomes remain unknown[5,6]. Here, we describe a comprehensive set of proteins critical to fungal cellulosome assembly, including conserved scaffolding proteins unique to the Neocallimastigomycota. High-quality genomes of the anaerobic fungi Anaeromyces robustus, Neocallimastix californiae and Piromyces finnis were assembled with long-read, single-molecule technology. Genomic analysis coupled with proteomic validation revealed an average of 312 NCDD-containing proteins per fungal strain, which were overwhelmingly carbohydrate active enzymes (CAZymes), with 95 large fungal scaffoldins identified across four genera that bind to NCDDs. Fungal dockerin and scaffoldin domains have no similarity to their bacterial counterparts, yet several catalytic domains originated via horizontal gene transfer with gut bacteria. However, the biocatalytic activity of anaerobic fungal cellulosomes is expanded by the inclusion of GH3, GH6 and GH45 enzymes. These findings suggest that the fungal cellulosome is an evolutionarily chimaeric structure-an independently evolved fungal complex that co-opted useful activities from bacterial neighbours within the gut microbiome.}, }
@article {pmid28551881, year = {2017}, author = {Tang, M and Dou, X and Wang, C and Tian, Z and Yang, M and Zhang, Y}, title = {Abundance and distribution of antibiotic resistance genes in a full-scale anaerobic-aerobic system alternately treating ribostamycin, spiramycin and paromomycin production wastewater.}, journal = {Environmental geochemistry and health}, volume = {39}, number = {6}, pages = {1595-1605}, pmid = {28551881}, issn = {1573-2983}, support = {No. 21437005//National Natural Scientific Foundation of China/ ; 15L03ESPC//State Key Joint Laboratory of Environmental Simulation and Pollution Control/ ; }, mesh = {Aerobiosis ; Anaerobiosis ; Bacteria/drug effects/genetics ; Drug Resistance, Microbial/*genetics ; Gene Transfer, Horizontal ; Mutation ; Paromomycin/*chemistry/pharmacology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Ribostamycin/*chemistry/pharmacology ; Sewage ; Spiramycin/*chemistry/pharmacology ; Wastewater/*chemistry ; }, abstract = {The occurrence of antibiotic-resistant bacteria and antibiotic resistance genes (ARGs) has been intensively investigated for wastewater treatment systems treating single class of antibiotic in recent years. However, the impacts of alternately occurring antibiotics in antibiotic production wastewater on the behavior of ARGs in biological treatment systems were not well understood yet. Herein, techniques including high-capacity quantitative PCR and quantitative PCR (qPCR) were used to investigate the behavior of ARGs in an anaerobic-aerobic full-scale system. The system alternately treated three kinds of antibiotic production wastewater including ribostamycin, spiramycin and paromomycin, which referred to stages 1, 2 and 3. The aminoglycoside ARGs (52.1-79.3%) determined using high-capacity quantitative PCR were the most abundant species in all sludge samples of the three stages. The total relative abundances of macrolide-lincosamide-streptogramin (MLS) resistance genes and aminoglycoside resistance genes measured using qPCR were significantly higher (P < 0.05) in aerobic sludge than in sewage sludge. However, the comparison of ARGs acquired from three alternate stages revealed that MLS genes and the aminoglycoside ARGs did not vary significantly (P > 0.05) in both aerobic and anaerobic sludge samples. In aerobic sludge, one acetyltransferase gene (aacA4) and the other three nucleotidyltransferase genes (aadB, aadA and aadE) exhibited positive correlations with intI1 (r [2] = 0.83-0.94; P < 0.05), implying the significance of horizontal transfer in their proliferation. These results and facts will be helpful to understand the abundance and distribution of ARGs from antibiotic production wastewater treatment systems.}, }
@article {pmid28551392, year = {2017}, author = {Toussaint, A and Rice, PA}, title = {Transposable phages, DNA reorganization and transfer.}, journal = {Current opinion in microbiology}, volume = {38}, number = {}, pages = {88-94}, doi = {10.1016/j.mib.2017.04.009}, pmid = {28551392}, issn = {1879-0364}, support = {R01 GM101989/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*genetics/*virology ; Bacteriophages/*genetics ; Conjugation, Genetic ; DNA, Viral/*genetics ; *Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences ; *Recombination, Genetic ; }, abstract = {Transposable bacteriophages have long been known to necessarily and randomly integrate their DNA in their host genome, where they amplify by successive rounds of replicative transposition, profoundly reorganizing that genome. As a result of such transposition, a conjugative element (plasmid or genomic island), can either become integrated in the chromosome or receive chromosome segments, which can then be transferred to new hosts by conjugation. In recent years, more and more transposable phages have been isolated or detected by sequence similarity searches in a wide range of bacteria, supporting the idea that this mode of HGT may be pervasive in natural bacterial populations.}, }
@article {pmid28550453, year = {2017}, author = {Weiss, RA}, title = {Exchange of Genetic Sequences Between Viruses and Hosts.}, journal = {Current topics in microbiology and immunology}, volume = {407}, number = {}, pages = {1-29}, doi = {10.1007/82_2017_21}, pmid = {28550453}, issn = {0070-217X}, mesh = {Animals ; Endogenous Retroviruses/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genes, Viral/*genetics ; Host Specificity/*genetics ; Proviruses/*genetics ; Viruses/*genetics ; }, abstract = {Although genetic transfer between viruses and vertebrate hosts occurs less frequently than gene flow between bacteriophages and prokaryotes, it is extensive and has affected the evolution of both parties. With retroviruses, the integration of proviral DNA into chromosomal DNA can result in the activation of adjacent host gene expression and in the transduction of host transcripts into retroviral genomes as oncogenes. Yet in contrast to lysogenic phage, there is little evidence that viral oncogenes persist in a chain of natural transmission or that retroviral transduction is a significant driver of the horizontal spread of host genes. Conversely, integration of proviruses into the host germ line has generated endogenous retroviral genomes (ERV) in all vertebrate genomes sequenced to date. Some of these genomes retain potential infectivity and upon reactivation may transmit to other host species. During mammalian evolution, sequences of retroviral origin have been repurposed to serve host functions, such as the viral envelope glycoproteins crucial to the development of the placenta. Beyond retroviruses, DNA viruses with complex genomes have acquired numerous genes of host origin which influence replication, pathogenesis and immune evasion, while host species have accumulated germline sequences of both DNA and RNA viruses. A codicil is added on lateral transmission of cancer cells between hosts and on migration of host mitochondria into cancer cells.}, }
@article {pmid28550284, year = {2017}, author = {Deakin, G and Dobbs, E and Bennett, JM and Jones, IM and Grogan, HM and Burton, KS}, title = {Multiple viral infections in Agaricus bisporus - Characterisation of 18 unique RNA viruses and 8 ORFans identified by deep sequencing.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {2469}, pmid = {28550284}, issn = {2045-2322}, support = {/WT_/Wellcome Trust/United Kingdom ; BB/G02040X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; G0900747/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Agaricus/*virology ; Fungal Viruses/classification/*genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; *Genome, Viral ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Open Reading Frames ; Phylogeny ; RNA Viruses/classification/*genetics/isolation &amp; purification ; RNA, Viral/*genetics ; *Transcriptome ; }, abstract = {Thirty unique non-host RNAs were sequenced in the cultivated fungus, Agaricus bisporus, comprising 18 viruses each encoding an RdRp domain with an additional 8 ORFans (non-host RNAs with no similarity to known sequences). Two viruses were multipartite with component RNAs showing correlative abundances and common 3' motifs. The viruses, all positive sense single-stranded, were classified into diverse orders/families. Multiple infections of Agaricus may represent a diverse, dynamic and interactive viral ecosystem with sequence variability ranging over 2 orders of magnitude and evidence of recombination, horizontal gene transfer and variable fragment numbers. Large numbers of viral RNAs were detected in multiple Agaricus samples; up to 24 in samples symptomatic for disease and 8-17 in asymptomatic samples, suggesting adaptive strategies for co-existence. The viral composition of growing cultures was dynamic, with evidence of gains and losses depending on the environment and included new hypothetical viruses when compared with the current transcriptome and EST databases. As the non-cellular transmission of mycoviruses is rare, the founding infections may be ancient, preserved in wild Agaricus populations, which act as reservoirs for subsequent cell-to-cell infection when host populations are expanded massively through fungiculture.}, }
@article {pmid28550056, year = {2017}, author = {Marti, R and Schmid, M and Kulli, S and Schneeberger, K and Naskova, J and Knøchel, S and Ahrens, CH and Hummerjohann, J}, title = {Biofilm Formation Potential of Heat-Resistant Escherichia coli Dairy Isolates and the Complete Genome of Multidrug-Resistant, Heat-Resistant Strain FAM21845.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {15}, pages = {}, pmid = {28550056}, issn = {1098-5336}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Biofilms ; Cattle ; Dairy Products/*microbiology ; Dairying ; *Drug Resistance, Bacterial ; Escherichia coli/drug effects/genetics/*isolation &amp; purification/*physiology ; Escherichia coli Proteins/genetics/metabolism ; Food Contamination/analysis ; *Genome, Bacterial ; Hot Temperature ; }, abstract = {We tested the biofilm formation potential of 30 heat-resistant and 6 heat-sensitive Escherichia coli dairy isolates. Production of curli and cellulose, static biofilm formation on polystyrene (PS) and stainless steel surfaces, biofilm formation under dynamic conditions (Bioflux), and initial adhesion rates (IAR) were evaluated. Biofilm formation varied greatly between strains, media, and assays. Our results highlight the importance of the experimental setup in determining biofilm formation under conditions of interest, as correlation between different assays was often not a given. The heat-resistant, multidrug-resistant (MDR) strain FAM21845 showed the strongest biofilm formation on PS and the highest IAR and was the only strain that formed significant biofilms on stainless steel under conditions relevant to the dairy industry, and it was therefore fully sequenced. Its chromosome is 4.9 Mb long, and it harbors a total of five plasmids (147.2, 54.2, 5.8, 2.5, and 1.9 kb). The strain carries a broad range of genes relevant to antimicrobial resistance and biofilm formation, including some on its two large conjugative plasmids, as demonstrated in plate mating assays.IMPORTANCE In biofilms, cells are embedded in an extracellular matrix that protects them from stresses, such as UV radiation, osmotic shock, desiccation, antibiotics, and predation. Biofilm formation is a major bacterial persistence factor of great concern in the clinic and the food industry. Many tested strains formed strong biofilms, and especially strains such as the heat-resistant, MDR strain FAM21845 may pose a serious issue for food production. Strong biofilm formation combined with diverse resistances (some encoded on conjugative plasmids) may allow for increased persistence, coselection, and possible transfer of these resistance factors. Horizontal gene transfer may conceivably occur in the food production setting or the gastrointestinal tract after consumption.}, }
@article {pmid28548042, year = {2017}, author = {Liu, L and Cheng, J and Fu, Y and Liu, H and Jiang, D and Xie, J}, title = {New insights into reovirus evolution: implications from a newly characterized mycoreovirus.}, journal = {The Journal of general virology}, volume = {98}, number = {5}, pages = {1132-1141}, doi = {10.1099/jgv.0.000752}, pmid = {28548042}, issn = {1465-2099}, abstract = {We performed molecular cloning and complete genome sequencing of a novel mycoreovirus, Sclerotinia sclerotiorumreovirus 1 (SsReV1), isolated from an isolate of the phytopathogenic fungus Sclerotinia sclerotiorum. SsReV1 has a genome of 28 055 bp and is composed of 11 double-stranded RNA segments. With a combination of unique molecular features, virion shape and composition, and phylogenetic analysis, SsReV1 is significantly distinct from all known reoviruses and defines a novel genus in the family Reoviridae. Interestingly, two conserved domains, double-stranded RNA binding motif (dsRBM, Pfam 00 035) and reovirus sigma C capsid protein (Reo_σC, pfam04 582), were identified in the genome of SsReV1, which are widespread in diverse virus lineages. Sequence comparison and phylogenetic analysis revealed that multiple cross-family horizontal gene transfer (HGT) events could occur between reoviruses and double-stranded DNA viruses, single-stranded RNA viruses and even cellular organisms. Interestingly, the dsRBM of SsReV1 was phylogenetically related to dsRNA-binding proteins of some insects, but not reoviruses. These results indicated that SsReV1 is a new taxonomic representative in Reoviridae, which provides new insights into the diversity and global ecology of reoviruses and other segmented double-stranded RNA viruses. More importantly, the present results provided evidence indicating that reoviruses indeed have HGT events with other virus lineages on a large scale and that HGT may serve as an important driving factor that plays a key role in the evolution of reoviruses.}, }
@article {pmid28544449, year = {2018}, author = {Hily, JM and Demanèche, S and Poulicard, N and Tannières, M and Djennane, S and Beuve, M and Vigne, E and Demangeat, G and Komar, V and Gertz, C and Marmonier, A and Hemmer, C and Vigneron, S and Marais, A and Candresse, T and Simonet, P and Lemaire, O}, title = {Metagenomic-based impact study of transgenic grapevine rootstock on its associated virome and soil bacteriome.}, journal = {Plant biotechnology journal}, volume = {16}, number = {1}, pages = {208-220}, pmid = {28544449}, issn = {1467-7652}, mesh = {Metagenomics/*methods ; Plants, Genetically Modified/*genetics/microbiology/virology ; Vitis/*genetics/microbiology/virology ; }, abstract = {For some crops, the only possible approach to gain a specific trait requires genome modification. The development of virus-resistant transgenic plants based on the pathogen-derived resistance strategy has been a success story for over three decades. However, potential risks associated with the technology, such as horizontal gene transfer (HGT) of any part of the transgene to an existing gene pool, have been raised. Here, we report no evidence of any undesirable impacts of genetically modified (GM) grapevine rootstock on its biotic environment. Using state of the art metagenomics, we analysed two compartments in depth, the targeted Grapevine fanleaf virus (GFLV) populations and nontargeted root-associated microbiota. Our results reveal no statistically significant differences in the genetic diversity of bacteria that can be linked to the GM trait. In addition, no novel virus or bacteria recombinants of biosafety concern can be associated with transgenic grapevine rootstocks cultivated in commercial vineyard soil under greenhouse conditions for over 6 years.}, }
@article {pmid28543018, year = {2017}, author = {Raymond, JA and Morgan-Kiss, R}, title = {Multiple ice-binding proteins of probable prokaryotic origin in an Antarctic lake alga, Chlamydomonas sp. ICE-MDV (Chlorophyceae).}, journal = {Journal of phycology}, volume = {53}, number = {4}, pages = {848-854}, pmid = {28543018}, issn = {1529-8817}, support = {P20 GM103440/GM/NIGMS NIH HHS/United States ; }, mesh = {Algal Proteins/chemistry/*genetics/metabolism ; Amino Acid Sequence ; Antarctic Regions ; Carrier Proteins/chemistry/*genetics/metabolism ; Chlamydomonas/*genetics/metabolism/microbiology ; *Gene Transfer, Horizontal ; Ice ; Lakes ; Phylogeny ; Prokaryotic Cells/physiology ; Protein Isoforms/genetics/metabolism ; }, abstract = {Ice-associated algae produce ice-binding proteins (IBPs) to prevent freezing damage. The IBPs of the three chlorophytes that have been examined so far share little similarity across species, making it likely that they were acquired by horizontal gene transfer (HGT). To clarify the importance and source of IBPs in chlorophytes, we sequenced the IBP genes of another Antarctic chlorophyte, Chlamydomonas sp. ICE-MDV (Chlamy-ICE). Genomic DNA and total RNA were sequenced and screened for known ice-associated genes. Chlamy-ICE has as many as 50 IBP isoforms, indicating that they have an important role in survival. The IBPs are of the DUF3494 type and have similar exon structures. The DUF3494 sequences are much more closely related to prokaryotic sequences than they are to sequences in other chlorophytes, and the chlorophyte IBP and ribosomal 18S phylogenies are dissimilar. The multiple IBP isoforms found in Chlamy-ICE and other algae may allow the algae to adapt to a greater variety of ice conditions than prokaryotes, which typically have a single IBP gene. The predicted structure of the DUF3494 domain has an ice-binding face with an orderly array of hydrophilic side chains. The results indicate that Chlamy-ICE acquired its IBP genes by HGT in a single event. The acquisitions of IBP genes by this and other species of Antarctic algae by HGT appear to be key evolutionary events that allowed algae to extend their ranges into polar environments.}, }
@article {pmid28542565, year = {2017}, author = {Kadam, A and Eutsey, RA and Rosch, J and Miao, X and Longwell, M and Xu, W and Woolford, CA and Hillman, T and Motib, AS and Yesilkaya, H and Mitchell, AP and Hiller, NL}, title = {Promiscuous signaling by a regulatory system unique to the pandemic PMEN1 pneumococcal lineage.}, journal = {PLoS pathogens}, volume = {13}, number = {5}, pages = {e1006339}, pmid = {28542565}, issn = {1553-7374}, support = {R00 DC011322/DC/NIDCD NIH HHS/United States ; }, mesh = {Aged ; Amino Acid Sequence ; Animals ; Bacterial Adhesion ; Bacterial Proteins/*genetics/metabolism ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genomics ; Humans ; Mice ; Models, Biological ; Mutation ; Nasopharynx/microbiology ; *Pandemics ; Phylogeny ; Pneumococcal Infections/epidemiology/*microbiology ; Regulon/genetics ; Sequence Alignment ; *Signal Transduction ; Streptococcus pneumoniae/*genetics/physiology ; }, abstract = {Streptococcus pneumoniae (pneumococcus) is a leading cause of death and disease in children and elderly. Genetic variability among isolates from this species is high. These differences, often the product of gene loss or gene acquisition via horizontal gene transfer, can endow strains with new molecular pathways, diverse phenotypes, and ecological advantages. PMEN1 is a widespread and multidrug-resistant pneumococcal lineage. Using comparative genomics we have determined that a regulator-peptide signal transduction system, TprA2/PhrA2, was acquired by a PMEN1 ancestor and is encoded by the vast majority of strains in this lineage. We show that TprA2 is a negative regulator of a PMEN1-specific gene encoding a lanthionine-containing peptide (lcpA). The activity of TprA2 is modulated by its cognate peptide, PhrA2. Expression of phrA2 is density-dependent and its C-terminus relieves TprA2-mediated inhibition leading to expression of lcpA. In the pneumococcal mouse model with intranasal inoculation, TprA2 had no effect on nasopharyngeal colonization but was associated with decreased lung disease via its control of lcpA levels. Furthermore, the TprA2/PhrA2 system has integrated into the pneumococcal regulatory circuitry, as PhrA2 activates TprA/PhrA, a second regulator-peptide signal transduction system widespread among pneumococci. Extracellular PhrA2 can release TprA-mediated inhibition, activating expression of TprA-repressed genes in both PMEN1 cells as well as another pneumococcal lineage. Acquisition of TprA2/PhrA2 has provided PMEN1 isolates with a mechanism to promote commensalism over dissemination and control inter-strain gene regulation.}, }
@article {pmid28541905, year = {2018}, author = {Mykowiecka, A and Szczesny, P and Gorecki, P}, title = {Inferring Gene-Species Assignments in the Presence of Horizontal Gene Transfer.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {15}, number = {5}, pages = {1571-1578}, doi = {10.1109/TCBB.2017.2707083}, pmid = {28541905}, issn = {1557-9964}, mesh = {Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/genetics ; Metagenomics/*methods ; Methanobrevibacter/genetics ; *Models, Genetic ; *Phylogeny ; }, abstract = {BACKGROUND: Microbial communities from environmental samples show great diversity as bacteria quickly responds to changes in their ecosystems. To assess the scenario of the actual changes, metagenomics experiments aimed at sequencing genomic DNA from such samples are performed. These new obtained sequences together with already known are used to infer phylogenetic trees assessing the taxonomic groups the species with these genes belong to. Here, we propose the first approach to the gene-species assignment problem by using reconciliation with horizontal gene transfer.<br><br>RESULTS: We propose efficient algorithms that search for optimal gene-species mappings taking into account gene duplication, loss and transfer events under two tractable models of HGT reconciliation.<br><br>CONCLUSIONS: We calculate both the optimal cost and all possible optimal scenarios. Furthermore as the number of optimal reconstructions can be large, we use a Monte-Carlo method for the inference of approximate distributions of gene-species assignments. We demonstrate the applicability on empirical and simulated datasets.}, }
@article {pmid28541467, year = {2017}, author = {Bevan, ER and Jones, AM and Hawkey, PM}, title = {Global epidemiology of CTX-M β-lactamases: temporal and geographical shifts in genotype.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {72}, number = {8}, pages = {2145-2155}, doi = {10.1093/jac/dkx146}, pmid = {28541467}, issn = {1460-2091}, mesh = {Animals ; Disease Transmission, Infectious ; Enterobacteriaceae/*enzymology/isolation &amp; purification ; Enterobacteriaceae Infections/*epidemiology/*microbiology ; Gene Transfer, Horizontal ; *Genotype ; Global Health ; Humans ; Molecular Epidemiology ; Phylogeography ; Spatio-Temporal Analysis ; beta-Lactamases/*genetics ; }, abstract = {Globally, rates of ESBL-producing Enterobacteriaceae are rising. We undertook a literature review, and present the temporal trends in blaCTX-M epidemiology, showing that blaCTX-M-15 and blaCTX-M-14 have displaced other genotypes in many parts of the world. Explanations for these changes can be attributed to: (i) horizontal gene transfer (HGT) of plasmids; (ii) successful Escherichia coli clones; (iii) ESBLs in food animals; (iv) the natural environment; and (v) human migration and access to basic sanitation. We also provide explanations for the changing epidemiology of blaCTX-M-2 and blaCTX-M-27. Modifiable anthropogenic factors, such as poor access to basic sanitary facilities, encourage the spread of blaCTX-M and other antimicrobial resistance (AMR) genes, such as blaNDM, blaKPC and mcr-1. We provide further justification for novel preventative and interventional strategies to reduce transmission of these AMR genes.}, }
@article {pmid28540258, year = {2017}, author = {Moses, AS and Millar, JA and Bonazzi, M and Beare, PA and Raghavan, R}, title = {Horizontally Acquired Biosynthesis Genes Boost Coxiella burnetii's Physiology.}, journal = {Frontiers in cellular and infection microbiology}, volume = {7}, number = {}, pages = {174}, pmid = {28540258}, issn = {2235-2988}, support = {R03 AI123464/AI/NIAID NIH HHS/United States ; R15 AI126385/AI/NIAID NIH HHS/United States ; }, mesh = {Biotin/*biosynthesis/genetics ; Coxiella burnetii/*genetics/growth &amp; development/*metabolism ; Fatty Acids/biosynthesis/genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Glutamic Acid/biosynthesis/genetics ; Heme/biosynthesis/genetics ; Lipopolysaccharides/biosynthesis/genetics ; Metabolic Networks and Pathways/genetics ; RNA, Ribosomal, 16S/classification/genetics ; Viral Proteins/genetics ; }, abstract = {Coxiella burnetii, the etiologic agent of acute Q fever and chronic endocarditis, has a unique biphasic life cycle, which includes a metabolically active intracellular form that occupies a large lysosome-derived acidic vacuole. C. burnetii is the only bacterium known to thrive within such an hostile intracellular niche, and this ability is fundamental to its pathogenicity; however, very little is known about genes that facilitate Coxiella's intracellular growth. Recent studies indicate that C. burnetii evolved from a tick-associated ancestor and that the metabolic capabilities of C. burnetii are different from that of Coxiella-like bacteria found in ticks. Horizontally acquired genes that allow C. burnetii to infect and grow within mammalian cells likely facilitated the host shift; however, because of its obligate intracellular replication, C. burnetii would have lost most genes that have been rendered redundant due to the availability of metabolites within the host cell. Based on these observations, we reasoned that horizontally derived biosynthetic genes that have been retained in the reduced genome of C. burnetii are ideal candidates to begin to uncover its intracellular metabolic requirements. Our analyses identified a large number of putative foreign-origin genes in C. burnetii, including tRNA[Glu]2 that is potentially required for heme biosynthesis, and genes involved in the production of lipopolysaccharide-a virulence factor, and of critical metabolites such as fatty acids and biotin. In comparison to wild-type C. burnetii, a strain that lacks tRNA[Glu]2 exhibited reduced growth, indicating its importance to Coxiella's physiology. Additionally, by using chemical agents that block heme and biotin biosyntheses, we show that these pathways are promising targets for the development of new anti-Coxiella therapies.}, }
@article {pmid28538166, year = {2017}, author = {Hülter, N and Ilhan, J and Wein, T and Kadibalban, AS and Hammerschmidt, K and Dagan, T}, title = {An evolutionary perspective on plasmid lifestyle modes.}, journal = {Current opinion in microbiology}, volume = {38}, number = {}, pages = {74-80}, doi = {10.1016/j.mib.2017.05.001}, pmid = {28538166}, issn = {1879-0364}, support = {281357/ERC_/European Research Council/International ; }, mesh = {*Adaptation, Biological ; *Gene Transfer, Horizontal ; Genomic Instability ; Host Specificity ; *Plasmids ; }, abstract = {Plasmids are extra-chromosomal genetic elements whose ecology and evolution depend on their genetic repertoire and interaction with the host. We review the events that lead to transitions between plasmid lifestyle modes - invasion, host range, plasmid persistence and adaptation - from a plasmid perspective. Plasmid lifestyle is determined by various traits, including mobility, stability and indispensability that vary in their magnitude. Transitions between the plasmid lifestyles, invasion, host range, plasmid persistence and adpatation, are caused by the interplay between plasmid traits and host biology. Mobility and indispensability are important in plasmid ecology, whereas plasmid stability is more relevant for long-term plasmid evolution. In transitioning into additional chromosomes plasmids loose their independence and enter the host lineage. Though plasmids are confined to their hosts, their evolution may be independent of prokaryotic chromosomes.}, }
@article {pmid28537231, year = {2017}, author = {Blinov, VM and Zverev, VV and Krasnov, GS and Filatov, FP and Shargunov, AV}, title = {[Viral component of the human genome].}, journal = {Molekuliarnaia biologiia}, volume = {51}, number = {2}, pages = {240-250}, doi = {10.7868/S0026898417020069}, pmid = {28537231}, issn = {0026-8984}, mesh = {*Gene Transfer, Horizontal ; *Genes, Viral ; *Genome, Human ; Humans ; Viral Proteins/*genetics ; Viruses/*genetics ; }, abstract = {Relationships between viruses and their human host are traditionally described from the point of view taking into consideration hosts as victims of viral aggression, which results in infectious diseases. However, these relations are in fact two-sided and involve modifications of both the virus and host genomes. Mutations that accumulate in the populations of viruses and hosts may provide them advantages such as the ability to overcome defense barriers of host cells or to create more efficient barriers to deal with the attack of the viral agent. One of the most common ways of reinforcing anti-viral barriers is the horizontal transfer of viral genes into the host genome. Within the host genome, these genes may be modified and extensively expressed to compete with viral copies and inhibit the synthesis of their products or modulate their functions in other ways. This review summarizes the available data on the horizontal gene transfer between viral and human genomes and discusses related problems.}, }
@article {pmid28536456, year = {2017}, author = {Wegmann, U and Carvalho, AL and Stocks, M and Carding, SR}, title = {Use of genetically modified bacteria for drug delivery in humans: Revisiting the safety aspect.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {2294}, pmid = {28536456}, issn = {2045-2322}, support = {BB/J004529/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/L004291/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bacteroides/*genetics ; Drug Delivery Systems/*methods ; Gastrointestinal Tract/microbiology ; Gene Transfer, Horizontal ; Genetic Engineering/*methods ; Humans ; Microbial Interactions ; Transgenes/*genetics ; }, abstract = {The use of live, genetically modified bacteria as delivery vehicles for biologics is of considerable interest scientifically and has attracted significant commercial investment. We have pioneered the use of the commensal gut bacterium Bacteroides ovatus for the oral delivery of therapeutics to the gastrointestinal tract. Here we report on our investigations of the biological safety of engineered B. ovatus bacteria that includes the use of thymineless death as a containment strategy and the potential for the spread of transgenes in vivo in the mammalian gastrointestinal tract. We demonstrate the ability of GM-strains of Bacteroides to survive thymine starvation and overcome it through the exchange of genetic material. We also provide evidence for horizontal gene transfer in the mammalian gastrointestinal tract resulting in transgene-carrying wild type bacteria. These findings sound a strong note of caution on the employment of live genetically modified bacteria for the delivery of biologics.}, }
@article {pmid28535261, year = {2017}, author = {Capela, D and Marchetti, M and Clérissi, C and Perrier, A and Guetta, D and Gris, C and Valls, M and Jauneau, A and Cruveiller, S and Rocha, EPC and Masson-Boivin, C}, title = {Recruitment of a Lineage-Specific Virulence Regulatory Pathway Promotes Intracellular Infection by a Plant Pathogen Experimentally Evolved into a Legume Symbiont.}, journal = {Molecular biology and evolution}, volume = {34}, number = {10}, pages = {2503-2521}, doi = {10.1093/molbev/msx165}, pmid = {28535261}, issn = {1537-1719}, mesh = {Directed Molecular Evolution ; Fabaceae/genetics ; Gene Regulatory Networks/genetics ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/genetics ; Genome, Bacterial/genetics ; Mimosa/*genetics ; Mutation ; Plasmids/genetics ; Ralstonia solanacearum/*genetics/pathogenicity ; Symbiosis/genetics ; Virulence/genetics ; }, abstract = {Ecological transitions between different lifestyles, such as pathogenicity, mutualism and saprophytism, have been very frequent in the course of microbial evolution, and often driven by horizontal gene transfer. Yet, how genomes achieve the ecological transition initiated by the transfer of complex biological traits remains poorly known. Here, we used experimental evolution, genomics, transcriptomics and high-resolution phenotyping to analyze the evolution of the plant pathogen Ralstonia solanacearum into legume symbionts, following the transfer of a natural plasmid encoding the essential mutualistic genes. We show that a regulatory pathway of the recipient R. solanacearum genome involved in extracellular infection of natural hosts was reused to improve intracellular symbiosis with the Mimosa pudica legume. Optimization of intracellular infection capacity was gained through mutations affecting two components of a new regulatory pathway, the transcriptional regulator efpR and a region upstream from the RSc0965-0967 genes of unknown functions. Adaptive mutations caused the downregulation of efpR and the over-expression of a downstream regulatory module, the three unknown genes RSc3146-3148, two of which encoding proteins likely associated to the membrane. This over-expression led to important metabolic and transcriptomic changes and a drastic qualitative and quantitative improvement of nodule intracellular infection. In addition, these adaptive mutations decreased the virulence of the original pathogen. The complete efpR/RSc3146-3148 pathway could only be identified in the genomes of the pathogenic R. solanacearum species complex. Our findings illustrate how the rewiring of a genetic network regulating virulence allows a radically different type of symbiotic interaction and contributes to ecological transitions and trade-offs.}, }
@article {pmid28534829, year = {2017}, author = {Finke, JF and Winget, DM and Chan, AM and Suttle, CA}, title = {Variation in the Genetic Repertoire of Viruses Infecting Micromonas pusilla Reflects Horizontal Gene Transfer and Links to Their Environmental Distribution.}, journal = {Viruses}, volume = {9}, number = {5}, pages = {}, pmid = {28534829}, issn = {1999-4915}, mesh = {Base Sequence ; Chlorophyta/classification/*genetics/*virology ; DNA Viruses/*genetics ; DNA-Directed DNA Polymerase/genetics ; Environment ; Gene Transfer, Horizontal/*genetics ; Genes, Viral ; Genetic Variation ; Genome, Viral/*genetics ; Marine Biology ; Phycodnaviridae/classification/*genetics/isolation &amp; purification/pathogenicity ; Phylogeny ; Phytoplankton/virology ; }, abstract = {Prasinophytes, a group of eukaryotic phytoplankton, has a global distribution and is infected by large double-stranded DNA viruses (prasinoviruses) in the family Phycodnaviridae. This study examines the genetic repertoire, phylogeny, and environmental distribution of phycodnaviruses infecting Micromonas pusilla, other prasinophytes and chlorophytes. Based on comparisons among the genomes of viruses infecting M. pusilla and other phycodnaviruses, as well as the genome from a host isolate of M. pusilla, viruses infecting M. pusilla (MpVs) share a limited set of core genes, but vary strongly in their flexible pan-genome that includes numerous metabolic genes, such as those associated with amino acid synthesis and sugar manipulation. Surprisingly, few of these presumably host-derived genes are shared with M. pusilla, but rather have their closest non-viral homologue in bacteria and other eukaryotes, indicating horizontal gene transfer. A comparative analysis of full-length DNA polymerase (DNApol) genes from prasinoviruses with their overall gene content, demonstrated that the phylogeny of DNApol gene fragments reflects the gene content of the viruses; hence, environmental DNApol gene sequences from prasinoviruses can be used to infer their overall genetic repertoire. Thus, the distribution of virus ecotypes across environmental samples based on DNApol sequences implies substantial underlying differences in gene content that reflect local environmental conditions. Moreover, the high diversity observed in the genetic repertoire of prasinoviruses has been driven by horizontal gene transfer throughout their evolutionary history, resulting in a broad suite of functional capabilities and a high diversity of prasinovirus ecotypes.}, }
@article {pmid28533395, year = {2017}, author = {Williams, TA and Szöllősi, GJ and Spang, A and Foster, PG and Heaps, SE and Boussau, B and Ettema, TJG and Embley, TM}, title = {Integrative modeling of gene and genome evolution roots the archaeal tree of life.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {23}, pages = {E4602-E4611}, pmid = {28533395}, issn = {1091-6490}, support = {/WT_/Wellcome Trust/United Kingdom ; 310039/ERC_/European Research Council/International ; BB/G024707/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Algorithms ; Archaea/classification/*genetics/metabolism ; Eukaryota/classification/genetics ; *Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; *Genome, Archaeal ; Metabolic Networks and Pathways/genetics ; *Models, Genetic ; Multigene Family ; Phylogeny ; Temperature ; }, abstract = {A root for the archaeal tree is essential for reconstructing the metabolism and ecology of early cells and for testing hypotheses that propose that the eukaryotic nuclear lineage originated from within the Archaea; however, published studies based on outgroup rooting disagree regarding the position of the archaeal root. Here we constructed a consensus unrooted archaeal topology using protein concatenation and a multigene supertree method based on 3,242 single gene trees, and then rooted this tree using a recently developed model of genome evolution. This model uses evidence from gene duplications, horizontal transfers, and gene losses contained in 31,236 archaeal gene families to identify the most likely root for the tree. Our analyses support the monophyly of DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaea), a recently discovered cosmopolitan and genetically diverse lineage, and, in contrast to previous work, place the tree root between DPANN and all other Archaea. The sister group to DPANN comprises the Euryarchaeota and the TACK Archaea, including Lokiarchaeum, which our analyses suggest are monophyletic sister lineages. Metabolic reconstructions on the rooted tree suggest that early Archaea were anaerobes that may have had the ability to reduce CO2 to acetate via the Wood-Ljungdahl pathway. In contrast to proposals suggesting that genome reduction has been the predominant mode of archaeal evolution, our analyses infer a relatively small-genomed archaeal ancestor that subsequently increased in complexity via gene duplication and horizontal gene transfer.}, }
@article {pmid28531298, year = {2017}, author = {Diard, M and Hardt, WD}, title = {Evolution of bacterial virulence.}, journal = {FEMS microbiology reviews}, volume = {41}, number = {5}, pages = {679-697}, doi = {10.1093/femsre/fux023}, pmid = {28531298}, issn = {1574-6976}, mesh = {Bacteria/*pathogenicity ; *Biological Evolution ; Host-Pathogen Interactions ; Virulence/*physiology ; }, abstract = {Bacterial virulence is highly dynamic and context-dependent. For this reason, it is challenging to predict how molecular changes affect the growth of a pathogen in a host and its spread in host population. Two schools of thought have taken quite different directions to decipher the underlying principles of bacterial virulence. While molecular infection biology is focusing on the basic mechanisms of the pathogen-host interaction, evolution biology takes virulence as one of several parameters affecting pathogen spread in a host population. We review both approaches and discuss how they can complement each other in order to obtain a comprehensive understanding of bacterial virulence, its emergence, maintenance and evolution.}, }
@article {pmid28529505, year = {2017}, author = {Zhang, X and Liu, X and Liang, Y and Xiao, Y and Ma, L and Guo, X and Miao, B and Liu, H and Peng, D and Huang, W and Yin, H}, title = {Comparative Genomics Unravels the Functional Roles of Co-occurring Acidophilic Bacteria in Bioleaching Heaps.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {790}, pmid = {28529505}, issn = {1664-302X}, abstract = {The spatial-temporal distribution of populations in various econiches is thought to be potentially related to individual differences in the utilization of nutrients or other resources, but their functional roles in the microbial communities remain elusive. We compared differentiation in gene repertoire and metabolic profiles, with a focus on the potential functional traits of three commonly recognized members (Acidithiobacillus caldus, Leptospirillum ferriphilum, and Sulfobacillus thermosulfidooxidans) in bioleaching heaps. Comparative genomics revealed that intra-species divergence might be driven by horizontal gene transfer. These co-occurring bacteria shared a few homologous genes, which significantly suggested the genomic differences between these organisms. Notably, relatively more genes assigned to the Clusters of Orthologous Groups category [G] (carbohydrate transport and metabolism) were identified in Sulfobacillus thermosulfidooxidans compared to the two other species, which probably indicated their mixotrophic capabilities that assimilate both organic and inorganic forms of carbon. Further inspection revealed distinctive metabolic capabilities involving carbon assimilation, nitrogen uptake, and iron-sulfur cycling, providing robust evidence for functional differences with respect to nutrient utilization. Therefore, we proposed that the mutual compensation of functionalities among these co-occurring organisms might provide a selective advantage for efficiently utilizing the limited resources in their habitats. Furthermore, it might be favorable to chemoautotrophs' lifestyles to form mutualistic interactions with these heterotrophic and/or mixotrophic acidophiles, whereby the latter could degrade organic compounds to effectively detoxify the environments. Collectively, the findings shed light on the genetic traits and potential metabolic activities of these organisms, and enable us to make some inferences about genomic and functional differences that might allow them to co-exist.}, }
@article {pmid28527384, year = {2017}, author = {Touchon, M and Moura de Sousa, JA and Rocha, EP}, title = {Embracing the enemy: the diversification of microbial gene repertoires by phage-mediated horizontal gene transfer.}, journal = {Current opinion in microbiology}, volume = {38}, number = {}, pages = {66-73}, doi = {10.1016/j.mib.2017.04.010}, pmid = {28527384}, issn = {1879-0364}, mesh = {Adaptation, Biological ; Archaea/*genetics/*virology ; Bacteria/*genetics/*virology ; Bacteriophages/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Lysogeny ; Transduction, Genetic ; }, abstract = {Bacteriophages and archaeal viruses contribute, through lysogenic conversion or transduction, to the horizontal transfer of genetic material between microbial genomes. Recent genomics, metagenomics, and single cell studies have shown that lysogenic conversion is widespread and provides hosts with adaptive traits often associated with biotic interactions. The quantification of the evolutionary impact of transduction has lagged behind and requires further theoretical and experimental work. Nevertheless, recent studies suggested that generalized transduction plays a role in the transfer of antibiotic resistance genes and in the acquisition of novel genes during intra-specific bacterial competition. The characteristics of transduction and lysogenic conversion complement those of other mechanisms of transfer, and could play a key role in the spread of adaptive genes between communities.}, }
@article {pmid28525986, year = {2017}, author = {Fu, P and Ge, Y and Wu, Y and Zhao, N and Yuan, Z and Hu, X}, title = {The LspC3-41I restriction-modification system is the major determinant for genetic manipulations of Lysinibacillus sphaericus C3-41.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {116}, pmid = {28525986}, issn = {1471-2180}, mesh = {Animals ; Bacillaceae/*enzymology/*genetics ; DNA Restriction-Modification Enzymes/*genetics/*isolation &amp; purification ; DNA, Bacterial/genetics ; Escherichia coli/genetics ; Gene Knockdown Techniques ; *Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Genetics, Microbial ; Methylation ; Mosquito Control ; Multigene Family ; Multilocus Sequence Typing/methods ; Plasmids ; }, abstract = {BACKGROUND: Lysinibacillus sphaericus has been widely used in integrated mosquito control program and it is one of the minority bacterial species unable to metabolize carbohydrates. In consideration of the high genetic conservation at genomic level and difficulty of genetic horizontal transfer, it is hypothesized that effective restriction-modification (R-M) systems existed in mosquitocidal L. sphaericus.<br><br>RESULTS: In this study, six type II R-M systems including LspC3-41I were predicted in L. sphaericus C3-41 genome. It was found that the cell free extracts (CFE) from this strain shown similar restriction and methylation activity on exogenous Bacillus/Escherichia coli shuttle vector pBU4 as the HaeIII, which is an isoschizomer of BspRI. The Bsph_0498 (encoding the predicted LspC3-41IR) knockout mutant &#x394;0498 and the complement strain RC0498 were constructed. It was found that the unmethylated pBU4 can be digested by the CFE of C3-41 and RC0498, but not by that of &#x394;0498. Furthermore, the exogenous plasmid pBU4 can be transformed at very high efficacy into &#x394;0498, low efficacy into RC0498, but no transformation into C3-41, indicating that LspC3-41I might be a major determinant for the genetic restriction barrier of strain C3-41. Besides, lspC3-41IR and lspC3-41IM genes are detected in other two strains besides C3-41 of the tested 16&#xa0;L. sphaericus strains, which all belonging to serotype H5 and MLST sequence type (ST) 1. Furthermore, the three strains are not horizontal transferred, and this restriction could be overcome by in vitro methylation either by the host CFE or by commercial methytransferase M. HaeIII. The results provide an insight to further study the genetic restriction, modification and evolution of mosquitocidal L. sphaericus, also a theoretical basis and a method for the genetic manipulations of L. sphaericus.<br><br>CONCLUSIONS: LspC3-41I is identified as the major determinant for the restriction barrier of L. sphaericus C3-41. Only three strains of the tested 16&#xa0;L. sphaericus strains, which all belonging to serotype H5 and ST1 by MLST scheme, contain LspC3-41I system. Two different methods can be used to overcome the restriction barrier of the three isolates to get transformants efficiently: 1) to methylate plasmid DNA prior to the electroporation; and 2) to delete the major restriction endonuclease encoding gene lspC3-41IR.}, }
@article {pmid28525572, year = {2017}, author = {Lorenzo-Díaz, F and Fernández-López, C and Lurz, R and Bravo, A and Espinosa, M}, title = {Crosstalk between vertical and horizontal gene transfer: plasmid replication control by a conjugative relaxase.}, journal = {Nucleic acids research}, volume = {45}, number = {13}, pages = {7774-7785}, pmid = {28525572}, issn = {1362-4962}, mesh = {Bacterial Proteins/genetics/*metabolism ; Binding Sites ; Conjugation, Genetic ; DNA Copy Number Variations ; DNA Replication ; DNA, Bacterial/chemistry/genetics/metabolism ; DNA, Superhelical/chemistry/genetics/metabolism ; Drug Resistance, Bacterial/genetics ; Endodeoxyribonucleases/genetics/*metabolism ; Escherichia coli/genetics/metabolism ; Evolution, Molecular ; Gene Flow ; *Gene Transfer, Horizontal ; Microscopy, Electron ; Models, Biological ; Plasmids/*genetics ; Promoter Regions, Genetic ; Replicon ; Streptococcus pneumoniae/genetics/metabolism ; }, abstract = {Horizontal gene transfer is a key process in the evolution of bacteria and also represents a source of genetic variation in eukaryotes. Among elements participating in gene transfer, thousands of small (<10 kb) mobile bacterial plasmids that replicate by the rolling circle mechanism represent a driving force in the spread of antibiotic resistances. In general, these plasmids are built as genetic modules that encode a replicase, an antibiotic-resistance determinant, and a relaxase that participates in their conjugative mobilization. Further, they control their relatively high copy number (∼30 copies per genome equivalent) by antisense RNAs alone or combined with a repressor protein. We report here that the MobM conjugative relaxase encoded by the promiscuous plasmid pMV158 participates in regulation of the plasmid copy number by transcriptional repression of the antisense RNA, thus increasing the number of plasmid molecules ready to be horizontally transferred (mobilization) and/or vertically inherited (replication). This type of crosstalk between genetic modules involved in vertical and horizontal gene flow has not been reported before.}, }
@article {pmid28525571, year = {2017}, author = {Mueller, L and Bertelli, C and Pillonel, T and Salamin, N and Greub, G}, title = {One Year Genome Evolution of Lausannevirus in Allopatric versus Sympatric Conditions.}, journal = {Genome biology and evolution}, volume = {9}, number = {6}, pages = {1432-1449}, pmid = {28525571}, issn = {1759-6653}, support = {P41 GM103311/GM/NIGMS NIH HHS/United States ; }, mesh = {Acanthamoeba castellanii/*virology ; Biological Evolution ; *Evolution, Molecular ; *Genetic Speciation ; *Genome, Viral ; Giant Viruses/classification/*genetics ; Mutation ; Phosphoenolpyruvate Sugar Phosphotransferase System/genetics ; Phosphotransferases (Nitrogenous Group Acceptor)/genetics ; Phylogeny ; Sequence Analysis, DNA ; Sympatry ; }, abstract = {Amoeba-resisting microorganisms raised a great interest during the last decade. Among them, some large DNA viruses present huge genomes up to 2.5 Mb long, exceeding the size of small bacterial genomes. The rate of genome evolution in terms of mutation, deletion, and gene acquisition in these genomes is yet unknown. Given the suspected high plasticity of viral genomes, the microevolution of the 346 kb genome of Lausannevirus, a member of Megavirales, was studied. Hence, Lausannevirus was co-cultured within the amoeba Acanthamoeba castellanii over one year. Despite a low number of mutations, the virus showed a genome reduction of 3.7% after 12 months. Lausannevirus genome evolution in sympatric conditions was investigated by its co-culture with Estrella lausannensis, an obligate intracellular bacterium, in the amoeba A. castellanii during one year. Cultures were split every 3 months. Genome sequencing revealed that in these conditions both, Lausannevirus and E. lausannensis, show stable genome, presenting no major rearrangement. In fact, after one year they acquired from 2 to 7 and from 4 to 10 mutations per culture for Lausannevirus and E. lausannensis, respectively. Interestingly, different mutations in the endonuclease encoding genes of Lausannevirus were observed in different subcultures, highlighting the importance of this gene product in the replication of Lausannevirus. Conversely, mutations in E. lausannensis were mainly located in a gene encoding for a phosphoenolpyruvate-protein phosphotransferase (PtsI), implicated in sugar metabolism. Moreover, in our conditions and with our analyses we detected no horizontal gene transfer during one year of co-culture.}, }
@article {pmid28523739, year = {2017}, author = {Chen, Y and Bandyopadhyay, A and Kozlowicz, BK and Haemig, HAH and Tai, A and Hu, WS and Dunny, GM}, title = {Mechanisms of peptide sex pheromone regulation of conjugation in Enterococcus faecalis.}, journal = {MicrobiologyOpen}, volume = {6}, number = {4}, pages = {}, pmid = {28523739}, issn = {2045-8827}, support = {R01 GM049530/GM/NIGMS NIH HHS/United States ; R01 GM081388/GM/NIGMS NIH HHS/United States ; R35 GM118079/GM/NIGMS NIH HHS/United States ; T32 GM008347/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Proteins/metabolism ; Binding Sites ; Conjugation, Genetic/*drug effects ; DNA, Bacterial/metabolism ; Enterococcus faecalis/*genetics/*metabolism ; Gene Expression Regulation, Bacterial/*drug effects ; Gene Transfer, Horizontal ; Nucleic Acid Conformation ; Peptides/*metabolism ; Pheromones/*metabolism ; Plasmids/chemistry/metabolism ; Protein Binding ; Repressor Proteins/metabolism ; }, abstract = {In many gram positive bacteria, horizontal transfer and virulence are regulated by peptide-mediated cell-cell signaling. The heptapeptide cCF10 (C) activates conjugative transfer of the Enterococcus faecalis plasmid pCF10, whereas the iCF10 (I) peptide inhibits transfer. Both peptides bind to the same domain of the master transcription regulator PrgX, a repressor of transcription of the prgQ operon encoding conjugation genes. We show that repression of prgQ by PrgX tetramers requires formation of a pCF10 DNA loop where each of two PrgX DNA-binding sites is occupied by a dimer. I binding to PrgX enhances prgQ repression, while C binding has the opposite effect. Previous models suggested that differential effects of these two peptides on the PrgX oligomerization state accounted for their distinct functions. Our new results demonstrate that both peptides have similar, high-binding affinity for PrgX, and that both peptides actually promote formation of PrgX tetramers with higher DNA-binding affinity than Apo-PrgX. We propose that differences in repression ability of PrgX/peptide complexes result from subtle differences in the structures of DNA-bound PrgX/peptide complexes. Changes in the induction state of a donor cell likely results from replacement of one type of DNA-bound peptide/PrgX tetramer with the other.}, }
@article {pmid28520501, year = {2018}, author = {Todorović, D and Velhner, M and Grego, E and Vidanović, D and Milanov, D and Krnjaić, D and Kehrenberg, C}, title = {Molecular Characterization of Multidrug-Resistant Escherichia coli Isolates from Bovine Clinical Mastitis and Pigs in the Vojvodina Province, Serbia.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {24}, number = {1}, pages = {95-103}, doi = {10.1089/mdr.2017.0016}, pmid = {28520501}, issn = {1931-8448}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacterial Typing Techniques ; Cattle ; Cattle Diseases/*epidemiology/microbiology/transmission ; Conjugation, Genetic ; DNA Gyrase/genetics/metabolism ; DNA Topoisomerase IV/genetics/metabolism ; Drug Resistance, Multiple, Bacterial/genetics ; Escherichia coli/classification/drug effects/*genetics/isolation &amp; purification ; Escherichia coli Infections/epidemiology/microbiology/transmission/*veterinary ; Female ; *Gene Expression Regulation, Bacterial ; Genotype ; Integrons ; Mastitis, Bovine/*epidemiology/microbiology/transmission ; Microbial Sensitivity Tests ; Phylogeny ; Plasmids/chemistry/metabolism ; Serbia/epidemiology ; Swine ; Swine Diseases/*epidemiology/microbiology/transmission ; }, abstract = {The aim of the study was to characterize multidrug-resistant (MDR) Escherichia coli isolates collected in Serbia from bovine clinical mastitis cases and diseased pigs, mainly with molecular methods. A total of 48 E. coli isolates was collected during the years 2013-2014, of which 22 were MDR and were included in further analysis. Phylogenetic typing showed that 17 isolates belonged to group A, while two isolates were classified in group B1 and a single one in group D. All isolates showed unique macrorestriction patterns. Phenotypic susceptibility testing revealed resistances of the isolates against up to 13 antimicrobial agents, including resistance to fluoroquinolones. A wide variety of resistance genes was detected by PCR amplification and sequencing of amplicons. Sequence analysis of the quinolone resistance determining regions of topoisomerase genes revealed mutations in gyrA, parC, and/or parE. Plasmid-mediated quinolone resistance genes were detected in two porcine (aac-6'-Ib-cr and qnrS, respectively) isolates and a single bovine (aac-6'-Ib-cr) isolate. Resistance genes were found to be located on conjugative plasmids in 16 cases, many of which conferred a multidrug resistance phenotype. In conclusion, the plentitude of resistance genes located on conjugative plasmids and integrons in E. coli from cows and pigs in Vojvodina, Serbia, pose a high risk for horizontal gene transfer in bacteria from livestock husbandry.}, }
@article {pmid28515720, year = {2017}, author = {Rajput, A and Kumar, M}, title = {Computational Exploration of Putative LuxR Solos in Archaea and Their Functional Implications in Quorum Sensing.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {798}, pmid = {28515720}, issn = {1664-302X}, abstract = {LuxR solos are unexplored in Archaea, despite their vital role in the bacterial regulatory network. They assist bacteria in perceiving acyl homoserine lactones (AHLs) and/or non-AHLs signaling molecules for establishing intraspecies, interspecies, and interkingdom communication. In this study, we explored the potential LuxR solos of Archaea from InterPro v62.0 meta-database employing taxonomic, probable function, distribution, and evolutionary aspects to decipher their role in quorum sensing (QS). Our bioinformatics analyses showed that putative LuxR solos of Archaea shared few conserved domains with bacterial LuxR despite having less similarity within proteins. Functional characterization revealed their ability to bind various AHLs and/or non-AHLs signaling molecules that involve in QS cascades alike bacteria. Further, the phylogenetic study indicates that Archaeal LuxR solos (with less substitution per site) evolved divergently from bacteria and share distant homology along with instances of horizontal gene transfer. Moreover, Archaea possessing putative LuxR solos, exhibit the correlation between taxonomy and ecological niche despite being the inhabitant of diverse habitats like halophilic, thermophilic, barophilic, methanogenic, and chemolithotrophic. Therefore, this study would shed light in deciphering the role of the putative LuxR solos of Archaea to adapt varied habitats via multilevel communication with other organisms using QS.}, }
@article {pmid28515215, year = {2017}, author = {Bosch, T and Lutgens, SPM and Hermans, MHA and Wever, PC and Schneeberger, PM and Renders, NHM and Leenders, ACAP and Kluytmans, JAJW and Schoffelen, A and Notermans, D and Witteveen, S and Bathoorn, E and Schouls, LM}, title = {Outbreak of NDM-1-Producing Klebsiella pneumoniae in a Dutch Hospital, with Interspecies Transfer of the Resistance Plasmid and Unexpected Occurrence in Unrelated Health Care Centers.}, journal = {Journal of clinical microbiology}, volume = {55}, number = {8}, pages = {2380-2390}, pmid = {28515215}, issn = {1098-660X}, mesh = {Cross Infection/*epidemiology/microbiology ; *Disease Outbreaks ; Enterobacteriaceae/classification/*enzymology/genetics/isolation &amp; purification ; *Gene Transfer, Horizontal ; Genotype ; Health Facilities ; Humans ; Klebsiella Infections/*epidemiology/microbiology ; Multilocus Sequence Typing ; Netherlands/epidemiology ; Plasmids/*analysis ; beta-Lactamases/*genetics ; }, abstract = {In the Netherlands, the number of cases of infection with New Delhi metallo-beta-lactamase (NDM)-positive Enterobacteriaceae is low. Here, we report an outbreak of NDM-1-producing Klebsiella pneumoniae infection in a Dutch hospital with interspecies transfer of the resistance plasmid and unexpected occurrence in other unrelated health care centers (HCCs). Next-generation sequencing was performed on 250 carbapenemase-producing Enterobacteriaceae isolates, including 42 NDM-positive isolates obtained from 29 persons at the outbreak site. Most outbreak isolates were K. pneumoniae (n = 26) and Escherichia coli (n = 11), but 5 isolates comprising three other Enterobacteriaceae species were also cultured. The 26 K. pneumoniae isolates had sequence type 873 (ST873), as did 7 unrelated K. pneumoniae isolates originating from five geographically dispersed HCCs. The 33 ST873 isolates that clustered closely together using whole-genome multilocus sequence typing (wgMLST) carried the same plasmids and had limited differences in the resistome. The 11 E. coli outbreak isolates showed great variety in STs, did not cluster using wgMLST, and showed considerable diversity in resistome and plasmid profiles. The blaNDM-1 gene-carrying plasmid present in the ST873 K. pneumoniae isolates was found in all the other Enterobacteriaceae species cultured at the outbreak location and in a single E. coli isolate from another HCC. We describe a hospital outbreak with an NDM-1-producing K. pneumoniae strain from an unknown source that was also found in patients from five other Dutch HCCs in the same time frame without an epidemiological link. Interspecies transfer of the resistance plasmid was observed in other Enterobacteriaceae species isolated at the outbreak location and in another HCC.}, }
@article {pmid28512626, year = {2017}, author = {Liang, W and Xie, Y and Xiong, W and Tang, Y and Li, G and Jiang, X and Lu, Y}, title = {Anti-Restriction Protein, KlcAHS, Promotes Dissemination of Carbapenem Resistance.}, journal = {Frontiers in cellular and infection microbiology}, volume = {7}, number = {}, pages = {150}, pmid = {28512626}, issn = {2235-2988}, mesh = {Bacterial Proteins/*genetics ; Carbapenem-Resistant Enterobacteriaceae/*drug effects/genetics ; Carbapenems/pharmacology ; China ; Escherichia coli/genetics ; Gene Transfer, Horizontal/*drug effects/genetics ; Genes, Bacterial/genetics ; Humans ; Klebsiella Infections/epidemiology/microbiology ; Klebsiella pneumoniae/*drug effects/*genetics/isolation &amp; purification ; Microbial Sensitivity Tests ; Molecular Epidemiology ; Multilocus Sequence Typing ; Plasmids/genetics ; Recombinant Proteins/genetics ; Retrospective Studies ; Sequence Alignment ; Sequence Analysis, DNA ; Transformation, Genetic/drug effects/genetics ; Viral Proteins/*pharmacology ; beta-Lactamases/*genetics ; }, abstract = {Carbapenemase-producing Klebsiella pneumoniae (KPC) has emerged and spread throughout the world. A retrospective analysis was performed on carbapenem-resistant K. pneumoniae isolated at our teaching hospital during the period 2009-2010, when the initial outbreak occurred. To determine the mechanism(s) that underlies the increased infectivity exhibited by KPC, Multilocus Sequence Typing (MLST) was conducted. A series of plasmids was also extracted, sequenced and analyzed. Concurrently, the complete sequences of blaKPC-2-harboring plasmids deposited in GenBank were summarized and aligned. The blaKPC-2 and KlcAHS genes in the carbapenem-resistant K. pneumoniae isolates were examined. E. coli strains, carrying different Type I Restriction and Modification (RM) systems, were selected to study the interaction between RM systems, anti-RM systems and horizontal gene transfer (HGT). The ST11 clone predominated among 102 carbapenem-resistant K. pneumoniae isolates, all harbored the blaKPC-2 gene; 98% contained the KlcAHS gene. KlcAHS was one of the core genes in the backbone region of most blaKPC-2 carrying plasmids. Type I RM systems in the host bacteria reduced the rate of pHS10842 plasmid transformation by 30- to 40-fold. Presence of the anti-restriction protein, KlcAHS, on the other hand, increased transformation efficiency by 3- to 6-fold. These results indicate that RM systems can significantly restrict HGT. In contrast, KlcAHS can disrupt the RM systems and promote HGT by transformation. These findings suggest that the anti-restriction protein, KlcAHS, represents a novel mechanism that facilitates the increased transfer of blaKPC-2 and KlcAHS -carrying plasmids among K. pneumoniae strains.}, }
@article {pmid28512127, year = {2017}, author = {Goulas, T and Ksiazek, M and Garcia-Ferrer, I and Sochaj-Gregorczyk, AM and Waligorska, I and Wasylewski, M and Potempa, J and Gomis-Rüth, FX}, title = {A structure-derived snap-trap mechanism of a multispecific serpin from the dysbiotic human oral microbiome.}, journal = {The Journal of biological chemistry}, volume = {292}, number = {26}, pages = {10883-10898}, pmid = {28512127}, issn = {1083-351X}, support = {R21 DE026280/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacterial Proteins/*chemistry/metabolism ; *Dysbiosis ; Gingiva/*microbiology ; Humans ; *Microbiota ; Peptide Hydrolases/*chemistry/metabolism ; Protein Structure, Secondary ; Serpins/*chemistry/metabolism ; Tannerella forsythia/*chemistry/metabolism ; }, abstract = {Enduring host-microbiome relationships are based on adaptive strategies within a particular ecological niche. Tannerella forsythia is a dysbiotic member of the human oral microbiome that inhabits periodontal pockets and contributes to chronic periodontitis. To counteract endopeptidases from the host or microbial competitors, T. forsythia possesses a serpin-type proteinase inhibitor called miropin. Although serpins from animals, plants, and viruses have been widely studied, those from prokaryotes have received only limited attention. Here we show that miropin uses the serpin-type suicidal mechanism. We found that, similar to a snap trap, the protein transits from a metastable native form to a relaxed triggered or induced form after cleavage of a reactive-site target bond in an exposed reactive-center loop. The prey peptidase becomes covalently attached to the inhibitor, is dragged 75 Å apart, and is irreversibly inhibited. This coincides with a large conformational rearrangement of miropin, which inserts the segment upstream of the cleavage site as an extra β-strand in a central β-sheet. Standard serpins possess a single target bond and inhibit selected endopeptidases of particular specificity and class. In contrast, miropin uniquely blocked many serine and cysteine endopeptidases of disparate architecture and substrate specificity owing to several potential target bonds within the reactive-center loop and to plasticity in accommodating extra β-strands of variable length. Phylogenetic studies revealed a patchy distribution of bacterial serpins incompatible with a vertical descent model. This finding suggests that miropin was acquired from the host through horizontal gene transfer, perhaps facilitated by the long and intimate association of T. forsythia with the human gingiva.}, }
@article {pmid28510761, year = {2017}, author = {Shen, C and Dupont, CL and Hopkinson, BM}, title = {The diversity of CO2-concentrating mechanisms in marine diatoms as inferred from their genetic content.}, journal = {Journal of experimental botany}, volume = {68}, number = {14}, pages = {3937-3948}, pmid = {28510761}, issn = {1460-2431}, mesh = {Algal Proteins/*genetics/metabolism ; Carbon Dioxide/*metabolism ; Diatoms/*genetics/metabolism ; Environment ; *Genome ; Phylogeny ; Phytoplankton/*genetics/metabolism ; Seawater ; Sequence Analysis, DNA ; *Transcriptome ; }, abstract = {Marine diatoms are one of the most ecologically significant primary producers in the ocean. Most diatoms use a CO2-concentrating mechanism (CCM) to overcome the scarcity of CO2 in the ocean and limitations of the carbon-fixing enzyme Rubisco. However, the CCMs in model diatoms differ substantially in their genetic make-up and structural organization. To assess the extent of CCM diversity in marine diatoms more generally, we analyzed genome and transcriptome data from 31 diatom strains to identify putative CCM genes, examine the overall CCM architecture, and study CCM development in the context of the evolutionary history of these diatoms. Key CCM genes [carbonic anhydrases (CAs) and solute carrier 4 (SLC4) bicarbonate transporters] identified in the diatoms were placed into groups of likely orthologs by sequence similarity (OrthoMCL) and phylogenetic methods. These analyses indicated that diatoms seem to share similar HCO3- transporters, but possess a variety of CAs that have either undergone extensive diversification within the diatom lineage or have been acquired through horizontal gene transfer. Hierarchical clustering of the diatom species based on their CCM gene content suggests that CCM development is largely congruent with evolution of diatom species, despite some notable differences in CCM genes even among closely related species.}, }
@article {pmid28509908, year = {2017}, author = {Webster, NS and Reusch, TBH}, title = {Microbial contributions to the persistence of coral reefs.}, journal = {The ISME journal}, volume = {11}, number = {10}, pages = {2167-2174}, pmid = {28509908}, issn = {1751-7370}, mesh = {Acclimatization ; Animals ; Anthozoa/*microbiology/physiology ; *Coral Reefs ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Microbiota/genetics ; }, abstract = {On contemplating the adaptive capacity of reef organisms to a rapidly changing environment, the microbiome offers significant and greatly unrecognised potential. Microbial symbionts contribute to the physiology, development, immunity and behaviour of their hosts, and can respond very rapidly to changing environmental conditions, providing a powerful mechanism for acclimatisation and also possibly rapid evolution of coral reef holobionts. Environmentally acquired fluctuations in the microbiome can have significant functional consequences for the holobiont phenotype upon which selection can act. Environmentally induced changes in microbial abundance may be analogous to host gene duplication, symbiont switching / shuffling as a result of environmental change can either remove or introduce raw genetic material into the holobiont; and horizontal gene transfer can facilitate rapid evolution within microbial strains. Vertical transmission of symbionts is a key feature of many reef holobionts and this would enable environmentally acquired microbial traits to be faithfully passed to future generations, ultimately facilitating microbiome-mediated transgenerational acclimatisation (MMTA) and potentially even adaptation of reef species in a rapidly changing climate. In this commentary, we highlight the capacity and mechanisms for MMTA in reef species, propose a modified Price equation as a framework for assessing MMTA and recommend future areas of research to better understand how microorganisms contribute to the transgenerational acclimatisation of reef organisms, which is essential if we are to reliably predict the consequences of global change for reef ecosystems.}, }
@article {pmid28505370, year = {2017}, author = {Botelho, J and Grosso, F and Quinteira, S and Mabrouk, A and Peixe, L}, title = {The complete nucleotide sequence of an IncP-2 megaplasmid unveils a mosaic architecture comprising a putative novel blaVIM-2-harbouring transposon in Pseudomonas aeruginosa.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {72}, number = {8}, pages = {2225-2229}, doi = {10.1093/jac/dkx143}, pmid = {28505370}, issn = {1460-2091}, mesh = {Conjugation, Genetic ; *DNA Transposable Elements ; Gene Transfer, Horizontal ; Humans ; *Plasmids ; Pseudomonas Infections/microbiology ; Pseudomonas aeruginosa/*enzymology/*genetics ; Sequence Analysis, DNA ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: In Pseudomonas aeruginosa , bla VIM-2 has been mostly associated with a chromosomal location and rarely with a plasmid backbone. Until now, only three complete bla VIM-2 -carrying plasmid sequences have been described in this species. Here we explore the modular structure of pJB37, the first bla VIM-2 -carrying megaplasmid described in P. aeruginosa .<br><br>METHODS: The complete nucleotide sequence of plasmid pJB37 was determined with an Illumina HiSeq, with de novo assembly by SPAdes, annotation by RAST and searching for antimicrobial resistance genes and virulence factors. Conjugation assays were conducted.<br><br>RESULTS: Megaplasmid pJB37 (464&#x202f;804&#x2009;bp long and GC content of 57.2%) comprised: an IncP-2 repA-oriV-parAB region; a conjugative transfer region (traF , traG , virD2 and trbBCDEJLFGI genes); Tn 6356 , a new putative bla VIM-2 -carrying transposon; heavy metal (mercury and tellurite) resistance operons; and an arsenal of virulence genes. Plasmid pJB37 was transferable by conjugation to a spontaneous rifampicin-resistant mutant of P. aeruginosa PAO1. Here, a bla VIM-2 -harbouring In58 integron was associated with a new complex transposable structure, herein named Tn 6356 , suggesting that In58 was most likely acquired by insertion of this element.<br><br>CONCLUSIONS: The mosaic arrangement exhibited by the pJB37 IncP-2 megaplasmid, which highlights the vast assembly potential of distinct genetic elements in a Pseudomonas widespread plasmid platform, gives new insights into bacterial adaptation and evolution.}, }
@article {pmid28505353, year = {2017}, author = {Dalmolin, TV and Castro, L and Mayer, FQ and Zavascki, AP and Martins, AF and Lima-Morales, D and Barth, AL}, title = {Co-occurrence of mcr-1 and blaKPC-2 in a clinical isolate of Escherichia coli in Brazil.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {72}, number = {8}, pages = {2404-2406}, doi = {10.1093/jac/dkx142}, pmid = {28505353}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/pharmacology ; Brazil ; Conjugation, Genetic ; Emergency Service, Hospital ; Escherichia coli/*genetics/*isolation &amp; purification ; Escherichia coli Infections/*microbiology ; Escherichia coli Proteins/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Hospitals ; Humans ; Microbial Sensitivity Tests ; Plasmids/analysis ; Rectum/microbiology ; Whole Genome Sequencing ; beta-Lactamases/*genetics ; }, }
@article {pmid28505330, year = {2017}, author = {Chatterjee, S and Mondal, A and Mitra, S and Basu, S}, title = {Acinetobacter baumannii transfers the blaNDM-1 gene via outer membrane vesicles.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {72}, number = {8}, pages = {2201-2207}, doi = {10.1093/jac/dkx131}, pmid = {28505330}, issn = {1460-2091}, mesh = {Acinetobacter Infections/microbiology ; Acinetobacter baumannii/drug effects/*enzymology/*genetics/isolation &amp; purification ; Biological Transport ; DNA, Bacterial/isolation &amp; purification/*metabolism ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/drug effects/genetics ; Exosomes/*metabolism ; Gene Transfer, Horizontal ; Humans ; Infant, Newborn ; Microbial Sensitivity Tests ; Plasmids/isolation &amp; purification ; Polymerase Chain Reaction ; Transformation, Bacterial ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: To investigate the transmission of the gene encoding New Delhi metallo-β-lactamase-1 (bla NDM-1) through outer membrane vesicles (OMVs) released from an Acinetobacter baumannii strain (A_115).<br><br>METHODS: Isolation and purification of OMVs by density gradient from a carbapenem-resistant clinical strain of A. baumannii harbouring plasmid-mediated bla NDM-1 and aac(6')-Ib-cr genes was performed. DNA was purified from the OMVs and used for PCR and dot-blot analysis. Vesicles treated with DNase I and proteinase K were used to transform A. baumannii ATCC 19606 and Escherichia coli JM109 strains. MIC values for the transformants were determined, followed by PCR and restriction digestion of plasmids. PFGE was done for A_115 and transformants of ATCC 19606 and JM109.<br><br>RESULTS: The A. baumannii strain (ST 1462) released vesicles (25-100&#x2009;nm) during in vitro growth at late log phase. PCR and dot-blot analysis confirmed the presence of bla NDM-1 and aac(6')-Ib-cr genes in intravesicular DNA. bla NDM-1 and aac(6')-Ib-cr genes were transferred to both the A. baumannii ATCC 19606 and E. coli JM109 recipient cells. The transformation frequency of the purified OMVs was in the range of 10 -5 -10 -6 and gradually reduced with storage of OMVs. The sizes of the plasmids in the transformants and their restriction digestion patterns were identical to the plasmid in A_115. The transformants showed elevated MIC values of the &#x3b2;-lactam group of antibiotics, which confirmed the presence of a bla NDM-1 -harbouring plasmid.<br><br>CONCLUSIONS: This is the first experimental evidence of intra- and inter-species transfer of a plasmid harbouring a bla NDM-1 gene in A. baumannii via OMVs with high transformation frequency.}, }
@article {pmid28504899, year = {2017}, author = {Judelson, HS}, title = {Metabolic Diversity and Novelties in the Oomycetes.}, journal = {Annual review of microbiology}, volume = {71}, number = {}, pages = {21-39}, doi = {10.1146/annurev-micro-090816-093609}, pmid = {28504899}, issn = {1545-3251}, mesh = {*Evolution, Molecular ; Gene Duplication ; Gene Fusion ; Gene Transfer, Horizontal ; *Genetic Variation ; Metabolic Networks and Pathways/*genetics ; Oomycetes/*enzymology/genetics/*metabolism ; Recombination, Genetic ; }, abstract = {The eukaryotic microbes called oomycetes include many important saprophytes and pathogens, with the latter exhibiting necrotrophy, biotrophy, or obligate biotrophy. Understanding oomycete metabolism is fundamental to understanding these lifestyles. Genome mining and biochemical studies have shown that oomycetes, which belong to the kingdom Stramenopila, secrete suites of carbohydrate- and protein-degrading enzymes adapted to their environmental niches and produce unusual lipids and energy storage compounds. Despite having limited secondary metabolism, many oomycetes make chemicals for communicating within their species or with their hosts. Horizontal and endosymbiotic gene transfer events have diversified oomycete metabolism, resulting in biochemical pathways that often depart from standard textbook descriptions by amalgamating enzymes from multiple sources. Gene fusions and duplications have further shaped the composition and expression of the enzymes. Current research is helping us learn how oomycetes interact with host and environment, understand eukaryotic diversity and evolution, and identify targets for drugs and crop protection chemicals.}, }
@article {pmid28502981, year = {2017}, author = {Wagner, A and Whitaker, RJ and Krause, DJ and Heilers, JH and van Wolferen, M and van der Does, C and Albers, SV}, title = {Mechanisms of gene flow in archaea.}, journal = {Nature reviews. Microbiology}, volume = {15}, number = {8}, pages = {492-501}, pmid = {28502981}, issn = {1740-1534}, mesh = {Archaea/*genetics ; Evolution, Molecular ; *Gene Flow ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Archaeal ; Genomics ; }, abstract = {Archaea are diverse, ecologically important, single-celled microorganisms. They have unique functions and features, such as methanogenesis and the composition of their cell envelope, although many characteristics are shared with the other domains of life, either through ancestry or through promiscuous horizontal gene transfer. The exchange of genetic material is a major driving force for genome evolution across the tree of life and has a role in archaeal speciation, adaptation and maintenance of diversity. In this Review, we discuss our current knowledge of archaeal mechanisms of DNA transfer and highlight the role of gene transfer in archaeal evolution.}, }
@article {pmid28500385, year = {2017}, author = {Shahi, A and Ince, B and Aydin, S and Ince, O}, title = {Assessment of the horizontal transfer of functional genes as a suitable approach for evaluation of the bioremediation potential of petroleum-contaminated sites: a mini-review.}, journal = {Applied microbiology and biotechnology}, volume = {101}, number = {11}, pages = {4341-4348}, doi = {10.1007/s00253-017-8306-5}, pmid = {28500385}, issn = {1432-0614}, mesh = {Bacteria/genetics/metabolism ; *Biodegradation, Environmental ; *Gene Transfer, Horizontal ; Microbial Consortia/*genetics/physiology ; Petroleum/metabolism ; *Petroleum Pollution/prevention &amp; control/statistics &amp; numerical data ; Sewage/microbiology ; *Soil Microbiology ; Soil Pollutants ; }, abstract = {Petroleum sludge contains recalcitrant residuals. These compounds because of being toxic to humans and other organism are of the major concerns. Therefore, petroleum sludge should be safely disposed. Physicochemical methods which are used by this sector are mostly expensive and need complex devices. Bioremediation methods because of being eco-friendly and cost-effective overcome most of the limitations of physicochemical treatments. Microbial strains capable to degrade petroleum hydrocarbons are practically present in all soils and sediments and their population density increases in contact with contaminants. Bacterial strains cannot degrade alone all kinds of petroleum hydrocarbons, rather microbial consortium should collaborate with each other for degradation of petroleum hydrocarbon mixtures. Horizontal transfer of functional genes between bacteria plays an important role in increasing the metabolic potential of the microbial community. Therefore, selecting a suitable degrading gene and tracking its horizontal transfer would be a useful approach to evaluate the bioremediation process and to assess the bioremediation potential of contaminated sites.}, }
@article {pmid28500327, year = {2017}, author = {Lapadula, WJ and Marcet, PL and Mascotti, ML and Sanchez-Puerta, MV and Juri Ayub, M}, title = {Metazoan Ribosome Inactivating Protein encoding genes acquired by Horizontal Gene Transfer.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {1863}, pmid = {28500327}, issn = {2045-2322}, mesh = {Animals ; Base Sequence ; Culex/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Insect ; Genomics/methods ; Insecta/genetics ; Open Reading Frames ; Phylogeny ; Ribosome Inactivating Proteins/*genetics ; Selection, Genetic ; Synteny ; }, abstract = {Ribosome inactivating proteins (RIPs) are RNA N-glycosidases that depurinate a specific adenine residue in the conserved sarcin/ricin loop of 28S rRNA. These enzymes are widely distributed among plants and their presence has also been confirmed in several bacterial species. Recently, we reported for the first time in silico evidence of RIP encoding genes in metazoans, in two closely related species of insects: Aedes aegypti and Culex quinquefasciatus. Here, we have experimentally confirmed the presence of these genes in mosquitoes and attempted to unveil their evolutionary history. A detailed study was conducted, including evaluation of taxonomic distribution, phylogenetic inferences and microsynteny analyses, indicating that mosquito RIP genes derived from a single Horizontal Gene Transfer (HGT) event, probably from a cyanobacterial donor species. Moreover, evolutionary analyses show that, after the HGT event, these genes evolved under purifying selection, strongly suggesting they play functional roles in these organisms.}, }
@article {pmid28499353, year = {2017}, author = {Liu, Y and Gao, Y and Liu, X and Liu, Q and Zhang, Y and Wang, Q and Xiao, J}, title = {Transposon insertion sequencing reveals T4SS as the major genetic trait for conjugation transfer of multi-drug resistance pEIB202 from Edwardsiella.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {112}, pmid = {28499353}, issn = {1471-2180}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic/genetics ; DNA Transposable Elements/*genetics ; DNA, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Edwardsiella/*genetics ; Fish Diseases/microbiology ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Microbial Sensitivity Tests ; Plasmids ; RNA, Bacterial/analysis ; Sequence Analysis ; Type IV Secretion Systems/*genetics ; Virulence Factors/genetics ; Zebrafish/microbiology ; }, abstract = {BACKGROUND: Conjugation is a major type of horizontal transmission of genes that involves transfer of a plasmid into a recipient using specific conjugation machinery, which results in an extended spectrum of bacterial antibiotics resistance. However, there is inadequate knowledge about the regulator and mechanisms that control the conjugation processes, especially in an aquaculture environment where a cocktail of antibiotics may be present. Here, we investigated these with pEIB202, a typical multi-drug resistant IncP plasmid encoding tetracycline, streptomycin, sulfonamide and chloramphenicol resistance in fish pathogen Edwardsiella piscicida strain EIB202.<br><br>RESULTS: We used transposon insertion sequencing (TIS) to identify genes that are responsible for conjugation transfer of pEIB202. All ten of the plasmid-borne type IV secretion system (T4SS) genes and a putative lipoprotein p007 were identified to play an important role in pEIB202 horizontal transfer. Antibiotics appear to modulate conjugation frequencies by repressing T4SS gene expression. In addition, we identified topA gene, which encodes topoisomerase I, as an inhibitor of pEIB202 transfer. Furthermore, the RNA-seq analysis of the response regulator EsrB encoded on the chromosome also revealed its essential role in facilitating the conjugation by upregulating the T4SS genes.<br><br>CONCLUSIONS: Collectively, our screens unraveled the genetic basis of the conjugation transfer of pEIB202 and the influence of horizontally acquired EsrB on this process. Our results will improve the understanding of the mechanism of plasmid conjugation processes that facilitate dissemination of antibiotic resistance especially in aquaculture industries.}, }
@article {pmid28498924, year = {2017}, author = {Doumith, M and Findlay, J and Hirani, H and Hopkins, KL and Livermore, DM and Dodgson, A and Woodford, N}, title = {Major role of pKpQIL-like plasmids in the early dissemination of KPC-type carbapenemases in the UK.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {72}, number = {8}, pages = {2241-2248}, doi = {10.1093/jac/dkx141}, pmid = {28498924}, issn = {1460-2091}, mesh = {Bacterial Proteins/*genetics ; Disease Transmission, Infectious ; Enterobacteriaceae/classification/*enzymology/genetics/isolation &amp; purification ; Enterobacteriaceae Infections/*epidemiology/*microbiology ; Gene Transfer, Horizontal ; Molecular Epidemiology ; Multilocus Sequence Typing ; *Plasmids ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; United Kingdom/epidemiology ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacteriaceae were first seen in the UK in 2003 and have been increasingly reported since 2010, largely owing to an ongoing outbreak in North-West England. We examined the role of clonal spread and plasmid transmission in their emergence.<br><br>METHODS: Isolates comprised KPC-positive K. pneumoniae (n&#x2009; = &#x2009; 33), Escherichia coli (n&#x2009; = &#x2009; 7) and Enterobacter spp. (n&#x2009; = &#x2009; 4) referred to the national reference laboratory between 2008 and 2010 from 17 UK centres, including three in North-West England. Isolates were typed by MLST. Plasmids were transferred by electroporation and characterized by PCR or sequencing. PCR screening assays were developed to distinguish plasmid pKpQIL variants.<br><br>RESULTS: The K. pneumoniae isolates included 10 STs, of which three belonged to clonal group (CG) 258. CG258 (n&#x2009; = &#x2009; 19) isolates were detected in 13 centres but accounted for only 7/19 (36.8%) of those from North-West England. Most KPC-producers (37/44, 84.1%), including 16/19 CG258 K. pneumoniae , carried bla KPC on IncFII K2 plasmids. Sequencing of a subset of these plasmids (n&#x2009; = &#x2009; 11) revealed similarities with published pKpQIL. One variant, pKpQIL-UK [identified in K. pneumoniae CG258 (n&#x2009; = &#x2009; 5) and ST468 (n&#x2009; = &#x2009; 1) isolates from distinct centres] had only a few nucleotide changes from classical pKpQIL, whereas pKpQIL-D1 (n&#x2009; = &#x2009; 1) and pKpQIL-D2 (n&#x2009; = &#x2009; 4), from isolates of various species in the North-West, harboured large variations, reflecting replacement of the partitioning and replication functions and potentially thereby facilitating spread. PCR revealed that 36/37 (97.3%) IncFII K2 -type plasmids in KPC-positive isolates had pKpQIL markers.<br><br>CONCLUSIONS: pKpQIL-like plasmids played a major role in the early dissemination of KPC enzymes in the UK.}, }
@article {pmid28496941, year = {2017}, author = {Jørgensen, SL and Kudirkiene, E and Li, L and Christensen, JP and Olsen, JE and Nolan, L and Olsen, RH}, title = {Chromosomal features of Escherichia coli serotype O2:K2, an avian pathogenic E. coli.}, journal = {Standards in genomic sciences}, volume = {12}, number = {}, pages = {33}, pmid = {28496941}, issn = {1944-3277}, abstract = {Escherichia coli causing infection outside the gastrointestinal system are referred to as extra-intestinal pathogenic E. coli. Avian pathogenic E. coli is a subgroup of extra-intestinal pathogenic E. coli and infections due to avian pathogenic E. coli have major impact on poultry production economy and welfare worldwide. An almost defining characteristic of avian pathogenic E. coli is the carriage of plasmids, which may encode virulence factors and antibiotic resistance determinates. For the same reason, plasmids of avian pathogenic E. coli have been intensively studied. However, genes encoded by the chromosome may also be important for disease manifestation and antimicrobial resistance. For the E. coli strain APEC_O2 the plasmids have been sequenced and analyzed in several studies, and E. coli APEC_O2 may therefore serve as a reference strain in future studies. Here we describe the chromosomal features of E. coli APEC_O2. E. coli APEC_O2 is a sequence type ST135, has a chromosome of 4,908,820 bp (plasmid removed), comprising 4672 protein-coding genes, 110 RNA genes, and 156 pseudogenes, with an average G + C content of 50.69%. We identified 82 insertion sequences as well as 4672 protein coding sequences, 12 predicated genomic islands, three prophage-related sequences, and two clustered regularly interspaced short palindromic repeats regions on the chromosome, suggesting the possible occurrence of horizontal gene transfer in this strain. The wildtype strain of E. coli APEC_O2 is resistant towards multiple antimicrobials, however, no (complete) antibiotic resistance genes were present on the chromosome, but a number of genes associated with extra-intestinal disease were identified. Together, the information provided here on E. coli APEC_O2 will assist in future studies of avian pathogenic E. coli strains, in particular regarding strain of E. coli APEC_O2, and aid in the general understanding of the pathogenesis of avian pathogenic E. coli.}, }
@article {pmid28489498, year = {2017}, author = {Gordon, TR}, title = {Fusarium oxysporum and the Fusarium Wilt Syndrome.}, journal = {Annual review of phytopathology}, volume = {55}, number = {}, pages = {23-39}, doi = {10.1146/annurev-phyto-080615-095919}, pmid = {28489498}, issn = {1545-2107}, mesh = {Crops, Agricultural/*microbiology ; Fusarium/*pathogenicity ; Plant Diseases/*microbiology ; Plant Roots/microbiology ; Soil Microbiology ; }, abstract = {The Fusarium oxysporum species complex (FOSC) comprises a multitude of strains that cause vascular wilt diseases of economically important crops throughout the world. Although sexual reproduction is unknown in the FOSC, horizontal gene transfer may contribute to the observed diversity in pathogenic strains. Development of disease in a susceptible crop requires F. oxysporum to advance through a series of transitions, beginning with spore germination and culminating with establishment of a systemic infection. In principle, each transition presents an opportunity to influence the risk of disease. This includes modifications of the microbial community in soil, which can affect the ability of pathogen propagules to survive, germinate, and infect plant roots. In addition, many host attributes, including the composition of root exudates, the structure of the root cortex, and the capacity to recognize and respond quickly to invasive growth of a pathogen, can impede development of F. oxysporum.}, }
@article {pmid28489343, year = {2017}, author = {Pancrace, C and Jokela, J and Sassoon, N and Ganneau, C and Desnos-Ollivier, M and Wahlsten, M and Humisto, A and Calteau, A and Bay, S and Fewer, DP and Sivonen, K and Gugger, M}, title = {Rearranged Biosynthetic Gene Cluster and Synthesis of Hassallidin E in Planktothrix serta PCC 8927.}, journal = {ACS chemical biology}, volume = {12}, number = {7}, pages = {1796-1804}, doi = {10.1021/acschembio.7b00093}, pmid = {28489343}, issn = {1554-8937}, mesh = {Anti-Bacterial Agents/biosynthesis/pharmacology ; Cyanobacteria/*genetics/metabolism ; Fungi/drug effects ; Gene Transfer, Horizontal ; Glycopeptides/*biosynthesis/chemistry/*genetics/isolation &amp; purification/pharmacology ; *Multigene Family ; Peptides, Cyclic/biosynthesis/*chemistry ; }, abstract = {Cyanobacteria produce a wide range of natural products with antifungal bioactivity. The cyclic glycosylated lipopeptides of the hassallidin family have potent antifungal activity and display a great degree of chemical diversity. Here, we report the discovery of a hassallidin biosynthetic gene cluster from the filamentous cyanobacterium Planktothrix serta PCC 8927. The hassallidin gene cluster showed heavy rearrangement and marks of genomic plasticity. Nucleotide bias, differences in GC content, and phylogenetic incongruence suggested the acquisition of the hassallidin biosynthetic gene cluster in Planktothrix serta PCC 8927 by horizontal gene transfer. Chemical analyses by liquid chromatography and mass spectrometry demonstrated that this strain produced hassallidin E, a new glycosylated hassallidin variant. Hassallidin E was the only structural variant produced by Planktothrix serta PCC 8927 in all tested conditions. Further evaluated on human pathogenic fungi, hassallidin E showed an antifungal bioactivity. Hassallidin production levels correlated with nitrogen availability, in the only nitrogen-fixing Planktothrix described so far. Our results provide insights into the distribution and chemical diversity of cyanobacterial antifungal compounds as well as raise questions on their ecological relevance.}, }
@article {pmid28488744, year = {2017}, author = {Devos, S and Van Putte, W and Vitse, J and Van Driessche, G and Stremersch, S and Van Den Broek, W and Raemdonck, K and Braeckmans, K and Stahlberg, H and Kudryashev, M and Savvides, SN and Devreese, B}, title = {Membrane vesicle secretion and prophage induction in multidrug-resistant Stenotrophomonas maltophilia in response to ciprofloxacin stress.}, journal = {Environmental microbiology}, volume = {19}, number = {10}, pages = {3930-3937}, doi = {10.1111/1462-2920.13793}, pmid = {28488744}, issn = {1462-2920}, mesh = {Anti-Bacterial Agents/*pharmacology ; Ciprofloxacin/*pharmacology ; Drug Resistance, Bacterial/drug effects ; Fluoroquinolones/metabolism ; Microbial Sensitivity Tests ; Prophages/genetics/*physiology ; Proteomics ; Secretory Vesicles/*drug effects/ultrastructure ; Stenotrophomonas maltophilia/*drug effects/ultrastructure/virology ; Virus Activation/*drug effects ; }, abstract = {Several bacterial species produce membrane vesicles (MVs) in response to antibiotic stress. However, the biogenesis and role of MVs in bacterial antibiotic resistance mechanisms have remained unclear. Here, we studied the effect of the fluoroquinolone ciprofloxacin on MV secretion by Stenotrophomonas maltophilia using a combination of electron microscopy and proteomic approaches. We found that in addition to the classical outer membrane vesicles (OMV), ciprofloxacin-stimulated cultures produced larger vesicles containing both outer and inner membranes termed outer-inner membrane vesicles (OIMV), and that such MVs are enriched with cytosolic proteins. Remarkably, OIMV were found to be decorated with filamentous structures identified as fimbriae. In addition, ciprofloxacin stress leads to the release of bacteriophages and phage tail-like particles. Prophage induction by ciprofloxacin has been linked to pathogenesis and horizontal gene transfer in several bacterial species. Together, our findings show that ciprofloxacin treatment of S. maltophilia leads to the secretion of a heterogeneous pool of MVs and the induction of prophages that are potentially involved in adverse side-effects during antibiotic treatment.}, }
@article {pmid28482857, year = {2017}, author = {Salzberg, SL}, title = {Horizontal gene transfer is not a hallmark of the human genome.}, journal = {Genome biology}, volume = {18}, number = {1}, pages = {85}, pmid = {28482857}, issn = {1474-760X}, support = {R01 GM083873/GM/NIGMS NIH HHS/United States ; R01 HG006677/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; *Gene Transfer, Horizontal ; *Genome, Human ; Humans ; Invertebrates ; Vertebrates ; }, abstract = {Crisp et al. recently reported that 145 human genes have been horizontally transferred from distant species. Here, I re-analyze those genes listed by Crisp et al. as having the highest certainty of having been horizontally transferred, as well as 17 further genes from the 2001 human genome article, and find little or no evidence to support claims of horizontal gene transfer (HGT).Please see related Research article: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0607-3.}, }
@article {pmid28481399, year = {2017}, author = {Lei, DJ and Zhao, G and Xie, P and Li, Y and Yuan, H and Zou, M and Niu, JG and Ma, XF}, title = {Analysis of genetic diversity of Leuciscus leuciscus baicalensis using novel microsatellite markers with cross-species transferability.}, journal = {Genetics and molecular research : GMR}, volume = {16}, number = {2}, pages = {}, doi = {10.4238/gmr16029376}, pmid = {28481399}, issn = {1676-5680}, mesh = {Alleles ; Animals ; Cyprinidae/*genetics ; Expressed Sequence Tags ; *Gene Transfer, Horizontal ; Heterozygote ; *Microsatellite Repeats ; *Polymorphism, Genetic ; }, abstract = {We used next-generation sequencing technology to characterize 19 genomic simple sequence repeat (SSR) markers and 11 expressed sequence tag (EST) SSR markers from Leuciscus leuciscus baicalensis, a small freshwater fish that is widely distributed in Xinjiang, China. Primers were used to test for polymorphisms in three L. leuciscus baicalensis populations in Xinjiang. There were 4-27 (average 11.3) alleles (NA), the expected heterozygosity (HE) was 0.36-0.94 (average 0.75 ± 0.14), the observed heterozygosity (HO) was 0.37-1.00 (average 0.68 ± 0.18), and the polymorphism information content (PIC) was 0.31-0.93 (average 0.71). The averages of HE and PIC for the EST-SSR markers were slightly lower than for the genomic SSR markers. Genetic analysis of the three populations showed similar results for PIC, HE, and NA. Amplifications were performed in nine other species; the top three transferability values were for Rutilus lacustris (80%), Leuciscus idus (76.7%), and Phoxinus ujmonensis (63.3%), with the following average values: PIC (0.56, 4.46, and 0.52); NA (0.40, 3.00, and 0.32); and HO (0.44, 2.74, and 0.22), respectively. L. leuciscus baicalensis is one of the most important commercial fish in Xinjiang, but in recent years, fishery resources have decreased sharply owing to water conservation projects, unreasonable utilization, and invasion by alien species. These novel SSR markers are appropriate for studies involving fingerprinting, gene flow, genetic diversity, population structure, and molecular-assisted breeding, and could contribute to the conservation of L. leuciscus baicalensis.}, }
@article {pmid28480148, year = {2017}, author = {Watkins, SC and Putonti, C}, title = {The use of informativity in the development of robust viromics-based examinations.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e3281}, pmid = {28480148}, issn = {2167-8359}, abstract = {Metagenomics-based studies have provided insight into many of the complex microbial communities responsible for maintaining life on this planet. Sequencing efforts often uncover novel genetic content; this is most evident for phage communities, in which upwards of 90% of all sequences exhibit no similarity to any sequence in current data repositories. For the small fraction that can be identified, the top BLAST hit is generally posited as being representative of a viral taxon present in the sample of origin. Homology-based classification, however, can be misleading as sequence repositories capture but a small fraction of phage diversity. Furthermore, lateral gene transfer is pervasive within phage communities. As such, the presence of a particular gene may not be indicative of the presence of a particular viral species. Rather, it is just that: an indication of the presence of a specific gene. To circumvent this limitation, we have developed a new method for the analysis of viral metagenomic datasets. BLAST hits are weighted, integrating the sequence identity and length of alignments as well as a taxonomic signal, such that each gene is evaluated with respect to its information content. Through this quantifiable metric, predictions of viral community structure can be made with confidence. As a proof-of-concept, the approach presented here was implemented and applied to seven freshwater viral metagenomes. While providing a robust method for evaluating viral metagenomic data, the tool is versatile and can easily be customized to investigations of any environment or biome.}, }
@article {pmid28477267, year = {2017}, author = {Toribio-Fernández, R and Bella, JL and Martínez-Rodríguez, P and Funkhouser-Jones, LJ and Bordenstein, SR and Pita, M}, title = {Chromosomal localization of Wolbachia inserts in the genomes of two subspecies of Chorthippus parallelus forming a Pyrenean hybrid zone.}, journal = {Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology}, volume = {25}, number = {3-4}, pages = {215-225}, pmid = {28477267}, issn = {1573-6849}, support = {P30 DK058404/DK/NIDDK NIH HHS/United States ; R21 HD086833/HD/NICHD NIH HHS/United States ; }, mesh = {Animals ; *Chromosomes, Bacterial ; *Genome, Insect ; Grasshoppers/*genetics ; Heterochromatin ; *Hybridization, Genetic ; In Situ Hybridization, Fluorescence ; Male ; *Mutagenesis, Insertional ; *Polytene Chromosomes ; Sequence Analysis, DNA ; Wolbachia/*genetics ; }, abstract = {Wolbachia are endosymbiotic bacteria of arthropods and nematodes that can manipulate the reproduction of various host organisms to facilitate their own maternal transmission. Moreover, Wolbachia's presence in host germ cells may contribute to the many cases of lateral gene transfer from Wolbachia to host genomes that have been described. A previous study in Chorthippus parallelus, a well-known orthopteroid forming a hybrid zone in the Pyrenees, identified Wolbachia sequences from two major supergroups in the genomes of infected and uninfected Chorthippus parallelus parallelus (Cpp) and Chorthippus parallelus erythropus (Cpe) subspecies. In this study, we map the Wolbachia genomic inserts to specific regions on the chromosomes of Cpp and Cpe by fluorescent in situ hybridization (FISH) using tyramides to increase the accuracy and detection of these insertions. Additionally, we consider some of the possible roles that these bacterial inserts play in the organization and function of the grasshopper genome, as well as how they can serve as markers for phylogenetic relationships of these organisms.}, }
@article {pmid28472331, year = {2017}, author = {van Hooff, JJE and Snel, B and Kops, GJPL}, title = {Unique Phylogenetic Distributions of the Ska and Dam1 Complexes Support Functional Analogy and Suggest Multiple Parallel Displacements of Ska by Dam1.}, journal = {Genome biology and evolution}, volume = {9}, number = {5}, pages = {1295-1303}, pmid = {28472331}, issn = {1759-6653}, mesh = {Chromosomal Proteins, Non-Histone/*genetics ; Evolution, Molecular ; *Gene Duplication ; *Gene Transfer, Horizontal ; Humans ; Kinetochores/metabolism ; Microtubule-Associated Proteins/*genetics ; Microtubules/metabolism ; Phylogeny ; Saccharomyces cerevisiae ; }, abstract = {Faithful chromosome segregation relies on kinetochores, the large protein complexes that connect chromatin to spindle microtubules. Although human and yeast kinetochores are largely homologous, they track microtubules with the unrelated protein complexes Ska (Ska-C, human) and Dam1 (Dam1-C, yeast). We here uncovered that Ska-C and Dam1-C are both widespread among eukaryotes, but in an exceptionally inverse manner, supporting their functional analogy. Within the complexes, all Ska-C and various Dam1-C subunits are ancient paralogs, showing that gene duplication shaped these complexes. We examined various evolutionary scenarios to explain the nearly mutually exclusive patterns of Ska-C and Dam1-C in present-day species. We propose that Ska-C was present in the last eukaryotic common ancestor, that subsequently Dam1-C displaced Ska-C in an early fungus and was horizontally transferred to diverse non-fungal lineages, displacing Ska-C in these lineages too.}, }
@article {pmid28461122, year = {2017}, author = {Werisch, M and Berger, U and Berendonk, TU}, title = {Conjugative plasmids enable the maintenance of low cost non-transmissible plasmids.}, journal = {Plasmid}, volume = {91}, number = {}, pages = {96-104}, doi = {10.1016/j.plasmid.2017.04.004}, pmid = {28461122}, issn = {1095-9890}, mesh = {Bacteria/*genetics/metabolism ; Computer Simulation ; *Conjugation, Genetic ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Genetic Fitness ; *Models, Statistical ; Plasmids/*chemistry/metabolism ; Selection, Genetic ; Time Factors ; }, abstract = {Some plasmids can be transferred by conjugation to other bacterial hosts. But almost half of the plasmids are non-transmissible. These plasmid types can only be transmitted to the daughter cells of their host after bacterial fission. Previous studies suggest that non-transmissible plasmids become extinct in the absence of selection of their encoded traits, as plasmid-free bacteria are more competitive. Here, we aim to identify mechanisms that enable non-transmissible plasmids to persist, even if they are not beneficial. For this purpose, an individual-based model for plasmid population dynamics was set up and carefully tested for structural consistency and plausibility. Our results demonstrate that non-transmissible plasmids can be stably maintained in a population, even if they impose a substantial burden on their host cells growth. A prerequisite is the co-occurrence of an incompatible and costly conjugative plasmid type, which indirectly facilitates the preservation of the non-transmissible type. We suggest that this constellation might be considered as a potential mechanism maintaining plasmids and associated antibiotic resistances. It should be investigated in upcoming laboratory experiments.}, }
@article {pmid28461121, year = {2017}, author = {Hall, JPJ and Brockhurst, MA and Dytham, C and Harrison, E}, title = {The evolution of plasmid stability: Are infectious transmission and compensatory evolution competing evolutionary trajectories?.}, journal = {Plasmid}, volume = {91}, number = {}, pages = {90-95}, doi = {10.1016/j.plasmid.2017.04.003}, pmid = {28461121}, issn = {1095-9890}, mesh = {Bacteria/*genetics/metabolism ; Biological Evolution ; Chromosomes, Bacterial/chemistry/metabolism ; *Conjugation, Genetic ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Genetic Fitness ; Genetic Loci ; *Models, Statistical ; Mutagenesis, Insertional ; Plasmids/*chemistry/metabolism ; Selection, Genetic ; }, abstract = {Conjugative plasmids are widespread and play an important role in bacterial evolution by accelerating adaptation through horizontal gene transfer. However, explaining the long-term stability of plasmids remains challenging because segregational loss and the costs of plasmid carriage should drive the loss of plasmids though purifying selection. Theoretical and experimental studies suggest two key evolutionary routes to plasmid stability: First, the evolution of high conjugation rates would allow plasmids to survive through horizontal transmission as infectious agents, and second, compensatory evolution to ameliorate the cost of plasmid carriage can weaken purifying selection against plasmids. How these two evolutionary strategies for plasmid stability interact is unclear. Here, we summarise the literature on the evolution of plasmid stability and then use individual based modelling to investigate the evolutionary interplay between the evolution of plasmid conjugation rate and cost amelioration. We find that, individually, both strategies promote plasmid stability, and that they act together to increase the likelihood of plasmid survival. However, due to the inherent costs of increasing conjugation rate, particularly where conjugation is unlikely to be successful, our model predicts that amelioration is the more likely long-term solution to evolving stable bacteria-plasmid associations. Our model therefore suggests that bacteria-plasmid relationships should evolve towards lower plasmid costs that may forestall the evolution of highly conjugative, 'infectious' plasmids.}, }
@article {pmid28460114, year = {2017}, author = {Reynolds, HT and Slot, JC and Divon, HH and Lysøe, E and Proctor, RH and Brown, DW}, title = {Differential Retention of Gene Functions in a Secondary Metabolite Cluster.}, journal = {Molecular biology and evolution}, volume = {34}, number = {8}, pages = {2002-2015}, doi = {10.1093/molbev/msx145}, pmid = {28460114}, issn = {1537-1719}, mesh = {Alkadienes/*metabolism ; Ascomycota/genetics ; Databases, Nucleic Acid ; Epoxy Compounds/*metabolism ; Evolution, Molecular ; Fatty Alcohols/*metabolism ; Fungal Proteins/genetics ; Fusarium/genetics ; Gene Expression Profiling/methods ; Gene Expression Regulation, Fungal/genetics ; Gene Transfer, Horizontal/genetics ; Genome, Fungal/*genetics ; Multigene Family/*genetics ; Phylogeny ; Secondary Metabolism/genetics ; Virulence/genetics ; }, abstract = {In fungi, distribution of secondary metabolite (SM) gene clusters is often associated with host- or environment-specific benefits provided by SMs. In the plant pathogen Alternaria brassicicola (Dothideomycetes), the DEP cluster confers an ability to synthesize the SM depudecin, a histone deacetylase inhibitor that contributes weakly to virulence. The DEP cluster includes genes encoding enzymes, a transporter, and a transcription regulator. We investigated the distribution and evolution of the DEP cluster in 585 fungal genomes and found a wide but sporadic distribution among Dothideomycetes, Sordariomycetes, and Eurotiomycetes. We confirmed DEP gene expression and depudecin production in one fungus, Fusarium langsethiae. Phylogenetic analyses suggested 6-10 horizontal gene transfers (HGTs) of the cluster, including a transfer that led to the presence of closely related cluster homologs in Alternaria and Fusarium. The analyses also indicated that HGTs were frequently followed by loss/pseudogenization of one or more DEP genes. Independent cluster inactivation was inferred in at least four fungal classes. Analyses of transitions among functional, pseudogenized, and absent states of DEP genes among Fusarium species suggest enzyme-encoding genes are lost at higher rates than the transporter (DEP3) and regulatory (DEP6) genes. The phenotype of an experimentally-induced DEP3 mutant of Fusarium did not support the hypothesis that selective retention of DEP3 and DEP6 protects fungi from exogenous depudecin. Together, the results suggest that HGT and gene loss have contributed significantly to DEP cluster distribution, and that some DEP genes provide a greater fitness benefit possibly due to a differential tendency to form network connections.}, }
@article {pmid28459967, year = {2017}, author = {Blanchard, LS and Monin, A and Ouertani, H and Touaibia, L and Michel, E and Buret, F and Simonet, P and Morris, CE and Demanèche, S}, title = {Survival and electrotransformation of Pseudomonas syringae strains under simulated cloud-like conditions.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {5}, pages = {}, doi = {10.1093/femsec/fix057}, pmid = {28459967}, issn = {1574-6941}, mesh = {Adaptation, Physiological/*genetics ; Biological Evolution ; DNA, Bacterial/metabolism ; Electric Stimulation ; Electroporation/methods ; Escherichia coli/genetics ; Gene Transfer, Horizontal/*genetics ; Ice ; Lightning ; Pseudomonas syringae/*genetics/growth &amp; development/*metabolism ; Weather ; }, abstract = {To diversify their genetic material, and thereby allow adaptation to environmental disturbances and colonization of new ecological niches, bacteria use various evolutionary processes, including the acquisition of new genetic material by horizontal transfer mechanisms such as conjugation, transduction and transformation. Electrotransformation mediated by lightning-related electrical phenomena may constitute an additional gene-transfer mechanism occurring in nature. The presence in clouds of bacteria such as Pseudomonas syringae capable of forming ice nuclei that lead to precipitation, and that are likely to be involved in triggering lightning, led us to postulate that natural electrotransformation in clouds may contribute to the adaptive potential of these bacteria. Here, we quantify the survival rate of 10 P. syringae strains in liquid and icy media under such electrical pulses and their capacity to acquire exogenous DNA. In comparison to two other bacteria (Pseudomonas sp. N3 and Escherichia coli TOP10), P. syringae CC0094 appears to be best adapted for survival and for genetic electrotransformation under these conditions, which suggests that this bacterium would be able to survive and to get a boost in its adaptive potential while being transported in clouds and falling back to Earth with precipitation from storms.}, }
@article {pmid28458094, year = {2017}, author = {Blokesch, M}, title = {In and out-contribution of natural transformation to the shuffling of large genomic regions.}, journal = {Current opinion in microbiology}, volume = {38}, number = {}, pages = {22-29}, doi = {10.1016/j.mib.2017.04.001}, pmid = {28458094}, issn = {1879-0364}, mesh = {DNA/*genetics/*metabolism ; DNA Repair ; DNA Transformation Competence ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Recombination, Genetic ; *Transformation, Genetic ; }, abstract = {Naturally competent bacteria can pull free DNA from their surroundings. This incoming DNA can serve various purposes, ranging from acting as a source of nutrients or DNA stretches for repair to the acquisition of novel genetic information. The latter process defines the natural competence for transformation as a mode of horizontal gene transfer (HGT) and led to its discovery almost a century ago. However, although it is widely accepted that natural competence can contribute to the spread of genetic material among prokaryotes, the question remains whether this mode of HGT can foster the transfer of larger DNA regions or only transfers shorter fragments, given that extracellular DNA is often heavily fragmented. Here, I outline examples of competence-mediated movement of large genomic segments. Moreover, I discuss a recent proposition that transformation is used to cure bacteria of selfish mobile genetic elements. Such a transformation-mediated genome maintenance mechanism could indeed be an important and underappreciated function of natural competence.}, }
@article {pmid28458051, year = {2017}, author = {Abdul Momin, MHF and Liakopoulos, A and Phee, LM and Wareham, DW}, title = {Emergence and nosocomial spread of carbapenem-resistant OXA-232-producing Klebsiella pneumoniae in Brunei Darussalam.}, journal = {Journal of global antimicrobial resistance}, volume = {9}, number = {}, pages = {96-99}, doi = {10.1016/j.jgar.2017.02.008}, pmid = {28458051}, issn = {2213-7173}, mesh = {Brunei/epidemiology ; Carbapenem-Resistant Enterobacteriaceae/classification/drug effects/*enzymology/isolation &amp; purification ; Carbapenems/*pharmacology ; Conjugation, Genetic ; *Disease Outbreaks ; Gene Order ; Gene Transfer, Horizontal ; Genotype ; Humans ; Klebsiella Infections/epidemiology/*microbiology ; Klebsiella pneumoniae/classification/drug effects/*enzymology/isolation &amp; purification ; Molecular Epidemiology ; Multilocus Sequence Typing ; Plasmids/analysis ; Random Amplified Polymorphic DNA Technique ; Sequence Analysis, DNA ; *beta-Lactam Resistance ; beta-Lactamases/*analysis ; }, abstract = {OBJECTIVES: Carbapenem-resistant Enterobacteriaceae (CRE) are identified as a major global health concern. The success of CRE is facilitated by the emergence, acquisition and spread of successful clones carrying plasmid-encoded resistance genes. In this study, an outbreak of carbapenem-resistant Klebsiella pneumoniae (CRKP) infections in patients hospitalised in Brunei Darussalam was investigated.<br><br>METHODS: Over a 3-month period (May-July 2015), five multidrug-resistant K. pneumoniae were recovered from individual patients admitted to intensive care units at two hospitals (RIPAS and PMMPMHAB) in Brunei. Antimicrobial susceptibility was determined by broth microtitre dilution using a Micronaut-S &#x3b2;-lactamase VII kit or by Etest. Carbapenemase production was confirmed using the RAPID CARB Blue screen, and classes A-D &#x3b2;-lactamases were detected by multiplex PCR. Molecular typing was performed by random amplified polymorphic DNA (RAPD) PCR and multilocus sequence typing (MLST), with associated virulence and capsular types identified by PCR and sequencing. Plasmids were extracted, sized and characterised by PCR-based replicon typing.<br><br>RESULTS: All isolates were resistant to cephalosporins, carbapenems, aminoglycosides, quinolones and sulfonamides but remained susceptible to polymyxins. Isolates were indistinguishable by RAPD-PCR and all belonged to sequence type (ST231). Resistance was due to the production of OXA-232 and CTX-M-15 &#x3b2;-lactamases, with the blaOXA-232 carbapenemase gene located on a ColE-like plasmid.<br><br>CONCLUSIONS: This is the first report of plasmid-encoded OXA-232-producing CRKP in Brunei hospitals. All isolates were members of ST231, which may be representatives of a high-risk CRKP clone disseminating across Southeast Asia.}, }
@article {pmid28456703, year = {2017}, author = {Bi, W and Li, B and Song, J and Hong, Y and Zhang, X and Liu, H and Lu, H and Zhou, T and Cao, J}, title = {Antimicrobial susceptibility and mechanisms of fosfomycin resistance in extended-spectrum β-lactamase-producing Escherichia coli strains from urinary tract infections in Wenzhou, China.}, journal = {International journal of antimicrobial agents}, volume = {50}, number = {1}, pages = {29-34}, doi = {10.1016/j.ijantimicag.2017.02.010}, pmid = {28456703}, issn = {1872-7913}, mesh = {Anti-Bacterial Agents/*pharmacology ; Blotting, Southern ; China ; Conjugation, Genetic ; *Drug Resistance, Bacterial ; Escherichia coli/*drug effects/enzymology/isolation &amp; purification ; Escherichia coli Infections/*microbiology ; Escherichia coli Proteins/genetics ; Fosfomycin/*pharmacology ; Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; Plasmids/analysis ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Urinary Tract Infections/*microbiology ; beta-Lactamases/genetics/*metabolism ; }, abstract = {Fosfomycin in combination with various antibiotics represents an excellent clinically efficacious regimen for the treatment of urinary tract infections (UTIs) caused by extended-spectrum β-lactamase (ESBL)-producing Escherichia coli. Underlying mechanisms of fosfomycin resistance remain largely uncharacterised. To investigate the antibacterial efficacy of fosfomycin against ESBL-producing E. coli, 356 non-repetitive ESBL-producing E. coli clinical isolates were collected from urine specimens from patients with UTI in Wenzhou, China, from January 2011 to December 2015. Antimicrobial sensitivity testing indicated that 6.7% (24/356) of the ESBL-producing E. coli strains were resistant to fosfomycin. The fosA3 gene encoding a fosfomycin-modifying enzyme was detected in 20 isolates by PCR and sequencing, alone or in combination with other ESBL determinants. Conjugation experiments and Southern blotting demonstrated that 70% (14/20) of the fosA3-positive isolates possessed transferable plasmids (ca. 54.2 kb) co-harbouring the ESBL resistance gene blaCTX-M and the fosfomycin resistance gene fosA3. Among the four fosfomycin-resistant fosA3-negative E. coli isolates, three contained amino acid substitutions (Ile28Asn and Phe30Leu in MurA and Leu297Phe in GlpT). The results indicate that presence of the fosA3 gene is the primary mechanism of fosfomycin resistance in ESBL-producing E. coli isolates in Wenzhou, China. In addition, a plasmid (ca. 54.2 kb) co-harbouring fosA3 and blaCTX-M genes is horizontally transferable. Furthermore, a low degree of homology in the fosfomycin-resistant E. coli was confirmed using multilocus sequence typing (MLST), suggesting that there is no obvious phenomenon of clonal dissemination.}, }
@article {pmid28451760, year = {2017}, author = {Cardona, G and Pons, JC}, title = {Reconstruction of LGT networks from tri-LGT-nets.}, journal = {Journal of mathematical biology}, volume = {75}, number = {6-7}, pages = {1669-1692}, pmid = {28451760}, issn = {1432-1416}, mesh = {Computer Simulation ; Evolution, Molecular ; Gene Regulatory Networks ; *Gene Transfer, Horizontal ; Mathematical Concepts ; *Models, Genetic ; *Phylogeny ; }, abstract = {Phylogenetic networks have gained attention from the scientific community due to the evidence of the existence of evolutionary events that cannot be represented using trees. A variant of phylogenetic networks, called LGT networks, models specifically lateral gene transfer events, which cannot be properly represented with generic phylogenetic networks. In this paper we treat the problem of the reconstruction of LGT networks from substructures induced by three leaves, which we call tri-LGT-nets. We first restrict ourselves to a class of LGT networks that are both mathematically treatable and biologically significant, called BAN-LGT networks. Then, we study the decomposition of such networks in subnetworks with three leaves and ask whether or not this decomposition determines the network. The answer to this question is negative, but if we further impose time-consistency (species involved in a later gene transfer must coexist) the answer is affirmative, up to some redundancy that can never be recovered but is fully characterized.}, }
@article {pmid28451057, year = {2017}, author = {Iranzo, J and Krupovic, M and Koonin, EV}, title = {A network perspective on the virus world.}, journal = {Communicative &amp; integrative biology}, volume = {10}, number = {2}, pages = {e1296614}, pmid = {28451057}, issn = {1942-0889}, abstract = {Viral evolution is characterized by high rates of horizontal gene transfer and fast sequence divergence. Furthermore, there are no universal genes shared by all viruses. As a result, distant relationships among viruses are better represented by a network than by a tree. Here we discuss 3 network representations of the virus world with decreasing levels of complexity, from a multilayer network that integrates sequence conservation and patterns of gene sharing to a classic genome similarity network. As new tools for network analysis are developed, we expect that novel insights into virus evolution will result from the study of more complex representations of the virus world.}, }
@article {pmid28450856, year = {2017}, author = {Heshiki, Y and Dissanayake, T and Zheng, T and Kang, K and Yueqiong, N and Xu, Z and Sarkar, C and Woo, PCY and Chow, BKC and Baker, D and Yan, A and Webster, CJ and Panagiotou, G and Li, J}, title = {Toward a Metagenomic Understanding on the Bacterial Composition and Resistome in Hong Kong Banknotes.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {632}, pmid = {28450856}, issn = {1664-302X}, abstract = {Currency is possibly one of the main media transmitting pathogens and drug resistance due to its wide circulation in daily life. In this study, we made a comprehensive characterization of the bacterial community present on banknotes collected from different geographical regions of Hong Kong (HK) by performing in vitro characterization of the bacterial presence and resistome profile, as well as metagenomic analysis including microbial diversity, the prevalence of potential pathogens, the dissemination potential of antibiotic-resistance genes (ARGs), among others. When comparing the bacterial community of HK banknotes with other HK environmental samples, including water and marine sediment, we revealed that HK banknotes cover nearly 50% of total genera found in all the environmental samples, implying that banknotes harbor diverse bacteria originated from a variety of environments. Furthermore, the banknotes have higher abundance of potential pathogenic species (~5 times more) and ARGs (~5 times more) with higher dissemination potential (~48 times more) compared with other environmental samples. These findings unveiled the capabilities of this common medium of exchange to accommodate various bacteria, and transmit pathogens and antibiotic resistance. Furthermore, the observed independence of microbiome profile from the city's topological indices led us to formulate a hypothesis that due to their high circulation banknotes may harbor a homogenized microbiome.}, }
@article {pmid28448436, year = {2017}, author = {Blesa, A and Quintans, NG and Baquedano, I and Mata, CP and Castón, JR and Berenguer, J}, title = {Role of Archaeal HerA Protein in the Biology of the Bacterium Thermus thermophilus.}, journal = {Genes}, volume = {8}, number = {5}, pages = {}, pmid = {28448436}, issn = {2073-4425}, abstract = {Intense gene flux between prokaryotes result in high percentage of archaeal genes in the genome of the thermophilic bacteria Thermus spp. Among these archaeal genes a homolog to the Sulfolobus spp. HerA protein appears in all of the Thermus spp. strains so far sequenced (HepA). The role of HepA in Thermus thermophilus HB27 has been analyzed using deletion mutants, and its structure resolved at low resolution by electron microscopy. Recombinant HepA shows DNA-dependent ATPase activity and its structure revealed a double ring, conically-shaped hexamer with an upper diameter of 150 Å and a bottom module of 95 Å. A central pore was detected in the structure that ranges from 13 Å at one extreme, to 30 Å at the other. Mutants lacking HepA show defective natural competence and DNA donation capability in a conjugation-like process termed "transjugation", and also high sensitivity to UV and dramatic sensitivity to high temperatures. These data support that acquisition of an ancestral archaeal HerA has been fundamental for the adaptation of Thermus spp. to high temperatures.}, }
@article {pmid28447371, year = {2017}, author = {Cavaliere, M and Feng, S and Soyer, OS and Jiménez, JI}, title = {Cooperation in microbial communities and their biotechnological applications.}, journal = {Environmental microbiology}, volume = {19}, number = {8}, pages = {2949-2963}, pmid = {28447371}, issn = {1462-2920}, support = {BB/M017982/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M018040/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M009769/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/K003240/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Biological Evolution ; Biotechnology ; Ecology ; Microbial Consortia/*physiology ; Microbial Interactions/*physiology ; *Models, Biological ; }, abstract = {Microbial communities are increasingly utilized in biotechnology. Efficiency and productivity in many of these applications depends on the presence of cooperative interactions between members of the community. Two key processes underlying these interactions are the production of public goods and metabolic cross-feeding, which can be understood in the general framework of ecological and evolutionary (eco-evo) dynamics. In this review, we illustrate the relevance of cooperative interactions in microbial biotechnological processes, discuss their mechanistic origins and analyse their evolutionary resilience. Cooperative behaviours can be damaged by the emergence of 'cheating' cells that benefit from the cooperative interactions but do not contribute to them. Despite this, cooperative interactions can be stabilized by spatial segregation, by the presence of feedbacks between the evolutionary dynamics and the ecology of the community, by the role of regulatory systems coupled to the environmental conditions and by the action of horizontal gene transfer. Cooperative interactions enrich microbial communities with a higher degree of robustness against environmental stress and can facilitate the evolution of more complex traits. Therefore, the evolutionary resilience of microbial communities and their ability to constraint detrimental mutants should be considered to design robust biotechnological applications.}, }
@article {pmid28447026, year = {2017}, author = {Porse, A and Gumpert, H and Kubicek-Sutherland, JZ and Karami, N and Adlerberth, I and Wold, AE and Andersson, DI and Sommer, MOA}, title = {Genome Dynamics of Escherichia coli during Antibiotic Treatment: Transfer, Loss, and Persistence of Genetic Elements In situ of the Infant Gut.}, journal = {Frontiers in cellular and infection microbiology}, volume = {7}, number = {}, pages = {126}, pmid = {28447026}, issn = {2235-2988}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; DNA, Bacterial ; Drug Resistance, Multiple, Bacterial ; Escherichia coli/*drug effects/*genetics/isolation &amp; purification ; Escherichia coli Infections/microbiology ; *Evolution, Molecular ; Feces/microbiology ; Female ; Gastrointestinal Tract/*microbiology ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Genome, Bacterial/genetics ; Humans ; Infant ; Infant, Newborn ; Mice ; Mice, Inbred BALB C ; Plasmids ; Sequence Analysis ; Virulence/genetics ; Virulence Factors/genetics ; }, abstract = {Elucidating the adaptive strategies and plasticity of bacterial genomes in situ is crucial for understanding the epidemiology and evolution of pathogens threatening human health. While much is known about the evolution of Escherichia coli in controlled laboratory environments, less effort has been made to elucidate the genome dynamics of E. coli in its native settings. Here, we follow the genome dynamics of co-existing E. coli lineages in situ of the infant gut during the first year of life. One E. coli lineage causes a urinary tract infection (UTI) and experiences several alterations of its genomic content during subsequent antibiotic treatment. Interestingly, all isolates of this uropathogenic E. coli strain carried a highly stable plasmid implicated in virulence of diverse pathogenic strains from all over the world. While virulence elements are certainly beneficial during infection scenarios, their role in gut colonization and pathogen persistence is poorly understood. We performed in vivo competitive fitness experiments to assess the role of this highly disseminated virulence plasmid in gut colonization, but found no evidence for a direct benefit of plasmid carriage. Through plasmid stability assays, we demonstrate that this plasmid is maintained in a parasitic manner, by strong first-line inheritance mechanisms, acting on the single-cell level, rather than providing a direct survival advantage in the gut. Investigating the ecology of endemic accessory genetic elements, in their pathogenic hosts and native environment, is of vital importance if we want to understand the evolution and persistence of highly virulent and drug resistant bacterial isolates.}, }
@article {pmid28443072, year = {2017}, author = {Singh, T and Das, S and Ramachandran, VG and Wani, S and Shah, D and Maroof, KA and Sharma, A}, title = {Distribution of Integrons and Phylogenetic Groups among Enteropathogenic Escherichia coli Isolates from Children &lt;5 Years of Age in Delhi, India.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {561}, pmid = {28443072}, issn = {1664-302X}, abstract = {Integrons by means of horizontal gene transfer carry multidrug resistance genes (MDR) among bacteria, including E. coli. The aim of this study was to determine the antibiotic resistance profiles and the genes associated with them, to gain insights in the distribution of phylogroups, prevalence, and characterization of class 1, 2 and 3 integrons among Enteropathogenic E. coli (EPEC) isolates, from children upto 5 years of age from Delhi and National Capital Region (NCR), India. A total of 120 E. coli isolates, including 80 from diarrheagenic E. coli (cases) and 40 from healthy isolates (controls) were recruited in this study. After isolation of E. coli, screening for EPEC was done by conventional multiplex PCR. Antibiotic suseptibility test was performed using disk diffusion method and further confirmed by minimum inhibitory concentration (MICs) by E-test. The presence and characterization of integrons and antimicrobial resistance genes were performed by PCR and DNA sequencing. Phylogeny determination was carried out by quadruplex PCR. EPEC strains were found in 64 of the 80 diarrheagenic cases, out of which 38 were MDR. In the 40 healthy controls, 23 were found to be EPEC strain, out of which only 2 were MDR. Amongst 80 diarrheagenic cases, class 1 integron were observed in 43 isolates, class 2 integron in 12 isolates and 9 isolates were found with co-existence of both. Similarly, in healthy controls; class 1 integron in 9 and class 2 integron in 7 isolates were observed with co-existence in 3 isolates. None of the isolates included class 3 integron. The dfr was the most commonly identified gene cassette within the integron-positive isolates. Phylogenetic studies showed considerable representation of phylogroup B2 in both diarrheagenic cases and healthy controls. This study reiterates the importance of class 1 integron predominantly for acquisition of antibiotic resistance genes among EPEC isolates. Furthermore, it also ascertains the possible association between multidrug resistance and presence of integrons. Approximately 91% of isolates were easily assigned to their respective phylogroups. Assessment of the relationship between antibiotic resistance and dominant phylogroups detected was also attempted. This study also highlights the increased burden of antimicrobial resistance in healthy controls.}, }
@article {pmid28442305, year = {2017}, author = {Martins, ER and Estofolete, CF and Zequini, AB and Cerdeira, L and de Oliveira Garcia, D and Bueno, MFC and Francisco, GR and de Andrade, LN and da Costa Darini, AL and Tolentino, FM and Casella, T and Lincopan, N and Nogueira, MCL}, title = {Transfer of KPC-2 carbapenemase from Klebsiella pneumoniae to Enterobacter cloacae in a patient receiving meropenem therapy.}, journal = {Diagnostic microbiology and infectious disease}, volume = {88}, number = {3}, pages = {287-289}, doi = {10.1016/j.diagmicrobio.2017.04.004}, pmid = {28442305}, issn = {1879-0070}, mesh = {Anti-Bacterial Agents/*therapeutic use ; Enterobacter cloacae/*genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Klebsiella Infections/*drug therapy/microbiology ; Klebsiella pneumoniae/*genetics ; Male ; Meropenem ; Middle Aged ; Plasmids/analysis ; Respiratory Tract Infections/drug therapy/microbiology ; Thienamycins/*therapeutic use ; beta-Lactamases/*genetics ; }, abstract = {The horizontal transfer of a plasmid bearing the blaKPC-2 gene from K. pneumoniae to E. cloacae infecting the respiratory tract of a patient during meropenem therapy was elucidated. This finding is particularly worrisome, since these drugs are of last resort for multidrug-resistant Gram-negative pathogens.}, }
@article {pmid28441577, year = {2017}, author = {Domingues, S and Nielsen, KM}, title = {Membrane vesicles and horizontal gene transfer in prokaryotes.}, journal = {Current opinion in microbiology}, volume = {38}, number = {}, pages = {16-21}, doi = {10.1016/j.mib.2017.03.012}, pmid = {28441577}, issn = {1879-0364}, mesh = {Archaea/*genetics/*metabolism ; Bacteria/*genetics/*metabolism ; DNA/genetics/metabolism ; Extracellular Vesicles/*metabolism ; *Gene Transfer, Horizontal ; Membranes/*metabolism ; RNA/genetics/metabolism ; }, abstract = {Membrane vesicles (MVs) are released from all living cells. MVs are lumen-containing spheres of lipid-bilayers derived from the cell surface. MVs are biologically active and contain various components, including genetic material. Both chromosomal and plasmid DNA, as well as different types of RNA have been detected in MVs. Vesicle-mediated transfer of genes coding for antibiotic resistance, virulence and metabolic traits has been reported in Gram-negative and Gram-positive bacteria and in Archaea. MVs can persist over time in natural environments. Here we review the characteristics of and the role of MVs in horizontal gene transfer (HGT) processes in prokaryotes.}, }
@article {pmid28439658, year = {2017}, author = {Lee, JY and Han, GG and Choi, J and Jin, GD and Kang, SK and Chae, BJ and Kim, EB and Choi, YJ}, title = {Pan-Genomic Approaches in Lactobacillus reuteri as a Porcine Probiotic: Investigation of Host Adaptation and Antipathogenic Activity.}, journal = {Microbial ecology}, volume = {74}, number = {3}, pages = {709-721}, pmid = {28439658}, issn = {1432-184X}, support = {914005-04//Strategic Initiative for Microbiomes in Agriculture and Food, Ministry of Agriculture, Food and Rural Affairs, Republic of Korea/ ; 520160476//2016 Research Grant from Kangwon National University/ ; }, mesh = {Animals ; Feces/microbiology ; *Genome, Bacterial ; Genomics/methods ; Limosilactobacillus reuteri/chemistry/*genetics ; Probiotics/*analysis/metabolism ; *Sus scrofa/genetics/metabolism/microbiology ; }, abstract = {After the introduction of a ban on the use of antibiotic growth promoters (AGPs) for livestock, reuterin-producing Lactobacillus reuteri is getting attention as an alternative to AGPs. In this study, we investigated genetic features of L. reuteri associated with host specificity and antipathogenic effect. We isolated 104 L. reuteri strains from porcine feces, and 16 strains, composed of eight strains exhibiting the higher antipathogenic effect (group HS) and eight strains exhibiting the lower effect (group LS), were selected for genomic comparison. We generated draft genomes of the 16 isolates and investigated their pan-genome together with the 26 National Center for Biotechnology Information-registered genomes. L. reuteri genomes organized six clades with multi-locus sequence analysis, and the clade IV includes the 16 isolates. First, we identified six L. reuteri clade IV-specific genes including three hypothetical protein-coding genes. The three annotated genes encode transposases and cell surface proteins, indicating that these genes are the result of adaptation to the host gastrointestinal epithelia and that these host-specific traits were acquired by horizontal gene transfer. We also identified differences between groups HS and LS in the pdu-cbi-cob-hem gene cluster, which is essential for reuterin and cobalamin synthesis, and six genes specific to group HS are revealed. While the strains of group HS possessed all genes of this cluster, LS strains have lost many genes of the cluster. This study provides a deeper understanding of the relationship between probiotic properties and genomic features of L. reuteri.}, }
@article {pmid28439261, year = {2017}, author = {Tashiro, Y and Hasegawa, Y and Shintani, M and Takaki, K and Ohkuma, M and Kimbara, K and Futamata, H}, title = {Interaction of Bacterial Membrane Vesicles with Specific Species and Their Potential for Delivery to Target Cells.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {571}, pmid = {28439261}, issn = {1664-302X}, abstract = {Membrane vesicles (MVs) are secreted from a wide range of microbial species and transfer their content to other cells. Although MVs play critical roles in bacterial communication, whether MVs selectively interact with bacterial cells in microbial communities is unclear. In this study, we investigated the specificity of the MV-cell interactions and evaluated the potential of MVs to target bacterial cells for delivery. MV association with bacterial cells was examined using a fluorescent membrane dye to label MVs. MVs derived from the enterobacterium Buttiauxella agrestis specifically interacted with cells of the parent strain but interacted less specifically with those of other genera tested in this study. Electron microscopic analyses showed that MVs were not only attached on B. agrestis cells but also fused to them. The interaction energy, which was characterized by hydrodynamic diameter and zeta potential based on the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory, was significant low between MVs and cells in B. agrestis, compared to those between B. agrestis MVs and cells of other genera. Similar specific interaction was also occurred between B. agrestis MVs and cells of six other species belonging to Buttiauxella spp. B. agrestis harboring plasmid pBBR1MCS-1 secreted plasmid-containing MVs (p-MVs), and plasmid DNA in p-MVs was transferred to the same species. Moreover, antibiotic-associated MVs enabled effective killing of target species; the survival rate of B. agrestis was lower than those of Escherichia coli and Pseudomonas aeruginosa in the presence of gentamicin-associated MVs derived from B. agrestis. Altogether, we provide the evidence that MVs selectively interact with target bacterial cells and offer a new avenue for controlling specific bacterial species using bacterial MVs in microbial communities.}, }
@article {pmid28438469, year = {2017}, author = {Bañuelos-Vazquez, LA and Torres Tejerizo, G and Brom, S}, title = {Regulation of conjugative transfer of plasmids and integrative conjugative elements.}, journal = {Plasmid}, volume = {91}, number = {}, pages = {82-89}, doi = {10.1016/j.plasmid.2017.04.002}, pmid = {28438469}, issn = {1095-9890}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/*genetics/metabolism ; Chromosomes, Bacterial/chemistry/metabolism ; *Conjugation, Genetic ; DNA Transposable Elements ; DNA, Bacterial/*genetics/metabolism ; Drug Resistance, Multiple, Bacterial/genetics ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Genetic Loci ; Mutagenesis, Insertional ; Plasmids/*chemistry/metabolism ; Quorum Sensing ; }, abstract = {Horizontal gene transfer has been recognized as one of the principal contributors to bacterial evolution and diversification. One of the mechanisms involved in this process is conjugative transfer of plasmids and Integrative Conjugative Elements (ICEs). Plasmids and ICEs often encode traits beneficial for bacterial survival in specific environments, or for the establishment of symbiosis or pathogenesis, in addition to genes allowing conjugative transfer. In this review, we analyze the mechanisms that regulate the expression of conjugative transfer genes. For traits such as antibiotic or metal resistance, the compounds involved may induce conjugative transfer directly, while symbiosis and pathogenesis are modulated by quorum-sensing and/or signal molecules released by the host. However, multiple layers of regulation are usually involved in modulating transfer. In addition to the plasmid-encoded regulatory elements, conjugation seems to be regulated by what we have labeled as the "internal environment", defined by the interaction between the host chromosome and the plasmids or ICEs. Another regulatory level depends on the "external environment", which affects conjugative transfer due to the composition and conditions of the community.}, }
@article {pmid28436748, year = {2017}, author = {Saranathan, R and Pagal, S and Sawant, AR and Tomar, A and Madhangi, M and Sah, S and Satti, A and Arunkumar, KP and Prashanth, K}, title = {Disruption of tetR type regulator adeN by mobile genetic element confers elevated virulence in Acinetobacter baumannii.}, journal = {Virulence}, volume = {8}, number = {7}, pages = {1316-1334}, pmid = {28436748}, issn = {2150-5608}, mesh = {Acinetobacter Infections/*microbiology ; Acinetobacter baumannii/*genetics/growth &amp; development/metabolism/*pathogenicity ; Bacterial Proteins/genetics/*metabolism ; Gene Expression Regulation, Bacterial ; Humans ; Interspersed Repetitive Sequences ; *Mutagenesis, Insertional ; Trans-Activators/genetics/*metabolism ; Virulence ; }, abstract = {Acinetobacter baumannii is an important human pathogen and considered as a major threat due to its extreme drug resistance. In this study, the genome of a hyper-virulent MDR strain PKAB07 of A. baumannii isolated from an Indian patient was sequenced and analyzed to understand its mechanisms of virulence, resistance and evolution. Comparative genome analysis of PKAB07 revealed virulence and resistance related genes scattered throughout the genome, instead of being organized as an island, indicating the highly mosaic nature of the genome. Many intermittent horizontal gene transfer events, insertion sequence (IS) element insertions identified were augmenting resistance machinery and elevating the SNP densities in A. baumannii eventually aiding in their swift evolution. ISAba1, the most widely distributed insertion sequence in A. baumannii was found in multiple sites in PKAB07. Out of many ISAba1 insertions, we identified novel insertions in 9 different genes wherein insertional inactivation of adeN (tetR type regulator) was significant. To assess the significance of this disruption in A. baumannii, adeN mutant and complement strains were constructed in A. baumannii ATCC 17978 strain and studied. Biofilm levels were abrogated in the adeN knockout when compared with the wild type and complemented strain of adeN knockout. Virulence of the adeN knockout mutant strain was observed to be high, which was validated by in vitro experiments and Galleria mellonella infection model. The overexpression of adeJ, a major component of AdeIJK efflux pump observed in adeN knockout strain could be the possible reason for the elevated virulence in adeN mutant and PKB07 strain. Knocking out of adeN in ATCC strain led to increased resistance and virulence at par with the PKAB07. Disruption of tetR type regulator adeN by ISAba1 consequently has led to elevated virulence in this pathogen.}, }
@article {pmid28435889, year = {2017}, author = {Schultz, E and Barraud, O and Madec, JY and Haenni, M and Cloeckaert, A and Ploy, MC and Doublet, B}, title = {Multidrug Resistance Salmonella Genomic Island 1 in a Morganella morganii subsp. morganii Human Clinical Isolate from France.}, journal = {mSphere}, volume = {2}, number = {2}, pages = {}, pmid = {28435889}, issn = {2379-5042}, abstract = {Salmonella genomic island 1 (SGI1) is a multidrug resistance integrative mobilizable element that harbors a great diversity of antimicrobial resistance gene clusters described in numerous Salmonella enterica serovars and also in Proteus mirabilis. A serious threat to public health was revealed in the recent description in P. mirabilis of a SGI1-derivative multidrug resistance island named PGI1 (Proteus genomic island 1) carrying extended-spectrum-β-lactamase (ESBL) and metallo-β-lactamase resistance genes, blaVEB-6 and blaNDM-1, respectively. Here, we report the first description of Salmonella genomic island 1 (SGI1) in a multidrug-resistant clinical Morganella morganii subsp. morganii strain isolated from a patient in France in 2013. Complete-genome sequencing of the strain revealed SGI1 variant SGI1-L carrying resistance genes dfrA15, floR, tetA(G), blaPSE-1 (now referred to as blaCARB-2), and sul1, conferring resistance to trimethoprim, phenicols, tetracyclines, amoxicillin, and sulfonamides, respectively. The SGI1-L variant was integrated into the usual chromosome-specific integration site at the 3' end of the trmE gene. Beyond Salmonella enterica and Proteus mirabilis, the SGI1 integrative mobilizable element may thus also disseminate its multidrug resistance phenotype in another genus belonging to the Proteae tribe of the family Enterobacteriaceae. IMPORTANCE Since its initial identification in epidemic multidrug-resistant Salmonella enterica serovar Typhimurium DT104 strains, several SGI1 variants, SGI1 lineages, and SGI1-related elements (SGI2, PGI1, and AGI1) have been described in many bacterial genera (Salmonella, Proteus, Morganella, Vibrio, Shewanella, etc.). They constitute a family of multidrug resistance site-specific integrative elements acquired by horizontal gene transfer, SGI1 being the best-characterized element. The horizontal transfer of SGI1/PGI1 elements into other genera is of public health concern, notably with regard to the spread of critically important resistance genes such as ESBL and carbapenemase genes. The identification of SGI1 in Morganella morganii raises the issue of (i) the potential for SGI1 to emerge in other human pathogens and (ii) its bacterial host range. Further surveillance and research are needed to understand the epidemiology, the spread, and the importance of the members of this SGI1 family of integrative elements in contributing to antibiotic resistance development.}, }
@article {pmid28435006, year = {2017}, author = {Makart, L and Commans, F and Gillis, A and Mahillon, J}, title = {Horizontal transfer of chromosomal markers mediated by the large conjugative plasmid pXO16 from Bacillus thuringiensis serovar israelensis.}, journal = {Plasmid}, volume = {91}, number = {}, pages = {76-81}, doi = {10.1016/j.plasmid.2017.04.001}, pmid = {28435006}, issn = {1095-9890}, mesh = {Bacillus thuringiensis/*genetics/metabolism ; Chromosome Mapping ; Chromosomes, Bacterial/chemistry/metabolism ; *Conjugation, Genetic ; *DNA Transposable Elements ; DNA, Bacterial/*genetics/metabolism ; *Gene Transfer, Horizontal ; Genetic Loci ; Genetic Markers ; Mutagenesis ; Plasmids/*chemistry/metabolism ; }, abstract = {pXO16, a large plasmid originating from Bacillus thuringiensis serovar israelensis, displays unique conjugation capacities: besides efficient self-transfer, it is able to mobilize and retro-mobilize non-conjugative plasmids, including those missing an oriT and/or a mob gene, also known as "non-mobilizable" plasmids. In this paper, another peculiar transfer property of pXO16 is described. This element is indeed able to transfer chromosomal loci at frequencies of ca. 10[-5]-10[-6] transconjugants/donor cell. Whereas most other chromosomal transfer systems occur via the integration of the conjugative elements into the chromosome prior to its transfer, pXO16 appears to transfer the chromosomal markers in the absence of physical integration, but rather through a "donation-type" mobilization.}, }
@article {pmid28434972, year = {2017}, author = {Allen, AR}, title = {One bacillus to rule them all? - Investigating broad range host adaptation in Mycobacterium bovis.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {53}, number = {}, pages = {68-76}, doi = {10.1016/j.meegid.2017.04.018}, pmid = {28434972}, issn = {1567-7257}, mesh = {Animals ; Cattle ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genotype ; Host Specificity ; Humans ; Mycobacterium bovis/genetics/*physiology ; Tuberculosis/*microbiology/veterinary ; Zoonoses/*microbiology ; }, }
@article {pmid28432093, year = {2017}, author = {Dahmane, N and Libante, V and Charron-Bourgoin, F and Guédon, E and Guédon, G and Leblond-Bourget, N and Payot, S}, title = {Diversity of Integrative and Conjugative Elements of Streptococcus salivarius and Their Intra- and Interspecies Transfer.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {13}, pages = {}, pmid = {28432093}, issn = {1098-5336}, mesh = {Bacterial Proteins/genetics ; Conjugation, Genetic ; *DNA Transposable Elements ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Variation ; Streptococcus salivarius/classification/*genetics/isolation &amp; purification ; Streptococcus thermophilus/classification/*genetics/isolation &amp; purification ; }, abstract = {Integrative and conjugative elements (ICEs) are widespread chromosomal mobile genetic elements which can transfer autonomously by conjugation in bacteria. Thirteen ICEs with a conjugation module closely related to that of ICESt3 of Streptococcus thermophilus were characterized in Streptococcus salivarius by whole-genome sequencing. Sequence comparison highlighted ICE evolution by shuffling of 3 different integration/excision modules (for integration in the 3' end of the fda, rpsI, or rpmG gene) with the conjugation module of the ICESt3 subfamily. Sequence analyses also pointed out a recombination occurring at oriT (likely mediated by the relaxase) as a mechanism of ICE evolution. Despite a similar organization in two operons including three conserved genes, the regulation modules show a high diversity (about 50% amino acid sequence divergence for the encoded regulators and presence of unrelated additional genes) with a probable impact on the regulation of ICE activity. Concerning the accessory genes, ICEs of the ICESt3 subfamily appear particularly rich in restriction-modification systems and orphan methyltransferase genes. Other cargo genes that could confer a selective advantage to the cell hosting the ICE were identified, in particular, genes for bacteriocin synthesis and cadmium resistance. The functionality of 2 ICEs of S. salivarius was investigated. Autonomous conjugative transfer to other S. salivarius strains, to S. thermophilus, and to Enterococcus faecalis was observed. The analysis of the ICE-fda border sequence in these transconjugants allowed the localization of the DNA cutting site of the ICE integrase.IMPORTANCE The ICESt3 subfamily of ICEs appears to be widespread in streptococci and targets diverse chromosomal integration sites. These ICEs carry diverse cargo genes that can confer a selective advantage to the host strain. The maintenance of these mobile genetic elements likely relies in part on self-encoded restriction-modification systems. In this study, intra- and interspecies transfer was demonstrated for 2 ICEs of S. salivarius Closely related ICEs were also detected in silico in other Streptococcus species (S. pneumoniae and S. parasanguinis), thus indicating that diffusion of ICESt3-related elements probably plays a significant role in horizontal gene transfer (HGT) occurring in the oral cavity but also in the digestive tract, where S. salivarius is present.}, }
@article {pmid28428775, year = {2017}, author = {Patil, PP and Mali, S and Midha, S and Gautam, V and Dash, L and Kumar, S and Shastri, J and Singhal, L and Patil, PB}, title = {Genomics Reveals a Unique Clone of Burkholderia cenocepacia Harboring an Actively Excising Novel Genomic Island.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {590}, pmid = {28428775}, issn = {1664-302X}, abstract = {Burkholderia cenocepacia is a clinically dominant form among the other virulent species of Burkholderia cepacia complex (Bcc). In the present study, we sequenced and analyzed the genomes of seven nosocomial Bcc isolates, five of which were isolated from the bloodstream infections and two isolates were recovered from the hospital setting during the surveillance. Genome-based species identification of the Bcc isolates using a type strain explicitly identified the species as B. cenocepacia. Moreover, single nucleotide polymorphism analysis revealed that the six isolates were clonal and phylogenetically distinct from the other B. cenocepacia. Comparative genomics distinctly revealed the larger genome size of six clonal isolates as well as the presence of a novel 107 kb genomic island named as BcenGI15, which encodes putative pathogenicity-associated genes. We have shown that the BcenGI15 has an ability to actively excise from the genome and forming an extrachromosomal circular form suggesting its mobile nature. Surprisingly, a homolog of BcenGI15 was also present in the genome of a clinical isolate named Burkholderia pseudomallei strain EY1. This novel genetic element is present only in the variants of B. cenocepacia and B. pseudomallei isolates suggesting its interspecies existence in the main pathogenic species of the genus Burkholderia. In conclusion, the whole genome analysis of the genomically distinct B. cenocepacia clinical isolates has advanced our understanding of the epidemiology and evolution of this important nosocomial pathogen as well as its relatives.}, }
@article {pmid28427794, year = {2017}, author = {Luk-In, S and Pulsrikarn, C and Bangtrakulnonth, A and Chatsuwan, T and Kulwichit, W}, title = {Occurrence of a novel class 1 integron harboring qnrVC4 in Salmonella Rissen.}, journal = {Diagnostic microbiology and infectious disease}, volume = {88}, number = {3}, pages = {282-286}, doi = {10.1016/j.diagmicrobio.2017.03.016}, pmid = {28427794}, issn = {1879-0070}, support = {001/WHO_/World Health Organization/International ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Integrons ; Microbial Sensitivity Tests ; Plasmids/analysis ; Quinolones/*pharmacology ; Salmonella enterica/*drug effects/*genetics/isolation &amp; purification ; Sequence Homology ; Swine ; Thailand ; }, abstract = {We described qnrVC4 in S. Rissen 166ANSS50, a swine isolate, which was detected in the study on quinolone resistance mechanisms of nontyphoidal Salmonella in Thailand. The isolate was found to harbor a ̴17-kb non-conjugative plasmid carrying qnrVC4 within 8.91kb of a novel In4-like class 1 integron (In805). It contained the multi-drug resistance gene cassettes of qnrVC4-qacH4-aacA4-cmlA7-blaOXA-10-aadA1-dfrA14 and unusual 3'-CS of mobC-IS6100. This 1014-bp qnrVC4 cassette included with promoter (PqnrVC4: -35 TTGAGA and -10 TAGTCT) showed high homology with qnrVC4 in superintegron of V. cholerae O1 El Tor. The qnrVC4 recombinant plasmid resulted in 4-, 8-, and 16-fold increase in the MICs of nalidixic acid (2-8μg/mL), ciprofloxacin (0.015-0.125μg/mL), and norfloxacin (0.03-0.5μg/mL), respectively. In addition, the backbone plasmid revealed a novel replicon belonging to the MOBQ1 group from the broad-host-range mobilisable IncQ1 plasmid RFS1010 based on relaxase sequences. This is the first known report of qnrVC in Salmonella enterica. The qnrVC4 gene was co-transferred with other resistance genes via a novel plasmid-borne In805. This allowed the spread of this resistance gene to Enterobacteriaceae.}, }
@article {pmid28427348, year = {2017}, author = {Haase, EM and Kou, Y and Sabharwal, A and Liao, YC and Lan, T and Lindqvist, C and Scannapieco, FA}, title = {Comparative genomics and evolution of the amylase-binding proteins of oral streptococci.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {94}, pmid = {28427348}, issn = {1471-2180}, support = {R01 DE022673/DE/NIDCR NIH HHS/United States ; }, mesh = {Adaptation, Biological ; Amylases/*metabolism ; Bacterial Outer Membrane Proteins/genetics ; Bacterial Proteins/chemistry/classification/genetics ; Base Sequence ; Carrier Proteins/*chemistry/classification/*genetics ; DNA, Bacterial/isolation &amp; purification ; Gene Transfer, Horizontal ; *Genomics ; Humans ; Models, Molecular ; Mouth/microbiology ; Phylogeny ; Protein Structure, Tertiary ; Saliva/enzymology ; Sequence Alignment ; Sequence Analysis, Protein ; Streptococcus/*genetics ; Symbiosis ; alpha-Amylases/metabolism ; }, abstract = {BACKGROUND: Successful commensal bacteria have evolved to maintain colonization in challenging environments. The oral viridans streptococci are pioneer colonizers of dental plaque biofilm. Some of these bacteria have adapted to life in the oral cavity by binding salivary α-amylase, which hydrolyzes dietary starch, thus providing a source of nutrition. Oral streptococcal species bind α-amylase by expressing a variety of amylase-binding proteins (ABPs). Here we determine the genotypic basis of amylase binding where proteins of diverse size and function share a common phenotype.<br><br>RESULTS: ABPs were detected in culture supernatants of 27 of 59 strains representing 13 oral Streptococcus species screened using the amylase-ligand binding assay. N-terminal sequences from ABPs of diverse size were obtained from 18 strains representing six oral streptococcal species. Genome sequencing and BLAST searches using N-terminal sequences, protein size, and key words identified the gene associated with each ABP. Among the sequenced ABPs, 14 matched amylase-binding protein A (AbpA), 6 matched amylase-binding protein B (AbpB), and 11 unique ABPs were identified as peptidoglycan-binding, glutamine ABC-type transporter, hypothetical, or choline-binding proteins. Alignment and phylogenetic analyses performed to ascertain evolutionary relationships revealed that ABPs cluster into at least six distinct, unrelated families (AbpA, AbpB, and&#xa0;four novel ABPs) with no phylogenetic evidence that one group evolved from another, and no single ancestral gene found within each group. AbpA-like sequences can be divided into five subgroups based on the N-terminal sequences. Comparative genomics focusing on the abpA gene locus provides evidence of horizontal gene transfer.<br><br>CONCLUSION: The acquisition of an ABP by oral streptococci provides an interesting example of adaptive evolution.}, }
@article {pmid28427330, year = {2017}, author = {Karlsen, C and Hjerde, E and Klemetsen, T and Willassen, NP}, title = {Pan genome and CRISPR analyses of the bacterial fish pathogen Moritella viscosa.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {313}, pmid = {28427330}, issn = {1471-2164}, mesh = {Animals ; CRISPR-Cas Systems/*genetics ; Evolution, Molecular ; Fishes/*microbiology ; *Genomics ; Moritella/*genetics/physiology/virology ; Plasmids/genetics ; Prophages/physiology ; }, abstract = {BACKGROUND: Winter-ulcer Moritella viscosa infections continue to be a significant burden in Atlantic salmon (Salmo salar L.) farming. M. viscosa comprises two main clusters that differ in genetic variation and phenotypes including virulence. Horizontal gene transfer through acquisition and loss of mobile genetic elements (MGEs) is a major driving force of bacterial diversification. To gain insight into genomic traits that could affect sublineage evolution within this bacterium we examined the genome sequences of twelve M. viscosa strains. Matches between M. viscosa clustered, regularly interspaced, short palindromic, repeats and associated cas genes (CRISPR-Cas) were analysed to correlate CRISPR-Cas with adaptive immunity against MGEs.<br><br>RESULTS: The comparative genomic analysis of M. viscosa isolates from across the North Atlantic region and from different fish species support delineation of M. viscosa into four phylogenetic lineages. The results showed that M. viscosa carries two distinct variants of the CRISPR-Cas subtype I-F systems and that CRISPR features follow the phylogenetic lineages. A subset of the spacer content match prophage and plasmid genes dispersed among the M. viscosa strains. Further analysis revealed that prophage and plasmid-like element distribution were reflected in the content of the CRISPR-spacer profiles.<br><br>CONCLUSIONS: Our data suggests that CRISPR-Cas mediated interactions with MGEs impact genome properties among M. viscosa, and that patterns in spacer and MGE distributions are linked to strain relationships.}, }
@article {pmid28426805, year = {2017}, author = {Cuecas, A and Kanoksilapatham, W and Gonzalez, JM}, title = {Evidence of horizontal gene transfer by transposase gene analyses in Fervidobacterium species.}, journal = {PloS one}, volume = {12}, number = {4}, pages = {e0173961}, pmid = {28426805}, issn = {1932-6203}, mesh = {Bacteria/*genetics ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Species Specificity ; Transposases/*genetics ; }, abstract = {Horizontal Gene Transfer (HGT) plays an important role in the physiology and evolution of microorganisms above all thermophilic prokaryotes. Some members of the Phylum Thermotogae (i.e., Thermotoga spp.) have been reported to present genomes constituted by a mosaic of genes from a variety of origins. This study presents a novel approach to search on the potential plasticity of Fervidobacterium genomes using putative transposase-encoding genes as the target of analysis. Transposases are key proteins involved in genomic DNA rearrangements. A comprehensive comparative analysis, including phylogeny, non-metric multidimensional scaling analysis of tetranucleotide frequencies, repetitive flanking sequences and divergence estimates, was performed on the transposase genes detected in four Fervidobacterium genomes: F. nodosum, F. pennivorans, F. islandicum and a new isolate (Fervidobacterium sp. FC2004). Transposase sequences were classified in different groups by their degree of similarity. The different methods used in this study pointed that over half of the transposase genes represented putative HGT events with closest relative sequences within the phylum Firmicutes, being Caldicellulosiruptor the genus showing highest gene sequence proximity. These results confirmed a direct evolutionary relationship through HGT between specific Fervidobacterium species and thermophilic Firmicutes leading to potential gene sequence and functionality sharing to thrive under similar environmental conditions. Transposase-encoding genes represent suitable targets to approach the plasticity and potential mosaicism of bacterial genomes.}, }
@article {pmid28426741, year = {2017}, author = {Palmgren, M and Engström, K and Hallström, BM and Wahlberg, K and Søndergaard, DA and Säll, T and Vahter, M and Broberg, K}, title = {AS3MT-mediated tolerance to arsenic evolved by multiple independent horizontal gene transfers from bacteria to eukaryotes.}, journal = {PloS one}, volume = {12}, number = {4}, pages = {e0175422}, pmid = {28426741}, issn = {1932-6203}, mesh = {Arsenic/metabolism/*toxicity ; Eukaryota/metabolism ; *Gene Transfer, Horizontal ; Methyltransferases/*metabolism ; Phylogeny ; }, abstract = {Organisms have evolved the ability to tolerate toxic substances in their environments, often by producing metabolic enzymes that efficiently detoxify the toxicant. Inorganic arsenic is one of the most toxic and carcinogenic substances in the environment, but many organisms, including humans, metabolise inorganic arsenic to less toxic metabolites. This multistep process produces mono-, di-, and trimethylated arsenic metabolites, which the organism excretes. In humans, arsenite methyltransferase (AS3MT) appears to be the main metabolic enzyme that methylates arsenic. In this study, we examined the evolutionary origin of AS3MT and assessed the ability of different genotypes to produce methylated arsenic metabolites. Phylogenetic analysis suggests that multiple, independent horizontal gene transfers between different bacteria, and from bacteria to eukaryotes, increased tolerance to environmental arsenic during evolution. These findings are supported by the observation that genetic variation in AS3MT correlates with the capacity to methylate arsenic. Adaptation to arsenic thus serves as a model for how organisms evolve to survive under toxic conditions.}, }
@article {pmid28426231, year = {2017}, author = {Ma, L and Li, AD and Yin, XL and Zhang, T}, title = {The Prevalence of Integrons as the Carrier of Antibiotic Resistance Genes in Natural and Man-Made Environments.}, journal = {Environmental science &amp; technology}, volume = {51}, number = {10}, pages = {5721-5728}, doi = {10.1021/acs.est.6b05887}, pmid = {28426231}, issn = {1520-5851}, mesh = {*Anti-Bacterial Agents ; Bacteria/genetics ; Drug Resistance, Microbial/*genetics ; Environment ; Environmental Monitoring ; Humans ; *Integrons ; Prevalence ; }, abstract = {Class 1 integrase intI1 has been considered as a good proxy for anthropogenic pollution because of being linked to genes conferring resistance to antibiotics. The gene cassettes of class 1 integrons could carry diverse antibiotic resistance genes (ARGs) and conduct horizontal gene transfer among microorganisms. The present study applied high-throughput sequencing technique combined with an intI1 database and genome assembly to quantify the abundance of intI1 in 64 environmental samples from 8 ecosystems, and to investigate the diverse arrangements of ARG-carrying gene cassettes (ACGCs) carried by class 1 integrons. The abundance of detected intI1 ranged from 3.83 × 10[-4] to 4.26 × 10° intI1/cell. High correlation (Pearson's r = 0.852) between intI1 and ARG abundance indicated that intI1 could be considered as an important indicator of ARGs in environments. Aminoglycoside resistance genes were most frequently observed on gene cassettes, carried by 57% assembled ACGCs, followed by trimethoprim and beta-lactam resistance genes. This study established the pipeline for broad monitoring of intI1 in various environmental samples and scanning the ARGs carried by integrons. These findings supplemented our knowledge on the distribution of class 1 integrons and ARGs carried on mobile genetic elements, benefiting future studies on horizontal gene transfer of ARGs.}, }
@article {pmid28425429, year = {2017}, author = {Paynter, AN and Metzger, MJ and Sessa, JA and Siddall, ME}, title = {Evidence of horizontal transmission of the cancer-associated Steamer retrotransposon among ecological cohort bivalve species.}, journal = {Diseases of aquatic organisms}, volume = {124}, number = {2}, pages = {165-168}, doi = {10.3354/dao03113}, pmid = {28425429}, issn = {0177-5103}, mesh = {Animals ; Bivalvia/*genetics ; DNA/genetics ; Ecosystem ; Gene Transfer, Horizontal/*genetics ; Mutation ; Retroelements/*genetics ; Terminal Repeat Sequences ; }, abstract = {Bivalve specimens from legacy frozen tissue collections, and others freshly obtained, were surveyed for the presence of the Steamer long terminal repeat (LTR)-retrotransposon associated with disseminated hemic neoplasia of the soft-shelled clam Mya areneria. Of 22 species investigated using primers for the pol region, only Atlantic M. arenaria, Atlantic and North Sea razor clams Ensis directus, and Baltic clams Macoma balthica from the North Sea were found to possess copies of Steamer in their genomes. Notably, close relatives like Mya truncata and Siliqua patula did not exhibit evidence of Steamer. Amplified Steamer sequences were uniformly identical in all M. areneria specimens, and were highly variable across specimens of E. directus. Variation in the latter included nucleotide polymorphisms among and within individuals as well as length variation in 2 specimens corresponding to the deletion of a predicted stable hairpin structure. Results implicate Atlantic razor clams as the proximal source for horizontal transmission of Steamer among ecologically similar yet markedly distantly related bivalves. The consequences of cross-species transmission of the Steamer retrotransposon are unknown, and the finding of Steamer in 3 bivalve species suggests that further spread is possible.}, }
@article {pmid28424528, year = {2017}, author = {Sekizuka, T and Kawanishi, M and Ohnishi, M and Shima, A and Kato, K and Yamashita, A and Matsui, M and Suzuki, S and Kuroda, M}, title = {Elucidation of quantitative structural diversity of remarkable rearrangement regions, shufflons, in IncI2 plasmids.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {928}, pmid = {28424528}, issn = {2045-2322}, mesh = {DNA, Bacterial/*chemistry/genetics ; Escherichia coli/chemistry/*genetics ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Models, Genetic ; Plasmids/chemistry/*genetics ; Sequence Analysis, DNA ; *Sequence Inversion ; }, abstract = {A multiple DNA inversion system, the shufflon, exists in incompatibility (Inc) I1 and I2 plasmids. The shufflon generates variants of the PilV protein, a minor component of the thin pilus. The shufflon is one of the most difficult regions for de novo genome assembly because of its structural diversity even in an isolated bacterial clone. We determined complete genome sequences, including those of IncI2 plasmids carrying mcr-1, of three Escherichia coli strains using single-molecule, real-time (SMRT) sequencing and Illumina sequencing. The sequences assembled using only SMRT sequencing contained misassembled regions in the shufflon. A hybrid analysis using SMRT and Illumina sequencing resolved the misassembled region and revealed that the three IncI2 plasmids, excluding the shufflon region, were highly conserved. Moreover, the abundance ratio of whole-shufflon structures could be determined by quantitative structural variation analysis of the SMRT data, suggesting that a remarkable heterogeneity of whole-shufflon structural variations exists in IncI2 plasmids. These findings indicate that remarkable rearrangement regions should be validated using both long-read and short-read sequencing data and that the structural variation of PilV in the shufflon might be closely related to phenotypic heterogeneity of plasmid-mediated transconjugation involved in horizontal gene transfer even in bacterial clonal populations.}, }
@article {pmid28424524, year = {2017}, author = {Torres, M and Uroz, S and Salto, R and Fauchery, L and Quesada, E and Llamas, I}, title = {HqiA, a novel quorum-quenching enzyme which expands the AHL lactonase family.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {943}, pmid = {28424524}, issn = {2045-2322}, mesh = {Bacterial Proteins/genetics/metabolism ; Carboxylic Ester Hydrolases/*genetics/*metabolism ; Chromatography, High Pressure Liquid ; Deltaproteobacteria/enzymology/genetics/*isolation &amp; purification ; Gene Transfer, Horizontal ; Mass Spectrometry ; Metagenomics/methods ; Multigene Family ; Open Reading Frames ; Pectobacterium carotovorum/enzymology/genetics/*physiology ; Quorum Sensing ; Sequence Analysis, DNA ; Soil Microbiology ; Spain ; }, abstract = {The screening of a metagenomic library of 250,000 clones generated from a hypersaline soil (Spain) allowed us to identify a single positive clone which confers the ability to degrade N-acyl homoserine lactones (AHLs). The sequencing of the fosmid revealed a 42,318 bp environmental insert characterized by 46 ORFs. The subcloning of these ORFs demonstrated that a single gene (hqiA) allowed AHL degradation. Enzymatic analysis using purified HqiA and HPLC/MS revealed that this protein has lactonase activity on a broad range of AHLs. The introduction of hqiA in the plant pathogen Pectobacterium carotovorum efficiently interfered with both the synthesis of AHLs and quorum-sensing regulated functions, such as swarming motility and the production of maceration enzymes. Bioinformatic analyses highlighted that HqiA showed no sequence homology with the known prototypic AHL lactonases or acylases, thus expanding the AHL-degrading enzymes with a new family related to the cysteine hydrolase (CHase) group. The complete sequence analysis of the fosmid showed that 31 ORFs out of the 46 identified were related to Deltaproteobacteria, whilst many intercalated ORFs presented high homology with other taxa. In this sense, hqiA appeared to be assigned to the Hyphomonas genus (Alphaproteobacteria), suggesting that horizontal gene transfer had occurred.}, }
@article {pmid28421047, year = {2017}, author = {Butler, RR and Schill, KM and Wang, Y and Pombert, JF}, title = {Genetic Characterization of the Exceptionally High Heat Resistance of the Non-toxic Surrogate Clostridium sporogenes PA 3679.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {545}, pmid = {28421047}, issn = {1664-302X}, abstract = {Clostridium sporogenes PA 3679 is a non-toxic endospore former that is widely used as a surrogate for Clostridium botulinum by the food processing industry to validate thermal processing strategies. PA 3679 produces spores of exceptionally high heat resistance without botulinum neurotoxins, permitting the use of PA 3679 in inoculated pack studies while ensuring the safety of food processing facilities. To identify genes associated with this heat resistance, the genomes of C. sporogenes PA 3679 isolates were compared to several other C. sporogenes strains. The most significant difference was the acquisition of a second spoVA operon, spoVA2, which is responsible for transport of dipicolinic acid into the spore core during sporulation. Interestingly, spoVA2 was also found in some C. botulinum species which phylogenetically cluster with PA 3679. Most other C. sporogenes strains examined both lack the spoVA2 locus and are phylogenetically distant within the group I Clostridium, adding to the understanding that C. sporogenes are dispersed C. botulinum strains which lack toxin genes. C. sporogenes strains are thus a very eclectic group, and few strains possess the characteristic heat resistance of PA 3679.}, }
@article {pmid28419869, year = {2017}, author = {Garcia-Fulgueiras, V and Araujo, L and Bado, I and Cordeiro, NF and Mota, MI and Laguna, G and Algorta, G and Vignoli, R}, title = {Allodemic distribution of plasmids co-harbouring blaCTX-M-15/aac(6')-Ib-cr/qnrB in Klebsiella pneumoniae is the main source of extended-spectrum β-lactamases in Uruguay's paediatric hospital.}, journal = {Journal of global antimicrobial resistance}, volume = {9}, number = {}, pages = {68-73}, doi = {10.1016/j.jgar.2017.01.008}, pmid = {28419869}, issn = {2213-7173}, mesh = {Acetyltransferases/*genetics ; Bacterial Proteins/*genetics ; Conjugation, Genetic ; *Gene Transfer, Horizontal ; Hospitals, Pediatric ; Humans ; Klebsiella Infections/*epidemiology/microbiology ; Klebsiella pneumoniae/classification/*genetics/isolation &amp; purification ; Multilocus Sequence Typing ; Plasmids/*classification ; Toxin-Antitoxin Systems/genetics ; Uruguay/epidemiology ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: This study aimed to describe the characteristics of clinical isolates of extended-spectrum β-lactamase (ESBL)-producing enterobacteria (EPE) in Uruguay's paediatric hospital.<br><br>METHODS: ESBLs, qnr alleles and aac(6')-Ib-cr were sought and characterised in EPE isolated between March 2010 and March 2012. Transfer of resistance determinants was assessed by conjugation. Incompatibility (Inc) groups, plasmid toxin-antitoxin systems (TAS) and plasmid size were determined in transconjugants. Clonality was analysed by pulsed-field gel electrophoresis. Multilocus sequence typing was done for ESBL-producing Klebsiella pneumoniae.<br><br>RESULTS: A total of 77 EPE isolates were characterised, comprising 43% K. pneumoniae, 19.5% Serratia marcescens, 19.5% Escherichia coli, 17% Enterobacter cloacae and 1% Klebsiella oxytoca. ESBLs belonged mainly to the blaCTX-M family (69.6%) [blaCTX-M-15 (45%) and blaCTX-M-2 (31%)]. The aac(6')-Ib-cr/qnrB duplex was the most frequently detected plasmid-mediated quinolone resistance mechanism; this association was detected in K. pneumoniae harbouring blaCTX-M-15. Transconjugants were obtained for 71% of the EPE. Amongst transconjugants, certain combinations were found between ESBLs and Inc group, e.g. IncA/C-blaCTX-M-2, IncHI1/HI2-blaCTX-M-9 and IncHI1/HI2-blaSHV-12. In addition, the combination ccdAB-blaCTX-M-15 was also found. K. pneumoniae isolates harbouring blaCTX-M-15/aac(6')-Ib-cr/qnrB showed allodemic behaviour, with a predominance of ST14, ST45 and ST48.<br><br>CONCLUSIONS: In this study, epidemiological changes in ESBL distribution could be explained by the spread of K. pneumoniae harbouring blaCTX-M-15/aac(6')-Ib-cr/qnrB, encoded mainly on conjugative plasmids featuring ccdAB TAS. Since reports of TAS in K. pneumoniae plasmids are scarce, new strategies are needed to combat intrinsic selection pressure exerted by the association, in conjugative plasmids, of resistance mechanisms with TAS.}, }
@article {pmid28419231, year = {2017}, author = {Foster, TJ}, title = {Antibiotic resistance in Staphylococcus aureus. Current status and future prospects.}, journal = {FEMS microbiology reviews}, volume = {41}, number = {3}, pages = {430-449}, doi = {10.1093/femsre/fux007}, pmid = {28419231}, issn = {1574-6976}, mesh = {Anti-Bacterial Agents/*pharmacology ; Cell Membrane/*drug effects ; Cell Wall/*drug effects ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal ; Staphylococcal Infections/drug therapy/microbiology ; Staphylococcus aureus/*drug effects/*genetics/growth &amp; development ; }, abstract = {The major targets for antibiotics in staphylococci are (i) the cell envelope, (ii) the ribosome and (iii) nucleic acids. Several novel targets emerged from recent targeted drug discovery programmes including the ClpP protease and FtsZ from the cell division machinery. Resistance can either develop by horizontal transfer of resistance determinants encoded by mobile genetic elements viz plasmids, transposons and the staphylococcal cassette chromosome or by mutations in chromosomal genes. Horizontally acquired resistance can occur by one of the following mechanisms: (i) enzymatic drug modification and inactivation, (ii) enzymatic modification of the drug binding site, (iii) drug efflux, (iv) bypass mechanisms involving acquisition of a novel drug-resistant target, (v) displacement of the drug to protect the target. Acquisition of resistance by mutation can result from (i) alteration of the drug target that prevents the inhibitor from binding, (ii) derepression of chromosomally encoded multidrug resistance efflux pumps and (iii) multiple stepwise mutations that alter the structure and composition of the cell wall and/or membrane to reduce drug access to its target. This review focuses on development of resistance to currently used antibiotics and examines future prospects for new antibiotics and informed use of drug combinations.}, }
@article {pmid28418075, year = {2017}, author = {McInerney, JO}, title = {Horizontal gene transfer is less frequent in eukaryotes than prokaryotes but can be important (retrospective on DOI 10.1002/bies.201300095).}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {39}, number = {6}, pages = {}, doi = {10.1002/bies.201700002}, pmid = {28418075}, issn = {1521-1878}, mesh = {*Eukaryota ; *Gene Transfer, Horizontal ; Humans ; Phylogeny ; Prokaryotic Cells ; Retrospective Studies ; }, }
@article {pmid28416709, year = {2017}, author = {Lynch, JB and Alegado, RA}, title = {Spheres of Hope, Packets of Doom: the Good and Bad of Outer Membrane Vesicles in Interspecies and Ecological Dynamics.}, journal = {Journal of bacteriology}, volume = {199}, number = {15}, pages = {}, pmid = {28416709}, issn = {1098-5530}, support = {F32 GM119238/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacterial Proteins/metabolism ; Gram-Negative Bacteria/*physiology ; Host-Pathogen Interactions ; Lipid Metabolism ; Nucleic Acids/metabolism ; Secretory Vesicles/*metabolism ; Symbiosis ; }, abstract = {Outer membrane vesicles (OMVs) are proteoliposome nanoparticles ubiquitously produced by Gram-negative bacteria. Typically bearing a composition similar to those of the outer membrane and periplasm of the cells from which they are derived, OMVs package an array of proteins, lipids, and nucleic acids. Once considered inconsequential by-products of bacterial growth, OMVs have since been demonstrated to mediate cellular stress relief, promote horizontal gene transfer and antimicrobial activity, and elicit metazoan inflammation. Recently, OMVs have gained appreciation as critical moderators of interorganismal dynamics. In this review, we focus on recent progress toward understanding the functions of OMVs with regard to symbiosis and ecological contexts, and we propose potential avenues for future OMV studies.}, }
@article {pmid28416702, year = {2017}, author = {Peccoud, J and Loiseau, V and Cordaux, R and Gilbert, C}, title = {Massive horizontal transfer of transposable elements in insects.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {18}, pages = {4721-4726}, pmid = {28416702}, issn = {1091-6490}, mesh = {Animals ; *DNA Transposable Elements ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Insect ; Insecta/*genetics ; }, abstract = {Horizontal transfer (HT) of genetic material is central to the architecture and evolution of prokaryote genomes. Within eukaryotes, the majority of HTs reported so far are transfers of transposable elements (TEs). These reports essentially come from studies focusing on specific lineages or types of TEs. Because of the lack of large-scale survey, the amount and impact of HT of TEs (HTT) in eukaryote evolution, as well as the trends and factors shaping these transfers, are poorly known. Here, we report a comprehensive analysis of HTT in 195 insect genomes, representing 123 genera and 13 of the 28 insect orders. We found that these insects were involved in at least 2,248 HTT events that essentially occurred during the last 10 My. We show that DNA transposons transfer horizontally more often than retrotransposons, and unveil phylogenetic relatedness and geographical proximity as major factors facilitating HTT in insects. Even though our study is restricted to a small fraction of insect biodiversity and to a recent evolutionary timeframe, the TEs we found to be horizontally transferred generated up to 24% (2.08% on average) of all nucleotides of insect genomes. Together, our results establish HTT as a major force shaping insect genome evolution.}, }
@article {pmid28414952, year = {2017}, author = {Gillings, MR}, title = {Class 1 integrons as invasive species.}, journal = {Current opinion in microbiology}, volume = {38}, number = {}, pages = {10-15}, doi = {10.1016/j.mib.2017.03.002}, pmid = {28414952}, issn = {1879-0364}, mesh = {Bacteria/*drug effects/*genetics ; *Drug Resistance, Bacterial ; *Gene Transfer, Horizontal ; *Integrons ; *Introduced Species ; *Recombination, Genetic ; }, abstract = {Clinical class 1 integrons are a major contributor to the evolution and dissemination of antibiotic resistance. The conserved motifs of these integrons suggest that a single, recent ancestor gave rise to all current variants. They have had a spectacular increase in distribution and abundance over the last 100 years, exhibiting many similarities to invasive species that prosper under human impacts. They have spread into over 70 bacterial species of medical importance, are commonly resident in the gut of humans and domesticated animals, and have invaded every continent, including Antarctica. They have done so via linkage with transposons, metal, disinfectant and antibiotic resistance genes. As a consequence of their invasive nature they have now become significant pollutants of natural environments.}, }
@article {pmid28414085, year = {2017}, author = {Bordewich, M and Linz, S and Semple, C}, title = {Lost in space? Generalising subtree prune and regraft to spaces of phylogenetic networks.}, journal = {Journal of theoretical biology}, volume = {423}, number = {}, pages = {1-12}, doi = {10.1016/j.jtbi.2017.03.032}, pmid = {28414085}, issn = {1095-8541}, mesh = {*Algorithms ; Computational Biology/methods ; Gene Regulatory Networks ; Gene Transfer, Horizontal ; *Hybridization, Genetic ; *Phylogeny ; Spatial Analysis ; }, abstract = {Over the last fifteen years, phylogenetic networks have become a popular tool to analyse relationships between species whose past includes reticulation events such as hybridisation or horizontal gene transfer. However, the space of phylogenetic networks is significantly larger than that of phylogenetic trees, and how to analyse and search this enlarged space remains a poorly understood problem. Inspired by the widely-used rooted subtree prune and regraft (rSPR) operation on rooted phylogenetic trees, we propose a new operation-called subnet prune and regraft (SNPR)-that induces a metric on the space of all rooted phylogenetic networks on a fixed set of leaves. We show that the spaces of several popular classes of rooted phylogenetic networks (e.g. tree child, reticulation visible, and tree based) are connected under SNPR and that connectedness remains for the subclasses of these networks with a fixed number of reticulations. Lastly, we bound the distance between two rooted phylogenetic networks under the SNPR operation, show that it is computationally hard to compute this distance exactly, and analyse how the SNPR-distance between two such networks relates to the rSPR-distance between rooted phylogenetic trees that are embedded in these networks.}, }
@article {pmid28412903, year = {2017}, author = {Olszak, T and Latka, A and Roszniowski, B and Valvano, MA and Drulis-Kawa, Z}, title = {Phage Life Cycles Behind Bacterial Biodiversity.}, journal = {Current medicinal chemistry}, volume = {24}, number = {36}, pages = {3987-4001}, doi = {10.2174/0929867324666170413100136}, pmid = {28412903}, issn = {1875-533X}, mesh = {Bacteria/genetics/*virology ; Bacteriophages/genetics/*physiology ; *Biodiversity ; CRISPR-Cas Systems/genetics ; Drug Resistance, Microbial ; Evolution, Molecular ; Gene Transfer, Horizontal ; Host-Pathogen Interactions ; }, abstract = {Bacteriophages (phages or bacterial viruses) are the most abundant biological entities in our planet; their influence reaches far beyond the microorganisms they parasitize. Phages are present in every environment and shape up every bacterial population in both active and passive ways. They participate in the circulation of organic matter and drive the evolution of microorganisms by horizontal gene transfer at unprecedented scales. The mass flow of genetic information in the microbial world influences the biosphere and poses challenges for science and medicine. The genetic flow, however, depends on the fate of the viral DNA injected into the bacterial cell. The archetypal notion of phages only engaging in predatorprey relationships is slowly fading. Because of their varied development cycles, environmental conditions, and the diversity of microorganisms they parasitize, phages form a dense and highly complex web of dependencies, which has important consequences for life on Earth. The sophisticated phage-bacteria interplay includes both aggressive action (bacterial lysis) and "diplomatic negotiations" (prophage domestication). Here, we review the most important mechanisms of interactions between phages and bacteria and their evolutionary consequences influencing their biodiversity.}, }
@article {pmid28412524, year = {2017}, author = {Mala, W and Faksri, K and Samerpitak, K and Yordpratum, U and Kaewkes, W and Tattawasart, U and Chomvarin, C}, title = {Antimicrobial resistance and genetic diversity of the SXT element in Vibrio cholerae from clinical and environmental water samples in northeastern Thailand.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {52}, number = {}, pages = {89-95}, doi = {10.1016/j.meegid.2017.04.013}, pmid = {28412524}, issn = {1567-7257}, mesh = {Bacterial Proteins/*genetics ; Cholera/*microbiology ; *Drug Resistance, Multiple, Bacterial ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genetic Variation ; Humans ; Integrons ; Phylogeny ; Thailand ; Vibrio cholerae/*classification/drug effects/genetics/isolation &amp; purification ; Water Microbiology ; }, abstract = {Multidrug resistance in V. cholerae has been increasing around the world including northeastern Thailand. The aquatic environment is a reservoir of V. cholerae and might be an important source of resistant strains. The aims of this study were to investigate the phylogenetic relationships of intSXT gene sequences from 31 clinical and 14 environmental V. cholerae O1 and non-O1/non-O139 isolates and 11 sequences amplified directly from environmental water samples. We also amplified class 1 integrons, the SXT elements (targeting the intSXT gene) and antimicrobial resistance genes directly from water samples. Phylogenetic analysis displayed two major distinct clusters (clusters 1 and 2). Most V. cholerae O1 (19/20, 95%) and non-O1/non-O139 isolates (8/11, 72.7%) from clinical sources, and all sequences obtained directly from water samples, belonged to cluster 1. Cluster 2 mostly comprised environmental non-O1/non-O139 isolates (10/12, 83.3%). We successfully amplified the SXT elements directly from17.5% of water samples. Associated resistance genes were also amplified as follows: sul2 (41.3% of water samples), dfrA1 (60%), dfr18 (33.8%), strB (70%) and tetA (2.5%). Class 1 integrons were not found in water samples, indicating that the SXT element was the major contributor of multidrug resistance determinants in this region. The SXT element and antimicrobial resistance genes could be transferred from clinical V. cholerae O1 to environmental V. cholerae non-O1/non-O139 was demonstrated by conjugation experiment. These findings indicate that there may have been cross dissemination and horizontal gene transfer (HGT) of the SXT element harbored by V. cholerae O1 and non-O1/non-O139 strains isolated from clinical and environmental water sources. Environmental water might be an important source of antimicrobial resistance genes in V. cholerae in this region. Direct detection of antimicrobial resistance genes in water samples can be used for monitoring the spread of such genes in the ecosystem.}, }
@article {pmid28411227, year = {2017}, author = {Mantilla-Calderon, D and Hong, PY}, title = {Fate and Persistence of a Pathogenic NDM-1-Positive Escherichia coli Strain in Anaerobic and Aerobic Sludge Microcosms.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {13}, pages = {}, pmid = {28411227}, issn = {1098-5336}, mesh = {Aerobiosis ; Anaerobiosis ; Escherichia coli/classification/enzymology/genetics/*isolation &amp; purification ; Escherichia coli Proteins/*genetics/metabolism ; Plasmids/genetics/metabolism ; Sewage/chemistry/*microbiology ; Wastewater/microbiology ; beta-Lactamases/genetics/*metabolism ; }, abstract = {The presence of emerging biological pollutants in treated wastewater effluents has gained attention due to increased interest in water reuse. To evaluate the effectiveness of the removal of such contaminants by the conventional wastewater treatment process, the fate and decay kinetics of NDM-1-positive Escherichia coli strain PI7 and its plasmid-encoded antibiotic resistance genes (ARGs) were assessed in microcosms of anaerobic and aerobic sludge. Results showed that E. coli PI7 decayed at a significantly lower rate under anaerobic conditions. Approximate half-lives were 32.4 ± 1.4 h and 5.9 ± 0.9 h in the anaerobic and aerobic microcosms, respectively. In the aerobic microcosms, after 72 h of operation, E. coli PI7 remained detectable, but no further decay was observed. Instead, 1 in every 10,000 E. coli cells was identified to be recalcitrant to decay and persist indefinitely in the sludge. ARGs associated with the E. coli PI7 strain were detected to have transferred to other native microorganisms in the sludge or were released to the liquid fraction upon host decay. Extracellular DNA quickly degraded in the liquid fraction of the aerobic sludge. In contrast, no DNA decay was detected in the anaerobic sludge water matrix throughout the 24-h sampling period. This study suggests an increased likelihood of environmental dispersion of ARGs associated with anaerobically treated wastewater effluents and highlights the potential importance of persister cells in the dissemination of E. coli in the environment during reuse events of treated wastewater.IMPORTANCE This study examines the decay kinetics of a pathogenic and antibiotic resistant strain of Escherichia coli in microcosms simulating biological treatment units of aerobic and anaerobic sludge. The results of this study point at a significantly prolonged persistence of the E. coli and the associated antibiotic resistance gene in the anaerobic sludge. However, horizontal transfer of the plasmid encoding the antibiotic resistance gene was detected in the aerobic sludge by a cultivation method. A subpopulation of persister E. coli cells was also detected in the aerobic sludge. The findings of this study suggest potential areas of concern arising from pathogenic and antibiotic-resistant E. coli during both anaerobic and aerobic sludge treatment processes.}, }
@article {pmid28411217, year = {2017}, author = {Mo, SS and Sunde, M and Ilag, HK and Langsrud, S and Heir, E}, title = {Transfer Potential of Plasmids Conferring Extended-Spectrum-Cephalosporin Resistance in Escherichia coli from Poultry.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {12}, pages = {}, pmid = {28411217}, issn = {1098-5336}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; *Cephalosporin Resistance ; Cephalosporins/*pharmacology ; Conjugation, Genetic ; Escherichia coli/drug effects/*genetics/isolation &amp; purification/metabolism ; Escherichia coli Infections/microbiology/*veterinary ; *Gene Transfer, Horizontal ; Plasmids/*genetics/metabolism ; Poultry ; Poultry Diseases/*microbiology ; Serratia marcescens/drug effects/*genetics/metabolism ; }, abstract = {Escherichia coli strains resistant to extended-spectrum cephalosporins (ESC) are widely distributed in Norwegian broiler production, and the majority harbor transferable IncK or IncI1 plasmids carrying blaCMY-2 Persistent occurrence in broiler farms may occur through the survival of ESC-resistant E. coli strains in the farm environment, or by transfer and maintenance of resistance plasmids within a population of environmental bacteria with high survival abilities. The aim of this study was to determine the transferability of two successful blaCMY-2-carrying plasmids belonging to the incompatibility groups IncK and IncI1 into E. coli and Serratia species recipients. Initially, conjugative plasmid transfer from two E. coli donors to potential recipients was tested in an agar assay. Conjugation was further investigated for selected mating pairs in surface and planktonic assays at temperatures from 12°C to 37°C. Transfer of plasmids was observed on agar, in broth, and in biofilm at temperatures down to 25°C. The IncK plasmid was able to transfer into Serratia marcescens, and transconjugants were able to act as secondary plasmid donors to different E. coli and Serratia species recipients. All transconjugants displayed an AmpC phenotype corresponding to the acquisition of blaCMY-2 In summary, the results indicate that the IncK plasmid may transfer between E. coli and Serratia spp. under conditions relevant for broiler production.IMPORTANCE Certain blaCMY-2-carrying plasmids are successful and disseminated in European broiler production. Traditionally, plasmid transferability has been studied under conditions that are optimal for bacterial growth. Plasmid transfer has previously been reported between E. coli bacteria in biofilms at 37°C and in broth at temperatures ranging from 8 to 37°C. However, intergenus transfer of blaCMY-2-carrying plasmids from E. coli to environmental bacteria in the food-processing chain has not been previously studied. We demonstrate that blaCMY-2-carrying plasmids are capable of conjugative transfer between different poultry-associated bacterial genera under conditions relevant for broiler production. Transfer to Serratia spp. and to hosts with good biofilm-forming abilities and with the potential to act as secondary plasmid donors to new hosts might contribute to the persistence of these resistance plasmids. These results contribute to increased knowledge of factors affecting the persistence of ESC resistance in broiler production and can provide a basis for improvement of routines and preventive measures.}, }
@article {pmid28407482, year = {2017}, author = {Wotzka, SY and Nguyen, BD and Hardt, WD}, title = {Salmonella Typhimurium Diarrhea Reveals Basic Principles of Enteropathogen Infection and Disease-Promoted DNA Exchange.}, journal = {Cell host &amp; microbe}, volume = {21}, number = {4}, pages = {443-454}, doi = {10.1016/j.chom.2017.03.009}, pmid = {28407482}, issn = {1934-6069}, mesh = {Diarrhea/*microbiology/*pathology ; *Gene Transfer, Horizontal ; *Host-Pathogen Interactions ; Immunity, Innate ; Interspersed Repetitive Sequences ; Intestinal Mucosa/microbiology/pathology ; Salmonella Infections/*microbiology/*pathology ; Salmonella typhimurium/genetics/growth &amp; development/*pathogenicity ; }, abstract = {Despite decades of research, efficient therapies for most enteropathogenic bacteria are still lacking. In this review, we focus on Salmonella enterica Typhimurium (S. Typhimurium), a frequent cause of acute, self-limiting food-borne diarrhea and a model that has revealed key principles of enteropathogen infection. We review the steps of gut infection and the mucosal innate-immune defenses limiting pathogen burdens, and we discuss how inflammation boosts gut luminal S. Typhimurium growth. We also discuss how S. Typhimurium-induced inflammation accelerates the transfer of plasmids and phages, which may promote the transmission of antibiotic resistance and facilitate emergence of pathobionts and pathogens with enhanced virulence. The targeted manipulation of the microbiota and vaccination might offer strategies to prevent this evolution. As gut luminal microbes impact various aspects of the host's physiology, improved strategies for preventing enteropathogen infection and disease-inflicted DNA exchange may be of broad interest well beyond the acute infection.}, }
@article {pmid28406168, year = {2017}, author = {Zeman, M and Mašlaňová, I and Indráková, A and Šiborová, M and Mikulášek, K and Bendíčková, K and Plevka, P and Vrbovská, V and Zdráhal, Z and Doškař, J and Pantůček, R}, title = {Staphylococcus sciuri bacteriophages double-convert for staphylokinase and phospholipase, mediate interspecies plasmid transduction, and package mecA gene.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {46319}, pmid = {28406168}, issn = {2045-2322}, mesh = {Gene Transfer, Horizontal ; *Genes, Bacterial ; Genome, Viral ; Genomics/methods ; Host Specificity ; Metalloendopeptidases/*metabolism ; Phospholipases/*metabolism ; Plasmids/*genetics ; Staphylococcus/*virology ; Staphylococcus Phages/*physiology/ultrastructure ; *Transduction, Genetic ; Virus Attachment ; }, abstract = {Staphylococcus sciuri is a bacterial pathogen associated with infections in animals and humans, and represents a reservoir for the mecA gene encoding methicillin-resistance in staphylococci. No S. sciuri siphophages were known. Here the identification and characterization of two temperate S. sciuri phages from the Siphoviridae family designated ϕ575 and ϕ879 are presented. The phages have icosahedral heads and flexible noncontractile tails that end with a tail spike. The genomes of the phages are 42,160 and 41,448 bp long and encode 58 and 55 ORFs, respectively, arranged in functional modules. Their head-tail morphogenesis modules are similar to those of Staphylococcus aureus ϕ13-like serogroup F phages, suggesting their common evolutionary origin. The genome of phage ϕ575 harbours genes for staphylokinase and phospholipase that might enhance the virulence of the bacterial hosts. In addition both of the phages package a homologue of the mecA gene, which is a requirement for its lateral transfer. Phage ϕ879 transduces tetracycline and aminoglycoside pSTS7-like resistance plasmids from its host to other S. sciuri strains and to S. aureus. Furthermore, both of the phages efficiently adsorb to numerous staphylococcal species, indicating that they may contribute to interspecies horizontal gene transfer.}, }
@article {pmid28405008, year = {2017}, author = {Dunning Hotopp, JC and Slatko, BE and Foster, JM}, title = {Targeted Enrichment and Sequencing of Recent Endosymbiont-Host Lateral Gene Transfers.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {857}, pmid = {28405008}, issn = {2045-2322}, support = {DP2 OD007372/OD/NIH HHS/United States ; U19 AI110820/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Genome, Helminth ; Nematoda/genetics/microbiology ; *Symbiosis ; Wolbachia/genetics/pathogenicity ; }, abstract = {Lateral gene transfer (LGT) from microbial symbionts to invertebrate animals is described at an increasing rate, particularly between Wolbachia endosymbionts and their diverse invertebrate hosts. We sought to assess the use of a capture system to cost-effectively sequence such LGT from the host genome. The sequencing depth of Illumina paired end data obtained with a Wolbachia capture system correlated well with that for an Illumina paired end data set used to detect LGT in Wolbachia-depleted B. malayi (p-value: <2e-16). Using a sequencing depth threshold of two or three standard deviations above the mean, 96.9% or 96.7% of positions, respectively, are predicted in the same manner between the two datasets, with 24.7% or 42.5% of the known 49.0 kbp of LGT sequence predicted correctly, respectively. Prior qPCR results for nuwts showed similar correlations for both datasets supporting our conclusion that oligonucleotide-based capture methods can be used to obtain sequences from Wolbachia-host LGT. However, at least 121 positions had a minority of the reads supporting the endosymbiont reference base call using the capture data, illustrating that sequence reads from endosymbiont-host LGTs can confound endosymbiont genome projects, erroneously altering the called consensus genome, a problem that is irrespective to the sequencing technology or platform.}, }
@article {pmid28401640, year = {2018}, author = {Ficarra, FA and Grandellis, C and Garavaglia, BS and Gottig, N and Ottado, J}, title = {Bacterial and plant natriuretic peptides improve plant defence responses against pathogens.}, journal = {Molecular plant pathology}, volume = {19}, number = {4}, pages = {801-811}, pmid = {28401640}, issn = {1364-3703}, mesh = {Arabidopsis/genetics/*metabolism/*microbiology ; Natriuretic Peptides/genetics/*metabolism ; Plant Diseases/microbiology ; Plant Leaves/genetics/metabolism/microbiology ; Plant Proteins/genetics/*metabolism ; Plants, Genetically Modified/genetics/metabolism/microbiology ; Pseudomonas syringae/pathogenicity ; Xanthomonas/*pathogenicity ; }, abstract = {Plant natriuretic peptides (PNPs) have been implicated in the regulation of ions and water homeostasis, and their participation in the plant immune response has also been proposed. Xanthomonas citri ssp. citri contains a gene encoding a PNP-like protein (XacPNP) which has no homologues in other bacteria. XacPNP mimics its Arabidopsis thaliana homologue AtPNP-A by modifying host responses to create favourable conditions for pathogen survival. However, the ability of XacPNP to induce plant defence responses has not been investigated. In order to study further the role of XacPNP in vivo, A. thaliana lines over-expressing XacPNP, lines over-expressing AtPNP-A and AtPNP-A-deficient plants were generated. Plants over-expressing XacPNP or AtPNP-A showed larger stomatal aperture and were more resistant to saline or oxidative stress than were PNP-deficient lines. In order to study further the role of PNP in biotic stress responses, A. thaliana leaves were infiltrated with pure recombinant XacPNP, and showed enhanced expression of genes related to the defence response and a higher resistance to pathogen infections. Moreover, AtPNP-A expression increased in A. thaliana on Pseudomonas syringae pv. tomato (Pst) infection. This evidence led us to analyse the responses of the transgenic plants to pathogens. Plants over-expressing XacPNP or AtPNP-A were more resistant to Pst infection than control plants, whereas PNP-deficient plants were more susceptible and showed a stronger hypersensitive response when challenged with non-host bacteria. Therefore, XacPNP, acquired by horizontal gene transfer, is able to mimic PNP functions, even with an increase in plant defence responses.}, }
@article {pmid28393265, year = {2017}, author = {Ash, KT and Drake, KM and Gibbs, WS and Ely, B}, title = {Genomic Diversity of Type B3 Bacteriophages of Caulobacter crescentus.}, journal = {Current microbiology}, volume = {74}, number = {7}, pages = {779-786}, pmid = {28393265}, issn = {1432-0991}, support = {R25 GM066526/GM/NIGMS NIH HHS/United States ; R25 GM076277/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteriophages/classification/*genetics/isolation &amp; purification ; Base Sequence ; Caulobacter crescentus/*virology ; Gene Order ; *Genome, Viral ; Genomics ; }, abstract = {The genomes of the type B3 bacteriophages that infect Caulobacter crescentus are among the largest phage genomes thus far deposited into GenBank with sizes over 200 kb. In this study, we introduce six new bacteriophage genomes which were obtained from phage collected from various water systems in the southeastern United States and from tropical locations across the globe. A comparative analysis of the 12 available genomes revealed a "core genome" which accounts for roughly 1/3 of these bacteriophage genomes and is predominately localized to the head, tail, and lysis gene regions. Despite being isolated from geographically distinct locations, the genomes of these bacteriophages are highly conserved in both genome sequence and gene order. We also identified the insertions, deletions, translocations, and horizontal gene transfer events which are responsible for the genomic diversity of this group of bacteriophages and demonstrated that these changes are not consistent with the idea that modular reassortment of genomes occurs in this group of bacteriophages.}, }
@article {pmid28392565, year = {2017}, author = {Crofts, TS and Gasparrini, AJ and Dantas, G}, title = {Next-generation approaches to understand and combat the antibiotic resistome.}, journal = {Nature reviews. Microbiology}, volume = {15}, number = {7}, pages = {422-434}, pmid = {28392565}, issn = {1740-1534}, support = {DP2 DK098089/DK/NIDDK NIH HHS/United States ; R01 GM099538/GM/NIGMS NIH HHS/United States ; T32 HD049305/HD/NICHD NIH HHS/United States ; R01 AI123394/AI/NIAID NIH HHS/United States ; U01 AI123394/AI/NIAID NIH HHS/United States ; T32 GM007067/GM/NIGMS NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics ; Communicable Diseases, Emerging/microbiology/prevention &amp; control/therapy ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial/drug effects ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome/*drug effects ; *Metagenomics/methods ; Phylogeny ; }, abstract = {Antibiotic resistance is a natural feature of diverse microbial ecosystems. Although recent studies of the antibiotic resistome have highlighted barriers to the horizontal transfer of antibiotic resistance genes between habitats, the rapid global spread of genes that confer resistance to carbapenem, colistin and quinolone antibiotics illustrates the dire clinical and societal consequences of such events. Over time, the study of antibiotic resistance has grown from focusing on single pathogenic organisms in axenic culture to studying antibiotic resistance in pathogenic, commensal and environmental bacteria at the level of microbial communities. As the study of antibiotic resistance advances, it is important to incorporate this comprehensive approach to better inform global antibiotic resistance surveillance and antibiotic development. It is increasingly becoming apparent that although not all resistance genes are likely to geographically and phylogenetically disseminate, the threat presented by those that are is serious and warrants an interdisciplinary research focus. In this Review, we highlight seminal work in the resistome field, discuss recent advances in the studies of resistomes, and propose a resistome paradigm that can pave the way for the improved proactive identification and mitigation of emerging antibiotic resistance threats.}, }
@article {pmid28391142, year = {2017}, author = {Ramsay, JP and Firth, N}, title = {Diverse mobilization strategies facilitate transfer of non-conjugative mobile genetic elements.}, journal = {Current opinion in microbiology}, volume = {38}, number = {}, pages = {1-9}, doi = {10.1016/j.mib.2017.03.003}, pmid = {28391142}, issn = {1879-0364}, mesh = {*Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences ; *Plasmids ; Staphylococcus aureus/*genetics ; }, abstract = {Conjugation is a dominant mechanism of horizontal gene transfer and substantially contributes to the plasticity and evolvability of prokaryotic genomes. The impact of conjugation on genetic flux extends well beyond self-transmissible conjugative elements, because non-conjugative 'mobilizable elements' utilize other elements' conjugative apparatus for transfer. Bacterial genome comparisons highlight plasmids as vehicles for dissemination of pathogenesis and antimicrobial-resistance determinants, but for most non-conjugative plasmids, a mobilization mechanism is not apparent. Recently we discovered many Staphylococcus aureus plasmids lacking mobilization genes carry oriT sequences that mimic those on conjugative plasmids, suggesting that significantly more elements may be mobilizable than previously recognized. Here we summarize our findings, review the diverse mobilization strategies employed by mobile genetic elements and discuss implications for future gene-transfer research.}, }
@article {pmid28390108, year = {2017}, author = {Jacquiod, S and Brejnrod, A and Morberg, SM and Abu Al-Soud, W and Sørensen, SJ and Riber, L}, title = {Deciphering conjugative plasmid permissiveness in wastewater microbiomes.}, journal = {Molecular ecology}, volume = {26}, number = {13}, pages = {3556-3571}, doi = {10.1111/mec.14138}, pmid = {28390108}, issn = {1365-294X}, mesh = {Bacteria/*genetics ; *Conjugation, Genetic ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; *Microbiota ; Plasmids/*genetics ; RNA, Ribosomal, 16S/genetics ; Sewage/microbiology ; Wastewater/*microbiology ; }, abstract = {Wastewater treatment plants (WWTPs) are designed to robustly treat polluted water. They are characterized by ceaseless flows of organic, chemical and microbial matter, followed by treatment steps before environmental release. WWTPs are hotspots of horizontal gene transfer between bacteria via conjugative plasmids, leading to dissemination of potentially hazardous genetic material such as antimicrobial resistance genes (AMRGs). While current focus is on the threat of AMRGs spreading and their environmental maintenance, conjugative plasmid transfer dynamics within and between bacterial communities still remains largely uncharted. Furthermore, current in vitro methods used to assess conjugation in complex microbiomes do not include in situ behaviours of recipient cells, resulting in partial understanding of transfers. We investigated the in vitro conjugation capacities of WWTP microbiomes from inlet sewage and outlet treated water using the broad-host range IncP-1 conjugative plasmid, pKJK5. A thorough molecular approach coupling metagenomes to 16S rRNA DNA/cDNA amplicon sequencing was established to characterize microbiomes using the ecological concept of functional response groups. A broad diversity of recipient bacterial phyla for the plasmid was observed, especially in WWTP outlets. We also identified permissive bacteria potentially able to cross WWTPs and engage in conjugation before and after water treatment. Bacterial activity and lifestyle seem to influence conjugation extent, as treated water copiotrophs were the most represented strategist amongst transconjugants. Correlation analysis highlighted possible plasmid transmission routes into communities between the sewage to the environment, with identification of keystone members (e.g., Arcobacter) potentially involved in cross-border exchanges between distant Gram-positive and Gram-negative phyla.}, }
@article {pmid28387730, year = {2017}, author = {Jain, S and Panda, A and Colson, P and Raoult, D and Pontarotti, P}, title = {MimiLook: A Phylogenetic Workflow for Detection of Gene Acquisition in Major Orthologous Groups of Megavirales.}, journal = {Viruses}, volume = {9}, number = {4}, pages = {}, pmid = {28387730}, issn = {1999-4915}, mesh = {Computational Biology/methods ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Viral ; Giant Viruses/*genetics ; *Phylogeny ; Workflow ; }, abstract = {With the inclusion of new members, understanding about evolutionary mechanisms and processes by which members of the proposed order, Megavirales, have evolved has become a key area of interest. The central role of gene acquisition has been shown in previous studies. However, the major drawback in gene acquisition studies is the focus on few MV families or putative families with large variation in their genetic structure. Thus, here we have tried to develop a methodology by which we can detect horizontal gene transfers (HGTs), taking into consideration orthologous groups of distantly related Megavirale families. Here, we report an automated workflow MimiLook, prepared as a Perl command line program, that deduces orthologous groups (OGs) from ORFomes of Megavirales and constructs phylogenetic trees by performing alignment generation, alignment editing and protein-protein BLAST (BLASTP) searching across the National Center for Biotechnology Information (NCBI) non-redundant (nr) protein sequence database. Finally, this tool detects statistically validated events of gene acquisitions with the help of the T-REX algorithm by comparing individual gene tree with NCBI species tree. In between the steps, the workflow decides about handling paralogs, filtering outputs, identifying Megavirale specific OGs, detection of HGTs, along with retrieval of information about those OGs that are monophyletic with organisms from cellular domains of life. By implementing MimiLook, we noticed that nine percent of Megavirale gene families (i.e., OGs) have been acquired by HGT, 80% OGs were Megaviralespecific and eight percent were found to be sharing common ancestry with members of cellular domains (Eukaryote, Bacteria, Archaea, Phages or other viruses) and three percent were ambivalent. The results are briefly discussed to emphasize methodology. Also, MimiLook is relevant for detecting evolutionary scenarios in other targeted phyla with user defined modifications. It can be accessed at following link 10.6084/m9.figshare.4653622.}, }
@article {pmid28383780, year = {2017}, author = {Farré, D and Martínez-Vicente, P and Engel, P and Angulo, A}, title = {Immunoglobulin superfamily members encoded by viruses and their multiple roles in immune evasion.}, journal = {European journal of immunology}, volume = {47}, number = {5}, pages = {780-796}, doi = {10.1002/eji.201746984}, pmid = {28383780}, issn = {1521-4141}, mesh = {Adenoviruses, Human/genetics/immunology/pathogenicity ; Animals ; Antigens, CD/immunology ; DNA Viruses/*genetics/immunology/*pathogenicity ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Immunoglobulin ; Herpesviridae/genetics/immunology/pathogenicity ; Humans ; *Immune Evasion ; Immunoglobulins/genetics/*immunology/metabolism ; Intercellular Signaling Peptides and Proteins/immunology ; Viral Proteins/genetics/*immunology ; }, abstract = {Pathogens have developed a plethora of strategies to undermine host immune defenses in order to guarantee their survival. For large DNA viruses, these immune evasion mechanisms frequently rely on the expression of genes acquired from host genomes. Horizontally transferred genes include members of the immunoglobulin superfamily, whose products constitute the most diverse group of proteins of vertebrate genomes. Their promiscuous immunoglobulin domains, which comprise the building blocks of these molecules, are involved in a large variety of functions mediated by ligand-binding interactions. The flexible structural nature of the immunoglobulin domains makes them appealing targets for viral capture due to their capacity to generate high functional diversity. Here, we present an up-to-date review of immunoglobulin superfamily gene homologs encoded by herpesviruses, poxviruses, and adenoviruses, that include CD200, CD47, Fc receptors, interleukin-1 receptor 2, interleukin-18 binding protein, CD80, carcinoembryonic antigen-related cell adhesion molecules, and signaling lymphocyte activation molecules. We discuss their distinct structural attributes, binding properties, and functions, shaped by evolutionary pressures to disarm specific immune pathways. We include several novel genes identified from extensive genome database surveys. An understanding of the properties and modes of action of these viral proteins may guide the development of novel immune-modulatory therapeutic tools.}, }
@article {pmid28383665, year = {2017}, author = {Jeukens, J and Freschi, L and Vincent, AT and Emond-Rheault, JG and Kukavica-Ibrulj, I and Charette, SJ and Levesque, RC}, title = {A Pan-Genomic Approach to Understand the Basis of Host Adaptation in Achromobacter.}, journal = {Genome biology and evolution}, volume = {9}, number = {4}, pages = {1030-1046}, pmid = {28383665}, issn = {1759-6653}, abstract = {Over the past decade, there has been a rising interest in Achromobacter sp., an emerging opportunistic pathogen responsible for nosocomial and cystic fibrosis lung infections. Species of this genus are ubiquitous in the environment, can outcompete resident microbiota, and are resistant to commonly used disinfectants as well as antibiotics. Nevertheless, the Achromobacter genus suffers from difficulties in diagnosis, unresolved taxonomy and limited understanding of how it adapts to the cystic fibrosis lung, not to mention other host environments. The goals of this first genus-wide comparative genomics study were to clarify the taxonomy of this genus and identify genomic features associated with pathogenicity and host adaptation. This was done with a widely applicable approach based on pan-genome analysis. First, using all publicly available genomes, a combination of phylogenetic analysis based on 1,780 conserved genes with average nucleotide identity and accessory genome composition allowed the identification of a largely clinical lineage composed of Achromobacter xylosoxidans, Achromobacter insuavis, Achromobacter dolens, and Achromobacter ruhlandii. Within this lineage, we identified 35 positively selected genes involved in metabolism, regulation and efflux-mediated antibiotic resistance. Second, resistome analysis showed that this clinical lineage carried additional antibiotic resistance genes compared with other isolates. Finally, we identified putative mobile elements that contribute 53% of the genus's resistome and support horizontal gene transfer between Achromobacter and other ecologically similar genera. This study provides strong phylogenetic and pan-genomic bases to motivate further research on Achromobacter, and contributes to the understanding of opportunistic pathogen evolution.}, }
@article {pmid28383641, year = {2017}, author = {Sullivan, AR and Schiffthaler, B and Thompson, SL and Street, NR and Wang, XR}, title = {Interspecific Plastome Recombination Reflects Ancient Reticulate Evolution in Picea (Pinaceae).}, journal = {Molecular biology and evolution}, volume = {34}, number = {7}, pages = {1689-1701}, pmid = {28383641}, issn = {1537-1719}, mesh = {Biological Evolution ; DNA, Plant/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Plant ; Genome, Plastid ; High-Throughput Nucleotide Sequencing/methods ; Hybridization, Genetic ; Phylogeny ; Picea/*genetics ; Plastids/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Plastid sequences are a cornerstone in plant systematic studies and key aspects of their evolution, such as uniparental inheritance and absent recombination, are often treated as axioms. While exceptions to these assumptions can profoundly influence evolutionary inference, detecting them can require extensive sampling, abundant sequence data, and detailed testing. Using advancements in high-throughput sequencing, we analyzed the whole plastomes of 65 accessions of Picea, a genus of ∼35 coniferous forest tree species, to test for deviations from canonical plastome evolution. Using complementary hypothesis and data-driven tests, we found evidence for chimeric plastomes generated by interspecific hybridization and recombination in the clade comprising Norway spruce (P. abies) and 10 other species. Support for interspecific recombination remained after controlling for sequence saturation, positive selection, and potential alignment artifacts. These results reconcile previous conflicting plastid-based phylogenies and strengthen the mounting evidence of reticulate evolution in Picea. Given the relatively high frequency of hybridization and biparental plastid inheritance in plants, we suggest interspecific plastome recombination may be more widespread than currently appreciated and could underlie reported cases of discordant plastid phylogenies.}, }
@article {pmid28382496, year = {2017}, author = {Prisilla, A and Prathiviraj, R and Chellapandi, P}, title = {Molecular Evolutionary Constraints that Determine the Avirulence State of Clostridium botulinum C2 Toxin.}, journal = {Journal of molecular evolution}, volume = {84}, number = {4}, pages = {174-186}, pmid = {28382496}, issn = {1432-1432}, mesh = {Amino Acid Sequence/genetics ; Base Sequence/genetics ; Botulinum Toxins/*genetics/metabolism/physiology ; Clostridium botulinum/genetics/pathogenicity ; Conserved Sequence/genetics ; Evolution, Molecular ; Genetic Variation ; Phylogeny ; Virulence/*genetics ; }, abstract = {Clostridium botulinum (group-III) is an anaerobic bacterium producing C2 toxin along with botulinum neurotoxins. C2 toxin is belonged to binary toxin A family in bacterial ADP-ribosylation superfamily. A structural and functional diversity of binary toxin A family was inferred from different evolutionary constraints to determine the avirulence state of C2 toxin. Evolutionary genetic analyses revealed evidence of C2 toxin cluster evolution through horizontal gene transfer from the phage or plasmid origins, site-specific insertion by gene divergence, and homologous recombination event. It has also described that residue in conserved NAD-binding core, family-specific domain structure, and functional motifs found to predetermine its virulence state. Any mutational changes in these residues destabilized its structure-function relationship. Avirulent mutants of C2 toxin were screened and selected from a crucial site required for catalytic function of C2I and pore-forming function of C2II. We found coevolved amino acid pairs contributing an essential role in stabilization of its local structural environment. Avirulent toxins selected in this study were evaluated by detecting evolutionary constraints in stability of protein backbone structure, folding and conformational dynamic space, and antigenic peptides. We found 4 avirulent mutants of C2I and 5 mutants of C2II showing more stability in their local structural environment and backbone structure with rapid fold rate, and low conformational flexibility at mutated sites. Since, evolutionary constraints-free mutants with lack of catalytic and pore-forming function suggested as potential immunogenic candidates for treating C. botulinum infected poultry and veterinary animals. Single amino acid substitution in C2 toxin thus provides a major importance to understand its structure-function link, not only of a molecule but also of the pathogenesis.}, }
@article {pmid28379381, year = {2017}, author = {Hopkins, KL and Findlay, J and Doumith, M and Mather, B and Meunier, D and D'Arcy, S and Pike, R and Mustafa, N and Howe, R and Wootton, M and Woodford, N}, title = {IMI-2 carbapenemase in a clinical Klebsiella variicola isolated in the UK.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {72}, number = {7}, pages = {2129-2131}, doi = {10.1093/jac/dkx103}, pmid = {28379381}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/*genetics ; Carbapenem-Resistant Enterobacteriaceae/drug effects/*enzymology/genetics/isolation &amp; purification ; Carbapenems/*pharmacology ; Cephalosporins/pharmacology ; Drug Resistance, Bacterial ; Ertapenem ; Gene Transfer, Horizontal ; Humans ; Imipenem/pharmacology ; Klebsiella/drug effects/*enzymology/genetics/isolation &amp; purification ; Meropenem ; Plasmids ; Thienamycins/pharmacology ; United Kingdom ; beta-Lactamases/*genetics ; beta-Lactams/pharmacology ; }, }
@article {pmid28377759, year = {2017}, author = {Wang, L and Wang, J and Jing, C}, title = {Comparative Genomic Analysis Reveals Organization, Function and Evolution of ars Genes in Pantoea spp.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {471}, pmid = {28377759}, issn = {1664-302X}, abstract = {Numerous genes are involved in various strategies to resist toxic arsenic (As). However, the As resistance strategy in genus Pantoea is poorly understood. In this study, a comparative genome analysis of 23 Pantoea genomes was conducted. Two vertical genetic arsC-like genes without any contribution to As resistance were found to exist in the 23 Pantoea strains. Besides the two arsC-like genes, As resistance gene clusters arsRBC or arsRBCH were found in 15 Pantoea genomes. These ars clusters were found to be acquired by horizontal gene transfer (HGT) from sources related to Franconibacter helveticus, Serratia marcescens, and Citrobacter freundii. During the history of evolution, the ars clusters were acquired more than once in some species, and were lost in some strains, producing strains without As resistance capability. This study revealed the organization, distribution and the complex evolutionary history of As resistance genes in Pantoea spp.. The insights gained in this study improved our understanding on the As resistance strategy of Pantoea spp. and its roles in the biogeochemical cycling of As.}, }
@article {pmid28377756, year = {2017}, author = {Malwade, A and Nguyen, A and Sadat-Mousavi, P and Ingalls, BP}, title = {Predictive Modeling of a Batch Filter Mating Process.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {461}, pmid = {28377756}, issn = {1664-302X}, abstract = {Quantitative characterizations of horizontal gene transfer are needed to accurately describe gene transfer processes in natural and engineered systems. A number of approaches to the quantitative description of plasmid conjugation have appeared in the literature. In this study, we seek to extend that work, motivated by the question of whether a mathematical model can accurately predict growth and conjugation dynamics in a batch process. We used flow cytometry to make time-point observations of a filter-associated mating between two E. coli strains, and fit ordinary differential equation models to the data. A model comparison analysis identified the model formulation that is best supported by the data. Identifiability analysis revealed that the parameters were estimated with acceptable accuracy. The predictive power of the model was assessed by comparison with test data that demanded extrapolation from the training experiments. This study represents the first attempt to assess the quality of model predictions for plasmid conjugation. Our successful application of this approach lays a foundation for predictive modeling that can be used both in the study of natural plasmid transmission and in model-based design of engineering approaches that employ conjugation, such as plasmid-mediated bioaugmentation.}, }
@article {pmid28376762, year = {2017}, author = {Huang, W and Tsai, L and Li, Y and Hua, N and Sun, C and Wei, C}, title = {Widespread of horizontal gene transfer in the human genome.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {274}, pmid = {28376762}, issn = {1471-2164}, mesh = {Base Composition ; Chromosomes, Human/genetics ; Computational Biology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Human ; Humans ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: A fundamental concept in biology is that heritable material is passed from parents to offspring, a process called vertical gene transfer. An alternative mechanism of gene acquisition is through horizontal gene transfer (HGT), which involves movement of genetic materials between different species. Horizontal gene transfer has been found prevalent in prokaryotes but very rare in eukaryote. In this paper, we investigate horizontal gene transfer in the human genome.<br><br>RESULTS: From the pair-wise alignments between human genome and 53 vertebrate genomes, 1,467 human genome regions (2.6&#xa0;M bases) from all chromosomes were found to be more conserved with non-mammals than with most mammals. These human genome regions involve 642 known genes, which are enriched with ion binding. Compared to known horizontal gene transfer regions in the human genome, there were few overlapping regions, which indicated horizontal gene transfer is more common than we expected in the human genome.<br><br>CONCLUSIONS: Horizontal gene transfer impacts hundreds of human genes and this study provided insight into potential mechanisms of HGT in the human genome.}, }
@article {pmid28376716, year = {2017}, author = {Bitrus, AA and Zunita, Z and Bejo, SK and Othman, S and Nadzir, NA}, title = {In vitro transfer of methicillin resistance determinants mecA from methicillin resistant Staphylococcus aureus (MRSA) to methicillin susceptible Staphylococcus aureus (MSSA).}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {83}, pmid = {28376716}, issn = {1471-2180}, mesh = {Bacterial Proteins/*genetics ; Base Sequence ; DNA, Bacterial ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial ; In Vitro Techniques ; Methicillin/*pharmacology ; Methicillin Resistance/*genetics ; Methicillin-Resistant Staphylococcus aureus/*drug effects/*genetics ; Microbial Sensitivity Tests ; Penicillin-Binding Proteins/*genetics ; Polymerase Chain Reaction ; Staphylococcus aureus/*genetics/pathogenicity ; Transcription Factors/genetics ; }, abstract = {BACKGROUND: Staphylococcus aureus more than any other human pathogen is a better model for the study of the adaptive evolution of bacterial resistance to antibiotics, as it has demonstrated a remarkable ability in its response to new antibiotics. This study was designed to investigate the in vitro transfer of mecA gene from methicillin resistant S. aureus to methicillin susceptible S. aureus.<br><br>RESULT: The recipient transconjugants were resistant to erythromycin, cefpodoxime and were mecA positive. PCR amplification of mecA after mix culture plating on Luria Bertani agar containing 100&#xa0;&#x3bc;g/mL showed that 75% of the donor and 58.3% of the recipient transconjugants were mecA positive. Additionally, 61.5% of both the donor cells and recipient transconjugants were mecA positive, while 46.2% and 41.75% of both donor and recipient transconjugants were mecA positive on LB agar containing 50&#xa0;&#x3bc;g/mL and 30&#xa0;&#x3bc;g/mL respectively.<br><br>CONCLUSION: In this study, the direction of transfer of phenotypic resistance as well as mecA was observed to have occurred from the donor to the recipient strains. This study affirmed the importance of horizontal transfer events in the dissemination of antibiotics resistance among different strains of MRSA.}, }
@article {pmid28373865, year = {2017}, author = {Coluzzi, C and Guédon, G and Devignes, MD and Ambroset, C and Loux, V and Lacroix, T and Payot, S and Leblond-Bourget, N}, title = {A Glimpse into the World of Integrative and Mobilizable Elements in Streptococci Reveals an Unexpected Diversity and Novel Families of Mobilization Proteins.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {443}, pmid = {28373865}, issn = {1664-302X}, abstract = {Recent analyses of bacterial genomes have shown that integrated elements that transfer by conjugation play an essential role in horizontal gene transfer. Among these elements, the integrative and mobilizable elements (IMEs) are known to encode their own excision and integration machinery, and to carry all the sequences or genes necessary to hijack the mating pore of a conjugative element for their own transfer. However, knowledge of their prevalence and diversity is still severely lacking. In this work, an extensive analysis of 124 genomes from 27 species of Streptococcus reveals 144 IMEs. These IMEs encode either tyrosine or serine integrases. The identification of IME boundaries shows that 141 are specifically integrated in 17 target sites. The IME-encoded relaxases belong to nine superfamilies, among which four are previously unknown in any mobilizable or conjugative element. A total of 118 IMEs are found to encode a non-canonical relaxase related to rolling circle replication initiators (belonging to the four novel families or to MobT). Surprisingly, among these, 83 encode a TcpA protein (i.e., a non-canonical coupling protein (CP) that is more closely related to FtsK than VirD4) that was not previously known to be encoded by mobilizable elements. Phylogenetic analyses reveal not only many integration/excision module replacements but also losses, acquisitions or replacements of TcpA genes between IMEs. This glimpse into the still poorly known world of IMEs reveals that mobilizable elements have a very high prevalence. Their diversity is even greater than expected, with most encoding a CP and/or a non-canonical relaxase.}, }
@article {pmid28371770, year = {2017}, author = {Tong, J and Lu, X and Zhang, J and Sui, Q and Wang, R and Chen, M and Wei, Y}, title = {Occurrence of antibiotic resistance genes and mobile genetic elements in enterococci and genomic DNA during anaerobic digestion of pharmaceutical waste sludge with different pretreatments.}, journal = {Bioresource technology}, volume = {235}, number = {}, pages = {316-324}, doi = {10.1016/j.biortech.2017.03.104}, pmid = {28371770}, issn = {1873-2976}, mesh = {Anaerobiosis ; Anti-Bacterial Agents/*metabolism ; DNA ; Drug Resistance, Microbial/genetics ; Enterococcus/genetics ; Genomics ; Interspersed Repetitive Sequences ; Pharmaceutical Preparations ; *Sewage ; Waste Disposal, Fluid ; }, abstract = {Pharmaceutical waste sludge harbors large amounts of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), and it is necessary to study the reduction of ARGs and MGEs during sludge treatment. Therefore, the antibiotic resistance phenotypes and genotypes of enterococci, and the ARGs and MGEs in genomic DNA were investigated during anaerobic digestion (AD) with microwave (MW), thermal hydrolysis (TH) and ozone pretreatment. Results showed that sludge pretreatment increased the occurrence of the resistance phenotypes and genotypes of enterococci. During AD, the resistance of enterococci to macrolides decreased, except for in the MW-pretreated sludge. Horizontal gene transfer and co-occurrence of ermB and tetM in enterococci resulted in increased tetracycline resistance of enterococci throughout the sludge treatment. MGEs such as intI1, ISCR1 and Tn916/1545 had a significant effect on the distribution of ARGs. AD with pretreatment, especially TH pretreatment, resulted in greater ARGs and MGEs reduction and improved methane production.}, }
@article {pmid28369623, year = {2017}, author = {Delavat, F and Miyazaki, R and Carraro, N and Pradervand, N and van der Meer, JR}, title = {The hidden life of integrative and conjugative elements.}, journal = {FEMS microbiology reviews}, volume = {41}, number = {4}, pages = {512-537}, pmid = {28369623}, issn = {1574-6976}, mesh = {DNA Transposable Elements/genetics/*physiology ; Host-Pathogen Interactions/physiology ; }, abstract = {Integrative and conjugative elements (ICEs) are widespread mobile DNA that transmit both vertically, in a host-integrated state, and horizontally, through excision and transfer to new recipients. Different families of ICEs have been discovered with more or less restricted host ranges, which operate by similar mechanisms but differ in regulatory networks, evolutionary origin and the types of variable genes they contribute to the host. Based on reviewing recent experimental data, we propose a general model of ICE life style that explains the transition between vertical and horizontal transmission as a result of a bistable decision in the ICE-host partnership. In the large majority of cells, the ICE remains silent and integrated, but hidden at low to very low frequencies in the population specialized host cells appear in which the ICE starts its process of horizontal transmission. This bistable process leads to host cell differentiation, ICE excision and transfer, when suitable recipients are present. The ratio of ICE bistability (i.e. ratio of horizontal to vertical transmission) is the outcome of a balance between fitness costs imposed by the ICE horizontal transmission process on the host cell, and selection for ICE distribution (i.e. ICE 'fitness'). From this emerges a picture of ICEs as elements that have adapted to a mostly confined life style within their host, but with a very effective and dynamic transfer from a subpopulation of dedicated cells.}, }
@article {pmid28369562, year = {2017}, author = {Stanczak-Mrozek, KI and Laing, KG and Lindsay, JA}, title = {Resistance gene transfer: induction of transducing phage by sub-inhibitory concentrations of antimicrobials is not correlated to induction of lytic phage.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {72}, number = {6}, pages = {1624-1631}, pmid = {28369562}, issn = {1460-2091}, support = {G0900205//Medical Research Council/United Kingdom ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteriolysis ; Bacteriophages/*drug effects/genetics/isolation &amp; purification/*physiology ; Drug Resistance, Multiple, Bacterial/genetics ; Humans ; Methicillin-Resistant Staphylococcus aureus/drug effects/*genetics/virology ; Microbial Sensitivity Tests ; Staphylococcal Infections/microbiology ; Staphylococcus aureus/drug effects/*genetics/virology ; *Transduction, Genetic ; *Virus Activation ; }, abstract = {OBJECTIVES: Horizontal gene transfer of antimicrobial resistance (AMR) genes between clinical isolates via transduction is poorly understood. MRSA are opportunistic pathogens resistant to all classes of antimicrobial agents but currently no strains are fully drug resistant. AMR gene transfer between Staphylococcus aureus isolates is predominantly due to generalized transduction via endogenous bacteriophage, and recent studies have suggested transfer is elevated during host colonization. The aim was to investigate whether exposure to sub-MIC concentrations of antimicrobials triggers bacteriophage induction and/or increased efficiency of AMR gene transfer.<br><br>METHODS: Isolates from MRSA carriers were exposed to nine antimicrobials and supernatants were compared for lytic phage particles and ability to transfer an AMR gene. A new technology, droplet digital PCR, was used to measure the concentration of genes in phage particles.<br><br>RESULTS: All antibiotics tested induced lytic phage and AMR gene transduction, although the ratio of transducing particles to lytic particles differed substantially for each antibiotic. Mupirocin induced the highest ratio of transducing versus lytic particles. Gentamicin and novobiocin reduced UV-induced AMR transduction. The genes carried in phage particles correlated with AMR transfer or lytic particle activity, suggesting antimicrobials influence which DNA sequences are packaged into phage particles.<br><br>CONCLUSIONS: Sub-inhibitory antibiotics induce AMR gene transfer between clinical MRSA, while combination therapy with an inhibiting antibiotic could potentially alter AMR gene packaging into phage particles, reducing AMR transfer. In a continually evolving environment, pathogens have an advantage if they can transfer DNA while lowering the risk of lytic death.}, }
@article {pmid28369538, year = {2017}, author = {Varela-Ramirez, A and Abendroth, J and Mejia, AA and Phan, IQ and Lorimer, DD and Edwards, TE and Aguilera, RJ}, title = {Structure of acid deoxyribonuclease.}, journal = {Nucleic acids research}, volume = {45}, number = {10}, pages = {6217-6227}, pmid = {28369538}, issn = {1362-4962}, support = {G12 MD007592/MD/NIMHD NIH HHS/United States ; R25 GM069621/GM/NIGMS NIH HHS/United States ; SC3 GM088069/GM/NIGMS NIH HHS/United States ; SC3 GM103713/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacterial Proteins/antagonists &amp; inhibitors/*chemistry/metabolism ; Burkholderia/*enzymology ; Catalytic Domain ; Copper/pharmacology ; Crystallography, X-Ray ; DNA, Bacterial/metabolism ; Endodeoxyribonucleases/antagonists &amp; inhibitors/*chemistry/metabolism ; Eukaryotic Cells/enzymology ; Evolution, Molecular ; Gene Transfer, Horizontal ; Hydrogen-Ion Concentration ; Models, Molecular ; Molecular Docking Simulation ; Phylogeny ; Prokaryotic Cells/enzymology ; Protein Conformation ; Protein Folding ; Recombinant Fusion Proteins/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {Deoxyribonuclease II (DNase II) is also known as acid deoxyribonuclease because it has optimal activity at the low pH environment of lysosomes where it is typically found in higher eukaryotes. Interestingly, DNase II has also been identified in a few genera of bacteria and is believed to have arisen via horizontal transfer. Here, we demonstrate that recombinant Burkholderia thailandensis DNase II is highly active at low pH in the absence of divalent metal ions, similar to eukaryotic DNase II. The crystal structure of B. thailandensis DNase II shows a dimeric quaternary structure which appears capable of binding double-stranded DNA. Each monomer of B. thailandensis DNase II exhibits a similar overall fold as phospholipase D (PLD), phosphatidylserine synthase (PSS) and tyrosyl-DNA phosphodiesterase (TDP), and conserved catalytic residues imply a similar mechanism. The structural and biochemical data presented here provide insights into the atomic structure and catalytic mechanism of DNase II.}, }
@article {pmid28369408, year = {2017}, author = {Roer, L and Hansen, F and Thomsen, MCF and Knudsen, JD and Hansen, DS and Wang, M and Samulioniené, J and Justesen, US and Røder, BL and Schumacher, H and Østergaard, C and Andersen, LP and Dzajic, E and Søndergaard, TS and Stegger, M and Hammerum, AM and Hasman, H}, title = {WGS-based surveillance of third-generation cephalosporin-resistant Escherichia coli from bloodstream infections in Denmark.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {72}, number = {7}, pages = {1922-1929}, doi = {10.1093/jac/dkx092}, pmid = {28369408}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteremia/epidemiology/*microbiology ; Bacterial Proteins/biosynthesis/genetics ; Cephalosporin Resistance/*genetics ; Cephalosporins/*pharmacology ; Electrophoresis, Gel, Pulsed-Field ; Epidemiological Monitoring ; Escherichia coli/*drug effects/enzymology/*genetics ; Escherichia coli Infections/epidemiology/*microbiology ; Gene Transfer, Horizontal ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Humans ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Phylogeny ; Polymerase Chain Reaction ; beta-Lactamases/biosynthesis/genetics ; }, abstract = {OBJECTIVES: To evaluate a genome-based surveillance of all Danish third-generation cephalosporin-resistant Escherichia coli (3GC-R Ec) from bloodstream infections between 2014 and 2015, focusing on horizontally transferable resistance mechanisms.<br><br>METHODS: A collection of 552 3GC-R Ec isolates were whole-genome sequenced and characterized by using the batch uploader from the Center for Genomic Epidemiology (CGE) and automatically analysed using the CGE tools according to resistance profile, MLST, serotype and fimH subtype. Additionally, the phylogenetic relationship of the isolates was analysed by SNP analysis.<br><br>RESULTS: The majority of the 552 isolates were ESBL producers (89%), with bla CTX-M-15 being the most prevalent (50%) gene, followed by bla CTX-M-14 (14%), bla CTX-M-27 (11%) and bla CTX-M-101 (5%). ST131 was detected in 50% of the E. coli isolates, with the remaining isolates belonging to 73 other STs, including globally disseminated STs (e.g. ST10, ST38, ST58, ST69 and ST410). Five of the bloodstream isolates were carbapenemase producers, carrying bla OXA-181 (3) and bla OXA-48 (2). Phylogenetic analysis revealed 15 possible national outbreaks during the 2&#x2009;year period, one caused by a novel ST131/ bla CTX-M-101 clone, here observed for the first time in Denmark. Additionally, the analysis revealed three individual cases with possible persistence of closely related clones collected more than 13&#x2009;months apart.<br><br>CONCLUSIONS: Continuous WGS-based national surveillance of 3GC-R Ec , in combination with more detailed epidemiological information, can improve the ability to follow the population dynamics of 3GC-R Ec , thus allowing for the detection of potential outbreaks and the effects of changing treatment regimens in the future.}, }
@article {pmid28366828, year = {2017}, author = {Ofir-Birin, Y and Heidenreich, M and Regev-Rudzki, N}, title = {Pathogen-derived extracellular vesicles coordinate social behaviour and host manipulation.}, journal = {Seminars in cell &amp; developmental biology}, volume = {67}, number = {}, pages = {83-90}, doi = {10.1016/j.semcdb.2017.03.004}, pmid = {28366828}, issn = {1096-3634}, mesh = {Bacteria/genetics/growth &amp; development/*metabolism/pathogenicity ; Biofilms/growth &amp; development ; Communicable Diseases/*immunology/microbiology/virology ; Extracellular Vesicles/*metabolism ; Fungi/genetics/growth &amp; development/*metabolism/pathogenicity ; Gene Transfer, Horizontal ; Host-Pathogen Interactions/*immunology ; Humans ; Immunity, Innate ; Lymphocyte Activation ; Lymphocytes/immunology/microbiology/virology ; Microbial Interactions/*physiology ; Quorum Sensing/physiology ; Social Behavior ; Virulence ; Viruses/genetics/growth &amp; development/*metabolism/pathogenicity ; }, abstract = {Infectious diseases are the leading cause of death of children worldwide, causing a tenacious and major public-health burden. The dynamic interplay between pathogens and their host is one of the most complicated themes of the disease progression. Pathogens excel in developing different means to facilitate cell-cell communication via secreted vesicles, among others. The released vesicles are involved in the transfer of biologically active molecules that induce phenotypic changes in the recipient cells. The messages within the vesicles are delivered to coordinate diverse processes, including virulence factor expression, differentiation state and control of their population density. Importantly, production of such vesicles promotes pathogen survival, as it provides a secure means of pathogen-pathogen communication and an ability to manipulate host responses for their own benefits. This review highlights intriguing findings, which show the important role of EVs in the social activity of pathogens, within and in between their communities. We further present examples of how pathogens use EVs to alter host immune and non-immune responses. Advancing our understanding of cell-cell communication in infectious diseases will be particularly useful to decipher the complexity of the cross-talk between pathogens themselves and their hosts, leading to the development of therapeutic strategies for fighting infectious agents.}, }
@article {pmid28364120, year = {2017}, author = {Chamosa, LS and Álvarez, VE and Nardelli, M and Quiroga, MP and Cassini, MH and Centrón, D}, title = {Lateral Antimicrobial Resistance Genetic Transfer is active in the open environment.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {513}, pmid = {28364120}, issn = {2045-2322}, mesh = {Alleles ; Argentina ; Bacteria/*drug effects/*genetics ; *Drug Resistance, Bacterial ; *Environmental Microbiology ; Gene Frequency ; *Gene Transfer, Horizontal ; Integrases/genetics ; Public Health Surveillance ; }, abstract = {Historically, the environment has been viewed as a passive deposit of antimicrobial resistance mechanisms, where bacteria show biological cost for maintenance of these genes. Thus, in the absence of antimicrobial pressure, it is expected that they disappear from environmental bacterial communities. To test this scenario, we studied native IntI1 functionality of 11 class 1 integron-positive environmental strains of distant genera collected in cold and subtropical forests of Argentina. We found natural competence and successful site-specific insertion with no significant fitness cost of both aadB and bla VIM-2 antimicrobial resistance gene cassettes, in a model system without antibiotic pressure. A bidirectional flow of antimicrobial resistance gene cassettes between natural and nosocomial habitats is proposed, which implies an active role of the open environment as a reservoir, recipient and source of antimicrobial resistance mechanisms, outlining an environmental threat where novel concepts of rational use of antibiotics are extremely urgent and mandatory.}, }
@article {pmid28362724, year = {2017}, author = {Stevenson, C and Hall, JP and Harrison, E and Wood, A and Brockhurst, MA}, title = {Gene mobility promotes the spread of resistance in bacterial populations.}, journal = {The ISME journal}, volume = {11}, number = {8}, pages = {1930-1932}, pmid = {28362724}, issn = {1751-7370}, support = {311490/ERC_/European Research Council/International ; }, mesh = {Drug Resistance, Bacterial/*genetics ; *Gene Transfer, Horizontal ; Mercury/*toxicity ; Plasmids/*genetics ; Pseudomonas fluorescens/*drug effects/*genetics ; }, abstract = {Theory predicts that horizontal gene transfer (HGT) expands the selective conditions under which genes spread in bacterial populations. Whereas vertically inherited genes can only spread by positively selected clonal expansion, mobile genetic elements can drive fixation of genes by infectious HGT. We tested this using populations of Pseudomonas fluorescens and the conjugative mercury resistance (Hg[R]) plasmid pQBR57. HGT expanded the selective conditions allowing the spread of Hg[R]: Chromosomal Hg[R] only increased in frequency under positive selection, whereas plasmid-encoded Hg[R] reached fixation with or without positive selection. Tracking plasmid dynamics over time revealed that the mode of Hg[R] inheritance varied across mercury environments. Under mercury selection, the spread of Hg[R] was driven primarily by clonal expansion while in the absence of mercury Hg[R] dynamics were dominated by infectious transfer. Thus, HGT is most likely to drive the spread of resistance genes in environments where resistance is useless.}, }
@article {pmid28362383, year = {2017}, author = {Cafini, F and Thi Le Thuy, N and Román, F and Prieto, J and Dubrac, S and Msadek, T and Morikawa, K}, title = {Methodology for the Study of Horizontal Gene Transfer in Staphylococcus aureus.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {121}, pages = {}, pmid = {28362383}, issn = {1940-087X}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics ; Conjugation, Genetic/genetics ; Drug Resistance, Bacterial/drug effects/*genetics ; *Gene Transfer, Horizontal ; *Genetic Techniques ; Humans ; Staphylococcus Phages/genetics ; Staphylococcus aureus/drug effects/*genetics ; Thiamphenicol/analogs &amp; derivatives/pharmacology ; Transduction, Genetic ; }, abstract = {One important feature of the major opportunistic human pathogen Staphylococcus aureus is its extraordinary ability to rapidly acquire resistance to antibiotics. Genomic studies reveal that S. aureus carries many virulence and resistance genes located in mobile genetic elements, suggesting that horizontal gene transfer (HGT) plays a critical role in S. aureus evolution. However, a full and detailed description of the methodology used to study HGT in S. aureus is still lacking, especially regarding natural transformation, which has been recently reported in this bacterium. This work describes three protocols that are useful for the in vitro investigation of HGT in S. aureus: conjugation, phage transduction, and natural transformation. To this aim, the cfr gene (chloramphenicol/florfenicol resistance), which confers the Phenicols, Lincosamides, Oxazolidinones, Pleuromutilins, and Streptogramin A (PhLOPSA)-resistance phenotype, was used. Understanding the mechanisms through which S. aureus transfers genetic materials to other strains is essential to comprehending the rapid acquisition of resistance and helps to clarify the modes of dissemination reported in surveillance programs or to further predict the spreading mode in the future.}, }
@article {pmid28361040, year = {2017}, author = {Levipan, HA and Avendaño-Herrera, R}, title = {Different Phenotypes of Mature Biofilm in Flavobacterium psychrophilum Share a Potential for Virulence That Differs from Planktonic State.}, journal = {Frontiers in cellular and infection microbiology}, volume = {7}, number = {}, pages = {76}, pmid = {28361040}, issn = {2235-2988}, mesh = {Biofilms/*growth &amp; development ; Flavobacterium/genetics/growth &amp; development/*physiology ; Gene Expression Profiling ; Phenotype ; Virulence ; }, abstract = {Flavobacterium psychrophilum is the etiological agent of bacterial coldwater disease and the rainbow trout fry syndrome in salmonid aquaculture worldwide. However, there have been few studies into the capacity of F. psychrophilum to form biofilms and how these cellular accretions differ from planktonic cells or how they affect potential virulence. We evaluated the biofilm formation by three Chilean isolates of F. psychrophilum (LM-02-Fp, LM-06-Fp, and LM-13-Fp) and two non-Chilean strains (JIP02/86 and NCMB1947[T]), and compared biofilm and planktonic states to obtain insights into expression differences of virulence- and biofilm-related genes (VBRGs). Our findings are based on scanning confocal laser microscopy (SCLM) and LIVE/DEAD staining, enzymatic reactions, reverse transcription-quantitative PCR (RT-qPCR) of genes encoding putative virulence factors, and transcriptomes (RNA-Seq). The LM-02-Fp and NCMB1947[T] strains were the strongest and weakest biofilm producers, respectively. The strong-biofilm producer showed different physiological cell states distributed in different layers of mature biofilms, whereas the NCMB1947[T] biofilms consisted of cells arranged in a monolayer. WGA-binding exopolysaccharides would be the main components of their corresponding extracellular matrices. Transcriptomes of F. psychrophilum NCMB1947[T] and LM-02-Fp were clustered by state (biofilm vs. planktonic) rather than by strain, indicating important state-dependent differences in gene expression. Analysis of differentially expressed genes between states identified putative VBRGs involved in polysaccharide biosynthesis, lateral gene transfer, membrane transport (e.g., for drugs and Fe[3+]), sensory mechanisms, and adhesion, and indicated that about 60-100% of VBRGs involved in these processes was significantly upregulated in the biofilm state. Conversely, upregulated motility-related genes in the biofilm state were not identified, whereas a lower fraction of proteolysis-related genes (33%) was upregulated in biofilms. In summary, F. psychrophilum strains that produce different biofilm phenotypes show global transcriptional activity in the mature biofilm state that differs significantly from their planktonic counterparts. Also, different biofilm phenotypes share a genetic potential for virulence that is transcriptionally enhanced with respect to free-living cells. Our results suggest that the F. psychrophilum biofilm lifestyle acts as a reservoir for a given set of putative virulence factors, and recommend a deeper understanding of which could help prevent recurring infections in salmonid farms.}, }
@article {pmid28360923, year = {2017}, author = {Ponce de León, I and Montesano, M}, title = {Adaptation Mechanisms in the Evolution of Moss Defenses to Microbes.}, journal = {Frontiers in plant science}, volume = {8}, number = {}, pages = {366}, pmid = {28360923}, issn = {1664-462X}, abstract = {Bryophytes, including mosses, liverworts and hornworts are early land plants that have evolved key adaptation mechanisms to cope with abiotic stresses and microorganisms. Microbial symbioses facilitated plant colonization of land by enhancing nutrient uptake leading to improved plant growth and fitness. In addition, early land plants acquired novel defense mechanisms to protect plant tissues from pre-existing microbial pathogens. Due to its evolutionary stage linking unicellular green algae to vascular plants, the non-vascular moss Physcomitrella patens is an interesting organism to explore the adaptation mechanisms developed in the evolution of plant defenses to microbes. Cellular and biochemical approaches, gene expression profiles, and functional analysis of genes by targeted gene disruption have revealed that several defense mechanisms against microbial pathogens are conserved between mosses and flowering plants. P. patens perceives pathogen associated molecular patterns by plasma membrane receptor(s) and transduces the signal through a MAP kinase (MAPK) cascade leading to the activation of cell wall associated defenses and expression of genes that encode proteins with different roles in plant resistance. After pathogen assault, P. patens also activates the production of ROS, induces a HR-like reaction and increases levels of some hormones. Furthermore, alternative metabolic pathways are present in P. patens leading to the production of a distinct metabolic scenario than flowering plants that could contribute to defense. P. patens has acquired genes by horizontal transfer from prokaryotes and fungi, and some of them could represent adaptive benefits for resistance to biotic stress. In this review, the current knowledge related to the evolution of plant defense responses against pathogens will be discussed, focusing on the latest advances made in the model plant P. patens.}, }
@article {pmid28359330, year = {2017}, author = {Szafranski, P}, title = {Evolutionarily recent, insertional fission of mitochondrial cox2 into complementary genes in bilaterian Metazoa.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {269}, pmid = {28359330}, issn = {1471-2164}, mesh = {Animals ; Electron Transport Complex IV/chemistry/*genetics ; *Evolution, Molecular ; Gene Expression Regulation ; *Genes, Mitochondrial ; Genome, Mitochondrial ; Hydrophobic and Hydrophilic Interactions ; Mitochondrial Dynamics/*genetics ; *Mutagenesis, Insertional ; Phylogeny ; Polyadenylation ; }, abstract = {BACKGROUND: Mitochondrial genomes (mtDNA) of multicellular animals (Metazoa) with bilateral symmetry (Bilateria) are compact and usually carry 13 protein-coding genes for subunits of three respiratory complexes and ATP synthase. However, occasionally reported exceptions to this typical mtDNA organization prompted speculation that, as in protists and plants, some bilaterian mitogenomes may continue to lose their canonical genes, or may even acquire new genes. To shed more light on this phenomenon, a PCR-based screen was conducted to assess fast-evolving mtDNAs of apocritan Hymenoptera (Arthropoda, Insecta) for genomic rearrangements that might be associated with the modification of mitochondrial gene content.<br><br>RESULTS: Sequencing of segmental inversions,&#xa0;identified in the screen, revealed that the cytochrome oxidase subunit II gene (cox2) of Campsomeris (Dielis) (Scoliidae) was split into two genes coding for COXIIA and COXIIB. The COXII-derived complementary polypeptides apparently form a heterodimer, have reduced hydrophobicity compared with the majority of mitogenome-encoded COX subunits, and one of them, COXIIB, features increased content of Cys residues. Analogous cox2 fragmentation is known only in two clades of protists (chlorophycean algae and alveolates), where it has been associated with piecewise relocation of this gene into the nucleus. In Campsomeris mtDNA, cox2a and cox2b loci are separated by&#xa0;a 3-kb large cluster of several antiparallel overlapping ORFs, one of which, qnu, seems to encode a nuclease that may have played a role in cox2 fission.<br><br>CONCLUSIONS: Although discontinuous mitochondrial protein genes encoding fragmented, complementary polypeptides are known in protists and some plants, split cox2 of Campsomeris is the first case of such a gene arrangement found in animals. The reported data also indicate that bilaterian animal mitogenomes may be carrying lineage-specific genes more often than previously thought, and suggest&#xa0;a homing endonuclease-based mechanism for insertional mitochondrial gene fission.}, }
@article {pmid28357330, year = {2016}, author = {Martin, WF and Weiss, MC and Neukirchen, S and Nelson-Sathi, S and Sousa, FL}, title = {Physiology, phylogeny, and LUCA.}, journal = {Microbial cell (Graz, Austria)}, volume = {3}, number = {12}, pages = {582-587}, pmid = {28357330}, issn = {2311-2638}, abstract = {Genomes record their own history. But if we want to look all the way back to life's beginnings some 4 billion years ago, the record of microbial evolution that is preserved in prokaryotic genomes is not easy to read. Microbiology has a lot in common with geology in that regard. Geologists know that plate tectonics and erosion have erased much of the geological record, with ancient rocks being truly rare. The same is true of microbes. Lateral gene transfer (LGT) and sequence divergence have erased much of the evolutionary record that was once written in genomes, and it is not obvious which genes among sequenced genomes are genuinely ancient. Which genes trace to the last universal ancestor, LUCA? The classical approach has been to look for genes that are universally distributed. Another approach is to make all trees for all genes, and sift out the trees where signals have been overwritten by LGT. What is left ought to be ancient. If we do that, what do we find?}, }
@article {pmid28352105, year = {2017}, author = {Mattila, S and Ruotsalainen, P and Ojala, V and Tuononen, T and Hiltunen, T and Jalasvuori, M}, title = {Conjugative ESBL plasmids differ in their potential to rescue susceptible bacteria via horizontal gene transfer in lethal antibiotic concentrations.}, journal = {The Journal of antibiotics}, volume = {70}, number = {6}, pages = {805-808}, pmid = {28352105}, issn = {1881-1469}, mesh = {Anti-Bacterial Agents/administration &amp; dosage/*pharmacology ; Drug Resistance, Bacterial ; Escherichia coli/*drug effects/enzymology/isolation &amp; purification ; Escherichia coli Infections/drug therapy/enzymology/microbiology ; *Gene Transfer, Horizontal ; Humans ; Plasmids ; beta-Lactamases/*genetics ; }, }
@article {pmid28350002, year = {2017}, author = {McInerney, JO and McNally, A and O'Connell, MJ}, title = {Why prokaryotes have pangenomes.}, journal = {Nature microbiology}, volume = {2}, number = {}, pages = {17040}, doi = {10.1038/nmicrobiol.2017.40}, pmid = {28350002}, issn = {2058-5276}, mesh = {Archaea/*classification/*genetics ; Bacteria/*classification/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Fitness ; *Genetic Variation ; Selection, Genetic ; }, }
@article {pmid28348879, year = {2017}, author = {Baltrus, DA and Dougherty, K and Arendt, KR and Huntemann, M and Clum, A and Pillay, M and Palaniappan, K and Varghese, N and Mikhailova, N and Stamatis, D and Reddy, TBK and Ngan, CY and Daum, C and Shapiro, N and Markowitz, V and Ivanova, N and Kyrpides, N and Woyke, T and Arnold, AE}, title = {Absence of genome reduction in diverse, facultative endohyphal bacteria.}, journal = {Microbial genomics}, volume = {3}, number = {2}, pages = {e000101}, pmid = {28348879}, issn = {2057-5858}, mesh = {Ascomycota/*physiology ; Bacteria/classification/*genetics/isolation &amp; purification ; Cupressaceae/microbiology ; Gene Transfer, Horizontal ; Genetic Variation ; *Genome, Bacterial ; Host Microbial Interactions/*genetics ; Hyphae/*physiology ; Plant Leaves/microbiology ; *Symbiosis ; Whole Genome Sequencing ; }, abstract = {Fungi interact closely with bacteria, both on the surfaces of the hyphae and within their living tissues (i.e. endohyphal bacteria, EHB). These EHB can be obligate or facultative symbionts and can mediate diverse phenotypic traits in their hosts. Although EHB have been observed in many lineages of fungi, it remains unclear how widespread and general these associations are, and whether there are unifying ecological and genomic features can be found across EHB strains as a whole. We cultured 11 bacterial strains after they emerged from the hyphae of diverse Ascomycota that were isolated as foliar endophytes of cupressaceous trees, and generated nearly complete genome sequences for all. Unlike the genomes of largely obligate EHB, the genomes of these facultative EHB resembled those of closely related strains isolated from environmental sources. Although all analysed genomes encoded structures that could be used to interact with eukaryotic hosts, pathways previously implicated in maintenance and establishment of EHB symbiosis were not universally present across all strains. Independent isolation of two nearly identical pairs of strains from different classes of fungi, coupled with recent experimental evidence, suggests horizontal transfer of EHB across endophytic hosts. Given the potential for EHB to influence fungal phenotypes, these genomes could shed light on the mechanisms of plant growth promotion or stress mitigation by fungal endophytes during the symbiotic phase, as well as degradation of plant material during the saprotrophic phase. As such, these findings contribute to the illumination of a new dimension of functional biodiversity in fungi.}, }
@article {pmid28348874, year = {2016}, author = {Page, AJ and De Silva, N and Hunt, M and Quail, MA and Parkhill, J and Harris, SR and Otto, TD and Keane, JA}, title = {Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data.}, journal = {Microbial genomics}, volume = {2}, number = {8}, pages = {e000083}, pmid = {28348874}, issn = {2057-5858}, support = {/WT_/Wellcome Trust/United Kingdom ; WT098051/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Genome, Bacterial/genetics ; Genomics/economics/*methods ; High-Throughput Nucleotide Sequencing ; Multilocus Sequence Typing ; Prokaryotic Cells ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {The rapidly reducing cost of bacterial genome sequencing has lead to its routine use in large-scale microbial analysis. Though mapping approaches can be used to find differences relative to the reference, many bacteria are subject to constant evolutionary pressures resulting in events such as the loss and gain of mobile genetic elements, horizontal gene transfer through recombination and genomic rearrangements. De novo assembly is the reconstruction of the underlying genome sequence, an essential step to understanding bacterial genome diversity. Here we present a high-throughput bacterial assembly and improvement pipeline that has been used to generate nearly 20 000 annotated draft genome assemblies in public databases. We demonstrate its performance on a public data set of 9404 genomes. We find all the genes used in multi-locus sequence typing schema present in 99.6 % of assembled genomes. When tested on low-, neutral- and high-GC organisms, more than 94 % of genes were present and completely intact. The pipeline has been proven to be scalable and robust with a wide variety of datasets without requiring human intervention. All of the software is available on GitHub under the GNU GPL open source license.}, }
@article {pmid28348867, year = {2016}, author = {Holmes, DE and Dang, Y and Walker, DJF and Lovley, DR}, title = {The electrically conductive pili of Geobacter species are a recently evolved feature for extracellular electron transfer.}, journal = {Microbial genomics}, volume = {2}, number = {8}, pages = {e000072}, pmid = {28348867}, issn = {2057-5858}, mesh = {*Electromagnetic Phenomena ; Electron Transport ; Ferric Compounds ; Fimbriae Proteins/genetics/metabolism ; Fimbriae, Bacterial/*genetics/metabolism ; Geobacter/classification/*physiology ; Phylogeny ; }, abstract = {The electrically conductive pili (e-pili) of Geobactersulfurreducens have environmental and practical significance because they can facilitate electron transfer to insoluble Fe(III) oxides; to other microbial species; and through electrically conductive biofilms. E-pili conductivity has been attributed to the truncated PilA monomer, which permits tight packing of aromatic amino acids to form a conductive path along the length of e-pili. In order to better understand the evolution and distribution of e-pili in the microbial world, type IVa PilA proteins from various Gram-negative and Gram-positive bacteria were examined with a particular emphasis on Fe(III)-respiring bacteria. E-pilin genes are primarily restricted to a tight phylogenetic group in the order Desulfuromonadales. The downstream gene in all but one of the Desulfuromonadales that possess an e-pilin gene is a gene previously annotated as 'pilA-C' that has characteristics suggesting that it may encode an outer-membrane protein. Other genes associated with pilin function are clustered with e-pilin and 'pilA-C' genes in the Desulfuromonadales. In contrast, in the few bacteria outside the Desulfuromonadales that contain e-pilin genes, the other genes required for pilin function may have been acquired through horizontal gene transfer. Of the 95 known Fe(III)-reducing micro-organisms for which genomes are available, 80 % lack e-pilin genes, suggesting that e-pili are just one of several mechanisms involved in extracellular electron transport. These studies provide insight into where and when e-pili are likely to contribute to extracellular electron transport processes that are biogeochemically important and involved in bioenergy conversions.}, }
@article {pmid28348864, year = {2016}, author = {Spencer-Smith, R and Roberts, S and Gurung, N and Snyder, LAS}, title = {DNA uptake sequences in Neisseria gonorrhoeae as intrinsic transcriptional terminators and markers of horizontal gene transfer.}, journal = {Microbial genomics}, volume = {2}, number = {8}, pages = {e000069}, pmid = {28348864}, issn = {2057-5858}, mesh = {DNA, Bacterial/genetics/*metabolism ; Gene Transfer, Horizontal/*genetics ; Neisseria gonorrhoeae/*genetics ; Repetitive Sequences, Nucleic Acid/genetics ; Sequence Inversion/genetics ; Terminator Regions, Genetic/*genetics ; Transcription, Genetic/genetics ; }, abstract = {DNA uptake sequences are widespread throughout the Neisseria gonorrhoeae genome. These short, conserved sequences facilitate the exchange of endogenous DNA between members of the genus Neisseria. Often the DNA uptake sequences are present as inverted repeats that are able to form hairpin structures. It has been suggested previously that DNA uptake sequence inverted repeats present 3' of genes play a role in rho-independent termination and attenuation. However, there is conflicting experimental evidence to support this role. The aim of this study was to determine the role of DNA uptake sequences in transcriptional termination. Both bioinformatics predictions, conducted using TransTermHP, and experimental evidence, from RNA-seq data, were used to determine which inverted repeat DNA uptake sequences are transcriptional terminators and in which direction. Here we show that DNA uptake sequences in the inverted repeat configuration occur in N. gonorrhoeae both where the DNA uptake sequence precedes the inverted version of the sequence and also, albeit less frequently, in reverse order. Due to their symmetrical configuration, inverted repeat DNA uptake sequences can potentially act as bi-directional terminators, therefore affecting transcription on both DNA strands. This work also provides evidence that gaps in DNA uptake sequence density in the gonococcal genome coincide with areas of DNA that are foreign in origin, such as prophage. This study differentiates for the first time, to our knowledge, between DNA uptake sequences that form intrinsic transcriptional terminators and those that do not, providing characteristic features within the flanking inverted repeat that can be identified.}, }
@article {pmid28348844, year = {2016}, author = {Holt, K and Kenyon, JJ and Hamidian, M and Schultz, MB and Pickard, DJ and Dougan, G and Hall, R}, title = {Five decades of genome evolution in the globally distributed, extensively antibiotic-resistant Acinetobacter baumannii global clone 1.}, journal = {Microbial genomics}, volume = {2}, number = {2}, pages = {e000052}, pmid = {28348844}, issn = {2057-5858}, support = {//Wellcome Trust/United Kingdom ; 098051//Wellcome Trust/United Kingdom ; }, mesh = {Acinetobacter baumannii/*genetics ; DNA Transposable Elements/genetics ; Drug Resistance, Bacterial/*genetics ; *Evolution, Molecular ; Genome, Bacterial/*genetics ; Plasmids/genetics ; }, abstract = {The majority of Acinetobacter baumannii isolates that are multiply, extensively and pan-antibiotic resistant belong to two globally disseminated clones, GC1 and GC2, that were first noticed in the 1970s. Here, we investigated microevolution and phylodynamics within GC1 via analysis of 45 whole-genome sequences, including 23 sequenced for this study. The most recent common ancestor of GC1 arose around 1960 and later diverged into two phylogenetically distinct lineages. In the 1970s, the main lineage acquired the AbaR resistance island, conferring resistance to older antibiotics, via a horizontal gene transfer event. We estimate a mutation rate of ∼5 SNPs genome[- 1] year[- 1] and detected extensive recombination within GC1 genomes, introducing nucleotide diversity into the population at >20 times the substitution rate (the ratio of SNPs introduced by recombination compared with mutation was 22). The recombination events were non-randomly distributed in the genome and created significant diversity within loci encoding outer surface molecules (including the capsular polysaccharide, the outer core lipooligosaccharide and the outer membrane protein CarO), and spread antimicrobial resistance-conferring mutations affecting the gyrA and parC genes and insertion sequence insertions activating the ampC gene. Both GC1 lineages accumulated resistance to newer antibiotics through various genetic mechanisms, including the acquisition of plasmids and transposons or mutations in chromosomal genes. Our data show that GC1 has diversified into multiple successful extensively antibiotic-resistant subclones that differ in their surface structures. This has important implications for all avenues of control, including epidemiological tracking, antimicrobial therapy and vaccination.}, }
@article {pmid28348054, year = {2017}, author = {Tseng, CW and Chiu, CJ and Kanci, A and Citti, C and Rosengarten, R and Browning, GF and Markham, PF}, title = {The oppD Gene and Putative Peptidase Genes May Be Required for Virulence in Mycoplasma gallisepticum.}, journal = {Infection and immunity}, volume = {85}, number = {6}, pages = {}, pmid = {28348054}, issn = {1098-5522}, mesh = {Animals ; Bacterial Proteins/genetics/*metabolism ; Chickens/*microbiology ; Mutagenesis, Insertional/*genetics ; Mycoplasma Infections/genetics/microbiology ; Mycoplasma gallisepticum/*genetics/*pathogenicity ; Poultry Diseases/genetics/*microbiology ; Virulence/genetics ; Virulence Factors/genetics ; }, abstract = {Relatively few virulence genes have been identified in pathogenic mycoplasmas, so we used signature-tagged mutagenesis to identify mutants of the avian pathogen Mycoplasma gallisepticum with a reduced capacity to persist in vivo and compared the levels of virulence of selected mutants in experimentally infected chickens. Four mutants had insertions in one of the two incomplete oppABCDF operons, and a further three had insertions in distinct hypothetical genes, two containing peptidase motifs and one containing a member of a gene family. The three hypothetical gene mutants and the two with insertions in oppD1 were used to infect chickens, and all five were shown to have a reduced capacity to induce respiratory tract lesions. One oppD1 mutant and the MGA_1102 and MGA_1079 mutants had a greatly reduced capacity to persist in the respiratory tract and to induce systemic antibody responses against M. gallisepticum The other oppD1 mutant and the MGA_0588 mutant had less capacity than the wild type to persist in the respiratory tract but did elicit systemic antibody responses. Although M. gallisepticum carries two incomplete opp operons, one of which has been acquired by horizontal gene transfer, our results suggest that one of the copies of oppD may be required for full expression of virulence. We have also shown that three hypothetical genes, two of which encode putative peptidases, may be required for full expression of virulence in M. gallisepticum. None of these genes has previously been shown to influence virulence in pathogenic mycoplasmas.}, }
@article {pmid28347342, year = {2017}, author = {Guo, FB and Xiong, L and Zhang, KY and Dong, C and Zhang, FZ and Woo, PC}, title = {Identification and analysis of genomic islands in Burkholderia cenocepacia AU 1054 with emphasis on pathogenicity islands.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {73}, pmid = {28347342}, issn = {1471-2180}, mesh = {A549 Cells ; Bacterial Adhesion ; Bacterial Proteins/genetics ; Base Composition ; Burkholderia Infections/microbiology ; Burkholderia cenocepacia/*genetics/growth &amp; development/pathogenicity ; Cell Culture Techniques ; Colony Count, Microbial ; Computational Biology/methods ; DNA, Bacterial ; Gene Deletion ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Genome, Bacterial/genetics ; Genomic Islands/*genetics ; *Genomics ; Humans ; Virulence Factors/*genetics/*isolation &amp; purification ; }, abstract = {BACKGROUND: Genomic islands (GIs) are genomic regions that reveal evidence of horizontal DNA transfer. They can code for many functions and may augment a bacterium's adaptation to its host or environment. GIs have been identified in strain J2315 of Burkholderia cenocepacia, whereas in strain AU 1054 there has been no published works on such regions according to our text mining and keyword search in Medline.<br><br>RESULTS: In this study, we identified 21 GIs in AU 1054 by combining two computational tools. Feature analyses suggested that the predictions are highly reliable and hence illustrated the advantage of joint predictions by two independent methods. Based on putative virulence factors, four GIs were further identified as pathogenicity islands (PAIs). Through experiments of gene deletion mutants in live bacteria, two putative PAIs were confirmed, and the virulence factors involved were identified as lipA and copR. The importance of the genes lipA (from PAI 1) and copR (from PAI 2) for bacterial invasion and replication indicates that they are required for the invasive properties of B. cenocepacia and may function as virulence determinants for bacterial pathogenesis and host infection.<br><br>CONCLUSIONS: This approach of in silico prediction of GIs and subsequent identification of potential virulence factors in the putative island regions with final validation using wet experiments could be used as an effective strategy to rapidly discover novel virulence factors in other bacterial species and strains.}, }
@article {pmid28346467, year = {2017}, author = {Li, G and Lu, S and Shen, M and Le, S and Shen, W and Tan, Y and Wang, J and Zhao, X and Zhao, Y and Gong, Y and Yang, Y and Zhu, H and Hu, F and Li, M}, title = {Characterization and interstrain transfer of prophage pp3 of Pseudomonas aeruginosa.}, journal = {PloS one}, volume = {12}, number = {3}, pages = {e0174429}, pmid = {28346467}, issn = {1932-6203}, mesh = {*Gene Transfer, Horizontal ; Integrases/*genetics ; Prophages/*genetics ; Pseudomonas aeruginosa/*genetics ; Recombination, Genetic ; }, abstract = {Prophages are major contributors to horizontal gene transfer and drive the evolution and diversification of bacteria. Here, we describe the characterization of a prophage element designated pp3 in the clinical Pseudomonas aeruginosa isolate PA1. pp3 spontaneously excises from the PA1 genome and circularizes at a very high frequency of 25%. pp3 is likely to be a defective prophage due to its inability to form plaques on P. aeruginosa indicator strains, and no phage particles could be detected in PA1 supernatants. The pp3-encoded integrase is essential for excision by mediating site-specific recombination at the 26-bp attachment sequence. Using a filter mating experiment, we demonstrated that pp3 can transfer into P. aeruginosa recipient strains that do not possess this element naturally. Upon transfer, pp3 integrates into the same attachment site as in PA1 and maintains the ability to excise and circularize. Furthermore, pp3 significantly promotes biofilm formation in the recipient. Sequence alignment reveals that the 26-bp attachment site recognized by pp3 is conserved in all P. aeruginosa strains sequenced to date, making it possible that pp3 could be extensively disseminated in P. aeruginosa. This work improves our understanding of the ways in which prophages influence bacterial behavior and evolution.}, }
@article {pmid28346388, year = {2017}, author = {Iqubal, MA and Sharma, R and Jheeta, S and Kamaluddin, }, title = {Thermal Condensation of Glycine and Alanine on Metal Ferrite Surface: Primitive Peptide Bond Formation Scenario.}, journal = {Life (Basel, Switzerland)}, volume = {7}, number = {2}, pages = {}, pmid = {28346388}, issn = {2075-1729}, abstract = {The amino acid condensation reaction on a heterogeneous mineral surface has been regarded as one of the important pathways for peptide bond formation. Keeping this in view, we have studied the oligomerization of the simple amino acids, glycine and alanine, on nickel ferrite (NiFe2O4), cobalt ferrite (CoFe2O4), copper ferrite (CuFe2O4), zinc ferrite (ZnFe2O4), and manganese ferrite (MnFe2O4) nanoparticles surfaces, in the temperature range from 50-120 °C for 1-35 days, without applying any wetting/drying cycles. Among the metal ferrites tested for their catalytic activity, NiFe2O4 produced the highest yield of products by oligomerizing glycine to the trimer level and alanine to the dimer level, whereas MnFe2O4 was the least efficient catalyst, producing the lowest yield of products, as well as shorter oligomers of amino acids under the same set of experimental conditions. It produced primarily diketopiperazine (Ala) with a trace amount of alanine dimer from alanine condensation, while glycine was oligomerized to the dimer level. The trend in product formation is in accordance with the surface area of the minerals used. A temperature as low as 50 °C can even favor peptide bond formation in the present study, which is important in the sense that the condensation process is highly feasible without any sort of localized heat that may originate from volcanoes or hydrothermal vents. However, at a high temperature of 120 °C, anhydrides of glycine and alanine formation are favored, while the optimum temperature for the highest yield of product formation was found to be 90 °C.}, }
@article {pmid28346361, year = {2017}, author = {Andrews, M and Andrews, ME}, title = {Specificity in Legume-Rhizobia Symbioses.}, journal = {International journal of molecular sciences}, volume = {18}, number = {4}, pages = {}, pmid = {28346361}, issn = {1422-0067}, mesh = {Bacterial Proteins/classification/genetics ; Bradyrhizobium/classification/genetics/physiology ; Cupriavidus/classification/physiology ; Fabaceae/metabolism/*microbiology ; Phylogeny ; Plant Roots/metabolism/microbiology ; RNA, Ribosomal, 16S/genetics/metabolism ; Rhizobium/classification/genetics/*physiology ; *Symbiosis ; }, abstract = {Most species in the Leguminosae (legume family) can fix atmospheric nitrogen (N2) via symbiotic bacteria (rhizobia) in root nodules. Here, the literature on legume-rhizobia symbioses in field soils was reviewed and genotypically characterised rhizobia related to the taxonomy of the legumes from which they were isolated. The Leguminosae was divided into three sub-families, the Caesalpinioideae, Mimosoideae and Papilionoideae. Bradyrhizobium spp. were the exclusive rhizobial symbionts of species in the Caesalpinioideae, but data are limited. Generally, a range of rhizobia genera nodulated legume species across the two Mimosoideae tribes Ingeae and Mimoseae, but Mimosa spp. show specificity towards Burkholderia in central and southern Brazil, Rhizobium/Ensifer in central Mexico and Cupriavidus in southern Uruguay. These specific symbioses are likely to be at least in part related to the relative occurrence of the potential symbionts in soils of the different regions. Generally, Papilionoideae species were promiscuous in relation to rhizobial symbionts, but specificity for rhizobial genus appears to hold at the tribe level for the Fabeae (Rhizobium), the genus level for Cytisus (Bradyrhizobium), Lupinus (Bradyrhizobium) and the New Zealand native Sophora spp. (Mesorhizobium) and species level for Cicer arietinum (Mesorhizobium), Listia bainesii (Methylobacterium) and Listia angolensis (Microvirga). Specificity for rhizobial species/symbiovar appears to hold for Galega officinalis (Neorhizobium galegeae sv. officinalis), Galega orientalis (Neorhizobium galegeae sv. orientalis), Hedysarum coronarium (Rhizobium sullae), Medicago laciniata (Ensifer meliloti sv. medicaginis), Medicago rigiduloides (Ensifer meliloti sv. rigiduloides) and Trifolium ambiguum (Rhizobium leguminosarum sv. trifolii). Lateral gene transfer of specific symbiosis genes within rhizobial genera is an important mechanism allowing legumes to form symbioses with rhizobia adapted to particular soils. Strain-specific legume rhizobia symbioses can develop in particular habitats.}, }
@article {pmid28345639, year = {2017}, author = {Fedrizzi, T and Meehan, CJ and Grottola, A and Giacobazzi, E and Fregni Serpini, G and Tagliazucchi, S and Fabio, A and Bettua, C and Bertorelli, R and De Sanctis, V and Rumpianesi, F and Pecorari, M and Jousson, O and Tortoli, E and Segata, N}, title = {Genomic characterization of Nontuberculous Mycobacteria.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {45258}, pmid = {28345639}, issn = {2045-2322}, mesh = {Chromosome Mapping/*methods ; Gene Transfer, Horizontal ; Genetic Variation ; Genome, Bacterial ; Humans ; Molecular Sequence Annotation ; Mycobacterium Infections, Nontuberculous/microbiology ; Nontuberculous Mycobacteria/classification/*genetics ; Open Reading Frames ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {Mycobacterium tuberculosis and Mycobacterium leprae have remained, for many years, the primary species of the genus Mycobacterium of clinical and microbiological interest. The other members of the genus, referred to as nontuberculous mycobacteria (NTM), have long been underinvestigated. In the last decades, however, the number of reports linking various NTM species with human diseases has steadily increased and treatment difficulties have emerged. Despite the availability of whole genome sequencing technologies, limited effort has been devoted to the genetic characterization of NTM species. As a consequence, the taxonomic and phylogenetic structure of the genus remains unsettled and genomic information is lacking to support the identification of these organisms in a clinical setting. In this work, we widen the knowledge of NTMs by reconstructing and analyzing the genomes of 41 previously uncharacterized NTM species. We provide the first comprehensive characterization of the genomic diversity of NTMs and open new venues for the clinical identification of opportunistic pathogens from this genus.}, }
@article {pmid28342123, year = {2017}, author = {Paridaens, H and Coussement, J and Argudín, MA and Delaere, B and Huang, TD and Glupczynski, Y and Denis, O}, title = {Clinical case of cfr-positive MRSA CC398 in Belgium.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {36}, number = {8}, pages = {1527-1529}, pmid = {28342123}, issn = {1435-4373}, mesh = {Aged ; Agricultural Workers' Diseases/drug therapy/*microbiology ; Animals ; Anti-Bacterial Agents/adverse effects/pharmacology/therapeutic use ; Bacterial Proteins/drug effects/*genetics ; Belgium ; Drug Resistance, Multiple, Bacterial ; Gene Transfer, Horizontal ; Humans ; Male ; Methicillin-Resistant Staphylococcus aureus/drug effects/genetics/*isolation &amp; purification ; Microbial Sensitivity Tests ; Postoperative Complications/drug therapy/microbiology ; Soft Tissue Infections/drug therapy/microbiology ; Staphylococcal Infections/drug therapy/*microbiology ; Staphylococcal Skin Infections/drug therapy/microbiology ; Zoonoses/microbiology ; }, }
@article {pmid28338786, year = {2017}, author = {Murray, S and Pascoe, B and Méric, G and Mageiros, L and Yahara, K and Hitchings, MD and Friedmann, Y and Wilkinson, TS and Gormley, FJ and Mack, D and Bray, JE and Lamble, S and Bowden, R and Jolley, KA and Maiden, MCJ and Wendlandt, S and Schwarz, S and Corander, J and Fitzgerald, JR and Sheppard, SK}, title = {Recombination-Mediated Host Adaptation by Avian Staphylococcus aureus.}, journal = {Genome biology and evolution}, volume = {9}, number = {4}, pages = {830-842}, pmid = {28338786}, issn = {1759-6653}, support = {BB/I013873/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/I02464X/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; G0801929/MRC_/Medical Research Council/United Kingdom ; MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; BB/K00638X/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; //Wellcome Trust/United Kingdom ; }, mesh = {Adaptation, Physiological/*genetics ; Animals ; Chickens/genetics/microbiology ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial ; Genotype ; Humans ; Poultry Diseases/*genetics/microbiology/transmission ; Species Specificity ; Staphylococcal Infections/*genetics/microbiology/transmission ; Staphylococcus aureus/*genetics/pathogenicity ; }, abstract = {Staphylococcus aureus are globally disseminated among farmed chickens causing skeletal muscle infections, dermatitis, and septicaemia. The emergence of poultry-associated lineages has involved zoonotic transmission from humans to chickens but questions remain about the specific adaptations that promote proliferation of chicken pathogens. We characterized genetic variation in a population of genome-sequenced S. aureus isolates of poultry and human origin. Genealogical analysis identified a dominant poultry-associated sequence cluster within the CC5 clonal complex. Poultry and human CC5 isolates were significantly distinct from each other and more recombination events were detected in the poultry isolates. We identified 44 recombination events in 33 genes along the branch extending to the poultry-specific CC5 cluster, and 47 genes were found more often in CC5 poultry isolates compared with those from humans. Many of these gene sequences were common in chicken isolates from other clonal complexes suggesting horizontal gene transfer among poultry associated lineages. Consistent with functional predictions for putative poultry-associated genes, poultry isolates showed enhanced growth at 42 °C and greater erythrocyte lysis on chicken blood agar in comparison with human isolates. By combining phenotype information with evolutionary analyses of staphylococcal genomes, we provide evidence of adaptation, following a human-to-poultry host transition. This has important implications for the emergence and dissemination of new pathogenic clones associated with modern agriculture.}, }
@article {pmid28335474, year = {2017}, author = {Nissimov, JI and Pagarete, A and Ma, F and Cody, S and Dunigan, DD and Kimmance, SA and Allen, MJ}, title = {Coccolithoviruses: A Review of Cross-Kingdom Genomic Thievery and Metabolic Thuggery.}, journal = {Viruses}, volume = {9}, number = {3}, pages = {}, pmid = {28335474}, issn = {1999-4915}, support = {P30 GM103509/GM/NIGMS NIH HHS/United States ; }, mesh = {Ecosystem ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Variation ; Genome Size ; Genome, Viral ; Haptophyta/virology ; Phycodnaviridae/classification/*genetics/physiology ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Coccolithoviruses (Phycodnaviridae) infect and lyse the most ubiquitous and successful coccolithophorid in modern oceans, Emiliania huxleyi. So far, the genomes of 13 of these giant lytic viruses (i.e., Emiliania huxleyi viruses-EhVs) have been sequenced, assembled, and annotated. Here, we performed an in-depth comparison of their genomes to try and contextualize the ecological and evolutionary traits of these viruses. The genomes of these EhVs have from 444 to 548 coding sequences (CDSs). Presence/absence analysis of CDSs identified putative genes with particular ecological significance, namely sialidase, phosphate permease, and sphingolipid biosynthesis. The viruses clustered into distinct clades, based on their DNA polymerase gene as well as full genome comparisons. We discuss the use of such clustering and suggest that a gene-by-gene investigation approach may be more useful when the goal is to reveal differences related to functionally important genes. A multi domain "Best BLAST hit" analysis revealed that 84% of the EhV genes have closer similarities to the domain Eukarya. However, 16% of the EhV CDSs were very similar to bacterial genes, contributing to the idea that a significant portion of the gene flow in the planktonic world inter-crosses the domains of life.}, }
@article {pmid28334919, year = {2017}, author = {Liu, P and Wu, Z and Xue, H and Zhao, X}, title = {Antibiotics trigger initiation of SCCmec transfer by inducing SOS responses.}, journal = {Nucleic acids research}, volume = {45}, number = {7}, pages = {3944-3952}, pmid = {28334919}, issn = {1362-4962}, mesh = {Anti-Bacterial Agents/toxicity ; Bacterial Proteins/metabolism ; Binding Sites ; DNA Damage ; *DNA Transposable Elements ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Methicillin Resistance/*genetics ; Promoter Regions, Genetic ; Rec A Recombinases/metabolism ; Recombinases/biosynthesis/*genetics ; *SOS Response, Genetics ; Serine Endopeptidases/metabolism ; Staphylococcus/drug effects/*genetics/metabolism ; }, abstract = {The rise of antimicrobial resistance limits therapeutic options for infections by methicillin-resistant staphylococci. The staphylococcal cassette chromosome mec (SCCmec) is a mobile genetic element as the only carrier of the methicillin-resistance determinants, the mecA or mecC gene. The use of antibiotics increases the spread of antibiotic resistance, but the mechanism by which antibiotics promote horizontal dissemination of SCCmec is largely unknown. In this study, we demonstrate that many antibiotics, including β-lactams, can induce the expression of ccrC1 and SCCmec excision from the bacterial chromosome. In particular, three widely used antibiotics targeting DNA replication and repair (sulfamethoxazole, ciprofloxacin and trimethoprim) induced higher levels of ccrC1 expression and higher rates of SCCmec excision even at low concentrations (1/8 × minimum inhibitory concentration). LexA was identified as a repressor of ccrC1 and ccrAB by binding to the promoter regions of ccrC1 and ccrAB. The activation of RecA after antibiotic induction alleviated the repression by LexA and increased the expression of ccrC1 or ccrAB, consequently increasing the excision frequency of the SCCmec for SCCmec transfer. These findings lead us to propose a mechanism by which antimicrobial agents can promote horizontal gene transfer of the mecA gene and facilitate the spread of methicillin resistance.}, }
@article {pmid28334205, year = {2017}, author = {Aijaz, I and Koudelka, GB}, title = {Tetrahymena phagocytic vesicles as ecological micro-niches of phage transfer.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {4}, pages = {}, doi = {10.1093/femsec/fix030}, pmid = {28334205}, issn = {1574-6941}, mesh = {Animals ; Bacteria/genetics ; Bacteriophages/genetics/*physiology ; Ecology ; Eukaryota ; Fresh Water ; Phagocytosis ; Tetrahymena thermophila ; }, abstract = {The microbial communities in natural environments such as soil, pond water, or animal rumens are composed of a diverse mixture of bacteria and protozoa including ciliates or flagellates. In such microbiomes, a major source of bacterial mortality is grazing by phagocytic protists. Many protists are omnivorous heterotrophs, feeding on a range of different bacterial species. Due to this indiscriminate feeding, different bacterial species can assemble together in the same phagocytic vesicles where they can potentially exchange genetic material. Here we show that Tetrahymena thermophila imports and accumulates phage donor and recipient bacterial strains in its phagocytic vesicles and that under laboratory conditions the ingested bacteria remain viable for ≥2 h. Prophages in the ingested bacteria induce immediately after ingestion, and the released phages are concentrated in the phagocytic vesicles of the ciliate. These phages retain their ability to infect phage-susceptible bacterial strains. As a consequence of being confined within the phagosome, the frequency of lysogen formation in these vesicles increases 6-fold as compared with the bulk solution. Collectively, these observations suggest that T. thermophila aids in dissemination of bacteriophages by accumulating susceptible bacteria and phages in their phagocytic vesicles.}, }
@article {pmid28333270, year = {2017}, author = {Hughes, D and Andersson, DI}, title = {Environmental and genetic modulation of the phenotypic expression of antibiotic resistance.}, journal = {FEMS microbiology reviews}, volume = {41}, number = {3}, pages = {374-391}, pmid = {28333270}, issn = {1574-6976}, mesh = {Adaptation, Physiological/*physiology ; Anti-Bacterial Agents/*pharmacology ; *Bacteria/drug effects/genetics/growth &amp; development ; Biofilms/*drug effects/growth &amp; development ; Drug Resistance, Multiple, Bacterial/*genetics ; Environment ; Gene Transfer, Horizontal/genetics ; Genotype ; Humans ; Mutation ; Phenotype ; }, abstract = {Antibiotic resistance can be acquired by mutation or horizontal transfer of a resistance gene, and generally an acquired mechanism results in a predictable increase in phenotypic resistance. However, recent findings suggest that the environment and/or the genetic context can modify the phenotypic expression of specific resistance genes/mutations. An important implication from these findings is that a given genotype does not always result in the expected phenotype. This dissociation of genotype and phenotype has important consequences for clinical bacteriology and for our ability to predict resistance phenotypes from genetics and DNA sequences. A related problem concerns the degree to which the genes/mutations currently identified in vitro can fully explain the in vivo resistance phenotype, or whether there is a significant additional amount of presently unknown mutations/genes (genetic 'dark matter') that could contribute to resistance in clinical isolates. Finally, a very important question is whether/how we can identify the genetic features that contribute to making a successful pathogen, and predict why some resistant clones are very successful and spread globally? In this review, we describe different environmental and genetic factors that influence phenotypic expression of antibiotic resistance genes/mutations and how this information is needed to understand why particular resistant clones spread worldwide and to what extent we can use DNA sequences to predict evolutionary success.}, }
@article {pmid28333234, year = {2017}, author = {Tanner, WD and Atkinson, RM and Goel, RK and Toleman, MA and Benson, LS and Porucznik, CA and VanDerslice, JA}, title = {Horizontal transfer of the blaNDM-1 gene to Pseudomonas aeruginosa and Acinetobacter baumannii in biofilms.}, journal = {FEMS microbiology letters}, volume = {364}, number = {8}, pages = {}, doi = {10.1093/femsle/fnx048}, pmid = {28333234}, issn = {1574-6968}, mesh = {Acinetobacter baumannii/drug effects/*genetics/physiology ; Anti-Bacterial Agents/pharmacology ; *Biofilms ; *Conjugation, Genetic ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/genetics ; *Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; Plasmids ; Pseudomonas aeruginosa/drug effects/*genetics/physiology ; beta-Lactamases/*genetics ; }, abstract = {Horizontal gene transfer has contributed to the global spread of the blaNDM-1 gene. Multiple studies have demonstrated plasmid transfer of blaNDM-1 between Gram-negative bacteria, primarily Enterobacteriaceae species, but conjugational transfer of natural blaNDM-1 plasmids from Enterobacteriaceae into Pseudomonas aeruginosa and Acinetobacter baumannii has not previously been shown. As P. aeruginosa and A. baumannii are both typically strong biofilm formers, transfer of natural blaNDM-1 plasmids could potentially occur more readily in this environment. To determine whether natural blaNDM-1 plasmids could transfer to P. aeruginosa or A. baumannii in biofilms, three clinical and environmental Enterobacteriaceae strains carrying NDM-1-encoding plasmids of different incompatibility types were mated with E. coli J53, producing E. coli J53- blaNDM-1 transconjugants. Subsequently, dual-species biofilms were created using the E. coli J53 transconjugants as plasmid donors and either P. aeruginosa or A. baumannii as recipients. Biofilm transfer of NDM-encoding plasmids to P. aeruginosa and A. baumannii was successful from one and two E. coli J53- blaNDM-1 transconjugants, respectively. This demonstrates the potential for the spread of blaNDM-1, genes to P. aeruginosa and A. baumannii in clinical and environmental settings.}, }
@article {pmid28333184, year = {2017}, author = {Alonso, CA and Michael, GB and Li, J and Somalo, S and Simón, C and Wang, Y and Kaspar, H and Kadlec, K and Torres, C and Schwarz, S}, title = {Analysis of blaSHV-12-carrying Escherichia coli clones and plasmids from human, animal and food sources.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {72}, number = {6}, pages = {1589-1596}, doi = {10.1093/jac/dkx024}, pmid = {28333184}, issn = {1460-2091}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Chickens/microbiology ; Chloramphenicol/pharmacology ; Dogs/microbiology ; Escherichia coli/drug effects/enzymology/*genetics/isolation &amp; purification ; *Food Microbiology ; Gene Transfer, Horizontal ; Genes, MDR ; Humans ; Integrons ; Meat/microbiology ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; *Plasmids/isolation &amp; purification ; Replicon ; Sequence Analysis, DNA ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: This study aimed at characterizing 23 Escherichia coli isolates from various sources and their respective bla SHV-12 -carrying plasmids and sequencing one of these plasmids completely.<br><br>METHODS: Isolates were typed by XbaI-PFGE, MLST and PCR-based phylotyping. Transformed bla SHV-12 -carrying plasmids were examined by replicon typing, S1-nuclease, conjugation, EcoRI-HindIII-BamHI digests and plasmid MLST. Co-located resistance genes and integrons as well as the bla SHV-12 genetic environment were analysed by PCR and sequencing. One IncI1 plasmid was sequenced completely using HiSeq 2500 and gap closure by PCRs and Sanger sequencing.<br><br>RESULTS: Among the 23 SHV-12-positive E. coli , some isolates from different sources showed the same characteristics: ST23/phylogroup A (human, dog, livestock), ST57/D (wild bird, chicken meat) and ST117/D (chicken meat, chicken). All bla SHV-12 genes were horizontally transferable via 30-120&#x2009;kb plasmids of incompatibility groups IncI1 (n &#x2009;=&#x2009;17), IncK (n &#x2009;=&#x2009;3), IncF (n &#x2009;=&#x2009;1), IncX3 (n &#x2009;=&#x2009;1) and a non-typeable plasmid. IncK plasmids, indistinguishable in size and restriction patterns, were found in isolates from different sources (ST57/D, meat; ST131/B2, meat; ST57/B1, dog). The IncI1- bla SHV-12 -carrying plasmids were mostly assigned to plasmid ST (pST) 26 and pST3. Three plasmids showed novel pSTs (pST214, pST215). The majority of the IncI1 transformants exhibited resistance to &#x3b2;-lactams, chloramphenicol and streptomycin (in relation with a class 1 integron containing an estX - psp - aadA2 - cmlA1 - aadA1 - qacI gene cassette array), and to tetracycline. A novel bla SHV-12 environment was detected and whole plasmid sequencing revealed a Tn 21 -derived- bla SHV12 -&#x394;Tn 1721 resistance complex.<br><br>CONCLUSIONS: Results from this study suggest that the dissemination of bla SHV-12 genes occurs by vertical (clonal) and horizontal transfer, the latter mainly mediated through IncI1 multidrug-resistance plasmids.}, }
@article {pmid28328284, year = {2017}, author = {Langereis, JD and de Jonge, MI}, title = {Non-encapsulated Streptococcus pneumoniae, vaccination as a measure to interfere with horizontal gene transfer.}, journal = {Virulence}, volume = {8}, number = {6}, pages = {637-639}, pmid = {28328284}, issn = {2150-5608}, mesh = {Anti-Bacterial Agents ; *Gene Transfer, Horizontal ; Humans ; *Streptococcus pneumoniae ; Vaccination ; }, }
@article {pmid28327641, year = {2017}, author = {Kirchberger, PC and Unterweger, D and Provenzano, D and Pukatzki, S and Boucher, Y}, title = {Sequential displacement of Type VI Secretion System effector genes leads to evolution of diverse immunity gene arrays in Vibrio cholerae.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {45133}, pmid = {28327641}, issn = {2045-2322}, mesh = {Computational Biology/methods ; Gene Transfer, Horizontal ; Genome, Bacterial ; Genomics/methods ; Immunity/*genetics ; Molecular Sequence Annotation ; Phylogeny ; Recombination, Genetic ; Type VI Secretion Systems/*genetics/*immunology ; Vibrio cholerae/classification/*genetics/*immunology ; }, abstract = {Type VI secretion systems (T6SS) enable bacteria to engage neighboring cells in contact-dependent competition. In Vibrio cholerae, three chromosomal clusters each encode a pair of effector and immunity genes downstream of those encoding the T6SS structural machinery for effector delivery. Different combinations of effector-immunity proteins lead to competition between strains of V. cholerae, which are thought to be protected only from the toxicity of their own effectors. Screening of all publically available V. cholerae genomes showed that numerous strains possess long arrays of orphan immunity genes encoded in the 3' region of their T6SS clusters. Phylogenetic analysis reveals that these genes are highly similar to those found in the effector-immunity pairs of other strains, indicating acquisition by horizontal gene transfer. Extensive genomic comparisons also suggest that successive addition of effector-immunity gene pairs replaces ancestral effectors, yet retains the cognate immunity genes. The retention of old immunity genes perhaps provides protection against nearby kin bacteria in which the old effector was not replaced. This mechanism, combined with frequent homologous recombination, is likely responsible for the high diversity of T6SS effector-immunity gene profiles observed for V. cholerae and closely related species.}, }
@article {pmid28327522, year = {2017}, author = {Leigh, B and Karrer, C and Cannon, JP and Breitbart, M and Dishaw, LJ}, title = {Isolation and Characterization of a Shewanella Phage-Host System from the Gut of the Tunicate, Ciona intestinalis.}, journal = {Viruses}, volume = {9}, number = {3}, pages = {}, pmid = {28327522}, issn = {1999-4915}, mesh = {Animals ; Bacteriolysis ; Bacteriophages/*growth &amp; development/*isolation &amp; purification ; Biofilms/growth &amp; development ; Ciona intestinalis/*microbiology/*virology ; Intestines/microbiology/virology ; Shewanella/*isolation &amp; purification/physiology/*virology ; }, abstract = {Outnumbering all other biological entities on earth, bacteriophages (phages) play critical roles in structuring microbial communities through bacterial infection and subsequent lysis, as well as through horizontal gene transfer. While numerous studies have examined the effects of phages on free-living bacterial cells, much less is known regarding the role of phage infection in host-associated biofilms, which help to stabilize adherent microbial communities. Here we report the cultivation and characterization of a novel strain of Shewanella fidelis from the gut of the marine tunicate Ciona intestinalis, inducible prophages from the S. fidelis genome, and a strain-specific lytic phage recovered from surrounding seawater. In vitro biofilm assays demonstrated that lytic phage infection affects biofilm formation in a process likely influenced by the accumulation and integration of the extracellular DNA released during cell lysis, similar to the mechanism that has been previously shown for prophage induction.}, }
@article {pmid28324738, year = {2017}, author = {Moreira, D and López-García, P}, title = {Protist Evolution: Stealing Genes to Gut It Out.}, journal = {Current biology : CB}, volume = {27}, number = {6}, pages = {R223-R225}, pmid = {28324738}, issn = {1879-0445}, support = {322669/ERC_/European Research Council/International ; }, mesh = {Animals ; Blastocystis/*genetics ; Eukaryota/*genetics ; Gene Transfer, Horizontal ; Humans ; *Parasites ; Phylogeny ; Theft ; }, abstract = {The amount and evolutionary impact of horizontal gene transfer in eukaryotes remain contentious issues. A new phylogenomic study suggests that gene transfer from prokaryotes has contributed significantly to the adaptation and metabolic evolution of Blastocystis, the most widespread human gut eukaryotic parasite.}, }
@article {pmid28323299, year = {2017}, author = {Esteves-Ferreira, AA and Cavalcanti, JHF and Vaz, MGMV and Alvarenga, LV and Nunes-Nesi, A and Araújo, WL}, title = {Cyanobacterial nitrogenases: phylogenetic diversity, regulation and functional predictions.}, journal = {Genetics and molecular biology}, volume = {40}, number = {1 suppl 1}, pages = {261-275}, pmid = {28323299}, issn = {1415-4757}, abstract = {Cyanobacteria is a remarkable group of prokaryotic photosynthetic microorganisms, with several genera capable of fixing atmospheric nitrogen (N2) and presenting a wide range of morphologies. Although the nitrogenase complex is not present in all cyanobacterial taxa, it is spread across several cyanobacterial strains. The nitrogenase complex has also a high theoretical potential for biofuel production, since H2 is a by-product produced during N2 fixation. In this review we discuss the significance of a relatively wide variety of cell morphologies and metabolic strategies that allow spatial and temporal separation of N2 fixation from photosynthesis in cyanobacteria. Phylogenetic reconstructions based on 16S rRNA and nifD gene sequences shed light on the evolutionary history of the two genes. Our results demonstrated that (i) sequences of genes involved in nitrogen fixation (nifD) from several morphologically distinct strains of cyanobacteria are grouped in similarity with their morphology classification and phylogeny, and (ii) nifD genes from heterocytous strains share a common ancestor. By using this data we also discuss the evolutionary importance of processes such as horizontal gene transfer and genetic duplication for nitrogenase evolution and diversification. Finally, we discuss the importance of H2 synthesis in cyanobacteria, as well as strategies and challenges to improve cyanobacterial H2 production.}, }
@article {pmid28323279, year = {2017}, author = {Sun, Y and Powell, KE and Sung, W and Lynch, M and Moran, MA and Luo, H}, title = {Spontaneous mutations of a model heterotrophic marine bacterium.}, journal = {The ISME journal}, volume = {11}, number = {7}, pages = {1713-1718}, pmid = {28323279}, issn = {1751-7370}, support = {R01 GM036827/GM/NIGMS NIH HHS/United States ; R35 GM122566/GM/NIGMS NIH HHS/United States ; }, mesh = {Aquatic Organisms ; Biological Evolution ; Genome Size ; *Genome, Bacterial ; *Genomics ; Mutation Rate ; Phytoplankton ; Rhodobacteraceae/*genetics ; }, abstract = {Heterotrophic marine bacterioplankton populations display substantive genomic diversity that is commonly explained to be the result of selective forces imposed by resource limitation or interactions with phage and predators. Here we use a mutation-accumulation experiment followed by whole-genome sequencing of mutation lines to determine an unbiased rate and molecular spectrum of spontaneous mutations for a model heterotrophic marine bacterium in the globally important Roseobacter clade, Ruegeria pomeroyi DSS-3. We find evidence for mutational bias towards deletions over insertions, and this process alone could account for a sizable portion of genome size diversity among roseobacters and also implies that lateral gene transfer and/or selection must also play a role in maintaining roseobacters with large genome sizes. We also find evidence for a mutational bias in favor of changes from A/T to G/C nucleobases, which explains widespread occurrences of G/C-enriched Roseobacter genomes. Using the calculated mutation rate of 1.39 × 10[-10] per base per generation, we implement a 'mutation-rate clock' approach to date the evolution of roseobacters by assuming a constant mutation rate along their evolutionary history. This approach gives an estimated date of Roseobacter genome expansion in good agreement with an earlier fossil-based estimate of ~250 million years ago and is consistent with a hypothesis of a correlated evolutionary history between roseobacters and marine eukaryotic phytoplankton groups.}, }
@article {pmid28321006, year = {2017}, author = {Habibi, S and Ayubi, AG and Ohkama-Ohtsu, N and Sekimoto, H and Yokoyama, T}, title = {Genetic Characterization of Soybean Rhizobia Isolated from Different Ecological Zones in North-Eastern Afghanistan.}, journal = {Microbes and environments}, volume = {32}, number = {1}, pages = {71-79}, pmid = {28321006}, issn = {1347-4405}, mesh = {Afghanistan ; Bacterial Proteins/genetics ; Bradyrhizobium/*classification/genetics/*isolation &amp; purification/physiology ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Nitrogen Fixation ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhizobiaceae/*classification/genetics/*isolation &amp; purification/physiology ; Root Nodules, Plant/*microbiology ; Sequence Analysis, DNA ; Glycine max/*microbiology ; Symbiosis ; }, abstract = {Seventy rhizobial isolates were obtained from the root nodules of two soybean (Glycine max) cultivars: Japanese cultivar Enrei and USA cultivar Stine3300, which were inoculated with different soil samples from Afghanistan. In order to study the genetic properties of the isolates, the DNA sequences of the 16S rRNA gene and symbiotic genes (nodD1 and nifD) were elucidated. Furthermore, the isolates were inoculated into the roots of two soybean cultivars, and root nodule numbers and nitrogen fixation abilities were subsequently evaluated in order to assess symbiotic performance. Based on 16S rRNA gene sequences, the Afghanistan isolates obtained from soybean root nodules were classified into two genera, Bradyrhizobium and Ensifer. Bradyrhizobium isolates accounted for 54.3% (38) of the isolates, and these isolates had a close relationship with Bradyrhizobium liaoningense and B. yuanmingense. Five out of the 38 Bradyrhizobium isolates showed a novel lineage for B. liaoningense and B. yuanmingense. Thirty-two out of the 70 isolates were identified as Ensifer fredii. An Ensifer isolate had identical nodD1 and nifD sequences to those in B. yuanmingense. This result indicated that the horizontal gene transfer of symbiotic genes occurred from Bradyrhizobium to Ensifer in Afghanistan soil. The symbiotic performance of the 14 tested isolates from the root nodules of the two soybean cultivars indicated that Bradyrhizobium isolates exhibited stronger acetylene reduction activities than Ensifer isolates. This is the first study to genetically characterize soybean-nodulating rhizobia in Afghanistan soil.}, }
@article {pmid28320396, year = {2017}, author = {Ingti, B and Paul, D and Maurya, AP and Bora, D and Chanda, DD and Chakravarty, A and Bhattacharjee, A}, title = {Occurrence of bla DHA-1 mediated cephalosporin resistance in Escherichia coli and their transcriptional response against cephalosporin stress: a report from India.}, journal = {Annals of clinical microbiology and antimicrobials}, volume = {16}, number = {1}, pages = {13}, pmid = {28320396}, issn = {1476-0711}, mesh = {Adult ; Aged, 80 and over ; Anti-Bacterial Agents/*pharmacology ; *Cephalosporin Resistance ; Cephalosporinase/*biosynthesis/genetics/metabolism ; Cephalosporins/*pharmacology ; Conjugation, Genetic ; Escherichia coli/drug effects/*enzymology/genetics ; Escherichia coli Infections/epidemiology/*microbiology ; Escherichia coli Proteins/*biosynthesis/genetics/metabolism ; Female ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial/drug effects ; Gene Transfer, Horizontal ; Genotyping Techniques ; Humans ; India/epidemiology ; Male ; Microbial Sensitivity Tests ; Prevalence ; Real-Time Polymerase Chain Reaction ; Transcription, Genetic/*drug effects ; }, abstract = {BACKGROUND: Treatment alternatives for DHA-1 harboring strains are challenging as it confers resistance to broad spectrum cephalosporins and may further limit treatment option when expressed at higher levels. Therefore, this study was designed to know the prevalence of DHA genes and analyse the transcription level of DHA-1 against different β-lactam stress.<br><br>METHODS: Screening of AmpC &#x3b2;-lactamase phenotypically by modified three dimensional extract method followed by Antimicrobial Susceptibility and MIC determination. Genotyping screening of &#x3b2;-lactamase genes was performed by PCR assay followed by their sequencing. The bla DHA-1 transcriptional response was evaluated under different cephalosporin stress by RT PCR. Transferability of bla DHA gene was performed by transformation and conjugation and plasmid incompatibility typing, DNA fingerprinting by enterobacterial repetitive intergenic consensus sequences PCR.<br><br>RESULTS: 16 DHA-1 genes were screened positive from 176 Escherichia coli isolates and primer extension analysis showed a significant increase in DHA-1 mRNA transcription in response to cefotaxime at 8&#xa0;&#xb5;g/ml (6.99&#xa0;&#xd7;&#xa0;10[2] fold), ceftriaxone at 2&#xa0;&#xb5;g/ml (2.63&#xa0;&#xd7;&#xa0;10[3] fold), ceftazidime at 8&#xa0;&#xb5;g/ml (7.06&#xa0;&#xd7;&#xa0;10[3] fold) and cefoxitin at 4&#xa0;&#xb5;g/ml (3.60&#xa0;&#xd7;&#xa0;10[4] fold) when compared with untreated strain. These transcription data were found significant when analyzed statistically using one way ANOVA. Four different ESBL genes were detected in 10 isolates which include CTX-M (n&#xa0;=&#xa0;6), SHV (n&#xa0;=&#xa0;4), TEM (n&#xa0;=&#xa0;3) and OXA-10 (n&#xa0;=&#xa0;1), whereas, carbapenemase gene (NDM) was detected only in one isolate. Other plasmid mediated AmpC &#x3b2;-lactamases CIT (n&#xa0;=&#xa0;9), EBC (n&#xa0;=&#xa0;2) were detected in nine isolates. All DHA-1 genes detected were encoded in plasmid and incompatibility typing from the transformants indicated that the plasmid encoding bla DHA-1 was carried mostly by the FIA and L/M Inc group.<br><br>CONCLUSION: This study demonstrates the prevalence of DHA-1 gene in this region and highlights high transcription of DHA-1 when induced with different &#x3b2;-lactam antibiotics. Therefore, cephalosporin treatment must be restricted for the patients infected with pathogen expressing this resistance determinant.}, }
@article {pmid28316142, year = {2017}, author = {Suring, W and Meusemann, K and Blanke, A and Mariën, J and Schol, T and Agamennone, V and Faddeeva-Vakhrusheva, A and Berg, MP and ,  and Brouwer, A and van Straalen, NM and Roelofs, D}, title = {Evolutionary ecology of beta-lactam gene clusters in animals.}, journal = {Molecular ecology}, volume = {26}, number = {12}, pages = {3217-3229}, doi = {10.1111/mec.14109}, pmid = {28316142}, issn = {1365-294X}, mesh = {Animals ; Arthropod Proteins/*genetics ; Arthropods/enzymology/*genetics ; Cephamycins ; *Multigene Family ; Oxidoreductases/genetics ; Peptide Synthases/genetics ; Phylogeny ; *beta-Lactams ; }, abstract = {Beta-lactam biosynthesis was thought to occur only in fungi and bacteria, but we recently reported the presence of isopenicillin N synthase in a soil-dwelling animal, Folsomia candida. However, it has remained unclear whether this gene is part of a larger beta-lactam biosynthesis pathway and how widespread the occurrence of penicillin biosynthesis is among animals. Here, we analysed the distribution of beta-lactam biosynthesis genes throughout the animal kingdom and identified a beta-lactam gene cluster in the genome of F. candida (Collembola), consisting of isopenicillin N synthase (IPNS), δ-(L-α-aminoadipoyl)-L-cysteinyl-D-valine synthetase (ACVS), and two cephamycin C genes (cmcI and cmcJ) on a genomic scaffold of 0.76 Mb. All genes are transcriptionally active and are inducible by stress (heat shock). A beta-lactam compound was detected in vivo using an ELISA beta-lactam assay. The gene cluster also contains an ABC transporter which is coregulated with IPNS and ACVS after heat shock. Furthermore, we show that different combinations of beta-lactam biosynthesis genes are present in over 60% of springtail families, but they are absent from genome- and transcript libraries of other animals including close relatives of springtails (Protura, Diplura and insects). The presence of beta-lactam genes is strongly correlated with an euedaphic (soil-living) lifestyle. Beta-lactam genes IPNS and ACVS each form a phylogenetic clade in between bacteria and fungi, while cmcI and cmcJ genes cluster within bacteria. This suggests a single horizontal gene transfer event most probably from a bacterial host, followed by differential loss in more recently evolving species.}, }
@article {pmid28303404, year = {2017}, author = {Ito, D and Ihara, Y and Nishihara, H and Masuda, S}, title = {Phylogenetic analysis of proteins involved in the stringent response in plant cells.}, journal = {Journal of plant research}, volume = {130}, number = {4}, pages = {625-634}, pmid = {28303404}, issn = {1618-0860}, mesh = {Bacteria/enzymology/*genetics ; Chloroplasts/genetics/physiology ; Gene Expression Regulation, Enzymologic ; *Gene Expression Regulation, Plant ; Gene Transfer, Horizontal ; Ligases/genetics ; Phosphoprotein Phosphatases/genetics ; Phylogeny ; Plant Cells/enzymology/physiology ; Plant Proteins/*genetics ; Plants/enzymology/*genetics ; }, abstract = {The nucleotide (p)ppGpp is a second messenger that controls the stringent response in bacteria. The stringent response modifies expression of a large number of genes and metabolic processes and allows bacteria to survive under fluctuating environmental conditions. Recent genome sequencing analyses have revealed that genes responsible for the stringent response are also found in plants. These include (p)ppGpp synthases and hydrolases, RelA/SpoT homologs (RSHs), and the pppGpp-specific phosphatase GppA/Ppx. However, phylogenetic relationship between enzymes involved in bacterial and plant stringent responses is as yet generally unclear. Here, we investigated the origin and evolution of genes involved in the stringent response in plants. Phylogenetic analysis and primary structures of RSH homologs from different plant phyla (including Embryophyta, Charophyta, Chlorophyta, Rhodophyta and Glaucophyta) indicate that RSH gene families were introduced into plant cells by at least two independent lateral gene transfers from the bacterial Deinococcus-Thermus phylum and an unidentified bacterial phylum; alternatively, they were introduced into a proto-plant cell by a lateral gene transfer from the endosymbiotic cyanobacterium followed by gene loss of an ancestral RSH gene in the cyanobacterial linage. Phylogenetic analysis of gppA/ppx families indicated that plant gppA/ppx homologs form an individual cluster in the phylogenetic tree, and show a sister relationship with some bacterial gppA/ppx homologs. Although RSHs contain a plastidial transit peptide at the N terminus, GppA/Ppx homologs do not, suggesting that plant GppA/Ppx homologs function in the cytosol. These results reveal that a proto-plant cell obtained genes for the stringent response by lateral gene transfer events from different bacterial phyla and have utilized them to control metabolism in plastids and the cytosol.}, }
@article {pmid28302951, year = {2017}, author = {Tashiro, Y and Eida, H and Ishii, S and Futamata, H and Okabe, S}, title = {Generation of Small Colony Variants in Biofilms by Escherichia coli Harboring a Conjugative F Plasmid.}, journal = {Microbes and environments}, volume = {32}, number = {1}, pages = {40-46}, pmid = {28302951}, issn = {1347-4405}, mesh = {Aminoglycosides/metabolism ; Anti-Bacterial Agents/metabolism ; Biofilms/drug effects/*growth &amp; development ; DNA Transposable Elements ; Escherichia coli/drug effects/genetics/*growth &amp; development ; Escherichia coli Proteins/genetics ; *F Factor ; Genetic Complementation Test ; Genetic Variation ; Genome, Bacterial ; Mutagenesis, Insertional ; *Phenotype ; }, abstract = {A conjugative F plasmid induces mature biofilm formation by Escherichia coli by promoting F-pili-mediated cell-cell interactions and increasing the expression of biofilm-related genes. We herein demonstrated another function for the F plasmid in E. coli biofilms; it contributes to the emergence of genetic and phenotypic variations by spontaneous mutations. Small colony variants (SCVs) were more frequently generated in a continuous flow-cell biofilm than in the planktonic state of E. coli harboring the F plasmid. E. coli SCVs represented typical phenotypic changes such as slower growth, less biofilm formation, and greater resistance to aminoglycoside antibiotics than the parent strain. Genomic and complementation analyses indicated that the small colony phenotype was caused by the insertion of Tn1000, which was originally localized in the F plasmid, into the hemB gene. Furthermore, the Tn1000 insertion was removed from hemB in the revertant, which showed a normal colony phenotype. This study revealed that the F plasmid has the potential to increase genetic variations not only by horizontal gene transfer via F pili, but also by site-specific recombination within a single cell.}, }
@article {pmid28293553, year = {2017}, author = {Miyazaki, K and Sato, M and Tsukuda, M}, title = {PCR Primer Design for 16S rRNAs for Experimental Horizontal Gene Transfer Test in Escherichia coli.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {5}, number = {}, pages = {14}, pmid = {28293553}, issn = {2296-4185}, abstract = {We recently demonstrated that the Escherichia coli ribosome is robust enough to accommodate foreign 16S rRNAs from diverse gamma- and betaproteobacteria bacteria (Kitahara et al., 2012). Therein, we used the common universal primers Bac8f and UN1541r to obtain a nearly full-length gene. However, we noticed that these primers overlap variable sites at 19[A/C] and 1527[U/C] in Bac8f and UN1541r, respectively, and thus, the amplicon could contain mutations. This is problematic, particularly for the former site, because the 19th nucleotide pairs with the 916th nucleotide, which is a part of the "central pseudoknot" and is critical for function. Therefore, we mutationally investigated the role of the base pair using several 16S rRNAs from gamma- and betaproteobacteria. We found that both the native base pairs (gammaproteobacterial 19A-916U and betaproteobacterial 19C-916G) and the non-native 19A-916G pair retained function, whereas the non-native 19C-916U was defective 16S rRNAs. We next designed a new primer set, Bac1f and UN1542r, so that they do not overlap the potential mismatch sites. 16S rRNA amplicons obtained from the environmental metagenome using the new primer set were dominated by proteobacterial species (~85%). Subsequent functional screening identified various 16S rRNAs from proteobacteria, all of which contained native 19A-916U or 19C-916G base pairs. The primers developed in this study are thus advantageous for functional characterization of foreign 16S rRNA in E. coli with no artifacts.}, }
@article {pmid28290510, year = {2017}, author = {Bartley, SN and Mowlaboccus, S and Mullally, CA and Stubbs, KA and Vrielink, A and Maiden, MC and Harrison, OB and Perkins, TT and Kahler, CM}, title = {Acquisition of the capsule locus by horizontal gene transfer in Neisseria meningitidis is often accompanied by the loss of UDP-GalNAc synthesis.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {44442}, pmid = {28290510}, issn = {2045-2322}, support = {/WT_/Wellcome Trust/United Kingdom ; 104992/WT_/Wellcome Trust/United Kingdom ; 087622/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacterial Capsules/genetics ; Gene Transfer, Horizontal/*genetics ; Humans ; Meningitis, Meningococcal/*genetics/microbiology ; Neisseria meningitidis/*genetics/pathogenicity ; Repetitive Sequences, Nucleic Acid/genetics ; UDPglucose 4-Epimerase/*genetics ; Uridine Diphosphate Galactose/biosynthesis ; }, abstract = {Pathogenic meningococci have acquired a 24 kb capsule synthesis island (cps) by horizontal gene transfer which consists of a synthetic locus and associated capsule transport genes flanked by repetitive Regions D and D'. Regions D and D' contain an intact gene encoding a UDP-galactose epimerase (galE1) and a truncated remnant (galE2), respectively. In this study, GalE protein alleles were shown to be either mono-functional, synthesising UDP-galactose (UDP-Gal), or bi-functional, synthesising UDP-Gal and UDP-galactosamine (UDP-GalNAc). Meningococci possessing a capsule null locus (cnl) typically possessed a single bi-functional galE. Separation of functionality between galE1 and galE2 alleles in meningococcal isolates was retained for all serogroups except serogroup E which has a synthetic requirement for UDP-GalNAc. The truncated galE2 remnant in Region D' was also phylogenetically related to the bi-functional galE of the cnl locus suggesting common ancestry. A model is proposed in which the illegitimate recombination of the cps island into the galE allele of the cnl locus results in the formation of Region D' containing the truncated galE2 locus and the capture of the cps island en bloc. The retention of the duplicated Regions D and D' enables inversion of the synthetic locus within the cps island during bacterial growth.}, }
@article {pmid28289083, year = {2017}, author = {Chubiz, LM and Marx, CJ}, title = {Growth Trade-Offs Accompany the Emergence of Glycolytic Metabolism in Shewanella oneidensis MR-1.}, journal = {Journal of bacteriology}, volume = {199}, number = {11}, pages = {}, pmid = {28289083}, issn = {1098-5530}, mesh = {Acetylglucosamine/metabolism ; Bacterial Proteins/genetics/metabolism ; *Gene Expression Regulation, Bacterial ; Glucose/*metabolism ; Glycolysis ; Monosaccharide Transport Proteins/genetics/metabolism ; Shewanella/enzymology/genetics/growth &amp; development/*metabolism ; }, abstract = {Bacteria increase their metabolic capacity via the acquisition of genetic material or by the mutation of genes already present in the genome. Here, we explore the mechanisms and trade-offs involved when Shewanella oneidensis, a bacterium that typically consumes small organic and amino acids, rapidly evolves to expand its metabolic capacity to catabolize glucose after a short period of adaptation to a glucose-rich environment. Using whole-genome sequencing and genetic approaches, we discovered that deletions in a region including the transcriptional repressor (nagR) that regulates the expression of genes associated with catabolism of N-acetylglucosamine are the common basis for evolved glucose metabolism across populations. The loss of nagR results in the constitutive expression of genes for an N-acetylglucosamine permease (nagP) and kinase (nagK). We demonstrate that promiscuous activities of both NagP and NagK toward glucose allow for the transport and phosphorylation of glucose to glucose-6-phosphate, the initial events of glycolysis otherwise thought to be absent in S. oneidensis[13]C-based metabolic flux analysis uncovered that subsequent utilization was mediated by the Entner-Doudoroff pathway. This is an example whereby gene loss and preexisting enzymatic promiscuity, and not gain-of-function mutations, were the drivers of increased metabolic capacity. However, we observed a significant decrease in the growth rate on lactate after adaptation to glucose catabolism, suggesting that trade-offs may explain why glycolytic function may not be readily observed in S. oneidensis in natural environments despite it being readily accessible through just a single mutational event.IMPORTANCE Gains in metabolic capacity are frequently associated with the acquisition of novel genetic material via natural or engineered horizontal gene transfer events. Here, we explored how a bacterium that typically consumes small organic acids and amino acids expands its metabolic capacity to include glucose via a loss of genetic material, a process frequently associated with a deterioration of metabolic function. Our findings highlight how the natural promiscuity of transporters and enzymes can be a key driver in expanding metabolic diversity and that many bacteria may possess a latent metabolic capacity accessible through one or a few mutations that remove regulatory functions. Our discovery of trade-offs between growth on lactate and on glucose suggests why this easily gained trait is not observed in nature.}, }
@article {pmid28283403, year = {2017}, author = {Choudoir, MJ and Panke-Buisse, K and Andam, CP and Buckley, DH}, title = {Genome Surfing As Driver of Microbial Genomic Diversity.}, journal = {Trends in microbiology}, volume = {25}, number = {8}, pages = {624-636}, doi = {10.1016/j.tim.2017.02.006}, pmid = {28283403}, issn = {1878-4380}, mesh = {*Gene Transfer, Horizontal ; *Genetic Variation ; *Genome, Microbial ; Genomics ; Models, Genetic ; Phylogeny ; Streptomyces/genetics ; }, abstract = {Historical changes in population size, such as those caused by demographic range expansions, can produce nonadaptive changes in genomic diversity through mechanisms such as gene surfing. We propose that demographic range expansion of a microbial population capable of horizontal gene exchange can result in genome surfing, a mechanism that can cause widespread increase in the pan-genome frequency of genes acquired by horizontal gene exchange. We explain that patterns of genetic diversity within Streptomyces are consistent with genome surfing, and we describe several predictions for testing this hypothesis both in Streptomyces and in other microorganisms.}, }
@article {pmid28283023, year = {2017}, author = {Chalker, V and Jironkin, A and Coelho, J and Al-Shahib, A and Platt, S and Kapatai, G and Daniel, R and Dhami, C and Laranjeira, M and Chambers, T and Guy, R and Lamagni, T and Harrison, T and Chand, M and Johnson, AP and Underwood, A and , }, title = {Genome analysis following a national increase in Scarlet Fever in England 2014.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {224}, pmid = {28283023}, issn = {1471-2164}, mesh = {Antigens, Bacterial/genetics ; Bacterial Outer Membrane Proteins/genetics ; Bacteriophages/genetics ; Carrier Proteins/genetics ; Cluster Analysis ; England/epidemiology ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genomics/methods ; Humans ; Multilocus Sequence Typing ; Phylogeny ; Population Surveillance ; Scarlet Fever/epidemiology/*microbiology ; Streptococcus pyogenes/classification/*genetics/virology ; }, abstract = {BACKGROUND: During a substantial elevation in scarlet fever (SF) notifications in 2014 a national genomic study was undertaken of Streptococcus pyogenes (Group A Streptococci, GAS) isolates from patients with SF with comparison to isolates from patients with invasive disease (iGAS) to test the hypotheses that the increase in SF was due to either the introduction of one or more new/emerging strains in the population in England or the transmission of a known genetic element through the population of GAS by horizontal gene transfer (HGT) resulting in infections with an increased likelihood of causing SF. Isolates were collected to provide geographical representation, for approximately 5% SF isolates from each region from 1[st] April 2014 to 18[th] June 2014. Contemporaneous iGAS isolates for which genomic data were available were included for comparison. Data were analysed in order to determine emm gene sequence type, phylogenetic lineage and genomic clade representation, the presence of known prophage elements and the presence of genes known to confer pathogenicity and resistance to antibiotics.<br><br>RESULTS: 555 isolates were analysed, 303 from patients with SF and 252 from patients with iGAS. Isolates from patients with SF were of multiple distinct emm sequence types and phylogenetic lineages. Prior to data normalisation, emm3 was the predominant type (accounting for 42.9% of SF isolates, 130/303 95%CI 37.5-48.5; 14.7% higher than the percentage of emm3 isolates found in the iGAS isolates). Post-normalisation emm types, 4 and 12, were found to be over-represented in patients with SF versus iGAS (p&#x2009;<&#x2009;0.001). A single gene, ssa, was over-represented in isolates from patients with SF. No single phage was found to be over represented in SF vs iGAS. However, a "meta-ssa" phage defined by the presence of :315.2, SPsP6, MGAS10750.3 or HK360ssa, was found to be over represented. The HKU360.vir phage was not detected yet the HKU360.ssa phage was present in 43/63 emm12 isolates but not found to be over-represented in isolates from patients with SF.<br><br>CONCLUSIONS: There is no evidence that the increased number of SF cases was a strain-specific or known mobile element specific phenomenon, as the increase in SF cases was associated with multiple lineages of GAS.}, }
@article {pmid28276126, year = {2017}, author = {Hehemann, JH and Truong, LV and Unfried, F and Welsch, N and Kabisch, J and Heiden, SE and Junker, S and Becher, D and Thürmer, A and Daniel, R and Amann, R and Schweder, T}, title = {Aquatic adaptation of a laterally acquired pectin degradation pathway in marine gammaproteobacteria.}, journal = {Environmental microbiology}, volume = {19}, number = {6}, pages = {2320-2333}, doi = {10.1111/1462-2920.13726}, pmid = {28276126}, issn = {1462-2920}, mesh = {Adaptation, Physiological/*genetics ; Amino Acid Sequence ; Gammaproteobacteria/genetics/*metabolism ; Gene Transfer, Horizontal/genetics ; Interspersed Repetitive Sequences/genetics ; Pectins/*metabolism ; Polysaccharide-Lyases/*genetics ; Proteomics ; }, abstract = {Mobile genomic islands distribute functional traits between microbes and habitats, yet it remains unclear how their proteins adapt to new environments. Here we used a comparative phylogenomic and proteomic approach to show that the marine bacterium Pseudoalteromonas haloplanktis ANT/505 acquired a genomic island with a functional pathway for pectin catabolism. Bioinformatics and biochemical experiments revealed that this pathway encodes a series of carbohydrate-active enzymes including two multi-modular pectate lyases, PelA and PelB. PelA is a large enzyme with a polysaccharide lyase family 1 (PL1) domain and a carbohydrate esterase family 8 domain, and PelB contains a PL1 domain and two carbohydrate-binding domains of family 13. Comparative phylogenomic analyses indicate that the pathway was most likely acquired from terrestrial microbes, yet we observed multi-modular orthologues only in marine bacteria. Proteomic experiments showed that P. haloplanktis ANT/505 secretes both pectate lyases into the environment in the presence of pectin. These multi-modular enzymes may therefore represent a marine innovation that enhances physical interaction with pectins to reduce loss of substrate and enzymes by diffusion. Our results revealed that marine bacteria can catabolize pectin, and highlight enzyme fusion as a potential adaptation that may facilitate microbial consumption of polymeric substrates in aquatic environments.}, }
@article {pmid28274848, year = {2017}, author = {Xiao, H and Li, Z and Li, F and Wen, J and Liu, D and Du, W and Hou, J and Li, Z and Zheng, R and Liu, D and Chu, T and Du, D and Tian, H}, title = {Preliminary study of tetracycline resistance genes in Treponema pallidum.}, journal = {Journal of global antimicrobial resistance}, volume = {9}, number = {}, pages = {1-2}, doi = {10.1016/j.jgar.2017.02.003}, pmid = {28274848}, issn = {2213-7173}, mesh = {*Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; *Point Mutation ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Syphilis/microbiology ; *Tetracycline Resistance ; Treponema pallidum/*genetics/isolation &amp; purification ; }, }
@article {pmid28274202, year = {2017}, author = {Pinos, S and Pontarotti, P and Raoult, D and Merhej, V}, title = {Identification of constraints influencing the bacterial genomes evolution in the PVC super-phylum.}, journal = {BMC evolutionary biology}, volume = {17}, number = {1}, pages = {75}, pmid = {28274202}, issn = {1471-2148}, mesh = {Bacteria/classification/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Phylogeny ; }, abstract = {BACKGROUND: Horizontal transfer plays an important role in the evolution of bacterial genomes, yet it obeys several constraints, including the ecological opportunity to meet other organisms, the presence of transfer systems, and the fitness of the transferred genes. Bacteria from the Planctomyctetes, Verrumicrobia, Chlamydiae (PVC) super-phylum have a compartmentalized cell plan delimited by an intracytoplasmic membrane that might constitute an additional constraint with particular impact on bacterial evolution. In this investigation, we studied the evolution of 33 genomes from PVC species and focused on the rate and the nature of horizontally transferred sequences in relation to their habitat and their cell plan.<br><br>RESULTS: Using a comparative phylogenomic approach, we showed that habitat influences the evolution of the bacterial genome's content and the flux of horizontal transfer of DNA (HT). Thus bacteria from soil, from insects and ubiquitous bacteria presented the highest average of horizontal transfer compared to bacteria living in water, extracellular bacteria in vertebrates, bacteria from amoeba and intracellular bacteria in vertebrates (with a mean of 379 versus 110 events per species, respectively and 7.6% of each genomes due to HT against 4.8%). The partners of these transfers were mainly bacterial organisms (94.9%); they allowed us to differentiate environmental bacteria, which exchanged more with Proteobacteria, and bacteria from vertebrates, which exchanged more with Firmicutes. The functional analysis of the horizontal transfers revealed a convergent evolution, with an over-representation of genes encoding for membrane biogenesis and lipid metabolism, among compartmentalized bacteria in the different habitats.<br><br>CONCLUSIONS: The presence of an intracytoplasmic membrane in PVC species seems to affect the genome's evolution through the selection of transferred DNA, according to their encoded functions.}, }
@article {pmid28270808, year = {2017}, author = {Cai, W and Cai, X and Yang, Y and Yan, S and Zhang, H}, title = {Transcriptional Control of Dual Transporters Involved in α-Ketoglutarate Utilization Reveals Their Distinct Roles in Uropathogenic Escherichia coli.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {275}, pmid = {28270808}, issn = {1664-302X}, abstract = {Uropathogenic Escherichia coli (UPEC) are the primary causative agents of urinary tract infections. Some UPEC isolates are able to infect renal proximal tubule cells, and can potentially cause pyelonephritis. We have previously shown that to fulfill their physiological roles renal proximal tubule cells accumulate high concentrations of α-ketoglutarate (KG) and that gene cluster c5032-c5039 contribute to anaerobic utilization of KG by UPEC str. CFT073, thereby promoting its in vivo fitness. Given the importance of utilizing KG for UPEC, this study is designed to investigate the roles of two transporters KgtP and C5038 in KG utilization, their transcriptional regulation, and their contributions to UPEC fitness in vivo. Our phylogenetic analyses support that kgtP is a widely conserved locus in commensal and pathogenic E. coli, while UPEC-associated c5038 was acquired through horizontal gene transfer. Global anaerobic transcriptional regulators Fumarate and nitrate reduction (FNR) and ArcA induced c5038 expression in anaerobiosis, and C5038 played a major role in anaerobic growth on KG. KgtP was required for aerobic growth on KG, and its expression was repressed by FNR and ArcA under anaerobic conditions. Analyses of FNR and ArcA binding sites and results of EMS assays suggest that FNR and ArcA likely inhibit kgtP expression through binding to the -35 region of kgtP promoter and occluding the occupancy of RNA polymerases. Gene c5038 can be specifically induced by KG, whereas the expression of kgtP does not respond to KG, yet can be stimulated during growth on glycerol. In addition, c5038 and kgtP expression were further shown to be controlled by different alternative sigma factors RpoN and RpoS, respectively. Furthermore, dual-strain competition assays in a murine model showed that c5038 mutant but not kgtP mutant was outcompeted by the wild-type strain during the colonization of murine bladders and kidneys, highlighting the importance of C5038 under in vivo conditions. Therefore, different transcriptional regulation led to distinct roles played by C5038 and KgtP in KG utilization and fitness in vivo. This study thus potentially expanded our understanding of UPEC pathobiology.}, }
@article {pmid28264195, year = {2017}, author = {Gold, DA and Caron, A and Fournier, GP and Summons, RE}, title = {Paleoproterozoic sterol biosynthesis and the rise of oxygen.}, journal = {Nature}, volume = {543}, number = {7645}, pages = {420-423}, doi = {10.1038/nature21412}, pmid = {28264195}, issn = {1476-4687}, mesh = {Atmosphere/chemistry ; Bacteria/genetics/metabolism ; Eukaryota/genetics/metabolism ; Gene Transfer, Horizontal ; History, Ancient ; Oceans and Seas ; Oxygen/*metabolism ; Phylogeny ; Seawater/chemistry ; Sterols/*biosynthesis ; Synteny ; }, abstract = {Natural products preserved in the geological record can function as 'molecular fossils', providing insight into organisms and physiologies that existed in the deep past. One important group of molecular fossils is the steroidal hydrocarbons (steranes), which are the diagenetic remains of sterol lipids. Complex sterols with modified side chains are unique to eukaryotes, although simpler sterols can also be synthesized by a few bacteria. Sterol biosynthesis is an oxygen-intensive process; thus, the presence of complex steranes in ancient rocks not only signals the presence of eukaryotes, but also aerobic metabolic processes. In 1999, steranes were reported in 2.7 billion year (Gyr)-old rocks from the Pilbara Craton in Australia, suggesting a long delay between photosynthetic oxygen production and its accumulation in the atmosphere (also known as the Great Oxidation Event) 2.45-2.32 Gyr ago. However, the recent reappraisal and rejection of these steranes as contaminants pushes the oldest reported steranes forward to around 1.64 Gyr ago (ref. 6). Here we use a molecular clock approach to improve constraints on the evolution of sterol biosynthesis. We infer that stem eukaryotes shared functionally modern sterol biosynthesis genes with bacteria via horizontal gene transfer. Comparing multiple molecular clock analyses, we find that the maximum marginal probability for the divergence time of bacterial and eukaryal sterol biosynthesis genes is around 2.31 Gyr ago, concurrent with the most recent geochemical evidence for the Great Oxidation Event. Our results therefore indicate that simple sterol biosynthesis existed well before the diversification of living eukaryotes, substantially predating the oldest detected sterane biomarkers (approximately 1.64 Gyr ago), and furthermore, that the evolutionary history of sterol biosynthesis is tied to the first widespread availability of molecular oxygen in the ocean-atmosphere system.}, }
@article {pmid28263596, year = {2017}, author = {Al-Jassim, N and Mantilla-Calderon, D and Wang, T and Hong, PY}, title = {Inactivation and Gene Expression of a Virulent Wastewater Escherichia coli Strain and the Nonvirulent Commensal Escherichia coli DSM1103 Strain upon Solar Irradiation.}, journal = {Environmental science &amp; technology}, volume = {51}, number = {7}, pages = {3649-3659}, doi = {10.1021/acs.est.6b05377}, pmid = {28263596}, issn = {1520-5851}, mesh = {Escherichia coli/*isolation &amp; purification ; Escherichia coli Infections ; Half-Life ; Solar Energy ; *Wastewater ; }, abstract = {This study examined the decay kinetics and molecular responses of two Escherichia coli strains upon solar irradiation. The first is E. coli PI-7, a virulent and antibiotic-resistant strain that was isolated from wastewater and carries the emerging NDM-1 antibiotic resistance gene. The other strain, E. coli DSM1103, displayed lower virulence and antibiotic resistance than E. coli PI-7. In a buffer solution, E. coli PI-7 displayed a longer lag phase prior to decay and a longer half-life compared with E. coli DSM1103 (6.64 ± 0.63 h and 2.85 ± 0.46 min vs 1.33 ± 0.52 h and 2.04 ± 0.36 min). In wastewater, both E. coli strains decayed slower than they did in buffer. Although solar irradiation remained effective in reducing the numbers of both strains by more than 5-log10 in <24 h, comparative genomics and transcriptomics revealed differences in the genomes and overall regulation of genes between the two E. coli strains. A wider arsenal of genes related to oxidative stress, cellular repair and protective mechanisms were upregulated in E. coli PI-7. Subpopulations of E. coli PI-7 expressed genes related to dormancy and persister cell formation during the late decay phase, which may have accounted for its prolonged persistence. Upon prolonged solar irradiation, both E. coli strains displayed upregulation of genes related to horizontal gene transfer and antibiotic resistance. Virulence functions unique to E. coli PI-7 were also upregulated. Our findings collectively indicated that, whereas solar irradiation is able to reduce total cell numbers, viable E. coli remained and expressed genes that enable survival despite solar treatment. There remains a need for heightened levels of concern regarding risks arising from the dissemination of E. coli that may remain viable in wastewater after solar irradiation.}, }
@article {pmid28262720, year = {2017}, author = {Gandini, CL and Sanchez-Puerta, MV}, title = {Foreign Plastid Sequences in Plant Mitochondria are Frequently Acquired Via Mitochondrion-to-Mitochondrion Horizontal Transfer.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {43402}, pmid = {28262720}, issn = {2045-2322}, mesh = {Arecaceae/classification/genetics ; Base Sequence ; DNA, Mitochondrial ; Evolution, Molecular ; Fagaceae/classification/genetics ; *Gene Transfer, Horizontal ; *Genome, Mitochondrial ; *Genome, Plastid ; Lamiaceae/classification/genetics ; Magnoliopsida/classification/*genetics ; Mitochondria/*genetics ; Phylogeny ; Plastids/*genetics ; Rosaceae/classification/genetics ; }, abstract = {Angiosperm mitochondrial genomes (mtDNA) exhibit variable quantities of alien sequences. Many of these sequences are acquired by intracellular gene transfer (IGT) from the plastid. In addition, frequent events of horizontal gene transfer (HGT) between mitochondria of different species also contribute to their expanded genomes. In contrast, alien sequences are rarely found in plastid genomes. Most of the plant-to-plant HGT events involve mitochondrion-to-mitochondrion transfers. Occasionally, foreign sequences in mtDNAs are plastid-derived (MTPT), raising questions about their origin, frequency, and mechanism of transfer. The rising number of complete mtDNAs allowed us to address these questions. We identified 15 new foreign MTPTs, increasing significantly the number of those previously reported. One out of five of the angiosperm species analyzed contained at least one foreign MTPT, suggesting a remarkable frequency of HGT among plants. By analyzing the flanking regions of the foreign MTPTs, we found strong evidence for mt-to-mt transfers in 65% of the cases. We hypothesize that plastid sequences were initially acquired by the native mtDNA via IGT and then transferred to a distantly-related plant via mitochondrial HGT, rather than directly from a foreign plastid to the mitochondrial genome. Finally, we describe three novel putative cases of mitochondrial-derived sequences among angiosperm plastomes.}, }
@article {pmid28262486, year = {2017}, author = {Eme, L and Gentekaki, E and Curtis, B and Archibald, JM and Roger, AJ}, title = {Lateral Gene Transfer in the Adaptation of the Anaerobic Parasite Blastocystis to the Gut.}, journal = {Current biology : CB}, volume = {27}, number = {6}, pages = {807-820}, doi = {10.1016/j.cub.2017.02.003}, pmid = {28262486}, issn = {1879-0445}, mesh = {Acclimatization ; Blastocystis/genetics/*physiology ; Blastocystis Infections/*parasitology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Humans ; Intestinal Diseases/*parasitology ; Intestines/*parasitology ; *Microbiota ; }, abstract = {Blastocystis spp. are the most prevalent eukaryotic microbes found in the intestinal tract of humans. Here we present an in-depth investigation of lateral gene transfer (LGT) in the genome of Blastocystis sp. subtype 1. Using rigorous phylogeny-based methods and strict validation criteria, we show that ∼2.5% of the genes of this organism were recently acquired by LGT. We identify LGTs both from prokaryote and eukaryote donors. Several transfers occurred specifically in ancestors of a subset of Blastocystis subtypes, demonstrating that LGT is an ongoing process. Functional predictions reveal that these genes are involved in diverse metabolic pathways, many of which appear related to adaptation of Blastocystis to the gut environment. Specifically, we identify genes involved in carbohydrate scavenging and metabolism, anaerobic amino acid and nitrogen metabolism, oxygen-stress resistance, and pH homeostasis. A number of the transferred genes encoded secreted proteins that are potentially involved in infection, escaping host defense, or most likely affect the prokaryotic microbiome and the inflammation state of the gut. We also show that Blastocystis subtypes differ in the nature and copy number of LGTs that could relate to variation in their prevalence and virulence. Finally, we identified bacterial-derived genes encoding NH3-dependent nicotinamide adenine dinucleotide (NAD) synthase in Blastocystis and other protozoan parasites, which are promising targets for drug development. Collectively, our results suggest new avenues for research into the role of Blastocystis in intestinal disease and unequivocally demonstrate that LGT is an important mechanism by which eukaryotic microbes adapt to new environments.}, }
@article {pmid28262000, year = {2017}, author = {Lindow, SE}, title = {Horizontal gene transfer gone wild: promiscuity in a kiwifruit pathogen leads to resistance to chemical control.}, journal = {Environmental microbiology}, volume = {19}, number = {4}, pages = {1363-1365}, doi = {10.1111/1462-2920.13717}, pmid = {28262000}, issn = {1462-2920}, mesh = {*Actinidia ; Fruit ; *Gene Transfer, Horizontal ; Serogroup ; }, }
@article {pmid28261178, year = {2017}, author = {Entfellner, E and Frei, M and Christiansen, G and Deng, L and Blom, J and Kurmayer, R}, title = {Evolution of Anabaenopeptin Peptide Structural Variability in the Cyanobacterium Planktothrix.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {219}, pmid = {28261178}, issn = {1664-302X}, support = {P 24070/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Cyanobacteria are frequently involved in the formation of harmful algal blooms wherein, apart from the toxic microcystins, other groups of bioactive peptides are abundant as well, such as anabaenopeptins (APs). The APs are synthesized nonribosomally as cyclic hexapeptides with various amino acids at the exocyclic position. We investigated the presence and recombination of the AP synthesis gene cluster (apnA-E) through comparing 125 strains of the bloom-forming cyanobacterium Planktothrix spp., which were isolated from numerous shallow and deep water habitats in the temperate and tropical climatic zone. Ten ecologically divergent strains were purified and genome sequenced to compare their entire apnA-E gene cluster. In order to quantify apn gene distribution patterns, all the strains were investigated by PCR amplification of 2 kbp portions of the entire apn gene cluster without interruption. Within the 11 strains assigned to P. pseudagardhii, P. mougeotii, or P. tepida (Lineage 3), neither apnA-E genes nor remnants were observed. Within the P. agardhii/P. rubescens strains from shallow waters (Lineage 1, 52 strains), strains both carrying and lacking apn genes occurred, while among the strains lacking the apnA-E genes, the presence of the 5'end flanking region indicated a gene cluster deletion. Among the strains of the more derived deep water ecotype (Lineage 2, 62 strains), apnA-E genes were always present. A high similarity of apn genes of the genus Planktothrix when compared with strains of the genus Microcystis suggested its horizontal gene transfer during the speciation of P. agardhii/P. rubescens. Genetic analysis of the first (A1-) domain of the apnA gene, encoding synthesis of the exocyclic position of the AP molecule, revealed four genotype groups that corresponded with substrate activation. Groups of genotypes were either related to Arginine only, the coproduction of Arginine and Tyrosine or Arginine and Lysine, or even the coproduction of Arginine, Tyrosine, and Lysine in the exocyclic position of the AP-molecule. The increased structural diversity resulted from the evolution of apnA A1 genotypes through a small number of positively selected point mutations that occurred repeatedly and independently from phylogenetic association.}, }
@article {pmid28261177, year = {2017}, author = {Wüthrich, D and Berthoud, H and Wechsler, D and Eugster, E and Irmler, S and Bruggmann, R}, title = {The Histidine Decarboxylase Gene Cluster of Lactobacillus parabuchneri Was Gained by Horizontal Gene Transfer and Is Mobile within the Species.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {218}, pmid = {28261177}, issn = {1664-302X}, abstract = {Histamine in food can cause intolerance reactions in consumers. Lactobacillus parabuchneri (L. parabuchneri) is one of the major causes of elevated histamine levels in cheese. Despite its significant economic impact and negative influence on human health, no genomic study has been published so far. We sequenced and analyzed 18 L. parabuchneri strains of which 12 were histamine positive and 6 were histamine negative. We determined the complete genome of the histamine positive strain FAM21731 with PacBio as well as Illumina and the genomes of the remaining 17 strains using the Illumina technology. We developed the synteny aware ortholog finding algorithm SynOrf to compare the genomes and we show that the histidine decarboxylase (HDC) gene cluster is located in a genomic island. It is very likely that the HDC gene cluster was transferred from other lactobacilli, as it is highly conserved within several lactobacilli species. Furthermore, we have evidence that the HDC gene cluster was transferred within the L. parabuchneri species.}, }
@article {pmid28258564, year = {2017}, author = {Ishibashi, K and Morishita, Y and Tanaka, Y}, title = {The Evolutionary Aspects of Aquaporin Family.}, journal = {Advances in experimental medicine and biology}, volume = {969}, number = {}, pages = {35-50}, doi = {10.1007/978-94-024-1057-0_2}, pmid = {28258564}, issn = {0065-2598}, mesh = {Amino Acid Sequence ; Animals ; Aquaporins/chemistry/classification/*genetics/metabolism ; Biological Evolution ; Biological Transport ; Conserved Sequence ; Fungi/classification/*genetics/metabolism ; Gene Duplication ; Gene Expression ; Gene Transfer, Horizontal ; Invertebrates/classification/*genetics/metabolism ; Phylogeny ; Plants/classification/*genetics/metabolism ; Prokaryotic Cells/classification/*metabolism ; Protein Domains ; Vertebrates/classification/*genetics/metabolism ; }, abstract = {Aquaporins (AQPs) are a family of transmembrane proteins present in almost all species including virus. They are grossly divided into three subfamilies based on the sequence around a highly conserved pore-forming NPA motif: (1) classical water -selective AQP (CAQP), (2) glycerol -permeable aquaglyceroporin (AQGP) and (3) AQP super-gene channel, superaquaporin (SAQP). AQP is composed of two tandem repeats of conserved three transmembrane domains and a NPA motif. AQP ancestors probably started in prokaryotes by the duplication of half AQP genes to be diversified into CAQPs or AQGPs by evolving a subfamily-specific carboxyl-terminal NPA motif. Both AQP subfamilies may have been carried over to unicellular eukaryotic ancestors, protists and further to multicellular organisms. Although fungus lineage has kept both AQP subfamilies, the plant lineage has lost AQGP after algal ancestors with extensive diversifications of CAQPs into PIP, TIP, SIP, XIP, HIP and LIP with a possible horizontal transfer of NIP from bacteria. Interestingly, the animal lineage has obtained new SAQP subfamily with highly deviated NPA motifs, especially at the amino-terminal halves in both prostomial and deuterostomial animals. The prostomial lineage has lost AQGP after hymenoptera, while the deuterostomial lineage has kept all three subfamilies up to the vertebrate with diversified CAQPs (AQP0, 1, 2, 4, 5, 6, 8) and AQGPs (AQP3, 7, 9, 10) with limited SAQPs (AQP11, 12) in mammals. Whole-genome duplications, local gene duplications and horizontal gene transfers may have produced the AQP diversity with adaptive selections and functional alternations in response to environment changes. With the above evolutionary perspective in mind, the function of each AQP could be speculated by comparison among species to get new insights into physiological roles of AQPs . This evolutionary guidance in AQP research will lead to deeper understandings of water and solute homeostasis.}, }
@article {pmid28258227, year = {2017}, author = {Mukerji, S and O'Dea, M and Barton, M and Kirkwood, R and Lee, T and Abraham, S}, title = {Development and transmission of antimicrobial resistance among Gram-negative bacteria in animals and their public health impact.}, journal = {Essays in biochemistry}, volume = {61}, number = {1}, pages = {23-35}, doi = {10.1042/EBC20160055}, pmid = {28258227}, issn = {1744-1358}, mesh = {Animals ; Anti-Infective Agents/*pharmacology ; DNA Transposable Elements/genetics ; Drug Resistance, Bacterial/*drug effects ; Gene Transfer, Horizontal/genetics ; Gram-Negative Bacteria/*drug effects ; Humans ; *Public Health ; }, abstract = {Gram-negative bacteria are known to cause severe infections in both humans and animals. Antimicrobial resistance (AMR) in Gram-negative bacteria is a major challenge in the treatment of clinical infections globally due to the propensity of these organisms to rapidly develop resistance against antimicrobials in use. In addition, Gram-negative bacteria possess highly efficient mechanisms through which the AMR can be disseminated between pathogenic and commensal bacteria of the same or different species. These unique traits of Gram-negative bacteria have resulted in evolution of Gram-negative bacterial strains demonstrating resistance to multiple classes of antimicrobials. The evergrowing resistance issue has not only resulted in limitation of treatment options but also led to increased treatment costs and mortality rates in humans and animals. With few or no new antimicrobials in production to combat severe life-threatening infections, AMR has been described as the one of the most severe, long-term threats to human health. Aside from overuse and misuse of antimicrobials in humans, another factor that has exacerbated the emergence of AMR in Gram-negative bacteria is the veterinary use of antimicrobials that belong to the same classes considered to be critically important for treating serious life-threatening infections in humans. Despite the fact that development of AMR dates back to before the introduction of antimicrobials, the recent surge in the resistance towards all available critically important antimicrobials has emerged as a major public health issue. This review thus focuses on discussing the development, transmission and public health impact of AMR in Gram-negative bacteria in animals.}, }
@article {pmid28258226, year = {2017}, author = {Tripathi, V and Cytryn, E}, title = {Impact of anthropogenic activities on the dissemination of antibiotic resistance across ecological boundaries.}, journal = {Essays in biochemistry}, volume = {61}, number = {1}, pages = {11-21}, doi = {10.1042/EBC20160054}, pmid = {28258226}, issn = {1744-1358}, mesh = {Animals ; *Drug Resistance, Microbial/genetics ; *Ecosystem ; Genes, Bacterial ; *Human Activities ; Humans ; Models, Biological ; Risk Assessment ; }, abstract = {Antibiotics are considered to be one of the major medical breakthroughs in history. Nonetheless, over the past four decades, antibiotic resistance has reached alarming levels worldwide and this trend is expected to continue to increase, leading some experts to forecast the coming of a 'post-antibiotic' era. Although antibiotic resistance in pathogens is traditionally linked to clinical environments, there is a rising concern that the global propagation of antibiotic resistance is also associated with environmental reservoirs that are linked to anthropogenic activities such as animal husbandry, agronomic practices and wastewater treatment. It is hypothesized that the emergence and dissemination of antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs) within and between environmental microbial communities can ultimately contribute to the acquisition of antibiotic resistance in human pathogens. Nonetheless, the scope of this phenomenon is not clear due to the complexity of microbial communities in the environment and methodological constraints that limit comprehensive in situ evaluation of microbial genomes. This review summarizes the current state of knowledge regarding antibiotic resistance in non-clinical environments, specifically focusing on the dissemination of antibiotic resistance across ecological boundaries and the contribution of this phenomenon to global antibiotic resistance.}, }
@article {pmid28258138, year = {2017}, author = {Wang, Y and Hatt, JK and Tsementzi, D and Rodriguez-R, LM and Ruiz-Pérez, CA and Weigand, MR and Kizer, H and Maresca, G and Krishnan, R and Poretsky, R and Spain, JC and Konstantinidis, KT}, title = {Quantifying the Importance of the Rare Biosphere for Microbial Community Response to Organic Pollutants in a Freshwater Ecosystem.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {8}, pages = {}, pmid = {28258138}, issn = {1098-5336}, mesh = {2,4-Dichlorophenoxyacetic Acid/metabolism/pharmacology ; Archaea/classification/genetics/metabolism ; Bacteria/classification/genetics/metabolism ; Biodegradation, Environmental ; *Biodiversity ; Caffeine/metabolism/pharmacology ; *Ecosystem ; Fresh Water/*microbiology ; Georgia ; Lakes/microbiology ; Metagenomics ; Microbial Consortia/drug effects/genetics/*physiology ; Nitrophenols/metabolism/pharmacology ; Phylogeny ; RNA, Ribosomal, 16S ; Real-Time Polymerase Chain Reaction ; Water Pollutants, Chemical/chemistry/*metabolism/*pharmacology ; }, abstract = {A single liter of water contains hundreds, if not thousands, of bacterial and archaeal species, each of which typically makes up a very small fraction of the total microbial community (<0.1%), the so-called "rare biosphere." How often, and via what mechanisms, e.g., clonal amplification versus horizontal gene transfer, the rare taxa and genes contribute to microbial community response to environmental perturbations represent important unanswered questions toward better understanding the value and modeling of microbial diversity. We tested whether rare species frequently responded to changing environmental conditions by establishing 20-liter planktonic mesocosms with water from Lake Lanier (Georgia, USA) and perturbing them with organic compounds that are rarely detected in the lake, including 2,4-dichlorophenoxyacetic acid (2,4-D), 4-nitrophenol (4-NP), and caffeine. The populations of the degraders of these compounds were initially below the detection limit of quantitative PCR (qPCR) or metagenomic sequencing methods, but they increased substantially in abundance after perturbation. Sequencing of several degraders (isolates) and time-series metagenomic data sets revealed distinct cooccurring alleles of degradation genes, frequently carried on transmissible plasmids, especially for the 2,4-D mesocosms, and distinct species dominating the post-enrichment microbial communities from each replicated mesocosm. This diversity of species and genes also underlies distinct degradation profiles among replicated mesocosms. Collectively, these results supported the hypothesis that the rare biosphere can serve as a genetic reservoir, which can be frequently missed by metagenomics but enables community response to changing environmental conditions caused by organic pollutants, and they provided insights into the size of the pool of rare genes and species.IMPORTANCE A single liter of water or gram of soil contains hundreds of low-abundance bacterial and archaeal species, the so called rare biosphere. The value of this astonishing biodiversity for ecosystem functioning remains poorly understood, primarily due to the fact that microbial community analysis frequently focuses on abundant organisms. Using a combination of culture-dependent and culture-independent (metagenomics) techniques, we showed that rare taxa and genes commonly contribute to the microbial community response to organic pollutants. Our findings should have implications for future studies that aim to study the role of rare species in environmental processes, including environmental bioremediation efforts of oil spills or other contaminants.}, }
@article {pmid28256033, year = {2017}, author = {Kawamura, Y and Yamamoto, Y and Sato, TA and Ochiya, T}, title = {Extracellular vesicles as trans-genomic agents: Emerging roles in disease and evolution.}, journal = {Cancer science}, volume = {108}, number = {5}, pages = {824-830}, pmid = {28256033}, issn = {1349-7006}, mesh = {DNA/*genetics ; Extracellular Vesicles/*metabolism/*physiology ; Genome/*genetics ; Genomics/methods ; Humans ; Tumor Microenvironment/*genetics ; }, abstract = {The composition of genetic material in extracellular vesicles (EV) has sparked interest particularly in the potential for horizontal gene transfer by EV. Although the RNA content of EV has been studied extensively, few reports have examined the DNA content of EV. It is still unclear how DNA is packaged inside EV, and whether they are functional in recipient cells. In this review, we describe the biological significance of genetic material in EV and their possible impacts in recipient cells, with focus on DNA from cancer cell-derived EV and the potential roles they may play in the cancer microenvironment. Another important feature of the genetic content of EV is the presence of retrotransposon elements. In this review, we discuss the possibility of an EV-mediated mechanism for the dispersal of retrotransposon elements, and their potential involvement in the development of genetically influenced diseases. In addition to this, we discuss the potential involvement of EV in the transfer of genetic material across species, and their possible impacts in modulating genome evolution.}, }
@article {pmid28253620, year = {2017}, author = {Gu, H and Kolewe, KW and Ren, D}, title = {Conjugation in Escherichia coli Biofilms on Poly(dimethylsiloxane) Surfaces with Microtopographic Patterns.}, journal = {Langmuir : the ACS journal of surfaces and colloids}, volume = {33}, number = {12}, pages = {3142-3150}, doi = {10.1021/acs.langmuir.6b04679}, pmid = {28253620}, issn = {1520-5827}, support = {R21 EY025750/EY/NEI NIH HHS/United States ; }, mesh = {*Biofilms ; Dimethylpolysiloxanes/*chemistry/metabolism ; Escherichia coli/*chemistry/metabolism ; Particle Size ; Surface Properties ; }, abstract = {Bacterial biofilms are highly tolerant to antimicrobials and play an important role in the development and spread of antibiotic resistance based on horizontal gene transfer due to close cell-to-cell contact. As an important surface property, topography has been shown to affect bacterial adhesion and biofilm formation. Here, we demonstrate that micrometer-scale surface topographies also affect horizontal gene transfer through conjugation in bacterial biofilms. Specifically, biofilm formation and associated conjugation on poly(dimethylsiloxane) (PDMS) surfaces with 10 μm tall protruding patterns were studied using fluorescently labeled donor and recipient strains of Escherichia coli. The results demonstrate that square-shaped topographic patterns with side length of 20, 50, and 100 μm and interpattern distance equal to or larger than 10 μm promote biofilm formation and conjugation compared to the smooth control. The vertical sides of these topographic features were found to be the "hot spots" for bacterial conjugation compared to the top of patterns and grooves between topographic features. The increase in conjugation frequency on the sides of topographic patterns was attributed to the high cell density of recipient cells at these locations. A motility (motB) mutant of the recipient strain exhibited defects in biofilm formation at the "hot spots" and conjugation, which were recovered by complementing the motB gene on a plasmid. These results also provided guidance for designing surface topographies that can reduce conjugation. Specifically, 10 μm tall hexagon-shaped topographic patterns with side length of 15 μm and interpattern distance of 2 μm were prepared to reduce biofilm formation on the side of protruding patterns and interrupt cell-cell interaction in the grooves. This topography exhibited 85% and 46% reduction of biofilm formation and associated conjugation, respectively, compared to the smooth control.}, }
@article {pmid28247474, year = {2017}, author = {Harrison, E and Hall, JPJ and Paterson, S and Spiers, AJ and Brockhurst, MA}, title = {Conflicting selection alters the trajectory of molecular evolution in a tripartite bacteria-plasmid-phage interaction.}, journal = {Molecular ecology}, volume = {26}, number = {10}, pages = {2757-2764}, pmid = {28247474}, issn = {1365-294X}, mesh = {Bacteriophages/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Plasmids/*genetics ; Pseudomonas fluorescens/*genetics/*virology ; *Selection, Genetic ; }, abstract = {Bacteria engage in a complex network of ecological interactions, which includes mobile genetic elements (MGEs) such as phages and plasmids. These elements play a key role in microbial communities as vectors of horizontal gene transfer but can also be important sources of selection for their bacterial hosts. In natural communities, bacteria are likely to encounter multiple MGEs simultaneously and conflicting selection among MGEs could alter the bacterial evolutionary response to each MGE. Here, we test the effect of interactions with multiple MGEs on bacterial molecular evolution in the tripartite interaction between the bacterium, Pseudomonas fluorescens, the lytic bacteriophage, SBW25φ2, and conjugative plasmid, pQBR103, using genome sequencing of experimentally evolved bacteria. We show that individually, both plasmids and phages impose selection leading to bacterial evolutionary responses that are distinct from bacterial populations evolving without MGEs, but that together, plasmids and phages impose conflicting selection on bacteria, constraining the evolutionary responses observed in pairwise interactions. Our findings highlight the likely difficulties of predicting evolutionary responses to multiple selective pressures from the observed evolutionary responses to each selective pressure alone. Understanding evolution in complex microbial communities comprising many species and MGEs will require that we go beyond studies of pairwise interactions.}, }
@article {pmid28243225, year = {2017}, author = {Bai, L and Wang, L and Yang, X and Wang, J and Gan, X and Wang, W and Xu, J and Chen, Q and Lan, R and Fanning, S and Li, F}, title = {Prevalence and Molecular Characteristics of Extended-Spectrum β-Lactamase Genes in Escherichia coli Isolated from Diarrheic Patients in China.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {144}, pmid = {28243225}, issn = {1664-302X}, abstract = {Background: The emergence and spread of antimicrobial resistance has become a major global public health concern. A component element of this is the spread of the plasmid-encoded extended-spectrum b-lactamase (ESBL) genes, conferring resistance to third-generation cephalosporins. The purpose of this study was to investigate the molecular characteristics of ESBL-encoding genes identified in Escherichia coli cultured from diarrheic patients in China from 2013 to 2014. Materials and Methods: A total of 51 E. coli were confirmed as ESBL producers by double-disk synergy testing of 912 E. coli isolates studied. Polymerase chain reaction (PCR) and DNA sequencing were performed to identify the corresponding ESBL genes. Susceptibility testing was tested by the disk diffusion method. Plasmids were typed by PCR-based replicon typing and their sizes were determined by S1-nuclease pulsed-field gel electrophoresis. Multi-locus sequence typing (MLST) and phylogrouping were also performed. Broth mating assays were carried out for all isolates to determine whether the ESBL marker could be transferred by conjugation. Results: Of the 51 ESBL-positive isolates identified, blaCTX-M, blaTEM, blaOXA, and blaSHV were detected in 51, 26, 3, 1 of these isolates, respectively. Sequencing revealed that 7 blaCTX-M subtypes were detected, with blaCTX-M-14 being the most common, followed by blaCTX-M-79 and blaCTX-M-28. Of the 26 TEM-positive isolates identified, all of these were blaTEM-1 genotypes. All isolates contained one to three large plasmids and 10 replicon types were detected. Of these, IncFrep (n = 50), IncK/B (n = 31), IncFIB (n = 26), IncB/O (n = 14), and IncI1-Ir (n = 8) replicon types were the predominating incompatibility groups. Twenty-six isolates demonstrated the ability to transfer their cefotaxime resistance marker at high transfer rates. MLST typing identified 31 sequence types and phylogenetic grouping showed that 12 of the 51 donor strains belonged to phylogroup B2. Conclusion: This study highlights the diversity of the ESBL producing E. coli and also the diversity of ESBL genes and plasmids carrying these genes in China, which poses a threat to public health.}, }
@article {pmid28242671, year = {2017}, author = {Yang, YQ and Li, YX and Song, T and Yang, YX and Jiang, W and Zhang, AY and Guo, XY and Liu, BH and Wang, YX and Lei, CW and Xiang, R and Wang, HN}, title = {Colistin Resistance Gene mcr-1 and Its Variant in Escherichia coli Isolates from Chickens in China.}, journal = {Antimicrobial agents and chemotherapy}, volume = {61}, number = {5}, pages = {}, pmid = {28242671}, issn = {1098-6596}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Base Sequence ; Chickens/*microbiology ; China ; Colistin/*pharmacology ; Drug Resistance, Bacterial/genetics ; Escherichia coli/drug effects/*genetics/isolation &amp; purification ; Escherichia coli Infections/drug therapy/veterinary ; Escherichia coli Proteins/*genetics ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Plasmids/genetics ; Poultry Diseases/*microbiology ; Sequence Analysis, DNA ; beta-Lactamases/genetics ; }, abstract = {The mcr-1 gene was detected in 5.11% (58/1136) of Escherichia coli isolates of chicken origin from 13 provinces in China. A novel mcr-1 variant, named mcr-1.3, encoding an Ile-to-Val functional variant of MCR-1 was identified in a sequence type 155 (ST155) strain. An mcr-1.3-containing IncI2 plasmid, pHeN867 (60,757 bp), was identified. The transfer of pHeN867 led to a 32-fold increase in the MIC of colistin in the recipient, exhibiting an effect on colistin resistance that was similar to that of mcr-1.}, }
@article {pmid28242668, year = {2017}, author = {Liu, Z and Wang, Y and Walsh, TR and Liu, D and Shen, Z and Zhang, R and Yin, W and Yao, H and Li, J and Shen, J}, title = {Plasmid-Mediated Novel blaNDM-17 Gene Encoding a Carbapenemase with Enhanced Activity in a Sequence Type 48 Escherichia coli Strain.}, journal = {Antimicrobial agents and chemotherapy}, volume = {61}, number = {5}, pages = {}, pmid = {28242668}, issn = {1098-6596}, support = {MR/P007295/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Amino Acid Substitution/genetics ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics ; Carbapenem-Resistant Enterobacteriaceae/drug effects/*genetics ; Chickens ; China ; Escherichia coli/*drug effects/*genetics/isolation &amp; purification ; Escherichia coli Proteins/*genetics ; Gene Transfer, Horizontal/genetics ; Microbial Sensitivity Tests ; Plasmids/*genetics ; beta-Lactamases/*genetics ; beta-Lactams/pharmacology ; }, abstract = {Carbapenem-resistant Enterobacteriaceae (CRE) have spread worldwide, leaving very few treatment options available. New Delhi metallo-beta-lactamase (NDM) is the main carbapenemase mediating CRE resistance and is of increasing concern. NDM-positive Enterobacteriaceae of human origin are frequently identified; however, the emergence of NDM, and particularly novel variants, in bacteria of food animal origin has never been reported. Here, we characterize a novel NDM variant (assigned NDM-17) identified in a β-lactam-resistant sequence type 48 (ST48) Escherichia coli strain that was isolated from a chicken in China. Compared to NDM-1, NDM-17 had three amino acid substitutions (V88L, M154L, and E170K) that confer significantly enhanced carbapenemase activity. Compared to NDM-5, NDM-17 had only one amino acid substitution (E170K) and slightly increased isolate resistance to carbapenem, as indicated by increased MIC values. The gene encoding NDM-17 (blaNDM-17) was located on an IncX3 plasmid, which was readily transferrable to recipient E. coli strain J53 by conjugation, suggesting the possibility of the rapid dissemination of blaNDM-17 Enzyme kinetics showed that NDM-17 could hydrolyze all β-lactams tested, except for aztreonam, and had a significantly higher affinity for all β-lactams tested than did NDM-5. The emergence of this novel NDM variant could pose a threat to public health because of its transferability and enhanced carbapenemase activity.}, }
@article {pmid28238801, year = {2017}, author = {He, D and Liu, L and Guo, B and Wu, S and Chen, X and Wang, J and Zeng, Z and Liu, JH}, title = {Chromosomal location of the fosA3 and blaCTX-M genes in Proteus mirabilis and clonal spread of Escherichia coli ST117 carrying fosA3-positive IncHI2/ST3 or F2:A-:B- plasmids in a chicken farm.}, journal = {International journal of antimicrobial agents}, volume = {49}, number = {4}, pages = {443-448}, doi = {10.1016/j.ijantimicag.2016.12.009}, pmid = {28238801}, issn = {1872-7913}, mesh = {Animals ; Bacterial Proteins/genetics ; Carrier State/microbiology/*veterinary ; Chickens/microbiology ; Enterobacteriaceae Infections/microbiology/*veterinary ; Escherichia coli/classification/*genetics/isolation &amp; purification ; Farms ; *Gene Transfer, Horizontal ; Molecular Typing ; Plasmids/*analysis/classification ; Polymerase Chain Reaction ; Proteus mirabilis/classification/*genetics/isolation &amp; purification ; beta-Lactamases/*genetics ; }, abstract = {The aim of this study was to investigate the spread and location of the fosA3 gene among Enterobacteriaceae from diseased broiler chickens. Twenty-nine Escherichia coli and seven Proteus mirabilis isolates recovered from one chicken farm were screened for the presence of plasmid-mediated fosfomycin resistance genes by PCR. The clonal relatedness of fosA3-positive isolates, the transferability and location of fosA3, and the genetic context of the fosA3 gene were determined. Seven P. mirabilis isolates with three different pulsed-field gel electrophoresis (PFGE) patterns and five E. coli isolates belonging to sequence type 117 (ST117) and phylogenetic group D were positive for fosA3 and all carried the blaCTX-M gene. In E. coli, the genetic structures IS26-ISEcp1-blaCTX-M-65-IS26-fosA3-1758 bp-IS26 and IS26-ISEcp1-blaCTX-M-3-blaTEM-1-IS26-fosA3-1758 bp-IS26 were present on transferable IncHI2/ST3 and F2:A-:B- plasmids, respectively. However, fosA3 was located on the chromosome of the seven P. mirabilis isolates. IS26-ISEcp1-blaCTX-M-65-IS26-fosA3-1758 bp-IS26 and IS26-blaCTX-M-14-611 bp-fosA3-1222 bp-IS26 were detected in three and four P. mirabilis isolates, respectively. Minicircles that contained both fosA3 and blaCTX-M-65 were shared between E. coli and P. mirabilis. This is the first report of the fosA3 gene integrated into the chromosome of P. mirabilis isolates with the blaCTX-M gene. The emergence and clonal spread of avian pathogenic E. coli ST117 with the feature of multidrug resistance and high virulence are a serious problem.}, }
@article {pmid28235827, year = {2017}, author = {Dupont, PY and Cox, MP}, title = {Genomic Data Quality Impacts Automated Detection of Lateral Gene Transfer in Fungi.}, journal = {G3 (Bethesda, Md.)}, volume = {7}, number = {4}, pages = {1301-1314}, pmid = {28235827}, issn = {2160-1836}, mesh = {Automation ; *Data Accuracy ; Epichloe/*genetics ; *Gene Transfer, Horizontal ; Genes, Fungal ; Genetic Variation ; Genomics/*standards ; Phylogeny ; Species Specificity ; Statistics as Topic ; }, abstract = {Lateral gene transfer (LGT, also known as horizontal gene transfer), an atypical mechanism of transferring genes between species, has almost become the default explanation for genes that display an unexpected composition or phylogeny. Numerous methods of detecting LGT events all rely on two fundamental strategies: primary structure composition or gene tree/species tree comparisons. Discouragingly, the results of these different approaches rarely coincide. With the wealth of genome data now available, detection of laterally transferred genes is increasingly being attempted in large uncurated eukaryotic datasets. However, detection methods depend greatly on the quality of the underlying genomic data, which are typically complex for eukaryotes. Furthermore, given the automated nature of genomic data collection, it is typically impractical to manually verify all protein or gene models, orthology predictions, and multiple sequence alignments, requiring researchers to accept a substantial margin of error in their datasets. Using a test case comprising plant-associated genomes across the fungal kingdom, this study reveals that composition- and phylogeny-based methods have little statistical power to detect laterally transferred genes. In particular, phylogenetic methods reveal extreme levels of topological variation in fungal gene trees, the vast majority of which show departures from the canonical species tree. Therefore, it is inherently challenging to detect LGT events in typical eukaryotic genomes. This finding is in striking contrast to the large number of claims for laterally transferred genes in eukaryotic species that routinely appear in the literature, and questions how many of these proposed examples are statistically well supported.}, }
@article {pmid28235561, year = {2017}, author = {Ccorahua-Santo, R and Eca, A and Abanto, M and Guerra, G and Ramírez, P}, title = {Physiological and comparative genomic analysis of Acidithiobacillus ferrivorans PQ33 provides psychrotolerant fitness evidence for oxidation at low temperature.}, journal = {Research in microbiology}, volume = {168}, number = {5}, pages = {482-492}, doi = {10.1016/j.resmic.2017.01.007}, pmid = {28235561}, issn = {1769-7123}, mesh = {Acidithiobacillus/enzymology/*genetics/*physiology ; Base Composition ; *Cold Temperature ; DNA, Bacterial/genetics ; Ferrous Compounds/*metabolism ; Gene Transfer, Horizontal ; *Genetic Fitness ; *Genome, Bacterial ; Genomic Islands ; Genomics ; Operon ; Oxidation-Reduction ; Peptidylprolyl Isomerase/genetics ; Phylogeny ; Trehalose/metabolism ; }, abstract = {Friendly environmental hydrometallurgy at low temperatures is principally promoted by Acidithiobacillus ferrivorans. Until recently, the synergy between cold tolerance and the molecular mechanism of ferrous iron (Fe[2+]) oxidation was unknown. In the present paper, we conducted a physiological and comparative genomics analysis of the new strain A. ferrivorans PQ33 to elucidate the oxidation mechanism at low temperatures, with emphasis placed on trehalose and the Rus operon. PQ33 exhibited a doubling time of 66.6 h in Fe[2+] at pH 1.6 and 63.6 h in CuS at 5 °C. Genomic island (GI) identification and comparative genome analysis were performed with four available genomes of Acidithiobacillus sp. The genome comprised 3,298,172 bp and 56.55% GC content. In contrast to ATCC Acidithiobacillus ferrooxidans strains, the genome of A. ferrivorans PQ33 harbors one GI, which contains a RusB gene. Moreover, five genes of peptidyl-prolyl cis-trans isomerase (PPIases) were observed. Furthermore, comparative analysis of the trehalose operon suggested the presence of a horizontal transfer event. In addition, comparison of rusticyanin proteins revealed that RusB has better intrinsic flexibility than RusA. This comparison suggests psychrotolerant fitness and supports the genetic canalization of A. ferrivorans PQ33 for oxidation at low temperature.}, }
@article {pmid28235127, year = {2017}, author = {Marcon, HS and Costa-Silva, J and Lorenzetti, APR and Marino, CL and Domingues, DS}, title = {Genome-wide analysis of EgEVE_1, a transcriptionally active endogenous viral element associated to small RNAs in Eucalyptus genomes.}, journal = {Genetics and molecular biology}, volume = {40}, number = {1 suppl 1}, pages = {217-225}, pmid = {28235127}, issn = {1415-4757}, abstract = {Endogenous viral elements (EVEs) are the result of heritable horizontal gene transfer from viruses to hosts. In the last years, several EVE integration events were reported in plants by the exponential availability of sequenced genomes. Eucalyptus grandis is a forest tree species with a sequenced genome that is poorly studied in terms of evolution and mobile genetic elements composition. Here we report the characterization of E. grandis endogenous viral element 1 (EgEVE_1), a transcriptionally active EVE with a size of 5,664 bp. Phylogenetic analysis and genomic distribution demonstrated that EgEVE_1 is a newly described member of the Caulimoviridae family, distinct from the recently characterized plant Florendoviruses. Genomic distribution of EgEVE_1 and Florendovirus is also distinct. EgEVE_1 qPCR quantification in Eucalyptus urophylla suggests that this genome has more EgEVE_1 copies than E. grandis. EgEVE_1 transcriptional activity was demonstrated by RT-qPCR in five Eucalyptus species and one intrageneric hybrid. We also identified that Eucalyptus EVEs can generate small RNAs (sRNAs),that might be involved in de novo DNA methylation and virus resistance. Our data suggest that EVE families in Eucalyptus have distinct properties, and we provide the first comparative analysis of EVEs in Eucalyptus genomes.}, }
@article {pmid28232822, year = {2017}, author = {Orlek, A and Stoesser, N and Anjum, MF and Doumith, M and Ellington, MJ and Peto, T and Crook, D and Woodford, N and Walker, AS and Phan, H and Sheppard, AE}, title = {Plasmid Classification in an Era of Whole-Genome Sequencing: Application in Studies of Antibiotic Resistance Epidemiology.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {182}, pmid = {28232822}, issn = {1664-302X}, abstract = {Plasmids are extra-chromosomal genetic elements ubiquitous in bacteria, and commonly transmissible between host cells. Their genomes include variable repertoires of 'accessory genes,' such as antibiotic resistance genes, as well as 'backbone' loci which are largely conserved within plasmid families, and often involved in key plasmid-specific functions (e.g., replication, stable inheritance, mobility). Classifying plasmids into different types according to their phylogenetic relatedness provides insight into the epidemiology of plasmid-mediated antibiotic resistance. Current typing schemes exploit backbone loci associated with replication (replicon typing), or plasmid mobility (MOB typing). Conventional PCR-based methods for plasmid typing remain widely used. With the emergence of whole-genome sequencing (WGS), large datasets can be analyzed using in silico plasmid typing methods. However, short reads from popular high-throughput sequencers can be challenging to assemble, so complete plasmid sequences may not be accurately reconstructed. Therefore, localizing resistance genes to specific plasmids may be difficult, limiting epidemiological insight. Long-read sequencing will become increasingly popular as costs decline, especially when resolving accurate plasmid structures is the primary goal. This review discusses the application of plasmid classification in WGS-based studies of antibiotic resistance epidemiology; novel in silico plasmid analysis tools are highlighted. Due to the diverse and plastic nature of plasmid genomes, current typing schemes do not classify all plasmids, and identifying conserved, phylogenetically concordant genes for subtyping and phylogenetics is challenging. Analyzing plasmids as nodes in a network that represents gene-sharing relationships between plasmids provides a complementary way to assess plasmid diversity, and allows inferences about horizontal gene transfer to be made.}, }
@article {pmid28230768, year = {2017}, author = {Mukai, T and Reynolds, NM and Crnković, A and Söll, D}, title = {Bioinformatic Analysis Reveals Archaeal tRNA[Tyr] and tRNA[Trp] Identities in Bacteria.}, journal = {Life (Basel, Switzerland)}, volume = {7}, number = {1}, pages = {}, pmid = {28230768}, issn = {2075-1729}, support = {R01 GM022854/GM/NIGMS NIH HHS/United States ; R35 GM122560/GM/NIGMS NIH HHS/United States ; R37 GM022854/GM/NIGMS NIH HHS/United States ; }, abstract = {The tRNA identity elements for some amino acids are distinct between the bacterial and archaeal domains. Searching in recent genomic and metagenomic sequence data, we found some candidate phyla radiation (CPR) bacteria with archaeal tRNA identity for Tyr-tRNA and Trp-tRNA synthesis. These bacteria possess genes for tyrosyl-tRNA synthetase (TyrRS) and tryptophanyl-tRNA synthetase (TrpRS) predicted to be derived from DPANN superphylum archaea, while the cognate tRNA[Tyr] and tRNA[Trp] genes reveal bacterial or archaeal origins. We identified a trace of domain fusion and swapping in the archaeal-type TyrRS gene of a bacterial lineage, suggesting that CPR bacteria may have used this mechanism to create diverse proteins. Archaeal-type TrpRS of bacteria and a few TrpRS species of DPANN archaea represent a new phylogenetic clade (named TrpRS-A). The TrpRS-A open reading frames (ORFs) are always associated with another ORF (named ORF1) encoding an unknown protein without global sequence identity to any known protein. However, our protein structure prediction identified a putative HIGH-motif and KMSKS-motif as well as many α-helices that are characteristic of class I aminoacyl-tRNA synthetase (aaRS) homologs. These results provide another example of the diversity of molecular components that implement the genetic code and provide a clue to the early evolution of life and the genetic code.}, }
@article {pmid28223970, year = {2017}, author = {Marti, H and Kim, H and Joseph, SJ and Dojiri, S and Read, TD and Dean, D}, title = {Tet(C) Gene Transfer between Chlamydia suis Strains Occurs by Homologous Recombination after Co-infection: Implications for Spread of Tetracycline-Resistance among Chlamydiaceae.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {156}, pmid = {28223970}, issn = {1664-302X}, abstract = {Chlamydia suis is a swine pathogen that has also recently been found to cause zoonotic infections of the human eye, pharynx, and gastrointestinal tract. Many strains contain a tetracycline class C gene [tet(C)] cassette that confers tetracycline resistance. The cassette was likely originally acquired by horizontal gene transfer from a Gram-negative donor after the introduction of tetracycline into animal feed in the 1950s. Various research groups have described the capacity for different Chlamydia species to exchange DNA by homologous recombination. Since over 90% of C. suis strains are tetracycline resistant, they represent a potential source for antibiotic-resistance spread within and between Chlamydiaceae species. Here, we examined the genetics of tet(C)-transfer among C. suis strains. Tetracycline-sensitive C. suis strain S45 was simultaneously or sequentially co-infected with tetracycline-resistant C. suis strains in McCoy cells. Potential recombinants were clonally purified by a harvest assay derived from the classic plaque assay. C. suis strain Rogers132, lacking transposases IS200 and IS605, was the most efficient donor, producing two unique recombinants detected in three of the 56 (5.4%) clones screened. Recombinants were found to have a minimal inhibitory concentration (MIC) of 8-16 μg/mL for tetracycline. Resistance remained stable over 10 passages as long as recombinants were initially grown in tetracycline at twice the MIC of S45 (0.032 μg/mL). Genomic analysis revealed that tet(C) had integrated into the S45 genome by homologous recombination at two unique sites depending on the recombinant: a 55 kb exchange between nrqF and pckG, and a 175 kb exchange between kdsA and cysQ. Neither site was associated with inverted repeats or motifs associated with recombination hotspots. Our findings show that cassette transfer into S45 has low frequency, does not require IS200/IS605 transposases, is stable if initially grown in tetracycline, and results in multiple genomic configurations. We provide a model for stable cassette transfer to better understand the capability for cassette acquisition by Chlamydiaceae species that infect humans, a matter of public health importance.}, }
@article {pmid28222679, year = {2017}, author = {Skippington, E and Barkman, TJ and Rice, DW and Palmer, JD}, title = {Comparative mitogenomics indicates respiratory competence in parasitic Viscum despite loss of complex I and extreme sequence divergence, and reveals horizontal gene transfer and remarkable variation in genome size.}, journal = {BMC plant biology}, volume = {17}, number = {1}, pages = {49}, pmid = {28222679}, issn = {1471-2229}, mesh = {DNA, Plant ; Electron Transport Chain Complex Proteins/genetics ; Electron Transport Complex I/*genetics/metabolism ; *Evolution, Molecular ; Gene Deletion ; *Gene Transfer, Horizontal ; Genes, Plant ; *Genetic Variation ; Genome, Mitochondrial ; *Genome, Plant ; Molecular Sequence Annotation ; Plant Proteins/genetics ; RNA, Plant ; RNA, Ribosomal ; Sequence Analysis, DNA ; Species Specificity ; Viscum/*genetics/metabolism ; Viscum album/genetics/metabolism ; }, abstract = {BACKGROUND: Aerobically respiring eukaryotes usually contain four respiratory-chain complexes (complexes I-IV) and an ATP synthase (complex V). In several lineages of aerobic microbial eukaryotes, complex I has been lost, with an alternative, nuclear-encoded NADH dehydrogenase shown in certain cases to bypass complex I and oxidize NADH without proton translocation. The first loss of complex I in any multicellular eukaryote was recently reported in two studies; one sequenced the complete mitogenome of the hemiparasitic aerial mistletoe, Viscum scurruloideum, and the other sequenced the V. album mitogenome. The V. scurruloideum study reported no significant additional loss of mitochondrial genes or genetic function, but the V. album study postulated that mitochondrial genes encoding all ribosomal RNAs and proteins of all respiratory complexes are either absent or pseudogenes, thus raising questions as to whether the mitogenome and oxidative respiration are functional in this plant.<br><br>RESULTS: To determine whether these opposing conclusions about the two Viscum mitogenomes reflect a greater degree of reductive/degenerative evolution in V. album or instead result from interpretative and analytical differences, we reannotated and reanalyzed the V. album mitogenome and compared it with the V. scurruloideum mitogenome. We find that the two genomes share a complete complement of mitochondrial rRNA genes and a typical complement of genes encoding respiratory complexes II-V. Most Viscum mitochondrial protein genes exhibit very high levels of divergence yet are evolving under purifying, albeit relaxed selection. We discover two cases of horizontal gene transfer in V. album and show that the two Viscum mitogenomes differ by 8.6-fold in size (66&#xa0;kb in V. scurruloideum; 565&#xa0;kb in V. album).<br><br>CONCLUSIONS: Viscum mitogenomes are extraordinary compared to other plant mitogenomes in terms of their wide size range, high rates of synonymous substitutions, degree of relaxed selection, and unprecedented loss of respiratory complex I. However, contrary to the initial conclusions regarding V. album, both Viscum mitogenomes possess conventional sets of rRNA and, excepting complex I, respiratory genes. Both plants should therefore be able to carry out aerobic respiration. Moreover, with respect to size, the V. scurruloideum mitogenome has experienced a greater level of reductive evolution.}, }
@article {pmid28219824, year = {2017}, author = {Horna, G and Velasquez, J and Fernández, N and Tamariz, J and Ruiz, J}, title = {Characterisation of the first KPC-2-producing Klebsiella pneumoniae ST340 from Peru.}, journal = {Journal of global antimicrobial resistance}, volume = {9}, number = {}, pages = {36-40}, doi = {10.1016/j.jgar.2016.12.011}, pmid = {28219824}, issn = {2213-7173}, mesh = {Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Disk Diffusion Antimicrobial Tests ; Gene Transfer, Horizontal ; Genotype ; Hospitals ; Humans ; Integrons ; Klebsiella Infections/*microbiology ; Klebsiella pneumoniae/classification/*enzymology/genetics/*isolation &amp; purification ; Molecular Typing ; Peru ; Plasmids/analysis ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; beta-Lactamases/genetics/*metabolism ; }, abstract = {OBJECTIVES: The aim of this study was to characterise a KPC-carrying Klebsiella pneumoniae isolate from a Peruvian hospital setting.<br><br>METHODS: The identity of the isolate was confirmed by amplification and sequencing of the 16S rRNA gene, and the antibiotic resistance profile was determined by disk diffusion and automated methods The sequence type (ST) and phylogenetic group were established by PCR. The presence of different &#x3b2;-lactamase genes was determined, including blaMBL, blaKPC, blaCTX-M, blaSHV, blaOXA-1-like, blaOXA-2-like, blaOXA-5-like, blaOXA-48-like and blaTEM and up to six different plasmid-encoded AmpC genes as well as class 1 integrons. The conjugability of &#x3b2;-lactam resistance was assessed by conjugation.<br><br>RESULTS: The isolate was confirmed to be K. pneumoniae classified as belonging to the KpI phylogenetic group within ST340, which belongs to the high-risk clonal complex 258 (CC258). The isolate was resistant to all &#x3b2;-lactam agents tested, with only the presence of a non-conjugative blaKPC-2 gene being detected and carried in a non-classical genetic structure.<br><br>CONCLUSIONS: This is the first description of a member of CC258 and of a blaKPC-2 gene in Peru. Intensive surveillance is needed to determine the relevance of both in this area.}, }
@article {pmid28217917, year = {2017}, author = {Cubillas, C and Miranda-Sánchez, F and González-Sánchez, A and Elizalde, JP and Vinuesa, P and Brom, S and García-de Los Santos, A}, title = {A comprehensive phylogenetic analysis of copper transporting P1B ATPases from bacteria of the Rhizobiales order uncovers multiplicity, diversity and novel taxonomic subtypes.}, journal = {MicrobiologyOpen}, volume = {6}, number = {4}, pages = {}, pmid = {28217917}, issn = {2045-8827}, mesh = {Bacterial Proteins/*genetics ; Computational Biology ; Copper-Transporting ATPases/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Phylogeny ; Rhizobiaceae/*classification/*enzymology/genetics ; Sequence Homology ; }, abstract = {The ubiquitous cytoplasmic membrane copper transporting P1B-1 and P1B-3 -type ATPases pump out Cu[+] and Cu[2+] , respectively, to prevent cytoplasmic accumulation and avoid toxicity. The presence of five copies of Cu-ATPases in the symbiotic nitrogen-fixing bacteria Sinorhizobium meliloti is remarkable; it is the largest number of Cu[+] -transporters in a bacterial genome reported to date. Since the prevalence of multiple Cu-ATPases in members of the Rhizobiales order is unknown, we performed an in silico analysis to understand the occurrence, diversity and evolution of Cu[+] -ATPases in members of the Rhizobiales order. Multiple copies of Cu-ATPase coding genes (2-8) were detected in 45 of the 53 analyzed genomes. The diversity inferred from a maximum-likelihood (ML) phylogenetic analysis classified Cu-ATPases into four monophyletic groups. Each group contained additional subtypes, based on the presence of conserved motifs. This novel phylogeny redefines the current classification, where they are divided into two subtypes (P1B-1 and P1B-3). Horizontal gene transfer (HGT) as well as the evolutionary dynamic of plasmid-borne genes may have played an important role in the functional diversification of Cu-ATPases. Homologous cytoplasmic and periplasmic Cu[+] -chaperones, CopZ, and CusF, that integrate a CopZ-CopA-CusF tripartite efflux system in gamma-proteobacteria and archeae, were found in 19 of the 53 surveyed genomes of the Rhizobiales. This result strongly suggests a high divergence of CopZ and CusF homologs, or the existence of unexplored proteins involved in cellular copper transport.}, }
@article {pmid28212383, year = {2017}, author = {Gupta, RS and Nanda, A and Khadka, B}, title = {Novel molecular, structural and evolutionary characteristics of the phosphoketolases from bifidobacteria and Coriobacteriales.}, journal = {PloS one}, volume = {12}, number = {2}, pages = {e0172176}, pmid = {28212383}, issn = {1932-6203}, mesh = {Actinobacteria/*enzymology ; Aldehyde-Lyases/*chemistry/genetics/*metabolism ; Amino Acid Sequence ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Phylogeny ; Protein Multimerization ; Protein Structure, Quaternary ; Sequence Homology, Amino Acid ; }, abstract = {Members from the order Bifidobacteriales, which include many species exhibiting health promoting effects, differ from all other organisms in using a unique pathway for carbohydrate metabolism, known as the "bifid shunt", which utilizes the enzyme phosphoketolase (PK) to carry out the phosphorolysis of both fructose-6-phosphate (F6P) and xylulose-5-phosphate (X5P). In contrast to bifidobacteria, the PKs found in other organisms (referred to XPK) are able to metabolize primarily X5P and show very little activity towards F6P. Presently, very little is known about the molecular or biochemical basis of the differences in the two forms of PKs. Comparative analyses of PK sequences from different organisms reported here have identified multiple high-specific sequence features in the forms of conserved signature inserts and deletions (CSIs) in the PK sequences that clearly distinguish the X5P/F6P phosphoketolases (XFPK) of bifidobacteria from the XPK homologs found in most other organisms. Interestingly, most of the molecular signatures that are specific for the XFPK from bifidobacteria are also shared by the PK homologs from the Coriobacteriales order of Actinobacteria. Similarly to the Bifidobacteriales, the order Coriobacteriales is also made up of commensal organisms, that are saccharolytic and able to metabolize wide variety of carbohydrates, producing lactate and other metabolites. Phylogenetic studies provide evidence that the XFPK from bifidobacteria are specifically related to those found in the Coriobacteriales and suggest that the gene for PK (XFPK) was horizontally transferred between these two groups. A number of the identified CSIs in the XFPK sequence, which serve to distinguish the XFPK homologs from XPK homologs, are located at the subunit interface in the structure of the XFPK dimer protein. The results of protein modelling and subunit docking studies indicate that these CSIs are involved in the formation/stabilization of the protein dimer. The significance of these observations regarding the differences in the activities of the XFPK and XPK homologs are discussed. Additionally, this work also discusses the significance of the XFPK-like homologs, similar to those found in bifidobacteria, in the order Coriobacteriales.}, }
@article {pmid28211334, year = {2017}, author = {Gardner, CM and Gunsch, CK}, title = {Adsorption capacity of multiple DNA sources to clay minerals and environmental soil matrices less than previously estimated.}, journal = {Chemosphere}, volume = {175}, number = {}, pages = {45-51}, doi = {10.1016/j.chemosphere.2017.02.030}, pmid = {28211334}, issn = {1879-1298}, mesh = {Adsorption ; Aluminum Silicates/*chemistry ; Bentonite ; Clay ; DNA/chemistry ; Gene Transfer, Horizontal ; Kaolin ; Minerals/chemistry ; Plants, Genetically Modified/*genetics ; Soil/*chemistry ; Soil Pollutants/analysis ; Transgenes/genetics ; Zea mays/genetics ; }, abstract = {The cultivation and consumption of transgenic crops continues to be a widely debated topic, as the potential ecological impacts are not fully understood. In particular, because antibiotic resistance genes (ARGs) have historically been used as selectable markers in the genetic engineering of transgenic crops, it is important to determine if the genetic constructs found in decomposing transgenic crops persist long enough in the environment and if they can be transferred horizontally to indigenous microorganisms. In the present study, we address the question of persistence. Others have also estimated the DNA adsorption capacity of various clays, but have done so by manipulating the surface charge and size of particles tested which may overestimate sorption and underestimate the DNA available for horizontal transfer. In the present study, isotherms were generated using model Calf Thymus DNA and transgenic maize DNA without surface modification. Montmorillonite, kaolinite, and 3 soil mixtures with varying clay content were used in this study. The adsorption capacity of pure montmorillonite and kaolinite minerals was found to be one to two orders of magnitude less than previously estimated likely due to the distribution of clay particle sizes and heteroionic particle surface charge. However, it appears that a substantial amount of DNA is still able to adsorb onto these matrices (up to 200 mg DNA per gram of clay) suggesting the potential availability of free transgenic DNA in the environment may still be significant. Future studies should be conducted to determine the fate of these genes in agricultural soils.}, }
@article {pmid28211331, year = {2017}, author = {Guo, X and Pang, W and Dou, C and Yin, D}, title = {Sulfamethoxazole and COD increase abundance of sulfonamide resistance genes and change bacterial community structures within sequencing batch reactors.}, journal = {Chemosphere}, volume = {175}, number = {}, pages = {21-27}, doi = {10.1016/j.chemosphere.2017.01.134}, pmid = {28211331}, issn = {1879-1298}, mesh = {Anti-Bacterial Agents/pharmacology ; Base Sequence ; Biodegradation, Environmental ; Bioreactors/microbiology ; Drug Resistance, Bacterial/*genetics ; Genes, Bacterial/*drug effects ; RNA, Ribosomal, 16S ; Sulfamethoxazole/*pharmacology ; Sulfonamides/metabolism ; Wastewater/*microbiology ; }, abstract = {The abundant microbial community in biological treatment processes in wastewater treatment plants (WWTPs) may potentially enhance the horizontal gene transfer of antibiotic resistance genes with the presence of antibiotics. A lab-scale sequencing batch reactor was designed to investigate response of sulfonamide resistance genes (sulI, sulII) and bacterial communities to various concentrations of sulfamethoxazole (SMX) and chemical oxygen demand (COD) of wastewater. The SMX concentrations (0.001 mg/L, 0.1 mg/L and 10 mg/L) decreased with treatment time and higher SMX level was more difficult to remove. The presence of SMX also significantly reduced the removal efficiency of ammonia nitrogen, affecting the normal function of WWTPs. All three concentrations of SMX raised both sulI and sulII genes with higher concentrations exhibiting greater increases. The abundance of sul genes was positive correlated with treatment time and followed the second-order reaction kinetic model. Interestingly, these two genes have rather similar activity. SulI and sulII gene abundance also performed similar response to COD. Simpson index and Shannon-Weiner index did not show changes in the microbial community diversity. However, the 16S rRNA gene cloning and sequencing results showed the bacterial community structures varied during different stages. The results demonstrated that influent antibiotics into WWTPs may facilitate selection of ARGs and affect the wastewater conventional treatment as well as the bacteria community structures.}, }
@article {pmid28207825, year = {2017}, author = {Ramachandran, G and Miguel-Arribas, A and Abia, D and Singh, PK and Crespo, I and Gago-Córdoba, C and Hao, JA and Luque-Ortega, JR and Alfonso, C and Wu, LJ and Boer, DR and Meijer, WJ}, title = {Discovery of a new family of relaxases in Firmicutes bacteria.}, journal = {PLoS genetics}, volume = {13}, number = {2}, pages = {e1006586}, pmid = {28207825}, issn = {1553-7404}, support = {/WT_/Wellcome Trust/United Kingdom ; WT098374AIA/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Sequence ; Bacillus subtilis/enzymology ; Bacterial Proteins/*genetics ; *Conjugation, Genetic ; DNA, Single-Stranded/genetics ; Drug Resistance, Bacterial/*genetics ; Endodeoxyribonucleases/*genetics/isolation &amp; purification ; Firmicutes/*enzymology/genetics ; Gastrointestinal Microbiome/genetics ; Gene Transfer, Horizontal ; Humans ; Plasmids/genetics ; }, abstract = {Antibiotic resistance is a serious global problem. Antibiotic resistance genes (ARG), which are widespread in environmental bacteria, can be transferred to pathogenic bacteria via horizontal gene transfer (HGT). Gut microbiomes are especially apt for the emergence and dissemination of ARG. Conjugation is the HGT route that is predominantly responsible for the spread of ARG. Little is known about conjugative elements of Gram-positive bacteria, including those of the phylum Firmicutes, which are abundantly present in gut microbiomes. A critical step in the conjugation process is the relaxase-mediated site- and strand-specific nick in the oriT region of the conjugative element. This generates a single-stranded DNA molecule that is transferred from the donor to the recipient cell via a connecting channel. Here we identified and characterized the relaxosome components oriT and the relaxase of the conjugative plasmid pLS20 of the Firmicute Bacillus subtilis. We show that the relaxase gene, named relLS20, is essential for conjugation, that it can function in trans and provide evidence that Tyr26 constitutes the active site residue. In vivo and in vitro analyses revealed that the oriT is located far upstream of the relaxase gene and that the nick site within oriT is located on the template strand of the conjugation genes. Surprisingly, the RelLS20 shows very limited similarity to known relaxases. However, more than 800 genes to which no function had been attributed so far are predicted to encode proteins showing significant similarity to RelLS20. Interestingly, these putative relaxases are encoded almost exclusively in Firmicutes bacteria. Thus, RelLS20 constitutes the prototype of a new family of relaxases. The identification of this novel relaxase family will have an important impact in different aspects of future research in the field of HGT in Gram-positive bacteria in general, and specifically in the phylum of Firmicutes, and in gut microbiome research.}, }
@article {pmid28206693, year = {2017}, author = {Bedhomme, S and Perez Pantoja, D and Bravo, IG}, title = {Plasmid and clonal interference during post horizontal gene transfer evolution.}, journal = {Molecular ecology}, volume = {26}, number = {7}, pages = {1832-1847}, pmid = {28206693}, issn = {1365-294X}, support = {647916/ERC_/European Research Council/International ; 682819/ERC_/European Research Council/International ; }, mesh = {Adaptation, Physiological ; Anti-Bacterial Agents/pharmacology ; Chromosomes, Bacterial/genetics ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; Escherichia coli/drug effects/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; High-Throughput Nucleotide Sequencing ; Plasmids/*genetics ; Sequence Analysis, DNA ; }, abstract = {Plasmids are nucleic acid molecules that can drive their own replication in a living cell. They can be transmitted horizontally and can thrive in the host cell to high-copy numbers. Plasmid replication and gene expression consume cellular resources and cells carrying plasmids incur fitness costs. But many plasmids carry genes that can be beneficial under certain conditions, allowing the cell to endure in the presence of antibiotics, toxins, competitors or parasites. Horizontal transfer of plasmid-encoded genes can thus instantaneously confer differential adaptation to local or transient selection conditions. This conflict between cellular fitness and plasmid spread sets the scene for multilevel selection processes. We have engineered a system to study the short-term evolutionary impact of different synonymous versions of a plasmid-encoded antibiotic resistance gene. Applying experimental evolution under different selection conditions and deep sequencing allowed us to show rapid local adaptation to the presence of antibiotic and to the specific version of the resistance gene transferred. We describe the presence of clonal interference at two different levels: at the within-cell level, because a single cell can carry several plasmids, and at the between-cell level, because a bacterial population may contain several clones carrying different plasmids and displaying different fitness in the presence/absence of antibiotic. Understanding the within-cell and between-cell dynamics of plasmids after horizontal gene transfer is essential to unravel the dense network of mobile elements underlying the worldwide threat to public health of antibiotic resistance.}, }
@article {pmid28204477, year = {2016}, author = {Lo, WS and Huang, YY and Kuo, CH}, title = {Winding paths to simplicity: genome evolution in facultative insect symbionts.}, journal = {FEMS microbiology reviews}, volume = {40}, number = {6}, pages = {855-874}, pmid = {28204477}, issn = {1574-6976}, mesh = {Animals ; Enterobacteriaceae/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/*genetics ; Insecta/*genetics/*microbiology ; Proteobacteria/genetics ; Spiroplasma/genetics ; Symbiosis/*genetics ; }, abstract = {Symbiosis between organisms is an important driving force in evolution. Among the diverse relationships described, extensive progress has been made in insect–bacteria symbiosis, which improved our understanding of the genome evolution in host-associated bacteria. Particularly, investigations on several obligate mutualists have pushed the limits of what we know about the minimal genomes for sustaining cellular life. To bridge the gap between those obligate symbionts with extremely reduced genomes and their non-host-restricted ancestors, this review focuses on the recent progress in genome characterization of facultative insect symbionts. Notable cases representing various types and stages of host associations, including those from multiple genera in the family Enterobacteriaceae (class Gammaproteobacteria), Wolbachia (Alphaproteobacteria) and Spiroplasma (Mollicutes), are discussed. Although several general patterns of genome reduction associated with the adoption of symbiotic relationships could be identified, extensive variation was found among these facultative symbionts. These findings are incorporated into the established conceptual frameworks to develop a more detailed evolutionary model for the discussion of possible trajectories. In summary, transitions from facultative to obligate symbiosis do not appear to be a universal one-way street; switches between hosts and lifestyles (e.g. commensalism, parasitism or mutualism) occur frequently and could be facilitated by horizontal gene transfer.}, }
@article {pmid28202954, year = {2017}, author = {Zarzycki, J and Sutter, M and Cortina, NS and Erb, TJ and Kerfeld, CA}, title = {In Vitro Characterization and Concerted Function of Three Core Enzymes of a Glycyl Radical Enzyme - Associated Bacterial Microcompartment.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {42757}, pmid = {28202954}, issn = {2045-2322}, support = {R01 AI114975/AI/NIAID NIH HHS/United States ; }, mesh = {Aldehyde Dehydrogenase/*chemistry/metabolism ; Bacterial Proteins/*chemistry/metabolism ; Cell Compartmentation ; Propanediol Dehydratase/*chemistry/metabolism ; Propylene Glycol/metabolism ; Protein Binding ; Rhodopseudomonas/enzymology ; }, abstract = {Many bacteria encode proteinaceous bacterial microcompartments (BMCs) that encapsulate sequential enzymatic reactions of diverse metabolic pathways. Well-characterized BMCs include carboxysomes for CO2-fixation, and propanediol- and ethanolamine-utilizing microcompartments that contain B12-dependent enzymes. Genes required to form BMCs are typically organized in gene clusters, which promoted their distribution across phyla by horizontal gene transfer. Recently, BMCs associated with glycyl radical enzymes (GREs) were discovered; these are widespread and comprise at least three functionally distinct types. Previously, we predicted one type of these GRE-associated microcompartments (GRMs) represents a B12-independent propanediol-utilizing BMC. Here we functionally and structurally characterize enzymes of the GRM of Rhodopseudomonas palustris BisB18 and demonstrate their concerted function in vitro. The GRM signature enzyme, the GRE, is a dedicated 1,2-propanediol dehydratase with a new type of intramolecular encapsulation peptide. It forms a complex with its activating enzyme and, in conjunction with an aldehyde dehydrogenase, converts 1,2-propanediol to propionyl-CoA. Notably, homologous GRMs are also encoded in pathogenic Escherichia coli strains. Our high-resolution crystal structures of the aldehyde dehydrogenase lead to a revised reaction mechanism. The successful in vitro reconstitution of a part of the GRM metabolism provides insights into the metabolic function and steps in the assembly of this BMC.}, }
@article {pmid28202049, year = {2017}, author = {Hülter, N and Sørum, V and Borch-Pedersen, K and Liljegren, MM and Utnes, AL and Primicerio, R and Harms, K and Johnsen, PJ}, title = {Costs and benefits of natural transformation in Acinetobacter baylyi.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {34}, pmid = {28202049}, issn = {1471-2180}, support = {281357/ERC_/European Research Council/International ; }, mesh = {Acinetobacter/enzymology/*genetics/metabolism/*radiation effects ; Bacterial Proteins/genetics/metabolism/radiation effects ; *Biological Evolution ; *Cost-Benefit Analysis ; DNA Damage/radiation effects ; DNA Repair/physiology/radiation effects ; DNA, Bacterial/genetics/radiation effects ; Exodeoxyribonuclease V/metabolism/radiation effects ; Gene Deletion ; Gene Transfer, Horizontal/genetics/radiation effects ; Genes, Bacterial/genetics/radiation effects ; Membrane Proteins/genetics/radiation effects ; Mutation/genetics/radiation effects ; Phenotype ; Recombination, Genetic/radiation effects ; Stress, Physiological ; Survival ; Transformation, Bacterial/*genetics/*radiation effects ; Ultraviolet Rays/adverse effects ; }, abstract = {BACKGROUND: Natural transformation enables acquisition of adaptive traits and drives genome evolution in prokaryotes. Yet, the selective forces responsible for the evolution and maintenance of natural transformation remain elusive since taken-up DNA has also been hypothesized to provide benefits such as nutrients or templates for DNA repair to individual cells.<br><br>RESULTS: We investigated the immediate effects of DNA uptake and recombination on the naturally competent bacterium Acinetobacter baylyi in both benign and genotoxic conditions. In head-to-head competition experiments between DNA uptake-proficient and -deficient strains, we observed a fitness benefit of DNA uptake independent of UV stress. This benefit was found with both homologous and heterologous DNA and was independent of recombination. Recombination with taken-up DNA reduced survival of transformed cells with increasing levels of UV-stress through interference with nucleotide excision repair, suggesting that DNA strand breaks occur during recombination attempts with taken-up DNA. Consistent with this, we show that absence of RecBCD and RecFOR recombinational DNA repair pathways strongly decrease natural transformation.<br><br>CONCLUSIONS: Our data show a physiological benefit of DNA uptake unrelated to recombination. In contrast, recombination during transformation is a strand break inducing process that represents a previously unrecognized cost of natural transformation.}, }
@article {pmid28199699, year = {2017}, author = {Verner-Jeffreys, DW and Brazier, T and Perez, RY and Ryder, D and Card, RM and Welch, TJ and Hoare, R and Ngo, T and McLaren, N and Ellis, R and Bartie, KL and Feist, SW and Rowe, WMP and Adams, A and Thompson, KD}, title = {Detection of the florfenicol resistance gene floR in Chryseobacterium isolates from rainbow trout. Exception to the general rule?.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {4}, pages = {}, doi = {10.1093/femsec/fix015}, pmid = {28199699}, issn = {1574-6941}, mesh = {Acetyltransferases/genetics ; Animals ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/*genetics ; Carrier Proteins/antagonists &amp; inhibitors/genetics ; Chloramphenicol O-Acetyltransferase/genetics ; Chryseobacterium/*drug effects/*genetics/isolation &amp; purification ; Genome, Bacterial/genetics ; Hemolysin Proteins/biosynthesis ; Humans ; Microbial Sensitivity Tests ; Oncorhynchus mykiss/*microbiology ; Phenylalanine/analogs &amp; derivatives/pharmacology ; Polymerase Chain Reaction ; Siderophores/biosynthesis ; Tetracycline Resistance/genetics ; Thiamphenicol/*analogs &amp; derivatives/pharmacology ; Virulence Factors/biosynthesis ; }, abstract = {Bacteria from the family Flavobacteriaceae often show low susceptibility to antibiotics. With the exception of two Chryseobacterium spp. isolates that were positive for the florfenicol resistance gene floR, no clinical resistance genes were identified by microarray in 36 Flavobacteriaceae isolates from salmonid fish that could grow in ≥ 4 mg/L florfenicol. Whole genome sequence analysis of the floR positive isolates revealed the presence of a region that contained the antimicrobial resistance genes floR, a tet(X) tetracycline resistance gene, a streptothricin resistance gene and a chloramphenicol acetyltransferase gene. In silico analysis of 377 published genomes for Flavobacteriaceae isolates from a range of sources confirmed that well-characterised resistance gene cassettes were not widely distributed in bacteria from this group. Efflux pump-mediated decreased susceptibility to a range of antimicrobials was confirmed in both floR positive isolates using an efflux pump inhibitor (phenylalanine-arginine β-naphthylamide) assay. The floR isolates possessed putative virulence factors, including production of siderophores and haemolysins, and were mildly pathogenic in rainbow trout. Results support the suggestion that, despite the detection of floR, susceptibility to antimicrobials in Flavobacteriaceae is mostly mediated via intrinsic mechanisms rather than the horizontally acquired resistance genes more normally associated with Gram-negative bacterial pathogens such as Enterobacteriaceae.}, }
@article {pmid28199335, year = {2017}, author = {Venner, S and Miele, V and Terzian, C and Biémont, C and Daubin, V and Feschotte, C and Pontier, D}, title = {Ecological networks to unravel the routes to horizontal transposon transfers.}, journal = {PLoS biology}, volume = {15}, number = {2}, pages = {e2001536}, pmid = {28199335}, issn = {1545-7885}, support = {R01 GM077582/GM/NIGMS NIH HHS/United States ; }, mesh = {Computer Simulation ; DNA Transposable Elements/*genetics ; *Ecosystem ; Gene Transfer, Horizontal/*genetics ; Genome ; }, abstract = {Transposable elements (TEs) represent the single largest component of numerous eukaryotic genomes, and their activity and dispersal constitute an important force fostering evolutionary innovation. The horizontal transfer of TEs (HTT) between eukaryotic species is a common and widespread phenomenon that has had a profound impact on TE dynamics and, consequently, on the evolutionary trajectory of many species' lineages. However, the mechanisms promoting HTT remain largely unknown. In this article, we argue that network theory combined with functional ecology provides a robust conceptual framework and tools to delineate how complex interactions between diverse organisms may act in synergy to promote HTTs.}, }
@article {pmid28199080, year = {2017}, author = {Nett, RS and Contreras, T and Peters, RJ}, title = {Characterization of CYP115 As a Gibberellin 3-Oxidase Indicates That Certain Rhizobia Can Produce Bioactive Gibberellin A4.}, journal = {ACS chemical biology}, volume = {12}, number = {4}, pages = {912-917}, pmid = {28199080}, issn = {1554-8937}, support = {R01 GM109773/GM/NIGMS NIH HHS/United States ; }, mesh = {Arabidopsis Proteins/*metabolism ; Gibberellins/*biosynthesis ; Mixed Function Oxygenases/*metabolism ; Rhizobium/*metabolism ; }, abstract = {The gibberellin (GA) phytohormones are produced not only by plants but also by fungi and bacteria. Previous characterization of a cytochrome P450 (CYP)-rich GA biosynthetic operon found in many symbiotic, nitrogen-fixing rhizobia led to the elucidation of bacterial GA biosynthesis and implicated GA9 as the final product. However, GA9 does not exhibit hormonal/biological activity and presumably requires further transformation to elicit an effect in the legume host plant. Some rhizobia that contain the GA operon also possess an additional CYP (CYP115), and here we show that this acts as a GA 3-oxidase to produce bioactive GA4 from GA9. This is the first GA 3-oxidase identified for rhizobia, and provides a more complete scheme for biosynthesis of bioactive GAs in bacteria. Furthermore, phylogenetic analyses suggest that rhizobia acquired CYP115 independently of the core GA operon, adding further complexity to the horizontal gene transfer of GA biosynthetic enzymes among bacteria.}, }
@article {pmid28197728, year = {2017}, author = {Gawryszewska, I and Żabicka, D and Hryniewicz, W and Sadowy, E}, title = {Linezolid-resistant enterococci in Polish hospitals: species, clonality and determinants of linezolid resistance.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {36}, number = {7}, pages = {1279-1286}, pmid = {28197728}, issn = {1435-4373}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Anti-Bacterial Agents/*pharmacokinetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Drug Resistance, Bacterial ; Enterococcus faecalis/classification/*drug effects/genetics/isolation &amp; purification ; Enterococcus faecium/classification/*drug effects/genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; Gram-Positive Bacterial Infections/*epidemiology/*microbiology ; Hospitals ; Humans ; Linezolid/*pharmacology ; Membrane Transport Proteins/genetics ; Minisatellite Repeats ; Multilocus Sequence Typing ; Mutation ; Plasmids/analysis ; Poland/epidemiology ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 23S/genetics ; }, abstract = {The significant increase of the linezolid-resistant enterococci (LRE) has been observed in Polish hospitals since 2012 and our study aimed at elucidating the possible reasons for this phenomenon. Polish LRE isolates were analysed by multilocus-sequence typing (MLST) and multiple locus variable-number tandem repeat (VNTR) analysis (MLVA), polymerase chain reaction (PCR) and PCR-restriction fragment length polymorphism (PCR-RFLP) to establish clonal relatedness and mechanism of linezolid resistance, respectively. Fifty analysed LRE (2008-2015) included mostly Enterococcus faecium (82%) and Enterococcus faecalis (16%). Enterococcus faecium belonged to the hospital-adapted lineages 17/18 and 78, while E. faecalis isolates represented ST6, a hospital-associated type, and ST116, found in both humans and food-production animals. The G2576T 23S rRNA mutation was the most frequent (94%) mechanism of linezolid/tedizolid resistance of LRE. None of the isolates carried the plasmid-associated gene of Cfr methyltransferase, whereas optrA, encoding the ABC-type drug transporter, was identified in two E. faecalis isolates. In these isolates, optrA was located on a plasmid, transferable to both E. faecium and E. faecalis, whose partial (36.3 kb) sequence was 100% identical to the pE394 plasmid, identified previously in China in both clinical and farm animal isolates. The optrA-E. faecium transconjugant displayed a significant growth deficiency, in contrast to the optrA-E. faecalis. Our study indicates the role of mutation acquisition by hospital-adapted clones of enterococci as a major driver of increasing resistance to linezolid and tedizolid. Transferability and apparent lack of a biological cost of resistance suggest that E. faecalis may be a natural reservoir of optrA, an emerging mechanism of oxazolidinone resistance.}, }
@article {pmid28197061, year = {2016}, author = {Saeb, AT}, title = {Presence of Bacterial Virulence Gene Homologues in the dibenzo-p-dioxins degrading bacterium Sphingomonas wittichii.}, journal = {Bioinformation}, volume = {12}, number = {4}, pages = {241-248}, pmid = {28197061}, issn = {0973-2063}, abstract = {Sphingomonas wittichii, a close relative of the human pathogen Sphingomonas paucimobilis, is a microorganism of great interest to the bioremediation community for its ability of biodegradation to a large number of toxic polychlorinated dioxins. In the present study we investigated the presence of different virulence factors and genes in S. wittichii. We utilized phylogenetic, comparative genomics and bioinformatics analysis to investigate the potentiality of S. wittichii as a potential virulent pathogen. The 16SrDNA phylogenetic tree showed that the closest bacterial taxon to S. wittichii is Brucella followed by Helicobacter, Campylobacter, Pseudomonas then Legionella. Despite their close phylogenetic relationship, S. wittichii did not share any virulence factors with Helicobacter or Campylobacter. On the contrary, in spite of the phylogenetic divergence between S. wittichii and Pseudomonas spp., they shared many major virulence factors, such as, adherence, antiphagocytosis, Iron uptake, proteases and quorum sensing. S. wittichii contains several major virulence factors resembling Pseudomonas sp., Legionella sp., Brucella sp. and Bordetella sp. virulence factors. Similarity of virulence factors did not match phylogenetic relationships. These findings suggest horizontal gene transfer of virulence factors rather than sharing a common pathogenic ancestor. S. wittichii is a potential virulent bacterium. Another possibility is that reductive evolution process attenuated S. wittichii pathogenic capabilities. Thus plenty of care must be taken when using this bacterium in soil remediation purposes.}, }
@article {pmid28195532, year = {2017}, author = {Dong, LF and Kovarova, J and Bajzikova, M and Bezawork-Geleta, A and Svec, D and Endaya, B and Sachaphibulkij, K and Coelho, AR and Sebkova, N and Ruzickova, A and Tan, AS and Kluckova, K and Judasova, K and Zamecnikova, K and Rychtarcikova, Z and Gopalan, V and Andera, L and Sobol, M and Yan, B and Pattnaik, B and Bhatraju, N and Truksa, J and Stopka, P and Hozak, P and Lam, AK and Sedlacek, R and Oliveira, PJ and Kubista, M and Agrawal, A and Dvorakova-Hortova, K and Rohlena, J and Berridge, MV and Neuzil, J}, title = {Horizontal transfer of whole mitochondria restores tumorigenic potential in mitochondrial DNA-deficient cancer cells.}, journal = {eLife}, volume = {6}, number = {}, pages = {}, pmid = {28195532}, issn = {2050-084X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Cell Line, Tumor ; Cell Respiration ; DNA, Mitochondrial/*genetics ; Disease Models, Animal ; *Gene Transfer, Horizontal ; Melanoma/*pathology ; Mice, Inbred C57BL ; }, abstract = {Recently, we showed that generation of tumours in syngeneic mice by cells devoid of mitochondrial (mt) DNA (ρ[0] cells) is linked to the acquisition of the host mtDNA. However, the mechanism of mtDNA movement between cells remains unresolved. To determine whether the transfer of mtDNA involves whole mitochondria, we injected B16ρ[0] mouse melanoma cells into syngeneic C57BL/6N[su9-DsRed2] mice that express red fluorescent protein in their mitochondria. We document that mtDNA is acquired by transfer of whole mitochondria from the host animal, leading to normalisation of mitochondrial respiration. Additionally, knockdown of key mitochondrial complex I (NDUFV1) and complex II (SDHC) subunits by shRNA in B16ρ[0] cells abolished or significantly retarded their ability to form tumours. Collectively, these results show that intact mitochondria with their mtDNA payload are transferred in the developing tumour, and provide functional evidence for an essential role of oxidative phosphorylation in cancer.}, }
@article {pmid28194158, year = {2017}, author = {Checcucci, A and Azzarello, E and Bazzicalupo, M and De Carlo, A and Emiliani, G and Mancuso, S and Spini, G and Viti, C and Mengoni, A}, title = {Role and Regulation of ACC Deaminase Gene in Sinorhizobium meliloti: Is It a Symbiotic, Rhizospheric or Endophytic Gene?.}, journal = {Frontiers in genetics}, volume = {8}, number = {}, pages = {6}, pmid = {28194158}, issn = {1664-8021}, abstract = {Plant-associated bacteria exhibit a number of different strategies and specific genes allow bacteria to communicate and metabolically interact with plant tissues. Among the genes found in the genomes of plant-associated bacteria, the gene encoding the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase (acdS) is one of the most diffused. This gene is supposed to be involved in the cleaving of plant-produced ACC, the precursor of the plant stress-hormone ethylene toning down the plant response to infection. However, few reports are present on the actual role in rhizobia, one of the most investigated groups of plant-associated bacteria. In particular, still unclear is the origin and the role of acdS in symbiotic competitiveness and on the selective benefit it may confer to plant symbiotic rhizobia. Here we present a phylogenetic and functional analysis of acdS orthologs in the rhizobium model-species Sinorhizobium meliloti. Results showed that acdS orthologs present in S. meliloti pangenome have polyphyletic origin and likely spread through horizontal gene transfer, mediated by mobile genetic elements. When acdS ortholog from AK83 strain was cloned and assayed in S. meliloti 1021 (lacking acdS), no modulation of plant ethylene levels was detected, as well as no increase in fitness for nodule occupancy was found in the acdS-derivative strain compared to the parental one. Surprisingly, AcdS was shown to confer the ability to utilize formamide and some dipeptides as sole nitrogen source. Finally, acdS was shown to be negatively regulated by a putative leucine-responsive regulator (LrpL) located upstream to acdS sequence (acdR). acdS expression was induced by root exudates of both legumes and non-leguminous plants. We conclude that acdS in S. meliloti is not directly related to symbiotic interaction, but it could likely be involved in the rhizospheric colonization or in the endophytic behavior.}, }
@article {pmid28193728, year = {2017}, author = {Repar, J and Warnecke, T}, title = {Mobile Introns Shape the Genetic Diversity of Their Host Genes.}, journal = {Genetics}, volume = {205}, number = {4}, pages = {1641-1648}, pmid = {28193728}, issn = {1943-2631}, support = {MC_UP_1102/7/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Endonucleases/genetics ; Gene Conversion ; Genes, Fungal ; *Introns ; Mutation ; *Polymorphism, Single Nucleotide ; Selection, Genetic ; Yeasts/*genetics ; }, abstract = {Self-splicing introns populate several highly conserved protein-coding genes in fungal and plant mitochondria. In fungi, many of these introns have retained their ability to spread to intron-free target sites, often assisted by intron-encoded endonucleases that initiate the homing process. Here, leveraging population genomic data from Saccharomyces cerevisiae, Schizosaccharomyces pombe, and Lachancea kluyveri, we expose nonrandom patterns of genetic diversity in exons that border self-splicing introns. In particular, we show that, in all three species, the density of single nucleotide polymorphisms increases as one approaches a mobile intron. Through multiple lines of evidence, we rule out relaxed purifying selection as the cause of uneven nucleotide diversity. Instead, our findings implicate intron mobility as a direct driver of host gene diversity. We discuss two mechanistic scenarios that are consistent with the data: either endonuclease activity and subsequent error-prone repair have left a mutational footprint on the insertion environment of mobile introns or nonrandom patterns of genetic diversity are caused by exonic coconversion, which occurs when introns spread to empty target sites via homologous recombination. Importantly, however, we show that exonic coconversion can only explain diversity gradients near intron-exon boundaries if the conversion template comes from outside the population. In other words, there must be pervasive and ongoing horizontal gene transfer of self-splicing introns into extant fungal populations.}, }
@article {pmid28193673, year = {2017}, author = {Gonzalez, GM and Hardwick, SW and Maslen, SL and Skehel, JM and Holmqvist, E and Vogel, J and Bateman, A and Luisi, BF and Broadhurst, RW}, title = {Structure of the Escherichia coli ProQ RNA-binding protein.}, journal = {RNA (New York, N.Y.)}, volume = {23}, number = {5}, pages = {696-711}, pmid = {28193673}, issn = {1469-9001}, support = {/WT_/Wellcome Trust/United Kingdom ; 200873/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; MC_EX_MR/K015680/1/MRC_/Medical Research Council/United Kingdom ; MC_U105178788/MRC_/Medical Research Council/United Kingdom ; }, mesh = {3' Untranslated Regions ; Binding Sites ; Escherichia coli Proteins/*chemistry/metabolism ; Host Factor 1 Protein/metabolism ; Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; Protein Domains ; RNA-Binding Proteins/*chemistry/metabolism ; }, abstract = {The protein ProQ has recently been identified as a global small noncoding RNA-binding protein in Salmonella, and a similar role is anticipated for its numerous homologs in divergent bacterial species. We report the solution structure of Escherichia coli ProQ, revealing an N-terminal FinO-like domain, a C-terminal domain that unexpectedly has a Tudor domain fold commonly found in eukaryotes, and an elongated bridging intradomain linker that is flexible but nonetheless incompressible. Structure-based sequence analysis suggests that the Tudor domain was acquired through horizontal gene transfer and gene fusion to the ancestral FinO-like domain. Through a combination of biochemical and biophysical approaches, we have mapped putative RNA-binding surfaces on all three domains of ProQ and modeled the protein's conformation in the apo and RNA-bound forms. Taken together, these data suggest how the FinO, Tudor, and linker domains of ProQ cooperate to recognize complex RNA structures and serve to promote RNA-mediated regulation.}, }
@article {pmid28193666, year = {2017}, author = {Albornoz, E and Tijet, N and De Belder, D and Gomez, S and Martino, F and Corso, A and Melano, RG and Petroni, A}, title = {qnrE1, a Member of a New Family of Plasmid-Located Quinolone Resistance Genes, Originated from the Chromosome of Enterobacter Species.}, journal = {Antimicrobial agents and chemotherapy}, volume = {61}, number = {5}, pages = {}, pmid = {28193666}, issn = {1098-6596}, mesh = {Aged ; Amino Acid Sequence ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/*genetics ; DNA Gyrase/genetics ; Drug Resistance, Bacterial/*genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Escherichia coli/drug effects/genetics ; Female ; Gene Transfer, Horizontal/genetics ; Humans ; Klebsiella pneumoniae/drug effects/*genetics ; Microbial Sensitivity Tests ; Plasmids/genetics ; Quinolones/*pharmacology ; }, abstract = {qnrE1, found in a clinical Klebsiella pneumoniae isolate, was undetectable by PCR assays used for the six qnr families. qnrE1 was located on a conjugative plasmid (ca. 185 kb) and differed from qnrB alleles by 25%. Phylogenetic reconstructions of qnr genes and proteins and analysis of the qnrE1 surroundings showed that this gene belongs to a new qnr family and was likely mobilized by ISEcp1 from the chromosome of Enterobacter spp. to plasmids of K. pneumoniae.}, }
@article {pmid28190803, year = {2017}, author = {Kojima, H and Shinohara, R and Itonori, S and Ito, M}, title = {Characterization of a Novel Rhamnose-containing Acidic Glycosphingolipid from the Ascidian Halocynthia aurantium.}, journal = {Journal of oleo science}, volume = {66}, number = {3}, pages = {285-295}, doi = {10.5650/jos.ess16150}, pmid = {28190803}, issn = {1347-3352}, mesh = {Acidic Glycosphingolipids/*chemistry/isolation &amp; purification ; Animals ; Carbohydrate Sequence ; Ceramides/chemistry ; Chromatography, Ion Exchange ; Mass Spectrometry ; Rhamnose/*chemistry ; Stereoisomerism ; Urochordata/*chemistry ; }, abstract = {Halocynthia aurantium, an edible ascidian species belonging to Urochordata, was subjected to structural characterization of acidic glycosphingolipids to investigate these molecules in ascidians: sulfatide from Ciona intestinalis and the glucuronic acid-containing acidic glycosphingolipid from H. roretzi. Acidic glycosphingolipids containing three or five sugars were isolated from soft parts of the ascidian H. aurantium by chloroform-methanol extraction, mild-alkaline hydrolysis, precipitation with cold acetone, and subsequent column chromatography using a DEAE-Sephadex A-25 column, a Florisil column, and an Iatrobead column. The structures of these glycosphingolipids were determined by methylation studies, sugar analysis, fatty acid analysis, sphingoid analysis, mass spectrometry, and proton nuclear magnetic resonance spectroscopy. A novel glucuronic acid-containing glycosphingolipid having a rhamnose residue was identified as Rhaα1-3GlcNAcβ1-3Galβ1-4(Fucα1-3)GlcAβ1-Cer (UGL-2). This novel structure is particularly unusual given that it contains both a rhamnose residue and a reducing terminal glucuronic acid residue within a single molecule. Rhamnose is a characteristic sugar, which is a component of cell wall pectin in plants and exopolysaccharides in bacteria. Ascidians acquired the cellulose synthase gene via lateral gene transfer, and therefore, it can be speculated that they also acquired the rhamnosyltransferase gene in the same manner. We also detected Galβ1-4(Fucα1-3)GlcAβ1-Cer (UGL-1), which was already identified in another ascidian, H. roretzi.}, }
@article {pmid28189899, year = {2017}, author = {Costantini, A and Doria, F and Saiz, JC and Garcia-Moruno, E}, title = {Phage-host interactions analysis of newly characterized Oenococcus oeni bacteriophages: Implications for malolactic fermentation in wine.}, journal = {International journal of food microbiology}, volume = {246}, number = {}, pages = {12-19}, doi = {10.1016/j.ijfoodmicro.2017.01.020}, pmid = {28189899}, issn = {1879-3460}, mesh = {Bacteriophages/*genetics ; *Fermentation ; Food Microbiology ; Gene Transfer, Horizontal ; Hydrogen-Ion Concentration ; Integrases/genetics ; Lactic Acid/chemistry ; Malates/chemistry ; Microscopy, Electron ; Oenococcus/*virology ; Sensitivity and Specificity ; Ultraviolet Rays ; Wine/*microbiology ; }, abstract = {Nowadays, only few phages infecting Oenococcus oeni, the principal lactic acid bacteria (LAB) species responsible for malolactic fermentation (MLF) in wine, have been characterized. In the present study, to better understanding the factors affecting the lytic activity of Oenococcus phages, fifteen O. oeni bacteriophages have been studied in detail, both with molecular and microbiological methods. No correlations were found between genome sizes, type of integrase genes, or morphology and the lytic activity of the 15 tested phages. Interestingly, though phage attack in a wine at the end of alcoholic fermentation seems not to be a problem, it can indeed represent a risk factor for MLF when the alcohol content is low, feature that may be a key point for choosing the appropriate time for malolactic starter inoculation. Additionally, it was observed that some phages genomes bear 2 or 3 types of integrase genes, which point to horizontal gene transfer between O. oeni bacteriophages.}, }
@article {pmid28189637, year = {2017}, author = {Sieber, KB and Bromley, RE and Dunning Hotopp, JC}, title = {Lateral gene transfer between prokaryotes and eukaryotes.}, journal = {Experimental cell research}, volume = {358}, number = {2}, pages = {421-426}, pmid = {28189637}, issn = {1090-2422}, support = {DP2 OD007372/OD/NIH HHS/United States ; R01 CA206188/CA/NCI NIH HHS/United States ; T32 DK067872/DK/NIDDK NIH HHS/United States ; 1-R01-CA206188/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics ; Eukaryota/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics/physiology ; Humans ; Mitochondria/metabolism ; Prokaryotic Cells/*cytology ; }, abstract = {Lateral gene transfer (LGT) is an all-encompassing term for the movement of DNA between diverse organisms. LGT is synonymous with horizontal gene transfer, and the terms are used interchangeably throughout the scientific literature. While LGT has been recognized within the bacteria domain of life for decades, inter-domain LGTs are being increasingly described. LGTs between bacteria and complex multicellular organisms are of interest because they challenge the long-held dogma that such transfers could only occur in closely-related, single-celled organisms. Scientists will continue to challenge our understanding of LGT as we sequence more, diverse organisms, as we sequence more endosymbiont-colonized arthropods, and as we continue to appreciate LGT events, both young and old.}, }
@article {pmid28189617, year = {2017}, author = {Peris, D and Arias, A and Orlić, S and Belloch, C and Pérez-Través, L and Querol, A and Barrio, E}, title = {Mitochondrial introgression suggests extensive ancestral hybridization events among Saccharomyces species.}, journal = {Molecular phylogenetics and evolution}, volume = {108}, number = {}, pages = {49-60}, doi = {10.1016/j.ympev.2017.02.008}, pmid = {28189617}, issn = {1095-9513}, mesh = {Base Sequence ; Electron Transport Complex IV/genetics ; Genome, Mitochondrial ; Geography ; Haplotypes/genetics ; *Hybridization, Genetic ; Mitochondria/*genetics ; Open Reading Frames/genetics ; Phylogeny ; Saccharomyces/*genetics ; Sequence Alignment ; Species Specificity ; }, abstract = {Horizontal gene transfer (HGT) in eukaryotic plastids and mitochondrial genomes is common, and plays an important role in organism evolution. In yeasts, recent mitochondrial HGT has been suggested between S. cerevisiae and S. paradoxus. However, few strains have been explored given the lack of accurate mitochondrial genome annotations. Mitochondrial genome sequences are important to understand how frequent these introgressions occur, and their role in cytonuclear incompatibilities and fitness. Indeed, most of the Bateson-Dobzhansky-Muller genetic incompatibilities described in yeasts are driven by cytonuclear incompatibilities. We herein explored the mitochondrial inheritance of several worldwide distributed wild Saccharomyces species and their hybrids isolated from different sources and geographic origins. We demonstrated the existence of several recombination points in mitochondrial region COX2-ORF1, likely mediated by either the activity of the protein encoded by the ORF1 (F-SceIII) gene, a free-standing homing endonuclease, or mostly facilitated by A+T tandem repeats and regions of integration of GC clusters. These introgressions were shown to occur among strains of the same species and among strains of different species, which suggests a complex model of Saccharomyces evolution that involves several ancestral hybridization events in wild environments.}, }
@article {pmid28187427, year = {2016}, author = {Soares, SC and Oliveira, LC and Jaiswal, AK and Azevedo, V}, title = {Genomic Islands: an overview of current software and future improvements.}, journal = {Journal of integrative bioinformatics}, volume = {13}, number = {1}, pages = {301}, doi = {10.2390/biecoll-jib-2016-301}, pmid = {28187427}, issn = {1613-4516}, mesh = {Bacteria/*genetics ; *Genome, Bacterial ; *Genomic Islands ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {Microbes are highly diverse and widely distributed organisms. They account for ~60% of Earth’s biomass and new predictions point for the existence of 1011 to 1012 species, which are constantly sharing genes through several different mechanisms. Genomic Islands (GI) are critical in this context, as they are large regions acquired through horizontal gene transfer. Also, they present common features like genomic signature deviation, transposase genes, flanking tRNAs and insertion sequences. GIs carry large numbers of genes related to specific lifestyle and are commonly classified in Pathogenicity, Resistance, Metabolic or Symbiotic Islands. With the advent of the next-generation sequencing technologies and the deluge of genomic data, many software tools have been developed that aim to tackle the problem of GI prediction and they are all based on the prediction of GI common features. However, there is still room for the development of new software tools that implements new approaches, such as, machine learning and pangenomics based analyses. Finally, GIs will always hold a potential application in every newly invented genomic approach as they are directly responsible for much of the genomic plasticity of bacteria.}, }
@article {pmid28185583, year = {2016}, author = {Khan, MA and Mahmudi, O and Ullah, I and Arvestad, L and Lagergren, J}, title = {Probabilistic inference of lateral gene transfer events.}, journal = {BMC bioinformatics}, volume = {17}, number = {Suppl 14}, pages = {431}, pmid = {28185583}, issn = {1471-2105}, mesh = {Biological Evolution ; Entomoplasmataceae/classification/genetics ; Gene Transfer, Horizontal/*genetics ; *Models, Genetic ; Phylogeny ; }, abstract = {BACKGROUND: Lateral gene transfer (LGT) is an evolutionary process that has an important role in biology. It challenges the traditional binary tree-like evolution of species and is attracting increasing attention of the molecular biologists due to its involvement in antibiotic resistance. A number of attempts have been made to model LGT in the presence of gene duplication and loss, but reliably placing LGT events in the species tree has remained a challenge.<br><br>RESULTS: In this paper, we propose probabilistic methods that samples reconciliations of the gene tree with a dated species tree and computes maximum a posteriori probabilities. The MCMC-based method uses the probabilistic model DLTRS, that integrates LGT, gene duplication, gene loss, and sequence evolution under a relaxed molecular clock for substitution rates. We can estimate posterior distributions on gene trees and, in contrast to previous work, the actual placement of potential LGT, which can be used to, e.g., identify "highways" of LGT.<br><br>CONCLUSIONS: Based on a simulation study, we conclude that the method is able to infer the true LGT events on gene tree and reconcile it to the correct edges on the species tree in most cases. Applied to two biological datasets, containing gene families from Cyanobacteria and Molicutes, we find potential LGTs highways that corroborate other studies as well as previously undetected examples.}, }
@article {pmid28184216, year = {2017}, author = {Dashper, SG and Mitchell, HL and Seers, CA and Gladman, SL and Seemann, T and Bulach, DM and Chandry, PS and Cross, KJ and Cleal, SM and Reynolds, EC}, title = {Porphyromonas gingivalis Uses Specific Domain Rearrangements and Allelic Exchange to Generate Diversity in Surface Virulence Factors.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {48}, pmid = {28184216}, issn = {1664-302X}, abstract = {Porphyromonas gingivalis is a keystone pathogen of chronic periodontitis. The virulence of P. gingivalis is reported to be strain related and there are currently a number of strain typing schemes based on variation in capsular polysaccharide, the major and minor fimbriae and adhesin domains of Lys-gingipain (Kgp), amongst other surface proteins. P. gingivalis can exchange chromosomal DNA between strains by natural competence and conjugation. The aim of this study was to determine the genetic variability of P. gingivalis strains sourced from international locations over a 25-year period and to determine if variability in surface virulence factors has a phylogenetic basis. Whole genome sequencing was performed on 13 strains and comparison made to 10 previously sequenced strains. A single nucleotide polymorphism-based phylogenetic analysis demonstrated a shallow tri-lobed phylogeny. There was a high level of reticulation in the phylogenetic network, demonstrating extensive horizontal gene transfer between the strains. Two highly conserved variants of the catalytic domain of the major virulence factor the Kgp proteinase (KgpcatI and KgpcatII) were found. There were three variants of the fourth Kgp C-terminal cleaved adhesin domain. Specific variants of the cell surface proteins FimA, FimCDE, MfaI, RagAB, Tpr, and PrtT were also identified. The occurrence of all these variants in the P. gingivalis strains formed a mosaic that was not related to the SNP-based phylogeny. In conclusion P. gingivalis uses domain rearrangements and genetic exchange to generate diversity in specific surface virulence factors.}, }
@article {pmid28182844, year = {2017}, author = {Guo, H and Pan, L and Li, L and Lu, J and Kwok, L and Menghe, B and Zhang, H and Zhang, W}, title = {Characterization of Antibiotic Resistance Genes from Lactobacillus Isolated from Traditional Dairy Products.}, journal = {Journal of food science}, volume = {82}, number = {3}, pages = {724-730}, doi = {10.1111/1750-3841.13645}, pmid = {28182844}, issn = {1750-3841}, mesh = {Anti-Bacterial Agents/*pharmacology ; China ; Ciprofloxacin/pharmacology ; Cultured Milk Products/*microbiology ; Drug Resistance, Bacterial/*genetics ; Fermentation ; *Food Microbiology ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Lactobacillus/drug effects/*genetics/isolation &amp; purification ; Microbial Sensitivity Tests ; *Probiotics ; Tetracycline/pharmacology ; Vancomycin/pharmacology ; }, abstract = {Lactobacilli are widely used as starter cultures or probiotics in yoghurt, cheese, beer, wine, pickles, preserved food, and silage. They are generally recognized as safe (GRAS). However, recent studies have shown that some lactic acid bacteria (LAB) strains carry antibiotic resistance genes and are resistant to antibiotics. Some of them may even transfer their intrinsic antibiotic resistance genes to other LAB or pathogens via horizontal gene transfer, thus threatening human health. A total of 33 Lactobacillus strains was isolated from fermented milk collected from different areas of China. We analyzed (1) their levels of antibiotic resistance using a standardized dilution method, (2) their antibiotic resistance gene profiles by polymerase chain reaction (PCR) using gene-specific primers, and (3) the transferability of some of the detected resistance markers by a filter mating assay. All Lactobacillus strains were found to be resistant to vancomycin, but susceptible to gentamicin, linezolid, neomycin, erythromycin, and clindamycin. Their susceptibilities to tetracycline, kanamycin, ciprofloxacin, streptomycin, quinupristin/dalfopristin, trimethoprim, ampicillin, rifampicin, and chloramphenicol was different. Results from our PCR analysis revealed 19 vancomycin, 10 ciprofloxacin, and 1 tetracycline-resistant bacteria that carried the van(X), van(E), gyr(A), and tet(M) genes, respectively. Finally, no transferal of the monitored antibiotic resistance genes was observed in the filter mating assay. Taken together, our study generated the antibiotic resistance profiles of some milk-originated lactobacilli isolates and preliminarily assessed their risk of transferring antibiotic gene to other bacteria. The study may provide important data concerning the safe use of LAB.}, }
@article {pmid28180287, year = {2017}, author = {Chaliotis, A and Vlastaridis, P and Mossialos, D and Ibba, M and Becker, HD and Stathopoulos, C and Amoutzias, GD}, title = {The complex evolutionary history of aminoacyl-tRNA synthetases.}, journal = {Nucleic acids research}, volume = {45}, number = {3}, pages = {1059-1068}, pmid = {28180287}, issn = {1362-4962}, support = {R21 AI127582/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Amino Acyl-tRNA Synthetases/chemistry/classification/*genetics ; Bacteria/drug effects/enzymology/genetics ; Computational Biology ; Conserved Sequence ; Databases, Protein ; *Evolution, Molecular ; Markov Chains ; Phylogeny ; Protein Domains ; }, abstract = {Aminoacyl-tRNA synthetases (AARSs) are a superfamily of enzymes responsible for the faithful translation of the genetic code and have lately become a prominent target for synthetic biologists. Our large-scale analysis of >2500 prokaryotic genomes reveals the complex evolutionary history of these enzymes and their paralogs, in which horizontal gene transfer played an important role. These results show that a widespread belief in the evolutionary stability of this superfamily is misconceived. Although AlaRS, GlyRS, LeuRS, IleRS, ValRS are the most stable members of the family, GluRS, LysRS and CysRS often have paralogs, whereas AsnRS, GlnRS, PylRS and SepRS are often absent from many genomes. In the course of this analysis, highly conserved protein motifs and domains within each of the AARS loci were identified and used to build a web-based computational tool for the genome-wide detection of AARS coding sequences. This is based on hidden Markov models (HMMs) and is available together with a cognate database that may be used for specific analyses. The bioinformatics tools that we have developed may also help to identify new antibiotic agents and targets using these essential enzymes. These tools also may help to identify organisms with alternative pathways that are involved in maintaining the fidelity of the genetic code.}, }
@article {pmid28180279, year = {2017}, author = {Cooper, LP and Roberts, GA and White, JH and Luyten, YA and Bower, EKM and Morgan, RD and Roberts, RJ and Lindsay, JA and Dryden, DTF}, title = {DNA target recognition domains in the Type I restriction and modification systems of Staphylococcus aureus.}, journal = {Nucleic acids research}, volume = {45}, number = {6}, pages = {3395-3406}, pmid = {28180279}, issn = {1362-4962}, support = {BB/K005804/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; GR080463MA//Wellcome Trust/United Kingdom ; 090288/Z/09/ZA//Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Sequence ; DNA/chemistry/metabolism ; DNA Modification Methylases/*chemistry/*metabolism ; Deoxyribonucleases, Type I Site-Specific/*chemistry/*metabolism ; Protein Domains ; Sequence Analysis, DNA ; Staphylococcus aureus/*enzymology/genetics ; Transformation, Bacterial ; }, abstract = {Staphylococcus aureus displays a clonal population structure in which horizontal gene transfer between different lineages is extremely rare. This is due, in part, to the presence of a Type I DNA restriction-modification (RM) system given the generic name of Sau1, which maintains different patterns of methylation on specific target sequences on the genomes of different lineages. We have determined the target sequences recognized by the Sau1 Type I RM systems present in a wide range of the most prevalent S. aureus lineages and assigned the sequences recognized to particular target recognition domains within the RM enzymes. We used a range of biochemical assays on purified enzymes and single molecule real-time sequencing on genomic DNA to determine these target sequences and their patterns of methylation. Knowledge of the main target sequences for Sau1 will facilitate the synthesis of new vectors for transformation of the most prevalent lineages of this 'untransformable' bacterium.}, }
@article {pmid28179896, year = {2017}, author = {Suzuki, S and Pruden, A and Virta, M and Zhang, T}, title = {Editorial: Antibiotic Resistance in Aquatic Systems.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {14}, pmid = {28179896}, issn = {1664-302X}, }
@article {pmid28177699, year = {2017}, author = {Bogdanowicz, D and Giaro, K}, title = {Comparing Phylogenetic Trees by Matching Nodes Using the Transfer Distance Between Partitions.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {24}, number = {5}, pages = {422-435}, pmid = {28177699}, issn = {1557-8666}, mesh = {Algorithms ; Computational Biology/*methods ; Gene Transfer, Horizontal ; Models, Genetic ; *Phylogeny ; }, abstract = {Ability to quantify dissimilarity of different phylogenetic trees describing the relationship between the same group of taxa is required in various types of phylogenetic studies. For example, such metrics are used to assess the quality of phylogeny construction methods, to define optimization criteria in supertree building algorithms, or to find horizontal gene transfer (HGT) events. Among the set of metrics described so far in the literature, the most commonly used seems to be the Robinson-Foulds distance. In this article, we define a new metric for rooted trees-the Matching Pair (MP) distance. The MP metric uses the concept of the minimum-weight perfect matching in a complete bipartite graph constructed from partitions of all pairs of leaves of the compared phylogenetic trees. We analyze the properties of the MP metric and present computational experiments showing its potential applicability in tasks related to finding the HGT events.}, }
@article {pmid28174620, year = {2017}, author = {Schäfers, C and Blank, S and Wiebusch, S and Elleuche, S and Antranikian, G}, title = {Complete genome sequence of Thermus brockianus GE-1 reveals key enzymes of xylan/xylose metabolism.}, journal = {Standards in genomic sciences}, volume = {12}, number = {}, pages = {22}, pmid = {28174620}, issn = {1944-3277}, abstract = {Thermus brockianus strain GE-1 is a thermophilic, Gram-negative, rod-shaped and non-motile bacterium that was isolated from the Geysir geothermal area, Iceland. Like other thermophiles, Thermus species are often used as model organisms to understand the mechanism of action of extremozymes, especially focusing on their heat-activity and thermostability. Genome-specific features of T. brockianus GE-1 and their properties further help to explain processes of the adaption of extremophiles at elevated temperatures. Here we analyze the first whole genome sequence of T. brockianus strain GE-1. Insights of the genome sequence and the methodologies that were applied during de novo assembly and annotation are given in detail. The finished genome shows a phred quality value of QV50. The complete genome size is 2.38 Mb, comprising the chromosome (2,035,182 bp), the megaplasmid pTB1 (342,792 bp) and the smaller plasmid pTB2 (10,299 bp). Gene prediction revealed 2,511 genes in total, including 2,458 protein-encoding genes, 53 RNA and 66 pseudo genes. A unique genomic region on megaplasmid pTB1 was identified encoding key enzymes for xylan depolymerization and xylose metabolism. This is in agreement with the growth experiments in which xylan is utilized as sole source of carbon. Accordingly, we identified sequences encoding the xylanase Xyn10, an endoglucanase, the membrane ABC sugar transporter XylH, the xylose-binding protein XylF, the xylose isomerase XylA catalyzing the first step of xylose metabolism and the xylulokinase XylB, responsible for the second step of xylose metabolism. Our data indicate that an ancestor of T. brockianus obtained the ability to use xylose as alternative carbon source by horizontal gene transfer.}, }
@article {pmid28173753, year = {2017}, author = {Hong, TP and Carter, MQ and Struffi, P and Casonato, S and Hao, Y and Lam, JS and Lory, S and Jousson, O}, title = {Conjugative type IVb pilus recognizes lipopolysaccharide of recipient cells to initiate PAPI-1 pathogenicity island transfer in Pseudomonas aeruginosa.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {31}, pmid = {28173753}, issn = {1471-2180}, mesh = {Bacterial Proteins/genetics/metabolism ; Cell Membrane/chemistry ; Chromosomes, Bacterial ; Conjugation, Genetic/genetics/physiology ; Fimbriae, Bacterial/genetics ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Genome, Bacterial/genetics/physiology ; Genomic Islands/drug effects/*genetics ; Humans ; Lipopolysaccharides/chemistry/*metabolism ; Multigene Family ; Mutation ; Pseudomonas Infections/microbiology ; Pseudomonas aeruginosa/*genetics/pathogenicity ; Rhamnose/pharmacology ; Virulence Factors/genetics ; }, abstract = {BACKGROUND: Pseudomonas aeruginosa pathogenicity island 1 (PAPI-1) is one of the largest genomic islands of this important opportunistic human pathogen. Previous studies have shown that PAPI-1 encodes several putative virulence factors, including a major regulator of biofilm formation and antibiotic-resistance traits. PAPI-1 is horizontally transferable into recipient strains lacking this island via conjugation mediated by the specialized type IV pilus. The PAPI-1 encodes a cluster of ten genes associated with the synthesis and assembly of the type IV pilus. The PAPI-1 acquisition mechanism is currently not well understood.<br><br>RESULTS: In this study, we performed a series of conjugation experiments and identified determinants of PAPI-1 acquisition by analyzing transfer efficiency between the donor and a series of mutant recipient strains. Our data show that common polysaccharide antigen (CPA) lipopolysaccharide (LPS), a homopolymer of D-rhamnose, is required for initiating PAPI-1 transfer, suggesting that this structure acts as a receptor for conjugative type IV pilus in recipient strains. These results were substantiated by experimental evidence from PAPI-1 transfer assay experiments, in which outer membrane or LPS preparations from well-defined LPS mutants were added to the transfer mix to assess the role of P. aeruginosa LPS in PAPI-1 transfer and in vitro binding experiments between pilin fusion protein GST-pilV2' and immobilized LPS molecules were performed. Our data also showed that P. aeruginosa strains that had already acquired a copy of PAPI-1 were unable to import additional copies of the island, and that such strains produced proportionally lower amounts of CPA LPS compared to the strains lacking PAPI-1.<br><br>CONCLUSIONS: These results suggest that a PAPI-1 exclusion mechanism exists in P. aeruginosa that might serve to regulate the avoidance of uncontrolled expansions of the bacterial genome.}, }
@article {pmid28169338, year = {2017}, author = {Xiao, J and Liu, L and Ke, Y and Li, X and Liu, Y and Pan, Y and Yan, S and Wang, Y}, title = {Shrimp AHPND-causing plasmids encoding the PirAB toxins as mediated by pirAB-Tn903 are prevalent in various Vibrio species.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {42177}, pmid = {28169338}, issn = {2045-2322}, mesh = {Animals ; Bacterial Toxins/*biosynthesis/genetics ; Base Sequence ; Biological Evolution ; *DNA Transposable Elements ; Gene Transfer, Horizontal ; Hepatopancreas/microbiology/pathology ; High-Throughput Nucleotide Sequencing ; Penaeidae/*microbiology ; Phylogeny ; Plasmids/*chemistry/metabolism ; Seafood ; Sequence Homology, Nucleic Acid ; Vibrio/classification/*genetics/isolation &amp; purification/pathogenicity ; Vibrio parahaemolyticus/classification/*genetics/isolation &amp; purification/pathogenicity ; }, abstract = {Acute hepatopancreatic necrosis disease (AHPND) is a newly emerging shrimp disease caused by pirAB toxins encoded by a plasmid found in Vibrio parahaemolyticus. The pirAB toxins are the homologs of the Photorhabdus insect-related (Pir) toxins. Here, we report the complete sequences of the AHPND-causing plasmid isolated from V. owensii, as well as those of its 11 siblings (pVH family). In addition, we also included 13 related plasmids (pVH-r family) without the pirAB genes isolated from a variety of species within the Vibrio Harveyi clade. Furthermore, the pirAB-Tn903 composite transposon was identified in pVH, and both ends of the transposon appeared to have inserted simultaneously into the ancestor plasmid at different sites. The homologue counterparts of pirAB were also detected in a non-pVH plasmid in V. campbellii. Taken together, our results provide novel insights into the acquisition and evolution of pirAB as well as related plasmids in the Vibrio Harveyi clade.}, }
@article {pmid28168224, year = {2017}, author = {Loy, A and Pfann, C and Steinberger, M and Hanson, B and Herp, S and Brugiroux, S and Gomes Neto, JC and Boekschoten, MV and Schwab, C and Urich, T and Ramer-Tait, AE and Rattei, T and Stecher, B and Berry, D}, title = {Lifestyle and Horizontal Gene Transfer-Mediated Evolution of Mucispirillum schaedleri, a Core Member of the Murine Gut Microbiota.}, journal = {mSystems}, volume = {2}, number = {1}, pages = {}, pmid = {28168224}, issn = {2379-5077}, support = {I 2320/FWF_/Austrian Science Fund FWF/Austria ; P 27831/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Mucispirillum schaedleri is an abundant inhabitant of the intestinal mucus layer of rodents and other animals and has been suggested to be a pathobiont, a commensal that plays a role in disease. In order to gain insights into its lifestyle, we analyzed the genome and transcriptome of M. schaedleri ASF 457 and performed physiological experiments to test traits predicted by its genome. Although described as a mucus inhabitant, M. schaedleri has limited capacity for degrading host-derived mucosal glycans and other complex polysaccharides. Additionally, M. schaedleri reduces nitrate and expresses systems for scavenging oxygen and reactive oxygen species in vivo, which may account for its localization close to the mucosal tissue and expansion during inflammation. Also of note, M. schaedleri harbors a type VI secretion system and putative effector proteins and can modify gene expression in mucosal tissue, suggesting intimate interactions with its host and a possible role in inflammation. The M. schaedleri genome has been shaped by extensive horizontal gene transfer, primarily from intestinal Epsilon- and Deltaproteobacteria, indicating that horizontal gene transfer has played a key role in defining its niche in the gut ecosystem. IMPORTANCE Shifts in gut microbiota composition have been associated with intestinal inflammation, but it remains unclear whether inflammation-associated bacteria are commensal or detrimental to their host. Here, we studied the lifestyle of the gut bacterium Mucispirillum schaedleri, which is associated with inflammation in widely used mouse models. We found that M. schaedleri has specialized systems to handle oxidative stress during inflammation. Additionally, it expresses secretion systems and effector proteins and can modify the mucosal gene expression of its host. This suggests that M. schaedleri undergoes intimate interactions with its host and may play a role in inflammation. The insights presented here aid our understanding of how commensal gut bacteria may be involved in altering susceptibility to disease.}, }
@article {pmid28167670, year = {2017}, author = {Kintz, E and Heiss, C and Black, I and Donohue, N and Brown, N and Davies, MR and Azadi, P and Baker, S and Kaye, PM and van der Woude, M}, title = {Salmonella enterica Serovar Typhi Lipopolysaccharide O-Antigen Modification Impact on Serum Resistance and Antibody Recognition.}, journal = {Infection and immunity}, volume = {85}, number = {4}, pages = {}, pmid = {28167670}, issn = {1098-5522}, support = {/WT_/Wellcome Trust/United Kingdom ; G1000230/MRC_/Medical Research Council/United Kingdom ; 100087/Z/12/Z/WT_/Wellcome Trust/United Kingdom ; WT094333MA/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Antibodies, Bacterial/*immunology/pharmacology ; Bacterial Proteins/genetics/immunology/metabolism ; Base Sequence ; Disease Models, Animal ; Female ; Gene Expression Regulation, Bacterial ; Humans ; Immune Sera/*immunology/pharmacology ; Immunization ; Methylation ; Mice ; O Antigens/*immunology/metabolism ; Operon ; Salmonella typhi/classification/drug effects/genetics/*immunology ; Typhoid Fever/immunology/microbiology ; }, abstract = {Salmonella enterica serovar Typhi is a human-restricted Gram-negative bacterial pathogen responsible for causing an estimated 27 million cases of typhoid fever annually, leading to 217,000 deaths, and current vaccines do not offer full protection. The O-antigen side chain of the lipopolysaccharide is an immunodominant antigen, can define host-pathogen interactions, and is under consideration as a vaccine target for some Gram-negative species. The composition of the O-antigen can be modified by the activity of glycosyltransferase (gtr) operons acquired by horizontal gene transfer. Here we investigate the role of two gtr operons that we identified in the S Typhi genome. Strains were engineered to express specific gtr operons. Full chemical analysis of the O-antigens of these strains identified gtr-dependent glucosylation and acetylation. The glucosylated form of the O-antigen mediated enhanced survival in human serum and decreased complement binding. A single nucleotide deviation from an epigenetic phase variation signature sequence rendered the expression of this glucosylating gtr operon uniform in the population. In contrast, the expression of the acetylating gtrC gene is controlled by epigenetic phase variation. Acetylation did not affect serum survival, but phase variation can be an immune evasion mechanism, and thus, this modification may contribute to persistence in a host. In murine immunization studies, both O-antigen modifications were generally immunodominant. Our results emphasize that natural O-antigen modifications should be taken into consideration when assessing responses to vaccines, especially O-antigen-based vaccines, and that the Salmonellagtr repertoire may confound the protective efficacy of broad-ranging Salmonella lipopolysaccharide conjugate vaccines.}, }
@article {pmid28167346, year = {2017}, author = {Okubo, T and Matushita, M and Ohara, Y and Matsuo, J and Oguri, S and Fukumoto, T and Hayasaka, K and Akizawa, K and Shibuya, H and Shimizu, C and Yamaguchi, H}, title = {Ciliates promote the transfer of a plasmid encoding blaNDM-5 from Escherichia coli, isolated from a hospital in Japan, to other human pathogens.}, journal = {International journal of antimicrobial agents}, volume = {49}, number = {3}, pages = {387-388}, doi = {10.1016/j.ijantimicag.2017.01.003}, pmid = {28167346}, issn = {1872-7913}, mesh = {Escherichia coli/*genetics ; *Gene Transfer, Horizontal ; Humans ; *Plasmids ; Tetrahymena/*genetics ; beta-Lactamases/*genetics ; }, }
@article {pmid28165062, year = {2017}, author = {Scavariello, C and Luchetti, A and Martoni, F and Bonandin, L and Mantovani, B}, title = {Hybridogenesis and a potential case of R2 non-LTR retrotransposon horizontal transmission in Bacillus stick insects (Insecta Phasmida).}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {41946}, pmid = {28165062}, issn = {2045-2322}, mesh = {Animals ; Evolution, Molecular ; *Gene Flow ; *Gene Transfer, Horizontal ; *Hybridization, Genetic ; Insecta/classification/*genetics ; Parthenogenesis/*genetics ; Phylogeny ; *Retroelements ; }, abstract = {Horizontal transfer (HT) is an event in which the genetic material is transferred from one species to another, even if distantly related, and it has been demonstrated as a possible essential part of the lifecycle of transposable elements (TEs). However, previous studies on the non-LTR R2 retrotransposon, a metazoan-wide distributed element, indicated its vertical transmission since the Radiata-Bilateria split. Here we present the first possible instances of R2 HT in stick insects of the genus Bacillus (Phasmida). Six R2 elements were characterized in the strictly bisexual subspecies B. grandii grandii, B. grandii benazzii and B. grandii maretimi and in the obligatory parthenogenetic taxon B. atticus. These elements were compared with those previously retrieved in the facultative parthenogenetic species B. rossius. Phylogenetic inconsistencies between element and host taxa, and age versus divergence analyses agree and support at least two HT events. These HT events can be explained by taking into consideration the complex Bacillus reproductive biology, which includes also hybridogenesis, gynogenesis and androgenesis. Through these non-canonical reproductive modes, R2 elements may have been transferred between Bacillus genomes. Our data suggest, therefore, a possible role of hybridization for TEs survival and the consequent reshaping of involved genomes.}, }
@article {pmid28164039, year = {2017}, author = {Lu, Y and Zeng, J and Wu, B and E, S and Wang, L and Cai, R and Zhang, N and Li, Y and Huang, X and Huang, B and Chen, C}, title = {Quorum Sensing N-acyl Homoserine Lactones-SdiA Suppresses Escherichia coli-Pseudomonas aeruginosa Conjugation through Inhibiting traI Expression.}, journal = {Frontiers in cellular and infection microbiology}, volume = {7}, number = {}, pages = {7}, pmid = {28164039}, issn = {2235-2988}, mesh = {Acyl-Butyrolactones/*metabolism ; Conjugation, Genetic/*drug effects ; DNA Helicases/*metabolism ; Escherichia coli/*drug effects/*genetics ; Escherichia coli Proteins/*metabolism ; Gene Expression Regulation, Bacterial/drug effects ; Pseudomonas aeruginosa/*genetics ; Trans-Activators/*metabolism ; }, abstract = {Conjugation is a key mechanism for horizontal gene transfer and plays an important role in bacterial evolution, especially with respect to antibiotic resistance. However, little is known about the role of donor and recipient cells in regulation of conjugation. Here, using an Escherichia coli (SM10λπ)-Pseudomonas aeruginosa (PAO1) conjugation model, we demonstrated that deficiency of lasI/rhlI, genes associated with generation of the quorum sensing signals N-acyl homoserine lactones (AHLs) in PAO1, or deletion of the AHLs receptor SdiA in the donor SM10λπ both facilitated conjugation. When using another AHLs-non-producing E. coli strain EC600 as recipient cells, deficiency of sdiA in donor SM10λπ hardly affect the conjugation. More importantly, in the presence of exogenous AHLs, the conjugation efficiency between SM10λπ and EC600 was dramatically decreased, while deficiency of sdiA in SM10λπ attenuated AHLs-inhibited conjugation. These data suggest the conjugation suppression function of AHLs-SdiA chemical signaling. Further bioinformatics analysis, β-galactosidase reporter system and electrophoretic mobility shift assays characterized the binding site of SdiA on the promoter region of traI gene. Furthermore, deletion of lasI/rhlI or sdiA promoted traI mRNA expression in SM10λπ and PAO1 co-culture system, which was abrogated by AHLs. Collectively, our results provide new insight into an important contribution of quorum sensing system AHLs-SdiA to the networks that regulate conjugation.}, }
@article {pmid28163827, year = {2017}, author = {Alexandraki, V and Kazou, M and Blom, J and Pot, B and Tsakalidou, E and Papadimitriou, K}, title = {The complete genome sequence of the yogurt isolate Streptococcus thermophilus ACA-DC 2.}, journal = {Standards in genomic sciences}, volume = {12}, number = {}, pages = {18}, pmid = {28163827}, issn = {1944-3277}, abstract = {Streptococcus thermophilus ACA-DC 2 is a newly sequenced strain isolated from traditional Greek yogurt. Among the 14 fully sequenced strains of S. thermophilus currently deposited in the NCBI database, the ACA-DC 2 strain has the smallest chromosome, containing 1,731,838 bp. The annotation of its genome revealed the presence of 1,850 genes, including 1,556 protein-coding genes, 70 RNA genes and 224 potential pseudogenes. A large number of pseudogenes were identified. This was also accompanied by the absence of pathogenic features suggesting evolution of strain ACA-DC 2 through genome decay processes, most probably due to adaptation to the milk ecosystem. Analysis revealed the existence of one complete lactose-galactose operon, several proteolytic enzymes, one exopolysaccharide cluster, stress response genes and four putative antimicrobial peptides. Interestingly, one CRISPR-cas system and one orphan CRISPR, both carrying only one spacer, were predicted indicating low activity or inactivation of the cas proteins. Nevertheless, four putative restriction-modification systems were determined that may compensate any deficiencies of the CRISPR-cas system. Furthermore, whole genome phylogeny indicated three distinct clades within S. thermophilus. Comparative analysis among selected strains representative for each clade, including strain ACA-DC 2, revealed a high degree of conservation at the genomic scale, but also strain specific regions. Unique genes and genomic islands of strain ACA-DC 2 contained a number of genes potentially acquired through horizontal gene transfer events, that could be related to important technological properties for dairy starters. Our study suggests genomic traits in strain ACA-DC 2 compatible to the production of dairy fermented foods.}, }
@article {pmid28163823, year = {2017}, author = {Aserse, AA and Woyke, T and Kyrpides, NC and Whitman, WB and Lindström, K}, title = {Draft genome sequence of type strain HBR26[T] and description of Rhizobium aethiopicum sp. nov.}, journal = {Standards in genomic sciences}, volume = {12}, number = {}, pages = {14}, pmid = {28163823}, issn = {1944-3277}, abstract = {Rhizobium aethiopicum sp. nov. is a newly proposed species within the genus Rhizobium. This species includes six rhizobial strains; which were isolated from root nodules of the legume plant Phaseolus vulgaris growing in soils of Ethiopia. The species fixes nitrogen effectively in symbiosis with the host plant P. vulgaris, and is composed of aerobic, Gram-negative staining, rod-shaped bacteria. The genome of type strain HBR26[T] of R. aethiopicum sp. nov. was one of the rhizobial genomes sequenced as a part of the DOE JGI 2014 Genomic Encyclopedia project designed for soil and plant-associated and newly described type strains. The genome sequence is arranged in 62 scaffolds and consists of 6,557,588 bp length, with a 61% G + C content and 6221 protein-coding and 86 RNAs genes. The genome of HBR26[T] contains repABC genes (plasmid replication genes) homologous to the genes found in five different Rhizobium etli CFN42[T] plasmids, suggesting that HBR26[T] may have five additional replicons other than the chromosome. In the genome of HBR26[T], the nodulation genes nodB, nodC, nodS, nodI, nodJ and nodD are located in the same module, and organized in a similar way as nod genes found in the genome of other known common bean-nodulating rhizobial species. nodA gene is found in a different scaffold, but it is also very similar to nodA genes of other bean-nodulating rhizobial strains. Though HBR26[T] is distinct on the phylogenetic tree and based on ANI analysis (the highest value 90.2% ANI with CFN42[T]) from other bean-nodulating species, these nod genes and most nitrogen-fixing genes found in the genome of HBR26[T] share high identity with the corresponding genes of known bean-nodulating rhizobial species (96-100% identity). This suggests that symbiotic genes might be shared between bean-nodulating rhizobia through horizontal gene transfer. R. aethiopicum sp. nov. was grouped into the genus Rhizobium but was distinct from all recognized species of that genus by phylogenetic analyses of combined sequences of the housekeeping genes recA and glnII. The closest reference type strains for HBR26[T] were R. etli CFN42[T] (94% similarity of the combined recA and glnII sequences) and Rhizobium bangladeshense BLR175[T] (93%). Genomic ANI calculation based on protein-coding genes also revealed that the closest reference strains were R. bangladeshense BLR175[T] and R. etli CFN42[T] with ANI values 91.8 and 90.2%, respectively. Nevertheless, the ANI values between HBR26[T] and BLR175[T] or CFN42[T] are far lower than the cutoff value of ANI (> = 96%) between strains in the same species, confirming that HBR26[T] belongs to a novel species. Thus, on the basis of phylogenetic, comparative genomic analyses and ANI results, we formally propose the creation of R. aethiopicum sp. nov. with strain HBR26[T] (=HAMBI 3550[T]=LMG 29711[T]) as the type strain. The genome assembly and annotation data is deposited in the DOE JGI portal and also available at European Nucleotide Archive under accession numbers FMAJ01000001-FMAJ01000062.}, }
@article {pmid28161438, year = {2018}, author = {Wong, MKS and Takei, Y}, title = {Molecular and evolutionary perspectives of the renin-angiotensin system from lamprey.}, journal = {General and comparative endocrinology}, volume = {257}, number = {}, pages = {137-142}, doi = {10.1016/j.ygcen.2017.01.031}, pmid = {28161438}, issn = {1095-6840}, mesh = {Animals ; Biological Evolution ; *Lampreys ; Renin-Angiotensin System/*physiology ; }, abstract = {The recent advance and revision on the renin-angiotensin system in lamprey were summarized and we emphasized that presence of two types of angiotensins (Angs) in lamprey. Due to the parasitic nature on fish blood, teleost-type Angs were produced in their buccal gland and secreted into the lamphredin to evade the host immunorejection. A native lamprey angiotensinogen (AGT) was identified in genome and it retains serine-protease inhibitor activity for thrombin that regulates the blood coagulation pathway. The native lamprey angiotensin II (Lp-Ang II) is hypotensive instead of hypertensive, suggesting a functional divergence on cardiovascular regulation from the main vertebrate groups. The renin gene was absent from the lamprey genome so far, and the mutation on the renin-recognition site on lamprey AGT suggested that other proteases may have replaced the role of renin. Lp-Ang II was shown to bind to AT1 receptor and internalized, but the downstream signaling was still unknown. Molecular and phylogenetic evidence on invertebrate ACE-like proteins indicated that they were not homologous to those in vertebrates and could be acting on other native peptides. Although it was generally believed that the RAS was a well-conserved hormone system in vertebrates and invertebrates, revision by molecular data indicated that invertebrates lack homologous RAS components while lamprey possess an almost complete RAS. This suggests that the hormone cascade system was first evolved around cyclostome emergence and invertebrates could have taken up the RAS components from vertebrates through horizontal gene transfer.}, }
@article {pmid28161329, year = {2017}, author = {Guerra, F and Arbini, AA and Moro, L}, title = {Mitochondria and cancer chemoresistance.}, journal = {Biochimica et biophysica acta. Bioenergetics}, volume = {1858}, number = {8}, pages = {686-699}, doi = {10.1016/j.bbabio.2017.01.012}, pmid = {28161329}, issn = {0005-2728}, mesh = {Animals ; Antineoplastic Agents/*pharmacology/therapeutic use ; Apoptosis/drug effects ; Cell Transformation, Neoplastic ; DNA, Mitochondrial/genetics ; Disease Progression ; Drug Design ; Drug Resistance, Neoplasm/drug effects/*physiology ; Energy Metabolism/*drug effects ; Gene Transfer, Horizontal ; Humans ; Mitochondria/*drug effects/metabolism ; Mitochondrial Proteins/genetics/physiology ; Models, Biological ; Neoplasm Metastasis ; Neoplasm Proteins/genetics/physiology ; Neoplasms/*drug therapy/metabolism ; Neoplastic Stem Cells/metabolism ; Oxidative Phosphorylation ; Sequence Deletion ; Signal Transduction/drug effects ; Tumor Microenvironment/drug effects ; }, abstract = {Mitochondria, known for more than a century as the energy powerhouse of a cell, represent key intracellular signaling hub that are emerging as important determinants of several aspects of cancer development and progression, including metabolic reprogramming, acquisition of metastatic capability, and response to chemotherapeutic drugs. The majority of cancer cells harbors somatic mutations in the mitochondrial genome (mtDNA) and/or alterations in the mtDNA content, leading to mitochondrial dysfunction. Decreased mtDNA content is also detected in tumor-initiating cells, a subpopulation of cancer cells that are believed to play an integral role in cancer recurrence following chemotherapy. Although mutations in mitochondrial genes are common in cancer cells, they do not shut down completely the mitochondrial energy metabolism and functionality. Instead, they promote rewiring of the bioenergetics and biosynthetic profile of a cancer cell through a mitochondria-to-nucleus signaling activated by "dysfunctional" mitochondria that results in changes in transcription and/or activity of cancer-related genes and signaling pathways. Different cancer cell types may undergo different bioenergetic changes, some to more glycolytic and some to more oxidative. These different metabolic signatures may coexist within the same tumor mass (intra-tumor heterogeneity). In this review we describe the current understanding of mitochondrial dysfunction in the context of cancer chemoresistance with special attention to the role of mtDNA alterations. We put emphasis on potential therapeutic strategies targeting different metabolic events specific to cancer cells, including glycolysis, glutaminolysis, oxidative phosphorylation, and the retrograde signaling, to prevent chemoresistance. We also highlight novel genome-editing strategies aimed at "correcting" mtDNA defects in cancer cells. We conclude on the importance of considering intratumor metabolic heterogeneity to develop effective metabolism-based cancer therapy that can overcome chemoresistance. This article is part of a Special Issue entitled Mitochondria in Cancer, edited by Giuseppe Gasparre, Rodrigue Rossignol and Pierre Sonveaux.}, }
@article {pmid28156112, year = {2017}, author = {Song, JM and Hong, SK and An, YJ and Kang, MH and Hong, KH and Lee, YH and Cha, SS}, title = {Genetic and Structural Characterization of a Thermo-Tolerant, Cold-Active, and Acidic Endo-β-1,4-glucanase from Antarctic Springtail, Cryptopygus antarcticus.}, journal = {Journal of agricultural and food chemistry}, volume = {65}, number = {8}, pages = {1630-1640}, doi = {10.1021/acs.jafc.6b05037}, pmid = {28156112}, issn = {1520-5118}, mesh = {Amino Acid Sequence ; Animals ; Arthropod Proteins/*chemistry/*genetics/metabolism ; Arthropods/chemistry/classification/*enzymology/genetics ; Cellulase/*chemistry/*genetics/metabolism ; Cloning, Molecular ; Cold Temperature ; Enzyme Stability ; Hot Temperature ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; }, abstract = {The CaCel gene from Antarctic springtail Cryptopygus antarcticus codes for a cellulase belonging to the glycosyl hydrolase family 45 (GHF45). Phylogenetic, biochemical, and structural analyses revealed that the CaCel gene product (CaCel) is closely related to fungal GHF45 endo-β-1,4-glucanases. The organization of five introns within the open reading frame of the CaCel gene indicates its endogenous origin in the genome of the species, which suggests the horizontal transfer of the gene from fungi to the springtail. CaCel exhibited optimal activity at pH 3.5, retained 80% of its activity at 0-10 °C, and maintained a half-life of 4 h at 70 °C. Based on the structural comparison between CaCel and a fungal homologue, we deduced the structural basis for the unusual characteristics of CaCel. Under acidic conditions at 50 °C, CaCel was effective to digest the green algae (Ulva pertusa), suggesting that it could be exploited for biofuel production from seaweeds.}, }
@article {pmid28156004, year = {2017}, author = {Shen, J and Lv, L and Wang, X and Xiu, Z and Chen, G}, title = {Comparative analysis of CRISPR-Cas systems in Klebsiella genomes.}, journal = {Journal of basic microbiology}, volume = {57}, number = {4}, pages = {325-336}, doi = {10.1002/jobm.201600589}, pmid = {28156004}, issn = {1521-4028}, mesh = {Adaptive Immunity ; *CRISPR-Cas Systems ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Computational Biology ; Gene Transfer, Horizontal ; Genetic Variation ; *Genome, Bacterial ; Klebsiella/*genetics/immunology ; Polymorphism, Genetic ; }, abstract = {Prokaryotic CRISPR-Cas system provides adaptive immunity against invasive genetic elements. Bacteria of the genus Klebsiella are important nosocomial opportunistic pathogens. However, information of CRISPR-Cas system in Klebsiella remains largely unknown. Here, we analyzed the CRISPR-Cas systems of 68 complete genomes of Klebsiella representing four species. All the elements for CRISPR-Cas system (cas genes, repeats, leader sequences, and PAMs) were characterized. Besides the typical Type I-E and I-F CRISPR-Cas systems, a new Subtype I system located in the ABC transport system-glyoxalase region was found. The conservation of the new subtype CRISPR system between different species showed new evidence for CRISPR horizontal transfer. CRISPR polymorphism was strongly correlated both with species and multilocus sequence types. Some results indicated the function of adaptive immunity: most spacers (112 of 124) matched to prophages and plasmids and no matching housekeeping genes; new spacer acquisition was observed within the same sequence type (ST) and same clonal complex; the identical spacers were observed only in the ancient position (far from the leader) between different STs and clonal complexes. Interestingly, a high ratio of self-targeting spacers (7.5%, 31 of 416) was found in CRISPR-bearing Klebsiella pneumoniae (61%, 11 of 18). In some strains, there even were multiple full matching self-targeting spacers. Some self-targeting spacers were conserved even between different STs. These results indicated that some unknown mechanisms existed to compromise the function of self-targets of CRISPR-Cas systems in K. pneumoniae.}, }
@article {pmid28152054, year = {2017}, author = {Zhang, G and Leclercq, SO and Tian, J and Wang, C and Yahara, K and Ai, G and Liu, S and Feng, J}, title = {A new subclass of intrinsic aminoglycoside nucleotidyltransferases, ANT(3")-II, is horizontally transferred among Acinetobacter spp. by homologous recombination.}, journal = {PLoS genetics}, volume = {13}, number = {2}, pages = {e1006602}, pmid = {28152054}, issn = {1553-7404}, mesh = {Acinetobacter/classification/enzymology/*genetics ; Acinetobacter Infections/microbiology ; Acinetobacter baumannii/enzymology/genetics ; Bacterial Proteins/*genetics/metabolism ; Drug Resistance, Microbial/drug effects/genetics ; Electrophoresis, Polyacrylamide Gel ; *Gene Transfer, Horizontal ; *Homologous Recombination ; Host-Pathogen Interactions ; Humans ; Microbial Sensitivity Tests ; Nucleotidyltransferases/*genetics/metabolism ; Phylogeny ; Species Specificity ; Spectinomycin/metabolism/pharmacology ; Streptomycin/metabolism/pharmacology ; }, abstract = {The emergence and spread of antibiotic resistance among Acinetobacter spp. have been investigated extensively. Most studies focused on the multiple antibiotic resistance genes located on plasmids or genomic resistance islands. On the other hand, the mechanisms controlling intrinsic resistance are still not well understood. In this study, we identified the novel subclass of aminoglycoside nucleotidyltransferase ANT(3")-II in Acinetobacter spp., which comprised numerous variants distributed among three main clades. All members of this subclass can inactivate streptomycin and spectinomycin. The three ant(3")-II genes, encoding for the three ANT(3")-II clades, are widely distributed in the genus Acinetobacter and always located in the same conserved genomic region. According to their prevalence, these genes are intrinsic in Acinetobacter baumannii, Acinetobacter pittii, and Acinetobacter gyllenbergii. We also demonstrated that the ant(3")-II genes are located in a homologous recombination hotspot and were recurrently transferred among Acinetobacter species. In conclusion, our findings demonstrated a novel mechanism of natural resistance in Acinetobacter spp., identified a novel subclass of aminoglycoside nucleotidyltransferase and provided new insight into the evolutionary history of intrinsic resistance genes.}, }
@article {pmid28151042, year = {2017}, author = {Paul, D and Garg, A and Bhattacharjee, A}, title = {Occurrence of blaNDM-1 and blaNDM-5 in a Tertiary Referral Hospital of North India.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {23}, number = {7}, pages = {815-821}, doi = {10.1089/mdr.2016.0124}, pmid = {28151042}, issn = {1931-8448}, mesh = {Acinetobacter/drug effects/enzymology/*genetics/isolation &amp; purification ; Acinetobacter Infections/drug therapy/epidemiology/microbiology/transmission ; Adolescent ; Adult ; Aged ; Anti-Bacterial Agents/pharmacology ; Carbapenems/pharmacology ; Conjugation, Genetic ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/drug effects/enzymology/*genetics/isolation &amp; purification ; Escherichia coli Infections/drug therapy/epidemiology/microbiology/transmission ; Female ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Humans ; India/epidemiology ; Male ; Microbial Sensitivity Tests ; Middle Aged ; Plasmids/chemistry/metabolism ; Pseudomonas Infections/drug therapy/epidemiology/microbiology/transmission ; Pseudomonas aeruginosa/drug effects/enzymology/*genetics/isolation &amp; purification ; Tertiary Care Centers ; Transcription, Genetic ; beta-Lactamases/*genetics/metabolism ; }, abstract = {Antimicrobial resistance poses a great challenge to clinicians leaving very limited treatment options available. A panel of carbapenem-resistant bacterial isolates was selected based on Rapidec Carba NP test from a total of 900 samples, which were collected from different specialities hospitals of Kanpur, India. Carba NP-positive isolates were screened for carbapenemases, extended-spectrum beta-lactamases (ESBLs), quinolone resistance, and 16s methyltransferase genes. Presence of diverse blaNDM (blaNDM-1 and blaNDM-5) were detected and horizontal transferability was determined by transformation and conjugation assay. Elimination of blaNDM-1 and blaNDM-5 harboring plasmid was done by treating the isolates with sodium dodecyl sulfate. The transcriptional response of blaNDM-1 and blaNDM-5 under the exposure of imipenem, meropenem, and ertapenem stress was determined by quantitative real-time polymerase chain reaction. blaNDM harboring isolates were found to be horizontally transferable through IncFrepB and K type plasmid and could be successfully eliminated after the single treatment with sodium dodecyl sulfate. A distinct pattern of transcriptional response was observed for blaNDM-1 and blaNDM-5 under the pressure of carbapenem antibiotics where an upregulated expression of both blaNDM-1 and blaNDM-5 was observed. Minimum inhibitory concentration (MIC) results revealed that blaNDM harboring strains showed a high MIC range against imipenem, meropenem, ertapenem, cefepime, and aztreonam. Thus, prudent action should be taken to control the spread of these multidrug-resistant determinants or at least slowing down their lateral transfer in the hospital settings.}, }
@article {pmid28149295, year = {2017}, author = {Grevskott, DH and Svanevik, CS and Sunde, M and Wester, AL and Lunestad, BT}, title = {Marine Bivalve Mollusks As Possible Indicators of Multidrug-Resistant Escherichia coli and Other Species of the Enterobacteriaceae Family.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {24}, pmid = {28149295}, issn = {1664-302X}, abstract = {The mechanisms for the development and spread of antibacterial resistance (ABR) in bacteria residing in environmental compartments, including the marine environment, are far from understood. The objective of this study was to examine the ABR rates in Escherichia coli and other Enterobacteriaceae isolates obtained from marine bivalve mollusks collected along the Norwegian coast during a period from October 2014 to November 2015. A total of 549 bivalve samples were examined by a five times three tube most probable number method for enumeration of E. coli in bivalves resulting in 199 isolates from the positive samples. These isolates were identified by biochemical reactions and matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry, showing that 90% were E. coli, while the remaining were species within the genera Klebsiella, Citrobacter, and Enterobacter. All 199 isolates recovered were susceptibility tested following the European Committee on Antimicrobial Susceptibility Testing disk diffusion method. In total, 75 of 199 (38%) isolates showed resistance to at least one antibacterial agent, while multidrug-resistance were seen in 9 (5%) isolates. One isolate conferred resistance toward 15 antibacterial agents. Among the 75 resistant isolates, resistance toward extended-spectrum penicillins (83%), aminoglycosides (16%), trimethoprim (13%), sulfonamides (11%), tetracyclines (8%), third-generation cephalosporins (7%), amphenicols (5%), nitrofurans (5%), and quinolones (5%), were observed. Whole-genome sequencing on a selection of 10 E. coli isolates identified the genes responsible for resistance, including blaCTX-M genes. To indicate the potential for horizontal gene transfer, conjugation experiments were performed on the same selected isolates. Conjugative transfer of resistance was observed for six of the 10 E. coli isolates. In order to compare E. coli isolates from bivalves with clinical strains, multiple-locus variable number tandem repeats analysis (MLVA) was applied on a selection of 30 resistant E. coli isolates. The MLVA-profiles were associated with community-acquired E. coli strains causing bacteremia. Our study indicates that bivalves represent an important tool for monitoring antibacterial resistant E. coli and other members of the Enterobacteriaceae family in the coastal environment.}, }
@article {pmid28138100, year = {2017}, author = {Sansevere, EA and Luo, X and Park, JY and Yoon, S and Seo, KS and Robinson, DA}, title = {Transposase-Mediated Excision, Conjugative Transfer, and Diversity of ICE6013 Elements in Staphylococcus aureus.}, journal = {Journal of bacteriology}, volume = {199}, number = {8}, pages = {}, pmid = {28138100}, issn = {1098-5530}, support = {P20 GM103646/GM/NIGMS NIH HHS/United States ; R01 GM080602/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/*metabolism ; Conjugation, Genetic/*physiology ; Gene Expression Regulation, Bacterial/physiology ; Genetic Variation ; Protein Domains ; Staphylococcus aureus/*enzymology/genetics/*physiology ; Transposases/*metabolism ; }, abstract = {ICE6013 represents one of two families of integrative conjugative elements (ICEs) identified in the pan-genome of the human and animal pathogen Staphylococcus aureus Here we investigated the excision and conjugation functions of ICE6013 and further characterized the diversity of this element. ICE6013 excision was not significantly affected by growth, temperature, pH, or UV exposure and did not depend on recA The IS30-like DDE transposase (Tpase; encoded by orf1 and orf2) of ICE6013 must be uninterrupted for excision to occur, whereas disrupting three of the other open reading frames (ORFs) on the element significantly affects the level of excision. We demonstrate that ICE6013 conjugatively transfers to different S. aureus backgrounds at frequencies approaching that of the conjugative plasmid pGO1. We found that excision is required for conjugation, that not all S. aureus backgrounds are successful recipients, and that transconjugants acquire the ability to transfer ICE6013 Sequencing of chromosomal integration sites in serially passaged transconjugants revealed a significant integration site preference for a 15-bp AT-rich palindromic consensus sequence, which surrounds the 3-bp target site that is duplicated upon integration. A sequence analysis of ICE6013 from different host strains of S. aureus and from eight other species of staphylococci identified seven divergent subfamilies of ICE6013 that include sequences previously classified as a transposon, a plasmid, and various ICEs. In summary, these results indicate that the IS30-like Tpase functions as the ICE6013 recombinase and that ICE6013 represents a diverse family of mobile genetic elements that mediate conjugation in staphylococci.IMPORTANCE Integrative conjugative elements (ICEs) encode the abilities to integrate into and excise from bacterial chromosomes and plasmids and mediate conjugation between bacteria. As agents of horizontal gene transfer, ICEs may affect bacterial evolution. ICE6013 represents one of two known families of ICEs in the pathogen Staphylococcus aureus, but its core functions of excision and conjugation are not well studied. Here, we show that ICE6013 depends on its IS30-like DDE transposase for excision, which is unique among ICEs, and we demonstrate the conjugative transfer and integration site preference of ICE6013 A sequence analysis revealed that ICE6013 has diverged into seven subfamilies that are dispersed among staphylococci.}, }
@article {pmid28137844, year = {2017}, author = {Mahelka, V and Krak, K and Kopecký, D and Fehrer, J and Šafář, J and Bartoš, J and Hobza, R and Blavet, N and Blattner, FR}, title = {Multiple horizontal transfers of nuclear ribosomal genes between phylogenetically distinct grass lineages.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {7}, pages = {1726-1731}, pmid = {28137844}, issn = {1091-6490}, mesh = {Cell Nucleus/*genetics ; DNA, Plant/chemistry/genetics ; DNA, Ribosomal/chemistry/*genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Diploidy ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Plant/genetics ; Hordeum/classification/genetics ; *Phylogeny ; Poaceae/classification/*genetics ; Sequence Analysis, DNA ; }, abstract = {The movement of nuclear DNA from one vascular plant species to another in the absence of fertilization is thought to be rare. Here, nonnative rRNA gene [ribosomal DNA (rDNA)] copies were identified in a set of 16 diploid barley (Hordeum) species; their origin was traceable via their internal transcribed spacer (ITS) sequence to five distinct Panicoideae genera, a lineage that split from the Pooideae about 60 Mya. Phylogenetic, cytogenetic, and genomic analyses implied that the nonnative sequences were acquired between 1 and 5 Mya after a series of multiple events, with the result that some current Hordeum sp. individuals harbor up to five different panicoid rDNA units in addition to the native Hordeum rDNA copies. There was no evidence that any of the nonnative rDNA units were transcribed; some showed indications of having been silenced via pseudogenization. A single copy of a Panicum sp. rDNA unit present in H. bogdanii had been interrupted by a native transposable element and was surrounded by about 70 kbp of mostly noncoding sequence of panicoid origin. The data suggest that horizontal gene transfer between vascular plants is not a rare event, that it is not necessarily restricted to one or a few genes only, and that it can be selectively neutral.}, }
@article {pmid28137804, year = {2017}, author = {Ramírez-Vargas, G and Quesada-Gómez, C and Acuña-Amador, L and López-Ureña, D and Murillo, T and Del Mar Gamboa-Coronado, M and Chaves-Olarte, E and Thomson, N and Rodríguez-Cavallini, E and Rodríguez, C}, title = {A Clostridium difficile Lineage Endemic to Costa Rican Hospitals Is Multidrug Resistant by Acquisition of Chromosomal Mutations and Novel Mobile Genetic Elements.}, journal = {Antimicrobial agents and chemotherapy}, volume = {61}, number = {4}, pages = {}, pmid = {28137804}, issn = {1098-6596}, support = {/WT_/Wellcome Trust/United Kingdom ; 098051/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Clostridioides difficile/classification/drug effects/*genetics/isolation &amp; purification ; Clostridium Infections/*epidemiology/microbiology/transmission ; Costa Rica/epidemiology ; DNA Gyrase/genetics/metabolism ; DNA-Directed RNA Polymerases/genetics/metabolism ; Drug Resistance, Multiple, Bacterial/*genetics ; *Endemic Diseases ; Gene Expression ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genotype ; High-Throughput Nucleotide Sequencing ; Hospitals ; Humans ; *Interspersed Repetitive Sequences ; Metronidazole/pharmacology ; *Mutation ; Phylogeny ; Polymorphism, Single Nucleotide ; Vancomycin/pharmacology ; }, abstract = {The antimicrobial resistance (AMR) rates and levels recorded for Clostridium difficile are on the rise. This study reports the nature, levels, diversity, and genomic context of the antimicrobial resistance of human C. difficile isolates of the NAPCR1/RT012/ST54 genotype, which caused an outbreak in 2009 and is endemic in Costa Rican hospitals. To this end, we determined the susceptibilities of 38 NAPCR1 isolates to 10 antibiotics from seven classes using Etests or macrodilution tests and examined 31 NAPCR1 whole-genome sequences to identify single nucleotide polymorphisms (SNPs) and genes that could explain the resistance phenotypes observed. The NAPCR1 isolates were multidrug resistant (MDR) and commonly exhibited very high resistance levels. By sequencing their genomes, we showed that they possessed resistance-associated SNPs in gyrA and rpoB and carried eight to nine acquired antimicrobial resistance (AMR) genes. Most of these genes were located on known or novel mobile genetic elements shared by isolates recovered at different hospitals and at different time points. Metronidazole and vancomycin remain the first-line treatment options for these isolates. Overall, the NAPCR1 lineage showed an enhanced ability to acquire AMR genes through lateral gene transfer. On the basis of this finding, we recommend further vigilance and the adoption of improved control measures to limit the dissemination of this lineage and the emergence of more C. difficile MDR strains.}, }
@article {pmid28137747, year = {2017}, author = {Willemsen, A and Zwart, MP and Ambrós, S and Carrasco, JL and Elena, SF}, title = {2b or Not 2b: Experimental Evolution of Functional Exogenous Sequences in a Plant RNA Virus.}, journal = {Genome biology and evolution}, volume = {9}, number = {2}, pages = {297-310}, pmid = {28137747}, issn = {1759-6653}, mesh = {AlkB Enzymes/chemistry/genetics ; Cucumovirus/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Viral ; Potyvirus/*genetics ; Protein Domains ; RNA, Viral/genetics ; Nicotiana/virology ; }, abstract = {Horizontal gene transfer (HGT) is pervasive in viruses and thought to be a key mechanism in their evolution. On the other hand, strong selective constraints against increasing genome size are an impediment for HGT, rapidly purging horizontally transferred sequences and thereby potentially hindering evolutionary innovation. Here, we explore experimentally the evolutionary fate of viruses with simulated HGT events, using the plant RNA virus Tobacco etch virus (TEV), by separately introducing two functional, exogenous sequences to its genome. One of the events simulates the acquisition of a new function though HGT of a conserved AlkB domain, responsible for the repair of alkylation or methylation damage in many organisms. The other event simulates the acquisition of a sequence that duplicates an existing function, through HGT of the 2b RNA silencing suppressor from Cucumber mosaic virus. We then evolved these two viruses, tracked the maintenance of the horizontally transferred sequences over time, and for the final virus populations, sequenced their genome and measured viral fitness. We found that the AlkB domain was rapidly purged from the TEV genome, restoring fitness to wild-type levels. Conversely, the 2b gene was stably maintained and did not have a major impact on viral fitness. Moreover, we found that 2b is functional in TEV, as it provides a replicative advantage when the RNA silencing suppression domain of HC-Pro is mutated. These observations suggest a potentially interesting role for HGT of short functional sequences in ameliorating evolutionary constraints on viruses, through the duplication of functions.}, }
@article {pmid28133574, year = {2017}, author = {Dsouza, R and Pinto, NA and Hwang, I and Cho, Y and Yong, D and Choi, J and Lee, K and Chong, Y}, title = {Panel strain of Klebsiella pneumoniae for beta-lactam antibiotic evaluation: their phenotypic and genotypic characterization.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e2896}, pmid = {28133574}, issn = {2167-8359}, abstract = {Klebsiella pneumoniae is responsible for numerous infections caused in hospitals, leading to mortality and morbidity. It has been evolving as a multi-drug resistant pathogen, acquiring multiple resistances such as such as horizontal gene transfer, transposon-mediated insertions or change in outer membrane permeability. Therefore, constant efforts are being carried out to control the infections using various antibiotic therapies. Considering the severity of the acquired resistance, we developed a panel of strains of K. pneumoniae expressing different resistance profiles such as high-level penicillinase and AmpC production, extended spectrum beta-lactamases and carbapenemases. Bacterial strains expressing different resistance phenotypes were collected and examined for resistance genes, mutations and porin alterations contributing to the detected phenotypes. Using the Massive parallel sequencing (MPS) technology we have constructed and genotypically characterized the panel strains to elucidate the multidrug resistance. These panel strains can be used in the clinical laboratory as standard reference strains. In addition, these strains could be significant in the field of pharmaceuticals for the antibiotic drug testing to verify its efficiency on pathogens expressing various resistances.}, }
@article {pmid28128333, year = {2017}, author = {Corbinais, C and Mathieu, A and Damke, PP and Kortulewski, T and Busso, D and Prado-Acosta, M and Radicella, JP and Marsin, S}, title = {ComB proteins expression levels determine Helicobacter pylori competence capacity.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {41495}, pmid = {28128333}, issn = {2045-2322}, mesh = {Bacterial Proteins/genetics/*metabolism ; DNA Damage ; DNA Repair ; DNA, Bacterial/genetics ; *Gene Expression Regulation, Bacterial ; Helicobacter pylori/*genetics/metabolism ; Mutation/genetics ; Operon/genetics ; Transformation, Genetic ; }, abstract = {Helicobacter pylori chronically colonises half of the world's human population and is the main cause of ulcers and gastric cancers. Its prevalence and the increase in antibiotic resistance observed recently reflect the high genetic adaptability of this pathogen. Together with high mutation rates and an efficient DNA recombination system, horizontal gene transfer through natural competence makes of H. pylori one of the most genetically diverse bacteria. We show here that transformation capacity is enhanced in strains defective for recN, extending previous work with other homologous recombination genes. However, inactivation of either mutY or polA has no effect on DNA transformation, suggesting that natural competence can be boosted in H. pylori by the persistence of DNA breaks but not by enhanced mutagenesis. The transformation efficiency of the different DNA repair impaired strains correlates with the number of transforming DNA foci formed on the cell surface and with the expression of comB8 and comB10 competence genes. Overexpression of the comB6-B10 operon is sufficient to increase the transformation capacity of a wild type strain, indicating that the ComB complex, present in the bacterial wall and essential for DNA uptake, can be a limiting factor for transformation efficiency.}, }
@article {pmid28127891, year = {2017}, author = {Vera, MA and Brune, A}, title = {Hand over that gun: lateral gene transfer provides an amoeba with a bacterial weapon.}, journal = {Environmental microbiology}, volume = {19}, number = {3}, pages = {847-848}, doi = {10.1111/1462-2920.13680}, pmid = {28127891}, issn = {1462-2920}, mesh = {*Amoeba ; Bacteria ; *Gene Transfer, Horizontal ; Weapons ; }, }
@article {pmid28125687, year = {2017}, author = {Castellanos, LR and Donado-Godoy, P and León, M and Clavijo, V and Arevalo, A and Bernal, JF and Timmerman, AJ and Mevius, DJ and Wagenaar, JA and Hordijk, J}, title = {High Heterogeneity of Escherichia coli Sequence Types Harbouring ESBL/AmpC Genes on IncI1 Plasmids in the Colombian Poultry Chain.}, journal = {PloS one}, volume = {12}, number = {1}, pages = {e0170777}, pmid = {28125687}, issn = {1932-6203}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics/metabolism ; Chickens/microbiology ; Colombia/epidemiology ; Epidemiological Monitoring ; Escherichia coli/classification/drug effects/*genetics/isolation &amp; purification ; Escherichia coli Infections/drug therapy/epidemiology/transmission/*veterinary ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genetic Heterogeneity ; Humans ; Phylogeny ; Plasmids/chemistry/*metabolism ; Poultry/microbiology ; Poultry Diseases/drug therapy/epidemiology/microbiology/transmission ; beta-Lactam Resistance/*genetics ; beta-Lactamases/*genetics/metabolism ; beta-Lactams/pharmacology ; }, abstract = {BACKGROUND: Escherichia coli producing ESBL/AmpC enzymes are unwanted in animal production chains as they may pose a risk to human and animal health. Molecular characterization of plasmids and strains carrying genes that encode these enzymes is essential to understand their local and global spread.<br><br>OBJECTIVES: To investigate the diversity of genes, plasmids and strains in ESBL/AmpC-producing E. coli from the Colombian poultry chain isolated within the Colombian Integrated Program for Antimicrobial Resistance Surveillance (Coipars).<br><br>METHODS: A total of 541 non-clinical E. coli strains from epidemiologically independent samples and randomly isolated between 2008 and 2013 within the Coipars program were tested for antimicrobial susceptibility. Poultry isolates resistant to cefotaxime (MIC &#x2265; 4 mg/L) were screened for ESBL/AmpC genes including blaCTX-M, blaSHV, blaTEM, blaCMY and blaOXA. Plasmid and strain characterization was performed for a selection of the ESBL/AmpC-producing isolates. Plasmids were purified and transformed into E. coli DH10B cells or transferred by conjugation to E. coli W3110. When applicable, PCR Based Replicon Typing (PBRT), plasmid Multi Locus Sequence Typing (pMLST), plasmid Double Locus Sequence Typing (pDLST) and/or plasmid Replicon Sequence Typing (pRST) was performed on resulting transformants and conjugants. Multi Locus Sequence Typing (MLST) was used for strain characterization.<br><br>RESULTS: In total, 132 of 541 isolates were resistant to cefotaxime and 122 were found to carry ESBL/AmpC genes. Ninety-two harboured blaCMY-2 (75%), fourteen blaSHV-12 (11%), three blaSHV-5 (2%), five blaCTX-M-2 (4%), one blaCTX-M-15 (1%), one blaCTX-M-8 (1%), four a combination of blaCMY-2 and blaSHV-12 (4%) and two a combination of blaCMY-2 and blaSHV-5 (2%). A selection of 39 ESBL/AmpC-producing isolates was characterized at the plasmid and strain level. ESBL/AmpC genes from 36 isolates were transferable by transformation or conjugation of which 22 were located on IncI1 plasmids. These IncI1 plasmids harboured predominantly blaCMY-2 (16/22), and to a lesser extend blaSHV-12 (5/22) and blaCTX-M-8 (1/22). Other plasmid families associated with ESBL/AmpC-genes were IncK (4/33), IncHI2 (3/33), IncA/C (2/33), Inc&#x392;/O (1/33) and a non-typeable replicon (1/33). Subtyping of IncI1 and IncHI2 demonstrated IncI1/ST12 was predominantly associated with blaCMY-2 (12/16) and IncHI2/ST7 with blaCTX-M-2 (2/3). Finally, 31 different STs were detected among the 39 selected isolates.<br><br>CONCLUSIONS: Resistance to extended spectrum cephalosporins in E. coli from Colombian poultry is mainly caused by blaCMY-2 and blaSHV-12. The high diversity of strain Sequence Types and the dissemination of homogeneous IncI1/ST12 plasmids suggest that spread of the resistance is mainly mediated by horizontal gene transfer.}, }
@article {pmid28125655, year = {2017}, author = {Baraúna, RA and Ramos, RT and Veras, AA and Pinheiro, KC and Benevides, LJ and Viana, MV and Guimarães, LC and Edman, JM and Spier, SJ and Azevedo, V and Silva, A}, title = {Assessing the Genotypic Differences between Strains of Corynebacterium pseudotuberculosis biovar equi through Comparative Genomics.}, journal = {PloS one}, volume = {12}, number = {1}, pages = {e0170676}, pmid = {28125655}, issn = {1932-6203}, mesh = {Animals ; Corynebacterium Infections/*genetics/microbiology ; Corynebacterium pseudotuberculosis/*genetics/pathogenicity ; Genome, Bacterial/*genetics ; Genotype ; High-Throughput Nucleotide Sequencing ; Horse Diseases/*genetics/microbiology ; Horses/microbiology ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Rhodococcus equi/*genetics/pathogenicity ; }, abstract = {Seven genomes of Corynebacterium pseudotuberculosis biovar equi were sequenced on the Ion Torrent PGM platform, generating high-quality scaffolds over 2.35 Mbp. This bacterium is the causative agent of disease known as "pigeon fever" which commonly affects horses worldwide. The pangenome of biovar equi was calculated and two phylogenomic approaches were used to identify clustering patterns within Corynebacterium genus. Furthermore, other comparative analyses were performed including the prediction of genomic islands and prophages, and SNP-based phylogeny. In the phylogenomic tree, C. pseudotuberculosis was divided into two distinct clades, one formed by nitrate non-reducing species (biovar ovis) and another formed by nitrate-reducing species (biovar equi). In the latter group, the strains isolated from California were more related to each other, while the strains CIP 52.97 and 1/06-A formed the outermost clade of the biovar equi. A total of 1,355 core genes were identified, corresponding to 42.5% of the pangenome. This pangenome has one of the smallest core genomes described in the literature, suggesting a high genetic variability of biovar equi of C. pseudotuberculosis. The analysis of the similarity between the resistance islands identified a higher proximity between the strains that caused more severe infectious conditions (infection in the internal organs). Pathogenicity islands were largely conserved between strains. Several genes that modulate the pathogenicity of C. pseudotuberculosis were described including peptidases, recombination enzymes, micoside synthesis enzymes, bacteriocins with antimicrobial activity and several others. Finally, no genotypic differences were observed between the strains that caused the three different types of infection (external abscess formation, infection with abscess formation in the internal organs, and ulcerative lymphangitis). Instead, it was noted that there is a higher phenetic correlation between strains isolated at California compared to the other strains. Additionally, high variability of resistance islands suggests gene acquisition through several events of horizontal gene transfer.}, }
@article {pmid28123115, year = {2017}, author = {Sanderson, MJ and Nicolae, M and McMahon, MM}, title = {Homology-Aware Phylogenomics at Gigabase Scales.}, journal = {Systematic biology}, volume = {66}, number = {4}, pages = {590-603}, pmid = {28123115}, issn = {1076-836X}, mesh = {Classification/*methods ; Gene Transfer, Horizontal/genetics ; *Genomics ; Oryza/classification/genetics ; *Phylogeny ; }, abstract = {Obstacles to inferring species trees from whole genome data sets range from algorithmic and data management challenges to the wholesale discordance in evolutionary history found in different parts of a genome. Recent work that builds trees directly from genomes by parsing them into sets of small $k$-mer strings holds promise to streamline and simplify these efforts, but existing approaches do not account well for gene tree discordance. We describe a "seed and extend" protocol that finds nearly exact matching sets of orthologous $k$-mers and extends them to construct data sets that can properly account for genomic heterogeneity. Exploiting an efficient suffix array data structure, sets of whole genomes can be parsed and converted into phylogenetic data matrices rapidly, with contiguous blocks of $k$-mers from the same chromosome, gene, or scaffold concatenated as needed. Phylogenetic trees constructed from highly curated rice genome data and a diverse set of six other eukaryotic whole genome, transcriptome, and organellar genome data sets recovered trees nearly identical to published phylogenomic analyses, in a small fraction of the time, and requiring many fewer parameter choices. Our method's ability to retain local homology information was demonstrated by using it to characterize gene tree discordance across the rice genome, and by its robustness to the high rate of interchromosomal gene transfer found in several rice species.}, }
@article {pmid28123114, year = {2017}, author = {Allman, ES and Kubatko, LS and Rhodes, JA}, title = {Split Scores: A Tool to Quantify Phylogenetic Signal in Genome-Scale Data.}, journal = {Systematic biology}, volume = {66}, number = {4}, pages = {620-636}, pmid = {28123114}, issn = {1076-836X}, support = {R01 GM117590/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Classification/*methods ; Culicidae/classification/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome/genetics ; *Phylogeny ; Primates/classification/genetics ; Software ; Viruses/classification/genetics ; }, abstract = {Detecting variation in the evolutionary process along chromosomes is increasingly important as whole-genome data become more widely available. For example, factors such as incomplete lineage sorting, horizontal gene transfer, and chromosomal inversion are expected to result in changes in the underlying gene trees along a chromosome, while changes in selective pressure and mutational rates for different genomic regions may lead to shifts in the underlying mutational process. We propose the split score as a general method for quantifying support for a particular phylogenetic relationship within a genomic data set. Because the split score is based on algebraic properties of a matrix of site pattern frequencies, it can be rapidly computed, even for data sets that are large in the number of taxa and/or in the length of the alignment, providing an advantage over other methods (e.g., maximum likelihood) that are often used to assess such support. Using simulation, we explore the properties of the split score, including its dependence on sequence length, branch length, size of a split and its ability to detect true splits in the underlying tree. Using a sliding window analysis, we show that split scores can be used to detect changes in the underlying evolutionary process for genome-scale data from primates, mosquitoes, and viruses in a computationally efficient manner. Computation of the split score has been implemented in the software package SplitSup.}, }
@article {pmid28117696, year = {2017}, author = {Gallot-Lavallée, L and Blanc, G}, title = {A Glimpse of Nucleo-Cytoplasmic Large DNA Virus Biodiversity through the Eukaryotic Genomics Window.}, journal = {Viruses}, volume = {9}, number = {1}, pages = {}, pmid = {28117696}, issn = {1999-4915}, mesh = {*Biodiversity ; Eukaryota/*genetics/*virology ; Genomics ; Giant Viruses/*classification/*genetics ; Recombination, Genetic ; }, abstract = {The nucleocytoplasmic large DNA viruses (NCLDV) are a group of extremely complex double-stranded DNA viruses, which are major parasites of a variety of eukaryotes. Recent studies showed that certain eukaryotes contain fragments of NCLDV DNA integrated in their genome, when surprisingly many of these organisms were not previously shown to be infected by NCLDVs. We performed an update survey of NCLDV genes hidden in eukaryotic sequences to measure the incidence of this phenomenon in common public sequence databases. A total of 66 eukaryotic genomic or transcriptomic datasets-many of which are from algae and aquatic protists-contained at least one of the five most consistently conserved NCLDV core genes. Phylogenetic study of the eukaryotic NCLDV-like sequences identified putative new members of already recognized viral families, as well as members of as yet unknown viral clades. Genomic evidence suggested that most of these sequences resulted from viral DNA integrations rather than contaminating viruses. Furthermore, the nature of the inserted viral genes helped predicting original functional capacities of the donor viruses. These insights confirm that genomic insertions of NCLDV DNA are common in eukaryotes and can be exploited to delineate the contours of NCLDV biodiversity.}, }
@article {pmid28115381, year = {2017}, author = {Zhang, X and Liu, X and Liang, Y and Guo, X and Xiao, Y and Ma, L and Miao, B and Liu, H and Peng, D and Huang, W and Zhang, Y and Yin, H}, title = {Adaptive Evolution of Extreme Acidophile Sulfobacillus thermosulfidooxidans Potentially Driven by Horizontal Gene Transfer and Gene Loss.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {7}, pages = {}, pmid = {28115381}, issn = {1098-5336}, mesh = {Clostridiales/*genetics ; Computational Biology ; *Evolution, Molecular ; *Gene Deletion ; *Gene Transfer, Horizontal ; *Genetic Variation ; Genome, Bacterial ; Genomics ; Metabolic Networks and Pathways ; Models, Genetic ; Phylogeny ; Stress, Physiological ; }, abstract = {Recent phylogenomic analysis has suggested that three strains isolated from different copper mine tailings around the world were taxonomically affiliated with Sulfobacillusthermosulfidooxidans Here, we present a detailed investigation of their genomic features, particularly with respect to metabolic potentials and stress tolerance mechanisms. Comprehensive analysis of the Sulfobacillus genomes identified a core set of essential genes with specialized biological functions in the survival of acidophiles in their habitats, despite differences in their metabolic pathways. The Sulfobacillus strains also showed evidence for stress management, thereby enabling them to efficiently respond to harsh environments. Further analysis of metabolic profiles provided novel insights into the presence of genomic streamlining, highlighting the importance of gene loss as a main mechanism that potentially contributes to cellular economization. Another important evolutionary force, especially in larger genomes, is gene acquisition via horizontal gene transfer (HGT), which might play a crucial role in the recruitment of novel functionalities. Also, a successful integration of genes acquired from archaeal donors appears to be an effective way of enhancing the adaptive capacity to cope with environmental changes. Taken together, the findings of this study significantly expand the spectrum of HGT and genome reduction in shaping the evolutionary history of Sulfobacillus strains.IMPORTANCE Horizontal gene transfer (HGT) and gene loss are recognized as major driving forces that contribute to the adaptive evolution of microbial genomes, although their relative importance remains elusive. The findings of this study suggest that highly frequent gene turnovers within microorganisms via HGT were necessary to incur additional novel functionalities to increase the capacity of acidophiles to adapt to changing environments. Evidence also reveals a fascinating phenomenon of potential cross-kingdom HGT. Furthermore, genome streamlining may be a critical force in driving the evolution of microbial genomes. Taken together, this study provides insights into the importance of both HGT and gene loss in the evolution and diversification of bacterial genomes.}, }
@article {pmid28113725, year = {2017}, author = {Weyenberg, G and Yoshida, R and Howe, D}, title = {Normalizing Kernels in the Billera-Holmes-Vogtmann Treespace.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {14}, number = {6}, pages = {1359-1365}, doi = {10.1109/TCBB.2016.2565475}, pmid = {28113725}, issn = {1557-9964}, mesh = {*Algorithms ; Computer Simulation ; Genome/*genetics ; Genomics/*methods ; *Phylogeny ; Sequence Alignment ; }, abstract = {As costs of genome sequencing have dropped precipitously, development of efficient bioinformatic methods to analyze genome structure and evolution have become ever more urgent. For example, most published phylogenomic studies involve either massive concatenation of sequences, or informal comparisons of phylogenies inferred on a small subset of orthologous genes, neither of which provides a comprehensive overview of evolution or systematic identification of genes with unusual and interesting evolution (e.g., horizontal gene transfers, gene duplication, and subsequent neofunctionalization). We are interested in identifying such "outlying" gene trees from the set of gene trees and estimating the distribution of trees over the "tree space". This paper describes an improvement to the kdetrees algorithm, an adaptation of classical kernel density estimation to the metric space of phylogenetic trees (Billera-Holmes-Vogtman treespace), whereby the kernel normalizing constants, are estimated through the use of the novel holonomic gradient methods. As in the original kdetrees paper, we have applied kdetrees to a set of Apicomplexa genes. The analysis identified several unreliable sequence alignments that had escaped previous detection, as well as a gene independently reported as a possible case of horizontal gene transfer. The updated version of the kdetrees software package is available both from CRAN (the official R package system), as well as from the official development repository on Github. (github.com/grady/kdetrees).}, }
@article {pmid28112239, year = {2017}, author = {Watkins, ER and Maiden, MC}, title = {Metabolic shift in the emergence of hyperinvasive pandemic meningococcal lineages.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {41126}, pmid = {28112239}, issn = {2045-2322}, support = {268904/ERC_/European Research Council/International ; 087622/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Africa South of the Sahara ; Cell Lineage/genetics ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/genetics ; Humans ; Meningitis/epidemiology/*genetics/microbiology ; *Molecular Epidemiology ; Neisseria meningitidis/*genetics/pathogenicity ; Pandemics ; Phylogeny ; Sepsis/epidemiology/*genetics/microbiology ; }, abstract = {Hyperinvasive lineages of Neisseria meningitidis, which persist despite extensive horizontal genetic exchange, are a major cause of meningitis and septicaemia worldwide. Over the past 50 years one such lineage of meningococci, known as serogroup A, clonal complex 5 (A:cc5), has caused three successive pandemics, including epidemics in sub-Saharan Africa. Although the principal antigens that invoke effective immunity have remained unchanged, distinct A:cc5 epidemic clones have nevertheless emerged. An analysis of whole genome sequence diversity among 153 A:cc5 isolates identified eleven genetic introgression events in the emergence of the epidemic clones, which primarily involved variants of core genes encoding metabolic processes. The acquired DNA was identical to that found over many years in other, unrelated, hyperinvasive meningococci, suggesting that the epidemic clones emerged by acquisition of pre-existing metabolic gene variants, rather than 'virulence' associated or antigen-encoding genes. This is consistent with mathematical models which predict the association of transmission fitness with the emergence and maintenance of virulence in recombining commensal organisms.}, }
@article {pmid28111326, year = {2017}, author = {Xu, X and Li, X and Luo, M and Liu, P and Su, K and Qing, Y and Chen, S and Qiu, J and Li, Y}, title = {Molecular characterisations of integrons in clinical isolates of Klebsiella pneumoniae in a Chinese tertiary hospital.}, journal = {Microbial pathogenesis}, volume = {104}, number = {}, pages = {164-170}, doi = {10.1016/j.micpath.2017.01.035}, pmid = {28111326}, issn = {1096-1208}, mesh = {Anti-Bacterial Agents/pharmacology ; China ; Conjugation, Genetic ; DNA, Bacterial/genetics ; Disk Diffusion Antimicrobial Tests ; *Drug Resistance, Multiple, Bacterial ; Gene Transfer, Horizontal ; Genetic Variation ; Genotype ; Humans ; *Integrons ; Klebsiella Infections/*microbiology ; Klebsiella pneumoniae/classification/*drug effects/*genetics/isolation &amp; purification ; Multilocus Sequence Typing ; Polymerase Chain Reaction ; Tertiary Care Centers ; }, abstract = {BACKGROUND: Integrons are mobile genetic elements that play an important role in the distribution of antibiotic-resistance genes among bacteria. This study aimed to investigate the distribution of integrons in clinical isolates of Klebsiella pneumoniae and explore the molecular mechanism of integron-mediated multiple-drug resistance in K. pneumoniae.<br><br>METHODS: Class 1, 2, and 3 integrases were identified by polymerase chain reaction (PCR) among 178 K.&#xa0;pneumoniae clinical isolates. Antibiotic susceptibility was examined by disk-diffusion method. Conjugation experiments were conducted to evaluate the horizontal-transfer capability, and multilocus sequence typing (MLST) assays were conducted to explore the genetic relationships among the isolates. Highly virulent serotypes were identified by PCR from the 44 integron-positive isolates with variable regions.<br><br>RESULTS: Class1 and 2 integrons were detected in 60.1% and 1.7% of isolates, respectively. One isolate carried both class 1 and 2 integrons. Class 3 integrons were not detected in all 178 isolates. Among the 44 integrons containing variable regions, 39 were located in conjugative plasmids. Dihydrofolate reductase (dfrA) and aminoglycoside adenyltransferase (aad) were found to be the most common in class 1 and 2 integrons. These gene cassettes encoded resistance to trimethoprim and aminoglycosides. Moreover, the association between integron carriage and antibiotic resistance was most significant for aminoglycosides, phenicols, and fluoroquinolones. Among the 44 integron-positive isolates with variable regions, 9 were classified as highly virulent serotypes (k1, k2, k20, and k54). In addition, MLST analysis detected 13 sequence types (STs), with the predominant ones being ST11 and ST15. The eBURST analysis revalued the existence of 11 singleton STs and one group, which is comprised of ST11 and ST437.<br><br>CONCLUSIONS: The wide diversity of detected integrons suggested that the horizontal transfer by mobile genetic elements played a major role in the distribution of antimicrobial resistance genes, thereby indicating the urgent need to use effective means of avoiding the spread of drug-resistant bacteria.}, }
@article {pmid28109845, year = {2017}, author = {Yu, J and Wang, Y and Chen, Z and Zhu, X and Tian, L and Li, L and Sun, Z}, title = {Outbreak of nosocomial NDM-1-producing Klebsiella pneumoniae ST1419 in a neonatal unit.}, journal = {Journal of global antimicrobial resistance}, volume = {8}, number = {}, pages = {135-139}, doi = {10.1016/j.jgar.2016.10.014}, pmid = {28109845}, issn = {2213-7173}, mesh = {Blotting, Southern ; Carbapenem-Resistant Enterobacteriaceae/*enzymology/isolation &amp; purification ; China/epidemiology ; Conjugation, Genetic ; *Disease Outbreaks ; Electrophoresis, Gel, Pulsed-Field ; Female ; Gene Transfer, Horizontal ; Humans ; Infant ; Infant, Newborn ; Klebsiella Infections/*epidemiology/microbiology ; Klebsiella pneumoniae/classification/drug effects/*enzymology/isolation &amp; purification ; Male ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Polymerase Chain Reaction ; Retrospective Studies ; beta-Lactamases/*analysis ; }, abstract = {OBJECTIVES: The aim of this study was to characterise carbapenem-resistant Klebsiella pneumoniae isolates recovered from neonatal clinical specimens over a 4-month period.<br><br>METHODS: Seven carbapenem-resistant K. pneumoniae isolates were analysed. Antibiotic susceptibilities of the isolates were determined by the agar dilution method, and the drug resistance genes were evaluated by PCR. Clonal relatedness of the isolates was assessed using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Conjugation experiments and Southern blot hybridisation were performed to determine the transferability of the plasmids.<br><br>RESULTS: All of the K. pneumoniae isolates carried the blaNDM-1 gene but were negative for all other carbapenemases tested. All of the isolates harboured blaSHV-12, and five isolates also carried blaCTX-M-15 and/or blaTEM-1. All of the isolates exhibited multidrug resistance. The isolates belonged to sequence types ST1419 and ST101 and formed three different PFGE patterns. Plasmids carrying blaNDM-1 were successfully transferred from six of the seven isolates to the Escherichia coli recipient. These six NDM-1-producing K. pneumoniae were clonal and carried blaNDM-1 on the same plasmid, but one isolate possibly carried chromosomal blaNDM-1.<br><br>CONCLUSIONS: This is the first report of NDM-1-positive K. pneumoniae ST1419 from neonates in China. Closer attention should be paid to monitoring blaNDM-1 gene dissemination because it is potentially transferred horizontally.}, }
@article {pmid28106797, year = {2017}, author = {Schroeder, M and Brooks, BD and Brooks, AE}, title = {The Complex Relationship between Virulence and Antibiotic Resistance.}, journal = {Genes}, volume = {8}, number = {1}, pages = {}, pmid = {28106797}, issn = {2073-4425}, abstract = {Antibiotic resistance, prompted by the overuse of antimicrobial agents, may arise from a variety of mechanisms, particularly horizontal gene transfer of virulence and antibiotic resistance genes, which is often facilitated by biofilm formation. The importance of phenotypic changes seen in a biofilm, which lead to genotypic alterations, cannot be overstated. Irrespective of if the biofilm is single microbe or polymicrobial, bacteria, protected within a biofilm from the external environment, communicate through signal transduction pathways (e.g., quorum sensing or two-component systems), leading to global changes in gene expression, enhancing virulence, and expediting the acquisition of antibiotic resistance. Thus, one must examine a genetic change in virulence and resistance not only in the context of the biofilm but also as inextricably linked pathologies. Observationally, it is clear that increased virulence and the advent of antibiotic resistance often arise almost simultaneously; however, their genetic connection has been relatively ignored. Although the complexities of genetic regulation in a multispecies community may obscure a causative relationship, uncovering key genetic interactions between virulence and resistance in biofilm bacteria is essential to identifying new druggable targets, ultimately providing a drug discovery and development pathway to improve treatment options for chronic and recurring infection.}, }
@article {pmid28104786, year = {2017}, author = {Green, DE and DeAngelis, PL}, title = {Identification of a chondroitin synthase from an unexpected source, the green sulfur bacterium Chlorobium phaeobacteroides.}, journal = {Glycobiology}, volume = {27}, number = {5}, pages = {469-476}, pmid = {28104786}, issn = {1460-2423}, support = {R01 HL062244/HL/NHLBI NIH HHS/United States ; }, mesh = {Amino Acid Sequence/genetics ; Chlorobium/*enzymology ; Chondroitin Sulfates/chemistry ; Escherichia coli/genetics ; Glycosaminoglycans/genetics/*metabolism ; N-Acetylgalactosaminyltransferases/*genetics/*isolation &amp; purification/metabolism ; Substrate Specificity ; }, abstract = {Glycosaminoglycans (GAGs) are known to be present in all animals as well as some pathogenic microbes. Chondroitin sulfate is the most abundant GAG in mammals where it has various structural and adhesion roles. The Gram-negative bacteria Pasteurella multocida Type F and Escherichia coli K4 produce extracellular capsules composed of unsulfated chondroitin or a fructosylated chondroitin, respectively. Such polysaccharides that are structurally related to host molecules do not generally provoke a strong antibody response thus are thought to be employed as molecular camouflage during infection. We observed a sequence from the photosynthetic green sulfur bacteria, Chlorobium phaeobacteroides DSM 266, which was very similar (~62% identical) to the open reading frames of the known bifunctional chondroitin synthases (PmCS and KfoC); some segments are strikingly conserved amongst the three proteins. Recombinant E. coli-derived Chlorobium enzyme preparations were found to possess bona fide chondroitin synthase activity in vitro. This new catalyst, CpCS, however, has a more promiscuous acceptor usage than the prototypical PmCS, which may be of utility in novel chimeric GAG syntheses. The finding of such a similar chondroitin synthase enzyme in C. phaeobacteroides is unexpected for several reasons including (a) a free-living nonpathogenic organism should not "need" an animal self molecule for protection, (b) the Proteobacteria and the green sulfur bacterial lineages diverged ~2.5-3 billion years ago and (c) the ecological niches of these bacteria are not thought to overlap substantially to facilitate horizontal gene transfer. CpCS provides insight into the structure/function relationship of this class of enzymes.}, }
@article {pmid28104347, year = {2017}, author = {Schulman, LS}, title = {Bacterial resistance to antibodies: a model evolutionary study.}, journal = {Journal of theoretical biology}, volume = {417}, number = {}, pages = {61-67}, doi = {10.1016/j.jtbi.2017.01.022}, pmid = {28104347}, issn = {1095-8541}, mesh = {Antibodies/*immunology ; Bacteria/genetics/*immunology ; *Biological Evolution ; *Gene Transfer, Horizontal ; Models, Biological ; }, abstract = {The tangled nature model of evolution (reviewed in the main text) is adapted for use in the study of antibody resistance acquired by horizontal gene transfer. Exchanges of DNA and the acquisition of resistant gene sequences are considered. For the parameters used, resistant strains rapidly proliferate and dominate, although initial intense antibiotic treatment can occasionally prevent this. Variation in genome distribution appears to be long tailed. If this is reflected in nature, the occurrence of resistant bacterial strains can be expected, as well as considerable variation in patient outcomes.}, }
@article {pmid28101896, year = {2017}, author = {Richard, D and Ravigné, V and Rieux, A and Facon, B and Boyer, C and Boyer, K and Grygiel, P and Javegny, S and Terville, M and Canteros, BI and Robène, I and Vernière, C and Chabirand, A and Pruvost, O and Lefeuvre, P}, title = {Adaptation of genetically monomorphic bacteria: evolution of copper resistance through multiple horizontal gene transfers of complex and versatile mobile genetic elements.}, journal = {Molecular ecology}, volume = {26}, number = {7}, pages = {2131-2149}, doi = {10.1111/mec.14007}, pmid = {28101896}, issn = {1365-294X}, mesh = {Adaptation, Physiological/genetics ; Argentina ; Citrus/microbiology ; Copper/*pharmacology ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/*genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genetics, Population ; Genotype ; *Interspersed Repetitive Sequences ; Martinique ; Microsatellite Repeats ; Plant Diseases/microbiology ; Reunion ; Xanthomonas/drug effects/*genetics ; }, abstract = {Copper-based antimicrobial compounds are widely used to control plant bacterial pathogens. Pathogens have adapted in response to this selective pressure. Xanthomonas citri pv. citri, a major citrus pathogen causing Asiatic citrus canker, was first reported to carry plasmid-encoded copper resistance in Argentina. This phenotype was conferred by the copLAB gene system. The emergence of resistant strains has since been reported in Réunion and Martinique. Using microsatellite-based genotyping and copLAB PCR, we demonstrated that the genetic structure of the copper-resistant strains from these three regions was made up of two distant clusters and varied for the detection of copLAB amplicons. In order to investigate this pattern more closely, we sequenced six copper-resistant X. citri pv. citri strains from Argentina, Martinique and Réunion, together with reference copper-resistant Xanthomonas and Stenotrophomonas strains using long-read sequencing technology. Genes involved in copper resistance were found to be strain dependent with the novel identification in X. citri pv. citri of copABCD and a cus heavy metal efflux resistance-nodulation-division system. The genes providing the adaptive trait were part of a mobile genetic element similar to Tn3-like transposons and included in a conjugative plasmid. This indicates the system's great versatility. The mining of all available bacterial genomes suggested that, within the bacterial community, the spread of copper resistance associated with mobile elements and their plasmid environments was primarily restricted to the Xanthomonadaceae family.}, }
@article {pmid28100665, year = {2017}, author = {Ren, Q and Wang, C and Jin, M and Lan, J and Ye, T and Hui, K and Tan, J and Wang, Z and Wyckoff, GJ and Wang, W and Han, GZ}, title = {Co-option of bacteriophage lysozyme genes by bivalve genomes.}, journal = {Open biology}, volume = {7}, number = {1}, pages = {}, pmid = {28100665}, issn = {2046-2441}, mesh = {Animals ; Anti-Bacterial Agents/chemistry/pharmacology ; Bacteriophages/*enzymology/genetics ; Bivalvia/*genetics/microbiology ; Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; Muramidase/chemistry/*genetics/pharmacology ; Phylogeny ; Protein Conformation ; Viral Proteins/chemistry/genetics/pharmacology ; }, abstract = {Eukaryotes have occasionally acquired genetic material through horizontal gene transfer (HGT). However, little is known about the evolutionary and functional significance of such acquisitions. Lysozymes are ubiquitous enzymes that degrade bacterial cell walls. Here, we provide evidence that two subclasses of bivalves (Heterodonta and Palaeoheterodonta) acquired a lysozyme gene via HGT, building on earlier findings. Phylogenetic analyses place the bivalve lysozyme genes within the clade of bacteriophage lysozyme genes, indicating that the bivalves acquired the phage-type lysozyme genes from bacteriophages, either directly or through intermediate hosts. These bivalve lysozyme genes underwent dramatic structural changes after their co-option, including intron gain and fusion with other genes. Moreover, evidence suggests that recurrent gene duplication occurred in the bivalve lysozyme genes. Finally, we show the co-opted lysozymes exhibit a capacity for antibacterial action, potentially augmenting the immune function of related bivalves. This represents an intriguing evolutionary strategy in the eukaryote-microbe arms race, in which the genetic materials of bacteriophages are co-opted by eukaryotes, and then used by eukaryotes to combat bacteria, using a shared weapon against a common enemy.}, }
@article {pmid28100194, year = {2017}, author = {Conwell, M and Daniels, V and Naughton, PJ and Dooley, JS}, title = {Interspecies transfer of vancomycin, erythromycin and tetracycline resistance among Enterococcus species recovered from agrarian sources.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {19}, pmid = {28100194}, issn = {1471-2180}, mesh = {Base Sequence ; Conjugation, Genetic/genetics ; Cross Infection ; DNA, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Enterococcus/drug effects/*genetics/*isolation &amp; purification ; Enterococcus faecalis/drug effects/genetics/isolation &amp; purification ; Enterococcus faecium/drug effects/genetics/isolation &amp; purification ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/genetics ; Microbial Sensitivity Tests/methods ; Phenotype ; Sex Attractants ; Tetracycline Resistance/*genetics ; Vancomycin Resistance/*genetics ; Water Microbiology ; }, abstract = {BACKGROUND: Enterococci are now well recognised for their ability to transfer antibiotic resistance and for their association with nosocomial infections, but less is known regarding their relevance in the wider environment. Enterococcus faecalis and Enterococcus faecium were isolated from a range of agrarian associated sources (low-flow water, septic tank, poultry litter, high flow water, slurry/soil) and were assessed for latent ability to transfer antimicrobial resistance.<br><br>RESULTS: The isolates were tested for phenotypic clumping in the presence of cell-free supernatant from other isolates. Some isolates were identified which demonstrated clumping, indicating that they possessed peptide sex pheromone conjugal machinery. All isolates were also tested for antibiotic resistance phenotypes using both disc diffusion and minimum inhibitory concentration (MIC) assays. These tests revealed that the enterococci demonstrated both phenotypic clumping and antibiotic resistance phenotypes. Based on these selection criteria, the isolates were identified as having the potential for horizontal gene transfer and were used to investigate the transfer of multiple antibiotic resistance phenotypes. Conjugal transfer of antibiotic resistance phenotypes was determined using a solid agar mating method followed by a standard antibiotic selection test resulting in different transfer patterns. An interspecies conjugal transfer of vancomycin resistance from E. faecalis to E. faecium was identified while the remaining reactions were within the same species. Transfer efficiencies ranging from 2&#x2009;&#xd7;&#x2009;10[-1] to 2.3&#x2009;&#xd7;&#x2009;10[-5] were determined based on the reactions of three donor isolates (MF06036, MF0410 and MF06035) and two recipient isolates (MW01105[Rif] and ST01109[Rif]), with the transfer of vancomycin, erythromycin and tetracycline resistance genes.<br><br>CONCLUSIONS: The conjugation reactions and selection conditions used in this study resulted in a variety of co-transferred resistance phenotypes suggesting the presence of different mobile elements in the set of natural isolates. This study highlights the potential for extensive horizontal gene transfer in a previously neglected reservoir for enterococci.}, }
@article {pmid28096488, year = {2017}, author = {Keen, EC and Bliskovsky, VV and Malagon, F and Baker, JD and Prince, JS and Klaus, JS and Adhya, SL}, title = {Novel "Superspreader" Bacteriophages Promote Horizontal Gene Transfer by Transformation.}, journal = {mBio}, volume = {8}, number = {1}, pages = {}, pmid = {28096488}, issn = {2150-7511}, mesh = {*Bacteriolysis ; Coliphages/*growth &amp; development ; DNA, Bacterial/*genetics ; Drug Resistance, Bacterial ; Escherichia coli/drug effects/*virology ; *Gene Transfer, Horizontal ; Maryland ; Plasmids ; *Transformation, Bacterial ; Wyoming ; }, abstract = {UNLABELLED: Bacteriophages infect an estimated 10[23] to 10[25] bacterial cells each second, many of which carry physiologically relevant plasmids (e.g., those encoding antibiotic resistance). However, even though phage-plasmid interactions occur on a massive scale and have potentially significant evolutionary, ecological, and biomedical implications, plasmid fate upon phage infection and lysis has not been investigated to date. Here we show that a subset of the natural lytic phage population, which we dub "superspreaders," releases substantial amounts of intact, transformable plasmid DNA upon lysis, thereby promoting horizontal gene transfer by transformation. Two novel Escherichia coli phage superspreaders, SUSP1 and SUSP2, liberated four evolutionarily distinct plasmids with equal efficiency, including two close relatives of prominent antibiotic resistance vectors in natural environments. SUSP2 also mediated the extensive lateral transfer of antibiotic resistance in unbiased communities of soil bacteria from Maryland and Wyoming. Furthermore, the addition of SUSP2 to cocultures of kanamycin-resistant E. coli and kanamycin-sensitive Bacillus sp. bacteria resulted in roughly 1,000-fold more kanamycin-resistant Bacillus sp. bacteria than arose in phage-free controls. Unlike many other lytic phages, neither SUSP1 nor SUSP2 encodes homologs to known hydrolytic endonucleases, suggesting a simple potential mechanism underlying the superspreading phenotype. Consistent with this model, the deletion of endonuclease IV and the nucleoid-disrupting protein ndd from coliphage T4, a phage known to extensively degrade chromosomal DNA, significantly increased its ability to promote plasmid transformation. Taken together, our results suggest that phage superspreaders may play key roles in microbial evolution and ecology but should be avoided in phage therapy and other medical applications.<br><br>IMPORTANCE: Bacteriophages (phages), viruses that infect bacteria, are the planet's most numerous biological entities and kill vast numbers of bacteria in natural environments. Many of these bacteria carry plasmids, extrachromosomal DNA elements that frequently encode antibiotic resistance. However, it is largely unknown whether plasmids are destroyed during phage infection or released intact upon phage lysis, whereupon their encoded resistance could be acquired and manifested by other bacteria (transformation). Because phages are being developed to combat antibiotic-resistant bacteria and because transformation is a principal form of horizontal gene transfer, this question has important implications for biomedicine and microbial evolution alike. Here we report the isolation and characterization of two novel Escherichia coli phages, dubbed "superspreaders," that promote extensive plasmid transformation and efficiently disperse antibiotic resistance genes. Our work suggests that phage superspreaders are not suitable for use in medicine but may help drive bacterial evolution in natural environments.}, }
@article {pmid28096446, year = {2017}, author = {Kingston, AW and Ponkratz, C and Raleigh, EA}, title = {Rpn (YhgA-Like) Proteins of Escherichia coli K-12 and Their Contribution to RecA-Independent Horizontal Transfer.}, journal = {Journal of bacteriology}, volume = {199}, number = {7}, pages = {}, pmid = {28096446}, issn = {1098-5530}, mesh = {Calcium/metabolism ; Deoxyribonuclease I/genetics/metabolism ; Escherichia coli K12/genetics/*metabolism ; Escherichia coli Proteins/genetics/*metabolism ; Gene Expression Regulation, Bacterial/*physiology ; Gene Expression Regulation, Enzymologic ; Gene Transfer, Horizontal/*physiology ; Magnesium/metabolism ; Protein Transport ; Rec A Recombinases/genetics/*metabolism ; Recombination, Genetic ; }, abstract = {Bacteria use a variety of DNA-mobilizing enzymes to facilitate environmental niche adaptation via horizontal gene transfer. This has led to real-world problems, like the spread of antibiotic resistance, yet many mobilization proteins remain undefined. In the study described here, we investigated the uncharacterized family of YhgA-like transposase_31 (Pfam PF04754) proteins. Our primary focus was the genetic and biochemical properties of the five Escherichia coli K-12 members of this family, which we designate RpnA to RpnE, where Rpn represents recombination-promoting nuclease. We employed a conjugal system developed by our lab that demanded RecA-independent recombination following transfer of chromosomal DNA. Overexpression of RpnA (YhgA), RpnB (YfcI), RpnC (YadD), and RpnD (YjiP) increased RecA-independent recombination, reduced cell viability, and induced the expression of reporter of DNA damage. For the exemplar of the family, RpnA, mutational changes in proposed catalytic residues reduced or abolished all three phenotypes in concert. In vitro, RpnA displayed magnesium-dependent, calcium-stimulated DNA endonuclease activity with little, if any, sequence specificity and a preference for double-strand cleavage. We propose that Rpn/YhgA-like family nucleases can participate in gene acquisition processes.IMPORTANCE Bacteria adapt to new environments by obtaining new genes from other bacteria. Here, we characterize a set of genes that can promote the acquisition process by a novel mechanism. Genome comparisons had suggested the horizontal spread of the genes for the YhgA-like family of proteins through bacteria. Although annotated as transposase_31, no member of the family has previously been characterized experimentally. We show that four Escherichia coli K-12 paralogs contribute to a novel RecA-independent recombination mechanism in vivo For RpnA, we demonstrate in vitro action as a magnesium-dependent, calcium-stimulated nonspecific DNA endonuclease. The cleavage products are capable of providing priming sites for DNA polymerase, which can enable DNA joining by primer-template switching.}, }
@article {pmid28096345, year = {2017}, author = {Urbach, JM and Ausubel, FM}, title = {The NBS-LRR architectures of plant R-proteins and metazoan NLRs evolved in independent events.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {5}, pages = {1063-1068}, pmid = {28096345}, issn = {1091-6490}, support = {P30 DK040561/DK/NIDDK NIH HHS/United States ; R01 GM048707/GM/NIGMS NIH HHS/United States ; R37 GM048707/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; Disease Resistance/*genetics ; *Evolution, Molecular ; Immunity, Innate ; Leucine-Rich Repeat Proteins ; Likelihood Functions ; Models, Genetic ; *Multigene Family ; NLR Proteins/chemistry/*genetics ; Nucleoside-Triphosphatase/chemistry/*genetics ; Phylogeny ; Plant Proteins/chemistry/*genetics ; Protein Domains ; Proteins/chemistry/*genetics ; Repetitive Sequences, Amino Acid ; Sequence Alignment ; Sequence Homology, Amino Acid ; Species Specificity ; Structure-Activity Relationship ; Tetratricopeptide Repeat ; }, abstract = {There are intriguing parallels between plants and animals, with respect to the structures of their innate immune receptors, that suggest universal principles of innate immunity. The cytosolic nucleotide binding site-leucine rich repeat (NBS-LRR) resistance proteins of plants (R-proteins) and the so-called NOD-like receptors of animals (NLRs) share a domain architecture that includes a STAND (signal transduction ATPases with numerous domains) family NTPase followed by a series of LRRs, suggesting inheritance from a common ancestor with that architecture. Focusing on the STAND NTPases of plant R-proteins, animal NLRs, and their homologs that represent the NB-ARC (nucleotide-binding adaptor shared by APAF-1, certain R gene products and CED-4) and NACHT (named for NAIP, CIIA, HET-E, and TEP1) subfamilies of the STAND NTPases, we analyzed the phylogenetic distribution of the NBS-LRR domain architecture, used maximum-likelihood methods to infer a phylogeny of the NTPase domains of R-proteins, and reconstructed the domain structure of the protein containing the common ancestor of the STAND NTPase domain of R-proteins and NLRs. Our analyses reject monophyly of plant R-proteins and NLRs and suggest that the protein containing the last common ancestor of the STAND NTPases of plant R-proteins and animal NLRs (and, by extension, all NB-ARC and NACHT domains) possessed a domain structure that included a STAND NTPase paired with a series of tetratricopeptide repeats. These analyses reject the hypothesis that the domain architecture of R-proteins and NLRs was inherited from a common ancestor and instead suggest the domain architecture evolved at least twice. It remains unclear whether the NBS-LRR architectures were innovations of plants and animals themselves or were acquired by one or both lineages through horizontal gene transfer.}, }
@article {pmid28096159, year = {2017}, author = {Falgenhauer, L and Ghosh, H and Doijad, S and Yao, Y and Bunk, B and Spröer, C and Kaase, M and Hilker, R and Overmann, J and Imirzalioglu, C and Chakraborty, T}, title = {Genome Analysis of the Carbapenem- and Colistin-Resistant Escherichia coli Isolate NRZ14408 Reveals Horizontal Gene Transfer Pathways towards Panresistance and Enhanced Virulence.}, journal = {Antimicrobial agents and chemotherapy}, volume = {61}, number = {4}, pages = {}, pmid = {28096159}, issn = {1098-6596}, mesh = {Anti-Bacterial Agents/*pharmacology ; Carbapenems/*pharmacology ; Colistin/*pharmacology ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/*drug effects/*genetics/isolation &amp; purification/pathogenicity ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial/genetics ; Humans ; Plasmids/genetics ; Virulence/genetics ; Whole Genome Sequencing ; }, }
@article {pmid28095778, year = {2017}, author = {Bosi, E and Fondi, M and Orlandini, V and Perrin, E and Maida, I and de Pascale, D and Tutino, ML and Parrilli, E and Lo Giudice, A and Filloux, A and Fani, R}, title = {The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {93}, pmid = {28095778}, issn = {1471-2164}, support = {MR/J006874/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Antarctic Regions ; Anti-Bacterial Agents/metabolism ; Bacterial Proteins/genetics/metabolism ; Cold Temperature ; Databases, Genetic ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Membrane Transport Proteins/genetics/metabolism ; Phylogeny ; Pseudoalteromonas/classification/*genetics ; Secondary Metabolism/genetics ; }, abstract = {BACKGROUND: Pseudoalteromonas is a genus of ubiquitous marine bacteria used as model organisms to study the biological mechanisms involved in the adaptation to cold conditions. A remarkable feature shared by these bacteria is their ability to produce secondary metabolites with a strong antimicrobial and antitumor activity. Despite their biotechnological relevance, representatives of this genus are still lacking (with few exceptions) an extensive genomic characterization, including features involved in the evolution of secondary metabolites production. Indeed, biotechnological applications would greatly benefit from such analysis.<br><br>RESULTS: Here, we analyzed the genomes of 38 strains belonging to different Pseudoalteromonas species and isolated from diverse ecological niches, including extreme ones (i.e. Antarctica). These sequences were used to reconstruct the largest Pseudoalteromonas pangenome computed so far, including also the two main groups of Pseudoalteromonas strains (pigmented and not pigmented strains). The downstream analyses were conducted to describe the genomic diversity, both at genus and group levels. This allowed highlighting a remarkable genomic heterogeneity, even for closely related strains. We drafted all the main evolutionary steps that led to the current structure and gene content of Pseudoalteromonas representatives. These, most likely, included an extensive genome reduction and a strong contribution of Horizontal Gene Transfer (HGT), which affected biotechnologically relevant gene sets and occurred in a strain-specific fashion. Furthermore, this study also identified the genomic determinants related to some of the most interesting features of the Pseudoalteromonas representatives, such as the production of secondary metabolites, the adaptation to cold temperatures and the resistance to abiotic compounds.<br><br>CONCLUSIONS: This study poses the bases for a comprehensive understanding of the evolutionary trajectories followed in time by this peculiar bacterial genus and for a focused exploitation of their biotechnological potential.}, }
@article {pmid28095611, year = {2017}, author = {Qiu, H and Lee, JM and Yoon, HS and Bhattacharya, D}, title = {Hypothesis: Gene-rich plastid genomes in red algae may be an outcome of nuclear genome reduction.}, journal = {Journal of phycology}, volume = {53}, number = {3}, pages = {715-719}, doi = {10.1111/jpy.12514}, pmid = {28095611}, issn = {1529-8817}, mesh = {*Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Plant/*genetics ; Genome, Plastid/*genetics ; Rhodophyta/*genetics ; Symbiosis ; }, abstract = {Red algae (Rhodophyta) putatively diverged from the eukaryote tree of life >1.2 billion years ago and are the source of plastids in the ecologically important diatoms, haptophytes, and dinoflagellates. In general, red algae contain the largest plastid gene inventory among all such organelles derived from primary, secondary, or additional rounds of endosymbiosis. In contrast, their nuclear gene inventory is reduced when compared to their putative sister lineage, the Viridiplantae, and other photosynthetic lineages. The latter is thought to have resulted from a phase of genome reduction that occurred in the stem lineage of Rhodophyta. A recent comparative analysis of a taxonomically broad collection of red algal and Viridiplantae plastid genomes demonstrates that the red algal ancestor encoded ~1.5× more plastid genes than Viridiplantae. This difference is primarily explained by more extensive endosymbiotic gene transfer (EGT) in the stem lineage of Viridiplantae, when compared to red algae. We postulate that limited EGT in Rhodophytes resulted from the countervailing force of ancient, and likely recurrent, nuclear genome reduction. In other words, the propensity for nuclear gene loss led to the retention of red algal plastid genes that would otherwise have undergone intracellular gene transfer to the nucleus. This hypothesis recognizes the primacy of nuclear genome evolution over that of plastids, which have no inherent control of their gene inventory and can change dramatically (e.g., secondarily non-photosynthetic eukaryotes, dinoflagellates) in response to selection acting on the host lineage.}, }
@article {pmid28093843, year = {2018}, author = {McDonald, MC and Ahren, D and Simpfendorfer, S and Milgate, A and Solomon, PS}, title = {The discovery of the virulence gene ToxA in the wheat and barley pathogen Bipolaris sorokiniana.}, journal = {Molecular plant pathology}, volume = {19}, number = {2}, pages = {432-439}, pmid = {28093843}, issn = {1364-3703}, mesh = {Ascomycota/*pathogenicity ; Fungal Proteins/genetics/*metabolism ; Gene Transfer, Horizontal/genetics ; Hordeum/*microbiology ; Triticum/*microbiology ; Virulence ; }, abstract = {Bipolaris sorokiniana is the causal agent of multiple diseases on wheat and barley and is the primary constraint to cereal production throughout South Asia. Despite its significance, the molecular basis of disease is poorly understood. To address this, the genomes of three Australian isolates of B. sorokiniana were sequenced and screened for known pathogenicity genes. Sequence analysis revealed that the isolate BRIP10943 harboured the ToxA gene, which has been associated previously with disease in the wheat pathogens Parastagonospora nodorum and Pyrenophora tritici-repentis. Analysis of the regions flanking ToxA within B. sorokiniana revealed that it was embedded within a 12-kb genomic element nearly identical to the corresponding regions in P. nodorum and P. tritici-repentis. A screen of 35 Australian B. sorokiniana isolates confirmed that ToxA was present in 12 isolates. Sequencing of the ToxA genes within these isolates revealed two haplotypes, which differed by a single non-synonymous nucleotide substitution. Pathogenicity assays showed that a B. sorokiniana isolate harbouring ToxA was more virulent on wheat lines that contained the sensitivity gene when compared with a non-ToxA isolate. This work demonstrates that proteins that confer host-specific virulence can be horizontally acquired across multiple species. This acquisition can dramatically increase the virulence of pathogenic strains on susceptible cultivars, which, in an agricultural setting, can have devastating economic and social impacts.}, }
@article {pmid28090382, year = {2016}, author = {Suhartono, S and Savin, M}, title = {Conjugative transmission of antibiotic-resistance from stream water Escherichia coli as related to number of sulfamethoxazole but not class 1 and 2 integrase genes.}, journal = {Mobile genetic elements}, volume = {6}, number = {6}, pages = {e1256851}, pmid = {28090382}, issn = {2159-2543}, abstract = {A conjugation assay was used to determine the effects of phenotypic resistance to one to up to 5 antibiotics, sampling site of origin, presence or absence of class 1 and/or class 2 integrase (intI) genes (intI1 and intI2), and the number of sulfamethoxazole resistance (sul) and trimethoprim resistance (dfr) genes on the transfer frequencies of plasmids from environmental, antibiotic-resistant Escherichia coli. Of 51 sulfamethoxazole and trimethoprim-resistant E. coli isolates conferring at least one mob gene (mobP51, mobF11, mobF12, mobQ11, mobQ12 , or mobQu), 38 produced transconjugants with an overall mean frequency of 1.60 × 10[-3] transconjugants/ donors (T/D) or 5.89 × 10[-3] transconjugants/recipients (T/R). The presence or absence of intI1 and intI2 and the presence or absence of different targeted dfr genes (dfrA1, dfrA8, dfrA12, dfrA14, dfrA17, and/or dfrB3) were not statistically related to plasmid transfer frequencies as determined by ANOVA (P ≥ 0.05). However, E. coli isolates recovered 2 km downstream of wastewater treatment plant effluent input, and those possessing resistance to 3 antibiotics had significantly greater plasmid transfer frequency than their counterparts when calculated as T/D (ANOVA followed by Fisher's least significant difference means comparison, P < 0.05). Greater plasmid transfer frequency calculated as T/D was also measured for E. coli possessing 3 compared to a single sul gene. The in-vitro frequency suggests that horizontal gene transfer of conjugative mediated-antibiotic (sul) resistance genes may be significant among resistant, stream bacteria.}, }
@article {pmid28090377, year = {2016}, author = {Snir, S}, title = {Ordered orthology as a tool in prokaryotic evolutionary inference.}, journal = {Mobile genetic elements}, volume = {6}, number = {6}, pages = {e1120576}, pmid = {28090377}, issn = {2159-2543}, abstract = {Molecular data is accumulated at exponentially increasing pace. This deluge of information should have brought us closer to resolving one of the most fundamental issues in biology - deciphering the history of life on Earth. So far, however, this abundance of data only seems to blur our understanding of the problem. This is largely due to horizontal gene transfer (HGT), the transfer of genetic material between evolutionarily unrelated organisms that transforms the prokaryotic tree into a network of relationships. Recently, we developed a method to infer evolutionary relationships among closely related species where the conventional evolutionary markers do not provide a strong enough signal. The method relies on the loss of synteny, gene order conservation among species that provides a stronger signal, sufficient to classify even strains of a given species. Here we elaborate on this method and suggest further uses of it in the context of detecting HGT events and genome architecture.}, }
@article {pmid28088766, year = {2017}, author = {Larsen, J and Andersen, PS and Winstel, V and Peschel, A}, title = {Staphylococcus aureus CC395 harbours a novel composite staphylococcal cassette chromosome mec element.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {72}, number = {4}, pages = {1002-1005}, pmid = {28088766}, issn = {1460-2091}, mesh = {*Chromosomes, Bacterial ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; *Interspersed Repetitive Sequences ; *Recombination, Genetic ; Sequence Analysis, DNA ; Staphylococcus aureus/*genetics ; }, abstract = {BACKGROUND: CoNS species are likely reservoirs of the staphylococcal cassette chromosome mec (SCC mec) in Staphylococcus aureus . S . aureus CC395 is unique as it is capable of exchanging DNA with CoNS via bacteriophages, which are also known to mediate transfer of SCC mec .<br><br>OBJECTIVES: To analyse the structure and putative origin of the SCC mec element in S . aureus CC395.<br><br>METHODS: The only MRSA CC395 strain described in the literature, JS395, was subjected to WGS, and its SCC mec element was compared with those found in CoNS species and other S. aureus strains.<br><br>RESULTS: JS395 was found to carry an unusually large 88&#x2005;kb composite SCC mec element. The 33&#x2005;kb region downstream of orfX harboured a type V SCC mec element and a CRISPR locus, which was most similar to those found in the CoNS species Staphylococcus capitis and Staphylococcus schleiferi . A 55&#x2005;kb SCC element was identified downstream of the type V SCC mec element and contained a mercury resistance region found in the composite SCC element of some Staphylococcus epidermidis and S . aureus strains, an integrated S . aureus plasmid containing genes for the detoxification of cadmium and arsenic, and a stretch of genes that was partially similar to the type IVg SCC mec element found in a bovine S . aureus strain.<br><br>CONCLUSIONS: The size and complexity of the SCC mec element support the idea that CC395 is highly prone to DNA uptake from CoNS. Thus CC395 may serve as an entry point for SCC mec and SCC structures into S . aureus .}, }
@article {pmid28088530, year = {2017}, author = {Ben, W and Wang, J and Cao, R and Yang, M and Zhang, Y and Qiang, Z}, title = {Distribution of antibiotic resistance in the effluents of ten municipal wastewater treatment plants in China and the effect of treatment processes.}, journal = {Chemosphere}, volume = {172}, number = {}, pages = {392-398}, doi = {10.1016/j.chemosphere.2017.01.041}, pmid = {28088530}, issn = {1879-1298}, mesh = {Anti-Bacterial Agents/analysis ; Bacteria/drug effects/*genetics ; China ; Disinfectants/chemistry ; Disinfection ; *Drug Resistance, Microbial ; Gene Transfer, Horizontal ; Genes, Bacterial ; RNA, Ribosomal, 16S/chemistry ; Sewage/microbiology ; Sulfonamides/analysis ; Tetracycline Resistance/genetics ; Tetracyclines/analysis ; Waste Disposal, Fluid/*methods ; Wastewater/*analysis ; *Water Microbiology ; Water Pollutants, Chemical/chemistry ; Water Purification/*methods ; }, abstract = {Municipal wastewater treatment plant (WWTP) effluents represent an important contamination source of antibiotic resistance, threatening the ecological safety of receiving environments. In this study, the release of antibiotic resistance to sulfonamides and tetracyclines in the effluents of ten WWTPs in China was investigated. Results indicate that the concentrations of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) ranged from 1.1 × 10[1] to 8.9 × 10[3] CFU mL[-1] and 3.6 × 10[1] (tetW) to 5.4 × 10[6] (tetX) copies mL[-1], respectively. There were insignificant correlations of the concentrations of ARB and ARGs with those of corresponding antibiotics. Strong correlations were observed between the total concentrations of tetracycline resistance genes and sulfonamide resistance genes, and both of which were significantly correlated with intI1 concentrations. Statistical analysis of the effluent ARG concentrations in different WWTPs revealed an important role of disinfection in eliminating antibiotic resistance. The release rates of ARB and ARGs through the effluents of ten WWTPs ranged from 5.9 × 10[12] to 4.8 × 10[15] CFU d[-1] and 6.4 × 10[12] (tetW) to 1.7 × 10[18] (sul1) copies d[-1], respectively. This study helps the effective assessment and scientific management of ecological risks induced by antibiotic resistance discharged from WWTPs.}, }
@article {pmid28087933, year = {2016}, author = {Termorshuizen, AJ}, title = {Ecology of Fungal Plant Pathogens.}, journal = {Microbiology spectrum}, volume = {4}, number = {6}, pages = {}, doi = {10.1128/microbiolspec.FUNK-0013-2016}, pmid = {28087933}, issn = {2165-0497}, mesh = {*Ecosystem ; Fungi/*growth &amp; development/*pathogenicity ; Plant Diseases/*microbiology ; Population Density ; }, abstract = {Fungal plant pathogens are ubiquitous and highly diverse. Key to their success is high host density, which notably is the case in agroecosystems. Several hypotheses related to the effects of plant pathogens on plant diversity (the Janzen-Connell hypothesis, the dilution effect hypothesis) and the phenomenon of higher biomass in plant mixtures (i.e., overyielding) can all be explained by the quantitative interplay between host and pathogen density. In many agroecosystems, fungal plant pathogens cause great losses, since in monocultures diseased plants cannot be replaced by healthy plants. On the other hand, in natural ecosystems fungal plant pathogens shape the succession of vegetation and enhance the biodiversity of forests and grasslands. When pathogens are introduced into areas outside their natural range, they may behave differently, causing severe damage. Once introduced, changes may occur such as hybridization with other closely related pathogens or host shifts, host jumps, or horizontal gene transfer. Such changes can be hazardous for both agricultural and natural ecosystems.}, }
@article {pmid28087696, year = {2017}, author = {Du, C and Cao, S and Shi, X and Nie, X and Zheng, J and Deng, Y and Ruan, L and Peng, D and Sun, M}, title = {Genetic and Biochemical Characterization of a Gene Operon for trans-Aconitic Acid, a Novel Nematicide from Bacillus thuringiensis.}, journal = {The Journal of biological chemistry}, volume = {292}, number = {8}, pages = {3517-3530}, pmid = {28087696}, issn = {1083-351X}, mesh = {Aconitic Acid/*metabolism ; Amino Acid Sequence ; Antinematodal Agents/*metabolism ; Bacillus thuringiensis/chemistry/*enzymology/*genetics/metabolism ; Bacterial Proteins/chemistry/genetics/metabolism ; Carrier Proteins/chemistry/*genetics/metabolism ; DNA Transposable Elements ; Genes, Bacterial ; Isomerases/chemistry/*genetics/metabolism ; Multigene Family ; *Operon ; Sequence Alignment ; }, abstract = {trans-Aconitic acid (TAA) is an isomer of cis-aconitic acid (CAA), an intermediate of the tricarboxylic acid cycle that is synthesized by aconitase. Although TAA production has been detected in bacteria and plants for many years and is known to be a potent inhibitor of aconitase, its biosynthetic origins and the physiological relevance of its activity have remained unclear. We have serendipitously uncovered key information relevant to both of these questions. Specifically, in a search for novel nematicidal factors from Bacillus thuringiensis, a significant nematode pathogen harboring many protein virulence factors, we discovered a high yielding component that showed activity against the plant-parasitic nematode Meloidogyne incognita and surprisingly identified it as TAA. Comparison with CAA, which displayed a much weaker nematicidal effect, suggested that TAA is specifically synthesized by B. thuringiensis as a virulence factor. Analysis of mutants deficient in plasmids that were anticipated to encode virulence factors allowed us to isolate a TAA biosynthesis-related (tbr) operon consisting of two genes, tbrA and tbrB We expressed the corresponding proteins, TbrA and TbrB, and characterized them as an aconitate isomerase and TAA transporter, respectively. Bioinformatics analysis of the TAA biosynthetic gene cluster revealed the association of the TAA genes with transposable elements relevant for horizontal gene transfer as well as a distribution across B. cereus bacteria and other B. thuringiensis strains, suggesting a general role for TAA in the interactions of B. cereus group bacteria with nematode hosts in the soil environment. This study reveals new bioactivity for TAA and the TAA biosynthetic pathway, improving our understanding of virulence factors employed by B. thuringiensis pathogenesis and providing potential implications for nematode management applications.}, }
@article {pmid28087420, year = {2017}, author = {Bryant, C and Fischer, M and Linz, S and Semple, C}, title = {On the quirks of maximum parsimony and likelihood on phylogenetic networks.}, journal = {Journal of theoretical biology}, volume = {417}, number = {}, pages = {100-108}, doi = {10.1016/j.jtbi.2017.01.013}, pmid = {28087420}, issn = {1095-8541}, mesh = {Animals ; *Biological Evolution ; Gene Regulatory Networks ; Humans ; *Likelihood Functions ; *Models, Genetic ; *Phylogeny ; }, abstract = {Maximum parsimony is one of the most frequently-discussed tree reconstruction methods in phylogenetic estimation. However, in recent years it has become more and more apparent that phylogenetic trees are often not sufficient to describe evolution accurately. For instance, processes like hybridization or lateral gene transfer that are commonplace in many groups of organisms and result in mosaic patterns of relationships cannot be represented by a single phylogenetic tree. This is why phylogenetic networks, which can display such events, are becoming of more and more interest in phylogenetic research. It is therefore necessary to extend concepts like maximum parsimony from phylogenetic trees to networks. Several suggestions for possible extensions can be found in recent literature, for instance the softwired and the hardwired parsimony concepts. In this paper, we analyze the so-called big parsimony problem under these two concepts, i.e. we investigate maximum parsimonious networks and analyze their properties. In particular, we show that finding a softwired maximum parsimony network is possible in polynomial time. We also show that the set of maximum parsimony networks for the hardwired definition always contains at least one phylogenetic tree. Lastly, we investigate some parallels of parsimony to different likelihood concepts on phylogenetic networks.}, }
@article {pmid28087277, year = {2017}, author = {Lehmann, G and Udasin, RG and Livneh, I and Ciechanover, A}, title = {Identification of UBact, a ubiquitin-like protein, along with other homologous components of a conjugation system and the proteasome in different gram-negative bacteria.}, journal = {Biochemical and biophysical research communications}, volume = {483}, number = {3}, pages = {946-950}, doi = {10.1016/j.bbrc.2017.01.037}, pmid = {28087277}, issn = {1090-2104}, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics/*metabolism ; Computational Biology ; Conserved Sequence ; Evolution, Molecular ; Gram-Negative Bacteria/classification/genetics/*metabolism ; Phylogeny ; Proteasome Endopeptidase Complex/genetics/*metabolism ; Sequence Homology, Amino Acid ; Ubiquitins/genetics/*metabolism ; }, abstract = {Systems analogous to the eukaryotic ubiquitin-proteasome system have been previously identified in Archaea, and Actinobacteria (gram-positive), but not in gram-negative bacteria. Here, we report the bioinformatic identification of a novel prokaryotic ubiquitin-like protein, which we name UBact. The phyletic distribution of UBact covers at least five gram-negative bacterial phyla, including Nitrospirae, Armatimonadetes, Verrucomicroba, Nitrospinae, and Planctomycetes. Additionally, it was identified in seven candidate (uncultured) phyla and one Archaeon. UBact might have been overlooked because only few species in the phyla where it is found have been sequenced. In most of the species where we identified UBact, its neighbors in the genome code for proteins homologous to those involved in conjugation and/or degradation of Pup and Pup-tagged substrates. Among them are PafA-, Dop-, Mpa- and proteasome-homologous proteins. This gene association as well as UBact's size and conserved C-terminal G[E/Q] motif, strongly suggest that UBact is used as a conjugatable tag for degradation. With regard to its C-terminus, UBact differs from ubiquitin and most ubiquitin-like proteins (including the mycobacterial Pup) in that it lacks the characteristic C-terminal di-glycine motif, and it usually ends with the sequence R[T/S]G[E/Q]. The phyla that contain UBact are thought to have diverged over 3000 million years ago, indicating that either this ubiquitin-like conjugation system evolved early in evolution or that its occurrence in distant gram-negative phyla is due to multiple instances of horizontal gene transfer.}, }
@article {pmid28086786, year = {2017}, author = {Breusing, C and Vrijenhoek, RC and Reusch, TB}, title = {Widespread introgression in deep-sea hydrothermal vent mussels.}, journal = {BMC evolutionary biology}, volume = {17}, number = {1}, pages = {13}, pmid = {28086786}, issn = {1471-2148}, mesh = {Animals ; Bivalvia/*genetics ; Ecosystem ; Gene Transfer, Horizontal ; Genetics, Population ; *Hybridization, Genetic ; Hydrothermal Vents ; Mytilidae/genetics ; }, abstract = {BACKGROUND: The analysis of hybrid zones is crucial for gaining a mechanistic understanding of the process of speciation and the maintenance of species boundaries. Hybrid zones have been studied intensively in terrestrial and shallow-water ecosystems, but very little is known about their occurrence in deep-sea environments. Here we used diagnostic, single nucleotide polymorphisms in combination with one mitochondrial gene to re-examine prior hypotheses about a contact zone involving deep-sea hydrothermal vent mussels, Bathymodiolus azoricus and B. puteoserpentis, living along the Mid-Atlantic Ridge.<br><br>RESULTS: Admixture was found to be asymmetric with respect to the parental species, while introgression was more widespread geographically than previously recognized. Admixed individuals with a majority of alleles from one of the parental species were most frequent in habitats corresponding to that species. Mussels found at a geographically intermediate vent field constituted a genetically mixed population that showed no evidence for hybrid incompatibilities, a finding that does not support a previously inferred tension zone model.<br><br>CONCLUSIONS: Our analyses indicate that B. azoricus and B. puteoserpentis hybridize introgressively across a large geographic area without evidence for general hybrid incompatibilities. While these findings shed new light onto the genetic structure of this hybrid zone, many aspects about its nature still remain obscure. Our study sets a baseline for further research that should primarily focus on the acquisition of additional mussel samples and environmental data, a detailed exploration of vent areas and hidden populations as well as genomic analyses in both mussel hosts and their bacterial symbionts.}, }
@article {pmid28083919, year = {2018}, author = {Ishihara, K}, title = {New approach for studying mobile genes using metagenomic analysis.}, journal = {Oral diseases}, volume = {24}, number = {4}, pages = {494-496}, doi = {10.1111/odi.12640}, pmid = {28083919}, issn = {1601-0825}, mesh = {Bacteria/*genetics ; Drug Resistance, Bacterial/genetics ; Fiji ; Gastrointestinal Microbiome/genetics ; Gene Transfer, Horizontal ; Humans ; *Metagenome ; Metagenomics ; Mouth/*microbiology ; Mouth Diseases/*microbiology ; North America ; }, }
@article {pmid28082953, year = {2016}, author = {González, C and Lazcano, M and Valdés, J and Holmes, DS}, title = {Bioinformatic Analyses of Unique (Orphan) Core Genes of the Genus Acidithiobacillus: Functional Inferences and Use As Molecular Probes for Genomic and Metagenomic/Transcriptomic Interrogation.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {2035}, pmid = {28082953}, issn = {1664-302X}, abstract = {Using phylogenomic and gene compositional analyses, five highly conserved gene families have been detected in the core genome of the phylogenetically coherent genus Acidithiobacillus of the class Acidithiobacillia. These core gene families are absent in the closest extant genus Thermithiobacillus tepidarius that subtends the Acidithiobacillus genus and roots the deepest in this class. The predicted proteins encoded by these core gene families are not detected by a BLAST search in the NCBI non-redundant database of more than 90 million proteins using a relaxed cut-off of 1.0e[-5]. None of the five families has a clear functional prediction. However, bioinformatic scrutiny, using pI prediction, motif/domain searches, cellular location predictions, genomic context analyses, and chromosome topology studies together with previously published transcriptomic and proteomic data, suggests that some may have functions associated with membrane remodeling during cell division perhaps in response to pH stress. Despite the high level of amino acid sequence conservation within each family, there is sufficient nucleotide variation of the respective genes to permit the use of the DNA sequences to distinguish different species of Acidithiobacillus, making them useful additions to the armamentarium of tools for phylogenetic analysis. Since the protein families are unique to the Acidithiobacillus genus, they can also be leveraged as probes to detect the genus in environmental metagenomes and metatranscriptomes, including industrial biomining operations, and acid mine drainage (AMD).}, }
@article {pmid28081925, year = {2017}, author = {Torpdahl, M and Hasman, H and Litrup, E and Skov, RL and Nielsen, EM and Hammerum, AM}, title = {Detection of mcr-1-encoding plasmid-mediated colistin-resistant Salmonella isolates from human infection in Denmark.}, journal = {International journal of antimicrobial agents}, volume = {49}, number = {2}, pages = {261-262}, doi = {10.1016/j.ijantimicag.2016.11.010}, pmid = {28081925}, issn = {1872-7913}, mesh = {Anti-Bacterial Agents/*pharmacology ; Colistin/*pharmacology ; Denmark ; *Drug Resistance, Bacterial ; Escherichia coli Proteins/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genotype ; Humans ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Phenotype ; Plasmids/*analysis/classification ; Salmonella/*drug effects/isolation &amp; purification ; Salmonella Infections/*microbiology ; }, }
@article {pmid28074180, year = {2016}, author = {Nakao, R and Abe, T and Funayama, S and Sugimoto, C}, title = {Horizontally Transferred Genetic Elements in the Tsetse Fly Genome: An Alignment-Free Clustering Approach Using Batch Learning Self-Organising Map (BLSOM).}, journal = {BioMed research international}, volume = {2016}, number = {}, pages = {3164624}, pmid = {28074180}, issn = {2314-6141}, mesh = {Animals ; Bacillus/genetics ; Chromosome Mapping/methods ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genetic Loci ; *Genome ; Tsetse Flies/*genetics/microbiology ; Wolbachia/genetics ; }, abstract = {Tsetse flies (Glossina spp.) are the primary vectors of trypanosomes, which can cause human and animal African trypanosomiasis in Sub-Saharan African countries. The objective of this study was to explore the genome of Glossina morsitans morsitans for evidence of horizontal gene transfer (HGT) from microorganisms. We employed an alignment-free clustering method, that is, batch learning self-organising map (BLSOM), in which sequence fragments are clustered based on the similarity of oligonucleotide frequencies independently of sequence homology. After an initial scan of HGT events using BLSOM, we identified 3.8% of the tsetse fly genome as HGT candidates. The predicted donors of these HGT candidates included known symbionts, such as Wolbachia, as well as bacteria that have not previously been associated with the tsetse fly. We detected HGT candidates from diverse bacteria such as Bacillus and Flavobacteria, suggesting a past association between these taxa. Functional annotation revealed that the HGT candidates encoded loci in various functional pathways, such as metabolic and antibiotic biosynthesis pathways. These findings provide a basis for understanding the coevolutionary history of the tsetse fly and its microbes and establish the effectiveness of BLSOM for the detection of HGT events.}, }
@article {pmid28073961, year = {2017}, author = {Li, R and Xie, M and Zhang, J and Yang, Z and Liu, L and Liu, X and Zheng, Z and Chan, EW and Chen, S}, title = {Genetic characterization of mcr-1-bearing plasmids to depict molecular mechanisms underlying dissemination of the colistin resistance determinant.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {72}, number = {2}, pages = {393-401}, doi = {10.1093/jac/dkw411}, pmid = {28073961}, issn = {1460-2091}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; China ; Colistin/*pharmacology ; Computational Biology ; *Drug Resistance, Bacterial ; Escherichia coli/*drug effects/genetics ; Escherichia coli Proteins/*genetics ; Farms ; Gene Transfer, Horizontal ; Genes, Bacterial ; Interspersed Repetitive Sequences ; Microbial Sensitivity Tests ; Plasmids/*classification ; Sequence Analysis, DNA ; Swine/*microbiology ; }, abstract = {OBJECTIVES: To analyse and compare mcr-1-bearing plasmids from animal Escherichia coli isolates, and to investigate potential mechanisms underlying dissemination of mcr-1.<br><br>METHODS: Ninety-seven ESBL-producing E. coli strains isolated from pig farms in China were screened for the mcr-1 gene. Fifteen mcr-1-positive strains were subjected to molecular characterization and bioinformatic analysis of the mcr-1-bearing plasmids that they harboured.<br><br>RESULTS: Three major types of mcr-1-bearing plasmids were recovered: IncX4 (&#x223c;33 kb), IncI2 (&#x223c;60 kb) and IncHI2 (&#x223c;216-280 kb), among which the IncX4 and IncI2 plasmids were found to harbour the mcr-1 gene only, whereas multiple resistance elements including blaCTX-M, blaCMY, blaTEM, fosA, qnrS, floR and oqxAB were detected, in various combinations, alongside mcr-1 in the IncHI2 plasmids. The profiles of mcr-1-bearing plasmids in the test strains were highly variable, with coexistence of two mcr-1-bearing plasmids being common. However, the MIC of colistin was not affected by the number of mcr-1-carrying plasmids harboured. Comparative analysis of the plasmids showed that they contained an mcr-1 gene cassette with varied structures (mcr-1-orf, ISApl1-mcr-1-orf and Tn6330), with the IncHI2 type being the most active in acquiring foreign resistance genes. A novel transposon, Tn6330, with the structure ISApl1-mcr-1-orf-ISApl1 was found to be the key element mediating translocation of mcr-1 into various plasmid backbones through formation of a circular intermediate.<br><br>CONCLUSIONS: The mcr-1 gene can be disseminated via multiple mobile elements including Tn6330, its circular intermediate and plasmids harbouring such elements. It is often co-transmitted with other resistance determinants through IncHI2 plasmids. The functional mechanism of Tn6330, a typical composite transposon harbouring mcr-1, should be further investigated.}, }
@article {pmid28069644, year = {2017}, author = {Liu, BT and Song, FJ and Zou, M and Zhang, QD and Shan, H}, title = {High Incidence of Escherichia coli Strains Coharboring mcr-1 and blaNDM from Chickens.}, journal = {Antimicrobial agents and chemotherapy}, volume = {61}, number = {3}, pages = {}, pmid = {28069644}, issn = {1098-6596}, mesh = {Animal Husbandry ; Animals ; Anti-Bacterial Agents/pharmacology ; Carbapenems/pharmacology ; Chickens ; China/epidemiology ; Clone Cells ; Colistin/pharmacology ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/drug effects/genetics/growth &amp; development ; Escherichia coli Infections/drug therapy/epidemiology/transmission/*veterinary ; Escherichia coli Proteins/*genetics/metabolism ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Plasmids/chemistry/*metabolism ; Poultry Diseases/drug therapy/*epidemiology/microbiology/transmission ; beta-Lactamases/*genetics/metabolism ; }, abstract = {This study investigated the characteristics of Escherichia coli isolates carrying mcr-1-blaNDM from a chicken farm in China. Of the 78 E. coli isolates, 21 clonally unrelated isolates carried mcr-1-blaNDM Diverse IncI2 plasmids disseminated mcr-1, while the dissemination of blaNDM was mediated by diverse IncB/O plasmids. More striking was the colocalization of resistance genes mcr-1 and blaNDM-4 in an IncHI2/ST3 plasmid, which might pose a great challenge for public health.}, }
@article {pmid28067866, year = {2017}, author = {Lamberte, LE and Baniulyte, G and Singh, SS and Stringer, AM and Bonocora, RP and Stracy, M and Kapanidis, AN and Wade, JT and Grainger, DC}, title = {Horizontally acquired AT-rich genes in Escherichia coli cause toxicity by sequestering RNA polymerase.}, journal = {Nature microbiology}, volume = {2}, number = {}, pages = {16249}, pmid = {28067866}, issn = {2058-5276}, support = {204684//Wellcome Trust/United Kingdom ; 204684/Z/16/Z//Wellcome Trust/United Kingdom ; DP2 OD007188/OD/NIH HHS/United States ; BB/H01795X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 110164//Wellcome Trust/United Kingdom ; 085092//Wellcome Trust/United Kingdom ; //Wellcome Trust/United Kingdom ; }, mesh = {AT Rich Sequence/*genetics ; Base Composition ; DNA, Bacterial/chemistry/*genetics/metabolism ; DNA-Binding Proteins/metabolism ; DNA-Directed RNA Polymerases/*genetics/*metabolism ; Escherichia coli/*genetics ; Escherichia coli Proteins/*metabolism ; Fimbriae Proteins/*metabolism ; Gene Expression Regulation, Bacterial ; Gene Silencing ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Fitness ; Genome ; Mutation ; Promoter Regions, Genetic ; Transcription, Genetic ; }, abstract = {Horizontal gene transfer permits rapid dissemination of genetic elements between individuals in bacterial populations. Transmitted DNA sequences may encode favourable traits. However, if the acquired DNA has an atypical base composition, it can reduce host fitness. Consequently, bacteria have evolved strategies to minimize the harmful effects of foreign genes. Most notably, xenogeneic silencing proteins bind incoming DNA that has a higher AT content than the host genome. An enduring question has been why such sequences are deleterious. Here, we showed that the toxicity of AT-rich DNA in Escherichia coli frequently results from constitutive transcription initiation within the coding regions of genes. Left unchecked, this causes titration of RNA polymerase and a global downshift in host gene expression. Accordingly, a mutation in RNA polymerase that diminished the impact of AT-rich DNA on host fitness reduced transcription from constitutive, but not activator-dependent, promoters.}, }
@article {pmid28067598, year = {2017}, author = {Coray, DS and Wheeler, NE and Heinemann, JA and Gardner, PP}, title = {Why so narrow: Distribution of anti-sense regulated, type I toxin-antitoxin systems compared with type II and type III systems.}, journal = {RNA biology}, volume = {14}, number = {3}, pages = {275-280}, pmid = {28067598}, issn = {1555-8584}, mesh = {Antitoxins/*genetics ; Bacterial Toxins/*genetics ; Databases, Genetic ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Interspersed Repetitive Sequences ; Multigene Family ; Operon ; Phylogeny ; RNA, Antisense/*genetics ; }, abstract = {Toxin-antitoxin (TA) systems are gene modules that appear to be horizontally mobile across a wide range of prokaryotes. It has been proposed that type I TA systems, with an antisense RNA-antitoxin, are less mobile than other TAs that rely on direct toxin-antitoxin binding but no direct comparisons have been made. We searched for type I, II and III toxin families using iterative searches with profile hidden Markov models across phyla and replicons. The distribution of type I toxin families were comparatively narrow, but these patterns weakened with recently discovered families. We discuss how the function and phenotypes of TA systems as well as biases in our search methods may account for differences in their distribution.}, }
@article {pmid28067311, year = {2017}, author = {Pang, TY and Lercher, MJ}, title = {Supra-operonic clusters of functionally related genes (SOCs) are a source of horizontal gene co-transfers.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {40294}, pmid = {28067311}, issn = {2045-2322}, mesh = {*Gene Transfer, Horizontal ; *Genes ; Multigene Family ; Operon/*genetics ; }, abstract = {Adaptation of bacteria occurs predominantly via horizontal gene transfer (HGT). While it is widely recognized that horizontal acquisitions frequently encompass multiple genes, it is unclear what the size distribution of successfully transferred DNA segments looks like and what evolutionary forces shape this distribution. Here, we identified 1790 gene family pairs that were consistently co-gained on the same branches across a phylogeny of 53 E. coli strains. We estimated a lower limit of their genomic distances at the time they were transferred to their host genomes; this distribution shows a sharp upper bound at 30 kb. The same gene-pairs can have larger distances (up to 70 kb) in other genomes. These more distant pairs likely represent recent acquisitions via transduction that involve the co-transfer of excised prophage genes, as they are almost always associated with intervening phage-associated genes. The observed distribution of genomic distances of co-transferred genes is much broader than expected from a model based on the co-transfer of genes within operons; instead, this distribution is highly consistent with the size distribution of supra-operonic clusters (SOCs), groups of co-occurring and co-functioning genes that extend beyond operons. Thus, we propose that SOCs form a basic unit of horizontal gene transfer.}, }
@article {pmid28066393, year = {2016}, author = {Kohn, T and Heuer, A and Jogler, M and Vollmers, J and Boedeker, C and Bunk, B and Rast, P and Borchert, D and Glöckner, I and Freese, HM and Klenk, HP and Overmann, J and Kaster, AK and Rohde, M and Wiegand, S and Jogler, C}, title = {Fuerstia marisgermanicae gen. nov., sp. nov., an Unusual Member of the Phylum Planctomycetes from the German Wadden Sea.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {2079}, pmid = {28066393}, issn = {1664-302X}, abstract = {Members of the phylum Planctomycetes are ubiquitous bacteria that dwell in aquatic and terrestrial habitats. While planctomycetal species are important players in the global carbon and nitrogen cycle, this phylum is still undersampled and only few genome sequences are available. Here we describe strain NH11[T], a novel planctomycete obtained from a crustacean shell (Wadden Sea, Germany). The phylogenetically closest related cultivated species is Gimesia maris, sharing only 87% 16S rRNA sequence identity. Previous isolation attempts have mostly yielded members of the genus Rhodopirellula from water of the German North Sea. On the other hand, only one axenic culture of the genus Pirellula was obtained from a crustacean thus far. However, the 16S rRNA gene sequence of strain NH11[T] shares only 80% sequence identity with the closest relative of both genera, Rhodopirellula and Pirellula. Thus, strain NH11[T] is unique in terms of origin and phylogeny. While the pear to ovoid shaped cells of strain NH11[T] are typical planctomycetal, light-, and electron microscopic observations point toward an unusual variation of cell division through budding: during the division process daughter- and mother cells are connected by an unseen thin tubular-like structure. Furthermore, the periplasmic space of strain NH11[T] was unusually enlarged and differed from previously known planctomycetes. The complete genome of strain NH11[T], with almost 9 Mb in size, is among the largest planctomycetal genomes sequenced thus far, but harbors only 6645 protein-coding genes. The acquisition of genomic components by horizontal gene transfer is indicated by the presence of numerous putative genomic islands. Strikingly, 45 "giant genes" were found within the genome of NH11[T]. Subsequent analysis of all available planctomycetal genomes revealed that Planctomycetes as such are especially rich in "giant genes". Furthermore, Multilocus Sequence Analysis (MLSA) tree reconstruction support the phylogenetic distance of strain NH11[T] from other cultivated Planctomycetes of the same phylogenetic cluster. Thus, based on our findings, we propose to classify strain NH11[T] as Fuerstia marisgermanicae gen. nov., sp. nov., with the type strain NH11[T], within the phylum Planctomycetes.}, }
@article {pmid28066362, year = {2016}, author = {Zhang, N and Yang, D and Kendall, JR and Borriss, R and Druzhinina, IS and Kubicek, CP and Shen, Q and Zhang, R}, title = {Comparative Genomic Analysis of Bacillus amyloliquefaciens and Bacillus subtilis Reveals Evolutional Traits for Adaptation to Plant-Associated Habitats.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {2039}, pmid = {28066362}, issn = {1664-302X}, abstract = {Bacillus subtilis and its sister species B. amyloliquefaciens comprise an evolutionary compact but physiologically versatile group of bacteria that includes strains isolated from diverse habitats. Many of these strains are used as plant growth-promoting rhizobacteria (PGPR) in agriculture and a plant-specialized subspecies of B. amyloliquefaciens-B. amyloliquefaciens subsp. plantarum, has recently been recognized, here we used 31 whole genomes [including two newly sequenced PGPR strains: B. amyloliquefaciens NJN-6 isolated from Musa sp. (banana) and B. subtilis HJ5 from Gossypium sp. (cotton)] to perform comparative analysis and investigate the genomic characteristics and evolution traits of both species in different niches. Phylogenomic analysis indicated that strains isolated from plant-associated (PA) habitats could be distinguished from those from non-plant-associated (nPA) niches in both species. The core genomes of PA strains are more abundant in genes relevant to intermediary metabolism and secondary metabolites biosynthesis as compared with those of nPA strains, and they also possess additional specific genes involved in utilization of plant-derived substrates and synthesis of antibiotics. A further gene gain/loss analysis indicated that only a few of these specific genes (18/192 for B. amyloliquefaciens and 53/688 for B. subtilis) were acquired by PA strains at the initial divergence event, but most were obtained successively by different subgroups of PA stains during the evolutional process. This study demonstrated the genomic differences between PA and nPA B. amyloliquefaciens and B. subtilis from different niches and the involved evolutional traits, and has implications for screening of PGPR strains in agricultural production.}, }
@article {pmid28066338, year = {2016}, author = {Naranjo-Ortíz, MA and Brock, M and Brunke, S and Hube, B and Marcet-Houben, M and Gabaldón, T}, title = {Widespread Inter- and Intra-Domain Horizontal Gene Transfer of d-Amino Acid Metabolism Enzymes in Eukaryotes.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {2001}, pmid = {28066338}, issn = {1664-302X}, support = {310325/ERC_/European Research Council/International ; }, abstract = {Analysis of the growing number of available fully-sequenced genomes has shown that Horizontal Gene Transfer (HGT) in eukaryotes is more common than previously thought. It has been proposed that genes with certain functions may be more prone to HGT than others, but we still have a very poor understanding of the selective forces driving eukaryotic HGT. Recent work uncovered that d-amino acid racemases have been commonly transferred from bacteria to fungi, but their role in the receiving organisms is currently unknown. Here, we set out to assess whether d-amino acid racemases are commonly transferred to and between eukaryotic groups. For this we performed a global survey that used a novel automated phylogeny-based HGT-detection algorithm (Abaccus). Our results revealed that at least 7.0% of the total eukaryotic racemase repertoire is the result of inter- or intra-domain HGT. These transfers are significantly enriched in plant-associated fungi. For these, we hypothesize a possible role for the acquired racemases allowing to exploit minoritary nitrogen sources in plant biomass, a nitrogen-poor environment. Finally, we performed experiments on a transferred aspartate-glutamate racemase in the fungal human pathogen Candida glabrata, which however revealed no obvious biological role.}, }
@article {pmid28063194, year = {2017}, author = {Colombi, E and Straub, C and Künzel, S and Templeton, MD and McCann, HC and Rainey, PB}, title = {Evolution of copper resistance in the kiwifruit pathogen Pseudomonas syringae pv. actinidiae through acquisition of integrative conjugative elements and plasmids.}, journal = {Environmental microbiology}, volume = {19}, number = {2}, pages = {819-832}, doi = {10.1111/1462-2920.13662}, pmid = {28063194}, issn = {1462-2920}, mesh = {Actinidia/*microbiology ; Biological Evolution ; *Conjugation, Genetic ; Copper/*pharmacology ; *Drug Resistance, Bacterial ; Fruit/microbiology ; Host Specificity ; Plant Diseases/*microbiology ; Plasmids/*genetics/metabolism ; Pseudomonas syringae/*drug effects/*genetics/physiology ; }, abstract = {Horizontal gene transfer can precipitate rapid evolutionary change. In 2010 the global pandemic of kiwifruit canker disease caused by Pseudomonas syringae pv. actinidiae (Psa) reached New Zealand. At the time of introduction, the single clone responsible for the outbreak was sensitive to copper, however, analysis of a sample of isolates taken in 2015 and 2016 showed that a quarter were copper resistant. Genome sequences of seven strains showed that copper resistance - comprising czc/cusABC and copABCD systems - along with resistance to arsenic and cadmium, was acquired via uptake of integrative conjugative elements (ICEs), but also plasmids. Comparative analysis showed ICEs to have a mosaic structure, with one being a tripartite arrangement of two different ICEs and a plasmid that were isolated in 1921 (USA), 1968 (NZ) and 1988 (Japan), from P. syringae pathogens of millet, wheat and kiwifruit respectively. Two of the Psa ICEs were nearly identical to two ICEs isolated from kiwifruit leaf colonists prior to the introduction of Psa into NZ. Additionally, we show ICE transfer in vitro and in planta, analyze fitness consequences of ICE carriage, capture the de novo formation of novel recombinant ICEs, and explore ICE host-range.}, }
@article {pmid28062463, year = {2017}, author = {Chou, WC and Huang, SC and Chiu, CH and Chen, YM}, title = {YMC-2011, a Temperate Phage of Streptococcus salivarius 57.I.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {6}, pages = {}, pmid = {28062463}, issn = {1098-5336}, mesh = {Base Sequence ; DNA, Viral/genetics ; Lysogeny/drug effects/*genetics ; Mitomycin/*pharmacology ; Mouth/microbiology ; Promoter Regions, Genetic/genetics ; Sequence Analysis, DNA ; Streptococcus Phages/classification/*genetics ; Streptococcus salivarius/genetics/isolation &amp; purification/*virology ; Virus Activation/*drug effects ; }, abstract = {Streptococcus salivarius is an abundant isolate of the oral cavity. The genome of S. salivarius 57.I consists of a 2-Mb chromosome and a 40,758-bp circular molecule, designated YMC-2011. Annotation of YMC-2011 revealed 55 open reading frames, most of them associated with phage production, although plaque formation is not observed in S. salivarius 57.I after lytic induction using mitomycin C. Results from Southern hybridization and quantitative real-time PCR confirmed that YMC-2011 exists extrachromosomally, with an estimated copy number of 3 to 4. Phage particles were isolated from the supernatant of mitomycin C-treated S. salivarius 57.I cultures, and transmission electron microscopic examination indicated that YMC-2011 belongs to the Siphoviridae family. Phylogenetic analysis suggests that phage YMC-2011 and the cos-type phages of Streptococcus thermophilus originated from a common ancestor. An extended -10 element (p L) and a σ[70]-like promoter (p R) were mapped 5' to Ssal_phage00013 (encoding a CI-like repressor) and Ssal_phage00014 (encoding a hypothetical protein), respectively, using 5' rapid amplification of cDNA ends, indicating that YMC-2011 transcribes at least two mRNAs in opposite orientations. Studies using promoter-chloramphenicol acetyltransferase reporter gene fusions revealed that p R , but not p L , was sensitive to mitomycin C induction, suggesting that the switch from lysogenic growth to lytic growth was controlled mainly by the activity of these two promoters. In conclusion, a lysogenic state is maintained in S. salivarius 57.I, presumably by the repression of genes encoding proteins for lytic growth.IMPORTANCE The movement of mobile genetic elements such as bacteriophages and the establishment of lysogens may have profound effects on the balance of microbial ecology where lysogenic bacteria reside. The discovery of phage YMC-2011 from Streptococcus salivarius 57.I suggests that YMC-2011 and Streptococcus thermophilus-infecting phages share an ancestor. Although S. salivarius and S. thermophilus are close phylogenetically, S. salivarius is a natural inhabitant of the human mouth, whereas S. thermophilus is commonly found in the mammary mucosa of bovine species. Thus, the identification of YMC-2011 suggests that horizontal gene transfer via phage infection could take place between species from different ecological niches.}, }
@article {pmid28061804, year = {2017}, author = {Vazquez-Gutierrez, P and Stevens, MJ and Gehrig, P and Barkow-Oesterreicher, S and Lacroix, C and Chassard, C}, title = {The extracellular proteome of two Bifidobacterium species reveals different adaptation strategies to low iron conditions.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {41}, pmid = {28061804}, issn = {1471-2164}, mesh = {Adaptation, Physiological/*drug effects ; Bifidobacterium/*cytology/drug effects/*metabolism/physiology ; Dose-Response Relationship, Drug ; Evolution, Molecular ; Extracellular Space/*drug effects/*metabolism ; Iron/*pharmacology ; *Proteomics ; Species Specificity ; }, abstract = {BACKGROUND: Bifidobacteria are among the first anaerobic bacteria colonizing the gut. Bifidobacteria require iron for growth and their iron-sequestration mechanisms are important for their fitness and possibly inhibit enteropathogens. Here we used combined genomic and proteomic analyses to characterize adaptations to low iron conditions of B. kashiwanohense PV20-2 and B. pseudolongum PV8-2, 2 strains isolated from the feces of iron-deficient African infants and selected for their high iron-sequestering ability.<br><br>RESULTS: Analyses of the genome contents revealed evolutionary adaptation to low iron conditions. A ferric and a ferrous iron operon encoding binding proteins and transporters were found in both strains. Remarkably, the ferric iron operon of B. pseudolongum PV8-2 is not found in other B. pseudolongum strains and likely acquired via horizontal gene transfer. The genome B. kashiwanohense PV20-2 harbors a unique region encoding genes putatively involved in siderophore production. Additionally, the secretomes of the two strains grown under low-iron conditions were analyzed using a combined genomic-proteomic approach. A ferric iron transporter was found in the secretome of B. pseudolongum PV8-2, while ferrous binding proteins were detected in the secretome of B. kashiwanohense PV20-2, suggesting different strategies to take up iron in the strains. In addition, proteins such as elongation factors, a glyceraldehyde-3-phosphate dehydrogenase, and the stress proteins GroEL and DnaK were identified in both secretomes. These proteins have been previously associated with adhesion of lactobacilli to epithelial cells.<br><br>CONCLUSION: Analyses of the genome and secretome of B. kashiwanohense PV20-2 and B. pseudolongum PV8-2 revealed different adaptations to low iron conditions and identified extracellular proteins for iron transport. The identified extracellular proteins might be involved in competition for iron in the gastrointestinal tract.}, }
@article {pmid28055898, year = {2017}, author = {Kordi, M and Bansal, MS}, title = {On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {14}, number = {3}, pages = {587-599}, doi = {10.1109/TCBB.2015.2511761}, pmid = {28055898}, issn = {1557-9964}, mesh = {Algorithms ; Chromosome Mapping/*methods ; *Evolution, Molecular ; *Gene Deletion ; Gene Duplication/*genetics ; Gene Transfer, Horizontal/*genetics ; Multigene Family/*genetics ; *Pedigree ; Phylogeny ; }, abstract = {Duplication-Transfer-Loss (DTL) reconciliation has emerged as a powerful technique for studying gene family evolution in the presence of horizontal gene transfer. DTL reconciliation takes as input a gene family phylogeny and the corresponding species phylogeny, and reconciles the two by postulating speciation, gene duplication, horizontal gene transfer, and gene loss events. Efficient algorithms exist for finding optimal DTL reconciliations when the gene tree is binary. However, gene trees are frequently non-binary. With such non-binary gene trees, the reconciliation problem seeks to find a binary resolution of the gene tree that minimizes the reconciliation cost. Given the prevalence of non-binary gene trees, many efficient algorithms have been developed for this problem in the context of the simpler Duplication-Loss (DL) reconciliation model. Yet, no efficient algorithms exist for DTL reconciliation with non-binary gene trees and the complexity of the problem remains unknown. In this work, we resolve this open question by showing that the problem is, in fact, NP-hard. Our reduction applies to both the dated and undated formulations of DTL reconciliation. By resolving this long-standing open problem, this work will spur the development of both exact and heuristic algorithms for this important problem.}, }
@article {pmid28054641, year = {2017}, author = {Tannières, M and Lang, J and Barnier, C and Shykoff, JA and Faure, D}, title = {Quorum-quenching limits quorum-sensing exploitation by signal-negative invaders.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {40126}, pmid = {28054641}, issn = {2045-2322}, mesh = {Agrobacterium tumefaciens/*genetics/*physiology ; DNA Mutational Analysis ; *Gene Transfer, Horizontal ; Mutation ; Plant Tumor-Inducing Plasmids/*metabolism ; *Quorum Sensing ; Whole Genome Sequencing ; }, abstract = {Some bacteria produce and perceive quorum-sensing (QS) signals that coordinate several behaviours, including the costly processes that are exoenzyme production and plasmid transfer. In the case of plasmid transfer, the emergence of QS signal-altered invaders and their policing are poorly documented. In Agrobacterium tumefaciens, the virulence Ti-plasmid encodes both synthesis and sensing of QS-signals, which promote its transfer from a donor to a recipient cell. Here, we reported that QS-altered A. tumefaciens mutants arose during experimental evolution. All showed improved growth compared to their ancestor. Genome sequencing revealed that, though some had lost the Ti-plasmid, most were defective for QS-signal synthesis and Ti-plasmid conjugation (traR mutations) and one exhibited a QS-signal exploitation behaviour, using signal produced by other cells to enhance its own Ti-plasmid transfer. We explored mechanisms that can limit this QS-hijacking. We showed that the A. tumefaciens capacity to inactivate QS-signals by expressing QS-degrading enzyme could attenuate dissemination of the QS signal-negative Ti-plasmids. This work shows that enzymatic QS-disruption whether encoded by the QS-producing Ti-plasmid itself, by a companion plasmid in the same donor cells, or by one in the recipient cells, in all cases can serve as a mechanism for controlling QS exploitation by QS signal-negative mutants.}, }
@article {pmid28049657, year = {2017}, author = {Macaisne, N and Liu, F and Scornet, D and Peters, AF and Lipinska, A and Perrineau, MM and Henry, A and Strittmatter, M and Coelho, SM and Cock, JM}, title = {The Ectocarpus IMMEDIATE UPRIGHT gene encodes a member of a novel family of cysteine-rich proteins with an unusual distribution across the eukaryotes.}, journal = {Development (Cambridge, England)}, volume = {144}, number = {3}, pages = {409-418}, doi = {10.1242/dev.141523}, pmid = {28049657}, issn = {1477-9129}, support = {638240/ERC_/European Research Council/International ; }, mesh = {Algal Proteins/antagonists &amp; inhibitors/chemistry/*genetics ; Amino Acid Sequence ; Cloning, Molecular ; Cysteine/chemistry ; Evolution, Molecular ; Gene Expression Profiling ; Gene Transfer, Horizontal ; Models, Genetic ; Multigene Family ; Mutation ; Phaeophyceae/*genetics/growth &amp; development/virology ; Phylogeny ; RNA Interference ; Sequence Homology, Amino Acid ; Viral Proteins/chemistry/genetics ; }, abstract = {The sporophyte generation of the brown alga Ectocarpus sp. exhibits an unusual pattern of development compared with the majority of brown algae. The first cell division is symmetrical and the apical-basal axis is established late in development. In the immediate upright (imm) mutant, the initial cell undergoes an asymmetric division to immediately establish the apical-basal axis. We provide evidence which suggests that this phenotype corresponds to the ancestral state of the sporophyte. The IMM gene encodes a protein of unknown function that contains a repeated motif also found in the EsV-1-7 gene of the Ectocarpus virus EsV-1. Brown algae possess large families of EsV-1-7 domain genes but these genes are rare in other stramenopiles, suggesting that the expansion of this family might have been linked with the emergence of multicellular complexity. EsV-1-7 domain genes have a patchy distribution across eukaryotic supergroups and occur in several viral genomes, suggesting possible horizontal transfer during eukaryote evolution.}, }
@article {pmid28049420, year = {2017}, author = {Matassi, G}, title = {Horizontal gene transfer drives the evolution of Rh50 permeases in prokaryotes.}, journal = {BMC evolutionary biology}, volume = {17}, number = {1}, pages = {2}, pmid = {28049420}, issn = {1471-2148}, mesh = {Archaea/genetics ; Bacteria/genetics ; Eukaryota/genetics ; *Evolution, Molecular ; Fungi/genetics ; *Gene Transfer, Horizontal ; Membrane Transport Proteins/*genetics ; Phylogeny ; *Prokaryotic Cells/enzymology ; }, abstract = {BACKGROUND: Rh50 proteins belong to the family of ammonia permeases together with their Amt/MEP homologs. Ammonia permeases increase the permeability of NH3/NH4[+] across cell membranes and are believed to be involved in excretion of toxic ammonia and in the maintenance of pH homeostasis. RH50 genes are widespread in eukaryotes but absent in land plants and fungi, and remarkably rare in prokaryotes. The evolutionary history of RH50 genes in prokaryotes is just beginning to be unveiled.<br><br>RESULTS: Here, a molecular phylogenetic approach suggests horizontal gene transfer (HGT) as a primary force driving the evolution and spread of RH50 among prokaryotes. In addition, the taxonomic distribution of the RH50 gene among prokaryotes turned out to be very narrow; a single-copy RH50 is present in the genome of only a small proportion of Bacteria, and, first evidence to date, in only three methanogens among Euryarchaea. The coexistence of RH50 and AMT in prokaryotes seems also a rare event. Finally, phylogenetic analyses were used to reconstruct the HGT network along which prokaryotic RH50 evolution has taken place.<br><br>CONCLUSIONS: The eukaryotic or bacterial "origin" of the RH50 gene remains unsolved. The RH50 prokaryotic HGT network suggests a preferential directionality of transfer from aerobic to anaerobic organisms. The observed HGT events between archaeal methanogens, anaerobic and aerobic ammonia-oxidizing bacteria suggest that syntrophic relationships play a major role in the structuring of the network, and point to oxygen minimum zones as an ecological niche that might be of crucial importance for HGT-driven evolution.}, }
@article {pmid28045495, year = {2017}, author = {Jahed, Z and Shahsavan, H and Verma, MS and Rogowski, JL and Seo, BB and Zhao, B and Tsui, TY and Gu, FX and Mofrad, MR}, title = {Bacterial Networks on Hydrophobic Micropillars.}, journal = {ACS nano}, volume = {11}, number = {1}, pages = {675-683}, doi = {10.1021/acsnano.6b06985}, pmid = {28045495}, issn = {1936-086X}, abstract = {Bacteria have evolved as intelligent microorganisms that can colonize and form highly structured and cooperative multicellular communities with sophisticated singular and collective behaviors. The initial stages of colony formation and intercellular communication are particularly important to understand and depend highly on the spatial organization of cells. Controlling the distribution and growth of bacterial cells at the nanoscale is, therefore, of great interest in understanding the mechanisms of cell-cell communication at the initial stages of colony formation. Staphyloccocus aureus, a ubiquitous human pathogen, is of specific clinical importance due to the rise of antibiotic resistant strains of this species, which can cause life-threatening infections. Although several methods have attempted to pattern bacterial cells onto solid surfaces at single cell resolution, no study has truly controlled the 3D architectures of growing colonies. Herein, we present a simple, low-cost method to pattern S. aureus bacterial colonies and control the architecture of their growth. Using the wetting properties of micropatterened poly(dimethyl siloxane) platforms, with help from the physiological activities of the S. aureus cells, we fabricated connected networks of bacterial microcolonies of various sizes. Unlike conventional heterogeneous growth of biofilms on surfaces, the patterned S. aureus microcolonies in this work grow radially from nanostrings of a few bacterial cells, to form micrometer-thick rods when provided with a nutrient rich environment. This simple, efficient, and low-cost method can be used as a platform for studies of cell-cell communication phenomena, such as quorum sensing, horizontal gene transfer, and metabolic cross-feeding especially during initial stages of colony formation.}, }
@article {pmid28045086, year = {2017}, author = {Uchiya, KI and Tomida, S and Nakagawa, T and Asahi, S and Nikai, T and Ogawa, K}, title = {Comparative genome analyses of Mycobacterium avium reveal genomic features of its subspecies and strains that cause progression of pulmonary disease.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {39750}, pmid = {28045086}, issn = {2045-2322}, mesh = {Animals ; Ecosystem ; Gene Transfer, Horizontal ; Genetic Speciation ; Genetics, Population ; Genome/*genetics ; Humans ; Japan ; Multigene Family ; Mycobacterium avium/*physiology ; Phylogeny ; Polymorphism, Single Nucleotide ; Species Specificity ; Tuberculosis, Pulmonary/genetics/*microbiology ; Whole Genome Sequencing ; }, abstract = {Pulmonary disease caused by nontuberculous mycobacteria (NTM) is increasing worldwide. Mycobacterium avium is the most clinically significant NTM species in humans and animals, and comprises four subspecies: M. avium subsp. avium (MAA), M. avium subsp. silvaticum (MAS), M. avium subsp. paratuberculosis (MAP), and M. avium subsp. hominissuis (MAH). To improve our understanding of the genetic landscape and diversity of M. avium and its role in disease, we performed a comparative genome analysis of 79 M. avium strains. Our analysis demonstrated that MAH is an open pan-genome species. Phylogenetic analysis based on single nucleotide variants showed that MAH had the highest degree of sequence variability among the subspecies, and MAH strains isolated in Japan and those isolated abroad possessed distinct phylogenetic features. Furthermore, MAP strains, MAS and MAA strains isolated from birds, and many MAH strains that cause the progression of pulmonary disease were grouped in each specific cluster. Comparative genome analysis revealed the presence of genetic elements specific to each lineage, which are thought to be acquired via horizontal gene transfer during the evolutionary process, and identified potential genetic determinants accounting for the pathogenic and host range characteristics of M. avium.}, }
@article {pmid28041851, year = {2017}, author = {Tzipilevich, E and Habusha, M and Ben-Yehuda, S}, title = {Acquisition of Phage Sensitivity by Bacteria through Exchange of Phage Receptors.}, journal = {Cell}, volume = {168}, number = {1-2}, pages = {186-199.e12}, doi = {10.1016/j.cell.2016.12.003}, pmid = {28041851}, issn = {1097-4172}, mesh = {Bacillus/virology ; Bacillus Phages/enzymology/*physiology ; Bacillus subtilis/metabolism/*virology ; *Bacteriolysis ; Host Specificity ; Receptors, Virus/*metabolism ; Staphylococcus aureus/virology ; Transduction, Genetic ; }, abstract = {Bacteriophages (phages) typically exhibit a narrow host range, yet they tremendously impact horizontal gene transfer (HGT). Here, we investigate phage dynamics in communities harboring phage-resistant (R) and sensitive (S) bacteria, a common scenario in nature. Using Bacillus subtilis and its lytic phage SPP1, we demonstrate that R cells, lacking SPP1 receptor, can be lysed by SPP1 when co-cultured with S cells. This unanticipated lysis was triggered in part by phage lytic enzymes released from nearby infected cells. Strikingly, we discovered that occasionally phages can invade R cells, a phenomenon we termed acquisition of sensitivity (ASEN). We found that ASEN is mediated by R cells transiently gaining phage attachment molecules from neighboring S cells and provide evidence that this molecular exchange is driven by membrane vesicles. Exchange of phage attachment molecules could even occur in an interspecies fashion, enabling phage adsorption to non-host species, providing an unexplored route for HGT. VIDEO ABSTRACT.}, }
@article {pmid28040181, year = {2017}, author = {Vendramin, V and Treu, L and Campanaro, S and Lombardi, A and Corich, V and Giacomini, A}, title = {Genome comparison and physiological characterization of eight Streptococcus thermophilus strains isolated from Italian dairy products.}, journal = {Food microbiology}, volume = {63}, number = {}, pages = {47-57}, doi = {10.1016/j.fm.2016.11.002}, pmid = {28040181}, issn = {1095-9998}, mesh = {Animals ; Bacteriocins/genetics ; DNA, Bacterial/genetics ; Dairy Products/*microbiology ; Genetic Variation ; *Genome, Bacterial ; Genomics ; Genotype ; Italy ; Milk/*microbiology ; Phenotype ; Phylogeny ; Polymorphism, Single Nucleotide ; Streptococcus thermophilus/classification/*genetics/isolation &amp; purification/*physiology ; }, abstract = {Eight Streptococcus thermophilus strains of dairy origin isolated in Italy were chosen to investigate autochthonous bacterial diversity in this important technological species. In the present study a comparative analysis of all the 17 S. thermophilus genomes publicly available was performed to identify the core and the variable genes, which vary among strains from 196 to 265. Additionally, correlation between the isolation site and the genetic distance was investigated at genomic level. Results highlight that the phylogenetic reconstruction differs from the geographical strain distribution. Moreover, strain M17PTZA496 has a genome of 2.15 Mbp, notably larger than that of the others, determined by lateral gene transfer (including phage-mediated incorporation) and duplication events. Important technological characters, such as growth kinetics, bacteriocin production, acidification kinetics and surface adhesion capability were studied in all the Italian strains. Results indicate a wide range of variability in adhesion properties that significantly clustered strains into four groups. Genomic differences among strains in relation to these characters were identified but a clear correlation between genotype and phenotype was not always found since most of the genomic modifications arise from single nucleotide polymorphisms. This research represents a step forward in the identification of strains-specific functions in Streptococcus thermophilus and it has also the potential to provide valuable information to predict strain specific behaviors in industrial processes.}, }
@article {pmid28036367, year = {2016}, author = {Scholz, HC and Mühldorfer, K and Shilton, C and Benedict, S and Whatmore, AM and Blom, J and Eisenberg, T}, title = {The Change of a Medically Important Genus: Worldwide Occurrence of Genetically Diverse Novel Brucella Species in Exotic Frogs.}, journal = {PloS one}, volume = {11}, number = {12}, pages = {e0168872}, pmid = {28036367}, issn = {1932-6203}, mesh = {Animals ; Anura/*microbiology ; Australia ; Brucella/*genetics ; Brucellosis/microbiology ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal/genetics ; Genetic Variation/genetics ; Humans ; Ochrobactrum/genetics ; Phylogeny ; Rodentia/microbiology ; Sequence Analysis, DNA/methods ; }, abstract = {The genus Brucella comprises various species of both veterinary and human medical importance. All species are genetically highly related to each other, sharing intra-species average nucleotide identities (ANI) of > 99%. Infections occur among various warm-blooded animal species, marine mammals, and humans. Until recently, amphibians had not been recognized as a host for Brucella. In this study, however, we show that novel Brucella species are distributed among exotic frogs worldwide. Comparative recA gene analysis of 36 frog isolates from various continents and different frog species revealed an unexpected high genetic diversity, not observed among classical Brucella species. In phylogenetic reconstructions the isolates consequently formed various clusters and grouped together with atypical more distantly related brucellae, like B. inopinata, strain BO2, and Australian isolates from rodents, some of which were isolated as human pathogens. Of one frog isolate (10RB9215) the genome sequence was determined. Comparative genome analysis of this isolate and the classical Brucella species revealed additional genetic material, absent from classical Brucella species but present in Ochrobactrum, the closest genetic neighbor of Brucella, and in other soil associated genera of the Alphaproteobacteria. The presence of gene clusters encoding for additional metabolic functions, flanked by tRNAs and mobile genetic elements, as well as by bacteriophages is suggestive for a different ecology compared to classical Brucella species. Furthermore it suggests that amphibian isolates may represent a link between free living soil saprophytes and the pathogenic Brucella with a preferred intracellular habitat. We therefore assume that brucellae from frogs have a reservoir in soil and, in contrast to classical brucellae, undergo extensive horizontal gene transfer.}, }
@article {pmid28034347, year = {2018}, author = {Ellenberger, S and Burmester, A and Wöstemeyer, J}, title = {The fate of mitochondria after infection of the Mucoralean fungus Absidia glauca by the fusion parasite Parasitella parasitica: comparison of mitochondrial genomes in zygomycetes.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {1}, pages = {113-120}, doi = {10.1080/24701394.2016.1248432}, pmid = {28034347}, issn = {2470-1408}, mesh = {Absidia/*genetics ; Base Sequence ; Gene Transfer, Horizontal ; Genome, Fungal ; *Genome, Mitochondrial ; *Introns ; Mitochondria/*genetics ; Mucorales/genetics ; Mucormycosis ; Sequence Alignment ; }, abstract = {Absidia glauca and Parasitella parasitica constitute a versatile experimental system for studying horizontal gene transfer between a mucoralean host and its fusion parasite. The A. glauca chondriome has a length of approximately 63 kb and a GC content of 28%. The chondriome of P. parasitica is larger, 83 kb, and contains 31% GC base pairs. These mtDNAs contain the standard fungal mitochondrial gene set, small and large subunit rRNAs, plus ribonuclease P RNA. Comparing zygomycete chondriomes reveals an unusually high number of homing endonuclease genes in P. parasitica, substantiating the mobility of intron elements independent of host-parasite interactions.}, }
@article {pmid28033323, year = {2016}, author = {Even-Tov, E and Omer Bendori, S and Pollak, S and Eldar, A}, title = {Transient Duplication-Dependent Divergence and Horizontal Transfer Underlie the Evolutionary Dynamics of Bacterial Cell-Cell Signaling.}, journal = {PLoS biology}, volume = {14}, number = {12}, pages = {e2000330}, pmid = {28033323}, issn = {1545-7885}, mesh = {Bacillus/*genetics/metabolism ; *Biological Evolution ; Databases, Genetic ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Phylogeny ; *Signal Transduction ; }, abstract = {Evolutionary expansion of signaling pathway families often underlies the evolution of regulatory complexity. Expansion requires the acquisition of a novel homologous pathway and the diversification of pathway specificity. Acquisition can occur either vertically, by duplication, or through horizontal transfer, while divergence of specificity is thought to occur through a promiscuous protein intermediate. The way by which these mechanisms shape the evolution of rapidly diverging signaling families is unclear. Here, we examine this question using the highly diversified Rap-Phr cell-cell signaling system, which has undergone massive expansion in the genus Bacillus. To this end, genomic sequence analysis of >300 Bacilli genomes was combined with experimental analysis of the interaction of Rap receptors with Phr autoinducers and downstream targets. Rap-Phr expansion is shown to have occurred independently in multiple Bacillus lineages, with >80 different putative rap-phr alleles evolving in the Bacillius subtilis group alone. The specificity of many rap-phr alleles and the rapid gain and loss of Rap targets are experimentally demonstrated. Strikingly, both horizontal and vertical processes were shown to participate in this expansion, each with a distinct role. Horizontal gene transfer governs the acquisition of already diverged rap-phr alleles, while intralocus duplication and divergence of the phr gene create the promiscuous intermediate required for the divergence of Rap-Phr specificity. Our results suggest a novel role for transient gene duplication and divergence during evolutionary shifts in specificity.}, }
@article {pmid28029340, year = {2016}, author = {Pasumarthi, R and Mutnuri, S}, title = {Horizontal gene transfer versus biostimulation: A strategy for bioremediation in Goa.}, journal = {Marine pollution bulletin}, volume = {113}, number = {1-2}, pages = {271-276}, doi = {10.1016/j.marpolbul.2016.09.044}, pmid = {28029340}, issn = {1879-3363}, mesh = {*Biodegradation, Environmental ; Gasoline ; *Gene Transfer, Horizontal ; Hydrocarbons ; India ; *Petroleum Pollution ; Pseudomonas aeruginosa ; Water Pollutants, Chemical ; }, abstract = {Bioaugmentation, Biostimulation and Horizontal gene transfer (HGT) of catabolic genes have been proven for their role in bioremediation of hydrocarbons. It also has been proved that selection of either biostimulation or bioremediation varies for every contaminated site. The reliability of HGT compared to biostimulation and bioremediation was not tested. The present study focuses on reliability of biostimulatiion, bioaugmentation and HGT during biodegradation of Diesel oil and Non aqueous phase liquids (NAPL). Pseudomonas aeruginosa (AEBBITS1) having alkB and NDO genes was used for bioaugmentation and the experiment was conducted using seawater as medium. Based on Gas chromatography results diesel was found to be degraded to 100% in both presence and absence of AEBBITS1. Denturing gradient gel electrophoresis result showed same pattern in presence and absence of AEBBITS1 indicating no HGT. NAPL degradation was found to be more by Biostimulated Bioaugmentation compared to biostimulation and bioaugmentation alone. This proves that biostimulated bioaugmentation is better strategy for oil contamination (tarabll) in Velsao beach, Goa.}, }
@article {pmid28028472, year = {2016}, author = {Wang, Y and Chandler, C}, title = {Candidate pathogenicity islands in the genome of 'Candidatus Rickettsiella isopodorum', an intracellular bacterium infecting terrestrial isopod crustaceans.}, journal = {PeerJ}, volume = {4}, number = {}, pages = {e2806}, pmid = {28028472}, issn = {2167-8359}, abstract = {The bacterial genus Rickettsiellabelongs to the order Legionellales in the Gammaproteobacteria, and consists of several described species and pathotypes, most of which are considered to be intracellular pathogens infecting arthropods. Two members of this genus, R. grylliand R. isopodorum, are known to infect terrestrial isopod crustaceans. In this study, we assembled a draft genomic sequence for R. isopodorum, and performed a comparative genomic analysis with R. grylli. We found evidence for several candidate genomic island regions in R. isopodorum, none of which appear in the previously available R. grylli genome sequence.Furthermore, one of these genomic island candidates in R. isopodorum contained a gene that encodes a cytotoxin partially homologous to those found in Photorhabdus luminescensand Xenorhabdus nematophilus (Enterobacteriaceae), suggesting that horizontal gene transfer may have played a role in the evolution of pathogenicity in Rickettsiella. These results lay the groundwork for future studies on the mechanisms underlying pathogenesis in R. isopodorum, and this system may provide a good model for studying the evolution of host-microbe interactions in nature.}, }
@article {pmid28027803, year = {2017}, author = {Joshi, A and Kostiuk, B and Rogers, A and Teschler, J and Pukatzki, S and Yildiz, FH}, title = {Rules of Engagement: The Type VI Secretion System in Vibrio cholerae.}, journal = {Trends in microbiology}, volume = {25}, number = {4}, pages = {267-279}, pmid = {28027803}, issn = {1878-4380}, support = {R01 AI102584/AI/NIAID NIH HHS/United States ; R01 AI114261/AI/NIAID NIH HHS/United States ; R56 AI102584/AI/NIAID NIH HHS/United States ; //CIHR/Canada ; }, mesh = {Antibiosis/genetics/*physiology ; Bacterial Toxins/biosynthesis/*metabolism ; Cholera/microbiology ; Gene Transfer, Horizontal/genetics ; Humans ; Quorum Sensing/*physiology ; Type VI Secretion Systems/genetics/*metabolism ; Vibrio cholerae/genetics/growth &amp; development/*pathogenicity ; }, abstract = {Microbial species often exist in complex communities where they must avoid predation and compete for favorable niches. The type VI secretion system (T6SS) is a contact-dependent bacterial weapon that allows for direct killing of competitors through the translocation of proteinaceous toxins. Vibrio cholerae is a Gram-negative pathogen that can use its T6SS during antagonistic interactions with neighboring prokaryotic and eukaryotic competitors. The T6SS not only promotes V. cholerae's survival during its aquatic and host life cycles, but also influences its evolution by facilitating horizontal gene transfer. This review details the recent insights regarding the structure and function of the T6SS as well as the diverse signals and regulatory pathways that control its activation in V. cholerae.}, }
@article {pmid28025496, year = {2016}, author = {Lukasik, A and Zielenkiewicz, P}, title = {Plant MicroRNAs-Novel Players in Natural Medicine?.}, journal = {International journal of molecular sciences}, volume = {18}, number = {1}, pages = {}, pmid = {28025496}, issn = {1422-0067}, mesh = {Animals ; Gene Transfer Techniques ; *Gene Transfer, Horizontal ; Genetic Therapy/*methods ; Humans ; MicroRNAs/*genetics/metabolism ; RNA, Plant/*genetics/metabolism ; }, abstract = {MicroRNAs (miRNAs) represent a class of small non-coding RNAs that act as efficient gene expression regulators and thus play many important roles in living organisms. Due to their involvement in several known human pathological and pathogenic states, miRNA molecules have become an important issue in medicine and gained the attention of scientists from the pharmaceutical industry. In recent few years, a growing number of studies have provided evidence that miRNAs may be transferred from one species to another and regulate gene expression in the recipients' cells. The most intriguing results revealed that stable miRNAs derived from food plants may enter the mammals' circulatory system and, after reaching the target, inhibit the production of specific mammalian protein. Part of the scientific community has perceived this as an attractive hypothesis that may provide a foundation for novel therapeutic approaches. In turn, others are convinced about the "false positive" effect of performed experiments from which the mentioned results were achieved. In this article, we review the recent literature that provides evidence (from both fronts) of dietary, plant miRNA uptake and functionality in various consumers. Additionally, we discuss possible miRNA transport mechanisms from plant food sources to human cells.}, }
@article {pmid28024527, year = {2017}, author = {Dutta, A and Katarkar, A and Chaudhuri, K}, title = {In-silico prediction of dual function of DksA like hypothetical protein in V. cholerae O395 genome.}, journal = {Microbiological research}, volume = {195}, number = {}, pages = {60-70}, doi = {10.1016/j.micres.2016.11.010}, pmid = {28024527}, issn = {1618-0623}, mesh = {Bacterial Proteins/*genetics/*metabolism ; Binding Sites ; Computer Simulation ; DNA, Bacterial/metabolism ; DNA-Binding Proteins/*genetics/*metabolism ; DNA-Directed RNA Polymerases/metabolism ; Gene Expression Profiling ; *Gene Expression Regulation, Bacterial ; Models, Molecular ; Protein Binding ; Protein Conformation ; Real-Time Polymerase Chain Reaction ; Vibrio cholerae/*genetics/*physiology ; }, abstract = {Cholera, an acute infection of the small intestine, is caused by Vibrio cholerae. The present study identified a hypothetical protein in V. cholerae O395, which was predicted to be acquired through horizontal gene transfer the origin of which was found to be from a phage. Its expression was further confirmed by RT-PCR. Homology based 3D model of the hypothetical protein indicated DksA like homologue. Protein binding site of 3D-model revealed a deep cleft which may influence the dimer formation and interaction with ds-DNA molecule. Also, canonical function of direct interaction with RNA polymerase (RNAP) holoenzyme in complex with ppGpp suggests its dual role in the pathogenesis of cholera.}, }
@article {pmid28018913, year = {2016}, author = {Yu, D and Yin, Z and Jin, Y and Zhou, J and Ren, H and Hu, M and Li, B and Zhou, W and Liang, L and Yue, J}, title = {Evolution of bopA Gene in Burkholderia: A Case of Convergent Evolution as a Mechanism for Bacterial Autophagy Evasion.}, journal = {BioMed research international}, volume = {2016}, number = {}, pages = {6745028}, pmid = {28018913}, issn = {2314-6141}, mesh = {Autophagy/*genetics/immunology ; Bacterial Proteins/*genetics/immunology ; Base Composition/genetics ; Burkholderia pseudomallei/*genetics/immunology/pathogenicity ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Host-Pathogen Interactions/immunology ; Humans ; Immune Evasion/*genetics ; Phylogeny ; }, abstract = {Autophagy is an important defense mechanism targeting intracellular bacteria to restrict their survival and growth. On the other hand, several intracellular pathogens have developed an antiautophagy mechanism to facilitate their own replication or intracellular survival. Up to now, no information about the origin or evolution of the antiautophagic genes in bacteria is available. BopA is an effector protein secreted by Burkholderia pseudomallei via the type three secretion system, and it has been shown to play a pivotal role in their escape from autophagy. The evolutionary origin of bopA was examined in this work. Sequence similarity searches for BopA showed that no homolog of BopA was detected in eukaryotes. However, eukaryotic linear motifs were detected in BopA. The phylogenetic tree of the BopA proteins in our analysis is congruent with the species phylogeny derived from housekeeping genes. Moreover, there was no obvious difference in GC content values of bopA gene and their respective genomes. Integrated information on the taxonomic distribution, phylogenetic relationships, and GC content of the bopA gene of Burkholderia revealed that this gene was acquired via convergent evolution, not from eukaryotic host through horizontal gene transfer (HGT) event. This work has, for the first time, characterized the evolutionary mechanism of bacterial evasion of autophagy. The results of this study clearly demonstrated the role of convergent evolution in the evolution of how bacteria evade autophagy.}, }
@article {pmid28018315, year = {2016}, author = {Imperial, IC and Ibana, JA}, title = {Addressing the Antibiotic Resistance Problem with Probiotics: Reducing the Risk of Its Double-Edged Sword Effect.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1983}, pmid = {28018315}, issn = {1664-302X}, abstract = {Antibiotic resistance is a global public health problem that requires our attention. Indiscriminate antibiotic use is a major contributor in the introduction of selective pressures in our natural environments that have significantly contributed in the rapid emergence of antibiotic-resistant microbial strains. The use of probiotics in lieu of antibiotic therapy to address certain health conditions in both animals and humans may alleviate these antibiotic-mediated selective pressures. Probiotic use is defined as the actual application of live beneficial microbes to obtain a desired outcome by preventing diseased state or improving general health. Multiple studies have confirmed the beneficial effects of probiotic use in the health of both livestock and humans. As such, probiotics consumption is gaining popularity worldwide. However, concerns have been raised in the use of some probiotics strains that carry antibiotic resistance genes themselves, as they have the potential to pass the antibiotic resistance genes to pathogenic bacteria through horizontal gene transfer. Therefore, with the current public health concern on antibiotic resistance globally, in this review, we underscore the need to screen probiotic strains that are used in both livestock and human applications to assure their safety and mitigate their potential in significantly contributing to the spread of antibiotic resistance genes in our natural environments.}, }
@article {pmid28018051, year = {2016}, author = {Msimbira, LA and Jaiswal, SK and Dakora, FD}, title = {Identification and characterization of phages parasitic on bradyrhizobia nodulating groundnut (Arachis hypogaea L.) in South Africa.}, journal = {Applied soil ecology : a section of Agriculture, Ecosystems &amp; Environment}, volume = {108}, number = {}, pages = {334-340}, pmid = {28018051}, issn = {0929-1393}, abstract = {In this study, three lytic phages (namely, PRSA-1, PRSA-2 and PRSA-26) were isolated and characterized for their morphology, host range, profile and restriction endonuclease banding pattern of genome size. The susceptible rhizobial isolates were identified by nifH and glnII sequence analysis. The results showed that all phages had polyhedral head with non-contractile tail which confirmed their relationship with the Siphoviridae family. All the three phages produced highly distinct plaques on their host bradyrhizobial lawn, and were highly sensitive to chloroform. The phage genome sizes ranged from 34.7 to 53.1 kbp. The phages were tested against groundnut-nodulating bradyrhizobial strains TUTAHSA75, TUTAHSA155 and TUTAHSA126 isolated from South African soils. The results revealed different bacterial susceptibilities to phages. Bradyrhizobial isolate TUTAHSA126 was susceptible to all three phages (i.e. PRSA-1, PRSA-2 and PRSA-26), TUTAHSA155 to two phages (i.e. PRSA-1, PRSA-2), and TUTAHSA75 to only one phage (i.e. PRSA-1). Phylogenetic analysis of nifH and glnII gene sequences of the phage-susceptible bradyrhizobial isolates revealed their close relatedness to a diverse group of Bradyrhizobium species. Phage PRSA-1 could parasitize on all three bradyrhizobial strains, which indicates its potential role in horizontal gene transfer through lysogenic conversion, and/or genetic transduction in soil microbial environments.}, }
@article {pmid28017588, year = {2017}, author = {Heler, R and Wright, AV and Vucelja, M and Bikard, D and Doudna, JA and Marraffini, LA}, title = {Mutations in Cas9 Enhance the Rate of Acquisition of Viral Spacer Sequences during the CRISPR-Cas Immune Response.}, journal = {Molecular cell}, volume = {65}, number = {1}, pages = {168-175}, pmid = {28017588}, issn = {1097-4164}, support = {DP2 AI104556/AI/NIAID NIH HHS/United States ; }, mesh = {*Adaptive Immunity ; Bacterial Proteins/*genetics/immunology/metabolism ; CRISPR-Associated Protein 9 ; CRISPR-Associated Proteins/*genetics/immunology/metabolism ; CRISPR-Cas Systems/*immunology ; Clustered Regularly Interspaced Short Palindromic Repeats/*immunology ; DNA, Intergenic/*genetics/immunology/metabolism ; DNA, Viral/*genetics/immunology/metabolism ; Endonucleases/*genetics/immunology/metabolism ; Genotype ; High-Throughput Nucleotide Sequencing ; Host-Pathogen Interactions ; *Mutation ; Phenotype ; Staphylococcus aureus/enzymology/genetics/immunology/virology ; Substrate Specificity ; Time Factors ; }, abstract = {CRISPR loci and their associated (Cas) proteins encode a prokaryotic immune system that protects against viruses and plasmids. Upon infection, a low fraction of cells acquire short DNA sequences from the invader. These sequences (spacers) are integrated in between the repeats of the CRISPR locus and immunize the host against the matching invader. Spacers specify the targets of the CRISPR immune response through transcription into short RNA guides that direct Cas nucleases to the invading DNA molecules. Here we performed random mutagenesis of the RNA-guided Cas9 nuclease to look for variants that provide enhanced immunity against viral infection. We identified a mutation, I473F, that increases the rate of spacer acquisition by more than two orders of magnitude. Our results highlight the role of Cas9 during CRISPR immunization and provide a useful tool to study this rare process and develop it as a biotechnological application.}, }
@article {pmid28012687, year = {2017}, author = {Manaia, CM}, title = {Assessing the Risk of Antibiotic Resistance Transmission from the Environment to Humans: Non-Direct Proportionality between Abundance and Risk.}, journal = {Trends in microbiology}, volume = {25}, number = {3}, pages = {173-181}, doi = {10.1016/j.tim.2016.11.014}, pmid = {28012687}, issn = {1878-4380}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/*drug effects/*genetics ; Bacterial Infections/drug therapy/microbiology/transmission ; Drug Resistance, Bacterial/*genetics ; Environment ; Gastrointestinal Microbiome/drug effects/*genetics ; Gene Transfer, Horizontal/*genetics ; Humans ; Models, Theoretical ; }, abstract = {The past decade has witnessed a burst of study regarding antibiotic resistance in the environment, mainly in areas under anthropogenic influence. Therefore, impacts of the contaminant resistome, that is, those related to human activities, are now recognized. However, a key issue refers to the risk of transmission of resistance to humans, for which a quantitative model is urgently needed. This opinion paper makes an overview of some risk-determinant variables and raises questions regarding research needs. A major conclusion is that the risks of transmission of antibiotic resistance from the environment to humans must be managed under the precautionary principle, because it may be too late to act if we wait until we have concrete risk values.}, }
@article {pmid28010735, year = {2016}, author = {Druzhinina, IS and Kubicek, EM and Kubicek, CP}, title = {Several steps of lateral gene transfer followed by events of 'birth-and-death' evolution shaped a fungal sorbicillinoid biosynthetic gene cluster.}, journal = {BMC evolutionary biology}, volume = {16}, number = {1}, pages = {269}, pmid = {28010735}, issn = {1471-2148}, mesh = {Ascomycota/classification/*genetics/metabolism ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Fungal ; Penicillium/classification/*genetics/metabolism ; Phylogeny ; Polyketide Synthases/genetics ; Polyketides/*metabolism ; }, abstract = {BACKGROUND: Sorbicillinoids are a family of complex cyclic polyketides produced by only a small number of distantly related ascomycete fungi such as Trichoderma (Sordariomycetes) and Penicillium (Eurotiomycetes). In T. reesei, they are synthesized by a gene cluster consisting of eight genes including two polyketide synthases (PKS). To reconstruct the evolutionary origin of this gene cluster, we examined the occurrence of these eight genes in ascomycetes.<br><br>RESULTS: A cluster comprising at least six of them was only found in Hypocreales (Acremonium chrysogenum, Ustilaginoidea virens, Trichoderma species from section Longibrachiatum) and in Penicillium rubens (Eurotiales). In addition, Colletotrichum graminicola contained the two pks (sor1 and sor2), but not the other sor genes. A. chrysogenum was the evolutionary eldest species in which sor1, sor2, sor3, sor4 and sor6 were present. Sor5 was gained by lateral gene transfer (LGT) from P. rubens. In the younger Hypocreales (U. virens, Trichoderma spp.), the cluster evolved by vertical transfer, but sor2 was lost and regained by LGT from C. graminicola. SorB (=sor2) and sorD (=sor4) were symplesiomorphic in P. rubens, whereas sorA, sorC and sorF were obtained by LGT from A. chrysogenum, and sorE by LGT from Pestalotiopsis fici (Xylariales). The sorbicillinoid gene cluster in Trichoderma section Longibrachiatum is under strong purifying selection. The T. reesei sor genes are expressed during fast vegetative growth, during antagonism of other fungi and regulated by the secondary metabolism regulator LAE1.<br><br>CONCLUSIONS: Our findings pinpoint the evolution of the fungal sorbicillinoid biosynthesis gene cluster. The core cluster arose in early Hypocreales, and was complemented by LGT. During further speciation in the Hypocreales, it became subject to birth and death evolution in selected lineages. In P. rubrens (Eurotiales), two cluster genes were symplesiomorphic, and the whole cluster formed by LGT from at least two different fungal donors.}, }
@article {pmid28009086, year = {2017}, author = {Vences-Guzmán, M&#xc1; and Paula Goetting-Minesky, M and Guan, Z and Castillo-Ramirez, S and Córdoba-Castro, LA and López-Lara, IM and Geiger, O and Sohlenkamp, C and Christopher Fenno, J}, title = {1,2-Diacylglycerol choline phosphotransferase catalyzes the final step in the unique Treponema denticola phosphatidylcholine biosynthesis pathway.}, journal = {Molecular microbiology}, volume = {103}, number = {5}, pages = {896-912}, pmid = {28009086}, issn = {1365-2958}, support = {R21 AI079325/AI/NIAID NIH HHS/United States ; R21 AI105362/AI/NIAID NIH HHS/United States ; U24 DK097153/DK/NIDDK NIH HHS/United States ; U54 GM069338/GM/NIGMS NIH HHS/United States ; }, mesh = {Alleles ; *Biosynthetic Pathways/genetics/physiology ; Catalysis ; Diacylglycerol Cholinephosphotransferase/*metabolism ; Kinetics ; Manganese/metabolism ; Mutagenesis ; Phosphatidylcholines/*biosynthesis ; Sequence Alignment ; Treponema denticola/genetics/*metabolism ; }, abstract = {Treponema denticola synthesizes phosphatidylcholine through a licCA-dependent CDP-choline pathway identified only in the genus Treponema. However, the mechanism of conversion of CDP-choline to phosphatidylcholine remained unclear. We report here characterization of TDE0021 (herein designated cpt) encoding a 1,2-diacylglycerol choline phosphotransferase homologous to choline phosphotransferases that catalyze the final step of the highly conserved Kennedy pathway for phosphatidylcholine synthesis in eukaryotes. T. denticola Cpt catalyzed in vitro phosphatidylcholine formation from CDP-choline and diacylglycerol, and full activity required divalent manganese. Allelic replacement mutagenesis of cpt in T. denticola resulted in abrogation of phosphatidylcholine synthesis. T. denticola Cpt complemented a Saccharomyces cerevisiae CPT1 mutant, and expression of the entire T. denticola LicCA-Cpt pathway in E. coli resulted in phosphatidylcholine biosynthesis. Our findings show that T. denticola possesses a unique phosphatidylcholine synthesis pathway combining conserved prokaryotic choline kinase and CTP:phosphocholine cytidylyltransferase activities with a 1,2-diacylglycerol choline phosphotransferase that is common in eukaryotes. Other than in a subset of mammalian host-associated Treponema that includes T. pallidum, this pathway is found in neither bacteria nor Archaea. Molecular dating analysis of the Cpt gene family suggests that a horizontal gene transfer event introduced this gene into an ancestral Treponema well after its divergence from other spirochetes.}, }
@article {pmid28008844, year = {2016}, author = {Gilbert, C and Peccoud, J}, title = {[Insect mobile elements jump frequently into viral genomes].}, journal = {Medecine sciences : M/S}, volume = {32}, number = {11}, pages = {1017-1019}, doi = {10.1051/medsci/20163211019}, pmid = {28008844}, issn = {1958-5381}, mesh = {Animals ; DNA Transposable Elements/*genetics ; DNA, Viral/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Viral/*genetics ; Host-Pathogen Interactions/genetics ; Humans ; Insecta/*genetics/*virology ; Mutagenesis, Insertional ; }, }
@article {pmid28003446, year = {2016}, author = {Sasakura, Y and Ogura, Y and Treen, N and Yokomori, R and Park, SJ and Nakai, K and Saiga, H and Sakuma, T and Yamamoto, T and Fujiwara, S and Yoshida, K}, title = {Transcriptional regulation of a horizontally transferred gene from bacterium to chordate.}, journal = {Proceedings. Biological sciences}, volume = {283}, number = {1845}, pages = {}, pmid = {28003446}, issn = {1471-2954}, mesh = {Actinobacteria/*genetics ; Animals ; Binding Sites ; Biological Evolution ; *Gene Expression Regulation ; *Gene Transfer, Horizontal ; Glucosyltransferases/genetics ; Phylogeny ; Transcription Factor AP-2/genetics ; Urochordata/*genetics ; }, abstract = {The horizontal transfer of genes between distantly related organisms is undoubtedly a major factor in the evolution of novel traits. Because genes are functionless without expression, horizontally transferred genes must acquire appropriate transcriptional regulations in their recipient organisms, although the evolutionary mechanism is not known well. The defining characteristic of tunicates is the presence of a cellulose containing tunic covering the adult and larval body surface. Cellulose synthase was acquired by horizontal gene transfer from Actinobacteria. We found that acquisition of the binding site of AP-2 transcription factor was essential for tunicate cellulose synthase to gain epidermal-specific expression. Actinobacteria have very GC-rich genomes, regions of which are capable of inducing specific expression in the tunicate epidermis as the AP-2 binds to a GC-rich region. Therefore, the actinobacterial cellulose synthase could have been potentiated to evolve its new function in the ancestor of tunicates with a higher probability than the evolution depending solely on a spontaneous event.}, }
@article {pmid28000570, year = {2017}, author = {Kesari, P and Neetu,  and Sharma, A and Katiki, M and Kumar, P and Gurjar, BR and Tomar, S and Sharma, AK and Kumar, P}, title = {Structural, Functional and Evolutionary Aspects of Seed Globulins.}, journal = {Protein and peptide letters}, volume = {24}, number = {3}, pages = {267-277}, doi = {10.2174/0929866523666161220112641}, pmid = {28000570}, issn = {1875-5305}, mesh = {Biological Evolution ; Gene Duplication ; Gene Expression ; Gene Transfer, Horizontal ; Globulins/genetics/metabolism ; Glycoproteins/*chemistry/genetics/metabolism ; Humans ; Immunoglobulin E/genetics/metabolism ; Plant Proteins/*chemistry/genetics/metabolism ; Plants/*chemistry/genetics/metabolism ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Seed Storage Proteins/*chemistry/genetics/metabolism ; Seeds/*chemistry/genetics/metabolism ; Sequence Homology, Amino Acid ; Legumins ; }, abstract = {Globulins are a major class of seed storage proteins which were thought to be enzymatically inactive. These proteins belong to the most ancient cupin superfamily. They can be graded into 11S legumin type and 7S vicilin type based on their sedimentation coefficients. Members from both classes share structural homology are thought to have evolved from either one-domain germin predecessor by duplication or by horizontal gene transfer of two-domain gene from bacteria to eukaryotes. Globulins are known to define the nutritional quality of the seeds, however, they are also involved in sucrose binding, desiccation, defense against microbes, hormone binding and oxidative stress etc. Major drawback with globulins is their tendency to bind to IgE. Studying structural-functional behavior of such protein can help in modifying proteins for enhanced functionality in food processing industries.}, }
@article {pmid27999667, year = {2016}, author = {Cameron, A and McAllister, TA}, title = {Antimicrobial usage and resistance in beef production.}, journal = {Journal of animal science and biotechnology}, volume = {7}, number = {}, pages = {68}, pmid = {27999667}, issn = {1674-9782}, abstract = {Antimicrobials are critical to contemporary high-intensity beef production. Many different antimicrobials are approved for beef cattle, and are used judiciously for animal welfare, and controversially, to promote growth and feed efficiency. Antimicrobial administration provides a powerful selective pressure that acts on the microbial community, selecting for resistance gene determinants and antimicrobial-resistant bacteria resident in the bovine flora. The bovine microbiota includes many harmless bacteria, but also opportunistic pathogens that may acquire and propagate resistance genes within the microbial community via horizontal gene transfer. Antimicrobial-resistant bovine pathogens can also complicate the prevention and treatment of infectious diseases in beef feedlots, threatening the efficiency of the beef production system. Likewise, the transmission of antimicrobial resistance genes to bovine-associated human pathogens is a potential public health concern. This review outlines current antimicrobial use practices pertaining to beef production, and explores the frequency of antimicrobial resistance in major bovine pathogens. The effect of antimicrobials on the composition of the bovine microbiota is examined, as are the effects on the beef production resistome. Antimicrobial resistance is further explored within the context of the wider beef production continuum, with emphasis on antimicrobial resistance genes in the food chain, and risk to the human population.}, }
@article {pmid27999570, year = {2016}, author = {Zhang, X and Liu, X and He, Q and Dong, W and Zhang, X and Fan, F and Peng, D and Huang, W and Yin, H}, title = {Gene Turnover Contributes to the Evolutionary Adaptation of Acidithiobacillus caldus: Insights from Comparative Genomics.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1960}, pmid = {27999570}, issn = {1664-302X}, abstract = {Acidithiobacillus caldus is an extremely acidophilic sulfur-oxidizer with specialized characteristics, such as tolerance to low pH and heavy metal resistance. To gain novel insights into its genetic complexity, we chosen six A. caldus strains for comparative survey. All strains analyzed in this study differ in geographic origins as well as in ecological preferences. Based on phylogenomic analysis, we clustered the six A. caldus strains isolated from various ecological niches into two groups: group 1 strains with smaller genomes and group 2 strains with larger genomes. We found no obvious intraspecific divergence with respect to predicted genes that are related to central metabolism and stress management strategies between these two groups. Although numerous highly homogeneous genes were observed, high genetic diversity was also detected. Preliminary inspection provided a first glimpse of the potential correlation between intraspecific diversity at the genome level and environmental variation, especially geochemical conditions. Evolutionary genetic analyses further showed evidence that the difference in environmental conditions might be a crucial factor to drive the divergent evolution of A. caldus species. We identified a diverse pool of mobile genetic elements including insertion sequences and genomic islands, which suggests a high frequency of genetic exchange in these harsh habitats. Comprehensive analysis revealed that gene gains and losses were both dominant evolutionary forces that directed the genomic diversification of A. caldus species. For instance, horizontal gene transfer and gene duplication events in group 2 strains might contribute to an increase in microbial DNA content and novel functions. Moreover, genomes undergo extensive changes in group 1 strains such as removal of potential non-functional DNA, which results in the formation of compact and streamlined genomes. Taken together, the findings presented herein show highly frequent gene turnover of A. caldus species that inhabit extremely acidic environments, and shed new light on the contribution of gene turnover to the evolutionary adaptation of acidophiles.}, }
@article {pmid27995274, year = {2017}, author = {Spitzer, J}, title = {Emergence of Life on Earth: A Physicochemical Jigsaw Puzzle.}, journal = {Journal of molecular evolution}, volume = {84}, number = {1}, pages = {1-7}, pmid = {27995274}, issn = {1432-1432}, mesh = {Biological Evolution ; Evolution, Chemical ; *Origin of Life ; Seawater ; Thermodynamics ; }, abstract = {We review physicochemical factors and processes that describe how cellular life can emerge from prebiotic chemical matter; they are: (1) prebiotic Earth is a multicomponent and multiphase reservoir of chemical compounds, to which (2) Earth-Moon rotations deliver two kinds of regular cycling energies: diurnal electromagnetic radiation and seawater tides. (3) Emerging colloidal phases cyclically nucleate and agglomerate in seawater and consolidate as geochemical sediments in tidal zones, creating a matrix of microspaces. (4) Some microspaces persist and retain memory from past cycles, and others re-dissolve and re-disperse back into the Earth's chemical reservoir. (5) Proto-metabolites and proto-biopolymers coevolve with and within persisting microspaces, where (6) Macromolecular crowding and other non-covalent molecular forces govern the evolution of hydrophilic, hydrophobic, and charged molecular surfaces. (7) The matrices of microspaces evolve into proto-biofilms of progenotes with rudimentary but evolving replication, transcription, and translation, enclosed in unstable cell envelopes. (8) Stabilization of cell envelopes 'crystallizes' bacteria-like genetics and metabolism with low horizontal gene transfer-life 'as we know it.' These factors and processes constitute the 'working pieces' of the jigsaw puzzle of life's emergence. They extend the concept of progenotes as the first proto-cellular life, connected backward in time to the cycling chemistries of the Earth-Moon planetary system, and forward to the ancient cell cycle of first bacteria-like organisms. Supra-macromolecular models of 'compartments first' are preferred: they facilitate macromolecular crowding-a key abiotic/biotic transition toward living states. Evolutionary models of metabolism or genetics 'first' could not have evolved in unconfined and uncrowded environments because of the diffusional drift to disorder mandated by the second law of thermodynamics.}, }
@article {pmid27993847, year = {2017}, author = {Kong, LH and Lei, CW and Ma, SZ and Jiang, W and Liu, BH and Wang, YX and Guan, R and Men, S and Yuan, QW and Cheng, GY and Zhou, WC and Wang, HN}, title = {Various Sequence Types of Escherichia coli Isolates Coharboring blaNDM-5 and mcr-1 Genes from a Commercial Swine Farm in China.}, journal = {Antimicrobial agents and chemotherapy}, volume = {61}, number = {3}, pages = {}, pmid = {27993847}, issn = {1098-6596}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Carbapenems/pharmacology ; China/epidemiology ; Colistin/pharmacology ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/drug effects/*genetics/growth &amp; development/isolation &amp; purification ; Escherichia coli Infections/epidemiology/microbiology/*veterinary ; Escherichia coli Proteins/*genetics/metabolism ; Gene Expression ; Gene Transfer, Horizontal ; Genetic Fitness ; Genotype ; Plasmids/chemistry/genetics/metabolism ; Swine ; Swine Diseases/*epidemiology/microbiology ; beta-Lactamases/*genetics/metabolism ; }, abstract = {Sixteen different sequence types (STs) of Escherichia coli isolates from a commercial swine farm in China were confirmed to coharbor the carbapenem resistance gene blaNDM-5 and the colistin resistance gene mcr-1 Whole-genome sequencing revealed that blaNDM-5 and mcr-1 were located on a 46-kb IncX3 plasmid and a 32-kb IncX4 plasmid, respectively. The two plasmids can transfer together with a low fitness cost, which might explain the presence of various STs of E. coli coharboring blaNDM-5 and mcr-1.}, }
@article {pmid27980385, year = {2016}, author = {Wang, Y and Tao, XF and Su, ZX and Liu, AK and Liu, TL and Sun, L and Yao, Q and Chen, KP and Gu, X}, title = {Current Bacterial Gene Encoding Capsule Biosynthesis Protein CapI Contains Nucleotides Derived from Exonization.}, journal = {Evolutionary bioinformatics online}, volume = {12}, number = {}, pages = {303-312}, pmid = {27980385}, issn = {1176-9343}, abstract = {Since the proposition of introns-early hypothesis, although many studies have shown that most eukaryotic ancestors possessed intron-rich genomes, evidence of intron existence in genomes of ancestral bacteria has still been absent. While not a single intron has been found in all protein-coding genes of current bacteria, analyses on bacterial genes horizontally transferred into eukaryotes at ancient time may provide evidence of intron existence in bacterial ancestors. In this study, a bacterial gene encoding capsule biosynthesis protein CapI was found in the genome of sea anemone, Nematostella vectensis. This horizontally transferred gene contains a phase 1 intron of 40 base pairs. The nucleotides of this intron have high sequence identity with those encoding amino acids in current bacterial CapI gene, indicating that the intron and the amino acid-coding nucleotides are originated from the same ancestor sequence. Moreover, 5'-splice site of this intron is located in a GT-poor region associated with a closely following AG-rich region, suggesting that deletion mutation at 5'-splice site has been employed to remove this intron and the intron-like amino acid-coding nucleotides in current bacterial CapI gene are derived from exonization. These data suggest that bacterial CapI gene contained intron(s) at ancient time. This is the first report providing the result of sequence analysis to suggest possible existence of spliceosomal introns in ancestral bacterial genes. The methodology employed in this study may be used to identify more such evidence that would aid in settlement of the dispute between introns-early and introns-late theories.}, }
@article {pmid27977935, year = {2017}, author = {Zhang, Y and Loria, R}, title = {Emergence of Novel Pathogenic Streptomyces Species by Site-Specific Accretion and cis-Mobilization of Pathogenicity Islands.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {30}, number = {1}, pages = {72-82}, doi = {10.1094/MPMI-09-16-0190-R}, pmid = {27977935}, issn = {0894-0282}, support = {2010-65110-20416//US Department of Agriculture/International ; }, mesh = {Base Sequence ; Biosynthetic Pathways/genetics ; Chromosomes, Bacterial/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial ; Genomic Islands/*genetics ; Indoles/metabolism ; Models, Biological ; Phylogeny ; Piperazines/metabolism ; Species Specificity ; Streptomyces/*genetics/isolation &amp; purification/*pathogenicity ; }, abstract = {The main pathogenicity factor of Streptomyces species associated with the potato common scab disease is a nitrated diketopiperazine called thaxtomin A (ThxA). In Streptomyces scabiei (syn. S. scabies), which is thought to be the most ancient pathogenic Streptomyces species, the ThxA biosynthetic cluster is located within a mobile genomic island called the toxicogenic region (TR). Three attachment (att) sites further separate TR into two subregions (TR1 and TR2). TR1 contains the ThxA biosynthetic cluster and is conserved among several pathogenic Streptomyces species. However, TR2, an integrative and conjugative element, is missing in most pathogenic species. In our previous study, we demonstrated the mobilization of the whole TR element or TR2 alone between S. scabiei and nonpathogenic Streptomyces species. TR1 alone did not mobilize in these experiments. These data suggest that TR2 is required for the mobilization of TR1. Here, we show that TR2 can self mobilize to pathogenic Streptomyces species harboring only TR1 and integrate into the att site of TR1, leading to the tandem accretion of resident TR1 and incoming TR2. The incoming TR2 can further mobilize resident TR1 in cis and transfer to a new recipient cell. Our study demonstrated that TR1 is a nonautonomous cis-mobilizable element and that it can hijack TR2 recombination and conjugation machinery to excise, transfer, and integrate, leading to the dissemination of pathogenicity genes and emergence of novel pathogenic species. Additionally, comparative genomic analysis of 23 pathogenic Streptomyces isolates from ten species revealed that the composite pathogenicity island (PAI) formed by TR1 and TR2 is dynamic and various compositions of the island exist within the population of newly emerged pathogenic species, indicating the structural instability of this composite PAI.}, }
@article {pmid27975296, year = {2016}, author = {Chen, K and Stephanou, AS and Roberts, GA and White, JH and Cooper, LP and Houston, PJ and Lindsay, JA and Dryden, DT}, title = {Erratum to: The Type I Restriction Enzymes as Barriers to Horizontal Gene Transfer: Determination of the DNA Target Sequences Recognised by Livestock-Associated Methicillin-Resistant Staphylococcus aureus Clonal Complexes 133/ST771 and 398.}, journal = {Advances in experimental medicine and biology}, volume = {915}, number = {}, pages = {E1-E3}, doi = {10.1007/978-3-319-32189-9_22}, pmid = {27975296}, issn = {0065-2598}, }
@article {pmid27973733, year = {2017}, author = {Carmona, LM and Schatz, DG}, title = {New insights into the evolutionary origins of the recombination-activating gene proteins and V(D)J recombination.}, journal = {The FEBS journal}, volume = {284}, number = {11}, pages = {1590-1605}, pmid = {27973733}, issn = {1742-4658}, support = {/HHMI/Howard Hughes Medical Institute/United States ; R37 AI032524/AI/NIAID NIH HHS/United States ; T32 AI007019/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Conserved Sequence ; DNA End-Joining Repair ; DNA Transposable Elements/*genetics ; DNA-Binding Proteins/genetics/*physiology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, RAG-1 ; Homeodomain Proteins/*physiology ; Humans ; Lancelets/genetics/immunology ; Models, Genetic ; Phylogeny ; Sea Urchins/genetics/immunology ; Starfish/genetics/immunology ; Transposases/genetics/physiology ; *V(D)J Recombination ; VDJ Recombinases/genetics/physiology ; Vertebrates/genetics/*immunology ; }, abstract = {The adaptive immune system of jawed vertebrates relies on V(D)J recombination as one of the main processes to generate the diverse array of receptors necessary for the recognition of a wide range of pathogens. The DNA cleavage reaction necessary for the assembly of the antigen receptor genes from an array of potential gene segments is mediated by the recombination-activating gene proteins RAG1 and RAG2. The RAG proteins have been proposed to originate from a transposable element (TE) as they share mechanistic and structural similarities with several families of transposases and are themselves capable of mediating transposition. A number of RAG-like proteins and TEs with sequence similarity to RAG1 and RAG2 have been identified, but only recently has their function begun to be characterized, revealing mechanistic links to the vertebrate RAGs. Of particular significance is the discovery of ProtoRAG, a transposon superfamily found in the genome of the basal chordate amphioxus. ProtoRAG has many of the sequence and mechanistic features predicted for the ancestral RAG transposon and is likely to be an evolutionary relative of RAG1 and RAG2. In addition, early observations suggesting that RAG1 is able to mediate V(D)J recombination in the absence of RAG2 have been confirmed, implying independent evolutionary origins for the two RAG genes. Here, recent progress in identifying and characterizing RAG-like proteins and the TEs that encode them is summarized and a refined model for the evolution of V(D)J recombination and the RAG proteins is presented.}, }
@article {pmid27966630, year = {2016}, author = {Wang, L and Zhuang, X and Zhuang, G and Jing, C}, title = {Arsenic resistance strategy in Pantoea sp. IMH: Organization, function and evolution of ars genes.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {39195}, pmid = {27966630}, issn = {2045-2322}, mesh = {Adaptation, Physiological ; Arsenic/*pharmacology ; Bacterial Proteins/*genetics/*metabolism ; Cloning, Molecular ; *Drug Resistance, Bacterial ; Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Multigene Family ; Pantoea/drug effects/genetics/*growth &amp; development ; Sequence Analysis, DNA ; Sequence Homology ; Temperature ; }, abstract = {Pantoea sp. IMH is the only bacterium found in genus Pantoea with a high As resistance capacity, but its molecular mechanism is unknown. Herein, the organization, function, and evolution of ars genes in IMH are studied starting with analysis of the whole genome. Two ars systems - ars1 (arsR1B1C1H1) and ars2 (arsR2B2C2H2) - with low sequence homology and two arsC-like genes, were found in the IMH genome. Both ars1 and ars2 are involved in the As resistance, where ars1 is the major contributor at 15 °C and ars2 at 30 °C. The difference in the behavior of these two ars systems is attributed to the disparate activities of their arsR promoters at different temperatures. Sequence analysis based on concatenated ArsRBC indicates that ars1 and ars2 clusters may be acquired from Franconibacter helveticus LMG23732 and Serratia marcescens (plasmid R478), respectively, by horizontal gene transfer (HGT). Nevertheless, two arsC-like genes, probably arising from the duplication of arsC, do not contribute to the As resistance. Our results indicate that Pantoea sp. IMH acquired two different As resistance genetic systems by HGT, allowing the colonization of changing ecosystems, and highlighting the flexible adaptation of microorganisms to resist As.}, }
@article {pmid27965650, year = {2016}, author = {Li, Z and Li, X and Xiao, X and Xu, J}, title = {An Integrative Genomic Island Affects the Adaptations of the Piezophilic Hyperthermophilic Archaeon Pyrococcus yayanosii to High Temperature and High Hydrostatic Pressure.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1927}, pmid = {27965650}, issn = {1664-302X}, abstract = {Deep-sea hydrothermal vent environments are characterized by high hydrostatic pressure and sharp temperature and chemical gradients. Horizontal gene transfer is thought to play an important role in the microbial adaptation to such an extreme environment. In this study, a 21.4-kb DNA fragment was identified as a genomic island, designated PYG1, in the genomic sequence of the piezophilic hyperthermophile Pyrococcus yayanosii. According to the sequence alignment and functional annotation, the genes in PYG1 could tentatively be divided into five modules, with functions related to mobility, DNA repair, metabolic processes and the toxin-antitoxin system. Integrase can mediate the site-specific integration and excision of PYG1 in the chromosome of P. yayanosii A1. Gene replacement of PYG1 with a Sim[R] cassette was successful. The growth of the mutant strain ΔPYG1 was compared with its parent strain P. yayanosii A2 under various stress conditions, including different pH, salinity, temperature, and hydrostatic pressure. The ΔPYG1 mutant strain showed reduced growth when grown at 100°C, while the biomass of ΔPYG1 increased significantly when cultured at 80 MPa. Differential expression of the genes in module III of PYG1 was observed under different temperature and pressure conditions. This study demonstrates the first example of an archaeal integrative genomic island that could affect the adaptation of the hyperthermophilic piezophile P. yayanosii to high temperature and high hydrostatic pressure.}, }
@article {pmid27965647, year = {2016}, author = {Whitaker, MR and Salzman, S and Sanders, J and Kaltenpoth, M and Pierce, NE}, title = {Microbial Communities of Lycaenid Butterflies Do Not Correlate with Larval Diet.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1920}, pmid = {27965647}, issn = {1664-302X}, abstract = {Herbivores possess many counteradaptations to plant defenses, and a growing body of research describes the role of symbiotic gut bacteria in mediating herbivorous diets among insects. However, persistent bacterial symbioses have not been found in Lepidoptera, despite the fact that perhaps 99% of the species in this order are herbivorous. We surveyed bacterial communities in the guts of larvae from 31 species of lycaenid butterflies whose caterpillars had diets ranging from obligate carnivory to strict herbivory. Contrary to our expectations, we found that the bacterial communities of carnivorous and herbivorous caterpillars do not differ in richness, diversity, or composition. Many of the observed bacterial genera are commonly found in soil and plant surfaces, and we detected known homopteran endosymbionts in the guts of homopterophagous species, suggesting that larvae acquire gut bacteria from their food and environment. These results indicate that lycaenid butterflies do not rely on specific bacterial symbioses to mediate their diverse diets, and provide further evidence of taxonomically depauperate bacterial communities among Lepidoptera.}, }
@article {pmid27965627, year = {2016}, author = {Wang, GH and Sun, BF and Xiong, TL and Wang, YK and Murfin, KE and Xiao, JH and Huang, DW}, title = {Bacteriophage WO Can Mediate Horizontal Gene Transfer in Endosymbiotic Wolbachia Genomes.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1867}, pmid = {27965627}, issn = {1664-302X}, support = {T32 HL007974/HL/NHLBI NIH HHS/United States ; }, abstract = {Phage-mediated horizontal gene transfer (HGT) is common in free-living bacteria, and many transferred genes can play a significant role in their new bacterial hosts. However, there are few reports concerning phage-mediated HGT in endosymbionts (obligate intracellular bacteria within animal or plant hosts), such as Wolbachia. The Wolbachia-infecting temperate phage WO can actively shift among Wolbachia genomes and has the potential to mediate HGT between Wolbachia strains. In the present study, we extend previous findings by validating that the phage WO can mediate transfer of non-phage genes. To do so, we utilized bioinformatic, phylogenetic, and molecular analyses based on all sequenced Wolbachia and phage WO genomes. Our results show that the phage WO can mediate HGT between Wolbachia strains, regardless of whether the transferred genes originate from Wolbachia or other unrelated bacteria.}, }
@article {pmid27965456, year = {2016}, author = {Chavda, KD and Chen, L and Fouts, DE and Sutton, G and Brinkac, L and Jenkins, SG and Bonomo, RA and Adams, MD and Kreiswirth, BN}, title = {Comprehensive Genome Analysis of Carbapenemase-Producing Enterobacter spp.: New Insights into Phylogeny, Population Structure, and Resistance Mechanisms.}, journal = {mBio}, volume = {7}, number = {6}, pages = {}, pmid = {27965456}, issn = {2150-7511}, support = {R01 AI100560/AI/NIAID NIH HHS/United States ; R21 AI117338/AI/NIAID NIH HHS/United States ; R01 AI090155/AI/NIAID NIH HHS/United States ; R01 AI072219/AI/NIAID NIH HHS/United States ; R01 AI063517/AI/NIAID NIH HHS/United States ; U19 AI110819/AI/NIAID NIH HHS/United States ; I01 BX001974/BX/BLRD VA/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/biosynthesis ; Carbapenems/pharmacology ; *Drug Resistance, Bacterial/genetics ; Enterobacter/*drug effects/enzymology/*genetics ; Enterobacter cloacae/drug effects/genetics ; Enterobacteriaceae Infections/microbiology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Humans ; Klebsiella pneumoniae/drug effects/genetics ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Phylogeny ; Plasmids ; beta-Lactamases/biosynthesis ; }, abstract = {UNLABELLED: Knowledge regarding the genomic structure of Enterobacter spp., the second most prevalent carbapenemase-producing Enterobacteriaceae, remains limited. Here we sequenced 97 clinical Enterobacter species isolates that were both carbapenem susceptible and resistant from various geographic regions to decipher the molecular origins of carbapenem resistance and to understand the changing phylogeny of these emerging and drug-resistant pathogens. Of the carbapenem-resistant isolates, 30 possessed blaKPC-2, 40 had blaKPC-3, 2 had blaKPC-4, and 2 had blaNDM-1 Twenty-three isolates were carbapenem susceptible. Six genomes were sequenced to completion, and their sizes ranged from 4.6 to 5.1 Mbp. Phylogenomic analysis placed 96 of these genomes, 351 additional Enterobacter genomes downloaded from NCBI GenBank, and six newly sequenced type strains into 19 phylogenomic groups-18 groups (A to R) in the Enterobacter cloacae complex and Enterobacter aerogenes Diverse mechanisms underlying the molecular evolutionary trajectory of these drug-resistant Enterobacter spp. were revealed, including the acquisition of an antibiotic resistance plasmid, followed by clonal spread, horizontal transfer of blaKPC-harboring plasmids between different phylogenomic groups, and repeated transposition of the blaKPC gene among different plasmid backbones. Group A, which comprises multilocus sequence type 171 (ST171), was the most commonly identified (23% of isolates). Genomic analysis showed that ST171 isolates evolved from a common ancestor and formed two different major clusters; each acquiring unique blaKPC-harboring plasmids, followed by clonal expansion. The data presented here represent the first comprehensive study of phylogenomic interrogation and the relationship between antibiotic resistance and plasmid discrimination among carbapenem-resistant Enterobacter spp., demonstrating the genetic diversity and complexity of the molecular mechanisms driving antibiotic resistance in this genus.<br><br>IMPORTANCE: Enterobacter spp., especially carbapenemase-producing Enterobacter spp., have emerged as a clinically significant cause of nosocomial infections. However, only limited information is available on the distribution of carbapenem resistance across this genus. Augmenting this problem is an erroneous identification of Enterobacter strains because of ambiguous typing methods and imprecise taxonomy. In this study, we used a whole-genome-based comparative phylogenetic approach to (i) revisit and redefine the genus Enterobacter and (ii) unravel the emergence and evolution of the Klebsiella pneumoniae carbapenemase-harboring Enterobacter spp. Using genomic analysis of 447 sequenced strains, we developed an improved understanding of the species designations within this complex genus and identified the diverse mechanisms driving the molecular evolution of carbapenem resistance. The findings in this study provide a solid genomic framework that will serve as an important resource in the future development of molecular diagnostics and in supporting drug discovery programs.}, }
@article {pmid27964731, year = {2016}, author = {Hargreaves, KR and Thanki, AM and Jose, BR and Oggioni, MR and Clokie, MR}, title = {Use of single molecule sequencing for comparative genomics of an environmental and a clinical isolate of Clostridium difficile ribotype 078.}, journal = {BMC genomics}, volume = {17}, number = {1}, pages = {1020}, pmid = {27964731}, issn = {1471-2164}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {CRISPR-Cas Systems ; Clostridioides difficile/*classification/*genetics/isolation &amp; purification ; Clustered Regularly Interspaced Short Palindromic Repeats ; Computational Biology/methods ; DNA Methylation ; DNA Transposable Elements ; *Environmental Microbiology ; *Genome, Bacterial ; *Genomics/methods ; High-Throughput Nucleotide Sequencing ; Humans ; *Ribotyping ; *Sequence Analysis, DNA ; }, abstract = {BACKGROUND: How the pathogen Clostridium difficile might survive, evolve and be transferred between reservoirs within the natural environment is poorly understood. Some ribotypes are found both in clinical and environmental settings. Whether these strains are distinct from each another and evolve in the specific environments is not established. The possession of a highly mobile genome has contributed to the genetic diversity and ongoing evolution of C. difficile. Interpretations of genetic diversity have been limited by fragmented assemblies resulting from short-read length sequencing approaches and by a limited understanding of epigenetic regulation of diversity. To address this, single molecule real time (SMRT) sequencing was used in this study as it produces high quality genome sequences, with resolution of repeat regions (including those found in mobile elements) and can generate data to determine methylation modifications across the sequence (the methylome).<br><br>RESULTS: Chromosomal rearrangements and ribosomal operon duplications were observed in both genomes. The rearrangements occurred at insertion sites within two mobile genetic elements (MGEs), Tn6164 and Tn6293, present only in the M120 and CD105HS27 genomes, respectively. The gene content of these two transposons differ considerably which could impact upon horizontal gene transfer; differences include CDSs encoding methylases and a conjugative prophage only in Tn6164. To investigate mechanisms which could affect MGE transfer, the methylome, restriction modification (RM) &#xa0;and the CRISPR/Cas systems were characterised for each strain. Notably, the environmental isolate, CD105HS27, does not share a consensus motif for [m4]C methylation, but has one additional spacer &#xa0;when compared to the clinical isolate M120.<br><br>CONCLUSIONS: These findings show key differences between the two strains in terms of their genetic capacity for MGE transfer. The carriage of horizontally transferred genes appear to have genome wide effects based on two different methylation patterns. The CRISPR/Cas system appears active although perhaps slow to evolve. Data suggests that both mechanisms are functional and impact upon horizontal gene transfer and genome evolution within C. difficile.}, }
@article {pmid27956618, year = {2016}, author = {Harms, K and Lunnan, A and Hülter, N and Mourier, T and Vinner, L and Andam, CP and Marttinen, P and Fridholm, H and Hansen, AJ and Hanage, WP and Nielsen, KM and Willerslev, E and Johnsen, PJ}, title = {Substitutions of short heterologous DNA segments of intragenomic or extragenomic origins produce clustered genomic polymorphisms.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {52}, pages = {15066-15071}, pmid = {27956618}, issn = {1091-6490}, support = {R01 AI106786/AI/NIAID NIH HHS/United States ; }, mesh = {Acinetobacter/genetics ; Alleles ; Computational Biology/methods ; Cytoplasm/metabolism ; DNA/*genetics ; DNA Replication ; DNA, Single-Stranded/genetics ; Gene Deletion ; Gene Transfer, Horizontal ; Genome, Human ; Genomics ; Genotype ; Humans ; Mutagens ; *Mutation ; Plasmids/metabolism ; *Polymorphism, Genetic ; Polymorphism, Single Nucleotide ; Recombination, Genetic ; Sequence Analysis, DNA ; Streptococcus pneumoniae/*genetics ; }, abstract = {In a screen for unexplained mutation events we identified a previously unrecognized mechanism generating clustered DNA polymorphisms such as microindels and cumulative SNPs. The mechanism, short-patch double illegitimate recombination (SPDIR), facilitates short single-stranded DNA molecules to invade and replace genomic DNA through two joint illegitimate recombination events. SPDIR is controlled by key components of the cellular genome maintenance machinery in the gram-negative bacterium Acinetobacter baylyi. The source DNA is primarily intragenomic but can also be acquired through horizontal gene transfer. The DNA replacements are nonreciprocal and locus independent. Bioinformatic approaches reveal occurrence of SPDIR events in the gram-positive human pathogen Streptococcus pneumoniae and in the human genome.}, }
@article {pmid27956257, year = {2017}, author = {Khowal, S and Siddiqui, MZ and Ali, S and Khan, MT and Khan, MA and Naqvi, SH and Wajid, S}, title = {A report on extensive lateral genetic reciprocation between arsenic resistant Bacillus subtilis and Bacillus pumilus strains analyzed using RAPD-PCR.}, journal = {Molecular phylogenetics and evolution}, volume = {107}, number = {}, pages = {443-454}, doi = {10.1016/j.ympev.2016.12.010}, pmid = {27956257}, issn = {1095-9513}, mesh = {Arsenic/*toxicity ; Bacillus pumilus/*drug effects/*genetics/isolation &amp; purification ; Bacillus subtilis/*drug effects/*genetics/isolation &amp; purification ; Evolution, Molecular ; Genes, Bacterial ; Hydrogen-Ion Concentration ; Likelihood Functions ; Phylogeny ; Polymerase Chain Reaction/*methods ; Random Amplified Polymorphic DNA Technique/*methods ; Soil ; }, abstract = {The study involves isolation of arsenic resistant bacteria from soil samples. The characterization of bacteria isolates was based on 16S rRNA gene sequences. The phylogenetic consanguinity among isolates was studied employing rpoB and gltX gene sequence. RAPD-PCR technique was used to analyze genetic similarity between arsenic resistant isolates. In accordance with the results Bacillus subtilis and Bacillus pumilus strains may exhibit extensive horizontal gene transfer. Arsenic resistant potency in Bacillus sonorensis and high arsenite tolerance in Bacillus pumilus strains was identified. The RAPD-PCR primer OPO-02 amplified a 0.5kb DNA band specific to B. pumilus 3ZZZ strain and 0.75kb DNA band specific to B. subtilis 3PP. These unique DNA bands may have potential use as SCAR (Sequenced Characterized Amplified Region) molecular markers for identification of arsenic resistant B. pumilus and B. subtilis strains.}, }
@article {pmid27955806, year = {2017}, author = {Hwang, D and Kim, SM and Kim, HJ}, title = {Modelling of tetracycline resistance gene transfer by commensal Escherichia coli food isolates that survived in gastric fluid conditions.}, journal = {International journal of antimicrobial agents}, volume = {49}, number = {1}, pages = {81-87}, doi = {10.1016/j.ijantimicag.2016.10.009}, pmid = {27955806}, issn = {1872-7913}, mesh = {Escherichia coli/*drug effects/*genetics/isolation &amp; purification/physiology ; *Food Microbiology ; Gastric Juice/*chemistry ; *Gene Transfer, Horizontal ; Humans ; Hydrogen-Ion Concentration ; Microbial Viability/*drug effects ; Models, Theoretical ; Republic of Korea ; *Tetracycline Resistance ; }, abstract = {Antimicrobial resistance (AR) is a major public health concern and a food safety issue worldwide. Escherichia coli strains, indicators of antibiotic resistance, are a source of horizontal gene transfer to other bacteria in the human intestinal system. A probabilistic exposure model was used to estimate the transfer of the AR gene tet(A). The acid resistance and kinetic behaviour of E. coli was analysed as a function of pH to describe the inactivation of E. coli in simulated gastric fluid (SGF), the major host barrier against exogenous micro-organisms. The kinetic parameters of microbial inactivation in SGF were estimated using GInaFiT, and log-linear + tail and Weibull models were found to be suitable for commensal and enterohaemorrhagic E. coli (EHEC), respectively. A probabilistic exposure model was developed to estimate E. coli survival in gastric pH conditions as well as gene transfer from resistant to susceptible cells in humans. E. coli-contaminated retail foods for consumption without further cooking and gastric pH data in South Korea were considered as an example. The model predicts that 22-33% of commensal E. coli can survive under gastric pH conditions of Koreans. The estimated total mean tet(A) transfer level by commensal E. coli was 1.68 × 10[-4]-8.15 × 10[-4] log CFU/mL/h. The inactivation kinetic parameters of E. coli in SGF and the quantitative exposure model can provide useful information regarding risk management options to control the spread of AR.}, }
@article {pmid27938421, year = {2017}, author = {Cao, XL and Shen, H and Xu, YY and Xu, XJ and Zhang, ZF and Cheng, L and Chen, JH and Arakawa, Y}, title = {High prevalence of fosfomycin resistance gene fosA3 in bla CTX-M-harbouring Escherichia coli from urine in a Chinese tertiary hospital during 2010-2014.}, journal = {Epidemiology and infection}, volume = {145}, number = {4}, pages = {818-824}, pmid = {27938421}, issn = {1469-4409}, mesh = {Anti-Bacterial Agents/pharmacology ; China/epidemiology ; Conjugation, Genetic ; *Drug Resistance, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/drug effects/enzymology/*genetics/isolation &amp; purification ; Escherichia coli Infections/*epidemiology/microbiology ; Escherichia coli Proteins/*genetics ; Fosfomycin/pharmacology ; Gene Transfer, Horizontal ; Genetic Variation ; Genotype ; Humans ; Multilocus Sequence Typing ; Plasmids/analysis/classification ; Prevalence ; Tertiary Care Centers ; Urinary Tract Infections/*epidemiology/microbiology ; Urine/*microbiology ; beta-Lactamases/*genetics ; }, abstract = {Fosfomycin has become a therapeutic option in urinary tract infections. We identified 57 fosfomycin-resistant Escherichia coli from 465 urine-derived extended-spectrum β-lactamase (ESBL)-producing isolates from a Chinese hospital during 2010-2014. Of the 57 fosfomycin-resistant isolates, 51 (89·5%) carried fosA3, and one carried fosA1. Divergent pulsed-field gel electrophoresis profiles and multi-locus sequence typing results revealed high clonal diversity in the fosA3-positive isolates. Conjugation experiments showed that the fosA3 genes from 50 isolates were transferable, with IncFII or IncI1 being the most prevalent types of plasmids. The high prevalence of fosA3 was closely associated with that of bla CTX-M. Horizontal transfer, rather than clonal expansion, might play a central role in dissemination. Such strains may constitute an important reservoir of fosA3 and bla CTX-M, which may well be readily disseminated to other potential human pathogens. Since most ESBL-producing E. coli have acquired resistance to fluoroquinolones worldwide, further spread of fosA3 in such E. coli isolates should be monitored closely.}, }
@article {pmid27938347, year = {2016}, author = {Schlegel, M and Münsterkötter, M and Güldener, U and Bruggmann, R and Duò, A and Hainaut, M and Henrissat, B and Sieber, CM and Hoffmeister, D and Grünig, CR}, title = {Globally distributed root endophyte Phialocephala subalpina links pathogenic and saprophytic lifestyles.}, journal = {BMC genomics}, volume = {17}, number = {1}, pages = {1015}, pmid = {27938347}, issn = {1471-2164}, mesh = {Ascomycota/*genetics/metabolism/ultrastructure ; Computational Biology/methods ; DNA Transposable Elements ; Endophytes/*genetics/metabolism/ultrastructure ; Gene Ontology ; Gene Transfer, Horizontal ; Genes, Fungal ; Genome, Fungal ; Genomics/methods ; Multigene Family ; Plant Roots/*microbiology ; RNA Interference ; Repetitive Sequences, Nucleic Acid ; Secondary Metabolism/genetics ; }, abstract = {BACKGROUND: Whereas an increasing number of pathogenic and mutualistic ascomycetous species were sequenced in the past decade, species showing a seemingly neutral association such as root endophytes received less attention. In the present study, the genome of Phialocephala subalpina, the most frequent species of the Phialocephala fortinii s.l. - Acephala applanata species complex, was sequenced for insight in the genome structure and gene inventory of these wide-spread root endophytes.<br><br>RESULTS: The genome of P. subalpina was sequenced using Roche/454 GS FLX technology and a whole genome shotgun strategy. The assembly resulted in 205 scaffolds and a genome size of 69.7 Mb. The expanded genome size in P. subalpina was not due to the proliferation of transposable elements or other repeats, as is the case with other ascomycetous genomes. Instead, P. subalpina revealed an expanded gene inventory that includes 20,173 gene models. Comparative genome analysis of P. subalpina with 13 ascomycetes shows that P. subalpina uses a versatile gene inventory including genes specific for pathogens and saprophytes. Moreover, the gene inventory for carbohydrate active enzymes (CAZymes) was expanded including genes involved in degradation of biopolymers, such as pectin, hemicellulose, cellulose and lignin.<br><br>CONCLUSIONS: The analysis of a globally distributed root endophyte allowed detailed insights in the gene inventory and genome organization of a yet largely neglected group of organisms. We showed that the ubiquitous root endophyte P. subalpina has a broad gene inventory that links pathogenic and saprophytic lifestyles.}, }
@article {pmid27937735, year = {2017}, author = {Hutinet, G and Swarjo, MA and de Crécy-Lagard, V}, title = {Deazaguanine derivatives, examples of crosstalk between RNA and DNA modification pathways.}, journal = {RNA biology}, volume = {14}, number = {9}, pages = {1175-1184}, pmid = {27937735}, issn = {1555-8584}, support = {R01 GM070641/GM/NIGMS NIH HHS/United States ; R01 GM110588/GM/NIGMS NIH HHS/United States ; }, mesh = {Archaea/genetics/metabolism ; Bacteria/genetics/metabolism ; Bacteriophages/genetics/metabolism ; DNA/chemistry/genetics/*metabolism ; Eukaryota/genetics/metabolism ; Gene Transfer, Horizontal ; Guanine/analogs &amp; derivatives/chemistry/metabolism ; Metabolic Networks and Pathways ; Nucleoside Q/chemistry/metabolism ; RNA/chemistry/genetics/*metabolism ; RNA, Transfer/chemistry/genetics/metabolism ; }, abstract = {Seven-deazapurine modifications were thought to be highly specific of tRNAs, but have now been discovered in DNA of phages and of phylogenetically diverse bacteria, illustrating the plasticity of these modification pathways. The intermediate 7-cyano-7-deazaguanine (preQ0) is a shared precursor in the pathways leading to the insetion of 7-deazapurine derivatives in both tRNA and DNA. It is also used as an intermediate in the synthesis of secondary metabolites such as toyocamacin. The presence of 7-deazapurine in DNA is proposed to be a protection mechanism against endonucleases. This makes preQ0 a metabolite of underappreaciated but central importance.}, }
@article {pmid27934695, year = {2016}, author = {Ratner, HK and Sampson, TR and Weiss, DS}, title = {Overview of CRISPR-Cas9 Biology.}, journal = {Cold Spring Harbor protocols}, volume = {2016}, number = {12}, pages = {pdb.top088849}, pmid = {27934695}, issn = {1559-6095}, support = {P51 OD011132/OD/NIH HHS/United States ; R01 AI110701/AI/NIAID NIH HHS/United States ; }, mesh = {Archaea/*enzymology/*genetics ; Bacteria/*enzymology/*genetics ; *CRISPR-Cas Systems ; Gene Targeting/methods ; Gene Transfer, Horizontal ; Interspersed Repetitive Sequences ; }, abstract = {Prokaryotes use diverse strategies to improve fitness in the face of different environmental threats and stresses, including those posed by mobile genetic elements (e.g., bacteriophages and plasmids). To defend against these elements, many bacteria and archaea use elegant, RNA-directed, nucleic acid-targeting adaptive restriction machineries called CRISPR -: Cas (CRISPR-associated) systems. While providing an effective defense against foreign genetic elements, these systems have also been observed to play critical roles in regulating bacterial physiology during environmental stress. Increasingly, CRISPR-Cas systems, in particular the Type II systems containing the Cas9 endonuclease, have been exploited for their ability to bind desired nucleic acid sequences, as well as direct sequence-specific cleavage of their targets. Cas9-mediated genome engineering is transcending biological research as a versatile and portable platform for manipulating genetic content in myriad systems. Here, we present a systematic overview of CRISPR-Cas history and biology, highlighting the revolutionary tools derived from these systems, which greatly expand the molecular biologists' toolkit.}, }
@article {pmid27933035, year = {2016}, author = {Kerepesi, C and Szabó, JE and Papp-Kádár, V and Dobay, O and Szabó, D and Grolmusz, V and Vértessy, BG}, title = {Life without dUTPase.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1768}, pmid = {27933035}, issn = {1664-302X}, abstract = {Fine-tuned regulation of the cellular nucleotide pools is indispensable for faithful replication of Deoxyribonucleic Acid (DNA). The genetic information is also safeguarded by DNA damage recognition and repair processes. Uracil is one of the most frequently occurring erroneous bases in DNA; it can arise from cytosine deamination or thymine-replacing incorporation. Two enzyme activities are primarily involved in keeping DNA uracil-free: dUTPase (dUTP pyrophosphatase) activity that prevent thymine-replacing incorporation and uracil-DNA glycosylase activity that excise uracil from DNA and initiate uracil-excision repair. Both dUTPase and the most efficient uracil-DNA glycosylase (UNG) is thought to be ubiquitous in free-living organisms. In the present work, we have systematically investigated the genotype of deposited fully sequenced bacterial and Archaeal genomes. We have performed bioinformatic searches in these genomes using the already well described dUTPase and UNG gene sequences. For dUTPases, we have included the trimeric all-beta and the dimeric all-alpha families and also, the bifunctional dCTP (deoxycytidine triphosphate) deaminase-dUTPase sequences. Surprisingly, we have found that in contrast to the generally held opinion, a wide number of bacterial and Archaeal species lack all of the previously described dUTPase gene(s). The dut- genotype is present in diverse bacterial phyla indicating that loss of this (or these) gene(s) has occurred multiple times during evolution. We discuss potential survival strategies in lack of dUTPases, such as simultaneous lack or inhibition of UNG and possession of exogenous or alternate metabolic enzymes involved in uracil-DNA metabolism. The potential that genes previously not associated with dUTPase activity may still encode enzymes capable of hydrolyzing dUTP is also discussed. Our data indicate that several unicellular microorganisms may efficiently cope with a dut- genotype lacking all of the previously described dUTPase genes, and potentially leading to an unusual uracil-enrichment in their genomic DNA.}, }
@article {pmid27930295, year = {2016}, author = {Leclercq, S and Thézé, J and Chebbi, MA and Giraud, I and Moumen, B and Ernenwein, L and Grève, P and Gilbert, C and Cordaux, R}, title = {Birth of a W sex chromosome by horizontal transfer of Wolbachia bacterial symbiont genome.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {52}, pages = {15036-15041}, pmid = {27930295}, issn = {1091-6490}, mesh = {Animals ; Biological Evolution ; Crosses, Genetic ; Cytoplasm/metabolism ; Female ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Genotype ; Isopoda/microbiology ; Male ; Microscopy, Electron, Transmission ; Phylogeny ; *Sex Chromosomes ; Sex Determination Processes ; Sex Ratio ; Symbiosis ; Wolbachia/*genetics ; }, abstract = {Sex determination is a fundamental developmental pathway governing male and female differentiation, with profound implications for morphology, reproductive strategies, and behavior. In animals, sex differences between males and females are generally determined by genetic factors carried by sex chromosomes. Sex chromosomes are remarkably variable in origin and can differ even between closely related species, indicating that transitions occur frequently and independently in different groups of organisms. The evolutionary causes underlying sex chromosome turnover are poorly understood, however. Here we provide evidence indicating that Wolbachia bacterial endosymbionts triggered the evolution of new sex chromosomes in the common pillbug Armadillidium vulgare We identified a 3-Mb insert of a feminizing Wolbachia genome that was recently transferred into the pillbug nuclear genome. The Wolbachia insert shows perfect linkage to the female sex, occurs in a male genetic background (i.e., lacking the ancestral W female sex chromosome), and is hemizygous. Our results support the conclusion that the Wolbachia insert is now acting as a female sex-determining region in pillbugs, and that the chromosome carrying the insert is a new W sex chromosome. Thus, bacteria-to-animal horizontal genome transfer represents a remarkable mechanism underpinning the birth of sex chromosomes. We conclude that sex ratio distorters, such as Wolbachia endosymbionts, can be powerful agents of evolutionary transitions in sex determination systems in animals.}, }
@article {pmid27928044, year = {2016}, author = {Bell, T and Tylianakis, JM}, title = {Microbes in the Anthropocene: spillover of agriculturally selected bacteria and their impact on natural ecosystems.}, journal = {Proceedings. Biological sciences}, volume = {283}, number = {1844}, pages = {}, pmid = {27928044}, issn = {1471-2954}, support = {311399/ERC_/European Research Council/International ; }, mesh = {*Agriculture ; Bacteria/*classification ; Crops, Agricultural ; *Ecosystem ; Humans ; *Soil Microbiology ; }, abstract = {Soil microbial communities are enormously diverse, with at least millions of species and trillions of genes unknown to science or poorly described. Soil microbial communities are key components of agriculture, for example, in provisioning nitrogen and protecting crops from pathogens, providing overall ecosystem services in excess of $1000bn per year. It is important to know how humans are affecting this hidden diversity. Much is known about the negative consequences of agricultural intensification on higher organisms, but almost nothing is known about how alterations to landscapes affect microbial diversity, distributions and processes. We review what is known about spatial flows of microbes and their response to land-use change, and outline nine hypotheses to advance research of microbiomes across landscapes. We hypothesize that intensified agriculture selects for certain taxa and genes, which then 'spill over' into adjacent unmodified areas and generate a halo of genetic differentiation around agricultural fields. Consequently, the spatial configuration and management intensity of different habitats combines with the dispersal ability of individual taxa to determine the extent of spillover, which can impact the functioning of adjacent unmodified habitats. When landscapes are heterogeneous and dispersal rates are high, this will select for large genomes that allow exploitation of multiple habitats, a process that may be accelerated through horizontal gene transfer. Continued expansion of agriculture will increase genotypic similarity, making microbial community functioning increasingly variable in human-dominated landscapes, potentially also impacting the consistent provisioning of ecosystem services. While the resulting economic costs have not been calculated, it is clear that dispersal dynamics of microbes should be taken into consideration to ensure that ecosystem functioning and services are maintained in agri-ecosystem mosaics.}, }
@article {pmid27924916, year = {2016}, author = {Trivedi, VD and Jangir, PK and Sharma, R and Phale, PS}, title = {Insights into functional and evolutionary analysis of carbaryl metabolic pathway from Pseudomonas sp. strain C5pp.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {38430}, pmid = {27924916}, issn = {2045-2322}, mesh = {Amidohydrolases/*genetics/metabolism ; Biodegradation, Environmental ; Carbamates/chemistry ; Carbaryl/*metabolism ; Dioxygenases/*genetics/metabolism ; Genome, Bacterial/genetics ; Metabolic Networks and Pathways/genetics ; Mixed Function Oxygenases/*genetics/metabolism ; Multienzyme Complexes/*genetics/metabolism ; Pesticides/chemistry ; Pseudomonas/enzymology/*genetics ; Soil Microbiology ; }, abstract = {Carbaryl (1-naphthyl N-methylcarbamate) is a most widely used carbamate pesticide in the agriculture field. Soil isolate, Pseudomonas sp. strain C5pp mineralizes carbaryl via 1-naphthol, salicylate and gentisate, however the genetic organization and evolutionary events of acquisition and assembly of pathway have not yet been studied. The draft genome analysis of strain C5pp reveals that the carbaryl catabolic genes are organized into three putative operons, 'upper', 'middle' and 'lower'. The sequence and functional analysis led to identification of new genes encoding: i) hitherto unidentified 1-naphthol 2-hydroxylase, sharing a common ancestry with 2,4-dichlorophenol monooxygenase; ii) carbaryl hydrolase, a member of a new family of esterase; and iii) 1,2-dihydroxy naphthalene dioxygenase, uncharacterized type-II extradiol dioxygenase. The 'upper' pathway genes were present as a part of a integron while the 'middle' and 'lower' pathway genes were present as two distinct class-I composite transposons. These findings suggest the role of horizontal gene transfer event(s) in the acquisition and evolution of the carbaryl degradation pathway in strain C5pp. The study presents an example of assembly of degradation pathway for carbaryl.}, }
@article {pmid27924551, year = {2017}, author = {Brown, DW and Baker, SE}, title = {Mycotoxins: A Fungal Genomics Perspective.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1542}, number = {}, pages = {367-379}, doi = {10.1007/978-1-4939-6707-0_24}, pmid = {27924551}, issn = {1940-6029}, mesh = {Aspergillus/classification/genetics ; Fumonisins ; Fusarium/classification/genetics ; *Gene Expression Regulation, Fungal ; *Genes, Fungal ; *Genome, Fungal ; *Genomics/methods ; Multigene Family ; Mycotoxins/*genetics ; Phylogeny ; }, abstract = {The chemical and enzymatic diversity in the fungal kingdom is staggering. Large-scale fungal genome sequencing projects are generating a massive catalog of secondary metabolite biosynthetic genes and pathways. Fungal natural products are a boon and bane to man as valuable pharmaceuticals and harmful toxins. Understanding how these chemicals are synthesized will aid the development of new strategies to limit mycotoxin contamination of food and feeds as well as expand drug discovery programs. A survey of work focused on the fumonisin family of mycotoxins highlights technological advances and provides a blueprint for future studies of other fungal natural products. Expressed sequence tags led to the discovery of new fumonisin genes (FUM) and hinted at a role for alternatively spliced transcripts in regulation. Phylogenetic studies of FUM genes uncovered a complex evolutionary history of the FUM cluster, as well as fungi with the potential to synthesize fumonisin or fumonisin-like chemicals. The application of new technologies (e.g., CRISPR) could substantially impact future efforts to harness fungal resources.}, }
@article {pmid27923578, year = {2017}, author = {Lee, J and Shin, SG and Jang, HM and Kim, YB and Lee, J and Kim, YM}, title = {Characterization of antibiotic resistance genes in representative organic solid wastes: Food waste-recycling wastewater, manure, and sewage sludge.}, journal = {The Science of the total environment}, volume = {579}, number = {}, pages = {1692-1698}, doi = {10.1016/j.scitotenv.2016.11.187}, pmid = {27923578}, issn = {1879-1026}, mesh = {Drug Resistance, Microbial/*genetics ; *Environmental Monitoring ; *Food Industry ; Industrial Waste ; Republic of Korea ; Sewage/microbiology ; Waste Disposal, Fluid/*methods ; Wastewater/*microbiology ; }, abstract = {In this research, the distribution of antibiotic resistance genes (ARGs) was characterized in representative organic solid waste (OSW) in Korea: food waste-recycling wastewater (FRW), manure, and sewage sludge. The amounts of total ARG (gene copies/16S rRNA gene copies) was greatest in manure followed by sewage sludge and FRW. Interestingly, there were significantly different patterns in the diversity and mechanisms of ARGs. For example, a significant proportion of ARGs were tetracycline resistant genes in all the OSW (40.4-78.2%). β-lactam antibiotics resistant genes were higher in the FRW samples than in other types of OSW but sulfonamides resistant genes represented the greatest proportion in sludge. Regarding the characteristics of antibiotic resistance mechanisms, there was a relatively higher proportion of the ribosomal protection mechanism to tetracycline observed in the FRW and manure samples. However, tetracycline resistant genes with direct interaction were relatively higher in the sewage sludge samples. sul1 was the dominant subtype in all the OSW types and detection of ermB was observed although there was no ermC detected in sewage sludge. There were significant correlations between the occurrences of ARG subtypes: tetB and tetG in all OSW (P<0.01); tetE and tetQ only in sludge (P<0.01). The Class 1 integron-integrase gene (intI1) was significantly correlated with total ARGs only in manure and sludge (P<0.05), revealing potential horizontal gene transfer in these OSW.}, }
@article {pmid27923069, year = {2016}, author = {Fischer, F and Robbe-Saule, M and Turlin, E and Mancuso, F and Michel, V and Richaud, P and Veyrier, FJ and De Reuse, H and Vinella, D}, title = {Characterization in Helicobacter pylori of a Nickel Transporter Essential for Colonization That Was Acquired during Evolution by Gastric Helicobacter Species.}, journal = {PLoS pathogens}, volume = {12}, number = {12}, pages = {e1006018}, pmid = {27923069}, issn = {1553-7374}, mesh = {ATP-Binding Cassette Transporters/genetics/*metabolism ; Animals ; Bacterial Proteins/genetics/*metabolism ; Biological Evolution ; Biological Transport/physiology ; Disease Models, Animal ; Helicobacter Infections/metabolism ; Helicobacter pylori/genetics/*metabolism/pathogenicity ; Mice ; Nickel/*metabolism ; Phylogeny ; Virulence/*physiology ; }, abstract = {Metal acquisition is crucial for all cells and for the virulence of many bacterial pathogens. In particular, nickel is a virulence determinant for the human gastric pathogen Helicobacter pylori as it is the cofactor of two enzymes essential for in vivo colonization, urease and a [NiFe] hydrogenase. To import nickel despite its scarcity in the human body, H. pylori requires efficient uptake mechanisms that are only partially defined. Indeed, alternative ways of nickel entry were predicted to exist in addition to the well-described NixA permease. Using a genetic screen, we identified an ABC transporter, that we designated NiuBDE, as a novel H. pylori nickel transport system. Unmarked mutants carrying deletions of nixA, niuD and/or niuB, were constructed and used to measure (i) tolerance to toxic nickel exposure, (ii) intracellular nickel content by ICP-OES, (iii) transport of radioactive nickel and (iv) expression of a reporter gene controlled by nickel concentration. We demonstrated that NiuBDE and NixA function separately and are the sole nickel transporters in H. pylori. NiuBDE, but not NixA, also transports cobalt and bismuth, a metal currently used in H. pylori eradication therapy. Both NiuBDE and NixA participate in nickel-dependent urease activation at pH 5 and survival under acidic conditions mimicking those encountered in the stomach. However, only NiuBDE is able to carry out this activity at neutral pH and is essential for colonization of the mouse stomach. Phylogenomic analyses indicated that both nixA and niuBDE genes have been acquired via horizontal gene transfer by the last common ancestor of the gastric Helicobacter species. Our work highlights the importance of this evolutionary event for the emergence of Helicobacter gastric species that are adapted to the hostile environment of the stomach where the capacity of Helicobacter to import nickel and thereby activate urease needs to be optimized.}, }
@article {pmid27922601, year = {2017}, author = {Bentkowski, P and van Oosterhout, C and Ashby, B and Mock, T}, title = {The effect of extrinsic mortality on genome size evolution in prokaryotes.}, journal = {The ISME journal}, volume = {11}, number = {4}, pages = {1011-1018}, pmid = {27922601}, issn = {1751-7370}, mesh = {Bacteria/*genetics/metabolism ; *Biological Evolution ; *Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genome Size ; Genome, Bacterial/*genetics ; *Selection, Genetic ; }, abstract = {Mortality has a significant role in prokaryotic ecology and evolution, yet the impact of variations in extrinsic mortality on prokaryotic genome evolution has received little attention. We used both mathematical and agent-based models to reveal how variations in extrinsic mortality affect prokaryotic genome evolution. Our results suggest that the genome size of bacteria increases with increased mortality. A high extrinsic mortality increases the pool of free resources and shortens life expectancy, which selects for faster reproduction, a phenotype we called 'scramblers'. This phenotype is realised by the expansion of gene families involved in nutrient acquisition and metabolism. In contrast, a low mortality rate increases an individual's life expectancy, which results in natural selection favouring tolerance to starvation when conditions are unfavourable. This leads to the evolution of small, streamlined genomes ('stayers'). Our models predict that large genomes, gene family expansion and horizontal gene transfer should be observed in prokaryotes occupying ecosystems exposed to high abiotic stress, as well as those under strong predator- and/or pathogen-mediated selection. A comparison of genome size of cyanobacteria in relatively stable marine versus more turbulent freshwater environments corroborates our predictions, although other factors between these environments could also be responsible.}, }
@article {pmid27922269, year = {2017}, author = {Zhang, W and Cheng, Y and Du, P and Zhang, Y and Jia, H and Li, X and Wang, J and Han, N and Qiang, Y and Chen, C and Lu, J}, title = {Genomic study of the Type IVC secretion system in Clostridium difficile: understanding C. difficile evolution via horizontal gene transfer.}, journal = {Genome}, volume = {60}, number = {1}, pages = {8-16}, doi = {10.1139/gen-2016-0053}, pmid = {27922269}, issn = {1480-3321}, mesh = {Biological Evolution ; Clostridioides difficile/*physiology ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomic Islands ; *Genomics/methods ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Polymorphism, Single Nucleotide ; *Type IV Secretion Systems/genetics ; }, abstract = {Clostridium difficile, the etiological agent of Clostridium difficile infection (CDI), is a gram-positive, spore-forming bacillus that is responsible for ∼20% of antibiotic-related cases of diarrhea and nearly all cases of pseudomembranous colitis. Previous data have shown that a substantial proportion (11%) of the C. difficile genome consists of mobile genetic elements, including seven conjugative transposons. However, the mechanism underlying the formation of a mosaic genome in C. difficile is unknown. The type-IV secretion system (T4SS) is the only secretion system known to transfer DNA segments among bacteria. We searched genome databases to identify a candidate T4SS in C. difficile that could transfer DNA among different C. difficile strains. All T4SS gene clusters in C. difficile are located within genomic islands (GIs), which have variable lengths and structures and are all conjugative transposons. During the horizontal-transfer process of T4SS GIs within the C. difficile population, the excision sites were altered, resulting in different short-tandem repeat sequences among the T4SS GIs, as well as different chromosomal insertion sites and additional regions in the GIs.}, }
@article {pmid27922098, year = {2016}, author = {Koehorst, JJ and van Dam, JC and van Heck, RG and Saccenti, E and Dos Santos, VA and Suarez-Diez, M and Schaap, PJ}, title = {Comparison of 432 Pseudomonas strains through integration of genomic, functional, metabolic and expression data.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {38699}, pmid = {27922098}, issn = {2045-2322}, mesh = {*Computational Biology/methods ; *Energy Metabolism ; *Gene Expression Regulation, Bacterial ; *Genome, Bacterial ; *Genomics/methods ; Humans ; Molecular Sequence Annotation ; Phylogeny ; Pseudomonas/classification/*genetics/*metabolism ; Workflow ; }, abstract = {Pseudomonas is a highly versatile genus containing species that can be harmful to humans and plants while others are widely used for bioengineering and bioremediation. We analysed 432 sequenced Pseudomonas strains by integrating results from a large scale functional comparison using protein domains with data from six metabolic models, nearly a thousand transcriptome measurements and four large scale transposon mutagenesis experiments. Through heterogeneous data integration we linked gene essentiality, persistence and expression variability. The pan-genome of Pseudomonas is closed indicating a limited role of horizontal gene transfer in the evolutionary history of this genus. A large fraction of essential genes are highly persistent, still non essential genes represent a considerable fraction of the core-genome. Our results emphasize the power of integrating large scale comparative functional genomics with heterogeneous data for exploring bacterial diversity and versatility.}, }
@article {pmid27920384, year = {2017}, author = {Hiltunen, T and Virta, M and Laine, AL}, title = {Antibiotic resistance in the wild: an eco-evolutionary perspective.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {372}, number = {1712}, pages = {}, pmid = {27920384}, issn = {1471-2970}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/drug effects/*genetics ; *Biological Evolution ; *Drug Resistance, Microbial ; Evolution, Molecular ; }, abstract = {The legacy of the use and misuse of antibiotics in recent decades has left us with a global public health crisis: antibiotic-resistant bacteria are on the rise, making it harder to treat infections. At the same time, evolution of antibiotic resistance is probably the best-documented case of contemporary evolution. To date, research on antibiotic resistance has largely ignored the complexity of interactions that bacteria engage in. However, in natural populations, bacteria interact with other species; for example, competition and grazing are import interactions influencing bacterial population dynamics. Furthermore, antibiotic leakage to natural environments can radically alter bacterial communities. Overall, we argue that eco-evolutionary feedback loops in microbial communities can be modified by residual antibiotics and evolution of antibiotic resistance. The aim of this review is to connect some of the well-established key concepts in evolutionary biology and recent advances in the study of eco-evolutionary dynamics to research on antibiotic resistance. We also identify some key knowledge gaps related to eco-evolutionary dynamics of antibiotic resistance, and review some of the recent technical advantages in molecular microbiology that offer new opportunities for tackling these questions. Finally, we argue that using the full potential of evolutionary theory and active communication across the different fields is needed for solving this global crisis more efficiently.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'.}, }
@article {pmid27919802, year = {2017}, author = {Jia, B and Jia, X and Kim, KH and Jeon, CO}, title = {Integrative view of 2-oxoglutarate/Fe(II)-dependent oxygenase diversity and functions in bacteria.}, journal = {Biochimica et biophysica acta. General subjects}, volume = {1861}, number = {2}, pages = {323-334}, doi = {10.1016/j.bbagen.2016.12.001}, pmid = {27919802}, issn = {0304-4165}, mesh = {Bacteria/*metabolism ; Binding Sites/physiology ; Catalysis ; Computational Biology/methods ; Ferrous Compounds/*metabolism ; Ketoglutaric Acids/*metabolism ; Oxidation-Reduction ; Oxygenases/*metabolism ; Peroxides/metabolism ; Peroxiredoxins/metabolism ; Protein Domains ; Sequence Homology, Amino Acid ; Tyrosine/metabolism ; }, abstract = {BACKGROUND: The 2-oxoglutarate/Fe(II)-dependent oxygenase (2OG oxygenase) superfamily is extremely diverse and includes enzymes responsible for protein modification, DNA and mRNA repair, and synthesis of secondary metabolites.<br><br>METHODS: To investigate the evolutionary relationship and make functional inferences within this remarkably diverse superfamily in bacteria, we used a protein sequence similarity network and other bioinformatics tools to analyze the bacterial proteins in the superfamily.<br><br>RESULTS: The network based on experimentally characterized 2OG oxygenases reflects functional clustering. Networks based on all of the bacterial 2OG oxygenases from the Interpro database indicate that only few proteins in this superfamily are functionally defined. The uneven distribution of the enzymes supports the hypothesis that horizontal gene transfer plays an important role in 2OG oxygenase evolution. A hydrophobic tyrosine residue binding the primary substrates at the N-termini is conserved. At the C-termini, the iron-binding, oxoglutarate-binding, and hydrophobic motifs are conserved and coevolved. Considering the proteins in the family are largely unexplored, we annotated them by the Pfam database and hundreds of novel and multi-domain proteins are discovered. Among them, a two-domain protein containing an N-terminal peroxiredoxin domain and a C-terminal 2OG oxygenase domain was characterized enzymatically. The results show that the enzyme could catalyze the reduction of peroxide using 2-oxoglutarate as an electron donor.<br><br>CONCLUSIONS: Our observations suggest relatively low evolutionary pressure on the bacterial 2OG oxygenases and a straightforward electron transfer pathway catalyzed by the two-domain 2OG oxygenase.<br><br>GENERAL SIGNIFICANCE: This work enables an expanded understanding of the diversity, evolution, and functions of bacterial 2OG oxygenases.}, }
@article {pmid27917155, year = {2016}, author = {Cardenas, JP and Quatrini, R and Holmes, DS}, title = {Aerobic Lineage of the Oxidative Stress Response Protein Rubrerythrin Emerged in an Ancient Microaerobic, (Hyper)Thermophilic Environment.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1822}, pmid = {27917155}, issn = {1664-302X}, abstract = {Rubrerythrins (RBRs) are non-heme di-iron proteins belonging to the ferritin-like superfamily. They are involved in oxidative stress defense as peroxide scavengers in a wide range of organisms. The vast majority of RBRs, including classical forms of this protein, contain a C-terminal rubredoxin-like domain involved in electron transport that is used during catalysis in anaerobic conditions. Rubredoxin is an ancient and large protein family of short length (<100 residues) that contains a Fe-S center involved in electron transfer. However, functional forms of the enzyme lacking the rubredoxin-like domain have been reported (e.g., sulerythrin and ferriperoxin). In this study, phylogenomic evidence is presented that suggests that a complete lineage of rubrerythrins, lacking the rubredoxin-like domain, arose in an ancient microaerobic and (hyper)thermophilic environments in the ancestors of the Archaea Thermoproteales and Sulfolobales. This lineage (termed the "aerobic-type" lineage) subsequently evolved to become adapted to environments with progressively lower temperatures and higher oxygen concentrations via the acquisition of two co-localized genes, termed DUF3501 and RFO, encoding a conserved protein of unknown function and a predicted Fe-S oxidoreductase, respectively. Proposed Horizontal Gene Transfer events from these archaeal ancestors to Bacteria expanded the opportunities for further evolution of this RBR including adaption to lower temperatures. The second lineage (termed the cyanobacterial lineage) is proposed to have evolved in cyanobacterial ancestors, maybe in direct response to the production of oxygen via oxygenic photosynthesis during the Great Oxygen Event (GOE). It is hypothesized that both lineages of RBR emerged in a largely anaerobic world with "whiffs" of oxygen and that their subsequent independent evolutionary trajectories allowed microorganisms to transition from this anaerobic world to an aerobic one.}, }
@article {pmid27916622, year = {2017}, author = {Oliva, M and Monno, R and D'Addabbo, P and Pesole, G and Dionisi, AM and Scrascia, M and Chiara, M and Horner, DS and Manzari, C and Luzzi, I and Calia, C and D'Erchia, AM and Pazzani, C}, title = {A novel group of IncQ1 plasmids conferring multidrug resistance.}, journal = {Plasmid}, volume = {89}, number = {}, pages = {22-26}, doi = {10.1016/j.plasmid.2016.11.005}, pmid = {27916622}, issn = {1095-9890}, mesh = {Anti-Bacterial Agents/pharmacology ; Antiporters/genetics ; Bacterial Proteins/genetics ; Computational Biology/methods ; Conjugation, Genetic ; *Drug Resistance, Multiple, Bacterial ; Gene Order ; Gene Transfer, Horizontal ; Genes, Bacterial ; Microbial Sensitivity Tests ; Plasmids/*genetics ; Salmonella typhimurium/drug effects/genetics ; Tetracycline Resistance/genetics ; }, abstract = {The IncQ is a group of non-conjugative but mobilisable plasmids that are found and stably maintained in a wide range of bacteria contributing to the spread of antimicrobial resistance genes and to the insurgence of multidrug resistant bacteria. Here we report the identification, in clinical Salmonella Typhimurium strains, of an IncQ1 plasmid (pNUC) which confers resistance to sulfamethoxazole, streptomycin and tetracycline through the presence of sul2, strAB and tetA genes, respectively. pNUC was detected in five multidrug resistant S. Typhimurium strains collected in Southern Italy from various hospitals and years of isolation. Bioinformatics analyses highlighted the presence of pNUC-like plasmids in pathogenic bacteria of various Enterobacteriaceae genera or species. Taken as a whole, these plasmids constitute a novel group of IncQ1 plasmids that might have originated through recombination events between a tetR-tetA gene cluster (possibly derived from a Tn1721) and a recipient IncQ1 plasmid related to RSF1010. Our findings raise concerns regarding the possible contribution of the newly identified group of IncQ1 plasmids to the spread of tetracycline resistance.}, }
@article {pmid27915286, year = {2017}, author = {Zinga, MK and Jaiswal, SK and Dakora, FD}, title = {Presence of diverse rhizobial communities responsible for nodulation of common bean (Phaseolus vulgaris) in South African and Mozambican soils.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {2}, pages = {}, doi = {10.1093/femsec/fiw236}, pmid = {27915286}, issn = {1574-6941}, mesh = {Africa, Southern ; DNA, Bacterial/genetics ; Molecular Sequence Data ; Mozambique ; Phaseolus/*microbiology/physiology ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Rhizobium/classification/*genetics ; Sequence Analysis, DNA ; Soil ; *Soil Microbiology ; South Africa ; Symbiosis ; }, abstract = {The diversity and phylogeny of root-nodule bacteria isolated from common bean grown in Mozambique and different provinces of South Africa was studied by restriction fragment length polymorphism (RFLP) and phylogenetic analysis. The combined restriction banding pattern of 16S rRNA and nifH profile-generated dendrogram grouped all test isolates into four major clusters with XXI restriction groups and three clusters with VIII restriction groups. Location-based clustering was observed with the 16S rRNA RFLP analysis. Phylogenetic analysis of 16S rRNA, glnII, gyrB and gltA sequences showed that common bean was nodulated specifically by Rhizobium etli in Mozambican soils, and by a diverse group of Rhizobium species in South African soils (e.g. R. etli, R. phaseoli, R. sophoriradicis, R. leucaenae and novel group of Rhizobium spp.). Isolates from the Eastern Cape region of South Africa were dominated by R. leucaenae Overall, the results suggested high nodulation promiscuity of common bean grown in Southern Africa. The nifH and nodC sequence analysis classified all the test isolates with R. etli group, except for isolates TUTPVSA117, TUTPVSA114 and TUTPVSA110 which delineated with R. tropici group. This finding was inconsistent with the phylogram of the housekeeping genes, and is probably an indication of horizontal gene transfer among the Rhizobium isolates tested.}, }
@article {pmid27915087, year = {2017}, author = {Santos, C and Ramalheira, E and Da Silva, G and Mendo, S}, title = {Genetically unrelated multidrug- and carbapenem-resistant Citrobacter freundii detected in outpatients admitted to a Portuguese hospital.}, journal = {Journal of global antimicrobial resistance}, volume = {8}, number = {}, pages = {18-22}, doi = {10.1016/j.jgar.2016.09.010}, pmid = {27915087}, issn = {2213-7173}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics/*metabolism ; Carbapenems/*pharmacology ; Citrobacter freundii/drug effects/enzymology/*genetics/*isolation &amp; purification ; DNA Fingerprinting ; Disk Diffusion Antimicrobial Tests ; Drug Resistance, Multiple, Bacterial/drug effects/*genetics ; Enterobacteriaceae/genetics ; Enterobacteriaceae Infections/microbiology ; Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Hospitals ; Humans ; Integrons/genetics ; Interspersed Repetitive Sequences/genetics ; Molecular Epidemiology ; Molecular Typing ; Outpatients ; Portugal ; RNA, Ribosomal, 16S/genetics ; beta-Lactamases/genetics ; }, abstract = {OBJECTIVES: Non-clonal, carbapenem- and multidrug-resistant Citrobacter freundii isolates were collected from unrelated outpatients admitted to a Portuguese hospital emergency department. One patient lived in a nursing home and was never hospitalised, whereas the other patient was repeatedly hospitalised in this hospital. The aim of this study was to unveil the molecular mechanisms associated with the carbapenem resistance of these isolates and to assess its potential dissemination.<br><br>METHODS: Isolate identification was performed by VITEK[&#xae;]2 and was confirmed by 16S rDNA sequencing. The clonal relationship of the isolates was evaluated by repetitive element palindromic PCR (rep-PCR). Antibiotic susceptibility was determined using the automatic VITEK[&#xae;]2 AES system and disk diffusion assay. &#x3b2;-Lactamases, porins and mobile genetic elements were characterised by PCR and sequencing. Pulsed-field gel electrophoresis (PFGE) and Southern blot hybridisation were used to determine the genetic location of integrons, and their transferability was tested by conjugation.<br><br>RESULTS: No genetic relatedness was found, suggesting different origins of the isolates. In isolate Cf254 a VIM-2 carbapenemase integrated in In58 was detected, located in a high-frequency conjugative IncL/M plasmid that also carried CTX-M-15 and CMY-39 genes. VIM-1 in isolate Cf872 was chromosomal. This is the first description in Portugal of VIM carbapenemases in C. freundii. Loss/alteration of porins was also detected.<br><br>CONCLUSIONS: Emergence of carbapenem-resistant Enterobacteria is not confined to the nosocomial environment. Community-acquired strains appear to be in circulation between inpatients and outpatients, spreading carbapenem resistance genes by horizontal gene transfer.}, }
@article {pmid27914300, year = {2017}, author = {Alotaibi, M and Reyes, BD and Le, T and Luong, P and Valafar, F and Metzger, RP and Fogel, GB and Hecht, D}, title = {Structure-based analysis of Bacilli and plasmid dihydrofolate reductase evolution.}, journal = {Journal of molecular graphics &amp; modelling}, volume = {71}, number = {}, pages = {135-153}, pmid = {27914300}, issn = {1873-4243}, support = {SC3 GM100791/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence/genetics ; Bacillus/chemistry/genetics ; Binding Sites ; Catalytic Domain/genetics ; Crystallography, X-Ray ; *Evolution, Molecular ; Models, Molecular ; Phylogeny ; Plasmids/chemistry/genetics ; *Protein Conformation ; Protein Structure, Secondary ; Sequence Alignment ; *Structural Homology, Protein ; Tetrahydrofolate Dehydrogenase/*chemistry/metabolism ; }, abstract = {Dihydrofolate reductase (DHFR), a key enzyme in tetrahydrofolate-mediated biosynthetic pathways, has a structural motif known to be highly conserved over a wide range of organisms. Given its critical role in purine and amino acid synthesis, DHFR is a well established therapeutic target for treating a wide range of prokaryotic and eukaryotic infections as well as certain types of cancer. Here we present a structural-based computer analysis of bacterial (Bacilli) and plasmid DHFR evolution. We generated a structure-based sequence alignment using 7 wild-type DHFR x-ray crystal structures obtained from the RCSB Protein Data Bank and 350 chromosomal and plasmid homology models we generated from sequences obtained from the NCBI Protein Database. We used these alignments to compare active site and non-active site conservation in terms of amino acid residues, secondary structure and amino acid residue class. With respect to amino acid sequences and residue classes, active-site positions in both plasmid and chromosomal DHFR are significantly more conserved than non-active site positions. Secondary structure conservation was similar for active site and non-active site positions. Plasmid-encoded DHFR proteins have greater degree of sequence and residue class conservation, particularly in sequence positions associated with a network of concerted protein motions, than chromosomal-encoded DHFR proteins. These structure-based were used to build DHFR specific phylogenetic trees from which evidence for horizontal gene transfer was identified.}, }
@article {pmid27913675, year = {2016}, author = {Piepenbrink, KH and Sundberg, EJ}, title = {Motility and adhesion through type IV pili in Gram-positive bacteria.}, journal = {Biochemical Society transactions}, volume = {44}, number = {6}, pages = {1659-1666}, pmid = {27913675}, issn = {1470-8752}, support = {F32 AI110045/AI/NIAID NIH HHS/United States ; K22 AI123467/AI/NIAID NIH HHS/United States ; R01 AI114902/AI/NIAID NIH HHS/United States ; T32 AI095190/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Adhesion/*physiology ; Fimbriae Proteins/chemistry/genetics/physiology ; Fimbriae, Bacterial/*physiology ; Gram-Positive Bacteria/classification/genetics/*physiology ; Models, Molecular ; Movement/physiology ; Mutation ; Protein Domains ; Species Specificity ; }, abstract = {Type IV pili are hair-like bacterial surface appendages that play a role in diverse processes such as cellular adhesion, colonization, twitching motility, biofilm formation, and horizontal gene transfer. These extracellular fibers are composed exclusively or primarily of many copies of one or more pilin proteins, tightly packed in a helix so that the highly hydrophobic amino-terminus of the pilin is buried in the pilus core. Type IV pili have been characterized extensively in Gram-negative bacteria, and recent advances in high-throughput genomic sequencing have revealed that they are also widespread in Gram-positive bacteria. Here, we review the current state of knowledge of type IV pilus systems in Gram-positive bacterial species and discuss them in the broader context of eubacterial type IV pili.}, }
@article {pmid27912842, year = {2016}, author = {Potter, RF and D'Souza, AW and Dantas, G}, title = {The rapid spread of carbapenem-resistant Enterobacteriaceae.}, journal = {Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy}, volume = {29}, number = {}, pages = {30-46}, pmid = {27912842}, issn = {1532-2084}, support = {R01 GM099538/GM/NIGMS NIH HHS/United States ; T32 GM007067/GM/NIGMS NIH HHS/United States ; T32 GM007200/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Proteins/classification/*genetics/metabolism ; Carbapenem-Resistant Enterobacteriaceae/*drug effects/enzymology/genetics/pathogenicity ; Carbapenems/*pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Drug Therapy, Combination ; Enterobacteriaceae Infections/drug therapy/epidemiology/microbiology/*transmission ; Epidemiological Monitoring ; Gene Expression ; Humans ; Isoenzymes/classification/genetics/metabolism ; Plasmids/chemistry/metabolism ; Replicon ; beta-Lactam Resistance/*genetics ; beta-Lactamase Inhibitors/*pharmacology ; beta-Lactamases/classification/*genetics/metabolism ; }, abstract = {Carbapenems, our one-time silver bullet for multidrug resistant bacterial infections, are now threatened by widespread dissemination of carbapenem-resistant Enterobacteriaceae (CRE). Successful expansion of Enterobacteriaceae clonal groups and frequent horizontal gene transfer of carbapenemase expressing plasmids are causing increasing carbapenem resistance. Recent advances in genetic and phenotypic detection facilitate global surveillance of CRE diversity and prevalence. In particular, whole genome sequencing enabled efficient tracking, annotation, and study of genetic elements colocalized with carbapenemase genes on chromosomes and on plasmids. Improved characterization helps detail the co-occurrence of other antibiotic resistance genes in CRE isolates and helps identify pan-drug resistance mechanisms. The novel β-lactamase inhibitor, avibactam, combined with ceftazidime or aztreonam, is a promising CRE treatment compared to current colistin or tigecycline regimens. To halt increasing CRE-associated morbidity and mortality, we must continue quality, cooperative monitoring and urgently investigate novel treatments.}, }
@article {pmid27908230, year = {2016}, author = {Konstantinov, YM and Dietrich, A and Weber-Lotfi, F and Ibrahim, N and Klimenko, ES and Tarasenko, VI and Bolotova, TA and Koulintchenko, MV}, title = {DNA Import into Mitochondria.}, journal = {Biochemistry. Biokhimiia}, volume = {81}, number = {10}, pages = {1044-1056}, doi = {10.1134/S0006297916100035}, pmid = {27908230}, issn = {1608-3040}, mesh = {Animals ; Cell Nucleus/genetics/metabolism ; *DNA, Plant/genetics/metabolism ; Humans ; *Mitochondria/genetics/metabolism ; Mitochondrial Membranes/metabolism ; *Plants/genetics/metabolism ; *RNA, Plant/genetics/metabolism ; *RNA, Transfer/genetics/metabolism ; }, abstract = {In recent decades, it has become evident that the condition for normal functioning of mitochondria in higher eukaryotes is the presence of membrane transport systems of macromolecules (proteins and nucleic acids). Natural competence of the mitochondria in plants, animals, and yeasts to actively uptake DNA may be directly related to horizontal gene transfer into these organelles occurring at much higher rate compared to the nuclear and chloroplast genomes. However, in contrast with import of proteins and tRNAs, little is known about the biological role and molecular mechanism underlying import of DNA into eukaryotic mitochondria. In this review, we discuss current state of investigations in this area, particularly specificity of DNA import into mitochondria and its features in plants, animals, and yeasts; a tentative mechanism of DNA import across the mitochondrial outer and inner membranes; experimental data evidencing several existing, but not yet fully understood mechanisms of DNA transfer into mitochondria. Currently available data regarding transport of informational macromolecules (DNA, RNA, and proteins) into the mitochondria do not rule out that the mechanism of protein and tRNA import as well as tRNA and DNA import into the mitochondria may partially overlap.}, }
@article {pmid27906133, year = {2016}, author = {Yurchenko, T and Ševčíková, T and Strnad, H and Butenko, A and Eliáš, M}, title = {The plastid genome of some eustigmatophyte algae harbours a bacteria-derived six-gene cluster for biosynthesis of a novel secondary metabolite.}, journal = {Open biology}, volume = {6}, number = {11}, pages = {}, pmid = {27906133}, issn = {2046-2441}, mesh = {DNA, Algal/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Plastid ; Molecular Sequence Annotation ; Multigene Family ; Sequence Analysis, DNA/*methods ; Stramenopiles/*genetics ; }, abstract = {Acquisition of genes by plastid genomes (plastomes) via horizontal gene transfer (HGT) seems to be a rare phenomenon. Here, we report an interesting case of HGT revealed by sequencing the plastomes of the eustigmatophyte algae Monodopsis sp. MarTras21 and Vischeria sp. CAUP Q 202. These plastomes proved to harbour a unique cluster of six genes, most probably acquired from a bacterium of the phylum Bacteroidetes, with homologues in various bacteria, typically organized in a conserved uncharacterized putative operon. Sequence analyses of the six proteins encoded by the operon yielded the following annotation for them: (i) a novel family without discernible homologues; (ii) a new family within the superfamily of metallo-dependent hydrolases; (iii) a novel subgroup of the UbiA superfamily of prenyl transferases; (iv) a new clade within the sugar phosphate cyclase superfamily; (v) a new family within the xylose isomerase-like superfamily; and (vi) a hydrolase for a phosphate moiety-containing substrate. We suggest that the operon encodes enzymes of a pathway synthesizing an isoprenoid-cyclitol-derived compound, possibly an antimicrobial or other protective substance. To the best of our knowledge, this is the first report of an expansion of the metabolic capacity of a plastid mediated by HGT into the plastid genome.}, }
@article {pmid27905116, year = {2017}, author = {Sanchez-Puerta, MV and García, LE and Wohlfeiler, J and Ceriotti, LF}, title = {Unparalleled replacement of native mitochondrial genes by foreign homologs in a holoparasitic plant.}, journal = {The New phytologist}, volume = {214}, number = {1}, pages = {376-387}, doi = {10.1111/nph.14361}, pmid = {27905116}, issn = {1469-8137}, mesh = {Base Sequence ; Chromosome Mapping ; DNA, Mitochondrial/genetics ; Fatty Acids, Unsaturated/genetics ; Gene Transfer, Horizontal ; *Genes, Mitochondrial ; Genes, Plant ; Genetic Speciation ; Genome, Mitochondrial ; Open Reading Frames/genetics ; Phylogeny ; Plants/*genetics ; Selection, Genetic ; *Sequence Homology, Nucleic Acid ; }, abstract = {Horizontal gene transfer (HGT) among flowering plant mitochondria occurs frequently and, in most cases, leads to nonfunctional transgenes in the recipient genome. Parasitic plants are particularly prone to this phenomenon, but their mitochondrial genomes (mtDNA) have been largely unexplored. We undertook a large-scale mitochondrial genomic study of the holoparasitic plant Lophophytum mirabile (Balanophoraceae). Comprehensive phylogenetic analyses were performed to address the frequency, origin, and impact of HGT. The sequencing of the complete mtDNA of L. mirabile revealed the unprecedented acquisition of host-derived mitochondrial genes, representing 80% of the protein-coding gene content. All but two of these foreign genes replaced the native homologs and are probably functional in energy metabolism. The genome consists of 54 circular-mapping chromosomes, 25 of which carry no intact genes. The likely functional replacement of up to 26 genes in L. mirabile represents a stunning example of the potential effect of rampant HGT on plant mitochondria. The use of host-derived genes may have a positive effect on the host-parasite relationship, but could also be the result of nonadaptive forces.}, }
@article {pmid27904954, year = {2017}, author = {Hellmuth, M and Stadler, PF and Wieseke, N}, title = {The mathematics of xenology: di-cographs, symbolic ultrametrics, 2-structures and tree-representable systems of binary relations.}, journal = {Journal of mathematical biology}, volume = {75}, number = {1}, pages = {199-237}, pmid = {27904954}, issn = {1432-1416}, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal ; *Models, Biological ; *Phylogeny ; }, abstract = {The concepts of orthology, paralogy, and xenology play a key role in molecular evolution. Orthology and paralogy distinguish whether a pair of genes originated by speciation or duplication. The corresponding binary relations on a set of genes form complementary cographs. Allowing more than two types of ancestral event types leads to symmetric symbolic ultrametrics. Horizontal gene transfer, which leads to xenologous gene pairs, however, is inherent asymmetric since one offspring copy "jumps" into another genome, while the other continues to be inherited vertically. We therefore explore here the mathematical structure of the non-symmetric generalization of symbolic ultrametrics. Our main results tie non-symmetric ultrametrics together with di-cographs (the directed generalization of cographs), so-called uniformly non-prime ([Formula: see text]) 2-structures, and hierarchical structures on the set of strong modules. This yields a characterization of relation structures that can be explained in terms of trees and types of ancestral events. This framework accommodates a horizontal-transfer relation in terms of an ancestral event and thus, is slightly different from the the most commonly used definition of xenology. As a first step towards a practical use, we present a simple polynomial-time recognition algorithm of [Formula: see text] 2-structures and investigate the computational complexity of several types of editing problems for [Formula: see text] 2-structures. We show, finally that these NP-complete problems can be solved exactly as Integer Linear Programs.}, }
@article {pmid27902886, year = {2017}, author = {Nývltová, E and Šut'ák, R and Žárský, V and Harant, K and Hrdý, I and Tachezy, J}, title = {Lateral gene transfer of p-cresol- and indole-producing enzymes from environmental bacteria to Mastigamoeba balamuthi.}, journal = {Environmental microbiology}, volume = {19}, number = {3}, pages = {1091-1102}, doi = {10.1111/1462-2920.13636}, pmid = {27902886}, issn = {1462-2920}, mesh = {Animals ; Archamoebae/*genetics ; Bacteria/genetics ; Carboxy-Lyases ; Cresols/*metabolism ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Indoles/*metabolism ; Operon ; S-Adenosylmethionine/metabolism ; }, abstract = {p-Cresol and indole are volatile biologically active products of the bacterial degradation of tyrosine and tryptophan respectively. They are typically produced by bacteria in animal intestines, soil and various sediments. Here, we demonstrate that the free-living eukaryote Mastigamoeba balamuthi and its pathogenic relative Entamoeba histolytica produce significant amounts of indole via tryptophanase activity. Unexpectedly, M. balamuthi also produces p-cresol in concentrations that are bacteriostatic to non-p-cresol-producing bacteria. The ability of M. balamuthi to produce p-cresol, which has not previously been observed in any eukaryotic microbe, was gained due to the lateral acquisition of a bacterial gene for 4-hydroxyphenylacetate decarboxylase (HPAD). In bacteria, the genes for HPAD and the S-adenosylmethionine-dependent activating enzyme (AE) are present in a common operon. In M. balamuthi, HPAD displays a unique fusion with the AE that suggests the operon-mediated transfer of genes from a bacterial donor. We also clarified that the tyrosine-to-4-hydroxyphenylacetate conversion proceeds via the Ehrlich pathway. The acquisition of the bacterial HPAD gene may provide M. balamuthi a competitive advantage over other microflora in its native habitat.}, }
@article {pmid27902329, year = {2016}, author = {Anand, T and Bera, BC and Vaid, RK and Barua, S and Riyesh, T and Virmani, N and Hussain, M and Singh, RK and Tripathi, BN}, title = {Abundance of antibiotic resistance genes in environmental bacteriophages.}, journal = {The Journal of general virology}, volume = {97}, number = {12}, pages = {3458-3466}, doi = {10.1099/jgv.0.000639}, pmid = {27902329}, issn = {1465-2099}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics/metabolism/*virology ; Bacteriophages/*genetics/isolation &amp; purification/metabolism ; *Drug Resistance, Bacterial ; Environmental Microbiology ; Gene Transfer, Horizontal ; Viral Proteins/*genetics/metabolism ; }, abstract = {The ecosystem is continuously exposed to a wide variety of antimicrobials through waste effluents, agricultural run-offs and animal-related and anthropogenic activities, which contribute to the spread of antibiotic resistance genes (ARGs). The contamination of ecosystems with ARGs may create increased opportunities for their transfer to naive microbes and eventually lead to entry into the human food chain. Transduction is a significant mechanism of horizontal gene transfer in natural environments, which has traditionally been underestimated as compared to transformation. We explored the presence of ARGs in environmental bacteriophages in order to recognize their contribution in the spread of ARGs in environmental settings. Bacteriophages were isolated against environmental bacterial isolates, purified and bulk cultured. They were characterized, and detection of ARG and intI genes including blaTEM, blaOXA-2, intI1, intI2, intI3, tetA and tetW was carried out by PCR. This study revealed the presence of various genes [tetA (12.7 %), intI1 (10.9 %), intI2 (10.9 %), intI3 (9.1 %), tetW (9.1 %) and blaOXA-2 (3.6 %)] and blaTEM in a significantly higher proportion (30.9 %). blaSHV, blaOXA-1, tetO, tetB, tetG, tetM and tetS were not detected in any of the phages. Soil phages were the most versatile in terms of ARG carriage. Also, the relative abundance of tetA differed significantly vis-à-vis source. The phages from organized farms showed varied ARGs as compared to the unorganized sector, although blaTEM ARG incidences did not differ significantly. The study reflects on the role of phages in dissemination of ARGs in environmental reservoirs, which may provide an early warning system for future clinically relevant resistance mechanisms.}, }
@article {pmid27901648, year = {2016}, author = {Wong, TY and Kuo, J}, title = {A new drug design strategy: Killing drug resistant bacteria by deactivating their hypothetical genes.}, journal = {Journal of environmental science and health. Part C, Environmental carcinogenesis &amp; ecotoxicology reviews}, volume = {34}, number = {4}, pages = {276-292}, doi = {10.1080/10590501.2016.1236605}, pmid = {27901648}, issn = {1532-4095}, mesh = {*Drug Design ; Drug Resistance, Bacterial/*genetics ; Escherichia coli K12/*genetics ; Gene Transfer, Horizontal/physiology ; Genes, Bacterial/physiology ; Genome, Bacterial/*physiology ; Humans ; }, abstract = {Despite that a bacterial genome is complicated by large numbers of horizontally transferred (HT) genes and function unknown hypothetical (FUN) genes, the Genic-Transcriptional-Stop-Signals-Ratio (TSSR) of a genome shows that HT and FUN genes are complementary to all other genes in the genome. When HT or certain FUN genes are omitted from the Escherichia coli K-12 genome, its Genomic-TSSR value becomes totally incomparable to other E. coli strains. The Genic-TSSR correlation tree of a pathogen shows that some FUN genes would form a unique cluster. Removing these genes by site-specific mutation or gene-knockout should lead to the demise of this pathogen.}, }
@article {pmid27899587, year = {2017}, author = {Woodard, LE and Downes, LM and Lee, YC and Kaja, A and Terefe, ES and Wilson, MH}, title = {Temporal self-regulation of transposition through host-independent transposase rodlet formation.}, journal = {Nucleic acids research}, volume = {45}, number = {1}, pages = {353-366}, pmid = {27899587}, issn = {1362-4962}, support = {I01 BX002190/BX/BLRD VA/United States ; IK2 BX002797/BX/BLRD VA/United States ; R01 DK093660/DK/NIDDK NIH HHS/United States ; R25 GM069234/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *DNA Transposable Elements ; Female ; *Gene Expression Regulation ; Genes, Reporter ; HEK293 Cells ; HeLa Cells ; Humans ; Insect Proteins/*genetics/metabolism ; Luciferases/genetics/metabolism ; Male ; Mice ; Optical Imaging ; Time-Lapse Imaging ; Transposases/*genetics/metabolism ; Tribolium ; }, abstract = {Transposons are highly abundant in eukaryotic genomes, but their mobilization must be finely tuned to maintain host organism fitness and allow for transposon propagation. Forty percent of the human genome is comprised of transposable element sequences, and the most abundant cut-and-paste transposons are from the hAT superfamily. We found that the hAT transposase TcBuster from Tribolium castaneum formed filamentous structures, or rodlets, in human tissue culture cells, after gene transfer to adult mice, and ex vivo in cell-free conditions, indicating that host co-factors or cellular structures were not required for rodlet formation. Time-lapsed imaging of GFP-laced rodlets in human cells revealed that they formed quickly in a dynamic process involving fusion and fission. We delayed the availability of the transposon DNA and found that transposition declined after transposase concentrations became high enough for visible transposase rodlets to appear. In combination with earlier findings for maize Ac elements, these results give insight into transposase overproduction inhibition by demonstrating that the appearance of transposase protein structures and the end of active transposition are simultaneous, an effect with implications for genetic engineering and horizontal gene transfer.}, }
@article {pmid27896732, year = {2017}, author = {de Oliveira Martins, L and Posada, D}, title = {Species Tree Estimation from Genome-Wide Data with guenomu.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1525}, number = {}, pages = {461-478}, doi = {10.1007/978-1-4939-6622-6_18}, pmid = {27896732}, issn = {1940-6029}, mesh = {Algorithms ; Bayes Theorem ; Computational Biology/*methods ; Evolution, Molecular ; Gene Duplication/genetics ; Gene Transfer, Horizontal/genetics ; *Phylogeny ; }, abstract = {The history of particular genes and that of the species that carry them can be different for a variety of reasons. In particular, gene trees and species trees can differ due to well-known evolutionary processes such as gene duplication and loss, lateral gene transfer, or incomplete lineage sorting. Species tree reconstruction methods have been developed to take this incongruence into account; these can be divided grossly into supertree and supermatrix approaches. Here we introduce a new Bayesian hierarchical model that we have recently developed and implemented in the program guenomu. The new model considers multiple sources of gene tree/species tree disagreement. Guenomu takes as input posterior distributions of unrooted gene tree topologies for multiple gene families, in order to estimate the posterior distribution of rooted species tree topologies.}, }
@article {pmid27896730, year = {2017}, author = {Chan, CX and Beiko, RG and Ragan, MA}, title = {Scaling Up the Phylogenetic Detection of Lateral Gene Transfer Events.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1525}, number = {}, pages = {421-432}, doi = {10.1007/978-1-4939-6622-6_16}, pmid = {27896730}, issn = {1940-6029}, support = {//CIHR/Canada ; }, mesh = {Algorithms ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genomics ; Phylogeny ; }, abstract = {Lateral genetic transfer (LGT) is the process by which genetic material moves between organisms (and viruses) in the biosphere. Among the many approaches developed for the inference of LGT events from DNA sequence data, methods based on the comparison of phylogenetic trees remain the gold standard for many types of problem. Identifying LGT events from sequenced genomes typically involves a series of steps in which homologous sequences are identified and aligned, phylogenetic trees are inferred, and their topologies are compared to identify unexpected or conflicting relationships. These types of approach have been used to elucidate the nature and extent of LGT and its physiological and ecological consequences throughout the Tree of Life. Advances in DNA sequencing technology have led to enormous increases in the number of sequenced genomes, including ultra-deep sampling of specific taxonomic groups and single cell-based sequencing of unculturable "microbial dark matter." Environmental shotgun sequencing enables the study of LGT among organisms that share the same habitat.This abundance of genomic data offers new opportunities for scientific discovery, but poses two key problems. As ever more genomes are generated, the assembly and annotation of each individual genome receives less scrutiny; and with so many genomes available it is tempting to include them all in a single analysis, but thousands of genomes and millions of genes can overwhelm key algorithms in the analysis pipeline. Identifying LGT events of interest therefore depends on choosing the right dataset, and on algorithms that appropriately balance speed and accuracy given the size and composition of the chosen set of genomes.}, }
@article {pmid27895636, year = {2016}, author = {Zhang, W and Ding, W and Yang, B and Tian, R and Gu, S and Luo, H and Qian, PY}, title = {Genomic and Transcriptomic Evidence for Carbohydrate Consumption among Microorganisms in a Cold Seep Brine Pool.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1825}, pmid = {27895636}, issn = {1664-302X}, abstract = {The detailed lifestyle of microorganisms in deep-sea brine environments remains largely unexplored. Using a carefully calibrated genome binning approach, we reconstructed partial to nearly-complete genomes of 51 microorganisms in biofilms from the Thuwal cold seep brine pool of the Red Sea. The recovered metagenome-assembled genomes (MAGs) belong to six different phyla: Actinobacteria, Proteobacteria, Candidatus Cloacimonetes, Candidatus Marinimicrobia, Bathyarchaeota, and Thaumarchaeota. By comparison with close relatives of these microorganisms, we identified a number of unique genes associated with organic carbon metabolism and energy generation. These genes included various glycoside hydrolases, nitrate and sulfate reductases, putative bacterial microcompartment biosynthetic clusters (BMC), and F420H2 dehydrogenases. Phylogenetic analysis suggested that the acquisition of these genes probably occurred through horizontal gene transfer (HGT). Metatranscriptomics illustrated that glycoside hydrolases are among the most highly expressed genes. Our results suggest that the microbial inhabitants are well adapted to this brine environment, and anaerobic carbohydrate consumption mediated by glycoside hydrolases and electron transport systems (ETSs) is a dominant process performed by microorganisms from various phyla within this ecosystem.}, }
@article {pmid27895624, year = {2016}, author = {MacGregor, BJ}, title = {Visualizing Evolutionary Relationships of Multidomain Proteins: An Example from Receiver (REC) Domains of Sensor Histidine Kinases in the Candidatus Maribeggiatoa str. Orange Guaymas Draft Genome.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1780}, pmid = {27895624}, issn = {1664-302X}, abstract = {For multidomain proteins, evolutionary changes may occur at the domain as well as the whole-protein level. An example is presented here, with suggestions for how such complicated relationships might be visualized. Earlier analysis of the Candidatus Maribeggiatoa str. Orange Guaymas (BOGUAY; Gammaproteobacteria) single-filament draft genome found evidence of gene exchange with the phylogenetically distant Cyanobacteria, particularly for sensory and signal transduction proteins. Because these are modular proteins, known to undergo frequent duplication, domain swapping, and horizontal gene transfer, a single domain was chosen for analysis. Recognition (REC) domains are short (~125 amino acids) and well conserved, simplifying sequence alignments and phylogenetic calculations. Over 100 of these were identified in the BOGUAY genome and found to have a wide range of inferred phylogenetic relationships. Two sets were chosen here for detailed study. One set of four BOGUAY ORFs has closest relatives among other Beggiatoaceae and Cyanobacteria. A second set of four has REC domains with more mixed affiliations, including other Beggiatoaceae, several sulfate-reducing Deltaproteobacteria and Firmicutes, magnetotactic Nitrospirae, one Shewanella and one Ferrimonas strain (both Gammaproteobacteria), and numerous Vibrio vulnificus and V. navarrensis strains (also Gammaproteobacteria). For an overview of the possible origins of the whole proteins and the surrounding genomic regions, color-coded BLASTP results were produced and displayed against cartoons showing protein domain structure of predicted genes. This is suggested as a visualization method for investigation of possible horizontally transferred regions, giving more detail than scans of DNA composition and codon usage but much faster than carrying out full phylogenetic analyses for multiple proteins. As expected, most of the predicted sensor histidine kinases investigated have two or more segments with distinct BLASTP affiliations. For the first set of BOGUAY ORFs, the flanking regions were also examined, and the results suggest they are embedded in genomic stretches with complex histories. An automated method of creating such visualizations could be generally useful; a wish list for its features is given.}, }
@article {pmid27892531, year = {2016}, author = {Suzuki, M and Shibayama, K and Yahara, K}, title = {A genome-wide association study identifies a horizontally transferred bacterial surface adhesin gene associated with antimicrobial resistant strains.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {37811}, pmid = {27892531}, issn = {2045-2322}, mesh = {Acinetobacter baumannii/drug effects/genetics ; Adhesins, Bacterial/*genetics ; Carbapenems/pharmacology ; Drug Resistance, Bacterial/drug effects/*genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Variation ; *Genome-Wide Association Study ; Nucleotide Motifs ; Phylogeny ; }, abstract = {Carbapenems are a class of last-resort antibiotics; thus, the increase in bacterial carbapenem-resistance is a serious public health threat. Acinetobacter baumannii is one of the microorganisms that can acquire carbapenem-resistance; it causes severe nosocomial infection, and is notoriously difficult to control in hospitals. Recently, a machine-learning approach was first used to analyze the genome sequences of hundreds of susceptible and resistant A. baumannii strains, including those carrying commonly acquired resistant mechanisms, to build a classifier that can predict strain resistance. A complementary approach is to explore novel genetic elements that could be associated with the antimicrobial resistance of strains, independent of known mechanisms. Therefore, we carefully selected A. baumannii strains, spanning various genotypes, from public genome databases, and conducted the first genome-wide association study (GWAS) of carbapenem resistance. We employed a recently developed method, capable of identifying any kind of genetic variation and accounting for bacterial population structure, and evaluated its effectiveness. Our study identified a surface adhesin gene that had been horizontally transferred to an ancestral branch of A. baumannii, as well as a specific region of that gene that appeared to accumulate multiple individual variations across the different branches of carbapenem-resistant A. baumannii strains.}, }
@article {pmid27892503, year = {2016}, author = {Brunel, R and Charpentier, X}, title = {Trans-translation is essential in the human pathogen Legionella pneumophila.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {37935}, pmid = {27892503}, issn = {2045-2322}, mesh = {Amoeba/microbiology ; Anti-Bacterial Agents/pharmacology ; Erythromycin/pharmacology ; Genes, Bacterial ; Humans ; Legionella pneumophila/drug effects/*genetics/growth &amp; development/*pathogenicity ; Legionnaires' Disease/microbiology ; Macrophages/microbiology ; *Protein Biosynthesis ; RNA, Bacterial ; Ribosomes/drug effects ; Rifampin/pharmacology ; }, abstract = {Trans-translation is a ubiquitous bacterial mechanism for ribosome rescue in the event of translation stalling. Although trans-translation is not essential in several bacterial species, it has been found essential for viability or virulence in a wide range of pathogens. We describe here that trans-translation is essential in the human pathogen Legionella pneumophila, the etiologic agent of Legionnaire's disease (LD), a severe form of nosocomial and community-acquired pneumonia. The ssrA gene coding for tmRNA, the key component of trans-translation, could not be deleted in L. pneumophila. To circumvent this and analyse the consequences of impaired trans-translation, we placed ssrA under the control of a chemical inducer. Phenotypes associated with the inhibition of ssrA expression include growth arrest in rich medium, hampered cell division, and hindered ability to infect eukaryotic cells (amoebae and human macrophages). LD is often associated with failure of antibiotic treatment and death (>10% of clinical cases). Decreasing tmRNA levels led to significantly higher sensitivity to ribosome-targeting antibiotics, including to erythromycin. We also detected a higher sensitivity to the transcription inhibitor rifampicin. Both antibiotics are recommended treatments for LD. Thus, interfering with trans-translation may not only halt the infection, but could also potentiate the recommended therapeutic treatments of LD.}, }
@article {pmid27890586, year = {2017}, author = {Lekunberri, I and Subirats, J and Borrego, CM and Balcázar, JL}, title = {Exploring the contribution of bacteriophages to antibiotic resistance.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {220}, number = {Pt B}, pages = {981-984}, doi = {10.1016/j.envpol.2016.11.059}, pmid = {27890586}, issn = {1873-6424}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/drug effects/*genetics ; Bacteriophages/genetics/*physiology ; Drug Resistance, Microbial/*genetics ; Feces/microbiology/virology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genes, Viral ; Genome, Viral ; Sewage/microbiology/virology ; Water Microbiology ; }, abstract = {Bacteriophages (phages) are the most abundant and diverse biological entities in our planet. They infect susceptible bacterial hosts into which they either multiply or persist. In the latter case, phages can confer new functions to their hosts as a result of gene transfer, thus contributing to their adaptation (short-term) and evolution (long-term). In this regard, the role of phages on the dissemination of antibiotic resistance genes (ARGs) among bacterial hosts in natural environments has not yet been clearly resolved. Here, we carry out a comprehensive analysis of thirty-three viromes from different habitats to investigate whether phages harbor ARGs. Our results demonstrate that while human-associated viromes do not or rarely carry ARGs, viromes from non-human sources (e.g. pig feces, raw sewage, and freshwater and marine environments) contain a large reservoir of ARGs, thus pointing out that phages could play a part on the spread of antibiotic resistance. Given this, the role of phages should not be underestimated and it should be considered when designing strategies to tackle the global crisis of antibiotic resistance.}, }
@article {pmid27889804, year = {2017}, author = {Furukawa, R and Nakagawa, M and Kuroyanagi, T and Yokobori, SI and Yamagishi, A}, title = {Quest for Ancestors of Eukaryal Cells Based on Phylogenetic Analyses of Aminoacyl-tRNA Synthetases.}, journal = {Journal of molecular evolution}, volume = {84}, number = {1}, pages = {51-66}, pmid = {27889804}, issn = {1432-1432}, mesh = {Amino Acid Sequence/genetics ; Amino Acyl-tRNA Synthetases/*genetics ; Archaea/genetics ; Bacteria/genetics ; Base Sequence/genetics ; Biological Evolution ; Computer Simulation ; Eukaryota/*genetics ; Eukaryotic Cells ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Models, Genetic ; Phylogeny ; Sequence Alignment/methods ; }, abstract = {The three-domain phylogenetic system of life has been challenged, particularly with regard to the position of Eukarya. The recent increase of known genome sequences has allowed phylogenetic analyses of all extant organisms using concatenated sequence alignment of universally conserved genes; these data supported the two-domain hypothesis, which place eukaryal species as ingroups of the Domain Archaea. However, the origin of Eukarya is complicated: the closest archaeal species to Eukarya differs in single-gene phylogenetic analyses depending on the genes. In this report, we performed molecular phylogenetic analyses of 23 aminoacyl-tRNA synthetases (ARS). Cytoplasmic ARSs in 12 trees showed a monophyletic Eukaryotic branch. One ARS originated from TACK superphylum. One ARS originated from Euryarchaeota and three originated from DPANN superphylum. Four ARSs originated from different bacterial species. The other 8 cytoplasmic ARSs were split into two or three groups in respective trees, which suggested that the cytoplasmic ARSs were replaced by secondary ARSs, and the original ARSs have been lost during evolution of Eukarya. In these trees, one original cytoplasmic ARS was derived from Euryarchaeota and three were derived from DPANN superphylum. Our results strongly support the two-domain hypothesis. We discovered that rampant-independent lateral gene transfers from several archaeal species of DPANN superphylum have contributed to the formation of Eukaryal cells. Based on our phylogenetic analyses, we proposed a model for the establishment of Eukarya.}, }
@article {pmid27881071, year = {2016}, author = {Gonçalves, IR and Brouillet, S and Soulié, MC and Gribaldo, S and Sirven, C and Charron, N and Boccara, M and Choquer, M}, title = {Genome-wide analyses of chitin synthases identify horizontal gene transfers towards bacteria and allow a robust and unifying classification into fungi.}, journal = {BMC evolutionary biology}, volume = {16}, number = {1}, pages = {252}, pmid = {27881071}, issn = {1471-2148}, mesh = {Animals ; Bacteria/*enzymology/genetics ; Chitin Synthase/*classification/*genetics/metabolism ; Eukaryota/enzymology ; Evolution, Molecular ; Fungi/*enzymology/genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial ; *Genome-Wide Association Study ; Multigene Family ; Phylogeny ; Recombination, Genetic/genetics ; Viruses/enzymology ; }, abstract = {BACKGROUND: Chitin, the second most abundant biopolymer on earth after cellulose, is found in probably all fungi, many animals (mainly invertebrates), several protists and a few algae, playing an essential role in the development of many of them. This polysaccharide is produced by type 2 glycosyltransferases, called chitin synthases (CHS). There are several contradictory classifications of CHS isoenzymes and, as regards their evolutionary history, their origin and diversity is still a matter of debate.<br><br>RESULTS: A genome-wide analysis resulted in the detection of more than eight hundred putative chitin synthases in proteomes associated with about 130 genomes. Phylogenetic analyses were performed with special care to avoid any pitfalls associated with the peculiarities of these sequences (e.g. highly variable regions, truncated or recombined sequences, long-branch attraction). This allowed us to revise and unify the fungal CHS classification and to study the evolutionary history of the CHS multigenic family. This update has the advantage of being user-friendly due to the development of a dedicated website (http://wwwabi.snv.jussieu.fr/public/CHSdb), and it includes any correspondences with previously published classifications and mutants. Concerning the evolutionary history of CHS, this family has mainly evolved via duplications and losses. However, it is likely that several horizontal gene transfers (HGT) also occurred in eukaryotic microorganisms and, even more surprisingly, in bacteria.<br><br>CONCLUSIONS: This comprehensive multi-species analysis contributes to the classification of fungal CHS, in particular by optimizing its robustness, consensuality and accessibility. It also highlights the importance of HGT in the evolutionary history of CHS and describes bacterial chs genes for the first time. Many of the bacteria that have acquired a chitin synthase are plant pathogens (e.g. Dickeya spp; Pectobacterium spp; Brenneria spp; Agrobacterium vitis and Pseudomonas cichorii). Whether they are able to produce a chitin exopolysaccharide or secrete chitooligosaccharides requires further investigation.}, }
@article {pmid27880757, year = {2016}, author = {Shi, M and Lin, XD and Tian, JH and Chen, LJ and Chen, X and Li, CX and Qin, XC and Li, J and Cao, JP and Eden, JS and Buchmann, J and Wang, W and Xu, J and Holmes, EC and Zhang, YZ}, title = {Redefining the invertebrate RNA virosphere.}, journal = {Nature}, volume = {540}, number = {7634}, pages = {539-543}, pmid = {27880757}, issn = {1476-4687}, abstract = {Current knowledge of RNA virus biodiversity is both biased and fragmentary, reflecting a focus on culturable or disease-causing agents. Here we profile the transcriptomes of over 220 invertebrate species sampled across nine animal phyla and report the discovery of 1,445 RNA viruses, including some that are sufficiently divergent to comprise new families. The identified viruses fill major gaps in the RNA virus phylogeny and reveal an evolutionary history that is characterized by both host switching and co-divergence. The invertebrate virome also reveals remarkable genomic flexibility that includes frequent recombination, lateral gene transfer among viruses and hosts, gene gain and loss, and complex genomic rearrangements. Together, these data present a view of the RNA virosphere that is more phylogenetically and genomically diverse than that depicted in current classification schemes and provide a more solid foundation for studies in virus ecology and evolution.}, }
@article {pmid27877158, year = {2016}, author = {Gambelli, L and Cremers, G and Mesman, R and Guerrero, S and Dutilh, BE and Jetten, MS and Op den Camp, HJ and van Niftrik, L}, title = {Ultrastructure and Viral Metagenome of Bacteriophages from an Anaerobic Methane Oxidizing Methylomirabilis Bioreactor Enrichment Culture.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1740}, pmid = {27877158}, issn = {1664-302X}, support = {339880/ERC_/European Research Council/International ; 669371/ERC_/European Research Council/International ; }, abstract = {With its capacity for anaerobic methane oxidation and denitrification, the bacterium Methylomirabilis oxyfera plays an important role in natural ecosystems. Its unique physiology can be exploited for more sustainable wastewater treatment technologies. However, operational stability of full-scale bioreactors can experience setbacks due to, for example, bacteriophage blooms. By shaping microbial communities through mortality, horizontal gene transfer, and metabolic reprogramming, bacteriophages are important players in most ecosystems. Here, we analyzed an infected Methylomirabilis sp. bioreactor enrichment culture using (advanced) electron microscopy, viral metagenomics and bioinformatics. Electron micrographs revealed four different viral morphotypes, one of which was observed to infect Methylomirabilis cells. The infected cells contained densely packed ~55 nm icosahedral bacteriophage particles with a putative internal membrane. Various stages of virion assembly were observed. Moreover, during the bacteriophage replication, the host cytoplasmic membrane appeared extremely patchy, which suggests that the bacteriophages may use host bacterial lipids to build their own putative internal membrane. The viral metagenome contained 1.87 million base pairs of assembled viral sequences, from which five putative complete viral genomes were assembled and manually annotated. Using bioinformatics analyses, we could not identify which viral genome belonged to the Methylomirabilis- infecting bacteriophage, in part because the obtained viral genome sequences were novel and unique to this reactor system. Taken together these results show that new bacteriophages can be detected in anaerobic cultivation systems and that the effect of bacteriophages on the microbial community in these systems is a topic for further study.}, }
@article {pmid27875695, year = {2016}, author = {Eme, L and Doolittle, WF}, title = {Microbial Evolution: Xenology (Apparently) Trumps Paralogy.}, journal = {Current biology : CB}, volume = {26}, number = {22}, pages = {R1181-R1183}, doi = {10.1016/j.cub.2016.09.049}, pmid = {27875695}, issn = {1879-0445}, abstract = {Within-genome gene duplication is generally considered the source of extra copies when higher dosage is required and a starting point for evolution of new function. A new study suggests that horizontal gene transfer can appear to play both roles.}, }
@article {pmid27875306, year = {2016}, author = {Zhang, W and Lu, L and Lai, Q and Zhu, B and Li, Z and Xu, Y and Shao, Z and Herrup, K and Moore, BS and Ross, AC and Qian, PY}, title = {Family-wide Structural Characterization and Genomic Comparisons Decode the Diversity-oriented Biosynthesis of Thalassospiramides by Marine Proteobacteria.}, journal = {The Journal of biological chemistry}, volume = {291}, number = {53}, pages = {27228-27238}, pmid = {27875306}, issn = {1083-351X}, support = {R01 GM097509/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacterial Proteins/chemistry/*genetics/metabolism ; Cells, Cultured ; Embryo, Mammalian/cytology/drug effects/metabolism ; Genomics/*methods ; Marine Biology ; Mice ; Mice, Inbred C57BL ; Multigene Family/genetics ; Neurons/cytology/*drug effects/metabolism ; Neuroprotective Agents/chemistry/*pharmacology ; Peptides, Cyclic/*pharmacology ; Phylogeny ; Proteobacteria/genetics/growth &amp; development/*metabolism ; }, abstract = {The thalassospiramide lipopeptides have great potential for therapeutic applications; however, their structural and functional diversity and biosynthesis are poorly understood. Here, by cultivating 130 Rhodospirillaceae strains sampled from oceans worldwide, we discovered 21 new thalassospiramide analogues and demonstrated their neuroprotective effects. To investigate the diversity of biosynthetic gene cluster (BGC) architectures, we sequenced the draft genomes of 28 Rhodospirillaceae strains. Our family-wide genomic analysis revealed three types of dysfunctional BGCs and four functional BGCs whose architectures correspond to four production patterns. This correlation allowed us to reassess the "diversity-oriented biosynthesis" proposed for the microbial production of thalassospiramides, which involves iteration of several key modules. Preliminary evolutionary investigation suggested that the functional BGCs could have arisen through module/domain loss, whereas the dysfunctional BGCs arose through horizontal gene transfer. Further comparative genomics indicated that thalassospiramide production is likely to be attendant on particular genes/pathways for amino acid metabolism, signaling transduction, and compound efflux. Our findings provide a systematic understanding of thalassospiramide production and new insights into the underlying mechanism.}, }
@article {pmid27873028, year = {2017}, author = {Caniaux, I and van Belkum, A and Zambardi, G and Poirel, L and Gros, MF}, title = {MCR: modern colistin resistance.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {36}, number = {3}, pages = {415-420}, pmid = {27873028}, issn = {1435-4373}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology/therapeutic use ; Carrier State/diagnosis/microbiology/veterinary ; Colistin/*pharmacology/therapeutic use ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Gram-Negative Bacteria/*drug effects/isolation &amp; purification ; Gram-Negative Bacterial Infections/diagnosis/*drug therapy/*microbiology/veterinary ; Humans ; Plasmids ; }, abstract = {Recently, plasmid-mediated and, therefore, transferable bacterial polymyxin resistance was discovered in strains from both humans and animals. Such a trait may widely spread geographically, while simultaneously crossing microbial species barriers. This may ultimately render the "last resort" polymyxin antibiotics therapeutically useless. Colistin is currently used to treat infections caused by Gram-negative carbapenemase producers and colistin resistance may lead to practical pan-antibiotic resistance. We here analyzed the medical and diagnostic consequences of (emerging) colistin resistance and propose pathways toward adequate diagnostics for timely detection of both asymptomatic carriage and infection. Culture-based testing using chromogenic and selective media for screening clinical (and veterinary) specimens may constitute key tools for that purpose. Relevant molecular tests are also discussed.}, }
@article {pmid27867010, year = {2016}, author = {Patterson, AG and Jackson, SA and Taylor, C and Evans, GB and Salmond, GPC and Przybilski, R and Staals, RHJ and Fineran, PC}, title = {Quorum Sensing Controls Adaptive Immunity through the Regulation of Multiple CRISPR-Cas Systems.}, journal = {Molecular cell}, volume = {64}, number = {6}, pages = {1102-1108}, pmid = {27867010}, issn = {1097-4164}, support = {BB/H002677/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {4-Butyrolactone/analogs &amp; derivatives/pharmacology ; Bacterial Proteins/*genetics/immunology ; CRISPR-Associated Proteins/genetics/immunology ; CRISPR-Cas Systems/*immunology ; Clustered Regularly Interspaced Short Palindromic Repeats ; Endodeoxyribonucleases/*genetics/immunology ; Gene Expression Regulation, Bacterial/*immunology ; Quorum Sensing/drug effects/*genetics/immunology ; Repressor Proteins/genetics/immunology ; Serratia/drug effects/*genetics/immunology ; }, abstract = {Bacteria commonly exist in high cell density populations, making them prone to viral predation and horizontal gene transfer (HGT) through transformation and conjugation. To combat these invaders, bacteria possess an arsenal of defenses, such as CRISPR-Cas adaptive immunity. Many bacterial populations coordinate their behavior as cell density increases, using quorum sensing (QS) signaling. In this study, we demonstrate that QS regulation results in increased expression of the type I-E, I-F, and III-A CRISPR-Cas systems in Serratia cells in high-density populations. Strains unable to communicate via QS were less effective at defending against invaders targeted by any of the three CRISPR-Cas systems. Additionally, the acquisition of immunity by the type I-E and I-F systems was impaired in the absence of QS signaling. We propose that bacteria can use chemical communication to modulate the balance between community-level defense requirements in high cell density populations and host fitness costs of basal CRISPR-Cas activity.}, }
@article {pmid27866935, year = {2016}, author = {Gomes, TA and Elias, WP and Scaletsky, IC and Guth, BE and Rodrigues, JF and Piazza, RM and Ferreira, LC and Martinez, MB}, title = {Diarrheagenic Escherichia coli.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {47 Suppl 1}, number = {Suppl 1}, pages = {3-30}, pmid = {27866935}, issn = {1678-4405}, mesh = {Diarrhea/*diagnosis/epidemiology/*microbiology ; Escherichia coli/*classification/pathogenicity/*physiology ; Escherichia coli Infections/*diagnosis/epidemiology/*microbiology ; Humans ; Prevalence ; Virulence Factors/genetics ; }, abstract = {Most Escherichia coli strains live harmlessly in the intestines and rarely cause disease in healthy individuals. Nonetheless, a number of pathogenic strains can cause diarrhea or extraintestinal diseases both in healthy and immunocompromised individuals. Diarrheal illnesses are a severe public health problem and a major cause of morbidity and mortality in infants and young children, especially in developing countries. E. coli strains that cause diarrhea have evolved by acquiring, through horizontal gene transfer, a particular set of characteristics that have successfully persisted in the host. According to the group of virulence determinants acquired, specific combinations were formed determining the currently known E. coli pathotypes, which are collectively known as diarrheagenic E. coli. In this review, we have gathered information on current definitions, serotypes, lineages, virulence mechanisms, epidemiology, and diagnosis of the major diarrheagenic E. coli pathotypes.}, }
@article {pmid27865985, year = {2017}, author = {Song, Y and Lv, Y and Cui, L and Li, Y and Ke, Q and Zhao, Y}, title = {cfr-mediated linezolid-resistant clinical isolates of methicillin-resistant coagulase-negative staphylococci from China.}, journal = {Journal of global antimicrobial resistance}, volume = {8}, number = {}, pages = {1-5}, doi = {10.1016/j.jgar.2016.09.008}, pmid = {27865985}, issn = {2213-7173}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics ; China ; Coagulase/*genetics ; DNA, Bacterial/analysis ; Drug Resistance, Bacterial/drug effects/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Genes, MDR/genetics ; Humans ; Interspersed Repetitive Sequences/genetics ; Linezolid/*pharmacology ; Methicillin Resistance/*genetics ; Microbial Sensitivity Tests ; Molecular Typing ; Mutation ; Plasmids/genetics ; Ribosomal Protein L3 ; Ribosomal Proteins/genetics ; Staphylococcal Infections/microbiology ; Staphylococcus/drug effects/*genetics/*isolation &amp; purification ; }, abstract = {Three linezolid-resistant coagulase-negative staphylococci (LR-CoNS), including two Staphylococcus cohnii and one Staphylococcus capitis, were isolated from 1104 clinical staphylococcal isolates across China in 2013-2014. Antibiotic susceptibilities of the bacteria were determined by the agar dilution method. PCR and DNA sequencing were performed to determine the potential molecular mechanism of linezolid resistance. The two linezolid-resistant S. cohnii isolates were subjected to pulsed-field gel electrophoresis (PFGE) to investigate their genetic relatedness. Primer walking, S1 nuclease PFGE and Southern blot hybridisation were conducted to ascertain the location and environment of the cfr gene. All three isolates were positive for the cfr gene. Amino acid mutations S158F and S158Y in the ribosomal protein L3 were identified in S. cohnii 13B289 and 13L105, respectively, both of which also had an additional substitution (D159Y) in L3. PFGE indicated that the two S. cohnii isolates belonged to diverse clonal strains. S1 nuclease PFGE and Southern blotting experiments indicated that the cfr gene of the three isolates resided on plasmids of similar size (ca. 35.4kb). The cfr-harbouring segments of S. capitis 13G350 and S. cohnii 13L105 were identical to plasmid pSS-01 reported previously. The cfr-carrying fragment of S. cohnii 13B289 was indistinguishable from the formerly described plasmid pSS-02. In conclusion, the presence of the cfr gene located on a plasmid was the main mechanism contributing to resistance to linezolid in the three staphylococcal isolates. Hence, timely detection and judicious use of antibiotics are essential to prevent further transmission of this resistance mechanism.}, }
@article {pmid27864136, year = {2017}, author = {Zhi, XY and Jiang, Z and Yang, LL and Huang, Y}, title = {The underlying mechanisms of genetic innovation and speciation in the family Corynebacteriaceae: A phylogenomics approach.}, journal = {Molecular phylogenetics and evolution}, volume = {107}, number = {}, pages = {246-255}, doi = {10.1016/j.ympev.2016.11.009}, pmid = {27864136}, issn = {1095-9513}, mesh = {Actinomycetales/*classification/*genetics ; Animals ; Gene Transfer, Horizontal ; *Genetic Speciation ; Genetic Variation ; *Genome, Bacterial ; *Genomics ; Metabolic Networks and Pathways/genetics ; *Phylogeny ; }, abstract = {The pangenome of a bacterial species population is formed by genetic reduction and genetic expansion over the long course of evolution. Gene loss is a pervasive source of genetic reduction, and (exogenous and endogenous) gene gain is the main driver of genetic expansion. To understand the genetic innovation and speciation of the family Corynebacteriaceae, which cause a wide range of serious infections in humans and animals, we analyzed the pangenome of this family, and reconstructed its phylogeny using a phylogenomics approach. Genetic variations have occurred throughout the whole evolutionary history of the Corynebacteriaceae. Gene loss has been the primary force causing genetic changes, not only in terms of the number of protein families affected, but also because of its continuity on the time series. The variation in metabolism caused by these genetic changes mainly occurred for membrane transporters, two-component systems, and metabolism related to amino acids and carbohydrates. Interestingly, horizontal gene transfer (HGT) not only caused changes related to pathogenicity, but also triggered the acquisition of antimicrobial resistance. The Darwinian theory of evolution did not adequately explain the effects of dispersive HGT and/or gene loss in the evolution of the Corynebacteriaceae. These findings provide new insight into the evolution and speciation of Corynebacteriaceae and advance our understanding of the genetic innovation in microbial populations.}, }
@article {pmid27863503, year = {2016}, author = {Danchin, EG}, title = {Lateral gene transfer in eukaryotes: tip of the iceberg or of the ice cube?.}, journal = {BMC biology}, volume = {14}, number = {1}, pages = {101}, pmid = {27863503}, issn = {1741-7007}, mesh = {Eukaryota/genetics ; *Gene Transfer, Horizontal ; Genome ; *Ice ; Phylogeny ; Prokaryotic Cells ; }, abstract = {Lateral gene transfer (LGT) is the transmission of genes, sometimes across species barriers, outwith the classic vertical inheritance from parent to offspring. LGT is recognized as an important phenomenon that has shaped the genomes and biology of prokaryotes. Whether LGT in eukaryotes is important and widespread remains controversial. A study in BMC Biology concludes that LGT in eukaryotes is neither continuous nor prevalent and suggests a rule of thumb for judging when apparent LGT may reflect contamination.See research article: http://bmcbiol.biomedcentral.com/articles/10.1186/s12915-016-0315-9 .}, }
@article {pmid27862505, year = {2016}, author = {Olofsson, JK and Bianconi, M and Besnard, G and Dunning, LT and Lundgren, MR and Holota, H and Vorontsova, MS and Hidalgo, O and Leitch, IJ and Nosil, P and Osborne, CP and Christin, PA}, title = {Genome biogeography reveals the intraspecific spread of adaptive mutations for a complex trait.}, journal = {Molecular ecology}, volume = {25}, number = {24}, pages = {6107-6123}, pmid = {27862505}, issn = {1365-294X}, mesh = {Adaptation, Biological/*genetics ; Africa ; *Biological Evolution ; Gene Flow ; *Mutation ; Photosynthesis/*genetics ; Phylogeography ; Poaceae/*genetics/physiology ; }, abstract = {Physiological novelties are often studied at macro-evolutionary scales such that their micro-evolutionary origins remain poorly understood. Here, we test the hypothesis that key components of a complex trait can evolve in isolation and later be combined by gene flow. We use C4 photosynthesis as a study system, a derived physiology that increases plant productivity in warm, dry conditions. The grass Alloteropsis semialata includes C4 and non-C4 genotypes, with some populations using laterally acquired C4 -adaptive loci, providing an outstanding system to track the spread of novel adaptive mutations. Using genome data from C4 and non-C4 A. semialata individuals spanning the species' range, we infer and date past migrations of different parts of the genome. Our results show that photosynthetic types initially diverged in isolated populations, where key C4 components were acquired. However, rare but recurrent subsequent gene flow allowed the spread of adaptive loci across genetic pools. Indeed, laterally acquired genes for key C4 functions were rapidly passed between populations with otherwise distinct genomic backgrounds. Thus, our intraspecific study of C4 -related genomic variation indicates that components of adaptive traits can evolve separately and later be combined through secondary gene flow, leading to the assembly and optimization of evolutionary innovations.}, }
@article {pmid27861576, year = {2016}, author = {Cihlář, J and Füssy, Z and Horák, A and Oborník, M}, title = {Evolution of the Tetrapyrrole Biosynthetic Pathway in Secondary Algae: Conservation, Redundancy and Replacement.}, journal = {PloS one}, volume = {11}, number = {11}, pages = {e0166338}, pmid = {27861576}, issn = {1932-6203}, mesh = {*Biological Evolution ; *Biosynthetic Pathways/genetics ; Cryptophyta/classification/genetics/*metabolism ; Diatoms/classification/genetics/*metabolism ; Dinoflagellida/classification/genetics/*metabolism ; Gene Expression Profiling ; Heme/metabolism ; Phylogeny ; Porphobilinogen Synthase/genetics/metabolism ; Tetrapyrroles/*metabolism ; }, abstract = {Tetrapyrroles such as chlorophyll and heme are indispensable for life because they are involved in energy fixation and consumption, i.e. photosynthesis and oxidative phosphorylation. In eukaryotes, the tetrapyrrole biosynthetic pathway is shaped by past endosymbioses. We investigated the origins and predicted locations of the enzymes of the heme pathway in the chlorarachniophyte Bigelowiella natans, the cryptophyte Guillardia theta, the "green" dinoflagellate Lepidodinium chlorophorum, and three dinoflagellates with diatom endosymbionts ("dinotoms"): Durinskia baltica, Glenodinium foliaceum and Kryptoperidinium foliaceum. Bigelowiella natans appears to contain two separate heme pathways analogous to those found in Euglena gracilis; one is predicted to be mitochondrial-cytosolic, while the second is predicted to be plastid-located. In the remaining algae, only plastid-type tetrapyrrole synthesis is present, with a single remnant of the mitochondrial-cytosolic pathway, a ferrochelatase of G. theta putatively located in the mitochondrion. The green dinoflagellate contains a single pathway composed of mostly rhodophyte-origin enzymes, and the dinotoms hold two heme pathways of apparently plastidal origin. We suggest that heme pathway enzymes in B. natans and L. chlorophorum share a predominantly rhodophytic origin. This implies the ancient presence of a rhodophyte-derived plastid in the chlorarachniophyte alga, analogous to the green dinoflagellate, or an exceptionally massive horizontal gene transfer.}, }
@article {pmid27861551, year = {2016}, author = {Malki, K and Shapiro, JW and Price, TK and Hilt, EE and Thomas-White, K and Sircar, T and Rosenfeld, AB and Kuffel, G and Zilliox, MJ and Wolfe, AJ and Putonti, C}, title = {Genomes of Gardnerella Strains Reveal an Abundance of Prophages within the Bladder Microbiome.}, journal = {PloS one}, volume = {11}, number = {11}, pages = {e0166757}, pmid = {27861551}, issn = {1932-6203}, support = {R01 DK104718/DK/NIDDK NIH HHS/United States ; R21 DK097435/DK/NIDDK NIH HHS/United States ; R56 DK104718/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Computational Biology/methods ; DNA Transposable Elements ; Female ; Gardnerella/*genetics/virology ; Genes, Viral ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Humans ; *Microbiota ; Open Reading Frames ; Phylogeny ; Prophages/*genetics ; Urinary Bladder/*microbiology ; }, abstract = {Bacterial surveys of the vaginal and bladder human microbiota have revealed an abundance of many similar bacterial taxa. As the bladder was once thought to be sterile, the complex interactions between microbes within the bladder have yet to be characterized. To initiate this process, we have begun sequencing isolates, including the clinically relevant genus Gardnerella. Herein, we present the genomic sequences of four Gardnerella strains isolated from the bladders of women with symptoms of urgency urinary incontinence; these are the first Gardnerella genomes produced from this niche. Congruent to genomic characterization of Gardnerella isolates from the reproductive tract, isolates from the bladder reveal a large pangenome, as well as evidence of high frequency horizontal gene transfer. Prophage gene sequences were found to be abundant amongst the strains isolated from the bladder, as well as amongst publicly available Gardnerella genomes from the vagina and endometrium, motivating an in depth examination of these sequences. Amongst the 39 Gardnerella strains examined here, there were more than 400 annotated prophage gene sequences that we could cluster into 95 homologous groups; 49 of these groups were unique to a single strain. While many of these prophages exhibited no sequence similarity to any lytic phage genome, estimation of the rate of phage acquisition suggests both vertical and horizontal acquisition. Furthermore, bioinformatic evidence indicates that prophage acquisition is ongoing within both vaginal and bladder Gardnerella populations. The abundance of prophage sequences within the strains examined here suggests that phages could play an important role in the species' evolutionary history and in its interactions within the complex communities found in the female urinary and reproductive tracts.}, }
@article {pmid27860150, year = {2017}, author = {Rybak, K and See, PT and Phan, HT and Syme, RA and Moffat, CS and Oliver, RP and Tan, KC}, title = {A functionally conserved Zn2 Cys6 binuclear cluster transcription factor class regulates necrotrophic effector gene expression and host-specific virulence of two major Pleosporales fungal pathogens of wheat.}, journal = {Molecular plant pathology}, volume = {18}, number = {3}, pages = {420-434}, pmid = {27860150}, issn = {1364-3703}, mesh = {Ascomycota/*genetics/growth &amp; development/*pathogenicity ; *Conserved Sequence ; Epistasis, Genetic ; Fungal Proteins/genetics/*metabolism ; Gene Deletion ; *Gene Expression Regulation, Fungal ; Host Specificity/*genetics ; Phylogeny ; Plant Diseases/microbiology ; Polymorphism, Genetic ; Promoter Regions, Genetic/genetics ; Sequence Alignment ; Spores, Fungal/physiology ; Transcription Factors/genetics/*metabolism ; Triticum/*microbiology ; Virulence/genetics ; Zinc Fingers ; }, abstract = {The fungus Parastagonospora nodorum is the causal agent of Septoria nodorum blotch of wheat (Triticum aestivum). The interaction is mediated by multiple fungal necrotrophic effector-dominant host sensitivity gene interactions. The three best-characterized effector-sensitivity gene systems are SnToxA-Tsn1, SnTox1-Snn1 and SnTox3-Snn3. These effector genes are highly expressed during early infection, but expression decreases as the infection progresses to tissue necrosis and sporulation. However, the mechanism of regulation is unknown. We have identified and functionally characterized a gene, referred to as PnPf2, which encodes a putative zinc finger transcription factor. PnPf2 deletion resulted in the down-regulation of SnToxA and SnTox3 expression. Virulence on Tsn1 and Snn3 wheat cultivars was strongly reduced. The SnTox1-Snn1 interaction remained unaffected. Furthermore, we have also identified and deleted an orthologous PtrPf2 from the tan spot fungus Pyrenophora tritici-repentis which possesses a near-identical ToxA that was acquired from P. nodorum via horizontal gene transfer. PtrPf2 deletion also resulted in the down-regulation of PtrToxA expression and a near-complete loss of virulence on Tsn1 wheat. We have demonstrated, for the first time, evidence for a functionally conserved signalling component that plays a role in the regulation of a common/horizontally transferred effector found in two major fungal pathogens of wheat.}, }
@article {pmid27859237, year = {2017}, author = {Lakey, B and Triemer, R}, title = {The tetrapyrrole synthesis pathway as a model of horizontal gene transfer in euglenoids.}, journal = {Journal of phycology}, volume = {53}, number = {1}, pages = {198-217}, doi = {10.1111/jpy.12491}, pmid = {27859237}, issn = {1529-8817}, mesh = {Biosynthetic Pathways ; Euglenozoa/classification/*genetics/*metabolism ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Phylogeny ; Symbiosis ; Tetrapyrroles/genetics/*metabolism ; }, abstract = {The history of euglenoids may have begun as early as ~2 bya. These early phagotrophs ate cyanobacteria, archaea, and eubacteria, and the subsequent appearance of red algae and chromalveolates provided euglenoids with additional food sources. Following the appearance of green algae, euglenoids acquired a chloroplast via a secondary endosymbiotic event with a green algal ancestor. This endosymbiosis also involved a massive transfer of nuclear-encoded genes from the symbiont nucleus to the host. Expecting these genes to have a green algal origin, this research has shown, through the use of DNA-sequences and the analysis of phylogenetic relationships, that many housekeeping genes have a red algal/chromalveolate ancestry. This suggested that many other endosymbiotic/horizontal gene transfers, which brought genes from chromalveolates to euglenoids, may have been taking place long before the acquisition of the chloroplast. The investigation of the origin of the enzymes involved in the tetrapyrrole synthesis pathway provided insights into horizontal gene transfer in euglenoids and demonstrated that the euglenoid nuclear genome is a mosaic comprised of genes from the ancestral lineage plus genes transferred endosymbiotically/horizontally from green, red, and chromalveolates lineages.}, }
@article {pmid27855283, year = {2017}, author = {Doore, SM and Schweers, NJ and Fane, BA}, title = {Elevating fitness after a horizontal gene exchange in bacteriophage φX174.}, journal = {Virology}, volume = {501}, number = {}, pages = {25-34}, doi = {10.1016/j.virol.2016.10.029}, pmid = {27855283}, issn = {1096-0341}, mesh = {Bacteriophage phi X 174/*genetics/physiology ; *Gene Transfer, Horizontal ; Mutation ; Viral Fusion Proteins/genetics ; Virus Assembly ; }, abstract = {In an earlier study, protein-based barriers to horizontal gene transfer were investigated by placing the bacteriophage G4 G gene, encoding the major spike protein, into the φX174 genome. The foreign G protein promoted off-pathway assembly reactions, resulting in a lethal phenotype. After three targeted genetic selections, one of two foreign spike proteins was productively integrated into the φX174 system: the complete G4 or a recombinant G4/φX174 protein (94% G4:6% φX174). However, strain fitness was very low. In this study, the chimeras were characterized and experimentally evolved. Inefficient assembly was the primary contributor to low fitness: accordingly, mutations affecting assembly restored fitness. The spike protein preference of the ancestral and evolved strains was determined in competition experiments between the foreign and φX174G proteins. Before adaptation, both G proteins were incorporated into virions; afterwards, the foreign proteins were strongly preferred. Thus, a previously inhibitory protein became the preferred substrate during assembly.}, }
@article {pmid27855212, year = {2016}, author = {Dean, P and Hirt, RP and Embley, TM}, title = {Microsporidia: Why Make Nucleotides if You Can Steal Them?.}, journal = {PLoS pathogens}, volume = {12}, number = {11}, pages = {e1005870}, pmid = {27855212}, issn = {1553-7374}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Host-Parasite Interactions/*physiology ; Humans ; Microsporidia/*metabolism ; Nucleotides/*metabolism ; }, abstract = {Microsporidia are strict obligate intracellular parasites that infect a wide range of eukaryotes including humans and economically important fish and insects. Surviving and flourishing inside another eukaryotic cell is a very specialised lifestyle that requires evolutionary innovation. Genome sequence analyses show that microsporidia have lost most of the genes needed for making primary metabolites, such as amino acids and nucleotides, and also that they have only a limited capacity for making adenosine triphosphate (ATP). Since microsporidia cannot grow and replicate without the enormous amounts of energy and nucleotide building blocks needed for protein, DNA, and RNA biosynthesis, they must have evolved ways of stealing these substrates from the infected host cell. Providing they can do this, genome analyses suggest that microsporidia have the enzyme repertoire needed to use and regenerate the imported nucleotides efficiently. Recent functional studies suggest that a critical innovation for adapting to intracellular life was the acquisition by lateral gene transfer of nucleotide transport (NTT) proteins that are now present in multiple copies in all microsporidian genomes. These proteins are expressed on the parasite surface and allow microsporidia to steal ATP and other purine nucleotides for energy and biosynthesis from their host. However, it remains unclear how other essential metabolites, such as pyrimidine nucleotides, are acquired. Transcriptomic and experimental studies suggest that microsporidia might manipulate host cell metabolism and cell biological processes to promote nucleotide synthesis and to maximise the potential for ATP and nucleotide import. In this review, we summarise recent genomic and functional data relating to how microsporidia exploit their hosts for energy and building blocks needed for growth and nucleic acid metabolism and we identify some remaining outstanding questions.}, }
@article {pmid27855160, year = {2016}, author = {van der Does, HC and Fokkens, L and Yang, A and Schmidt, SM and Langereis, L and Lukasiewicz, JM and Hughes, TR and Rep, M}, title = {Transcription Factors Encoded on Core and Accessory Chromosomes of Fusarium oxysporum Induce Expression of Effector Genes.}, journal = {PLoS genetics}, volume = {12}, number = {11}, pages = {e1006401}, pmid = {27855160}, issn = {1553-7404}, mesh = {Chromosomes, Fungal ; DNA-Binding Proteins/*genetics/metabolism ; Fusarium/*genetics/growth &amp; development/pathogenicity ; Gene Expression Regulation, Fungal ; Gene Transfer, Horizontal/genetics ; Genome, Fungal ; High-Throughput Nucleotide Sequencing ; Host-Pathogen Interactions/genetics ; Solanum lycopersicum/growth &amp; development/microbiology ; Phylogeny ; Plant Diseases/*genetics/microbiology ; Promoter Regions, Genetic ; Transcription Factors/*genetics/metabolism ; }, abstract = {Proteins secreted by pathogens during host colonization largely determine the outcome of pathogen-host interactions and are commonly called 'effectors'. In fungal plant pathogens, coordinated transcriptional up-regulation of effector genes is a key feature of pathogenesis and effectors are often encoded in genomic regions with distinct repeat content, histone code and rate of evolution. In the tomato pathogen Fusarium oxysporum f. sp. lycopersici (Fol), effector genes reside on one of four accessory chromosomes, known as the 'pathogenicity' chromosome, which can be exchanged between strains through horizontal transfer. The three other accessory chromosomes in the Fol reference strain may also be important for virulence towards tomato. Expression of effector genes in Fol is highly up-regulated upon infection and requires Sge1, a transcription factor encoded on the core genome. Interestingly, the pathogenicity chromosome itself contains 13 predicted transcription factor genes and for all except one, there is a homolog on the core genome. We determined DNA binding specificity for nine transcription factors using oligonucleotide arrays. The binding sites for homologous transcription factors were highly similar, suggesting that extensive neofunctionalization of DNA binding specificity has not occurred. Several DNA binding sites are enriched on accessory chromosomes, and expression of FTF1, its core homolog FTF2 and SGE1 from a constitutive promoter can induce expression of effector genes. The DNA binding sites of only these three transcription factors are enriched among genes up-regulated during infection. We further show that Ftf1, Ftf2 and Sge1 can activate transcription from their binding sites in yeast. RNAseq analysis revealed that in strains with constitutive expression of FTF1, FTF2 or SGE1, expression of a similar set of plant-responsive genes on the pathogenicity chromosome is induced, including most effector genes. We conclude that the Fol pathogenicity chromosome may be partially transcriptionally autonomous, but there are also extensive transcriptional connections between core and accessory chromosomes.}, }
@article {pmid27855079, year = {2017}, author = {Girlich, D and Bonnin, RA and Bogaerts, P and De Laveleye, M and Huang, DT and Dortet, L and Glaser, P and Glupczynski, Y and Naas, T}, title = {Chromosomal Amplification of the blaOXA-58 Carbapenemase Gene in a Proteus mirabilis Clinical Isolate.}, journal = {Antimicrobial agents and chemotherapy}, volume = {61}, number = {2}, pages = {}, pmid = {27855079}, issn = {1098-6596}, mesh = {Adult ; Bacterial Proteins/*genetics/metabolism ; Binding Sites ; Chromosomes, Bacterial ; Drug Resistance, Bacterial/genetics ; Escherichia coli/genetics ; Escherichia coli Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Humans ; Integrases/genetics/metabolism ; Male ; Microbial Sensitivity Tests ; Multigene Family ; Prophages/*genetics ; Proteus Infections/drug therapy/*etiology/microbiology ; Proteus mirabilis/drug effects/*genetics/isolation &amp; purification ; beta-Lactamases/*genetics ; }, abstract = {Horizontal gene transfer may occur between distantly related bacteria, thus leading to genetic plasticity and in some cases to acquisition of novel resistance traits. Proteus mirabilis is an enterobacterial species responsible for human infections that may express various acquired β-lactam resistance genes, including different classes of carbapenemase genes. Here we report a Proteus mirabilis clinical isolate (strain 1091) displaying resistance to penicillin, including temocillin, together with reduced susceptibility to carbapenems and susceptibility to expanded-spectrum cephalosporins. Using biochemical tests, significant carbapenem hydrolysis was detected in P. mirabilis 1091. Since PCR failed to detect acquired carbapenemase genes commonly found in Enterobacteriaceae, we used a whole-genome sequencing approach that revealed the presence of blaOXA-58 class D carbapenemase gene, so far identified only in Acinetobacter species. This gene was located on a 3.1-kb element coharboring a blaAmpC-like gene. Remarkably, these two genes were bracketed by putative XerC-XerD binding sites and inserted at a XerC-XerD site located between the terminase-like small- and large-subunit genes of a bacteriophage. Increased expression of the two bla genes resulted from a 6-time tandem amplification of the element as revealed by Southern blotting. This is the first isolation of a clinical P. mirabilis strain producing OXA-58, a class D carbapenemase, and the first description of a XerC-XerD-dependent insertion of antibiotic resistance genes within a bacteriophage. This study revealed a new role for the XerC-XerD recombinase in bacteriophage biology.}, }
@article {pmid27855076, year = {2017}, author = {Skalova, A and Chudejova, K and Rotova, V and Medvecky, M and Studentova, V and Chudackova, E and Lavicka, P and Bergerova, T and Jakubu, V and Zemlickova, H and Papagiannitsis, CC and Hrabak, J}, title = {Molecular Characterization of OXA-48-Like-Producing Enterobacteriaceae in the Czech Republic and Evidence for Horizontal Transfer of pOXA-48-Like Plasmids.}, journal = {Antimicrobial agents and chemotherapy}, volume = {61}, number = {2}, pages = {}, pmid = {27855076}, issn = {1098-6596}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics/metabolism ; Chromosomes, Bacterial/genetics ; Czech Republic ; Enterobacteriaceae/drug effects/*enzymology/*genetics ; Escherichia coli/drug effects/enzymology/genetics ; Gene Transfer, Horizontal/genetics ; Klebsiella pneumoniae/drug effects/enzymology/genetics ; Microbial Sensitivity Tests ; Plasmids/genetics ; beta-Lactamases/genetics/metabolism ; }, abstract = {The aim of this study was to characterize the first cases and outbreaks of OXA-48-like-producing Enterobacteriaceae recovered from hospital settings in the Czech Republic. From 2013 to 2015, 22 Klebsiella pneumoniae isolates, 3 Escherichia coli isolates, and 1 Enterobacter cloacae isolate producing OXA-48-like carbapenemases were isolated from 20 patients. Four of the patients were colonized or infected by two or three different OXA-48-like producers. The K. pneumoniae isolates were classified into nine sequence types (STs), with ST101 being predominant (n = 8). The E. coli isolates were of different STs, while the E. cloacae isolate belonged to ST109. Twenty-four isolates carried blaOXA-48, while two isolates carried blaOXA-181 or blaOXA-232 Almost all isolates (n = 22) carried blaOXA-48-positive plasmids of a similar size (∼60 kb), except the two isolates producing OXA-181 or OXA-232. In an ST45 K. pneumoniae isolate and an ST38 E. coli isolate, S1 nuclease profiling plus hybridization indicated a chromosomal location of blaOXA-48 Sequencing showed that the majority of blaOXA-48-carrying plasmids exhibited high degrees of identity with the pOXA-48-like plasmid pE71T. Additionally, two novel pE71T derivatives, pOXA-48_30715 and pOXA-48_30891, were observed. The blaOXA-181-carrying plasmid was identical to the IncX3 plasmid pOXA181_EC14828, while the blaOXA-232-carrying plasmid was a ColE2-type plasmid, being a novel derivative of pOXA-232. Finally, sequencing data showed that the ST45 K. pneumoniae and ST38 E. coli isolates harbored the IS1R-based composite transposon Tn6237 containing blaOXA-48 integrated into their chromosomes. These findings underlined that the horizontal transfer of pOXA-48-like plasmids has played a major role in the dissemination of blaOXA-48 in the Czech Republic. In combination with the difficulties with their detection, OXA-48 producers constitute an important public threat.}, }
@article {pmid27853884, year = {2017}, author = {Zhang, HH and Li, GY and Xiong, XM and Han, MJ and Dai, FY}, title = {Horizontal transfer of a novel Helentron in insects.}, journal = {Molecular genetics and genomics : MGG}, volume = {292}, number = {1}, pages = {243-250}, pmid = {27853884}, issn = {1617-4623}, mesh = {Animals ; Bombyx/*genetics ; *DNA Transposable Elements ; *Gene Transfer, Horizontal ; Genome ; Insecta/genetics ; Phylogeny ; }, abstract = {Helentrons represent a novel subtype of Helitrons. However, the evolutionary history of Helentrons in organisms is not clearly understood. In this study, we performed structure and autonomous partner analyses, which revealed that bm_455, a TE obtained from the Bombyx mori TE database, BmTEdb, was a member of Helentrons but not a long-terminal repeat (LTR) retrotransposon. Further analyses showed that bm_455 was also present in a wide range of insects including lepidopterans, coleopterans and hymenopterans using a homology-based search strategy. Several lines of evidence (high sequence identity, discontinuous distribution and lack of intense purifying selection) suggested that these elements could have been transferred into these species in part by horizontal transfers (HTs). Because Helentrons can capture host gene fragments, HTs of Helentrons might have a huge impact on their host genome evolution.}, }
@article {pmid27852226, year = {2016}, author = {Gregory, AC and Solonenko, SA and Ignacio-Espinoza, JC and LaButti, K and Copeland, A and Sudek, S and Maitland, A and Chittick, L and Dos Santos, F and Weitz, JS and Worden, AZ and Woyke, T and Sullivan, MB}, title = {Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer.}, journal = {BMC genomics}, volume = {17}, number = {1}, pages = {930}, pmid = {27852226}, issn = {1471-2164}, mesh = {Bacteriophages/classification/*genetics ; Biological Evolution ; Comparative Genomic Hybridization ; DNA/metabolism ; DNA, Viral/chemistry/isolation &amp; purification/metabolism ; Gene Transfer, Horizontal/*genetics ; Genetic Linkage ; *Genome, Viral ; Host Specificity ; Metagenomics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Genetic recombination is a driving force in genome evolution. Among viruses it has a dual role. For genomes with higher fitness, it maintains genome integrity in the face of high mutation rates. Conversely, for genomes with lower fitness, it provides immediate access to sequence space that cannot be reached by mutation alone. Understanding how recombination impacts the cohesion and dissolution of individual whole genomes within viral sequence space is poorly understood across double-stranded DNA bacteriophages (a.k.a phages) due to the challenges of obtaining appropriately scaled genomic datasets.<br><br>RESULTS: Here we explore the role of recombination in both maintaining and differentiating whole genomes of 142 wild double-stranded DNA marine cyanophages. Phylogenomic analysis across the 51 core genes revealed ten lineages, six of which were well represented. These phylogenomic lineages represent discrete genotypic populations based on comparisons of intra- and inter- lineage shared gene content, genome-wide average nucleotide identity, as well as detected gaps in the distribution of pairwise differences between genomes. McDonald-Kreitman selection tests identified putative niche-differentiating genes under positive selection that differed across the six well-represented genotypic populations and that may have driven initial divergence. Concurrent with patterns of recombination of discrete populations, recombination analyses of both genic and intergenic regions largely revealed decreased genetic exchange across individual genomes between relative to within populations.<br><br>CONCLUSIONS: These findings suggest that discrete double-stranded DNA marine cyanophage populations occur in nature and are maintained by patterns of recombination akin to those observed in bacteria, archaea and in sexual eukaryotes.}, }
@article {pmid27849579, year = {2016}, author = {Ling, J and Wang, H and Wu, P and Li, T and Tang, Y and Naseer, N and Zheng, H and Masson-Boivin, C and Zhong, Z and Zhu, J}, title = {Plant nodulation inducers enhance horizontal gene transfer of Azorhizobium caulinodans symbiosis island.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {48}, pages = {13875-13880}, pmid = {27849579}, issn = {1091-6490}, support = {R01 AI120489/AI/NIAID NIH HHS/United States ; }, mesh = {Azorhizobium caulinodans/*genetics/metabolism ; Fabaceae/genetics/microbiology ; Gene Transfer, Horizontal/*genetics ; Genomic Islands/genetics ; Nitrogen Fixation/genetics ; Plant Root Nodulation/*genetics ; Symbiosis/*genetics ; }, abstract = {Horizontal gene transfer (HGT) of genomic islands is a driving force of bacterial evolution. Many pathogens and symbionts use this mechanism to spread mobile genetic elements that carry genes important for interaction with their eukaryotic hosts. However, the role of the host in this process remains unclear. Here, we show that plant compounds inducing the nodulation process in the rhizobium-legume mutualistic symbiosis also enhance the transfer of symbiosis islands. We demonstrate that the symbiosis island of the Sesbania rostrata symbiont, Azorhizobium caulinodans, is an 87.6-kb integrative and conjugative element (ICE[Ac]) that is able to excise, form a circular DNA, and conjugatively transfer to a specific site of gly-tRNA gene of other rhizobial genera, expanding their host range. The HGT frequency was significantly increased in the rhizosphere. An ICE[Ac]-located LysR-family transcriptional regulatory protein AhaR triggered the HGT process in response to plant flavonoids that induce the expression of nodulation genes through another LysR-type protein, NodD. Our study suggests that rhizobia may sense rhizosphere environments and transfer their symbiosis gene contents to other genera of rhizobia, thereby broadening rhizobial host-range specificity.}, }
@article {pmid27846272, year = {2016}, author = {Domazet-Lošo, M and Domazet-Lošo, T}, title = {gmos: Rapid Detection of Genome Mosaicism over Short Evolutionary Distances.}, journal = {PloS one}, volume = {11}, number = {11}, pages = {e0166602}, pmid = {27846272}, issn = {1932-6203}, mesh = {Algorithms ; *Computational Biology ; Enterococcus faecium/genetics ; Gene Transfer, Horizontal ; Genome, Bacterial/*genetics ; Mosaicism ; Sequence Alignment/*methods ; Sequence Analysis, DNA/methods ; *Software ; }, abstract = {Prokaryotic and viral genomes are often altered by recombination and horizontal gene transfer. The existing methods for detecting recombination are primarily aimed at viral genomes or sets of loci, since the expensive computation of underlying statistical models often hinders the comparison of complete prokaryotic genomes. As an alternative, alignment-free solutions are more efficient, but cannot map (align) a query to subject genomes. To address this problem, we have developed gmos (Genome MOsaic Structure), a new program that determines the mosaic structure of query genomes when compared to a set of closely related subject genomes. The program first computes local alignments between query and subject genomes and then reconstructs the query mosaic structure by choosing the best local alignment for each query region. To accomplish the analysis quickly, the program mostly relies on pairwise alignments and constructs multiple sequence alignments over short overlapping subject regions only when necessary. This fine-tuned implementation achieves an efficiency comparable to an alignment-free tool. The program performs well for simulated and real data sets of closely related genomes and can be used for fast recombination detection; for instance, when a new prokaryotic pathogen is discovered. As an example, gmos was used to detect genome mosaicism in a pathogenic Enterococcus faecium strain compared to seven closely related genomes. The analysis took less than two minutes on a single 2.1 GHz processor. The output is available in fasta format and can be visualized using an accessory program, gmosDraw (freely available with gmos).}, }
@article {pmid27833663, year = {2016}, author = {Kaur, G and Arora, A and Sathyabama, S and Mubin, N and Verma, S and Mayilraj, S and Agrewala, JN}, title = {Genome sequencing, assembly, annotation and analysis of Staphylococcus xylosus strain DMB3-Bh1 reveals genes responsible for pathogenicity.}, journal = {Gut pathogens}, volume = {8}, number = {}, pages = {55}, pmid = {27833663}, issn = {1757-4749}, abstract = {BACKGROUND: Staphylococcus xylosus is coagulase-negative staphylococci (CNS), found occasionally on the skin of humans but recurrently on other mammals. Recent reports suggest that this commensal bacterium may cause diseases in humans and other animals. In this study, we present the first report of whole genome sequencing of S. xylosus strain DMB3-Bh1, which was isolated from the stool of a mouse.<br><br>RESULTS: The draft genome of S. xylosus strain DMB3-Bh1 consisted of 2,81,0255&#xa0;bp with G+C content of 32.7&#xa0;mol%, 2623 predicted coding sequences (CDSs) and 58 RNAs. The final assembly contained 12 contigs of total size 2,81,0255&#xa0;bp with N50 contig length of 4,37,962&#xa0;bp and the largest contig assembled measured 7,61,338&#xa0;bp. Further, an interspecies comparative genomic analysis through rapid annotation using subsystem technology server was achieved with Staphylococcus aureus RF122 that revealed 36 genes having similarity with S. xylosus DMB3-Bh1. 35 genes encoded for virulence, disease and defense and 1 gene encoded for phages, prophages and transposable elements.<br><br>CONCLUSIONS: These results suggest co linearity in genes between S. xylosus DMB3-Bh1 and S. aureus RF122 that contribute to pathogenicity and might be the result of horizontal gene transfer. The study indicates that S. xylosus DMB3-Bh1 may be a potential emerging pathogen for rodents.}, }
@article {pmid27833021, year = {2016}, author = {Matsumoto, A and Sekoguchi, A and Imai, J and Kondo, K and Shibata, Y and Maeda, S}, title = {Natural Escherichia coli strains undergo cell-to-cell plasmid transformation.}, journal = {Biochemical and biophysical research communications}, volume = {481}, number = {1-2}, pages = {59-62}, doi = {10.1016/j.bbrc.2016.11.018}, pmid = {27833021}, issn = {1090-2104}, mesh = {Cell Communication/genetics ; DNA, Bacterial/*genetics ; Escherichia coli/classification/*cytology/*genetics ; Gene Transfer, Horizontal/*genetics ; Plasmids/*genetics ; Species Specificity ; Transformation, Bacterial/*genetics ; }, abstract = {Horizontal gene transfer is a strong tool that allows bacteria to adapt to various environments. Although three conventional mechanisms of horizontal gene transfer (transformation, transduction, and conjugation) are well known, new variations of these mechanisms have also been observed. We recently reported that DNase-sensitive cell-to-cell transfer of nonconjugative plasmids occurs between laboratory strains of Escherichia coli in co-culture. We termed this phenomenon "cell-to-cell transformation." In this report, we found that several combinations of Escherichia coli collection of reference (ECOR) strains, which were co-cultured in liquid media, resulted in DNase-sensitive cell-to-cell transfer of antibiotic resistance genes. Plasmid isolation of these new transformants demonstrated cell-to-cell plasmid transfer between the ECOR strains. Natural transformation experiments, using a combination of purified plasmid DNA and the same ECOR strains, revealed that cell-to-cell transformation occurs much more frequently than natural transformation under the same culture conditions. Thus, cell-to-cell transformation is both unique and effective. In conclusion, this study is the first to demonstrate cell-to-cell plasmid transformation in natural E. coli strains.}, }
@article {pmid27832824, year = {2016}, author = {McKenna, DD and Scully, ED and Pauchet, Y and Hoover, K and Kirsch, R and Geib, SM and Mitchell, RF and Waterhouse, RM and Ahn, SJ and Arsala, D and Benoit, JB and Blackmon, H and Bledsoe, T and Bowsher, JH and Busch, A and Calla, B and Chao, H and Childers, AK and Childers, C and Clarke, DJ and Cohen, L and Demuth, JP and Dinh, H and Doddapaneni, H and Dolan, A and Duan, JJ and Dugan, S and Friedrich, M and Glastad, KM and Goodisman, MA and Haddad, S and Han, Y and Hughes, DS and Ioannidis, P and Johnston, JS and Jones, JW and Kuhn, LA and Lance, DR and Lee, CY and Lee, SL and Lin, H and Lynch, JA and Moczek, AP and Murali, SC and Muzny, DM and Nelson, DR and Palli, SR and Panfilio, KA and Pers, D and Poelchau, MF and Quan, H and Qu, J and Ray, AM and Rinehart, JP and Robertson, HM and Roehrdanz, R and Rosendale, AJ and Shin, S and Silva, C and Torson, AS and Jentzsch, IM and Werren, JH and Worley, KC and Yocum, G and Zdobnov, EM and Gibbs, RA and Richards, S}, title = {Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface.}, journal = {Genome biology}, volume = {17}, number = {1}, pages = {227}, pmid = {27832824}, issn = {1474-760X}, support = {K12 GM000708/GM/NIGMS NIH HHS/United States ; U54 HG003273/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Coleoptera/*genetics/pathogenicity ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Insect/*genetics ; Host-Parasite Interactions/genetics ; Introduced Species ; Larva ; *Sequence Analysis, DNA ; Trees/parasitology ; }, abstract = {BACKGROUND: Relatively little is known about the genomic basis and evolution of wood-feeding in beetles. We undertook genome sequencing and annotation, gene expression assays, studies of plant cell wall degrading enzymes, and other functional and comparative studies of the Asian longhorned beetle, Anoplophora glabripennis, a globally significant invasive species capable of inflicting severe feeding damage on many important tree species. Complementary studies of genes encoding enzymes involved in digestion of woody plant tissues or detoxification of plant allelochemicals were undertaken with the genomes of 14 additional insects, including the newly sequenced emerald ash borer and bull-headed dung beetle.<br><br>RESULTS: The Asian longhorned beetle genome encodes a uniquely diverse arsenal of enzymes that can degrade the main polysaccharide networks in plant cell walls, detoxify plant allelochemicals, and otherwise facilitate feeding on woody plants. It has the metabolic plasticity needed to feed on diverse plant species, contributing to its highly invasive nature. Large expansions of chemosensory genes involved in the reception of pheromones and plant kairomones are consistent with the complexity of chemical cues it uses to find host plants and mates.<br><br>CONCLUSIONS: Amplification and functional divergence of genes associated with specialized feeding on plants, including genes originally obtained via horizontal gene transfer from fungi and bacteria, contributed to the addition, expansion, and enhancement of the metabolic repertoire of the Asian longhorned beetle, certain other phytophagous beetles, and to a lesser degree, other phytophagous insects. Our results thus begin to establish a genomic basis for the evolutionary success of beetles on plants.}, }
@article {pmid27831476, year = {2016}, author = {Michael, CA and Franks, AE and Labbate, M}, title = {The antimicrobial resistance crisis: management through gene monitoring.}, journal = {Open biology}, volume = {6}, number = {11}, pages = {}, pmid = {27831476}, issn = {2046-2441}, mesh = {Anti-Bacterial Agents ; Bacteria/*genetics ; Bacterial Proteins/*genetics ; *Drug Resistance, Bacterial ; Evolution, Molecular ; Gene Frequency ; Genome, Bacterial ; Humans ; Prospective Studies ; Selection, Genetic ; }, abstract = {Antimicrobial resistance (AMR) is an acknowledged crisis for humanity. Its genetic origins and dire potential outcomes are increasingly well understood. However, diagnostic techniques for monitoring the crisis are currently largely limited to enumerating the increasing incidence of resistant pathogens. Being the end-stage of the evolutionary process that produces antimicrobial resistant pathogens, these measurements, while diagnostic, are not prognostic, and so are not optimal in managing this crisis. A better test is required. Here, using insights from an understanding of evolutionary processes ruling the changing abundance of genes under selective pressure, we suggest a predictive framework for the AMR crisis. We then discuss the likely progression of resistance for both existing and prospective antimicrobial therapies. Finally, we suggest that by the environmental monitoring of resistance gene frequency, resistance may be detected and tracked presumptively, and how this tool may be used to guide decision-making in the local and global use of antimicrobials.}, }
@article {pmid27828759, year = {2017}, author = {Fernandes, SA and Camargo, CH and Francisco, GR and Bueno, MFC and Garcia, DO and Doi, Y and Casas, MRT}, title = {Prevalence of Extended-Spectrum β-Lactamases CTX-M-8 and CTX-M-2-Producing Salmonella Serotypes from Clinical and Nonhuman Isolates in Brazil.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {23}, number = {5}, pages = {580-589}, doi = {10.1089/mdr.2016.0085}, pmid = {27828759}, issn = {1931-8448}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Brazil/epidemiology ; Chickens ; Conjugation, Genetic ; Drug Resistance, Multiple, Bacterial/*genetics ; Electrophoresis, Gel, Pulsed-Field ; Gene Expression ; Gene Transfer, Horizontal ; Genetic Variation ; Humans ; Isoenzymes/genetics/metabolism ; Meat Products/microbiology ; Microbial Sensitivity Tests ; Plasmids/chemistry/metabolism ; Prevalence ; Public Health Surveillance ; Salmonella/classification/drug effects/*genetics/isolation &amp; purification ; Salmonella Infections/drug therapy/*epidemiology/microbiology ; Salmonella typhimurium/classification/drug effects/*genetics/isolation &amp; purification ; *Serogroup ; Sewage/microbiology ; beta-Lactamases/*genetics/metabolism ; }, abstract = {We characterized extended-spectrum β-lactamases (ESBL) enzymes among Salmonella strains isolated in Brazil from 2009 to 2014. Salmonella recovered from both clinical and nonhuman (food, poultry, and environment) sources were subjected to antimicrobial susceptibility testing. β-lactamases genes were detected by polymerase chain reaction/sequencing; plasmid profiles and transferability were assessed by S1-pulsed field gel electrophoresis (PFGE). Genetic diversity was evaluated by XbaI-PFGE. Out of 630 Salmonella strains screened, 46 displayed ESBL phenotype, distributed across 11 different serotypes. blaCTX-M-8 and blaCTX-M-2 genes were detected at frequencies of 47% and 41%, respectively. blaSHV-5 and blaSHV-2 were also detected but in lower frequencies (4%, 2%). blaTEM-1 gene was detected in 22% of the strains. Most of the ESBL genes were transferable by conjugation, and the respective blaESBL gene was detected in the recipient strain, indicating the location of ESBL determinants on transferable plasmids. XbaI-PFGE revealed genomic diversity of Salmonella Typhimurium bearing blaCTX-M-2, blaCTX-M-8, blaTEM-1, and blaSHV-2 genes. Salmonella Muenchen (harboring blaCTX-M-2) and Salmonella Corvallis (blaCTX-M-8 and blaSHV-5) showed clonal relatedness within respective serotypes. Our findings underscore the occurrence of diverse ESBL genes in several Salmonella serotypes, reinforcing the need for continuous surveillance of resistance genes circulating in human and nonhuman sources.}, }
@article {pmid27825443, year = {2016}, author = {Blokesch, M}, title = {Natural competence for transformation.}, journal = {Current biology : CB}, volume = {26}, number = {21}, pages = {R1126-R1130}, doi = {10.1016/j.cub.2016.08.058}, pmid = {27825443}, issn = {1879-0445}, mesh = {Bacteria/*genetics ; Bacteriophages/genetics ; *Conjugation, Genetic ; *Gene Transfer, Horizontal ; *Transduction, Genetic ; }, abstract = {While most molecular biologists are familiar with the artificial transformation of bacteria in the context of laboratory cloning experiments, natural competence for transformation refers to a specific physiological state in which prokaryotes are able to take up genetic material from their surroundings. Occasionally, such absorbed DNA is recombined into the organism's own genome, resulting in natural transformation (Figure 1). As a consequence, natural competence for transformation is considered a primary mode of horizontal gene transfer (HGT) in prokaryotes, together with conjugation (direct cell to cell transfer of DNA via a specialized conjugal pilus) and phage transduction (DNA transfer mediated by viruses). HGT plays a major role in bacterial evolution, and past research has demonstrated that HGT, including natural competence for transformation, contributes to the emergence of pathogens and the spread of virulence factors. Indeed, Frederick Griffith discovered natural competence for transformation in 1928 while he was investigating the exchange of pathogenic traits in pneumococci. Due to the increase in the abundance and spread of multidrug-resistant microbes, research on HGT is even more important today than ever before.}, }
@article {pmid27824124, year = {2016}, author = {Watanabe, T and Kojima, H and Fukui, M}, title = {Identity of major sulfur-cycle prokaryotes in freshwater lake ecosystems revealed by a comprehensive phylogenetic study of the dissimilatory adenylylsulfate reductase.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {36262}, pmid = {27824124}, issn = {2045-2322}, mesh = {Bacteria/classification/*enzymology/genetics ; Bacterial Proteins/genetics ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Ecosystem ; Evolution, Molecular ; Fresh Water/*microbiology ; Gene Transfer, Horizontal ; Lakes ; Oxidoreductases Acting on Sulfur Group Donors/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Adenylylsulfate reductase is a heterodimeric complex of two subunits, AprB and AprA, and is a key enzyme in dissimilatory sulfate reduction and sulfur oxidation. Common use of aprA as a functional marker gene has revealed the diversity of sulfur-cycle prokaryotes in diverse environments. In this study, we established a comprehensive sequence set of apr genes and employed it to reanalyze apr phylogeny, evaluate the coverage of a widely used primer set (AprA-1-FW/AprA-5-RV), and categorize environmental aprA sequences. Phylogenetic tree construction revealed new members of Apr lineage II and several previously unrecognized lateral gene transfer events. Using the established phylogenetic tree, we classified all previously reported aprA sequences amplified from freshwater lakes with the primer pair AprA-1-FW/AprA-5-RV in addition to the aprA sequences newly retrieved from freshwater lakes; the obtained results were complemented by 16S rRNA clone library analysis. Apr-based classifications of some of operational taxonomic units were supported by 16S rRNA-based analysis. This study updates our knowledge on the phylogeny of aprBA and shows the identities of several sulfur-cycle bacteria, which could not be classified to a known taxa until now. The established apr sequence set is publicly available and can be applied to assign environmental sequences to known lineages.}, }
@article {pmid27822532, year = {2016}, author = {Roer, L and Hendriksen, RS and Leekitcharoenphon, P and Lukjancenko, O and Kaas, RS and Hasman, H and Aarestrup, FM}, title = {Is the Evolution of Salmonella enterica subsp. enterica Linked to Restriction-Modification Systems?.}, journal = {mSystems}, volume = {1}, number = {3}, pages = {}, pmid = {27822532}, issn = {2379-5077}, abstract = {Salmonella enterica subsp. enterica bacteria are highly diverse foodborne pathogens that are subdivided into more than 1,500 serovars. The diversity is believed to result from mutational evolution, as well as intra- and interspecies recombination that potentially could be influenced by restriction-modification (RM) systems. The aim of this study was to investigate whether RM systems were linked to the evolution of Salmonella enterica subsp. enterica. The study included 221 Salmonella enterica genomes, of which 68 were de novo sequenced and 153 were public available genomes from ENA. The data set covered 97 different serovars of Salmonella enterica subsp. enterica and an additional five genomes from four other Salmonella subspecies as an outgroup for constructing the phylogenetic trees. The phylogenetic trees were constructed based on multiple alignment of core genes, as well as the presence or absence of pangenes. The topology of the trees was compared to the presence of RM systems, antimicrobial resistance (AMR) genes, Salmonella pathogenicity islands (SPIs), and plasmid replicons. We did not observe any correlation between evolution and the RM systems in S. enterica subsp. enterica. However, sublineage correlations and serovar-specific patterns were observed. Additionally, we conclude that plasmid replicons, SPIs, and AMR were all better correlated to serovars than to RM systems. This study suggests a limited influence of RM systems on the evolution of Salmonella enterica subsp. enterica, which could be due to the conjugational mode of horizontal gene transfer in Salmonella. Thus, we conclude that other factors must be involved in shaping the evolution of bacteria. IMPORTANCE The evolution of bacterial pathogens, their plasticity and ability to rapidly change and adapt to new surroundings are crucial for understanding the epidemiology and public health. With the application of genomics, it became clear that horizontal gene transfer played a key role in evolution. To understand the evolution and diversification of pathogens, we need to understand the processes that drive the horizontal gene transfer. Restriction-modification systems are thought to cause rearrangements within the chromosome, as well as act as a barrier to horizontal gene transfer. However, here we show that the correlation between restriction-modification systems and evolution in other bacterial species does not apply to Salmonella enterica subsp. enterica. In summary, from this work, we conclude that other mechanisms might be involved in controlling and shaping the evolution of Salmonella enterica subsp. enterica.}, }
@article {pmid27819663, year = {2016}, author = {Wolf, YI and Makarova, KS and Lobkovsky, AE and Koonin, EV}, title = {Two fundamentally different classes of microbial genes.}, journal = {Nature microbiology}, volume = {2}, number = {}, pages = {16208}, doi = {10.1038/nmicrobiol.2016.208}, pmid = {27819663}, issn = {2058-5276}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Evolution, Molecular ; *Genes, Microbial ; Genetic Variation ; Synteny ; }, abstract = {The evolution of bacterial and archaeal genomes is highly dynamic and involves extensive horizontal gene transfer and gene loss[1-4]. Furthermore, many microbial species appear to have open pangenomes, where each newly sequenced genome contains more than 10% ORFans, that is, genes without detectable homologues in other species[5,6]. Here, we report a quantitative analysis of microbial genome evolution by fitting the parameters of a simple, steady-state evolutionary model to the comparative genomic data on the gene content and gene order similarity between archaeal genomes. The results reveal two sharply distinct classes of microbial genes, one of which is characterized by effectively instantaneous gene replacement, and the other consists of genes with finite, distributed replacement rates. These findings imply a conservative estimate of the size of the prokaryotic genomic universe, which appears to consist of at least a billion distinct genes. Furthermore, the same distribution of constraints is shown to govern the evolution of gene complement and gene order, without the need to invoke long-range conservation or the selfish operon concept[7].}, }
@article {pmid27819286, year = {2016}, author = {Haaber, J and Leisner, JJ and Cohn, MT and Catalan-Moreno, A and Nielsen, JB and Westh, H and Penadés, JR and Ingmer, H}, title = {Bacterial viruses enable their host to acquire antibiotic resistance genes from neighbouring cells.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {13333}, pmid = {27819286}, issn = {2041-1723}, mesh = {Anti-Bacterial Agents/*pharmacology/therapeutic use ; DNA, Bacterial/genetics ; Drug Resistance, Microbial/*genetics ; Gene Transfer, Horizontal/genetics ; Host-Pathogen Interactions/genetics ; Humans ; Prophages/*physiology ; Staphylococcal Infections/*drug therapy/microbiology ; Staphylococcus aureus/*physiology/virology ; }, abstract = {Prophages are quiescent viruses located in the chromosomes of bacteria. In the human pathogen, Staphylococcus aureus, prophages are omnipresent and are believed to be responsible for the spread of some antibiotic resistance genes. Here we demonstrate that release of phages from a subpopulation of S. aureus cells enables the intact, prophage-containing population to acquire beneficial genes from competing, phage-susceptible strains present in the same environment. Phage infection kills competitor cells and bits of their DNA are occasionally captured in viral transducing particles. Return of such particles to the prophage-containing population can drive the transfer of genes encoding potentially useful traits such as antibiotic resistance. This process, which can be viewed as 'auto-transduction', allows S. aureus to efficiently acquire antibiotic resistance both in vitro and in an in vivo virulence model (wax moth larvae) and enables it to proliferate under strong antibiotic selection pressure. Our results may help to explain the rapid exchange of antibiotic resistance genes observed in S. aureus.}, }
@article {pmid27816285, year = {2017}, author = {Huang, L and Xu, YB and Xu, JX and Ling, JY and Chen, JL and Zhou, JL and Zheng, L and Du, QP}, title = {Antibiotic resistance genes (ARGs) in duck and fish production ponds with integrated or non-integrated mode.}, journal = {Chemosphere}, volume = {168}, number = {}, pages = {1107-1114}, doi = {10.1016/j.chemosphere.2016.10.096}, pmid = {27816285}, issn = {1879-1298}, mesh = {Animals ; Aquaculture ; Bacterial Proteins/genetics ; China ; Drug Resistance, Microbial/*genetics ; Ducks ; Environmental Monitoring ; Fishes ; *Genes, Bacterial ; Geologic Sediments/analysis ; Ponds/analysis ; Water Pollutants/*analysis ; }, abstract = {Antibiotic resistance genes (ARGs) are emerging micropollutants with environmental persistence. Aquaculture environments are considered as potential reservoirs for ARGs pollution and horizontal gene transfer (HGT). This study analyzed water and sediment from eight culture ponds (integrated culture: duck-fish pond; monoculture: duck pond and fish pond) and a control pond (without any aquaculture activity) in Zhongshan, South China. Seventeen types of ARGs were detected in all ponds, which conferring resistance to four classes of antibiotics including tetracycline (tetA, tetB, tetC, tetE, tetG, tetL, tetA-P, tetM, tetO, tetS, tetW and tetX), AmpC beta-lactamase products (EBC and FOX), sulfonamide (sul1 and sul2) and erythromycin (ermA), with class 1 integron (intI1) as motility gene. The total concentrations of detected ARGs in culture pond water were much higher than control (about 1.6-4.0 times). Integrated culture showed lowest absolute abundance of ∑ARGs in water (3.686 × 10[7] copies mL[-1]) and the highest in sediment (4.574 × 10[8] copies g[-1]). Monoculture ponds showed higher relative abundance of ∑ARGs both in water (fish pond: 0.5149) and sediment (duck pond: 0.4919). As the main contributor to the ARGs abundance and significant correlations with ∑tet, ∑ARGs and intI1 (P < 0.01), tetA was suggested to be a potential indicator for the abundance of tetracycline resistance genes in these classes of aquaculture modes in the Pearl River Delta. This study provides a case for the ARGs abundance in aquaculture and as a reference for the upcoming health risk assessment in aquatic environment.}, }
@article {pmid27812423, year = {2016}, author = {Brouard, JS and Turmel, M and Otis, C and Lemieux, C}, title = {Proliferation of group II introns in the chloroplast genome of the green alga Oedocladium carolinianum (Chlorophyceae).}, journal = {PeerJ}, volume = {4}, number = {}, pages = {e2627}, pmid = {27812423}, issn = {2167-8359}, abstract = {BACKGROUND: The chloroplast genome sustained extensive changes in architecture during the evolution of the Chlorophyceae, a morphologically and ecologically diverse class of green algae belonging to the Chlorophyta; however, the forces driving these changes are poorly understood. The five orders recognized in the Chlorophyceae form two major clades: the CS clade consisting of the Chlamydomonadales and Sphaeropleales, and the OCC clade consisting of the Oedogoniales, Chaetophorales, and Chaetopeltidales. In the OCC clade, considerable variations in chloroplast DNA (cpDNA) structure, size, gene order, and intron content have been observed. The large inverted repeat (IR), an ancestral feature characteristic of most green plants, is present in Oedogonium cardiacum (Oedogoniales) but is lacking in the examined members of the Chaetophorales and Chaetopeltidales. Remarkably, the Oedogonium 35.5-kb IR houses genes that were putatively acquired through horizontal DNA transfer. To better understand the dynamics of chloroplast genome evolution in the Oedogoniales, we analyzed the cpDNA of a second representative of this order, Oedocladium carolinianum.<br><br>METHODS: The Oedocladium cpDNA was sequenced and annotated. The evolutionary distances separating Oedocladium and Oedogonium cpDNAs and two other pairs of chlorophycean cpDNAs were estimated using a 61-gene data set. Phylogenetic analysis of an alignment of group IIA introns from members of the OCC clade was performed. Secondary structures and insertion sites of oedogonialean group IIA introns were analyzed.<br><br>RESULTS: The 204,438-bp Oedocladium genome is 7.9 kb larger than the Oedogonium genome, but its repertoire of conserved genes is remarkably similar and gene order differs by only one reversal. Although the 23.7-kb IR is missing the putative foreign genes found in Oedogonium, it contains sequences coding for a putative phage or bacterial DNA primase and a hypothetical protein. Intergenic sequences are 1.5-fold longer and dispersed repeats are more abundant, but a smaller fraction of the Oedocladium genome is occupied by introns. Six additional group II introns are present, five of which lack ORFs and carry highly similar sequences to that of the ORF-less IIA intron shared with Oedogonium. Secondary structure analysis of the group IIA introns disclosed marked differences in the exon-binding sites; however, each intron showed perfect or nearly perfect base pairing interactions with its target site.<br><br>DISCUSSION: Our results suggest that chloroplast genes rearrange more slowly in the Oedogoniales than in the Chaetophorales and raise questions as to what was the nature of the foreign coding sequences in the IR of the common ancestor of the Oedogoniales. They provide the first evidence for intragenomic proliferation of group IIA introns in the Viridiplantae, revealing that intron spread in the Oedocladium lineage likely occurred by retrohoming after sequence divergence of the exon-binding sites.}, }
@article {pmid27811990, year = {2016}, author = {Berthold, T and Centler, F and Hübschmann, T and Remer, R and Thullner, M and Harms, H and Wick, LY}, title = {Mycelia as a focal point for horizontal gene transfer among soil bacteria.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {36390}, pmid = {27811990}, issn = {2045-2322}, mesh = {Bacteria/*genetics ; Bacterial Physiological Phenomena ; *Gene Transfer, Horizontal ; Genetic Variation ; Mycelium/*physiology ; Soil Microbiology ; }, abstract = {Horizontal gene transfer (HGT) is a main mechanism of bacterial evolution endowing bacteria with new genetic traits. The transfer of mobile genetic elements such as plasmids (conjugation) requires the close proximity of cells. HGT between genetically distinct bacteria largely depends on cell movement in water films, which are typically discontinuous in natural systems like soil. Using laboratory microcosms, a bacterial reporter system and flow cytometry, we here investigated if and to which degree mycelial networks facilitate contact of and HGT between spatially separated bacteria. Our study shows that the network structures of mycelia promote bacterial HGT by providing continuous liquid films in which bacterial migration and contacts are favoured. This finding was confirmed by individual-based simulations, revealing that the tendency of migrating bacteria to concentrate in the liquid film around hyphae is a key factor for improved HGT along mycelial networks. Given their ubiquity, we propose that hyphae can act as focal point for HGT and genetic adaptation in soil.}, }
@article {pmid27811174, year = {2016}, author = {Maumus, F and Blanc, G}, title = {Study of Gene Trafficking between Acanthamoeba and Giant Viruses Suggests an Undiscovered Family of Amoeba-Infecting Viruses.}, journal = {Genome biology and evolution}, volume = {8}, number = {11}, pages = {3351-3363}, pmid = {27811174}, issn = {1759-6653}, mesh = {Acanthamoeba/*genetics/virology ; DNA Viruses/classification/*genetics/pathogenicity ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Protozoan ; *Genes, Viral ; Phylogeny ; }, abstract = {The nucleocytoplasmic large DNA viruses (NCLDV) are a group of extremely complex double-stranded DNA viruses, which are major parasites of a variety of eukaryotes. Recent studies showed that certain unicellular eukaryotes contain fragments of NCLDV DNA integrated in their genome, when surprisingly many of these organisms were not previously shown to be infected by NCLDVs. These findings prompted us to search the genome of Acanthamoeba castellanii strain Neff (Neff), one of the most prolific hosts in the discovery of giant NCLDVs, for possible DNA inserts of viral origin. We report the identification of 267 markers of lateral gene transfer with viruses, approximately half of which are clustered in Neff genome regions of viral origins, transcriptionally inactive or exhibit nucleotide-composition signatures suggestive of a foreign origin. The integrated viral genes had diverse origin among relatives of viruses that infect Neff, including Mollivirus, Pandoravirus, Marseillevirus, Pithovirus, and Mimivirus However, phylogenetic analysis suggests the existence of a yet-undiscovered family of amoeba-infecting NCLDV in addition to the five already characterized. The active transcription of some apparently anciently integrated virus-like genes suggests that some viral genes might have been domesticated during the amoeba evolution. These insights confirm that genomic insertion of NCLDV DNA is a common theme in eukaryotes. This gene flow contributed fertilizing the eukaryotic gene repertoire and participated in the occurrence of orphan genes, a long standing issue in genomics. Search for viral inserts in eukaryotic genomes followed by environmental screening of the original viruses should be used to isolate radically new NCLDVs.}, }
@article {pmid27811049, year = {2016}, author = {Eggers, CH and Gray, CM and Preisig, AM and Glenn, DM and Pereira, J and Ayers, RW and Alshahrani, M and Acabbo, C and Becker, MR and Bruenn, KN and Cheung, T and Jendras, TM and Shepley, AB and Moeller, JT}, title = {Phage-mediated horizontal gene transfer of both prophage and heterologous DNA by ϕBB-1, a bacteriophage of Borrelia burgdorferi.}, journal = {Pathogens and disease}, volume = {74}, number = {9}, pages = {}, doi = {10.1093/femspd/ftw107}, pmid = {27811049}, issn = {2049-632X}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteriophages/drug effects/*physiology ; Borrelia burgdorferi/drug effects/*genetics/*virology ; *DNA ; DNA, Bacterial ; Ethanol/pharmacology ; *Gene Transfer, Horizontal ; Humans ; Lyme Disease/microbiology ; Microbial Sensitivity Tests ; }, abstract = {Horizontal gene transfer (HGT) in Borrelia burgdorferi, the Lyme disease agent, is likely mediated by bacteriophage. Studies of the B. burgdorferi phage, ϕBB-1 and its role in HGT have been hindered by the lack of an assay for readily characterizing phage-mediated DNA movement (transduction). Here we describe an in vitro assay in which a clone of B. burgdorferi strain CA-11.2A encoding kanamycin resistance on a ϕBB-1 prophage is co-cultured with different clones encoding gentamicin resistance on a shuttle vector; transduction is monitored by enumerating colonies selected in the presence of both kanamycin and gentamicin. When both clones used in the assay were derived from CA-11.2A, the frequency of transduction was 1.23 × 10[-6] transductants per cell, and could be increased 5-fold by exposing the phage-producing strain to 5% ethanol. Transduction was also demonstrated between the CA-11.2A clone and clones of both high-passage B. burgdorferi strain B31 and low-passage, virulent B. burgdorferi strain 297, although with lower transduction frequencies. The transductant in the 297 background produced phage capable of transducing another B. burgdorferi clone: this is the first experimental demonstration of transduction from a clone of a virulent strain. In addition to prophage DNA, small Escherichia coli-derived shuttle vectors were also transduced between co-cultured B. burgdorferi strains, suggesting both a broad role for the phage in the HGT of heterologous DNA and a potential use of the phage as a molecular tool. These results enhance our understanding of phage-mediated transduction as a mechanism of HGT in the Lyme disease spirochetes. Furthermore, the reagents and techniques developed herein will facilitate future studies of phage-mediated HGT, especially within the tick vector and vertebrate host.}, }
@article {pmid27810499, year = {2016}, author = {Artuso, MC and Roldán, JS and Scolaro, LA and Carlucci, MJ}, title = {Viruses: As mediators in "Élan vital" of the "creative" evolution.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {46}, number = {}, pages = {78-84}, doi = {10.1016/j.meegid.2016.10.028}, pmid = {27810499}, issn = {1567-7257}, mesh = {Animals ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Life ; Mice ; Polysaccharides ; Simplexvirus ; Sulfates ; *Viruses ; }, abstract = {The understanding of the processes occurring in Nature has been a continuing concern throughout the history of mankind. Intellectual tools employed towards this goal were specific for each period and have been largely based on the prevailing paradigms that reigned in the past. In this work we present evidence that supports the idea of viruses as key agents mediating natural processes linked to the evolution of organisms, particularly those involved in the flux of genes in the environment. This point of view tinges our perception of Nature and prompts us to include "viral" creativity and plasticity among the tools we employ to analyze those processes far beyond actual paradigms. Experimental data to support this proposal arose during the study of the interaction of the human pathogen, herpes simplex virus (HSV) with sulfated polysaccharides during multiplication of the virus in vitro. Sulfated polysaccharides are the main chemical structures found in carrageenans (CGNs) that are natural products obtained from seaweeds, which proved to be strong inhibitors for the virus. Here we describe the interaction between virus and CGNs as a suitable scenario for the emergence of viral variants which proved to be markedly attenuated for mice. A striking feature of these variants is that they showed changes at the level of conserved regions of the genome such as the DNA polymerase and thymidine kinase genes. In view of these findings, the importance of HSV evolution towards attenuated variants by the action of polysaccharides is also discussed. Attenuation may be considered part of a natural evolutionary process enabling the virus to contribute with valuable information for the host.}, }
@article {pmid27810477, year = {2017}, author = {Bolotin, A and Gillis, A and Sanchis, V and Nielsen-LeRoux, C and Mahillon, J and Lereclus, D and Sorokin, A}, title = {Comparative genomics of extrachromosomal elements in Bacillus thuringiensis subsp. israelensis.}, journal = {Research in microbiology}, volume = {168}, number = {4}, pages = {331-344}, doi = {10.1016/j.resmic.2016.10.008}, pmid = {27810477}, issn = {1769-7123}, mesh = {Animals ; Bacillus thuringiensis/*genetics/pathogenicity ; Bacterial Toxins/genetics ; Base Sequence ; Biological Control Agents ; Culicidae/microbiology ; DNA Transposable Elements/*genetics ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/*genetics ; Multilocus Sequence Typing ; Plasmids/*genetics ; Sequence Analysis, DNA ; }, abstract = {Bacillus thuringiensis subsp. israelensis is one of the most important microorganisms used against mosquitoes. It was intensively studied following its discovery and became a model bacterium of the B. thuringiensis species. Those studies focused on toxin genes, aggregation-associated conjugation, linear genome phages, etc. Recent announcements of genomic sequences of different strains have not been explicitly related to the biological properties studied. We report data on plasmid content analysis of four strains using ultra-high-throughput sequencing. The strains were commercial product isolates, with their putative ancestor and type B. thuringiensis subsp. israelensis strain sequenced earlier. The assembled contigs corresponding to published and novel data were assigned to plasmids described earlier in B. thuringiensis subsp. israelensis and other B. thuringiensis strains. A new 360 kb plasmid was identified, encoding multiple transporters, also found in most of the earlier sequenced strains. Our genomic data show the presence of two toxin-coding plasmids of 128 and 100 kb instead of the reported 225 kb plasmid, a co-integrate of the former two. In two of the sequenced strains, only a 100 kb plasmid was present. Some heterogeneity exists in the small plasmid content and structure between strains. These data support the perception of active plasmid exchange among B. thuringiensis subsp. israelensis strains in nature.}, }
@article {pmid27681363, year = {2016}, author = {Ni, Q and Tian, Y and Zhang, L and Jiang, C and Dong, D and Li, Z and Mao, E and Peng, Y}, title = {Prevalence and quinolone resistance of fecal carriage of extended-spectrum β-lactamase-producing Escherichia coli in 6 communities and 2 physical examination center populations in Shanghai, China.}, journal = {Diagnostic microbiology and infectious disease}, volume = {86}, number = {4}, pages = {428-433}, doi = {10.1016/j.diagmicrobio.2016.07.010}, pmid = {27681363}, issn = {1879-0070}, mesh = {Adult ; Aged ; Aged, 80 and over ; Anti-Bacterial Agents/*pharmacology ; Carrier State/*epidemiology/microbiology ; China/epidemiology ; Community-Acquired Infections/*epidemiology/microbiology ; *Drug Resistance, Bacterial ; Escherichia coli/*drug effects/enzymology/genetics/isolation &amp; purification ; Escherichia coli Infections/*epidemiology/microbiology ; Feces/microbiology ; Female ; Gene Transfer, Horizontal ; Humans ; Male ; Microbial Sensitivity Tests ; Middle Aged ; Plasmids/analysis ; Polymerase Chain Reaction ; Prevalence ; Quinolones/*pharmacology ; Sequence Analysis, DNA ; Young Adult ; beta-Lactamases/*metabolism ; }, abstract = {OBJECTIVES: To characterize extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolates from the community, determine their antibiotic sensitivity profiles and quinolone resistance mechanisms, and identify any horizontal transfer of ESBL genes.<br><br>METHODS: One thousand seven hundred thirty-two stool samples were collected from healthy individuals in 6 communities and 2 physical examination centers in Shanghai, China. ESBL-producing E. coli was screened and confirmed by confirmatory test and E. coli-identifying agars. PCR was used to amplify ESBL-encoding genes blaCTX-M, blaTEM, blaSHV genes, and quinolone resistance-relating genes gyrA, gryB, parC, parE, qnrS, aac (6')-Ib-cr, oqxA, and oqxB, followed by sequencing. Antimicrobial susceptibility tests and conjugation assays were also performed.<br><br>RESULTS: Overall, 528 isolates were identified as ESBL-producing E. coli, and all were positive for blaCTX-M. CTX-M-14 was found most frequently (48.9%). S83L&#xb1;D87N in gyrA and S80I in parC were the most common topoisomerase mutations. Plasmid-mediated quinolone resistance (PMQR) determinants were also detected, including qnrS1 (11.7%), qnrS2 (3.7%), aac (6')-Ib-cr(12.8%), oqxA(8.5%), and oqxB(11.0%). The rate of multidrug resistance was very high (92.2%). ESBL genes transferred successfully in 39.4% isolates.<br><br>CONCLUSIONS: There is a high prevalence of fecal carriage of ESBL-producing E. coli in the community in Shanghai, with high-level quinolone resistance and CTX-M-14 being the predominant CTX-M enzyme.}, }
@article {pmid27809244, year = {2016}, author = {Andersen, KL and Beckert, B and Masquida, B and Johansen, SD and Nielsen, H}, title = {Accumulation of Stable Full-Length Circular Group I Intron RNAs during Heat-Shock.}, journal = {Molecules (Basel, Switzerland)}, volume = {21}, number = {11}, pages = {}, pmid = {27809244}, issn = {1420-3049}, mesh = {Heat-Shock Response/*physiology ; *Introns ; Myxomycetes/genetics/*metabolism ; RNA, Catalytic/*biosynthesis/genetics ; }, abstract = {Group I introns in nuclear ribosomal RNA of eukaryotic microorganisms are processed by splicing or circularization. The latter results in formation of full-length circular introns without ligation of the exons and has been proposed to be active in intron mobility. We applied qRT-PCR to estimate the copy number of circular intron RNA from the myxomycete Didymium iridis. In exponentially growing amoebae, the circular introns are nuclear and found in 70 copies per cell. During heat-shock, the circular form is up-regulated to more than 500 copies per cell. The intron harbours two ribozymes that have the potential to linearize the circle. To understand the structural features that maintain circle integrity, we performed chemical and enzymatic probing of the splicing ribozyme combined with molecular modeling to arrive at models of the inactive circular form and its active linear counterpart. We show that the two forms have the same overall structure but differ in key parts, including the catalytic core element P7 and the junctions at which reactions take place. These differences explain the relative stability of the circular species, demonstrate how it is prone to react with a target molecule for circle integration and thus supports the notion that the circular form is a biologically significant molecule possibly with a role in intron mobility.}, }
@article {pmid27806928, year = {2016}, author = {Zhang, G and Feng, J}, title = {The intrinsic resistance of bacteria.}, journal = {Yi chuan = Hereditas}, volume = {38}, number = {10}, pages = {872-880}, doi = {10.16288/j.yczz.16-159}, pmid = {27806928}, issn = {0253-9772}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics/metabolism ; Bacterial Infections/*microbiology ; Bacterial Proteins/genetics/metabolism ; *Drug Resistance, Bacterial ; Humans ; Membrane Transport Proteins/genetics/metabolism ; }, abstract = {Antibiotic resistance is often considered to be a trait acquired by previously susceptible bacteria, on the basis of which can be attributed to the horizontal acquisition of new genes or the occurrence of spontaneous mutation. In addition to acquired resistance, bacteria have a trait of intrinsic resistance to different classes of antibiotics. An intrinsic resistance gene is involved in intrinsic resistance, and its presence in bacterial strains is independent of previous antibiotic exposure and is not caused by horizontal gene transfer. Recently, interest in intrinsic resistance genes has increased, because these gene products not only may provide attractive therapeutic targets for development of novel drugs that rejuvenate the activity of existing antibiotics, and but also might predict future emergence of resistant pathogens if they become mobilized. In the present review, we summarize the conventional examples of intrinsic resistance, including the impermeability of cellular envelopes, the activity of multidrug efflux pumps or lack of drug targets. We also demonstrate that transferases and enzymes involved in basic bacterial metabolic processes confer intrinsic resistance in Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus. We present as well information on the cryptic intrinsic resistance genes that do not confer resistance to their native hosts but are capable of conferring resistance when their expression levels are increased and the activation of the cryptic genes. Finally, we discuss that intrinsic genes could be the origin of acquired resistance, especially in the genus Acinetobacter.}, }
@article {pmid27804963, year = {2017}, author = {Theriault, G and Nkongolo, KK}, title = {Evidence of prokaryote like protein associated with nickel resistance in higher plants: horizontal transfer of TonB-dependent receptor/protein in Betula genus or de novo mechanisms?.}, journal = {Heredity}, volume = {118}, number = {4}, pages = {358-365}, pmid = {27804963}, issn = {1365-2540}, mesh = {Bacterial Proteins/genetics ; Base Sequence ; Betula/drug effects/*genetics ; Biological Transport ; *Gene Transfer, Horizontal ; Genotype ; High-Throughput Nucleotide Sequencing ; Membrane Proteins/genetics ; *Nickel ; Plant Proteins/*genetics ; }, abstract = {Mechanisms of metal resistance have been reported in many plants but knowledge in woody species is scarce. The TonB-dependent receptors family (TBDTs) is a large group of proteins that facilitate the transport of molecules across the membrane of Gram-negative bacteria. Some evidence exists that TBDTs are involved in metal stress. The existence of a TonB-like mechanism in non-prokaryotes has not been established. The recent development of the Betula papyrifera (white birch) transcriptome has allowed the discovery of genes involved in plant adaptation to stress. The main objective of the present study was to identify novel genes associated with nickel resistance in B. papyrifera. Our results from next generation sequencing and RT-qPCR analyses show that genes involved in transport activities are upregulated in nickel-resistant genotypes compared with susceptible forms. Detailed analysis of gene expression and genome analysis shows for the first time the existence of a TonB-dependent receptor and TonB-like family protein in non-prokaryotes. In addition, we have found that these proteins are associated with nickel resistance in B. papyrifera. Our experiments suggest that the TonB-dependent receptor may be exclusive to the Betula genus, suggesting that Betula species may have acquired the gene via horizontal gene transfer from prokaryotes or fungi.}, }
@article {pmid27803895, year = {2016}, author = {Ceccarelli, D and Alam, M and Huq, A and Colwell, RR}, title = {Reduced Susceptibility to Extended-Spectrum β-Lactams in Vibrio cholerae Isolated in Bangladesh.}, journal = {Frontiers in public health}, volume = {4}, number = {}, pages = {231}, pmid = {27803895}, issn = {2296-2565}, abstract = {β-lactams are antibiotic molecules able to inhibit cell wall biosynthesis. Among other mechanisms, resistance in Gram-negative bacteria is mostly associated with production of β-lactamase enzymes able to bind and hydrolyze the β-lactam ring. Extended-spectrum β-lactamases extend this ability also to third- and fourth-generation cephalosporins, as well as to carbapenems and monobactams. Vibrio cholerae is the causative agent of epidemic cholera and a public health burden for developing countries like Bangladesh. Although appropriate oral or intravenous rehydration is the therapy of choice for cholera, severe infections and V. cholerae-associated septicemia are treated with antimicrobial drugs, including doxycycline, erythromycin, azithromycin, ciprofloxacin, and/or third-generation cephalosporins. In the years after the introduction of antibiotics in clinical practice, V. cholerae developed resistance to commonly used drugs worldwide mostly through gene acquisition via horizontal gene transfer. Reduced susceptibility of V. cholerae to third-generation cephalosporins has been occasionally documented. However, carbapenemase-producing V. cholerae has been reported at higher rates than resistance to extended-spectrum β-lactams, mainly associated with blaNDM-1 emergence and successful plasmid dissemination. Recent findings suggest limited β-lactam resistance is present in V. cholerae O1 isolates collected during ecological and epidemiological surveillance in Bangladesh. However, a trend to intermediate-susceptibility insurgence was observed. Horizontal gene transfer of β-lactam resistance from enteric pathogens to environmental microorganisms should not be underrated, given the ability of V. cholerae to acquire new genetic information.}, }
@article {pmid27803316, year = {2016}, author = {Van Arnam, EB and Ruzzini, AC and Sit, CS and Horn, H and Pinto-Tomás, AA and Currie, CR and Clardy, J}, title = {Selvamicin, an atypical antifungal polyene from two alternative genomic contexts.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {46}, pages = {12940-12945}, pmid = {27803316}, issn = {1091-6490}, support = {R01 AT009874/AT/NCCIH NIH HHS/United States ; R01 GM086258/GM/NIGMS NIH HHS/United States ; U19 AI109673/AI/NIAID NIH HHS/United States ; //CIHR/Canada ; F32 GM117661/GM/NIGMS NIH HHS/United States ; }, mesh = {Actinobacteria/*genetics/isolation &amp; purification/*metabolism ; Animals ; Antifungal Agents/chemistry/*metabolism/pharmacology ; Ants/microbiology ; Candida albicans/drug effects/growth &amp; development ; Gene Transfer, Horizontal ; Genome, Bacterial ; Genomics ; Glycosylation ; Macrolides/chemistry/*metabolism/pharmacology ; Multigene Family ; Plasmids ; Polyenes/chemistry/*metabolism/pharmacology ; }, abstract = {The bacteria harbored by fungus-growing ants produce a variety of small molecules that help maintain a complex multilateral symbiosis. In a survey of antifungal compounds from these bacteria, we discovered selvamicin, an unusual antifungal polyene macrolide, in bacterial isolates from two neighboring ant nests. Selvamicin resembles the clinically important antifungals nystatin A1 and amphotericin B, but it has several distinctive structural features: a noncationic 6-deoxymannose sugar at the canonical glycosylation site and a second sugar, an unusual 4-O-methyldigitoxose, at the opposite end of selvamicin's shortened polyene macrolide. It also lacks some of the pharmacokinetic liabilities of the clinical agents and appears to have a different target. Whole genome sequencing revealed the putative type I polyketide gene cluster responsible for selvamicin's biosynthesis including a subcluster of genes consistent with selvamicin's 4-O-methyldigitoxose sugar. Although the selvamicin biosynthetic cluster is virtually identical in both bacterial producers, in one it is on the chromosome, in the other it is on a plasmid. These alternative genomic contexts illustrate the biosynthetic gene cluster mobility that underlies the diversity and distribution of chemical defenses by the specialized bacteria in this multilateral symbiosis.}, }
@article {pmid27803186, year = {2016}, author = {Zheng, H and Nishida, A and Kwong, WK and Koch, H and Engel, P and Steele, MI and Moran, NA}, title = {Metabolism of Toxic Sugars by Strains of the Bee Gut Symbiont Gilliamella apicola.}, journal = {mBio}, volume = {7}, number = {6}, pages = {}, pmid = {27803186}, issn = {2150-7511}, support = {R01 GM108477/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bees/*microbiology ; Biotransformation ; *Carbohydrate Metabolism ; Gammaproteobacteria/genetics/growth &amp; development/metabolism/*physiology ; Gastrointestinal Tract/microbiology ; Genome, Bacterial ; Metabolic Networks and Pathways/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {UNLABELLED: Social bees collect carbohydrate-rich food to support their colonies, and yet, certain carbohydrates present in their diet or produced through the breakdown of pollen are toxic to bees. The gut microbiota of social bees is dominated by a few core bacterial species, including the Gram-negative species Gilliamella apicola We isolated 42 strains of G. apicola from guts of honey bees and bumble bees and sequenced their genomes. All of the G. apicola strains share high 16S rRNA gene similarity, but they vary extensively in gene repertoires related to carbohydrate metabolism. Predicted abilities to utilize different sugars were verified experimentally. Some strains can utilize mannose, arabinose, xylose, or rhamnose (monosaccharides that can cause toxicity in bees) as their sole carbon and energy source. All of the G. apicola strains possess a manO-associated mannose family phosphotransferase system; phylogenetic analyses suggest that this was acquired from Firmicutes through horizontal gene transfer. The metabolism of mannose is specifically dependent on the presence of mannose-6-phosphate isomerase (MPI). Neither growth rates nor the utilization of glucose and fructose are affected in the presence of mannose when the gene encoding MPI is absent from the genome, suggesting that mannose is not taken up by G. apicola strains which harbor the phosphotransferase system but do not encode the MPI. Given their ability to simultaneously utilize glucose, fructose, and mannose, as well as the ability of many strains to break down other potentially toxic carbohydrates, G. apicola bacteria may have key roles in improving dietary tolerances and maintaining the health of their bee hosts.<br><br>IMPORTANCE: Bees are important pollinators of agricultural plants. Our study documents the ability of Gilliamella apicola, a dominant gut bacterium in honey bees and bumble bees, to utilize several sugars that are harmful to bee hosts. Using genome sequencing and growth assays, we found that the ability to metabolize certain toxic carbohydrates is directly correlated with the presence of their respective degradation pathways, indicating that metabolic potential can be accurately predicted from genomic data in these gut symbionts. Strains vary considerably in their range of utilizable carbohydrates, which likely reflects historical horizontal gene transfer and gene deletion events. Unlike their bee hosts, G.&#xa0;apicola bacteria are not detrimentally affected by growth on mannose-containing medium, even in strains that cannot metabolize this sugar. These results suggest that G.&#xa0;apicola may be an important player in modulating nutrition in the bee gut, with ultimate effects on host health.}, }
@article {pmid27791096, year = {2016}, author = {Hepp, C and Maier, B}, title = {Kinetics of DNA uptake during transformation provide evidence for a translocation ratchet mechanism.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {44}, pages = {12467-12472}, pmid = {27791096}, issn = {1091-6490}, mesh = {Algorithms ; Bacterial Proteins/genetics/*metabolism ; Biological Transport ; DNA, Bacterial/genetics/metabolism ; DNA-Binding Proteins/genetics/*metabolism ; Fimbriae, Bacterial/genetics/*metabolism ; Kinetics ; Models, Genetic ; Neisseria gonorrhoeae/genetics/metabolism ; Periplasm/metabolism ; Protein Binding ; *Transformation, Bacterial ; }, abstract = {Horizontal gene transfer can speed up adaptive evolution and support chromosomal DNA repair. A particularly widespread mechanism of gene transfer is transformation. The initial step to transformation, namely the uptake of DNA from the environment, is supported by the type IV pilus system in most species. However, the molecular mechanism of DNA uptake remains elusive. Here, we used single-molecule techniques for characterizing the force-dependent velocity of DNA uptake by Neisseria gonorrhoeae We found that the DNA uptake velocity depends on the concentration of the periplasmic DNA-binding protein ComE, indicating that ComE is directly involved in the uptake process. The velocity-force relation of DNA uptake is in very good agreement with a translocation ratchet model where binding of chaperones in the periplasm biases DNA diffusion through a membrane pore in the direction of uptake. The model yields a speed of DNA uptake of 900 bp⋅s[-1] and a reversal force of 17 pN. Moreover, by comparing the velocity-force relation of DNA uptake and type IV pilus retraction, we can exclude pilus retraction as a mechanism for DNA uptake. In conclusion, our data strongly support the model of a translocation ratchet with ComE acting as a ratcheting chaperone.}, }
@article {pmid27801909, year = {2017}, author = {Kuwahara, H and Yuki, M and Izawa, K and Ohkuma, M and Hongoh, Y}, title = {Genome of 'Ca. Desulfovibrio trichonymphae', an H2-oxidizing bacterium in a tripartite symbiotic system within a protist cell in the termite gut.}, journal = {The ISME journal}, volume = {11}, number = {3}, pages = {766-776}, pmid = {27801909}, issn = {1751-7370}, mesh = {Animals ; Desulfovibrio/*genetics/physiology ; Gene Expression Regulation, Bacterial ; *Genome, Bacterial ; Hypermastigia/*microbiology/physiology ; Isoptera/*microbiology ; Molecular Sequence Data ; Phylogeny ; Symbiosis/*physiology ; }, abstract = {The cellulolytic protist Trichonympha agilis in the termite gut permanently hosts two symbiotic bacteria, 'Candidatus Endomicrobium trichonymphae' and 'Candidatus Desulfovibrio trichonymphae'. The former is an intracellular symbiont, and the latter is almost intracellular but still connected to the outside via a small pore. The complete genome of 'Ca. Endomicrobium trichonymphae' has previously been reported, and we here present the complete genome of 'Ca. Desulfovibrio trichonymphae'. The genome is small (1 410 056 bp), has many pseudogenes, and retains biosynthetic pathways for various amino acids and cofactors, which are partially complementary to those of 'Ca. Endomicrobium trichonymphae'. An amino acid permease gene has apparently been transferred between the ancestors of these two symbionts; a lateral gene transfer has affected their metabolic capacity. Notably, 'Ca. Desulfovibrio trichonymphae' retains the complex system to oxidize hydrogen by sulfate and/or fumarate, while genes for utilizing other substrates common in desulfovibrios are pseudogenized or missing. Thus, 'Ca. Desulfovibrio trichonymphae' is specialized to consume hydrogen that may otherwise inhibit fermentation processes in both T. agilis and 'Ca. Endomicrobium trichonymphae'. The small pore may be necessary to take up sulfate. This study depicts a genome-based model of a multipartite symbiotic system within a cellulolytic protist cell in the termite gut.}, }
@article {pmid27801295, year = {2016}, author = {Sbaraini, N and Guedes, RL and Andreis, FC and Junges, &#xc2; and de Morais, GL and Vainstein, MH and de Vasconcelos, AT and Schrank, A}, title = {Secondary metabolite gene clusters in the entomopathogen fungus Metarhizium anisopliae: genome identification and patterns of expression in a cuticle infection model.}, journal = {BMC genomics}, volume = {17}, number = {Suppl 8}, pages = {736}, pmid = {27801295}, issn = {1471-2164}, mesh = {Animals ; Evolution, Molecular ; Gene Expression Profiling ; Gene Expression Regulation ; Gene Order ; *Genome, Fungal ; *Genomics/methods ; Host-Pathogen Interactions ; Metarhizium/classification/*genetics/*metabolism ; Phylogeny ; Quantitative Trait, Heritable ; Secondary Metabolism/*genetics ; Ticks/microbiology ; *Transcriptome ; }, abstract = {BACKGROUND: The described species from the Metarhizium genus are cosmopolitan fungi that infect arthropod hosts. Interestingly, while some species infect a wide range of hosts (host-generalists), other species infect only a few arthropods (host-specialists). This singular evolutionary trait permits unique comparisons to determine how pathogens and virulence determinants emerge. Among the several virulence determinants that have been described, secondary metabolites (SMs) are suggested to play essential roles during fungal infection. Despite progress in the study of pathogen-host relationships, the majority of genes related to SM production in Metarhizium spp. are uncharacterized, and little is known about their genomic organization, expression and regulation. To better understand how infection conditions may affect SM production in Metarhizium anisopliae, we have performed a deep survey and description of SM biosynthetic gene clusters (BGCs) in M. anisopliae, analyzed RNA-seq data from fungi grown on cattle-tick cuticles, evaluated the differential expression of BGCs, and assessed conservation among the Metarhizium genus. Furthermore, our analysis extended to the construction of a phylogeny for the following three BGCs: a tropolone/citrinin-related compound (MaPKS1), a pseurotin-related compound (MaNRPS-PKS2), and a putative helvolic acid (MaTERP1).<br><br>RESULTS: Among 73 BGCs identified in M. anisopliae, 20&#xa0;% were up-regulated during initial tick cuticle infection and presumably possess virulence-related roles. These up-regulated BGCs include known clusters, such as destruxin, NG39x and ferricrocin, together with putative helvolic acid and, pseurotin and tropolone/citrinin-related compound clusters as well as uncharacterized clusters. Furthermore, several previously characterized and putative BGCs were silent or down-regulated in initial infection conditions, indicating minor participation over the course of infection. Interestingly, several up-regulated BGCs were not conserved in host-specialist species from the Metarhizium genus, indicating differences in the metabolic strategies employed by generalist and specialist species to overcome and kill their host. These differences in metabolic potential may have been partially shaped by horizontal gene transfer (HGT) events, as our phylogenetic analysis provided evidence that the putative helvolic acid cluster in Metarhizium spp. originated&#xa0;from an HGT event.<br><br>CONCLUSIONS: Several unknown BGCs are described, and aspects of their organization, regulation and origin are discussed, providing further support for the impact of SM on the Metarhizium genus lifestyle and infection process.}, }
@article {pmid27793835, year = {2016}, author = {Suring, W and Mariën, J and Broekman, R and van Straalen, NM and Roelofs, D}, title = {Biochemical pathways supporting beta-lactam biosynthesis in the springtail Folsomia candida.}, journal = {Biology open}, volume = {5}, number = {12}, pages = {1784-1789}, pmid = {27793835}, issn = {2046-6390}, abstract = {Recently, an active set of beta-lactam biosynthesis genes was reported in the genome of the arthropod springtail Folsomia candida (Collembola). Evidence was provided that these genes were acquired through horizontal gene transfer. However, successful integration of fungal- or bacterial-derived beta-lactam biosynthesis into the metabolism of an animal requires the beta-lactam precursor L-α-aminoadipic acid and a phosphopantetheinyl transferase for activation of the first enzyme of the pathway, δ-(L-α-aminoadipoyl)-L-cysteinyl-D-valine synthetase (ACVS). In this study, we characterized these supporting pathways and their transcriptional regulation in F. candida We identified one phosphopantetheinyl transferase and three pathways for L-α-aminoadipic acid production, distinct from the pathways utilized by microorganisms. We found that after heat shock, the phosphopantetheinyl transferase was co-regulated with ACVS, confirming its role in activating ACVS. Two of the three L-α-aminoadipic acid production pathways were downregulated, while PIPOX, an enzyme participating in the pipecolate pathway, was slightly co-regulated with ACVS. This indicates that L-α-aminoadipic acid may not be a limiting factor in beta-lactam biosynthesis in F. candida, in contrast to microorganisms. In conclusion, we show that all components for L-α-aminoadipic acid synthesis are present and transcriptionally active in F. candida This demonstrates how springtails could have recruited native enzymes to integrate a beta-lactam biosynthesis pathway into their metabolism after horizontal gene transfer.}, }
@article {pmid27796645, year = {2017}, author = {Datta, S and Mitra, S and Chattopadhyay, P and Som, T and Mukherjee, S and Basu, S}, title = {Spread and exchange of bla NDM-1 in hospitalized neonates: role of mobilizable genetic elements.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {36}, number = {2}, pages = {255-265}, pmid = {27796645}, issn = {1435-4373}, mesh = {Conjugation, Genetic ; Enterobacteriaceae/*enzymology/*genetics/isolation &amp; purification ; Enterobacteriaceae Infections/*microbiology ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genotype ; Hospitalization ; Humans ; India ; Infant, Newborn ; *Interspersed Repetitive Sequences ; Plasmids/analysis ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Sepsis/*microbiology ; Transformation, Bacterial ; beta-Lactamases/*genetics ; }, abstract = {To investigate the mobilizable elements associated with bla NDM-1 in Enterobacteriaceae isolated from septicaemic neonates at a NICU in India, during December, 2008-2011. An attempt was also made to understand whether there was a pattern in the temporal acquisition of bla NDM-1 within the unit. Transferability of carbapenem resistance was tested by conjugation and transformation. Plasmid types and addiction systems were analysed. The genetic background of bla NDM-1 and association with class 1 integron were evaluated by PCR mapping. RFLP was carried out to discriminate plasmids of same incompatibility group. Transfer of carbapenem resistance was successful in 13/15 cases. bla NDM-1 was associated with different plasmid scaffolds (IncFII, IncL/M, IncN, IncR, IncHIB-M/FIB-M), IncF type being the prevalent one. Addiction systems ccdAB and hok/sok were associated with transferable plasmids. Genetic structures surrounding bla NDM-1 showed its association with at least a remnant of ISAba125 at its 5'-end. The spread of NDM-1 was not related to class 1 integron which possessed resistance determinants against trimethoprim (dfrA12, dfrA1, dfrA5), streptomycin (aadA2, aacA4), and rifampicin (arr-3). RFLP showed that three isolates possessed the same FII/FIIs plasmid; two of these three isolates were from a single neonate, implying interspecies transfer of bla NDM-1. The predominance of FII plasmids and ISAba125 along with bla NDM-1 was noted, but no specific pattern in the temporal acquisition of mobile genetic elements could be identified. To the best of our knowledge, this report is the first to inform the in-vivo interspecies plasmid transfer event of bla NDM-1 in a neonate.}, }
@article {pmid27796355, year = {2016}, author = {Tan, SY and Tan, IK and Tan, MF and Dutta, A and Choo, SW}, title = {Evolutionary study of Yersinia genomes deciphers emergence of human pathogenic species.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {36116}, pmid = {27796355}, issn = {2045-2322}, mesh = {Adhesins, Bacterial/chemistry/genetics ; Bacterial Outer Membrane Proteins/chemistry/genetics ; CRISPR-Cas Systems/genetics ; *Evolution, Molecular ; *Genome, Bacterial ; Humans ; Phylogeny ; Plasmids/genetics/metabolism ; Virulence/genetics ; Yersinia/classification/*genetics/pathogenicity ; Yersinia Infections/microbiology/pathology ; }, abstract = {On record, there are 17 species in the Yersinia genus, of which three are known to be pathogenic to human. While the chromosomal and pYV (or pCD1) plasmid-borne virulence genes as well as pathogenesis of these three species are well studied, their genomic evolution is poorly understood. Our study aims to predict the key evolutionary events that led to the emergence of pathogenic Yersinia species by analyzing gene gain-and-loss, virulence genes, and "Clustered regularly-interspaced short palindromic repeats". Our results suggest that the most recent ancestor shared by the human pathogenic Yersinia was most probably an environmental species that had adapted to the human body. This might have led to ecological specialization that diverged Yersinia into ecotypes and distinct lineages based on differential gene gain-and-loss in different niches. Our data also suggest that Y. pseudotuberculosis group might be the donor of the ail virulence gene to Y. enterocolitica. Hence, we postulate that evolution of human pathogenic Yersinia might not be totally in parallel, but instead, there were lateral gene transfer events. Furthermore, the presence of virulence genes seems to be important for the positive selection of virulence plasmid. Our studies provide better insights into the evolutionary biology of these bacteria.}, }
@article {pmid27793962, year = {2017}, author = {Beyrouthy, R and Robin, F and Hamze, M and Bonnet, R}, title = {IncFIIk plasmid harbouring an amplification of 16S rRNA methyltransferase-encoding gene rmtH associated with mobile element ISCR2.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {72}, number = {2}, pages = {402-406}, doi = {10.1093/jac/dkw435}, pmid = {27793962}, issn = {1460-2091}, mesh = {Aminoglycosides/*pharmacology ; Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Humans ; Infant, Newborn ; *Interspersed Repetitive Sequences ; Klebsiella Infections/microbiology ; Klebsiella pneumoniae/*drug effects/genetics/isolation &amp; purification ; Methyltransferases/*genetics ; Microbial Sensitivity Tests ; Plasmids/*analysis/classification ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; beta-Lactams/*pharmacology ; }, abstract = {OBJECTIVES: To investigate the resistance mechanisms and genetic support underlying the high resistance level of the Klebsiella pneumoniae strain CMUL78 to aminoglycoside and β-lactam antibiotics.<br><br>METHODS: Antibiotic susceptibility was assessed by the disc diffusion method and MICs were determined by the microdilution method. Antibiotic resistance genes and their genetic environment were characterized by PCR and Sanger sequencing. Plasmid contents were analysed in the clinical strain and transconjugants obtained by mating-out assays. Complete plasmid sequencing was performed with PacBio and Illumina technology.<br><br>RESULTS: Strain CMUL78 co-produced the 16S rRNA methyltransferase (RMTase) RmtH, carbapenemase OXA-48 and ESBL SHV-12. The rmtH- and blaSHV-12-encoding genes were harboured by a novel &#x223c;115 kb IncFIIk plasmid designated pRmtH, and blaOXA-48 by a &#x223c;62 kb IncL/M plasmid related to pOXA-48a. pRmtH plasmid possessed seven different stability modules, one of which is a novel hybrid toxin-antitoxin system. Interestingly, pRmtH plasmid harboured a 4-fold amplification of an rmtH-ISCR2 unit arranged in tandem and inserted within a novel IS26-based composite transposon designated Tn6329.<br><br>CONCLUSIONS: This is the first known report of the 16S RMTase-encoding gene rmtH in a plasmid. The rmtH-ISCR2 unit was inserted in a composite transposon as a 4-fold tandem repeat, a scarcely reported organization.}, }
@article {pmid27664178, year = {2016}, author = {Grewe, F and Zhu, A and Mower, JP}, title = {Loss of a Trans-Splicing nad1 Intron from Geraniaceae and Transfer of the Maturase Gene matR to the Nucleus in Pelargonium.}, journal = {Genome biology and evolution}, volume = {8}, number = {10}, pages = {3193-3201}, pmid = {27664178}, issn = {1759-6653}, mesh = {Cell Nucleus/metabolism ; Endoribonucleases/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Introns ; NADH Dehydrogenase/*genetics ; Nucleotidyltransferases/*genetics ; Pelargonium/*genetics ; Plant Proteins/*genetics ; Sequence Deletion ; Trans-Splicing ; }, abstract = {The mitochondrial nad1 gene of seed plants has a complex structure, including four introns in cis or trans configurations and a maturase gene (matR) hosted within the final intron. In the geranium family (Geraniaceae), however, sequencing of representative species revealed that three of the four introns, including one in a trans configuration and another that hosts matR, were lost from the nad1 gene in their common ancestor. Despite the loss of the host intron, matR has been retained as a freestanding gene in most genera of the family, indicating that this maturase has additional functions beyond the splicing of its host intron. In the common ancestor of Pelargonium, matR was transferred to the nuclear genome, where it was split into two unlinked genes that encode either its reverse transcriptase or maturase domain. Both nuclear genes are transcribed and contain predicted mitochondrial targeting signals, suggesting that they express functional proteins that are imported into mitochondria. The nuclear localization and split domain structure of matR in the Pelargonium nuclear genome offers a unique opportunity to assess the function of these two domains using transgenic approaches.}, }
@article {pmid27791104, year = {2016}, author = {Yang, Z and Zhang, Y and Wafula, EK and Honaas, LA and Ralph, PE and Jones, S and Clarke, CR and Liu, S and Su, C and Zhang, H and Altman, NS and Schuster, SC and Timko, MP and Yoder, JI and Westwood, JH and dePamphilis, CW}, title = {Horizontal gene transfer is more frequent with increased heterotrophy and contributes to parasite adaptation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {45}, pages = {E7010-E7019}, pmid = {27791104}, issn = {1091-6490}, abstract = {Horizontal gene transfer (HGT) is the transfer of genetic material across species boundaries and has been a driving force in prokaryotic evolution. HGT involving eukaryotes appears to be much less frequent, and the functional implications of HGT in eukaryotes are poorly understood. We test the hypothesis that parasitic plants, because of their intimate feeding contacts with host plant tissues, are especially prone to horizontal gene acquisition. We sought evidence of HGTs in transcriptomes of three parasitic members of Orobanchaceae, a plant family containing species spanning the full spectrum of parasitic capabilities, plus the free-living Lindenbergia Following initial phylogenetic detection and an extensive validation procedure, 52 high-confidence horizontal transfer events were detected, often from lineages of known host plants and with an increasing number of HGT events in species with the greatest parasitic dependence. Analyses of intron sequences in putative donor and recipient lineages provide evidence for integration of genomic fragments far more often than retro-processed RNA sequences. Purifying selection predominates in functionally transferred sequences, with a small fraction of adaptively evolving sites. HGT-acquired genes are preferentially expressed in the haustorium-the organ of parasitic plants-and are strongly biased in predicted gene functions, suggesting that expression products of horizontally acquired genes are contributing to the unique adaptive feeding structure of parasitic plants.}, }
@article {pmid27791007, year = {2016}, author = {Nowack, EC and Price, DC and Bhattacharya, D and Singer, A and Melkonian, M and Grossman, AR}, title = {Gene transfers from diverse bacteria compensate for reductive genome evolution in the chromatophore of Paulinella chromatophora.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {43}, pages = {12214-12219}, pmid = {27791007}, issn = {1091-6490}, mesh = {Amoeba/*genetics/growth &amp; development ; Biological Evolution ; *Chromatophores ; Cyanobacteria/*genetics ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial/genetics ; Molecular Sequence Annotation ; Plastids/genetics ; Symbiosis/genetics ; Transcriptome/genetics ; }, abstract = {Plastids, the photosynthetic organelles, originated >1 billion y ago via the endosymbiosis of a cyanobacterium. The resulting proliferation of primary producers fundamentally changed global ecology. Endosymbiotic gene transfer (EGT) from the intracellular cyanobacterium to the nucleus is widely recognized as a critical factor in the evolution of photosynthetic eukaryotes. The contribution of horizontal gene transfers (HGTs) from other bacteria to plastid establishment remains more controversial. A novel perspective on this issue is provided by the amoeba Paulinella chromatophora, which contains photosynthetic organelles (chromatophores) that are only 60-200 million years old. Chromatophore genome reduction entailed the loss of many biosynthetic pathways including those for numerous amino acids and cofactors. How the host cell compensates for these losses remains unknown, because the presence of bacteria in all available P. chromatophora cultures excluded elucidation of the full metabolic capacity and occurrence of HGT in this species. Here we generated a high-quality transcriptome and draft genome assembly from the first bacteria-free P. chromatophora culture to deduce rules that govern organelle integration into cellular metabolism. Our analyses revealed that nuclear and chromatophore gene inventories provide highly complementary functions. At least 229 nuclear genes were acquired via HGT from various bacteria, of which only 25% putatively arose through EGT from the chromatophore genome. Many HGT-derived bacterial genes encode proteins that fill gaps in critical chromatophore pathways/processes. Our results demonstrate a dominant role for HGT in compensating for organelle genome reduction and suggest that phagotrophy may be a major driver of HGT.}, }
@article {pmid27790412, year = {2016}, author = {Lv, J and Qi, X and Zhang, D and Zheng, Z and Chen, Y and Guo, Y and Wang, S and Chen, L and Kreiswirth, BN and Tang, YW and Chen, Z and Hu, L and Wang, L and Yu, F}, title = {First Report of Complete Sequence of a blaNDM-13-Harboring Plasmid from an Escherichia coli ST5138 Clinical Isolate.}, journal = {Frontiers in cellular and infection microbiology}, volume = {6}, number = {}, pages = {130}, pmid = {27790412}, issn = {2235-2988}, support = {P30 CA008748/CA/NCI NIH HHS/United States ; R01 AI090155/AI/NIAID NIH HHS/United States ; R21 AI117338/AI/NIAID NIH HHS/United States ; }, mesh = {China ; Conjugation, Genetic ; Cross Infection/microbiology ; Escherichia coli/enzymology/genetics/*isolation &amp; purification ; Escherichia coli Infections/*microbiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Plasmids/*analysis ; *Sequence Analysis, DNA ; Urinary Tract Infections/microbiology ; beta-Lactamases/*genetics ; }, abstract = {Since the first report of blaNDM-1, 16 blaNDM variants have been identified among Gram-negative bacteria worldwide. Recently, a novel blaNDM variant, blaNDM-13, was identified in the chromosome of an ST101 Escherichia coli isolate from Nepal. Here we first reported plasmid-mediated blaNDM-13 in a carbapenem-resistant E. coli ST5138 clinical isolate associated with hospital-acquired urinary tract infection from China. blaNDM-13 and blaSHV-12 coexisted on the a ~54 Kb self-transferable plasmid. Compared with NDM-1, NDM-13, NDM-3, and NDM-4 had two amino acid substitutions (D95N and M154L), one amino acid substitution (D95N) and one amino acid substitutions (M154L), respectively. Complete plasmid sequencing showed that blaNDM-13-harboring plasmid (pNDM13-DC33) was highly similar to the blaNDM-1-harboring IncX3 plasmid pNDM-HN380, a common blaNDM-harboring vector circulating in China. In accordance with the structure of pNDM-HN380, pNDM13-DC33 consists of a 33-kb backbone encoding plasmid replication (repB), stability partitioning, and transfer (tra, trb, and pil) functions, and a 21-kb antimicrobial resistance region with high GC content between umuD and mpr genes. In conclusion, the present study is the first report of a plasmid-encoded blaNDM-13 and the complete sequence of a blaNDM-13-harboring plasmid (pNDM13-DC33). blaNDM-13 maybe originate from blaNDM-1 located on a pNDM-HN380-like plasmid by sequential mutations.}, }
@article {pmid27789039, year = {2017}, author = {Njage, PM and Buys, EM}, title = {Quantitative assessment of human exposure to extended spectrum and AmpC β-lactamases bearing E. coli in lettuce attributable to irrigation water and subsequent horizontal gene transfer.}, journal = {International journal of food microbiology}, volume = {240}, number = {}, pages = {141-151}, doi = {10.1016/j.ijfoodmicro.2016.10.011}, pmid = {27789039}, issn = {1879-3460}, mesh = {Bacterial Proteins/*genetics ; Chlorine/pharmacology ; Disinfectants/pharmacology ; Disinfection/methods ; Escherichia coli/drug effects/*genetics/*growth &amp; development/isolation &amp; purification ; Escherichia coli Infections/microbiology ; Food Contamination/*analysis ; Foodborne Diseases/microbiology ; *Gene Transfer, Horizontal ; Humans ; Lactuca/*microbiology ; Microbial Sensitivity Tests ; Prevalence ; South Africa ; *Water Microbiology ; beta-Lactamases/*genetics ; }, abstract = {The contribution of the fresh produce production environment to human exposure with bacteria bearing extended spectrum β-lactamases and AmpC β-lactamases (ESBL/AmpC) has not been reported. High prevalence of ESBLs/AmpC bearing E. coli as well as a high gene transfer efficiency of lettuce and irrigation water E. coli isolates was previously reported. This stochastic modeling was aimed at quantitatively assessing human exposure to ESBL/AmpC bearing E. coli through lettuce attributable to irrigation water and subsequent horizontal gene transfer. Modular process risk approach was used for the quantitative exposure assessment and models were constructed in Ms. Excel spreadsheet with farm to consumption chain accounted for by primary production, processing, retail and consumer storage. Probability distributions were utilised to take into account the variability of the exposure estimates. Exposure resulting from ESBL/AmpC positive E. coli and gene transfer was taken into account. Monte Carlo simulation was carried out using @Risk software followed by sensitivity and scenario analysis to assess most effective single or combinations of mitigation strategies for the ESBL/AmpC positive E. coli events from farm to fork. Three percent of South African lettuce consumers are exposed to lettuce contaminated with about 10[6.4]±10[6.7] (95% CI: 10[5.1]-10[7]) cfu of ESBL/AmpC positive E. coli per serving. The contribution of originally positive isolates and conjugative genetic transfer was 10[6]±10[6.7] (95% CI: 10[5]-10[7]) and 10[5.2]±10[5.6] (95% CI: 10[3.9]-10[5.8]) cfu per serving respectively. Proportion of ESBL/AmpC positive E. coli (Spearman's correlation coefficient (ρ)=0.85), conjugative gene transfer (ρ=0.05-0.14), washing in chlorine water (ρ=0.18), further rinsing (ρ=0.15), and prevalence of E. coli in irrigation water (ρ=0.16) had highest influence on consumer exposure. The most effective single methods in reducing consumer exposure were reduction in irrigation water microbial quality variation (87.4% reduction), storage period (49.9-87.4% reduction) and growth rate reduction by 75% (90% reduction). Reduction in growth rate together with storage time (92.1-99.4%) and reduction in storage time combined with E. coli concentration in irrigation water (95-96% reduction) were most effective combinations of mitigation measures. The high variation in exposure reflected the high irrigation water quality variation. The exposure levels may impose higher consumer risk than acceptable for irrigation water risk. E. coli contamination and growth related measures, as well as measures to reduce contamination with antimicrobial resistant E. coli from lettuce production environment are recommended. This exposure model could form a basis for the development of similar models assessing the impact of contaminated irrigation water and gene transfer in other microbial hazards, antimicrobial resistance types and fresh produce types.}, }
@article {pmid27788691, year = {2017}, author = {Vubil, D and Figueiredo, R and Reis, T and Canha, C and Boaventura, L and DA Silva, GJ}, title = {Outbreak of KPC-3-producing ST15 and ST348 Klebsiella pneumoniae in a Portuguese hospital.}, journal = {Epidemiology and infection}, volume = {145}, number = {3}, pages = {595-599}, pmid = {27788691}, issn = {1469-4409}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics/*metabolism ; Blood/microbiology ; Cluster Analysis ; Cross Infection/*epidemiology/microbiology ; *Disease Outbreaks ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/drug effects/genetics ; Gene Transfer, Horizontal ; *Genotype ; Humans ; Klebsiella Infections/*epidemiology/microbiology ; Klebsiella pneumoniae/classification/*enzymology/genetics/isolation &amp; purification ; Multilocus Sequence Typing ; Plasmids/analysis ; Portugal/epidemiology ; Tertiary Care Centers ; Urine/microbiology ; beta-Lactam Resistance ; beta-Lactamases/genetics/*metabolism ; }, abstract = {To date, only a few sporadic cases of infections due to Klebsiella pneumoniae carbapenemase (KPC) producers have been reported in Portugal. Here, we report for the first time an outbreak of K. pneumoniae KPC-3 producers in a tertiary-care hospital during 2013. Twenty-seven ertapenem-resistant K. pneumoniae were identified in patients at a tertiary-care hospital during 2013 isolated predominantly from urine (48·1%) and blood (25·9%) cultures. All isolates were highly resistant to β-lactam antibiotics and most showed intermediate resistance to imipenem. The more frequent β-lactamases were TEM- (77·7%), CTX-M- (70·3%) and KPC-type (66·6%). KPC-3 was identified by sequencing. The bla KPC-3 gene was associated with an IncF plasmid, and efficiently transferred to E. coli J53. Pulsed-field gel electrophoresis typing revealed three clusters of isolates which were further characterized by multi-locus sequence typing as ST11, ST15 and ST348. Ertapenem-resistant ST15 was already in circulation in the hospital, related to expression of OmpK36 modified porin, but the other two sequence types had not been previously found in the hospital. We conclude that the IncF plasmid mediated transfer of KPC-3 in the outbreak and that implementation of carbapenemase gene screening in isolates from patients on admission to hospital is advisable in order to control dissemination of these antimicrobial resistance elements.}, }
@article {pmid27733511, year = {2016}, author = {Haskett, TL and Terpolilli, JJ and Bekuma, A and O'Hara, GW and Sullivan, JT and Wang, P and Ronson, CW and Ramsay, JP}, title = {Assembly and transfer of tripartite integrative and conjugative genetic elements.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {43}, pages = {12268-12273}, pmid = {27733511}, issn = {1091-6490}, mesh = {Conjugation, Genetic/genetics ; DNA Transposable Elements/*genetics ; Fabaceae/*genetics/growth &amp; development ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial ; Genomic Islands/genetics ; Integrases/genetics ; Mesorhizobium/genetics/growth &amp; development ; Plasmids ; *Recombination, Genetic ; Symbiosis/genetics ; }, abstract = {Integrative and conjugative elements (ICEs) are ubiquitous mobile genetic elements present as "genomic islands" within bacterial chromosomes. Symbiosis islands are ICEs that convert nonsymbiotic mesorhizobia into symbionts of legumes. Here we report the discovery of symbiosis ICEs that exist as three separate chromosomal regions when integrated in their hosts, but through recombination assemble as a single circular ICE for conjugative transfer. Whole-genome comparisons revealed exconjugants derived from nonsymbiotic mesorhizobia received three separate chromosomal regions from the donor Mesorhizobium ciceri WSM1271. The three regions were each bordered by two nonhomologous integrase attachment (att) sites, which together comprised three homologous pairs of attL and attR sites. Sequential recombination between each attL and attR pair produced corresponding attP and attB sites and joined the three fragments to produce a single circular ICE, ICEMcSym[1271] A plasmid carrying the three attP sites was used to recreate the process of tripartite ICE integration and to confirm the role of integrase genes intS, intM, and intG in this process. Nine additional tripartite ICEs were identified in diverse mesorhizobia and transfer was demonstrated for three of them. The transfer of tripartite ICEs to nonsymbiotic mesorhizobia explains the evolution of competitive but suboptimal N2-fixing strains found in Western Australian soils. The unheralded existence of tripartite ICEs raises the possibility that multipartite elements reside in other organisms, but have been overlooked because of their unusual biology. These discoveries reveal mechanisms by which integrases dramatically manipulate bacterial genomes to allow cotransfer of disparate chromosomal regions.}, }
@article {pmid27613685, year = {2016}, author = {Peabody, G and Winkler, J and Fountain, W and Castro, DA and Leiva-Aravena, E and Kao, KC}, title = {Benefits of a Recombination-Proficient Escherichia coli System for Adaptive Laboratory Evolution.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {22}, pages = {6736-6747}, pmid = {27613685}, issn = {1098-5336}, mesh = {Chromosomes, Bacterial ; Directed Molecular Evolution/*methods ; Escherichia coli/*genetics ; Genotype ; Models, Genetic ; Mutation ; Phenotype ; *Recombination, Genetic ; Selection, Genetic ; }, abstract = {UNLABELLED: Adaptive laboratory evolution typically involves the propagation of organisms asexually to select for mutants with the desired phenotypes. However, asexual evolution is prone to competition among beneficial mutations (clonal interference) and the accumulation of hitchhiking and neutral mutations. The benefits of horizontal gene transfer toward overcoming these known disadvantages of asexual evolution were characterized in a strain of Escherichia coli engineered for superior sexual recombination (genderless). Specifically, we experimentally validated the capacity of the genderless strain to reduce the mutational load and recombine beneficial mutations. We also confirmed that inclusion of multiple origins of transfer influences both the frequency of genetic exchange throughout the chromosome and the linkage of donor DNA. We built a simple kinetic model to estimate recombination frequency as a function of transfer size and relative genotype enrichment in batch transfers; the model output correlated well with the experimental data. Our results provide strong support for the advantages of utilizing the genderless strain over its asexual counterpart during adaptive laboratory evolution for generating beneficial mutants with reduced mutational load.<br><br>IMPORTANCE: Over 80 years ago Fisher and Muller began a debate on the origins of sexual recombination. Although many aspects of sexual recombination have been examined at length, experimental evidence behind the behaviors of recombination in many systems and the means to harness it remain elusive. In this study, we sought to experimentally validate some advantages of recombination in typically asexual Escherichia coli and determine if a sexual strain of E. coli can become an effective tool for strain development.}, }
@article {pmid27613679, year = {2016}, author = {Hu, Y and Yang, X and Li, J and Lv, N and Liu, F and Wu, J and Lin, IY and Wu, N and Weimer, BC and Gao, GF and Liu, Y and Zhu, B}, title = {The Bacterial Mobile Resistome Transfer Network Connecting the Animal and Human Microbiomes.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {22}, pages = {6672-6681}, pmid = {27613679}, issn = {1098-5336}, mesh = {Animals ; Animals, Domestic/microbiology ; Bacteria/genetics/pathogenicity ; Drug Resistance, Bacterial/*genetics ; Ecosystem ; Gastrointestinal Tract/microbiology ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; *Metagenome ; Microbiota/*genetics ; Phylogeny ; Proteobacteria/genetics ; RNA, Ribosomal, 16S ; *Soil Microbiology ; }, abstract = {UNLABELLED: Horizontally acquired antibiotic resistance genes (ARGs) in bacteria are highly mobile and have been ranked as principal risk resistance determinants. However, the transfer network of the mobile resistome and the forces driving mobile ARG transfer are largely unknown. Here, we present the whole profile of the mobile resistome in 23,425 bacterial genomes and explore the effects of phylogeny and ecology on the recent transfer (≥99% nucleotide identity) of mobile ARGs. We found that mobile ARGs are mainly present in four bacterial phyla and are significantly enriched in Proteobacteria The recent mobile ARG transfer network, which comprises 703 bacterial species and 16,859 species pairs, is shaped by the bacterial phylogeny, while an ecological barrier also exists, especially when interrogating bacteria colonizing different human body sites. Phylogeny is still a driving force for the transfer of mobile ARGs between farm animals and the human gut, and, interestingly, the mobile ARGs that are shared between the human and animal gut microbiomes are also harbored by diverse human pathogens. Taking these results together, we suggest that phylogeny and ecology are complementary in shaping the bacterial mobile resistome and exert synergistic effects on the development of antibiotic resistance in human pathogens.<br><br>IMPORTANCE: The development of antibiotic resistance threatens our modern medical achievements. The dissemination of antibiotic resistance can be largely attributed to the transfer of bacterial mobile antibiotic resistance genes (ARGs). Revealing the transfer network of these genes in bacteria and the forces driving the gene flow is of great importance for controlling and predicting the emergence of antibiotic resistance in the clinic. Here, by analyzing tens of thousands of bacterial genomes and millions of human and animal gut bacterial genes, we reveal that the transfer of mobile ARGs is mainly controlled by bacterial phylogeny but under ecological constraints. We also found that dozens of ARGs are transferred between the human and animal gut and human pathogens. This work demonstrates the whole profile of mobile ARGs and their transfer network in bacteria and provides further insight into the evolution and spread of antibiotic resistance in nature.}, }
@article {pmid27776538, year = {2016}, author = {Narechania, A and Baker, R and DeSalle, R and Mathema, B and Kolokotronis, SO and Kreiswirth, B and Planet, PJ}, title = {Clusterflock: a flocking algorithm for isolating congruent phylogenomic datasets.}, journal = {GigaScience}, volume = {5}, number = {1}, pages = {44}, pmid = {27776538}, issn = {2047-217X}, mesh = {Algorithms ; Cluster Analysis ; Evolution, Molecular ; Genes, Bacterial ; Genomics/*methods ; Phylogeny ; Recombination, Genetic ; Staphylococcus aureus/*classification/genetics ; }, abstract = {BACKGROUND: Collective animal behavior, such as the flocking of birds or the shoaling of fish, has inspired a class of algorithms designed to optimize distance-based clusters in various applications, including document analysis and DNA microarrays. In a flocking model, individual agents respond only to their immediate environment and move according to a few simple rules. After several iterations the agents self-organize, and clusters emerge without the need for partitional seeds. In addition to its unsupervised nature, flocking offers several computational advantages, including the potential to reduce the number of required comparisons.<br><br>FINDINGS: In the tool presented here, Clusterflock, we have implemented a flocking algorithm designed to locate groups (flocks) of orthologous gene families (OGFs) that share an evolutionary history. Pairwise distances that measure phylogenetic incongruence between OGFs guide flock formation. We tested this approach on several simulated datasets by varying the number of underlying topologies, the proportion of missing data, and evolutionary rates, and show that in datasets containing high levels of missing data and rate heterogeneity, Clusterflock outperforms other well-established clustering techniques. We also verified its utility on a known, large-scale recombination event in Staphylococcus aureus. By isolating sets of OGFs with divergent phylogenetic signals, we were able to pinpoint the recombined region without forcing a pre-determined number of groupings or defining a pre-determined incongruence threshold.<br><br>CONCLUSIONS: Clusterflock is an open-source tool that can be used to discover horizontally transferred genes, recombined areas of chromosomes, and the phylogenetic 'core' of a genome. Although we used it here in an evolutionary context, it is generalizable to any clustering problem. Users can write extensions to calculate any distance metric on the unit interval, and can use these distances to 'flock' any type of data.}, }
@article {pmid27776307, year = {2016}, author = {Yu, Z and He, P and Shao, L and Zhang, H and Lü, F}, title = {Co-occurrence of mobile genetic elements and antibiotic resistance genes in municipal solid waste landfill leachates: A preliminary insight into the role of landfill age.}, journal = {Water research}, volume = {106}, number = {}, pages = {583-592}, doi = {10.1016/j.watres.2016.10.042}, pmid = {27776307}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Refuse Disposal ; *Solid Waste ; Waste Disposal Facilities ; *Water Pollutants, Chemical ; }, abstract = {Since municipal solid waste (MSW) landfill harbours miscellaneous wastes, pollutants and microorganisms, it gradually becomes a huge potential reservoir for breeding antibiotic resistance genes (ARGs). The objective of this study was to determine the prevalence and diversity of ARGs associated with various mobile genetic elements (MGEs) in MSW landfill leachates. The relationship of ARGs with leachate characteristics was also studied to explore the influence of landfill age. Seven sulfonamides (sulfapyridine, sulfadiazine, sulfathiazole, sulfamethoxazole, sulfamerazine, sulfamethazine and sulfaquinoxaline), three encoded ARGs (sul-I, sul-II and sul-III) and four types of MGEs (plasmids, transposons, integrons and insertion sequences) were quantified in leachates with landfill ages ranging from 3 months-6 years. ARGs increased to an absolute concentration of 10[6] copies/μL and were positively correlated (p < 0.05) to MGEs. Significant correlations (p < 0.05) were also discovered among ARGs and the increasing humic acids, heavy metals (Zn, Cu and Co) and antibiotics (except for sulfathiazole and sulfaquinoxaline), implying landfilling might contribute to the enrichment of ARGs in the long-term. Non-target full scans revealed the role of persistent unknown compounds in stimulating the ARGs dissemination. Overall, this study demonstrates the exacerbation of ARGs pollution in landfill environment and a detailed delineation of the complex inter-relationships between ARGs and the substances harbouring in landfills is badly required.}, }
@article {pmid27774436, year = {2016}, author = {Huang, J and Ma, J and Shang, K and Hu, X and Liang, Y and Li, D and Wu, Z and Dai, L and Chen, L and Wang, L}, title = {Evolution and Diversity of the Antimicrobial Resistance Associated Mobilome in Streptococcus suis: A Probable Mobile Genetic Elements Reservoir for Other Streptococci.}, journal = {Frontiers in cellular and infection microbiology}, volume = {6}, number = {}, pages = {118}, pmid = {27774436}, issn = {2235-2988}, mesh = {Conjugation, Genetic ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Genetic Loci ; *Interspersed Repetitive Sequences ; Recombination, Genetic ; Sequence Analysis, DNA ; Streptococcus/*drug effects/*genetics/growth &amp; development ; }, abstract = {Streptococcus suis is a previously neglected, newly emerging multidrug-resistant zoonotic pathogen. Mobile genetic elements (MGEs) play a key role in intra- and interspecies horizontal transfer of antimicrobial resistance (AMR) determinants. Although, previous studies showed the presence of several MGEs, a comprehensive analysis of AMR-associated mobilome as well as their interaction and evolution has not been performed. In this study, we presented the AMR-associated mobilome and their insertion hotspots in S. suis. Integrative conjugative elements (ICEs), prophages and tandem MGEs were located at different insertion sites, while 86% of the AMR-associated MGEs were inserted at rplL and rum loci. Comprehensive analysis of insertions at rplL and rum loci among four pathogenic Streptococcus species (Streptococcus agalactiae, Streptococcus pneumoniae, Streptococcus pyogenes, and S. suis) revealed the existence of different groups of MGEs, including Tn5252, ICESp1108, and TnGBS2 groups ICEs, Φm46.1 group prophage, ICE_ICE and ICE_prophage tandem MGEs. Comparative ICE genomics of ICESa2603 family revealed that module exchange and acquisition/deletion were the main mechanisms in MGEs' expansion and evolution. Furthermore, the observation of tandem MGEs reflected a novel mechanism for MGE diversity. Moreover, an in vitro competition assay showed no visible fitness cost was observed between different MGE-carrying isolates and a conjugation assay revealed the transferability of ICESa2603 family of ICEs. Our statistics further indicated that the prevalence and diversity of MGEs in S. suis is much greater than in other three species which prompted our hypothesis that S. suis is probably a MGEs reservoir for other streptococci. In conclusion, our results showed that acquisition of MGEs confers S. suis not only its capability as a multidrug resistance pathogen, but also represents a paradigm to study the modular evolution and matryoshkas of MGEs.}, }
@article {pmid27773878, year = {2017}, author = {Bonacina, J and Suárez, N and Hormigo, R and Fadda, S and Lechner, M and Saavedra, L}, title = {A genomic view of food-related and probiotic Enterococcus strains.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {24}, number = {1}, pages = {11-24}, pmid = {27773878}, issn = {1756-1663}, mesh = {Bacteriocins/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats ; Drug Resistance, Microbial/genetics ; Enterococcus/classification/*genetics ; *Food Microbiology ; Gene Transfer, Horizontal ; Genetic Markers ; *Genome, Bacterial ; Phylogeny ; *Probiotics ; }, abstract = {The study of enterococcal genomes has grown considerably in recent years. While special attention is paid to comparative genomic analysis among clinical relevant isolates, in this study we performed an exhaustive comparative analysis of enterococcal genomes of food origin and/or with potential to be used as probiotics. Beyond common genetic features, we especially aimed to identify those that are specific to enterococcal strains isolated from a certain food-related source as well as features present in a species-specific manner. Thus, the genome sequences of 25 Enterococcus strains, from 7 different species, were examined and compared. Their phylogenetic relationship was reconstructed based on orthologous proteins and whole genomes. Likewise, markers associated with a successful colonization (bacteriocin genes and genomic islands) and genome plasticity (phages and clustered regularly interspaced short palindromic repeats) were investigated for lifestyle specific genetic features. At the same time, a search for antibiotic resistance genes was carried out, since they are of big concern in the food industry. Finally, it was possible to locate 1617 FIGfam families as a core proteome universally present among the genera and to determine that most of the accessory genes code for hypothetical proteins, providing reasonable hints to support their functional characterization.}, }
@article {pmid27771149, year = {2017}, author = {Muzslay, M and Moore, G and Alhussaini, N and Wilson, AP}, title = {ESBL-producing Gram-negative organisms in the healthcare environment as a source of genetic material for resistance in human infections.}, journal = {The Journal of hospital infection}, volume = {95}, number = {1}, pages = {59-64}, doi = {10.1016/j.jhin.2016.09.009}, pmid = {27771149}, issn = {1532-2939}, mesh = {Bacteriological Techniques ; Cephalosporin Resistance ; Conjugation, Genetic ; *Disease Reservoirs ; *Environmental Microbiology ; Gene Transfer, Horizontal ; *Genes ; Gram-Negative Bacteria/enzymology/genetics/*isolation &amp; purification ; *Health Facilities ; Humans ; Surveys and Questionnaires ; beta-Lactamases/*genetics ; }, abstract = {BACKGROUND: The increasing prevalence of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae in the healthcare setting and in the community despite established infection control guidelines indicates that these microorganisms may possess survival strategies that allow them to persist in the environment.<br><br>AIMS: To determine the extent and variation in endemic ESBL-carrying species in different ward environments, and to investigate the potential for cephalosporin resistance to be transferred from environmental isolates to human pathogens.<br><br>METHODS: Conventional microbiological methods were used to sample 1436 environmental surfaces for ESBL-producing bacteria. Transconjugation assays (broth mating experiments) were performed using environmental ESBL-producing isolates as donors and streptomycin-resistant Escherichia coli (NCTC 50237) as the recipient.<br><br>FINDINGS: The prevalence of ESBL-producing bacteria on surfaces in a non-outbreak setting was low (45/1436; 3.1%). The sites most likely to be contaminated were the drains of handwash basins (28/105; 26.7%) and floors (14/160; 8.8%). Fifty-nine ESBL-carrying organisms were isolated. Of these, Klebsiella spp. (33.9%), Enterobacter spp. (20.3%), Pantoea spp. (15.3%) and Citrobacter spp. (13.6%) were the most common isolates. ESBL determinants were transferred successfully from three representative environmental isolates (Pantoea calida, Klebsiella oxytoca, Raoultella ornithinolytica) to the human pathogen E.&#xa0;coli.<br><br>CONCLUSION: ESBL-producing Gram-negative isolates were recovered from the hospital environment in the absence of any ESBL infection on the wards. The drains of handwash basins should be considered potential long-term reservoirs of multi-drug-resistant bacteria and drug resistance genes. These genes can reside in various genera of hardy environmental organisms and be a potential source of ESBL for more common human pathogens.}, }
@article {pmid27751837, year = {2016}, author = {Cai, J and Wu, G and Jose, PA and Zeng, C}, title = {Functional transferred DNA within extracellular vesicles.}, journal = {Experimental cell research}, volume = {349}, number = {1}, pages = {179-183}, doi = {10.1016/j.yexcr.2016.10.012}, pmid = {27751837}, issn = {1090-2422}, mesh = {Animals ; DNA/*metabolism ; Disease ; Extracellular Vesicles/*metabolism ; Gene Transfer Techniques ; Humans ; Models, Biological ; }, abstract = {Extracellular vesicles (EVs) are small membrane vesicles including exosomes and shedding vesicles that mediated a cell-to-cell communication. EVs are released from almost all cell types under both physiological and pathological conditions and incorporate nuclear and cytoplasmic molecules for intercellular delivery. Besides protein, mRNA, and microRNA of these molecules, as recent studies show, specific DNA are prominently packaged into EVs. It appears likely that some of exosomes or shedding vesicles, bearing nuclear molecules are released upon bubble-like blebs. Specific interaction of EVs with susceptible recipients performs the uptake of EVs into the target cells, discharging their cargo including nuclear and cytoplasmic macromolecules into the cytosol. These findings expand the nucleic acid content of EVs to include increased levels of specific DNA. Thus, EVs contain a repertoire of genetic information available for horizontal gene transfer and potential use as blood biomarkers for cancer and atherosclerosis. In this review, the focus is on the characteristics, biological functions, and roles in diseases of DNA within EVs.}, }
@article {pmid27742260, year = {2016}, author = {Billiard, S and Collet, P and Ferrière, R and Méléard, S and Tran, VC}, title = {The effect of competition and horizontal trait inheritance on invasion, fixation, and polymorphism.}, journal = {Journal of theoretical biology}, volume = {411}, number = {}, pages = {48-58}, doi = {10.1016/j.jtbi.2016.10.003}, pmid = {27742260}, issn = {1095-8541}, mesh = {Adaptation, Physiological/genetics ; *Algorithms ; Animals ; Competitive Behavior ; Ecosystem ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genetics, Population ; *Models, Genetic ; Phenotype ; Polymorphism, Genetic/*genetics ; Population Density ; Population Dynamics ; Probability ; Stochastic Processes ; Time Factors ; }, abstract = {Horizontal transfer (HT) of heritable information or 'traits' (carried by genetic elements, plasmids, endosymbionts, or culture) is widespread among living organisms. Yet current ecological and evolutionary theory addressing HT is scant. We present a modeling framework for the dynamics of two populations that compete for resources and horizontally exchange (transfer) an otherwise vertically inherited trait. Competition influences individual demographics, thereby affecting population size, which feeds back on the dynamics of transfer. This feedback is captured in a stochastic individual-based model, from which we derive a general model for the contact rate, with frequency-dependent (FD) and density-dependent (DD) rates as special cases. Taking a large-population limit on the stochastic individual-level model yields a deterministic Lotka-Volterra competition system with additional terms accounting for HT. The stability analysis of this system shows that HT can revert the direction of selection: HT can drive invasion of a deleterious trait, or prevent invasion of an advantageous trait. Due to HT, invasion does not necessarily imply fixation. Two trait values may coexist in a stable polymorphism even if their invasion fitnesses have opposite signs, or both are negative. Addressing the question of how the stochasticity of individual processes influences population fluctuations, we identify conditions on competition and mode of transfer (FD versus DD) under which the stochasticity of transfer events overwhelms demographic stochasticity. Assuming that one trait is initially rare, we derive invasion and fixation probabilities and time. In the case of costly plasmids, which are transfered unilaterally, invasion is always possible if the transfer rate is large enough; under DD and for intermediate values of the transfer rate, maintenance of the plasmid in a polymorphic population is possible. In conclusion, HT interacts with ecology (competition) in non-trivial ways. Our model provides a basis to model the influence of HT on evolutionary adaptation.}, }
@article {pmid27704560, year = {2017}, author = {Pandey, RS and Saxena, G and Bhattacharya, D and Qiu, H and Azad, RK}, title = {Using complementary approaches to identify trans-domain nuclear gene transfers in the extremophile Galdieria sulphuraria (Rhodophyta).}, journal = {Journal of phycology}, volume = {53}, number = {1}, pages = {7-11}, doi = {10.1111/jpy.12466}, pmid = {27704560}, issn = {1529-8817}, mesh = {Archaea/genetics ; Bacteria/genetics ; *Evolution, Molecular ; Extremophiles/classification/*genetics ; *Gene Transfer, Horizontal ; Microalgae/classification/*genetics ; Phylogeny ; Rhodophyta/classification/*genetics ; Sequence Analysis, DNA ; }, abstract = {Identification of horizontal gene transfers (HGTs) has primarily relied on phylogenetic tree based methods, which require a rich sampling of sequenced genomes to ensure a reliable inference. Because the success of phylogenetic approaches depends on the breadth and depth of the database, researchers usually apply stringent filters to detect only the most likely gene transfers in the genomes of interest. One such study focused on a highly conservative estimate of trans-domain gene transfers in the extremophile eukaryote, Galdieria sulphuraria (Galdieri) Merola (Rhodophyta), by applying multiple filters in their phylogenetic pipeline. This led to the identification of 75 inter-domain acquisitions from Bacteria or Archaea. Because of the evolutionary, ecological, and potential biotechnological significance of foreign genes in algae, alternative approaches and pipelines complementing phylogenetics are needed for a more comprehensive assessment of HGT. We present here a novel pipeline that uncovered 17 novel foreign genes of prokaryotic origin in G. sulphuraria, results that are supported by multiple lines of evidence including composition-based, comparative data, and phylogenetics. These genes encode a variety of potentially adaptive functions, from metabolite transport to DNA repair.}, }
@article {pmid27652382, year = {2016}, author = {Aucamp, J and Bronkhorst, AJ and Badenhorst, CP and Pretorius, PJ}, title = {A historical and evolutionary perspective on the biological significance of circulating DNA and extracellular vesicles.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {73}, number = {23}, pages = {4355-4381}, pmid = {27652382}, issn = {1420-9071}, mesh = {Animals ; *Biological Evolution ; DNA/*blood/metabolism ; Extracellular Vesicles/*metabolism ; Heredity ; Humans ; Inheritance Patterns/genetics ; Multiprotein Complexes/metabolism ; }, abstract = {The discovery of quantitative and qualitative differences of the circulating DNA (cirDNA) between healthy and diseased individuals inclined researchers to investigate these molecules as potential biomarkers for non-invasive diagnosis and prognosis of various pathologies. However, except for some prenatal tests, cirDNA analyses have not been readily translated to clinical practice due to a lack of knowledge regarding its composition, function, and biological and evolutionary origins. We believe that, to fully grasp the nature of cirDNA and the extracellular vesicles (EVs) and protein complexes with which it is associated, it is necessary to probe the early and badly neglected work that contributed to the discovery and development of these concepts. Accordingly, this review consists of a schematic summary of the major events that developed and integrated the concepts of heredity, genetic information, cirDNA, EVs, and protein complexes. CirDNA enters target cells and provokes a myriad of gene regulatory effects associated with the messaging functions of various natures, disease progression, somatic genome variation, and transgenerational inheritance. This challenges the traditional views on each of the former topics. All of these discoveries can be traced directly back to the iconic works of Darwin, Lamarck, and their followers. The history of cirDNA that has been revisited here is rich in information that should be considered in clinical practice, when designing new experiments, and should be very useful for generating an empirically up-to-date view of cirDNA and EVs. Furthermore, we hope that it will invite many flights of speculation and stimulate further inquiry into its biological and evolutionary origins.}, }
@article {pmid27587336, year = {2016}, author = {Patel, S}, title = {Drivers of bacterial genomes plasticity and roles they play in pathogen virulence, persistence and drug resistance.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {45}, number = {}, pages = {151-164}, doi = {10.1016/j.meegid.2016.08.030}, pmid = {27587336}, issn = {1567-7257}, mesh = {Bacterial Infections/microbiology ; Drug Resistance, Bacterial/*genetics ; Gene Rearrangement/genetics ; Gene Transfer, Horizontal ; Genome, Bacterial/*genetics ; Humans ; Interspersed Repetitive Sequences/genetics ; Virulence/*genetics ; }, abstract = {Despite the advent of next-generation sequencing (NGS) technologies, sophisticated data analysis and drug development efforts, bacterial drug resistance persists and is escalating in magnitude. To better control the pathogens, a thorough understanding of their genomic architecture and dynamics is vital. Bacterial genome is extremely complex, a mosaic of numerous co-operating and antagonizing components, altruistic and self-interested entities, behavior of which are predictable and conserved to some extent, yet largely dictated by an array of variables. In this regard, mobile genetic elements (MGE), DNA repair systems, post-segregation killing systems, toxin-antitoxin (TA) systems, restriction-modification (RM) systems etc. are dominant agents and horizontal gene transfer (HGT), gene redundancy, epigenetics, phase and antigenic variation etc. processes shape the genome. By illegitimate recombinations, deletions, insertions, duplications, amplifications, inversions, conversions, translocations, modification of intergenic regions and other alterations, bacterial genome is modified to tackle stressors like drugs, and host immune effectors. Over the years, thousands of studies have investigated this aspect and mammoth amount of insights have been accumulated. This review strives to distillate the existing information, formulate hypotheses and to suggest directions, that might contribute towards improved mitigation of the vicious pathogens.}, }
@article {pmid27768816, year = {2016}, author = {Gibert, M and Paytubi, S and Beltrán, S and Juárez, A and Balsalobre, C and Madrid, C}, title = {Growth phase-dependent control of R27 conjugation is mediated by the interplay between the plasmid-encoded regulatory circuit TrhR/TrhY-HtdA and the cAMP regulon.}, journal = {Environmental microbiology}, volume = {18}, number = {12}, pages = {5277-5287}, doi = {10.1111/1462-2920.13579}, pmid = {27768816}, issn = {1462-2920}, mesh = {*Conjugation, Genetic ; Cyclic AMP/*metabolism ; Escherichia coli/*genetics/*growth &amp; development/metabolism ; Escherichia coli Proteins/genetics/*metabolism ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Plasmids/*genetics/metabolism ; Regulon ; }, abstract = {Plasmids of the incompatibility group HI1 (IncHI1) have been isolated from several Gram-negative pathogens and are associated with the spread of multidrug resistance. Their conjugation is tightly regulated and it is inhibited at temperatures higher than 30°C, indicating that conjugation occurs outside warm-blooded hosts. Using R27, the prototype of IncHI1 plasmids, we report that plasmid transfer efficiency in E. coli strongly depends on the physiological state of the donor cells. Conjugation frequency is high when cells are actively growing, dropping sharply when cells enter the stationary phase of growth. Accordingly, our transcriptomic assays show significant downregulation of numerous R27 genes during the stationary phase, including several tra (transfer) genes. Growth phase-dependent regulation of tra genes transcription is independent of H-NS, a silencer of horizontal gene transfer, and ppGpp and RpoS, regulators of the stationary phase, but highly dependent on the plasmid-encoded regulatory circuit TrhR/TrhY-HtdA. The metabolic sensor cAMP, whose synthesis is chromosomally encoded, is also involved in the growth phase regulation of R27 conjugation by modulating htdA expression. Our data suggest that the involvement of regulators encoded by both chromosome and plasmid are required for efficient physiological control of IncHI1 plasmid conjugation.}, }
@article {pmid27767072, year = {2016}, author = {Pärnänen, K and Karkman, A and Tamminen, M and Lyra, C and Hultman, J and Paulin, L and Virta, M}, title = {Evaluating the mobility potential of antibiotic resistance genes in environmental resistomes without metagenomics.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {35790}, pmid = {27767072}, issn = {2045-2322}, mesh = {Bacteria/drug effects/genetics/pathogenicity ; DNA, Bacterial/genetics ; Drug Resistance, Microbial/*genetics ; *Environmental Microbiology ; Environmental Monitoring/methods ; Gene Transfer, Horizontal ; Geologic Sediments/microbiology ; Humans ; *Interspersed Repetitive Sequences ; Metagenomics ; Multigene Family ; Polymerase Chain Reaction/methods ; }, abstract = {Antibiotic resistance genes are ubiquitous in the environment. However, only a fraction of them are mobile and able to spread to pathogenic bacteria. Until now, studying the mobility of antibiotic resistance genes in environmental resistomes has been challenging due to inadequate sensitivity and difficulties in contig assembly of metagenome based methods. We developed a new cost and labor efficient method based on Inverse PCR and long read sequencing for studying mobility potential of environmental resistance genes. We applied Inverse PCR on sediment samples and identified 79 different MGE clusters associated with the studied resistance genes, including novel mobile genetic elements, co-selected resistance genes and a new putative antibiotic resistance gene. The results show that the method can be used in antibiotic resistance early warning systems. In comparison to metagenomics, Inverse PCR was markedly more sensitive and provided more data on resistance gene mobility and co-selected resistances.}, }
@article {pmid27766095, year = {2016}, author = {Novais, C and Tedim, AP and Lanza, VF and Freitas, AR and Silveira, E and Escada, R and Roberts, AP and Al-Haroni, M and Baquero, F and Peixe, L and Coque, TM}, title = {Co-diversification of Enterococcus faecium Core Genomes and PBP5: Evidences of pbp5 Horizontal Transfer.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1581}, pmid = {27766095}, issn = {1664-302X}, support = {L60 MD002414/MD/NIMHD NIH HHS/United States ; }, abstract = {Ampicillin resistance has greatly contributed to the recent dramatic increase of a cluster of human adapted Enterococcus faecium lineages (ST17, ST18, and ST78) in hospital-based infections. Changes in the chromosomal pbp5 gene have been associated with different levels of ampicillin susceptibility, leading to protein variants (designated as PBP5 C-types to keep the nomenclature used in previous works) with diverse degrees of reduction in penicillin affinity. Our goal was to use a comparative genomics approach to evaluate the relationship between the diversity of PBP5 among E. faecium isolates of different phylogenomic groups as well as to assess the pbp5 transferability among isolates of disparate clonal lineages. The analyses of 78 selected E. faecium strains as well as published E. faecium genomes, suggested that the diversity of pbp5 mirrors the phylogenomic diversification of E. faecium. The presence of identical PBP5 C-types as well as similar pbp5 genetic environments in different E. faecium lineages and clones from quite different geographical and environmental origin was also documented and would indicate their horizontal gene transfer among E. faecium populations. This was supported by experimental assays showing transfer of large (≈180-280 kb) chromosomal genetic platforms containing pbp5 alleles, ponA (transglycosilase) and other metabolic and adaptive features, from E. faecium donor isolates to suitable E. faecium recipient strains. Mutation profile analysis of PBP5 from available genomes and strains from this study suggests that the spread of PBP5 C-types might have occurred even in the absence of a significant ampicillin resistance phenotype. In summary, genetic platforms containing pbp5 sequences were stably maintained in particular E. faecium lineages, but were also able to be transferred among E. faecium clones of different origins, emphasizing the growing risk of further spread of ampicillin resistance in this nosocomial pathogen.}, }
@article {pmid27765811, year = {2016}, author = {Li, G and Shen, M and Le, S and Tan, Y and Li, M and Zhao, X and Shen, W and Yang, Y and Wang, J and Zhu, H and Li, S and Rao, X and Hu, F and Lu, S}, title = {Genomic analyses of multidrug resistant Pseudomonas aeruginosa PA1 resequenced by single-molecule real-time sequencing.}, journal = {Bioscience reports}, volume = {36}, number = {6}, pages = {}, pmid = {27765811}, issn = {1573-4935}, mesh = {Bacterial Proteins/*genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Genome, Bacterial/*genetics ; Genomic Islands/genetics ; Genomics/methods ; Phylogeny ; Pseudomonas aeruginosa/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {As a third-generation sequencing (TGS) method, single-molecule real-time (SMRT) technology provides long read length, and it is well suited for resequencing projects and de novo assembly. In the present study, Pseudomonas aeruginosa PA1 was characterized and resequenced using SMRT technology. PA1 was also subjected to genomic, comparative and pan-genomic analyses. The multidrug resistant strain PA1 possesses a 6,498,072 bp genome and a sequence type of ST-782. The genome of PA1 was also visualized, and the results revealed the details of general genome annotations, virulence factors, regulatory proteins (RPs), secretion system proteins, type II toxin-antitoxin (T-A) pairs and genomic islands. Whole genome comparison analysis suggested that PA1 exhibits similarity to other P. aeruginosa strains but differs in terms of horizontal gene transfer (HGT) regions, such as prophages and genomic islands. Phylogenetic analyses based on 16S rRNA sequences demonstrated that PA1 is closely related to PAO1, and P. aeruginosa strains can be divided into two main groups. The pan-genome of P. aeruginosa consists of a core genome of approximately 4,000 genes and an accessory genome of at least 6,600 genes. The present study presented a detailed, visualized and comparative analysis of the PA1 genome, to enhance our understanding of this notorious pathogen.}, }
@article {pmid27765015, year = {2016}, author = {LaRoche-Johnston, F and Monat, C and Cousineau, B}, title = {Recent horizontal transfer, functional adaptation and dissemination of a bacterial group II intron.}, journal = {BMC evolutionary biology}, volume = {16}, number = {1}, pages = {223}, pmid = {27765015}, issn = {1471-2148}, mesh = {Bacteria/*genetics ; Bacterial Proteins/genetics ; DNA Transposable Elements ; Enterococcus faecalis/*genetics ; *Gene Transfer, Horizontal ; *Introns ; Lactococcus lactis/*genetics ; Mutation ; Phylogeny ; RNA Splicing ; RNA, Catalytic/genetics ; }, abstract = {BACKGROUND: Group II introns are catalytically active RNA and mobile retroelements present in certain eukaryotic organelles, bacteria and archaea. These ribozymes self-splice from the pre-mRNA of interrupted genes and reinsert within target DNA sequences by retrohoming and retrotransposition. Evolutionary hypotheses place these retromobile elements at the origin of over half the human genome. Nevertheless, the evolution and dissemination of group II introns was found to be quite difficult to infer.<br><br>RESULTS: We characterized the functional and evolutionary relationship between the model group II intron from Lactococcus lactis, Ll.LtrB, and Ef.PcfG, a newly discovered intron from a clinical strain of Enterococcus faecalis. Ef.PcfG was found to be homologous to Ll.LtrB and to splice and mobilize in its native environment as well as in L. lactis. Interestingly, Ef.PcfG was shown to splice at the same level as Ll.LtrB but to be significantly less efficient to invade the Ll.LtrB recognition site. We also demonstrated that specific point mutations between the IEPs of both introns correspond to functional adaptations which developed in L. lactis as a response to selective pressure on mobility efficiency independently of splicing. The sequence of all the homologous full-length variants of Ll.LtrB were compared and shown to share a conserved pattern of mutation acquisition.<br><br>CONCLUSIONS: This work shows that Ll.LtrB and Ef.PcfG are homologous and have a common origin resulting from a recent lateral transfer event followed by further adaptation to the new target site and/or host environment. We hypothesize that Ef.PcfG is the ancestor of Ll.LtrB and was initially acquired by L. lactis, most probably by conjugation, via a single event of horizontal transfer. Strong selective pressure on homing site invasion efficiency then led to the emergence of beneficial point mutations in the IEP, enabling the successful establishment and survival of the group II intron in its novel lactococcal environment. The current colonization state of Ll.LtrB in L. lactis was probably later achieved through recurring episodes of conjugation-based horizontal transfer as well as independent intron mobility events. Overall, our data provide the first evidence of functional adaptation of a group II intron upon invading a new host, offering strong experimental support to the theory that bacterial group II introns, in sharp contrast to their organellar counterparts, behave mostly as mobile elements.}, }
@article {pmid27707801, year = {2016}, author = {Zeman, I and Neboháčová, M and Gérecová, G and Katonová, K and Jánošíková, E and Jakúbková, M and Centárová, I and Dunčková, I and Tomáška, L and Pryszcz, LP and Gabaldón, T and Nosek, J}, title = {Mitochondrial Carriers Link the Catabolism of Hydroxyaromatic Compounds to the Central Metabolism in Candida parapsilosis.}, journal = {G3 (Bethesda, Md.)}, volume = {6}, number = {12}, pages = {4047-4058}, pmid = {27707801}, issn = {2160-1836}, support = {310325/ERC_/European Research Council/International ; }, mesh = {Acetyl-CoA C-Acyltransferase/genetics/metabolism ; Ascomycota/classification/genetics/*metabolism ; Biological Evolution ; Coenzyme A-Transferases/genetics/metabolism ; Fungal Proteins/genetics/metabolism ; Gene Expression Regulation, Fungal ; Hydrocarbons, Aromatic/*metabolism ; Metabolic Networks and Pathways ; Mitochondria/genetics/*metabolism ; Mutation ; Phylogeny ; Protein Transport ; Saccharomyces cerevisiae/genetics/metabolism ; Substrate Specificity ; }, abstract = {The pathogenic yeast Candida parapsilosis metabolizes hydroxyderivatives of benzene and benzoic acid to compounds channeled into central metabolism, including the mitochondrially localized tricarboxylic acid cycle, via the 3-oxoadipate and gentisate pathways. The orchestration of both catabolic pathways with mitochondrial metabolism as well as their evolutionary origin is not fully understood. Our results show that the enzymes involved in these two pathways operate in the cytoplasm with the exception of the mitochondrially targeted 3-oxoadipate CoA-transferase (Osc1p) and 3-oxoadipyl-CoA thiolase (Oct1p) catalyzing the last two reactions of the 3-oxoadipate pathway. The cellular localization of the enzymes indicates that degradation of hydroxyaromatic compounds requires a shuttling of intermediates, cofactors, and products of the corresponding biochemical reactions between cytosol and mitochondria. Indeed, we found that yeast cells assimilating hydroxybenzoates increase the expression of genes SFC1, LEU5, YHM2, and MPC1 coding for succinate/fumarate carrier, coenzyme A carrier, oxoglutarate/citrate carrier, and the subunit of pyruvate carrier, respectively. A phylogenetic analysis uncovered distinct evolutionary trajectories for sparsely distributed gene clusters coding for enzymes of both pathways. Whereas the 3-oxoadipate pathway appears to have evolved by vertical descent combined with multiple losses, the gentisate pathway shows a striking pattern suggestive of horizontal gene transfer to the evolutionarily distant Mucorales.}, }
@article {pmid27611183, year = {2016}, author = {Brenzinger, S and Dewenter, L and Delalez, NJ and Leicht, O and Berndt, V and Paulick, A and Berry, RM and Thanbichler, M and Armitage, JP and Maier, B and Thormann, KM}, title = {Mutations targeting the plug-domain of the Shewanella oneidensis proton-driven stator allow swimming at increased viscosity and under anaerobic conditions.}, journal = {Molecular microbiology}, volume = {102}, number = {5}, pages = {925-938}, doi = {10.1111/mmi.13499}, pmid = {27611183}, issn = {1365-2958}, support = {BB/E00458X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/H01991X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Anaerobiosis ; Bacterial Outer Membrane Proteins/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Flagella/*genetics/metabolism ; Molecular Motor Proteins/*genetics/metabolism ; Mutation ; Protons ; Shewanella/*genetics/metabolism ; Viscosity ; }, abstract = {Shewanella oneidensis MR-1 possesses two different stator units to drive flagellar rotation, the Na[+] -dependent PomAB stator and the H[+] -driven MotAB stator, the latter possibly acquired by lateral gene transfer. Although either stator can independently drive swimming through liquid, MotAB-driven motors cannot support efficient motility in structured environments or swimming under anaerobic conditions. Using ΔpomAB cells we isolated spontaneous mutants able to move through soft agar. We show that a mutation that alters the structure of the plug domain in MotB affects motor functions and allows cells to swim through media of increased viscosity and under anaerobic conditions. The number and exchange rates of the mutant stator around the rotor were not significantly different from wild-type stators, suggesting that the number of stators engaged is not the cause of increased swimming efficiency. The swimming speeds of planktonic mutant MotAB-driven cells was reduced, and overexpression of some of these stators caused reduced growth rates, implying that mutant stators not engaged with the rotor allow some proton leakage. The results suggest that the mutations in the MotB plug domain alter the proton interactions with the stator ion channel in a way that both increases torque output and allows swimming at decreased pmf values.}, }
@article {pmid27764198, year = {2016}, author = {Tandberg, JI and Lagos, LX and Langlete, P and Berger, E and Rishovd, AL and Roos, N and Varkey, D and Paulsen, IT and Winther-Larsen, HC}, title = {Comparative Analysis of Membrane Vesicles from Three Piscirickettsia salmonis Isolates Reveals Differences in Vesicle Characteristics.}, journal = {PloS one}, volume = {11}, number = {10}, pages = {e0165099}, pmid = {27764198}, issn = {1932-6203}, mesh = {Animals ; Bacterial Proteins/*metabolism ; Canada ; Chile ; Cytoplasmic Vesicles/immunology/*metabolism ; Mass Spectrometry/methods ; Norway ; Piscirickettsia/*isolation &amp; purification/metabolism ; Piscirickettsiaceae Infections/*immunology ; Proteomics/*methods ; Salmonidae/microbiology ; Virulence Factors/metabolism ; Zebrafish/immunology/microbiology ; }, abstract = {Membrane vesicles (MVs) are spherical particles naturally released from the membrane of Gram-negative bacteria. Bacterial MV production is associated with a range of phenotypes including biofilm formation, horizontal gene transfer, toxin delivery, modulation of host immune responses and virulence. This study reports comparative profiling of MVs from bacterial strains isolated from three widely disperse geographical areas. Mass spectrometry identified 119, 159 and 142 proteins in MVs from three different strains of Piscirickettsia salmonis isolated from salmonids in Chile (LF-89), Norway (NVI 5692) and Canada (NVI 5892), respectively. MV comparison revealed several strain-specific differences related to higher virulence capability for LF-89 MVs, both in vivo and in vitro, and stronger similarities between the NVI 5692 and NVI 5892 MV proteome. The MVs were similar in size and appearance as analyzed by electron microscopy and dynamic light scattering. The MVs from all three strains were internalized by both commercial and primary immune cell cultures, which suggest a potential role of the MVs in the bacterium's utilization of leukocytes. When MVs were injected into an adult zebrafish infection model, an upregulation of several pro-inflammatory genes were observed in spleen and kidney, indicating a modulating effect on the immune system. The present study is the first comparative analysis of P. salmonis derived MVs, highlighting strain-specific vesicle characteristics. The results further illustrate that the MV proteome from one bacterial strain is not representative of all bacterial strains within one species.}, }
@article {pmid27758703, year = {2017}, author = {Hemlata,  and Jan, AT and Tiwari, A}, title = {The Ever Changing Face of Antibiotic Resistance: Prevailing Problems and Preventive Measures.}, journal = {Current drug metabolism}, volume = {18}, number = {1}, pages = {69-77}, doi = {10.2174/1389200217666161014163324}, pmid = {27758703}, issn = {1875-5453}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects ; *Drug Resistance, Multiple, Bacterial ; Global Health ; Humans ; }, abstract = {BACKGROUND: Antibiotic resistance is a global problem that presents significant risk to human health. Driven by selective pressure of antimicrobial agents, spontaneous mutation, recombination and horizontal gene transfer events, inappropriate antibiotic prescribing and use outside healthcare settings has increased their impact on healthcare system. Increasing risk for human health lead us to study resistance development mechanisms, associated factors that increase dissemination of resistance genes along with information of imperative measures necessary to curtail the growing menace.<br><br>METHODS: In this article, we emphasized on the state of knowledge regarding imprudent use of antibiotics that act as promoters of resistance development. For this, literature based search for articles and entries related to antimicrobial resistance was done. With ample of data available, selected was performed for the epidemiological and clinical based study to curtail the facts present in these data sets so as to get accurate and important information.<br><br>RESULTS: Resistance mediated by different determinants such as TEM, SHV, OXA and CTX-M, methods of mobilization that increase spread across species and as such failure to available treatment regimens was studied. Addition to detection methods, information of the inhibitors and natural substance useful in mitigating the effect of multidrug resistance was included to strategies the policies and plans for restricting their spread.<br><br>CONCLUSION: As intervention to this growing problem, modified use of antimicrobial agents, employment of different formulations of herbs along with public health interventions in restricting antibiotic use, are believed to be of great help in restricting their dissemination and as such spread to non-pathogenic bacterial isolates.}, }
@article {pmid27756908, year = {2016}, author = {Song, T and Xu, H and Wei, C and Jiang, T and Qin, S and Zhang, W and Cao, Y and Hu, C and Zhang, F and Qiao, D and Cao, Y}, title = {Horizontal Transfer of a Novel Soil Agarase Gene from Marine Bacteria to Soil Bacteria via Human Microbiota.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {34103}, pmid = {27756908}, issn = {2045-2322}, mesh = {Bacterial Proteins/*genetics/metabolism ; *Gastrointestinal Microbiome ; Gene Transfer, Horizontal/*physiology ; Glycoside Hydrolases/*genetics/metabolism ; Humans ; *Paenibacillus/enzymology/genetics ; *Soil Microbiology ; *Water Microbiology ; }, abstract = {Seaweed is receiving an increasing amount of attention as a "sea vegetable". The microbiota of coastal populations may acquire seaweed associated enzymes through marine food. Several agarases have been found in non-marine environments; however, their origin is unknown. In this study, a hypothetical protein, Aga1, was identified as an agarase from an inland soil agar-degrading bacterium, Paenibacillus sp. SSG-1.Having low similarity to known glycoside hydrolases, Aga1 may be a distant member of the glycoside hydrolase family 86. Aga1 has good pH stability (pH 3-11) and is stable in the presence of various metal ions. Aga1 is an exo-type β-agarase that produces NA 4 (neoagarotetraose) and NA 6 (neoagarohexaose) as its main products. In addition, Aga1 may be a cell-surface-binding protein. The bioinformatic analysis showed aga1 may have been transfered together with its surrounding genes, from marine bacteria to soil bacteria via human microbiota. The use of seaweed as food and the disposal of human faeces or saliva were the most likely reasons for this gene transfer pathway. Notably, the results also indicated that microbes from inland humans may degrade agar and that these microbes may have acquired seaweed associated genes because of increased seaweed in diets.}, }
@article {pmid27568050, year = {2016}, author = {Marti, R and Muniesa, M and Schmid, M and Ahrens, CH and Naskova, J and Hummerjohann, J}, title = {Short communication: Heat-resistant Escherichia coli as potential persistent reservoir of extended-spectrum β-lactamases and Shiga toxin-encoding phages in dairy.}, journal = {Journal of dairy science}, volume = {99}, number = {11}, pages = {8622-8632}, doi = {10.3168/jds.2016-11076}, pmid = {27568050}, issn = {1525-3198}, mesh = {Animals ; Cheese/*microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Escherichia coli Proteins/*genetics/metabolism ; Food Contamination/analysis ; Food Microbiology ; Genes, Bacterial ; *Hot Temperature ; Milk/microbiology ; Plasmids/genetics/metabolism ; Shiga Toxin/*genetics/metabolism ; Shiga-Toxigenic Escherichia coli/genetics/growth &amp; development/*isolation &amp; purification ; beta-Lactamases/*genetics/metabolism ; }, abstract = {Here we report the isolation of heat-resistant Escherichia coli from raw milk cheeses. Detection of the heat-resistance markers clpK and orfI by PCR was followed by phenotypical confirmation of increased heat-resistance. These strains were Shiga toxin-negative and, although several were found to be multidrug resistant, no plasmids encoding extended-spectrum β-lactamases (ESBL) were found in any of the isolates. The aim of this study was to assess the potential of these strains to acquire ESBL plasmids and a modified Shiga toxin-encoding phage. Only 4 ESBL-encoding, heat-sensitive E. coli strains were isolated from 1,251 dairy samples (2/455 raw milk and 2/796 raw milk cheese samples). One incompatibility group FII plasmid (CTX-M-14, 79.0 kb) and 3 incompatibility group I1 plasmids (CTX-M-15, 95.2, 96.1, and 97.8 kb) were fully sequenced and de novo assembled. All 4 plasmids are readily transferred to heat-resistant E. coli isolates in plate matings (9.7×10[-5] to 3.7×10[-1] exconjugants per recipient) and, to a lesser extent, in milk (up to 7.4×10[-5] exconjugants per recipient). Importantly, the plasmids are stably maintained during passaging in liquid media without antimicrobial pressure. The heat-resistant isolate FAM21805 was also shown to be capable of acting as donor of all 4 ESBL plasmids. In addition, 3 of 11 tested ESBL exconjugants of heat-resistant strains were lysogenized by the modified Shiga toxin-encoding phage 933W ∆stx::gfp::cat. The higher fraction of heat-resistant E. coli (93 of 256 isolates) compared with the estimated 2% previously predicted based on genomic prevalence of heat resistance genes seems to indicate a selection advantage in the raw milk cheese production environment. The combination of 2 factors may lead to said advantage: increased survival during thermization of raw milk (heating to subpasteurization temperatures) and increased survival rates during cheese ripening. Should these strains acquire ESBL-encoding plasmids, Shiga toxin-encoding phages, or both, these genetic elements would profit from the selection advantage of their host and become more abundant in this particular environment, which in turn could lead to an increased threat to consumers of raw milk products.}, }
@article {pmid27751626, year = {2017}, author = {Planet, PJ and Narechania, A and Chen, L and Mathema, B and Boundy, S and Archer, G and Kreiswirth, B}, title = {Architecture of a Species: Phylogenomics of Staphylococcus aureus.}, journal = {Trends in microbiology}, volume = {25}, number = {2}, pages = {153-166}, doi = {10.1016/j.tim.2016.09.009}, pmid = {27751626}, issn = {1878-4380}, mesh = {Anti-Bacterial Agents/pharmacology ; Base Sequence ; Drug Resistance, Multiple, Bacterial/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/*physiology ; Genome, Bacterial/*genetics ; Humans ; Methicillin-Resistant Staphylococcus aureus/classification/*genetics/*pathogenicity ; Microbial Sensitivity Tests ; Sequence Analysis, DNA ; Staphylococcal Infections/microbiology ; Virulence Factors/genetics ; }, abstract = {A deluge of whole-genome sequencing has begun to give insights into the patterns and processes of microbial evolution, but genome sequences have accrued in a haphazard manner, with biased sampling of natural variation that is driven largely by medical and epidemiological priorities. For instance, there is a strong bias for sequencing epidemic lineages of methicillin-resistant Staphylococcus aureus (MRSA) over sensitive isolates (methicillin-sensitive S. aureus: MSSA). As more diverse genomes are sequenced the emerging picture is of a highly subdivided species with a handful of relatively clonal groups (complexes) that, at any given moment, dominate in particular geographical regions. The establishment of hegemony of particular clones appears to be a dynamic process of successive waves of replacement of the previously dominant clone. Here we review the phylogenomic structure of a diverse range of S. aureus, including both MRSA and MSSA. We consider the utility of the concept of the 'core' genome and the impact of recombination and horizontal transfer. We argue that whole-genome surveillance of S. aureus populations could lead to better forecasting of antibiotic resistance and virulence of emerging clones, and a better understanding of the elusive biological factors that determine repeated strain replacement.}, }
@article {pmid27751184, year = {2016}, author = {Ku, C and Martin, WF}, title = {A natural barrier to lateral gene transfer from prokaryotes to eukaryotes revealed from genomes: the 70 % rule.}, journal = {BMC biology}, volume = {14}, number = {1}, pages = {89}, pmid = {27751184}, issn = {1741-7007}, mesh = {Eukaryotic Cells/*metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome/genetics ; Prokaryotic Cells/*metabolism ; }, abstract = {BACKGROUND: The literature harbors many claims for lateral gene transfer (LGT) from prokaryotes to eukaryotes. Such claims are typically founded in analyses of genome sequences. It is undisputed that many genes entered the eukaryotic lineage via the origin of mitochondria and the origin of plastids. Claims for lineage-specific LGT to eukaryotes outside the context of organelle origins and claims of continuous LGT to eukaryotic lineages are more problematic. If eukaryotes acquire genes from prokaryotes continuously during evolution, then sequenced eukaryote genomes should harbor evidence for recent LGT, like prokaryotic genomes do.<br><br>RESULTS: Here we devise an approach to investigate 30,358 eukaryotic sequences in the context of 1,035,375 prokaryotic homologs among 2585 phylogenetic trees containing homologs from prokaryotes and eukaryotes. Prokaryote genomes reflect a continuous process of gene acquisition and inheritance, with abundant recent acquisitions showing 80-100&#xa0;% amino acid sequence identity to their phylogenetic sister-group homologs from other phyla. By contrast, eukaryote genomes show no evidence for either continuous or recent gene acquisitions from prokaryotes. We find that, in general, genes in eukaryotic genomes that share &#x2265;70&#xa0;% amino acid identity to prokaryotic homologs are genome-specific; that is, they are not found outside individual genome assemblies.<br><br>CONCLUSIONS: Our analyses indicate that eukaryotes do not acquire genes through continual LGT like prokaryotes do. We propose a 70&#xa0;% rule: Coding sequences in eukaryotic genomes that share more than 70&#xa0;% amino acid sequence identity to prokaryotic homologs are most likely assembly or annotation artifacts. The findings further uncover that the role of differential loss in eukaryote genome evolution has been vastly underestimated.}, }
@article {pmid27748310, year = {2016}, author = {Paul, D and Maurya, AP and Chanda, DD and Sharma, GD and Chakravarty, A and Bhattacharjee, A}, title = {Carriage of blaNDM-1 in Pseudomonas aeruginosa through multiple Inc type plasmids in a tertiary referral hospital of northeast India.}, journal = {The Indian journal of medical research}, volume = {143}, number = {6}, pages = {826-829}, pmid = {27748310}, issn = {0971-5916}, mesh = {Adolescent ; Adult ; Child ; Child, Preschool ; Female ; Gene Transfer, Horizontal/genetics ; Humans ; India ; Infant ; Infant, Newborn ; Male ; Middle Aged ; Plasmids/*genetics ; Pseudomonas Infections/*drug therapy/enzymology/genetics/microbiology ; Pseudomonas aeruginosa/drug effects/*enzymology/pathogenicity ; Tertiary Care Centers ; beta-Lactamases/*genetics ; }, }
@article {pmid27739374, year = {2017}, author = {Cheung, RCF and Ng, TB and Wong, JH}, title = {Antifreeze Proteins from Diverse Organisms and their Applications: An Overview.}, journal = {Current protein &amp; peptide science}, volume = {18}, number = {3}, pages = {262-283}, doi = {10.2174/1389203717666161013095027}, pmid = {27739374}, issn = {1875-5550}, mesh = {Animals ; Antifreeze Proteins/*chemistry/*metabolism ; Bacterial Proteins/chemistry/metabolism ; Cryopreservation/methods ; Evolution, Molecular ; Fish Proteins/chemistry/metabolism ; Food Additives/chemistry ; Food Handling ; Fungal Proteins/chemistry/metabolism ; Insect Proteins/chemistry/metabolism ; Marinomonas/chemistry ; Plant Proteins/chemistry/metabolism ; }, abstract = {Antifreeze proteins are ice-binding or ice-structuring proteins that prevent water from freezing by adsorbing to the ice surface and stopping the growth of minute ice crystals to large crystals in a non-colligative manner. The antifreeze proteins are found in species like fish, arthropods, plants, algae, fungi, yeasts and bacteria. The diversity, distribution and classification of antifreeze proteins were highlighted in this review. Antifreeze proteins help the organisms adapt to and survive in subzero temperature environments. The distribution of antifreeze proteins in different species appears to be the outcome of a combination of independent evolutionary events, probably the convergent evolution or horizontal gene transfer. Benefits can be derived from the frost resistance of these organisms. Their potential applications have been recognized in food processing, cryopreservation, cryosurgery, fishery and agricultural industries and anti-icing materials development. This review includes information on the current understanding of antifreeze proteins. A discussion on interactions and mechanisms involving ice recognition and adsorption was also included.}, }
@article {pmid27732651, year = {2016}, author = {Nakashima, Y and Egami, Y and Kimura, M and Wakimoto, T and Abe, I}, title = {Metagenomic Analysis of the Sponge Discodermia Reveals the Production of the Cyanobacterial Natural Product Kasumigamide by 'Entotheonella'.}, journal = {PloS one}, volume = {11}, number = {10}, pages = {e0164468}, pmid = {27732651}, issn = {1932-6203}, mesh = {Animals ; Cyanobacteria/enzymology/*genetics/physiology ; Gene Transfer, Horizontal ; *Metagenome ; Metagenomics ; Multigene Family ; Oligopeptides/*genetics/metabolism ; Phylogeny ; Polyketide Synthases/genetics/metabolism ; Porifera/*genetics/*microbiology/physiology ; *Symbiosis ; }, abstract = {Sponge metagenomes are a useful platform to mine cryptic biosynthetic gene clusters responsible for production of natural products involved in the sponge-microbe association. Since numerous sponge-derived bioactive metabolites are biosynthesized by the symbiotic bacteria, this strategy may concurrently reveal sponge-symbiont produced compounds. Accordingly, a metagenomic analysis of the Japanese marine sponge Discodermia calyx has resulted in the identification of a hybrid type I polyketide synthase-nonribosomal peptide synthetase gene (kas). Bioinformatic analysis of the gene product suggested its involvement in the biosynthesis of kasumigamide, a tetrapeptide originally isolated from freshwater free-living cyanobacterium Microcystis aeruginosa NIES-87. Subsequent investigation of the sponge metabolic profile revealed the presence of kasumigamide in the sponge extract. The kasumigamide producing bacterium was identified as an 'Entotheonella' sp. Moreover, an in silico analysis of kas gene homologs uncovered the presence of kas family genes in two additional bacteria from different phyla. The production of kasumigamide by distantly related multiple bacterial strains implicates horizontal gene transfer and raises the potential for a wider distribution across other bacterial groups.}, }
@article {pmid27727237, year = {2016}, author = {Bordenstein, SR and Bordenstein, SR}, title = {Eukaryotic association module in phage WO genomes from Wolbachia.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {13155}, pmid = {27727237}, issn = {2041-1723}, support = {R01 GM085163/GM/NIGMS NIH HHS/United States ; R21 HD086833/HD/NICHD NIH HHS/United States ; }, mesh = {Ankyrin Repeat ; Bacteriophages/*genetics ; Conserved Sequence ; Eukaryota/*metabolism ; Furin/metabolism ; Gene Transfer, Horizontal ; Genes, Viral ; *Genome, Viral ; Models, Biological ; Phylogeny ; Spider Venoms/chemistry ; Tetratricopeptide Repeat ; Viral Proteins/metabolism ; Wolbachia/*virology ; }, abstract = {Viruses are trifurcated into eukaryotic, archaeal and bacterial categories. This domain-specific ecology underscores why eukaryotic viruses typically co-opt eukaryotic genes and bacteriophages commonly harbour bacterial genes. However, the presence of bacteriophages in obligate intracellular bacteria of eukaryotes may promote DNA transfers between eukaryotes and bacteriophages. Here we report a metagenomic analysis of purified bacteriophage WO particles of Wolbachia and uncover a eukaryotic association module in the complete WO genome. It harbours predicted domains, such as the black widow latrotoxin C-terminal domain, that are uninterrupted in bacteriophage genomes, enriched with eukaryotic protease cleavage sites and combined with additional domains to forge one of the largest bacteriophage genes to date (14,256 bp). To the best of our knowledge, these eukaryotic-like domains have never before been reported in packaged bacteriophages and their phylogeny, distribution and sequence diversity imply lateral transfers between bacteriophage/prophage and animal genomes. Finally, the WO genome sequences and identification of attachment sites will potentially advance genetic manipulation of Wolbachia.}, }
@article {pmid27723601, year = {2018}, author = {Jetten, L and van Iersel, L}, title = {Nonbinary Tree-Based Phylogenetic Networks.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {15}, number = {1}, pages = {205-217}, doi = {10.1109/TCBB.2016.2615918}, pmid = {27723601}, issn = {1557-9964}, mesh = {Algorithms ; Animals ; Computational Biology/*methods ; *Evolution, Molecular ; *Models, Genetic ; *Phylogeny ; Plants/genetics ; Viruses/genetics ; }, abstract = {Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic base-tree with additional linking arcs, which can, for example, represent gene transfer events. Such phylogenetic networks are called tree-based. Here, we consider two possible generalizations of this concept to nonbinary networks, which we call tree-based and strictly-tree-based nonbinary phylogenetic networks. We give simple graph-theoretic characterizations of tree-based and strictly-tree-based nonbinary phylogenetic networks. Moreover, we show for each of these two classes that it can be decided in polynomial time whether a given network is contained in the class. Our approach also provides a new view on tree-based binary phylogenetic networks. Finally, we discuss two examples of nonbinary phylogenetic networks in biology and show how our results can be applied to them.}, }
@article {pmid27723009, year = {2017}, author = {Parmar, KM and Hathi, ZJ and Dafale, NA}, title = {Control of Multidrug-Resistant Gene Flow in the Environment Through Bacteriophage Intervention.}, journal = {Applied biochemistry and biotechnology}, volume = {181}, number = {3}, pages = {1007-1029}, doi = {10.1007/s12010-016-2265-7}, pmid = {27723009}, issn = {1559-0291}, mesh = {*Bacteria/genetics/metabolism/virology ; Bacteriophages/*physiology ; *Drug Resistance, Multiple, Bacterial ; Gene Transfer, Horizontal/*physiology ; }, abstract = {The spread of multidrug-resistant (MDR) bacteria is an emerging threat to the environment and public wellness. Inappropriate use and indiscriminate release of antibiotics in the environment through un-metabolized form create a scenario for the emergence of virulent pathogens and MDR bugs in the surroundings. Mechanisms underlying the spread of resistance include horizontal and vertical gene transfers causing the transmittance of MDR genes packed in different host, which pass across different food webs. Several controlling agents have been used for combating pathogens; however, the use of lytic bacteriophages proves to be one of the most eco-friendly due to their specificity, killing only target bacteria without damaging the indigenous beneficial flora of the habitat. Phages are part of the natural microflora present in different environmental niches and are remarkably stable in the environment. Diverse range of phage products, such as phage enzymes, phage peptides having antimicrobial properties, and phage cocktails also have been used to eradicate pathogens along with whole phages. Recently, the ability of phages to control pathogens has extended from the different areas of medicine, agriculture, aquaculture, food industry, and into the environment. To avoid the arrival of pre-antibiotic epoch, phage intervention proves to be a potential option to eradicate harmful pathogens generated by the MDR gene flow which are uneasy to cure by conventional treatments.}, }
@article {pmid27720010, year = {2016}, author = {Navarre, WW}, title = {The Impact of Gene Silencing on Horizontal Gene Transfer and Bacterial Evolution.}, journal = {Advances in microbial physiology}, volume = {69}, number = {}, pages = {157-186}, doi = {10.1016/bs.ampbs.2016.07.004}, pmid = {27720010}, issn = {2162-5468}, mesh = {AT Rich Sequence/genetics ; Bacterial Proteins/genetics ; DNA-Binding Proteins/genetics ; Escherichia coli/*genetics/pathogenicity ; Escherichia coli Proteins/genetics ; *Evolution, Molecular ; Gene Expression Regulation, Bacterial/*genetics ; Gene Regulatory Networks/genetics ; Gene Silencing/*physiology ; Gene Transfer, Horizontal/*genetics ; Protein Structure, Tertiary/genetics ; Repressor Proteins/genetics ; Trans-Activators/genetics ; Virulence/genetics ; }, abstract = {The H-NS family of DNA-binding proteins is the subject of intense study due to its important roles in the regulation of horizontally acquired genes critical for virulence, antibiotic resistance, and metabolism. Xenogeneic silencing proteins, typified by the H-NS protein of Escherichia coli, specifically target and downregulate expression from AT-rich genes by selectively recognizing specific structural features unique to the AT-rich minor groove. In doing so, these proteins facilitate bacterial evolution; enabling these cells to engage in horizontal gene transfer while buffering potential any detrimental fitness consequences that may result from it. Xenogeneic silencing and counter-silencing explain how bacterial cells can evolve effective gene regulatory strategies in the face of rampant gene gain and loss and it has extended our understanding of bacterial gene regulation beyond the classic operon model. Here we review the structures and mechanisms of xenogeneic silencers as well as their impact on bacterial evolution. Several H-NS-like proteins appear to play a role in facilitating gene transfer by other mechanisms including by regulating transposition, conjugation, and participating in the activation of virulence loci like the locus of enterocyte effacement pathogenicity island of pathogenic strains of E. coli. Evidence suggests that the critical determinants that dictate whether an H-NS-like protein will be a silencer or will perform a different function do not lie in the DNA-binding domain but, rather, in the domains that control oligomerization. This suggests that H-NS-like proteins are transcription factors that both recognize and alter the shape of DNA to exert specific effects that include but are not limited to gene silencing.}, }
@article {pmid27717408, year = {2016}, author = {Pal, C and Bengtsson-Palme, J and Kristiansson, E and Larsson, DG}, title = {The structure and diversity of human, animal and environmental resistomes.}, journal = {Microbiome}, volume = {4}, number = {1}, pages = {54}, pmid = {27717408}, issn = {2049-2618}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/drug effects/*genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Gastrointestinal Microbiome/drug effects/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Interspersed Repetitive Sequences/*genetics ; Metals/pharmacology ; Selection, Genetic/drug effects/*genetics ; Sewage/microbiology ; Smog ; Soil Microbiology ; Tetracycline Resistance/genetics ; }, abstract = {BACKGROUND: Antibiotic resistance genes (ARGs) are widespread but cause problems only when present in pathogens. Environments where selection and transmission of antibiotic resistance frequently take place are likely to be characterized by high abundance and diversity of horizontally transferable ARGs. Large-scale quantitative data on ARGs is, however, lacking for most types of environments, including humans and animals, as is data on resistance genes to potential co-selective agents, such as biocides and metals. This paucity prevents efficient identification of risk environments.<br><br>RESULTS: We provide a comprehensive characterization of resistance genes, mobile genetic elements (MGEs) and bacterial taxonomic compositions for 864 metagenomes from humans (n&#x2009;=&#x2009;350), animals (n&#x2009;=&#x2009;145) and external environments (n&#x2009;=&#x2009;369), all deeply sequenced using Illumina technology. Environment types showed clear differences in both resistance profiles and bacterial community compositions. Human and animal microbial communities were characterized by limited taxonomic diversity and low abundance and diversity of biocide/metal resistance genes and MGEs but a relatively high abundance of ARGs. In contrast, external environments showed consistently high taxonomic diversity which in turn was linked to high diversity of both biocide/metal resistance genes and MGEs. Water, sediment and soil generally carried low relative abundance and few varieties of known ARGs, whereas wastewater/sludge was on par with the human gut. The environments with the largest relative abundance and/or diversity of ARGs, including genes encoding resistance to last resort antibiotics, were those subjected to industrial antibiotic pollution and a limited set of deeply sequenced air samples from a Beijing smog event.<br><br>CONCLUSIONS: Our study identifies air and antibiotic-polluted environments as under-investigated transmission routes and reservoirs for antibiotic resistance. The high taxonomic and genetic diversity of external environments supports the hypothesis that these also form vast sources of unknown resistance genes, with potential to be transferred to pathogens in the future.}, }
@article {pmid27717306, year = {2016}, author = {Wang, X and Liu, X}, title = {Close ecological relationship among species facilitated horizontal transfer of retrotransposons.}, journal = {BMC evolutionary biology}, volume = {16}, number = {1}, pages = {201}, pmid = {27717306}, issn = {1471-2148}, mesh = {Amino Acid Sequence ; Animals ; Ecosystem ; *Gene Transfer, Horizontal ; Genome Size ; Penaeidae/*genetics ; Phylogeny ; Retroelements/*genetics ; }, abstract = {BACKGROUND: Horizontal transfer (HT) of genetic materials is increasingly being found in both animals and plants and mainly concerns transposable elements (TEs). Many crustaceans have big genome sizes and are thus likely to harbor high TE contents. Their habitat might offer them ample opportunities to exchange genetic materials with organisms that are ecologically close but taxonomically distant to them.<br><br>RESULTS: In this study, we analyzed the transcriptome of Pacific white shrimp (Litopenaeus vannamei), an important economic crustacean, to explore traces of HT events. From a collection of newly assembled transcripts, we identified 395 high reliable TE transcripts, most of which were retrotransposon transcripts. One hundred fifty-seven of those transcripts showed highest similarity to sequences from non-arthropod organisms, including ray-finned fishes, mollusks and putative parasites. In total, 16 already known L. vannamei TE families are likely to be involved in horizontal transfer events. Phylogenetic analyses of 10&#x2009;L. vannamei TE families and their homologues (protein sequences) revealed that L. vannamei TE families were generally more close to sequences from aquatic species. Furthermore, TEs from other aquatic species also tend to group together, although they are often distantly related in taxonomy. Sequences from parasites and microorganisms were also widely present, indicating their possible important roles in HT events. Expression profile analyses of transcripts in two NCBI BioProjects revealed that transcripts involved in HT events are likely to play important roles in antiviral immunity. More specifically, those transcripts might act as inhibitors of antiviral immunity.<br><br>CONCLUSIONS: Close ecological relationship, especially predation, might greatly facilitate HT events among aquatic species. This could be achieved through exchange of parasites and microorganisms, or through direct DNA flow. The occurrence of HT events may be largely incidental, but the effects could be beneficial for recipients.}, }
@article {pmid27716041, year = {2016}, author = {Olivera, IE and Fins, KC and Rodriguez, SA and Abiff, SK and Tartar, JL and Tartar, A}, title = {Glycoside hydrolases family 20 (GH20) represent putative virulence factors that are shared by animal pathogenic oomycetes, but are absent in phytopathogens.}, journal = {BMC microbiology}, volume = {16}, number = {1}, pages = {232}, pmid = {27716041}, issn = {1471-2180}, mesh = {Aedes/microbiology ; Amino Acid Sequence ; Animal Diseases/*microbiology ; Animals ; Base Sequence ; Genomics ; Glycoside Hydrolases/genetics/*metabolism ; Hexosaminidases/genetics/metabolism ; Host-Pathogen Interactions ; Lagenidium/enzymology/genetics/pathogenicity ; Larva/microbiology ; Oomycetes/enzymology/genetics/*pathogenicity ; Phylogeny ; Plant Diseases/*microbiology ; Transcriptome ; Virulence Factors/genetics/*metabolism ; }, abstract = {BACKGROUND: Although interest in animal pathogenic oomycetes is increasing, the molecular basis mediating oomycete-animal relationships remains virtually unknown. Crinkler (CRN) genes, which have been traditionally associated with the cytotoxic activity displayed by plant pathogenic oomycetes, were recently detected in transcriptome sequences from the entomopathogenic oomycete Lagenidium giganteum, suggesting that these genes may represent virulence factors conserved in both animal and plant pathogenic oomycetes. In order to further characterize the L. giganteum pathogenome, an on-going genomic survey was mined to reveal novel putative virulence factors, including canonical oomycete effectors Crinkler 13 (CRN13) orthologs. These novel sequences provided a basis to initiate gene expression analyses and determine if the proposed L. giganteum virulence factors are differentially expressed in the presence of mosquito larvae (Aedes aegypti).<br><br>RESULTS: Sequence analyses revealed that L. giganteum express CRN13 transcripts. The predicted proteins, like other L. giganteum CRNs, contained a conserved LYLA motif at the N terminal, but did not display signal peptides. In contrast, other potential virulence factors, such as Glycoside Hydrolases family 20 (hexosaminidase) and 37 (trehalase) proteins (GH20 and GH37), contained identifiable signal peptides. Genome mining demonstrated that GH20 genes are absent from phytopathogenic oomycete genomes, and that the L. giganteum GH20 sequence is the only reported peronosporalean GH20 gene. All other oomycete GH20 homologs were retrieved from animal pathogenic, saprolegnialean genomes. Furthermore, phylogenetic analyses demonstrated that saprolegnialean and peronosporalean GH20 protein sequences clustered in unrelated clades. The saprolegnialean GH20 sequences appeared as a strongly supported, monophyletic group nested within an arthropod-specific clade, suggesting that this gene was acquired via a lateral gene transfer event from an insect or crustacean genome. In contrast, the L. giganteum GH20 protein sequence appeared as a sister taxon to a plant-specific clade that included exochitinases with demonstrated insecticidal activities. Finally, gene expression analyses demonstrated that the L. giganteum GH20 gene expression level is significantly modulated in the presence of mosquito larvae. In agreement with the protein secretion predictions, CRN transcripts did not show any differential expression.<br><br>CONCLUSIONS: These results identified GH20 enzymes, and not CRNs, as potential pathogenicity factors shared by all animal pathogenic oomycetes.}, }
@article {pmid27714987, year = {2017}, author = {Kaplan, JB and Sampathkumar, V and Bendaoud, M and Giannakakis, AK and Lally, ET and Balashova, NV}, title = {In vitro characterization of biofilms formed by Kingella kingae.}, journal = {Molecular oral microbiology}, volume = {32}, number = {4}, pages = {341-353}, pmid = {27714987}, issn = {2041-1014}, support = {R01 DE009517/DE/NIDCR NIH HHS/United States ; R21 AI082392/AI/NIAID NIH HHS/United States ; }, mesh = {Biofilms/drug effects/*growth &amp; development ; Child ; Child, Preschool ; Deoxyribonuclease I/pharmacology ; Endopeptidase K/pharmacology ; Fimbriae Proteins/deficiency/genetics ; Fimbriae, Bacterial/metabolism ; Gene Transfer, Horizontal ; Humans ; Kingella kingae/genetics/pathogenicity/*physiology ; Neisseriaceae Infections/microbiology/transmission ; Osteomyelitis/microbiology ; }, abstract = {The Gram-negative bacterium Kingella kingae is part of the normal oropharyngeal mucosal flora of children <4 years old. K. kingae can enter the submucosa and cause infections of the skeletal system in children, including septic arthritis and osteomyelitis. The organism is also associated with infective endocarditis in children and adults. Although biofilm formation has been coupled with pharyngeal colonization, osteoarticular infections, and infective endocarditis, no studies have investigated biofilm formation in K. kingae. In this study we measured biofilm formation by 79 K. kingae clinical isolates using a 96-well microtiter plate crystal violet binding assay. We found that 37 of 79 strains (47%) formed biofilms. All strains that formed biofilms produced corroding colonies on agar. Biofilm formation was inhibited by proteinase K and DNase I. DNase I also caused the detachment of pre-formed K. kingae biofilm colonies. A mutant strain carrying a deletion of the pilus gene cluster pilA1pilA2fimB did not produce corroding colonies on agar, autoaggregate in broth, or form biofilms. Biofilm forming strains have higher levels of pilA1 expression. The extracellular components of biofilms contained 490 μg cm[-2] of protein, 0.68 μg cm[-2] of DNA, and 0.4 μg cm[-2] of total carbohydrates. We concluded that biofilm formation is common among K. kingae clinical isolates, and that biofilm formation is dependent on the production of proteinaceous pili and extracellular DNA. Biofilm development may have relevance to the colonization, transmission, and pathogenesis of this bacterium. Extracellular DNA production by K. kingae may facilitate horizontal gene transfer within the oral microbial community.}, }
@article {pmid27708749, year = {2016}, author = {Boden, R and Hutt, LP and Huntemann, M and Clum, A and Pillay, M and Palaniappan, K and Varghese, N and Mikhailova, N and Stamatis, D and Reddy, T and Ngan, CY and Daum, C and Shapiro, N and Markowitz, V and Ivanova, N and Woyke, T and Kyrpides, N}, title = {Permanent draft genome of Thermithiobaclillus tepidarius DSM 3134[T], a moderately thermophilic, obligately chemolithoautotrophic member of the Acidithiobacillia.}, journal = {Standards in genomic sciences}, volume = {11}, number = {}, pages = {74}, pmid = {27708749}, issn = {1944-3277}, abstract = {Thermithiobacillus tepidarius DSM 3134[T] was originally isolated (1983) from the waters of a sulfidic spring entering the Roman Baths (Temple of Sulis-Minerva) at Bath, United Kingdom and is an obligate chemolithoautotroph growing at the expense of reduced sulfur species. This strain has a genome size of 2,958,498 bp. Here we report the genome sequence, annotation and characteristics. The genome comprises 2,902 protein coding and 66 RNA coding genes. Genes responsible for the transaldolase variant of the Calvin-Benson-Bassham cycle were identified along with a biosynthetic horseshoe in lieu of Krebs' cycle sensu stricto. Terminal oxidases were identified, viz. cytochrome c oxidase (cbb3, EC 1.9.3.1) and ubiquinol oxidase (bd, EC 1.10.3.10). Metalloresistance genes involved in pathways of arsenic and cadmium resistance were found. Evidence of horizontal gene transfer accounting for 5.9 % of the protein-coding genes was found, including transfer from Thiobacillus spp. and Methylococcus capsulatus Bath, isolated from the same spring. A sox gene cluster was found, similar in structure to those from other Acidithiobacillia - by comparison with Thiobacillus thioparus and Paracoccus denitrificans, an additional gene between soxA and soxB was found, annotated as a DUF302-family protein of unknown function. As the Kelly-Friedrich pathway of thiosulfate oxidation (encoded by sox) is not used in Thermithiobacillus spp., the role of the operon (if any) in this species remains unknown. We speculate that DUF302 and sox genes may have a role in periplasmic trithionate oxidation.}, }
@article {pmid27708147, year = {2016}, author = {Hofstatter, PG and Tice, AK and Kang, S and Brown, MW and Lahr, DJ}, title = {Evolution of bacterial recombinase A (recA) in eukaryotes explained by addition of genomic data of key microbial lineages.}, journal = {Proceedings. Biological sciences}, volume = {283}, number = {1840}, pages = {}, pmid = {27708147}, issn = {1471-2954}, support = {P20 GM103476/GM/NIGMS NIH HHS/United States ; }, mesh = {Amoebozoa/enzymology/genetics ; Bacterial Proteins/*genetics ; Dictyostelium/enzymology/genetics ; Eukaryota/enzymology/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Phylogeny ; Rec A Recombinases/*genetics ; }, abstract = {Recombinase enzymes promote DNA repair by homologous recombination. The genes that encode them are ancestral to life, occurring in all known dominions: viruses, Eubacteria, Archaea and Eukaryota. Bacterial recombinases are also present in viruses and eukaryotic groups (supergroups), presumably via ancestral events of lateral gene transfer. The eukaryotic recA genes have two distinct origins (mitochondrial and plastidial), whose acquisition by eukaryotes was possible via primary (bacteria-eukaryote) and/or secondary (eukaryote-eukaryote) endosymbiotic gene transfers (EGTs). Here we present a comprehensive phylogenetic analysis of the recA genealogy, with substantially increased taxonomic sampling in the bacteria, viruses, eukaryotes and a special focus on the key eukaryotic supergroup Amoebozoa, earlier represented only by Dictyostelium We demonstrate that several major eukaryotic lineages have lost the bacterial recombinases (including Opisthokonta and Excavata), whereas others have retained them (Amoebozoa, Archaeplastida and the SAR-supergroups). When absent, the bacterial recA homologues may have been lost entirely (secondary loss of canonical mitochondria) or replaced by other eukaryotic recombinases. RecA proteins have a transit peptide for organellar import, where they act. The reconstruction of the RecA phylogeny with its EGT events presented here retells the intertwined evolutionary history of eukaryotes and bacteria, while further illuminating the events of endosymbiosis in eukaryotes by expanding the collection of widespread genes that provide insight to this deep history.}, }
@article {pmid27707895, year = {2016}, author = {Lorenzo-Diaz, F and Fernández-Lopez, C and Douarre, PE and Baez-Ortega, A and Flores, C and Glaser, P and Espinosa, M}, title = {Streptococcal group B integrative and mobilizable element IMESag-rpsI encodes a functional relaxase involved in its transfer.}, journal = {Open biology}, volume = {6}, number = {10}, pages = {}, pmid = {27707895}, issn = {2046-2441}, mesh = {Bacterial Proteins/genetics/metabolism ; Chromosomes, Bacterial/genetics ; Cloning, Molecular/*methods ; DNA Nucleotidyltransferases/*genetics/metabolism ; Gene Transfer, Horizontal ; Genetic Variation ; *Interspersed Repetitive Sequences ; Open Reading Frames ; Ribosomal Protein S9 ; Ribosomal Proteins/genetics ; Sequence Analysis, DNA ; Streptococcus agalactiae/enzymology/*genetics ; }, abstract = {Streptococcus agalactiae or Group B Streptococcus (GBS) are opportunistic bacteria that can cause lethal sepsis in children and immuno-compromised patients. Their genome is a reservoir of mobile genetic elements that can be horizontally transferred. Among them, integrative and conjugative elements (ICEs) and the smaller integrative and mobilizable elements (IMEs) primarily reside in the bacterial chromosome, yet have the ability to be transferred between cells by conjugation. ICEs and IMEs are therefore a source of genetic variability that participates in the spread of antibiotic resistance. Although IMEs seem to be the most prevalent class of elements transferable by conjugation, they are poorly known. Here, we have studied a GBS-IME, termed IMESag-rpsI, which is widely distributed in GBS despite not carrying any apparent virulence trait. Analyses of 240 whole genomes showed that IMESag-rpsI is present in approximately 47% of the genomes, has a roughly constant size (approx. 9 kb) and is always integrated at a single location, the 3'-end of the gene encoding the ribosomal protein S9 (rpsI). Based on their genetic variation, several IMESag-rpsI types were defined (A-J) and classified in clonal complexes (CCs). CC1 was the most populated by IMESag-rpsI (more than 95%), mostly of type-A (71%). One CC1 strain (S. agalactiae HRC) was deep-sequenced to understand the rationale underlying type-A IMESag-rpsI enrichment in GBS. Thirteen open reading frames were identified, one of them encoding a protein (MobSag) belonging to the broadly distributed family of relaxases MOBV1 Protein MobSag was purified and, by a newly developed method, shown to cleave DNA at a specific dinucleotide. The S. agalactiae HRC-IMESag-rpsI is able to excise from the chromosome, as shown by the presence of circular intermediates, and it harbours a fully functional mobilization module. Further, the mobSag gene encoded by this mobile element is able to promote plasmid transfer among pneumococcal strains, suggesting that MobSag facilitates the spread of IMESag-rpsI and that this spread would explain the presence of the same IMESag-rpsI type in GBS strains belonging to different CCs.}, }
@article {pmid27706829, year = {2017}, author = {Gillings, MR}, title = {Lateral gene transfer, bacterial genome evolution, and the Anthropocene.}, journal = {Annals of the New York Academy of Sciences}, volume = {1389}, number = {1}, pages = {20-36}, doi = {10.1111/nyas.13213}, pmid = {27706829}, issn = {1749-6632}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Anti-Infective Agents ; Bacteria/drug effects/*genetics ; Bacterial Infections/genetics ; *Biological Evolution ; DNA, Bacterial/analysis ; Ecosystem ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; Humans ; Phenotype ; }, abstract = {Lateral gene transfer (LGT) has significantly influenced bacterial evolution since the origins of life. It helped bacteria generate flexible, mosaic genomes and enables individual cells to rapidly acquire adaptive phenotypes. In turn, this allowed bacteria to mount strong defenses against human attempts to control their growth. The widespread dissemination of genes conferring resistance to antimicrobial agents has precipitated a crisis for modern medicine. Our actions can promote increased rates of LGT and also provide selective forces to fix such events in bacterial populations. For instance, the use of selective agents induces the bacterial SOS response, which stimulates LGT. We create hotspots for lateral transfer, such as wastewater systems, hospitals, and animal production facilities. Conduits of gene transfer between humans and animals ensure rapid dissemination of recent transfer events, as does modern transport and globalization. As resistance to antibacterial compounds becomes universal, there is likely to be increasing selection pressure for phenotypes with adverse consequences for human welfare, such as enhanced virulence, pathogenicity, and transmission. Improved understanding of the ecology of LGT could help us devise strategies to control this fundamental evolutionary process.}, }
@article {pmid27706589, year = {2016}, author = {An, MM and Guo, C and Lin, PP and Zhou, MB}, title = {Heterogeneous evolution of Ty3-gypsy retroelements among bamboo species.}, journal = {Genetics and molecular research : GMR}, volume = {15}, number = {3}, pages = {}, doi = {10.4238/gmr.15038515}, pmid = {27706589}, issn = {1676-5680}, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Plant ; Phylogeny ; *Retroelements ; Sasa/*genetics ; Sequence Analysis, DNA ; Terminal Repeat Sequences ; }, abstract = {Ty3-gypsy long-terminal repeat retroelements are ubiquitously found in many plant genomes. This study reports the occurrence of heterogeneous Ty3-gypsy retroelements in four representative bamboo species: Phyllostachys heterocycla (Carr.) Mitford cv. pubescens, P. heterocycla (Carr.) Mitford cv. heterocycla, Dendrocalamopsis oldhami, and Pleioblastus fortunei. Using degenerate oligonucleotide primers corresponding to the conserved domains of reverse transcriptase (rt) genes of Ty3-gypsy retroelements, 165 distinct sequences were amplified from genomic DNA. The length of the nucleotide sequences varied from 366 to 438 bp. The sequences demonstrated a high heterogeneity, with homology ranging from 52.2 to 99.8%. A phylogenetic tree was constructed, including Arabidopsis thaliana and Oryza sativa. Bamboo Ty3-gypsy sequences formed three distinct retroelement clusters (gypsy I-III). Further analysis indicated that there were not only nearly identical Ty3-gypsy retroelements found in distantly related species, but also highly diverse Ty3-gypsy retroelements observed in closely related species. The results of this study provide genetic and evolutionary information about the bamboo genome that could contribute to further studies of repetitive elements in bamboo as well as in other species.}, }
@article {pmid27706188, year = {2016}, author = {Zhao, K and Ren, F and Han, F and Liu, Q and Wu, G and Xu, Y and Zhang, J and Wu, X and Wang, J and Li, P and Shi, W and Zhu, H and Lv, J and Zhao, X and Tang, X}, title = {Edible Safety Assessment of Genetically Modified Rice T1C-1 for Sprague Dawley Rats through Horizontal Gene Transfer, Allergenicity and Intestinal Microbiota.}, journal = {PloS one}, volume = {11}, number = {10}, pages = {e0163352}, pmid = {27706188}, issn = {1932-6203}, mesh = {Allergens/*immunology ; Animals ; Bacillus thuringiensis/genetics/metabolism ; Bacteria/classification/genetics/isolation &amp; purification ; Bacterial Proteins/*genetics/immunology/metabolism ; Cluster Analysis ; Feces/microbiology ; Female ; Food, Genetically Modified/toxicity ; Gene Transfer, Horizontal/*physiology ; Genetic Variation ; Immunoglobulin G/blood/immunology ; Immunoglobulin M/blood/immunology ; Insect Proteins ; Intestinal Mucosa/metabolism ; Intestines/*microbiology ; Male ; Microbiota ; Muscles/metabolism ; Oryza/*genetics/metabolism ; Phylogeny ; Plants, Genetically Modified/genetics ; RNA, Ribosomal, 16S/genetics/metabolism ; Rats ; Rats, Sprague-Dawley ; Receptors, Cell Surface/*genetics/immunology/metabolism ; Toxicity Tests, Acute ; }, abstract = {In this study, assessment of the safety of transgenic rice T1C-1 expressing Cry1C was carried out by: (1) studying horizontal gene transfer (HGT) in Sprague Dawley rats fed transgenic rice for 90 d; (2) examining the effect of Cry1C protein in vitro on digestibility and allergenicity; and (3) studying the changes of intestinal microbiota in rats fed with transgenic rice T1C-1 in acute and subchronic toxicity tests. Sprague Dawley rats were fed a diet containing either 60% GM Bacillus thuringiensis (Bt) rice T1C-1 expressing Cry1C protein, the parental rice Minghui 63, or a basic diet for 90 d. The GM Bt rice T1C-1 showed no evidence of HGT between rats and transgenic rice. Sequence searching of the Cry1C protein showed no homology with known allergens or toxins. Cry1C protein was rapidly degraded in vitro with simulated gastric and intestinal fluids. The expressed Cry1C protein did not induce high levels of specific IgG and IgE antibodies in rats. The intestinal microbiota of rats fed T1C-1 was also analyzed in acute and subchronic toxicity tests by DGGE. Cluster analysis of DGGE profiles revealed significant individual differences in the rats' intestinal microbiota.}, }
@article {pmid27705609, year = {2016}, author = {Goic-Barisic, I and Hrenovic, J and Kovacic, A and Musić, M&#x160;}, title = {Emergence of Oxacillinases in Environmental Carbapenem-Resistant Acinetobacter baumannii Associated with Clinical Isolates.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {22}, number = {7}, pages = {559-563}, doi = {10.1089/mdr.2015.0275}, pmid = {27705609}, issn = {1931-8448}, mesh = {Acinetobacter baumannii/classification/drug effects/*genetics/isolation &amp; purification ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics/metabolism ; Carbapenems/pharmacology ; Croatia ; DNA-Directed RNA Polymerases/genetics/metabolism ; Gene Expression ; *Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; Multiplex Polymerase Chain Reaction ; Phylogeny ; Sequence Analysis, DNA ; Wastewater/microbiology ; *Water Microbiology ; beta-Lactam Resistance/*genetics ; beta-Lactamases/*genetics/metabolism ; }, abstract = {Six carbapenem-resistant isolates of Acinetobacter baumannii were recovered from untreated and treated municipal wastewater of the capital city of Zagreb, Croatia. Molecular identification of environmental isolates of A. baumannii was performed by amplification, sequencing, and phylogenetic analyses of rpoB gene. The presence of blaOXA genes encoding OXA-type carbapenemases (OXA-51-like, OXA-23, and OXA-40-like) was confirmed by multiplex PCR and sequencing. Phylogenetic analyses corroborated the affiliation of detected blaOXA genes to three different clusters and showed association of environmental OXAs with those described from clinical isolates. This result suggests that isolates recovered from municipal wastewater are most probably of clinical origin. Furthermore, the presence of OXA-40-like (OXA-72) in an environmental A. baumannii isolate is reported for the first time. Persistence of A. baumannii harboring the clinically important OXAs in the wastewater treatment process poses a potentially significant source for horizontal gene transfer and implications for wider spread of antibiotic resistance genes.}, }
@article {pmid27703073, year = {2016}, author = {Kelley, DS and Lennon, CW and ,  and Belfort, M and Novikova, O}, title = {Mycobacteriophages as Incubators for Intein Dissemination and Evolution.}, journal = {mBio}, volume = {7}, number = {5}, pages = {}, pmid = {27703073}, issn = {2150-7511}, support = {/HHMI/Howard Hughes Medical Institute/United States ; R37 GM039422/GM/NIGMS NIH HHS/United States ; F32 GM121000/GM/NIGMS NIH HHS/United States ; R01 GM039422/GM/NIGMS NIH HHS/United States ; T32 AI055429/AI/NIAID NIH HHS/United States ; R01 GM044844/GM/NIGMS NIH HHS/United States ; }, mesh = {Computational Biology ; Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Gene Expression Regulation, Viral ; *Gene Transfer, Horizontal ; Inteins/*genetics ; Mycobacteriophages/*genetics ; Mycobacterium leprae/*genetics/*virology ; Mycobacterium tuberculosis/*genetics/*virology ; }, abstract = {UNLABELLED: Inteins are self-splicing protein elements that are mobile at the DNA level and are sporadically distributed across microbial genomes. Inteins appear to be horizontally transferred, and it has been speculated that phages may play a role in intein distribution. Our attention turns to mycobacteriophages, which infect mycobacteria, where both phage and host harbor inteins. Using bioinformatics, mycobacteriophage genomes were mined for inteins. This study reveals that these mobile elements are present across multiple mycobacteriophage clusters and are pervasive in certain genes, like the large terminase subunit TerL and a RecB-like nuclease, with the majority of intein-containing genes being phage specific. Strikingly, despite this phage specificity, inteins localize to functional motifs shared with bacteria, such that intein-containing genes have similar roles, like hydrolase activity and nucleic acid binding, indicating a global commonality among intein-hosting proteins. Additionally, there are multiple insertion points within active centers, implying independent invasion events, with regulatory implications. Several phage inteins were shown to be splicing competent and to encode functional homing endonucleases, important for mobility. Further, bioinformatic analysis supports the potential for phages as facilitators of intein movement among mycobacteria and related genera. Analysis of catalytic intein residues finds the highly conserved penultimate histidine inconsistently maintained among mycobacteriophages. Biochemical characterization of a noncanonical phage intein shows that this residue influences precursor accumulation, suggesting that splicing has been tuned in phages to modulate generation of important proteins. Together, this work expands our understanding of phage-based intein dissemination and evolution and implies that phages provide a context for evolution of splicing-based regulation.<br><br>IMPORTANCE: Inteins are mobile protein splicing elements found in critical genes across all domains of life. Mycobacterial inteins are of particular interest because of their occurrence in pathogenic species, such as Mycobacterium tuberculosis and Mycobacterium&#xa0;leprae, which harbor inteins in important proteins. We have discovered a similarity in activities of intein-containing proteins among mycobacteriophages and their intein-rich actinobacterial hosts, with implications for both posttranslational regulation by inteins and phages participating in horizontal intein transfer. Our demonstration of multiple insertion points within active centers of phage proteins implies independent invasion events, indicating the importance of intein maintenance at specific functional sites. The variable conservation of a catalytic splicing residue, leading to profoundly altered splicing rates, points to the regulatory potential of inteins and to mycobacteriophages playing a role in intein evolution. Collectively, these results suggest inteins as posttranslational regulators and mycobacteriophages as both vehicles for intein distribution and incubators for intein evolution.}, }
@article {pmid27699821, year = {2016}, author = {Lopatkin, AJ and Sysoeva, TA and You, L}, title = {Dissecting the effects of antibiotics on horizontal gene transfer: Analysis suggests a critical role of selection dynamics.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {38}, number = {12}, pages = {1283-1292}, pmid = {27699821}, issn = {1521-1878}, support = {R01 GM098642/GM/NIGMS NIH HHS/United States ; R01 GM110494/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; Drug Resistance, Bacterial/*genetics ; *Gene Transfer, Horizontal ; }, abstract = {Horizontal gene transfer (HGT) is a major mechanism responsible for the spread of antibiotic resistance. Conversely, it is often assumed that antibiotics promote HGT. Careful dissection of the literature, however, suggests a lack of conclusive evidence supporting this notion in general. This is largely due to the lack of well-defined quantitative experiments to address this question in an unambiguous manner. In this review, we discuss the extent to which HGT is responsible for the spread of antibiotic resistance and examine what is known about the effect of antibiotics on the HGT dynamics. We focus on conjugation, which is the dominant mode of HGT responsible for spreading antibiotic resistance on the global scale. Our analysis reveals a need to design experiments to quantify HGT in such a way to facilitate rigorous data interpretation. Such measurements are critical for developing novel strategies to combat resistance spread through HGT.}, }
@article {pmid27698087, year = {2016}, author = {Wright, LD and Grossman, AD}, title = {Autonomous Replication of the Conjugative Transposon Tn916.}, journal = {Journal of bacteriology}, volume = {198}, number = {24}, pages = {3355-3366}, pmid = {27698087}, issn = {1098-5530}, support = {R01 GM050895/GM/NIGMS NIH HHS/United States ; T32 GM007287/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacillus subtilis/*genetics/metabolism ; *Conjugation, Genetic ; *DNA Replication ; *DNA Transposable Elements ; DNA, Bacterial/genetics/metabolism ; Plasmids/genetics/metabolism ; }, abstract = {UNLABELLED: Integrative and conjugative elements (ICEs), also known as conjugative transposons, are self-transferable elements that are widely distributed among bacterial phyla and are important drivers of horizontal gene transfer. Many ICEs carry genes that confer antibiotic resistances to their host cells and are involved in the dissemination of these resistance genes. ICEs reside in host chromosomes but under certain conditions can excise to form a plasmid that is typically the substrate for transfer. A few ICEs are known to undergo autonomous replication following activation. However, it is not clear if autonomous replication is a general property of many ICEs. We found that Tn916, the first conjugative transposon identified, replicates autonomously via a rolling-circle mechanism. Replication of Tn916 was dependent on the relaxase encoded by orf20 of Tn916 The origin of transfer of Tn916, oriT(916), also functioned as an origin of replication. Using immunoprecipitation and mass spectrometry, we found that the relaxase (Orf20) and the two putative helicase processivity factors (Orf22 and Orf23) encoded by Tn916 likely interact in a complex and that the Tn916 relaxase contains a previously unidentified conserved helix-turn-helix domain in its N-terminal region that is required for relaxase function and replication. Lastly, we identified a functional single-strand origin of replication (sso) in Tn916 that we predict primes second-strand synthesis during rolling-circle replication. Together these results add to the emerging data that show that several ICEs replicate via a conserved, rolling-circle mechanism.<br><br>IMPORTANCE: Integrative and conjugative elements (ICEs) drive horizontal gene transfer and the spread of antibiotic resistances in bacteria. ICEs reside integrated in a host genome but can excise to create a plasmid that is the substrate for transfer to other cells. Here we show that Tn916, an ICE with broad host range, undergoes autonomous rolling-circle replication when in the plasmid form. We found that the origin of transfer functions as a double-stranded origin of replication and identified a single-stranded origin of replication. It was long thought that ICEs do not undergo autonomous replication. Our work adds to the evidence that ICEs replicate autonomously as part of their normal life cycle and indicates that diverse ICEs use the same replicative mechanism.}, }
@article {pmid27697685, year = {2016}, author = {Zhang, J and Sui, Q and Tong, J and Buhe, C and Wang, R and Chen, M and Wei, Y}, title = {Sludge bio-drying: Effective to reduce both antibiotic resistance genes and mobile genetic elements.}, journal = {Water research}, volume = {106}, number = {}, pages = {62-70}, doi = {10.1016/j.watres.2016.09.055}, pmid = {27697685}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents/*pharmacology ; Desiccation ; Drug Resistance, Microbial/genetics ; Genes, Bacterial/drug effects ; Interspersed Repetitive Sequences ; Sewage/*microbiology ; }, abstract = {Sewage sludge is considered as one of major contributors to the increased environmental burden of ARGs. Sludge bio-drying was increasingly adopted due to its faster sludge reduction compared with composting. The fate of ARGs during full-scale sludge bio-drying was investigated to determine whether it could effectively reduce ARGs, and the contributions of bacterial community, horizontal gene transfer (HGT) through mobile genetic elements (MGEs) and co-selection from heavy metals to ARGs profiles were discussed in detail. Two piles with different aeration strategies (Pile I, the improved and Pile II, the control) were operated to elucidate effects of aeration strategy on ARGs profiles. Results showed that sludge bio-drying could effectively reduce both most of targeted ARGs (0.4-3.1 logs) and MGEs (0.8-3.3 logs) by the improved aeration strategy, which also enhanced both the sludge bio-drying performance and ARGs reduction. The enrichment of ARGs including ermF, tetX and sulII could be well explained by the evolution of bioavailable heavy metals, not HGT through MGEs, and their potential host bacteria mainly existed in Bacteroidetes. Although changes of bacterial community contributed the most to ARGs profiles, HGT through MGEs should be paid more attention especially in the thermophilic stage of sludge bio-drying.}, }
@article {pmid27697167, year = {2017}, author = {Stefanovic, E and Fitzgerald, G and McAuliffe, O}, title = {Advances in the genomics and metabolomics of dairy lactobacilli: A review.}, journal = {Food microbiology}, volume = {61}, number = {}, pages = {33-49}, doi = {10.1016/j.fm.2016.08.009}, pmid = {27697167}, issn = {1095-9998}, mesh = {Dairy Products/*microbiology ; Food Microbiology ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomics ; Lactobacillus/classification/*genetics/*metabolism/physiology ; *Metabolic Engineering ; *Metabolome ; Metabolomics ; Phylogeny ; }, abstract = {The Lactobacillus genus represents the largest and most diverse genera of all the lactic acid bacteria (LAB), encompassing species with applications in industrial, biotechnological and medical fields. The increasing number of available Lactobacillus genome sequences has allowed understanding of genetic and metabolic potential of this LAB group. Pangenome and core genome studies are available for numerous species, demonstrating the plasticity of the Lactobacillus genomes and providing the evidence of niche adaptability. Advancements in the application of lactobacilli in the dairy industry lie in exploring the genetic background of their commercially important characteristics, such as flavour development potential or resistance to the phage attack. The integration of available genomic and metabolomic data through the generation of genome scale metabolic models has enabled the development of computational models that predict the behaviour of organisms under specific conditions and present a route to metabolic engineering. Lactobacilli are recognised as potential cell factories, confirmed by the successful production of many compounds. In this review, we discuss the current knowledge of genomics, metabolomics and metabolic engineering of the prevalent Lactobacillus species associated with the production of fermented dairy foods. In-depth understanding of their characteristics opens the possibilities for their future knowledge-based applications.}, }
@article {pmid27697043, year = {2017}, author = {Viganor, L and Howe, O and McCarron, P and McCann, M and Devereux, M}, title = {The Antibacterial Activity of Metal Complexes Containing 1,10- phenanthroline: Potential as Alternative Therapeutics in the Era of Antibiotic Resistance.}, journal = {Current topics in medicinal chemistry}, volume = {17}, number = {11}, pages = {1280-1302}, doi = {10.2174/1568026616666161003143333}, pmid = {27697043}, issn = {1873-4294}, mesh = {Anti-Bacterial Agents/chemical synthesis/*chemistry/*pharmacology ; Bacteria/drug effects ; Bacterial Infections/*drug therapy/microbiology ; Drug Discovery ; Drug Resistance, Multiple, Bacterial/*drug effects ; Humans ; Microbial Sensitivity Tests ; Organometallic Compounds/chemical synthesis/*chemistry/*pharmacology ; Phenanthrolines/chemistry/*pharmacology ; }, abstract = {The "antibiotic era", characterized by the overuse and misuse of antibiotics, over the last half-century has culminated in the present critical "era of resistance". The treatment of bacterial infections is challenging because of a decline in the current arsenal of useful antibiotics and the slow rate of new drug development. The discovery of a new gene (mcr-1) in 2015, which enables bacteria to be highly resistant to polymyxins (such as colistin), the last line of antibiotic defence left, heralds a new level of concern as this gene is susceptible to horizontal gene transfer, with alarming potential to be spread between different bacterial populations, suggesting that the progression from "extensive drug resistance" to "pan-drug resistance" may be inevitable. Clearly there is a need for the development of novel classes of anti-bacterial agents capable of killing bacteria through mechanisms that are different to those of the known classes of antibiotics. 1,10-phenanthroline (phen) is a heterocyclic organic compound which exerts in vitro antimicrobial activity against a broad-spectrum of bacteria. The antimicrobial activity of phen can be significantly modulated by modifying its structure. The development of metal-phen complexes offers the medicinal chemist an opportunity to expand such structural diversity by controlling the geometry and varying the oxidation states of the metal centre, with the inclusion of appropriate auxiliary ligands in the structure, offering the opportunity to target different biochemical pathways in bacteria. In this review, we summarize what is currently known about the antibacterial capability of metal-phen complexes and their mechanisms of action.}, }
@article {pmid27693467, year = {2017}, author = {Tian, Y and Kubatko, LS}, title = {Expected pairwise congruence among gene trees under the coalescent model.}, journal = {Molecular phylogenetics and evolution}, volume = {106}, number = {}, pages = {144-150}, doi = {10.1016/j.ympev.2016.09.023}, pmid = {27693467}, issn = {1095-9513}, mesh = {Genetic Loci ; Genetic Speciation ; *Models, Genetic ; Phylogeny ; Recombination, Genetic ; }, abstract = {Although it is widely appreciated that gene trees may differ from the overall species tree and from one another due to various evolutionary processes (e.g., incomplete lineage sorting (ILS), horizontal gene transfer, etc.), the extent of this incongruence is rarely quantified and discussed. Here we consider the expected amount of incongruence arising from ILS, as modeled by the coalescent process. In particular, we compute the probability that two gene trees randomly sampled from the same species tree agree with one another as well as the distribution of the Robinson-Foulds distance between them, for species trees with three to eight taxa. We demonstrate that, as expected under the coalescent model, the amount of discordance is affected by species tree-specific factors such as speciation times and effective population sizes for the species under consideration. Our results highlight the fact that substantial discordance may occur, even when the number of species is very small, which has implications both for larger taxon samples and for any method that uses estimated gene trees as the basis for further statistical inference. The amount of incongruence is substantial enough that such methods may need to be modified to account for variability in the underlying gene trees.}, }
@article {pmid27681923, year = {2016}, author = {Da Silva, GJ and Domingues, S}, title = {Insights on the Horizontal Gene Transfer of Carbapenemase Determinants in the Opportunistic Pathogen Acinetobacter baumannii.}, journal = {Microorganisms}, volume = {4}, number = {3}, pages = {}, pmid = {27681923}, issn = {2076-2607}, abstract = {Horizontal gene transfer (HGT) is a driving force to the evolution of bacteria. The fast emergence of antimicrobial resistance reflects the ability of genetic adaptation of pathogens. Acinetobacter baumannii has emerged in the last few decades as an important opportunistic nosocomial pathogen, in part due to its high capacity of acquiring resistance to diverse antibiotic families, including to the so-called last line drugs such as carbapenems. The rampant selective pressure and genetic exchange of resistance genes hinder the effective treatment of resistant infections. A. baumannii uses all the resistance mechanisms to survive against carbapenems but production of carbapenemases are the major mechanism, which may act in synergy with others. A. baumannii appears to use all the mechanisms of gene dissemination. Beyond conjugation, the mostly reported recent studies point to natural transformation, transduction and outer membrane vesicles-mediated transfer as mechanisms that may play a role in carbapenemase determinants spread. Understanding the genetic mobilization of carbapenemase genes is paramount in preventing their dissemination. Here we review the carbapenemases found in A. baumannii and present an overview of the current knowledge of contributions of the various HGT mechanisms to the molecular epidemiology of carbapenem resistance in this relevant opportunistic pathogen.}, }
@article {pmid27681232, year = {2016}, author = {Zámocký, M and Tafer, H and Chovanová, K and Lopandic, K and Kamlárová, A and Obinger, C}, title = {Genome sequence of the filamentous soil fungus Chaetomium cochliodes reveals abundance of genes for heme enzymes from all peroxidase and catalase superfamilies.}, journal = {BMC genomics}, volume = {17}, number = {1}, pages = {763}, pmid = {27681232}, issn = {1471-2164}, support = {P 27474/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {BACKGROUND: The ascomycetous family Chaetomiaceae (class Sordariomycetes) includes numerous soilborn, saprophytic, endophytic and pathogenic fungi which can adapt to various growth conditions and living niches by providing a broad armory of oxidative and antioxidant enzymes.<br><br>RESULTS: We release the 34.7 Mbp draft genome of Chaetomium cochliodes CCM F-232 consisting of 6036 contigs with an average size of 5756&#xa0;bp and reconstructed its phylogeny. We show that this filamentous fungus is closely related but not identical to Chaetomium globosum and Chaetomium elatum. We screened and critically analysed this genome for open reading frames coding for essential antioxidant enzymes. It is demonstrated that the genome of C. cochliodes contains genes encoding putative enzymes from all four known heme peroxidase superfamilies including bifunctional catalase-peroxidase (KatG), cytochrome c peroxidase (CcP), manganese peroxidase, two paralogs of hybrid B peroxidases (HyBpox), cyclooxygenase, linoleate diol synthase, dye-decolorizing peroxidase (DyP) of type B and three paralogs of heme thiolate peroxidases. Both KatG and DyP-type B are shown to be introduced into ascomycetes genomes by horizontal gene transfer from various bacteria. In addition, two putative large subunit secretory and two small-subunit typical catalases are found in C. cochliodes. We support our genomic findings with quantitative transcription analysis of nine peroxidase &amp; catalase genes.<br><br>CONCLUSIONS: We delineate molecular phylogeny of five distinct gene superfamilies coding for essential heme oxidoreductases in Chaetomia and from the transcription analysis the role of this antioxidant enzymatic armory for the survival of a peculiar soil ascomycete in various harsh environments.}, }
@article {pmid27678195, year = {2016}, author = {Zhong, Y and Cheng, ZM}, title = {A unique RPW8-encoding class of genes that originated in early land plants and evolved through domain fission, fusion, and duplication.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {32923}, pmid = {27678195}, issn = {2045-2322}, abstract = {Duplication, lateral gene transfer, domain fusion/fission and de novo domain creation play a key role in formation of initial common ancestral protein. Abundant protein diversities are produced by domain rearrangements, including fusions, fissions, duplications, and terminal domain losses. In this report, we explored the origin of the RPW8 domain and examined the domain rearrangements that have driven the evolution of RPW8-encoding genes in land plants. The RPW8 domain first emerged in the early land plant, Physcomitrella patens, and it likely originated de novo from a non-coding sequence or domain divergence after duplication. It was then incorporated into the NBS-LRR protein to create a main sub-class of RPW8-encoding genes, the RPW8-NBS-encoding genes. They evolved by a series of genetic events of domain fissions, fusions, and duplications. Many species-specific duplication events and tandemly duplicated clusters clearly demonstrated that species-specific and tandem duplications played important roles in expansion of RPW8-encoding genes, especially in gymnosperms and species of the Rosaceae. RPW8 domains with greater Ka/Ks values than those of the NBS domains indicated that they evolved faster than the NBS domains in RPW8-NBSs.}, }
@article {pmid27676308, year = {2016}, author = {Ruzzini, AC and Clardy, J}, title = {Gene Flow and Molecular Innovation in Bacteria.}, journal = {Current biology : CB}, volume = {26}, number = {18}, pages = {R859-R864}, pmid = {27676308}, issn = {1879-0445}, support = {R01 GM086258/GM/NIGMS NIH HHS/United States ; U19 AI109673/AI/NIAID NIH HHS/United States ; U19 TW009872/TW/FIC NIH HHS/United States ; }, mesh = {Actinobacteria/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genomic Islands/*genetics ; Plasmids/*genetics ; }, abstract = {The small molecules produced by environmental bacteria have been mainstays of both chemical and biological research for decades, and some have led to important therapeutic interventions. These small molecules have been shaped by natural selection as they evolved to fulfill changing functional roles in their native environments. This minireview describes some recent systematic studies providing illustrative examples that involve the acquisition and alteration of genetic information for molecular innovation by bacteria in well-defined environments. Two different bacterial genera are featured, Pseudonocardia and Salinispora, and, although the small-molecule repertoires of both have benefited from horizontal gene transfer, Pseudonocardia spp. have relied on plasmid-based tactics while Salinispora spp. have relied on chromosomally integrated genomic islands.}, }
@article {pmid27667524, year = {2016}, author = {Furushita, M and Akagi, H and Kaneoka, A and Maeda, T and Fukuda, T and Tatsuno, R and Shiba, T}, title = {Similarity in the Structure of tetD-Carrying Mobile Genetic Elements in Bacterial Strains of Different Genera Isolated from Cultured Yellowtail.}, journal = {Biocontrol science}, volume = {21}, number = {3}, pages = {183-186}, doi = {10.4265/bio.21.183}, pmid = {27667524}, issn = {1884-0205}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/*genetics/isolation &amp; purification ; *DNA Transposable Elements ; Drug Resistance, Bacterial ; Fishes/*microbiology ; Gene Order ; *Genes, Bacterial ; Microbial Sensitivity Tests ; Tetracycline/pharmacology ; }, abstract = {Structure analysis was performed on the antibiotic-resistance-gene region of conjugative plasmids of four fish farm bacteria.The kanamycin resistance gene, IS26, and tetracycline resistance gene (tetA(D)) were flanked by two IS26s in opposite orientation in Citrobacter sp. TA3 and TA6, and Alteromonas sp. TA55 from fish farm A. IS26-Inner was disrupted with ISRSB101. The chloramphenicol resistance gene, IS26 and tetA (D) were flanked by two IS26s in direct orientation in Salmonella sp. TC67 from farm C. Structures of tetA (D) and IS26 were identical among the four bacteria, but there was no insertion within the IS26-Inner of Salmonella sp. TC67. Horizontal gene transfer between the strains of two different genera in fish farm A was suggested by the structure homologies of mobile genetic elements and antibiotic resistance genes.}, }
@article {pmid27667131, year = {2016}, author = {Zhang, HH and Li, GY and Xiong, XM and Han, MJ and Zhang, XG and Dai, FY}, title = {TRT, a Vertebrate and Protozoan Tc1-Like Transposon: Current Activity and Horizontal Transfer.}, journal = {Genome biology and evolution}, volume = {8}, number = {9}, pages = {2994-3005}, pmid = {27667131}, issn = {1759-6653}, mesh = {Amino Acid Motifs ; Animals ; Catalytic Domain ; Codon, Terminator ; *DNA Transposable Elements ; DNA-Binding Proteins/chemistry/*genetics/metabolism ; *Gene Transfer, Horizontal ; Phylogeny ; Protozoan Proteins/chemistry/*genetics/metabolism ; Transposases/chemistry/*genetics/metabolism ; Zebrafish/genetics ; Zebrafish Proteins/chemistry/*genetics/metabolism ; }, abstract = {We report a Danio rerio transposon named DrTRT, for D. rerio Transposon Related to Tc1 The complete sequence of the DrTRT transposon is 1,563 base pairs (bp) in length, and its transposase putatively encodes a 338-amino acid protein that harbors a DD37E motif in its catalytic domain. We present evidence based on searches of publicly available genomes that TRT elements commonly occur in vertebrates and protozoa. Phylogenetic and functional domain comparisons confirm that TRT constitutes a new subfamily within the Tc1 family. Hallmark features of having no premature termination codons within the transposase, the presence of all expected functional domains, and its occurrence in the bony fish transcriptome suggest that TRT might have current or recent activity in these species. Further analysis showed that the activity of TRT elements in these species might have arisen about between 4 and 19 Ma. Interestingly, our results also implied that the widespread distribution of TRT among fishes, frog, and snakes is the result of multiple independent HT events, probably from bony fishes to snakes or frog. Finally, the mechanisms underlying horizontal transfer of TRT elements are discussed.}, }
@article {pmid27664091, year = {2016}, author = {Bamba, M and Nakata, S and Aoki, S and Takayama, K and Núñez-Farfán, J and Ito, M and Miya, M and Kajita, T}, title = {Wide distribution range of rhizobial symbionts associated with pantropical sea-dispersed legumes.}, journal = {Antonie van Leeuwenhoek}, volume = {109}, number = {12}, pages = {1605-1614}, doi = {10.1007/s10482-016-0761-y}, pmid = {27664091}, issn = {1572-9699}, mesh = {Bacterial Proteins/genetics ; Bradyrhizobium/classification/isolation &amp; purification ; Fabaceae/*microbiology ; Genes, Bacterial ; Molecular Typing ; N-Acetylglucosaminyltransferases/genetics ; Pacific Ocean ; Phylogeny ; RNA, Bacterial ; RNA, Ribosomal, 16S/genetics ; Rhizobiaceae/classification/genetics/*isolation &amp; purification ; Rhizobium/classification/isolation &amp; purification ; Sinorhizobium/classification/isolation &amp; purification ; Symbiosis ; }, abstract = {To understand the geographic distributions of rhizobia that associated with widely distributed wild legumes, 66 nodules obtained from 41 individuals including three sea-dispersed legumes (Vigna marina, Vigna luteola, and Canavalia rosea) distributed across the tropical and subtropical coastal regions of the world were studied. Partial sequences of 16S rRNA and nodC genes extracted from the nodules showed that only Bradyrhizobium and Sinorhizobium were associated with the pantropical legumes, and some of the symbiont strains were widely distributed over the Pacific. Horizontal gene transfer of nodulation genes were observed within the Bradyrhizobium and Sinorhizobium lineages. BLAST searches in GenBank also identified records of these strains from various legumes across the world, including crop species. However, one of the rhizobial strains was not found in GenBank, which implies the strain may have adapted to the littoral environment. Our results suggested that some rhizobia, which associate with the widespread sea-dispersed legume, distribute across a broad geographic range. By establishing symbiotic relationships with widely distributed rhizobia, the pantropical legumes may also be able to extend their range much further than other legume species.}, }
@article {pmid27660623, year = {2016}, author = {Ross, A and Ward, S and Hyman, P}, title = {More Is Better: Selecting for Broad Host Range Bacteriophages.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1352}, pmid = {27660623}, issn = {1664-302X}, abstract = {Bacteriophages are viruses that infect bacteria. In this perspective, we discuss several aspects of a characteristic feature of bacteriophages, their host range. Each phage has its own particular host range, the range of bacteria that it can infect. While some phages can only infect one or a few bacterial strains, other phages can infect many species or even bacteria from different genera. Different methods for determining host range may give different results, reflecting the multiple mechanisms bacteria have to resist phage infection and reflecting the different steps of infection each method depends on. This makes defining host range difficult. Another difficulty in describing host range arises from the inconsistent use of the words "narrow" and especially "broad" when describing the breadth of the host range. Nearly all bacteriophages have been isolated using a single host strain of bacteria. While this procedure is fairly standard, it may more likely produce narrow rather than broad host range phage. Our results and those of others suggest that using multiple host strains during isolation can more reliably produce broader host range phages. This challenges the common belief that most bacteriophages have a narrow host range. We highlight the implications of this for several areas that are affected by host range including horizontal gene transfer and phage therapy.}, }
@article {pmid27659024, year = {2016}, author = {Gambette, P and van Iersel, L and Kelk, S and Pardi, F and Scornavacca, C}, title = {Do Branch Lengths Help to Locate a Tree in a Phylogenetic Network?.}, journal = {Bulletin of mathematical biology}, volume = {78}, number = {9}, pages = {1773-1795}, doi = {10.1007/s11538-016-0199-4}, pmid = {27659024}, issn = {1522-9602}, mesh = {Algorithms ; Evolution, Molecular ; Mathematical Concepts ; *Models, Genetic ; *Phylogeny ; }, abstract = {Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental questions that arise in this context is whether the evolution of a gene with one copy in all species can be explained by a given network. In mathematical terms, this is often translated in the following way: is a given phylogenetic tree contained in a given phylogenetic network? Recently this tree containment problem has been widely investigated from a computational perspective, but most studies have only focused on the topology of the phylogenies, ignoring a piece of information that, in the case of phylogenetic trees, is routinely inferred by evolutionary analyses: branch lengths. These measure the amount of change (e.g., nucleotide substitutions) that has occurred along each branch of the phylogeny. Here, we study a number of versions of the tree containment problem that explicitly account for branch lengths. We show that, although length information has the potential to locate more precisely a tree within a network, the problem is computationally hard in its most general form. On a positive note, for a number of special cases of biological relevance, we provide algorithms that solve this problem efficiently. This includes the case of networks of limited complexity, for which it is possible to recover, among the trees contained by the network with the same topology as the input tree, the closest one in terms of branch lengths.}, }
@article {pmid27655214, year = {2017}, author = {Ruck, EC and Linard, SR and Nakov, T and Theriot, EC and Alverson, AJ}, title = {Hoarding and horizontal transfer led to an expanded gene and intron repertoire in the plastid genome of the diatom, Toxarium undulatum (Bacillariophyta).}, journal = {Current genetics}, volume = {63}, number = {3}, pages = {499-507}, pmid = {27655214}, issn = {1432-0983}, mesh = {Chlorophyll/*biosynthesis/genetics ; Chlorophyll A ; Diatoms/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome, Plastid/genetics ; Introns/genetics ; Phylogeny ; Plastids/genetics ; Sequence Analysis, DNA ; }, abstract = {Although the plastid genomes of diatoms maintain a conserved architecture and core gene set, considerable variation about this core theme exists and can be traced to several different processes. Gene duplication, pseudogenization, and loss, as well as intracellular transfer of genes to the nuclear genome, have all contributed to variation in gene content among diatom species. In addition, some noncoding sequences have highly restricted phylogenetic distributions that suggest a recent foreign origin. We sequenced the plastid genome of the marine diatom, Toxarium undulatum, and found that the genome contains three genes (chlB, chlL, and chlN) involved in light-independent chlorophyll a biosynthesis that were not previously known from diatoms. Phylogenetic and syntenic data suggest that these genes were differentially retained in this one lineage as they were repeatedly lost from most other diatoms. Unique among diatoms and other heterokont algae sequenced so far, the genome also contains a large group II intron within an otherwise intact psaA gene. Although the intron is most similar to one in the plastid-encoded psaA gene of some green algae, high sequence divergence between the diatom and green algal introns rules out recent shared ancestry. We conclude that the psaA intron was likely introduced into the plastid genome of T. undulatum, or some earlier ancestor, by horizontal transfer from an unknown donor. This genome further highlights the myriad processes driving variation in gene and intron content in the plastid genomes of diatoms, one of the world's foremost primary producers.}, }
@article {pmid27653556, year = {2016}, author = {Hehemann, JH and Arevalo, P and Datta, MS and Yu, X and Corzett, CH and Henschel, A and Preheim, SP and Timberlake, S and Alm, EJ and Polz, MF}, title = {Adaptive radiation by waves of gene transfer leads to fine-scale resource partitioning in marine microbes.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {12860}, pmid = {27653556}, issn = {2041-1723}, support = {T32 GM087237/GM/NIGMS NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; }, abstract = {Adaptive radiations are important drivers of niche filling, since they rapidly adapt a single clade of organisms to ecological opportunities. Although thought to be common for animals and plants, adaptive radiations have remained difficult to document for microbes in the wild. Here we describe a recent adaptive radiation leading to fine-scale ecophysiological differentiation in the degradation of an algal glycan in a clade of closely related marine bacteria. Horizontal gene transfer is the primary driver in the diversification of the pathway leading to several ecophysiologically differentiated Vibrionaceae populations adapted to different physical forms of alginate. Pathway architecture is predictive of function and ecology, underscoring that horizontal gene transfer without extensive regulatory changes can rapidly assemble fully functional pathways in microbes.}, }
@article {pmid27649274, year = {2016}, author = {Hashimoto, T and Horikawa, DD and Saito, Y and Kuwahara, H and Kozuka-Hata, H and Shin-I, T and Minakuchi, Y and Ohishi, K and Motoyama, A and Aizu, T and Enomoto, A and Kondo, K and Tanaka, S and Hara, Y and Koshikawa, S and Sagara, H and Miura, T and Yokobori, SI and Miyagawa, K and Suzuki, Y and Kubo, T and Oyama, M and Kohara, Y and Fujiyama, A and Arakawa, K and Katayama, T and Toyoda, A and Kunieda, T}, title = {Extremotolerant tardigrade genome and improved radiotolerance of human cultured cells by tardigrade-unique protein.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {12808}, pmid = {27649274}, issn = {2041-1723}, mesh = {Adaptation, Physiological/*genetics ; Animals ; DNA Damage ; Gene Transfer, Horizontal ; *Genome ; HEK293 Cells ; Humans ; Peroxisomes ; Stress, Physiological/genetics ; Tardigrada/*genetics ; X-Rays ; }, abstract = {Tardigrades, also known as water bears, are small aquatic animals. Some tardigrade species tolerate almost complete dehydration and exhibit extraordinary tolerance to various physical extremes in the dehydrated state. Here we determine a high-quality genome sequence of Ramazzottius varieornatus, one of the most stress-tolerant tardigrade species. Precise gene repertoire analyses reveal the presence of a small proportion (1.2% or less) of putative foreign genes, loss of gene pathways that promote stress damage, expansion of gene families related to ameliorating damage, and evolution and high expression of novel tardigrade-unique proteins. Minor changes in the gene expression profiles during dehydration and rehydration suggest constitutive expression of tolerance-related genes. Using human cultured cells, we demonstrate that a tardigrade-unique DNA-associating protein suppresses X-ray-induced DNA damage by ∼40% and improves radiotolerance. These findings indicate the relevance of tardigrade-unique proteins to tolerability and tardigrades could be a bountiful source of new protection genes and mechanisms.}, }
@article {pmid27649032, year = {2016}, author = {Chowdhury, G and Pazhani, GP and Sarkar, A and Rajendran, K and Mukhopadhyay, AK and Bhattacharya, MK and Ghosh, A and Ramamurthy, T}, title = {Carbapenem Resistance in Clonally Distinct Clinical Strains of Vibrio fluvialis Isolated from Diarrheal Samples.}, journal = {Emerging infectious diseases}, volume = {22}, number = {10}, pages = {1754-1761}, pmid = {27649032}, issn = {1080-6059}, mesh = {Anti-Bacterial Agents/*pharmacology ; Carbapenems/*pharmacology ; Conjugation, Genetic ; Diarrhea/*microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Enterobacteriaceae/genetics ; Enterobacteriaceae Infections/microbiology ; Escherichia coli/drug effects/genetics ; Gene Transfer, Horizontal ; Humans ; India ; Microbial Sensitivity Tests ; R Factors ; Species Specificity ; Vibrio/*drug effects/enzymology/genetics/isolation &amp; purification ; beta-Lactam Resistance/*genetics ; beta-Lactamases/*genetics ; }, abstract = {Carbapenems have been used for many years to treat severe nosocomial Enterobacteriaceae infections. The spread of resistance to these drugs among other bacterial families is an emerging problem worldwide, mostly caused by New Delhi metallo-β-lactamase (NDM-1). We screened for the prevalence of NDM-1-expressing enteric pathogens from hospitalized patients with acute diarrhea in Kolkata, India, and identified 27 Vibrio fluvialis-harboring blaNDM-1 (NDM-VF) strains. These isolates were also resistant to all the tested antimicrobial drugs except doxycycline. The large plasmid of V. fluvialis harboring blaNDM-1 could be easily transferred to other enteric pathogens. Genes flanking the blaNDM-1 were found to be identical to the reported sequence from an Escherichia coli isolate. Analyses showed that the V. fluvialis possessing the NDM-VF region belonged to different clones. The pathogenicity of V. fluvialis to humans and its ubiquitous presence in the environment call for constant monitoring of this species for emerging antimicrobial drug resistance.}, }
@article {pmid27648812, year = {2017}, author = {Popa, O and Landan, G and Dagan, T}, title = {Phylogenomic networks reveal limited phylogenetic range of lateral gene transfer by transduction.}, journal = {The ISME journal}, volume = {11}, number = {2}, pages = {543-554}, pmid = {27648812}, issn = {1751-7370}, support = {281357/ERC_/European Research Council/International ; }, mesh = {Bacteria/classification/*genetics/virology ; Bacteriophages/*physiology ; Biological Evolution ; *Gene Transfer, Horizontal ; Genome, Bacterial/*genetics ; Host Specificity ; Phylogeny ; *Transduction, Genetic ; }, abstract = {Bacteriophages are recognized DNA vectors and transduction is considered as a common mechanism of lateral gene transfer (LGT) during microbial evolution. Anecdotal events of phage-mediated gene transfer were studied extensively, however, a coherent evolutionary viewpoint of LGT by transduction, its extent and characteristics, is still lacking. Here we report a large-scale evolutionary reconstruction of transduction events in 3982 genomes. We inferred 17 158 recent transduction events linking donors, phages and recipients into a phylogenomic transduction network view. We find that LGT by transduction is mostly restricted to closely related donors and recipients. Furthermore, a substantial number of the transduction events (9%) are best described as gene duplications that are mediated by mobile DNA vectors. We propose to distinguish this type of paralogy by the term autology. A comparison of donor and recipient genomes revealed that genome similarity is a superior predictor of species connectivity in the network in comparison to common habitat. This indicates that genetic similarity, rather than ecological opportunity, is a driver of successful transduction during microbial evolution. A striking difference in the connectivity pattern of donors and recipients shows that while lysogenic interactions are highly species-specific, the host range for lytic phage infections can be much wider, serving to connect dense clusters of closely related species. Our results thus demonstrate that DNA transfer via transduction occurs within the context of phage-host specificity, but that this tight constraint can be breached, on rare occasions, to produce long-range LGTs of profound evolutionary consequences.}, }
@article {pmid27647002, year = {2016}, author = {Yang, Z and Liu, L and Fang, H and Li, P and Xu, S and Cao, W and Xu, C and Huang, J and Zhou, Y}, title = {Origin of the plant Tm-1-like gene via two independent horizontal transfer events and one gene fusion event.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {33691}, pmid = {27647002}, issn = {2045-2322}, mesh = {Disease Resistance/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Plant ; Solanum lycopersicum/genetics/virology ; Phylogeny ; Plant Diseases/virology ; *Recombination, Genetic ; Streptophyta/classification/genetics ; Tobamovirus/genetics ; }, abstract = {The Tomato mosaic virus (ToMV) resistance gene Tm-1 encodes a direct inhibitor of ToMV RNA replication to protect tomato from infection. The plant Tm-1-like (Tm-1L) protein is predicted to contain an uncharacterized N-terminal UPF0261 domain and a C-terminal TIM-barrel signal transduction (TBST) domain. Homologous searches revealed that proteins containing both of these two domains are mainly present in charophyte green algae and land plants but absent from glaucophytes, red algae and chlorophyte green algae. Although Tm-1 homologs are widely present in bacteria, archaea and fungi, UPF0261- and TBST-domain-containing proteins are generally encoded by different genes in these linages. A co-evolution analysis also suggested a putative interaction between UPF0261- and TBST-domain-containing proteins. Phylogenetic analyses based on homologs of these two domains revealed that plants have acquired UPF0261- and TBST-domain-encoding genes through two independent horizontal gene transfer (HGT) events before the origin of land plants from charophytes. Subsequently, gene fusion occurred between these two horizontally acquired genes and resulted in the origin of the Tm-1L gene in streptophytes. Our results demonstrate a novel evolutionary mechanism through which the recipient organism may acquire genes with functional interaction through two different HGT events and further fuse them into one functional gene.}, }
@article {pmid27645387, year = {2016}, author = {Renda, BA and Chan, C and Parent, KN and Barrick, JE}, title = {Emergence of a Competence-Reducing Filamentous Phage from the Genome of Acinetobacter baylyi ADP1.}, journal = {Journal of bacteriology}, volume = {198}, number = {23}, pages = {3209-3219}, pmid = {27645387}, issn = {1098-5530}, support = {R00 GM087550/GM/NIGMS NIH HHS/United States ; }, mesh = {Acinetobacter baumannii/genetics/*virology ; Bacterial Proteins/genetics/metabolism ; Genome, Bacterial ; Genome, Viral ; Inovirus/classification/genetics/*isolation &amp; purification/physiology ; Prophages/classification/genetics/*isolation &amp; purification/physiology ; }, abstract = {UNLABELLED: Bacterial genomes commonly contain prophage sequences as a result of past infections with lysogenic phages. Many of these integrated viral sequences are believed to be cryptic, but prophage genes are sometimes coopted by the host, and some prophages may be reactivated to form infectious particles when cells are stressed or mutate. We found that a previously uncharacterized filamentous phage emerged from the genome of Acinetobacter baylyi ADP1 during a laboratory evolution experiment. This phage has a genetic organization similar to that of the Vibrio cholerae CTXϕ phage. The emergence of the ADP1 phage was associated with the evolution of reduced transformability in our experimental populations, so we named it the competence-reducing acinetobacter phage (CRAϕ). Knocking out ADP1 genes required for competence leads to resistance to CRAϕ infection. Although filamentous bacteriophages are known to target type IV pili, this is the first report of a phage that apparently uses a competence pilus as a receptor. A. baylyi may be especially susceptible to this route of infection because every cell is competent during normal growth, whereas competence is induced only under certain environmental conditions or in a subpopulation of cells in other bacterial species. It is possible that CRAϕ-like phages restrict horizontal gene transfer in nature by inhibiting the growth of naturally transformable strains. We also found that prophages with homology to CRAϕ exist in several strains of Acinetobacter baumannii These CRAϕ-like A. baumannii prophages encode toxins similar to CTXϕ that might contribute to the virulence of this opportunistic multidrug-resistant pathogen.<br><br>IMPORTANCE: We observed the emergence of a novel filamentous phage (CRA&#x3d5;) from the genome of Acinetobacter baylyi ADP1 during a long-term laboratory evolution experiment. CRA&#x3d5; is the first bacteriophage reported to require the molecular machinery involved in the uptake of environmental DNA for infection. Reactivation and evolution of CRA&#x3d5; reduced the potential for horizontal transfer of genes via natural transformation in our experiment. Risk of infection by similar phages may limit the expression and maintenance of bacterial competence in nature. The closest studied relative of CRA&#x3d5; is the Vibrio cholerae CTX&#x3d5; phage. Variants of CRA&#x3d5; are found in the genomes of Acinetobacter baumannii strains, and it is possible that phage-encoded toxins contribute to the virulence of this opportunistic multidrug-resistant pathogen.}, }
@article {pmid27642638, year = {2016}, author = {McCarthy, CG and Fitzpatrick, DA}, title = {Systematic Search for Evidence of Interdomain Horizontal Gene Transfer from Prokaryotes to Oomycete Lineages.}, journal = {mSphere}, volume = {1}, number = {5}, pages = {}, pmid = {27642638}, issn = {2379-5042}, abstract = {While most commonly associated with prokaryotes, horizontal gene transfer (HGT) can also have a significant influence on the evolution of microscopic eukaryotes. Systematic analysis of HGT in the genomes of the oomycetes, filamentous eukaryotic microorganisms in the Stramenopiles-Alveolates-Rhizaria (SAR) supergroup, has to date focused mainly on intradomain transfer events between oomycetes and fungi. Using systematic whole-genome analysis followed by phylogenetic reconstruction, we have investigated the extent of interdomain HGT between bacteria and plant-pathogenic oomycetes. We report five putative instances of HGT from bacteria into the oomycetes. Two transfers were found in Phytophthora species, including one unique to the cucurbit pathogen Phytophthora capsici. Two were found in Pythium species only, and the final transfer event was present in Phytopythium and Pythium species, the first reported bacterium-inherited genes in these genera. Our putative transfers included one protein that appears to be a member of the Pythium secretome, metabolic proteins, and enzymes that could potentially break down xenobiotics within the cell. Our findings complement both previous reports of bacterial genes in oomycete and SAR genomes and the growing body of evidence suggesting that interdomain transfer from prokaryotes into eukaryotes occurs more frequently than previously thought. IMPORTANCE Horizontal gene transfer (HGT) is the nonvertical inheritance of genetic material by transfer between different species. HGT is an important evolutionary mechanism for prokaryotes and in some cases is responsible for the spread of antibiotic resistance from resistant to benign species. Genome analysis has shown that examples of HGT are not as frequent in eukaryotes, but when they do occur they may have important evolutionary consequences. For example, the acquisition of fungal genes by an ancestral Phytophthora (plant destroyer) species is responsible for the large repertoire of enzymes in the plant-degrading arsenal of modern-day Phytophthora species. In this analysis, we set out to systematically search oomycete genomes for evidence of interdomain HGT (transfer of bacterial genes into oomycete species). Our results show that interdomain HGT is rare in oomycetes but has occurred. We located five well-supported examples, including one that could potentially break down xenobiotics within the cell.}, }
@article {pmid27642089, year = {2017}, author = {Drezen, JM and Gauthier, J and Josse, T and Bézier, A and Herniou, E and Huguet, E}, title = {Foreign DNA acquisition by invertebrate genomes.}, journal = {Journal of invertebrate pathology}, volume = {147}, number = {}, pages = {157-168}, doi = {10.1016/j.jip.2016.09.004}, pmid = {27642089}, issn = {1096-0805}, mesh = {Animals ; *Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome ; Invertebrates/*genetics/microbiology ; Symbiosis/genetics ; }, abstract = {Recent studies have highlighted that the accidental acquisition of DNA from other species by invertebrate genomes is much more common than originally thought. The transferred DNAs are of bacterial or eukaryote origin and in both cases the receiver species may end up utilising the transferred genes for its own benefit. Frequent contact with prokaryotic DNA from symbiotic endocellular bacteria may predispose invertebrates to incorporate this genetic material into their genomes. Increasing evidence also points to viruses as major players in transferring genes and mobile elements between the species they infect. Unexpectedly a gene flux between Hymenoptera and Lepidoptera mediated by endogenous viruses of parasitic wasps has been recently unravelled, suggesting we are probably just seeing the tip of the iceberg concerning horizontal gene transfers in invertebrates. In the context of insect for feed and food, if the new technology of insect genome editing (such as Crisper/Cas9) were used to modify the genome of reared insects it is important to take into account the risk that an introduced gene can be transferred. More generally, although insects are traditionally consumed in Asia and Africa, knowledge on insect viruses is still limited rendering it difficult to predict the impact they might have in the context of insect rearing at an industrial scale.}, }
@article {pmid27635331, year = {2016}, author = {DeBlasio, DF and Wisecaver, JH}, title = {SICLE: a high-throughput tool for extracting evolutionary relationships from phylogenetic trees.}, journal = {PeerJ}, volume = {4}, number = {}, pages = {e2359}, pmid = {27635331}, issn = {2167-8359}, abstract = {We present the phylogeny analysis software SICLE (Sister Clade Extractor), an easy-to-use, high-throughput tool to describe the nearest neighbors to a node of interest in a phylogenetic tree as well as the support value for the relationship. The application is a command line utility that can be embedded into a phylogenetic analysis pipeline or can be used as a subroutine within another C++ program. As a test case, we applied this new tool to the published phylome of Salinibacter ruber, a species of halophilic Bacteriodetes, identifying 13 unique sister relationships to S. ruber across the 4,589 gene phylogenies. S. ruber grouped with bacteria, most often other Bacteriodetes, in the majority of phylogenies, but 91 phylogenies showed a branch-supported sister association between S. ruber and Archaea, an evolutionarily intriguing relationship indicative of horizontal gene transfer. This test case demonstrates how SICLE makes it possible to summarize the phylogenetic information produced by automated phylogenetic pipelines to rapidly identify and quantify the possible evolutionary relationships that merit further investigation. SICLE is available for free for noncommercial use at http://eebweb.arizona.edu/sicle/.}, }
@article {pmid27634406, year = {2016}, author = {Yin, Z and Zhu, B and Feng, H and Huang, L}, title = {Horizontal gene transfer drives adaptive colonization of apple trees by the fungal pathogen Valsa mali.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {33129}, pmid = {27634406}, issn = {2045-2322}, mesh = {Actinobacteria/genetics ; Ascomycota/*genetics/*pathogenicity ; Bacteria/genetics/pathogenicity ; Bleomycin/metabolism ; Cell Wall/genetics ; China ; Eukaryota/genetics ; Gene Transfer, Horizontal/*genetics ; Malus/*genetics/*microbiology ; Nitrogen/metabolism ; Phylogeny ; Virulence/genetics ; Virulence Factors/genetics ; }, abstract = {Horizontal gene transfer (HGT) often has strong benefits for fungi. In a study of samples from apple canker in Shaanxi Province, China, diverse microbes, along with the necrotrophic pathogen Valsa mali, were found to colonize the apple bark, thus providing ample opportunity for HGT to occur. In the present study, we identified 32 HGT events in V. mali by combining phyletic distribution-based methods with phylogenetic analyses. Most of these HGTs were from bacteria, whereas several others were from eukaryotes. Three HGTs putatively functioned in competition with actinomycetes, some of which showed a significant inhibitory effect on V. mali. Three HGTs that were probably involved in nitrogen uptake were also identified. Ten HGTs were thought to be involved in pathogenicity because they were related to known virulence factors, including cell wall-degrading enzymes and candidate effector proteins. HGT14, together with HGT32, was shown to contribute to bleomycin resistance of V. mali.These results suggest that HGT drives the adaptive evolution of V. mali. The HGTs identified here provide new clues for unveiling the adaptation mechanisms and virulence determinants of V. mali.}, }
@article {pmid27633769, year = {2016}, author = {Joseph, SJ and Cox, D and Wolff, B and Morrison, SS and Kozak-Muiznieks, NA and Frace, M and Didelot, X and Castillo-Ramirez, S and Winchell, J and Read, TD and Dean, D}, title = {Dynamics of genome change among Legionella species.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {33442}, pmid = {27633769}, issn = {2045-2322}, support = {MR/K010174/1/MRC_/Medical Research Council/United Kingdom ; R01 AI098843/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Secretion Systems/genetics ; Base Sequence ; CRISPR-Cas Systems/genetics ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial ; *Genome, Bacterial ; Genomics ; Legionella/*genetics ; Phylogeny ; Recombination, Genetic/genetics ; Selection, Genetic ; Species Specificity ; }, abstract = {Legionella species inhabit freshwater and soil ecosystems where they parasitize protozoa. L. pneumonphila (LP) serogroup-1 (Lp1) is the major cause of Legionnaires' Disease (LD), a life-threatening pulmonary infection that can spread systemically. The increased global frequency of LD caused by Lp and non-Lp species underscores the need to expand our knowledge of evolutionary forces underlying disease pathogenesis. Whole genome analyses of 43 strains, including all known Lp serogroups 1-17 and 17 emergent LD-causing Legionella species (of which 33 were sequenced in this study) in addition to 10 publicly available genomes, resolved the strains into four phylogenetic clades along host virulence demarcations. Clade-specific genes were distinct for genetic exchange and signal-transduction, indicating adaptation to specific cellular and/or environmental niches. CRISPR spacer comparisons hinted at larger pools of accessory DNA sequences in Lp than predicted by the pan-genome analyses. While recombination within Lp was frequent and has been reported previously, population structure analysis identified surprisingly few DNA admixture events between species. In summary, diverse Legionella LD-causing species share a conserved core-genome, are genetically isolated from each other, and selectively acquire genes with potential for enhanced virulence.}, }
@article {pmid27630622, year = {2016}, author = {Sun, B and Li, T and Xiao, J and Liu, L and Zhang, P and Murphy, RW and He, S and Huang, D}, title = {Contribution of Multiple Inter-Kingdom Horizontal Gene Transfers to Evolution and Adaptation of Amphibian-Killing Chytrid, Batrachochytrium dendrobatidis.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1360}, pmid = {27630622}, issn = {1664-302X}, abstract = {Amphibian populations are experiencing catastrophic declines driven by the fungal pathogen Batrachochytrium dendrobatidis (Bd). Although horizontal gene transfer (HGT) facilitates the evolution and adaptation in many fungi by conferring novel function genes to the recipient fungi, inter-kingdom HGT in Bd remains largely unexplored. In this study, our investigation detects 19 bacterial genes transferred to Bd, including metallo-beta-lactamase and arsenate reductase that play important roles in the resistance to antibiotics and arsenates. Moreover, three probable HGT gene families in Bd are from plants and one gene family coding the ankyrin repeat-containing protein appears to come from oomycetes. The observed multi-copy gene families associated with HGT are probably due to the independent transfer events or gene duplications. Five HGT genes with extracellular locations may relate to infection, and some other genes may participate in a variety of metabolic pathways, and in doing so add important metabolic traits to the recipient. The evolutionary analysis indicates that all the transferred genes evolved under purifying selection, suggesting that their functions in Bd are similar to those of the donors. Collectively, our results indicate that HGT from diverse donors may be an important evolutionary driver of Bd, and improve its adaptations for infecting and colonizing host amphibians.}, }
@article {pmid27630250, year = {2016}, author = {Pinhassi, J and DeLong, EF and Béjà, O and González, JM and Pedrós-Alió, C}, title = {Marine Bacterial and Archaeal Ion-Pumping Rhodopsins: Genetic Diversity, Physiology, and Ecology.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {80}, number = {4}, pages = {929-954}, pmid = {27630250}, issn = {1098-5557}, mesh = {Aquatic Organisms/metabolism ; Archaea/genetics/*metabolism ; Bacteria/genetics/*metabolism ; Gene Expression/genetics ; Gene Transfer, Horizontal/genetics ; Genetic Variation/genetics ; Ion Transport/*physiology ; Light ; Rhodopsins, Microbial/genetics/*metabolism ; Seawater/microbiology ; Sodium-Potassium-Exchanging ATPase/genetics/metabolism ; }, abstract = {The recognition of a new family of rhodopsins in marine planktonic bacteria, proton-pumping proteorhodopsin, expanded the known phylogenetic range, environmental distribution, and sequence diversity of retinylidene photoproteins. At the time of this discovery, microbial ion-pumping rhodopsins were known solely in haloarchaea inhabiting extreme hypersaline environments. Shortly thereafter, proteorhodopsins and other light-activated energy-generating rhodopsins were recognized to be widespread among marine bacteria. The ubiquity of marine rhodopsin photosystems now challenges prior understanding of the nature and contributions of "heterotrophic" bacteria to biogeochemical carbon cycling and energy fluxes. Subsequent investigations have focused on the biophysics and biochemistry of these novel microbial rhodopsins, their distribution across the tree of life, evolutionary trajectories, and functional expression in nature. Later discoveries included the identification of proteorhodopsin genes in all three domains of life, the spectral tuning of rhodopsin variants to wavelengths prevailing in the sea, variable light-activated ion-pumping specificities among bacterial rhodopsin variants, and the widespread lateral gene transfer of biosynthetic genes for bacterial rhodopsins and their associated photopigments. Heterologous expression experiments with marine rhodopsin genes (and associated retinal chromophore genes) provided early evidence that light energy harvested by rhodopsins could be harnessed to provide biochemical energy. Importantly, some studies with native marine bacteria show that rhodopsin-containing bacteria use light to enhance growth or promote survival during starvation. We infer from the distribution of rhodopsin genes in diverse genomic contexts that different marine bacteria probably use rhodopsins to support light-dependent fitness strategies somewhere between these two extremes.}, }
@article {pmid27629899, year = {2016}, author = {Mulhall, RM and Brehony, C and O'Connor, L and Meyler, K and Jolley, KA and Bray, J and Bennett, D and Maiden, MC and Cunney, R}, title = {Resolution of a Protracted Serogroup B Meningococcal Outbreak with Whole-Genome Sequencing Shows Interspecies Genetic Transfer.}, journal = {Journal of clinical microbiology}, volume = {54}, number = {12}, pages = {2891-2899}, pmid = {27629899}, issn = {1098-660X}, support = {/WT_/Wellcome Trust/United Kingdom ; 087622/WT_/Wellcome Trust/United Kingdom ; 104992/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Adolescent ; Adult ; Child ; Child, Preschool ; *Disease Outbreaks ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/genetics ; Humans ; Infant ; Meningococcal Infections/*epidemiology/microbiology/*transmission ; Multilocus Sequence Typing ; Neisseria lactamica/genetics/*isolation &amp; purification ; Neisseria meningitidis, Serogroup B/genetics/*isolation &amp; purification ; *Population Density ; Young Adult ; }, abstract = {A carriage study was undertaken (n = 112) to ascertain the prevalence of Neisseria spp. following the eighth case of invasive meningococcal disease in young children (5 to 46 months) and members of a large extended indigenous ethnic minority Traveller family (n = 123), typically associated with high-occupancy living conditions. Nested multilocus sequence typing (MLST) was employed for case specimen extracts. Isolates were genome sequenced and then were assembled de novo and deposited into the Bacterial Isolate Genome Sequencing Database (BIGSdb). This facilitated an expanded MLST approach utilizing large numbers of loci for isolate characterization and discrimination. A rare sequence type, ST-6697, predominated in disease specimens and isolates that were carried (n = 8/14), persisting for at least 44 months, likely driven by the high population density of houses (n = 67/112) and trailers (n = 45/112). Carriage for Neisseria meningitidis (P < 0.05) and Neisseria lactamica (P < 0.002) (2-sided Fisher's exact test) was more likely in the smaller, more densely populated trailers. Meningococcal carriage was highest in 24- to 39-year-olds (45%, n = 9/20). Evidence of horizontal gene transfer (HGT) was observed in four individuals cocolonized by Neisseria lactamica and Neisseria meningitidis One HGT event resulted in the acquisition of 26 consecutive N. lactamica alleles. This study demonstrates how housing density can drive meningococcal transmission and carriage, which likely facilitated the persistence of ST-6697 and prolonged the outbreak. Whole-genome MLST effectively distinguished between highly similar outbreak strain isolates, including those isolated from person-to-person transmission, and also highlighted how a few HGT events can distort the true phylogenetic relationship between highly similar clonal isolates.}, }
@article {pmid27627107, year = {2016}, author = {Madsen, JS and Riber, L and Kot, W and Basfeld, A and Burmølle, M and Hansen, LH and Sørensen, SJ}, title = {Type 3 Fimbriae Encoded on Plasmids Are Expressed from a Unique Promoter without Affecting Host Motility, Facilitating an Exceptional Phenotype That Enhances Conjugal Plasmid Transfer.}, journal = {PloS one}, volume = {11}, number = {9}, pages = {e0162390}, pmid = {27627107}, issn = {1932-6203}, mesh = {Biofilms ; Fimbriae, Bacterial/*metabolism ; Gene Transfer, Horizontal ; Phenotype ; *Plasmids ; *Promoter Regions, Genetic ; }, abstract = {Horizontal gene transfer (HGT), the transmission of genetic material to a recipient that is not the progeny of the donor, is fundamental in bacterial evolution. HGT is often mediated by mobile genetic elements such as conjugative plasmids, which may be in conflict with the chromosomal elements of the genome because they are independent replicons that may petition their own evolutionary strategy. Here we study differences between type 3 fimbriae encoded on wild type plasmids and in chromosomes. Using known and newly characterized plasmids we show that the expression of type 3 fimbriae encoded on plasmids is systematically different, as MrkH, a c-di-GMP dependent transcriptional activator is not needed for strong expression of the fimbriae. MrkH is required for expression of type 3 fimbriae of the Klebsiella pneumoniae chromosome, wherefrom the fimbriae operon (mrkABCDF) of plasmids is believed to have originated. We find that mrkABCDFs of plasmids are highly expressed via a unique promoter that differs from the original Klebsiella promoter resulting in fundamental behavioral consequences. Plasmid associated mrkABCDFs did not influence the swimming behavior of the host, that hereby acquired an exceptional phenotype being able to both actively swim (planktonic behavior) and express biofilm associated fimbriae (sessile behavior). We show that this exceptional phenotype enhances the conjugal transfer of the plasmid.}, }
@article {pmid27621177, year = {2017}, author = {He, T and Wang, Y and Sun, L and Pang, M and Zhang, L and Wang, R}, title = {Occurrence and characterization of blaNDM-5-positive Klebsiella pneumoniae isolates from dairy cows in Jiangsu, China.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {72}, number = {1}, pages = {90-94}, doi = {10.1093/jac/dkw357}, pmid = {27621177}, issn = {1460-2091}, mesh = {Animals ; Blotting, Southern ; Cattle ; Cattle Diseases/*microbiology ; China ; Conjugation, Genetic ; DNA, Bacterial/analysis/genetics ; Electrophoresis, Gel, Pulsed-Field ; Gene Order ; Gene Transfer, Horizontal ; Genotype ; Klebsiella Infections/microbiology/*veterinary ; Klebsiella pneumoniae/classification/genetics/*isolation &amp; purification ; Multilocus Sequence Typing ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; beta-Lactamases/*analysis/genetics ; }, abstract = {OBJECTIVES: To investigate the epidemiological characteristics and the surrounding genetic structure of the blaNDM-5 gene in Klebsiella pneumoniae derived from dairy cows in Jiangsu Province, China.<br><br>METHODS: Ten carbapenem-resistant K. pneumoniae were collected from three dairy farms and were screened for the presence of carbapenemase genes using PCR and sequencing. PFGE and MLST were conducted to analyse the genetic relatedness of the blaNDM-5-harbouring K. pneumoniae isolates. The location of blaNDM-5 was identified by S1 nuclease-PFGE and Southern blotting. The transferability and profiles of blaNDM-5-carrying plasmids were analysed by conjugation experiments, and PCR-based replicon typing and RFLP, respectively. The surrounding genetic structure of the blaNDM-5 gene was obtained using WGS and PCR mapping.<br><br>RESULTS: All 10 K. pneumoniae from dairy cows harboured the blaNDM-5 gene, exhibited resistance to multiple antimicrobials and belonged to five STs, of which ST1661 and ST2108 were the most prevalent. The blaNDM-5 gene was located on the &#x223c;46 kb IncX3 plasmid in all isolates and these plasmids could be conjugated to an Escherichia coli recipient with no additional resistance profiles transferred. All blaNDM-5-carrying plasmids shared similar genetic contexts and were nearly identical to that of the human K. pneumoniae plasmid (pNDM-MGR194) previously reported in India.<br><br>CONCLUSIONS: This was the first case of blaNDM-5-positive K. pneumoniae identified from dairy cows in China. The IncX3 pNDM-MGR194-like plasmid disseminated among cow farms should be highlighted and its potential role in mediating transmission of the blaNDM gene between bacteria from humans and animals requires further monitoring.}, }
@article {pmid27621174, year = {2017}, author = {Morici, E and Simoni, S and Brenciani, A and Giovanetti, E and Varaldo, PE and Mingoia, M}, title = {A new mosaic integrative and conjugative element from Streptococcus agalactiae carrying resistance genes for chloramphenicol (catQ) and macrolides [mef(I) and erm(TR)].}, journal = {The Journal of antimicrobial chemotherapy}, volume = {72}, number = {1}, pages = {64-67}, doi = {10.1093/jac/dkw367}, pmid = {27621174}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/*pharmacology ; Chloramphenicol/*pharmacology ; *Drug Resistance, Bacterial ; Female ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genotype ; Host Specificity ; Humans ; *Interspersed Repetitive Sequences ; Macrolides/*pharmacology ; Male ; Recombination, Genetic ; Streptococcal Infections/microbiology ; Streptococcus agalactiae/classification/*genetics/isolation &amp; purification ; }, abstract = {OBJECTIVES: To investigate the genetic basis of catQ-mediated chloramphenicol resistance in Streptococcus agalactiae.<br><br>METHODS: Two clinical strains of catQ-positive chloramphenicol-resistant S. agalactiae (Sag236 and Sag403) were recently isolated, typed (MLST, PFGE pulsotypes, capsular types) and their antibiotic resistances investigated by phenotypic and genotypic approaches. Several molecular methods (PCR mapping, restriction assays, Southern blotting, sequencing and sequence analysis, conjugal transfer assays) were used to determine the genetic context of catQ and characterize a genetic element detected in the isolates.<br><br>RESULTS: Sag236 and Sag403 shared the same ST (ST19), but exhibited a different capsular type (III and V, respectively) and pulsotype. Both harboured the macrolide resistance genes mef(I) and erm(TR) and the tetracycline resistance gene tet(M). Accordingly, they were resistant to chloramphenicol, erythromycin and tetracycline. catQ and mef(I) were associated in an IQ module that was indistinguishable in Sag236 and Sag403. In mating assays, chloramphenicol and erythromycin resistance proved transferable, at low frequency, only from Sag236. Transconjugants carried not only catQ and mef(I), but also erm(TR), suggesting a linkage of the three resistance genes in a mobile element, which, though seemingly non-mobile, was also detected in Sag403. The new element (designated ICESag236, &#x223c;110 kb) results from recombination of two integrative and conjugative elements (ICEs) originally described in different streptococcal species: S. agalactiae ICESagTR7, carrying erm(TR); and Streptococcus pneumoniae ICESpn529IQ, carrying the prototype IQ module.<br><br>CONCLUSIONS: These findings strengthen the notion that widespread streptococcal ICEs may form mosaics that enhance their diversity and spread, broaden their host range and carry new cargo genes.}, }
@article {pmid27610568, year = {2016}, author = {Costa, TRD and Ilangovan, A and Ukleja, M and Redzej, A and Santini, JM and Smith, TK and Egelman, EH and Waksman, G}, title = {Structure of the Bacterial Sex F Pilus Reveals an Assembly of a Stoichiometric Protein-Phospholipid Complex.}, journal = {Cell}, volume = {166}, number = {6}, pages = {1436-1444.e10}, pmid = {27610568}, issn = {1097-4172}, support = {BB/L014211/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; R01 GM035269/GM/NIGMS NIH HHS/United States ; 093228/WT_/Wellcome Trust/United Kingdom ; 098302/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Attachment Sites, Microbiological/genetics ; Cryoelectron Microscopy ; Escherichia coli/*physiology ; Escherichia coli Proteins/*chemistry/metabolism ; F Factor/*chemistry/genetics ; Fimbriae, Bacterial/*chemistry/genetics/metabolism ; Lipids/chemistry ; *Models, Molecular ; Mutation ; Phospholipids/*chemistry/metabolism ; Protein Binding ; Protein Subunits/genetics/metabolism ; Type V Secretion Systems/chemistry/metabolism ; }, abstract = {Conjugative pili are widespread bacterial appendages that play important roles in horizontal gene transfer, in spread of antibiotic resistance genes, and as sites of phage attachment. Among conjugative pili, the F "sex" pilus encoded by the F plasmid is the best functionally characterized, and it is also historically the most important, as the discovery of F-plasmid-mediated conjugation ushered in the era of molecular biology and genetics. Yet, its structure is unknown. Here, we present atomic models of two F family pili, the F and pED208 pili, generated from cryoelectron microscopy reconstructions at 5.0 and 3.6 Å resolution, respectively. These structures reveal that conjugative pili are assemblies of stoichiometric protein-phospholipid units. We further demonstrate that each pilus type binds preferentially to particular phospholipids. These structures provide the molecular basis for F pilus assembly and also shed light on the remarkable properties of conjugative pili in bacterial secretion and phage infection.}, }
@article {pmid27610108, year = {2016}, author = {Lopes, LD and Pereira E Silva, Mde C and Andreote, FD}, title = {Bacterial Abilities and Adaptation Toward the Rhizosphere Colonization.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1341}, pmid = {27610108}, issn = {1664-302X}, abstract = {The rhizosphere harbors one of the most complex, diverse, and active plant-associated microbial communities. This community can be recruited by the plant host to either supply it with nutrients or to help in the survival under stressful conditions. Although selection for the rhizosphere community is evident, the specific bacterial traits that make them able to colonize this environment are still poorly understood. Thus, here we used a combination of community level physiological profile (CLPP) analysis and 16S rRNA gene quantification and sequencing (coupled with in silico analysis and metagenome prediction), to get insights on bacterial features and processes involved in rhizosphere colonization of sugarcane. CLPP revealed a higher metabolic activity in the rhizosphere compared to bulk soil, and suggested that D-galacturonic acid plays a role in bacterial selection by the plant roots (supported by results of metagenome prediction). Quantification of the 16S rRNA gene confirmed the higher abundance of bacteria in the rhizosphere. Sequence analysis showed that of the 252 classified families sampled, 24 were significantly more abundant in the bulk soil and 29 were more abundant in the rhizosphere. Furthermore, metagenomes predicted from the 16S rRNA gene sequences revealed a significant higher abundance of predicted genes associated with biofilm formation and with horizontal gene transfer (HGT) processes. In sum, this study identified major bacterial groups and their potential abilities to occupy the sugarcane rhizosphere, and indicated that polygalacturonase activity and HGT events may be important features for rhizosphere colonization.}, }
@article {pmid27609232, year = {2016}, author = {Mašlaňová, I and Stříbná, S and Doškař, J and Pantůček, R}, title = {Efficient plasmid transduction to Staphylococcus aureus strains insensitive to the lytic action of transducing phage.}, journal = {FEMS microbiology letters}, volume = {363}, number = {19}, pages = {}, doi = {10.1093/femsle/fnw211}, pmid = {27609232}, issn = {1574-6968}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial ; Lysogeny ; Penicillinase/genetics ; *Plasmids ; Prophages/genetics/physiology ; Staphylococcal Infections/microbiology ; Staphylococcus Phages/*genetics/physiology ; Staphylococcus aureus/*genetics/virology ; Tetracycline/pharmacology ; *Transduction, Genetic ; }, abstract = {The transduction mediated by bacteriophages is considered to be one of the primary driving forces in horizontal gene transfer in staphylococci, which is crucial to their adaptation and successful evolution. For a transduction to be effective, it is generally accepted that the recipient strain should be susceptible to the transducing phage. In this study, we demonstrate that the plasmid DNAs are effectively transduced into the recipient Staphylococcus aureus strains in spite of their insensitivity to the lytic action of the transducing phage, provided that these phages adsorb effectively to the bacterial cells. The tetracycline and penicillinase plasmids were transduced to insensitive laboratory and clinical strains by bacteriophages ϕ29, ϕ52A and ϕ80α as well as by prophage ϕ53 and naturally occurring prophages induced from donor lysogenic strains. Comparable frequencies of transduction were achieved in both phage-sensitive and phage-insensitive recipient strains. We have demonstrated that such mechanisms as the restriction of DNA and lysogenic immunity which are responsible for insensitivity of cells to phages may not be a barrier to the transfer, maintenance and effective spread of plasmids to a wider range of potential recipients in the staphylococcal population.}, }
@article {pmid27609231, year = {2016}, author = {Ter Kuile, BH and Kraupner, N and Brul, S}, title = {The risk of low concentrations of antibiotics in agriculture for resistance in human health care.}, journal = {FEMS microbiology letters}, volume = {363}, number = {19}, pages = {}, doi = {10.1093/femsle/fnw210}, pmid = {27609231}, issn = {1574-6968}, mesh = {*Agriculture ; Agrochemicals/*analysis/*pharmacology ; Animals ; Anti-Bacterial Agents/administration &amp; dosage/*analysis/*pharmacology ; Drug Dosage Calculations ; Drug Resistance, Microbial/*genetics ; Food Chain ; Food Microbiology ; Gene Transfer, Horizontal ; Humans ; Symbiosis ; Zoonoses ; }, abstract = {The contribution of antibiotic resistance originally selected for in the agricultural sector to resistance in human pathogens is not known exactly, but is unlikely to be negligible. It is estimated that 50% to 80% of all antibiotics used are applied in agriculture and the remainder for treating infections in humans. Since dosing regimens are less controlled in agriculture than in human health care, veterinary and environmental microbes are often exposed to sublethal levels of antibiotics. Exposure to sublethal drug concentrations must be considered a risk factor for de novo resistance, transfer of antimicrobial resistant (AMR) genes, and selection for already existing resistance. Resistant zoonotic agents and commensal strains carrying AMR genes reach the human population by a variety of routes, foodstuffs being only one of these. Based on the present knowledge, short treatments with the highest dose that does not cause unacceptable side-effects may be optimal for achieving therapeutic goals while minimizing development of resistance. Novel approaches such as combination or alternating therapy are promising, but need to be explored further before they can be implemented in daily practice.}, }
@article {pmid27609049, year = {2017}, author = {Wang, Y and Lo, WU and Lai, RW and Tse, CW and Lee, RA and Luk, WK and Cheng, VC and Que, TL and Chow, KH and Ho, PL}, title = {IncN ST7 epidemic plasmid carrying blaIMP-4 in Enterobacteriaceae isolates with epidemiological links to multiple geographical areas in China.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {72}, number = {1}, pages = {99-103}, doi = {10.1093/jac/dkw353}, pmid = {27609049}, issn = {1460-2091}, mesh = {Aged ; Aged, 80 and over ; Cross Infection/epidemiology/*microbiology ; Enterobacteriaceae/*enzymology/genetics/isolation &amp; purification ; Enterobacteriaceae Infections/epidemiology/*microbiology ; Female ; Gene Transfer, Horizontal ; Hong Kong/epidemiology ; Humans ; Infant ; Male ; Middle Aged ; Plasmids/*analysis/classification ; Retrospective Studies ; Sequence Alignment ; Sequence Analysis, DNA ; *Topography, Medical ; }, abstract = {OBJECTIVES: To characterize blaIMP-4-carrying plasmids originating from inpatients in Hong Kong.<br><br>METHODS: Sixteen blaIMP-4-carrying plasmids identified among Enterobacteriaceae (nine Escherichia coli, four Klebsiella pneumoniae, two Citrobacter freundii and one Enterobacter cloacae) recovered from 15 patients were characterized. The isolates, collected during January 2010 to December 2013, were retrospectively investigated by plasmid sequencing, molecular and fitness studies.<br><br>RESULTS: The blaIMP-4-carrying plasmids belonged to the IncN ST7 lineage (&#x223c;50 kb). Twelve of the 16 plasmids were epidemiologically linked to seven different regions in China. Alignment of the complete plasmid sequences showed identical plasmid backbones and two highly similar resistance regions, each carrying one of two resistance genes (blaIMP-4 and qnrS1). The blaIMP-4 was detected in a class 1 integron (containing blaIMP-4 and intron Kl.pn.13) that is part of an IS6100-IS26 transposon-like structure. The nine E. coli carrying the epidemic plasmid belonged to multiple multilocus STs (six ST542, one ST131, one ST657 and one ST3177). Fitness assays performed on E. coli J53 recipients showed that the presence of the epidemic plasmid did not have a significant biological cost.<br><br>CONCLUSIONS: This study identified a blaIMP-4-carrying IncN ST7 plasmid disseminated among multiple enterobacterial species originating from patients with epidemiological links to different regions in China.}, }
@article {pmid27608044, year = {2016}, author = {Bininda-Emonds, OR and Hinz, C and Ahlrichs, WH}, title = {Evidence Supporting the Uptake and Genomic Incorporation of Environmental DNA in the "Ancient Asexual" Bdelloid Rotifer Philodina roseola.}, journal = {Life (Basel, Switzerland)}, volume = {6}, number = {3}, pages = {}, pmid = {27608044}, issn = {2075-1729}, abstract = {Increasing evidence suggests that bdelloid rotifers regularly undergo horizontal gene transfer, apparently as a surrogate mechanism of genetic exchange in the absence of true sexual reproduction, in part because of their ability to withstand desiccation. We provide empirical support for this latter hypothesis using the bdelloid Philodina roseola, which we demonstrate to readily internalize environmental DNA in contrast to a representative monogonont rotifer (Brachionus rubens), which, like other monogononts, is facultative sexual and cannot withstand desiccation. In addition, environmental DNA that was more similar to the host DNA was retained more often and for a longer period of time. Indirect evidence (increased variance in the reproductive output of the untreated F1 generation) suggests that environmental DNA can be incorporated into the genome during desiccation and is thus heritable. Our observed fitness effects agree with sexual theory and also occurred when the animals were desiccated in groups (thereby acting as DNA donors), but not individually, indicating the mechanism could occur in nature. Thus, although DNA uptake and its genomic incorporation appears proximally related to anhydrobiosis in bdelloids, it might also facilitate accidental genetic exchange with closely related taxa, thereby maintaining higher levels of genetic diversity than is otherwise expected for this group of "ancient asexuals".}, }
@article {pmid27605596, year = {2017}, author = {Pinholt, M and Gumpert, H and Bayliss, S and Nielsen, JB and Vorobieva, V and Pedersen, M and Feil, E and Worning, P and Westh, H}, title = {Genomic analysis of 495 vancomycin-resistant Enterococcus faecium reveals broad dissemination of a vanA plasmid in more than 19 clones from Copenhagen, Denmark.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {72}, number = {1}, pages = {40-47}, doi = {10.1093/jac/dkw360}, pmid = {27605596}, issn = {1460-2091}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Bacterial Proteins/*genetics ; Carbon-Oxygen Ligases/*genetics ; Child ; Child, Preschool ; DNA Transposable Elements ; Denmark/epidemiology ; Enterococcus faecium/classification/*genetics/isolation &amp; purification ; Female ; Gene Transfer, Horizontal ; *Genetic Variation ; Genotype ; Gram-Positive Bacterial Infections/epidemiology/*microbiology ; Humans ; Male ; Middle Aged ; Molecular Epidemiology ; Molecular Typing ; Phylogeny ; Plasmids/*analysis ; Sequence Analysis, DNA ; Vancomycin-Resistant Enterococci/classification/*genetics/isolation &amp; purification ; Young Adult ; }, abstract = {OBJECTIVES: From 2012 to 2014, there has been a huge increase in vancomycin-resistant (vanA) Enterococcus faecium (VREfm) in Copenhagen, Denmark, with 602 patients infected or colonized with VREfm in 2014 compared with just 22 in 2012. The objective of this study was to describe the genetic epidemiology of VREfm to assess the contribution of clonal spread and horizontal transfer of the vanA transposon (Tn1546) and plasmid in the dissemination of VREfm in hospitals.<br><br>METHODS: VREfm from Copenhagen, Denmark (2012-14) were whole-genome sequenced. The clonal structure was determined and the structure of Tn1546-like transposons was characterized. One VREfm isolate belonging to the largest clonal group was sequenced using long-read technology to close a 37 kb vanA plasmid.<br><br>RESULTS: Phylogeny revealed a polyclonal structure where 495 VREfm isolates were divided into 13 main groups and 7 small groups. The majority of the isolates were located in three groups (n&#x200a;=&#x200a;44, 100 and 218) and clonal spread of VREfm between wards and hospitals was identified. Five Tn1546-like transposon types were identified. A dominant truncated transposon (type 4, 92%) was spread across all but one VREfm group. The closed vanA plasmid was highly covered by reads from isolates containing the type 4 transposon.<br><br>CONCLUSIONS: This study suggests that it was the dissemination of the type 4 Tn1546-like transposon and plasmid via horizontal transfer to multiple populations of E. faecium, followed by clonal spread of new VREfm clones, that contributed to the increase in and diversity of VREfm in Danish hospitals.}, }
@article {pmid27604878, year = {2016}, author = {Gilbert, MJ and Miller, WG and Yee, E and Kik, M and Zomer, AL and Wagenaar, JA and Duim, B}, title = {Comparative Genomics of Campylobacter iguaniorum to Unravel Genetic Regions Associated with Reptilian Hosts.}, journal = {Genome biology and evolution}, volume = {8}, number = {9}, pages = {3022-3029}, pmid = {27604878}, issn = {1759-6653}, mesh = {Animals ; Base Composition ; Campylobacter/classification/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Host-Pathogen Interactions/genetics ; Reptiles/microbiology ; Selection, Genetic ; }, abstract = {Campylobacter iguaniorum is most closely related to the species C fetus, C hyointestinalis, and C lanienae Reptiles, chelonians and lizards in particular, appear to be a primary reservoir of this Campylobacter species. Here we report the genome comparison of C iguaniorum strain 1485E, isolated from a bearded dragon (Pogona vitticeps), and strain 2463D, isolated from a green iguana (Iguana iguana), with the genomes of closely related taxa, in particular with reptile-associated C fetus subsp. testudinum In contrast to C fetus, C iguaniorum is lacking an S-layer encoding region. Furthermore, a defined lipooligosaccharide biosynthesis locus, encoding multiple glycosyltransferases and bounded by waa genes, is absent from C iguaniorum Instead, multiple predicted glycosylation regions were identified in C iguaniorum One of these regions is > 50 kb with deviant G + C content, suggesting acquisition via lateral transfer. These similar, but non-homologous glycosylation regions were located at the same position on the genome in both strains. Multiple genes encoding respiratory enzymes not identified to date within the C. fetus clade were present. C iguaniorum shared highest homology with C hyointestinalis and C fetus. As in reptile-associated C fetus subsp. testudinum, a putative tricarballylate catabolism locus was identified. However, despite colonizing a shared host, no recent recombination between both taxa was detected. This genomic study provides a better understanding of host adaptation, virulence, phylogeny, and evolution of C iguaniorum and related Campylobacter taxa.}, }
@article {pmid27601577, year = {2016}, author = {Aviv, G and Rahav, G and Gal-Mor, O}, title = {Horizontal Transfer of the Salmonella enterica Serovar Infantis Resistance and Virulence Plasmid pESI to the Gut Microbiota of Warm-Blooded Hosts.}, journal = {mBio}, volume = {7}, number = {5}, pages = {}, pmid = {27601577}, issn = {2150-7511}, mesh = {Animals ; Conjugation, Genetic/drug effects/radiation effects ; Disease Models, Animal ; *Drug Resistance, Bacterial ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; *Gene Transfer, Horizontal ; Mice ; *Plasmids ; Salmonella Infections/microbiology ; Salmonella enterica/*genetics ; Virulence ; }, abstract = {UNLABELLED: Salmonella enterica serovar Infantis is one of the prevalent salmonellae worldwide. Recently, we showed that the emergence of S Infantis in Israel was facilitated by the acquisition of a unique megaplasmid (pESI) conferring multidrug resistance and increased virulence phenotypes. Here we elucidate the ecology, transmission properties, and regulation of pESI. We show that despite its large size (~280 kb), pESI does not impose a significant metabolic burden in vitro and that it has been recently fixed in the domestic S Infantis population. pESI conjugation and the transcription of its pilus (pil) genes are inhibited at the ambient temperature (27°C) and by ≥1% bile but increased under temperatures of 37 to 41°C, oxidative stress, moderate osmolarity, and the microaerobic conditions characterizing the intestinal environment of warm-blooded animals. The pESI-encoded protein TraB and the oxygen homeostasis regulator Fnr were identified as transcriptional regulators of pESI conjugation. Using the mouse model, we show that following S Infantis infection, pESI can be horizontally transferred to the gut microbiota, including to commensal Escherichia coli strains. Possible transfer, but not persistence, of pESI was also observed into Gram-positive mouse microbiota species, especially Lactobacillus reuteri Moreover, pESI was demonstrated to further disseminate from gut microbiota to S. enterica serovar Typhimurium, in the context of gastrointestinal infection. These findings exhibit the ability of a selfish clinically relevant megaplasmid to distribute to and from the microbiota and suggest an overlooked role of the microbiota as a reservoir of mobile genetic elements and intermediator in the spread of resistance and virulence genes between commensals and pathogenic bacteria.<br><br>IMPORTANCE: Plasmid conjugation plays a key role in microbial evolution, enabling the acquisition of new phenotypes, including resistance and virulence. Salmonella enterica serovar Infantis is one of the ubiquitous salmonellae worldwide and a major cause of foodborne infections. Previously, we showed that the emergence of S&#xa0;Infantis in Israel has involved the acquisition of a unique megaplasmid (pESI) conferring multidrug resistance and increased virulence phenotypes. Recently, the emergence of another S&#xa0;Infantis strain carrying a pESI-like plasmid was identified in Italy, suggesting that the acquisition of pESI may be common to different emergent S&#xa0;Infantis populations globally. Transmission of this plasmid to other strains or bacterial species is an alarming scenario. Understanding the ecology, regulation, and transmission properties of clinically relevant plasmids and the role of the microbiota in their spreading offers a new mechanism explaining the emergence of new pathogenic and resistant biotypes and may assist in the development of appropriate surveillance and prevention measures.}, }
@article {pmid27600442, year = {2016}, author = {Willems, M and Lord, E and Laforest, L and Labelle, G and Lapointe, FJ and Di Sciullo, AM and Makarenkov, V}, title = {Using hybridization networks to retrace the evolution of Indo-European languages.}, journal = {BMC evolutionary biology}, volume = {16}, number = {1}, pages = {180}, pmid = {27600442}, issn = {1471-2148}, mesh = {Algorithms ; Computational Biology ; Databases, Factual ; Europe ; India ; *Language ; Linguistics ; *Models, Theoretical ; Phylogeny ; }, abstract = {BACKGROUND: Curious parallels between the processes of species and language evolution have been observed by many researchers. Retracing the evolution of Indo-European (IE) languages remains one of the most intriguing intellectual challenges in historical linguistics. Most of the IE language studies use the traditional phylogenetic tree model to represent the evolution of natural languages, thus not taking into account reticulate evolutionary events, such as language hybridization and word borrowing which can be associated with species hybridization and horizontal gene transfer, respectively. More recently, implicit evolutionary networks, such as split graphs and minimal lateral networks, have been used to account for reticulate evolution in linguistics.<br><br>RESULTS: Striking parallels existing between the evolution of species and natural languages allowed us to apply three computational biology methods for reconstruction of phylogenetic networks to model the evolution of IE languages. We show how the transfer of methods between the two disciplines can be achieved, making necessary methodological adaptations. Considering basic vocabulary data from the well-known Dyen's lexical database, which contains word forms in 84&#xa0;IE languages for the meanings of a 200-meaning Swadesh list, we adapt a recently developed computational biology algorithm for building explicit hybridization networks to study the evolution of IE languages and compare our findings to the results provided by the split graph and galled network methods.<br><br>CONCLUSION: We conclude that explicit phylogenetic networks can be successfully used to identify donors and recipients of lexical material as well as the degree of influence of each donor language on the corresponding recipient languages. We show that our algorithm is well suited to detect reticulate relationships among languages, and present some historical and linguistic justification for the results obtained. Our findings could be further refined if relevant syntactic, phonological and morphological data could be analyzed along with the available lexical data.}, }
@article {pmid27600408, year = {2016}, author = {Cao, L and Gao, CH and Zhu, J and Zhao, L and Wu, Q and Li, M and Sun, B}, title = {Identification and functional study of type III-A CRISPR-Cas systems in clinical isolates of Staphylococcus aureus.}, journal = {International journal of medical microbiology : IJMM}, volume = {306}, number = {8}, pages = {686-696}, doi = {10.1016/j.ijmm.2016.08.005}, pmid = {27600408}, issn = {1618-0607}, mesh = {*CRISPR-Cas Systems ; Gene Order ; Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; Sequence Analysis, DNA ; Staphylococcal Infections/microbiology ; Staphylococcus aureus/*enzymology/*genetics/isolation &amp; purification ; Transcription, Genetic ; Transformation, Bacterial ; }, abstract = {The CRISPR-Cas (clustered regularly interspaced short palindromic repeats [CRISPR]-CRISPR associated proteins [Cas]) system can provide prokaryote with immunity against invading mobile genetic elements (MGEs) such as phages and plasmids, which are the main sources of staphylococcal accessory genes. To date, only a few Staphylococcus aureus strains containing CRISPR-Cas systems have been identified, but no functional study in these strains has been reported. In this study, 6 clinical isolates of S. aureus with type III-A CRISPR-Cas systems were identified, and whole-genome sequencing and functional study were conducted subsequently. Genome sequence analysis revealed a close linkage between the CRISPR-Cas system and the staphylococcal cassette chromosome mec (SCCmec) element in five strains. Comparative sequence analysis showed that the type III-A repeats are conserved within staphylococci, despite of the decreased conservation in trailer-end repeats. Highly homologous sequences of some spacers were identified in staphylococcal MGEs, and partially complementary sequences of spacers were mostly found in the coding strand of lytic regions in staphylococcal phages. Transformation experiments showed that S. aureus type III-A CRISPR-Cas system can specifically prevent plasmid transfer in a transcription-dependent manner. Base paring between crRNA and target sequence, the endoribonuclease, and the Csm complex were proved to be necessary for type III-A CRISPR-Cas immunity.}, }
@article {pmid27598571, year = {2016}, author = {Qian, X and Sun, W and Gu, J and Wang, XJ and Zhang, YJ and Duan, ML and Li, HC and Zhang, RR}, title = {Reducing antibiotic resistance genes, integrons, and pathogens in dairy manure by continuous thermophilic composting.}, journal = {Bioresource technology}, volume = {220}, number = {}, pages = {425-432}, doi = {10.1016/j.biortech.2016.08.101}, pmid = {27598571}, issn = {1873-2976}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Biodegradation, Environmental ; Drug Resistance, Microbial/*genetics ; *Genes, Bacterial ; *Integrons ; Manure/*microbiology ; Nucleic Acid Denaturation ; Sequence Analysis, DNA ; *Soil Microbiology ; Temperature ; }, abstract = {This study explored the effects of composting using three temperature regimes, namely, insufficient thermophilic composting (ITC), normal thermophilic composting (NTC), and continuous thermophilic composting (CTC), on antibiotic resistance genes (ARGs), integrons, and human pathogenic bacteria (HPB), as well as the mechanisms involved. The NTC and CTC treatments led to greater decreases in 5/10 ARGs and two integrons than ITC, and the abundances of ARGs (tetC, tetG, and tetQ) and int1 only declined in the NTC and CTC treatments. The abundances of HPB decreased by 82.8%, 76.9%, and 96.9% under ITC, NTC, CTC, respectively. Redundancy analysis showed that both bacterial succession and horizontal gene transfer play important roles in the variation of ARGs, and the changes in different ARGs were due to diverse mechanisms. CTC performed significantly better at reducing ARGs, integrons, and HPB, thus it may be used to manage the public health risks of ARGs in animal manure.}, }
@article {pmid27596223, year = {2016}, author = {Adel, M and Elbehery, AH and Aziz, SK and Aziz, RK and Grossart, HP and Siam, R}, title = {Viruses-to-mobile genetic elements skew in the deep Atlantis II brine pool sediments.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {32704}, pmid = {27596223}, issn = {2045-2322}, mesh = {*Genes, Viral ; Geologic Sediments ; *Interspersed Repetitive Sequences ; *Metagenome ; Phylogeny ; *Seawater ; Viruses/*genetics ; }, abstract = {The central rift of the Red Sea has 25 brine pools with different physical and geochemical characteristics. Atlantis II (ATIID), Discovery Deeps (DD) and Chain Deep (CD) are characterized by high salinity, temperature and metal content. Several studies reported microbial communities in these brine pools, but few studies addressed the brine pool sediments. Therefore, sediment cores were collected from ATIID, DD, CD brine pools and an adjacent brine-influenced site. Sixteen different lithologic sediment sections were subjected to shotgun DNA pyrosequencing to generate 1.47 billion base pairs (1.47 × 10(9) bp). We generated sediment-specific reads and attempted to annotate all reads. We report the phylogenetic and biochemical uniqueness of the deepest ATIID sulfur-rich brine pool sediments. In contrary to all other sediment sections, bacteria dominate the deepest ATIID sulfur-rich brine pool sediments. This decrease in virus-to-bacteria ratio in selected sections and depth coincided with an overrepresentation of mobile genetic elements. Skewing in the composition of viruses-to-mobile genetic elements may uniquely contribute to the distinct microbial consortium in sediments in proximity to hydrothermally active vents of the Red Sea and possibly in their surroundings, through differential horizontal gene transfer.}, }
@article {pmid27595771, year = {2016}, author = {Gómez-Garzón, C and Hernández-Santana, A and Dussán, J}, title = {Comparative genomics reveals Lysinibacillus sphaericus group comprises a novel species.}, journal = {BMC genomics}, volume = {17}, number = {1}, pages = {709}, pmid = {27595771}, issn = {1471-2164}, mesh = {Bacillus/*classification/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial ; Genomics/*methods ; Phylogeny ; Sequence Analysis, DNA/*methods ; Species Specificity ; }, abstract = {BACKGROUND: Early in the 1990s, it was recognized that Lysinibacillus sphaericus, one of the most popular and effective entomopathogenic bacteria, was a highly heterogeneous group. Many authors have even proposed it comprises more than one species, but the lack of phenotypic traits that guarantee an accurate differentiation has not allowed this issue to be clarified. Now that genomic technologies are rapidly advancing, it is possible to address the problem from a whole genome perspective, getting insights into the phylogeny, evolutive history and biology itself.<br><br>RESULTS: The genome of the Colombian strain L. sphaericus OT4b.49 was sequenced, assembled and annotated, obtaining 3 chromosomal contigs and no evidence of plasmids. Using these sequences and the 13 other L. sphaericus genomes available on the NCBI database, we carried out comparative genomic analyses that included whole genome alignments, searching for mobile elements, phylogenomic metrics (TETRA, ANI and in-silico DDH) and pan-genome assessments. The results support the hypothesis about this species as a very heterogeneous group. The entomopathogenic lineage is actually a single and independent species with 3728 core genes and 2153 accessory genes, whereas each non-toxic strain seems to be a separate species, though without a clear circumscription. Toxin-encoding genes, binA, B and mtx1, 2, 3 could be acquired via horizontal gene transfer in a single evolutionary event. The non-toxic strain OT4b.31 is the most related with the type strain KCTC 3346.<br><br>CONCLUSIONS: The current L. sphaericus is actually a sensu lato due to a sub-estimation of diversity accrued using traditional non-genomics based classification strategies. The toxic lineage is the most studied with regards to its larvicidal activity, which is a greatly conserved trait among these strains and thus, their differentiating feature. Further studies are needed in order to establish a univocal classification of the non-toxic strains that, according to our results, seem to be a paraphyletic group.}, }
@article {pmid27595093, year = {2016}, author = {Warrier, I and Walter, MC and Frangoulidis, D and Raghavan, R and Hicks, LD and Minnick, MF}, title = {The Intervening Sequence of Coxiella burnetii: Characterization and Evolution.}, journal = {Frontiers in cellular and infection microbiology}, volume = {6}, number = {}, pages = {83}, pmid = {27595093}, issn = {2235-2988}, support = {R21 AI078125/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Base Sequence ; Coxiella burnetii/*genetics/growth &amp; development/metabolism ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Escherichia coli/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Introns ; Nucleic Acid Conformation ; Phylogeny ; Protein Structure, Secondary ; Q Fever/microbiology ; RNA Splicing ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/*genetics ; Ribonuclease III/genetics ; }, abstract = {The intervening sequence (IVS) of Coxiella burnetii, the agent of Q fever, is a 428-nt selfish genetic element located in helix 45 of the precursor 23S rRNA. The IVS element, in turn, contains an ORF that encodes a hypothetical ribosomal S23 protein (S23p). Although S23p can be synthesized in vitro in the presence of an engineered E. coli promoter and ribosome binding site, results suggest that the protein is not synthesized in vivo. In spite of a high degree of IVS conservation among different strains of C. burnetii, the region immediately upstream of the S23p start codon is prone to change, and the S23p-encoding ORF is evidently undergoing reductive evolution. We determined that IVS excision from 23S rRNA was mediated by RNase III, and IVS RNA was rapidly degraded, thereafter. Levels of the resulting 23S rRNA fragments that flank the IVS, F1 (~1.2 kb) and F2 (~1.7 kb), were quantified over C. burnetii's logarithmic growth phase (1-5 d). Results showed that 23S F1 quantities were consistently higher than those of F2 and 16S rRNA. The disparity between levels of the two 23S rRNA fragments following excision of IVS is an interesting phenomenon of unknown significance. Based upon phylogenetic analyses, IVS was acquired through horizontal transfer after C. burnetii's divergence from an ancestral bacterium and has been subsequently maintained by vertical transfer. The widespread occurrence, maintenance and conservation of the IVS in C. burnetii imply that it plays an adaptive role or has a neutral effect on fitness.}, }
@article {pmid27593176, year = {2017}, author = {van Duin, D and Doi, Y}, title = {The global epidemiology of carbapenemase-producing Enterobacteriaceae.}, journal = {Virulence}, volume = {8}, number = {4}, pages = {460-469}, pmid = {27593176}, issn = {2150-5608}, support = {R21 AI114508/AI/NIAID NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; }, mesh = {Carbapenem-Resistant Enterobacteriaceae/*isolation &amp; purification ; Disease Transmission, Infectious ; Enterobacteriaceae Infections/*epidemiology/*microbiology/transmission ; Gene Transfer, Horizontal ; Global Health ; Humans ; *Pandemics ; }, abstract = {Carbapenemase-producing Enterobacteriaceae (CPE) are an important and increasing threat to global health. Both clonal spread and plasmid-mediated transmission contribute to the ongoing rise in incidence of these bacteria. Among the 4 classes of β-lactamases defined by the Ambler classification system, the carbapenemases that confer carbapenem resistance in Enterobacteriaceae belong to 3 of them: Class A (K. pneumoniae carbapenemases, KPC), Class B (metallo-β-lactamases, MBL including New Delhi metallo-β-lactamases, NDM) and Class D (OXA-48-like carbapenemases). KPC-producing CPE are the most commonly occurring CPE in the United States. MBL-producing CPE have been most commonly associated with the Indian Subcontinent as well as with specific countries in Europe, including Romania, Denmark, Spain, and Hungary. The epicenter of OXA-48-like-producing is in Turkey and surrounding countries. Detailed knowledge of the epidemiology and molecular characteristics of CPE is essential to stem the spread of these pathogens.}, }
@article {pmid27592346, year = {2017}, author = {Olsson, S and Penacho, V and Puente-Sánchez, F and Díaz, S and Gonzalez-Pastor, JE and Aguilera, A}, title = {Horizontal Gene Transfer of Phytochelatin Synthases from Bacteria to Extremophilic Green Algae.}, journal = {Microbial ecology}, volume = {73}, number = {1}, pages = {50-60}, pmid = {27592346}, issn = {1432-184X}, mesh = {Aminoacyltransferases/*genetics ; Cadmium/*pharmacology ; Chlamydomonas/*genetics/metabolism ; Escherichia coli/*drug effects/*genetics ; Extremophiles/*genetics ; Polymerase Chain Reaction ; Water Pollutants/pharmacology ; Water Pollution, Chemical ; }, abstract = {Transcriptomic sequencing together with bioinformatic analyses and an automated annotation process led us to identify novel phytochelatin synthase (PCS) genes from two extremophilic green algae (Chlamydomonas acidophila and Dunaliella acidophila). These genes are of intermediate length compared to known PCS genes from eukaryotes and PCS-like genes from prokaryotes. A detailed phylogenetic analysis gives new insight into the complicated evolutionary history of PCS genes and provides evidence for multiple horizontal gene transfer events from bacteria to eukaryotes within the gene family. A separate subgroup containing PCS-like genes within the PCS gene family is not supported since the PCS genes are monophyletic only when the PCS-like genes are included. The presence and functionality of the novel genes in the organisms were verified by genomic sequencing and qRT-PCR. Furthermore, the novel PCS gene in Chlamydomonas acidophila showed very strong induction by cadmium. Cloning and expression of the gene in Escherichia coli clearly improves its cadmium resistance. The gene in Dunaliella was not induced, most likely due to gene duplication.}, }
@article {pmid27591293, year = {2017}, author = {Di Luca, MC and Sørum, V and Starikova, I and Kloos, J and Hülter, N and Naseer, U and Johnsen, PJ and Samuelsen, &#xd8;}, title = {Low biological cost of carbapenemase-encoding plasmids following transfer from Klebsiella pneumoniae to Escherichia coli.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {72}, number = {1}, pages = {85-89}, doi = {10.1093/jac/dkw350}, pmid = {27591293}, issn = {1460-2091}, mesh = {Bacterial Proteins/*genetics/*metabolism ; *Gene Transfer, Horizontal ; Genomic Instability ; Klebsiella pneumoniae/*genetics ; *Plasmids ; Transformation, Bacterial ; Uropathogenic Escherichia coli/*drug effects/genetics/*growth &amp; development ; Virulence ; beta-Lactamases/*genetics/*metabolism ; }, abstract = {OBJECTIVES: The objective of this study was to determine the biological cost, stability and sequence of two carbapenemase-encoding plasmids containing blaKPC-2 (pG12-KPC-2) and blaVIM-1 (pG06-VIM-1) isolated from Klebsiella pneumoniae when newly acquired by uropathogenic Escherichia coli clinical isolates of different genetic backgrounds.<br><br>METHODS: The two plasmids were transferred into plasmid-free E. coli clinical isolates by transformation. The fitness effect of newly acquired plasmids on the host cell was assessed in head-to-head competitions with the corresponding isogenic strain. Plasmid stability was estimated by propagating monocultures for &#x223c;312 generations. Plasmid nucleotide sequences were determined using next-generation sequencing technology. Assembly, gap closure, annotation and comparative analyses were performed.<br><br>RESULTS: Both plasmids were stably maintained in three of four E. coli backgrounds and resulted in low to moderate reductions in host fitness ranging from 1.1% to 3.6%. A difference in fitness cost was observed for pG12-KPC-2 between two different genetic backgrounds, while no difference was detected for pG06-VIM-1 between three different genetic backgrounds. In addition, a difference was observed between pG12-KPC-2 and pG06-VIM-1 in the same genetic background. In general, the magnitude of biological cost of plasmid carriage was both host and plasmid dependent. The sequences of the two plasmids showed high backbone similarity to previously circulating plasmids in K. pneumoniae.<br><br>CONCLUSIONS: The low to modest fitness cost of newly acquired and stably maintained carbapenemase-encoding plasmids in E. coli indicates a potential for establishment and further dissemination into other Enterobacteriaceae species. We also show that the fitness cost is both plasmid and host specific.}, }
@article {pmid27587679, year = {2016}, author = {Trappe, K and Marschall, T and Renard, BY}, title = {Detecting horizontal gene transfer by mapping sequencing reads across species boundaries.}, journal = {Bioinformatics (Oxford, England)}, volume = {32}, number = {17}, pages = {i595-i604}, doi = {10.1093/bioinformatics/btw423}, pmid = {27587679}, issn = {1367-4811}, mesh = {Chromosome Mapping/*methods ; Computational Biology/methods ; *Gene Transfer, Horizontal ; Genome ; *High-Throughput Nucleotide Sequencing ; *Phylogeny ; }, abstract = {MOTIVATION: Horizontal gene transfer (HGT) is a fundamental mechanism that enables organisms such as bacteria to directly transfer genetic material between distant species. This way, bacteria can acquire new traits such as antibiotic resistance or pathogenic toxins. Current bioinformatics approaches focus on the detection of past HGT events by exploring phylogenetic trees or genome composition inconsistencies. However, these techniques normally require the availability of finished and fully annotated genomes and of sufficiently large deviations that allow detection and are thus not widely applicable. Especially in outbreak scenarios with HGT-mediated emergence of new pathogens, like the enterohemorrhagic Escherichia coli outbreak in Germany 2011, there is need for fast and precise HGT detection. Next-generation sequencing (NGS) technologies facilitate rapid analysis of unknown pathogens but, to the best of our knowledge, so far no approach detects HGTs directly from NGS reads.<br><br>RESULTS: We present Daisy, a novel mapping-based tool for HGT detection. Daisy determines HGT boundaries with split-read mapping and evaluates candidate regions relying on read pair and coverage information. Daisy successfully detects HGT regions with base pair resolution in both simulated and real data, and outperforms alternative approaches using a genome assembly of the reads. We see our approach as a powerful complement for a comprehensive analysis of HGT in the context of NGS data.<br><br>Daisy is freely available from http://github.com/ktrappe/daisy<br><br>CONTACT: renardb@rki.de<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid27583185, year = {2016}, author = {Ramsay, JP and Kwong, SM and Murphy, RJ and Yui Eto, K and Price, KJ and Nguyen, QT and O'Brien, FG and Grubb, WB and Coombs, GW and Firth, N}, title = {An updated view of plasmid conjugation and mobilization in Staphylococcus.}, journal = {Mobile genetic elements}, volume = {6}, number = {4}, pages = {e1208317}, pmid = {27583185}, issn = {2159-2543}, abstract = {The horizontal gene transfer facilitated by mobile genetic elements impacts almost all areas of bacterial evolution, including the accretion and dissemination of antimicrobial-resistance genes in the human and animal pathogen Staphylococcus aureus. Genome surveys of staphylococcal plasmids have revealed an unexpected paucity of conjugation and mobilization loci, perhaps suggesting that conjugation plays only a minor role in the evolution of this genus. In this letter we present the DNA sequences of historically documented staphylococcal conjugative plasmids and highlight that at least 3 distinct and widely distributed families of conjugative plasmids currently contribute to the dissemination of antimicrobial resistance in Staphylococcus. We also review the recently documented "relaxase-in trans" mechanism of conjugative mobilization facilitated by conjugative plasmids pWBG749 and pSK41, and discuss how this may facilitate the horizontal transmission of around 90% of plasmids that were previously considered non-mobilizable. Finally, we enumerate unique sequenced S. aureus plasmids with a potential mechanism of mobilization and predict that at least 80% of all non-conjugative S. aureus plasmids are mobilizable by at least one mechanism. We suggest that a greater research focus on the molecular biology of conjugation is essential if we are to recognize gene-transfer mechanisms from our increasingly in silico analyses.}, }
@article {pmid27581938, year = {2016}, author = {Mehra, V and Ghosh, TS and Mande, SS}, title = {Insights into horizontal acquisition patterns of dormancy and reactivation regulon genes in mycobacterial species using a partitioning-based framework.}, journal = {Journal of biosciences}, volume = {41}, number = {3}, pages = {475-485}, pmid = {27581938}, issn = {0973-7138}, mesh = {Algorithms ; Burkholderia/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial ; Humans ; Mycobacterium tuberculosis/*genetics/pathogenicity ; Operon/genetics ; Phylogeny ; Tuberculosis/*genetics/microbiology ; }, abstract = {Horizontal Gene Transfer (HGT) events, initially thought to be rare in Mycobacterium tuberculosis, have recently been shown to be involved in the acquisition of virulence operons in M. tuberculosis. We have developed a new partitioning framework based HGT prediction algorithm, called Grid3M, and applied the same for the prediction of HGTs in Mycobacteria. Validation and testing using simulated and real microbial genomes indicated better performance of Grid3M as compared with other widely used HGT prediction methods. Specific analysis of the genes belonging to dormancy/reactivation regulons across 14 mycobacterial genomes indicated that horizontal acquisition is specifically restricted to important accessory proteins. The results also revealed Burkholderia species to be a probable source of HGT genes belonging to these regulons. The current study provides a basis for similar analyses investigating the functional/evolutionary aspects of HGT genes in other pathogens. A database of Grid3M predicted HGTs in completely sequenced genomes is available at https://metagenomics.atc.tcs.com/Grid3M/.}, }
@article {pmid27578962, year = {2016}, author = {Stenkova, AM and Bystritskaya, EP and Guzev, KV and Rakin, AV and Isaeva, MP}, title = {Molecular Evolution of the Yersinia Major Outer Membrane Protein C (OmpC).}, journal = {Evolutionary bioinformatics online}, volume = {12}, number = {}, pages = {185-191}, pmid = {27578962}, issn = {1176-9343}, abstract = {The genus Yersinia includes species with a wide range of eukaryotic hosts (from fish, insects, and plants to mammals and humans). One of the major outer membrane proteins, the porin OmpC, is preferentially expressed in the host gut, where osmotic pressure, temperature, and the concentrations of nutrients and toxic products are relatively high. We consider here the molecular evolution and phylogeny of Yersinia ompC. The maximum likelihood gene tree reflects the macroevolution processes occurring within the genus Yersinia. Positive selection and horizontal gene transfer are the key factors of ompC diversification, and intraspecies recombination was revealed in two Yersinia species. The impact of recombination on ompC evolution was different from that of another major porin gene, ompF, possibly due to the emergence of additional functions and conservation of the basic transport function. The predicted antigenic determinants of OmpC were located in rapidly evolving regions, which may indicate the evolutionary mechanisms of Yersinia adaptation to the host immune system.}, }
@article {pmid27576537, year = {2016}, author = {Joseph, SJ and Marti, H and Didelot, X and Read, TD and Dean, D}, title = {Tetracycline Selective Pressure and Homologous Recombination Shape the Evolution of Chlamydia suis: A Recently Identified Zoonotic Pathogen.}, journal = {Genome biology and evolution}, volume = {8}, number = {8}, pages = {2613-2623}, pmid = {27576537}, issn = {1759-6653}, support = {MR/K010174/1/MRC_/Medical Research Council/United Kingdom ; R01 AI098843/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Betaproteobacteria/drug effects/genetics ; Chlamydia/drug effects/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Homologous Recombination ; *Selection, Genetic ; Tetracycline/pharmacology ; Tetracycline Resistance/*genetics ; }, abstract = {Species closely related to the human pathogen Chlamydia trachomatis (Ct) have recently been found to cause zoonotic infections, posing a public health threat especially in the case of tetracycline resistant Chlamydia suis (Cs) strains. These strains acquired a tet(C)-containing cassette via horizontal gene transfer (HGT). Genomes of 11 Cs strains from various tissues were sequenced to reconstruct evolutionary pathway(s) for tet(C) HGT. Cs had the highest recombination rate of Chlamydia species studied to date. Admixture occurred among Cs strains and with Chlamydia muridarum but not with Ct Although in vitro tet(C) cassette exchange with Ct has been documented, in vivo evidence may require examining human samples from Ct and Cs co-infected sites. Molecular-clock dating indicated that ancestral clades of resistant Cs strains predated the 1947 discovery of tetracycline, which was subsequently used in animal feed. The cassette likely spread throughout Cs strains by homologous recombination after acquisition from an external source, and our analysis suggests Betaproteobacteria as the origin. Selective pressure from tetracycline may be responsible for recent bottlenecks in Cs populations. Since tetracycline is an important antibiotic for treating Ct, zoonotic infections at mutual sites of infection indicate the possibility for cassette transfer and major public health repercussions.}, }
@article {pmid27575913, year = {2017}, author = {Khalil, MAF and Elgaml, A and El-Mowafy, M}, title = {Emergence of Multidrug-Resistant New Delhi Metallo-β-Lactamase-1-Producing Klebsiella pneumoniae in Egypt.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {23}, number = {4}, pages = {480-487}, doi = {10.1089/mdr.2016.0003}, pmid = {27575913}, issn = {1931-8448}, mesh = {Anti-Bacterial Agents/pharmacology ; Carbapenems/pharmacology ; DNA, Bacterial/*genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Egypt/epidemiology ; Female ; Gene Expression ; Gene Transfer, Horizontal ; Humans ; Integrons ; Klebsiella Infections/drug therapy/*epidemiology/microbiology/transmission ; Klebsiella pneumoniae/classification/*drug effects/genetics/isolation &amp; purification ; Male ; Microbial Sensitivity Tests ; Phylogeny ; Plasmids/chemistry/*metabolism ; beta-Lactamases/*genetics/metabolism ; }, abstract = {Despite expansion of the New Delhi metallo-β-lactamase-1 (NDM-1) worldwide, the incident of outbreaks regarding Egypt is still uncommon. In this survey, we denounce the emanation of multidrug-resistant NDM-1-producing Klebsiella pneumoniae in Egypt. We have reclaimed 46 unrepeatable carbapenem-resistant K. pneumoniae isolates at El-demerdash hospital, Ain Shams University, Cairo, Egypt. All the isolates showed a decreased sensitivity to imipenem and meropenem via the disc diffusion method. Among the isolates, 10 were proven as NDM-1 producers by utilizing the phenotypic methods (modified Hodge test and EDTA synergistic test) and specific PCR detection of NDM-1 encoding gene, blaNDM-1. The isolates hosting the blaNDM-1 showed an elevated resistance to several classes of β-lactam and non β-lactam antibiotics. All blaNDM-1-harboring isolates have showed positivity for one or more other plasmid-mediated bla genes; in addition, the isolates carried class 1 integron. Enterobacterial repetitive intergenic consensus (ERIC)-PCR results revealed that majority of the isolates, including the NDM-1 producers, are unrelated to each other. This highlights the danger of horizontal transfer of plasmids encoding for such carbapenemases, including NDM-1, between the isolates of K. pneumoniae. In summary, this study has confirmed the incidence of blaNDM-1 together with other bla genes among the K. pneumoniae isolates in Egypt. Control and prevention of infection can be achieved through early detection of resistance genes among bacterial isolates; through limiting the dispersal of these organisms.}, }
@article {pmid27573819, year = {2016}, author = {Husnik, F and McCutcheon, JP}, title = {Repeated replacement of an intrabacterial symbiont in the tripartite nested mealybug symbiosis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {37}, pages = {E5416-24}, pmid = {27573819}, issn = {1091-6490}, mesh = {Animals ; Betaproteobacteria/*genetics/growth &amp; development ; Gammaproteobacteria/*genetics/growth &amp; development ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial ; Phylogeny ; Planococcus Insect/genetics/*microbiology ; Sequence Analysis, DNA ; Symbiosis/*genetics ; }, abstract = {Stable endosymbiosis of a bacterium into a host cell promotes cellular and genomic complexity. The mealybug Planococcus citri has two bacterial endosymbionts with an unusual nested arrangement: the γ-proteobacterium Moranella endobia lives in the cytoplasm of the β-proteobacterium Tremblaya princeps These two bacteria, along with genes horizontally transferred from other bacteria to the P. citri genome, encode gene sets that form an interdependent metabolic patchwork. Here, we test the stability of this three-way symbiosis by sequencing host and symbiont genomes for five diverse mealybug species and find marked fluidity over evolutionary time. Although Tremblaya is the result of a single infection in the ancestor of mealybugs, the γ-proteobacterial symbionts result from multiple replacements of inferred different ages from related but distinct bacterial lineages. Our data show that symbiont replacement can happen even in the most intricate symbiotic arrangements and that preexisting horizontally transferred genes can remain stable on genomes in the face of extensive symbiont turnover.}, }
@article {pmid27573108, year = {2016}, author = {Pawluk, A and Staals, RH and Taylor, C and Watson, BN and Saha, S and Fineran, PC and Maxwell, KL and Davidson, AR}, title = {Inactivation of CRISPR-Cas systems by anti-CRISPR proteins in diverse bacterial species.}, journal = {Nature microbiology}, volume = {1}, number = {8}, pages = {16085}, pmid = {27573108}, issn = {2058-5276}, support = {MOP-130482//CIHR/Canada ; MOP-136845//CIHR/Canada ; }, mesh = {Bacteria/*enzymology ; Bacteriophages/*genetics ; *CRISPR-Cas Systems ; Enzyme Inhibitors/*metabolism ; Viral Proteins/genetics/*metabolism ; }, abstract = {CRISPR-Cas systems provide sequence-specific adaptive immunity against foreign nucleic acids(1,2). They are present in approximately half of all sequenced prokaryotes(3) and are expected to constitute a major barrier to horizontal gene transfer. We previously described nine distinct families of proteins encoded in Pseudomonas phage genomes that inhibit CRISPR-Cas function(4,5). We have developed a bioinformatic approach that enabled us to discover additional anti-CRISPR proteins encoded in phages and other mobile genetic elements of diverse bacterial species. We show that five previously undiscovered families of anti-CRISPRs inhibit the type I-F CRISPR-Cas systems of both Pseudomonas aeruginosa and Pectobacterium atrosepticum, and a dual specificity anti-CRISPR inactivates both type I-F and I-E CRISPR-Cas systems. Mirroring the distribution of the CRISPR-Cas systems they inactivate, these anti-CRISPRs were found in species distributed broadly across the phylum Proteobacteria. Importantly, anti-CRISPRs originating from species with divergent type I-F CRISPR-Cas systems were able to inhibit the two systems we tested, highlighting their broad specificity. These results suggest that all type I-F CRISPR-Cas systems are vulnerable to inhibition by anti-CRISPRs. Given the widespread occurrence and promiscuous activity of the anti-CRISPRs described here, we propose that anti-CRISPRs play an influential role in facilitating the movement of DNA between prokaryotes by breaching the barrier imposed by CRISPR-Cas systems.}, }
@article {pmid27572835, year = {2016}, author = {Lopatkin, AJ and Huang, S and Smith, RP and Srimani, JK and Sysoeva, TA and Bewick, S and Karig, DK and You, L}, title = {Antibiotics as a selective driver for conjugation dynamics.}, journal = {Nature microbiology}, volume = {1}, number = {6}, pages = {16044}, pmid = {27572835}, issn = {2058-5276}, support = {F31 DA028102/DA/NIDA NIH HHS/United States ; R01 GM098642/GM/NIGMS NIH HHS/United States ; R01 GM110494/GM/NIGMS NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/adverse effects/*pharmacology/therapeutic use ; Conjugation, Genetic/*drug effects ; Drug Resistance, Bacterial/drug effects ; Escherichia coli/*drug effects/*genetics ; Humans ; Microbial Sensitivity Tests ; Microfluidic Analytical Techniques ; Models, Biological ; Molecular Dynamics Simulation ; Plasmids/drug effects ; *Selection, Genetic ; }, abstract = {It is generally assumed that antibiotics can promote horizontal gene transfer. However, because of a variety of confounding factors that complicate the interpretation of previous studies, the mechanisms by which antibiotics modulate horizontal gene transfer remain poorly understood. In particular, it is unclear whether antibiotics directly regulate the efficiency of horizontal gene transfer, serve as a selection force to modulate population dynamics after such gene transfer has occurred, or both. Here, we address this question by quantifying conjugation dynamics in the presence and absence of antibiotic-mediated selection. Surprisingly, we find that sublethal concentrations of antibiotics from the most widely used classes do not significantly increase the conjugation efficiency. Instead, our modelling and experimental results demonstrate that conjugation dynamics are dictated by antibiotic-mediated selection, which can both promote and suppress conjugation dynamics. Our findings suggest that the contribution of antibiotics to the promotion of horizontal gene transfer may have been overestimated. These findings have implications for designing effective antibiotic treatment protocols and for assessing the risks of antibiotic use.}, }
@article {pmid27572415, year = {2016}, author = {Lee, JJ and Kim, MN and Park, KS and Lee, JH and Karim, AM and Park, M and Kim, JH and Lee, SH}, title = {Complex Class 1 Integron Carrying qnrB62 and blaVIM-2 in a Citrobacter freundii Clinical Isolate.}, journal = {Antimicrobial agents and chemotherapy}, volume = {60}, number = {11}, pages = {6937-6940}, pmid = {27572415}, issn = {1098-6596}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/*genetics ; Citrobacter freundii/drug effects/*genetics/isolation &amp; purification ; Conjugation, Genetic ; Drug Resistance, Bacterial/drug effects/*genetics ; Fluoroquinolones/pharmacology ; Gene Transfer, Horizontal ; Humans ; Integrons/genetics ; Microbial Sensitivity Tests ; Mutation ; Republic of Korea ; beta-Lactamases/*genetics ; }, abstract = {The coexistence of qnrB62 and blaVIM-2 was detected in a Citrobacter clinical isolate. The reduced fluoroquinolone susceptibility is attributable to qnrB62, mutations of quinolone-resistance-determining regions, and an efflux pump or pumps. The genetic context surrounding chromosomal qnrB62 was a novel complex class 1 integron (In1184::ISCR1::qnrB62) containing a unique gene array (blaVIM-2-aacA4'-8-gucD). An 18-nucleotide deletion at the 3' end of the pspA gene [pspA(Δ18)], upstream of qnrB62, and an inverted repeat region (IRR2) were detected in In1184::ISCR1::qnrB62, indicating past transposition events.}, }
@article {pmid27572409, year = {2016}, author = {Wong, MH and Chan, EW and Xie, L and Li, R and Chen, S}, title = {IncHI2 Plasmids Are the Key Vectors Responsible for oqxAB Transmission among Salmonella Species.}, journal = {Antimicrobial agents and chemotherapy}, volume = {60}, number = {11}, pages = {6911-6915}, pmid = {27572409}, issn = {1098-6596}, mesh = {Animals ; Chickens/microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Gene Transfer, Horizontal ; Humans ; Plasmids/*genetics ; Quinoxalines/pharmacology ; Salmonella/drug effects/*genetics/isolation &amp; purification ; Salmonella typhimurium/drug effects/genetics/isolation &amp; purification ; }, abstract = {This study reported and analyzed the complete sequences of two oqxAB-bearing IncHI2 plasmids harbored by a clinical Salmonella enterica serovar Typhimurium strain and an S Indiana strain of animal origin, respectively. In particular, pA3T recovered from S Indiana comprised the resistance determinants oqxAB, aac(6')Ib-cr, fosA3, and blaCTX-M-14 Further genetic screening of 63 oqxAB-positive Salmonella isolates revealed that the majority carried IncHI2 plasmids, confirming that such plasmids play a pivotal role in dissemination of oqxAB in Salmonella spp.}, }
@article {pmid27572405, year = {2016}, author = {Guo, Q and Ding, B and Jové, T and Stoesser, N and Cooper, VS and Wang, M and Doi, Y}, title = {Characterization of a Novel IncHI2 Plasmid Carrying Tandem Copies of blaCTX-M-2 in a fosA6-Harboring Escherichia coli Sequence Type 410 Strain.}, journal = {Antimicrobial agents and chemotherapy}, volume = {60}, number = {11}, pages = {6742-6747}, pmid = {27572405}, issn = {1098-6596}, support = {R01 AI104895/AI/NIAID NIH HHS/United States ; R21 AI123747/AI/NIAID NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; }, mesh = {Adult ; Animals ; Anti-Bacterial Agents/pharmacology ; *DNA Transposable Elements ; Drug Resistance, Multiple, Bacterial/genetics ; Escherichia coli/classification/drug effects/*genetics/isolation &amp; purification ; Escherichia coli Infections/*diagnosis/microbiology/transmission ; Europe ; Female ; Fosfomycin/pharmacology ; Gene Expression ; *Gene Transfer, Horizontal ; Hong Kong ; Humans ; Integrons ; Phylogeny ; Plasmids/chemistry/*metabolism ; Sequence Analysis, DNA ; South America ; United States ; beta-Lactamases/*genetics/metabolism ; }, abstract = {The extended-spectrum β-lactamase gene blaCTX-M-2 is mainly associated with ISCR1 embedded in complex sul1-type integrons, but information on the genetic context of plasmids harboring the ISCR1-blaCTX-M-2 module remains limited. In this study, a blaCTX-M-2-harboring plasmid (pYD786-1) belonging to the sequence type 2 (ST2)-IncHI2 plasmid type and isolated from an Escherichia coli ST410 clinical strain was sequenced and analyzed. pYD786-1 belongs to the APEC-O1-R-type IncHI2 plasmids, which are widely distributed in human, poultry, and livestock strains. It contains a multidrug resistance mosaic region (MRR) consisting of a Tn21::In2 transposon backbone augmented by acquisition of duplicate ISCR1-blaCTX-M-2 modules. Tn2411, a Tn21::In2 precursor, likely played a role in the generation of the MRR in pN13-01290_23, the putative progenitor plasmid of pYD786-1, found in a foodborne Salmonella strain. Tn21/Tn2411::In::ISCR1-blaCTX-M-2 derivatives, including pYD786-1, have been identified in strains from Europe, South America, and the United States, suggesting potential global dissemination of the blaCTX-M-2 modules mediated by this vehicle.}, }
@article {pmid27571176, year = {2016}, author = {Mir-Sanchis, I and Roman, CA and Misiura, A and Pigli, YZ and Boyle-Vavra, S and Rice, PA}, title = {Staphylococcal SCCmec elements encode an active MCM-like helicase and thus may be replicative.}, journal = {Nature structural &amp; molecular biology}, volume = {23}, number = {10}, pages = {891-898}, pmid = {27571176}, issn = {1545-9985}, support = {R21 AI117593/AI/NIAID NIH HHS/United States ; R25 GM066522/GM/NIGMS NIH HHS/United States ; T32 GM008720/GM/NIGMS NIH HHS/United States ; }, mesh = {Adenosine Triphosphatases/chemistry/genetics/metabolism ; Bacterial Proteins/chemistry/*genetics/metabolism ; Chromosomes, Bacterial/*genetics ; Crystallography, X-Ray ; DNA Helicases/chemistry/*genetics/metabolism ; DNA Replication ; DNA, Bacterial/genetics/metabolism ; DNA-Binding Proteins/chemistry/genetics/metabolism ; Humans ; Methicillin-Resistant Staphylococcus aureus/chemistry/*genetics/metabolism ; Models, Molecular ; Open Reading Frames ; Protein Conformation ; Protein Domains ; Protein Multimerization ; Staphylococcal Infections/microbiology ; }, abstract = {Methicillin-resistant Staphylococcus aureus (MRSA) is a public-health threat worldwide. Although the mobile genomic island responsible for this phenotype, staphylococcal cassette chromosome (SCC), has been thought to be nonreplicative, we predicted DNA-replication-related functions for some of the conserved proteins encoded by SCC. We show that one of these, Cch, is homologous to the self-loading initiator helicases of an unrelated family of genomic islands, that it is an active 3'-to-5' helicase and that the adjacent ORF encodes a single-stranded DNA-binding protein. Our 2.9-Å crystal structure of intact Cch shows that it forms a hexameric ring. Cch, like the archaeal and eukaryotic MCM-family replicative helicases, belongs to the pre-sensor II insert clade of AAA+ ATPases. Additionally, we found that SCC elements are part of a broader family of mobile elements, all of which encode a replication initiator upstream of their recombinases. Replication after excision would enhance the efficiency of horizontal gene transfer.}, }
@article {pmid27565162, year = {2016}, author = {Dang, UJ and Devault, AM and Mortimer, TD and Pepperell, CS and Poinar, HN and Golding, GB}, title = {Estimation of Gene Insertion/Deletion Rates with Missing Data.}, journal = {Genetics}, volume = {204}, number = {2}, pages = {513-529}, pmid = {27565162}, issn = {1943-2631}, support = {R01 AI113287/AI/NIAID NIH HHS/United States ; T32 GM007215/GM/NIGMS NIH HHS/United States ; }, mesh = {Data Interpretation, Statistical ; *Evolution, Molecular ; Gardnerella vaginalis/genetics ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial ; INDEL Mutation/*genetics ; Mutagenesis, Insertional/genetics ; *Mutation Rate ; Mycobacterium/genetics ; }, abstract = {Lateral gene transfer is an important mechanism for evolution among bacteria. Here, genome-wide gene insertion and deletion rates are modeled in a maximum-likelihood framework with the additional flexibility of modeling potential missing data. The performance of the models is illustrated using simulations and a data set on gene family phyletic patterns from Gardnerella vaginalis that includes an ancient taxon. A novel application involving pseudogenization/genome reduction magnitudes is also illustrated, using gene family data from Mycobacterium spp. Finally, an R package called indelmiss is available from the Comprehensive R Archive Network at https://cran.r-project.org/package=indelmiss, with support documentation and examples.}, }
@article {pmid27558983, year = {2017}, author = {Groth, SB and Blumenstiel, JP}, title = {Horizontal Transfer Can Drive a Greater Transposable Element Load in Large Populations.}, journal = {The Journal of heredity}, volume = {108}, number = {1}, pages = {36-44}, doi = {10.1093/jhered/esw050}, pmid = {27558983}, issn = {1465-7333}, mesh = {Algorithms ; Animals ; Computer Simulation ; *DNA Transposable Elements ; Drosophila melanogaster/genetics ; Evolution, Molecular ; Gene Dosage ; *Gene Transfer, Horizontal ; Genetic Drift ; *Genetics, Population ; Models, Genetic ; Probability ; Selection, Genetic ; }, abstract = {Genomes are comprised of contrasting domains of euchromatin and heterochromatin, and transposable elements (TEs) play an important role in defining these genomic regions. Therefore, understanding the forces that control TE abundance can help us understand the chromatin landscape of the genome. What determines the burden of TEs in populations? Some have proposed that drift plays a determining role. In small populations, mildly deleterious TE insertion alleles are allowed to fix, leading to increased copy number. However, it is not clear how the rate of exposure to new TE families, via horizontal transfer (HT), can contribute to broader patterns of genomic TE abundance. Here, using simulation and analytical approaches, we show that when the effects of drift are weak, exposure rate to new TE families via HT can be an important determinant of genomic copy number. If population exposure rate is proportional to population size, larger populations are expected to have a higher rate of exposure to rare HT events. This leads to the counterintuitive prediction that larger populations may carry a higher TE load. We also find that increased rates of recombination can lead to greater probabilities of TE establishment. This work has implications for our understanding of the evolution of chromatin landscapes, genome defense by RNA silencing, and recombination rates.}, }
@article {pmid27554651, year = {2016}, author = {Flot, JF and Debortoli, N and Hallet, B and Van Doninck, K}, title = {Response to Signorovitch et al.}, journal = {Current biology : CB}, volume = {26}, number = {16}, pages = {R755}, doi = {10.1016/j.cub.2016.06.052}, pmid = {27554651}, issn = {1879-0445}, mesh = {Animals ; DNA Breaks, Double-Stranded ; DNA Repair ; *Gene Transfer, Horizontal ; Genome ; Rotifera/*genetics ; }, abstract = {Signorovitch et al.[1] comment that an Oenothera-like meiosis [2] could produce a pattern similar to what we observed in our study of natural isolates of the bdelloid rotifer Adineta vaga, which we attributed to horizontal gene transfers (HGTs) [3]. Indeed, our HGT hypothesis appears at first sight difficult to conciliate with their observation of a congruent pattern of allele sharing at four large loci possibly located on different chromosomes [4]. However, one might imagine conditions under which massive horizontal gene transfer between bdelloid individuals could produce such a pattern, notably if the individuals involved had previously lost most of their heterozygosity because of their exposure to frequent desiccation (which produces DNA double-strand breaks [5]). In the published A. vaga genome the loss of heterozygosity due to large-scale gene conversion events or break-induced replication covers only about 10% of the genome [6], but this percentage may be much higher in environmental isolates that often experience dessication. Besides, if an Oenothera-like mode of meiosis occurs in bdelloids frequently enough to be detected in a single sampling of 29 individuals (as in [4]), one would expect males and meiosis to be observed at least occasionally, and instances of congruent allele sharing across loci should turn up frequently in genetic surveys. This was not the case in [3]: among the 82 A. vaga individuals sequenced for four nuclear markers, no trio of individuals presented congruent patterns of shared sequences at different loci. For these reasons, and in the absence of any direct evidence for an Oenothera-like meiosis in bdelloids, we still consider inter-bdelloid HGTs a more parsimonious explanation for our results.}, }
@article {pmid27554650, year = {2016}, author = {Signorovitch, A and Hur, J and Gladyshev, E and Meselson, M}, title = {Evidence for meiotic sex in bdelloid rotifers.}, journal = {Current biology : CB}, volume = {26}, number = {16}, pages = {R754-5}, doi = {10.1016/j.cub.2016.06.051}, pmid = {27554650}, issn = {1879-0445}, mesh = {Animals ; *Gene Transfer, Horizontal ; Genomics ; Haplotypes ; Meiosis ; *Rotifera ; }, abstract = {In their study of genetic exchange in the bdelloid rotifer Adineta vaga, Debortoli et al. [1] conclude that the patchwork pattern of allele sharing among three individuals in the genomic regions they examined is "…unlikely to arise in cases of PTH (Oenothera-like) meiosis since haplotypes are transferred as entire blocks…" and therefore that "Genetic exchange among bdelloid rotifers is more likely due to horizontal gene transfer than to meiotic sex." This assumes without justification that horizontal gene transfer (HGT) in bdelloids precludes the sexual transmission of entire haplotypes, for which we have reported evidence in the bdelloid Macrotrachela quadricornifera[2]. And it does not consider the contribution to such a patchwork pattern that would result from conversion and subsequent outcrossing, even in Oenothera-like systems.}, }
@article {pmid27551073, year = {2016}, author = {}, title = {Correction for Boothby et al., Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {36}, pages = {E5364}, doi = {10.1073/pnas.1613046113}, pmid = {27551073}, issn = {1091-6490}, }
@article {pmid27548264, year = {2016}, author = {Montaña, S and Schramm, ST and Traglia, GM and Chiem, K and Parmeciano Di Noto, G and Almuzara, M and Barberis, C and Vay, C and Quiroga, C and Tolmasky, ME and Iriarte, A and Ramírez, MS}, title = {The Genetic Analysis of an Acinetobacter johnsonii Clinical Strain Evidenced the Presence of Horizontal Genetic Transfer.}, journal = {PloS one}, volume = {11}, number = {8}, pages = {e0161528}, pmid = {27548264}, issn = {1932-6203}, support = {T37 MD001368/MD/NIMHD NIH HHS/United States ; }, mesh = {Acinetobacter/classification/drug effects/*genetics/isolation &amp; purification ; Acinetobacter Infections/drug therapy/microbiology/*transmission ; Anti-Bacterial Agents/pharmacology ; Argentina ; Base Sequence ; Disease Reservoirs/*microbiology ; Gene Expression ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Hospitals ; Humans ; Microbial Sensitivity Tests ; Multigene Family ; Mutagenesis, Insertional ; Phylogeny ; Plasmids/chemistry/metabolism ; Prophages/genetics ; Sequence Alignment ; beta-Lactam Resistance/genetics ; beta-Lactamases/*genetics/metabolism ; }, abstract = {Acinetobacter johnsonii rarely causes human infections. While most A. johnsonii isolates are susceptible to virtually all antibiotics, strains harboring a variety of β-lactamases have recently been described. An A. johnsonii Aj2199 clinical strain recovered from a hospital in Buenos Aires produces PER-2 and OXA-58. We decided to delve into its genome by obtaining the whole genome sequence of the Aj2199 strain. Genome comparison studies on Aj2199 revealed 240 unique genes and a close relation to strain WJ10621, isolated from the urine of a patient in China. Genomic analysis showed evidence of horizontal genetic transfer (HGT) events. Forty-five insertion sequences and two intact prophages were found in addition to several resistance determinants such as blaPER-2, blaOXA-58, blaTEM-1, strA, strB, ereA, sul1, aacC2 and a new variant of blaOXA-211, called blaOXA-498. In particular, blaPER-2 and blaTEM-1 are present within the typical contexts previously described in the Enterobacteriaceae family. These results suggest that A. johnsonii actively acquires exogenous DNA from other bacterial species and concomitantly becomes a reservoir of resistance genes.}, }
@article {pmid27548157, year = {2016}, author = {Zhang, X and Feng, X and Tao, J and Ma, L and Xiao, Y and Liang, Y and Liu, X and Yin, H}, title = {Comparative Genomics of the Extreme Acidophile Acidithiobacillus thiooxidans Reveals Intraspecific Divergence and Niche Adaptation.}, journal = {International journal of molecular sciences}, volume = {17}, number = {8}, pages = {}, pmid = {27548157}, issn = {1422-0067}, mesh = {Acidithiobacillus thiooxidans/*genetics ; Genome, Bacterial/genetics ; Genomic Islands/genetics ; Genomics/*methods ; }, abstract = {Acidithiobacillus thiooxidans known for its ubiquity in diverse acidic and sulfur-bearing environments worldwide was used as the research subject in this study. To explore the genomic fluidity and intraspecific diversity of Acidithiobacillus thiooxidans (A. thiooxidans) species, comparative genomics based on nine draft genomes was performed. Phylogenomic scrutiny provided first insights into the multiple groupings of these strains, suggesting that genetic diversity might be potentially correlated with their geographic distribution as well as geochemical conditions. While these strains shared a large number of common genes, they displayed differences in gene content. Functional assignment indicated that the core genome was essential for microbial basic activities such as energy acquisition and uptake of nutrients, whereas the accessory genome was thought to be involved in niche adaptation. Comprehensive analysis of their predicted central metabolism revealed that few differences were observed among these strains. Further analyses showed evidences of relevance between environmental conditions and genomic diversification. Furthermore, a diverse pool of mobile genetic elements including insertion sequences and genomic islands in all A. thiooxidans strains probably demonstrated the frequent genetic flow (such as lateral gene transfer) in the extremely acidic environments. From another perspective, these elements might endow A. thiooxidans species with capacities to withstand the chemical constraints of their natural habitats. Taken together, our findings bring some valuable data to better understand the genomic diversity and econiche adaptation within A. thiooxidans strains.}, }
@article {pmid27540086, year = {2016}, author = {Ang, MY and Dutta, A and Wee, WY and Dymock, D and Paterson, IC and Choo, SW}, title = {Comparative Genome Analysis of Fusobacterium nucleatum.}, journal = {Genome biology and evolution}, volume = {8}, number = {9}, pages = {2928-2938}, pmid = {27540086}, issn = {1759-6653}, mesh = {Fusobacterium nucleatum/classification/*genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomic Islands ; Phylogeny ; }, abstract = {Fusobacterium nucleatum is considered to be a key oral bacterium in recruiting periodontal pathogens into subgingival dental plaque. Currently F. nucleatum can be subdivided into five subspecies. Our previous genome analysis of F. nucleatum W1481 (referred to hereafter as W1481), isolated from an 8-mm periodontal pocket in a patient with chronic periodontitis, suggested the possibility of a new subspecies. To further investigate the biology and relationships of this possible subspecies with other known subspecies, we performed comparative analysis between W1481 and 35 genome sequences represented by the five known Fusobacterium subspecies. Our analyses suggest that W1481 is most likely a new F. nucleatum subspecies, supported by evidence from phylogenetic analyses and maximal unique match indices (MUMi). Interestingly, we found a horizontally transferred W1481-specific genomic island harboring the tripartite ATP-independent (TRAP)-like transporter genes, suggesting this bacterium might have a high-affinity transport system for the C4-dicarboxylates malate, succinate, and fumarate. Moreover, we found virulence genes in the W1481 genome that may provide a strong defense mechanism which might enable it to colonize and survive within the host by evading immune surveillance. This comparative study provides better understanding of F. nucleatum and the basis for future functional work on this important pathogen.}, }
@article {pmid27532335, year = {2016}, author = {Wachter, J and Hill, S}, title = {Positive Selection Pressure Drives Variation on the Surface-Exposed Variable Proteins of the Pathogenic Neisseria.}, journal = {PloS one}, volume = {11}, number = {8}, pages = {e0161348}, pmid = {27532335}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Antigens, Bacterial/*genetics/*immunology ; Bacterial Outer Membrane Proteins/*genetics/immunology ; Base Sequence ; Biological Evolution ; Fimbriae Proteins/*genetics/immunology ; Humans ; Neisseria gonorrhoeae/*genetics/immunology ; Neisseria meningitidis/*genetics/immunology ; Polymorphism, Genetic ; Selection, Genetic/genetics/immunology ; }, abstract = {Pathogenic species of Neisseria utilize variable outer membrane proteins to facilitate infection and proliferation within the human host. However, the mechanisms behind the evolution of these variable alleles remain largely unknown due to analysis of previously limited datasets. In this study, we have expanded upon the previous analyses to substantially increase the number of analyzed sequences by including multiple diverse strains, from various geographic locations, to determine whether positive selective pressure is exerted on the evolution of these variable genes. Although Neisseria are naturally competent, this analysis indicates that only intrastrain horizontal gene transfer among the pathogenic Neisseria principally account for these genes exhibiting linkage equilibrium which drives the polymorphisms evidenced within these alleles. As the majority of polymorphisms occur across species, the divergence of these variable genes is dependent upon the species and is independent of geographical location, disease severity, or serogroup. Tests of neutrality were able to detect strong selection pressures acting upon both the opa and pil gene families, and were able to locate the majority of these sites within the exposed variable regions of the encoded proteins. Evidence of positive selection acting upon the hypervariable domains of Opa contradicts previous beliefs and provides evidence for selection of receptor binding. As the pathogenic Neisseria reside exclusively within the human host, the strong selection pressures acting upon both the opa and pil gene families provide support for host immune system pressure driving sequence polymorphisms within these variable genes.}, }
@article {pmid27532298, year = {2016}, author = {Cámara, PG and Levine, AJ and Rabadán, R}, title = {Inference of Ancestral Recombination Graphs through Topological Data Analysis.}, journal = {PLoS computational biology}, volume = {12}, number = {8}, pages = {e1005071}, pmid = {27532298}, issn = {1553-7358}, support = {R01 GM117591/GM/NIGMS NIH HHS/United States ; U54 CA193313/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Computational Biology/*methods ; *Evolution, Molecular ; Finches/genetics ; Gene Transfer, Horizontal ; Humans ; Models, Genetic ; Phylogeny ; Recombination, Genetic/*genetics ; *Software ; }, abstract = {The recent explosion of genomic data has underscored the need for interpretable and comprehensive analyses that can capture complex phylogenetic relationships within and across species. Recombination, reassortment and horizontal gene transfer constitute examples of pervasive biological phenomena that cannot be captured by tree-like representations. Starting from hundreds of genomes, we are interested in the reconstruction of potential evolutionary histories leading to the observed data. Ancestral recombination graphs represent potential histories that explicitly accommodate recombination and mutation events across orthologous genomes. However, they are computationally costly to reconstruct, usually being infeasible for more than few tens of genomes. Recently, Topological Data Analysis (TDA) methods have been proposed as robust and scalable methods that can capture the genetic scale and frequency of recombination. We build upon previous TDA developments for detecting and quantifying recombination, and present a novel framework that can be applied to hundreds of genomes and can be interpreted in terms of minimal histories of mutation and recombination events, quantifying the scales and identifying the genomic locations of recombinations. We implement this framework in a software package, called TARGet, and apply it to several examples, including small migration between different populations, human recombination, and horizontal evolution in finches inhabiting the Galápagos Islands.}, }
@article {pmid27532207, year = {2016}, author = {Pathak, A and Chauhan, A and Blom, J and Indest, KJ and Jung, CM and Stothard, P and Bera, G and Green, SJ and Ogram, A}, title = {Comparative Genomics and Metabolic Analysis Reveals Peculiar Characteristics of Rhodococcus opacus Strain M213 Particularly for Naphthalene Degradation.}, journal = {PloS one}, volume = {11}, number = {8}, pages = {e0161032}, pmid = {27532207}, issn = {1932-6203}, mesh = {Bacterial Proteins/genetics ; Biodegradation, Environmental ; Dioxygenases/genetics ; Environmental Pollutants/metabolism ; Gene Rearrangement ; Genome, Bacterial ; Genomic Islands ; Metabolic Networks and Pathways/genetics ; Multienzyme Complexes/genetics ; Naphthalenes/*metabolism ; Phylogeny ; Replicon ; Rhodococcus/*genetics/isolation &amp; purification/*metabolism ; Soil Microbiology ; Species Specificity ; }, abstract = {The genome of Rhodococcus opacus strain M213, isolated from a fuel-oil contaminated soil, was sequenced and annotated which revealed a genome size of 9,194,165 bp encoding 8680 putative genes and a G+C content of 66.72%. Among the protein coding genes, 71.77% were annotated as clusters of orthologous groups of proteins (COGs); 55% of the COGs were present as paralog clusters. Pulsed field gel electrophoresis (PFGE) analysis of M213 revealed the presence of three different sized replicons- a circular chromosome and two megaplasmids (pNUO1 and pNUO2) estimated to be of 750Kb 350Kb in size, respectively. Conversely, using an alternative approach of optical mapping, the plasmid replicons appeared as a circular ~1.2 Mb megaplasmid and a linear, ~0.7 Mb megaplasmid. Genome-wide comparative analysis of M213 with a cohort of sequenced Rhodococcus species revealed low syntenic affiliation with other R. opacus species including strains B4 and PD630. Conversely, a closer affiliation of M213, at the functional (COG) level, was observed with the catabolically versatile R. jostii strain RHA1 and other Rhodococcii such as R. wratislaviensis strain IFP 2016, R. imtechensis strain RKJ300, Rhodococcus sp. strain JVH1, and Rhodococcus sp. strain DK17, respectively. An in-depth, genome-wide comparison between these functional relatives revealed 971 unique genes in M213 representing 11% of its total genome; many associating with catabolic functions. Of major interest was the identification of as many as 154 genomic islands (GEIs), many with duplicated catabolic genes, in particular for PAHs; a trait that was confirmed by PCR-based identification of naphthalene dioxygenase (NDO) as a representative gene, across PFGE-resolved replicons of strain M213. Interestingly, several plasmid/GEI-encoded genes, that likely participate in degrading naphthalene (NAP) via a peculiar pathway, were also identified in strain M213 using a combination of bioinformatics, metabolic analysis and gene expression measurements of selected catabolic genes by RT-PCR. Taken together, this study provides a comprehensive understanding of the genome plasticity and ecological competitiveness of strain M213 likely facilitated by horizontal gene transfer (HGT), bacteriophage attacks and genomic reshuffling- aspects that continue to be understudied and thus poorly understood, in particular for the soil-borne Rhodococcii.}, }
@article {pmid27530855, year = {2016}, author = {Pagaling, E and Gatica, J and Yang, K and Cytryn, E and Yan, T}, title = {Phylogenetic diversity of ceftriaxone resistance and the presence of extended-spectrum β-lactamase genes in the culturable soil resistome.}, journal = {Journal of global antimicrobial resistance}, volume = {6}, number = {}, pages = {128-135}, doi = {10.1016/j.jgar.2016.05.002}, pmid = {27530855}, issn = {2213-7173}, mesh = {Bacteria/*classification ; *Ceftriaxone ; *Drug Resistance, Bacterial ; Hawaii ; Israel ; Phylogeny ; Soil ; *Soil Microbiology ; beta-Lactamases/*genetics ; }, abstract = {The aim of this study was to determine the phylogenetic diversity of ceftriaxone resistance and the presence of known extended-spectrum β-lactamase (ESBL) genes in culturable soil resistomes. Libraries of soil bacterial isolates resistant to ceftriaxone were established from six physicochemically diverse soils collected in Hawaii (USA) and Israel. The phylogenetic affiliation, ceftriaxone and multidrug resistance levels, and presence of known ESBL genes of the isolates were determined. The soil bacterial isolates were phylogenetically grouped with the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Actinobacteria, Firmicutes and Bacteroidetes. Ceftriaxone minimum inhibitory concentrations (MICs) largely followed the phylogeny structure and higher levels of ceftriaxone resistance corresponded to higher multidrug resistance. Three distinct blaTEM variants were detected in soil bacterial isolates belonging to nine different genera. In conclusion, the culturable soil resistomes for ceftriaxone exhibited high phylogenetic diversity and multidrug resistance. blaTEM was the only known ESBL detected in the soil resistomes, and its distribution in different phylogenetic groups suggests its ubiquitous presence and/or possible horizontal gene transfer within the soil microbiomes.}, }
@article {pmid27530756, year = {2016}, author = {Freitas, AR and Tedim, AP and Francia, MV and Jensen, LB and Novais, C and Peixe, L and Sánchez-Valenzuela, A and Sundsfjord, A and Hegstad, K and Werner, G and Sadowy, E and Hammerum, AM and Garcia-Migura, L and Willems, RJ and Baquero, F and Coque, TM}, title = {Multilevel population genetic analysis of vanA and vanB Enterococcus faecium causing nosocomial outbreaks in 27 countries (1986-2012).}, journal = {The Journal of antimicrobial chemotherapy}, volume = {71}, number = {12}, pages = {3351-3366}, doi = {10.1093/jac/dkw312}, pmid = {27530756}, issn = {1460-2091}, mesh = {Bacterial Proteins/*genetics ; Bacteriocins/analysis ; Carbon-Oxygen Ligases/*genetics ; Cross Infection/epidemiology/microbiology ; DNA Transposable Elements ; *Disease Outbreaks ; Electrophoresis, Gel, Pulsed-Field ; Enterococcus faecium/*classification/genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; *Genetic Variation ; Genetics, Population ; Genotype ; Global Health ; Gram-Positive Bacterial Infections/*epidemiology/microbiology ; Humans ; Multilocus Sequence Typing ; Plasmids/analysis ; Vancomycin-Resistant Enterococci/*classification/genetics/isolation &amp; purification ; Virulence Factors/genetics ; }, abstract = {OBJECTIVES: Vancomycin-resistant Enterococcus faecium (VREfm) have been increasingly reported since the 1980s. Despite the high number of published studies about VRE epidemiology, the dynamics and evolvability of these microorganisms are still not fully understood. A multilevel population genetic analysis of VREfm outbreak strains since 1986, representing the first comprehensive characterization of plasmid content in E. faecium, was performed to provide a detailed view of potential transmissible units.<br><br>METHODS: From a comprehensive MeSH search, we identified VREfm strains causing hospital outbreaks (1986-2012). In total, 53 VanA and 18 VanB isolates (27 countries, 5 continents) were analysed and 82 vancomycin-susceptible E. faecium (VSEfm) were included for comparison. Clonal relatedness was established by PFGE and MLST (goeBURST/Bayesian Analysis of Population Structure, BAPS). Characterization of van transposons (PCR mapping, RFLP, sequencing), plasmids (transfer, ClaI-RFLP, PCR typing of relaxases, replication-initiation proteins and toxin-antitoxin systems, hybridization, sequencing), bacteriocins and virulence determinants (PCR, hybridization, sequencing) was performed.<br><br>RESULTS: VREfm were mainly associated with major human lineages ST17, ST18 and ST78. VREfm and VSEfm harboured plasmids of different families [RCR, small theta plasmids, RepA_N (pRUM/pLG1) and Inc18] able to yield mosaic elements. Tn1546-vanA was mainly located on pRUM/Axe-Txe (USA) and Inc18-pIP186 (Europe) plasmids. The VanB2 type (Tn5382/Tn1549) was predominant among VanB strains (chromosome and plasmids).<br><br>CONCLUSIONS: Both strains and plasmids contributed to the spread and persistence of vancomycin resistance among E. faecium. Horizontal gene transfer events among genetic elements from different clonal lineages (same or different species) result in chimeras with different stability and host range, complicating the surveillance of epidemic plasmids.}, }
@article {pmid27530704, year = {2017}, author = {Armijos-Jaramillo, V and Santander-Gordón, D and Soria, R and Pazmiño-Betancourth, M and Echeverría, MC}, title = {A whole genome analysis reveals the presence of a plant PR1 sequence in the potato pathogen Streptomyces scabies and other Streptomyces species.}, journal = {Molecular phylogenetics and evolution}, volume = {114}, number = {}, pages = {346-352}, doi = {10.1016/j.ympev.2016.08.006}, pmid = {27530704}, issn = {1095-9513}, mesh = {*Genome, Bacterial ; Phylogeny ; Plant Diseases/microbiology ; Plant Proteins/chemistry/*genetics ; Protein Structure, Tertiary ; Solanum tuberosum/*microbiology ; Streptomyces/classification/*genetics ; }, abstract = {Streptomyces scabies is a common soil bacterium that causes scab symptoms in potatoes. Strong evidence indicates horizontal gene transfer (HGT) among bacteria has influenced the evolution of this plant pathogen and other Streptomyces spp. To extend the study of the HGT to the Streptomyces genus, we explored the effects of the inter-domain HGT in the S. scabies genome. We employed a semi-automatic pipeline based on BLASTp searches and phylogenetic reconstruction. The data show low impact of inter-domain HGT in the S. scabies genome; however, we found a putative plant pathogenesis related 1 (PR1) sequence in the genome of S. scabies and other species of the genus. It is possible that this gene could be used by S. scabies to out-compete other soil organisms.}, }
@article {pmid27530353, year = {2016}, author = {Venter, HJ and Bøhn, T}, title = {Interactions between Bt crops and aquatic ecosystems: A review.}, journal = {Environmental toxicology and chemistry}, volume = {35}, number = {12}, pages = {2891-2902}, doi = {10.1002/etc.3583}, pmid = {27530353}, issn = {1552-8618}, mesh = {Animals ; Aquatic Organisms/drug effects/*physiology ; Bacillus thuringiensis/genetics/*metabolism ; Bacterial Proteins/metabolism ; Bacterial Toxins/toxicity ; Crops, Agricultural ; *Ecosystem ; Gene Transfer, Horizontal ; Plants, Genetically Modified/genetics ; }, abstract = {The term Bt crops collectively refers to crops that have been genetically modified to include a gene (or genes) sourced from Bacillus thuringiensis (Bt) bacteria. These genes confer the ability to produce proteins toxic to certain insect pests. The interaction between Bt crops and adjacent aquatic ecosystems has received limited attention in research and risk assessment, despite the fact that some Bt crops have been in commercial use for 20 yr. Reports of effects on aquatic organisms such as Daphnia magna, Elliptio complanata, and Chironomus dilutus suggest that some aquatic species may be negatively affected, whereas other reports suggest that the decreased use of insecticides precipitated by Bt crops may benefit aquatic communities. The present study reviews the literature regarding entry routes and exposure pathways by which aquatic organisms may be exposed to Bt crop material, as well as feeding trials and field surveys that have investigated the effects of Bt-expressing plant material on such organisms. The present review also discusses how Bt crop development has moved past single-gene events, toward multigene stacked varieties that often contain herbicide resistance genes in addition to multiple Bt genes, and how their use (in conjunction with co-technology such as glyphosate/Roundup) may impact and interact with aquatic ecosystems. Lastly, suggestions for further research in this field are provided. Environ Toxicol Chem 2016;35:2891-2902. © 2016 SETAC.}, }
@article {pmid27528665, year = {2016}, author = {Boritsch, EC and Khanna, V and Pawlik, A and Honoré, N and Navas, VH and Ma, L and Bouchier, C and Seemann, T and Supply, P and Stinear, TP and Brosch, R}, title = {Key experimental evidence of chromosomal DNA transfer among selected tuberculosis-causing mycobacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {35}, pages = {9876-9881}, pmid = {27528665}, issn = {1091-6490}, mesh = {DNA, Bacterial/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Bacterial/*genetics ; Humans ; Mycobacterium/classification/*genetics/physiology ; Mycobacterium tuberculosis/classification/genetics/physiology ; Species Specificity ; Tuberculosis/microbiology ; Whole Genome Sequencing/methods ; }, abstract = {Horizontal gene transfer (HGT) is a major driving force of bacterial diversification and evolution. For tuberculosis-causing mycobacteria, the impact of HGT in the emergence and distribution of dominant lineages remains a matter of debate. Here, by using fluorescence-assisted mating assays and whole genome sequencing, we present unique experimental evidence of chromosomal DNA transfer between tubercle bacilli of the early-branching Mycobacterium canettii clade. We found that the obtained recombinants had received multiple donor-derived DNA fragments in the size range of 100 bp to 118 kbp, fragments large enough to contain whole operons. Although the transfer frequency between M. canettii strains was low and no transfer could be observed among classical Mycobacterium tuberculosis complex (MTBC) strains, our study provides the proof of concept for genetic exchange in tubercle bacilli. This outstanding, now experimentally validated phenomenon presumably played a key role in the early evolution of the MTBC toward pathogenicity. Moreover, our findings also provide important information for the risk evaluation of potential transfer of drug resistance and fitness mutations among clinically relevant mycobacterial strains.}, }
@article {pmid27527758, year = {2016}, author = {Chen, Y and Sun, J and Liao, XP and Shao, Y and Li, L and Fang, LX and Liu, YH}, title = {Impact of enrofloxacin and florfenicol therapy on the spread of OqxAB gene and intestinal microbiota in chickens.}, journal = {Veterinary microbiology}, volume = {192}, number = {}, pages = {1-9}, doi = {10.1016/j.vetmic.2016.05.014}, pmid = {27527758}, issn = {1873-2542}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Chickens/*microbiology ; Cloaca/microbiology ; DNA, Bacterial ; Drug Resistance, Multiple, Bacterial/*genetics ; Enrofloxacin ; Escherichia coli/*drug effects/genetics ; Feces/microbiology ; Fluoroquinolones/*pharmacology ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genes, Bacterial ; Intestines/microbiology ; Microbial Sensitivity Tests ; Salmonella typhimurium/*drug effects/genetics ; Thiamphenicol/*analogs &amp; derivatives/pharmacology ; }, abstract = {Horizontal transfer of plasmid-encoded multidrug-resistant determinants is a major health problem and has attracted much public attention. We studied the dissemination of the efflux pump gene oqxAB located on transferable plasmid pHXY0908 between Salmonella Typhimurium and Escherichia coli in the gut of chickens. After an inoculation with Salmonella Typhimurium harboring oqxAB-bearing plasmid pHXY0908, chickens were treated with enrofloxacin and florfenicol. Inoculated, but non-treated chickens were included as a control group. Our results revealed that commensal E. coli isolates from the gut of chickens acquired the oqxAB-bearing plasmid in both treated and non-treated groups. Additionally, in the florfenicol treatment group, the average isolation rate of oqxAB-positive E. coli was significantly higher than that in the non-treated group. PFGE analysis showed that oqxAB-positive E. coli strains belonged to different patterns with one predominating. Moreover, multilocus sequence typing analysis revealed that E. coli ST533 was closely associated with the spread of oqxAB gene. qPCR analysis indicated that antibiotic administration provided selective advantages for sustaining a significantly high level of oqxAB gene from the DNA extracted from the feces. There was also a fluctuation in the intestinal microbiota with antibiotic therapy. In conclusion, the present study indicates that the oqxAB gene could be readily spread within the intestinal microflora. This could be enhanced by administrated with clinical doses of florfenicol and enrofloxacin, resulting in the enlargement of resistance gene reservoirs. In addition, ST533 E. coli isolates were found to contribute to transfer of the oqxAB gene.}, }
@article {pmid27521636, year = {2016}, author = {de Sena Filho, JG and Quin, MB and Spakowicz, DJ and Shaw, JJ and Kucera, K and Dunican, B and Strobel, SA and Schmidt-Dannert, C}, title = {Genome of Diaporthe sp. provides insights into the potential inter-phylum transfer of a fungal sesquiterpenoid biosynthetic pathway.}, journal = {Fungal biology}, volume = {120}, number = {8}, pages = {1050-1063}, pmid = {27521636}, issn = {1878-6146}, support = {R01 GM080299/GM/NIGMS NIH HHS/United States ; T15 LM007056/LM/NLM NIH HHS/United States ; T32 GM007223/GM/NIGMS NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; }, mesh = {Antineoplastic Agents/metabolism ; Ascomycota/*genetics/isolation &amp; purification/*metabolism ; *Biosynthetic Pathways ; Computational Biology ; Endophytes/genetics/isolation &amp; purification/metabolism ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Fungal ; Sequence Analysis, DNA ; Sequence Homology ; Sesquiterpenes/*metabolism ; }, abstract = {Fungi have highly active secondary metabolic pathways which enable them to produce a wealth of sesquiterpenoids that are bioactive. One example is Δ6-protoilludene, the precursor to the cytotoxic illudins, which are pharmaceutically relevant as anticancer therapeutics. To date, this valuable sesquiterpene has only been identified in members of the fungal division Basidiomycota. To explore the untapped potential of fungi belonging to the division Ascomycota in producing Δ6-protoilludene, we isolated a fungal endophyte Diaporthe sp. BR109 and show that it produces a diversity of terpenoids including Δ6-protoilludene. Using a genome sequencing and mining approach 17 putative novel sesquiterpene synthases were identified in Diaporthe sp. BR109. A phylogenetic approach was used to predict which gene encodes Δ6-protoilludene synthase, which was then confirmed experimentally. These analyses reveal that the sesquiterpene synthase and its putative sesquiterpene scaffold modifying cytochrome P450(s) may have been acquired by inter-phylum horizontal gene transfer from Basidiomycota to Ascomycota. Bioinformatic analyses indicate that inter-phylum transfer of these minimal sequiterpenoid secondary metabolic pathways may have occurred in other fungi. This work provides insights into the evolution of fungal sesquiterpenoid secondary metabolic pathways in the production of pharmaceutically relevant bioactive natural products.}, }
@article {pmid27516530, year = {2016}, author = {Bertelli, C and Cissé, OH and Rusconi, B and Kebbi-Beghdadi, C and Croxatto, A and Goesmann, A and Collyn, F and Greub, G}, title = {CRISPR System Acquisition and Evolution of an Obligate Intracellular Chlamydia-Related Bacterium.}, journal = {Genome biology and evolution}, volume = {8}, number = {8}, pages = {2376-2386}, pmid = {27516530}, issn = {1759-6653}, support = {T32 DK077653/DK/NIDDK NIH HHS/United States ; }, mesh = {CRISPR-Cas Systems/*genetics ; Chlamydia/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomic Islands/genetics ; Molecular Sequence Annotation ; Naegleria/genetics/microbiology ; Plasmids/genetics ; }, abstract = {Recently, a new Chlamydia-related organism, Protochlamydia naegleriophila KNic, was discovered within a Naegleria amoeba. To decipher the mechanisms at play in the modeling of genomes from the Protochlamydia genus, we sequenced the full genome of Pr. naegleriophila, which includes a 2,885,090 bp chromosome and a 145,285 bp megaplasmid. For the first time within the Chlamydiales order, we describe the presence of a clustered regularly interspaced short palindromic repeats (CRISPR) system, the immune system of bacteria, located on the chromosome. It is composed of a small CRISPR locus comprising eight repeats and associated cas-cse genes of the subtype I-E. A CRISPR locus is also present within Chlamydia sp. Diamant, another Pr. naegleriophila strain, suggesting that the CRISPR system was acquired by a common ancestor of Pr. naegleriophila, after its divergence from Pr. amoebophila. Both nucleotide bias and comparative genomics approaches identified probable horizontal gene acquisitions within two and four genomic islands in Pr. naegleriophila KNic and Diamant genomes, respectively. The plasmid encodes an F-type conjugative system highly similar to 1) that found in the Pam100G genomic island of Pr. amoebophila UWE25 chromosome, as well as on the plasmid of Rubidus massiliensis and 2) to the three genes remaining in the chromosome of Parachlamydia acanthamoebae strains. Therefore, this conjugative system was likely acquired on an ancestral plasmid before the divergence of Parachlamydiaceae Overall, this new complete Pr. naegleriophila genome sequence enables further investigation of the dynamic processes shaping the genomes of the family Parachlamydiaceae and the genus Protochlamydia.}, }
@article {pmid27515739, year = {2016}, author = {Hanson, NW and Konwar, KM and Hallam, SJ}, title = {LCA*: an entropy-based measure for taxonomic assignment within assembled metagenomes.}, journal = {Bioinformatics (Oxford, England)}, volume = {32}, number = {23}, pages = {3535-3542}, pmid = {27515739}, issn = {1367-4811}, mesh = {*Algorithms ; Entropy ; *Metagenome ; Models, Statistical ; *Phylogeny ; }, abstract = {MOTIVATION: A perennial problem in the analysis of environmental sequence information is the assignment of reads or assembled sequences, e.g. contigs or scaffolds, to discrete taxonomic bins. In the absence of reference genomes for most environmental microorganisms, the use of intrinsic nucleotide patterns and phylogenetic anchors can improve assembly-dependent binning needed for more accurate taxonomic and functional annotation in communities of microorganisms, and assist in identifying mobile genetic elements or lateral gene transfer events.<br><br>RESULTS: Here, we present a statistic called LCA* inspired by Information and Voting theories that uses the NCBI Taxonomic Database hierarchy to assign taxonomy to contigs assembled from environmental sequence information. The LCA* algorithm identifies a sufficiently strong majority on the hierarchy while minimizing entropy changes to the observed taxonomic distribution resulting in improved statistical properties. Moreover, we apply results from the order-statistic literature to formulate a likelihood-ratio hypothesis test and P-value for testing the supremacy of the assigned LCA* taxonomy. Using simulated and real-world datasets, we empirically demonstrate that voting-based methods, majority vote and LCA*, in the presence of known reference annotations, are consistently more accurate in identifying contig taxonomy than the lowest common ancestor algorithm popularized by MEGAN, and that LCA* taxonomy strikes a balance between specificity and confidence to provide an estimate appropriate to the available information in the data.<br><br>The LCA* has been implemented as a stand-alone Python library compatible with the MetaPathways pipeline; both of which are available on GitHub with installation instructions and use-cases (http://www.github.com/hallamlab/LCAStar/).<br><br>CONTACT: shallam@mail.ubc.caSupplementary information: Supplementary data are available at Bioinformatics online.}, }
@article {pmid27510852, year = {2016}, author = {Harrison, E and Dytham, C and Hall, JP and Guymer, D and Spiers, AJ and Paterson, S and Brockhurst, MA}, title = {Rapid compensatory evolution promotes the survival of conjugative plasmids.}, journal = {Mobile genetic elements}, volume = {6}, number = {3}, pages = {e1179074}, pmid = {27510852}, issn = {2159-2543}, abstract = {Conjugative plasmids play a vital role in bacterial adaptation through horizontal gene transfer. Explaining how plasmids persist in host populations however is difficult, given the high costs often associated with plasmid carriage. Compensatory evolution to ameliorate this cost can rescue plasmids from extinction. In a recently published study we showed that compensatory evolution repeatedly targeted the same bacterial regulatory system, GacA/GacS, in populations of plasmid-carrying bacteria evolving across a range of selective environments. Mutations in these genes arose rapidly and completely eliminated the cost of plasmid carriage. Here we extend our analysis using an individual based model to explore the dynamics of compensatory evolution in this system. We show that mutations which ameliorate the cost of plasmid carriage can prevent both the loss of plasmids from the population and the fixation of accessory traits on the bacterial chromosome. We discuss how dependent the outcome of compensatory evolution is on the strength and availability of such mutations and the rate at which beneficial accessory traits integrate on the host chromosome.}, }
@article {pmid27510669, year = {2016}, author = {Ogbolu, DO and Alli, AO and Anorue, MC and Daini, OA and Oluwadun, A}, title = {Distribution of plasmid-mediated quinolone resistance in Gram-negative bacteria from a tertiary hospital in Nigeria.}, journal = {Indian journal of pathology &amp; microbiology}, volume = {59}, number = {3}, pages = {322-326}, doi = {10.4103/0377-4929.188108}, pmid = {27510669}, issn = {0974-5130}, mesh = {Anti-Bacterial Agents/*pharmacology ; Conjugation, Genetic ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genetic Variation ; Gram-Negative Bacteria/classification/*drug effects/genetics/isolation &amp; purification ; Gram-Negative Bacterial Infections/epidemiology/*microbiology ; Humans ; Microbial Sensitivity Tests ; Molecular Typing ; Nigeria/epidemiology ; Plasmids/*analysis ; Prevalence ; Quinolones/*pharmacology ; Random Amplified Polymorphic DNA Technique ; Tertiary Care Centers ; }, abstract = {BACKGROUND: Until recently, mechanisms of resistance to quinolones in Gram-negative bacteria were believed to be only chromosome encoded. However, emergence of plasmid-mediated quinolone resistance (PMQR) has been reported worldwide.<br><br>AIM: This study investigated distribution of PMQR in Gram-negative bacteria from a tertiary hospital in eastern part of Nigeria.<br><br>MATERIALS AND METHODS: Seventy-one nonduplicate Gram-negative bacterial isolates of eight species were analyzed for antimicrobial susceptibility, genotypic detection of various PMQRs, typed by random amplified polymorphic DNA (RAPD) and analysis of plasmids present, including replicon typing.<br><br>RESULTS: The minimum inhibitory concentrations showed MIC90values as high as 256 &#x3bc;g/ml for fluoroquinolones. Carriage of PMQR was found to be 35.2%. Twenty (28.2%) isolates carried various qnr genes, of which seven (9.9%) qnrA1; four (5.6%) qnrB1; eight (11.3%) qnrS1 while one (1.4%) encoded qnrD1. Eighteen (25.4%) isolates were positive for aac(6')-Ib-cr while carriage of multiple genes exists in some strains. Similarly, 13 isolates (18.7%) were found to carry PMQR efflux pump gene, qepA. Conjugation experiments revealed that the plasmids once transferred coded for fluoroquinolone resistance. The transconjugant strains carried a common plasmid estimated to be 65 kb. These plasmids were untypable for replicon/incompatibility. Typing revealed high diversity among all species tested with no identical RAPD pattern seen.<br><br>CONCLUSION: This study further confirms high level resistance to many antimicrobials in different species of Gram-negative bacteria including fluoroquinolones and spread of PMQR genes in Southern Nigeria.}, }
@article {pmid27508073, year = {2016}, author = {Koonin, EV}, title = {Horizontal gene transfer: essentiality and evolvability in prokaryotes, and roles in evolutionary transitions.}, journal = {F1000Research}, volume = {5}, number = {}, pages = {}, pmid = {27508073}, issn = {2046-1402}, abstract = {The wide spread of gene exchange and loss in the prokaryotic world has prompted the concept of 'lateral genomics' to the point of an outright denial of the relevance of phylogenetic trees for evolution. However, the pronounced coherence congruence of the topologies of numerous gene trees, particularly those for (nearly) universal genes, translates into the notion of a statistical tree of life (STOL), which reflects a central trend of vertical evolution. The STOL can be employed as a framework for reconstruction of the evolutionary processes in the prokaryotic world. Quantitatively, however, horizontal gene transfer (HGT) dominates microbial evolution, with the rate of gene gain and loss being comparable to the rate of point mutations and much greater than the duplication rate. Theoretical models of evolution suggest that HGT is essential for the survival of microbial populations that otherwise deteriorate due to the Muller's ratchet effect. Apparently, at least some bacteria and archaea evolved dedicated vehicles for gene transfer that evolved from selfish elements such as plasmids and viruses. Recent phylogenomic analyses suggest that episodes of massive HGT were pivotal for the emergence of major groups of organisms such as multiple archaeal phyla as well as eukaryotes. Similar analyses appear to indicate that, in addition to donating hundreds of genes to the emerging eukaryotic lineage, mitochondrial endosymbiosis severely curtailed HGT. These results shed new light on the routes of evolutionary transitions, but caution is due given the inherent uncertainty of deep phylogenies.}, }
@article {pmid27507612, year = {2016}, author = {Miyashita, S and Sagane, Y and Suzuki, T and Matsumoto, T and Niwa, K and Watanabe, T}, title = {"Non-Toxic" Proteins of the Botulinum Toxin Complex Exert In-vivo Toxicity.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {31043}, pmid = {27507612}, issn = {2045-2322}, mesh = {Animals ; Apoptosis ; Bacterial Proteins/toxicity ; Botulinum Toxins/*toxicity ; Cell Line ; Clostridium botulinum/*physiology ; Helicobacter pylori/physiology ; Hemolysin Factors/toxicity ; Intestinal Mucosa/*metabolism/ultrastructure ; Multiprotein Complexes ; Rats ; Vacuoles/*ultrastructure ; Vibrio cholerae/physiology ; }, abstract = {The botulinum neurotoxin (BoNT) causes muscle paralysis and is the most potent toxin in nature. BoNT is associated with a complex of auxiliary "Non-Toxic" proteins, which constitute a large-sized toxin complex (L-TC). However, here we report that the "Non-Toxic" complex of serotype D botulinum L-TC, when administered to rats, exerts in-vivo toxicity on small-intestinal villi. Moreover, Serotype C and D of the "Non-Toxic" complex, but not BoNT, induced vacuole-formation in a rat intestinal epithelial cell line (IEC-6), resulting in cell death. Our results suggest that the vacuole was formed in a manner distinct from the mechanism by which Helicobacter pylori vacuolating toxin (VacA) and Vibrio cholerae haemolysin induce vacuolation. We therefore hypothesise that the serotype C and D botulinum toxin complex is a functional hybrid of the neurotoxin and vacuolating toxin (VT) which arose from horizontal gene transfer from an ancestral BoNT-producing bacterium to a hypothetical VT-producing bacterium.}, }
@article {pmid27507344, year = {2016}, author = {Brouwer, MS and Mullany, P and Allan, E and Roberts, AP}, title = {Investigating Transfer of Large Chromosomal Regions Containing the Pathogenicity Locus Between Clostridium difficile Strains.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1476}, number = {}, pages = {215-222}, doi = {10.1007/978-1-4939-6361-4_16}, pmid = {27507344}, issn = {1940-6029}, support = {G0601176//Medical Research Council/United Kingdom ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics/metabolism ; Bacterial Toxins/genetics/metabolism ; Bacteriophages/drug effects/*genetics/metabolism ; Chromosomes, Bacterial/*chemistry/metabolism/virology ; Clostridioides difficile/drug effects/*genetics/metabolism/virology ; *Conjugation, Genetic ; DNA Primers/chemistry/metabolism ; *DNA Transposable Elements ; DNA, Bacterial/genetics/metabolism ; Enterotoxins/genetics/metabolism ; *Gene Transfer, Horizontal ; Genetic Loci ; *Genomic Islands ; High-Throughput Nucleotide Sequencing ; Homologous Recombination ; Mitomycin/pharmacology ; Polymerase Chain Reaction ; Virus Activation/drug effects ; }, abstract = {The genomes of all sequenced Clostridium difficile isolates contain multiple mobile genetic elements. The chromosomally located pathogenicity locus (PaLoc), encoding the cytotoxins TcdA and TcdB, was previously hypothesized to be a mobile genetic element; however, mobility was not demonstrated. Here we describe the methods used to facilitate and detect the transfer of the PaLoc from a toxigenic strain into non-toxigenic strains of C. difficile. Although the precise mechanism of transfer has not yet been elucidated, a number of controls are described which indicate transfer occurs via a cell-to-cell-mediated conjugation-like transfer mechanism. Importantly, transfer of the PaLoc was shown to occur on large chromosomal fragments of variable sizes, indicating that homologous recombination is likely to be responsible for the insertion events.}, }
@article {pmid27507343, year = {2016}, author = {Johanesen, P and Lyras, D}, title = {Methods for Determining Transfer of Mobile Genetic Elements in Clostridium difficile.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1476}, number = {}, pages = {199-213}, doi = {10.1007/978-1-4939-6361-4_15}, pmid = {27507343}, issn = {1940-6029}, mesh = {Anti-Bacterial Agents/pharmacology ; Clostridioides difficile/drug effects/*genetics/metabolism ; *Conjugation, Genetic ; DNA Primers/chemistry/metabolism ; *DNA Transposable Elements ; DNA, Bacterial/genetics/metabolism ; DNA, Circular/genetics/metabolism ; Erythromycin/pharmacology ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Plasmids/chemistry/metabolism ; Polymerase Chain Reaction/*methods ; Rifampin/pharmacology ; Tetracycline/pharmacology ; Thiamphenicol/pharmacology ; }, abstract = {Horizontal gene transfer by mobile genetic elements plays an important role in the evolution of bacteria, allowing them to rapidly acquire new traits, including antibiotic resistance. Mobile genetic elements such as conjugative and mobilizable transposons make up a considerable part of the C. difficile genome. While sequence analysis has identified a large number of these elements, experimental analysis is required to demonstrate mobility and function. This chapter describes the experimental methods utilized for determining function and transfer of mobile genetic elements in C. difficile including detection of the circular transfer intermediate and the analysis and confirmation of mobile genetic element transfer to recipient cells.}, }
@article {pmid27507342, year = {2016}, author = {Barbanti, F and Wasels, F and Spigaglia, P}, title = {Transfer of Clostridium difficile Genetic Elements Conferring Resistance to Macrolide-Lincosamide-Streptogramin B (MLSB) Antibiotics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1476}, number = {}, pages = {187-198}, doi = {10.1007/978-1-4939-6361-4_14}, pmid = {27507342}, issn = {1940-6029}, mesh = {Anaerobiosis ; Anti-Bacterial Agents/*pharmacology ; Clindamycin/pharmacology ; Clostridioides difficile/*drug effects/genetics/growth &amp; development/metabolism ; DNA, Bacterial/*genetics/metabolism ; Drug Resistance, Multiple, Bacterial/*genetics ; Erythromycin/pharmacology ; Gene Expression ; *Gene Transfer, Horizontal ; Lincosamides/pharmacology ; Macrolides/pharmacology ; Methyltransferases/genetics/metabolism ; Microbial Sensitivity Tests ; Polymerase Chain Reaction ; Ribotyping ; Rifampin/pharmacology ; Streptogramin B/pharmacology ; }, abstract = {Molecular analysis is an important tool to investigate Clostridium difficile resistance to macrolide-lincosamide-streptogramin B (MLSB). In particular, the protocols described in this chapter have been designed to investigate the genetic organization of erm(B)-containing elements and to evaluate the capability of these elements to transfer in C. difficile recipient strains using filter mating assay.}, }
@article {pmid27507341, year = {2016}, author = {Goh, S}, title = {Phage Transduction.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1476}, number = {}, pages = {177-185}, doi = {10.1007/978-1-4939-6361-4_13}, pmid = {27507341}, issn = {1940-6029}, mesh = {Bacteriophages/drug effects/*genetics/growth &amp; development/isolation &amp; purification ; Clostridioides difficile/genetics/*virology ; DNA, Viral/*genetics/metabolism ; *Gene Transfer, Horizontal ; High-Throughput Nucleotide Sequencing ; Host Specificity ; *Lysogeny ; Microscopy, Electron, Transmission ; Taurocholic Acid/pharmacology ; Tetracycline/pharmacology ; *Transduction, Genetic ; Virus Activation/drug effects ; }, abstract = {Bacteriophages mediate horizontal gene transfer through a mechanism known as transduction. Phage transduction carried out in the laboratory involves a bacterial donor and a recipient, both of which are susceptible to infection by the phage of interest. Phage is propagated in the donor, concentrated, and exposed transiently to recipient at different multiplicity of infection ratios. Transductants are selected for the desired phenotype by culture on selective medium. Here we describe transduction of ermB conferring resistance to erythromycin by the C. difficile phage ϕC2.}, }
@article {pmid27507339, year = {2016}, author = {Sekulović, O and Fortier, LC}, title = {Characterization of Functional Prophages in Clostridium difficile.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1476}, number = {}, pages = {143-165}, doi = {10.1007/978-1-4939-6361-4_11}, pmid = {27507339}, issn = {1940-6029}, mesh = {Clostridioides difficile/genetics/*virology ; DNA, Viral/*genetics/metabolism ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genome, Viral ; High-Throughput Nucleotide Sequencing ; Host Specificity ; *Lysogeny ; Microscopy, Electron, Transmission ; Mitomycin/pharmacology ; Myoviridae/classification/genetics/growth &amp; development/isolation &amp; purification ; Prophages/classification/*genetics/growth &amp; development/isolation &amp; purification ; Siphoviridae/classification/genetics/growth &amp; development/isolation &amp; purification ; Transduction, Genetic ; Ultraviolet Rays ; Viral Plaque Assay ; Virus Activation/drug effects/radiation effects ; }, abstract = {Bacteriophages (phages) are present in almost, if not all ecosystems. Some of these bacterial viruses are present as latent "prophages," either integrated within the chromosome of their host, or as episomal DNAs. Since prophages are ubiquitous throughout the bacterial world, there has been a sustained interest in trying to understand their contribution to the biology of their host. Clostridium difficile is no exception to that rule and with the recent release of hundreds of bacterial genome sequences, there has been a growing interest in trying to identify and classify these prophages. Besides their identification in bacterial genomes, there is also growing interest in determining the functionality of C. difficile prophages, i.e., their capacity to escape their host and reinfect a different strain, thereby promoting genomic evolution and horizontal transfer of genes through transduction, for example of antibiotic resistance genes. There is also some interest in using therapeutic phages to fight C. difficile infections.The objective of this chapter is to share with the broader C. difficile research community the expertise we developed in the study of C. difficile temperate phages. In this chapter, we describe a general "pipeline" comprising a series of experiments that we use in our lab to identify, induce, isolate, propagate, and characterize prophages. Our aim is to provide readers with the necessary basic tools to start studying C. difficile phages.}, }
@article {pmid27507008, year = {2016}, author = {Pinos, S and Pontarotti, P and Raoult, D and Baudoin, JP and Pagnier, I}, title = {Compartmentalization in PVC super-phylum: evolution and impact.}, journal = {Biology direct}, volume = {11}, number = {}, pages = {38}, pmid = {27507008}, issn = {1745-6150}, mesh = {Bacteria/*genetics ; Cell Membrane/metabolism ; Cytoplasm/metabolism ; DNA, Bacterial/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Phylogeny ; }, abstract = {BACKGROUND: The PVC super-phylum gathers bacteria from seven phyla (Planctomycetes, Verrucomicrobiae, Chlamydiae, Lentisphaera, Poribacteria, OP3, WWE2) presenting different lifestyles, cell plans and environments. Planctomyces and several Verrucomicrobiae exhibit a complex cell plan, with an intracytoplasmic membrane inducing the compartmentalization of the cytoplasm into two regions (pirellulosome and paryphoplasm). The evolution and function of this cell plan is still subject to debate. In this work, we hypothesized that it could play a role in protection of the bacterial DNA, especially against Horizontal Genes Transfers (HGT). Therefore, 64 bacterial genomes belonging to seven different phyla (whose four PVC phyla) were studied. We reconstructed the evolution of the cell plan as precisely as possible, thanks to information obtained by bibliographic study and electronic microscopy. We used a strategy based on comparative phylogenomic in order to determine the part occupied by the horizontal transfers for each studied genomes.<br><br>RESULTS: Our results show that the bacteria Simkania negevensis (Chlamydiae) and Coraliomargarita akajimensis (Verrucomicrobiae), whose cell plan were unknown before, are compartmentalized, as we can see on the micrographies. This is one of the first indication of the presence of an intracytoplasmic membrane in a Chlamydiae. The proportion of HGT does not seems to be related to the cell plan of bacteria, suggesting that compartmentalization does not induce a protection of bacterial DNA against HGT. Conversely, lifestyle of bacteria seems to impact the ability of bacteria to exchange genes.<br><br>CONCLUSIONS: Our study allows a best reconstruction of the evolution of intracytoplasmic membrane, but this structure seems to have no impact on HGT occurrences.<br><br>REVIEWERS: This article was reviewed by Mircea Podar and Olivier Tenaillon.}, }
@article {pmid27506509, year = {2016}, author = {Michael, GB and Schwarz, S}, title = {Antimicrobial resistance in zoonotic nontyphoidal Salmonella: an alarming trend?.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {22}, number = {12}, pages = {968-974}, doi = {10.1016/j.cmi.2016.07.033}, pmid = {27506509}, issn = {1469-0691}, mesh = {Animals ; Anti-Infective Agents/*pharmacology ; Drug Resistance, Multiple, Bacterial/*genetics ; Europe ; Genes, Bacterial ; Genomic Islands ; Humans ; Microbial Sensitivity Tests ; Salmonella/classification/*drug effects/genetics ; Salmonella Infections/drug therapy ; United States ; Zoonoses/drug therapy/*microbiology ; }, abstract = {Zoonotic bacteria of the genus Salmonella have acquired various antimicrobial resistance properties over the years. The corresponding resistance genes are commonly located on plasmids, transposons, gene cassettes, or variants of the Salmonella Genomic Islands SGI1 and SGI2. Human infections by nontyphoidal Salmonella isolates mainly result from ingestion of contaminated food. The two predominantly found Salmonella enterica subsp. enterica serovars in the USA and in Europe are S. Enteritidis and S. Typhimurium. Many other nontyphoidal Salmonella serovars have been implicated in foodborne Salmonella outbreaks. Summary reports of the antimicrobial susceptibility patterns of nontyphoidal Salmonella isolates over time suggest a moderate to low level of antimicrobial resistance and multidrug-resistance. However, serovar-specific analyses showed in part a steady state, a continuous decline, or a recent increase in resistance to certain antimicrobial agents. Resistance to critically important antimicrobial agents, e.g. third-generation cephalosporins and (fluoro)quinolones is part of many monitoring programmes and the corresponding results confirm that extended-spectrum β-lactamases are still rarely found in nontyphoidal Salmonella serovars, whereas resistance to (fluoro)quinolones is prevalent at variable frequencies among different serovars from humans and animals in different countries. Although it is likely that nontyphoidal Salmonella isolates from animals represent a reservoir for resistance determinants, it is mostly unknown where and when Salmonella isolates acquired resistance properties and which exchange processes have happened since then.}, }
@article {pmid27503765, year = {2016}, author = {Ojala, V and Mattila, S and Hoikkala, V and Bamford, JKh and Hiltunen, T and Jalasvuori, M}, title = {Scoping the effectiveness and evolutionary obstacles in using plasmid-dependent phages to fight antibiotic resistance.}, journal = {Future microbiology}, volume = {11}, number = {}, pages = {999-1009}, doi = {10.2217/fmb-2016-0038}, pmid = {27503765}, issn = {1746-0921}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteriophages/genetics/*physiology ; Conjugation, Genetic ; *Drug Resistance, Bacterial ; Escherichia coli/drug effects/genetics/physiology/*virology ; Escherichia coli Infections/*microbiology ; Humans ; Plasmids/*genetics/metabolism ; }, abstract = {AIM: To investigate the potential evolutionary obstacles in the sustainable therapeutic use of plasmid-dependent phages to control the clinically important conjugative plasmid-mediated dissemination of antibiotic resistance genes to pathogenic bacteria.<br><br>MATERIALS &amp; METHODS: The lytic plasmid-dependent phage PRD1 and the multiresistance conferring plasmid RP4 in an Escherichia coli host were utilized to assess the genetic and phenotypic changes induced by combined phage and antibiotic selection.<br><br>RESULTS &amp; CONCLUSIONS: Resistance to PRD1 was always coupled with either completely lost or greatly reduced conjugation ability. Reversion to full conjugation efficiency was found to be rare, and it also restored the susceptibility to plasmid-dependent phages. Consequently, plasmid-dependent phages constitute an interesting candidate for development of sustainable anticonjugation/antiresistance therapeutic applications.}, }
@article {pmid27503291, year = {2016}, author = {Iranzo, J and Puigbò, P and Lobkovsky, AE and Wolf, YI and Koonin, EV}, title = {Inevitability of Genetic Parasites.}, journal = {Genome biology and evolution}, volume = {8}, number = {9}, pages = {2856-2869}, pmid = {27503291}, issn = {1759-6653}, mesh = {Animals ; DNA Transposable Elements ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genetic Variation ; Genome ; *Host-Parasite Interactions ; *Models, Genetic ; Mutation ; Parasites/*genetics ; Viruses/*genetics ; }, abstract = {Almost all cellular life forms are hosts to diverse genetic parasites with various levels of autonomy including plasmids, transposons and viruses. Theoretical modeling of the evolution of primordial replicators indicates that parasites (cheaters) necessarily evolve in such systems and can be kept at bay primarily via compartmentalization. Given the (near) ubiquity, abundance and diversity of genetic parasites, the question becomes pertinent: are such parasites intrinsic to life? At least in prokaryotes, the persistence of parasites is linked to the rate of horizontal gene transfer (HGT). We mathematically derive the threshold value of the minimal transfer rate required for selfish element persistence, depending on the element duplication and loss rates as well as the cost to the host. Estimation of the characteristic gene duplication, loss and transfer rates for transposons, plasmids and virus-related elements in multiple groups of diverse bacteria and archaea indicates that most of these rates are compatible with the long term persistence of parasites. Notably, a small but non-zero rate of HGT is also required for the persistence of non-parasitic genes. We hypothesize that cells cannot tune their horizontal transfer rates to be below the threshold required for parasite persistence without experiencing highly detrimental side-effects. As a lower boundary to the minimum DNA transfer rate that a cell can withstand, we consider the process of genome degradation and mutational meltdown of populations through Muller's ratchet. A numerical assessment of this hypothesis suggests that microbial populations cannot purge parasites while escaping Muller's ratchet. Thus, genetic parasites appear to be virtually inevitable in cellular organisms.}, }
@article {pmid27501945, year = {2016}, author = {Porse, A and Schønning, K and Munck, C and Sommer, MO}, title = {Survival and Evolution of a Large Multidrug Resistance Plasmid in New Clinical Bacterial Hosts.}, journal = {Molecular biology and evolution}, volume = {33}, number = {11}, pages = {2860-2873}, pmid = {27501945}, issn = {1537-1719}, mesh = {Adaptation, Biological/*genetics ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Conjugation, Genetic ; DNA Transposable Elements ; Drug Resistance, Microbial ; Drug Resistance, Multiple ; Escherichia coli/genetics ; Evolution, Molecular ; Klebsiella pneumoniae/genetics ; Microbial Sensitivity Tests ; Plasmids/*drug effects/*genetics/metabolism ; }, abstract = {Large conjugative plasmids are important drivers of bacterial evolution and contribute significantly to the dissemination of antibiotic resistance. Although plasmid borne multidrug resistance is recognized as one of the main challenges in modern medicine, the adaptive forces shaping the evolution of these plasmids within pathogenic hosts are poorly understood. Here we study plasmid-host adaptations following transfer of a 73 kb conjugative multidrug resistance plasmid to naïve clinical isolates of Klebsiella pneumoniae and Escherichia coli. We use experimental evolution, mathematical modelling and population sequencing to show that the long-term persistence and molecular integrity of the plasmid is highly influenced by multiple factors within a 25 kb plasmid region constituting a host-dependent burden. In the E. coli hosts investigated here, improved plasmid stability readily evolves via IS26 mediated deletions of costly regions from the plasmid backbone, effectively expanding the host-range of the plasmid. Although these adaptations were also beneficial to plasmid persistence in a naïve K. pneumoniae host, they were never observed in this species, indicating that differential evolvability can limit opportunities of plasmid adaptation. While insertion sequences are well known to supply plasmids with adaptive traits, our findings suggest that they also play an important role in plasmid evolution by maintaining the plasticity necessary to alleviate plasmid-host constrains. Further, the observed evolutionary strategy consistently followed by all evolved E. coli lineages exposes a trade-off between horizontal and vertical transmission that may ultimately limit the dissemination potential of clinical multidrug resistance plasmids in these hosts.}, }
@article {pmid27495169, year = {2016}, author = {Miranda-CasoLuengo, AA and Staunton, PM and Dinan, AM and Lohan, AJ and Loftus, BJ}, title = {Functional characterization of the Mycobacterium abscessus genome coupled with condition specific transcriptomics reveals conserved molecular strategies for host adaptation and persistence.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {553}, pmid = {27495169}, issn = {1471-2164}, support = {/WT_/Wellcome Trust/United Kingdom ; 099817/Z/12/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Adaptation, Biological/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; *Evolution, Molecular ; Fatty Acids/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; *Host-Pathogen Interactions ; Hypoxia ; Iron/metabolism ; Mycobacterium/*genetics/metabolism ; Open Reading Frames ; Protein Isoforms ; RNA, Bacterial ; Siderophores/biosynthesis ; Stress, Physiological/genetics ; *Transcriptome ; }, abstract = {BACKGROUND: Mycobacterium abscessus subsp. abscessus (MAB) is a highly drug resistant mycobacterium and the most common respiratory pathogen among the rapidly growing non-tuberculous mycobacteria. MAB is also one of the most deadly of the emerging cystic fibrosis (CF) pathogens requiring prolonged treatment with multiple antibiotics. In addition to its "mycobacterial" virulence genes, the genome of MAB harbours a large accessory genome, presumably acquired via lateral gene transfer including homologs shared with the CF pathogens Pseudomonas aeruginosa and Burkholderia cepacia. While multiple genome sequences are available there is little functional genomics data available for this important pathogen.<br><br>RESULTS: We report here the first multi-omics approach to characterize the primary transcriptome, coding potential and potential regulatory regions of the MAB genome utilizing differential RNA sequencing (dRNA-seq), RNA-seq, Ribosome profiling and LC-MS proteomics. In addition we attempt to address the genomes contribution to the molecular systems that underlie MAB's adaptation and persistence in the human host through an examination of MABs transcriptional response to a number of clinically relevant conditions. These include hypoxia, exposure to sub-inhibitory concentrations of antibiotics and growth in an artificial sputum designed to mimic the conditions within the cystic fibrosis lung.<br><br>CONCLUSIONS: Our integrated map provides the first comprehensive view of the primary transcriptome of MAB and evidence for the translation of over one hundred new short open reading frames (sORFs). Our map will act as a resource for ongoing functional genomics characterization of MAB and our transcriptome data from clinically relevant stresses informs our understanding of MAB's adaptation to life in the CF lung. MAB's adaptation to growth in artificial CF sputum highlights shared metabolic strategies with other CF pathogens including P. aeruginosa and mirrors the transcriptional responses that lead to persistence in mycobacteria. These strategies include an increased reliance on amino acid metabolism, and fatty acid catabolism and highlights the relevance of the glyoxylate shunt to growth in the CF lung. Our data suggests that, similar to what is seen in chronically persisting P. aeruginosa, progression towards a biofilm mode of growth would play a more prominent role in a longer-term MAB infection. Finally, MAB's transcriptional response to antibiotics highlights the role of antibiotic modifications enzymes, active transport and the evolutionarily conserved WhiB7 driven antibiotic resistance regulon.}, }
@article {pmid27494919, year = {2016}, author = {Hammerum, AM and Hansen, F and Nielsen, HL and Jakobsen, L and Stegger, M and Andersen, PS and Jensen, P and Nielsen, TK and Hansen, LH and Hasman, H and Fuglsang-Damgaard, D}, title = {Use of WGS data for investigation of a long-term NDM-1-producing Citrobacter freundii outbreak and secondary in vivo spread of blaNDM-1 to Escherichia coli, Klebsiella pneumoniae and Klebsiella oxytoca.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {71}, number = {11}, pages = {3117-3124}, doi = {10.1093/jac/dkw289}, pmid = {27494919}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/pharmacology ; Citrobacter freundii/classification/*enzymology/genetics/isolation &amp; purification ; Denmark/epidemiology ; *Disease Outbreaks ; Enterobacteriaceae Infections/*epidemiology/microbiology ; Escherichia coli/*enzymology/genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; Genome, Bacterial ; *Genotype ; Humans ; Klebsiella/*enzymology/genetics/isolation &amp; purification ; Meropenem ; Microbial Sensitivity Tests ; Phylogeny ; Plasmids/analysis/classification ; Sequence Analysis, DNA ; Thienamycins/pharmacology ; beta-Lactam Resistance ; beta-Lactamases/genetics/*metabolism ; }, abstract = {OBJECTIVES: An outbreak of NDM-1-producing Citrobacter freundii and possible secondary in vivo spread of blaNDM-1 to other Enterobacteriaceae were investigated.<br><br>METHODS: From October 2012 to March 2015, meropenem-resistant Enterobacteriaceae were detected in 45 samples from seven patients at Aalborg University Hospital, Aalborg, Denmark. In silico resistance genes, Inc plasmid types and STs (MLST) were obtained from WGS data from 24 meropenem-resistant isolates (13 C. freundii, 6 Klebsiella pneumoniae, 4 Escherichia coli and 1 Klebsiella oxytoca) and 1 meropenem-susceptible K. oxytoca. The sequences of the meropenem-resistant C. freundii isolates were compared by phylogenetic analyses. In vitro susceptibility to 21 antimicrobial agents was tested. Furthermore, in vitro conjugation and plasmid characterization was performed.<br><br>RESULTS: From the seven patients, 13 highly clonal ST18 NDM-1-producing C. freundii were isolated. The ST18 NDM-1-producing C. freundii isolates were only susceptible to tetracycline, tigecycline, colistin and fosfomycin (except for the C. freundii isolates from Patient 2 and Patient 7, which were additionally resistant to tetracycline). The E. coli and K. pneumoniae from different patients belonged to different STs, indicating in vivo transfer of blaNDM-1 in the individual patients. This was further supported by in vitro conjugation and detection of a 154 kb IncA/C2 plasmid with blaNDM-1. Patient screenings failed to reveal any additional cases. None of the patients had a history of recent travel abroad and the source of the blaNDM-1 plasmid was unknown.<br><br>CONCLUSIONS: To our knowledge, this is the first report of an NDM-1-producing C. freundii outbreak and secondary in vivo spread of an IncA/C2 plasmid with blaNDM-1 to other Enterobacteriaceae.}, }
@article {pmid27494913, year = {2016}, author = {Khong, WX and Marimuthu, K and Teo, J and Ding, Y and Xia, E and Lee, JJ and Ong, RT and Venkatachalam, I and Cherng, B and Pada, SK and Choong, WL and Smitasin, N and Ooi, ST and Deepak, RN and Kurup, A and Fong, R and Van La, M and Tan, TY and Koh, TH and Lin, RT and Tan, EL and Krishnan, PU and Singh, S and Pitout, JD and Teo, YY and Yang, L and Ng, OT and , }, title = {Tracking inter-institutional spread of NDM and identification of a novel NDM-positive plasmid, pSg1-NDM, using next-generation sequencing approaches.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {71}, number = {11}, pages = {3081-3089}, doi = {10.1093/jac/dkw277}, pmid = {27494913}, issn = {1460-2091}, mesh = {Enterobacteriaceae/classification/*enzymology/genetics/*isolation &amp; purification ; Enterobacteriaceae Infections/epidemiology/*microbiology/transmission ; Gene Transfer, Horizontal ; Health Facilities ; *High-Throughput Nucleotide Sequencing ; Humans ; Molecular Epidemiology ; Plasmids/classification/*isolation &amp; purification ; *Sequence Analysis, DNA ; Singapore/epidemiology ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: Owing to gene transposition and plasmid conjugation, New Delhi metallo-β-lactamase (NDM) is typically identified among varied Enterobacteriaceae species and STs. We used WGS to characterize the chromosomal and plasmid molecular epidemiology of NDM transmission involving four institutions in Singapore.<br><br>METHODS: Thirty-three Enterobacteriaceae isolates (collection years 2010-14) were sequenced using short-read sequencing-by-synthesis and analysed. Long-read single molecule, real-time sequencing (SMRTS) was used to characterize genetically a novel plasmid pSg1-NDM carried on Klebsiella pneumoniae ST147.<br><br>RESULTS: In 20 (61%) isolates, blaNDM was located on the pNDM-ECS01 plasmid in the background of multiple bacterial STs, including eight K. pneumoniae STs and five Escherichia coli STs. In six (18%) isolates, a novel blaNDM-positive plasmid, pSg1-NDM, was found only in K. pneumoniae ST147. The pSg1-NDM-K. pneumoniae ST147 clone (Sg1-NDM) was fully sequenced using SMRTS. pSg1-NDM, a 90&#x200a;103 bp IncR plasmid, carried genes responsible for resistance to six classes of antimicrobials. A large portion of pSg1-NDM had no significant homology to any known plasmids in GenBank. pSg1-NDM had no conjugative transfer region. Combined chromosomal-plasmid phylogenetic analysis revealed five clusters of clonal bacterial NDM-positive plasmid transmission, of which two were inter-institution clusters. The largest inter-institution cluster involved six K. pneumoniae ST147-pSg1-NDM isolates. Fifteen patients were involved in transmission clusters, of which four had ward contact, six had hospital contact and five had an unknown transmission link.<br><br>CONCLUSIONS: A combined sequencing-by-synthesis and SMRTS approach can determine effectively the transmission clusters of blaNDM and genetically characterize novel plasmids. Plasmid molecular epidemiology is important to understanding NDM spread as blaNDM-positive plasmids can conjugate extensively across species and STs.}, }
@article {pmid27494616, year = {2016}, author = {Das, A and Natarajan, M and Mandal, J}, title = {The Emergence of Quinolone Resistant Shigella sonnei, Pondicherry, India.}, journal = {PloS one}, volume = {11}, number = {8}, pages = {e0160290}, pmid = {27494616}, issn = {1932-6203}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics ; Ciprofloxacin/pharmacology ; Drug Resistance, Bacterial/*drug effects/genetics ; Dysentery, Bacillary/microbiology ; Feces/microbiology ; Humans ; India ; Levofloxacin/pharmacology ; Microbial Sensitivity Tests ; Plasmids/genetics ; Quinolones/*pharmacology ; Shigella sonnei/*drug effects/*genetics/isolation &amp; purification/pathogenicity ; }, abstract = {Ciprofloxacin resistant Shigella sonnei across the globe have been increasing alarmingly. In order to understand the emergence of S.sonnei with respect to ciprofloxacin resistance in our patient population, the following study was carried out. Of the 184 Shigella sp. Isolated from 2012 to 2015, 34 S.sonnei which were confirmed by standard methods and subjected to antimicrobial susceptibility testing were selected. The minimum inhibitory concentrations (MICs) of 16/34 quinolone resistant isolates tested ranged from 4micrograms/ml to 16micrograms/ml for ciprofloxacin, from 16 micrograms/ml to 64 micrograms/ml for ofloxacin and from 16micrograms/ml to 64micrograms/ml for levofloxacin. Sequence determination of the quinolone resistance determining regions of gyrA, gyrB, parC, and parE genes showed mutations in GyrA at Gln69/Trp, Phe71/Ser, Ser72/Pro, Met75/Leu, Ser90/Cys, Met94/Leu, His106/Pro, Asn161/His, Thr163/Ala and in ParC at Ala64/Asp. Among the plasmid-mediated quinolone resistance (PMQRs) targets investigated,qnrB was the most (93.7%) prevalent followed by qnrC (18.7%). None hadqnrA, qnrS and qepA. Two (0.1%) of the isolates harboured theaac(6')-lb gene. Drug accumulation assay detected the presence of efflux pump activity in 9/15 (60%) among ciprofloxacin resistant isolates. All isolates harboured the ipaH gene followed by ial (17.6%), sen (11.7%), set1A&amp;set1B (5.8%) genes. None had stx1 element. PCR for Enterobacterial repetitive intergenic consensus (ERIC) sequences resulted in 4 unique clusters, of which Type III was the most (44%) dominant but there was no correlation between the ERIC types and the antibiotic resistance pattern or the virulence profile. A documented increase in S.sonnei harbouring the qnrgenes and some unusual genes like set1Aand indicate an ongoing process of horizontal gene transfer. The accumulation of novel mutations in GyrA and ParC in the presence of efflux pump and PMQR genes contributed to the raised MIC to quinolones. These findings are crucial in our understanding of quinolone resistance in these isolates.}, }
@article {pmid27492287, year = {2016}, author = {Pfeifer, E and Hünnefeld, M and Popa, O and Polen, T and Kohlheyer, D and Baumgart, M and Frunzke, J}, title = {Silencing of cryptic prophages in Corynebacterium glutamicum.}, journal = {Nucleic acids research}, volume = {44}, number = {21}, pages = {10117-10131}, pmid = {27492287}, issn = {1362-4962}, mesh = {AT Rich Sequence ; Actinobacteria/genetics ; Corynebacterium glutamicum/*genetics ; DNA, Viral/metabolism ; Gene Silencing ; Gene Transfer, Horizontal ; Genome, Bacterial ; Genome-Wide Association Study ; Prophages/*genetics/physiology ; Sequence Homology, Amino Acid ; Viral Proteins/genetics/*metabolism ; }, abstract = {DNA of viral origin represents a ubiquitous element of bacterial genomes. Its integration into host regulatory circuits is a pivotal driver of microbial evolution but requires the stringent regulation of phage gene activity. In this study, we describe the nucleoid-associated protein CgpS, which represents an essential protein functioning as a xenogeneic silencer in the Gram-positive Corynebacterium glutamicum CgpS is encoded by the cryptic prophage CGP3 of the C. glutamicum strain ATCC 13032 and was first identified by DNA affinity chromatography using an early phage promoter of CGP3. Genome-wide profiling of CgpS binding using chromatin affinity purification and sequencing (ChAP-Seq) revealed its association with AT-rich DNA elements, including the entire CGP3 prophage region (187 kbp), as well as several other elements acquired by horizontal gene transfer. Countersilencing of CgpS resulted in a significantly increased induction frequency of the CGP3 prophage. In contrast, a strain lacking the CGP3 prophage was not affected and displayed stable growth. In a bioinformatics approach, cgpS orthologs were identified primarily in actinobacterial genomes as well as several phage and prophage genomes. Sequence analysis of 618 orthologous proteins revealed a strong conservation of the secondary structure, supporting an ancient function of these xenogeneic silencers in phage-host interaction.}, }
@article {pmid27490553, year = {2016}, author = {Morohoshi, T and Okutsu, N and Xie, X and Ikeda, T}, title = {Identification of Quorum-Sensing Signal Molecules and a Biosynthetic Gene in Alicycliphilus sp. Isolated from Activated Sludge.}, journal = {Sensors (Basel, Switzerland)}, volume = {16}, number = {8}, pages = {}, pmid = {27490553}, issn = {1424-8220}, mesh = {Acyl-Butyrolactones/chemistry ; Alicyclobacillus/genetics/*isolation &amp; purification ; Bacteria/genetics/*isolation &amp; purification ; Biosensing Techniques/*methods ; Escherichia coli/genetics ; Quorum Sensing/*genetics ; Sewage/microbiology ; Wastewater/chemistry/microbiology ; }, abstract = {Activated sludge is a complicated mixture of various microorganisms that is used to treat sewage and industrial wastewater. Many bacteria produce N-acylhomoserine lactone (AHL) as a quorum-sensing signal molecule to regulate the expression of the exoenzymes used for wastewater treatment. Here, we isolated an AHL-producing bacteria from an activated sludge sample collected from an electronic component factory, which we named Alicycliphilus sp. B1. Clone library analysis revealed that Alicycliphilus was a subdominant genus in this sample. When we screened the activated sludge sample for AHL-producing strains, 12 of 14 the AHL-producing isolates were assigned to the genus Alicycliphilus. A putative AHL-synthase gene, ALISP_0667, was cloned from the genome of B1 and transformed into Escherichia coli DH5α. The AHLs were extracted from the culture supernatants of the B1 strain and E. coli DH5α cells harboring the ALISP_0667 gene and were identified by liquid chromatography-mass spectrometry as N-(3-hydroxydecanoyl)-l-homoserine lactone and N-(3-hydroxydodecanoyl)-l-homoserine lactone. The results of comparative genomic analysis suggested that the quorum-sensing genes in the B1 strain might have been acquired by horizontal gene transfer within activated sludge.}, }
@article {pmid27490492, year = {2016}, author = {Janek, D and Zipperer, A and Kulik, A and Krismer, B and Peschel, A}, title = {High Frequency and Diversity of Antimicrobial Activities Produced by Nasal Staphylococcus Strains against Bacterial Competitors.}, journal = {PLoS pathogens}, volume = {12}, number = {8}, pages = {e1005812}, pmid = {27490492}, issn = {1553-7374}, mesh = {Antibiosis/*physiology ; Bacteriocins/*biosynthesis ; Chromatography, High Pressure Liquid ; Humans ; Microbiota ; Nose/*microbiology ; Polymerase Chain Reaction ; Spectrometry, Mass, Electrospray Ionization ; Staphylococcus/*metabolism ; }, abstract = {The human nasal microbiota is highly variable and dynamic often enclosing major pathogens such as Staphylococcus aureus. The potential roles of bacteriocins or other mechanisms allowing certain bacterial clones to prevail in this nutrient-poor habitat have hardly been studied. Of 89 nasal Staphylococcus isolates, unexpectedly, the vast majority (84%) was found to produce antimicrobial substances in particular under habitat-specific stress conditions, such as iron limitation or exposure to hydrogen peroxide. Activity spectra were generally narrow but highly variable with activities against certain nasal members of the Actinobacteria, Proteobacteria, Firmicutes, or several groups of bacteria. Staphylococcus species and many other Firmicutes were insusceptible to most of the compounds. A representative bacteriocin was identified as a nukacin-related peptide whose inactivation reduced the capacity of the producer Staphylococcus epidermidis IVK45 to limit growth of other nasal bacteria. Of note, the bacteriocin genes were found on mobile genetic elements exhibiting signs of extensive horizontal gene transfer and rearrangements. Thus, continuously evolving bacteriocins appear to govern bacterial competition in the human nose and specific bacteriocins may become important agents for eradication of notorious opportunistic pathogens from human microbiota.}, }
@article {pmid27489797, year = {2016}, author = {Miranda, A and Ávila, B and Díaz, P and Rivas, L and Bravo, K and Astudillo, J and Bueno, C and Ulloa, MT and Hermosilla, G and Del Canto, F and Salazar, JC and Toro, CS}, title = {Emergence of Plasmid-Borne dfrA14 Trimethoprim Resistance Gene in Shigella sonnei.}, journal = {Frontiers in cellular and infection microbiology}, volume = {6}, number = {}, pages = {77}, pmid = {27489797}, issn = {2235-2988}, mesh = {Chile/epidemiology ; Cloning, Molecular ; Disease Outbreaks ; Dysentery, Bacillary/epidemiology/microbiology ; Gene Order ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; *Plasmids ; Sequence Analysis, DNA ; Shigella sonnei/*drug effects/*genetics/isolation &amp; purification ; Tetrahydrofolate Dehydrogenase/*genetics ; *Trimethoprim Resistance ; }, abstract = {The most common mechanism of trimethoprim (TMP)-resistance is the acquisition of dihydrofolate reductase enzyme resistant to this drug. Previous molecular characterization of TMP-genes resistance in Chilean isolates of Shigella sonnei searching for dfrA1 and dfrA8, showed solely the presence of dfrA8 (formerly dhfrIIIc). However, these genetic markers were absent in S. sonnei strains further isolated during an outbreak in 2009. To identify the TMP-resistance gene in these strains, a genomic DNA library from a TMP-resistant (TMP(R)) S. sonnei representative strain for the outbreak was used to clone, select and identify a TMP-resistance marker. The TMP(R) clone was sequenced by primer walking, identifying the presence of the dfrA14 gene in the sul2-strA'-dfrA14-'strA-strB gene arrangement, harbored in a native 6779-bp plasmid. The same plasmid was isolated by transforming with a ~4.2 MDa plasmid extracted from several TMP(R) S. sonnei strains into Escherichia coli. This plasmid, named pABC-3, was present only in dfrA14-positive strains and was homologous to a previously described pCERC-1, but different due to the absence of an 11-bp repetitive unit. The distribution of dfrA1, dfrA8, and dfrA14 TMP-resistance genes was determined in 126 TMP(R) S. sonnei isolates. Most of the strains (96%) carried only one of the three TMP-resistance genes assessed. Thus, all strains obtained during the 2009-outbreak harbored only dfrA14, whereas, dfrA8 was the most abundant gene marker before outbreak and, after the outbreak dfrA1 seems have appeared in circulating strains. According to PFGE, dfrA14-positive strains were clustered in a genetically related group including some dfrA1- and dfrA8-positive strains; meanwhile other genetic group included most of the dfrA8-positive strains. This distribution also correlated with the isolation period, showing a dynamics of trimethoprim genetic markers prevalent in Chilean S. sonnei strains. To our knowledge, dfrA14 gene associated to a small non-conjugative plasmid was detected for the first time in Shigella. Apparently, the strain causing the outbreak must have been introduced, changing drastically the genetic distribution of trimethoprim resistance in Chilean S. sonnei strains.}, }
@article {pmid27489097, year = {2016}, author = {Acevedo-Rocha, CG and Budisa, N}, title = {Xenomicrobiology: a roadmap for genetic code engineering.}, journal = {Microbial biotechnology}, volume = {9}, number = {5}, pages = {666-676}, pmid = {27489097}, issn = {1751-7915}, mesh = {Biotechnology/methods/trends ; *Genetic Code ; Metabolic Engineering/*methods ; Synthetic Biology/*methods ; Technology, Pharmaceutical/methods/trends ; }, abstract = {Biology is an analytical and informational science that is becoming increasingly dependent on chemical synthesis. One example is the high-throughput and low-cost synthesis of DNA, which is a foundation for the research field of synthetic biology (SB). The aim of SB is to provide biotechnological solutions to health, energy and environmental issues as well as unsustainable manufacturing processes in the frame of naturally existing chemical building blocks. Xenobiology (XB) goes a step further by implementing non-natural building blocks in living cells. In this context, genetic code engineering respectively enables the re-design of genes/genomes and proteins/proteomes with non-canonical nucleic (XNAs) and amino (ncAAs) acids. Besides studying information flow and evolutionary innovation in living systems, XB allows the development of new-to-nature therapeutic proteins/peptides, new biocatalysts for potential applications in synthetic organic chemistry and biocontainment strategies for enhanced biosafety. In this perspective, we provide a brief history and evolution of the genetic code in the context of XB. We then discuss the latest efforts and challenges ahead for engineering the genetic code with focus on substitutions and additions of ncAAs as well as standard amino acid reductions. Finally, we present a roadmap for the directed evolution of artificial microbes for emancipating rare sense codons that could be used to introduce novel building blocks. The development of such xenomicroorganisms endowed with a 'genetic firewall' will also allow to study and understand the relation between code evolution and horizontal gene transfer.}, }
@article {pmid28480050, year = {2016}, author = {Stalder, T and Top, E}, title = {Plasmid transfer in biofilms: a perspective on limitations and opportunities.}, journal = {NPJ biofilms and microbiomes}, volume = {2}, number = {}, pages = {16022-}, pmid = {28480050}, issn = {2055-5008}, support = {R01 AI084918/AI/NIAID NIH HHS/United States ; }, abstract = {Biofilms dominate microbial life, and their importance for human health and the environment can no longer be dismissed. Nevertheless many of the processes governing this form of microbial growth are still poorly understood. This includes the horizontal exchange of genetic information, which is a major driver in bacterial evolution and rapid adaptation, exemplified by the alarming spread of multi-drug resistance among pathogens mediated by plasmids. Biofilms are often considered hot spot for horizontal gene transfer, yet several studies have shown that plasmid transfer is limited to the outer layers. On the basis of results from decades of research we analyse this paradox and discuss the mechanisms by which biofilm growth can promote the initial transfer of some plasmids, but also limit further plasmid invasion into the population or community. If we want to adequately promote or combat horizontal gene spread in biofilms, we need to gain better insight into the physicochemical and biological mechanisms that control this process.}, }
@article {pmid28433315, year = {2015}, author = {Abriouel, H and Casado Muñoz, MDC and Lavilla Lerma, L and Pérez Montoro, B and Bockelmann, W and Pichner, R and Kabisch, J and Cho, GS and Franz, CMAP and Gálvez, A and Benomar, N}, title = {New insights in antibiotic resistance of Lactobacillus species from fermented foods.}, journal = {Food research international (Ottawa, Ont.)}, volume = {78}, number = {}, pages = {465-481}, doi = {10.1016/j.foodres.2015.09.016}, pmid = {28433315}, issn = {1873-7145}, }
@article {pmid28348822, year = {2015}, author = {Marttinen, P and Croucher, NJ and Gutmann, MU and Corander, J and Hanage, WP}, title = {Recombination produces coherent bacterial species clusters in both core and accessory genomes.}, journal = {Microbial genomics}, volume = {1}, number = {5}, pages = {e000038}, pmid = {28348822}, issn = {2057-5858}, abstract = {BACKGROUND: Population samples show bacterial genomes can be divided into a core of ubiquitous genes and accessory genes that are present in a fraction of isolates. The ecological significance of this variation in gene content remains unclear. However, microbiologists agree that a bacterial species should be 'genomically coherent', even though there is no consensus on how this should be determined.<br><br>RESULTS: We use a parsimonious model combining diversification in both the core and accessory genome, including mutation, homologous recombination (HR) and horizontal gene transfer (HGT) introducing new loci, to produce a population of interacting clusters of strains with varying genome content. New loci introduced by HGT may then be transferred on by HR. The model fits well to a systematic population sample of 616 pneumococcal genomes, capturing the major features of the population structure with parameter values that agree well with empirical estimates.<br><br>CONCLUSIONS: The model does not include explicit selection on individual genes, suggesting that crude comparisons of gene content may be a poor predictor of ecological function. We identify a clearly divergent subpopulation of pneumococci that are inconsistent with the model and may be considered genomically incoherent with the rest of the population. These strains have a distinct disease tropism and may be rationally defined as a separate species. We also find deviations from the model that may be explained by recent population bottlenecks or spatial structure.}, }
@article {pmid29124226, year = {2015}, author = {Nagao, N and Yamamoto, J and Komatsu, H and Suzuki, H and Hirose, Y and Umekage, S and Ohyama, T and Kikuchi, Y}, title = {The gene transfer agent-like particle of the marine phototrophic bacterium Rhodovulum sulfidophilum.}, journal = {Biochemistry and biophysics reports}, volume = {4}, number = {}, pages = {369-374}, pmid = {29124226}, issn = {2405-5808}, abstract = {Gene transfer agents (GTAs) are shaped like bacteriophage particles but have many properties that distinguish them from bacteriophages. GTAs play a role in horizontal gene transfer in nature and thus affect the evolution of prokaryotic genomes. In the course of studies on the extracellular production of designed RNAs using the marine bacterium Rhodovulum sulfidophilum, we found that this bacterium produces a GTA-like particle. The particle contains DNA fragments of 4.5 kb, which consist of randomly fragmented genomic DNA from the bacterium. This 4.5-kb DNA production was prevented while quorum sensing was inhibited. Direct observation of the particle by transmission electron microscopy revealed that the particle resembles a tailed phage and has a head diameter of about 40 nm and a tail length of about 60 nm. We also identified the structural genes for the GTA in the genome. Translated amino acid sequences and gene positions are closely related to those of the genes that encode the Rhodobacter capsulatus GTA. This is the first report of a GTA-like particle from the genus Rhodovulum. However, gene transfer activity of this particle has not yet been confirmed. The differences between this particle and other GTAs are discussed.}, }
@article {pmid28357301, year = {2015}, author = {Taylor, TB and Mulley, G and McGuffin, LJ and Johnson, LJ and Brockhurst, MA and Arseneault, T and Silby, MW and Jackson, RW}, title = {Evolutionary rewiring of bacterial regulatory networks.}, journal = {Microbial cell (Graz, Austria)}, volume = {2}, number = {7}, pages = {256-258}, doi = {10.15698/mic2015.07.215}, pmid = {28357301}, issn = {2311-2638}, abstract = {Bacteria have evolved complex regulatory networks that enable integration of multiple intracellular and extracellular signals to coordinate responses to environmental changes. However, our knowledge of how regulatory systems function and evolve is still relatively limited. There is often extensive homology between components of different networks, due to past cycles of gene duplication, divergence, and horizontal gene transfer, raising the possibility of cross-talk or redundancy. Consequently, evolutionary resilience is built into gene networks - homology between regulators can potentially allow rapid rescue of lost regulatory function across distant regions of the genome. In our recent study [Taylor, et al. Science (2015), 347(6225)] we find that mutations that facilitate cross-talk between pathways can contribute to gene network evolution, but that such mutations come with severe pleiotropic costs. Arising from this work are a number of questions surrounding how this phenomenon occurs.}, }
@article {pmid27774277, year = {2015}, author = {Martin, DP and Murrell, B and Golden, M and Khoosal, A and Muhire, B}, title = {RDP4: Detection and analysis of recombination patterns in virus genomes.}, journal = {Virus evolution}, volume = {1}, number = {1}, pages = {vev003}, pmid = {27774277}, issn = {2057-1577}, support = {K24 AI100665/AI/NIAID NIH HHS/United States ; U01 GM110749/GM/NIGMS NIH HHS/United States ; U19 AI090970/AI/NIAID NIH HHS/United States ; }, abstract = {RDP4 is the latest version of recombination detection program (RDP), a Windows computer program that implements an extensive array of methods for detecting and visualising recombination in, and stripping evidence of recombination from, virus genome sequence alignments. RDP4 is capable of analysing twice as many sequences (up to 2,500) that are up to three times longer (up to 10 Mb) than those that could be analysed by older versions of the program. RDP4 is therefore also applicable to the analysis of bacterial full-genome sequence datasets. Other novelties in RDP4 include (1) the capacity to differentiate between recombination and genome segment reassortment, (2) the estimation of recombination breakpoint confidence intervals, (3) a variety of 'recombination aware' phylogenetic tree construction and comparison tools, (4) new matrix-based visualisation tools for examining both individual recombination events and the overall phylogenetic impacts of multiple recombination events and (5) new tests to detect the influences of gene arrangements, encoded protein structure, nucleic acid secondary structure, nucleotide composition, and nucleotide diversity on recombination breakpoint patterns. The key feature of RDP4 that differentiates it from other recombination detection tools is its flexibility. It can be run either in fully automated mode from the command line interface or with a graphically rich user interface that enables detailed exploration of both individual recombination events and overall recombination patterns.}, }
@article {pmid28362003, year = {2015}, author = {Zíková, A and Oborník, M and Lukeš, J}, title = {Fancy a gene? A surprisingly complex evolutionary history of peroxiredoxins.}, journal = {Microbial cell (Graz, Austria)}, volume = {2}, number = {2}, pages = {33-37}, pmid = {28362003}, issn = {2311-2638}, abstract = {While the phylum Apicomplexa includes "only" several thousand described species of obligatory parasites of animals, it may in fact be the most specious group of parasitic protists with over a million species 1. The best known representatives are Plasmodium spp., Toxoplasma gondii and Cryptosporidium spp., which belong to the most important and widespread human parasites exacting an enormous disease burden. On the other hand, dinoflagellates and colpodellids, which are monophyletic with the apicomplexans, are ecologically highly significant, as they belong to the most abundant marine protists 2. As the common ancestor of these groups was most likely a free-living photosynthesizing protist, one wonders, which evolutionary forces contributed to the dramatic transition of some of its descendants into the arguably most successful intracellular parasites? Although a range of various processes and mechanisms contributed to this transition, most likely it also involved an acquisition of genes via horizontal gene transfer (HGT), which might have provided typical characteristics of a parasitic cell, such as immune escape, nutritional dependence and the capacity to invade other cells.}, }
@article {pmid28357258, year = {2015}, author = {Djuika, CF and Huerta-Cepas, J and Przyborski, JM and Deil, S and Sanchez, CP and Doerks, T and Bork, P and Lanzer, M and Deponte, M}, title = {Prokaryotic ancestry and gene fusion of a dual localized peroxiredoxin in malaria parasites.}, journal = {Microbial cell (Graz, Austria)}, volume = {2}, number = {1}, pages = {5-13}, pmid = {28357258}, issn = {2311-2638}, abstract = {Horizontal gene transfer has emerged as a crucial driving force for the evolution of eukaryotes. This also includes Plasmodium falciparum and related economically and clinically relevant apicomplexan parasites, whose rather small genomes have been shaped not only by natural selection in different host populations but also by horizontal gene transfer following endosymbiosis. However, there is rather little reliable data on horizontal gene transfer between animal hosts or bacteria and apicomplexan parasites. Here we show that apicomplexan homologues of peroxiredoxin 5 (Prx5) have a prokaryotic ancestry and therefore represent a special subclass of Prx5 isoforms in eukaryotes. Using two different immunobiochemical approaches, we found that the P. falciparum Prx5 homologue is dually localized to the parasite plastid and cytosol. This dual localization is reflected by a modular Plasmodium-specific gene architecture consisting of two exons. Despite the plastid localization, our phylogenetic analyses contradict an acquisition by secondary endosymbiosis and support a gene fusion event following a horizontal prokaryote-to-eukaryote gene transfer in early apicomplexans. The results provide unexpected insights into the evolution of apicomplexan parasites as well as the molecular evolution of peroxiredoxins, an important family of ubiquitous, usually highly concentrated thiol-dependent hydroperoxidases that exert functions as detoxifying enzymes, redox sensors and chaperones.}, }
@article {pmid27682088, year = {2015}, author = {Downing, T}, title = {Tackling Drug Resistant Infection Outbreaks of Global Pandemic Escherichia coli ST131 Using Evolutionary and Epidemiological Genomics.}, journal = {Microorganisms}, volume = {3}, number = {2}, pages = {236-267}, pmid = {27682088}, issn = {2076-2607}, abstract = {High-throughput molecular screening is required to investigate the origin and diffusion of antimicrobial resistance in pathogen outbreaks. The most frequent cause of human infection is Escherichia coli, which is dominated by sequence type 131 (ST131)-a set of rapidly radiating pandemic clones. The highly infectious clades of ST131 originated firstly by a mutation enhancing conjugation and adhesion. Secondly, single-nucleotide polymorphisms occurred enabling fluoroquinolone-resistance, which is near-fixed in all ST131. Thirdly, broader resistance through beta-lactamases has been gained and lost frequently, symptomatic of conflicting environmental selective effects. This flexible approach to gene exchange is worrying and supports the proposition that ST131 will develop an even wider range of plasmid and chromosomal elements promoting antimicrobial resistance. To stop ST131, deep genome sequencing is required to understand the origin, evolution and spread of antimicrobial resistance genes. Phylogenetic methods that decipher past events can predict future patterns of virulence and transmission based on genetic signatures of adaptation and gene exchange. Both the effect of partial antimicrobial exposure and cell dormancy caused by variation in gene expression may accelerate the development of resistance. High-throughput sequencing can decode measurable evolution of cell populations within patients associated with systems-wide changes in gene expression during treatments. A multi-faceted approach can enhance assessment of antimicrobial resistance in E. coli ST131 by examining transmission dynamics between hosts to achieve a goal of pre-empting resistance before it emerges by optimising antimicrobial treatment protocols.}, }
@article {pmid27682079, year = {2015}, author = {Nayak, DD and Marx, CJ}, title = {Experimental Horizontal Gene Transfer of Methylamine Dehydrogenase Mimics Prevalent Exchange in Nature and Overcomes the Methylamine Growth Constraints Posed by the Sub-Optimal N-Methylglutamate Pathway.}, journal = {Microorganisms}, volume = {3}, number = {1}, pages = {60-79}, pmid = {27682079}, issn = {2076-2607}, support = {R01 GM078209/GM/NIGMS NIH HHS/United States ; }, abstract = {Methylamine plays an important role in the global carbon and nitrogen budget; microorganisms that grow on reduced single carbon compounds, methylotrophs, serve as a major biological sink for methylamine in aerobic environments. Two non-orthologous, functionally degenerate routes for methylamine oxidation have been studied in methylotrophic Proteobacteria: Methylamine dehydrogenase and the N-methylglutamate pathway. Recent work suggests the N-methylglutamate (NMG) pathway may be more common in nature than the well-studied methylamine dehydrogenase (MaDH, encoded by the mau gene cluster). However, the distribution of these pathways across methylotrophs has never been analyzed. Furthermore, even though horizontal gene transfer (HGT) is commonly invoked as a means to transfer these pathways between strains, the physiological barriers to doing so have not been investigated. We found that the NMG pathway is both more abundant and more universally distributed across methylotrophic Proteobacteria compared to MaDH, which displays a patchy distribution and has clearly been transmitted by HGT even amongst very closely related strains. This trend was especially prominent in well-characterized strains of the Methylobacterium extroquens species, which also display significant phenotypic variability during methylamine growth. Strains like Methylobacterium extorquens PA1 that only encode the NMG pathway grew on methylamine at least five-fold slower than strains like Methylobacterium extorquens AM1 that also possess the mau gene cluster. By mimicking a HGT event through the introduction of the M. extorquens AM1 mau gene cluster into the PA1 genome, the resulting strain instantaneously achieved a 4.5-fold increase in growth rate on methylamine and a 11-fold increase in fitness on methylamine, which even surpassed the fitness of M. extorquens AM1. In contrast, when three replicate populations of wild type M. extorquens PA1 were evolved on methylamine as the sole carbon and energy source for 150 generations neither fitness nor growth rate improved. These results suggest that the NMG pathway permits slow growth on methylamine and is widely distributed in methylotrophs; however, rapid growth on methylamine can be achieved quite readily through acquisition of the mau cluster by HGT.}, }
@article {pmid27873693, year = {2014}, author = {Narciso-da-Rocha, C and Varela, AR and Schwartz, T and Nunes, OC and Manaia, CM}, title = {blaTEM and vanA as indicator genes of antibiotic resistance contamination in a hospital-urban wastewater treatment plant system.}, journal = {Journal of global antimicrobial resistance}, volume = {2}, number = {4}, pages = {309-315}, doi = {10.1016/j.jgar.2014.10.001}, pmid = {27873693}, issn = {2213-7173}, abstract = {Four indicator genes were monitored by quantitative PCR in hospital effluent (HE) and in the raw and treated wastewater of the municipal wastewater treatment plant receiving the hospital discharge. The indicator genes were the class 1 integrase gene intI1, to assess the capacity of bacteria to be involved in horizontal gene transfer processes; blaTEM, one of the most widespread antibiotic resistance genes in the environment, associated with Enterobacteriaceae; vanA, an antibiotic resistance gene uncommon in the environment and frequent in clinical isolates; and marA, part of a locus related to the stress response in Enterobacteriaceae. Variation in the abundance of these genes was analysed as a function of the type of water, and possible correlations with cultivable bacteria, antimicrobial residue concentrations, and bacterial community composition and structure were analysed. HE was confirmed as an important source of blaTEM and vanA genes, and wastewater treatment showed a limited capacity to remove these resistance genes. The genes blaTEM and vanA presented the strongest correlations with culturable bacteria, antimicrobial residues and some bacterial populations, representing interesting candidates as indicator genes to monitor resistance in environmental samples. The intI1 gene was the most abundant in all samples, demonstrating that wastewater bacterial populations hold a high potential for gene acquisition.}, }
@article {pmid28626679, year = {2015}, author = {Hu, X and Kang, F and Gao, Y and Zhou, Q}, title = {Bacterial diversity losses: A potential extracellular driving mechanism involving the molecular ecological function of hydrophobic polycyclic aromatic hydrocarbons.}, journal = {Biotechnology reports (Amsterdam, Netherlands)}, volume = {5}, number = {}, pages = {27-30}, pmid = {28626679}, issn = {2215-017X}, abstract = {The DNA transformation is vital to the horizontal gene transfer (HGT). The low-efficiency transformation of bare plasmid exposed to hydrophobic polycyclic aromatic hydrocarbons (PAHs) decreases the gene transfer level, and is possibly related to the loss of bacterial diversity at present. PAHs have great affinity for bare DNA through dispersion force and π-π overlap between PAHs and bases. These noncovalent interactions between PAHs and bases reduced the transformational efficiency of plasmid into bacterial recipients. Meanwhile these low-efficiency transformations for plasmid are controlled by the ions like Ca[2+] in environment, in turn, presence of 0.5 mmol L[-1] Ca[2+] recovered the efficiency from 3.2 (phenanthrene), 3.5 (pyrene) to about 4.45 and 4.75, respectively. The combination of Ca[2+] with the -POO[-]- groups in DNA forms strong electrovalent bonds, weakening the molecular effect of DNA on PAHs and in turn promoting the gene transfer exposed to PAHs.}, }
@article {pmid27873730, year = {2014}, author = {Ojala, V and Mattila, S and Hoikkala, V and Bamford, JK and Jalasvuori, M}, title = {Evolutionary rescue of bacteria via horizontal gene transfer under a lethal β-lactam concentration.}, journal = {Journal of global antimicrobial resistance}, volume = {2}, number = {3}, pages = {198-200}, doi = {10.1016/j.jgar.2014.02.005}, pmid = {27873730}, issn = {2213-7173}, abstract = {β-Lactams are a commonly used class of bactericidal antibiotics. The number of β-lactam-resistant pathogens is constantly increasing in hospitals around the world. Interestingly, most of the β-lactam-resistant bacteria carry mobile genetic elements, such as conjugative plasmids, that render the pathogen resistant. These elements mediate their own transfer from one bacterium to another, producing new resistant strains via horizontal gene transfer. Here we investigated whether it is possible that transfer of the resistance element from another bacterium may evolutionarily rescue a susceptible bacterium exposed to a lethal concentration of the β-lactam ampicillin. Indeed, the rescuing occurs even at very high, clinically significant antibiotic levels, suggesting that pathogens may acquire the resistance 'on the fly' from commensal bacteria during treatment.}, }
@article {pmid27873593, year = {2014}, author = {Purrello, SM and Daum, RS and Edwards, GF and Lina, G and Lindsay, J and Peters, G and Stefani, S}, title = {Meticillin-resistant Staphylococcus aureus (MRSA) update: New insights into bacterial adaptation and therapeutic targets.}, journal = {Journal of global antimicrobial resistance}, volume = {2}, number = {2}, pages = {61-69}, doi = {10.1016/j.jgar.2014.02.003}, pmid = {27873593}, issn = {2213-7173}, abstract = {Successful meticillin-resistant Staphylococcus aureus (MRSA) clones have evolved to adapt to healthcare, community and livestock environments. This review will bring together recent studies into clone adaptation and the importance of genes acquired during horizontal gene transfer to survival in specific environments. It will also discuss the role of global regulators controlling virulence gene expression and resistance to antibiotics, such as the agr and vraRS systems. Understanding these processes in successful clones could reveal novel targets for therapeutic agents, which are urgently required to reduce the infection burden and improve treatment options.}, }
@article {pmid28206911, year = {2013}, author = {Sangal, V and Fineran, PC and Hoskisson, PA}, title = {Novel configurations of type I and II CRISPR-Cas systems in Corynebacterium diphtheriae.}, journal = {Microbiology (Reading, England)}, volume = {159}, number = {10}, pages = {2118-2126}, doi = {10.1099/mic.0.070235-0}, pmid = {28206911}, issn = {1465-2080}, abstract = {Clustered regularly interspaced short palindromic repeats (CRISPRs) are major barriers to recombination through recognition of invading nucleic acids, such as phage and plasmids, and promoting their degredation through the action of CRISPR associated (Cas) proteins. The genomic comparison of 17 Corynebacterium diphtheriae strains led to the identification of three novel CRISPR-Cas system variants, based on the Type II (Type II-C) or type I-E systems. The type II-C system was the most common (11/17 isolates) but it lacked the csn2 and cas4 genes that are involved in spacer acquisition. We also identified that this variant type II-C CRISPR-Cas system is present in other bacteria, and the first system was recently characterized in Neisseria meningitidis. In the remaining isolates, the type II-C system was replaced by a variant of type I-E (I-E-a), where the repeat arrays are inserted between the cas3 and cse1 genes. Three isolates with the type II-C system also possess an additional variant of type I-E (I-E-b), elsewhere in the genome, that exhibits a novel divergent gene organization within the cas operon. The nucleotide sequences of the palindromic repeats and the cas1 gene were phylogenetically incongruent to the core genome. The G+C content of the systems is lower (46.0-49.5 mol%) than the overall DNA G+C content (53 mol%), and they are flanked by mobile genetic elements, providing evidence that they were acquired in three independent horizontal gene transfer events. The majority of spacers lack identity with known phage or plasmid sequences, indicating that there is an unexplored reservoir of corynebacteriophages and plasmids. These novel CRISPR-Cas systems may represent a unique mechanism for spacer acquisitions and defence against invading DNA.}, }
@article {pmid27873623, year = {2013}, author = {Martinez, E and Pérez, JE and Márquez, C and Vilacoba, E and Centrón, D and Leal, AL and Saavedra, C and Saavedra, SY and Tovar, C and Vanegas, N and Stokes, HW}, title = {Emerging and existing mechanisms co-operate in generating diverse β-lactam resistance phenotypes in geographically dispersed and genetically disparate Pseudomonas aeruginosa strains.}, journal = {Journal of global antimicrobial resistance}, volume = {1}, number = {3}, pages = {135-142}, doi = {10.1016/j.jgar.2013.03.013}, pmid = {27873623}, issn = {2213-7173}, abstract = {β-Lactam resistance in Pseudomonas aeruginosa clinical isolates is driven by a number of mechanisms. Whilst several are understood, how they act co-operatively in pathogenic strains is less clear. In some isolates, resistance profiles cannot always be explained by identifying the common resistance-determining pathways, suggesting that other mechanisms may be important. Pathogenic P. aeruginosa isolates from four countries were characterised by PCR. Quantitative expression analysis was also assessed for the activity of several pathways that influence antibiotic resistance, and culture experiments were conducted to test how random transposition of the insertion sequence IS26 during growth may influence resistance to some antibiotics. In most strains, antibiotic resistance was being driven by changes in multiple pathways and by the presence or absence of genes acquired by lateral gene transfer. Multiple mechanisms of resistance were prevalent in strains from all of the countries examined, although regional differences in the type of interacting mechanisms were apparent. Changes in chromosomal pathways included overexpression of AmpC and two efflux pumps. Also, gain or loss of IS26 at some chromosomal locations, most notably oprD, could influence resistance to carbapenems. IS26-related resistance was found in strains from Argentina and geographically linked Uruguay, but not in strains from either Colombia or Australia. Pseudomonas aeruginosa pathogenic strains are evolving to become multidrug-resistant in more complex ways. This is being influenced by single strains acquiring changes in numerous known pathways as well as by newly emerging resistance mechanisms in this species.}, }
@article {pmid28206910, year = {2010}, author = {Díez-Villaseñor, C and Almendros, C and García-Martínez, J and Mojica, FJ}, title = {Diversity of CRISPR loci in Escherichia coli.}, journal = {Microbiology (Reading, England)}, volume = {156}, number = {5}, pages = {1351-1361}, doi = {10.1099/mic.0.036046-0}, pmid = {28206910}, issn = {1465-2080}, abstract = {CRISPR (clustered regularly interspaced short palindromic repeats) and CAS (CRISPR-associated sequence) proteins are constituents of a novel genetic barrier that limits horizontal gene transfer in prokaryotes by means of an uncharacterized mechanism. The fundamental discovery of small RNAs as the guides of the defence apparatus arose as a result of Escherichia coli studies. However, a survey of the system diversity in this species in order to further contribute to the understanding of the CRISPR mode of action has not yet been performed. Here we describe two CRISPR/CAS systems found in E. coli, following the analysis of 100 strains representative of the species' diversity. Our results substantiate different levels of activity between loci of both CRISPR types, as well as different target preferences and CRISPR relevances for particular groups of strains. Interestingly, the data suggest that the degeneration of one CRISPR/CAS system in E. coli ancestors could have been brought about by self-interference.}, }
@article {pmid28621897, year = {1997}, author = {Dowson, CG and Barcus, V and King, S and Pickerill, P and Whatmore, A and Yeo, M}, title = {Horizontal gene transfer and the evolution of resistance and virulence determinants in Streptococcus.}, journal = {Journal of applied microbiology}, volume = {83}, number = {S1}, pages = {42S-51S}, doi = {10.1046/j.1365-2672.83.s1.5.x}, pmid = {28621897}, issn = {1365-2672}, }
@article {pmid28565713, year = {1996}, author = {Hart, MW}, title = {TESTING COLD FUSION OF PHYLA: MATERNITY IN A TUNICATE × SEA URCHIN HYBRID DETERMINED FROM DNA COMPARISONS.}, journal = {Evolution; international journal of organic evolution}, volume = {50}, number = {4}, pages = {1713-1718}, doi = {10.1111/j.1558-5646.1996.tb03943.x}, pmid = {28565713}, issn = {1558-5646}, }
@article {pmid28568654, year = {1992}, author = {Valdés, AM and Piñero, D}, title = {PHYLOGENETIC ESTIMATION OF PLASMID EXCHANGE IN BACTERIA.}, journal = {Evolution; international journal of organic evolution}, volume = {46}, number = {3}, pages = {641-656}, doi = {10.1111/j.1558-5646.1992.tb02072.x}, pmid = {28568654}, issn = {1558-5646}, abstract = {The existence of differential horizontal gene transfer may be assessed by comparing the phylogenetic trees derived from two different genes. We use this concept to estimate quantitatively the amount of plasmid exchange that has occurred in a bacterial population. By means of computer simulations we studied the effect of gene transfer on the topological distortion between two phylogenetic trees: one obtained from an euchromosomal gene and another from a plasmid-borne sequence, which may be subjected to horizontal transfer. The basic assumptions of our simulations were (a) that plasmid exchange had occurred recently (after the last population split); and (b) that either the amount of chromosomal horizontal exchange was negligible or that it was only a fraction of the amount of plasmid exchange in which case we will be estimating relative amounts of plasmid transfer. We found that the topological difference between two such trees is a function of the number of plasmid exchange events that have occurred. It can be explained by a logistic model that relates the average distortion index between two trees (dT) to the number of transfer events (x). The behavior remains the same under different conditions that were tested (symmetry of the topology, number of taxa in the tree, effect of reconstruction errors, mutation after plasmid transfer). We have also tried our method on empirical data from the literature and estimated the amount of gene transfer that may have occurred among Sym plasmids in agricultural field populations of Rhizobium leguminosarum biovar phaseoli. We found that between 15.77 to 29.98% of all genetic types in these populations have been either the source or the target of a plasmid transfer event. When the comparisons were made among trees derived exclusively from plasmid probes this value dropped to 2.00%. Phylogenetic trees derived from symbiotic and nonsymbiotic sequences were also used to infer the number of gene transfer events among 11 isolates from R. galegae. The estimated number of transfer events of symbiotic sequences was 10.515 (although we do not know out of how many genetic types). We concluded that intraspecific transfer of symbiotic sequences is widespread in these two species of the genus Rhizobium.}, }
@article {pmid26513533, year = {2016}, author = {Dufour, D and Villemin, C and Perry, JA and Lévesque, CM}, title = {Escape from the competence state in Streptococcus mutans is governed by the bacterial population density.}, journal = {Molecular oral microbiology}, volume = {31}, number = {6}, pages = {501-514}, doi = {10.1111/omi.12145}, pmid = {26513533}, issn = {2041-1014}, mesh = {Bacterial Load ; Bacterial Proteins/*genetics ; Coculture Techniques ; *DNA Transformation Competence ; *Gene Expression Regulation, Bacterial ; Humans ; Quorum Sensing/genetics ; Streptococcus mutans/*genetics/growth &amp; development ; Transcriptome ; }, abstract = {Horizontal gene transfer through natural DNA transformation is an important evolutionary mechanism among bacteria. Transformation requires that the bacteria are physiologically competent to take and incorporate free DNA directly from the environment. Although natural genetic transformation is a remarkable feature of many naturally competent bacteria, the process is energetically expensive for the cells. Consequently, a tight control of the competence state is necessary. The objective of the present work was to help decipher the molecular mechanisms regulating the escape from the competence state in Streptococcus mutans, the principal etiological agent responsible for tooth decay in humans. Our results showed that the cessation of competence in S. mutans was abrupt, and did not involve the accumulation of a competence inhibitor nor the depletion of a competence activator in the extracellular environment. The competence state was repressed at high cell population density via concomitant repression of sigX gene encoding the master regulator of the competence regulon. Co-culture experiments performed with oral and non-oral bacteria showed that S. mutans assesses its own population density and also the microbial density of its surroundings to regulate its competence escape. Interestingly, neither the intra-species and extra-species quorum-sensing systems nor the other 13 two-component regulatory systems identified in S. mutans were involved in the cell-density-dependent escape of the competence state. Altogether, our results suggest a complex mechanism regulating the competence shut-off involving cell-density-dependent repression of sigX through an as yet undefined system, and possibly SigX protein stability.}, }
@article {pmid27481640, year = {2016}, author = {Sanchini, A and Semmler, T and Mao, L and Kumar, N and Dematheis, F and Tandon, K and Peddireddy, V and Ahmed, N and Lewin, A}, title = {A hypervariable genomic island identified in clinical and environmental Mycobacterium avium subsp. hominissuis isolates from Germany.}, journal = {International journal of medical microbiology : IJMM}, volume = {306}, number = {7}, pages = {495-503}, doi = {10.1016/j.ijmm.2016.07.001}, pmid = {27481640}, issn = {1618-0607}, mesh = {Adult ; Child ; Child, Preschool ; *Environmental Microbiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genetic Variation ; Genome, Bacterial ; *Genomic Islands ; Genotype ; Germany ; Humans ; Mycobacterium avium/classification/*genetics/isolation &amp; purification ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Tuberculosis/*microbiology ; }, abstract = {Mycobacterium avium subsp. hominissuis (MAH) is an opportunistic human pathogen widespread in the environment. Genomic islands (GI)s represent a part of the accessory genome of bacteria and influence virulence, drug-resistance or fitness and trigger bacterial evolution. We previously identified a novel GI in four MAH genomes. Here, we further explored this GI in a larger collection of MAH isolates from Germany (n=41), including 20 clinical and 21 environmental isolates. Based on comparative whole genome analysis, we detected this GI in 39/41 (95.1%) isolates. Although all these GIs integrated in the same insertion hotspot, there is high variability in the genetic structure of this GI: eight different types of GI have been identified, designated A-H (sized 6.2-73.3kb). These GIs were arranged as single GI (23/41, 56.1%), combination of two different GIs (14/41, 34.1%) or combination of three different GIs (2/41, 4.9%) in the insertion hotspot. Moreover, two GI types shared more than 80% sequence identity with sequences of M. canettii, responsible for Tuberculosis. A total of 253 different genes were identified in all GIs, among which the previously documented virulence-related genes mmpL10 and mce. The diversity of the GI and the sequence similarity with other mycobacteria suggests cross-species transfer, involving also highly pathogenic species. Shuffling of potential virulence genes such as mmpL10 via this GI may create new pathogens that can cause future outbreaks.}, }
@article {pmid27058504, year = {2016}, author = {Miyasaka, H and Ogata, T and Tanaka, S and Ohama, T and Kano, S and Kazuhiro, F and Hayashi, S and Yamamoto, S and Takahashi, H and Matsuura, H and Hirata, K}, title = {Is chloroplastic class IIA aldolase a marine enzyme?.}, journal = {The ISME journal}, volume = {10}, number = {11}, pages = {2767-2772}, pmid = {27058504}, issn = {1751-7370}, mesh = {Biological Evolution ; Chlorophyta/classification/*enzymology/genetics ; Chloroplasts/*enzymology/genetics ; Fructose-Bisphosphate Aldolase/genetics/*metabolism ; Gene Transfer, Horizontal ; Genome ; Genomics ; Molecular Sequence Data ; Phylogeny ; Seawater/chemistry ; }, abstract = {Expressed sequence tag analyses revealed that two marine Chlorophyceae green algae, Chlamydomonas sp. W80 and Chlamydomonas sp. HS5, contain genes coding for chloroplastic class IIA aldolase (fructose-1, 6-bisphosphate aldolase: FBA). These genes show robust monophyly with those of the marine Prasinophyceae algae genera Micromonas, Ostreococcus and Bathycoccus, indicating that the acquisition of this gene through horizontal gene transfer by an ancestor of the green algal lineage occurred prior to the divergence of the core chlorophytes (Chlorophyceae and Trebouxiophyceae) and the prasinophytes. The absence of this gene in some freshwater chlorophytes, such as Chlamydomonas reinhardtii, Volvox carteri, Chlorella vulgaris, Chlorella variabilis and Coccomyxa subellipsoidea, can therefore be explained by the loss of this gene somewhere in the evolutionary process. Our survey on the distribution of this gene in genomic and transcriptome databases suggests that this gene occurs almost exclusively in marine algae, with a few exceptions, and as such, we propose that chloroplastic class IIA FBA is a marine environment-adapted enzyme. This hypothesis was also experimentally tested using Chlamydomonas W80, for which we found that the transcript levels of this gene to be significantly lower under low-salt (that is, simulated terrestrial) conditions. Expression analyses of transcriptome data for two algae, Prymnesium parvum and Emiliania huxleyi, taken from the Sequence Read Archive database also indicated that the expression of this gene under terrestrial conditions (low NaCl and low sulfate) is significantly downregulated. Thus, these experimental and transcriptome data provide support for our hypothesis.}, }
@article {pmid27453497, year = {2016}, author = {Saha, C and Mukherjee, G and Agarwal-Banka, P and Seal, A}, title = {A consortium of non-rhizobial endophytic microbes from Typha angustifolia functions as probiotic in rice and improves nitrogen metabolism.}, journal = {Plant biology (Stuttgart, Germany)}, volume = {18}, number = {6}, pages = {938-946}, doi = {10.1111/plb.12485}, pmid = {27453497}, issn = {1438-8677}, mesh = {Biomass ; Endophytes/cytology/*physiology ; Nitrogen/*metabolism ; Nitrogen Fixation ; Oryza/cytology/metabolism/*microbiology ; Sequence Analysis, DNA ; Typhaceae/*microbiology ; }, abstract = {Endophytic microbes isolated from plants growing in nutrient-deficient environments often possess properties that improve nutrition of agriculturally important plants. A consortium of non-rhizobial endophytic microbes isolated from a macrophyte Typha angustifolia growing in the marginal wetlands associated with a Uranium mine was characterized for their beneficial effect on rice and the mechanisms of growth promotion were investigated. The microbes were identified and characterized for their potential plant growth promoting (PGP) properties. Effect of these microbes on nitrogen (N)-metabolism of rice was tested as Typha endophytes were predominantly (N)-fixing. Relative N-use efficiency and expression of genes involved in N-uptake and assimilation were investigated in treated plants. Evidence of horizontal gene transfer (HGT) of dinitrogen reductase gene was observed within the consortium from a Pseudomonas stutzeri strain. The consortium behaved as plant probiotic and showed substantial growth benefits to Typha, their natural host as well as to rice. Typha endophytes colonized rice endosphere significantly increasing biomass, shoot length and chlorophyll content in rice plants both under N-sufficient and N-deficient conditions. N-uptake and assimilation genes were upregulated in plants treated with the endophytes even after three weeks post infection. Our results suggested, HGT of nitrogen-fixation trait to be highly prevalent among endophytes isolated from nutrient-poor habitats of the uranium mine. A long-term nitrogen deficiency response in the treated plants was elicited by the consortium improving N-uptake, assimilation and relative N-use efficiency of rice plants. This appeared to be at least one of the main strategies of plant growth promotion.}, }
@article {pmid27335204, year = {2016}, author = {Durkin, CA and Koester, JA and Bender, SJ and Armbrust, EV}, title = {The evolution of silicon transporters in diatoms.}, journal = {Journal of phycology}, volume = {52}, number = {5}, pages = {716-731}, pmid = {27335204}, issn = {1529-8817}, mesh = {Algal Proteins/*genetics ; Biological Transport ; Diatoms/classification/*genetics/*metabolism ; *Evolution, Molecular ; Membrane Transport Proteins/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Silicon/*metabolism ; }, abstract = {Diatoms are highly productive single-celled algae that form an intricately patterned silica cell wall after every cell division. They take up and utilize silicic acid from seawater via silicon transporter (SIT) proteins. This study examined the evolution of the SIT gene family to identify potential genetic adaptations that enable diatoms to thrive in the modern ocean. By searching for sequence homologs in available databases, the diversity of organisms found to encode SITs increased substantially and included all major diatom lineages and other algal protists. A bacterial-encoded gene with homology to SIT sequences was also identified, suggesting that a lateral gene transfer event occurred between bacterial and protist lineages. In diatoms, the SIT genes diverged and diversified to produce five distinct clades. The most basal SIT clades were widely distributed across diatom lineages, while the more derived clades were lineage-specific, which together produced a distinct repertoire of SIT types among major diatom lineages. Differences in the predicted protein functional domains encoded among SIT clades suggest that the divergence of clades resulted in functional diversification among SITs. Both laboratory cultures and natural communities changed transcription of each SIT clade in response to experimental or environmental growth conditions, with distinct transcriptional patterns observed among clades. Together, these data suggest that the diversification of SITs within diatoms led to specialized adaptations among diatoms lineages, and perhaps their dominant ability to take up silicic acid from seawater in diverse environmental conditions.}, }
@article {pmid27487482, year = {2016}, author = {Milton, ME and Choe, JY and Honzatko, RB and Nelson, SW}, title = {Crystal Structure of the Apicoplast DNA Polymerase from Plasmodium falciparum: The First Look at a Plastidic A-Family DNA Polymerase.}, journal = {Journal of molecular biology}, volume = {428}, number = {20}, pages = {3920-3934}, doi = {10.1016/j.jmb.2016.07.016}, pmid = {27487482}, issn = {1089-8638}, mesh = {Apicoplasts/*enzymology ; Crystallography, X-Ray ; DNA-Directed DNA Polymerase/*chemistry ; Models, Molecular ; Plasmodium falciparum/*enzymology ; Protein Conformation ; Protein Domains ; }, abstract = {Plasmodium falciparum, the primary cause of malaria, contains a non-photosynthetic plastid called the apicoplast. The apicoplast exists in most members of the phylum Apicomplexa and has its own genome along with organelle-specific enzymes for its replication. The only DNA polymerase found in the apicoplast (apPOL) was putatively acquired through horizontal gene transfer from a bacteriophage and is classified as an atypical A-family polymerase. Here, we present its crystal structure at a resolution of 2.9Å. P. falciparum apPOL, the first structural representative of a plastidic A-family polymerase, diverges from typical A-family members in two of three previously identified signature motifs and in a region not implicated by sequence. Moreover, apPOL has an additional N-terminal subdomain, the absence of which severely diminishes its 3' to 5' exonuclease activity. A compound known to be toxic to Plasmodium is a potent inhibitor of apPOL, suggesting that apPOL is a viable drug target. The structure provides new insights into the structural diversity of A-family polymerases and may facilitate structurally guided antimalarial drug design.}, }
@article {pmid27486448, year = {2016}, author = {Michener, JK and Vuilleumier, S and Bringel, F and Marx, CJ}, title = {Transfer of a Catabolic Pathway for Chloromethane in Methylobacterium Strains Highlights Different Limitations for Growth with Chloromethane or with Dichloromethane.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1116}, pmid = {27486448}, issn = {1664-302X}, support = {F32 GM106629/GM/NIGMS NIH HHS/United States ; }, abstract = {Chloromethane (CM) is an ozone-depleting gas, produced predominantly from natural sources, that provides an important carbon source for microbes capable of consuming it. CM catabolism has been difficult to study owing to the challenging genetics of its native microbial hosts. Since the pathways for CM catabolism show evidence of horizontal gene transfer, we reproduced this transfer process in the laboratory to generate new CM-catabolizing strains in tractable hosts. We demonstrate that six putative accessory genes improve CM catabolism, though heterologous expression of only one of the six is strictly necessary for growth on CM. In contrast to growth of Methylobacterium strains with the closely related compound dichloromethane (DCM), we find that chloride export does not limit growth on CM and, in general that the ability of a strain to grow on DCM is uncorrelated with its ability to grow on CM. This heterologous expression system allows us to investigate the components required for effective CM catabolism and the factors that limit effective catabolism after horizontal transfer.}, }
@article {pmid27485833, year = {2016}, author = {Jaffe, AL and Corel, E and Pathmanathan, JS and Lopez, P and Bapteste, E}, title = {Bipartite graph analyses reveal interdomain LGT involving ultrasmall prokaryotes and their divergent, membrane-related proteins.}, journal = {Environmental microbiology}, volume = {18}, number = {12}, pages = {5072-5081}, doi = {10.1111/1462-2920.13477}, pmid = {27485833}, issn = {1462-2920}, mesh = {Archaea/classification/*genetics/isolation &amp; purification ; Bacteria/classification/*genetics/isolation &amp; purification ; Bacterial Proteins/*genetics/metabolism ; *Gene Transfer, Horizontal ; Genome, Archaeal ; Genome, Bacterial ; Membrane Proteins/*genetics/metabolism ; Phylogeny ; Symbiosis ; }, abstract = {Based on their small size and genomic properties, ultrasmall prokaryotic groups like the Candidate Phyla Radiation have been proposed as possible symbionts dependent on other bacteria or archaea. In this study, we use a bipartite graph analysis to examine patterns of sequence similarity between draft and complete genomes from ultrasmall bacteria and other complete prokaryotic genomes, assessing whether the former group might engage in significant gene transfer (or even endosymbioses) with other community members. Our results provide preliminary evidence for many lateral gene transfers with other prokaryotes, including members of the archaea, and report the presence of divergent, membrane-associated proteins among these ultrasmall taxa. In particular, these divergent genes were found in TM6 relatives of the intracellular parasite Babela massiliensis.}, }
@article {pmid27485281, year = {2016}, author = {Huang, H and Chen, Y and Zheng, X and Su, Y and Wan, R and Yang, S}, title = {Distribution of tetracycline resistance genes in anaerobic treatment of waste sludge: The role of pH in regulating tetracycline resistant bacteria and horizontal gene transfer.}, journal = {Bioresource technology}, volume = {218}, number = {}, pages = {1284-1289}, doi = {10.1016/j.biortech.2016.07.097}, pmid = {27485281}, issn = {1873-2976}, mesh = {Anaerobiosis ; *Bacteria/drug effects/genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/*genetics ; Hydrogen-Ion Concentration ; Sewage/*microbiology ; Tetracycline Resistance/*genetics ; }, abstract = {Although pH value has been widely regarded as an important factor that affects resource recovery of waste sludge, the potential influence of diverse pHs on the distribution of tetracycline resistance genes (TRGs) during sludge anaerobic treatment is largely unknown. Here we reported that in the range of pH 4-10, 0.58-1.18 log unit increase of target TRGs was observed at pH 4, compared with that at pH 7, while 0.70-1.31 log unit further removal were obtained at pH 10. Mechanism study revealed that varied pHs not only altered the community structures of tetracycline resistant bacteria (TRB), but also changed their relative abundances, benefitting the propagation (acidic pHs) or attenuation (alkaline pHs) of TRB. Further investigation indicated that the amount and gene-possessing abilities of key genetic vectors for horizontal TRGs transfer were greatly promoted at acidic pHs but restricted under alkaline conditions.}, }
@article {pmid27482924, year = {2017}, author = {Klümper, U and Dechesne, A and Riber, L and Brandt, KK and Gülay, A and Sørensen, SJ and Smets, BF}, title = {Metal stressors consistently modulate bacterial conjugal plasmid uptake potential in a phylogenetically conserved manner.}, journal = {The ISME journal}, volume = {11}, number = {1}, pages = {152-165}, pmid = {27482924}, issn = {1751-7370}, support = {MR/N007174/1/MRC_/Medical Research Council/United Kingdom ; //Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteria/classification/*genetics/isolation &amp; purification/metabolism ; *Conjugation, Genetic ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Metals/*metabolism ; *Phylogeny ; Plasmids/*genetics ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; }, abstract = {The environmental stimulants and inhibitors of conjugal plasmid transfer in microbial communities are poorly understood. Specifically, it is not known whether exposure to stressors may cause a community to alter its plasmid uptake ability. We assessed whether metals (Cu, Cd, Ni, Zn) and one metalloid (As), at concentrations causing partial growth inhibition, modulate community permissiveness (that is, uptake ability) against a broad-host-range IncP-type plasmid (pKJK5). Cells were extracted from an agricultural soil as recipient community and a cultivation-minimal filter mating assay was conducted with an exogenous E. coli donor strain. The donor hosted a gfp-tagged pKJK5 derivative from which conjugation events could be microscopically quantified and transconjugants isolated and phylogenetically described at high resolution via FACS and 16S rRNA amplicon sequencing. Metal stress consistently decreased plasmid transfer frequencies to the community, while the transconjugal pool richness remained unaffected with OTUs belonging to 12 bacterial phyla. The taxonomic composition of the transconjugal pools was distinct from their respective recipient communities and clustered dependent on the stress type and dose. However, for certain OTUs, stress increased or decreased permissiveness by more than 1000-fold and this response was typically correlated across different metals and doses. The response to some stresses was, in addition, phylogenetically conserved. This is the first demonstration that community permissiveness is sensitive to metal(loid) stress in a manner that is both partially consistent across stressors and phylogenetically conserved.}, }
@article {pmid27482743, year = {2016}, author = {Booth, A and Mariscal, C and Doolittle, WF}, title = {The Modern Synthesis in the Light of Microbial Genomics.}, journal = {Annual review of microbiology}, volume = {70}, number = {}, pages = {279-297}, doi = {10.1146/annurev-micro-102215-095456}, pmid = {27482743}, issn = {1545-3251}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; Evolution, Molecular ; *Genes, Synthetic ; *Genome, Bacterial ; *Genomics ; Phylogeny ; }, abstract = {We review the theoretical implications of findings in genomics for evolutionary biology since the Modern Synthesis. We examine the ways in which microbial genomics has influenced our understanding of the last universal common ancestor, the tree of life, species, lineages, and evolutionary transitions. We conclude by advocating a piecemeal toolkit approach to evolutionary biology, in lieu of any grand unified theory updated to include microbial genomics.}, }
@article {pmid27481787, year = {2016}, author = {Mallo, D and Posada, D}, title = {Multilocus inference of species trees and DNA barcoding.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {371}, number = {1702}, pages = {}, pmid = {27481787}, issn = {1471-2970}, support = {203161/ERC_/European Research Council/International ; }, mesh = {*Biological Evolution ; *DNA Barcoding, Taxonomic ; *Genetic Speciation ; *Phylogeny ; }, abstract = {The unprecedented amount of data resulting from next-generation sequencing has opened a new era in phylogenetic estimation. Although large datasets should, in theory, increase phylogenetic resolution, massive, multilocus datasets have uncovered a great deal of phylogenetic incongruence among different genomic regions, due both to stochastic error and to the action of different evolutionary process such as incomplete lineage sorting, gene duplication and loss and horizontal gene transfer. This incongruence violates one of the fundamental assumptions of the DNA barcoding approach, which assumes that gene history and species history are identical. In this review, we explain some of the most important challenges we will have to face to reconstruct the history of species, and the advantages and disadvantages of different strategies for the phylogenetic analysis of multilocus data. In particular, we describe the evolutionary events that can generate species tree-gene tree discordance, compare the most popular methods for species tree reconstruction, highlight the challenges we need to face when using them and discuss their potential utility in barcoding. Current barcoding methods sacrifice a great amount of statistical power by only considering one locus, and a transition to multilocus barcodes would not only improve current barcoding methods, but also facilitate an eventual transition to species-tree-based barcoding strategies, which could better accommodate scenarios where the barcode gap is too small or inexistent.This article is part of the themed issue 'From DNA barcodes to biomes'.}, }
@article {pmid27480862, year = {2016}, author = {Wan, TW and Hung, WC and Tsai, JC and Lin, YT and Lee, H and Hsueh, PR and Lee, TF and Teng, LJ}, title = {Novel Structure of Enterococcus faecium-Originated ermB-Positive Tn1546-Like Element in Staphylococcus aureus.}, journal = {Antimicrobial agents and chemotherapy}, volume = {60}, number = {10}, pages = {6108-6114}, pmid = {27480862}, issn = {1098-6596}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics/metabolism ; Chromosomes, Bacterial/chemistry ; Conjugation, Genetic ; *DNA Transposable Elements ; Disk Diffusion Antimicrobial Tests ; Drug Resistance, Multiple, Bacterial/*genetics ; Electrophoresis, Gel, Pulsed-Field ; Enterococcus faecium/drug effects/*genetics/metabolism/pathogenicity ; Gene Expression ; *Gene Transfer, Horizontal ; Isoenzymes/genetics/metabolism ; Lincosamides/pharmacology ; Macrolides/pharmacology ; Methicillin-Resistant Staphylococcus aureus/drug effects/*genetics/metabolism/pathogenicity ; Methyltransferases/genetics/metabolism ; Phenotype ; Plasmids/chemistry/*metabolism ; Sequence Analysis, DNA ; Streptogramins/pharmacology ; }, abstract = {We determined the resistance determinants in 274 erythromycin-resistant methicillin-susceptible Staphylococcus aureus (MSSA) isolates during a 13-year period, 2000 to 2012. The resistance phenotypes, inducible macrolide-lincosamide-streptogramin (iMLS), constitutive MLS (cMLS), and macrolide-streptogramin (MS) resistance phenotypes, were examined by a double-disk diffusion D test. The ermB gene was more frequent (35%; 97/274) than ermC (27%; 75/274) or ermA (21%; 58/274). All 97 ermB-positive isolates harbored Tn551 and IS1216V The majority (89/97) of ermB-positive isolates displayed the cMLS phenotype and carried mobile element structure (MES)-like structures, which has been previously reported in sequence type 59 (ST59) methicillin-resistant S. aureus (MRSA). The remaining 8 ermB-carrying isolates, belonging to ST7 (n = 4), ST5 (n = 3), and ST59 (n = 1), were sasK intact and did not carry MES-like structures. Unlike a MES-like structure that was located on the chromosome, the ermB elements on sasK-intact isolates were located on plasmids by S1 nuclease pulsed-field gel electrophoresis (PFGE) analysis and conjugation tests. Sequence data for the ermB-containing region (14,566 bp) from ST59 NTUH_3874 revealed that the best match was a Tn1546-like element in plasmid pMCCL2 DNA (GenBank accession number AP009486) of Macrococcus caseolyticus Tn1546 is recognized as an enterococcal transposon and was known from the vancomycin resistance gene cluster in vancomycin-resistant Enterococcus (VRE). So far, acquisitions of Tn1546 in S. aureus have occurred in clonal complex 5 (CC5) MRSA, but not in MSSA. This is the first report that MSSA harbors an Enterococcus faecium-originated ermB-positive Tn1546-like element located on a plasmid.}, }
@article {pmid27480115, year = {2016}, author = {Xu, F and Jerlström-Hultqvist, J and Kolisko, M and Simpson, AG and Roger, AJ and Svärd, SG and Andersson, JO}, title = {On the reversibility of parasitism: adaptation to a free-living lifestyle via gene acquisitions in the diplomonad Trepomonas sp. PC1.}, journal = {BMC biology}, volume = {14}, number = {}, pages = {62}, pmid = {27480115}, issn = {1741-7007}, mesh = {Adaptation, Physiological/*genetics ; Animals ; Cell Wall/metabolism ; Diplomonadida/enzymology/*genetics/*physiology ; *Genes, Protozoan ; Intramolecular Transferases/genetics ; Likelihood Functions ; Lysosomes/metabolism ; Parasites/enzymology/*genetics/*physiology ; Phylogeny ; Transcriptome/genetics ; }, abstract = {BACKGROUND: It is generally thought that the evolutionary transition to parasitism is irreversible because it is associated with the loss of functions needed for a free-living lifestyle. Nevertheless, free-living taxa are sometimes nested within parasite clades in phylogenetic trees, which could indicate that they are secondarily free-living. Herein, we test this hypothesis by studying the genomic basis for evolutionary transitions between lifestyles in diplomonads, a group of anaerobic eukaryotes. Most described diplomonads are intestinal parasites or commensals of various animals, but there are also free-living diplomonads found in oxygen-poor environments such as marine and freshwater sediments. All these nest well within groups of parasitic diplomonads in phylogenetic trees, suggesting that they could be secondarily free-living.<br><br>RESULTS: We present a transcriptome study of Trepomonas sp. PC1, a diplomonad isolated from marine sediment. Analysis of the metabolic genes revealed a number of proteins involved in degradation of the bacterial membrane and cell wall, as well as an extended set of enzymes involved in carbohydrate degradation and nucleotide metabolism. Phylogenetic analyses showed that most of the differences in metabolic capacity between free-living Trepomonas and the parasitic diplomonads are due to recent acquisitions of bacterial genes via gene transfer. Interestingly, one of the acquired genes encodes a ribonucleotide reductase, which frees Trepomonas from the need to scavenge deoxyribonucleosides. The transcriptome included a gene encoding squalene-tetrahymanol cyclase. This enzyme synthesizes the sterol substitute tetrahymanol in the absence of oxygen, potentially allowing Trepomonas to thrive under anaerobic conditions as a free-living bacterivore, without depending on sterols from other eukaryotes.<br><br>CONCLUSIONS: Our findings are consistent with the phylogenetic evidence that the last common ancestor of diplomonads was dependent on a host and that Trepomonas has adapted secondarily to a free-living lifestyle. We believe that similar studies of other groups where free-living taxa are nested within parasites could reveal more examples of secondarily free-living eukaryotes.}, }
@article {pmid27476981, year = {2017}, author = {Feßler, AT and Zhao, Q and Schoenfelder, S and Kadlec, K and Brenner Michael, G and Wang, Y and Ziebuhr, W and Shen, J and Schwarz, S}, title = {Complete sequence of a plasmid from a bovine methicillin-resistant Staphylococcus aureus harbouring a novel ica-like gene cluster in addition to antimicrobial and heavy metal resistance genes.}, journal = {Veterinary microbiology}, volume = {200}, number = {}, pages = {95-100}, doi = {10.1016/j.vetmic.2016.07.010}, pmid = {27476981}, issn = {1873-2542}, mesh = {Animals ; Anti-Infective Agents/pharmacology ; Bacterial Proteins/genetics ; Biofilms/*growth &amp; development ; Cattle ; Cattle Diseases/epidemiology/*microbiology ; Drug Resistance, Multiple, Bacterial/*genetics ; Metals, Heavy/toxicity ; Methicillin-Resistant Staphylococcus aureus/drug effects/*genetics/isolation &amp; purification/pathogenicity ; Microbial Sensitivity Tests/veterinary ; Multigene Family ; Plasmids/*genetics ; Sequence Analysis, DNA/veterinary ; Staphylococcal Infections/epidemiology/microbiology/*veterinary ; Virulence/genetics ; }, abstract = {The multiresistance plasmid pAFS11, obtained from a bovine methicillin-resistant Staphylococcus aureus (MRSA) isolate, was completely sequenced and analysed for its structure and organisation. Moreover, the susceptibility to the heavy metals cadmium and copper was determined by broth macrodilution. The 49,189-bp plasmid harboured the apramycin resistance gene apmA, two copies of the macrolide/lincosamide/streptogramin B resistance gene erm(B) (both located on remnants of a truncated transposon Tn917), the kanamycin/neomycin resistance gene aadD, the tetracycline resistance gene tet(L) and the trimethoprim resistance gene dfrK. The latter three genes were part of a 7,284-bp segment which was bracketed by two copies of IS431. In addition, the cadmium resistance operon cadDX as well as the copper resistance genes copA and mco were located on the plasmid and mediated a reduced susceptibility to cadmium and copper. Moreover, a complete novel ica-like gene cluster of so far unknown genetic origin was detected on this plasmid. The ica-like gene cluster comprised four different genes whose products showed 64.4-76.9% homology to the Ica proteins known to be involved in biofilm formation of the S. aureus strains Mu50, Mu3 and N315. However, 96.2-99.4% homology was seen to proteins from S. sciuri NS1 indicating an S. sciuri origin. The finding of five different antibiotic resistance genes co-located on a plasmid with heavy metal resistance genes and an ica-like gene cluster is alarming. With the acquisition of this plasmid, antimicrobial multiresistance, heavy metal resistances and potential virulence properties may be co-selected and spread via a single horizontal gene transfer event.}, }
@article {pmid27476200, year = {2016}, author = {Provorov, NA and Andronov, EE}, title = {[Evolution of Root Nodule Bacteria: Reconstruction of the Speciation Processes Resulting from Genomic Rearrangements in a Symbiotic System].}, journal = {Mikrobiologiia}, volume = {85}, number = {2}, pages = {115-125}, pmid = {27476200}, issn = {0026-3656}, mesh = {*Bacteria/genetics/metabolism ; *Evolution, Molecular ; Genome, Bacterial/*physiology ; Root Nodules, Plant/*microbiology ; Symbiosis/*physiology ; }, abstract = {The processes of speciation and macroevolution of root nodule bacteria (rhizobia), based on deep rearrangements of their genomes and occurring in the N2-fixing symbiotic system, are reconstructed. At the first stage of rhizobial evolution, transformation of free-living diazotrophs (related to Rhodopseudomonas) to symbiotic N2-fixers (Bradyrhizobium) occurred due to the acquisition of the fix gene system, which is responsible for providing nitrogenase with electrons and reducing equivalents, as well as for oxygen-dependent regulation of nitrogenase synthesis in planta, and then of the nod genes responsible for the synthesis of the lipo- chito-oligosaccharide Nod factors, which induce root nodule development. The subsequent rearrangements of bacterial genomes included: (1) increased volume of hereditary information supported by species, genera (pan-genome), and individual strains; (2) transition from the unitary genome to a multicomponent one; and (3) enhanced levels of bacterial genetic plasticity and horizontal gene transfer, resulting in formation of new genera, of which Mesorhizobium, Rhizobium, and Sinorhizobium are the largest, and of over 100 species. Rhizobial evolution caused by development and diversification of the Nod factor synthesizing systems may result in both increased host specificity range (transition of Bradyrhizobium from autotrophic to symbiotrophic carbon metabolism in interaction with a broad spectrum of legumes) and to its contraction (transition of Rhizobium and Sinorhizobium to "altruistic" interaction with legumes of the galegoid clade). Reconstruction of the evolutionary pathway from symbiotic N2-fixers to their free-living ancestors makes it possible to initiate the studies based on up-to-date genome screening technologies and aimed at the issues of genetic integration of organisms into supracpecies complexes, ratios of the macro- and microevolutionary mechanisms, and developmetn of cooperative adaptations based on altruistic relationship between the symbiotic partners.}, }
@article {pmid27472489, year = {2016}, author = {Harrison, RL and Rowley, DL and Funk, CJ}, title = {The Complete Genome Sequence of Plodia Interpunctella Granulovirus: Evidence for Horizontal Gene Transfer and Discovery of an Unusual Inhibitor-of-Apoptosis Gene.}, journal = {PloS one}, volume = {11}, number = {7}, pages = {e0160389}, pmid = {27472489}, issn = {1932-6203}, support = {P20 GM103429/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; *Gene Transfer, Horizontal ; *Genes, Viral ; Granulovirus/*genetics ; Inhibitor of Apoptosis Proteins/*genetics ; Open Reading Frames ; Phylogeny ; Sequence Homology, Amino Acid ; }, abstract = {The Indianmeal moth, Plodia interpunctella (Lepidoptera: Pyralidae), is a common pest of stored goods with a worldwide distribution. The complete genome sequence for a larval pathogen of this moth, the baculovirus Plodia interpunctella granulovirus (PiGV), was determined by next-generation sequencing. The PiGV genome was found to be 112, 536 bp in length with a 44.2% G+C nucleotide distribution. A total of 123 open reading frames (ORFs) and seven homologous regions (hrs) were identified and annotated. Phylogenetic inference using concatenated alignments of 36 baculovirus core genes placed PiGV in the "b" clade of viruses from genus Betabaculovirus with a branch length suggesting that PiGV represents a distinct betabaculovirus species. In addition to the baculovirus core genes and orthologues of other genes found in other betabaculovirus genomes, the PiGV genome sequence contained orthologues of the bidensovirus NS3 gene, as well as ORFs that occur in alphabaculoviruses but not betabaculoviruses. While PiGV contained an orthologue of inhibitor of apoptosis-5 (iap-5), an orthologue of inhibitor of apoptosis-3 (iap-3) was not present. Instead, the PiGV sequence contained an ORF (PiGV ORF81) encoding an IAP homologue with sequence similarity to insect cellular IAPs, but not to viral IAPs. Phylogenetic analysis of baculovirus and insect IAP amino acid sequences suggested that the baculovirus IAP-3 genes and the PiGV ORF81 IAP homologue represent different lineages arising from more than one acquisition event. The presence of genes from other sources in the PiGV genome highlights the extent to which baculovirus gene content is shaped by horizontal gene transfer.}, }
@article {pmid27465983, year = {2017}, author = {Muteeb, G and Rehman, MT and Ali, SZ and Al-Shahrani, AM and Kamal, MA and Ashraf, GM}, title = {Phage Display Technique: A Novel Medicinal Approach to Overcome An tibiotic Resistance by Using Peptide-Based Inhibitors Against β-Lactamases.}, journal = {Current drug metabolism}, volume = {18}, number = {2}, pages = {90-95}, doi = {10.2174/1389200217666160727100434}, pmid = {27465983}, issn = {1875-5453}, mesh = {Anti-Bacterial Agents/classification/*pharmacology ; *Cell Surface Display Techniques ; Humans ; Peptides/classification/*pharmacology ; *beta-Lactam Resistance ; beta-Lactamase Inhibitors/classification/*pharmacology ; }, abstract = {The emergence of antibiotic resistance in bacteria is a serious threat with enormous social and economic implications. The distribution of resistance genes/markers through horizontal gene transfer leads to the dissemination of resistant strains in different parts of the world. The resistant bacteria acquire the ability to overcome resistance by different modes amongst which the expression of β-lactamases is a major factor. The β-lactamase enzymes cleave the amide bond of the β-lactam antibiotics, which constitute about one-third of the antibiotics used all over the world. In a quest to control the spread of resistant bacteria, advanced generations of antibiotics are used either alone or in combination with inhibitors. However, these antibiotics and inhibitors also contain β-lactam ring in their structure and hence are prone to be hydrolyzed by β-lactamase enzymes in the near future. Thus, the severity of the problem is manifested due to the paucity of novel non-β-lactam core containing antibiotics in the drug development stage. One approach to overcome these shortcomings is to use peptide-based inhibitors. Here, we describe the potential use of phage display technique to screen commercially available libraries to pan against β-lactamase enzymes. The main advantage of using peptide-based inhibitors is that the bacteria will not be able to recruit pre-existing defense mechanisms and it will take a long time to evolve a new mechanism in its defense against peptide-based inhibitors.}, }
@article {pmid27465908, year = {2016}, author = {Wen, Z and Liu, Y and Qu, F and Zhang, JR}, title = {Allelic Variation of the Capsule Promoter Diversifies Encapsulation and Virulence In Streptococcus pneumoniae.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {30176}, pmid = {27465908}, issn = {2045-2322}, mesh = {A549 Cells ; Alleles ; Animals ; Bacterial Capsules/*genetics ; Cell Line, Tumor ; Female ; Gene Expression Regulation, Bacterial/genetics ; Genetic Variation/*genetics ; Humans ; Mice ; Pneumococcal Infections/microbiology ; Promoter Regions, Genetic/*genetics ; RAW 264.7 Cells ; Streptococcus pneumoniae/*genetics ; Virulence/*genetics ; Virulence Factors/*genetics ; }, abstract = {The polysaccharide capsule is the major virulence factor of Streptococcus pneumoniae (pneumococcus), a major human pathogen. The sequences in the promoter and coding regions of the capsule gene locus undergo extensive variations through the natural transformation-mediated horizontal gene transfer. The sequence variations in the coding region have led to at least 97 capsular serotypes. However, it remains unclear whether the sequence polymorphisms in the promoter region have any biological significance. In this study, we determined the sequences of the cps promoter region from 225 invasive pneumococcal isolates, and identified modular composition and remarkable inter-strain sequence variations in this region. The strain-to strain variations in the cps promoter are characterized by diversity in sequence and size, mosaic combinations of nucleotide polymorphisms and sequence modules, selective preservation of the sequence combinations, and promiscuous assortments of the sequences between the promoter and coding regions. Isogenic pneumococci carrying allelic variants of the cps promoter displayed significant differences in the transcription of the capsule genes, capsule production, adhesion to host epithelial cells, anti-phagocytosis and virulence in mouse bacteremia model. This study has thus indicated that the sequence polymorphisms in the cps promoter represent a novel mechanism for fine-tuning the level of encapsulation and virulence among S. pneumoniae strains.}, }
@article {pmid27465241, year = {2016}, author = {Wu, W and Espedido, B and Feng, Y and Zong, Z}, title = {Citrobacter freundii carrying blaKPC-2 and blaNDM-1: characterization by whole genome sequencing.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {30670}, pmid = {27465241}, issn = {2045-2322}, mesh = {Anti-Bacterial Agents/pharmacology ; Carbapenems/pharmacology ; Citrobacter freundii/*enzymology/*genetics/isolation &amp; purification ; Conjugation, Genetic ; DNA Transposable Elements ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Hospitals ; Plasmids/analysis ; Sewage/microbiology ; Whole Genome Sequencing ; beta-Lactam Resistance ; beta-Lactamases/*genetics ; }, abstract = {A carbapenem-resistant Citrobacter freundii strain WCHCF65 was recovered from hospital sewage and was characterized by genome sequencing and conjugation experiments. The strain carried nine genes encoding β-lactamases including two carbapenemase genes, blaNDM-1 and blaKPC-2. blaNDM-1 was carried on an IncX3 plasmid, which was identical to a plasmid found in a local Escherichia coli, suggesting interspecies horizontal transfer. blaKPC-2 was bracketed by two copies of insertion sequence ISKpn19, which could form a composite transposon with the potential to mobilize blaKPC-2, on a new type of plasmid. The coexistence of blaNDM-1 and blaKPC-2 conferred higher levels of resistance to carbapenems compared with blaNDM-1 or blaKPC-2 alone. The coexistence of these carbapenemase genes, on two different plasmids, in one strain may allow new genetic platforms to be generated to mediate their spread.}, }
@article {pmid27462108, year = {2016}, author = {Naor, A and Altman-Price, N and Soucy, SM and Green, AG and Mitiagin, Y and Turgeman-Grott, I and Davidovich, N and Gogarten, JP and Gophna, U}, title = {Impact of a homing intein on recombination frequency and organismal fitness.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {32}, pages = {E4654-61}, pmid = {27462108}, issn = {1091-6490}, mesh = {Cell Fusion ; DNA Polymerase beta/physiology ; Haloferax volcanii/*genetics ; Inteins/*physiology ; *Recombination, Genetic ; }, abstract = {Inteins are parasitic genetic elements that excise themselves at the protein level by self-splicing, allowing the formation of functional, nondisrupted proteins. Many inteins contain a homing endonuclease (HEN) domain and rely on its activity for horizontal propagation. However, successful invasion of an entire population will make this activity redundant, and the HEN domain is expected to degenerate quickly under these conditions. Several theories have been proposed for the continued existence of the both active HEN and noninvaded alleles within a population. However, to date, these models were not directly tested experimentally. Using the natural cell fusion ability of the halophilic archaeon Haloferax volcanii we were able to examine this question in vivo, by mating polB intein-positive [insertion site c in the gene encoding DNA polymerase B (polB-c)] and intein-negative cells and examining the dispersal efficiency of this intein in a natural, polyploid population. Through competition between otherwise isogenic intein-positive and intein-negative strains we determined a surprisingly high fitness cost of over 7% for the polB-c intein. Our laboratory culture experiments and samples taken from Israel's Mediterranean coastline show that the polB-c inteins do not efficiently take over an inteinless population through mating, even under ideal conditions. The presence of the HEN/intein promoted recombination when intein-positive and intein-negative cells were mated. Increased recombination due to HEN activity contributes not only to intein dissemination but also to variation at the population level because recombination tracts during repair extend substantially from the homing site.}, }
@article {pmid27461509, year = {2016}, author = {Breurec, S and Criscuolo, A and Diancourt, L and Rendueles, O and Vandenbogaert, M and Passet, V and Caro, V and Rocha, EP and Touchon, M and Brisse, S}, title = {Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {30379}, pmid = {27461509}, issn = {2045-2322}, support = {281605/ERC_/European Research Council/International ; }, mesh = {Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; DNA Transposable Elements ; Evolution, Molecular ; Flavobacteriaceae/classification/*genetics/pathogenicity ; Gene Transfer, Horizontal ; *Genetic Variation ; *Genome, Bacterial ; *Phylogeny ; Virulence/genetics ; }, abstract = {Elizabethkingia anophelis is an emerging pathogen involved in human infections and outbreaks in distinct world regions. We investigated the phylogenetic relationships and pathogenesis-associated genomic features of two neonatal meningitis isolates isolated 5 years apart from one hospital in Central African Republic and compared them with Elizabethkingia from other regions and sources. Average nucleotide identity firmly confirmed that E. anophelis, E. meningoseptica and E. miricola represent demarcated genomic species. A core genome multilocus sequence typing scheme, broadly applicable to Elizabethkingia species, was developed and made publicly available (http://bigsdb.pasteur.fr/elizabethkingia). Phylogenetic analysis revealed distinct E. anophelis sublineages and demonstrated high genetic relatedness between the African isolates, compatible with persistence of the strain in the hospital environment. CRISPR spacer variation between the African isolates was mirrored by the presence of a large mobile genetic element. The pan-genome of E. anophelis comprised 6,880 gene families, underlining genomic heterogeneity of this species. African isolates carried unique resistance genes acquired by horizontal transfer. We demonstrated the presence of extensive variation of the capsular polysaccharide synthesis gene cluster in E. anophelis. Our results demonstrate the dynamic evolution of this emerging pathogen and the power of genomic approaches for Elizabethkingia identification, population biology and epidemiology.}, }
@article {pmid27460800, year = {2016}, author = {Ray, A and Kinch, LN and de Souza Santos, M and Grishin, NV and Orth, K and Salomon, D}, title = {Proteomics Analysis Reveals Previously Uncharacterized Virulence Factors in Vibrio proteolyticus.}, journal = {mBio}, volume = {7}, number = {4}, pages = {}, pmid = {27460800}, issn = {2150-7511}, support = {K99 AI116948/AI/NIAID NIH HHS/United States ; R01 AI056404/AI/NIAID NIH HHS/United States ; R01 GM094575/GM/NIGMS NIH HHS/United States ; T32 DK007745/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Aquatic Organisms/chemistry ; Cell Survival/drug effects ; Cytoskeleton/metabolism ; Epithelial Cells/microbiology/physiology ; HeLa Cells ; Hemolysin Proteins/*analysis/metabolism ; Humans ; Macrophages/microbiology/physiology ; Mice ; *Proteomics ; RAW 264.7 Cells ; Vibrio/*chemistry ; Virulence Factors/*analysis ; }, abstract = {UNLABELLED: Members of the genus Vibrio include many pathogens of humans and marine animals that share genetic information via horizontal gene transfer. Hence, the Vibrio pan-genome carries the potential to establish new pathogenic strains by sharing virulence determinants, many of which have yet to be characterized. Here, we investigated the virulence properties of Vibrio proteolyticus, a Gram-negative marine bacterium previously identified as part of the Vibrio consortium isolated from diseased corals. We found that V. proteolyticus causes actin cytoskeleton rearrangements followed by cell lysis in HeLa cells in a contact-independent manner. In search of the responsible virulence factor involved, we determined the V. proteolyticus secretome. This proteomics approach revealed various putative virulence factors, including active type VI secretion systems and effectors with virulence toxin domains; however, these type VI secretion systems were not responsible for the observed cytotoxic effects. Further examination of the V. proteolyticus secretome led us to hypothesize and subsequently demonstrate that a secreted hemolysin, belonging to a previously uncharacterized clan of the leukocidin superfamily, was the toxin responsible for the V. proteolyticus-mediated cytotoxicity in both HeLa cells and macrophages. Clearly, there remains an armory of yet-to-be-discovered virulence factors in the Vibrio pan-genome that will undoubtedly provide a wealth of knowledge on how a pathogen can manipulate host cells.<br><br>IMPORTANCE: The pan-genome of the genus Vibrio is a potential reservoir of unidentified toxins that can provide insight into how members of this genus have successfully risen as emerging pathogens worldwide. We focused on Vibrio proteolyticus, a marine bacterium that was previously implicated in virulence toward marine animals, and characterized its interaction with eukaryotic cells. We found that this bacterium causes actin cytoskeleton rearrangements and leads to cell death. Using a proteomics approach, we identified a previously unstudied member of the leukocidin family of pore-forming toxins as the virulence factor responsible for the observed cytotoxicity in eukaryotic cells, as well as a plethora of additional putative virulence factors secreted by this bacterium. Our findings reveal a functional new clan of the leukocidin toxin superfamily and establish this pathogen as a reservoir of potential toxins that can be used for biomedical applications.}, }
@article {pmid27460588, year = {2016}, author = {Rabbani, M and Wahl, LM}, title = {The dynamics of mobile promoters: Enhanced stability in promoter regions.}, journal = {Journal of theoretical biology}, volume = {407}, number = {}, pages = {401-408}, doi = {10.1016/j.jtbi.2016.07.030}, pmid = {27460588}, issn = {1095-8541}, mesh = {DNA Transposable Elements/*genetics ; *Genomic Instability ; Models, Genetic ; *Promoter Regions, Genetic ; Statistics as Topic ; }, abstract = {Mobile promoters are emerging as a new class of mobile genetic elements, first identified by examining prokaryote genome sequences, and more recently confirmed by experimental observations in bacteria. Recent datasets have identified over 40,000 putative mobile promoters in sequenced prokaryote genomes, however only one-third of these are in regions of the genome directly upstream from coding sequences, that is, in promoter regions. The presence of many promoter sequences in non-promoter regions is unexplained. Here we develop a general mathematical model for the dynamics of mobile promoters, extending previous work to capture the dynamics both within and outside promoter regions. From this general model, we apply rigorous model selection techniques to identify which parameters are statistically justified in describing the available mobile promoter data, and find best-fit values of these parameters. Our results suggest that high rates of horizontal gene transfer maintain the population of mobile promoters in promoter regions, and that once established at these sites, mobile promoters are rarely lost, but are commonly copied to other genomic regions. In contrast, mobile promoter copies in non-promoter regions are more numerous and more volatile, experiencing substantially higher rates of duplication, loss and diversification.}, }
@article {pmid27458785, year = {2017}, author = {Wang, H and Sangwan, N and Li, HY and Su, JQ and Oyang, WY and Zhang, ZJ and Gilbert, JA and Zhu, YG and Ping, F and Zhang, HL}, title = {The antibiotic resistome of swine manure is significantly altered by association with the Musca domestica larvae gut microbiome.}, journal = {The ISME journal}, volume = {11}, number = {1}, pages = {100-111}, pmid = {27458785}, issn = {1751-7370}, mesh = {Agriculture ; Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/*drug effects/genetics/isolation &amp; purification ; *Drug Resistance, Bacterial ; Gastrointestinal Microbiome/*drug effects ; Gastrointestinal Tract/microbiology ; Houseflies/*microbiology ; Larva/microbiology ; Manure/*microbiology ; Swine ; }, abstract = {The overuse of antibiotics as veterinary feed additives is potentially contributing to a significant reservoir of antibiotic resistance in agricultural farmlands via the application of antibiotic-contaminated manure. Vermicomposting of swine manure using housefly larvae is a promising biotechnology for waste reduction and control of antibiotic pollution. To determine how vermicomposting influences antibiotic resistance traits in swine manure, we explored the resistome and associated bacterial community dynamics during larvae gut transit over 6 days of treatment. In total, 94 out of 158 antibiotic resistance genes (ARGs) were significantly attenuated (by 85%), while 23 were significantly enriched (3.9-fold) following vermicomposting. The manure-borne bacterial community showed a decrease in the relative abundance of Bacteroidetes, and an increase in Proteobacteria, specifically Ignatzschineria, following gut transit. ARG attenuation was significantly correlated with changes in microbial community succession, especially reduction in Clostridiales and Bacteroidales. Six genomes were assembled from the manure, vermicompost (final product) and gut samples, including Pseudomonas, Providencia, Enterococcus, Bacteroides and Alcanivorax. Transposon-linked ARGs were more abundant in gut-associated bacteria compared with those from manure and vermicompost. Further, ARG-transposon gene cassettes had a high degree of synteny between metagenomic assemblies from gut and vermicompost samples, highlighting the significant contribution of gut microbiota through horizontal gene transfer to the resistome of vermicompost. In conclusion, the larvae gut microbiome significantly influences manure-borne community succession and the antibiotic resistome during animal manure processing.}, }
@article {pmid27457081, year = {2016}, author = {Boucher, N and Noll, KM}, title = {Substrate adaptabilities of Thermotogae mannan binding proteins as a function of their evolutionary histories.}, journal = {Extremophiles : life under extreme conditions}, volume = {20}, number = {5}, pages = {771-783}, pmid = {27457081}, issn = {1433-4909}, mesh = {ATP-Binding Cassette Transporters/*genetics/metabolism ; Bacterial Proteins/*genetics/metabolism ; Binding Sites ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Mannans/*metabolism ; Phylogeny ; Protein Binding ; Selection, Genetic ; Substrate Specificity ; Thermotoga maritima/enzymology/*genetics ; Thermotoga neapolitana/enzymology/*genetics ; }, abstract = {The Thermotogae possess a large number of ATP-binding cassette (ABC) transporters, including two mannan binding proteins, ManD and CelE (previously called ManE). We show that a gene encoding an ancestor of these was acquired by the Thermotogae from the archaea followed by gene duplication. To address the functional evolution of these proteins as a consequence of their evolutionary histories, we measured the binding affinities of ManD and CelE orthologs from representative Thermotogae. Both proteins bind cellobiose, cellotriose, cellotetraose, β-1,4-mannotriose, and β-1,4-mannotetraose. The CelE orthologs additionally bind β-1,4-mannobiose, laminaribiose, laminaritriose and sophorose while the ManD orthologs additionally only weakly bind β-1,4-mannobiose. The CelE orthologs have higher unfolding temperatures than the ManD orthologs. An examination of codon sites under positive selection revealed that many of these encode residues located near or in the binding site, suggesting that the proteins experienced selective pressures in regions that might have changed their functions. The gene arrangement, phylogeny, binding properties, and putative regulatory networks suggest that the ancestral mannan binding protein was a CelE ortholog which gave rise to the ManD orthologs. This study provides a window on how one class of proteins adapted to new functions and temperatures to fit the physiologies of their new hosts.}, }
@article {pmid27453035, year = {2016}, author = {Cong, Y and Chan, YB and Ragan, MA}, title = {A novel alignment-free method for detection of lateral genetic transfer based on TF-IDF.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {30308}, pmid = {27453035}, issn = {2045-2322}, mesh = {Computational Biology/methods ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome ; Phylogeny ; Sequence Analysis, DNA/*methods ; Sequence Analysis, Protein/*methods ; }, abstract = {Lateral genetic transfer (LGT) plays an important role in the evolution of microbes. Existing computational methods for detecting genomic regions of putative lateral origin scale poorly to large data. Here, we propose a novel method based on TF-IDF (Term Frequency-Inverse Document Frequency) statistics to detect not only regions of lateral origin, but also their origin and direction of transfer, in sets of hierarchically structured nucleotide or protein sequences. This approach is based on the frequency distributions of k-mers in the sequences. If a set of contiguous k-mers appears sufficiently more frequently in another phyletic group than in its own, we infer that they have been transferred from the first group to the second. We performed rigorous tests of TF-IDF using simulated and empirical datasets. With the simulated data, we tested our method under different parameter settings for sequence length, substitution rate between and within groups and post-LGT, deletion rate, length of transferred region and k size, and found that we can detect LGT events with high precision and recall. Our method performs better than an established method, ALFY, which has high recall but low precision. Our method is efficient, with runtime increasing approximately linearly with sequence length.}, }
@article {pmid27452976, year = {2016}, author = {Cong, Y and Chan, YB and Ragan, MA}, title = {Exploring lateral genetic transfer among microbial genomes using TF-IDF.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {29319}, pmid = {27452976}, issn = {2045-2322}, mesh = {Bacteria/genetics ; Databases, Genetic ; Gene Regulatory Networks ; *Gene Transfer, Horizontal ; *Genome, Microbial ; Phylogeny ; }, abstract = {Many microbes can acquire genetic material from their environment and incorporate it into their genome, a process known as lateral genetic transfer (LGT). Computational approaches have been developed to detect genomic regions of lateral origin, but typically lack sensitivity, ability to distinguish donor from recipient, and scalability to very large datasets. To address these issues we have introduced an alignment-free method based on ideas from document analysis, term frequency-inverse document frequency (TF-IDF). Here we examine the performance of TF-IDF on three empirical datasets: 27 genomes of Escherichia coli and Shigella, 110 genomes of enteric bacteria, and 143 genomes across 12 bacterial and three archaeal phyla. We investigate the effect of k-mer size, gap size and delineation of groups on the inference of genomic regions of lateral origin, finding an interplay among these parameters and sequence divergence. Because TF-IDF identifies donor groups and delineates regions of lateral origin within recipient genomes, aggregating these regions by gene enables us to explore, for the first time, the mosaic nature of lateral genes including the multiplicity of biological sources, ancestry of transfer and over-writing by subsequent transfers. We carry out Gene Ontology enrichment tests to investigate which biological processes are potentially affected by LGT.}, }
@article {pmid27452947, year = {2016}, author = {Sun, T and Renner, SS and Xu, Y and Qin, Y and Wu, J and Sun, G}, title = {Two hAT transposon genes were transferred from Brassicaceae to broomrapes and are actively expressed in some recipients.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {30192}, pmid = {27452947}, issn = {2045-2322}, mesh = {Amino Acid Sequence ; Brassicaceae/*genetics ; DNA Transposable Elements/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genes, Plant/*genetics ; Molecular Sequence Annotation/methods ; Orobanchaceae/genetics ; Orobanche/*genetics ; Phylogeny ; Plant Roots/genetics ; Sequence Analysis, DNA ; Transposases/genetics ; }, abstract = {A growing body of evidence is pointing to an important role of horizontal gene transfer (HGT) in the evolution of higher plants. However, reports of HGTs of transposable elements (TEs) in plants are still scarce, and only one case is known of a class II transposon horizontally transferred between grasses. To investigate possible TE transfers in dicots, we performed transcriptome screening in the obligate root parasite Phelipanche aegyptiaca (Orobanchaceae), data-mining in the draft genome assemblies of four other Orobanchaceae, gene cloning, gene annotation in species with genomic information, and a molecular phylogenetic analysis. We discovered that the broomrape genera Phelipanche and Orobanche acquired two related nuclear genes (christened BO transposase genes), a new group of the hAT superfamily of class II transposons, from Asian Sisymbrieae or a closely related tribe of Brassicaceae, by HGT. The collinearity of the flanking genes, lack of a classic border structure, and low expression levels suggest that BO transposase genes cannot transpose in Brassicaceae, whereas they are highly expressed in P. aegyptiaca.}, }
@article {pmid27449596, year = {2016}, author = {Wang, X and Wood, TK}, title = {Cryptic prophages as targets for drug development.}, journal = {Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy}, volume = {27}, number = {}, pages = {30-38}, doi = {10.1016/j.drup.2016.06.001}, pmid = {27449596}, issn = {1532-2084}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/*drug effects/genetics/pathogenicity/virology ; Chromosomes, Bacterial/chemistry/*virology ; Drug Resistance, Microbial/*genetics ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Lysogeny/genetics ; Prophages/*drug effects/genetics/pathogenicity ; SOS Response, Genetics ; Toxin-Antitoxin Systems/genetics ; Virulence ; Virulence Factors/genetics/metabolism ; }, abstract = {Bacterial chromosomes may contain up to 20% phage DNA that encodes diverse proteins ranging from those for photosynthesis to those for autoimmunity; hence, phages contribute greatly to the metabolic potential of pathogens. Active prophages carrying genes encoding virulence factors and antibiotic resistance can be excised from the host chromosome to form active phages and are transmissible among different bacterial hosts upon SOS responses. Cryptic prophages are artifacts of mutagenesis in which lysogenic phage are captured in the bacterial chromosome: they may excise but they do not form active phage particles or lyse their captors. Hence, cryptic prophages are relatively permanent reservoirs of genes, many of which benefit pathogens, in ways we are just beginning to discern. Here we explore the role of active prophage- and cryptic prophage-derived proteins in terms of (i) virulence, (ii) antibiotic resistance, and (iii) antibiotic tolerance; antibiotic tolerance occurs as a result of the non-heritable phenotype of dormancy which is a result of activation of toxins of toxin/antitoxin loci that are frequently encoded in cryptic prophages. Therefore, cryptic prophages are promising targets for drug development.}, }
@article {pmid27446814, year = {2016}, author = {Cenci, U and Ducatez, M and Kadouche, D and Colleoni, C and Ball, SG}, title = {Was the Chlamydial Adaptative Strategy to Tryptophan Starvation an Early Determinant of Plastid Endosymbiosis?.}, journal = {Frontiers in cellular and infection microbiology}, volume = {6}, number = {}, pages = {67}, pmid = {27446814}, issn = {2235-2988}, mesh = {Amino Acids/metabolism ; Biological Evolution ; Chlamydia/enzymology/genetics/*metabolism ; Cyanobacteria/metabolism ; Escherichia coli/metabolism ; Gene Transfer, Horizontal ; Host-Pathogen Interactions ; Phylogeny ; Plants/enzymology/metabolism/microbiology ; Plastids/genetics/*metabolism/*microbiology ; Symbiosis ; Tryptophan/biosynthesis/*deficiency/genetics/*metabolism ; }, abstract = {Chlamydiales were recently proposed to have sheltered the future cyanobacterial ancestor of plastids in a common inclusion. The intracellular pathogens are thought to have donated those critical transporters that triggered the efflux of photosynthetic carbon and the consequent onset of symbiosis. Chlamydiales are also suspected to have encoded glycogen metabolism TTS (Type Three Secretion) effectors responsible for photosynthetic carbon assimilation in the eukaryotic cytosol. We now review the reasons underlying other chlamydial lateral gene transfers evidenced in the descendants of plastid endosymbiosis. In particular we show that half of the genes encoding enzymes of tryptophan synthesis in Archaeplastida are of chlamydial origin. Tryptophan concentration is an essential cue triggering two alternative modes of replication in Chlamydiales. In addition, sophisticated tryptophan starvation mechanisms are known to act as antibacterial defenses in animal hosts. We propose that Chlamydiales have donated their tryptophan operon to the emerging plastid to ensure increased synthesis of tryptophan by the plastid ancestor. This would have allowed massive expression of the tryptophan rich chlamydial transporters responsible for symbiosis. It would also have allowed possible export of this valuable amino-acid in the inclusion of the tryptophan hungry pathogens. Free-living single cell cyanobacteria are devoid of proteins able to transport this amino-acid. We therefore investigated the phylogeny of the Tyr/Trp transporters homologous to E. coli TyrP/Mre and found yet another LGT from Chlamydiales to Archaeplastida thereby considerably strengthening our proposal.}, }
@article {pmid27446038, year = {2016}, author = {Tian, X and Zhang, Z and Yang, T and Chen, M and Li, J and Chen, F and Yang, J and Li, W and Zhang, B and Zhang, Z and Wu, J and Zhang, C and Long, L and Xiao, J}, title = {Comparative Genomics Analysis of Streptomyces Species Reveals Their Adaptation to the Marine Environment and Their Diversity at the Genomic Level.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {998}, pmid = {27446038}, issn = {1664-302X}, abstract = {Over 200 genomes of streptomycete strains that were isolated from various environments are available from the NCBI. However, little is known about the characteristics that are linked to marine adaptation in marine-derived streptomycetes. The particularity and complexity of the marine environment suggest that marine streptomycetes are genetically diverse. Here, we sequenced nine strains from the Streptomyces genus that were isolated from different longitudes, latitudes, and depths of the South China Sea. Then we compared these strains to 22 NCBI downloaded streptomycete strains. Thirty-one streptomycete strains are clearly grouped into a marine-derived subgroup and multiple source subgroup-based phylogenetic tree. The phylogenetic analyses have revealed the dynamic process underlying streptomycete genome evolution, and lateral gene transfer is an important driving force during the process. Pan-genomics analyses have revealed that streptomycetes have an open pan-genome, which reflects the diversity of these streptomycetes and guarantees the species a quick and economical response to diverse environments. Functional and comparative genomics analyses indicate that the marine-derived streptomycetes subgroup possesses some common characteristics of marine adaptation. Our findings have expanded our knowledge of how ocean isolates of streptomycete strains adapt to marine environments. The availability of streptomycete genomes from the South China Sea will be beneficial for further analysis on marine streptomycetes and will enrich the South China Sea's genetic data sources.}, }
@article {pmid27445996, year = {2016}, author = {Badalamenti, JP and Summers, ZM and Chan, CH and Gralnick, JA and Bond, DR}, title = {Isolation and Genomic Characterization of 'Desulfuromonas soudanensis WTL', a Metal- and Electrode-Respiring Bacterium from Anoxic Deep Subsurface Brine.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {913}, pmid = {27445996}, issn = {1664-302X}, abstract = {Reaching a depth of 713 m below the surface, the Soudan Underground Iron Mine (Soudan, MN, USA) transects a massive Archaean (2.7 Ga) banded iron formation, providing a remarkably accessible window into the terrestrial deep biosphere. Despite organic carbon limitation, metal-reducing microbial communities are present in potentially ancient anoxic brines continuously emanating from exploratory boreholes on Level 27. Using graphite electrodes deposited in situ as bait, we electrochemically enriched and isolated a novel halophilic iron-reducing Deltaproteobacterium, 'Desulfuromonas soudanensis' strain WTL, from an acetate-fed three-electrode bioreactor poised at +0.24 V (vs. standard hydrogen electrode). Cyclic voltammetry revealed that 'D. soudanensis' releases electrons at redox potentials approximately 100 mV more positive than the model freshwater surface isolate Geobacter sulfurreducens, suggesting that its extracellular respiration is tuned for higher potential electron acceptors. 'D. soudanensis' contains a 3,958,620-bp circular genome, assembled to completion using single-molecule real-time (SMRT) sequencing reads, which encodes a complete TCA cycle, 38 putative multiheme c-type cytochromes, one of which contains 69 heme-binding motifs, and a LuxI/LuxR quorum sensing cassette that produces an unidentified N-acyl homoserine lactone. Another cytochrome is predicted to lie within a putative prophage, suggesting that horizontal gene transfer plays a role in respiratory flexibility among metal reducers. Isolation of 'D. soudanensis' underscores the utility of electrode-based approaches for enriching rare metal reducers from a wide range of habitats.}, }
@article {pmid27445994, year = {2016}, author = {Zhang, M and Brons, JK and van Elsas, JD}, title = {The Complete Sequences and Ecological Roles of Two IncP-1β Plasmids, pHB44 and pBS64, Isolated from the Mycosphere of Laccaria proxima.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {909}, pmid = {27445994}, issn = {1664-302X}, abstract = {Two novel plasmids, coined pHB44 and pBS64, were recently found in Variovorax paradoxus strains HB44 and BS64 isolated from the mycosphere of Laccaria proxima, on two different sampling occasions. We here describe the full sequences of pHB44 and pBS64 and establish their evolutionary placement and ecological function. Both plasmids, unique for mycospheric V. paradoxus, were around 58 kb in size. They possessed, in a very similar fashion, three main plasmid backbone regions, which were predicted to be involved in plasmid replication, central control of maintenance, and conjugational transfer. Phylogenetic inference on the basis of seven selected and concatenated plasmid backbone genes provided solid evidence for the placement of the two plasmids in the IncP-1β1 group, with the recently isolated IncP-1β1 plasmid pMBUI8 as the closest relative. A comparative analysis of the sequences present in each of the recombinational hot spots (RHS) I to III across plasmids pHB44, pBS64, and pMBUI8 revealed the insertions found in plasmids pHB44 and pBS64 to be different from those of pMBUI8. Whereas, in the former two plasmids, RHS I and III were devoid of any major inserts, their RHS II regions contained inserts of 15,043 (pHB44) and 16,406 kb (pBS64), against about 9,3 kb for pMBUI8. Interestingly, these regions were highly similar across plasmids pHB44 and pBS64, and differed from that of pMBUI8. Closer inspection revealed the insert in the former plasmids to contain, next to transposases, an "mmf" gene cassette previously reported to encode metal "responsiveness" in the PromA plasmid pMOL98. Whereas the plasmid pHB44 RHS II contained the canonical mmf sequence, that in pBS64 contained, in addition, a "two-gene duplicated region" flanking the mmf C2 gene. In vitro experiments on the growth and survival of strains with or without plasmid pHB44 suggested this plasmid was involved in the binding and import of Fe(3+) as well as V(3+) ions into the host cells, thus yielding a growth advantage under "metal ion-limiting" conditions. In addition, pHB44 was found to confer a bacitracin resistance phenotype to its host strain HB44. The metal import and bacitracin resistance traits were tentatively attributed to specific genes present in the RHS II inserts.}, }
@article {pmid27442015, year = {2016}, author = {Llanes, A and Restrepo, CM and Rajeev, S}, title = {Whole Genome Sequencing Allows Better Understanding of the Evolutionary History of Leptospira interrogans Serovar Hardjo.}, journal = {PloS one}, volume = {11}, number = {7}, pages = {e0159387}, pmid = {27442015}, issn = {1932-6203}, mesh = {Base Sequence ; *Biological Evolution ; *Genome, Bacterial ; Genomics ; Leptospira interrogans/*classification/*genetics ; Likelihood Functions ; Molecular Sequence Annotation ; Phylogeny ; Sequence Analysis, DNA/*methods ; *Serogroup ; }, abstract = {The genome of a laboratory-adapted strain of Leptospira interrogans serovar Hardjo was sequenced and analyzed. Comparison of the sequenced genome with that recently published for a field isolate of the same serovar revealed relatively high sequence conservation at the nucleotide level, despite the different biological background of both samples. Conversely, comparison of both serovar Hardjo genomes with those of L. borgpetersenii serovar Hardjo showed extensive differences between the corresponding chromosomes, except for the region occupied by their rfb loci. Additionally, comparison of the serovar Hardjo genomes with those of different L. interrogans serovars allowed us to detect several genomic features that may confer an adaptive advantage to L. interrogans serovar Hardjo, including a possible integrated plasmid and an additional copy of a cluster encoding a membrane transport system known to be involved in drug resistance. A phylogenomic strategy was used to better understand the evolutionary position of the Hardjo serovar among L. interrogans serovars and other Leptospira species. The proposed phylogeny supports the hypothesis that the presence of similar rfb loci in two different species may be the result of a lateral gene transfer event.}, }
@article {pmid27438026, year = {2016}, author = {Chen, X and Yang, Y and Shi, Z and Gao, MQ and Zhang, Y}, title = {Effects of Genetically Modified Milk Containing Human Beta-Defensin-3 on Gastrointestinal Health of Mice.}, journal = {PloS one}, volume = {11}, number = {7}, pages = {e0159700}, pmid = {27438026}, issn = {1932-6203}, mesh = {Animals ; Consumer Product Safety ; Digestion ; Food, Genetically Modified/*adverse effects ; Gastrointestinal Tract/drug effects ; Humans ; Mice ; Milk/*adverse effects/metabolism ; beta-Defensins/*genetics ; }, abstract = {This study was performed to investigate the effects of genetically modified (GM) milk containing human beta-defensin-3 (HBD3) on mice by a 90-day feeding study. The examined parameters included the digestibility of GM milk, general physical examination, gastric emptying function, intestinal permeability, intestinal microflora composition of mice, and the possibility of horizontal gene transfer (HGT). The emphasis was placed on the effects on gastrointestinal (GI) tract due to the fact that GI tract was the first site contacting with food and played crucial roles in metabolic reactions, nutrition absorption and immunity regulation in the host. However, the traditional methods for analyzing the potential toxicological risk of GM product pay little attention on GI health. In this study, the results showed GM milk was easy to be digested in simulated gastric fluid, and it did not have adverse effects on general and GI health compared to conventional milk. And there is little possibility of HGT. This study may enrich the safety assessment of GM product on GI health.}, }
@article {pmid27435459, year = {2016}, author = {Carraro, N and Rivard, N and Ceccarelli, D and Colwell, RR and Burrus, V}, title = {IncA/C Conjugative Plasmids Mobilize a New Family of Multidrug Resistance Islands in Clinical Vibrio cholerae Non-O1/Non-O139 Isolates from Haiti.}, journal = {mBio}, volume = {7}, number = {4}, pages = {}, pmid = {27435459}, issn = {2150-7511}, mesh = {Anti-Bacterial Agents/pharmacology ; Cholera/microbiology ; *Conjugation, Genetic ; DNA Transposable Elements ; *Drug Resistance, Multiple, Bacterial ; *Gene Transfer, Horizontal ; *Genomic Islands ; Haiti ; Humans ; Integrons ; *Plasmids ; Vibrio cholerae non-O1/*drug effects/*genetics/isolation &amp; purification ; }, abstract = {UNLABELLED: Mobile genetic elements play a pivotal role in the adaptation of bacterial populations, allowing them to rapidly cope with hostile conditions, including the presence of antimicrobial compounds. IncA/C conjugative plasmids (ACPs) are efficient vehicles for dissemination of multidrug resistance genes in a broad range of pathogenic species of Enterobacteriaceae ACPs have sporadically been reported in Vibrio cholerae, the infectious agent of the diarrheal disease cholera. The regulatory network that controls ACP mobility ultimately depends on the transcriptional activation of multiple ACP-borne operons by the master activator AcaCD. Beyond ACP conjugation, AcaCD has also recently been shown to activate the expression of genes located in the Salmonella genomic island 1 (SGI1). Here, we describe MGIVchHai6, a novel and unrelated mobilizable genomic island (MGI) integrated into the 3' end of trmE in chromosome I of V. cholerae HC-36A1, a non-O1/non-O139 multidrug-resistant clinical isolate recovered from Haiti in 2010. MGIVchHai6 contains a mercury resistance transposon and an integron In104-like multidrug resistance element similar to the one of SGI1. We show that MGIVchHai6 excises from the chromosome in an AcaCD-dependent manner and is mobilized by ACPs. Acquisition of MGIVchHai6 confers resistance to β-lactams, sulfamethoxazole, tetracycline, chloramphenicol, trimethoprim, and streptomycin/spectinomycin. In silico analyses revealed that MGIVchHai6-like elements are carried by several environmental and clinical V. cholerae strains recovered from the Indian subcontinent, as well as from North and South America, including all non-O1/non-O139 clinical isolates from Haiti.<br><br>IMPORTANCE: Vibrio cholerae, the causative agent of cholera, remains a global public health threat. Seventh-pandemic V.&#xa0;cholerae acquired multidrug resistance genes primarily through circulation of SXT/R391 integrative and conjugative elements. IncA/C conjugative plasmids have sporadically been reported to mediate antimicrobial resistance in environmental and clinical V.&#xa0;cholerae isolates. Our results showed that while IncA/C plasmids are rare in V.&#xa0;cholerae populations, they play an important yet insidious role by specifically propagating a new family of genomic islands conferring resistance to multiple antibiotics. These results suggest that nonepidemic V.&#xa0;cholerae non-O1/non-O139 strains bearing these genomic islands constitute a reservoir of transmissible resistance genes that can be propagated by IncA/C plasmids to V.&#xa0;cholerae populations in epidemic geographical areas as well to pathogenic species of Enterobacteriaceae We recommend future epidemiological surveys take into account the circulation of these genomic islands.}, }
@article {pmid27433121, year = {2016}, author = {Choi, J and Park, JG and Ali, MS and Choi, SJ and Baek, KH}, title = {Systematic Analysis of the Anticancer Agent Taxol-Producing Capacity in Colletotrichum Species and Use of the Species for Taxol Production.}, journal = {Mycobiology}, volume = {44}, number = {2}, pages = {105-111}, pmid = {27433121}, issn = {1229-8093}, abstract = {Paclitaxel (taxol) has long been used as a potent anticancer agent for the treatment of many cancers. Ever since the fungal species Taxomyces andreanae was first shown to produce taxol in 1993, many endophytic fungal species have been recognized as taxol accumulators. In this study, we analyzed the taxol-producing capacity of different Colletotrichum spp. to determine the distribution of a taxol biosynthetic gene within this genus. Distribution of the taxadiene synthase (TS) gene, which cyclizes geranylgeranyl diphosphate to produce taxadiene, was analyzed in 12 Colletotrichum spp., of which 8 were found to contain the unique skeletal core structure of paclitaxel. However, distribution of the gene was not limited to closely related species. The production of taxol by Colletotrichum dematium, which causes pepper anthracnose, depended on the method in which the fungus was stored, with the highest production being in samples stored under mineral oil. Based on its distribution among Colletotrichum spp., the TS gene was either integrated into or deleted from the bacterial genome in a species-specific manner. In addition to their taxol-producing capacity, the simple genome structure and easy gene manipulation of these endophytic fungal species make them valuable resources for identifying genes in the taxol biosynthetic pathway.}, }
@article {pmid27432973, year = {2016}, author = {Attaiech, L and Boughammoura, A and Brochier-Armanet, C and Allatif, O and Peillard-Fiorente, F and Edwards, RA and Omar, AR and MacMillan, AM and Glover, M and Charpentier, X}, title = {Silencing of natural transformation by an RNA chaperone and a multitarget small RNA.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {31}, pages = {8813-8818}, pmid = {27432973}, issn = {1091-6490}, mesh = {Bacterial Proteins/genetics/metabolism ; DNA, Bacterial/genetics ; Gene Expression Profiling/methods ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Humans ; Legionella pneumophila/*genetics/metabolism ; Legionnaires' Disease/microbiology ; Models, Genetic ; RNA, Bacterial/*genetics ; Regulon/genetics ; Transformation, Bacterial ; }, abstract = {A highly conserved DNA uptake system allows many bacteria to actively import and integrate exogenous DNA. This process, called natural transformation, represents a major mechanism of horizontal gene transfer (HGT) involved in the acquisition of virulence and antibiotic resistance determinants. Despite evidence of HGT and the high level of conservation of the genes coding the DNA uptake system, most bacterial species appear non-transformable under laboratory conditions. In naturally transformable species, the DNA uptake system is only expressed when bacteria enter a physiological state called competence, which develops under specific conditions. Here, we investigated the mechanism that controls expression of the DNA uptake system in the human pathogen Legionella pneumophila We found that a repressor of this system displays a conserved ProQ/FinO domain and interacts with a newly characterized trans-acting sRNA, RocR. Together, they target mRNAs of the genes coding the DNA uptake system to control natural transformation. This RNA-based silencing represents a previously unknown regulatory means to control this major mechanism of HGT. Importantly, these findings also show that chromosome-encoded ProQ/FinO domain-containing proteins can assist trans-acting sRNAs and that this class of RNA chaperones could play key roles in post-transcriptional gene regulation throughout bacterial species.}, }
@article {pmid27430533, year = {2016}, author = {Azizi, O and Shakibaie, MR and Badmasti, F and Modarresi, F and Ramazanzadeh, R and Mansouri, S and Shahcheraghi, F}, title = {Class 1 integrons in non-clonal multidrug-resistant Acinetobacter baumannii from Iran, description of the new blaIMP-55 allele in In1243.}, journal = {Journal of medical microbiology}, volume = {65}, number = {9}, pages = {928-936}, doi = {10.1099/jmm.0.000315}, pmid = {27430533}, issn = {1473-5644}, mesh = {Acinetobacter Infections/*microbiology ; Acinetobacter baumannii/classification/enzymology/*genetics/*isolation &amp; purification ; Adult ; Alleles ; Bacterial Proteins/*genetics ; Conjugation, Genetic ; DNA Fingerprinting ; *Drug Resistance, Multiple, Bacterial ; Female ; Gene Transfer, Horizontal ; Genotype ; Hospitals ; Humans ; *Integrons ; Iran ; Male ; Middle Aged ; Molecular Typing ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; beta-Lactamases/*genetics ; }, abstract = {Infections and outbreaks caused by multidrug-resistant Acinetobacter baumannii (MDR-AB) are prevalent and have been reported worldwide over the past 20 or more years. Class 1 integron in MDR-AB plays an important role in the spread of antibiotic resistance in clinical settings. This study has been conducted to evaluate the detection of metallo-β-lactamase, characterization of class 1 integron and determination of clonal relatedness among A. baumannii hospital isolates. Sixty-five clinical isolates of MDR-AB were recovered from two Iranian hospital's intensive care units from February to August 2013. Integrase (intI1) and blaIMP genes were detected in 70.8 % (n=46/65) and 9.23 % (n=6/65) of the isolates using PCR assay, respectively. No other metallo-β-lactamase genes (blaVIM, blaSIM and blaNDM) were detected. PCR sequencing of integron gene cassette revealed the following arrays: blaOXA10-aacA4-blaIMP-55-cmlA5 (as a novel array was designated In1243), aacC1 and aadA1. Analysis of blaIMP gene revealed a new allele designated as blaIMP-55. Gene transfer experiment by conjugation showed the 36 kb conjugative plasmid harbouring In1243. The clonal assessment by repetitive extragenic palindromic PCR demonstrated a high-degree relatedness among the strains, but strains harbouring In1243 displayed a different repetitive extragenic palindromic PCR profile. In this study, we found that a novel class 1 integron (In1243) that encoded a new blaIMP allele resided on a transferable plasmid in non-clonal strains of MDR-AB.}, }
@article {pmid27428829, year = {2016}, author = {Pereira, MB and Wallroth, M and Kristiansson, E and Axelson-Fisk, M}, title = {HattCI: Fast and Accurate attC site Identification Using Hidden Markov Models.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {23}, number = {11}, pages = {891-902}, doi = {10.1089/cmb.2016.0024}, pmid = {27428829}, issn = {1557-8666}, mesh = {Bacteria/*genetics ; Computational Biology/*methods ; Databases, Nucleic Acid ; Gene Transfer, Horizontal ; Integrons ; *Inverted Repeat Sequences ; Markov Chains ; Metagenomics/methods ; }, abstract = {Integrons are genetic elements that facilitate the horizontal gene transfer in bacteria and are known to harbor genes associated with antibiotic resistance. The gene mobility in the integrons is governed by the presence of attC sites, which are 55 to 141-nucleotide-long imperfect inverted repeats. Here we present HattCI, a new method for fast and accurate identification of attC sites in large DNA data sets. The method is based on a generalized hidden Markov model that describes each core component of an attC site individually. Using twofold cross-validation experiments on a manually curated reference data set of 231 attC sites from class 1 and 2 integrons, HattCI showed high sensitivities of up to 91.9% while maintaining satisfactory false-positive rates. When applied to a metagenomic data set of 35 microbial communities from different environments, HattCI found a substantially higher number of attC sites in the samples that are known to contain more horizontally transferred elements. HattCI will significantly increase the ability to identify attC sites and thus integron-mediated genes in genomic and metagenomic data. HattCI is implemented in C and is freely available at http://bioinformatics.math.chalmers.se/HattCI .}, }
@article {pmid27425574, year = {2016}, author = {Zarlenga, D and Wang, Z and Mitreva, M}, title = {Trichinella spiralis: Adaptation and parasitism.}, journal = {Veterinary parasitology}, volume = {231}, number = {}, pages = {8-21}, pmid = {27425574}, issn = {1873-2550}, support = {R01 AI081803/AI/NIAID NIH HHS/United States ; R01 GM097435/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Physiological/*genetics ; Animals ; *Biological Evolution ; *Genome, Helminth ; *Genomics ; Nematoda/*genetics/physiology ; Phylogeny ; Proteomics ; Trichinella spiralis/*genetics/physiology ; }, abstract = {Publication of the genome from the clade I organism, Trichinella spiralis, has provided us an avenue to address more holistic problems in parasitology; namely the processes of adaptation and the evolution of parasitism. Parasitism among nematodes has evolved in multiple, independent events. Deciphering processes that drive species diversity and adaptation are keys to understanding parasitism and advancing control strategies. Studies have been put forth on morphological and physiological aspects of parasitism and adaptation in nematodes; however, data is now coming available to investigate adaptation, host switching and parasitism at the genomic level. Herein we compare proteomic data from the clade I parasite, Trichinella spiralis with data from Brugia malayi (clade III), Meloidogyne hapla and Meloidogyne incognita (clade IV), and free-living nematodes belonging to the genera Caenorhabditis and Pristionchus (clade V). We explore changes in protein family birth/death and expansion/reduction over the course of metazoan evolution using Homo sapiens, Drosophila melanogaster and Saccharomyces cerevisiae as outgroups for the phylum Nematoda. We further examine relationships between these changes and the ability and/or result of nematodes adapting to their environments. Data are consistent with gene loss occurring in conjunction with nematode specialization resulting from parasitic worms acclimating to well-defined, environmental niches. We observed evidence for independent, lateral gene transfer events involving conserved genes that may have played a role in the evolution of nematode parasitism. In general, parasitic nematodes gained proteins through duplication and lateral gene transfer, and lost proteins through random mutation and deletions. Data suggest independent acquisition rather than ancestral inheritance among the Nematoda followed by selective gene loss over evolutionary time. Data also show that parasitism and adaptation affected a broad range of proteins, especially those involved in sensory perception, metabolism, and transcription/translation. New protein gains with functions related to regulating transcription and translation, and protein family expansions with functions related to morphology and body development have occurred in association with parasitism. Further gains occurred as a result of lateral gene transfer and in particular, with the cyanase protein family In contrast, reductions and/or losses have occurred in protein families with functions related to metabolic process and signal transduction. Taking advantage of the independent occurrences of parasitism in nematodes, which enabled us to distinguish changes associated with parasitism from species specific niche adaptation, our study provides valuable insights into nematode parasitism at a proteome level using T. spiralis as a benchmark for early adaptation to or acquisition of parasitism.}, }
@article {pmid27421564, year = {2016}, author = {Harman, A and Manna, S}, title = {Identification of Pif1 helicases with novel accessory domains in various amoebae.}, journal = {Molecular phylogenetics and evolution}, volume = {103}, number = {}, pages = {64-74}, doi = {10.1016/j.ympev.2016.07.015}, pmid = {27421564}, issn = {1095-9513}, mesh = {Amino Acid Sequence ; Amoeba/*classification/metabolism ; Basidiomycota/enzymology ; DNA Helicases/classification/*genetics ; DNA Replication ; DNA Topoisomerases, Type I/classification/genetics ; DNA, Protozoan/chemistry/isolation &amp; purification/metabolism ; Gene Transfer, Horizontal ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Zinc Fingers/genetics ; }, abstract = {Pif1 helicases are a conserved family of eukaryotic proteins involved in the maintenance of both nuclear and mitochondrial DNA. These enzymes possess a number of known and putative functions, which facilitate overall genome integrity. Here we have identified multiple subtypes of Pif1 proteins in various pathogenic and non-pathogenic amoeboid species which possess additional domains not present in other Pif1 helicases. These helicases each possess one of five different accessory domains, which have roles in ubiquitination, origin of DNA replication recognition or single-stranded nucleic acid binding activity. Using a robust phylogenetic approach we examined each Pif1 class, which revealed that gene duplication, fusion and horizontal gene transfer events have all contributed to the evolution of these enzymes. This study has identified the first collection of Pif1 helicases to contain additional domains, which likely confer novel enzymatic activity, or improve existing functionality. Furthermore, the potential functions of these helicases may shed further light on the overall role the Pif1 family plays in genome maintenance.}, }
@article {pmid27419137, year = {2016}, author = {Wang, J}, title = {A Metric on the Space of Partly Reduced Phylogenetic Networks.}, journal = {BioMed research international}, volume = {2016}, number = {}, pages = {7534258}, pmid = {27419137}, issn = {2314-6141}, mesh = {*Models, Genetic ; *Phylogeny ; }, abstract = {Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of evolutionary events acting at the population level, such as recombination between genes, hybridization between lineages, and horizontal gene transfer. The researchers have designed several measures for computing the dissimilarity between two phylogenetic networks, and each measure has been proven to be a metric on a special kind of phylogenetic networks. However, none of the existing measures is a metric on the space of partly reduced phylogenetic networks. In this paper, we provide a metric, d e -distance, on the space of partly reduced phylogenetic networks, which is polynomial-time computable.}, }
@article {pmid27412985, year = {2016}, author = {Müller, WJ and Tlalajoe, N and Cason, ED and Litthauer, D and Reva, O and Brzuszkiewicz, E and van Heerden, E}, title = {Whole Genome Comparison of Thermus sp. NMX2.A1 Reveals Principle Carbon Metabolism Differences with Closest Relation Thermus scotoductus SA-01.}, journal = {G3 (Bethesda, Md.)}, volume = {6}, number = {9}, pages = {2791-2797}, pmid = {27412985}, issn = {2160-1836}, mesh = {Carbon/metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome ; Molecular Sequence Data ; Phylogeography ; *Proteomics ; Thermus/*genetics ; }, abstract = {Genome sequencing of the yellow-pigmented, thermophilic bacterium Thermus sp. NMX2.A1 resulted in a 2.29 Mb draft genome that encodes for 2312 proteins. The genetic relationship between various strains from the genus Thermus was assessed based on phylogenomic analyses using a concatenated set of conserved proteins. The resulting phylogenetic tree illustrated that Thermus sp. NMX2 A.1 clusters together with Thermus scotoductus SA-01, despite being isolated from vastly different geographical locations. The close evolutionary relationship and metabolic parallels between the two strains has previously been recognized; however, neither strain's genome data were available at that point in time. Genomic comparison of the Thermus sp. NMX2.A1 and T. scotoductus SA-01, as well as other closely related Thermus strains, revealed a high degree of synteny at both the genomic and proteomic level, with processes such as denitrification and natural cell competence appearing to be conserved. However, despite this high level of similarity, analysis revealed a complete, putative Calvin-Benson-Bassham (CBB) cycle in NMX2.A1 that is absent in SA-01. Analysis of horizontally transferred gene islands provide evidence that NMX2 selected these genes due to pressure from its HCO3 (-) rich environment, which is in stark contrast to that of the deep subsurface isolated SA-01.}, }
@article {pmid27411639, year = {2016}, author = {Campisi, E and Rinaudo, CD and Donati, C and Barucco, M and Torricelli, G and Edwards, MS and Baker, CJ and Margarit, I and Rosini, R}, title = {Serotype IV Streptococcus agalactiae ST-452 has arisen from large genomic recombination events between CC23 and the hypervirulent CC17 lineages.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {29799}, pmid = {27411639}, issn = {2045-2322}, mesh = {Adult ; DNA, Bacterial/chemistry/genetics ; Genome, Bacterial/*genetics ; Genomics/*methods ; Humans ; Infant, Newborn ; Phylogeny ; Polymorphism, Single Nucleotide ; Recombination, Genetic ; Serotyping ; Species Specificity ; Streptococcal Infections/microbiology ; Streptococcus agalactiae/classification/*genetics/pathogenicity ; Virulence/genetics ; Whole Genome Sequencing/*methods ; }, abstract = {Streptococcus agalactiae (Group B Streptococcus, GBS) causes life-threatening infections in newborns and adults with chronic medical conditions. Serotype IV strains are emerging both among carriers and as cause of invasive disease and recent studies revealed two main Sequence Types (STs), ST-452 and ST-459 assigned to Clonal Complexes CC23 and CC1, respectively. Whole genome sequencing of 70 type IV GBS and subsequent phylogenetic analysis elucidated the localization of type IV isolates in a SNP-based phylogenetic tree and suggested that ST-452 could have originated through genetic recombination. SNPs density analysis of the core genome confirmed that the founder strain of this lineage originated from a single large horizontal gene transfer event between CC23 and the hypervirulent CC17. Indeed, ST-452 genomes are composed by two parts that are nearly identical to corresponding regions in ST-24 (CC23) and ST-291 (CC17). Chromosome mapping of the major GBS virulence factors showed that ST-452 strains have an intermediate yet unique profile among CC23 and CC17 strains. We described unreported large recombination events, involving the cps IV operon and resulting in the expansion of serotype IV to CC23. This work sheds further light on the evolution of GBS providing new insights on the recent emergence of serotype IV.}, }
@article {pmid27409808, year = {2016}, author = {Brito, IL and Yilmaz, S and Huang, K and Xu, L and Jupiter, SD and Jenkins, AP and Naisilisili, W and Tamminen, M and Smillie, CS and Wortman, JR and Birren, BW and Xavier, RJ and Blainey, PC and Singh, AK and Gevers, D and Alm, EJ}, title = {Mobile genes in the human microbiome are structured from global to individual scales.}, journal = {Nature}, volume = {535}, number = {7612}, pages = {435-439}, pmid = {27409808}, issn = {1476-4687}, support = {U54 HG003067/HG/NHGRI NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; U54HG003067/HG/NHGRI NIH HHS/United States ; T32 GM087237/GM/NIGMS NIH HHS/United States ; R01 DE020891/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacteriophages/genetics ; Cohort Studies ; DNA Transposable Elements/genetics ; Diet ; Fiji ; Gene Pool ; Gene Transfer, Horizontal/*genetics ; *Gene-Environment Interaction ; Genetic Variation/*genetics ; Humans ; *Metagenomics ; Microbiota/*genetics ; North America ; Plasmids/genetics ; Recombination, Genetic/genetics ; Selection, Genetic/*genetics ; Single-Cell Analysis ; }, abstract = {Recent work has underscored the importance of the microbiome in human health, and has largely attributed differences in phenotype to differences in the species present among individuals. However, mobile genes can confer profoundly different phenotypes on different strains of the same species. Little is known about the function and distribution of mobile genes in the human microbiome, and in particular whether the gene pool is globally homogenous or constrained by human population structure. Here, we investigate this question by comparing the mobile genes found in the microbiomes of 81 metropolitan North Americans with those of 172 agrarian Fiji islanders using a combination of single-cell genomics and metagenomics. We find large differences in mobile gene content between the Fijian and North American microbiomes, with functional variation that mirrors known dietary differences such as the excess of plant-based starch degradation genes found in Fijian individuals. Notably, we also observed differences between the mobile gene pools of neighbouring Fijian villages, even though microbiome composition across villages is similar. Finally, we observe high rates of recombination leading to individual-specific mobile elements, suggesting that the abundance of some genes may reflect environmental selection rather than dispersal limitation. Together, these data support the hypothesis that human activities and behaviours provide selective pressures that shape mobile gene pools, and that acquisition of mobile genes is important for colonizing specific human populations.}, }
@article {pmid27406565, year = {2016}, author = {Lacroix, B and Citovsky, V}, title = {Transfer of DNA from Bacteria to Eukaryotes.}, journal = {mBio}, volume = {7}, number = {4}, pages = {}, pmid = {27406565}, issn = {2150-7511}, mesh = {Bacteria/*genetics ; DNA, Bacterial/*genetics/*metabolism ; Eukaryota/*genetics ; *Gene Transfer, Horizontal ; *Transformation, Genetic ; Type IV Secretion Systems/metabolism ; }, abstract = {Historically, the members of the Agrobacterium genus have been considered the only bacterial species naturally able to transfer and integrate DNA into the genomes of their eukaryotic hosts. Yet, increasing evidence suggests that this ability to genetically transform eukaryotic host cells might be more widespread in the bacterial world. Indeed, analyses of accumulating genomic data reveal cases of horizontal gene transfer from bacteria to eukaryotes and suggest that it represents a significant force in adaptive evolution of eukaryotic species. Specifically, recent reports indicate that bacteria other than Agrobacterium, such as Bartonella henselae (a zoonotic pathogen), Rhizobium etli (a plant-symbiotic bacterium related to Agrobacterium), or even Escherichia coli, have the ability to genetically transform their host cells under laboratory conditions. This DNA transfer relies on type IV secretion systems (T4SSs), the molecular machines that transport macromolecules during conjugative plasmid transfer and also during transport of proteins and/or DNA to the eukaryotic recipient cells. In this review article, we explore the extent of possible transfer of genetic information from bacteria to eukaryotic cells as well as the evolutionary implications and potential applications of this transfer.}, }
@article {pmid27402429, year = {2016}, author = {Reinecke, DL and Zarka, A and Leu, S and Boussiba, S}, title = {Cloning, molecular characterization, and phylogeny of two evolutionary distinct glutamine synthetase isoforms in the green microalga Haematococcus pluvialis (Chlorophyceae).}, journal = {Journal of phycology}, volume = {52}, number = {6}, pages = {961-972}, doi = {10.1111/jpy.12444}, pmid = {27402429}, issn = {1529-8817}, mesh = {Algal Proteins/*genetics ; Amino Acid Sequence ; Chlorophyta/*classification/*enzymology/genetics ; Cloning, Molecular ; Glutamate-Ammonia Ligase/*genetics ; Microalgae/classification/enzymology/genetics ; *Phylogeny ; Sequence Alignment ; }, abstract = {Haematococcus pluvialis (Chlorophyta) is a widely used microalga of great economic potential, yet its molecular genetics and evolution are largely unknown. We present new detailed molecular and phylogenetic analysis of two glutamine synthetase (GS) enzymes and genes (gln) under the Astaxanthin-inducing conditions of light- and nitrogen-stress. Structure analysis identified key residues and confirmed two decameric GS2 holoenzymes, a cytoplasmic enzyme, termed GS2c , and a plastidic form, termed GS2p , due to chloroplast-transit peptides at its N-terminus. Gene expression analysis showed dissociation of mRNA, protein, and enzyme activity levels for both GS2 under different growth conditions, indicating the strong post-transcriptional regulation. Data-mining identified novel and specified published gln genes from Prasinophyceae, Chlorophyta, Trebouxiophyceae, Charophyceae, Bryophyta, Lycopodiophyta, Spermatophyta, and Rhodophyta. Phylogenetic analysis found homologues to the cytosolic GS2c of H. pluvialis in all other photo- and non-photosynthetic Eukaryota. The chloroplastic GS2p was restricted to Chlorophyta, Bryophyta, some Proteobacteria and Fungii; no homologues were identified in Spermatophyta or other Eukaryota. This indicates two independent prokaryotic donors for these two gln genes in H. pluvialis. Combined phylogenetic analysis of GS, chl-b synthase, elongation factor, and light harvesting complex homologues project a newly refined model of Viridiplantae evolution. Herein, a GS1 evolved into the cytosolic GS2c and was passed on to all Eukaryota. Later, the chloroplastic GS2p entered the Archaeplastida lineage via a horizontal gene transfer at the divergence of Chlorophyta and Rhodophyta lineages. GS2p persisted in Chlorophyta and Bryophyta, but was lost during Spermatophyta evolution. These data suggest the revision of GS classification and nomenclature, and extend our understanding of the photosynthetic Eukaryota evolution.}, }
@article {pmid27396565, year = {2016}, author = {Proto, WR}, title = {Unravelling the Laverania.}, journal = {Nature reviews. Microbiology}, volume = {14}, number = {8}, pages = {478}, pmid = {27396565}, issn = {1740-1534}, mesh = {Animals ; Ape Diseases/*parasitology/transmission ; Biological Evolution ; Gene Transfer, Horizontal ; *Genome, Protozoan ; Gorilla gorilla/parasitology ; Hominidae/*parasitology ; Host Specificity ; Humans ; Malaria/parasitology/transmission/*veterinary ; Phylogeny ; Plasmodium/*genetics/physiology ; Plasmodium falciparum/*genetics ; Protozoan Proteins/genetics ; }, abstract = {How did an ape-infecting Plasmodium species jump to a human host?}, }
@article {pmid27395779, year = {2016}, author = {Tucker, DB and Colli, GR and Giugliano, LG and Hedges, SB and Hendry, CR and Lemmon, EM and Lemmon, AR and Sites, JW and Pyron, RA}, title = {Methodological congruence in phylogenomic analyses with morphological support for teiid lizards (Sauria: Teiidae).}, journal = {Molecular phylogenetics and evolution}, volume = {103}, number = {}, pages = {75-84}, doi = {10.1016/j.ympev.2016.07.002}, pmid = {27395779}, issn = {1095-9513}, mesh = {Animals ; Chromosomes/genetics ; Expressed Sequence Tags ; Genetic Loci ; Lizards/anatomy &amp; histology/*classification/genetics ; Phylogeny ; }, abstract = {A well-known issue in phylogenetics is discordance among gene trees, species trees, morphology, and other data types. Gene-tree discordance is often caused by incomplete lineage sorting, lateral gene transfer, and gene duplication. Multispecies-coalescent methods can account for incomplete lineage sorting and are believed by many to be more accurate than concatenation. However, simulation studies and empirical data have demonstrated that concatenation and species tree methods often recover similar topologies. We use three popular methods of phylogenetic reconstruction (one concatenation, two species tree) to evaluate relationships within Teiidae. These lizards are distributed across the United States to Argentina and the West Indies, and their classification has been controversial due to incomplete sampling and the discordance among various character types (chromosomes, DNA, musculature, osteology, etc.) used to reconstruct phylogenetic relationships. Recent morphological and molecular analyses of the group resurrected three genera and created five new genera to resolve non-monophyly in three historically ill-defined genera: Ameiva, Cnemidophorus, and Tupinambis. Here, we assess the phylogenetic relationships of the Teiidae using "next-generation" anchored-phylogenomics sequencing. Our final alignment includes 316 loci (488,656bp DNA) for 244 individuals (56 species of teiids, representing all currently recognized genera) and all three methods (ExaML, MP-EST, and ASTRAL-II) recovered essentially identical topologies. Our results are basically in agreement with recent results from morphology and smaller molecular datasets, showing support for monophyly of the eight new genera. Interestingly, even with hundreds of loci, the relationships among some genera in Tupinambinae remain ambiguous (i.e. low nodal support for the position of Salvator and Dracaena).}, }
@article {pmid27392085, year = {2017}, author = {Llorens-Marès, T and Liu, Z and Allen, LZ and Rusch, DB and Craig, MT and Dupont, CL and Bryant, DA and Casamayor, EO}, title = {Speciation and ecological success in dimly lit waters: horizontal gene transfer in a green sulfur bacteria bloom unveiled by metagenomic assembly.}, journal = {The ISME journal}, volume = {11}, number = {1}, pages = {201-211}, pmid = {27392085}, issn = {1751-7370}, mesh = {Bacterial Proteins/metabolism ; Bacteriochlorophylls/metabolism ; Chlorobium/classification/genetics/isolation &amp; purification/*metabolism ; Ecosystem ; *Gene Transfer, Horizontal ; Lakes/*microbiology ; Metagenomics ; Photosynthesis ; RNA, Ribosomal, 16S/genetics ; Spain ; Sulfur/*metabolism ; }, abstract = {A natural planktonic bloom of a brown-pigmented photosynthetic green sulfur bacteria (GSB) from the disphotic zone of karstic Lake Banyoles (NE Spain) was studied as a natural enrichment culture from which a nearly complete genome was obtained after metagenomic assembly. We showed in situ a case where horizontal gene transfer (HGT) explained the ecological success of a natural population unveiling ecosystem-specific adaptations. The uncultured brown-pigmented GSB was 99.7% identical in the 16S rRNA gene sequence to its green-pigmented cultured counterpart Chlorobium luteolum DSM 273[T]. Several differences were detected for ferrous iron acquisition potential, ATP synthesis and gas vesicle formation, although the most striking trait was related to pigment biosynthesis strategy. Chl. luteolum DSM 273[T] synthesizes bacteriochlorophyll (BChl) c, whereas Chl. luteolum CIII incorporated by HGT a 18-kbp cluster with the genes needed for BChl e and specific carotenoids biosynthesis that provided ecophysiological advantages to successfully colonize the dimly lit waters. We also genomically characterized what we believe to be the first described GSB phage, which based on the metagenomic coverage was likely in an active state of lytic infection. Overall, we observed spread HGT and we unveiled clear evidence for virus-mediated HGT in a natural population of photosynthetic GSB.}, }
@article {pmid27389688, year = {2016}, author = {Levasseur, A and Andreani, J and Delerce, J and Bou Khalil, J and Robert, C and La Scola, B and Raoult, D}, title = {Comparison of a Modern and Fossil Pithovirus Reveals Its Genetic Conservation and Evolution.}, journal = {Genome biology and evolution}, volume = {8}, number = {8}, pages = {2333-2339}, pmid = {27389688}, issn = {1759-6653}, mesh = {*Evolution, Molecular ; Fossils/*virology ; Gene Transfer, Horizontal ; Genome, Viral/*genetics ; Giant Viruses/*genetics ; Mosaicism ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Most theories on viral evolution are speculative and lack fossil comparison. Here, we isolated a modern Pithovirus-like virus from sewage samples. This giant virus, named Pithovirus massiliensis, was compared with its prehistoric counterpart, Pithovirus sibericum, found in Siberian permafrost. Our analysis revealed near-complete gene repertoire conservation, including horizontal gene transfer and ORFans. Furthermore, all orthologous genes evolved under strong purifying selection with a non-synonymous and synonymous ratio in the same range as the ratio found in the prokaryotic world. The comparison between fossil and modern Pithovirus species provided an estimation of the cadence of the molecular clock, reaching up to 3 × 10(-6) mutations/site/year. In addition, the strict conservation of HGTs and ORFans in P. massiliensis revealed the stable genetic mosaicism in giant viruses and excludes the concept of a bag of genes. The genetic stability for 30,000 years of P. massiliensis demonstrates that giant viruses evolve similarly to prokaryotes by classical mechanisms of evolution, including selection and fixation of genes, followed by selective constraints.}, }
@article {pmid27386932, year = {2016}, author = {Pirogov, S and Rybko, A and Kalinina, A and Gelfand, M}, title = {Recombination Processes and Nonlinear Markov Chains.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {23}, number = {9}, pages = {711-717}, doi = {10.1089/cmb.2016.0051}, pmid = {27386932}, issn = {1557-8666}, mesh = {Bacteria/*genetics ; Genetics, Population ; Genome, Bacterial ; *Markov Chains ; *Models, Genetic ; *Mutation ; Probability ; *Recombination, Genetic ; }, abstract = {Bacteria are known to exchange genetic information by horizontal gene transfer. Since the frequency of homologous recombination depends on the similarity between the recombining segments, several studies examined whether this could lead to the emergence of subspecies. Most of them simulated fixed-size Wright-Fisher populations, in which the genetic drift should be taken into account. Here, we use nonlinear Markov processes to describe a bacterial population evolving under mutation and recombination. We consider a population structure as a probability measure on the space of genomes. This approach implies the infinite population size limit, and thus, the genetic drift is not assumed. We prove that under these conditions, the emergence of subspecies is impossible.}, }
@article {pmid27386606, year = {2016}, author = {Olaitan, AO and Diene, SM and Assous, MV and Rolain, JM}, title = {Genomic Plasticity of Multidrug-Resistant NDM-1 Positive Clinical Isolate of Providencia rettgeri.}, journal = {Genome biology and evolution}, volume = {8}, number = {3}, pages = {723-728}, pmid = {27386606}, issn = {1759-6653}, mesh = {Anti-Bacterial Agents/therapeutic use ; Drug Resistance, Multiple/*genetics ; Enterobacteriaceae Infections/*genetics/microbiology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial/genetics ; Humans ; Molecular Sequence Annotation ; Phylogeny ; Providencia/*genetics/pathogenicity ; Sequence Analysis, DNA ; beta-Lactamases/*genetics ; }, abstract = {We performed a detailed whole-genome sequence analysis of Providencia rettgeri H1736, a multidrug-resistant clinical pathogen isolated in Israel in 2011. The objective was to describe the genomic flexibility of this bacterium that has greatly contributed to its pathogenicity. The genome has a chromosome size of 4,609,352 bp with 40.22% GC content. Five plasmids were predicted, as well as other mobile genetic elements (MGEs) including phages, genomic islands, and integrative and conjugative elements. The resistome consisted of a total of 27 different antibiotic resistance genes including blaNDM-1, mostly located on MGEs. Phenotypically, the bacteria displayed resistance to a total of ten different antimicrobial classes. Various features such as metabolic operons (including a novel carbapenem biosynthesis operon) and virulence genes were also borne on the MGEs, making P. rettgeri H1736 significantly different from other P. rettgeri isolates. A large quantity of the genetic diversity that exists in P. rettgeri H1736 was due to extensive horizontal gene transfer events, leading to an enormous presence of MGEs in its genome. Most of these changes contributed toward the pathogenic evolution of this bacterium.}, }
@article {pmid27385827, year = {2016}, author = {Hall, JP and Wood, AJ and Harrison, E and Brockhurst, MA}, title = {Source-sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {29}, pages = {8260-8265}, pmid = {27385827}, issn = {1091-6490}, support = {311490/ERC_/European Research Council/International ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Mercury/pharmacology ; Plasmids/*genetics ; Pseudomonas fluorescens/drug effects/*genetics ; Pseudomonas putida/drug effects/*genetics ; *Soil Microbiology ; }, abstract = {Horizontal gene transfer is a fundamental process in bacterial evolution that can accelerate adaptation via the sharing of genes between lineages. Conjugative plasmids are the principal genetic elements mediating the horizontal transfer of genes, both within and between bacterial species. In some species, plasmids are unstable and likely to be lost through purifying selection, but when alternative hosts are available, interspecific plasmid transfer could counteract this and maintain access to plasmid-borne genes. To investigate the evolutionary importance of alternative hosts to plasmid population dynamics in an ecologically relevant environment, we established simple soil microcosm communities comprising two species of common soil bacteria, Pseudomonas fluorescens and Pseudomonas putida, and a mercury resistance (Hg(R)) plasmid, pQBR57, both with and without positive selection [i.e., addition of Hg(II)]. In single-species populations, plasmid stability varied between species: although pQBR57 survived both with and without positive selection in P. fluorescens, it was lost or replaced by nontransferable Hg(R) captured to the chromosome in P. putida A simple mathematical model suggests these differences were likely due to pQBR57's lower intraspecific conjugation rate in P. putida By contrast, in two-species communities, both models and experiments show that interspecific conjugation from P. fluorescens allowed pQBR57 to persist in P. putida via source-sink transfer dynamics. Moreover, the replacement of pQBR57 by nontransferable chromosomal Hg(R) in P. putida was slowed in coculture. Interspecific transfer allows plasmid survival in host species unable to sustain the plasmid in monoculture, promoting community-wide access to the plasmid-borne accessory gene pool and thus potentiating future evolvability.}, }
@article {pmid27383577, year = {2016}, author = {Godziszewska, J and Guzek, D and Głąbski, K and Wierzbicka, A}, title = {Mobile antibiotic resistance - the spread of genes determining the resistance of bacteria through food products.}, journal = {Postepy higieny i medycyny doswiadczalnej (Online)}, volume = {70}, number = {0}, pages = {803-810}, doi = {10.5604/17322693.1209214}, pmid = {27383577}, issn = {1732-2693}, mesh = {Bacteria/*genetics ; *Conjugation, Genetic ; Drug Resistance, Bacterial/*genetics ; *Food Microbiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; }, abstract = {In recent years, more and more antibiotics have become ineffective in the treatment of bacterial nfections. The acquisition of antibiotic resistance by bacteria is associated with circulation of genes in the environment. Determinants of antibiotic resistance may be transferred to pathogenic bacteria. It has been shown that conjugation is one of the key mechanisms responsible for spread of antibiotic resistance genes, which is highly efficient and allows the barrier to restrictions and modifications to be avoided. Some conjugative modules enable the transfer of plasmids even between phylogenetically distant bacterial species. Many scientific reports indicate that food is one of the main reservoirs of these genes. Antibiotic resistance genes have been identified in meat products, milk, fruits and vegetables. The reason for such a wide spread of antibiotic resistance genes is the overuse of antibiotics by breeders of plants and animals, as well as by horizontal gene transfer. It was shown, that resistance determinants located on mobile genetic elements, which are isolated from food products, can easily be transferred to another niche. The antibiotic resistance genes have been in the environment for 30 000 years. Their removal from food products is not possible, but the risks associated with the emergence of multiresistant pathogenic strains are very large. The only option is to control the emergence, selection and spread of these genes. Therefore measures are sought to prevent horizontal transfer of genes. Promising concepts involve the combination of developmental biology, evolution and ecology in the fight against the spread of antibiotic resistance.}, }
@article {pmid27381852, year = {2016}, author = {Auchtung, JM and Aleksanyan, N and Bulku, A and Berkmen, MB}, title = {Biology of ICEBs1, an integrative and conjugative element in Bacillus subtilis.}, journal = {Plasmid}, volume = {86}, number = {}, pages = {14-25}, doi = {10.1016/j.plasmid.2016.07.001}, pmid = {27381852}, issn = {1095-9890}, mesh = {Bacillus subtilis/*genetics ; Conjugation, Genetic/*genetics ; DNA Replication/*physiology ; DNA Transposable Elements/*genetics ; DNA, Bacterial/genetics ; DNA, Circular/genetics ; Gene Transfer, Horizontal/*physiology ; Plasmids/*genetics ; }, abstract = {Horizontal gene transfer plays a profound role in bacterial evolution by propelling the rapid transfer of genes and gene cassettes. Integrative and conjugative elements (ICEs) are one important mechanism driving horizontal gene transfer. ICEs, also known as conjugative transposons, reside on the host chromosome but can excise to form a conjugative DNA circle that is capable of transfer to other cells. Analysis of the large number of completed bacterial genome sequences has revealed many previously unrecognized ICEs, including ICEBs1, found in the Gram-positive model bacterium Bacillus subtilis. The discovery of ICEBs1 in an organism with such an impressive array of molecular tools for genetics and molecular biology was fortuitous. Significant insights into ICE biology have resulted since its discovery <15years ago. In this review, we describe aspects of ICEBs1 biology, such as excision, conjugative transfer, and reintegration, likely to be conserved across many ICEs. We will also highlight some of the more unexpected aspects of ICEBs1 biology, such as its ability to undergo plasmid-like replication after excision and its ability to mobilize plasmids lacking dedicated mobilization functions. A molecular understanding of ICEBs1 has led to additional insights into signals and mechanisms that promote horizontal gene transfer and shape bacterial evolution.}, }
@article {pmid27381397, year = {2016}, author = {Yamamoto, M and Matsumura, Y and Gomi, R and Matsuda, T and Tanaka, M and Nagao, M and Takakura, S and Uemoto, S and Ichiyama, S}, title = {Interspecies Dissemination of a Mobilizable Plasmid Harboring blaIMP-19 and the Possibility of Horizontal Gene Transfer in a Single Patient.}, journal = {Antimicrobial agents and chemotherapy}, volume = {60}, number = {9}, pages = {5412-5419}, pmid = {27381397}, issn = {1098-6596}, mesh = {Achromobacter denitrificans/*genetics/metabolism ; Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; Drug Resistance, Multiple, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Gene Expression ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; Klebsiella pneumoniae/*genetics/metabolism ; Male ; Middle Aged ; Multilocus Sequence Typing ; Phylogeny ; Plasmids/*chemistry/classification/metabolism ; beta-Lactamases/*genetics/metabolism ; }, abstract = {Carbapenemase-producing Gram-negative bacilli have been a global concern over the past 2 decades because these organisms can cause severe infections with high mortality rates. Carbapenemase genes are often carried by mobile genetic elements, and resistance plasmids can be transferred through conjugation. We conducted whole-genome sequencing (WGS) to demonstrate that the same plasmid harboring a metallo-β-lactamase gene was detected in two different species isolated from a single patient. Metallo-β-lactamase-producing Achromobacter xylosoxidans (KUN4507), non-metallo-β-lactamase-producing Klebsiella pneumoniae (KUN4843), and metallo-β-lactamase-producing K. pneumoniae (KUN5033) were sequentially isolated from a single patient and then analyzed in this study. Antimicrobial susceptibility testing, molecular typing (pulsed-field gel electrophoresis and multilocus sequence typing), and conjugation analyses were performed by conventional methods. Phylogenetic and molecular clock analysis of K. pneumoniae isolates were performed with WGS, and the nucleotide sequences of plasmids detected from these isolates were determined using WGS. Conventional molecular typing revealed that KUN4843 and KUN5033 were identical, whereas the phylogenetic tree analysis revealed a slight difference. These two isolates were separated from the most recent common ancestor 0.74 years before they were isolated. The same resistance plasmid harboring blaIMP-19 was detected in metallo-β-lactamase-producing A. xylosoxidans and K. pneumoniae Although this plasmid was not self-transferable, the conjugation of this plasmid from A. xylosoxidans to non-metallo-β-lactamase-producing K. pneumoniae was successfully performed. The susceptibility patterns for metallo-β-lactamase-producing K. pneumoniae and the transconjugant were similar. These findings supported the possibility of the horizontal transfer of plasmid-borne blaIMP-19 from A. xylosoxidans to K. pneumoniae in a single patient.}, }
@article {pmid27381348, year = {2016}, author = {Willemse, N and Howell, KJ and Weinert, LA and Heuvelink, A and Pannekoek, Y and Wagenaar, JA and Smith, HE and van der Ende, A and Schultsz, C}, title = {An emerging zoonotic clone in the Netherlands provides clues to virulence and zoonotic potential of Streptococcus suis.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {28984}, pmid = {27381348}, issn = {2045-2322}, mesh = {Animals ; Genomics/methods ; Host-Pathogen Interactions/genetics ; Humans ; Meningitis, Bacterial/microbiology ; Netherlands ; Streptococcal Infections/*microbiology ; Streptococcus suis/*genetics ; Swine/microbiology ; Swine Diseases/microbiology ; Virulence/*genetics ; Virulence Factors/*genetics ; Zoonoses/*microbiology ; }, abstract = {Streptococcus suis is a zoonotic swine pathogen and a major public health concern in Asia, where it emerged as an important cause of bacterial meningitis in adults. While associated with food-borne transmission in Asia, zoonotic S. suis infections are mainly occupational hazards elsewhere. To identify genomic differences that can explain zoonotic potential, we compared whole genomes of 98 S. suis isolates from human patients and pigs with invasive disease in the Netherlands, and validated our observations with 18 complete and publicly available sequences. Zoonotic isolates have smaller genomes than non-zoonotic isolates, but contain more virulence factors. We identified a zoonotic S. suis clone that diverged from a non-zoonotic clone by means of gene loss, a capsule switch, and acquisition of a two-component signalling system in the late 19th century, when foreign pig breeds were introduced. Our results indicate that zoonotic potential of S. suis results from gene loss, recombination and horizontal gene transfer events.}, }
@article {pmid27381333, year = {2017}, author = {Kraeva, N and Horáková, E and Kostygov, AY and Kořený, L and Butenko, A and Yurchenko, V and Lukeš, J}, title = {Catalase in Leishmaniinae: With me or against me?.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {50}, number = {}, pages = {121-127}, doi = {10.1016/j.meegid.2016.06.054}, pmid = {27381333}, issn = {1567-7257}, mesh = {Animals ; Bacteria/genetics ; Catalase/*genetics ; Fungi/genetics ; *Gene Deletion ; Gene Expression ; *Genome ; Host-Parasite Interactions ; Humans ; Hydrogen Peroxide/*metabolism/pharmacology ; Leishmania/drug effects/genetics/growth &amp; development/*metabolism ; Life Cycle Stages/*drug effects/genetics ; Phylogeny ; Psychodidae/parasitology ; Signal Transduction ; Trypanosomatina/classification/genetics ; }, abstract = {The catalase gene is a virtually ubiquitous component of the eukaryotic genomes. It is also present in the monoxenous (i.e. parasitizing solely insects) trypanosomatids of the subfamily Leishmaniinae, which have acquired the enzyme by horizontal gene transfer from a bacterium. However, as shown here, the catalase gene was secondarily lost from the genomes of all Leishmania sequenced so far. Due to the potentially key regulatory role of hydrogen peroxide in the inter-stagial transformation of Leishmania spp., this loss seems to be a necessary prerequisite for the emergence of a complex life cycle of these important human pathogens. Hence, in this group of protists, the advantages of keeping catalase were uniquely outweighed by its disadvantages.}, }
@article {pmid27380549, year = {2016}, author = {Oikonomou, O and Liakopoulos, A and Phee, LM and Betts, J and Mevius, D and Wareham, DW}, title = {Providencia stuartii Isolates from Greece: Co-Carriage of Cephalosporin (blaSHV-5, blaVEB-1), Carbapenem (blaVIM-1), and Aminoglycoside (rmtB) Resistance Determinants by a Multidrug-Resistant Outbreak Clone.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {22}, number = {5}, pages = {379-386}, doi = {10.1089/mdr.2015.0215}, pmid = {27380549}, issn = {1931-8448}, mesh = {Adult ; Aged ; Aminoglycosides/pharmacology ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics ; Carbapenems/pharmacology ; Cephalosporins/pharmacology ; Clone Cells ; Conjugation, Genetic ; Cross Infection/drug therapy/*epidemiology/microbiology/mortality ; *Disease Outbreaks ; Drug Resistance, Multiple, Bacterial/*genetics ; Enterobacteriaceae Infections/drug therapy/*epidemiology/microbiology/mortality ; Female ; Gene Expression ; Gene Transfer, Horizontal ; Greece/epidemiology ; Humans ; Male ; Methyltransferases/genetics ; Microbial Sensitivity Tests ; Middle Aged ; Plasmids/chemistry/metabolism ; Providencia/drug effects/enzymology/*genetics/isolation &amp; purification ; Quinolones/pharmacology ; Replicon ; Survival Analysis ; beta-Lactamases/genetics ; }, abstract = {Providencia stuartii has emerged as an important nosocomial pathogen. We describe an outbreak due to a multidrug-resistant strain over a 4-month period in a critical care unit in Athens. Molecular typing revealed each of the isolates to be clonally related with coresistance to cephalosporins, carbapenems, aminoglycosides, and quinolones. Each isolate contained a 220-kb multi-replicon (IncA/C and IncR) conjugative plasmid encoding TEM-1, SHV-5, VEB-1, and VIM-1 β-lactamases and the 16S rDNA methylase RmtB. Antimicrobial therapy was unsuccessful in 3 of 6 cases, and resistance was readily transmissible to susceptible strains of Escherichia coli by transformation and conjugation. This highlights the clinical importance of P. stuartii and its ability to disseminate critical resistance determinants to other bacterial pathogens.}, }
@article {pmid27378198, year = {2016}, author = {Czobor, I and Novais, &#xc2; and Rodrigues, C and Chifiriuc, MC and Mihăescu, G and Lazăr, V and Peixe, L}, title = {Efficient transmission of IncFIIY and IncL plasmids and Klebsiella pneumoniae ST101 clone producing OXA-48, NDM-1 or OXA-181 in Bucharest hospitals.}, journal = {International journal of antimicrobial agents}, volume = {48}, number = {2}, pages = {223-224}, doi = {10.1016/j.ijantimicag.2016.05.004}, pmid = {27378198}, issn = {1872-7913}, mesh = {Cross Infection/epidemiology/*microbiology ; *Gene Transfer, Horizontal ; *Genotype ; Hospitals ; Humans ; Klebsiella Infections/epidemiology/*microbiology ; Klebsiella pneumoniae/*classification/enzymology/genetics/isolation &amp; purification ; Molecular Epidemiology ; Plasmids/*analysis/classification ; Romania/epidemiology ; beta-Lactamases/*metabolism ; }, }
@article {pmid27375573, year = {2016}, author = {Marcoleta, AE and Berríos-Pastén, C and Nuñez, G and Monasterio, O and Lagos, R}, title = {Klebsiella pneumoniae Asparagine tDNAs Are Integration Hotspots for Different Genomic Islands Encoding Microcin E492 Production Determinants and Other Putative Virulence Factors Present in Hypervirulent Strains.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {849}, pmid = {27375573}, issn = {1664-302X}, abstract = {Due to the developing of multi-resistant and invasive hypervirulent strains, Klebsiella pneumoniae has become one of the most urgent bacterial pathogen threats in the last years. Genomic comparison of a growing number of sequenced isolates has allowed the identification of putative virulence factors, proposed to be acquirable mainly through horizontal gene transfer. In particular, those related with synthesizing the antibacterial peptide microcin E492 (MccE492) and salmochelin siderophores were found to be highly prevalent among hypervirulent strains. The determinants for the production of both molecules were first reported as part of a 13-kbp segment of K. pneumoniae RYC492 chromosome, and were cloned and characterized in E. coli. However, the genomic context of this segment in K. pneumoniae remained uncharacterized. In this work, we provided experimental and bioinformatics evidence indicating that the MccE492 cluster is part of a highly conserved 23-kbp genomic island (GI) named GIE492, that was integrated in a specific asparagine-tRNA gene (asn-tDNA) and was found in a high proportion of isolates from liver abscesses sampled around the world. This element resulted to be unstable and its excision frequency increased after treating bacteria with mitomycin C and upon the overexpression of the island-encoded integrase. Besides the MccE492 genetic cluster, it invariably included an integrase-coding gene, at least seven protein-coding genes of unknown function, and a putative transfer origin that possibly allows this GI to be mobilized through conjugation. In addition, we analyzed the asn-tDNA loci of all the available K. pneumoniae assembled chromosomes to evaluate them as GI-integration sites. Remarkably, 73% of the strains harbored at least one GI integrated in one of the four asn-tDNA present in this species, confirming them as integration hotspots. Each of these tDNAs was occupied with different frequencies, although they were 100% identical. Also, we identified a total of 47 asn-tDNA-associated GIs that were classified into 12 groups of homology differing in theencoded functionalities but sharing with GIE492 a conserved recombination module and potentially its mobility features. Most of these GIs encoded factors with proven or potential role in pathogenesis, constituting a major reservoir of virulence factors in this species.}, }
@article {pmid27375355, year = {2016}, author = {Bruder, K and Malki, K and Cooper, A and Sible, E and Shapiro, JW and Watkins, SC and Putonti, C}, title = {Freshwater Metaviromics and Bacteriophages: A Current Assessment of the State of the Art in Relation to Bioinformatic Challenges.}, journal = {Evolutionary bioinformatics online}, volume = {12}, number = {Suppl 1}, pages = {25-33}, pmid = {27375355}, issn = {1176-9343}, abstract = {Advances in bioinformatics and sequencing technologies have allowed for the analysis of complex microbial communities at an unprecedented rate. While much focus is often placed on the cellular members of these communities, viruses play a pivotal role, particularly bacteria-infecting viruses (bacteriophages); phages mediate global biogeochemical processes and drive microbial evolution through bacterial grazing and horizontal gene transfer. Despite their importance and ubiquity in nature, very little is known about the diversity and structure of viral communities. Though the need for culture-based methods for viral identification has been somewhat circumvented through metagenomic techniques, the analysis of metaviromic data is marred with many unique issues. In this review, we examine the current bioinformatic approaches for metavirome analyses and the inherent challenges facing the field as illustrated by the ongoing efforts in the exploration of freshwater phage populations.}, }
@article {pmid27371582, year = {2016}, author = {Steinum, TM and Karataş, S and Martinussen, NT and Meirelles, PM and Thompson, FL and Colquhoun, DJ}, title = {Multilocus Sequence Analysis of Close Relatives Vibrio anguillarum and Vibrio ordalii.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {18}, pages = {5496-5504}, pmid = {27371582}, issn = {1098-5336}, mesh = {Animals ; DNA Gyrase/genetics ; Fish Diseases/*microbiology ; Fishes ; *Genes, Essential ; *Genetic Variation ; Ireland ; *Multilocus Sequence Typing ; Norway ; Nucleic Acid Hybridization ; Scotland ; Vibrio/*classification/*genetics/isolation &amp; purification ; Vibrio Infections/microbiology/*veterinary ; }, abstract = {UNLABELLED: The genetic heterogeneity of the close relatives Vibrio anguillarum and Vibrio ordalii, both serious pathogens of fish causing extensive losses in aquaculture, was studied. Eight housekeeping genes, i.e., atpA, ftsZ, gapA, gyrB, mreB, rpoA, topA, and pyrH, were partially sequenced in 116 isolates from diverse fish species and geographical areas. The eight genes appear to be under purifying selection, and the genetic diversity in the total data set was estimated to be 0.767 ± 0.026. Our multilocus sequence analysis (MLSA) scheme identified several widespread clonal complexes and resolved the isolates, for the most part, according to serotype. Serotype O2b isolates from diseased cod in Norway, Ireland, and Scotland were found to be extremely homogeneous. Horizontal gene transfer appears to be fairly common within and between clonal complexes. Taken together, MLSA and in silico DNA-DNA hybridization (DDH) calculations suggest that some isolates previously characterized as V ordalii, i.e., 12B09, FF93, FS144, and FS238, are in fact V. anguillarum isolates. The precise taxonomic situation for two isolates from Atlantic cod that display several traits consistent with V. ordalii, i.e., NVI 5286 and NVI 5918, and a single environmental strain that was previously considered to represent V. ordalii, i.e., FF167, is less clear.<br><br>IMPORTANCE: It is still being debated whether V. anguillarum and V ordalii represent separate bacterial species. Our study addresses this issue and elucidates the degree of genetic variability within this group of closely related bacteria, based on a substantial number of isolates. Our results clearly illustrate the existence of different populations among putative V ordalii isolates. On the basis of additional full-length genomic analysis, we conclude that most environmental isolates previously identified as V ordalii lie firmly within the species V. anguillarum While bona fide fish-pathogenic V ordalii isolates display a very close genetic relationship with V. anguillarum, they combine a clearly divergent evolutionary pattern with clear phenotypic differences. The study also highlights the need for further characterization of fish-pathogenic isolates from the northern Atlantic region that share phenotypic characteristics with V. ordalii but are genetically closer to V. anguillarum The retention of taxonomic distinctions between the phenotypically different groups of bacteria is of practical advantage to microbial ecologists and veterinarians.}, }
@article {pmid27363362, year = {2016}, author = {Bernard, G and Chan, CX and Ragan, MA}, title = {Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {28970}, pmid = {27363362}, issn = {2045-2322}, mesh = {Bacteria/*classification/genetics ; Computer Simulation ; Evolution, Molecular ; Gene Rearrangement ; Gene Transfer, Horizontal ; Genomics/*methods ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {Alignment-free (AF) approaches have recently been highlighted as alternatives to methods based on multiple sequence alignment in phylogenetic inference. However, the sensitivity of AF methods to genome-scale evolutionary scenarios is little known. Here, using simulated microbial genome data we systematically assess the sensitivity of nine AF methods to three important evolutionary scenarios: sequence divergence, lateral genetic transfer (LGT) and genome rearrangement. Among these, AF methods are most sensitive to the extent of sequence divergence, less sensitive to low and moderate frequencies of LGT, and most robust against genome rearrangement. We describe the application of AF methods to three well-studied empirical genome datasets, and introduce a new application of the jackknife to assess node support. Our results demonstrate that AF phylogenomics is computationally scalable to multi-genome data and can generate biologically meaningful phylogenies and insights into microbial evolution.}, }
@article {pmid27359365, year = {2016}, author = {Gilbert, GS and Parker, IM}, title = {The Evolutionary Ecology of Plant Disease: A Phylogenetic Perspective.}, journal = {Annual review of phytopathology}, volume = {54}, number = {}, pages = {549-578}, doi = {10.1146/annurev-phyto-102313-045959}, pmid = {27359365}, issn = {1545-2107}, mesh = {Biodiversity ; *Biological Evolution ; Ecology/*methods ; *Host Specificity ; Phylogeny ; *Plant Diseases/genetics/microbiology/parasitology ; *Plants/genetics/microbiology/parasitology ; }, abstract = {An explicit phylogenetic perspective provides useful tools for phytopathology and plant disease ecology because the traits of both plants and microbes are shaped by their evolutionary histories. We present brief primers on phylogenetic signal and the analytical tools of phylogenetic ecology. We review the literature and find abundant evidence of phylogenetic signal in pathogens and plants for most traits involved in disease interactions. Plant nonhost resistance mechanisms and pathogen housekeeping functions are conserved at deeper phylogenetic levels, whereas molecular traits associated with rapid coevolutionary dynamics are more labile at branch tips. Horizontal gene transfer disrupts the phylogenetic signal for some microbial traits. Emergent traits, such as host range and disease severity, show clear phylogenetic signals. Therefore pathogen spread and disease impact are influenced by the phylogenetic structure of host assemblages. Phylogenetically rare species escape disease pressure. Phylogenetic tools could be used to develop predictive tools for phytosanitary risk analysis and reduce disease pressure in multispecies cropping systems.}, }
@article {pmid27359215, year = {2016}, author = {Singh, K and Milstein, JN and Navarre, WW}, title = {Xenogeneic Silencing and Its Impact on Bacterial Genomes.}, journal = {Annual review of microbiology}, volume = {70}, number = {}, pages = {199-213}, doi = {10.1146/annurev-micro-102215-095301}, pmid = {27359215}, issn = {1545-3251}, mesh = {Bacteria/*genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; DNA-Binding Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Gene Silencing ; *Genome, Bacterial ; }, abstract = {The H-NS (heat-stable nucleoid structuring) protein affects both nucleoid compaction and global gene regulation. H-NS appears to act primarily as a silencer of AT-rich genetic material acquired by horizontal gene transfer. As such, it is key in the regulation of most genes involved in virulence and in adaptation to new environmental niches. Here we review recent progress in understanding the biochemistry of H-NS and how xenogeneic silencing affects bacterial evolution. We highlight the strengths and weaknesses of some of the models proposed in H-NS-mediated nucleoprotein complex formation. Based on recent single-molecule studies, we also propose a novel mode of DNA compaction by H-NS termed intrabridging to explain over two decades of observations of the H-NS molecule.}, }
@article {pmid27358425, year = {2016}, author = {Bellot, S and Cusimano, N and Luo, S and Sun, G and Zarre, S and Gröger, A and Temsch, E and Renner, SS}, title = {Assembled Plastid and Mitochondrial Genomes, as well as Nuclear Genes, Place the Parasite Family Cynomoriaceae in the Saxifragales.}, journal = {Genome biology and evolution}, volume = {8}, number = {7}, pages = {2214-2230}, pmid = {27358425}, issn = {1759-6653}, mesh = {Contig Mapping ; Cynomorium/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Mitochondrial ; *Genome, Plastid ; RNA, Ribosomal/genetics ; Saxifragaceae/*genetics ; }, abstract = {Cynomoriaceae, one of the last unplaced families of flowering plants, comprise one or two species or subspecies of root parasites that occur from the Mediterranean to the Gobi Desert. Using Illumina sequencing, we assembled the mitochondrial and plastid genomes as well as some nuclear genes of a Cynomorium specimen from Italy. Selected genes were also obtained by Sanger sequencing from individuals collected in China and Iran, resulting in matrices of 33 mitochondrial, 6 nuclear, and 14 plastid genes and rDNAs enlarged to include a representative angiosperm taxon sampling based on data available in GenBank. We also compiled a new geographic map to discern possible discontinuities in the parasites' occurrence. Cynomorium has large genomes of 13.70-13.61 (Italy) to 13.95-13.76 pg (China). Its mitochondrial genome consists of up to 49 circular subgenomes and has an overall gene content similar to that of photosynthetic angiosperms, while its plastome retains only 27 of the normally 116 genes. Nuclear, plastid and mitochondrial phylogenies place Cynomoriaceae in Saxifragales, and we found evidence for several horizontal gene transfers from different hosts, as well as intracellular gene transfers.}, }
@article {pmid27358423, year = {2016}, author = {Ceapa, C and Davids, M and Ritari, J and Lambert, J and Wels, M and Douillard, FP and Smokvina, T and de Vos, WM and Knol, J and Kleerebezem, M}, title = {The Variable Regions of Lactobacillus rhamnosus Genomes Reveal the Dynamic Evolution of Metabolic and Host-Adaptation Repertoires.}, journal = {Genome biology and evolution}, volume = {8}, number = {6}, pages = {1889-1905}, pmid = {27358423}, issn = {1759-6653}, support = {250172/ERC_/European Research Council/International ; }, mesh = {CRISPR-Cas Systems ; Carbohydrate Metabolism/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Lacticaseibacillus rhamnosus/*genetics ; Molecular Sequence Annotation ; Phylogeny ; }, abstract = {Lactobacillus rhamnosus is a diverse Gram-positive species with strains isolated from different ecological niches. Here, we report the genome sequence analysis of 40 diverse strains of L. rhamnosus and their genomic comparison, with a focus on the variable genome. Genomic comparison of 40 L. rhamnosus strains discriminated the conserved genes (core genome) and regions of plasticity involving frequent rearrangements and horizontal transfer (variome). The L. rhamnosus core genome encompasses 2,164 genes, out of 4,711 genes in total (the pan-genome). The accessory genome is dominated by genes encoding carbohydrate transport and metabolism, extracellular polysaccharides (EPS) biosynthesis, bacteriocin production, pili production, the cas system, and the associated clustered regularly interspaced short palindromic repeat (CRISPR) loci, and more than 100 transporter functions and mobile genetic elements like phages, plasmid genes, and transposons. A clade distribution based on amino acid differences between core (shared) proteins matched with the clade distribution obtained from the presence-absence of variable genes. The phylogenetic and variome tree overlap indicated that frequent events of gene acquisition and loss dominated the evolutionary segregation of the strains within this species, which is paralleled by evolutionary diversification of core gene functions. The CRISPR-Cas system could have contributed to this evolutionary segregation. Lactobacillus rhamnosus strains contain the genetic and metabolic machinery with strain-specific gene functions required to adapt to a large range of environments. A remarkable congruency of the evolutionary relatedness of the strains' core and variome functions, possibly favoring interspecies genetic exchanges, underlines the importance of gene-acquisition and loss within the L. rhamnosus strain diversification.}, }
@article {pmid27357338, year = {2016}, author = {Glöckner, G and Lawal, HM and Felder, M and Singh, R and Singer, G and Weijer, CJ and Schaap, P}, title = {The multicellularity genes of dictyostelid social amoebas.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {12085}, pmid = {27357338}, issn = {2041-1723}, support = {//Wellcome Trust/United Kingdom ; BB/G020426/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Biological Evolution ; Cell Differentiation/genetics ; Dictyostelium/*genetics ; Gene Expression Profiling ; Gene Transfer, Horizontal ; *Genes, Essential ; Whole Genome Sequencing ; }, abstract = {The evolution of multicellularity enabled specialization of cells, but required novel signalling mechanisms for regulating cell differentiation. Early multicellular organisms are mostly extinct and the origins of these mechanisms are unknown. Here using comparative genome and transcriptome analysis across eight uni- and multicellular amoebozoan genomes, we find that 80% of proteins essential for the development of multicellular Dictyostelia are already present in their unicellular relatives. This set is enriched in cytosolic and nuclear proteins, and protein kinases. The remaining 20%, unique to Dictyostelia, mostly consists of extracellularly exposed and secreted proteins, with roles in sensing and recognition, while several genes for synthesis of signals that induce cell-type specialization were acquired by lateral gene transfer. Across Dictyostelia, changes in gene expression correspond more strongly with phenotypic innovation than changes in protein functional domains. We conclude that the transition to multicellularity required novel signals and sensors rather than novel signal processing mechanisms.}, }
@article {pmid27355474, year = {2016}, author = {Ruhe, ZC and Nguyen, JY and Chen, AJ and Leung, NY and Hayes, CS and Low, DA}, title = {CDI Systems Are Stably Maintained by a Cell-Contact Mediated Surveillance Mechanism.}, journal = {PLoS genetics}, volume = {12}, number = {6}, pages = {e1006145}, pmid = {27355474}, issn = {1553-7404}, mesh = {Bacterial Toxins/metabolism ; Biofilms/growth &amp; development ; Contact Inhibition/*genetics/*physiology ; Escherichia coli/*metabolism/*physiology ; Escherichia coli Proteins/*metabolism ; F Factor/metabolism ; Membrane Proteins/*metabolism ; }, abstract = {Contact-dependent growth inhibition (CDI) systems are widespread amongst Gram-negative bacteria where they play important roles in inter-cellular competition and biofilm formation. CDI+ bacteria use cell-surface CdiA proteins to bind neighboring bacteria and deliver C-terminal toxin domains. CDI+ cells also express CdiI immunity proteins that specifically neutralize toxins delivered from adjacent siblings. Genomic analyses indicate that cdi loci are commonly found on plasmids and genomic islands, suggesting that these Type 5 secretion systems are spread through horizontal gene transfer. Here, we examine whether CDI toxin and immunity activities serve to stabilize mobile genetic elements using a minimal F plasmid that fails to partition properly during cell division. This F plasmid is lost from Escherichia coli populations within 50 cell generations, but is maintained in ~60% of the cells after 100 generations when the plasmid carries the cdi gene cluster from E. coli strain EC93. By contrast, the ccdAB "plasmid addiction" module normally found on F exerts only a modest stabilizing effect. cdi-dependent plasmid stabilization requires the BamA receptor for CdiA, suggesting that plasmid-free daughter cells are inhibited by siblings that retain the CDI+ plasmid. In support of this model, the CDI+ F plasmid is lost rapidly from cells that carry an additional cdiI immunity gene on a separate plasmid. These results indicate that plasmid stabilization occurs through elimination of non-immune cells arising in the population via plasmid loss. Thus, genetic stabilization reflects a strong selection for immunity to CDI. After long-term passage for more than 300 generations, CDI+ plasmids acquire mutations that increase copy number and result in 100% carriage in the population. Together, these results show that CDI stabilizes genetic elements through a toxin-mediated surveillance mechanism in which cells that lose the CDI system are detected and eliminated by their siblings.}, }
@article {pmid27355362, year = {2016}, author = {Prudhomme, M and Berge, M and Martin, B and Polard, P}, title = {Pneumococcal Competence Coordination Relies on a Cell-Contact Sensing Mechanism.}, journal = {PLoS genetics}, volume = {12}, number = {6}, pages = {e1006113}, pmid = {27355362}, issn = {1553-7404}, mesh = {Bacterial Proteins/*genetics ; Cell Communication/*genetics ; DNA Transformation Competence/*genetics ; Gene Expression Regulation, Bacterial/genetics ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/genetics ; Membrane Proteins/genetics ; Peptides/genetics ; Streptococcus pneumoniae/*genetics ; }, abstract = {Bacteria have evolved various inducible genetic programs to face many types of stress that challenge their growth and survival. Competence is one such program. It enables genetic transformation, a major horizontal gene transfer process. Competence development in liquid cultures of Streptococcus pneumoniae is synchronized within the whole cell population. This collective behavior is known to depend on an exported signaling Competence Stimulating Peptide (CSP), whose action generates a positive feedback loop. However, it is unclear how this CSP-dependent population switch is coordinated. By monitoring spontaneous competence development in real time during growth of four distinct pneumococcal lineages, we have found that competence shift in the population relies on a self-activated cell fraction that arises via a growth time-dependent mechanism. We demonstrate that CSP remains bound to cells during this event, and conclude that the rate of competence development corresponds to the propagation of competence by contact between activated and quiescent cells. We validated this two-step cell-contact sensing mechanism by measuring competence development during co-cultivation of strains with altered capacity to produce or respond to CSP. Finally, we found that the membrane protein ComD retains the CSP, limiting its free diffusion in the medium. We propose that competence initiator cells originate stochastically in response to stress, to form a distinct subpopulation that then transmits the CSP by cell-cell contact.}, }
@article {pmid27354706, year = {2016}, author = {Knie, N and Grewe, F and Knoop, V}, title = {Monilophyte mitochondrial rps1 genes carry a unique group II intron that likely originated from an ancient paralog in rpl2.}, journal = {RNA (New York, N.Y.)}, volume = {22}, number = {9}, pages = {1338-1348}, pmid = {27354706}, issn = {1469-9001}, mesh = {*Evolution, Molecular ; Ferns/classification/*genetics ; Gene Transfer, Horizontal ; *Introns ; Mitochondrial Proteins/*genetics ; Phylogeny ; Plant Proteins/*genetics ; RNA Editing ; RNA-Binding Proteins/*genetics ; }, abstract = {Intron patterns in plant mitochondrial genomes differ significantly between the major land plant clades. We here report on a new, clade-specific group II intron in the rps1 gene of monilophytes (ferns). This intron, rps1i25g2, is strikingly similar to rpl2i846g2 previously identified in the mitochondrial rpl2 gene of seed plants, ferns, and the lycophyte Phlegmariurus squarrosus Although mitochondrial ribosomal protein genes are frequently subject to endosymbiotic gene transfer among plants, we could retrieve the mitochondrial rps1 gene in a taxonomically wide sampling of 44 monilophyte taxa including basal lineages such as the Ophioglossales, Psilotales, and Marattiales with the only exception being the Equisetales (horsetails). Introns rps1i25g2 and rpl2i846g2 were likewise consistently present with only two exceptions: Intron rps1i25g2 is lost in the genus Ophioglossum and intron rpl2i846g2 is lost in Equisetum bogotense Both intron sequences are moderately affected by RNA editing. The unprecedented primary and secondary structure similarity of rps1i25g2 and rpl2i846g2 suggests an ancient retrotransposition event copying rpl2i846g2 into rps1, for which we suggest a model. Our phylogenetic analysis adding the new rps1 locus to a previous data set is fully congruent with recent insights on monilophyte phylogeny and further supports a sister relationship of Gleicheniales and Hymenophyllales.}, }
@article {pmid27353756, year = {2016}, author = {Conlan, S and Park, M and Deming, C and Thomas, PJ and Young, AC and Coleman, H and Sison, C and ,  and Weingarten, RA and Lau, AF and Dekker, JP and Palmore, TN and Frank, KM and Segre, JA}, title = {Plasmid Dynamics in KPC-Positive Klebsiella pneumoniae during Long-Term Patient Colonization.}, journal = {mBio}, volume = {7}, number = {3}, pages = {}, pmid = {27353756}, issn = {2150-7511}, support = {ZIA HG200382/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Bacterial Proteins/biosynthesis/*genetics ; Cross Infection ; DNA, Bacterial/genetics ; Disease Outbreaks ; Drug Resistance, Multiple, Bacterial/*genetics ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli ; Female ; Gene Transfer, Horizontal ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Humans ; Klebsiella Infections/*microbiology/transmission ; Klebsiella pneumoniae/enzymology/*genetics/*growth &amp; development/isolation &amp; purification ; Male ; *Plasmids ; Time Factors ; beta-Lactamases/biosynthesis/*genetics ; }, abstract = {UNLABELLED: Carbapenem-resistant Klebsiella pneumoniae strains are formidable hospital pathogens that pose a serious threat to patients around the globe due to a rising incidence in health care facilities, high mortality rates associated with infection, and potential to spread antibiotic resistance to other bacterial species, such as Escherichia coli Over 6 months in 2011, 17 patients at the National Institutes of Health (NIH) Clinical Center became colonized with a highly virulent, transmissible carbapenem-resistant strain of K. pneumoniae Our real-time genomic sequencing tracked patient-to-patient routes of transmission and informed epidemiologists' actions to monitor and control this outbreak. Two of these patients remained colonized with carbapenemase-producing organisms for at least 2 to 4 years, providing the opportunity to undertake a focused genomic study of long-term colonization with antibiotic-resistant bacteria. Whole-genome sequencing studies shed light on the underlying complex microbial colonization, including mixed or evolving bacterial populations and gain or loss of plasmids. Isolates from NIH patient 15 showed complex plasmid rearrangements, leaving the chromosome and the blaKPC-carrying plasmid intact but rearranging the two other plasmids of this outbreak strain. NIH patient 16 has shown continuous colonization with blaKPC-positive organisms across multiple time points spanning 2011 to 2015. Genomic studies defined a complex pattern of succession and plasmid transmission across two different K. pneumoniae sequence types and an E. coli isolate. These findings demonstrate the utility of genomic methods for understanding strain succession, genome plasticity, and long-term carriage of antibiotic-resistant organisms.<br><br>IMPORTANCE: In 2011, the NIH Clinical Center had a nosocomial outbreak involving 19 patients who became colonized or infected with blaKPC-positive Klebsiella pneumoniae Patients who have intestinal colonization with blaKPC-positive K.&#xa0;pneumoniae are at risk for developing infections that are difficult or nearly impossible to treat with existing antibiotic options. Two of those patients remained colonized with blaKPC-positive Klebsiella pneumoniae for over a year, leading to the initiation of a detailed genomic analysis exploring mixed colonization, plasmid recombination, and plasmid diversification. Whole-genome sequence analysis identified a variety of changes, both subtle and large, in the blaKPC-positive organisms. Long-term colonization of patients with blaKPC-positive Klebsiella pneumoniae creates new opportunities for horizontal gene transfer of plasmids encoding antibiotic resistance genes and poses complications for the delivery of health care.}, }
@article {pmid27353650, year = {2016}, author = {Tovpeko, Y and Bai, J and Morrison, DA}, title = {Competence for Genetic Transformation in Streptococcus pneumoniae: Mutations in σA Bypass the ComW Requirement for Late Gene Expression.}, journal = {Journal of bacteriology}, volume = {198}, number = {17}, pages = {2370-2378}, pmid = {27353650}, issn = {1098-5530}, mesh = {Bacterial Proteins/genetics/*metabolism ; Gene Expression Regulation, Bacterial/*physiology ; Mutation ; Sigma Factor/genetics/*metabolism ; Streptococcus pneumoniae/*genetics ; *Transformation, Genetic ; }, abstract = {UNLABELLED: Streptococcus pneumoniae is able to integrate exogenous DNA into its genome by natural genetic transformation. Transient accumulation of high levels of the only S. pneumoniae alternative σ factor is insufficient for development of full competence without expression of a second competence-specific protein, ComW. The ΔcomW mutant is 10(4)-fold deficient in the yield of recombinants, 10-fold deficient in the amount of σ(X) activity, and 10-fold deficient in the amount of σ(X) protein. The critical role of ComW during transformation can be partially obviated by σ(A) mutations clustered on surfaces controlling affinity for core RNA polymerase (RNAP). While strains harboring σ(A) mutations in the comW mutant background were transforming at higher rates, the mechanism of transformation restoration was not clear. To investigate the mechanism of transformation restoration, we measured late gene expression in σ(A)* suppressor strains. Restoration of late gene expression was observed in ΔcomW σ(A)* mutants, indicating that a consequence of the σ(A)* mutations is, at least, to restore σ(X) activity. Competence kinetics were normal in ΔcomW σ(A)* strains, indicating that strains with restored competence exhibit the same pattern of transience as wild-type (WT) strains. We also identified a direct interaction between ComW and σ(X) using the yeast two-hybrid (Y2H) assay. Taken together, these data are consistent with the idea that ComW increases σ(X) access to core RNAP, pointing to a direct role of ComW in σ factor exchange during genetic transformation. However, the lack of late gene shutoff in ΔcomW mutants also points to a potential new role for ComW in competence shutoff.<br><br>IMPORTANCE: The sole alternative sigma factor of the streptococci, SigX, regulates development of competence for genetic transformation, a widespread mechanism of adaptation by horizontal gene transfer in this genus. The transient appearance of this sigma factor is strictly controlled at the levels of transcription and stability. This report shows that it is also controlled at the point of its substitution for SigA by a second transient competence-specific protein, ComW.}, }
@article {pmid27353489, year = {2016}, author = {Alam, SI and Dwivedi, P}, title = {Putative function of hypothetical proteins expressed by Clostridium perfringens type A strains and their protective efficacy in mouse model.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {44}, number = {}, pages = {147-156}, doi = {10.1016/j.meegid.2016.06.040}, pmid = {27353489}, issn = {1567-7257}, mesh = {Animals ; Bacterial Proteins/*genetics/*immunology/metabolism ; Cloning, Molecular ; Clostridium perfringens/genetics/*pathogenicity ; Disease Models, Animal ; Escherichia coli/genetics ; Female ; Gas Gangrene/immunology ; Mice, Inbred BALB C ; Phylogeny ; Recombinant Proteins/genetics/immunology/metabolism ; }, abstract = {The whole genome sequencing and annotation of Clostridium perfringens strains revealed several genes coding for proteins of unknown function with no significant similarities to genes in other organisms. Our previous studies clearly demonstrated that hypothetical proteins CPF_2500, CPF_1441, CPF_0876, CPF_0093, CPF_2002, CPF_2314, CPF_1179, CPF_1132, CPF_2853, CPF_0552, CPF_2032, CPF_0438, CPF_1440, CPF_2918, CPF_0656, and CPF_2364 are genuine proteins of C. perfringens expressed in high abundance. This study explored the putative role of these hypothetical proteins using bioinformatic tools and evaluated their potential as putative candidates for prophylaxis. Apart from a group of eight hypothetical proteins (HPs), a putative function was predicted for the rest of the hypothetical proteins using one or more of the algorithms used. The phylogenetic analysis did not suggest an evidence of a horizontal gene transfer event except for HP CPF_0876. HP CPF_2918 is an abundant extracellular protein, unique to C. perfringens species with maximum strain coverage and did not show any significant match in the database. CPF_2918 was cloned, recombinant protein was purified to near homogeneity, and probing with mouse anti-CPF_2918 serum revealed surface localization of the protein in C. perfringens ATCC13124 cultures. The purified recombinant CPF_2918 protein induced antibody production, a mixed Th1 and Th2 kind of response, and provided partial protection to immunized mice in direct C. perfringens challenge.}, }
@article {pmid27351410, year = {2017}, author = {Jakovac, S and Bojić, EF and Ibrišimović, MA and Tutiš, B and Ostojić, M and Hukić, M}, title = {Characteristics of Vancomycin-Resistant Enterococcus Strains in the West Balkans: A First Report.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {23}, number = {1}, pages = {122-126}, doi = {10.1089/mdr.2015.0355}, pmid = {27351410}, issn = {1931-8448}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics/metabolism ; Bacterial Typing Techniques ; Bosnia and Herzegovina/epidemiology ; Carbon-Oxygen Ligases/genetics/metabolism ; Croatia/epidemiology ; Enterococcus faecalis/drug effects/*genetics/growth &amp; development/isolation &amp; purification ; Enterococcus faecium/drug effects/*genetics/growth &amp; development/isolation &amp; purification ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Gram-Positive Bacterial Infections/drug therapy/*epidemiology/microbiology/transmission ; Humans ; Microbial Sensitivity Tests ; Pilot Projects ; Plasmids/chemistry/metabolism ; Prospective Studies ; Public Health Surveillance ; Vancomycin/pharmacology ; Vancomycin Resistance/*genetics ; Vancomycin-Resistant Enterococci/drug effects/*genetics/growth &amp; development/isolation &amp; purification ; }, abstract = {Vancomycin-resistant enterococci are among the major causes of nosocomial infections and represent a growing problem in many European countries. Among the most common enterococcal isolates, Enterococcus faecium is considered to be the reservoir of VanA and VanB-mediated resistance to glycopeptides. Enterococci with VanA-mediated resistance can transfer resistance genes to other enterococci and gram-positive bacteria. Hence, monitoring and surveillance of vancomycin-resistant enterococci (VREs) are crucial for the prevention of the spread of glycopeptide resistance. No reports have yet been published that document the resistance rates and typization of VREs in the region of Bosnia and Herzegovina as well as Croatia. In this study, 64 clinical enterococcal strains that were isolated in clinical centers, Mostar, Sarajevo, and Zagreb, were studied and findings regarding characteristics of vancomycin-resistant strains found in the West Balkan region are reported for the first time. All of the strains were identified using conventional phenotypic methods, and the resistance to glycopeptides was determined using the disk diffusion method, Vitek 2, and genotypic Enterococcus assay. The results of genotyping showed that 40 strains were identified as VREs (30% Enterococcus faecalis and 70% E. faecium), while the sensitivity of the phenotypic methods was 87.5%. Furthermore, VanA and VanB resistance types were found in Bosnia and Herzegovina and Croatia, with slightly higher prevalence of the latter (72.5%) over the former (27.5%).}, }
@article {pmid27345842, year = {2016}, author = {Yakimov, MM and Crisafi, F and Messina, E and Smedile, F and Lopatina, A and Denaro, R and Pieper, DH and Golyshin, PN and Giuliano, L}, title = {Analysis of defence systems and a conjugative IncP-1 plasmid in the marine polyaromatic hydrocarbons-degrading bacterium Cycloclasticus sp. 78-ME.}, journal = {Environmental microbiology reports}, volume = {8}, number = {4}, pages = {508-519}, doi = {10.1111/1758-2229.12424}, pmid = {27345842}, issn = {1758-2229}, mesh = {Biotransformation ; *CRISPR-Cas Systems ; *DNA Restriction-Modification Enzymes ; Genes, Bacterial ; Genomic Islands ; Hydrocarbons/*metabolism ; Piscirickettsiaceae/*genetics/*metabolism ; Plasmids/*analysis/*classification ; Seawater/microbiology ; }, abstract = {Marine prokaryotes have evolved a broad repertoire of defence systems to protect their genomes from lateral gene transfer including innate or acquired immune systems and infection-induced programmed cell suicide and dormancy. Here we report on the analysis of multiple defence systems present in the genome of the strain Cycloclasticus sp. 78-ME isolated from petroleum deposits of the tanker 'Amoco Milford Haven'. Cycloclasticus are ubiquitous bacteria globally important in polyaromatic hydrocarbons degradation in marine environments. Two 'defence islands' were identified in 78-ME genome: the first harbouring CRISPR-Cas with toxin-antitoxin system, while the second was composed by an array of genes for toxin-antitoxin and restriction-modification proteins. Among all identified spacers of CRISPR-Cas system only seven spacers match sequences of phages and plasmids. Furthermore, a conjugative plasmid p7ME01, which belongs to a new IncP-1θ ancestral archetype without any accessory mobile elements was found in 78-ME. Our results provide the context to the co-occurrence of diverse defence mechanisms in the genome of Cycloclasticus sp. 78-ME, which protect the genome of this highly specialized PAH-degrader. This study contributes to the further understanding of complex networks established in petroleum-based microbial communities.}, }
@article {pmid27343289, year = {2016}, author = {Wang, Y and White, MM and Kvist, S and Moncalvo, JM}, title = {Genome-Wide Survey of Gut Fungi (Harpellales) Reveals the First Horizontally Transferred Ubiquitin Gene from a Mosquito Host.}, journal = {Molecular biology and evolution}, volume = {33}, number = {10}, pages = {2544-2554}, pmid = {27343289}, issn = {1537-1719}, mesh = {Animals ; Biological Evolution ; Culicidae/*microbiology ; Fungi/*genetics ; Gastrointestinal Tract/microbiology ; *Gene Transfer, Horizontal ; Genome ; Phenotype ; Phylogeny ; Symbiosis/genetics ; Ubiquitin/*genetics ; Ubiquitination/genetics ; }, abstract = {Harpellales, an early-diverging fungal lineage, is associated with the digestive tracts of aquatic arthropod hosts. Concurrent with the production and annotation of the first four Harpellales genomes, we discovered that Zancudomyces culisetae, one of the most widely distributed Harpellales species, encodes an insect-like polyubiquitin chain. Ubiquitin and ubiquitin-like proteins are universally involved in protein degradation and regulation of immune response in eukaryotic organisms. Phylogenetic analyses inferred that this polyubiquitin variant has a mosquito origin. In addition, its amino acid composition, animal-like secondary structure, as well as the fungal nature of flanking genes all further support this as a horizontal gene transfer event. The single-copy polyubiquitin gene from Z. culisetae has lower GC ratio compared with homologs of insect taxa, which implies homogenization of the gene since its putatively ancient transfer. The acquired polyubiquitin gene may have served to improve important functions within Z. culisetae, by perhaps exploiting the insect hosts' ubiquitin-proteasome systems in the gut environment. Preliminary comparisons among the four Harpellales genomes highlight the reduced genome size of Z. culisetae, which corroborates its distinguishable symbiotic lifestyle. This is the first record of a horizontally transferred ubiquitin gene from disease-bearing insects to the gut-dwelling fungal endobiont and should invite further exploration in an evolutionary context.}, }
@article {pmid27343288, year = {2016}, author = {Hynes, AP and Shakya, M and Mercer, RG and Grüll, MP and Bown, L and Davidson, F and Steffen, E and Matchem, H and Peach, ME and Berger, T and Grebe, K and Zhaxybayeva, O and Lang, AS}, title = {Functional and Evolutionary Characterization of a Gene Transfer Agent's Multilocus "Genome".}, journal = {Molecular biology and evolution}, volume = {33}, number = {10}, pages = {2530-2543}, pmid = {27343288}, issn = {1537-1719}, mesh = {Bacterial Proteins/genetics ; Bacteriophages/genetics ; *Biological Evolution ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal/genetics ; Prophages/genetics ; Rhodobacter capsulatus/*genetics ; }, abstract = {Gene transfer agents (GTAs) are phage-like particles that can package and transfer a random piece of the producing cell's genome, but are unable to transfer all the genes required for their own production. As such, GTAs represent an evolutionary conundrum: are they selfish genetic elements propagating through an unknown mechanism, defective viruses, or viral structures "repurposed" by cells for gene exchange, as their name implies? In Rhodobacter capsulatus, production of the R. capsulatus GTA (RcGTA) particles is associated with a cluster of genes resembling a small prophage. Utilizing transcriptomic, genetic and biochemical approaches, we report that the RcGTA "genome" consists of at least 24 genes distributed across five distinct loci. We demonstrate that, of these additional loci, two are involved in cell recognition and binding and one in the production and maturation of RcGTA particles. The five RcGTA "genome" loci are widespread within Rhodobacterales, but not all loci have the same evolutionary histories. Specifically, two of the loci have been subject to frequent, probably virus-mediated, gene transfer events. We argue that it is unlikely that RcGTA is a selfish genetic element. Instead, our findings are compatible with the scenario that RcGTA is a virus-derived element maintained by the producing organism due to a selective advantage of within-population gene exchange. The modularity of the RcGTA "genome" is presumably a result of selection on the host organism to retain GTA functionality.}, }
@article {pmid27342545, year = {2016}, author = {Schwarz, S and Johnson, AP}, title = {Transferable resistance to colistin: a new but old threat.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {71}, number = {8}, pages = {2066-2070}, doi = {10.1093/jac/dkw274}, pmid = {27342545}, issn = {1460-2091}, mesh = {Animal Husbandry/methods ; Animals ; Anti-Bacterial Agents/*pharmacology/therapeutic use ; China ; Colistin/*pharmacology/therapeutic use ; *Drug Resistance, Bacterial ; Drug Utilization/standards ; Enterobacteriaceae/*drug effects/*genetics ; Enterobacteriaceae Infections/microbiology/veterinary ; *Gene Transfer, Horizontal ; Health Policy ; Humans ; Poultry ; Swine ; }, abstract = {In this Leading article, we summarize current knowledge of the occurrence of the first and so far only transferable colistin resistance gene, mcr-1 Its location on a conjugative plasmid is likely to have driven its spread into a range of enteric bacteria in humans and animals. Screening studies have identified mcr-1 in five of the seven continents and retrospective studies in China have identified this gene in Escherichia coli originally isolated in the 1980s, while the first European isolate dates back to 2005. Based on the widespread use of colistin in pigs and poultry in several countries and the higher number of mcr-1-carrying isolates of animal origin than of human origin, it is tempting to assume that this resistance may have emerged in the animal sector. Whatever its origin, interventions to reduce its further spread will require an integrated global one-health approach, comprising robust antibiotic stewardship to reduce unnecessary colistin use, improved infection prevention, and control and surveillance of colistin usage and resistance in both veterinary and human medicine.}, }
@article {pmid27337454, year = {2016}, author = {Mathers, A}, title = {Mobilization of Carbapenemase-Mediated Resistance in Enterobacteriaceae.}, journal = {Microbiology spectrum}, volume = {4}, number = {3}, pages = {}, doi = {10.1128/microbiolspec.EI10-0010-2015}, pmid = {27337454}, issn = {2165-0497}, mesh = {Anti-Bacterial Agents/*therapeutic use ; Bacterial Proteins/*genetics ; Carbapenems/*therapeutic use ; Drug Resistance, Multiple, Bacterial/*genetics ; Enterobacteriaceae/*drug effects/*genetics ; Enterobacteriaceae Infections/*drug therapy/epidemiology ; Humans ; Interspersed Repetitive Sequences/genetics ; Microbial Sensitivity Tests ; beta-Lactamases/*genetics ; }, abstract = {There has been a dramatic increase in the last decade in the number of carbapenem-resistant Enterobacteriaceae, often leaving patients and their providers with few treatment options and resultant poor outcomes when an infection develops. The majority of the carbapenem resistance is mediated by bacterial acquisition of one of three carbapenemases (Klebsiella pneumoniae carbapenemase [KPC], oxacillinase-48-like [OXA-48], and the New Delhi metallo-β-lactamase [NDM]). Each of these enzymes has a unique global epidemiology and microbiology. The genes which encode the most globally widespread carbapenemases are typically carried on mobile pieces of DNA which can be freely exchanged between bacterial strains and species via horizontal gene transfer. Unfortunately, most of the antimicrobial surveillance systems target specific strains or species and therefore are not well equipped for examining genes of drug resistance. Examination of not only the carbapenemase gene itself but also the genetic context which can predispose a gene to mobilize within a diversity of species and environments will likely be central to understanding the factors contributing to the global dissemination of carbapenem resistance. Using the three most prevalent carbapenemase genes as examples, this chapter highlights the potential impact the associated genetic mobile elements have on the epidemiology and microbiology for each carbapenemase. Understanding how a carbapenemase gene mobilizes through a bacterial population will be critical for detection methods and ultimately inform infection control practices. Understanding gene mobilization and tracking will require novel approaches to surveillance, which will be required to slow the spread of this emerging resistance.}, }
@article {pmid27336621, year = {2016}, author = {Alvarez-Carreño, C and Becerra, A and Lazcano, A}, title = {Molecular Evolution of the Oxygen-Binding Hemerythrin Domain.}, journal = {PloS one}, volume = {11}, number = {6}, pages = {e0157904}, pmid = {27336621}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Cluster Analysis ; *Evolution, Molecular ; Gene Dosage ; Genome, Bacterial ; Hemerythrin/chemistry/classification/*genetics/*metabolism ; Oxygen/*metabolism ; Phylogeny ; Protein Binding ; *Protein Interaction Domains and Motifs ; }, abstract = {BACKGROUND: The evolution of oxygenic photosynthesis during Precambrian times entailed the diversification of strategies minimizing reactive oxygen species-associated damage. Four families of oxygen-carrier proteins (hemoglobin, hemerythrin and the two non-homologous families of arthropodan and molluscan hemocyanins) are known to have evolved independently the capacity to bind oxygen reversibly, providing cells with strategies to cope with the evolutionary pressure of oxygen accumulation. Oxygen-binding hemerythrin was first studied in marine invertebrates but further research has made it clear that it is present in the three domains of life, strongly suggesting that its origin predated the emergence of eukaryotes.<br><br>RESULTS: Oxygen-binding hemerythrins are a monophyletic sub-group of the hemerythrin/HHE (histidine, histidine, glutamic acid) cation-binding domain. Oxygen-binding hemerythrin homologs were unambiguously identified in 367/2236 bacterial, 21/150 archaeal and 4/135 eukaryotic genomes. Overall, oxygen-binding hemerythrin homologues were found in the same proportion as single-domain and as long protein sequences. The associated functions of protein domains in long hemerythrin sequences can be classified in three major groups: signal transduction, phosphorelay response regulation, and protein binding. This suggests that in many organisms the reversible oxygen-binding capacity was incorporated in signaling pathways. A maximum-likelihood tree of oxygen-binding hemerythrin homologues revealed a complex evolutionary history in which lateral gene transfer, duplications and gene losses appear to have played an important role.<br><br>CONCLUSIONS: Hemerythrin is an ancient protein domain with a complex evolutionary history. The distinctive iron-binding coordination site of oxygen-binding hemerythrins evolved first in prokaryotes, very likely prior to the divergence of Firmicutes and Proteobacteria, and spread into many bacterial, archaeal and eukaryotic species. The later evolution of the oxygen-binding hemerythrin domain in both prokaryotes and eukaryotes led to a wide variety of functions, ranging from protection against oxidative damage in anaerobic and microaerophilic organisms, to oxygen supplying to particular enzymes and pathways in aerobic and facultative species.}, }
@article {pmid27336403, year = {2016}, author = {Bromberg, R and Grishin, NV and Otwinowski, Z}, title = {Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer.}, journal = {PLoS computational biology}, volume = {12}, number = {6}, pages = {e1004985}, pmid = {27336403}, issn = {1553-7358}, support = {R01 GM053163/GM/NIGMS NIH HHS/United States ; R01 GM094575/GM/NIGMS NIH HHS/United States ; R01 GM117080/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Algorithms ; Archaea/*genetics ; Bacteria/*genetics ; Computational Biology/*methods ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome, Archaeal/*genetics ; Genome, Bacterial/*genetics ; Phylogeny ; }, abstract = {Advances in sequencing have generated a large number of complete genomes. Traditionally, phylogenetic analysis relies on alignments of orthologs, but defining orthologs and separating them from paralogs is a complex task that may not always be suited to the large datasets of the future. An alternative to traditional, alignment-based approaches are whole-genome, alignment-free methods. These methods are scalable and require minimal manual intervention. We developed SlopeTree, a new alignment-free method that estimates evolutionary distances by measuring the decay of exact substring matches as a function of match length. SlopeTree corrects for horizontal gene transfer, for composition variation and low complexity sequences, and for branch-length nonlinearity caused by multiple mutations at the same site. We tested SlopeTree on 495 bacteria, 73 archaea, and 72 strains of Escherichia coli and Shigella. We compared our trees to the NCBI taxonomy, to trees based on concatenated alignments, and to trees produced by other alignment-free methods. The results were consistent with current knowledge about prokaryotic evolution. We assessed differences in tree topology over different methods and settings and found that the majority of bacteria and archaea have a core set of proteins that evolves by descent. In trees built from complete genomes rather than sets of core genes, we observed some grouping by phenotype rather than phylogeny, for instance with a cluster of sulfur-reducing thermophilic bacteria coming together irrespective of their phyla. The source-code for SlopeTree is available at: http://prodata.swmed.edu/download/pub/slopetree_v1/slopetree.tar.gz.}, }
@article {pmid27333878, year = {2016}, author = {Gilbert, MJ and Miller, WG and Yee, E and Zomer, AL and van der Graaf-van Bloois, L and Fitzgerald, C and Forbes, KJ and Méric, G and Sheppard, SK and Wagenaar, JA and Duim, B}, title = {Comparative Genomics of Campylobacter fetus from Reptiles and Mammals Reveals Divergent Evolution in Host-Associated Lineages.}, journal = {Genome biology and evolution}, volume = {8}, number = {6}, pages = {2006-2019}, pmid = {27333878}, issn = {1759-6653}, support = {MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Campylobacter Infections/*genetics/microbiology ; Campylobacter fetus/*genetics/pathogenicity ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; Host-Pathogen Interactions/*genetics ; Humans ; Mammals/genetics/microbiology ; Phylogeny ; Reptiles/genetics/microbiology ; Species Specificity ; }, abstract = {Campylobacter fetus currently comprises three recognized subspecies, which display distinct host association. Campylobacter fetus subsp. fetus and C fetus subsp. venerealis are both associated with endothermic mammals, primarily ruminants, whereas C fetus subsp. testudinum is primarily associated with ectothermic reptiles. Both C. fetus subsp. testudinum and C. fetus subsp. fetus have been associated with severe infections, often with a systemic component, in immunocompromised humans. To study the genetic factors associated with the distinct host dichotomy in C. fetus, whole-genome sequencing and comparison of mammal- and reptile-associated C fetus was performed. The genomes of C fetus subsp. testudinum isolated from either reptiles or humans were compared with elucidate the genetic factors associated with pathogenicity in humans. Genomic comparisons showed conservation of gene content and organization among C fetus subspecies, but a clear distinction between mammal- and reptile-associated C fetus was observed. Several genomic regions appeared to be subspecies specific, including a putative tricarballylate catabolism pathway, exclusively present in C fetus subsp. testudinum strains. Within C fetus subsp. testudinum, sapA, sapB, and sapAB type strains were observed. The recombinant locus iamABC (mlaFED) was exclusively associated with invasive C fetus subsp. testudinum strains isolated from humans. A phylogenetic reconstruction was consistent with divergent evolution in host-associated strains and the existence of a barrier to lateral gene transfer between mammal- and reptile-associated C fetus Overall, this study shows that reptile-associated C fetus subsp. testudinum is genetically divergent from mammal-associated C fetus subspecies.}, }
@article {pmid27330141, year = {2016}, author = {Xu, T and Qin, S and Hu, Y and Song, Z and Ying, J and Li, P and Dong, W and Zhao, F and Yang, H and Bao, Q}, title = {Whole genomic DNA sequencing and comparative genomic analysis of Arthrospira platensis: high genome plasticity and genetic diversity.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {23}, number = {4}, pages = {325-338}, pmid = {27330141}, issn = {1756-1663}, mesh = {Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomic Instability ; Phylogeny ; *Polymorphism, Genetic ; Repetitive Sequences, Nucleic Acid ; Spirulina/classification/*genetics ; }, abstract = {Arthrospira platensis is a multi-cellular and filamentous non-N2-fixing cyanobacterium that is capable of performing oxygenic photosynthesis. In this study, we determined the nearly complete genome sequence of A. platensis YZ. A. platensis YZ genome is a single, circular chromosome of 6.62 Mb in size. Phylogenetic and comparative genomic analyses revealed that A. platensis YZ was more closely related to A. platensis NIES-39 than Arthrospira sp. PCC 8005 and A. platensis C1. Broad gene gains were identified between A. platensis YZ and three other Arthrospira speices, some of which have been previously demonstrated that can be laterally transferred among different species, such as restriction-modification systems-coding genes. Moreover, unprecedented extensive chromosomal rearrangements among different strains were observed. The chromosomal rearrangements, particularly the chromosomal inversions, were analysed and estimated to be closely related to palindromes that involved long inverted repeat sequences and the extensively distributed type IIR restriction enzyme in the Arthrospira genome. In addition, species from genus Arthrospira unanimously contained the highest rate of repetitive sequence compared with the other species of order Oscillatoriales, suggested that sequence duplication significantly contributed to Arthrospira genome phylogeny. These results provided in-depth views into the genomic phylogeny and structural variation of A. platensis, as well as provide a valuable resource for functional genomics studies.}, }
@article {pmid27329941, year = {2016}, author = {Cheng, K and Rong, X and Huang, Y}, title = {Widespread interspecies homologous recombination reveals reticulate evolution within the genus Streptomyces.}, journal = {Molecular phylogenetics and evolution}, volume = {102}, number = {}, pages = {246-254}, doi = {10.1016/j.ympev.2016.06.004}, pmid = {27329941}, issn = {1095-9513}, mesh = {Bacterial Proteins/chemistry/genetics/metabolism ; Biological Evolution ; DNA, Bacterial/chemistry/genetics/metabolism ; Gene Transfer, Horizontal/*genetics ; Genetic Linkage ; Homologous Recombination ; Phylogeny ; RNA, Ribosomal, 16S/chemistry/genetics/metabolism ; Sequence Analysis, DNA ; Streptomyces/*classification/genetics ; }, abstract = {Homologous recombination is increasingly being recognized as a driving force in microbial evolution. However, recombination in streptomycetes, a rich source of diverse secondary metabolites, particularly among different species, remains minimally investigated. In this study, the largest sample of Streptomyces species to date, consisting of 142 type strains spanning the genus, with available sequences of 16S rRNA, atpD, gyrB, recA, rpoB and trpB genes, were collected and subjected to a comprehensive population genetic analysis to generate an overall estimate of the level of Streptomyces interspecies genetic exchange and its effect on the evolution of this genus. The results indicate frequent homologous recombination among Streptomyces species, which occurred three times more frequently and was nearly 14 times more important than point mutation in nucleotide sequence divergence (ρ/θw=3.10, r/m=13.74). As a result, a facilitating effect on the evolutionary process and confusion in phylogenetic relationships were observed, as well as a number of specific transfer events of the six gene fragments. A resultant phylogenetic network depicted extensive horizontal genetic exchange which decays clonality in streptomycetes. Moreover, seven evolutionary lineage groups were identified in the present sample in the Structure analysis, generally consistent with morphological and physiological data, and the contribution of recombination was detected to be varied among them. Our analyses demonstrated a reticulate evolution within Streptomyces due to the high level of interspecies gene exchange, which greatly challenges the traditional tree-shaped phylogeny in this genus and may advance our evolutionary understanding of a genuine Streptomyces species.}, }
@article {pmid27329036, year = {2016}, author = {Jans, C and de Wouters, T and Bonfoh, B and Lacroix, C and Kaindi, DW and Anderegg, J and Böck, D and Vitali, S and Schmid, T and Isenring, J and Kurt, F and Kogi-Makau, W and Meile, L}, title = {Phylogenetic, epidemiological and functional analyses of the Streptococcus bovis/Streptococcus equinus complex through an overarching MLST scheme.}, journal = {BMC microbiology}, volume = {16}, number = {1}, pages = {117}, pmid = {27329036}, issn = {1471-2180}, mesh = {Animals ; Bacterial Adhesion ; Base Sequence ; Chaperonin 60/genetics ; DNA, Bacterial/genetics ; Gastric Juice/microbiology ; Genes, Essential ; Humans ; Multilocus Sequence Typing/methods ; NF-kappa B/immunology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Streptococcal Infections/blood/*epidemiology/microbiology ; Streptococcus/*genetics/*isolation &amp; purification ; Streptococcus bovis/genetics/isolation &amp; purification ; Streptococcus gallolyticus/genetics/isolation &amp; purification ; }, abstract = {BACKGROUND: The Streptococcus bovis/Streptococcus equinus complex (SBSEC) comprises seven (sub)species classified as human and animal commensals, emerging opportunistic pathogens and food fermentative organisms. Changing taxonomy, shared habitats, natural competence and evidence for horizontal gene transfer pose difficulties for determining their phylogeny, epidemiology and virulence mechanisms. Thus, novel phylogenetic and functional classifications are required. An SBSEC overarching multi locus sequence type (MLST) scheme targeting 10 housekeeping genes was developed, validated and combined with host-related properties of adhesion to extracellular matrix proteins (ECM), activation of the immune responses via NF-KB and survival in simulated gastric juice (SGJ).<br><br>RESULTS: Commensal and pathogenic SBSEC strains (n&#x2009;=&#x2009;74) of human, animal and food origin from Europe, Asia, America and Africa were used in the MLST scheme yielding 66 sequence types and 10 clonal complexes differentiated into distinct habitat-associated and mixed lineages. Adhesion to ECMs collagen I and mucin type II was a common characteristic (23&#xa0;% of strains) followed by adhesion to fibronectin and fibrinogen (19.7&#xa0;%). High adhesion abilities were found for East African dairy and human blood isolate branches whereas commensal fecal SBSEC displayed low adhesion. NF-KB activation was observed for a limited number of dairy and blood isolates suggesting the potential of some pathogenic strains for reduced immune activation. Strains from dairy MLST clades displayed the highest relative survival to SGJ independently of dairy adaptation markers lacS/lacZ.<br><br>CONCLUSION: Combining phylogenetic and functional analyses via SBSEC MLST enabled the clear delineation of strain clades to unravel the complexity of this bacterial group. High adhesion values shared between certain dairy and blood strains as well as the behavior of NF-KB activation are concerning for specific lineages. They highlighted the health risk among shared lineages and establish the basis to elucidate (zoonotic-) transmission, host specificity, virulence mechanisms and enhanced risk assessment as pathobionts in an overarching One Health approach.}, }
@article {pmid27325351, year = {2016}, author = {Valente, C and Hinds, J and Gould, KA and Pinto, FR and de Lencastre, H and Sá-Leão, R}, title = {Impact of the 13-valent pneumococcal conjugate vaccine on Streptococcus pneumoniae multiple serotype carriage.}, journal = {Vaccine}, volume = {34}, number = {34}, pages = {4072-4078}, doi = {10.1016/j.vaccine.2016.06.017}, pmid = {27325351}, issn = {1873-2518}, mesh = {Carrier State/*epidemiology/microbiology ; Child ; Child, Preschool ; Humans ; Infant ; Nasopharynx/microbiology ; Pneumococcal Infections/*prevention &amp; control ; Pneumococcal Vaccines/*administration &amp; dosage/therapeutic use ; Portugal ; Serogroup ; Streptococcus pneumoniae/classification ; }, abstract = {INTRODUCTION: Pneumococcal multiple serotype carriage is important for evolution of the species and to understand how the pneumococcal population is changing with vaccination. We aimed to determine the impact of the 13-valent pneumococcal conjugate vaccine (PCV13) on multiple serotype carriage.<br><br>METHODS AND MATERIALS: Nasopharyngeal samples from fully vaccinated pneumococcal carriers (4 doses of PCV13, n=141, aged 18-72months) or from non-vaccinated pneumococcal carriers (0 doses of any PCV, n=140, same age group) were analyzed. Multiple serotype carriage was evaluated by DNA hybridization with a molecular serotyping microarray that detects all known serotypes.<br><br>RESULTS: Vaccinated children had a lower prevalence of multiple serotype carriage than the non-vaccinated group (20.6% vs 29.3%, p=0.097), and a significantly lower proportion of PCV13 serotypes (6.4% vs 38.5%, p=0.0001). PCV13 serotypes found among vaccinated children were mostly detected as a minor serotype in co-colonization with a more abundant non-vaccine serotype. Vaccinated children were colonized by a significantly higher proportion of commensal non-pneumococcal Streptococcus spp. (58.2% vs 42.8%, p=0.012). In vaccinated children there were significantly less non-vaccine type (NVT) co-colonization events than expected based on the distribution of these serotypes in non-vaccinated children.<br><br>CONCLUSIONS: The results suggest that vaccinated children have lower pneumococcal multiple serotype carriage prevalence due to higher competitive abilities of non-vaccine serotypes expanding after PCV13 use. This might represent an additional benefit of PCV13, as decreased co-colonization rates translate into decreased opportunities for horizontal gene transfer and might have implications for the evolution and virulence of pneumococci.}, }
@article {pmid27324571, year = {2016}, author = {Naamala, J and Jaiswal, SK and Dakora, FD}, title = {Microsymbiont diversity and phylogeny of native bradyrhizobia associated with soybean (Glycine max L. Merr.) nodulation in South African soils.}, journal = {Systematic and applied microbiology}, volume = {39}, number = {5}, pages = {336-344}, pmid = {27324571}, issn = {1618-0984}, mesh = {Base Sequence ; *Bradyrhizobium/classification/genetics/isolation &amp; purification ; DNA Gyrase/genetics ; DNA, Bacterial/genetics ; Genes, Essential/genetics ; Genetic Variation/genetics ; Molecular Typing ; Oxidoreductases/genetics ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Root Nodules, Plant/*microbiology ; Sequence Analysis, DNA ; Soil Microbiology ; South Africa ; Glycine max/*microbiology ; Symbiosis ; Transcription Factors/genetics ; }, abstract = {The genetic diversity and identification of slow- and fast-growing soybean root nodule bacterial isolates from different agro-climatic regions in Mpumalanga, Limpopo and Gauteng Provinces of South Africa were evaluated. The 16S-rDNA-RFLP analysis of 100 rhizobial isolates and eight reference type strains placed the isolates into six major clusters, and revealed their site-dependent genomic diversity. Sequence analysis of single and concatenated housekeeping genes (atpD, glnII and gyrB), as well as the symbiotic gene nifH captured a considerably higher level of genetic diversity and indicated the dominance of Bradyrhizobium diazoefficiens and Bradyrhizobium japonicum in Mpumalanga, Limpopo and Gauteng Provinces. Gene sequence similarities of isolates with type strains of Bradyrhizobium ranged from 97.3 to 100% for the 16S rDNA, and 83.4 to 100% for the housekeeping genes. The glnII gene phylogeny showed discordance with the other genes, suggesting lateral gene transfer or recombination events. Concatenated gene sequence analysis showed that most of the isolates did not align with known type strains and might represent new species from South Africa. This underscores the high genetic variability associated with soybean Bradyrhizobium in South African soils, and the presence of an important reservoir of novel soybean-nodulating bradyrhizobia in the country. In this study, the grouping of isolates was influenced by site origin, with Group I isolates originating from Limpopo Province and Groups II and III from Mpumlanga Province in the 16S rDNA-RFLP analysis.}, }
@article {pmid27321040, year = {2016}, author = {Martini, MC and Wibberg, D and Lozano, M and Torres Tejerizo, G and Albicoro, FJ and Jaenicke, S and van Elsas, JD and Petroni, A and Garcillán-Barcia, MP and de la Cruz, F and Schlüter, A and Pühler, A and Pistorio, M and Lagares, A and Del Papa, MF}, title = {Genomics of high molecular weight plasmids isolated from an on-farm biopurification system.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {28284}, pmid = {27321040}, issn = {2045-2322}, mesh = {Escherichia coli/chemistry/*genetics ; Molecular Weight ; *Plasmids/chemistry/genetics/isolation &amp; purification ; *Replicon ; }, abstract = {The use of biopurification systems (BPS) constitutes an efficient strategy to eliminate pesticides from polluted wastewaters from farm activities. BPS environments contain a high microbial density and diversity facilitating the exchange of information among bacteria, mediated by mobile genetic elements (MGEs), which play a key role in bacterial adaptation and evolution in such environments. Here we sequenced and characterized high-molecular-weight plasmids from a bacterial collection of an on-farm BPS. The high-throughput-sequencing of the plasmid pool yielded a total of several Mb sequence information. Assembly of the sequence data resulted in six complete replicons. Using in silico analyses we identified plasmid replication genes whose encoding proteins represent 13 different Pfam families, as well as proteins involved in plasmid conjugation, indicating a large diversity of plasmid replicons and suggesting the occurrence of horizontal gene transfer (HGT) events within the habitat analyzed. In addition, genes conferring resistance to 10 classes of antimicrobial compounds and those encoding enzymes potentially involved in pesticide and aromatic hydrocarbon degradation were found. Global analysis of the plasmid pool suggest that the analyzed BPS represents a key environment for further studies addressing the dissemination of MGEs carrying catabolic genes and pathway assembly regarding degradation capabilities.}, }
@article {pmid27320224, year = {2016}, author = {Mangwani, N and Kumari, S and Das, S}, title = {Bacterial biofilms and quorum sensing: fidelity in bioremediation technology.}, journal = {Biotechnology &amp; genetic engineering reviews}, volume = {32}, number = {1-2}, pages = {43-73}, doi = {10.1080/02648725.2016.1196554}, pmid = {27320224}, issn = {2046-5556}, mesh = {Bacteria/genetics/growth &amp; development ; *Bacterial Physiological Phenomena ; Bacterial Proteins/genetics/metabolism ; Biodegradation, Environmental ; Biofilms/*growth &amp; development ; Mutation ; *Quorum Sensing ; Signal Transduction ; }, abstract = {Increased contamination of the environment with toxic pollutants has paved the way for efficient strategies which can be implemented for environmental restoration. The major problem with conventional methods used for cleaning of pollutants is inefficiency and high economic costs. Bioremediation is a growing technology having advanced potential of cleaning pollutants. Biofilm formed by various micro-organisms potentially provide a suitable microenvironment for efficient bioremediation processes. High cell density and stress resistance properties of the biofilm environment provide opportunities for efficient metabolism of number of hydrophobic and toxic compounds. Bacterial biofilm formation is often regulated by quorum sensing (QS) which is a population density-based cell-cell communication process via signaling molecules. Numerous signaling molecules such as acyl homoserine lactones, peptides, autoinducer-2, diffusion signaling factors, and α-hydroxyketones have been studied in bacteria. Genetic alteration of QS machinery can be useful to modulate vital characters valuable for environmental applications such as biofilm formation, biosurfactant production, exopolysaccharide synthesis, horizontal gene transfer, catabolic gene expression, motility, and chemotaxis. These qualities are imperative for bacteria during degradation or detoxification of any pollutant. QS signals can be used for the fabrication of engineered biofilms with enhanced degradation kinetics. This review discusses the connection between QS and biofilm formation by bacteria in relation to bioremediation technology.}, }
@article {pmid27316956, year = {2016}, author = {Valente, C and Dawid, S and Pinto, FR and Hinds, J and Simões, AS and Gould, KA and Mendes, LA and de Lencastre, H and Sá-Leão, R}, title = {The blp Locus of Streptococcus pneumoniae Plays a Limited Role in the Selection of Strains That Can Cocolonize the Human Nasopharynx.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {17}, pages = {5206-5215}, pmid = {27316956}, issn = {1098-5336}, support = {R01 AI101285/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/*metabolism ; Gene Expression Regulation, Bacterial ; Humans ; Nasopharynx/*microbiology ; Pneumococcal Infections/*microbiology ; Streptococcus pneumoniae/genetics/*growth &amp; development/isolation &amp; purification/*metabolism ; }, abstract = {UNLABELLED: Nasopharyngeal colonization is important for Streptococcus pneumoniae evolution, providing the opportunity for horizontal gene transfer when multiple strains co-occur. Although colonization with more than one strain of pneumococcus is common, the factors that influence the ability of strains to coexist are not known. A highly variable blp (bacteriocin-like peptide) locus has been identified in all sequenced strains of S. pneumoniae This locus controls the regulation and secretion of bacteriocins, small peptides that target other bacteria. In this study, we analyzed a series of cocolonizing isolates to evaluate the impact of the blp locus on human colonization to determine whether competitive phenotypes of bacteriocin secretion restrict cocolonization. We identified a collection of 135 nasopharyngeal samples cocolonized with two or more strains, totaling 285 isolates. The blp locus of all strains was characterized genetically with regard to pheromone type, bacteriocin/immunity content, and potential for locus functionality. Inhibitory phenotypes of bacteriocin secretion and locus activity were assessed through overlay assays. Isolates from single colonizations (n = 298) were characterized for comparison. Cocolonizing strains had a high diversity of blp cassettes; approximately one-third displayed an inhibitory phenotype in vitro Despite in vitro evidence of competition, pneumococci cocolonized the subjects independently of blp pheromone type (P = 0.577), bacteriocin/immunity content, blp locus activity (P = 0.798), and inhibitory phenotype (P = 0.716). In addition, no significant differences were observed when single and cocolonizing strains were compared. Despite clear evidence of blp-mediated competition in experimental models, the results of our study suggest that the blp locus plays a limited role in restricting pneumococcal cocolonization in humans.<br><br>IMPORTANCE: Nasopharyngeal colonization with Streptococcus pneumoniae (pneumococcus) is important for pneumococcal evolution, as the nasopharynx represents the major site for horizontal gene transfer when multiple strains co-occur, a phenomenon known as cocolonization. Understanding how pneumococcal strains interact within the competitive environment of the nasopharynx is of chief importance in the context of pneumococcal ecology. In this study, we used an unbiased collection of naturally co-occurring pneumococcal strains and showed that a biological process frequently used by bacteria for competition-bacteriocin production-is not decisive in the coexistence of pneumococci in the host, in contrast to what has been shown in experimental models.}, }
@article {pmid27312952, year = {2016}, author = {Barbosa, EG and Crisp, A and Broadbent, SE and Carrillo, M and Boschetti, C and Tunnacliffe, A}, title = {A functional difference between native and horizontally acquired genes in bdelloid rotifers.}, journal = {Gene}, volume = {590}, number = {1}, pages = {186-191}, doi = {10.1016/j.gene.2016.06.019}, pmid = {27312952}, issn = {1879-0038}, mesh = {Alternative Splicing ; Amino Acid Sequence ; Animals ; Biological Evolution ; Gene Expression Profiling ; Gene Ontology ; *Gene Transfer, Horizontal ; *Genome, Helminth ; Molecular Sequence Annotation ; RNA, Helminth/*genetics/metabolism ; RNA, Messenger/*genetics/metabolism ; RNA, Spliced Leader/*genetics/metabolism ; Rotifera/*genetics ; Sequence Alignment ; *Trans-Splicing ; Transcriptome ; Transgenes ; }, abstract = {The form of RNA processing known as SL trans-splicing involves the transfer of a short conserved sequence, the spliced leader (SL), from a noncoding SL RNA to the 5' ends of mRNA molecules. SL trans-splicing occurs in several animal taxa, including bdelloid rotifers (Rotifera, Bdelloidea). One striking feature of these aquatic microinvertebrates is the large proportion of foreign genes, i.e. those acquired by horizontal gene transfer from other organisms, in their genomes. However, whether such foreign genes behave similarly to native genes has not been tested in bdelloids or any other animal. We therefore used a combination of experimental and computational methods to examine whether transcripts of foreign genes in bdelloids were SL trans-spliced, like their native counterparts. We found that many foreign transcripts contain SLs, use similar splice acceptor sequences to native genes, and are able to undergo alternative trans-splicing. However, a significantly lower proportion of foreign mRNAs contains SL sequences than native transcripts. This demonstrates a novel functional difference between foreign and native genes in bdelloids and suggests that SL trans-splicing is not essential for the expression of foreign genes, but is acquired during their domestication.}, }
@article {pmid27312355, year = {2016}, author = {Subirats, J and Sànchez-Melsió, A and Borrego, CM and Balcázar, JL and Simonet, P}, title = {Metagenomic analysis reveals that bacteriophages are reservoirs of antibiotic resistance genes.}, journal = {International journal of antimicrobial agents}, volume = {48}, number = {2}, pages = {163-167}, doi = {10.1016/j.ijantimicag.2016.04.028}, pmid = {27312355}, issn = {1872-7913}, mesh = {Bacteria/drug effects/*virology ; Bacteriophages/classification/*genetics/isolation &amp; purification ; Caudovirales/classification/genetics/isolation &amp; purification ; *Drug Resistance, Bacterial ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genes, Viral ; Hospitals ; Metagenomics ; Wastewater/*virology ; }, abstract = {A metagenomics approach was applied to explore the presence of antibiotic resistance genes (ARGs) in bacteriophages from hospital wastewater. Metagenomic analysis showed that most phage sequences affiliated to the order Caudovirales, comprising the tailed phage families Podoviridae, Siphoviridae and Myoviridae. Moreover, the relative abundance of ARGs in the phage DNA fraction (0.26%) was higher than in the bacterial DNA fraction (0.18%). These differences were particularly evident for genes encoding ATP-binding cassette (ABC) and resistance-nodulation-cell division (RND) proteins, phosphotransferases, β-lactamases and plasmid-mediated quinolone resistance. Analysis of assembled contigs also revealed that blaOXA-10, blaOXA-58 and blaOXA-24 genes belonging to class D β-lactamases as well as a novel blaTEM (98.9% sequence similarity to the blaTEM-1 gene) belonging to class A β-lactamases were detected in a higher proportion in phage DNA. Although preliminary, these findings corroborate the role of bacteriophages as reservoirs of resistance genes and thus highlight the necessity to include them in future studies on the emergence and spread of antibiotic resistance in the environment.}, }
@article {pmid27312345, year = {2016}, author = {Öztürk, B and Ghequire, M and Nguyen, TP and De Mot, R and Wattiez, R and Springael, D}, title = {Expanded insecticide catabolic activity gained by a single nucleotide substitution in a bacterial carbamate hydrolase gene.}, journal = {Environmental microbiology}, volume = {18}, number = {12}, pages = {4878-4887}, doi = {10.1111/1462-2920.13409}, pmid = {27312345}, issn = {1462-2920}, mesh = {Amino Acid Substitution/genetics ; Carbamates/metabolism ; Carbaryl/metabolism ; Carbofuran/*metabolism ; Carboxylic Ester Hydrolases/genetics/*metabolism ; Insecticides/*metabolism ; Interspersed Repetitive Sequences/genetics ; Nucleotides ; Rhizobium/enzymology/*metabolism ; Sphingomonadaceae/enzymology/*metabolism ; }, abstract = {Carbofuran-mineralizing strain Novosphingobium sp. KN65.2 produces the CfdJ enzyme that converts the N-methylcarbamate insecticide to carbofuran phenol. Purified CfdJ shows a remarkably low KM towards carbofuran. Together with the carbaryl hydrolase CehA of Rhizobium sp. strain AC100, CfdJ represents a new protein family with several uncharacterized bacterial members outside the proteobacteria. Although both enzymes differ by only four amino acids, CehA does not recognize carbofuran as a substrate whereas CfdJ also hydrolyzes carbaryl. None of the CfdJ amino acids that differ from CehA were shown to be silent regarding carbofuran hydrolytic activity but one particular amino acid substitution, i.e., L152 to F152, proved crucial. CfdJ is more efficient in degrading methylcarbamate pesticides with an aromatic side chain whereas CehA is more efficient in degrading the oxime carbamate nematicide oxamyl. The presence of common flanking sequences suggest that the cfdJ gene is located on a remnant of the mobile genetic element Tnceh carrying cehA. Our results suggest that these enzymes can be acquired through horizontal gene transfer and can evolve to degrade new carbamate substrates by limited amino acid substitutions. We demonstrate that a carbaryl hydrolase can gain the additional capacity to degrade carbofuran by a single nucleotide transversion.}, }
@article {pmid27311567, year = {2016}, author = {Yue, JX and Holland, ND and Holland, LZ and Deheyn, DD}, title = {The evolution of genes encoding for green fluorescent proteins: insights from cephalochordates (amphioxus).}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {28350}, pmid = {27311567}, issn = {2045-2322}, mesh = {Animals ; Cephalochordata/classification/*genetics ; Evolution, Molecular ; Female ; Green Fluorescent Proteins/*genetics ; Multigene Family ; Ovary/chemistry ; Phylogeny ; }, abstract = {Green Fluorescent Protein (GFP) was originally found in cnidarians, and later in copepods and cephalochordates (amphioxus) (Branchiostoma spp). Here, we looked for GFP-encoding genes in Asymmetron, an early-diverged cephalochordate lineage, and found two such genes closely related to some of the Branchiostoma GFPs. Dim fluorescence was found throughout the body in adults of Asymmetron lucayanum, and, as in Branchiostoma floridae, was especially intense in the ripe ovaries. Spectra of the fluorescence were similar between Asymmetron and Branchiostoma. Lineage-specific expansion of GFP-encoding genes in the genus Branchiostoma was observed, largely driven by tandem duplications. Despite such expansion, purifying selection has strongly shaped the evolution of GFP-encoding genes in cephalochordates, with apparent relaxation for highly duplicated clades. All cephalochordate GFP-encoding genes are quite different from those of copepods and cnidarians. Thus, the ancestral cephalochordates probably had GFP, but since GFP appears to be lacking in more early-diverged deuterostomes (echinoderms, hemichordates), it is uncertain whether the ancestral cephalochordates (i.e. the common ancestor of Asymmetron and Branchiostoma) acquired GFP by horizontal gene transfer (HGT) from copepods or cnidarians or inherited it from the common ancestor of copepods and deuterostomes, i.e. the ancestral bilaterians.}, }
@article {pmid27307274, year = {2016}, author = {Wybouw, N and Pauchet, Y and Heckel, DG and Van Leeuwen, T}, title = {Horizontal Gene Transfer Contributes to the Evolution of Arthropod Herbivory.}, journal = {Genome biology and evolution}, volume = {8}, number = {6}, pages = {1785-1801}, pmid = {27307274}, issn = {1759-6653}, mesh = {Animals ; Arthropods/*genetics/metabolism/physiology ; Biological Evolution ; Ecosystem ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Herbivory/*genetics/physiology ; Phylogeny ; Plants/genetics/*metabolism ; }, abstract = {Within animals, evolutionary transition toward herbivory is severely limited by the hostile characteristics of plants. Arthropods have nonetheless counteracted many nutritional and defensive barriers imposed by plants and are currently considered as the most successful animal herbivores in terrestrial ecosystems. We gather a body of evidence showing that genomes of various plant feeding insects and mites possess genes whose presence can only be explained by horizontal gene transfer (HGT). HGT is the asexual transmission of genetic information between reproductively isolated species. Although HGT is known to have great adaptive significance in prokaryotes, its impact on eukaryotic evolution remains obscure. Here, we show that laterally transferred genes into arthropods underpin many adaptations to phytophagy, including efficient assimilation and detoxification of plant produced metabolites. Horizontally acquired genes and the traits they encode often functionally diversify within arthropod recipients, enabling the colonization of more host plant species and organs. We demonstrate that HGT can drive metazoan evolution by uncovering its prominent role in the adaptations of arthropods to exploit plants.}, }
@article {pmid27305774, year = {2016}, author = {Sun, D and Qiu, J}, title = {[Advances in molecular mechanisms of adaptive immunity mediated by type I-E CRISPR/Cas system--A review].}, journal = {Wei sheng wu xue bao = Acta microbiologica Sinica}, volume = {56}, number = {1}, pages = {1-7}, pmid = {27305774}, issn = {0001-6209}, mesh = {Bacteria/genetics/*immunology ; *CRISPR-Cas Systems ; Clustered Regularly Interspaced Short Palindromic Repeats ; Gene Transfer, Horizontal ; }, abstract = {To better adapt to the environment, prokaryocyte can take up exogenous genes (from bacteriophages, plasmids or genomes of other species) through horizontal gene transfer. Accompanied by the acquisition of exogenous genes, prokaryocyte is challenged by the invasion of 'selfish genes'. Therefore, to protect against the risk of gene transfer, prokaryocyte needs to establish mechanisms for selectively taking up or degrading exogenous DNA. In recent years, researchers discovered an adaptive immunity, which is mediated by the small RNA guided DNA degradation, prevents the invasion of exogenous genes in prokaryocyte. During the immune process, partial DNA fragments are firstly integrated.to the clustered regularly interspaced short palindromic repeats (CRISPR) located within the genome DNA, and then the mature CRISPR RNA transcript and the CRISPR associated proteins (Cas) form a complex CRISPR/Cas for degrading exogenous DNA. In this review, we will first briefly describe the CRISPR/Cas systems and then mainly focus on the recent advances of the function mechanism and the regulation mechanism of the type I-E CRISPR/Cas system in Escherichia coli.}, }
@article {pmid27303749, year = {2016}, author = {Price, VJ and Huo, W and Sharifi, A and Palmer, KL}, title = {CRISPR-Cas and Restriction-Modification Act Additively against Conjugative Antibiotic Resistance Plasmid Transfer in Enterococcus faecalis.}, journal = {mSphere}, volume = {1}, number = {3}, pages = {}, pmid = {27303749}, issn = {2379-5042}, support = {K22 AI099088/AI/NIAID NIH HHS/United States ; R01 AI116610/AI/NIAID NIH HHS/United States ; }, abstract = {Enterococcus faecalis is an opportunistic pathogen and a leading cause of nosocomial infections. Conjugative pheromone-responsive plasmids are narrow-host-range mobile genetic elements (MGEs) that are rapid disseminators of antibiotic resistance in the faecalis species. Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas and restriction-modification confer acquired and innate immunity, respectively, against MGE acquisition in bacteria. Most multidrug-resistant E. faecalis isolates lack CRISPR-Cas and possess an orphan locus lacking cas genes, CRISPR2, that is of unknown function. Little is known about restriction-modification defense in E. faecalis. Here, we explore the hypothesis that multidrug-resistant E. faecalis strains are immunocompromised. We assessed MGE acquisition by E. faecalis T11, a strain closely related to the multidrug-resistant hospital isolate V583 but which lacks the ~620 kb of horizontally acquired genome content that characterizes V583. T11 possesses the E. faecalis CRISPR3-cas locus and a predicted restriction-modification system, neither of which occurs in V583. We demonstrate that CRISPR-Cas and restriction-modification together confer a 4-log reduction in acquisition of the pheromone-responsive plasmid pAM714 in biofilm matings. Additionally, we show that the orphan CRISPR2 locus is functional for genome defense against another pheromone-responsive plasmid, pCF10, only in the presence of cas9 derived from the E. faecalis CRISPR1-cas locus, which most multidrug-resistant E. faecalis isolates lack. Overall, our work demonstrated that the loss of only two loci led to a dramatic reduction in genome defense against a clinically relevant MGE, highlighting the critical importance of the E. faecalis accessory genome in modulating horizontal gene transfer. Our results rationalize the development of antimicrobial strategies that capitalize upon the immunocompromised status of multidrug-resistant E. faecalis. IMPORTANCE Enterococcus faecalis is a bacterium that normally inhabits the gastrointestinal tracts of humans and other animals. Although these bacteria are members of our native gut flora, they can cause life-threatening infections in hospitalized patients. Antibiotic resistance genes appear to be readily shared among high-risk E. faecalis strains, and multidrug resistance in these bacteria limits treatment options for infections. Here, we find that CRISPR-Cas and restriction-modification systems, which function as adaptive and innate immune systems in bacteria, significantly impact the spread of antibiotic resistance genes in E. faecalis populations. The loss of these systems in high-risk E. faecalis suggests that they are immunocompromised, a tradeoff that allows them to readily acquire new genes and adapt to new antibiotics.}, }
@article {pmid27303743, year = {2016}, author = {Stutzmann, S and Blokesch, M}, title = {Circulation of a Quorum-Sensing-Impaired Variant of Vibrio cholerae Strain C6706 Masks Important Phenotypes.}, journal = {mSphere}, volume = {1}, number = {3}, pages = {}, pmid = {27303743}, issn = {2379-5042}, abstract = {Vibrio cholerae, the causative agent of cholera, is a model organism for studying virulence regulation, biofilm formation, horizontal gene transfer, and the cell-to-cell communication known as quorum sensing (QS). As in any research field, discrepancies between data from diverse laboratories are sometimes observed for V. cholerae. Such discrepancies are often caused by the use of diverse patient or environmental isolates. In this study, we investigated the inability of a few laboratories to reproduce high levels of natural transformation, a mode of horizontal gene transfer that is specifically induced on chitinous surfaces. This irreproducibility was mostly related to one specific isolate of V. cholerae: the O1 El Tor C6706 strain. C6706 was previously described as QS proficient, an important prerequisite for the induction of natural competence for transformation. To elucidate the underlying problem, we collected seven isolates of the same C6706 strain from different research laboratories in North America and Europe and compared their phenotypes. Importantly, we observed a split response with respect to QS-related gene expression, including chitin-induced natural competence and type VI secretion (T6S). While approximately half of the strains behaved as reported for several other O1 El Tor pandemic isolates that are commonly studied in the laboratory, the other half were significantly impaired in QS-related expression patterns. This impairment was caused by a mutation in a QS-related gene (luxO). We conclude that the circulation of such QS-impaired wild-type strains is responsible for masking several important phenotypes of V. cholerae, including natural competence for transformation and T6S. IMPORTANCE Phenotypic diversity between laboratory-domesticated bacterial strains is a common problem and often results in the failed reproduction of published data. However, researchers rarely compare such strains to elucidate the underlying mutation(s). In this study, we tested one of the best-studied V. cholerae isolates, O1 El Tor strain C6706 (a patient isolate from Peru), with respect to two main phenotypes: natural competence for transformation and type VI secretion. We recently demonstrated that the two phenotypes are coregulated and specifically induced upon the growth of pandemic V. cholerae O1 El Tor strains on chitinous surfaces. We provide evidence that of seven C6706 strains collected from different laboratories, four were impaired in the tested phenotypes due to a mutation in a QS gene. Collectively, our data indicate that the circulation of such a mutated wild-type strain of C6706 might have had important consequences for QS-related data.}, }
@article {pmid27303717, year = {2016}, author = {Denapaite, D and Rieger, M and Köndgen, S and Brückner, R and Ochigava, I and Kappeler, P and Mätz-Rensing, K and Leendertz, F and Hakenbeck, R}, title = {Highly Variable Streptococcus oralis Strains Are Common among Viridans Streptococci Isolated from Primates.}, journal = {mSphere}, volume = {1}, number = {2}, pages = {}, pmid = {27303717}, issn = {2379-5042}, abstract = {Viridans streptococci were obtained from primates (great apes, rhesus monkeys, and ring-tailed lemurs) held in captivity, as well as from free-living animals (chimpanzees and lemurs) for whom contact with humans is highly restricted. Isolates represented a variety of viridans streptococci, including unknown species. Streptococcus oralis was frequently isolated from samples from great apes. Genotypic methods revealed that most of the strains clustered on separate lineages outside the main cluster of human S. oralis strains. This suggests that S. oralis is part of the commensal flora in higher primates and evolved prior to humans. Many genes described as virulence factors in Streptococcus pneumoniae were present also in other viridans streptococcal genomes. Unlike in S. pneumoniae, clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR-associated protein (Cas) gene clusters were common among viridans streptococci, and many S. oralis strains were type PI-2 (pilus islet 2) variants. S. oralis displayed a remarkable diversity of genes involved in the biosynthesis of peptidoglycan (penicillin-binding proteins and MurMN) and choline-containing teichoic acid. The small noncoding cia-dependent small RNAs (csRNAs) controlled by the response regulator CiaR might contribute to the genomic diversity, since we observed novel genomic islands between duplicated csRNAs, variably present in some isolates. All S. oralis genomes contained a β-N-acetyl-hexosaminidase gene absent in S. pneumoniae, which in contrast frequently harbors the neuraminidases NanB/C, which are absent in S. oralis. The identification of S. oralis-specific genes will help us to understand their adaptation to diverse habitats. IMPORTANCE Streptococcus pneumoniae is a rare example of a human-pathogenic bacterium among viridans streptococci, which consist of commensal symbionts, such as the close relatives Streptococcus mitis and S. oralis. We have shown that S. oralis can frequently be isolated from primates and a variety of other viridans streptococci as well. Genes and genomic islands which are known pneumococcal virulence factors are present in S. oralis and S. mitis, documenting the widespread occurrence of these compounds, which encode surface and secreted proteins. The frequent occurrence of CRISP-Cas gene clusters and a surprising variation of a set of small noncoding RNAs are factors to be considered in future research to further our understanding of mechanisms involved in the genomic diversity driven by horizontal gene transfer among viridans streptococci.}, }
@article {pmid27303384, year = {2016}, author = {Ullrich, SR and González, C and Poehlein, A and Tischler, JS and Daniel, R and Schlömann, M and Holmes, DS and Mühling, M}, title = {Gene Loss and Horizontal Gene Transfer Contributed to the Genome Evolution of the Extreme Acidophile "Ferrovum".}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {797}, pmid = {27303384}, issn = {1664-302X}, abstract = {Acid mine drainage (AMD), associated with active and abandoned mining sites, is a habitat for acidophilic microorganisms that gain energy from the oxidation of reduced sulfur compounds and ferrous iron and that thrive at pH below 4. Members of the recently proposed genus "Ferrovum" are the first acidophilic iron oxidizers to be described within the Betaproteobacteria. Although they have been detected as typical community members in AMD habitats worldwide, knowledge of their phylogenetic and metabolic diversity is scarce. Genomics approaches appear to be most promising in addressing this lacuna since isolation and cultivation of "Ferrovum" has proven to be extremely difficult and has so far only been successful for the designated type strain "Ferrovum myxofaciens" P3G. In this study, the genomes of two novel strains of "Ferrovum" (PN-J185 and Z-31) derived from water samples of a mine water treatment plant were sequenced. These genomes were compared with those of "Ferrovum" sp. JA12 that also originated from the mine water treatment plant, and of the type strain (P3G). Phylogenomic scrutiny suggests that the four strains represent three "Ferrovum" species that cluster in two groups (1 and 2). Comprehensive analysis of their predicted metabolic pathways revealed that these groups harbor characteristic metabolic profiles, notably with respect to motility, chemotaxis, nitrogen metabolism, biofilm formation and their potential strategies to cope with the acidic environment. For example, while the "F. myxofaciens" strains (group 1) appear to be motile and diazotrophic, the non-motile group 2 strains have the predicted potential to use a greater variety of fixed nitrogen sources. Furthermore, analysis of their genome synteny provides first insights into their genome evolution, suggesting that horizontal gene transfer and genome reduction in the group 2 strains by loss of genes encoding complete metabolic pathways or physiological features contributed to the observed diversification.}, }
@article {pmid27302758, year = {2016}, author = {Chénard, C and Wirth, JF and Suttle, CA}, title = {Viruses Infecting a Freshwater Filamentous Cyanobacterium (Nostoc sp.) Encode a Functional CRISPR Array and a Proteobacterial DNA Polymerase B.}, journal = {mBio}, volume = {7}, number = {3}, pages = {}, pmid = {27302758}, issn = {2150-7511}, mesh = {Bacteriophages/*enzymology/*genetics/isolation &amp; purification ; *Clustered Regularly Interspaced Short Palindromic Repeats ; DNA-Directed DNA Polymerase/*genetics ; Evolution, Molecular ; Fresh Water/microbiology ; Gene Transfer, Horizontal ; Nostoc/*virology ; Phylogeny ; Recombination, Genetic ; Sequence Homology ; Viral Proteins/*genetics ; }, abstract = {UNLABELLED: Here we present the first genomic characterization of viruses infecting Nostoc, a genus of ecologically important cyanobacteria that are widespread in freshwater. Cyanophages A-1 and N-1 were isolated in the 1970s and infect Nostoc sp. strain PCC 7210 but remained genomically uncharacterized. Their 68,304- and 64,960-bp genomes are strikingly different from those of other sequenced cyanophages. Many putative genes that code for proteins with known functions are similar to those found in filamentous cyanobacteria, showing a long evolutionary history in their host. Cyanophage N-1 encodes a CRISPR array that is transcribed during infection and is similar to the DR5 family of CRISPRs commonly found in cyanobacteria. The presence of a host-related CRISPR array in a cyanophage suggests that the phage can transfer the CRISPR among related cyanobacteria and thereby provide resistance to infection with competing phages. Both viruses also encode a distinct DNA polymerase B that is closely related to those found in plasmids of Cyanothece sp. strain PCC 7424, Nostoc sp. strain PCC 7120, and Anabaena variabilis ATCC 29413. These polymerases form a distinct evolutionary group that is more closely related to DNA polymerases of proteobacteria than to those of other viruses. This suggests that the polymerase was acquired from a proteobacterium by an ancestral virus and transferred to the cyanobacterial plasmid. Many other open reading frames are similar to a prophage-like element in the genome of Nostoc sp. strain PCC 7524. The Nostoc cyanophages reveal a history of gene transfers between filamentous cyanobacteria and their viruses that have helped to forge the evolutionary trajectory of this previously unrecognized group of phages.<br><br>IMPORTANCE: Filamentous cyanobacteria belonging to the genus Nostoc are widespread and ecologically important in freshwater, yet little is known about the genomic content of their viruses. Here we report the first genomic analysis of cyanophages infecting filamentous freshwater cyanobacteria, revealing that their gene content is unlike that of other cyanophages. In addition to sharing many gene homologues with freshwater cyanobacteria, cyanophage N-1 encodes a CRISPR array and expresses it upon infection. Also, both viruses contain a DNA polymerase B-encoding gene with high similarity to genes found in proteobacterial plasmids of filamentous cyanobacteria. The observation that phages can acquire CRISPRs from their hosts suggests that phages can also move them among hosts, thereby conferring resistance to competing phages. The presence in these cyanophages of CRISPR and DNA polymerase B sequences, as well as a suite of other host-related genes, illustrates the long and complex evolutionary history of these viruses and their hosts.}, }
@article {pmid27301340, year = {2016}, author = {Corbinais, C and Mathieu, A and Kortulewski, T and Radicella, JP and Marsin, S}, title = {Following transforming DNA in Helicobacter pylori from uptake to expression.}, journal = {Molecular microbiology}, volume = {101}, number = {6}, pages = {1039-1053}, doi = {10.1111/mmi.13440}, pmid = {27301340}, issn = {1365-2958}, mesh = {DNA, Bacterial/*genetics/metabolism ; Gene Expression ; Gene Transfer, Horizontal ; Helicobacter pylori/*genetics/metabolism ; Transformation, Bacterial/*genetics ; }, abstract = {Natural transformation is a potent driver for genetic diversification in bacterial populations. It involves exogenous DNA binding, uptake, transport and internalization into the cytoplasm, where DNA can be processed and integrated into the host chromosome. Direct visualisation of transforming DNA (tDNA) has been limited to its binding to the surface or, in the case of Gram-negative species, to its entrance into the periplasm. We present here for the first time the direct visualisation of tDNA entering the bacterial cytoplasm. We used as a model the Gram-negative pathogen Helicobacter pylori, characterised by a large intraspecies variability that results from high mutation rates and efficient horizontal gene transfer. Using fluorescently labelled DNA, we followed for up to 3 h the fate of tDNA foci formed in the periplasm and eventually internalised into the cytoplasm. By tracking at the single cell level the expression of a fluorescent protein coded by the tDNA, we show that up to 50% of the cells express the transforming phenotype. The overall transformation process in H. pylori, from tDNA uptake to expression of the recombinant gene, can take place in less than 1 h, without requiring a growth arrest, and prior to the replication of the chromosome.}, }
@article {pmid27294956, year = {2016}, author = {Gabriško, M and Barák, I}, title = {Evolution of the SpoIISABC Toxin-Antitoxin-Antitoxin System in Bacilli.}, journal = {Toxins}, volume = {8}, number = {6}, pages = {}, pmid = {27294956}, issn = {2072-6651}, mesh = {Amino Acid Sequence ; Antitoxins/genetics/*metabolism ; Bacillus/genetics/*metabolism ; Bacterial Proteins/genetics/*metabolism ; Bacterial Toxins/genetics/*metabolism ; Conserved Sequence ; *Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Phylogeny ; Sequence Alignment ; Sequence Homology, Amino Acid ; Species Specificity ; }, abstract = {Programmed cell death in bacteria is generally associated with two-component toxin-antitoxin systems. The SpoIISABC system, originally identified in Bacillus subtilis, consists of three components: a SpoIISA toxin and the SpoIISB and SpoIISC antitoxins. SpoIISA is a membrane-bound protein, while SpoIISB and SpoIISC are small cytosolic antitoxins, which are able to bind SpoIISA and neutralize its toxicity. In the presented bioinformatics analysis, a taxonomic distribution of the genes of the SpoIISABC system is investigated; their conserved regions and residues are identified; and their phylogenetic relationships are inferred. The SpoIISABC system is part of the core genome in members of the Bacillus genus of the Firmicutes phylum. Its presence in some non-bacillus species is likely the result of horizontal gene transfer. The SpoIISB and SpoIISC antitoxins originated by gene duplications, which occurred independently in the B. subtilis and B. cereus lineages. In the B. cereus lineage, the SpoIIS module is present in two different architectures.}, }
@article {pmid27293536, year = {2016}, author = {Lu, B and Leong, HW}, title = {Computational methods for predicting genomic islands in microbial genomes.}, journal = {Computational and structural biotechnology journal}, volume = {14}, number = {}, pages = {200-206}, pmid = {27293536}, issn = {2001-0370}, abstract = {Clusters of genes acquired by lateral gene transfer in microbial genomes, are broadly referred to as genomic islands (GIs). GIs often carry genes important for genome evolution and adaptation to niches, such as genes involved in pathogenesis and antibiotic resistance. Therefore, GI prediction has gradually become an important part of microbial genome analysis. Despite inherent difficulties in identifying GIs, many computational methods have been developed and show good performance. In this mini-review, we first summarize the general challenges in predicting GIs. Then we group existing GI detection methods by their input, briefly describe representative methods in each group, and discuss their advantages as well as limitations. Finally, we look into the potential improvements for better GI prediction.}, }
@article {pmid27289192, year = {2016}, author = {Wu, H and Wang, M and Liu, Y and Wang, X and Wang, Y and Lu, J and Xu, H}, title = {Characterization of antimicrobial resistance in Klebsiella species isolated from chicken broilers.}, journal = {International journal of food microbiology}, volume = {232}, number = {}, pages = {95-102}, doi = {10.1016/j.ijfoodmicro.2016.06.001}, pmid = {27289192}, issn = {1879-3460}, mesh = {Abattoirs ; Animals ; Anti-Bacterial Agents/*pharmacology ; Chickens/*microbiology ; China ; DNA Gyrase/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Humans ; Integrons/genetics ; Klebsiella pneumoniae/*classification/*drug effects/genetics/isolation &amp; purification ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Phylogeny ; Plasmids/genetics ; Poultry Diseases/*microbiology ; beta-Lactamases/*genetics ; }, abstract = {The prevalence of antimicrobial resistant Klebsiella pneumoniae in poultry products has been a public concern, as it severely endangers food safety and human health. In this study, we investigated 90 antimicrobial resistant Klebsiella strains that were isolated from a commercial broiler slaughter plant in Shandong province of China. Nearly all (89/90) of the isolates were identified as infectious phylogenetic group KpI-type K. pneumoniae. Out of these 90 strains, 87 (96.7%) were multidrug-resistant isolates, and 87 (96.7%) were extended-spectrum beta-lactamase (ESBL)-producing isolates. An analysis of the prevalence of quinolone resistance genes showed that 7.8%, 77.8%, 26.7%, and 2.2% of the strains carried the qnrA, qnrB, qnrS, and qepA genes, respectively. An analysis of beta-lactam resistance genes showed that a high percentage of the strains contain the blaTEM (76.7%), blaSHV (88.9%), and blaCTX-M (75.6%) genes, among which three blaSHV subtypes (blaSHV-1, n=30; blaSHV-11, n=38; blaSHV-12, n=12) and three blaCTX-M subtypes (blaCTX-M-14, n=14; blaCTX-M-15, n=35; blaCTX-M-55, n=19) were found. A further investigation of mobile genetic elements involved in horizontal multidrug resistance gene transfer showed the presence of class 1 and 2 integrons in 77 (85.6%) and five (5.6%) isolates, respectively, while no class 3 integrons were detected. Four types of class 1 integrons containing specific gene cassette arrays (dfrA12-orfF-aadA2, dfrA17-aadA5, dfrA1-aadA1, and empty) were identified. Only one gene cassette array (dfrA1-sat2-aadA1) was detected in the class 2 integrons. Furthermore, four different types of insertion sequence common region 1 (ISCR1)-mediated downstream structures were successfully identified in 46 class 1 integron-positive isolates, among which ISCR1-sapA-like-qnrB2-qacEΔ1 was the most commonly observed structure. Chi-square tests revealed a significant association between ESBL genes, plasmid-mediated quinolone resistance (PMQR) genes, and class 1 integrons (p<0.01). Additional conjugation experiments confirmed this relationship (p<0.01) in transconjugants by finding that a high percentage of PMQR genes (74.0%) and class 1 integrons (73.7%) were co-transferred with ESBL genes. Finally, multilocus sequence typing (MLST) was performed, and it revealed that the isolates from chickens are widely distributed in humans, and that antimicrobial resistance is not only disseminated by clonal spreading, but largely by horizontal gene transfer. These results suggest that horizontal transfer of antimicrobial resistance genes by mobile genetic elements, such as integrons, plays a major role in the spread of antimicrobial resistance. Therefore, elucidating the structures of drug resistance integrons is of great importance to the commercial broiler slaughter plant in Shandong, China.}, }
@article {pmid27289101, year = {2016}, author = {Faddeeva-Vakhrusheva, A and Derks, MF and Anvar, SY and Agamennone, V and Suring, W and Smit, S and van Straalen, NM and Roelofs, D}, title = {Gene Family Evolution Reflects Adaptation to Soil Environmental Stressors in the Genome of the Collembolan Orchesella cincta.}, journal = {Genome biology and evolution}, volume = {8}, number = {7}, pages = {2106-2117}, pmid = {27289101}, issn = {1759-6653}, mesh = {*Adaptation, Physiological ; Animals ; Arthropods/*genetics/physiology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Insect ; *Multigene Family ; Selection, Genetic ; Soil ; Stress, Physiological ; }, abstract = {Collembola (springtails) are detritivorous hexapods that inhabit the soil and its litter layer. The ecology of the springtail Orchesella cincta is extensively studied in the context of adaptation to anthropogenically disturbed areas. Here, we present a draft genome of an O. cincta reference strain with an estimated size of 286.8 Mbp, containing 20,249 genes. In total, 446 gene families are expanded and 1,169 gene families evolved specific to this lineage. Besides these gene families involved in general biological processes, we observe gene clusters participating in xenobiotic biotransformation. Furthermore, we identified 253 cases of horizontal gene transfer (HGT). Although the largest percentage of them originated from bacteria (37.5%), we observe an unusually high percentage (30.4%) of such genes of fungal origin. The majority of foreign genes are involved in carbohydrate metabolism and cellulose degradation. Moreover, some foreign genes (e.g., bacillopeptidases) expanded after HGT. We hypothesize that horizontally transferred genes could be advantageous for food processing in a soil environment that is full of decaying organic material. Finally, we identified several lineage-specific genes, expanded gene families, and horizontally transferred genes, associated with altered gene expression as a consequence of genetic adaptation to metal stress. This suggests that these genome features may be preadaptations allowing natural selection to act on. In conclusion, this genome study provides a solid foundation for further analysis of evolutionary mechanisms of adaptation to environmental stressors.}, }
@article {pmid27289093, year = {2016}, author = {Mustapha, MM and Marsh, JW and Krauland, MG and Fernandez, JO and de Lemos, AP and Dunning Hotopp, JC and Wang, X and Mayer, LW and Lawrence, JG and Hiller, NL and Harrison, LH}, title = {Genomic Investigation Reveals Highly Conserved, Mosaic, Recombination Events Associated with Capsular Switching among Invasive Neisseria meningitidis Serogroup W Sequence Type (ST)-11 Strains.}, journal = {Genome biology and evolution}, volume = {8}, number = {6}, pages = {2065-2075}, pmid = {27289093}, issn = {1759-6653}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Genome, Bacterial ; Genomics ; Humans ; Meningococcal Infections/*genetics/microbiology ; Multigene Family ; Neisseria meningitidis/*genetics/pathogenicity ; *Phylogeny ; *Recombination, Genetic ; Serogroup ; }, abstract = {Neisseria meningitidis is an important cause of meningococcal disease globally. Sequence type (ST)-11 clonal complex (cc11) is a hypervirulent meningococcal lineage historically associated with serogroup C capsule and is believed to have acquired the W capsule through a C to W capsular switching event. We studied the sequence of capsule gene cluster (cps) and adjoining genomic regions of 524 invasive W cc11 strains isolated globally. We identified recombination breakpoints corresponding to two distinct recombination events within W cc11: A 8.4-kb recombinant region likely acquired from W cc22 including the sialic acid/glycosyl-transferase gene, csw resulted in a C→W change in capsular phenotype and a 13.7-kb recombinant segment likely acquired from Y cc23 lineage includes 4.5 kb of cps genes and 8.2 kb downstream of the cps cluster resulting in allelic changes in capsule translocation genes. A vast majority of W cc11 strains (497/524, 94.8%) retain both recombination events as evidenced by sharing identical or very closely related capsular allelic profiles. These data suggest that the W cc11 capsular switch involved two separate recombination events and that current global W cc11 meningococcal disease is caused by strains bearing this mosaic capsular switch.}, }
@article {pmid27289092, year = {2016}, author = {Meyer, JM and Markov, GV and Baskaran, P and Herrmann, M and Sommer, RJ and Rödelsperger, C}, title = {Draft Genome of the Scarab Beetle Oryctes borbonicus on La Réunion Island.}, journal = {Genome biology and evolution}, volume = {8}, number = {7}, pages = {2093-2105}, pmid = {27289092}, issn = {1759-6653}, mesh = {Animals ; Coleoptera/classification/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Insect ; Phylogeny ; }, abstract = {Beetles represent the largest insect order and they display extreme morphological, ecological and behavioral diversity, which makes them ideal models for evolutionary studies. Here, we present the draft genome of the scarab beetle Oryctes borbonicus, which has a more basal phylogenetic position than the two previously sequenced pest species Tribolium castaneum and Dendroctonus ponderosae providing the potential for sequence polarization. Oryctes borbonicus is endemic to La Réunion, an island located in the Indian Ocean, and is the host of the nematode Pristionchus pacificus, a well-established model organism for integrative evolutionary biology. At 518 Mb, the O. borbonicus genome is substantially larger and encodes more genes than T. castaneum and D. ponderosae We found that only 25% of the predicted genes of O. borbonicus are conserved as single copy genes across the nine investigated insect genomes, suggesting substantial gene turnover within insects. Even within beetles, up to 21% of genes are restricted to only one species, whereas most other genes have undergone lineage-specific duplications and losses. We illustrate lineage-specific duplications using detailed phylogenetic analysis of two gene families. This study serves as a reference point for insect/coleopteran genomics, although its original motivation was to find evidence for potential horizontal gene transfer (HGT) between O. borbonicus and P. pacificus The latter was previously shown to be the recipient of multiple horizontally transferred genes including some genes from insect donors. However, our study failed to provide any clear evidence for additional HGTs between the two species.}, }
@article {pmid27286965, year = {2016}, author = {Eves-van den Akker, S and Laetsch, DR and Thorpe, P and Lilley, CJ and Danchin, EG and Da Rocha, M and Rancurel, C and Holroyd, NE and Cotton, JA and Szitenberg, A and Grenier, E and Montarry, J and Mimee, B and Duceppe, MO and Boyes, I and Marvin, JM and Jones, LM and Yusup, HB and Lafond-Lapalme, J and Esquibet, M and Sabeh, M and Rott, M and Overmars, H and Finkers-Tomczak, A and Smant, G and Koutsovoulos, G and Blok, V and Mantelin, S and Cock, PJ and Phillips, W and Henrissat, B and Urwin, PE and Blaxter, M and Jones, JT}, title = {The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence.}, journal = {Genome biology}, volume = {17}, number = {1}, pages = {124}, pmid = {27286965}, issn = {1474-760X}, support = {BB/G007071/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/F000642/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/F00334X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 098051/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Enhancer Elements, Genetic ; Gene Expression Profiling ; Gene Transfer, Horizontal ; *Genome, Protozoan ; Genomic Islands ; Genomics/methods ; High-Throughput Nucleotide Sequencing ; Life Cycle Stages ; Nucleotide Motifs ; Plant Diseases/*parasitology ; Position-Specific Scoring Matrices ; RNA Splice Sites ; RNA Splicing ; Solanum tuberosum/*parasitology ; Transcriptome ; Tylenchoidea/*genetics/growth &amp; development/*pathogenicity ; Virulence/genetics ; }, abstract = {BACKGROUND: The yellow potato cyst nematode, Globodera rostochiensis, is a devastating plant pathogen of global economic importance. This biotrophic parasite secretes effectors from pharyngeal glands, some of which were acquired by horizontal gene transfer, to manipulate host processes and promote parasitism. G. rostochiensis is classified into pathotypes with different plant resistance-breaking phenotypes.<br><br>RESULTS: We generate a high quality genome assembly for G. rostochiensis pathotype Ro1, identify putative effectors and horizontal gene transfer events, map gene expression through the life cycle focusing on key parasitic transitions and sequence the genomes of eight populations including four additional pathotypes to identify variation. Horizontal gene transfer contributes 3.5&#xa0;% of the predicted genes, of which approximately 8.5&#xa0;% are deployed as effectors. Over one-third of all effector genes are clustered in 21 putative 'effector islands' in the genome. We identify a dorsal gland promoter element motif (termed DOG Box) present upstream in representatives from 26 out of 28 dorsal gland effector families, and predict a putative effector superset associated with this motif. We validate gland cell expression in two novel genes by in situ hybridisation and catalogue dorsal gland promoter element-containing effectors from available cyst nematode genomes. Comparison of effector diversity between pathotypes highlights correlation with plant resistance-breaking.<br><br>CONCLUSIONS: These G. rostochiensis genome resources will facilitate major advances in understanding nematode plant-parasitism. Dorsal gland promoter element-containing effectors are at the front line of the evolutionary arms race between plant and parasite and the ability to predict gland cell expression a priori promises rapid advances in understanding their roles and mechanisms of action.}, }
@article {pmid27284988, year = {2016}, author = {Venditti, C and Villa, L and Capone, A and Fortini, D and D'Arezzo, S and Nisii, C and Bordi, E and Puro, V and Antonini, M and Carattoli, A and Cataldo, MA and Petrosillo, N and Di Caro, A}, title = {Isolation of KPC 3-producing Enterobacter aerogenes in a patient colonized by MDR Klebsiella pneumoniae.}, journal = {The new microbiologica}, volume = {39}, number = {4}, pages = {310-313}, pmid = {27284988}, issn = {1121-7138}, mesh = {Bacterial Proteins/*genetics ; Enterobacter aerogenes/*genetics ; Gene Transfer, Horizontal ; Humans ; Klebsiella pneumoniae/*genetics ; Male ; Plasmids ; beta-Lactamases/*genetics ; }, abstract = {We describe the interspecies transmission of the plasmid-mediated blaKPC-3 gene, which confers carbapenem resistance, between clinically relevant gram-negative bacteria in a single patient. A KPC-3 producing Enterobacter aerogenes was isolated from a hospitalized patient previously colonized and then infected by a Klebsiella pneumoniae ST101 carrying the blaKPC-3 gene. The strains showed identical plasmids. Since intense horizontal exchanges among bacteria can occur in the gut, clinicians should be aware that patients colonized by carbapenem-resistant K. pneumoniae could become carriers of other carbapenem-resistant Enterobacteriaceae.}, }
@article {pmid27282807, year = {2016}, author = {Aragão-Silva, CW and Andrade, MS and Ardisson-Araújo, DM and Fernandes, JE and Morgado, FS and Báo, SN and Moraes, RH and Wolff, JL and Melo, FL and Ribeiro, BM}, title = {The complete genome of a baculovirus isolated from an insect of medical interest: Lonomia obliqua (Lepidoptera: Saturniidae).}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {23127}, pmid = {27282807}, issn = {2045-2322}, mesh = {Animals ; Base Sequence ; DNA, Viral/chemistry/isolation &amp; purification/metabolism ; Gene Transfer, Horizontal ; *Genome, Viral ; Insect Proteins/classification/genetics ; Larva/metabolism/virology ; Moths/growth &amp; development/metabolism/*virology ; Nucleopolyhedroviruses/classification/*genetics/isolation &amp; purification ; Open Reading Frames/genetics ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Trans-Activators/classification/genetics ; Transcription Factors/classification/genetics ; }, abstract = {Lonomia obliqua (Lepidoptera: Saturniidae) is a species of medical importance due to the severity of reactions caused by accidental contact with the caterpillar bristles. Several natural pathogens have been identified in L. obliqua, and among them the baculovirus Lonomia obliqua multiple nucleopolyhedrovirus (LoobMNPV). The complete genome of LoobMNPV was sequenced and shown to have 120,022 bp long with 134 putative open reading frames (ORFs). Phylogenetic analysis of the LoobMNPV genome showed that it belongs to Alphabaculovirus group I (lepidopteran-infective NPV). A total of 12 unique ORFs were identified with no homologs in other sequenced baculovirus genomes. One of these, the predicted protein encoded by loob035, showed significant identity to an eukaryotic transcription terminator factor (TTF2) from the Lepidoptera Danaus plexippus, suggesting an independent acquisition through horizontal gene transfer. Homologs of cathepsin and chitinase genes, which are involved in host integument liquefaction and viral spread, were not found in this genome. As L. obliqua presents a gregarious behavior during the larvae stage the impact of this deletion might be neglectable.}, }
@article {pmid27282556, year = {2016}, author = {Orosz, F}, title = {Wider than Thought Phylogenetic Occurrence of Apicortin, A Characteristic Protein of Apicomplexan Parasites.}, journal = {Journal of molecular evolution}, volume = {82}, number = {6}, pages = {303-314}, pmid = {27282556}, issn = {1432-1432}, mesh = {Amino Acid Sequence ; Animals ; Apicomplexa/*genetics ; Databases, Nucleic Acid ; Parasites/genetics ; Phylogeny ; Proteins/genetics ; Sequence Alignment ; }, abstract = {Apicomplexan parasites cause serious illnesses, including malaria, in humans and domestic animals. The presence of apicortins is predominantly characteristic of this phylum. All the apicomplexan species sequenced contain an apicortin which unites two conserved domains: DCX and partial p25alpha. This paper identifies novel apicortin orthologs in silico and corrects in several cases the erroneous sequences of hypothetical apicortin proteins of Cryptosporidium, Eimeria, and Theileria genera published in databases. Plasmodium apicortins, except from Plasmodium gallinaceum, differ significantly from the other apicomplexan apicortins. The feature of this ortholog suggests that only orthologs of Plasmodiums hosted by mammals altered significantly. The free-living Chromerida, Chromera velia, and Vitrella brassicaformis, contain three paralogs. Their apicomplexan-type and nonapicomplexan-type apicortins might be "outparalogs." The fungal ortholog, Rozella allomycis, found at protein level, and the algal Nitella mirabilis, found as Transcriptome Shotgun Assembly (TSA), are similar to the known Opisthokont (Trichoplax adhaerens, Spizellomyces punctatus) and Viridiplantae (Nicotiana tabacum) ones, since they do not contain the long, unstructured N-terminal part present in apicomplexan apicortins. A few eumetazoan animals possess apicortin-like (partial) sequences at TSA level, which may be either contaminations or the result of horizontal gene transfer; in some cases the contamination has been proved.}, }
@article {pmid27279642, year = {2016}, author = {Gupta, RS}, title = {Impact of genomics on the understanding of microbial evolution and classification: the importance of Darwin's views on classification.}, journal = {FEMS microbiology reviews}, volume = {40}, number = {4}, pages = {520-553}, doi = {10.1093/femsre/fuw011}, pmid = {27279642}, issn = {1574-6976}, mesh = {Bacteria/*classification/genetics ; *Classification ; Genetic Markers/genetics ; Genetic Speciation ; Genome, Bacterial/genetics ; *Genomics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Analyses of genome sequences, by some approaches, suggest that the widespread occurrence of horizontal gene transfers (HGTs) in prokaryotes disguises their evolutionary relationships and have led to questioning of the Darwinian model of evolution for prokaryotes. These inferences are critically examined in the light of comparative genome analysis, characteristic synapomorphies, phylogenetic trees and Darwin's views on examining evolutionary relationships. Genome sequences are enabling discovery of numerous molecular markers (synapomorphies) such as conserved signature indels (CSIs) and conserved signature proteins (CSPs), which are distinctive characteristics of different prokaryotic taxa. Based on these molecular markers, exhibiting high degree of specificity and predictive ability, numerous prokaryotic taxa of different ranks, currently identified based on the 16S rRNA gene trees, can now be reliably demarcated in molecular terms. Within all studied groups, multiple CSIs and CSPs have been identified for successive nested clades providing reliable information regarding their hierarchical relationships and these inferences are not affected by HGTs. These results strongly support Darwin's views on evolution and classification and supplement the current phylogenetic framework based on 16S rRNA in important respects. The identified molecular markers provide important means for developing novel diagnostics, therapeutics and for functional studies providing important insights regarding prokaryotic taxa.}, }
@article {pmid27277956, year = {2016}, author = {Markov, AV and Kaznacheev, IS}, title = {Evolutionary consequences of polyploidy in prokaryotes and the origin of mitosis and meiosis.}, journal = {Biology direct}, volume = {11}, number = {}, pages = {28}, pmid = {27277956}, issn = {1745-6150}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Computer Simulation ; *Evolution, Molecular ; *Meiosis ; *Mitosis ; Models, Genetic ; *Polyploidy ; }, abstract = {BACKGROUND: The origin of eukaryote-specific traits such as mitosis and sexual reproduction remains disputable. There is growing evidence that both mitosis and eukaryotic sex (i.e., the alternation of syngamy and meiosis) may have already existed in the basal eukaryotes. The mating system of the halophilic archaeon Haloferax volcanii probably represents an intermediate stage between typical prokaryotic and eukaryotic sex. H. volcanii is highly polyploid, as well as many other Archaea. Here, we use computer simulation to explore genetic and evolutionary outcomes of polyploidy in amitotic prokaryotes and its possible role in the origin of mitosis, meiosis and eukaryotic sex.<br><br>RESULTS: Modeling suggests that polyploidy can confer strong short-term evolutionary advantage to amitotic prokaryotes. However, it also promotes the accumulation of recessive deleterious mutations and the risk of extinction in the long term, especially in highly mutagenic environment. There are several possible strategies that amitotic polyploids can use in order to reduce the genetic costs of polyploidy while retaining its benefits. Interestingly, most of these strategies resemble different components or aspects of eukaryotic sex. They include asexual ploidy cycles, equalization of genome copies by gene conversion, high-frequency lateral gene transfer between relatives, chromosome exchange coupled with homologous recombination, and the evolution of more accurate chromosome distribution during cell division (mitosis). Acquisition of mitosis by an amitotic polyploid results in chromosome diversification and specialization. Ultimately, it transforms a polyploid cell into a functionally monoploid one with multiple unique, highly redundant chromosomes. Specialization of chromosomes makes the previously evolved modes of promiscuous chromosome shuffling deleterious. This can result in selective pressure to develop accurate mechanisms of homolog pairing, and, ultimately, meiosis.<br><br>CONCLUSION: Emergence of mitosis and the first evolutionary steps towards eukaryotic sex could have taken place in the ancestral polyploid, amitotic proto-eukaryotes, as they were struggling to survive in the highly mutagenic environment of the Early Proterozoic shallow water microbial communities, through the succession of the following stages: (1) acquisition of high-frequency between-individual genetic exchange coupled with homologous recombination; (2) acquisition of mitosis, followed by rapid chromosome diversification and specialization; (3) evolution of homolog synapsis and meiosis. Additional evidence compatible with this scenario includes mass acquisition of new families of paralogous genes by the basal eukaryotes, and recently discovered correlation between polyploidy and the presence of histones in Archaea.<br><br>REVIEWER: This article was reviewed by Eugene Koonin, Uri Gophna and Armen Mulkidjanian. For the full reviews, please go to the Reviewers' comments section.}, }
@article {pmid27273536, year = {2016}, author = {Du, Q and Bi, G and Mao, Y and Sui, Z}, title = {The complete chloroplast genome of Gracilariopsis lemaneiformis (Rhodophyta) gives new insight into the evolution of family Gracilariaceae.}, journal = {Journal of phycology}, volume = {52}, number = {3}, pages = {441-450}, doi = {10.1111/jpy.12406}, pmid = {27273536}, issn = {1529-8817}, mesh = {Biological Evolution ; *Genome, Chloroplast ; High-Throughput Nucleotide Sequencing ; *Phylogeny ; Rhodophyta/*genetics ; Sequence Analysis, DNA ; }, abstract = {The complete chloroplast genome of Gracilariopsis lemaneiformis was recovered from a Next Generation Sequencing data set. Without quadripartite structure, this chloroplast genome (183,013 bp, 27.40% GC content) contains 202 protein-coding genes, 34 tRNA genes, 3 rRNA genes, and 1 tmRNA gene. Synteny analysis showed plasmid incorporation regions in chloroplast genomes of three species of family Gracilariaceae and in Grateloupia taiwanensis of family Halymeniaceae. Combined with reported red algal plasmid sequences in nuclear and mitochondrial genomes, we postulated that red algal plasmids may have played an important role in ancient horizontal gene transfer among nuclear, chloroplast, and mitochondrial genomes. Substitution rate analysis showed that purifying selective forces maintaining stability of protein-coding genes of nine red algal chloroplast genomes over long periods must be strong and that the forces acting on gene groups and single genes of nine red algal chloroplast genomes were similar and consistent. The divergence of Gp. lemaneiformis occurred ~447.98 million years ago (Mya), close to the divergence time of genus Pyropia and Porphyra (443.62 Mya).}, }
@article {pmid27270455, year = {2016}, author = {Dimitriu, T and Misevic, D and Lotton, C and Brown, SP and Lindner, AB and Taddei, F}, title = {Indirect Fitness Benefits Enable the Spread of Host Genes Promoting Costly Transfer of Beneficial Plasmids.}, journal = {PLoS biology}, volume = {14}, number = {6}, pages = {e1002478}, pmid = {27270455}, issn = {1545-7885}, mesh = {Algorithms ; Bacteria/*genetics ; Conjugation, Genetic ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Genetic Fitness ; Genetics, Population ; Interspersed Repetitive Sequences/genetics ; Models, Genetic ; Plasmids/genetics ; Selection, Genetic ; }, abstract = {Bacterial genes that confer crucial phenotypes, such as antibiotic resistance, can spread horizontally by residing on mobile genetic elements (MGEs). Although many mobile genes provide strong benefits to their hosts, the fitness consequences of the process of transfer itself are less clear. In previous studies, transfer has been interpreted as a parasitic trait of the MGEs because of its costs to the host but also as a trait benefiting host populations through the sharing of a common gene pool. Here, we show that costly donation is an altruistic act when it spreads beneficial MGEs favoured when it increases the inclusive fitness of donor ability alleles. We show mathematically that donor ability can be selected when relatedness at the locus modulating transfer is sufficiently high between donor and recipients, ensuring high frequency of transfer between cells sharing donor alleles. We further experimentally demonstrate that either population structure or discrimination in transfer can increase relatedness to a level selecting for chromosomal transfer alleles. Both mechanisms are likely to occur in natural environments. The simple process of strong dilution can create sufficient population structure to select for donor ability. Another mechanism observed in natural isolates, discrimination in transfer, can emerge through coselection of transfer and discrimination alleles. Our work shows that horizontal gene transfer in bacteria can be promoted by bacterial hosts themselves and not only by MGEs. In the longer term, the success of cells bearing beneficial MGEs combined with biased transfer leads to an association between high donor ability, discrimination, and mobile beneficial genes. However, in conditions that do not select for altruism, host bacteria promoting transfer are outcompeted by hosts with lower transfer rate, an aspect that could be relevant in the fight against the spread of antibiotic resistance.}, }
@article {pmid27270289, year = {2016}, author = {Hardiman, CA and Weingarten, RA and Conlan, S and Khil, P and Dekker, JP and Mathers, AJ and Sheppard, AE and Segre, JA and Frank, KM}, title = {Horizontal Transfer of Carbapenemase-Encoding Plasmids and Comparison with Hospital Epidemiology Data.}, journal = {Antimicrobial agents and chemotherapy}, volume = {60}, number = {8}, pages = {4910-4919}, pmid = {27270289}, issn = {1098-6596}, support = {G0800778/MRC_/Medical Research Council/United Kingdom ; 087646/Z/08/Z/WT_/Wellcome Trust/United Kingdom ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacterial Proteins/*genetics ; Cross Infection/genetics/microbiology ; Escherichia coli/genetics ; Escherichia coli Infections/genetics ; Gene Transfer, Horizontal/*genetics ; Hospitals ; Humans ; Klebsiella Infections/genetics/microbiology ; Klebsiella pneumoniae/genetics ; Multilocus Sequence Typing/methods ; Plasmids/*genetics ; beta-Lactamases/*genetics ; }, abstract = {Carbapenemase-producing organisms have spread worldwide, and infections with these bacteria cause significant morbidity. Horizontal transfer of plasmids carrying genes that encode carbapenemases plays an important role in the spread of multidrug-resistant Gram-negative bacteria. Here we investigate parameters regulating conjugation using an Escherichia coli laboratory strain that lacks plasmids or restriction enzyme modification systems as a recipient and also using patient isolates as donors and recipients. Because conjugation is tightly regulated, we performed a systematic analysis of the transfer of Klebsiella pneumoniae carbapenemase (blaKPC)-encoding plasmids into multiple strains under different environmental conditions to investigate critical variables. We used four blaKPC-carrying plasmids isolated from patient strains obtained from two hospitals: pKpQIL and pKPC-47e from the National Institutes of Health, and pKPC_UVA01 and pKPC_UVA02 from the University of Virginia. Plasmid transfer frequency differed substantially between different donor and recipient pairs, and the frequency was influenced by plasmid content, temperature, and substrate, in addition to donor and recipient strain. pKPC-47e was attenuated in conjugation efficiency across all conditions tested. Despite its presence in multiple clinical species, pKPC_UVA01 had lower conjugation efficiencies than pKpQIL into recipient strains. The conjugation frequency of these plasmids into K. pneumoniae and E. coli patient isolates ranged widely without a clear correlation with clinical epidemiological data. Our results highlight the importance of each variable examined in these controlled experiments. The in vitro models did not reliably predict plasmid mobilization observed in a patient population, indicating that further studies are needed to understand the most important variables affecting horizontal transfer in vivo.}, }
@article {pmid27270286, year = {2016}, author = {Traglia, GM and Quinn, B and Schramm, ST and Soler-Bistue, A and Ramirez, MS}, title = {Serum Albumin and Ca2+ Are Natural Competence Inducers in the Human Pathogen Acinetobacter baumannii.}, journal = {Antimicrobial agents and chemotherapy}, volume = {60}, number = {8}, pages = {4920-4929}, pmid = {27270286}, issn = {1098-6596}, mesh = {Acinetobacter Infections/*microbiology ; Acinetobacter baumannii/*drug effects/*genetics ; Calcium/*pharmacology ; Cross Infection/*microbiology ; DNA/genetics ; DNA Transformation Competence/*drug effects/genetics ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal/drug effects/genetics ; Genes, Bacterial/genetics ; Humans ; Serum Albumin/*pharmacology ; }, abstract = {The increasing frequency of bacteria showing antimicrobial resistance (AMR) raises the menace of entering into a postantibiotic era. Horizontal gene transfer (HGT) is one of the prime reasons for AMR acquisition. Acinetobacter baumannii is a nosocomial pathogen with outstanding abilities to survive in the hospital environment and to acquire resistance determinants. Its capacity to incorporate exogenous DNA is a major source of AMR genes; however, few studies have addressed this subject. The transformation machinery as well as the factors that induce natural competence in A. baumannii are unknown. In this study, we demonstrate that naturally competent strain A118 increases its natural transformation frequency upon the addition of Ca(2+)or albumin. We show that comEA and pilQ are involved in this process since their expression levels are increased upon the addition of these compounds. An unspecific protein, like casein, does not reproduce this effect, showing that albumin's effect is specific. Our work describes the first specific inducers of natural competence in A. baumannii Overall, our results suggest that the main protein in blood enhances HGT in A. baumannii, contributing to the increase of AMR in this threatening human pathogen.}, }
@article {pmid27270140, year = {2016}, author = {Chen, DS and Wu, YQ and Zhang, W and Jiang, SJ and Chen, SZ}, title = {Horizontal gene transfer events reshape the global landscape of arm race between viruses and homo sapiens.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {26934}, pmid = {27270140}, issn = {2045-2322}, mesh = {Amino Acid Sequence ; Chemokines/genetics ; Conserved Sequence ; *Evolution, Molecular ; Gene Ontology ; *Gene Transfer, Horizontal ; Genes, Viral ; Host-Pathogen Interactions ; Human Genetics ; Humans ; Phylogeny ; Receptors, Chemokine/genetics ; Viruses/*genetics ; }, abstract = {Horizontal gene transfer (HGT) drives the evolution of recipient organism particularly if it provides a novel function which enhances the fitness or its adaption to the environment. Virus-host co-evolution is attractive for studying co-evolutionary processes, since viruses strictly replicate inside of the host cells and thus their evolution is inexorably tangled with host biology. HGT, as a mechanism of co-evolution between human and viruses, has been widely documented, however, the roles HGT play during the interaction between human and viruses are still in their infancy. In this study, we performed a comprehensive analysis on the genes horizontally transferred between viruses and their corresponding human hosts. Our study suggests that the HGT genes in human are predominantly enriched in immune related GO terms while viral HGT genes are tend to be encoded by viruses which promote the invasion of immune system of hosts. Based on our results, it gives us a hint about the evolution trajectory of HGT events. Overall, our study suggests that the HGT between human and viruses are highly relevant to immune interaction and probably reshaped the arm race between hosts and viruses.}, }
@article {pmid27269511, year = {2016}, author = {De Meyer, SE and Briscoe, L and Martínez-Hidalgo, P and Agapakis, CM and de-Los Santos, PE and Seshadri, R and Reeve, W and Weinstock, G and O'Hara, G and Howieson, JG and Hirsch, AM}, title = {Symbiotic Burkholderia Species Show Diverse Arrangements of nif/fix and nod Genes and Lack Typical High-Affinity Cytochrome cbb3 Oxidase Genes.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {29}, number = {8}, pages = {609-619}, doi = {10.1094/MPMI-05-16-0091-R}, pmid = {27269511}, issn = {0894-0282}, support = {IOB-0537497//National Science Foundation/International ; IOS-1201735//National Science Foundation/International ; DE-AC02-05CH11231//US Department of Energy/International ; }, mesh = {Bacterial Proteins/*genetics ; Burkholderia/enzymology/*genetics/physiology ; Cupriavidus/enzymology/genetics/physiology ; Electron Transport Complex IV/genetics ; Gene Transfer, Horizontal ; Genome, Bacterial/*genetics ; Mimosa/*microbiology ; Nitrogen/metabolism ; Nitrogen Fixation ; Phylogeny ; Plant Root Nodulation/genetics ; RNA, Ribosomal, 16S/genetics ; Symbiosis/*genetics ; Transcription Factors/genetics ; }, abstract = {Genome analysis of fourteen mimosoid and four papilionoid beta-rhizobia together with fourteen reference alpha-rhizobia for both nodulation (nod) and nitrogen-fixing (nif/fix) genes has shown phylogenetic congruence between 16S rRNA/MLSA (combined 16S rRNA gene sequencing and multilocus sequence analysis) and nif/fix genes, indicating a free-living diazotrophic ancestry of the beta-rhizobia. However, deeper genomic analysis revealed a complex symbiosis acquisition history in the beta-rhizobia that clearly separates the mimosoid and papilionoid nodulating groups. Mimosoid-nodulating beta-rhizobia have nod genes tightly clustered in the nodBCIJHASU operon, whereas papilionoid-nodulating Burkholderia have nodUSDABC and nodIJ genes, although their arrangement is not canonical because the nod genes are subdivided by the insertion of nif and other genes. Furthermore, the papilionoid Burkholderia spp. contain duplications of several nod and nif genes. The Burkholderia nifHDKEN and fixABC genes are very closely related to those found in free-living diazotrophs. In contrast, nifA is highly divergent between both groups, but the papilionoid species nifA is more similar to alpha-rhizobia nifA than to other groups. Surprisingly, for all Burkholderia, the fixNOQP and fixGHIS genes required for cbb3 cytochrome oxidase production and assembly are missing. In contrast, symbiotic Cupriavidus strains have fixNOQPGHIS genes, revealing a divergence in the evolution of two distinct electron transport chains required for nitrogen fixation within the beta-rhizobia.}, }
@article {pmid27268252, year = {2016}, author = {Michael, AJ}, title = {Polyamines in Eukaryotes, Bacteria, and Archaea.}, journal = {The Journal of biological chemistry}, volume = {291}, number = {29}, pages = {14896-14903}, pmid = {27268252}, issn = {1083-351X}, mesh = {Archaea/*metabolism ; Bacteria/*metabolism ; Biosynthetic Pathways ; Eukaryota/*metabolism ; Gene Transfer, Horizontal/genetics ; Polyamines/*metabolism ; }, abstract = {Polyamines are primordial polycations found in most cells and perform different functions in different organisms. Although polyamines are mainly known for their essential roles in cell growth and proliferation, their functions range from a critical role in cellular translation in eukaryotes and archaea, to bacterial biofilm formation and specialized roles in natural product biosynthesis. At first glance, the diversity of polyamine structures in different organisms appears chaotic; however, biosynthetic flexibility and evolutionary and ecological processes largely explain this heterogeneity. In this review, I discuss the biosynthetic, evolutionary, and physiological processes that constrain or expand polyamine structural and functional diversity.}, }
@article {pmid27257491, year = {2016}, author = {Montaña, S and Cittadini, R and Del Castillo, M and Uong, S and Lazzaro, T and Almuzara, M and Barberis, C and Vay, C and Ramírez, MS}, title = {Presence of New Delhi metallo-β-lactamase gene (NDM-1) in a clinical isolate of Acinetobacter junii in Argentina.}, journal = {New microbes and new infections}, volume = {11}, number = {}, pages = {43-44}, pmid = {27257491}, issn = {2052-2975}, }
@article {pmid27254463, year = {2016}, author = {Wang, H and Li, Z and Jia, R and Hou, Y and Yin, J and Bian, X and Li, A and Müller, R and Stewart, AF and Fu, J and Zhang, Y}, title = {RecET direct cloning and Redαβ recombineering of biosynthetic gene clusters, large operons or single genes for heterologous expression.}, journal = {Nature protocols}, volume = {11}, number = {7}, pages = {1175-1190}, pmid = {27254463}, issn = {1750-2799}, mesh = {Bacteriophage lambda/*genetics ; Biosynthetic Pathways ; Cloning, Molecular/*methods ; Escherichia coli/*genetics ; Genetic Engineering/*methods ; Genetic Vectors/genetics ; Homologous Recombination ; Industrial Microbiology/methods ; *Multigene Family ; Operon ; Plasmids/genetics ; Prophages/*genetics ; Recombination, Genetic ; Transgenes ; Viral Proteins/*genetics ; }, abstract = {Full-length RecE and RecT from Rac prophage mediate highly efficient linear-linear homologous recombination that can be used to clone large DNA regions directly from genomic DNA into expression vectors, bypassing library construction and screening. Homologous recombination mediated by Redαβ from lambda phage has been widely used for recombinant DNA engineering. Here we present a protocol for direct cloning and engineering of biosynthetic gene clusters, large operons or single genes from genomic DNA using one Escherichia coli host that harbors both RecET and Redαβ systems. The pipeline uses standardized cassettes for horizontal gene transfer options, as well as vectors with different replication origins configured to minimize recombineering background through the use of selectively replicating templates or CcdB counterselection. These optimized reagents and protocols facilitate fast acquisition of transgenes from genomic DNA preparations, which are ready for heterologous expression within 1 week.}, }
@article {pmid27252683, year = {2016}, author = {Bezuidt, OK and Pierneef, R and Gomri, AM and Adesioye, F and Makhalanyane, TP and Kharroub, K and Cowan, DA}, title = {The Geobacillus Pan-Genome: Implications for the Evolution of the Genus.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {723}, pmid = {27252683}, issn = {1664-302X}, abstract = {The genus Geobacillus is comprised of a diverse group of spore-forming Gram-positive thermophilic bacterial species and is well known for both its ecological diversity and as a source of novel thermostable enzymes. Although the mechanisms underlying the thermophilicity of the organism and the thermostability of its macromolecules are reasonably well understood, relatively little is known of the evolutionary mechanisms, which underlie the structural and functional properties of members of this genus. In this study, we have compared 29 Geobacillus genomes, with a specific focus on the elements, which comprise the conserved core and flexible genomes. Based on comparisons of conserved core and flexible genomes, we present evidence of habitat delineation with specific Geobacillus genomes linked to specific niches. Our analysis revealed that Geobacillus and Anoxybacillus share a high proportion of genes. Moreover, the results strongly suggest that horizontal gene transfer is a major factor deriving the evolution of Geobacillus from Bacillus, with genetic contributions from other phylogenetically distant taxa.}, }
@article {pmid27252403, year = {2016}, author = {Dorman, CJ and Colgan, A and Dorman, MJ}, title = {Bacterial pathogen gene regulation: a DNA-structure-centred view of a protein-dominated domain.}, journal = {Clinical science (London, England : 1979)}, volume = {130}, number = {14}, pages = {1165-1177}, doi = {10.1042/CS20160024}, pmid = {27252403}, issn = {1470-8736}, mesh = {DNA, Bacterial/*chemistry ; DNA, Superhelical/chemistry ; DNA-Binding Proteins/*chemistry ; *Gene Expression Regulation, Bacterial ; *Protein Domains ; Virulence/genetics ; }, abstract = {The mechanisms used by bacterial pathogens to regulate the expression of their genes, especially their virulence genes, have been the subject of intense investigation for several decades. Whole genome sequencing projects, together with more targeted studies, have identified hundreds of DNA-binding proteins that contribute to the patterns of gene expression observed during infection as well as providing important insights into the nature of the gene products whose expression is being controlled by these proteins. Themes that have emerged include the importance of horizontal gene transfer to the evolution of pathogens, the need to impose regulatory discipline upon these imported genes and the important roles played by factors normally associated with the organization of genome architecture as regulatory principles in the control of virulence gene expression. Among these architectural elements is the structure of DNA itself, its variable nature at a topological rather than just at a base-sequence level and its ability to play an active (as well as a passive) part in the gene regulation process.}, }
@article {pmid27250633, year = {2016}, author = {Ghosh, B and Mukherjee, M}, title = {Emergence of co-production of plasmid-mediated AmpC beta-lactamase and ESBL in cefoxitin-resistant uropathogenic Escherichia coli.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {35}, number = {9}, pages = {1449-1454}, pmid = {27250633}, issn = {1435-4373}, mesh = {Anti-Bacterial Agents/*pharmacology ; Cefoxitin/*pharmacology ; Conjugation, Genetic ; Disk Diffusion Antimicrobial Tests ; Escherichia coli Infections/microbiology ; Gene Transfer, Horizontal ; Genetic Variation ; Genotype ; Humans ; India ; Molecular Typing ; Plasmids/analysis/classification ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Urinary Tract Infections/microbiology ; Uropathogenic Escherichia coli/*drug effects/*enzymology/genetics/isolation &amp; purification ; *beta-Lactam Resistance ; beta-Lactamases/genetics/*metabolism ; }, abstract = {Plasmid-mediated AmpC (pAmpC) and ESBL co-production was detected in Escherichia coli a major etiologic agent of urinary tract infection. Isolates resistant to cefoxitin by CLSI methodology were tested for pAmpC beta-lactamase using phenylboronic acid and ESBLs by combined disk diffusion method. pAmpC/ESBL genes were characterized by PCR and sequencing. Transconjugation experiments were done to study the transfer of pAmpC and ESBL production from clinical isolates as donor to E. coli J53 AziR as recipient. Incompatibility groups of transmissible plasmids were classified by PCR-based replicon typing (PBRT). Among 148 urine culture positive isolates, E. coli was reported in 39.86 % (59/148), with 93.22 % (55/59) of cefoxitin resistance. pAmpC production was detected in 25, with varied distribution of blaCMY-2 and blaDHA-1type genes alone (n = 13 and 7 respectively) or in combination (n = 5). ESBL co-production was observed in 88 % (22/25) of pAmpC producing isolates with predominance of blaTEM (n = 20). Twenty-three transconjugants showed transmission of pAmpC-and ESBL-resistant genes with co-carriage of blaCMY-2 and blaTEM (n = 15) in plasmids of IncF type (n = 9) being predominant, followed by IncI1 (n = 4) and IncH1 (n = 2) in combination. All clinical isolates were clonally diverse. Resistance against different beta-lactams in uropathogenic E. coli has been an emerging concern in resource- poor countries such as India. Knowledge on the occurrence of AmpC beta-lactamases and ESBL amongst this pathogen and its transmission dynamics may aid in hospital infection control.}, }
@article {pmid27249582, year = {2016}, author = {Andrey, DO and Posfay-Barbe, KM}, title = {Re-emergence of scarlet fever: old players return?.}, journal = {Expert review of anti-infective therapy}, volume = {14}, number = {8}, pages = {687-689}, doi = {10.1080/14787210.2016.1195684}, pmid = {27249582}, issn = {1744-8336}, mesh = {China/epidemiology ; Communicable Diseases, Emerging/*epidemiology/microbiology ; Disease Outbreaks ; Gene Transfer, Horizontal ; Genome, Bacterial/genetics ; Hong Kong/epidemiology ; Humans ; Interspersed Repetitive Sequences ; Scarlet Fever/*epidemiology/microbiology ; Streptococcus pyogenes/genetics ; United Kingdom/epidemiology ; Vietnam/epidemiology ; }, }
@article {pmid27247406, year = {2016}, author = {Delavat, F and Mitri, S and Pelet, S and van der Meer, JR}, title = {Highly variable individual donor cell fates characterize robust horizontal gene transfer of an integrative and conjugative element.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {24}, pages = {E3375-83}, pmid = {27247406}, issn = {1091-6490}, mesh = {Cell Division/*physiology ; Conjugation, Genetic/*physiology ; DNA, Bacterial/genetics/*metabolism ; Gene Transfer, Horizontal/*physiology ; *Models, Biological ; Pseudomonas putida/genetics/*metabolism ; }, abstract = {Horizontal gene transfer is an important evolutionary mechanism for bacterial adaptation. However, given the typical low transfer frequencies in a bacterial population, little is known about the fate and interplay of donor cells and the mobilized DNA during transfer. Here we study transfer of an integrative and conjugative element (ICE) among individual live bacterial cells. ICEs are widely distributed mobile DNA elements that are different than plasmids because they reside silent in the host chromosome and are maintained through vertical descent. Occasionally, ICEs become active, excise, and transmit their DNA to a new recipient, where it is reintegrated. We develop a fluorescent tool to differentiate excision, transfer, and reintegration of a model ICE named ICEclc (for carrying the clc genes for chlorocatechol metabolism) among single Pseudomonas cells by using time-lapse microscopy. We find that ICEclc activation is initiated in stationary phase cells, but excision and transfer predominantly occur only when such cells have been presented with new nutrients. Donors with activated ICE develop a number of different states, characterized by reduced cell division rates or growth arrest, persistence, or lysis, concomitant with ICE excision, and likely, ICE loss or replication. The donor cell state transitions can be described by using a stochastic model, which predicts that ICE fitness is optimal at low initiation rates in stationary phase. Despite highly variable donor cell fates, ICE transfer is remarkably robust overall, with 75% success after excision. Our results help to better understand ICE behavior and shed a new light on bacterial cellular differentiation during horizontal gene transfer.}, }
@article {pmid27247229, year = {2016}, author = {Beres, SB and Kachroo, P and Nasser, W and Olsen, RJ and Zhu, L and Flores, AR and de la Riva, I and Paez-Mayorga, J and Jimenez, FE and Cantu, C and Vuopio, J and Jalava, J and Kristinsson, KG and Gottfredsson, M and Corander, J and Fittipaldi, N and Di Luca, MC and Petrelli, D and Vitali, LA and Raiford, A and Jenkins, L and Musser, JM}, title = {Transcriptome Remodeling Contributes to Epidemic Disease Caused by the Human Pathogen Streptococcus pyogenes.}, journal = {mBio}, volume = {7}, number = {3}, pages = {}, pmid = {27247229}, issn = {2150-7511}, mesh = {Bacterial Proteins/*genetics ; *Epidemics/prevention &amp; control ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial ; Genotype ; *Host-Pathogen Interactions ; Humans ; Immune Evasion ; Polymorphism, Single Nucleotide ; Recombination, Genetic ; Streptococcal Infections/*epidemiology/*microbiology ; Streptococcus pyogenes/*genetics/immunology/pathogenicity ; *Transcriptome ; Virulence/genetics ; Virulence Factors/genetics ; }, abstract = {UNLABELLED: For over a century, a fundamental objective in infection biology research has been to understand the molecular processes contributing to the origin and perpetuation of epidemics. Divergent hypotheses have emerged concerning the extent to which environmental events or pathogen evolution dominates in these processes. Remarkably few studies bear on this important issue. Based on population pathogenomic analysis of 1,200 Streptococcus pyogenes type emm89 infection isolates, we report that a series of horizontal gene transfer events produced a new pathogenic genotype with increased ability to cause infection, leading to an epidemic wave of disease on at least two continents. In the aggregate, these and other genetic changes substantially remodeled the transcriptomes of the evolved progeny, causing extensive differential expression of virulence genes and altered pathogen-host interaction, including enhanced immune evasion. Our findings delineate the precise molecular genetic changes that occurred and enhance our understanding of the evolutionary processes that contribute to the emergence and persistence of epidemically successful pathogen clones. The data have significant implications for understanding bacterial epidemics and for translational research efforts to blunt their detrimental effects.<br><br>IMPORTANCE: The confluence of studies of molecular events underlying pathogen strain emergence, evolutionary genetic processes mediating altered virulence, and epidemics is in its infancy. Although understanding these events is necessary to develop new or improved strategies to protect health, surprisingly few studies have addressed this issue, in particular, at the comprehensive population genomic level. Herein we establish that substantial remodeling of the transcriptome of the human-specific pathogen Streptococcus pyogenes by horizontal gene flow and other evolutionary genetic changes is a central factor in precipitating and perpetuating epidemic disease. The data unambiguously show that the key outcome of these molecular events is evolution of a new, more virulent pathogenic genotype. Our findings provide new understanding of epidemic disease.}, }
@article {pmid27246235, year = {2016}, author = {Pham Thanh, D and Thanh Tuyen, H and Nguyen Thi Nguyen, T and Chung The, H and Wick, RR and Thwaites, GE and Baker, S and Holt, KE}, title = {Inducible colistin resistance via a disrupted plasmid-borne mcr-1 gene in a 2008 Vietnamese Shigella sonnei isolate.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {71}, number = {8}, pages = {2314-2317}, pmid = {27246235}, issn = {1460-2091}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Colistin/*pharmacology ; Conjugation, Genetic ; *Drug Resistance, Bacterial ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genome, Bacterial ; Humans ; *Plasmids ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Shigella sonnei/*drug effects/genetics/isolation &amp; purification ; Transcriptional Activation ; Vietnam ; }, abstract = {OBJECTIVES: The objective of this study was to assess the presence of mcr-1 in Shigella sonnei isolated in Vietnam.<br><br>METHODS: WGS data were analysed for the presence of the mcr-1 gene sequence. The association of mcr-1 with a plasmid was assessed by PCR and by conjugation.<br><br>RESULTS: Through genome sequencing we identified a plasmid-associated inactive form of mcr-1 in a 2008 Vietnamese isolate of Shigella sonnei. The plasmid was conjugated into Escherichia coli and mcr-1 was activated upon exposure to colistin, resulting in highly colistin-resistant transconjugants.<br><br>CONCLUSIONS: This is the first description of the mcr-1 gene in Shigella, which is atypical given that colistin is not ordinarily used to treat diarrhoea. Our data suggest the mcr-1 gene has been circulating in human-restricted pathogens for some time but likely carries a selective fitness cost.}, }
@article {pmid27246231, year = {2016}, author = {Sóki, J and Hedberg, M and Patrick, S and Bálint, B and Herczeg, R and Nagy, I and Hecht, DW and Nagy, E and Urbán, E}, title = {Emergence and evolution of an international cluster of MDR Bacteroides fragilis isolates.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {71}, number = {9}, pages = {2441-2448}, doi = {10.1093/jac/dkw175}, pmid = {27246231}, issn = {1460-2091}, mesh = {Bacteroides Infections/epidemiology/*microbiology ; Bacteroides fragilis/*classification/*drug effects/genetics/isolation &amp; purification ; Cluster Analysis ; Conjugation, Genetic ; DNA Transposable Elements ; Disk Diffusion Antimicrobial Tests ; *Drug Resistance, Multiple, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Gene Order ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; *Genotype ; Global Health ; High-Throughput Nucleotide Sequencing ; Humans ; Molecular Typing ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {OBJECTIVES: The aim of this study was to examine the antibiotic resistance profiles, antibiotic resistance mechanisms and possible 'clonal' nature of some MDR Bacteroides fragilis strains that simultaneously harboured cfiA, nimB, IS1186 and IS4351.<br><br>METHODS: Antibiotic susceptibilities were determined by Etests and antibiotic resistance genes and different genetic elements were detected by applying PCR methods. The environments of the cfiA and nimB genes were also determined by sequencing. The transferability of the cfiA, nimB and tet(Q) genes was tested by conjugation. The genetic relatedness of the test strains was tested by ERIC-PCR or PFGE. The complete genome sequences of two strains (B. fragilis BF8 and O:21) were determined by next-generation sequencing.<br><br>RESULTS: Most of the seven B. fragilis strains tested displayed multidrug resistance phenotypes; five strains were resistant to at least five types of antibiotics. Besides the common genetic constitution, ERIC-PCR implied high genetic relatedness. Similarities in some of the antibiotic resistance mechanisms [carbapenems (cfiA) and metronidazole (nimB)] also confirmed their common origin, but some other resistance mechanisms {MLSB [erm(F)] and tetracycline [tet(Q)]} and PFGE typing revealed differences. In B. fragilis BF8 and O:21, erm(F) and tet(X) genes were found with IS4351 borders, thus constituting Tn4351. All the strains were tet(Q) positive and transferred this gene in conjugation experiments, but not the cfiA and nimB genes.<br><br>CONCLUSIONS: An international cluster of MDR B. fragilis strains has been identified and characterized. This 'clone' may have emerged early in the evolution of division II B. fragilis strains, which was suggested by the low-complexity ERIC profiles and differences in the PFGE patterns.}, }
@article {pmid27242152, year = {2016}, author = {Kim, JN}, title = {Roles of two RyhB paralogs in the physiology of Salmonella enterica.}, journal = {Microbiological research}, volume = {186-187}, number = {}, pages = {146-152}, doi = {10.1016/j.micres.2016.04.004}, pmid = {27242152}, issn = {1618-0623}, mesh = {*Gene Expression Regulation, Bacterial ; RNA, Bacterial/*metabolism ; RNA, Small Untranslated/*metabolism ; Salmonella enterica/*genetics/*physiology ; *Stress, Physiological ; Virulence Factors/*biosynthesis ; }, abstract = {Salmonella has evolved complicated regulatory systems to regulate the expression of virulence determinants that are acquired by horizontal gene transfer in response to various environmental niches. Among these, small RNA (sRNA)-mediated regulation exhibits unique features, distinct from those of protein factor-mediated regulation, which may provide benefits for a pathogen coping with the complex stress conditions encountered during host infection. Specifically, iron acquisition by this pathogenic bacterium is important for cellular processes such as energy metabolism and DNA replication. Many studies on the role of RyhB sRNA have begun to unveil the essential nature of iron acquisition in allowing the organism to persist and develop pathogenicity. The Salmonella genome encodes two RyhB paralogs, RyhB-1 and RyhB-2, which are known to act singularly or together on target expression. Based on the mechanism of Escherichia coli RyhB function, this review proposes a possible model to show how two Salmonella RyhB paralogs regulate the level of target mRNAs by sensing environmental inputs or conditions. This review also describes the involvement of Salmonella RyhBs in diverse functions including nitrate homeostasis, adaptive system to oxidative stress, and intracellular survival. Thus, the two Salmonella RyhBs play a critical role in the regulation of gene expression that appears to be essential for persistence and pathogenesis of Salmonella spp.}, }
@article {pmid27242148, year = {2016}, author = {Nowicka, B and Kruk, J}, title = {Powered by light: Phototrophy and photosynthesis in prokaryotes and its evolution.}, journal = {Microbiological research}, volume = {186-187}, number = {}, pages = {99-118}, doi = {10.1016/j.micres.2016.04.001}, pmid = {27242148}, issn = {1618-0623}, mesh = {Bacteria/genetics/*metabolism ; *Biological Evolution ; Carbon Dioxide/metabolism ; *Light ; Oxygen/metabolism ; *Photosynthesis ; *Phototrophic Processes ; }, abstract = {Photosynthesis is a complex metabolic process enabling photosynthetic organisms to use solar energy for the reduction of carbon dioxide into biomass. This ancient pathway has revolutionized life on Earth. The most important event was the development of oxygenic photosynthesis. It had a tremendous impact on the Earth's geochemistry and the evolution of living beings, as the rise of atmospheric molecular oxygen enabled the development of a highly efficient aerobic metabolism, which later led to the evolution of complex multicellular organisms. The mechanism of photosynthesis has been the subject of intensive research and a great body of data has been accumulated. However, the evolution of this process is not fully understood, and the development of photosynthesis in prokaryota in particular remains an unresolved question. This review is devoted to the occurrence and main features of phototrophy and photosynthesis in prokaryotes. Hypotheses concerning the origin and spread of photosynthetic traits in bacteria are also discussed.}, }
@article {pmid27239333, year = {2016}, author = {Romero, M and Cerritos, R and Ximenez, C}, title = {Horizontal Gene Transfers from Bacteria to Entamoeba Complex: A Strategy for Dating Events along Species Divergence.}, journal = {Journal of parasitology research}, volume = {2016}, number = {}, pages = {3241027}, pmid = {27239333}, issn = {2090-0023}, abstract = {Horizontal gene transfer has proved to be relevant in eukaryotic evolution, as it has been found more often than expected and related to adaptation to certain niches. A relatively large list of laterally transferred genes has been proposed and evaluated for the parasite Entamoeba histolytica. The goals of this work were to elucidate the importance of lateral gene transfer along the evolutionary history of some members of the genus Entamoeba, through identifying donor groups and estimating the divergence time of some of these events. In order to estimate the divergence time of some of the horizontal gene transfer events, the dating of some Entamoeba species was necessary, following an indirect dating strategy based on the fossil record of plausible hosts. The divergence between E. histolytica and E. nuttallii probably occurred 5.93 million years ago (Mya); this lineage diverged from E. dispar 9.97 Mya, while the ancestor of the latter separated from E. invadens 68.18 Mya. We estimated times for 22 transferences; the most recent occurred 31.45 Mya and the oldest 253.59 Mya. Indeed, the acquisition of genes through lateral transfer may have triggered a period of adaptive radiation, thus playing a major role in the evolution of the Entamoeba genus.}, }
@article {pmid27234675, year = {2016}, author = {Rhouma, M and Beaudry, F and Letellier, A}, title = {Resistance to colistin: what is the fate for this antibiotic in pig production?.}, journal = {International journal of antimicrobial agents}, volume = {48}, number = {2}, pages = {119-126}, doi = {10.1016/j.ijantimicag.2016.04.008}, pmid = {27234675}, issn = {1872-7913}, mesh = {Animal Husbandry/*methods ; Animals ; Anti-Bacterial Agents/*administration &amp; dosage/pharmacokinetics ; Biological Evolution ; Colistin/*administration &amp; dosage/pharmacokinetics ; *Drug Resistance, Bacterial ; Enterobacteriaceae/*drug effects ; Enterobacteriaceae Infections/*drug therapy/*veterinary ; Gene Transfer, Horizontal ; Humans ; Selection, Genetic ; Swine ; }, abstract = {Colistin, a cationic polypeptide antibiotic, has reappeared in human medicine as a last-line treatment option for multidrug-resistant Gram-negative bacteria (MDR-GNB). Colistin is widely used in veterinary medicine for the treatment of gastrointestinal infections caused by Enterobacteriaceae. GNB resistant to colistin owing to chromosomal mutations have already been reported both in human and veterinary medicine, however several recent studies have just identified a plasmid-mediated mcr-1 gene encoding for colistin resistance in Escherichia coli colistin resistance. The discovery of a non-chromosomal mechanism of colistin resistance in E. coli has led to strong reactions in the scientific community and to concern among physicians and veterinarians. Colistin use in food animals and particularly in pig production has been singled out as responsible for the emergence of colistin resistance. The present review will focus mainly on the possible link between colistin use in pigs and the spread of colistin resistance in Enterobacteriaceae. First we demonstrate a possible link between Enterobacteriaceae resistance emergence and oral colistin pharmacokinetics/pharmacodynamics and its administration modalities in pigs. We then discuss the potential impact of colistin use in pigs on public health with respect to resistance. We believe that colistin use in pig production should be re-evaluated and its dosing and usage optimised. Moreover, the search for competitive alternatives to using colistin with swine is of paramount importance to preserve the effectiveness of this antibiotic for the treatment of MDR-GNB infections in human medicine.}, }
@article {pmid27234293, year = {2016}, author = {Panaud, O}, title = {Horizontal transfers of transposable elements in eukaryotes: The flying genes.}, journal = {Comptes rendus biologies}, volume = {339}, number = {7-8}, pages = {296-299}, doi = {10.1016/j.crvi.2016.04.013}, pmid = {27234293}, issn = {1768-3238}, mesh = {Animals ; DNA Transposable Elements/*genetics ; Eukaryota/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genomics ; Parasites/genetics ; }, abstract = {Transposable elements (TEs) are the major components of eukaryotic genomes. Their propensity to densely populate and in some cases invade the genomes of plants and animals is in contradiction with the fact that transposition is strictly controlled by several molecular pathways acting at either transcriptional or post-transcriptional levels. Horizontal transfers, defined as the transmission of genetic material between sexually isolated species, have long been considered as rare phenomena. Here, we show that the horizontal transfers of transposable elements (HTTs) are very frequent in ecosystems. The exact mechanisms of such transfers are not well understood, but species involved in close biotic interactions, like parasitism, show a propensity to exchange genetic material horizontally. We propose that HTTs allow TEs to escape the silencing machinery of their host genome and may therefore be an important mechanism for their survival and their dissemination in eukaryotes.}, }
@article {pmid27233666, year = {2016}, author = {Ahmed, MZ and Breinholt, JW and Kawahara, AY}, title = {Evidence for common horizontal transmission of Wolbachia among butterflies and moths.}, journal = {BMC evolutionary biology}, volume = {16}, number = {1}, pages = {118}, pmid = {27233666}, issn = {1471-2148}, mesh = {Animals ; Biodiversity ; Butterflies/*microbiology ; Gene Regulatory Networks ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Geography ; Likelihood Functions ; Moths/*microbiology ; Phylogeny ; Wolbachia/genetics/*physiology ; }, abstract = {BACKGROUND: Wolbachia is one of the most widespread bacteria on Earth. Previous research on Wolbachia-host interactions indicates that the bacterium is typically transferred vertically, from mother to offspring, through the egg cytoplasm. Although horizontal transmission of Wolbachia from one species to another is reported to be common in arthropods, limited direct ecological evidence is available. In this study, we examine horizontal transmission of Wolbachia using a multilocus sequence typing (MLST) strains dataset and used Wolbachia and Lepidoptera genomes to search for evidence for lateral gene transfer (LGT) in Lepidoptera, one of the most diverse cosmopolitan insect orders. We constructed a phylogeny of arthropod-associated MLST Wolbachia strains and calibrated the age of Wolbachia strains associated with lepidopteran species.<br><br>RESULTS: Our results reveal inter-specific, inter-generic, inter-familial, and inter-ordinal horizontal transmission of Wolbachia strains, without discernible geographic patterns. We found at least seven probable cases of horizontal transmission among 31 species within Lepidoptera and between Lepidoptera and other arthropod hosts. The divergence time analysis revealed that Wolbachia is recently (22.6-4.7 mya, 95&#xa0;% HPD) introduced in Lepidoptera. Analysis of nine Lepidoptera genomes (Bombyx mori, Danaus plexippus, Heliconius melpomene, Manduca sexta, Melitaea cinxia, Papilio glaucus, P. polytes, P. xuthus and Plutella xylostella) yielded one possible instance of Wolbachia LGT.<br><br>CONCLUSIONS: Our results provide evidence of high incidence of identical and multiple strains of Wolbachia among butterflies and moths, adding Lepidoptera to the growing body of evidence for common horizontal transmission of Wolbachia. This study demonstrates interesting dynamics of this remarkable and influential microorganism.}, }
@article {pmid27232957, year = {2016}, author = {Aggarwal, N and Bandhu, AV and Sengupta, S}, title = {Finite population analysis of the effect of horizontal gene transfer on the origin of an universal and optimal genetic code.}, journal = {Physical biology}, volume = {13}, number = {3}, pages = {036007}, doi = {10.1088/1478-3975/13/3/036007}, pmid = {27232957}, issn = {1478-3975}, mesh = {Amino Acids/*genetics ; Gene Transfer, Horizontal/*genetics ; Genetic Code/*genetics ; }, abstract = {The origin of a universal and optimal genetic code remains a compelling mystery in molecular biology and marks an essential step in the origin of DNA and protein based life. We examine a collective evolution model of genetic code origin that allows for unconstrained horizontal transfer of genetic elements within a finite population of sequences each of which is associated with a genetic code selected from a pool of primordial codes. We find that when horizontal transfer of genetic elements is incorporated in this more realistic model of code-sequence coevolution in a finite population, it can increase the likelihood of emergence of a more optimal code eventually leading to its universality through fixation in the population. The establishment of such an optimal code depends on the probability of HGT events. Only when the probability of HGT events is above a critical threshold, we find that the ten amino acid code having a structure that is most consistent with the standard genetic code (SGC) often gets fixed in the population with the highest probability. We examine how the threshold is determined by factors like the population size, length of the sequences and selection coefficient. Our simulation results reveal the conditions under which sharing of coding innovations through horizontal transfer of genetic elements may have facilitated the emergence of a universal code having a structure similar to that of the SGC.}, }
@article {pmid27232692, year = {2016}, author = {Fröhlich, KS and Papenfort, K}, title = {Interplay of regulatory RNAs and mobile genetic elements in enteric pathogens.}, journal = {Molecular microbiology}, volume = {101}, number = {5}, pages = {701-713}, doi = {10.1111/mmi.13428}, pmid = {27232692}, issn = {1365-2958}, mesh = {Enterobacteriaceae/*genetics ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences ; RNA, Bacterial/metabolism ; RNA, Small Cytoplasmic/genetics ; *Regulatory Sequences, Ribonucleic Acid ; }, abstract = {Horizontal transfer of genetic information is a major driving force of evolution. In bacteria, genome plasticity is intimately linked to the ability of the bacterium to integrate novel material into existing gene expression circuits. Small RNAs (sRNAs) are a versatile class of regulatory molecules, and have recently been discovered to perform important tasks in the interplay between core genomic elements and horizontally-acquired DNA. Together with auxiliary proteins such as the RNA-chaperone Hfq and cellular ribonucleases, sRNAs typically act post-transcriptionally to either promote or restrict the expression of multiple target genes. Bacterial sRNAs have been identified in core and peripheral (acquired) genome sequences, and their target suites may likewise include genes from both locations. In this review, we discuss how sRNAs influence the expression of foreign genetic material in enterobacterial pathogens, and outline the processes that foster the integration of horizontally-acquired RNAs into existing regulatory networks. We also consider potential benefits and risks of horizontal gene transfer for RNA-based gene regulation.}, }
@article {pmid27232438, year = {2016}, author = {Li, L and Ye, L and Yu, L and Zhou, C and Meng, H}, title = {Characterization of Extended Spectrum Β-Lactamase Producing Enterobacteria and Methicillin-Resistant Staphylococcus aureus Isolated from Raw Pork and Cooked Pork Products in South China.}, journal = {Journal of food science}, volume = {81}, number = {7}, pages = {M1773-7}, doi = {10.1111/1750-3841.13346}, pmid = {27232438}, issn = {1750-3841}, mesh = {Animals ; China ; Cooking ; Drug Resistance ; Enterobacteriaceae/genetics/isolation &amp; purification/metabolism ; Escherichia coli/*genetics/metabolism ; Food Handling ; *Food Microbiology ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Livestock ; Meat/microbiology ; Methicillin/pharmacology ; Methicillin-Resistant Staphylococcus aureus/*genetics/isolation &amp; purification/metabolism ; Multilocus Sequence Typing ; Red Meat/*microbiology ; Swine ; beta-Lactamases/*genetics/metabolism ; }, abstract = {In this study, we assessed the co-colonization with extended spectrum β-lactamase producing Enterobacteria (ESBL-E) and methicillin-resistant Staphylococcus aureus (MRSA) in raw pork and cooked pork products in south China. In total, 240 raw pork and 240 cooked pork samples collected from supermarkets (n = 20) and local butcher shops (n = 20) in the city of Guangzhou (China) were investigated. Raw pork and cooked pork was more frequent colonization with ESBL-E (7.5% in raw pork and 0.4% in cooked pork products) than with MRSA (4.2% in raw pork). Two of samples were contaminated with both tested types of multidrug-resistant bacteria. High antibiotic-resistance rate with wide spectrums of both ESBL-E and MRSA isolated were observed. In ESBL-E isolates, TEM (n = 15), CTX-M-1 (n = 3), CTX-M-9 (n = 1), and SHV (n = 1) genes were detected. TEM and SHV genes were associated with CTX-M-1 in 2 isolates, respectively. The CTX-M-9 gene of 1 isolate from cooked pork samples was found to be transferred to Escherichia coli J53 by conjugation. Detected MLST-types of MRSA were livestock-associated ST7 (n = 5) and ST9 (n = 4), as well as hospital-acquired ST239 (n = 1), suggesting contamination from human source(s) during meat processing. These findings confirmed a contamination of raw pork and cooked pork with ESBL-E and MRSA and emphasized the necessity of enforcing hygienic practices and specific detection of MRSA and ESBL-producing bacteria in meat processing and storage.}, }
@article {pmid27231649, year = {2016}, author = {Trubl, G and Solonenko, N and Chittick, L and Solonenko, SA and Rich, VI and Sullivan, MB}, title = {Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient.}, journal = {PeerJ}, volume = {4}, number = {}, pages = {e1999}, pmid = {27231649}, issn = {2167-8359}, abstract = {Permafrost stores approximately 50% of global soil carbon (C) in a frozen form; it is thawing rapidly under climate change, and little is known about viral communities in these soils or their roles in C cycling. In permafrost soils, microorganisms contribute significantly to C cycling, and characterizing them has recently been shown to improve prediction of ecosystem function. In other ecosystems, viruses have broad ecosystem and community impacts ranging from host cell mortality and organic matter cycling to horizontal gene transfer and reprogramming of core microbial metabolisms. Here we developed an optimized protocol to extract viruses from three types of high organic-matter peatland soils across a permafrost thaw gradient (palsa, moss-dominated bog, and sedge-dominated fen). Three separate experiments were used to evaluate the impact of chemical buffers, physical dispersion, storage conditions, and concentration and purification methods on viral yields. The most successful protocol, amended potassium citrate buffer with bead-beating or vortexing and BSA, yielded on average as much as 2-fold more virus-like particles (VLPs) g(-1) of soil than other methods tested. All method combinations yielded VLPs g(-1) of soil on the 10(8) order of magnitude across all three soil types. The different storage and concentration methods did not yield significantly more VLPs g(-1) of soil among the soil types. This research provides much-needed guidelines for resuspending viruses from soils, specifically carbon-rich soils, paving the way for incorporating viruses into soil ecology studies.}, }
@article {pmid27230650, year = {2016}, author = {Rodríguez-Blanco, A and Lemos, ML and Osorio, CR}, title = {Unveiling the pan-genome of the SXT/R391 family of ICEs: molecular characterisation of new variable regions of SXT/R391-like ICEs detected in Pseudoalteromonas sp. and Vibrio scophthalmi.}, journal = {Antonie van Leeuwenhoek}, volume = {109}, number = {8}, pages = {1141-1152}, doi = {10.1007/s10482-016-0716-3}, pmid = {27230650}, issn = {1572-9699}, mesh = {Animals ; Aquaculture ; Bacterial Proteins/genetics ; Base Sequence ; *Conjugation, Genetic ; DNA Replication ; DNA Transposable Elements ; DNA, Bacterial/genetics ; Fishes/*microbiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Phylogeny ; Pseudoalteromonas/*genetics ; Sequence Analysis, DNA ; Vibrio/*genetics ; }, abstract = {Integrating conjugative elements (ICEs) of the SXT/R391 family have been identified in fish-isolated bacterial strains collected from marine aquaculture environments of the northwestern Iberian Peninsula. Here we analysed the variable regions of two ICEs, one preliminarily characterised in a previous study (ICEVscSpa3) and one newly identified (ICEPspSpa1). Bacterial strains harboring these ICEs were phylogenetically assigned to Vibrio scophthalmi and Pseudoalteromonas sp., thus constituting the first evidence of SXT/R391-like ICEs in the genus Pseudoalteromonas to date. Variable DNA regions, which confer element-specific properties to ICEs of this family, were characterised. Interestingly, the two ICEs contained 29 genes not found in variable DNA insertions of previously described ICEs. Most notably, variable gene content for ICEVscSpa3 showed similarity to genes potentially involved in housekeeping functions of replication, nucleotide metabolism and transcription. For these genes, closest homologues were found clustered in the genome of Pseudomonas psychrotolerans L19, suggesting a transfer as a block to ICEVscSpa3. Genes encoding antibiotic resistance, restriction modification systems and toxin/antitoxin systems were absent from hotspots of ICEVscSpa3. In contrast, the variable gene content of ICEPspSpa1 included genes involved in restriction/modification functions in two different hotspots and genes related to ICE maintenance. The present study unveils a relatively large number of novel genes in SXT/R391-ICEs, and demonstrates the major role of ICE elements as contributors to horizontal gene transfer.}, }
@article {pmid27229510, year = {2016}, author = {Xu, P and Li, Q and Jiang, K and Yang, Q and Bi, M and Jiang, C and Wang, X and Wang, C and Li, L and Qiao, C and Gong, H and Xing, Y and Ren, J}, title = {BAC mediated transgenic Large White boars with FSHα/β genes from Chinese Erhualian pigs.}, journal = {Transgenic research}, volume = {25}, number = {5}, pages = {693-709}, pmid = {27229510}, issn = {1573-9368}, mesh = {Animals ; Animals, Genetically Modified/genetics/growth &amp; development ; Breeding ; Chromosomes, Artificial, Bacterial/*genetics ; Female ; Follicle Stimulating Hormone/*genetics ; Gastrointestinal Microbiome/*genetics ; Genome ; Male ; Nuclear Transfer Techniques ; RNA, Ribosomal, 16S/genetics ; Reproduction/genetics ; Spermatogenesis/genetics ; Sus scrofa/*genetics/growth &amp; development ; }, abstract = {Follicle-stimulating hormone (FSH) is a critical hormone regulating reproduction in mammals. Transgenic mice show that overexpression of FSH can improve female fecundity. Using a bacterial artificial chromosome (BAC) system and somatic cell nuclear transfer, we herein generated 67 Large White transgenic (TG) boars harboring FSHα/β genes from Chinese Erhualian pigs, the most prolific breed in the world. We selected two F0 TG boars for further breeding and conducted molecular characterization and biosafety assessment for F1 boars. We showed that 8-9 copies of exogenous FSHα and 5-6 copies of exogenous FSHβ were integrated into the genome of transgenic pigs. The inheritance of exogenous genes conforms to the Mendel's law of segregation. TG boars had higher levels of serum FSH, FSHα mRNA in multiple tissues, FSHβ protein in pituitary and more germ cells per seminiferous tubule compared with their wild-type half sibs without any reproductive defects. Analysis of growth curve, hematological and biochemical parameters and histopathology illustrated that TG boars grew healthily and normally. By applying 16S rRNA gene sequencing, we demonstrated that exogenous genes had no impact on the bacterial community structures of pig guts. Moreover, foreign gene drift did not occur as verified by horizontal gene transfer. Our findings indicate that overexpression of FSH could improve spermatogenesis ability of boars. This work provides insight into the effect of FSHα/β genes on male reproductive performance on pigs by a BAC-mediated transgenic approach.}, }
@article {pmid27228397, year = {2016}, author = {Zhang, L}, title = {On Tree-Based Phylogenetic Networks.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {23}, number = {7}, pages = {553-565}, doi = {10.1089/cmb.2015.0228}, pmid = {27228397}, issn = {1557-8666}, mesh = {Algorithms ; Computational Biology/*methods ; Models, Genetic ; *Phylogeny ; }, abstract = {A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree-based networks. We present a simple necessary and sufficient condition for tree-based networks and prove that a universal tree-based network exists for any number of taxa that contains as its base every phylogenetic tree on the same set of taxa. This answers two problems posted by Francis and Steel recently. A byproduct is a computer program for generating random binary phylogenetic networks under the uniform distribution model.}, }
@article {pmid27227308, year = {2016}, author = {Lyte, M}, title = {Microbial Endocrinology in the Pathogenesis of Infectious Disease.}, journal = {Microbiology spectrum}, volume = {4}, number = {2}, pages = {}, doi = {10.1128/microbiolspec.VMBF-0021-2015}, pmid = {27227308}, issn = {2165-0497}, mesh = {Animals ; Brain/metabolism/microbiology ; Communicable Diseases/metabolism/*microbiology/*physiopathology ; Digestive System/metabolism/microbiology ; Endocrinology ; Gastrointestinal Microbiome/*physiology ; Host-Pathogen Interactions ; Humans ; Microbial Interactions ; Neurotransmitter Agents/metabolism ; Stress, Physiological ; }, abstract = {Microbial endocrinology represents the intersection of two seemingly disparate fields, microbiology and neurobiology, and is based on the shared presence of neurochemicals that are exactly the same in host as well as in the microorganism. The ability of microorganisms to not only respond to, but also produce, many of the same neurochemicals that are produced by the host, such as during periods of stress, has led to the introduction of this evolutionary-based mechanism which has a role in the pathogenesis of infectious disease. The consideration of microbial endocrinology-based mechanisms has demonstrated, for example, that the prevalent use of catecholamine-based synthetic drugs in the clinical setting contributes to the formation of biofilms in indwelling medical devices. Production of neurochemicals by microorganisms most often employs the same biosynthetic pathways as those utilized by the host, indicating that acquisition of host neurochemical-based signaling system in the host may have been acquired due to lateral gene transfer from microorganisms. That both host and microorganism produce and respond to the very same neurochemicals means that there is bidirectionality contained with the theoretical underpinnings of microbial endocrinology. This can be seen in the role of microbial endocrinology in the microbiota-gut-brain axis and its relevance to infectious disease. Such shared pathways argue for a role of microorganism-neurochemical interactions in infectious disease.}, }
@article {pmid27223632, year = {2016}, author = {Agnew-Crumpton, R and Vaz, PK and Devlin, JM and O'Rourke, D and Blacker-Smith, HP and Konsak-Ilievski, B and Hartley, CA and Noormohammadi, AH}, title = {Spread of the newly emerging infectious laryngotracheitis viruses in Australia.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {43}, number = {}, pages = {67-73}, doi = {10.1016/j.meegid.2016.05.023}, pmid = {27223632}, issn = {1567-7257}, mesh = {Animals ; Australia/epidemiology ; Chickens/*virology ; Gene Transfer, Horizontal ; Herpesviridae Infections/*epidemiology/*veterinary/virology ; Herpesvirus 1, Gallid/*classification/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing/veterinary ; Phylogeny ; Poultry Diseases/epidemiology/*virology ; Sequence Analysis, DNA/veterinary ; Virulence ; Virus Replication ; }, abstract = {Infectious laryngotracheitis (ILT) is a significant viral disease of chickens in many countries around the globe. In this report the status of ILT in Australia has been used as a model to evaluate the evolution of the ILT viruses (ILTVs). Due to its geographical isolation, Australia harbored a distinct lineage of ILT viruses (ILTV) up to 2007. However examination of the ILT viruses (ILTV) involved in outbreaks between 2007 and 2009 has revealed that many of the outbreaks were caused by two new viral genotypes, class 8 and class 9. These two recombinant viruses were found to emerge as a result of recombination between previously existing live vaccine strains (SA2 and A20), and another live vaccine strain (Serva) introduced into the country in 2007. The new recombinant ILTVs were also shown to possess significantly higher virulence and replication capacity compared with a previously predominant ILTV, class 2. In the current study, examination of a large number of ILTVs isolated from outbreaks between 2009 and 2015 revealed the emergence of yet another recombinant virus (class 10) that appears to have become a predominant genotype in New South Wales. In Victoria however, the recombinant class 9 gradually became the predominant virus, replacing class 2. Therefore, there was an unusual pattern in geographical spread of the newly emerged viruses in different states of the country. These results suggest that ILTV is fast evolving towards a greater transmissibility and therefore greater capacity to spread into ILTV-free areas.}, }
@article {pmid27222845, year = {2016}, author = {Mahajan, V and Gaymalov, Z and Alakhova, D and Gupta, R and Zucker, IH and Kabanov, AV}, title = {Data on macrophage mediated muscle transfection upon delivery of naked plasmid DNA with block copolymers.}, journal = {Data in brief}, volume = {7}, number = {}, pages = {1269-1282}, pmid = {27222845}, issn = {2352-3409}, support = {P20 GM103480/GM/NIGMS NIH HHS/United States ; P20 RR021937/RR/NCRR NIH HHS/United States ; R01 CA116591/CA/NCI NIH HHS/United States ; }, abstract = {The data contains 14 figures supporting the research article "Horizontal gene transfer from macrophages to ischemic muscles upon delivery of naked DNA with Pluronic block copolymers" [1]. The data explains the surgical procedure and histological characterization of Murine Hind Limb Ischemia. The data also shows the kinetics of luciferase gene expression, spread of GFP expression through muscle and the colocalization of GFP with cellular markers in ischemic muscles injected with pDNA alone or pDNA/Pluronic. Finally the data shows the effect of Pluronic Block Copolymer to enhance total gene expression (cmv-promoter driven luciferase gene) in coculture of DNA transfected MØs with muscle cells.}, }
@article {pmid27222803, year = {2016}, author = {Gohil, KN and Neurgaonkar, PS and Paranjpe, A and Dastager, SG and Dharne, MS}, title = {Peeping into genomic architecture by re-sequencing of Ochrobactrum intermedium M86 strain during laboratory adapted conditions.}, journal = {Genomics data}, volume = {8}, number = {}, pages = {72-76}, pmid = {27222803}, issn = {2213-5960}, abstract = {Advances in de novo sequencing technologies allow us to track deeper insights into microbial genomes for restructuring events during the course of their evolution inside and outside the host. Bacterial species belonging to Ochrobactrum genus are being reported as emerging, and opportunistic pathogens in this technology driven era probably due to insertion and deletion of genes. The Ochrobactrum intermedium M86 was isolated in 2005 from a case of non-ulcer dyspeptic human stomach followed by its first draft genome sequence in 2009. Here we report re-sequencing of O. intermedium M86 laboratory adapted strain in terms of gain and loss of genes. We also attempted for finer scale genome sequence with 10 times more genome coverage than earlier one followed by comparative evaluation on Ion PGM and Illumina MiSeq. Despite their similarities at genomic level, lab-adapted strain mainly lacked genes encoding for transposase protein, insertion elements family, phage tail-proteins that were not detected in original strain on both chromosomes. Interestingly, a 5 kb indel was detected in chromosome 2 that was absent in original strain mapped with phage integrase gene of Rhizobium spp. and may be acquired and integrated through horizontal gene transfer indicating the gene loss and gene gain phenomenon in this genus. Majority of indel fragments did not match with known genes indicating more bioinformatic dissection of this fragment. Additionally we report genes related to antibiotic resistance, heavy metal tolerance in earlier and re-sequenced strain. Though SNPs detected, there did not span urease and flagellar genes. We also conclude that third generation sequencing technologies might be useful for understanding genomic architecture and re-arrangement of genes in the genome due to their ability of larger coverage that can be used to trace evolutionary aspects in microbial system.}, }
@article {pmid27219870, year = {2016}, author = {Berridge, MV and McConnell, MJ and Grasso, C and Bajzikova, M and Kovarova, J and Neuzil, J}, title = {Horizontal transfer of mitochondria between mammalian cells: beyond co-culture approaches.}, journal = {Current opinion in genetics &amp; development}, volume = {38}, number = {}, pages = {75-82}, doi = {10.1016/j.gde.2016.04.003}, pmid = {27219870}, issn = {1879-0380}, mesh = {Animals ; Cell Communication/*genetics ; Cell Division/genetics ; DNA, Mitochondrial/*genetics ; Gene Transfer, Horizontal/*genetics ; Humans ; Mitochondria/*genetics ; }, abstract = {Current dogma holds that genes are the property of individual mammalian cells and partition between daughter cells during cell division. However, and rather unexpectedly, recent research has demonstrated horizontal cell-to-cell transfer of mitochondria and mitochondrial DNA in several mammalian cell culture systems. Furthermore, unequivocal evidence that mitochondrial DNA transfer occurs in vivo has now been published. While these studies show horizontal transfer of mitochondrial DNA in pathological settings, it is also possible that intercellular mitochondrial transfer is a fundamental physiological process with a role in development and tissue homeostasis.}, }
@article {pmid27218454, year = {2016}, author = {Bhattacharya, D and Agrawal, S and Aranda, M and Baumgarten, S and Belcaid, M and Drake, JL and Erwin, D and Foret, S and Gates, RD and Gruber, DF and Kamel, B and Lesser, MP and Levy, O and Liew, YJ and MacManes, M and Mass, T and Medina, M and Mehr, S and Meyer, E and Price, DC and Putnam, HM and Qiu, H and Shinzato, C and Shoguchi, E and Stokes, AJ and Tambutté, S and Tchernov, D and Voolstra, CR and Wagner, N and Walker, CW and Weber, AP and Weis, V and Zelzion, E and Zoccola, D and Falkowski, PG}, title = {Comparative genomics explains the evolutionary success of reef-forming corals.}, journal = {eLife}, volume = {5}, number = {}, pages = {}, pmid = {27218454}, issn = {2050-084X}, support = {P20 GM103466/GM/NIGMS NIH HHS/United States ; P20 MD006084/MD/NIMHD NIH HHS/United States ; U54 MD007584/MD/NIMHD NIH HHS/United States ; }, mesh = {Adaptation, Physiological/*genetics ; Animals ; Anthozoa/classification/*genetics/growth &amp; development/metabolism ; Biological Evolution ; Calcification, Physiologic/*genetics ; Calcium Carbonate/chemistry/metabolism ; Coral Reefs ; Gene Transfer, Horizontal ; *Genome ; Genomics/*methods ; Hydrogen-Ion Concentration ; Light ; Metabolic Networks and Pathways/*genetics ; Photosynthesis/physiology ; Phylogeny ; Reactive Nitrogen Species/metabolism ; Reactive Oxygen Species/metabolism ; Stress, Physiological ; Symbiosis/physiology ; Temperature ; }, abstract = {Transcriptome and genome data from twenty stony coral species and a selection of reference bilaterians were studied to elucidate coral evolutionary history. We identified genes that encode the proteins responsible for the precipitation and aggregation of the aragonite skeleton on which the organisms live, and revealed a network of environmental sensors that coordinate responses of the host animals to temperature, light, and pH. Furthermore, we describe a variety of stress-related pathways, including apoptotic pathways that allow the host animals to detoxify reactive oxygen and nitrogen species that are generated by their intracellular photosynthetic symbionts, and determine the fate of corals under environmental stress. Some of these genes arose through horizontal gene transfer and comprise at least 0.2% of the animal gene inventory. Our analysis elucidates the evolutionary strategies that have allowed symbiotic corals to adapt and thrive for hundreds of millions of years.}, }
@article {pmid27216071, year = {2016}, author = {Cuzon, G and Bogaerts, P and Bauraing, C and Huang, TD and Bonnin, RA and Glupczynski, Y and Naas, T}, title = {Spread of Plasmids Carrying Multiple GES Variants.}, journal = {Antimicrobial agents and chemotherapy}, volume = {60}, number = {8}, pages = {5040-5043}, pmid = {27216071}, issn = {1098-6596}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics/*metabolism ; Enterobacter cloacae/drug effects/enzymology/genetics ; Enterobacteriaceae/*drug effects/*enzymology/genetics ; Gene Transfer, Horizontal/genetics ; Microbial Sensitivity Tests ; Plasmids/*genetics ; beta-Lactamases/genetics/*metabolism ; }, abstract = {Five GES-producing Enterobacteriaceae isolates that displayed an extended-spectrum β-lactamase (ESBL) phenotype harbored two GES variants: GES-7 ESBL and GES-6 carbapenemase. In all isolates, the two GES alleles were located on the same integron that was inserted into an 80-kb IncM1 self-conjugative plasmid. Whole-genome sequencing suggested in vivo horizontal gene transfer of the plasmid along with clonal diffusion of Enterobacter cloacae To our knowledge, this is the first description in Europe of clustered Enterobacteriaceae isolates carrying two GES β-lactamases, of which one has extended activity toward carbapenems.}, }
@article {pmid27215567, year = {2016}, author = {Qiu, H and Cai, G and Luo, J and Bhattacharya, D and Zhang, N}, title = {Extensive horizontal gene transfers between plant pathogenic fungi.}, journal = {BMC biology}, volume = {14}, number = {}, pages = {41}, pmid = {27215567}, issn = {1741-7007}, mesh = {Ascomycota/*genetics ; Colletotrichum/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genetic Markers ; *Genome, Fungal ; Host-Pathogen Interactions ; Phylogeny ; Plant Diseases/microbiology ; Plants/*microbiology ; Symbiosis ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT) plays an important role in the adaptation of lineages to changing environments. The extent of this process in eukaryotes, however, remains controversial. The most well-known and dramatic form of HGT represents intracellular gene transfer from endosymbionts to the host nuclear genome. Such episodes of transfer typically involve hundreds of genes and are thought to be possible only in the case of endosymbiosis.<br><br>RESULTS: Using a conservative phylogenomic approach, we analyzed genomic data from the fungal pathogen Magnaporthiopsis incrustans in the order Magnaporthales and identified two instances of exclusive sharing of HGT-derived gene markers between Magnaporthales and another lineage of plant-pathogenic fungi in the genus Colletotrichum. Surprisingly, inspection of these data demonstrated that HGT is far more widespread than anticipated, with more than 90 genes (including 33 highly supported candidates) being putatively transferred between Magnaporthales and Colletotrichum. These gene transfers are often physically linked in the genome and show more than two-fold functional enrichment in carbohydrate activating enzymes associated with plant cell wall degradation.<br><br>CONCLUSIONS: Our work provides a novel perspective on the scale of HGT between eukaryotes. These results challenge the notion that recognized HGT plays a minor role in the evolution of fungal lineages, and in the case we describe, is likely implicated in the evolution of plant pathogenesis. More generally, we suggest that the expanding database of closely related eukaryotic genomes and the application of novel analytic methods will further underline the significant impact of foreign gene acquisition across the tree of life. Major lifestyle transitions such as those accompanying the origin of extremophily or pathogenesis are expected to be ideal candidates for studying the mode and tempo of HGT.}, }
@article {pmid27215217, year = {2016}, author = {Parmeciano Di Noto, G and Jara, E and Iriarte, A and Centrón, D and Quiroga, C}, title = {Genome analysis of a clinical isolate of Shewanella sp. uncovered an active hybrid integrative and conjugative element carrying an integron platform inserted in a novel genomic locus.}, journal = {Microbiology (Reading, England)}, volume = {162}, number = {8}, pages = {1335-1345}, doi = {10.1099/mic.0.000310}, pmid = {27215217}, issn = {1465-2080}, mesh = {Bacterial Proteins/*genetics ; Base Sequence ; DNA, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial/genetics ; Humans ; Integrons/*genetics ; Membrane Transport Proteins/*genetics ; Sequence Analysis, DNA ; Shewanella/*genetics/isolation &amp; purification ; beta-Lactamases/*genetics ; }, abstract = {Shewanella spp. are currently considered to be emerging pathogens that can code for a blaOXA carbapenemase in their chromosome. Complete genome analysis of the clinical isolate Shewanella sp. Sh95 revealed that this strain is a novel species, which shares a lineage with marine isolates. Characterization of its resistome showed that it codes for genes drfA15, qacH and blaOXA-48. We propose that Shewanella sp. Sh95 acts as reservoir of blaOXA-48. Moreover, analysis of mobilome showed that it contains a novel integrative and conjugative element (ICE), named ICESh95. Comparative analysis between the close relatives ICESpuPO1 from Shewanella sp. W3-18-1 and ICE SXTMO10 from Vibrio cholerae showed that ICESh95 encompassed two new regions, a type III restriction modification system and a multidrug resistance integron. The integron platform contained a novel arrangement formed by gene cassettes drfA15 and qacH, and a class C-attC group II intron. Furthermore, insertion of ICESh95 occurred at a unique target site, which correlated with the presence of a different xis/int module. Mobility of ICESh95 was assessed and demonstrated its ability to self-transfer with high efficiency to different species of bacteria. Our results show that ICESh95 is a self-transmissible, mobile element, which can contribute to the dissemination of antimicrobial resistance; this is clearly a threat when natural bacteria from water ecosystems, such as Shewanella, act as vectors in its propagation.}, }
@article {pmid27213270, year = {2016}, author = {Palazzo, A and Lovero, D and D'Addabbo, P and Caizzi, R and Marsano, RM}, title = {Identification of Bari Transposons in 23 Sequenced Drosophila Genomes Reveals Novel Structural Variants, MITEs and Horizontal Transfer.}, journal = {PloS one}, volume = {11}, number = {5}, pages = {e0156014}, pmid = {27213270}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; Chromosome Mapping ; DNA Transposable Elements/*genetics ; Drosophila melanogaster/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; *Genetic Variation ; Genome, Insect/genetics ; Mutagenesis, Insertional/*genetics ; Phylogeny ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Terminal Repeat Sequences ; }, abstract = {Bari elements are members of the Tc1-mariner superfamily of DNA transposons, originally discovered in Drosophila melanogaster, and subsequently identified in silico in 11 sequenced Drosophila genomes and as experimentally isolated in four non-sequenced Drosophila species. Bari-like elements have been also studied for their mobility both in vivo and in vitro. We analyzed 23 Drosophila genomes and carried out a detailed characterization of the Bari elements identified, including those from the heterochromatic Bari1 cluster in D. melanogaster. We have annotated 401 copies of Bari elements classified either as putatively autonomous or inactive according to the structure of the terminal sequences and the presence of a complete transposase-coding region. Analyses of the integration sites revealed that Bari transposase prefers AT-rich sequences in which the TA target is cleaved and duplicated. Furthermore evaluation of transposon's co-occurrence near the integration sites of Bari elements showed a non-random distribution of other transposable elements. We also unveil the existence of a putatively autonomous Bari1 variant characterized by two identical long Terminal Inverted Repeats, in D. rhopaloa. In addition, we detected MITEs related to Bari transposons in 9 species. Phylogenetic analyses based on transposase gene and the terminal sequences confirmed that Bari-like elements are distributed into three subfamilies. A few inconsistencies in Bari phylogenetic tree with respect to the Drosophila species tree could be explained by the occurrence of horizontal transfer events as also suggested by the results of dS analyses. This study further clarifies the Bari transposon's evolutionary dynamics and increases our understanding on the Tc1-mariner elements' biology.}, }
@article {pmid27212064, year = {2016}, author = {Li, X and Koç, C and Kühner, P and Stierhof, YD and Krismer, B and Enright, MC and Penadés, JR and Wolz, C and Stehle, T and Cambillau, C and Peschel, A and Xia, G}, title = {An essential role for the baseplate protein Gp45 in phage adsorption to Staphylococcus aureus.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {26455}, pmid = {27212064}, issn = {2045-2322}, mesh = {Acetylglucosamine/metabolism ; Adsorption ; Antibodies/metabolism ; Cell Wall/metabolism ; Gene Knockout Techniques ; Gene Transfer, Horizontal ; Siphoviridae/metabolism/*physiology ; Staphylococcus aureus/genetics/metabolism/*virology ; Teichoic Acids/*metabolism ; Viral Envelope Proteins/chemistry/*metabolism ; }, abstract = {Despite the importance of phages in driving horizontal gene transfer (HGT) among pathogenic bacteria, the underlying molecular mechanisms mediating phage adsorption to S. aureus are still unclear. Phage ϕ11 is a siphovirus with a high transducing efficiency. Here, we show that the tail protein Gp45 localized within the ϕ11 baseplate. Phage ϕ11 was efficiently neutralized by anti-Gp45 serum, and its adsorption to host cells was inhibited by recombinant Gp45 in a dose-dependent manner. Flow cytometry analysis demonstrated that biotin-labelled Gp45 efficiently stained the wild-type S. aureus cell but not the double knockout mutant ΔtarM/S, which lacks both α- and β-O-GlcNAc residues on its wall teichoic acids (WTAs). Additionally, adsorption assays indicate that GlcNAc residues on WTAs and O-acetyl groups at the 6-position of muramic acid residues in peptidoglycan are essential components of the ϕ11 receptor. The elucidation of Gp45-involved molecular interactions not only broadens our understanding of siphovirus-mediated HGT, but also lays the groundwork for the development of sensitive affinity-based diagnostics and therapeutics for S. aureus infection.}, }
@article {pmid27210832, year = {2016}, author = {Shelomi, M and Danchin, EG and Heckel, D and Wipfler, B and Bradler, S and Zhou, X and Pauchet, Y}, title = {Horizontal Gene Transfer of Pectinases from Bacteria Preceded the Diversification of Stick and Leaf Insects.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {26388}, pmid = {27210832}, issn = {2045-2322}, mesh = {Animals ; Bacteria/enzymology/*genetics ; Evolution, Molecular ; Gastrointestinal Microbiome ; *Gene Transfer, Horizontal ; Insect Proteins/genetics ; Neoptera/*enzymology/genetics ; Phylogeny ; Polygalacturonase/*genetics ; Sequence Analysis, RNA ; }, abstract = {Genes acquired by horizontal transfer are increasingly being found in animal genomes. Understanding their origin and evolution requires knowledge about the phylogenetic relationships from both source and recipient organisms. We used RNASeq data and respective assembled transcript libraries to trace the evolutionary history of polygalacturonase (pectinase) genes in stick insects (Phasmatodea). By mapping the distribution of pectinase genes on a Polyneoptera phylogeny, we identified the transfer of pectinase genes from known phasmatodean gut microbes into the genome of an early euphasmatodean ancestor that took place between 60 and 100 million years ago. This transfer preceded the rapid diversification of the suborder, enabling symbiont-free pectinase production that would increase the insects' digestive efficiency and reduce dependence on microbes. Bacteria-to-insect gene transfer was thought to be uncommon, however the increasing availability of large-scale genomic data may change this prevailing notion.}, }
@article {pmid27206480, year = {2016}, author = {De Maayer, P and Cowan, DA}, title = {Flashy flagella: flagellin modification is relatively common and highly versatile among the Enterobacteriaceae.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {377}, pmid = {27206480}, issn = {1471-2164}, mesh = {Enterobacteriaceae/classification/*genetics/*metabolism ; Flagella/*genetics/*metabolism ; Flagellin/*genetics/*metabolism ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Loci ; Glycosylation ; Phylogeny ; Polysaccharides ; Protein Processing, Post-Translational ; }, abstract = {BACKGROUND: Post-translational glycosylation of the flagellin protein is relatively common among Gram-negative bacteria, and has been linked to several phenotypes, including flagellar biosynthesis and motility, biofilm formation, host immune evasion and manipulation and virulence. However to date, despite extensive physiological and genetic characterization, it has never been reported for the peritrichously flagellate Enterobacteriaceae.<br><br>RESULTS: Using comparative genomic approaches we analyzed 2,000 representative genomes of Enterobacteriaceae, and show that flagellin glycosylation islands are relatively common and extremely versatile among members of this family. Differences in the G&#x2009;+&#x2009;C content of the FGIs and the rest of the genome and the presence of mobile genetic elements provide evidence of horizontal gene transfer occurring within the FGI loci. These loci therefore encode highly variable flagellin glycan structures, with distinct sugar backbones, heavily substituted with formyl, methyl, acetyl, lipoyl and amino groups. Additionally, an N-lysine methylase, FliB, previously identified only in the enterobacterial pathogen Salmonella enterica, is relatively common among several distinct taxa within the family. These flagellin methylase island loci (FMIs), in contrast to the FGI loci, appear to be stably maintained within these diverse lineages.<br><br>CONCLUSIONS: The prevalence and versatility of flagellin modification loci, both glycosylation and methylation loci, suggests they play important biological roles among the Enterobacteriaceae.}, }
@article {pmid27199920, year = {2016}, author = {Kittinger, C and Lipp, M and Baumert, R and Folli, B and Koraimann, G and Toplitsch, D and Liebmann, A and Grisold, AJ and Farnleitner, AH and Kirschner, A and Zarfel, G}, title = {Antibiotic Resistance Patterns of Pseudomonas spp. Isolated from the River Danube.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {586}, pmid = {27199920}, issn = {1664-302X}, support = {P 25817/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Spread and persistence of antibiotic resistance pose a severe threat to human health, yet there is still lack of knowledge about reservoirs of antibiotic resistant bacteria in the environment. We took the opportunity of the Joint Danube Survey 3 (JDS3), the world's biggest river research expedition of its kind in 2013, to analyse samples originating from different sampling points along the whole length of the river. Due to its high clinical relevance, we concentrated on the characterization of Pseudomonas spp. and evaluated the resistance profiles of Pseudomonas spp. which were isolated from eight sampling points. In total, 520 Pseudomonas isolates were found, 344 (66.0%) isolates were identified as Pseudomonas putida, and 141 (27.1%) as Pseudomonas fluorescens, all other Pseudomonas species were represented by less than five isolates, among those two P. aeruginosa isolates. Thirty seven percent (37%) of all isolated Pseudomonas species showed resistance to at least one out of 10 tested antibiotics. The most common resistance was against meropenem (30.4%/158 isolates) piperacillin/tazobactam (10.6%/55 isolates) and ceftazidime (4.2%/22 isolates). 16 isolates (3.1%/16 isolates) were multi-resistant. For each tested antibiotic at least one resistant isolate could be detected. Sampling points from the upper stretch of the River Danube showed more resistant isolates than downriver. Our results suggest that antibiotic resistance can be acquired by and persists even in Pseudomonas species that are normally not in direct contact with humans. A possible scenario is that these bacteria provide a reservoir of antibiotic resistance genes that can spread to related human pathogens by horizontal gene transfer.}, }
@article {pmid27199915, year = {2016}, author = {López-Leal, G and Cevallos, MA and Castillo-Ramírez, S}, title = {Evolution of a Sigma Factor: An All-In-One of Gene Duplication, Horizontal Gene Transfer, Purifying Selection, and Promoter Differentiation.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {581}, pmid = {27199915}, issn = {1664-302X}, abstract = {Sigma factors are an essential part of bacterial gene regulation and have been extensively studied as far as their molecular mechanisms and protein structure are concerned. However, their molecular evolution, especially for the alternative sigma factors, is poorly understood. Here, we analyze the evolutionary forces that have shaped the rpoH sigma factors within the alphaproteobacteria. We found that an ancient duplication gave rise to two major groups of rpoH sigma factors and that after this event horizontal gene transfer (HGT) occurred in rpoH 1 group. We also noted that purifying selection has differentially affected distinct parts of the gene; singularly, the gene segment that encodes the region 4.2, which interacts with the -35 motif of the RpoH-dependent genes, has been under relaxed purifying selection. Furthermore, these two major groups are clearly differentiated from one another regarding their promoter selectivity, as rpoH 1 is under the transcriptional control of σ(70) and σ(32), whereas rpoH 2 is under the transcriptional control of σ(24). Our results suggest a scenario in which HGT, gene loss, variable purifying selection and clear promoter specialization occurred after the ancestral duplication event. More generally, our study offers insights into the molecular evolution of alternative sigma factors and highlights the importance of analyzing not only the coding regions but also the promoter regions.}, }
@article {pmid27199912, year = {2016}, author = {de Vries, LE and Hasman, H and Jurado Rabadán, S and Agersø, Y}, title = {Sequence-Based Characterization of Tn5801-Like Genomic Islands in Tetracycline-Resistant Staphylococcus pseudintermedius and Other Gram-positive Bacteria from Humans and Animals.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {576}, pmid = {27199912}, issn = {1664-302X}, abstract = {Antibiotic resistance in pathogens is often associated with mobile genetic elements, such as genomic islands (GI) including integrative and conjugative elements (ICEs). These can transfer resistance genes within and between bacteria from humans and/or animals. The aim of this study was to investigate whether Tn5801-like GIs carrying the tetracycline resistance gene, tet(M), are common in Staphylococcus pseudintermedius from pets, and to do an overall sequences-based characterization of Tn5801-like GIs detected in Gram-positive bacteria from humans and animals. A total of 27 tetracycline-resistant S. pseudintermedius isolates from Danish pets (1998-2005) were screened for tet(M) by PCR. Selected isolates (13) were screened for GI- or ICE-specific genes (int Tn5801 or xis Tn916) and their tet(M) gene was sequenced (Sanger-method). Long-range PCR mappings and whole-genome-sequencing (Illumina) were performed for selected S. pseudintermedius-isolates (seven and three isolates, respectively) as well as for human S. aureus isolates (seven and one isolates, respectively) and one porcine Enterococcus faecium isolate known to carry Tn5801-like GIs. All 27 S. pseudintermedius were positive for tet(M). Out of 13 selected isolates, seven contained Tn5801-like GIs and six contained Tn916-like ICEs. Two different Tn5801-like GI types were detected among S. pseudintermedius (Tn5801 and GI6287) - both showed high similarity compared to GenBank sequences from human pathogens. Two distinct Tn5801-like GI types were detected among the porcine E. faecium and human S. aureus isolates (Tn6014 and GI6288). Tn5801-like GIs were detected in GenBank-sequences from Gram-positive bacteria of human, animal or food origin worldwide. Known Tn5801-like GIs were divided into seven types. The results showed that Tn5801-like GIs appear to be relatively common in tetracycline-resistant S. pseudintermedius in Denmark. Almost identical Tn5801-like GIs were identified in different Gram-positive species of pet and human origin, suggesting that horizontal transfer of these elements has occurred between S. pseudintermedius from pets and human pathogens, including S. aureus.}, }
@article {pmid27197212, year = {2016}, author = {Press, MO and Queitsch, C and Borenstein, E}, title = {Evolutionary assembly patterns of prokaryotic genomes.}, journal = {Genome research}, volume = {26}, number = {6}, pages = {826-833}, pmid = {27197212}, issn = {1549-5469}, support = {DP2 OD008371/OD/NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; Computational Biology ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Models, Genetic ; Phylogeny ; }, abstract = {Evolutionary innovation must occur in the context of some genomic background, which limits available evolutionary paths. For example, protein evolution by sequence substitution is constrained by epistasis between residues. In prokaryotes, evolutionary innovation frequently happens by macrogenomic events such as horizontal gene transfer (HGT). Previous work has suggested that HGT can be influenced by ancestral genomic content, yet the extent of such gene-level constraints has not yet been systematically characterized. Here, we evaluated the evolutionary impact of such constraints in prokaryotes, using probabilistic ancestral reconstructions from 634 extant prokaryotic genomes and a novel framework for detecting evolutionary constraints on HGT events. We identified 8228 directional dependencies between genes and demonstrated that many such dependencies reflect known functional relationships, including for example, evolutionary dependencies of the photosynthetic enzyme RuBisCO. Modeling all dependencies as a network, we adapted an approach from graph theory to establish chronological precedence in the acquisition of different genomic functions. Specifically, we demonstrated that specific functions tend to be gained sequentially, suggesting that evolution in prokaryotes is governed by functional assembly patterns. Finally, we showed that these dependencies are universal rather than clade-specific and are often sufficient for predicting whether or not a given ancestral genome will acquire specific genes. Combined, our results indicate that evolutionary innovation via HGT is profoundly constrained by epistasis and historical contingency, similar to the evolution of proteins and phenotypic characters, and suggest that the emergence of specific metabolic and pathological phenotypes in prokaryotes can be predictable from current genomes.}, }
@article {pmid27193539, year = {2016}, author = {Chen, K and Stephanou, AS and Roberts, GA and White, JH and Cooper, LP and Houston, PJ and Lindsay, JA and Dryden, DT}, title = {The Type I Restriction Enzymes as Barriers to Horizontal Gene Transfer: Determination of the DNA Target Sequences Recognised by Livestock-Associated Methicillin-Resistant Staphylococcus aureus Clonal Complexes 133/ST771 and 398.}, journal = {Advances in experimental medicine and biology}, volume = {915}, number = {}, pages = {81-97}, doi = {10.1007/978-3-319-32189-9_7}, pmid = {27193539}, issn = {0065-2598}, support = {090288/Z/09/ZA//Wellcome Trust/United Kingdom ; GR080463MA//Wellcome Trust/United Kingdom ; }, mesh = {Adenine/metabolism ; Amino Acid Sequence ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics/*metabolism ; Base Sequence ; Cattle ; DNA Methylation ; DNA, Bacterial/genetics/*metabolism ; Deoxyribonucleases, Type I Site-Specific/genetics/*metabolism ; Drug Resistance, Bacterial/genetics ; *Gene Transfer, Horizontal ; Genotype ; Host-Pathogen Interactions ; Livestock/*microbiology ; Methicillin-Resistant Staphylococcus aureus/drug effects/*enzymology/genetics/isolation &amp; purification ; Milk/*microbiology ; Molecular Sequence Data ; Phenotype ; Staphylococcal Infections/drug therapy/*microbiology/transmission ; Substrate Specificity ; Virulence/genetics ; }, abstract = {The Type I DNA restriction-modification (RM) systems of Staphylococcus aureus are known to act as a significant barrier to horizontal gene transfer between S. aureus strains belonging to different clonal complexes. The livestock-associated clonal complexes CC133/771 and CC398 contain Type I RM systems not found in human MRSA strains as yet but at some point transfer will occur. When this does take place, horizontal gene transfer of resistance will happen more easily between these strains. The reservoir of antibiotic resistance, virulence and host-adaptation genes present in livestock-associated MRSA will then potentially contribute to the development of newly evolving MRSA clones. The target sites recognised by the Type I RM systems of CC133/771 and CC398 were identified as CAG(N)5RTGA and ACC(N)5RTGA, respectively. Assuming that these enzymes recognise the methylation state of adenine, the underlined A and T bases indicate the unique positions of methylation. Target methylation points for enzymes from CC1 were also identified. The methylation points for CC1-1 are CCAY(N)5TTAA and those for CC1-2 are CCAY(N)6 TGT with the underline indicating the adenine methylation site thus clearing up the ambiguity noted previously (Roberts et al. 2013, Nucleic Acids Res 41:7472-7484) for the half sites containing two adenine bases.}, }
@article {pmid27193376, year = {2016}, author = {Cenci, U and Moog, D and Curtis, BA and Tanifuji, G and Eme, L and Lukeš, J and Archibald, JM}, title = {Heme pathway evolution in kinetoplastid protists.}, journal = {BMC evolutionary biology}, volume = {16}, number = {1}, pages = {109}, pmid = {27193376}, issn = {1471-2148}, support = {MOP-115141//CIHR/Canada ; }, mesh = {Animals ; Biological Evolution ; Eukaryota/classification/*physiology ; Gene Transfer, Horizontal ; Heme/*metabolism ; Kinetoplastida/classification/*genetics/*physiology ; Phylogeny ; Symbiosis ; }, abstract = {BACKGROUND: Kinetoplastea is a diverse protist lineage composed of several of the most successful parasites on Earth, organisms whose metabolisms have coevolved with those of the organisms they infect. Parasitic kinetoplastids have emerged from free-living, non-pathogenic ancestors on multiple occasions during the evolutionary history of the group. Interestingly, in both parasitic and free-living kinetoplastids, the heme pathway-a core metabolic pathway in a wide range of organisms-is incomplete or entirely absent. Indeed, Kinetoplastea investigated thus far seem to bypass the need for heme biosynthesis by acquiring heme or intermediate metabolites directly from their environment.<br><br>RESULTS: Here we report the existence of a near-complete heme biosynthetic pathway in Perkinsela spp., kinetoplastids that live as obligate endosymbionts inside amoebozoans belonging to the genus Paramoeba/Neoparamoeba. We also use phylogenetic analysis to infer the evolution of the heme pathway in Kinetoplastea.<br><br>CONCLUSION: We show that Perkinsela spp. is a deep-branching kinetoplastid lineage, and that lateral gene transfer has played a role in the evolution of heme biosynthesis in Perkinsela spp. and other Kinetoplastea. We also discuss the significance of the presence of seven of eight heme pathway genes in the Perkinsela genome as it relates to its endosymbiotic relationship with Paramoeba.}, }
@article {pmid27190206, year = {2016}, author = {Fondi, M and Karkman, A and Tamminen, MV and Bosi, E and Virta, M and Fani, R and Alm, E and McInerney, JO}, title = {"Every Gene Is Everywhere but the Environment Selects": Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis.}, journal = {Genome biology and evolution}, volume = {8}, number = {5}, pages = {1388-1400}, pmid = {27190206}, issn = {1759-6653}, mesh = {*Biodiversity ; Ecology ; *Environment ; Gene Flow ; *Gene Regulatory Networks ; *Genetic Determinism ; *Genetic Speciation ; Geography ; Humans ; *Microbiological Phenomena ; }, abstract = {The spatial distribution of microbes on our planet is famously formulated in the Baas Becking hypothesis as "everything is everywhere but the environment selects." While this hypothesis does not strictly rule out patterns caused by geographical effects on ecology and historical founder effects, it does propose that the remarkable dispersal potential of microbes leads to distributions generally shaped by environmental factors rather than geographical distance. By constructing sequence similarity networks from uncultured environmental samples, we show that microbial gene pool distributions are not influenced nearly as much by geography as ecology, thus extending the Bass Becking hypothesis from whole organisms to microbial genes. We find that gene pools are shaped by their broad ecological niche (such as sea water, fresh water, host, and airborne). We find that freshwater habitats act as a gene exchange bridge between otherwise disconnected habitats. Finally, certain antibiotic resistance genes deviate from the general trend of habitat specificity by exhibiting a high degree of cross-habitat mobility. The strong cross-habitat mobility of antibiotic resistance genes is a cause for concern and provides a paradigmatic example of the rate by which genes colonize new habitats when new selective forces emerge.}, }
@article {pmid27190150, year = {2016}, author = {Santala, V and Karp, M and Santala, S}, title = {Bioluminescence-based system for rapid detection of natural transformation.}, journal = {FEMS microbiology letters}, volume = {363}, number = {13}, pages = {}, doi = {10.1093/femsle/fnw125}, pmid = {27190150}, issn = {1574-6968}, mesh = {Acinetobacter/genetics/growth &amp; development ; Biofilms/growth &amp; development ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; Homologous Recombination ; Luciferases/genetics ; Luminescent Measurements/*methods ; Operon ; *Transformation, Bacterial ; }, abstract = {Horizontal gene transfer plays a significant role in bacterial evolution and has major clinical importance. Thus, it is vital to understand the mechanisms and kinetics of genetic transformations. Natural transformation is the driving mechanism for horizontal gene transfer in diverse genera of bacteria. Our study introduces a simple and rapid method for the investigation of natural transformation. This highly sensitive system allows the detection of a transformation event directly from a bacterial population without any separation step or selection of cells. The system is based on the bacterial luciferase operon from Photorhabdus luminescens The studied molecular tools consist of the functional modules luxCDE and luxAB, which involve a replicative plasmid and an integrative gene cassette. A well-established host for bacterial genetic investigations, Acinetobacter baylyi ADP1, is used as the model bacterium. We show that natural transformation followed by homologous recombination or plasmid recircularization can be readily detected in both actively growing and static biofilm-like cultures, including very rare transformation events. The system allows the detection of natural transformation within 1 h of introducing sample DNA into the culture. The introduced method provides a convenient means to study the kinetics of natural transformation under variable conditions and perturbations.}, }
@article {pmid27190138, year = {2016}, author = {Lin, X and Faridi, N and Casola, C}, title = {An Ancient Transkingdom Horizontal Transfer of Penelope-Like Retroelements from Arthropods to Conifers.}, journal = {Genome biology and evolution}, volume = {8}, number = {4}, pages = {1252-1266}, pmid = {27190138}, issn = {1759-6653}, mesh = {Animals ; Arthropods/*genetics ; Cycadopsida/genetics ; Gene Dosage ; *Gene Transfer, Horizontal ; Phylogeny ; *Retroelements ; Tracheophyta/*genetics ; }, abstract = {Comparative genomics analyses empowered by the wealth of sequenced genomes have revealed numerous instances of horizontal DNA transfers between distantly related species. In eukaryotes, repetitive DNA sequences known as transposable elements (TEs) are especially prone to move across species boundaries. Such horizontal transposon transfers, or HTTs, are relatively common within major eukaryotic kingdoms, including animals, plants, and fungi, while rarely occurring across these kingdoms. Here, we describe the first case of HTT from animals to plants, involving TEs known as Penelope-like elements, or PLEs, a group of retrotransposons closely related to eukaryotic telomerases. Using a combination of in situ hybridization on chromosomes, polymerase chain reaction experiments, and computational analyses we show that the predominant PLE lineage, EN(+)PLEs, is highly diversified in loblolly pine and other conifers, but appears to be absent in other gymnosperms. Phylogenetic analyses of both protein and DNA sequences reveal that conifers EN(+)PLEs, or Dryads, form a monophyletic group clustering within a clade of primarily arthropod elements. Additionally, no EN(+)PLEs were detected in 1,928 genome assemblies from 1,029 nonmetazoan and nonconifer genomes from 14 major eukaryotic lineages. These findings indicate that Dryads emerged following an ancient horizontal transfer of EN(+)PLEs from arthropods to a common ancestor of conifers approximately 340 Ma. This represents one of the oldest known interspecific transmissions of TEs, and the most conspicuous case of DNA transfer between animals and plants.}, }
@article {pmid27189567, year = {2016}, author = {Wisecaver, JH and Alexander, WG and King, SB and Hittinger, CT and Rokas, A}, title = {Dynamic Evolution of Nitric Oxide Detoxifying Flavohemoglobins, a Family of Single-Protein Metabolic Modules in Bacteria and Eukaryotes.}, journal = {Molecular biology and evolution}, volume = {33}, number = {8}, pages = {1979-1987}, doi = {10.1093/molbev/msw073}, pmid = {27189567}, issn = {1537-1719}, mesh = {Adaptation, Biological/genetics ; Amino Acid Sequence ; Bacteria/*genetics/*metabolism ; Bacterial Proteins/*genetics/*metabolism ; Biological Evolution ; Computational Biology ; Databases, Nucleic Acid ; Dihydropteridine Reductase/genetics/metabolism ; Escherichia coli Proteins/genetics/metabolism ; Eukaryota/*genetics/*metabolism ; Evolution, Molecular ; Fungi/genetics ; Gene Duplication ; Gene Transfer, Horizontal ; Hemeproteins/*genetics/*metabolism ; NADH, NADPH Oxidoreductases/genetics/metabolism ; Nitric Oxide/*metabolism ; Phylogeny ; }, abstract = {Due to their functional independence, proteins that comprise standalone metabolic units, which we name single-protein metabolic modules, may be particularly prone to gene duplication (GD) and horizontal gene transfer (HGT). Flavohemoglobins (flavoHbs) are prime examples of single-protein metabolic modules, detoxifying nitric oxide (NO), a ubiquitous toxin whose antimicrobial properties many life forms exploit, to nitrate, a common source of nitrogen for organisms. FlavoHbs appear widespread in bacteria and have been identified in a handful of microbial eukaryotes, but how the distribution of this ecologically and biomedically important protein family evolved remains unknown. Reconstruction of the evolutionary history of 3,318 flavoHb protein sequences covering the family's known diversity showed evidence of recurrent HGT at multiple evolutionary scales including intrabacterial HGT, as well as HGT from bacteria to eukaryotes. One of the most striking examples of HGT is the acquisition of a flavoHb by the dandruff- and eczema-causing fungus Malassezia from Corynebacterium Actinobacteria, a transfer that growth experiments show is capable of mediating NO resistance in fungi. Other flavoHbs arose via GD; for example, many filamentous fungi possess two flavoHbs that are differentially targeted to the cytosol and mitochondria, likely conferring protection against external and internal sources of NO, respectively. Because single-protein metabolic modules such as flavoHb function independently, readily undergo GD and HGT, and are frequently involved in organismal defense and competition, we suggest that they represent "plug-and-play" proteins for ecological arms races.}, }
@article {pmid27189546, year = {2016}, author = {Zamani-Dahaj, SA and Okasha, M and Kosakowski, J and Higgs, PG}, title = {Estimating the Frequency of Horizontal Gene Transfer Using Phylogenetic Models of Gene Gain and Loss.}, journal = {Molecular biology and evolution}, volume = {33}, number = {7}, pages = {1843-1857}, doi = {10.1093/molbev/msw062}, pmid = {27189546}, issn = {1537-1719}, mesh = {Archaea/genetics ; Bacterial Proteins/genetics ; Computational Biology ; Computer Simulation ; Cyanobacteria/genetics ; Evolution, Molecular ; *Gene Deletion ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Archaeal ; Genome, Bacterial ; *Models, Genetic ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {We analyze patterns of gene presence and absence in a maximum likelihood framework with rate parameters for gene gain and loss. Standard methods allow independent gains and losses in different parts of a tree. While losses of the same gene are likely to be frequent, multiple gains need to be considered carefully. A gene gain could occur by horizontal transfer or by origin of a gene within the lineage being studied. If a gene is gained more than once, then at least one of these gains must be a horizontal transfer. A key parameter is the ratio of gain to loss rates, a/v We consider the limiting case known as the infinitely many genes model, where a/v tends to zero and a gene cannot be gained more than once. The infinitely many genes model is used as a null model in comparison to models that allow multiple gains. Using genome data from cyanobacteria and archaea, it is found that the likelihood is significantly improved by allowing for multiple gains, but the average a/v is very small. The fraction of genes whose presence/absence pattern is best explained by multiple gains is only 15% in the cyanobacteria and 20% and 39% in two data sets of archaea. The distribution of rates of gene loss is very broad, which explains why many genes follow a treelike pattern of vertical inheritance, despite the presence of a significant minority of genes that undergo horizontal transfer.}, }
@article {pmid27186981, year = {2016}, author = {Wei, FJ and Tsai, YC and Hsu, YM and Chen, YA and Huang, CT and Wu, HP and Huang, LT and Lai, MH and Kuang, LY and Lo, SF and Yu, SM and Lin, YR and Hsing, YI}, title = {Lack of Genotype and Phenotype Correlation in a Rice T-DNA Tagged Line Is Likely Caused by Introgression in the Seed Source.}, journal = {PloS one}, volume = {11}, number = {5}, pages = {e0155768}, pmid = {27186981}, issn = {1932-6203}, mesh = {*DNA, Bacterial ; *DNA, Plant ; Gene Transfer, Horizontal ; Genome, Plant ; Genotype ; Mutation ; Oryza/*genetics ; Phenotype ; Polymorphism, Single Nucleotide ; Recombination, Genetic ; Seeds/*genetics ; Sequence Analysis, DNA ; }, abstract = {Rice (Oryza sativa) is one of the most important crops in the world. Several rice insertional mutant libraries are publicly available for systematic analysis of gene functions. However, the tagging efficiency of these mutant resources-the relationship between genotype and phenotype-is very low. We used whole-genome sequencing to analyze a T-DNA-tagged transformant from the Taiwan Rice Insertional Mutants (TRIM) resource. The phenomics records for M0028590, one of the TRIM lines, revealed three phenotypes-wild type, large grains, and tillering dwarf-in the 12 T1 plants. Using the sequencing data for 7 plants from three generations of this specific line, we demonstrate that introgression from an indica rice variety might occur in one generation before the seed was used for callus generation and transformation of this line. In addition, the large-grain trait came from the GS3 gene of the introgressed region and the tillering dwarf phenotype came from a single nucleotide change in the D17 gene that occurred during the callus induction to regeneration of the transformant. As well, another regenerant showed completely heterozygous single-nucleotide polymorphisms across the whole genome. In addition to the known sequence changes such as T-DNA integration, single nucleotide polymorphism, insertion, deletion, chromosome rearrangement and doubling, spontaneous outcrossing occurred in the rice field may also explain some mutated traits in a tagged mutant population. Thus, the co-segregation of an integration event and the phenotype should be checked when using these mutant populations.}, }
@article {pmid27185914, year = {2016}, author = {Hubbard, TP and Chao, MC and Abel, S and Blondel, CJ and Abel Zur Wiesch, P and Zhou, X and Davis, BM and Waldor, MK}, title = {Genetic analysis of Vibrio parahaemolyticus intestinal colonization.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {22}, pages = {6283-6288}, pmid = {27185914}, issn = {1091-6490}, support = {F31 AI120665/AI/NIAID NIH HHS/United States ; F32 GM108355/GM/NIGMS NIH HHS/United States ; R37 AI042347/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacterial Proteins/*genetics/metabolism ; DNA, Bacterial/genetics ; *Gene Expression Regulation, Bacterial ; Genetic Testing/*methods ; Humans ; Intestinal Mucosa/metabolism ; Intestines/*virology ; Rabbits ; Transcription Factors/metabolism ; Type III Secretion Systems ; Vibrio Infections/*genetics/virology ; Vibrio parahaemolyticus/*genetics/metabolism/pathogenicity ; Virulence/*genetics ; }, abstract = {Vibrio parahaemolyticus is the most common cause of seafood-borne gastroenteritis worldwide and a blight on global aquaculture. This organism requires a horizontally acquired type III secretion system (T3SS2) to infect the small intestine, but knowledge of additional factors that underlie V. parahaemolyticus pathogenicity is limited. We used transposon-insertion sequencing to screen for genes that contribute to viability of V. parahaemolyticus in vitro and in the mammalian intestine. Our analysis enumerated and controlled for the host infection bottleneck, enabling robust assessment of genetic contributions to in vivo fitness. We identified genes that contribute to V. parahaemolyticus colonization of the intestine independent of known virulence mechanisms in addition to uncharacterized components of T3SS2. Our study revealed that toxR, an ancestral locus in Vibrio species, is required for V. parahaemolyticus fitness in vivo and for induction of T3SS2 gene expression. The regulatory mechanism by which V. parahaemolyticus ToxR activates expression of T3SS2 resembles Vibrio cholerae ToxR regulation of distinct virulence elements acquired via lateral gene transfer. Thus, disparate horizontally acquired virulence systems have been placed under the control of this ancestral transcription factor across independently evolved human pathogens.}, }
@article {pmid27185558, year = {2016}, author = {Karnkowska, A and Vacek, V and Zubáčová, Z and Treitli, SC and Petrželková, R and Eme, L and Novák, L and Žárský, V and Barlow, LD and Herman, EK and Soukal, P and Hroudová, M and Doležal, P and Stairs, CW and Roger, AJ and Eliáš, M and Dacks, JB and Vlček, &#x10c; and Hampl, V}, title = {A Eukaryote without a Mitochondrial Organelle.}, journal = {Current biology : CB}, volume = {26}, number = {10}, pages = {1274-1284}, doi = {10.1016/j.cub.2016.03.053}, pmid = {27185558}, issn = {1879-0445}, support = {62809//CIHR/Canada ; }, mesh = {Biological Evolution ; Cytosol/metabolism ; Mitochondria/*physiology ; Oxymonadida/*cytology/genetics/*physiology ; Phylogeny ; Sulfur/*metabolism ; Transcriptome ; }, abstract = {The presence of mitochondria and related organelles in every studied eukaryote supports the view that mitochondria are essential cellular components. Here, we report the genome sequence of a microbial eukaryote, the oxymonad Monocercomonoides sp., which revealed that this organism lacks all hallmark mitochondrial proteins. Crucially, the mitochondrial iron-sulfur cluster assembly pathway, thought to be conserved in virtually all eukaryotic cells, has been replaced by a cytosolic sulfur mobilization system (SUF) acquired by lateral gene transfer from bacteria. In the context of eukaryotic phylogeny, our data suggest that Monocercomonoides is not primitively amitochondrial but has lost the mitochondrion secondarily. This is the first example of a eukaryote lacking any form of a mitochondrion, demonstrating that this organelle is not absolutely essential for the viability of a eukaryotic cell.}, }
@article {pmid27184979, year = {2016}, author = {Biswas, A and Staals, RH and Morales, SE and Fineran, PC and Brown, CM}, title = {CRISPRDetect: A flexible algorithm to define CRISPR arrays.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {356}, pmid = {27184979}, issn = {1471-2164}, mesh = {Algorithms ; Bacteria/genetics ; *CRISPR-Cas Systems ; *Clustered Regularly Interspaced Short Palindromic Repeats ; DNA, Intergenic ; Databases, Nucleic Acid ; Genome ; Genomics/methods ; Mutagenesis, Insertional ; Mutation ; Prokaryotic Cells/metabolism ; Sequence Deletion ; *Software ; Tandem Repeat Sequences ; User-Computer Interface ; Workflow ; }, abstract = {BACKGROUND: CRISPR (clustered regularly interspaced short palindromic repeats) RNAs provide the specificity for noncoding RNA-guided adaptive immune defence systems in prokaryotes. CRISPR arrays consist of repeat sequences separated by specific spacer sequences. CRISPR arrays have previously been identified in a large proportion of prokaryotic genomes. However, currently available detection algorithms do not utilise recently discovered features regarding CRISPR loci.<br><br>RESULTS: We have developed a new approach to automatically detect, predict and interactively refine CRISPR arrays. It is available as a web program and command line from bioanalysis.otago.ac.nz/CRISPRDetect. CRISPRDetect discovers putative arrays, extends the array by detecting additional variant repeats, corrects the direction of arrays, refines the repeat/spacer boundaries, and annotates different types of sequence variations (e.g. insertion/deletion) in near identical repeats. Due to these features, CRISPRDetect has significant advantages when compared to existing identification tools. As well as further support for small medium and large repeats, CRISPRDetect identified a class of arrays with 'extra-large' repeats in bacteria (repeats 44-50&#xa0;nt). The CRISPRDetect output is integrated with other analysis tools. Notably, the predicted spacers can be directly utilised by CRISPRTarget to predict targets.<br><br>CONCLUSION: CRISPRDetect enables more accurate detection of arrays and spacers and its gff output is suitable for inclusion in genome annotation pipelines and visualisation. It has been used to analyse all complete bacterial and archaeal reference genomes.}, }
@article {pmid27183895, year = {2016}, author = {Sukumar, S and Roberts, AP and Martin, FE and Adler, CJ}, title = {Metagenomic Insights into Transferable Antibiotic Resistance in Oral Bacteria.}, journal = {Journal of dental research}, volume = {95}, number = {9}, pages = {969-976}, doi = {10.1177/0022034516648944}, pmid = {27183895}, issn = {1544-0591}, mesh = {Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/genetics ; Humans ; *Metagenomics ; Microbiota/*drug effects/genetics ; Mouth/*microbiology ; }, abstract = {Antibiotic resistance is considered one of the greatest threats to global public health. Resistance is often conferred by the presence of antibiotic resistance genes (ARGs), which are readily found in the oral microbiome. In-depth genetic analyses of the oral microbiome through metagenomic techniques reveal a broad distribution of ARGs (including novel ARGs) in individuals not recently exposed to antibiotics, including humans in isolated indigenous populations. This has resulted in a paradigm shift from focusing on the carriage of antibiotic resistance in pathogenic bacteria to a broader concept of an oral resistome, which includes all resistance genes in the microbiome. Metagenomics is beginning to demonstrate the role of the oral resistome and horizontal gene transfer within and between commensals in the absence of selective pressure, such as an antibiotic. At the chairside, metagenomic data reinforce our need to adhere to current antibiotic guidelines to minimize the spread of resistance, as such data reveal the extent of ARGs without exposure to antimicrobials and the ecologic changes created in the oral microbiome by even a single dose of antibiotics. The aim of this review is to discuss the role of metagenomics in the investigation of the oral resistome, including the transmission of antibiotic resistance in the oral microbiome. Future perspectives, including clinical implications of the findings from metagenomic investigations of oral ARGs, are also considered.}, }
@article {pmid27183715, year = {2016}, author = {Godakova, SA and Sevast'yanova, GA and Semyenova, SK}, title = {[STRUCTURE AND DISTRIBUTION OF THE RETROTRANSPOSON BOV-B LINE].}, journal = {Molekuliarnaia genetika, mikrobiologiia i virusologiia}, volume = {34}, number = {1}, pages = {9-12}, doi = {10.3103/s0891416816010043}, pmid = {27183715}, issn = {0208-0613}, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal/*physiology ; Retroelements/*physiology ; }, abstract = {The classification of mobile elements was discussed. Special attention was devoted to the retroelement of the LINE group: retrotransposon Bov-B LINE. The history of its origin and distribution in the nature was considered. The results of the phenomenon of horizontal transition of the retrotransposon Bov-B LINE between evolutionally distant classes were discussed.}, }
@article {pmid27183378, year = {2017}, author = {El-Mahdy, TS and Al-Agamy, MH and Al-Qahtani, AA and Shibl, AM}, title = {Detection of blaOXA-23-like and blaNDM-1 in Acinetobacter baumannii from the Eastern Region, Saudi Arabia.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {23}, number = {1}, pages = {115-121}, doi = {10.1089/mdr.2015.0304}, pmid = {27183378}, issn = {1931-8448}, mesh = {Acinetobacter Infections/drug therapy/*epidemiology/microbiology ; Acinetobacter baumannii/classification/drug effects/genetics/isolation &amp; purification ; Aminoglycosides/pharmacology ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics/metabolism ; Carbapenems/pharmacology ; Ciprofloxacin/pharmacology ; Drug Resistance, Multiple, Bacterial/*genetics ; Electrophoresis, Gel, Pulsed-Field ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; Minocycline/analogs &amp; derivatives/pharmacology ; Phylogeny ; Plasmids/chemistry/classification/*metabolism ; Polymerase Chain Reaction ; Prevalence ; Public Health Surveillance ; Saudi Arabia/epidemiology ; Tigecycline ; beta-Lactamases/*genetics/metabolism ; }, abstract = {Acinetobacter baumannii is currently considered as one of the most common successful pathogens in the healthcare system due to its ability to quickly develop resistance. Ten carbapenem-resistant A. calcoaceticus-baumannii complex were isolated from the eastern region, Saudi Arabia in 2014. All isolates were resistant to ciprofloxacin, however, 8 of 10 isolates were tigecycline resistant. Susceptibility test was also carried out for three aminoglycosides, resistance to gentamicin was 80%, amikacin was 90%, and tobramycin was 50%. Colistin susceptibility was seen in all isolates. The 10 isolates harbored blaOXA-23-like and ISAba1 and 9 of them also carried blaADC. Three isolates of 10 harbored blaNDM-1 coding for NDM metallo-β-lactamase (MBL) with coexistence of blaADC together with either blaGES or blaTEM or both. Those three isolates exhibited negative Etest MBL screening test. Pulsed-field gel electrophoresis revealed the high clonal variability of the isolates, although two isolates were indistinguishable. The risk of dissemination of carbapenem resistance through presence of ISAba1 upstream of OXA-23-like in all isolates raises the concern about emergence of higher carbapenem prevalence rates in the future in our region. This study also demonstrated the importance of molecular surveillance to provide accurate and reliable data about the resistance rates of A. baumannii. Finally, the high incidence of NDM-1 among our isolates requires a routine surveillance to monitor the future prevalence of this enzyme in the region.}, }
@article {pmid27173902, year = {2016}, author = {Bemm, F and Weiß, CL and Schultz, J and Förster, F}, title = {Genome of a tardigrade: Horizontal gene transfer or bacterial contamination?.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {22}, pages = {E3054-6}, pmid = {27173902}, issn = {1091-6490}, mesh = {*Gene Transfer, Horizontal ; *Genome ; Tardigrada ; }, }
@article {pmid27173901, year = {2016}, author = {Arakawa, K}, title = {No evidence for extensive horizontal gene transfer from the draft genome of a tardigrade.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {22}, pages = {E3057}, pmid = {27173901}, issn = {1091-6490}, mesh = {Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome ; Genome, Bacterial ; Humans ; Phylogeny ; Tardigrada/genetics ; }, }
@article {pmid27172044, year = {2016}, author = {Pehrsson, EC and Tsukayama, P and Patel, S and Mejía-Bautista, M and Sosa-Soto, G and Navarrete, KM and Calderon, M and Cabrera, L and Hoyos-Arango, W and Bertoli, MT and Berg, DE and Gilman, RH and Dantas, G}, title = {Interconnected microbiomes and resistomes in low-income human habitats.}, journal = {Nature}, volume = {533}, number = {7602}, pages = {212-216}, pmid = {27172044}, issn = {1476-4687}, support = {MR/K007467/1/MRC_/Medical Research Council/United Kingdom ; R01 GM099538/GM/NIGMS NIH HHS/United States ; R01-GM099538/GM/NIGMS NIH HHS/United States ; }, mesh = {Agriculture ; Bacteria/classification/*genetics ; Developing Countries/*economics ; Drug Resistance, Microbial/*genetics ; *Ecosystem ; El Salvador ; Environmental Monitoring ; Feces/microbiology ; *Gene Transfer, Horizontal ; Humans ; Metagenomics ; Microbiota/*genetics ; Molecular Epidemiology ; Peru ; Phylogeny ; Residence Characteristics ; Risk Assessment ; Sewage/microbiology ; Socioeconomic Factors ; }, abstract = {Antibiotic-resistant infections annually claim hundreds of thousands of lives worldwide. This problem is exacerbated by exchange of resistance genes between pathogens and benign microbes from diverse habitats. Mapping resistance gene dissemination between humans and their environment is a public health priority. Here we characterized the bacterial community structure and resistance exchange networks of hundreds of interconnected human faecal and environmental samples from two low-income Latin American communities. We found that resistomes across habitats are generally structured by bacterial phylogeny along ecological gradients, but identified key resistance genes that cross habitat boundaries and determined their association with mobile genetic elements. We also assessed the effectiveness of widely used excreta management strategies in reducing faecal bacteria and resistance genes in these settings representative of low- and middle-income countries. Our results lay the foundation for quantitative risk assessment and surveillance of resistance gene dissemination across interconnected habitats in settings representing over two-thirds of the world's population.}, }
@article {pmid27167505, year = {2017}, author = {Xue, G and Li, J and Feng, Y and Xu, W and Li, S and Yan, C and Zhao, H and Sun, H}, title = {High Prevalence of Plasmid-Mediated Quinolone Resistance Determinants in Escherichia coli and Klebsiella pneumoniae Isolates from Pediatric Patients in China.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {23}, number = {1}, pages = {107-114}, doi = {10.1089/mdr.2016.0004}, pmid = {27167505}, issn = {1931-8448}, mesh = {Anti-Bacterial Agents/pharmacology ; Child ; Child, Preschool ; China/epidemiology ; Conjugation, Genetic ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/classification/drug effects/genetics/isolation &amp; purification ; Escherichia coli Infections/drug therapy/*epidemiology/microbiology ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Humans ; Infant ; Klebsiella Infections/drug therapy/*epidemiology/microbiology ; Klebsiella pneumoniae/classification/drug effects/genetics/isolation &amp; purification ; Microbial Sensitivity Tests ; Phylogeny ; Plasmids/chemistry/classification/*metabolism ; Polymerase Chain Reaction ; Prevalence ; Public Health Surveillance ; Quinolones/pharmacology ; Sequence Analysis, DNA ; beta-Lactamases/*genetics/metabolism ; beta-Lactams/pharmacology ; }, abstract = {In this study, the prevalence of the plasmid-mediated quinolone resistance (PMQR) genes among pediatric clinical isolates of Escherichia coli and Klebsiella pneumoniae was investigated. A total of 243 nonduplicate clinical isolates of E. coli and K. pneumoniae collected between January 2010 and December 2012 from Beijing, China, were studied. In total, 55 isolates (22.63%) were positive for PMQR genes, the most frequently detected gene was qnrS (13.2%), followed by aac(6')-Ib-cr (6.2%) and qnrB (3.7%). The qnrA and qepA genes were not detected. Furthermore, 92.73% (51/55) produced extended-spectrum β-lactamases (ESBLs) and 21.82% (12/55) were resistant to quinolones. DNA sequencing results showed that 14.55% (8/55) of isolates possessed gyrA mutations, while 1.82% (1/55) had parC mutations in the quinolone resistance-determining region (QRDR). Nalidixic acid or ciprofloxacin resistance of the transconjugants increased from 2- to 32-fold. Enterobacterial repetitive intergenic consensus sequence polymerase chain reaction typing indicated that most isolates were not clonally related. Our findings showed that the PMQR detection rate among pediatric clinical isolates of E. coli and K. pneumoniae was high in China. PMQR-positive strains were more common among ESBL-producing and ciprofloxacin-susceptible isolates. Conjugation experiments showed that these isolates could be transferred horizontally. The present study highlights the high prevalence of PMQR in Chinese pediatrics who are not treated with quinolones.}, }
@article {pmid27165784, year = {2016}, author = {Dobiasova, H and Dolejska, M}, title = {Prevalence and diversity of IncX plasmids carrying fluoroquinolone and β-lactam resistance genes in Escherichia coli originating from diverse sources and geographical areas.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {71}, number = {8}, pages = {2118-2124}, doi = {10.1093/jac/dkw144}, pmid = {27165784}, issn = {1460-2091}, mesh = {Animals ; Animals, Wild ; Cluster Analysis ; Conjugation, Genetic ; *Drug Resistance, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/*drug effects/genetics/isolation &amp; purification ; Escherichia coli Infections/microbiology/veterinary ; Fluoroquinolones/*pharmacology ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genetic Variation ; Genotype ; Global Health ; Humans ; Molecular Typing ; Plasmids/*analysis/*classification ; Polymerase Chain Reaction ; Prevalence ; Sequence Analysis, DNA ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Transformation, Bacterial ; beta-Lactams/*pharmacology ; }, abstract = {OBJECTIVES: To describe the prevalence and diversity of IncX plasmids with antibiotic resistance genes in Enterobacteriaceae and to identify the most disseminated lineages of the plasmid family.<br><br>METHODS: IncX plasmids were screened in 1894 Enterobacteriaceae isolates resistant to cefotaxime (2 mg/L) or with reduced susceptibility to ciprofloxacin (0.05 mg/L) obtained from various sources in five continents using PCR. IncX plasmid-harbouring isolates were identified using MALDI-TOF or biochemical tests, and screened for antibiotic resistance genes using PCR and sequencing; their clonality was determined by PFGE. Horizontal transfer of plasmids was tested using transformation and conjugation. IncX plasmids were characterized by S1-nuclease and PFGE, RFLP and hybridization.<br><br>RESULTS: A total of 164 Escherichia coli isolates (8.7%, n&#x200a;=&#x200a;1894) carried at least one IncX subgroup. Seven isolates harboured two distinct subgroups. IncX1 subgroup was found in 93 isolates, followed by IncX2 (35 isolates), IncX4 (28) and IncX3 (15). IncX4 plasmids were not transferred horizontally as single plasmids and therefore excluded from further analysis. The most disseminated lineages of IncX plasmids included IncX1 harbouring qnrS1 and blaTEM-1,-135 found in 36 E. coli from different sources in Europe and Australia and IncX2 carrying qnrS1 and tet(A) detected in nine E. coli from wildlife in Europe. IncX3 plasmids harboured predominantly blaSHV-12 and qnrS1 or qnrB7.<br><br>CONCLUSIONS: IncX plasmids were widely distributed in E. coli from wildlife in Europe and were predominantly associated with fluoroquinolone resistance genes. Plasmids showing indistinguishable restriction profiles were identified in E. coli from different sources and countries suggesting wide dissemination of certain plasmid lineages.}, }
@article {pmid27162172, year = {2016}, author = {Medina, EM and Turner, JJ and Gordân, R and Skotheim, JM and Buchler, NE}, title = {Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi.}, journal = {eLife}, volume = {5}, number = {}, pages = {}, pmid = {27162172}, issn = {2050-084X}, support = {DP2 OD008654/OD/NIH HHS/United States ; P50 GM107615/GM/NIGMS NIH HHS/United States ; R01 GM092925/GM/NIGMS NIH HHS/United States ; }, mesh = {*Cell Cycle ; Cell Cycle Proteins/*genetics/*metabolism ; *Evolution, Molecular ; Fungi/*cytology/*genetics/physiology ; Gene Transfer, Horizontal ; Transcription Factors/genetics/metabolism ; }, abstract = {Although cell cycle control is an ancient, conserved, and essential process, some core animal and fungal cell cycle regulators share no more sequence identity than non-homologous proteins. Here, we show that evolution along the fungal lineage was punctuated by the early acquisition and entrainment of the SBF transcription factor through horizontal gene transfer. Cell cycle evolution in the fungal ancestor then proceeded through a hybrid network containing both SBF and its ancestral animal counterpart E2F, which is still maintained in many basal fungi. We hypothesize that a virally-derived SBF may have initially hijacked cell cycle control by activating transcription via the cis-regulatory elements targeted by the ancestral cell cycle regulator E2F, much like extant viral oncogenes. Consistent with this hypothesis, we show that SBF can regulate promoters with E2F binding sites in budding yeast.}, }
@article {pmid27161450, year = {2016}, author = {Liu, C and Wang, X and Wang, X and Sun, C}, title = {Acclimation of Antarctic Chlamydomonas to the sea-ice environment: a transcriptomic analysis.}, journal = {Extremophiles : life under extreme conditions}, volume = {20}, number = {4}, pages = {437-450}, pmid = {27161450}, issn = {1433-4909}, mesh = {Acclimatization/*genetics ; Antarctic Regions ; Chlamydomonas/*genetics/metabolism ; *Cold Temperature ; Gene Transfer, Horizontal ; Ice Cover ; Lipid Metabolism ; Membrane Transport Proteins/genetics/metabolism ; Molecular Chaperones/genetics/metabolism ; Plant Proteins/genetics/metabolism ; Seawater ; Signal Transduction/genetics ; *Transcriptome ; }, abstract = {The Antarctic green alga Chlamydomonas sp. ICE-L was isolated from sea ice. As a psychrophilic microalga, it can tolerate the environmental stress in the sea-ice brine, such as freezing temperature and high salinity. We performed a transcriptome analysis to identify freezing stress responding genes and explore the extreme environmental acclimation-related strategies. Here, we show that many genes in ICE-L transcriptome that encoding PUFA synthesis enzymes, molecular chaperon proteins, and cell membrane transport proteins have high similarity to the gens from Antarctic bacteria. These ICE-L genes are supposed to be acquired through horizontal gene transfer from its symbiotic microbes in the sea-ice brine. The presence of these genes in both sea-ice microalgae and bacteria indicated the biological processes they involved in are possibly contributing to ICE-L success in sea ice. In addition, the biological pathways were compared between ICE-L and its closely related sister species, Chlamydomonas reinhardtii and Volvox carteri. In ICE-L transcripome, many sequences homologous to the plant or bacteria proteins in the post-transcriptional, post-translational modification, and signal-transduction KEGG pathways, are absent in the nonpsychrophilic green algae. These complex structural components might imply enhanced stress adaptation capacity. At last, differential gene expression analysis at the transcriptome level of ICE-L indicated that genes that associated with post-translational modification, lipid metabolism, and nitrogen metabolism are responding to the freezing treatment. In conclusion, the transcriptome of Chlamydomonas sp. ICE-L is very useful for exploring the mutualistic interaction between microalgae and bacteria in sea ice; and discovering the specific genes and metabolism pathways responding to the freezing acclimation in psychrophilic microalgae.}, }
@article {pmid27152022, year = {2016}, author = {Sanfilippo, JE and Nguyen, AA and Karty, JA and Shukla, A and Schluchter, WM and Garczarek, L and Partensky, F and Kehoe, DM}, title = {Self-regulating genomic island encoding tandem regulators confers chromatic acclimation to marine Synechococcus.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {21}, pages = {6077-6082}, pmid = {27152022}, issn = {1091-6490}, support = {T32 GM007757/GM/NIGMS NIH HHS/United States ; }, mesh = {Acclimatization/*physiology ; *Aquatic Organisms/genetics/metabolism ; *Bacterial Proteins/genetics/metabolism ; *Genomic Islands ; *Phycoerythrin/genetics/metabolism ; *Synechococcus/genetics/metabolism ; }, abstract = {The evolutionary success of marine Synechococcus, the second-most abundant phototrophic group in the marine environment, is partly attributable to this group's ability to use the entire visible spectrum of light for photosynthesis. This group possesses a remarkable diversity of light-harvesting pigments, and most of the group's members are orange and pink because of their use of phycourobilin and phycoerythrobilin chromophores, which are attached to antennae proteins called phycoerythrins. Many strains can alter phycoerythrin chromophore ratios to optimize photon capture in changing blue-green environments using type IV chromatic acclimation (CA4). Although CA4 is common in most marine Synechococcus lineages, the regulation of this process remains unexplored. Here, we show that a widely distributed genomic island encoding tandem master regulators named FciA (for type four chromatic acclimation island) and FciB plays a central role in controlling CA4. FciA and FciB have diametric effects on CA4. Interruption of fciA causes a constitutive green light phenotype, and interruption of fciB causes a constitutive blue light phenotype. These proteins regulate all of the molecular responses occurring during CA4, and the proteins' activity is apparently regulated posttranscriptionally, although their cellular ratio appears to be critical for establishing the set point for the blue-green switch in ecologically relevant light environments. Surprisingly, FciA and FciB coregulate only three genes within the Synechococcus genome, all located within the same genomic island as fciA and fciB These findings, along with the widespread distribution of strains possessing this island, suggest that horizontal transfer of a small, self-regulating DNA region has conferred CA4 capability to marine Synechococcus throughout many oceanic areas.}, }
@article {pmid27151933, year = {2016}, author = {Sharma, A and Gilbert, JA and Lal, R}, title = {(Meta)genomic insights into the pathogenome of Cellulosimicrobium cellulans.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {25527}, pmid = {27151933}, issn = {2045-2322}, mesh = {Actinobacteria/*genetics/*pathogenicity ; Base Composition ; Codon ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genomic Islands ; Humans ; Metagenomics ; Synteny ; Virulence Factors/*genetics ; }, abstract = {Despite having serious clinical manifestations, Cellulosimicrobium cellulans remain under-reported with only three genome sequences available at the time of writing. Genome sequences of C. cellulans LMG16121, C. cellulans J36 and Cellulosimicrobium sp. strain MM were used to determine distribution of pathogenicity islands (PAIs) across C. cellulans, which revealed 49 potential marker genes with known association to human infections, e.g. Fic and VbhA toxin-antitoxin system. Oligonucleotide composition-based analysis of orthologous proteins (n = 791) across three genomes revealed significant negative correlation (P < 0.05) between frequency of optimal codons (Fopt) and gene G+C content, highlighting the G+C-biased gene conversion (gBGC) effect across Cellulosimicrobium strains. Bayesian molecular-clock analysis performed on three virulent PAI proteins (Fic; D-alanyl-D-alanine-carboxypeptidase; transposase) dated the divergence event at 300 million years ago from the most common recent ancestor. Synteny-based annotation of hypothetical proteins highlighted gene transfers from non-pathogenic bacteria as a key factor in the evolution of PAIs. Additonally, deciphering the metagenomic islands using strain MM's genome with environmental data from the site of isolation (hot-spring biofilm) revealed (an)aerobic respiration as population segregation factor across the in situ cohorts. Using reference genomes and metagenomic data, our results highlight the emergence and evolution of PAIs in the genus Cellulosimicrobium.}, }
@article {pmid27151790, year = {2016}, author = {Parmeciano Di Noto, G and Vázquez, SC and MacCormack, WP and Iriarte, A and Quiroga, C}, title = {Draft Genome of Shewanella frigidimarina Ag06-30, a Marine Bacterium Isolated from Potter Peninsula, King George Island, Antarctica.}, journal = {Genome announcements}, volume = {4}, number = {3}, pages = {}, pmid = {27151790}, issn = {2169-8287}, abstract = {We present the draft genome of Shewanella frigidimarina Ag06-30, a marine bacterium from King George Island, Antarctica, which encodes the carbapenemase SFP-1. The assembly contains 4,799,218 bp (G+C content 41.24%). This strain harbors several mobile genetic elements that provide insight into lateral gene transfer and bacterial plasticity and evolution.}, }
@article {pmid27150396, year = {2016}, author = {Siebor, E and de Curraize, C and Amoureux, L and Neuwirth, C}, title = {Mobilization of the Salmonella genomic island SGI1 and the Proteus genomic island PGI1 by the A/C2 plasmid carrying blaTEM-24 harboured by various clinical species of Enterobacteriaceae.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {71}, number = {8}, pages = {2167-2170}, doi = {10.1093/jac/dkw151}, pmid = {27150396}, issn = {1460-2091}, mesh = {Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; Enterobacteriaceae/*genetics/isolation &amp; purification ; Enterobacteriaceae Infections/microbiology ; *Gene Transfer, Horizontal ; *Genomic Islands ; *Plasmids ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; beta-Lactamases/genetics ; }, abstract = {OBJECTIVES: The objective of this study was to transfer the Salmonella genomic islands (GIs) SGI1 and SGI1-V and the Proteus GI PGI1-PmESC to clinical isolates of Enterobacteriaceae harbouring an A/C2 plasmid.<br><br>METHODS: The entire genetic structures of SGI1 and PGI1-PmESC from Salmonella Typhimurium and Proteus mirabilis, respectively, were characterized by PCR and DNA sequencing. Ten enterobacterial isolates from different species carrying blaTEM-24 on an A/C2 plasmid were used for the mobilization of SGI1: Escherichia coli, Enterobacter cloacae, Klebsiella pneumoniae, Proteus mirabilis, Enterobacter aerogenes, Citrobacter freundii, Klebsiella oxytoca, Proteus vulgaris, Providencia stuartii and Serratia marcescens. SGI1-V and PGI1-PmESC were transferred to E. aerogenes. Conjugation attempts were also performed using the wild strain E. aerogenes BOL and E. coli K-12 with or without pA/C2. Detection and location of the GI in the transconjugants were assessed by PCR targeting their junctions.<br><br>RESULTS: The multidrug resistance region of PGI1-PmESC contained a class 1 integron (aadB and aadA2) and regions deriving from transposon Tn501 and a hybrid Tn502/Tn5053 transposon, whereas SGI1 harboured the known determinants responsible for the pentaresistance. The transfer of SGI1 occurred from Salmonella Typhimurium to the 10 enterobacterial isolates, and transfer of SGI1-V and PGI1-PmESC occurred from P. mirabilis to E. aerogenes. In all transconjugants the GI was located at the 3'-end of trmE. SGI1 was also transferred to E. aerogenes BOL (pA/C2) and E. coli K-12 (pA/C2), but not to E. aerogenes BOL and E. coli K-12.<br><br>CONCLUSIONS: This is the first known description of SGI1 mobilization into a broad range of enterobacterial species harbouring an A/C2 plasmid and the first demonstration of PGI1 movement. The A/C2 plasmid is responsible for the GI mobilization.}, }
@article {pmid27149698, year = {2016}, author = {Toll-Riera, M and San Millan, A and Wagner, A and MacLean, RC}, title = {The Genomic Basis of Evolutionary Innovation in Pseudomonas aeruginosa.}, journal = {PLoS genetics}, volume = {12}, number = {5}, pages = {e1006005}, pmid = {27149698}, issn = {1553-7404}, support = {/WT_/Wellcome Trust/United Kingdom ; G0900747/MRC_/Medical Research Council/United Kingdom ; G090074791070/MRC_/Medical Research Council/United Kingdom ; 090532/Z/09/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Evolution, Molecular ; Gene Duplication/genetics ; Gene Transfer, Horizontal ; Genetic Pleiotropy ; Genome, Bacterial ; *Genomics ; Mutation ; Pseudomonas Infections/*genetics/microbiology ; Pseudomonas aeruginosa/*genetics/pathogenicity ; Transcription, Genetic ; }, abstract = {Novel traits play a key role in evolution, but their origins remain poorly understood. Here we address this problem by using experimental evolution to study bacterial innovation in real time. We allowed 380 populations of Pseudomonas aeruginosa to adapt to 95 different carbon sources that challenged bacteria with either evolving novel metabolic traits or optimizing existing traits. Whole genome sequencing of more than 80 clones revealed profound differences in the genetic basis of innovation and optimization. Innovation was associated with the rapid acquisition of mutations in genes involved in transcription and metabolism. Mutations in pre-existing duplicate genes in the P. aeruginosa genome were common during innovation, but not optimization. These duplicate genes may have been acquired by P. aeruginosa due to either spontaneous gene amplification or horizontal gene transfer. High throughput phenotype assays revealed that novelty was associated with increased pleiotropic costs that are likely to constrain innovation. However, mutations in duplicate genes with close homologs in the P. aeruginosa genome were associated with low pleiotropic costs compared to mutations in duplicate genes with distant homologs in the P. aeruginosa genome, suggesting that functional redundancy between duplicates facilitates innovation by buffering pleiotropic costs.}, }
@article {pmid27148814, year = {2017}, author = {Chang, CY and Lin, HJ and Chang, LL and Ma, L and Siu, LK and Tung, YC and Lu, PL}, title = {Characterization of Extended-Spectrum β-Lactamase-Carrying Plasmids in Clinical Isolates of Klebsiella pneumoniae from Taiwan.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {23}, number = {1}, pages = {98-106}, doi = {10.1089/mdr.2015.0212}, pmid = {27148814}, issn = {1931-8448}, mesh = {Anti-Bacterial Agents/pharmacology ; Clone Cells ; Conjugation, Genetic ; Drug Resistance, Multiple, Bacterial/*genetics ; Electrophoresis, Gel, Pulsed-Field ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Humans ; Klebsiella Infections/drug therapy/*epidemiology/microbiology ; Klebsiella pneumoniae/classification/*drug effects/genetics/isolation &amp; purification ; Microbial Sensitivity Tests ; Phylogeny ; Plasmids/chemistry/classification/*metabolism ; Polymorphism, Restriction Fragment Length ; Public Health Surveillance ; Replicon ; Taiwan/epidemiology ; Trimethoprim, Sulfamethoxazole Drug Combination/pharmacology ; beta-Lactamases/*genetics/metabolism ; beta-Lactams/pharmacology ; }, abstract = {We analyzed the replicon types, sizes, and restriction fragment length polymorphism (RFLP) typing of plasmids carrying extended-spectrum β-lactamase (ESBL) genes in Klebsiella pneumoniae isolates from Taiwan. Fifty-one Escherichia coli transconjugant strains with plasmids from ESBL-producing K. pneumoniae from the Taiwan Surveillance of Antimicrobial Resistance III Program in 2002 were included. All the 51 plasmids carried a blaCTX-M gene, the majority of which were blaCTX-M-3 (28/51 [54.9%]). Plasmids ranged in size from 126 to 241 kb by S1 nuclease digestion and subsequent pulsed-field gel electrophoresis, and the most common plasmid size (37.3%) was 161-170 kb. The most common replicon type of plasmids was incompatibility group (Inc)A/C (60.8%). The IncA/C plasmids all carried blaCTX-M (blaCTX-M-3, -14, -15), and some also carried blaSHV (blaSHV-5, -12) genes. All 51 plasmids could be typed with PstI, and 27 (52.9%) belonged to 10 clusters. Thirty-eight of the 51 plasmids were typable with BamHI, and 21 plasmids (55.3%) fell into 7 clusters. Plasmids in the same cluster belonged to the same incompatibility group, with the exception of cluster C6. In conclusion, IncA/C plasmids are the main plasmid type responsible for the dissemination of ESBL genes of K. pneumoniae from Taiwan. RFLP with PstI possessed better discriminatory power than that with BamHI and PCR-based replicon typing for ESBL-carrying plasmids in K. pneumoniae in this study. Greater than 50% of plasmids fell into clusters, and >60% of cluster-classified plasmids were present in clonally unrelated isolates, indicating that horizontal transfer of plasmids plays an important role in the spread of ESBL genes.}, }
@article {pmid27147933, year = {2016}, author = {Kong, HG and Kim, NH and Lee, SY and Lee, SW}, title = {Impact of a Recombinant Biocontrol Bacterium, Pseudomonas fluorescens pc78, on Microbial Community in Tomato Rhizosphere.}, journal = {The plant pathology journal}, volume = {32}, number = {2}, pages = {136-144}, pmid = {27147933}, issn = {1598-2254}, abstract = {Pseudomonas fluorescens pc78 is an effective biocontrol agent for soil-borne fungal diseases. We previously constructed a P43-gfp tagged biocontrol bacteria P. fluorescens pc78-48 to investigate bacterial traits in natural ecosystem and the environmental risk of genetically modified biocontrol bacteria in tomato rhizosphere. Fluctuation of culturable bacteria profile, microbial community structure, and potential horizontal gene transfer was investigated over time after the bacteria treatment to the tomato rhizosphere. Tagged gene transfer to other organisms such as tomato plants and bacteria cultured on various media was examined by polymerase chain reaction, using gene specific primers. Transfer of chromosomally integrated P43-gfp from pc78 to other organisms was not apparent. Population and colony types of culturable bacteria were not significantly affected by the introduction of P. fluorescens pc78 or pc78-48 into tomato rhizosphere. Additionally, terminal restriction fragment length polymorphism profiles were investigated to estimate the influence on the microbial community structure in tomato rhizosphere between non-treated and pc78-48-treated samples. Interestingly, rhizosphere soil treated with strain pc78-48 exhibited a significantly different bacterial community structure compared to that of non-treated rhizosphere soil. Our results suggest that biocontrol bacteria treatment influences microbial community in tomato rhizosphere, while the chromosomally modified biocontrol bacteria may not pose any specific environmental risk in terms of gene transfer.}, }
@article {pmid27147305, year = {2016}, author = {Anjum, MF and Duggett, NA and AbuOun, M and Randall, L and Nunez-Garcia, J and Ellis, RJ and Rogers, J and Horton, R and Brena, C and Williamson, S and Martelli, F and Davies, R and Teale, C}, title = {Colistin resistance in Salmonella and Escherichia coli isolates from a pig farm in Great Britain.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {71}, number = {8}, pages = {2306-2313}, doi = {10.1093/jac/dkw149}, pmid = {27147305}, issn = {1460-2091}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Colistin/*pharmacology ; Conjugation, Genetic ; *Drug Resistance, Bacterial ; Escherichia coli/*drug effects/isolation &amp; purification ; Farms ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Microbial Sensitivity Tests ; Plasmids/analysis ; Salmonella/*drug effects/isolation &amp; purification ; Sequence Analysis, DNA ; Swine/*microbiology ; United Kingdom ; }, abstract = {OBJECTIVES: The objective of this study was to characterize colistin-resistant bacteria isolated from pigs on a farm in Great Britain following identification of a plasmid-borne colistin resistance mechanism in Escherichia coli from China.<br><br>METHODS: Phenotypic antimicrobial susceptibility testing was undertaken by broth dilution and WGS was performed to detect the presence of genes encoding resistance and virulence. Transferable colistin resistance was investigated by conjugation.<br><br>RESULTS: Two E. coli and one Salmonella Typhimurium variant Copenhagen were shown to be MDR, including resistance to colistin, with one E. coli and the Salmonella carrying the mcr-1 gene; all three harboured chromosomal mutations in genes conferring colistin resistance and both E. coli harboured &#x3b2;-lactamase resistance. The Salmonella mcr-1 plasmid was highly similar to pHNSHP45, from China, while the E. coli mcr-1 plasmid only had the ISApII and mcr-1 genes in common. The frequency of mcr-1 plasmid transfer by conjugation to recipient Enterobacteriaceae from Salmonella was low, lying between 10(-7) and 10(-9) cfu/recipient cfu. We were unable to demonstrate mcr-1 plasmid transfer from the E. coli. Plasmid profiling indicated transfer of multiple plasmids from the Salmonella resulting in some MDR transconjugants.<br><br>CONCLUSIONS: Identification of the mcr-1 gene in Enterobacteriaceae from pigs confirms its presence in livestock in Great Britain. The results suggest dissemination of resistance through different horizontally transferable elements. The in vitro transfer of multiple plasmids carrying colistin and other resistances from the Salmonella isolate underlines the potential for wider dissemination and recombination.}, }
@article {pmid27144273, year = {2016}, author = {Wen, D and Yu, Y and Nakhleh, L}, title = {Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent.}, journal = {PLoS genetics}, volume = {12}, number = {5}, pages = {e1006006}, pmid = {27144273}, issn = {1553-7404}, mesh = {Bayes Theorem ; Computational Biology/methods ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome ; Markov Chains ; *Models, Genetic ; *Phylogeny ; }, abstract = {The multispecies coalescent (MSC) is a statistical framework that models how gene genealogies grow within the branches of a species tree. The field of computational phylogenetics has witnessed an explosion in the development of methods for species tree inference under MSC, owing mainly to the accumulating evidence of incomplete lineage sorting in phylogenomic analyses. However, the evolutionary history of a set of genomes, or species, could be reticulate due to the occurrence of evolutionary processes such as hybridization or horizontal gene transfer. We report on a novel method for Bayesian inference of genome and species phylogenies under the multispecies network coalescent (MSNC). This framework models gene evolution within the branches of a phylogenetic network, thus incorporating reticulate evolutionary processes, such as hybridization, in addition to incomplete lineage sorting. As phylogenetic networks with different numbers of reticulation events correspond to points of different dimensions in the space of models, we devise a reversible-jump Markov chain Monte Carlo (RJMCMC) technique for sampling the posterior distribution of phylogenetic networks under MSNC. We implemented the methods in the publicly available, open-source software package PhyloNet and studied their performance on simulated and biological data. The work extends the reach of Bayesian inference to phylogenetic networks and enables new evolutionary analyses that account for reticulation.}, }
@article {pmid27144084, year = {2016}, author = {Yosef, I and Manor, M and Qimron, U}, title = {Counteracting selection for antibiotic-resistant bacteria.}, journal = {Bacteriophage}, volume = {6}, number = {1}, pages = {e1096996}, pmid = {27144084}, issn = {2159-7073}, abstract = {The occurrence of antibiotic-resistant bacterial pathogens is on the rise because antibiotics exert selection pressure that kills only the antibiotic-sensitive pathogens. Sanitation and cleansing of hospital surfaces and the skin of medical personnel do not counteract this selective pressure, but rather indiscriminately reduce total pathogens on treated surfaces. Here, we discuss two recently introduced genetic strategies, based on temperate bacteriophages as DNA-delivery vehicles, that aim to sensitize bacteria to antibiotics and selectively kill the antibiotic-resistant ones. Outlooks for rendering one such approach more efficient and applicable are proposed. We believe that using an end product designed according to the provided principles on hospital surfaces and in hand-sanitizers will facilitate substitution of antibiotic-resistant pathogens with sensitive ones.}, }
@article {pmid27143648, year = {2016}, author = {Fang, L and Li, X and Li, L and Li, S and Liao, X and Sun, J and Liu, Y}, title = {Co-spread of metal and antibiotic resistance within ST3-IncHI2 plasmids from E. coli isolates of food-producing animals.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {25312}, pmid = {27143648}, issn = {2045-2322}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; DNA Transposable Elements ; *Drug Resistance, Bacterial ; Escherichia coli/*drug effects/*genetics/isolation &amp; purification ; Escherichia coli Infections/microbiology/*veterinary ; Gene Transfer, Horizontal ; Genes, Bacterial ; Livestock ; Metals/*pharmacology ; Microbial Sensitivity Tests ; Operon ; Plasmids/*classification ; Selection, Genetic ; Sequence Analysis, DNA ; }, abstract = {Concerns have been raised in recent years regarding co-selection for antibiotic resistance among bacteria exposed to heavy metals, particularly copper and zinc, used as growth promoters for some livestock species. In this study, 25 IncHI2 plasmids harboring oqxAB (20/25)/blaCTX-M (18/25) were found with sizes ranging from ∼260 to ∼350 kb and 22 belonged to the ST3-IncHI2 group. In addition to blaCTX-M and oqxAB, pcoA-E (5/25) and silE-P (5/25), as well as aac(6')-Ib-cr (18/25), floR (16/25), rmtB (6/25), qnrS1(3/25) and fosA3 (2/25), were also identified on these IncHI2 plasmids. The plasmids carried pco and sil contributed to increasing in the MICs of CuSO4 and AgNO3. The genetic context surrounding the two operons was well conserved except some variations within the pco operon. The ~32 kb region containing the two operons identified in the IncHI2 plasmids was also found in chromosomes of different Enterobacteriaceae species. Further, phylogenetic analysis of this structure showed that Tn7-like transposon might play an important role in cross-genus transfer of the sil and pco operons among Enterobacteriaceae. In conclusion, co-existence of the pco and sil operons, and oqxAB/blaCTX-M as well as other antibiotic resistance genes on IncHI2 plasmids may promote the development of multidrug-resistant bacteria.}, }
@article {pmid27141324, year = {2016}, author = {Kejnovsky, E and Trifonov, EN}, title = {Horizontal transfer - imperative mission of acellular life forms, Acytota.}, journal = {Mobile genetic elements}, volume = {6}, number = {2}, pages = {e1154636}, pmid = {27141324}, issn = {2159-2543}, abstract = {Acytota is a kingdom of life covering satellites, plasmids, transposable elements, viroids and viruses, all outside the conventional tree of life but satisfying most life definitions. This review focuses on some aspects of Acytota, their "genomes" and life styles, the dominance of transposable elements and their evolutionary influence on other life forms in order to vindicate the Acytota as a life kingdom no more polyphyletic than other kingdoms and its members no more parasitic than other life forms.}, }
@article {pmid27140615, year = {2016}, author = {Oliveira, PH and Touchon, M and Rocha, EP}, title = {Regulation of genetic flux between bacteria by restriction-modification systems.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {20}, pages = {5658-5663}, pmid = {27140615}, issn = {1091-6490}, support = {281605/ERC_/European Research Council/International ; }, mesh = {Bacteria/*genetics/*immunology ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Homologous Recombination ; *Immunity, Innate ; }, abstract = {Restriction-modification (R-M) systems are often regarded as bacteria's innate immune systems, protecting cells from infection by mobile genetic elements (MGEs). Their diversification has been recently associated with the emergence of particularly virulent lineages. However, we have previously found more R-M systems in genomes carrying more MGEs. Furthermore, it has been suggested that R-M systems might favor genetic transfer by producing recombinogenic double-stranded DNA ends. To test whether R-M systems favor or disfavor genetic exchanges, we analyzed their frequency with respect to the inferred events of homologous recombination and horizontal gene transfer within 79 bacterial species. Genetic exchanges were more frequent in bacteria with larger genomes and in those encoding more R-M systems. We created a recognition target motif predictor for Type II R-M systems that identifies genomes encoding systems with similar restriction sites. We found more genetic exchanges between these genomes, independently of their evolutionary distance. Our results reconcile previous studies by showing that R-M systems are more abundant in promiscuous species, wherein they establish preferential paths of genetic exchange within and between lineages with cognate R-M systems. Because the repertoire and/or specificity of R-M systems in bacterial lineages vary quickly, the preferential fluxes of genetic transfer within species are expected to constantly change, producing time-dependent networks of gene transfer.}, }
@article {pmid27139503, year = {2016}, author = {Jensen, L and Grant, JR and Laughinghouse, HD and Katz, LA}, title = {Assessing the effects of a sequestered germline on interdomain lateral gene transfer in Metazoa.}, journal = {Evolution; international journal of organic evolution}, volume = {70}, number = {6}, pages = {1322-1333}, doi = {10.1111/evo.12935}, pmid = {27139503}, issn = {1558-5646}, mesh = {Animals ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Germ Cells ; Phylogeny ; }, abstract = {A sequestered germline in Metazoa has been argued to be an obstacle to lateral gene transfer (LGT), though few studies have specifically assessed this claim. Here, we test the hypothesis that the origin of a sequestered germline reduced LGT events in Bilateria (i.e., triploblast lineages) as compared to early-diverging Metazoa (i.e., Ctenophora, Cnidaria, Porifera, and Placozoa). We analyze single-gene phylogenies generated with over 900 species sampled from among Bacteria, Archaea, and Eukaryota to identify well-supported interdomain LGTs. We focus on ancient interdomain LGT (i.e., those between prokaryotes and multiple lineages of Metazoa) as systematic errors in single-gene tree reconstruction create uncertainties for interpreting eukaryote-to-eukaryote transfer. The breadth of the sampled Metazoa enables us to estimate the timing of LGTs, and to examine the pattern before versus after the evolution of a sequestered germline. We identified 58 LGTs found only in Metazoa and prokaryotes (i.e., bacteria and/or archaea), and seven genes transferred from prokaryotes into Metazoa plus one other eukaryotic clade. Our analyses indicate that more interdomain transfers occurred before the development of a sequestered germline, consistent with the hypothesis that this feature is an obstacle to LGT.}, }
@article {pmid27138047, year = {2016}, author = {Zelaya-Molina, LX and Hernández-Soto, LM and Guerra-Camacho, JE and Monterrubio-López, R and Patiño-Siciliano, A and Villa-Tanaca, L and Hernández-Rodríguez, C}, title = {Ammonia-Oligotrophic and Diazotrophic Heavy Metal-Resistant Serratia liquefaciens Strains from Pioneer Plants and Mine Tailings.}, journal = {Microbial ecology}, volume = {72}, number = {2}, pages = {324-346}, pmid = {27138047}, issn = {1432-184X}, mesh = {Ammonia/*analysis ; Biofilms ; DNA, Bacterial/genetics ; Genes, Bacterial ; Genetic Variation ; Hydrogen-Ion Concentration ; Indoleacetic Acids/analysis ; Metagenomics ; Metals, Heavy/*analysis ; Mexico ; Microbial Sensitivity Tests ; *Mining ; Nitrogen Fixation ; *Phylogeny ; Plant Roots/*microbiology ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Serratia liquefaciens/*classification/genetics/isolation &amp; purification ; Soil Microbiology ; Stress, Physiological ; }, abstract = {Mine tailings are man-made environments characterized by low levels of organic carbon and assimilable nitrogen, as well as moderate concentrations of heavy metals. For the introduction of nitrogen into these environments, a key role is played by ammonia-oligotrophic/diazotrophic heavy metal-resistant guilds. In mine tailings from Zacatecas, Mexico, Serratia liquefaciens was the dominant heterotrophic culturable species isolated in N-free media from bulk mine tailings as well as the rhizosphere, roots, and aerial parts of pioneer plants. S. liquefaciens strains proved to be a meta-population with high intraspecific genetic diversity and a potential to respond to these extreme conditions. The phenotypic and genotypic features of these strains reveal the potential adaptation of S. liquefaciens to oligotrophic and nitrogen-limited mine tailings with high concentrations of heavy metals. These features include ammonia-oligotrophic growth, nitrogen fixation, siderophore and indoleacetic acid production, phosphate solubilization, biofilm formation, moderate tolerance to heavy metals under conditions of diverse nitrogen availability, and the presence of zntA, amtB, and nifH genes. The acetylene reduction assay suggests low nitrogen-fixing activity. The nifH gene was harbored in a plasmid of ∼60 kb and probably was acquired by a horizontal gene transfer event from Klebsiella variicola.}, }
@article {pmid27131323, year = {2016}, author = {Wang, JB and St Leger, RJ and Wang, C}, title = {Advances in Genomics of Entomopathogenic Fungi.}, journal = {Advances in genetics}, volume = {94}, number = {}, pages = {67-105}, doi = {10.1016/bs.adgen.2016.01.002}, pmid = {27131323}, issn = {0065-2660}, support = {R01 AI106998/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Beauveria/genetics/pathogenicity ; Biological Evolution ; Cordyceps/genetics/pathogenicity ; Fungal Proteins/genetics/metabolism ; Fungi/*genetics/*pathogenicity ; Gene Transfer, Horizontal ; Genomics/*methods ; Host Specificity ; Host-Pathogen Interactions/genetics ; Insecta/*microbiology ; Metarhizium/genetics/pathogenicity ; }, abstract = {Fungi are the commonest pathogens of insects and crucial regulators of insect populations. The rapid advance of genome technologies has revolutionized our understanding of entomopathogenic fungi with multiple Metarhizium spp. sequenced, as well as Beauveria bassiana, Cordyceps militaris, and Ophiocordyceps sinensis among others. Phylogenomic analysis suggests that the ancestors of many of these fungi were plant endophytes or pathogens, with entomopathogenicity being an acquired characteristic. These fungi now occupy a wide range of habitats and hosts, and their genomes have provided a wealth of information on the evolution of virulence-related characteristics, as well as the protein families and genomic structure associated with ecological and econutritional heterogeneity, genome evolution, and host range diversification. In particular, their evolutionary transition from plant pathogens or endophytes to insect pathogens provides a novel perspective on how new functional mechanisms important for host switching and virulence are acquired. Importantly, genomic resources have helped make entomopathogenic fungi ideal model systems for answering basic questions in parasitology, entomology, and speciation. At the same time, identifying the selective forces that act upon entomopathogen fitness traits could underpin both the development of new mycoinsecticides and further our understanding of the natural roles of these fungi in nature. These roles frequently include mutualistic relationships with plants. Genomics has also facilitated the rapid identification of genes encoding biologically useful molecules, with implications for the development of pharmaceuticals and the use of these fungi as bioreactors.}, }
@article {pmid27130825, year = {2016}, author = {Zhu, J and Wang, G and Pelosi, P}, title = {Plant transcriptomes reveal hidden guests.}, journal = {Biochemical and biophysical research communications}, volume = {474}, number = {3}, pages = {497-502}, doi = {10.1016/j.bbrc.2016.04.134}, pmid = {27130825}, issn = {1090-2104}, mesh = {Gene Expression Profiling/methods ; Gene Expression Regulation, Plant/*physiology ; Insect Proteins/*metabolism ; Plant Proteins/*metabolism ; Plants/*metabolism ; Proteome/*metabolism ; Transcriptome/*physiology ; }, abstract = {With the wide adoption of transcriptome sequencing an ever increasing amount of information is becoming available, together with spurious data originating from contamination. We show that sometimes errors and inaccuracy can turn beneficial, revealing insect and arthropod pests when analysing plant transcriptomes. We have found a large number of soluble olfactory proteins, odorant-binding proteins (OBPs) and chemosensory proteins (CSPs), in plant databases, likely due to contamination by guest insects. In fact, both classes of proteins are only expressed in insects, with few CSPs also present in other arthropods. In addition, we found many sequences of the Niemann-Pick (Npc2) family, proteins dedicated to cholesterol transport in vertebrates and hypothesised to be involved in chemical communication in insects, but absent in plants. In several cases we were able to trace down members of the three classes of proteins to the insect or arthopod species responsible for contamination. Our work suggests that genes found in plants and recognised as contaminants can be turned into useful information to investigate plant-insect relationships or to identify new sequences from insects species not yet investigated.}, }
@article {pmid27128993, year = {2016}, author = {Oyserman, BO and Moya, F and Lawson, CE and Garcia, AL and Vogt, M and Heffernen, M and Noguera, DR and McMahon, KD}, title = {Ancestral genome reconstruction identifies the evolutionary basis for trait acquisition in polyphosphate accumulating bacteria.}, journal = {The ISME journal}, volume = {10}, number = {12}, pages = {2931-2945}, pmid = {27128993}, issn = {1751-7370}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification/*metabolism ; Bioreactors/microbiology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Glycogen/metabolism ; Phosphorus/metabolism ; Phylogeny ; Polyphosphates/*metabolism ; }, abstract = {The evolution of complex traits is hypothesized to occur incrementally. Identifying the transitions that lead to extant complex traits may provide a better understanding of the genetic nature of the observed phenotype. A keystone functional group in wastewater treatment processes are polyphosphate accumulating organisms (PAOs), however the evolution of the PAO phenotype has yet to be explicitly investigated and the specific metabolic traits that discriminate non-PAO from PAO are currently unknown. Here we perform the first comprehensive investigation on the evolution of the PAO phenotype using the model uncultured organism Candidatus Accumulibacter phosphatis (Accumulibacter) through ancestral genome reconstruction, identification of horizontal gene transfer, and a kinetic/stoichiometric characterization of Accumulibacter Clade IIA. The analysis of Accumulibacter's last common ancestor identified 135 laterally derived genes, including genes involved in glycogen, polyhydroxyalkanoate, pyruvate and NADH/NADPH metabolisms, as well as inorganic ion transport and regulatory mechanisms. In contrast, pathways such as the TCA cycle and polyphosphate metabolism displayed minimal horizontal gene transfer. We show that the transition from non-PAO to PAO coincided with horizontal gene transfer within Accumulibacter's core metabolism; likely alleviating key kinetic and stoichiometric bottlenecks, such as anaerobically linking glycogen degradation to polyhydroxyalkanoate synthesis. These results demonstrate the utility of investigating the derived genome of a lineage to identify key transitions leading to an extant complex phenotype.}, }
@article {pmid27128469, year = {2016}, author = {Yoshida, S and Cui, S and Ichihashi, Y and Shirasu, K}, title = {The Haustorium, a Specialized Invasive Organ in Parasitic Plants.}, journal = {Annual review of plant biology}, volume = {67}, number = {}, pages = {643-667}, doi = {10.1146/annurev-arplant-043015-111702}, pmid = {27128469}, issn = {1545-2123}, mesh = {Biological Transport ; Convolvulaceae/growth &amp; development/*physiology ; Orobanchaceae/growth &amp; development/*physiology ; *Plant Roots ; *Plant Stems ; Plant Weeds/growth &amp; development/*physiology ; }, abstract = {Parasitic plants thrive by infecting other plants. Flowering plants evolved parasitism independently at least 12 times, in all cases developing a unique multicellular organ called the haustorium that forms upon detection of haustorium-inducing factors derived from the host plant. This organ penetrates into the host stem or root and connects to its vasculature, allowing exchange of materials such as water, nutrients, proteins, nucleotides, pathogens, and retrotransposons between the host and the parasite. In this review, we focus on the formation and function of the haustorium in parasitic plants, with a specific emphasis on recent advances in molecular studies of root parasites in the Orobanchaceae and stem parasites in the Convolvulaceae.}, }
@article {pmid27117415, year = {2016}, author = {Metzger, LC and Stutzmann, S and Scrignari, T and Van der Henst, C and Matthey, N and Blokesch, M}, title = {Independent Regulation of Type VI Secretion in Vibrio cholerae by TfoX and TfoY.}, journal = {Cell reports}, volume = {15}, number = {5}, pages = {951-958}, pmid = {27117415}, issn = {2211-1247}, support = {309064/ERC_/European Research Council/International ; }, mesh = {Bacterial Proteins/genetics/*metabolism ; *Bacterial Secretion Systems/drug effects ; Cyclic GMP/analogs &amp; derivatives/pharmacology ; Gene Expression Regulation, Bacterial/drug effects ; Models, Biological ; Sequence Homology, Amino Acid ; Vibrio cholerae/drug effects/genetics/*metabolism ; }, abstract = {Type VI secretion systems (T6SSs) are nanomachines used for interbacterial killing and intoxication of eukaryotes. Although Vibrio cholerae is a model organism for structural studies on T6SSs, the underlying regulatory network is less understood. A recent study showed that the T6SS is part of the natural competence regulon in V. cholerae and is activated by the regulator TfoX. Here, we identify the TfoX homolog TfoY as a second activator of the T6SS. Importantly, despite inducing the same T6SS core machinery, the overall regulons differ significantly for TfoX and TfoY. We show that TfoY does not contribute to competence induction. Instead, TfoY drives the production of T6SS-dependent and T6SS-independent toxins, together with an increased motility phenotype. Hence, we conclude that V. cholerae uses its sole T6SS in response to diverse cues and for distinctive outcomes: either to kill for the prey's DNA, leading to horizontal gene transfer, or as part of a defensive escape reaction.}, }
@article {pmid27114507, year = {2016}, author = {Arfi, Y and Minder, L and Di Primo, C and Le Roy, A and Ebel, C and Coquet, L and Claverol, S and Vashee, S and Jores, J and Blanchard, A and Sirand-Pugnet, P}, title = {MIB-MIP is a mycoplasma system that captures and cleaves immunoglobulin G.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {19}, pages = {5406-5411}, pmid = {27114507}, issn = {1091-6490}, mesh = {Bacterial Proteins/*metabolism ; Immunoglobulin G/*metabolism ; Multiprotein Complexes/*metabolism ; Mycoplasma mycoides/*metabolism ; Protein Binding ; }, abstract = {Mycoplasmas are "minimal" bacteria able to infect humans, wildlife, and a large number of economically important livestock species. Mycoplasma infections include a spectrum of clinical manifestations ranging from simple fever to fulminant inflammatory diseases with high mortality rates. These infections are mostly chronic, suggesting that mycoplasmas have developed means to evade the host immune response. Here we present and functionally characterize a two-protein system from Mycoplasma mycoides subspecies capri that is involved in the capture and cleavage of IgG. The first component, Mycoplasma Ig binding protein (MIB), is an 83-kDa protein that is able to tightly bind to the Fv region of a wide range of IgG. The second component, Mycoplasma Ig protease (MIP), is a 97-kDa serine protease that is able to cleave off the VH domain of IgG. We demonstrate that MIB is necessary for the proteolytic activity of MIP. Cleavage of IgG requires a sequential interaction of the different partners of the system: first MIB captures the IgG, and then MIP is recruited to the MIB-IgG complex, enabling protease activity. MIB and MIP are encoded by two genes organized in tandem, with homologs found in the majority of pathogenic mycoplasmas and often in multiple copies. Phylogenetic studies suggest that genes encoding the MIB-MIP system are specific to mycoplasmas and have been disseminated by horizontal gene transfer. These results highlight an original and complex system targeting the host immunoglobulins, playing a potentially key role in the immunity evasion by mycoplasmas.}, }
@article {pmid27112795, year = {2016}, author = {Cavalié, L and Mantion, B and Fayet, O and Prère, MF}, title = {blaNDM-1-positive Citrobacter sedlakii: emergence after horizontal gene transfer from Klebsiella pneumoniae in the human intestinal tract.}, journal = {International journal of antimicrobial agents}, volume = {47}, number = {5}, pages = {411-413}, doi = {10.1016/j.ijantimicag.2016.02.012}, pmid = {27112795}, issn = {1872-7913}, mesh = {Adolescent ; Anti-Bacterial Agents/pharmacology ; Citrobacter/drug effects/*genetics/isolation &amp; purification ; Gastrointestinal Tract/*microbiology ; *Gene Transfer, Horizontal ; Humans ; Klebsiella pneumoniae/drug effects/*genetics/isolation &amp; purification ; Male ; Microbial Sensitivity Tests ; beta-Lactam Resistance ; beta-Lactamases/*genetics ; }, }
@article {pmid27112572, year = {2016}, author = {Kazlauskas, D and Krupovic, M and Venclovas, &#x10c;}, title = {The logic of DNA replication in double-stranded DNA viruses: insights from global analysis of viral genomes.}, journal = {Nucleic acids research}, volume = {44}, number = {10}, pages = {4551-4564}, pmid = {27112572}, issn = {1362-4962}, mesh = {DNA ; DNA Helicases/genetics/metabolism ; DNA Primase/genetics/metabolism ; *DNA Replication ; DNA Topoisomerases/genetics/metabolism ; DNA Viruses/*genetics ; Gene Transfer, Horizontal ; Genome Size ; *Genome, Viral ; Host-Pathogen Interactions/genetics ; Phylogeny ; RNA-Dependent RNA Polymerase/genetics/metabolism ; Viral Proteins/*genetics/metabolism ; }, abstract = {Genomic DNA replication is a complex process that involves multiple proteins. Cellular DNA replication systems are broadly classified into only two types, bacterial and archaeo-eukaryotic. In contrast, double-stranded (ds) DNA viruses feature a much broader diversity of DNA replication machineries. Viruses differ greatly in both completeness and composition of their sets of DNA replication proteins. In this study, we explored whether there are common patterns underlying this extreme diversity. We identified and analyzed all major functional groups of DNA replication proteins in all available proteomes of dsDNA viruses. Our results show that some proteins are common to viruses infecting all domains of life and likely represent components of the ancestral core set. These include B-family polymerases, SF3 helicases, archaeo-eukaryotic primases, clamps and clamp loaders of the archaeo-eukaryotic type, RNase H and ATP-dependent DNA ligases. We also discovered a clear correlation between genome size and self-sufficiency of viral DNA replication, the unanticipated dominance of replicative helicases and pervasive functional associations among certain groups of DNA replication proteins. Altogether, our results provide a comprehensive view on the diversity and evolution of replication systems in the DNA virome and uncover fundamental principles underlying the orchestration of viral DNA replication.}, }
@article {pmid27111883, year = {2016}, author = {Lyngwi, NA and Nongkhlaw, M and Kalita, D and Joshi, SR}, title = {Bioprospecting of Plant Growth Promoting Bacilli and Related Genera Prevalent in Soils of Pristine Sacred Groves: Biochemical and Molecular Approach.}, journal = {PloS one}, volume = {11}, number = {4}, pages = {e0152951}, pmid = {27111883}, issn = {1932-6203}, mesh = {Bacillus/classification/genetics/*physiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Phylogeny ; *Plant Development ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {Bacillus spp. and related genera native to soils of the pristine sacred groves from Meghalaya, India were characterized using biochemical and 16S rRNA gene analysis which revealed dominance of Bacillus, Paenibacillus, Lysinibacillus and Viridibacillus in the groves. Biochemical estimation was carried out for in vitro testing of plant growth promoting traits present in these isolates. PCR screening were performed for plant growth-promoting related genes involved in the biosynthesis of acid phosphatase (AcPho), indolepyruvate decarboxylase (ipdC), 1-aminocyclopropane-1-carboxylate deaminase (accd) and siderophore biosynthesis protein (asbA). 76% of the sacred grove isolates gave an amplified fragment for AcPho. Three of the isolates gave an amplified fragment for IpdC gene. Apart from 2 isolates, all the other isolates including the reference strains were positive for the amplification of the accd gene indicating their potential to produce ACC deaminase enzyme. 42% of the isolates gave an amplified fragment for asbA gene indicating the potential ability of these isolates to produce the catechol type siderophore, petrobactin. Overall findings indicated multiple PGP genetic traits present in these isolates which suggested that these isolates are capable of expressing multiple PGP traits. Phylogenetic and sequence analysis of accd and asbA genes from the isolates revealed that asbA genes from Paenibacillus taichungiensis SG3 and Paenibacillus tylopili SG24 indicated the occurrence of intergeneric horizontal transfer between Paenibacillus and Bacillus.}, }
@article {pmid27109772, year = {2016}, author = {Khalil, RK and Skinner, C and Patfield, S and He, X}, title = {Phage-mediated Shiga toxin (Stx) horizontal gene transfer and expression in non-Shiga toxigenic Enterobacter and Escherichia coli strains.}, journal = {Pathogens and disease}, volume = {74}, number = {5}, pages = {}, doi = {10.1093/femspd/ftw037}, pmid = {27109772}, issn = {2049-632X}, mesh = {Bacteriolysis ; Bacteriophages/*physiology ; Enterobacter/*genetics/*virology ; Escherichia coli/*genetics/*virology ; *Gene Expression ; *Gene Transfer, Horizontal ; Host Specificity ; Shiga Toxin/*genetics ; Transduction, Genetic ; }, abstract = {Enterobacter cloacae M12X01451 strain recently identified from a clinical specimen produces a new Stx1 subtype (Stx1e) that was not neutralized by existing anti-Stx1 monoclonal antibodies. Acquisition of stx by Ent. cloacae is rare and origin/stability of stx1e in M12X01451 is not known. In this study, we confirmed the ability of Stx1a- and Stx1e-converting phages from an Escherichia coli O157:H7 strain RM8530 and M12X01451 respectively to infect several E. coli and Ent. cloacae strains. stx1e was detected in 97.5% and 72.5% of progenies of strains lysogenized by stx1e phage after 10 (T10) and 20 (T20) subcultures, versus 65% and 17.5% for stx1a gene. Infection of M12X01451 and RM8530 with each other's phages generated double lysogens containing both phages. stx1a was lost after T10, whereas the stx1e was maintained even after T20 in M12X01451 lysogens. In RM8530 lysogens, the acquired stx1e was retained with no mutations, but 20% of stx1a was lost after T20 ELISA and western blot analyses demonstrated that Stx1e was produced in all strains lysogenized by stx1e phage; however, Stx1a was not detected in any lysogenized strain. The study results highlight the potential risks of emerging Stx-producing strains via bacteriophages either in the human gastrointestinal tract or in food production environments, which are matters of great concern and may have serious impacts on human health.}, }
@article {pmid27105286, year = {2016}, author = {Marreiros, BC and Sena, FV and Sousa, FM and Batista, AP and Pereira, MM}, title = {Type II NADH:quinone oxidoreductase family: phylogenetic distribution, structural diversity and evolutionary divergences.}, journal = {Environmental microbiology}, volume = {18}, number = {12}, pages = {4697-4709}, doi = {10.1111/1462-2920.13352}, pmid = {27105286}, issn = {1462-2920}, mesh = {Archaea/enzymology/genetics/metabolism ; Base Sequence ; Cyanobacteria/enzymology/genetics/*metabolism ; *Evolution, Molecular ; NADH, NADPH Oxidoreductases/*metabolism ; NADP/metabolism ; Oxidation-Reduction ; Phylogeny ; Prokaryotic Cells/enzymology/metabolism ; Quinones/metabolism ; }, abstract = {Type II NADH:quinone oxidoreductases (NDH-2s) are membrane proteins, crucial for the catabolic metabolism, because they contribute to the maintenance of the NADH/NAD[+] balance. In several pathogenic bacteria and protists, NDH-2s are the only enzymes performing respiratory NADH:quinone oxidoreductase activity. For this reason and for being considered absent in mammals, NDH-2s were proposed as suitable targets for novel antimicrobial therapies. We selected all sequences of genes encoding NDH-2s from fully sequenced genomes present in the KEGG database. These genes were present in 61% of the 1805 species belonging to Eukarya (83%), Bacteria (60%) and Archaea (32%). Notably sequences from mammal species including humans were retrieved in our selection as NDH-2s. The data obtained and the already available information allowed systematizing several properties of NDH-2s: (i) the existence of additional sequence motifs with putative regulatory functions, (ii) specificity towards NADH or NADPH and (iii) the type of quinone binding motif. We observed that NDH-2 family distribution is not congruent with the taxonomic tree, suggesting different origins for the eukaryotic sequences and possible lateral gene transfer among prokaryotes. We note the absence of genes coding for NDH-2 in anaerobic phyla and the presence of multiple copies in several genomes, specifically in cyanobacteria. These observations inspired us to propose a metabolic hypothesis for the appearance of NDH-2s.}, }
@article {pmid27103580, year = {2016}, author = {Fercher, C and Probst, I and Kohler, V and Goessweiner-Mohr, N and Arends, K and Grohmann, E and Zangger, K and Meyer, NH and Keller, W}, title = {VirB8-like protein TraH is crucial for DNA transfer in Enterococcus faecalis.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {24643}, pmid = {27103580}, issn = {2045-2322}, mesh = {Bacterial Proteins/chemistry/genetics/*metabolism ; *Biological Transport ; *Conjugation, Genetic ; DNA/*metabolism ; Enterococcus faecalis/genetics/*metabolism ; Gene Deletion ; *Gene Transfer, Horizontal ; Humans ; Magnetic Resonance Spectroscopy ; Nuclear Proteins/chemistry/genetics/*metabolism ; Plasmids ; Protein Conformation ; }, abstract = {Untreatable bacterial infections caused by a perpetual increase of antibiotic resistant strains represent a serious threat to human healthcare in the 21(st) century. Conjugative DNA transfer is the most important mechanism for antibiotic resistance and virulence gene dissemination among bacteria and is mediated by a protein complex, known as type IV secretion system (T4SS). The core of the T4SS is a multiprotein complex that spans the bacterial envelope as a channel for macromolecular secretion. We report the NMR structure and functional characterization of the transfer protein TraH encoded by the conjugative Gram-positive broad-host range plasmid pIP501. The structure exhibits a striking similarity to VirB8 proteins of Gram-negative secretion systems where they play an essential role in the scaffold of the secretion machinery. Considering TraM as the first VirB8-like protein discovered in pIP501, TraH represents the second protein affiliated with this family in the respective transfer operon. A markerless traH deletion in pIP501 resulted in a total loss of transfer in Enterococcus faecalis as compared with the pIP501 wild type (wt) plasmid, demonstrating that TraH is essential for pIP501 mediated conjugation. Moreover, oligomerization state and topology of TraH in the native membrane were determined providing insights in molecular organization of a Gram-positive T4SS.}, }
@article {pmid27102205, year = {2017}, author = {Cuny, C and Arnold, P and Hermes, J and Eckmanns, T and Mehraj, J and Schoenfelder, S and Ziebuhr, W and Zhao, Q and Wang, Y and Feßler, AT and Krause, G and Schwarz, S and Witte, W}, title = {Occurrence of cfr-mediated multiresistance in staphylococci from veal calves and pigs, from humans at the corresponding farms, and from veterinarians and their family members.}, journal = {Veterinary microbiology}, volume = {200}, number = {}, pages = {88-94}, doi = {10.1016/j.vetmic.2016.04.002}, pmid = {27102205}, issn = {1873-2542}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacterial Proteins/*genetics ; Cattle ; Cattle Diseases/epidemiology/*microbiology ; Drug Resistance, Multiple, Bacterial/*genetics ; Family ; Farms ; Gene Transfer, Horizontal ; Germany/epidemiology ; Humans ; Livestock/microbiology ; Microbial Sensitivity Tests ; Plasmids/genetics ; Staphylococcal Infections/epidemiology/*microbiology ; Staphylococcus/classification/drug effects/*genetics/isolation &amp; purification ; Staphylococcus aureus/classification/drug effects/genetics/isolation &amp; purification ; Swine ; Swine Diseases/epidemiology/*microbiology ; Thiamphenicol/analogs &amp; derivatives/pharmacology/therapeutic use ; Veterinarians ; }, abstract = {This study reports on the emergence of linezolid-resistant coagulase-negative staphylococci (CoNS) containing the multiresistance gene cfr in veal calves and pigs, as well as in humans exposed to these animals. CoNS (Staphylococcus auricularis, Staphylococcus cohnii, Staphylococcus lentus, Staphylococcus kloosii, Staphylococcus sciuri, Staphylococcus simulans), but not Staphylococcus aureus, carrying the gene cfr were detected in samples of 12 out of 52 calves at three farms which had a history of florfenicol use. Nasal swabs from 10 humans living on these farms were negative for cfr-carrying staphylococci. Nasal swabs taken from 142 calves at 16 farms in the same area that did not use florfenicol were also negative for cfr-carrying staphylococci. 14 cfr-carrying CoNS (S. kloosii, S. saprophyticus, S. simulans) were detected in three of eight conventional pig farms investigated. One of 12 humans living on these farms harboured a cfr-carrying S. cohnii. Among the nasal swabs taken from 169 veterinarians from all over Germany, four (2.3%) were positive for cfr-carrying CoNS (three S. epidermidis, one S. saprophyticus), and three (1.1%) of 263 contact persons of this group also harboured cfr-carrying CoNS (one S. epidermidis, two S. saprophyticus). In vitro conjugation of cfr by filter mating to S. aureus 8325-4 was possible for 10 of 34CoNS and the cfr gene was associated with plasmids of 38-40kb. Moreover, a total of 363 humans of a German municipal community were investigated for nasal carriage of cfr-carrying staphylococci to get an idea whether such isolates are disseminated as nasal colonizers in non-hospitalized humans in the community, were all negative.}, }
@article {pmid27101788, year = {2016}, author = {Zhai, Y and He, Z and Kang, Y and Yu, H and Wang, J and Du, P and Zhang, Z and Hu, S and Gao, Z}, title = {Complete nucleotide sequence of pH11, an IncHI2 plasmid conferring multi-antibiotic resistance and multi-heavy metal resistance genes in a clinical Klebsiella pneumoniae isolate.}, journal = {Plasmid}, volume = {86}, number = {}, pages = {26-31}, doi = {10.1016/j.plasmid.2016.04.001}, pmid = {27101788}, issn = {1095-9890}, mesh = {Anti-Bacterial Agents/*pharmacology ; Base Sequence ; DNA, Bacterial/genetics ; DNA-Binding Proteins/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal ; Klebsiella Infections/microbiology ; Klebsiella pneumoniae/*drug effects/*genetics/isolation &amp; purification ; Metals, Heavy/*toxicity ; Methyltransferases/genetics ; Microbial Sensitivity Tests ; Plasmids/*genetics ; Retroelements/genetics ; Sequence Analysis, DNA ; }, abstract = {The complete 284,628bp sequence of pH11, an IncHI2 plasmid, was determined through single-molecule, real-time (SMRT) sequencing. Harbored by a clinical Klebsiella pneumoniae strain H11, and isolated in Beijing, this plasmid contains multiple antibiotic resistance genes, including catA2, aac(6')-Ib, strB, strA, dfrA19, blaTEM-1, blaSHV-12, sul1, qacE delta 1, ereA, arr2, and aac3. The aac(6')-Ib is carried by a class I integron. Plasmid pH11 also carries several genes associated with resistance to heavy metals, such as tellurium, mercury, cobalt, zinc, nickel, copper, lead and cadmium. This plasmid exhibits numerous characteristics, including HipBA and RelBE toxin-antitoxin systems, two major transfer (Tra) regions closely related to those of Salmonella enterica serovar plasmid pRH-R27, a type II restriction modification system (EcoRII R-M system), several methyltransferases and methylases and genes encoding Hha and StpA. These characteristics suggest that pH11 may adapt to various hosts and environments. Multiple insertion sequence elements, transposases, recombinases, resolvases and integrases are scattered throughout pH11. The presence of these genes may indicate that horizontal gene transfer occurs frequently in pH11 and thus may facilitate the dissemination of antimicrobial resistance determinants. Our data suggest that pH11 is a chimera gradually assembled through the integration of different horizontally acquired DNA segments via transposition or homologous recombination.}, }
@article {pmid27101775, year = {2016}, author = {Godziszewska, J and Moncalián, G and Cabezas, M and Bartosik, AA and de la Cruz, F and Jagura-Burdzy, G}, title = {Concerted action of NIC relaxase and auxiliary protein MobC in RA3 plasmid conjugation.}, journal = {Molecular microbiology}, volume = {101}, number = {3}, pages = {439-456}, doi = {10.1111/mmi.13401}, pmid = {27101775}, issn = {1365-2958}, mesh = {Bacterial Proteins/genetics/metabolism ; Base Sequence ; Binding Sites ; Conjugation, Genetic ; DNA ; DNA, Bacterial/genetics/metabolism ; DNA, Superhelical/genetics/metabolism ; Endodeoxyribonucleases/*genetics/metabolism ; Escherichia coli/genetics/metabolism ; Gene Transfer Techniques ; Gene Transfer, Horizontal ; Operon ; Plasmids/*genetics ; Protein Domains ; Structure-Activity Relationship ; }, abstract = {Conjugative transfer of the broad-host-range RA3 plasmid, the archetype of the IncU group, relies on the relaxase NIC that belongs to the as yet uncharacterized MOBP4 subfamily. NIC contains the signature motifs of HUH relaxases involved in Tyr nucleophilic attack. However, it differs in the residue involved in His activation for cation coordination and was shown here to have altered divalent cation requirements. NIC is encoded in the mobC-nic operon preceded directly by oriT, where mobC encodes an auxiliary transfer protein with a dual function: autorepressor and stimulator of conjugative transfer. Here an interplay between MobC and NIC was demonstrated. MobC is required for efficient NIC cleavage of oriT in supercoiled DNA whereas NIC assists MobC in repression of the mobC-nic operon. A 7-bp arm of IR3 (IR3a) was identified as the binding site for NIC and the crucial nucleotides in IR3a for NIC recognition were defined. Fully active oriTRA3 was delineated to a 47-bp DNA segment encompassing a conserved cleavage site sequence, the NIC binding site IR3a and the MobC binding site OM . This highly efficient RA3 conjugative system with defined requirements for minimal oriT could find ample applications in biotechnology and computational biology where simple conjugative systems are needed.}, }
@article {pmid27099691, year = {2016}, author = {Shahbazi Dastjerdeh, M and Kouhpayeh, S and Sabzehei, F and Khanahmad, H and Salehi, M and Mohammadi, Z and Shariati, L and Hejazi, Z and Rabiei, P and Manian, M}, title = {Zinc Finger Nuclease: A New Approach to Overcome Beta-Lactam Antibiotic Resistance.}, journal = {Jundishapur journal of microbiology}, volume = {9}, number = {1}, pages = {e29384}, pmid = {27099691}, issn = {2008-3645}, abstract = {BACKGROUND: The evolution of antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs) has been accelerated recently by the indiscriminate application of antibiotics. Antibiotic resistance has challenged the success of medical interventions and therefore is considered a hazardous threat to human health.<br><br>OBJECTIVES: The present study aimed to describe the use of zinc finger nuclease (ZFN) technology to target and disrupt a plasmid-encoded &#x3b2;-lactamase, which prevents horizontal gene transfer-mediated evolution of ARBs.<br><br>MATERIALS AND METHODS: An engineered ZFN was designed to target a specific sequence in the ampicillin resistance gene (amp(R)) of the pTZ57R plasmid. The Escherichia coli bacteria already contained the pZFN kanamycin-resistant (kana(R)) plasmid as the case or the pP15A, kana(R) empty vector as the control, were transformed with the pTZ57R; the ability of the designed ZFN to disrupt the &#x3b2;-lactamase gene was evaluated with the subsequent disturbed ability of the bacteria to grow on ampicillin (amp) and ampicillin-kanamycin (amp-kana)-containing media. The effect of mild hypothermia on the ZFN gene targeting efficiency was also evaluated.<br><br>RESULTS: The growth of bacteria in the case group on the amp and amp-kana-containing media was significantly lower compared with the control group at 37&#xb0;C (P < 0.001). Despite being more efficient in hypothermic conditions at 30&#xb0;C (P < 0.001), there were no significant associations between the incubation temperature and the ZFN gene targeting efficiency.<br><br>CONCLUSIONS: Our findings revealed that the ZFN technology could be employed to overcome ampicillin resistance by the targeted disruption of the ampicillin resistance gene, which leads to inactivation of &#x3b2;-lactam synthesis. Therefore, ZFN technology could be engaged to decrease the antibiotic resistance issue with the construction of a ZFN archive against different ARGs. To tackle the resistance issue at the environmental level, recombinant phages expressing ZFNs against different ARGs could be constructed and released into both hospital and urban wastewater systems.}, }
@article {pmid27097561, year = {2016}, author = {Suh, A and Witt, CC and Menger, J and Sadanandan, KR and Podsiadlowski, L and Gerth, M and Weigert, A and McGuire, JA and Mudge, J and Edwards, SV and Rheindt, FE}, title = {Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {11396}, pmid = {27097561}, issn = {2041-1723}, mesh = {Animals ; Biological Evolution ; Bird Diseases/epidemiology/*history/parasitology/transmission ; Birds/classification/parasitology ; Brugia/classification/*genetics ; Elephantiasis, Filarial/epidemiology/*history/parasitology/transmission ; Filariasis/epidemiology/*history/parasitology/transmission ; *Gene Transfer, Horizontal ; History, Ancient ; Humans ; Loa/classification/*genetics ; Loiasis/epidemiology/*history/parasitology/transmission ; Phylogeny ; Phylogeography ; Retroelements ; Wuchereria/classification/*genetics ; }, abstract = {Parasite host switches may trigger disease emergence, but prehistoric host ranges are often unknowable. Lymphatic filariasis and loiasis are major human diseases caused by the insect-borne filarial nematodes Brugia, Wuchereria and Loa. Here we show that the genomes of these nematodes and seven tropical bird lineages exclusively share a novel retrotransposon, AviRTE, resulting from horizontal transfer (HT). AviRTE subfamilies exhibit 83-99% nucleotide identity between genomes, and their phylogenetic distribution, paleobiogeography and invasion times suggest that HTs involved filarial nematodes. The HTs between bird and nematode genomes took place in two pantropical waves, >25-22 million years ago (Myr ago) involving the Brugia/Wuchereria lineage and >20-17 Myr ago involving the Loa lineage. Contrary to the expectation from the mammal-dominated host range of filarial nematodes, we hypothesize that these major human pathogens may have independently evolved from bird endoparasites that formerly infected the global breadth of avian biodiversity.}, }
@article {pmid27092125, year = {2016}, author = {Cheng, G and Dai, M and Ahmed, S and Hao, H and Wang, X and Yuan, Z}, title = {Antimicrobial Drugs in Fighting against Antimicrobial Resistance.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {470}, pmid = {27092125}, issn = {1664-302X}, abstract = {The outbreak of antimicrobial resistance, together with the lack of newly developed antimicrobial drugs, represents an alarming signal for both human and animal healthcare worldwide. Selection of rational dosage regimens for traditional antimicrobial drugs based on pharmacokinetic/pharmacodynamic principles as well as development of novel antimicrobials targeting new bacterial targets or resistance mechanisms are key approaches in tackling AMR. In addition to the cellular level resistance (i.e., mutation and horizontal gene transfer of resistance determinants), the community level resistance (i.e., bilofilms and persisters) is also an issue causing antimicrobial therapy difficulties. Therefore, anti-resistance and antibiofilm strategies have currently become research hotspot to combat antimicrobial resistance. Although metallic nanoparticles can both kill bacteria and inhibit biofilm formation, the toxicity is still a big challenge for their clinical applications. In conclusion, rational use of the existing antimicrobials and combinational use of new strategies fighting against antimicrobial resistance are powerful warranties to preserve potent antimicrobial drugs for both humans and animals.}, }
@article {pmid27092114, year = {2016}, author = {Eckshtain-Levi, N and Shkedy, D and Gershovits, M and Da Silva, GM and Tamir-Ariel, D and Walcott, R and Pupko, T and Burdman, S}, title = {Insights from the Genome Sequence of Acidovorax citrulli M6, a Group I Strain of the Causal Agent of Bacterial Fruit Blotch of Cucurbits.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {430}, pmid = {27092114}, issn = {1664-302X}, abstract = {Acidovorax citrulli is a seedborne bacterium that causes bacterial fruit blotch of cucurbit plants including watermelon and melon. A. citrulli strains can be divided into two major groups based on DNA fingerprint analyses and biochemical properties. Group I strains have been generally isolated from non-watermelon cucurbits, while group II strains are closely associated with watermelon. In the present study, we report the genome sequence of M6, a group I model A. citrulli strain, isolated from melon. We used comparative genome analysis to investigate differences between the genome of strain M6 and the genome of the group II model strain AAC00-1. The draft genome sequence of A. citrulli M6 harbors 139 contigs, with an overall approximate size of 4.85 Mb. The genome of M6 is ∼500 Kb shorter than that of strain AAC00-1. Comparative analysis revealed that this size difference is mainly explained by eight fragments, ranging from ∼35-120 Kb and distributed throughout the AAC00-1 genome, which are absent in the M6 genome. In agreement with this finding, while AAC00-1 was found to possess 532 open reading frames (ORFs) that are absent in strain M6, only 123 ORFs in M6 were absent in AAC00-1. Most of these M6 ORFs are hypothetical proteins and most of them were also detected in two group I strains that were recently sequenced, tw6 and pslb65. Further analyses by PCR assays and coverage analyses with other A. citrulli strains support the notion that some of these fragments or significant portions of them are discriminative between groups I and II strains of A. citrulli. Moreover, GC content, effective number of codon values and cluster of orthologs' analyses indicate that these fragments were introduced into group II strains by horizontal gene transfer events. Our study reports the genome sequence of a model group I strain of A. citrulli, one of the most important pathogens of cucurbits. It also provides the first comprehensive comparison at the genomic level between the two major groups of strains of this pathogen.}, }
@article {pmid27091964, year = {2016}, author = {Wang, Y and Diaz Arenas, C and Stoebel, DM and Flynn, K and Knapp, E and Dillon, MM and Wünsche, A and Hatcher, PJ and Moore, FB and Cooper, VS and Cooper, TF}, title = {Benefit of transferred mutations is better predicted by the fitness of recipients than by their ecological or genetic relatedness.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {18}, pages = {5047-5052}, pmid = {27091964}, issn = {1091-6490}, mesh = {Computer Simulation ; Ecosystem ; Epistasis, Genetic ; Escherichia coli/classification/*genetics ; *Gene-Environment Interaction ; Genetic Fitness/*genetics ; *Models, Genetic ; Mutation/*genetics ; Risk Assessment/methods ; Selection, Genetic/*genetics ; }, abstract = {The effect of a mutation depends on its interaction with the genetic background in which it is assessed. Studies in experimental systems have demonstrated that such interactions are common among beneficial mutations and often follow a pattern consistent with declining evolvability of more fit genotypes. However, these studies generally examine the consequences of interactions between a small number of focal mutations. It is not clear, therefore, that findings can be extrapolated to natural populations, where new mutations may be transferred between genetically divergent backgrounds. We build on work that examined interactions between four beneficial mutations selected in a laboratory-evolved population of Escherichia coli to test how they interact with the genomes of diverse natural isolates of the same species. We find that the fitness effect of transferred mutations depends weakly on the genetic and ecological similarity of recipient strains relative to the donor strain in which the mutations were selected. By contrast, mutation effects were strongly inversely correlated to the initial fitness of the recipient strain. That is, there was a pattern of diminishing returns whereby fit strains benefited proportionally less from an added mutation. Our results strengthen the view that the fitness of a strain can be a major determinant of its ability to adapt. They also support a role for barriers of transmission, rather than differential selection of transferred DNA, as an explanation of observed phylogenetically determined patterns of restricted recombination among E. coli strains.}, }
@article {pmid27088665, year = {2016}, author = {Bristow, CC and Dong, H and Klausner, JD}, title = {Technological Solutions to Address Drug-Resistant Neisseria gonorrhoeae.}, journal = {Emerging infectious diseases}, volume = {22}, number = {5}, pages = {939-940}, pmid = {27088665}, issn = {1080-6059}, support = {D43 TW009343/TW/FIC NIH HHS/United States ; R01 DA037773-01A1/DA/NIDA NIH HHS/United States ; R21 AI109005/AI/NIAID NIH HHS/United States ; T32 DA023356/DA/NIDA NIH HHS/United States ; R21AI109005/AI/NIAID NIH HHS/United States ; R01 DA037773/DA/NIDA NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*pharmacology/therapeutic use ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Genes, Bacterial ; Gonorrhea/drug therapy/*epidemiology/*microbiology ; Humans ; Microbial Sensitivity Tests ; Mutation ; Neisseria gonorrhoeae/*drug effects/genetics ; Selection, Genetic ; }, }
@article {pmid27087920, year = {2016}, author = {Gordon, BR and Klinger, CR and Weese, DJ and Lau, JA and Burke, PV and Dentinger, BT and Heath, KD}, title = {Decoupled genomic elements and the evolution of partner quality in nitrogen-fixing rhizobia.}, journal = {Ecology and evolution}, volume = {6}, number = {5}, pages = {1317-1327}, pmid = {27087920}, issn = {2045-7758}, abstract = {Understanding how mutualisms evolve in response to a changing environment will be critical for predicting the long-term impacts of global changes, such as increased N (nitrogen) deposition. Bacterial mutualists in particular might evolve quickly, thanks to short generation times and the potential for independent evolution of plasmids through recombination and/or HGT (horizontal gene transfer). In a previous work using the legume/rhizobia mutualism, we demonstrated that long-term nitrogen fertilization caused the evolution of less-mutualistic rhizobia. Here, we use our 63 previously isolated rhizobium strains in comparative phylogenetic and quantitative genetic analyses to determine the degree to which variation in partner quality is attributable to phylogenetic relationships among strains versus recent genetic changes in response to N fertilization. We find evidence of distinct evolutionary relationships between chromosomal and pSym genes, and broad similarity between pSym genes. We also find that nifD has a unique evolutionary history that explains much of the variation in partner quality, and suggest MoFe subunit interaction sites in the evolution of less-mutualistic rhizobia. These results provide insight into the mechanisms behind the evolutionary response of rhizobia to long-term N fertilization, and we discuss the implications of our results for the evolution of the mutualism.}, }
@article {pmid27084942, year = {2016}, author = {Shin, JE and Lin, C and Lim, HN}, title = {Horizontal transfer of DNA methylation patterns into bacterial chromosomes.}, journal = {Nucleic acids research}, volume = {44}, number = {9}, pages = {4460-4471}, pmid = {27084942}, issn = {1362-4962}, mesh = {Chromosomes, Bacterial/*genetics ; *DNA Methylation ; DNA, Bacterial/genetics ; Escherichia coli/*genetics ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Genetic Engineering ; }, abstract = {Horizontal gene transfer (HGT) is the non-inherited acquisition of novel DNA sequences. HGT is common and important in bacteria because it enables the rapid generation of new phenotypes such as antibiotic resistance. Here we show that in vivo and in vitro DNA methylation patterns can be horizontally transferred into bacterial chromosomes to program cell phenotypes. The experiments were performed using a synthetic system in Escherichia coli where different DNA methylation patterns within the cis-regulatory sequence of the agn43 gene turn on or off a fluorescent reporter (CFP). With this system we demonstrated that DNA methylation patterns not only accompany the horizontal transfer of genes into the bacterial cytoplasm but can be transferred into chromosomes by: (i) bacteriophage P1 transduction; and (ii) transformation of extracellular synthetic DNA. We also modified the experimental system by replacing CFP with the SgrS small RNA, which regulates glucose and methyl α-D-glucoside uptake, and showed that horizontally acquired DNA methylation patterns can increase or decrease cell fitness. That is, horizontally acquired DNA methylation patterns can result in the selection for and against cells that have HGT. Findings from these proof-of-concept experiments have applications in synthetic biology and potentially broad implications for bacterial adaptation and evolution.}, }
@article {pmid27084016, year = {2016}, author = {Nguyen, NT and Nguyen, HM and Nguyen, CV and Nguyen, TV and Nguyen, MT and Thai, HQ and Ho, MH and Thwaites, G and Ngo, HT and Baker, S and Carrique-Mas, J}, title = {Use of Colistin and Other Critical Antimicrobials on Pig and Chicken Farms in Southern Vietnam and Its Association with Resistance in Commensal Escherichia coli Bacteria.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {13}, pages = {3727-3735}, pmid = {27084016}, issn = {1098-5336}, support = {/WT_/Wellcome Trust/United Kingdom ; 110085/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; 100087/Z/12/Z/WT_/Wellcome Trust/United Kingdom ; 089276/Z/09/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology/*therapeutic use ; Chickens ; Colistin/*pharmacology/*therapeutic use ; Conjugation, Genetic ; *Drug Resistance, Bacterial ; Drug Utilization ; Escherichia coli/*drug effects/isolation &amp; purification ; Escherichia coli Infections/microbiology/*veterinary ; Farms ; Gene Transfer, Horizontal ; Plasmids/analysis ; Swine ; Vietnam ; }, abstract = {UNLABELLED: Antimicrobial resistance (AMR) is a global health problem, and emerging semi-intensive farming systems in Southeast Asia are major contributors to the AMR burden. We accessed 12 pig and chicken farms at key stages of production in Tien Giang Province, Vietnam, to measure antimicrobial usage and to investigate the prevalence of AMR to five critical antimicrobials (β-lactams, third-generation cephalosporins, quinolones, aminoglycosides, and polymyxins) and their corresponding molecular mechanisms among 180 Escherichia coli isolates. Overall, 94.7 mg (interquartile range [IQR], 65.3 to 151.1) and 563.6 mg (IQR, 398.9 to 943.6) of antimicrobials was used to produce 1 kg (live weight) of chicken and pig, respectively. A median of 3 (out of 8) critical antimicrobials were used on pig farms. E. coli isolates exhibited a high prevalence of resistance to ampicillin (97.8% and 94.4% for chickens and pigs, respectively), ciprofloxacin (73.3% and 21.1%), gentamicin (42.2% and 35.6%), and colistin (22.2% and 24.4%). The prevalence of a recently discovered colistin resistance gene, mcr-1, was 19 to 22% and had strong agreement with phenotypic colistin resistance. We conducted plasmid conjugation experiments with 37 mcr-1 gene-positive E. coli isolates and successfully observed transfer of the gene in 54.0% of isolates through a plasmid of approximately 63 kb, consistent with one recently identified in China. We found no significant correlation between total use of antimicrobials at the farm level and AMR. These data provide additional insight into the role of mcr-1 in colistin resistance on farms and outline the dynamics of phenotypic and genotypic AMR in semi-intensive farming systems in Vietnam.<br><br>IMPORTANCE: Our study provides accurate baseline information on levels of antimicrobial use, as well as on the dynamics of phenotypic and genotypic resistance for antimicrobials of critical importance among E. coli over the different stages of production in emerging pig and poultry production systems in Vietnam. E. coli isolates showed a high prevalence of resistance (>20%) to critically important antimicrobials, such as colistin, ciprofloxacin, and gentamicin. The underlying genetic mechanisms identified for colistin (the mcr-1 gene) and quinolone (gyrA gene mutations) are likely to play a major role in AMR to those compounds. Conjugation experiments led to the identification of a 63-kb plasmid, similar to one recently identified in China, as the potential carrier of the mcr-1 gene. These results should encourage greater restrictions of such antimicrobials in Southeast Asian farming systems.}, }
@article {pmid27083976, year = {2016}, author = {Cabello, FC and Godfrey, HP and Buschmann, AH and Dölz, HJ}, title = {Aquaculture as yet another environmental gateway to the development and globalisation of antimicrobial resistance.}, journal = {The Lancet. Infectious diseases}, volume = {16}, number = {7}, pages = {e127-e133}, doi = {10.1016/S1473-3099(16)00100-6}, pmid = {27083976}, issn = {1474-4457}, mesh = {Animals ; Anti-Bacterial Agents/therapeutic use ; Aquaculture/*methods ; Bacteria/drug effects ; Bacterial Infections/drug therapy/*prevention &amp; control ; Drug Resistance, Bacterial/*drug effects ; Fishes ; Humans ; Internationality ; }, abstract = {Aquaculture uses hundreds of tonnes of antimicrobials annually to prevent and treat bacterial infection. The passage of these antimicrobials into the aquatic environment selects for resistant bacteria and resistance genes and stimulates bacterial mutation, recombination, and horizontal gene transfer. The potential bridging of aquatic and human pathogen resistomes leads to emergence of new antimicrobial-resistant bacteria and global dissemination of them and their antimicrobial resistance genes into animal and human populations. Efforts to prevent antimicrobial overuse in aquaculture must include education of all stakeholders about its detrimental effects on the health of fish, human beings, and the aquatic ecosystem (the notion of One Health), and encouragement of environmentally friendly measures of disease prevention, including vaccines, probiotics, and bacteriophages. Adoption of these measures is a crucial supplement to efforts dealing with antimicrobial resistance by developing new therapeutic agents, if headway is to be made against the increasing problem of antimicrobial resistance in human and veterinary medicine.}, }
@article {pmid27083193, year = {2016}, author = {Kyselková, M and Chrudimský, T and Husník, F and Chroňáková, A and Heuer, H and Smalla, K and Elhottová, D}, title = {Characterization of tet(Y)-carrying LowGC plasmids exogenously captured from cow manure at a conventional dairy farm.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {6}, pages = {fiw075}, doi = {10.1093/femsec/fiw075}, pmid = {27083193}, issn = {1574-6941}, mesh = {Acinetobacter/drug effects/*genetics ; Agriculture ; Animals ; Anti-Bacterial Agents/*pharmacology ; Base Composition/*genetics ; Base Sequence/genetics ; Cattle ; Chlortetracycline/*pharmacology ; Chromosome Mapping ; Farms ; Female ; Manure/*analysis ; Plasmids/*genetics ; Sequence Analysis, DNA ; Soil ; Soil Microbiology ; Streptomycin/*pharmacology ; Swine ; Tetracycline Resistance/*genetics ; }, abstract = {Manure from dairy farms has been shown to contain diverse tetracycline resistance genes that are transferable to soil. Here, we focus on conjugative plasmids that may spread tetracycline resistance at a conventional dairy farm. We performed exogenous plasmid isolation from cattle feces using chlortetracycline for transconjugant selection. The transconjugants obtained harbored LowGC-type plasmids and tet(Y). A representative plasmid (pFK2-7) was fully sequenced and this was compared with previously described LowGC plasmids from piggery manure-treated soil and a GenBank record from Acinetobacter nosocomialis that we also identified as a LowGC plasmid. The pFK2-7 plasmid had the conservative backbone typical of LowGC plasmids, though this region was interrupted with an insert containing the tet(Y)-tet(R) tetracycline resistance genes and the strA-strB streptomycin resistance genes. Despite Acinetobacter populations being considered natural hosts of LowGC plasmids, these plasmids were not found in three Acinetobacter isolates from the study farm. The isolates harbored tet(Y)-tet(R) genes in identical genetic surroundings as pFK2-7, however, suggesting genetic exchange between Acinetobacter and LowGC plasmids. Abundance of LowGC plasmids and tet(Y) was correlated in manure and soil samples from the farm, indicating that LowGC plasmids may be involved in the spread of tet(Y) in the environment.}, }
@article {pmid27075565, year = {2016}, author = {Boto, L}, title = {Accepting Foreign Genes.}, journal = {Journal of molecular evolution}, volume = {82}, number = {4-5}, pages = {173-175}, pmid = {27075565}, issn = {1432-1432}, mesh = {Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial ; Integration Host Factors ; Phylogeny ; }, abstract = {Three recent papers underline the importance of the host genomic background in allowing the stable maintenance of horizontally acquired genes. These studies suggest that post-transfer changes in both host genome and acquired genes contribute to the stable integration of foreign genes.}, }
@article {pmid27075453, year = {2016}, author = {Ghatak, S and Blom, J and Das, S and Sanjukta, R and Puro, K and Mawlong, M and Shakuntala, I and Sen, A and Goesmann, A and Kumar, A and Ngachan, SV}, title = {Pan-genome analysis of Aeromonas hydrophila, Aeromonas veronii and Aeromonas caviae indicates phylogenomic diversity and greater pathogenic potential for Aeromonas hydrophila.}, journal = {Antonie van Leeuwenhoek}, volume = {109}, number = {7}, pages = {945-956}, doi = {10.1007/s10482-016-0693-6}, pmid = {27075453}, issn = {1572-9699}, mesh = {Aeromonas caviae/drug effects/*genetics/pathogenicity ; Aeromonas hydrophila/drug effects/*genetics/pathogenicity ; Aeromonas veronii/drug effects/*genetics/pathogenicity ; Animals ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; Genome, Bacterial ; Genotype ; Homologous Recombination ; Humans ; Microbial Sensitivity Tests ; Phylogeny ; Virulence/genetics ; Virulence Factors/genetics ; }, abstract = {Aeromonas species are important pathogens of fishes and aquatic animals capable of infecting humans and other animals via food. Due to the paucity of pan-genomic studies on aeromonads, the present study was undertaken to analyse the pan-genome of three clinically important Aeromonas species (A. hydrophila, A. veronii, A. caviae). Results of pan-genome analysis revealed an open pan-genome for all three species with pan-genome sizes of 9181, 7214 and 6884 genes for A. hydrophila, A. veronii and A. caviae, respectively. Core-genome: pan-genome ratio (RCP) indicated greater genomic diversity for A. hydrophila and interestingly RCP emerged as an effective indicator to gauge genomic diversity which could possibly be extended to other organisms too. Phylogenomic network analysis highlighted the influence of homologous recombination and lateral gene transfer in the evolution of Aeromonas spp. Prediction of virulence factors indicated no significant difference among the three species though analysis of pathogenic potential and acquired antimicrobial resistance genes revealed greater hazards from A. hydrophila. In conclusion, the present study highlighted the usefulness of whole genome analyses to infer evolutionary cues for Aeromonas species which indicated considerable phylogenomic diversity for A. hydrophila and hitherto unknown genomic evidence for pathogenic potential of A. hydrophila compared to A. veronii and A. caviae.}, }
@article {pmid27073266, year = {2016}, author = {Adler, A and Khabra, E and Paikin, S and Carmeli, Y}, title = {Dissemination of the blaKPC gene by clonal spread and horizontal gene transfer: comparative study of incidence and molecular mechanisms.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {71}, number = {8}, pages = {2143-2146}, doi = {10.1093/jac/dkw106}, pmid = {27073266}, issn = {1460-2091}, mesh = {Enterobacteriaceae/classification/*enzymology/genetics/isolation &amp; purification ; Enterobacteriaceae Infections/*epidemiology/*microbiology ; Gene Order ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Incidence ; Multilocus Sequence Typing ; Multiplex Polymerase Chain Reaction ; Plasmids/classification ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: In addition to the global spread of the KPC-producing Klebsiella pneumoniae (KPC-KP) clonal complex (CC)-258 clone, the blaKPC gene may also spread by horizontal gene transfer (HGT), as suspected when more than one KPC-producing Enterobacteriaceae (KPC-Ent) species are isolated in a single patient. We aimed to characterize the incidence and molecular features of KPC-KP that were isolated alone (singular KPC-KP) versus KPC-KP that were isolated together with another KPC-Ent species (joint KPC-KP).<br><br>METHODS: Isolates were collected from April 2011 to August 2012 at the Laniado Medical Center. Typing was done by CC-258 multiplex PCR and MLST. Plasmids were characterized by plasmid MLST (pMLST). The genetic environment of the blaKPC gene was studied by sequencing.<br><br>RESULTS: During the 17 month period, there were 281 cases of singular KPC-KP and 8 cases of joint KPC-KP (P&#x200a;<&#x200a;0.0001). Among the patients with joint KPC-KP, the additional KPC-Ent species were Escherichia coli (n&#x200a;=&#x200a;6), Enterobacter aerogenes (n&#x200a;=&#x200a;1), Enterobacter cloacae (n&#x200a;=&#x200a;1) and Citrobacter freundii (n&#x200a;=&#x200a;1). All singular KPC-KP isolates tested (n&#x200a;=&#x200a;27) belonged to the CC-258 clone and carried the blaKPC-3 allele, located inside a Tn4401a transposon. In contrast, joint KPC-KP/KPC-Ent isolates belonged to different STs and all but one carried the blaKPC-2 allele. The blaKPC-2 gene was located inside &#x394;Tn4401c transposons that were harboured by IncN/pMLST ST-15-type plasmids possessing high conjugation efficiency.<br><br>CONCLUSIONS: This study highlights two dissemination modes of the blaKPC gene: clonal spread of the CC-258 clone and, far less commonly, HGT-related spread, mediated by ST-15 plasmids that shuttle between a variety of species and clones.}, }
@article {pmid27073099, year = {2016}, author = {McDonald, ND and Lubin, JB and Chowdhury, N and Boyd, EF}, title = {Host-Derived Sialic Acids Are an Important Nutrient Source Required for Optimal Bacterial Fitness In Vivo.}, journal = {mBio}, volume = {7}, number = {2}, pages = {e02237-15}, pmid = {27073099}, issn = {2150-7511}, mesh = {Animals ; Cholera/*metabolism/microbiology ; Host-Pathogen Interactions ; Humans ; Male ; Mice ; Mice, Inbred C57BL ; Phylogeny ; Sialic Acids/*metabolism ; Vibrio cholerae/classification/genetics/isolation &amp; purification/*physiology ; }, abstract = {UNLABELLED: A major challenge facing bacterial intestinal pathogens is competition for nutrient sources with the host microbiota.Vibrio cholerae is an intestinal pathogen that causes cholera, which affects millions each year; however, our knowledge of its nutritional requirements in the intestinal milieu is limited. In this study, we demonstrated that V. cholerae can grow efficiently on intestinal mucus and its component sialic acids and that a tripartite ATP-independent periplasmic SiaPQM strain, transporter-deficient mutant NC1777, was attenuated for colonization using a streptomycin-pretreated adult mouse model. In in vivo competition assays, NC1777 was significantly outcompeted for up to 3 days postinfection. NC1777 was also significantly outcompeted in in vitro competition assays in M9 minimal medium supplemented with intestinal mucus, indicating that sialic acid uptake is essential for fitness. Phylogenetic analyses demonstrated that the ability to utilize sialic acid was distributed among 452 bacterial species from eight phyla. The majority of species belonged to four phyla, Actinobacteria (members of Actinobacillus, Corynebacterium, Mycoplasma, and Streptomyces), Bacteroidetes (mainly Bacteroides, Capnocytophaga, and Prevotella), Firmicutes (members of Streptococcus, Staphylococcus, Clostridium, and Lactobacillus), and Proteobacteria (including Escherichia, Shigella, Salmonella, Citrobacter, Haemophilus, Klebsiella, Pasteurella, Photobacterium, Vibrio, and Yersinia species), mostly commensals and/or pathogens. Overall, our data demonstrate that the ability to take up host-derived sugars and sialic acid specifically allows V. cholerae a competitive advantage in intestinal colonization and that this is a trait that is sporadic in its occurrence and phylogenetic distribution and ancestral in some genera but horizontally acquired in others.<br><br>IMPORTANCE: Sialic acids are nine carbon amino sugars that are abundant on all mucous surfaces. The deadly human pathogen Vibrio cholerae contains the genes required for scavenging, transport, and catabolism of sialic acid. We determined that the V. cholerae SiaPQM transporter is essential for sialic acid transport and that this trait allows the bacterium to outcompete noncatabolizers in vivo. We also showed that the ability to take up and catabolize sialic acid is prevalent among both commensals and pathogens that colonize the oral cavity and the respiratory, intestinal, and urogenital tracts. Phylogenetic analysis determined that the sialic acid catabolism phenotype is ancestral in some genera such as Yersinia, Streptococcus, and Staphylococcus and is acquired by horizontal gene transfer in others such as Vibrio, Aeromonas, and Klebsiella. The data demonstrate that this trait has evolved multiple times in different lineages, indicating the importance of specialized metabolism to niche expansion.}, }
@article {pmid27073098, year = {2016}, author = {Johnson, TA and Stedtfeld, RD and Wang, Q and Cole, JR and Hashsham, SA and Looft, T and Zhu, YG and Tiedje, JM}, title = {Clusters of Antibiotic Resistance Genes Enriched Together Stay Together in Swine Agriculture.}, journal = {mBio}, volume = {7}, number = {2}, pages = {e02214-15}, pmid = {27073098}, issn = {2150-7511}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/drug effects/*genetics/isolation &amp; purification ; Bacterial Proteins/*genetics ; China ; Drug Resistance, Bacterial ; Interspersed Repetitive Sequences ; Phylogeny ; Swine/growth &amp; development/*microbiology ; }, abstract = {UNLABELLED: Antibiotic resistance is a worldwide health risk, but the influence of animal agriculture on the genetic context and enrichment of individual antibiotic resistance alleles remains unclear. Using quantitative PCR followed by amplicon sequencing, we quantified and sequenced 44 genes related to antibiotic resistance, mobile genetic elements, and bacterial phylogeny in microbiomes from U.S. laboratory swine and from swine farms from three Chinese regions. We identified highly abundant resistance clusters: groups of resistance and mobile genetic element alleles that cooccur. For example, the abundance of genes conferring resistance to six classes of antibiotics together with class 1 integrase and the abundance of IS6100-type transposons in three Chinese regions are directly correlated. These resistance cluster genes likely colocalize in microbial genomes in the farms. Resistance cluster alleles were dramatically enriched (up to 1 to 10% as abundant as 16S rRNA) and indicate that multidrug-resistant bacteria are likely the norm rather than an exception in these communities. This enrichment largely occurred independently of phylogenetic composition; thus, resistance clusters are likely present in many bacterial taxa. Furthermore, resistance clusters contain resistance genes that confer resistance to antibiotics independently of their particular use on the farms. Selection for these clusters is likely due to the use of only a subset of the broad range of chemicals to which the clusters confer resistance. The scale of animal agriculture and its wastes, the enrichment and horizontal gene transfer potential of the clusters, and the vicinity of large human populations suggest that managing this resistance reservoir is important for minimizing human risk.<br><br>IMPORTANCE: Agricultural antibiotic use results in clusters of cooccurring resistance genes that together confer resistance to multiple antibiotics. The use of a single antibiotic could select for an entire suite of resistance genes if they are genetically linked. No links to bacterial membership were observed for these clusters of resistance genes. These findings urge deeper understanding of colocalization of resistance genes and mobile genetic elements in resistance islands and their distribution throughout antibiotic-exposed microbiomes. As governments seek to combat the rise in antibiotic resistance, a balance is sought between ensuring proper animal health and welfare and preserving medically important antibiotics for therapeutic use. Metagenomic and genomic monitoring will be critical to determine if resistance genes can be reduced in animal microbiomes, or if these gene clusters will continue to be coselected by antibiotics not deemed medically important for human health but used for growth promotion or by medically important antibiotics used therapeutically.}, }
@article {pmid27072110, year = {2016}, author = {Magalhães, P and Pinto, L and Gonçalves, A and Araújo, JE and Santos, HM and Capelo, JL and Saénz, Y and de Toro, M and Torres, C and Chambon, C and Hébraud, M and Poeta, P and Igrejas, G}, title = {Could transformation mechanisms of acetylase-harboring pMdT1 plasmid be evaluated through proteomic tools in Escherichia coli?.}, journal = {Journal of proteomics}, volume = {145}, number = {}, pages = {103-111}, doi = {10.1016/j.jprot.2016.03.042}, pmid = {27072110}, issn = {1876-7737}, mesh = {Acetylesterase/*genetics ; Amino Acid Sequence ; Computational Biology ; Drug Resistance, Microbial ; Escherichia coli/*genetics ; Gene Transfer, Horizontal ; Plasmids/*genetics ; Proteomics/*methods ; *Transformation, Genetic ; }, abstract = {UNLABELLED: Escherichia coli is a commensal microorganism of the gastrointestinal tract of animals and humans and it is an excellent model organism for the study of antibiotic resistance mechanisms. The resistance transmission and other characteristics of bacteria are based on different types of gene transfer occurring throughout the bacterial evolution. One of which is horizontal gene transfer that allows us to understand the ability of bacteria to acquire new genes. One dimensional and two dimensional electrophoresis (2-DE) techniques were performed in order to identify and characterize the proteome of two E. coli strains: Electromax DH10B, a transformation-ready strain; and TF-Se20, the Electromax DH10B that contains the aac(6')-Ib-cr4-harboring pMdT1 plasmid. After 2-DE and subsequent analysis by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), it was possible to identify 76 distinct proteins on the TF-Se20 strain, whereas 71 had a known function. From Electromax DH10B strain, 72 different proteins were identified of which 71 were associated with a biological process. The protein of interest, aminoglycoside N-(6')-acetyltransferase type 1, was identified by MALDI-TOF MS. The liquid chromatography-tandem mass spectrometry (LC-MS/MS) technique was performed to determine its sequence. Seventy six percent of the acetylase sequence was reconstructed only in the TF-Se20 strain, representing the single protein associated to antibiotic resistance. MALDI-TOF MS and LC-MS/MS approaches allowed us to determine the total proteome of both strains, as well as the acetylase sequence. Both of them enhance the ability to obtain more accurate information about the mechanisms of antimicrobial resistance. The pMdT1 plasmid brings a new perspective in understanding the metabolic processes that lead to antibiotic resistance.<br><br>BIOLOGICAL SIGNIFICANCE: This study highlights the importance of proteomics and bioinformatics in understanding mechanisms of gene transfer and antibiotic resistance. These two approaches allow to compare the protein expression in different samples, as well as different biological processes related to each protein.}, }
@article {pmid27071651, year = {2016}, author = {Lange, A and Beier, S and Steimle, A and Autenrieth, IB and Huson, DH and Frick, JS}, title = {Extensive Mobilome-Driven Genome Diversification in Mouse Gut-Associated Bacteroides vulgatus mpk.}, journal = {Genome biology and evolution}, volume = {8}, number = {4}, pages = {1197-1207}, pmid = {27071651}, issn = {1759-6653}, mesh = {Animals ; Bacteroides/*genetics ; Base Sequence ; CRISPR-Cas Systems ; DNA, Bacterial/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Intestines/microbiology ; Mice/*microbiology ; Phylogeny ; }, abstract = {Like many other Bacteroides species, Bacteroides vulgatus strain mpk, a mouse fecal isolate which was shown to promote intestinal homeostasis, utilizes a variety of mobile elements for genome evolution. Based on sequences collected by Pacific Biosciences SMRT sequencing technology, we discuss the challenges of assembling and studying a bacterial genome of high plasticity. Additionally, we conducted comparative genomics comparing this commensal strain with the B. vulgatus type strain ATCC 8482 as well as multiple other Bacteroides and Parabacteroides strains to reveal the most important differences and identify the unique features of B. vulgatus mpk. The genome of B. vulgatus mpk harbors a large and diverse set of mobile element proteins compared with other sequenced Bacteroides strains. We found evidence of a number of different horizontal gene transfer events and a genome landscape that has been extensively altered by different mobilization events. A CRISPR/Cas system could be identified that provides a possible mechanism for preventing the integration of invading external DNA. We propose that the high genome plasticity and the introduced genome instabilities of B. vulgatus mpk arising from the various mobilization events might play an important role not only in its adaptation to the challenging intestinal environment in general, but also in its ability to interact with the gut microbiota.}, }
@article {pmid27071628, year = {2016}, author = {Shen, G and Gan, F and Bryant, DA}, title = {The siderophilic cyanobacterium Leptolyngbya sp. strain JSC-1 acclimates to iron starvation by expressing multiple isiA-family genes.}, journal = {Photosynthesis research}, volume = {128}, number = {3}, pages = {325-340}, doi = {10.1007/s11120-016-0257-7}, pmid = {27071628}, issn = {1573-5079}, mesh = {*Acclimatization ; Animals ; Antibodies/genetics ; Bacterial Proteins/chemistry/*genetics/metabolism ; Cyanobacteria/genetics/*physiology/ultrastructure ; Evolution, Molecular ; Gene Duplication ; Gene Expression Profiling ; Gene Transfer, Horizontal ; Homeostasis ; *Iron Deficiencies ; Light-Harvesting Protein Complexes/chemistry/*genetics/metabolism ; Photosynthesis ; Photosystem I Protein Complex/genetics/metabolism ; Phylogeny ; Rabbits ; Sequence Analysis, RNA ; }, abstract = {In the evolution of different cyanobacteria performing oxygenic photosynthesis, the core complexes of the two photosystems were highly conserved. However, cyanobacteria exhibit significant diversification in their light-harvesting complexes and have flexible regulatory mechanisms to acclimate to changes in their growth environments. In the siderophilic, filamentous cyanobacterium, Leptolyngbya sp. strain JSC-1, five different isiA-family genes occur in two gene clusters. During acclimation to Fe limitation, relative transcript levels for more than 600 genes increased more than twofold. Relative transcript levels were ~250 to 300 times higher for the isiA1 gene cluster (isiA1-isiB-isiC), and ~440- to 540-fold for the isiA2-isiA3-isiA4-cpcG2-isiA5 gene cluster after 48 h of iron starvation. Chl-protein complexes were isolated and further purified from cells grown under Fe-replete and Fe-depleted conditions. A single class of particles, trimeric PSI, was identified by image analysis of electron micrographs of negatively stained PSI complexes from Fe-replete cells. However, three major classes of particles were observed for the Chl-protein supercomplexes from cells grown under iron starvation conditions. Based on LC-MS-MS analyses, the five IsiA-family proteins were found in the largest supercomplexes together with core components of the two photosystems; however, IsiA5 was not present in complexes in which only the core subunits of PSI were detected. IsiA5 belongs to the same clade as PcbC proteins in a phylogenetic classification, and it is proposed that IsiA5 is most likely involved in supercomplexes containing PSII dimers. IsiA4, which is a fusion of an IsiA domain and a C-terminal PsaL domain, was found together with IsiA1, IsiA2, and IsiA3 in complexes with monomeric PSI. The data indicate that horizontal gene transfer, gene duplication, and divergence have played important roles in the adaptive evolution of this cyanobacterium to iron starvation conditions.}, }
@article {pmid27070545, year = {2016}, author = {Kazi, MI and Conrado, AR and Mey, AR and Payne, SM and Davies, BW}, title = {ToxR Antagonizes H-NS Regulation of Horizontally Acquired Genes to Drive Host Colonization.}, journal = {PLoS pathogens}, volume = {12}, number = {4}, pages = {e1005570}, pmid = {27070545}, issn = {1553-7374}, support = {R01 AI091957/AI/NIAID NIH HHS/United States ; R01AI091957/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacterial Proteins/*genetics ; Base Sequence ; Blotting, Northern ; Cholera/genetics ; Chromatin Immunoprecipitation ; DNA-Binding Proteins/*genetics ; Gene Expression Regulation, Bacterial/*genetics ; Gene Transfer, Horizontal ; Mice ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Reverse Transcriptase Polymerase Chain Reaction ; Transcription Factors/*genetics ; Vibrio cholerae/*pathogenicity ; Virulence/*genetics ; Virulence Factors/genetics ; }, abstract = {The virulence regulator ToxR initiates and coordinates gene expression needed by Vibrio cholerae to colonize the small intestine and cause disease. Despite its prominence in V. cholerae virulence, our understanding of the direct ToxR regulon is limited to four genes: toxT, ompT, ompU and ctxA. Here, we determine ToxR's genome-wide DNA-binding profile and demonstrate that ToxR is a global regulator of both progenitor genome-encoded genes and horizontally acquired islands that encode V. cholerae's major virulence factors and define pandemic lineages. We show that ToxR shares more than a third of its regulon with the histone-like nucleoid structuring protein H-NS, and antagonizes H-NS binding at shared binding locations. Importantly, we demonstrate that this regulatory interaction is the critical function of ToxR in V. cholerae colonization and biofilm formation. In the absence of H-NS, ToxR is no longer required for V. cholerae to colonize the infant mouse intestine or for robust biofilm formation. We further illustrate a dramatic difference in regulatory scope between ToxR and other prominent virulence regulators, despite similar predicted requirements for DNA binding. Our results suggest that factors in addition to primary DNA structure influence the ability of ToxR to recognize its target promoters.}, }
@article {pmid27068610, year = {2016}, author = {Noon, JB and Baum, TJ}, title = {Horizontal gene transfer of acetyltransferases, invertases and chorismate mutases from different bacteria to diverse recipients.}, journal = {BMC evolutionary biology}, volume = {16}, number = {}, pages = {74}, pmid = {27068610}, issn = {1471-2148}, mesh = {Acetyltransferases/genetics ; Animals ; Bacteria/genetics ; Biological Evolution ; Chorismate Mutase/genetics ; *Gene Transfer, Horizontal ; Nematoda/classification/*enzymology/*genetics ; Phylogeny ; beta-Fructofuranosidase/genetics ; }, abstract = {BACKGROUND: Hoplolaimina plant-parasitic nematodes (PPN) are a lineage of animals with many documented cases of horizontal gene transfer (HGT). In a recent study, we reported on three likely HGT candidate genes in the soybean cyst nematode Heterodera glycines, all of which encode secreted candidate effectors with putative functions in the host plant. Hg-GLAND1 is a putative GCN5-related N-acetyltransferase (GNAT), Hg-GLAND13 is a putative invertase (INV), and Hg-GLAND16 is a putative chorismate mutase (CM), and blastp searches of the non-redundant database resulted in highest similarity to bacterial sequences. Here, we searched nematode and non-nematode sequence databases to identify all the nematodes possible that contain these three genes, and to formulate hypotheses about when they most likely appeared in the phylum Nematoda. We then performed phylogenetic analyses combined with model selection tests of alternative models of sequence evolution to determine whether these genes were horizontally acquired from bacteria.<br><br>RESULTS: Mining of nematode sequence databases determined that GNATs appeared in Hoplolaimina PPN late in evolution, while both INVs and CMs appeared before the radiation of the Hoplolaimina suborder. Also, Hoplolaimina GNATs, INVs and CMs formed well-supported clusters with different rhizosphere bacteria in the phylogenetic trees, and the model selection tests greatly supported models of HGT over descent via common ancestry. Surprisingly, the phylogenetic trees also revealed additional, well-supported clusters of bacterial GNATs, INVs and CMs with diverse eukaryotes and archaea. There were at least eleven and eight well-supported clusters of GNATs and INVs, respectively, from different bacteria with diverse eukaryotes and archaea. Though less frequent, CMs from different bacteria formed supported clusters with multiple different eukaryotes. Moreover, almost all individual clusters containing bacteria and eukaryotes or archaea contained species that inhabit very similar niches.<br><br>CONCLUSIONS: GNATs were horizontally acquired late in Hoplolaimina PPN evolution from bacteria most similar to the saprophytic and plant-pathogenic actinomycetes. INVs and CMs were horizontally acquired from bacteria most similar to rhizobacteria and Burkholderia soil bacteria, respectively, before the radiation of Hoplolaimina. Also, these three gene groups appear to have been frequent subjects of HGT from different bacteria to numerous, diverse lineages of eukaryotes and archaea, which suggests that these genes may confer important evolutionary advantages to many taxa. In the case of Hoplolaimina PPN, this advantage likely was an improved ability to parasitize plants.}, }
@article {pmid27068531, year = {2016}, author = {Eldholm, V and Balloux, F}, title = {Antimicrobial Resistance in Mycobacterium tuberculosis: The Odd One Out.}, journal = {Trends in microbiology}, volume = {24}, number = {8}, pages = {637-648}, doi = {10.1016/j.tim.2016.03.007}, pmid = {27068531}, issn = {1878-4380}, mesh = {Anti-Bacterial Agents/pharmacology ; Biofilms ; Biological Evolution ; Drug Resistance, Bacterial/*genetics/physiology ; *Gene Transfer, Horizontal ; Genetic Variation ; Humans ; Latent Tuberculosis ; Life Cycle Stages ; Mutation ; Mycobacterium tuberculosis/*genetics/physiology ; Tuberculosis/epidemiology/microbiology/transmission ; }, abstract = {Antimicrobial resistance (AMR) threats are typically represented by bacteria capable of extensive horizontal gene transfer (HGT). One clear exception is Mycobacterium tuberculosis (Mtb). It is an obligate human pathogen with limited genetic diversity and a low mutation rate which lacks any evidence for HGT. Such features should, in principle, reduce its ability to rapidly evolve AMR. We identify key features in its biology and epidemiology that allow it to overcome its low adaptive potential. We focus in particular on its innate resistance to drugs, its unusual life cycle, including an often extensive latent phase, and its ability to shelter from exposure to antimicrobial drugs within cavities it induces in the lungs.}, }
@article {pmid27068094, year = {2016}, author = {Li, G and Liang, Z and Wang, X and Yang, Y and Shao, Z and Li, M and Ma, Y and Qu, F and Morrison, DA and Zhang, JR}, title = {Addiction of Hypertransformable Pneumococcal Isolates to Natural Transformation for In Vivo Fitness and Virulence.}, journal = {Infection and immunity}, volume = {84}, number = {6}, pages = {1887-1901}, pmid = {27068094}, issn = {1098-5522}, mesh = {Animals ; Disease Models, Animal ; Female ; Gene Expression Profiling ; *Gene Expression Regulation, Bacterial ; Genes, Bacterial/*immunology ; Genetic Fitness ; Genetic Heterogeneity ; Humans ; Immune Evasion/*genetics ; Mice ; Mice, Inbred BALB C ; Nasopharynx/immunology/microbiology ; Phenotype ; Pneumonia, Pneumococcal/*immunology/microbiology/pathology ; Serogroup ; Streptococcus pneumoniae/*genetics/immunology/*pathogenicity ; Transformation, Bacterial/*immunology ; Virulence ; }, abstract = {Natural genetic transformation of Streptococcus pneumoniae, an important human pathogen, mediates horizontal gene transfer for the development of drug resistance, modulation of carriage and virulence traits, and evasion of host immunity. Transformation frequency differs greatly among pneumococcal clinical isolates, but the molecular basis and biological importance of this interstrain variability remain unclear. In this study, we characterized the transformation frequency and other associated phenotypes of 208 S. pneumoniae clinical isolates representing at least 30 serotypes. While the vast majority of these isolates (94.7%) were transformable, the transformation frequency differed by up to 5 orders of magnitude between the least and most transformable isolates. The strain-to-strain differences in transformation frequency were observed among many isolates producing the same capsule types, indicating no general association between transformation frequency and serotype. However, a statistically significant association was observed between the levels of transformation and colonization fitness/virulence in the hypertransformable isolates. Although nontransformable mutants of all the selected hypertransformable isolates were significantly attenuated in colonization fitness and virulence in mouse infection models, such mutants of the strains with relatively low transformability had no or marginal fitness phenotypes under the same experimental settings. This finding strongly suggests that the pneumococci with high transformation capability are "addicted" to a "hypertransformable" state for optimal fitness in the human host. This work has thus provided an intriguing hint for further investigation into how the competence system impacts the fitness, virulence, and other transformation-associated traits of this important human pathogen.}, }
@article {pmid27067320, year = {2016}, author = {Sheppard, AE and Stoesser, N and Wilson, DJ and Sebra, R and Kasarskis, A and Anson, LW and Giess, A and Pankhurst, LJ and Vaughan, A and Grim, CJ and Cox, HL and Yeh, AJ and ,  and Sifri, CD and Walker, AS and Peto, TE and Crook, DW and Mathers, AJ}, title = {Nested Russian Doll-Like Genetic Mobility Drives Rapid Dissemination of the Carbapenem Resistance Gene blaKPC.}, journal = {Antimicrobial agents and chemotherapy}, volume = {60}, number = {6}, pages = {3767-3778}, pmid = {27067320}, issn = {1098-6596}, support = {/WT_/Wellcome Trust/United Kingdom ; /DH_/Department of Health/United Kingdom ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Typing Techniques ; Carbapenems/pharmacology ; Conjugation, Genetic ; DNA Transposable Elements ; Enterobacteriaceae/classification/drug effects/*genetics/isolation &amp; purification ; Enterobacteriaceae Infections/drug therapy/*epidemiology/microbiology ; Gene Expression ; *Gene Transfer, Horizontal ; High-Throughput Nucleotide Sequencing ; Homologous Recombination ; Humans ; Phylogeny ; Plasmids/chemistry/metabolism ; Public Health Surveillance ; Tertiary Care Centers ; Virginia/epidemiology ; beta-Lactam Resistance/*genetics ; beta-Lactamases/*genetics/metabolism ; }, abstract = {The recent widespread emergence of carbapenem resistance in Enterobacteriaceae is a major public health concern, as carbapenems are a therapy of last resort against this family of common bacterial pathogens. Resistance genes can mobilize via various mechanisms, including conjugation and transposition; however, the importance of this mobility in short-term evolution, such as within nosocomial outbreaks, is unknown. Using a combination of short- and long-read whole-genome sequencing of 281 blaKPC-positive Enterobacteriaceae isolates from a single hospital over 5 years, we demonstrate rapid dissemination of this carbapenem resistance gene to multiple species, strains, and plasmids. Mobility of blaKPC occurs at multiple nested genetic levels, with transmission of blaKPC strains between individuals, frequent transfer of blaKPC plasmids between strains/species, and frequent transposition of blaKPC transposon Tn4401 between plasmids. We also identify a common insertion site for Tn4401 within various Tn2-like elements, suggesting that homologous recombination between Tn2-like elements has enhanced the spread of Tn4401 between different plasmid vectors. Furthermore, while short-read sequencing has known limitations for plasmid assembly, various studies have attempted to overcome this by the use of reference-based methods. We also demonstrate that, as a consequence of the genetic mobility observed in this study, plasmid structures can be extremely dynamic, and therefore these reference-based methods, as well as traditional partial typing methods, can produce very misleading conclusions. Overall, our findings demonstrate that nonclonal resistance gene dissemination can be extremely rapid, presenting significant challenges for public health surveillance and achieving effective control of antibiotic resistance.}, }
@article {pmid27067073, year = {2016}, author = {Kotnik, T and Weaver, JC}, title = {Abiotic Gene Transfer: Rare or Rampant?.}, journal = {The Journal of membrane biology}, volume = {249}, number = {5}, pages = {623-631}, pmid = {27067073}, issn = {1432-1424}, support = {R01 GM063857/GM/NIGMS NIH HHS/United States ; }, mesh = {*Electroporation ; *Gene Transfer, Horizontal ; *Transformation, Genetic ; }, abstract = {Phylogenetic studies reveal that horizontal gene transfer (HGT) plays a prominent role in evolution and genetic variability of life. Five biotic mechanisms of HGT among prokaryotic organisms have been extensively characterized: conjugation, competence, transduction, gene transfer agent particles, and transitory fusion with recombination, but it is not known whether they can account for all natural HGT. It is even less clear how HGT could have occurred before any of these mechanisms had developed. Here, we consider contemporary conditions and experiments on microorganisms to estimate possible roles of abiotic HGT-currently and throughout evolution. Candidate mechanisms include freeze-and-thaw, microbeads-agitation, and electroporation-based transformation, and we posit that these laboratory techniques have analogues in nature acting as mechanisms of abiotic HGT: freeze-and-thaw cycles in polar waters, agitation by sand at foreshores and riverbeds, and lightning-triggered electroporation in near-surface aqueous habitats. We derive conservative order-of-magnitude estimates for rates of microorganisms subjected to freeze-and-thaw cycles, sand agitation, and lightning-triggered electroporation, at 10[24], 10[19], and 10[17] per year, respectively. Considering the yield of viable transformants, which is by far the highest in electroporation, we argue this may still favor lightning-triggered transformation over the other two mechanisms. Electroporation-based gene transfer also appears to be the most general of these abiotic candidates, and perhaps even of all known HGT mechanisms. Future studies should provide improved estimates of gene transfer rates and cell viability, currently and in the past, but to assess the importance of abiotic HGT in nature will likely require substantial progress-also in knowledge of biotic HGT.}, }
@article {pmid27066305, year = {2016}, author = {Salomon, D}, title = {MIX and match: mobile T6SS MIX-effectors enhance bacterial fitness.}, journal = {Mobile genetic elements}, volume = {6}, number = {1}, pages = {e1123796}, pmid = {27066305}, issn = {2159-2543}, support = {K99 AI116948/AI/NIAID NIH HHS/United States ; }, abstract = {Protein secretion systems that mediate interbacterial competition secret a wide repertoire of antibacterial toxins. A major player in these competitions is the newly discovered bacterial type VI secretion system (T6SS). We recently found that a subset of polymorphic MIX-effectors, which are a widespread class of effectors secreted by T6SSs, are horizontally shared between marine bacteria and are used to diversify their T6SS effector repertoires, thus enhancing their environmental fitness. In this commentary, I expand on the ideas that were introduced in the previous report, and further speculate on the possible mobility of other MIX-effectors. In addition, I discuss the possible role of horizontal gene transfer in the dissemination of MIX-effectors through bacterial genomes, as well as its possible role in diversifying the T6SS effector repertoire.}, }
@article {pmid27066024, year = {2016}, author = {McDonald, TR and Ward, JM}, title = {Evolution of Electrogenic Ammonium Transporters (AMTs).}, journal = {Frontiers in plant science}, volume = {7}, number = {}, pages = {352}, pmid = {27066024}, issn = {1664-462X}, abstract = {The ammonium transporter gene family consists of three main clades, AMT, MEP, and Rh. The evolutionary history of the AMT/MEP/Rh gene family is characterized by multiple horizontal gene transfer events, gene family expansion and contraction, and gene loss; thus the gene tree for this family of transporters is unlike the organismal tree. The genomes of angiosperms contain genes for both electrogenic and electroneutral ammonium transporters, but it is not clear how far back in the land plant lineage electrogenic ammonium transporters occur. Here, we place Marchantia polymorpha ammonium transporters in the AMT/MEP/Rh phylogeny and we show that AMTs from the liverwort M. polymorpha are electrogenic. This information suggests that electrogenic ammonium transport evolved at least as early as the divergence of bryophytes in the land plant lineage.}, }
@article {pmid27065978, year = {2016}, author = {Bajaj, P and Singh, NS and Virdi, JS}, title = {Escherichia coli β-Lactamases: What Really Matters.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {417}, pmid = {27065978}, issn = {1664-302X}, abstract = {Escherichia coli strains belonging to diverse pathotypes have increasingly been recognized as a major public health concern. The β-lactam antibiotics have been used successfully to treat infections caused by pathogenic E. coli. However, currently, the utility of β-lactams is being challenged severely by a large number of hydrolytic enzymes - the β-lactamases expressed by bacteria. The menace is further compounded by the highly flexible genome of E. coli, and propensity of resistance dissemination through horizontal gene transfer and clonal spread. Successful management of infections caused by such resistant strains requires an understanding of the diversity of β-lactamases, their unambiguous detection, and molecular mechanisms underlying their expression and spread with regard to the most relevant information about individual bacterial species. Thus, this review comprises first such effort in this direction for E. coli, a bacterial species known to be associated with production of diverse classes of β-lactamases. The review also highlights the role of commensal E. coli as a potential but under-estimated reservoir of β-lactamases-encoding genes.}, }
@article {pmid27065965, year = {2016}, author = {Panda, P and Vanga, BR and Lu, A and Fiers, M and Fineran, PC and Butler, R and Armstrong, K and Ronson, CW and Pitman, AR}, title = {Pectobacterium atrosepticum and Pectobacterium carotovorum Harbor Distinct, Independently Acquired Integrative and Conjugative Elements Encoding Coronafacic Acid that Enhance Virulence on Potato Stems.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {397}, pmid = {27065965}, issn = {1664-302X}, abstract = {Integrative and conjugative elements (ICEs) play a central role in the evolution of bacterial virulence, their transmission between bacteria often leading to the acquisition of virulence factors that alter host range or aggressiveness. Much is known about the functions of the virulence determinants that ICEs harbor, but little is understood about the cryptic effects of ICEs on their host cell. In this study, the importance of horizontally acquired island 2 (HAI2), an ICE in the genome of Pectobacterium atrosepticum SCRI1043, was studied using a strain in which the entire ICE had been removed by CRISPR-Cas-mediated genome editing. HAI2 encodes coronafacic acid, a virulence factor that enhances blackleg disease of potato stems caused by P. atrosepticum SCRI1043. As expected, deletion of HAI2 resulted in reduced blackleg symptoms in potato stems. A subsequent screen for HAI2-related ICEs in other strains of the Pectobacterium genus revealed their ubiquitous nature in P. atrosepticum. Yet, HAI2-related ICEs were only detected in the genomes of a few P. carotovorum strains. These strains were notable as blackleg causing strains belonging to two different subspecies of P. carotovorum. Sequence analysis of the ICEs in different strains of both P. atrosepticum and P. carotovorum confirmed that they were diverse and were present in different locations on the genomes of their bacterial host, suggesting that the cfa cluster was probably acquired independently on a number of occasions via chromosomal insertion of related ICEs. Excision assays also demonstrated that the ICEs in both P. atrosepticum and P. carotovorum are mobilized from the host chromosome. Thus, the future spread of these ICEs via lateral gene transfer might contribute to an increase in the prevalence of blackleg-causing strains of P. carotovorum.}, }
@article {pmid27065964, year = {2016}, author = {Taylor, VL and Hoage, JF and Thrane, SW and Huszczynski, SM and Jelsbak, L and Lam, JS}, title = {A Bacteriophage-Acquired O-Antigen Polymerase (Wzyβ) from P. aeruginosa Serotype O16 Performs a Varied Mechanism Compared to Its Cognate Wzyα.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {393}, pmid = {27065964}, issn = {1664-302X}, abstract = {Pseudomonas aeruginosa is a Gram-negative bacterium that produces highly varied lipopolysaccharide (LPS) structures. The O antigen (O-Ag) in the LPS is synthesized through the Wzx/Wzy-dependent pathway where lipid-linked O-Ag repeats are polymerized by Wzy. Horizontal-gene transfer has been associated with O-Ag diversity. The O-Ag present on the surface of serotypes O5 and O16, differ in the intra-molecular bonds, α and β, respectively; the latter arose from the action of three genes in a serotype converting unit acquired from bacteriophage D3, including a β-polymerase (Wzyβ). To further our understanding of O-polymerases, the inner membrane (IM) topology of Wzyβ was determined using a dual phoA-lacZα reporter system wherein random 3' gene truncations were localized to specific loci with respect to the IM by normalized reporter activities as determined through the ratio of alkaline phosphatase activity to β-galactosidase activity. The topology of Wzyβ developed through this approach was shown to contain two predominant periplasmic loops, PL3 (containing an RX10G motif) and PL4 (having an O-Ag ligase superfamily motif), associated with inverting glycosyltransferase reaction. Through site-directed mutagenesis and complementation assays, residues Arg(254), Arg(270), Arg(272), and His(300) were found to be essential for Wzyβ function. Additionally, like-charge substitutions, R254K and R270K, could not complement the wzy β knockout, highlighting the essential guanidium side group of Arg residues. The O-Ag ligase domain is conserved among heterologous Wzy proteins that produce β-linked O-Ag repeat units. Taking advantage of the recently obtained whole-genome sequence of serotype O16 a candidate promoter was identified. Wzy β under its native promoter was integrated in the PAO1 genome, which resulted in simultaneous production of α- and β-linked O-Ag. These observations established that members of Wzy-like family consistently exhibit a dual-periplasmic loops topology, and identifies motifs that are plausible to be involved in enzymatic activities. Based on these results, the phage-derived Wzyβ utilizes a different reaction mechanism in the P. aeruginosa host to avoid self-inhibition during serotype conversion.}, }
@article {pmid27065390, year = {2016}, author = {Luby, E and Ibekwe, AM and Zilles, J and Pruden, A}, title = {Molecular Methods for Assessment of Antibiotic Resistance in Agricultural Ecosystems: Prospects and Challenges.}, journal = {Journal of environmental quality}, volume = {45}, number = {2}, pages = {441-453}, doi = {10.2134/jeq2015.07.0367}, pmid = {27065390}, issn = {0047-2425}, mesh = {Agriculture ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/*genetics ; *Ecosystem ; Humans ; }, abstract = {Agricultural ecosystems are of special interest for monitoring the potential for antibiotic resistance to spread through the environment and contribute to human exposure. Molecular methods, which target DNA, RNA, and other molecular components of bacterial cells, present certain advantages for characterizing and quantifying markers of antibiotic resistance and their horizontal gene transfer. These include rapid, unambiguous detection of targets; consistent results; and avoidance of culture bias. However, molecular methods are also subject to limitations that are not always clearly addressed or taken into consideration in the interpretation of scientific data. In particular, DNA-based methods do not directly assess viability or presence within an intact bacterial host, but such information may be inferred based on appropriate experimental design or in concert with complementary methods. The purpose of this review is to provide an overview of existing molecular methods for tracking antibiotic resistance in agricultural ecosystems, to define their strengths and weaknesses, and to recommend a path forward for future applications of molecular methods and standardized reporting in the literature. This will guide research along the farm-to-fork continuum and support comparability of the growing number of studies in the literature in a manner that informs management decisions and policy development.}, }
@article {pmid27065386, year = {2016}, author = {Williams-Nguyen, J and Sallach, JB and Bartelt-Hunt, S and Boxall, AB and Durso, LM and McLain, JE and Singer, RS and Snow, DD and Zilles, JL}, title = {Antibiotics and Antibiotic Resistance in Agroecosystems: State of the Science.}, journal = {Journal of environmental quality}, volume = {45}, number = {2}, pages = {394-406}, doi = {10.2134/jeq2015.07.0336}, pmid = {27065386}, issn = {0047-2425}, mesh = {Agriculture ; *Anti-Bacterial Agents ; Bacteria ; *Drug Resistance, Microbial ; *Ecosystem ; Humans ; }, abstract = {We propose a simple causal model depicting relationships involved in dissemination of antibiotics and antibiotic resistance in agroecosystems and potential effects on human health, functioning of natural ecosystems, and agricultural productivity. Available evidence for each causal link is briefly summarized, and key knowledge gaps are highlighted. A lack of quantitative estimates of human exposure to environmental bacteria, in general, and antibiotic-resistant bacteria, specifically, is a significant data gap hindering the assessment of effects on human health. The contribution of horizontal gene transfer to resistance in the environment and conditions that might foster the horizontal transfer of antibiotic resistance genes into human pathogens also need further research. Existing research has focused heavily on human health effects, with relatively little known about the effects of antibiotics and antibiotic resistance on natural and agricultural ecosystems. The proposed causal model is used to elucidate gaps in knowledge that must be addressed by the research community and may provide a useful starting point for the design and analysis of future research efforts.}, }
@article {pmid27060669, year = {2016}, author = {Kerfeld, CA and Melnicki, MR}, title = {Assembly, function and evolution of cyanobacterial carboxysomes.}, journal = {Current opinion in plant biology}, volume = {31}, number = {}, pages = {66-75}, doi = {10.1016/j.pbi.2016.03.009}, pmid = {27060669}, issn = {1879-0356}, mesh = {Bacterial Proteins/*metabolism ; Cyanobacteria/*metabolism ; Ribulose-Bisphosphate Carboxylase/metabolism ; }, abstract = {All cyanobacteria contain carboxysomes, RuBisCO-encapsulating bacterial microcompartments that function as prokaryotic organelles. The two carboxysome types, alpha and beta, differ fundamentally in components, assembly, and species distribution. Alpha carboxysomes share a highly-conserved gene organization, with evidence of horizontal gene transfer from chemoautotrophic proteobacteria to the picocyanobacteria, and seem to co-assemble shells concomitantly with aggregation of cargo enzymes. In contrast, beta carboxysomes assemble an enzymatic core first, with an encapsulation peptide playing a critical role in formation of the surrounding shell. Based on similarities in assembly, and phylogenetic analysis of the pentameric shell protein conserved across all bacterial microcompartments, beta carboxysomes appear to be more closely related to the microcompartments of heterotrophic bacteria (metabolosomes) than to alpha carboxysomes, which appear deeply divergent. Beta carboxysomes can be found in the basal cyanobacterial clades that diverged before the ancestor of the chloroplast and have recently been shown to be able to encapsulate functional RuBisCO enzymes resurrected from ancestrally-reconstructed sequences, consistent with an ancient origin. Alpha and beta carboxysomes are not only distinct units of evolution, but are now emerging as genetic/metabolic modules for synthetic biology; heterologous expression and redesign of both the shell and the enzymatic core have recently been achieved.}, }
@article {pmid27060121, year = {2016}, author = {Wendel, AF and Ressina, S and Kolbe-Busch, S and Pfeffer, K and MacKenzie, CR}, title = {Species Diversity of Environmental GIM-1-Producing Bacteria Collected during a Long-Term Outbreak.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {12}, pages = {3605-3610}, pmid = {27060121}, issn = {1098-5336}, mesh = {Bacterial Proteins/*analysis/genetics ; Conjugation, Genetic ; Cross Infection/*epidemiology ; *Disease Outbreaks ; Drug Resistance, Bacterial ; Enterobacter cloacae/*enzymology/isolation &amp; purification ; *Environmental Microbiology ; Gene Transfer, Horizontal ; Gram-Negative Bacterial Infections/*epidemiology ; Humans ; Microbial Sensitivity Tests ; Plasmids/analysis ; Pseudomonas aeruginosa/*enzymology/isolation &amp; purification ; beta-Lactamases/*analysis/genetics ; }, abstract = {UNLABELLED: Reports of outbreaks concerning carbapenemase-producing Gram-negative bacteria in which the main source of transmission is the hospital environment are increasing. This study describes the results of environmental sampling in a protracted polyspecies metallo-beta-lactamase GIM-1 outbreak driven by plasmids and bacterial clones of Enterobacter cloacae and Pseudomonas aeruginosa in a tertiary care center. Environmental sampling targeting wet locations (especially sinks) was carried out on a surgical intensive care unit and on a medical ward on several occasions in 2012 and 2013. We were able to demonstrate 43 blaGIM-1-carrying bacteria (mainly nonfermenters but also Enterobacteriaceae) that were either related or unrelated to clinical strains in 30 sinks and one hair washbasin. GIM-1 was found in 12 different species, some of which are described here as carriers of GIM-1. Forty out of 43 bacteria displayed resistance to carbapenems and, in addition, to various non-beta-lactam antibiotics. Colistin resistance was observed in two E. cloacae isolates with MICs above 256 mg/liter. The blaGIM-1 gene was harbored in 12 different class 1 integrons, some without the typical 3' end. The blaGIM-1 gene was localized on plasmids in five isolates. In vitro plasmid transfer by conjugation was successful in one isolate. The environment, with putatively multispecies biofilms, seems to be an important biological niche for multidrug-resistant bacteria and resistance genes. Biofilms may serve as a "melting pot" for horizontal gene transfer, for dissemination into new species, and as a reservoir to propagate future hospital outbreaks.<br><br>IMPORTANCE: In Gram-negative bacteria, resistance to the clinically relevant broad-spectrum carbapenem antibiotics is a major public health concern. Major reservoirs for these resistant organisms are not only the gastrointestinal tracts of animals and humans but also the (hospital) environment. Due to the difficulty in eradicating biofilm formation in the latter, a sustained dissemination of multidrug-resistant bacteria from the environment can occur. In addition, horizontal transfer of resistance genes on mobile genetic elements within biofilms adds to the total "resistance gene pool" in the environment. To gain insight into the transmission pathways of a rare and locally restricted carbapenemases resistance gene (blaGIM-1), we analyzed the genetic background of the blaGIM-1 gene in environmental bacteria during a long-term polyspecies outbreak in a German hospital.}, }
@article {pmid27059897, year = {2016}, author = {Merda, D and Bonneau, S and Guimbaud, JF and Durand, K and Brin, C and Boureau, T and Lemaire, C and Jacques, MA and Fischer-Le Saux, M}, title = {Recombination-prone bacterial strains form a reservoir from which epidemic clones emerge in agroecosystems.}, journal = {Environmental microbiology reports}, volume = {8}, number = {5}, pages = {572-581}, doi = {10.1111/1758-2229.12397}, pmid = {27059897}, issn = {1758-2229}, abstract = {The acquisition of virulence-related genes through horizontal gene transfer can modify the pathogenic profiles of strains and lead to the emergence of new diseases. Xanthomonas arboricola is a bacterial species largely known for the damage it causes to stone and nut fruit trees worldwide. In addition to these host-specific populations called pathovars, many nonpathogenic strains have been identified in this species. Their evolutionary significance in the context of pathogen emergence is unknown. We looked at seven housekeeping genes amplified from 187 pathogenic and nonpathogenic strains isolated from various plants worldwide to analyze population genetics and recombination dynamics. We also examined the dynamics of the gains and losses of genes associated with life history traits (LHTs) during X. arboricola evolution. We discovered that X. arboricola presents an epidemic population structure. Successful pathovars of trees (i.e. pruni, corylina and juglandis) are epidemic clones whose emergence appears to be linked to the acquisition of eight genes coding for Type III effectors. The other strains of this species are part of a recombinant network, within which LHT-associated genes might have been lost. We suggest that nonpathogenic strains, because of their high genetic diversity and propensity for recombination, may promote the emergence of pathogenic strains.}, }
@article {pmid27057964, year = {2016}, author = {Shapiro, BJ}, title = {How clonal are bacteria over time?.}, journal = {Current opinion in microbiology}, volume = {31}, number = {}, pages = {116-123}, doi = {10.1016/j.mib.2016.03.013}, pmid = {27057964}, issn = {1879-0364}, mesh = {Archaea/genetics/growth &amp; development ; Bacteria/*genetics/*growth &amp; development ; Clonal Evolution/*genetics ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial/genetics ; Lakes/microbiology ; Recombination, Genetic/*genetics ; Selection, Genetic/genetics ; }, abstract = {Bacteria and archaea reproduce clonally (vertical descent), but exchange genes by recombination (horizontal transfer). Recombination allows adaptive mutations or genes to spread rapidly within (or even between) species, and reduces the burden of deleterious mutations. Clonality-defined here as the balance between vertical and horizontal inheritance-is therefore a key microbial trait, determining how quickly a population can adapt and the size of its gene pool. Here, I discuss whether clonality varies over time and if it can be considered a stable trait of a given population. I show that, in some cases, clonality is clearly not static. For example, non-clonal (highly recombining) populations can give rise to clonal expansions, often of pathogens. However, an analysis of time-course metagenomic data from a lake suggests that a bacterial population's past clonality (as measured by its genetic diversity) is a good predictor of its future clonality. Clonality therefore appears to be relatively-but not completely-stable over evolutionary time.}, }
@article {pmid27055295, year = {2015}, author = {Baymiev, AKh and Ivanova, ES and Gumenko, RS and Chubukova, OV and Baymiev, AKh}, title = {[Analysis of Symbiotic Genes of Leguminous Plants Nodule Bacteria Grown in the Southern Urals].}, journal = {Genetika}, volume = {51}, number = {12}, pages = {1359-1367}, pmid = {27055295}, issn = {0016-6758}, mesh = {*Fabaceae/genetics/microbiology ; Gene Transfer, Horizontal/*physiology ; *Genes, Plant ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Rhizobiaceae/*physiology ; *Root Nodules, Plant/genetics/microbiology ; Russia ; Symbiosis/*physiology ; }, abstract = {Bacterial strains isolated from the nodules, tissues, and root surface of wild legumes growing in the Southern Urals related to the tribes Galegeae, Hedysareae, Genisteae, Trifolieae, and Loteae were examined for the presence in their genomes of symbiotic (sym) genes. It was found that the sym-genes are present in microorganisms isolated only from the nodules of the analyzed plants (sym+ -strains). Phylogenetic analysis of sym+ -strains on the basis of a comparative analysis of 16S rRNA gene sequences showed that sym+ -strains belong to five families of nodule bacteria: Mesorhizobium, Bradyrhizobium, Sinorhizobium, Rhizobium, and Phyllobacterium. A study the phylogeny of the sym-genes showed that the nodule bacteria of leguminous plants of the Southern Urals at the genus level are mainly characterized by a parallel evolution of symbiotic genes and the 16S rRNA gene. Thus, cases of horizontal transfer of sym genes, which sometimes leads to the formation of certain types of atypical rhizobial strains ofleguminous plants, are detected in nodule bacteria populations.}, }
@article {pmid27049518, year = {2016}, author = {Graaf-van Bloois, Lv and Miller, WG and Yee, E and Gorkiewicz, G and Forbes, KJ and Zomer, AL and Wagenaar, JA and Duim, B}, title = {Campylobacter fetus Subspecies Contain Conserved Type IV Secretion Systems on Multiple Genomic Islands and Plasmids.}, journal = {PloS one}, volume = {11}, number = {4}, pages = {e0152832}, pmid = {27049518}, issn = {1932-6203}, mesh = {Bacterial Proteins/classification/genetics ; Campylobacter fetus/genetics/*physiology ; *Genome, Bacterial ; Phylogeny ; *Plasmids ; }, abstract = {The features contributing to differences in pathogenicity of the Campylobacter fetus subspecies are unknown. Putative factors involved in pathogenesis are located in genomic islands that encode a type IV secretion system (T4SS) and fic domain (filamentation induced by cyclic AMP) proteins, which may disrupt host cell processes. In the genomes of 27 C. fetus strains, three phylogenetically-different T4SS-encoding regions (T4SSs) were identified: one was located in both the chromosome and in extra-chromosomal plasmids; one was located exclusively in the chromosome; and one exclusively in extra-chromosomal plasmids. We observed that C. fetus strains can contain multiple T4SSs and that homologous T4SSs can be present both in chromosomal genomic islands (GI) and on plasmids in the C. fetus strains. The GIs of the chromosomally located T4SS differed mainly by the presence of fic genes, insertion sequence elements and phage-related or hypothetical proteins. Comparative analysis showed that T4SS sequences, inserted in the same locations, were conserved in the studied C. fetus genomes. Using phylogenetic analysis of the T4SSs, it was shown that C. fetus may have acquired the T4SS regions from other Campylobacter species by horizontal gene transfer. The identified T4SSs and fic genes were found in Cff and Cfv strains, although the presence of T4SSs and fic genes were significantly associated with Cfv strains. The T4SSs and fic genes could not be associated with S-layer serotypes or geographical origin of the strains.}, }
@article {pmid27048805, year = {2016}, author = {Hemme, CL and Green, SJ and Rishishwar, L and Prakash, O and Pettenato, A and Chakraborty, R and Deutschbauer, AM and Van Nostrand, JD and Wu, L and He, Z and Jordan, IK and Hazen, TC and Arkin, AP and Kostka, JE and Zhou, J}, title = {Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community.}, journal = {mBio}, volume = {7}, number = {2}, pages = {e02234-15}, pmid = {27048805}, issn = {2150-7511}, mesh = {Gammaproteobacteria/*genetics/metabolism ; *Gene Transfer, Horizontal ; Groundwater/analysis/*microbiology ; Metals, Heavy/*analysis/metabolism ; Microbiota ; Water Pollutants, Chemical/*analysis/metabolism ; }, abstract = {UNLABELLED: Unraveling the drivers controlling the response and adaptation of biological communities to environmental change, especially anthropogenic activities, is a central but poorly understood issue in ecology and evolution. Comparative genomics studies suggest that lateral gene transfer (LGT) is a major force driving microbial genome evolution, but its role in the evolution of microbial communities remains elusive. To delineate the importance of LGT in mediating the response of a groundwater microbial community to heavy metal contamination, representative Rhodanobacter reference genomes were sequenced and compared to shotgun metagenome sequences. 16S rRNA gene-based amplicon sequence analysis indicated that Rhodanobacter populations were highly abundant in contaminated wells with low pHs and high levels of nitrate and heavy metals but remained rare in the uncontaminated wells. Sequence comparisons revealed that multiple geochemically important genes, including genes encoding Fe(2+)/Pb(2+) permeases, most denitrification enzymes, and cytochrome c553, were native to Rhodanobacter and not subjected to LGT. In contrast, the Rhodanobacter pangenome contained a recombinational hot spot in which numerous metal resistance genes were subjected to LGT and/or duplication. In particular, Co(2+)/Zn(2+)/Cd(2+) efflux and mercuric resistance operon genes appeared to be highly mobile within Rhodanobacter populations. Evidence of multiple duplications of a mercuric resistance operon common to most Rhodanobacter strains was also observed. Collectively, our analyses indicated the importance of LGT during the evolution of groundwater microbial communities in response to heavy metal contamination, and a conceptual model was developed to display such adaptive evolutionary processes for explaining the extreme dominance of Rhodanobacter populations in the contaminated groundwater microbiome.<br><br>IMPORTANCE: Lateral gene transfer (LGT), along with positive selection and gene duplication, are the three main mechanisms that drive adaptive evolution of microbial genomes and communities, but their relative importance is unclear. Some recent studies suggested that LGT is a major adaptive mechanism for microbial populations in response to changing environments, and hence, it could also be critical in shaping microbial community structure. However, direct evidence of LGT and its rates in extant natural microbial communities in response to changing environments is still lacking. Our results presented in this study provide explicit evidence that LGT played a crucial role in driving the evolution of a groundwater microbial community in response to extreme heavy metal contamination. It appears that acquisition of genes critical for survival, growth, and reproduction via LGT is the most rapid and effective way to enable microorganisms and associated microbial communities to quickly adapt to abrupt harsh environmental stresses.}, }
@article {pmid27048799, year = {2016}, author = {Lee, MJ and Geller, AM and Bamford, NC and Liu, H and Gravelat, FN and Snarr, BD and Le Mauff, F and Chabot, J and Ralph, B and Ostapska, H and Lehoux, M and Cerone, RP and Baptista, SD and Vinogradov, E and Stajich, JE and Filler, SG and Howell, PL and Sheppard, DC}, title = {Deacetylation of Fungal Exopolysaccharide Mediates Adhesion and Biofilm Formation.}, journal = {mBio}, volume = {7}, number = {2}, pages = {e00252-16}, pmid = {27048799}, issn = {2150-7511}, support = {236182//Canadian Institutes of Health Research/Canada ; 81361//Canadian Institutes of Health Research/Canada ; R01AI073829/AI/NIAID NIH HHS/United States ; S10 OD016290/OD/NIH HHS/United States ; 13337//Canadian Institutes of Health Research/Canada ; R01 AI073829/AI/NIAID NIH HHS/United States ; }, mesh = {Acetylation ; Aspergillosis/*microbiology ; Aspergillus fumigatus/genetics/growth &amp; development/*physiology ; *Biofilms ; Fungal Proteins/genetics/metabolism ; Humans ; Polysaccharides/*metabolism ; }, abstract = {UNLABELLED: The mold Aspergillus fumigatus causes invasive infection in immunocompromised patients. Recently, galactosaminogalactan (GAG), an exopolysaccharide composed of galactose and N-acetylgalactosamine (GalNAc), was identified as a virulence factor required for biofilm formation. The molecular mechanisms underlying GAG biosynthesis and GAG-mediated biofilm formation were unknown. We identified a cluster of five coregulated genes that were dysregulated in GAG-deficient mutants and whose gene products share functional similarity with proteins that mediate the synthesis of the bacterial biofilm exopolysaccharide poly-(β1-6)-N-acetyl-D-glucosamine (PNAG). Bioinformatic analyses suggested that the GAG cluster gene agd3 encodes a protein containing a deacetylase domain. Because deacetylation of N-acetylglucosamine residues is critical for the function of PNAG, we investigated the role of GAG deacetylation in fungal biofilm formation. Agd3 was found to mediate deacetylation of GalNAc residues within GAG and render the polysaccharide polycationic. As with PNAG, deacetylation is required for the adherence of GAG to hyphae and for biofilm formation. Growth of the Δagd3 mutant in the presence of culture supernatants of the GAG-deficient Δuge3 mutant rescued the biofilm defect of the Δagd3 mutant and restored the adhesive properties of GAG, suggesting that deacetylation is an extracellular process. The GAG biosynthetic gene cluster is present in the genomes of members of the Pezizomycotina subphylum of the Ascomycota including a number of plant-pathogenic fungi and a single basidiomycete species,Trichosporon asahii, likely a result of recent horizontal gene transfer. The current study demonstrates that the production of cationic, deacetylated exopolysaccharides is a strategy used by both fungi and bacteria for biofilm formation.<br><br>IMPORTANCE: This study sheds light on the biosynthetic pathways governing the synthesis of galactosaminogalactan (GAG), which plays a key role in A. fumigatus virulence and biofilm formation. We find that bacteria and fungi use similar strategies to synthesize adhesive biofilm exopolysaccharides. The presence of orthologs of the GAG biosynthetic gene clusters in multiple fungi suggests that this exopolysaccharide may also be important in the virulence of other fungal pathogens. Further, these studies establish a molecular mechanism of adhesion in which GAG interacts via charge-charge interactions to bind to both fungal hyphae and other substrates. Finally, the importance of deacetylation in the synthesis of functional GAG and the extracellular localization of this process suggest that inhibition of deacetylation may be an attractive target for the development of novel antifungal therapies.}, }
@article {pmid27047141, year = {2015}, author = {Warjri, I and Dutta, TK and Lalzampuia, H and Chandra, R}, title = {Detection and characterization of extended-spectrum β-lactamases (blaCTX-M-1 and blaSHV) producing Escherichia coli, Salmonella spp. and Klebsiella pneumoniae isolated from humans in Mizoram.}, journal = {Veterinary world}, volume = {8}, number = {5}, pages = {599-604}, pmid = {27047141}, issn = {0972-8988}, abstract = {AIM: The present study was conducted to isolate and characterize the extended spectrum β-lactamases (ESBLs) producing enteric bacteria in human beings in Mizoram, India.<br><br>MATERIALS AND METHODS: Fecal samples were collected from human beings with or without the history of diarrhea from different hospitals of Mizoram. Samples were processed for isolation and identification of Escherichia coli, Salmonella and Klebsiella pneumoniae. All the isolates were subjected to antibiotic sensitivity assays. Phenotypically, ESBLs production ability was determined by double discs synergy test (DDST) method. ESBLs producing isolates were subjected to polymerase chain reaction (PCR) for detection of ESBLs genes. Plasmids were cured by acridine orange. Transfer of resistance from a donor to recipient strains was done by in vitro horizontal method.<br><br>RESULTS: A total of 414 enteric bacteria were isolated from 180 fecal samples (113 were from diarrheic patients and 67 were from non-diarrheic patients), of which 333 (80.44%), 52 (12.56%), and 29 (7.00%) were E. coli, K. pneumoniae and Salmonella spp., respectively. Double discs synergy test (DDST) exhibited 72 (21.62%) E. coli, 12 (23.08%) K. pneumoniae and 4 (13.79%) Salmonella spp. were ESBLs producers. Altogether, 24 (13.04%) isolates were found to be positive for at least one resistance genes under this study. A total of 36 (8.70%) E. coli, 4 (0.97%) K. pneumoniae and 2 (0.48%) Salmonella spp. were found to be positive for blaCTX-M-1 gene by PCR. Similarly, 5 (1.21%) E. coli and 4 (0.97%) K. pneumoniae isolates were found to be positive for blaSHV gene. A total of 3 (0.72%) K. pneumoniae isolates were recorded as positive for both blaCTX-M-1 and blaSHV genes. All the isolates were carrying plasmids ranging between 0.9 kb and ~30 kb. The resistance plasmid could not be transferred to a recipient by in vitro horizontal gene transfer method.<br><br>CONCLUSION: ESBLs producing enteric bacteria are circulating in human population in North Eastern Region of India. Indiscriminate use of antibiotics should be avoided to control the menace of multidrug resistance bacteria in the environment, animals, and human beings.}, }
@article {pmid27046731, year = {2016}, author = {Pitta, DW and Dou, Z and Kumar, S and Indugu, N and Toth, JD and Vecchiarelli, B and Bhukya, B}, title = {Metagenomic Evidence of the Prevalence and Distribution Patterns of Antimicrobial Resistance Genes in Dairy Agroecosystems.}, journal = {Foodborne pathogens and disease}, volume = {13}, number = {6}, pages = {296-302}, doi = {10.1089/fpd.2015.2092}, pmid = {27046731}, issn = {1556-7125}, mesh = {Animal Husbandry ; Animals ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteroides/drug effects ; Cattle ; Cattle Diseases/drug therapy/*epidemiology/microbiology ; *Dairying ; Drug Resistance, Bacterial/*genetics ; Feces/microbiology ; Female ; *Food Microbiology ; Manure/microbiology ; Pennsylvania/epidemiology ; Prevalence ; Soil Microbiology ; }, abstract = {Antimicrobial resistance (AR) is a global problem with serious implications for public health. AR genes are frequently detected on animal farms, but little is known about their origin and distribution patterns. We hypothesized that AR genes can transfer from animal feces to the environment through manure, and to this end, we characterized and compared the resistomes (collections of AR genes) of animal feces, manure, and soil samples collected from five dairy farms using a metagenomics approach. Resistomes constituted only up to 1% of the total gene content, but were variable by sector and also farm. Broadly, the identified AR genes were associated with 18 antibiotic resistances classes across all samples; however, the most abundant genes were classified under multidrug transporters (44.75%), followed by resistance to vancomycin (12.48%), tetracycline (10.52%), bacitracin (10.43%), beta-lactam resistance (7.12%), and MLS efflux pump (6.86%) antimicrobials. The AR gene profiles were variable between farms. Farm 09 was categorized as a high risk farm, as a greater proportion of AR genes were common to at least three sectors, suggesting possible horizontal transfer of AR genes. Taxonomic characterization of AR genes revealed that a majority of AR genes were associated with the phylum Proteobacteria. Nonetheless, there were several members of Bacteroidetes, particularly Bacteroides genus and several lineages from Firmicutes that carried similar AR genes in different sectors, suggesting a strong potential for horizontal transfer of AR genes between unrelated bacterial hosts in different sectors of the farms. Further studies are required to affirm the horizontal gene transfer mechanisms between microbiomes of different sectors in animal agroecosystems.}, }
@article {pmid27046628, year = {2016}, author = {Milanović, V and Osimani, A and Pasquini, M and Aquilanti, L and Garofalo, C and Taccari, M and Cardinali, F and Riolo, P and Clementi, F}, title = {Getting insight into the prevalence of antibiotic resistance genes in specimens of marketed edible insects.}, journal = {International journal of food microbiology}, volume = {227}, number = {}, pages = {22-28}, doi = {10.1016/j.ijfoodmicro.2016.03.018}, pmid = {27046628}, issn = {1879-3460}, mesh = {Animals ; Bacteria/classification/drug effects/*genetics ; Bacterial Load ; *Drug Resistance, Bacterial ; Food Chain ; *Food Safety ; *Gene Transfer, Horizontal ; Insecta/classification/genetics/*microbiology ; Netherlands ; Polymerase Chain Reaction ; Scorpions/classification/genetics/*microbiology ; Thailand ; }, abstract = {This study was aimed at investigating the occurrence of 11 transferable antibiotic resistance (AR) genes [erm(A), erm(B), erm(C), vanA, vanB, tet(M), tet(O), tet(S), tet(K), mecA, blaZ] in 11 species of marketed edible insects (small crickets powder, small crickets, locusts, mealworm larvae, giant waterbugs, black ants, winged termite alates, rhino beetles, mole crickets, silkworm pupae, and black scorpions) in order to provide a first baseline for risk assessment. Among the AR genes under study, tet(K) occurred with the highest frequency, followed by erm(B), tet(S) and blaZ. A high variability was seen among the samples, in terms of occurrence of different AR determinants. Cluster Analysis and Principal Coordinates Analysis allowed the 11 samples to be grouped in two main clusters, one including all but one samples produced in Thailand and the other including those produced in the Netherlands.}, }
@article {pmid27043971, year = {2016}, author = {Chen, Q and An, X and Li, H and Su, J and Ma, Y and Zhu, YG}, title = {Long-term field application of sewage sludge increases the abundance of antibiotic resistance genes in soil.}, journal = {Environment international}, volume = {92-93}, number = {}, pages = {1-10}, doi = {10.1016/j.envint.2016.03.026}, pmid = {27043971}, issn = {1873-6750}, mesh = {Anti-Bacterial Agents/*analysis/pharmacology ; China ; Drug Resistance, Microbial/*genetics ; *Genes, Bacterial ; High-Throughput Screening Assays ; Manure/microbiology ; Real-Time Polymerase Chain Reaction ; Sewage/*microbiology ; Soil/chemistry/standards ; *Soil Microbiology ; Soil Pollutants/*analysis/pharmacology ; }, abstract = {Sewage sludge and manure are common soil amendments in crop production; however, their impact on the abundance and diversity of the antibiotic resistome in soil remains elusive. In this study, by using high-throughput sequencing and high-throughput quantitative PCR, the patterns of bacterial community and antibiotic resistance genes (ARGs) in a long-term field experiment were investigated to gain insights into these impacts. A total of 130 unique ARGs and 5 mobile genetic elements (MGEs) were detected and the long-term application of sewage sludge and chicken manure significantly increased the abundance and diversity of ARGs in the soil. Genes conferring resistance to beta-lactams, tetracyclines, and multiple drugs were dominant in the samples. Sewage sludge or chicken manure applications caused significant enrichment of 108 unique ARGs and MGEs with a maximum enrichment of up to 3845 folds for mexF. The enrichment of MGEs suggested that the application of sewage sludge or manure may accelerate the dissemination of ARGs in soil through horizontal gene transfer (HGT). Based on the co-occurrence pattern of ARGs subtypes revealed by network analysis, aacC, oprD and mphA-02, were proposed to be potential indicators for quantitative estimation of the co-occurring ARGs subtypes abundance by power functions. The application of sewage sludge and manure resulted in significant increase of bacterial diversity in soil, Proteobacteria, Acidobacteria, Actinobacteria and Chloroflexi were the dominant phyla (>10% in each sample). Five bacterial phyla (Chloroflexi, Planctomycetes, Firmicutes, Gemmatimonadetes and Bacteroidetes) were found to be significantly correlated with the ARGs in soil. Mantel test and variation partitioning analysis (VPA) suggested that bacterial community shifts, rather than MGEs, is the major driver shaping the antibiotic resistome. Additionally, the co-occurrence pattern between ARGs and microbial taxa revealed by network analysis indicated that four bacterial families might be potential hosts of ARGs. These results may shed light on the mechanism underlining the effects of amendments of sewage sludge or manure on the occurrence and dissemination of ARGs in soil.}, }
@article {pmid27042356, year = {2016}, author = {Javadi, M and Oloomi, M and Bouzari, S}, title = {Genotype Cluster Analysis in Pathogenic Escherichia coli Isolates Producing Different CDT Types.}, journal = {Journal of pathogens}, volume = {2016}, number = {}, pages = {9237127}, pmid = {27042356}, issn = {2090-3057}, abstract = {Diarrheagenic and uropathogenic E. coli types are mainly characterized by the expression of distinctive bacterial virulent factors. stx1, stx2 (Shiga toxins), and cdt (cytolethal distending toxin) genes have been acquired by horizontal gene transfer. Some virulent genes such as espP (serine protease), etpD (part of secretion pathway), and katP (catalase-peroxidase), or sfpA gene (Sfp fimbriae), are on plasmids and the others like fliC (flagellin) and the fimH gene (fimbriae type-I) are located on chromosome. Genomic pathogenicity islands (PAIs) carry some virulent genes such as hly gene. To determine the existence of virulence genes in cdt clinical isolates, genes including stx1, stx2, cdt, hly, espP, katP, sfpA, etpD, fliC, and fimH were assessed by Polymerase Chain Reaction (PCR). The most prevalent isolates for etpD and katP genes were 85.7% in cdtII. katP gene was also observed 83.3% in cdtI. However, in 42.85% of cdtIII isolates, espP gene was the most detected. Moreover, hly gene was also the most prominent gene in cdtIII (71.42%). sfpA gene was observed in 66.6% of cdtV. stx1 gene was detected in 100% of cdtII, cdtIV, and cdtV types. Presence and pattern of virulence genes were considered among cdt positive isotypes and used for their clustering and profiling.}, }
@article {pmid27039285, year = {2016}, author = {Kottara, A and Hall, JP and Harrison, E and Brockhurst, MA}, title = {Multi-host environments select for host-generalist conjugative plasmids.}, journal = {BMC evolutionary biology}, volume = {16}, number = {}, pages = {70}, pmid = {27039285}, issn = {1471-2148}, support = {311490/ERC_/European Research Council/International ; }, mesh = {*Biological Evolution ; Drug Resistance, Bacterial ; *Gene Transfer, Horizontal ; Genetic Fitness ; Mercury/toxicity ; *Plasmids ; Pseudomonas fluorescens/*genetics ; Pseudomonas putida/*genetics ; }, abstract = {BACKGROUND: Conjugative plasmids play an important role in bacterial evolution by transferring ecologically important genes within and between species. A key limit on interspecific horizontal gene transfer is plasmid host range. Here, we experimentally test the effect of single and multi-host environments on the host-range evolution of a large conjugative mercury resistance plasmid, pQBR57. Specifically, pQBR57 was conjugated between strains of a single host species, either P. fluorescens or P. putida, or alternating between P. fluorescens and P. putida. Crucially, the bacterial hosts were not permitted to evolve allowing us to observe plasmid evolutionary responses in isolation.<br><br>RESULTS: In all treatments plasmids evolved higher conjugation rates over time. Plasmids evolved in single-host environments adapted to their host bacterial species becoming less costly, but in the case of P. fluorescens-adapted plasmids, became costlier in P. putida, suggesting an evolutionary trade-off. When evolved in the multi-host environment plasmids adapted to P. fluorescens without a higher cost in P. putida.<br><br>CONCLUSION: Whereas evolution in a single-host environment selected for host-specialist plasmids due to a fitness trade-off, this trade-off could be circumvented in the multi-host environment, leading to the evolution of host-generalist plasmids.}, }
@article {pmid27038795, year = {2016}, author = {Ohmine, Y and Satoh, Y and Kiyokawa, K and Yamamoto, S and Moriguchi, K and Suzuki, K}, title = {DNA repair genes RAD52 and SRS2, a cell wall synthesis regulator gene SMI1, and the membrane sterol synthesis scaffold gene ERG28 are important in efficient Agrobacterium-mediated yeast transformation with chromosomal T-DNA.}, journal = {BMC microbiology}, volume = {16}, number = {}, pages = {58}, pmid = {27038795}, issn = {1471-2180}, mesh = {Agrobacterium/*genetics/growth &amp; development ; Cell Wall/metabolism ; DNA Helicases/genetics ; DNA, Bacterial/*genetics ; Gene Library ; Membrane Proteins/genetics ; Mutation ; Rad52 DNA Repair and Recombination Protein/genetics ; Saccharomyces cerevisiae/genetics/*growth &amp; development/metabolism ; Saccharomyces cerevisiae Proteins/*genetics ; Transcription Factors/genetics ; *Transformation, Genetic ; }, abstract = {BACKGROUND: Plant pathogenic Agrobacterium strains can transfer T-DNA regions of their Ti plasmids to a broad range of eukaryotic hosts, including fungi, in vitro. In the recent decade, the yeast Saccharomyces cerevisiae is used as a model host to reveal important host proteins for the Agrobacterium-mediated transformation (AMT). Further investigation is required to understand the fundamental mechanism of AMT, including interaction at the cell surface, to expand the host range, and to develop new tools. In this study, we screened a yeast mutant library for low AMT mutant strains by advantage of a chromosome type T-DNA, which transfer is efficient and independent on integration into host chromosome.<br><br>RESULTS: By the mutant screening, we identified four mutant strains (srs2&#x394;, rad52&#x394;, smi1&#x394; and erg28&#x394;), which showed considerably low AMT efficiency. Structural analysis of T-DNA product replicons in AMT colonies of mutants lacking each of the two DNA repair genes, SRS2 and RAD52, suggested that the genes act soon after T-DNA entry for modification of the chromosomal T-DNA to stably maintain them as linear replicons and to circularize certain T-DNA simultaneously. The cell wall synthesis regulator SMI1 might have a role in the cell surface interaction between the donor and recipient cells, but the smi1&#x394; mutant exhibited pleiotropic effect, i.e. low effector protein transport as well as low AMT for the chromosomal T-DNA, but relatively high AMT for integrative T-DNAs. The ergosterol synthesis regulator/enzyme-scaffold gene ERG28 probably contributes by sensing a congested environment, because growth of erg28&#x394; strain was unaffected by the presence of donor bacterial cells, while the growth of the wild-type and other mutant yeast strains was suppressed by their presence.<br><br>CONCLUSIONS: RAD52 and the DNA helicase/anti-recombinase gene SRS2 are necessary to form and maintain artificial chromosomes through the AMT of chromosomal T-DNA. A sterol synthesis scaffold gene ERG28 is important in the high-efficiency AMT, possibly by avoiding congestion. The involvement of the cell wall synthesis regulator SMI1 remains to be elucidated.}, }
@article {pmid27036745, year = {2015}, author = {Blesa, A and Berenguer, J}, title = {Contribution of vesicle-protected extracellular DNA to horizontal gene transfer in Thermus spp.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {18}, number = {3}, pages = {177-187}, doi = {10.2436/20.1501.01.248}, pmid = {27036745}, issn = {1139-6709}, mesh = {DNA, Bacterial/genetics/metabolism ; Extracellular Vesicles/*metabolism ; *Gene Transfer, Horizontal ; Thermus/*genetics/growth &amp; development/metabolism ; }, abstract = {Highly efficient apparatus for natural competence and conjugation have been shown as the major contributors to horizontal gene transfer (HGT) in Thermus thermophilus. In practical terms, both mechanisms can be distinguished by the sensitivity of the former to the presence of DNAse, and the requirement for cell to cell contacts in the second. Here we demonstrate that culture supernatants of different strains of Thermus spp. produce DNAse-resistant extracellular DNA (eDNA) in a growth-rate dependent manner. This eDNA was double stranded, similar in size to isolated genomic DNA (around 20 kbp), and represented the whole genome of the producer strain. Protection against DNAse was the consequence of association of the eDNA to membrane vesicles which composition was shown to include a great diversity of cell envelope proteins with minor content of cytoplasmic proteins. Access of the recipient cell to the protected eDNA depended on the natural competence apparatus and elicited the DNA-DNA interference defence mediated by the Argonaute protein. We hypothesize on the lytic origin of the eDNA carrying vesicles and discuss the relevance of this alternative mechanism for HGT in natural thermal environments.}, }
@article {pmid27035985, year = {2016}, author = {Koutsovoulos, G and Kumar, S and Laetsch, DR and Stevens, L and Daub, J and Conlon, C and Maroon, H and Thomas, F and Aboobaker, AA and Blaxter, M}, title = {No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {18}, pages = {5053-5058}, pmid = {27035985}, issn = {1091-6490}, mesh = {Animals ; Arthropods/genetics ; *Gene Transfer, Horizontal ; Genome ; Molecular Sequence Data ; Phylogeny ; Tardigrada/*genetics ; }, abstract = {Tardigrades are meiofaunal ecdysozoans that are key to understanding the origins of Arthropoda. Many species of Tardigrada can survive extreme conditions through cryptobiosis. In a recent paper [Boothby TC, et al. (2015) Proc Natl Acad Sci USA 112(52):15976-15981], the authors concluded that the tardigrade Hypsibius dujardini had an unprecedented proportion (17%) of genes originating through functional horizontal gene transfer (fHGT) and speculated that fHGT was likely formative in the evolution of cryptobiosis. We independently sequenced the genome of H. dujardini As expected from whole-organism DNA sampling, our raw data contained reads from nontarget genomes. Filtering using metagenomics approaches generated a draft H. dujardini genome assembly of 135 Mb with superior assembly metrics to the previously published assembly. Additional microbial contamination likely remains. We found no support for extensive fHGT. Among 23,021 gene predictions we identified 0.2% strong candidates for fHGT from bacteria and 0.2% strong candidates for fHGT from nonmetazoan eukaryotes. Cross-comparison of assemblies showed that the overwhelming majority of HGT candidates in the Boothby et al. genome derived from contaminants. We conclude that fHGT into H. dujardini accounts for at most 1-2% of genes and that the proposal that one-sixth of tardigrade genes originate from functional HGT events is an artifact of undetected contamination.}, }
@article {pmid27035945, year = {2016}, author = {Alexander, WG and Wisecaver, JH and Rokas, A and Hittinger, CT}, title = {Horizontally acquired genes in early-diverging pathogenic fungi enable the use of host nucleosides and nucleotides.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {15}, pages = {4116-4121}, pmid = {27035945}, issn = {1091-6490}, mesh = {Fungi/*genetics/metabolism ; *Gene Transfer, Horizontal ; *Genes, Fungal ; *Host-Pathogen Interactions ; Nucleosides/*metabolism ; Nucleotides/*metabolism ; Phylogeny ; }, abstract = {Horizontal gene transfer (HGT) among bacteria, archaea, and viruses is widespread, but the extent of transfers from these lineages into eukaryotic organisms is contentious. Here we systematically identify hundreds of genes that were likely acquired horizontally from a variety of sources by the early-diverging fungal phyla Microsporidia and Cryptomycota. Interestingly, the Microsporidia have acquired via HGT several genes involved in nucleic acid synthesis and salvage, such as those encoding thymidine kinase (TK), cytidylate kinase, and purine nucleotide phosphorylase. We show that these HGT-derived nucleic acid synthesis genes tend to function at the interface between the metabolic networks of the host and pathogen. Thus, these genes likely play vital roles in diversifying the useable nucleic acid components available to the intracellular parasite, often through the direct capture of resources from the host. Using an in vivo viability assay, we also demonstrate that one of these genes, TK, encodes an enzyme that is capable of activating known prodrugs to their active form, which suggests a possible treatment route for microsporidiosis. We further argue that interfacial genes with well-understood activities, especially those horizontally transferred from bacteria or viruses, could provide medical treatments for microsporidian infections.}, }
@article {pmid27031100, year = {2016}, author = {Kim, BJ and Kim, BR and Lee, SY and Kim, GN and Kook, YH and Kim, BJ}, title = {Molecular Taxonomic Evidence for Two Distinct Genotypes of Mycobacterium yongonense via Genome-Based Phylogenetic Analysis.}, journal = {PloS one}, volume = {11}, number = {3}, pages = {e0152703}, pmid = {27031100}, issn = {1932-6203}, mesh = {Bacterial Proteins/*genetics ; *Genome, Bacterial ; *Genotype ; Mycobacterium/*genetics ; *Phylogeny ; Species Specificity ; }, abstract = {Recently, we introduced a distinct Mycobacterium intracellulare INT-5 genotype, distantly related to other genotypes of M. intracellulare (INT-1 to -4). The aim of this study is to determine the exact taxonomic status of the M. intracellulare INT-5 genotype via genome-based phylogenetic analysis. To this end, genome sequences of the two INT-5 strains, MOTT-H4Y and MOTT-36Y were compared with M. intracellulare ATCC 13950(T) and Mycobacterium yongonense DSM 45126(T). Our phylogenetic analysis based on complete genome sequences, multi-locus sequence typing (MLST) of 35 target genes, and single nucleotide polymorphism (SNP) analysis indicated that the two INT-5 strains were more closely related to M. yongonense DSM 45126(T) than the M. intracellulare strains. These results suggest their taxonomic transfer from M. intracellulare into M. yongonense. Finally, we selected 5 target genes (argH, dnaA, deaD, hsp65, and recF) and used SNPs for the identification of M. yongonese strains from other M. avium complex (MAC) strains. The application of the SNP analysis to 14 MAC clinical isolates enabled the selective identification of 4 M. yongonense clinical isolates from the other MACs. In conclusion, our genome-based phylogenetic analysis showed that the taxonomic status of two INT-5 strains, MOTT-H4Y and MOTT-36Y should be revised into M. yongonense. Our results also suggest that M. yongonense could be divided into 2 distinct genotypes (the Type I genotype with the M. parascrofulaceum rpoB gene and the Type II genotype with the M. intracellulare rpoB gene) depending on the presence of the lateral gene transfer of rpoB from M. parascrofulaceum.}, }
@article {pmid27030977, year = {2016}, author = {Shapiro, BJ and Leducq, JB and Mallet, J}, title = {What Is Speciation?.}, journal = {PLoS genetics}, volume = {12}, number = {3}, pages = {e1005860}, pmid = {27030977}, issn = {1553-7404}, mesh = {Bacteria/genetics ; Ecology ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; *Genetic Speciation ; Genetic Variation ; *Genome, Bacterial ; Genomics ; Recombination, Genetic ; Selection, Genetic ; }, abstract = {Concepts and definitions of species have been debated by generations of biologists and remain controversial. Microbes pose a particular challenge because of their genetic diversity, asexual reproduction, and often promiscuous horizontal gene transfer (HGT). However, microbes also present an opportunity to study and understand speciation because of their rapid evolution, both in nature and in the lab, and small, easily sequenced genomes. Here, we review how microbial population genomics has enabled us to catch speciation "in the act" and how the results have challenged and enriched our concepts of species, with implications for all domains of life. We describe how recombination (including HGT and introgression) has shaped the genomes of nascent microbial, animal, and plant species and argue for a prominent role of natural selection in initiating and maintaining speciation. We ask how universal is the process of speciation across the tree of life, and what lessons can be drawn from microbes? Comparative genomics showing the extent of HGT in natural populations certainly jeopardizes the relevance of vertical descent (i.e., the species tree) in speciation. Nevertheless, we conclude that species do indeed exist as clusters of genetic and ecological similarity and that speciation is driven primarily by natural selection, regardless of the balance between horizontal and vertical descent.}, }
@article {pmid27030726, year = {2016}, author = {Hurwitz, BL and U'Ren, JM and Youens-Clark, K}, title = {Computational prospecting the great viral unknown.}, journal = {FEMS microbiology letters}, volume = {363}, number = {10}, pages = {}, doi = {10.1093/femsle/fnw077}, pmid = {27030726}, issn = {1574-6968}, mesh = {Bacteria/genetics ; Bacteriophages/*genetics/physiology ; Computational Biology ; DNA, Viral/genetics ; Gene Transfer, Horizontal ; *Genome, Viral ; Host-Pathogen Interactions/genetics ; Humans ; Metagenome ; *Metagenomics ; Skin/virology ; }, abstract = {Bacteriophages play an important role in host-driven biological processes by controlling bacterial population size, horizontally transferring genes between hosts and expressing host-derived genes to alter host metabolism. Metagenomics provides the genetic basis for understanding the interplay between uncultured bacteria, their phage and the environment. In particular, viral metagenomes (viromes) are providing new insight into phage-encoded host genes (i.e. auxiliary metabolic genes; AMGs) that reprogram host metabolism during infection. Yet, despite deep sequencing efforts of viral communities, the majority of sequences have no match to known proteins. Reference-independent computational techniques, such as protein clustering, contig spectra and ecological profiling are overcoming these barriers to examine both the known and unknown components of viromes. As the field of viral metagenomics progresses, a critical assessment of tools is required as the majority of algorithms have been developed for analyzing bacteria. The aim of this paper is to offer an overview of current computational methodologies for virome analysis and to provide an example of reference-independent approaches using human skin viromes. Additionally, we present methods to carefully validate AMGs from host contamination. Despite computational challenges, these new methods offer novel insights into the diversity and functional roles of phages in diverse environments.}, }
@article {pmid27030552, year = {2016}, author = {Bastidas, RJ and Valdivia, RH}, title = {Emancipating Chlamydia: Advances in the Genetic Manipulation of a Recalcitrant Intracellular Pathogen.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {80}, number = {2}, pages = {411-427}, pmid = {27030552}, issn = {1098-5557}, support = {R01 AI100759/AI/NIAID NIH HHS/United States ; AI081694/AI/NIAID NIH HHS/United States ; AI100759/AI/NIAID NIH HHS/United States ; R21 AI085238/AI/NIAID NIH HHS/United States ; R01 AI081694/AI/NIAID NIH HHS/United States ; AI085238/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Chlamydia/*genetics/physiology ; Chlamydia Infections/*microbiology ; DNA, Bacterial ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Engineering ; Host-Pathogen Interactions ; Humans ; }, abstract = {Chlamydia species infect millions of individuals worldwide and are important etiological agents of sexually transmitted disease, infertility, and blinding trachoma. Historically, the genetic intractability of this intracellular pathogen has hindered the molecular dissection of virulence factors contributing to its pathogenesis. The obligate intracellular life cycle of Chlamydia and restrictions on the use of antibiotics as selectable markers have impeded the development of molecular tools to genetically manipulate these pathogens. However, recent developments in the field have resulted in significant gains in our ability to alter the genome of Chlamydia, which will expedite the elucidation of virulence mechanisms. In this review, we discuss the challenges affecting the development of molecular genetic tools for Chlamydia and the work that laid the foundation for recent advancements in the genetic analysis of this recalcitrant pathogen.}, }
@article {pmid27030297, year = {2016}, author = {Lee, J and Kim, KM and Yang, EC and Miller, KA and Boo, SM and Bhattacharya, D and Yoon, HS}, title = {Reconstructing the complex evolutionary history of mobile plasmids in red algal genomes.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {23744}, pmid = {27030297}, issn = {2045-2322}, mesh = {DNA Copy Number Variations ; DNA, Mitochondrial/*genetics ; DNA, Plant/*genetics ; *Evolution, Molecular ; Gene Ontology ; Gene Transfer, Horizontal ; *Genome, Plastid ; Molecular Sequence Annotation ; Open Reading Frames ; Phylogeny ; Plasmids/chemistry/*metabolism ; Plastids/genetics ; Rhodophyta/classification/*genetics ; }, abstract = {The integration of foreign DNA into algal and plant plastid genomes is a rare event, with only a few known examples of horizontal gene transfer (HGT). Plasmids, which are well-studied drivers of HGT in prokaryotes, have been reported previously in red algae (Rhodophyta). However, the distribution of these mobile DNA elements and their sites of integration into the plastid (ptDNA), mitochondrial (mtDNA), and nuclear genomes of Rhodophyta remain unknown. Here we reconstructed the complex evolutionary history of plasmid-derived DNAs in red algae. Comparative analysis of 21 rhodophyte ptDNAs, including new genome data for 5 species, turned up 22 plasmid-derived open reading frames (ORFs) that showed syntenic and copy number variation among species, but were conserved within different individuals in three lineages. Several plasmid-derived homologs were found not only in ptDNA but also in mtDNA and in the nuclear genome of green plants, stramenopiles, and rhizarians. Phylogenetic and plasmid-derived ORF analyses showed that the majority of plasmid DNAs originated within red algae, whereas others were derived from cyanobacteria, other bacteria, and viruses. Our results elucidate the evolution of plasmid DNAs in red algae and suggest that they spread as parasitic genetic elements. This hypothesis is consistent with their sporadic distribution within Rhodophyta.}, }
@article {pmid27029902, year = {2016}, author = {Čelešnik, H and Tanšek, A and Tahirović, A and Vižintin, A and Mustar, J and Vidmar, V and Dolinar, M}, title = {Biosafety of biotechnologically important microalgae: intrinsic suicide switch implementation in cyanobacterium Synechocystis sp. PCC 6803.}, journal = {Biology open}, volume = {5}, number = {4}, pages = {519-528}, pmid = {27029902}, issn = {2046-6390}, abstract = {In recent years, photosynthetic autotrophic cyanobacteria have attracted interest for biotechnological applications for sustainable production of valuable metabolites. Although biosafety issues can have a great impact on public acceptance of cyanobacterial biotechnology, biosafety of genetically modified cyanobacteria has remained largely unexplored. We set out to incorporate biocontainment systems in the model cyanobacteriumSynechocystissp. PCC 6803. Plasmid-encoded safeguards were constructed using the nonspecific nuclease NucA fromAnabaenacombined with different metal-ion inducible promoters. In this manner, conditional lethality was dependent on intracellular DNA degradation for regulated autokilling as well as preclusion of horizontal gene transfer. In cells carrying the suicide switch comprising thenucAgene fused to a variant of thecopMpromoter, efficient inducible autokilling was elicited. Parallel to nuclease-based safeguards, cyanobacterial toxin/antitoxin (TA) modules were examined in biosafety switches. Rewiring ofSynechocystisTA pairsssr1114/slr0664andslr6101/slr6100for conditional lethality using metal-ion responsive promoters resulted in reduced growth, rather than cell killing, suggesting cells could cope with elevated toxin levels. Overall, promoter properties and translation efficiency influenced the efficacy of biocontainment systems. Several metal-ion promoters were tested in the context of safeguards, and selected promoters, including anrsBvariant, were characterized by beta-galactosidase reporter assay.}, }
@article {pmid27028821, year = {2016}, author = {Naumoff, DG}, title = {[GH10 Family of Glycoside Hydrolases: Structure and Evolutionary Connections].}, journal = {Molekuliarnaia biologiia}, volume = {50}, number = {1}, pages = {151-160}, doi = {10.7868/S0026898415060208}, pmid = {27028821}, issn = {0026-8984}, mesh = {Bacteria/*enzymology/*genetics ; Bacterial Proteins/chemistry/classification/genetics ; Catalytic Domain/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Glycoside Hydrolases/chemistry/*classification/*genetics ; }, abstract = {Evolutionary connections were analyzed for endo-β-xylanases, which possess the GH10 family catalytic domains. A homology search yielded thrice as many proteins as are available from the Carbohydrate-Active Enzymes (CAZy) database. Lateral gene transfer was shown to play an important role in evolution of bacterial proteins of the family, especially in the phyla Acidobacteria, Cyanobacteria, Planctomycetes, Spirochaetes, and Verrucomicrobia. In the case of Verrucomicrobia, 23 lateral transfers from organisms of other phyla were detected. Evolutionary relationships were observed between the GH10 family domains and domains with the TIM-barrel tertiary structure from several other glycosidase families. The GH39 family of glycoside hydrolases showed the closest relationship. Unclassified homologs were grouped into 12 novel families of putative glycoside hydrolases (GHL51-GHL62).}, }
@article {pmid27021419, year = {2016}, author = {Nordmann, P and Poirel, L}, title = {Plasmid-mediated colistin resistance: an additional antibiotic resistance menace.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {22}, number = {5}, pages = {398-400}, doi = {10.1016/j.cmi.2016.03.009}, pmid = {27021419}, issn = {1469-0691}, mesh = {Anti-Bacterial Agents/*pharmacology/therapeutic use ; Bacterial Infections/drug therapy/*microbiology ; Colistin/*pharmacology/therapeutic use ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Humans ; Interspersed Repetitive Sequences ; *Plasmids ; }, }
@article {pmid27017950, year = {2016}, author = {Zheng, W and Mutha, NV and Heydari, H and Dutta, A and Siow, CC and Jakubovics, NS and Wee, WY and Tan, SY and Ang, MY and Wong, GJ and Choo, SW}, title = {NeisseriaBase: a specialised Neisseria genomic resource and analysis platform.}, journal = {PeerJ}, volume = {4}, number = {}, pages = {e1698}, pmid = {27017950}, issn = {2167-8359}, abstract = {Background. The gram-negative Neisseria is associated with two of the most potent human epidemic diseases: meningococcal meningitis and gonorrhoea. In both cases, disease is caused by bacteria colonizing human mucosal membrane surfaces. Overall, the genus shows great diversity and genetic variation mainly due to its ability to acquire and incorporate genetic material from a diverse range of sources through horizontal gene transfer. Although a number of databases exist for the Neisseria genomes, they are mostly focused on the pathogenic species. In this present study we present the freely available NeisseriaBase, a database dedicated to the genus Neisseria encompassing the complete and draft genomes of 15 pathogenic and commensal Neisseria species. Methods. The genomic data were retrieved from National Center for Biotechnology Information (NCBI) and annotated using the RAST server which were then stored into the MySQL database. The protein-coding genes were further analyzed to obtain information such as calculation of GC content (%), predicted hydrophobicity and molecular weight (Da) using in-house Perl scripts. The web application was developed following the secure four-tier web application architecture: (1) client workstation, (2) web server, (3) application server, and (4) database server. The web interface was constructed using PHP, JavaScript, jQuery, AJAX and CSS, utilizing the model-view-controller (MVC) framework. The in-house developed bioinformatics tools implemented in NeisseraBase were developed using Python, Perl, BioPerl and R languages. Results. Currently, NeisseriaBase houses 603,500 Coding Sequences (CDSs), 16,071 RNAs and 13,119 tRNA genes from 227 Neisseria genomes. The database is equipped with interactive web interfaces. Incorporation of the JBrowse genome browser in the database enables fast and smooth browsing of Neisseria genomes. NeisseriaBase includes the standard BLAST program to facilitate homology searching, and for Virulence Factor Database (VFDB) specific homology searches, the VFDB BLAST is also incorporated into the database. In addition, NeisseriaBase is equipped with in-house designed tools such as the Pairwise Genome Comparison tool (PGC) for comparative genomic analysis and the Pathogenomics Profiling Tool (PathoProT) for the comparative pathogenomics analysis of Neisseria strains. Discussion. This user-friendly database not only provides access to a host of genomic resources on Neisseria but also enables high-quality comparative genome analysis, which is crucial for the expanding scientific community interested in Neisseria research. This database is freely available at http://neisseria.um.edu.my.}, }
@article {pmid27017627, year = {2016}, author = {Rodriguez, F and Arkhipova, IR}, title = {Multitasking of the piRNA Silencing Machinery: Targeting Transposable Elements and Foreign Genes in the Bdelloid Rotifer Adineta vaga.}, journal = {Genetics}, volume = {203}, number = {1}, pages = {255-268}, pmid = {27017627}, issn = {1943-2631}, support = {R01 GM111917/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA Transposable Elements ; Gene Expression Profiling ; Gene Library ; *Gene Silencing ; High-Throughput Nucleotide Sequencing ; Multigene Family ; Phylogeny ; *RNA Interference ; RNA, Small Interfering/*genetics ; RNA, Small Untranslated/genetics ; Rotifera/*genetics ; }, abstract = {RNA-mediated silencing processes play a key role in silencing of transposable elements, especially in the germ line, where piwi-interacting RNAs (piRNAs) are responsible for suppressing transposon mobility and maintaining genome integrity. We previously reported that the genome of Adineta vaga, the first sequenced representative of the phylum Rotifera (class Bdelloidea), is characterized by massive levels of horizontal gene transfer, by unusually low transposon content, and by highly diversified RNA-mediated silencing machinery. Here, we investigate genome-wide distribution of pi-like small RNAs, which in A. vaga are 25-31 nucleotides in length and have a strong 5'-uridine bias, while lacking ping-pong amplification signatures. In agreement with expectations, 71% of mapped reads corresponded to annotated transposons, with 93% of these reads being in the antisense orientation. Unexpectedly, a significant fraction of piRNAs originate from predicted coding regions corresponding to genes of putatively foreign origin. The distribution of piRNAs across foreign genes is not biased toward 3'-UTRs, instead resembling transposons in uniform distribution pattern throughout the gene body, and in predominantly antisense orientation. We also find that genes with small RNA coverage, including a number of genes of metazoan origin, are characterized by higher occurrence of telomeric repeats in the surrounding genomic regions, and by higher density of transposons in the vicinity, which have the potential to promote antisense transcription. Our findings highlight the complex interplay between RNA-based silencing processes and acquisition of genes at the genome periphery, which can result either in their loss or eventual domestication and integration into the host genome.}, }
@article {pmid27015628, year = {2016}, author = {Kim, JW and Brawley, SH and Prochnik, S and Chovatia, M and Grimwood, J and Jenkins, J and LaButti, K and Mavromatis, K and Nolan, M and Zane, M and Schmutz, J and Stiller, JW and Grossman, AR}, title = {Genome Analysis of Planctomycetes Inhabiting Blades of the Red Alga Porphyra umbilicalis.}, journal = {PloS one}, volume = {11}, number = {3}, pages = {e0151883}, pmid = {27015628}, issn = {1932-6203}, mesh = {Gene Transfer, Horizontal ; *Genome, Bacterial ; *Phylogeny ; Planctomycetales/*genetics ; Porphyra/genetics/*microbiology ; Sulfatases/genetics ; }, abstract = {Porphyra is a macrophytic red alga of the Bangiales that is important ecologically and economically. We describe the genomes of three bacteria in the phylum Planctomycetes (designated P1, P2 and P3) that were isolated from blades of Porphyra umbilicalis (P.um.1). These three Operational Taxonomic Units (OTUs) belong to distinct genera; P2 belongs to the genus Rhodopirellula, while P1 and P3 represent undescribed genera within the Planctomycetes. Comparative analyses of the P1, P2 and P3 genomes show large expansions of distinct gene families, which can be widespread throughout the Planctomycetes (e.g., protein kinases, sensors/response regulators) and may relate to specific habitat (e.g., sulfatase gene expansions in marine Planctomycetes) or phylogenetic position. Notably, there are major differences among the Planctomycetes in the numbers and sub-functional diversity of enzymes (e.g., sulfatases, glycoside hydrolases, polysaccharide lyases) that allow these bacteria to access a range of sulfated polysaccharides in macroalgal cell walls. These differences suggest that the microbes have varied capacities for feeding on fixed carbon in the cell walls of P.um.1 and other macrophytic algae, although the activities among the various bacteria might be functionally complementary in situ. Additionally, phylogenetic analyses indicate augmentation of gene functions through expansions arising from gene duplications and horizontal gene transfers; examples include genes involved in cell wall degradation (e.g., κ-carrageenase, alginate lyase, fucosidase) and stress responses (e.g., efflux pump, amino acid transporter). Finally P1 and P2 contain various genes encoding selenoproteins, many of which are enzymes that ameliorate the impact of environmental stresses that occur in the intertidal habitat.}, }
@article {pmid27014291, year = {2016}, author = {Zhou, D and Xu, L and Gao, S and Guo, J and Luo, J and You, Q and Que, Y}, title = {Cry1Ac Transgenic Sugarcane Does Not Affect the Diversity of Microbial Communities and Has No Significant Effect on Enzyme Activities in Rhizosphere Soil within One Crop Season.}, journal = {Frontiers in plant science}, volume = {7}, number = {}, pages = {265}, pmid = {27014291}, issn = {1664-462X}, abstract = {Cry1Ac transgenic sugarcane provides a promising way to control stem-borer pests. Biosafety assessment of soil ecosystem for cry1Ac transgenic sugarcane is urgently needed because of the important role of soil microorganisms in nutrient transformations and element cycling, however little is known. This study aimed to explore the potential impact of cry1Ac transgenic sugarcane on rhizosphere soil enzyme activities and microbial community diversity, and also to investigate whether the gene flow occurs through horizontal gene transfer. We found no horizontal gene flow from cry1Ac sugarcane to soil. No significant difference in the population of culturable microorganisms between the non-GM and cry1Ac transgenic sugarcane was observed, and there were no significant interactions between the sugarcane lines and the growth stages. A relatively consistent trend at community-level, represented by the functional diversity index, was found between the cry1Ac sugarcane and the non-transgenic lines. Most soil samples showed no significant difference in the activities of four soil enzymes: urease, protease, sucrose, and acid phosphate monoester between the non-transgenic and cry1Ac sugarcane lines. We conclude, based on one crop season, that the cry1Ac sugarcane lines may not affect the microbial community structure and functional diversity of the rhizosphere soil and have few negative effects on soil enzymes.}, }
@article {pmid27014196, year = {2016}, author = {Miller, JH and Novak, JT and Knocke, WR and Pruden, A}, title = {Survival of Antibiotic Resistant Bacteria and Horizontal Gene Transfer Control Antibiotic Resistance Gene Content in Anaerobic Digesters.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {263}, pmid = {27014196}, issn = {1664-302X}, abstract = {Understanding fate of antibiotic resistant bacteria (ARB) vs. their antibiotic resistance genes (ARGs) during wastewater sludge treatment is critical in order to reduce the spread of antibiotic resistance through process optimization. Here, we spiked high concentrations of tetracycline-resistant bacteria, isolated from mesophilic (Iso M1-1-a Pseudomonas sp.) and thermophilic (Iso T10-a Bacillus sp.) anaerobic digested sludge, into batch digesters and monitored their fate by plate counts and quantitative polymerase chain reaction (QPCR) of their corresponding tetracycline ARGs. In batch studies, spiked ARB plate counts returned to baseline (thermophilic) or 1-log above baseline (mesophilic) while levels of the ARG present in the spiked isolate [tet(G)] remained high in mesophilic batch reactors. To compare results under semi-continuous flow conditions with natural influent variation, tet(O), tet(W), and sul1 ARGs, along with the intI1 integrase gene, were monitored over a 9-month period in the raw feed sludge and effluent sludge of lab-scale thermophilic and mesophilic anaerobic digesters. sul1 and intI1 in mesophilic and thermophilic digesters correlated positively (Spearman rho = 0.457-0.829, P < 0.05) with the raw feed sludge. There was no correlation in tet(O) or tet(W) ratios in raw sludge and mesophilic digested sludge or thermophilic digested sludge (Spearman rho = 0.130-0.486, P = 0.075-0.612). However, in the thermophilic digester, the tet(O) and tet(W) ratios remained consistently low over the entire monitoring period. We conclude that the influent sludge microbial composition can influence the ARG content of a digester, apparently as a result of differential survival or death of ARBs or horizontal gene transfer of genes between raw sludge ARBs and the digester microbial community. Notably, mesophilic digestion was more susceptible to ARG intrusion than thermophilic digestion, which may be attributed to a higher rate of ARB survival and/or horizontal gene transfer between raw sludge bacteria and the digester microbial community.}, }
@article {pmid27013267, year = {2016}, author = {Shahi, S and Beerens, B and Bosch, M and Linmans, J and Rep, M}, title = {Nuclear dynamics and genetic rearrangement in heterokaryotic colonies of Fusarium oxysporum.}, journal = {Fungal genetics and biology : FG &amp; B}, volume = {91}, number = {}, pages = {20-31}, doi = {10.1016/j.fgb.2016.03.003}, pmid = {27013267}, issn = {1096-0937}, mesh = {Cell Nucleus/*genetics ; Chromosomes, Fungal/*genetics ; Fusarium/*genetics/pathogenicity ; Gene Rearrangement/genetics ; Gene Transfer, Horizontal/*genetics ; Genome, Fungal/genetics ; Green Fluorescent Proteins/genetics ; Hyphae/genetics/growth &amp; development ; Solanum lycopersicum/microbiology ; Spores, Fungal/genetics/growth &amp; development ; }, abstract = {Recent studies have shown horizontal transfer of chromosomes to be a potential key contributor to genome plasticity in asexual fungal pathogens. However, the mechanisms behind horizontal chromosome transfer in eukaryotes are not well understood. Here we investigated the role of conidial anastomosis in heterokaryon formation between incompatible strains of Fusarium oxysporum and determined the importance of heterokaryons for horizontal chromosome transfer. Using live-cell imaging we demonstrate that conidial pairing of incompatible strains under carbon starvation can result in the formation of viable heterokaryotic hyphae in F. oxysporum. Nuclei of the parental lines presumably fuse at some stage as conidia with a single nucleus harboring both marker histones (GFP- and RFP-tagged) are produced. Upon colony formation, this hybrid offspring is subject to progressive and gradual genome rearrangement. The parental genomes appear to become spatially separated and RFP-tagged histones, deriving from one of the strains, Fol4287, are eventually lost. With a PCR-based method we showed that markers for most of the chromosomes of this strain are lost, indicating a lack of Fol4287 chromosomes. This leaves offspring with the genomic background of the other strain (Fo47), but in some cases together with one or two chromosomes from Fol4287, including the chromosome that confers pathogenicity towards tomato.}, }
@article {pmid27013042, year = {2016}, author = {Ellenberger, S and Burmester, A and Wöstemeyer, J}, title = {Complete Mitochondrial DNA Sequence of the Mucoralean Fungus Absidia glauca, a Model for Studying Host-Parasite Interactions.}, journal = {Genome announcements}, volume = {4}, number = {2}, pages = {}, pmid = {27013042}, issn = {2169-8287}, abstract = {The mitochondrial DNA (mtDNA) ofAbsidia glaucahas been completely sequenced. It is 63,080 bp long, has a G+C content of 28%, and contains the standard fungal gene set.A. glaucais the recipient in a laboratory model for horizontal gene transfer withParasitella parasiticaas a donor of nuclei and mitochondria.}, }
@article {pmid27009761, year = {2016}, author = {Opperdoes, FR and Butenko, A and Flegontov, P and Yurchenko, V and Lukeš, J}, title = {Comparative Metabolism of Free-living Bodo saltans and Parasitic Trypanosomatids.}, journal = {The Journal of eukaryotic microbiology}, volume = {63}, number = {5}, pages = {657-678}, doi = {10.1111/jeu.12315}, pmid = {27009761}, issn = {1550-7408}, mesh = {Amino Acids/metabolism ; Bacteria/genetics/metabolism ; Carbohydrate Metabolism ; Coenzymes/metabolism ; Dolichols/metabolism ; Ergosterol/biosynthesis ; Eukaryota/genetics/metabolism ; Folic Acid/metabolism ; Genes, Protozoan/genetics ; Gluconeogenesis ; Glycolysis ; Kinetoplastida/enzymology/*genetics/*metabolism ; Lipid Metabolism ; Mevalonic Acid/metabolism ; Microbodies/metabolism ; Mitochondria/enzymology/metabolism ; Oxidoreductases/metabolism ; Pentose Phosphate Pathway ; Peroxisomes/metabolism ; Phospholipids/metabolism ; Polyamines/metabolism ; Protein Prenylation ; Protozoan Proteins/genetics ; Purines/biosynthesis/metabolism ; Pyrimidines/biosynthesis/metabolism ; Reactive Oxygen Species ; Trypanosomatina/enzymology/*genetics/*metabolism ; Ubiquinone/metabolism ; Urea/metabolism ; Vitamins/metabolism ; }, abstract = {Comparison of the genomes of free-living Bodo saltans and those of parasitic trypanosomatids reveals that the transition from a free-living to a parasitic life style has resulted in the loss of approximately 50% of protein-coding genes. Despite this dramatic reduction in genome size, B. saltans and trypanosomatids still share a significant number of common metabolic traits: glycosomes; a unique set of the pyrimidine biosynthetic pathway genes; an ATP-PFK which is homologous to the bacterial PPi -PFKs rather than to the canonical eukaryotic ATP-PFKs; an alternative oxidase; three phosphoglycerate kinases and two GAPDH isoenzymes; a pyruvate kinase regulated by fructose-2,6-bisphosphate; trypanothione as a substitute for glutathione; synthesis of fatty acids via a unique set of elongase enzymes; and a mitochondrial acetate:succinate coenzyme A transferase. B. saltans has lost the capacity to synthesize ubiquinone. Among genes that are present in B. saltans and lost in all trypanosomatids are those involved in the degradation of mureine, tryptophan and lysine. Novel acquisitions of trypanosomatids are components of pentose sugar metabolism, pteridine reductase and bromodomain-factor proteins. In addition, only the subfamily Leishmaniinae has acquired a gene for catalase and the capacity to convert diaminopimelic acid to lysine.}, }
@article {pmid27003885, year = {2016}, author = {Schwander, T}, title = {Evolution: The End of an Ancient Asexual Scandal.}, journal = {Current biology : CB}, volume = {26}, number = {6}, pages = {R233-5}, doi = {10.1016/j.cub.2016.01.034}, pmid = {27003885}, issn = {1879-0445}, mesh = {Animals ; *Biological Evolution ; Gene Transfer, Horizontal ; Phylogeny ; Reproduction, Asexual/genetics ; *Rotifera ; }, abstract = {Bdelloid rotifers were believed to have persisted and diversified in the absence of sex. Two papers now show they exchange genes with each other, via horizontal gene transfers as known in bacteria and/or via other forms of non-canonical sex.}, }
@article {pmid26999399, year = {2016}, author = {Bliven, KA and Maurelli, AT}, title = {Evolution of Bacterial Pathogens Within the Human Host.}, journal = {Microbiology spectrum}, volume = {4}, number = {1}, pages = {}, pmid = {26999399}, issn = {2165-0497}, support = {R01 AI024656/AI/NIAID NIH HHS/United States ; R01 AI044033/AI/NIAID NIH HHS/United States ; R01 AI024656-23/AI/NIAID NIH HHS/United States ; R01 AI044033-12/AI/NIAID NIH HHS/United States ; }, mesh = {Adaptation, Physiological ; Animals ; *Bacteria ; Bacterial Infections/*microbiology ; Bacterial Physiological Phenomena ; *Biological Evolution ; Humans ; Selection, Genetic ; }, abstract = {Selective pressures within the human host, including interactions with innate and adaptive immune responses, exposure to medical interventions such as antibiotics, and competition with commensal microbiota all facilitate the evolution of bacterial pathogens. In this chapter, we present examples of pathogen strategies that emerged as a result of selective pressures within the human host niche and discuss the resulting coevolutionary "arms race" between these organisms. In bacterial pathogens, many of the genes responsible for these strategies are encoded on mobile pathogenicity islands or plasmids, underscoring the importance of horizontal gene transfer in the emergence of virulent microbial species.}, }
@article {pmid26999398, year = {2016}, author = {Ates, LS and Houben, ENG and Bitter, W}, title = {Type VII Secretion: A Highly Versatile Secretion System.}, journal = {Microbiology spectrum}, volume = {4}, number = {1}, pages = {}, doi = {10.1128/microbiolspec.VMBF-0011-2015}, pmid = {26999398}, issn = {2165-0497}, mesh = {Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Mycobacterium/genetics/*metabolism/pathogenicity ; Mycobacterium Infections/microbiology ; Type VII Secretion Systems/genetics/*physiology ; }, abstract = {Type VII secretion (T7S) systems of mycobacteria secrete substrates over the unusual diderm cell envelope. Furthermore, T7S gene clusters are present throughout the phylum Actinobacteria, and functional T7S-like systems have been identified in Firmicutes. Most of the T7S substrates can be divided into two families: the Esx proteins, which are found in both Firmicutes and Actinobacteria, and the PE and PPE proteins, which are more mycobacterium-specific. Members of both families have been shown to be secreted as folded heterodimers, suggesting that this is a conserved feature of T7S substrates. Most knowledge of the mechanism of T7S and the roles of T7S systems in virulence comes from studies of pathogenic mycobacteria. These bacteria can contain up to five T7S systems, called ESX-1 to ESX-5, each having its own role in bacterial physiology and virulence. In this article, we discuss the general composition of T7S systems and the role of the individual components in secretion. These conserved components include two membrane proteins with (predicted) enzymatic activities: a predicted ATPase (EccC), likely to be required for energy provision of T7S, and a subtilisin-like protease (MycP) involved in processing of specific substrates. Additionally, we describe the role of a conserved intracellular chaperone in T7S substrate recognition, based on recently published crystal structures and molecular analysis. Finally, we discuss system-specific features of the different T7S systems in mycobacteria and their role in pathogenesis and provide an overview of the role of T7S in virulence of other pathogenic bacteria.}, }
@article {pmid26997548, year = {2016}, author = {Wang, GH and Jia, LY and Xiao, JH and Huang, DW}, title = {Discovery of a new Wolbachia supergroup in cave spider species and the lateral transfer of phage WO among distant hosts.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {41}, number = {}, pages = {1-7}, doi = {10.1016/j.meegid.2016.03.015}, pmid = {26997548}, issn = {1567-7257}, mesh = {Animals ; Bacterial Outer Membrane Proteins/genetics ; Bacterial Proteins/genetics ; Bacteriophages/classification/*genetics ; Caves ; Chaperonin 60/genetics ; China ; Cytoskeletal Proteins/genetics ; Electron Transport Complex IV/genetics ; Gene Expression ; Gene Transfer, Horizontal ; Host Specificity ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Spiders/*microbiology ; Symbiosis/physiology ; Wolbachia/classification/*genetics/virology ; }, abstract = {Wolbachia are widespread intracellular bacteria infecting the major classes of arthropods and some filarial nematodes. In arthropods, Wolbachia have evolved various intriguing reproductive manipulations, including cytoplasmic incompatibility, parthenogenesis, feminization, and male killing. Sixteen supergroups of Wolbachia have been identified, named A-Q (except G). Though Wolbachia present great diversity in arthropods, spiders, especially cave spiders, are still a poorly surveyed group of Wolbachia hosts. Here, we report a novel Wolbachia supergroup from nine Telema cave spiders (Araneae: Telemidae) based on five molecular markers (16S rRNA, ftsZ, gltA, groEL, and coxA). In addition, phage WO, which was previously reported only in Wolbachia supergroups A, B, and F, infects this new Wolbachia supergroup. We detected a 100% infection rate for phage WO and Wolbachia in Telema species. The phylogenetic trees of phage WO and Wolbachia are not congruent, which suggests that horizontal transfer of phage WO has occurred in these secluded species. Additionally, these data indicate Telema-Wolbachia-phage WO may be a good model for exploring the horizontal transfer history of WO among different host species.}, }
@article {pmid26994934, year = {2016}, author = {Morgan, GJ}, title = {What is a virus species? Radical pluralism in viral taxonomy.}, journal = {Studies in history and philosophy of biological and biomedical sciences}, volume = {59}, number = {}, pages = {64-70}, doi = {10.1016/j.shpsc.2016.02.009}, pmid = {26994934}, issn = {1879-2499}, mesh = {Biological Evolution ; Gene Transfer, Horizontal ; *Genetic Speciation ; Phylogeny ; Viruses/*classification/genetics ; }, abstract = {Early attempts in the 1960s at constructing a classification scheme for viruses were phenetic and focused on structural properties of the virion. Over time, the International Committee on the Taxonomy of Viruses (ICTV) has refined its definition of a virus species to include an appeal to evolutionary history. The current ICTV definition defines a viral species in terms of monophyly. The existence of prolific horizontal genetic transfer (HGT) among various groups of viruses presents a challenge to this definition. I argue that the proper response to this mode of evolution is to allow for radical pluralism. Some viruses can be members of more than one species; others don't form species at all and should be classified using new reticulate categories.}, }
@article {pmid26993236, year = {2016}, author = {da Fonseca, GC and de Oliveira, LFV and de Morais, GL and Abdelnor, RV and Nepomuceno, AL and Waterhouse, PM and Farinelli, L and Margis, R}, title = {Unusual RNA plant virus integration in the soybean genome leads to the production of small RNAs.}, journal = {Plant science : an international journal of experimental plant biology}, volume = {246}, number = {}, pages = {62-69}, doi = {10.1016/j.plantsci.2016.01.011}, pmid = {26993236}, issn = {1873-2259}, mesh = {Base Sequence ; Cucumovirus/physiology ; Gene Expression Regulation, Plant ; Gene Library ; *Genome, Plant ; Phylogeny ; Plant Viruses/*physiology ; RNA, Messenger/genetics/metabolism ; RNA, Plant/*genetics/metabolism ; Glycine max/*genetics/*virology ; Virus Integration/*physiology ; }, abstract = {Horizontal gene transfer (HGT) is known to be a major force in genome evolution. The acquisition of genes from viruses by eukaryotic genomes is a well-studied example of HGT, including rare cases of non-retroviral RNA virus integration. The present study describes the integration of cucumber mosaic virus RNA-1 into soybean genome. After an initial metatranscriptomic analysis of small RNAs derived from soybean, the de novo assembly resulted a 3029-nt contig homologous to RNA-1. The integration of this sequence in the soybean genome was confirmed by DNA deep sequencing. The locus where the integration occurred harbors the full RNA-1 sequence followed by the partial sequence of an endogenous mRNA and another sequence of RNA-1 as an inverted repeat and allowing the formation of a hairpin structure. This region recombined into a retrotransposon located inside an exon of a soybean gene. The nucleotide similarity of the integrated sequence compared to other Cucumber mosaic virus sequences indicates that the integration event occurred recently. We described a rare event of non-retroviral RNA virus integration in soybean that leads to the production of a double-stranded RNA in a similar fashion to virus resistance RNAi plants.}, }
@article {pmid26992913, year = {2016}, author = {Shapiro, LR and Scully, ED and Straub, TJ and Park, J and Stephenson, AG and Beattie, GA and Gleason, ML and Kolter, R and Coelho, MC and De Moraes, CM and Mescher, MC and Zhaxybayeva, O}, title = {Horizontal Gene Acquisitions, Mobile Element Proliferation, and Genome Decay in the Host-Restricted Plant Pathogen Erwinia Tracheiphila.}, journal = {Genome biology and evolution}, volume = {8}, number = {3}, pages = {649-664}, pmid = {26992913}, issn = {1759-6653}, mesh = {Cucurbita/*genetics ; Erwinia/*genetics/pathogenicity ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Plant/genetics ; Host-Pathogen Interactions/genetics ; Interspersed Repetitive Sequences/genetics ; Plant Diseases/*genetics/parasitology ; }, abstract = {Modern industrial agriculture depends on high-density cultivation of genetically similar crop plants, creating favorable conditions for the emergence of novel pathogens with increased fitness in managed compared with ecologically intact settings. Here, we present the genome sequence of six strains of the cucurbit bacterial wilt pathogen Erwinia tracheiphila (Enterobacteriaceae) isolated from infected squash plants in New York, Pennsylvania, Kentucky, and Michigan. These genomes exhibit a high proportion of recent horizontal gene acquisitions, invasion and remarkable amplification of mobile genetic elements, and pseudogenization of approximately 20% of the coding sequences. These genome attributes indicate that E. tracheiphila recently emerged as a host-restricted pathogen. Furthermore, chromosomal rearrangements associated with phage and transposable element proliferation contribute to substantial differences in gene content and genetic architecture between the six E. tracheiphila strains and other Erwinia species. Together, these data lead us to hypothesize that E. tracheiphila has undergone recent evolution through both genome decay (pseudogenization) and genome expansion (horizontal gene transfer and mobile element amplification). Despite evidence of dramatic genomic changes, the six strains are genetically monomorphic, suggesting a recent population bottleneck and emergence into E. tracheiphila's current ecological niche.}, }
@article {pmid26992400, year = {2016}, author = {Carniel, FC and Gerdol, M and Montagner, A and Banchi, E and De Moro, G and Manfrin, C and Muggia, L and Pallavicini, A and Tretiach, M}, title = {New features of desiccation tolerance in the lichen photobiont Trebouxia gelatinosa are revealed by a transcriptomic approach.}, journal = {Plant molecular biology}, volume = {91}, number = {3}, pages = {319-339}, pmid = {26992400}, issn = {1573-5028}, mesh = {Chlorophyta/genetics/*physiology ; Dehydration ; Desiccation ; Lichens/genetics/*physiology ; Phylogeny ; Polymerase Chain Reaction ; Transcriptome/genetics/physiology ; }, abstract = {Trebouxia is the most common lichen-forming genus of aero-terrestrial green algae and all its species are desiccation tolerant (DT). The molecular bases of this remarkable adaptation are, however, still largely unknown. We applied a transcriptomic approach to a common member of the genus, T. gelatinosa, to investigate the alteration of gene expression occurring after dehydration and subsequent rehydration in comparison to cells kept constantly hydrated. We sequenced, de novo assembled and annotated the transcriptome of axenically cultured T. gelatinosa by using Illumina sequencing technology. We tracked the expression profiles of over 13,000 protein-coding transcripts. During the dehydration/rehydration cycle c. 92 % of the total protein-coding transcripts displayed a stable expression, suggesting that the desiccation tolerance of T. gelatinosa mostly relies on constitutive mechanisms. Dehydration and rehydration affected mainly the gene expression for components of the photosynthetic apparatus, the ROS-scavenging system, Heat Shock Proteins, aquaporins, expansins, and desiccation related proteins (DRPs), which are highly diversified in T. gelatinosa, whereas Late Embryogenesis Abundant Proteins were not affected. Only some of these phenomena were previously observed in other DT green algae, bryophytes and resurrection plants, other traits being distinctive of T. gelatinosa, and perhaps related to its symbiotic lifestyle. Finally, the phylogenetic inference extended to DRPs of other chlorophytes, embryophytes and bacteria clearly pointed out that DRPs of chlorophytes are not orthologous to those of embryophytes: some of them were likely acquired through horizontal gene transfer from extremophile bacteria which live in symbiosis within the lichen thallus.}, }
@article {pmid26991103, year = {2016}, author = {Alam, MK and Alhhazmi, A and DeCoteau, JF and Luo, Y and Geyer, CR}, title = {RecA Inhibitors Potentiate Antibiotic Activity and Block Evolution of Antibiotic Resistance.}, journal = {Cell chemical biology}, volume = {23}, number = {3}, pages = {381-391}, doi = {10.1016/j.chembiol.2016.02.010}, pmid = {26991103}, issn = {2451-9448}, mesh = {Animals ; Anti-Bacterial Agents/chemistry/*pharmacology ; Drug Resistance, Microbial/*drug effects ; Enzyme Inhibitors/chemistry/*pharmacology ; Female ; Gram-Negative Bacteria/*drug effects/enzymology ; Gram-Positive Bacteria/*drug effects/enzymology ; Indoles/chemistry/*pharmacology ; Mice ; Microbial Sensitivity Tests ; Molecular Structure ; Rec A Recombinases/*antagonists &amp; inhibitors/genetics/metabolism ; Structure-Activity Relationship ; }, abstract = {Antibiotic resistance arises from the maintenance of resistance mutations or genes acquired from the acquisition of adaptive de novo mutations or the transfer of resistance genes. Antibiotic resistance is acquired in response to antibiotic therapy by activating SOS-mediated DNA repair and mutagenesis and horizontal gene transfer pathways. Initiation of the SOS pathway promotes activation of RecA, inactivation of LexA repressor, and induction of SOS genes. Here, we have identified and characterized phthalocyanine tetrasulfonic acid RecA inhibitors that block antibiotic-induced activation of the SOS response. These inhibitors potentiate the activity of bactericidal antibiotics, including members of the quinolone, β-lactam, and aminoglycoside families in both Gram-negative and Gram-positive bacteria. They reduce the ability of bacteria to acquire antibiotic resistance mutations and to transfer mobile genetic elements conferring resistance. This study highlights the advantage of including RecA inhibitors in bactericidal antibiotic therapies and provides a new strategy for prolonging antibiotic shelf life.}, }
@article {pmid26987049, year = {2016}, author = {Rocha, EP}, title = {Using Sex to Cure the Genome.}, journal = {PLoS biology}, volume = {14}, number = {3}, pages = {e1002417}, pmid = {26987049}, issn = {1545-7885}, mesh = {*Gene Transfer, Horizontal ; *Genome, Microbial ; *Interspersed Repetitive Sequences ; *Transformation, Bacterial ; }, abstract = {The diversification of prokaryotes is accelerated by their ability to acquire DNA from other genomes. However, the underlying processes also facilitate genome infection by costly mobile genetic elements. The discovery that cells can uptake DNA by natural transformation was instrumental to the birth of molecular biology nearly a century ago. Surprisingly, a new study shows that this mechanism could efficiently cure the genome of mobile elements acquired through previous sexual exchanges.}, }
@article {pmid26986998, year = {2015}, author = {Graham, LE and Wilcox, LW and Knack, JJ}, title = {Why we need more algal metagenomes(1).}, journal = {Journal of phycology}, volume = {51}, number = {6}, pages = {1029-1036}, doi = {10.1111/jpy.12344}, pmid = {26986998}, issn = {1529-8817}, abstract = {A recent perspective article ably argued that fully sequencing more algal genomes would enable progress in diverse areas of fundamental and applied studies. More algal genomes would add resources needed to build well-supported phylogenies, improve our understanding of how horizontal gene transfer has influenced the evolution of algal genomes, provide useful ecological insights, and generate information essential to manipulating the genomes of industrially useful algae (J. Phycol. 51:1). We agree that more algal genomes would be quite beneficial, and also propose that more algal metagenomes would enable progress in both predictable and unforeseen directions.}, }
@article {pmid26986787, year = {2015}, author = {Qiu, H and Price, DC and Yang, EC and Yoon, HS and Bhattacharya, D}, title = {Evidence of ancient genome reduction in red algae (Rhodophyta).}, journal = {Journal of phycology}, volume = {51}, number = {4}, pages = {624-636}, doi = {10.1111/jpy.12294}, pmid = {26986787}, issn = {1529-8817}, abstract = {Red algae (Rhodophyta) comprise a monophyletic eukaryotic lineage of ~6,500 species with a fossil record that extends back 1.2 billion years. A surprising aspect of red algal evolution is that sequenced genomes encode a relatively limited gene inventory (~5-10 thousand genes) when compared with other free-living algae or to other eukaryotes. This suggests that the common ancestor of red algae may have undergone extensive genome reduction, which can result from lineage specialization to a symbiotic or parasitic lifestyle or adaptation to an extreme or oligotrophic environment. We gathered genome and transcriptome data from a total of 14 red algal genera that represent the major branches of this phylum to study genome evolution in Rhodophyta. Analysis of orthologous gene gains and losses identifies two putative major phases of genome reduction: (i) in the stem lineage leading to all red algae resulting in the loss of major functions such as flagellae and basal bodies, the glycosyl-phosphatidylinositol anchor biosynthesis pathway, and the autophagy regulation pathway; and (ii) in the common ancestor of the extremophilic Cyanidiophytina. Red algal genomes are also characterized by the recruitment of hundreds of bacterial genes through horizontal gene transfer that have taken on multiple functions in shared pathways and have replaced eukaryotic gene homologs. Our results suggest that Rhodophyta may trace their origin to a gene depauperate ancestor. Unlike plants, it appears that a limited gene inventory is sufficient to support the diversification of a major eukaryote lineage that possesses sophisticated multicellular reproductive structures and an elaborate triphasic sexual cycle.}, }
@article {pmid26983858, year = {2016}, author = {Zolfaghari Emameh, R and Barker, HR and Tolvanen, ME and Parkkila, S and Hytönen, VP}, title = {Horizontal transfer of β-carbonic anhydrase genes from prokaryotes to protozoans, insects, and nematodes.}, journal = {Parasites &amp; vectors}, volume = {9}, number = {}, pages = {152}, pmid = {26983858}, issn = {1756-3305}, mesh = {Animals ; Bacteria/*enzymology ; Carbonic Anhydrases/chemistry/*genetics ; Eukaryota/*enzymology ; *Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences ; Models, Molecular ; Sequence Homology ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT) is a movement of genetic information occurring outside of normal mating activities. It is especially common between prokaryotic endosymbionts and their protozoan, insect, and nematode hosts. Although beta carbonic anhydrase (β-CA) plays a crucial role in metabolic functions of many living organisms, the origin of β-CA genes in eukaryotic species remains unclear.<br><br>METHODS: This study was conducted using phylogenetics, prediction of subcellular localization, and identification of &#x3b2;-CA, transposase, integrase, and resolvase genes on the MGEs of bacteria. We also structurally analyzed &#x3b2;-CAs from protozoans, insects, and nematodes and their putative prokaryotic common ancestors, by homology modelling.<br><br>RESULTS: Our investigations of a number of target genomes revealed that genes coding for transposase, integrase, resolvase, and conjugation complex proteins have been integrated with &#x3b2;-CA gene sequences on mobile genetic elements (MGEs) which have facilitated the mobility of &#x3b2;-CA genes from bacteria to protozoan, insect, and nematode species. The prokaryotic origin of protozoan, insect, and nematode &#x3b2;-CA enzymes is supported by phylogenetic analyses, prediction of subcellular localization, and homology modelling.<br><br>CONCLUSION: MGEs form a complete set of enzymatic tools, which are relevant to HGT of &#x3b2;-CA gene sequences from prokaryotes to protozoans, insects, and nematodes.}, }
@article {pmid26983646, year = {2016}, author = {Grover, S and Gupta, P and Kahlon, PS and Goyal, S and Grover, A and Dalal, K and Sabeeha,  and Ehtesham, NZ and Hasnain, SE}, title = {Analyses of methyltransferases across the pathogenicity spectrum of different mycobacterial species point to an extremophile connection.}, journal = {Molecular bioSystems}, volume = {12}, number = {5}, pages = {1615-1625}, doi = {10.1039/c5mb00810g}, pmid = {26983646}, issn = {1742-2051}, mesh = {Antigens, Bacterial/metabolism ; DNA/metabolism ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial ; Genes, Essential ; Methyltransferases/classification/genetics/*metabolism ; Mycobacterium/*enzymology/genetics/immunology/*pathogenicity ; Proteomics ; Species Specificity ; Virulence Factors/metabolism ; }, abstract = {Tuberculosis is a devastating disease, taking one human life every 20 seconds globally. We hypothesize that professional pathogens such as M.tb have acquired specific features that might assist in causing infection, persistence and transmissible pathology in their host. We have identified 121 methyltransferases (MTases) in the M.tb proteome, which use a variety of substrates - DNA, RNA, protein, intermediates of mycolic acid biosynthesis and other fatty acids - that are involved in cellular maintenance within the host. A comparative analysis of the proteome of the virulent strain H37Rv and the avirulent strain H37Ra identified 3 MTases, which displayed significant variations in terms of N-terminal extension/deletion and point mutations, possibly impacting various physicochemical properties. The cross-proteomic comparison of MTases of M.tb H37Rv with 15 different Mycobacterium species revealed the acquisition of novel MTases in a MTB complex as a function of evolution. Phylogenetic analysis revealed that these newly acquired MTases showed common roots with certain extremophiles such as halophilic and acidophilic organisms. Our results establish an evolutionary relationship of M.tb with halotolerant organisms and also the role of MTases of M.tb in withstanding the host osmotic stress, thereby pointing to their likely role in pathogenesis, virulence and niche adaptation.}, }
@article {pmid26982444, year = {2016}, author = {Van Leeuwen, T and Dermauw, W}, title = {The Molecular Evolution of Xenobiotic Metabolism and Resistance in Chelicerate Mites.}, journal = {Annual review of entomology}, volume = {61}, number = {}, pages = {475-498}, doi = {10.1146/annurev-ento-010715-023907}, pmid = {26982444}, issn = {1545-4487}, mesh = {Adaptation, Biological ; Animals ; *Biological Evolution ; *Evolution, Molecular ; Mites/*genetics/metabolism ; Xenobiotics/*metabolism ; }, abstract = {Chelicerate mites diverged from other arthropod lineages more than 400 million years ago and subsequently developed specific and remarkable xenobiotic adaptations. The study of the two-spotted spider mite, Tetranychus urticae, for which a high-quality Sanger-sequenced genome was first available, revealed expansions and radiations in all major detoxification gene families, including P450 monooxygenases, carboxyl/cholinesterases, glutathione-S-transferases, and ATP-binding cassette transporters. Novel gene families that are not well studied in other arthropods, such as major facilitator family transporters and lipocalins, also reflect the evolution of xenobiotic adaptation. The acquisition of genes by horizontal gene transfer provided new routes to handle toxins, for example, the β-cyanoalanine synthase enzyme that metabolizes cyanide. The availability of genomic resources for other mite species has allowed researchers to study the lineage specificity of these gene family expansions and the distinct evolution of genes involved in xenobiotic metabolism in mites. Genome-based tools have been crucial in supporting the idiosyncrasies of mite detoxification and will further support the expanding field of mite-plant interactions.}, }
@article {pmid26982016, year = {2016}, author = {Morroni, G and Di Cesare, A and Di Sante, L and Brenciani, A and Vignaroli, C and Pasquaroli, S and Giovanetti, E and Sabatino, R and Rossi, L and Magnani, M and Biavasco, F}, title = {Enterococcus faecium ST17 from Coastal Marine Sediment Carrying Transferable Multidrug Resistance Plasmids.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {22}, number = {7}, pages = {523-530}, doi = {10.1089/mdr.2015.0222}, pmid = {26982016}, issn = {1931-8448}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Toxins/genetics ; Conjugation, Genetic ; Disease Reservoirs ; Drug Resistance, Multiple, Bacterial/*genetics ; Enterococcus faecium/drug effects/*genetics/growth &amp; development/isolation &amp; purification ; Erythromycin/pharmacology ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Geologic Sediments/microbiology ; Humans ; Plasmids/chemistry/*metabolism ; Replicon ; Tetracycline/pharmacology ; *Water Microbiology ; }, abstract = {The multidrug-resistant Enterococcus faecium 17i48, sequence type 17, from marine sediment, carrying erm(B), tet(M), and tet(L) genes, was analyzed for the presence of antibiotic resistance plasmids and for the ability to transfer resistance genes. The strain was found to harbor the replicon type (repA) of pRE25, pRUM, pHTβ, and the axe-txe toxin-antitoxin (TA) system. In mating experiments, tet(M) and tet(L) were cotransferred with the repApRE25, whereas erm(B) was consistently cotransferred with the axe-txe and repApRUM, suggesting that tetracycline and erythromycin resistance genes were carried on different elements both transferable by conjugation, likely via pHTβ-mediated mobilization. Hybridization and PCR mapping demonstrated that tet(M) and tet(L) were located in tandem on a pDO1-like plasmid that also carried the repApRE25, whereas erm(B) was carried by a pRUM-like plasmid. Sequencing of the latter plasmid showed a high nucleotide identity with pRUM and the presence of cat, aadE, sat4, and a complete aphA resistance genes. These findings show that the genetic features of E. faecium 17i48 are consistent with a hospital-adapted clone and suggest that antibiotic resistance may spread in the environment, also in the absence of antibiotic pressure, due to TA system plasmid maintenance.}, }
@article {pmid26978165, year = {2016}, author = {Pinto-Carbó, M and Sieber, S and Dessein, S and Wicker, T and Verstraete, B and Gademann, K and Eberl, L and Carlier, A}, title = {Evidence of horizontal gene transfer between obligate leaf nodule symbionts.}, journal = {The ISME journal}, volume = {10}, number = {9}, pages = {2092-2105}, pmid = {26978165}, issn = {1751-7370}, mesh = {Base Sequence ; Biological Evolution ; Burkholderia/*genetics/metabolism ; *Gene Transfer, Horizontal ; Plant Leaves/microbiology ; Secondary Metabolism ; Symbiosis/*genetics ; }, abstract = {Bacteria of the genus Burkholderia establish an obligate symbiosis with plant species of the Rubiaceae and Primulaceae families. The bacteria, housed within the leaves, are transmitted hereditarily and have not yet been cultured. We have sequenced and compared the genomes of eight bacterial leaf nodule symbionts of the Rubiaceae plant family. All of the genomes exhibit features consistent with genome erosion. Genes potentially involved in the biosynthesis of kirkamide, an insecticidal C7N aminocyclitol, are conserved in most Rubiaceae symbionts. However, some have partially lost the kirkamide pathway due to genome erosion and are unable to synthesize the compound. Kirkamide synthesis is therefore not responsible for the obligate nature of the symbiosis. More importantly, we find evidence of intra-clade horizontal gene transfer (HGT) events affecting genes of the secondary metabolism. This indicates that substantial gene flow can occur at the early stages following host restriction in leaf nodule symbioses. We propose that host-switching events and plasmid conjugative transfers could have promoted these HGTs. This genomic analysis of leaf nodule symbionts gives, for the first time, new insights in the genome evolution of obligate symbionts in their early stages of the association with plants.}, }
@article {pmid26973693, year = {2016}, author = {Cardona, T}, title = {Reconstructing the Origin of Oxygenic Photosynthesis: Do Assembly and Photoactivation Recapitulate Evolution?.}, journal = {Frontiers in plant science}, volume = {7}, number = {}, pages = {257}, pmid = {26973693}, issn = {1664-462X}, support = {BB/K002627/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {Due to the great abundance of genomes and protein structures that today span a broad diversity of organisms, now more than ever before, it is possible to reconstruct the molecular evolution of protein complexes at an incredible level of detail. Here, I recount the story of oxygenic photosynthesis or how an ancestral reaction center was transformed into a sophisticated photochemical machine capable of water oxidation. First, I review the evolution of all reaction center proteins in order to highlight that Photosystem II and Photosystem I, today only found in the phylum Cyanobacteria, branched out very early in the history of photosynthesis. Therefore, it is very unlikely that they were acquired via horizontal gene transfer from any of the described phyla of anoxygenic phototrophic bacteria. Second, I present a new evolutionary scenario for the origin of the CP43 and CP47 antenna of Photosystem II. I suggest that the antenna proteins originated from the remodeling of an entire Type I reaction center protein and not from the partial gene duplication of a Type I reaction center gene. Third, I highlight how Photosystem II and Photosystem I reaction center proteins interact with small peripheral subunits in remarkably similar patterns and hypothesize that some of this complexity may be traced back to the most ancestral reaction center. Fourth, I outline the sequence of events that led to the origin of the Mn4CaO5 cluster and show that the most ancestral Type II reaction center had some of the basic structural components that would become essential in the coordination of the water-oxidizing complex. Finally, I collect all these ideas, starting at the origin of the first reaction center proteins and ending with the emergence of the water-oxidizing cluster, to hypothesize that the complex and well-organized process of assembly and photoactivation of Photosystem II recapitulate evolutionary transitions in the path to oxygenic photosynthesis.}, }
@article {pmid26972562, year = {2016}, author = {Ershova, A and Rusinov, I and Vasiliev, M and Spirin, S and Karyagina, A}, title = {Restriction-Modification systems interplay causes avoidance of GATC site in prokaryotic genomes.}, journal = {Journal of bioinformatics and computational biology}, volume = {14}, number = {2}, pages = {1641003}, doi = {10.1142/S0219720016410031}, pmid = {26972562}, issn = {1757-6334}, mesh = {DNA Methylation ; DNA Restriction-Modification Enzymes/classification/genetics/*metabolism ; Genome ; Inverted Repeat Sequences/*genetics ; Models, Biological ; Multigene Family ; Prokaryotic Cells ; Site-Specific DNA-Methyltransferase (Adenine-Specific)/genetics/metabolism ; }, abstract = {Palindromes are frequently underrepresented in prokaryotic genomes. Palindromic 5[Formula: see text]-GATC-3[Formula: see text] site is a recognition site of different Restriction-Modification (R-M) systems, as well as solitary methyltransferase Dam. Classical GATC-specific R-M systems methylate GATC and cleave unmethylated GATC. On the contrary, methyl-directed Type II restriction endonucleases cleave methylated GATC. Methylation of GATC by Dam methyltransferase is involved in the regulation of different cellular processes. The diversity of functions of GATC-recognizing proteins makes GATC sequence a good model for studying the reasons of palindrome avoidance in prokaryotic genomes. In this work, the influence of R-M systems and solitary proteins on the GATC site avoidance is described by a mathematical model. GATC avoidance is strongly associated with the presence of alternate (methyl-directed or classical Type II R-M system) genes in different strains of the same species, as we have shown for Streptococcus pneumoniae, Neisseria meningitidis, Eubacterium rectale, and Moraxella catarrhalis. We hypothesize that GATC avoidance can result from a DNA exchange between strains with different methylation status of GATC site within the process of natural transformation. If this hypothesis is correct, the GATC avoidance is a sign of a DNA exchange between bacteria with different methylation status in a mixed population.}, }
@article {pmid26971465, year = {2016}, author = {Fulton, KM and Smith, JC and Twine, SM}, title = {Clinical applications of bacterial glycoproteins.}, journal = {Expert review of proteomics}, volume = {13}, number = {4}, pages = {345-353}, doi = {10.1586/14789450.2016.1166054}, pmid = {26971465}, issn = {1744-8387}, mesh = {Animals ; Bacterial Proteins/*metabolism ; Biomarkers/metabolism ; Communicable Diseases/*diagnosis/metabolism/microbiology/therapy ; Glycoproteins/*metabolism ; Host-Pathogen Interactions ; Humans ; Virulence Factors/metabolism ; }, abstract = {There is an ongoing race between bacterial evolution and medical advances. Pathogens have the advantages of short generation times and horizontal gene transfer that enable rapid adaptation to new host environments and therapeutics that currently outpaces clinical research. Antibiotic resistance, the growing impact of nosocomial infections, cancer-causing bacteria, the risk of zoonosis, and the possibility of biowarfare all emphasize the increasingly urgent need for medical research focussed on bacterial pathogens. Bacterial glycoproteins are promising targets for alternative therapeutic intervention since they are often surface exposed, involved in host-pathogen interactions, required for virulence, and contain distinctive glycan structures. The potential exists to exploit these unique structures to improve clinical prevention, diagnosis, and treatment strategies. Translation of the potential in this field to actual clinical impact is an exciting prospect for fighting infectious diseases.}, }
@article {pmid26971047, year = {2016}, author = {Roy Chowdhury, P and DeMaere, M and Chapman, T and Worden, P and Charles, IG and Darling, AE and Djordjevic, SP}, title = {Comparative genomic analysis of toxin-negative strains of Clostridium difficile from humans and animals with symptoms of gastrointestinal disease.}, journal = {BMC microbiology}, volume = {16}, number = {}, pages = {41}, pmid = {26971047}, issn = {1471-2180}, mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins/chemistry/genetics ; Bacterial Toxins/metabolism ; Clostridioides difficile/classification/*genetics/*isolation &amp; purification/metabolism ; Clostridium Infections/*microbiology/*veterinary ; Gastrointestinal Diseases/*microbiology/*veterinary ; Horse Diseases/*microbiology ; Horses ; Humans ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Swine ; Swine Diseases/*microbiology ; }, abstract = {BACKGROUND: Clostridium difficile infections (CDI) are a significant health problem to humans and food animals. Clostridial toxins ToxA and ToxB encoded by genes tcdA and tcdB are located on a pathogenicity locus known as the PaLoc and are the major virulence factors of C. difficile. While toxin-negative strains of C. difficile are often isolated from faeces of animals and patients suffering from CDI, they are not considered to play a role in disease. Toxin-negative strains of C. difficile have been used successfully to treat recurring CDI but their propensity to acquire the PaLoc via lateral gene transfer and express clinically relevant levels of toxins has reinforced the need to characterise them genetically. In addition, further studies that examine the pathogenic potential of toxin-negative strains of C. difficile and the frequency by which toxin-negative strains may acquire the PaLoc are needed.<br><br>RESULTS: We undertook a comparative genomic analysis of five Australian toxin-negative isolates of C. difficile that lack tcdA, tcdB and both binary toxin genes cdtA and cdtB that were recovered from humans and farm animals with symptoms of gastrointestinal disease. Our analyses show that the five C. difficile isolates cluster closely with virulent toxigenic strains of C. difficile belonging to the same sequence type (ST) and have virulence gene profiles akin to those in toxigenic strains. Furthermore, phage acquisition appears to have played a key role in the evolution of C. difficile.<br><br>CONCLUSIONS: Our results are consistent with the C. difficile global population structure comprising six clades each containing both toxin-positive and toxin-negative strains. Our data also suggests that toxin-negative strains of C. difficile encode a repertoire of putative virulence factors that are similar to those found in toxigenic strains of C. difficile, raising the possibility that acquisition of PaLoc by toxin-negative strains poses a threat to human health. Studies in appropriate animal models are needed to examine the pathogenic potential of toxin-negative strains of C. difficile and to determine the frequency by which toxin-negative strains may acquire the PaLoc.}, }
@article {pmid26970895, year = {2016}, author = {van Regenmortel, MH}, title = {The metaphor that viruses are living is alive and well, but it is no more than a metaphor.}, journal = {Studies in history and philosophy of biological and biomedical sciences}, volume = {59}, number = {}, pages = {117-124}, doi = {10.1016/j.shpsc.2016.02.017}, pmid = {26970895}, issn = {1879-2499}, mesh = {*Biological Evolution ; Life ; Metaphor ; *Virus Physiological Phenomena ; Viruses/classification ; }, abstract = {Virologists often use anthropomorphic metaphors to vividly describe the properties of viruses and this has led some virologists to claim that viruses are living microorganisms. The discovery of giant viruses that are larger and have a more complex genome than small bacteria has fostered the interpretation that viral factories, which are the compartments in virus-infected cells where the virus is being replicated, are able to transform themselves into a new type of living viral organism called a virocell. However, because of the widespread occurrence of horizontal gene transfer, endosymbiosis and hybridization in the evolution of viral genomes, it has not been possible to include metaphorical virocells in the so-called Tree of Life which itself is a metaphor. In the case of viruses that cause human diseases, the infection process is usually presented metaphorically as a war between host and virus and it is assumed that a virus such as the human immunodeficiency virus (HIV) is able to develop new strategies and mechanisms for escaping protective host immune responses. However, the ability of the virus to defeat the immune system is solely due to stochastic mutations arising from the error-prone activity of the viral enzyme reverse transcriptase. The following two types of metaphors will be distinguished: an intentionality metaphor commonly used for attributing goals and intentions to organisms and the living virus metaphor that considers viruses to be actually living organisms.}, }
@article {pmid26968003, year = {2016}, author = {Lacroix, B and Citovsky, V}, title = {A Functional Bacterium-to-Plant DNA Transfer Machinery of Rhizobium etli.}, journal = {PLoS pathogens}, volume = {12}, number = {3}, pages = {e1005502}, pmid = {26968003}, issn = {1553-7374}, support = {5R01GM05022418/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; Bacterial Proteins/genetics ; DNA, Bacterial/genetics ; DNA, Plant/genetics ; *Gene Transfer, Horizontal ; Genes, Reporter ; Mutation ; Plasmids/genetics ; Rhizobium etli/*genetics ; Virulence ; }, abstract = {Different strains and species of the soil phytopathogen Agrobacterium possess the ability to transfer and integrate a segment of DNA (T-DNA) into the genome of their eukaryotic hosts, which is mainly mediated by a set of virulence (vir) genes located on the bacterial Ti-plasmid that also contains the T-DNA. To date, Agrobacterium is considered to be unique in its capacity to mediate genetic transformation of eukaryotes. However, close homologs of the vir genes are encoded by the p42a plasmid of Rhizobium etli; this microorganism is related to Agrobacterium, but known only as a symbiotic bacterium that forms nitrogen-fixing nodules in several species of beans. Here, we show that R. etli can mediate functional DNA transfer and stable genetic transformation of plant cells, when provided with a plasmid containing a T-DNA segment. Thus, R. etli represents another bacterial species, besides Agrobacterium, that encodes a protein machinery for DNA transfer to eukaryotic cells and their subsequent genetic modification.}, }
@article {pmid26967674, year = {2016}, author = {La Rosa, SL and Montealegre, MC and Singh, KV and Murray, BE}, title = {Enterococcus faecalis Ebp pili are important for cell-cell aggregation and intraspecies gene transfer.}, journal = {Microbiology (Reading, England)}, volume = {162}, number = {5}, pages = {798-802}, pmid = {26967674}, issn = {1465-2080}, support = {R01 AI047923/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Adhesion/genetics/*physiology ; Biofilms/growth &amp; development ; Conjugation, Genetic/*genetics ; DNA, Bacterial/genetics/*metabolism ; Enterococcus faecalis/*genetics/metabolism/*pathogenicity ; Fimbriae, Bacterial/*genetics ; Gene Transfer, Horizontal/*genetics ; Virulence Factors/genetics ; }, abstract = {Enterococcus faecalis is an opportunistic pathogen that ranks among the leading causes of biofilm-associated infections. We previously demonstrated that the endocarditis- and biofilm-associated pili (Ebp) of E. faecalis play a major role in biofilm formation, adherence to abiotic surfaces and experimental infections. In this study, derivatives of E. faecalis strain OG1 were engineered to further characterize functions of Ebp pili. Loss of pili resulted in a 36-fold decrease in the number of closely associated cells when OG1RFΔebpABC was mixed with OG1SSpΔebpABC, compared with mixing the Ebp+ parental strains. In addition, using the Ebp+ parental strains as donor and recipient, we found a statistically significant increase (280-360 %, P < 0.05) in the frequency of plasmid transfer versus using Ebp- mutants in the conjugation experiments. These results demonstrate a previously unrecognized role of Ebp pili, namely, as important contributors to microscale cell aggregation and horizontal spread of genetic material.}, }
@article {pmid26966911, year = {2016}, author = {Wang, Q and Qian, L and Jiang, S and Cai, C and Ma, D and Gao, P and Li, H and Jiang, K and Tang, M and Hou, J and Liu, J and Cui, W}, title = {Safety Evaluation of Neo Transgenic Pigs by Studying Changes in Gut Microbiota Using High-Throughput Sequencing Technology.}, journal = {PloS one}, volume = {11}, number = {3}, pages = {e0150937}, pmid = {26966911}, issn = {1932-6203}, mesh = {Animals ; Animals, Genetically Modified/*microbiology ; Bacteroidetes/genetics/isolation &amp; purification ; Drug Resistance, Bacterial/genetics ; Escherichia coli/genetics/isolation &amp; purification ; Feces/microbiology ; Firmicutes/genetics/isolation &amp; purification ; Gastrointestinal Microbiome/*drug effects ; Gastrointestinal Tract/*microbiology ; Gene Transfer, Horizontal ; Hafnia/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Kanamycin Kinase/*genetics ; Lactobacillus/genetics/isolation &amp; purification ; Neomycin/pharmacology ; Proteobacteria/genetics/isolation &amp; purification ; Shigella/genetics/isolation &amp; purification ; Swine/*genetics ; Transgenes ; }, abstract = {The neo (neomycin phosphotransferase) gene is widely used as a selection marker in the production of genetically engineered animals and plants. Recent attention has been focused on safety concerns regarding neo transgene expression. In this study, neo transgenic and non-transgenic piglets were randomly assigned into Group A and Group B to evaluate effects of neo transgene by studying changes in gut microbiota using high-throughput sequencing. Group A pigs were fed a standard diet supplemented with antibiotic neomycin; Group B pigs were fed a standard diet. We examined horizontal transfer of exogenous neo gene using multiplex PCR; and investigated if the presence of secreted NPT II (neo expression product) in the intestine could lead to some protection against neomycin in transgenic pigs by monitoring different patterns of changes in gut microbiota in Group A animals. The unintended effects of neo transgene on gut microbiota were studied in Group B animals. Horizontal gene transfer was not detected in gut microbiota of any transgenic pigs. In Group A, a significant difference was observed between transgenic pigs and non-transgenic pigs in pattern of changes in Proteobacteria populations in fecal samples during and post neomycin feeding. In Group B, there were significant differences in the relative abundance of phyla Firmicutes, Bacteroidetes and Proteobacteria, and genera Lactobacillus and Escherichia-Shigella-Hafnia between transgenic pigs and non-transgenic pigs. We speculate that the secretion of NPT II from transgenic tissues/cells into gut microbiota results in the inhibition of neomycin activity and the different patterns of changes in bacterial populations. Furthermore, the neo gene also leads to unintended effects on gut microbiota in transgenic pigs that were fed with basic diet (not supplemented with neomycin). Thus, our data in this study caution that wide use of the neo transgene in genetically engineered animals should be carefully considered and fully assessed.}, }
@article {pmid26966063, year = {2016}, author = {Wang, L and Cao, Y and Wang, ET and Qiao, YJ and Jiao, S and Liu, ZS and Zhao, L and Wei, GH}, title = {Biodiversity and biogeography of rhizobia associated with common bean (Phaseolus vulgaris L.) in Shaanxi Province.}, journal = {Systematic and applied microbiology}, volume = {39}, number = {3}, pages = {211-219}, doi = {10.1016/j.syapm.2016.02.001}, pmid = {26966063}, issn = {1618-0984}, mesh = {Agrobacterium/*classification/genetics/isolation &amp; purification ; Bacterial Proteins/genetics ; *Bacterial Typing Techniques ; Base Sequence ; Biodiversity ; Bradyrhizobium/*classification/genetics/isolation &amp; purification ; China ; DNA, Bacterial/genetics ; Genetic Variation/genetics ; N-Acetylglucosaminyltransferases/genetics ; Ochrobactrum/*classification/genetics/isolation &amp; purification ; Oxidoreductases/genetics ; Phaseolus/*microbiology ; RNA, Ribosomal, 16S/genetics ; Rec A Recombinases/genetics ; Rhizobium/*classification/genetics/isolation &amp; purification ; Root Nodules, Plant/*microbiology ; Sequence Analysis, DNA ; Transcription Factors/genetics ; }, abstract = {The biodiversity and biogeography of rhizobia associated with bean in Shaanxi Province were investigated. A total of 194 bacterial isolates from bean nodules collected from 13 sampling sites were characterized based on phylogenetic analyses of the 16S rRNA gene, the housekeeping genes recA, glnII and atpD, and the symbiotic genes nodC and nifH. Fifteen genospecies belonging to the genera Rhizobium, Agrobacterium, Ensifer, Bradyrhizobium and Ochrobactrum were defined among the isolates, with Rhizobium sp. II, Agrobacterium sp. II, E. fredii and R. phaseoli being the dominant groups. Four symbiotic gene lineages corresponding to Rhizobium sp. I, Rhizobium sp. II, R. phaseoli and B. liaoningense were detected in the nodC and nifH sequence analyses, indicating different origins for the symbiotic genes and their co-evolution with the chromosome of the bacteria. Moreover, the Ensifer isolates harbored symbiotic genes closely related to bean-nodulating Pararhizobium giardinii, indicating possible lateral gene transfer from Rhizobium to Ensifer. Correlation of rhizobial community composition with moisture, temperature, intercropping, soil features and nutrients were detected. All the results demonstrated a great diversity of bean rhizobia in Shaanxi that might be due to the adaptable evolution of the bean-nodulating rhizobia subjected to the diverse ecological conditions in the area.}, }
@article {pmid26959720, year = {2016}, author = {Zhang, HH and Shen, YH and Xiong, XM and Han, MJ and Qi, DW and Zhang, XG}, title = {Evidence for horizontal transfer of a recently active Academ transposon.}, journal = {Insect molecular biology}, volume = {25}, number = {3}, pages = {338-346}, doi = {10.1111/imb.12225}, pmid = {26959720}, issn = {1365-2583}, mesh = {Animals ; *DNA Transposable Elements ; *Gene Transfer, Horizontal ; Host-Parasite Interactions ; Insecta/*genetics/parasitology ; }, abstract = {Horizontal transfer (HT), the exchange of genetic material between species, plays important roles in transposon biology and genome evolution. In this study, we provide the first documented example of a new Academ transposon involved in recent and distant HTs into the genomes of species belonging to seven different orders of insects: Lepidoptera, Hymenoptera, Neuroptera, Embioptera, Dermaptera, Trichoptera and Zoraptera. These results suggest that HT of DNA transposons amongst insects has occurred on a broader scale than previously appreciated. The Academ transposon discovered in the Lepidoptera and parasitic wasps is of particular interest because the intimate association between wasps and their lepidopteran hosts might provide an opportunity for HT of transposons.}, }
@article {pmid26959231, year = {2016}, author = {Conaco, C and Tsoulfas, P and Sakarya, O and Dolan, A and Werren, J and Kosik, KS}, title = {Detection of Prokaryotic Genes in the Amphimedon queenslandica Genome.}, journal = {PloS one}, volume = {11}, number = {3}, pages = {e0151092}, pmid = {26959231}, issn = {1932-6203}, mesh = {Animals ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genome/*genetics ; Phylogeny ; Porifera/*genetics ; }, abstract = {Horizontal gene transfer (HGT) is common between prokaryotes and phagotrophic eukaryotes. In metazoans, the scale and significance of HGT remains largely unexplored but is usually linked to a close association with parasites and endosymbionts. Marine sponges (Porifera), which host many microorganisms in their tissues and lack an isolated germ line, are potential carriers of genes transferred from prokaryotes. In this study, we identified a number of potential horizontally transferred genes within the genome of the sponge, Amphimedon queenslandica. We further identified homologs of some of these genes in other sponges. The transferred genes, most of which possess catalytic activity for carbohydrate or protein metabolism, have assimilated host genome characteristics and are actively expressed. The diversity of functions contributed by the horizontally transferred genes is likely an important factor in the adaptation and evolution of A. queenslandica. These findings highlight the potential importance of HGT on the success of sponges in diverse ecological niches.}, }
@article {pmid26958912, year = {2015}, author = {Penadés, JR and Christie, GE}, title = {The Phage-Inducible Chromosomal Islands: A Family of Highly Evolved Molecular Parasites.}, journal = {Annual review of virology}, volume = {2}, number = {1}, pages = {181-201}, doi = {10.1146/annurev-virology-031413-085446}, pmid = {26958912}, issn = {2327-0578}, support = {1R56 AI081837/AI/NIAID NIH HHS/United States ; MR/M003876/1//Medical Research Council/United Kingdom ; }, mesh = {Bacteria/genetics/*virology ; Bacteriophages/classification/*genetics/physiology ; Genomic Islands ; *Interspersed Repetitive Sequences ; }, abstract = {The phage-inducible chromosomal islands (PICIs) are a family of highly mobile genetic elements that contribute substantively to horizontal gene transfer, host adaptation, and virulence. Initially identified in Staphylococcus aureus, these elements are now thought to occur widely in gram-positive bacteria. They are molecular parasites that exploit certain temperate phages as helpers, using a variety of elegant strategies to manipulate the phage life cycle and promote their own spread, both intra- and intergenerically. At the same time, these PICI-encoded mechanisms severely interfere with helper phage reproduction, thereby enhancing survival of the bacterial population. In this review we discuss the genetics and the life cycle of these elements, with special emphasis on how they interact and interfere with the helper phage machinery for their own benefit. We also analyze the role that these elements play in driving bacterial and viral evolution.}, }
@article {pmid26956583, year = {2016}, author = {Bergstrand, LH and Cardenas, E and Holert, J and Van Hamme, JD and Mohn, WW}, title = {Delineation of Steroid-Degrading Microorganisms through Comparative Genomic Analysis.}, journal = {mBio}, volume = {7}, number = {2}, pages = {e00166}, pmid = {26956583}, issn = {2150-7511}, mesh = {Actinobacteria/genetics/*metabolism ; Aerobiosis ; Biotransformation ; *Genomics ; Metabolic Networks and Pathways/*genetics ; Proteobacteria/genetics/*metabolism ; Steroids/*metabolism ; }, abstract = {UNLABELLED: Steroids are ubiquitous in natural environments and are a significant growth substrate for microorganisms. Microbial steroid metabolism is also important for some pathogens and for biotechnical applications. This study delineated the distribution of aerobic steroid catabolism pathways among over 8,000 microorganisms whose genomes are available in the NCBI RefSeq database. Combined analysis of bacterial, archaeal, and fungal genomes with both hidden Markov models and reciprocal BLAST identified 265 putative steroid degraders within only Actinobacteria and Proteobacteria, which mainly originated from soil, eukaryotic host, and aquatic environments. These bacteria include members of 17 genera not previously known to contain steroid degraders. A pathway for cholesterol degradation was conserved in many actinobacterial genera, particularly in members of the Corynebacterineae, and a pathway for cholate degradation was conserved in members of the genus Rhodococcus. A pathway for testosterone and, sometimes, cholate degradation had a patchy distribution among Proteobacteria. The steroid degradation genes tended to occur within large gene clusters. Growth experiments confirmed bioinformatic predictions of steroid metabolism capacity in nine bacterial strains. The results indicate there was a single ancestral 9,10-seco-steroid degradation pathway. Gene duplication, likely in a progenitor of Rhodococcus, later gave rise to a cholate degradation pathway. Proteobacteria and additional Actinobacteria subsequently obtained a cholate degradation pathway via horizontal gene transfer, in some cases facilitated by plasmids. Catabolism of steroids appears to be an important component of the ecological niches of broad groups of Actinobacteria and individual species of Proteobacteria.<br><br>IMPORTANCE: Steroids are ubiquitous growth substrates for environmental and pathogenic bacteria, and bacterial steroid metabolism has important pharmaceutical and health applications. To date, the genetics and biochemistry of microbial steroid degradation have mainly been studied in a few model bacteria, and the diversity of this metabolism remains largely unexplored. Here, we provide a bioinformatically derived perspective of the taxonomic distribution of aerobic microbial steroid catabolism pathways. We identified several novel steroid-degrading bacterial groups, including ones from marine environments. In several cases, we confirmed bioinformatic predictions of metabolism in cultures. We found that cholesterol and cholate catabolism pathways are highly conserved among certain actinobacterial taxa. We found evidence for horizontal transfer of a pathway to several proteobacterial genera, conferring testosterone and, sometimes, cholate catabolism. The results of this study greatly expand our ecological and evolutionary understanding of microbial steroid metabolism and provide a basis for better exploiting this metabolism for biotechnology.}, }
@article {pmid26954687, year = {2016}, author = {Athey, TB and Teatero, S and Takamatsu, D and Wasserscheid, J and Dewar, K and Gottschalk, M and Fittipaldi, N}, title = {Population Structure and Antimicrobial Resistance Profiles of Streptococcus suis Serotype 2 Sequence Type 25 Strains.}, journal = {PloS one}, volume = {11}, number = {3}, pages = {e0150908}, pmid = {26954687}, issn = {1932-6203}, mesh = {Anti-Bacterial Agents/*pharmacology ; DNA Transposable Elements ; *Drug Resistance, Bacterial ; Gene Order ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Microbial Sensitivity Tests ; Phylogeny ; Polymorphism, Single Nucleotide ; Recombination, Genetic ; Serogroup ; Streptococcus suis/classification/*drug effects/*genetics ; }, abstract = {Strains of serotype 2 Streptococcus suis are responsible for swine and human infections. Different serotype 2 genetic backgrounds have been defined using multilocus sequence typing (MLST). However, little is known about the genetic diversity within each MLST sequence type (ST). Here, we used whole-genome sequencing to test the hypothesis that S. suis serotype 2 strains of the ST25 lineage are genetically heterogeneous. We evaluated 51 serotype 2 ST25 S. suis strains isolated from diseased pigs and humans in Canada, the United States of America, and Thailand. Whole-genome sequencing revealed numerous large-scale rearrangements in the ST25 genome, compared to the genomes of ST1 and ST28 S. suis strains, which result, among other changes, in disruption of a pilus island locus. We report that recombination and lateral gene transfer contribute to ST25 genetic diversity. Phylogenetic analysis identified two main and distinct Thai and North American clades grouping most strains investigated. These clades also possessed distinct patterns of antimicrobial resistance genes, which correlated with acquisition of different integrative and conjugative elements (ICEs). Some of these ICEs were found to be integrated at a recombination hot spot, previously identified as the site of integration of the 89K pathogenicity island in serotype 2 ST7 S. suis strains. Our results highlight the limitations of MLST for phylogenetic analysis of S. suis, and the importance of lateral gene transfer and recombination as drivers of diversity in this swine pathogen and zoonotic agent.}, }
@article {pmid26953198, year = {2016}, author = {Krahn, T and Wibberg, D and Maus, I and Winkler, A and Bontron, S and Sczyrba, A and Nordmann, P and Pühler, A and Poirel, L and Schlüter, A}, title = {Intraspecies Transfer of the Chromosomal Acinetobacter baumannii blaNDM-1 Carbapenemase Gene.}, journal = {Antimicrobial agents and chemotherapy}, volume = {60}, number = {5}, pages = {3032-3040}, pmid = {26953198}, issn = {1098-6596}, mesh = {Acinetobacter baumannii/drug effects/*genetics ; Bacterial Proteins/genetics ; Carbapenems/pharmacology ; DNA Transposable Elements/genetics ; Gene Transfer, Horizontal/*genetics ; Microbial Sensitivity Tests ; Plasmids/genetics ; beta-Lactamases/genetics ; }, abstract = {The species Acinetobacter baumannii is one of the most important multidrug-resistant human pathogens. To determine its virulence and antibiotic resistance determinants, the genome of the nosocomial blaNDM-1-positive A. baumannii strain R2090 originating from Egypt was completely sequenced. Genome analysis revealed that strain R2090 is highly related to the community-acquired Australian A. baumannii strain D1279779. The two strains belong to sequence type 267 (ST267). Isolate R2090 harbored the chromosomally integrated transposon Tn125 carrying the carbapenemase gene blaNDM-1 that is not present in the D1279779 genome. To test the transferability of the metallo-β-lactamase (MBL) gene region, the clinical isolate R2090 was mated with the susceptible A. baumannii recipient CIP 70.10, and the carbapenem-resistant derivative R2091 was obtained. Genome sequencing of the R2091 derivative revealed that it had received an approximately 66-kb region comprising the transposon Tn125 embedding the blaNDM-1 gene. This region had integrated into the chromosome of the recipient strain CIP 70.10. From the four known mechanisms for horizontal gene transfer (conjugation, outer membrane vesicle-mediated transfer, transformation, and transduction), conjugation could be ruled out, since strain R2090 lacks any plasmid, and a type IV secretion system is not encoded in its chromosome. However, strain R2090 possesses three putative prophages, two of which were predicted to be complete and therefore functional. Accordingly, it was supposed that the transfer of the resistance gene region from the clinical isolate R2090 to the recipient occurred by general transduction facilitated by one of the prophages present in the R2090 genome. Hence, phage-mediated transduction has to be taken into account for the dissemination of antibiotic resistance genes within the species A. baumannii.}, }
@article {pmid26951647, year = {2016}, author = {Gurdon, C and Svab, Z and Feng, Y and Kumar, D and Maliga, P}, title = {Cell-to-cell movement of mitochondria in plants.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {12}, pages = {3395-3400}, pmid = {26951647}, issn = {1091-6490}, support = {T32 AT004094/AT/NCCIH NIH HHS/United States ; }, mesh = {*Cell Movement ; DNA, Mitochondrial/genetics ; Mitochondria/*physiology ; *Plant Physiological Phenomena ; Plastids ; }, abstract = {We report cell-to-cell movement of mitochondria through a graft junction. Mitochondrial movement was discovered in an experiment designed to select for chloroplast transfer from Nicotiana sylvestris into Nicotiana tabacum cells. The alloplasmic N. tabacum line we used carries Nicotiana undulata cytoplasmic genomes, and its flowers are male sterile due to the foreign mitochondrial genome. Thus, rare mitochondrial DNA transfer from N. sylvestris to N. tabacum could be recognized by restoration of fertile flower anatomy. Analyses of the mitochondrial genomes revealed extensive recombination, tentatively linking male sterility to orf293, a mitochondrial gene causing homeotic conversion of anthers into petals. Demonstrating cell-to-cell movement of mitochondria reconstructs the evolutionary process of horizontal mitochondrial DNA transfer and enables modification of the mitochondrial genome by DNA transmitted from a sexually incompatible species. Conversion of anthers into petals is a visual marker that can be useful for mitochondrial transformation.}, }
@article {pmid26950302, year = {2016}, author = {Solís-Lemus, C and Ané, C}, title = {Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting.}, journal = {PLoS genetics}, volume = {12}, number = {3}, pages = {e1005896}, pmid = {26950302}, issn = {1553-7404}, mesh = {Computer Simulation ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Likelihood Functions ; Models, Genetic ; *Phylogeny ; }, abstract = {Phylogenetic networks are necessary to represent the tree of life expanded by edges to represent events such as horizontal gene transfers, hybridizations or gene flow. Not all species follow the paradigm of vertical inheritance of their genetic material. While a great deal of research has flourished into the inference of phylogenetic trees, statistical methods to infer phylogenetic networks are still limited and under development. The main disadvantage of existing methods is a lack of scalability. Here, we present a statistical method to infer phylogenetic networks from multi-locus genetic data in a pseudolikelihood framework. Our model accounts for incomplete lineage sorting through the coalescent model, and for horizontal inheritance of genes through reticulation nodes in the network. Computation of the pseudolikelihood is fast and simple, and it avoids the burdensome calculation of the full likelihood which can be intractable with many species. Moreover, estimation at the quartet-level has the added computational benefit that it is easily parallelizable. Simulation studies comparing our method to a full likelihood approach show that our pseudolikelihood approach is much faster without compromising accuracy. We applied our method to reconstruct the evolutionary relationships among swordtails and platyfishes (Xiphophorus: Poeciliidae), which is characterized by widespread hybridizations.}, }
@article {pmid26948882, year = {2016}, author = {Debortoli, N and Li, X and Eyres, I and Fontaneto, D and Hespeels, B and Tang, CQ and Flot, JF and Van Doninck, K}, title = {Genetic Exchange among Bdelloid Rotifers Is More Likely Due to Horizontal Gene Transfer Than to Meiotic Sex.}, journal = {Current biology : CB}, volume = {26}, number = {6}, pages = {723-732}, doi = {10.1016/j.cub.2016.01.031}, pmid = {26948882}, issn = {1879-0445}, support = {BB/F020856/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Belgium ; *Gene Transfer, Horizontal ; Genetics, Population ; Genome ; Haplotypes ; Meiosis ; Reproduction, Asexual/genetics ; Rotifera/*genetics ; }, abstract = {Although strict asexuality is supposed to be an evolutionary dead end, morphological, cytogenetic, and genomic data suggest that bdelloid rotifers, a clade of microscopic animals, have persisted and diversified for more than 60 Myr in an ameiotic fashion. Moreover, the genome of bdelloids of the genus Adineta comprises 8%-10% of genes of putative non-metazoan origin, indicating that horizontal gene transfers are frequent within this group and suggesting that this mechanism may also promote genetic exchanges among bdelloids as well. To test this hypothesis, we used five independent sequence markers to study the genetic diversity of 576 Adineta vaga individuals from a park in Belgium. Haplowebs and GMYC analyses revealed the existence of six species among our sampled A. vaga individuals, with strong evidence of both intra- and interspecific recombination. Comparison of genomic regions of three allele-sharing individuals further revealed signatures of genetic exchanges scattered among regions evolving asexually. Our findings suggest that bdelloids evolve asexually but exchange DNA horizontally both within and between species.}, }
@article {pmid26946995, year = {2016}, author = {Ding, C and Pan, J and Jin, M and Yang, D and Shen, Z and Wang, J and Zhang, B and Liu, W and Fu, J and Guo, X and Wang, D and Chen, Z and Yin, J and Qiu, Z and Li, J}, title = {Enhanced uptake of antibiotic resistance genes in the presence of nanoalumina.}, journal = {Nanotoxicology}, volume = {10}, number = {8}, pages = {1051-1060}, doi = {10.3109/17435390.2016.1161856}, pmid = {26946995}, issn = {1743-5404}, mesh = {Aluminum Oxide/chemistry/*toxicity ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/*drug effects/genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; In Situ Hybridization, Fluorescence ; Nanostructures/chemistry/*toxicity ; Plasmids/genetics ; Real-Time Polymerase Chain Reaction ; Staphylococcus aureus/*drug effects/genetics ; }, abstract = {Nanomaterial pollution and the spread of antibiotic resistance genes (ARGs) are global public health and environmental concerns. Whether nanomaterials could aid the transfer of ARGs released from dead bacteria into live bacteria to cause spread of ARGs is still unknown. Here, we demonstrated that nano-Al2O3 could significantly promote plasmid-mediated ARGs transformation into Gram-negative Escherichia coli strains and into Gram-positive Staphylococcus aureus; however, bulk Al2O3 did not have this effect. Under suitable conditions, 7.4 × 10(6) transformants of E. coli and 2.9 × 10(5) transformants of S. aureus were obtained from 100 ng of a pBR322-based plasmid when bacteria were treated with nano-Al2O3. Nanoparticles concentrations, plasmid concentrations, bacterial concentrations, interaction time between the nanomaterial and bacterial cells and the vortexing time affected the transformation efficiency. We also explored the mechanisms underlying this phenomenon. Using fluorescence in situ hybridization and scanning electron microscopy, we found that nano-Al2O3 damaged the cell membrane to produce pores, through which plasmid could enter bacterial cells. Results from reactive oxygen species (ROS) assays, genome-wide expression microarray profiling and quantitative real-time polymerase chain reactions suggested that intracellular ROS damaged the cell membrane, and that an SOS response promoted plasmid transformation. Our results indicated the environmental and health risk resulting from nanomaterials helping sensitive bacteria to obtain antibiotic resistance.}, }
@article {pmid26943624, year = {2016}, author = {Morrissey, EM and Mau, RL and Schwartz, E and Caporaso, JG and Dijkstra, P and van Gestel, N and Koch, BJ and Liu, CM and Hayer, M and McHugh, TA and Marks, JC and Price, LB and Hungate, BA}, title = {Phylogenetic organization of bacterial activity.}, journal = {The ISME journal}, volume = {10}, number = {9}, pages = {2336-2340}, pmid = {26943624}, issn = {1751-7370}, mesh = {Bacteria/*genetics/metabolism ; Biological Evolution ; Carbon Isotopes/analysis ; Ecology ; Ecosystem ; Oxygen Isotopes/analysis ; Phenotype ; Phylogeny ; }, abstract = {Phylogeny is an ecologically meaningful way to classify plants and animals, as closely related taxa frequently have similar ecological characteristics, functional traits and effects on ecosystem processes. For bacteria, however, phylogeny has been argued to be an unreliable indicator of an organism's ecology owing to evolutionary processes more common to microbes such as gene loss and lateral gene transfer, as well as convergent evolution. Here we use advanced stable isotope probing with (13)C and (18)O to show that evolutionary history has ecological significance for in situ bacterial activity. Phylogenetic organization in the activity of bacteria sets the stage for characterizing the functional attributes of bacterial taxonomic groups. Connecting identity with function in this way will allow scientists to begin building a mechanistic understanding of how bacterial community composition regulates critical ecosystem functions.}, }
@article {pmid26941228, year = {2016}, author = {Das, S and Pettersson, BM and Behra, PR and Ramesh, M and Dasgupta, S and Bhattacharya, A and Kirsebom, LA}, title = {The Mycobacterium phlei Genome: Expectations and Surprises.}, journal = {Genome biology and evolution}, volume = {8}, number = {4}, pages = {975-985}, pmid = {26941228}, issn = {1759-6653}, mesh = {Animals ; CRISPR-Cas Systems ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Glycerol/metabolism ; Mycobacterium phlei/*genetics/growth &amp; development/metabolism ; Phylogeny ; Polyamines/metabolism ; }, abstract = {Mycobacterium phlei, a nontuberculosis mycobacterial species, was first described in 1898-1899. We present the complete genome sequence for theM. phlei CCUG21000(T)type strain and the draft genomes for four additional strains. The genome size for all five is 5.3 Mb with 69.4% Guanine-Cytosine content. This is ≈0.35 Mbp smaller than the previously reported M. phlei RIVM draft genome. The size difference is attributed partly to large bacteriophage sequence fragments in theM. phlei RIVM genome. Comparative analysis revealed the following: 1) A CRISPR system similar to Type 1E (cas3) in M. phlei RIVM; 2) genes involved in polyamine metabolism and transport (potAD,potF) that are absent in other mycobacteria, and 3) strain-specific variations in the number of σ-factor genes. Moreover,M. phlei has as many as 82 mce(mammalian cell entry) homologs and many of the horizontally acquired genes in M. phlei are present in other environmental bacteria including mycobacteria that share similar habitat. Phylogenetic analysis based on 693 Mycobacterium core genes present in all complete mycobacterial genomes suggested that its closest neighbor is Mycobacterium smegmatis JS623 and Mycobacterium rhodesiae NBB3, while it is more distant toM. smegmatis mc2 155.}, }
@article {pmid26941045, year = {2016}, author = {Vlaardingerbroek, I and Beerens, B and Rose, L and Fokkens, L and Cornelissen, BJ and Rep, M}, title = {Exchange of core chromosomes and horizontal transfer of lineage-specific chromosomes in Fusarium oxysporum.}, journal = {Environmental microbiology}, volume = {18}, number = {11}, pages = {3702-3713}, doi = {10.1111/1462-2920.13281}, pmid = {26941045}, issn = {1462-2920}, mesh = {Chromosomes, Fungal/*genetics/metabolism ; Fusarium/*classification/*genetics/metabolism ; *Gene Transfer, Horizontal ; Solanum lycopersicum/microbiology ; Plant Diseases/*microbiology ; }, abstract = {Horizontal transfer of supernumerary or lineage-specific (LS) chromosomes has been described in a number of plant pathogenic filamentous fungi. So far it was not known whether transfer is restricted to chromosomes of certain size or properties, or whether 'core' chromosomes can also undergo horizontal transfer. We combined a directed and a non-biased approach to determine whether such restrictions exist. Selection genes were integrated into the genome of a strain of Fusarium oxysporum pathogenic on tomato, either targeted to specific chromosomes by homologous recombination or integrated randomly into the genome. By testing these strains for transfer of the marker to another strain we could confirm transfer of a previously described mobile pathogenicity chromosome. Surprisingly, we also identified strains in which (parts of) core chromosomes were transferred. Whole genome sequencing revealed that this was accompanied by the loss of the homologous region from the recipient strain. Remarkably, transfer of the mobile pathogenicity chromosome always accompanied this exchange of core chromosomes.}, }
@article {pmid26939857, year = {2016}, author = {Gaca, AO and Gilmore, MS}, title = {Killing of VRE Enterococcus faecalis by commensal strains: Evidence for evolution and accumulation of mobile elements in the absence of competition.}, journal = {Gut microbes}, volume = {7}, number = {1}, pages = {90-96}, pmid = {26939857}, issn = {1949-0984}, support = {R01 AI108710/AI/NIAID NIH HHS/United States ; AI083214/AI/NIAID NIH HHS/United States ; R01 AI072360/AI/NIAID NIH HHS/United States ; AI072360/AI/NIAID NIH HHS/United States ; AI108710/AI/NIAID NIH HHS/United States ; EY007145/EY/NEI NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/*genetics ; Enterococcus faecalis/*drug effects/*genetics ; Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract/microbiology ; *Gene Transfer, Horizontal ; Humans ; Interspersed Repetitive Sequences/*genetics ; Symbiosis ; Vancomycin Resistance/*genetics ; Vancomycin-Resistant Enterococci/drug effects/*genetics ; }, abstract = {Enterococci are members of the gastrointestinal tract of humans and most animals that, over the past 3 decades, have emerged as leading causes of multidrug resistant hospital acquired infection (HAI). In addition to their general hardiness, many traits have entered enterococcal lineages through horizontal gene transfer, which has led to the evolution of pathogenic hospital-associated lineages uniquely adapted for survival and proliferation in the antibiotic perturbed ecology of the gastrointestinal tract. We recently observed that the accretion of mobile genetic elements in the prototype vancomycin resistant E. faecalis, clinical isolate V583, renders it unable to co-exist with native enterococci in healthy human fecal flora. In this addendum, we discuss how these findings inform our understanding of how multidrug resistant enterococci evolve, and the implications for the development of treatments that limit colonization and spread of highly antibiotic refractory microbes of this type.}, }
@article {pmid26939722, year = {2016}, author = {Nieto, PA and Pardo-Roa, C and Salazar-Echegarai, FJ and Tobar, HE and Coronado-Arrázola, I and Riedel, CA and Kalergis, AM and Bueno, SM}, title = {New insights about excisable pathogenicity islands in Salmonella and their contribution to virulence.}, journal = {Microbes and infection}, volume = {18}, number = {5}, pages = {302-309}, doi = {10.1016/j.micinf.2016.02.001}, pmid = {26939722}, issn = {1769-714X}, mesh = {Animals ; Disease Models, Animal ; *Genomic Islands ; Humans ; *Interspersed Repetitive Sequences ; Recombination, Genetic ; Salmonella Infections/microbiology ; Salmonella enterica/*genetics/*pathogenicity ; Virulence ; }, abstract = {Pathogenicity islands (PAIs) are regions of the chromosome of pathogenic bacteria that harbor virulence genes, which were probably acquired by lateral gene transfer. Several PAIs can excise from the bacterial chromosome by site-specific recombination and in this review have been denominated "excisable PAIs". Here, the characteristic of some of the excisable PAIs from Salmonella enterica and the possible role and impact of the excision process on bacterial virulence is discussed. Understanding the role of PAI excision could provide important insights relative to the emergence, evolution and virulence of pathogenic enterobacteria.}, }
@article {pmid26939583, year = {2016}, author = {Liu, S and Feng, M and Guan, W}, title = {Mitochondrial DNA sensing by STING signaling participates in inflammation, cancer and beyond.}, journal = {International journal of cancer}, volume = {139}, number = {4}, pages = {736-741}, doi = {10.1002/ijc.30074}, pmid = {26939583}, issn = {1097-0215}, mesh = {Animals ; Apoptosis ; Autophagy ; DNA, Mitochondrial/*immunology ; Extracellular Traps/immunology/metabolism ; Gene Transfer, Horizontal ; Host-Pathogen Interactions/*immunology ; Humans ; Immunity ; Inflammation/*etiology/*metabolism ; Membrane Proteins/*metabolism ; Mitochondria/genetics/metabolism ; Neoplasms/*etiology/*metabolism ; Nucleotidyltransferases/metabolism ; *Signal Transduction ; }, abstract = {Recent studies have revealed the diverse pathophysiological functions of mitochondria beyond traditional energetic metabolism in cells. Mitochondria-released damage-associated molecular patterns, particularly mitochondrial deoxyribonucleic acid (mtDNA), play a central role in host immune defenses against foreign pathogens. Newly discovered cGAS-STING signaling is responsible for microbial DNA recognition, and potentially participates in mitochondrial DNA sensing. Inappropriate inflammatory signaling mediated by mtDNA is implicated in various human diseases, especially infectious/inflammatory disease and cancer. In addition, mtDNA horizontal transfer between tumor cells and surrounding somatic cells has been recently observed and been associated with tumorigenesis and cancer progression. In this review, we will summarize the molecular signaling of mtDNA recognition (especially STING signaling), and discuss the underlying mechanism by which mtDNA transfer triggers cancer progression in human. Besides, we will highlight the central role of mtDNA in host immunity, with particular emphasis on mtDNA-induced NETs (neutrophil extracellular traps) formation, apoptosis and autophagy.}, }
@article {pmid26938861, year = {2016}, author = {Martins-Pinheiro, M and Lima, WC and Asif, H and Oller, CA and Menck, CF}, title = {Evolutionary and Functional Relationships of the dha Regulon by Genomic Context Analysis.}, journal = {PloS one}, volume = {11}, number = {3}, pages = {e0150772}, pmid = {26938861}, issn = {1932-6203}, mesh = {Aerobiosis ; Algorithms ; Amino Acid Sequence ; Archaea/*genetics ; Bacteria/*genetics ; *Evolution, Molecular ; Fermentation ; Gene Transfer, Horizontal ; Genome, Archaeal ; Genome, Bacterial ; Genomics ; Glyceraldehyde/*analogs &amp; derivatives/chemistry ; Glycerol/chemistry/metabolism ; Likelihood Functions ; Molecular Sequence Data ; Phylogeny ; Propane/*chemistry ; Propylene Glycols/*chemistry ; *Regulon ; Sequence Homology, Amino Acid ; Species Specificity ; }, abstract = {3-hydroxypropionaldehyde (3-HPA) and 1,3-propanediol (1,3-PD) are subproducts of glycerol degradation and of economical interest as they are used for polymers synthesis, such as polyesters and polyurethanes. Some few characterized bacterial species (mostly from Firmicutes and Gamma-proteobacteria groups) are able to catabolize these monomers from glycerol using the gene products from the dha regulon. To expand our knowledge and direct further experimental studies on the regulon and related genes for the anaerobic glycerol metabolism, an extensive genomic screening was performed to identify the presence of the dha genes in fully sequenced prokaryotic genomes. Interestingly, this work shows that although only few bacteria species are known to produce 3-HPA or 1,3-PD, the incomplete regulon is found in more than 100 prokaryotic genomes. However, the complete pathway is found only in a few dozen species belonging to five different taxonomic groups, including one Archaea species, Halalkalicoccus jeotgali. Phylogenetic analysis and conservation of both gene synteny and primary sequence similarity reinforce the idea that these genes have a common origin and were possibly acquired by lateral gene transfer (LGT). Besides the evolutionary aspect, the identification of homologs from several different organisms may predict potential alternative targets for faster or more efficient biological synthesis of 3-HPA or 1,3-PD.}, }
@article {pmid26938451, year = {2016}, author = {Sateriale, A and Striepen, B}, title = {Beg, Borrow and Steal: Three Aspects of Horizontal Gene Transfer in the Protozoan Parasite, Cryptosporidium parvum.}, journal = {PLoS pathogens}, volume = {12}, number = {3}, pages = {e1005429}, pmid = {26938451}, issn = {1553-7374}, support = {/WT_/Wellcome Trust/United Kingdom ; R37 AI112427/AI/NIAID NIH HHS/United States ; }, mesh = {Cryptosporidiosis/*parasitology ; Cryptosporidium parvum/*genetics/immunology/metabolism ; *Gene Transfer, Horizontal ; Humans ; Immune Evasion ; Oxygen/metabolism ; }, }
@article {pmid26936890, year = {2016}, author = {Carter, AT and Austin, JW and Weedmark, KA and Peck, MW}, title = {Evolution of Chromosomal Clostridium botulinum Type E Neurotoxin Gene Clusters: Evidence Provided by Their Rare Plasmid-Borne Counterparts.}, journal = {Genome biology and evolution}, volume = {8}, number = {3}, pages = {540-555}, pmid = {26936890}, issn = {1759-6653}, support = {BB/J004529/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Botulinum Toxins/*genetics ; Botulism/*genetics/microbiology ; Clostridium botulinum type E/*genetics/pathogenicity ; Genome, Bacterial ; Humans ; Multigene Family ; *Phylogeny ; Plasmids/genetics ; }, abstract = {Analysis of more than 150 Clostridium botulinum Group II type E genomes identified a small fraction (6%) where neurotoxin-encoding genes were located on plasmids. Seven closely related (134-144 kb) neurotoxigenic plasmids of subtypes E1, E3, and E10 were characterized; all carried genes associated with plasmid mobility via conjugation. Each plasmid contained the same 24-kb neurotoxin cluster cassette (six neurotoxin cluster and six flanking genes) that had split a helicase gene, rather than the more common chromosomal rarA. The neurotoxin cluster cassettes had evolved as separate genetic units which had either exited their chromosomal rarA locus in a series of parallel events, inserting into the plasmid-borne helicase gene, or vice versa. A single intact version of the helicase gene was discovered on a nonneurotoxigenic form of this plasmid. The observed low frequency for the plasmid location may reflect one or more of the following: 1) Less efficient recombination mechanism for the helicase gene target, 2) lack of suitable target plasmids, and 3) loss of neurotoxigenic plasmids. Type E1 and E10 plasmids possessed a Clustered Regularly Interspaced Short Palindromic Repeats locus with spacers that recognized C. botulinum Group II plasmids, but not C. botulinum Group I plasmids, demonstrating their long-term separation. Clostridium botulinum Group II type E strains also carry nonneurotoxigenic plasmids closely related to C. botulinum Group II types B and F plasmids. Here, the absence of neurotoxin cassettes may be because recombination requires both a specific mechanism and specific target sequence, which are rarely found together.}, }
@article {pmid26934590, year = {2016}, author = {Croucher, NJ and Mostowy, R and Wymant, C and Turner, P and Bentley, SD and Fraser, C}, title = {Horizontal DNA Transfer Mechanisms of Bacteria as Weapons of Intragenomic Conflict.}, journal = {PLoS biology}, volume = {14}, number = {3}, pages = {e1002394}, pmid = {26934590}, issn = {1545-7885}, support = {//Wellcome Trust/United Kingdom ; 104169//Wellcome Trust/United Kingdom ; MR/K010174/1/MRC_/Medical Research Council/United Kingdom ; 104169/Z/14/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {DNA Transformation Competence ; *Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences ; Prophages/physiology ; Streptococcus/*genetics/virology ; }, abstract = {Horizontal DNA transfer (HDT) is a pervasive mechanism of diversification in many microbial species, but its primary evolutionary role remains controversial. Much recent research has emphasised the adaptive benefit of acquiring novel DNA, but here we argue instead that intragenomic conflict provides a coherent framework for understanding the evolutionary origins of HDT. To test this hypothesis, we developed a mathematical model of a clonally descended bacterial population undergoing HDT through transmission of mobile genetic elements (MGEs) and genetic transformation. Including the known bias of transformation toward the acquisition of shorter alleles into the model suggested it could be an effective means of counteracting the spread of MGEs. Both constitutive and transient competence for transformation were found to provide an effective defence against parasitic MGEs; transient competence could also be effective at permitting the selective spread of MGEs conferring a benefit on their host bacterium. The coordination of transient competence with cell-cell killing, observed in multiple species, was found to result in synergistic blocking of MGE transmission through releasing genomic DNA for homologous recombination while simultaneously reducing horizontal MGE spread by lowering the local cell density. To evaluate the feasibility of the functions suggested by the modelling analysis, we analysed genomic data from longitudinal sampling of individuals carrying Streptococcus pneumoniae. This revealed the frequent within-host coexistence of clonally descended cells that differed in their MGE infection status, a necessary condition for the proposed mechanism to operate. Additionally, we found multiple examples of MGEs inhibiting transformation through integrative disruption of genes encoding the competence machinery across many species, providing evidence of an ongoing "arms race." Reduced rates of transformation have also been observed in cells infected by MGEs that reduce the concentration of extracellular DNA through secretion of DNases. Simulations predicted that either mechanism of limiting transformation would benefit individual MGEs, but also that this tactic's effectiveness was limited by competition with other MGEs coinfecting the same cell. A further observed behaviour we hypothesised to reduce elimination by transformation was MGE activation when cells become competent. Our model predicted that this response was effective at counteracting transformation independently of competing MGEs. Therefore, this framework is able to explain both common properties of MGEs, and the seemingly paradoxical bacterial behaviours of transformation and cell-cell killing within clonally related populations, as the consequences of intragenomic conflict between self-replicating chromosomes and parasitic MGEs. The antagonistic nature of the different mechanisms of HDT over short timescales means their contribution to bacterial evolution is likely to be substantially greater than previously appreciated.}, }
@article {pmid26930396, year = {2016}, author = {Arya, P and Acharya, V}, title = {Computational Identification Raises a Riddle for Distribution of Putative NACHT NTPases in the Genome of Early Green Plants.}, journal = {PloS one}, volume = {11}, number = {3}, pages = {e0150634}, pmid = {26930396}, issn = {1932-6203}, mesh = {Conserved Sequence/genetics ; Evolution, Molecular ; Genome, Plant/*genetics ; Neuronal Apoptosis-Inhibitory Protein/*genetics ; Nucleoside-Triphosphatase/*genetics ; Phylogeny ; Plants/genetics ; Sequence Alignment ; }, abstract = {NACHT NTPases and AP-ATPases belongs to STAND (signal transduction ATPases with numerous domain) P-loop NTPase class, which are known to be involved in defense signaling pathways and apoptosis regulation. The AP-ATPases (also known as NB-ARC) and NACHT NTPases are widely spread throughout all kingdoms of life except in plants, where only AP-ATPases have been extensively studied in the scenario of plant defense response against pathogen invasion and in hypersensitive response (HR). In the present study, we have employed a genome-wide survey (using stringent computational analysis) of 67 diverse organisms viz., archaebacteria, cyanobacteria, fungi, animalia and plantae to revisit the evolutionary history of these two STAND P-loop NTPases. This analysis divulged the presence of NACHT NTPases in the early green plants (green algae and the lycophyte) which had not been previously reported. These NACHT NTPases were known to be involved in diverse functional activities such as transcription regulation in addition to the defense signaling cascades depending on the domain association. In Chalmydomonas reinhardtii, a green algae, WD40 repeats found to be at the carboxyl-terminus of NACHT NTPases suggest probable role in apoptosis regulation. Moreover, the genome of Selaginella moellendorffii, an extant lycophyte, intriguingly shows the considerable number of both AP-ATPases and NACHT NTPases in contrast to a large repertoire of AP-ATPases in plants and emerge as an important node in the evolutionary tree of life. The large complement of AP-ATPases overtakes the function of NACHT NTPases and plausible reason behind the absence of the later in the plant lineages. The presence of NACHT NTPases in the early green plants and phyletic patterns results from this study raises a quandary for the distribution of this STAND P-loop NTPase with the apparent horizontal gene transfer from cyanobacteria.}, }
@article {pmid26929403, year = {2016}, author = {Wilkinson, ME and Nakatani, Y and Staals, RH and Kieper, SN and Opel-Reading, HK and McKenzie, RE and Fineran, PC and Krause, KL}, title = {Structural plasticity and in vivo activity of Cas1 from the type I-F CRISPR-Cas system.}, journal = {The Biochemical journal}, volume = {473}, number = {8}, pages = {1063-1072}, doi = {10.1042/BCJ20160078}, pmid = {26929403}, issn = {1470-8728}, mesh = {CRISPR-Associated Proteins/*chemistry/*metabolism ; CRISPR-Cas Systems/*physiology ; Crystallization ; Crystallography, X-Ray ; Endodeoxyribonucleases/*chemistry/*metabolism ; Escherichia coli Proteins/*chemistry/*metabolism ; Pectobacterium/metabolism ; Protein Structure, Secondary ; Protein Structure, Tertiary ; }, abstract = {CRISPR-Cas systems are adaptive immune systems in prokaryotes that provide protection against viruses and other foreign DNA. In the adaptation stage, foreign DNA is integrated into CRISPR (clustered regularly interspaced short palindromic repeat) arrays as new spacers. These spacers are used in the interference stage to guide effector CRISPR associated (Cas) protein(s) to target complementary foreign invading DNA. Cas1 is the integrase enzyme that is central to the catalysis of spacer integration. There are many diverse types of CRISPR-Cas systems, including type I-F systems, which are typified by a unique Cas1-Cas2-3 adaptation complex. In the present study we characterize the Cas1 protein of the potato phytopathogen Pectobacterium atrosepticum, an important model organism for understanding spacer acquisition in type I-F CRISPR-Cas systems. We demonstrate by mutagenesis that Cas1 is essential for adaptation in vivo and requires a conserved aspartic acid residue. By X-ray crystallography, we show that although P. atrosepticum Cas1 adopts a fold conserved among other Cas1 proteins, it possesses remarkable asymmetry as a result of structural plasticity. In particular, we resolve for the first time a flexible, asymmetric loop that may be unique to type I-F Cas1 proteins, and we discuss the implications of these structural features for DNA binding and enzymatic activity.}, }
@article {pmid26929322, year = {2016}, author = {Thiaville, JJ and Kellner, SM and Yuan, Y and Hutinet, G and Thiaville, PC and Jumpathong, W and Mohapatra, S and Brochier-Armanet, C and Letarov, AV and Hillebrand, R and Malik, CK and Rizzo, CJ and Dedon, PC and de Crécy-Lagard, V}, title = {Novel genomic island modifies DNA with 7-deazaguanine derivatives.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {11}, pages = {E1452-9}, pmid = {26929322}, issn = {1091-6490}, support = {P01 CA160032/CA/NCI NIH HHS/United States ; GM70641/GM/NIGMS NIH HHS/United States ; P30 ES002109/ES/NIEHS NIH HHS/United States ; ES002109/ES/NIEHS NIH HHS/United States ; R01 GM070641/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics/*metabolism ; Coliphages/genetics/metabolism ; DNA, Bacterial/*chemistry/genetics/metabolism ; Deoxyguanosine/analogs &amp; derivatives/analysis/metabolism ; Gene Transfer, Horizontal ; *Genomic Islands ; Guanine/*analogs &amp; derivatives/chemistry/metabolism ; Guanosine/analogs &amp; derivatives/metabolism ; Molecular Sequence Data ; Multigene Family ; Mutation ; Phylogeny ; Purines/analysis ; RNA, Transfer/genetics/metabolism ; Salmonella enterica/*genetics/metabolism ; Salmonella typhimurium/genetics ; }, abstract = {The discovery of ∼20-kb gene clusters containing a family of paralogs of tRNA guanosine transglycosylase genes, called tgtA5, alongside 7-cyano-7-deazaguanine (preQ0) synthesis and DNA metabolism genes, led to the hypothesis that 7-deazaguanine derivatives are inserted in DNA. This was established by detecting 2'-deoxy-preQ0 and 2'-deoxy-7-amido-7-deazaguanosine in enzymatic hydrolysates of DNA extracted from the pathogenic, Gram-negative bacteria Salmonella enterica serovar Montevideo. These modifications were absent in the closely related S. enterica serovar Typhimurium LT2 and from a mutant of S Montevideo, each lacking the gene cluster. This led us to rename the genes of the S. Montevideo cluster as dpdA-K for 7-deazapurine in DNA. Similar gene clusters were analyzed in ∼150 phylogenetically diverse bacteria, and the modifications were detected in DNA from other organisms containing these clusters, including Kineococcus radiotolerans, Comamonas testosteroni, and Sphingopyxis alaskensis Comparative genomic analysis shows that, in Enterobacteriaceae, the cluster is a genomic island integrated at the leuX locus, and the phylogenetic analysis of the TgtA5 family is consistent with widespread horizontal gene transfer. Comparison of transformation efficiencies of modified or unmodified plasmids into isogenic S. Montevideo strains containing or lacking the cluster strongly suggests a restriction-modification role for the cluster in Enterobacteriaceae. Another preQ0 derivative, 2'-deoxy-7-formamidino-7-deazaguanosine, was found in the Escherichia coli bacteriophage 9 g, as predicted from the presence of homologs of genes involved in the synthesis of the archaeosine tRNA modification. These results illustrate a deep and unexpected evolutionary connection between DNA and tRNA metabolism.}, }
@article {pmid26928176, year = {2016}, author = {Du, XH and Zhao, Q and Xu, J and Yang, ZL}, title = {High inbreeding, limited recombination and divergent evolutionary patterns between two sympatric morel species in China.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {22434}, pmid = {26928176}, issn = {2045-2322}, mesh = {Ascomycota/*genetics ; Base Sequence ; China ; DNA, Fungal/genetics ; Gene Transfer, Horizontal ; Genetic Variation/*genetics ; Geography ; Phylogeny ; Recombination, Genetic/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {As highly prized, popular mushrooms, morels are widely distributed in the northern hemisphere, with China as a modern centre of speciation and diversity. Overharvesting of morels has caused concern over how to effectively preserve their biological and genetic diversity. However, little is known about their population biology and life cycle. In this study, we selected two sympatric phylogenetic species, Mel-13 (124 collections from 11 geographical locations) and Morchella eohespera (156 collections from 14 geographical locations), using fragments of 4 DNA sequences, to analyse their genetic structure. Our results indicated significant differentiation among geographic locations in both species, whereas no obvious correlation between genetic and geographic distance was identified in either species. M. eohespera exhibited a predominantly clonal population structure with limited recombination detected in only 1 of the 14 geographic locations. In contrast, relatively frequent recombination was identified in 6 of the 11 geographic locations of Mel-13. Our analysis indicated that the sympatric species Mel-13 and M. eohespera might have divergent evolutionary patterns, with the former showing signatures of recent population expansion and the latter being relatively stable. Interestingly, we found no heterozygosity but strong evidence for genealogical incongruence, indicating a high level of inbreeding and hybridisation among morel species.}, }
@article {pmid26927519, year = {2016}, author = {Gong, M and Wang, H and Chen, M and Bao, D and Zhu, Q and Tan, Q}, title = {A newly discovered ubiquitin-conjugating enzyme E2 correlated with the cryogenic autolysis of Volvariella volvacea.}, journal = {Gene}, volume = {583}, number = {1}, pages = {58-63}, doi = {10.1016/j.gene.2016.02.038}, pmid = {26927519}, issn = {1879-0038}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Fungal Proteins/genetics/*metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Fungal ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; Selection, Genetic ; Ubiquitin-Conjugating Enzymes/*genetics/*metabolism ; Volvariella/enzymology/genetics/*metabolism ; }, abstract = {In Volvariella volvacea, a species of edible mushroom, cryogenic autolysis is a typical part of abnormal metabolism. Previous functional annotation cluster analyses of cold-induced gene expression profiles have shown that the ubiquitin-conjugating enzyme E2 (UBE2), rather than the cyclin-like F-box domain alone, forms the functional cluster. In this study, analysis of gene expression profiling showed that only one type of UBE2 in V. volvacea (UBEV2) was significantly up-regulated. Further quantitative real-time PCR analysis confirmed that the expression of UBEV2 was significantly up-regulated (P<0.05) after cold-treatment lasting 4, 6, and 8h. This provided evidence that UBEV2 was closely correlated with cryogenic autolysis. The specific distribution of UBEV2 in recently diverged herb decay fungi indicated that UBEV2 was not evolutionarily correlated with early diverging fungi. Phylogenetic analysis indicated that UBEV2 was generated by horizontal gene transfer (HGT) from the ancestry of Selaginella moellendorffii UBE2. Further relative time estimation and detection of natural selection showed that there has been recent positive selection after HGT in UBEV2. Molecular modeling and logo analysis showed that the cysteine-cysteine motif is the characteristic of the UBEV2 family. These observations indicate that UBEV2 is a new type of UBE2 correlated with the cryogenic autolysis of V. volvacea.}, }
@article {pmid26926999, year = {2016}, author = {Bahar, O and Mordukhovich, G and Luu, DD and Schwessinger, B and Daudi, A and Jehle, AK and Felix, G and Ronald, PC}, title = {Bacterial Outer Membrane Vesicles Induce Plant Immune Responses.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {29}, number = {5}, pages = {374-384}, doi = {10.1094/MPMI-12-15-0270-R}, pmid = {26926999}, issn = {0894-0282}, support = {GM 59962/GM/NIGMS NIH HHS/United States ; }, mesh = {Arabidopsis/*immunology ; Arabidopsis Proteins/genetics/metabolism ; Bacteria/classification/*metabolism ; Cell Membrane/*physiology ; Gene Expression Regulation, Plant/immunology ; Plant Diseases/*immunology ; }, abstract = {Gram-negative bacteria continuously pinch off portions of their outer membrane, releasing membrane vesicles. These outer membrane vesicles (OMVs) are involved in multiple processes including cell-to-cell communication, biofilm formation, stress tolerance, horizontal gene transfer, and virulence. OMVs are also known modulators of the mammalian immune response. Despite the well-documented role of OMVs in mammalian-bacterial communication, their interaction with plants is not well studied. To examine whether OMVs of plant pathogens modulate the plant immune response, we purified OMVs from four different plant pathogens and used them to treat Arabidopsis thaliana. OMVs rapidly induced a reactive oxygen species burst, medium alkalinization, and defense gene expression in A. thaliana leaf discs, cell cultures, and seedlings, respectively. Western blot analysis revealed that EF-Tu is present in OMVs and that it serves as an elicitor of the plant immune response in this form. Our results further show that the immune coreceptors BAK1 and SOBIR1 mediate OMV perception and response. Taken together, our results demonstrate that plants can detect and respond to OMV-associated molecules by activation of their immune system, revealing a new facet of plant-bacterial interactions.}, }
@article {pmid26925045, year = {2016}, author = {von Wintersdorff, CJ and Penders, J and van Niekerk, JM and Mills, ND and Majumder, S and van Alphen, LB and Savelkoul, PH and Wolffs, PF}, title = {Dissemination of Antimicrobial Resistance in Microbial Ecosystems through Horizontal Gene Transfer.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {173}, pmid = {26925045}, issn = {1664-302X}, abstract = {The emergence and spread of antibiotic resistance among pathogenic bacteria has been a rising problem for public health in recent decades. It is becoming increasingly recognized that not only antibiotic resistance genes (ARGs) encountered in clinical pathogens are of relevance, but rather, all pathogenic, commensal as well as environmental bacteria-and also mobile genetic elements and bacteriophages-form a reservoir of ARGs (the resistome) from which pathogenic bacteria can acquire resistance via horizontal gene transfer (HGT). HGT has caused antibiotic resistance to spread from commensal and environmental species to pathogenic ones, as has been shown for some clinically important ARGs. Of the three canonical mechanisms of HGT, conjugation is thought to have the greatest influence on the dissemination of ARGs. While transformation and transduction are deemed less important, recent discoveries suggest their role may be larger than previously thought. Understanding the extent of the resistome and how its mobilization to pathogenic bacteria takes place is essential for efforts to control the dissemination of these genes. Here, we will discuss the concept of the resistome, provide examples of HGT of clinically relevant ARGs and present an overview of the current knowledge of the contributions the various HGT mechanisms make to the spread of antibiotic resistance.}, }
@article {pmid26923784, year = {2016}, author = {Lyons, NA and Kraigher, B and Stefanic, P and Mandic-Mulec, I and Kolter, R}, title = {A Combinatorial Kin Discrimination System in Bacillus subtilis.}, journal = {Current biology : CB}, volume = {26}, number = {6}, pages = {733-742}, pmid = {26923784}, issn = {1879-0445}, support = {R01 GM058213/GM/NIGMS NIH HHS/United States ; GM058213/GM/NIGMS NIH HHS/United States ; }, mesh = {ATP-Binding Cassette Transporters/genetics ; Adenosine Triphosphatases/genetics ; Antigens, Bacterial/genetics ; Bacillus subtilis/genetics/*physiology ; Bacterial Physiological Phenomena ; Bacterial Proteins/genetics ; DNA Transposable Elements ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Microbial Interactions ; Mutation ; Phenotype ; Sigma Factor/genetics ; }, abstract = {Multicellularity inherently involves a number of cooperative behaviors that are potentially susceptible to exploitation but can be protected by mechanisms such as kin discrimination. Discrimination of kin from non-kin has been observed in swarms of the bacterium Bacillus subtilis, but the underlying molecular mechanism has been unknown. We used genetic, transcriptomic, and bioinformatic analyses to uncover kin recognition factors in this organism. Our results identified many molecules involved in cell-surface modification and antimicrobial production and response. These genes varied significantly in expression level and mutation phenotype among B. subtilis strains, suggesting interstrain variation in the exact kin discrimination mechanism used. Genome analyses revealed a substantial diversity of antimicrobial genes present in unique combinations in different strains, with many likely acquired by horizontal gene transfer. The dynamic combinatorial effect derived from this plethora of kin discrimination genes creates a tight relatedness cutoff for cooperation that has likely led to rapid diversification within the species. Our data suggest that genes likely originally selected for competitive purposes also generate preferential interactions among kin, thus stabilizing multicellular lifestyles.}, }
@article {pmid26915958, year = {2016}, author = {Danchin, EG and Guzeeva, EA and Mantelin, S and Berepiki, A and Jones, JT}, title = {Horizontal Gene Transfer from Bacteria Has Enabled the Plant-Parasitic Nematode Globodera pallida to Feed on Host-Derived Sucrose.}, journal = {Molecular biology and evolution}, volume = {33}, number = {6}, pages = {1571-1579}, doi = {10.1093/molbev/msw041}, pmid = {26915958}, issn = {1537-1719}, mesh = {Animals ; Bacteria/genetics ; Base Sequence ; Biological Evolution ; Evolution, Molecular ; Gene Expression ; *Gene Transfer, Horizontal ; Genome, Plant ; Nematoda/*genetics/metabolism/*microbiology ; Phylogeny ; Plant Diseases/*parasitology ; Plants/genetics/parasitology ; Sequence Alignment ; Sucrose/*metabolism ; beta-Fructofuranosidase/genetics/metabolism ; }, abstract = {The evolution of plant-parasitic nematodes (PPN) is unusual in that these organisms have acquired a range of genes from bacteria via horizontal gene transfer (HGT). The proteins encoded by most of these genes are involved in metabolism of various components of the plant cell wall during invasion of the host. Recent genome sequencing projects for PPN have shown that Glycosyl Hydrolase Family 32 (GH32) sequences are present in several PPN species. These sequences are absent from almost all other animals. Here, we show that the GH32 sequences from an economically important cyst nematode species, Globodera pallida are functional invertases, are expressed during feeding and are restricted in expression to the nematode digestive system. These data are consistent with a role in metabolizing host-derived sucrose. In addition, a detailed phylogenetic analysis shows that the GH32 sequences from PPN and those present in some insect species have distinct bacterial origins and do not therefore derive from a gene present in the last common ancestor of ecdysozoan species. HGT has therefore played at least two critical roles in the evolution of PPN, enabling both invasion of the host and feeding on the main translocation carbohydrate of the plant.}, }
@article {pmid26914459, year = {2016}, author = {Ikeda-Ohtsubo, W and Strassert, JF and Köhler, T and Mikaelyan, A and Gregor, I and McHardy, AC and Tringe, SG and Hugenholtz, P and Radek, R and Brune, A}, title = {'Candidatus Adiutrix intracellularis', an endosymbiont of termite gut flagellates, is the first representative of a deep-branching clade of Deltaproteobacteria and a putative homoacetogen.}, journal = {Environmental microbiology}, volume = {18}, number = {8}, pages = {2548-2564}, doi = {10.1111/1462-2920.13234}, pmid = {26914459}, issn = {1462-2920}, mesh = {Animals ; Deltaproteobacteria/*classification/genetics/*isolation &amp; purification ; Desulfovibrio/genetics ; Formate Dehydrogenases/genetics ; Gene Transfer, Horizontal/genetics ; Hypermastigia/*microbiology ; In Situ Hybridization, Fluorescence ; Intestines/*microbiology ; Isoptera/*parasitology ; Nitrogen Fixation/genetics ; Phylogeny ; Symbiosis ; }, abstract = {Termite gut flagellates are typically colonized by specific bacterial symbionts. Here we describe the phylogeny, ultrastructure and subcellular location of 'Candidatus Adiutrix intracellularis', an intracellular symbiont of Trichonympha collaris in the termite Zootermopsis nevadensis. It represents a novel, deep-branching clade of uncultured Deltaproteobacteria widely distributed in intestinal tracts of termites and cockroaches. Fluorescence in situ hybridization and transmission electron microscopy localized the endosymbiont near hydrogenosomes in the posterior part and near the ectosymbiont 'Candidatus Desulfovibrio trichonymphae' in the anterior part of the host cell. The draft genome of 'Ca. Adiutrix intracellularis' obtained from a metagenomic library revealed the presence of a complete gene set encoding the Wood-Ljungdahl pathway, including two homologs of fdhF encoding hydrogenase-linked formate dehydrogenases (FDHH) and all other components of the recently described hydrogen-dependent carbon dioxide reductase (HDCR) complex, which substantiates previous claims that the symbiont is capable of reductive acetogenesis from CO2 and H2 . The close phylogenetic relationship between the HDCR components and their homologs in homoacetogenic Firmicutes and Spirochaetes suggests that the deltaproteobacterium acquired the capacity for homoacetogenesis via lateral gene transfer. The presence of genes for nitrogen fixation and the biosynthesis of amino acids and cofactors indicate the nutritional nature of the symbiosis.}, }
@article {pmid26913819, year = {2016}, author = {Kolman, MA and Salerno, GL}, title = {Sucrose in bloom-forming cyanobacteria: loss and gain of genes involved in its biosynthesis.}, journal = {Environmental microbiology}, volume = {18}, number = {2}, pages = {439-449}, doi = {10.1111/1462-2920.13071}, pmid = {26913819}, issn = {1462-2920}, mesh = {Cyanobacteria/*genetics/*metabolism ; Fresh Water/microbiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial/genetics ; Molecular Sequence Data ; Multigene Family/genetics ; Osmotic Pressure ; Salinity ; Sucrose/*metabolism ; }, abstract = {Bloom-forming cyanobacteria are widely distributed in freshwater ecosystems. To cope with salinity fluctuations, cyanobacteria synthesize compatible solutes, such as sucrose, to maintain the intracellular osmotic balance. The screening of cyanobacterial genomes revealed that homologues to sucrose metabolism-related genes only occur in few bloom-forming strains, mostly belonging to Nostocales and Stigonematales orders. Remarkably, among Chroococcales and Oscillatoriales strains, homologues were only found in M. aeruginosa PCC 7806 and Leptolyngbya boryana PCC 6306, suggesting a massive loss of sucrose metabolism in bloom-forming strains of these orders. After a complete functional characterization of sucrose genes in M. aeruginosa PCC 7806, we showed that sucrose metabolism depends on the expression of a gene cluster that defines a transcriptional unit, unique among all sucrose-containing cyanobacteria. It was also demonstrated that the expression of the encoding genes of sucrose-related proteins is stimulated by salt. In view of its ancestral origin in cyanobacteria, the fact that most bloom-forming strains lack sucrose metabolism indicates that the genes involved might have been lost during evolution. However, in a particular strain, like M. aeruginosa PCC 7806, sucrose synthesis genes were probably regained by horizontal gene transfer, which could be hypothesized as a response to salinity fluctuations.}, }
@article {pmid26912753, year = {2016}, author = {Gniadek, TJ and Carroll, KC and Simner, PJ}, title = {Carbapenem-Resistant Non-Glucose-Fermenting Gram-Negative Bacilli: the Missing Piece to the Puzzle.}, journal = {Journal of clinical microbiology}, volume = {54}, number = {7}, pages = {1700-1710}, pmid = {26912753}, issn = {1098-660X}, mesh = {Acinetobacter Infections/epidemiology/microbiology/prevention &amp; control ; Acinetobacter baumannii/*drug effects/genetics ; Anti-Bacterial Agents/*pharmacology ; Carbapenems/*pharmacology ; Cross Infection/epidemiology/microbiology/prevention &amp; control ; Disease Transmission, Infectious/*prevention &amp; control ; Gene Transfer, Horizontal ; Humans ; Infection Control/*methods ; Pseudomonas Infections/epidemiology/microbiology/prevention &amp; control ; Pseudomonas aeruginosa/*drug effects/genetics ; *beta-Lactam Resistance ; }, abstract = {The non-glucose-fermenting Gram-negative bacilli Pseudomonas aeruginosa and Acinetobacter baumannii are increasingly acquiring carbapenem resistance. Given their intrinsic antibiotic resistance, this can cause extremely difficult-to-treat infections. Additionally, resistance gene transfer can occur between Gram-negative species, regardless of their ability to ferment glucose. Thus, the acquisition of carbapenemase genes by these organisms increases the risk of carbapenemase spread in general. Ultimately, infection control practitioners and clinical microbiologists need to work together to determine the risk carried by carbapenem-resistant non-glucose-fermenting Gram-negative bacilli (CR-NF) in their institution and what methods should be considered for surveillance and detection of CR-NF.}, }
@article {pmid26912404, year = {2016}, author = {Earl, JP and de Vries, SP and Ahmed, A and Powell, E and Schultz, MP and Hermans, PW and Hill, DJ and Zhou, Z and Constantinidou, CI and Hu, FZ and Bootsma, HJ and Ehrlich, GD}, title = {Comparative Genomic Analyses of the Moraxella catarrhalis Serosensitive and Seroresistant Lineages Demonstrate Their Independent Evolution.}, journal = {Genome biology and evolution}, volume = {8}, number = {4}, pages = {955-974}, pmid = {26912404}, issn = {1759-6653}, support = {AI080935/AI/NIAID NIH HHS/United States ; R01 DC002148/DC/NIDCD NIH HHS/United States ; R01 DC005659/DC/NIDCD NIH HHS/United States ; DC02148/DC/NIDCD NIH HHS/United States ; DC05659/DC/NIDCD NIH HHS/United States ; R01 AI080935/AI/NIAID NIH HHS/United States ; }, mesh = {Cell Line ; Evolution, Molecular ; *Genome, Bacterial ; Genomics ; Humans ; Moraxella catarrhalis/*genetics/growth &amp; development ; Moraxellaceae Infections/microbiology ; Multigene Family ; Phylogeny ; Virulence Factors/genetics ; }, abstract = {The bacterial speciesMoraxella catarrhalishas been hypothesized as being composed of two distinct lineages (referred to as the seroresistant [SR] and serosensitive [SS]) with separate evolutionary histories based on several molecular typing methods, whereas 16S ribotyping has suggested an additional split within the SS lineage. Previously, we characterized whole-genome sequences of 12 SR-lineage isolates, which revealed a relatively small supragenome when compared with other opportunistic nasopharyngeal pathogens, suggestive of a relatively short evolutionary history. Here, we performed whole-genome sequencing on 18 strains from both ribotypes of the SS lineage, an additional SR strain, as well as four previously identified highly divergent strains based on multilocus sequence typing analyses. All 35 strains were subjected to a battery of comparative genomic analyses which clearly show that there are three lineages-the SR, SS, and the divergent. The SR and SS lineages are closely related, but distinct from each other based on three different methods of comparison: Allelic differences observed among core genes; possession of lineage-specific sets of core and distributed genes; and by an alignment of concatenated core sequences irrespective of gene annotation. All these methods show that the SS lineage has much longer interstrain branches than the SR lineage indicating that this lineage has likely been evolving either longer or faster than the SR lineage. There is evidence of extensive horizontal gene transfer (HGT) within both of these lineages, and to a lesser degree between them. In particular, we identified very high rates of HGT between these two lineages for ß-lactamase genes. The four divergent strains aresui generis, being much more distantly related to both the SR and SS groups than these other two groups are to each other. Based on average nucleotide identities, gene content, GC content, and genome size, this group could be considered as a separate taxonomic group. The SR and SS lineages, although distinct, clearly form a single species based on multiple criteria including a large common core genome, average nucleotide identity values, GC content, and genome size. Although neither of these lineages arose from within the other based on phylogenetic analyses, the question of how and when these lineages split and then subsequently reunited in the human nasopharynx is explored.}, }
@article {pmid26910229, year = {2016}, author = {Sistrom, M and Evans, B and Benoit, J and Balmer, O and Aksoy, S and Caccone, A}, title = {De Novo Genome Assembly Shows Genome Wide Similarity between Trypanosoma brucei brucei and Trypanosoma brucei rhodesiense.}, journal = {PloS one}, volume = {11}, number = {2}, pages = {e0147660}, pmid = {26910229}, issn = {1932-6203}, support = {R21 AI094615-01/AI/NIAID NIH HHS/United States ; T32 AI007404/AI/NIAID NIH HHS/United States ; R21 AI094615/AI/NIAID NIH HHS/United States ; R01 AI068932/AI/NIAID NIH HHS/United States ; R21 AI076879/AI/NIAID NIH HHS/United States ; }, mesh = {Evolution, Molecular ; Gene Transfer, Horizontal ; *Genomics ; Humans ; Membrane Glycoproteins/genetics ; Protozoan Proteins/genetics ; Sequence Analysis ; Trypanosoma brucei brucei/*genetics/physiology ; Trypanosoma brucei rhodesiense/*genetics/physiology ; Trypanosomiasis, African/epidemiology ; }, abstract = {BACKGROUND: Trypanosoma brucei is a eukaryotic pathogen which causes African trypanosomiasis. It is notable for its variant surface glycoprotein (VSG) coat, which undergoes antigenic variation enabled by a large suite of VSG pseudogenes, allowing for persistent evasion of host adaptive immunity. While Trypanosoma brucei rhodesiense (Tbr) and T. b gambiense (Tbg) are human infective, related T. b. brucei (Tbb) is cleared by human sera. A single gene, the Serum Resistance Associated (SRA) gene, confers Tbr its human infectivity phenotype. Potential genetic recombination of this gene between Tbr and non-human infective Tbb strains has significant epidemiological consequences for Human African Trypanosomiasis outbreaks.<br><br>RESULTS: Using long and short read whole genome sequencing, we generated a hybrid de novo assembly of a Tbr strain, producing 4,210 scaffolds totaling approximately 38.8 megabases, which comprise a significant proportion of the Tbr genome, and thus represents a valuable tool for a comparative genomics analyses among human and non-human infective T. brucei and future complete genome assembly. We detected 5,970 putative genes, of which two, an alcohol oxidoreductase and a pentatricopeptide repeat-containing protein, were members of gene families common to all T. brucei subspecies, but variants specific to the Tbr strain sequenced in this study. Our findings confirmed the extremely high level of genomic similarity between the two parasite subspecies found in other studies.<br><br>CONCLUSIONS: We confirm at the whole genome level high similarity between the two Tbb and Tbr strains studied. The discovery of extremely minor genomic differentiation between Tbb and Tbr suggests that the transference of the SRA gene via genetic recombination could potentially result in novel human infective strains, thus all genetic backgrounds of T. brucei should be considered potentially human infective in regions where Tbr is prevalent.}, }
@article {pmid26909097, year = {2016}, author = {Wang, C and Li, SS and Han, GZ}, title = {Commentary: Plant Auxin Biosynthesis Did Not Originate in Charophytes.}, journal = {Frontiers in plant science}, volume = {7}, number = {}, pages = {158}, pmid = {26909097}, issn = {1664-462X}, }
@article {pmid26907990, year = {2016}, author = {Lu, B and Leong, HW}, title = {GI-SVM: A sensitive method for predicting genomic islands based on unannotated sequence of a single genome.}, journal = {Journal of bioinformatics and computational biology}, volume = {14}, number = {1}, pages = {1640003}, doi = {10.1142/S0219720016400035}, pmid = {26907990}, issn = {1757-6334}, mesh = {Corynebacterium diphtheriae/genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genomic Islands ; Genomics/*methods ; Pseudomonas aeruginosa/genetics ; Salmonella typhi/genetics ; Sequence Analysis, DNA ; *Support Vector Machine ; }, abstract = {Genomic islands (GIs) are clusters of functionally related genes acquired by lateral genetic transfer (LGT), and they are present in many bacterial genomes. GIs are extremely important for bacterial research, because they not only promote genome evolution but also contain genes that enhance adaption and enable antibiotic resistance. Many methods have been proposed to predict GI. But most of them rely on either annotations or comparisons with other closely related genomes. Hence these methods cannot be easily applied to new genomes. As the number of newly sequenced bacterial genomes rapidly increases, there is a need for methods to detect GI based solely on sequences of a single genome. In this paper, we propose a novel method, GI-SVM, to predict GIs given only the unannotated genome sequence. GI-SVM is based on one-class support vector machine (SVM), utilizing composition bias in terms of k-mer content. From our evaluations on three real genomes, GI-SVM can achieve higher recall compared with current methods, without much loss of precision. Besides, GI-SVM allows flexible parameter tuning to get optimal results for each genome. In short, GI-SVM provides a more sensitive method for researchers interested in a first-pass detection of GI in newly sequenced genomes.}, }
@article {pmid26907777, year = {2016}, author = {Yang, XW and Yang, RF and Cui, YJ}, title = {[Homologous recombination among bacterial genomes: the measurement and identification].}, journal = {Yi chuan = Hereditas}, volume = {38}, number = {2}, pages = {137-143}, doi = {10.16288/j.yczz.15-382}, pmid = {26907777}, issn = {0253-9772}, mesh = {Bacteria/classification/*genetics ; Biological Evolution ; Computational Biology/methods ; Gene Transfer, Horizontal/genetics ; *Genetic Variation ; Genetics, Population ; Genome, Bacterial/*genetics ; *Homologous Recombination ; Phylogeny ; Species Specificity ; }, abstract = {Homologous recombination is one of important sources in shaping the bacterial population diversity, which disrupts the clonal relationship among different lineages through horizontal transferring of DNA-segments. As consequence of blurring the vertical inheritance signals, the homologous recombination raises difficulties in phylogenetic analysis and reconstruction of population structure. Here we discuss the impacts of homologous recombination in inferring phylogenetic relationship among bacterial isolates, and summarize the tools and models separately used in recombination measurement and identification. We also highlight the merits and drawbacks of various approaches, aiming to assist in the practical application for the analysis of homologous recombination in bacterial evolution research.}, }
@article {pmid26906100, year = {2016}, author = {Baker, M and Hobman, JL and Dodd, CE and Ramsden, SJ and Stekel, DJ}, title = {Mathematical modelling of antimicrobial resistance in agricultural waste highlights importance of gene transfer rate.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {4}, pages = {fiw040}, doi = {10.1093/femsec/fiw040}, pmid = {26906100}, issn = {1574-6941}, mesh = {Agriculture ; Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/*genetics ; Drug Resistance, Bacterial/drug effects/*genetics ; Gene Transfer, Horizontal/*genetics ; Manure/microbiology ; Microbial Sensitivity Tests ; *Models, Theoretical ; }, abstract = {Antimicrobial resistance is of global concern. Most antimicrobial use is in agriculture; manures and slurry are especially important because they contain a mix of bacteria, including potential pathogens, antimicrobial resistance genes and antimicrobials. In many countries, manures and slurry are stored, especially over winter, before spreading onto fields as organic fertilizer. Thus, these are a potential location for gene exchange and selection for resistance. We develop and analyse a mathematical model to quantify the spread of antimicrobial resistance in stored agricultural waste. We use parameters from a slurry tank on a UK dairy farm as an exemplar. We show that the spread of resistance depends in a subtle way on the rates of gene transfer and antibiotic inflow. If the gene transfer rate is high, then its reduction controls resistance, while cutting antibiotic inflow has little impact. If the gene transfer rate is low, then reducing antibiotic inflow controls resistance. Reducing length of storage can also control spread of resistance. Bacterial growth rate, fitness costs of carrying antimicrobial resistance and proportion of resistant bacteria in animal faeces have little impact on spread of resistance. Therefore, effective treatment strategies depend critically on knowledge of gene transfer rates.}, }
@article {pmid26903978, year = {2016}, author = {Hansen, M and Perner, M}, title = {Hydrogenase Gene Distribution and H2 Consumption Ability within the Thiomicrospira Lineage.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {99}, pmid = {26903978}, issn = {1664-302X}, abstract = {Thiomicrospira were originally characterized as sulfur-oxidizing chemolithoautotrophs. Attempts to grow them on hydrogen failed for many years. Only recently we demonstrated hydrogen consumption among two of three tested Thiomicrospira and posited that hydrogen consumption may be more widespread among Thiomicrospira than previously assumed. Here, we investigate and compare the hydrogen consumption ability and the presence of group 1 [NiFe]-hydrogenase genes (enzyme catalyzes H2↔2H(+) + 2e(-)) for sixteen different Thiomicrospira species. Seven of these Thiomicrospira species encoded group 1 [NiFe]-hydrogenase genes and five of these species could also consume hydrogen. All Thiomicrospira species exhibiting hydrogen consumption were from hydrothermal vents along the Mid-Atlantic ridge or Eastern Pacific ridges. The tested Thiomicrospira from Mediterranean and Western Pacific vents could not consume hydrogen. The [NiFe]-hydrogenase genes were categorized into two clusters: those resembling the hydrogenase from Hydrogenovibrio are in cluster I and are related to those from Alpha- and other Gammaproteobacteria. In cluster II, hydrogenases found exclusively in Thiomicrospira crunogena strains are combined and form a monophyletic group with those from Epsilonproteobacteria suggesting they were acquired through horizontal gene transfer. Hydrogen consumption appears to be common among some Thiomicrospira, given that five of the tested sixteen strains carried this trait. The hydrogen consumption ability expands their competitiveness within an environment.}, }
@article {pmid26903279, year = {2016}, author = {Sennati, S and Riccobono, E and Di Pilato, V and Villagran, AL and Pallecchi, L and Bartoloni, A and Rossolini, GM}, title = {pHN7A8-related multiresistance plasmids (blaCTX-M-65, fosA3 and rmtB) detected in clinical isolates of Klebsiella pneumoniae from Bolivia: intercontinental plasmid dissemination?.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {71}, number = {6}, pages = {1732-1734}, doi = {10.1093/jac/dkv506}, pmid = {26903279}, issn = {1460-2091}, mesh = {Adult ; Aged ; Anti-Bacterial Agents/pharmacology ; Bolivia ; *Drug Resistance, Multiple, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Female ; Gene Order ; *Gene Transfer, Horizontal ; Genotype ; Humans ; Klebsiella Infections/*microbiology ; Klebsiella pneumoniae/classification/*genetics/*isolation &amp; purification ; Microbial Sensitivity Tests ; Molecular Epidemiology ; Multilocus Sequence Typing ; Plasmids/*analysis ; Sequence Analysis, DNA ; }, }
@article {pmid26903276, year = {2016}, author = {He, T and Shen, Y and Schwarz, S and Cai, J and Lv, Y and Li, J and Feßler, AT and Zhang, R and Wu, C and Shen, J and Wang, Y}, title = {Genetic environment of the transferable oxazolidinone/phenicol resistance gene optrA in Enterococcus faecalis isolates of human and animal origin.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {71}, number = {6}, pages = {1466-1473}, doi = {10.1093/jac/dkw016}, pmid = {26903276}, issn = {1460-2091}, mesh = {Animals ; Anti-Infective Agents/*pharmacology ; Chickens ; Conjugation, Genetic ; DNA Transposable Elements ; Drug Resistance, Bacterial ; Enterococcus faecalis/*drug effects/*genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; Genes, Bacterial ; Gram-Positive Bacterial Infections/*microbiology/*veterinary ; Humans ; Oxazolidinones/*pharmacology ; Plasmids/analysis ; Sequence Analysis, DNA ; Swine ; Thiamphenicol/*pharmacology ; }, abstract = {OBJECTIVES: Aim of this study was to analyse 17 non-related Enterococcus faecalis isolates of human and animal origin for the genetic environment of the novel oxazolidinone/phenicol resistance gene optrA.<br><br>METHODS: WGS and de novo assembly were conducted to analyse the flanking sequences of the optrA gene in the 17 E. faecalis isolates. When optrA was located on a plasmid, conjugation assays were performed to check whether the plasmids are conjugative and to confirm the resistance phenotype associated with these plasmids.<br><br>RESULTS: All nine optrA-carrying plasmids were conjugated into E. faecalis JH2-2 and the transconjugants exhibited the optrA-associated phenotype. In these plasmids, an IS1216E element was detected either upstream and/or downstream of the optrA gene. In eight plasmids, the phenicol exporter gene fexA was found upstream of optrA and in six plasmids, a novel erm(A)-related gene for macrolide-lincosamide-streptogramin B resistance was detected downstream of optrA. When located in the chromosomal DNA, the optrA gene was found downstream of the transcriptional regulator gene araC in four isolates, or downstream of the fexA gene in another four isolates. Integration of the optrA region into a Tn558-Tn554 hybrid, located in the chromosomal radC gene, was seen in two isolates.<br><br>CONCLUSIONS: The findings of the present study extend the current knowledge about the genetic environment of optrA and suggest that IS1216E elements play an important role in the dissemination of optrA among different types of enterococcal plasmids. The mechanism underlying the integration of optrA into the chromosomal DNA requires further investigation.}, }
@article {pmid26901318, year = {2016}, author = {Fukui, N and Oshima, T and Ueda, T and Ogasawara, N and Tobe, T}, title = {Gene Activation through the Modulation of Nucleoid Structures by a Horizontally Transferred Regulator, Pch, in Enterohemorrhagic Escherichia coli.}, journal = {PloS one}, volume = {11}, number = {2}, pages = {e0149718}, pmid = {26901318}, issn = {1932-6203}, mesh = {DNA, Bacterial/genetics/metabolism ; Escherichia coli/genetics/*metabolism ; Escherichia coli Proteins/genetics/*metabolism ; *Gene Transfer, Horizontal ; Multiprotein Complexes/genetics/*metabolism ; Phosphoproteins/genetics/metabolism ; Promoter Regions, Genetic/*physiology ; RNA-Binding Proteins/genetics/metabolism ; Trans-Activators/genetics/*metabolism ; Transcriptional Activation/*physiology ; Nucleolin ; }, abstract = {The horizontally transferred chromosomal segments, which are the main source of genetic diversity among bacterial pathogens, are bound by the nucleoid protein H-NS, resulting in the formation of a nucleoprotein complex and the silencing of gene expression. The de-silencing or activation of virulence genes necessary for the colonization of enterohemorrhagic Escherichia coli is achieved mainly by the action of two regulators, Pch and Ler, which are encoded by horizontally transferred elements. Although Ler has been shown to activate transcription by counteracting H-NS silencing, the mechanism for Pch is poorly understood. We show here that Pch activates the LEE1 promoter and also enhances the Ler-mediated activation of other LEE promoters. Transcriptional activation was completely dependent on repression by the H-NS/StpA/Hha/YdgT complex, indicating that Pch-derived activation was achieved by alleviating H-NS-mediated silencing. Expression of pch reduced the binding of H-NS at LEE1 promoter and altered the nucleoprotein complex. Furthermore, in vitro reconstruction of the protein-DNA complex on LEE1 promoter DNA confirmed the exclusive effect of Pch on H-NS binding. These results demonstrated that Pch is another anti-silencing regulator and a modulator of H-NS-containing nucleoprotein complexes. Thus, the anti-silencing mechanism plays a key role in the coordinated regulation of virulence genes in EHEC.}, }
@article {pmid26899322, year = {2016}, author = {Kirsch, R and Heckel, DG and Pauchet, Y}, title = {How the rice weevil breaks down the pectin network: Enzymatic synergism and sub-functionalization.}, journal = {Insect biochemistry and molecular biology}, volume = {71}, number = {}, pages = {72-82}, doi = {10.1016/j.ibmb.2016.02.007}, pmid = {26899322}, issn = {1879-0240}, mesh = {Animals ; Carboxylic Ester Hydrolases/genetics/*metabolism ; Insect Proteins/genetics/*metabolism ; Multigene Family ; Oryza/metabolism/*parasitology ; Pectins/*metabolism ; Phylogeny ; Polygalacturonase/genetics/*metabolism ; Weevils/enzymology/genetics/*metabolism ; }, abstract = {Pectin is the most complex polysaccharide in nature and highly abundant in plant cell walls and middle lamellae, where it functions in plant growth and development. Phytopathogens utilize plant pectin as an energy source through enzyme-mediated degradation. These pectolytic enzymes include polygalacturonases (PGs) of the GH28 family and pectin methylesterases (PMEs) of the CE8 family. Recently, PGs were also identified in herbivorous insects of the distantly related plant bug, stick insect and Phytophaga beetle lineages. Unlike all other insects, weevils possess PMEs in addition to PGs. To investigate pectin digestion in insects and the role of PMEs in weevils, all PME and PG family members of the rice weevil Sitophilus oryzae were heterologously expressed and functionally characterized. Enzymatically active and inactive PG and PME family members were identified. The loss of activity can be explained by a lack of substrate binding correlating with substitutions of functionally important amino acid residues. We found subfunctionalization in both enzyme families, supported by expression pattern and substrate specificities as well as evidence for synergistic pectin breakdown. Our data suggest that the rice weevil might be able to use pectin as an energy source, and illustrates the potential of both PG and PME enzyme families to functionally diversify after horizontal gene transfer.}, }
@article {pmid26896789, year = {2016}, author = {Kurakov, A and Mindlin, S and Beletsky, A and Shcherbatova, N and Rakitin, A and Ermakova, A and Mardanov, A and Petrova, M}, title = {The ancient small mobilizable plasmid pALWED1.8 harboring a new variant of the non-cassette streptomycin/spectinomycin resistance gene aadA27.}, journal = {Plasmid}, volume = {84-85}, number = {}, pages = {36-43}, doi = {10.1016/j.plasmid.2016.02.005}, pmid = {26896789}, issn = {1095-9890}, mesh = {Acinetobacter baumannii/*drug effects/*genetics ; Amino Acid Sequence ; Anti-Bacterial Agents/*pharmacology ; Base Sequence ; Genes, Bacterial/genetics ; Microbial Sensitivity Tests ; Nucleotidyltransferases/*genetics ; Plasmids/*genetics/isolation &amp; purification ; Sequence Analysis, DNA ; Spectinomycin/*pharmacology ; Streptomycin/*pharmacology ; }, abstract = {The small mobilizable plasmid pALWED1.8 containing a novel variant of the streptomycin/spectinomycin resistance gene aadA27 was isolated from the permafrost strains of Acinetobacter lwoffii. The 4135bp plasmid carries mobА and mobC genes that mediate its mobilization by conjugative plasmids. The nucleotide sequences of mobА and mobC are similar to those of mobilization genes of the modern plasmid pRAY* and its variants, which contain aadB gene, and are widespread among the pathogenic strains of Acinetobacter baumannii. Almost identical pALWED1.8 variants were detected in modern environmental Аcinetobacter strains. A highly similar plasmid was revealed in a strain of Acinetobacter parvus isolated from mouse intestine. Furthermore, we discovered six previously unidentified variants of plasmids related to pALWED1.8 and pRAY* in public databases. In contrast to most known variants of aadA which are cassette genes associated with integrons, the aadA27 variant harbored by pALWED1.8 is a non-cassette, autonomously transcribed gene. Non-cassette aadA genes with 96% sequence identity to aadA27 were detected in the chromosomes of Acinetobacter gyllenbergii and several uncharacterized strains of Аcinetobacter sp. Moreover, we revealed that the autonomous aadA-like genes are present in the chromosomes of many gram-positive and gram-negative bacteria. The phylogenetic analysis of amino acid sequences of all identified AadA proteins showed the following: (i) cassette aadA genes form a separate monophyletic group and mainly reside on plasmids and (ii) chromosomal non-cassette aadA genes are extremely diverse and can be inherited both vertical and via horizontal gene transfer.}, }
@article {pmid26893455, year = {2016}, author = {Staehlin, BM and Gibbons, JG and Rokas, A and O'Halloran, TV and Slot, JC}, title = {Evolution of a Heavy Metal Homeostasis/Resistance Island Reflects Increasing Copper Stress in Enterobacteria.}, journal = {Genome biology and evolution}, volume = {8}, number = {3}, pages = {811-826}, pmid = {26893455}, issn = {1759-6653}, support = {P30 CA060553/CA/NCI NIH HHS/United States ; R01 GM038784/GM/NIGMS NIH HHS/United States ; R01GM038784/GM/NIGMS NIH HHS/United States ; }, mesh = {Chromosomes, Bacterial/drug effects/genetics ; Copper/metabolism/*toxicity ; Enterobacteriaceae/drug effects/*genetics/metabolism ; Gene Transfer, Horizontal ; Homeostasis/genetics ; Humans ; Metals, Heavy/metabolism/*toxicity ; *Phylogeny ; Plasmids/genetics ; Shewanella/genetics ; }, abstract = {Copper homeostasis in bacteria is challenged by periodic elevation of copper levels in the environment, arising from both natural sources and human inputs. Several mechanisms have evolved to efflux copper from bacterial cells, including thecus(copper sensing copper efflux system), andpco(plasmid-borne copper resistance system) systems. The genes belonging to these two systems can be physically clustered in a Copper Homeostasis and Silver Resistance Island (CHASRI) on both plasmids and chromosomes in Enterobacteria. Increasing use of copper in agricultural and industrial applications raises questions about the role of human activity in the evolution of novel copper resistance mechanisms. Here we present evidence that CHASRI emerged and diversified in response to copper deposition across aerobic and anaerobic environments. An analysis of diversification rates and a molecular clock model suggest that CHASRI experienced repeated episodes of elevated diversification that could correspond to peaks in human copper production. Phylogenetic analyses suggest that CHASRI originated in a relative ofEnterobacter cloacaeas the ultimate product of sequential assembly of several pre-existing two-gene modules. Once assembled, CHASRI dispersed via horizontal gene transfer within Enterobacteriaceae and also to certain members of Shewanellaceae, where the originalpcomodule was replaced by a divergentpcohomolog. Analyses of copper stress mitigation suggest that CHASRI confers increased resistance aerobically, anaerobically, and during shifts between aerobic and anaerobic environments, which could explain its persistence in facultative anaerobes and emergent enteric pathogens.}, }
@article {pmid26893301, year = {2016}, author = {Gori, K and Suchan, T and Alvarez, N and Goldman, N and Dessimoz, C}, title = {Clustering Genes of Common Evolutionary History.}, journal = {Molecular biology and evolution}, volume = {33}, number = {6}, pages = {1590-1605}, pmid = {26893301}, issn = {1537-1719}, mesh = {Base Sequence ; *Biological Evolution ; Cluster Analysis ; Computer Simulation ; *Models, Genetic ; *Multigene Family ; Phylogeny ; Sequence Analysis, DNA/methods ; Software ; Yeasts/genetics ; }, abstract = {Phylogenetic inference can potentially result in a more accurate tree using data from multiple loci. However, if the loci are incongruent-due to events such as incomplete lineage sorting or horizontal gene transfer-it can be misleading to infer a single tree. To address this, many previous contributions have taken a mechanistic approach, by modeling specific processes. Alternatively, one can cluster loci without assuming how these incongruencies might arise. Such "process-agnostic" approaches typically infer a tree for each locus and cluster these. There are, however, many possible combinations of tree distance and clustering methods; their comparative performance in the context of tree incongruence is largely unknown. Furthermore, because standard model selection criteria such as AIC cannot be applied to problems with a variable number of topologies, the issue of inferring the optimal number of clusters is poorly understood. Here, we perform a large-scale simulation study of phylogenetic distances and clustering methods to infer loci of common evolutionary history. We observe that the best-performing combinations are distances accounting for branch lengths followed by spectral clustering or Ward's method. We also introduce two statistical tests to infer the optimal number of clusters and show that they strongly outperform the silhouette criterion, a general-purpose heuristic. We illustrate the usefulness of the approach by 1) identifying errors in a previous phylogenetic analysis of yeast species and 2) identifying topological incongruence among newly sequenced loci of the globeflower fly genus Chiastocheta We release treeCl, a new program to cluster genes of common evolutionary history (http://git.io/treeCl).}, }
@article {pmid26888909, year = {2016}, author = {Ribeiro, TG and Novais, &#xc2; and Peixe, L and Machado, E}, title = {Atypical epidemiology of CTX-M-15 among Enterobacteriaceae from a high diversity of non-clinical niches in Angola.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {71}, number = {5}, pages = {1169-1173}, doi = {10.1093/jac/dkv489}, pmid = {26888909}, issn = {1460-2091}, mesh = {Angola ; Animals ; Conjugation, Genetic ; Electrophoresis, Gel, Pulsed-Field ; Enterobacteriaceae/classification/*enzymology/genetics/*isolation &amp; purification ; Environmental Microbiology ; Gene Transfer, Horizontal ; Genotype ; Healthy Volunteers ; Humans ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Plasmids/analysis ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: The objective of this study was to investigate the distribution and molecular epidemiology of ESBLs, acquired AmpCs and carbapenemases in Enterobacteriaceae from non-clinical niches in Angola, an under-researched sub-Saharan country.<br><br>METHODS: Eighty-one samples were recovered from healthy persons (n&#x200a;=&#x200a;18), healthy animals (n&#x200a;=&#x200a;33) and their environments (n&#x200a;=&#x200a;10) or aquatic settings (n&#x200a;=&#x200a;20) in south Angola (2013). Samples were plated onto CHROMagar&#x2122; Orientation with/without antibiotics. Standard methods were used for bacterial identification, characterization of bla genes, antibiotic susceptibility testing and conjugation assays. Clonal analysis (XbaI-PFGE, MLST&#xa0;and Escherichia coli phylogroups), location of bla and plasmid characterization (S1-PFGE, I-CeuI-PFGE, replicon typing&#xa0;and hybridization) were also performed.<br><br>RESULTS: ESBLs (almost exclusively CTX-M-15, 98%) were detected in 21% (45/216) of the isolates, recovered from diverse non-clinical niches and belonging to different Enterobacteriaceae species (mainly E. coli). Acquired AmpCs or carbapenemases were not found. The pandemic B2-ST131 E. coli clone was not identified, but some widespread clonal complexes (CCs) from A (CC10 and CC168), B1 (CC156) or D (CC38) phylogroups were detected. blaCTX-M-15 was variably identified on typeable (29%; 100-335 kb; IncFII, IncFIIK6, IncHI2 and IncY) or non-typeable (16%; 70-330 kb) plasmids or on the chromosome (14%), while for 41% of the isolates its specific location was not determined.<br><br>CONCLUSIONS: This study reports, for the first time in Angola, an unexpected high occurrence of CTX-M-15 in diverse non-clinical niches and Enterobacteriaceae species, and uncovers novel plasmid replicons in under-researched geographical regions. The diffusion of blaCTX-M-15 through such a high diversity of genetic backgrounds (clones, typeable/non-typeable plasmids and genetic environments) unveils an extraordinary ability for blaCTX-M-15 acquisition and mobilization favoured by unrecognized ecological factors.}, }
@article {pmid26888293, year = {2016}, author = {Tanifuji, G and Archibald, JM and Hashimoto, T}, title = {Comparative genomics of mitochondria in chlorarachniophyte algae: endosymbiotic gene transfer and organellar genome dynamics.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {21016}, pmid = {26888293}, issn = {2045-2322}, support = {MOP-115141//Canadian Institutes of Health Research/Canada ; }, mesh = {Cercozoa/*genetics ; DNA, Mitochondrial/*genetics ; DNA, Protozoan/*genetics ; *Gene Transfer, Horizontal ; *Genome, Mitochondrial ; *Genome, Protozoan ; Species Specificity ; *Symbiosis ; }, abstract = {Chlorarachniophyte algae possess four DNA-containing compartments per cell, the nucleus, mitochondrion, plastid and nucleomorph, the latter being a relic nucleus derived from a secondary endosymbiont. While the evolutionary dynamics of plastid and nucleomorph genomes have been investigated, a comparative investigation of mitochondrial genomes (mtDNAs) has not been carried out. We have sequenced the complete mtDNA of Lotharella oceanica and compared it to that of another chlorarachniophyte, Bigelowiella natans. The linear mtDNA of L. oceanica is 36.7 kbp in size and contains 35 protein genes, three rRNAs and 24 tRNAs. The codons GUG and UUG appear to be capable of acting as initiation codons in the chlorarachniophyte mtDNAs, in addition to AUG. Rpl16, rps4 and atp8 genes are missing in L.oceanica mtDNA, despite being present in B. natans mtDNA. We searched for, and found, mitochondrial rpl16 and rps4 genes with spliceosomal introns in the L. oceanica nuclear genome, indicating that mitochondrion-to-host-nucleus gene transfer occurred after the divergence of these two genera. Despite being of similar size and coding capacity, the level of synteny between L. oceanica and B. natans mtDNA is low, suggesting frequent rearrangements. Overall, our results suggest that chlorarachniophyte mtDNAs are more evolutionarily dynamic than their plastid counterparts.}, }
@article {pmid26887391, year = {2016}, author = {Morozov, AA and Likhoshway, YV}, title = {Evolutionary history of the chitin synthases of eukaryotes.}, journal = {Glycobiology}, volume = {26}, number = {6}, pages = {635-639}, doi = {10.1093/glycob/cww018}, pmid = {26887391}, issn = {1460-2423}, mesh = {Acanthamoeba/classification/enzymology/*genetics ; Chitin Synthase/*genetics/metabolism ; Ciliophora/classification/enzymology/*genetics ; Diatoms/classification/enzymology/*genetics ; Evolution, Molecular ; Fungi/classification/enzymology/*genetics ; Gene Expression ; Gene Transfer, Horizontal ; Isoenzymes/genetics/metabolism ; Oomycetes/classification/enzymology/*genetics ; Phylogeny ; }, abstract = {Chitin synthases are widespread among eukaryotes and known to have a complex evolutionary history in some of the groups. We have reconstructed the chitin synthase phylogeny using the most taxonomically comprehensive dataset currently available and have shown the presence of independently formed paralogous groups in oomycetes, ciliates, fungi, and all diatoms except raphid pennates. There were also two cases of horizontal gene transfer (HGT): transfer from fungus to early diatoms gave rise to diatom paralogous group, while transfer from raphid pennate diatom to Acantamoeba ancestor is, to our knowledge, restricted to a single gene in amoeba. Early evolution of chitin synthases is heavily obscured by paralogy, and further sequencing effort is necessary.}, }
@article {pmid26884275, year = {2016}, author = {Sapriel, G and Konjek, J and Orgeur, M and Bouri, L and Frézal, L and Roux, AL and Dumas, E and Brosch, R and Bouchier, C and Brisse, S and Vandenbogaert, M and Thiberge, JM and Caro, V and Ngeow, YF and Tan, JL and Herrmann, JL and Gaillard, JL and Heym, B and Wirth, T}, title = {Genome-wide mosaicism within Mycobacterium abscessus: evolutionary and epidemiological implications.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {118}, pmid = {26884275}, issn = {1471-2164}, mesh = {Bacterial Typing Techniques ; Comparative Genomic Hybridization ; Conjugation, Genetic ; DNA, Bacterial/genetics ; *Evolution, Molecular ; Gene Flow ; Gene Frequency ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; Models, Genetic ; *Mosaicism ; Multilocus Sequence Typing ; Mycobacterium/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: In mycobacteria, conjugation differs from the canonical Hfr model, but is still poorly understood. Here, we quantified this evolutionary processe in a natural mycobacterial population, taking advantage of a large clinical strain collection of the emerging pathogen Mycobacterium abscessus (MAB).<br><br>RESULTS: Multilocus sequence typing confirmed the existence of three M. abscessus subspecies, and unravelled extensive allelic exchange between them. Furthermore, an asymmetrical gene flow occurring between these main lineages was detected, resulting in highly admixed strains. Intriguingly, these mosaic strains were significantly associated with cystic fibrosis patients with lung infections or chronic colonization. Genome sequencing of those hybrid strains confirmed that half of their genomic content was remodelled in large genomic blocks, leading to original tri-modal 'patchwork' architecture. One of these hybrid strains acquired a locus conferring inducible macrolide resistance, and a large genomic insertion from a slowly growing pathogenic mycobacteria, suggesting an adaptive gene transfer. This atypical genomic architecture of the highly recombinogenic strains is consistent with the distributive conjugal transfer (DCT) observed in M. smegmatis. Intriguingly, no known DCT function was found in M. abscessus chromosome, however, a p-RAW-like genetic element was detected in one of the highly admixed strains.<br><br>CONCLUSION: Taken together, our results strongly suggest that MAB evolution is sporadically punctuated by dramatic genome wide remodelling events. These findings might have far reaching epidemiological consequences for emerging mycobacterial pathogens survey in the context of increasing numbers of rapidly growing mycobacteria and M. tuberculosis co-infections.}, }
@article {pmid26875189, year = {2016}, author = {Anacarso, I and Iseppi, R and Sabia, C and Messi, P and Condò, C and Bondi, M and de Niederhäusern, S}, title = {Conjugation-Mediated Transfer of Antibiotic-Resistance Plasmids Between Enterobacteriaceae in the Digestive Tract of Blaberus craniifer (Blattodea: Blaberidae).}, journal = {Journal of medical entomology}, volume = {53}, number = {3}, pages = {591-597}, doi = {10.1093/jme/tjw005}, pmid = {26875189}, issn = {1938-2928}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Cockroaches/*microbiology ; *Conjugation, Genetic ; Enterobacteriaceae/classification/*drug effects/*genetics/isolation &amp; purification ; Gastrointestinal Tract/microbiology ; Gene Transfer, Horizontal ; Plasmids/*genetics/metabolism ; }, abstract = {Cockroaches, insects of the order Blattodea, seem to play a crucial role in the possible conjugation-mediated genetic exchanges that occur among bacteria that harbor in the cockroach intestinal tract. The gut of these insects can be thought of as an effective in vivo model for the natural transfer of antimicrobial resistance plasmids among bacteria. In our study, we evaluated the conjugation-mediated horizontal transfer of resistance genes between Escherichia coli and other microorganisms of the same Enterobacteriaceae family within the intestinal tract of Blaberus craniifer Burmeister, 1838 (Blattodea: Blaberidae). Different in vivo mating experiments were performed using E. coli RP4 harboring the RP4 plasmid carrying ampicillin, kanamycin, and tetracycline resistance genes as the donor and E. coli K12 resistant to nalidixic acid or Salmonella enterica serovar Enteritidis IMM39 resistant to streptomycin as the recipients. The RP4 plasmid was successfully transferred to both recipients, producing E. coli K12-RP4 and S. Enteritidis IMM39-RP4 transconjugants. Conjugation frequencies in vivo were similar to those previously observed in vitro. The transfer of the RP4 plasmid in all transconjugants was confirmed by small-scale plasmid isolation and agar gel electrophoresis, suggesting that the intestinal tract of cockroaches is an effective in vivo model for natural gene transfer. Our results confirm that cockroaches allow for the exchange of antimicrobial resistance plasmids among bacteria and may represent a potential reservoir for the dissemination of antibiotic-resistant bacteria in different environments. These findings are particularly significant to human health in the context of health care settings such as hospitals.}, }
@article {pmid26874261, year = {2016}, author = {Schmidt, M and de Lorenzo, V}, title = {Synthetic bugs on the loose: containment options for deeply engineered (micro)organisms.}, journal = {Current opinion in biotechnology}, volume = {38}, number = {}, pages = {90-96}, doi = {10.1016/j.copbio.2016.01.006}, pmid = {26874261}, issn = {1879-0429}, mesh = {Animals ; Biotechnology/methods ; Containment of Biohazards/*methods ; Humans ; Risk Factors ; Synthetic Biology/*methods ; }, abstract = {Synthetic Biology (SynBio) has brought up again questions on the environmental fate of microorganisms carrying genetic modifications. The growing capacity of editing genomes for deployment of man-made programs opens unprecedented biotechnological opportunities. But the same exacerbate concerns regarding fortuitous or deliberate releases to the natural medium. Most approaches to tackle these worries involve endowing SynBio agents with containment devices for halting horizontal gene transfer and survival of the live agents only at given times and places. Genetic circuits and trophic restraint schemes have been proposed to this end in the pursuit of complete containment. The most promising include adoption of alternative genetic codes and/or dependency on xenobiotic amino acids and nucleotides. But the field has to still overcome serious bottlenecks.}, }
@article {pmid26872493, year = {2016}, author = {Piffaretti, JC}, title = {Antibiotic resistance: the emergence of plasmid-mediated colistin resistance enhances the need of a proactive one-health approach.}, journal = {FEMS microbiology letters}, volume = {363}, number = {5}, pages = {fnw034}, doi = {10.1093/femsle/fnw034}, pmid = {26872493}, issn = {1574-6968}, mesh = {Colistin/*pharmacology ; Communicable Diseases/*drug therapy/microbiology ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/*drug effects/genetics ; Gene Transfer, Horizontal/genetics ; Humans ; Klebsiella pneumoniae/*drug effects/genetics ; Plasmids/genetics ; }, }
@article {pmid26871586, year = {2016}, author = {De Paepe, M and Tournier, L and Moncaut, E and Son, O and Langella, P and Petit, MA}, title = {Carriage of λ Latent Virus Is Costly for Its Bacterial Host due to Frequent Reactivation in Monoxenic Mouse Intestine.}, journal = {PLoS genetics}, volume = {12}, number = {2}, pages = {e1005861}, pmid = {26871586}, issn = {1553-7404}, mesh = {Animals ; Bacteriophage lambda/growth &amp; development/pathogenicity/*physiology ; Colony Count, Microbial ; Escherichia coli/*virology ; Gastrointestinal Tract/*virology ; Gene Transfer, Horizontal ; Host-Pathogen Interactions/*physiology ; Lysogeny ; Mice ; Models, Biological ; Mutation/genetics ; Virulence ; Virus Activation/*physiology ; Virus Latency/*physiology ; }, abstract = {Temperate phages, the bacterial viruses able to enter in a dormant prophage state in bacterial genomes, are present in the majority of bacterial strains for which the genome sequence is available. Although these prophages are generally considered to increase their hosts' fitness by bringing beneficial genes, studies demonstrating such effects in ecologically relevant environments are relatively limited to few bacterial species. Here, we investigated the impact of prophage carriage in the gastrointestinal tract of monoxenic mice. Combined with mathematical modelling, these experimental results provided a quantitative estimation of key parameters governing phage-bacteria interactions within this model ecosystem. We used wild-type and mutant strains of the best known host/phage pair, Escherichia coli and phage λ. Unexpectedly, λ prophage caused a significant fitness cost for its carrier, due to an induction rate 50-fold higher than in vitro, with 1 to 2% of the prophage being induced. However, when prophage carriers were in competition with isogenic phage susceptible bacteria, the prophage indirectly benefited its carrier by killing competitors: infection of susceptible bacteria led to phage lytic development in about 80% of cases. The remaining infected bacteria were lysogenized, resulting overall in the rapid lysogenization of the susceptible lineage. Moreover, our setup enabled to demonstrate that rare events of phage gene capture by homologous recombination occurred in the intestine of monoxenic mice. To our knowledge, this study constitutes the first quantitative characterization of temperate phage-bacteria interactions in a simplified gut environment. The high prophage induction rate detected reveals DNA damage-mediated SOS response in monoxenic mouse intestine. We propose that the mammalian gut, the most densely populated bacterial ecosystem on earth, might foster bacterial evolution through high temperate phage activity.}, }
@article {pmid26870017, year = {2016}, author = {Huang, J and Liang, Y and Guo, D and Shang, K and Ge, L and Kashif, J and Wang, L}, title = {Comparative Genomic Analysis of the ICESa2603 Family ICEs and Spread of erm(B)- and tet(O)-Carrying Transferable 89K-Subtype ICEs in Swine and Bovine Isolates in China.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {55}, pmid = {26870017}, issn = {1664-302X}, abstract = {Integrative and conjugative elements (ICEs) of the ICESa2603 family have been isolated from several species of Streptococcus spp.; however, the comparative genomic and evolutionary analyses of these particular ICEs are currently only at their initial stages. By investigating 13 ICEs of the ICESa2603 family and two ICESa2603 family-like ICEs derived from diverse hosts and locations, we have determined that ICEs comprised a backbone of 30 identical syntenic core genes and accessory genes that were restricted to the intergenic sites or the 3'-end of the non-conserved domain of core genes to maintain its function. ICESa2603 family integrase IntICE Sa 2603 specifically recognized a 15-bp att sequence (TTATTTAAGAGTAAC) at the 3'-end of rplL, which was highly conserved in genus Streptococcus. Phylogenetic analyses suggest that extensive recombination/insertion and the occurrence of a hybrid/mosaic in the ICESa2603 family were responsible for the significant increase in ICE diversity, thereby broadening its host range. Approximately 42.5 and 38.1% of the tested Streptococcus suis and Streptococcus agalactiae clinical isolates respectively contained ICESa2603 family Type IV secretion system (T4SS) genes, and 80.5 and 62.5% of which also respectively carried int ICE Sa 2603, indicating that ICESa2603 family is widely distributed across these bacteria. Sequencing and conjugation transfer of a novel sequence type ST303 clinical S. suis isolate HB1011 demonstrated that the 89K-subtype ICESsuHB1011 retained its transferrable function, thereby conferring tetracycline and macrolide resistance.}, }
@article {pmid26867773, year = {2016}, author = {Sakrouhi, I and Belfquih, M and Sbabou, L and Moulin, P and Bena, G and Filali-Maltouf, A and Le Quéré, A}, title = {Recovery of symbiotic nitrogen fixing acacia rhizobia from Merzouga Desert sand dunes in South East Morocco--Identification of a probable new species of Ensifer adapted to stressed environments.}, journal = {Systematic and applied microbiology}, volume = {39}, number = {2}, pages = {122-131}, doi = {10.1016/j.syapm.2016.01.001}, pmid = {26867773}, issn = {1618-0984}, mesh = {Acacia/*microbiology ; Carbon/chemistry ; *Desert Climate ; Hydrogen-Ion Concentration ; Molecular Typing ; Morocco ; Nitrogen/chemistry ; *Nitrogen Fixation ; Phenotype ; Phosphates/chemistry ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhizobium/*classification/isolation &amp; purification/*physiology ; *Stress, Physiological ; }, abstract = {Bacteria capable of nodulating Acacia tortilis and A. gummifera could be recovered from sand dunes collected in the Moroccan Merzouga desert. The trapping approach enabled the recovery of 17 desert rhizobia that all clustered within the Ensifer (Sinorhizobium) genus. Four isolates of the dominant genotype comprising 15 strains as well as 2 divergent strains were further characterized by MLSA. Phylogenetic analyzes indicated that the dominant genetic type was belonging to a new and yet undefined species within the Ensifer genus. Interestingly, housekeeping gene phylogenies showed that this possibly new species is also present in another desert but in India. Phylogenetic analyses of nifH and nodC sequences showed high sequence conservation among the Moroccan strains belonging to the dominant genotype but high divergence with sequences from Indian isolates suggesting acquisition of symbiotic genes through Horizontal Gene Transfer. These desert rhizobia were capable of growing in media containing high salt concentrations, under high pH and most of the strains showed growth at 45°C. Only recovered from desert type of Biome, yet, this new taxon appears particularly adapted to such harsh environment.}, }
@article {pmid26866478, year = {2016}, author = {El Karkouri, K and Pontarotti, P and Raoult, D and Fournier, PE}, title = {Origin and Evolution of Rickettsial Plasmids.}, journal = {PloS one}, volume = {11}, number = {2}, pages = {e0147492}, pmid = {26866478}, issn = {1932-6203}, mesh = {Alphaproteobacteria/genetics ; *Biological Evolution ; Chromosomes, Bacterial ; DNA, Bacterial/genetics ; *Evolution, Molecular ; Gammaproteobacteria/genetics ; Gene Duplication ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Molecular Sequence Annotation ; Phylogeny ; *Plasmids/genetics ; Rickettsia/classification/*genetics/metabolism ; Sequence Alignment ; Species Specificity ; }, abstract = {BACKGROUND: Rickettsia species are strictly intracellular bacteria that have undergone a reductive genomic evolution. Despite their allopatric lifestyle, almost half of the 26 currently validated Rickettsia species have plasmids. In order to study the origin, evolutionary history and putative roles of rickettsial plasmids, we investigated the evolutionary processes that have shaped 20 plasmids belonging to 11 species, using comparative genomics and phylogenetic analysis between rickettsial, microbial and non-microbial genomes.<br><br>RESULTS: Plasmids were differentially present among Rickettsia species. The 11 species had 1 to 4 plasmid (s) with a size ranging from 12 kb to 83 kb. We reconstructed pRICO, the last common ancestor of the current rickettsial plasmids. pRICO was vertically inherited mainly from Rickettsia/Orientia chromosomes and diverged vertically into a single or multiple plasmid(s) in each species. These plasmids also underwent a reductive evolution by progressive gene loss, similar to that observed in rickettsial chromosomes, possibly leading to cryptic plasmids or complete plasmid loss. Moreover, rickettsial plasmids exhibited ORFans, recent gene duplications and evidence of horizontal gene transfer events with rickettsial and non-rickettsial genomes mainly from the &#x3b1;/&#x3b3;-proteobacteria lineages. Genes related to maintenance and plasticity of plasmids, and to adaptation and resistance to stress mostly evolved under vertical and/or horizontal processes. Those involved in nucleotide/carbohydrate transport and metabolism were under the influence of vertical evolution only, whereas genes involved in cell wall/membrane/envelope biogenesis, cycle control, amino acid/lipid/coenzyme and secondary metabolites biosynthesis, transport and metabolism underwent mainly horizontal transfer events.<br><br>CONCLUSION: Rickettsial plasmids had a complex evolution, starting with a vertical inheritance followed by a reductive evolution associated with increased complexity via horizontal gene transfer as well as gene duplication and genesis. The plasmids are plastic and mosaic structures that may play biological roles similar to or distinct from their co-residing chromosomes in an obligate intracellular lifestyle.}, }
@article {pmid26859773, year = {2016}, author = {Zhu, B and Ibrahim, M and Cui, Z and Xie, G and Jin, G and Kube, M and Li, B and Zhou, X}, title = {Multi-omics analysis of niche specificity provides new insights into ecological adaptation in bacteria.}, journal = {The ISME journal}, volume = {10}, number = {8}, pages = {2072-2075}, pmid = {26859773}, issn = {1751-7370}, mesh = {*Adaptation, Physiological ; Burkholderia/genetics/*physiology ; Ecology ; Gene Transfer, Horizontal ; Genome, Bacterial/*genetics ; *Genomics ; Humans ; Plants/microbiology ; Soil ; Soil Microbiology ; Species Specificity ; }, abstract = {Different lifestyles, ranging from a saprophyte to a pathogen, have been reported in bacteria of one species. Here, we performed genome-wide survey of the ecological adaptation in four Burkholderia seminalis strains, distinguished by their origin as part of the saprophytic microbial community of soil or water but also including human and plant pathogens. The results indicated that each strain is separated from the others by increased fitness in medium simulating its original niche corresponding to the difference between strains in metabolic capacities. Furthermore, strain-specific metabolism and niche survival was generally linked with genomic variants and niche-dependent differential expression of the corresponding genes. In particular, the importance of iron, trehalose and d-arabitol utilization was highlighted by the involvement of DNA-methylation and horizontal gene transfer in niche-adapted regulation of the corresponding operons based on the integrated analysis of our multi-omics data. Overall, our results provided insights of niche-specific adaptation in bacteria.}, }
@article {pmid26859724, year = {2016}, author = {Keroack, CD and Wurster, JI and Decker, CG and Williams, KM and Slatko, BE and Foster, JM and Williams, SA}, title = {Absence of the Filarial Endosymbiont Wolbachia in Seal Heartworm (Acanthocheilonema spirocauda) but Evidence of Ancient Lateral Gene Transfer.}, journal = {The Journal of parasitology}, volume = {102}, number = {3}, pages = {312-318}, doi = {10.1645/15-872}, pmid = {26859724}, issn = {1937-2345}, mesh = {Acanthocheilonema/genetics/*microbiology ; Acanthocheilonemiasis/microbiology/parasitology/*veterinary ; Animals ; Biological Evolution ; Blotting, Western ; DNA Barcoding, Taxonomic ; DNA, Helminth/chemistry/isolation &amp; purification ; Female ; *Gene Transfer, Horizontal/physiology ; Hydroxymethylbilane Synthase/genetics ; Phoca/*parasitology ; Phylogeny ; Polymerase Chain Reaction/methods ; Pseudogenes ; Sequence Analysis, DNA ; Symbiosis ; Wolbachia/*genetics/immunology/physiology ; }, abstract = {The symbiotic relationship of Wolbachia spp. was first observed in insects and subsequently in many parasitic filarial nematodes. This bacterium is believed to provide metabolic and developmental assistance to filarial parasitic nematodes, although the exact nature of this relationship remains to be fully elucidated. While Wolbachia is present in most filarial nematodes in the family Onchocercidae, it is absent in several disparate species such as the human parasite Loa loa . All tested members of the genus Acanthocheilonema, such as Acanthocheilonema viteae, have been shown to lack Wolbachia. Consistent with this, we show that Wolbachia is absent from the seal heartworm (Acanthocheilonema spirocauda), but lateral gene transfer (LGT) of DNA sequences between Wolbachia and A. spirocauda has occurred, indicating a past evolutionary association. Seal heartworm is an important pathogen of phocid seals and understanding its basic biology is essential for conservation of the host. The findings presented here may allow for the development of future treatments or diagnostics for the disease and also aid in clarification of the complicated nematode-Wolbachia relationship.}, }
@article {pmid26858706, year = {2016}, author = {Schut, GJ and Lipscomb, GL and Nguyen, DM and Kelly, RM and Adams, MW}, title = {Heterologous Production of an Energy-Conserving Carbon Monoxide Dehydrogenase Complex in the Hyperthermophile Pyrococcus furiosus.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {29}, pmid = {26858706}, issn = {1664-302X}, abstract = {Carbon monoxide (CO) is an important intermediate in anaerobic carbon fixation pathways in acetogenesis and methanogenesis. In addition, some anaerobes can utilize CO as an energy source. In the hyperthermophilic archaeon Thermococcus onnurineus, which grows optimally at 80°C, CO oxidation and energy conservation is accomplished by a respiratory complex encoded by a 16-gene cluster containing a CO dehydrogenase, a membrane-bound [NiFe]-hydrogenase and a Na(+)/H(+) antiporter module. This complex oxidizes CO, evolves CO2 and H2, and generates a Na(+) motive force that is used to conserve energy by a Na(+)-dependent ATP synthase. Herein we used a bacterial artificial chromosome to insert the 13.2 kb gene cluster encoding the CO-oxidizing respiratory complex of T. onnurineus into the genome of the heterotrophic archaeon, Pyrococcus furiosus, which grows optimally at 100°C. P. furiosus is normally unable to utilize CO, however, the recombinant strain readily oxidized CO and generated H2 at 80°C. Moreover, CO also served as an energy source and allowed the P. furiosus strain to grow with a limiting concentration of sugar or with peptides as the carbon source. Moreover, CO oxidation by P. furiosus was also coupled to the re-utilization, presumably for biosynthesis, of acetate generated by fermentation. The functional transfer of CO utilization between Thermococcus and Pyrococcus species demonstrated herein is representative of the horizontal gene transfer of an environmentally relevant metabolic capability. The transfer of CO utilizing, hydrogen-producing genetic modules also has applications for biohydrogen production and a CO-based industrial platform for various thermophilic organisms.}, }
@article {pmid26858702, year = {2016}, author = {Hammerl, JA and Göllner, C and Al Dahouk, S and Nöckler, K and Reetz, J and Hertwig, S}, title = {Analysis of the First Temperate Broad Host Range Brucellaphage (BiPBO1) Isolated from B. inopinata.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {24}, pmid = {26858702}, issn = {1664-302X}, abstract = {Brucella species are important human and animal pathogens. Though, only little is known about mobile genetic elements of these highly pathogenic bacteria. To date, neither plasmids nor temperate phages have been described in brucellae. We analyzed genomic sequences of various reference and type strains and identified a number of putative prophages residing within the Brucella chromosomes. By induction, phage BiPBO1 was isolated from Brucella inopinata. BiPBO1 is a siphovirus that infects several Brucella species including Brucella abortus and Brucella melitensis. Integration of the phage genome occurs adjacent to a tRNA gene in chromosome 1 (chr 1). The bacterial (attB) and phage (attP) attachment sites comprise an identical sequence of 46 bp. This sequence exists in many Brucella and Ochrobactrum species. The BiPBO1 genome is composed of a 46,877 bp double-stranded DNA. Eighty-seven putative gene products were determined, of which 32 could be functionally assigned. Strongest similarities were found to a temperate phage residing in the chromosome of Ochrobactrum anthropi ATCC 49188 and to prophages identified in several families belonging to the order rhizobiales. The data suggest that horizontal gene transfer may occur between Brucella and Ochrobactrum and underpin the close relationship of these environmental and pathogenic bacteria.}, }
@article {pmid26856837, year = {2016}, author = {Baines, SL and Howden, BP and Heffernan, H and Stinear, TP and Carter, GP and Seemann, T and Kwong, JC and Ritchie, SR and Williamson, DA}, title = {Rapid Emergence and Evolution of Staphylococcus aureus Clones Harboring fusC-Containing Staphylococcal Cassette Chromosome Elements.}, journal = {Antimicrobial agents and chemotherapy}, volume = {60}, number = {4}, pages = {2359-2365}, pmid = {26856837}, issn = {1098-6596}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/*genetics/metabolism ; Chromosomes, Bacterial/*chemistry ; *Clonal Evolution ; Clone Cells ; Drug Resistance, Multiple, Bacterial/genetics ; Fusidic Acid/*pharmacology ; Gene Expression ; Gene Transfer, Horizontal ; Genetic Variation ; Humans ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; New Zealand/epidemiology ; Penicillin-Binding Proteins/genetics/metabolism ; Phylogeny ; Prevalence ; Staphylococcal Infections/drug therapy/*epidemiology/microbiology ; Staphylococcus aureus/classification/drug effects/*genetics/growth &amp; development ; Virulence Factors/genetics/metabolism ; }, abstract = {The prevalence of fusidic acid (FA) resistance amongStaphylococcus aureusstrains in New Zealand (NZ) is among the highest reported globally, with a recent study describing a resistance rate of approximately 28%. Three FA-resistantS. aureusclones (ST5 MRSA, ST1 MSSA, and ST1 MRSA) have emerged over the past decade and now predominate in NZ, and in all three clones FA resistance is mediated by thefusCgene. In particular, ST5 MRSA has rapidly become the dominant MRSA clone in NZ, although the origin of FA-resistant ST5 MRSA has not been explored, and the genetic context offusCin FA-resistant NZ isolates is unknown. To better understand the rapid emergence of FA-resistantS. aureus, we used population-based comparative genomics to characterize a collection of FA-resistant and FA-susceptible isolates from NZ. FA-resistant NZ ST5 MRSA displayed minimal genetic diversity and represented a phylogenetically distinct clade within a global population model of clonal complex 5 (CC5)S. aureus In all lineages,fusCwas invariably located within staphylococcal cassette chromosome (SCC) elements, suggesting that SCC-mediated horizontal transfer is the primary mechanism offusCdissemination. The genotypic association offusCwithmecAhas important implications for the emergence of MRSA clones in populations with high usage of fusidic acid. In addition, we found thatfusCwas colocated with a recently described virulence factor (tirS) in dominant NZS. aureusclones, suggesting a fitness advantage. This study points to the likely molecular mechanisms responsible for the successful emergence and spread of FA-resistantS. aureus.}, }
@article {pmid26850442, year = {2016}, author = {Székely, AJ and Breitbart, M}, title = {Single-stranded DNA phages: from early molecular biology tools to recent revolutions in environmental microbiology.}, journal = {FEMS microbiology letters}, volume = {363}, number = {6}, pages = {}, doi = {10.1093/femsle/fnw027}, pmid = {26850442}, issn = {1574-6968}, mesh = {Bacteriophages/classification/*genetics/physiology ; DNA ; *DNA, Single-Stranded ; *DNA, Viral ; Environmental Microbiology ; Evolution, Molecular ; *Genome, Viral ; Viral Tropism ; }, abstract = {Single-stranded DNA (ssDNA) phages are profoundly different from tailed phages in many aspects including the nature and size of their genome, virion size and morphology, mutation rate, involvement in horizontal gene transfer, infection dynamics and cell lysis mechanisms. Despite the importance of ssDNA phages as molecular biology tools and model systems, the environmental distribution and ecological roles of these phages have been largely unexplored. Viral metagenomics and other culture-independent viral diversity studies have recently challenged the perspective of tailed, double-stranded DNA (dsDNA) phages, dominance by demonstrating the prevalence of ssDNA phages in diverse habitats. However, the differences between ssDNA and dsDNA phages also substantially limit the efficacy of simultaneously assessing the abundance and diversity of these two phage groups. Here we provide an overview of the major differences between ssDNA and tailed dsDNA phages that may influence their effects on bacterial communities. Furthermore, through the analysis of 181 published metaviromes we demonstrate the environmental distribution of ssDNA phages and present an analysis of the methodological biases that distort their study through metagenomics.}, }
@article {pmid26849349, year = {2016}, author = {Mondal, M and Chatterjee, NS}, title = {Role of Vibrio cholerae exochitinase ChiA2 in horizontal gene transfer.}, journal = {Canadian journal of microbiology}, volume = {62}, number = {3}, pages = {201-209}, doi = {10.1139/cjm-2015-0556}, pmid = {26849349}, issn = {1480-3275}, mesh = {*Gene Transfer, Horizontal ; Hexosaminidases/*genetics/physiology ; Transformation, Genetic ; Vibrio cholerae/enzymology/*genetics/growth &amp; development ; }, abstract = {Vibrio cholerae exochitinase ChiA2 plays a key role in acquisition of nutrients by chitin hydrolysis in the natural environment as well as in pathogenesis in the intestinal milieu. In this study we demonstrate the importance of ChiA2 in horizontal gene transfer in the natural environment. We found that the expression of ChiA2 and TfoX, the central regulator of V. cholerae horizontal gene transfer, varied with changes in environmental conditions. The activity of ChiA2 was also dependent on these conditions. In 3 different environmental conditions tested here, we observed that the supporting environmental condition for maximum expression and activity of ChiA2 was 20 °C, pH 5.5, and 100 mmol/L salinity in the presence of chitin. The same condition also induced TfoX expression and was favorable for horizontal gene transfer in V. cholerae. High-performance liquid chromatography analysis showed that ChiA2 released a significant amount of (GlcNAc)2 from chitin hydrolysis under the favorable condition. We hypothesized that under the favorable environmental condition, ChiA2 was upregulated and maximally active to produce a significant amount of (GlcNAc)2 from chitin. The same environmental condition also induced tfoX expression, followed by its translational activation by the (GlcNAc)2 produced, leading to efficient horizontal gene transfer.}, }
@article {pmid26849314, year = {2016}, author = {Engelstädter, J and Harms, K and Johnsen, PJ}, title = {The evolutionary dynamics of integrons in changing environments.}, journal = {The ISME journal}, volume = {10}, number = {6}, pages = {1296-1307}, pmid = {26849314}, issn = {1751-7370}, mesh = {Bacteria/*genetics ; Bacterial Proteins/genetics ; Environment ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Variation ; Integrases/*genetics ; Integrons/*genetics ; *Models, Theoretical ; }, abstract = {Integrons are genetic elements that are common in bacteria and are hotspots for genome evolution. They facilitate the acquisition and reassembly of gene cassettes encoding a variety of functions, including drug resistance. Despite their importance in clinical settings, the selective forces responsible for the evolution and maintenance of integrons are poorly understood. We present a mathematical model of integron evolution within bacterial populations subject to fluctuating antibiotic exposures. Bacteria carrying a functional integrase that mediates reshuffling of cassette genes and thereby modulates gene expression patterns compete with bacteria without a functional integrase. Our results indicate that for a wide range of parameters, the functional integrase can be stably maintained in the population despite substantial fitness costs. This selective advantage arises because gene-cassette shuffling generates genetic diversity, thus enabling the population to respond rapidly to changing selective pressures. We also show that horizontal gene transfer promotes stable maintenance of the integrase and can also lead to de novo assembly of integrons. Our model generates testable predictions for integron evolution, including loss of functional integrases in stable environments and selection for intermediate gene-shuffling rates in changing environments. Our results highlight the need for experimental studies of integron population biology.}, }
@article {pmid26849244, year = {2016}, author = {Quirós, P and Brown-Jaque, M and Muniesa, M}, title = {Spread of bacterial genomes in packaged particles.}, journal = {Future microbiology}, volume = {11}, number = {2}, pages = {171-173}, doi = {10.2217/fmb.15.145}, pmid = {26849244}, issn = {1746-0921}, mesh = {Bacteria/*genetics ; Bacteriophages/genetics ; *Gene Transfer, Horizontal ; Genetic Vectors ; *Genome, Bacterial ; Humans ; }, }
@article {pmid26848973, year = {2016}, author = {Werbowy, O and Kaczorowski, T}, title = {Plasmid pEC156, a Naturally Occurring Escherichia coli Genetic Element That Carries Genes of the EcoVIII Restriction-Modification System, Is Mobilizable among Enterobacteria.}, journal = {PloS one}, volume = {11}, number = {2}, pages = {e0148355}, pmid = {26848973}, issn = {1932-6203}, mesh = {Base Sequence ; DNA Restriction Enzymes/*metabolism ; Escherichia coli/cytology/*enzymology/*genetics ; Interspersed Repetitive Sequences/*genetics ; Molecular Sequence Data ; Plasmids/*genetics ; Transformation, Genetic ; }, abstract = {Type II restriction-modification systems are ubiquitous in prokaryotes. Some of them are present in naturally occurring plasmids, which may facilitate the spread of these systems in bacterial populations by horizontal gene transfer. However, little is known about the routes of their dissemination. As a model to study this, we have chosen an Escherichia coli natural plasmid pEC156 that carries the EcoVIII restriction modification system. The presence of this system as well as the cis-acting cer site involved in resolution of plasmid multimers determines the stable maintenance of pEC156 not only in Escherichia coli but also in other enterobacteria. We have shown that due to the presence of oriT-type F and oriT-type R64 loci it is possible to mobilize pEC156 by conjugative plasmids (F and R64, respectively). The highest mobilization frequency was observed when pEC156-derivatives were transferred between Escherichia coli strains, Enterobacter cloacae and Citrobacter freundii representing coliform bacteria. We found that a pEC156-derivative with a functional EcoVIII restriction-modification system was mobilized in enterobacteria at a frequency lower than a plasmid lacking this system. In addition, we found that bacteria that possess the EcoVIII restriction-modification system can efficiently release plasmid content to the environment. We have shown that E. coli cells can be naturally transformed with pEC156-derivatives, however, with low efficiency. The transformation protocol employed neither involved chemical agents (e.g. CaCl2) nor temperature shift which could induce plasmid DNA uptake.}, }
@article {pmid26848752, year = {2016}, author = {Han, G and Xu, J and Liu, Q and Li, C and Xu, H and Lu, Z}, title = {Genome of Cnaphalocrocis medinalis Granulovirus, the First Crambidae-Infecting Betabaculovirus Isolated from Rice Leaffolder to Sequenced.}, journal = {PloS one}, volume = {11}, number = {2}, pages = {e0147882}, pmid = {26848752}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Animals ; Baculoviridae/classification/genetics ; Base Sequence ; Conserved Sequence ; Gene Order ; Genes, Viral ; *Genome, Viral ; Genomics/methods ; Granulovirus/classification/*genetics/isolation &amp; purification ; Molecular Sequence Data ; Moths/*virology ; Nucleic Acid Conformation ; Open Reading Frames ; Phylogeny ; Sequence Alignment ; Tandem Repeat Sequences ; Transcription, Genetic ; }, abstract = {Cnaphalocrocis medinalis is a major pest of rice in South and South-East Asia. Insecticides are the major means farmers use for management. A naturally occurring baculovirus, C. medinalis granulovirus (CnmeGV), has been isolated from the larvae and this has the potential for use as microbial agent. Here, we described the complete genome sequence of CnmeGV and compared it to other baculovirus genomes. The genome of CnmeGV is 112,060 base pairs in length, has a G+C content of 35.2%. It contains 133 putative open reading frames (ORFs) of at least 150 nucleotides. A hundred and one (101) of these ORFs are homologous to other baculovirus genes including 37 baculovirus core genes. Thirty-two (32) ORFs are unique to CnmeGV with no homologues detected in the GeneBank and 53 tandem repeats (TRs) with sequence length from 25 to 551 nt intersperse throughout the genome of CnmeGV. Six (6) homologous regions (hrs) were identified interspersed throughout the genome. Hr2 contains 11 imperfect palindromes and a high content of AT sequence (about 73%). The unique ORF28 contains a coiled-coil region and a zinc finger-like domain of 4-50 residues specialized by two C2C2 zinc finger motifs that putatively bound two atoms of zinc. ORF21 encoding a chit-1 protein suggesting a horizontal gene transfer from alphabaculovirus. The putative protein presents two carbohydrate-binding module family 14 (CBM_14) domains rather than other homologues detected from betabaculovirus that only contains one chit-binding region. Gene synteny maps showed the colinearity of sequenced betabaculovirus. Phylogenetic analysis indicated that CnmeGV grouped in the betabaculovirus, with a close relation to AdorGV. The cladogram obtained in this work grouped the 17 complete GV genomes in one monophyletic clade. CnmeGV represents a new crambidae host-isolated virus species from the genus Betabaculovirus and is most closely relative of AdorGV. The analyses and information derived from this study will provide a better understanding of the pathological symptoms caused by this virus and its potential use as a microbial pesticide.}, }
@article {pmid26847793, year = {2016}, author = {García-Romero, I and Pérez-Pulido, AJ and González-Flores, YE and Reyes-Ramírez, F and Santero, E and Floriano, B}, title = {Genomic analysis of the nitrate-respiring Sphingopyxis granuli (formerly Sphingomonas macrogoltabida) strain TFA.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {93}, pmid = {26847793}, issn = {1471-2164}, mesh = {Bacteriophages/physiology ; Chromosomes, Bacterial ; Computational Biology ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomic Islands ; *Genomics ; High-Throughput Nucleotide Sequencing ; Nitrates/metabolism ; Phylogeny ; Proteome ; Proteomics/methods ; Secondary Metabolism ; Sequence Analysis, DNA ; Sphingomonas/*genetics/metabolism/virology ; }, abstract = {BACKGROUND: Sphingomonads are Alphaproteobacteria that belong to the Sphingomonas, Novosphingobium, Sphingopyxis or Sphingobium genera, They are physiologically diverse and broadly distributed in nature, playing important roles in oligotrophic environments and in the degradation of recalcitrant polyaromatic compounds, Sphingopyxis is a poorly studied genus of which only one representative (S. alaskensis RB2256) has been deeply characterized. In this paper we analyze the genomic features of S. granuli strain TFA (formerly Sphingomonas macrogoltabida) in comparison with the available Sphingopyxis sequenced genomes, to describe common characteristics of this genus and to highlight unique characteristics of strain TFA.<br><br>RESULTS: The TFA genome has been assembled in a single circular chromosome of 4.7 Mb. Genomic sequence analysis and proteome comparison re-assigned the TFA strain to the Sphingopyxis genus and the S. granuli species. Some regions of the TFA genome show high similarity (ca. 100%) to other bacteria and several genomic islands have been detected. Pathways for aromatic compound degradation have been predicted but no growth of TFA has been detected using these as carbon or nitrogen sources. Genes for nitrate respiration have been identified as TFA exclusive. Experimental data on anaerobic growth of TFA using nitrate as a terminal electron acceptor are also provided.<br><br>CONCLUSIONS: Sphingopyxis representatives form a compact phylogenetic group (with the exception of S. baekryungensis DSM 16222) that share several characteristics, such as being naturally resistant to streptomycin, having only one ribosomal operon, a low number of prophages and CRISPR sequences, absence of selenoproteins and presence of ectoin and other biosynthesis pathways for secondary metabolites. Moreover, the TFA genome organization shows evidence of the presence of putative integrative and conjugative elements (ICE) responsible for the acquisition of several characteristics by horizontal transfer mechanisms. Sphingopyxis representatives have been described as strict aerobes but anaerobic growth using nitrate as a terminal electron acceptor might confer an environmental advantage to the first S. granuli strain characterized at genomic level.}, }
@article {pmid26847652, year = {2016}, author = {Ardisson-Araújo, DM and Pereira, BT and Melo, FL and Ribeiro, BM and Báo, SN and de A Zanotto, PM and Moscardi, F and Kitajima, EW and Sosa-Gomez, DR and Wolff, JL}, title = {A betabaculovirus encoding a gp64 homolog.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {94}, pmid = {26847652}, issn = {1471-2164}, mesh = {Baculoviridae/classification/*genetics/isolation &amp; purification/ultrastructure ; Base Composition ; Base Sequence ; Brazil ; Gene Order ; Genome, Viral ; Genomics ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Saccharum/virology ; Viral Envelope Proteins/chemistry/*genetics ; Viral Proteins/genetics ; }, abstract = {BACKGROUND: A betabaculovirus (DisaGV) was isolated from Diatraea saccharalis (Lepidoptera: Crambidae), one of the most important insect pests of the sugarcane and other monocot cultures in Brazil.<br><br>RESULTS: The complete genome sequence of DisaGV was determined using the 454-pyrosequencing method. The genome was 98,392 bp long, which makes it the smallest lepidopteran-infecting baculovirus sequenced to date. It had a G + C content of 29.7% encoding 125 putative open reading frames (ORF). All the 37 baculovirus core genes and a set of 19 betabaculovirus-specific genes were found. A group of 13 putative genes was not found in any other baculovirus genome sequenced so far. A phylogenetic analysis indicated that DisaGV is a member of Betabaculovirus genus and that it is a sister group to a cluster formed by ChocGV, ErelGV, PiraGV isolates, ClanGV, CaLGV, CpGV, CrleGV, AdorGV, PhopGV and EpapGV. Surprisingly, we found in the DisaGV genome a G protein-coupled receptor related to lepidopteran and other insect virus genes and a gp64 homolog, which is likely a product of horizontal gene transfer from Group 1 alphabaculoviruses.<br><br>CONCLUSION: DisaGV represents a distinct lineage of the genus Betabaculovirus. It is closely related to the CpGV-related group and presents the smallest genome in size so far. Remarkably, we found a homolog of gp64, which was reported solely in group 1 alphabaculovirus genomes so far.}, }
@article {pmid26847371, year = {2016}, author = {Mengual-Chuliá, B and Bedhomme, S and Lafforgue, G and Elena, SF and Bravo, IG}, title = {Assessing parallel gene histories in viral genomes.}, journal = {BMC evolutionary biology}, volume = {16}, number = {}, pages = {32}, pmid = {26847371}, issn = {1471-2148}, mesh = {Cluster Analysis ; *Evolution, Molecular ; *Genes, Viral ; *Genome, Viral ; Papillomaviridae/*genetics ; *Phylogeny ; Potyviridae/*genetics ; Recombination, Genetic ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The increasing abundance of sequence data has exacerbated a long known problem: gene trees and species trees for the same terminal taxa are often incongruent. Indeed, genes within a genome have not all followed the same evolutionary path due to events such as incomplete lineage sorting, horizontal gene transfer, gene duplication and deletion, or recombination. Considering conflicts between gene trees as an obstacle, numerous methods have been developed to deal with these incongruences and to reconstruct consensus evolutionary histories of species despite the heterogeneity in the history of their genes. However, inconsistencies can also be seen as a source of information about the specific evolutionary processes that have shaped genomes.<br><br>RESULTS: The goal of the approach here proposed is to exploit this conflicting information: we have compiled eleven variables describing phylogenetic relationships and evolutionary pressures and submitted them to dimensionality reduction techniques to identify genes with similar evolutionary histories. To illustrate the applicability of the method, we have chosen two viral datasets, namely papillomaviruses and Turnip mosaic virus (TuMV) isolates, largely dissimilar in genome, evolutionary distance and biology. Our method pinpoints viral genes with common evolutionary patterns. In the case of papillomaviruses, gene clusters match well our knowledge on viral biology and life cycle, illustrating the potential of our approach. For the less known TuMV, our results trigger new hypotheses about viral evolution and gene interaction.<br><br>CONCLUSIONS: The approach here presented allows turning phylogenetic inconsistencies into evolutionary information, detecting gene assemblies with similar histories, and could be a powerful tool for comparative pathogenomics.}, }
@article {pmid26843557, year = {2016}, author = {Cairns, J and Jalasvuori, M and Ojala, V and Brockhurst, M and Hiltunen, T}, title = {Conjugation is necessary for a bacterial plasmid to survive under protozoan predation.}, journal = {Biology letters}, volume = {12}, number = {2}, pages = {20150953}, pmid = {26843557}, issn = {1744-957X}, mesh = {*Conjugation, Genetic ; *Food Chain ; Plasmids/*genetics ; Serratia marcescens/*genetics ; Tetrahymena thermophila/*physiology ; }, abstract = {Horizontal gene transfer by conjugative plasmids plays a critical role in the evolution of antibiotic resistance. Interactions between bacteria and other organisms can affect the persistence and spread of conjugative plasmids. Here we show that protozoan predation increased the persistence and spread of the antibiotic resistance plasmid RP4 in populations of the opportunist bacterial pathogen Serratia marcescens. A conjugation-defective mutant plasmid was unable to survive under predation, suggesting that conjugative transfer is required for plasmid persistence under the realistic condition of predation. These results indicate that multi-trophic interactions can affect the maintenance of conjugative plasmids with implications for bacterial evolution and the spread of antibiotic resistance genes.}, }
@article {pmid26840222, year = {2017}, author = {Cemazar, M and Ambrozic Avgustin, J and Pavlin, D and Sersa, G and Poli, A and Krhac Levacic, A and Tesic, N and Lampreht Tratar, U and Rak, M and Tozon, N}, title = {Efficacy and safety of electrochemotherapy combined with peritumoral IL-12 gene electrotransfer of canine mast cell tumours.}, journal = {Veterinary and comparative oncology}, volume = {15}, number = {2}, pages = {641-654}, doi = {10.1111/vco.12208}, pmid = {26840222}, issn = {1476-5829}, mesh = {Animals ; Combined Modality Therapy/veterinary ; Dog Diseases/*drug therapy ; Dogs ; Electrochemotherapy/adverse effects/methods/*veterinary ; Female ; Gene Transfer Techniques/adverse effects/*veterinary ; Interleukin-12/*genetics ; Male ; Mastocytosis, Cutaneous/drug therapy/*veterinary ; }, abstract = {Electrochemotherapy combined with peritumoral interleukin-12 (IL-12) gene electrotransfer was used for treatment of mast cell tumours in 18 client-owned dogs. Local tumour control, recurrence rate, as well as safety of combined therapy were evaluated. One month after the therapy, no side effects were recorded and good local tumour control was observed with high complete responses rate which even increased during the observation period to 72%. IL-12 gene electrotransfer resulted in 78% of patients with detectable serum IFN-γ and/or IL-12 levels. In the treated tumours vascular changes as well as minimal T-lymphocytes infiltration was observed. After 1 week, the plasmid DNA was not detected intra- or peritumorally and no horizontal gene transfer was observed. In summary, our study demonstrates high antitumour efficacy of electrochemotherapy combined with IL-12 electrotransfer, which also prevented recurrences or distant metastases, as well as its safety and feasibility in treatment of canine mast cell tumours.}, }
@article {pmid26836814, year = {2016}, author = {Benoit, JB and Adelman, ZN and Reinhardt, K and Dolan, A and Poelchau, M and Jennings, EC and Szuter, EM and Hagan, RW and Gujar, H and Shukla, JN and Zhu, F and Mohan, M and Nelson, DR and Rosendale, AJ and Derst, C and Resnik, V and Wernig, S and Menegazzi, P and Wegener, C and Peschel, N and Hendershot, JM and Blenau, W and Predel, R and Johnston, PR and Ioannidis, P and Waterhouse, RM and Nauen, R and Schorn, C and Ott, MC and Maiwald, F and Johnston, JS and Gondhalekar, AD and Scharf, ME and Peterson, BF and Raje, KR and Hottel, BA and Armisén, D and Crumière, AJJ and Refki, PN and Santos, ME and Sghaier, E and Viala, S and Khila, A and Ahn, SJ and Childers, C and Lee, CY and Lin, H and Hughes, DST and Duncan, EJ and Murali, SC and Qu, J and Dugan, S and Lee, SL and Chao, H and Dinh, H and Han, Y and Doddapaneni, H and Worley, KC and Muzny, DM and Wheeler, D and Panfilio, KA and Vargas Jentzsch, IM and Vargo, EL and Booth, W and Friedrich, M and Weirauch, MT and Anderson, MAE and Jones, JW and Mittapalli, O and Zhao, C and Zhou, JJ and Evans, JD and Attardo, GM and Robertson, HM and Zdobnov, EM and Ribeiro, JMC and Gibbs, RA and Werren, JH and Palli, SR and Schal, C and Richards, S}, title = {Unique features of a global human ectoparasite identified through sequencing of the bed bug genome.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {10165}, pmid = {26836814}, issn = {2041-1723}, support = {GM070559-9/GM/NIGMS NIH HHS/United States ; R01 GM070559/GM/NIGMS NIH HHS/United States ; U54 HG003273/HG/NHGRI NIH HHS/United States ; 260986/ERC_/European Research Council/International ; UL1 TR001427/TR/NCATS NIH HHS/United States ; 616346/ERC_/European Research Council/International ; }, mesh = {Animals ; Bedbugs/*genetics ; *Ectoparasitic Infestations ; *Feeding Behavior ; Gene Transfer, Horizontal/*genetics ; Genome ; Host-Parasite Interactions/*genetics ; Humans ; Insecticide Resistance/*genetics ; *Insecticides ; Sequence Analysis, DNA ; }, abstract = {The bed bug, Cimex lectularius, has re-established itself as a ubiquitous human ectoparasite throughout much of the world during the past two decades. This global resurgence is likely linked to increased international travel and commerce in addition to widespread insecticide resistance. Analyses of the C. lectularius sequenced genome (650 Mb) and 14,220 predicted protein-coding genes provide a comprehensive representation of genes that are linked to traumatic insemination, a reduced chemosensory repertoire of genes related to obligate hematophagy, host-symbiont interactions, and several mechanisms of insecticide resistance. In addition, we document the presence of multiple putative lateral gene transfer events. Genome sequencing and annotation establish a solid foundation for future research on mechanisms of insecticide resistance, human-bed bug and symbiont-bed bug associations, and unique features of bed bug biology that contribute to the unprecedented success of C. lectularius as a human ectoparasite.}, }
@article {pmid26834729, year = {2016}, author = {Sitaraman, R}, title = {The Role of DNA Restriction-Modification Systems in the Biology of Bacillus anthracis.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {11}, pmid = {26834729}, issn = {1664-302X}, abstract = {Restriction-modification (R-M) systems are widespread among prokaryotes and, depending on their type, may be viewed as selfish genetic elements that persist as toxin-antitoxin modules, or as cellular defense systems against phage infection that confer a selective advantage to the host bacterium. Studies in the last decade have made it amply clear that these two options do not exhaust the list of possible biological roles for R-M systems. Their presence in a cell may also have a bearing on other processes such as horizontal gene transfer and gene regulation. From genome sequencing and experimental data, we know that Bacillus anthracis encodes at least three methylation-dependent (typeIV) restriction endonucleases (RE), and an orphan DNA methyltransferase. In this article, we first present an outline of our current knowledge of R-M systems in B. anthracis. Based on available DNA sequence data, and on our current understanding of the functions of similar genes in other systems, we conclude with hypotheses on the possible roles of the three REs and the orphan DNA methyltransferase.}, }
@article {pmid26834726, year = {2016}, author = {Gong, C and Zhang, W and Zhou, X and Wang, H and Sun, G and Xiao, J and Pan, Y and Yan, S and Wang, Y}, title = {Novel Virophages Discovered in a Freshwater Lake in China.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {5}, pmid = {26834726}, issn = {1664-302X}, abstract = {Virophages are small double-stranded DNA viruses that are parasites of giant DNA viruses that infect unicellular eukaryotes. Here we identify a novel group of virophages, named Dishui Lake virophages (DSLVs) that were discovered in Dishui Lake (DSL): an artificial freshwater lake in Shanghai, China. Based on PCR and metagenomic analysis, the complete genome of DSLV1 was found to be circular and 28,788 base pairs in length, with a G+C content 43.2%, and 28 predicted open reading frames (ORFs). Fifteen of the DSLV1 ORFs have sequence similarity to known virophages. Two DSLV1 ORFs exhibited sequence similarity to that of prasinoviruses (Phycodnaviridae) and chloroviruses (Phycodnaviridae), respectively, suggesting horizontal gene transfer occurred between these large algal DNA viruses and DSLV1. 46 other virophages-related contigs were also obtained, including six homologous major capsid protein (MCP) gene. Phylogenetic analysis of these MCPs showed that DSLVs are closely related to OLV (Organic Lake virophage) and YSLVs (Yellowstone Lake virophages), especially to YSLV3, except for YSLV7. These results indicate that freshwater ecotopes are the hotbed for discovering novel virophages as well as understanding their diversity and properties.}, }
@article {pmid26833415, year = {2016}, author = {Johnson, CM and Grossman, AD}, title = {The Composition of the Cell Envelope Affects Conjugation in Bacillus subtilis.}, journal = {Journal of bacteriology}, volume = {198}, number = {8}, pages = {1241-1249}, pmid = {26833415}, issn = {1098-5530}, support = {GM050895/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacillus subtilis/*physiology ; Bacterial Proteins/genetics/metabolism ; Cell Membrane/*physiology ; Conjugation, Genetic/*physiology ; Gene Expression Regulation, Bacterial/physiology ; Mutation ; Phospholipids/biosynthesis ; }, abstract = {UNLABELLED: Conjugation in bacteria is the contact-dependent transfer of DNA from one cell to another via donor-encoded conjugation machinery. It is a major type of horizontal gene transfer between bacteria. Conjugation of the integrative and conjugative element ICEBs1 into Bacillus subtilis is affected by the composition of phospholipids in the cell membranes of the donor and recipient. We found that reduction (or elimination) of lysyl-phosphatidylglycerol caused by loss of mpr F caused a decrease in conjugation efficiency. Conversely, alterations that caused an increase in lysyl-phosphatidylglycerol, including loss of ugtP or overproduction of mprF, caused an increase in conjugation efficiency. In addition, we found that mutations that alter production of other phospholipids, e.g., loss of clsA and yfnI, also affected conjugation, apparently without substantively altering levels of lysyl-phosphatidylglycerol, indicating that there are multiple pathways by which changes to the cell envelope affect conjugation. We found that the contribution of mprF to conjugation was affected by the chemical environment. Wild-type cells were generally more responsive to addition of anions that enhanced conjugation, whereas mprF mutant cells were more sensitive to combinations of anions that inhibited conjugation at pH 7. Our results indicate that mprF and lysyl-phosphatidylglycerol allow cells to maintain relatively consistent conjugation efficiencies under a variety of ionic conditions.<br><br>IMPORTANCE: Horizontal gene transfer is a driving force in microbial evolution, enabling cells that receive DNA to acquire new genes and phenotypes. Conjugation, the contact-dependent transfer of DNA from a donor to a recipient by a donor-encoded secretion machine, is a prevalent type of horizontal gene transfer. Although critically important, it is not well understood how the recipient influences the success of conjugation. We found that the composition of phospholipids in the membranes of donors and recipients influences the success of transfer of the integrative and conjugative element ICEBs1 in Bacillus subtilis Specifically, the presence of lysyl-phosphatidylglycerol enables relatively constant conjugation efficiencies in a range of diverse chemical environments.}, }
@article {pmid26833181, year = {2016}, author = {Xu, Y and Zhu, Y and Wang, Y and Chang, YF and Zhang, Y and Jiang, X and Zhuang, X and Zhu, Y and Zhang, J and Zeng, L and Yang, M and Li, S and Wang, S and Ye, Q and Xin, X and Zhao, G and Zheng, H and Guo, X and Wang, J}, title = {Whole genome sequencing revealed host adaptation-focused genomic plasticity of pathogenic Leptospira.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {20020}, pmid = {26833181}, issn = {2045-2322}, mesh = {Adaptation, Physiological/*physiology ; Animals ; Genome, Bacterial/*physiology ; High-Throughput Nucleotide Sequencing ; Humans ; Leptospira/*genetics ; Leptospirosis/genetics ; Virulence Factors/*genetics ; }, abstract = {Leptospirosis, caused by pathogenic Leptospira spp., has recently been recognized as an emerging infectious disease worldwide. Despite its severity and global importance, knowledge about the molecular pathogenesis and virulence evolution of Leptospira spp. remains limited. Here we sequenced and analyzed 102 isolates representing global sources. A high genomic variability were observed among different Leptospira species, which was attributed to massive gene gain and loss events allowing for adaptation to specific niche conditions and changing host environments. Horizontal gene transfer and gene duplication allowed the stepwise acquisition of virulence factors in pathogenic Leptospira evolved from a recent common ancestor. More importantly, the abundant expansion of specific virulence-related protein families, such as metalloproteases-associated paralogs, were exclusively identified in pathogenic species, reflecting the importance of these protein families in the pathogenesis of leptospirosis. Our observations also indicated that positive selection played a crucial role on this bacteria adaptation to hosts. These novel findings may lead to greater understanding of the global diversity and virulence evolution of Leptospira spp.}, }
@article {pmid26832755, year = {2016}, author = {Jost, C and Bidet, P and Carrère, T and Mariani-Kurkdjian, P and Bonacorsi, S}, title = {Susceptibility of enterohaemorrhagic Escherichia coli to azithromycin in France and analysis of resistance mechanisms.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {71}, number = {5}, pages = {1183-1187}, doi = {10.1093/jac/dkv477}, pmid = {26832755}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/*pharmacology ; Azithromycin/*pharmacology ; Blotting, Southern ; Conjugation, Genetic ; Disk Diffusion Antimicrobial Tests ; *Drug Resistance, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Enterohemorrhagic Escherichia coli/*drug effects/isolation &amp; purification ; Escherichia coli Infections/*microbiology ; France ; Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; Plasmids/analysis ; Polymerase Chain Reaction ; }, abstract = {OBJECTIVES: Antibiotic therapy is not recommended during enterohaemorrhagic Escherichia coli (EHEC) infection. However, the potential benefit of azithromycin has recently been described. This study was conducted to evaluate the macrolide susceptibility of EHEC isolates from France and to analyse the mechanisms of resistance to azithromycin in EHEC.<br><br>METHODS: Strains from patients with EHEC infections were collected by the associated French National Reference Laboratory for E. coli from 2004 to 2014. Antimicrobial susceptibility testing was performed by disc diffusion and Etest methods. For strains presenting macrolide resistance, antibiotic resistance genes were searched for by PCR. Genetic transfer was performed by conjugation and plasmid analysis was done by Southern-blot hybridization after PFGE.<br><br>RESULTS: We tested 508 isolates of EHEC. Azithromycin MICs ranged between 0.25 and 16 mg/L (median&#x200a;=&#x200a;3 mg/L), except for two atypical strains, 34396 and 36493, for which MICs were >256 mg/L. Plasmid transferability of macrolide resistance was demonstrated. Strain 34396, of serotype O106:H18, harboured two macrolide resistance genes [mph(A) and erm(B)] and two other antimicrobial resistance genes (blaDHA-1 for &#x3b2;-lactam resistance and qnrB4 for quinolone resistance). mph(A), blaDHA-1 and qnrB4 were localized on the same plasmid. Strain 36493 belonging to the highly virulent O26:H11 EHEC clonal group harboured a plasmid containing mph(A).<br><br>CONCLUSIONS: For the first time we describe plasmid-borne macrolide resistance genes in EHEC strains. Dissemination of such plasmids may threaten the potential benefit of azithromycin during the management of patients infected or colonized with EHEC. Determination of azithromycin MICs should be considered prior to its therapeutic use and 16 mg/L may be used as the epidemiological cut-off value.}, }
@article {pmid26832203, year = {2016}, author = {Karkman, A and Johnson, TA and Lyra, C and Stedtfeld, RD and Tamminen, M and Tiedje, JM and Virta, M}, title = {High-throughput quantification of antibiotic resistance genes from an urban wastewater treatment plant.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {3}, pages = {}, doi = {10.1093/femsec/fiw014}, pmid = {26832203}, issn = {1574-6941}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/*drug effects/genetics/*isolation &amp; purification ; Bacterial Proteins/*genetics ; Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Integrons ; Sewage/microbiology ; Wastewater/*microbiology ; Water Purification/*instrumentation ; }, abstract = {Antibiotic resistance among bacteria is a growing problem worldwide, and wastewater treatment plants have been considered as one of the major contributors to the dissemination of antibiotic resistance to the environment. There is a lack of comprehensive quantitative molecular data on extensive numbers of antibiotic resistance genes (ARGs) in different seasons with a sampling strategy that would cover both incoming and outgoing water together with the excess sludge that is removed from the process. In order to fill that gap we present a highly parallel quantitative analysis of ARGs and horizontal gene transfer potential over four seasons at an urban wastewater treatment plant using a high-throughput qPCR array. All analysed transposases and two-thirds of primer sets targeting ARGs were detected in the wastewater. The relative abundance of most of the genes was highest in influent and lower in effluent water and sludge. The resistance profiles of the samples cluster by sample location with a shift from raw influent through the final effluents and dried sludge to the sediments. Wastewater discharge enriched only a few genes, namely Tn25 type transposase gene and clinical class 1 integrons, in the sediment near the discharge pipe, but those enriched genes may indicate a potential for horizontal gene transfer.}, }
@article {pmid26831115, year = {2016}, author = {Rolando, M and Escoll, P and Nora, T and Botti, J and Boitez, V and Bedia, C and Daniels, C and Abraham, G and Stogios, PJ and Skarina, T and Christophe, C and Dervins-Ravault, D and Cazalet, C and Hilbi, H and Rupasinghe, TW and Tull, D and McConville, MJ and Ong, SY and Hartland, EL and Codogno, P and Levade, T and Naderer, T and Savchenko, A and Buchrieser, C}, title = {Legionella pneumophila S1P-lyase targets host sphingolipid metabolism and restrains autophagy.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {7}, pages = {1901-1906}, pmid = {26831115}, issn = {1091-6490}, support = {U54 GM074942/GM/NIGMS NIH HHS/United States ; U54 GM094585/GM/NIGMS NIH HHS/United States ; GM074942/GM/NIGMS NIH HHS/United States ; GM094585/GM/NIGMS NIH HHS/United States ; }, mesh = {Aldehyde-Lyases/chemistry/*metabolism ; Animals ; *Autophagy ; Catalytic Domain ; Crystallography, X-Ray ; Legionella pneumophila/*enzymology ; Legionnaires' Disease/immunology ; Mice ; Protein Conformation ; Sphingolipids/*metabolism ; }, abstract = {Autophagy is an essential component of innate immunity, enabling the detection and elimination of intracellular pathogens. Legionella pneumophila, an intracellular pathogen that can cause a severe pneumonia in humans, is able to modulate autophagy through the action of effector proteins that are translocated into the host cell by the pathogen's Dot/Icm type IV secretion system. Many of these effectors share structural and sequence similarity with eukaryotic proteins. Indeed, phylogenetic analyses have indicated their acquisition by horizontal gene transfer from a eukaryotic host. Here we report that L. pneumophila translocates the effector protein sphingosine-1 phosphate lyase (LpSpl) to target the host sphingosine biosynthesis and to curtail autophagy. Our structural characterization of LpSpl and its comparison with human SPL reveals high structural conservation, thus supporting prior phylogenetic analysis. We show that LpSpl possesses S1P lyase activity that was abrogated by mutation of the catalytic site residues. L. pneumophila triggers the reduction of several sphingolipids critical for macrophage function in an LpSpl-dependent and -independent manner. LpSpl activity alone was sufficient to prevent an increase in sphingosine levels in infected host cells and to inhibit autophagy during macrophage infection. LpSpl was required for efficient infection of A/J mice, highlighting an important virulence role for this effector. Thus, we have uncovered a previously unidentified mechanism used by intracellular pathogens to inhibit autophagy, namely the disruption of host sphingolipid biosynthesis.}, }
@article {pmid26830052, year = {2016}, author = {Agyekum, A and Fajardo-Lubián, A and Ansong, D and Partridge, SR and Agbenyega, T and Iredell, JR}, title = {blaCTX-M-15 carried by IncF-type plasmids is the dominant ESBL gene in Escherichia coli and Klebsiella pneumoniae at a hospital in Ghana.}, journal = {Diagnostic microbiology and infectious disease}, volume = {84}, number = {4}, pages = {328-333}, doi = {10.1016/j.diagmicrobio.2015.12.010}, pmid = {26830052}, issn = {1879-0070}, mesh = {Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/classification/*enzymology/genetics/isolation &amp; purification ; Escherichia coli Infections/*microbiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Variation ; Ghana ; Hospitals ; Humans ; Klebsiella Infections/*microbiology ; Klebsiella pneumoniae/classification/*enzymology/genetics/isolation &amp; purification ; Molecular Typing ; Plasmids/classification/*isolation &amp; purification ; Sequence Analysis, DNA ; beta-Lactamases/*genetics ; }, abstract = {Escherichia coli and Klebsiella pneumoniae producing extended-spectrum β-lactamases (ESBLs) are among the most multidrug-resistant pathogens in hospitals and are spreading worldwide. Horizontal gene transfer and spread of high-risk clones are involved in ESBL dissemination. Investigation of the resistance phenotypes of 101 consecutive clinical E. coli (n=58) and K. pneumoniae (n=43) isolated at the Komfo Anokye Teaching Hospital in Ghana over 3 months revealed 63 (62%) with an ESBL phenotype. All 63 had a blaCTX-M gene, and sequence analysis showed that 62 of these were blaCTX-M-15. blaCTX-M-15 was linked to ISEcp1 and orf477Δ in all isolates, and most isolates also carried blaTEM, aac(3)-II, aacA4cr, and/or blaOXA-30 genes on IncF plasmids. XbaI/pulsed-field electrophoresis showed heterogeneity among isolates of both species, suggesting that blaCTX-M-15 dissemination is caused by horizontal gene transfer rather than clonal spread of these species in Ghana.}, }
@article {pmid26829539, year = {2016}, author = {Yu, T and Zhang, J and Jiang, X and Wu, J and Dai, Z and Wu, Z and Liang, Y and Wang, X}, title = {Characterization and horizontal transfer of class 1 integrons in Escherichia coli isolates from cooked meat products.}, journal = {Journal of infection in developing countries}, volume = {10}, number = {1}, pages = {68-73}, doi = {10.3855/jidc.6858}, pmid = {26829539}, issn = {1972-2680}, mesh = {China ; Conjugation, Genetic ; Escherichia coli/*genetics/*isolation &amp; purification ; *Gene Transfer, Horizontal ; Humans ; *Integrons ; Meat Products/*microbiology ; Transformation, Bacterial ; }, abstract = {INTRODUCTION: Escherichia coli is a commensal bacterium in humans, animals, and the environment that is one of the microorganisms commonly resistant to antimicrobials. Cooked meat products, which are popular in China, are easily contaminated by E. coli during processing and storage.<br><br>METHODOLOGY: In this study, a total of 75 E. coli isolates from cooked meat products in Henan province, China, were assayed for the presence of and horizontal transfer of class 1 integrons.<br><br>RESULTS: Class 1 integrons were detected in 11 (14.7%) of these isolates, and contained four groups of resistance gene cassettes, including dfrA17-aadA5, dfrA1-aadA1, dfrA12-orfF-aadA2, and an uncommon array of aacA4-catB8-aadA1. The transfer frequency of selected integron-positve donors ranged from 10(-6) to 10(-4) transconjugants per recipient cell, and the integron-containing DNA from the donors could be transferred to E. coli J53Azr with the transformation frequency of 10(-7) to 10(-5).<br><br>CONCLUSIONS: Class 1 integrons could be transferred to recipient E. coli J53 by conjugation and natural transformation. These findings suggest the role of commensal E. coli isolates from cooked meats as an important reservoir for integrons and the possible transfer of antimicrobial resistance genes to humans via the food chain.}, }
@article {pmid26829536, year = {2016}, author = {Vignoli, R and García-Fulgueiras, V and Cordeiro, NF and Bado, I and Seija, V and Aguerrebere, P and Laguna, G and Araújo, L and Bazet, C and Gutkind, G and Chabalgoity, J}, title = {Extended-spectrum β-lactamases, transferable quinolone resistance, and virulotyping in extra-intestinal E. coli in Uruguay.}, journal = {Journal of infection in developing countries}, volume = {10}, number = {1}, pages = {43-52}, doi = {10.3855/jidc.6918}, pmid = {26829536}, issn = {1972-2680}, mesh = {Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/classification/*enzymology/genetics/isolation &amp; purification ; Escherichia coli Infections/*microbiology ; Gene Transfer, Horizontal ; *Genotype ; Humans ; Multilocus Sequence Typing ; Plasmids/analysis ; Polymerase Chain Reaction ; Quinolones/*pharmacology ; Uruguay ; Virulence Factors/*genetics ; beta-Lactamases/*genetics ; }, abstract = {INTRODUCTION: To characterize extended-spectrum β-lactamases (ESBLs) and plasmid-mediated quinolone resistance (PMQR) genes in Escherichia coli isolates obtained from extra-intestinal samples in three Uruguayan hospitals.<br><br>METHODOLOGY: Fifty-five ESBL-producing E. coli isolates were studied. Virulence genes, ESBLs, and PMQR genes were detected by polymerase chain reaction. ESBL-producing isolates were compared by pulsed-field gel electrophoresis. Multi-locus sequence typing was also performed on 13 selected isolates.<br><br>RESULTS: Thirty-seven isolates harbored blaCTX-M-15 (67.3%), eight blaCTX-M-2 (14.6%), five blaCTX-M-14 (9.1%), three carried both blaCTX-M-2 and blaCTX-M-14, one blaCTX-M-9, and one blaCTX-M-8. Among the CTX-M-15 producers, 92% belonged to sequence types ST131 and ST405, and carried aac(6')Ib-cr as well. Isolates harboring blaCTX-M-2, blaCTX-M-14, blaCTX-M-9, or blaCTX-M-8 were found to be genetically unrelated.<br><br>CONCLUSIONS: The successful dissemination of CTX-M-15-producing E.coli isolates seems to be linked to the spreading of high-risk clones and horizontal gene transfer. A trade-off between carrying more antibiotic resistance and less virulence-related genes could partially account for the evolutionary advantages featured by successful clones.}, }
@article {pmid26829124, year = {2016}, author = {Gilbert, C and Peccoud, J and Chateigner, A and Moumen, B and Cordaux, R and Herniou, EA}, title = {Continuous Influx of Genetic Material from Host to Virus Populations.}, journal = {PLoS genetics}, volume = {12}, number = {2}, pages = {e1005838}, pmid = {26829124}, issn = {1553-7404}, mesh = {Animals ; Baculoviridae/*genetics ; Base Sequence ; DNA Transposable Elements/genetics ; Gene Transfer, Horizontal ; Genome, Viral ; Host-Pathogen Interactions/*genetics ; Inheritance Patterns/genetics ; Moths/*genetics/*virology ; Nucleotide Motifs/genetics ; Sequence Analysis, DNA ; }, abstract = {Many genes of large double-stranded DNA viruses have a cellular origin, suggesting that host-to-virus horizontal transfer (HT) of DNA is recurrent. Yet, the frequency of these transfers has never been assessed in viral populations. Here we used ultra-deep DNA sequencing of 21 baculovirus populations extracted from two moth species to show that a large diversity of moth DNA sequences (n = 86) can integrate into viral genomes during the course of a viral infection. The majority of the 86 different moth DNA sequences are transposable elements (TEs, n = 69) belonging to 10 superfamilies of DNA transposons and three superfamilies of retrotransposons. The remaining 17 sequences are moth sequences of unknown nature. In addition to bona fide DNA transposition, we uncover microhomology-mediated recombination as a mechanism explaining integration of moth sequences into viral genomes. Many sequences integrated multiple times at multiple positions along the viral genome. We detected a total of 27,504 insertions of moth sequences in the 21 viral populations and we calculate that on average, 4.8% of viruses harbor at least one moth sequence in these populations. Despite this substantial proportion, no insertion of moth DNA was maintained in any viral population after 10 successive infection cycles. Hence, there is a constant turnover of host DNA inserted into viral genomes each time the virus infects a moth. Finally, we found that at least 21 of the moth TEs integrated into viral genomes underwent repeated horizontal transfers between various insect species, including some lepidopterans susceptible to baculoviruses. Our results identify host DNA influx as a potent source of genetic diversity in viral populations. They also support a role for baculoviruses as vectors of DNA HT between insects, and call for an evaluation of possible gene or TE spread when using viruses as biopesticides or gene delivery vectors.}, }
@article {pmid26826602, year = {2016}, author = {Pánek, T and Zadrobílková, E and Walker, G and Brown, MW and Gentekaki, E and Hroudová, M and Kang, S and Roger, AJ and Tice, AK and Vlček, &#x10c; and Čepička, I}, title = {First multigene analysis of Archamoebae (Amoebozoa: Conosa) robustly reveals its phylogeny and shows that Entamoebidae represents a deep lineage of the group.}, journal = {Molecular phylogenetics and evolution}, volume = {98}, number = {}, pages = {41-51}, doi = {10.1016/j.ympev.2016.01.011}, pmid = {26826602}, issn = {1095-9513}, mesh = {Archamoebae/*classification/*genetics/metabolism/ultrastructure ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Mitochondria/metabolism ; Multigene Family/*genetics ; Nitrogen Fixation/genetics ; *Phylogeny ; Sulfates/metabolism ; }, abstract = {Archamoebae is an understudied group of anaerobic free-living or endobiotic protists that constitutes the major anaerobic lineage of the supergroup Amoebozoa. Hitherto, the phylogeny of Archamoebae was based solely on SSU rRNA and actin genes, which did not resolve relationships among the main lineages of the group. Because of this uncertainty, several different scenarios had been proposed for the phylogeny of the Archamoebae. In this study, we present the first multigene phylogenetic analysis that includes members of Pelomyxidae, and Rhizomastixidae. The analysis clearly shows that Mastigamoebidae, Pelomyxidae and Rhizomastixidae form a clade of mostly free-living, amoeboid flagellates, here called Pelobiontida. The predominantly endobiotic and aflagellated Entamoebidae represents a separate, deep-branching lineage, Entamoebida. Therefore, two unique evolutionary events, horizontal transfer of the nitrogen fixation system from bacteria and transfer of the sulfate activation pathway to mitochondrial derivatives, predate the radiation of recent lineages of Archamoebae. The endobiotic lifestyle has arisen at least three times independently during the evolution of the group. We also present new ultrastructural data that clarifies the primary divergence among the family Mastigamoebidae which had previously been inferred from phylogenetic analyses based on SSU rDNA.}, }
@article {pmid26826232, year = {2016}, author = {Huguet-Tapia, JC and Lefebure, T and Badger, JH and Guan, D and Pettis, GS and Stanhope, MJ and Loria, R}, title = {Genome Content and Phylogenomics Reveal both Ancestral and Lateral Evolutionary Pathways in Plant-Pathogenic Streptomyces Species.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {7}, pages = {2146-2155}, pmid = {26826232}, issn = {1098-5336}, mesh = {Bacterial Proteins/genetics/metabolism ; *Evolution, Molecular ; *Genome, Bacterial ; *Phylogeny ; Plant Diseases/*genetics/*microbiology ; Plants/microbiology ; Streptomyces/classification/*genetics/metabolism ; }, abstract = {Streptomyces spp. are highly differentiated actinomycetes with large, linear chromosomes that encode an arsenal of biologically active molecules and catabolic enzymes. Members of this genus are well equipped for life in nutrient-limited environments and are common soil saprophytes. Out of the hundreds of species in the genus Streptomyces, a small group has evolved the ability to infect plants. The recent availability of Streptomyces genome sequences, including four genomes of pathogenic species, provided an opportunity to characterize the gene content specific to these pathogens and to study phylogenetic relationships among them. Genome sequencing, comparative genomics, and phylogenetic analysis enabled us to discriminate pathogenic from saprophytic Streptomyces strains; moreover, we calculated that the pathogen-specific genome contains 4,662 orthologs. Phylogenetic reconstruction suggested that Streptomyces scabies and S. ipomoeae share an ancestor but that their biosynthetic clusters encoding the required virulence factor thaxtomin have diverged. In contrast, S. turgidiscabies and S. acidiscabies, two relatively unrelated pathogens, possess highly similar thaxtomin biosynthesis clusters, which suggests that the acquisition of these genes was through lateral gene transfer.}, }
@article {pmid26826226, year = {2016}, author = {Warnes, SL and Keevil, CW}, title = {Lack of Involvement of Fenton Chemistry in Death of Methicillin-Resistant and Methicillin-Sensitive Strains of Staphylococcus aureus and Destruction of Their Genomes on Wet or Dry Copper Alloy Surfaces.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {7}, pages = {2132-2136}, pmid = {26826226}, issn = {1098-5336}, mesh = {Alloys/*pharmacology ; Anti-Bacterial Agents/*pharmacology ; Copper/*pharmacology ; Genome, Bacterial/*drug effects ; Humans ; Methicillin/pharmacology ; Methicillin Resistance ; Methicillin-Resistant Staphylococcus aureus/*drug effects/genetics/growth &amp; development ; Nickel/pharmacology ; Staphylococcal Infections/microbiology ; Staphylococcus aureus/*drug effects/genetics/growth &amp; development ; Zinc/pharmacology ; }, abstract = {The pandemic of hospital-acquired infections caused by methicillin-resistant Staphylococcus aureus (MRSA) has declined, but the evolution of strains with enhanced virulence and toxins and the increase of community-associated infections are still a threat. In previous studies, 10(7) MRSA bacteria applied as simulated droplet contamination were killed on copper and brass surfaces within 90 min. However, contamination of surfaces is often via finger tips and dries rapidly, and it may be overlooked by cleaning regimes (unlike visible droplets). In this new study, a 5-log reduction of a hardy epidemic strain of MRSA (epidemic methicillin-resistant S. aureus 16 [EMRSA-16]) was observed following 10 min of contact with copper, and a 4-log reduction was observed on copper nickel and cartridge brass alloys in 15 min. A methicillin-sensitive S. aureus (MSSA) strain from an osteomyelitis patient was killed on copper surfaces in 15 min, and 4-log and 3-log reductions occurred within 20 min of contact with copper nickel and cartridge brass, respectively. Bacterial respiration was compromised on copper surfaces, and superoxide was generated as part of the killing mechanism. In addition, destruction of genomic DNA occurs on copper and brass surfaces, allaying concerns about horizontal gene transfer and copper resistance. Incorporation of copper alloy biocidal surfaces may help to reduce the spread of this dangerous pathogen.}, }
@article {pmid26823959, year = {2016}, author = {Wang, X and Wei, L and Wang, B and Zhang, R and Liu, C and Bi, D and Chen, H and Tan, C}, title = {Complete genome sequence and characterization of avian pathogenic Escherichia coli field isolate ACN001.}, journal = {Standards in genomic sciences}, volume = {11}, number = {}, pages = {13}, pmid = {26823959}, issn = {1944-3277}, abstract = {Avian pathogenic Escherichia coli is an important etiological agent of avian colibacillosis, which manifests as respiratory, hematogenous, meningitic, and enteric infections in poultry. It is also a potential zoonotic threat to human health. The diverse genomes of APEC strains largely hinder disease prevention and control measures. In the current study, pyrosequencing was used to analyze and characterize APEC strain ACN001 (= CCTCC 2015182(T) = DSMZ 29979(T)), which was isolated from the liver of a diseased chicken in China in 2010. Strain ACN001 belongs to extraintestinal pathogenic E. coli phylogenetic group B1, and was highly virulent in chicken and mouse models. Whole genome analysis showed that it consists of six different plasmids along with a circular chromosome of 4,936,576 bp, comprising 4,794 protein-coding genes, 108 RNA genes, and 51 pseudogenes, with an average G + C content of 50.56 %. As well as 237 coding sequences, we identified 39 insertion sequences, 12 predicated genomic islands, 8 prophage-related sequences, and 2 clustered regularly interspaced short palindromic repeats regions on the chromosome, suggesting the possible occurrence of horizontal gene transfer in this strain. In addition, most of the virulence and antibiotic resistance genes were located on the plasmids, which would assist in the distribution of pathogenicity and multidrug resistance elements among E. coli populations. Together, the information provided here on APEC isolate ACN001 will assist in future study of APEC strains, and aid in the development of control measures.}, }
@article {pmid26806259, year = {2016}, author = {Courvalin, P}, title = {Why is antibiotic resistance a deadly emerging disease?.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {22}, number = {5}, pages = {405-407}, doi = {10.1016/j.cmi.2016.01.012}, pmid = {26806259}, issn = {1469-0691}, mesh = {Anti-Bacterial Agents/*pharmacology/therapeutic use ; Bacteria/*drug effects/*genetics ; Bacterial Infections/drug therapy/*microbiology ; Biological Evolution ; Communicable Diseases, Emerging/drug therapy/*microbiology ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Humans ; Selection, Genetic ; Treatment Failure ; }, abstract = {Evolution of bacteria towards resistance to antimicrobial agents, including multidrug resistance, is unavoidable because it represents a particular aspect of the general evolution of bacteria that is unstoppable. Therefore, the only means of dealing with this situation is to delay the emergence and subsequent dissemination of resistant bacteria or resistance genes. In this review, we will consider the biochemical mechanisms and the genetics that bacteria use to offset antibiotic selective pressure. The data provided are mainly, if not exclusively, taken from the work carried out in the laboratory, although there are numerous other examples in the literature.}, }
@article {pmid26806196, year = {2016}, author = {Yanagida, K and Sakuda, A and Suzuki-Minakuchi, C and Shintani, M and Matsui, K and Okada, K and Nojiri, H}, title = {Comparisons of the transferability of plasmids pCAR1, pB10, R388, and NAH7 among Pseudomonas putida at different cell densities.}, journal = {Bioscience, biotechnology, and biochemistry}, volume = {80}, number = {5}, pages = {1020-1023}, doi = {10.1080/09168451.2015.1127131}, pmid = {26806196}, issn = {1347-6947}, mesh = {Bacterial Load ; *Conjugation, Genetic ; Culture Media/chemistry ; DNA, Bacterial/*genetics/metabolism ; Gene Expression Profiling ; *Gene Transfer, Horizontal ; Plasmids/chemistry/*metabolism ; Pseudomonas putida/*genetics/metabolism ; }, abstract = {The transferability of plasmids pCAR1, pB10, R388, and NAH7 was compared using the same donor-recipient system at different cell density combinations in liquid or on a solid surface. pCAR1 was efficiently transferred in liquid, whereas the other plasmids were preferentially transferred on a solid surface. Difference of liquid or solid affected the transfer frequency especially at lower cell densities.}, }
@article {pmid26803822, year = {2016}, author = {Zhu, J and Sun, L and Ding, B and Yang, Y and Xu, X and Liu, W and Zhu, D and Yang, F and Zhang, H and Hu, F}, title = {Outbreak of NDM-1-producing Klebsiella pneumoniae ST76 and ST37 isolates in neonates.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {35}, number = {4}, pages = {611-618}, pmid = {26803822}, issn = {1435-4373}, mesh = {Child ; China/epidemiology ; Conjugation, Genetic ; Cross Infection/*epidemiology/microbiology ; *Disease Outbreaks ; Female ; Gene Transfer, Horizontal ; Genotype ; Hospitals, Pediatric ; Humans ; Infant ; Infant, Newborn ; Klebsiella Infections/*epidemiology/microbiology ; Klebsiella pneumoniae/classification/*enzymology/genetics/isolation &amp; purification ; Male ; Microbial Sensitivity Tests ; Molecular Typing ; Plasmids/analysis ; Polymerase Chain Reaction ; Retrospective Studies ; Sequence Analysis, DNA ; beta-Lactam Resistance ; beta-Lactamases/genetics/*metabolism ; }, abstract = {The purpose of this study was to investigate the epidemiological characteristics of carbapenem-resistant Klebsiella pneumoniae (CRKP) in Shanghai Children's Hospital in China. Twenty-two non-duplicate CRKP strains were collected from pediatric patients between March and June in 2014. Antimicrobial susceptibility testing was conducted by the agar dilution method. Beta-lactamases were characterized by polymerase chain reaction (PCR) and DNA sequencing. The transferability of bla NDM-1 was investigated by conjugation experiment. The plasmids bearing antibiotic resistance genes were characterized by S1 nuclease pulsed-field gel electrophoresis (S1-PFGE) and Southern hybridization. Clonal relatedness was evaluated by PFGE and multilocus sequence typing (MLST). The clinical data of patients were retrospectively reviewed. The 22 CRKP strains were resistant to most of the antimicrobial agents tested, except tigecycline and colistin. Overall, 59, 77, and 100 % of these strains were resistant to imipenem, meropenem, and ertapenem, respectively. The bla NDM-1 was positive in 77.3 % (17/22) of the CRKP strains, of which the 16 isolates from inpatients were designated as ST37 (n = 9) and ST76 (n =7) and one isolate from an outpatient belonged to ST846. The 17 bla NDM-1-positive isolates belonged to PFGE type A (n = 9), type C (n = 7), or type B (n = 1). The plasmids bearing bla NDM-1 could be transferred into recipient Escherichia coli J53 through conjugation in 88.2 % (15/17) of the strains. The hybridization results showed that the plasmids carrying the bla NDM-1 gene were approximately 50-240 kb in size. This is the first report of an outbreak caused by NDM-1-producing K. pneumoniae ST76 and ST37 among neonates.}, }
@article {pmid26803268, year = {2016}, author = {Lin, W and Li, S and Zhang, S and Yu, X}, title = {Reduction in horizontal transfer of conjugative plasmid by UV irradiation and low-level chlorination.}, journal = {Water research}, volume = {91}, number = {}, pages = {331-338}, doi = {10.1016/j.watres.2016.01.020}, pmid = {26803268}, issn = {1879-2448}, mesh = {Bacteria/drug effects/*genetics/radiation effects ; Disinfection ; Drinking Water/*microbiology ; Gene Transfer, Horizontal/*drug effects/*radiation effects ; *Halogenation ; Plasmids/drug effects/radiation effects ; *Ultraviolet Rays ; }, abstract = {The widespread presence of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) in the drinking water system facilitates their horizontal gene transfer among microbiota. In this study, the conjugative gene transfer of RP4 plasmid after disinfection including ultraviolet (UV) irradiation and low-level chlorine treatment was investigated. It was found that both UV irradiation and low-level chlorine treatment reduced the conjugative gene transfer frequency. The transfer frequency gradually decreased from 2.75 × 10(-3) to 2.44 × 10(-5) after exposure to UV doses ranging from 5 to 20 mJ/cm(2). With higher UV dose of 50 and 100 mJ/cm(2), the transfer frequency was reduced to 1.77 × 10(-6) and 2.44 × 10(-8). The RP4 plasmid transfer frequency was not significantly affected by chlorine treatment at dosages ranging from 0.05 to 0.2 mg/l, but treatment with 0.3-0.5 mg/l chlorine induced a decrease in conjugative transfer to 4.40 × 10(-5) or below the detection limit. The mechanisms underlying these phenomena were also explored, and the results demonstrated that UV irradiation and chlorine treatment (0.3 and 0.5 mg/l) significantly reduced the viability of bacteria, thereby lowering the conjugative transfer frequency. Although the lower chlorine concentrations tested (0.05-0.2 mg/l) were not sufficient to damage the cells, exposure to these concentrations may still depress the expression of a flagellar gene (FlgC), an outer membrane porin gene (ompF), and a DNA transport-related gene (TraG). Additionally, fewer pili were scattered on the bacteria after chlorine treatment. These findings are important in assessing and controlling the risk of ARG transfer and dissemination in the drinking water system.}, }
@article {pmid26802341, year = {2016}, author = {Jutkina, J and Rutgersson, C and Flach, CF and Joakim Larsson, DG}, title = {An assay for determining minimal concentrations of antibiotics that drive horizontal transfer of resistance.}, journal = {The Science of the total environment}, volume = {548-549}, number = {}, pages = {131-138}, doi = {10.1016/j.scitotenv.2016.01.044}, pmid = {26802341}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents/*pharmacology ; Biological Assay/*methods ; Drug Resistance, Microbial/*genetics ; *Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; }, abstract = {Ability to understand the factors driving horizontal transfer of antibiotic resistance from unknown, harmless bacteria to pathogens is crucial in order to tackle the growing resistance problem. However, current methods to measure effects of stressors on horizontal gene transfer have limitations and often fall short, as the estimated endpoints can be a mix of both the number of transfer events and clonal growth of transconjugants. Our aim was therefore to achieve a proper strategy for assessing the minimal concentration of a stressor (exemplified by tetracycline) that drives horizontal transfer of antibiotic resistance from a complex community to a model pathogen. Conditions were optimized to improve a culture-based approach using the bacterial community of treated sewage effluent as donor, and fluorescent, traceable Escherichia coli as recipient. Reduced level of background resistance, differentiation of isolates as well as decreased risk for measuring effects of selection were achieved through the use of chromogenic medium, optimization of conjugation time as well as applying a different antibiotic for isolation of transconjugants than the one tested for its ability to drive transfer. Using this assay, we showed that a very low concentration of tetracycline, 10μg/L i.e. 150 times below the minimal inhibitory concentration of the recipient, promoted horizontal transfer of multiple antibiotic-resistance determinants. Higher concentrations favoured selection of a tetracycline-resistance phenotype along with a decline in the number of detectable transfer events. The described method can be used to evaluate different environmental conditions and factors that trigger horizontal dissemination of mobile resistance elements, eventually resulting in the formation of drug-resistant pathogens.}, }
@article {pmid26802071, year = {2016}, author = {Matsui, K and Yoshinami, S and Narita, M and Chien, MF and Phung, le T and Silver, S and Endo, G}, title = {Mercury resistance transposons in Bacilli strains from different geographical regions.}, journal = {FEMS microbiology letters}, volume = {363}, number = {5}, pages = {fnw013}, doi = {10.1093/femsle/fnw013}, pmid = {26802071}, issn = {1574-6968}, mesh = {Bacillus/*drug effects/*genetics/isolation &amp; purification ; Bacterial Proteins/*genetics ; Base Sequence ; DNA Transposable Elements/*genetics ; DNA, Bacterial/genetics ; DNA-Binding Proteins/*genetics ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal/physiology ; Geography ; Lyases/*genetics ; Mercury/*pharmacology ; Molecular Sequence Data ; Oxidoreductases/*genetics ; Sequence Analysis, DNA ; Transposases/genetics ; }, abstract = {A total of 65 spore-forming mercury-resistant bacteria were isolated from natural environments worldwide in order to understand the acquisition of additional genes by and dissemination of mercury resistance transposons across related Bacilli genera by horizontal gene movement. PCR amplification using a single primer complementary to the inverted repeat sequence of TnMERI1-like transposons showed that 12 of 65 isolates had a transposon-like structure. There were four types of amplified fragments: Tn5084, Tn5085, Tn(d)MER3 (a newly identified deleted transposon-like fragment) and Tn6294 (a newly identified transposon). Tn(d)MER3 is a 3.5-kb sequence that carries a merRETPA operon with no merB or transposase genes. It is related to the mer operon of Bacillus licheniformis strain FA6-12 from Russia. DNA homology analysis shows that Tn6294 is an 8.5-kb sequence that is possibly derived from Tn(d)MER3 by integration of a TnMERI1-type transposase and resolvase genes and in addition the merR2 and merB1 genes. Bacteria harboring Tn6294 exhibited broad-spectrum mercury resistance to organomercurial compounds, although Tn6294 had only merB1 and did not have the merB2 and merB3 sequences for organomercurial lyases found in Tn5084 of B. cereus strain RC607. Strains with Tn6294 encode mercuric reductase (MerA) of less than 600 amino acids in length with a single N-terminal mercury-binding domain, whereas MerA encoded by strains MB1 and RC607 has two tandem domains. Thus, Tn(d)MER3 and Tn6294 are shorter prototypes for TnMERI1-like transposons. Identification of Tn6294 in Bacillus sp. from Taiwan and in Paenibacillus sp. from Antarctica indicates the wide horizontal dissemination of TnMERI1-like transposons across bacterial species and geographical barriers.}, }
@article {pmid26801681, year = {2016}, author = {Daubin, V and Szöllősi, GJ}, title = {Horizontal Gene Transfer and the History of Life.}, journal = {Cold Spring Harbor perspectives in biology}, volume = {8}, number = {4}, pages = {a018036}, pmid = {26801681}, issn = {1943-0264}, mesh = {Adaptation, Biological ; Bacteria/genetics ; *Biological Evolution ; *Gene Transfer, Horizontal ; Phylogeny ; Prokaryotic Cells/physiology ; }, abstract = {Microbes acquire DNA from a variety of sources. The last decades, which have seen the development of genome sequencing, have revealed that horizontal gene transfer has been a major evolutionary force that has constantly reshaped genomes throughout evolution. However, because the history of life must ultimately be deduced from gene phylogenies, the lack of methods to account for horizontal gene transfer has thrown into confusion the very concept of the tree of life. As a result, many questions remain open, but emerging methodological developments promise to use information conveyed by horizontal gene transfer that remains unexploited today.}, }
@article {pmid26800233, year = {2016}, author = {Peng, T and Lin, J and Xu, YZ and Zhang, Y}, title = {Comparative genomics reveals new evolutionary and ecological patterns of selenium utilization in bacteria.}, journal = {The ISME journal}, volume = {10}, number = {8}, pages = {2048-2059}, pmid = {26800233}, issn = {1751-7370}, mesh = {Bacteria/*genetics/metabolism ; Bacterial Proteins/genetics ; Biological Evolution ; Ecology ; Gene Transfer, Horizontal ; *Genomics ; Phosphotransferases/genetics ; Phylogeny ; Selenium/*metabolism ; Selenoproteins/genetics ; Trace Elements/*metabolism ; }, abstract = {Selenium (Se) is an important micronutrient for many organisms, which is required for the biosynthesis of selenocysteine, selenouridine and Se-containing cofactor. Several key genes involved in different Se utilization traits have been characterized; however, systematic studies on the evolution and ecological niches of Se utilization are very limited. Here, we analyzed more than 5200 sequenced organisms to examine the occurrence patterns of all Se traits in bacteria. A global species map of all Se utilization pathways has been generated, which demonstrates the most detailed understanding of Se utilization in bacteria so far. In addition, the selenophosphate synthetase gene, which is used to define the overall Se utilization, was also detected in some organisms that do not have any of the known Se traits, implying the presence of a novel Se form in this domain. Phylogenetic analyses of components of different Se utilization traits revealed new horizontal gene transfer events for each of them. Moreover, by characterizing the selenoproteomes of all organisms, we found a new selenoprotein-rich phylum and additional selenoprotein-rich species. Finally, the relationship between ecological environments and Se utilization was investigated and further verified by metagenomic analysis of environmental samples, which indicates new macroevolutionary trends of each Se utilization trait in bacteria. Our data provide insights into the general features of Se utilization in bacteria and should be useful for a further understanding of the evolutionary dynamics of Se utilization in nature.}, }
@article {pmid26799070, year = {2016}, author = {Semmler, T and Harrison, EM and Lübke-Becker, A and Ulrich, RG and Wieler, LH and Guenther, S and Stamm, I and Hanssen, AM and Holmes, MA and Vincze, S and Walther, B}, title = {A Look into the Melting Pot: The mecC-Harboring Region Is a Recombination Hot Spot in Staphylococcus stepanovicii.}, journal = {PloS one}, volume = {11}, number = {1}, pages = {e0147150}, pmid = {26799070}, issn = {1932-6203}, support = {G1001787/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Genes, Bacterial ; *Recombination, Genetic ; Staphylococcus/*genetics ; }, abstract = {INTRODUCTION: Horizontal gene transfer (HGT) is an important driver for resistance- and virulence factor accumulation in pathogenic bacteria such as Staphylococcus aureus.<br><br>METHODS: Here, we have investigated the downstream region of the bacterial chromosomal attachment site (attB) for the staphylococcal cassette chromosome mec (SCCmec) element of a commensal mecC-positive Staphylococcus stepanovicii strain (IMT28705; ODD4) with respect to genetic composition and indications of HGT. S. stepanovicii IMT28705 was isolated from a fecal sample of a trapped wild bank vole (Myodes glareolus) during a screening study (National Network on "Rodent-Borne Pathogens") in Germany. Whole genome sequencing (WGS) of IMT28705 together with the mecC-negative type strain CM7717 was conducted in order to comparatively investigate the genomic region downstream of attB (GenBank accession no. KR732654 and KR732653).<br><br>RESULTS: The bank vole isolate (IMT28705) harbors a mecC gene which shares 99.2% nucleotide (and 98.5% amino acid) sequence identity with mecC of MRSA_LGA251. In addition, the mecC-encoding region harbors the typical blaZ-mecC-mecR1-mecI structure, corresponding with the class E mec complex. While the sequences downstream of attB in both S. stepanovicii isolates (IMT28705 and CM7717) are partitioned by 15 bp direct repeats, further comparison revealed a remarkable low concordance of gene content, indicating a chromosomal "hot spot" for foreign DNA integration and exchange.<br><br>CONCLUSION: Our data highlight the necessity for further research on transmission routes of resistance encoding factors from the environmental and wildlife resistome.}, }
@article {pmid26793174, year = {2015}, author = {Anderson, AC and Jonas, D and Huber, I and Karygianni, L and Wölber, J and Hellwig, E and Arweiler, N and Vach, K and Wittmer, A and Al-Ahmad, A}, title = {Enterococcus faecalis from Food, Clinical Specimens, and Oral Sites: Prevalence of Virulence Factors in Association with Biofilm Formation.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1534}, pmid = {26793174}, issn = {1664-302X}, abstract = {Enterococci have gained significance as the cause of nosocomial infections; they occur as food contaminants and have also been linked to dental diseases. E. faecalis has a great potential to spread virulence as well as antibiotic resistance genes via horizontal gene transfer. The integration of food-borne enterococci into the oral biofilm in-vivo has been observed. Therefore, we investigated the virulence determinants and antibiotic resistance of 97 E. faecalis isolates from the oral cavity, food, and clinical specimens. In addition, phenotypic expression of gelatinase and cytolysin were tested, in-vitro biofilm formation was quantified and isolates were compared for strain relatedness via pulsed field gel electrophoresis (PFGE). Each isolate was found to possess two or more virulence genes, most frequently gelE, efaA, and asa1. Notably, plaque/saliva isolates possessed the highest abundance of virulence genes, the highest levels of phenotypic gelatinase and hemolysin activity and concurrently a high ability to form biofilm. The presence of asa1 was associated with biofilm formation. The biofilm formation capacity of clinical and plaque/saliva isolates was considerably higher than that of food isolates and they also showed similar antibiotic resistance patterns. These results indicate that the oral cavity can constitute a reservoir for virulent E. faecalis strains possessing antibiotic resistance traits and at the same time distinct biofilm formation capabilities facilitating exchange of genetic material.}, }
@article {pmid26789284, year = {2016}, author = {Higashi, K and Tobe, T and Kanai, A and Uyar, E and Ishikawa, S and Suzuki, Y and Ogasawara, N and Kurokawa, K and Oshima, T}, title = {H-NS Facilitates Sequence Diversification of Horizontally Transferred DNAs during Their Integration in Host Chromosomes.}, journal = {PLoS genetics}, volume = {12}, number = {1}, pages = {e1005796}, pmid = {26789284}, issn = {1553-7404}, mesh = {Adaptation, Biological/genetics ; Chromosomes, Bacterial ; DNA-Binding Proteins/*genetics ; Escherichia coli/*genetics ; Escherichia coli Proteins/*genetics/metabolism ; Evolution, Molecular ; Fimbriae Proteins/*genetics/metabolism ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal/*genetics ; Phylogeny ; Promoter Regions, Genetic ; Protein Binding ; Transcription Factors/*genetics ; }, abstract = {Bacteria can acquire new traits through horizontal gene transfer. Inappropriate expression of transferred genes, however, can disrupt the physiology of the host bacteria. To reduce this risk, Escherichia coli expresses the nucleoid-associated protein, H-NS, which preferentially binds to horizontally transferred genes to control their expression. Once expression is optimized, the horizontally transferred genes may actually contribute to E. coli survival in new habitats. Therefore, we investigated whether and how H-NS contributes to this optimization process. A comparison of H-NS binding profiles on common chromosomal segments of three E. coli strains belonging to different phylogenetic groups indicated that the positions of H-NS-bound regions have been conserved in E. coli strains. The sequences of the H-NS-bound regions appear to have diverged more so than H-NS-unbound regions only when H-NS-bound regions are located upstream or in coding regions of genes. Because these regions generally contain regulatory elements for gene expression, sequence divergence in these regions may be associated with alteration of gene expression. Indeed, nucleotide substitutions in H-NS-bound regions of the ybdO promoter and coding regions have diversified the potential for H-NS-independent negative regulation among E. coli strains. The ybdO expression in these strains was still negatively regulated by H-NS, which reduced the effect of H-NS-independent regulation under normal growth conditions. Hence, we propose that, during E. coli evolution, the conservation of H-NS binding sites resulted in the diversification of the regulation of horizontally transferred genes, which may have facilitated E. coli adaptation to new ecological niches.}, }
@article {pmid26787686, year = {2016}, author = {Devos, S and Stremersch, S and Raemdonck, K and Braeckmans, K and Devreese, B}, title = {Intra- and Interspecies Effects of Outer Membrane Vesicles from Stenotrophomonas maltophilia on β-Lactam Resistance.}, journal = {Antimicrobial agents and chemotherapy}, volume = {60}, number = {4}, pages = {2516-2518}, pmid = {26787686}, issn = {1098-6596}, mesh = {Anti-Bacterial Agents/pharmacology ; Burkholderia cenocepacia/drug effects/enzymology/*genetics ; Cell Membrane/chemistry ; Conjugation, Genetic ; Extracellular Vesicles/chemistry/*enzymology ; Gene Expression ; Gene Transfer, Horizontal ; Hydrolysis ; Imipenem/pharmacology ; Microbial Sensitivity Tests ; Pseudomonas aeruginosa/drug effects/enzymology/*genetics ; Stenotrophomonas maltophilia/drug effects/enzymology/*genetics ; Ticarcillin/pharmacology ; beta-Lactam Resistance/*genetics ; beta-Lactamases/genetics/*metabolism ; }, abstract = {The treatment ofStenotrophomonas maltophiliainfection with β-lactam antibiotics leads to increased release of outer membrane vesicles (OMVs), which are packed with two chromosomally encoded β-lactamases. Here, we show that these β-lactamase-packed OMVs are capable of establishing extracellular β-lactam degradation. We also show that they dramatically increase the apparent MICs of imipenem and ticarcillin for the cohabituating speciesPseudomonas aeruginosaandBurkholderia cenocepacia.}, }
@article {pmid26784237, year = {2016}, author = {Mobley, HL}, title = {Measuring Escherichia coli Gene Expression during Human Urinary Tract Infections.}, journal = {Pathogens (Basel, Switzerland)}, volume = {5}, number = {1}, pages = {}, pmid = {26784237}, issn = {2076-0817}, support = {R01 AI059722/AI/NIAID NIH HHS/United States ; R01 AI116791/AI/NIAID NIH HHS/United States ; R01 DK094777/DK/NIDDK NIH HHS/United States ; }, abstract = {Extraintestinal Escherichia coli (E. coli) evolved by acquisition of pathogenicity islands, phage, plasmids, and DNA segments by horizontal gene transfer. Strains are heterogeneous but virulent uropathogenic isolates more often have specific fimbriae, toxins, and iron receptors than commensal strains. One may ask whether it is the virulence factors alone that are required to establish infection. While these virulence factors clearly contribute strongly to pathogenesis, bacteria must survive by metabolizing nutrients available to them. By constructing mutants in all major metabolic pathways and co-challenging mice transurethrally with each mutant and the wild type strain, we identified which major metabolic pathways are required to infect the urinary tract. We must also ask what else is E. coli doing in vivo? To answer this question, we examined the transcriptome of E. coli CFT073 in the murine model of urinary tract infection (UTI) as well as for E. coli strains collected and analyzed directly from the urine of patients attending either a urology clinic or a university health clinic for symptoms of UTI. Using microarrays and RNA-seq, we measured in vivo gene expression for these uropathogenic E. coli strains, identifying genes upregulated during murine and human UTI. Our findings allow us to propose a new definition of bacterial virulence.}, }
@article {pmid26782935, year = {2016}, author = {Horiike, T and Minai, R and Miyata, D and Nakamura, Y and Tateno, Y}, title = {Ortholog-Finder: A Tool for Constructing an Ortholog Data Set.}, journal = {Genome biology and evolution}, volume = {8}, number = {2}, pages = {446-457}, pmid = {26782935}, issn = {1759-6653}, mesh = {*Gene Transfer, Horizontal ; Genome, Bacterial ; Gram-Positive Bacteria/classification/genetics ; *Open Reading Frames ; Phylogeny ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {Orthologs are widely used for phylogenetic analysis of species; however, identifying genuine orthologs among distantly related species is challenging, because genes obtained through horizontal gene transfer (HGT) and out-paralogs derived from gene duplication before speciation are often present among the predicted orthologs. We developed a program, "Ortholog-Finder," to obtain ortholog data sets for performing phylogenetic analysis by using all open-reading frame data of species. The program includes five processes for minimizing the effects of HGT and out-paralogs in phylogeny construction: 1) HGT filtering: Genes derived from HGT could be detected and deleted from the initial sequence data set by examining their base compositions. 2) Out-paralog filtering: Out-paralogs are detected and deleted from the data set based on sequence similarity. 3) Classification of phylogenetic trees: Phylogenetic trees generated for ortholog candidates are classified as monophyletic or polyphyletic trees. 4) Tree splitting: Polyphyletic trees are bisected to obtain monophyletic trees and remove HGT genes and out-paralogs. 5) Threshold changing: Out-paralogs are further excluded from the data set based on the difference in the similarity scores of genuine orthologs and out-paralogs. We examined how out-paralogs and HGTs affected phylogenetic trees constructed for species based on ortholog data sets obtained by Ortholog-Finder with the use of simulation data, and we determined the effects of confounding factors. We then used Ortholog-Finder in phylogeny construction for 12 Gram-positive bacteria from two phyla and validated each node of the constructed tree by comparison with individually constructed ortholog trees.}, }
@article {pmid26779166, year = {2015}, author = {Stagars, MH and Ruff, SE and Amann, R and Knittel, K}, title = {High Diversity of Anaerobic Alkane-Degrading Microbial Communities in Marine Seep Sediments Based on (1-methylalkyl)succinate Synthase Genes.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1511}, pmid = {26779166}, issn = {1664-302X}, abstract = {Alkanes comprise a substantial fraction of crude oil and are prevalent at marine seeps. These environments are typically anoxic and host diverse microbial communities that grow on alkanes. The most widely distributed mechanism of anaerobic alkane activation is the addition of alkanes to fumarate by (1-methylalkyl)succinate synthase (Mas). Here we studied the diversity of MasD, the catalytic subunit of the enzyme, in 12 marine sediments sampled at seven seeps. We aimed to identify cosmopolitan species as well as to identify factors structuring the alkane-degrading community. Using next generation sequencing we obtained a total of 420 MasD species-level operational taxonomic units (OTU0.96) at 96% amino acid identity. Diversity analysis shows a high richness and evenness of alkane-degrading bacteria. Sites with similar hydrocarbon composition harbored similar alkane-degrading communities based on MasD genes; the MasD community structure is clearly driven by the hydrocarbon source available at the various seeps. Two of the detected OTU0.96 were cosmopolitan and abundant while 75% were locally restricted, suggesting the presence of few abundant and globally distributed alkane degraders as well as specialized variants that have developed under specific conditions at the diverse seep environments. Of the three MasD clades identified, the most diverse was affiliated with Deltaproteobacteria. A second clade was affiliated with both Deltaproteobacteria and Firmicutes likely indicating lateral gene transfer events. The third clade was only distantly related to known alkane-degrading organisms and comprises new divergent lineages of MasD homologs, which might belong to an overlooked phylum of alkane-degrading bacteria. In addition, masD geneFISH allowed for the in situ identification and quantification of the target guild in alkane-degrading enrichment cultures. Altogether, these findings suggest an unexpectedly high number of yet unknown groups of anaerobic alkane degraders and underline the need for comprehensive surveys of microbial diversity based on metabolic genes in addition to ribosomal genes.}, }
@article {pmid26779119, year = {2015}, author = {Skennerton, CT and Ward, LM and Michel, A and Metcalfe, K and Valiente, C and Mullin, S and Chan, KY and Gradinaru, V and Orphan, VJ}, title = {Genomic Reconstruction of an Uncultured Hydrothermal Vent Gammaproteobacterial Methanotroph (Family Methylothermaceae) Indicates Multiple Adaptations to Oxygen Limitation.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1425}, pmid = {26779119}, issn = {1664-302X}, support = {R21 MH103824/MH/NIMH NIH HHS/United States ; T32 GM007616/GM/NIGMS NIH HHS/United States ; }, abstract = {Hydrothermal vents are an important contributor to marine biogeochemistry, producing large volumes of reduced fluids, gasses, and metals and housing unique, productive microbial and animal communities fueled by chemosynthesis. Methane is a common constituent of hydrothermal vent fluid and is frequently consumed at vent sites by methanotrophic bacteria that serve to control escape of this greenhouse gas into the atmosphere. Despite their ecological and geochemical importance, little is known about the ecophysiology of uncultured hydrothermal vent-associated methanotrophic bacteria. Using metagenomic binning techniques, we recovered and analyzed a near-complete genome from a novel gammaproteobacterial methanotroph (B42) associated with a white smoker chimney in the Southern Lau basin. B42 was the dominant methanotroph in the community, at ∼80x coverage, with only four others detected in the metagenome, all on low coverage contigs (7x-12x). Phylogenetic placement of B42 showed it is a member of the Methylothermaceae, a family currently represented by only one sequenced genome. Metabolic inferences based on the presence of known pathways in the genome showed that B42 possesses a branched respiratory chain with A- and B-family heme copper oxidases, cytochrome bd oxidase and a partial denitrification pathway. These genes could allow B42 to respire over a wide range of oxygen concentrations within the highly dynamic vent environment. Phylogenies of the denitrification genes revealed they are the result of separate horizontal gene transfer from other Proteobacteria and suggest that denitrification is a selective advantage in conditions where extremely low oxygen concentrations require all oxygen to be used for methane activation.}, }
@article {pmid26776116, year = {2016}, author = {Maurya, AP and Das Talukdar, A and Chanda, DD and Chakravarty, A and Bhattacharjee, A}, title = {First description of SHV-148 mediated extended-spectrum cephalosporin resistance among clinical isolates of Escherichia coli from India.}, journal = {Indian journal of medical microbiology}, volume = {34}, number = {1}, pages = {33-37}, doi = {10.4103/0255-0857.174110}, pmid = {26776116}, issn = {1998-3646}, mesh = {Adult ; *Cephalosporin Resistance ; DNA Transposable Elements ; Deoxyribonucleases, Type II Site-Specific/metabolism ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/classification/*drug effects/genetics/isolation &amp; purification ; Escherichia coli Infections/*microbiology ; Female ; Gene Transfer, Horizontal ; Humans ; India ; Integrons ; Male ; Microbial Sensitivity Tests ; Middle Aged ; Molecular Typing ; Plasmids/analysis/classification ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Tertiary Care Centers ; Young Adult ; beta-Lactamases/*analysis/genetics ; }, abstract = {PURPOSE: The present study was aimed to investigate the genetic context, association with IS26 and horizontal transmission of SHV-148 among Escherichia coli in Tertiary Referral Hospital of India.<br><br>METHODOLOGY: Phenotypic characterisation of extended-spectrum beta-lactamases (ESBLs) was carried out as per CLSI criteria. Molecular characterisation of blaSHVand integron was carried out by polymerase chain reaction (PCR) assay and confirmed by sequencing. Linkage of IS26 with blaSHV-148was achieved by PCR. Purified products were cloned on pGEM-T vector and sequenced. Strain typing was performed by pulsed field gel electrophoresis with Xba I digestion. Transferability experiment and antimicrobial susceptibility was performed.<br><br>RESULTS: A total of 33 isolates showed the presence of SHV-148 variant by sequencing and all were Class 1 integron borne. PCR and sequencing results suggested that all blaSHV-148 showed linkage with IS26 and were present in the upstream portion of the gene cassette and were also horizontally transferable through F type of Inc group. Susceptibility results suggest that tigecycline was most effective.<br><br>CONCLUSION: The present study reports for the first time of SHV-148 mediated extended spectrum cephalosporin resistance from India. Association of their resistance gene with IS26 and Class 1 integron and carriage within IncF plasmid signifies the potential mobilising unit for the horizontal transfer.}, }
@article {pmid26775188, year = {2016}, author = {Sharma, VK and Johnson, N and Cizmas, L and McDonald, TJ and Kim, H}, title = {A review of the influence of treatment strategies on antibiotic resistant bacteria and antibiotic resistance genes.}, journal = {Chemosphere}, volume = {150}, number = {}, pages = {702-714}, doi = {10.1016/j.chemosphere.2015.12.084}, pmid = {26775188}, issn = {1879-1298}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/*genetics/isolation &amp; purification/metabolism ; Bacterial Proteins/*genetics/metabolism ; *Drug Resistance, Bacterial ; Drug Resistance, Microbial/genetics ; Fresh Water/*microbiology ; Humans ; }, abstract = {Antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARG) in the aquatic environment have become an emerging contaminant issue, which has implications for human and ecological health. This review begins with an introduction to the occurrence of ARB and ARG in different environmental systems such as natural environments and drinking water resources. For example, ARG or ARB with resistance to ciprofloxacin, sulfamethoxazole, trimethoprim, quinolone, vancomycin, or tetracycline (e.g., tet(A), tet(B), tet(C), tet(G), tet(O), tet(M), tet(W), sul I, and sul II) have been detected in the environment. The development of resistance may be intrinsic, may be acquired through spontaneous mutations (de novo), or may occur due to horizontal gene transfer from donor bacteria, phages, or free DNA to recipient bacteria. An overview is also provided of the current knowledge regarding inactivation of ARB and ARG, and the mechanism of the effects of different disinfection processes in water and wastewater (chlorination, UV irradiation, Fenton reaction, ozonation, and photocatalytic oxidation). The effects of constructed wetlands and nanotechnology on ARB and ARG are also summarized.}, }
@article {pmid26774999, year = {2016}, author = {Corel, E and Lopez, P and Méheust, R and Bapteste, E}, title = {Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution.}, journal = {Trends in microbiology}, volume = {24}, number = {3}, pages = {224-237}, pmid = {26774999}, issn = {1878-4380}, mesh = {Bacteria/*genetics ; *Evolution, Molecular ; *Gene Regulatory Networks ; Gene Transfer, Horizontal ; Genome ; *Models, Genetic ; Symbiosis ; }, abstract = {The tree model and tree-based methods have played a major, fruitful role in evolutionary studies. However, with the increasing realization of the quantitative and qualitative importance of reticulate evolutionary processes, affecting all levels of biological organization, complementary network-based models and methods are now flourishing, inviting evolutionary biology to experience a network-thinking era. We show how relatively recent comers in this field of study, that is, sequence-similarity networks, genome networks, and gene families-genomes bipartite graphs, already allow for a significantly enhanced usage of molecular datasets in comparative studies. Analyses of these networks provide tools for tackling a multitude of complex phenomena, including the evolution of gene transfer, composite genes and genomes, evolutionary transitions, and holobionts.}, }
@article {pmid26773550, year = {2016}, author = {Kumar, D and Mondal, AK and Kutum, R and Dash, D}, title = {Proteogenomics of rare taxonomic phyla: A prospective treasure trove of protein coding genes.}, journal = {Proteomics}, volume = {16}, number = {2}, pages = {226-240}, doi = {10.1002/pmic.201500263}, pmid = {26773550}, issn = {1615-9861}, mesh = {Archaeal Proteins/*genetics ; Bacterial Proteins/*genetics ; Gene Transfer, Horizontal ; Genome, Archaeal ; Genome, Bacterial ; Humans ; Molecular Sequence Annotation ; Open Reading Frames ; Phylogeny ; Proteome/*genetics ; *Proteomics ; }, abstract = {Sustainable innovations in sequencing technologies have resulted in a torrent of microbial genome sequencing projects. However, the prokaryotic genomes sequenced so far are unequally distributed along their phylogenetic tree; few phyla contain the majority, the rest only a few representatives. Accurate genome annotation lags far behind genome sequencing. While automated computational prediction, aided by comparative genomics, remains a popular choice for genome annotation, substantial fraction of these annotations are erroneous. Proteogenomics utilizes protein level experimental observations to annotate protein coding genes on a genome wide scale. Benefits of proteogenomics include discovery and correction of gene annotations regardless of their phylogenetic conservation. This not only allows detection of common, conserved proteins but also the discovery of protein products of rare genes that may be horizontally transferred or taxonomy specific. Chances of encountering such genes are more in rare phyla that comprise a small number of complete genome sequences. We collated all bacterial and archaeal proteogenomic studies carried out to date and reviewed them in the context of genome sequencing projects. Here, we present a comprehensive list of microbial proteogenomic studies, their taxonomic distribution, and also urge for targeted proteogenomics of underexplored taxa to build an extensive reference of protein coding genes.}, }
@article {pmid26769930, year = {2016}, author = {Beye, M and Bakour, S and Labas, N and Raoult, D and Fournier, PE}, title = {Draft Genome Sequence of Actinobaculum massiliense Strain FC3.}, journal = {Genome announcements}, volume = {4}, number = {1}, pages = {}, pmid = {26769930}, issn = {2169-8287}, abstract = {Actinobaculum massiliense strain FC3 was isolated from the urine of a patient with acute cystitis. The 2.06-Mb genome of strain FC3 contains 17 toxin/antitoxin modules and 9 bacteriocin-encoding genes that may play a role in virulence. The genome also exhibits 693 genes acquired by lateral gene transfer.}, }
@article {pmid26769030, year = {2016}, author = {Karcagi, I and Draskovits, G and Umenhoffer, K and Fekete, G and Kovács, K and Méhi, O and Balikó, G and Szappanos, B and Györfy, Z and Fehér, T and Bogos, B and Blattner, FR and Pál, C and Pósfai, G and Papp, B}, title = {Indispensability of Horizontally Transferred Genes and Its Impact on Bacterial Genome Streamlining.}, journal = {Molecular biology and evolution}, volume = {33}, number = {5}, pages = {1257-1269}, pmid = {26769030}, issn = {1537-1719}, support = {//Wellcome Trust/United Kingdom ; 098016//Wellcome Trust/United Kingdom ; }, mesh = {Biological Evolution ; Escherichia coli/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome Size ; *Genome, Bacterial ; Phylogeny ; }, abstract = {Why are certain bacterial genomes so small and compact? The adaptive genome streamlining hypothesis posits that selection acts to reduce genome size because of the metabolic burden of replicating DNA. To reveal the impact of genome streamlining on cellular traits, we reduced the Escherichia coli genome by up to 20% by deleting regions which have been repeatedly subjects of horizontal transfer in nature. Unexpectedly, horizontally transferred genes not only confer utilization of specific nutrients and elevate tolerance to stresses, but also allow efficient usage of resources to build new cells, and hence influence fitness in routine and stressful environments alike. Genome reduction affected fitness not only by gene loss, but also by induction of a general stress response. Finally, we failed to find evidence that the advantage of smaller genomes would be due to a reduced metabolic burden of replicating DNA or a link with smaller cell size. We conclude that as the potential energetic benefit gained by deletion of short genomic segments is vanishingly small compared with the deleterious side effects of these deletions, selection for reduced DNA synthesis costs is unlikely to shape the evolution of small genomes.}, }
@article {pmid26764427, year = {2016}, author = {Krupovic, M and Shmakov, S and Makarova, KS and Forterre, P and Koonin, EV}, title = {Recent Mobility of Casposons, Self-Synthesizing Transposons at the Origin of the CRISPR-Cas Immunity.}, journal = {Genome biology and evolution}, volume = {8}, number = {2}, pages = {375-386}, pmid = {26764427}, issn = {1759-6653}, support = {340440/ERC_/European Research Council/International ; /ImNIH/Intramural NIH HHS/United States ; }, mesh = {Archaeal Proteins/*genetics ; Base Sequence ; *Clustered Regularly Interspaced Short Palindromic Repeats ; DNA Transposable Elements/*genetics ; Endodeoxyribonucleases/*genetics ; *Gene Transfer, Horizontal ; Genome, Archaeal ; Methanosarcina barkeri/classification/genetics ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Casposons are a superfamily of putative self-synthesizing transposable elements that are predicted to employ a homolog of Cas1 protein as a recombinase and could have contributed to the origin of the CRISPR-Cas adaptive immunity systems in archaea and bacteria. Casposons remain uncharacterized experimentally, except for the recent demonstration of the integrase activity of the Cas1 homolog, and given their relative rarity in archaea and bacteria, original comparative genomic analysis has not provided direct indications of their mobility. Here, we report evidence of casposon mobility obtained by comparison of the genomes of 62 strains of the archaeon Methanosarcina mazei. In these genomes, casposons are variably inserted in three distinct sites indicative of multiple, recent gains, and losses. Some casposons are inserted into other mobile genetic elements that might provide vehicles for horizontal transfer of the casposons. Additionally, many M. mazei genomes contain previously undetected solo terminal inverted repeats that apparently are derived from casposons and could resemble intermediates in CRISPR evolution. We further demonstrate the sequence specificity of casposon insertion and note clear parallels with the adaptation mechanism of CRISPR-Cas. Finally, besides identifying additional representatives in each of the three originally defined families, we describe a new, fourth, family of casposons.}, }
@article {pmid26759362, year = {2016}, author = {Warren, JM and Simmons, MP and Wu, Z and Sloan, DB}, title = {Linear Plasmids and the Rate of Sequence Evolution in Plant Mitochondrial Genomes.}, journal = {Genome biology and evolution}, volume = {8}, number = {2}, pages = {364-374}, pmid = {26759362}, issn = {1759-6653}, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Mitochondrial ; *Genome, Plant ; Magnoliopsida/classification/*genetics ; Mutagenesis, Insertional ; Mutation Rate ; Plasmids/*genetics ; }, abstract = {The mitochondrial genomes of flowering plants experience frequent insertions of foreign sequences, including linear plasmids that also exist in standalone forms within mitochondria, but the history and phylogenetic distribution of plasmid insertions is not well known. Taking advantage of the increased availability of plant mitochondrial genome sequences, we performed phylogenetic analyses to reconstruct the evolutionary history of these plasmids and plasmid-derived insertions. Mitochondrial genomes from multiple land plant lineages (including liverworts, lycophytes, ferns, and gymnosperms) include fragmented remnants from ancient plasmid insertions. Such insertions are much more recent and widespread in angiosperms, in which approximately 75% of sequenced mitochondrial genomes contain identifiable plasmid insertions. Although conflicts between plasmid and angiosperm phylogenies provide clear evidence of repeated horizontal transfers, we were still able to detect significant phylogenetic concordance, indicating that mitochondrial plasmids have also experienced sustained periods of (effectively) vertical transmission in angiosperms. The observed levels of sequence divergence in plasmid-derived genes suggest that nucleotide substitution rates in these plasmids, which often encode their own viral-like DNA polymerases, are orders of magnitude higher than in mitochondrial chromosomes. Based on these results, we hypothesize that the periodic incorporation of mitochondrial genes into plasmids contributes to the remarkable heterogeneity in substitution rates among genes that has recently been discovered in some angiosperm mitochondrial genomes. In support of this hypothesis, we show that the recently acquired ψtrnP-trnW gene region in a maize linear plasmid is evolving significantly faster than homologous sequences that have been retained in the mitochondrial chromosome in closely related grasses.}, }
@article {pmid26758181, year = {2016}, author = {Zhang, YZ and Li, Y and Xie, BB and Chen, XL and Yao, QQ and Zhang, XY and Kempher, ML and Zhou, J and Oren, A and Qin, QL}, title = {Nascent Genomic Evolution and Allopatric Speciation of Myroides profundi D25 in Its Transition from Land to Ocean.}, journal = {mBio}, volume = {7}, number = {1}, pages = {e01946-15}, pmid = {26758181}, issn = {2150-7511}, mesh = {Bacteroidetes/*genetics/*growth &amp; development/isolation &amp; purification ; China ; Culture Media/chemistry ; Gene Expression Profiling ; Gene Transfer, Horizontal ; *Genetic Speciation ; *Genome, Bacterial ; Geologic Sediments/microbiology ; Molecular Sequence Data ; Phylogeny ; Salinity ; Sequence Analysis, DNA ; }, abstract = {UNLABELLED: A large amount of bacterial biomass is transferred from land to ocean annually. Most transferred bacteria should not survive, but undoubtedly some do. It is unclear what mechanisms these bacteria use in order to survive and even thrive in a new marine environment. Myroides profundi D25(T), a member of the Bacteroidetes phylum, was isolated from deep-sea sediment of the southern Okinawa Trough near the China mainland and had high genomic sequence identity to and synteny with the human opportunistic pathogen Myroides odoratimimus. Phylogenetic and physiological analyses suggested that M. profundi recently transitioned from land to the ocean. This provided an opportunity to explore how a bacterial genome evolved to survive in a novel environment. Changes in the transcriptome were evaluated when both species were cultured under low-salinity conditions and then transferred to high-salinity conditions. Comparative genomic and transcriptomic analyses showed that M. profundi altered transcription regulation in the early stages of survival. In these stages, vertically inherited genes played a key role in the survival of M. profundi. The contribution of M. profundi unique genes, some possibly acquired by horizontal gene transfer (HGT), appeared relatively small, and expression levels of unique genes were diminished under the high-salinity conditions. We postulate that HGT genes might play an important role in longer-term adaptation. These results suggested that some human pathogens might have the ability to survive in and adapt to the marine environment, which may have important implications for public health control in coastal regions.<br><br>IMPORTANCE: Horizontal gene transfer (HGT) is considered to be important for bacteria to adapt to a different microhabitat. However, our results showed that vertically inherited genes might play more important roles than HGT genes in the nascent adaptation to the marine environment in the bacterium Myroides profundi, which has recently been transferred from land to ocean. M.&#xa0;profundi unique genes had low expression levels and were less regulated under high-salinity conditions, indicating that the contribution of HGT genes to survival of this bacterium under marine high-salinity conditions was limited. In the early adaptation stages, M.&#xa0;profundi apparently survived and adapted mainly by regulating the expression of inherited core genes. These results may explain in part why human pathogens can easily be detected in marine environments.}, }
@article {pmid26750147, year = {2016}, author = {Llorente, B and de Souza, FSJ and Soto, G and Meyer, C and Alonso, GD and Flawiá, MM and Bravo-Almonacid, F and Ayub, ND and Rodríguez-Concepción, M}, title = {Selective pressure against horizontally acquired prokaryotic genes as a driving force of plastid evolution.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {19036}, pmid = {26750147}, issn = {2045-2322}, mesh = {Arabidopsis/classification/enzymology/*genetics ; Bacteria/classification/enzymology/genetics ; *Biological Evolution ; Catechol Oxidase/*genetics/metabolism ; Cell Nucleus/enzymology/genetics ; Chlorophyta/classification/enzymology/genetics ; Eukaryotic Cells/cytology ; Fungi/classification/enzymology/genetics ; Gene Expression ; *Gene Transfer, Horizontal ; *Genome, Plant ; Models, Molecular ; Phylogeny ; Plastids/enzymology/*genetics ; Prokaryotic Cells/cytology/enzymology ; Protein Sorting Signals ; Protein Transport ; Selection, Genetic ; Symbiosis/physiology ; }, abstract = {The plastid organelle comprises a high proportion of nucleus-encoded proteins that were acquired from different prokaryotic donors via independent horizontal gene transfers following its primary endosymbiotic origin. What forces drove the targeting of these alien proteins to the plastid remains an unresolved evolutionary question. To better understand this process we screened for suitable candidate proteins to recapitulate their prokaryote-to-eukaryote transition. Here we identify the ancient horizontal transfer of a bacterial polyphenol oxidase (PPO) gene to the nuclear genome of an early land plant ancestor and infer the possible mechanism behind the plastidial localization of the encoded enzyme. Arabidopsis plants expressing PPO versions either lacking or harbouring a plastid-targeting signal allowed examining fitness consequences associated with its subcellular localization. Markedly, a deleterious effect on plant growth was highly correlated with PPO activity only when producing the non-targeted enzyme, suggesting that selection favoured the fixation of plastid-targeted protein versions. Our results reveal a possible evolutionary mechanism of how selection against heterologous genes encoding cytosolic proteins contributed in incrementing plastid proteome complexity from non-endosymbiotic gene sources, a process that may also impact mitochondrial evolution.}, }
@article {pmid26748339, year = {2016}, author = {Dumas, E and Christina Boritsch, E and Vandenbogaert, M and Rodríguez de la Vega, RC and Thiberge, JM and Caro, V and Gaillard, JL and Heym, B and Girard-Misguich, F and Brosch, R and Sapriel, G}, title = {Mycobacterial Pan-Genome Analysis Suggests Important Role of Plasmids in the Radiation of Type VII Secretion Systems.}, journal = {Genome biology and evolution}, volume = {8}, number = {2}, pages = {387-402}, pmid = {26748339}, issn = {1759-6653}, mesh = {*Evolution, Molecular ; Gene Rearrangement ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Mycobacterium/classification/*genetics ; Phylogeny ; Plasmids/*genetics ; Synteny ; Type IV Secretion Systems/*genetics ; }, abstract = {In mycobacteria, various type VII secretion systems corresponding to different ESX (ESAT-6 secretory) types, are contributing to pathogenicity, iron acquisition, and/or conjugation. In addition to the known chromosomal ESX loci, the existence of plasmid-encoded ESX systems was recently reported. To investigate the potential role of ESX-encoding plasmids on mycobacterial evolution, we analyzed a large representative collection of mycobacterial genomes, including both chromosomal and plasmid-borne sequences. Data obtained for chromosomal ESX loci confirmed the previous five classical ESX types and identified a novel mycobacterial ESX-4-like type, termed ESX-4-bis. Moreover, analysis of the plasmid-encoded ESX loci showed extensive diversification, with at least seven new ESX profiles, identified. Three of them (ESX-P clusters 1-3) were found in multiple plasmids, while four corresponded to singletons. Our phylogenetic and gene-order-analyses revealed two main groups of ESX types: 1) ancestral types, including ESX-4 and ESX-4-like systems from mycobacterial and non-mycobacterial actinobacteria and 2) mycobacteria-specific ESX systems, including ESX-1-2-3-5 systems and the plasmid-encoded ESX types. Synteny analysis revealed that ESX-P systems are part of phylogenetic groups that derived from a common ancestor, which diversified and resulted in the different ESX types through extensive gene rearrangements. A converging body of evidence, derived from composition bias-, phylogenetic-, and synteny analyses points to a scenario in which ESX-encoding plasmids have been a major driving force for acquisition and diversification of type VII systems in mycobacteria, which likely played (and possibly still play) important roles in the adaptation to new environments and hosts during evolution of mycobacterial pathogenesis.}, }
@article {pmid26746714, year = {2016}, author = {Nakane, K and Kawamura, K and Goto, K and Arakawa, Y}, title = {Long-Term Colonization by bla(CTX-M)-Harboring Escherichia coli in Healthy Japanese People Engaged in Food Handling.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {6}, pages = {1818-1827}, pmid = {26746714}, issn = {1098-5336}, mesh = {Anti-Bacterial Agents/pharmacology ; Asian People ; Bacterial Typing Techniques ; Carrier State/*epidemiology/*microbiology ; Conjugation, Genetic ; Disk Diffusion Antimicrobial Tests ; Escherichia coli/classification/*enzymology/genetics/isolation &amp; purification ; Escherichia coli Infections/*epidemiology/*microbiology ; Feces/microbiology ; *Food Handling ; Gene Transfer, Horizontal ; Genotyping Techniques ; Healthy Volunteers ; Humans ; Japan/epidemiology ; Plasmids ; Serotyping ; beta-Lactamases/*metabolism ; beta-Lactams/pharmacology ; }, abstract = {The actual state of intestinal long-term colonization by extended-spectrum β-lactamase (ESBL)-producing Escherichia coli in healthy Japanese people remains unclear. Therefore, a total of 4,314 fecal samples were collected from 2,563 food handlers from January 2010 to December 2011. Approximately 0.1 g of each fecal sample was inoculated onto a MacConkey agar plate containing cefotaxime (1 μg/ml). The bacterial colonies that grew on each plate were checked for ESBL production by the double-disk synergy test, as recommended by the Clinical and Laboratory Standards Institute. The bacterial serotype, antimicrobial susceptibility, pulsotype, sequence type (ST), and ESBL genotype were checked, and the replicon types of plasmids harboring the ESBL gene were also determined after conjugation experiments. ESBL producers were recovered from 70 (3.1%) of 2,230 participants who were checked only once. On the other hand, ESBL producers were isolated at least once from 52 (15.6%) of 333 participants who were checked more than twice, and 13 of the 52 participants carried ESBL producers for from more than 3 months to up to 2 years. Fluoroquinolone (FQ)-resistant E. coli strains harboring bla(CTX-M) were repeatedly recovered from 11 of the 13 carriers of bla(CTX-M)-harboring E. coli. A genetically related FQ-resistant E. coli O25b:H4-ST131 isolate harboring bla(CTX-M)-27 was recovered from 4 of the 13 carriers for more than 6 months. Three FQ-resistant E. coli O1:H6-ST648 isolates that harbored bla(CTX-M-15) or bla(CTX-M)-14 were recovered from 3 carriers. Moreover, multiple CTX-M-14- or CTX-M-15-producing E. coli isolates with different serotypes were recovered from 2 respective carriers. These findings predict a provable further spread of ESBL producers in both community and clinical settings.}, }
@article {pmid26745984, year = {2016}, author = {Yan, S and Wu, G}, title = {Analysis on evolutionary relationship of amylases from archaea, bacteria and eukaryota.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {32}, number = {2}, pages = {24}, pmid = {26745984}, issn = {1573-0972}, mesh = {Amino Acid Sequence ; Amylases/classification/*genetics/metabolism ; Archaea/*enzymology/genetics ; Bacteria/*enzymology/genetics ; Data Interpretation, Statistical ; Eukaryota/*enzymology/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Engineering ; Genetic Variation ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; }, abstract = {Amylase is one of the earliest characterized enzymes and has many applications in clinical and industrial settings. In biotechnological industries, the amylase activity is enhanced through modifying amylase structure and through cloning and expressing targeted amylases in different species. It is important to understand how engineered amylases can survive from generation to generation. This study used phylogenetic and statistical approaches to explore general patterns of amylases evolution, including 3118 α-amylases and 280 β-amylases from archaea, eukaryota and bacteria with fully documented taxonomic lineage. First, the phylogenetic tree was created to analyze the evolution of amylases with focus on individual amylases used in biofuel industry. Second, the average pairwise p-distance was computed for each kingdom, phylum, class, order, family and genus, and its diversity implies multi-time and multi-clan evolution. Finally, the variance was further partitioned into inter-clan variance and intra-clan variance for each taxonomic group, and they represent horizontal and vertical gene transfer. Theoretically, the results show a full picture on the evolution of amylases in manners of vertical and horizontal gene transfer, and multi-time and multi-clan evolution as well. Practically, this study provides the information on the surviving chance of desired amylase in a given taxonomic group, which may potentially enhance the successful rate of cloning and expression of amylase gene in different species.}, }
@article {pmid26745978, year = {2016}, author = {Rosnina, AG and Tan, YS and Abdullah, N and Vikineswary, S}, title = {Morphological and molecular characterization of yellow oyster mushroom, Pleurotus citrinopileatus, hybrids obtained by interspecies mating.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {32}, number = {2}, pages = {18}, pmid = {26745978}, issn = {1573-0972}, mesh = {Base Sequence ; Crosses, Genetic ; DNA, Fungal/genetics ; Gene Transfer, Horizontal ; Genes, Fungal ; Genes, rRNA ; *Hybridization, Genetic ; Phylogeny ; Pleurotus/*classification/cytology/*genetics/isolation &amp; purification ; Sequence Homology ; }, abstract = {Pleurotus citrinopileatus (yellow oyster mushroom) has an attractive shape and yellow colour but the fragile texture complicates packaging, and its strong aroma is unappealing to consumers. This study aimed to improve the characteristics and yield of P. citrinopileatus by interspecies mating between monokaryotic cultures of P. citrinopileatus and P. pulmonarius. Ten monokaryon cultures of the parental lines were crossed in all combinations to obtain hybrids. Eleven compatible mating pairs were obtained and cultivated to observe their sporophore morphology and yield. The selected hybrid, i.e. P1xC9, was beige in colour while hybrid P3xC8 was yellow in colour. Their sporophores had less offensive aroma, improved texture and higher yield. The DNA sequences of these hybrids were found to be in the same clade as the P. citrinopileatus parent with a bootstrap value of 99%. High bootstrap values indicate high genetic homology between hybrids and the P. citrinopileatus parent. The biological efficiencies of these hybrids P1xC9 (70.97%) and P3xC8 (52.14%) were also higher than the P. citrinopileatus parent (35.63%). Interspecies hybrids obtained by this mating technique can lead to better strains of mushrooms for genetic improvement of the Pleurotus species.}, }
@article {pmid26745428, year = {2016}, author = {Mao, J and Lu, T}, title = {Population-Dynamic Modeling of Bacterial Horizontal Gene Transfer by Natural Transformation.}, journal = {Biophysical journal}, volume = {110}, number = {1}, pages = {258-268}, pmid = {26745428}, issn = {1542-0086}, mesh = {Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/genetics ; Genomic Islands/genetics ; *Models, Genetic ; Neisseria gonorrhoeae/cytology/*genetics ; Nonlinear Dynamics ; Stochastic Processes ; *Transformation, Genetic ; }, abstract = {Natural transformation is a major mechanism of horizontal gene transfer (HGT) and plays an essential role in bacterial adaptation, evolution, and speciation. Although its molecular underpinnings have been increasingly revealed, natural transformation is not well characterized in terms of its quantitative ecological roles. Here, by using Neisseria gonorrhoeae as an example, we developed a population-dynamic model for natural transformation and analyzed its dynamic characteristics with nonlinear tools and simulations. Our study showed that bacteria capable of natural transformation can display distinct population behaviors ranging from extinction to coexistence and to bistability, depending on their HGT rate and selection coefficient. With the model, we also illustrated the roles of environmental DNA sources-active secretion and passive release-in impacting population dynamics. Additionally, by constructing and utilizing a stochastic version of the model, we examined how noise shapes the steady and dynamic behaviors of the system. Notably, we found that distinct waiting time statistics for HGT events, namely a power-law distribution, an exponential distribution, and a mix of the both, are associated with the dynamics in the regimes of extinction, coexistence, and bistability accordingly. This work offers a quantitative illustration of natural transformation by revealing its complex population dynamics and associated characteristics, therefore advancing our ecological understanding of natural transformation as well as HGT in general.}, }
@article {pmid26745326, year = {2016}, author = {Chmielarczyk, A and Pilarczyk-Żurek, M and Kamińska, W and Pobiega, M and Romaniszyn, D and Ziółkowski, G and Wójkowska-Mach, J and Bulanda, M}, title = {Molecular Epidemiology and Drug Resistance of Acinetobacter baumannii Isolated from Hospitals in Southern Poland: ICU as a Risk Factor for XDR Strains.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {22}, number = {4}, pages = {328-335}, doi = {10.1089/mdr.2015.0224}, pmid = {26745326}, issn = {1931-8448}, mesh = {Acinetobacter Infections/drug therapy/*epidemiology/microbiology ; Acinetobacter baumannii/classification/drug effects/*genetics/isolation &amp; purification ; Adult ; Aged ; Anti-Bacterial Agents/pharmacology ; Bacteremia/drug therapy/*epidemiology/microbiology ; Clone Cells ; Drug Resistance, Multiple, Bacterial/*genetics ; Female ; Gene Expression ; Gene Transfer, Horizontal ; Hospitals ; Humans ; Incidence ; Intensive Care Units ; Male ; Middle Aged ; Molecular Epidemiology ; Phylogeny ; Plasmids/chemistry/metabolism ; Pneumonia, Bacterial/drug therapy/*epidemiology/microbiology ; Poland/epidemiology ; Real-Time Polymerase Chain Reaction ; beta-Lactamases/classification/*genetics ; }, abstract = {The objectives of the present study were to investigate the carbapenemase and metallo-beta-lactamase genes of Acinetobacter baumannii clinical isolates by polymerase chain reaction (PCR) and real time PCR and to determine the molecular epidemiology of the strains using the DiversiLab tool. From these data, correlations between drug resistance, resistance genes, and epidemiological clones may be revealed. The study was conducted on 125 A. baumannii collected over the 2013 year. The majority of the isolates from both intensive care unit (ICU) and non-ICU cases originated from pneumonia infections (79.2%), isolates from blood infections accounted for 17.6% and 3.2% were from meningitis infections. In the ICU cases compared with the non-ICU cases, bloodstream infections were more frequently diagnosed (19.2% vs. 11.5%). Sixty percent of A. baumannii strains were resistant to all the antimicrobials tested with the exception of colistin. All strains were susceptible to colistin and polymyxin B. Extensively drug-resistant (XDR) strains accounted for 80.8% of the isolates tested and these XDR strains were more frequently isolated from ICU cases than from non-ICU cases (93.9% vs. 30.8%). Among the 101 isolates of A. baumannii exhibiting the XDR pattern of resistance, 80 possessed the blaOXA-24 gene and 29 had the blaOXA-23 gene. Only two isolates possessed the blaVIM gene. The presence of the ISAba1element was confirmed among 10 strains from patients hospitalized in the ICU. Using repetitive extragenic palindromic sequence PCR (DiversiLab typing), six clones and 12 unique strains were identified, of which two clones dominated. Most isolates belonging to clone 1 (66.7%) and clone 2 (85.5%) were susceptible only to colistin. In summary, it is clear from our findings and those of other studies that carbapenem resistance among A. baumannii strains presents a serious clinical problem worldwide. Furthermore, the presence of XDR international clone II in ICUs poses a potential risk for future outbreaks of A. baumannii infection and controlling A. baumannii infections in hospitals presents a serious challenge.}, }
@article {pmid26744223, year = {2016}, author = {Novick, RP and Ram, G}, title = {The Floating (Pathogenicity) Island: A Genomic Dessert.}, journal = {Trends in genetics : TIG}, volume = {32}, number = {2}, pages = {114-126}, pmid = {26744223}, issn = {0168-9525}, support = {R01 AI022159/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteriophages/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genomic Islands/*genetics ; Staphylococcus/genetics ; }, abstract = {Among the prokaryotic genomic islands (GIs) involved in horizontal gene transfer (HGT) are the classical pathogenicity islands, including the integrative and conjugative elements (ICEs), the gene-transfer agents (GTAs), and the staphylococcal pathogenicity islands (SaPIs), the primary focus of this review. While the ICEs and GTAs mediate HGT autonomously, the SaPIs are dependent on specific phages. The ICEs transfer primarily their own DNA, the GTAs exclusively transfer unlinked host DNA, and the SaPIs combine the capabilities of both. Thus the SaPIs derive their importance from the genes they carry (their genetic cargo) and the genes they move. They act not only as versatile high-frequency mobilizers but also as mediators of phage interference and consequently are major benefactors of their host bacteria.}, }
@article {pmid26738553, year = {2016}, author = {Colombo, S and Arioli, S and Guglielmetti, S and Lunelli, F and Mora, D}, title = {Virome-associated antibiotic-resistance genes in an experimental aquaculture facility.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {3}, pages = {}, doi = {10.1093/femsec/fiw003}, pmid = {26738553}, issn = {1574-6941}, mesh = {Anti-Bacterial Agents/*pharmacology ; Aquaculture ; Bacteria/classification/*drug effects/*genetics/isolation &amp; purification ; Bacterial Proteins/*genetics ; Bacteriophages/classification/genetics/*isolation &amp; purification ; Drug Resistance, Microbial/genetics ; Metagenome/drug effects ; Metagenomics ; Microbiota ; Open Reading Frames ; Wastewater/microbiology/virology ; }, abstract = {We report the comprehensive characterization of viral and microbial communities within an aquaculture wastewater sample, by a shotgun sequencing and 16S rRNA gene profiling metagenomic approach. Caudovirales had the largest representation within the sample, with over 50% of the total taxonomic abundance, whereas approximately 30% of the total open reading frames (ORFs) identified were from eukaryotic viruses (Mimiviridae and Phycodnaviridae). Antibiotic resistance genes (ARGs) within the virome accounted for 0.85% of the total viral ORFs and showed a similar distribution both in virome and in microbiome. Among the ARGs, those encoding proteins involved in the modulation of antibiotic efflux pumps were the most abundant. Interestingly, the taxonomy of the bacterial ORFs identified in the viral metagenome did not reflect the microbial taxonomy as deduced by 16S rRNA gene profiling and shotgun metagenomic analysis. A limited number of ARGs appeared to be mobilized from bacteria to phages or vice versa, together with other bacterial genes encoding products involved in general metabolic functions, even in the absence of any antibiotic treatment within the aquaculture plant. Thus, these results confirm the presence of a complex phage-bacterial network in the aquaculture environment.}, }
@article {pmid26736055, year = {2016}, author = {Han, XM and Hu, HW and Shi, XZ and Wang, JT and Han, LL and Chen, D and He, JZ}, title = {Impacts of reclaimed water irrigation on soil antibiotic resistome in urban parks of Victoria, Australia.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {211}, number = {}, pages = {48-57}, doi = {10.1016/j.envpol.2015.12.033}, pmid = {26736055}, issn = {1873-6424}, mesh = {Anti-Bacterial Agents/analysis ; Bacteria/drug effects/*genetics ; Drug Resistance, Microbial/*genetics ; Environment ; Genes, Bacterial ; Parks, Recreational ; Soil/chemistry ; Soil Microbiology ; Victoria ; Waste Disposal, Fluid ; Wastewater/analysis/chemistry/*microbiology ; Water/analysis ; }, abstract = {UNLABELLED: The effluents from wastewater treatment plants have been recognized as a significant environmental reservoir of antibiotics and antibiotic resistance genes (ARGs). Reclaimed water irrigation (RWI) is increasingly used as a practical solution for combating water scarcity in arid and semiarid regions, however, impacts of RWI on the patterns of ARGs and the soil bacterial community remain unclear. Here, we used high-throughput quantitative PCR and terminal restriction fragment length polymorphism techniques to compare the diversity, abundance and composition of a broad-spectrum of ARGs and total bacteria in 12 urban parks with and without RWI in Victoria, Australia. A total of 40 unique ARGs were detected across all park soils, with genes conferring resistance to β-lactam being the most prevalent ARG type. The total numbers and the fold changes of the detected ARGs were significantly increased by RWI, and marked shifts in ARG patterns were also observed in urban parks with RWI compared to those without RWI. The changes in ARG patterns were paralleled by a significant effect of RWI on the bacterial community structure and a co-occurrence pattern of the detected ARG types. There were significant and positive correlations between the fold changes of the integrase intI1 gene and two β-lactam resistance genes (KPC and IMP-2 groups), but no significant impacts of RWI on the abundances of intI1 and the transposase tnpA gene were found, indicating that RWI did not improve the potential for horizontal gene transfer of soil ARGs. Taken together, our findings suggested that irrigation of urban parks with reclaimed water could influence the abundance, diversity, and compositions of a wide variety of soil ARGs of clinical relevance.<br><br>ONE-SENTENCE SUMMARY: Irrigation of urban parks with treated wastewater significantly increased the abundance and diversity of various antibiotic resistance genes, but did not significantly enhance their potential for horizontal gene transfer.}, }
@article {pmid26730948, year = {2016}, author = {Vikeved, E and Backlund, A and Alsmark, C}, title = {The Dynamics of Lateral Gene Transfer in Genus Leishmania - A Route for Adaptation and Species Diversification.}, journal = {PLoS neglected tropical diseases}, volume = {10}, number = {1}, pages = {e0004326}, pmid = {26730948}, issn = {1935-2735}, mesh = {Adaptation, Physiological/*genetics ; *Genetic Speciation ; Genome, Protozoan ; Leishmania/*genetics/*physiology ; }, abstract = {BACKGROUND: The genome of Leishmania major harbours a comparably high proportion of genes of prokaryote origin, acquired by lateral gene transfer (LGT). Some of these are present in closely related trypanosomatids, while some are detected in Leishmania only. We have evaluated the impact and destiny of LGT in genus Leishmania.<br><br>To study the dynamics and fate of LGTs we have performed phylogenetic, as well as nucleotide and amino acid composition analyses within orthologous groups of LGTs detected in Leishmania. A set of universal trypanosomatid LGTs was added as a reference group. Both groups of LGTs have, to some extent, ameliorated to resemble the recipient genomes. However, while virtually all of the universal trypanosomatid LGTs are distributed and conserved in the entire genus Leishmania, the LGTs uniquely present in genus Leishmania are more prone to gene loss and display faster rates of evolution. Furthermore, a PCR based approach has been employed to ascertain the presence of a set of twenty LGTs uniquely present in genus Leishmania, and three universal trypanosomatid LGTs, in ten additional strains of Leishmania. Evolutionary rates and predicted expression levels of these LGTs have also been estimated. Ten of the twenty LGTs are distributed and conserved in all species investigated, while the remainder have been subjected to modifications, or undergone pseudogenization, degradation or loss in one or more species.<br><br>CONCLUSIONS/SIGNIFICANCE: LGTs unique to the genus Leishmania have been acquired after the divergence of Leishmania from the other trypanosomatids, and are evolving faster than their recipient genomes. This implies that LGT in genus Leishmania is a continuous and dynamic process contributing to species differentiation and speciation. This study also highlights the importance of carefully evaluating these dynamic genes, e.g. as LGTs have been suggested as potential drug targets.}, }
@article {pmid26729648, year = {2016}, author = {Touchon, M and Rocha, EP}, title = {Coevolution of the Organization and Structure of Prokaryotic Genomes.}, journal = {Cold Spring Harbor perspectives in biology}, volume = {8}, number = {1}, pages = {a018168}, pmid = {26729648}, issn = {1943-0264}, support = {281605/ERC_/European Research Council/International ; }, mesh = {*Biological Evolution ; Chromosome Segregation ; Chromosomes/chemistry ; DNA Replication ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; *Genome ; Genome Size ; Models, Genetic ; Operon/genetics/physiology ; Ploidies ; *Prokaryotic Cells ; Recombination, Genetic ; }, abstract = {The cytoplasm of prokaryotes contains many molecular machines interacting directly with the chromosome. These vital interactions depend on the chromosome structure, as a molecule, and on the genome organization, as a unit of genetic information. Strong selection for the organization of the genetic elements implicated in these interactions drives replicon ploidy, gene distribution, operon conservation, and the formation of replication-associated traits. The genomes of prokaryotes are also very plastic with high rates of horizontal gene transfer and gene loss. The evolutionary conflicts between plasticity and organization lead to the formation of regions with high genetic diversity whose impact on chromosome structure is poorly understood. Prokaryotic genomes are remarkable documents of natural history because they carry the imprint of all of these selective and mutational forces. Their study allows a better understanding of molecular mechanisms, their impact on microbial evolution, and how they can be tinkered in synthetic biology.}, }
@article {pmid26728193, year = {2016}, author = {Pollet, RM and Ingle, JD and Hymes, JP and Eakes, TC and Eto, KY and Kwong, SM and Ramsay, JP and Firth, N and Redinbo, MR}, title = {Processing of Nonconjugative Resistance Plasmids by Conjugation Nicking Enzyme of Staphylococci.}, journal = {Journal of bacteriology}, volume = {198}, number = {6}, pages = {888-897}, pmid = {26728193}, issn = {1098-5530}, support = {AI78924/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/*metabolism ; *Conjugation, Genetic ; *DNA Breaks, Single-Stranded ; DNA, Bacterial/metabolism ; Endonucleases/*metabolism ; *Gene Transfer, Horizontal ; Nucleic Acid Conformation ; *Plasmids ; Protein Binding ; Replication Origin ; Staphylococcus aureus/*enzymology/*genetics ; }, abstract = {UNLABELLED: Antimicrobial resistance in Staphylococcus aureus presents an increasing threat to human health. This resistance is often encoded on mobile plasmids, such as pSK41; however, the mechanism of transfer of these plasmids is not well understood. In this study, we first examine key protein-DNA interactions formed by the relaxase enzyme, NES, which initiates and terminates the transfer of the multidrug resistance plasmid pSK41. Two loops on the NES protein, hairpin loops 1 and 2, form extensive contacts with the DNA hairpin formed at the oriT region of pSK41, and here we establish that these contacts are essential for proper DNA cleavage and religation by the full 665-residue NES protein in vitro. Second, pSK156 and pCA347 are nonconjugative Staphylococcus aureus plasmids that contain sequences similar to the oriT region of pSK41 but differ in the sequence predicted to form a DNA hairpin. We show that pSK41-encoded NES is able to bind, cleave, and religate the oriT sequences of these nonconjugative plasmids in vitro. Although pSK41 could mobilize a coresident plasmid harboring its cognate oriT, it was unable to mobilize plasmids containing the pSK156 and pCA347 variant oriT mimics, suggesting that an accessory protein like that previously shown to confer specificity in the pWBG749 system may also be involved in transmission of plasmids containing a pSK41-like oriT. These data indicate that the conjugative relaxase in trans mechanism recently described for the pWBG749 family of plasmids also applies to the pSK41 family of plasmids, further heightening the potential significance of this mechanism in the horizontal transfer of staphylococcal plasmids.<br><br>IMPORTANCE: Understanding the mechanism of antimicrobial resistance transfer in bacteria such as Staphylococcus aureus is an important step toward potentially slowing the spread of antimicrobial-resistant infections. This work establishes protein-DNA interactions essential for the transfer of the Staphylococcus aureus multiresistance plasmid pSK41 by its relaxase, NES. This enzyme also processed variant oriT-like sequences found on numerous plasmids previously considered nontransmissible, suggesting that in conjunction with an uncharacterized accessory protein, these plasmids may be transferred horizontally via a relaxase in trans mechanism. These findings have important implications for our understanding of staphylococcal resistance plasmid evolution.}, }
@article {pmid26728065, year = {2016}, author = {Siddaramappa, S}, title = {Histophilus somni Genomics and Genetics.}, journal = {Current topics in microbiology and immunology}, volume = {396}, number = {}, pages = {49-70}, doi = {10.1007/82_2015_5009}, pmid = {26728065}, issn = {0070-217X}, mesh = {Base Sequence ; Genomics ; Molecular Sequence Data ; Mutagenesis ; Pasteurellaceae/*genetics ; Plasmids ; Transcriptome ; }, abstract = {Histophilus somni is a commensal and an opportunistic bacterial pathogen associated with multisystemic diseases in cattle and sheep. Some strains of H. somni isolated from the genital tract of cattle are biochemically and serologically similar to the pathogenic strains, but are relatively innocuous. Several virulence factors/mechanisms have been identified in H. somni, of which the phase-variable lipooligosaccharide, induction of apoptosis of host cells, intraphagocytic survival, and immunoglobulin Fc-binding proteins have been well characterized. The genomes of H. somni pneumonia strain 2336 and preputial strain 129Pt have also been sequenced, and comparative analyses of these genomes have provided novel insights into the role of horizontal gene transfer in the evolution of the respective strains. Continued analyses of the genomes of H. somni strains and comparing them to the newly sequenced genomes of other bacteria facilitated the identification of a putative integrative and conjugative element (designated ICEHso2336) encoding tetracycline resistance. Comparative genomics also showed that the uptake signal sequence (5'-AAGTGCGGT) of Haemophilus influenzae is abundant in H. somni and provided a genetic basis for the recalcitrance of some strains of this species to natural transformation. The post-genomic era for H. somni offered an opportunity for the functional characterization of genes identified by computational methods. This opportunity has been realized to a great extent by transcriptomic studies that have identified several small noncoding RNAs and new genes. These new discoveries and developments are expected to stimulate further in-depth investigations of H. somni, especially from the systems biology viewpoint.}, }
@article {pmid26722009, year = {2016}, author = {Mendonça, AA and de Lucena, BT and de Morais, MM and de Morais, MA}, title = {First identification of Tn916-like element in industrial strains of Lactobacillus vini that spread the tet-M resistance gene.}, journal = {FEMS microbiology letters}, volume = {363}, number = {3}, pages = {}, doi = {10.1093/femsle/fnv240}, pmid = {26722009}, issn = {1574-6968}, mesh = {Anti-Bacterial Agents/metabolism ; Conjugation, Genetic ; DNA Fingerprinting ; *DNA Transposable Elements ; DNA, Bacterial/genetics ; Doxycycline/metabolism ; Enterococcus faecalis/drug effects/genetics ; Gene Transfer, Horizontal ; Genotype ; *Industrial Microbiology ; Lactobacillus/classification/*drug effects/*genetics ; Polymerase Chain Reaction ; *Tetracycline Resistance ; }, abstract = {The open process used to ferment sugar cane juice or molasses to produce ethanol fuel is prone to contamination by bacterial cells of different species, in particular Lactobacilli. The situation can be exacerbated by the emergence of resistant cells to industrial antibiotics that are normally used to combat this contamination. In this work, two Lactobacillus vini isolates from ethanol distilleries were identified and found to be resistant to doxycycline, a tetracycline derivative, although sensitive to other antibiotics tested. The identification of these isolates was confirmed by sequencing the pheS gene and their clonal origin was shown by PCR-fingerprinting analysis. Moreover, the isolates were shown to carry the transposable element Tn916 that harboured the tet-M gene. Furthermore, conjugation experiments showed that both isolates were capable of transferring this element, and as a result, the tet-M gene, to Enterococcus faecalis reference strain. Finally, the identification of tetracycline resistance in the same distilleries in other Lactobacilli, suggested that inter-species transfer of antibiotic resistance may be occurring in the industrial environment, and thus impairing the efficiency of the antibiotic treatment and causing serious health concerns.}, }
@article {pmid26715828, year = {2015}, author = {Zhang, YC and Lin, K}, title = {Phylogeny Inference of Closely Related Bacterial Genomes: Combining the Features of Both Overlapping Genes and Collinear Genomic Regions.}, journal = {Evolutionary bioinformatics online}, volume = {11}, number = {Suppl 2}, pages = {1-9}, pmid = {26715828}, issn = {1176-9343}, abstract = {Overlapping genes (OGs) represent one type of widespread genomic feature in bacterial genomes and have been used as rare genomic markers in phylogeny inference of closely related bacterial species. However, the inference may experience a decrease in performance for phylogenomic analysis of too closely or too distantly related genomes. Another drawback of OGs as phylogenetic markers is that they usually take little account of the effects of genomic rearrangement on the similarity estimation, such as intra-chromosome/genome translocations, horizontal gene transfer, and gene losses. To explore such effects on the accuracy of phylogeny reconstruction, we combine phylogenetic signals of OGs with collinear genomic regions, here called locally collinear blocks (LCBs). By putting these together, we refine our previous metric of pairwise similarity between two closely related bacterial genomes. As a case study, we used this new method to reconstruct the phylogenies of 88 Enterobacteriale genomes of the class Gammaproteobacteria. Our results demonstrated that the topological accuracy of the inferred phylogeny was improved when both OGs and LCBs were simultaneously considered, suggesting that combining these two phylogenetic markers may reduce, to some extent, the influence of gene loss on phylogeny inference. Such phylogenomic studies, we believe, will help us to explore a more effective approach to increasing the robustness of phylogeny reconstruction of closely related bacterial organisms.}, }
@article {pmid26715630, year = {2016}, author = {Martinson, EO and Martinson, VG and Edwards, R and Mrinalini,  and Werren, JH}, title = {Laterally Transferred Gene Recruited as a Venom in Parasitoid Wasps.}, journal = {Molecular biology and evolution}, volume = {33}, number = {4}, pages = {1042-1052}, pmid = {26715630}, issn = {1537-1719}, support = {R01 GM098667/GM/NIGMS NIH HHS/United States ; R01GM098667/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Chitinases/*genetics ; Gene Transfer, Horizontal/*genetics ; Genome, Insect ; Host-Parasite Interactions/genetics ; Microsporidia/genetics ; *Phylogeny ; Wasp Venoms/*genetics ; Wasps/genetics/pathogenicity ; }, abstract = {Parasitoid wasps use venom to manipulate the immunity and metabolism of their host insects in a variety of ways to provide resources for their offspring. Yet, how genes are recruited and evolve to perform venom functions remain open questions. A recently recognized source of eukaryotic genome innovation is lateral gene transfer (LGT). Glycoside hydrolase family 19 (GH19) chitinases are widespread in bacteria, microsporidia, and plants where they are used in nutrient acquisition or defense, but have previously not been known in metazoans. In this study, a GH19 chitinase LGT is described from the unicellular microsporidia/Rozella clade into parasitoid wasps of the superfamily Chalcidoidea, where it has become recruited as a venom protein. The GH19 chitinase is present in 15 species of chalcidoid wasps representing four families, and phylogenetic analysis indicates that it was laterally transferred near or before the origin of Chalcidoidea (∼95 Ma). The GH19 chitinase gene is highly expressed in the venom gland of at least seven species, indicating a role in the complex host manipulations performed by parasitoid wasp venom. RNAi knockdown in the model parasitoid Nasonia vitripennis reveals that-following envenomation-the GH19 chitinase induces fly hosts to upregulate genes involved in an immune response to fungi. A second, independent LGT of GH19 chitinase from microsporidia into mosquitoes was also found, also supported by phylogenetic reconstructions. Besides these two LGT events, GH19 chitinase is not found in any other sequenced animal genome, or in any fungi outside the microsporidia/Rozella clade.}, }
@article {pmid26712939, year = {2015}, author = {Wang, J and Moolji, J and Dufort, A and Staffa, A and Domenech, P and Reed, MB and Behr, MA}, title = {Iron Acquisition in Mycobacterium avium subsp. paratuberculosis.}, journal = {Journal of bacteriology}, volume = {198}, number = {5}, pages = {857-866}, pmid = {26712939}, issn = {1098-5530}, support = {MOP-115133//Canadian Institutes of Health Research/Canada ; MOP-97813//Canadian Institutes of Health Research/Canada ; }, mesh = {Bacterial Proteins/genetics/metabolism ; Biological Transport ; Gene Expression Regulation, Bacterial/physiology ; Iron/*metabolism ; Mutation ; Mycobacterium avium subsp. paratuberculosis/*metabolism ; Oxazoles/*metabolism ; }, abstract = {UNLABELLED: Mycobacterium avium subsp. paratuberculosis is a host-adapted pathogen that evolved from the environmental bacterium M. avium subsp. hominissuis through gene loss and gene acquisition. Growth of M. avium subsp. paratuberculosis in the laboratory is enhanced by supplementation of the media with the iron-binding siderophore mycobactin J. Here we examined the production of mycobactins by related organisms and searched for an alternative iron uptake system in M. avium subsp. paratuberculosis. Through thin-layer chromatography and radiolabeled iron-uptake studies, we showed that M. avium subsp. paratuberculosis is impaired for both mycobactin synthesis and iron acquisition. Consistent with these observations, we identified several mutations, including deletions, in M. avium subsp. paratuberculosis genes coding for mycobactin synthesis. Using a transposon-mediated mutagenesis screen conditional on growth without myobactin, we identified a potential mycobactin-independent iron uptake system on a M. avium subsp. paratuberculosis-specific genomic island, LSP(P)15. We obtained a transposon (Tn) mutant with a disruption in the LSP(P)15 gene MAP3776c for targeted study. The mutant manifests increased iron uptake as well as intracellular iron content, with genes downstream of the transposon insertion (MAP3775c to MAP3772c [MAP3775-2c]) upregulated as the result of a polar effect. As an independent confirmation, we observed the same iron uptake phenotypes by overexpressing MAP3775-2c in wild-type M. avium subsp. paratuberculosis. These data indicate that the horizontally acquired LSP(P)15 genes contribute to iron acquisition by M. avium subsp. paratuberculosis, potentially allowing the subsequent loss of siderophore production by this pathogen.<br><br>IMPORTANCE: Many microbes are able to scavenge iron from their surroundings by producing iron-chelating siderophores. One exception is Mycobacterium avium subsp. paratuberculosis, a fastidious, slow-growing animal pathogen whose growth needs to be supported by exogenous mycobacterial siderophore (mycobactin) in the laboratory. Data presented here demonstrate that, compared to other closely related M. avium subspecies, mycobactin production and iron uptake are different in M. avium subsp. paratuberculosis, and these phenotypes may be caused by numerous deletions in its mycobactin biosynthesis pathway. Using a genomic approach, supplemented by targeted genetic and biochemical studies, we identified that LSP(P)15, a horizontally acquired genomic island, may encode an alternative iron uptake system. These findings shed light on the potential physiological consequence of horizontal gene transfer in M. avium subsp. paratuberculosis evolution.}, }
@article {pmid26711897, year = {2016}, author = {Fischer, S and Klockgether, J and Morán Losada, P and Chouvarine, P and Cramer, N and Davenport, CF and Dethlefsen, S and Dorda, M and Goesmann, A and Hilker, R and Mielke, S and Schönfelder, T and Suerbaum, S and Türk, O and Woltemate, S and Wiehlmann, L and Tümmler, B}, title = {Intraclonal genome diversity of the major Pseudomonas aeruginosa clones C and PA14.}, journal = {Environmental microbiology reports}, volume = {8}, number = {2}, pages = {227-234}, pmid = {26711897}, issn = {1758-2229}, mesh = {Conserved Sequence ; Environmental Microbiology ; Gene Transfer, Horizontal ; *Genetic Variation ; Genome, Bacterial ; *Genotype ; Humans ; Pseudomonas Infections/microbiology ; Pseudomonas aeruginosa/*classification/*genetics/isolation &amp; purification ; }, abstract = {Bacterial populations differentiate at the subspecies level into clonal complexes. Intraclonal genome diversity was studied in 100 isolates of the two dominant Pseudomonas aeruginosa clones C and PA14 collected from the inanimate environment, acute and chronic infections. The core genome was highly conserved among clone members with a median pairwise within-clone single nucleotide sequence diversity of 8 × 10(-6) for clone C and 2 × 10(-5) for clone PA14. The composition of the accessory genome was, on the other hand, as variable within the clone as between unrelated clones. Each strain carried a large cargo of unique genes. The two dominant worldwide distributed P. aeruginosa clones combine an almost invariant core with the flexible gain and loss of genetic elements that spread by horizontal transfer.}, }
@article {pmid26711767, year = {2015}, author = {Mandras, N and Tullio, V and Furneri, PM and Roana, J and Allizond, V and Scalas, D and Petronio Petronio, G and Fuochi, V and Banche, G and Cuffini, AM}, title = {Key Roles of Human Polymorphonuclear Cells and Ciprofloxacin in Lactobacillus Species Infection Control.}, journal = {Antimicrobial agents and chemotherapy}, volume = {60}, number = {3}, pages = {1638-1641}, pmid = {26711767}, issn = {1098-6596}, mesh = {Anti-Bacterial Agents/*pharmacology ; Cells, Cultured ; Ciprofloxacin/*pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Gene Transfer, Horizontal/genetics ; Humans ; Lactobacillus/*drug effects/genetics/*immunology ; Neutrophils/*immunology ; Phagocytosis/*immunology ; }, abstract = {Lactobacilli have the potential to act as reservoirs of antibiotic resistance genes similar to those found in human pathogens, with the risk of transferring these genes to many pathogenic bacteria. In this study, we investigated the role of human polymorphonuclear cells (PMNs) against Lactobacillus spp. both resistant and susceptible to ciprofloxacin (a fluoroquinolone) and the effect of ciprofloxacin on the interaction between PMNs and three Lactobacillus spp. with different patterns of susceptibility to this drug. Hence, the primary functions of PMNs, such as phagocytosis and bacterial intracellular killing, against lactobacilli were investigated. The rate of PMN phagocytosis was high for ciprofloxacin-sensitive and ciprofloxacin-resistant strains. The patterns of intracellular killing of ciprofloxacin-sensitive and ciprofloxacin-resistant strains by PMNs underline that PMNs alone were able to kill lactobacilli. The addition of ciprofloxacin to PMNs did not result in a significant increase in the bacterial uptake by phagocytes. On the contrary, ciprofloxacin had a marked effect on PMN intracellular killing, resulting in increased numbers of killed ciprofloxacin-sensitive bacteria in comparison with antibiotic-free controls. Our data show that by itself, the profile of antibiotic resistance does not constitute an intrinsic factor of greater or lesser pathogenicity toward the host. The ability of PMNs to kill a diverse array of bacterial pathogens is essential for human innate host defense, primarily in immunocompromised patients.}, }
@article {pmid26710854, year = {2015}, author = {van Dijk, B and Hogeweg, P}, title = {In Silico Gene-Level Evolution Explains Microbial Population Diversity through Differential Gene Mobility.}, journal = {Genome biology and evolution}, volume = {8}, number = {1}, pages = {176-188}, pmid = {26710854}, issn = {1759-6653}, mesh = {Antibiosis/genetics ; Bacterial Toxins/genetics ; Computer Simulation ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; *Polymorphism, Genetic ; Vibrionaceae/genetics ; }, abstract = {Microbial communities can show astonishing ecological and phylogenetic diversity. What is the role of pervasive horizontal gene transfer (HGT) in shaping this diversity in the presence of clonally expanding "killer strains"? Does HGT of antibiotic production and resistance genes erase phylogenetic structure? To answer these questions, we study a spatial eco-evolutionary model of prokaryotes, inspired by recent findings on antagonistic interactions in Vibrionaceae populations. We find toxin genes evolve to be highly mobile, whereas resistance genes minimize mobility. This differential gene mobility is a requirement to maintain a diverse and dynamic ecosystem. The resistance gene repertoire acts as a core genome that corresponds to the phylogeny of cells, whereas toxin genes do not follow this phylogeny and have a patchy distribution. We also show that interstrain HGT makes the emergent phylogenetic structure robust to selective sweeps. Finally, in this evolved ecosystem we observe antagonistic interactions between, rather than within, spatially structure subpopulations, as has been previously observed for prokaryotes in soils and oceans. In contrast to ascribing the diversification and evolution of microbial communities to clonal dynamics, we show that multilevel evolution can elegantly explain the observed phylogenetic structure and ecosystem diversity.}, }
@article {pmid26710853, year = {2015}, author = {Tran, TT and Belahbib, H and Bonnefoy, V and Talla, E}, title = {A Comprehensive tRNA Genomic Survey Unravels the Evolutionary History of tRNA Arrays in Prokaryotes.}, journal = {Genome biology and evolution}, volume = {8}, number = {1}, pages = {282-295}, pmid = {26710853}, issn = {1759-6653}, mesh = {Acidithiobacillus/*genetics ; *Evolution, Molecular ; Genetic Speciation ; *Genome, Bacterial ; Genomic Instability ; RNA, Transfer/*genetics ; }, abstract = {Considering the importance of tRNAs in the translation machinery, scant attention has been paid to tRNA array units defined as genomic regions containing at least 20 tRNA genes with a minimal tRNA gene density of two tRNA genes per kilobase. Our analysis of Acidithiobacillus ferrivorans CF27 and Acidithiobacillus ferrooxidans ATCC 23270(T) genomes showed that both display a tRNA array unit with syntenic conservation which mainly contributed to the tRNA gene redundancy in these two organisms. Our investigations into the occurrence and distribution of tRNA array units revealed that 1) this tRNA organization is limited to few phyla and mainly found in Gram-positive bacteria; and 2) the presence of tRNA arrays favors the redundancy of tRNA genes, in particular those encoding the core tRNA isoacceptors. Finally, comparative array organization revealed that tRNA arrays were acquired through horizontal gene transfer (from Firmicutes or unknown donor), before being subjected to tRNA rearrangements, deletions, and duplications. In Bacilli, the most parsimonious evolutionary history involved two common ancestors and the acquisition of their arrays arose late in evolution, in the genera branches. Functional roles of the array units in organism lifestyle, selective genetic advantage and translation efficiency, as well as the evolutionary advantages of organisms harboring them were proposed. Our study offers new insight into the structural organization and evolution of tRNA arrays in prokaryotic organisms.}, }
@article {pmid26709836, year = {2016}, author = {Mallet, J and Besansky, N and Hahn, MW}, title = {How reticulated are species?.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {38}, number = {2}, pages = {140-149}, pmid = {26709836}, issn = {1521-1878}, support = {BB/G006903/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; R01 AI076584/AI/NIAID NIH HHS/United States ; R01 AI76584/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Eukaryota/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; *Genetic Speciation ; Genomics/methods ; Organisms, Genetically Modified/genetics ; *Phylogeny ; Plants/genetics ; }, abstract = {Many groups of closely related species have reticulate phylogenies. Recent genomic analyses are showing this in many insects and vertebrates, as well as in microbes and plants. In microbes, lateral gene transfer is the dominant process that spoils strictly tree-like phylogenies, but in multicellular eukaryotes hybridization and introgression among related species is probably more important. Because many species, including the ancestors of ancient major lineages, seem to evolve rapidly in adaptive radiations, some sexual compatibility may exist among them. Introgression and reticulation can thereby affect all parts of the tree of life, not just the recent species at the tips. Our understanding of adaptive evolution, speciation, phylogenetics, and comparative biology must adapt to these mostly recent findings. Introgression has important practical implications as well, not least for the management of genetically modified organisms in pest and disease control.}, }
@article {pmid26706616, year = {2016}, author = {Bortolaia, V and Espinosa-Gongora, C and Guardabassi, L}, title = {Human health risks associated with antimicrobial-resistant enterococci and Staphylococcus aureus on poultry meat.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {22}, number = {2}, pages = {130-140}, doi = {10.1016/j.cmi.2015.12.003}, pmid = {26706616}, issn = {1469-0691}, mesh = {Animals ; Drug Resistance, Bacterial ; Enterococcus faecalis/classification/*genetics ; Enterococcus faecium/classification/*genetics ; Food Microbiology ; Gene Transfer, Horizontal ; Humans ; Livestock/microbiology ; Meat/*microbiology ; Methicillin-Resistant Staphylococcus aureus/classification/*genetics ; Poultry/microbiology ; Poultry Diseases/*microbiology ; }, abstract = {Enterococci and staphylococci are frequent contaminants on poultry meat. Enterococcus faecalis, Enterococcus faecium and Staphylococcus aureus are also well-known aetiological agents of a wide variety of infections resulting in major healthcare costs. This review provides an overview of the human health risks associated with the occurrence of these opportunistic human pathogens on poultry meat with particular focus on the risk of food-borne transmission of antimicrobial resistance. In the absence of conclusive evidence of transmission, this risk was inferred using data from scientific articles and national reports on prevalence, bacterial load, antimicrobial resistance and clonal distribution of these three species on poultry meat. The risks associated with ingestion of antimicrobial-resistant enterococci of poultry origin comprise horizontal transfer of resistance genes and transmission of multidrug-resistant E. faecalis lineages such as sequence type ST16. Enterococcus faecium lineages occurring in poultry meat products are distantly related to those causing hospital-acquired infections but may act as donors of quinupristin/dalfopristin resistance and other resistance determinants of clinical interest to the human gut microbiota. Ingestion of poultry meat contaminated with S. aureus may lead to food poisoning. However, antimicrobial resistance in the toxin-producing strains does not have clinical implications because food poisoning is not managed by antimicrobial therapy. Recently methicillin-resistant S. aureus of livestock origin has been reported on poultry meat. In theory handling or ingestion of contaminated meat is a potential risk factor for colonization by methicillin-resistant S. aureus. However, this risk is presently regarded as negligible by public health authorities.}, }
@article {pmid26705573, year = {2016}, author = {Zhang, M and Yang, P and van Elsas, JD}, title = {Effect of the IncP-1β plasmid pHB44 on the population dynamics of Burkholderia terrae BS001 in the Lyophyllum sp. strain Karsten mycosphere under different iron conditions.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {2}, pages = {}, doi = {10.1093/femsec/fiv167}, pmid = {26705573}, issn = {1574-6941}, mesh = {Agaricales/genetics/*metabolism ; Burkholderia/*genetics/*metabolism ; Comamonadaceae/*genetics/*metabolism ; Ecosystem ; Gene Transfer Techniques ; Iron/metabolism ; Plasmids/*genetics ; Population Dynamics ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Burkholderia terrae strain BS001 is a well-described inhabitant of the mycosphere of diverse fungi. In the interaction between this bacterium and its fungal host in soil, competition for iron might be a key process. Here, we address the capacity of the broad-host-range IncP-1β plasmid pHB44, originally isolated in Variovorax paradoxus HB44, to enhance or modulate the competitiveness of B. terrae BS001 under different soil iron levels when confronted with (young versus ageing) mycelia of Lyophyllum sp. strain Karsten in microcosms. The data revealed that, in most cases, plasmid pHB44 reduced the fitness of its host in the mycosphere, possibly due to a metabolic burden effect. However, an opposite effect was found under low-iron conditions at the extreme tips of the soil-exploring Lyophyllum sp. strain Karsten mycelium. The negative effect of plasmid pHB44 on strain BS001 population sizes was clearly offset by fitness enhancement under these conditions. Moreover, as evidenced by using plasmid pSUP104 as a tracer, plasmid pHB44 was transferred from the B. terrae BS001 host into V. paradoxus BS64 in the ageing mycosphere, but not in bulk soil. Strikingly, successful plasmid establishment in the new host was more prominent in the iron-limited than in the 'high-iron' mycosphere habitat, indicating plasmid pHB44 was required in the V. paradoxus host as a fitness stimulator in the iron-limited condition. Taken together, the data suggest that efficiency of iron acquisition only served as the selective mechanism under certain conditions of iron availability in the soil, specifically promoting the fitness of V. paradoxus transconjugants. Not only is the mycosphere to be regarded as a selective arena in which horizontal gene transfer across the bacterial inhabitants is spurred, but the outcome of the adaptive processes is strongly shaped by competitive events among the local organisms.}, }
@article {pmid26701821, year = {2016}, author = {Puglisi, E and Guerrieri, MC and Morelli, L}, title = {Mutations in rpoB sequences of Actinobacteria: a confounding factor in conjugal transfer experiments.}, journal = {International journal of antimicrobial agents}, volume = {47}, number = {1}, pages = {105-106}, doi = {10.1016/j.ijantimicag.2015.11.003}, pmid = {26701821}, issn = {1872-7913}, mesh = {Actinobacteria/*genetics ; Base Sequence ; Conjugation, Genetic ; DNA-Directed RNA Polymerases/*genetics ; Gene Transfer, Horizontal ; Molecular Sequence Data ; *Mutation, Missense ; *Point Mutation ; }, }
@article {pmid26699528, year = {2015}, author = {Gordon, JL and Lefeuvre, P and Escalon, A and Barbe, V and Cruveiller, S and Gagnevin, L and Pruvost, O}, title = {Comparative genomics of 43 strains of Xanthomonas citri pv. citri reveals the evolutionary events giving rise to pathotypes with different host ranges.}, journal = {BMC genomics}, volume = {16}, number = {}, pages = {1098}, pmid = {26699528}, issn = {1471-2164}, mesh = {Evolution, Molecular ; *Genome, Plant ; Host Specificity ; Metagenomics/methods ; Phylogeny ; Polymorphism, Single Nucleotide ; Recombination, Genetic ; Sequence Analysis, DNA/*methods ; Xanthomonas/*classification/*genetics ; }, abstract = {BACKGROUND: The identification of factors involved in the host range definition and evolution is a pivotal challenge in the goal to predict and prevent the emergence of plant bacterial disease. To trace the evolution and find molecular differences between three pathotypes of Xanthomonas citri pv. citri that may explain their distinctive host ranges, 42 strains of X. citri pv. citri and one outgroup strain, Xanthomonas citri pv. bilvae were sequenced and compared.<br><br>RESULTS: The strains from each pathotype form monophyletic clades, with a short branch shared by the A(w) and A pathotypes. Pathotype-specific recombination was detected in seven regions of the alignment. Using Ancestral Character Estimation, 426 SNPs were mapped to the four branches at the base of the A, A*, A(w) and A/A(w) clades. Several genes containing pathotype-specific nonsynonymous mutations have functions related to pathogenicity. The A pathotype is enriched for SNP-containing genes involved in defense mechanisms, while A* is significantly depleted for genes that are involved in transcription. The pathotypes differ by four gene islands that largely coincide with regions of recombination and include genes with a role in virulence. Both A* and A(w) are missing genes involved in defense mechanisms. In contrast to a recent study, we find that there are an extremely small number of pathotype-specific gene presences and absences.<br><br>CONCLUSIONS: The three pathotypes of X. citri pv. citri that differ in their host ranges largely show genomic differences related to recombination, horizontal gene transfer and single nucleotide polymorphism. We detail the phylogenetic relationship of the pathotypes and provide a set of candidate genes involved in pathotype-specific evolutionary events that could explain to the differences in host range and pathogenicity between them.}, }
@article {pmid26698649, year = {2016}, author = {Putnam, CD}, title = {Evolution of the methyl directed mismatch repair system in Escherichia coli.}, journal = {DNA repair}, volume = {38}, number = {}, pages = {32-41}, pmid = {26698649}, issn = {1568-7856}, support = {R01 GM050006/GM/NIGMS NIH HHS/United States ; GM50006/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; *Biological Evolution ; *DNA Mismatch Repair ; Escherichia coli/*metabolism ; Gene Transfer, Horizontal/genetics ; Methylation ; Molecular Sequence Data ; Phylogeny ; }, abstract = {DNA mismatch repair (MMR) repairs mispaired bases in DNA generated by replication errors. MutS or MutS homologs recognize mispairs and coordinate with MutL or MutL homologs to direct excision of the newly synthesized DNA strand. In most organisms, the signal that discriminates between the newly synthesized and template DNA strands has not been definitively identified. In contrast, Escherichia coli and some related gammaproteobacteria use a highly elaborated methyl-directed MMR system that recognizes Dam methyltransferase modification sites that are transiently unmethylated on the newly synthesized strand after DNA replication. Evolution of methyl-directed MMR is characterized by the acquisition of Dam and the MutH nuclease and by the loss of the MutL endonuclease activity. Methyl-directed MMR is present in a subset of Gammaproteobacteria belonging to the orders Enterobacteriales, Pasteurellales, Vibrionales, Aeromonadales, and a subset of the Alteromonadales (the EPVAA group) as well as in gammaproteobacteria that have obtained these genes by horizontal gene transfer, including the medically relevant bacteria Fluoribacter, Legionella, and Tatlockia and the marine bacteria Methylophaga and Nitrosococcus.}, }
@article {pmid26697056, year = {2015}, author = {Han, L and Luan, YS}, title = {Horizontal Transfer of Small RNAs to and from Plants.}, journal = {Frontiers in plant science}, volume = {6}, number = {}, pages = {1113}, pmid = {26697056}, issn = {1664-462X}, abstract = {Genetic information is traditionally thought to be transferred from parents to offspring. However, there is evidence indicating that gene transfer can also occur from microbes to higher species, such as plants, invertebrates, and vertebrates. This horizontal transfer can be carried out by small RNAs (sRNAs). sRNAs have been recently reported to move across kingdoms as mobile signals, spreading silencing information toward targeted genes. sRNAs, especially microRNAs (miRNAs) and small interfering RNAs (siRNAs), are non-coding molecules that control gene expression at the transcriptional or post-transcriptional level. Some sRNAs act in a cross-kingdom manner between animals and their parasites, but little is known about such sRNAs associated with plants. In this report, we provide a brief introduction to miRNAs that are transferred from plants to mammals/viruses and siRNAs that are transferred from microbes to plants. Both miRNAs and siRNAs can exert corresponding functions in the target organisms. Additionally, we provide information concerning a host-induced gene silencing system as a potential application that utilizes the transgenic trafficking of RNA molecules to silence the genes of interacting organisms. Moreover, we lay out the controversial views regarding cross-kingdom miRNAs and call for better methodology and experimental design to confirm this unique function of miRNAs.}, }
@article {pmid26691555, year = {2015}, author = {Cardona, G and Pons, JC and Rosselló, F}, title = {A reconstruction problem for a class of phylogenetic networks with lateral gene transfers.}, journal = {Algorithms for molecular biology : AMB}, volume = {10}, number = {}, pages = {28}, pmid = {26691555}, issn = {1748-7188}, abstract = {BACKGROUND: Lateral, or Horizontal, Gene Transfers are a type of asymmetric evolutionary events where genetic material is transferred from one species to another. In this paper we consider LGT networks, a general model of phylogenetic networks with lateral gene transfers which consist, roughly, of a principal rooted tree with its leaves labelled on a set of taxa, and a set of extra secondary arcs between nodes in this tree representing lateral gene transfers. An LGT network gives rise in a natural way to a principal phylogenetic subtree and a set of secondary phylogenetic subtrees, which, roughly, represent, respectively, the main line of evolution of most genes and the secondary lines of evolution through lateral gene transfers.<br><br>RESULTS: We introduce a set of simple conditions on an LGT network that guarantee that its principal and secondary phylogenetic subtrees are pairwise different and that these subtrees determine, up to isomorphism, the LGT network. We then give an algorithm that, given a set of pairwise different phylogenetic trees [Formula: see text] on the same set of taxa, outputs, when it exists, the LGT network that satisfies these conditions and such that its principal phylogenetic tree is [Formula: see text] and its secondary phylogenetic trees are [Formula: see text].}, }
@article {pmid26691285, year = {2015}, author = {Sun, BF and Li, T and Xiao, JH and Jia, LY and Liu, L and Zhang, P and Murphy, RW and He, SM and Huang, DW}, title = {Horizontal functional gene transfer from bacteria to fishes.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {18676}, pmid = {26691285}, issn = {2045-2322}, mesh = {Animals ; Bacteria/*genetics ; Conserved Sequence ; Fishes/*genetics ; *Gene Transfer, Horizontal ; Phylogeny ; Physical Chromosome Mapping ; Seawater/microbiology ; Selection, Genetic ; Species Specificity ; Zebrafish/genetics ; }, abstract = {Invertebrates can acquire functional genes via horizontal gene transfer (HGT) from bacteria but fishes are not known to do so. We provide the first reliable evidence of one HGT event from marine bacteria to fishes. The HGT appears to have occurred after emergence of the teleosts. The transferred gene is expressed and regulated developmentally. Its successful integration and expression may change the genetic and metabolic repertoire of fishes. In addition, this gene contains conserved domains and similar tertiary structures in fishes and their putative donor bacteria. Thus, it may function similarly in both groups. Evolutionary analyses indicate that it evolved under purifying selection, further indicating its conserved function. We document the first likely case of HGT of functional gene from prokaryote to fishes. This discovery certifies that HGT can influence vertebrate evolution.}, }
@article {pmid26690348, year = {2015}, author = {Wu, Y and Aandahl, RZ and Tanaka, MM}, title = {Dynamics of bacterial insertion sequences: can transposition bursts help the elements persist?.}, journal = {BMC evolutionary biology}, volume = {15}, number = {}, pages = {288}, pmid = {26690348}, issn = {1471-2148}, mesh = {Bacteria/*genetics ; *DNA Transposable Elements ; Gene Transfer, Horizontal ; Genetic Fitness ; Genetic Variation ; Genome, Bacterial ; Models, Genetic ; *Mutagenesis, Insertional ; Mutation ; Selection, Genetic ; }, abstract = {BACKGROUND: Currently there is no satisfactory explanation for why bacterial insertion sequences (ISs) widely occur across prokaryotes despite being mostly harmful to their host genomes. Rates of horizontal gene transfer are likely to be too low to maintain ISs within a population. IS-induced beneficial mutations may be important for both prevalence of ISs and microbial adaptation to changing environments but may be too rare to sustain IS elements in the long run. Environmental stress can induce elevated rates of IS transposition activities; such episodes are known as 'transposition bursts'. By examining how selective forces and transposition events interact to influence IS dynamics, this study asks whether transposition bursts can lead to IS persistence.<br><br>RESULTS: We show through a simulation model that ISs are gradually eliminated from a population even if IS transpositions occasionally cause advantageous mutations. With beneficial mutations, transposition bursts create variation in IS copy numbers and improve cell fitness on average. However, these benefits are not usually sufficient to overcome the negative selection against the elements, and transposition bursts amplify the mean fitness effect which, if negative, simply accelerates the extinction of ISs. If down regulation of transposition occurs, IS extinctions are reduced while ISs still generate variation amongst bacterial genomes.<br><br>CONCLUSIONS: Transposition bursts do not help ISs persist in a bacterial population in the long run because most burst-induced mutations are deleterious and therefore not favoured by natural selection. However, bursts do create more genetic variation through which occasional advantageous mutations can help organisms adapt. Regulation of IS transposition bursts and stronger positive selection of the elements interact to slow down the burst-induced extinction of ISs.}, }
@article {pmid26690249, year = {2015}, author = {Dilthey, A and Lercher, MJ}, title = {Horizontally transferred genes cluster spatially and metabolically.}, journal = {Biology direct}, volume = {10}, number = {}, pages = {72}, pmid = {26690249}, issn = {1745-6150}, mesh = {Gammaproteobacteria/*genetics/metabolism ; *Gene Regulatory Networks ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; *Multigene Family ; }, abstract = {BACKGROUND: Genomic uptake of DNA by prokaryotes often encompasses more than a single gene. In many cases, several horizontally transferred genes may be acquired together. Accordingly, we expect that horizontally transferred genes cluster spatially in the genome more often than expected if transfers were independent. Further, genes that depend on each other functionally may be unlikely to have beneficial fitness effects when taken up individually by a foreign genome. Hence, we also expect the co-acquisition of functionally related genes, resulting in the clustering of horizontally transferred genes in functional networks.<br><br>RESULTS: Analysing spatial and metabolic clustering of recent horizontal (or lateral) gene transfers among 21 &#x3b3;-proteobacteria, we confirm both predictions. When comparing two datasets of predicted transfers that differ in their expected false-positive rate, we find that the more stringent dataset shows a stronger enrichment of clustered pairs.<br><br>CONCLUSIONS: The enrichment of interdependent metabolic genes among predicted transfers supports a biologically significant role of horizontally transferred genes in metabolic adaptation. Our results further suggest that spatial and metabolic clustering may be used as a benchmark for methods that predict recent horizontal gene transfers.}, }
@article {pmid26688693, year = {2015}, author = {Roffler, S and Menardo, F and Wicker, T}, title = {The making of a genomic parasite - the Mothra family sheds light on the evolution of Helitrons in plants.}, journal = {Mobile DNA}, volume = {6}, number = {}, pages = {23}, pmid = {26688693}, issn = {1759-8753}, abstract = {BACKGROUND: Helitrons are Class II transposons which are highly abundant in almost all eukaryotes. However, most Helitrons lack protein coding sequence. These non-autonomous elements are thought to hijack recombinase/helicase (RepHel) and possibly further enzymes from related, autonomous elements. Interestingly, many plant Helitrons contain an additional gene encoding a single-strand binding protein homologous to Replication Factor A (RPA), a highly conserved, single-copy gene found in all eukaryotes.<br><br>RESULTS: Here, we describe the analysis of DHH_Mothra, a high-copy non-autonomous Helitron in the genome of rice (Oryza sativa). Mothra has a low GC-content and consists of two distinct blocs of tandem repeats. Based on homology between their termini, we identified a putative mother element which encodes an RPA-like protein but has no RepHel gene. Additionally, we found a putative autonomous sister-family with strong homology to the Mothra mother element in the RPA protein and terminal sequences, which we propose provides the RepHel domain for the Mothra family. Furthermore, we phylogenetically analyzed the evolutionary history of RPA-like proteins. Interestingly, plant Helitron RPAs (PHRPAs) are only found in monocotyledonous and dicotyledonous plants and they form a monophyletic group which branched off before the eukaryotic "core" RPAs.<br><br>CONCLUSIONS: Our data show how erosion of autonomous Helitrons can lead to different "levels" of autonomy within Helitron families and can create highly successful subfamilies of non-autonomous elements. Most importantly, our phylogenetic analysis showed that the PHRPA gene was most likely acquired via horizontal gene transfer from an unknown eukaryotic donor at least 145-300 million years ago in the common ancestor of monocotyledonous and dicotyledonous plants. This might have led to the evolution of a separate branch of the Helitron superfamily in plants.}, }
@article {pmid26688468, year = {2016}, author = {Marcet-Houben, M and Gabaldón, T}, title = {Horizontal acquisition of toxic alkaloid synthesis in a clade of plant associated fungi.}, journal = {Fungal genetics and biology : FG &amp; B}, volume = {86}, number = {}, pages = {71-80}, pmid = {26688468}, issn = {1096-0937}, support = {310325/ERC_/European Research Council/International ; }, mesh = {Alkaloids/biosynthesis/*genetics ; Ergot Alkaloids/biosynthesis/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Hypocreales/classification/*genetics/metabolism ; Multigene Family ; Phylogeny ; }, abstract = {Clavicipitaceae is a fungal group that comprises species that closely interact with plants as pathogens, parasites or symbionts. A key factor in these interactions is the ability of these fungi to synthesize toxic alkaloid compounds that contribute to the protection of the plant host against herbivores. Some of these compounds such as ergot alkaloids are toxic to humans and have caused important epidemics throughout history. The gene clusters encoding the proteins responsible for the synthesis of ergot alkaloids and lolines in Clavicipitaceae have been elucidated. Notably, homologs to these gene clusters can be found in distantly related species such as Aspergillus fumigatus and Penicillium expansum, which diverged from Clavicipitaceae more than 400 million years ago. We here use a phylogenetic approach to analyze the evolution of these gene clusters. We found that the gene clusters conferring the ability to synthesize ergot alkaloids and loline emerged first in Eurotiomycetes and were then likely transferred horizontally to Clavicipitaceae. Horizontal gene transfer is known to play a role in shaping the distribution of secondary metabolism clusters across distantly related fungal species. We propose that HGT events have played an important role in the capability of Clavicipitaceae to produce two key secondary metabolites that have enhanced the ability of these species to protect their plant hosts, therefore favoring their interactions.}, }
@article {pmid26685788, year = {2016}, author = {Shahi, A and Aydin, S and Ince, B and Ince, O}, title = {Evaluation of microbial population and functional genes during the bioremediation of petroleum-contaminated soil as an effective monitoring approach.}, journal = {Ecotoxicology and environmental safety}, volume = {125}, number = {}, pages = {153-160}, doi = {10.1016/j.ecoenv.2015.11.029}, pmid = {26685788}, issn = {1090-2414}, mesh = {Bacterial Proteins/*genetics ; Biodegradation, Environmental ; Environmental Monitoring ; Gram-Negative Bacteria/genetics/isolation &amp; purification ; Gram-Positive Bacteria/genetics/isolation &amp; purification ; Petroleum/*microbiology ; Polycyclic Aromatic Hydrocarbons/chemistry ; Pseudomonas/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Soil Pollutants/*chemistry ; }, abstract = {This study investigated the abundance and diversity of soil n-alkane and polycyclic aromatic hydrocarbon (PAH)-degrading bacterial communities. It also investigated the quantity of the functional genes, the occurrence of horizontal gene transfer (HGT) in the identified bacterial communities and the effect that such HGT can have on biostimulation process. Illumina sequencing was used to detect the microbial diversity of petroleum-polluted soil prior to the biostimulation process, and quantitative real-time PCR was used to determine changes in the bacterial community and functional genes (alkB, phnAc and nah) expressions throughout the biostimulation of petroleum-contaminated soil. The illumine results revealed that γ-proteobacteria, Chloroflexi, Firmicutes, and δ-proteobacteria were the most dominant bacterial phyla in the contaminated site, and that most of the strains were Gram-negative. The results of the gene expression results revealed that gram-negative bacteria and alkB are critical to successful bioremediation. Failure to maintain the stability of hydrocarbon-degrading bacteria and functional gene will reduce the extend to which alkanes and PAHs are degraded. According to the results of the study, the application of a C:N:P ratio of was 100:15:1 in the biodegradation experiment resulted in the highest rate at which petroleum hydrocarbons were biodegraded. The diversity of pollutant-degrading bacteria and the effective transfer of degrading genes among resident microorganisms are essential factors for the successful biostimulation of petroleum hydrocarbons. As such, screening these factors throughout the biostimulation process represents an effective monitoring approach by which the success of the biostimulation can be assessed.}, }
@article {pmid26685176, year = {2016}, author = {Wallau, GL and Capy, P and Loreto, E and Le Rouzic, A and Hua-Van, A}, title = {VHICA, a New Method to Discriminate between Vertical and Horizontal Transposon Transfer: Application to the Mariner Family within Drosophila.}, journal = {Molecular biology and evolution}, volume = {33}, number = {4}, pages = {1094-1109}, pmid = {26685176}, issn = {1537-1719}, mesh = {Animals ; DNA Transposable Elements/*genetics ; DNA-Binding Proteins/*genetics ; Drosophila/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genetic Variation ; Genomics ; Phylogeny ; Species Specificity ; Transposases/*genetics ; }, abstract = {Transposable elements (TEs) are genomic repeated sequences that display complex evolutionary patterns. They are usually inherited vertically, but can occasionally be transmitted between sexually independent species, through so-called horizontal transposon transfers (HTTs). Recurrent HTTs are supposed to be essential in life cycle of TEs, which are otherwise destined for eventual decay. HTTs also impact the host genome evolution. However, the extent of HTTs in eukaryotes is largely unknown, due to the lack of efficient, statistically supported methods that can be applied to multiple species sequence data sets. Here, we developed a new automated method available as a R package "vhica" that discriminates whether a given TE family was vertically or horizontally transferred, and potentially infers donor and receptor species. The method is well suited for TE sequences extracted from complete genomes, and applicable to multiple TEs and species at the same time. We first validated our method using Drosophila TE families with well-known evolutionary histories, displaying both HTTs and vertical transmission. We then tested 26 different lineages of mariner elements recently characterized in 20 Drosophila genomes, and found HTTs in 24 of them. Furthermore, several independent HTT events could often be detected within the same mariner lineage. The VHICA (Vertical and Horizontal Inheritance Consistence Analysis) method thus appears as a valuable tool to analyze the evolutionary history of TEs across a large range of species.}, }
@article {pmid26683492, year = {2016}, author = {Fukuda, A and Usui, M and Okubo, T and Tamura, Y}, title = {Horizontal Transfer of Plasmid-Mediated Cephalosporin Resistance Genes in the Intestine of Houseflies (Musca domestica).}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {22}, number = {4}, pages = {336-341}, doi = {10.1089/mdr.2015.0125}, pmid = {26683492}, issn = {1931-8448}, mesh = {Achromobacter/genetics/metabolism ; Animals ; Anti-Bacterial Agents/pharmacology ; Cephalosporin Resistance/*genetics ; Cephalosporins/pharmacology ; *Conjugation, Genetic ; Escherichia coli/drug effects/*genetics/metabolism ; Escherichia coli Proteins/genetics/metabolism ; Gastrointestinal Tract/*microbiology ; Gene Expression ; *Gene Transfer, Horizontal ; Houseflies/*microbiology ; Insect Vectors/*microbiology ; Plasmids/chemistry/metabolism ; Pseudomonas fluorescens/genetics/metabolism ; Rifampin/pharmacology ; }, abstract = {Houseflies are a mechanical vector for various types of bacteria, including antimicrobial-resistant bacteria (ARB). If the intestine of houseflies is a suitable site for the transfer of antimicrobial resistance genes (ARGs), houseflies could also serve as a biological vector for ARB. To clarify whether cephalosporin resistance genes are transferred efficiently in the housefly intestine, we compared with conjugation experiments in vivo (in the intestine) and in vitro by using Escherichia coli with eight combinations of four donor and two recipient strains harboring plasmid-mediated cephalosporin resistance genes and chromosomal-encoded rifampicin resistance genes, respectively. In the in vivo conjugation experiment, houseflies ingested donor strains for 6 hr and then recipient strains for 3 hr, and 24 hr later, the houseflies were surface sterilized and analyzed. In vitro conjugation experiments were conducted using the broth-mating method. In 3/8 combinations, the in vitro transfer frequency (Transconjugants/Donor) was ≥1.3 × 10(-4); the in vivo transfer rates of cephalosporin resistance genes ranged from 2.0 × 10(-4) to 5.7 × 10(-5). Moreover, cephalosporin resistance genes were transferred to other species of enteric bacteria of houseflies such as Achromobacter sp. and Pseudomonas fluorescens. These results suggest that houseflies are not only a mechanical vector for ARB but also a biological vector for the occurrence of new ARB through the horizontal transfer of ARGs in their intestine.}, }
@article {pmid26674953, year = {2015}, author = {Prentice, HC and Li, Y and Lönn, M and Tunlid, A and Ghatnekar, L}, title = {A horizontally transferred nuclear gene is associated with microhabitat variation in a natural plant population.}, journal = {Proceedings. Biological sciences}, volume = {282}, number = {1821}, pages = {20152453}, pmid = {26674953}, issn = {1471-2954}, mesh = {*Ecosystem ; Festuca/*genetics ; *Gene Transfer, Horizontal ; *Genes, Plant ; Genetic Variation ; Glucose-6-Phosphate Isomerase/genetics ; Grassland ; Soil ; Sweden ; }, abstract = {Horizontal gene transfer involves the non-sexual interspecific transmission of genetic material. Even if they are initially functional, horizontally transferred genes are expected to deteriorate into non-expressed pseudogenes, unless they become adaptively relevant in the recipient organism. However, little is known about the distributions of natural transgenes within wild species or the adaptive significance of natural transgenes within wild populations. Here, we examine the distribution of a natural plant-to-plant nuclear transgene in relation to environmental variation within a wild population. Festuca ovina is polymorphic for an extra (second) expressed copy of the nuclear gene (PgiC) encoding cytosolic phosphoglucose isomerase, with the extra PgiC locus having been acquired horizontally from the distantly related grass genus Poa. We investigated variation at PgiC in samples of F. ovina from a fine-scale, repeating patchwork of grassland microhabitats, replicated within spatially separated sites. Even after accounting for spatial effects, the distributions of F. ovina individuals carrying the additional PgiC locus, and one of the enzyme products encoded by the locus, are significantly associated with fine-scale habitat variation. Our results suggest that the PgiC transgene contributes, together with the unlinked 'native' PgiC locus, to local adaptation to a fine-scale mosaic of edaphic and biotic grassland microhabitats.}, }
@article {pmid26670152, year = {2016}, author = {Rocha, DA and Campos, JC and Passadore, LF and Sampaio, SC and Nicodemo, AC and Sampaio, JL}, title = {Frequency of Plasmid-Mediated AmpC β-Lactamases in Escherichia coli Isolates from Urine Samples in São Paulo, Brazil.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {22}, number = {4}, pages = {321-327}, doi = {10.1089/mdr.2015.0190}, pmid = {26670152}, issn = {1931-8448}, mesh = {Aged ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/classification/*genetics ; Brazil/epidemiology ; Cefoxitin/pharmacology ; Cephalosporin Resistance/*genetics ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/classification/drug effects/*genetics/isolation &amp; purification ; Escherichia coli Infections/drug therapy/*epidemiology/microbiology/urine ; Female ; Gene Expression ; Gene Transfer, Horizontal ; Humans ; Incidence ; Inpatients ; Male ; Molecular Epidemiology ; Multiplex Polymerase Chain Reaction ; Outpatients ; Phylogeny ; Plasmids/chemistry/*metabolism ; Urinary Tract Infections/drug therapy/*epidemiology/microbiology/urine ; beta-Lactamases/classification/*genetics ; }, abstract = {Plasmid-mediated AmpC β-lactamases (PMACBLs) in Enterobacteriaceae encode resistance to third-generation cephalosporins, and these can mediate carbapenem resistance when associated with porin loss. However, no standardized phenotypic method is available for detecting these enzymes in the clinical microbiology laboratory. Limited data are available concerning the frequency of PMACBLs in Enterobacteriaceae in Brazil. This study was conducted in response to an increased cefoxitin (CFO) resistance rate of 3.7% in Escherichia coli isolates from urine samples from patients with suspected urinary tract infections during 2010. We collected 2,266 E. coli isolates prospectively during January 2012. A total of 109 (4.8%) isolates were nonsusceptible to CFO. These strains were further examined using multiplex PCR for the presence of genes encoding PMACBLs and using inhibitor assays with CFO and ceftazidime (CAZ) disks with and without phenylboronic acid. Pulsed-field gel electrophoresis was used to evaluate clonal dissemination. Genes encoding PMACBLs were detected in 1.8% of the isolates from inpatients and 0.46% of isolates from outpatients. The most prevalent gene was blaCMY-2 and blaCMY-4 was also detected. The phenotypic analysis showed 100% sensitivity and specificity for CMY-2 and CMY-4 when CFO-resistant isolates with a minimum zone diameter difference of 5 mm for CAZ or CAZ and CFO were considered positive. Although most of the isolates were nonclonal, one clonal group with two isolates was observed. Thus, the most frequent PMACBL in E. coli from São Paulo, Brazil is CMY-2, and both clonal and plasmid-mediated dissemination occur.}, }
@article {pmid26669767, year = {2016}, author = {Rocha, FR and Pinto, VP and Barbosa, FC}, title = {The Spread of CTX-M-Type Extended-Spectrum β-Lactamases in Brazil: A Systematic Review.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {22}, number = {4}, pages = {301-311}, doi = {10.1089/mdr.2015.0180}, pmid = {26669767}, issn = {1931-8448}, mesh = {Anti-Bacterial Agents/pharmacology ; Brazil/epidemiology ; Community-Acquired Infections ; Escherichia coli/classification/drug effects/*genetics/isolation &amp; purification ; Escherichia coli Infections/drug therapy/*epidemiology/microbiology ; Escherichia coli Proteins/classification/*genetics ; Gene Expression ; Gene Transfer, Horizontal ; Hospitals ; Humans ; Incidence ; Klebsiella Infections/drug therapy/*epidemiology/microbiology ; Klebsiella pneumoniae/classification/drug effects/*genetics/isolation &amp; purification ; Molecular Epidemiology ; beta-Lactam Resistance/*genetics ; beta-Lactamases/classification/*genetics ; beta-Lactams/pharmacology ; }, abstract = {The aim of this study was evaluate the spread of CTX-M-type extended-spectrum β-lactamase variants in microorganisms involved in both hospital- and community-acquired infections in different regions of Brazil to determine their epidemiology and identify areas for further research. Thirty-six studies were included and analyzed. Most of the studies were conducted in the southeastern (66.7%, 24/36), southern (22.2%, 8/36), and northeastern (8.3%, 3/36) regions of Brazil. No study was conducted in the northern or midwestern region. CTX-M-producing bacteria were isolated exclusively from humans in both hospital and community environments. The microorganisms that were most commonly associated with the presence of the blaCTX-M gene were Klebsiella pneumoniae and Escherichia coli. The β-lactamases of the CTX-M family that were most frequently identified in Brazil were CTX-M-2 and CTX-M-15, especially in the southeast where these variants are often detected. In this systematic review, the microorganisms that were most commonly associated with the presence of the blaCTX-M gene were K. pneumoniae and E. coli. CTX-M-2 and CTX-M-15 were the most dominant variants of the CTX-M family, followed by CTX-M-8, CTX-M-9, and CTX-M-59. A higher frequency of CTX-M variants was found in the southeastern region, especially in the states of São Paulo and Rio de Janeiro, where CTX-M-2 and CTX-M-15 are predominant.}, }
@article {pmid26668183, year = {2016}, author = {Loftie-Eaton, W and Yano, H and Burleigh, S and Simmons, RS and Hughes, JM and Rogers, LM and Hunter, SS and Settles, ML and Forney, LJ and Ponciano, JM and Top, EM}, title = {Evolutionary Paths That Expand Plasmid Host-Range: Implications for Spread of Antibiotic Resistance.}, journal = {Molecular biology and evolution}, volume = {33}, number = {4}, pages = {885-897}, pmid = {26668183}, issn = {1537-1719}, support = {P20 RR016448/RR/NCRR NIH HHS/United States ; P20GM103397/GM/NIGMS NIH HHS/United States ; R01 AI084918/AI/NIAID NIH HHS/United States ; P20 GM103397/GM/NIGMS NIH HHS/United States ; P20RR16448/RR/NCRR NIH HHS/United States ; }, mesh = {DNA Transposable Elements/genetics ; Drug Resistance, Microbial/*genetics ; *Evolution, Molecular ; Host Specificity/genetics ; Host-Pathogen Interactions/genetics ; Humans ; Plasmids/*genetics ; Pseudomonas/drug effects/*genetics/pathogenicity ; Sequence Analysis, DNA ; }, abstract = {The World Health Organization has declared the emergence of antibiotic resistance to be a global threat to human health. Broad-host-range plasmids have a key role in causing this health crisis because they transfer multiple resistance genes to a wide range of bacteria. To limit the spread of antibiotic resistance, we need to gain insight into the mechanisms by which the host range of plasmids evolves. Although initially unstable plasmids have been shown to improve their persistence through evolution of the plasmid, the host, or both, the means by which this occurs are poorly understood. Here, we sought to identify the underlying genetic basis of expanded plasmid host-range and increased persistence of an antibiotic resistance plasmid using a combined experimental-modeling approach that included whole-genome resequencing, molecular genetics and a plasmid population dynamics model. In nine of the ten previously evolved clones, changes in host and plasmid each slightly improved plasmid persistence, but their combination resulted in a much larger improvement, which indicated positive epistasis. The only genetic change in the plasmid was the acquisition of a transposable element from a plasmid native to the Pseudomonas host used in these studies. The analysis of genetic deletions showed that the critical genes on this transposon encode a putative toxin-antitoxin (TA) and a cointegrate resolution system. As evolved plasmids were able to persist longer in multiple naïve hosts, acquisition of this transposon also expanded the plasmid's host range, which has important implications for the spread of antibiotic resistance.}, }
@article {pmid26668029, year = {2016}, author = {Martín, JF and Liras, P}, title = {Evolutionary formation of gene clusters by reorganization: the meleagrin/roquefortine paradigm in different fungi.}, journal = {Applied microbiology and biotechnology}, volume = {100}, number = {4}, pages = {1579-1587}, doi = {10.1007/s00253-015-7192-y}, pmid = {26668029}, issn = {1432-0614}, mesh = {Alkaloids/*metabolism ; Evolution, Molecular ; *Gene Rearrangement ; Heterocyclic Compounds, 4 or More Rings/metabolism ; Indoles/*metabolism ; Metabolic Networks and Pathways/*genetics ; *Multigene Family ; Ovomucin/*metabolism ; Penicillium/*genetics ; Piperazines/metabolism ; }, abstract = {The biosynthesis of secondary metabolites in fungi is catalyzed by enzymes encoded by genes linked in clusters that are frequently co-regulated at the transcriptional level. Formation of gene clusters may take place by de novo assembly of genes recruited from other cellular functions, but also novel gene clusters are formed by reorganization of progenitor clusters and are distributed by horizontal gene transfer. This article reviews (i) the published information on the roquefortine/meleagrin/neoxaline gene clusters of Penicillium chrysogenum (Penicillium rubens) and the short roquefortine cluster of Penicillium roqueforti, and (ii) the correlation of the genes present in those clusters with the enzymes and metabolites derived from these pathways. The P. chrysogenum roq/mel cluster consists of seven genes and includes a gene (roqT) encoding a 12-TMS transporter protein of the MFS family. Interestingly, the orthologous P. roquefortine gene cluster has only four genes and the roqT gene is present as a residual pseudogene that encodes only small peptides. Two of the genes present in the central region of the P. chrysogenum roq/mel cluster have been lost during the evolutionary formation of the short cluster and the order of the structural genes in the cluster has been rearranged. The two lost genes encode a N1 atom hydroxylase (nox) and a roquefortine scaffold-reorganizing oxygenase (sro). As a consequence P. roqueforti has lost the ability to convert the roquefortine-type carbon skeleton to the glandicoline/meleagrin-type scaffold and is unable to produce glandicoline B, meleagrin and neoxaline. The loss of this genetic information is not recent and occurred probably millions of years ago when a progenitor Penicillium strain got adapted to life in a few rich habitats such as cheese, fermented cereal grains or silage. P. roqueforti may be considered as a "domesticated" variant of a progenitor common to contemporary P. chrysogenum and related Penicillia.}, }
@article {pmid26667220, year = {2016}, author = {Ramisetty, BC and Santhosh, RS}, title = {Horizontal gene transfer of chromosomal Type II toxin-antitoxin systems of Escherichia coli.}, journal = {FEMS microbiology letters}, volume = {363}, number = {3}, pages = {}, doi = {10.1093/femsle/fnv238}, pmid = {26667220}, issn = {1574-6968}, mesh = {Bacterial Toxins/*genetics ; Computational Biology ; Escherichia coli/*genetics ; *Gene Transfer, Horizontal ; Genetic Variation ; }, abstract = {Type II toxin-antitoxin systems (TAs) are small autoregulated bicistronic operons that encode a toxin protein with the potential to inhibit metabolic processes and an antitoxin protein to neutralize the toxin. Most of the bacterial genomes encode multiple TAs. However, the diversity and accumulation of TAs on bacterial genomes and its physiological implications are highly debated. Here we provide evidence that Escherichia coli chromosomal TAs (encoding RNase toxins) are 'acquired' DNA likely originated from heterologous DNA and are the smallest known autoregulated operons with the potential for horizontal propagation. Sequence analyses revealed that integration of TAs into the bacterial genome is unique and contributes to variations in the coding and/or regulatory regions of flanking host genome sequences. Plasmids and genomes encoding identical TAs of natural isolates are mutually exclusive. Chromosomal TAs might play significant roles in the evolution and ecology of bacteria by contributing to host genome variation and by moderation of plasmid maintenance.}, }
@article {pmid26666222, year = {2015}, author = {Filée, J and Rouault, JD and Harry, M and Hua-Van, A}, title = {Mariner transposons are sailing in the genome of the blood-sucking bug Rhodnius prolixus.}, journal = {BMC genomics}, volume = {16}, number = {}, pages = {1061}, pmid = {26666222}, issn = {1471-2164}, mesh = {Animals ; *DNA Transposable Elements ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome Size ; Genome, Insect ; Phylogeny ; Rhodnius/*genetics ; }, abstract = {BACKGROUND: The Triatomine bug Rhodnius prolixus is a vector of Trypanosoma cruzi, which causes the Chagas disease in Latin America. R. prolixus can also transfer transposable elements horizontally across a wide range of species. We have taken advantage of the availability of the 700 Mbp complete genome sequence of R. prolixus to study the dynamics of invasion and persistence of transposable elements in this species.<br><br>RESULTS: Using both library-based and de novo methods of transposon detection, we found less than 6 % of transposable elements in the R. prolixus genome, a relatively low percentage compared to other insect genomes with a similar genome size. DNA transposons are surprisingly abundant and elements belonging to the mariner family are by far the most preponderant components of the mobile part of this genome with 11,015 mariner transposons that could be clustered in 89 groups (75 % of the mobilome). Our analysis allowed the detection of a new mariner clade in the R. prolixus genome, that we called nosferatis. We demonstrated that a large diversity of mariner elements invaded the genome and expanded successfully over time via three main processes. (i) several families experienced recent and massive expansion, for example an explosive burst of a single mariner family led to the generation of more than 8000 copies. These recent expansion events explain the unusual prevalence of mariner transposons in the R. prolixus genome. Other families expanded via older bursts of transposition demonstrating the long lasting permissibility of mariner transposons in the R. prolixus genome. (ii) Many non-autonomous families generated by internal deletions were also identified. Interestingly, two non autonomous families were generated by atypical recombinations (5' part replacement with 3' part). (iii) at least 10 cases of horizontal transfers were found, supporting the idea that host/vector relationships played a pivotal role in the transmission and subsequent persistence of transposable elements in this genome.<br><br>CONCLUSION: These data provide a new insight into the evolution of transposons in the genomes of hematophagous insects and bring additional evidences that lateral exchanges of mobile genetics elements occur frequently in the R. prolixus genome.}, }
@article {pmid26665738, year = {2015}, author = {Bodoev, IN and Il'ina, EN}, title = {[MOLECULAR MECHANISMS OF DRUG RESISTANCE NEISSERIA GONORRHOEAE HISTORY AND PROSPECTS].}, journal = {Molekuliarnaia genetika, mikrobiologiia i virusologiia}, volume = {33}, number = {3}, pages = {22-27}, pmid = {26665738}, issn = {0208-0613}, mesh = {*Anti-Bacterial Agents/history/therapeutic use ; *Drug Resistance, Bacterial ; *Gonorrhea/drug therapy/epidemiology/genetics/history/metabolism ; History, 20th Century ; History, 21st Century ; Humans ; Neisseria gonorrhoeae/*genetics/*metabolism ; }, abstract = {Neisseria gonorrhoeae (gonococcus) is a strict human pathogen, which causes gonorrhea--an infectious disease, whose origin dates back to more than two thousand years. Due to the unique plasticity of the genetic material, these bacteria have acquired the capacity to adapt to the host immune system, cause repeated infections, as well as withstand antimicrobials. Since the introduction of antibiotics in 1930s, gonococcus has displayed its propensity to develop resistance to all clinically useful antibiotics. It is important to note that the known resistance determinants of N. gonorrhoeae were acquired through horizontal gene transfer, recombination and spontaneous mutagenesis, and may be located both in the chromosome and on the plasmid. After introduction of a new antimicrobial drug, gonococcus becomes resistant within two decades and replaces sensitive bacterial population. Currently Ceftriaxone is the last remaining antibiotic for first-line treatment of gonorrhea. However, the first gonococcus displaying high-level resistance to Ceftriaxone was isolated in Japan a few years ago. Therefore, in the near future, gonorrhea may become untreatable. In the present review, we discuss the chronology of the anti-gonorrhea drugs (antibiotics) replacement, the evolution of resistance mechanisms emergence and future perspectives of N. gonorrhoeae treatment.}, }
@article {pmid26665736, year = {2015}, author = {Zakharova, IB and Viktorov, DV}, title = {[CONJUGATIVE INTEGRATIVE ELEMENTS (ICEs) OF MICROORGANISMS].}, journal = {Molekuliarnaia genetika, mikrobiologiia i virusologiia}, volume = {33}, number = {3}, pages = {9-16}, pmid = {26665736}, issn = {0208-0613}, mesh = {Conjugation, Genetic/*physiology ; Gene Transfer, Horizontal/*physiology ; *Gram-Negative Bacteria/genetics/metabolism ; *Gram-Positive Bacteria/genetics/metabolism ; }, abstract = {Integrative conjugative elements (ICEs) are an extensive group of mobile genetic elements found in the Gram-positive and Gram-negative bacteria. These genetic elements are replicated being incorporated into host chromosome, but retain the ability for excision and conjugative transfer. Given a set of the genes of the conjugative transfer, control of removal and integration, ICEs are directly involved in the processes of horizontal transfer of genetic determinants, which increase the adaptive potential of the bacterial species, as well as act as a mobilizing factor for other genetic elements.}, }
@article {pmid26664808, year = {2015}, author = {Funkhouser-Jones, LJ and Sehnert, SR and Martínez-Rodríguez, P and Toribio-Fernández, R and Pita, M and Bella, JL and Bordenstein, SR}, title = {Wolbachia co-infection in a hybrid zone: discovery of horizontal gene transfers from two Wolbachia supergroups into an animal genome.}, journal = {PeerJ}, volume = {3}, number = {}, pages = {e1479}, pmid = {26664808}, issn = {2167-8359}, support = {R01 GM085163/GM/NIGMS NIH HHS/United States ; T32 GM008554/GM/NIGMS NIH HHS/United States ; }, abstract = {Hybrid zones and the consequences of hybridization have contributed greatly to our understanding of evolutionary processes. Hybrid zones also provide valuable insight into the dynamics of symbiosis since each subspecies or species brings its unique microbial symbionts, including germline bacteria such as Wolbachia, to the hybrid zone. Here, we investigate a natural hybrid zone of two subspecies of the meadow grasshopper Chorthippus parallelus in the Pyrenees Mountains. We set out to test whether co-infections of B and F Wolbachia in hybrid grasshoppers enabled horizontal transfer of phage WO, similar to the numerous examples of phage WO transfer between A and B Wolbachia co-infections. While we found no evidence for transfer between the divergent co-infections, we discovered horizontal transfer of at least three phage WO haplotypes to the grasshopper genome. Subsequent genome sequencing of uninfected grasshoppers uncovered the first evidence for two discrete Wolbachia supergroups (B and F) contributing at least 448 kb and 144 kb of DNA, respectively, into the host nuclear genome. Fluorescent in situ hybridization verified the presence of Wolbachia DNA in C. parallelus chromosomes and revealed that some inserts are subspecies-specific while others are present in both subspecies. We discuss our findings in light of symbiont dynamics in an animal hybrid zone.}, }
@article {pmid26664710, year = {2015}, author = {Mittra, I}, title = {Circulating nucleic acids: a new class of physiological mobile genetic elements.}, journal = {F1000Research}, volume = {4}, number = {}, pages = {924}, pmid = {26664710}, issn = {2046-1402}, abstract = {Mobile genetic elements play a major role in shaping biotic genomes and bringing about evolutionary transformations. Herein, a new class of mobile genetic elements is proposed in the form of circulating nucleic acids (CNAs) derived from the billions of cells that die in the body every day due to normal physiology and that act intra-corporeally. A recent study shows that CNAs can freely enter into healthy cells, integrate into their genomes by a unique mechanism and cause damage to their DNA. Being ubiquitous and continuously arising, CNA-induced DNA damage may be the underlying cause of ageing, ageing-related disabilities and the ultimate demise of the organism. Thus, DNA seems to act in the paradoxical roles of both preserver and destroyer of life. This new class of mobile genetic element may be relevant not only to multi-cellular organisms with established circulatory systems, but also to other multi-cellular organisms in which intra-corporeal mobility of nucleic acids may be mediated via the medium of extra-cellular fluid.}, }
@article {pmid26661395, year = {2016}, author = {Cafini, F and Nguyen, le TT and Higashide, M and Román, F and Prieto, J and Morikawa, K}, title = {Horizontal gene transmission of the cfr gene to MRSA and Enterococcus: role of Staphylococcus epidermidis as a reservoir and alternative pathway for the spread of linezolid resistance.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {71}, number = {3}, pages = {587-592}, doi = {10.1093/jac/dkv391}, pmid = {26661395}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteriophages ; Conjugation, Genetic ; *Drug Resistance, Bacterial ; Enterococcus/drug effects/*genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Japan ; Linezolid/*pharmacology ; Methicillin-Resistant Staphylococcus aureus/drug effects/*genetics ; Plasmids ; Spain ; Staphylococcus epidermidis/drug effects/*genetics ; Transduction, Genetic ; Transformation, Bacterial ; }, abstract = {OBJECTIVES: Linezolid resistance mediated by the cfr gene represents a global concern due to its dissemination among multiresistant nosocomial pathogens such as MRSA and Enterococcus. In the present work, we have evaluated the in vitro transmission of cfr pSCFS7-like plasmids from two Staphylococcus epidermidis ST2 strains (SE45 and SE50) isolated in Spanish hospitals, to clinical MRSA and Enterococcus spp. isolates obtained in Japan, a country in which cfr has not been detected yet. We have also investigated alternative mechanisms of horizontal gene transfer involved in the spread of the cfr gene.<br><br>METHODS: MRSA (n&#x200a;=&#x200a;16) and Enterococcus spp. (n&#x200a;=&#x200a;8) clinical isolates were used as recipients in conjugative experiments. Bacteriophage-mediated transmission was tested using MR83a phage and N315, COL and Mu50 strains. A transformation assay was carried out using a natural competent strain derived from N315.<br><br>RESULTS: The SE45 strain was able to transfer the cfr gene to all strains tested, while transmission from SE50 was observed only to a few strains and with less efficiency. No transmission was observed to Enterococcus spp. isolates. Even though conjugation is thought to be the main mechanism of cfr dissemination, we have demonstrated that transduction can be considered an alternative pathway for transmission of the cfr gene between MRSA strains. However, the results suggest an absence of transmission by natural transformation.<br><br>CONCLUSIONS: Linezolid resistance mediated by cfr vectors, such as pSCFS7-like plasmids, can be efficiently transferred to clinical MRSA in Japanese isolates. After reaching the staphylococcal pool, the cfr gene could be spread among MRSA strains by either conjugation or transduction.}, }
@article {pmid26658054, year = {2016}, author = {Hetem, DJ and Bootsma, MC and Bonten, MJ}, title = {Prevention of Surgical Site Infections: Decontamination With Mupirocin Based on Preoperative Screening for Staphylococcus aureus Carriers or Universal Decontamination?.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {62}, number = {5}, pages = {631-636}, doi = {10.1093/cid/civ990}, pmid = {26658054}, issn = {1537-6591}, mesh = {Administration, Intranasal ; Baths ; Chlorhexidine/administration &amp; dosage/*therapeutic use ; Decontamination ; Drug Resistance, Bacterial ; Humans ; Models, Biological ; Mupirocin/administration &amp; dosage/*therapeutic use ; Nose/microbiology ; Ointments ; Staphylococcal Infections/*prevention &amp; control ; Staphylococcus aureus/drug effects ; Surgical Wound Infection/*prevention &amp; control ; }, abstract = {Perioperative decolonization of Staphylococcus aureus nasal carriers with mupirocin together with chlorhexidine body washing reduces the incidence of S. aureus surgical site infection. A targeted strategy, applied in S. aureus carriers only, is costly, and implementation may reduce effectiveness. Universal decolonization is more cost-effective but increases exposure of noncarriers to mupirocin and the risk of resistance to mupirocin in staphylococci. High-level mupirocin resistance in S. aureus can emerge through horizontal gene transfer originating from coagulase-negative staphylococci (CoNS) and through clonal transmission. The current evidence on the occurrence of high-level mupirocin resistance in S. aureus and CoNS, in combination with the results of mathematical modeling, strongly suggests that the increased selection of high-level mupirocin resistance in CoNS does not constitute an important risk for high-level mupirocin resistance in S. aureus. Compared with a targeted strategy, universal decolonization seems associated with an equally low risk of mupirocin resistance in S. aureus.}, }
@article {pmid26656489, year = {2016}, author = {Rezulak, M and Borsuk, I and Mruk, I}, title = {Natural C-independent expression of restriction endonuclease in a C protein-associated restriction-modification system.}, journal = {Nucleic acids research}, volume = {44}, number = {6}, pages = {2646-2660}, pmid = {26656489}, issn = {1362-4962}, mesh = {Amino Acid Sequence ; Bacterial Proteins/*genetics/metabolism ; Base Sequence ; Citrobacter/*genetics/metabolism ; DNA Restriction Enzymes/*genetics/metabolism ; DNA-Cytosine Methylases/*genetics/metabolism ; Escherichia coli/*genetics/metabolism ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genes, Reporter ; Lac Operon ; Molecular Sequence Data ; Plasmids/chemistry/genetics/metabolism ; Promoter Regions, Genetic ; RNA, Messenger/genetics/metabolism ; Recombinant Proteins/genetics/metabolism ; Transcription Initiation, Genetic ; Transformation, Bacterial ; }, abstract = {Restriction-modification (R-M) systems are highly prevalent among bacteria and archaea, and appear to play crucial roles in modulating horizontal gene transfer and protection against phage. There is much to learn about these diverse enzymes systems, especially their regulation. Type II R-M systems specify two independent enzymes: a restriction endonuclease (REase) and protective DNA methyltransferase (MTase). Their activities need to be finely balanced in vivo Some R-M systems rely on specialized transcription factors called C (controller) proteins. These proteins play a vital role in the temporal regulation of R-M gene expression, and function to indirectly modulate the horizontal transfer of their genes across the species. We report novel regulation of a C-responsive R-M system that involves a C protein of a poorly-studied structural class - C.Csp231I. Here, the C and REase genes share a bicistronic transcript, and some of the transcriptional auto-control features seen in other C-regulated R-M systems are conserved. However, separate tandem promoters drive most transcription of the REase gene, a distinctive property not seen in other tested C-linked R-M systems. Further, C protein only partially controls REase expression, yet plays a role in system stability and propagation. Consequently, high REase activity was observed after deletion of the entire C gene, and cells bearing the ΔC R-M system were outcompeted in mixed culture assays by those with the WT R-M system. Overall, our data reveal unexpected regulatory variation among R-M systems.}, }
@article {pmid26653218, year = {2015}, author = {Huchon, D and Szitenberg, A and Shefer, S and Ilan, M and Feldstein, T}, title = {Mitochondrial group I and group II introns in the sponge orders Agelasida and Axinellida.}, journal = {BMC evolutionary biology}, volume = {15}, number = {}, pages = {278}, pmid = {26653218}, issn = {1471-2148}, mesh = {Animals ; Base Sequence ; Electron Transport Complex IV/genetics ; Gene Transfer, Horizontal ; Genome, Mitochondrial ; *Introns ; Molecular Sequence Data ; Phylogeny ; Porifera/*classification/*genetics ; RNA Splicing ; }, abstract = {BACKGROUND: Self-splicing introns are present in the mitochondria of members of most eukaryotic lineages. They are divided into Group I and Group II introns, according to their secondary structure and splicing mechanism. Being rare in animals, self-splicing introns were only described in a few sponges, cnidarians, placozoans and one annelid species. In sponges, three types of mitochondrial Group I introns were previously described in two demosponge families (Tetillidae, and Aplysinellidae) and in the homoscleromorph family Plakinidae. These three introns differ in their insertion site, secondary structure and in the sequence of the LAGLIDADG gene they encode. Notably, no group II introns have been previously described in sponges.<br><br>RESULTS: We report here the presence of mitochondrial introns in the cytochrome oxidase subunit 1 (COI) gene of three additional sponge species from three different families: Agelas oroides (Agelasidae, Agelasida), Cymbaxinella (p) verrucosa (Hymerhabdiidae, Agelasida) and Axinella polypoides (Axinellidae, Axinellida). We show, for the first time, that sponges can also harbour Group II introns in their COI gene, whose presence in animals' mitochondria has so far been described in only two phyla, Placozoa and Annelida. Surprisingly, two different Group II introns were discovered in the COI gene of C. verrucosa. Phylogenetic analysis indicates that the Group II introns present in C. verrucosa are related to red algae (Rhodophyta) introns.<br><br>CONCLUSIONS: The differences found among intron secondary structures and the phylogenetic inferences support the hypothesis that the introns originated from independent horizontal gene transfer events. Our results thus suggest that self-splicing introns are more diverse in the mitochondrial genome of sponges than previously anticipated.}, }
@article {pmid26652286, year = {2016}, author = {Yang, J and Jiang, Y and Guo, L and Ye, L and Ma, Y and Luo, Y}, title = {Prevalence of Diverse Clones of Vancomycin-Resistant Enterococcus faecium ST78 in a Chinese Hospital.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {22}, number = {4}, pages = {294-300}, doi = {10.1089/mdr.2015.0069}, pmid = {26652286}, issn = {1931-8448}, mesh = {Aged ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics ; Bacterial Typing Techniques ; Carbon-Oxygen Ligases/*genetics ; China/epidemiology ; Clone Cells ; Cross Infection/drug therapy/*epidemiology/microbiology ; Electrophoresis, Gel, Pulsed-Field ; Enterococcus faecium/drug effects/*genetics/isolation &amp; purification/pathogenicity ; Female ; Gene Expression ; Gene Transfer, Horizontal ; Genotype ; Gram-Positive Bacterial Infections/drug therapy/*epidemiology/microbiology ; Hospitals ; Humans ; Male ; Plasmids/chemistry/metabolism ; Prevalence ; Sequence Analysis, DNA ; Vancomycin/pharmacology ; Vancomycin-Resistant Enterococci/drug effects/*genetics/isolation &amp; purification/pathogenicity ; Virulence Factors/*genetics ; }, abstract = {BACKGROUND: Vancomycin-resistant Enterococcus (VRE) has been identified in China. However, little is known about the spread of VRE isolates.<br><br>METHODS: The genetic relatedness of vancomycin-resistant Enterococcus faecium (VREfm) isolates was analyzed by pulsed-field gel electrophoresis (PFGE), their antimicrobial susceptibilities were analyzed by E-test and the VITEK 2 AST-GP67 test Kit, and their sequence types (STs) were investigated by multilocus sequence typing (MLST). S1-PFGE was used for plasmid profiling, and PCR and subsequent sequencing were performed to identify the virulence genes.<br><br>RESULTS: A total of 96 nonduplicated VREfm isolates were obtained and categorized into 38 PFGE types (type 1-38). The predominant MLST type was ST78, while ST17, ST341, and ST342 were also sporadically identified. All types of clinical VREfm strains harbored the vanA gene; however, they carried plasmids of different sizes. While 92.1%, 71.1%, and 60.5% of VREfm strains carried hyl, scm, and ecbA genes, respectively, all of them were positive for esp, acm, sgrA, pilA, and pilB genes.<br><br>CONCLUSIONS: Clonal VREfm spread was observed, and nonplasmid-mediated horizontal transfer of vancomycin-resistant gene might have conveyed resistance to some vancomycin-susceptible E. faecium strains. E. faecium ST78 carrying vanA gene was the most prevalent clone in this study. The high prevalence of virulence genes, including esp, hyl, acm, scm, ecbA, sgrA, pilA, and pilB, confirmed their important roles in the emergence of VREfm ST78 in nosocomial infections.}, }
@article {pmid26651764, year = {2015}, author = {Arnoldt, H and Strogatz, SH and Timme, M}, title = {Toward the Darwinian transition: Switching between distributed and speciated states in a simple model of early life.}, journal = {Physical review. E, Statistical, nonlinear, and soft matter physics}, volume = {92}, number = {5}, pages = {052909}, doi = {10.1103/PhysRevE.92.052909}, pmid = {26651764}, issn = {1550-2376}, mesh = {*Evolution, Molecular ; *Gene Transfer, Horizontal ; *Models, Genetic ; Stochastic Processes ; }, abstract = {It has been hypothesized that in the era just before the last universal common ancestor emerged, life on earth was fundamentally collective. Ancient life forms shared their genetic material freely through massive horizontal gene transfer (HGT). At a certain point, however, life made a transition to the modern era of individuality and vertical descent. Here we present a minimal model for stochastic processes potentially contributing to this hypothesized "Darwinian transition." The model suggests that HGT-dominated dynamics may have been intermittently interrupted by selection-driven processes during which genotypes became fitter and decreased their inclination toward HGT. Stochastic switching in the population dynamics with three-point (hypernetwork) interactions may have destabilized the HGT-dominated collective state and essentially contributed to the emergence of vertical descent and the first well-defined species in early evolution. A systematic nonlinear analysis of the stochastic model dynamics covering key features of evolutionary processes (such as selection, mutation, drift and HGT) supports this view. Our findings thus suggest a viable direction out of early collective evolution, potentially enabling the start of individuality and vertical Darwinian evolution.}, }
@article {pmid26650381, year = {2016}, author = {Anjum, R and Krakat, N}, title = {Detection of Multiple Resistances, Biofilm Formation and Conjugative Transfer of Bacillus cereus from Contaminated Soils.}, journal = {Current microbiology}, volume = {72}, number = {3}, pages = {321-328}, pmid = {26650381}, issn = {1432-0991}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/classification/*drug effects/genetics/*isolation &amp; purification ; Biofilms/*growth &amp; development ; Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Drug Resistance, Bacterial ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Molecular Sequence Data ; Pesticides/pharmacology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {The purpose of this study was to detect microbial resistances to a set of antibiotics/pesticides (multi-resistance) within pesticide and antibiotic-contaminated alluvial soils and to identify the corresponding antibiotic resistance genes (ARGs). To assess whether identified multi-resistant isolates are able to construct biofilms, several biofilm formation and conjugation experiments were conducted. Out of 35 isolates, six strains were used for filter mating experiments. Nine strains were identified by 16S rDNA gene sequence analyses and those were closely related to Pseudomonas sp., Citrobacter sp., Acinetobacter sp., Enterobacter sp., and in addition, Bacillus cereus was chosen for multi-resistant and pesticide-tolerant studies. Antibiotic-resistant and pesticide-tolerant bacterial strains were tested for the presence of ARGs. All nine strains were containing multiple ARGs (ampC, ermB, ermD, ermG, mecA, tetM) in different combinations. Interestingly, only strain WR34 (strongly related to Bacillus cereus) exhibited a high biofilm forming capacity on glass beads. Results obtained by filter mating experiments demonstrated gene transfer frequencies from 10(-5) to 10(-8). This study provides evidence that alluvial soils are hot spots for the accumulation of antibiotics, pesticides and biofilm formation. Particularly high resistances to tetracycline, ampicillin, amoxicillin and methicillin were proved. Apparently, isolate WR34 strongly correlated to a pathogenic organism had high potential to deploy biofilms in alluvial soils. Thus, we assume that loosened and unconsolidated soils investigated pose a high risk of an enhanced ARG prevalence.}, }
@article {pmid26645270, year = {2016}, author = {Yoon, EJ and Goussard, S and Nemec, A and Lambert, T and Courvalin, P and Grillot-Courvalin, C}, title = {Origin in Acinetobacter gyllenbergii and dissemination of aminoglycoside-modifying enzyme AAC(6')-Ih.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {71}, number = {3}, pages = {601-606}, pmid = {26645270}, issn = {1460-2091}, support = {HHSN272200900018C/AI/NIAID NIH HHS/United States ; HHSN272200900018C/AI/NIAID NIH HHS/United States ; }, mesh = {Acetyltransferases/*genetics/*metabolism ; Acinetobacter Infections/microbiology ; Acinetobacter baumannii/*classification/drug effects/*enzymology/genetics ; Aminoglycosides/metabolism/*pharmacology ; Anti-Bacterial Agents/metabolism/*pharmacology ; DNA Transposable Elements ; *Drug Resistance, Bacterial ; Gene Dosage ; Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; Plasmids/analysis ; Promoter Regions, Genetic ; Real-Time Polymerase Chain Reaction ; }, abstract = {OBJECTIVES: The aac(6')-Ih gene encoding aminoglycoside 6'-N-acetyltransferase type I subtype h [AAC(6')-Ih] is plasmid-borne in Acinetobacter baumannii where it confers high-level amikacin resistance, but its origin remains unknown. We searched for the gene in the genomes of a collection of 133 Acinetobacter spp. and studied its species specificity, expression and dissemination.<br><br>METHODS: Gene copy number was determined by quantitative PCR, expression by quantitative RT-PCR, MIC by microdilution and transfer by plasmid mobilization.<br><br>RESULTS: The aac(6')-Ih gene was present in the chromosome of the two Acinetobacter gyllenbergii of the collection and was detected in all seven A. gyllenbergii clinical isolates. They had indistinguishable flanking regions indicating that the gene was intrinsic to this species. A. baumannii PIS Aba23 promoters were provided by insertion of ISAba23, which disrupted the Pnative promoter in A. gyllenbergii. Both types of promoters were similarly potent in Escherichia coli and A. baumannii. Aminoglycoside MICs for A. baumannii harbouring pIP1858 were higher than for A. gyllenbergii due to gene dosage. The non-self-transferable plasmid could be mobilized to other A. baumannii cells by the broad host range plasmid RP4.<br><br>CONCLUSIONS: We have found the origin of aac(6')-Ih in A. gyllenbergii, a species isolated, although rarely, in humans, and documented that dissemination of this gene is restricted to the Acinetobacter genus.}, }
@article {pmid26644001, year = {2015}, author = {Scales, BS and Erb-Downward, JR and Huffnagle, IM and LiPuma, JJ and Huffnagle, GB}, title = {Comparative genomics of Pseudomonas fluorescens subclade III strains from human lungs.}, journal = {BMC genomics}, volume = {16}, number = {}, pages = {1032}, pmid = {26644001}, issn = {1471-2164}, support = {T32 AI007528/AI/NIAID NIH HHS/United States ; U19 AI090871/AI/NIAID NIH HHS/United States ; T32-AI007528/AI/NIAID NIH HHS/United States ; R01 HL114447/HL/NHLBI NIH HHS/United States ; U19-AI090871/AI/NIAID NIH HHS/United States ; R0I-HL114447/HL/NHLBI NIH HHS/United States ; }, mesh = {Bacterial Secretion Systems/genetics ; Base Composition ; Cystic Fibrosis/complications ; Genetic Loci ; *Genome, Bacterial ; *Genomics/methods ; Genotype ; Humans ; Metals/metabolism ; Multigene Family ; Phenotype ; Phylogeny ; Pneumonia, Bacterial/*microbiology ; Pseudomonas Infections/*microbiology ; Pseudomonas fluorescens/*classification/*genetics/isolation &amp; purification/metabolism ; Secondary Metabolism/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: While the taxonomy and genomics of environmental strains from the P. fluorescens species-complex has been reported, little is known about P. fluorescens strains from clinical samples. In this report, we provide the first genomic analysis of P. fluorescens strains in which human vs. environmental isolates are compared.<br><br>RESULTS: Seven P. fluorescens strains were isolated from respiratory samples from cystic fibrosis (CF) patients. The clinical strains could grow at a higher temperature (>34 &#xb0;C) than has been reported for environmental strains. Draft genomes were generated for all of the clinical strains, and multi-locus sequence analysis placed them within subclade III of the P. fluorescens species-complex. All strains encoded type- II, -III, -IV, and -VI secretion systems, as well as the widespread colonization island (WCI). This is the first description of a WCI in P. fluorescens strains. All strains also encoded a complete I2/PfiT locus and showed evidence of horizontal gene transfer. The clinical strains were found to differ from the environmental strains in the number of genes involved in metal resistance, which may be a possible adaptation to chronic antibiotic exposure in the CF lung.<br><br>CONCLUSIONS: This is the largest comparative genomics analysis of P. fluorescens subclade III strains to date and includes the first clinical isolates. At a global level, the clinical P. fluorescens subclade III strains were largely indistinguishable from environmental P. fluorescens subclade III strains, supporting the idea that identifying strains as 'environmental' vs 'clinical' is not a phenotypic trait. Rather, strains within P. fluorescens subclade III will colonize and persist in any niche that provides the requirements necessary for growth.}, }
@article {pmid26636559, year = {2016}, author = {Widderich, N and Czech, L and Elling, FJ and Könneke, M and Stöveken, N and Pittelkow, M and Riclea, R and Dickschat, JS and Heider, J and Bremer, E}, title = {Strangers in the archaeal world: osmostress-responsive biosynthesis of ectoine and hydroxyectoine by the marine thaumarchaeon Nitrosopumilus maritimus.}, journal = {Environmental microbiology}, volume = {18}, number = {4}, pages = {1227-1248}, doi = {10.1111/1462-2920.13156}, pmid = {26636559}, issn = {1462-2920}, mesh = {Amino Acid Sequence ; Amino Acids, Diamino/*biosynthesis/genetics ; Archaea/genetics/*metabolism ; Escherichia coli/genetics ; Gene Transfer, Horizontal/genetics ; Hydro-Lyases/*genetics ; Mechanoreceptors/metabolism ; Mixed Function Oxygenases/genetics ; Multigene Family/genetics ; Osmotic Pressure/*physiology ; Phylogeny ; }, abstract = {Ectoine and hydroxyectoine are compatible solutes widely synthesized by members of the Bacteria to cope with high osmolarity surroundings. Inspection of 557 archaeal genomes revealed that only 12 strains affiliated with the Nitrosopumilus, Methanothrix or Methanobacterium genera harbour ectoine/hydroxyectoine gene clusters. Phylogenetic considerations suggest that these Archaea have acquired these genes through horizontal gene transfer events. Using the Thaumarchaeon 'Candidatus Nitrosopumilus maritimus' as an example, we demonstrate that the transcription of its ectABCD genes is osmotically induced and functional since it leads to the production of both ectoine and hydroxyectoine. The ectoine synthase and the ectoine hydroxylase were biochemically characterized, and their properties resemble those of their counterparts from Bacteria. Transcriptional analysis of osmotically stressed 'Ca. N. maritimus' cells demonstrated that they possess an ectoine/hydroxyectoine gene cluster (hyp-ectABCD-mscS) different from those recognized previously since it contains a gene for an MscS-type mechanosensitive channel. Complementation experiments with an Escherichia coli mutant lacking all known mechanosensitive channel proteins demonstrated that the (Nm)MscS protein is functional. Hence, 'Ca. N. maritimus' cells cope with high salinity not only through enhanced synthesis of osmostress-protective ectoines but they already prepare themselves simultaneously for an eventually occurring osmotic down-shock by enhancing the production of a safety-valve (NmMscS).}, }
@article {pmid26635412, year = {2016}, author = {Li, X and Wang, Y and Brown, CJ and Yao, F and Jiang, Y and Top, EM and Li, H}, title = {Diversification of broad host range plasmids correlates with the presence of antibiotic resistance genes.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {1}, pages = {}, pmid = {26635412}, issn = {1574-6941}, support = {R01AI084918/AI/NIAID NIH HHS/United States ; P20RR016454/RR/NCRR NIH HHS/United States ; R01 AI084918/AI/NIAID NIH HHS/United States ; P20 GM103408/GM/NIGMS NIH HHS/United States ; P20 RR016454/RR/NCRR NIH HHS/United States ; P20GM103408/GM/NIGMS NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Base Sequence ; China ; DNA Helicases/genetics ; Drug Resistance, Bacterial/*genetics ; Environmental Pollution ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/genetics ; Genomics/*methods ; Host Specificity ; Petroleum/metabolism ; Phylogeny ; Plasmids/*genetics/isolation &amp; purification ; Proteobacteria/drug effects/genetics/virology ; Sequence Analysis, DNA ; Soil Pollutants/metabolism ; Wastewater/microbiology ; }, abstract = {The IncP-1ε subgroup is a recently identified phylogenetic clade within IncP-1 plasmids, which plays an important role in the spread of antibiotic resistance and degradation of xenobiotic pollutants. Here, four IncP-1ε plasmids were exogenously captured from a petroleum-contaminated habitat in China and compared phylogenetically and genomically with previously reported IncP-1ε and other IncP-1 plasmids. The IncP-1ε plasmids can be clearly subdivided into two subclades, designated as ε-I and ε-II, based on phylogenetic analysis of backbone proteins TraI and TrfA. This was further supported by comparison of concatenated backbone genes. Moreover, the two subclades differed in the transposon types, phenotypes and insertion locations of the accessory elements. The accessory genes on ε-I plasmids were inserted between parA and traC, and harbored ISPa17 and Tn402-like transposon modules, typically carrying antibiotic resistance genes. In contrast, the accessory elements on ε-II plasmids were typically located between trfA and oriV, and contained IS1071, which was commonly inserted within the Tn501-like transposon, typically harboring a cluster of genes encoding mercury resistance and/or catabolic pathways. Our study is one of the first to compare IncP-1 plasmid genomes from China, expands the available collection of IncP-1ε plasmids and enhances our understanding of their diversity, biogeography and evolutionary history.}, }
@article {pmid26634393, year = {2016}, author = {Sarkar, A and Paul, D and Kazy, SK and Sar, P}, title = {Molecular analysis of microbial community in arsenic-rich groundwater of Kolsor, West Bengal.}, journal = {Journal of environmental science and health. Part A, Toxic/hazardous substances &amp; environmental engineering}, volume = {51}, number = {3}, pages = {229-239}, doi = {10.1080/10934529.2015.1094339}, pmid = {26634393}, issn = {1532-4117}, mesh = {Arsenic/*analysis/metabolism ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Groundwater/chemistry/*microbiology ; India ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Water Pollutants, Chemical/*analysis/metabolism ; }, abstract = {Bacterial community composition within the highly arsenic (As) contaminated groundwater from Kolsur, West Bengal was analyzed over a period of 3 years using 16S rRNA gene clone library and Denaturing Gradient Gel Electrophoresis (DGGE). Molecular phylogenetic study revealed abundance of α-Proteobacteria (56%) and Firmicutes (29%) along with members of β-Proteobacteria, Verrucomicrobia and Sphingobacteria as relatively minor groups. Along with consistent physicochemical environment, a stable microbial community structure comprising of bacterial genera Agrobacterium-Rhizobium, Ochrobactrum, Pseudomonas, Anoxybacillus and Penibacillus was recorded over the three years study period. Presence of cytosolic arsenate reductase (arsC) gene was observed within the microbial community. Phylogenetic analyses revealed that all the arsC sequences were closely related to the same gene from γ-proteobacterial members while the community was consisted of mainly α-proteobacterial groups. Such phylogenetic incongruence between 16S rRNA and arsC genes possibly indicated horizontal gene transfer (HGT) of the ars genes within the groundwater community. Overall, the study reported a nearly stable geomicrobial environment and genetic determinant related to As homeostasis gene, and provided a better insight on biogeochemistry of As contaminated aquifer of West Bengal.}, }
@article {pmid26632584, year = {2015}, author = {Rohwer, F and Segall, AM}, title = {In retrospect: A century of phage lessons.}, journal = {Nature}, volume = {528}, number = {7580}, pages = {46-48}, pmid = {26632584}, issn = {1476-4687}, mesh = {*Bacteriophages/genetics/immunology/pathogenicity/physiology ; CRISPR-Cas Systems/genetics ; Cyanobacteria/genetics/metabolism/virology ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genome, Viral/genetics ; History, 20th Century ; History, 21st Century ; Host-Pathogen Interactions/genetics ; Humans ; Molecular Biology/*history ; Mutagenesis/genetics ; Neoplasms/genetics/pathology ; Oncogenes/genetics ; Photosynthesis ; Sequence Analysis, DNA/history ; Synthetic Biology/trends ; }, }
@article {pmid26627243, year = {2015}, author = {Mesquita, RD and Vionette-Amaral, RJ and Lowenberger, C and Rivera-Pomar, R and Monteiro, FA and Minx, P and Spieth, J and Carvalho, AB and Panzera, F and Lawson, D and Torres, AQ and Ribeiro, JM and Sorgine, MH and Waterhouse, RM and Montague, MJ and Abad-Franch, F and Alves-Bezerra, M and Amaral, LR and Araujo, HM and Araujo, RN and Aravind, L and Atella, GC and Azambuja, P and Berni, M and Bittencourt-Cunha, PR and Braz, GR and Calderón-Fernández, G and Carareto, CM and Christensen, MB and Costa, IR and Costa, SG and Dansa, M and Daumas-Filho, CR and De-Paula, IF and Dias, FA and Dimopoulos, G and Emrich, SJ and Esponda-Behrens, N and Fampa, P and Fernandez-Medina, RD and da Fonseca, RN and Fontenele, M and Fronick, C and Fulton, LA and Gandara, AC and Garcia, ES and Genta, FA and Giraldo-Calderón, GI and Gomes, B and Gondim, KC and Granzotto, A and Guarneri, AA and Guigó, R and Harry, M and Hughes, DS and Jablonka, W and Jacquin-Joly, E and Juárez, MP and Koerich, LB and Lange, AB and Latorre-Estivalis, JM and Lavore, A and Lawrence, GG and Lazoski, C and Lazzari, CR and Lopes, RR and Lorenzo, MG and Lugon, MD and Majerowicz, D and Marcet, PL and Mariotti, M and Masuda, H and Megy, K and Melo, AC and Missirlis, F and Mota, T and Noriega, FG and Nouzova, M and Nunes, RD and Oliveira, RL and Oliveira-Silveira, G and Ons, S and Orchard, I and Pagola, L and Paiva-Silva, GO and Pascual, A and Pavan, MG and Pedrini, N and Peixoto, AA and Pereira, MH and Pike, A and Polycarpo, C and Prosdocimi, F and Ribeiro-Rodrigues, R and Robertson, HM and Salerno, AP and Salmon, D and Santesmasses, D and Schama, R and Seabra-Junior, ES and Silva-Cardoso, L and Silva-Neto, MA and Souza-Gomes, M and Sterkel, M and Taracena, ML and Tojo, M and Tu, ZJ and Tubio, JM and Ursic-Bedoya, R and Venancio, TM and Walter-Nuno, AB and Wilson, D and Warren, WC and Wilson, RK and Huebner, E and Dotson, EM and Oliveira, PL}, title = {Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {48}, pages = {14936-14941}, pmid = {26627243}, issn = {1091-6490}, support = {NHGRI-HG003079//PHS HHS/United States ; HHSN272200900039C//PHS HHS/United States ; R01 AI045545/AI/NIAID NIH HHS/United States ; HHSN272200900039C/AI/NIAID NIH HHS/United States ; U54 HG003079/HG/NHGRI NIH HHS/United States ; }, mesh = {Adaptation, Physiological/*genetics ; Animals ; Base Sequence ; *Chagas Disease ; Gene Transfer, Horizontal ; Host-Parasite Interactions/*genetics ; Humans ; *Insect Vectors/genetics/parasitology ; Molecular Sequence Data ; *Rhodnius/genetics/parasitology ; Trypanosoma cruzi/*physiology ; Wolbachia/genetics ; }, abstract = {Rhodnius prolixus not only has served as a model organism for the study of insect physiology, but also is a major vector of Chagas disease, an illness that affects approximately seven million people worldwide. We sequenced the genome of R. prolixus, generated assembled sequences covering 95% of the genome (∼ 702 Mb), including 15,456 putative protein-coding genes, and completed comprehensive genomic analyses of this obligate blood-feeding insect. Although immune-deficiency (IMD)-mediated immune responses were observed, R. prolixus putatively lacks key components of the IMD pathway, suggesting a reorganization of the canonical immune signaling network. Although both Toll and IMD effectors controlled intestinal microbiota, neither affected Trypanosoma cruzi, the causal agent of Chagas disease, implying the existence of evasion or tolerance mechanisms. R. prolixus has experienced an extensive loss of selenoprotein genes, with its repertoire reduced to only two proteins, one of which is a selenocysteine-based glutathione peroxidase, the first found in insects. The genome contained actively transcribed, horizontally transferred genes from Wolbachia sp., which showed evidence of codon use evolution toward the insect use pattern. Comparative protein analyses revealed many lineage-specific expansions and putative gene absences in R. prolixus, including tandem expansions of genes related to chemoreception, feeding, and digestion that possibly contributed to the evolution of a blood-feeding lifestyle. The genome assembly and these associated analyses provide critical information on the physiology and evolution of this important vector species and should be instrumental for the development of innovative disease control methods.}, }
@article {pmid26626322, year = {2015}, author = {Wegmann, U and MacKenzie, DA and Zheng, J and Goesmann, A and Roos, S and Swarbreck, D and Walter, J and Crossman, LC and Juge, N}, title = {The pan-genome of Lactobacillus reuteri strains originating from the pig gastrointestinal tract.}, journal = {BMC genomics}, volume = {16}, number = {}, pages = {1023}, pmid = {26626322}, issn = {1471-2164}, support = {BB/J004529/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/K019554/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/00044452/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bacterial Outer Membrane Proteins/genetics ; Bacterial Secretion Systems/genetics ; Bacteriophages ; Basal Metabolism/genetics ; Chromosomes, Bacterial ; Gastrointestinal Tract/microbiology ; Gene Order ; Gene Transfer, Horizontal ; Genetic Structures ; *Genome, Bacterial ; *Genomics/methods ; High-Throughput Nucleotide Sequencing ; Host-Pathogen Interactions ; Limosilactobacillus reuteri/*genetics/isolation &amp; purification/metabolism/virology ; Multigene Family ; Phylogeny ; Pseudogenes ; Swine ; }, abstract = {BACKGROUND: Lactobacillus reuteri is a gut symbiont of a wide variety of vertebrate species that has diversified into distinct phylogenetic clades which are to a large degree host-specific. Previous work demonstrated host specificity in mice and begun to determine the mechanisms by which gut colonisation and host restriction is achieved. However, how L. reuteri strains colonise the gastrointestinal (GI) tract of pigs is unknown.<br><br>RESULTS: To gain insight into the ecology of L. reuteri in the pig gut, the genome sequence of the porcine small intestinal isolate L. reuteri ATCC 53608 was completed and consisted of a chromosome of 1.94 Mbp and two plasmids of 138.5 kbp and 9.09 kbp, respectively. Furthermore, we generated draft genomes of four additional L. reuteri strains isolated from pig faeces or lower GI tract, lp167-67, pg-3b, 20-2 and 3c6, and subjected all five genomes to a comparative genomic analysis together with the previously completed genome of strain I5007. A phylogenetic analysis based on whole genomes showed that porcine L. reuteri strains fall into two distinct clades, as previously suggested by multi-locus sequence analysis. These six pig L. reuteri genomes contained a core set of 1364 orthologous gene clusters, as determined by OrthoMCL analysis, that contributed to a pan-genome totalling 3373 gene clusters. Genome comparisons of the six pig L. reuteri strains with 14&#x2009;L. reuteri strains from other host origins gave a total pan-genome of 5225 gene clusters that included a core genome of 851 gene clusters but revealed that there were no pig-specific genes per se. However, genes specific for and conserved among strains of the two pig phylogenetic lineages were detected, some of which encoded cell surface proteins that could contribute to the diversification of the two lineages and their observed host specificity.<br><br>CONCLUSIONS: This study extends the phylogenetic analysis of L. reuteri strains at a genome-wide level, pointing to distinct evolutionary trajectories of porcine L. reuteri lineages, and providing new insights into the genomic events in L. reuteri that occurred during specialisation to their hosts. The occurrence of two distinct pig-derived clades may reflect differences in host genotype, environmental factors such as dietary components or to evolution from ancestral strains of human and rodent origin following contact with pig populations.}, }
@article {pmid26618540, year = {2015}, author = {Kingston, AW and Roussel-Rossin, C and Dupont, C and Raleigh, EA}, title = {Correction: Novel recA-Independent Horizontal Gene Transfer in Escherichia coli K-12.}, journal = {PloS one}, volume = {10}, number = {11}, pages = {e0143991}, pmid = {26618540}, issn = {1932-6203}, }
@article {pmid26616601, year = {2016}, author = {Le Devendec, L and Mourand, G and Bougeard, S and Léaustic, J and Jouy, E and Keita, A and Couet, W and Rousset, N and Kempf, I}, title = {Impact of colistin sulfate treatment of broilers on the presence of resistant bacteria and resistance genes in stored or composted manure.}, journal = {Veterinary microbiology}, volume = {194}, number = {}, pages = {98-106}, doi = {10.1016/j.vetmic.2015.11.012}, pmid = {26616601}, issn = {1873-2542}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bedding and Linens/microbiology ; Chickens ; Colistin/*pharmacology ; Drug Resistance, Bacterial/drug effects/*genetics ; Feces/microbiology ; Gene Transfer, Horizontal ; Gram-Negative Bacteria/*drug effects/genetics/*physiology ; Intestines/microbiology ; Manure/*microbiology ; Plasmids/genetics ; *Soil Microbiology ; Time Factors ; }, abstract = {The application of manure may result in contamination of the environment with antimicrobials, antimicrobial-resistant bacteria, resistance genes and plasmids. The aim of this study was to investigate the impact of the administration of colistin and of manure management on (i) the presence of colistin-resistant Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa and (ii) the prevalence of various antimicrobial resistance genes in feces and in composted or stored manure. One flock of chickens was treated with colistin at the recommended dosage and a second flock was kept as an untreated control. Samples of feces, litter and stored or composted manure from both flocks were collected for isolation and determination of the colistin-susceptibility of E. coli, K. pneumoniae and P. aeruginosa and quantification of genes coding for resistance to different antimicrobials. The persistence of plasmids in stored or composted manure from colistin-treated broilers was also evaluated by plasmid capturing experiments. Results revealed that colistin administration to chickens had no apparent impact on the antimicrobial resistance of the dominant Enterobacteriaceae and P. aeruginosa populations in the chicken gut. Composting stimulated an apparently limited decrease in genes coding for resistance to different antimicrobial families. Importantly, it was shown that even after six weeks of composting or storage, plasmids carrying antimicrobial resistance genes could still be transferred to a recipient E. coli. In conclusion, composting is insufficient to completely eliminate the risk of spreading antimicrobial resistance through chicken manure.}, }
@article {pmid26615332, year = {2016}, author = {Metzger, LC and Blokesch, M}, title = {Regulation of competence-mediated horizontal gene transfer in the natural habitat of Vibrio cholerae.}, journal = {Current opinion in microbiology}, volume = {30}, number = {}, pages = {1-7}, doi = {10.1016/j.mib.2015.10.007}, pmid = {26615332}, issn = {1879-0364}, mesh = {Bacterial Secretion Systems/genetics/metabolism ; Ecosystem ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Vibrio cholerae/*genetics/metabolism ; }, abstract = {The human pathogen Vibrio cholerae is an autochthonous inhabitant of aquatic environments where it often interacts with zooplankton and their chitinous molts. Chitin induces natural competence for transformation in V. cholerae, a key mode of horizontal gene transfer (HGT). Recent comparative genomic analyses were indicative of extensive HGT in this species. However, we can still expand our understanding of the complex regulatory network that drives competence in V. cholerae. Here, we present recent advances, including the elucidation of bipartite competence regulation mediated by QstR, the inclusion of the type VI secretion system in the competence regulon of pandemic O1 El Tor strains, and the identification of TfoS as a transcriptional regulator that links chitin to competence induction in V. cholerae.}, }
@article {pmid26615220, year = {2015}, author = {Brito, AF and Braconi, CT and Weidmann, M and Dilcher, M and Alves, JM and Gruber, A and Zanotto, PM}, title = {The Pangenome of the Anticarsia gemmatalis Multiple Nucleopolyhedrovirus (AgMNPV).}, journal = {Genome biology and evolution}, volume = {8}, number = {1}, pages = {94-108}, pmid = {26615220}, issn = {1759-6653}, mesh = {Animals ; Baculoviridae/*genetics ; Base Sequence ; *Genome, Viral ; Genomic Instability ; Lepidoptera/*virology ; Molecular Sequence Data ; Open Reading Frames ; Polymorphism, Genetic ; Recombination, Genetic ; Ubiquitins/genetics ; Viral Proteins/genetics ; }, abstract = {The alphabaculovirus Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV) is the world's most successful viral bioinsecticide. Through the 1980s and 1990s, this virus was extensively used for biological control of populations of Anticarsia gemmatalis (Velvetbean caterpillar) in soybean crops. During this period, genetic studies identified several variable loci in the AgMNPV; however, most of them were not characterized at the sequence level. In this study we report a full genome comparison among 17 wild-type isolates of AgMNPV. We found the pangenome of this virus to contain at least 167 hypothetical genes, 151 of which are shared by all genomes. The gene bro-a that might be involved in host specificity and carrying transporter is absent in some genomes, and new hypothetical genes were observed. Among these genes there is a unique rnf12-like gene, probably implicated in ubiquitination. Events of gene fission and fusion are common, as four genes have been observed as single or split open reading frames. Gains and losses of genomic fragments (from 20 to 900 bp) are observed within tandem repeats, such as in eight direct repeats and four homologous regions. Most AgMNPV genes present low nucleotide diversity, and variable genes are mainly located in a locus known to evolve through homologous recombination. The evolution of AgMNPV is mainly driven by small indels, substitutions, gain and loss of nucleotide stretches or entire coding sequences. These variations may cause relevant phenotypic alterations, which probably affect the infectivity of AgMNPV. This work provides novel information on genomic evolution of the AgMNPV in particular and of baculoviruses in general.}, }
@article {pmid26615215, year = {2015}, author = {Schaap, P and Barrantes, I and Minx, P and Sasaki, N and Anderson, RW and Bénard, M and Biggar, KK and Buchler, NE and Bundschuh, R and Chen, X and Fronick, C and Fulton, L and Golderer, G and Jahn, N and Knoop, V and Landweber, LF and Maric, C and Miller, D and Noegel, AA and Peace, R and Pierron, G and Sasaki, T and Schallenberg-Rüdinger, M and Schleicher, M and Singh, R and Spaller, T and Storey, KB and Suzuki, T and Tomlinson, C and Tyson, JJ and Warren, WC and Werner, ER and Werner-Felmayer, G and Wilson, RK and Winckler, T and Gott, JM and Glöckner, G and Marwan, W}, title = {The Physarum polycephalum Genome Reveals Extensive Use of Prokaryotic Two-Component and Metazoan-Type Tyrosine Kinase Signaling.}, journal = {Genome biology and evolution}, volume = {8}, number = {1}, pages = {109-125}, pmid = {26615215}, issn = {1759-6653}, support = {HG003079/HG/NHGRI NIH HHS/United States ; 100293/Z/12/Z/WT_/Wellcome Trust/United Kingdom ; R01 GM054663/GM/NIGMS NIH HHS/United States ; 100293/WT_/Wellcome Trust/United Kingdom ; GM54663/GM/NIGMS NIH HHS/United States ; P 22406/FWF_/Austrian Science Fund FWF/Austria ; U54 HG003079/HG/NHGRI NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; BB/K000799/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Cell Cycle Proteins/genetics/metabolism ; *Evolution, Molecular ; Genetic Loci ; *Genome, Protozoan ; Physarum polycephalum/*genetics ; Protozoan Proteins/*genetics/metabolism ; Receptor Protein-Tyrosine Kinases/*genetics/metabolism ; *Signal Transduction ; Transcriptome ; }, abstract = {Physarum polycephalum is a well-studied microbial eukaryote with unique experimental attributes relative to other experimental model organisms. It has a sophisticated life cycle with several distinct stages including amoebal, flagellated, and plasmodial cells. It is unusual in switching between open and closed mitosis according to specific life-cycle stages. Here we present the analysis of the genome of this enigmatic and important model organism and compare it with closely related species. The genome is littered with simple and complex repeats and the coding regions are frequently interrupted by introns with a mean size of 100 bases. Complemented with extensive transcriptome data, we define approximately 31,000 gene loci, providing unexpected insights into early eukaryote evolution. We describe extensive use of histidine kinase-based two-component systems and tyrosine kinase signaling, the presence of bacterial and plant type photoreceptors (phytochromes, cryptochrome, and phototropin) and of plant-type pentatricopeptide repeat proteins, as well as metabolic pathways, and a cell cycle control system typically found in more complex eukaryotes. Our analysis characterizes P. polycephalum as a prototypical eukaryote with features attributed to the last common ancestor of Amorphea, that is, the Amoebozoa and Opisthokonts. Specifically, the presence of tyrosine kinases in Acanthamoeba and Physarum as representatives of two distantly related subdivisions of Amoebozoa argues against the later emergence of tyrosine kinase signaling in the opisthokont lineage and also against the acquisition by horizontal gene transfer.}, }
@article {pmid26612499, year = {2016}, author = {Remigi, P and Zhu, J and Young, JPW and Masson-Boivin, C}, title = {Symbiosis within Symbiosis: Evolving Nitrogen-Fixing Legume Symbionts.}, journal = {Trends in microbiology}, volume = {24}, number = {1}, pages = {63-75}, doi = {10.1016/j.tim.2015.10.007}, pmid = {26612499}, issn = {1878-4380}, mesh = {Alphaproteobacteria/genetics/physiology ; Biological Evolution ; *Evolution, Molecular ; Fabaceae/genetics/*microbiology/physiology ; Genes, Bacterial ; Nitrogen/metabolism ; Nitrogen Fixation/*physiology ; Phylogeny ; Rhizobium/genetics/physiology ; Soil Microbiology ; Symbiosis/genetics/*physiology ; }, abstract = {Bacterial accessory genes are genomic symbionts with an evolutionary history and future that is different from that of their hosts. Packages of accessory genes move from strain to strain and confer important adaptations, such as interaction with eukaryotes. The ability to fix nitrogen with legumes is a remarkable example of a complex trait spread by horizontal transfer of a few key symbiotic genes, converting soil bacteria into legume symbionts. Rhizobia belong to hundreds of species restricted to a dozen genera of the Alphaproteobacteria and Betaproteobacteria, suggesting infrequent successful transfer between genera but frequent successful transfer within genera. Here we review the genetic and environmental conditions and selective forces that have shaped evolution of this complex symbiotic trait.}, }
@article {pmid26612095, year = {2016}, author = {Kyrillos, A and Arora, G and Murray, B and Rosenwald, AG}, title = {The Presence of Phage Orthologous Genes in Helicobacter pylori Correlates with the Presence of the Virulence Factors CagA and VacA.}, journal = {Helicobacter}, volume = {21}, number = {3}, pages = {226-233}, doi = {10.1111/hel.12282}, pmid = {26612095}, issn = {1523-5378}, mesh = {Antigens, Bacterial/*genetics ; Bacterial Proteins/*genetics ; Bacteriophages/*genetics ; Helicobacter Infections/*microbiology ; Helicobacter pylori/*genetics/pathogenicity ; Humans ; Phylogeny ; Stomach Neoplasms/*microbiology ; Stomach Ulcer/*microbiology ; Virulence Factors/genetics ; }, abstract = {BACKGROUND: The bacterium Helicobacter pylori is associated with ulcers and the development of gastric cancer. Several genes, including cytotoxin-associated gene A (CagA) and vacuolating cytotoxin A (VacA), are associated with increased gastric cancer risk. Some strains of H. pylori also contain sequences related to bacteriophage phiHP33; however, the significance of these phage-related sequences remains unknown.<br><br>MATERIALS AND METHODS: We assessed the extent to which phiHP33-related sequences are present in 335 H.&#xa0;pylori strains using homology searches then mapped shared genes between phiHP33 and H.&#xa0;pylori strains onto an existing phylogeny.<br><br>RESULTS: One hundred and twenty-one H.&#xa0;pylori strains contain phage orthologous sequences, and the presence of the phage-related sequences correlates with the presence of CagA and VacA. Mapping of the phage orthologs onto a phylogeny of H.&#xa0;pylori is consistent with the hypothesis that these genes were acquired by horizontal gene transfer.<br><br>CONCLUSIONS: phiHP33 phage orthologous sequences might be of significance in understanding virulence of different H.&#xa0;pylori strains.}, }
@article {pmid26610025, year = {2015}, author = {van Kessel, MA and Speth, DR and Albertsen, M and Nielsen, PH and Op den Camp, HJ and Kartal, B and Jetten, MS and Lücker, S}, title = {Complete nitrification by a single microorganism.}, journal = {Nature}, volume = {528}, number = {7583}, pages = {555-559}, pmid = {26610025}, issn = {1476-4687}, support = {232937/ERC_/European Research Council/International ; 339880/ERC_/European Research Council/International ; }, mesh = {Ammonia/*metabolism ; Bacteria/enzymology/genetics/*metabolism ; Evolution, Molecular ; Genome, Bacterial/genetics ; Nitrates/*metabolism ; *Nitrification/genetics ; Nitrites/*metabolism ; Oxidation-Reduction ; Oxidoreductases/genetics/metabolism ; Phylogeny ; }, abstract = {Nitrification is a two-step process where ammonia is first oxidized to nitrite by ammonia-oxidizing bacteria and/or archaea, and subsequently to nitrate by nitrite-oxidizing bacteria. Already described by Winogradsky in 1890, this division of labour between the two functional groups is a generally accepted characteristic of the biogeochemical nitrogen cycle. Complete oxidation of ammonia to nitrate in one organism (complete ammonia oxidation; comammox) is energetically feasible, and it was postulated that this process could occur under conditions selecting for species with lower growth rates but higher growth yields than canonical ammonia-oxidizing microorganisms. Still, organisms catalysing this process have not yet been discovered. Here we report the enrichment and initial characterization of two Nitrospira species that encode all the enzymes necessary for ammonia oxidation via nitrite to nitrate in their genomes, and indeed completely oxidize ammonium to nitrate to conserve energy. Their ammonia monooxygenase (AMO) enzymes are phylogenetically distinct from currently identified AMOs, rendering recent acquisition by horizontal gene transfer from known ammonia-oxidizing microorganisms unlikely. We also found highly similar amoA sequences (encoding the AMO subunit A) in public sequence databases, which were apparently misclassified as methane monooxygenases. This recognition of a novel amoA sequence group will lead to an improved understanding of the environmental abundance and distribution of ammonia-oxidizing microorganisms. Furthermore, the discovery of the long-sought-after comammox process will change our perception of the nitrogen cycle.}, }
@article {pmid26607739, year = {2015}, author = {Li, X and Li, J and Hu, X and Huang, L and Xiao, J and Chan, J and Mi, K}, title = {Differential roles of the hemerythrin-like proteins of Mycobacterium smegmatis in hydrogen peroxide and erythromycin susceptibility.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {16130}, pmid = {26607739}, issn = {2045-2322}, mesh = {Adaptation, Physiological/drug effects ; Bacterial Proteins/*metabolism ; Erythromycin/*pharmacology ; Gene Knockout Techniques ; Hemerythrin/*metabolism ; Hydrogen Peroxide/*pharmacology ; Microbial Sensitivity Tests ; Models, Biological ; Mycobacterium smegmatis/*drug effects/*metabolism ; Phylogeny ; }, abstract = {Hemerythrin-like proteins are oxygen-carrying non-heme di-iron binding proteins and their functions have effect on oxidation-reduction regulation and antibiotic resistance. Recent studies using bioinformatic analyses suggest that multiple hemerythrin-like protein coding sequences might have been acquired by lateral gene transfer and the number of hemerythrin-like proteins varies amongst different species. Mycobacterium smegmatis contains three hemerythrin-like proteins, MSMEG_3312, MSMEG_2415 and MSMEG_6212. In this study, we have systematically analyzed all three hemerythrin-like proteins in M. smegmatis and our results identified and characterized two functional classes: MSMEG_2415 plays an important role in H2O2 susceptibility, and MSMEG_3312 and MSMEG_6212 are associated with erythromycin susceptibility. Phylogenetic analysis indicated that these three proteins have different evolutionary origins, possibly explaining their different physiological functions. Here, combined with biological and phylogenetic analyses, our results provide new insights into the evolutionary divergence of the hemerythrin-like proteins in M. smegmatis.}, }
@article {pmid26607569, year = {2015}, author = {Barrera, GP and Belaich, MN and Patarroyo, MA and Villamizar, LF and Ghiringhelli, PD}, title = {Evidence of recent interspecies horizontal gene transfer regarding nucleopolyhedrovirus infection of Spodoptera frugiperda.}, journal = {BMC genomics}, volume = {16}, number = {}, pages = {1008}, pmid = {26607569}, issn = {1471-2164}, mesh = {Animals ; Computational Biology/methods ; Gene Expression Regulation, Viral ; Gene Order ; *Gene Transfer, Horizontal ; Genes, Viral ; Genome, Viral ; Genomics ; Insect Control ; Nucleopolyhedroviruses/classification/*genetics ; Open Reading Frames ; Phylogeny ; Spodoptera/*genetics/*virology ; }, abstract = {BACKGROUND: Baculoviruses are insect-associated viruses carrying large, circular double-stranded-DNA genomes with significant biotechnological applications such as biological pest control, recombinant protein production, gene delivery in mammals and as a model of DNA genome evolution. These pathogens infect insects from the orders Lepidoptera, Hymenoptera and Diptera, and have high species diversity which is expressed in their diverse biological properties including morphology, virulence or pathogenicity. Spodoptera frugiperda (Lepidoptera: Noctuidae), the fall armyworm, represents a significant pest for agriculture in America; it is a host for baculoviruses such as the Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV) (Colombia strain, genotype A) having been classified as a Group II alphabaculovirus making it a very attractive target for bioinsecticidal use.<br><br>RESULTS: Genome analysis by pyrosequencing revealed that SfMNPV ColA has 145 ORFs, 2 of which were not present in the other sequenced genotypes of the virus (SfMNPV-NicB, SfMNPV-NicG, SfMNPV-19 and SfMNPV-3AP2). An in-depth bioinformatics study showed that ORF023 and ORF024 were acquired by a recent homologous recombination process between Spodoptera frugiperda and Spodoptera litura (the Oriental leafworm moth) nucleopolyhedroviruses. Auxiliary genes are numerous in the affected locus which has a homologous region (hr3), a repetitive sequence associated with genome replication which became lost in SfColA along with 1 ORF. Besides, the mRNAs associated with two acquired genes appeared in the virus' life-cycle during the larval stage. Predictive studies concerning the theoretical proteins identified that ORF023 protein would be a phosphatase involved in DNA repair and that the ORF024 protein would be a membrane polypeptide associated with cell transport.<br><br>CONCLUSIONS: The SfColA genome was thus revealed to be a natural recombinant virus showing evidence of recent horizontal gene transfer between different baculovirus species occurring in nature. This feature could be the cause of its high insecticidal power and therefore SfColA becomes a great candidate for bioinsecticide formulations.}, }
@article {pmid26607338, year = {2016}, author = {Klochko, VV and Zelena, LB and Kim, JY and Avdeeva, LV and Reva, ON}, title = {Prospects of a new antistaphylococcal drug batumin revealed by molecular docking and analysis of the complete genome sequence of the batumin-producer Pseudomonas batumici UCM B-321.}, journal = {International journal of antimicrobial agents}, volume = {47}, number = {1}, pages = {56-61}, doi = {10.1016/j.ijantimicag.2015.10.006}, pmid = {26607338}, issn = {1872-7913}, mesh = {Amino Acyl-tRNA Synthetases/antagonists &amp; inhibitors ; Anti-Bacterial Agents/chemistry/*pharmacology ; DNA, Bacterial/*chemistry/genetics ; Genome, Bacterial ; Humans ; Methicillin-Resistant Staphylococcus aureus/*drug effects ; *Molecular Docking Simulation ; Molecular Sequence Data ; Organic Chemicals/chemistry/pharmacology ; Pseudomonas/*genetics/metabolism ; *Sequence Analysis, DNA ; }, abstract = {Meticillin-resistant Staphylococcus aureus (MRSA) is a serious public health threat causing outbreaks of clinical infection around the world. Mupirocin is a promising anti-MRSA drug, however mupirocin-resistant strains of S. aureus are emerging at an increasing rate. The newly discovered antibiotic batumin may contribute to anti-MRSA therapy. The objective of this work was to identify possible molecular targets for batumin as well as mechanisms of its antistaphylococcal activity using computational molecular docking and by analysing the complete genome sequence of the batumin-producer Pseudomonas batumici UCM B-321. It was found that batumin acted very similarly to mupirocin by inhibiting aminoacyl tRNA synthetases. A previous hypothesis considering the trans-enoyl-CoA reductase FabI as a prime molecular target of batumin was rejected. However, indirect inhibition of fatty acid biosynthesis in sensitive bacteria does take place as a part of stringent response repression triggered by accumulation of uncharged tRNA molecules. Paralogues of diverse leucine-tRNA synthetases in the genome of P. batumici indicated that this protein might be the prime target of batumin. A batumin biosynthesis operon comprising 28 genes was found to be acquired through horizontal gene transfer. It was hypothesised that, in contrast to mupirocin, batumin could inhibit a broader range of aminoacyl tRNA synthetases and that acquired resistance to mupirocin might not endow S. aureus strains with resistance against batumin.}, }
@article {pmid26607336, year = {2016}, author = {Alonso, N and Miró, E and Pascual, V and Rivera, A and Simó, M and Garcia, MC and Xercavins, M and Morera, MA and Espejo, E and Gurguí, M and Pérez, J and Rodríguez-Carballeira, M and Garau, J and Calbo, E and Navarro, F and Mirelis, B and Coll, P}, title = {Molecular characterisation of acquired and overproduced chromosomal blaAmpC in Escherichia coli clinical isolates.}, journal = {International journal of antimicrobial agents}, volume = {47}, number = {1}, pages = {62-68}, doi = {10.1016/j.ijantimicag.2015.10.007}, pmid = {26607336}, issn = {1872-7913}, mesh = {Bacterial Proteins/*genetics/*metabolism ; Chromosomes, Bacterial ; DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; Drug Resistance, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/classification/*enzymology/*genetics ; Escherichia coli Infections/*microbiology ; Gene Expression ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Variation ; Humans ; Multilocus Sequence Typing ; Mutation ; Plasmids ; Polymerase Chain Reaction ; Quinolones/metabolism ; Sequence Analysis, DNA ; Spain ; beta-Lactamases/*genetics/*metabolism ; }, abstract = {Escherichia coli recovered from three hospitals in Barcelona (Spain) were studied to determine the prevalence of isolates with acquired AmpC (ac-AmpC) and/or overproduced chromosomal AmpC (c-AmpC). Mechanisms involved in blac-AmpC overexpression, blaac-AmpC and the plasmids associated with their distribution as well as the prevalence of plasmid-mediated quinolone resistance (PMQR) in AmpC-producing isolates were also determined. Isolates were selected according to their resistance phenotype. blaac-AmpC, alterations in the blac-AmpC promoter/attenuator, and PMQR genes [qnrA, qnrB, qnrS, aac(6')-Ib-cr and qepA] were characterised by PCR and sequencing. blac-AmpC expression was determined by qRT-PCR. Population structure analysis was performed using PFGE, MLST and phylogenetic group PCR. Plasmids carrying blaac-AmpC were characterised by PCR-based replicon typing and S1-PFGE. IncI1 and IncF plasmids were also analysed by plasmid MLST and replicon sequence typing, respectively. Among 21563 E. coli isolates, 240 (1.1%) overproduced AmpC β-lactamases, including 180 (75.0%) harbouring ac-AmpC (132 CMY-2 variants and 48 DHA-1) and 60 (25.0%) c-AmpC enzymes. Three mutation profiles in the blac-AmpC promoter/attenuator were associated with a 72.5-, 19.9- and 5.8-fold increased expression, respectively. Moreover, 63.3% of ac-AmpC and 43.3% of c-AmpC isolates belonged to B2, D, E or F phylogenetic groups. PMQR was found in 31% of ac-AmpC isolates [38 qnrB4, 8 aac(6')-Ib-cr, 6 qnrS1 and 3 qnrB19] and in 10% of c-AmpC isolates [5 aac(6')-Ib-cr and 1 qnrS1]. IncI1-ST12 and IncF were associated with blaCMY-2 and blaDHA-1, respectively. These results suggest that ac-AmpC β-lactamases were the main mechanism of AmpC production. Isolates and plasmids both showed high genetic diversity.}, }
@article {pmid26603172, year = {2016}, author = {Liu, YY and Wang, Y and Walsh, TR and Yi, LX and Zhang, R and Spencer, J and Doi, Y and Tian, G and Dong, B and Huang, X and Yu, LF and Gu, D and Ren, H and Chen, X and Lv, L and He, D and Zhou, H and Liang, Z and Liu, JH and Shen, J}, title = {Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study.}, journal = {The Lancet. Infectious diseases}, volume = {16}, number = {2}, pages = {161-168}, doi = {10.1016/S1473-3099(15)00424-7}, pmid = {26603172}, issn = {1474-4457}, support = {G1100135/MRC_/Medical Research Council/United Kingdom ; MR/P007295/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; China ; Colistin/*therapeutic use ; Drug Resistance, Bacterial/immunology ; Enterobacteriaceae/*drug effects ; Enterobacteriaceae Infections/*drug therapy/*immunology ; Humans ; Meat/microbiology ; Mice ; Plasmids/*immunology ; Polymyxins/*therapeutic use ; Swine ; Swine Diseases/*drug therapy ; }, abstract = {BACKGROUND: Until now, polymyxin resistance has involved chromosomal mutations but has never been reported via horizontal gene transfer. During a routine surveillance project on antimicrobial resistance in commensal Escherichia coli from food animals in China, a major increase of colistin resistance was observed. When an E coli strain, SHP45, possessing colistin resistance that could be transferred to another strain, was isolated from a pig, we conducted further analysis of possible plasmid-mediated polymyxin resistance. Herein, we report the emergence of the first plasmid-mediated polymyxin resistance mechanism, MCR-1, in Enterobacteriaceae.<br><br>METHODS: The mcr-1 gene in E coli strain SHP45 was identified by whole plasmid sequencing and subcloning. MCR-1 mechanistic studies were done with sequence comparisons, homology modelling, and electrospray ionisation mass spectrometry. The prevalence of mcr-1 was investigated in E coli and Klebsiella pneumoniae strains collected from five provinces between April, 2011, and November, 2014. The ability of MCR-1 to confer polymyxin resistance in vivo was examined in a murine thigh model.<br><br>FINDINGS: Polymyxin resistance was shown to be singularly due to the plasmid-mediated mcr-1 gene. The plasmid carrying mcr-1 was mobilised to an E coli recipient at a frequency of 10(-1) to 10(-3) cells per recipient cell by conjugation, and maintained in K pneumoniae and Pseudomonas aeruginosa. In an in-vivo model, production of MCR-1 negated the efficacy of colistin. MCR-1 is a member of the phosphoethanolamine transferase enzyme family, with expression in E coli resulting in the addition of phosphoethanolamine to lipid A. We observed mcr-1 carriage in E coli isolates collected from 78 (15%) of 523 samples of raw meat and 166 (21%) of 804 animals during 2011-14, and 16 (1%) of 1322 samples from inpatients with infection.<br><br>INTERPRETATION: The emergence of MCR-1 heralds the breach of the last group of antibiotics, polymyxins, by plasmid-mediated resistance. Although currently confined to China, MCR-1 is likely to emulate other global resistance mechanisms such as NDM-1. Our findings emphasise the urgent need for coordinated global action in the fight against pan-drug-resistant Gram-negative bacteria.<br><br>FUNDING: Ministry of Science and Technology of China, National Natural Science Foundation of China.}, }
@article {pmid26601271, year = {2015}, author = {Nasir, A and Caetano-Anollés, G}, title = {A phylogenomic data-driven exploration of viral origins and evolution.}, journal = {Science advances}, volume = {1}, number = {8}, pages = {e1500527}, pmid = {26601271}, issn = {2375-2548}, abstract = {The origin of viruses remains mysterious because of their diverse and patchy molecular and functional makeup. Although numerous hypotheses have attempted to explain viral origins, none is backed by substantive data. We take full advantage of the wealth of available protein structural and functional data to explore the evolution of the proteomic makeup of thousands of cells and viruses. Despite the extremely reduced nature of viral proteomes, we established an ancient origin of the "viral supergroup" and the existence of widespread episodes of horizontal transfer of genetic information. Viruses harboring different replicon types and infecting distantly related hosts shared many metabolic and informational protein structural domains of ancient origin that were also widespread in cellular proteomes. Phylogenomic analysis uncovered a universal tree of life and revealed that modern viruses reduced from multiple ancient cells that harbored segmented RNA genomes and coexisted with the ancestors of modern cells. The model for the origin and evolution of viruses and cells is backed by strong genomic and structural evidence and can be reconciled with existing models of viral evolution if one considers viruses to have originated from ancient cells and not from modern counterparts.}, }
@article {pmid26598659, year = {2015}, author = {Boothby, TC and Tenlen, JR and Smith, FW and Wang, JR and Patanella, KA and Nishimura, EO and Tintori, SC and Li, Q and Jones, CD and Yandell, M and Messina, DN and Glasscock, J and Goldstein, B}, title = {Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {52}, pages = {15976-15981}, pmid = {26598659}, issn = {1091-6490}, support = {K12 GM000678/GM/NIGMS NIH HHS/United States ; K12GM000678/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Fungal/chemistry/genetics ; DNA, Plant/chemistry/genetics ; DNA, Viral/chemistry/genetics ; *Gene Transfer, Horizontal ; Genome/*genetics ; *Genomic Library ; Phylogeny ; Sequence Analysis, DNA/*methods ; Tardigrada/classification/*genetics ; }, abstract = {Horizontal gene transfer (HGT), or the transfer of genes between species, has been recognized recently as more pervasive than previously suspected. Here, we report evidence for an unprecedented degree of HGT into an animal genome, based on a draft genome of a tardigrade, Hypsibius dujardini. Tardigrades are microscopic eight-legged animals that are famous for their ability to survive extreme conditions. Genome sequencing, direct confirmation of physical linkage, and phylogenetic analysis revealed that a large fraction of the H. dujardini genome is derived from diverse bacteria as well as plants, fungi, and Archaea. We estimate that approximately one-sixth of tardigrade genes entered by HGT, nearly double the fraction found in the most extreme cases of HGT into animals known to date. Foreign genes have supplemented, expanded, and even replaced some metazoan gene families within the tardigrade genome. Our results demonstrate that an unexpectedly large fraction of an animal genome can be derived from foreign sources. We speculate that animals that can survive extremes may be particularly prone to acquiring foreign genes.}, }
@article {pmid26598365, year = {2016}, author = {Yáñez-Cuna, FO and Castellanos, M and Romero, D}, title = {Biased Gene Conversion in Rhizobium etli Is Caused by Preferential Double-Strand Breaks on One of the Recombining Homologs.}, journal = {Journal of bacteriology}, volume = {198}, number = {3}, pages = {591-599}, pmid = {26598365}, issn = {1098-5530}, mesh = {*DNA Breaks, Double-Stranded ; DNA Repair ; *DNA, Bacterial ; Recombination, Genetic/*physiology ; Rhizobium etli/*genetics ; }, abstract = {UNLABELLED: Gene conversion, the nonreciprocal transfer of information during homologous recombination, is the main process that maintains identity between members of multigene families. Gene conversion in the nitrogenase (nifH) multigene family of Rhizobium etli was analyzed by using a two-plasmid system, where each plasmid carried a copy of nifH. One of the nifH copies was modified, creating restriction fragment length polymorphisms (RFLPs) spaced along the gene. Once the modified plasmid was introduced into R. etli, selection was done for cointegration with a resident plasmid lacking the RFLPs. Most of the cointegrate molecules harbor gene conversion events, biased toward a gain of RFLPs. This bias may be explained under the double-strand break repair model by proposing that the nifH gene lacking the RFLPs suffers a DNA double-strand break, so the incoming plasmid functions as a template for repairing the homolog on the resident plasmid. To support this proposal, we cloned an SceI site into the nifH homolog that had the RFLPs used for scoring gene conversion. In vivo expression of the meganuclease I-SceI allowed the generation of a double-strand break on this homolog. Upon introduction of this modified plasmid into an R. etli strain lacking I-SceI, biased gene conversion still favored the retention of markers on the incoming plasmid. In contrast, when the recipient strain ectopically expressed I-SceI, a dramatic reversal in gene conversion bias was seen, favoring the preservation of resident sequences. These results show that biased gene conversion is caused by preferential double-strand breaks on one of the recombining homologs.<br><br>IMPORTANCE: In this work, we analyzed gene conversion by using a system that entails horizontal gene transfer followed by homologous recombination in the recipient cell. Most gene conversion events are biased toward the acquisition of the incoming sequences, ranging in size from 120 bp to 800 bp. This bias is due to preferential cutting of resident DNA and can be reversed upon introduction of a double-strand break on the incoming sequence. Since conditions used in this work are similar to those in horizontal gene transfer, it provides evidence that, upon transfer, the resident DNA preferentially acquires gene variants.}, }
@article {pmid26596936, year = {2016}, author = {Linkevicius, M and Sandegren, L and Andersson, DI}, title = {Potential of Tetracycline Resistance Proteins To Evolve Tigecycline Resistance.}, journal = {Antimicrobial agents and chemotherapy}, volume = {60}, number = {2}, pages = {789-796}, pmid = {26596936}, issn = {1098-6596}, mesh = {Anti-Bacterial Agents/*pharmacology ; Escherichia coli/*drug effects/*genetics ; Membrane Proteins/*genetics ; Microbial Sensitivity Tests ; Minocycline/*analogs &amp; derivatives/pharmacology ; Tetracycline Resistance/*genetics ; Tigecycline ; }, abstract = {Tigecycline is a glycylcycline antibiotic active against multidrug-resistant bacterial pathogens. The objectives of our study were to examine the potential of the Tet(A), Tet(K), Tet(M), and Tet(X) tetracycline resistance proteins to acquire mutations causing tigecycline resistance and to determine how this affects resistance to earlier classes of tetracyclines. Mutations in all four tet genes caused a significant increase in the tigecycline MIC in Escherichia coli, and strains expressing mutant Tet(A) and Tet(X) variants reached clinically relevant MICs (2 mg/liter and 3 mg/liter, respectively). Mutations predominantly accumulated in transmembrane domains of the efflux pumps, most likely increasing the accommodation of tigecycline as a substrate. All selected Tet(M) mutants contained at least one mutation in the functionally most important loop III of domain IV. Deletion of leucine 505 of this loop led to the highest increase of the tigecycline MIC (0.5 mg/liter) among Tet(M) mutants. It also caused collateral sensitivity to earlier classes of tetracyclines. A majority of the Tet(X) mutants showed increased activity against all three classes of tetracylines. All tested Tet proteins have the potential to acquire mutations leading to increased MICs of tigecycline. As tet genes are widely found in pathogenic bacteria and spread easily by horizontal gene transfer, resistance development by alteration of existing Tet proteins might compromise the future medical use of tigecycline. We predict that Tet(X) might become the most problematic future Tet determinant, since its weak intrinsic tigecycline activity can be mutationally improved to reach clinically relevant levels without collateral loss in activity to other tetracyclines.}, }
@article {pmid26596631, year = {2015}, author = {Li, X and Gerlach, D and Du, X and Larsen, J and Stegger, M and Kühner, P and Peschel, A and Xia, G and Winstel, V}, title = {An accessory wall teichoic acid glycosyltransferase protects Staphylococcus aureus from the lytic activity of Podoviridae.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {17219}, pmid = {26596631}, issn = {2045-2322}, mesh = {Amino Acid Sequence ; Bacterial Proteins/*physiology ; Evolution, Molecular ; Glycosyltransferases/*physiology ; Host-Pathogen Interactions ; Molecular Sequence Data ; Phylogeny ; Podoviridae/*physiology ; Staphylococcus aureus/*enzymology/virology ; }, abstract = {Many Staphylococcus aureus have lost a major genetic barrier against phage infection, termed clustered regularly interspaced palindromic repeats (CRISPR/cas). Hence, S. aureus strains frequently exchange genetic material via phage-mediated horizontal gene transfer events, but, in turn, are vulnerable in particular to lytic phages. Here, a novel strategy of S. aureus is described, which protects S. aureus against the lytic activity of Podoviridae, a unique family of staphylococcal lytic phages with short, non-contractile tails. Unlike most staphylococcal phages, Podoviridae require a precise wall teichoic acid (WTA) glycosylation pattern for infection. Notably, TarM-mediated WTA α-O-GlcNAcylation prevents infection of Podoviridae while TarS-mediated WTA β-O-GlcNAcylation is required for S. aureus susceptibility to podoviruses. Tracking the evolution of TarM revealed an ancient origin in other staphylococci and vertical inheritance during S. aureus evolution. However, certain phylogenetic branches have lost tarM during evolution, which rendered them podovirus-susceptible. Accordingly, lack of tarM correlates with podovirus susceptibility and can be converted into a podovirus-resistant phenotype upon ectopic expression of tarM indicating that a "glyco-switch" of WTA O-GlcNAcylation can prevent the infection by certain staphylococcal phages. Since lytic staphylococcal phages are considered as anti-S. aureus agents, these data may help to establish valuable strategies for treatment of infections.}, }
@article {pmid26592443, year = {2015}, author = {Niehus, R and Mitri, S and Fletcher, AG and Foster, KR}, title = {Migration and horizontal gene transfer divide microbial genomes into multiple niches.}, journal = {Nature communications}, volume = {6}, number = {}, pages = {8924}, pmid = {26592443}, issn = {2041-1723}, support = {242670/ERC_/European Research Council/International ; }, mesh = {Bacteria/*genetics ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Models, Genetic ; }, abstract = {Horizontal gene transfer is central to microbial evolution, because it enables genetic regions to spread horizontally through diverse communities. However, how gene transfer exerts such a strong effect is not understood. Here we develop an eco-evolutionary model and show how genetic transfer, even when rare, can transform the evolution and ecology of microbes. We recapitulate existing models, which suggest that asexual reproduction will overpower horizontal transfer and greatly limit its effects. We then show that allowing immigration completely changes these predictions. With migration, the rates and impacts of horizontal transfer are greatly increased, and transfer is most frequent for loci under positive natural selection. Our analysis explains how ecologically important loci can sweep through competing strains and species. In this way, microbial genomes can evolve to become ecologically diverse where different genomic regions encode for partially overlapping, but distinct, ecologies. Under these conditions ecological species do not exist, because genes, not species, inhabit niches.}, }
@article {pmid26590289, year = {2016}, author = {Zablocki, O and Adriaenssens, EM and Cowan, D}, title = {Diversity and Ecology of Viruses in Hyperarid Desert Soils.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {3}, pages = {770-777}, pmid = {26590289}, issn = {1098-5336}, mesh = {Bacteriophages/classification/genetics/isolation &amp; purification/*physiology ; *Desert Climate ; *Ecosystem ; *Genetic Variation ; Genome, Viral ; Phylogeny ; RNA, Ribosomal, 16S ; *Soil Microbiology ; Virus Physiological Phenomena ; Viruses/classification/genetics/isolation &amp; purification ; }, abstract = {In recent years, remarkable progress has been made in the field of virus environmental ecology. In marine ecosystems, for example, viruses are now thought to play pivotal roles in the biogeochemical cycling of nutrients and to be mediators of microbial evolution through horizontal gene transfer. The diversity and ecology of viruses in soils are poorly understood, but evidence supports the view that the diversity and ecology of viruses in soils differ substantially from those in aquatic systems. Desert biomes cover ∼ 33% of global land masses, and yet the diversity and roles of viruses in these dominant ecosystems remain poorly understood. There is evidence that hot hyperarid desert soils are characterized by high levels of bacterial lysogens and low extracellular virus counts. In contrast, cold desert soils contain high extracellular virus titers. We suggest that the prevalence of microbial biofilms in hyperarid soils, combined with extreme thermal regimens, exerts strong selection pressures on both temperate and virulent viruses. Many desert soil virus sequences show low values of identity to virus genomes in public databases, suggesting the existence of distinct and as-yet-uncharacterized soil phylogenetic lineages (e.g., cyanophages). We strongly advocate for amplification-free metavirome analyses while encouraging the classical isolation of phages from dominant and culturable microbial isolates in order to populate sequence databases. This review provides an overview of recent advances in the study of viruses in hyperarid soils and of the factors that contribute to viral abundance and diversity in hot and cold deserts and offers technical recommendations for future studies.}, }
@article {pmid26590286, year = {2016}, author = {Bergholz, TM and den Bakker, HC and Katz, LS and Silk, BJ and Jackson, KA and Kucerova, Z and Joseph, LA and Turnsek, M and Gladney, LM and Halpin, JL and Xavier, K and Gossack, J and Ward, TJ and Frace, M and Tarr, CL}, title = {Determination of Evolutionary Relationships of Outbreak-Associated Listeria monocytogenes Strains of Serotypes 1/2a and 1/2b by Whole-Genome Sequencing.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {3}, pages = {928-938}, pmid = {26590286}, issn = {1098-5336}, mesh = {*Disease Outbreaks ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Variation ; Genome, Bacterial ; Humans ; Listeria monocytogenes/*genetics/isolation &amp; purification ; Listeriosis/*epidemiology/*microbiology ; Phylogeny ; Point Mutation ; Sequence Analysis, DNA ; Serogroup ; Serotyping ; United States/epidemiology ; }, abstract = {We used whole-genome sequencing to determine evolutionary relationships among 20 outbreak-associated clinical isolates of Listeria monocytogenes serotypes 1/2a and 1/2b. Isolates from 6 of 11 outbreaks fell outside the clonal groups or "epidemic clones" that have been previously associated with outbreaks, suggesting that epidemic potential may be widespread in L. monocytogenes and is not limited to the recognized epidemic clones. Pairwise comparisons between epidemiologically related isolates within clonal complexes showed that genome-level variation differed by 2 orders of magnitude between different comparisons, and the distribution of point mutations (core versus accessory genome) also varied. In addition, genetic divergence between one closely related pair of isolates from a single outbreak was driven primarily by changes in phage regions. The evolutionary analysis showed that the changes could be attributed to horizontal gene transfer; members of the diverse bacterial community found in the production facility could have served as the source of novel genetic material at some point in the production chain. The results raise the question of how to best utilize information contained within the accessory genome in outbreak investigations. The full magnitude and complexity of genetic changes revealed by genome sequencing could not be discerned from traditional subtyping methods, and the results demonstrate the challenges of interpreting genetic variation among isolates recovered from a single outbreak. Epidemiological information remains critical for proper interpretation of nucleotide and structural diversity among isolates recovered during outbreaks and will remain so until we understand more about how various population histories influence genetic variation.}, }
@article {pmid26590210, year = {2015}, author = {Wetzel, ME and Olsen, GJ and Chakravartty, V and Farrand, SK}, title = {The repABC Plasmids with Quorum-Regulated Transfer Systems in Members of the Rhizobiales Divide into Two Structurally and Separately Evolving Groups.}, journal = {Genome biology and evolution}, volume = {7}, number = {12}, pages = {3337-3357}, pmid = {26590210}, issn = {1759-6653}, support = {R01 GM052465/GM/NIGMS NIH HHS/United States ; R01 GM52465/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Proteins/*genetics ; DNA Helicases/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Plasmids/genetics ; Quorum Sensing/*genetics ; Rhizobiaceae/*genetics ; Trans-Activators/*genetics ; }, abstract = {The large repABC plasmids of the order Rhizobiales with Class I quorum-regulated conjugative transfer systems often define the nature of the bacterium that harbors them. These otherwise diverse plasmids contain a core of highly conserved genes for replication and conjugation raising the question of their evolutionary relationships. In an analysis of 18 such plasmids these elements fall into two organizational classes, Group I and Group II, based on the sites at which cargo DNA is located. Cladograms constructed from proteins of the transfer and quorum-sensing components indicated that those of the Group I plasmids, while coevolving, have diverged from those coevolving proteins of the Group II plasmids. Moreover, within these groups the phylogenies of the proteins usually occupy similar, if not identical, tree topologies. Remarkably, such relationships were not seen among proteins of the replication system; although RepA and RepB coevolve, RepC does not. Nor do the replication proteins coevolve with the proteins of the transfer and quorum-sensing systems. Functional analysis was mostly consistent with phylogenies. TraR activated promoters from plasmids within its group, but not between groups and dimerized with TraR proteins from within but not between groups. However, oriT sequences, which are highly conserved, were processed by the transfer system of plasmids regardless of group. We conclude that these plasmids diverged into two classes based on the locations at which cargo DNA is inserted, that the quorum-sensing and transfer functions are coevolving within but not between the two groups, and that this divergent evolution extends to function.}, }
@article {pmid26589282, year = {2015}, author = {Watson, AK and Williams, TA and Williams, BA and Moore, KA and Hirt, RP and Embley, TM}, title = {Transcriptomic profiling of host-parasite interactions in the microsporidian Trachipleistophora hominis.}, journal = {BMC genomics}, volume = {16}, number = {}, pages = {983}, pmid = {26589282}, issn = {1471-2164}, support = {045404//Wellcome Trust/United Kingdom ; WT097835MF//Wellcome Trust/United Kingdom ; //Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Alleles ; Animals ; Cell Line ; Cells, Cultured ; Computational Biology/methods ; DNA Transposable Elements ; Diploidy ; Evolution, Molecular ; *Gene Expression Profiling ; Gene Expression Regulation, Fungal ; Gene Frequency ; Gene Transfer, Horizontal ; Genes, Fungal ; Genome, Fungal ; Host-Pathogen Interactions/*genetics ; Insecta/genetics/microbiology ; Life Cycle Stages/genetics ; Microsporidia/*genetics/growth &amp; development/metabolism ; Multigene Family ; Phylogeny ; Polymorphism, Single Nucleotide ; RNA Splicing ; Rabbits ; Reproducibility of Results ; Transcription, Genetic ; *Transcriptome ; }, abstract = {BACKGROUND: Trachipleistophora hominis was isolated from an HIV/AIDS patient and is a member of a highly successful group of obligate intracellular parasites.<br><br>METHODS: Here we have investigated the evolution of the parasite and the interplay between host and parasite gene expression using transcriptomics of T. hominis-infected rabbit kidney cells.<br><br>RESULTS: T. hominis has about 30% more genes than small-genome microsporidians. Highly expressed genes include those involved in growth, replication, defence against oxidative stress, and a large fraction of uncharacterised genes. Chaperones are also highly expressed and may buffer the deleterious effects of the large number of non-synonymous mutations observed in essential T. hominis genes. Host expression suggests a general cellular shutdown upon infection, but ATP, amino sugar and nucleotide sugar production appear enhanced, potentially providing the parasite with substrates it cannot make itself. Expression divergence of duplicated genes, including transporters used to acquire host metabolites, demonstrates ongoing functional diversification during microsporidian evolution. We identified overlapping transcription at more than 100 loci in the sparse T. hominis genome, demonstrating that this feature is not caused by genome compaction. The detection of additional transposons of insect origin strongly suggests that the natural host for T. hominis is an insect.<br><br>CONCLUSIONS: Our results reveal that the evolution of contemporary microsporidian genomes is highly dynamic and innovative. Moreover, highly expressed T. hominis genes of unknown function include a cohort that are shared among all microsporidians, indicating that some strongly conserved features of the biology of these enormously successful parasites remain uncharacterised.}, }
@article {pmid26589218, year = {2016}, author = {Bearson, BL}, title = {Molecular Profiling: Catecholamine Modulation of Gene Expression in Escherichia coli O157:H7 and Salmonella enterica Serovar Typhimurium.}, journal = {Advances in experimental medicine and biology}, volume = {874}, number = {}, pages = {167-182}, doi = {10.1007/978-3-319-20215-0_7}, pmid = {26589218}, issn = {0065-2598}, mesh = {Catecholamines/*pharmacology ; Escherichia coli O157/*drug effects/genetics/physiology ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; Iron/metabolism ; Salmonella typhimurium/*drug effects/genetics/physiology ; }, abstract = {Investigations of Escherichia coli O157:H7 and Salmonella enterica serovar Typhimurium have demonstrated that these bacterial pathogens can respond to the presence of catecholamines including norepinephrine and/or epinephrine in their environment by modulating gene expression and exhibiting various phenotypes. For example, one of the most intensively investigated phenotypes following exposure of E. coli and S. Typhimurium to norepinephrine is enhanced bacterial growth in a serum-based medium. Host-pathogen investigations have demonstrated that the mammalian host utilizes nutritional immunity to sequester iron and prevent extraintestinal growth by bacterial pathogens. However, Salmonella and certain E. coli strains have a genetic arsenal designed for subversion and subterfuge of the host. Norepinephrine enhances bacterial growth due, in part, to increased iron availability, and transcriptional profiling indicates differential expression of genes encoding iron acquisition and transport proteins. Bacterial motility of E. coli and S. Typhimurium is also enhanced in the presence of catecholamines and increased flagellar gene expression has been described. Furthermore, epinephrine and norepinephrine are chemoattractants for E. coli O157:H7. In S. Typhimurium, norepinephrine enhances horizontal gene transfer and increases expression of genes involved in plasmid transfer. Exposure of E. coli O157:H7 to norepinephrine increases expression of the genes encoding Shiga toxin and operons within the locus of enterocyte effacement (LEE). Alterations in the transcriptional response of enteric bacteria to catecholamine exposure in vivo are predicted to enhance bacterial colonization and pathogen virulence. This chapter will review the current literature on the transcriptional response of E. coli and S. Typhimurium to catecholamines.}, }
@article {pmid26588876, year = {2016}, author = {Stratev, D and Odeyemi, OA}, title = {Antimicrobial resistance of Aeromonas hydrophila isolated from different food sources: A mini-review.}, journal = {Journal of infection and public health}, volume = {9}, number = {5}, pages = {535-544}, doi = {10.1016/j.jiph.2015.10.006}, pmid = {26588876}, issn = {1876-035X}, mesh = {Aeromonas hydrophila/*drug effects/isolation &amp; purification ; Animals ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial ; *Food Microbiology ; Humans ; }, abstract = {Aeromonas hydrophila is a Gram-negative, oxidase-positive, facultative, anaerobic, opportunistic aquatic pathogen. A. hydrophila produces virulence factors, such as hemolysins, aerolysins, adhesins, enterotoxins, phospholipase and lipase. In addition to isolation from aquatic sources, A. hydrophila has been isolated from meat and meat products, milk and dairy products, and vegetables. However, various studies showed that this opportunistic pathogen is resistant to commercial antibiotics. This is attributed to factors such as the indiscriminate use of antibiotics in aquaculture, plasmids or horizontal gene transfer. In this report, we highlight the occurrence, prevalence and antimicrobial resistance of A. hydrophila isolated from different food samples. The presence of antimicrobial-resistant A. hydrophila in food poses threats to public and aquatic animal health.}, }
@article {pmid26585401, year = {2016}, author = {Hill, RLL and Dokland, T}, title = {The Type 2 dUTPase of Bacteriophage ϕNM1 Initiates Mobilization of Staphylococcus aureus Bovine Pathogenicity Island 1.}, journal = {Journal of molecular biology}, volume = {428}, number = {1}, pages = {142-152}, pmid = {26585401}, issn = {1089-8638}, support = {R01 AI083255/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteriophages/*enzymology ; Gene Deletion ; *Gene Transfer, Horizontal ; *Genomic Islands ; Protein Binding ; Protein Conformation ; Pyrophosphatases/chemistry/*metabolism ; Repressor Proteins/metabolism ; Staphylococcus aureus/*genetics/*virology ; }, abstract = {Staphylococcus aureus pathogenicity islands (SaPIs) are genetic elements that are mobilized by specific helper phages. The initial step in mobilization is the derepression of the SaPI by the interaction of a phage protein with the SaPI master repressor Stl. Stl proteins are highly divergent between different SaPIs and respond to different phage-encoded derepressors. One such SaPI, SaPIbov1, is derepressed by the dUTPase (Dut) of bacteriophage 80α (Dut80α) and its phage ϕ11 homolog, Dut11. We previously showed that SaPIbov1 could also be mobilized by phage ϕNM1, even though its dut gene is not homologous with that of 80α. Here, we show that ϕNM1 dut encodes a type 2 dUTPase (DutNM1), which has an α-helical structure that is distinct from the type 1 trimeric, β-sheet structure of Dut80α. Deletion of dutNM1 abolishes the ability of ϕNM1 to mobilize SaPIbov1. Like Dut80α, DutNM1 forms a direct interaction with SaPIbov1 Stl both in vivo and in vitro, leading to inhibition of the dUTPase activity and Stl release from its target DNA. This work provides novel insights into the diverse mechanisms of genetic mobilization in S. aureus.}, }
@article {pmid26581334, year = {2015}, author = {Bajda, S and Dermauw, W and Greenhalgh, R and Nauen, R and Tirry, L and Clark, RM and Van Leeuwen, T}, title = {Transcriptome profiling of a spirodiclofen susceptible and resistant strain of the European red mite Panonychus ulmi using strand-specific RNA-seq.}, journal = {BMC genomics}, volume = {16}, number = {}, pages = {974}, pmid = {26581334}, issn = {1471-2164}, support = {T32 GM007464/GM/NIGMS NIH HHS/United States ; }, mesh = {4-Butyrolactone/*analogs &amp; derivatives/pharmacology ; Acaricides/*pharmacology ; Animals ; Drug Resistance/*genetics ; *Gene Expression Profiling ; Gene Ontology ; Gene Transfer, Horizontal ; Sequence Analysis, RNA ; Species Specificity ; Spiro Compounds/*pharmacology ; Tetranychidae/*drug effects/enzymology/*genetics ; Xenobiotics/pharmacology ; }, abstract = {BACKGROUND: The European red mite, Panonychus ulmi, is among the most important mite pests in fruit orchards, where it is controlled primarily by acaricide application. However, the species rapidly develops pesticide resistance, and the elucidation of resistance mechanisms for P. ulmi has not kept pace with insects or with the closely related spider mite Tetranychus urticae. The main reason for this lack of knowledge has been the absence of genomic resources needed to investigate the molecular biology of resistance mechanisms.<br><br>RESULTS: Here, we provide a comprehensive strand-specific RNA-seq based transcriptome resource for P. ulmi derived from strains susceptible and resistant to the widely used acaricide spirodiclofen. From a de novo assembly of the P. ulmi transcriptome, we manually annotated detoxification enzyme families, target-sites of commonly used acaricides, and horizontally transferred genes implicated in plant-mite interactions and pesticide resistance. In a comparative analysis that incorporated sequences available for Panonychus citri, T. urticae, and insects, we identified radiations for detoxification gene families following the divergence of Panonychus and Tetranychus genera. Finally, we used the replicated RNA-seq data from the spirodiclofen susceptible and resistant strains to describe gene expression changes associated with resistance. A cytochrome P450 monooxygenase, as well as multiple carboxylcholinesterases, were differentially expressed between the susceptible and resistant strains, and provide a molecular entry point for understanding resistance to spirodiclofen, widely used to control P. ulmi populations.<br><br>CONCLUSIONS: The new genomic resources and data that we present in this study for P. ulmi will substantially facilitate molecular studies of underlying mechanisms involved in acaricide resistance.}, }
@article {pmid26578597, year = {2016}, author = {Jeong, H and Sung, S and Kwon, T and Seo, M and Caetano-Anollés, K and Choi, SH and Cho, S and Nasir, A and Kim, H}, title = {HGTree: database of horizontally transferred genes determined by tree reconciliation.}, journal = {Nucleic acids research}, volume = {44}, number = {D1}, pages = {D610-9}, pmid = {26578597}, issn = {1362-4962}, mesh = {*Databases, Genetic ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Archaeal ; *Genes, Bacterial ; Genome, Microbial ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The HGTree database provides putative genome-wide horizontal gene transfer (HGT) information for 2472 completely sequenced prokaryotic genomes. This task is accomplished by reconstructing approximate maximum likelihood phylogenetic trees for each orthologous gene and corresponding 16S rRNA reference species sets and then reconciling the two trees under parsimony framework. The tree reconciliation method is generally considered to be a reliable way to detect HGT events but its practical use has remained limited because the method is computationally intensive and conceptually challenging. In this regard, HGTree (http://hgtree.snu.ac.kr) represents a useful addition to the biological community and enables quick and easy retrieval of information for HGT-acquired genes to better understand microbial taxonomy and evolution. The database is freely available and can be easily scaled and updated to keep pace with the rapid rise in genomic information.}, }
@article {pmid26578204, year = {2016}, author = {Wilson, BA and Garud, NR and Feder, AF and Assaf, ZJ and Pennings, PS}, title = {The population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens.}, journal = {Molecular ecology}, volume = {25}, number = {1}, pages = {42-66}, pmid = {26578204}, issn = {1365-294X}, support = {T32 HG000044/HG/NHGRI NIH HHS/United States ; }, mesh = {Drug Resistance/*genetics ; Epistasis, Genetic ; *Evolution, Molecular ; Gene Rearrangement ; Genetic Variation ; *Genetics, Population ; HIV/genetics ; Mycobacterium tuberculosis/genetics ; Orthomyxoviridae/genetics ; Plasmodium falciparum/genetics ; Recombination, Genetic ; Selection, Genetic ; Staphylococcus aureus/genetics ; }, abstract = {Drug resistance is a costly consequence of pathogen evolution and a major concern in public health. In this review, we show how population genetics can be used to study the evolution of drug resistance and also how drug resistance evolution is informative as an evolutionary model system. We highlight five examples from diverse organisms with particular focus on: (i) identifying drug resistance loci in the malaria parasite Plasmodium falciparum using the genomic signatures of selective sweeps, (ii) determining the role of epistasis in drug resistance evolution in influenza, (iii) quantifying the role of standing genetic variation in the evolution of drug resistance in HIV, (iv) using drug resistance mutations to study clonal interference dynamics in tuberculosis and (v) analysing the population structure of the core and accessory genome of Staphylococcus aureus to understand the spread of methicillin resistance. Throughout this review, we discuss the uses of sequence data and population genetic theory in studying the evolution of drug resistance.}, }
@article {pmid26578069, year = {2015}, author = {Gallagher, KA and Jensen, PR}, title = {Genomic insights into the evolution of hybrid isoprenoid biosynthetic gene clusters in the MAR4 marine streptomycete clade.}, journal = {BMC genomics}, volume = {16}, number = {}, pages = {960}, pmid = {26578069}, issn = {1471-2164}, support = {R01 GM085770/GM/NIGMS NIH HHS/United States ; T32 GM067550/GM/NIGMS NIH HHS/United States ; GM067550/GM/NIGMS NIH HHS/United States ; R01GM085770/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics ; Dimethylallyltranstransferase/genetics ; Evolution, Molecular ; *Genomics ; Mevalonic Acid/metabolism ; Multigene Family/*genetics ; *Phylogeny ; Streptomyces/enzymology/*genetics/*metabolism ; Terpenes/*metabolism ; }, abstract = {BACKGROUND: Considerable advances have been made in our understanding of the molecular genetics of secondary metabolite biosynthesis. Coupled with increased access to genome sequence data, new insight can be gained into the diversity and distributions of secondary metabolite biosynthetic gene clusters and the evolutionary processes that generate them. Here we examine the distribution of gene clusters predicted to encode the biosynthesis of a structurally diverse class of molecules called hybrid isoprenoids (HIs) in the genus Streptomyces. These compounds are derived from a mixed biosynthetic origin that is characterized by the incorporation of a terpene moiety onto a variety of chemical scaffolds and include many potent antibiotic and cytotoxic agents.<br><br>RESULTS: One hundred and twenty Streptomyces genomes were searched for HI biosynthetic gene clusters using ABBA prenyltransferases (PTases) as queries. These enzymes are responsible for a key step in HI biosynthesis. The strains included 12 that belong to the 'MAR4' clade, a largely marine-derived lineage linked to the production of diverse HI secondary metabolites. We found ABBA PTase homologs in all of the MAR4 genomes, which averaged five copies per strain, compared with 21 % of the non-MAR4 genomes, which averaged one copy per strain. Phylogenetic analyses suggest that MAR4 PTase diversity has arisen by a combination of horizontal gene transfer and gene duplication. Furthermore, there is evidence that HI gene cluster diversity is generated by the horizontal exchange of orthologous PTases among clusters. Many putative HI gene clusters have not been linked to their secondary metabolic products, suggesting that MAR4 strains will yield additional new compounds in this structure class. Finally, we confirm that the mevalonate pathway is not always present in genomes that contain HI gene clusters and thus is not a reliable query for identifying strains with the potential to produce HI secondary metabolites.<br><br>CONCLUSIONS: We found that marine-derived MAR4 streptomycetes possess a relatively high genetic potential for HI biosynthesis. The combination of horizontal gene transfer, duplication, and rearrangement indicate that complex evolutionary processes account for the high level of HI gene cluster diversity in these bacteria, the products of which may provide a yet to be defined adaptation to the marine environment.}, }
@article {pmid26572696, year = {2016}, author = {Porto, WF and Miranda, VJ and Pinto, MF and Dohms, SM and Franco, OL}, title = {High-performance computational analysis and peptide screening from databases of cyclotides from poaceae.}, journal = {Biopolymers}, volume = {106}, number = {1}, pages = {109-118}, doi = {10.1002/bip.22771}, pmid = {26572696}, issn = {1097-0282}, mesh = {Amino Acid Sequence ; Cyclotides/*chemistry ; *Databases, Protein ; Molecular Dynamics Simulation ; Poaceae/*chemistry ; Sequence Homology, Amino Acid ; Zea mays/chemistry ; }, abstract = {Cyclotides are a family of head-to-tail cyclized peptides containing three conserved disulfide bonds, in a structural scaffold also known as a cyclic cysteine knot. Due to the high degree of cysteine conservation, novel members from this peptide family can be identified in protein databases through a search through regular expression (REGEX). In this work, six novel cyclotide-like precursors from the Poaceae were identified from NCBI's non-redundant protein database by the use of REGEX. Two out of six sequences (named Zea mays L and M) showed an Asp residue in the C-terminal, which indicated that they could be cyclic. Gene expression in maize tissues was investigated, showing that the previously described cyclotide-like Z. mays J is expressed in the roots. According to molecular dynamics, the structure of Z. mays J seems to be stable, despite the putative absence of cyclization. As regards cyclotide evolution, it was hypothesized that this is an outcome from convergent evolution and/or horizontal gene transfer. The results showed that peptide screening from databases should be performed periodically in order to include novel sequences, which are deposited as the databases grow. Indeed, the advances in computational and experimental methods will together help to answer key questions and reach new horizons in defense-related peptide identification.}, }
@article {pmid26571622, year = {2015}, author = {Tsukuda, M and Miyazaki, K}, title = {[Functional plasticity of bacterial ribosome: Experimental horizontal gene transfer of 16S rRNA genes in Escherichia coli].}, journal = {Seikagaku. The Journal of Japanese Biochemical Society}, volume = {87}, number = {4}, pages = {475-477}, pmid = {26571622}, issn = {0037-1017}, mesh = {Animals ; Cell Plasticity/*physiology ; Escherichia coli/genetics ; Gene Transfer, Horizontal/*genetics ; Humans ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*metabolism ; Ribosomes/*genetics ; }, }
@article {pmid26566594, year = {2016}, author = {Markunas, CM and Triemer, RE}, title = {Evolutionary History of the Enzymes Involved in the Calvin-Benson Cycle in Euglenids.}, journal = {The Journal of eukaryotic microbiology}, volume = {63}, number = {3}, pages = {326-339}, doi = {10.1111/jeu.12282}, pmid = {26566594}, issn = {1550-7408}, mesh = {Aldose-Ketose Isomerases/classification/genetics/metabolism ; Bayes Theorem ; *Biological Evolution ; Chlorophyta/enzymology/genetics/physiology ; Chloroplasts/genetics ; Enzymes/classification/genetics/metabolism ; Euglenida/*enzymology/*genetics/metabolism ; Fructose-Bisphosphatase/classification/genetics/metabolism ; Gene Transfer, Horizontal ; Glyceraldehyde-3-Phosphate Dehydrogenases/classification/genetics/metabolism ; Phosphoric Monoester Hydrolases/classification/genetics/metabolism ; Photosynthesis/genetics/*physiology ; Phylogeny ; Rhodophyta/enzymology ; Symbiosis ; Triose-Phosphate Isomerase/classification/genetics/metabolism ; }, abstract = {Euglenids are an ancient lineage that may have existed as early as 2 billion years ago. A mere 65 years ago, Melvin Calvin and Andrew A. Benson performed experiments on Euglena gracilis and elucidated the series of reactions by which carbon was fixed and reduced during photosynthesis. However, the evolutionary history of this pathway (Calvin-Benson cycle) in euglenids was more complex than Calvin and Benson could have imagined. The chloroplast present today in euglenophytes arose from a secondary endosymbiosis between a phagotrophic euglenid and a prasinophyte green alga. A long period of evolutionary time existed before this secondary endosymbiotic event took place, which allowed for other endosymbiotic events or gene transfers to occur prior to the establishment of the green chloroplast. This research revealed the evolutionary history of the major enzymes of the Calvin-Benson cycle throughout the euglenid lineage and showed that the majority of genes for Calvin-Benson cycle enzymes shared an ancestry with red algae and/or chromophytes suggesting they may have been transferred to the nucleus prior to the acquisition of the green chloroplast.}, }
@article {pmid26566111, year = {2015}, author = {Badrinarayanan, A and Le, TB and Laub, MT}, title = {Bacterial chromosome organization and segregation.}, journal = {Annual review of cell and developmental biology}, volume = {31}, number = {}, pages = {171-199}, pmid = {26566111}, issn = {1530-8995}, support = {R01 GM082899/GM/NIGMS NIH HHS/United States ; R01GM082899/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*genetics ; Bacterial Proteins/genetics ; Chromosome Segregation/*genetics ; Chromosomes, Bacterial/*genetics ; DNA Repair/genetics ; DNA Replication/genetics ; DNA-Binding Proteins/genetics ; }, abstract = {If fully stretched out, a typical bacterial chromosome would be nearly 1 mm long, approximately 1,000 times the length of a cell. Not only must cells massively compact their genetic material, but they must also organize their DNA in a manner that is compatible with a range of cellular processes, including DNA replication, DNA repair, homologous recombination, and horizontal gene transfer. Recent work, driven in part by technological advances, has begun to reveal the general principles of chromosome organization in bacteria. Here, drawing on studies of many different organisms, we review the emerging picture of how bacterial chromosomes are structured at multiple length scales, highlighting the functions of various DNA-binding proteins and the impact of physical forces. Additionally, we discuss the spatial dynamics of chromosomes, particularly during their segregation to daughter cells. Although there has been tremendous progress, we also highlight gaps that remain in understanding chromosome organization and segregation.}, }
@article {pmid26562692, year = {2016}, author = {Lee, YD and Park, JH}, title = {Phage Conversion for β-Lactam Antibiotic Resistance of Staphylococcus aureus from Foods.}, journal = {Journal of microbiology and biotechnology}, volume = {26}, number = {2}, pages = {263-269}, doi = {10.4014/jmb.1508.08042}, pmid = {26562692}, issn = {1738-8872}, mesh = {Antineoplastic Agents/pharmacology ; Computational Biology ; *Food Microbiology ; Food Safety ; Genome, Viral ; Microscopy, Electron ; Open Reading Frames ; Siphoviridae/classification/*genetics/*isolation &amp; purification/*ultrastructure ; Staphylococcus Phages/classification/*genetics/*isolation &amp; purification/ultrastructure ; Staphylococcus aureus/drug effects/genetics/*virology ; Transduction, Genetic ; *beta-Lactam Resistance/genetics ; beta-Lactamases/genetics ; beta-Lactams/pharmacology ; }, abstract = {Temperate phages have been suggested to carry virulence factors and other lysogenic conversion genes that play important roles in pathogenicity. In this study, phage TEM123 in wild-type Staphylococcus aureus from food sources was analyzed with respect to its morphology, genome sequence, and antibiotic resistance conversion ability. Phage TEM123 from a mitomycin C-induced lysate of S. aureus was isolated from foods. Morphological analysis under a transmission electron microscope revealed that it belonged to the family Siphoviridae. The genome of phage TEM123 consisted of a double-stranded DNA of 43,786 bp with a G+C content of 34.06%. A bioinformatics analysis of the phage genome identified 43 putative open reading frames (ORFs). ORF1 encoded a protein that was nearly identical to the metallo-β-lactamase enzymes that degrade β-lactam antibiotics. After transduction to S. aureus with phage TEM123, the metallo-β-lactamase gene was confirmed in the transductant by PCR and sequencing analyses. In a β-lactam antibiotic susceptibility test, the transductant was more highly resistant to β-lactam antibiotics than S. aureus S133. Phage TEM123 might play a role in the transfer of β-lactam antibiotic resistance determinants in S. aureus. Therefore, we suggest that the prophage of S. aureus with its exotoxin is a risk factor for food safety in the food chain through lateral gene transfer.}, }
@article {pmid26561016, year = {2015}, author = {Kesavan, B and Srividhya, KV and Krishnaswamy, S and Raja, M and Vidya, N and Mohan, AV}, title = {Understanding the virulence of the entero-aggregative E. coli O104:H4.}, journal = {International journal of bioinformatics research and applications}, volume = {11}, number = {3}, pages = {187-199}, doi = {10.1504/ijbra.2015.069185}, pmid = {26561016}, issn = {1744-5485}, mesh = {Adult ; Disease Outbreaks ; Escherichia coli/genetics/*pathogenicity ; Escherichia coli Infections/epidemiology/*microbiology ; Female ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/genetics ; Germany ; Humans ; Prophages/genetics ; Republic of Korea ; Virulence/*genetics ; }, abstract = {O104:H4 is a new strain of E. coli that has caused an outbreak in Germany. It was isolated from patients with bloody diarrhoea and Haemolytic Uremic Syndrome (HUS). BGI (www.genomics.cn) sequenced and assembled this new strain. It was reported to show resistance to a number of drugs that are toxic to other E. coli and causes serious complications during infections, which ultimately lead to death. Multi-drug resistance and high virulence of this strain is thought to be acquired from different sources, by horizontal gene transfer. A total of 38 prophage elements were detected from the new strain by using three computational tools viz., DRAD, Prophage Finder and PHAST. Analysis on these prophage elements shows a number of virulence proteins like Shiga toxin and multi-drug resistance protein encoding genes. The high virulence of the strain could be attributed by the prophage elements acquired from its micro environment.}, }
@article {pmid26559010, year = {2016}, author = {Murray, GG and Weinert, LA and Rhule, EL and Welch, JJ}, title = {The Phylogeny of Rickettsia Using Different Evolutionary Signatures: How Tree-Like is Bacterial Evolution?.}, journal = {Systematic biology}, volume = {65}, number = {2}, pages = {265-279}, pmid = {26559010}, issn = {1076-836X}, support = {//Medical Research Council/United Kingdom ; //Wellcome Trust/United Kingdom ; }, mesh = {Biological Evolution ; Classification ; Computer Simulation/*standards ; Genome, Bacterial/*genetics ; *Phylogeny ; Rickettsia/*classification/*genetics ; }, abstract = {Rickettsia is a genus of intracellular bacteria whose hosts and transmission strategies are both impressively diverse, and this is reflected in a highly dynamic genome. Some previous studies have described the evolutionary history of Rickettsia as non-tree-like, due to incongruity between phylogenetic reconstructions using different portions of the genome. Here, we reconstruct the Rickettsia phylogeny using whole-genome data, including two new genomes from previously unsampled host groups. We find that a single topology, which is supported by multiple sources of phylogenetic signal, well describes the evolutionary history of the core genome. We do observe extensive incongruence between individual gene trees, but analyses of simulations over a single topology and interspersed partitions of sites show that this is more plausibly attributed to systematic error than to horizontal gene transfer. Some conflicting placements also result from phylogenetic analyses of accessory genome content (i.e., gene presence/absence), but we argue that these are also due to systematic error, stemming from convergent genome reduction, which cannot be accommodated by existing phylogenetic methods. Our results show that, even within a single genus, tests for gene exchange based on phylogenetic incongruence may be susceptible to false positives.}, }
@article {pmid26555390, year = {2015}, author = {Böhm, ME and Huptas, C and Krey, VM and Scherer, S}, title = {Massive horizontal gene transfer, strictly vertical inheritance and ancient duplications differentially shape the evolution of Bacillus cereus enterotoxin operons hbl, cytK and nhe.}, journal = {BMC evolutionary biology}, volume = {15}, number = {}, pages = {246}, pmid = {26555390}, issn = {1471-2148}, mesh = {Bacillaceae Infections/microbiology ; Bacillus cereus/classification/*genetics/*pathogenicity ; Bacterial Proteins/genetics ; Enterotoxins/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Hemolysin Proteins/genetics ; Operon ; Phylogeny ; Virulence Factors/*genetics ; }, abstract = {BACKGROUND: Bacillus cereus sensu lato comprises eight closely related species including the human pathogens Bacillus anthracis and Bacillus cereus. Within B. cereus sensu lato, chromosomally and plasmid-encoded toxins exist. While plasmid-mediated horizontal gene transfer of the emetic toxin, anthrax and insecticidal toxins is known, evolution of enterotoxin genes within the group has not been studied.<br><br>RESULTS: We report draft genome assemblies of 25 strains, a phylogenetic network of 142 strains based on ANI derived from genome sequences and a phylogeny based on whole-genome SNP analysis. The data clearly support subdivision of B. cereus sensu lato into seven phylogenetic groups. While group I, V and VII represent B. pseudomycoides, B. toyonensis and B. cytotoxicus, which are distinguishable at species level (ANI border &#x2265; 96 %), strains ascribed to the other five species do not match phylogenic groups. The chromosomal enterotoxin operons nheABC and hblCDAB are abundant within B. cereus both isolated from infections and from the environment. While the duplicated hbl variant hbl a is present in 22 % of all strains investigated, duplication of nheABC is extremely rare (0.02 %) and appears to be phylogenetically unstable. Distribution of toxin genes was matched to a master tree based on seven concatenated housekeeping genes, which depicts species relationships in B. cereus sensu lato as accurately as whole-genome comparisons. Comparison to the phylogeny of enterotoxin genes uncovered ample evidence for horizontal transfer of hbl, cytK and plcR, as well as frequent deletion of both toxins and duplication of hbl. No evidence for nhe deletion was found and stable horizontal transfer of nhe is rare. Therefore, evolution of B. cereus enterotoxin operons is shaped unexpectedly different for yet unknown reasons.<br><br>CONCLUSIONS: Frequent exchange of the pathogenicity factors hbl, cytK and plcR in B. cereus sensu lato appears to be an important mechanism of B. cereus virulence evolution, including so-called probiotic or non-pathogenic species, which might have consequences for risk assessment procedures. In contrast, exclusively vertical inheritance of nhe was observed, and since nhe-negative strains appear to be extremely rare, we suggest that fitness loss may be associated with deletion or horizontal transfer of the nhe operon.}, }
@article {pmid26549518, year = {2016}, author = {Marsit, S and Sanchez, I and Galeote, V and Dequin, S}, title = {Horizontally acquired oligopeptide transporters favour adaptation of Saccharomyces cerevisiae wine yeast to oenological environment.}, journal = {Environmental microbiology}, volume = {18}, number = {4}, pages = {1148-1161}, doi = {10.1111/1462-2920.13117}, pmid = {26549518}, issn = {1462-2920}, mesh = {Adaptation, Physiological/*genetics ; Amino Acids/*metabolism ; Biological Transport/genetics ; Environment ; Fermentation ; Gene Expression Profiling ; Gene Transfer, Horizontal ; Metabolic Networks and Pathways ; Oligopeptides/metabolism ; Saccharomyces cerevisiae/*genetics/*metabolism ; Vitis/microbiology ; Wine/*microbiology ; }, abstract = {In the past decade, horizontal gene transfer (HGT) has emerged as a major evolutionary process that has shaped the genome of Saccharomyces cerevisiae wine yeasts. We recently showed that a large Torulaspora microellipsoides genomic island carrying two oligopeptide transporters encoded by FOT genes increases the fitness of wine yeast during fermentation of grape must. However, the impact of these genes on the metabolic network of S. cerevisiae remained uncharacterized. Here we show that Fot-mediated peptide uptake substantially affects the glutamate node and the NADPH/NADP(+) balance, resulting in the delayed uptake of free amino acids and altered profiles of metabolites and volatile compounds. Transcriptome analysis revealed that cells using a higher amount of oligopeptides from grape must are less stressed and display substantial variation in the expression of genes in the central pathways of carbon and nitrogen metabolism, amino acid and protein biosynthesis, and the oxidative stress response. These regulations shed light on the molecular and metabolic mechanisms involved in the higher performance and fitness conferred by the HGT-acquired FOT genes, pinpointing metabolic effects that can positively affect the organoleptic balance of wines.}, }
@article {pmid26543265, year = {2015}, author = {Rathinasabapathi, P and Hiremath, DS and Arunraj, R and Parani, M}, title = {Molecular Detection of New Delhi Metallo-Beta-Lactamase-1 (NDM-1) Positive Bacteria from Environmental and Drinking Water Samples by Loop Mediated Isothermal Amplification of bla NDM-1.}, journal = {Indian journal of microbiology}, volume = {55}, number = {4}, pages = {400-405}, pmid = {26543265}, issn = {0046-8991}, abstract = {New Delhi metallo-β-lactamase-1 gene (bla NDM-1) codes for New Delhi metallo-beta-lactamase-1 (NDM-1) enzyme that cleaves the amide bond of β-lactam ring, and provides resistance against major classes of β-lactam antibiotics. Dissemination of the plasmid borne bla NDM-1 through horizontal gene transfer is a potential threat to the society. In this study, a rapid non-culture method for detecting NDM-1 positive bacteria was developed by Loop Mediated Isothermal Amplification (LAMP) of bla NDM-1 . Sensitivity of this method was found to be one femtogram of plasmid DNA, which translates into 2.6-25.8 copies depending on the size of the plasmid DNA. This method was applied to detect NDM-1 positive bacteria in 81 water samples that were collected from environmental and drinking water sources. NDM-1 positive bacteria were detected in three drinking water samples by LAMP but not by PCR. These three samples were collected from the water sources that were treated with chlorine for decontamination before public distribution. NDM-1 positive bacteria were not detected in lake water samples or in the samples that were collected from the water sources that were purified by reverse osmosis before public distribution. Detection of NDM-1 positive bacteria using LAMP was found to be safe, sensitive and rapid for screening large number of samples from diverse sources. This method could be developed as on-field detection kit by using fluorescent dyes to visualize the amplified bla NDM-1 gene.}, }
@article {pmid26542581, year = {2015}, author = {Martiny, JB and Jones, SE and Lennon, JT and Martiny, AC}, title = {Microbiomes in light of traits: A phylogenetic perspective.}, journal = {Science (New York, N.Y.)}, volume = {350}, number = {6261}, pages = {aac9323}, doi = {10.1126/science.aac9323}, pmid = {26542581}, issn = {1095-9203}, mesh = {Environment ; Gene Transfer, Horizontal ; *Gene-Environment Interaction ; Genetic Loci ; *Genetic Variation ; Humans ; Microbiota/*genetics ; Phylogeny ; Phylogeography ; Prochlorococcus/classification/genetics ; }, abstract = {A focus on the phenotypic characteristics of microorganisms-their traits-offers a path for interpreting the growing amount of microbiome data. We review key aspects of microbial traits, as well as approaches used to assay their phylogenetic distribution. Recent studies reveal that microbial traits are differentially conserved across the tree of life and appear to be conserved in a hierarchical fashion, possibly linked to their biochemical complexity. These results suggest a predictive framework whereby the genetic (or taxonomic) resolution of microbiome variation among samples provides information about the traits under selection. The organizational parallels seen among human and free-living microbiomes seem to support this idea. Developments in this framework may offer predictions not only for how microbial composition responds to changing environmental conditions, but also for how these changes may alter the health or functioning in human, engineered, and environmental systems.}, }
@article {pmid26542305, year = {2016}, author = {Chen, D and Gong, L and Walsh, TR and Lan, R and Wang, T and Zhang, J and Mai, W and Ni, N and Lu, J and Xu, J and Li, J}, title = {Infection by and dissemination of NDM-5-producing Escherichia coli in China.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {71}, number = {2}, pages = {563-565}, doi = {10.1093/jac/dkv352}, pmid = {26542305}, issn = {1460-2091}, support = {G1100135/MRC_/Medical Research Council/United Kingdom ; MR/P007295/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adult ; Aged, 80 and over ; China/epidemiology ; Escherichia coli/*enzymology/genetics/isolation &amp; purification ; Escherichia coli Infections/*epidemiology/*microbiology ; Female ; Gene Transfer, Horizontal ; Humans ; Male ; Molecular Sequence Data ; Plasmids/analysis ; Sequence Analysis, DNA ; Young Adult ; beta-Lactamases/*metabolism ; }, }
@article {pmid26542048, year = {2015}, author = {Boyd, EF and Carpenter, MR and Chowdhury, N and Cohen, AL and Haines-Menges, BL and Kalburge, SS and Kingston, JJ and Lubin, JB and Ongagna-Yhombi, SY and Whitaker, WB}, title = {Post-Genomic Analysis of Members of the Family Vibrionaceae.}, journal = {Microbiology spectrum}, volume = {3}, number = {5}, pages = {}, pmid = {26542048}, issn = {2165-0497}, support = {T32 GM008550/GM/NIGMS NIH HHS/United States ; }, mesh = {Aliivibrio/*classification/genetics ; Animals ; Bacterial Typing Techniques ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Essential ; Genes, Regulator ; *Genetic Variation ; *Genome, Bacterial ; Gram-Negative Bacterial Infections/microbiology/veterinary ; Host-Pathogen Interactions ; Humans ; Photobacterium/*classification/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sigma Factor/genetics ; Vibrio/*classification/genetics ; }, abstract = {Similar to other genera and species of bacteria, whole genomic sequencing has revolutionized how we think about and address questions of basic Vibrio biology. In this review we examined 36 completely sequenced and annotated members of the Vibrionaceae family, encompassing 12 different species of the genera Vibrio, Aliivibrio, and Photobacterium. We reconstructed the phylogenetic relationships among representatives of this group of bacteria by using three housekeeping genes and 16S rRNA sequences. With an evolutionary framework in place, we describe the occurrence and distribution of primary and alternative sigma factors, global regulators present in all bacteria. Among Vibrio we show that the number and function of many of these sigma factors differs from species to species. We also describe the role of the Vibrio-specific regulator ToxRS in fitness and survival. Examination of the biochemical capabilities was and still is the foundation of classifying and identifying new Vibrio species. Using comparative genomics, we examine the distribution of carbon utilization patterns among Vibrio species as a possible marker for understanding bacteria-host interactions. Finally, we discuss the significant role that horizontal gene transfer, specifically, the distribution and structure of integrons, has played in Vibrio evolution.}, }
@article {pmid26541173, year = {2016}, author = {Groussin, M and Boussau, B and Szöllõsi, G and Eme, L and Gouy, M and Brochier-Armanet, C and Daubin, V}, title = {Gene Acquisitions from Bacteria at the Origins of Major Archaeal Clades Are Vastly Overestimated.}, journal = {Molecular biology and evolution}, volume = {33}, number = {2}, pages = {305-310}, pmid = {26541173}, issn = {1537-1719}, mesh = {Archaea/classification/*genetics ; Bacteria/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; Genomics ; *Genotype ; Phylogeny ; }, abstract = {In a recent article, Nelson-Sathi et al. (NS) report that the origins of major archaeal lineages (MAL) correspond to massive group-specific gene acquisitions via HGT from bacteria (Nelson-Sathi et al. 2015. Origins of major archaeal clades correspond to gene acquisitions from bacteria. Nature 517(7532):77-80.). If correct, this would have fundamental implications for the process of diversification in microbes. However, a reexamination of these data and results shows that the methodology used by NS systematically inflates the number of genes acquired at the root of each MAL, and incorrectly assumes bacterial origins for these genes. A reanalysis of their data with appropriate phylogenetic models accounting for the dynamics of gene gain and loss between lineages supports the continuous acquisition of genes over long periods in the evolution of Archaea.}, }
@article {pmid26539826, year = {2015}, author = {Wu, G and Zhao, H and Li, C and Rajapakse, MP and Wong, WC and Xu, J and Saunders, CW and Reeder, NL and Reilman, RA and Scheynius, A and Sun, S and Billmyre, BR and Li, W and Averette, AF and Mieczkowski, P and Heitman, J and Theelen, B and Schröder, MS and De Sessions, PF and Butler, G and Maurer-Stroh, S and Boekhout, T and Nagarajan, N and Dawson, TL}, title = {Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin.}, journal = {PLoS genetics}, volume = {11}, number = {11}, pages = {e1005614}, pmid = {26539826}, issn = {1553-7404}, support = {R37 AI039115/AI/NIAID NIH HHS/United States ; T32 GM007184/GM/NIGMS NIH HHS/United States ; R01 AI039115/AI/NIAID NIH HHS/United States ; R01 AI050113/AI/NIAID NIH HHS/United States ; R37 AI39115-18/AI/NIAID NIH HHS/United States ; R01 AI50113-11/AI/NIAID NIH HHS/United States ; }, mesh = {*Adaptation, Physiological ; Gene Transfer, Horizontal ; *Genes, Fungal ; Humans ; Malassezia/classification/genetics/physiology ; *Phylogeny ; Skin/*microbiology ; }, abstract = {Malassezia is a unique lipophilic genus in class Malasseziomycetes in Ustilaginomycotina, (Basidiomycota, fungi) that otherwise consists almost exclusively of plant pathogens. Malassezia are typically isolated from warm-blooded animals, are dominant members of the human skin mycobiome and are associated with common skin disorders. To characterize the genetic basis of the unique phenotypes of Malassezia spp., we sequenced the genomes of all 14 accepted species and used comparative genomics against a broad panel of fungal genomes to comprehensively identify distinct features that define the Malassezia gene repertoire: gene gain and loss; selection signatures; and lineage-specific gene family expansions. Our analysis revealed key gene gain events (64) with a single gene conserved across all Malassezia but absent in all other sequenced Basidiomycota. These likely horizontally transferred genes provide intriguing gain-of-function events and prime candidates to explain the emergence of Malassezia. A larger set of genes (741) were lost, with enrichment for glycosyl hydrolases and carbohydrate metabolism, concordant with adaptation to skin's carbohydrate-deficient environment. Gene family analysis revealed extensive turnover and underlined the importance of secretory lipases, phospholipases, aspartyl proteases, and other peptidases. Combining genomic analysis with a re-evaluation of culture characteristics, we establish the likely lipid-dependence of all Malassezia. Our phylogenetic analysis sheds new light on the relationship between Malassezia and other members of Ustilaginomycotina, as well as phylogenetic lineages within the genus. Overall, our study provides a unique genomic resource for understanding Malassezia niche-specificity and potential virulence, as well as their abundance and distribution in the environment and on human skin.}, }
@article {pmid26539367, year = {2015}, author = {Oloomi, M and Javadi, M and Bouzari, S}, title = {Presence of pathogenicity island related and plasmid encoded virulence genes in cytolethal distending toxin producing Escherichia coli isolates from diarrheal cases.}, journal = {International journal of applied &amp; basic medical research}, volume = {5}, number = {3}, pages = {181-186}, pmid = {26539367}, issn = {2229-516X}, abstract = {CONTEXT: Mobile genetic elements such as plasmids, bacteriophages, insertion elements, and genomic islands play a critical role in virulence of bacterial pathogens. These elements transfer horizontally and could play an important role in the evolution and virulence of many pathogens. A broad spectrum of gram-negative bacterial species has been shown to produce a cytolethal distending toxin (CDT). On the other hand, Shiga toxin producing Escherichia coli are the one carry virulence genes such as stx 1 and stx 2 (Shiga toxin) and these genes can be acquired by horizontal gene transfer.<br><br>AIM: The aim of this study was to investigate the presence of other virulence associated genes among CDT producing E. coli strains.<br><br>MATERIALS AND METHODS: Thirty CDT positive strains isolated from patients with diarrhea were characterized. Thereafter, the association with virulent genetic elements in known pathogenicity islands (PAIs) was assessed by polymerase chain reaction.<br><br>RESULTS: In this study, it was shown that the most CDT producing E. coli isolates express Shiga toxin. Moreover, the presence of prophages framing cdt genes (like P2 phage) was also identified in each cdt-type genomic group. Flanked regions of cdt-I, cdt-IV, and cdt-V-type was similar to plasmid sequences while cdt-II and cdt-III-type regions similarity with hypothetical protein (orf3) was observed.<br><br>CONCLUSION: The occurrence of each cdt-type groups with specific virulence genes and PAI genetic elements is indicative of horizontal gene transfer by these mobile genetic elements, which could lead to diversity among the isolates.}, }
@article {pmid26537974, year = {2016}, author = {Varga, M and Pantu Ček, R and Ru Žičková, V and Doškarˇ, J}, title = {Molecular characterization of a new efficiently transducing bacteriophage identified in meticillin-resistant Staphylococcus aureus.}, journal = {The Journal of general virology}, volume = {97}, number = {1}, pages = {258-268}, doi = {10.1099/jgv.0.000329}, pmid = {26537974}, issn = {1465-2099}, mesh = {Computational Biology ; DNA, Viral/chemistry/genetics ; Drug Resistance, Bacterial ; Gene Order ; Gene Transfer, Horizontal ; Genome, Viral ; Lysogeny ; Methicillin-Resistant Staphylococcus aureus/*virology ; Microscopy, Electron, Transmission ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Plasmids ; Prophages/*genetics/*isolation &amp; purification/ultrastructure ; Sequence Analysis, DNA ; Sequence Homology ; Siphoviridae/genetics/isolation &amp; purification/ultrastructure ; Synteny ; *Transduction, Genetic ; Virus Activation ; }, abstract = {In Staphylococcus aureus, generalized transduction mediated by temperate bacteriophages represents a highly efficient way of transferring antibiotic resistance genes between strains. In the present study, we identified and characterized in detail a new efficiently transducing bacteriophage of the family Siphoviridae, designated ϕJB, which resides as a prophage in the meticillin-resistant S. aureus (MRSA) strain Jevons B. Whole-genome sequencing followed by detailed in silico analysis uncovered a linear dsDNA genome consisting of 43 ,12 bp and comprising 70 ORFs, of which ∼40 encoded proteins with unknown function. A global genome alignment of ϕJB and other efficiently transducing phages ϕ11, ϕ53, ϕ80, ϕ80α and ϕNM4 showed a high degree of homology with ϕNM4 and substantial differences with regard to other phages. Using a model transduction system with a well-defined donor and recipient, ϕJB transferred the tetracycline resistance plasmid pT181 and a penicillinase plasmid with outstanding frequencies, beating most of the above-mentioned phages by an order of magnitude. Moreover, ϕJB demonstrated high frequencies of transferring antibiotic resistance plasmids even upon induction from a lysogenic donor strain. Considering such transducing potential, ϕJB and related bacteriophages may serve as a suitable tool for elucidating the nature of transduction and its contribution to the spread of antibiotic resistance genes in naturally occurring MRSA populations.}, }
@article {pmid26537913, year = {2015}, author = {Eyres, I and Boschetti, C and Crisp, A and Smith, TP and Fontaneto, D and Tunnacliffe, A and Barraclough, TG}, title = {Horizontal gene transfer in bdelloid rotifers is ancient, ongoing and more frequent in species from desiccating habitats.}, journal = {BMC biology}, volume = {13}, number = {}, pages = {90}, pmid = {26537913}, issn = {1741-7007}, support = {233232/ERC_/European Research Council/International ; BB/F020562/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/F020856/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Desiccation ; *Ecosystem ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; Rotifera/*genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {BACKGROUND: Although prevalent in prokaryotes, horizontal gene transfer (HGT) is rarer in multicellular eukaryotes. Bdelloid rotifers are microscopic animals that contain a higher proportion of horizontally transferred, non-metazoan genes in their genomes than typical of animals. It has been hypothesized that bdelloids incorporate foreign DNA when they repair their chromosomes following double-strand breaks caused by desiccation. HGT might thereby contribute to species divergence and adaptation, as in prokaryotes. If so, we expect that species should differ in their complement of foreign genes, rather than sharing the same set of foreign genes inherited from a common ancestor. Furthermore, there should be more foreign genes in species that desiccate more frequently. We tested these hypotheses by surveying HGT in four congeneric species of bdelloids from different habitats: two from permanent aquatic habitats and two from temporary aquatic habitats that desiccate regularly.<br><br>RESULTS: Transcriptomes of all four species contain many genes with a closer match to non-metazoan genes than to metazoan genes. Whole genome sequencing of one species confirmed the presence of these foreign genes in the genome. Nearly half of foreign genes are shared between all four species and an outgroup from another family, but many hundreds are unique to particular species, which indicates that HGT is ongoing. Using a dated phylogeny, we estimate an average of 12.8 gains versus 2.0 losses of foreign genes per million years. Consistent with the desiccation hypothesis, the level of HGT is higher in the species that experience regular desiccation events than those that do not. However, HGT still contributed hundreds of foreign genes to the species from permanently aquatic habitats. Foreign genes were mainly enzymes with various annotated functions that include catabolism of complex polysaccharides and stress responses. We found evidence of differential loss of ancestral foreign genes previously associated with desiccation protection in the two non-desiccating species.<br><br>CONCLUSIONS: Nearly half of foreign genes were acquired before the divergence of bdelloid families over 60 Mya. Nonetheless, HGT is ongoing in bdelloids and has contributed to putative functional differences among species. Variation among our study species is consistent with the hypothesis that desiccating habitats promote HGT.}, }
@article {pmid26537224, year = {2015}, author = {Ooka, T and Ogura, Y and Katsura, K and Seto, K and Kobayashi, H and Kawano, K and Tokuoka, E and Furukawa, M and Harada, S and Yoshino, S and Seto, J and Ikeda, T and Yamaguchi, K and Murase, K and Gotoh, Y and Imuta, N and Nishi, J and Gomes, TA and Beutin, L and Hayashi, T}, title = {Defining the Genome Features of Escherichia albertii, an Emerging Enteropathogen Closely Related to Escherichia coli.}, journal = {Genome biology and evolution}, volume = {7}, number = {12}, pages = {3170-3179}, pmid = {26537224}, issn = {1759-6653}, mesh = {Base Sequence ; Enteropathogenic Escherichia coli/*genetics/isolation &amp; purification/pathogenicity ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Molecular Sequence Data ; Virulence/genetics ; }, abstract = {Escherichia albertii is a recently recognized close relative of Escherichia coli. This emerging enteropathogen possesses a type III secretion system (T3SS) encoded by the locus of enterocyte effacement, similar to enteropathogenic and enterohemorrhagic E. coli (EPEC and EHEC). Shiga toxin-producing strains have also been identified. The genomic features of E. albertii, particularly differences from other Escherichia species, have not yet been well clarified. Here, we sequenced the genome of 29 E. albertii strains (3 complete and 26 draft sequences) isolated from multiple sources and performed intraspecies and intragenus genomic comparisons. The sizes of the E. albertii genomes range from 4.5 to 5.1 Mb, smaller than those of E. coli strains. Intraspecies genomic comparisons identified five phylogroups of E. albertii. Intragenus genomic comparison revealed that the possible core genome of E. albertii comprises 3,250 genes, whereas that of the genus Escherichia comprises 1,345 genes. Our analysis further revealed several unique or notable genetic features of E. albertii, including those responsible for known biochemical features and virulence factors and a possibly active second T3SS known as ETT2 (E. coli T3SS 2) that is inactivated in E. coli. Although this organism has been observed to be nonmotile in vitro, genes for flagellar biosynthesis are fully conserved; chemotaxis-related genes have been selectively deleted. Based on these results, we have developed a nested polymerase chain reaction system to directly detect E. albertii. Our data define the genomic features of E. albertii and provide a valuable basis for future studies of this important emerging enteropathogen.}, }
@article {pmid26537223, year = {2015}, author = {Koczyk, G and Dawidziuk, A and Popiel, D}, title = {The Distant Siblings-A Phylogenomic Roadmap Illuminates the Origins of Extant Diversity in Fungal Aromatic Polyketide Biosynthesis.}, journal = {Genome biology and evolution}, volume = {7}, number = {11}, pages = {3132-3154}, pmid = {26537223}, issn = {1759-6653}, mesh = {Ascomycota/enzymology/*genetics ; Bayes Theorem ; Conserved Sequence ; Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; Genetic Speciation ; *Genome, Fungal ; Likelihood Functions ; Models, Genetic ; *Phylogeny ; Polyketide Synthases/*genetics ; Polyketides/*metabolism ; Protein Structure, Tertiary ; Synteny ; }, abstract = {In recent years, the influx of newly sequenced fungal genomes has enabled sampling of secondary metabolite biosynthesis on an unprecedented scale. However, explanations of extant diversity which take into account both large-scale phylogeny reconstructions and knowledge gained from multiple genome projects are still lacking. We analyzed the evolutionary sources of genetic diversity in aromatic polyketide biosynthesis in over 100 model fungal genomes. By reconciling the history of over 400 nonreducing polyketide synthases (NR-PKSs) with corresponding species history, we demonstrate that extant fungal NR-PKSs are clades of distant siblings, originating from a burst of duplications in early Pezizomycotina and thinned by extensive losses. The capability of higher fungi to biosynthesize the simplest precursor molecule (orsellinic acid) is highlighted as an ancestral trait underlying biosynthesis of aromatic compounds. This base activity was modified during early evolution of filamentous fungi, toward divergent reaction schemes associated with biosynthesis of, for example, aflatoxins and fusarubins (C4-C9 cyclization) or various anthraquinone derivatives (C6-C11 cyclization). The functional plasticity is further shown to have been supplemented by modularization of domain architecture into discrete pieces (conserved splice junctions within product template domain), as well as tight linkage of key accessory enzyme families and divergence in employed transcriptional factors. Although the majority of discord between species and gene history is explained by ancient duplications, this landscape has been altered by more recent duplications, as well as multiple horizontal gene transfers. The 25 detected transfers include previously undescribed events leading to emergence of, for example, fusarubin biosynthesis in Fusarium genus. Both the underlying data and the results of present analysis (including alternative scenarios revealed by sampling multiple reconciliation optima) are maintained as a freely available web-based resource: http://cropnet.pl/metasites/sekmet/nrpks_2014.}, }
@article {pmid26535959, year = {2016}, author = {Goodman, KE and Simner, PJ and Tamma, PD and Milstone, AM}, title = {Infection control implications of heterogeneous resistance mechanisms in carbapenem-resistant Enterobacteriaceae (CRE).}, journal = {Expert review of anti-infective therapy}, volume = {14}, number = {1}, pages = {95-108}, doi = {10.1586/14787210.2016.1106940}, pmid = {26535959}, issn = {1744-8336}, mesh = {Anti-Bacterial Agents/*therapeutic use ; Bacterial Proteins/*genetics/metabolism ; Carbapenems/*therapeutic use ; Communicable Disease Control/methods ; Cross Infection/*drug therapy/epidemiology/microbiology/transmission ; Enterobacteriaceae/drug effects/enzymology/*genetics ; Enterobacteriaceae Infections/*drug therapy/epidemiology/microbiology/transmission ; Epidemiological Monitoring ; Gene Expression ; Gene Transfer, Horizontal ; Humans ; Molecular Epidemiology ; Mutation ; Plasmids/chemistry/metabolism ; United States/epidemiology ; beta-Lactam Resistance/*genetics ; beta-Lactamases/*genetics/metabolism ; }, abstract = {The Centers for Disease Control and Prevention (CDC) defines carbapenem-resistant Enterobacteriaceae (CRE) based upon a phenotypic demonstration of carbapenem resistance. However, considerable heterogeneity exists within this definitional umbrella. CRE may mechanistically differ by whether they do or do not produce carbapenemases. Moreover, patients can acquire CRE through multiple pathways: endogenously through antibiotic selective pressure on intestinal microbiota, exogenously through horizontal transmission or through a combination of these factors. Some evidence suggests that non-carbapenemase-producing CRE may be more frequently acquired by antibiotic exposure and carbapenemase-producing CRE via horizontal transmission, but definitive data are lacking. This review examines types of CRE resistance mechanisms, antibiotic exposure and horizontal transmission pathways of CRE acquisition, and the implications of these heterogeneities to the development of evidence-based CRE healthcare epidemiology policies. In our Expert Commentary &amp; Five-Year View, we outline specific nosocomial CRE knowledge gaps and potential methodological approaches for their resolution.}, }
@article {pmid26535725, year = {2015}, author = {Andrade, BS and Góes-Neto, A}, title = {Phylogenetic analysis of DNA and RNA polymerases from a Moniliophthora perniciosa mitochondrial plasmid reveals probable lateral gene transfer.}, journal = {Genetics and molecular research : GMR}, volume = {14}, number = {4}, pages = {14105-14114}, doi = {10.4238/2015.October.29.30}, pmid = {26535725}, issn = {1676-5680}, mesh = {Agaricales/*enzymology/*genetics ; Cacao/microbiology ; DNA-Directed DNA Polymerase/*genetics ; DNA-Directed RNA Polymerases/*genetics ; *Gene Transfer, Horizontal ; Genome, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; Plant Diseases/microbiology ; Plasmids/genetics ; Sequence Analysis, DNA ; Sequence Analysis, Protein ; }, abstract = {The filamentous fungus Moniliophthora perniciosa is a hemibiotrophic basidiomycete that causes witches' broom disease of cacao (Theobroma cacao L.). Many fungal mitochondrial plasmids are DNA and RNA polymerase-encoding invertrons with terminal inverted repeats and 5'-linked proteins. The aim of this study was to carry out comparative and phylogenetic analyses of DNA and RNA polymerases for all known linear mitochondrial plasmids in fungi. We performed these analyses at both gene and protein levels and assessed differences between fungal and viral polymerases in order to test the lateral gene transfer (LGT) hypothesis. We analyzed all mitochondrial plasmids of the invertron type within the fungal clade, including five from Ascomycota, seven from Basidiomycota, and one from Chytridiomycota. All phylogenetic analyses generated similar tree topologies regardless of the methods and datasets used. It is likely that DNA and RNA polymerase genes were inserted into the mitochondrial genomes of the 13 fungal species examined in our study as a result of different LGT events. These findings are important for a better understanding of the evolutionary relationships between fungal mitochondrial plasmids.}, }
@article {pmid26528406, year = {2015}, author = {Sackman, AM and Reed, D and Rokyta, DR}, title = {Intergenic incompatibilities reduce fitness in hybrids of extremely closely related bacteriophages.}, journal = {PeerJ}, volume = {3}, number = {}, pages = {e1320}, pmid = {26528406}, issn = {2167-8359}, support = {R01 GM099723/GM/NIGMS NIH HHS/United States ; }, abstract = {Horizontal gene transfer and recombination occur across many groups of viruses and play key roles in important viral processes such as host-range expansion and immune-system avoidance. To have any predictive power regarding the ability of viruses to readily recombine, we must determine the extent to which epistasis restricts the success of recombinants, particularly as it relates to the genetic divergence between parental strains. In any hybridization event, the evolutionary success or failure of hybrids is largely determined by the pervasiveness of epistasis in the parental genomes. Recombination has previously been shown to incur steep fitness costs in highly divergent viruses as a result of disrupted epistatic interactions. We used a pair of bacteriophages of the family Microviridae to demonstrate that epistasis may evidence itself in the form of fitness costs even in the case of the exchange of alleles at a locus with amino acid divergence as low as 1%. We explored a possible biophysical source of epistasis in the interaction of viral coat and scaffolding proteins and examined a recovery mutation that likely repairs interactions disrupted by recombination.}, }
@article {pmid26527411, year = {2015}, author = {Rawlings, ND}, title = {Bacterial calpains and the evolution of the calpain (C2) family of peptidases.}, journal = {Biology direct}, volume = {10}, number = {}, pages = {66}, pmid = {26527411}, issn = {1745-6150}, support = {/WT_/Wellcome Trust/United Kingdom ; WT077044/Z/05/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacteria/*enzymology/*genetics ; Bacterial Proteins/*genetics/metabolism ; Calpain/*genetics/metabolism ; Eukaryota/*enzymology/*genetics/metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Phylogeny ; }, abstract = {Homologues of calpain, often thought to be an essential, cytoplasmic, calcium-dependent cysteine endopeptidase found exclusively in eukaryotes, have been found in bacterial proteomes. The homologues lack calcium-binding sites, have differing domain architectures, and can be secreted or membrane-associated. Homologues are rare and occur in a minority of bacterial phyla and often in a minority of species in a genus. However, the differences in domain architecture argue against a recent, horizontal gene transfer from a eukaryote. From analysis of a phylogenetic tree and absence of homologues in archaea, calpains in eukaryotes may be derived from genes horizontally transferred from a bacterium.}, }
@article {pmid26527082, year = {2016}, author = {Martins-Pinheiro, M and Schons-Fonseca, L and da Silva, JB and Domingos, RH and Momo, LH and Simões, AC and Ho, PL and da Costa, RM}, title = {Genomic survey and expression analysis of DNA repair genes in the genus Leptospira.}, journal = {Molecular genetics and genomics : MGG}, volume = {291}, number = {2}, pages = {703-722}, pmid = {26527082}, issn = {1617-4623}, mesh = {Animals ; DNA Repair/*genetics ; Gene Expression Regulation, Bacterial ; Genome, Bacterial ; Host-Pathogen Interactions/genetics ; Leptospira/*genetics ; Leptospirosis/*genetics/microbiology ; Mesocricetus ; Models, Animal ; Phylogeny ; Zoonoses/genetics/microbiology ; }, abstract = {Leptospirosis is an emerging zoonosis with important economic and public health consequences and is caused by pathogenic leptospires. The genus Leptospira belongs to the order Spirochaetales and comprises saprophytic (L. biflexa), pathogenic (L. interrogans) and host-dependent (L. borgpetersenii) members. Here, we present an in silico search for DNA repair pathways in Leptospira spp. The relevance of such DNA repair pathways was assessed through the identification of mRNA levels of some genes during infection in animal model and after exposition to spleen cells. The search was performed by comparison of available Leptospira spp. genomes in public databases with known DNA repair-related genes. Leptospires exhibit some distinct and unexpected characteristics, for instance the existence of a redundant mechanism for repairing a chemically diverse spectrum of alkylated nucleobases, a new mutS-like gene and a new shorter version of uvrD. Leptospira spp. shares some characteristics from Gram-positive, as the presence of PcrA, two RecQ paralogs and two SSB proteins; the latter is considered a feature shared by naturally competent bacteria. We did not find a significant reduction in the number of DNA repair-related genes in both pathogenic and host-dependent species. Pathogenic leptospires were enriched for genes dedicated to base excision repair and non-homologous end joining. Their evolutionary history reveals a remarkable importance of lateral gene transfer events for the evolution of the genus. Up-regulation of specific DNA repair genes, including components of SOS regulon, during infection in animal model validates the critical role of DNA repair mechanisms for the complex interplay between host/pathogen.}, }
@article {pmid26526427, year = {2016}, author = {Mallo, D and De Oliveira Martins, L and Posada, D}, title = {SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees.}, journal = {Systematic biology}, volume = {65}, number = {2}, pages = {334-344}, pmid = {26526427}, issn = {1076-836X}, mesh = {Classification/*methods ; *Computer Simulation ; Genes/genetics ; Genetic Loci/genetics ; Genetic Speciation ; *Phylogeny ; Reproducibility of Results ; Software/*standards ; }, abstract = {We present a fast and flexible software package--SimPhy--for the simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer--all three potentially leading to species tree/gene tree discordance--and gene conversion. SimPhy implements a hierarchical phylogenetic model in which the evolution of species, locus, and gene trees is governed by global and local parameters (e.g., genome-wide, species-specific, locus-specific), that can be fixed or be sampled from a priori statistical distributions. SimPhy also incorporates comprehensive models of substitution rate variation among lineages (uncorrelated relaxed clocks) and the capability of simulating partitioned nucleotide, codon, and protein multilocus sequence alignments under a plethora of substitution models using the program INDELible. We validate SimPhy's output using theoretical expectations and other programs, and show that it scales extremely well with complex models and/or large trees, being an order of magnitude faster than the most similar program (DLCoal-Sim). In addition, we demonstrate how SimPhy can be useful to understand interactions among different evolutionary processes, conducting a simulation study to characterize the systematic overestimation of the duplication time when using standard reconciliation methods. SimPhy is available at https://github.com/adamallo/SimPhy, where users can find the source code, precompiled executables, a detailed manual and example cases.}, }
@article {pmid26525488, year = {2016}, author = {Militello, KT and Chang, MM and Simon, RD and Lazatin, JC}, title = {Blue genes: An integrative laboratory to differentiate genetic transformation from gene mutation for underclassmen.}, journal = {Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology}, volume = {44}, number = {1}, pages = {55-62}, doi = {10.1002/bmb.20923}, pmid = {26525488}, issn = {1539-3429}, mesh = {Escherichia coli/genetics ; *Genes, Bacterial ; Genotype ; Molecular Biology/*education ; *Mutation ; Phenotype ; *Students ; *Transformation, Genetic ; }, abstract = {The ability of students to understand the relationship between genotype and phenotype, and the mechanisms by which genotypes and phenotypes can change is essential for students studying genetics. To this end, we have developed a four-week laboratory called Blue Genes, which is designed to help novice students discriminate between two mechanisms by which the genetic material can be altered: genetic transformation and gene mutation. In the first week of the laboratory, students incubate a plasmid DNA with calcium chloride-treated Escherichia coli JM109 cells and observe a phenotype change from ampicillin sensitive to ampicillin resistant and from white color to blue color on plates containing 5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside (X-gal) and isopropyl β-D-thiogalactopyranoside (IPTG). Over the course of the next three weeks, students use a battery of approaches including plasmid DNA isolation experiments, restriction maps, and PCR to differentiate between mutation and transformation. The students ultimately come to the conclusion that the changes in phenotypes are due to genetic transformation and not mutation based on the evidence generated over the four-week period. Pre-laboratory tests and post-laboratory tests indicate that this set of exercises is successful in helping students differentiate between transformation and mutation. The laboratory is designed for underclassmen and is a good prerequisite for an apprentice-based research opportunity, although it is not designed as a class based research experience. Potential modifications and future directions of the laboratory based upon student experiences and assessment are presented.}, }
@article {pmid26519859, year = {2015}, author = {Alex, A and Antunes, A}, title = {Whole Genome Sequencing of the Symbiont Pseudovibrio sp. from the Intertidal Marine Sponge Polymastia penicillus Revealed a Gene Repertoire for Host-Switching Permissive Lifestyle.}, journal = {Genome biology and evolution}, volume = {7}, number = {11}, pages = {3022-3032}, pmid = {26519859}, issn = {1759-6653}, mesh = {Animals ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Molecular Sequence Data ; Multigene Family ; *Phylogeny ; Porifera/*microbiology ; Sequence Analysis, DNA ; *Symbiosis ; Vibrionaceae/*genetics/isolation &amp; purification ; }, abstract = {Sponges harbor a complex consortium of microbial communities living in symbiotic relationship benefiting each other through the integration of metabolites. The mechanisms influencing a successful microbial association with a sponge partner are yet to be fully understood. Here, we sequenced the genome of Pseudovibrio sp. POLY-S9 strain isolated from the intertidal marine sponge Polymastia penicillus sampled from the Atlantic coast of Portugal to identify the genomic features favoring the symbiotic relationship. The draft genome revealed an exceptionally large genome size of 6.6 Mbp compared with the previously reported genomes of the genus Pseudovibrio isolated from a coral and a sponge larva. Our genomic study detected the presence of several biosynthetic gene clusters-polyketide synthase, nonribosomal peptide synthetase and siderophore-affirming the potential ability of the genus Pseudovibrio to produce a wide variety of metabolic compounds. Moreover, we identified a repertoire of genes encoding adaptive symbioses factors (eukaryotic-like proteins), such as the ankyrin repeats, tetratrico peptide repeats, and Sel1 repeats that improve the attachment to the eukaryotic hosts and the avoidance of the host's immune response : The genome also harbored a large number of mobile elements (∼5%) and gene transfer agents, which explains the massive genome expansion and suggests a possible mechanism of horizontal gene transfer. In conclusion, the genome of POLY-S9 exhibited an increase in size, number of mobile DNA, multiple metabolite gene clusters, and secretion systems, likely to influence the genome diversification and the evolvability.}, }
@article {pmid26518052, year = {2016}, author = {Tijet, N and Muller, MP and Matukas, LM and Khan, A and Patel, SN and Melano, RG}, title = {Lateral dissemination and inter-patient transmission of blaKPC-3: role of a conjugative plasmid in spreading carbapenem resistance.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {71}, number = {2}, pages = {344-347}, doi = {10.1093/jac/dkv356}, pmid = {26518052}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/pharmacology ; Blotting, Southern ; Citrobacter freundii/*enzymology/genetics/isolation &amp; purification ; Conjugation, Genetic ; Cross Infection/microbiology ; Disk Diffusion Antimicrobial Tests ; Electrophoresis, Gel, Pulsed-Field ; Enterobacteriaceae Infections/*microbiology ; Escherichia coli/*enzymology/genetics/isolation &amp; purification ; Female ; Gene Transfer, Horizontal ; Genotype ; Humans ; Klebsiella pneumoniae/*enzymology/genetics/isolation &amp; purification ; Middle Aged ; Multilocus Sequence Typing ; Plasmids/*analysis ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; *beta-Lactam Resistance ; beta-Lactamases/genetics/*metabolism ; }, abstract = {OBJECTIVES: The objective of this study was to describe the nosocomial spread of carbapenemase-producing enterobacteria and characterize a plasmid involved in KPC dissemination.<br><br>METHODS: Two Klebsiella pneumoniae, one Escherichia coli and one Citrobacter freundii isolated from two patients were studied. Susceptibility profiles were obtained using Etest. Carbapenemase activity was detected using the Carba NP test. &#x3b2;-Lactamase gene content was screened by PCR and sequencing. K. pneumoniae isolates were genotyped by MLST and PFGE. KPC plasmid sizes were estimated by S1-DNA digestion and PFGE-Southern blot. Plasmids were sequenced using Illumina's technology and Sanger sequencing.<br><br>RESULTS: Two patients sharing a room on a surgical unit were positive for carbapenemase-producing K. pneumoniae. One patient was also colonized with carbapenemase-producing C. freundii and E. coli. Neither patient had known risk factors for carbapenemase acquisition, although one patient had recent surgery at another Toronto hospital; the other patient's husband had surgery in New York City 3 years prior to her presentation. An extensive investigation was conducted at both hospitals, but no additional cases were identified. blaKPC-3 was detected in all clinical isolates. Variable carbapenem resistance levels were observed. Both K. pneumoniae belonged to the same clone by PFGE and MLST (ST277). pKPC-SMH (&#x223c; 53 kb) was identified in all the clinical isolates, showing identity only with structurally similar IncN plasmids.<br><br>CONCLUSIONS: We describe intra- and inter-patient dissemination of blaKPC. The involvement of a clone related to the successful K. pneumoniae ST258 and the blaKPC-3 gene detected in an active Tn4401 transposon carried on a conjugative broad-host-range plasmid increased the potential for this horizontal transmission.}, }
@article {pmid26513927, year = {2015}, author = {Siriwan-Sirikaew,  and Rattanachuay, P and Nakaguchi, Y and Sukhumungoonl, P}, title = {IMMUNO-MAGNETIC ISOLATION, CHARACTERIZATION AND GENETIC RELATIONSHIP OF ESCHERICHIA COLI O26 FROM RAW MEATS, HAT YAI CITY, SONGKHLA, THAILAND.}, journal = {The Southeast Asian journal of tropical medicine and public health}, volume = {46}, number = {2}, pages = {241-253}, pmid = {26513927}, issn = {0125-1562}, mesh = {Animals ; Cattle/microbiology ; Chickens/microbiology ; Diarrhea/microbiology ; Drug Resistance, Multiple, Bacterial ; Escherichia coli/genetics/*isolation &amp; purification/pathogenicity ; Escherichia coli Infections/microbiology ; Escherichia coli Proteins ; Food Microbiology ; Immunomagnetic Separation ; Meat/*microbiology ; Microbial Sensitivity Tests ; *Phylogeny ; Polymerase Chain Reaction ; Swine/microbiology ; Thailand ; }, abstract = {Escherichia coli O26 is the most important serotype in non-O157 group, which plays a significant role in gastrointestinal illnesses. However, information regarding the prevalence and its characteristics are lacking in Thailand. As raw meat is frequently a source of diarrheagenic E. coli, a total of 1,279 E. coli colonies were obtained from 157 raw meat samples obtained from retail markets in Hat Yai City, Songkhla Province, Thailand and E. coli O26 isolated using an immunemagnetic separation technique. Twenty-seven E. coli O26 strains were isolated from 18 samples of raw beef, chicken and pork meats. These E. coli O26 strains could not be classified into the six diarrheagenic E. coli categories and did not harbor virulence genes, except 5 strains carrying escV, encoding type III secretion system component. Phylogenetic group examination demonstrated that 26 strains belonged to phylogenetic group A, and one to group D. Antimicrobial susceptibility test revealed that the E. coli O26 strains were the multi-drug resistant strains. Genetic relatedness employing (GTG)5-PCR and ERIC2-PCR showed that some of O26 which isolated from different samples and different time intervals revealed the identical fingerprint pattern, suggesting that they were derived from the same clone. Examination of five stx2-containing phage integration sites showed that 6 strains had prophage occupancy at sbcB, suggesting that these isolates have the potential in horizontal gene transfer of virulence trait. Moreover, the intactness of yecE and wrbA, the important integration sites in E. coli O26, indicated the possibility of stx2-phage lysogenization in the future.}, }
@article {pmid26513155, year = {2015}, author = {Gluck-Thaler, E and Slot, JC}, title = {Dimensions of Horizontal Gene Transfer in Eukaryotic Microbial Pathogens.}, journal = {PLoS pathogens}, volume = {11}, number = {10}, pages = {e1005156}, pmid = {26513155}, issn = {1553-7374}, mesh = {Bacteria/*genetics ; Gene Regulatory Networks ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; }, }
@article {pmid26509691, year = {2015}, author = {Eberlein, C and Leducq, JB and Landry, CR}, title = {The genomics of wild yeast populations sheds light on the domestication of man's best (micro) friend.}, journal = {Molecular ecology}, volume = {24}, number = {21}, pages = {5309-5311}, doi = {10.1111/mec.13380}, pmid = {26509691}, issn = {1365-294X}, mesh = {*Evolution, Molecular ; *Genetics, Population ; *Genome, Fungal ; Saccharomyces cerevisiae/*genetics ; Wine/*microbiology ; }, abstract = {The domestication of plants, animals and microbes by humans are the longest artificial evolution experiments ever performed. The study of these long-term experiments can teach us about the genomics of adaptation through the identification of the genetic bases underlying the traits favoured by humans. In laboratory evolution, the characterization of the molecular changes that evolved specifically in some lineages is straightforward because the ancestors are readily available, for instance in the freezer. However, in the case of domesticated species, the ancestor is often missing, which leads to the necessity of going back to nature in order to infer the most likely ancestral state. Significant and relatively recent examples of this approach include wolves as the closest wild relative to domestic dogs (Axelsson et al. 2013) and teosinte as the closest relative to maize (reviewed in Hake &amp; Ross-Ibarra 2015). In both cases, the joint analysis of domesticated lineages and their wild cousins has been key in reconstructing the molecular history of their domestication. While the identification of closest wild relatives has been done for many plants and animals, these comparisons represent challenges for micro-organisms. This has been the case for the budding yeast Saccharomyces cerevisiae, whose natural ecological niche is particularly challenging to define. For centuries, this unicellular fungus has been the cellular factory for wine, beer and bread crafting, and currently for bioethanol and drug production. While the recent development of genomics has lead to the identification of many genetic elements associated with important wine characteristics, the historical origin of some of the domesticated wine strains has remained elusive due to the lack of knowledge of their close wild relatives. In this issue of Molecular Ecology, Almeida et al. (2015) identified what is to date the closest known wild population of the wine yeast. This population is found associated with oak trees in Europe, presumably its natural host. Using population genomics analyses, Almeida and colleagues discovered that the initial divergence between natural and domesticated wine yeasts in the Mediterranean region took place around the early days of wine production. Surprisingly, genomic regions that are key to wine production today appeared not to be derived from these natural populations but from genes gained from other yeast species.}, }
@article {pmid26505690, year = {2015}, author = {Nešvera, J and Rucká, L and Pátek, M}, title = {Catabolism of Phenol and Its Derivatives in Bacteria: Genes, Their Regulation, and Use in the Biodegradation of Toxic Pollutants.}, journal = {Advances in applied microbiology}, volume = {93}, number = {}, pages = {107-160}, doi = {10.1016/bs.aambs.2015.06.002}, pmid = {26505690}, issn = {0065-2164}, mesh = {Bacteria/*genetics/*metabolism ; Bacterial Proteins/*genetics/metabolism ; Biodegradation, Environmental ; *Gene Expression Regulation ; Hazardous Substances/*metabolism/toxicity ; Phenol/*metabolism/toxicity ; }, abstract = {Phenol and its derivatives (alkylphenols, halogenated phenols, nitrophenols) are natural or man-made aromatic compounds that are ubiquitous in nature and in human-polluted environments. Many of these substances are toxic and/or suspected of mutagenic, carcinogenic, and teratogenic effects. Bioremediation of the polluted soil and water using various bacteria has proved to be a promising option for the removal of these compounds. In this review, we describe a number of peripheral pathways of aerobic and anaerobic catabolism of various natural and xenobiotic phenolic compounds, which funnel these substances into a smaller number of central catabolic pathways. Finally, the metabolites are used as carbon and energy sources in the citric acid cycle. We provide here the characteristics of the enzymes that convert the phenolic compounds and their catabolites, show their genes, and describe regulatory features. The genes, which encode these enzymes, are organized on chromosomes and plasmids of the natural bacterial degraders in various patterns. The accumulated data on similarities and the differences of the genes, their varied organization, and particularly, an astonishingly broad range of intricate regulatory mechanism may be read as an exciting adventurous book on divergent evolutionary processes and horizontal gene transfer events inscribed in the bacterial genomes. In the end, the use of this wealth of bacterial biodegradation potential and the manipulation of its genetic basis for purposes of bioremediation is exemplified. It is envisioned that the integrated high-throughput techniques and genome-level approaches will enable us to manipulate systems rather than separated genes, which will give birth to systems biotechnology.}, }
@article {pmid26503660, year = {2016}, author = {Ocampo, AM and Chen, L and Cienfuegos, AV and Roncancio, G and Chavda, KD and Kreiswirth, BN and Jiménez, JN}, title = {A Two-Year Surveillance in Five Colombian Tertiary Care Hospitals Reveals High Frequency of Non-CG258 Clones of Carbapenem-Resistant Klebsiella pneumoniae with Distinct Clinical Characteristics.}, journal = {Antimicrobial agents and chemotherapy}, volume = {60}, number = {1}, pages = {332-342}, pmid = {26503660}, issn = {1098-6596}, support = {R01AI090155/AI/NIAID NIH HHS/United States ; }, mesh = {Adult ; Aged ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics/metabolism ; Carbapenems/pharmacology ; Clone Cells ; Colombia/epidemiology ; Cross-Sectional Studies ; DNA, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Electrophoresis, Gel, Pulsed-Field ; Epidemiological Monitoring ; Female ; Gene Expression ; Gene Transfer, Horizontal ; Humans ; Klebsiella Infections/drug therapy/*epidemiology/microbiology/transmission ; Klebsiella pneumoniae/classification/drug effects/enzymology/*genetics ; Male ; Microbial Sensitivity Tests ; Middle Aged ; Molecular Epidemiology ; Multilocus Sequence Typing ; *Phylogeny ; Plasmids/chemistry/metabolism ; Tertiary Care Centers ; beta-Lactamases/*genetics/metabolism ; }, abstract = {The global spread of carbapenem-resistant Klebsiella pneumoniae (CR-Kp) has been largely associated with sequence type 258 (ST258) and its related variants (clonal group 258 [CG258]). Here we describe the molecular epidemiology of CR-Kp from five tertiary care hospitals in Medellín, the second largest city in Colombia. All CR-Kp-infected patients admitted from June 2012 to June 2014 were included (n = 193). Patients' clinical information was obtained from medical records. Carbapenemase KPC, VIM, IMP, NDM, and OXA-48 genes were detected by PCR. A CG258-tonB79 cluster-specific real-time PCR (targeting the multilocus sequence type [MLST] tonB79 allele), pulsed-field gel electrophoresis (PFGE), and MLST analysis were performed for typing. Remarkably, 62.2% (n = 120) of isolates were from STs unrelated to CG258 (non-CG258). KPC-3 predominated in CG258 isolates (86.3%), while KPC-2 prevailed in non-CG258 isolates (75.5%) (P < 0.001). Multidrug resistance (MDR) frequency was significantly higher in CG258 strains (91.4% versus 56.1%; P < 0.001). ST512 (a single-locus variant of ST258) is the main ST in CG258 (96.3%), and isolates in this group showed closely related pulsotype and similar resistance gene profiles, suggesting the clonal spread of this strain. In contrast, high heterogeneity of STs (34/54), including eight novel STs, was found in non-CG258 isolates. Among non-CG258 isolates, ST14 (13.3%; n = 16) and ST307 (14.2%; n = 17) were the most frequent, and they showed distinct molecular and clinical characteristics in comparison to CG258 isolates. Our results suggest that the dissemination of carbapenem resistance in Medellín is due to heterogeneous K. pneumoniae clones, likely the result of horizontal transmission of KPC in different unrelated lineages, further highlighting the challenge in CR-Kp infection control and the need for a multifocal intervention.}, }
@article {pmid26502932, year = {2015}, author = {Ivanov, YV and Shariat, N and Register, KB and Linz, B and Rivera, I and Hu, K and Dudley, EG and Harvill, ET}, title = {A newly discovered Bordetella species carries a transcriptionally active CRISPR-Cas with a small Cas9 endonuclease.}, journal = {BMC genomics}, volume = {16}, number = {}, pages = {863}, pmid = {26502932}, issn = {1471-2164}, support = {R21 AI116186/AI/NIAID NIH HHS/United States ; R56 AI107016/AI/NIAID NIH HHS/United States ; R01 GM113681/GM/NIGMS NIH HHS/United States ; AI107016/AI/NIAID NIH HHS/United States ; R01 GM083113/GM/NIGMS NIH HHS/United States ; GM083113/GM/NIGMS NIH HHS/United States ; GM113681/GM/NIGMS NIH HHS/United States ; R56 AI065507/AI/NIAID NIH HHS/United States ; AI116186/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/metabolism ; Base Composition/genetics ; Bordetella/*enzymology/*genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/*genetics ; Endonucleases/*genetics/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {BACKGROUND: Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated genes (cas) are widely distributed among bacteria. These systems provide adaptive immunity against mobile genetic elements specified by the spacer sequences stored within the CRISPR.<br><br>METHODS: The CRISPR-Cas system has been identified using Basic Local Alignment Search Tool (BLAST) against other sequenced and annotated genomes and confirmed via CRISPRfinder program. Using Polymerase Chain Reactions (PCR) and Sanger DNA sequencing, we discovered CRISPRs in additional bacterial isolates of the same species of Bordetella. Transcriptional activity and processing of the CRISPR have been assessed via RT-PCR.<br><br>RESULTS: Here we describe a novel Type II-C CRISPR and its associated genes-cas1, cas2, and cas9-in several isolates of a newly discovered Bordetella species. The CRISPR-cas locus, which is absent in all other Bordetella species, has a significantly lower GC-content than the genome-wide average, suggesting acquisition of this locus via horizontal gene transfer from a currently unknown source. The CRISPR array is transcribed and processed into mature CRISPR RNAs (crRNA), some of which have homology to prophages found in closely related species B. hinzii.<br><br>CONCLUSIONS: Expression of the CRISPR-Cas system and processing of crRNAs with perfect homology to prophages present in closely related species, but absent in that containing this CRISPR-Cas system, suggest it provides protection against phage predation. The 3,117-bp cas9 endonuclease gene from this novel CRISPR-Cas system is 990&#xa0;bp smaller than that of Streptococcus pyogenes, the 4,017-bp allele currently used for genome editing, and which may make it a useful tool in various CRISPR-Cas technologies.}, }
@article {pmid26502901, year = {2015}, author = {Melnyk, RA and Coates, JD}, title = {The Perchlorate Reduction Genomic Island: Mechanisms and Pathways of Evolution by Horizontal Gene Transfer.}, journal = {BMC genomics}, volume = {16}, number = {}, pages = {862}, pmid = {26502901}, issn = {1471-2164}, support = {S10 RR027303/RR/NCRR NIH HHS/United States ; S10 RR029668/RR/NCRR NIH HHS/United States ; S10RR027303/RR/NCRR NIH HHS/United States ; S10RR029668/RR/NCRR NIH HHS/United States ; }, mesh = {*Biological Evolution ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial/*genetics ; Genomic Islands/*genetics ; Perchlorates/*metabolism ; }, abstract = {BACKGROUND: Perchlorate is a widely distributed anion that is toxic to humans, but serves as a valuable electron acceptor for several lineages of bacteria. The ability to utilize perchlorate is conferred by a horizontally transferred piece of DNA called the perchlorate reduction genomic island (PRI).<br><br>METHODS: We compared genomes of perchlorate reducers using phylogenomics, SNP mapping, and differences in genomic architecture to interrogate the evolutionary history of perchlorate respiration.<br><br>RESULTS: Here we report on the PRI of 13 genomes of perchlorate-reducing bacteria from four different classes of Phylum Proteobacteria (the Alpha-, Beta-, Gamma- and Epsilonproteobacteria). Among the different phylogenetic classes, the island varies considerably in genetic content as well as in its putative mechanism and location of integration. However, the islands of the densely sampled genera Azospira and Magnetospirillum have striking nucleotide identity despite divergent genomes, implying horizontal transfer and positive selection within narrow phylogenetic taxa. We also assess the phylogenetic origin of accessory genes in the various incarnations of the island, which can be traced to chromosomal paralogs from phylogenetically similar organisms.<br><br>CONCLUSION: These observations suggest a complex phylogenetic history where the island is rarely transferred at the class level but undergoes frequent and continuous transfer within narrow phylogenetic groups. This restricted transfer is seen directly by the independent integration of near-identical islands within a genus and indirectly due to the acquisition of lineage-specific accessory genes. The genomic reversibility of perchlorate reduction may present a unique equilibrium for a metabolism that confers a competitive advantage only in the presence of an electron acceptor, which although widely distributed, is generally present at low concentrations in nature.}, }
@article {pmid26502735, year = {2016}, author = {Kim, JS and Cho, DH and Park, M and Chung, WJ and Shin, D and Ko, KS and Kweon, DH}, title = {CRISPR/Cas9-Mediated Re-Sensitization of Antibiotic-Resistant Escherichia coli Harboring Extended-Spectrum β-Lactamases.}, journal = {Journal of microbiology and biotechnology}, volume = {26}, number = {2}, pages = {394-401}, doi = {10.4014/jmb.1508.08080}, pmid = {26502735}, issn = {1738-8872}, mesh = {Anti-Bacterial Agents/pharmacology ; CRISPR-Cas Systems/*genetics ; Drug Resistance, Multiple, Bacterial ; Escherichia coli/drug effects/*enzymology/*genetics/growth &amp; development ; Genes, MDR ; Plasmids/genetics ; *beta-Lactam Resistance ; beta-Lactamases/*biosynthesis/genetics ; }, abstract = {Recently, the clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (CRISPR/Cas9) system, a genome editing technology, was shown to be versatile in treating several antibiotic-resistant bacteria. In the present study, we applied the CRISPR/ Cas9 technology to kill extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli. ESBL bacteria are mostly multidrug resistant (MDR), and have plasmid-mediated antibiotic resistance genes that can be easily transferred to other members of the bacterial community by horizontal gene transfer. To restore sensitivity to antibiotics in these bacteria, we searched for a CRISPR/Cas9 target sequence that was conserved among >1,000 ESBL mutants. There was only one target sequence for each TEM- and SHV-type ESBL, with each of these sequences found in ~200 ESBL strains of each type. Furthermore, we showed that these target sequences can be exploited to re-sensitize MDR cells in which resistance is mediated by genes that are not the target of the CRISPR/Cas9 system, but by genes that are present on the same plasmid as target genes. We believe our Re-Sensitization to Antibiotics from Resistance (ReSAFR) technology, which enhances the practical value of the CRISPR/Cas9 system, will be an effective method of treatment against plasmid-carrying MDR bacteria.}, }
@article {pmid26498963, year = {2015}, author = {Pivetal, J and Frénéa-Robin, M and Haddour, N and Vézy, C and Zanini, LF and Ciuta, G and Dempsey, NM and Dumas-Bouchiat, F and Reyne, G and Bégin-Colin, S and Felder-Flesh, D and Ghobril, C and Pourroy, G and Simonet, P}, title = {Development and applications of a DNA labeling method with magnetic nanoparticles to study the role of horizontal gene transfer events between bacteria in soil pollutant bioremediation processes.}, journal = {Environmental science and pollution research international}, volume = {22}, number = {24}, pages = {20322-20327}, pmid = {26498963}, issn = {1614-7499}, mesh = {Bacteria/*drug effects/genetics/growth &amp; development ; Biodegradation, Environmental ; DNA/chemistry/*genetics ; Equipment Design ; Escherichia coli/drug effects/genetics/growth &amp; development ; France ; *Gene Transfer, Horizontal ; Magnetite Nanoparticles/*chemistry ; Microfluidics ; Plasmids ; Soil Pollutants/*analysis ; }, abstract = {Horizontal gene transfers are critical mechanisms of bacterial evolution and adaptation that are involved to a significant level in the degradation of toxic molecules such as xenobiotic pesticides. However, understanding how these mechanisms are regulated in situ and how they could be used by man to increase the degradation potential of soil microbes is compromised by conceptual and technical limitations. This includes the physical and chemical complexity and heterogeneity in such environments leading to an extreme bacterial taxonomical diversity and a strong redundancy of genes and functions. In addition, more than 99 % of soil bacteria fail to develop colonies in vitro, and even new DNA-based investigation methods (metagenomics) are not specific and sensitive enough to consider lysis recalcitrant bacteria and those belonging to the rare biosphere. The objective of the ANR funded project “Emergent” was to develop a new culture independent approach to monitor gene transfer among soil bacteria by labeling plasmid DNA with magnetic nanoparticles in order to specifically capture and isolate recombinant cells using magnetic microfluidic devices. We showed the feasibility of the approach by using electrotransformation to transform a suspension of Escherichia coli cells with biotin-functionalized plasmid DNA molecules linked to streptavidin-coated superparamagnetic nanoparticles. Our results have demonstrated that magnetically labeled cells could be specifically retained on micromagnets integrated in a microfluidic channel and that an efficient selective separation can be achieved with the microfluidic device. Altogether, the project offers a promising alternative to traditional culture-based approaches for deciphering the extent of horizontal gene transfer events mediated by electro or natural genetic transformation mechanisms in complex environments such as soil.}, }
@article {pmid26498126, year = {2015}, author = {Niu, XN and Wei, ZQ and Zou, HF and Xie, GG and Wu, F and Li, KJ and Jiang, W and Tang, JL and He, YQ}, title = {Complete sequence and detailed analysis of the first indigenous plasmid from Xanthomonas oryzae pv. oryzicola.}, journal = {BMC microbiology}, volume = {15}, number = {}, pages = {233}, pmid = {26498126}, issn = {1471-2180}, mesh = {China ; Computational Biology ; Conjugation, Genetic ; DNA Replication ; Drug Resistance, Bacterial ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Metals, Heavy/toxicity ; Molecular Sequence Annotation ; Molecular Sequence Data ; Open Reading Frames ; Oryza/microbiology ; Phylogeny ; Plant Diseases/microbiology ; Plasmids/*isolation &amp; purification ; Sequence Analysis, DNA ; Sequence Homology ; Xanthomonas/*genetics/isolation &amp; purification ; }, abstract = {BACKGROUND: Bacterial plasmids have a major impact on metabolic function and adaptation of their hosts. An indigenous plasmid was identified in a Chinese isolate (GX01) of the invasive phytopathogen Xanthomonas oryzae pv. oryzicola (Xoc), the causal agent of rice bacterial leaf streak (BLS). To elucidate the biological functions of the plasmid, we have sequenced and comprehensively annotated the plasmid.<br><br>METHODS: The plasmid DNA was extracted from Xoc strain GX01 by alkaline lysis and digested with restriction enzymes. The cloned and subcloned DNA fragments in pUC19 were sequenced by Sanger sequencing. Sequences were assembled by using Sequencher software. Gaps were closed by primer walking and sequencing, and multi-PCRs were conducted through the whole plasmid sequence for verification. BLAST, phylogenetic analysis and dinucleotide calculation were performed for gene annotation and DNA structure analysis. Transformation, transconjugation and stress tolerance tests were carried out for plasmid function assays.<br><br>RESULTS: The indigenous plasmid from Xoc strain GX01, designated pXOCgx01, is 53,206-bp long and has been annotated to possess 64 open reading frames (ORFs), including genes encoding type IV secretion system, heavy metal exporter, plasmid stability factors, and DNA mobile factors, i.e., the Tn3-like transposon. Bioinformatics analysis showed that pXOCgx01 has a mosaic structure containing different genome contexts with distinct genomic heterogeneities. Phylogenetic analysis indicated that the closest relative of pXOCgx01 is pXAC64 from Xanthomonas axonopodis pv. citri str. 306. It was estimated that there are four copies of pXOCgx01 per cell of Xoc GX01 by PCR assay and the calculation of whole genome shotgun sequencing data. We demonstrate that pXOCgx01 is a self-transmissible plasmid and can replicate in some Xanthomonas spp. strains, but not in Escherichia coli DH5&#x3b1;. It could significantly enhance the tolerance of Xanthomonas oryzae pv. oryzae PXO99A to the stresses of heavy metal ions. The plasmid survey indicated that nine out of 257 Xoc Chinese isolates contain plasmids.<br><br>CONCLUSIONS: pXOCgx01 is the first report of indigenous plasmid from Xanthomonas oryzae pv. oryzicola, and the first completely sequenced plasmid from Xanthomonas oryzae species. It is a self-transmissible plasmid and has a mosaic structure, containing genes for macromolecule secretion, heavy metal exportation, and DNA mobile factors, especially the Tn3-like transposon which may provide transposition function for mobile insertion cassette and play a major role in the spread of pathogenicity determinants. The results will be helpful to elucidate the biological significance of this cryptic plasmid and the adaptive evolution of Xoc.}, }
@article {pmid26497940, year = {2015}, author = {Maier, B and Wong, GCL}, title = {How Bacteria Use Type IV Pili Machinery on Surfaces.}, journal = {Trends in microbiology}, volume = {23}, number = {12}, pages = {775-788}, doi = {10.1016/j.tim.2015.09.002}, pmid = {26497940}, issn = {1878-4380}, mesh = {Bacteria/*cytology ; Bacterial Adhesion/physiology ; Bacterial Physiological Phenomena ; Biomechanical Phenomena ; Elasticity ; Evolution, Molecular ; Fimbriae Proteins/*chemistry/metabolism/*physiology/ultrastructure ; Fimbriae, Bacterial/*chemistry/metabolism/*physiology/ultrastructure ; Locomotion/physiology ; Models, Molecular ; Mutation ; Pseudomonas aeruginosa/metabolism/physiology ; }, abstract = {The bacterial type IV pilus (T4P) is a versatile molecular machine with a broad range of functions. Recent advances revealed that the molecular components and the biophysical properties of the machine are well conserved among phylogenetically distant bacterial species. However, its functions are diverse, and include adhesion, motility, and horizontal gene transfer. This review focusses on the role of T4P in surface motility and bacterial interactions. Different species have evolved distinct mechanisms for intracellular coordination of multiple pili and of pili with other motility machines, ranging from physical coordination to biochemical clocks. Coordinated behavior between multiple bacteria on a surface is achieved by active manipulation of surfaces and modulation of pilus-pilus interactions. An emerging picture is that the T4P actively senses and responds to environmental conditions.}, }
@article {pmid26497507, year = {2015}, author = {Werner, FM and Covenas, R}, title = {Methicillin-Resistant Staphylococcus aureus: Treatment with Cultures of Non Drug-Resistant Staphylococcus epidermidis.}, journal = {Recent patents on anti-infective drug discovery}, volume = {10}, number = {2}, pages = {124-127}, doi = {10.2174/1574891x10666150827103448}, pmid = {26497507}, issn = {2212-4071}, mesh = {*Coinfection ; *Gene Transfer, Horizontal ; Humans ; Methicillin-Resistant Staphylococcus aureus/*genetics ; Staphylococcal Infections/*microbiology/*therapy ; Staphylococcus epidermidis/*genetics ; }, abstract = {The colonization and infection with methicillin-resistant Staphylococcus aureus is a major health problem in hospitals and long-term care facilities. Although bacteriaemias with MRSA (methicillin-resistant Staphylococcus aureus) can be treated with vancomycin and other reserve antibiotics, 20% of patients cannot be successfully cured. Inpatients colonized with MRSA are isolated in hospitals according to the guidelines of the Robert-Koch-Institute, although in long-term care facilities these patients are not urgently isolated. Active decolonization measures are taken to eradicate colonization with MRSA. In order to reduce MRSA colonization, it could be possible to administer cultures of Staphylococcus epidermidis which have no antibiotic resistance, so that physiological genes could be conferred from Staphylococcus epidermidis to MRSA bacteria.}, }
@article {pmid26494050, year = {2015}, author = {Goldberg, GW and Marraffini, LA}, title = {Resistance and tolerance to foreign elements by prokaryotic immune systems - curating the genome.}, journal = {Nature reviews. Immunology}, volume = {15}, number = {11}, pages = {717-724}, pmid = {26494050}, issn = {1474-1741}, support = {DP2 AI104556/AI/NIAID NIH HHS/United States ; 1DP2AI104556&#x2011;01/AI/NIAID NIH HHS/United States ; }, mesh = {*Adaptive Immunity ; CRISPR-Cas Systems/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome ; Humans ; Immune System/*immunology ; *Immune Tolerance ; }, abstract = {To engage in adaptive symbioses or genetic exchange, organisms must interact with foreign, non-self elements despite the risks of predation and parasitism. By surveying the interface between self and non-self, immune systems can help ensure the benevolence of these interactions without isolating their hosts altogether. In this Essay, we examine prokaryotic restriction-modification and CRISPR-Cas (clustered, regularly interspaced palindromic repeat-CRISPR-associated proteins) activities and discuss their analogy to mammalian immune pathways. We further explain how their capacities for resistance and tolerance are optimized to reduce parasitism and immunopathology during encounters with non-self.}, }
@article {pmid26492264, year = {2015}, author = {Caprari, S and Metzler, S and Lengauer, T and Kalinina, OV}, title = {Sequence and Structure Analysis of Distantly-Related Viruses Reveals Extensive Gene Transfer between Viruses and Hosts and among Viruses.}, journal = {Viruses}, volume = {7}, number = {10}, pages = {5388-5409}, pmid = {26492264}, issn = {1999-4915}, mesh = {Animals ; Computational Biology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Viral ; *Host-Pathogen Interactions ; Humans ; RNA Viruses/*genetics ; *Recombination, Genetic ; Sequence Analysis, DNA ; }, abstract = {The origin and evolution of viruses is a subject of ongoing debate. In this study, we provide a full account of the evolutionary relationships between proteins of significant sequence and structural similarity found in viruses that belong to different classes according to the Baltimore classification. We show that such proteins can be found in viruses from all Baltimore classes. For protein families that include these proteins, we observe two patterns of the taxonomic spread. In the first pattern, they can be found in a large number of viruses from all implicated Baltimore classes. In the other pattern, the instances of the corresponding protein in species from each Baltimore class are restricted to a few compact clades. Proteins with the first pattern of distribution are products of so-called viral hallmark genes reported previously. Additionally, this pattern is displayed by the envelope glycoproteins from Flaviviridae and Bunyaviridae and helicases of superfamilies 1 and 2 that have homologs in cellular organisms. The second pattern can often be explained by horizontal gene transfer from the host or between viruses, an example being Orthomyxoviridae and Coronaviridae hemagglutinin esterases. Another facet of horizontal gene transfer comprises multiple independent introduction events of genes from cellular organisms into otherwise unrelated viruses.}, }
@article {pmid26490946, year = {2015}, author = {Ulrich, A and Becker, R and Ulrich, K and Ewald, D}, title = {Conjugative transfer of a derivative of the IncP-1α plasmid RP4 and establishment of transconjugants in the indigenous bacterial community of poplar plants.}, journal = {FEMS microbiology letters}, volume = {362}, number = {23}, pages = {fnv201}, pmid = {26490946}, issn = {1574-6968}, mesh = {*Conjugation, Genetic ; DNA, Bacterial ; Gene Transfer, Horizontal ; Microbial Consortia/genetics ; Phylogeny ; Plasmids ; Populus/*microbiology ; Proteobacteria/classification/*genetics/isolation &amp; purification ; Real-Time Polymerase Chain Reaction ; }, abstract = {The persistence of traits introduced into the indigenous bacterial community of poplar plants was investigated using bioluminescence mediated by the luc gene. Three endophytic bacterial strains provided with the IncP-1α plasmid RP4-Tn-luc were used to inoculate poplar cuttings at different phenological stages. Screening of isolates by bioluminescence and real-time PCR detection of the luc gene revealed stable persistence for at least 10 weeks. Although the inoculated strains became established with a high population density after inoculation at leaf development (April) and senescence (October), the strains were suppressed by the indigenous bacteria at stem elongation (June). Transconjugants could be detected only at this phenological stage. Indigenous bacteria harbouring RP4-Tn-luc became established with densities ranging from 2 × 10(5) to 9 × 10(6) CFU g(-1) fresh weight 3 and 10 weeks after inoculation. The increased colonization of the cuttings by indigenous bacteria at stem elongation seemed to strongly compete with the introduced strains. Otherwise, the phenological stage of the plants as well as the density of the indigenous recipients could serve as the driver for a more frequent conjugative plasmid transfer. A phylogenetic assignment of transconjugants indicated the transfer of RP4-Tn-luc into six genera of Proteobacteria, mainly Sphingomonas, Stenotrophomonas and Xanthomonas.}, }
@article {pmid26490380, year = {2016}, author = {Baddela, VS and Nayan, V and Rani, P and Onteru, SK and Singh, D}, title = {Physicochemical Biomolecular Insights into Buffalo Milk-Derived Nanovesicles.}, journal = {Applied biochemistry and biotechnology}, volume = {178}, number = {3}, pages = {544-557}, doi = {10.1007/s12010-015-1893-7}, pmid = {26490380}, issn = {1559-0291}, mesh = {Animals ; Buffaloes ; Exosomes ; MicroRNAs/chemistry ; Microscopy, Electron, Scanning ; Milk/*chemistry ; *Nanoparticles ; Spectroscopy, Fourier Transform Infrared ; }, abstract = {Milk is a natural nutraceutical produced by mammals. The nanovesicles of milk play a role in horizontal gene transfer and confer health-benefits to milk consumers. These nanovesicles contain miRNA, mRNA, and proteins which mediate the intercellular communication. In this work, we isolated and characterized the buffalo milk-derived nanovesicles by dynamic light scattering (DLS), nanoparticle tracking analysis (NTA), scanning electron microscopy (SEM), Western probing, and Fourier transform infrared (FTIR) spectroscopy. The DLS data suggested a bimodal size distribution with one mode near 50 nm and the other around 200 nm for the nanovesicles. The NTA and SEM data also supported the size of nanovesicles within a range of 50-200 nm. The FTIR measurements of nanovesicles identified some prominent absorption bands attributable to the proteins (1300-1700 cm(-1), amide A and amide B bands), lipids (2800-3100 cm(-1)), polysaccharides, and nucleic acids (900-1200 cm(-1)). The comparative expression profiles of immune miRNA signatures (miR-15b, miR-21, miR-27b, miR-125b, miR-155, and miR-500) in nanovesicles isolated from milk, serum, and urine revealed that these miRNAs are present abundantly (P < 0.05) in milk-derived nanovesicles. Milk miRNAs (miR-21 and 500) that were also found stable under different household storage conditions indicated that these could be biologically available to milk consumers. Overall, nanovesicles are a new class of bioactive compounds from buffalo milk with high proportion of stable immune miRNAs compared to urine and plasma of same animals.}, }
@article {pmid26489830, year = {2015}, author = {Borland, S and Oudart, A and Prigent-Combaret, C and Brochier-Armanet, C and Wisniewski-Dyé, F}, title = {Genome-wide survey of two-component signal transduction systems in the plant growth-promoting bacterium Azospirillum.}, journal = {BMC genomics}, volume = {16}, number = {}, pages = {833}, pmid = {26489830}, issn = {1471-2164}, mesh = {Azospirillum/*genetics/*metabolism ; Biological Evolution ; Databases, Genetic ; Genes, Bacterial ; *Genome, Bacterial ; *Genome-Wide Association Study ; *Genomics/methods ; Phylogeny ; *Signal Transduction ; }, abstract = {BACKGROUND: Two-component systems (TCS) play critical roles in sensing and responding to environmental cues. Azospirillum is a plant growth-promoting rhizobacterium living in the rhizosphere of many important crops. Despite numerous studies about its plant beneficial properties, little is known about how the bacterium senses and responds to its rhizospheric environment. The availability of complete genome sequenced from four Azospirillum strains (A. brasilense Sp245 and CBG 497, A. lipoferum 4B and Azospirillum sp. B510) offers the opportunity to conduct a comprehensive comparative analysis of the TCS gene family.<br><br>RESULTS: Azospirillum genomes harbour a very large number of genes encoding TCS, and are especially enriched in hybrid histidine kinases (HyHK) genes compared to other plant-associated bacteria of similar genome sizes. We gained further insight into HyHK structure and architecture, revealing an intriguing complexity of these systems. An unusual proportion of TCS genes were orphaned or in complex clusters, and a high proportion of predicted soluble HKs compared to other plant-associated bacteria are reported. Phylogenetic analyses of the transmitter and receiver domains of A. lipoferum 4B HyHK indicate that expansion of this family mainly arose through horizontal gene transfer but also through gene duplications all along the diversification of the Azospirillum genus. By performing a genome-wide comparison of TCS, we unraveled important 'genus-defining' and 'plant-specifying' TCS.<br><br>CONCLUSIONS: This study shed light on Azospirillum TCS which may confer important regulatory flexibility. Collectively, these findings highlight that Azospirillum genomes have broad potential for adaptation to fluctuating environments.}, }
@article {pmid26486592, year = {2015}, author = {Fan, J and Ning, K and Zeng, X and Luo, Y and Wang, D and Hu, J and Li, J and Xu, H and Huang, J and Wan, M and Wang, W and Zhang, D and Shen, G and Run, C and Liao, J and Fang, L and Huang, S and Jing, X and Su, X and Wang, A and Bai, L and Hu, Z and Xu, J and Li, Y}, title = {Genomic Foundation of Starch-to-Lipid Switch in Oleaginous Chlorella spp.}, journal = {Plant physiology}, volume = {169}, number = {4}, pages = {2444-2461}, pmid = {26486592}, issn = {1532-2548}, mesh = {Base Sequence ; Carbohydrate Metabolism ; Carbon/metabolism ; Chlorella/genetics/*metabolism ; Citric Acid Cycle ; Electron Transport ; Fatty Acids/metabolism ; *Genomics ; Heterotrophic Processes ; *Lipid Metabolism ; Molecular Sequence Data ; Oxidative Phosphorylation ; Photosynthesis ; Sequence Analysis, DNA ; Starch/*metabolism ; }, abstract = {The ability to rapidly switch the intracellular energy storage form from starch to lipids is an advantageous trait for microalgae feedstock. To probe this mechanism, we sequenced the 56.8-Mbp genome of Chlorella pyrenoidosa FACHB-9, an industrial production strain for protein, starch, and lipids. The genome exhibits positive selection and gene family expansion in lipid and carbohydrate metabolism and genes related to cell cycle and stress response. Moreover, 10 lipid metabolism genes might be originated from bacteria via horizontal gene transfer. Transcriptomic dynamics tracked via messenger RNA sequencing over six time points during metabolic switch from starch-rich heterotrophy to lipid-rich photoautotrophy revealed that under heterotrophy, genes most strongly expressed were from the tricarboxylic acid cycle, respiratory chain, oxidative phosphorylation, gluconeogenesis, glyoxylate cycle, and amino acid metabolisms, whereas those most down-regulated were from fatty acid and oxidative pentose phosphate metabolism. The shift from heterotrophy into photoautotrophy highlights up-regulation of genes from carbon fixation, photosynthesis, fatty acid biosynthesis, the oxidative pentose phosphate pathway, and starch catabolism, which resulted in a marked redirection of metabolism, where the primary carbon source of glycine is no longer supplied to cell building blocks by the tricarboxylic acid cycle and gluconeogenesis, whereas carbon skeletons from photosynthesis and starch degradation may be directly channeled into fatty acid and protein biosynthesis. By establishing the first genetic transformation in industrial oleaginous C. pyrenoidosa, we further showed that overexpression of an NAD(H) kinase from Arabidopsis (Arabidopsis thaliana) increased cellular lipid content by 110.4%, yet without reducing growth rate. These findings provide a foundation for exploiting the metabolic switch in microalgae for improved photosynthetic production of food and fuels.}, }
@article {pmid26486372, year = {2015}, author = {Xiong, J and Wang, G and Cheng, J and Tian, M and Pan, X and Warren, A and Jiang, C and Yuan, D and Miao, W}, title = {Genome of the facultative scuticociliatosis pathogen Pseudocohnilembus persalinus provides insight into its virulence through horizontal gene transfer.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {15470}, pmid = {26486372}, issn = {2045-2322}, mesh = {Animals ; Base Sequence ; Cell Adhesion/genetics ; Flounder/parasitology ; *Gene Transfer, Horizontal ; *Genome ; Molecular Sequence Annotation ; Oligohymenophorea/*genetics/pathogenicity ; Phylogeny ; *Sequence Analysis, DNA ; }, abstract = {Certain ciliates of the subclass Scuticociliatia (scuticociliates) are facultative parasites of fishes in which they cause a suite of diseases collectively termed scuticociliatosis. Hitherto, comparatively little was known about genetics and genomics of scuticociliates or the mechanism of scuticociliatosis. In this study, a laboratory culture of the facultatively pathogenic scuticociliate Pseudocohnilembus persalinus was established and its genome sequenced, giving the first genome of a marine ciliate. Genome-wide horizontal gene transfer (HGT) analysis showed P. persalinus has acquired many unique prokaryote-derived genes that potentially contribute to the virulence of this organism, including cell adhesion, hemolysis and heme utilization genes. These findings give new insights into our understanding of the pathology of scuticociliates.}, }
@article {pmid26485437, year = {2015}, author = {Haverkate, MR and Dautzenberg, MJ and Ossewaarde, TJ and van der Zee, A and den Hollander, JG and Troelstra, A and Bonten, MJ and Bootsma, MC}, title = {Within-Host and Population Transmission of blaOXA-48 in K. pneumoniae and E. coli.}, journal = {PloS one}, volume = {10}, number = {10}, pages = {e0140960}, pmid = {26485437}, issn = {1932-6203}, mesh = {Drug Resistance, Bacterial/*genetics ; Escherichia coli/*genetics/metabolism ; Escherichia coli Infections/microbiology/transmission ; Escherichia coli Proteins/*genetics/metabolism ; *Gene Transfer, Horizontal ; Humans ; Klebsiella Infections/microbiology/transmission ; Klebsiella pneumoniae/*genetics/metabolism ; beta-Lactamases/*genetics/metabolism ; }, abstract = {During a large hospital outbreak of OXA-48 producing bacteria, most K. pneumoniaeOXA-48 isolates were phenotypically resistant to meropenem or imipenem, whereas most E. coliOXA-48 isolates were phenotypically susceptible to these antibiotics. In the absence of molecular gene-detection E. coliOXA-48 could remain undetected, facilitating cross-transmission and horizontal gene transfer of blaOXA-48. Based on 868 longitudinal molecular microbiological screening results from patients carrying K. pneumoniaeOXA-48 (n = 24), E. coliOXA-48 (n = 17), or both (n = 40) and mathematical modelling we determined mean durations of colonisation (278 and 225 days for K. pneumoniaeOXA-48 and E. coliOXA-48, respectively), and horizontal gene transfer rates (0.0091/day from K. pneumoniae to E. coli and 0.0015/day vice versa). Based on these findings the maximum effect of horizontal gene transfer of blaOXA-48 originating from E. coliOXA-48 on the basic reproduction number (R0) is 1.9%, and it is, therefore, unlikely that phenotypically susceptible E. coliOXA-48 will contribute significantly to the spread of blaOXA-48.}, }
@article {pmid26484862, year = {2015}, author = {Bershtein, S and Serohijos, AW and Bhattacharyya, S and Manhart, M and Choi, JM and Mu, W and Zhou, J and Shakhnovich, EI}, title = {Protein Homeostasis Imposes a Barrier on Functional Integration of Horizontally Transferred Genes in Bacteria.}, journal = {PLoS genetics}, volume = {11}, number = {10}, pages = {e1005612}, pmid = {26484862}, issn = {1553-7404}, support = {R01 GM068670/GM/NIGMS NIH HHS/United States ; R01GM068670/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence/genetics ; Escherichia coli/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; High-Throughput Nucleotide Sequencing ; Homeostasis/genetics ; Mutation ; *Phylogeny ; Species Specificity ; Tetrahydrofolate Dehydrogenase/*genetics ; }, abstract = {Horizontal gene transfer (HGT) plays a central role in bacterial evolution, yet the molecular and cellular constraints on functional integration of the foreign genes are poorly understood. Here we performed inter-species replacement of the chromosomal folA gene, encoding an essential metabolic enzyme dihydrofolate reductase (DHFR), with orthologs from 35 other mesophilic bacteria. The orthologous inter-species replacements caused a marked drop (in the range 10-90%) in bacterial growth rate despite the fact that most orthologous DHFRs are as stable as E.coli DHFR at 37°C and are more catalytically active than E. coli DHFR. Although phylogenetic distance between E. coli and orthologous DHFRs as well as their individual molecular properties correlate poorly with growth rates, the product of the intracellular DHFR abundance and catalytic activity (kcat/KM), correlates strongly with growth rates, indicating that the drop in DHFR abundance constitutes the major fitness barrier to HGT. Serial propagation of the orthologous strains for ~600 generations dramatically improved growth rates by largely alleviating the fitness barriers. Whole genome sequencing and global proteome quantification revealed that the evolved strains with the largest fitness improvements have accumulated mutations that inactivated the ATP-dependent Lon protease, causing an increase in the intracellular DHFR abundance. In one case DHFR abundance increased further due to mutations accumulated in folA promoter, but only after the lon inactivating mutations were fixed in the population. Thus, by apparently distinguishing between self and non-self proteins, protein homeostasis imposes an immediate and global barrier to the functional integration of foreign genes by decreasing the intracellular abundance of their products. Once this barrier is alleviated, more fine-tuned evolution occurs to adjust the function/expression of the transferred proteins to the constraints imposed by the intracellular environment of the host organism.}, }
@article {pmid26484663, year = {2015}, author = {Spring-Pearson, SM and Stone, JK and Doyle, A and Allender, CJ and Okinaka, RT and Mayo, M and Broomall, SM and Hill, JM and Karavis, MA and Hubbard, KS and Insalaco, JM and McNew, LA and Rosenzweig, CN and Gibbons, HS and Currie, BJ and Wagner, DM and Keim, P and Tuanyok, A}, title = {Pangenome Analysis of Burkholderia pseudomallei: Genome Evolution Preserves Gene Order despite High Recombination Rates.}, journal = {PloS one}, volume = {10}, number = {10}, pages = {e0140274}, pmid = {26484663}, issn = {1932-6203}, mesh = {Algorithms ; Burkholderia pseudomallei/classification/*genetics/isolation &amp; purification ; Evolution, Molecular ; *Gene Order ; Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Genetic Variation ; Genome, Bacterial/*genetics ; Models, Genetic ; Recombination, Genetic ; Species Specificity ; }, abstract = {The pangenomic diversity in Burkholderia pseudomallei is high, with approximately 5.8% of the genome consisting of genomic islands. Genomic islands are known hotspots for recombination driven primarily by site-specific recombination associated with tRNAs. However, recombination rates in other portions of the genome are also high, a feature we expected to disrupt gene order. We analyzed the pangenome of 37 isolates of B. pseudomallei and demonstrate that the pangenome is 'open', with approximately 136 new genes identified with each new genome sequenced, and that the global core genome consists of 4568±16 homologs. Genes associated with metabolism were statistically overrepresented in the core genome, and genes associated with mobile elements, disease, and motility were primarily associated with accessory portions of the pangenome. The frequency distribution of genes present in between 1 and 37 of the genomes analyzed matches well with a model of genome evolution in which 96% of the genome has very low recombination rates but 4% of the genome recombines readily. Using homologous genes among pairs of genomes, we found that gene order was highly conserved among strains, despite the high recombination rates previously observed. High rates of gene transfer and recombination are incompatible with retaining gene order unless these processes are either highly localized to specific sites within the genome, or are characterized by symmetrical gene gain and loss. Our results demonstrate that both processes occur: localized recombination introduces many new genes at relatively few sites, and recombination throughout the genome generates the novel multi-locus sequence types previously observed while preserving gene order.}, }
@article {pmid26484384, year = {2016}, author = {Kocsis, E and Gužvinec, M and Butić, I and Krešić, S and Crnek, S&#x160; and Tambić, A and Cornaglia, G and Mazzariol, A}, title = {blaNDM-1 Carriage on IncR Plasmid in Enterobacteriaceae Strains.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {22}, number = {2}, pages = {123-128}, doi = {10.1089/mdr.2015.0083}, pmid = {26484384}, issn = {1931-8448}, mesh = {Anti-Bacterial Agents/*pharmacology ; Carbapenems/pharmacology ; Citrobacter koseri/drug effects/enzymology/*genetics/isolation &amp; purification ; Colistin/pharmacology ; Conjugation, Genetic ; Croatia ; DNA, Bacterial/*genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Enterobacteriaceae Infections/drug therapy/microbiology ; Gene Expression ; Gene Transfer, Horizontal ; Humans ; Isoenzymes/genetics/metabolism ; Klebsiella pneumoniae/drug effects/enzymology/*genetics/isolation &amp; purification ; Microbial Sensitivity Tests ; Minocycline/analogs &amp; derivatives/pharmacology ; Plasmids/chemistry/*metabolism ; Sequence Analysis, DNA ; Tigecycline ; beta-Lactamases/*genetics/metabolism ; }, abstract = {Four NDM-1-producing Enterobacteriaceae strains (three Klebsiella pneumoniae and one Citrobacter koseri) were isolated between 2009 and 2011 through a nationwide surveillance for carbapenem-resistant Enterobacteriaceae in Croatia to study the molecular genetic background of blaNDM and the responsible plasmid types. Phenotypically, the clinical strains proved to be multidrug resistant. All strains remained susceptible to tigecycline and colistin. The clinical strains harbored variable antibiotic resistance determinants, notably, blaNDM-1, blaTEM-1, blaSHV-1, blaSHV-12, blaOXA-1, blaOXA-9, blaCTX-M-15, blaCMY-4, qnrB1, and aac(6')Ib-cr in different combinations. Two K. pneumoniae belonged to sequence type ST15 and one strain to ST16. As for the plasmid types, C. koseri and one of the ST15 K. pneumoniae carried IncR, and the second ST15 K. pneumoniae carried IncR and colE. The K. pneumoniae ST16 strain hosted A/C and colE plasmids. The blaNDM-1 gene was detected on conjugative high-molecular-weight plasmids, namely, A/C and IncR types. It is noteworthy that this is the first description of K. pneumoniae ST16 expressing NDM-1 in Europe. Remarkably, our study underscores the importance of the IncR plasmid as a reservoir of multidrug resistance. To the best of our knowledge, the IncR plasmid carrying blaNDM-1 in C. koseri is reported for the first time.}, }
@article {pmid26483054, year = {2015}, author = {Fischer, MJ and Rustenhloz, C and Leh-Louis, V and Perrière, G}, title = {Molecular and functional evolution of the fungal diterpene synthase genes.}, journal = {BMC microbiology}, volume = {15}, number = {}, pages = {221}, pmid = {26483054}, issn = {1471-2180}, mesh = {Ascomycota/*genetics/*metabolism ; Basidiomycota/*genetics/*metabolism ; Diterpenes/*metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Fungal ; Metabolic Networks and Pathways/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {BACKGROUND: Terpenes represent one of the largest and most diversified families of natural compounds and are used in numerous industrial applications. Terpene synthase (TPS) genes originated in bacteria as diterpene synthase (di-TPS) genes. They are also found in plant and fungal genomes. The recent availability of a large number of fungal genomes represents an opportunity to investigate how genes involved in diterpene synthesis were acquired by fungi, and to assess the consequences of this process on the fungal metabolism.<br><br>RESULTS: In order to investigate the origin of fungal di-TPS, we implemented a search for potential fungal di-TPS genes and identified their presence in several unrelated Ascomycota and Basidiomycota species. The fungal di-TPS phylogenetic tree is function-related but is not associated with the phylogeny based on housekeeping genes. The lack of agreement between fungal and di-TPS-based phylogenies suggests the presence of Horizontal Gene Transfer (HGTs) events. Further evidence for HGT was provided by conservation of synteny of di-TPS and neighbouring genes in distantly related fungi.<br><br>CONCLUSIONS: The results obtained here suggest that fungal di-TPSs originated from an ancient HGT event of a single di-TPS gene from a plant to a fungus in Ascomycota. In fungi, these di-TPSs allowed for the formation of clusters consisting in di-TPS, GGPPS and P450 genes to create functional clusters that were transferred between fungal species, producing diterpenes acting as hormones or toxins, thus affecting fungal development and pathogenicity.}, }
@article {pmid26481237, year = {2016}, author = {Liu, GX and Ma, HM and Xie, HY and Xuan, N and Picimbon, JF}, title = {Sequence variation of Bemisia tabaci Chemosensory Protein 2 in cryptic species B and Q: New DNA markers for whitefly recognition.}, journal = {Gene}, volume = {576}, number = {1 Pt 2}, pages = {284-291}, doi = {10.1016/j.gene.2015.10.036}, pmid = {26481237}, issn = {1879-0038}, mesh = {Animals ; Base Sequence ; China ; Deoxyribonucleases, Type II Site-Specific/genetics/metabolism ; Electron Transport Complex IV/genetics ; Gene Transfer, Horizontal ; *Genetic Markers ; Genetic Variation ; Genetics, Population ; Hemiptera/*genetics ; Insect Proteins/*genetics ; Introns ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Bemisia tabaci Gennadius biotypes B and Q are two of the most important worldwide agricultural insect pests. Genomic sequences of Type-2 B. tabaci chemosensory protein (BtabCSP2) were cloned and sequenced in B and Q biotypes, revealing key biotype-specific variations in the intron sequence. A Q260 sequence was found specifically in Q-BtabCSP2 and Cucumis melo LN692399, suggesting ancestral horizontal transfer of gene between the insect and the plant through bacteria. A cleaved amplified polymorphic sequences (CAPS) method was then developed to differentiate B and Q based on the sequence variation in exon of BtabCSP2 gene. The performances of CSP2-based CAPS for whitefly recognition were assessed using B. tabaci field collections from Shandong Province (P.R. China). Our SacII based CAPS method led to the same result compared to mitochondrial cytochrome oxidase-based CAPS method in the field collections. We therefore propose an explanation for CSP origin and a new rapid simple molecular method based on genomic DNA and chemosensory gene to differentiate accurately the B and Q whiteflies of the Bemisia complex around the world.}, }
@article {pmid26481232, year = {2016}, author = {Abbasian, F and Lockington, R and Megharaj, M and Naidu, R}, title = {A Review on the Genetics of Aliphatic and Aromatic Hydrocarbon Degradation.}, journal = {Applied biochemistry and biotechnology}, volume = {178}, number = {2}, pages = {224-250}, doi = {10.1007/s12010-015-1881-y}, pmid = {26481232}, issn = {1559-0291}, mesh = {Adaptation, Physiological ; Anaerobiosis ; Bacteria/classification/genetics/*metabolism ; Genes, Bacterial ; Hydrocarbons/*metabolism ; Hydrolysis ; Plasmids ; }, abstract = {Because of the high diversity of hydrocarbons, degradation of each class of these compounds is activated by a specific enzyme. However, most of other downstream enzymes necessary for complete degradation of hydrocarbons maybe common between different hydrocarbons. The genes encoding proteins for degradation of hydrocarbons, including the proteins required for the uptake of these molecules, the specific enzyme used for the initial activation of the molecules and other necessary degrading enzymes are usually arranged as an operon. Although the corresponding genes in many phylogenetic groups of microbial species show different levels of diversity in terms of the gene sequence, the organisation of the genes in the genome or on plasmids and the activation mode (inductive or constitutive), some organisms show identical hydrocarbon-degrading genes, probably as a result of horizontal gene transfer between microorganisms.}, }
@article {pmid26480472, year = {2016}, author = {Mahajan, V and Gaymalov, Z and Alakhova, D and Gupta, R and Zucker, IH and Kabanov, AV}, title = {Horizontal gene transfer from macrophages to ischemic muscles upon delivery of naked DNA with Pluronic block copolymers.}, journal = {Biomaterials}, volume = {75}, number = {}, pages = {58-70}, pmid = {26480472}, issn = {1878-5905}, support = {P20 GM103480/GM/NIGMS NIH HHS/United States ; R01 CA116591/CA/NCI NIH HHS/United States ; P20GM103480/GM/NIGMS NIH HHS/United States ; }, mesh = {Adoptive Transfer ; Animals ; Coculture Techniques ; DNA/*metabolism ; Disease Models, Animal ; Female ; Gene Expression Regulation ; *Gene Transfer Techniques ; Green Fluorescent Proteins/metabolism ; Hindlimb/blood supply/pathology ; Inflammation/genetics/pathology ; Ischemia/genetics/*pathology ; Macrophages/*metabolism ; Mice ; Mice, Inbred BALB C ; Muscle, Skeletal/*blood supply/pathology ; Peritonitis/pathology ; Plasmids/metabolism ; Poloxamer/*chemistry ; RAW 264.7 Cells ; Transfection ; Transgenes ; }, abstract = {Intramuscular administration of plasmid DNA (pDNA) with non-ionic Pluronic block copolymers increases gene expression in injected muscles and lymphoid organs. We studied the role of immune cells in muscle transfection upon inflammation. Local inflammation in murine hind limb ischemia model (MHLIM) drastically increased DNA, RNA and expressed protein levels in ischemic muscles injected with pDNA/Pluronic. The systemic inflammation (MHLIM or peritonitis) also increased expression of pDNA/Pluronic in the muscles. When pDNA/Pluronic was injected in ischemic muscles the reporter gene, Green Fluorescent Protein (GFP) co-localized with desmin(+) muscle fibers and CD11b(+) macrophages (MØs), suggesting transfection of MØs along with the muscle cells. P85 enhanced (∼ 4 orders) transfection of MØs with pDNA in vitro. Moreover, adoptively transferred MØs were shown to pass the transgene to inflamed muscle cells in MHLIM. Using a co-culture of myotubes (MTs) and transfected MØs expressing a reporter gene under constitutive (cmv-luciferase) or muscle specific (desmin-luciferase) promoter we demonstrated that P85 enhances horizontal gene transfer from MØ to MTs. Therefore, MØs can play an important role in muscle transfection with pDNA/Pluronic during inflammation, with both inflammation and Pluronic contributing to the increased gene expression. pDNA/Pluronic has potential for therapeutic gene delivery in muscle pathologies that involve inflammation.}, }
@article {pmid26475454, year = {2015}, author = {Durzyńska, J and Goździcka-Józefiak, A}, title = {Viruses and cells intertwined since the dawn of evolution.}, journal = {Virology journal}, volume = {12}, number = {}, pages = {169}, pmid = {26475454}, issn = {1743-422X}, mesh = {*Biological Evolution ; Eukaryotic Cells/*physiology/*virology ; Viruses/genetics/*growth &amp; development ; }, abstract = {Many attempts have been made to define nature of viruses and to uncover their origin. Our aim within this work was to show that there are different perceptions of viruses and many concepts to explain their emergence: the virus-first concept (also called co-evolution), the escape and the reduction theories. Moreover, a relatively new concept of polyphyletic virus origin called "three RNA cells, three DNA viruses" proposed by Forterre is described herein. In this paper, not only is each thesis supported by a body of evidence but also counter-argued in the light of various findings to give more insightful considerations to the readers. As the origin of viruses and that of living cells are most probably interdependent, we decided to reveal ideas concerning nature of cellular last universal common ancestor (LUCA). Furthermore, we discuss monophyletic ancestry of cellular domains and their relationships at the molecular level of membrane lipids and replication strategies of these three types of cells. In this review, we also present the emergence of DNA viruses requiring an evolutionary transition from RNA to DNA and recently discovered giant DNA viruses possibly involved in eukaryogenesis. In the course of evolution viruses emerged many times. They have always played a key role through horizontal gene transfer in evolutionary events and in formation of the tree of life or netlike routes of evolution providing a great deal of genetic diversity. In our opinion, future findings are crucial to better understand past relations between viruses and cells and the origin of both.}, }
@article {pmid26475319, year = {2015}, author = {Chiara, M and Fanelli, F and Mulè, G and Logrieco, AF and Pesole, G and Leslie, JF and Horner, DS and Toomajian, C}, title = {Genome Sequencing of Multiple Isolates Highlights Subtelomeric Genomic Diversity within Fusarium fujikuroi.}, journal = {Genome biology and evolution}, volume = {7}, number = {11}, pages = {3062-3069}, pmid = {26475319}, issn = {1759-6653}, mesh = {Adaptation, Physiological/genetics ; DNA, Fungal/genetics ; *Evolution, Molecular ; Fusarium/*genetics ; Gene Duplication ; Gene Transfer, Horizontal ; Genetic Variation ; Genetics, Population ; *Genome, Fungal ; Genomics ; Host-Pathogen Interactions/genetics ; Multigene Family ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Comparisons of draft genome sequences of three geographically distinct isolates of Fusarium fujikuroi with two recently published genome sequences from the same species suggest diverse profiles of secondary metabolite production within F. fujikuroi. Species- and lineage-specific genes, many of which appear to exhibit expression profiles that are consistent with roles in host-pathogen interactions and adaptation to environmental changes, are concentrated in subtelomeric regions. These genomic compartments also exhibit distinct gene densities and compositional characteristics with respect to other genomic partitions, and likely play a role in the generation of molecular diversity. Our data provide additional evidence that gene duplication, divergence, and differential loss play important roles in F. fujikuroi genome evolution and suggest that hundreds of lineage-specific genes might have been acquired through horizontal gene transfer.}, }
@article {pmid26474848, year = {2016}, author = {Gonçalves, C and Coelho, MA and Salema-Oom, M and Gonçalves, P}, title = {Stepwise Functional Evolution in a Fungal Sugar Transporter Family.}, journal = {Molecular biology and evolution}, volume = {33}, number = {2}, pages = {352-366}, doi = {10.1093/molbev/msv220}, pmid = {26474848}, issn = {1537-1719}, mesh = {Antiporters/genetics/metabolism ; Basidiomycota/genetics/metabolism ; *Biological Evolution ; Biological Transport ; *Carbohydrate Metabolism ; Carbohydrates ; Evolution, Molecular ; Fungi/classification/*genetics/*metabolism ; Monosaccharide Transport Proteins/*genetics/*metabolism ; *Multigene Family ; Phylogeny ; }, abstract = {Sugar transport is of the utmost importance for most cells and is central to a wide range of applied fields. However, despite the straightforward in silico assignment of many novel transporters, including sugar porters, to existing families, their exact biological role and evolutionary trajectory often remain unclear, mainly because biochemical characterization of membrane proteins is inherently challenging, but also owing to their uncommonly turbulent evolutionary histories. In addition, many important shifts in membrane carrier function are apparently ancient, which further limits our ability to reconstruct evolutionary trajectories in a reliable manner. Here, we circumvented some of these obstacles by examining the relatively recent emergence of a unique family of fungal sugar facilitators, related to drug antiporters. The former transporters, named Ffz, were previously shown to be required for fructophilic metabolism in yeasts. We first exploited the wealth of fungal genomic data available to define a comprehensive but well-delimited family of Ffz-like transporters, showing that they are only present in Dikarya. Subsequently, a combination of phylogenetic analyses and in vivo functional characterization was used to retrace important changes in function, while highlighting the evolutionary events that are most likely to have determined extant distribution of the gene, such as horizontal gene transfers (HGTs). One such HGT event is proposed to have set the stage for the onset of fructophilic metabolism in yeasts, a trait that according to our results may be the metabolic hallmark of close to 100 yeast species that thrive in sugar rich environments.}, }
@article {pmid26473921, year = {2015}, author = {Nguyen, M and Ekstrom, A and Li, X and Yin, Y}, title = {HGT-Finder: A New Tool for Horizontal Gene Transfer Finding and Application to Aspergillus genomes.}, journal = {Toxins}, volume = {7}, number = {10}, pages = {4035-4053}, pmid = {26473921}, issn = {2072-6651}, support = {R15 GM114706/GM/NIGMS NIH HHS/United States ; 1R15GM114706/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Biological/genetics ; Algorithms ; Aspergillus/*genetics ; Computational Biology/*methods ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Fungal ; *Genome, Fungal ; Multigene Family ; Phylogeny ; *Software ; Species Specificity ; }, abstract = {Horizontal gene transfer (HGT) is a fast-track mechanism that allows genetically unrelated organisms to exchange genes for rapid environmental adaptation. We developed a new phyletic distribution-based software, HGT-Finder, which implements a novel bioinformatics algorithm to calculate a horizontal transfer index and a probability value for each query gene. Applying this new tool to the Aspergillus fumigatus, Aspergillus flavus, and Aspergillus nidulans genomes, we found 273, 542, and 715 transferred genes (HTGs), respectively. HTGs have shorter length, higher guanine-cytosine (GC) content, and relaxed selection pressure. Metabolic process and secondary metabolism functions are significantly enriched in HTGs. Gene clustering analysis showed that 61%, 41% and 74% of HTGs in the three genomes form physically linked gene clusters (HTGCs). Overlapping manually curated, secondary metabolite gene clusters (SMGCs) with HTGCs found that 9 of the 33 A. fumigatus SMGCs and 31 of the 65 A. nidulans SMGCs share genes with HTGCs, and that HTGs are significantly enriched in SMGCs. Our genome-wide analysis thus presented very strong evidence to support the hypothesis that HGT has played a very critical role in the evolution of SMGCs. The program is freely available at http://cys.bios.niu.edu/HGTFinder/ HGTFinder.tar.gz.}, }
@article {pmid26473380, year = {2015}, author = {Johnson, CM and Grossman, AD}, title = {Integrative and Conjugative Elements (ICEs): What They Do and How They Work.}, journal = {Annual review of genetics}, volume = {49}, number = {}, pages = {577-601}, pmid = {26473380}, issn = {1545-2948}, support = {R01 GM050895/GM/NIGMS NIH HHS/United States ; GM050895/GM/NIGMS NIH HHS/United States ; }, mesh = {*Conjugation, Genetic ; DNA Replication ; DNA Transposable Elements/*physiology ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; Gene Expression Regulation ; *Gene Transfer, Horizontal ; Plasmids ; Recombination, Genetic ; }, abstract = {Horizontal gene transfer plays a major role in microbial evolution, allowing microbes to acquire new genes and phenotypes. Integrative and conjugative elements (ICEs, a.k.a. conjugative transposons) are modular mobile genetic elements integrated into a host genome and are passively propagated during chromosomal replication and cell division. Induction of ICE gene expression leads to excision, production of the conserved conjugation machinery (a type IV secretion system), and the potential to transfer DNA to appropriate recipients. ICEs typically contain cargo genes that are not usually related to the ICE life cycle and that confer phenotypes to host cells. We summarize the life cycle and discovery of ICEs, some of the regulatory mechanisms, and how the types of cargo have influenced our view of ICEs. We discuss how ICEs can acquire new cargo genes and describe challenges to the field and various perspectives on ICE biology.}, }
@article {pmid26472766, year = {2016}, author = {Brenciani, A and Morroni, G and Pollini, S and Tiberi, E and Mingoia, M and Varaldo, PE and Rossolini, GM and Giovanetti, E}, title = {Characterization of novel conjugative multiresistance plasmids carrying cfr from linezolid-resistant Staphylococcus epidermidis clinical isolates from Italy.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {71}, number = {2}, pages = {307-313}, doi = {10.1093/jac/dkv341}, pmid = {26472766}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/*pharmacology ; Cluster Analysis ; *Conjugation, Genetic ; DNA, Bacterial/genetics ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Italy ; Linezolid/*pharmacology ; Molecular Sequence Data ; Phylogeny ; Plasmids/*analysis ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Staphylococcal Infections/*microbiology ; Staphylococcus epidermidis/drug effects/*genetics/isolation &amp; purification ; }, abstract = {OBJECTIVES: The objective of this study was to investigate the genetic environment of the cfr gene from two linezolid-resistant clinical isolates of Staphylococcus epidermidis from Italy.<br><br>METHODS: The two strains (SP1 and SP2) were phenotypically and genotypically characterized. Transferability of cfr was assessed by electrotransformation and conjugation. The genetic contexts of cfr were investigated by PCR mapping, sequencing and comparative sequence analyses.<br><br>RESULTS: SP1 and SP2 belonged to ST23 and ST83, respectively. In both strains, the cfr gene was located on a plasmid, which could be transferred to Staphylococcus aureus by transformation and conjugation. In isolate SP1, linezolid resistance mediated by mutations in 23S rRNA and the L3 ribosomal protein was also detected. pSP01, the cfr-carrying plasmid from strain SP1, had a larger number of additional resistance genes and was sequenced (76&#x200a;991 bp). It disclosed a distinctive mosaic structure, with four cargo regions interpolated into a backbone 95% identical to that of S. aureus plasmid pPR9. Besides cfr, resistance genes distributed in the cargo regions included blaZ, lsa(B), msr(A) and aad, and a gene cluster for resistance to heavy metals. A closely related cfr plasmid (pSP01.1, &#x223c; 49 kb), differing from pSP01 by the lack of a large cargo region with some resistance genes, was detected in strain SP2.<br><br>CONCLUSIONS: The conjugative multiresistance plasmid pSP01 is the first cfr-carrying plasmid to be sequenced in Italy. This is the first time cfr has been found: (i) in association with blaZ, msr(A) and heavy metal resistance genes; and (ii) in an S. epidermidis strain (SP2) belonging to ST83.}, }
@article {pmid26472620, year = {2016}, author = {Elling, FJ and Becker, KW and Könneke, M and Schröder, JM and Kellermann, MY and Thomm, M and Hinrichs, KU}, title = {Respiratory quinones in Archaea: phylogenetic distribution and application as biomarkers in the marine environment.}, journal = {Environmental microbiology}, volume = {18}, number = {2}, pages = {692-707}, doi = {10.1111/1462-2920.13086}, pmid = {26472620}, issn = {1462-2920}, mesh = {Archaea/*classification/genetics/*metabolism ; Bacteria/metabolism ; Biomarkers/metabolism ; Biomass ; Black Sea ; Ecology ; Gene Transfer, Horizontal ; Membrane Lipids/metabolism ; Oxidation-Reduction ; Phylogeny ; Quinones/*chemistry ; Terpenes/*chemistry ; }, abstract = {The distribution of respiratory quinone electron carriers among cultivated organisms provides clues on both the taxonomy of their producers and the redox processes these are mediating. Our study of the quinone inventories of 25 archaeal species belonging to the phyla Eury-, Cren- and Thaumarchaeota facilitates their use as chemotaxonomic markers for ecologically important archaeal clades. Saturated and monounsaturated menaquinones with six isoprenoid units forming the alkyl chain may serve as chemotaxonomic markers for Thaumarchaeota. Other diagnostic biomarkers are thiophene-bearing quinones for Sulfolobales and methanophenazines as functional quinone analogues of the Methanosarcinales. The ubiquity of saturated menaquinones in the Archaea in comparison to Bacteria suggests that these compounds may represent an ancestral and diagnostic feature of the Archaea. Overlap between quinone compositions of distinct thermophilic and halophilic archaea and bacteria may indicate lateral gene transfer. The biomarker potential of thaumarchaeal quinones was exemplarily demonstrated on a water column profile of the Black Sea. Both, thaumarchaeal quinones and membrane lipids showed similar distributions with maxima at the chemocline. Quinone distributions indicate that Thaumarchaeota dominate respiratory activity at a narrow interval in the chemocline, while they contribute only 9% to the microbial biomass at this depth, as determined by membrane lipid analysis.}, }
@article {pmid26469217, year = {2016}, author = {Pu, XY and Pan, JC and Gu, YM and Zheng, W and Li, J and Yu, H}, title = {Complete Sequences and Characterization of Two Novel Plasmids Carrying aac(6')-Ib-cr and qnrS Gene in Shigella flexneri.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {22}, number = {2}, pages = {115-122}, doi = {10.1089/mdr.2015.0082}, pmid = {26469217}, issn = {1931-8448}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/*genetics/metabolism ; Base Sequence ; China ; Ciprofloxacin/pharmacology ; Conjugation, Genetic ; Conserved Sequence ; DNA, Bacterial/*genetics ; Drug Resistance, Bacterial/*genetics ; Dysentery, Bacillary/drug therapy/microbiology ; Escherichia coli/genetics/metabolism ; Gene Expression ; Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; Plasmids/chemistry/*metabolism ; Shigella flexneri/drug effects/enzymology/*genetics/isolation &amp; purification ; beta-Lactamases/genetics/metabolism ; }, abstract = {The complete sequences of two previously reported plasmids carrying plasmid-mediated quinolone resistance genes from Shigella flexneri in China have not been available. The present study using the p5-C3 assembly method revealed that (1) the plasmid pSF07201 with aac(6')-Ib-cr had 75,335 bp with antibiotic resistance genes CTX-M-3, TEM-1, and FosA3; (2) seven fragments of pSF07201 had more than 99% homology with the seven corresponding plasmids; (3) the other plasmid pSF07202 with qnrS had 47,669 bp with antibiotic resistance gene TEM-1 and 99.95% homology with a segment of pKF362122, which has the qnrS gene from location 162,490 to 163,146. A conjugation and electrotransformation experiment suggested that these two plasmids might horizontally transfer between and coexist in Escherichia coli J53 and S. flexneri 2a 301. Either the aac(6')-Ib-cr or qnrS gene contributed to, but only the coexistence of the two genes conferred to the resistance to ciprofloxacin in these two strains. To the best of our knowledge, this is the first report of the complete sequences of the aac(6')-Ib-cr- and qnrS-positive plasmids in Shigella isolates. Our findings indicate that two genes probably evolve through horizontal plasmid transfer between the different bacterial types.}, }
@article {pmid26467299, year = {2015}, author = {Khayi, S and Blin, P and Pédron, J and Chong, TM and Chan, KG and Moumni, M and Hélias, V and Van Gijsegem, F and Faure, D}, title = {Population genomics reveals additive and replacing horizontal gene transfers in the emerging pathogen Dickeya solani.}, journal = {BMC genomics}, volume = {16}, number = {}, pages = {788}, pmid = {26467299}, issn = {1471-2164}, mesh = {Base Sequence ; Chromosome Mapping ; Enterobacteriaceae/*genetics/pathogenicity ; Gene Transfer, Horizontal/*genetics ; *Genetics, Population ; Genome, Bacterial ; *Metagenomics ; Phylogeny ; Plant Diseases/genetics/microbiology ; Polymorphism, Single Nucleotide ; Solanum tuberosum/microbiology ; }, abstract = {BACKGROUND: Dickeya solani is an emerging pathogen that causes soft rot and blackleg diseases in several crops including Solanum tuberosum, but little is known about its genomic diversity and evolution.<br><br>RESULTS: We combined Illumina and PacBio technologies to complete the genome sequence of D. solani strain 3337 that was used as a reference to compare with 19 other genomes (including that of the type strain IPO2222(T)) which were generated by Illumina technology. This population genomic analysis highlighted an unexpected variability among D. solani isolates since it led to the characterization of two distinct sub-groups within the D. solani species. This approach also revealed different types of variations such as scattered SNP/InDel variations as well as replacing and additive horizontal gene transfers (HGT). Infra-species (between the two D. solani sub-groups) and inter-species (between D. solani and D. dianthicola) replacing HGTs were observed. Finally, this work pointed that genetic and functional variation in the motility trait could contribute to aggressiveness variability in D. solani.<br><br>CONCLUSIONS: This work revealed that D. solani genomic variability may be caused by SNPs/InDels as well as replacing and additive HGT events, including plasmid acquisition; hence the D. solani genomes are more dynamic than that were previously proposed. This work alerts on precautions in molecular diagnosis of this emerging pathogen.}, }
@article {pmid26465111, year = {2015}, author = {de Mendoza, A and Suga, H and Permanyer, J and Irimia, M and Ruiz-Trillo, I}, title = {Complex transcriptional regulation and independent evolution of fungal-like traits in a relative of animals.}, journal = {eLife}, volume = {4}, number = {}, pages = {e08904}, pmid = {26465111}, issn = {2050-084X}, support = {206883/ERC_/European Research Council/International ; 616960/ERC_/European Research Council/International ; }, mesh = {Animals ; *Cell Differentiation ; *Gene Expression Regulation ; Mesomycetozoea/*genetics/growth &amp; development/*physiology ; Proteome/analysis ; }, abstract = {Cell-type specification through differential genome regulation is a hallmark of complex multicellularity. However, it remains unclear how this process evolved during the transition from unicellular to multicellular organisms. To address this question, we investigated transcriptional dynamics in the ichthyosporean Creolimax fragrantissima, a relative of animals that undergoes coenocytic development. We find that Creolimax utilizes dynamic regulation of alternative splicing, long inter-genic non-coding RNAs and co-regulated gene modules associated with animal multicellularity in a cell-type specific manner. Moreover, our study suggests that the different cell types of the three closest animal relatives (ichthyosporeans, filastereans and choanoflagellates) are the product of lineage-specific innovations. Additionally, a proteomic survey of the secretome reveals adaptations to a fungal-like lifestyle. In summary, the diversity of cell types among protistan relatives of animals and their complex genome regulation demonstrates that the last unicellular ancestor of animals was already capable of elaborate specification of cell types.}, }
@article {pmid26464609, year = {2015}, author = {Papaleo, MC and Fondi, M and Maida, I and Perrin, E and Bevivino, A and Dalmastri, C and Fani, R}, title = {Analysis of a Pool of Small Plasmids from Soil Heterotrophic Cultivable Bacterial Communities.}, journal = {The open microbiology journal}, volume = {9}, number = {}, pages = {98-109}, pmid = {26464609}, issn = {1874-2858}, abstract = {In this work the analysis of the plasmid presence on soil aerobic cultivable heterotrophic bacterial communities was carried out checking a panel of 1,200 isolates, in order to establish the frequency of plasmid presence as well as the degree of plasmid flow between strains affiliated to the same or different taxon. Bacterial communities were isolated from two different sites of a 13-year experimental field with a clay-silt texture. Plasmid molecules were detected at low frequency (27 isolates, 2%) with a size ranging between 2 Kb and 40 Kb. The RAPD analysis performed on the plasmid-harboring isolates and the phylogenetic analysis of the whole community using the 16S rRNA gene sequences revealed the existence of transfer of the same plasmids between strains belonging to the same species and, in some cases, to different species of the same genus. As it might be expected, even though the viable cells title did not differ significantly between the two samplings, the overall data disclosed an uneven distribution of both species and plasmid-harboring strains.}, }
@article {pmid26463362, year = {2016}, author = {Sun, Y and Li, M and Chen, L and Chen, H and Yu, X and Ye, J and Zhang, Y and Ma, C and Zhou, T}, title = {Prevalence and molecular characterization of carbapenemase-producing gram-negative bacteria from a university hospital in China.}, journal = {Infectious diseases (London, England)}, volume = {48}, number = {2}, pages = {138-146}, doi = {10.3109/23744235.2015.1094822}, pmid = {26463362}, issn = {2374-4243}, mesh = {Acinetobacter baumannii/classification/drug effects/*enzymology/genetics ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*metabolism ; China/epidemiology ; Conjugation, Genetic ; DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; Electrophoresis, Gel, Pulsed-Field ; Enterobacteriaceae/classification/drug effects/*enzymology/genetics ; Gene Transfer, Horizontal ; Genotype ; Gram-Negative Bacterial Infections/*epidemiology/*microbiology ; Hospitals, University ; Humans ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Phenotype ; Plasmids ; Polymerase Chain Reaction ; Prevalence ; Pseudomonas aeruginosa/classification/drug effects/*enzymology/genetics ; Sequence Analysis, DNA ; beta-Lactamases/*metabolism ; }, abstract = {BACKGROUND: The increasing emergence of carbapenem resistance in gram-negative bacteria associated with carbapenemase prompted the initiation of this study.<br><br>METHODS: A total of 3139 gram-negative bacteria were recovered from a 3380-bed university hospital in Wenzhou during 2008 and 2012. Antimicrobial susceptibility was determined using the VITEK2 Compact System and agar dilution method. The phenotype and genotype of carbapenemase were demonstrated using the modified Hodge test, PCR and sequencing. A conjugation experiment was performed to reveal the transferability of resistant genes. The location of the carbapenemase gene was studied by plasmid analysis and southern blot hybridization. Clonal relatedness of the isolates was investigated by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST).<br><br>RESULTS: Overall, 751 of 3139 isolates (71/2055 Enterobacteriaceae, 510/620 Acinetobacter baumannii and 170/464 Pseudomonas aeruginosa) exhibited resistance to carbapenem. Carbapenemase-encoding genes were detected in 70.4% (50/71) of carbapenem-resistant Enterobacteriaceae, including blaKPC (80%) and blaIMP (20%). All A. baumannii subjected to genotype analysis were positive for blaOXA-51-like and co-harboured blaOXA-23-like (80.4%) and blaIMP (7.8%). ISAba1 was found upstream of blaOXA-23-like and blaOXA-51-like. Eight and seven strains of 170 P. aeruginosa carried blaIMP and blaVIM, respectively. PFGE analysis identified at least one dominant genotype in certain species. Four KPC-2-producing Klebsiella pneumoniae belonged to the same sequence type ST11. The plasmids carrying blaKPC were successfully transferred into recipient strains.<br><br>CONCLUSION: This study highlights the challenge of increasing prevalence of carbapenem resistance associated with carbapenemase genes and dissemination of epidemic clones in Wenzhou, China.}, }
@article {pmid26459929, year = {2015}, author = {Zhang, W and Zhou, J and Liu, T and Yu, Y and Pan, Y and Yan, S and Wang, Y}, title = {Four novel algal virus genomes discovered from Yellowstone Lake metagenomes.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {15131}, pmid = {26459929}, issn = {2045-2322}, mesh = {Evolution, Molecular ; Gene Order ; Genetic Variation ; *Genome, Viral ; Lakes/*virology ; *Metagenome ; *Metagenomics/methods ; Multigene Family ; Open Reading Frames ; Phycodnaviridae/*genetics ; Phylogeny ; }, abstract = {Phycodnaviruses are algae-infecting large dsDNA viruses that are widely distributed in aquatic environments. Here, partial genomic sequences of four novel algal viruses were assembled from a Yellowstone Lake metagenomic data set. Genomic analyses revealed that three Yellowstone Lake phycodnaviruses (YSLPVs) had genome lengths of 178,262 bp, 171,045 bp, and 171,454 bp, respectively, and were phylogenetically closely related to prasinoviruses (Phycodnaviridae). The fourth (YSLGV), with a genome length of 73,689 bp, was related to group III in the extended family Mimiviridae comprising Organic Lake phycodnaviruses and Phaeocystis globosa virus 16 T (OLPG). A pair of inverted terminal repeats was detected in YSLPV1, suggesting that its genome is nearly complete. Interestingly, these four putative YSL giant viruses also bear some genetic similarities to Yellowstone Lake virophages (YSLVs). For example, they share nine non-redundant homologous genes, including ribonucleotide reductase small subunit (a gene conserved in nucleo-cytoplasmic large DNA viruses) and Organic Lake virophage OLV2 (conserved in the majority of YSLVs). Additionally, putative multidrug resistance genes (emrE) were found in YSLPV1 and YSLPV2 but not in other viruses. Phylogenetic trees of emrE grouped YSLPVs with algae, suggesting that horizontal gene transfer occurred between giant viruses and their potential algal hosts.}, }
@article {pmid26459858, year = {2015}, author = {Tang, M and Chen, Z and Grover, CE and Wang, Y and Li, S and Liu, G and Ma, Z and Wendel, JF and Hua, J}, title = {Rapid evolutionary divergence of Gossypium barbadense and G. hirsutum mitochondrial genomes.}, journal = {BMC genomics}, volume = {16}, number = {}, pages = {770}, pmid = {26459858}, issn = {1471-2164}, mesh = {Base Sequence ; Computational Biology ; *Evolution, Molecular ; Gene Rearrangement ; Gene Transfer, Horizontal ; Genes, Mitochondrial ; *Genetic Variation ; *Genome, Mitochondrial ; Gossypium/*genetics ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Data ; Mutation ; Phylogeny ; Pseudogenes ; RNA, Transfer/chemistry/genetics ; Sequence Alignment ; Synteny/genetics ; }, abstract = {BACKGROUND: The mitochondrial genome from upland cotton, G. hirsutum, was previously sequenced. To elucidate the evolution of mitochondrial genomic diversity within a single genus, we sequenced the mitochondrial genome from Sea Island cotton (Gossypium barbadense L.).<br><br>METHODS: Mitochondrial DNA from week-old etiolated seedlings was extracted from isolated organelles using discontinuous sucrose density gradient method. Mitochondrial genome was sequenced with Solexa using paired-end, 90 bp read. The clean reads were assembled into contigs using ABySS and finished via additional fosmid and BAC sequencing. Finally, the genome was annotated and analyzed using different softwares.<br><br>RESULTS: The G. barbadense (Sea Island cotton) mitochondrial genome was fully sequenced (677,434-bp) and compared to the mitogenome of upland cotton. The G. barbadense mitochondrial DNA contains seven more genes than that of upland cotton, with a total of 40 protein coding genes (excluding possible pseudogenes), 6 rRNA genes, and 29 tRNA genes. Of these 75 genes, atp1, mttB, nad4, nad9, rrn5, rrn18, and trnD(GTC)-cp were each represented by two identical copies. A single 64 kb repeat was largely responsible for the 9 % difference in genome size between the two mtDNAs. Comparison of genome structures between the two mitochondrial genomes revealed 8 rearranged syntenic regions and several large repeats. The largest repeat was missing from the master chromosome in G. hirsutum. Both mitochondrial genomes contain a duplicated copy of rps3 (rps3-2) in conjunction with a duplication of repeated sequences. Phylogenetic and divergence considerations suggest that a 544-bp fragment of rps3 was transferred to the nuclear genome shortly after divergence of the A- and D- genome diploid cottons.<br><br>CONCLUSION: These results highlight the insights to the evolution of structural variation between Sea Island and upland cotton mitochondrial genomes.}, }
@article {pmid26459829, year = {2015}, author = {Park, J and Zhang, Y and Chen, C and Dudley, EG and Harvill, ET}, title = {Diversity of secretion systems associated with virulence characteristics of the classical bordetellae.}, journal = {Microbiology (Reading, England)}, volume = {161}, number = {12}, pages = {2328-2340}, pmid = {26459829}, issn = {1465-2080}, support = {R01 GM083113/GM/NIGMS NIH HHS/United States ; R01 GM113681/GM/NIGMS NIH HHS/United States ; R21 AI116186/AI/NIAID NIH HHS/United States ; 5R01GM083113/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/*metabolism ; Bacterial Secretion Systems/genetics/*metabolism ; Bordetella Infections/*microbiology ; Bordetella bronchiseptica/classification/genetics/*metabolism/*pathogenicity ; Bordetella pertussis/classification/genetics/*metabolism/*pathogenicity ; Humans ; Phylogeny ; Virulence ; }, abstract = {Secretion systems are key virulence factors, modulating interactions between pathogens and the host's immune response. Six potential secretion systems (types 1-6; T1SS-T6SS) have been discussed in classical bordetellae, respiratory commensals/pathogens of mammals. The prototypical Bordetella bronchiseptica strain RB50 genome seems to contain all six systems, whilst two human-restricted subspecies, Bordetella parapertussis and Bordetella pertussis, have lost different subsets of these. This implicates secretion systems in the divergent evolutionary histories that have led to their success in different niches. Based on our previous work demonstrating that changes in secretion systems are associated with virulence characteristics, we hypothesized there would be substantial divergence of the loci encoding each amongst sequenced strains. Here, we describe extensive differences in secretion system loci; 10 of the 11 sequenced strains had lost subsets of genes or one entire secretion system locus. These loci contained genes homologous to those present in the respective loci in distantly related organisms, as well as genes unique to bordetellae, suggesting novel and/or auxiliary functions. The high degree of conservation of the T3SS locus, a complex machine with interdependent parts that must be conserved, stands in dramatic contrast to repeated loss of T5aSS 'autotransporters', which function as an autonomous unit. This comparative analysis provided insights into critical aspects of each pathogen's adaptation to its different niche, and the relative contributions of recombination, mutation and horizontal gene transfer. In addition, the relative conservation of various secretion systems is an important consideration in the ongoing search for more highly conserved protective antigens for the next generation of pertussis vaccines.}, }
@article {pmid26456591, year = {2015}, author = {Paul, S and Bhardwaj, A and Bag, SK and Sokurenko, EV and Chattopadhyay, S}, title = {PanCoreGen - Profiling, detecting, annotating protein-coding genes in microbial genomes.}, journal = {Genomics}, volume = {106}, number = {6}, pages = {367-372}, pmid = {26456591}, issn = {1089-8646}, support = {R01 AI106007/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics ; Computational Biology/*methods ; Gene Expression Profiling/*methods ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/genetics ; Genome, Microbial/*genetics ; Molecular Sequence Annotation/*methods ; Open Reading Frames/*genetics ; Phylogeny ; Reproducibility of Results ; Salmonella enterica/classification/genetics ; Species Specificity ; }, abstract = {A large amount of genomic data, especially from multiple isolates of a single species, has opened new vistas for microbial genomics analysis. Analyzing the pan-genome (i.e. the sum of genetic repertoire) of microbial species is crucial in understanding the dynamics of molecular evolution, where virulence evolution is of major interest. Here we present PanCoreGen - a standalone application for pan- and core-genomic profiling of microbial protein-coding genes. PanCoreGen overcomes key limitations of the existing pan-genomic analysis tools, and develops an integrated annotation-structure for a species-specific pan-genomic profile. It provides important new features for annotating draft genomes/contigs and detecting unidentified genes in annotated genomes. It also generates user-defined group-specific datasets within the pan-genome. Interestingly, analyzing an example-set of Salmonella genomes, we detect potential footprints of adaptive convergence of horizontally transferred genes in two human-restricted pathogenic serovars - Typhi and Paratyphi A. Overall, PanCoreGen represents a state-of-the-art tool for microbial phylogenomics and pathogenomics study.}, }
@article {pmid26454015, year = {2015}, author = {Orata, FD and Kirchberger, PC and Méheust, R and Barlow, EJ and Tarr, CL and Boucher, Y}, title = {The Dynamics of Genetic Interactions between Vibrio metoecus and Vibrio cholerae, Two Close Relatives Co-Occurring in the Environment.}, journal = {Genome biology and evolution}, volume = {7}, number = {10}, pages = {2941-2954}, pmid = {26454015}, issn = {1759-6653}, mesh = {Base Sequence ; Comparative Genomic Hybridization ; DNA, Bacterial/*genetics ; Environmental Microbiology ; Evolution, Molecular ; Gene-Environment Interaction ; *Genes, Bacterial ; Genomic Islands ; Humans ; Integrons ; Molecular Sequence Data ; Phylogeny ; Vibrio/*genetics/isolation &amp; purification ; Vibrio cholerae/*genetics/isolation &amp; purification ; Virulence Factors/genetics ; }, abstract = {Vibrio metoecus is the closest relative of Vibrio cholerae, the causative agent of the potent diarrheal disease cholera. Although the pathogenic potential of this new species is yet to be studied in depth, it has been co-isolated with V. cholerae in coastal waters and found in clinical specimens in the United States. We used these two organisms to investigate the genetic interaction between closely related species in their natural environment. The genomes of 20 V. cholerae and 4 V. metoecus strains isolated from a brackish coastal pond on the US east coast, as well as 4 clinical V. metoecus strains were sequenced and compared with reference strains. Whole genome comparison shows 86-87% average nucleotide identity (ANI) in their core genes between the two species. On the other hand, the chromosomal integron, which occupies approximately 3% of their genomes, shows higher conservation in ANI between species than any other region of their genomes. The ANI of 93-94% observed in this region is not significantly greater within than between species, meaning that it does not follow species boundaries. Vibrio metoecus does not encode toxigenic V. cholerae major virulence factors, the cholera toxin and toxin-coregulated pilus. However, some of the pathogenicity islands found in pandemic V. cholerae were either present in the common ancestor it shares with V. metoecus, or acquired by clinical and environmental V. metoecus in partial fragments. The virulence factors of V. cholerae are therefore both more ancient and more widespread than previously believed. There is high interspecies recombination in the core genome, which has been detected in 24% of the single-copy core genes, including genes involved in pathogenicity. Vibrio metoecus was six times more often the recipient of DNA from V. cholerae as it was the donor, indicating a strong bias in the direction of gene transfer in the environment.}, }
@article {pmid26453985, year = {2016}, author = {Baer, B and Millar, AH}, title = {Proteomics in evolutionary ecology.}, journal = {Journal of proteomics}, volume = {135}, number = {}, pages = {4-11}, doi = {10.1016/j.jprot.2015.09.031}, pmid = {26453985}, issn = {1876-7737}, mesh = {Animals ; Ecology/*methods/trends ; *Evolution, Molecular ; Humans ; Proteomics/*methods/trends ; }, abstract = {Evolutionary ecologists are traditionally gene-focused, as genes propagate phenotypic traits across generations and mutations and recombination in the DNA generate genetic diversity required for evolutionary processes. As a consequence, the inheritance of changed DNA provides a molecular explanation for the functional changes associated with natural selection. A direct focus on proteins on the other hand, the actual molecular agents responsible for the expression of a phenotypic trait, receives far less interest from ecologists and evolutionary biologists. This is partially due to the central dogma of molecular biology that appears to define proteins as the 'dead-end of molecular information flow' as well as technical limitations in identifying and studying proteins and their diversity in the field and in many of the more exotic genera often favored in ecological studies. Here we provide an overview of a newly forming field of research that we refer to as 'Evolutionary Proteomics'. We point out that the origins of cellular function are related to the properties of polypeptide and RNA and their interactions with the environment, rather than DNA descent, and that the critical role of horizontal gene transfer in evolution is more about coopting new proteins to impact cellular processes than it is about modifying gene function. Furthermore, post-transcriptional and post-translational processes generate a remarkable diversity of mature proteins from a single gene, and the properties of these mature proteins can also influence inheritance through genetic and perhaps epigenetic mechanisms. The influence of post-transcriptional diversification on evolutionary processes could provide a novel mechanistic underpinning for elements of rapid, directed evolutionary changes and adaptations as observed for a variety of evolutionary processes. Modern state-of the art technologies based on mass spectrometry are now available to identify and quantify peptides, proteins, protein modifications and protein interactions of interest with high accuracy and assess protein diversity and function. Therefore, proteomic technologies can be viewed as providing evolutionary biologist with exciting novel opportunities to understand very early events in functional variation of cellular molecular machinery that are acting as part of evolutionary processes.}, }
@article {pmid26452554, year = {2016}, author = {Molenda, O and Quaile, AT and Edwards, EA}, title = {Dehalogenimonas sp. Strain WBC-2 Genome and Identification of Its trans-Dichloroethene Reductive Dehalogenase, TdrA.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {1}, pages = {40-50}, pmid = {26452554}, issn = {1098-5336}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/*genetics/metabolism ; Chloroflexi/chemistry/classification/*enzymology/genetics ; Ethylene Dichlorides/metabolism ; *Genome, Bacterial ; Hydrolases/chemistry/*genetics/metabolism ; Molecular Sequence Data ; Native Polyacrylamide Gel Electrophoresis ; Operon ; Phylogeny ; Protein Structure, Tertiary ; Sequence Alignment ; }, abstract = {The Dehalogenimonas population in a dechlorinating enrichment culture referred to as WBC-2 was previously shown to be responsible for trans-dichloroethene (tDCE) hydrogenolysis to vinyl chloride (VC). In this study, blue native polyacrylamide gel electrophoresis (BN-PAGE) followed by enzymatic assays and protein identification using liquid chromatography coupled with mass spectrometry (LC-MS/MS) led to the functional characterization of a novel dehalogenase, TdrA. This new reductive dehalogenase (RDase) catalyzes the dechlorination of tDCE to VC. A metagenome of the WBC-2 culture was sequenced, and a complete Dehalogenimonas genome, only the second Dehalogenimonas genome to become publicly available, was closed. The tdrA dehalogenase found within the Dehalogenimonas genome appears to be on a genomic island similar to genomic islands found in Dehalococcoides. TdrA itself is most similar to TceA from Dehalococcoides sp. strain FL2 with 76.4% amino acid pairwise identity. It is likely that the horizontal transfer of rdhA genes is not only a feature of Dehalococcoides but also a feature of other Dehalococcoidia, including Dehalogenimonas. A set of primers was developed to track tdrA in WBC-2 subcultures maintained on different electron acceptors. This newest dehalogenase is an addition to the short list of functionally defined RDases sharing the usual characteristic motifs (including an AB operon, a TAT export sequence, two iron-sulfur clusters, and a corrinoid binding domain), substrate flexibility, and evidence for horizontal gene transfer within the Dehalococcoidia.}, }
@article {pmid26451825, year = {2015}, author = {Zrimec, J and Lapanje, A}, title = {Fast Prediction of DNA Melting Bubbles Using DNA Thermodynamic Stability.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {12}, number = {5}, pages = {1137-1145}, doi = {10.1109/TCBB.2015.2396057}, pmid = {26451825}, issn = {1557-9964}, mesh = {Base Sequence ; Computer Simulation ; DNA/*chemistry/genetics/*ultrastructure ; *Models, Chemical ; *Models, Molecular ; Models, Statistical ; Molecular Sequence Data ; Nucleic Acid Conformation ; Nucleic Acid Denaturation ; Regression Analysis ; Sequence Analysis, DNA/*methods ; Thermodynamics ; Transition Temperature ; }, abstract = {DNA melting bubbles are the basis of many DNA-protein interactions, such as those in regulatory DNA regions driving gene expression, DNA replication and bacterial horizontal gene transfer. Bubble formation is affected by DNA duplex stability and thermally induced duplex destabilization (TIDD). Although prediction of duplex stability with the nearest neighbor (NN) method is much faster than prediction of TIDD with the Peyrard-Bishop-Dauxois (PBD) model, PBD predicted TIDD defines regulatory DNA regions with higher accuracy and detail. Here, we considered that PBD predicted TIDD is inherently related to the intrinsic duplex stabilities of destabilization regions. We show by regression modeling that NN duplex stabilities can be used to predict TIDD almost as accurately as is predicted with PBD. Predicted TIDD is in fact ascribed to non-linear transformation of NN duplex stabilities in destabilization regions as well as effects of neighboring regions relative to destabilization size. Since the prediction time of our models is over six orders of magnitude shorter than that of PBD, the models present an accessible tool for researchers. TIDD can be predicted on our webserver at http://tidd.immt.eu.}, }
@article {pmid26450506, year = {2015}, author = {Davidson, R and Vachaspati, P and Mirarab, S and Warnow, T}, title = {Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer.}, journal = {BMC genomics}, volume = {16 Suppl 10}, number = {Suppl 10}, pages = {S1}, pmid = {26450506}, issn = {1471-2164}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {Computational Biology ; Computer Simulation ; Gene Transfer, Horizontal/*genetics ; *Genetic Speciation ; Genome ; *Models, Theoretical ; *Phylogeny ; Probability ; Regression Analysis ; }, abstract = {BACKGROUND: Species tree estimation is challenged by gene tree heterogeneity resulting from biological processes such as duplication and loss, hybridization, incomplete lineage sorting (ILS), and horizontal gene transfer (HGT). Mathematical theory about reconstructing species trees in the presence of HGT alone or ILS alone suggests that quartet-based species tree methods (known to be statistically consistent under ILS, or under bounded amounts of HGT) might be effective techniques for estimating species trees when both HGT and ILS are present.<br><br>RESULTS: We evaluated several publicly available coalescent-based methods and concatenation under maximum likelihood on simulated datasets with moderate ILS and varying levels of HGT. Our study shows that two quartet-based species tree estimation methods (ASTRAL-2 and weighted Quartets MaxCut) are both highly accurate, even on datasets with high rates of HGT. In contrast, although NJst and concatenation using maximum likelihood are highly accurate under low HGT, they are less robust to high HGT rates.<br><br>CONCLUSION: Our study shows that quartet-based species-tree estimation methods can be highly accurate under the presence of both HGT and ILS. The study suggests the possibility that some quartet-based methods might be statistically consistent under phylogenomic models of gene tree heterogeneity with both HGT and ILS.}, }
@article {pmid26448648, year = {2015}, author = {Lee, JH and Jeong, DW}, title = {Characterization of Mobile Staphylococcus equorum Plasmids Isolated from Fermented Seafood That Confer Lincomycin Resistance.}, journal = {PloS one}, volume = {10}, number = {10}, pages = {e0140190}, pmid = {26448648}, issn = {1932-6203}, mesh = {Anti-Bacterial Agents/*pharmacology ; Base Sequence ; Drug Resistance, Bacterial/genetics ; Fermentation ; Food Microbiology ; Gene Transfer, Horizontal ; Lincomycin/*pharmacology ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Plasmids/*genetics ; Seafood/*microbiology ; Staphylococcus/*genetics/isolation &amp; purification ; }, abstract = {The complete nucleotide sequences of lincomycin-resistance gene (lnuA)-containing plasmids in Staphylococcus equorum strains isolated from the high-salt-fermented seafood jeotgal were determined. These plasmids, designated pSELNU1-3, are 2638-bp long, have two polymorphic sites, and encode typical elements found in plasmids that replicate via a rolling-circle mechanism including the replication protein gene (rep), a double-stranded origin of replication, a single-stranded origin of replication, and counter-transcribed RNA sequence, as well as lnuA. Plasmid sequences exhibit over 83% identity to other Staphylococcus plasmids that harbor rep and lnuA genes. Further, three pairs of identified direct repeats may be involved in inter-plasmid recombination. One plasmid, pSELNU1, was successfully transferred to other Staphylococcus species, Enterococcus faecalis, and Tetragenococcus halophilus in vitro. Antibiotic susceptibility of the transconjugants was host-dependent, and transconjugants maintained a lincomycin resistance phenotype in the absence of selective pressure over 60 generations.}, }
@article {pmid26446804, year = {2015}, author = {Sant'Anna, FH and Lebedinsky, AV and Sokolova, TG and Robb, FT and Gonzalez, JM}, title = {Analysis of three genomes within the thermophilic bacterial species Caldanaerobacter subterraneus with a focus on carbon monoxide dehydrogenase evolution and hydrolase diversity.}, journal = {BMC genomics}, volume = {16}, number = {}, pages = {757}, pmid = {26446804}, issn = {1471-2164}, mesh = {Aldehyde Oxidoreductases/*genetics ; *Evolution, Molecular ; Firmicutes/genetics ; Gene Transfer, Horizontal/genetics ; Genetic Variation ; *Genome, Bacterial ; Hydrolases/genetics ; Multienzyme Complexes/*genetics ; *Phylogeny ; }, abstract = {BACKGROUND: The Caldanaerobacter subterraneus species includes thermophilic fermentative bacteria able to grow on carbohydrates substrates with acetate and L-alanine as the main products. In this study, comprehensive analysis of three genomes of C. subterraneus subspecies was carried in order to identify genes encoding key metabolic enzymes and to document the genomic basis for the evolution of these organisms.<br><br>METHODS: Average nucleotide identity and in silico DNA relatedness were estimated for the studied C. subterraneus genomes. Genome synteny was evaluated using R2CAT software. Protein conservation was analyzed using mGenome Subtractor. Horizontal gene transfer was predicted through the GOHTAM pipeline (using tetranucleotide composition) and phylogenetic analyses (by maximum likelihood). Hydrolases were identified through the MEROPS and CAZy platforms.<br><br>RESULTS: The three genomes of C. subterraneus showed high similarity, although there are substantial differences in their gene composition and organization. Each subspecies possesses a gene cluster encoding a carbon monoxide dehydrogenase (CODH) and an energy converting hydrogenase (ECH). The CODH gene is associated with an operon that resembles the Escherichia coli hydrogenase hyc/hyf operons, a novel genetic context distinct from that found in archetypical hydrogenogenic carboxydotrophs. Apart from the CODH-associated hydrogenase, these bacteria also contain other hydrogenases, encoded by ech and hyd genes. An Mbx ferredoxin:NADP oxidoreductase homolog similar to that originally described in the archaeon Pyrococcus furiosus was uniquely encoded in the C. subterraneus subsp. yonseiensis genome. Compositional analysis demonstrated that some genes of the CODH-ECH and mbx operons present distinct sequence patterns in relation to the majority of the other genes of each genome. Phylogenetic reconstructions of the genes from these operons and those from the ech operon are incongruent to the species tree. Notably, the cooS gene of C. subterraneus subsp. pacificus and its homologs in C. subterraneus subsp. tengcongensis and C. subterraneus subsp. yonseiensis form distinct clades. The strains have diverse hydrolytic enzymes and they appear to be proteolytic and glycolytic. Divergent glycosidases from 14 families, among them amylases, chitinases, alpha-glucosidases, beta-glucosidases, and cellulases, were identified. Each of the three genomes also contains around 100 proteases from 50 subfamilies, as well about ten different esterases.<br><br>CONCLUSIONS: Genomic information suggests that multiple horizontal gene transfers conferred the adaptation of C. subterraneus subspecies to extreme niches throughout the carbon monoxide utilization and hydrogen production. The variety of hydrolases found in their genomes indicate the versatility of the species in obtaining energy and carbon from diverse substrates, therefore these organisms constitute a remarkable resource of enzymes with biotechnological potential.}, }
@article {pmid26445136, year = {2015}, author = {Bao, Z and Gao, X and Zhang, Q and Lin, J and Hu, W and Yu, H and Chen, J and Yang, Q and Yu, Q}, title = {The Effects of GH Transgenic Goats on the Microflora of the Intestine, Feces and Surrounding Soil.}, journal = {PloS one}, volume = {10}, number = {10}, pages = {e0139822}, pmid = {26445136}, issn = {1932-6203}, mesh = {Animals ; Animals, Genetically Modified/microbiology ; Bacteria/genetics ; DNA, Bacterial/genetics ; Feces/*microbiology ; Goats/*genetics/*microbiology ; Growth Hormone/*genetics ; Intestines/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil ; Soil Microbiology ; }, abstract = {The development of genetically engineered animals has brought with it increasing concerns about biosafety issues. We therefore evaluated the risks of growth hormone from transgenic goats, including the probability of horizontal gene transfer and the impact on the microbial community of the goats' gastrointestinal tracts, feces and the surrounding soil. The results showed that neither the GH nor the neoR gene could be detected in the samples. Moreover, there was no significant change in the microbial community of the gastrointestinal tracts, feces and soil, as tested with PCR-denaturing gradient gel electrophoresis and 16S rDNA sequencing. Finally, phylogenetic analysis showed that the intestinal content, feces and soil samples all contained the same dominant group of bacteria. These results demonstrated that expression of goat growth hormone in the mammary of GH transgenic goat does not influence the microflora of the intestine, feces and surrounding soil.}, }
@article {pmid26445388, year = {2015}, author = {Blokesch, M}, title = {Competence-induced type VI secretion might foster intestinal colonization by Vibrio cholerae: Intestinal interbacterial killing by competence-induced V. cholerae.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {37}, number = {11}, pages = {1163-1168}, doi = {10.1002/bies.201500101}, pmid = {26445388}, issn = {1521-1878}, mesh = {Bacterial Adhesion/physiology ; Biofilms/growth &amp; development ; Chitin/metabolism ; Cholera/microbiology/transmission ; Gastrointestinal Microbiome ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal/genetics ; Host-Pathogen Interactions/*genetics ; Humans ; Intestines/*microbiology ; Type VI Secretion Systems/*genetics ; Vibrio cholerae/genetics/*pathogenicity ; }, abstract = {The human pathogen Vibrio cholerae exhibits two distinct lifestyles: one in the aquatic environment where it often associates with chitinous surfaces and the other as the causative agent of the disease cholera. While much of the research on V. cholerae has focused on the host-pathogen interaction, knowledge about the environmental lifestyle of the pathogen remains limited. We recently showed that the polymer chitin, which is extremely abundant in aquatic environments, induces natural competence as a mode of horizontal gene transfer and that this competence regulon also includes the type VI secretion system (T6SS), a molecular killing device. Here, I discuss the putative consequences that chitin-induced T6SS activation could have on intestinal colonization and how the transmission route might influence disease outcome. Moreover, I propose that common infant animal models for cholera might not sufficiently take into account T6SS-mediated interbacterial warfare between V. cholerae and the intestinal microbiota.}, }
@article {pmid26442180, year = {2015}, author = {Peña-Miller, R and Rodríguez-González, R and MacLean, RC and San Millan, A}, title = {Evaluating the effect of horizontal transmission on the stability of plasmids under different selection regimes.}, journal = {Mobile genetic elements}, volume = {5}, number = {3}, pages = {1-5}, pmid = {26442180}, issn = {2159-2543}, abstract = {In theory, plasmids can only be maintained in a population when the rate of horizontal gene transfer is larger than the combined effect of segregational loss and the decrease of fitness associated with plasmid carriage. Recent advances in genome sequencing have shown, however, that a large fraction of plasmids do not carry the genes necessary for conjugation or mobilization. So, how are so-called non-transmissible plasmids able to persist? In order to address this question, we examined a previously published evolutionary model based on the interaction between P. aeruginosa and the non-transmissible plasmid pNUK73. Both our in silico and in vitro results demonstrated that, although compensatory adaptation can decrease the rate of plasmid decay, the conditions for the maintenance of a non-transmissible plasmid are very stringent if the genes it carries are not beneficial to the bacterial host. This result suggests that apparently non-transmissible plasmids may still experience episodes of horizontal gene transfer occurring at very low frequencies, and that these scattered transmission events are sufficient to stabilize these plasmids. We conclude by discussing different genomic and microbiological approaches that could allow for the detection of these rare transmission events and thus to obtain a reliable estimate of the rate of horizontal gene transfer.}, }
@article {pmid26442174, year = {2014}, author = {Szuplewska, M and Czarnecki, J and Bartosik, D}, title = {Autonomous and non-autonomous Tn3-family transposons and their role in the evolution of mobile genetic elements.}, journal = {Mobile genetic elements}, volume = {4}, number = {6}, pages = {1-4}, pmid = {26442174}, issn = {2159-2543}, abstract = {The Tn3 family of transposons includes diverse elements that encode homologous transposases and contain conserved terminal inverted repeat sequences (IRs). The recent identification of non-autonomous elements, named TIMEs (Tn3-derived Inverted-repeat Miniature Elements), has shed new light on the diversity and evolution of this transposon family. A common feature of TIMEs and other members of this family is their ability to mobilize genomic DNA for transposition as part of composite transposons. These elements significantly influence the structure and properties of plasmids and other mobile genetic elements (MGEs). They may contain and move by transposition (i) plasmid replication systems, (ii) toxin-antitoxin systems and (iii) site-specific recombination modules that can resolve plasmid multimers. Some Tn3 family elements may also transfer large segments of chromosomal DNA into plasmids, which increases the pool of mobile DNA that can take part in horizontal gene transfer.}, }
@article {pmid26442172, year = {2014}, author = {Fernandez-Lopez, R and de la Cruz, F}, title = {Rebooting the genome: The role of negative feedback in horizontal gene transfer.}, journal = {Mobile genetic elements}, volume = {4}, number = {6}, pages = {1-6}, pmid = {26442172}, issn = {2159-2543}, abstract = {Horizontal Gene Transfer (HGT) is one of the key mechanisms driving bacterial evolution. Conjugative plasmids are fundamental vehicles for HGT in bacteria, playing an essential role in the spread of antibiotic resistances. Although the classical view has stressed the instrumental role of these mobile genetic elements in the dissemination of antibiotic resistance genes, plasmids contain a rich physiology devoted to horizontal and vertical reproduction. This particular lifestyle imposes specific constrains and trade-offs on plasmid physiology, and plasmids have evolved dedicated circuits to balance the opposing demands of vertical and horizontal reproduction. Recent studies on the transcriptional networks of IncW plasmids and other incompatibility groups have unveiled common architectures in the regulatory networks of different plasmid groups. Comparative studies show that negative feedback loops (NFLs) with strong gains are preferred, opening the question of a possible convergent evolution dictated by certain adaptive properties of this particular network motif. System analysis of NFLs with strong feedback gains indicate that this architecture exhibits transient overshooting after horizontal gene transfer. Since plasmid burden is dependent on the expression of plasmid functions, transcriptional overshooting results in a transient increase of the burden immediately after conjugation. We discuss the possible implications of this phenomenon on plasmid propagation, and the regulatory networks that plasmids have evolved to counteract the detrimental side effects of transient overshooting.}, }
@article {pmid26441947, year = {2015}, author = {Li, AD and Li, LG and Zhang, T}, title = {Exploring antibiotic resistance genes and metal resistance genes in plasmid metagenomes from wastewater treatment plants.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1025}, pmid = {26441947}, issn = {1664-302X}, abstract = {Plasmids operate as independent genetic elements in microorganism communities. Through horizontal gene transfer (HGT), they can provide their host microorganisms with important functions such as antibiotic resistance and heavy metal resistance. In this study, six metagenomic libraries were constructed with plasmid DNA extracted from influent, activated sludge (AS) and digested sludge (DS) of two wastewater treatment plants (WWTPs). Compared with the metagenomes of the total DNA extracted from the same sectors of the wastewater treatment plant, the plasmid metagenomes had significantly higher annotation rates, indicating that the functional genes on plasmids are commonly shared by those studied microorganisms. Meanwhile, the plasmid metagenomes also encoded many more genes related to defense mechanisms, including ARGs. Searching against an antibiotic resistance genes (ARGs) database and a metal resistance genes (MRGs) database revealed a broad-spectrum of antibiotic (323 out of a total 618 subtypes) and MRGs (23 out of a total 23 types) on these plasmid metagenomes. The influent plasmid metagenomes contained many more resistance genes (both ARGs and MRGs) than the AS and the DS metagenomes. Sixteen novel plasmids with a complete circular structure that carried these resistance genes were assembled from the plasmid metagenomes. The results of this study demonstrated that the plasmids in WWTPs could be important reservoirs for resistance genes, and may play a significant role in the horizontal transfer of these genes.}, }
@article {pmid26441918, year = {2015}, author = {Han, Y and Perner, M}, title = {The globally widespread genus Sulfurimonas: versatile energy metabolisms and adaptations to redox clines.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {989}, pmid = {26441918}, issn = {1664-302X}, abstract = {Sulfurimonas species are commonly isolated from sulfidic habitats and numerous 16S rRNA sequences related to Sulfurimonas species have been identified in chemically distinct environments, such as hydrothermal deep-sea vents, marine sediments, the ocean's water column, and terrestrial habitats. In some of these habitats, Sulfurimonas have been demonstrated to play an important role in chemoautotrophic processes. Sulfurimonas species can grow with a variety of electron donors and acceptors, which may contribute to their widespread distribution. Multiple copies of one type of enzyme (e.g., sulfide:quinone reductases and hydrogenases) may play a pivotal role in Sulfurimonas' flexibility to colonize disparate environments. Many of these genes appear to have been acquired through horizontal gene transfer which has promoted adaptations to the distinct habitats. Here we summarize Sulfurimonas' versatile energy metabolisms and link their physiological properties to their global distribution.}, }
@article {pmid26441907, year = {2015}, author = {Chattopadhyay, MK and Jagannadham, MV}, title = {Corrigendum: Vesicles-mediated resistance to antibiotics in bacteria.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {974}, doi = {10.3389/fmicb.2015.00974}, pmid = {26441907}, issn = {1664-302X}, abstract = {[This corrects the article on p. 758 in vol. 6, PMID: 26257725.].}, }
@article {pmid26441873, year = {2015}, author = {Singh, RP and Shelke, GM and Kumar, A and Jha, PN}, title = {Biochemistry and genetics of ACC deaminase: a weapon to "stress ethylene" produced in plants.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {937}, pmid = {26441873}, issn = {1664-302X}, abstract = {1-aminocyclopropane-1-carboxylate deaminase (ACCD), a pyridoxal phosphate-dependent enzyme, is widespread in diverse bacterial and fungal species. Owing to ACCD activity, certain plant associated bacteria help plant to grow under biotic and abiotic stresses by decreasing the level of "stress ethylene" which is inhibitory to plant growth. ACCD breaks down ACC, an immediate precursor of ethylene, to ammonia and α-ketobutyrate, which can be further metabolized by bacteria for their growth. ACC deaminase is an inducible enzyme whose synthesis is induced in the presence of its substrate ACC. This enzyme encoded by gene AcdS is under tight regulation and regulated differentially under different environmental conditions. Regulatory elements of gene AcdS are comprised of the regulatory gene encoding LRP protein and other regulatory elements which are activated differentially under aerobic and anaerobic conditions. The role of some additional regulatory genes such as AcdB or LysR may also be required for expression of AcdS. Phylogenetic analysis of AcdS has revealed that distribution of this gene among different bacteria might have resulted from vertical gene transfer with occasional horizontal gene transfer (HGT). Application of bacterial AcdS gene has been extended by developing transgenic plants with ACCD gene which showed increased tolerance to biotic and abiotic stresses in plants. Moreover, distribution of ACCD gene or its homolog's in a wide range of species belonging to all three domains indicate an alternative role of ACCD in the physiology of an organism. Therefore, this review is an attempt to explore current knowledge of bacterial ACC deaminase mediated physiological effects in plants, mode of enzyme action, genetics, distribution among different species, ecological role of ACCD and, future research avenues to develop transgenic plants expressing foreign AcdS gene to cope with biotic and abiotic stressors. Systemic identification of regulatory circuits would be highly valuable to express the gene under diverse environmental conditions.}, }
@article {pmid26440206, year = {2015}, author = {Wright, LD and Johnson, CM and Grossman, AD}, title = {Identification of a Single Strand Origin of Replication in the Integrative and Conjugative Element ICEBs1 of Bacillus subtilis.}, journal = {PLoS genetics}, volume = {11}, number = {10}, pages = {e1005556}, pmid = {26440206}, issn = {1553-7404}, support = {R01 GM050895/GM/NIGMS NIH HHS/United States ; T32 GM007287/GM/NIGMS NIH HHS/United States ; R01GM050895/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacillus subtilis/genetics ; Conjugation, Genetic ; DNA/genetics ; DNA Replication/*genetics ; DNA, Single-Stranded/genetics ; *Gene Transfer, Horizontal ; Interspersed Repetitive Sequences/*genetics ; Replication Origin/*genetics ; }, abstract = {We identified a functional single strand origin of replication (sso) in the integrative and conjugative element ICEBs1 of Bacillus subtilis. Integrative and conjugative elements (ICEs, also known as conjugative transposons) are DNA elements typically found integrated into a bacterial chromosome where they are transmitted to daughter cells by chromosomal replication and cell division. Under certain conditions, ICEs become activated and excise from the host chromosome and can transfer to neighboring cells via the element-encoded conjugation machinery. Activated ICEBs1 undergoes autonomous rolling circle replication that is needed for the maintenance of the excised element in growing and dividing cells. Rolling circle replication, used by many plasmids and phages, generates single-stranded DNA (ssDNA). In many cases, the presence of an sso enhances the conversion of the ssDNA to double-stranded DNA (dsDNA) by enabling priming of synthesis of the second DNA strand. We initially identified sso1 in ICEBs1 based on sequence similarity to the sso of an RCR plasmid. Several functional assays confirmed Sso activity. Genetic analyses indicated that ICEBs1 uses sso1 and at least one other region for second strand DNA synthesis. We found that Sso activity was important for two key aspects of the ICEBs1 lifecycle: 1) maintenance of the plasmid form of ICEBs1 in cells after excision from the chromosome, and 2) stable acquisition of ICEBs1 following transfer to a new host. We identified sequences similar to known plasmid sso's in several other ICEs. Together, our results indicate that many other ICEs contain at least one single strand origin of replication, that these ICEs likely undergo autonomous replication, and that replication contributes to the stability and spread of these elements.}, }
@article {pmid26439115, year = {2015}, author = {Adato, O and Ninyo, N and Gophna, U and Snir, S}, title = {Detecting Horizontal Gene Transfer between Closely Related Taxa.}, journal = {PLoS computational biology}, volume = {11}, number = {10}, pages = {e1004408}, pmid = {26439115}, issn = {1553-7358}, mesh = {Algorithms ; Chromosome Mapping/*methods ; Escherichia coli/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial/*genetics ; Models, Genetic ; Phylogeny ; Synteny/*genetics ; }, abstract = {Horizontal gene transfer (HGT), the transfer of genetic material between organisms, is crucial for genetic innovation and the evolution of genome architecture. Existing HGT detection algorithms rely on a strong phylogenetic signal distinguishing the transferred sequence from ancestral (vertically derived) genes in its recipient genome. Detecting HGT between closely related species or strains is challenging, as the phylogenetic signal is usually weak and the nucleotide composition is normally nearly identical. Nevertheless, there is a great importance in detecting HGT between congeneric species or strains, especially in clinical microbiology, where understanding the emergence of new virulent and drug-resistant strains is crucial, and often time-sensitive. We developed a novel, self-contained technique named Near HGT, based on the synteny index, to measure the divergence of a gene from its native genomic environment and used it to identify candidate HGT events between closely related strains. The method confirms candidate transferred genes based on the constant relative mutability (CRM). Using CRM, the algorithm assigns a confidence score based on "unusual" sequence divergence. A gene exhibiting exceptional deviations according to both synteny and mutability criteria, is considered a validated HGT product. We first employed the technique to a set of three E. coli strains and detected several highly probable horizontally acquired genes. We then compared the method to existing HGT detection tools using a larger strain data set. When combined with additional approaches our new algorithm provides richer picture and brings us closer to the goal of detecting all newly acquired genes in a particular strain.}, }
@article {pmid26438860, year = {2015}, author = {Sit, CS and Ruzzini, AC and Van Arnam, EB and Ramadhar, TR and Currie, CR and Clardy, J}, title = {Variable genetic architectures produce virtually identical molecules in bacterial symbionts of fungus-growing ants.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {43}, pages = {13150-13154}, pmid = {26438860}, issn = {1091-6490}, support = {U19AI09673/AI/NIAID NIH HHS/United States ; R01 GM086258/GM/NIGMS NIH HHS/United States ; U19 AI109673/AI/NIAID NIH HHS/United States ; U19 TW009872/TW/FIC NIH HHS/United States ; F32 GM108415/GM/NIGMS NIH HHS/United States ; }, mesh = {Actinobacteria/genetics/*physiology ; Animals ; Ants/*physiology ; Fungi/*growth &amp; development ; Genes, Bacterial ; Molecular Sequence Data ; *Symbiosis ; }, abstract = {Small molecules produced by Actinobacteria have played a prominent role in both drug discovery and organic chemistry. As part of a larger study of the actinobacterial symbionts of fungus-growing ants, we discovered a small family of three previously unreported piperazic acid-containing cyclic depsipeptides, gerumycins A-C. The gerumycins are slightly smaller versions of dentigerumycin, a cyclic depsipeptide that selectively inhibits a common fungal pathogen, Escovopsis. We had previously identified this molecule from a Pseudonocardia associated with Apterostigma dentigerum, and now we report the molecule from an associate of the more highly derived ant Trachymyrmex cornetzi. The three previously unidentified compounds, gerumycins A-C, have essentially identical structures and were produced by two different symbiotic Pseudonocardia spp. from ants in the genus Apterostigma found in both Panama and Costa Rica. To understand the similarities and differences in the biosynthetic pathways that produced these closely related molecules, the genomes of the three producing Pseudonocardia were sequenced and the biosynthetic gene clusters identified. This analysis revealed that dramatically different biosynthetic architectures, including genomic islands, a plasmid, and the use of spatially separated genetic loci, can lead to molecules with virtually identical core structures. A plausible evolutionary model that unifies these disparate architectures is presented.}, }
@article {pmid26435881, year = {2015}, author = {Dimitriu, T and Misevic, D and Lindner, AB and Taddei, F}, title = {Mobile genetic elements are involved in bacterial sociality.}, journal = {Mobile genetic elements}, volume = {5}, number = {1}, pages = {7-11}, pmid = {26435881}, issn = {2159-2543}, abstract = {Mobile genetic elements in bacteria are enriched in genes participating in social behaviors, suggesting an evolutionary link between gene mobility and social evolution. Cooperative behaviors, like the production of secreted public good molecules, are susceptible to the invasion of non-cooperative individuals, and their evolutionary maintenance requires mechanisms ensuring that benefits are directed preferentially to cooperators. In order to investigate the reasons for the mobility of public good genes, we designed a synthetic bacterial system where we control and quantify the transfer of public good production genes. In our recent study, we have experimentally shown that horizontal transfer helps maintain public good production in the face of both non-producer organisms and non-producer plasmids. Transfer spreads genes to neighboring cells, thus increasing relatedness and directing a higher proportion of public good benefits to producers. The effect is the strongest when public good genes undergo epidemics dynamics, making horizontal transfer especially relevant for pathogenic bacteria that repeatedly infect new hosts and base their virulence on costly public goods. The promotion of cooperation may be a general consequence of horizontal gene transfer in prokaryotes. Our work has an intriguing parallel, cultural transmission, where horizontal transfer, such as teaching, may preferentially promote cooperative behaviors.}, }
@article {pmid26435002, year = {2016}, author = {Manna, S and Harman, A}, title = {Horizontal gene transfer of a Chlamydial tRNA-guanine transglycosylase gene to eukaryotic microbes.}, journal = {Molecular phylogenetics and evolution}, volume = {94}, number = {Pt A}, pages = {392-396}, doi = {10.1016/j.ympev.2015.09.022}, pmid = {26435002}, issn = {1095-9513}, mesh = {Acanthamoeba/*genetics ; Amebiasis/genetics/parasitology ; Chlamydia/enzymology/*genetics ; Deltaproteobacteria/enzymology/genetics ; Dysentery, Bacillary/microbiology ; Eukaryota/genetics ; *Gene Transfer, Horizontal ; Pentosyltransferases/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Shigella flexneri/enzymology/genetics ; }, abstract = {tRNA-guanine transglycosylases are found in all domains of life and mediate the base exchange of guanine with queuine in the anticodon loop of tRNAs. They can also regulate virulence in bacteria such as Shigella flexneri, which has prompted the development of drugs that inhibit the function of these enzymes. Here we report a group of tRNA-guanine transglycosylases in eukaryotic microbes (algae and protozoa) which are more similar to their bacterial counterparts than previously characterized eukaryotic tRNA-guanine transglycosylases. We provide evidence demonstrating that the genes encoding these enzymes were acquired by these eukaryotic lineages via horizontal gene transfer from the Chlamydiae group of bacteria. Given that the S. flexneri tRNA-guanine transglycosylase can be targeted by drugs, we propose that the bacterial-like tRNA-guanine transglycosylases could potentially be targeted in a similar fashion in pathogenic amoebae that possess these enzymes such as Acanthamoeba castellanii. This work also presents ancient prokaryote-to-eukaryote horizontal gene transfer events as an untapped resource of potential drug target identification in pathogenic eukaryotes.}, }
@article {pmid26433693, year = {2015}, author = {Vos, M and Hesselman, MC and Te Beek, TA and van Passel, MWJ and Eyre-Walker, A}, title = {Rates of Lateral Gene Transfer in Prokaryotes: High but Why?.}, journal = {Trends in microbiology}, volume = {23}, number = {10}, pages = {598-605}, doi = {10.1016/j.tim.2015.07.006}, pmid = {26433693}, issn = {1878-4380}, mesh = {Evolution, Molecular ; Gene Transfer, Horizontal/*genetics/physiology ; Genome, Archaeal/genetics ; Genome, Bacterial/genetics ; Prokaryotic Cells/*metabolism ; }, abstract = {Lateral gene transfer is of fundamental importance to the evolution of prokaryote genomes and has important practical consequences, as evidenced by the rapid dissemination of antibiotic resistance and virulence determinants. Relatively little effort has so far been devoted to explicitly quantifying the rate at which accessory genes are taken up and lost, but it is possible that the combined rate of lateral gene transfer and gene loss is higher than that of point mutation. What evolutionary forces underlie the rate of lateral gene transfer are not well understood. We here use theory developed to explain the evolution of mutation rates to address this question and explore its consequences for the study of prokaryote evolution.}, }
@article {pmid26433010, year = {2015}, author = {Lemaire, B and Van Cauwenberghe, J and Chimphango, S and Stirton, C and Honnay, O and Smets, E and Muasya, AM}, title = {Recombination and horizontal transfer of nodulation and ACC deaminase (acdS) genes within Alpha- and Betaproteobacteria nodulating legumes of the Cape Fynbos biome.}, journal = {FEMS microbiology ecology}, volume = {91}, number = {11}, pages = {}, doi = {10.1093/femsec/fiv118}, pmid = {26433010}, issn = {1574-6941}, mesh = {Alphaproteobacteria/classification/enzymology/*genetics/physiology ; Betaproteobacteria/classification/enzymology/*genetics/physiology ; Carbon-Carbon Lyases/*genetics ; Ecosystem ; Evolution, Molecular ; Fabaceae/*microbiology/physiology ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Phylogeny ; South Africa ; Symbiosis ; }, abstract = {The goal of this work is to study the evolution and the degree of horizontal gene transfer (HGT) within rhizobial genera of both Alphaproteobacteria (Mesorhizobium, Rhizobium) and Betaproteobacteria (Burkholderia), originating from South African Fynbos legumes. By using a phylogenetic approach and comparing multiple chromosomal and symbiosis genes, we revealed conclusive evidence of high degrees of horizontal transfer of nodulation genes among closely related species of both groups of rhizobia, but also among species with distant genetic backgrounds (Rhizobium and Mesorhizobium), underscoring the importance of lateral transfer of symbiosis traits as an important evolutionary force among rhizobia of the Cape Fynbos biome. The extensive exchange of symbiosis genes in the Fynbos is in contrast with a lack of significant events of HGT among Burkholderia symbionts from the South American Cerrado and Caatinga biome. Furthermore, homologous recombination among selected housekeeping genes had a substantial impact on sequence evolution within Burkholderia and Mesorhizobium. Finally, phylogenetic analyses of the non-symbiosis acdS gene in Mesorhizobium, a gene often located on symbiosis islands, revealed distinct relationships compared to the chromosomal and symbiosis genes, suggesting a different evolutionary history and independent events of gene transfer. The observed events of HGT and incongruence between different genes necessitate caution in interpreting topologies from individual data types.}, }
@article {pmid26432822, year = {2016}, author = {Grandclément, C and Tannières, M and Moréra, S and Dessaux, Y and Faure, D}, title = {Quorum quenching: role in nature and applied developments.}, journal = {FEMS microbiology reviews}, volume = {40}, number = {1}, pages = {86-116}, doi = {10.1093/femsre/fuv038}, pmid = {26432822}, issn = {1574-6976}, mesh = {Acyl-Butyrolactones/metabolism ; Bacteria/enzymology ; *Bacterial Physiological Phenomena ; *Biofilms ; Quorum Sensing/*physiology ; Signal Transduction ; }, abstract = {Quorum sensing (QS) refers to the capacity of bacteria to monitor their population density and regulate gene expression accordingly: the QS-regulated processes deal with multicellular behaviors (e.g. growth and development of biofilm), horizontal gene transfer and host-microbe (symbiosis and pathogenesis) and microbe-microbe interactions. QS signaling requires the synthesis, exchange and perception of bacterial compounds, called autoinducers or QS signals (e.g. N-acylhomoserine lactones). The disruption of QS signaling, also termed quorum quenching (QQ), encompasses very diverse phenomena and mechanisms which are presented and discussed in this review. First, we surveyed the QS-signal diversity and QS-associated responses for a better understanding of the targets of the QQ phenomena that organisms have naturally evolved and are currently actively investigated in applied perspectives. Next the mechanisms, targets and molecular actors associated with QS interference are presented, with a special emphasis on the description of natural QQ enzymes and chemicals acting as QS inhibitors. Selected QQ paradigms are detailed to exemplify the mechanisms and biological roles of QS inhibition in microbe-microbe and host-microbe interactions. Finally, some QQ strategies are presented as promising tools in different fields such as medicine, aquaculture, crop production and anti-biofouling area.}, }
@article {pmid26430060, year = {2016}, author = {Pérez-Escobar, OA and Balbuena, JA and Gottschling, M}, title = {Rumbling Orchids: How To Assess Divergent Evolution Between Chloroplast Endosymbionts and the Nuclear Host.}, journal = {Systematic biology}, volume = {65}, number = {1}, pages = {51-65}, doi = {10.1093/sysbio/syv070}, pmid = {26430060}, issn = {1076-836X}, mesh = {*Biological Evolution ; Chloroplasts/*classification/*genetics ; Classification/*methods ; DNA, Chloroplast/genetics ; DNA, Plant/genetics ; Orchidaceae/*classification/*genetics ; Phylogeny ; Software ; Symbiosis/*genetics ; }, abstract = {Phylogenetic relationships inferred from multilocus organellar and nuclear DNA data are often difficult to resolve because of evolutionary conflicts among gene trees. However, conflicting or "outlier" associations (i.e., linked pairs of "operational terminal units" in two phylogenies) among these data sets often provide valuable information on evolutionary processes such as chloroplast capture following hybridization, incomplete lineage sorting, and horizontal gene transfer. Statistical tools that to date have been used in cophylogenetic studies only also have the potential to test for the degree of topological congruence between organellar and nuclear data sets and reliably detect outlier associations. Two distance-based methods, namely ParaFit and Procrustean Approach to Cophylogeny (PACo), were used in conjunction to detect those outliers contributing to conflicting phylogenies independently derived from chloroplast and nuclear sequence data. We explored their efficiency of retrieving outlier associations, and the impact of input data (unit branch length and additive trees) between data sets, by using several simulation approaches. To test their performance using real data sets, we additionally inferred the phylogenetic relationships within Neotropical Catasetinae (Epidendroideae, Orchidaceae), which is a suitable group to investigate phylogenetic incongruence because of hybridization processes between some of its constituent species. A comparison between trees derived from chloroplast and nuclear sequence data reflected strong, well-supported incongruence within Catasetum, Cycnoches, and Mormodes. As a result, outliers among chloroplast and nuclear data sets, and in experimental simulations, were successfully detected by PACo when using patristic distance matrices obtained from phylograms, but not from unit branch length trees. The performance of ParaFit was overall inferior compared to PACo, using either phylograms or unit branch lengths as input data. Because workflows for applying cophylogenetic analyses are not standardized yet, we provide a pipeline for executing PACo and ParaFit as well as displaying outlier associations in plots and trees by using the software R. The pipeline renders a method to identify outliers with high reliability and to assess the combinability of the independently derived data sets by means of statistical analyses.}, }
@article {pmid26429294, year = {2016}, author = {Vitali, LA and Di Luca, MC and Prenna, M and Petrelli, D}, title = {Correlation between genetic features of the mef(A)-msr(D) locus and erythromycin resistance in Streptococcus pyogenes.}, journal = {Diagnostic microbiology and infectious disease}, volume = {84}, number = {1}, pages = {57-62}, doi = {10.1016/j.diagmicrobio.2015.08.007}, pmid = {26429294}, issn = {1879-0070}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteriophages/genetics ; DNA, Bacterial/chemistry/genetics ; *Drug Resistance, Bacterial ; Erythromycin/*pharmacology ; Gene Transfer, Horizontal ; Genetic Loci ; *Genetic Variation ; Humans ; Lysogeny ; Membrane Transport Proteins/*genetics ; Microbial Sensitivity Tests ; Prophages/genetics ; Sequence Analysis, DNA ; Streptococcus pyogenes/*drug effects/*genetics/isolation &amp; purification/virology ; }, abstract = {We investigated the correlation between the genetic variation within mef(A)-msr(D) determinants of efflux-mediated erythromycin resistance in Streptococcus pyogenes and the level of erythromycin resistance. Twenty-eight mef(A)-positive strains were selected according to erythromycin MIC (4-32 μg/mL), and their mef(A)-msr(D) regions were sequenced. Strains were classified according to the bacteriophage carrying mef(A)-msr(D). A new Φm46.1 genetic variant was found in 8 strains out of 28 and named VP_00501.1. Degree of allelic variation was higher in mef(A) than in msr(D). Hotspots for recombination were mapped within the locus that could have shaped the apparent mosaic structure of the region. There was a general correlation between mef(A)-msr(D) sequence and erythromycin resistance level. However, lysogenic conversion of susceptible strains by mef(A)-msr(D)-carrying Φm46.1 indicated that key determinants may not all reside within the mef(A)-msr(D) locus and that horizontal gene transfer could contribute to changes in the level of antibiotic resistance in S. pyogenes.}, }
@article {pmid26427709, year = {2016}, author = {Baldridge, GD and Markowski, TW and Witthuhn, BA and Higgins, L and Baldridge, AS and Fallon, AM}, title = {The Wolbachia WO bacteriophage proteome in the Aedes albopictus C/wStr1 cell line: evidence for lytic activity?.}, journal = {In vitro cellular &amp; developmental biology. Animal}, volume = {52}, number = {1}, pages = {77-88}, pmid = {26427709}, issn = {1543-706X}, support = {R01 AI081322/AI/NIAID NIH HHS/United States ; R01 AI 081322/AI/NIAID NIH HHS/United States ; }, mesh = {Aedes/genetics/microbiology ; Animals ; Bacteriophages/*genetics ; Drosophila melanogaster/*genetics/microbiology ; Gene Transfer Techniques ; Genome, Bacterial ; Hemiptera/genetics ; *Pest Control, Biological ; Phylogeny ; Proteome/*genetics ; Wolbachia/genetics/pathogenicity ; }, abstract = {Wolbachia pipientis (Rickettsiales), an obligate intracellular alphaproteobacterium in insects, manipulates host reproduction to maximize invasion of uninfected insect populations. Modification of host population structure has potential applications for control of pest species, particularly if Wolbachia can be maintained, manipulated, and genetically engineered in vitro. Although Wolbachia maintains an obligate mutualism with genome stability in nematodes, arthropods can be co-infected with distinct Wolbachia strains, and horizontal gene transfer between strains is potentially mediated by WO phages encoded within Wolbachia genomes. Proteomic analysis of a robust, persistent infection of a mosquito cell line with wStr from the planthopper, Laodelphax striatellus, revealed expression of a full array of WO phage genes, as well as nine of ten non-phage genes that occur between two distinct clusters of WOMelB genes in the genome of wMel, which infects Drosophila melanogaster. These non-phage genes encode potential host-adaptive proteins and are expressed in wStr at higher levels than phage structural proteins. A subset of seven of the non-phage genes is flanked by highly conserved non-coding sequences, including a putative promoter element, that are not present in a syntenically arranged array of homologs in plasmids from three tick-associated Rickettsia spp. These studies expand our understanding of wStr in a host cell line derived from the mosquito, Aedes albopictus, and provide a basis for investigating conditions that favor the lytic phase of the WO phage life cycle and recovery of infectious phage particles.}, }
@article {pmid26424139, year = {2016}, author = {Koczura, R and Mokracka, J and Makowska, N}, title = {Environmental Isolate of Rahnella aquatilis Harbors Class 1 Integron.}, journal = {Current microbiology}, volume = {72}, number = {1}, pages = {64-67}, pmid = {26424139}, issn = {1432-0991}, mesh = {Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; *Integrons ; Plasmids/analysis ; Poland ; Polymerase Chain Reaction ; Rahnella/drug effects/*genetics/*isolation &amp; purification ; Rivers/*microbiology ; }, abstract = {The paper presents first description of class 1 integron in an environmental strain of Rahnella aquatilis, a rarely isolated Gram-negative bacterium of the family Enterobacteriaceae. The strain was isolated from the Warta river water, Poland. Class 1 integrase gene was detected by a PCR assay. Sequencing of the integron's variable region showed the presence of a dfrA1-aadA1 gene cassette array. The integron was located in a 54-kbp plasmid that was transferable to Escherichia coli J-53 recipient strain in a conjugation assay. The integron-bearing R. aquatilis strain was resistant to aminoglycosides, penicillins, trimethoprim, sulfamethoxazole, and trimethoprim/sulfamethoxazole. This paper confirms that water environment play a major role in the spread of integrons and, consequently, antimicrobial resistance, among bacteria of various genera.}, }
@article {pmid26422847, year = {2015}, author = {Moazami Goudarzi, S and Eftekhar, F}, title = {Multidrug resistance and integron carriage in clinical isolates of Pseudomonas aeruginosa in Tehran, Iran.}, journal = {Turkish journal of medical sciences}, volume = {45}, number = {4}, pages = {789-793}, doi = {10.3906/sag-1408-120}, pmid = {26422847}, issn = {1300-0144}, mesh = {Anti-Bacterial Agents/classification/pharmacology ; Burn Units/statistics &amp; numerical data ; Cross Infection/epidemiology/*microbiology/prevention &amp; control ; DNA, Bacterial/*analysis ; Drug Resistance, Multiple, Bacterial ; Female ; Gene Transfer, Horizontal ; Hospitals/statistics &amp; numerical data ; Humans ; *Integrons ; Iran/epidemiology ; Male ; Microbial Sensitivity Tests ; Pseudomonas Infections/epidemiology/*microbiology/prevention &amp; control ; *Pseudomonas aeruginosa/drug effects/genetics ; }, abstract = {BACKGROUND/AIM: Pseudomonas aeruginosa is the cause of 10% of hospital-acquired infections. The organisms are often multidrug- resistant, mediated mostly by antibiotic-resistant integrons. The aim of this research was to study integron carriage and its association with multidrug resistance in burn and nonburn clinical isolates of P. aeruginosa.<br><br>MATERIALS AND METHODS: A total of 112 P. aeruginosa clinical isolates were collected from the Motahari and Shohadaye Tajrish hospitals in Tehran between July and December 2011. Antibiotic susceptibility to 13 antibiotics was determined by disk diffusion. Detection of integron classes 1 and 2 and amplifications of internal variable regions (IVRs) of class 1 integrons were carried out by PCR and specific primers.<br><br>RESULTS: Among the 112 isolates, 77 were from burn patients and 35 were nonburn isolates. Multidrug resistance and class 1 integron carriage were both significantly higher in the burn isolates compared to the nonburn strains (97.4% vs. 22.8% and 82.3% vs. 17.7%, respectively). Class 2 integron (2.7%) was only present in the burn isolates. Amplification of IVRs of class 1 integrons revealed 3 different fragment arrays.<br><br>CONCLUSION: The significant association between multidrug resistance and integron carriage among P. aeruginosa burn isolates suggests a dissemination of resistance determinants by horizontal gene transfer.}, }
@article {pmid26420795, year = {2016}, author = {Kittichotirat, W and Bumgarner, RE and Chen, C}, title = {Evolutionary Divergence of Aggregatibacter actinomycetemcomitans.}, journal = {Journal of dental research}, volume = {95}, number = {1}, pages = {94-101}, pmid = {26420795}, issn = {1544-0591}, support = {R01 DE012212/DE/NIDCR NIH HHS/United States ; }, mesh = {Aggregatibacter actinomycetemcomitans/*genetics ; Aggregatibacter aphrophilus/*genetics ; Bacterial Toxins/genetics ; Base Composition/genetics ; DNA, Bacterial/genetics ; DNA, Concatenated/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/genetics ; Genetic Heterogeneity ; Genetic Speciation ; Genetic Variation/genetics ; Genome, Bacterial/genetics ; Genomic Islands/genetics ; Humans ; Mouth/microbiology ; Phylogeny ; Protein Subunits/genetics ; Sequence Analysis, DNA ; Serogroup ; }, abstract = {Gram-negative facultative Aggregatibacter actinomycetemcomitans is an oral pathogen associated with periodontitis. The genetic heterogeneity among A. actinomycetemcomitans strains has been long recognized. This study provides a comprehensive genomic analysis of A. actinomycetemcomitans and the closely related nonpathogenic Aggregatibacter aphrophilus. Whole genome sequencing by Illumina MiSeq platform was performed for 31 A. actinomycetemcomitans and 2 A. aphrophilus strains. Sequence similarity analysis shows a total of 3,220 unique genes across the 2 species, where 1,550 are core genes present in all genomes and 1,670 are variable genes (accessory genes) missing in at least 1 genome. Phylogenetic analysis based on 397 concatenated core genes distinguished A. aphrophilus and A. actinomycetemcomitans. The latter was in turn divided into 5 clades: clade b (serotype b), clade c (serotype c), clade e/f (serotypes e and f), clade a/d (serotypes a and d), and clade e' (serotype e strains). Accessory genes accounted for 14.1% to 23.2% of the A. actinomycetemcomitans genomes, with a majority belonging to the category of poorly characterized by Cluster of Orthologous Groups classification. These accessory genes were often organized into genomic islands (n = 387) with base composition biases, suggesting their acquisitions via horizontal gene transfer. There was a greater degree of similarity in gene content and genomic islands among strains within clades than between clades. Strains of clade e' isolated from human were found to be missing the genomic island that carries genes encoding cytolethal distending toxins. Taken together, the results suggest a pattern of sequential divergence, starting from the separation of A. aphrophilus and A. actinomycetemcomitans through gain and loss of genes and ending with the divergence of the latter species into distinct clades and serotypes. With differing constellations of genes, the A. actinomycetemcomitans clades may have evolved distinct adaptation strategies to the human oral cavity.}, }
@article {pmid26419330, year = {2015}, author = {Munck, C and Albertsen, M and Telke, A and Ellabaan, M and Nielsen, PH and Sommer, MOA}, title = {Limited dissemination of the wastewater treatment plant core resistome.}, journal = {Nature communications}, volume = {6}, number = {}, pages = {8452}, pmid = {26419330}, issn = {2041-1723}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics/*isolation &amp; purification ; *Drug Resistance, Bacterial ; Molecular Sequence Data ; Phylogeny ; Wastewater/*microbiology ; Water Purification/*instrumentation ; }, abstract = {Horizontal gene transfer is a major contributor to the evolution of bacterial genomes and can facilitate the dissemination of antibiotic resistance genes between environmental reservoirs and potential pathogens. Wastewater treatment plants (WWTPs) are believed to play a central role in the dissemination of antibiotic resistance genes. However, the contribution of the dominant members of the WWTP resistome to resistance in human pathogens remains poorly understood. Here we use a combination of metagenomic functional selections and comprehensive metagenomic sequencing to uncover the dominant genes of the WWTP resistome. We find that this core resistome is unique to the WWTP environment, with <10% of the resistance genes found outside the WWTP environment. Our data highlight that, despite an abundance of functional resistance genes within WWTPs, only few genes are found in other environments, suggesting that the overall dissemination of the WWTP resistome is comparable to that of the soil resistome.}, }
@article {pmid26412445, year = {2016}, author = {He, D and Fu, CJ and Baldauf, SL}, title = {Multiple Origins of Eukaryotic cox15 Suggest Horizontal Gene Transfer from Bacteria to Jakobid Mitochondrial DNA.}, journal = {Molecular biology and evolution}, volume = {33}, number = {1}, pages = {122-133}, doi = {10.1093/molbev/msv201}, pmid = {26412445}, issn = {1537-1719}, mesh = {Alphaproteobacteria/*genetics ; Amino Acid Sequence ; DNA, Mitochondrial/*genetics ; Eukaryota/genetics ; Gene Transfer, Horizontal/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Symbiosis/*genetics ; }, abstract = {The most gene-rich and bacterial-like mitochondrial genomes known are those of Jakobida (Excavata). Of these, the most extreme example to date is the Andalucia godoyi mitochondrial DNA (mtDNA), including a cox15 gene encoding the respiratory enzyme heme A synthase (HAS), which is nuclear-encoded in nearly all other mitochondriate eukaryotes. Thus cox15 in eukaryotes appears to be a classic example of mitochondrion-to-nucleus (endosymbiotic) gene transfer, with A. godoyi uniquely retaining the ancestral state. However, our analyses reveal two highly distinct HAS types (encoded by cox15-1 and cox15-2 genes) and identify A. godoyi mitochondrial cox15-encoded HAS as type-1 and all other eukaryotic cox15-encoded HAS as type-2. Molecular phylogeny places the two HAS types in widely separated clades with eukaryotic type-2 HAS clustering with the bulk of α-proteobacteria (>670 sequences), whereas A. godoyi type-1 HAS clusters with an eclectic set of bacteria and archaea including two α-proteobacteria missing from the type-2 clade. This wide phylogenetic separation of the two HAS types is reinforced by unique features of their predicted protein structures. Meanwhile, RNA-sequencing and genomic analyses fail to detect either cox15 type in the nuclear genome of any jakobid including A. godoyi. This suggests that not only is cox15-1 a relatively recent acquisition unique to the Andalucia lineage but also the jakobid last common ancestor probably lacked both cox15 types. These results indicate that uptake of foreign genes by mtDNA is more taxonomically widespread than previously thought. They also caution against the assumption that all α-proteobacterial-like features of eukaryotes are ancient remnants of endosymbiosis.}, }
@article {pmid26412136, year = {2015}, author = {Ropars, J and Rodríguez de la Vega, RC and López-Villavicencio, M and Gouzy, J and Sallet, E and Dumas, &#xc9; and Lacoste, S and Debuchy, R and Dupont, J and Branca, A and Giraud, T}, title = {Adaptive Horizontal Gene Transfers between Multiple Cheese-Associated Fungi.}, journal = {Current biology : CB}, volume = {25}, number = {19}, pages = {2562-2569}, pmid = {26412136}, issn = {1879-0445}, support = {309403/ERC_/European Research Council/International ; }, mesh = {Adaptation, Biological/physiology ; Cheese/*microbiology ; DNA, Fungal/metabolism ; Food Microbiology ; Fungi/*genetics ; *Gene Transfer, Horizontal ; Penicillium/metabolism ; Phenotype ; }, abstract = {Domestication is an excellent model for studies of adaptation because it involves recent and strong selection on a few, identified traits [1-5]. Few studies have focused on the domestication of fungi, with notable exceptions [6-11], despite their importance to bioindustry [12] and to a general understanding of adaptation in eukaryotes [5]. Penicillium fungi are ubiquitous molds among which two distantly related species have been independently selected for cheese making-P. roqueforti for blue cheeses like Roquefort and P. camemberti for soft cheeses like Camembert. The selected traits include morphology, aromatic profile, lipolytic and proteolytic activities, and ability to grow at low temperatures, in a matrix containing bacterial and fungal competitors [13-15]. By comparing the genomes of ten Penicillium species, we show that adaptation to cheese was associated with multiple recent horizontal transfers of large genomic regions carrying crucial metabolic genes. We identified seven horizontally transferred regions (HTRs) spanning more than 10 kb each, flanked by specific transposable elements, and displaying nearly 100% identity between distant Penicillium species. Two HTRs carried genes with functions involved in the utilization of cheese nutrients or competition and were found nearly identical in multiple strains and species of cheese-associated Penicillium fungi, indicating recent selective sweeps; they were experimentally associated with faster growth and greater competitiveness on cheese and contained genes highly expressed in the early stage of cheese maturation. These findings have industrial and food safety implications and improve our understanding of the processes of adaptation to rapid environmental changes.}, }
@article {pmid26411640, year = {2015}, author = {Lee, SH and Choe, H and Kim, BK and Nasir, A and Kim, KM}, title = {Complete genome of the marine bacterium Wenzhouxiangella marina KCTC 42284(T).}, journal = {Marine genomics}, volume = {24 Pt 3}, number = {}, pages = {277-280}, doi = {10.1016/j.margen.2015.09.006}, pmid = {26411640}, issn = {1876-7478}, mesh = {Chromosome Mapping ; Chromosomes, Bacterial ; Gene Expression Regulation, Bacterial ; Gram-Negative Aerobic Bacteria/*genetics ; Microalgae/microbiology ; RNA, Bacterial/genetics ; }, abstract = {Wenzhouxiangella marina is an obligatory aerobic, Gram-negative, non-motile, rod-shaped bacterium that was isolated from the culture broth of marine microalgae, Picochlorum sp. 122. Here we report the 3.67 MB complete genome (65.26 G+C%) of W. marina KCTC 42284(T) encoding 3,016 protein-coding genes, 43 tRNAs and one rRNA operon. The genomic information supports multiple horizontal gene transfer (HGT) events in the history of W. marina, possibly with other marine bacteria co-existing in marine habitats. Evaluation of genomic signatures revealed 19 such HGT-derived genomic islands. Of these, eight were also supported by "genomic context" that refers to the existence of integrases, transposases and tmRNA genes either inside or in near vicinity to the island. The addition of W. marina genome expands the repertoire of marine bacterial genomic diversity, especially because the strain represents the sole genomic resource of a novel taxonomic family in the bacterial order Chromatiales.}, }
@article {pmid26410170, year = {2015}, author = {Douarre, PE and Sauvage, E and Poyart, C and Glaser, P}, title = {Host specificity in the diversity and transfer of lsa resistance genes in group B Streptococcus.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {70}, number = {12}, pages = {3205-3213}, doi = {10.1093/jac/dkv277}, pmid = {26410170}, issn = {1460-2091}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Cattle ; Cattle Diseases/microbiology ; Diterpenes/pharmacology ; *Drug Resistance, Bacterial ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Genetic Variation ; Gram-Positive Bacterial Infections/microbiology/veterinary ; *Host Specificity ; Lincosamides/pharmacology ; Microbial Sensitivity Tests ; Polycyclic Compounds ; Recombination, Genetic ; Sequence Analysis, DNA ; Sequence Homology ; Streptococcus agalactiae/*drug effects/*genetics/isolation &amp; purification ; Streptogramin A/pharmacology ; Pleuromutilins ; }, abstract = {OBJECTIVES: In group B Streptococcus (GBS), cross-resistance to lincosamides, streptogramin A and pleuromutilins (LSAP) is mediated by the acquisition of lsa genes. Here, we characterized the diversity, mobility and ecology of lsa genes in this species.<br><br>METHODS: lsa variants were systematically identified by BLAST searches in the genomes of 531 GBS strains from different hosts and geographical origins. The associated phenotypes were determined by a microdilution MIC method. Acquisition of resistance genes was deduced from comparative genomics and phylogeny. Their mobility was tested by conjugation experiments.<br><br>RESULTS: lsa(E) and three variants of lsa(C) were identified in GBS strains. Two lsa(C) variants had not been previously reported. All four variants conferred LSAP phenotypes. lsa(E) was located in a multiresistance gene cluster of a single human strain. This gene was transferred by a high-frequency recombination-type mechanism between GBS strains. Two lsa(C) variants are carried in six unrelated human strains by two similar elements specifically integrated in the oriT site of four different classes of integrative and conjugative elements (ICEs). Strikingly, the acquisition of the resistance gene always occurred by the integration of the element into a resident ICE. The third lsa(C) variant was located at the same site in the core genome of 11 genetically distant bovine strains and was likely propagated by horizontal transfer of the corresponding chromosomal region.<br><br>CONCLUSIONS: lsa genes in GBS show distinct host specificities and modes of transfer. In general, their dissemination is mediated by recombination rather than by the transfer of conjugative elements.}, }
@article {pmid26403231, year = {2016}, author = {Lin, J and Zhu, L and Lau, GW}, title = {Disentangling competence for genetic transformation and virulence in Streptococcus pneumoniae.}, journal = {Current genetics}, volume = {62}, number = {1}, pages = {97-103}, pmid = {26403231}, issn = {1432-0983}, support = {R01 HL090699/HL/NHLBI NIH HHS/United States ; HL090699/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Bacterial Proteins/genetics/metabolism ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Mutation ; Operon ; Recombination, Genetic ; Streptococcus pneumoniae/pathogenicity/*physiology ; Streptolysins/genetics/metabolism ; *Transformation, Bacterial ; Virulence/genetics ; }, abstract = {Horizontal gene transfer mediated by the competence regulon is a major driver of genome plasticity in Streptococcus pneumoniae. When pneumococcal cells enter the competent state, about 6% of the genes in the genome are up-regulated. Among these, some genes are essential for genetic transformation while others are dispensable for the process. Exhaustive deletion analyses show that some up-regulated genes dispensable for genetic transformation contribute to pneumococcal-mediated pneumonia and bacteremia infections. Interestingly, virulence functions of such genes are either dependent or independent of the competent state. Among the competent-state-dependent genes are those mediating allolysis, a process where small fraction of non-competent cells within the pneumococcal population are lysed by their competent counterparts, releasing DNA presumably for transformation. Inadvertently, the pore-forming toxin pneumolysin is also released during allolysis, contributing to virulence. In this review, we discuss recent advances in our understanding of pneumococcal virulence processes mediated by the competence regulon. We proposed that coupling of competence induction and bacterial fitness drives the natural selection to favor an intact competence regulon, which in turn, provides the long-term benefits of genetic plasticity.}, }
@article {pmid26401445, year = {2015}, author = {Ormerod, KL and George, NM and Fraser, JA and Wainwright, C and Hugenholtz, P}, title = {Comparative genomics of non-pseudomonal bacterial species colonising paediatric cystic fibrosis patients.}, journal = {PeerJ}, volume = {3}, number = {}, pages = {e1223}, pmid = {26401445}, issn = {2167-8359}, abstract = {The genetic disorder cystic fibrosis is a life-limiting condition affecting ∼70,000 people worldwide. Targeted, early, treatment of the dominant infecting species, Pseudomonas aeruginosa, has improved patient outcomes; however, there is concern that other species are now stepping in to take its place. In addition, the necessarily long-term antibiotic therapy received by these patients may be providing a suitable environment for the emergence of antibiotic resistance. To investigate these issues, we employed whole-genome sequencing of 28 non-Pseudomonas bacterial strains isolated from three paediatric patients. We did not find any trend of increasing antibiotic resistance (either by mutation or lateral gene transfer) in these isolates in comparison with other examples of the same species. In addition, each isolate contained a virulence gene repertoire that was similar to other examples of the relevant species. These results support the impaired clearance of the CF lung not demanding extensive virulence for survival in this habitat. By analysing serial isolates of the same species we uncovered several examples of strain persistence. The same strain of Staphylococcus aureus persisted for nearly a year, despite administration of antibiotics to which it was shown to be sensitive. This is consistent with previous studies showing antibiotic therapy to be inadequate in cystic fibrosis patients, which may also explain the lack of increasing antibiotic resistance over time. Serial isolates of two naturally multi-drug resistant organisms, Achromobacter xylosoxidans and Stenotrophomonas maltophilia, revealed that while all S. maltophilia strains were unique, A. xylosoxidans persisted for nearly five years, making this a species of particular concern. The data generated by this study will assist in developing an understanding of the non-Pseudomonas species associated with cystic fibrosis.}, }
@article {pmid26400439, year = {2015}, author = {Aswad, A and Katzourakis, A}, title = {Convergent capture of retroviral superantigens by mammalian herpesviruses.}, journal = {Nature communications}, volume = {6}, number = {}, pages = {8299}, pmid = {26400439}, issn = {2041-1723}, mesh = {Animals ; Antigens, Viral/*genetics ; Aotidae ; Chiroptera ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genes, Viral/*genetics ; Herpesviridae/*genetics ; Herpesvirus 2, Saimiriine ; Hylobates ; Mammary Tumor Virus, Mouse/genetics ; Mice ; Phylogeny ; Rats ; Retroviridae/*genetics ; Rhadinovirus/genetics ; Sheep ; South America ; Superantigens/*genetics ; }, abstract = {Horizontal gene transfer from retroviruses to mammals is well documented and extensive, but is rare between unrelated viruses with distinct genome types. Three herpesviruses encode a gene with similarity to a retroviral superantigen gene (sag) of the unrelated mouse mammary tumour virus (MMTV). We uncover ancient retroviral sags in over 20 mammals to reconstruct their shared history with herpesviral sags, revealing that the acquisition is a convergent evolutionary event. A retrovirus circulating in South American primates over 10 million years ago was the source of sag in two monkey herpesviruses, and a different retrovirus was the source of sag in a Peruvian rodent herpesvirus. We further show through a timescaled phylogenetic analysis that a cross-species transmission of monkey herpesviruses occurred after the acquisition of sag. These results reveal that a diverse range of ancient sag-containing retroviruses independently donated sag twice from two separate lineages that are distinct from MMTV.}, }
@article {pmid26399243, year = {2015}, author = {Ou, T and Gao, XC and Li, SH and Zhang, QY}, title = {Genome analysis and gene nblA identification of Microcystis aeruginosa myovirus (MaMV-DC) reveal the evidence for horizontal gene transfer events between cyanomyovirus and host.}, journal = {The Journal of general virology}, volume = {96}, number = {12}, pages = {3681-3697}, doi = {10.1099/jgv.0.000290}, pmid = {26399243}, issn = {1465-2099}, mesh = {DNA, Viral/genetics ; Gene Expression Regulation, Viral/*physiology ; Gene Transfer, Horizontal/*physiology ; Genome, Viral ; Microcystis/*genetics/*virology ; Myoviridae/*genetics ; Phylogeny ; RNA, Transfer/genetics ; RNA, Viral/genetics ; Viral Proteins/genetics/*metabolism ; }, abstract = {The genome sequence, genetic characterization and nblA gene function of Microcystis aeruginosa myovirus isolated from Lake Dianchi in China (MaMV-DC) have been analysed. The genome DNA is 169 223 bp long, with 170 predicted protein-coding genes (001L–170L) and a tRNA gene. About one-sixth of these genes have homologues in the host cyanobacteria M. aeruginosa. The genome carries a gene homologous to host nblA, which encodes a protein involved in the degradation of cyanobacterial phycobilisome. Its expression during MaMV-DC infection was confirmed by reverse transcriptase PCR and Western blot detection and abundant expression was companied by the significant decline of phycocyanin content and massive release of progeny MaMV-DC. In addition, expressing MaMV-DC nblA reduced the phycocyanin peak and the phycocyanin to chlorophyll ratio in model cyanobacteria. These results confirm that horizontal gene transfer events have occurred between cyanobacterial host and cyanomyovirus and suggest that MaMV-DC carrying host-derived genes (such as 005L, that codes for NblA) is responsible for more efficient expression of cyanophage genes and release of progeny cyanophage. This study provides novel insight into the horizontal gene transfer in cyanophage and the interactions between cyanophage and their host.}, }
@article {pmid26399182, year = {2015}, author = {Ford, KL and Baumgartner, K and Henricot, B and Bailey, AM and Foster, GD}, title = {A reliable in vitro fruiting system for Armillaria mellea for evaluation of Agrobacterium tumefaciens transformation vectors.}, journal = {Fungal biology}, volume = {119}, number = {10}, pages = {859-869}, doi = {10.1016/j.funbio.2015.06.007}, pmid = {26399182}, issn = {1878-6146}, mesh = {Agrobacterium tumefaciens/*genetics ; Armillaria/genetics/*growth &amp; development/isolation &amp; purification ; Fruiting Bodies, Fungal/*growth &amp; development ; *Gene Transfer Techniques ; Gene Transfer, Horizontal ; Genetics, Microbial/*methods ; In Vitro Techniques/methods ; Light ; Mycology/*methods ; Temperature ; *Transformation, Genetic ; United States ; }, abstract = {Armillaria mellea is a serious pathogen of horticultural and agricultural systems in Europe and North America. The lack of a reliable in vitro fruiting system for heterothallic A. mellea has hindered research and required dependence on intermittently available wild-collected basidiospores of endemic genotypes, necessitating the use of variable genetic material in transformation studies. Here we describe a reliable, reproducible in vitro fruiting method for heterothallic A. mellea from the western US. Isolates and growth conditions were evaluated to determine effective fruiting conditions. Following medium colonisation for 4 weeks, cultures were incubated under warm/bright conditions for 4-6 weeks before incubation in dim/cool conditions. Primordia emerged within 3-4 weeks following a temperature decrease and this was most efficient when coupled with a light reduction. Basidiocarps matured within 3-4 weeks and produced viable basidiospores. Agrobacterium tumefaciens and vectors were evaluated by transformation of in vitro-produced basidiospores and a versatile transformation vector was constructed to simplify promoter and marker gene exchange using homologous recombination in yeast. Fruiting bodies and viable basidiospores of A. mellea have been reliably produced in vitro which, coupled with the enhanced knowledge of suitable A. tumefaciens strains and vectors for transformation, will assist future genetic research into this important pathogen.}, }
@article {pmid26396243, year = {2015}, author = {Thrane, SW and Taylor, VL and Freschi, L and Kukavica-Ibrulj, I and Boyle, B and Laroche, J and Pirnay, JP and Lévesque, RC and Lam, JS and Jelsbak, L}, title = {The Widespread Multidrug-Resistant Serotype O12 Pseudomonas aeruginosa Clone Emerged through Concomitant Horizontal Transfer of Serotype Antigen and Antibiotic Resistance Gene Clusters.}, journal = {mBio}, volume = {6}, number = {5}, pages = {e01396-15}, pmid = {26396243}, issn = {2150-7511}, support = {MOP-114045//Canadian Institutes of Health Research/Canada ; MOP-14687//Canadian Institutes of Health Research/Canada ; MOP-86644//Canadian Institutes of Health Research/Canada ; }, mesh = {*Drug Resistance, Bacterial ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genomic Islands ; Genotype ; Multigene Family ; O Antigens/*genetics ; Pseudomonas aeruginosa/classification/*drug effects/*genetics ; Recombination, Genetic ; *Serogroup ; }, abstract = {UNLABELLED: The O-specific antigen (OSA) in Pseudomonas aeruginosa lipopolysaccharide is highly varied by sugar identity, side chains, and bond between O-repeats. These differences classified P. aeruginosa into 20 distinct serotypes. In the past few decades, O12 has emerged as the predominant serotype in clinical settings and outbreaks. These serotype O12 isolates exhibit high levels of resistance to various classes of antibiotics. Here, we explore how the P. aeruginosa OSA biosynthesis gene clusters evolve in the population by investigating the association between the phylogenetic relationships among 83 P. aeruginosa strains and their serotypes. While most serotypes were closely linked to the core genome phylogeny, we observed horizontal exchange of OSA biosynthesis genes among phylogenetically distinct P. aeruginosa strains. Specifically, we identified a "serotype island" ranging from 62 kb to 185 kb containing the P. aeruginosa O12 OSA gene cluster, an antibiotic resistance determinant (gyrA(C248T)), and other genes that have been transferred between P. aeruginosa strains with distinct core genome architectures. We showed that these genes were likely acquired from an O12 serotype strain that is closely related to P. aeruginosa PA7. Acquisition and recombination of the "serotype island" resulted in displacement of the native OSA gene cluster and expression of the O12 serotype in the recipients. Serotype switching by recombination has apparently occurred multiple times involving bacteria of various genomic backgrounds. In conclusion, serotype switching in combination with acquisition of an antibiotic resistance determinant most likely contributed to the dissemination of the O12 serotype in clinical settings.<br><br>IMPORTANCE: Infection rates in hospital settings by multidrug-resistant (MDR) Pseudomonas aeruginosa clones have increased during the past decades, and serotype O12 is predominant among these epidemic strains. It is not known why the MDR phenotype is associated with serotype O12 and how this clone type has emerged. This study shows that evolution of MDR O12 strains involved a switch from an ancestral O4 serotype to O12. Serotype switching was the result of horizontal transfer and genetic recombination of lipopolysaccharide (LPS) biosynthesis genes originating from an MDR taxonomic outlier P.&#xa0;aeruginosa strain. Moreover, the recombination event also resulted in acquisition of antibiotic resistance genes. These results impact on our understanding of MDR outbreak strain and serotype evolution and can potentially assist in better monitoring and prevention.}, }
@article {pmid26395902, year = {2015}, author = {Warren, IA and Naville, M and Chalopin, D and Levin, P and Berger, CS and Galiana, D and Volff, JN}, title = {Evolutionary impact of transposable elements on genomic diversity and lineage-specific innovation in vertebrates.}, journal = {Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology}, volume = {23}, number = {3}, pages = {505-531}, pmid = {26395902}, issn = {1573-6849}, mesh = {Animals ; *DNA Transposable Elements ; *Evolution, Molecular ; Female ; Gene Expression Regulation ; Gene Rearrangement ; Gene Regulatory Networks ; Gene Transfer, Horizontal ; *Genetic Variation ; *Genome ; Genomics/methods ; Humans ; Nucleic Acid Conformation ; Open Reading Frames/genetics ; Placenta/metabolism ; Pregnancy ; Promoter Regions, Genetic ; RNA, Untranslated/chemistry/genetics ; Regulatory Sequences, Nucleic Acid ; Retroelements ; Transcription Factors/metabolism ; Transduction, Genetic ; Vertebrates/*genetics/metabolism ; }, abstract = {Since their discovery, a growing body of evidence has emerged demonstrating that transposable elements are important drivers of species diversity. These mobile elements exhibit a great variety in structure, size and mechanisms of transposition, making them important putative actors in organism evolution. The vertebrates represent a highly diverse and successful lineage that has adapted to a wide range of different environments. These animals also possess a rich repertoire of transposable elements, with highly diverse content between lineages and even between species. Here, we review how transposable elements are driving genomic diversity and lineage-specific innovation within vertebrates. We discuss the large differences in TE content between different vertebrate groups and then go on to look at how they affect organisms at a variety of levels: from the structure of chromosomes to their involvement in the regulation of gene expression, as well as in the formation and evolution of non-coding RNAs and protein-coding genes. In the process of doing this, we highlight how transposable elements have been involved in the evolution of some of the key innovations observed within the vertebrate lineage, driving the group's diversity and success.}, }
@article {pmid26394708, year = {2016}, author = {Ward, BJ and van Oosterhout, C}, title = {HYBRIDCHECK: software for the rapid detection, visualization and dating of recombinant regions in genome sequence data.}, journal = {Molecular ecology resources}, volume = {16}, number = {2}, pages = {534-539}, doi = {10.1111/1755-0998.12469}, pmid = {26394708}, issn = {1755-0998}, mesh = {Computational Biology/*methods ; Genomics/*methods ; *Recombination, Genetic ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {HYBRIDCHECK is a software package to visualize the recombination signal in large DNA sequence data set, and it can be used to analyse recombination, genetic introgression, hybridization and horizontal gene transfer. It can scan large (multiple kb) contigs and whole-genome sequences of three or more individuals. HYBRIDCHECK is written in the r software for OS X, Linux and Windows operating systems, and it has a simple graphical user interface. In addition, the r code can be readily incorporated in scripts and analysis pipelines. HYBRIDCHECK implements several ABBA-BABA tests and visualizes the effects of hybridization and the resulting mosaic-like genome structure in high-density graphics. The package also reports the following: (i) the breakpoint positions, (ii) the number of mutations in each introgressed block, (iii) the probability that the identified region is not caused by recombination and (iv) the estimated age of each recombination event. The divergence times between the donor and recombinant sequence are calculated using a JC, K80, F81, HKY or GTR correction, and the dating algorithm is exceedingly fast. By estimating the coalescence time of introgressed blocks, it is possible to distinguish between hybridization and incomplete lineage sorting. HYBRIDCHECK is libré software and it and its manual are free to download from http://ward9250.github.io/HybridCheck/.}, }
@article {pmid26394010, year = {2016}, author = {Spencer, SJ and Tamminen, MV and Preheim, SP and Guo, MT and Briggs, AW and Brito, IL and A Weitz, D and Pitkänen, LK and Vigneault, F and Juhani Virta, MP and Alm, EJ}, title = {Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers.}, journal = {The ISME journal}, volume = {10}, number = {2}, pages = {427-436}, pmid = {26394010}, issn = {1751-7370}, support = {P30 ES002109/ES/NIEHS NIH HHS/United States ; P30-ES002109/ES/NIEHS NIH HHS/United States ; }, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; Bacterial Proteins/genetics ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Lakes/*microbiology ; Metagenomics ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Many microbial communities are characterized by high genetic diversity. 16S ribosomal RNA sequencing can determine community members, and metagenomics can determine the functional diversity, but resolving the functional role of individual cells in high throughput remains an unsolved challenge. Here, we describe epicPCR (Emulsion, Paired Isolation and Concatenation PCR), a new technique that links functional genes and phylogenetic markers in uncultured single cells, providing a throughput of hundreds of thousands of cells with costs comparable to one genomic library preparation. We demonstrate the utility of our technique in a natural environment by profiling a sulfate-reducing community in a freshwater lake, revealing both known sulfate reducers and discovering new putative sulfate reducers. Our method is adaptable to any conserved genetic trait and translates genetic associations from diverse microbial samples into a sequencing library that answers targeted ecological questions. Potential applications include identifying functional community members, tracing horizontal gene transfer networks and mapping ecological interactions between microbial cells.}, }
@article {pmid26391376, year = {2015}, author = {Goedbloed, DJ and van Hooft, P and Lutz, W and Megens, HJ and van Wieren, SE and Ydenberg, RC and Prins, HH}, title = {Increased Mycoplasma hyopneumoniae Disease Prevalence in Domestic Hybrids Among Free-Living Wild Boar.}, journal = {EcoHealth}, volume = {12}, number = {4}, pages = {571-579}, pmid = {26391376}, issn = {1612-9210}, mesh = {Animals ; Animals, Wild/*microbiology ; Chimera/*genetics ; Epidemiological Monitoring/*veterinary ; Gene Transfer, Horizontal ; Germany ; Mycoplasma hyopneumoniae/*isolation &amp; purification ; Netherlands ; Pneumonia of Swine, Mycoplasmal/*epidemiology ; Prevalence ; Sus scrofa/*microbiology ; Swine/*microbiology ; }, abstract = {Wildlife immune genes are subject to natural selection exerted by pathogens. In contrast, domestic immune genes are largely protected from pathogen selection by veterinary care. Introgression of domestic alleles into the wild could lead to increased disease susceptibility, but observations are scarce due to low introgression rates, low disease prevalence and reduced survival of domestic hybrids. Here we report the first observation of a deleterious effect of domestic introgression on disease prevalence in a free-living large mammal. A fraction of 462 randomly sampled free-living European wild boar (Sus scrofa) was genetically identified as recent wild boar-domestic pig hybrids based on 351 SNP data. Analysis of antibody prevalence against the bacterial pathogen Mycoplasma hyopneumoniae (Mhyo) showed an increased Mhyo prevalence in wild-domestic hybrids. We argue that the most likely mechanism explaining the observed association between domestic hybrid status and Mhyo antibody prevalence would be introgression of deleterious domestic alleles. We hypothesise that large-scale use of antibiotics in the swine breeding sector may have played a role in shaping the relatively deleterious properties of domestic swine immune genes and that domestic introgression may also lead to increased wildlife disease susceptibility in the case of other species.}, }
@article {pmid26389644, year = {2015}, author = {Rebersek, M and Marjanovic, I and Begus, S and Pillet, F and Rols, MP and Miklavcic, D and Kotnik, T}, title = {Generator and Setup for Emulating Exposures of Biological Samples to Lightning Strokes.}, journal = {IEEE transactions on bio-medical engineering}, volume = {62}, number = {10}, pages = {2535-2543}, doi = {10.1109/TBME.2015.2437359}, pmid = {26389644}, issn = {1558-2531}, mesh = {Bacillus/radiation effects ; Electricity ; Equipment Design ; Gene Transfer, Horizontal/*radiation effects ; *Lightning ; *Models, Theoretical ; Research/*instrumentation ; Sound ; Spores, Bacterial/*radiation effects ; }, abstract = {GOAL: We aimed to develop a system for controlled exposure of biological samples to conditions they experience when lightning strikes their habitats.<br><br>METHODS: We based the generator on a capacitor charged via a bridge rectifier and a dc-dc converter, and discharged via a relay, delivering arcs similar to natural lightning strokes in electric current waveform and similarly accompanied by acoustic shock waves. We coupled the generator to our exposure chamber described previously, measured electrical and acoustic properties of arc discharges delivered, and assessed their ability to inactivate bacterial spores.<br><br>RESULTS: Submicrosecond discharges descended vertically from the conical emitting electrode across the air gap, entering the sample centrally and dissipating radially toward the ring-shaped receiving electrode. In contrast, longer discharges tended to short-circuit the electrodes. Recording at 341 000 FPS with Vision Research Phantom v2010 camera revealed that initial arc descent was still vertical, but became accompanied by arcs leaning increasingly sideways; after 8-12 &#x3bc;s, as the first of these arcs formed direct contact with the receiving electrode, it evolved into a channel of plasmified air and short-circuited the electrodes. We eliminated this artefact by incorporating an insulating cylinder concentrically between the electrodes, precluding short-circuiting between them. While bacterial spores are highly resistant to electric pulses delivered through direct contact, we showed that with arc discharges accompanied by an acoustic shock wave, spore inactivation is readily obtained.<br><br>CONCLUSION: The presented system allows scientific investigation of effects of arc discharges on biological samples.<br><br>SIGNIFICANCE: This system will allow realistic experimental studies of lightning-triggered horizontal gene transfer and assessment of its role in evolution.}, }
@article {pmid26386745, year = {2016}, author = {Baraniak, A and Izdebski, R and Fiett, J and Gawryszewska, I and Bojarska, K and Herda, M and Literacka, E and Żabicka, D and Tomczak, H and Pewińska, N and Szarata, M and Ozorowski, T and Milner, A and Hryniewicz, W and Gniadkowski, M}, title = {NDM-producing Enterobacteriaceae in Poland, 2012-14: inter-regional outbreak of Klebsiella pneumoniae ST11 and sporadic cases.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {71}, number = {1}, pages = {85-91}, doi = {10.1093/jac/dkv282}, pmid = {26386745}, issn = {1460-2091}, mesh = {Adolescent ; Adult ; DNA, Bacterial/chemistry/genetics ; *Disease Outbreaks ; Female ; Gene Transfer, Horizontal ; Genotype ; Humans ; Klebsiella Infections/*epidemiology/*microbiology ; Klebsiella pneumoniae/classification/*enzymology/genetics/*isolation &amp; purification ; Male ; Middle Aged ; Molecular Typing ; Nucleic Acid Hybridization ; Plasmids/analysis ; Poland/epidemiology ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: The objective of this study was to characterize New Delhi metallo-β-lactamase (NDM)-producing Enterobacteriaceae isolates reported in Poland in 2012-14.<br><br>METHODS: Representative isolates were typed by PFGE and MLST. NDM and other &#x3b2;-lactamase genes were amplified and sequenced. Plasmids with blaNDM genes were analysed by nuclease S1 plus hybridization profiling, by transfer assays and by PCR-based replicon typing. The blaNDM genetic context was studied by PCR mapping assays.<br><br>RESULTS: Of 374 cases of infection/colonization with NDM-positive Enterobacteriaceae identified in 2012-14, 370 cases in 40 hospitals, 10 outpatient clinics and 1 nursing home were associated with a Klebsiella pneumoniae outbreak with epicentres in Pozna&#x144; and Warsaw. The outbreak strain of K. pneumoniae ST11 was similar to an isolate from the Czech Republic from 2013. Like the Czech strain, many of the isolates had two blaNDM-1-carrying IncFII- and IncR-type plasmids of variable size, sharing a blaNDM-1-containing segment. The early isolates also produced CTX-M-15 co-encoded by the IncR-type plasmids, and differentiated later by extensive plasmid rearrangements. Four other NDM cases were reported in 2013, three being associated with arrivals from Montenegro, India or Afghanistan. The Indian Escherichia coli ST448 NDM-5 isolate revealed similarity to a recent isolate from Spain, including the blaNDM genetic context observed previously in E. coli strains in Poland and France (of Congolese and Indian origins, respectively). The Afghani Proteus mirabilis was the second isolate of this species with a chromosomal blaNDM-1 location.<br><br>CONCLUSIONS: The largest NDM outbreak in a non-endemic country has been observed, being an alarming phenomenon in resistance epidemiology in Poland.}, }
@article {pmid26385192, year = {2015}, author = {Morrow, JL and Frommer, M and Royer, JE and Shearman, DC and Riegler, M}, title = {Wolbachia pseudogenes and low prevalence infections in tropical but not temperate Australian tephritid fruit flies: manifestations of lateral gene transfer and endosymbiont spillover?.}, journal = {BMC evolutionary biology}, volume = {15}, number = {}, pages = {202}, pmid = {26385192}, issn = {1471-2148}, mesh = {Animals ; Australia ; Cloning, Molecular ; Gene Transfer, Horizontal ; Haplotypes ; Multilocus Sequence Typing ; Phylogeny ; Pseudogenes ; Tephritidae/*classification/*microbiology/physiology ; Wolbachia/*genetics/*isolation &amp; purification/physiology ; }, abstract = {BACKGROUND: Maternally inherited Wolbachia bacteria infect many insect species. They can also be transferred horizontally into uninfected host lineages. A Wolbachia spillover from an infected source population must occur prior to the establishment of heritable infections, but this spillover may be transient. In a previous study of tephritid fruit fly species of tropical Australia we detected a high incidence of identical Wolbachia strains in several species as well as Wolbachia pseudogenes. Here, we have investigated this further by analysing field specimens of 24 species collected along a 3,000 km climate gradient of eastern Australia.<br><br>RESULTS: Wolbachia sequences were detected in individuals of nine of the 24 (37 %) species. Seven (29 %) species displayed four distinct Wolbachia strains based on characterisation of full multi locus sequencing (MLST) profiles; the strains occurred as single and double infections in a small number of individuals (2-17 %). For the two remaining species all individuals had incomplete MLST profiles and Wolbachia pseudogenes that may be indicative of lateral gene transfer into host genomes. The detection of Wolbachia was restricted to northern Australia, including in five species that only occur in the tropics. Within the more widely distributed Bactrocera tryoni and Bactrocera neohumeralis, Wolbachia also only occurred in the north, and was not linked to any particular mitochondrial haplotypes.<br><br>CONCLUSIONS: The presence of Wolbachia pseudogenes at high prevalence in two species in absence of complete MLST profiles may represent footprints of historic infections that have been lost. The detection of identical low prevalence strains in a small number of individuals of seven species may question their role as reproductive manipulator and their vertical inheritance. Instead, the findings may be indicative of transient infections that result from spillover events from a yet unknown source. These spillover events appear to be restricted to northern Australia, without proliferation in host lineages further south. Our study highlights that tropical fruit fly communities contain Wolbachia pseudogenes and may be exposed to frequent horizontal Wolbachia transfer. It also emphasises that global estimates of Wolbachia frequencies may need to consider lateral gene transfer and Wolbachia spillover that may be regionally restricted, transient and not inherited.}, }
@article {pmid26383090, year = {2015}, author = {Drakos, NE and Wahl, LM}, title = {Extinction probabilities and stationary distributions of mobile genetic elements in prokaryotes: The birth-death-diversification model.}, journal = {Theoretical population biology}, volume = {106}, number = {}, pages = {22-31}, doi = {10.1016/j.tpb.2015.09.001}, pmid = {26383090}, issn = {1096-0325}, mesh = {Bacteria/genetics ; Computer Simulation ; *Extinction, Biological ; Gene Transfer, Horizontal ; Genome ; *Interspersed Repetitive Sequences ; Markov Chains ; *Models, Genetic ; Prokaryotic Cells/*physiology ; Promoter Regions, Genetic ; }, abstract = {Theoretical approaches are essential to our understanding of the complex dynamics of mobile genetic elements (MGEs) within genomes. Recently, the birth-death-diversification model was developed to describe the dynamics of mobile promoters (MPs), a particular class of MGEs in prokaryotes. A unique feature of this model is that genetic diversification of elements was included. To explore the implications of diversification on the longterm fate of MGE lineages, in this contribution we analyze the extinction probabilities, extinction times and equilibrium solutions of the birth-death-diversification model. We find that diversification increases both the survival and growth rate of MGE families, but the strength of this effect depends on the rate of horizontal gene transfer (HGT). We also find that the distribution of MGE families per genome is not necessarily monotonically decreasing, as observed for MPs, but may have a peak in the distribution that is related to the HGT rate. For MPs specifically, we find that new families have a high extinction probability, and predict that the number of MPs is increasing, albeit at a very slow rate. Additionally, we develop an extension of the birth-death-diversification model which allows MGEs in different regions of the genome, for example coding and non-coding, to be described by different rates. This extension may offer a potential explanation as to why the majority of MPs are located in non-promoter regions of the genome.}, }
@article {pmid26379286, year = {2015}, author = {Gasmi, L and Boulain, H and Gauthier, J and Hua-Van, A and Musset, K and Jakubowska, AK and Aury, JM and Volkoff, AN and Huguet, E and Herrero, S and Drezen, JM}, title = {Recurrent Domestication by Lepidoptera of Genes from Their Parasites Mediated by Bracoviruses.}, journal = {PLoS genetics}, volume = {11}, number = {9}, pages = {e1005470}, pmid = {26379286}, issn = {1553-7404}, mesh = {Animals ; Base Sequence ; DNA, Viral ; *Genes, Insect ; Lepidoptera/*parasitology ; Molecular Sequence Data ; Polydnaviridae/genetics/*physiology ; Spodoptera/genetics ; Wasps/*genetics ; }, abstract = {Bracoviruses are symbiotic viruses associated with tens of thousands of species of parasitic wasps that develop within the body of lepidopteran hosts and that collectively parasitize caterpillars of virtually every lepidopteran species. Viral particles are produced in the wasp ovaries and injected into host larvae with the wasp eggs. Once in the host body, the viral DNA circles enclosed in the particles integrate into lepidopteran host cell DNA. Here we show that bracovirus DNA sequences have been inserted repeatedly into lepidopteran genomes, indicating this viral DNA can also enter germline cells. The original mode of Horizontal Gene Transfer (HGT) unveiled here is based on the integrative properties of an endogenous virus that has evolved as a gene transfer agent within parasitic wasp genomes for ≈100 million years. Among the bracovirus genes thus transferred, a phylogenetic analysis indicated that those encoding C-type-lectins most likely originated from the wasp gene set, showing that a bracovirus-mediated gene flux exists between the 2 insect orders Hymenoptera and Lepidoptera. Furthermore, the acquisition of bracovirus sequences that can be expressed by Lepidoptera has resulted in the domestication of several genes that could result in adaptive advantages for the host. Indeed, functional analyses suggest that two of the acquired genes could have a protective role against a common pathogen in the field, baculovirus. From these results, we hypothesize that bracovirus-mediated HGT has played an important role in the evolutionary arms race between Lepidoptera and their pathogens.}, }
@article {pmid26377943, year = {2016}, author = {Halmillawewa, AP and Restrepo-Córdoba, M and Perry, BJ and Yost, CK and Hynes, MF}, title = {Characterization of the temperate phage vB_RleM_PPF1 and its site-specific integration into the Rhizobium leguminosarum F1 genome.}, journal = {Molecular genetics and genomics : MGG}, volume = {291}, number = {1}, pages = {349-362}, pmid = {26377943}, issn = {1617-4623}, mesh = {Bacteriophages/*genetics ; Base Composition/genetics ; Base Sequence ; DNA, Viral/*genetics ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial/*genetics ; Genome, Viral/genetics ; Lysogeny/genetics ; Molecular Sequence Data ; Open Reading Frames/genetics ; Phylogeny ; RNA, Transfer/genetics ; Rhizobium leguminosarum/*genetics/*virology ; Sequence Analysis, DNA/methods ; Sequence Homology ; Viral Proteins/*genetics ; }, abstract = {Bacteriophages may play an important role in regulating population size and diversity of the root nodule symbiont Rhizobium leguminosarum, as well as participating in horizontal gene transfer. Although phages that infect this species have been isolated in the past, our knowledge of their molecular biology, and especially of genome composition, is extremely limited, and this lack of information impacts on the ability to assess phage population dynamics and limits potential agricultural applications of rhizobiophages. To help address this deficit in available sequence and biological information, the complete genome sequence of the Myoviridae temperate phage PPF1 that infects R. leguminosarum biovar viciae strain F1 was determined. The genome is 54,506 bp in length with an average G+C content of 61.9 %. The genome contains 94 putative open reading frames (ORFs) and 74.5 % of these predicted ORFs share homology at the protein level with previously reported sequences in the database. However, putative functions could only be assigned to 25.5 % (24 ORFs) of the predicted genes. PPF1 was capable of efficiently lysogenizing its rhizobial host R. leguminosarum F1. The site-specific recombination system of the phage targets an integration site that lies within a putative tRNA-Pro (CGG) gene in R. leguminosarum F1. Upon integration, the phage is capable of restoring the disrupted tRNA gene, owing to the 50 bp homologous sequence (att core region) it shares with its rhizobial host genome. Phage PPF1 is the first temperate phage infecting members of the genus Rhizobium for which a complete genome sequence, as well as other biological data such as the integration site, is available.}, }
@article {pmid26377866, year = {2015}, author = {Anastasi, E and Giguère, S and Berghaus, LJ and Hondalus, MK and Willingham-Lane, JM and MacArthur, I and Cohen, ND and Roberts, MC and Vazquez-Boland, JA}, title = {Novel transferable erm(46) determinant responsible for emerging macrolide resistance in Rhodococcus equi.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {70}, number = {12}, pages = {3184-3190}, doi = {10.1093/jac/dkv279}, pmid = {26377866}, issn = {1460-2091}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Actinomycetales Infections/microbiology/veterinary ; Animals ; Animals, Newborn ; Anti-Bacterial Agents/*pharmacology ; Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; *Drug Resistance, Bacterial ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Horse Diseases/microbiology ; Horses ; Lincosamides/pharmacology ; Macrolides/*pharmacology ; Rhodococcus equi/*drug effects/*genetics/isolation &amp; purification ; Sequence Analysis, DNA ; Streptogramin B/pharmacology ; United States ; }, abstract = {OBJECTIVES: The objective of this study was to identify the molecular mechanism of macrolide resistance in the actinomycete Rhodococcus equi, a major equine pathogen and zoonotic agent causing opportunistic infections in people.<br><br>METHODS: Macrolide-resistant (n&#x200a;=&#x200a;62) and macrolide-susceptible (n&#x200a;=&#x200a;62) clinical isolates of R. equi from foals in the USA were studied. WGS of 18 macrolide-resistant and 6 macrolide-susceptible R. equi was performed. Representative sequences of all known macrolide resistance genes identified to date were used to search the genome assemblies for putative homologues. PCR was used to screen for the presence of the identified resistance determinant in the rest of the isolates. Mating experiments were performed to verify mobility of the gene.<br><br>RESULTS: A novel erm gene, erm(46), was identified in all sequenced resistant isolates, but not in susceptible isolates. There was complete association between macrolide resistance and the presence of erm(46) as detected by PCR screening of all 124 clinical isolates of R. equi. Expression of erm(46) in a macrolide-susceptible strain of R. equi induced high-level resistance to macrolides, lincosamides and streptogramins B, but not to other classes of antimicrobial agents. Transfer of erm(46) to macrolide-susceptible R. equi was confirmed. The transfer frequency ranged from 3&#x200a;&#xd7;&#x200a;10(-3) to 1&#x200a;&#xd7;&#x200a;10(-2).<br><br>CONCLUSIONS: This is the first molecular characterization of resistance to macrolides, lincosamides and streptogramins B in R. equi. Resistance was due to the presence of a novel erm(46) gene mobilizable likely by conjugation, which has spread among equine isolates of R. equi in the USA.}, }
@article {pmid26377567, year = {2015}, author = {Luan, JB and Chen, W and Hasegawa, DK and Simmons, AM and Wintermantel, WM and Ling, KS and Fei, Z and Liu, SS and Douglas, AE}, title = {Metabolic Coevolution in the Bacterial Symbiosis of Whiteflies and Related Plant Sap-Feeding Insects.}, journal = {Genome biology and evolution}, volume = {7}, number = {9}, pages = {2635-2647}, pmid = {26377567}, issn = {1759-6653}, mesh = {Animals ; Enterobacteriaceae/*genetics/metabolism ; *Evolution, Molecular ; Gene Duplication ; Genome, Insect ; Halomonadaceae/*genetics/metabolism ; Hemiptera/*genetics/metabolism/*microbiology ; Metabolic Networks and Pathways/genetics ; Symbiosis/*genetics ; Transcriptome ; }, abstract = {Genomic decay is a common feature of intracellular bacteria that have entered into symbiosis with plant sap-feeding insects. This study of the whitefly Bemisia tabaci and two bacteria (Portiera aleyrodidarum and Hamiltonella defensa) cohoused in each host cell investigated whether the decay of Portiera metabolism genes is complemented by host and Hamiltonella genes, and compared the metabolic traits of the whitefly symbiosis with other sap-feeding insects (aphids, psyllids, and mealybugs). Parallel genomic and transcriptomic analysis revealed that the host genome contributes multiple metabolic reactions that complement or duplicate Portiera function, and that Hamiltonella may contribute multiple cofactors and one essential amino acid, lysine. Homologs of the Bemisia metabolism genes of insect origin have also been implicated in essential amino acid synthesis in other sap-feeding insect hosts, indicative of parallel coevolution of shared metabolic pathways across multiple symbioses. Further metabolism genes coded in the Bemisia genome are of bacterial origin, but phylogenetically distinct from Portiera, Hamiltonella and horizontally transferred genes identified in other sap-feeding insects. Overall, 75% of the metabolism genes of bacterial origin are functionally unique to one symbiosis, indicating that the evolutionary history of metabolic integration in these symbioses is strongly contingent on the pattern of horizontally acquired genes. Our analysis, further, shows that bacteria with genomic decay enable host acquisition of complex metabolic pathways by multiple independent horizontal gene transfers from exogenous bacteria. Specifically, each horizontally acquired gene can function with other genes in the pathway coded by the symbiont, while facilitating the decay of the symbiont gene coding the same reaction.}, }
@article {pmid26376473, year = {2016}, author = {Soares, SC and Geyik, H and Ramos, RT and de Sá, PH and Barbosa, EG and Baumbach, J and Figueiredo, HC and Miyoshi, A and Tauch, A and Silva, A and Azevedo, V}, title = {GIPSy: Genomic island prediction software.}, journal = {Journal of biotechnology}, volume = {232}, number = {}, pages = {2-11}, doi = {10.1016/j.jbiotec.2015.09.008}, pmid = {26376473}, issn = {1873-4863}, mesh = {Escherichia coli/genetics ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial/*genetics ; Genomic Islands/*genetics ; Genomics/*methods ; *Software ; }, abstract = {Bacteria are highly diverse organisms that are able to adapt to a broad range of environments and hosts due to their high genomic plasticity. Horizontal gene transfer plays a pivotal role in this genome plasticity and in evolution by leaps through the incorporation of large blocks of genome sequences, ordinarily known as genomic islands (GEIs). GEIs may harbor genes encoding virulence, metabolism, antibiotic resistance and symbiosis-related functions, namely pathogenicity islands (PAIs), metabolic islands (MIs), resistance islands (RIs) and symbiotic islands (SIs). Although many software for the prediction of GEIs exist, they only focus on PAI prediction and present other limitations, such as complicated installation and inconvenient user interfaces. Here, we present GIPSy, the genomic island prediction software, a standalone and user-friendly software for the prediction of GEIs, built on our previously developed pathogenicity island prediction software (PIPS). We also present four application cases in which we crosslink data from literature to PAIs, MIs, RIs and SIs predicted by GIPSy. Briefly, GIPSy correctly predicted the following previously described GEIs: 13 PAIs larger than 30kb in Escherichia coli CFT073; 1 MI for Burkholderia pseudomallei K96243, which seems to be a miscellaneous island; 1 RI of Acinetobacter baumannii AYE, named AbaR1; and, 1 SI of Mesorhizobium loti MAFF303099 presenting a mosaic structure. GIPSy is the first life-style-specific genomic island prediction software to perform analyses of PAIs, MIs, RIs and SIs, opening a door for a better understanding of bacterial genome plasticity and the adaptation to new traits.}, }
@article {pmid26374754, year = {2015}, author = {Pascuan, C and Fox, AR and Soto, G and Ayub, ND}, title = {Exploring the Ancestral Mechanisms of Regulation of Horizontally Acquired Nitrogenases.}, journal = {Journal of molecular evolution}, volume = {81}, number = {3-4}, pages = {84-89}, pmid = {26374754}, issn = {1432-1432}, mesh = {Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; Nitrogen Fixation/genetics ; Nitrogenase/biosynthesis/*genetics ; Phylogeny ; Pseudomonas/*enzymology/genetics ; Pseudomonas stutzeri/enzymology/genetics ; }, abstract = {The vast majority of Pseudomonas species are unable to fix atmospheric nitrogen. Although several studies have demonstrated that some strains belonging to the genus Pseudomonas sensu stricto do have the ability to fix nitrogen by the expression of horizontally acquired nitrogenase, little is known about the mechanisms of nitrogenase adaptation to the new bacterial host. Recently, we transferred the nitrogen fixation island from Pseudomonas stutzeri A1501 to the non-nitrogen-fixing bacterium Pseudomonas protegens Pf-5, and interestingly, the resulting recombinant strain Pf-5 X940 showed an uncommon phenotype of constitutive nitrogenase activity. Here, we integrated evolutionary and functional approaches to elucidate this unusual phenotype. Phylogenetic analysis showed that polyhydroxybutyrate (PHB) biosynthesis genes from natural nitrogen-fixing Pseudomonas strains have been acquired by horizontal transfer. Contrary to Pf-5 X940, its derived PHB-producing strain Pf-5 X940-PHB exhibited the inhibition of nitrogenase activity under nitrogen-excess conditions, and displayed the typical switch-on phenotype observed in natural nitrogen-fixing strains after nitrogen deficiency. This indicates a competition between PHB production and nitrogen fixation. Therefore, we propose that horizontal transfer of PHB biosynthesis genes could be an ancestral mechanism of regulation of horizontally acquired nitrogenases in the genus Pseudomonas.}, }
@article {pmid26374538, year = {2015}, author = {Scheid, P}, title = {Viruses in close associations with free-living amoebae.}, journal = {Parasitology research}, volume = {114}, number = {11}, pages = {3959-3967}, pmid = {26374538}, issn = {1432-1955}, mesh = {Amoeba/ultrastructure/*virology ; Biological Evolution ; Cytoplasm/virology ; DNA Viruses/*genetics/ultrastructure ; Genome, Viral/*genetics ; Mimiviridae/genetics ; Phylogeny ; }, abstract = {As both groups of organisms, free-living amoebae (FLA) and viruses, can be found in aquatic environments side by side, it appears obvious that there are multiple interactions with respect to host-endocytobiont relationships. Several relationships between viruses and protozoan hosts are described and it was the discovery of the so called "giant viruses," associated with amoebae, which gave another dimension to these interactions. Mimiviruses, Pandoraviruses and Pithoviruses are examples for interesting viral endocytobionts within FLA. In the Mimivirus viral factories, viral DNA undergoes replication and transcription, and the DNA is prepared to be packed in procapsids. Theses Mimivirus factories can be considered as efficient "production lines" where, at any given moment, all stages of viral generation including membrane biogenesis, capsid assembly and genome encapsidation, are occurring concomitantly. There are some hints that similar replication factories are involved as well during the Pandoravirus development. Some scientists favour the assumption that the giant viruses have received many of their genes from their hosts or from sympatric occurring endocytobionts via lateral gene transfer. This hypothesis would mean that this type of transfer has been an important process in the evolution of genomes in the context of the intracellular parasitic or endocytobiotic lifestyle. In turn, that would migitate against hypothesizing development of a new branch in the tree of life. Based on the described scenarios to explain the presence of genes related to translation, it is also possible that earlier ancestors of today's DNA viruses were involved in the origin of eukaryotes. That possibly could in turn support the idea that cellular organisms could have evolved from viruses with growing autarkic properties. In future we expect the discovery of further (giant) viruses within free-living amoebae and other protozoa through genomic, transcriptomic and proteomic analyses.}, }
@article {pmid26371554, year = {2015}, author = {Sayavedra, L and Kleiner, M and Ponnudurai, R and Wetzel, S and Pelletier, E and Barbe, V and Satoh, N and Shoguchi, E and Fink, D and Breusing, C and Reusch, TB and Rosenstiel, P and Schilhabel, MB and Becher, D and Schweder, T and Markert, S and Dubilier, N and Petersen, JM}, title = {Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels.}, journal = {eLife}, volume = {4}, number = {}, pages = {e07966}, pmid = {26371554}, issn = {2050-084X}, mesh = {Animals ; Aquatic Organisms/*microbiology ; Bacteria/*genetics/growth &amp; development ; Bacterial Toxins/biosynthesis/*genetics ; Bivalvia/*microbiology ; DNA, Bacterial/chemistry/genetics ; Gene Expression Profiling ; Genome, Bacterial ; *Hydrothermal Vents ; Molecular Sequence Data ; Proteome/analysis ; Seawater ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {Bathymodiolus mussels live in symbiosis with intracellular sulfur-oxidizing (SOX) bacteria that provide them with nutrition. We sequenced the SOX symbiont genomes from two Bathymodiolus species. Comparison of these symbiont genomes with those of their closest relatives revealed that the symbionts have undergone genome rearrangements, and up to 35% of their genes may have been acquired by horizontal gene transfer. Many of the genes specific to the symbionts were homologs of virulence genes. We discovered an abundant and diverse array of genes similar to insecticidal toxins of nematode and aphid symbionts, and toxins of pathogens such as Yersinia and Vibrio. Transcriptomics and proteomics revealed that the SOX symbionts express the toxin-related genes (TRGs) in their hosts. We hypothesize that the symbionts use these TRGs in beneficial interactions with their host, including protection against parasites. This would explain why a mutualistic symbiont would contain such a remarkable 'arsenal' of TRGs.}, }
@article {pmid26368006, year = {2015}, author = {Hill, KK and Xie, G and Foley, BT and Smith, TJ}, title = {Genetic diversity within the botulinum neurotoxin-producing bacteria and their neurotoxins.}, journal = {Toxicon : official journal of the International Society on Toxinology}, volume = {107}, number = {Pt A}, pages = {2-8}, doi = {10.1016/j.toxicon.2015.09.011}, pmid = {26368006}, issn = {1879-3150}, support = {U01 AI056493/AI/NIAID NIH HHS/United States ; }, mesh = {Botulinum Toxins/*genetics/metabolism ; Botulinum Toxins, Type A/genetics ; Clostridium botulinum/*genetics/metabolism ; Genes, Bacterial/genetics ; Genetic Variation ; Genome, Bacterial/genetics ; }, abstract = {The recent availability of multiple Clostridium botulinum genomic sequences has initiated a new genomics era that strengthens our understanding of the bacterial species that produce botulinum neurotoxins (BoNTs). Analysis of the genomes has reinforced the historical Group I-VI designations and provided evidence that the bont genes can be located within the chromosome, phage or plasmids. The sequences provide the opportunity to examine closely the variation among the toxin genes, the composition and organization of the toxin complex, the regions flanking the toxin complex and the location of the toxin within different bacterial strains. These comparisons provide evidence of horizontal gene transfer and site-specific insertion and recombination events that have contributed to the variation observed among the neurotoxins. Here, examples that have contributed to the variation observed in serotypes A-H strains are presented to illustrate the mechanisms that have contributed to their variation.}, }
@article {pmid26362924, year = {2015}, author = {Li, Z and Chang, S and Ye, S and Chen, M and Lin, L and Li, Y and Li, S and An, Q}, title = {Differentiation of 1-aminocyclopropane-1-carboxylate (ACC) deaminase from its homologs is the key for identifying bacteria containing ACC deaminase.}, journal = {FEMS microbiology ecology}, volume = {91}, number = {10}, pages = {}, doi = {10.1093/femsec/fiv112}, pmid = {26362924}, issn = {1574-6941}, mesh = {Actinobacteria/*classification/enzymology/genetics ; Amino Acid Sequence ; Carbon-Carbon Lyases/*genetics ; DNA Primers/genetics ; Ethylenes/metabolism ; Molecular Sequence Data ; Phylogeny ; *Plant Development ; Plants/*microbiology ; Polymerase Chain Reaction ; Proteobacteria/*classification/enzymology/genetics ; }, abstract = {1-Aminocyclopropane-1-carboxylate (ACC) deaminase-mediated reduction of ethylene generation in plants under abiotic stresses is a key mechanism by which bacteria can promote plant growth. Misidentification of ACC deaminase and the ACC deaminase structure gene (acdS) can lead to overestimation of the number of bacteria containing ACC deaminase and their function in ecosystems. Previous non-specific amplification of acdS homologs has led to an overestimation of the horizontal transfer of acdS genes. Here, we designed consensus-degenerate hybrid oligonucleotide primers (acdSf3, acdSr3 and acdSr4) based on differentiating the key residues in ACC deaminases from those of homologs for specific amplification of partial acdS genes. PCR amplification, sequencing and phylogenetic analysis identified acdS genes from a wide range of proteobacteria and actinobacteria. PCR amplification and a genomic search did not find the acdS gene in bacteria belonging to Pseudomonas stutzeri or in the genera Enterobacter, Klebsiella or Bacillus. We showed that differentiating the acdS gene and ACC deaminase from their homologs was crucial for the molecular identification of bacteria containing ACC deaminase and for understanding the evolution of the acdS gene. We provide an effective method for screening and identifying bacteria containing ACC deaminase.}, }
@article {pmid26362160, year = {2016}, author = {Nongkhlaw, FM and Joshi, SR}, title = {Horizontal Gene Transfer of the Non-ribosomal Peptide Synthetase Gene Among Endophytic and Epiphytic Bacteria Associated with Ethnomedicinal Plants.}, journal = {Current microbiology}, volume = {72}, number = {1}, pages = {1-11}, pmid = {26362160}, issn = {1432-0991}, mesh = {Bacteria/classification/*enzymology/*genetics ; Base Composition ; Cluster Analysis ; Codon ; DNA, Ribosomal/chemistry/genetics ; Endophytes/enzymology/genetics ; *Gene Transfer, Horizontal ; Peptide Synthases/*genetics ; Phylogeny ; Plants, Medicinal/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {This study genetically screened endophytic and epiphytic bacteria associated with ethnomedicinal plants for the presence of the non-ribosomal peptide synthetase (NRPS) gene and identified horizontal gene transfer (HGT) of the NRPS gene between the bacterial species. NRPSs are large multimodular enzymes that synthesize a wide range of biologically active natural compounds that are pharmacologically important. Twenty-nine plant-associated culturable bacteria were screened for the presence of the NRPS gene, of which seven bacterial NRPS gene fragments were successfully detected. According to our findings the presence of NRPS gene among the isolates does not always equate to their antagonistic ability. Phylogenetic analysis of the NRPS and 16S rRNA-encoding genes was used to predict HGT that may have occurred during gene evolution. The occurrence of HGT was demonstrated in the isolates (one inter-phylum and four intra-phyla) and was supported by phylogenetic analysis, mol% G+C content, and tetranucleotide usage pattern and codon usage frequency. Among the four intra-phyla HGT, one isolate showed inter-class HGT and three other isolates showed intra-class HGT.}, }
@article {pmid26361395, year = {2015}, author = {Upadhyay, S and Hussain, A and Mishra, S and Maurya, AP and Bhattacharjee, A and Joshi, SR}, title = {Genetic Environment of Plasmid Mediated CTX-M-15 Extended Spectrum Beta-Lactamases from Clinical and Food Borne Bacteria in North-Eastern India.}, journal = {PloS one}, volume = {10}, number = {9}, pages = {e0138056}, pmid = {26361395}, issn = {1932-6203}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Typing Techniques ; Cross Infection/*microbiology ; Food Microbiology ; Gene Transfer, Horizontal ; Gram-Negative Bacteria/classification/drug effects/genetics/*isolation &amp; purification ; Gram-Negative Bacterial Infections/*microbiology ; Humans ; India ; Microbial Sensitivity Tests ; Multiplex Polymerase Chain Reaction ; Plasmids/*genetics ; Prevalence ; beta-Lactamases/*genetics ; }, abstract = {BACKGROUND: The study investigated the presence of CTX-M-15 type extended spectrum beta-lactamases (ESBL), compared their genetic arrangements and plasmid types in gram negative isolates of hospital and food origin in north-east India. From September 2013 to April 2014, a total of 252 consecutive, non-duplicate clinical isolates and 88 gram negative food isolates were selected. Phenotypic and molecular characterization of ESBL genes was performed. Presence of integrons and gene cassettes were analyzed by integrase and 59 base-element PCR respectively. The molecular environments surrounding blaCTX-M and plasmid types were investigated by PCR and PCR-based replicon typing respectively. Transformation was carried out to assess plasmid transfer. Southern blotting was conducted to localize the blaCTX-M-15 genes. DNA fingerprinting was performed by ERIC-PCR.<br><br>RESULTS: Prevalence of ESBL was found to be 40.8% (103/252) in clinical and 31.8% (28/88) in food-borne isolates. Molecular characterization revealed the presence of 56.3% (58/103) and 53.5% (15/28) blaCTX-M-15 in clinical and food isolates respectively. Strains of clinical and food origin were non-clonal. Replicon typing revealed that IncI1 and IncFII plasmid were carrying blaCTX-M-15 in clinical and food isolates and were horizontally transferable. The ISEcp1 element was associated with blaCTX-M-15 in both clinical and food isolates.<br><br>CONCLUSIONS: The simultaneous presence of resistance determinants in non-clonal isolates of two different groups thus suggests that the microbiota of common food products consumed may serve as a reservoir for some of the drug resistance genes prevalent in human pathogens.}, }
@article {pmid26358917, year = {2015}, author = {Rydzewski, K and Tlapák, H and Niehaus, IP and Dabrowski, PW and Grunow, R and Heuner, K}, title = {Identification and characterization of episomal forms of integrative genomic islands in the genus Francisella.}, journal = {International journal of medical microbiology : IJMM}, volume = {305}, number = {8}, pages = {874-880}, doi = {10.1016/j.ijmm.2015.08.037}, pmid = {26358917}, issn = {1618-0607}, mesh = {Escherichia coli/genetics ; Francisella/*genetics ; *Genomic Islands ; Integrases/genetics/metabolism ; Interspersed Repetitive Sequences ; *Plasmids ; Prophages/genetics ; RNA, Transfer, Val/genetics ; Recombination, Genetic ; }, abstract = {Recently, we identified a putative prophage on a genomic island (GI) within the genome sequence of Francisella hispaniensis isolate AS0-814 (Francisella tularensis subsp. novicida-like 3523) by the analysis of the CRISPR-Cas systems of Francisella. Various spacer DNAs within the CRISPR region of different F. tularensis subsp. novicida strains were found to be homologous to the putative prophage (Schunder et al., 2013, Int. J. Med. Microbiol. 303:51-60). Now we identified the GI (FhaGI-1) as a mobile element which is able to form a circular episomal structure. The circular episomal form of FhaGI-1 is generated by F. hispaniensis, and the excision of the island is an integrase-dependent and site-specific process. Furthermore, we could demonstrate that the excision of the island is also possible in other bacterial species (Escherichia coli). In addition, we could show that a genetically generated small variant of the island is also functional and, after its electroporation into strain F. tularensis subsp. holarctica LVS, the GI was stable and site-specifically integrated into the genome of the transformants. The integrase is sufficient for the integration and excision of the small variant into and from the DNA backbone, respectively. Thus, the element may be suitable to be used as a genetic tool in F. tularensis research. Furthermore, we identified the tRNA(Val) gene of Francisella as an integration site for GIs. Genomic island FphGI-1 was identified in Francisella philomiragia ATCC 25016. We were not able to detect the episomal form of this GI, probably due to a mutated attR site. However, we could demonstrate that integrative GIs are present in Francisella and that they may allow horizontal gene transfer between different Francisella species.}, }
@article {pmid26356096, year = {2015}, author = {Berglund, B}, title = {Environmental dissemination of antibiotic resistance genes and correlation to anthropogenic contamination with antibiotics.}, journal = {Infection ecology &amp; epidemiology}, volume = {5}, number = {}, pages = {28564}, pmid = {26356096}, issn = {2000-8686}, abstract = {Antibiotic resistance is a growing problem which threatens modern healthcare globally. Resistance has traditionally been viewed as a clinical problem, but recently non-clinical environments have been highlighted as an important factor in the dissemination of antibiotic resistance genes (ARGs). Horizontal gene transfer (HGT) events are likely to be common in aquatic environments; integrons in particular are well suited for mediating environmental dissemination of ARGs. A growing body of evidence suggests that ARGs are ubiquitous in natural environments. Particularly, elevated levels of ARGs and integrons in aquatic environments are correlated to proximity to anthropogenic activities. The source of this increase is likely to be routine discharge of antibiotics and resistance genes, for example, via wastewater or run-off from livestock facilities and agriculture. While very high levels of antibiotic contamination are likely to select for resistant bacteria directly, the role of sub-inhibitory concentrations of antibiotics in environmental antibiotic resistance dissemination remains unclear. In vitro studies have shown that low levels of antibiotics can select for resistant mutants and also facilitate HGT, indicating the need for caution. Overall, it is becoming increasingly clear that the environment plays an important role in dissemination of antibiotic resistance; further studies are needed to elucidate key aspects of this process. Importantly, the levels of environmental antibiotic contamination at which resistant bacteria are selected for and HGT is facilitated at should be determined. This would enable better risk analyses and facilitate measures for preventing dissemination and development of antibiotic resistance in the environment.}, }
@article {pmid26355747, year = {2015}, author = {Markova, DN and Mason-Gamer, RJ}, title = {The Role of Vertical and Horizontal Transfer in the Evolutionary Dynamics of PIF-Like Transposable Elements in Triticeae.}, journal = {PloS one}, volume = {10}, number = {9}, pages = {e0137648}, pmid = {26355747}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Cloning, Molecular ; *DNA Transposable Elements ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Open Reading Frames ; Phylogeny ; Poaceae/*genetics ; Protein Interaction Domains and Motifs ; Sequence Alignment ; Transposases/chemistry/genetics ; }, abstract = {PIF-like transposable elements are members of the PIF/Harbinger superfamily of DNA transposons found in the genomes of many plants, animals, and fungi. The evolution of the gene that encodes the transposase responsible for mobilizing PIF-like elements has been studied in both plants and animals, but the elements' history in flowering plants remains poorly known. In this work, we describe the phylogenetic distribution and evolution of PIF-like elements in the genomes of 21 diploid species from the wheat tribe, Triticeae, and we present the first convincing evidence of horizontal transfer of PIF elements in plant genomes. A phylogenetic analysis of 240 PIF sequences based on the conserved region of the transposase domain revealed at least four main transposase lineages. Their complex evolutionary history can be best explained by a combination of vertical transmission with differential evolutionary success among lineages, and occasional horizontal transfer between phylogenetically distant Triticeae genera. In addition, we identified 127 potentially functional transposase sequences indicating possible recent activity of PIF.}, }
@article {pmid26351664, year = {2015}, author = {Legendre, M and Lartigue, A and Bertaux, L and Jeudy, S and Bartoli, J and Lescot, M and Alempic, JM and Ramus, C and Bruley, C and Labadie, K and Shmakova, L and Rivkina, E and Couté, Y and Abergel, C and Claverie, JM}, title = {In-depth study of Mollivirus sibericum, a new 30,000-y-old giant virus infecting Acanthamoeba.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {38}, pages = {E5327-35}, pmid = {26351664}, issn = {1091-6490}, mesh = {Acanthamoeba/*virology ; Acanthamoeba castellanii/virology ; Biological Evolution ; Cloning, Molecular ; Computational Biology ; DNA Replication ; Gene Library ; Gene Transfer, Horizontal ; Genome, Viral ; Genomics ; Global Warming ; Mass Spectrometry ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Molecular Sequence Data ; Multigene Family ; Permafrost ; Phylogeny ; Proteome ; Proteomics/methods ; Sequence Analysis, DNA ; Viral Proteins/genetics ; Virion/genetics ; Viruses/*genetics ; }, abstract = {Acanthamoeba species are infected by the largest known DNA viruses. These include icosahedral Mimiviruses, amphora-shaped Pandoraviruses, and Pithovirus sibericum, the latter one isolated from 30,000-y-old permafrost. Mollivirus sibericum, a fourth type of giant virus, was isolated from the same permafrost sample. Its approximately spherical virion (0.6-µm diameter) encloses a 651-kb GC-rich genome encoding 523 proteins of which 64% are ORFans; 16% have their closest homolog in Pandoraviruses and 10% in Acanthamoeba castellanii probably through horizontal gene transfer. The Mollivirus nucleocytoplasmic replication cycle was analyzed using a combination of "omic" approaches that revealed how the virus highjacks its host machinery to actively replicate. Surprisingly, the host's ribosomal proteins are packaged in the virion. Metagenomic analysis of the permafrost sample uncovered the presence of both viruses, yet in very low amount. The fact that two different viruses retain their infectivity in prehistorical permafrost layers should be of concern in a context of global warming. Giant viruses' diversity remains to be fully explored.}, }
@article {pmid26348789, year = {2016}, author = {Lajoie, MJ and Söll, D and Church, GM}, title = {Overcoming Challenges in Engineering the Genetic Code.}, journal = {Journal of molecular biology}, volume = {428}, number = {5 Pt B}, pages = {1004-1021}, pmid = {26348789}, issn = {1089-8638}, support = {R01 GM022854/GM/NIGMS NIH HHS/United States ; R37 GM022854/GM/NIGMS NIH HHS/United States ; RF1 AG048056/AG/NIA NIH HHS/United States ; GM22854/GM/NIGMS NIH HHS/United States ; }, mesh = {Gene Targeting/*methods ; *Genetic Code ; Metabolic Engineering/*methods ; }, abstract = {Withstanding 3.5 billion years of genetic drift, the canonical genetic code remains such a fundamental foundation for the complexity of life that it is highly conserved across all three phylogenetic domains. Genome engineering technologies are now making it possible to rationally change the genetic code, offering resistance to viruses, genetic isolation from horizontal gene transfer, and prevention of environmental escape by genetically modified organisms. We discuss the biochemical, genetic, and technological challenges that must be overcome in order to engineer the genetic code.}, }
@article {pmid26347724, year = {2015}, author = {Poulin-Laprade, D and Carraro, N and Burrus, V}, title = {The extended regulatory networks of SXT/R391 integrative and conjugative elements and IncA/C conjugative plasmids.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {837}, pmid = {26347724}, issn = {1664-302X}, abstract = {Nowadays, healthcare systems are challenged by a major worldwide drug resistance crisis caused by the massive and rapid dissemination of antibiotic resistance genes and associated emergence of multidrug resistant pathogenic bacteria, in both clinical and environmental settings. Conjugation is the main driving force of gene transfer among microorganisms. This mechanism of horizontal gene transfer mediates the translocation of large DNA fragments between two bacterial cells in direct contact. Integrative and conjugative elements (ICEs) of the SXT/R391 family (SRIs) and IncA/C conjugative plasmids (ACPs) are responsible for the dissemination of a broad spectrum of antibiotic resistance genes among diverse species of Enterobacteriaceae and Vibrionaceae. The biology, diversity, prevalence and distribution of these two families of conjugative elements have been the subject of extensive studies for the past 15 years. Recently, the transcriptional regulators that govern their dissemination through the expression of ICE- or plasmid-encoded transfer genes have been described. Unrelated repressors control the activation of conjugation by preventing the expression of two related master activator complexes in both types of elements, i.e., SetCD in SXT/R391 ICEs and AcaCD in IncA/C plasmids. Finally, in addition to activating ICE- or plasmid-borne genes, these master activators have been shown to specifically activate phylogenetically unrelated mobilizable genomic islands (MGIs) that also disseminate antibiotic resistance genes and other adaptive traits among a plethora of pathogens such as Vibrio cholerae and Salmonella enterica.}, }
@article {pmid26347723, year = {2015}, author = {Ying, J and Wu, S and Zhang, K and Wang, Z and Zhu, W and Zhu, M and Zhang, Y and Cheng, C and Wang, H and Tou, H and Zhu, C and Li, P and Ying, J and Xu, T and Yi, H and Li, J and Ni, L and Xu, Z and Bao, Q and Lu, J}, title = {Comparative genomics analysis of pKF3-94 in Klebsiella pneumoniae reveals plasmid compatibility and horizontal gene transfer.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {831}, pmid = {26347723}, issn = {1664-302X}, abstract = {In order to get insights into plasmid evolution and the dissemination of multidrug resistance, we performed extensive comparative genomics analyses of the Klebsiella pneumoniae plasmid pKF3-94 and some of its related plasmids. pKF3-94 is one of three plasmids isolated from the K. pneumoniae strain KF3. Of the 144 putative genes it harbors, 69 can be functionally assigned to be involved in transfer conjugation, transfer leading, antimicrobial resistance, transposon function, and plasmid replication. Comparison of plasmid replicon sequence types revealed that pKF3-94 carries two replicons that are distinct from those carried on the two sibling K. pneumonia plasmids pKF3-70 and pKF3-140, thereby allowing pKF3-94 to coexist with these latter plasmids in the same host cell. Comparative genomics analyses further showed that pKF3-94 is more similar to plasmids pK1HV and pC15-k, which were isolated from different K. pneumonia strains, than to pKF3-70 and pKF3-140. Interestingly, pK1HV contains a unique 49 kb region rich in mobile genetic elements and drug resistance genes, while pKF3-94 and pC15-k share a 15 kb homology region partitioned into a region rich in drug resistance genes and one containing a replicon. It is conceivable, therefore, that pK1HV and pC15-k have both arisen from a common pKF3-94-like plasmid. The comparisons lend further support for the role horizontal gene transfer plays in genome evolution and in the dissemination of genetic elements including drug resistance genes.}, }
@article {pmid26338866, year = {2015}, author = {Finn, RN and Cerdà, J}, title = {Evolution and functional diversity of aquaporins.}, journal = {The Biological bulletin}, volume = {229}, number = {1}, pages = {6-23}, doi = {10.1086/BBLv229n1p6}, pmid = {26338866}, issn = {1939-8697}, mesh = {Animals ; Aquaporins/genetics/metabolism/*physiology ; Archaea/classification/*genetics ; Bacteria/classification/*genetics ; Eukaryota/classification/*genetics/metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; }, abstract = {In this review, we provide a brief synopsis of the evolution and functional diversity of the aquaporin gene superfamily in prokaryotic and eukaryotic organisms. Based upon the latest data, we discuss the expanding list of molecules shown to permeate the central pore of aquaporins, and the unexpected diversity of water channel genes in Archaea and Bacteria. We further provide new insight into the origin by horizontal gene transfer of plant glycerol-transporting aquaporins (NIPs), and the functional co-option and gene replacement of insect glycerol transporters. Finally, we discuss the origins of four major grades of aquaporins in Eukaryota, together with the increasing repertoires of aquaporins in vertebrates.}, }
@article {pmid26338497, year = {2015}, author = {Gibbons, JG and Rinker, DC}, title = {The genomics of microbial domestication in the fermented food environment.}, journal = {Current opinion in genetics &amp; development}, volume = {35}, number = {}, pages = {1-8}, pmid = {26338497}, issn = {1879-0380}, support = {F31 DC012991/DC/NIDCD NIH HHS/United States ; }, mesh = {Bacteria/*metabolism ; Fermentation/*physiology ; Food ; *Food Microbiology ; Genome, Bacterial/genetics ; Genome, Fungal/genetics ; *Genomics ; Humans ; Yeasts/*metabolism ; }, abstract = {Shortly after the agricultural revolution, the domestication of bacteria, yeasts, and molds, played an essential role in enhancing the stability, quality, flavor, and texture of food products. These domestication events were probably the result of human food production practices that entailed the continual recycling of isolated microbial communities in the presence of abundant agricultural food sources. We suggest that within these novel agrarian food niches the metabolic requirements of those microbes became regular and predictable resulting in rapid genomic specialization through such mechanisms as pseudogenization, genome decay, interspecific hybridization, gene duplication, and horizontal gene transfer. The ultimate result was domesticated strains of microorganisms with enhanced fermentative capacities.}, }
@article {pmid26338188, year = {2015}, author = {Pearson, BM and Louwen, R and van Baarlen, P and van Vliet, AH}, title = {Differential Distribution of Type II CRISPR-Cas Systems in Agricultural and Nonagricultural Campylobacter coli and Campylobacter jejuni Isolates Correlates with Lack of Shared Environments.}, journal = {Genome biology and evolution}, volume = {7}, number = {9}, pages = {2663-2679}, pmid = {26338188}, issn = {1759-6653}, support = {/WT_/Wellcome Trust/United Kingdom ; BB/J004529/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Alleles ; Bacteria/classification/genetics ; CRISPR-Associated Proteins/*genetics ; *CRISPR-Cas Systems ; Campylobacter coli/*genetics/isolation &amp; purification ; Campylobacter jejuni/classification/*genetics/isolation &amp; purification ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Environmental Microbiology ; Genome, Bacterial ; Nucleotide Motifs ; Phylogeny ; RNA, Bacterial/chemistry ; }, abstract = {CRISPR (clustered regularly interspaced palindromic repeats)-Cas (CRISPR-associated) systems are sequence-specific adaptive defenses against phages and plasmids which are widespread in prokaryotes. Here we have studied whether phylogenetic relatedness or sharing of environmental niches affects the distribution and dissemination of Type II CRISPR-Cas systems, first in 132 bacterial genomes from 15 phylogenetic classes, ranging from Proteobacteria to Actinobacteria. There was clustering of distinct Type II CRISPR-Cas systems in phylogenetically distinct genera with varying G+C%, which share environmental niches. The distribution of CRISPR-Cas within a genus was studied using a large collection of genome sequences of the closely related Campylobacter species Campylobacter jejuni (N = 3,746) and Campylobacter coli (N = 486). The Cas gene cas9 and CRISPR-repeat are almost universally present in C. jejuni genomes (98.0% positive) but relatively rare in C. coli genomes (9.6% positive). Campylobacter jejuni and agricultural C. coli isolates share the C. jejuni CRISPR-Cas system, which is closely related to, but distinct from the C. coli CRISPR-Cas system found in C. coli isolates from nonagricultural sources. Analysis of the genomic position of CRISPR-Cas insertion suggests that the C. jejuni-type CRISPR-Cas has been transferred to agricultural C. coli. Conversely, the absence of the C. coli-type CRISPR-Cas in agricultural C. coli isolates may be due to these isolates not sharing the same environmental niche, and may be affected by farm hygiene and biosecurity practices in the agricultural sector. Finally, many CRISPR spacer alleles were linked with specific multilocus sequence types, suggesting that these can assist molecular epidemiology applications for C. jejuni and C. coli.}, }
@article {pmid26337177, year = {2016}, author = {Ranwez, V and Scornavacca, C and Doyon, JP and Berry, V}, title = {Inferring gene duplications, transfers and losses can be done in a discrete framework.}, journal = {Journal of mathematical biology}, volume = {72}, number = {7}, pages = {1811-1844}, pmid = {26337177}, issn = {1432-1416}, mesh = {Algorithms ; *Biological Evolution ; Evolution, Molecular ; Gene Deletion ; *Gene Duplication ; Gene Transfer, Horizontal ; Genetic Speciation ; *Models, Biological ; Phylogeny ; }, abstract = {In the field of phylogenetics, the evolutionary history of a set of organisms is commonly depicted by a species tree-whose internal nodes represent speciation events-while the evolutionary history of a gene family is depicted by a gene tree-whose internal nodes can also represent macro-evolutionary events such as gene duplications and transfers. As speciation events are only part of the events shaping a gene history, the topology of a gene tree can show incongruences with that of the corresponding species tree. These incongruences can be used to infer the macro-evolutionary events undergone by the gene family. This is done by embedding the gene tree inside the species tree and hence providing a reconciliation of those trees. In the past decade, several parsimony-based methods have been developed to infer such reconciliations, accounting for gene duplications ([Formula: see text]), transfers ([Formula: see text]) and losses ([Formula: see text]). The main contribution of this paper is to formally prove an important assumption implicitly made by previous works on these reconciliations, namely that solving the (maximum) parsimony [Formula: see text] reconciliation problem in the discrete framework is equivalent to finding a most parsimonious [Formula: see text] scenario in the continuous framework. In the process, we also prove several intermediate results that are useful on their own and constitute a theoretical toolbox that will likely facilitate future theoretical contributions in the field.}, }
@article {pmid26336091, year = {2015}, author = {Bosacchi, M and Gurdon, C and Maliga, P}, title = {Plastid Genotyping Reveals the Uniformity of Cytoplasmic Male Sterile-T Maize Cytoplasms.}, journal = {Plant physiology}, volume = {169}, number = {3}, pages = {2129-2137}, pmid = {26336091}, issn = {1532-2548}, mesh = {Cytoplasm/genetics ; *Genetic Variation ; Genome, Mitochondrial/*genetics ; Genome, Plastid/genetics ; Genotype ; Genotyping Techniques ; Mitochondria/genetics ; Phylogeny ; Plant Infertility/*genetics ; Plastids/genetics/metabolism ; Pollen/genetics/physiology ; Sequence Analysis, DNA ; Zea mays/*genetics/physiology ; }, abstract = {Cytoplasmic male-sterile (CMS) lines in maize (Zea mays) have been classified by their response to specific restorer genes into three categories: cms-C, cms-S, and cms-T. A mitochondrial genome representing each of the CMS cytotypes has been sequenced, and male sterility in the cms-S and cms-T cytotypes is linked to chimeric mitochondrial genes. To identify markers for plastid genotyping, we sequenced the plastid genomes of three fertile maize lines (B37, B73, and A188) and the B37 cms-C, cms-S, and cms-T cytoplasmic substitution lines. We found that the plastid genomes of B37 and B73 lines are identical. Furthermore, the fertile and CMS plastid genomes are conserved, differing only by zero to three single-nucleotide polymorphisms (SNPs) in coding regions and by eight to 22 SNPs and 10 to 21 short insertions/deletions in noncoding regions. To gain insight into the origin and transmission of the cms-T trait, we identified three SNPs unique to the cms-T plastids and tested the three diagnostic SNPs in 27 cms-T lines, representing the HA, I, Q, RS, and T male-sterile cytoplasms. We report that each of the tested 27 cms-T group accessions have the same three diagnostic plastid SNPs, indicating a single origin and maternal cotransmission of the cms-T mitochondria and plastids to the seed progeny. Our data exclude exceptional pollen transmission of organelles or multiple horizontal gene transfer events as the source of the mitochondrial urf13-T (unidentified reading frame encoding 13-kD cms-T protein) gene in the cms-T cytoplasms. Plastid genotyping enables a reassessment of the evolutionary relationships of cytoplasms in cultivated maize.}, }
@article {pmid26330514, year = {2015}, author = {Getino, M and Sanabria-Ríos, DJ and Fernández-López, R and Campos-Gómez, J and Sánchez-López, JM and Fernández, A and Carballeira, NM and de la Cruz, F}, title = {Synthetic Fatty Acids Prevent Plasmid-Mediated Horizontal Gene Transfer.}, journal = {mBio}, volume = {6}, number = {5}, pages = {e01032-15}, pmid = {26330514}, issn = {2150-7511}, support = {P20 GM103475/GM/NIGMS NIH HHS/United States ; 5P20GM103475-13/GM/NIGMS NIH HHS/United States ; }, mesh = {Conjugation, Genetic/*drug effects ; Fatty Acids/chemical synthesis/*metabolism ; Gene Transfer, Horizontal/*drug effects ; Gram-Negative Bacteria/*drug effects/genetics ; Plasmids/*metabolism ; }, abstract = {UNLABELLED: Bacterial conjugation constitutes a major horizontal gene transfer mechanism for the dissemination of antibiotic resistance genes among human pathogens. Antibiotic resistance spread could be halted or diminished by molecules that interfere with the conjugation process. In this work, synthetic 2-alkynoic fatty acids were identified as a novel class of conjugation inhibitors. Their chemical properties were investigated by using the prototype 2-hexadecynoic acid and its derivatives. Essential features of effective inhibitors were the carboxylic group, an optimal long aliphatic chain of 16 carbon atoms, and one unsaturation. Chemical modification of these groups led to inactive or less-active derivatives. Conjugation inhibitors were found to act on the donor cell, affecting a wide number of pathogenic bacterial hosts, including Escherichia, Salmonella, Pseudomonas, and Acinetobacter spp. Conjugation inhibitors were active in inhibiting transfer of IncF, IncW, and IncH plasmids, moderately active against IncI, IncL/M, and IncX plasmids, and inactive against IncP and IncN plasmids. Importantly, the use of 2-hexadecynoic acid avoided the spread of a derepressed IncF plasmid into a recipient population, demonstrating the feasibility of abolishing the dissemination of antimicrobial resistances by blocking bacterial conjugation.<br><br>IMPORTANCE: Diseases caused by multidrug-resistant bacteria are taking an important toll with respect to human morbidity and mortality. The most relevant antibiotic resistance genes come to human pathogens carried by plasmids, mainly using conjugation as a transmission mechanism. Here, we identified and characterized a series of compounds that were active against several plasmid groups of clinical relevance, in a wide variety of bacterial hosts. These inhibitors might be used for fighting antibiotic-resistance dissemination by inhibiting conjugation. Potential inhibitors could be used in specific settings (e.g., farm, fish factory, or even clinical settings) to investigate their effect in the eradication of undesired resistances.}, }
@article {pmid26328805, year = {2016}, author = {Vorkapic, D and Pressler, K and Schild, S}, title = {Multifaceted roles of extracellular DNA in bacterial physiology.}, journal = {Current genetics}, volume = {62}, number = {1}, pages = {71-79}, pmid = {26328805}, issn = {1432-0983}, support = {P 22986/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Bacterial Physiological Phenomena ; Biofilms ; DNA, Bacterial/*genetics/*metabolism ; Energy Metabolism ; Extracellular Matrix ; Extracellular Space/metabolism ; Gene Transfer, Horizontal ; Quorum Sensing ; }, abstract = {In textbooks, DNA is generally defined as the universal storage material for genetic information in all branches of life. Beyond this important intracellular role, DNA can also be present outside of living cells and is an abundant biopolymer in aquatic and terrestrial ecosystems. The origin of extracellular DNA in such ecological niches is diverse: it can be actively secreted or released by prokaryotic and eukaryotic cells by means of autolysis, apoptosis, necrosis, bacterial secretion systems or found in association with extracellular bacterial membrane vesicles. Especially for bacteria, extracellular DNA represents a significant and convenient element that can be enzymatically modulated and utilized for multiple purposes. Herein, we discuss briefly the main origins of extracellular DNA and the most relevant roles for the bacterial physiology, such as biofilm formation, nutrient source, antimicrobial means and horizontal gene transfer.}, }
@article {pmid26327493, year = {2015}, author = {Walia, Y and Dhir, S and Zaidi, AA and Hallan, V}, title = {Apple scar skin viroid naked RNA is actively transmitted by the whitefly Trialeurodes vaporariorum.}, journal = {RNA biology}, volume = {12}, number = {10}, pages = {1131-1138}, pmid = {26327493}, issn = {1555-8584}, mesh = {Animals ; Cucumis sativus/*genetics/virology ; DNA, Single-Stranded/genetics ; Gene Transfer, Horizontal ; Hemiptera ; Nucleic Acids/*genetics ; Plant Lectins/*genetics/metabolism ; RNA, Plant/genetics ; Viroids/*genetics ; }, abstract = {Nucleic acid transfer between plants is a phenomenon which is likely to occur in many ways in nature. We report here the active transmission of Apple scar skin viroid (ASSVd) naked ssRNA species by the whitefly Trialeurodes vaporariorum (Tv). Not only the viroid RNA, its DNA form was also identified from the insect. The viroid transfer efficiency was enhanced with the help of Cucumis sativus Phloem protein 2 (CsPP2), a plant protein known to translocate viroid RNAs. This PP2/ASSVd complex is stably present in the viroid infected cucumber plants, as was identified with the help of immunological reaction. As viroid-like secondary structures are found in some plant RNAs, and PP2 is known to bind and translocate several RNAs, the results have huge implications in transfer of these RNA species between plants visited by the whitefly.}, }
@article {pmid26327282, year = {2015}, author = {Yang, C and Li, P and Su, W and Li, H and Liu, H and Yang, G and Xie, J and Yi, S and Wang, J and Cui, X and Wu, Z and Wang, L and Hao, R and Jia, L and Qiu, S and Song, H}, title = {Polymorphism of CRISPR shows separated natural groupings of Shigella subtypes and evidence of horizontal transfer of CRISPR.}, journal = {RNA biology}, volume = {12}, number = {10}, pages = {1109-1120}, pmid = {26327282}, issn = {1555-8584}, mesh = {Clustered Regularly Interspaced Short Palindromic Repeats/*genetics ; Escherichia coli/*genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Phylogeny ; Polymorphism, Genetic ; Sequence Analysis, DNA ; Shigella/*genetics ; }, abstract = {Clustered, regularly interspaced, short palindromic repeats (CRISPR) act as an adaptive RNA-mediated immune mechanism in bacteria. They can also be used for identification and evolutionary studies based on polymorphisms within the CRISPR locus. We amplified and analyzed 6 CRISPR loci from 237 Shigella strains belonging to the 4 species groups, as well as 13 Escherichia coli strains. The CRISPR-associated (cas) gene sequence arrays of these strains were screened and compared. The CRISPR sequences from Shigella were conserved among subtypes, suggesting that CRISPR may represent a new identification tool for the detection and discrimination of Shigella species. Secondary structure analysis showed a different stem-loop structure at the terminal repeat, suggesting a distinct recognition mechanism in the formation of crRNA. In addition, the presence of "self-target" spacers and polymorphisms within CRISPR in Shigella indicated a selective pressure for inhibition of this system, which has the potential to damage "self DNA." Homology analysis of spacers showed that CRISPR might be involved in the regulation of virulence transmission. Phylogenetic analysis based on CRISPR sequences from Shigella and E. coli indicated that although phenotypic properties maintain convergent evolution, the 4 Shigella species do not represent natural groupings. Surprisingly, comparative analysis of Shigella repeats with other species provided new evidence for CRISPR horizontal transfer. Our results suggested that CRISPR analysis is applicable for the detection of Shigella species and for investigation of evolutionary relationships.}, }
@article {pmid26324906, year = {2015}, author = {Baumgarten, S and Simakov, O and Esherick, LY and Liew, YJ and Lehnert, EM and Michell, CT and Li, Y and Hambleton, EA and Guse, A and Oates, ME and Gough, J and Weis, VM and Aranda, M and Pringle, JR and Voolstra, CR}, title = {The genome of Aiptasia, a sea anemone model for coral symbiosis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {38}, pages = {11893-11898}, pmid = {26324906}, issn = {1091-6490}, support = {BB/G022771/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; T32 HG000044/HG/NHGRI NIH HHS/United States ; 5 T32 HG000044/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Anthozoa/*physiology ; Chromosomes/genetics ; Evolution, Molecular ; Gene Expression Profiling ; Gene Transfer, Horizontal/genetics ; Genome/*genetics ; Genome Size ; Microbial Interactions/genetics ; Models, Biological ; Molecular Sequence Annotation ; Phylogeny ; Repetitive Sequences, Nucleic Acid/genetics ; Sea Anemones/*genetics ; Symbiosis/*genetics ; Synteny/genetics ; }, abstract = {The most diverse marine ecosystems, coral reefs, depend upon a functional symbiosis between a cnidarian animal host (the coral) and intracellular photosynthetic dinoflagellate algae. The molecular and cellular mechanisms underlying this endosymbiosis are not well understood, in part because of the difficulties of experimental work with corals. The small sea anemone Aiptasia provides a tractable laboratory model for investigating these mechanisms. Here we report on the assembly and analysis of the Aiptasia genome, which will provide a foundation for future studies and has revealed several features that may be key to understanding the evolution and function of the endosymbiosis. These features include genomic rearrangements and taxonomically restricted genes that may be functionally related to the symbiosis, aspects of host dependence on alga-derived nutrients, a novel and expanded cnidarian-specific family of putative pattern-recognition receptors that might be involved in the animal-algal interactions, and extensive lineage-specific horizontal gene transfer. Extensive integration of genes of prokaryotic origin, including genes for antimicrobial peptides, presumably reflects an intimate association of the animal-algal pair also with its prokaryotic microbiome.}, }
@article {pmid26323765, year = {2015}, author = {Szöllősi, GJ and Davín, AA and Tannier, E and Daubin, V and Boussau, B}, title = {Genome-scale phylogenetic analysis finds extensive gene transfer among fungi.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1678}, pages = {20140335}, pmid = {26323765}, issn = {1471-2970}, mesh = {Computer Simulation ; Cyanobacteria/genetics ; Fungi/*genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial ; *Genome, Fungal ; Models, Genetic ; *Phylogeny ; }, abstract = {Although the role of lateral gene transfer is well recognized in the evolution of bacteria, it is generally assumed that it has had less influence among eukaryotes. To explore this hypothesis, we compare the dynamics of genome evolution in two groups of organisms: cyanobacteria and fungi. Ancestral genomes are inferred in both clades using two types of methods: first, Count, a gene tree unaware method that models gene duplications, gains and losses to explain the observed numbers of genes present in a genome; second, ALE, a more recent gene tree-aware method that reconciles gene trees with a species tree using a model of gene duplication, loss and transfer. We compare their merits and their ability to quantify the role of transfers, and assess the impact of taxonomic sampling on their inferences. We present what we believe is compelling evidence that gene transfer plays a significant role in the evolution of fungi.}, }
@article {pmid26323764, year = {2015}, author = {Koonin, EV}, title = {Origin of eukaryotes from within archaea, archaeal eukaryome and bursts of gene gain: eukaryogenesis just made easier?.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1678}, pages = {20140333}, pmid = {26323764}, issn = {1471-2970}, mesh = {Archaea/*genetics ; *Biological Evolution ; Eukaryota/genetics ; *Eukaryotic Cells ; *Genome, Archaeal ; }, abstract = {The origin of eukaryotes is a fundamental, forbidding evolutionary puzzle. Comparative genomic analysis clearly shows that the last eukaryotic common ancestor (LECA) possessed most of the signature complex features of modern eukaryotic cells, in particular the mitochondria, the endomembrane system including the nucleus, an advanced cytoskeleton and the ubiquitin network. Numerous duplications of ancestral genes, e.g. DNA polymerases, RNA polymerases and proteasome subunits, also can be traced back to the LECA. Thus, the LECA was not a primitive organism and its emergence must have resulted from extensive evolution towards cellular complexity. However, the scenario of eukaryogenesis, and in particular the relationship between endosymbiosis and the origin of eukaryotes, is far from being clear. Four recent developments provide new clues to the likely routes of eukaryogenesis. First, evolutionary reconstructions suggest complex ancestors for most of the major groups of archaea, with the subsequent evolution dominated by gene loss. Second, homologues of signature eukaryotic proteins, such as actin and tubulin that form the core of the cytoskeleton or the ubiquitin system, have been detected in diverse archaea. The discovery of this 'dispersed eukaryome' implies that the archaeal ancestor of eukaryotes was a complex cell that might have been capable of a primitive form of phagocytosis and thus conducive to endosymbiont capture. Third, phylogenomic analyses converge on the origin of most eukaryotic genes of archaeal descent from within the archaeal evolutionary tree, specifically, the TACK superphylum. Fourth, evidence has been presented that the origin of the major archaeal phyla involved massive acquisition of bacterial genes. Taken together, these findings make the symbiogenetic scenario for the origin of eukaryotes considerably more plausible and the origin of the organizational complexity of eukaryotic cells more readily explainable than they appeared until recently.}, }
@article {pmid26323758, year = {2015}, author = {Moreira, D and López-García, P}, title = {Evolution of viruses and cells: do we need a fourth domain of life to explain the origin of eukaryotes?.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1678}, pages = {20140327}, pmid = {26323758}, issn = {1471-2970}, support = {322669/ERC_/European Research Council/International ; }, mesh = {*Biological Evolution ; Eukaryotic Cells/*classification/*cytology ; Gene Transfer, Horizontal ; Genome, Viral ; Viruses/*classification/*genetics ; }, abstract = {The recent discovery of diverse very large viruses, such as the mimivirus, has fostered a profusion of hypotheses positing that these viruses define a new domain of life together with the three cellular ones (Archaea, Bacteria and Eucarya). It has also been speculated that they have played a key role in the origin of eukaryotes as donors of important genes or even as the structures at the origin of the nucleus. Thanks to the increasing availability of genome sequences for these giant viruses, those hypotheses are amenable to testing via comparative genomic and phylogenetic analyses. This task is made very difficult by the high evolutionary rate of viruses, which induces phylogenetic artefacts, such as long branch attraction, when inadequate methods are applied. It can be demonstrated that phylogenetic trees supporting viruses as a fourth domain of life are artefactual. In most cases, the presence of homologues of cellular genes in viruses is best explained by recurrent horizontal gene transfer from cellular hosts to their infecting viruses and not the opposite. Today, there is no solid evidence for the existence of a viral domain of life or for a significant implication of viruses in the origin of the cellular domains.}, }
@article {pmid26323756, year = {2015}, author = {Katz, LA}, title = {Recent events dominate interdomain lateral gene transfers between prokaryotes and eukaryotes and, with the exception of endosymbiotic gene transfers, few ancient transfer events persist.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1678}, pages = {20140324}, pmid = {26323756}, issn = {1471-2970}, support = {R15 GM113177/GM/NIGMS NIH HHS/United States ; 1R15GM113177/GM/NIGMS NIH HHS/United States ; }, mesh = {*Biological Evolution ; *Eukaryotic Cells ; Gene Transfer, Horizontal ; Genetics, Microbial ; Photosynthesis/genetics ; Symbiosis/*genetics/*physiology ; }, abstract = {While there is compelling evidence for the impact of endosymbiotic gene transfer (EGT; transfer from either mitochondrion or chloroplast to the nucleus) on genome evolution in eukaryotes, the role of interdomain transfer from bacteria and/or archaea (i.e. prokaryotes) is less clear. Lateral gene transfers (LGTs) have been argued to be potential sources of phylogenetic information, particularly for reconstructing deep nodes that are difficult to recover with traditional phylogenetic methods. We sought to identify interdomain LGTs by using a phylogenomic pipeline that generated 13 465 single gene trees and included up to 487 eukaryotes, 303 bacteria and 118 archaea. Our goals include searching for LGTs that unite major eukaryotic clades, and describing the relative contributions of LGT and EGT across the eukaryotic tree of life. Given the difficulties in interpreting single gene trees that aim to capture the approximately 1.8 billion years of eukaryotic evolution, we focus on presence-absence data to identify interdomain transfer events. Specifically, we identify 1138 genes found only in prokaryotes and representatives of three or fewer major clades of eukaryotes (e.g. Amoebozoa, Archaeplastida, Excavata, Opisthokonta, SAR and orphan lineages). The majority of these genes have phylogenetic patterns that are consistent with recent interdomain LGTs and, with the notable exception of EGTs involving photosynthetic eukaryotes, we detect few ancient interdomain LGTs. These analyses suggest that LGTs have probably occurred throughout the history of eukaryotes, but that ancient events are not maintained unless they are associated with endosymbiotic gene transfer among photosynthetic lineages.}, }
@article {pmid26321009, year = {2015}, author = {Kaase, M and Pfennigwerth, N and Lange, F and Anders, A and Gatermann, SG}, title = {Molecular epidemiology of VIM-1 producing Escherichia coli from Germany referred to the National Reference Laboratory.}, journal = {International journal of medical microbiology : IJMM}, volume = {305}, number = {7}, pages = {784-789}, doi = {10.1016/j.ijmm.2015.08.032}, pmid = {26321009}, issn = {1618-0607}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Child ; Child, Preschool ; Cluster Analysis ; Drug Resistance, Bacterial ; Escherichia coli/*enzymology/genetics/isolation &amp; purification ; Escherichia coli Infections/*epidemiology/*microbiology ; Female ; Gene Transfer, Horizontal ; Genetic Variation ; Genotype ; Germany/epidemiology ; Humans ; Infant ; Infant, Newborn ; Male ; Microbial Sensitivity Tests ; Middle Aged ; Molecular Epidemiology ; Multilocus Sequence Typing ; Prevalence ; Young Adult ; beta-Lactamases/genetics ; }, abstract = {The distribution of carbapenemase genes in Escherichia coli strains isolated between September 2009 and May 2013 in Germany was investigated. Out of 192 isolates with carbapenemase production OXA-48 was found in 44.8%, VIM-1 in 18.8%, NDM-1 in 11.5% and KPC-2 in 6.8%. Patients with VIM-1 producing E. coli (n=36) differed from patients with OXA-48 by an older age, less frequent mention of travel history and an increased proportion of clinical over screening specimens. These data might indicate that introduction from abroad is of minor importance for VIM-1 producing E. coli compared to other carbapenemases. Multilocus sequence typing revealed that E. coli with VIM-1 were mostly multiclonal, emphasizing the role of horizontal gene transfer in its spread. Susceptibility testing of VIM-1 producing E. coli demonstrated aztreonam susceptibility in 55.6%. Among non-β-lactams susceptibility rates of >90% were observed for amikacin, tigecycline, colistin, fosfomycin and nitrofurantoin.}, }
@article {pmid26321007, year = {2015}, author = {Karch, A and Vogel, U and Claus, H}, title = {Role of penA polymorphisms for penicillin susceptibility in Neisseria lactamica and Neisseria meningitidis.}, journal = {International journal of medical microbiology : IJMM}, volume = {305}, number = {7}, pages = {729-735}, doi = {10.1016/j.ijmm.2015.08.025}, pmid = {26321007}, issn = {1618-0607}, mesh = {Amino Acid Substitution ; Gene Transfer, Horizontal ; Genotype ; Germany ; Humans ; Microbial Sensitivity Tests ; Mutation, Missense ; Neisseria lactamica/*drug effects/genetics/isolation &amp; purification ; Neisseria meningitidis/*drug effects/genetics/isolation &amp; purification ; Neisseriaceae Infections/microbiology ; *Penicillin Resistance ; Penicillin-Binding Proteins/*genetics ; Penicillins/*pharmacology ; *Polymorphism, Genetic ; Transformation, Bacterial ; }, abstract = {In meningococci, reduced penicillin susceptibility is associated with five specific mutations in the transpeptidase region of penicillin binding protein 2 (PBP2). We showed that the same set of mutations was present in 64 of 123 Neisseria lactamica strains obtained from a carriage study (MIC range: 0.125-2.0mg/L). The PBP2 encoding penA alleles in these strains were genetically similar to those found in intermediate resistant meningococci suggesting frequent interspecies genetic exchange. Fifty-six N. lactamica isolates with mostly lower penicillin MICs (range: 0.064-0.38mg/L) exhibited only three of the five mutations. The corresponding penA alleles were unique to N. lactamica and formed a distinct genetic clade. PenA alleles with no mutations on the other hand were unique to meningococci. Under penicillin selective pressure, genetic transformation of N. lactamica penA alleles in meningococci was only possible for alleles encoding five mutations, but not for those encoding three mutations; the transfer resulted in MICs comparable to those of meningococci harboring penA alleles that encoded PBP2 with five mutations, but considerably lower than those of the corresponding N. lactamica donor strains. Due to a transformation barrier the complete N. lactamica penA could not be transformed into N. meningitidis. In summary, penicillin MICs in N. lactamica were associated with the number of mutations in the transpeptidase region of PBP2. Evidence for interspecific genetic transfer was only observed for penA alleles associated with higher MICs, suggesting that alleles encoding only three mutations in the transpeptidase region are biologically not effective in N. meningitidis. Factors other than PBP2 seem to be responsible for the high levels of penicillin resistance in N. lactamica. A reduction of penicillin susceptibility in N. meningitidis by horizontal gene transfer from N. lactamica is unlikely to happen.}, }
@article {pmid26319575, year = {2015}, author = {Rauch, C and Vries, Jd and Rommel, S and Rose, LE and Woehle, C and Christa, G and Laetz, EM and Wägele, H and Tielens, AG and Nickelsen, J and Schumann, T and Jahns, P and Gould, SB}, title = {Why It Is Time to Look Beyond Algal Genes in Photosynthetic Slugs.}, journal = {Genome biology and evolution}, volume = {7}, number = {9}, pages = {2602-2607}, pmid = {26319575}, issn = {1759-6653}, mesh = {Animals ; *Evolution, Molecular ; Gastropoda/*genetics ; Gene Transfer, Horizontal ; Photosynthesis/genetics ; Plastids/*genetics ; }, abstract = {Eukaryotic organelles depend on nuclear genes to perpetuate their biochemical integrity. This is true for mitochondria in all eukaryotes and plastids in plants and algae. Then how do kleptoplasts, plastids that are sequestered by some sacoglossan sea slugs, survive in the animals' digestive gland cells in the absence of the algal nucleus encoding the vast majority of organellar proteins? For almost two decades, lateral gene transfer (LGT) from algae to slugs appeared to offer a solution, but RNA-seq analysis, later supported by genome sequencing of slug DNA, failed to find any evidence for such LGT events. Yet, isolated reports continue to be published and are readily discussed by the popular press and social media, making the data on LGT and its support for kleptoplast longevity appear controversial. However, when we take a sober look at the methods used, we realize that caution is warranted in how the results are interpreted. There is no evidence that the evolution of kleptoplasty in sea slugs involves LGT events. Based on what we know about photosystem maintenance in embryophyte plastids, we assume kleptoplasts depend on nuclear genes. However, studies have shown that some isolated algal plastids are, by nature, more robust than those of land plants. The evolution of kleptoplasty in green sea slugs involves many promising and unexplored phenomena, but there is no evidence that any of these require the expression of slug genes of algal origin.}, }
@article {pmid26316424, year = {2015}, author = {Krause, DJ and Whitaker, RJ}, title = {Inferring Speciation Processes from Patterns of Natural Variation in Microbial Genomes.}, journal = {Systematic biology}, volume = {64}, number = {6}, pages = {926-935}, pmid = {26316424}, issn = {1076-836X}, mesh = {Bacteria/*classification ; *Genetic Speciation ; *Genetic Variation ; Genome, Bacterial/genetics ; Genomics ; Models, Genetic ; }, abstract = {Microbial species concepts have long been the focus of contentious debate, fueled by technological limitations to the genetic resolution of species, by the daunting task of investigating phenotypic variation among individual microscopic organisms, and by a lack of understanding of gene flow in reproductively asexual organisms that are prone to promiscuous horizontal gene transfer. Population genomics, the emerging approach of analyzing the complete genomes of a multitude of closely related organisms, is poised to overcome these limitations by providing a window into patterns of genome variation revealing the evolutionary processes through which species diverge. This new approach is more than just an extension of previous multilocus sequencing technologies, in that it provides a comprehensive view of interacting evolutionary processes. Here we argue that the application of population genomic tools in a rigorous population genetic framework will help to identify the processes of microbial speciation and ultimately lead to a general species concept based on the unique biology and ecology of microorganisms.}, }
@article {pmid26309202, year = {2015}, author = {Huber, HJ and Holvoet, P}, title = {Exosomes: emerging roles in communication between blood cells and vascular tissues during atherosclerosis.}, journal = {Current opinion in lipidology}, volume = {26}, number = {5}, pages = {412-419}, pmid = {26309202}, issn = {1473-6535}, mesh = {Animals ; Apoptosis ; Atherosclerosis/*metabolism ; Endothelial Cells/physiology ; Exosomes/*physiology ; Gene Transfer, Horizontal ; Humans ; Microvessels/*metabolism/pathology ; Oxidative Stress ; Paracrine Communication ; Signal Transduction ; }, abstract = {PURPOSE OF REVIEW: Microvesicles, in general, and exosomes together with their delivered content in particular, are now being widely recognized as key players in atherosclerosis. We have previously reviewed the role of microvesicles in atherosclerosis pathogenesis, diagnosis and therapy. Here, we focus on the roles of exosomes and discuss their emergent role in mediating activation and response to inflammation, vessel infiltration and induction of coagulation. We will finally give an outlook to discuss novel detection techniques and systems biology based data analyses to investigate exosome-mediated cell-to-cell communication.<br><br>RECENT FINDINGS: Recent research points to a role of exosomes in delivering apoptotic and inflammatory content between blood cells and vascular cells, with a potential contribution of exosomes secreted by adipose tissue. An atheroprotective role of exosomes in response to coagulation that may contrast with the procoagulatory role of platelet-derived larger microvesicles is envisaged. New detection and separation methods and systems biology techniques are emerging.<br><br>CONCLUSION: We project that the development of novel detection, separation and analysis mechanism and systems-based analysis methods will further unravel the paracrine and endocrine 'communication protocol' between cellular players in atherosclerosis, mediating inflammation, oxidative stress and apoptosis.}, }
@article {pmid26307765, year = {2015}, author = {Papenfort, K and Espinosa, E and Casadesús, J and Vogel, J}, title = {Small RNA-based feedforward loop with AND-gate logic regulates extrachromosomal DNA transfer in Salmonella.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {34}, pages = {E4772-81}, pmid = {26307765}, issn = {1091-6490}, mesh = {Base Sequence ; *Chromosomes, Bacterial ; DNA, Bacterial/*genetics ; Molecular Sequence Data ; RNA, Bacterial/*genetics ; Salmonella/*genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {Horizontal gene transfer via plasmid conjugation is a major driving force in microbial evolution but constitutes a complex process that requires synchronization with the physiological state of the host bacteria. Although several host transcription factors are known to regulate plasmid-borne transfer genes, RNA-based regulatory circuits for host-plasmid communication remain unknown. We describe a posttranscriptional mechanism whereby the Hfq-dependent small RNA, RprA, inhibits transfer of pSLT, the virulence plasmid of Salmonella enterica. RprA employs two separate seed-pairing domains to activate the mRNAs of both the sigma-factor σ(S) and the RicI protein, a previously uncharacterized membrane protein here shown to inhibit conjugation. Transcription of ricI requires σ(S) and, together, RprA and σ(S) orchestrate a coherent feedforward loop with AND-gate logic to tightly control the activation of RicI synthesis. RicI interacts with the conjugation apparatus protein TraV and limits plasmid transfer under membrane-damaging conditions. To our knowledge, this study reports the first small RNA-controlled feedforward loop relying on posttranscriptional activation of two independent targets and an unexpected role of the conserved RprA small RNA in controlling extrachromosomal DNA transfer.}, }
@article {pmid26305100, year = {2015}, author = {Salomon, D and Klimko, JA and Trudgian, DC and Kinch, LN and Grishin, NV and Mirzaei, H and Orth, K}, title = {Type VI Secretion System Toxins Horizontally Shared between Marine Bacteria.}, journal = {PLoS pathogens}, volume = {11}, number = {8}, pages = {e1005128}, pmid = {26305100}, issn = {1553-7374}, support = {R01-AI056404/AI/NIAID NIH HHS/United States ; R01 AI056404/AI/NIAID NIH HHS/United States ; K99 AI116948/AI/NIAID NIH HHS/United States ; R01 GM094575/GM/NIGMS NIH HHS/United States ; K99AI116948/AI/NIAID NIH HHS/United States ; GM094575/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacterial Toxins/*genetics ; Base Sequence ; Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Genetic Fitness/genetics ; Mass Spectrometry ; Molecular Sequence Data ; Type VI Secretion Systems/*genetics ; Vibrio alginolyticus/*genetics ; }, abstract = {The type VI secretion system (T6SS) is a widespread protein secretion apparatus used by Gram-negative bacteria to deliver toxic effector proteins into adjacent bacterial or host cells. Here, we uncovered a role in interbacterial competition for the two T6SSs encoded by the marine pathogen Vibrio alginolyticus. Using comparative proteomics and genetics, we identified their effector repertoires. In addition to the previously described effector V12G01_02265, we identified three new effectors secreted by T6SS1, indicating that the T6SS1 secretes at least four antibacterial effectors, of which three are members of the MIX-effector class. We also showed that the T6SS2 secretes at least three antibacterial effectors. Our findings revealed that many MIX-effectors belonging to clan V are "orphan" effectors that neighbor mobile elements and are shared between marine bacteria via horizontal gene transfer. We demonstrated that a MIX V-effector from V. alginolyticus is a functional T6SS effector when ectopically expressed in another Vibrio species. We propose that mobile MIX V-effectors serve as an environmental reservoir of T6SS effectors that are shared and used to diversify antibacterial toxin repertoires in marine bacteria, resulting in enhanced competitive fitness.}, }
@article {pmid26303003, year = {2015}, author = {Silveira, AC and Cunha, GR and Caierão, J and Cordova, CM and d'Azevedo, PA}, title = {Molecular epidemiology of heteroresistant vancomycin-intermediate Staphylococcus aureus in Brazil.}, journal = {The Brazilian journal of infectious diseases : an official publication of the Brazilian Society of Infectious Diseases}, volume = {19}, number = {5}, pages = {466-472}, pmid = {26303003}, issn = {1678-4391}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Typing Techniques ; Brazil/epidemiology ; Cross Infection/epidemiology/microbiology ; DNA, Bacterial/analysis ; Electrophoresis, Gel, Pulsed-Field ; Humans ; Methicillin-Resistant Staphylococcus aureus/classification/*drug effects/genetics ; Microbial Sensitivity Tests ; Molecular Epidemiology ; Multiplex Polymerase Chain Reaction ; Phenotype ; Staphylococcal Infections/epidemiology/microbiology ; Vancomycin/*pharmacology ; }, abstract = {To determine the epidemiological and molecular characteristics of 12 Staphylococcus aureus isolates presenting heteroresistance to vancomycin in laboratories of two cities in Santa Catarina, southern Brazil. Epidemiological data, including the city of isolation, health institution, and date of isolation were considered, as well as the associated clinical specimen. For molecular characterization, we analyzed the staphylococcal cassette chromosome types, the erm gene presence, and the genomic diversity of isolates using pulsed-field gel electrophoresis. The 12 isolates of S. aureus were previously confirmed as heteroresistance to vancomycin using the population analysis profile-area under curve. Regarding genetic variability, two clones were detected: the main one (clone A) composed of four isolates and the clones B, with two isolates. For clone A, two isolates presented identical band patterns and were related to the same hospital, with an interval of 57 days between their isolation. The other isolates of this clone showed no epidemiological link between them because they were isolated in different hospitals and had no temporal relationship. The other clone showed no detectable epidemiological relationship. The heteroresistance to vancomycin recovered in Santa Catarina State from 2009 to 2012 had, in general, heterogeneous genomic patterns based on pulsed-field gel electrophoresis results, which is in accordance with the fact that these isolates had little or no epidemiological relationship among them. Due to the characteristic phenotypic instability and often prolonged vancomycin therapy for selection, clonal spread is not as common as for other resistance mechanisms disseminated through horizontal gene transfer.}, }
@article {pmid26300902, year = {2015}, author = {Urban, M and Irvine, AG and Cuzick, A and Hammond-Kosack, KE}, title = {Using the pathogen-host interactions database (PHI-base) to investigate plant pathogen genomes and genes implicated in virulence.}, journal = {Frontiers in plant science}, volume = {6}, number = {}, pages = {605}, pmid = {26300902}, issn = {1664-462X}, support = {BB/I000488/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/I001077/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {New pathogen-host interaction mechanisms can be revealed by integrating mutant phenotype data with genetic information. PHI-base is a multi-species manually curated database combining peer-reviewed published phenotype data from plant and animal pathogens and gene/protein information in a single database.}, }
@article {pmid26300877, year = {2015}, author = {Petříčková, K and Chroňáková, A and Zelenka, T and Chrudimský, T and Pospíšil, S and Petříček, M and Krištůfek, V}, title = {Evolution of cyclizing 5-aminolevulinate synthases in the biosynthesis of actinomycete secondary metabolites: outcomes for genetic screening techniques.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {814}, pmid = {26300877}, issn = {1664-302X}, abstract = {A combined approach, comprising PCR screening and genome mining, was used to unravel the diversity and phylogeny of genes encoding 5-aminolevulinic acid synthases (ALASs, hemA gene products) in streptomycetes-related strains. In actinomycetes, these genes were believed to be directly connected with the production of secondary metabolites carrying the C5N unit, 2-amino-3-hydroxycyclopent-2-enone, with biological activities making them attractive for future use in medicine and agriculture. Unlike "classical" primary metabolism ALAS, the C5N unit-forming cyclizing ALAS (cALAS) catalyses intramolecular cyclization of nascent 5-aminolevulinate. Specific amino acid sequence changes can be traced by comparison of "classical" ALASs against cALASs. PCR screening revealed 226 hemA gene-carrying strains from 1,500 tested, with 87% putatively encoding cALAS. Phylogenetic analysis of the hemA homologs revealed strain clustering according to putative type of metabolic product, which could be used to select producers of specific C5N compound classes. Supporting information was acquired through analysis of actinomycete genomic sequence data available in GenBank and further genetic or metabolic characterization of selected strains. Comparison of 16S rRNA taxonomic identification and BOX-PCR profiles provided evidence for numerous horizontal gene transfers of biosynthetic genes or gene clusters within actinomycete populations and even from non-actinomycete organisms. Our results underline the importance of environmental and evolutionary data in the design of efficient techniques for identification of novel producers.}, }
@article {pmid26300869, year = {2015}, author = {Chow, L and Waldron, L and Gillings, MR}, title = {Potential impacts of aquatic pollutants: sub-clinical antibiotic concentrations induce genome changes and promote antibiotic resistance.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {803}, pmid = {26300869}, issn = {1664-302X}, abstract = {Antibiotics are disseminated into aquatic environments via human waste streams and agricultural run-off. Here they can persist at low, but biologically relevant, concentrations. Antibiotic pollution establishes a selection gradient for resistance and may also raise the frequency of events that generate resistance: point mutations; recombination; and lateral gene transfer. This study examined the response of bacteria to sub-inhibitory levels of antibiotics. Pseudomonas aeruginosa and Pseudomonas protegens were exposed kanamycin, tetracycline or ciprofloxacin at 1/10 the minimal inhibitory concentration (MIC) in a serial streaking experiment over 40 passages. Significant changes in rep-PCR fingerprints were noted in both species when exposed to sub-inhibitory antibiotic concentrations. These changes were observed in as few as five passages, despite the fact that the protocols used sample less than 0.3% of the genome, in turn suggesting much more widespread alterations to sequence and genome architecture. Experimental lines also displayed variant colony morphologies. The final MICs were significantly higher in some experimental lineages of P. protegens, suggesting that 1/10 the MIC induces de-novo mutation events that generate resistance phenotypes. The implications of these results are clear: exposure of the environmental microbiome to antibiotic pollution will induce similar changes, including generating newly resistant species that may be of significant concern for human health.}, }
@article {pmid26296664, year = {2015}, author = {Siampour, M and Izadpanah, K and Marzachi, C and Salehi Abarkoohi, M}, title = {Identification and characterization of conserved and variable regions of lime witches' broom phytoplasma genome.}, journal = {Microbiology (Reading, England)}, volume = {161}, number = {Pt 9}, pages = {1741-1751}, doi = {10.1099/mic.0.000133}, pmid = {26296664}, issn = {1465-2080}, mesh = {Conserved Sequence ; DNA, Bacterial/genetics ; *Genome, Bacterial ; Minisatellite Repeats ; Phylogeny ; Phytoplasma/classification/*genetics/isolation &amp; purification ; Plant Diseases/*microbiology ; RNA, Ribosomal, 16S/genetics ; Vinca/*microbiology ; }, abstract = {Several segments (∼20 kbp) of the lime witches' broom (LWB) phytoplasma genome (16SrII group) were sequenced and analysed. A 5.7 kbp segment (LWB-C) included conserved genes whose phylogenetic tree was consistent with that generated using 16S rRNA genes. Another 6.4 kbp LWB phytoplasma genome segment (LWB-NC) was structurally similar to the putative mobile unit or sequence variable mosaic genomic region of phytoplasmas, although it represented a new arrangement of genes or pseudogenes such as phage-related protein genes and tra5 insertion sequences. Sequence- and phylogenetic-based evidence suggested that LWB-NC is a genomic region which includes horizontally transferred genes and could be regarded as a hot region to incorporate more foreign genes into the genome of LWB phytoplasma. The presence of phylogenetically related fragments of retroelements was also verified in the LWB phytoplasma genome. Putative intragenomic retrotransposition or retrohoming of these elements might have been determinant in shaping and manipulating the LWB phytoplasma genome. Altogether, the results of this study suggested that the genome of LWB phytoplasma is colonized by a variety of genes that have been acquired through horizontal gene transfer events, which may have further affected the genome through intragenomic mobility and insertion at cognate or incognate sites. Some of these genes are expected to have been involved in the development of features specific to LWB phytoplasma.}, }
@article {pmid26296655, year = {2015}, author = {Bhadauria, V and MacLachlan, R and Pozniak, C and Banniza, S}, title = {Candidate effectors contribute to race differentiation and virulence of the lentil anthracnose pathogen Colletotrichum lentis.}, journal = {BMC genomics}, volume = {16}, number = {1}, pages = {628}, pmid = {26296655}, issn = {1471-2164}, mesh = {Colletotrichum/*genetics/physiology ; Computer Simulation ; Expressed Sequence Tags ; Fungal Proteins/*genetics ; Gene Expression Profiling/*methods ; Gene Transfer, Horizontal ; Host Specificity ; Lens Plant/*microbiology ; Phylogeny ; Plant Leaves/microbiology ; Virulence Factors/*genetics ; }, abstract = {BACKGROUND: The hemibiotroph Colletotrichum lentis, causative agent of anthracnose on Lens culinaris (lentil) was recently described as a new species. During its interaction with the host plant, C. lentis likely secretes numerous effector proteins, including toxins to alter the plant's innate immunity, thereby gaining access to the host tissues for nutrition and reproduction.<br><br>RESULTS: In silico analysis of 2000 ESTs generated from C. lentis-infected lentil leaf tissues identified 15 candidate effectors. In planta infection stage-specific gene expression waves among candidate effectors were revealed for the appressorial penetration phase, biotrophic phase and necrotrophic phase. No sign of positive selection pressure [&#x3c9; (dN/dS)&#x2009;<&#x2009;1] in effectors was detected at the intraspecific level. A single nucleotide polymorphism in the ORF of candidate effector ClCE6, used to develop a KASPar marker, differentiated perfectly between pathogenic race 0 and race 1 isolates when tested on 52 isolates arbitrarily selected from a large culture collection representing the western Canadian population of C. lentis. Furthermore, an EST encoding argininosuccinate lyase (Arg) was identified as a bacterial gene. A toxin protein ClToxB was further characterized as a potential host-specific toxin through heterologous in planta expression. The knock-down of ClToxB transcripts by RNAi resulted in reduced virulence, suggesting that ClToxB is a virulence factor. In silico analysis of the ClToxB sequence and comparative genomics revealed that ToxB is unlikely a foreign gene in the C. lentis genome. Incongruency between established species relationships and that established based on gene sequence data confirmed ToxB arose through evolution from a common ancestor, whereas the bacterial gene Arg identified in C. lentis was horizontally transferred from bacteria.<br><br>CONCLUSIONS: EST mining and expression profiling revealed a set of in planta expressed candidate effectors. We developed a KASPar assay using effector polymorphism to differentiate C. lentis races. Comparative genomics revealed a foreign gene encoding a potential virulence factor Arg, which was horizontally transferred from bacteria into the genus Colletotrichum. ClToxB is further characterized as a host-specific toxin that is likely to contribute to quantitative differences in virulence between the races 0 and 1.}, }
@article {pmid26291765, year = {2015}, author = {Suzuki, K and Moriguchi, K and Yamamoto, S}, title = {Horizontal DNA transfer from bacteria to eukaryotes and a lesson from experimental transfers.}, journal = {Research in microbiology}, volume = {166}, number = {10}, pages = {753-763}, doi = {10.1016/j.resmic.2015.08.001}, pmid = {26291765}, issn = {1769-7123}, mesh = {Animals ; Bacteria/*genetics ; DNA, Bacterial/genetics ; Eukaryota/*genetics ; Evolution, Molecular ; Gene Transfer Techniques ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Phylogeny ; Type IV Secretion Systems/genetics/metabolism ; }, abstract = {Horizontal gene transfer (HGT) is widespread among bacteria and plays a key role in genome dynamics. HGT is much less common in eukaryotes, but is being reported with increasing frequency in eukaryotes. The mechanism as to how eukaryotes acquired genes from distantly related organisms remains obscure yet. This paper cites examples of bacteria-derived genes found in eukaryotic organisms, and then describes experimental DNA transports to eukaryotes by bacterial type 4 secretion systems in optimized conditions. The mechanisms of the latter are efficient, quite reproducible in vitro and predictable, and thereby would provide insight into natural HGT and to the development of new research tools.}, }
@article {pmid26287458, year = {2015}, author = {Ku, C and Nelson-Sathi, S and Roettger, M and Sousa, FL and Lockhart, PJ and Bryant, D and Hazkani-Covo, E and McInerney, JO and Landan, G and Martin, WF}, title = {Endosymbiotic origin and differential loss of eukaryotic genes.}, journal = {Nature}, volume = {524}, number = {7566}, pages = {427-432}, pmid = {26287458}, issn = {1476-4687}, mesh = {Archaea/genetics ; Bacteria/genetics ; Cluster Analysis ; Eukaryota/classification/*genetics ; Eukaryotic Cells/metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genome/genetics ; Mitochondria/genetics ; *Models, Genetic ; Organelles/*genetics ; Phylogeny ; Plastids/genetics ; Prokaryotic Cells/metabolism ; Proteome/genetics ; Symbiosis/*genetics ; Time Factors ; }, abstract = {Chloroplasts arose from cyanobacteria, mitochondria arose from proteobacteria. Both organelles have conserved their prokaryotic biochemistry, but their genomes are reduced, and most organelle proteins are encoded in the nucleus. Endosymbiotic theory posits that bacterial genes in eukaryotic genomes entered the eukaryotic lineage via organelle ancestors. It predicts episodic influx of prokaryotic genes into the eukaryotic lineage, with acquisition corresponding to endosymbiotic events. Eukaryotic genome sequences, however, increasingly implicate lateral gene transfer, both from prokaryotes to eukaryotes and among eukaryotes, as a source of gene content variation in eukaryotic genomes, which predicts continuous, lineage-specific acquisition of prokaryotic genes in divergent eukaryotic groups. Here we discriminate between these two alternatives by clustering and phylogenetic analysis of eukaryotic gene families having prokaryotic homologues. Our results indicate (1) that gene transfer from bacteria to eukaryotes is episodic, as revealed by gene distributions, and coincides with major evolutionary transitions at the origin of chloroplasts and mitochondria; (2) that gene inheritance in eukaryotes is vertical, as revealed by extensive topological comparison, sparse gene distributions stemming from differential loss; and (3) that continuous, lineage-specific lateral gene transfer, although it sometimes occurs, does not contribute to long-term gene content evolution in eukaryotic genomes.}, }
@article {pmid26286020, year = {2015}, author = {Li, X and Zhu, YG and Shaban, B and Bruxner, TJ and Bond, PL and Huang, L}, title = {Assessing the genetic diversity of Cu resistance in mine tailings through high-throughput recovery of full-length copA genes.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {13258}, pmid = {26286020}, issn = {2045-2322}, mesh = {Adenosine Triphosphatases/*genetics ; Biological Evolution ; Cation Transport Proteins/*genetics ; Copper/*toxicity ; Copper-Transporting ATPases ; *Genes, Bacterial ; *Genetic Variation ; *Industrial Waste ; Metagenome ; *Mining ; Phylogeny ; }, abstract = {Characterizing the genetic diversity of microbial copper (Cu) resistance at the community level remains challenging, mainly due to the polymorphism of the core functional gene copA. In this study, a local BLASTN method using a copA database built in this study was developed to recover full-length putative copA sequences from an assembled tailings metagenome; these sequences were then screened for potentially functioning CopA using conserved metal-binding motifs, inferred by evolutionary trace analysis of CopA sequences from known Cu resistant microorganisms. In total, 99 putative copA sequences were recovered from the tailings metagenome, out of which 70 were found with high potential to be functioning in Cu resistance. Phylogenetic analysis of selected copA sequences detected in the tailings metagenome showed that topology of the copA phylogeny is largely congruent with that of the 16S-based phylogeny of the tailings microbial community obtained in our previous study, indicating that the development of copA diversity in the tailings might be mainly through vertical descent with few lateral gene transfer events. The method established here can be used to explore copA (and potentially other metal resistance genes) diversity in any metagenome and has the potential to exhaust the full-length gene sequences for downstream analyses.}, }
@article {pmid26282127, year = {2015}, author = {McDonald, MJ and Chou, CH and Swamy, KB and Huang, HD and Leu, JY}, title = {The evolutionary dynamics of tRNA-gene copy number and codon-use in E. coli.}, journal = {BMC evolutionary biology}, volume = {15}, number = {}, pages = {163}, pmid = {26282127}, issn = {1471-2148}, mesh = {Amino Acids/genetics ; Biological Evolution ; *Codon ; Escherichia coli/*genetics ; Escherichia coli O157/genetics ; Gene Dosage ; *Gene Transfer, Horizontal ; Protein Biosynthesis ; RNA, Transfer/*genetics ; Shigella/classification/genetics ; }, abstract = {BACKGROUND: The introduction of foreign DNA by Lateral Gene Transfer (LGT) can quickly and drastically alter genome composition. Problems can arise if the genes introduced by LGT use codons that are not suited to the host's translational machinery. Here we investigate compensatory adaptation of E. coli in response to the introduction of large volumes of codons that are rarely used by the host genome.<br><br>RESULTS: We analyze genome sequences from the E. coli/Shigella complex, and find that certain tRNA genes are present in multiple copies in two pathogenic Shigella and O157:H7 subgroups of E. coli. Furthermore, we show that the codons that correspond to these multi-copy number tRNA genes are enriched in the high copy number Selfish Genetic Elements (SGE's) in Shigella and laterally introduced genes in O157:H7. We analyze the duplicate copies and find evidence for the selective retention of tRNA genes introduced by LGT in response to the changed codon content of the genome.<br><br>CONCLUSION: These data support a model where the relatively rapid influx of LGT genes and SGE's introduces a large number of genes maladapted to the host's translational machinery. Under these conditions, it becomes advantageous for the host to retain tRNA genes that are required for the incorporation of amino acids at these codons. Subsequently, the increased number of copies of these specific tRNA genes adjusts the cellular tRNA pool to the demands set by global shifts in codon usage.}, }
@article {pmid26276674, year = {2015}, author = {Youenou, B and Favre-Bonté, S and Bodilis, J and Brothier, E and Dubost, A and Muller, D and Nazaret, S}, title = {Comparative Genomics of Environmental and Clinical Stenotrophomonas maltophilia Strains with Different Antibiotic Resistance Profiles.}, journal = {Genome biology and evolution}, volume = {7}, number = {9}, pages = {2484-2505}, pmid = {26276674}, issn = {1759-6653}, mesh = {ATP-Binding Cassette Transporters/genetics ; Bacterial Proteins/genetics ; Drug Resistance, Bacterial/*genetics ; Environmental Microbiology ; Fusaric Acid/metabolism ; *Genome, Bacterial ; Genomics ; Humans ; Membrane Transport Proteins/genetics ; Phylogeny ; Stenotrophomonas maltophilia/classification/*drug effects/*genetics/isolation &amp; purification ; }, abstract = {Stenotrophomonas maltophilia, a ubiquitous Gram-negative γ-proteobacterium, has emerged as an important opportunistic pathogen responsible for nosocomial infections. A major characteristic of clinical isolates is their high intrinsic or acquired antibiotic resistance level. The aim of this study was to decipher the genetic determinism of antibiotic resistance among strains from different origins (i.e., natural environment and clinical origin) showing various antibiotic resistance profiles. To this purpose, we selected three strains isolated from soil collected in France or Burkina Faso that showed contrasting antibiotic resistance profiles. After whole-genome sequencing, the phylogenetic relationships of these 3 strains and 11 strains with available genome sequences were determined. Results showed that a strain's phylogeny did not match their origin or antibiotic resistance profiles. Numerous antibiotic resistance coding genes and efflux pump operons were revealed by the genome analysis, with 57% of the identified genes not previously described. No major variation in the antibiotic resistance gene content was observed between strains irrespective of their origin and antibiotic resistance profiles. Although environmental strains generally carry as many multidrug resistant (MDR) efflux pumps as clinical strains, the absence of resistance-nodulation-division (RND) pumps (i.e., SmeABC) previously described to be specific to S. maltophilia was revealed in two environmental strains (BurA1 and PierC1). Furthermore the genome analysis of the environmental MDR strain BurA1 showed the absence of SmeABC but the presence of another putative MDR RND efflux pump, named EbyCAB on a genomic island probably acquired through horizontal gene transfer.}, }
@article {pmid26275904, year = {2015}, author = {Xiao, L and Ptacek, T and Osborne, JD and Crabb, DM and Simmons, WL and Lefkowitz, EJ and Waites, KB and Atkinson, TP and Dybvig, K}, title = {Comparative genome analysis of Mycoplasma pneumoniae.}, journal = {BMC genomics}, volume = {16}, number = {1}, pages = {610}, pmid = {26275904}, issn = {1471-2164}, support = {UL1TR00165/TR/NCATS NIH HHS/United States ; UL1 TR000165/TR/NCATS NIH HHS/United States ; R01AI63909/AI/NIAID NIH HHS/United States ; R01 AI063909/AI/NIAID NIH HHS/United States ; UL1 TR001417/TR/NCATS NIH HHS/United States ; }, mesh = {China ; Comparative Genomic Hybridization ; England ; Evolution, Molecular ; Genetic Variation ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Mycoplasma pneumoniae/*classification/genetics/*isolation &amp; purification ; Phylogeny ; Sequence Analysis, DNA/*methods ; Sequence Homology, Nucleic Acid ; United States ; }, abstract = {BACKGROUND: Mycoplasma pneumoniae is a common pathogen that causes upper and lower respiratory tract infections in people of all ages, responsible for up to 40% of community-acquired pneumonias. It also causes a wide array of extrapulmonary infections and autoimmune phenomena. Phylogenetic studies of the organism have been generally restricted to specific genes or regions of the genome, because whole genome sequencing has been completed for only 4 strains. To better understand the physiology and pathogenicity of this important human pathogen, we performed comparative genomic analysis of 15 strains of M. pneumoniae that were isolated between the 1940s to 2009 from respiratory specimens and cerebrospinal fluid originating from the USA, China and England.<br><br>RESULTS: Illumina MiSeq whole genome sequencing was performed on the 15 strains and all genome sequences were completed. Results from the comparative genomic analysis indicate that although about 1500 SNP and indel variants exist between type1 and type 2 strains, there is an overall high degree of sequence similarity among the strains (>99% identical to each other). Within the two subtypes, conservation of most genes, including the CARDS toxin gene and arginine deiminase genes, was observed. The major variation occurs in the P1 and ORF6 genes associated with the adhesin complex. Multiple hsdS genes (encodes S subunit of type I restriction enzyme) with variable tandem repeat copy numbers were found in all 15 genomes.<br><br>CONCLUSIONS: These data indicate that despite conclusions drawn from 16S rRNA sequences suggesting rapid evolution, the M. pneumoniae genome is extraordinarily stable over time and geographic distance across the globe with a striking lack of evidence of horizontal gene transfer.}, }
@article {pmid26275815, year = {2015}, author = {Ruffner, B and Péchy-Tarr, M and Höfte, M and Bloemberg, G and Grunder, J and Keel, C and Maurhofer, M}, title = {Evolutionary patchwork of an insecticidal toxin shared between plant-associated pseudomonads and the insect pathogens Photorhabdus and Xenorhabdus.}, journal = {BMC genomics}, volume = {16}, number = {1}, pages = {609}, pmid = {26275815}, issn = {1471-2164}, mesh = {Animals ; Bacterial Toxins/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Insecta/microbiology ; Insecticides/pharmacology ; Multigene Family ; Photorhabdus/genetics/*metabolism ; Phylogeny ; Plants/microbiology ; Pseudomonas fluorescens/genetics/*metabolism ; Xenorhabdus/genetics/*metabolism ; }, abstract = {BACKGROUND: Root-colonizing fluorescent pseudomonads are known for their excellent abilities to protect plants against soil-borne fungal pathogens. Some of these bacteria produce an insecticidal toxin (Fit) suggesting that they may exploit insect hosts as a secondary niche. However, the ecological relevance of insect toxicity and the mechanisms driving the evolution of toxin production remain puzzling.<br><br>RESULTS: Screening a large collection of plant-associated pseudomonads for insecticidal activity and presence of the Fit toxin revealed that Fit is highly indicative of insecticidal activity and predicts that Pseudomonas protegens and P. chlororaphis are exclusive Fit producers. A comparative evolutionary analysis of Fit toxin-producing Pseudomonas including the insect-pathogenic bacteria Photorhabdus and Xenorhadus, which produce the Fit related Mcf toxin, showed that fit genes are part of a dynamic genomic region with substantial presence/absence polymorphism and local variation in GC base composition. The patchy distribution and phylogenetic incongruence of fit genes indicate that the Fit cluster evolved via horizontal transfer, followed by functional integration of vertically transmitted genes, generating a unique Pseudomonas-specific insect toxin cluster.<br><br>CONCLUSIONS: Our findings suggest that multiple independent evolutionary events led to formation of at least three versions of the Mcf/Fit toxin highlighting the dynamic nature of insect toxin evolution.}, }
@article {pmid26275230, year = {2015}, author = {Chaplin, AV and Efimov, BA and Smeianov, VV and Kafarskaia, LI and Pikina, AP and Shkoporov, AN}, title = {Intraspecies Genomic Diversity and Long-Term Persistence of Bifidobacterium longum.}, journal = {PloS one}, volume = {10}, number = {8}, pages = {e0135658}, pmid = {26275230}, issn = {1932-6203}, mesh = {Bifidobacterium/*genetics/isolation &amp; purification ; Child ; Child, Preschool ; Clustered Regularly Interspaced Short Palindromic Repeats ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; *Genetic Variation ; Genome, Bacterial ; Glycoside Hydrolases/genetics ; Humans ; Infant ; Longitudinal Studies ; Minisatellite Repeats ; Molecular Sequence Data ; *Phylogeny ; Plasmids ; }, abstract = {Members of genus Bifidobacterium are Gram-positive bacteria, representing a large part of the human infant microbiota and moderately common in adults. However, our knowledge about their diversity, intraspecific phylogeny and long-term persistence in humans is still limited. Bifidobacterium longum is generally considered to be the most common and prevalent species in the intestinal microbiota. In this work we studied whole genome sequences of 28 strains of B. longum, including 8 sequences described in this paper. Part of these strains were isolated from healthy children during a long observation period (up to 10 years between isolation from the same patient). The three known subspecies (longum, infantis and suis) could be clearly divided using sequence-based phylogenetic methods, gene content and the average nucleotide identity. The profiles of glycoside hydrolase genes reflected the different ecological specializations of these three subspecies. The high impact of horizontal gene transfer on genomic diversity was observed, which is possibly due to a large number of prophages and rapidly spreading plasmids. The pan-genome characteristics of the subspecies longum corresponded to the open pan-genome model. While the major part of the strain-specific genetic loci represented transposons and phage-derived regions, a large number of cell envelope synthesis genes were also observed within this category, representing high variability of cell surface molecules. We observed the cases of isolation of high genetically similar strains of B. longum from the same patients after long periods of time, however, we didn't succeed in the isolation of genetically identical bacteria: a fact, reflecting the high plasticity of microbiota in children.}, }
@article {pmid26273559, year = {2015}, author = {da Silva, SM and Amaral, C and Neves, SS and Santos, C and Pimentel, C and Rodrigues-Pousada, C}, title = {An HcpR paralog of Desulfovibrio gigas provides protection against nitrosative stress.}, journal = {FEBS open bio}, volume = {5}, number = {}, pages = {594-604}, pmid = {26273559}, issn = {2211-5463}, abstract = {Desulfovibrio gigas belongs to the group of sulfate reducing bacteria (SRB). These ubiquitous and metabolically versatile microorganisms are often exposed to reactive nitrogen species (RNS). Nonetheless, the mechanisms and regulatory elements involved in nitrosative stress protection are still poorly understood. The transcription factor HcpR has emerged as a putative regulator of nitrosative stress response among anaerobic bacteria. HcpR is known to orchestrate the expression of the hybrid cluster protein gene, hcp, proposed to be involved in cellular defense against RNS. According to phylogenetic analyses, the occurrence of hcpR paralog genes is a common feature among several Desulfovibrio species. Within the D. gigas genome we have identified two HcpR-related sequences. One of these sequences, hcpR1, was found in the close vicinity of the hcp gene and this finding prompted us to proceed with its functional characterization. We observed that the growth of a D. gigas strain lacking hcpR1 is severely impaired under nitrosative stress. An in silico search revealed several putative targets of HcpR1 that were experimentally validated. The fact that HcpR1 regulates several genes encoding proteins involved in nitrite and nitrate metabolism, together with the sensitive growth phenotype to NO displayed by an hcpR1 mutant strain, strongly supports a relevant role of this factor under nitrosative stress. Moreover, the finding that several Desulfovibrio species possess HcpR paralogs, which have been transmitted vertically in the evolution and diversification of the genus, suggests that these sequences may confer adaptive or survival advantage to these organisms, possibly by increasing their tolerance to nitrosative stress.}, }
@article {pmid26271942, year = {2015}, author = {Vanga, BR and Ramakrishnan, P and Butler, RC and Toth, IK and Ronson, CW and Jacobs, JM and Pitman, AR}, title = {Mobilization of horizontally acquired island 2 is induced in planta in the phytopathogen Pectobacterium atrosepticum SCRI1043 and involves the putative relaxase ECA0613 and quorum sensing.}, journal = {Environmental microbiology}, volume = {17}, number = {11}, pages = {4730-4744}, doi = {10.1111/1462-2920.13024}, pmid = {26271942}, issn = {1462-2920}, mesh = {Amino Acid Sequence ; Gene Transfer, Horizontal ; Indenes/metabolism ; Islands ; Molecular Sequence Data ; Pectobacterium/*genetics/metabolism/*pathogenicity ; Plant Diseases/*microbiology ; Quorum Sensing/genetics ; Sequence Alignment ; Solanum tuberosum/*microbiology ; Virulence Factors/*genetics/metabolism ; }, abstract = {Integrative and conjugative elements (ICEs) contribute to the rapid evolution of bacterial pathogens via horizontal gene transfer of virulence determinants. ICEs have common mechanisms for transmission, yet the cues triggering this process under natural environmental or physiological conditions are largely unknown. In this study, mobilization of the putative ICE horizontally acquired island 2 (HAI2), present in the chromosome of the phytopathogen Pectobacterium atrosepticum SCRI1043, was examined during infection of the host plant potato. Under these conditions, mobilization of HAI2 increased markedly compared with in vitro cultures. In planta-induced mobilization of HAI2 was regulated by quorum sensing and involved the putative ICE-encoded relaxase ECA0613. Disruption of ECA0613 also reduced transcription of genes involved in production of coronafacic acid (Cfa), the major virulence factor harboured on HAI2, whereas their expression was unaffected in the quorum-sensing (expI) mutant. Thus, suppression of cfa gene expression was not regulated by the mobilization of the ICE per se, but was due directly to inactivation of the relaxase. The identification of genetic factors associated solely with in planta mobilization of an ICE demonstrates that this process is highly adapted to the natural environment of the bacterial host and can influence the expression of virulence determinants.}, }
@article {pmid26262891, year = {2015}, author = {Kang, F and Hu, X and Liu, J and Gao, Y}, title = {Noncovalent Binding of Polycyclic Aromatic Hydrocarbons with Genetic Bases Reducing the in Vitro Lateral Transfer of Antibiotic Resistant Genes.}, journal = {Environmental science &amp; technology}, volume = {49}, number = {17}, pages = {10340-10348}, doi = {10.1021/acs.est.5b02293}, pmid = {26262891}, issn = {1520-5851}, mesh = {Ampicillin Resistance/*genetics ; *Base Pairing ; Binding Sites ; Fluorescence ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Microscopy, Atomic Force ; Plasmids/genetics ; Polycyclic Aromatic Hydrocarbons/*metabolism ; Spectroscopy, Fourier Transform Infrared ; Thermodynamics ; }, abstract = {In current studies of noncovalent interactions of polycyclic aromatic hydrocarbons (PAHs) with genetic units, the impact of such interactions on gene transfer has not been explored. In this study, we examined the association of some widely occurring PAHs (phenanthrene, pyrene, benzo[g,h,i]perylene, and other congeners) with antibiotic resistant plasmids (pUC19). Small molecular PAHs (e.g., phenanthrene) bind effectively with plasmids to form a loosely clew-like plasmid-PAH complex (16.5-49.5 nm), resulting in reduced transformation of ampicillin resistance gene (Ampr). The in vitro transcription analysis demonstrated that reduced transformation of Ampr in plasmids results from the PAH-inhibited Ampr transcription to RNA. Fluorescence microtitration coupled with Fourier transform infrared spectroscopy (FTIR) and theoretical interaction models showed that adenine in plasmid has a stronger capacity to sequester small Phen and Pyre molecules via a π-π attraction. Changes in Gibbs free energy (ΔG) suggest that the CT-PAH model reliably depicts the plasmid-PAH interaction through a noncovalently physical sorption mechanism. Considering the wide occurrence of PAHs and antibiotic resistant genes (ARGs) in the environment, our findings suggest that small-sized PAHs can well affect the behavior of ARGs via above-described noncovalent interactions.}, }
@article {pmid26261348, year = {2015}, author = {Lee, CT and Chen, IT and Yang, YT and Ko, TP and Huang, YT and Huang, JY and Huang, MF and Lin, SJ and Chen, CY and Lin, SS and Lightner, DV and Wang, HC and Wang, AH and Wang, HC and Hor, LI and Lo, CF}, title = {The opportunistic marine pathogen Vibrio parahaemolyticus becomes virulent by acquiring a plasmid that expresses a deadly toxin.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {34}, pages = {10798-10803}, pmid = {26261348}, issn = {1091-6490}, mesh = {Animals ; Bacterial Proteins/genetics/*isolation &amp; purification ; Bacterial Toxins/genetics/*isolation &amp; purification ; Conjugation, Genetic ; DNA, Bacterial/genetics ; Genes, Bacterial ; Models, Molecular ; Molecular Sequence Data ; Open Reading Frames/genetics ; Penaeidae/microbiology ; Plasmids/genetics/*metabolism ; Porins/chemistry ; Protein Conformation ; Sequence Homology, Nucleic Acid ; Vibrio parahaemolyticus/genetics/*pathogenicity ; Virulence/genetics ; }, abstract = {Acute hepatopancreatic necrosis disease (AHPND) is a severe, newly emergent penaeid shrimp disease caused by Vibrio parahaemolyticus that has already led to tremendous losses in the cultured shrimp industry. Until now, its disease-causing mechanism has remained unclear. Here we show that an AHPND-causing strain of V. parahaemolyticus contains a 70-kbp plasmid (pVA1) with a postsegregational killing system, and that the ability to cause disease is abolished by the natural absence or experimental deletion of the plasmid-encoded homologs of the Photorhabdus insect-related (Pir) toxins PirA and PirB. We determined the crystal structure of the V. parahaemolyticus PirA and PirB (PirA(vp) and PirB(vp)) proteins and found that the overall structural topology of PirA(vp)/PirB(vp) is very similar to that of the Bacillus Cry insecticidal toxin-like proteins, despite the low sequence identity (<10%). This structural similarity suggests that the putative PirAB(vp) heterodimer might emulate the functional domains of the Cry protein, and in particular its pore-forming activity. The gene organization of pVA1 further suggested that pirAB(vp) may be lost or acquired by horizontal gene transfer via transposition or homologous recombination.}, }
@article {pmid26260129, year = {2015}, author = {Feng, J and Qiu, Y and Yin, Z and Chen, W and Yang, H and Yang, W and Wang, J and Gao, Y and Zhou, D}, title = {Coexistence of a novel KPC-2-encoding MDR plasmid and an NDM-1-encoding pNDM-HN380-like plasmid in a clinical isolate of Citrobacter freundii.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {70}, number = {11}, pages = {2987-2991}, doi = {10.1093/jac/dkv232}, pmid = {26260129}, issn = {1460-2091}, mesh = {China ; Citrobacter freundii/drug effects/*enzymology/*genetics/isolation &amp; purification ; Conjugation, Genetic ; Enterobacteriaceae Infections/*microbiology ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Hospitals ; Humans ; Male ; Microbial Sensitivity Tests ; Middle Aged ; Plasmids/*analysis ; Polymerase Chain Reaction ; Shock, Septic/microbiology ; beta-Lactamases/*genetics/metabolism ; }, abstract = {OBJECTIVES: The objective of this study was to characterize the molecular mechanism of coproduction of KPC-2 and NDM-1 in Citrobacter freundii.<br><br>METHODS: C. freundii strain 112298 was isolated from a human case of septic shock in a Chinese teaching hospital. The major carbapenemase and ESBL genes were detected by PCR. The MIC values were determined by using VITEK 2 and antimicrobial susceptibility was judged by CLSI standards. The resistance plasmid was transferred into Escherichia coli by electroporation, followed by plasmid DNA isolation from the electroporant, and then fully sequenced and compared with closely related plasmids.<br><br>RESULTS: Strain 112298 produces KPC-2 and NDM-1, encoded by the novel non-typeable plasmid p112298-KPC and an IncX3-type plasmid p112298-NDM, respectively. In p112298-KPC, a Tn1722-based blaKPC-2-carrying transposon is associated with several additional resistance modules, constituting a single MDR region. Assembly of these resistance modules is likely mediated by homologous recombination between five copies of IS26 elements at different sites within the MDR region. p112298-NDM is a very close relation of pNDM-HN380. blaNDM-1 in p112298-NDM is carried by a Tn125 variant, which differs from the prototype Tn125 as observed in pNDM-BJ01 by disruption of an upstream copy of ISAba125 by IS5 and absence of a downstream copy of ISAba125.<br><br>CONCLUSIONS: Production of KPC-2 and NDM-1 by p112298-KPC and p112298-NDM, respectively, makes C. freundii 112298 highly resistant to carbapenems and, moreover, these two plasmids still harbour genes for resistance to cephalosporins, chloramphenicol, chromate, fosfomycin, quaternary ammonium, rifampicin and sulphonamides.}, }
@article {pmid26259823, year = {2015}, author = {Martín-Moldes, Z and Zamarro, MT and Del Cerro, C and Valencia, A and Gómez, MJ and Arcas, A and Udaondo, Z and García, JL and Nogales, J and Carmona, M and Díaz, E}, title = {Whole-genome analysis of Azoarcus sp. strain CIB provides genetic insights to its different lifestyles and predicts novel metabolic features.}, journal = {Systematic and applied microbiology}, volume = {38}, number = {7}, pages = {462-471}, doi = {10.1016/j.syapm.2015.07.002}, pmid = {26259823}, issn = {1618-0984}, mesh = {Adaptation, Biological ; Aerobiosis ; Anaerobiosis ; Azoarcus/*genetics/*physiology ; *Computational Biology ; Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Interspersed Repetitive Sequences ; Metabolic Networks and Pathways/*genetics ; Metals, Heavy/metabolism/toxicity ; Molecular Sequence Data ; *Multigene Family ; Nitrogen Fixation ; *Sequence Analysis, DNA ; }, abstract = {The genomic features of Azoarcus sp. CIB reflect its most distinguishing phenotypes as a diazotroph, facultative anaerobe, capable of degrading either aerobically and/or anaerobically a wide range of aromatic compounds, including some toxic hydrocarbons such as toluene and m-xylene, as well as its endophytic lifestyle. The analyses of its genome have expanded the catabolic potential of strain CIB toward common natural compounds, such as certain diterpenes, that were not anticipated as carbon sources. The high number of predicted solvent efflux pumps and heavy metal resistance gene clusters has provided the first evidence for two environmentally relevant features of this bacterium that remained unknown. Genome mining has revealed several gene clusters likely involved in the endophytic lifestyle of strain CIB, opening the door to the molecular characterization of some plant growth promoting traits. Horizontal gene transfer and mobile genetic elements appear to have played a major role as a mechanism of adaptation of this bacterium to different lifestyles. This work paves the way for a systems biology-based understanding of the abilities of Azoarcus sp. CIB to integrate aerobic and anaerobic metabolism of aromatic compounds, tolerate stress conditions, and interact with plants as an endophyte of great potential for phytostimulation and phytoremediation strategies. Comparative genomics provides an Azoarcus pan genome that confirms the global metabolic flexibility of this genus, and suggests that its phylogeny should be revisited.}, }
@article {pmid26259681, year = {2015}, author = {Tomova, A and Ivanova, L and Buschmann, AH and Rioseco, ML and Kalsi, RK and Godfrey, HP and Cabello, FC}, title = {Antimicrobial resistance genes in marine bacteria and human uropathogenic Escherichia coli from a region of intensive aquaculture.}, journal = {Environmental microbiology reports}, volume = {7}, number = {5}, pages = {803-809}, doi = {10.1111/1758-2229.12327}, pmid = {26259681}, issn = {1758-2229}, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Aquaculture/*methods ; Chile ; DNA, Bacterial/chemistry/genetics ; *Drug Resistance, Bacterial ; *Environmental Microbiology ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Molecular Sequence Data ; New York City ; Plasmids/analysis ; Sequence Analysis, DNA ; Sequence Homology ; Urinary Tract Infections/*microbiology ; Uropathogenic Escherichia coli/*isolation &amp; purification ; }, abstract = {Antimicrobials are heavily used in Chilean salmon aquaculture. We previously found significant differences in antimicrobial-resistant bacteria between sediments from an aquaculture and a non-aquaculture site. We now show that levels of antimicrobial resistance genes (ARG) are significantly higher in antimicrobial-selected marine bacteria than in unselected bacteria from these sites. While ARG in tetracycline- and florfenicol-selected bacteria from aquaculture and non-aquaculture sites were equally frequent, there were significantly more plasmid-mediated quinolone resistance genes per bacterium and significantly higher numbers of qnrB genes in quinolone-selected bacteria from the aquaculture site. Quinolone-resistant urinary Escherichia coli from patients in the Chilean aquacultural region were significantly enriched for qnrB (including a novel qnrB gene), qnrS, qnrA and aac(6')-1b, compared with isolates from New York City. Sequences of qnrA1, qnrB1 and qnrS1 in quinolone-resistant Chilean E. coli and Chilean marine bacteria were identical, suggesting horizontal gene transfer between antimicrobial-resistant marine bacteria and human pathogens.}, }
@article {pmid26257749, year = {2015}, author = {Wilkins, KE and Booher, NJ and Wang, L and Bogdanove, AJ}, title = {TAL effectors and activation of predicted host targets distinguish Asian from African strains of the rice pathogen Xanthomonas oryzae pv. oryzicola while strict conservation suggests universal importance of five TAL effectors.}, journal = {Frontiers in plant science}, volume = {6}, number = {}, pages = {536}, pmid = {26257749}, issn = {1664-462X}, abstract = {Xanthomonas oryzae pv. oryzicola (Xoc) causes the increasingly important disease bacterial leaf streak of rice (BLS) in part by type III delivery of repeat-rich transcription activator-like (TAL) effectors to upregulate host susceptibility genes. By pathogen whole genome, single molecule, real-time sequencing and host RNA sequencing, we compared TAL effector content and rice transcriptional responses across 10 geographically diverse Xoc strains. TAL effector content is surprisingly conserved overall, yet distinguishes Asian from African isolates. Five TAL effectors are conserved across all strains. In a prior laboratory assay in rice cv. Nipponbare, only two contributed to virulence in strain BLS256 but the strict conservation indicates all five may be important, in different rice genotypes or in the field. Concatenated and aligned, TAL effector content across strains largely reflects relationships based on housekeeping genes, suggesting predominantly vertical transmission. Rice transcriptional responses did not reflect these relationships, and on average, only 28% of genes upregulated and 22% of genes downregulated by a strain are up- and down- regulated (respectively) by all strains. However, when only known TAL effector targets were considered, the relationships resembled those of the TAL effectors. Toward identifying new targets, we used the TAL effector-DNA recognition code to predict effector binding elements in promoters of genes upregulated by each strain, but found that for every strain, all upregulated genes had at least one. Filtering with a classifier we developed previously decreases the number of predicted binding elements across the genome, suggesting that it may reduce false positives among upregulated genes. Applying this filter and eliminating genes for which upregulation did not strictly correlate with presence of the corresponding TAL effector, we generated testable numbers of candidate targets for four of the five strictly conserved TAL effectors.}, }
@article {pmid26257725, year = {2015}, author = {Chattopadhyay, MK and Jaganandham, MV}, title = {Vesicles-mediated resistance to antibiotics in bacteria.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {758}, pmid = {26257725}, issn = {1664-302X}, }
@article {pmid26254486, year = {2015}, author = {Choi, JY and Bubnell, JE and Aquadro, CF}, title = {Population Genomics of Infectious and Integrated Wolbachia pipientis Genomes in Drosophila ananassae.}, journal = {Genome biology and evolution}, volume = {7}, number = {8}, pages = {2362-2382}, pmid = {26254486}, issn = {1759-6653}, support = {R01 GM095793/GM/NIGMS NIH HHS/United States ; R01GM095793/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Drosophila/*microbiology ; *Evolution, Molecular ; Female ; *Genetic Variation ; *Genome, Bacterial ; Genome, Mitochondrial ; Genomics ; Heterozygote ; Polymorphism, Genetic ; Sequence Alignment ; Wolbachia/*genetics ; }, abstract = {Coevolution between Drosophila and its endosymbiont Wolbachia pipientis has many intriguing aspects. For example, Drosophila ananassae hosts two forms of W. pipientis genomes: One being the infectious bacterial genome and the other integrated into the host nuclear genome. Here, we characterize the infectious and integrated genomes of W. pipientis infecting D. ananassae (wAna), by genome sequencing 15 strains of D. ananassae that have either the infectious or integrated wAna genomes. Results indicate evolutionarily stable maternal transmission for the infectious wAna genome suggesting a relatively long-term coevolution with its host. In contrast, the integrated wAna genome showed pseudogene-like characteristics accumulating many variants that are predicted to have deleterious effects if present in an infectious bacterial genome. Phylogenomic analysis of sequence variation together with genotyping by polymerase chain reaction of large structural variations indicated several wAna variants among the eight infectious wAna genomes. In contrast, only a single wAna variant was found among the seven integrated wAna genomes examined in lines from Africa, south Asia, and south Pacific islands suggesting that the integration occurred once from a single infectious wAna genome and then spread geographically. Further analysis revealed that for all D. ananassae we examined with the integrated wAna genomes, the majority of the integrated wAna genomic regions is represented in at least two copies suggesting a double integration or single integration followed by an integrated genome duplication. The possible evolutionary mechanism underlying the widespread geographical presence of the duplicate integration of the wAna genome is an intriguing question remaining to be answered.}, }
@article {pmid26254485, year = {2015}, author = {Lo, WS and Gasparich, GE and Kuo, CH}, title = {Found and Lost: The Fates of Horizontally Acquired Genes in Arthropod-Symbiotic Spiroplasma.}, journal = {Genome biology and evolution}, volume = {7}, number = {9}, pages = {2458-2472}, pmid = {26254485}, issn = {1759-6653}, mesh = {Animals ; Arthropods/microbiology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Interspersed Repetitive Sequences ; Phylogeny ; Spiroplasma/classification/*genetics ; Symbiosis ; }, abstract = {Horizontal gene transfer (HGT) is an important mechanism that contributed to biological diversity, particularly in bacteria. Through acquisition of novel genes, the recipient cell may change its ecological preference and the process could promote speciation. In this study, we determined the complete genome sequence of two Spiroplasma species for comparative analyses and inferred the putative gene gains and losses. Although most Spiroplasma species are symbionts of terrestrial insects, Spiroplasma eriocheiris has evolved to be a lethal pathogen of freshwater crustaceans. We found that approximately 7% of the genes in this genome may have originated from HGT and these genes expanded the metabolic capacity of this organism. Through comparison with the closely related Spiroplasma atrichopogonis, as well as other more divergent lineages, our results indicated that these HGT events could be traced back to the most recent common ancestor of these two species. However, most of these horizontally acquired genes have been pseudogenized in S. atrichopogonis, suggesting that they did not contribute to the fitness of this lineage that maintained the association with terrestrial insects. Thus, accumulation of small deletions that disrupted these foreign genes was not countered by natural selection. On the other hand, the long-term survival of these horizontally acquired genes in the S. eriocheiris genome hinted that they might play a role in the ecological shift of this species. Finally, the implications of these findings and the conflicts among gene content, 16S rRNA gene sequencing, and serological typing, are discussed in light of defining bacterial species.}, }
@article {pmid26248371, year = {2015}, author = {Zhang, S and Ma, R and Liu, X and Zhang, X and Sun, B}, title = {Modulation of ccrAB Expression and SCCmec Excision by an Inverted Repeat Element and SarS in Methicillin-Resistant Staphylococcus aureus.}, journal = {Antimicrobial agents and chemotherapy}, volume = {59}, number = {10}, pages = {6223-6232}, pmid = {26248371}, issn = {1098-6596}, mesh = {Amino Acid Sequence ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics/metabolism ; Base Sequence ; Binding Sites ; DNA-Binding Proteins/*genetics/metabolism ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; *Inverted Repeat Sequences ; Methicillin/*pharmacology ; Methicillin-Resistant Staphylococcus aureus/drug effects/*genetics/metabolism ; Molecular Sequence Data ; Promoter Regions, Genetic ; Protein Binding ; Recombinases/chemistry/*genetics/metabolism ; Repressor Proteins ; Sequence Alignment ; beta-Lactam Resistance ; }, abstract = {Methicillin-resistant Staphylococcus aureus (MRSA) is a notorious human pathogen that can cause a broad spectrum of infections. MRSA strains are resistant to almost the entire family of β-lactam antibiotics due to the acquisition of staphylococcal cassette chromosome mec (SCCmec). The chromosome cassette recombinases A and B, encoded by ccrAB genes located on SCCmec, play a key role in the excision of SCCmec. Studies have shown that ccrAB genes are expressed in only a minority of cells, suggesting the involvement of a subtle regulatory mechanism in ccrAB expression which has not been uncovered. Here, we found that an inverted repeat (IR) element, existing extensively and conservatively within the ccrAB promoter of different SCCmec types, played a repressive role in ccrAB expression and SCCmec excision in MRSA strain N315. Replacement of the IR sequence led to a significant increase in ccrAB expression and curing of SCCmec from strain N315 cells. In addition, we identified the transcriptional regulator SarS using DNA-affinity chromatography and further demonstrated that SarS can bind to the IR sequence and upregulate ccrAB expression and SCCmec excision. These findings reveal a molecular mechanism regulating ccrAB expression and SCCmec excision and may provide mechanic insights into the lateral transfer of SCCmec and spread of antibiotic resistance in S. aureus.}, }
@article {pmid26247891, year = {2015}, author = {Caniça, M and Manageiro, V and Jones-Dias, D and Clemente, L and Gomes-Neves, E and Poeta, P and Dias, E and Ferreira, E}, title = {Current perspectives on the dynamics of antibiotic resistance in different reservoirs.}, journal = {Research in microbiology}, volume = {166}, number = {7}, pages = {594-600}, doi = {10.1016/j.resmic.2015.07.009}, pmid = {26247891}, issn = {1769-7123}, mesh = {Animals ; Bacteria/*drug effects/genetics ; Bacterial Infections/*microbiology/*veterinary ; *Drug Resistance, Bacterial ; *Environmental Microbiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Interspersed Repetitive Sequences ; }, abstract = {Antibiotic resistance consists of a dynamic web. In this review, we describe the path by which different antibiotic residues and antibiotic resistance genes disseminate among relevant reservoirs (human, animal, and environmental settings), evaluating how these events contribute to the current scenario of antibiotic resistance. The relationship between the spread of resistance and the contribution of different genetic elements and events is revisited, exploring examples of the processes by which successful mobile resistance genes spread across different niches. The importance of classic and next generation molecular approaches, as well as action plans and policies which might aid in the fight against antibiotic resistance, are also reviewed.}, }
@article {pmid26247404, year = {2015}, author = {Perez-Rueda, E and Ibarra, JA}, title = {Distribution of putative xenogeneic silencers in prokaryote genomes.}, journal = {Computational biology and chemistry}, volume = {58}, number = {}, pages = {167-172}, doi = {10.1016/j.compbiolchem.2015.06.007}, pmid = {26247404}, issn = {1476-928X}, mesh = {Bacterial Proteins/*genetics ; DNA-Binding Proteins/*genetics ; Gene Transfer, Horizontal/genetics ; *Genome, Archaeal ; *Genome, Bacterial ; Repressor Proteins/*genetics ; }, abstract = {Gene silencing is an important function as it keeps newly acquired foreign DNA repressed, thereby avoiding possible deleterious effects in the host organism. Known transcriptional regulators associated with this process are called xenogeneic silencers (XS) and belong to either the H-NS, Lsr2, MvaT or Rok families. In the work described here we looked for XS-like regulators and their distribution in prokaryotic organisms was evaluated. Our analysis showed that putative XS regulators similar to H-NS, Lsr2, MvaT or Rok are present only in bacteria (31.7%). This does not exclude the existence of alternative XS in the rest of the organisms analyzed. Additionally, of the four XS groups evaluated in this work, those from the H-NS family have diversified more than the other groups. In order to compare the distribution of these putative XS regulators we also searched for other nucleoid-associated proteins (NAPs) not included in this group such as Fis, EbfC/YbaB, HU/IHF and Alba. Results showed that NAPs from the Fis, EbfC/YbaB, HU/IHF and Alba families are widely (94%) distributed among prokaryotes. These NAPs were found in multiple combinations with or without XS-like proteins. In regard with XS regulators, results showed that only XS proteins from one family were found in those organisms containing them. This suggests specificity for this type of regulators and their corresponding genomes.}, }
@article {pmid26243776, year = {2015}, author = {O'Brien, FG and Yui Eto, K and Murphy, RJ and Fairhurst, HM and Coombs, GW and Grubb, WB and Ramsay, JP}, title = {Origin-of-transfer sequences facilitate mobilisation of non-conjugative antimicrobial-resistance plasmids in Staphylococcus aureus.}, journal = {Nucleic acids research}, volume = {43}, number = {16}, pages = {7971-7983}, pmid = {26243776}, issn = {1362-4962}, mesh = {Bacterial Proteins/genetics ; Base Sequence ; Conjugation, Genetic ; Conserved Sequence ; DNA, Bacterial/*chemistry ; Drug Resistance, Bacterial/*genetics ; *Gene Transfer, Horizontal ; Inverted Repeat Sequences ; Plasmids/*genetics ; Recombination, Genetic ; Sequence Alignment ; Sequence Analysis, DNA ; Staphylococcus aureus/*genetics ; }, abstract = {Staphylococcus aureus is a common cause of hospital, community and livestock-associated infections and is increasingly resistant to multiple antimicrobials. A significant proportion of antimicrobial-resistance genes are plasmid-borne, but only a minority of S. aureus plasmids encode proteins required for conjugative transfer or Mob relaxase proteins required for mobilisation. The pWBG749 family of S. aureus conjugative plasmids can facilitate the horizontal transfer of diverse antimicrobial-resistance plasmids that lack Mob genes. Here we reveal that these mobilisable plasmids carry copies of the pWBG749 origin-of-transfer (oriT) sequence and that these oriT sequences facilitate mobilisation by pWBG749. Sequences resembling the pWBG749 oriT were identified on half of all sequenced S. aureus plasmids, including the most prevalent large antimicrobial-resistance/virulence-gene plasmids, pIB485, pMW2 and pUSA300HOUMR. oriT sequences formed five subfamilies with distinct inverted-repeat-2 (IR2) sequences. pWBG749-family plasmids encoding each IR2 were identified and pWBG749 mobilisation was found to be specific for plasmids carrying matching IR2 sequences. Specificity of mobilisation was conferred by a putative ribbon-helix-helix-protein gene smpO. Several plasmids carried 2-3 oriT variants and pWBG749-mediated recombination occurred between distinct oriT sites during mobilisation. These observations suggest this relaxase-in trans mechanism of mobilisation by pWBG749-family plasmids is a common mechanism of plasmid dissemination in S. aureus.}, }
@article {pmid26242601, year = {2015}, author = {Bentkowski, P and Van Oosterhout, C and Mock, T}, title = {A Model of Genome Size Evolution for Prokaryotes in Stable and Fluctuating Environments.}, journal = {Genome biology and evolution}, volume = {7}, number = {8}, pages = {2344-2351}, pmid = {26242601}, issn = {1759-6653}, mesh = {Computer Simulation ; *Evolution, Molecular ; *Gene-Environment Interaction ; Genetic Fitness ; *Genome Size ; *Genome, Microbial ; *Models, Genetic ; Prokaryotic Cells ; }, abstract = {Temporal variability in ecosystems significantly impacts species diversity and ecosystem productivity and therefore the evolution of organisms. Different levels of environmental perturbations such as seasonal fluctuations, natural disasters, and global change have different impacts on organisms and therefore their ability to acclimatize and adapt. Thus, to understand how organisms evolve under different perturbations is a key for predicting how environmental change will impact species diversity and ecosystem productivity. Here, we developed a computer simulation utilizing the individual-based model approach to investigate genome size evolution of a haploid, clonal and free-living prokaryotic population across different levels of environmental perturbations. Our results show that a greater variability of the environment resulted in genomes with a larger number of genes. Environmental perturbations were more effectively buffered by populations of individuals with relatively large genomes. Unpredictable changes of the environment led to a series of population bottlenecks followed by adaptive radiations. Our model shows that the evolution of genome size is indirectly driven by the temporal variability of the environment. This complements the effects of natural selection directly acting on genome optimization. Furthermore, species that have evolved in relatively stable environments may face the greatest risk of extinction under global change as genome streamlining genetically constrains their ability to acclimatize to the new environmental conditions, unless mechanisms of genetic diversification such as horizontal gene transfer will enrich their gene pool and therefore their potential to adapt.}, }
@article {pmid26240317, year = {2015}, author = {Dalia, AB and Seed, KD and Calderwood, SB and Camilli, A}, title = {A globally distributed mobile genetic element inhibits natural transformation of Vibrio cholerae.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {33}, pages = {10485-10490}, pmid = {26240317}, issn = {1091-6490}, support = {AI058935/AI/NIAID NIH HHS/United States ; R01 AI055058/AI/NIAID NIH HHS/United States ; AI055058/AI/NIAID NIH HHS/United States ; //Howard Hughes Medical Institute/United States ; U01 AI058935/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/*genetics/physiology ; Bangladesh ; Chitin/chemistry ; Cholera/genetics/microbiology ; Conjugation, Genetic ; DNA/metabolism ; DNA, Bacterial/genetics ; Deoxyribonuclease I/metabolism ; Deoxyribonucleases/chemistry ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Haiti ; Humans ; *Interspersed Repetitive Sequences ; Lac Operon ; Models, Genetic ; Mutation ; Periplasm/metabolism ; Phylogeny ; Prevalence ; *Transformation, Bacterial ; Vibrio cholerae/*genetics/metabolism ; beta-Lactamases/metabolism ; }, abstract = {Natural transformation is one mechanism of horizontal gene transfer (HGT) in Vibrio cholerae, the causative agent of cholera. Recently, it was found that V. cholerae isolates from the Haiti outbreak were poorly transformed by this mechanism. Here, we show that an integrating conjugative element (ICE)-encoded DNase, which we name IdeA, is necessary and sufficient for inhibiting natural transformation of Haiti outbreak strains. We demonstrate that IdeA inhibits this mechanism of HGT in cis via DNA endonuclease activity that is localized to the periplasm. Furthermore, we show that natural transformation between cholera strains in a relevant environmental context is inhibited by IdeA. The ICE encoding IdeA is globally distributed. Therefore, we analyzed the prevalence and role for this ICE in limiting natural transformation of isolates from Bangladesh collected between 2001 and 2011. We found that IdeA(+) ICEs were nearly ubiquitous in isolates from 2001 to 2005; however, their prevalence decreased to ∼40% from 2006 to 2011. Thus, IdeA(+) ICEs may have limited the role of natural transformation in V. cholerae. However, the rise in prevalence of strains lacking IdeA may now increase the role of this conserved mechanism of HGT in the evolution of this pathogen.}, }
@article {pmid26239726, year = {2015}, author = {Zhou, J and Cheng, Y and Lv, M and Liao, L and Chen, Y and Gu, Y and Liu, S and Jiang, Z and Xiong, Y and Zhang, L}, title = {The complete genome sequence of Dickeya zeae EC1 reveals substantial divergence from other Dickeya strains and species.}, journal = {BMC genomics}, volume = {16}, number = {1}, pages = {571}, pmid = {26239726}, issn = {1471-2164}, mesh = {Base Sequence ; Chromosome Mapping ; Enterobacteriaceae/*genetics/pathogenicity ; *Genome, Bacterial ; *Genomics ; Macrolides/metabolism ; Oryza/genetics/microbiology ; Phylogeny ; Plant Diseases/*genetics/microbiology ; Polyamines/metabolism ; }, abstract = {BACKGROUND: Dickeya zeae is a bacterial species that infects monocotyledons and dicotyledons. Two antibiotic-like phytotoxins named zeamine and zeamine II were reported to play an important role in rice seed germination, and two genes associated with zeamines production, i.e., zmsA and zmsK, have been thoroughly characterized. However, other virulence factors and its molecular mechanisms of host specificity and pathogenesis are hardly known.<br><br>RESULTS: The complete genome of D. zeae strain EC1 isolated from diseased rice plants was sequenced, annotated, and compared with the genomes of other Dickeya spp.. The pathogen contains a chromosome of 4,532,364 bp with 4,154 predicted protein-coding genes. Comparative genomics analysis indicates that D. zeae EC1 is most co-linear with D. chrysanthemi Ech1591, most conserved with D. zeae Ech586 and least similar to D. paradisiaca Ech703. Substantial genomic rearrangement was revealed by comparing EC1 with Ech586 and Ech703. Most virulence genes were well-conserved in Dickeya strains except Ech703. Significantly, the zms gene cluster involved in biosynthesis of zeamines, which were shown previously as key virulence determinants, is present in D. zeae strains isolated from rice, and some D. solani strains, but absent in other Dickeya species and the D. zeae strains isolated from other plants or sources. In addition, a DNA fragment containing 9 genes associated with fatty acid biosynthesis was found inserted in the fli gene cluster encoding flagellar biosynthesis of strain EC1 and other two rice isolates but not in other strains. This gene cluster shares a high protein similarity to the fatty acid genes from Pantoea ananatis.<br><br>CONLUSION: Our findings delineate the genetic background of D. zeae EC1, which infects both dicotyledons and monocotyledons, and suggest that D. zeae strains isolated from rice could be grouped into a distinct pathovar, i.e., D. zeae subsp. oryzae. In addition, the results of this study also unveiled that the zms gene cluster presented in the genomes of D. zeae rice isolates and D. solani strains, and the fatty acid genes inserted in the fli gene cluster of strain EC1 were likely derived from horizontal gene transfer during later stage of bacterial evolution.}, }
@article {pmid26239519, year = {2015}, author = {Smith, SA and Moore, MJ and Brown, JW and Yang, Y}, title = {Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants.}, journal = {BMC evolutionary biology}, volume = {15}, number = {}, pages = {150}, pmid = {26239519}, issn = {1471-2148}, mesh = {Animals ; *Gene Duplication ; *Gene Transfer, Horizontal ; Genomics ; Magnoliopsida/*genetics/physiology ; Phylogeny ; Software ; Wasps/classification/genetics ; }, abstract = {BACKGROUND: The use of transcriptomic and genomic datasets for phylogenetic reconstruction has become increasingly common as researchers attempt to resolve recalcitrant nodes with increasing amounts of data. The large size and complexity of these datasets introduce significant phylogenetic noise and conflict into subsequent analyses. The sources of conflict may include hybridization, incomplete lineage sorting, or horizontal gene transfer, and may vary across the phylogeny. For phylogenetic analysis, this noise and conflict has been accommodated in one of several ways: by binning gene regions into subsets to isolate consistent phylogenetic signal; by using gene-tree methods for reconstruction, where conflict is presumed to be explained by incomplete lineage sorting (ILS); or through concatenation, where noise is presumed to be the dominant source of conflict. The results provided herein emphasize that analysis of individual homologous gene regions can greatly improve our understanding of the underlying conflict within these datasets.<br><br>RESULTS: Here we examined two published transcriptomic datasets, the angiosperm group Caryophyllales and the aculeate Hymenoptera, for the presence of conflict, concordance, and gene duplications in individual homologs across the phylogeny. We found significant conflict throughout the phylogeny in both datasets and in particular along the backbone. While some nodes in each phylogeny showed patterns of conflict similar to what might be expected with ILS alone, the backbone nodes also exhibited low levels of phylogenetic signal. In addition, certain nodes, especially in the Caryophyllales, had highly elevated levels of strongly supported conflict that cannot be explained by ILS alone.<br><br>CONCLUSION: This study demonstrates that phylogenetic signal is highly variable in phylogenomic data sampled across related species and poses challenges when conducting species tree analyses on large genomic and transcriptomic datasets. Further insight into the conflict and processes underlying these complex datasets is necessary to improve and develop adequate models for sequence analysis and downstream applications. To aid this effort, we developed the open source software phyparts (https://bitbucket.org/blackrim/phyparts), which calculates unique, conflicting, and concordant bipartitions, maps gene duplications, and outputs summary statistics such as internode certainy (ICA) scores and node-specific counts of gene duplications.}, }
@article {pmid26238987, year = {2016}, author = {Patokar, C and Sepsi, A and Schwarzacher, T and Kishii, M and Heslop-Harrison, JS}, title = {Molecular cytogenetic characterization of novel wheat-Thinopyrum bessarabicum recombinant lines carrying intercalary translocations.}, journal = {Chromosoma}, volume = {125}, number = {1}, pages = {163-172}, pmid = {26238987}, issn = {1432-0886}, mesh = {*Chromosomes, Plant ; Cytogenetic Analysis ; *Gene Transfer, Horizontal ; In Situ Hybridization ; Inbreeding ; Poaceae/*genetics ; *Translocation, Genetic ; }, abstract = {Thinopyrum bessarabicum (2n = 2x = 14, JJ or E(b)E(b)) is a valuable source of genes for bread wheat (2n = 6x = 42) improvement because of its salinity tolerance and disease resistance. Development of wheat-Th. bessarabicum translocation lines by backcrossing the amphiploid in the absence of the Ph1 gene (allowing intergenomic recombination) can assist its utilization in wheat improvement. In this study, six novel wheat-Th. bessarabicum translocation lines involving different chromosome segments (T4BS.4BL-4JL, T6BS.6BL-6JL, T5AS.5AL-5JL, T5DL.5DS-5JS, T2BS.2BL-2JL, and the whole arm translocation T1JS.1AL) were identified and characterized using genomic in situ hybridization (GISH) and fluorescent in situ hybridization (FISH). No background translocations between wheat genomes were observed. The involvement of five of the seven chromosomes and small terminal segments of Th. bessarabicum chromosome arm were important, contributing to both reduced linkage drag of the derived lines by minimizing agronomically deleterious genes from the alien species and high stability including transmission of the alien segment. All three wheat genomes were involved in the translocations with the alien chromosome, and GISH showed the Th. bessarabicum genome was more closely related to the D genome in wheat. All the introgression lines were disomic, stable, and with good morphological characters.}, }
@article {pmid26236726, year = {2015}, author = {Adamczuk, M and Zaleski, P and Dziewit, L and Wolinowska, R and Nieckarz, M and Wawrzyniak, P and Kieryl, P and Plucienniczak, A and Bartosik, D}, title = {Diversity and Global Distribution of IncL/M Plasmids Enabling Horizontal Dissemination of β-Lactam Resistance Genes among the Enterobacteriaceae.}, journal = {BioMed research international}, volume = {2015}, number = {}, pages = {414681}, pmid = {26236726}, issn = {2314-6141}, mesh = {DNA, Circular/genetics ; Enterobacteriaceae/*genetics ; Gene Transfer, Horizontal/*genetics ; *Genes, Bacterial ; *Genetic Variation ; Genomics ; Phylogeography ; Plasmids/*genetics ; beta-Lactam Resistance/*genetics ; beta-Lactamases/genetics ; }, abstract = {Antibiotic resistance determinants are frequently associated with plasmids and other mobile genetic elements, which simplifies their horizontal transmission. Several groups of plasmids (including replicons of the IncL/M incompatibility group) were found to play an important role in the dissemination of resistance genes encoding β-lactamases. The IncL/M plasmids are large, broad host range, and self-transmissible replicons. We have identified and characterized two novel members of this group: pARM26 (isolated from bacteria inhabiting activated sludge from a wastewater treatment plant) and pIGT15 (originating from a clinical strain of Escherichia coli). This instigated a detailed comparative analysis of all available sequences of IncL/M plasmids encoding β-lactamases. The core genome of these plasmids is comprised of 20 genes with conserved synteny. Phylogenetic analyses of these core genes allowed clustering of the plasmids into four separate groups, which reflect their antibiotic resistance profiles. Examination of the biogeography of the IncL/M plasmids revealed that they are most frequently found in bacteria of the family Enterobacteriaceae originating from the Mediterranean region and Western Europe and that they are able to persist in various ecological niches even in the absence of direct antibiotic selection pressure.}, }
@article {pmid26234735, year = {2015}, author = {Kurland, CG and Harish, A}, title = {The phylogenomics of protein structures: The backstory.}, journal = {Biochimie}, volume = {119}, number = {}, pages = {284-302}, doi = {10.1016/j.biochi.2015.07.027}, pmid = {26234735}, issn = {1638-6183}, mesh = {Amino Acid Sequence ; Animals ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome ; Humans ; *Models, Genetic ; Mutation ; *Phylogeny ; Protein Conformation ; Protein Isoforms/chemistry/genetics/metabolism ; Protein Structure, Tertiary ; Proteome/*chemistry/genetics/metabolism ; }, abstract = {In this introductory retrospective, evolution as viewed through gene trees is inspected through a lens compounded from its founding operational assumptions. The four assumptions of the gene tree culture that are singularly important to evolutionary interpretations are: a. that protein-coding sequences are molecular fossils; b. that gene trees are equivalent to species trees; c. that the tree of life is assumed to be rooted in a simple akaryote cell implying that akaryotes are primitive, and d. that the notion that all or most incongruities between alignment-based gene trees are due to horizontal gene transfer (HGT), which includes the endosymbiotic models postulated for the origins of eukaryotes. What has been unusual about these particular assumptions is that though each was taken on board explicitly, they are defended in the face of factual challenge by a stolid disregard for the conflicting observations. The factual challenges to the mainstream gene tree-inspired evolutionary view are numerous and most convincingly summarized as: Genome trees tell a very different story. Phylogeny inferred from genomic assortments of homologous protein structural-domains does not support any one of the four principle evolutionary interpretations of gene trees: a. 3D protein domain structures are the molecular fossils of evolution, while coding sequences are transients; b. Species trees are very different from gene trees; c. The ToL is rooted in a surprisingly complex universal common ancestor (UCA) that is distinct from any specific modern descendant and d. HGT including endosymbiosis is a negligible player in genome evolution from UCA to the present.}, }
@article {pmid26232566, year = {2015}, author = {Somensi, CA and Souza, AL and Simionatto, EL and Gaspareto, P and Millet, M and Radetski, CM}, title = {Genetic material present in hospital wastewaters: Evaluation of the efficiency of DNA denaturation by ozonolysis and ozonolysis/sonolysis treatments.}, journal = {Journal of environmental management}, volume = {162}, number = {}, pages = {74-80}, doi = {10.1016/j.jenvman.2015.07.039}, pmid = {26232566}, issn = {1095-8630}, mesh = {Brazil ; DNA/*chemistry ; Disinfection/methods ; Electrophoresis, Agar Gel ; *Hospitals ; Medical Waste Disposal/*methods ; Nucleic Acid Denaturation ; Ozone/chemistry ; Plasmids/genetics ; Waste Disposal, Fluid/methods ; Wastewater/*analysis/microbiology ; }, abstract = {Hospital wastewater treatments must ensure that all genetic material is destroyed, since nuclear and extra-nuclear DNA can show antimicrobial resistance and contain recombinant genes, which promote vertical and/or horizontal gene transfer, amplifying the current problem of the emergence of antibiotic-resistant microorganisms. In this study, we investigated whether ozonolysis or ozonolysis/sonolysis in combination can denature genetic material, i.e., destroy the integrity of DNA molecules, present in hospital wastewaters. To achieve this goal, hospital wastewaters were treated by ozonolysis or ozonolysis/sonolysis in combination (at 70 and 100 W L(-1)) and both raw and treated wastewaters were analyzed in terms of disinfection and DNA denaturation efficiency quantified by viable cell counts and by agarose gel electrophoresis. In the ozonolysis treatment, the agarose gel electrophoresis technique showed that the ozone-treated samples contained DNA molecules, while combined ozonolysis/sonolysis destroyed the DNA in a power density-dependent manner (64% at 70 W L(-1) and 81% at 100 W L(-1)). Care must be taken by environmental managers to distinguish disinfection processes from DNA denaturation processes, since these two terms are not synonymous.}, }
@article {pmid26228545, year = {2015}, author = {Vega, FE and Brown, SM and Chen, H and Shen, E and Nair, MB and Ceja-Navarro, JA and Brodie, EL and Infante, F and Dowd, PF and Pain, A}, title = {Draft genome of the most devastating insect pest of coffee worldwide: the coffee berry borer, Hypothenemus hampei.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {12525}, pmid = {26228545}, issn = {2045-2322}, mesh = {ATP-Binding Cassette Transporters/genetics/metabolism ; Animals ; Caffeine/pharmacokinetics ; Carboxylesterase/genetics/metabolism ; Coffea ; Crops, Agricultural ; Cytochrome P-450 Enzyme System/genetics/metabolism ; Enzymes/genetics/metabolism ; Female ; Gene Transfer, Horizontal ; *Genome, Insect ; Inactivation, Metabolic ; Insect Proteins/*genetics/metabolism ; Multigene Family ; Phylogeny ; RNA, Untranslated ; Weevils/drug effects/*genetics/physiology ; }, abstract = {The coffee berry borer, Hypothenemus hampei, is the most economically important insect pest of coffee worldwide. We present an analysis of the draft genome of the coffee berry borer, the third genome for a Coleopteran species. The genome size is ca. 163 Mb with 19,222 predicted protein-coding genes. Analysis was focused on genes involved in primary digestion as well as gene families involved in detoxification of plant defense molecules and insecticides, such as carboxylesterases, cytochrome P450, gluthathione S-transferases, ATP-binding cassette transporters, and a gene that confers resistance to the insecticide dieldrin. A broad range of enzymes capable of degrading complex polysaccharides were identified. We also evaluated the pathogen defense system and found homologs to antimicrobial genes reported in the Drosophila genome. Ten cases of horizontal gene transfer were identified with evidence for expression, integration into the H. hampei genome, and phylogenetic evidence that the sequences are more closely related to bacterial rather than eukaryotic genes. The draft genome analysis broadly expands our knowledge on the biology of a devastating tropical insect pest and suggests new pest management strategies.}, }
@article {pmid26224621, year = {2015}, author = {Burmeister, AR}, title = {Horizontal Gene Transfer.}, journal = {Evolution, medicine, and public health}, volume = {2015}, number = {1}, pages = {193-194}, pmid = {26224621}, issn = {2050-6201}, }
@article {pmid26223152, year = {2015}, author = {Chen, CM and Yu, WL and Huang, M and Liu, JJ and Chen, IC and Chen, HF and Wu, LT}, title = {Characterization of IS26-composite transposons and multidrug resistance in conjugative plasmids from Enterobacter cloacae.}, journal = {Microbiology and immunology}, volume = {59}, number = {9}, pages = {516-525}, doi = {10.1111/1348-0421.12289}, pmid = {26223152}, issn = {1348-0421}, mesh = {Cloning, Molecular ; Conjugation, Genetic ; *DNA Transposable Elements ; DNA, Bacterial/chemistry/genetics ; *Drug Resistance, Multiple, Bacterial ; Enterobacter cloacae/*drug effects/*genetics/isolation &amp; purification ; Enterobacteriaceae Infections/microbiology ; Evolution, Molecular ; Gene Transfer, Horizontal ; Homologous Recombination ; Humans ; Integrons ; Plasmids/*analysis/classification ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Taiwan ; beta-Lactamases/genetics ; }, abstract = {SHV-12 is the most widespread resistance determinant of Enterobacter cloacae in Taiwan; however, blaSHV-12 has rarely been mobilized. Six multidrug-resistant E. cloacae isolates were collected. After conjugal transfer, plasmid profiling and analysis of incompatibility groups was performed to characterize the genetic context of blaSHV-12 -containing fragments. The presence of mobile genetic elements was demonstrated by PCR, cloning, sequencing and bioinformatics analyses. Four different β-lactamase genes (blaTEM-1 , blaSHV-12 , blaCTX-M-3 and/or blaCTX-M-14) were observed in the conjugative plasmids belonging to the IncHI2 (n = 4), IncI1 or IncP incompatibility groups. The IS26-blaSHV-12 -IS26 locus was located in five different genetic environments. A novel structural organization of a class 1 integron with the aac(6')-IIc cassette truncated by IS26 was identified in one isolate. Thus, blaSHV-12 was obtained from different plasmids through IS26-mediated homologous recombination. IS26 plays a vital role in the distribution of mobile resistance elements between different plasmids found in multidrug-resistant E. cloacae isolates.}, }
@article {pmid26220935, year = {2015}, author = {Tian, RM and Cai, L and Zhang, WP and Cao, HL and Qian, PY}, title = {Rare Events of Intragenus and Intraspecies Horizontal Transfer of the 16S rRNA Gene.}, journal = {Genome biology and evolution}, volume = {7}, number = {8}, pages = {2310-2320}, pmid = {26220935}, issn = {1759-6653}, mesh = {Chlamydia/genetics ; Escherichia coli/genetics ; Gene Dosage ; *Gene Transfer, Horizontal ; *Genes, Archaeal ; *Genes, Bacterial ; Genetic Variation ; Genome, Archaeal ; Genome, Bacterial ; Mutation ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Thermoanaerobacter/genetics ; }, abstract = {Horizontal gene transfer (HGT) of operational genes has been widely reported in prokaryotic organisms. However, informational genes such as those involved in transcription and translation processes are very difficult to be horizontally transferred, as described by Woese's complexity hypothesis. Here, we analyzed all of the completed prokaryotic genome sequences (2,143 genomes) in the NCBI (National Center for Biotechnology Information) database, scanned for genomes with high intragenomic heterogeneity of 16S rRNA gene copies, and explored potential HGT events of ribosomal RNA genes based on the phylogeny, genomic organization, and secondary structures of the ribosomal RNA genes. Our results revealed 28 genomes with relatively high intragenomic heterogeneity of multiple 16S rRNA gene copies (lowest pairwise identity <98.0%), and further analysis revealed HGT events and potential donors of the heterogeneous copies (such as HGT from Chlamydia suis to Chlamydia trachomatis) and mutation events of some heterogeneous copies (such as Streptococcus suis JS14). Interestingly, HGT of the 16S rRNA gene only occurred at intragenus or intraspecies levels, which is quite different from the HGT of operational genes. Our results improve our understanding regarding the exchange of informational genes.}, }
@article {pmid26215153, year = {2015}, author = {Quandt, CA and Bushley, KE and Spatafora, JW}, title = {The genome of the truffle-parasite Tolypocladium ophioglossoides and the evolution of antifungal peptaibiotics.}, journal = {BMC genomics}, volume = {16}, number = {1}, pages = {553}, pmid = {26215153}, issn = {1471-2164}, mesh = {Animals ; Antifungal Agents/*metabolism ; Evolution, Molecular ; Fungal Proteins/*genetics/metabolism ; *Genome, Fungal ; Hypocreales/classification/*genetics/metabolism ; Insecta/microbiology ; Multigene Family ; Phylogeny ; Plants/microbiology ; Secondary Metabolism ; }, abstract = {BACKGROUND: Two major mycoparasitic lineages, the family Hypocreaceae and the genus Tolypocladium, exist within the fungal order, Hypocreales. Peptaibiotics are a group of secondary metabolites almost exclusively described from Trichoderma species of Hypocreaceae. Peptaibiotics are produced by nonribosomal peptide synthetases (NRPSs) and have antibiotic and antifungal activities. Tolypocladium species are mainly truffle parasites, but a few species are insect pathogens.<br><br>RESULTS: The draft genome sequence of the truffle parasite Tolypocladium ophioglossoides was generated and numerous secondary metabolite clusters were discovered, many of which have no known putative product. However, three large peptaibiotic gene clusters were identified using phylogenetic analyses. Peptaibiotic genes are absent from the predominantly plant and insect pathogenic lineages of Hypocreales, and are therefore exclusive to the largely mycoparasitic lineages. Using NRPS adenylation domain phylogenies and reconciliation of the domain tree with the organismal phylogeny, it is demonstrated that the distribution of these domains is likely not the product of horizontal gene transfer between mycoparasitic lineages, but represents independent losses in insect pathogenic lineages. Peptaibiotic genes are less conserved between species of Tolypocladium and are the product of complex patterns of lineage sorting and module duplication. In contrast, these genes are more conserved within the genus Trichoderma and consistent with diversification through speciation.<br><br>CONCLUSIONS: Peptaibiotic NRPS genes are restricted to mycoparasitic lineages of Hypocreales, based on current sampling. Phylogenomics and comparative genomics can provide insights into the evolution of secondary metabolite genes, their distribution across a broader range of taxa, and their possible function related to host specificity.}, }
@article {pmid26212213, year = {2015}, author = {Liu, CJ and Wang, R and Gong, FM and Liu, XF and Zheng, HJ and Luo, YY and Li, XR}, title = {Complete genome sequences and comparative genome analysis of Lactobacillus plantarum strain 5-2 isolated from fermented soybean.}, journal = {Genomics}, volume = {106}, number = {6}, pages = {404-411}, doi = {10.1016/j.ygeno.2015.07.007}, pmid = {26212213}, issn = {1089-8646}, mesh = {Bacterial Proteins/classification/genetics/metabolism ; Chromosomes, Bacterial/genetics ; DNA Transposable Elements/genetics ; Evolution, Molecular ; Fermentation ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Genome, Bacterial/*genetics ; Genomics/*methods ; Lactobacillus plantarum/classification/*genetics/virology ; Mutagenesis, Insertional ; Phylogeny ; Prophages/genetics/physiology ; Sequence Analysis, DNA/*methods ; Glycine max/metabolism/*microbiology ; Species Specificity ; }, abstract = {Lactobacillus plantarum is an important probiotic and is mostly isolated from fermented foods. We sequenced the genome of L. plantarum strain 5-2, which was derived from fermented soybean isolated from Yunnan province, China. The strain was determined to contain 3114 genes. Fourteen complete insertion sequence (IS) elements were found in 5-2 chromosome. There were 24 DNA replication proteins and 76 DNA repair proteins in the 5-2 genome. Consistent with the classification of L. plantarum as a facultative heterofermentative lactobacillus, the 5-2 genome encodes key enzymes required for the EMP (Embden-Meyerhof-Parnas) and phosphoketolase (PK) pathways. Several components of the secretion machinery are found in the 5-2 genome, which was compared with L. plantarum ST-III, JDM1 and WCFS1. Most of the specific proteins in the four genomes appeared to be related to their prophage elements.}, }
@article {pmid26211682, year = {2015}, author = {Pollo, SM and Zhaxybayeva, O and Nesbø, CL}, title = {Insights into thermoadaptation and the evolution of mesophily from the bacterial phylum Thermotogae.}, journal = {Canadian journal of microbiology}, volume = {61}, number = {9}, pages = {655-670}, doi = {10.1139/cjm-2015-0073}, pmid = {26211682}, issn = {1480-3275}, mesh = {Adaptation, Physiological/genetics ; Archaea/classification/genetics/*physiology ; Archaeal Proteins/genetics/metabolism ; *Biological Evolution ; Hot Temperature ; Proteomics ; }, abstract = {Thermophiles are extremophiles that grow optimally at temperatures >45 °C. To survive and maintain function of their biological molecules, they have a suite of characteristics not found in organisms that grow at moderate temperature (mesophiles). At the cellular level, thermophiles have mechanisms for maintaining their membranes, nucleic acids, and other cellular structures. At the protein level, each of their proteins remains stable and retains activity at temperatures that would denature their mesophilic homologs. Conversely, cellular structures and proteins from thermophiles may not function optimally at moderate temperatures. These differences between thermophiles and mesophiles presumably present a barrier for evolutionary transitioning between the 2 lifestyles. Therefore, studying closely related thermophiles and mesophiles can help us determine how such lifestyle transitions may happen. The bacterial phylum Thermotogae contains hyperthermophiles, thermophiles, mesophiles, and organisms with temperature ranges wide enough to span both thermophilic and mesophilic temperatures. Genomic, proteomic, and physiological differences noted between other bacterial thermophiles and mesophiles are evident within the Thermotogae. We argue that the Thermotogae is an ideal group of organisms for understanding of the response to fluctuating temperature and of long-term evolutionary adaptation to a different growth temperature range.}, }
@article {pmid26205244, year = {2015}, author = {Marsit, S and Dequin, S}, title = {Diversity and adaptive evolution of Saccharomyces wine yeast: a review.}, journal = {FEMS yeast research}, volume = {15}, number = {7}, pages = {}, pmid = {26205244}, issn = {1567-1364}, mesh = {*Adaptation, Biological ; *Evolution, Molecular ; *Genetic Variation ; Saccharomyces/*classification/*genetics ; Wine/*microbiology ; }, abstract = {Saccharomyces cerevisiae and related species, the main workhorses of wine fermentation, have been exposed to stressful conditions for millennia, potentially resulting in adaptive differentiation. As a result, wine yeasts have recently attracted considerable interest for studying the evolutionary effects of domestication. The widespread use of whole-genome sequencing during the last decade has provided new insights into the biodiversity, population structure, phylogeography and evolutionary history of wine yeasts. Comparisons between S. cerevisiae isolates from various origins have indicated that a variety of mechanisms, including heterozygosity, nucleotide and structural variations, introgressions, horizontal gene transfer and hybridization, contribute to the genetic and phenotypic diversity of S. cerevisiae. This review will summarize the current knowledge on the diversity and evolutionary history of wine yeasts, focusing on the domestication fingerprints identified in these strains.}, }
@article {pmid26202678, year = {2015}, author = {Zuchowska, M and Jaenicke, E and König, H and Claus, H}, title = {Allelic variants of hexose transporter Hxt3p and hexokinases Hxk1p/Hxk2p in strains of Saccharomyces cerevisiae and interspecies hybrids.}, journal = {Yeast (Chichester, England)}, volume = {32}, number = {11}, pages = {657-669}, doi = {10.1002/yea.3087}, pmid = {26202678}, issn = {1097-0061}, mesh = {*Alleles ; Base Sequence ; Chimera ; Ethanol/metabolism ; Fermentation ; Fructose/metabolism ; *Gene Transfer, Horizontal ; Glucose/metabolism ; Glucose Transport Proteins, Facilitative/genetics/metabolism ; Hexokinase/*genetics/metabolism ; Protein Conformation ; Saccharomyces cerevisiae/enzymology/*genetics/*metabolism ; Saccharomyces cerevisiae Proteins/*genetics/metabolism ; Wine/*microbiology ; }, abstract = {The transport of sugars across the plasma membrane is a critical step in the utilization of glucose and fructose by Saccharomyces cerevisiae during must fermentations. Variations in the molecular structure of hexose transporters and kinases may affect the ability of wine yeast strains to finish sugar fermentation, even under stressful wine conditions. In this context, we sequenced and compared genes encoding the hexose transporter Hxt3p and the kinases Hxk1p/Hxk2p of Saccharomyces strains and interspecies hybrids with different industrial usages and regional backgrounds. The Hxt3p primary structure varied in a small set of amino acids, which characterized robust yeast strains used for the production of sparkling wine or to restart stuck fermentations. In addition, interspecies hybrid strains, previously isolated at the end of spontaneous fermentations, revealed a common amino acid signature. The location and potential influence of the amino acids exchanges is discussed by means of a first modelled Hxt3p structure. In comparison, hexokinase genes were more conserved in different Saccharomyces strains and hybrids. Thus, molecular variants of the hexose carrier Hxt3p, but not of kinases, correlate with different fermentation performances of yeast.}, }
@article {pmid26200753, year = {2015}, author = {Pierneef, R and Cronje, L and Bezuidt, O and Reva, ON}, title = {Pre_GI: a global map of ontological links between horizontally transferred genomic islands in bacterial and archaeal genomes.}, journal = {Database : the journal of biological databases and curation}, volume = {2015}, number = {}, pages = {bav058}, pmid = {26200753}, issn = {1758-0463}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Databases, Nucleic Acid ; *Gene Ontology ; *Gene Transfer, Horizontal ; *Genome, Archaeal ; *Genome, Bacterial ; }, abstract = {The Predicted Genomic Islands database (Pre_GI) is a comprehensive repository of prokaryotic genomic islands (islands, GIs) freely accessible at http://pregi.bi.up.ac.za/index.php. Pre_GI, Version 2015, catalogues 26 744 islands identified in 2407 bacterial/archaeal chromosomes and plasmids. It provides an easy-to-use interface which allows users the ability to query against the database with a variety of fields, parameters and associations. Pre_GI is constructed to be a web-resource for the analysis of ontological roads between islands and cartographic analysis of the global fluxes of mobile genetic elements through bacterial and archaeal taxonomic borders. Comparison of newly identified islands against Pre_GI presents an alternative avenue to identify their ontology, origin and relative time of acquisition. Pre_GI aims to aid research on horizontal transfer events and materials through providing data and tools for holistic investigation of migration of genes through ecological niches and taxonomic boundaries.}, }
@article {pmid26199375, year = {2015}, author = {Maddamsetti, R and Hatcher, PJ and Cruveiller, S and Médigue, C and Barrick, JE and Lenski, RE}, title = {Synonymous Genetic Variation in Natural Isolates of Escherichia coli Does Not Predict Where Synonymous Substitutions Occur in a Long-Term Experiment.}, journal = {Molecular biology and evolution}, volume = {32}, number = {11}, pages = {2897-2904}, pmid = {26199375}, issn = {1537-1719}, mesh = {Biological Evolution ; Escherichia coli/*genetics ; Evolution, Molecular ; Genetic Variation ; Genomics ; Mutation Rate ; Phylogeny ; Selection, Genetic ; *Silent Mutation ; }, abstract = {Synonymous genetic differences vary by more than 20-fold among genes in natural isolates of Escherichia coli. One hypothesis to explain this heterogeneity is that genes with high levels of synonymous variation mutate at higher rates than genes with low synonymous variation. If so, then one would expect to observe similar mutational patterns in evolution experiments. In fact, however, the pattern of synonymous substitutions in a long-term evolution experiment with E. coli does not support this hypothesis. In particular, the extent of synonymous variation across genes in that experiment does not reflect the variation observed in natural isolates of E. coli. Instead, gene length alone predicts with high accuracy the prevalence of synonymous changes in the experimental populations. We hypothesize that patterns of synonymous variation in natural E. coli populations are instead caused by differences across genomic regions in their effective population size that, in turn, reflect different histories of recombination, horizontal gene transfer, selection, and population structure.}, }
@article {pmid26195306, year = {2015}, author = {Corradi, N}, title = {Microsporidia: Eukaryotic Intracellular Parasites Shaped by Gene Loss and Horizontal Gene Transfers.}, journal = {Annual review of microbiology}, volume = {69}, number = {}, pages = {167-183}, doi = {10.1146/annurev-micro-091014-104136}, pmid = {26195306}, issn = {1545-3251}, mesh = {Animals ; Ecosystem ; Gene Transfer, Horizontal ; Humans ; Microsporidia/classification/genetics/*physiology ; Microsporidiosis/microbiology/veterinary ; }, abstract = {Microsporidia are eukaryotic parasites of many animals that appear to have adapted to an obligate intracellular lifestyle by modifying the morphology and content of their cells. Living inside other cells, they have lost many, or all, metabolic functions, resulting in genomes that are always gene poor and often very small. The minute content of microsporidian genomes led many to assume that these parasites are biochemically static and uninteresting. However, recent studies have demonstrated that these organisms can be surprisingly complex and dynamic. In this review I detail the most significant recent advances in microsporidian genomics and discuss how these have affected our understanding of many biological aspects of these peculiar eukaryotic intracellular pathogens.}, }
@article {pmid26195134, year = {2015}, author = {Palomeque, T and Sanllorente, O and Maside, X and Vela, J and Mora, P and Torres, MI and Periquet, G and Lorite, P}, title = {Evolutionary history of the Azteca-like mariner transposons and their host ants.}, journal = {Die Naturwissenschaften}, volume = {102}, number = {7-8}, pages = {44}, pmid = {26195134}, issn = {1432-1904}, mesh = {Animals ; Ants/*classification/*enzymology/genetics ; DNA-Binding Proteins/*genetics ; Gene Transfer, Horizontal ; Genetic Variation ; Genome, Insect/genetics ; *Phylogeny ; Transposases/*genetics ; }, abstract = {Three different complete mariner elements were found in the genome of the ant Tapinoma nigerrimum. One (Tnigmar-Mr) was interrupted by a 900-bp insertion that corresponded to an incomplete member of a fourth mariner element, called Azteca. In this work, we isolate and characterize full-length Tnigmar-Az elements in T. nigerrimum. The purpose of this study is to clarify the evolutionary history of Azteca elements and their hosts as well as the possible existence of horizontal transfer processes. For this, Azteca-like elements were also retrieved from the available sequences of various ant genomes, representing four different ant subfamilies: Dolichoderinae, Formicinae, Myrmicinae, and Ponerinae. The tree topology resulting for the Azteca-like elements bore very little resemblance to that of their respective hosts. The pervasive presence of Azteca-like elements in all ant genomes, together with the observation that extant copies are usually younger than the genomes that host them, could be explained either by lineage sorting or by recent horizontal transfer of active elements. However, the finding of closer genetic relationships between elements than between the ants that host them is consistent with the latter scenario. This is clearly observed in Sinvmar-Az, Tnigmar-Az, Acepmar-Az, and Cflomar-Az elements, suggesting the existence of horizontal transfer processes. On the contrary, some elements displayed more divergence than did the hosts harboring them. This may reflect either further horizontal transfer events or random lineage sorting.}, }
@article {pmid26193304, year = {2015}, author = {Pagarete, A and Grébert, T and Stepanova, O and Sandaa, RA and Bratbak, G}, title = {Tsv-N1: A Novel DNA Algal Virus that Infects Tetraselmis striata.}, journal = {Viruses}, volume = {7}, number = {7}, pages = {3937-3953}, pmid = {26193304}, issn = {1999-4915}, mesh = {Chlorophyta/*virology ; Genome, Viral ; Host Specificity ; Humans ; Molecular Sequence Data ; Phycodnaviridae/genetics/isolation &amp; purification/*physiology ; Phylogeny ; }, abstract = {Numbering in excess of 10 million per milliliter of water, it is now undisputed that aquatic viruses are one of the major factors shaping the ecology and evolution of Earth's microbial world. Nonetheless, environmental viral diversity and roles remain poorly understood. Here we report the first thorough characterization of a virus (designated TsV) that infects the coastal marine microalga Tetraselmis striata. Unlike previously known microalgae-infecting viruses, TsV is a small (60 nm) DNA virus, with a 31 kb genome. From a range of eight different strains belonging to the Chlamydomonadaceae family, TsV was only able to infect T. striata. Gene expression dynamics revealed an up-regulation of viral transcripts already 1 h post-infection (p.i.). First clear signs of infection were observed 24 h p.i., with the appearance of viral factories inside the nucleus. TsV assembly was exclusively nuclear. TsV-N1 genome revealed very different from previously known algae viruses (Phycodnaviridae). Putative function and/or homology could be resolved for only 9 of the 33 ORFs encoded. Among those was a surprising DNA polymerase type Delta (only found in Eukaryotes), and two genes with closest homology to genes from human parasites of the urogenital tract. These results support the idea that the diversity of microalgae viruses goes far beyond the Phycodnaviridae family and leave the door open for future studies on implications of microalgae viruses for human health.}, }
@article {pmid26191043, year = {2015}, author = {Hasegawa, Y and Futamata, H and Tashiro, Y}, title = {Complexities of cell-to-cell communication through membrane vesicles: implications for selective interaction of membrane vesicles with microbial cells.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {633}, pmid = {26191043}, issn = {1664-302X}, }
@article {pmid26190075, year = {2015}, author = {Harrison, E and Guymer, D and Spiers, AJ and Paterson, S and Brockhurst, MA}, title = {Parallel compensatory evolution stabilizes plasmids across the parasitism-mutualism continuum.}, journal = {Current biology : CB}, volume = {25}, number = {15}, pages = {2034-2039}, doi = {10.1016/j.cub.2015.06.024}, pmid = {26190075}, issn = {1879-0445}, mesh = {Animals ; *Biological Evolution ; *Genetic Variation ; *Genome, Bacterial ; Host-Parasite Interactions ; Plasmids/genetics/*physiology ; Pseudomonas fluorescens/genetics/*physiology ; Symbiosis ; }, abstract = {Plasmids drive genomic diversity in bacteria via horizontal gene transfer [1, 2]; nevertheless, explaining their survival in bacterial populations is challenging [3]. Theory predicts that irrespective of their net fitness effects, plasmids should be lost: when parasitic (costs outweigh benefits), plasmids should decline due to purifying selection [4-6], yet under mutualism (benefits outweigh costs), selection favors the capture of beneficial accessory genes by the chromosome and loss of the costly plasmid backbone [4]. While compensatory evolution can enhance plasmid stability within populations [7-15], the propensity for this to occur across the parasitism-mutualism continuum is unknown. We experimentally evolved Pseudomonas fluorescens and its mercury resistance mega-plasmid, pQBR103 [16], across an environment-mediated parasitism-mutualism continuum. Compensatory evolution stabilized plasmids by rapidly ameliorating the cost of plasmid carriage in all environments. Genomic analysis revealed that, in both parasitic and mutualistic treatments, evolution repeatedly targeted the gacA/gacS bacterial two-component global regulatory system while leaving the plasmid sequence intact. Deletion of either gacA or gacS was sufficient to completely ameliorate the cost of plasmid carriage. Mutation of gacA/gacS downregulated the expression of ∼17% of chromosomal and plasmid genes and appears to have relieved the translational demand imposed by the plasmid. Chromosomal capture of mercury resistance accompanied by plasmid loss occurred throughout the experiment but very rarely invaded to high frequency, suggesting that rapid compensatory evolution can limit this process. Compensatory evolution can explain the widespread occurrence of plasmids and allows bacteria to retain horizontally acquired plasmids even in environments where their accessory genes are not immediately useful.}, }
@article {pmid26188514, year = {2015}, author = {Yang, S and Liu, J and Shao, F and Wang, P and Duan, G and Yang, H}, title = {Analysis of the features of 45 identified CRISPR loci in 32 Staphylococcus aureus.}, journal = {Biochemical and biophysical research communications}, volume = {464}, number = {3}, pages = {894-900}, doi = {10.1016/j.bbrc.2015.07.062}, pmid = {26188514}, issn = {1090-2104}, mesh = {Bacterial Proteins/genetics ; Bacterial Toxins/genetics ; Cluster Analysis ; *Clustered Regularly Interspaced Short Palindromic Repeats ; DNA, Intergenic ; Exotoxins/genetics ; Leukocidins/genetics ; Multilocus Sequence Typing ; RNA Stability ; RNA, Bacterial/chemistry ; Staphylococcus Phages/genetics ; Staphylococcus aureus/*genetics/pathogenicity ; }, abstract = {Staphylococcus aureus (S. aureus) is a common pathogen that can cause serious infections, even death. Because of the horizontal gene transfer (HGT) of antibiotic resistance genes, the drug resistant condition is becoming increasingly prevalent. Recently, an adaptive immunity system, named clustered regularly interspaced short palindromic repeats (CRISPR), was discovered and demonstrated to confer a defense against foreign invading elements that may carry the antibiotic resistance genes. In this study, we reveal the features of 45 identified CRISPR loci and the CRISPR associated gene (Cas) in 32 S. aureus strains from CRISPR database. Five spacers of S. aureus 08BA02176 and MSHR1132 were homologous with foreign genetic sequences from phages or plasmids, even containing a spacer sequence identical to part of some phages' genomes containing lukPV gene that encodes the PVL toxin. Many S. aureus strains with the same CRISPR type shared the same MLST type. CRISPR loci that had 3 or more similar protein loci mostly belonged to the same CRISPR type. We came to the conclusion that the CRISPR/Cas of strains 08BA02176 and MSHR1132 were inherited from a common ancestor or recombined from Staphylococcus lugdunensis. CRISPR loci can be mobilized and can transfer among different but closely related species, and the same types of MLST strains exhibit a higher affinity to the same types of CRISPR loci. Bacteriophages may be the predominant challenge facing S. aureus. The CRISPR/Cas structure may limit the transmission of bacterial virulence among S. aureus.}, }
@article {pmid26188331, year = {2015}, author = {Messenger, LA and Miles, MA}, title = {Evidence and importance of genetic exchange among field populations of Trypanosoma cruzi.}, journal = {Acta tropica}, volume = {151}, number = {}, pages = {150-155}, pmid = {26188331}, issn = {1873-6254}, support = {/WT_/Wellcome Trust/United Kingdom ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Chagas Disease/*parasitology/*transmission ; *Gene Transfer, Horizontal ; Genetic Variation ; *Hybridization, Genetic ; North America ; *Recombination, Genetic ; South America ; Trypanosoma cruzi/*genetics ; }, abstract = {Many eukaryotic pathogenic microorganisms that were previously assumed to propagate clonally have retained cryptic sexual cycles. The principal reproductive mode of Trypanosoma cruzi, the aetiological agent of Chagas disease, remains a controversial topic. Despite the existence of two recent natural hybrid lineages, a pervasive view is that recombination has been restrained at an evolutionary scale and is of little epidemiological relevance to contemporary parasite populations. This article reviews the growing number of field studies which indicate that natural hybridization in T. cruzi may be frequent, non-obligatory and idiosyncratic; potentially involving independent exchange of kinetoplast and nuclear genetic material as well as canonical meiotic mechanisms. Together these observations now challenge the traditional paradigm of preponderate clonal evolution in T. cruzi and highlight the need for additional, intensive and appropriately sampled field surveys, complemented by high resolution, combined nuclear and mitochondrial population genetics analyses.}, }
@article {pmid26185097, year = {2015}, author = {Chiara, M and Caruso, M and D'Erchia, AM and Manzari, C and Fraccalvieri, R and Goffredo, E and Latorre, L and Miccolupo, A and Padalino, I and Santagada, G and Chiocco, D and Pesole, G and Horner, DS and Parisi, A}, title = {Comparative Genomics of Listeria Sensu Lato: Genus-Wide Differences in Evolutionary Dynamics and the Progressive Gain of Complex, Potentially Pathogenicity-Related Traits through Lateral Gene Transfer.}, journal = {Genome biology and evolution}, volume = {7}, number = {8}, pages = {2154-2172}, pmid = {26185097}, issn = {1759-6653}, mesh = {DNA, Bacterial/chemistry ; Ethanolamine/metabolism ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; Genomics ; Italy ; Listeria/classification/*genetics/isolation &amp; purification/metabolism ; Phylogeny ; Propylene Glycols/metabolism ; Repetitive Sequences, Nucleic Acid ; Riboflavin/biosynthesis ; }, abstract = {Historically, genome-wide and molecular characterization of the genus Listeria has concentrated on the important human pathogen Listeria monocytogenes and a small number of closely related species, together termed Listeria sensu strictu. More recently, a number of genome sequences for more basal, and nonpathogenic, members of the Listeria genus have become available, facilitating a wider perspective on the evolution of pathogenicity and genome level evolutionary dynamics within the entire genus (termed Listeria sensu lato). Here, we have sequenced the genomes of additional Listeria fleischmannii and Listeria newyorkensis isolates and explored the dynamics of genome evolution in Listeria sensu lato. Our analyses suggest that acquisition of genetic material through gene duplication and divergence as well as through lateral gene transfer (mostly from outside Listeria) is widespread throughout the genus. Novel genetic material is apparently subject to rapid turnover. Multiple lines of evidence point to significant differences in evolutionary dynamics between the most basal Listeria subclade and all other congeners, including both sensu strictu and other sensu lato isolates. Strikingly, these differences are likely attributable to stochastic, population-level processes and contribute to observed variation in genome size across the genus. Notably, our analyses indicate that the common ancestor of Listeria sensu lato lacked flagella, which were acquired by lateral gene transfer by a common ancestor of Listeria grayi and Listeria sensu strictu, whereas a recently functionally characterized pathogenicity island, responsible for the capacity to produce cobalamin and utilize ethanolamine/propane-2-diol, was acquired in an ancestor of Listeria sensu strictu.}, }
@article {pmid26185080, year = {2015}, author = {Amaro, C and Sanjuán, E and Fouz, B and Pajuelo, D and Lee, CT and Hor, LI and Barrera, R}, title = {The Fish Pathogen Vibrio vulnificus Biotype 2: Epidemiology, Phylogeny, and Virulence Factors Involved in Warm-Water Vibriosis.}, journal = {Microbiology spectrum}, volume = {3}, number = {3}, pages = {}, doi = {10.1128/microbiolspec.VE-0005-2014}, pmid = {26185080}, issn = {2165-0497}, mesh = {Animals ; Bacterial Toxins/genetics/*metabolism ; Eels/*microbiology ; Fish Diseases/epidemiology/*microbiology/transmission ; Gene Transfer, Horizontal ; Humans ; Immunity, Innate ; Mice ; Phylogeny ; Plasmids/genetics ; Receptors, Transferrin/metabolism ; Vibrio Infections/epidemiology/*microbiology/transmission ; Vibrio vulnificus/classification/genetics/*pathogenicity ; Virulence Factors/genetics/*metabolism ; *Water Microbiology ; }, abstract = {Vibrio vulnificus biotype 2 is the etiological agent of warm-water vibriosis, a disease that affects eels and other teleosts, especially in fish farms. Biotype 2 is polyphyletic and probably emerged from aquatic bacteria by acquisition of a transferable virulence plasmid that encodes resistance to innate immunity of eels and other teleosts. Interestingly, biotype 2 comprises a zoonotic clonal complex designated as serovar E that has extended worldwide. One of the most interesting virulence factors produced by serovar E is RtxA13, a multifunctional protein that acts as a lethal factor for fish, an invasion factor for mice, and a survival factor outside the host. Two practically identical copies of rtxA13 are present in all biotype 2 strains regardless of the serovar, one in the virulence plasmid and the other in chromosome II. The plasmid also contains other genes involved in survival and growth in eel blood: vep07, a gene for an outer membrane (OM) lipoprotein involved in resistance to eel serum and vep20, a gene for an OM receptor specific for eel-transferrin and, probably, other related fish transferrins. All the three genes are highly conserved within biotype 2, which suggests that they are under a strong selective pressure. Interestingly, the three genes are related with transferable plasmids, which emphasizes the role of horizontal gene transfer in the evolution of V. vulnificus in nutrient-enriched aquatic environments, such as fish farms.}, }
@article {pmid26185067, year = {2015}, author = {Antonova, ES and Hammer, BK}, title = {Genetics of Natural Competence in Vibrio cholerae and other Vibrios.}, journal = {Microbiology spectrum}, volume = {3}, number = {3}, pages = {}, doi = {10.1128/microbiolspec.VE-0010-2014}, pmid = {26185067}, issn = {2165-0497}, mesh = {Biological Transport/genetics ; Chitin/metabolism ; Cyclic AMP Receptor Protein/metabolism ; DNA/metabolism ; DNA Transformation Competence/*genetics ; DNA, Bacterial/*genetics ; DNA-Binding Proteins/genetics ; Enzyme Activation ; Fimbriae Proteins/genetics ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal/*genetics ; Pili, Sex/genetics ; Quorum Sensing/genetics/physiology ; Signal Transduction/genetics ; Vibrio cholerae/*genetics/pathogenicity ; }, abstract = {Many Gram-positive and Gram-negative bacteria can become naturally competent to take up extracellular DNA from the environment via a dedicated uptake apparatus. The genetic material that is acquired can (i) be used for nutrients, (ii) aid in genome repair, and (iii) promote horizontal gene transfer when incorporated onto the genome by homologous recombination, the process of "transformation." Recent studies have identified multiple environmental cues sufficient to induce natural transformation in Vibrio cholerae and several other Vibrio species. In V. cholerae, nutrient limitation activates the cAMP receptor protein regulator, quorum-sensing signals promote synthesis of HapR-controlled QstR, chitin stimulates production of TfoX, and low extracellular nucleosides allow CytR to serve as an additional positive regulator. The network of signaling systems that trigger expression of each of these required regulators is well described, but the mechanisms by which each in turn controls competence apparatus genes is poorly understood. Recent work has defined a minimal set of genes that encode apparatus components and begun to characterize the architecture of the machinery by fluorescence microscopy. While studies with a small set of V. cholerae reference isolates have identified regulatory and competence genes required for DNA uptake, future studies may identify additional genes and regulatory connections, as well as revealing how common natural competence is among diverse V. cholerae isolates and other Vibrio species.}, }
@article {pmid26184597, year = {2015}, author = {Soucy, SM and Huang, J and Gogarten, JP}, title = {Horizontal gene transfer: building the web of life.}, journal = {Nature reviews. Genetics}, volume = {16}, number = {8}, pages = {472-482}, pmid = {26184597}, issn = {1471-0064}, mesh = {Eukaryota/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics/*physiology ; *Models, Genetic ; *Phylogeny ; *Selection, Genetic ; Symbiosis/*genetics ; }, abstract = {Horizontal gene transfer (HGT) is the sharing of genetic material between organisms that are not in a parent-offspring relationship. HGT is a widely recognized mechanism for adaptation in bacteria and archaea. Microbial antibiotic resistance and pathogenicity are often associated with HGT, but the scope of HGT extends far beyond disease-causing organisms. In this Review, we describe how HGT has shaped the web of life using examples of HGT among prokaryotes, between prokaryotes and eukaryotes, and even between multicellular eukaryotes. We discuss replacement and additive HGT, the proposed mechanisms of HGT, selective forces that influence HGT, and the evolutionary impact of HGT on ancestral populations and existing populations such as the human microbiome.}, }
@article {pmid26180132, year = {2015}, author = {Huang, TW and Lauderdale, TL and Liao, TL and Hsu, MC and Chang, FY and Chang, SC and Khong, WX and Ng, OT and Chen, YT and Kuo, SC and Chen, TL and Mu, JJ and Tsai, SF}, title = {Effective transfer of a 47 kb NDM-1-positive plasmid among Acinetobacter species.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {70}, number = {10}, pages = {2734-2738}, doi = {10.1093/jac/dkv191}, pmid = {26180132}, issn = {1460-2091}, mesh = {Acinetobacter/drug effects/*genetics ; Acinetobacter Infections/*microbiology ; Anti-Bacterial Agents/pharmacology ; *Conjugation, Genetic ; Cross Infection ; DNA Transposable Elements ; Gene Order ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; Microbial Sensitivity Tests ; Plasmids/*genetics ; beta-Lactam Resistance ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: To investigate the link between two NDM-1-positive Acinetobacter isolates from the same hospital, the plasmid profiles of the isolates were examined. These two isolates were found from a surveillance programme within 3 months from two patients without obvious physical contact or hospitalization time overlap.<br><br>METHODS: Antimicrobial susceptibility tests, genome sequencing of both isolates and plasmid transfer experiments were performed. A comparative study of similar plasmids was performed using BLAST analysis.<br><br>RESULTS: The antimicrobial susceptibility of the isolates (Acinetobacter soli M131 and Acinetobacter pittii MS32) and their Escherichia coli transconjugants revealed a conjugative plasmid that carried the carbapenem resistance determinant. Eleven plasmids were observed in M131 and three in MS32. Each isolate shared an identical plasmid that carried the blaNDM-1 gene. This 47&#x200a;271 bp plasmid harbours a conserved blaNDM-1-containing region that is flanked by ISAba125 and ISAba11 elements, and also contains a Ti-type conjugative operon. The plasmid is nearly identical in sequence to those of Acinetobacter isolates from China. In contrast to the mobilization of the blaNDM-1 sequence in Enterobacteriaceae, which is mainly by transposition, this plasmid moves as a whole among Acinetobacter species. Consistently, this plasmid was found to transfer effectively by in vitro conjugation to several Acinetobacter species.<br><br>CONCLUSIONS: The clinical and laboratory findings suggest that Acinetobacter species may serve as a reservoir of this blaNDM-1 plasmid. Our study demonstrates the potential of applying genome sequencing to the surveillance of antimicrobial-resistant bacteria.}, }
@article {pmid26177821, year = {2015}, author = {Takemura, M and Yokobori, S and Ogata, H}, title = {Evolution of Eukaryotic DNA Polymerases via Interaction Between Cells and Large DNA Viruses.}, journal = {Journal of molecular evolution}, volume = {81}, number = {1-2}, pages = {24-33}, pmid = {26177821}, issn = {1432-1432}, mesh = {Cell Nucleus/genetics ; DNA Viruses/*enzymology/*genetics ; DNA-Directed DNA Polymerase/*genetics ; Eukaryota/*enzymology/genetics ; Eukaryotic Cells/metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Phylogeny ; Sequence Alignment ; }, abstract = {B-family DNA-directed DNA polymerases are DNA replication enzymes found in Eukaryota, Archaea, large DNA viruses, and in some, but not all, bacteria. Several polymerase domains are conserved among the B-family DNA polymerases from these organisms, suggesting that the B-family DNA polymerases evolved from a common ancestor. Eukaryotes retain at least three replicative B-family DNA polymerases, DNA polymerase α, δ, and ε, and one translesion B-family DNA polymerase, DNA polymerase ζ. Here, we present molecular evolutionary evidence that suggests DNA polymerase genes evolved through horizontal gene transfer between the viral and archaeal-eukaryotic lineages. Molecular phylogenetic analyses of the B-family DNA polymerases from nucleo-cytoplasmic large DNA viruses (NCLDVs), eukaryotes, and archaea suggest that different NCLDV lineages such as Poxviridae and Mimiviridae were involved in the evolution of different DNA polymerases (pol-α-, δ-, ε-, and ζ-like genes) in archaeal-eukaryotic cell lineages, putatively through horizontal gene transfer. These results support existing theories that link the evolution of NCLDVs and the origin of the eukaryotic nucleus.}, }
@article {pmid26175724, year = {2015}, author = {Sánchez, MB}, title = {Antibiotic resistance in the opportunistic pathogen Stenotrophomonas maltophilia.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {658}, pmid = {26175724}, issn = {1664-302X}, abstract = {Stenotrophomonas maltophilia is an environmental bacterium found in the soil, associated with plants and animals, and in aquatic environments. It is also an opportunistic pathogen now causing an increasing number of nosocomial infections. The treatment of S. maltophilia is quite difficult given its intrinsic resistance to a number of antibiotics, and because it is able to acquire new resistances via horizontal gene transfer and mutations. Certainly, strains resistant to quinolones, cotrimoxale and/or cephalosporins-antibiotics commonly used to treat S. maltophilia infections-have emerged. The increasing number of available S. maltophilia genomes has allowed the identification and annotation of a large number of antimicrobial resistance genes. Most encode inactivating enzymes and efflux pumps, but information on their role in intrinsic and acquired resistance is limited. Non-typical antibiotic resistance mechanisms that also form part of the intrinsic resistome have been identified via mutant library screening. These include non-typical antibiotic resistance genes, such as bacterial metabolism genes, and non-inheritable resistant phenotypes, such as biofilm formation and persistence. Their relationships with resistance are complex and require further study.}, }
@article {pmid26173980, year = {2015}, author = {Wong, DH and Beiko, RG}, title = {Transfer of energy pathway genes in microbial enhanced biological phosphorus removal communities.}, journal = {BMC genomics}, volume = {16}, number = {1}, pages = {526}, pmid = {26173980}, issn = {1471-2164}, mesh = {Bacteria/enzymology/genetics ; Bacterial Proteins/genetics/metabolism ; Contig Mapping ; Energy Metabolism/genetics ; Enzymes/genetics/metabolism ; *Gene Transfer, Horizontal ; Phosphorus/*metabolism ; Sewage/microbiology ; }, abstract = {BACKGROUND: Lateral gene transfer (LGT) is an important evolutionary process in microbial evolution. In sewage treatment plants, LGT of antibiotic resistance and xenobiotic degradation-related proteins has been suggested, but the role of LGT outside these processes is unknown. Microbial communities involved in Enhanced Biological Phosphorus Removal (EBPR) have been used to treat wastewater in the last 50 years and may provide insights into adaptation to an engineered environment. We introduce two different types of analysis to identify LGT in EBPR sewage communities, based on identifying assembled sequences with more than one strong taxonomic match, and on unusual phylogenetic patterns. We applied these methods to investigate the role of LGT in six energy-related metabolic pathways.<br><br>RESULTS: The analyses identified overlapping but non-identical sets of transferred enzymes. All of these were homologous with sequences from known mobile genetic elements, and many were also in close proximity to transposases and integrases in the EBPR data set. The taxonomic method had higher sensitivity than the phylogenetic method, identifying more potential LGTs. Both analyses identified the putative transfer of five enzymes within an Australian community, two in a Danish community, and none in a US-derived culture.<br><br>CONCLUSIONS: Our methods were able to identify sequences with unusual phylogenetic or compositional properties as candidate LGT events. The association of these candidates with known mobile elements supports the hypothesis of transfer. The results of our analysis strongly suggest that LGT has influenced the development of functionally important energy-related pathways in EBPR systems, but transfers may be unique to each community due to different operating conditions or taxonomic composition.}, }
@article {pmid26173199, year = {2015}, author = {Wu, H and Xia, S and Bu, F and Qi, J and Liu, Y and Xu, H}, title = {Identification of integrons and phylogenetic groups of drug-resistant Escherichia coli from broiler carcasses in China.}, journal = {International journal of food microbiology}, volume = {211}, number = {}, pages = {51-56}, doi = {10.1016/j.ijfoodmicro.2015.07.004}, pmid = {26173199}, issn = {1879-3460}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Chickens/microbiology ; China ; *Drug Resistance, Bacterial ; Escherichia coli/classification/drug effects/genetics/*isolation &amp; purification ; Escherichia coli Infections/microbiology/*veterinary ; Escherichia coli Proteins/genetics ; *Integrons ; Meat/*microbiology ; *Phylogeny ; Poultry Diseases/*microbiology ; }, abstract = {The dissemination of drug-resistant Escherichia coli in poultry products is becoming a public concern, as it endangers food security and human health. It is very common for E. coli to exhibit drug resistance in the poultry industry in China due to the excessive use of antibiotics. However, few studies have examined the drug resistance endowed by integrons and integron-associated gene cassettes in different phylogenetic groups of E. coli isolated from broiler carcasses. In this study, 373 antibiotic-resistant E. coli strains were isolated from the surfaces or insides of broiler carcasses from a slaughterhouse in Shandong Province, China. According to phylogenetic assays of chuA, yjaA, and an anonymous DNA fragment, TSPE4-C2, these isolates belong to four phylogenetic groups (A, B1, B2, and D) and seven subgroups (A0, A1, B1, B21, B22, D1, and D2). Of the tested isolates, 95.71% (n=357) are multi-drug resistant, among which group B1 was predominant, accounting for 33.51% (n=125) of the tested isolates. A high percentage of the E. coli isolates were resistant to amoxicillin-clavulanic acid (99.20%, n=370), doxycycline (92.23%, n=344), sulfamethoxazole-trimethoprim (90.88%, n=339), ciprofloxacin, (64.61%, n=241), sulbactam-cefoperazone (51.21%, n=191), and amikacin (33.78%, n=126). Furthermore, among the 373 isolates, class 1 and 2 integrons were identified in 292 (78.28%) and 49 (13.14%) of the isolates, respectively, while no class 3 integrons were detected. The most prevalent gene cassette arrays were dfrA17-aadA5 and dfrA12-orfF-aadA2 in the variable region of class 1 integrons, while only one gene cassette array (dfrA1-sat2-aadA1) was detected in the variable region of class 2 integrons. Class 1 integrons were distributed in various physiological subtypes, whereas no predominant phylogenetic groups could be identified. The presence of class 2 integrons in the B21 subtype was significantly higher than in the other subtypes, and it coexisted with the class 1 integron. This study suggests that broiler products are potential sources of multi-drug resistant E. coli, and that resistance genes could be spread by lateral gene transfer.}, }
@article {pmid26163675, year = {2015}, author = {Bolotin, E and Hershberg, R}, title = {Gene Loss Dominates As a Source of Genetic Variation within Clonal Pathogenic Bacterial Species.}, journal = {Genome biology and evolution}, volume = {7}, number = {8}, pages = {2173-2187}, pmid = {26163675}, issn = {1759-6653}, mesh = {Bacteria/genetics ; Bacterial Proteins/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genetic Variation ; Genome, Bacterial ; Molecular Sequence Annotation ; Pseudogenes ; }, abstract = {Some of the most dangerous pathogens such as Mycobacterium tuberculosis and Yersinia pestis evolve clonally. This means that little or no recombination occurs between strains belonging to these species. Paradoxically, although different members of these species show extreme sequence similarity of orthologous genes, some show considerable intraspecies phenotypic variation, the source of which remains elusive. To examine the possible sources of phenotypic variation within clonal pathogenic bacterial species, we carried out an extensive genomic and pan-genomic analysis of the sources of genetic variation available to a large collection of clonal and nonclonal pathogenic bacterial species. We show that while nonclonal species diversify through a combination of changes to gene sequences, gene loss and gene gain, gene loss completely dominates as a source of genetic variation within clonal species. Indeed, gene loss is so prevalent within clonal species as to lead to levels of gene content variation comparable to those found in some nonclonal species that are much more diverged in their gene sequences and that acquire a substantial number of genes horizontally. Gene loss therefore needs to be taken into account as a potential dominant source of phenotypic variation within clonal bacterial species.}, }
@article {pmid26162088, year = {2015}, author = {Kingston, AW and Roussel-Rossin, C and Dupont, C and Raleigh, EA}, title = {Novel recA-Independent Horizontal Gene Transfer in Escherichia coli K-12.}, journal = {PloS one}, volume = {10}, number = {7}, pages = {e0130813}, pmid = {26162088}, issn = {1932-6203}, mesh = {Chromosomes, Bacterial/genetics ; Conjugation, Genetic ; DNA, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Escherichia coli K12/*genetics/metabolism ; Escherichia coli Proteins/*genetics/metabolism ; *Gene Transfer, Horizontal ; Genome, Bacterial/genetics ; Genomic Islands/genetics ; Homologous Recombination ; Models, Genetic ; Rec A Recombinases/*genetics/metabolism ; }, abstract = {In bacteria, mechanisms that incorporate DNA into a genome without strand-transfer proteins such as RecA play a major role in generating novelty by horizontal gene transfer. We describe a new illegitimate recombination event in Escherichia coli K-12: RecA-independent homologous replacements, with very large (megabase-length) donor patches replacing recipient DNA. A previously uncharacterized gene (yjiP) increases the frequency of RecA-independent replacement recombination. To show this, we used conjugal DNA transfer, combining a classical conjugation donor, HfrH, with modern genome engineering methods and whole genome sequencing analysis to enable interrogation of genetic dependence of integration mechanisms and characterization of recombination products. As in classical experiments, genomic DNA transfer begins at a unique position in the donor, entering the recipient via conjugation; antibiotic resistance markers are then used to select recombinant progeny. Different configurations of this system were used to compare known mechanisms for stable DNA incorporation, including homologous recombination, F'-plasmid formation, and genome duplication. A genome island of interest known as the immigration control region was specifically replaced in a minority of recombinants, at a frequency of 3 X 10(-12) CFU/recipient per hour.}, }
@article {pmid26161978, year = {2015}, author = {Driebe, EM and Sahl, JW and Roe, C and Bowers, JR and Schupp, JM and Gillece, JD and Kelley, E and Price, LB and Pearson, TR and Hepp, CM and Brzoska, PM and Cummings, CA and Furtado, MR and Andersen, PS and Stegger, M and Engelthaler, DM and Keim, PS}, title = {Using Whole Genome Analysis to Examine Recombination across Diverse Sequence Types of Staphylococcus aureus.}, journal = {PloS one}, volume = {10}, number = {7}, pages = {e0130955}, pmid = {26161978}, issn = {1932-6203}, support = {R01 AI090782/AI/NIAID NIH HHS/United States ; R01 AI101371/AI/NIAID NIH HHS/United States ; U01 AI066581/AI/NIAID NIH HHS/United States ; R01AI090782/AI/NIAID NIH HHS/United States ; }, mesh = {Bayes Theorem ; Cluster Analysis ; Evolution, Molecular ; Genes, Bacterial/genetics ; *Genetic Variation ; Genome, Bacterial/*genetics ; Genotype ; Mutation ; Mutation Rate ; Phylogeny ; Polymorphism, Single Nucleotide ; *Recombination, Genetic ; Sequence Analysis, DNA/*methods ; Staphylococcus aureus/classification/*genetics/pathogenicity ; Virulence/genetics ; }, abstract = {Staphylococcus aureus is an important clinical pathogen worldwide and understanding this organism's phylogeny and, in particular, the role of recombination, is important both to understand the overall spread of virulent lineages and to characterize outbreaks. To further elucidate the phylogeny of S. aureus, 35 diverse strains were sequenced using whole genome sequencing. In addition, 29 publicly available whole genome sequences were included to create a single nucleotide polymorphism (SNP)-based phylogenetic tree encompassing 11 distinct lineages. All strains of a particular sequence type fell into the same clade with clear groupings of the major clonal complexes of CC8, CC5, CC30, CC45 and CC1. Using a novel analysis method, we plotted the homoplasy density and SNP density across the whole genome and found evidence of recombination throughout the entire chromosome, but when we examined individual clonal lineages we found very little recombination. However, when we analyzed three branches of multiple lineages, we saw intermediate and differing levels of recombination between them. These data demonstrate that in S. aureus, recombination occurs across major lineages that subsequently expand in a clonal manner. Estimated mutation rates for the CC8 and CC5 lineages were different from each other. While the CC8 lineage rate was similar to previous studies, the CC5 lineage was 100-fold greater. Fifty known virulence genes were screened in all genomes in silico to determine their distribution across major clades. Thirty-three genes were present variably across clades, most of which were not constrained by ancestry, indicating horizontal gene transfer or gene loss.}, }
@article {pmid26161530, year = {2015}, author = {Hespeels, B and Li, X and Flot, JF and Pigneur, LM and Malaisse, J and Da Silva, C and Van Doninck, K}, title = {Against All Odds: Trehalose-6-Phosphate Synthase and Trehalase Genes in the Bdelloid Rotifer Adineta vaga Were Acquired by Horizontal Gene Transfer and Are Upregulated during Desiccation.}, journal = {PloS one}, volume = {10}, number = {7}, pages = {e0131313}, pmid = {26161530}, issn = {1932-6203}, mesh = {Animals ; Desiccation/methods ; Gene Dosage ; *Gene Transfer, Horizontal ; Glucosyltransferases/classification/*genetics/metabolism ; Helminth Proteins/*genetics/metabolism ; Metabolic Networks and Pathways ; Phosphoric Monoester Hydrolases/genetics/metabolism ; Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction ; Rotifera/enzymology/*genetics ; Transcriptional Activation ; Trehalase/*genetics/metabolism ; Trehalose/metabolism ; *Up-Regulation ; }, abstract = {The disaccharide sugar trehalose is essential for desiccation resistance in most metazoans that survive dryness; however, neither trehalose nor the enzymes involved in its metabolism have ever been detected in bdelloid rotifers despite their extreme resistance to desiccation. Here we screened the genome of the bdelloid rotifer Adineta vaga for genes involved in trehalose metabolism. We discovered a total of four putative trehalose-6-phosphate synthase (TPS) and seven putative trehalase (TRE) gene copies in the genome of this ameiotic organism; however, no trehalose-6-phosphate phosphatase (TPP) gene or domain was detected. The four TPS copies of A. vaga appear more closely related to plant and fungi proteins, as well as to some protists, whereas the seven TRE copies fall in bacterial clades. Therefore, A. vaga likely acquired its trehalose biosynthesis and hydrolysis genes by horizontal gene transfers. Nearly all residues important for substrate binding in the predicted TPS domains are highly conserved, supporting the hypothesis that several copies of the genes might be functional. Besides, RNAseq library screening showed that trehalase genes were highly expressed compared to TPS genes, explaining probably why trehalose had not been detected in previous studies of bdelloids. A strong overexpression of their TPS genes was observed when bdelloids enter desiccation, suggesting a possible signaling role of trehalose-6-phosphate or trehalose in this process.}, }
@article {pmid26159623, year = {2015}, author = {Parker, MA}, title = {A single sym plasmid type predominates across diverse chromosomal lineages of Cupriavidus nodule symbionts.}, journal = {Systematic and applied microbiology}, volume = {38}, number = {6}, pages = {417-423}, doi = {10.1016/j.syapm.2015.06.003}, pmid = {26159623}, issn = {1618-0984}, mesh = {Caribbean Region ; Cluster Analysis ; Cupriavidus/*classification/*genetics ; Gene Transfer, Horizontal ; Genes, Essential ; *Genetic Variation ; Mimosa/growth &amp; development/*microbiology ; Molecular Sequence Data ; Phylogeny ; Plant Development ; Plasmids/*analysis/*classification ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {Cupriavidus nodule symbionts from Mimosa host legumes indigenous to five locations around the Caribbean region were analyzed by sequencing portions of five chromosomal housekeeping loci and five sym plasmid loci in 80 isolates. Nodule symbionts did not form a single clade separated from non-symbiotic reference strains of Cupriavidus and Ralstonia, implying that either convergent losses or independent gains of the trait of legume symbiosis have taken place. Chromosomal genes exhibited significantly higher nucleotide polymorphism and haplotype diversity than sym plasmid loci. A single derived sym plasmid haplotype (A1) was found to predominate in four of the populations, and was shared by multiple housekeeping gene clades. This suggests that one sym plasmid variant has recently spread geographically and has been acquired by diverse chromosomal lineages within the region. Inoculation of two Mimosa host species indicated that strains carrying the predominant A1 haplotype ranked either first or second among the five major sym plasmid haplotype groups with respect to plant growth enhancement. Symbiotic outcomes also varied greatly among chromosomally diverse strains that all shared the A1 haplotype. Thus, chromosomal as well as sym plasmid variants likely contribute to differential interactions with Mimosa host species.}, }
@article {pmid26158727, year = {2015}, author = {Reck, M and Tomasch, J and Wagner-Döbler, I}, title = {The Alternative Sigma Factor SigX Controls Bacteriocin Synthesis and Competence, the Two Quorum Sensing Regulated Traits in Streptococcus mutans.}, journal = {PLoS genetics}, volume = {11}, number = {7}, pages = {e1005353}, pmid = {26158727}, issn = {1553-7404}, mesh = {Bacterial Proteins/genetics ; Bacteriocins/*biosynthesis/metabolism ; DNA Transformation Competence/genetics ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal/genetics ; Promoter Regions, Genetic/genetics ; Quorum Sensing/*genetics ; Sigma Factor/*genetics ; Signal Transduction/genetics ; Streptococcus mutans/*genetics ; Trans-Activators/genetics ; Transcriptome/genetics ; }, abstract = {Two small quorum sensing (QS) peptides regulate competence in S. mutans in a cell density dependent manner: XIP (sigX inducing peptide) and CSP (competence stimulating peptide). Depending on the environmental conditions isogenic S. mutans cells can split into a competent and non-competent subpopulation. The origin of this population heterogeneity has not been experimentally determined and it is unknown how the two QS systems are connected. We developed a toolbox of single and dual fluorescent reporter strains and systematically knocked out key genes of the competence signaling cascade in the reporter strain backgrounds. By following signal propagation on the single cell level we discovered that the master regulator of competence, the alternative sigma factor SigX, directly controls expression of the response regulator for bacteriocin synthesis ComE. Consequently, a SigX binding motif (cin-box) was identified in the promoter region of comE. Overexpressing the genetic components involved in competence development demonstrated that ComRS represents the origin of bimodality and determines the modality of the downstream regulators SigX and ComE. Moreover these analysis showed that there is no direct regulatory link between the two QS signaling cascades. Competence is induced through a hierarchical XIP signaling cascade, which has no regulatory input from the CSP cascade. CSP exclusively regulates bacteriocin synthesis. We suggest renaming it mutacin inducing peptide (MIP). Finally, using phosphomimetic comE mutants we show that unimodal bacteriocin production is controlled posttranslationally, thus solving the puzzling observation that in complex media competence is observed in a subpopulation only, while at the same time all cells produce bacteriocins. The control of both bacteriocin synthesis and competence through the alternative sigma-factor SigX suggests that S. mutans increases its genetic repertoire via QS controlled predation on neighboring species in its natural habitat.}, }
@article {pmid26149779, year = {2015}, author = {Kanchan, S and Mehrotra, R and Chowdhury, S}, title = {In Silico Analysis of the Endonuclease III Protein Family Identifies Key Residues and Processes During Evolution.}, journal = {Journal of molecular evolution}, volume = {81}, number = {1-2}, pages = {54-67}, pmid = {26149779}, issn = {1432-1432}, mesh = {Computer Simulation ; Databases, Protein ; Deoxyribonuclease (Pyrimidine Dimer)/*genetics ; Endonucleases/*genetics ; Escherichia coli/genetics ; Escherichia coli Proteins/*genetics ; *Evolution, Molecular ; Models, Theoretical ; Phylogeny ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {DNA repair refers to a collection of processes by which a cell identifies and corrects damage to genomic DNA molecules. DNA repair processes significantly overcome DNA damage and restore the normal nucleotide sequence and DNA structure. This study focuses on the evolution of the endonuclease III gene/protein family, which plays a key role in the base excision repair pathway. We analyzed 463 homologs of the endonuclease III protein and compared them with the corresponding gene and 16S/18S rRNA sequences to understand the evolutionary processes of this protein family. The sequence analysis and comparison reveal consensus sequence motifs within the ENDO3c and iron-sulfur cluster loop domains that are functionally and structurally important. On the basis of phylogenetic analysis, we propose an evolutionary model of the endonuclease III protein family. Horizontal gene transfer was identified as the key event among bacteria, archaea, and eukaryotic organisms that occurred during the evolution of the endonuclease III gene family among bacteria, archaea, and eukaryotic organisms. This analysis may be exploited to achieve a better prediction of the endonuclease III family gene/protein in unannotated organisms or families of organisms that are completely sequenced as well as in those for which sequencing is ongoing.}, }
@article {pmid26147573, year = {2015}, author = {Noor Uddin, GM and Larsen, MH and Christensen, H and Aarestrup, FM and Phu, TM and Dalsgaard, A}, title = {Identification and Antimicrobial Resistance of Bacteria Isolated from Probiotic Products Used in Shrimp Culture.}, journal = {PloS one}, volume = {10}, number = {7}, pages = {e0132338}, pmid = {26147573}, issn = {1932-6203}, mesh = {Aerococcus/drug effects/isolation &amp; purification ; Animals ; *Aquaculture ; Bacillus/classification/drug effects/genetics/isolation &amp; purification ; Bacteria/*drug effects/isolation &amp; purification ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; *Drug Resistance, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Genes, Bacterial ; Klebsiella/drug effects/isolation &amp; purification ; *Penaeidae ; Phylogeny ; *Probiotics ; R Factors/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Ribotyping ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Vietnam ; }, abstract = {Probiotics are increasingly used in aquaculture to control diseases and improve feed digestion and pond water quality; however, little is known about the antimicrobial resistance properties of such probiotic bacteria and to what extent they may contribute to the development of bacterial resistance in aquaculture ponds. Concerns have been raised that the declared information on probiotic product labels are incorrect and information on bacterial composition are often missing. We therefore evaluated seven probiotics commonly used in Vietnamese shrimp culture for their bacterial species content, phenotypic antimicrobial resistance and associated transferable resistance genes. The bacterial species was established by 16S rRNA sequence analysis of 125 representative bacterial isolates. MIC testing was done for a range of antimicrobials and whole genome sequencing of six multiple antimicrobial resistant Bacillus spp. used to identify resistance genes and genetic elements associated with horizontal gene transfer. Thirteen bacterial species declared on the probiotic products could not be identified and 11 non-declared Bacillus spp. were identified. Although our culture-based isolation and identification may have missed a few bacterial species present in the tested products this would represent minor bias, but future studies may apply culture independent identification methods like pyro sequencing. Only 6/60 isolates were resistant to more than four antimicrobials and whole genome sequencing showed that they contained macrolide (ermD), tetracycline (tetL), phenicol (fexA) and trimethoprim (dfrD, dfrG and dfrK) resistance genes, but not known structures associated with horizontal gene transfer. Probiotic bacterial strains used in Vietnamese shrimp culture seem to contribute with very limited types and numbers of resistance genes compared to the naturally occurring bacterial species in aquaculture environments. Approval procedures of probiotic products must be strengthened through scientific-based efficacy trials and product labels should allow identification of individual bacterial strains and inform the farmer on specific purpose, dosage and correct application measures.}, }
@article {pmid26147248, year = {2015}, author = {Ruan, L and Wang, H and Cai, G and Peng, D and Zhou, H and Zheng, J and Zhu, L and Wang, X and Yu, H and Li, S and Geng, C and Sun, M}, title = {A two-domain protein triggers heat shock pathway and necrosis pathway both in model plant and nematode.}, journal = {Environmental microbiology}, volume = {17}, number = {11}, pages = {4547-4565}, doi = {10.1111/1462-2920.12968}, pmid = {26147248}, issn = {1462-2920}, mesh = {Animals ; Arabidopsis/*microbiology ; Bacillus thuringiensis/genetics/*pathogenicity ; Base Sequence ; Biological Evolution ; Caenorhabditis elegans/drug effects/genetics/*microbiology ; Gene Transfer, Horizontal ; Heat-Shock Response/genetics/*physiology ; Methylgalactosides/pharmacology ; Molecular Sequence Data ; Plant Diseases/*microbiology ; Protein Structure, Tertiary/genetics ; Soil Microbiology ; Nicotiana/*microbiology ; Virulence/genetics ; }, abstract = {The entomopathogen Bacillus thuringiensis is equipped with multiple virulent factors. The genome sequence of B. thuringiensis YBT1520 revealed the presence of a two-domain protein named Nel which is composed of a necrosis-inducing phytophthora protein 1-like domain found in phytopathogens and a ricin B-like lectin domain. The merging of two distantly related domains is relatively rare. Nel induced necrosis and pathogen-triggered immunity (PTI) on model plants. The Nel also exhibited inhibition activity to nematode. Microscopic observation showed that the toxicity of Nel to nematodes targets the intestine. Quantitative proteomics revealed that Nel stimulated the host defence. The Nel thus possesses dual roles, as both toxin and elicitor. Remarkably, the Nel protein triggered a similar response, induction of the heat shock pathway and the necrosis pathway, in both model plants and nematodes. The unusual ability of Nel to function across kingdom suggests a highly conserved mechanism in eukaryotes that predates the divergence of plants and animal. It is also speculated that the two-domain protein is the result of horizontal gene transfer (HGT) between phytopathogens and entomopathogens. Our results provide an example that HGT occurs between members of different species or even genera with lower frequency are particularly important for evolution of new bacterial pathogen lineages with new virulence. Bacillus thuringiensis occupies the same ecological niches, plant and soil, as phytopathogens, providing the opportunity for gene exchange.}, }
@article {pmid26147218, year = {2015}, author = {Marcelletti, S and Scortichini, M}, title = {Comparative Genomic Analyses of Multiple Pseudomonas Strains Infecting Corylus avellana Trees Reveal the Occurrence of Two Genetic Clusters with Both Common and Distinctive Virulence and Fitness Traits.}, journal = {PloS one}, volume = {10}, number = {7}, pages = {e0131112}, pmid = {26147218}, issn = {1932-6203}, mesh = {Adaptation, Physiological/genetics ; Base Composition ; Clustered Regularly Interspaced Short Palindromic Repeats ; Coinfection ; Comparative Genomic Hybridization ; Corylus/*microbiology ; DNA, Bacterial/genetics ; Europe ; Evolution, Molecular ; Gene Flow ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genetic Fitness ; Genetic Speciation ; Genomic Islands/*genetics ; Host-Pathogen Interactions/genetics ; Molecular Sequence Data ; *Multigene Family ; Phylogeny ; Plant Diseases/*microbiology ; Pseudomonas/*genetics/isolation &amp; purification/pathogenicity ; Recombination, Genetic ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Species Specificity ; Virulence/genetics ; }, abstract = {The European hazelnut (Corylus avellana) is threatened in Europe by several pseudomonads which cause symptoms ranging from twig dieback to tree death. A comparison of the draft genomes of nine Pseudomonas strains isolated from symptomatic C. avellana trees was performed to identify common and distinctive genomic traits. The thorough assessment of genetic relationships among the strains revealed two clearly distinct clusters: P. avellanae and P. syringae. The latter including the pathovars avellanae, coryli and syringae. Between these two clusters, no recombination event was found. A genomic island of approximately 20 kb, containing the hrp/hrc type III secretion system gene cluster, was found to be present without any genomic difference in all nine pseudomonads. The type III secretion system effector repertoires were remarkably different in the two groups, with P. avellanae showing a higher number of effectors. Homologue genes of the antimetabolite mangotoxin and ice nucleation activity clusters were found solely in all P. syringae pathovar strains, whereas the siderophore yersiniabactin was only present in P. avellanae. All nine strains have genes coding for pectic enzymes and sucrose metabolism. By contrast, they do not have genes coding for indolacetic acid and anti-insect toxin. Collectively, this study reveals that genomically different Pseudomonas can converge on the same host plant by suppressing the host defence mechanisms with the use of different virulence weapons. The integration into their genomes of a horizontally acquired genomic island could play a fundamental role in their evolution, perhaps giving them the ability to exploit new ecological niches.}, }
@article {pmid26142678, year = {2015}, author = {Sumbana, J and Taviani, E and Manjate, A and Paglietti, B and Santona, A and Colombo, MM}, title = {Genetic determinants of pathogenicity of Escherichia coli isolated from children with acute diarrhea in Maputo, Mozambique.}, journal = {Journal of infection in developing countries}, volume = {9}, number = {6}, pages = {661-664}, doi = {10.3855/jidc.6122}, pmid = {26142678}, issn = {1972-2680}, mesh = {Child ; Child, Preschool ; Diarrhea/epidemiology/*microbiology ; Escherichia coli/classification/*genetics/isolation &amp; purification ; Escherichia coli Infections/epidemiology/*microbiology ; Escherichia coli Proteins/*genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genetic Variation ; Genotype ; Humans ; Infant ; Mozambique/epidemiology ; Polymerase Chain Reaction ; Virulence Factors/*genetics ; }, abstract = {INTRODUCTION: Diarrheagenic Escherichia coli (DEC) represents one of the leading cause of diarrhoea in developing countries. In this study a molecular approach was applied for the detection of diarrheagenic Escherichia coli (DEC) circulating in Maputo, Mozambique.<br><br>METHODOLOGY: All isolates were PCR tested for species-specific genes and for 11 molecular markers: stx1, stx2, eae, bfpA, lt, st, ipaH, aap, aggR CVD432 and daaE.<br><br>RESULTS: Of the 80 E. coli isolated, 74% were potential DEC: 21% EIEC, 19% EPEC, 15% EAEC, 13% ETEC, 5% DAEC and 1% hybrids.<br><br>CONCLISION: This study revealed the complexity of the etiology of diarrhea caused by pathogenic E. coli in Mozambique, and the risk of the emergence of new pathogenic variants due to the horizontal transmission of pathogenicity factors.}, }
@article {pmid26141154, year = {2015}, author = {Guo, J and Wang, Q and Wang, X and Wang, F and Yao, J and Zhu, H}, title = {Horizontal gene transfer in an acid mine drainage microbial community.}, journal = {BMC genomics}, volume = {16}, number = {1}, pages = {496}, pmid = {26141154}, issn = {1471-2164}, mesh = {Acids/*chemistry ; Bacteria/*genetics ; Drainage, Sanitary ; Environment ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial/genetics ; Metagenome/*genetics ; Metagenomics/methods ; Mining/methods ; Phylogeny ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT) has been widely identified in complete prokaryotic genomes. However, the roles of HGT among members of a microbial community and in evolution remain largely unknown. With the emergence of metagenomics, it is nontrivial to investigate such horizontal flow of genetic materials among members in a microbial community from the natural environment. Because of the lack of suitable methods for metagenomics gene transfer detection, microorganisms from a low-complexity community acid mine drainage (AMD) with near-complete genomes were used to detect possible gene transfer events and suggest the biological significance.<br><br>RESULTS: Using the annotation of coding regions by the current tools, a phylogenetic approach, and an approximately unbiased test, we found that HGTs in AMD organisms are not rare, and we predicted 119 putative transferred genes. Among them, 14 HGT events were determined to be transfer events among the AMD members. Further analysis of the 14 transferred genes revealed that the HGT events affected the functional evolution of archaea or bacteria in AMD, and it probably shaped the community structure, such as the dominance of G-plasma in archaea in AMD through HGT.<br><br>CONCLUSIONS: Our study provides a novel insight into HGT events among microorganisms in natural communities. The interconnectedness between HGT and community evolution is essential to understand microbial community formation and development.}, }
@article {pmid26140533, year = {2016}, author = {Oton, EV and Quince, C and Nicol, GW and Prosser, JI and Gubry-Rangin, C}, title = {Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota.}, journal = {The ISME journal}, volume = {10}, number = {1}, pages = {85-96}, pmid = {26140533}, issn = {1751-7370}, support = {MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; MR/M50161X/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adaptation, Biological ; Ammonia/analysis ; Archaea/*genetics ; *Biodiversity ; Biological Evolution ; DNA, Bacterial/genetics ; Ecology ; Ecosystem ; Multivariate Analysis ; Nitrogen/analysis ; Oxidation-Reduction ; Oxidoreductases ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Thaumarchaeota form a ubiquitously distributed archaeal phylum, comprising both the ammonia-oxidising archaea (AOA) and other archaeal groups in which ammonia oxidation has not been demonstrated (including Group 1.1c and Group 1.3). The ecology of AOA in terrestrial environments has been extensively studied using either a functional gene, encoding ammonia monooxygenase subunit A (amoA) or 16S ribosomal RNA (rRNA) genes, which show phylogenetic coherence with respect to soil pH. To test phylogenetic congruence between these two markers and to determine ecological coherence in all Thaumarchaeota, we performed high-throughput sequencing of 16S rRNA and amoA genes in 46 UK soils presenting 29 available contextual soil characteristics. Adaptation to pH and organic matter content reflected strong ecological coherence at various levels of taxonomic resolution for Thaumarchaeota (AOA and non-AOA), whereas nitrogen, total mineralisable nitrogen and zinc concentration were also important factors associated with AOA thaumarchaeotal community distribution. Other significant associations with environmental factors were also detected for amoA and 16S rRNA genes, reflecting different diversity characteristics between these two markers. Nonetheless, there was significant statistical congruence between the markers at fine phylogenetic resolution, supporting the hypothesis of low horizontal gene transfer between Thaumarchaeota. Group 1.1c Thaumarchaeota were also widely distributed, with two clusters predominating, particularly in environments with higher moisture content and organic matter, whereas a similar ecological pattern was observed for Group 1.3 Thaumarchaeota. The ecological and phylogenetic congruence identified is fundamental to understand better the life strategies, evolutionary history and ecosystem function of the Thaumarchaeota.}, }
@article {pmid26138219, year = {2015}, author = {Losi, A and Mandalari, C and Gärtner, W}, title = {The Evolution and Functional Role of Flavin-based Prokaryotic Photoreceptors.}, journal = {Photochemistry and photobiology}, volume = {91}, number = {5}, pages = {1021-1031}, doi = {10.1111/php.12489}, pmid = {26138219}, issn = {1751-1097}, mesh = {Bacteria/classification/*metabolism ; *Biological Evolution ; Flavins/*chemistry ; Photoreceptors, Microbial/*physiology ; Phylogeny ; }, abstract = {Flavin-based photoreceptor proteins of the LOV (light, oxygen and voltage) superfamily are ubiquitous and appear to be essential blue-light sensing systems not only in plants, algae and fungi, but also in prokaryotes, where they are represented in more than 10% of known species. Despite their broad occurrence, only in few cases LOV proteins have been correlated with important phenomena such as bacterial infectivity, selective growth patterns or/and stress responses; nevertheless these few known roles are helping us understand the multiple ways by which prokaryotes can exploit these soluble blue-light photoreceptors. Given the large number of sequences now deposited in databases, it becomes meaningful to define a signature for bona fide LOV domains, a procedure that facilitates identification of proteins with new properties and phylogenetic analysis. The latter clearly evidences that a class of LOV proteins from alpha-proteobacteria is the closest prokaryotic relative of eukaryotic LOV domains, whereas cyanobacterial sequences cluster with the archaeal and the other bacterial LOV domains. Distance trees built for LOV domains suggest complex evolutionary patterns, possibly involving multiple horizontal gene transfer events. Based on available data, the in vivo relevance and evolution of prokaryotic LOV is discussed.}, }
@article {pmid26136734, year = {2015}, author = {Filée, J}, title = {Genomic comparison of closely related Giant Viruses supports an accordion-like model of evolution.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {593}, pmid = {26136734}, issn = {1664-302X}, abstract = {Genome gigantism occurs so far in Phycodnaviridae and Mimiviridae (order Megavirales). Origin and evolution of these Giant Viruses (GVs) remain open questions. Interestingly, availability of a collection of closely related GV genomes enabling genomic comparisons offer the opportunity to better understand the different evolutionary forces acting on these genomes. Whole genome alignment for five groups of viruses belonging to the Mimiviridae and Phycodnaviridae families show that there is no trend of genome expansion or general tendency of genome contraction. Instead, GV genomes accumulated genomic mutations over the time with gene gains compensating the different losses. In addition, each lineage displays specific patterns of genome evolution. Mimiviridae (megaviruses and mimiviruses) and Chlorella Phycodnaviruses evolved mainly by duplications and losses of genes belonging to large paralogous families (including movements of diverse mobiles genetic elements), whereas Micromonas and Ostreococcus Phycodnaviruses derive most of their genetic novelties thought lateral gene transfers. Taken together, these data support an accordion-like model of evolution in which GV genomes have undergone successive steps of gene gain and gene loss, accrediting the hypothesis that genome gigantism appears early, before the diversification of the different GV lineages.}, }
@article {pmid26135711, year = {2016}, author = {Brolund, A and Sandegren, L}, title = {Characterization of ESBL disseminating plasmids.}, journal = {Infectious diseases (London, England)}, volume = {48}, number = {1}, pages = {18-25}, doi = {10.3109/23744235.2015.1062536}, pmid = {26135711}, issn = {2374-4243}, mesh = {Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; Enterobacteriaceae/drug effects/*enzymology/*genetics ; Enterobacteriaceae Infections/epidemiology/*microbiology ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Molecular Epidemiology ; *Plasmids ; beta-Lactam Resistance/*genetics ; beta-Lactamases/biosynthesis/*genetics ; beta-Lactams/pharmacology ; }, abstract = {Bacteria producing extended-spectrum β-lactamases (ESBLs) constitute a globally increasing problem that contributes to treatment complications and elevated death rates. The extremely successful dissemination by ESBL-producing Enterobacteriaceae during the latest decades is a result of the combination of mobilization, evolution and horizontal spread of β-lactamase genes on plasmids. In parallel, spread of these plasmids to particularly well-adapted bacterial clones (outbreak clones) has expanded. In this review we describe ESBL-producing bacteria and the genetic mechanisms for dissemination of ESBL resistance. We describe available methodology for studying plasmids and the importance of including plasmids in epidemiological typing as natural parts of the organisms. Plasmids play a fundamental role in how resistance arises and disseminates.}, }
@article {pmid26135320, year = {2015}, author = {Botka, T and Růžičková, V and Konečná, H and Pantůček, R and Rychlík, I and Zdráhal, Z and Petráš, P and Doškař, J}, title = {Complete genome analysis of two new bacteriophages isolated from impetigo strains of Staphylococcus aureus.}, journal = {Virus genes}, volume = {51}, number = {1}, pages = {122-131}, pmid = {26135320}, issn = {1572-994X}, mesh = {Cluster Analysis ; Cross Infection/epidemiology ; Czech Republic/epidemiology ; DNA Viruses/*genetics/isolation &amp; purification ; DNA, Viral/*chemistry/*genetics ; Disease Outbreaks ; Exfoliatins/genetics ; Gene Order ; Gene Transfer, Horizontal ; *Genome, Viral ; Hospitals, Maternity ; Humans ; Impetigo/epidemiology/microbiology ; Infant, Newborn ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Prophages/classification/genetics/isolation &amp; purification ; Sequence Analysis, DNA ; Sequence Homology ; Staphylococcal Infections/epidemiology/microbiology ; Staphylococcus Phages/*classification/genetics/*isolation &amp; purification ; Staphylococcus aureus/isolation &amp; purification/*virology ; Synteny ; Transduction, Genetic ; }, abstract = {Exfoliative toxin A (ETA)-coding temperate bacteriophages are leading contributors to the toxic phenotype of impetigo strains of Staphylococcus aureus. Two distinct eta gene-positive bacteriophages isolated from S. aureus strains which recently caused massive outbreaks of pemphigus neonatorum in Czech maternity hospitals were characterized. The phages, designated ϕB166 and ϕB236, were able to transfer the eta gene into a prophageless S. aureus strain which afterwards converted into an ETA producer. Complete phage genome sequences were determined, and a comparative analysis of five designed genomic regions revealed major variances between them. They differed in the genome size, number of open reading frames, genome architecture, and virion protein patterns. Their high mutual sequence similarity was detected only in the terminal regions of the genome. When compared with the so far described eta phage genomes, noticeable differences were found. Thus, both phages represent two new lineages of as yet not characterized bacteriophages of the Siphoviridae family having impact on pathogenicity of impetigo strains of S. aureus.}, }
@article {pmid26135212, year = {2015}, author = {Ruhe, ZC and Townsley, L and Wallace, AB and King, A and Van der Woude, MW and Low, DA and Yildiz, FH and Hayes, CS}, title = {CdiA promotes receptor-independent intercellular adhesion.}, journal = {Molecular microbiology}, volume = {98}, number = {1}, pages = {175-192}, pmid = {26135212}, issn = {1365-2958}, support = {R01 AI114261/AI/NIAID NIH HHS/United States ; GM102318/GM/NIGMS NIH HHS/United States ; U01 GM102318/GM/NIGMS NIH HHS/United States ; AI114261/AI/NIAID NIH HHS/United States ; BB/F003692/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Bacterial Adhesion ; Bacterial Outer Membrane Proteins/genetics/*metabolism ; Biofilms/*growth &amp; development ; Contact Inhibition ; Escherichia coli/genetics/*physiology ; Escherichia coli Proteins/*genetics/*metabolism ; Gene Transfer, Horizontal ; Membrane Glycoproteins/metabolism ; Membrane Proteins/*genetics/*metabolism ; Mutation ; }, abstract = {CdiB/CdiA proteins mediate inter-bacterial competition in a process termed contact-dependent growth inhibition (CDI). Filamentous CdiA exoproteins extend from CDI(+) cells and bind specific receptors to deliver toxins into susceptible target bacteria. CDI has also been implicated in auto-aggregation and biofilm formation in several species, but the contribution of CdiA-receptor interactions to these multi-cellular behaviors has not been examined. Using Escherichia coli isolate EC93 as a model, we show that cdiA and bamA receptor mutants are defective in biofilm formation, suggesting a prominent role for CdiA-BamA mediated cell-cell adhesion. However, CdiA also promotes auto-aggregation in a BamA-independent manner, indicating that the exoprotein possesses an additional adhesin activity. Cells must express CdiA in order to participate in BamA-independent aggregates, suggesting that adhesion could be mediated by homotypic CdiA-CdiA interactions. The BamA-dependent and BamA-independent interaction domains map to distinct regions within the CdiA filament. Thus, CdiA orchestrates a collective behavior that is independent of its growth-inhibition activity. This adhesion should enable 'greenbeard' discrimination, in which genetically unrelated individuals cooperate with one another based on a single shared trait. This kind-selective social behavior could provide immediate fitness benefits to bacteria that acquire the systems through horizontal gene transfer.}, }
@article {pmid26132232, year = {2015}, author = {Waldron, LS and Gillings, MR}, title = {Screening Foodstuffs for Class 1 Integrons and Gene Cassettes.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {100}, pages = {e52889}, pmid = {26132232}, issn = {1940-087X}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; Food Microbiology/*methods ; Fruit/microbiology ; Humans ; *Integrons ; Mutagenesis, Insertional ; Polymerase Chain Reaction/methods ; Seafood/microbiology ; Vegetables/microbiology ; }, abstract = {Antibiotic resistance is one of the greatest threats to health in the 21st century. Acquisition of resistance genes via lateral gene transfer is a major factor in the spread of diverse resistance mechanisms. Amongst the DNA elements facilitating lateral transfer, the class 1 integrons have largely been responsible for spreading antibiotic resistance determinants amongst Gram negative pathogens. In total, these integrons have acquired and disseminated over 130 different antibiotic resistance genes. With continued antibiotic use, class 1 integrons have become ubiquitous in commensals and pathogens of humans and their domesticated animals. As a consequence, they can now be found in all human waste streams, where they continue to acquire new genes, and have the potential to cycle back into humans via the food chain. This protocol details a streamlined approach for detecting class 1 integrons and their associated resistance gene cassettes in foodstuffs, using culturing and PCR. Using this protocol, researchers should be able to: collect and prepare samples to make enriched cultures and screen for class 1 integrons; isolate single bacterial colonies to identify integron-positive isolates; identify bacterial species that contain class 1 integrons; and characterize these integrons and their associated gene cassettes.}, }
@article {pmid26131555, year = {2015}, author = {Huerlimann, R and Zenger, KR and Jerry, DR and Heimann, K}, title = {Phylogenetic Analysis of Nucleus-Encoded Acetyl-CoA Carboxylases Targeted at the Cytosol and Plastid of Algae.}, journal = {PloS one}, volume = {10}, number = {7}, pages = {e0131099}, pmid = {26131555}, issn = {1932-6203}, mesh = {Acetyl-CoA Carboxylase/*genetics/metabolism ; Base Sequence ; Cell Nucleus/metabolism ; Chlorophyta/enzymology/*genetics/metabolism ; Cytosol/metabolism ; Molecular Sequence Data ; *Phylogeny ; Plant Proteins/*genetics/metabolism ; Plastids/metabolism ; Protein Transport ; }, abstract = {The understanding of algal phylogeny is being impeded by an unknown number of events of horizontal gene transfer (HGT), and primary and secondary/tertiary endosymbiosis. Through these events, previously heterotrophic eukaryotes developed photosynthesis and acquired new biochemical pathways. Acetyl-CoA carboxylase (ACCase) is a key enzyme in the fatty acid synthesis and elongation pathways in algae, where ACCase exists in two locations (cytosol and plastid) and in two forms (homomeric and heteromeric). All algae contain nucleus-encoded homomeric ACCase in the cytosol, independent of the origin of the plastid. Nucleus-encoded homomeric ACCase is also found in plastids of algae that arose from a secondary/tertiary endosymbiotic event. In contrast, plastids of algae that arose from a primary endosymbiotic event contain heteromeric ACCase, which consists of three nucleus-encoded and one plastid-encoded subunits. These properties of ACCase provide the potential to inform on the phylogenetic relationships of hosts and their plastids, allowing different hypothesis of endosymbiotic events to be tested. Alveolata (Dinoflagellata and Apicomplexa) and Chromista (Stramenopiles, Haptophyta and Cryptophyta) have traditionally been grouped together as Chromalveolata, forming the red lineage. However, recent genetic evidence groups the Stramenopiles, Alveolata and green plastid containing Rhizaria as SAR, excluding Haptophyta and Cryptophyta. Sequences coding for plastid and cytosol targeted homomeric ACCases were isolated from Isochrysis aff. galbana (TISO), Chromera velia and Nannochloropsis oculata, representing three taxonomic groups for which sequences were lacking. Phylogenetic analyses show that cytosolic ACCase strongly supports the SAR grouping. Conversely, plastidial ACCase groups the SAR with the Haptophyta, Cryptophyta and Prasinophyceae (Chlorophyta). These two ACCase based, phylogenetic relationships suggest that the plastidial homomeric ACCase was acquired by the Haptophyta, Cryptophyta and SAR, before the photosynthetic Rhizaria acquired their green plastid. Additionally, plastidial ACCase was derived by HGT from an ancestor or relative of the Prasinophyceae and not by duplication of cytosolic ACCase.}, }
@article {pmid26130822, year = {2015}, author = {Parker, MA and Jankowiak, JG and Landrigan, GK}, title = {Diversifying selection by Desmodiinae legume species on Bradyrhizobium symbionts.}, journal = {FEMS microbiology ecology}, volume = {91}, number = {7}, pages = {}, doi = {10.1093/femsec/fiv075}, pmid = {26130822}, issn = {1574-6941}, mesh = {Bradyrhizobium/*classification ; Fabaceae/*microbiology ; Gene Transfer, Horizontal ; Genomic Islands/genetics ; Molecular Sequence Data ; Phylogeny ; Root Nodules, Plant/*microbiology ; Sequence Analysis, DNA ; Symbiosis/*genetics ; }, abstract = {Desmodium and Hylodesmum (Papilionoideae Subtribe Desmodiinae) are among the most common herbaceous perennial legumes native to eastern North America. To analyze the population structure of their Bradyrhizobium sp. root-nodule bacteria, 159 isolates were sampled from ten host species across a 1000 km region. Phylogenetic analysis of four housekeeping loci (2164 bp) and two loci in the symbiosis island (SI) chromosomal region (1374 bp) indicated extensive overlap in symbiont utilization, with each common bacterial clade found on 2-7 species of these legume genera. However, host species differed considerably in the relative proportion of symbionts belonging to different Bradyrhizobium clades. High phylogenetic incongruence between trees for housekeeping loci and SI loci suggested that diversification of these Bradyrhizobium lineages involved substantial horizontal gene transfer. Plant inoculation with strains from six Bradyrhizobium clades revealed marked disparity in relative bacterial reproductive success across four Desmodium species. Estimated yield of Bradyrhizobium progeny cells per plant ranged from zero to >10(9), and strains with high fitness on one host sometimes reproduced poorly on other host species. Diversifying selection on bacteria, arising from differential success in habitats with different Desmodium and Hylodesmum taxa, is therefore likely to affect Bradyrhizobium diversity patterns at the landscape level.}, }
@article {pmid26126852, year = {2015}, author = {Attaiech, L and Minnen, A and Kjos, M and Gruber, S and Veening, JW}, title = {The ParB-parS Chromosome Segregation System Modulates Competence Development in Streptococcus pneumoniae.}, journal = {mBio}, volume = {6}, number = {4}, pages = {e00662}, pmid = {26126852}, issn = {2150-7511}, support = {260853/ERC_/European Research Council/International ; 337399/ERC_/European Research Council/International ; }, mesh = {Bacterial Proteins/genetics/*metabolism ; Binding Sites ; Chromatin Immunoprecipitation ; *Chromosome Segregation ; *DNA Transformation Competence ; Gene Order ; Models, Biological ; Operon ; Protein Binding ; Repressor Proteins/*metabolism ; Streptococcus pneumoniae/*genetics/*physiology ; }, abstract = {UNLABELLED: ParB proteins bind centromere-like DNA sequences called parS sites and are involved in plasmid and chromosome segregation in bacteria. We previously showed that the opportunistic human pathogen Streptococcus pneumoniae contains four parS sequences located close to the origin of replication which are bound by ParB. Using chromatin immunoprecipitation (ChIP), we found here that ParB spreads out from one of these parS sites, parS(-1.6°), for more than 5 kb and occupies the nearby comCDE operon, which drives competence development. Competence allows S. pneumoniae to take up DNA from its environment, thereby mediating horizontal gene transfer, and is also employed as a general stress response. Mutating parS(-1.6°) or deleting parB resulted in transcriptional up-regulation of comCDE and ssbB (a gene belonging to the competence regulon), demonstrating that ParB acts as a repressor of competence. However, genome-wide transcription analysis showed that ParB is not a global transcriptional regulator. Different factors, such as the composition of the growth medium and antibiotic-induced stress, can trigger the sensitive switch driving competence. This work shows that the ParB-parS chromosome segregation machinery also influences this developmental process.<br><br>IMPORTANCE: Streptococcus pneumoniae (pneumococcus) is an important human pathogen responsible for more than a million deaths each year. Like all other organisms, S. pneumoniae must be able to segregate its chromosomes properly. Not only is understanding the molecular mechanisms underlying chromosome segregation in S. pneumoniae therefore of fundamental importance, but also, this knowledge might offer new leads for ways to target this pathogen. Here, we identified a link between the pneumococcal chromosome segregation system and the competence-developmental system. Competence allows S. pneumoniae to take up and integrate exogenous DNA in its chromosome. This process plays a crucial role in successful adaptation to--and escape from--host defenses, antibiotic treatments, and vaccination strategies. We show that the chromosome segregation protein ParB acts as a repressor of competence. To the best of our knowledge, this is the first example of a ParB protein controlling bacterial competence.}, }
@article {pmid26124240, year = {2015}, author = {de la Mora, J and Uchida, K and del Campo, AM and Camarena, L and Aizawa, S and Dreyfus, G}, title = {Structural Characterization of the Fla2 Flagellum of Rhodobacter sphaeroides.}, journal = {Journal of bacteriology}, volume = {197}, number = {17}, pages = {2859-2866}, pmid = {26124240}, issn = {1098-5530}, mesh = {Bacterial Proteins/genetics/*metabolism ; Flagella/*ultrastructure ; Flagellin/*genetics/metabolism ; Gene Expression Regulation, Bacterial/*physiology ; Polymorphism, Genetic ; Rhodobacter sphaeroides/genetics/metabolism/*ultrastructure ; }, abstract = {UNLABELLED: Rhodobacter sphaeroides is a free-living alphaproteobacterium that contains two clusters of functional flagellar genes in its genome: one acquired by horizontal gene transfer (fla1) and one that is endogenous (fla2). We have shown that the Fla2 system is normally quiescent and under certain conditions produces polar flagella, while the Fla1 system is always active and produces a single flagellum at a nonpolar position. In this work we purified and characterized the structure and analyzed the composition of the Fla2 flagellum. The number of polar filaments per cell is 4.6 on average. By comparison with the Fla1 flagellum, the prominent features of the ultra structure of the Fla2 HBB are the absence of an H ring, thick and long hooks, and a smoother zone at the hook-filament junction. The Fla2 helical filaments have a pitch of 2.64 μm and a diameter of 1.4 μm, which are smaller than those of the Fla1 filaments. Fla2 filaments undergo polymorphic transitions in vitro and showed two polymorphs: curly (right-handed) and coiled. However, in vivo in free-swimming cells, we observed only a bundle of filaments, which should probably be left-handed. Together, our results indicate that Fla2 cell produces multiple right-handed polar flagella, which are not conventional but exceptional.<br><br>IMPORTANCE: R. sphaeroides possesses two functional sets of flagellar genes. The fla1 genes are normally expressed in the laboratory and were acquired by horizontal transfer. The fla2 genes are endogenous and are expressed in a Fla1(-) mutant grown phototrophically and in the absence of organic acids. The Fla1 system produces a single lateral or subpolar flagellum, and the Fla2 system produces multiple polar flagella. The two kinds of flagella are never expressed simultaneously, and both are used for swimming in liquid media. The two sets of genes are certainly ready for responding to specific environmental conditions. The characterization of the Fla2 system will help us to understand its role in the physiology of this microorganism.}, }
@article {pmid26124213, year = {2015}, author = {Flach, CF and Johnning, A and Nilsson, I and Smalla, K and Kristiansson, E and Larsson, DG}, title = {Isolation of novel IncA/C and IncN fluoroquinolone resistance plasmids from an antibiotic-polluted lake.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {70}, number = {10}, pages = {2709-2717}, doi = {10.1093/jac/dkv167}, pmid = {26124213}, issn = {1460-2091}, mesh = {Bacteria/drug effects/genetics ; Bacterial Proteins/*genetics ; Conjugation, Genetic ; *Drug Resistance, Bacterial ; Drug Resistance, Multiple, Bacterial ; Escherichia coli/drug effects/genetics ; Fluoroquinolones/*pharmacology ; Gene Order ; Gene Transfer, Horizontal ; Genetic Variation ; Geologic Sediments/microbiology ; Humans ; Lakes/*microbiology ; Microbial Sensitivity Tests ; Phosphoproteins/*genetics ; Plasmids/*genetics ; Water Pollution, Chemical ; }, abstract = {OBJECTIVES: Antibiotic-polluted environments may function as reservoirs for novel resistance plasmids not yet encountered in pathogens. The aims of this study were to assess the potential of resistance transfer between bacteria from such environments and Escherichia coli, and to characterize the conjugative elements involved.<br><br>METHODS: Sediment samples from Kazipally lake and Asanikunta tank, two Indian lakes with a history of severe pollution with fluoroquinolones, were investigated. Proportions of resistant bacteria were determined by selective cultivation, while horizontal gene transfer was studied using a GFP-tagged E. coli as recipient. Retrieved transconjugants were tested for susceptibility by Etest(&#xae;) and captured conjugative resistance elements were characterized by WGS.<br><br>RESULTS: The polluted lakes harboured considerably higher proportions of ciprofloxacin-resistant and sulfamethoxazole-resistant bacteria than did other Indian and Swedish lakes included for comparison (52% versus 2% and 60% versus 7%, respectively). Resistance plasmids were captured from Kazipally lake, but not from any of the other lakes; in the case of Asanikunta tank because of high sediment toxicity. Eight unique IncA/C and IncN resistance plasmids were identified among 11 sequenced transconjugants. Five plasmids were fully assembled, and four of these carried the quinolone resistance gene qnrVC1, which has previously only been found on chromosomes. Acquired resistance genes, in the majority of cases associated with class 1 integrons, could be linked to decreased susceptibility to several different classes of antibiotics.<br><br>CONCLUSIONS: Our study shows that environments heavily polluted with antibiotics contain novel multiresistance plasmids transferrable to E. coli.}, }
@article {pmid26123917, year = {2015}, author = {Gallus, S and Kumar, V and Bertelsen, MF and Janke, A and Nilsson, MA}, title = {A genome survey sequencing of the Java mouse deer (Tragulus javanicus) adds new aspects to the evolution of lineage specific retrotransposons in Ruminantia (Cetartiodactyla).}, journal = {Gene}, volume = {571}, number = {2}, pages = {271-278}, doi = {10.1016/j.gene.2015.06.064}, pmid = {26123917}, issn = {1879-0038}, mesh = {Animals ; Chromosome Mapping ; *Evolution, Molecular ; *Genome ; Genome, Mitochondrial ; Long Interspersed Nucleotide Elements ; Phylogeny ; Retroelements/*genetics ; Ruminants/*classification/*genetics ; *Sequence Analysis, DNA/veterinary ; Short Interspersed Nucleotide Elements ; Species Specificity ; }, abstract = {Ruminantia, the ruminating, hoofed mammals (cow, deer, giraffe and allies) are an unranked artiodactylan clade. Around 50-60 million years ago the BovB retrotransposon entered the ancestral ruminantian genome through horizontal gene transfer. A survey genome screen using 454-pyrosequencing of the Java mouse deer (Tragulus javanicus) and the lesser kudu (Tragelaphus imberbis) was done to investigate and to compare the landscape of transposable elements within Ruminantia. The family Tragulidae (mouse deer) is the only representative of Tragulina and phylogenetically important, because it represents the earliest divergence in Ruminantia. The data analyses show that, relative to other ruminantian species, the lesser kudu genome has seen an expansion of BovB Long INterspersed Elements (LINEs) and BovB related Short INterspersed Elements (SINEs) like BOVA2. In comparison the genome of Java mouse deer has fewer BovB elements than other ruminants, especially Bovinae, and has in addition a novel CHR-3 SINE most likely propagated by LINE-1. By contrast the other ruminants have low amounts of CHR SINEs but high numbers of actively propagating BovB-derived and BovB-propagated SINEs. The survey sequencing data suggest that the transposable element landscape in mouse deer (Tragulina) is unique among Ruminantia, suggesting a lineage specific evolutionary trajectory that does not involve BovB mediated retrotransposition. This shows that the genomic landscape of mobile genetic elements can rapidly change in any lineage.}, }
@article {pmid26120784, year = {2015}, author = {Wang, Q and Mao, D and Luo, Y}, title = {Ionic Liquid Facilitates the Conjugative Transfer of Antibiotic Resistance Genes Mediated by Plasmid RP4.}, journal = {Environmental science &amp; technology}, volume = {49}, number = {14}, pages = {8731-8740}, doi = {10.1021/acs.est.5b01129}, pmid = {26120784}, issn = {1520-5851}, mesh = {Anti-Bacterial Agents/pharmacology ; Cell Membrane Permeability/drug effects ; Conjugation, Genetic/drug effects ; Drug Resistance, Microbial/*genetics ; Electrophoresis, Polyacrylamide Gel ; Escherichia coli/drug effects/genetics ; Fimbriae Proteins/metabolism ; Gene Expression Regulation, Bacterial/drug effects ; Gene Transfer, Horizontal/*drug effects ; Genes, Bacterial ; Imidazoles/pharmacology ; Ionic Liquids/*pharmacology ; Plasmids/*metabolism ; Porins/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Salmonella enterica/drug effects/genetics ; }, abstract = {The dissemination and propagation of antibiotic resistance genes (ARGs) is an emerging global health concern. In our previous study, the ionic liquid (IL) 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIm][PF6]) had been proven to facilitate the dissemination of ARGs via horizontal gene transfer. In this study, we further confirm that this compound facilitates the horizontal transfer of plasmid RP4 through a conjugation mechanism and not by natural transformation. The mechanisms for [BMIm][PF6] promoting conjugative transfer are attributable to enhancing the mRNA expression levels of conjugative and global regulatory genes, as well as by inhibiting the genes that are responsible for the vertical transfer of cell growth. [BMIm][PF6] significantly enhanced the expression of the outer membrane porin proteins (OMPs) OmpC and OmpA and the corresponding mRNA expression levels of ompC and ompA genes in recipient bacteria, which contributed to pore formation and increased cell membrane permeability. The increased expression of pilin and pili allowed the donor pilus to attach to and access the recipient cells, thereby assisting cell-to-cell contact to facilitate the conjugative transfer of plasmid RP4. To the best of our knowledge, this is the first insightful exploration of [BMIm][PF6] facilitating the conjugative transfer of ARGs mediated by plasmid RP4 and of several other ILs with different cations or anions that are capable of promoting plasmid transfer. It is therefore suggested that the application of some ILs in industrial processes should be carefully evaluated before their bulk emission into the environment.}, }
@article {pmid26117543, year = {2015}, author = {Betat, H and Mede, T and Tretbar, S and Steiner, L and Stadler, PF and Mörl, M and Prohaska, SJ}, title = {The ancestor of modern Holozoa acquired the CCA-adding enzyme from Alphaproteobacteria by horizontal gene transfer.}, journal = {Nucleic acids research}, volume = {43}, number = {14}, pages = {6739-6746}, pmid = {26117543}, issn = {1362-4962}, mesh = {Alphaproteobacteria/classification/*genetics ; Animals ; Choanoflagellata/genetics ; Eukaryota/classification/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Phylogeny ; RNA Nucleotidyltransferases/*genetics ; }, abstract = {Transfer RNAs (tRNAs) require the absolutely conserved sequence motif CCA at their 3'-ends, representing the site of aminoacylation. In the majority of organisms, this trinucleotide sequence is not encoded in the genome and thus has to be added post-transcriptionally by the CCA-adding enzyme, a specialized nucleotidyltransferase. In eukaryotic genomes this ubiquitous and highly conserved enzyme family is usually represented by a single gene copy. Analysis of published sequence data allows us to pin down the unusual evolution of eukaryotic CCA-adding enzymes. We show that the CCA-adding enzymes of animals originated from a horizontal gene transfer event in the stem lineage of Holozoa, i.e. Metazoa (animals) and their unicellular relatives, the Choanozoa. The tRNA nucleotidyltransferase, acquired from an α-proteobacterium, replaced the ancestral enzyme in Metazoa. However, in Choanoflagellata, the group of Choanozoa that is closest to Metazoa, both the ancestral and the horizontally transferred CCA-adding enzymes have survived. Furthermore, our data refute a mitochondrial origin of the animal tRNA nucleotidyltransferases.}, }
@article {pmid26114501, year = {2015}, author = {Zeytuni, N and Cronin, S and Lefèvre, CT and Arnoux, P and Baran, D and Shtein, Z and Davidov, G and Zarivach, R}, title = {MamA as a Model Protein for Structure-Based Insight into the Evolutionary Origins of Magnetotactic Bacteria.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0130394}, pmid = {26114501}, issn = {1932-6203}, mesh = {Bacterial Proteins/*chemistry/genetics ; Crystallography, X-Ray ; Desulfovibrio/*chemistry/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Phylogeny ; Protein Structure, Tertiary ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {MamA is a highly conserved protein found in magnetotactic bacteria (MTB), a diverse group of prokaryotes capable of navigating according to magnetic fields - an ability known as magnetotaxis. Questions surround the acquisition of this magnetic navigation ability; namely, whether it arose through horizontal or vertical gene transfer. Though its exact function is unknown, MamA surrounds the magnetosome, the magnetic organelle embedding a biomineralised nanoparticle and responsible for magnetotaxis. Several structures for MamA from a variety of species have been determined and show a high degree of structural similarity. By determining the structure of MamA from Desulfovibrio magneticus RS-1 using X-ray crystallography, we have opened up the structure-sequence landscape. As such, this allows us to perform structural- and phylogenetic-based analyses using a variety of previously determined MamA from a diverse range of MTB species across various phylogenetic groups. We found that MamA has remained remarkably constant throughout evolution with minimal change between different taxa despite sequence variations. These findings, coupled with the generation of phylogenetic trees using both amino acid sequences and 16S rRNA, indicate that magnetotaxis likely did not spread via horizontal gene transfer and instead has a significantly earlier, primordial origin.}, }
@article {pmid26108467, year = {2015}, author = {Morel, G and Sterck, L and Swennen, D and Marcet-Houben, M and Onesime, D and Levasseur, A and Jacques, N and Mallet, S and Couloux, A and Labadie, K and Amselem, J and Beckerich, JM and Henrissat, B and Van de Peer, Y and Wincker, P and Souciet, JL and Gabaldón, T and Tinsley, CR and Casaregola, S}, title = {Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {11571}, pmid = {26108467}, issn = {2045-2322}, mesh = {Adaptation, Physiological/*genetics ; Biodiversity ; DNA, Fungal/chemistry/genetics ; *Evolution, Molecular ; Fungal Proteins/genetics ; Gene Transfer, Horizontal ; Genes, Fungal/*genetics ; *Genetic Variation ; Genome, Fungal/genetics ; Genome, Mitochondrial/genetics ; Geotrichum/*genetics/growth &amp; development ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Yeasts/classification/*genetics/growth &amp; development ; }, abstract = {The evolutionary history of the characters underlying the adaptation of microorganisms to food and biotechnological uses is poorly understood. We undertook comparative genomics to investigate evolutionary relationships of the dairy yeast Geotrichum candidum within Saccharomycotina. Surprisingly, a remarkable proportion of genes showed discordant phylogenies, clustering with the filamentous fungus subphylum (Pezizomycotina), rather than the yeast subphylum (Saccharomycotina), of the Ascomycota. These genes appear not to be the result of Horizontal Gene Transfer (HGT), but to have been specifically retained by G. candidum after the filamentous fungi-yeasts split concomitant with the yeasts' genome contraction. We refer to these genes as SRAGs (Specifically Retained Ancestral Genes), having been lost by all or nearly all other yeasts, and thus contributing to the phenotypic specificity of lineages. SRAG functions include lipases consistent with a role in cheese making and novel endoglucanases associated with degradation of plant material. Similar gene retention was observed in three other distantly related yeasts representative of this ecologically diverse subphylum. The phenomenon thus appears to be widespread in the Saccharomycotina and argues that, alongside neo-functionalization following gene duplication and HGT, specific gene retention must be recognized as an important mechanism for generation of biodiversity and adaptation in yeasts.}, }
@article {pmid26104702, year = {2015}, author = {Lanza, VF and Tedim, AP and Martínez, JL and Baquero, F and Coque, TM}, title = {The Plasmidome of Firmicutes: Impact on the Emergence and the Spread of Resistance to Antimicrobials.}, journal = {Microbiology spectrum}, volume = {3}, number = {2}, pages = {PLAS-0039-2014}, doi = {10.1128/microbiolspec.PLAS-0039-2014}, pmid = {26104702}, issn = {2165-0497}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; *Drug Resistance, Bacterial ; Firmicutes/*drug effects/*genetics ; *Gene Transfer, Horizontal ; Global Health ; Gram-Positive Bacterial Infections/epidemiology/*microbiology ; Humans ; Plasmids/*isolation &amp; purification ; }, abstract = {The phylum Firmicutes is one of the most abundant groups of prokaryotes in the microbiota of humans and animals and includes genera of outstanding relevance in biomedicine, health care, and industry. Antimicrobial drug resistance is now considered a global health security challenge of the 21st century, and this heterogeneous group of microorganisms represents a significant part of this public health issue.The presence of the same resistant genes in unrelated bacterial genera indicates a complex history of genetic interactions. Plasmids have largely contributed to the spread of resistance genes among Staphylococcus, Enterococcus, and Streptococcus species, also influencing the selection and ecological variation of specific populations. However, this information is fragmented and often omits species outside these genera. To date, the antimicrobial resistance problem has been analyzed under a "single centric" perspective ("gene tracking" or "vehicle centric" in "single host-single pathogen" systems) that has greatly delayed the understanding of gene and plasmid dynamics and their role in the evolution of bacterial communities.This work analyzes the dynamics of antimicrobial resistance genes using gene exchange networks; the role of plasmids in the emergence, dissemination, and maintenance of genes encoding resistance to antimicrobials (antibiotics, heavy metals, and biocides); and their influence on the genomic diversity of the main Gram-positive opportunistic pathogens under the light of evolutionary ecology. A revision of the approaches to categorize plasmids in this group of microorganisms is given using the 1,326 fully sequenced plasmids of Gram-positive bacteria available in the GenBank database at the time the article was written.}, }
@article {pmid26104695, year = {2015}, author = {Escudero, JA and Loot, C and Nivina, A and Mazel, D}, title = {The Integron: Adaptation On Demand.}, journal = {Microbiology spectrum}, volume = {3}, number = {2}, pages = {MDNA3-0019-2014}, doi = {10.1128/microbiolspec.MDNA3-0019-2014}, pmid = {26104695}, issn = {2165-0497}, mesh = {*Adaptation, Biological ; Attachment Sites, Microbiological ; Gene Rearrangement ; Gene Transfer, Horizontal ; Gram-Negative Bacteria/*genetics ; *Integrons ; Interspersed Repetitive Sequences ; Recombination, Genetic ; }, abstract = {The integron is a powerful system which, by capturing, stockpiling, and rearranging new functions carried by gene encoding cassettes, confers upon bacteria a rapid adaptation capability in changing environments. Chromosomally located integrons (CI) have been identified in a large number of environmental Gram-negative bacteria. Integron evolutionary history suggests that these sedentary CIs acquired mobility among bacterial species through their association with transposable elements and conjugative plasmids. As a result of massive antibiotic use, these so-called mobile integrons are now widespread in clinically relevant bacteria and are considered to be the principal agent in the emergence and rise of antibiotic multiresistance in Gram-negative bacteria. Cassette rearrangements are catalyzed by the integron integrase, a site-specific tyrosine recombinase. Central to these reactions is the single-stranded DNA nature of one of the recombination partners, the attC site. This makes the integron a unique recombination system. This review describes the current knowledge on this atypical recombination mechanism, its implications in the reactions involving the different types of sites, attC and attI, and focuses on the tight regulation exerted by the host on integron activity through the control of attC site folding. Furthermore, cassette and integrase expression are also highly controlled by host regulatory networks and the bacterial stress (SOS) response. These intimate connections to the host make the integron a genetically stable and efficient system, granting the bacteria a low cost, highly adaptive evolution potential "on demand".}, }
@article {pmid26104560, year = {2015}, author = {Smalla, K and Jechalke, S and Top, EM}, title = {Plasmid Detection, Characterization, and Ecology.}, journal = {Microbiology spectrum}, volume = {3}, number = {1}, pages = {PLAS-0038-2014}, pmid = {26104560}, issn = {2165-0497}, support = {R01 AI084918/AI/NIAID NIH HHS/United States ; }, mesh = {Adaptation, Biological ; Bacteria/*genetics ; Ecology ; Environmental Microbiology ; Gene Transfer, Horizontal ; Genetic Variation ; Host Specificity ; Plasmids/*analysis/*biosynthesis/classification ; }, abstract = {Plasmids are important vehicles for rapid adaptation of bacterial populations to changing environmental conditions. It is thought that to reduce the cost of plasmid carriage, only a fraction of a local population carries plasmids or is permissive to plasmid uptake. Plasmids provide various accessory traits which might be beneficial under particular conditions. The genetic variation generated by plasmid carriage within populations ensures the robustness toward environmental changes. Plasmid-mediated gene transfer plays an important role not only in the mobilization and dissemination of antibiotic resistance genes but also in the spread of degradative pathways and pathogenicity determinants of pathogens. Here we summarize the state-of-the-art methods to study the occurrence, abundance, and diversity of plasmids in environmental bacteria. Increasingly, cultivation-independent total-community DNA-based methods are being used to characterize and quantify the diversity and abundance of plasmids in relation to various biotic and abiotic factors. An improved understanding of the ecology of plasmids and their hosts is crucial in the development of intervention strategies for antibiotic-resistance-gene spread. We discuss the potentials and limitations of methods used to determine the host range of plasmids, as the ecology of plasmids is tightly linked to their hosts. The recent advances in sequencing technologies provide an enormous potential for plasmid classification, diversity, and evolution studies, but numerous challenges still exist.}, }
@article {pmid26104549, year = {2015}, author = {Samson, JE and Magadan, AH and Moineau, S}, title = {The CRISPR-Cas Immune System and Genetic Transfers: Reaching an Equilibrium.}, journal = {Microbiology spectrum}, volume = {3}, number = {1}, pages = {PLAS-0034-2014}, doi = {10.1128/microbiolspec.PLAS-0034-2014}, pmid = {26104549}, issn = {2165-0497}, mesh = {Bacteria/*genetics ; *CRISPR-Cas Systems ; Conjugation, Genetic ; DNA/genetics/metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal ; Interspersed Repetitive Sequences ; Transformation, Genetic ; }, abstract = {Horizontal gene transfer drives the evolution of bacterial genomes, including the adaptation to changing environmental conditions. Exogenous DNA can enter a bacterial cell through transformation (free DNA or plasmids) or through the transfer of mobile genetic elements by conjugation (plasmids) and transduction (bacteriophages). Favorable genes can be acquired, but undesirable traits can also be inadvertently acquired through these processes. Bacteria have systems, such as clustered regularly interspaced short palindromic repeat CRISPR-associated genes (CRISPR-Cas), that can cleave foreign nucleic acid molecules. In this review, we discuss recent advances in understanding CRISPR-Cas system activity against mobile genetic element transfer through transformation and conjugation. We also highlight how CRISPR-Cas systems influence bacterial evolution and how CRISPR-Cas components affect plasmid replication.}, }
@article {pmid26104453, year = {2014}, author = {Schwarz, S and Shen, J and Wendlandt, S and Feßler, AT and Wang, Y and Kadlec, K and Wu, CM}, title = {Plasmid-Mediated Antimicrobial Resistance in Staphylococci and Other Firmicutes.}, journal = {Microbiology spectrum}, volume = {2}, number = {6}, pages = {}, doi = {10.1128/microbiolspec.PLAS-0020-2014}, pmid = {26104453}, issn = {2165-0497}, mesh = {Anti-Bacterial Agents/*pharmacology ; *Drug Resistance, Bacterial ; Firmicutes/*drug effects/*genetics ; Gene Transfer, Horizontal ; Genetic Variation ; Humans ; *Plasmids ; }, abstract = {In staphylococci and other Firmicutes, resistance to numerous classes of antimicrobial agents, which are commonly used in human and veterinary medicine, is mediated by genes that are associated with mobile genetic elements. The gene products of some of these antimicrobial resistance genes confer resistance to only specific members of a certain class of antimicrobial agents, whereas others confer resistance to the entire class or even to members of different classes of antimicrobial agents. The resistance mechanisms specified by the resistance genes fall into any of three major categories: active efflux, enzymatic inactivation, and modification/replacement/protection of the target sites of the antimicrobial agents. Among the mobile genetic elements that carry such resistance genes, plasmids play an important role as carriers of primarily plasmid-borne resistance genes, but also as vectors for nonconjugative and conjugative transposons that harbor resistance genes. Plasmids can be exchanged by horizontal gene transfer between members of the same species but also between bacteria belonging to different species and genera. Plasmids are highly flexible elements, and various mechanisms exist by which plasmids can recombine, form cointegrates, or become integrated in part or in toto into the chromosomal DNA or into other plasmids. As such, plasmids play a key role in the dissemination of antimicrobial resistance genes within the gene pool to which staphylococci and other Firmicutes have access. This chapter is intended to provide an overview of the current knowledge of plasmid-mediated antimicrobial resistance in staphylococci and other Firmicutes.}, }
@article {pmid26104437, year = {2014}, author = {Carraro, N and Burrus, V}, title = {Biology of Three ICE Families: SXT/R391, ICEBs1, and ICESt1/ICESt3.}, journal = {Microbiology spectrum}, volume = {2}, number = {6}, pages = {}, doi = {10.1128/microbiolspec.MDNA3-0008-2014}, pmid = {26104437}, issn = {2165-0497}, mesh = {Bacteria/*genetics ; Drug Resistance, Bacterial ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genetic Variation ; *Interspersed Repetitive Sequences ; *Recombination, Genetic ; }, abstract = {Integrative and Conjugative Elements (ICEs) are bacterial mobile genetic elements that play a key role in bacterial genomes dynamics and evolution. ICEs are widely distributed among virtually all bacterial genera. Recent extensive studies have unraveled their high diversity and complexity. The present review depicts the general conserved features of ICEs and describes more precisely three major families of ICEs that have been extensively studied in the past decade for their biology, their evolution and their impact on genomes dynamics. First, the large SXT/R391 family of ICEs disseminates antibiotic resistance genes and drives the exchange of mobilizable genomic islands (MGIs) between many enteric pathogens such as Vibrio cholerae. Second, ICEBs1 of Bacillus subtilis is the most well understood ICE of Gram-positive bacteria, notably regarding the regulation of its dissemination and its initially unforeseen extrachromosomal replication, which could be a common feature of ICEs of both Gram-positive and Gram-negative bacteria. Finally, ICESt1 and ICESt3 of Streptococcus thermophilus are the prototypes of a large family of ICEs widely distributed among various streptococci. These ICEs carry an original regulation module that associates regulators related to those of both SXT/R391 and ICEBs1. Study of ICESt1 and ICESt3 uncovered the cis-mobilization of related genomic islands (CIMEs) by a mechanism called accretion-mobilization, which likely represents a paradigm for the evolution of many ICEs and genomic islands. These three major families of ICEs give a glimpse about ICEs dynamics and their high impact on bacterial adaptation.}, }
@article {pmid26104375, year = {2014}, author = {Fernández-López, C and Bravo, A and Ruiz-Cruz, S and Solano-Collado, V and Garsin, DA and Lorenzo-Díaz, F and Espinosa, M}, title = {Mobilizable Rolling-Circle Replicating Plasmids from Gram-Positive Bacteria: A Low-Cost Conjugative Transfer.}, journal = {Microbiology spectrum}, volume = {2}, number = {5}, pages = {}, doi = {10.1128/microbiolspec.PLAS-0008-2013}, pmid = {26104375}, issn = {2165-0497}, support = {R01AI076406/AI/NIAID NIH HHS/United States ; R56AI093699/AI/NIAID NIH HHS/United States ; }, mesh = {*Conjugation, Genetic ; *DNA Replication ; DNA, Bacterial/*metabolism ; *Gene Transfer, Horizontal ; Gram-Positive Bacteria/*genetics/*metabolism ; Models, Biological ; Plasmids/*metabolism ; Transfer, Psychology ; }, abstract = {Conjugation is a key mechanism for horizontal gene transfer in bacteria. Some plasmids are not self-transmissible but can be mobilized by functions encoded in trans provided by other auxiliary conjugative elements. Although the transfer efficiency of mobilizable plasmids is usually lower than that of conjugative elements, mobilizable plasmids are more frequently found in nature. In this sense, replication and mobilization can be considered important mechanisms influencing plasmid promiscuity. Here we review the currently available information on two families of small mobilizable plasmids from Gram-positive bacteria that replicate via the rolling-circle mechanism. One of these families, represented by the streptococcal plasmid pMV158, is an interesting model since it contains a specific mobilization module (MOBV) that is widely distributed among mobilizable plasmids. We discuss a mechanism in which the promiscuity of the pMV158 replicon is based on the presence of two origins of lagging strand synthesis. The current strategies to assess plasmid transfer efficiency as well as to inhibit conjugative plasmid transfer are presented. Some applications of these plasmids as biotechnological tools are also reviewed.}, }
@article {pmid26104371, year = {2014}, author = {Lagares, A and Sanjuán, J and Pistorio, M}, title = {The Plasmid Mobilome of the Model Plant-Symbiont Sinorhizobium meliloti: Coming up with New Questions and Answers.}, journal = {Microbiology spectrum}, volume = {2}, number = {5}, pages = {}, doi = {10.1128/microbiolspec.PLAS-0005-2013}, pmid = {26104371}, issn = {2165-0497}, mesh = {Conjugation, Genetic ; DNA Replication ; Gene Transfer, Horizontal ; Genetic Variation ; Medicago/microbiology ; Melilotus/microbiology ; *Plasmids ; Sinorhizobium meliloti/*genetics/physiology ; Symbiosis ; Trigonella/microbiology ; }, abstract = {Rhizobia are Gram-negative Alpha- and Betaproteobacteria living in the underground which have the ability to associate with legumes for the establishment of nitrogen-fixing symbioses. Sinorhizobium meliloti in particular-the symbiont of Medicago, Melilotus, and Trigonella spp.-has for the past decades served as a model organism for investigating, at the molecular level, the biology, biochemistry, and genetics of a free-living and symbiotic soil bacterium of agricultural relevance. To date, the genomes of seven different S. meliloti strains have been fully sequenced and annotated, and several other draft genomic sequences are also available. The vast amount of plasmid DNA that S. meliloti frequently bears (up to 45% of its total genome), the conjugative ability of some of those plasmids, and the extent of the plasmid diversity has provided researchers with an extraordinary system to investigate functional and structural plasmid molecular biology within the evolutionary context surrounding a plant-associated model bacterium. Current evidence indicates that the plasmid mobilome in S. meliloti is composed of replicons varying greatly in size and having diverse conjugative systems and properties along with different evolutionary stabilities and biological roles. While plasmids carrying symbiotic functions (pSyms) are known to have high structural stability (approaching that of chromosomes), the remaining plasmid mobilome (referred to as the non-pSym, functionally cryptic, or accessory compartment) has been shown to possess remarkable diversity and to be highly active in conjugation. In light of the modern genomic and current biochemical data on the plasmids of S. meliloti, the current article revises their main structural components, their transfer and regulatory mechanisms, and their potential as vehicles in shaping the evolution of the rhizobial genome.}, }
@article {pmid26104369, year = {2014}, author = {Kado, CI}, title = {Historical Events That Spawned the Field of Plasmid Biology.}, journal = {Microbiology spectrum}, volume = {2}, number = {5}, pages = {}, doi = {10.1128/microbiolspec.PLAS-0019-2013}, pmid = {26104369}, issn = {2165-0497}, mesh = {Adaptation, Biological ; Biology/*history ; Evolution, Molecular ; *Extrachromosomal Inheritance ; Gene Transfer, Horizontal ; Genetics, Microbial/*history ; History, 20th Century ; History, 21st Century ; Molecular Biology/*history ; *Plasmids ; Selection, Genetic ; }, abstract = {This chapter revisits the historical development and outcome of studies focused on the transmissible, extrachromosomal genetic elements called plasmids. Early work on plasmids involved structural and genetic mapping of these molecules, followed by the development of an understanding of how plasmids replicate and segregate during cell division. The intriguing property of plasmid transmission between bacteria and between bacteria and higher cells has received considerable attention. The utilitarian aspects of plasmids are described, including examples of various plasmid vector systems. This chapter also discusses the functional attributes of plasmids needed for their persistence and survival in nature and in man-made environments. The term plasmid biology was first conceived at the Fallen Leaf Lake Conference on Promiscuous Plasmids, 1990, Lake Tahoe, California. The International Society for Plasmid Biology was established in 2004 (www.ISPB.org).}, }
@article {pmid26104358, year = {2014}, author = {Ramirez, MS and Traglia, GM and Lin, DL and Tran, T and Tolmasky, ME}, title = {Plasmid-Mediated Antibiotic Resistance and Virulence in Gram-Negatives: the Klebsiella pneumoniae Paradigm.}, journal = {Microbiology spectrum}, volume = {2}, number = {5}, pages = {}, doi = {10.1128/microbiolspec.PLAS-0016-2013}, pmid = {26104358}, issn = {2165-0497}, support = {2R15AI047115/AI/NIAID NIH HHS/United States ; }, mesh = {Adaptation, Biological ; Community-Acquired Infections/epidemiology/microbiology ; Cross Infection/epidemiology/microbiology ; *Drug Resistance, Multiple, Bacterial ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Klebsiella pneumoniae/*drug effects/genetics/*pathogenicity ; *Plasmids ; Virulence ; Virulence Factors/*genetics ; }, abstract = {Plasmids harbor genes coding for specific functions including virulence factors and antibiotic resistance that permit bacteria to survive the hostile environment found in the host and resist treatment. Together with other genetic elements such as integrons and transposons, and using a variety of mechanisms, plasmids participate in the dissemination of these traits, resulting in the virtual elimination of barriers among different kinds of bacteria. In this article we review the current information about the physiology of plasmids and their role in virulence and antibiotic resistance from the Gram-negative opportunistic pathogen Klebsiella pneumoniae. This bacterium has acquired multidrug resistance and is the causative agent of serious community- and hospital-acquired infections. It is also included in the recently defined ESKAPE group of bacteria that cause most U.S. hospital infections.}, }
@article {pmid26104356, year = {2014}, author = {Cook, LC and Dunny, GM}, title = {The Influence of Biofilms in the Biology of Plasmids.}, journal = {Microbiology spectrum}, volume = {2}, number = {5}, pages = {}, doi = {10.1128/microbiolspec.PLAS-0012-2013}, pmid = {26104356}, issn = {2165-0497}, support = {1R01AI58134/AI/NIAID NIH HHS/United States ; R01 GM049530/GM/NIGMS NIH HHS/United States ; 1R01GM49530/GM/NIGMS NIH HHS/United States ; R01 AI058134/AI/NIAID NIH HHS/United States ; T32GM008347/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; *Bacterial Physiological Phenomena ; Biofilms/*growth &amp; development ; DNA Replication ; Gene Transfer, Horizontal ; Genomic Instability ; *Plasmids ; }, abstract = {The field of plasmid biology has historically focused on bacteria growing in liquid culture. Surface-attached communities of bacterial biofilms have recently been understood to be the normal environment of bacteria in the natural world. Thus, studies examining plasmid replication, maintenance, and transfer in biofilms are essential for a true understanding of bacterial plasmid biology. This article reviews the current knowledge of the interplay between bacterial biofilms and plasmids, focusing on the role of plasmids in biofilm development and the role of biofilms in plasmid maintenance, copy-number control, and transfer. The studies examined herein highlight the importance of biofilms as an important ecological niche in which bacterial plasmids play an essential role.}, }
@article {pmid26104311, year = {2016}, author = {Liebensteiner, MG and Oosterkamp, MJ and Stams, AJ}, title = {Microbial respiration with chlorine oxyanions: diversity and physiological and biochemical properties of chlorate- and perchlorate-reducing microorganisms.}, journal = {Annals of the New York Academy of Sciences}, volume = {1365}, number = {1}, pages = {59-72}, doi = {10.1111/nyas.12806}, pmid = {26104311}, issn = {1749-6632}, mesh = {Animals ; Chlorates/*metabolism ; Chlorine/*metabolism ; Humans ; *Microbiological Phenomena ; Perchlorates/*metabolism ; Phylogeny ; }, abstract = {Chlorine oxyanions are valuable electron acceptors for microorganisms. Recent findings have shed light on the natural formation of chlorine oxyanions in the environment. These suggest a permanent introduction of respective compounds on Earth, long before their anthropogenic manufacture. Microorganisms that are able to grow by the reduction of chlorate and perchlorate are affiliated with phylogenetically diverse lineages, spanning from the Proteobacteria to the Firmicutes and archaeal microorganisms. Microbial reduction of chlorine oxyanions can be found in diverse environments and different environmental conditions (temperature, salinities, pH). It commonly involves the enzymes perchlorate reductase (Pcr) or chlorate reductase (Clr) and chlorite dismutase (Cld). Horizontal gene transfer seems to play an important role for the acquisition of functional genes. Novel and efficient Clds were isolated from microorganisms incapable of growing on chlorine oxyanions. Archaea seem to use a periplasmic Nar-type reductase (pNar) for perchlorate reduction and lack a functional Cld. Chlorite is possibly eliminated by alternative (abiotic) reactions. This was already demonstrated for Archaeoglobus fulgidus, which uses reduced sulfur compounds to detoxify chlorite. A broad biochemical diversity of the trait, its environmental dispersal, and the occurrence of relevant enzymes in diverse lineages may indicate early adaptations of life toward chlorine oxyanions on Earth.}, }
@article {pmid26104193, year = {2014}, author = {Goessweiner-Mohr, N and Arends, K and Keller, W and Grohmann, E}, title = {Conjugation in Gram-Positive Bacteria.}, journal = {Microbiology spectrum}, volume = {2}, number = {4}, pages = {PLAS-0004-2013}, doi = {10.1128/microbiolspec.PLAS-0004-2013}, pmid = {26104193}, issn = {2165-0497}, mesh = {*Conjugation, Genetic ; DNA, Bacterial/genetics/metabolism ; Gene Transfer, Horizontal ; Genes, Bacterial ; Gram-Positive Bacteria/*genetics/physiology ; Macromolecular Substances/metabolism ; Membrane Transport Proteins/genetics/metabolism ; Operon ; Type IV Secretion Systems/genetics/metabolism ; }, abstract = {Conjugative transfer is the most important means of spreading antibiotic resistance and virulence factors among bacteria. The key vehicles of this horizontal gene transfer are a group of mobile genetic elements, termed conjugative plasmids. Conjugative plasmids contain as minimum instrumentation an origin of transfer (oriT), DNA-processing factors (a relaxase and accessory proteins), as well as proteins that constitute the trans-envelope transport channel, the so-called mating pair formation (Mpf) proteins. All these protein factors are encoded by one or more transfer (tra) operons that together form the DNA transport machinery, the Gram-positive type IV secretion system. However, multicellular Gram-positive bacteria belonging to the streptomycetes appear to have evolved another mechanism for conjugative plasmid spread reminiscent of the machinery involved in bacterial cell division and sporulation, which transports double-stranded DNA from donor to recipient cells. Here, we focus on the protein key players involved in the plasmid spread through the two different modes and present a new secondary structure homology-based classification system for type IV secretion protein families. Moreover, we discuss the relevance of conjugative plasmid transfer in the environment and summarize novel techniques to visualize and quantify conjugative transfer in situ.}, }
@article {pmid26101080, year = {2015}, author = {Sheppard, SK and Maiden, MC}, title = {The evolution of Campylobacter jejuni and Campylobacter coli.}, journal = {Cold Spring Harbor perspectives in biology}, volume = {7}, number = {8}, pages = {a018119}, pmid = {26101080}, issn = {1943-0264}, support = {087622//Wellcome Trust/United Kingdom ; }, mesh = {Adaptation, Physiological/genetics ; Campylobacter coli/*genetics/physiology ; Campylobacter jejuni/*genetics/physiology ; *Evolution, Molecular ; Recombination, Genetic ; }, abstract = {The global significance of Campylobacter jejuni and Campylobacter coli as gastrointestinal human pathogens has motivated numerous studies to characterize their population biology and evolution. These bacteria are a common component of the intestinal microbiota of numerous bird and mammal species and cause disease in humans, typically via consumption of contaminated meat products, especially poultry meat. Sequence-based molecular typing methods, such as multilocus sequence typing (MLST) and whole genome sequencing (WGS), have been instructive for understanding the epidemiology and evolution of these bacteria and how phenotypic variation relates to the high degree of genetic structuring in C. coli and C. jejuni populations. Here, we describe aspects of the relatively short history of coevolution between humans and pathogenic Campylobacter, by reviewing research investigating how mutation and lateral or horizontal gene transfer (LGT or HGT, respectively) interact to create the observed population structure. These genetic changes occur in a complex fitness landscape with divergent ecologies, including multiple host species, which can lead to rapid adaptation, for example, through frame-shift mutations that alter gene expression or the acquisition of novel genetic elements by HGT. Recombination is a particularly strong evolutionary force in Campylobacter, leading to the emergence of new lineages and even large-scale genome-wide interspecies introgression between C. jejuni and C. coli. The increasing availability of large genome datasets is enhancing understanding of Campylobacter evolution through the application of methods, such as genome-wide association studies, but MLST-derived clonal complex designations remain a useful method for describing population structure.}, }
@article {pmid26100509, year = {2015}, author = {Ma, PF and Zhang, YX and Guo, ZH and Li, DZ}, title = {Evidence for horizontal transfer of mitochondrial DNA to the plastid genome in a bamboo genus.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {11608}, pmid = {26100509}, issn = {2045-2322}, mesh = {Bambusa/*genetics ; Base Sequence ; DNA, Intergenic/genetics ; DNA, Mitochondrial/*genetics ; Gene Transfer, Horizontal/*genetics ; Genetic Variation ; Genome, Plant ; Genome, Plastid/*genetics ; Likelihood Functions ; Mutagenesis, Insertional/genetics ; Phylogeny ; Reproducibility of Results ; Sequence Analysis, DNA ; }, abstract = {In flowering plants, three genomes (nuclear, mitochondrial, and plastid) coexist and intracellular horizontal transfer of DNA is prevalent, especially from the plastid to the mitochondrion genome. However, the plastid genomes are generally conserved in evolution and have long been considered immune to foreign DNA. Recently, the opposite direction of DNA transfer from the mitochondrial to the plastid genome has been reported in two eudicot lineages. Here we sequenced 6 plastid genomes of bamboos, three of which are neotropical woody species and three are herbaceous ones. Several unusual features were found, including the duplication of trnT-GGU and loss of one copy of rps19 due to contraction of inverted repeats (IRs). The most intriguing was the ~2.7 kb insertion in the plastid IR regions in the three herbaceous bamboos. Furthermore, the insertion was documented to be horizontally transferred from the mitochondrial to the plastid genome. Our study provided evidence of the mitochondrial-to-plastid DNA transfer in the monocots, demonstrating again that this rare event does occur in other angiosperm lineages. However, the mechanism underlying the transfer remains obscure, and more studies in other plants may elucidate it in the future.}, }
@article {pmid26099939, year = {2015}, author = {Arora, AK and Forshaw, A and Miller, TA and Durvasula, R}, title = {A delivery system for field application of paratransgenic control.}, journal = {BMC biotechnology}, volume = {15}, number = {}, pages = {59}, pmid = {26099939}, issn = {1472-6750}, mesh = {Bacteria/*genetics/pathogenicity ; Drug Compounding ; *Gene Transfer Techniques ; Pantoea/*genetics ; }, abstract = {BACKGROUND: As an alternative to chemical pesticides, paratransgenesis relies on transformation of symbiotic bacteria of an arthropod vector to deliver molecules that disrupt pathogen transmission. For over a decade paratransgenesis has remained a laboratory-based endeavor owing to regulatory concerns regarding introduction of transformed microorganisms into the environment. To facilitate field application of paratransgenic strategies, risk mitigation approaches that address environmental contamination and gene spread must be developed.<br><br>RESULTS: Using biopolymer manipulation, we introduce a novel microencapsulation platform for containment and targeted delivery of engineered bacteria to the gut of a disease-transmitting arthropod. We demonstrate the first proof of principle of targeted delivery of EPA-approved Pantoea agglomerans E325 in a paratransgenic system to control spread of Pierce's Disease by glassy-winged sharpshooters, (Homalodisca vitripennis) under simulated field conditions. Engineered microcapsules may address regulatory concerns regarding containment of recombinant bacteria and environmental spread of foreign genetic material and may represent an important step in translating paratransgenic science beyond the lab and into the field.<br><br>CONCLUSIONS: We present, for the first time, a microencapsulation strategy to deliver recombinant bacteria to an insect and demonstrate targeted release of bacteria into the physiologically relevant region of the insect gut. This is a first step toward addressing concerns related to field application of recombinant bacteria. Engineered microparticles may decrease environmental contamination, horizontal gene transfer and competition with native species by acting as a barrier between recombinant bacteria and the environment.}, }
@article {pmid26097806, year = {2015}, author = {Ayala, JC and Wang, H and Benitez, JA and Silva, AJ}, title = {RNA-Seq analysis and whole genome DNA-binding profile of the Vibrio cholerae histone-like nucleoid structuring protein (H-NS).}, journal = {Genomics data}, volume = {5}, number = {}, pages = {147-150}, pmid = {26097806}, issn = {2213-5960}, support = {F31 AI106288/AI/NIAID NIH HHS/United States ; R21 AI103693/AI/NIAID NIH HHS/United States ; SC1 AI104993/AI/NIAID NIH HHS/United States ; }, abstract = {The data described in this article pertain to the genome-wide transcription profiling of a Vibrio cholerae mutant lacking the histone-like nucleoid structuring protein (H-NS) and the mapping of the H-NS chromosome binding sites [1, 2]. H-NS is a nucleoid-associated protein with two interrelated functions: organization of the bacterial nucleoid and transcriptional silencing [3]. Both functions require DNA binding and protein oligomerization [4, 5]. H-NS commonly silences the expression of virulence factors acquired by lateral gene transfer [6]. The highly pleiotropic nature of hns mutants in V. cholerae indicates that H-NS impacts a broad range of cellular processes such as virulence, stress response, surface attachment, biofilm development, motility and chemotaxis. We used a V. cholerae strain harboring a deletion of hns and a strain expressing H-NS tagged at the C-terminus with the FLAG epitope to generate datasets representing the hns transcriptome and DNA binding profile under laboratory conditions (LB medium, 37°C). The datasets are publicly available at the Gene Expression Omnibus (GEO) repository (http://www.ncbi.nlm.nih.gov/geo/) with accession numbers GSE62785 and GSE64249.}, }
@article {pmid26097040, year = {2015}, author = {Heiniger, EK and Harwood, CS}, title = {Posttranslational modification of a vanadium nitrogenase.}, journal = {MicrobiologyOpen}, volume = {4}, number = {4}, pages = {597-603}, pmid = {26097040}, issn = {2045-8827}, mesh = {Ammonia/*metabolism ; Cluster Analysis ; Gene Expression Regulation, Bacterial/*drug effects ; Gene Expression Regulation, Enzymologic/*drug effects ; Nitrogenase/genetics/*metabolism ; Phylogeny ; *Protein Processing, Post-Translational ; Rhodopseudomonas/*enzymology/metabolism ; Sequence Homology ; }, abstract = {In microbes that fix nitrogen, nitrogenase catalyzes the conversion of N2 to ammonia in an ATP-demanding reaction. To help conserve energy some bacteria inhibit nitrogenase activity upon exposure to ammonium. The purple nonsulfur phototrophic bacterium Rhodopseudomonas palustris strain CGA009 can synthesize three functional nitrogenase isoenzymes: a molybdenum nitrogenase, a vanadium nitrogenase, and an iron nitrogenase. Previous studies showed that in some alphaproteobacteria, including R. palustris, molybdenum nitrogenase activity is inhibited by ADP-ribosylation when cells are exposed to ammonium. Some iron nitrogenases are also posttranslationally modified. However, the posttranslational modification of vanadium nitrogenase has not been reported. Here, we investigated the regulation of the alternative nitrogenases of R. palustris and determined that both its vanadium nitrogenase and its iron nitrogenase activities were inhibited and posttranslationally modified when cells are exposed to ammonium. Vanadium nitrogenase is not found in all strains of R. palustris, suggesting that it may have been acquired by horizontal gene transfer. Also, phylogenetic analyses of the three nitrogenases suggest that VnfH, the target of ADP-ribosylation, may be the product of a gene duplication of nifH, the molybdenum nitrogenase homolog.}, }
@article {pmid26097034, year = {2015}, author = {Forsberg, KJ and Patel, S and Wencewicz, TA and Dantas, G}, title = {The Tetracycline Destructases: A Novel Family of Tetracycline-Inactivating Enzymes.}, journal = {Chemistry &amp; biology}, volume = {22}, number = {7}, pages = {888-897}, pmid = {26097034}, issn = {1879-1301}, support = {DP2 DK098089/DK/NIDDK NIH HHS/United States ; R01 GM099538/GM/NIGMS NIH HHS/United States ; DP2DK098089/DK/NIDDK NIH HHS/United States ; R01GM099538/GM/NIGMS NIH HHS/United States ; T32 HG000045/HG/NHGRI NIH HHS/United States ; R01 AI123394/AI/NIAID NIH HHS/United States ; T32HG000045/HG/NHGRI NIH HHS/United States ; U01 AI123394/AI/NIAID NIH HHS/United States ; T32 GM007067/GM/NIGMS NIH HHS/United States ; T32GM007067/GM/NIGMS NIH HHS/United States ; }, mesh = {Activation, Metabolic ; Escherichia coli/enzymology/genetics ; Molecular Sequence Data ; Oxygenases/*genetics/*metabolism ; Soil Microbiology ; Tetracycline/*pharmacokinetics/pharmacology ; Tetracycline Resistance/*genetics ; }, abstract = {Enzymes capable of inactivating tetracycline are paradoxically rare compared with enzymes that inactivate other natural-product antibiotics. We describe a family of flavoenzymes, previously unrecognizable as resistance genes, which are capable of degrading tetracycline antibiotics. From soil functional metagenomic selections, we discovered nine genes that confer high-level tetracycline resistance by enzymatic inactivation. We also demonstrate that a tenth enzyme, an uncharacterized homolog in the human pathogen Legionella longbeachae, similarly inactivates tetracycline. These enzymes catalyze the oxidation of tetracyclines in vitro both by known mechanisms and via previously undescribed activity. Tetracycline-inactivation genes were identified in diverse soil types, encompass substantial sequence diversity, and are adjacent to genes implicated in horizontal gene transfer. Because tetracycline inactivation is scarcely observed in hospitals, these enzymes may fill an empty niche in pathogenic organisms, and should therefore be monitored for their dissemination potential into the clinic.}, }
@article {pmid26092457, year = {2015}, author = {Osorio, CR and Rivas, AJ and Balado, M and Fuentes-Monteverde, JC and Rodríguez, J and Jiménez, C and Lemos, ML and Waldor, MK}, title = {A Transmissible Plasmid-Borne Pathogenicity Island Confers Piscibactin Biosynthesis in the Fish Pathogen Photobacterium damselae subsp. piscicida.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {17}, pages = {5867-5879}, pmid = {26092457}, issn = {1098-5336}, support = {R37 AI042347/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Fish Diseases/*microbiology ; *Gene Transfer, Horizontal ; *Genomic Islands ; Gram-Negative Bacterial Infections/microbiology/*veterinary ; Iron/metabolism ; Molecular Sequence Data ; Photobacterium/*genetics/*metabolism/pathogenicity ; Plasmids/*genetics/metabolism ; Siderophores/*biosynthesis ; Virulence ; }, abstract = {The fish pathogen Photobacterium damselae subsp. piscicida produces the siderophore piscibactin. A gene cluster that resembles the Yersinia high-pathogenicity island (HPI) encodes piscibactin biosynthesis. Here, we report that this HPI-like cluster is part of a hitherto-uncharacterized 68-kb plasmid dubbed pPHDP70. This plasmid lacks homologs of genes that mediate conjugation, but we found that it could be transferred at low frequencies from P. damselae subsp. piscicida to a mollusk pathogenic Vibrio alginolyticus strain and to other Gram-negative bacteria, likely dependent on the conjugative functions of the coresident plasmid pPHDP60. Following its conjugative transfer, pPHDP70 restored the capacity of a vibrioferrin mutant of V. alginolyticus to grow under low-iron conditions, and piscibactin became detectable in its supernatant. Thus, pPHDP70 appears to harbor all the genes required for piscibactin biosynthesis and transport. P. damselae subsp. piscicida strains cured of pPHDP70 no longer produced piscibactin, had impaired growth under iron-limited conditions, and exhibited markedly decreased virulence in fish. Collectively, our findings highlight the importance of pPHDP70, with its capacity for piscibactin-mediated iron acquisition, in the virulence of P. damselae subsp. piscicida. Horizontal transmission of this plasmid-borne piscibactin synthesis gene cluster in the marine environment may facilitate the emergence of new pathogens.}, }
@article {pmid26088623, year = {2015}, author = {Kamng'ona, AW and Hinds, J and Bar-Zeev, N and Gould, KA and Chaguza, C and Msefula, C and Cornick, JE and Kulohoma, BW and Gray, K and Bentley, SD and French, N and Heyderman, RS and Everett, DB}, title = {High multiple carriage and emergence of Streptococcus pneumoniae vaccine serotype variants in Malawian children.}, journal = {BMC infectious diseases}, volume = {15}, number = {}, pages = {234}, pmid = {26088623}, issn = {1471-2334}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Adolescent ; Bacterial Capsules/genetics ; Bacteriological Techniques ; Child ; Child, Preschool ; Cross Protection/immunology ; DNA, Bacterial/analysis/isolation &amp; purification ; Female ; Genetic Variation ; HIV Infections/complications/diagnosis ; Humans ; Infant ; Infant, Newborn ; Malawi ; Male ; Nasopharynx/microbiology ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; Pneumococcal Infections/complications/*microbiology/prevention &amp; control ; Pneumococcal Vaccines/immunology ; Sequence Analysis, DNA ; Serogroup ; Streptococcus pneumoniae/classification/*genetics/isolation &amp; purification ; }, abstract = {BACKGROUND: Carriage of either single or multiple pneumococcal serotypes (multiple carriage) is a prerequisite for developing invasive pneumococcal disease. However, despite the reported high rates of pneumococcal carriage in Malawi, no data on carriage of multiple serotypes has been reported previously. Our study provides the first description of the prevalence of multiple pneumococcal carriage in Malawi.<br><br>METHODS: The study was conducted in Blantyre and Karonga districts in Malawi, from 2008 to 2012. We recruited 116 children aged 0-13 years. These children were either HIV-infected (N = 44) or uninfected (N = 72). Nasopharyngeal samples were collected using sterile swabs. Pneumococcal serotypes in the samples were identified by microarray. Strains that could not be typed by microarray were sequenced to characterise possible genetic alterations within the capsular polysaccharide (CPS) locus.<br><br>RESULTS: The microarray identified 179 pneumococcal strains (from 116 subjects), encompassing 43 distinct serotypes and non-typeable (NT) strains. Forty per cent (46/116) of children carried multiple serotypes. Carriage of vaccine type (VT) strains was higher (p = 0.028) in younger (0-2 years) children (71 %, 40/56) compared to older (3-13 years) children (50 %, 30/60). Genetic variations within the CPS locus of known serotypes were observed in 19 % (34/179) of the strains identified. The variants included 13-valent pneumococcal conjugate vaccine (PCV13) serotypes 6B and 19A, and the polysaccharide vaccine serotype 20. Serotype 6B variants were the most frequently isolated (47 %, 16/34). Unlike the wild type, the CPS locus of the 6B variants contained an insertion of the licD-family phosphotransferase gene. The CPS locus of 19A- and 20-variants contained an inversion in the sugar-biosynthesis (rmlD) gene and a 717 bp deletion within the transferase (whaF) gene, respectively.<br><br>CONCLUSIONS: The high multiple carriage in Malawian children provides opportunities for genetic exchange through horizontal gene transfer. This may potentially lead to CPS locus variants and vaccine escape. Variants reported here occurred naturally, however, PCV13 introduction could exacerbate the CPS genetic variations. Further studies are therefore recommended to assess the invasive potential of these variants and establish whether PCV13 would offer cross-protection. We have shown that younger children (0-2 years) are a reservoir of VT serotypes, which makes them an ideal target for vaccination.}, }
@article {pmid26087621, year = {2015}, author = {Provorov, NA and Tikhonovich, IA}, title = {[Bacterial Genome Evolution in Superspecies Systems: an Approach to the Reconstruction of Symbiogenesis Processes].}, journal = {Genetika}, volume = {51}, number = {4}, pages = {456-465}, pmid = {26087621}, issn = {0016-6758}, mesh = {Alphaproteobacteria/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*physiology ; Genome, Bacterial/*physiology ; Symbiosis/*physiology ; }, abstract = {Bacteria form a broad spectrum of symbioses with eukaryotes. This permits reconstruction of the symbiogenesis processes providing the transformation of free-living microorganisms into cellular organelles. In ecologically (conditionally) obligate symbioses, an increase in the size and complexity of the bacterial genome structure was observed. This was associated with segregation of the regions controlling symbiosis into gene clusters, islands, and plasmids. In genetically (strictly) obligate symbioses, a reduction of "nonsymbiotic" regions of microbial genome occurs, which could begin from genes encoding metabolic and regulatory functions. It is extended towards genes encoding template processes. Conditionally obligate symbioses are characterised by the activation of horizontal gene transfer between various forms of microsymbionts, while for strictly obligate intracellular symbioses an activation of endo-symbiotic gene transfer between microsymbionts and their hosts was detected. The latter is responsible for bacterial transition from the functional (based on gene cross-regulation) to structural (based on recombination) genetic integration with hosts, which later could be followed by the complete assimilation of microbial genomes. In α-proteobacteria this evolutionary pathway could result in the formation of cellular organelles that are deficient in their own genomes but capable of preserving proteomic and cytological traits as a result of the gene-product import synthesized in cytosol (hydrogenosomes and mitosomes). The symbiogenic evolution of cyanobacteria could result in the loss of the plasmids generated from them, while the host maintains a significant part of their genome in nuclear chromosomes.}, }
@article {pmid26085541, year = {2015}, author = {Kupczok, A and Landan, G and Dagan, T}, title = {The Contribution of Genetic Recombination to CRISPR Array Evolution.}, journal = {Genome biology and evolution}, volume = {7}, number = {7}, pages = {1925-1939}, pmid = {26085541}, issn = {1759-6653}, support = {281357/ERC_/European Research Council/International ; }, mesh = {Algorithms ; *Clustered Regularly Interspaced Short Palindromic Repeats ; *Evolution, Molecular ; Gammaproteobacteria/genetics ; *Recombination, Genetic ; Sequence Deletion ; Streptococcus/genetics ; }, abstract = {CRISPR (clustered regularly interspaced short palindromic repeats) is a microbial immune system against foreign DNA. Recognition sequences (spacers) encoded within the CRISPR array mediate the immune reaction in a sequence-specific manner. The known mechanisms for the evolution of CRISPR arrays include spacer acquisition from foreign DNA elements at the time of invasion and array erosion through spacer deletion. Here, we consider the contribution of genetic recombination between homologous CRISPR arrays to the evolution of spacer repertoire. Acquisition of spacers from exogenic arrays via recombination may confer the recipient with immunity against unencountered antagonists. For this purpose, we develop a novel method for the detection of recombination in CRISPR arrays by modeling the spacer order in arrays from multiple strains from the same species. Because the evolutionary signal of spacer recombination may be similar to that of pervasive spacer deletions or independent spacer acquisition, our method entails a robustness analysis of the recombination inference by a statistical comparison to resampled and perturbed data sets. We analyze CRISPR data sets from four bacterial species: two Gammaproteobacteria species harboring CRISPR type I and two Streptococcus species harboring CRISPR type II loci. We find that CRISPR array evolution in Escherichia coli and Streptococcus agalactiae can be explained solely by vertical inheritance and differential spacer deletion. In Pseudomonas aeruginosa, we find an excess of single spacers potentially incorporated into the CRISPR locus during independent acquisition events. In Streptococcus thermophilus, evidence for spacer acquisition by recombination is present in 5 out of 70 strains. Genetic recombination has been proposed to accelerate adaptation by combining beneficial mutations that arose in independent lineages. However, for most species under study, we find that CRISPR evolution is shaped mainly by spacer acquisition and loss rather than recombination. Since the evolution of spacer content is characterized by a rapid turnover, it is likely that recombination is not beneficial for improving phage resistance in the strains under study, or that it cannot be detected in the resolution of intraspecies comparisons.}, }
@article {pmid26085102, year = {2015}, author = {Cordeiro, TN and García, J and Bernadó, P and Millet, O and Pons, M}, title = {A Three-protein Charge Zipper Stabilizes a Complex Modulating Bacterial Gene Silencing.}, journal = {The Journal of biological chemistry}, volume = {290}, number = {35}, pages = {21200-21212}, pmid = {26085102}, issn = {1083-351X}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/*metabolism ; DNA-Binding Proteins/chemistry/*metabolism ; Enterobacteriaceae/*genetics/*metabolism ; Enterobacteriaceae Infections/microbiology ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Humans ; Models, Molecular ; Molecular Sequence Data ; Nuclear Magnetic Resonance, Biomolecular ; Protein Conformation ; Protein Interaction Maps ; Protein Multimerization ; Static Electricity ; }, abstract = {The Hha/YmoA nucleoid-associated proteins help selectively silence horizontally acquired genetic material, including pathogenicity and antibiotic resistance genes and their maintenance in the absence of selective pressure. Members of the Hha family contribute to gene silencing by binding to the N-terminal dimerization domain of H-NS and modifying its selectivity. Hha-like proteins and the H-NS N-terminal domain are unusually rich in charged residues, and their interaction is mostly electrostatic-driven but, nonetheless, highly selective. The NMR-based structural model of the complex between Hha/YmoA and the H-NS N-terminal dimerization domain reveals that the origin of the selectivity is the formation of a three-protein charge zipper with interdigitated complementary charged residues from Hha and the two units of the H-NS dimer. The free form of YmoA shows collective microsecond-millisecond dynamics that can by measured by NMR relaxation dispersion experiments and shows a linear dependence with the salt concentration. The number of residues sensing the collective dynamics and the population of the minor form increased in the presence of H-NS. Additionally, a single residue mutation in YmoA (D43N) abolished H-NS binding and the dynamics of the apo-form, suggesting the dynamics and binding are functionally related.}, }
@article {pmid26081716, year = {2015}, author = {Baudoux, AC and Lebredonchel, H and Dehmer, H and Latimier, M and Edern, R and Rigaut-Jalabert, F and Ge, P and Guillou, L and Foulon, E and Bozec, Y and Cariou, T and Desdevises, Y and Derelle, E and Grimsley, N and Moreau, H and Simon, N}, title = {Interplay between the genetic clades of Micromonas and their viruses in the Western English Channel.}, journal = {Environmental microbiology reports}, volume = {7}, number = {5}, pages = {765-773}, doi = {10.1111/1758-2229.12309}, pmid = {26081716}, issn = {1758-2229}, mesh = {Chlorophyta/*classification/*genetics/virology ; Ecosystem ; *Genetic Variation ; Phycodnaviridae/*classification/*genetics ; Seasons ; Seawater/*microbiology ; Viral Plaque Assay ; }, abstract = {The genus Micromonas comprises distinct genetic clades that commonly dominate eukaryotic phytoplankton community from polar to tropical waters. This phytoplankter is also recurrently infected by abundant and genetically diverse prasinoviruses. Here we report on the interplay between prasinoviruses and Micromonas with regard to the genetic diversity of this host. For 1 year, we monitored the abundance of three clades of Micromonas and their viruses in the Western English Channel, both in the environment using clade-specific probes and flow cytometry, and in the laboratory using clonal strains of Micromonas clades to assay for their viruses by plaque-forming units. We showed that the seasonal fluctuations of Micromonas clades were closely mirrored by the abundance of their corresponding viruses, indicating that the members of Micromonas genus are susceptible to viral infection, regardless of their genetic affiliation. The characterization of 45 viral isolates revealed that Micromonas clades are attacked by specific virus populations, which exhibit distinctive clade specificity, life strategies and genetic diversity. However, some viruses can also cross-infect different host clades, suggesting a mechanism of horizontal gene transfer within the Micromonas genus. This study provides novel insights into the impact of viral infection for the ecology and evolution of the prominent phytoplankter Micromonas.}, }
@article {pmid26081635, year = {2015}, author = {Yue, Q and Chen, L and Li, Y and Bills, GF and Zhang, X and Xiang, M and Li, S and Che, Y and Wang, C and Niu, X and An, Z and Liu, X}, title = {Functional Operons in Secondary Metabolic Gene Clusters in Glarea lozoyensis (Fungi, Ascomycota, Leotiomycetes).}, journal = {mBio}, volume = {6}, number = {3}, pages = {e00703}, pmid = {26081635}, issn = {2150-7511}, mesh = {Ascomycota/*enzymology/genetics/metabolism ; Aspergillus nidulans/genetics/metabolism ; DNA, Fungal/chemistry/genetics ; Gene Expression ; *Gene Expression Regulation, Fungal ; Molecular Sequence Data ; *Multigene Family ; *Operon ; Peptide Synthases/*genetics/metabolism ; Polyketide Synthases/*genetics/metabolism ; Promoter Regions, Genetic ; Protein Biosynthesis ; Secondary Metabolism ; Sequence Analysis, DNA ; Transcription, Genetic ; }, abstract = {UNLABELLED: Operons are multigene transcriptional units which occur mostly in prokaryotes but rarely in eukaryotes. Protein-coding operons have not been reported in the Fungi even though they represent a very diverse kingdom of organisms. Here, we report a functional operon involved in the secondary metabolism of the fungus Glarea lozoyensis belonging to Leotiomycetes (Ascomycota). Two contiguous genes, glpks3 and glnrps7, encoding polyketide synthase and nonribosomal peptide synthetase, respectively, are cotranscribed into one dicistronic mRNA under the control of the same promoter, and the mRNA is then translated into two individual proteins, GLPKS3 and GLNRPS7. Heterologous expression in Aspergillus nidulans shows that the GLPKS3-GLNRPS7 enzyme complex catalyzes the biosynthesis of a novel pyrrolidinedione-containing compound, xenolozoyenone (compound 1), which indicates the operon is functional. Although it is structurally similar to prokaryotic operons, the glpks3-glnrps7 operon locus has a monophylogenic origin from fungi rather than having been horizontally transferred from prokaryotes. Moreover, two additional operons, glpks28-glnrps8 and glpks29-glnrps9, were verified at the transcriptional level in the same fungus. This is the first report of protein-coding operons in a member of the Fungi.<br><br>IMPORTANCE: Operons are multigene transcriptional units which occur mostly in prokaryotes but rarely in eukaryotes. Three operon-like gene structures for secondary metabolism that were discovered in the filamentous fungus Glarea lozoyensis are the first examples of protein-coding operons identified in a member of the Fungi. Among them, the glpks3-glnrps7 operon is responsible for the biosynthesis of xenolozoyenone, which is a novel tetramic acid-containing compound. Although structurally similar to prokaryotic operons, the glpks3-glnrps7 operon locus did not result from horizontal gene transfer from prokaryotes. In addition, operonlike structures have been predicted in silico to be common in other fungi. The common occurrence and operonlike structure in fungi provide evolutionary insight and essential data for eukaryotic gene transcription.}, }
@article {pmid26081630, year = {2015}, author = {Eutsey, RA and Powell, E and Dordel, J and Salter, SJ and Clark, TA and Korlach, J and Ehrlich, GD and Hiller, NL}, title = {Genetic Stabilization of the Drug-Resistant PMEN1 Pneumococcus Lineage by Its Distinctive DpnIII Restriction-Modification System.}, journal = {mBio}, volume = {6}, number = {3}, pages = {e00173}, pmid = {26081630}, issn = {2150-7511}, support = {R00 DC011322/DC/NIDCD NIH HHS/United States ; R00-DC-011322/DC/NIDCD NIH HHS/United States ; 098051/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; R01 AI080935/AI/NIAID NIH HHS/United States ; }, mesh = {*DNA Restriction-Modification Enzymes ; DNA, Bacterial/chemistry/genetics ; Gene Transfer, Horizontal ; Genotype ; Molecular Sequence Data ; Recombination, Genetic ; Sequence Analysis, DNA ; Streptococcus pneumoniae/classification/*enzymology/*genetics ; }, abstract = {UNLABELLED: The human pathogen Streptococcus pneumoniae (pneumococcus) exhibits a high degree of genomic diversity and plasticity. Isolates with high genomic similarity are grouped into lineages that undergo homologous recombination at variable rates. PMEN1 is a pandemic, multidrug-resistant lineage. Heterologous gene exchange between PMEN1 and non-PMEN1 isolates is directional, with extensive gene transfer from PMEN1 strains and only modest transfer into PMEN1 strains. Restriction-modification (R-M) systems can restrict horizontal gene transfer, yet most pneumococcal strains code for either the DpnI or DpnII R-M system and neither limits homologous recombination. Our comparative genomic analysis revealed that PMEN1 isolates code for DpnIII, a third R-M system syntenic to the other Dpn systems. Characterization of DpnIII demonstrated that the endonuclease cleaves unmethylated double-stranded DNA at the tetramer sequence 5' GATC 3', and the cognate methylase is a C5 cytosine-specific DNA methylase. We show that DpnIII decreases the frequency of recombination under in vitro conditions, such that the number of transformants is lower for strains transformed with unmethylated DNA than in those transformed with cognately methylated DNA. Furthermore, we have identified two PMEN1 isolates where the DpnIII endonuclease is disrupted, and phylogenetic work by Croucher and colleagues suggests that these strains have accumulated genomic differences at a higher rate than other PMEN1 strains. We propose that the R-M locus is a major determinant of genetic acquisition; the resident R-M system governs the extent of genome plasticity.<br><br>IMPORTANCE: Pneumococcus is one of the most important community-acquired bacterial pathogens. Pneumococcal strains can develop resistance to antibiotics and to serotype vaccines by acquiring genes from other strains or species. Thus, genomic plasticity is associated with strain adaptability and pneumococcal success. PMEN1 is a widespread and multidrug-resistant highly pathogenic pneumococcal lineage, which has evolved over the past century and displays a relatively stable genome. In this study, we characterize DpnIII, a restriction-modification (R-M) system that limits recombination. DpnIII is encountered in the PMEN1 lineage, where it replaces other R-M systems that do not decrease plasticity. Our hypothesis is that this genomic region, where different pneumococcal lineages code for variable R-M systems, plays a role in the fine-tuning of the extent of genomic plasticity. It is possible that well-adapted lineages such as PMEN1 have a mechanism to increase genomic stability, rather than foster genomic plasticity.}, }
@article {pmid26079817, year = {2015}, author = {Das, S and Pettersson, BM and Behra, PR and Ramesh, M and Dasgupta, S and Bhattacharya, A and Kirsebom, LA}, title = {Characterization of Three Mycobacterium spp. with Potential Use in Bioremediation by Genome Sequencing and Comparative Genomics.}, journal = {Genome biology and evolution}, volume = {7}, number = {7}, pages = {1871-1886}, pmid = {26079817}, issn = {1759-6653}, mesh = {Biodegradation, Environmental ; Copper/metabolism ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; Genomics ; Molecular Sequence Data ; Mycobacterium/classification/*genetics/metabolism ; Oxygenases/genetics ; Phylogeny ; RNA, Untranslated/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {We provide the genome sequences of the type strains of the polychlorophenol-degrading Mycobacterium chlorophenolicum (DSM43826), the degrader of chlorinated aliphatics Mycobacterium chubuense (DSM44219) and Mycobacterium obuense (DSM44075) that has been tested for use in cancer immunotherapy. The genome sizes of M. chlorophenolicum, M. chubuense, and M. obuense are 6.93, 5.95, and 5.58 Mb with GC-contents of 68.4%, 69.2%, and 67.9%, respectively. Comparative genomic analysis revealed that 3,254 genes are common and we predicted approximately 250 genes acquired through horizontal gene transfer from different sources including proteobacteria. The data also showed that the biodegrading Mycobacterium spp. NBB4, also referred to as M. chubuense NBB4, is distantly related to the M. chubuense type strain and should be considered as a separate species, we suggest it to be named Mycobacterium ethylenense NBB4. Among different categories we identified genes with potential roles in: biodegradation of aromatic compounds and copper homeostasis. These are the first nonpathogenic Mycobacterium spp. found harboring genes involved in copper homeostasis. These findings would therefore provide insight into the role of this group of Mycobacterium spp. in bioremediation as well as the evolution of copper homeostasis within the Mycobacterium genus.}, }
@article {pmid26079188, year = {2015}, author = {Lang, KS and Johnson, TJ}, title = {Transcriptome modulations due to A/C2 plasmid acquisition.}, journal = {Plasmid}, volume = {80}, number = {}, pages = {83-89}, doi = {10.1016/j.plasmid.2015.05.005}, pmid = {26079188}, issn = {1095-9890}, mesh = {Bacterial Proteins/biosynthesis/genetics ; Biosynthetic Pathways ; Chromosomes, Bacterial/genetics ; Escherichia coli/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genes, Bacterial ; Plasmids/*genetics ; Salmonella enterica/genetics/metabolism ; Shewanella/genetics/metabolism ; *Transcriptome ; }, abstract = {Plasmids play an important role in driving the genetic diversity of bacteria. Horizontal gene transfer via plasmids is crucial for the dissemination of antimicrobial resistance genes. Many factors contribute to the persistence of plasmids within bacterial populations, and it has been suggested that epistatic interactions between the host chromosome and plasmid contribute to the fitness of a particular plasmid-host combination. However, such interactions have been shown to differ between bacterial hosts. In this study, RNA-Seq was performed in six different strains, spanning three species, to characterize the influence of host background on the A/C2 plasmid transcriptome. In five of these strains, chromosomal transcriptomes were compared in the presence and absence of A/C2 plasmid pAR060302. Host-specific effects on plasmid gene expression were identified, and acquisition of pAR060302 resulted in changes in the expression of chromosomal genes involved in metabolism and energy production. These results suggest that A/C2 plasmid fitness is, in part, dependent on host chromosome content, as well as environmental factors.}, }
@article {pmid26078016, year = {2015}, author = {Bearson, BL and Brunelle, BW}, title = {Fluoroquinolone induction of phage-mediated gene transfer in multidrug-resistant Salmonella.}, journal = {International journal of antimicrobial agents}, volume = {46}, number = {2}, pages = {201-204}, doi = {10.1016/j.ijantimicag.2015.04.008}, pmid = {26078016}, issn = {1872-7913}, mesh = {Anti-Bacterial Agents/adverse effects/*metabolism ; *Drug Resistance, Multiple, Bacterial ; Fluoroquinolones/adverse effects/*metabolism ; Gene Transfer, Horizontal/*drug effects ; Prophages/genetics ; Salmonella Phages/*genetics ; Salmonella typhimurium/*drug effects ; *Transduction, Genetic ; }, abstract = {Fluoroquinolones are broad-spectrum antibiotics that inhibit bacterial DNA gyrase and topoisomerase activity, which can cause DNA damage and result in bacterial cell death. In response to DNA damage, bacteria induce an SOS response to stimulate DNA repair. However, the SOS response may also induce prophage with production of infectious virions. Salmonella strains typically contain multiple prophages, and certain strains including phage types DT120 and DT104 contain prophage that upon induction are capable of generalised transduction. In this study, strains of multidrug-resistant (MDR) Salmonella enterica serovar Typhimurium DT120 and DT104 were exposed to fluoroquinolones important for use in human and veterinary disease therapy to determine whether prophage(s) are induced that could facilitate phage-mediated gene transfer. Cultures of MDR S. Typhimurium DT120 and DT104 containing a kanamycin resistance plasmid were lysed after exposure to fluoroquinolones (ciprofloxacin, enrofloxacin and danofloxacin). Bacterial cell lysates were able to transfer the plasmid to a recipient kanamycin-susceptible Salmonella strain by generalised transduction. In addition, exposure of DT120 to ciprofloxacin induced the recA gene of the bacterial SOS response and genes encoded in a P22-like generalised transducing prophage. This research indicates that fluoroquinolone exposure of MDR Salmonella can facilitate horizontal gene transfer, suggesting that fluoroquinolone usage in human and veterinary medicine may have unintended consequences, including the induction of phage-mediated gene transfer from MDR Salmonella. Stimulation of gene transfer following bacterial exposure to fluoroquinolones should be considered an adverse effect, and clinical decisions regarding antibiotic selection for infectious disease therapy should include this potential risk.}, }
@article {pmid26075508, year = {2015}, author = {Melvin, WJ and McMichael, TM and Chesarino, NM and Hach, JC and Yount, JS}, title = {IFITMs from Mycobacteria Confer Resistance to Influenza Virus When Expressed in Human Cells.}, journal = {Viruses}, volume = {7}, number = {6}, pages = {3035-3052}, pmid = {26075508}, issn = {1999-4915}, support = {R00 AI095348/AI/NIAID NIH HHS/United States ; R56AI114826/AI/NIAID NIH HHS/United States ; T32GM068412/GM/NIGMS NIH HHS/United States ; R00AI095348/AI/NIAID NIH HHS/United States ; R56 AI114826/AI/NIAID NIH HHS/United States ; T32 GM068412/GM/NIGMS NIH HHS/United States ; }, mesh = {Antiviral Agents/*metabolism ; Bacterial Proteins/genetics/*metabolism ; Cell Line ; Conserved Sequence ; Endosomes/chemistry ; Epithelial Cells/chemistry/immunology/virology ; *Gene Expression ; Humans ; Interferon Inducers/*metabolism ; Lipoylation ; Mycobacterium/genetics/*immunology ; Orthomyxoviridae/*immunology ; Protein Processing, Post-Translational ; Protein Transport ; Recombinant Proteins/genetics/metabolism ; Sequence Homology, Amino Acid ; }, abstract = {Interferon induced transmembrane proteins (IFITMs) found in vertebrates restrict infections by specific viruses. IFITM3 is known to be essential for restriction of influenza virus infections in both mice and humans. Vertebrate IFITMs are hypothesized to have derived from a horizontal gene transfer from bacteria to a primitive unicellular eukaryote. Since bacterial IFITMs share minimal amino acid identity with human IFITM3, we hypothesized that examination of bacterial IFITMs in human cells would provide insight into the essential characteristics necessary for antiviral activity of IFITMs. We examined IFITMs from Mycobacterium avium and Mycobacterium abscessus for potential antiviral activity. Both of these IFITMs conferred a moderate level of resistance to influenza virus in human cells, identifying them as functional homologues of IFITM3. Analysis of sequence elements shared by bacterial IFITMs and IFITM3 identified two hydrophobic domains, putative S-palmitoylation sites, and conserved phenylalanine residues associated with IFITM3 interactions, which are all necessary for IFITM3 antiviral activity. We observed that, like IFITM3, bacterial IFITMs were S-palmitoylated, albeit to a lesser degree. We also demonstrated the ability of a bacterial IFITM to co-immunoprecipitate with IFITM3 suggesting formation of a complex, and also visualized strong co-localization of bacterial IFITMs with IFITM3. However, the mycobacterial IFITMs lack the endocytic-targeting motif conserved in vertebrate IFITM3. As such, these bacterial proteins, when expressed alone, had diminished colocalization with cathepsin B-positive endolysosomal compartments that are the primary site of IFITM3-dependent influenza virus restriction. Though the precise evolutionary origin of vertebrate IFITMs is not known, our results support a model whereby transfer of a bacterial IFITM gene to eukaryotic cells may have provided a selective advantage against viral infection that was refined through the course of vertebrate evolution to include more robust signals for S-palmitoylation and localization to sites of endocytic virus trafficking.}, }
@article {pmid26075362, year = {2015}, author = {López-García, P and Zivanovic, Y and Deschamps, P and Moreira, D}, title = {Bacterial gene import and mesophilic adaptation in archaea.}, journal = {Nature reviews. Microbiology}, volume = {13}, number = {7}, pages = {447-456}, pmid = {26075362}, issn = {1740-1534}, support = {322669/ERC_/European Research Council/International ; }, mesh = {Adaptation, Biological ; Archaea/*classification/*genetics/physiology ; *Evolution, Molecular ; Phylogeny ; Temperature ; }, abstract = {It is widely believed that the archaeal ancestor was hyperthermophilic, but during archaeal evolution, several lineages - including haloarchaea and their sister methanogens, the Thaumarchaeota, and the uncultured Marine Group II and Marine Group III Euryarchaeota (MGII/III) - independently adapted to lower temperatures. Recent phylogenomic studies suggest that the ancestors of these lineages were recipients of massive horizontal gene transfer from bacteria. Many of the acquired genes, which are often involved in metabolism and cell envelope biogenesis, were convergently acquired by distant mesophilic archaea. In this Opinion article, we explore the intriguing hypothesis that the import of these bacterial genes was crucial for the adaptation of archaea to mesophilic lifestyles.}, }
@article {pmid26074893, year = {2015}, author = {Piotrowska, M and Popowska, M}, title = {Insight into the mobilome of Aeromonas strains.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {494}, pmid = {26074893}, issn = {1664-302X}, abstract = {The mobilome is a pool of genes located within mobile genetic elements (MGE), such as plasmids, IS elements, transposons, genomic/pathogenicity islands, and integron-associated gene cassettes. These genes are often referred to as "flexible" and may encode virulence factors, toxic compounds as well as resistance to antibiotics. The phenomenon of MGE transfer between bacteria, known as horizontal gene transfer (HGT), is well documented. The genes present on MGE are subject to continuous processes of evolution and environmental changes, largely induced or significantly accelerated by man. For bacteria, the only chance of survival in an environment contaminated with toxic chemicals, heavy metals and antibiotics is the acquisition of genes providing the ability to survive in such conditions. The process of acquiring and spreading antibiotic resistance genes (ARG) is of particular significance, as it is important for the health of humans and animals. Therefore, it is important to thoroughly study the mobilome of Aeromonas spp. that is widely distributed in various environments, causing many diseases in fishes and humans. This review discusses the recently published information on MGE prevalent in Aeromonas spp. with special emphasis on plasmids belonging to different incompatibility groups, i.e., IncA/C, IncU, IncQ, IncF, IncI, and ColE-type. The vast majority of plasmids carry a number of different transposons (Tn3, Tn21, Tn1213, Tn1721, Tn4401), the 1st, 2nd, or 3rd class of integrons, IS elements (e.g., IS26, ISPa12, ISPa13, ISKpn8, ISKpn6) and encode determinants such as antibiotic and mercury resistance genes, as well as virulence factors. Although the actual role of Aeromonas spp. as a human pathogen remains controversial, species of this genus may pose a serious risk to human health. This is due to the considerable potential of their mobilome, particularly in terms of antibiotic resistance and the possibility of the horizontal transfer of resistance genes.}, }
@article {pmid26068099, year = {2015}, author = {Ding, P and McFarland, KA and Jin, S and Tong, G and Duan, B and Yang, A and Hughes, TR and Liu, J and Dove, SL and Navarre, WW and Xia, B}, title = {A Novel AT-Rich DNA Recognition Mechanism for Bacterial Xenogeneic Silencer MvaT.}, journal = {PLoS pathogens}, volume = {11}, number = {6}, pages = {e1004967}, pmid = {26068099}, issn = {1553-7374}, support = {R01 AI105013/AI/NIAID NIH HHS/United States ; AI105013/AI/NIAID NIH HHS/United States ; MOP-111007//Canadian Institutes of Health Research/Canada ; MOP-86683//Canadian Institutes of Health Research/Canada ; }, mesh = {Bacterial Proteins/chemistry/*genetics ; Biological Evolution ; Blotting, Western ; Electrophoretic Mobility Shift Assay ; Gene Expression Regulation, Bacterial/*genetics ; Gene Silencing/*physiology ; Gene Transfer, Horizontal ; High-Throughput Screening Assays ; Magnetic Resonance Spectroscopy ; Protein Array Analysis ; Pseudomonas aeruginosa/chemistry/*genetics ; *Structure-Activity Relationship ; Trans-Activators/chemistry/*genetics ; }, abstract = {Bacterial xenogeneic silencing proteins selectively bind to and silence expression from many AT rich regions of the chromosome. They serve as master regulators of horizontally acquired DNA, including a large number of virulence genes. To date, three distinct families of xenogeneic silencers have been identified: H-NS of Proteobacteria, Lsr2 of the Actinomycetes, and MvaT of Pseudomonas sp. Although H-NS and Lsr2 family proteins are structurally different, they all recognize the AT-rich DNA minor groove through a common AT-hook-like motif, which is absent in the MvaT family. Thus, the DNA binding mechanism of MvaT has not been determined. Here, we report the characteristics of DNA sequences targeted by MvaT with protein binding microarrays, which indicates that MvaT prefers binding flexible DNA sequences with multiple TpA steps. We demonstrate that there are clear differences in sequence preferences between MvaT and the other two xenogeneic silencer families. We also determined the structure of the DNA-binding domain of MvaT in complex with a high affinity DNA dodecamer using solution NMR. This is the first experimental structure of a xenogeneic silencer in complex with DNA, which reveals that MvaT recognizes the AT-rich DNA both through base readout by an "AT-pincer" motif inserted into the minor groove and through shape readout by multiple lysine side chains interacting with the DNA sugar-phosphate backbone. Mutations of key MvaT residues for DNA binding confirm their importance with both in vitro and in vivo assays. This novel DNA binding mode enables MvaT to better tolerate GC-base pair interruptions in the binding site and less prefer A tract DNA when compared to H-NS and Lsr2. Comparison of MvaT with other bacterial xenogeneic silencers provides a clear picture that nature has evolved unique solutions for different bacterial genera to distinguish foreign from self DNA.}, }
@article {pmid26066582, year = {2015}, author = {Schultz, E and Haenni, M and Mereghetti, L and Siebor, E and Neuwirth, C and Madec, JY and Cloeckaert, A and Doublet, B}, title = {Survey of multidrug resistance integrative mobilizable elements SGI1 and PGI1 in Proteus mirabilis in humans and dogs in France, 2010-13.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {70}, number = {9}, pages = {2543-2546}, doi = {10.1093/jac/dkv154}, pmid = {26066582}, issn = {1460-2091}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; DNA, Bacterial/genetics ; Dogs ; *Drug Resistance, Multiple, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; France ; Gene Transfer, Horizontal ; Genetic Variation ; Genomic Islands ; Genotype ; Humans ; *Interspersed Repetitive Sequences ; Microbial Sensitivity Tests ; Molecular Typing ; Polymerase Chain Reaction ; Proteus Infections/*microbiology/*veterinary ; Proteus mirabilis/classification/*drug effects/genetics/*isolation &amp; purification ; }, abstract = {OBJECTIVES: To characterize MDR genomic islands related to Salmonella genomic island 1 (SGI1) and Proteus genomic island 1 (PGI1) in Proteus mirabilis from human and animal sources in France in light of the previously reported cases.<br><br>METHODS: A total of 52 and 46 P. mirabilis clinical strains from human and animal sources, respectively, were studied for the period 2010-13. MDR was assessed by antimicrobial susceptibility testing, PCR detection of SGI1 and PGI1 and PCR mapping of the MDR regions. The diversity of the SGI1/PGI1-positive P. mirabilis strains was assessed by PFGE.<br><br>RESULTS: Twelve P. mirabilis strains (5 humans and 7 dogs) were found to harbour an MDR island related to SGI1 or PGI1. Among them, several SGI1 variants were identified in diverse P. mirabilis genetic backgrounds. The variant SGI1-V, which harbours the ESBL bla VEB-6 gene, was found in closely genetically related human and dog P. mirabilis strains. The recently described PGI1 element was also identified in human and dog strains. Finally, one strain harboured a novel SGI genomic island closely related to SGI1 and SGI2 without an insertion of the MDR region.<br><br>CONCLUSION: This study reports for the first time, to our knowledge, SGI1-positive and PGI1-positive P. mirabilis strains from dogs in France. The genetic diversity of the strains suggests several independent horizontal acquisitions of these MDR elements. The potential transmission of SGI1/PGI1-positive P. mirabilis strains between animals and humans is of public health concern, notably with regard to the spread of ESBL and carbapenemase genes, i.e. bla VEB-6 and bla NDM-1.}, }
@article {pmid26063817, year = {2015}, author = {Fasani, RA and Savageau, MA}, title = {Unrelated toxin-antitoxin systems cooperate to induce persistence.}, journal = {Journal of the Royal Society, Interface}, volume = {12}, number = {108}, pages = {20150130}, pmid = {26063817}, issn = {1742-5662}, support = {R01 GM030054/GM/NIGMS NIH HHS/United States ; R01-GM30054/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/genetics/*metabolism ; Bacterial Proteins/genetics/*metabolism ; Gene Expression Regulation, Bacterial/*physiology ; *Models, Biological ; }, abstract = {Persisters are drug-tolerant bacteria that account for the majority of bacterial infections. They are not mutants, rather, they are slow-growing cells in an otherwise normally growing population. It is known that the frequency of persisters in a population is correlated with the number of toxin-antitoxin systems in the organism. Our previous work provided a mechanistic link between the two by showing how multiple toxin-antitoxin systems, which are present in nearly all bacteria, can cooperate to induce bistable toxin concentrations that result in a heterogeneous population of slow- and fast-growing cells. As such, the slow-growing persisters are a bet-hedging subpopulation maintained under normal conditions. For technical reasons, the model assumed that the kinetic parameters of the various toxin-antitoxin systems in the cell are identical, but experimental data indicate that they differ, sometimes dramatically. Thus, a critical question remains: whether toxin-antitoxin systems from the diverse families, often found together in a cell, with significantly different kinetics, can cooperate in a similar manner. Here, we characterize the interaction of toxin-antitoxin systems from many families that are unrelated and kinetically diverse, and identify the essential determinant for their cooperation. The generic architecture of toxin-antitoxin systems provides the potential for bistability, and our results show that even when they do not exhibit bistability alone, unrelated systems can be coupled by the growth rate to create a strongly bistable, hysteretic switch between normal (fast-growing) and persistent (slow-growing) states. Different combinations of kinetic parameters can produce similar toxic switching thresholds, and the proximity of the thresholds is the primary determinant of bistability. Stochastic fluctuations can spontaneously switch all of the toxin-antitoxin systems in a cell at once. The spontaneous switch creates a heterogeneous population of growing and non-growing cells, typical of persisters, that exist under normal conditions, rather than only as an induced response. The frequency of persisters in the population can be tuned for a particular environmental niche by mixing and matching unrelated systems via mutation, horizontal gene transfer and selection.}, }
@article {pmid26063429, year = {2015}, author = {Wang, M and Wang, Y and Sun, X and Cheng, J and Fu, Y and Liu, H and Jiang, D and Ghabrial, SA and Xie, J}, title = {Characterization of a Novel Megabirnavirus from Sclerotinia sclerotiorum Reveals Horizontal Gene Transfer from Single-Stranded RNA Virus to Double-Stranded RNA Virus.}, journal = {Journal of virology}, volume = {89}, number = {16}, pages = {8567-8579}, pmid = {26063429}, issn = {1098-5514}, mesh = {Ascomycota/*virology ; Base Sequence ; Cluster Analysis ; DNA, Complementary/genetics ; Gene Transfer, Horizontal/*genetics ; Microscopy, Electron ; Molecular Sequence Data ; Nucleic Acid Conformation ; Open Reading Frames/genetics ; Phylogeny ; RNA Viruses/*genetics ; RNA, Double-Stranded/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {UNLABELLED: Mycoviruses have been detected in all major groups of filamentous fungi, and their study represents an important branch of virology. Here, we characterized a novel double-stranded RNA (dsRNA) mycovirus, Sclerotinia sclerotiorum megabirnavirus 1 (SsMBV1), in an apparently hypovirulent strain (SX466) of Sclerotinia sclerotiorum. Two similarly sized dsRNA segments (L1- and L2-dsRNA), the genome of SsMBV1, are packaged in rigid spherical particles purified from strain SX466. The full-length cDNA sequence of L1-dsRNA/SsMBV1 comprises two large open reading frames (ORF1 and ORF2), which encode a putative coat protein and an RNA-dependent RNA polymerase (RdRp), respectively. Phylogenetic analysis of the RdRp domain clearly indicates that SsMBV1 is related to Rosellinia necatrix megabirnavirus 1 (RnMBV1). L2-dsRNA/SsMBV1 comprises two nonoverlapping ORFs (ORFA and ORFB) encoding two hypothetical proteins with unknown functions. The 5'-terminal regions of L1- and L2-dsRNA/SsMBV1 share strictly conserved sequences and form stable stem-loop structures. Although L2-dsRNA/SsMBV1 is dispensable for replication, genome packaging, and pathogenicity of SsMBV1, it enhances transcript accumulation of L1-dsRNA/SsMBV1 and stability of virus-like particles (VLPs). Interestingly, a conserved papain-like protease domain similar to a multifunctional protein (p29) of Cryphonectria hypovirus 1 was detected in the ORFA-encoded protein of L2-dsRNA/SsMBV1. Phylogenetic analysis based on the protease domain suggests that horizontal gene transfer may have occurred from a single-stranded RNA (ssRNA) virus (hypovirus) to a dsRNA virus, SsMBV1. Our results reveal that SsMBV1 has a slight impact on the fundamental biological characteristics of its host regardless of the presence or absence of L2-dsRNA/SsMBV1.<br><br>IMPORTANCE: Mycoviruses are widespread in all major fungal groups, and they possess diverse genomes of mostly ssRNA and dsRNA and, recently, circular ssDNA. Here, we have characterized a novel dsRNA virus (Sclerotinia sclerotiorum megabirnavirus 1 [SsMBV1]) that was isolated from an apparently hypovirulent strain, SX466, of Sclerotinia sclerotiorum. Although SsMBV1 is phylogenetically related to RnMBV1, SsMBV1 is markedly distinct from other reported megabirnaviruses with two features of VLPs and conserved domains. Our results convincingly showed that SsMBV1 is viable in the absence of L2-dsRNA/SsMBV1 (a potential large satellite-like RNA or genuine genomic virus component). More interestingly, we detected a conserved papain-like protease domain that commonly exists in ssRNA viruses, including members of the families Potyviridae and Hypoviridae. Phylogenetic analysis based on the protease domain suggests that horizontal gene transfer might have occurred from an ssRNA virus to a dsRNA virus, which may provide new insights into the evolutionary history of dsRNA and ssRNA viruses.}, }
@article {pmid26062812, year = {2016}, author = {Willemsen, I and van Esser, J and Kluytmans-van den Bergh, M and Zhou, K and Rossen, JW and Verhulst, C and Verduin, K and Kluytmans, J}, title = {Retrospective identification of a previously undetected clinical case of OXA-48-producing K. pneumoniae and E. coli: the importance of adequate detection guidelines.}, journal = {Infection}, volume = {44}, number = {1}, pages = {107-110}, pmid = {26062812}, issn = {1439-0973}, mesh = {Bacteriological Techniques/*methods/standards ; Escherichia coli/*enzymology/genetics/isolation &amp; purification ; Escherichia coli Infections/microbiology ; Escherichia coli Proteins/*analysis ; Female ; Gene Transfer, Horizontal ; Genome, Bacterial ; *Guideline Adherence ; Humans ; Klebsiella Infections/microbiology ; Klebsiella pneumoniae/*enzymology/genetics/isolation &amp; purification ; Lymphoma, Non-Hodgkin/complications ; Mass Screening/methods/standards ; Middle Aged ; Netherlands ; Plasmids/analysis ; Sequence Analysis, DNA ; beta-Lactamases/*analysis ; }, abstract = {INTRODUCTION: The laboratory detection of OXA-48-carbapenemase-producing Enterobacteriaceae is difficult, as minimum inhibition concentrations for carbapenems are often below the clinical breakpoint. In 2011, the Dutch national guideline for the detection of highly resistant micro-organisms was issued, which includes recommendations on the use of carbapenem screening breakpoints for the detection of carbapenemase-producing Enterobacteriaceae.<br><br>MATERIALS AND METHODS: During a validation study of the Check-MDR CT103 microarray (Check-Points, Wageningen, The Netherlands) in 2013, an OXA-48-like carbapenemase gen was identified in two isolates that were previously obtained from a patient with non-Hodgkin lymphoma in 2007. Whole-genome sequencing (WGS) and subsequent BLAST Ringe Image Generator (BRIG) analysis were performed to establish the presence of OXA-48 carbapenemase encoding plasmids and their similarity.<br><br>RESULTS: This case report describes the first documented OXA-48-producing Klebsiella pneumonia (ST648) and Escherichia coli (ST866) in the Netherlands. A similar IncL/M plasmid was identified in both strains, suggesting within-patient horizontal transfer.<br><br>CONCLUSION: This case illustrates that OXA-48-carbapenemase-producing Enterobacteriaceae can be unnoticed without adequate laboratory detection procedures. Our observation stresses the importance of uniform and adequate laboratory methods for the timely and accurate detection of important antimicrobial resistance.}, }
@article {pmid26062772, year = {2016}, author = {Bartoli, C and Roux, F and Lamichhane, JR}, title = {Molecular mechanisms underlying the emergence of bacterial pathogens: an ecological perspective.}, journal = {Molecular plant pathology}, volume = {17}, number = {2}, pages = {303-310}, pmid = {26062772}, issn = {1364-3703}, mesh = {Bacteria/*genetics ; Biological Evolution ; *Ecosystem ; Gene Rearrangement/genetics ; Host-Pathogen Interactions/*genetics ; Mutation/genetics ; }, abstract = {The rapid emergence of new bacterial diseases negatively affects both human health and agricultural productivity. Although the molecular mechanisms underlying these disease emergences are shared between human- and plant-pathogenic bacteria, not much effort has been made to date to understand disease emergences caused by plant-pathogenic bacteria. In particular, there is a paucity of information in the literature on the role of environmental habitats in which plant-pathogenic bacteria evolve and on the stress factors to which these microbes are unceasingly exposed. In this microreview, we focus on three molecular mechanisms underlying pathogenicity in bacteria, namely mutations, genomic rearrangements and the acquisition of new DNA sequences through horizontal gene transfer (HGT). We briefly discuss the role of these mechanisms in bacterial disease emergence and elucidate how the environment can influence the occurrence and regulation of these molecular mechanisms by directly impacting disease emergence. The understanding of such molecular evolutionary mechanisms and their environmental drivers will represent an important step towards predicting bacterial disease emergence and developing sustainable management strategies for crops.}, }
@article {pmid26061996, year = {2015}, author = {Chen, Y and Wang, Y and Zhao, T and Yang, J and Feng, S and Nazeer, W and Zhang, T and Zhou, B}, title = {A New Synthetic Amphiploid (AADDAA) between Gossypium hirsutum and G. arboreum Lays the Foundation for Transferring Resistances to Verticillium and Drought.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0128981}, pmid = {26061996}, issn = {1932-6203}, mesh = {*Adaptation, Biological ; Chimera/*genetics/growth &amp; development ; *Disease Resistance ; Droughts ; Gene Transfer, Horizontal ; Genes, Plant ; Gossypium/classification/*genetics/growth &amp; development ; Plant Breeding/*methods ; Plant Diseases/microbiology ; Quantitative Trait Loci ; Self-Fertilization ; Tetraploidy ; Verticillium/physiology ; }, abstract = {Gossypium arboreum, a cultivated cotton species (2n = 26, AA) native to Asia, possesses invaluable characteristics unavailable in the tetraploid cultivated cotton gene pool, such as resistance to pests and diseases and tolerance to abiotic stresses. However, it is quite difficult to transfer favorable traits into Upland cotton through conventional methods due to the cross-incompatibility of G. hirsutum (2n = 52, AADD) and G. arboreum. Here, we improved an embryo rescue technique to overcome the cross-incompatibility between these two parents for transferring favorable genes from G. arboreum into G. hirsutum. Our results indicate that MSB2K supplemented with 0.5 mg l(-1) kinetin and 250 mg(-1) casein hydrolysate is an efficient initial medium for rescuing early (3 d after pollination) hybrid embryos. Eight putative hybrids were successfully obtained, which were further verified and characterized by cytology, molecular markers and morphological analysis. The putative hybrids were subsequently treated with different concentrations of colchicine solution to double their chromosomes. The results demonstrate that four putative hybrid plants were successfully chromosome-doubled by treatment with 0.1% colchicine for 24 h and become amphiploid, which were confirmed by cytological observation, self-fertilization and backcrossing. Preliminary assessments of resistance at seedling stage indicate that the synthetic amphiploid showed highly resistant to Verticillium and drought. The synthetic amphiploid between G. hirsutum × G. arboreum would lay the foundation for developing G. arboreum-introgressed lines with the uniform genetic background of G. hirsutum acc TM-1, which would greatly enhance and simplify the mining, isolation, characterization, cloning and use of G. arboreum-specific desirable genes in future cotton breeding programs.}, }
@article {pmid26060280, year = {2015}, author = {Beabout, K and Hammerstrom, TG and Wang, TT and Bhatty, M and Christie, PJ and Saxer, G and Shamoo, Y}, title = {Rampant Parasexuality Evolves in a Hospital Pathogen during Antibiotic Selection.}, journal = {Molecular biology and evolution}, volume = {32}, number = {10}, pages = {2585-2597}, pmid = {26060280}, issn = {1537-1719}, support = {R01 AI080714/AI/NIAID NIH HHS/United States ; R01 GM048746/GM/NIGMS NIH HHS/United States ; R01 A1080714//PHS HHS/United States ; }, mesh = {ATP-Binding Cassette Transporters/metabolism ; Adaptation, Physiological/drug effects ; Alleles ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/metabolism ; Base Sequence ; Chromosomes, Bacterial/genetics ; Directed Molecular Evolution ; Drug Resistance, Microbial/drug effects/*genetics ; Enterococcus faecalis/drug effects/*genetics ; Gene Dosage ; *Hospitals ; Humans ; Minocycline/analogs &amp; derivatives/pharmacology ; Molecular Sequence Data ; Mutagenesis, Insertional/genetics ; Phenotype ; Regulatory Sequences, Nucleic Acid/genetics ; Ribosomes/drug effects/metabolism ; Sequence Deletion ; Tigecycline ; Treatment Outcome ; }, abstract = {Horizontal gene transfer threatens the therapeutic success of antibiotics by facilitating the rapid dissemination of resistance alleles among bacterial species. The conjugative mobile element Tn916 provides an excellent context for examining the role of adaptive parasexuality as it carries the tetracycline-resistance allele tetM and has been identified in a wide range of pathogens. We have used a combination of experimental evolution and allelic frequency measurements to gain insights into the adaptive trajectories leading to tigecycline resistance in a hospital strain of Enterococcus faecalis and predict what mechanisms of resistance are most likely to appear in the clinical setting. Here, we show that antibiotic selection led to the near fixation of adaptive alleles that simultaneously altered TetM expression and produced remarkably increased levels of Tn916 horizontal gene transfer. In the absence of drug, approximately 1 in 120,000 of the nonadapted E. faecalis S613 cells had an excised copy of Tn916, whereas nearly 1 in 50 cells had an excised copy of Tn916 upon selection for resistance resulting in a more than 1,000-fold increase in conjugation rates. We also show that tigecycline, a translation inhibitor, selected for a mutation in the ribosomal S10 protein. Our results show the first example of mutations that concurrently confer resistance to an antibiotic and lead to constitutive conjugal-transfer of the resistance allele. Selection created a highly parasexual phenotype and high frequency of Tn916 jumping demonstrating how the use of antibiotics can lead directly to the proliferation of resistance in, and potentially among, pathogens.}, }
@article {pmid26057871, year = {2015}, author = {Jheeta, S}, title = {The Routes of Emergence of Life from LUCA during the RNA and Viral World: A Conspectus.}, journal = {Life (Basel, Switzerland)}, volume = {5}, number = {2}, pages = {1445-1453}, pmid = {26057871}, issn = {2075-1729}, abstract = {How did life emerge on Earth? The aim of the Network of Researchers on Horizontal Gene Transfer and the Last Universal Cellular Ancestor (NoR HGT &amp; LUCA) is to understand how the genetics of LUCAs were reorganised prior to the advent of the three domains of life. This paper reports the research of eminent scientists who have come together within the network and are making significant contributions to the wider knowledge base surrounding this, one of science's remaining mysteries. I also report on their relevance in relation to LUCAs and life's origins, as well as ask a question: what next?}, }
@article {pmid26057853, year = {2015}, author = {Chen, M and Guo, Q and Wang, Y and Zou, Y and Wang, G and Zhang, X and Xu, X and Zhao, M and Hu, F and Qu, D and Chen, M and Wang, M}, title = {Shifts in the Antibiotic Susceptibility, Serogroups, and Clonal Complexes of Neisseria meningitidis in Shanghai, China: A Time Trend Analysis of the Pre-Quinolone and Quinolone Eras.}, journal = {PLoS medicine}, volume = {12}, number = {6}, pages = {e1001838; discussion e1001838}, pmid = {26057853}, issn = {1549-1676}, mesh = {Anti-Bacterial Agents/*therapeutic use ; China/epidemiology ; Humans ; Meningitis, Meningococcal/*drug therapy/epidemiology ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Neisseria meningitidis/*drug effects ; Prevalence ; Quinolones/*therapeutic use ; Serogroup ; Urban Health ; }, abstract = {BACKGROUND: Fluoroquinolones have been used broadly since the end of the 1980s and have been recommended for Neisseria meningitidis prophylaxis since 2005 in China. The aim of this study was to determine whether and how N. meningitidis antimicrobial susceptibility, serogroup prevalence, and clonal complex (CC) prevalence shifted in association with the introduction and expanding use of quinolones in Shanghai, a region with a traditionally high incidence of invasive disease due to N. meningitidis.<br><br>METHODS AND FINDINGS: A total of 374 N. meningitidis isolates collected by the Shanghai Municipal Center for Disease Control and Prevention between 1965 and 2013 were studied. Shifts in the serogroups and CCs were observed, from predominantly serogroup A CC5 (84%) in 1965-1973 to serogroup A CC1 (58%) in 1974-1985, then to serogroup C or B CC4821 (62%) in 2005-2013. The rates of ciprofloxacin nonsusceptibility in N. meningitidis disease isolates increased from 0% in 1965-1985 to 84% (31/37) in 2005-2013 (p < 0.001). Among the ciprofloxacin-nonsusceptible isolates, 87% (27/31) were assigned to either CC4821 (n = 20) or CC5 (n = 7). The two predominant ciprofloxacin-resistant clones were designated ChinaCC4821-R1-C/B and ChinaCC5-R14-A. The ChinaCC4821-R1-C/B clone acquired ciprofloxacin resistance by a point mutation, and was present in 52% (16/31) of the ciprofloxacin-nonsusceptible disease isolates. The ChinaCC5-R14-A clone acquired ciprofloxacin resistance by horizontal gene transfer, and was found in 23% (7/31) of the ciprofloxacin-nonsusceptible disease isolates. The ciprofloxacin nonsusceptibility rate was 47% (7/15) among isolates from asymptomatic carriers, and nonsusceptibility was associated with diverse multi-locus sequence typing profiles and pulsed-field gel electrophoresis patterns. As detected after 2005, ciprofloxacin-nonsusceptible strains were shared between some of the patients and their close contacts. A limitation of this study is that isolates from 1986-2004 were not available and that only a small sample of convenience isolates from 1965-1985 were available.<br><br>CONCLUSIONS: The increasing prevalence of ciprofloxacin resistance since 2005 in Shanghai was associated with the spread of hypervirulent lineages CC4821 and CC5. Two resistant meningococcal clones ChinaCC4821-R1-C/B and ChinaCC5-R14-A have emerged in Shanghai during the quinolone era. Ciprofloxacin should be utilized with caution for the chemoprophylaxis of N. meningitidis in China.}, }
@article {pmid26053634, year = {2015}, author = {Shterzer, N and Mizrahi, I}, title = {The animal gut as a melting pot for horizontal gene transfer.}, journal = {Canadian journal of microbiology}, volume = {61}, number = {9}, pages = {603-605}, doi = {10.1139/cjm-2015-0049}, pmid = {26053634}, issn = {1480-3275}, mesh = {Animals ; Bacteria/*genetics ; Biological Evolution ; Gastrointestinal Tract/*microbiology ; *Gene Transfer, Horizontal ; Humans ; }, abstract = {In this minireview, we examine horizontal gene transfer (HGT) events in the mammalian gastrointestinal tract and their role in the evolutionary adaptation of microorganisms to the gut environment. We explore the notion of the mammalian gut as a melting pot of genetic exchange, resulting in the large extent of HGT occurrence.}, }
@article {pmid26051213, year = {2015}, author = {Davis, CC and Xi, Z}, title = {Horizontal gene transfer in parasitic plants.}, journal = {Current opinion in plant biology}, volume = {26}, number = {}, pages = {14-19}, doi = {10.1016/j.pbi.2015.05.008}, pmid = {26051213}, issn = {1879-0356}, mesh = {Gene Transfer, Horizontal/*genetics ; Genome, Mitochondrial/genetics ; Phylogeny ; Plants/*genetics ; Symbiosis/genetics ; }, abstract = {Horizontal gene transfer (HGT) between species has been a major focus of plant evolutionary research during the past decade. Parasitic plants, which establish a direct connection with their hosts, have provided excellent examples of how these transfers are facilitated via the intimacy of this symbiosis. In particular, phylogenetic studies from diverse clades indicate that parasitic plants represent a rich system for studying this phenomenon. Here, HGT has been shown to be astonishingly high in the mitochondrial genome, and appreciable in the nuclear genome. Although explicit tests remain to be performed, some transgenes have been hypothesized to be functional in their recipient species, thus providing a new perspective on the evolution of novelty in parasitic plants.}, }
@article {pmid26048939, year = {2015}, author = {Weigand, MR and Pena-Gonzalez, A and Shirey, TB and Broeker, RG and Ishaq, MK and Konstantinidis, KT and Raphael, BH}, title = {Implications of Genome-Based Discrimination between Clostridium botulinum Group I and Clostridium sporogenes Strains for Bacterial Taxonomy.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {16}, pages = {5420-5429}, pmid = {26048939}, issn = {1098-5336}, mesh = {Chromosomes ; Clostridium/*classification/*genetics ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; Genetic Loci ; *Genome, Bacterial ; Genotype ; Molecular Sequence Data ; Phylogeny ; Plasmids ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {Taxonomic classification of Clostridium botulinum is based on the production of botulinum neurotoxin (BoNT), while closely related, nontoxic organisms are classified as Clostridium sporogenes. However, this taxonomic organization does not accurately mirror phylogenetic relationships between these species. A phylogenetic reconstruction using 2,016 orthologous genes shared among strains of C. botulinum group I and C. sporogenes clearly separated these two species into discrete clades which showed ∼93% average nucleotide identity (ANI) between them. Clustering of strains based on the presence of variable orthologs revealed 143 C. sporogenes clade-specific genetic signatures, a subset of which were further evaluated for their ability to correctly classify a panel of presumptive C. sporogenes strains by PCR. Genome sequencing of several C. sporogenes strains lacking these signatures confirmed that they clustered with C. botulinum strains in a core genome phylogenetic tree. Our analysis also identified C. botulinum strains that contained C. sporogenes clade-specific signatures and phylogenetically clustered with C. sporogenes strains. The genome sequences of two bont/B2-containing strains belonging to the C. sporogenes clade contained regions with similarity to a bont-bearing plasmid (pCLD), while two different strains belonging to the C. botulinum clade carried bont/B2 on the chromosome. These results indicate that bont/B2 was likely acquired by C. sporogenes strains through horizontal gene transfer. The genome-based classification of these species used to identify candidate genes for the development of rapid assays for molecular identification may be applicable to additional bacterial species that are challenging with respect to their classification.}, }
@article {pmid26048929, year = {2015}, author = {Shin, SW and Shin, MK and Jung, M and Belaynehe, KM and Yoo, HS}, title = {Prevalence of Antimicrobial Resistance and Transfer of Tetracycline Resistance Genes in Escherichia coli Isolates from Beef Cattle.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {16}, pages = {5560-5566}, pmid = {26048929}, issn = {1098-5336}, mesh = {Animals ; Cattle ; Conjugation, Genetic ; Escherichia coli/classification/*drug effects/genetics/isolation &amp; purification ; Escherichia coli Infections/microbiology/*veterinary ; Feces/*microbiology ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genotype ; Microbial Sensitivity Tests ; Molecular Typing ; Prevalence ; Red Meat ; Republic of Korea ; Tetracycline Resistance ; }, abstract = {The aim of this study was to investigate the prevalence and transferability of resistance in tetracycline-resistant Escherichia coli isolates recovered from beef cattle in South Korea. A total of 155 E. coli isolates were collected from feces in South Korea, and 146 were confirmed to be resistant to tetracycline. The tetracycline resistance gene tet(A) (46.5%) was the most prevalent, followed by tet(B) (45.1%) and tet(C) (5.8%). Strains carrying tet(A) plus tet(B) and tet(B) plus tet(C) were detected in two isolates each. In terms of phylogenetic grouping, 101 (65.2%) isolates were classified as phylogenetic group B1, followed in decreasing order by D (17.4%), A (14.2%), and B2 (3.2%). Ninety-one (62.3%) isolates were determined to be multidrug resistant by the disk diffusion method. MIC testing using the principal tetracyclines, namely, tetracycline, chlortetracycline, oxytetracycline, doxycycline, and minocycline, revealed that isolates carrying tet(B) had higher MIC values than isolates carrying tet(A). Conjugation assays showed that 121 (82.9%) isolates could transfer a tetracycline resistance gene to a recipient via the IncFIB replicon (65.1%). This study suggests that the high prevalence of tetracycline-resistant E. coli isolates in beef cattle is due to the transferability of tetracycline resistance genes between E. coli populations which have survived the selective pressure caused by the use of antimicrobial agents.}, }
@article {pmid26048565, year = {2015}, author = {Wijayawardena, BK and Minchella, DJ and DeWoody, JA}, title = {Horizontal gene transfer in schistosomes: A critical assessment.}, journal = {Molecular and biochemical parasitology}, volume = {201}, number = {1}, pages = {57-65}, doi = {10.1016/j.molbiopara.2015.05.008}, pmid = {26048565}, issn = {1872-9428}, mesh = {Animals ; Computational Biology ; *Gene Transfer, Horizontal ; *Host-Parasite Interactions ; Phylogeny ; Schistosoma/*genetics ; Sequence Homology ; }, abstract = {Horizontal gene transfer (HGT), the movement of genetic material between distinct evolutionary lineages, has long been known as a principal force of diversification and adaptation of prokaryotes. More recently, genomic and transcriptomic datasets have suggested gene transfers among various eukaryotic taxa (e.g., Porifera, Cnidaria, Nematoda, Arthropoda, Rotifera, Craniata, and Plantae). Although the exact mechanism of eukaryotic HGT is often unknown, host-parasite interactions may provide ample opportunities for HGT. Schistosomes are trematode blood parasites with complex life cycles that have been repeatedly implicated in HGT. We employed molecular, bioinformatic and phylogenetic approaches to critically analyze 13 published reports of direct HGTs between schistosomes and their hosts to better understand host-parasite co-evolution. Our research suggests that reported cases of schistosome-associated HGT may be due to technical artifacts as opposed to biological reality as we were unable to substantiate them. HGT clearly occurs in eukaryotic organisms, but the burden of proof is high and we emphasize the importance of multiple lines of evidence to conclusively document HGT.}, }
@article {pmid26048440, year = {2015}, author = {Fang, LX and Sun, J and Li, L and Deng, H and Huang, T and Yang, QE and Li, X and Chen, MY and Liao, XP and Liu, YH}, title = {Dissemination of the chromosomally encoded CMY-2 cephalosporinase gene in Escherichia coli isolated from animals.}, journal = {International journal of antimicrobial agents}, volume = {46}, number = {2}, pages = {209-213}, doi = {10.1016/j.ijantimicag.2015.04.003}, pmid = {26048440}, issn = {1872-7913}, mesh = {Animals ; Animals, Domestic ; Anti-Bacterial Agents/pharmacology ; Chromosomes, Bacterial ; Conserved Sequence ; Drug Resistance, Multiple, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/classification/drug effects/*enzymology/genetics ; Escherichia coli Infections/microbiology/*veterinary ; Gene Order ; Gene Transfer, Horizontal ; Genes, Bacterial ; Molecular Typing ; Pets ; Plasmids/analysis ; beta-Lactamases/*genetics ; }, abstract = {In this study, 619 individual Escherichia coli isolates from food-producing and companion animals were analysed to determine the prevalence of the cephalosporinase gene blaCMY-2. In total, 18 CMY-2-producers (2.9%) were detected and exhibited multidrug-resistant phenotypes. One of the CMY-2-producers was found to possess a novel blaCMY-2-like allele, blaCMY-130. The isolates belonged to distinct pulsotypes, suggesting that the blaCMY-2 gene was not disseminated by clonal expansion of blaCMY-2-positive strains. The blaCMY-2 genes were located on IncA/C-, IncHI2- or IncX-type plasmids in 9 (50%) of the 18 E. coli isolates. However, in the other nine isolates I-CeuI-PFGE and hybridisation analyses revealed that the blaCMY-2 gene was chromosomally located. A CMY gene-containing region composed of five open reading frames (ORFs) (ISEcp1-blaCMY-2-blc-sugE-ΔencR) was observed in plasmids from eight strains. A CMY gene-containing region composed of ten ORFs was observed in all of the nine chromosomally encoded blaCMY-2 genes, including a putative IS66-like element inserted in this conserved CMY genetic region in three strains. This conserved CMY genetic region was also found to be inserted into the oriVγ (putative gamma origin), part of the IncX plasmid backbone, by a complete transposition unit flanked by 5-bp DRs (direct repeat sequence) in pS62T. These results demonstrate the high prevalence of the chromosomally encoded blaCMY-2 gene in E. coli. This is the first study reporting a chromosomally encoded blaCMY-2 gene in E. coli. Chromosomally encoded blaCMY-2 might be a source of some plasmid-mediated blaCMY-2 genes and this probably facilitates the spread of cephalosporin-resistant strains.}, }
@article {pmid26047569, year = {2015}, author = {Quist, CW and Smant, G and Helder, J}, title = {Evolution of plant parasitism in the phylum Nematoda.}, journal = {Annual review of phytopathology}, volume = {53}, number = {}, pages = {289-310}, doi = {10.1146/annurev-phyto-080614-120057}, pmid = {26047569}, issn = {1545-2107}, mesh = {Animals ; *Biological Evolution ; Crops, Agricultural/parasitology ; DNA, Ribosomal/genetics ; Helminth Proteins/genetics ; Nematoda/classification/genetics/*physiology ; Plants/*parasitology ; Sequence Analysis, DNA ; }, abstract = {Within the species-rich and trophically diverse phylum Nematoda, at least four independent major lineages of plant parasites have evolved, and in at least one of these major lineages plant parasitism arose independently multiple times. Ribosomal DNA data, sequence information from nematode-produced, plant cell wall-modifying enzymes, and the morphology and origin of the style(t), a protrusible piercing device used to penetrate the plant cell wall, all suggest that facultative and obligate plant parasites originate from fungivorous ancestors. Data on the nature and diversification of plant cell wall-modifying enzymes point at multiple horizontal gene transfer events from soil bacteria to bacterivorous nematodes resulting in several distinct lineages of fungal or oomycete-feeding nematodes. Ribosomal DNA frameworks with sequence data from more than 2,700 nematode taxa combined with detailed morphological information allow for explicit hypotheses on the origin of agronomically important plant parasites, such as root-knot, cyst, and lesion nematodes.}, }
@article {pmid26047475, year = {2015}, author = {Kim, JI and Yoon, HS and Yi, G and Kim, HS and Yih, W and Shin, W}, title = {The Plastid Genome of the Cryptomonad Teleaulax amphioxeia.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0129284}, pmid = {26047475}, issn = {1932-6203}, mesh = {Chloroplast Proteins/genetics ; Cryptophyta/*genetics ; DNA, Chloroplast/chemistry/genetics ; DNA, Circular/chemistry/genetics ; Gene Order ; Gene Transfer, Horizontal ; Genes, Chloroplast/*genetics ; Genome, Plastid/*genetics ; Photosynthesis/genetics ; Photosystem I Protein Complex/genetics ; Photosystem II Protein Complex/genetics ; Phylogeny ; Plastids/classification/*genetics ; Sequence Analysis, DNA ; }, abstract = {Teleaulax amphioxeia is a photosynthetic unicellular cryptophyte alga that is distributed throughout marine habitats worldwide. This alga is an important plastid donor to the dinoflagellate Dinophysis caudata through the ciliate Mesodinium rubrum in the marine food web. To better understand the genomic characteristics of T. amphioxeia, we have sequenced and analyzed its plastid genome. The plastid genome sequence of T. amphioxeia is similar to that of Rhodomonas salina, and they share significant synteny. This sequence exhibits less similarity to that of Guillardia theta, the representative plastid genome of photosynthetic cryptophytes. The gene content and order of the three photosynthetic cryptomonad plastid genomes studied is highly conserved. The plastid genome of T. amphioxeia is composed of 129,772 bp and includes 143 protein-coding genes, 2 rRNA operons and 30 tRNA sequences. The DNA polymerase III gene (dnaX) was most likely acquired via lateral gene transfer (LGT) from a firmicute bacterium, identical to what occurred in R. salina. On the other hand, the psbN gene was independently encoded by the plastid genome without a reverse transcriptase gene as an intron. To clarify the phylogenetic relationships of the algae with red-algal derived plastids, phylogenetic analyses of 32 taxa were performed, including three previously sequenced cryptophyte plastid genomes containing 93 protein-coding genes. The stramenopiles were found to have branched out from the Chromista taxa (cryptophytes, haptophytes, and stramenopiles), while the cryptophytes and haptophytes were consistently grouped into sister relationships with high resolution.}, }
@article {pmid26044078, year = {2015}, author = {Garushyants, SK and Kazanov, MD and Gelfand, MS}, title = {Horizontal gene transfer and genome evolution in Methanosarcina.}, journal = {BMC evolutionary biology}, volume = {15}, number = {}, pages = {102}, pmid = {26044078}, issn = {1471-2148}, mesh = {Archaea/classification/genetics ; Bacteria/genetics ; Databases, Genetic ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Archaeal ; Methanosarcina/*genetics ; Operon ; Phylogeny ; }, abstract = {BACKGROUND: Genomes of Methanosarcina spp. are among the largest archaeal genomes. One suggested reason for that is massive horizontal gene transfer (HGT) from bacteria. Genes of bacterial origin may be involved in the central metabolism and solute transport, in particular sugar synthesis, sulfur metabolism, phosphate metabolism, DNA repair, transport of small molecules etc. Horizontally transferred (HT) genes are considered to play the key role in the ability of Methanosarcina spp. to inhabit diverse environments. At the moment, genomes of three Methanosarcina spp. have been sequenced, and while these genomes vary in length and number of protein-coding genes, they all have been shown to accumulate HT genes. However, previous estimates had been made when fewer archaeal genomes were known. Moreover, several Methanosarcinaceae genomes from other genera have been sequenced recently. Here, we revise the census of genes of bacterial origin in Methanosarcinaceae.<br><br>RESULTS: About 5% of Methanosarcina genes have been shown to be horizontally transferred from various bacterial groups to the last common ancestor either of Methanosarcinaceae, or Methanosarcina, or later in the evolution. Simulation of the composition of the NCBI protein non-redundant database for different years demonstrates that the estimates of the HGT rate have decreased drastically since 2002, the year of publication of the first Methanosarcina genome. The phylogenetic distribution of HT gene donors is non-uniform. Most HT genes were transferred from Firmicutes and Proteobacteria, while no HGT events from Actinobacteria to the common ancestor of Methanosarcinaceae were found. About 50% of HT genes are involved in metabolism. Horizontal transfer of transcription factors is not common, while 46% of horizontally transferred genes have demonstrated differential expression in a variety of conditions. HGT of complete operons is relatively infrequent and half of HT genes do not belong to operons.<br><br>CONCLUSIONS: While genes of bacterial origin are still more frequent in Methanosarcinaceae than in other Archaea, most HGT events described earlier as Methanosarcina-specific seem to have occurred before the divergence of Methanosarcinaceae. Genes horizontally transferred from bacteria to archaea neither tend to be transferred with their regulators, nor in long operons.}, }
@article {pmid26042118, year = {2015}, author = {Morozov, SY and Solovyev, AG}, title = {Phylogenetic relationship of some "accessory" helicases of plant positive-stranded RNA viruses: toward understanding the evolution of triple gene block.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {508}, pmid = {26042118}, issn = {1664-302X}, abstract = {Recently, we hypothesized that silencing suppression activity gained by a viral replicative helicase led to the emergence of the second helicase possessing activity of the viral silencing suppressor and/or movement protein (MP). Our hypothesis accounted for the evolutionary origin of the specialized 'triple gene block' (TGB) in plant virus genomes encoding the MPs TGB1, TGB2, and TGB3 required for viral cell-to-cell transport through plasmodesmata. Here, we used public transcriptome databases to identify previously unrecognized viruses. The analysis of novel viral genomes further supported the previously proposed scenario of TGB origin and evolution, which included the following steps. First, the accessory helicase gene could have been acquired by horizontal gene transfer (HGT) presumably occured independently in different virus groups. Second, the TGB2 gene evolved by HGT or autonomization of the C-terminal transmembrane domain found in at least one TGB1 helicase. Third, the TGB3 gene has most likely emerged in the genomic block consisting of the TGB1 and TGB2 genes.}, }
@article {pmid26042098, year = {2015}, author = {Woegerbauer, M and Kuffner, M and Domingues, S and Nielsen, KM}, title = {Involvement of aph(3')-IIa in the formation of mosaic aminoglycoside resistance genes in natural environments.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {442}, pmid = {26042098}, issn = {1664-302X}, abstract = {Intragenic recombination leading to mosaic gene formation is known to alter resistance profiles for particular genes and bacterial species. Few studies have examined to what extent aminoglycoside resistance genes undergo intragenic recombination. We screened the GenBank database for mosaic gene formation in homologs of the aph(3')-IIa (nptII) gene. APH(3')-IIa inactivates important aminoglycoside antibiotics. The gene is widely used as a selectable marker in biotechnology and enters the environment via laboratory discharges and the release of transgenic organisms. Such releases may provide opportunities for recombination in competent environmental bacteria. The retrieved GenBank sequences were grouped in three datasets comprising river water samples, duck pathogens and full-length variants from various bacterial genomes and plasmids. Analysis for recombination in these datasets was performed with the Recombination Detection Program (RDP4), and the Genetic Algorithm for Recombination Detection (GARD). From a total of 89 homologous sequences, 83% showed 99-100% sequence identity with aph(3')-IIa originally described as part of transposon Tn5. Fifty one were unique sequence variants eligible for recombination analysis. Only a single recombination event was identified with high confidence and indicated the involvement of aph(3')-IIa in the formation of a mosaic gene located on a plasmid of environmental origin in the multi-resistant isolate Pseudomonas aeruginosa PA96. The available data suggest that aph(3')-IIa is not an archetypical mosaic gene as the divergence between the described sequence variants and the number of detectable recombination events is low. This is in contrast to the numerous mosaic alleles reported for certain penicillin or tetracycline resistance determinants.}, }
@article {pmid26041051, year = {2015}, author = {Guimarães, L and Soares, S and Trost, E and Blom, J and Ramos, R and Silva, A and Barh, D and Azevedo, V}, title = {Genome informatics and vaccine targets in Corynebacterium urealyticum using two whole genomes, comparative genomics, and reverse vaccinology.}, journal = {BMC genomics}, volume = {16 Suppl 5}, number = {Suppl 5}, pages = {S7}, pmid = {26041051}, issn = {1471-2164}, mesh = {Comparative Genomic Hybridization/*methods ; Computational Biology/*methods ; Corynebacterium/classification/*genetics/pathogenicity ; Corynebacterium Infections/drug therapy/microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Genome, Bacterial/*genetics ; Genomics/methods ; Humans ; Virulence Factors/*genetics ; }, abstract = {BACKGROUND: Corynebacterium urealyticum is an opportunistic pathogen that normally lives on skin and mucous membranes in humans. This high Gram-positive bacteria can cause acute or encrusted cystitis, encrusted pyelitis, and pyelonephritis in immunocompromised patients. The bacteria is multi-drug resistant, and knowledge about the genes that contribute to its virulence is very limited. Two complete genome sequences were used in this comparative genomic study: C. urealyticum DSM 7109 and C. urealyticum DSM 7111.<br><br>RESULTS: We used comparative genomics strategies to compare the two strains, DSM 7109 and DSM 7111, and to analyze their metabolic pathways, genome plasticity, and to predict putative antigenic targets. The genomes of these two strains together encode 2,115 non-redundant coding sequences, 1,823 of which are common to both genomes. We identified 188 strain-specific genes in DSM 7109 and 104 strain-specific genes in DSM 7111. The high number of strain-specific genes may be a result of horizontal gene transfer triggered by the large number of transposons in the genomes of these two strains. Screening for virulence factors revealed the presence of the spaDEF operon that encodes pili forming proteins. Therefore, spaDEF may play a pivotal role in facilitating the adhesion of the pathogen to the host tissue. Application of the reverse vaccinology method revealed 19 putative antigenic proteins that may be used in future studies as candidate drug or vaccine targets.<br><br>CONCLUSIONS: The genome features and the presence of virulence factors in genomic islands in the two strains of C. urealyticum provide insights in the lifestyle of this opportunistic pathogen and may be useful in developing future therapeutic strategies.}, }
@article {pmid26040248, year = {2015}, author = {Álvarez-Canales, G and Arellano-Álvarez, G and González-Domenech, CM and de la Cruz, F and Moya, A and Delaye, L}, title = {Identification of Xenologs and Their Characteristic Low Expression Levels in the Cyanobacterium Synechococcus elongatus.}, journal = {Journal of molecular evolution}, volume = {80}, number = {5-6}, pages = {292-304}, pmid = {26040248}, issn = {1432-1432}, mesh = {Adaptation, Physiological/genetics ; Algorithms ; Bacterial Proteins/*genetics/metabolism ; Chromosome Mapping ; Codon ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Genetic Fitness ; *Genome, Bacterial ; Iron/metabolism ; Molecular Sequence Annotation ; Nitrates/metabolism ; Open Reading Frames ; Oxidation-Reduction ; Synechococcus/*genetics/metabolism ; }, abstract = {Horizontal gene transfer (HGT) is a central process in prokaryotic evolution. Once a gene is introduced into a genome by HGT, its contribution to the fitness of the recipient cell depends in part on its expression level. Here we show that in Synechococcus elongatus PCC 7942, xenologs derived from non-cyanobacterial sources exhibited lower expression levels than native genes in the genome. In accord with our observation, xenolog codon adaptation indexes also displayed relatively low expression values. These results are in agreement with previous reports that suggested the relative neutrality of most xenologs. However, we also demonstrated that some of the xenologs detected participated in cellular functions, including iron starvation acclimation and nitrate reduction, which corroborate the role of HGT in bacterial adaptation. For example, the expression levels of some of the xenologs detected are known to increase under iron-limiting conditions. We interpreted the overall pattern as an indication that there is a selection pressure against high expression levels of xenologs. However, when a xenolog protein product confers a selective advantage, natural selection can further modulate its expression level to meet the requirements of the recipient cell. In addition, we show that ORFans did not exhibit significantly lower expression levels than native genes in the genome, which suggested an origin other than xenology.}, }
@article {pmid26039986, year = {2015}, author = {Wilson, AC and Duncan, RP}, title = {Signatures of host/symbiont genome coevolution in insect nutritional endosymbioses.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {33}, pages = {10255-10261}, pmid = {26039986}, issn = {1091-6490}, mesh = {Amino Acids/chemistry ; Amino Acids, Branched-Chain/chemistry ; Animals ; Bacteria/genetics ; Buchnera/genetics ; Cell Lineage ; Cytoplasm/metabolism ; *Evolution, Molecular ; Gene Expression Profiling ; Gene Transfer, Horizontal ; Genome ; Genome, Bacterial ; Hemiptera/*genetics/*microbiology ; Pantothenic Acid/chemistry ; *Symbiosis ; }, abstract = {The role of symbiosis in bacterial symbiont genome evolution is well understood, yet the ways that symbiosis shapes host genomes or more particularly, host/symbiont genome coevolution in the holobiont is only now being revealed. Here, we identify three coevolutionary signatures that characterize holobiont genomes. The first signature, host/symbiont collaboration, arises when completion of essential pathways requires host/endosymbiont genome complementarity. Metabolic collaboration has evolved numerous times in the pathways of amino acid and vitamin biosynthesis. Here, we highlight collaboration in branched-chain amino acid and pantothenate (vitamin B5) biosynthesis. The second coevolutionary signature is acquisition, referring to the observation that holobiont genomes acquire novel genetic material through various means, including gene duplication, lateral gene transfer from bacteria that are not their current obligate symbionts, and full or partial endosymbiont replacement. The third signature, constraint, introduces the idea that holobiont genome evolution is constrained by the processes governing symbiont genome evolution. In addition, we propose that collaboration is constrained by the expression profile of the cell lineage from which endosymbiont-containing host cells, called bacteriocytes, are derived. In particular, we propose that such differences in bacteriocyte cell lineage may explain differences in patterns of host/endosymbiont metabolic collaboration between the sap-feeding suborders Sternorrhyncha and Auchenorrhynca. Finally, we review recent studies at the frontier of symbiosis research that are applying functional genomic approaches to characterization of the developmental and cellular mechanisms of host/endosymbiont integration, work that heralds a new era in symbiosis research.}, }
@article {pmid26039278, year = {2015}, author = {Khater, S and Mohanty, D}, title = {In silico identification of AMPylating enzymes and study of their divergent evolution.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {10804}, pmid = {26039278}, issn = {2045-2322}, mesh = {Adenosine Monophosphate/*metabolism ; Amino Acid Motifs ; *Biological Evolution ; Conserved Sequence ; Gene Transfer, Horizontal ; Genomic Islands ; Genomics/methods ; Humans ; Markov Chains ; Models, Molecular ; Multigene Family ; Phylogeny ; Protein Conformation ; Protein Interaction Domains and Motifs ; *Protein Processing, Post-Translational ; Substrate Specificity ; Support Vector Machine ; }, abstract = {AMPylation is a novel post-translational modification (PTM) involving covalent attachment of an AMP moiety to threonine/tyrosine side chains of a protein. AMPylating enzymes belonging to three different families, namely Fic/Doc, GS-ATase and DrrA have been experimentally characterized. Involvement of these novel enzymes in a myriad of biological processes makes them interesting candidates for genome-wide search. We have used SVM and HMM to develop a computational protocol for identification of AMPylation domains and their classification into various functional subfamilies catalyzing AMPylation, deAMPylation, phosphorylation and phosphocholine transfer. Our analysis has not only identified novel PTM catalyzing enzymes among unannotated proteins, but has also revealed how this novel enzyme family has evolved to generate functional diversity by subtle changes in sequence/structures of the proteins. Phylogenetic analysis of Fic/Doc has revealed three new isofunctional subfamilies, thus adding to their functional divergence. Also, frequent occurrence of Fic/Doc proteins on highly mobile and unstable genomic islands indicated their evolution via extensive horizontal gene transfers. On the other hand phylogenetic analyses indicate lateral evolution of GS-ATase family and an early duplication event responsible for AMPylation and deAMPylation activity of GS-ATase. Our analysis also reveals molecular basis of substrate specificity of DrrA proteins.}, }
@article {pmid26039067, year = {2015}, author = {Csefalvay, E and Lapkouski, M and Guzanova, A and Csefalvay, L and Baikova, T and Shevelev, I and Bialevich, V and Shamayeva, K and Janscak, P and Kuta Smatanova, I and Panjikar, S and Carey, J and Weiserova, M and Ettrich, R}, title = {Functional coupling of duplex translocation to DNA cleavage in a type I restriction enzyme.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0128700}, pmid = {26039067}, issn = {1932-6203}, mesh = {Adenosine Triphosphate/*chemistry/metabolism ; Crystallography, X-Ray ; DNA Cleavage ; DNA, Bacterial ; Deoxyribonucleases, Type I Site-Specific/*chemistry/genetics/metabolism ; Escherichia coli/*genetics/metabolism ; Escherichia coli Proteins/*chemistry/genetics/metabolism ; Exodeoxyribonuclease V/*chemistry/genetics/metabolism ; Gene Expression ; Models, Molecular ; Mutation ; Nucleic Acid Conformation ; Plasmids/chemistry/metabolism ; Protein Sorting Signals ; Protein Structure, Tertiary ; Protein Subunits/*chemistry/genetics/metabolism ; Signal Transduction ; }, abstract = {Type I restriction-modification enzymes are multifunctional heteromeric complexes with DNA cleavage and ATP-dependent DNA translocation activities located on motor subunit HsdR. Functional coupling of DNA cleavage and translocation is a hallmark of the Type I restriction systems that is consistent with their proposed role in horizontal gene transfer. DNA cleavage occurs at nonspecific sites distant from the cognate recognition sequence, apparently triggered by stalled translocation. The X-ray crystal structure of the complete HsdR subunit from E. coli plasmid R124 suggested that the triggering mechanism involves interdomain contacts mediated by ATP. In the present work, in vivo and in vitro activity assays and crystal structures of three mutants of EcoR124I HsdR designed to probe this mechanism are reported. The results indicate that interdomain engagement via ATP is indeed responsible for signal transmission between the endonuclease and helicase domains of the motor subunit. A previously identified sequence motif that is shared by the RecB nucleases and some Type I endonucleases is implicated in signaling.}, }
@article {pmid26039056, year = {2015}, author = {Matthews, TD and Schmieder, R and Silva, GG and Busch, J and Cassman, N and Dutilh, BE and Green, D and Matlock, B and Heffernan, B and Olsen, GJ and Farris Hanna, L and Schifferli, DM and Maloy, S and Dinsdale, EA and Edwards, RA}, title = {Genomic Comparison of the Closely-Related Salmonella enterica Serovars Enteritidis, Dublin and Gallinarum.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0126883}, pmid = {26039056}, issn = {1932-6203}, support = {R01 GM098736/GM/NIGMS NIH HHS/United States ; }, mesh = {*Genome, Bacterial ; *Mutation ; *Polymorphism, Single Nucleotide ; Salmonella enteritidis/*genetics/*pathogenicity ; *Serogroup ; }, abstract = {The Salmonella enterica serovars Enteritidis, Dublin, and Gallinarum are closely related but differ in virulence and host range. To identify the genetic elements responsible for these differences and to better understand how these serovars are evolving, we sequenced the genomes of Enteritidis strain LK5 and Dublin strain SARB12 and compared these genomes to the publicly available Enteritidis P125109, Dublin CT 02021853 and Dublin SD3246 genome sequences. We also compared the publicly available Gallinarum genome sequences from biotype Gallinarum 287/91 and Pullorum RKS5078. Using bioinformatic approaches, we identified single nucleotide polymorphisms, insertions, deletions, and differences in prophage and pseudogene content between strains belonging to the same serovar. Through our analysis we also identified several prophage cargo genes and pseudogenes that affect virulence and may contribute to a host-specific, systemic lifestyle. These results strongly argue that the Enteritidis, Dublin and Gallinarum serovars of Salmonella enterica evolve by acquiring new genes through horizontal gene transfer, followed by the formation of pseudogenes. The loss of genes necessary for a gastrointestinal lifestyle ultimately leads to a systemic lifestyle and niche exclusion in the host-specific serovars.}, }
@article {pmid26037461, year = {2015}, author = {Feng, Y and Kumar, R and Ravcheev, DA and Zhang, H}, title = {Paracoccus denitrificans possesses two BioR homologs having a role in regulation of biotin metabolism.}, journal = {MicrobiologyOpen}, volume = {4}, number = {4}, pages = {644-659}, pmid = {26037461}, issn = {2045-8827}, mesh = {Agrobacterium tumefaciens/genetics/metabolism ; Artificial Gene Fusion ; Binding Sites ; Biotin/*metabolism ; DNA, Bacterial/metabolism ; Electrophoretic Mobility Shift Assay ; *Gene Expression Regulation, Bacterial ; Genes, Reporter ; Genetic Variation ; Paracoccus denitrificans/*genetics/*metabolism ; Phylogeny ; Promoter Regions, Genetic ; Protein Binding ; Repressor Proteins/*genetics/*metabolism ; Sequence Homology ; beta-Galactosidase/analysis/genetics ; }, abstract = {Recently, we determined that BioR, the GntR family of transcription factor, acts as a repressor for biotin metabolism exclusively distributed in certain species of α-proteobacteria, including the zoonotic agent Brucella melitensis and the plant pathogen Agrobacterium tumefaciens. However, the scenario is unusual in Paracoccus denitrificans, another closely related member of the same phylum α-proteobacteria featuring with denitrification. Not only does it encode two BioR homologs Pden_1431 and Pden_2922 (designated as BioR1 and BioR2, respectively), but also has six predictive BioR-recognizable sites (the two bioR homolog each has one site, whereas the two bio operons (bioBFDAGC and bioYB) each contains two tandem BioR boxes). It raised the possibility that unexpected complexity is present in BioR-mediated biotin regulation. Here we report that this is the case. The identity of the purified BioR proteins (BioR1 and BioR2) was confirmed with LC-QToF-MS. Phylogenetic analyses combined with GC percentage raised a possibility that the bioR2 gene might be acquired by horizontal gene transfer. Gel shift assays revealed that the predicted BioR-binding sites are functional for the two BioR homologs, in much similarity to the scenario seen with the BioR site of A. tumefaciens bioBFDAZ. Using the A. tumefaciens reporter system carrying a plasmid-borne LacZ fusion, we revealed that the two homologs of P. denitrificans BioR are functional repressors for biotin metabolism. As anticipated, not only does the addition of exogenous biotin stimulate efficiently the expression of bioYB operon encoding biotin transport/uptake system BioY, but also inhibits the transcription of the bioBFDAGC operon resembling the de novo biotin synthetic pathway. EMSA-based screening failed to demonstrate that the biotin-related metabolite is involved in BioR-DNA interplay, which is consistent with our former observation with Brucella BioR. Our finding defined a complex regulatory network for biotin metabolism in P. denitrificans by two BioR proteins.}, }
@article {pmid26035711, year = {2015}, author = {Petit, E and Coppi, MV and Hayes, JC and Tolonen, AC and Warnick, T and Latouf, WG and Amisano, D and Biddle, A and Mukherjee, S and Ivanova, N and Lykidis, A and Land, M and Hauser, L and Kyrpides, N and Henrissat, B and Lau, J and Schnell, DJ and Church, GM and Leschine, SB and Blanchard, JL}, title = {Genome and Transcriptome of Clostridium phytofermentans, Catalyst for the Direct Conversion of Plant Feedstocks to Fuels.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0118285}, pmid = {26035711}, issn = {1932-6203}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {Alcohol Dehydrogenase/genetics/metabolism ; Biofuels ; Biological Transport ; Carbohydrate Metabolism/*genetics ; Clostridium/*genetics/*metabolism ; Enzymes/genetics/*metabolism ; Ethanol/metabolism ; Fermentation ; Gene Expression Regulation, Bacterial ; *Genome, Bacterial ; Phylogeny ; Plants/*metabolism ; RNA, Ribosomal, 16S ; Transcriptome ; }, abstract = {Clostridium phytofermentans was isolated from forest soil and is distinguished by its capacity to directly ferment plant cell wall polysaccharides into ethanol as the primary product, suggesting that it possesses unusual catabolic pathways. The objective of the present study was to understand the molecular mechanisms of biomass conversion to ethanol in a single organism, Clostridium phytofermentans, by analyzing its complete genome and transcriptome during growth on plant carbohydrates. The saccharolytic versatility of C. phytofermentans is reflected in a diversity of genes encoding ATP-binding cassette sugar transporters and glycoside hydrolases, many of which may have been acquired through horizontal gene transfer. These genes are frequently organized as operons that may be controlled individually by the many transcriptional regulators identified in the genome. Preferential ethanol production may be due to high levels of expression of multiple ethanol dehydrogenases and additional pathways maximizing ethanol yield. The genome also encodes three different proteinaceous bacterial microcompartments with the capacity to compartmentalize pathways that divert fermentation intermediates to various products. These characteristics make C. phytofermentans an attractive resource for improving the efficiency and speed of biomass conversion to biofuels.}, }
@article {pmid26032716, year = {2015}, author = {Andersson, DI and Jerlström-Hultqvist, J and Näsvall, J}, title = {Evolution of new functions de novo and from preexisting genes.}, journal = {Cold Spring Harbor perspectives in biology}, volume = {7}, number = {6}, pages = {}, pmid = {26032716}, issn = {1943-0264}, mesh = {*Evolution, Molecular ; *Gene Duplication ; }, abstract = {How the enormous structural and functional diversity of new genes and proteins was generated (estimated to be 10(10)-10(12) different proteins in all organisms on earth [Choi I-G, Kim S-H. 2006. Evolution of protein structural classes and protein sequence families. Proc Natl Acad Sci 103: 14056-14061] is a central biological question that has a long and rich history. Extensive work during the last 80 years have shown that new genes that play important roles in lineage-specific phenotypes and adaptation can originate through a multitude of different mechanisms, including duplication, lateral gene transfer, gene fusion/fission, and de novo origination. In this review, we focus on two main processes as generators of new functions: evolution of new genes by duplication and divergence of pre-existing genes and de novo gene origination in which a whole protein-coding gene evolves from a noncoding sequence.}, }
@article {pmid26031909, year = {2015}, author = {Brimacombe, CA and Ding, H and Johnson, JA and Beatty, JT}, title = {Homologues of Genetic Transformation DNA Import Genes Are Required for Rhodobacter capsulatus Gene Transfer Agent Recipient Capability Regulated by the Response Regulator CtrA.}, journal = {Journal of bacteriology}, volume = {197}, number = {16}, pages = {2653-2663}, pmid = {26031909}, issn = {1098-5530}, mesh = {Bacterial Proteins/*genetics/metabolism ; Bacteriophages/genetics ; Computational Biology ; DNA, Bacterial/genetics ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Plasmids/genetics ; Recombinant Proteins/genetics ; Rhodobacter capsulatus/*genetics ; }, abstract = {UNLABELLED: Gene transfer agents (GTAs) morphologically resemble small, double-stranded DNA (dsDNA) bacteriophages; however, their only known role is to package and transfer random pieces of the producing cell genome to recipient cells. The best understood GTA is that of Rhodobacter capsulatus, termed RcGTA. We discovered that homologues of three genes involved in natural transformation in other bacteria, comEC, comF, and comM, are essential for RcGTA-mediated gene acquisition. This paper gives genetic and biochemical evidence that RcGTA-borne DNA entry into cells requires the ComEC and ComF putative DNA transport proteins and genetic evidence that putative cytoplasmic ComM protein of unknown function is required for recipient capability. Furthermore, the master regulator of RcGTA production in <1% of a cell population, CtrA, which is also required for gene acquisition in recipient cells, is expressed in the vast majority of the population. Our results indicate that RcGTA-mediated gene transfer combines key aspects of two bacterial horizontal gene transfer mechanisms, where donor DNA is packaged in transducing phage-like particles and recipient cells take up DNA using natural transformation-related machinery. Both of these differentiated subsets of a culture population, donors and recipients, are dependent on the same response regulator, CtrA.<br><br>IMPORTANCE: Horizontal gene transfer (HGT) is a major driver of bacterial evolution and adaptation to environmental stresses. Traits such as antibiotic resistance or metabolic properties can be transferred between bacteria via HGT; thus, HGT can have a tremendous effect on the fitness of a bacterial population. The three classically described HGT mechanisms are conjugation, transformation, and phage-mediated transduction. More recently, the HGT factor GTA was described, where random pieces of producing cell genome are packaged into phage-like particles that deliver DNA to recipient cells. In this report, we show that transport of DNA borne by the R. capsulatus RcGTA into recipient cells requires key genes previously thought to be specific to natural transformation pathways. These findings indicate that RcGTA combines central aspects of phage-mediated transduction and natural transformation in an efficient, regulated mode of HGT.}, }
@article {pmid26029174, year = {2015}, author = {Yang, C and Lin, F and Li, Q and Li, T and Zhao, J}, title = {Comparative genomics reveals diversified CRISPR-Cas systems of globally distributed Microcystis aeruginosa, a freshwater bloom-forming cyanobacterium.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {394}, pmid = {26029174}, issn = {1664-302X}, abstract = {Microcystis aeruginosa is one of the most common and dominant bloom-forming cyanobacteria in freshwater lakes around the world. Microcystis cells can produce toxic secondary metabolites, such as microcystins, which are harmful to human health. Two M. aeruginosa strains were isolated from two highly eutrophic lakes in China and their genomes were sequenced. Comparative genomic analysis was performed with the 12 other available M. aeruginosa genomes and closely related unicellular cyanobacterium. Each genome of M. aeruginosa containing at least one clustered regularly interspaced short palindromic repeat (CRISPR) locus and total 71 loci were identified, suggesting it is ubiquitous in M. aeruginosa genomes. In addition to the previously reported subtype I-D cas gene sets, three CAS subtypes I-A, III-A and III-B were identified and characterized in this study. Seven types of CRISPR direct repeat have close association with CAS subtype, confirming that different and specific secondary structures of CRISPR repeats are important for the recognition, binding and process of corresponding cas gene sets. Homology search of the CRISPR spacer sequences provides a history of not only resistance to bacteriophages and plasmids known to be associated with M. aeruginosa, but also the ability to target much more exogenous genetic material in the natural environment. These adaptive and heritable defense mechanisms play a vital role in keeping genomic stability and self-maintenance by restriction of horizontal gene transfer. Maintaining genomic stability and modulating genomic plasticity are both important evolutionary strategies for M. aeruginosa in adaptation and survival in various habitats.}, }
@article {pmid26025979, year = {2015}, author = {Doore, SM and Fane, BA}, title = {The Kinetic and Thermodynamic Aftermath of Horizontal Gene Transfer Governs Evolutionary Recovery.}, journal = {Molecular biology and evolution}, volume = {32}, number = {10}, pages = {2571-2584}, doi = {10.1093/molbev/msv130}, pmid = {26025979}, issn = {1537-1719}, mesh = {Amino Acid Sequence ; Bacteriophage phi X 174/genetics/physiology ; *Biological Evolution ; Codon, Terminator/genetics ; Gene Expression Regulation, Viral ; *Gene Transfer, Horizontal ; Genes, Viral ; Kinetics ; Microvirus/genetics/physiology ; Molecular Sequence Data ; Mutation/genetics ; Phenotype ; Phylogeny ; Sequence Alignment ; Temperature ; Thermodynamics ; Viral Proteins/chemistry/metabolism ; Virion/metabolism ; Virus Assembly ; }, abstract = {Shared host cells can serve as melting pots for viral genomes, giving many phylogenies a web-like appearance due to horizontal gene transfer. However, not all virus families exhibit web-like phylogenies. Microviruses form three distinct clades, represented by φX174, G4, and α3. Here, we investigate protein-based barriers to horizontal gene transfer between clades. We transferred gene G, which encodes a structural protein, between φX174 and G4, and monitored the evolutionary recovery of the resulting chimeras. In both cases, particle assembly was the major barrier after gene transfer. The G4φXG chimera displayed a temperature-sensitive assembly defect that could easily be corrected through single mutations that promote productive assembly. Gene transfer in the other direction was more problematic. The initial φXG4G chimera required an exogenous supply of both the φX174 major spike G and DNA pilot H proteins. Elevated DNA pilot protein levels may be required to compensate for off-pathway reactions that may have become thermodynamically and/or kinetically favored when the foreign spike protein was present. After three targeted genetic selections, the foreign spike protein was productively integrated into the φX174 background. The first adaption involved a global decrease in gene expression. This was followed by modifications affecting key protein-protein interactions that govern assembly. Finally, gene expression was re-elevated. Although the first selection suppresses nonproductive reactions, subsequent selections promote productive assembly and ultimately viability. However, viable chimeric strains exhibited reduced fitness compared with wild-type. This chimera's path to recovery may partially explain how unusual recombinant viruses could persist long enough to naturally emerge.}, }
@article {pmid26025898, year = {2015}, author = {Pavan, ME and Pavan, EE and López, NI and Levin, L and Pettinari, MJ}, title = {Living in an Extremely Polluted Environment: Clues from the Genome of Melanin-Producing Aeromonas salmonicida subsp. pectinolytica 34melT.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {15}, pages = {5235-5248}, pmid = {26025898}, issn = {1098-5336}, mesh = {Adaptation, Biological ; Aeromonas salmonicida/*genetics/isolation &amp; purification/metabolism ; Biotransformation ; DNA, Bacterial/*chemistry/*genetics ; Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Melanins/metabolism ; Metabolic Networks and Pathways/*genetics ; Metals, Heavy/toxicity ; Molecular Sequence Data ; Pectins/metabolism ; Rivers/microbiology ; *Sequence Analysis, DNA ; Water Pollution, Chemical ; }, abstract = {Aeromonas salmonicida subsp. pectinolytica 34mel(T) can be considered an extremophile due to the characteristics of the heavily polluted river from which it was isolated. While four subspecies of A. salmonicida are known fish pathogens, 34mel(T) belongs to the only subspecies isolated solely from the environment. Genome analysis revealed a high metabolic versatility, the capability to cope with diverse stress agents, and the lack of several virulence factors found in pathogenic Aeromonas. The most relevant phenotypic characteristics of 34mel(T) are pectin degradation, a distinctive trait of A. salmonicida subsp. pectinolytica, and melanin production. Genes coding for three pectate lyases were detected in a cluster, unique to this microorganism, that contains all genes needed for pectin degradation. Melanin synthesis in 34mel(T) is hypothesized to occur through the homogentisate pathway, as no tyrosinases or laccases were detected and the homogentisate 1,2-dioxygenase gene is inactivated by a transposon insertion, leading to the accumulation of the melanin precursor homogentisate. Comparative genome analysis of other melanogenic Aeromonas strains revealed that this gene was inactivated by transposon insertions or point mutations, indicating that melanin biosynthesis in Aeromonas occurs through the homogentisate pathway. Horizontal gene transfer could have contributed to the adaptation of 34mel(T) to a highly polluted environment, as 13 genomic islands were identified in its genome, some of them containing genes coding for fitness-related traits. Heavy metal resistance genes were also found, along with others associated with oxidative and nitrosative stresses. These characteristics, together with melanin production and the ability to use different substrates, may explain the ability of this microorganism to live in an extremely polluted environment.}, }
@article {pmid26025427, year = {2015}, author = {Gawryluk, RM and Eme, L and Roger, AJ}, title = {Gene fusion, fission, lateral transfer, and loss: Not-so-rare events in the evolution of eukaryotic ATP citrate lyase.}, journal = {Molecular phylogenetics and evolution}, volume = {91}, number = {}, pages = {12-16}, doi = {10.1016/j.ympev.2015.05.010}, pmid = {26025427}, issn = {1095-9513}, mesh = {ATP Citrate (pro-S)-Lyase/classification/*genetics ; Animals ; Eukaryota/enzymology/*genetics ; *Evolution, Molecular ; Gene Deletion ; *Gene Fusion ; *Gene Transfer, Horizontal ; Phylogeny ; }, abstract = {ATP citrate lyase (ACL) is an enzyme critical to the generation of cytosolic acetyl-CoA in eukaryotes. In most studied organisms, ACL activity is conferred in combination by two proteins, ACLA and ACLB (dsACL); however, animals encode a single-subunit ACL (ssACL) - the result of a gene fusion event. Through phylogenetic analyses, we investigated the evolution of ACL in a broad range of eukaryotes, including numerous microbes (protists). We show that the fused form is not restricted to animals, and is instead widely distributed among eukaryotes. Furthermore, ssACL and dsACL are patchily distributed and appear to be mutually exclusive; both types arose early in eukaryotic evolution. Finally, we present several compelling hypotheses of lateral gene transfer and gene loss, along with the secondary gene fission of ssACL in Ascomycota. Collectively, our in-depth analyses suggest that a complex suite of evolutionary events, usually considered rare, has shaped the evolution of ACL in eukaryotes.}, }
@article {pmid26022423, year = {2015}, author = {Li, G and Xu, J and Wu, L and Ren, D and Ye, W and Dong, G and Zhu, L and Zeng, D and Guo, L}, title = {Full genome sequence of Brevibacillus laterosporus strain B9, a biological control strain isolated from Zhejiang, China.}, journal = {Journal of biotechnology}, volume = {207}, number = {}, pages = {77-78}, doi = {10.1016/j.jbiotec.2015.05.011}, pmid = {26022423}, issn = {1873-4863}, mesh = {Brevibacillus/*genetics/*isolation &amp; purification ; China ; Gene Transfer, Horizontal ; Genome Size ; *Genome, Bacterial ; Molecular Sequence Data ; Oryza/growth &amp; development ; Plant Diseases/microbiology/prevention &amp; control ; Sequence Analysis, DNA/*methods ; Soil Microbiology ; }, abstract = {Brevibacillus laterosporus was newly classified from Bacillus laterosporus, which has ability to be used as a biological control agent in crop field. B. laterosporus strain B9 is an aerobic, motile, Gram-positive, spore-forming rod that was isolated from a field of Oryza sativa in Zhejiang, China in 2011. This bacterium has been confirmed to be a strong antagonist against bacterial brown strip of rice caused by Acidovorex avenae subsp. avenae. Here we describe the features of B. laterosporus strain B9, together with the complete genome sequence and its annotation. The 5,272,435bp genome contains 4804 protein-coding genes and 227 RNA-only encoding genes with 2 plasmids.}, }
@article {pmid26020646, year = {2015}, author = {Ravenhall, M and Škunca, N and Lassalle, F and Dessimoz, C}, title = {Inferring horizontal gene transfer.}, journal = {PLoS computational biology}, volume = {11}, number = {5}, pages = {e1004095}, pmid = {26020646}, issn = {1553-7358}, mesh = {Base Composition ; Computational Biology ; Computer Simulation ; DNA, Bacterial/genetics ; Databases, Genetic ; Drug Resistance, Bacterial/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genomics/statistics &amp; numerical data ; Humans ; Models, Genetic ; Models, Statistical ; Phylogeny ; }, abstract = {Horizontal or Lateral Gene Transfer (HGT or LGT) is the transmission of portions of genomic DNA between organisms through a process decoupled from vertical inheritance. In the presence of HGT events, different fragments of the genome are the result of different evolutionary histories. This can therefore complicate the investigations of evolutionary relatedness of lineages and species. Also, as HGT can bring into genomes radically different genotypes from distant lineages, or even new genes bearing new functions, it is a major source of phenotypic innovation and a mechanism of niche adaptation. For example, of particular relevance to human health is the lateral transfer of antibiotic resistance and pathogenicity determinants, leading to the emergence of pathogenic lineages. Computational identification of HGT events relies upon the investigation of sequence composition or evolutionary history of genes. Sequence composition-based ("parametric") methods search for deviations from the genomic average, whereas evolutionary history-based ("phylogenetic") approaches identify genes whose evolutionary history significantly differs from that of the host species. The evaluation and benchmarking of HGT inference methods typically rely upon simulated genomes, for which the true history is known. On real data, different methods tend to infer different HGT events, and as a result it can be difficult to ascertain all but simple and clear-cut HGT events.}, }
@article {pmid26020232, year = {2015}, author = {Savory, F and Leonard, G and Richards, TA}, title = {The role of horizontal gene transfer in the evolution of the oomycetes.}, journal = {PLoS pathogens}, volume = {11}, number = {5}, pages = {e1004805}, pmid = {26020232}, issn = {1553-7374}, mesh = {*Biological Evolution ; *Gene Transfer, Horizontal ; Oomycetes/*genetics/*growth &amp; development ; }, }
@article {pmid26018571, year = {2015}, author = {Wu, B and Buljic, A and Hao, W}, title = {Extensive Horizontal Transfer and Homologous Recombination Generate Highly Chimeric Mitochondrial Genomes in Yeast.}, journal = {Molecular biology and evolution}, volume = {32}, number = {10}, pages = {2559-2570}, doi = {10.1093/molbev/msv127}, pmid = {26018571}, issn = {1537-1719}, mesh = {Base Sequence ; Chimera/*genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Fungal ; *Genome, Mitochondrial ; Homologous Recombination/*genetics ; Introns/genetics ; Molecular Sequence Data ; Phylogeny ; Saccharomyces cerevisiae/*genetics ; Saccharomyces cerevisiae Proteins/genetics ; Sequence Alignment ; }, abstract = {The frequency of horizontal gene transfer (HGT) in mitochondrial DNA varies substantially. In plants, HGT is relatively common, whereas in animals it appears to be quite rare. It is of considerable importance to understand mitochondrial HGT across the major groups of eukaryotes at a genome-wide level, but so far this has been well studied only in plants. In this study, we generated ten new mitochondrial genome sequences and analyzed 40 mitochondrial genomes from the Saccharomycetaceae to assess the magnitude and nature of mitochondrial HGT in yeasts. We provide evidence for extensive, homologous-recombination-mediated, mitochondrial-to-mitochondrial HGT occurring throughout yeast mitochondrial genomes, leading to genomes that are highly chimeric evolutionarily. This HGT has led to substantial intraspecific polymorphism in both sequence content and sequence divergence, which to our knowledge has not been previously documented in any mitochondrial genome. The unexpectedly high frequency of mitochondrial HGT in yeast may be driven by frequent mitochondrial fusion, relatively low mitochondrial substitution rates and pseudohyphal fusion to produce heterokaryons. These findings suggest that mitochondrial HGT may play an important role in genome evolution of a much broader spectrum of eukaryotes than previously appreciated and that there is a critical need to systematically study the frequency, extent, and importance of mitochondrial HGT across eukaryotes.}, }
@article {pmid26018138, year = {2015}, author = {Baktavachalam, GB and Delaney, B and Fisher, TL and Ladics, GS and Layton, RJ and Locke, ME and Schmidt, J and Anderson, JA and Weber, NN and Herman, RA and Evans, SL}, title = {Transgenic maize event TC1507: Global status of food, feed, and environmental safety.}, journal = {GM crops &amp; food}, volume = {6}, number = {2}, pages = {80-102}, pmid = {26018138}, issn = {2164-5701}, mesh = {Animal Feed/adverse effects ; Animals ; Consumer Product Safety ; Food Safety ; Humans ; Plants, Genetically Modified/*adverse effects ; Risk Assessment ; United States ; Zea mays/*genetics ; }, abstract = {Maize (Zea mays) is a widely cultivated cereal that has been safely consumed by humans and animals for centuries. Transgenic or genetically engineered insect-resistant and herbicide-tolerant maize, are commercially grown on a broad scale. Event TC1507 (OECD unique identifier: DAS-Ø15Ø7-1) or the Herculex®(#) I trait, an insect-resistant and herbicide-tolerant maize expressing Cry1F and PAT proteins, has been registered for commercial cultivation in the US since 2001. A science-based safety assessment was conducted on TC1507 prior to commercialization. The safety assessment addressed allergenicity; acute oral toxicity; subchronic toxicity; substantial equivalence with conventional comparators, as well as environmental impact. Results from biochemical, physicochemical, and in silico investigations supported the conclusion that Cry1F and PAT proteins are unlikely to be either allergenic or toxic to humans. Also, findings from toxicological and animal feeding studies supported that maize with TC1507 is as safe and nutritious as conventional maize. Maize with TC1507 is not expected to behave differently than conventional maize in terms of its potential for invasiveness, gene flow to wild and weedy relatives, or impact on non-target organisms. These safety conclusions regarding TC1507 were acknowledged by over 20 regulatory agencies including United States Environment Protection Agency (US EPA), US Department of Agriculture (USDA), Canadian Food Inspection Agency (CFIA), and European Food Safety Authority (EFSA) before authorizing cultivation and/or food and feed uses. A comprehensive review of the safety studies on TC1507, as well as some benefits, are presented here to serve as a reference for regulatory agencies and decision makers in other countries where authorization of TC1507 is or will be pursued.}, }
@article {pmid26016604, year = {2015}, author = {Culyba, MJ and Mo, CY and Kohli, RM}, title = {Targets for Combating the Evolution of Acquired Antibiotic Resistance.}, journal = {Biochemistry}, volume = {54}, number = {23}, pages = {3573-3582}, pmid = {26016604}, issn = {1520-4995}, support = {T32 GM007229/GM/NIGMS NIH HHS/United States ; T32 AR007442/AR/NIAMS NIH HHS/United States ; T32 GM7229/GM/NIGMS NIH HHS/United States ; 2012071/DDCF_/Doris Duke Charitable Foundation/United States ; DP2 GM105444/GM/NIGMS NIH HHS/United States ; DP2-GM105444/DP/NCCDPHP CDC HHS/United States ; }, mesh = {Anti-Bacterial Agents/*pharmacology/therapeutic use ; *Drug Resistance, Bacterial/drug effects ; *Evolution, Molecular ; Gene Transfer, Horizontal/drug effects ; Gram-Negative Bacteria/*drug effects/genetics/growth &amp; development/metabolism ; Gram-Positive Bacteria/*drug effects/genetics/growth &amp; development/metabolism ; Humans ; *Models, Genetic ; Mutagenesis/drug effects ; SOS Response, Genetics/*drug effects ; }, abstract = {Bacteria possess a remarkable ability to rapidly adapt and evolve in response to antibiotics. Acquired antibiotic resistance can arise by multiple mechanisms but commonly involves altering the target site of the drug, enzymatically inactivating the drug, or preventing the drug from accessing its target. These mechanisms involve new genetic changes in the pathogen leading to heritable resistance. This recognition underscores the importance of understanding how such genetic changes can arise. Here, we review recent advances in our understanding of the processes that contribute to the evolution of antibiotic resistance, with a particular focus on hypermutation mediated by the SOS pathway and horizontal gene transfer. We explore the molecular mechanisms involved in acquired resistance and discuss their viability as potential targets. We propose that additional studies into these adaptive mechanisms not only can provide insights into evolution but also can offer a strategy for potentiating our current antibiotic arsenal.}, }
@article {pmid26015502, year = {2015}, author = {Thoma, L and Dobrowinski, H and Finger, C and Guezguez, J and Linke, D and Sepulveda, E and Muth, G}, title = {A Multiprotein DNA Translocation Complex Directs Intramycelial Plasmid Spreading during Streptomyces Conjugation.}, journal = {mBio}, volume = {6}, number = {3}, pages = {e02559-14}, pmid = {26015502}, issn = {2150-7511}, mesh = {Biological Transport ; *Conjugation, Genetic ; DNA, Bacterial/*metabolism ; Gene Deletion ; Multiprotein Complexes/*metabolism ; Plasmids/*metabolism ; Protein Binding ; Protein Interaction Mapping ; Protein Multimerization ; Streptomyces/genetics/*metabolism ; Two-Hybrid System Techniques ; }, abstract = {UNLABELLED: Conjugative DNA transfer in mycelial Streptomyces is a unique process involving the transfer of a double-stranded plasmid from the donor into the recipient and the subsequent spreading of the transferred plasmid within the recipient mycelium. This process is associated with growth retardation of the recipient and manifested by the formation of circular inhibition zones, named pocks. To characterize the unique Streptomyces DNA transfer machinery, we replaced each gene of the conjugative 12.1-kbp Streptomyces venezuelae plasmid pSVH1, with the exception of the rep gene required for plasmid replication, with a hexanucleotide sequence. Only deletion of traB, encoding the FtsK-like DNA translocase, affected efficiency of the transfer dramatically and abolished pock formation. Deletion of spdB3, spd79, or spdB2 had a minor effect on transfer but prevented pock formation and intramycelial plasmid spreading. Biochemical characterization of the encoded proteins revealed that the GntR-type regulator TraR recognizes a specific sequence upstream of spdB3, while Orf108, SpdB2, and TraR bind to peptidoglycan. SpdB2 promoted spheroplast formation by T7 lysozyme and formed pores in artificial membranes. Bacterial two-hybrid analyses and chemical cross-linking revealed that most of the pSVH1-encoded proteins interacted with each other, suggesting a multiprotein DNA translocation complex of TraB and Spd proteins which directs intramycelial plasmid spreading.<br><br>IMPORTANCE: Mycelial soil bacteria of the genus Streptomyces evolved specific resistance genes as part of the biosynthetic gene clusters to protect themselves from their own antibiotic, making streptomycetes a huge natural reservoir of antibiotic resistance genes for dissemination by horizontal gene transfer. Streptomyces conjugation is a unique process, visible on agar plates with the mere eye by the formation of circular inhibition zones, called pocks. To understand the Streptomyces conjugative DNA transfer machinery, which does not involve a type IV secretion system (T4SS), we made a thorough investigation of almost all genes/proteins of the model plasmid pSVH1. We identified all genes involved in transfer and intramycelial plasmid spreading and showed that the FtsK-like DNA translocase TraB interacts with multiple plasmid-encoded proteins. Our results suggest the existence of a macromolecular DNA translocation complex that directs intramycelial plasmid spreading.}, }
@article {pmid26013486, year = {2015}, author = {Leonetti, CT and Hamada, MA and Laurer, SJ and Broulidakis, MP and Swerdlow, KJ and Lee, CA and Grossman, AD and Berkmen, MB}, title = {Critical Components of the Conjugation Machinery of the Integrative and Conjugative Element ICEBs1 of Bacillus subtilis.}, journal = {Journal of bacteriology}, volume = {197}, number = {15}, pages = {2558-2567}, pmid = {26013486}, issn = {1098-5530}, support = {R01 GM050895/GM/NIGMS NIH HHS/United States ; R01GM50895/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacillus subtilis/*metabolism ; Bacterial Proteins/genetics/*metabolism ; Conjugation, Genetic/*physiology ; Gene Expression Regulation, Bacterial/physiology ; Gene Transfer, Horizontal ; Plasmids ; }, abstract = {UNLABELLED: Conjugation, or mating, plays a profound role in bacterial evolution by spreading genes that allow bacteria to adapt to and colonize new niches. ICEBs1, an integrative and conjugative element of Bacillus subtilis, can transfer itself and mobilize resident plasmids. DNA transfer is mediated by a type IV secretion system (T4SS). Characterized components of the ICEBs1 T4SS include the conserved VirB4-like ATPase ConE, the bifunctional cell wall hydrolase CwlT, and the presumed VirD4-like coupling protein ConQ. A fusion of ConE to green fluorescent protein (GFP) localizes to the membrane preferentially at the cell poles. One or more ICEBs1 proteins are required for ConE's localization at the membrane, as ConE lacks predicted transmembrane segments and ConE-GFP is found dispersed throughout the cytoplasm in cells lacking ICEBs1. Here, we analyzed five ICEBs1 genes to determine if they are required for DNA transfer and/or ConE-GFP localization. We found that conB, conC, conD, and conG, but not yddF, are required for both ICEBs1 transfer and plasmid mobilization. All four required genes encode predicted integral membrane proteins. conB and, to some extent, conD were required for localization of ConE-GFP to the membrane. Using an adenylate cyclase-based bacterial two-hybrid system, we found that ConE interacts with ConB. We propose a model in which the ICEBs1 conjugation machinery is composed of ConB, ConC, ConD, ConE, ConG, CwlT, ConQ, and possibly other ICEBs1 proteins, and that ConB interacts with ConE, helping to recruit and/or maintain ConE at the membrane.<br><br>IMPORTANCE: Conjugation is a major form of horizontal gene transfer and has played a profound role in bacterial evolution by moving genes, including those involved in antibiotic resistance, metabolism, symbiosis, and infectious disease. During conjugation, DNA is transferred from cell to cell through the conjugation machinery, a type of secretion system. Relatively little is known about the conjugation machinery of Gram-positive bacteria. Here, we analyzed five genes of the integrative and conjugative element ICEBs1 of Bacillus subtilis. Our research identifies four new components of the ICEBs1 conjugation machinery (ConB, ConC, ConD, and ConG) and shows an interaction between ConB and ConE that is required for ConE to associate with the cell membrane.}, }
@article {pmid26004171, year = {2015}, author = {Hammoudi, D and Moubareck, CA and Hakime, N and Houmani, M and Barakat, A and Najjar, Z and Suleiman, M and Fayad, N and Sarraf, R and Sarkis, DK}, title = {Spread of imipenem-resistant Acinetobacter baumannii co-expressing OXA-23 and GES-11 carbapenemases in Lebanon.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {36}, number = {}, pages = {56-61}, doi = {10.1016/j.ijid.2015.05.015}, pmid = {26004171}, issn = {1878-3511}, mesh = {Acinetobacter baumannii/*drug effects/enzymology/genetics/isolation &amp; purification ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/*genetics ; Cloxacillin/pharmacology ; Drug Resistance, Bacterial ; Humans ; Imipenem/*pharmacology ; Lebanon ; Polymerase Chain Reaction ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: The acquisition of carbapenemases by Acinetobacter baumannii is reported increasingly worldwide, but data from Lebanon are limited. The aims of this study were to evaluate the prevalence of imipenem-resistant A. baumannii in Lebanon, identify resistance determinants, and detect clonal relatedness.<br><br>METHODS: Imipenem-resistant A. baumannii were collected from nine Lebanese hospitals during 2012. Antimicrobial susceptibility, the cloxacillin effect, and ethylenediaminetetraacetic acid (EDTA) synergy were determined. Genes encoding carbapenemases and insertion sequence ISAba1 were screened via PCR sequencing. ISAba1 position relative to genes encoding Acinetobacter-derived cephalosporinases (ADCs) and OXA-23 was studied by PCR mapping. Clonal linkage was examined by enterobacterial repetitive intergenic consensus PCR (ERIC-PCR).<br><br>RESULTS: Out of 724 A. baumannii isolated in 2012, 638 (88%) were imipenem-resistant. Of these, 142 were analyzed. Clavulanic acid-imipenem synergy suggested carbapenem-hydrolyzing extended-spectrum &#x3b2;-lactamase. A positive cloxacillin test indicated ADCs, while EDTA detection strips were negative. Genotyping indicated that 90% of isolates co-harbored blaOXA-23 and blaGES-11. The remaining strains had blaOXA-23, blaOXA-24, blaGES-11, or blaOXA-24 with blaGES-11. ISAba1 was located upstream of blaADC and blaOXA-23 in 97% and 100% of isolates, respectively. ERIC-PCR fingerprinting revealed 18 pulsotypes spread via horizontal gene transfer and clonal dissemination.<br><br>CONCLUSION: This survey established baseline evidence of OXA-23 and GES-11-producing A. baumannii in Lebanon, indicating the need for further surveillance.}, }
@article {pmid26003279, year = {2015}, author = {Andersson, DI}, title = {Improving predictions of the risk of resistance development against new and old antibiotics.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {21}, number = {10}, pages = {894-898}, doi = {10.1016/j.cmi.2015.05.012}, pmid = {26003279}, issn = {1469-0691}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects ; Drug Discovery/*methods ; *Drug Resistance, Bacterial ; Risk Assessment ; }, abstract = {The methods used today by academic researchers and the pharmaceutical industry to assess the risk of emergence of resistance, for example during development of new antibiotics or when assessing an old antibiotic, are sub-optimal. Even though easy to perform, the presently used serial passage procedures, minimal prevention concentration measurements and determination of mutation rates in vitro are generally providing inadequate knowledge for risk assessment and making decisions to continue/discontinue drug development. These methods need to be complemented and replaced with more relevant methods such as determination of whether resistance genes already pre-exist in various metagenomes, and the likelihood that these genes can transfer into the relevant pathogens and be stably maintained. Furthermore, to determine the risk of emergence of mutationally conferred resistance the fitness effect of the resistance mechanism is key, as this parameter will determine the ability of the resistant mutants to be maintained and enriched in the host after they have emerged. This information combined with knowledge of bacterial population sizes and growth and killing dynamics at relevant infection sites should allow for better forecasting of the risk of resistance emerging in clinical settings.}, }
@article {pmid26000655, year = {2015}, author = {Zhao, WH and Hu, ZQ}, title = {Acquired metallo-β-lactamases and their genetic association with class 1 integrons and ISCR elements in Gram-negative bacteria.}, journal = {Future microbiology}, volume = {10}, number = {5}, pages = {873-887}, doi = {10.2217/fmb.15.18}, pmid = {26000655}, issn = {1746-0921}, mesh = {Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Gram-Negative Bacteria/drug effects/*genetics ; *Interspersed Repetitive Sequences ; beta-Lactamases/*genetics ; }, abstract = {Metallo-β-lactamases (MBLs) can hydrolyze almost all β-lactam antibiotics and are resistant to clinically available β-lactamase inhibitors. Numerous types of acquired MBLs have been identified, including IMP, VIM, NDM, SPM, GIM, SIM, DIM, KHM, TMB, FIM and AIM. IMPs and VIMs are the most frequent MBLs and disseminate in members of the family Enterobacteriaceae, Pseudomonas spp. and Acinetobacter spp. Acquired MBL genes are often embedded in integrons, and some are associated with insertion sequence (IS) elements. The class 1 integrons and IS common region (ISCR) elements are usually harbored in transposons and/or plasmids, forming so-called mobile vesicles for horizontal transfer of captured genes between bacteria. Here, we review the MBL superfamily identified in Gram-negative bacteria, with an emphasis on the phylogeny of acquired MBLs and their genetic association with class 1 integrons and IS common region elements.}, }
@article {pmid25997110, year = {2015}, author = {Papke, RT and Corral, P and Ram-Mohan, N and de la Haba, RR and Sánchez-Porro, C and Makkay, A and Ventosa, A}, title = {Horizontal gene transfer, dispersal and haloarchaeal speciation.}, journal = {Life (Basel, Switzerland)}, volume = {5}, number = {2}, pages = {1405-1426}, pmid = {25997110}, issn = {2075-1729}, abstract = {The Halobacteria are a well-studied archaeal class and numerous investigations are showing how their diversity is distributed amongst genomes and geographic locations. Evidence indicates that recombination between species continuously facilitates the arrival of new genes, and within species, it is frequent enough to spread acquired genes amongst all individuals in the population. To create permanent independent diversity and generate new species, barriers to recombination are probably required. The data support an interpretation that rates of evolution (e.g., horizontal gene transfer and mutation) are faster at creating geographically localized variation than dispersal and invasion are at homogenizing genetic differences between locations. Therefore, we suggest that recurrent episodes of dispersal followed by variable periods of endemism break the homogenizing forces of intrapopulation recombination and that this process might be the principal stimulus leading to divergence and speciation in Halobacteria.}, }
@article {pmid25997086, year = {2014}, author = {Seshasayee, AS}, title = {Gene expression homeostasis and chromosome architecture.}, journal = {Bioarchitecture}, volume = {4}, number = {6}, pages = {221-225}, pmid = {25997086}, issn = {1949-100X}, mesh = {Bacterial Proteins/*genetics/metabolism ; *Chromosomes, Bacterial ; DNA-Binding Proteins/genetics/metabolism ; Directed Molecular Evolution ; Escherichia coli/*genetics ; *Gene Expression Regulation, Bacterial ; Gene Silencing ; Gene Transfer Techniques ; Homeostasis ; Transcription Factors/genetics/metabolism ; Transcription, Genetic ; }, abstract = {In rapidly growing populations of bacterial cells, including those of the model organism Escherichia coli, genes essential for growth--such as those involved in protein synthesis--are expressed at high levels; this is in contrast to many horizontally-acquired genes, which are maintained at low transcriptional levels. (1) This balance in gene expression states between 2 distinct classes of genes is established by a galaxy of transcriptional regulators, including the so-called nucleoid associated proteins (NAP) that contribute to shaping the chromosome. (2) Besides these active players in gene regulation, it is not too far-fetched to anticipate that genome organization in terms of how genes are arranged on the chromosome, (3) which is the result of long-drawn transactions among genome rearrangement processes and selection, and the manner in which it is structured inside the cell, plays a role in establishing this balance. A recent study from our group has contributed to the literature investigating the interplay between global transcriptional regulators and genome organization in establishing gene expression homeostasis. (4) In particular, we address a triangle of functional interactions among genome organization, gene expression homeostasis and horizontal gene transfer.}, }
@article {pmid25994183, year = {2015}, author = {Labeeuw, L and Martone, PT and Boucher, Y and Case, RJ}, title = {Ancient origin of the biosynthesis of lignin precursors.}, journal = {Biology direct}, volume = {10}, number = {}, pages = {23}, pmid = {25994183}, issn = {1745-6150}, mesh = {Alcohols/chemistry ; Aldehyde Oxidoreductases/metabolism ; Arabidopsis/genetics ; Biological Evolution ; Chlamydomonas/*genetics ; Chlorella/*genetics ; Computational Biology ; Dinoflagellida/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Haptophyta/genetics ; Lignin/*biosynthesis ; Likelihood Functions ; Photosynthesis ; Phylogeny ; Selaginellaceae/genetics ; }, abstract = {BACKGROUND: Lignin plays an important role in plant structural support and water transport, and is considered one of the hallmarks of land plants. The recent discovery of lignin or its precursors in various algae has raised questions on the evolution of its biosynthetic pathway, which could be much more ancient than previously thought. To determine the taxonomic distribution of the lignin biosynthesis genes, we screened all publicly available genomes of algae and their closest non-photosynthetic relatives, as well as representative land plants. We also performed phylogenetic analysis of these genes to decipher the evolution and origin(s) of lignin biosynthesis.<br><br>RESULTS: Enzymes involved in making p-coumaryl alcohol, the simplest lignin monomer, are found in a variety of photosynthetic eukaryotes, including diatoms, dinoflagellates, haptophytes, cryptophytes as well as green and red algae. Phylogenetic analysis of these enzymes suggests that they are ancient and spread to some secondarily photosynthetic lineages when they acquired red and/or green algal endosymbionts. In some cases, one or more of these enzymes was likely acquired through lateral gene transfer (LGT) from bacteria.<br><br>CONCLUSIONS: Genes associated with p-coumaryl alcohol biosynthesis are likely to have evolved long before the transition of photosynthetic eukaryotes to land. The original function of this lignin precursor is therefore unlikely to have been related to water transport. We suggest that it participates in the biological defense of some unicellular and multicellular algae.}, }
@article {pmid25991925, year = {2015}, author = {Kwak, MJ and Kwon, SK and Cho, SH and Kim, JF}, title = {Genome sequences of the Shiga-like toxin-producing Escherichia coli NCCP15655 and NCCP15656.}, journal = {Gut pathogens}, volume = {7}, number = {}, pages = {13}, pmid = {25991925}, issn = {1757-4749}, abstract = {BACKGROUND: Virulence genes can spread among commensal bacteria through horizontal gene transfer. The bacterium with novel virulence factors may pose a severe threat to public health because of the absence of a management system unlike known pathogens. Especially, when a pathogenic bacterium acquires a new kind of virulence genes, it tends to exhibit stronger virulence. In this study, we analyzed the genomes of the two strains of Escherichia coli that were isolated from the feces of patients with diarrhea and produce Shiga-like toxin.<br><br>RESULTS: Phylogenetic analysis of conserved genes and average nucleotide identity values of the draft genome sequences indicate that strains NCCP15655 and NCCP15656, isolated from diarrhea patients, belong to the B1 group of E. coli and form a sister clade with strain E24377A. However, the proportion the genes belonging to the subsystem category "phages, prophages, transposable elements, plasmids" and "virulence, disease and defense" are higher than E24377A. Indeed, in their genomes, genes encoding Shiga toxin type 1, Shiga toxin type 2, and type 1 fimbriae were detected. Moreover, a plasmid encoding hemolysin and entropathogenic E. coli secreted protein C was identified in both genomes.<br><br>CONCLUSIONS: Through the genome analysis of NCCP15655 and NCCP15656, we identified two types of Shiga-like toxin genes that could be responsible for the manifestation of the diarrhea symptom. However, the LEE island, which is one of the major virulence factors of enterohemorrhagic E. coli, was not detected and they are most similar with non-Shiga-like toxin-producing E. coli at the genomic level. NCCP15655 and NCCP15656 will be good examples of Shiga-like toxin-producing E. coli whose genomes are not as similar with typical enterohemorrhagic E. coli as non-Shiga-like toxin-producing E. coli.}, }
@article {pmid25991681, year = {2015}, author = {Clark, IC and Melnyk, RA and Youngblut, MD and Carlson, HK and Iavarone, AT and Coates, JD}, title = {Synthetic and Evolutionary Construction of a Chlorate-Reducing Shewanella oneidensis MR-1.}, journal = {mBio}, volume = {6}, number = {3}, pages = {e00282-15}, pmid = {25991681}, issn = {2150-7511}, support = {S10 RR027303/RR/NCRR NIH HHS/United States ; S10 RR029668/RR/NCRR NIH HHS/United States ; S10RR027303.418/RR/NCRR NIH HHS/United States ; S10RR029668/RR/NCRR NIH HHS/United States ; }, mesh = {Bacterial Proteins/*genetics ; Chlorates/*metabolism ; *DNA Transposable Elements ; Evolution, Molecular ; Gene Deletion ; Gene Dosage ; Gene Expression Regulation, Bacterial ; *Genes, Bacterial ; Mutagenesis, Insertional ; Nitrates/metabolism ; Oxidation-Reduction ; Oxidoreductases/genetics ; Polymorphism, Single Nucleotide ; Shewanella/*genetics/*metabolism ; Transcription, Genetic ; }, abstract = {UNLABELLED: Despite evidence for the prevalence of horizontal gene transfer of respiratory genes, little is known about how pathways functionally integrate within new hosts. One example of a mobile respiratory metabolism is bacterial chlorate reduction, which is frequently encoded on composite transposons. This implies that the essential components of the metabolism are encoded on these mobile elements. To test this, we heterologously expressed genes for chlorate reduction from Shewanella algae ACDC in the non-chlorate-reducing Shewanella oneidensis MR-1. The construct that ultimately endowed robust growth on chlorate included cld, a cytochrome c gene, clrABDC, and two genes of unknown function. Although strain MR-1 was unable to grow on chlorate after initial insertion of these genes into the chromosome, 11 derived strains capable of chlorate respiration were obtained through adaptive evolution. Genome resequencing indicated that all of the evolved chlorate-reducing strains replicated a large genomic region containing chlorate reduction genes. Contraction in copy number and loss of the ability to reduce chlorate were also observed, indicating that this phenomenon was extremely dynamic. Although most strains contained more than six copies of the replicated region, a single strain with less duplication also grew rapidly. This strain contained three additional mutations that we hypothesized compensated for the low copy number. We remade the mutations combinatorially in the unevolved strain and determined that a single nucleotide polymorphism (SNP) upstream of cld enabled growth on chlorate and was epistatic to a second base pair change in the NarP binding sequence between narQP and nrfA that enhanced growth.<br><br>IMPORTANCE: The ability of chlorate reduction composite transposons to form functional metabolisms after transfer to a new host is an important part of their propagation. To study this phenomenon, we engineered Shewanella oneidensis MR-1 into a chlorate reducer. We defined a set of genes sufficient to endow growth on chlorate from a plasmid, but found that chromosomal insertion of these genes was nonfunctional. Evolution of this inoperative strain into a chlorate reducer showed that tandem duplication was a dominant mechanism of activation. While copy number changes are a relatively rapid way of increasing gene dosage, replicating almost 1 megabase of extra DNA is costly. Mutations that alleviate the need for high copy number are expected to arise and eventually predominate, and we identified a single nucleotide polymorphism (SNP) that relieved the copy number requirement. This study uses both rational and evolutionary approaches to gain insight into the evolution of a fascinating respiratory metabolism.}, }
@article {pmid25989702, year = {2015}, author = {Park, S and Grewe, F and Zhu, A and Ruhlman, TA and Sabir, J and Mower, JP and Jansen, RK}, title = {Dynamic evolution of Geranium mitochondrial genomes through multiple horizontal and intracellular gene transfers.}, journal = {The New phytologist}, volume = {208}, number = {2}, pages = {570-583}, doi = {10.1111/nph.13467}, pmid = {25989702}, issn = {1469-8137}, mesh = {Base Sequence ; DNA, Mitochondrial/genetics ; DNA, Plant/genetics ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Gene Conversion ; *Gene Transfer, Horizontal ; *Genes, Plant ; *Genome, Mitochondrial ; *Genome, Plant ; Geranium/*genetics ; Intracellular Space/*genetics ; Introns/genetics ; Molecular Sequence Data ; Phylogeny ; Time Factors ; }, abstract = {The exchange of genetic material between cellular organelles through intracellular gene transfer (IGT) or between species by horizontal gene transfer (HGT) has played an important role in plant mitochondrial genome evolution. The mitochondrial genomes of Geraniaceae display a number of unusual phenomena including highly accelerated rates of synonymous substitutions, extensive gene loss and reduction in RNA editing. Mitochondrial DNA sequences assembled for 17 species of Geranium revealed substantial reduction in gene and intron content relative to the ancestor of the Geranium lineage. Comparative analyses of nuclear transcriptome data suggest that a number of these sequences have been functionally relocated to the nucleus via IGT. Evidence for rampant HGT was detected in several Geranium species containing foreign organellar DNA from diverse eudicots, including many transfers from parasitic plants. One lineage has experienced multiple, independent HGT episodes, many of which occurred within the past 5.5 Myr. Both duplicative and recapture HGT were documented in Geranium lineages. The mitochondrial genome of Geranium brycei contains at least four independent HGT tracts that are absent in its nearest relative. Furthermore, G. brycei mitochondria carry two copies of the cox1 gene that differ in intron content, providing insight into contrasting hypotheses on cox1 intron evolution.}, }
@article {pmid25986903, year = {2015}, author = {Sanchez-Alberola, N and Campoy, S and Emerson, D and Barbé, J and Erill, I}, title = {An SOS Regulon under Control of a Noncanonical LexA-Binding Motif in the Betaproteobacteria.}, journal = {Journal of bacteriology}, volume = {197}, number = {16}, pages = {2622-2630}, pmid = {25986903}, issn = {1098-5530}, mesh = {Bacillus subtilis/genetics/metabolism ; Bacterial Proteins/genetics/*metabolism ; Base Sequence ; Betaproteobacteria/classification/*genetics/metabolism ; Comparative Genomic Hybridization ; Consensus Sequence ; DNA, Bacterial/genetics ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; Promoter Regions, Genetic ; Protein Binding ; Protein Structure, Tertiary ; *Regulon ; *SOS Response, Genetics ; Sequence Alignment ; Serine Endopeptidases/genetics/*metabolism ; Transcriptional Activation ; }, abstract = {UNLABELLED: The SOS response is a transcriptional regulatory network governed by the LexA repressor that activates in response to DNA damage. In the Betaproteobacteria, LexA is known to target a palindromic sequence with the consensus sequence CTGT-N8-ACAG. We report the characterization of a LexA regulon in the iron-oxidizing betaproteobacterium Sideroxydans lithotrophicus. In silico and in vitro analyses show that LexA targets six genes by recognizing a binding motif with the consensus sequence GAACGaaCGTTC, which is strongly reminiscent of the Bacillus subtilis LexA-binding motif. We confirm that the closely related Gallionella capsiferriformans shares the same LexA-binding motif, and in silico analyses indicate that this motif is also conserved in the Nitrosomonadales and the Methylophilales. Phylogenetic analysis of LexA and the alpha subunit of DNA polymerase III (DnaE) reveal that the organisms harboring this noncanonical LexA form a compact taxonomic cluster within the Betaproteobacteria. However, their lexA gene is unrelated to the standard Betaproteobacteria lexA, and there is evidence of its spread through lateral gene transfer. In contrast to other reported cases of noncanonical LexA-binding motifs, the regulon of S. lithotrophicus is comparable in size and function to that of many other Betaproteobacteria, suggesting that a convergent SOS regulon has reevolved under the control of a new LexA protein. Analysis of the DNA-binding domain of S. lithotrophicus LexA reveals little sequence similarity with that of other LexA proteins targeting similar binding motifs, suggesting that network structure may limit site evolution or that structural constrains make the B. subtilis-type motif an optimal interface for multiple LexA sequences.<br><br>IMPORTANCE: Understanding the evolution of transcriptional systems enables us to address important questions in microbiology, such as the emergence and transfer potential of different regulatory systems to regulate virulence or mediate responses to stress. The results reported here constitute the first characterization of a noncanonical LexA protein regulating a standard SOS regulon. This is significant because it illustrates how a complex transcriptional program can be put under the control of a novel transcriptional regulator. Our results also reveal a substantial degree of plasticity in the LexA recognition domain, raising intriguing questions about the space of protein-DNA interfaces and the specific evolutionary constrains faced by these elements.}, }
@article {pmid25984558, year = {2015}, author = {Harrison, OB and Bray, JE and Maiden, MC and Caugant, DA}, title = {Genomic Analysis of the Evolution and Global Spread of Hyper-invasive Meningococcal Lineage 5.}, journal = {EBioMedicine}, volume = {2}, number = {3}, pages = {234-243}, pmid = {25984558}, issn = {2352-3964}, support = {087622//Wellcome Trust/United Kingdom ; }, abstract = {BACKGROUND: The predominant model for bacterial pandemics is the emergence of a virulent variant that diversifies as it spreads in human populations. We investigated a 40-year meningococcal disease pandemic caused by the hyper-invasive ET-5/ST-32 complex.<br><br>METHODS: A global collection of Neisseria meningitidis isolates dating from 1969 to 2008 was whole genome sequenced (WGS) and analysed using a gene-by-gene approach at http://pubmlst.org/neisseria.<br><br>FINDINGS: Analysis of WGS data identified a 'Lineage 5 pan genome' of 1940 genes, 1752 (92%) of which were present in all isolates (Lineage 5 'core genome'). Genetic diversity, which was mostly generated by horizontal gene transfer, was unevenly distributed in the genome; however, genealogical analysis of diverse and conserved core genes, accessory genes, and antigen encoding genes, robustly identified a star phylogeny with a number of sub-lineages. Most European and American isolates belonged to one of two closely related sub-lineages, which had diversified before the identification of the pandemic in the 1970s. A third, genetically more diverse sub-lineage, was associated with Asian isolates. Several isolates had acquired DNA from the related gonococcus.<br><br>INTERPRETATION: These data were inconsistent with a single point of origin followed by pandemic spread, rather suggesting that the sub-lineages had diversified and spread by asymptomatic transmission, with multiple distinct strains causing localised hyperendemic outbreaks.}, }
@article {pmid25982743, year = {2015}, author = {Kirzinger, MW and Butz, CJ and Stavrinides, J}, title = {Inheritance of Pantoea type III secretion systems through both vertical and horizontal transfer.}, journal = {Molecular genetics and genomics : MGG}, volume = {290}, number = {6}, pages = {2075-2088}, pmid = {25982743}, issn = {1617-4623}, mesh = {Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Pantoea/classification/*genetics ; Phylogeny ; }, abstract = {The type III secretion system (T3SS) is an extracellular apparatus used by many Gram-negative bacteria to deliver effector proteins directly into plant and animal cells, thereby facilitating host-specific association. Strains of the enterobacterial genus, Pantoea, have been isolated from a wide variety of hosts, including plants, insects, and humans, yet it is unclear whether the T3SS may be involved in these associations. In this study, we use comparative genomics and phylogenetic methods to examine the origin and distribution of T3SSs in 35 sequenced environmental and clinical strains of Pantoea. We began our analysis by examining the distribution of the previously characterized plant cell-specific PSI-1 and animal cell-specific PSI-2 of the plant pathogenic Pantoea stewartii subsp. stewartii DC283 (PstDC283), and showed that both had a somewhat limited distribution. Our analysis, however, identified two variants of a unique plant cell-specific T3SS (PSI-1a and PSI-1b) in six Pantoea strains, including a clinical isolate. Our genome analysis of PstDC283 also identified a third T3SS that we named PSI-3, which has a similar genetic content and organization to the Salmonella, animal cell-specific SPI-2 system. Phylogenetic analysis of all three systems suggests that the PSI-1 system has been inherited vertically, whereas the newly identified PSI-1a and PSI-1b systems have been acquired independently from other genera within the Enterobacteriaceae. PSI-2 appears to have been acquired horizontally as far back as the Erwinia/Pantoea common ancestor, with evidence of more recent horizontal acquisition of the PSI-3 system. Our results suggest that Pantoea is a relatively old plant pathogen that has lost and subsequently regained different plant-associated T3SSs. This work has broad implications for understanding the host-associating capacity of Pantoea strains, and reveals the propensity for Pantoea isolates to exchange pathogenicity determinants with human-pathogenic members of the Enterobacteriaceae.}, }
@article {pmid25981746, year = {2015}, author = {Couchman, EC and Browne, HP and Dunn, M and Lawley, TD and Songer, JG and Hall, V and Petrovska, L and Vidor, C and Awad, M and Lyras, D and Fairweather, NF}, title = {Clostridium sordellii genome analysis reveals plasmid localized toxin genes encoded within pathogenicity loci.}, journal = {BMC genomics}, volume = {16}, number = {1}, pages = {392}, pmid = {25981746}, issn = {1471-2164}, support = {/WT_/Wellcome Trust/United Kingdom ; 086418/WT_/Wellcome Trust/United Kingdom ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 098051/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacterial Toxins/*genetics ; Chromosome Mapping ; Clostridium sordellii/classification/*genetics/*pathogenicity ; Gene Transfer, Horizontal ; Genetic Loci/genetics ; Genome, Bacterial/*genetics ; Neuraminidase/genetics ; Phylogeny ; Plasmids/genetics/*metabolism ; Sequence Analysis, DNA ; Type C Phospholipases/genetics ; Virulence Factors/*genetics ; }, abstract = {BACKGROUND: Clostridium sordellii can cause severe infections in animals and humans, the latter associated with trauma, toxic shock and often-fatal gynaecological infections. Strains can produce two large clostridial cytotoxins (LCCs), TcsL and TcsH, related to those produced by Clostridium difficile, Clostridium novyi and Clostridium perfringens, but the genetic basis of toxin production remains uncharacterised.<br><br>RESULTS: Phylogenetic analysis of the genome sequences of 44 strains isolated from human and animal infections in the UK, US and Australia placed the species into four clades. Although all strains originated from animal or clinical disease, only 5 strains contained LCC genes: 4 strains contain tcsL alone and one strain contains tcsL and tcsH. Four toxin-positive strains were found within one clade. Where present, tcsL and tcsH were localised in a pathogenicity locus, similar to but distinct from that present in C. difficile. In contrast to C. difficile, where the LCCs are chromosomally localised, the C. sordellii tcsL and tcsH genes are localised on plasmids. Our data suggest gain and loss of entire toxigenic plasmids in addition to horizontal transfer of the pathogenicity locus. A high quality, annotated sequence of ATCC9714 reveals many putative virulence factors including neuraminidase, phospholipase C and the cholesterol-dependent cytolysin sordellilysin that are highly conserved between all strains studied.<br><br>CONCLUSIONS: Genome analysis of C. sordellii reveals that the LCCs, the major virulence factors, are localised on plasmids. Many strains do not contain the LCC genes; it is probable that in several of these cases the plasmid has been lost upon laboratory subculture. Our data are consistent with LCCs being the primary virulence factors in the majority of infections, but LCC-negative strains may precipitate certain categories of infection. A high quality genome sequence reveals putative virulence factors whose role in virulence can be investigated.}, }
@article {pmid25980356, year = {2015}, author = {Wang, YC and Lee, YT and Yang, YS and Chen, CT and Chiu, CH and Yin, T and Kuo, SC and Chen, TL and Lin, JC and Wang, FD and Fung, CP and Chang, FY}, title = {Risk factors and outcome for colistin-resistant Acinetobacter nosocomialis bacteraemia in patients without previous colistin exposure.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {21}, number = {8}, pages = {758-764}, doi = {10.1016/j.cmi.2015.05.005}, pmid = {25980356}, issn = {1469-0691}, mesh = {Acinetobacter/classification/*drug effects/genetics/isolation &amp; purification ; Acinetobacter Infections/drug therapy/*epidemiology/mortality ; Adult ; Aged ; Aged, 80 and over ; Anti-Bacterial Agents/*pharmacology/*therapeutic use ; Bacteremia/drug therapy/*epidemiology/mortality ; Colistin/*pharmacology ; Conjugation, Genetic ; *Drug Resistance, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Female ; Gene Transfer, Horizontal ; Humans ; Male ; Microbial Sensitivity Tests ; Middle Aged ; Molecular Typing ; Retrospective Studies ; Risk Factors ; Survival Analysis ; Treatment Outcome ; Young Adult ; }, abstract = {The clinical characteristics of patients with colistin-resistant Acinetobacter baumannii bacteraemia have been documented, but those of patients with bacteraemia caused by other Acinetobacter species remain unknown. Previous exposure to colistin has been shown to be associated with the emergence of colistin resistance, but may be not the only predisposing factor. In the current study, we highlight the risk and outcome of patients without previous exposure to colistin who acquired colistin-resistant Acinetobacter nosocomialis (ColRAN) bacteraemia. This 11-year single-centre retrospective study analysed 58 patients with ColRAN bacteraemia and 213 patients with colistin-susceptible A. nosocomialis (ColSAN) bacteraemia. Antimicrobial susceptibilities were determined with an agar dilution method. The clonal relationship of ColRAN isolates was determined with pulsed-field gel electrophoresis. A conjugation mating-out assay was conducted to delineate the potential transfer of colistin resistance genes. Multivariable analysis was performed to evaluate the risk factors for ColRAN bacteraemia. Chronic obstructive pulmonary disease (COPD) was independently associated with ColRAN bacteraemia (OR 3.04; 95% CI 1.45-6.37; p 0.003). Patients with ColRAN bacteraemia had higher APACHE II scores, but the two groups showed no significant differences in 14-day mortality (10.3% vs. 10.3%) or 28-day mortality (15.5% vs. 15.0%). ColRAN isolates had greater resistance than ColSAN isolates to all antimicrobial agents except for ciprofloxacin (0% vs. 6.6%). There were 16 different ColRAN pulsotypes, and two major clones were found. Colistin resistance did not transfer to colistin-susceptible A. baumannii or A. nosocomialis. These results show that COPD is an independent risk factor for acquisition of ColRAN bacteraemia. The mortality rates were similar between patients with ColRAN and ColSAN bacteraemia.}, }
@article {pmid25977399, year = {2015}, author = {Belotti, PT and Thabet, L and Laffargue, A and André, C and Coulange-Mayonnove, L and Arpin, C and Messadi, A and M'Zali, F and Quentin, C and Dubois, V}, title = {Description of an original integron encompassing blaVIM-2, qnrVC1 and genes encoding bacterial group II intron proteins in Pseudomonas aeruginosa.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {70}, number = {8}, pages = {2237-2240}, doi = {10.1093/jac/dkv103}, pmid = {25977399}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/pharmacology ; Burn Units ; Burns/complications/epidemiology ; Conjugation, Genetic ; Endemic Diseases ; Gene Expression Profiling ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Imipenem/pharmacology ; *Integrons ; Introns ; Molecular Sequence Data ; Pseudomonas Infections/*microbiology ; Pseudomonas aeruginosa/enzymology/*genetics/isolation &amp; purification ; Sequence Analysis, DNA ; Transformation, Bacterial ; Tunisia/epidemiology ; beta-Lactam Resistance ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: A burn unit of a hospital in Tunis underwent an endemic situation caused by imipenem-resistant Pseudomonas aeruginosa. For nine non-repetitive isolates of a clonal VIM-2-producing strain, the blaVIM-2 genetic background was characterized and the associated qnrVC1 gene molecularly analysed.<br><br>METHODS: The imipenem resistance mechanism was investigated by phenotypic and molecular tests, and resistance transfer was studied by conjugation and transformation experiments. The integron's structure was characterized by sequencing, and qnrVC1 expression was explored after cloning experiments.<br><br>RESULTS: The nine VIM-2-producing strains were collected from eight patients and one environmental sample. All transfer assays failed, suggesting a chromosomal location of blaVIM-2. This latter was found to be part of a class 1 integron of &#x223c;7500 bp, which also contains blaOXA-2, aadA1 and two copies of the aadB, arr-6 and qnrVC1 genes. qnrVC1 exhibited higher homology with the chromosomally encoded qnr genes of Vibrionaceae than with plasmid-mediated qnr genes of Enterobacteriaceae. The qnrVC1 gene cassette possesses a promoter allowing its expression, and it conferred decreased fluoroquinolone susceptibility to Escherichia coli. Additionally, on the same integron, genes encoding an uncommon group IIC-attC intron were detected.<br><br>CONCLUSIONS: A VIM-2-producing P. aeruginosa outbreak led us to characterize an integron harbouring a qnrVC1 cassette and a new group IIC-attC intron. This is the first known description of a qnr determinant in a P. aeruginosa strain. Its presence conferred a low level of resistance to quinolones in E. coli, which might favour the emergence of highly resistant mutants.}, }
@article {pmid25977397, year = {2015}, author = {Wang, Y and Lv, Y and Cai, J and Schwarz, S and Cui, L and Hu, Z and Zhang, R and Li, J and Zhao, Q and He, T and Wang, D and Wang, Z and Shen, Y and Li, Y and Feßler, AT and Wu, C and Yu, H and Deng, X and Xia, X and Shen, J}, title = {A novel gene, optrA, that confers transferable resistance to oxazolidinones and phenicols and its presence in Enterococcus faecalis and Enterococcus faecium of human and animal origin.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {70}, number = {8}, pages = {2182-2190}, doi = {10.1093/jac/dkv116}, pmid = {25977397}, issn = {1460-2091}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Chloramphenicol/analogs &amp; derivatives/*pharmacology ; Cluster Analysis ; Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; *Drug Resistance, Bacterial ; Enterococcus faecalis/*drug effects/genetics/isolation &amp; purification ; Enterococcus faecium/*drug effects/genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Gram-Positive Bacterial Infections/microbiology/veterinary ; Humans ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Oxazolidinones/*pharmacology ; Phylogeny ; Plasmids ; Sequence Analysis, DNA ; Sequence Homology ; Transformation, Bacterial ; }, abstract = {OBJECTIVES: The oxazolidinone-resistant Enterococcus faecalis E349 from a human patient tested negative for the cfr gene and 23S rRNA mutations. Here we report the identification of a novel oxazolidinone resistance gene, optrA, and a first investigation of the extent to which this gene was present in E. faecalis and Enterococcus faecium from humans and food-producing animals.<br><br>METHODS: The resistance gene optrA was identified by whole-plasmid sequencing and subsequent cloning and expression in a susceptible Enterococcus host. Transformation and conjugation assays served to investigate the transferability of optrA. All optrA-positive E. faecalis and E. faecium isolates of human and animal origin were analysed for their MICs and their genotype, as well as the location of optrA.<br><br>RESULTS: The novel plasmid-borne ABC transporter gene optrA from E. faecalis E349 conferred combined resistance or elevated MICs (when no clinical breakpoints were available) to oxazolidinones (linezolid and tedizolid) and phenicols (chloramphenicol and florfenicol). The corresponding conjugative plasmid pE349, on which optrA was located, had a size of 36&#x200a;331 bp and also carried the phenicol exporter gene fexA. The optrA gene was functionally expressed in E. faecalis, E. faecium and Staphylococcus aureus. It was detected more frequently in E. faecalis and E. faecium from food-producing animals (20.3% and 5.7%, respectively) than from humans (4.2% and 0.6%, respectively).<br><br>CONCLUSIONS: Enterococci with elevated MICs of linezolid and tedizolid should be tested not only for 23S rRNA mutations and the gene cfr, but also for the novel resistance gene optrA.}, }
@article {pmid25973398, year = {2015}, author = {Zaura, E and Mira, A}, title = {Editorial: the oral microbiome in an ecological perspective.}, journal = {Frontiers in cellular and infection microbiology}, volume = {5}, number = {}, pages = {39}, pmid = {25973398}, issn = {2235-2988}, mesh = {*Biota ; Host-Pathogen Interactions ; Humans ; Microbial Interactions ; *Microbiota ; Mouth/*microbiology ; }, }
@article {pmid25969927, year = {2015}, author = {Hall, JP and Harrison, E and Lilley, AK and Paterson, S and Spiers, AJ and Brockhurst, MA}, title = {Environmentally co-occurring mercury resistance plasmids are genetically and phenotypically diverse and confer variable context-dependent fitness effects.}, journal = {Environmental microbiology}, volume = {17}, number = {12}, pages = {5008-5022}, pmid = {25969927}, issn = {1462-2920}, support = {311490/ERC_/European Research Council/International ; }, mesh = {Arylsulfatases/genetics ; DNA Transposable Elements/*genetics ; Drug Resistance, Bacterial/*genetics ; Environment ; Gene Transfer, Horizontal ; Mercury/*pharmacology ; Operon/genetics ; Plasmids/*genetics ; Pseudomonas fluorescens/*drug effects/*genetics/isolation &amp; purification ; Soil Microbiology ; Sucrose/metabolism ; }, abstract = {Plasmids are important mobile elements that can facilitate genetic exchange and local adaptation within microbial communities. We compared the sequences of four co-occurring pQBR family environmental mercury resistance plasmids and measured their effects on competitive fitness of a Pseudomonas fluorescens SBW25 host, which was isolated at the same field site. Fitness effects of carriage differed between plasmids and were strongly context dependent, varying with medium, plasmid status of competitor and levels of environmental mercury. The plasmids also varied widely in their rates of conjugation and segregational loss. We found that few of the plasmid-borne accessory genes could be ascribed functions, although we identified a putative chemotaxis operon, a type IV pilus-encoding cluster and a region encoding putative arylsulfatase enzymes, which were conserved across geographically distant isolates. One plasmid, pQBR55, conferred the ability to catabolize sucrose. Transposons, including the mercury resistance Tn5042, appeared to have been acquired by different pQBR plasmids by recombination, indicating an important role for horizontal gene transfer in the recent evolution of pQBR plasmids. Our findings demonstrate extensive genetic and phenotypic diversity among co-occurring members of a plasmid community and suggest a role for environmental heterogeneity in the maintenance of plasmid diversity.}, }
@article {pmid25964349, year = {2015}, author = {Kofler, R and Hill, T and Nolte, V and Betancourt, AJ and Schlötterer, C}, title = {The recent invasion of natural Drosophila simulans populations by the P-element.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {21}, pages = {6659-6663}, pmid = {25964349}, issn = {1091-6490}, support = {294485/ERC_/European Research Council/International ; P 27048/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Base Sequence ; DNA/genetics ; *DNA Transposable Elements ; Drosophila/*genetics ; Drosophila melanogaster/genetics ; Evolution, Molecular ; Female ; Gene Frequency ; Gene Transfer, Horizontal ; Genetics, Population ; Genome, Insect ; Male ; Molecular Sequence Data ; Phylogeny ; RNA/genetics ; Species Specificity ; Time Factors ; }, abstract = {The P-element is one of the best understood eukaryotic transposable elements. It invaded Drosophila melanogaster populations within a few decades but was thought to be absent from close relatives, including Drosophila simulans. Five decades after the spread in D. melanogaster, we provide evidence that the P-element has also invaded D. simulans. P-elements in D. simulans appear to have been acquired recently from D. melanogaster probably via a single horizontal transfer event. Expression data indicate that the P-element is processed in the germ line of D. simulans, and genomic data show an enrichment of P-element insertions in putative origins of replication, similar to that seen in D. melanogaster. This ongoing spread of the P-element in natural populations provides a unique opportunity to understand the dynamics of transposable element spread and the associated piwi-interacting RNAs defense mechanisms.}, }
@article {pmid25964335, year = {2015}, author = {Torres-Cortés, G and Ghignone, S and Bonfante, P and Schüßler, A}, title = {Mosaic genome of endobacteria in arbuscular mycorrhizal fungi: Transkingdom gene transfer in an ancient mycoplasma-fungus association.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {25}, pages = {7785-7790}, pmid = {25964335}, issn = {1091-6490}, mesh = {Bacteria/*genetics ; *Gene Transfer Techniques ; Genome, Bacterial ; Molecular Sequence Data ; *Mosaicism ; *Mycorrhizae ; }, abstract = {For more than 450 million years, arbuscular mycorrhizal fungi (AMF) have formed intimate, mutualistic symbioses with the vast majority of land plants and are major drivers in almost all terrestrial ecosystems. The obligate plant-symbiotic AMF host additional symbionts, so-called Mollicutes-related endobacteria (MRE). To uncover putative functional roles of these widespread but yet enigmatic MRE, we sequenced the genome of DhMRE living in the AMF Dentiscutata heterogama. Multilocus phylogenetic analyses showed that MRE form a previously unidentified lineage sister to the hominis group of Mycoplasma species. DhMRE possesses a strongly reduced metabolic capacity with 55% of the proteins having unknown function, which reflects unique adaptations to an intracellular lifestyle. We found evidence for transkingdom gene transfer between MRE and their AMF host. At least 27 annotated DhMRE proteins show similarities to nuclear-encoded proteins of the AMF Rhizophagus irregularis, which itself lacks MRE. Nuclear-encoded homologs could moreover be identified for another AMF, Gigaspora margarita, and surprisingly, also the non-AMF Mortierella verticillata. Our data indicate a possible origin of the MRE-fungus association in ancestors of the Glomeromycota and Mucoromycotina. The DhMRE genome encodes an arsenal of putative regulatory proteins with eukaryotic-like domains, some of them encoded in putative genomic islands. MRE are highly interesting candidates to study the evolution and interactions between an ancient, obligate endosymbiotic prokaryote with its obligate plant-symbiotic fungal host. Our data moreover may be used for further targeted searches for ancient effector-like proteins that may be key components in the regulation of the arbuscular mycorrhiza symbiosis.}, }
@article {pmid25964324, year = {2015}, author = {Naito, M and Morton, JB and Pawlowska, TE}, title = {Minimal genomes of mycoplasma-related endobacteria are plastic and contain host-derived genes for sustained life within Glomeromycota.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {25}, pages = {7791-7796}, pmid = {25964324}, issn = {1091-6490}, mesh = {*Genome, Bacterial ; Glomeromycota/classification/*physiology ; Molecular Sequence Data ; Mycoplasma/*genetics ; Phylogeny ; }, abstract = {Arbuscular mycorrhizal fungi (AMF, Glomeromycota) colonize roots of the majority of terrestrial plants. They provide essential minerals to their plant hosts and receive photosynthates in return. All major lineages of AMF harbor endobacteria classified as Mollicutes, and known as mycoplasma-related endobacteria (MRE). Except for their substantial intrahost genetic diversity and ability to transmit vertically, virtually nothing is known about the life history of these endobacteria. To understand MRE biology, we sequenced metagenomes of three MRE populations, each associated with divergent AMF hosts. We found that each AMF species harbored a genetically distinct group of MRE. Despite vertical transmission, all MRE populations showed extensive chromosomal rearrangements, which we attributed to genetic recombination, activity of mobile elements, and a history of plectroviral invasion. The MRE genomes are characterized by a highly reduced gene content, indicating metabolic dependence on the fungal host, with the mechanism of energy production remaining unclear. Several MRE genes encode proteins with domains involved in protein-protein interactions with eukaryotic hosts. In addition, the MRE genomes harbor genes horizontally acquired from AMF. Some of these genes encode small ubiquitin-like modifier (SUMO) proteases specific to the SUMOylation systems of eukaryotes, which MRE likely use to manipulate their fungal host. The extent of MRE genome plasticity and reduction, along with the large number of horizontally acquired host genes, suggests a high degree of adaptation to the fungal host. These features, together with the ubiquity of the MRE-Glomeromycota associations, emphasize the significance of MRE in the biology of Glomeromycota.}, }
@article {pmid25963270, year = {2015}, author = {Boto, L}, title = {Evolutionary change and phylogenetic relationships in light of horizontal gene transfer.}, journal = {Journal of biosciences}, volume = {40}, number = {2}, pages = {465-472}, pmid = {25963270}, issn = {0973-7138}, mesh = {*Biological Evolution ; Eukaryotic Cells/*cytology ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Phylogeny ; Prokaryotic Cells/*cytology ; Selection, Genetic/genetics ; }, abstract = {Horizontal gene transfer has, over the past 25 years, become a part of evolutionary thinking. In the present paper I discuss horizontal gene transfer (HGT) in relation to contingency, natural selection, evolutionary change speed and the Tree-of-Life endeavour, with the aim of contributing to the understanding of the role of HGT in evolutionary processes. In addition, the challenges that HGT imposes on the current view of evolution are emphasized.}, }
@article {pmid25963197, year = {2015}, author = {Szabó, R and Ferrier, DE}, title = {Another biomineralising protostome with an msp130 gene and conservation of msp130 gene structure across Bilateria.}, journal = {Evolution &amp; development}, volume = {17}, number = {3}, pages = {195-197}, doi = {10.1111/ede.12122}, pmid = {25963197}, issn = {1525-142X}, mesh = {Amino Acid Sequence ; Animals ; *Evolution, Molecular ; Glycoproteins/chemistry/*genetics/metabolism ; Membrane Proteins/chemistry/*genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; Polychaeta/*genetics/metabolism ; Sequence Alignment ; }, abstract = {Msp130 genes are known for their association with biomineralisation, principally in echinoderm skeletogenesis. Recently, msp130 genes were shown to exist more widely across the animal kingdom, including in molluscs, and a hypothesis was formed that the genes had arisen independently in the deuterostome and mollusc lineages via horizontal gene transfer, thus facilitating the evolution of biomineralisation in these distinct lineages (Ettensohn, 2014). Here we show that another biomineralising protostome, the polychaete Spirobranchus (formerly Pomatoceros) lamarcki also possesses an msp130 gene, and expresses it during a biomineralisation process. However, based on analysis of gene structure, we hypothesize that the protostome and deuterostome msp130 genes did not originate from independent horizontal gene transfers, but instead are descended from a gene already present in the bilaterian ancestor, with the gene being secondarily lost from several lineages.}, }
@article {pmid25962915, year = {2015}, author = {Kouzel, N and Oldewurtel, ER and Maier, B}, title = {Gene Transfer Efficiency in Gonococcal Biofilms: Role of Biofilm Age, Architecture, and Pilin Antigenic Variation.}, journal = {Journal of bacteriology}, volume = {197}, number = {14}, pages = {2422-2431}, pmid = {25962915}, issn = {1098-5530}, mesh = {Anti-Bacterial Agents/pharmacology ; Antigens, Bacterial/genetics/*metabolism ; Biofilms/*growth &amp; development ; Drug Resistance, Bacterial/genetics ; Fimbriae Proteins/genetics/*metabolism ; Gene Expression Regulation, Bacterial/physiology ; Gene Transfer, Horizontal/*physiology ; *Genetic Variation ; Neisseria gonorrhoeae/drug effects/genetics/*physiology ; }, abstract = {UNLABELLED: Extracellular DNA is an important structural component of many bacterial biofilms. It is unknown, however, to which extent external DNA is used to transfer genes by means of transformation. Here, we quantified the acquisition of multidrug resistance and visualized its spread under selective and nonselective conditions in biofilms formed by Neisseria gonorrhoeae. The density and architecture of the biofilms were controlled by microstructuring the substratum for bacterial adhesion. Horizontal transfer of antibiotic resistance genes between cocultured strains, each carrying a single resistance, occurred efficiently in early biofilms. The efficiency of gene transfer was higher in early biofilms than between planktonic cells. It was strongly reduced after 24 h and independent of biofilm density. Pilin antigenic variation caused a high fraction of nonpiliated bacteria but was not responsible for the reduced gene transfer at later stages. When selective pressure was applied to dense biofilms using antibiotics at their MIC, the double-resistant bacteria did not show a significant growth advantage. In loosely connected biofilms, the spreading of double-resistant clones was prominent. We conclude that multidrug resistance readily develops in early gonococcal biofilms through horizontal gene transfer. However, selection and spreading of the multiresistant clones are heavily suppressed in dense biofilms.<br><br>IMPORTANCE: Biofilms are considered ideal reaction chambers for horizontal gene transfer and development of multidrug resistances. The rate at which genes are exchanged within biofilms is unknown. Here, we quantified the acquisition of double-drug resistance by gene transfer between gonococci with single resistances. At early biofilm stages, the transfer efficiency was higher than for planktonic cells but then decreased with biofilm age. The surface topography affected the architecture of the biofilm. While the efficiency of gene transfer was independent of the architecture, spreading of double-resistant bacteria under selective conditions was strongly enhanced in loose biofilms. We propose that while biofilms help generating multiresistant strains, selection takes place mostly after dispersal from the biofilm.}, }
@article {pmid25962149, year = {2015}, author = {Arkhipova, OV and Meer, MV and Mikoulinskaia, GV and Zakharova, MV and Galushko, AS and Akimenko, VK and Kondrashov, FA}, title = {Recent Origin of the Methacrylate Redox System in Geobacter sulfurreducens AM-1 through Horizontal Gene Transfer.}, journal = {PloS one}, volume = {10}, number = {5}, pages = {e0125888}, pmid = {25962149}, issn = {1932-6203}, support = {55007424//Howard Hughes Medical Institute/United States ; }, mesh = {Bacterial Proteins/genetics/metabolism ; Biological Evolution ; Gene Order ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Geobacter/classification/*genetics/*metabolism ; Methacrylates/*metabolism ; Molecular Sequence Data ; Operon ; *Oxidation-Reduction ; Phylogeny ; }, abstract = {The origin and evolution of novel biochemical functions remains one of the key questions in molecular evolution. We study recently emerged methacrylate reductase function that is thought to have emerged in the last century and reported in Geobacter sulfurreducens strain AM-1. We report the sequence and study the evolution of the operon coding for the flavin-containing methacrylate reductase (Mrd) and tetraheme cytochrome с (Mcc) in the genome of G. sulfurreducens AM-1. Different types of signal peptides in functionally interlinked proteins Mrd and Mcc suggest a possible complex mechanism of biogenesis for chromoproteids of the methacrylate redox system. The homologs of the Mrd and Mcc sequence found in δ-Proteobacteria and Deferribacteres are also organized into an operon and their phylogenetic distribution suggested that these two genes tend to be horizontally transferred together. Specifically, the mrd and mcc genes from G. sulfurreducens AM-1 are not monophyletic with any of the homologs found in other Geobacter genomes. The acquisition of methacrylate reductase function by G. sulfurreducens AM-1 appears linked to a horizontal gene transfer event. However, the new function of the products of mrd and mcc may have evolved either prior or subsequent to their acquisition by G. sulfurreducens AM-1.}, }
@article {pmid25957384, year = {2015}, author = {Stanczak-Mrozek, KI and Manne, A and Knight, GM and Gould, K and Witney, AA and Lindsay, JA}, title = {Within-host diversity of MRSA antimicrobial resistances.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {70}, number = {8}, pages = {2191-2198}, pmid = {25957384}, issn = {1460-2091}, support = {G0900205//Medical Research Council/United Kingdom ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteriophages/isolation &amp; purification ; Carrier State/*microbiology ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; *Genetic Variation ; Genotype ; Humans ; Methicillin-Resistant Staphylococcus aureus/*drug effects/isolation &amp; purification ; Microbial Sensitivity Tests ; Nasal Mucosa/microbiology ; Phenotype ; Plasmids/analysis ; Staphylococcal Infections/*microbiology ; Transduction, Genetic ; }, abstract = {OBJECTIVES: MRSA is a major antimicrobial resistance (AMR) pathogen. The reservoir of infecting isolates is colonization, which is the site of evolutionary selection. The aim was to identify if AMRs in colonizing MRSA populations diversified and potential mechanisms of resistance gene transfer in vivo.<br><br>METHODS: Nasal swabs from 38 MRSA carriers admitted to hospital were plated and 20 individual colonies from each patient tested for phenotypic antibiotic susceptibility and genetically for lineage, carriage of four prophages and three plasmid families. Free bacteriophages were detected in swabs as well as their capacity for transducing resistance genes.<br><br>RESULTS: Nine (24%) patients carried phenotypic AMR variants and 24 (63%) carried prophage and plasmid variants. If a single colony was selected for testing, the probability of detecting all AMR in that patient was 87%. Sixty-four different AMR and mobile genetic element (MGE) profiles were detected, mostly in the MRSA CC22 background (where CC stands for clonal complex), with up to 8 profiles per patient. Nearly half of the patients carried detectable free bacteriophages and phages successfully transduced resistance genes between laboratory and patient isolates in vitro. WGS showed MRSA core genomes were stable, while AMR and MGEs varied.<br><br>CONCLUSIONS: 'Clouds' of MRSA variants that have acquired or lost AMR and MGEs are common in nasal colonizing populations and bacteriophages may play an important role in gene transfer. Accurate estimation of AMR and genetic variability has implications for diagnostics, epidemiology, antimicrobial stewardship and understanding the evolutionary selection of AMR in colonizing populations.}, }
@article {pmid25955384, year = {2015}, author = {Jalasvuori, M and Mattila, S and Hoikkala, V}, title = {Chasing the Origin of Viruses: Capsid-Forming Genes as a Life-Saving Preadaptation within a Community of Early Replicators.}, journal = {PloS one}, volume = {10}, number = {5}, pages = {e0126094}, pmid = {25955384}, issn = {1932-6203}, mesh = {Biological Evolution ; Capsid Proteins/*genetics ; Evolution, Molecular ; *Genes, Viral ; Models, Genetic ; *Virus Physiological Phenomena ; Virus Replication ; }, abstract = {Virus capsids mediate the transfer of viral genetic information from one cell to another, thus the origin of the first viruses arguably coincides with the origin of the viral capsid. Capsid genes are evolutionarily ancient and their emergence potentially predated even the origin of first free-living cells. But does the origin of the capsid coincide with the origin of viruses, or is it possible that capsid-like functionalities emerged before the appearance of true viral entities? We set to investigate this question by using a computational simulator comprising primitive replicators and replication parasites within a compartment matrix. We observe that systems with no horizontal gene transfer between compartments collapse due to the rapidly emerging replication parasites. However, introduction of capsid-like genes that induce the movement of randomly selected genes from one compartment to another rescues life by providing the non-parasitic replicators a mean to escape their current compartments before the emergence of replication parasites. Capsid-forming genes can mediate the establishment of a stable meta-population where parasites cause only local tragedies but cannot overtake the whole community. The long-term survival of replicators is dependent on the frequency of horizontal transfer events, as systems with either too much or too little genetic exchange are doomed to succumb to replication-parasites. This study provides a possible scenario for explaining the origin of viral capsids before the emergence of genuine viruses: in the absence of other means of horizontal gene transfer between compartments, evolution of capsid-like functionalities may have been necessary for early life to prevail.}, }
@article {pmid25954269, year = {2015}, author = {Labonté, JM and Field, EK and Lau, M and Chivian, D and Van Heerden, E and Wommack, KE and Kieft, TL and Onstott, TC and Stepanauskas, R}, title = {Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {349}, pmid = {25954269}, issn = {1664-302X}, abstract = {A major fraction of Earth's prokaryotic biomass dwells in the deep subsurface, where cellular abundances per volume of sample are lower, metabolism is slower, and generation times are longer than those in surface terrestrial and marine environments. How these conditions impact biotic interactions and evolutionary processes is largely unknown. Here we employed single cell genomics to analyze cell-to-cell genome content variability and signatures of horizontal gene transfer (HGT) and viral infections in five cells of Candidatus Desulforudis audaxviator, which were collected from a 3 km-deep fracture water in the 2.9 Ga-old Witwatersrand Basin of South Africa. Between 0 and 32% of genes recovered from single cells were not present in the original, metagenomic assembly of Desulforudis, which was obtained from a neighboring subsurface fracture. We found a transposable prophage, a retron, multiple clustered regularly interspaced short palindromic repeats (CRISPRs) and restriction-modification systems, and an unusually high frequency of transposases in the analyzed single cell genomes. This indicates that recombination, HGT and viral infections are prevalent evolutionary events in the studied population of microorganisms inhabiting a highly stable deep subsurface environment.}, }
@article {pmid25953738, year = {2015}, author = {Tamarit, D and Ellegaard, KM and Wikander, J and Olofsson, T and Vásquez, A and Andersson, SG}, title = {Functionally Structured Genomes in Lactobacillus kunkeei Colonizing the Honey Crop and Food Products of Honeybees and Stingless Bees.}, journal = {Genome biology and evolution}, volume = {7}, number = {6}, pages = {1455-1473}, pmid = {25953738}, issn = {1759-6653}, mesh = {Animals ; Bacterial Proteins/genetics ; Bees/*microbiology ; Gene Transfer, Horizontal ; Genome Size ; *Genome, Bacterial ; Lactobacillus/classification/*genetics ; Phylogeny ; Recombination, Genetic ; }, abstract = {Lactobacillus kunkeei is the most abundant bacterial species in the honey crop and food products of honeybees. The 16 S rRNA genes of strains isolated from different bee species are nearly identical in sequence and therefore inadequate as markers for studies of coevolutionary patterns. Here, we have compared the 1.5 Mb genomes of ten L. kunkeei strains isolated from all recognized Apis species and another two strains from Meliponini species. A gene flux analysis, including previously sequenced Lactobacillus species as outgroups, indicated the influence of reductive evolution. The genome architecture is unique in that vertically inherited core genes are located near the terminus of replication, whereas genes for secreted proteins and putative host-adaptive traits are located near the origin of replication. We suggest that these features have resulted from a genome-wide loss of genes, with integrations of novel genes mostly occurring in regions flanking the origin of replication. The phylogenetic analyses showed that the bacterial topology was incongruent with the host topology, and that strains of the same microcluster have recombined frequently across the host species barriers, arguing against codiversification. Multiple genotypes were recovered in the individual hosts and transfers of mobile elements could be demonstrated for strains isolated from the same host species. Unlike other bacteria with small genomes, short generation times and multiple rRNA operons suggest that L. kunkeei evolves under selection for rapid growth in its natural growth habitat. The results provide an extended framework for reductive genome evolution and functional genome organization in bacteria.}, }
@article {pmid25951456, year = {2015}, author = {Wang, Q and Mao, D and Mu, Q and Luo, Y}, title = {Enhanced horizontal transfer of antibiotic resistance genes in freshwater microcosms induced by an ionic liquid.}, journal = {PloS one}, volume = {10}, number = {5}, pages = {e0126784}, pmid = {25951456}, issn = {1932-6203}, mesh = {Acinetobacter/drug effects/genetics ; Cell Membrane Permeability/genetics ; Drug Resistance, Bacterial/*genetics ; *Ecosystem ; *Fresh Water ; *Gene Transfer, Horizontal ; Genes, Bacterial ; *Ionic Liquids ; Plasmids ; Salmonella/drug effects/genetics ; }, abstract = {The spread and propagation of antibiotic resistance genes (ARGs) is a worldwide public health concern. Ionic liquids (ILs), considered as "environmentally friendly" replacements for industrial organic solvents, have been widely applied in modern industry. However, few data have been collected regarding the potential ecological and environmental risks of ILs, which are important for preparing for their potential discharge into the environment. In this paper, the IL 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIm][PF6]) (0.001-5.0 g/L) was tested for its effects on facilitating ARGs horizontal transfer mediated by plasmid RP4 in freshwater microcosms. In the horizontal transfer microcosms, the transfer frequency of plasmid RP4 was significantly enhanced (60-fold higher than untreated groups) by the IL [BMIm][PF6] (1.0 g/L). Meanwhile, two strains of opportunistic pathogen Acinetobacter spp. and Salmonella spp. were isolated among the transconjugants, illustrating plasmid RP4 mediated horizontal transfer of ARGs occurred in pathogen. This could increase the risk of ARGs dissemination to human pathogens and pose great threat to public health. The cause that [BMIm[PF6] enhanced the transfer frequency of plasmid RP4 was proposed by suppressed cell membrane barrier and enhanced cell membrane permeability, which was evidenced by flow cytometry (FCM). This is the first report that some ILs facilitate horizontal transfer of plasmid RP4 which is widely distributed in the environment and thus add the adverse effects of the environmental risk of ILs.}, }
@article {pmid25944863, year = {2015}, author = {Xue, H and Cordero, OX and Camas, FM and Trimble, W and Meyer, F and Guglielmini, J and Rocha, EP and Polz, MF}, title = {Eco-Evolutionary Dynamics of Episomes among Ecologically Cohesive Bacterial Populations.}, journal = {mBio}, volume = {6}, number = {3}, pages = {e00552-15}, pmid = {25944863}, issn = {2150-7511}, mesh = {DNA, Bacterial/chemistry/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; *Plasmids ; Sequence Analysis, DNA ; Vibrionaceae/*genetics ; }, abstract = {UNLABELLED: Although plasmids and other episomes are recognized as key players in horizontal gene transfer among microbes, their diversity and dynamics among ecologically structured host populations in the wild remain poorly understood. Here, we show that natural populations of marine Vibrionaceae bacteria host large numbers of families of episomes, consisting of plasmids and a surprisingly high fraction of plasmid-like temperate phages. Episomes are unevenly distributed among host populations, and contrary to the notion that high-density communities in biofilms act as hot spots of gene transfer, we identified a strong bias for episomes to occur in free-living as opposed to particle-attached cells. Mapping of episomal families onto host phylogeny shows that, with the exception of all phage and a few plasmid families, most are of recent evolutionary origin and appear to have spread rapidly by horizontal transfer. Such high eco-evolutionary turnover is particularly surprising for plasmids that are, based on previously suggested categorization, putatively nontransmissible, indicating that this type of plasmid is indeed frequently transferred by currently unknown mechanisms. Finally, analysis of recent gene transfer among plasmids reveals a network of extensive exchange connecting nearly all episomes. Genes functioning in plasmid transfer and maintenance are frequently exchanged, suggesting that plasmids can be rapidly transformed from one category to another. The broad distribution of episomes among distantly related hosts and the observed promiscuous recombination patterns show how episomes can offer their hosts rapid assembly and dissemination of novel functions.<br><br>IMPORTANCE: Plasmids and other episomes are an integral part of bacterial biology in all environments, yet their study is heavily biased toward their role as vectors for antibiotic resistance genes. This study presents a comprehensive analysis of all episomes within several coexisting bacterial populations of Vibrionaceae from the coastal ocean and represents the largest-yet genomic survey of episomes from a single bacterial family. The host population framework allows analysis of the eco-evolutionary dynamics at unprecedented resolution, yielding several unexpected results. These include (i) discovery of novel, nonintegrative temperate phages, (ii) revision of a class of episomes, previously termed "nontransmissible," as highly transmissible, and (iii) surprisingly high evolutionary turnover of episomes, manifest as frequent birth, spread, and loss.}, }
@article {pmid25944581, year = {2016}, author = {Morrow, BL and McNatt, R and Joyce, L and McBride, S and Morgan, D and Tressler, C and Mellits, C}, title = {Highly pathogenic beta-hemolytic streptococcal infections in cats from an institutionalized hoarding facility and a multi-species comparison.}, journal = {Journal of feline medicine and surgery}, volume = {18}, number = {4}, pages = {318-327}, pmid = {25944581}, issn = {1532-2750}, mesh = {Abscess/microbiology/*veterinary ; Animals ; Cat Diseases/*microbiology ; Cats ; Hoarding Disorder ; Polymerase Chain Reaction/veterinary ; RNA, Ribosomal, 16S ; Streptococcal Infections/*veterinary ; *Streptococcus milleri Group ; }, abstract = {OBJECTIVES: Two hundred and thirty-four cats removed from an institutionalized hoarding facility (IHF) demonstrated severe, atypical pyogenic infections. The objective of this study was to document the various syndromes and determine the etiology of the infections.<br><br>METHODS: All cats were evaluated initially after removal from the IHF and on a daily basis for at least 15 months. Samples were collected and sent for culture/susceptibility and histopathology to commercial laboratories or stored at -20(o)C. PCR was performed using universal bacterial primers to amplify the 16S-23S rRNA intergenic spacer region. PCR products were sequenced to determine the identity of the bacteria.<br><br>RESULTS: Multiple pyogenic syndromes were documented, including abscesses of the paws and carpal/tarsal regions in 82 cats, acute rhinitis with profuse purulent nasal discharge in 68 cats and cervical lymphadenitis with abscessation unassociated with any wounding in 51 cats. Many cats exhibited septic arthritis with total joint destruction, necrotizing fasciitis, meningitis, otitis and septic shock, often leading to death. These infections appeared to be caused by beta-hemolytic streptococci (BHS) based on initial culture results (n = 10), though speciation was unclear and some samples (n = 6) produced no growth. Based on PCR results (n = 26), Streptococcus canis was the only bacterial species or the dominant species identified in each sample, and was the only species present in all the regions associated with the pyogenic infections.<br><br>CONCLUSIONS AND RELEVANCE: Horizontal gene transfer and loss of the cell wall may account for the discrepancy between the culture and PCR results and the highly pathogenic nature of S canis in this particular population of cats. A large-scale hoarding situation with multiple animal species, overcrowding, stress and mixing of animals from many geographical regions created ideal conditions for these events to occur. The specific virulence factors present may be more useful in predicting the pathophysiology of BHS infections than the species of Streptococcus found in the host per se.}, }
@article {pmid25943580, year = {2015}, author = {Bishnoi, R and Khatri, I and Subramanian, S and Ramya, TN}, title = {Prevalence of the F-type lectin domain.}, journal = {Glycobiology}, volume = {25}, number = {8}, pages = {888-901}, doi = {10.1093/glycob/cwv029}, pmid = {25943580}, issn = {1460-2423}, mesh = {Amino Acid Sequence ; Amphibians/classification/genetics ; Animals ; Bacteria/chemistry/classification/genetics ; Birds/classification/genetics ; Fucose/chemistry ; Gene Expression ; *Gene Transfer, Horizontal ; Lancelets/chemistry/classification/genetics ; Lectins/*chemistry/genetics ; Mammals/classification/genetics ; Models, Molecular ; Molecular Sequence Data ; Mollusca/chemistry/classification/genetics ; *Phylogeny ; Protein Structure, Tertiary ; Reptiles/classification/genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {F-type lectins are fucolectins with characteristic fucose and calcium-binding sequence motifs and a unique lectin fold (the "F-type" fold). F-type lectins are phylogenetically widespread with selective distribution. Several eukaryotic F-type lectins have been biochemically and structurally characterized, and the F-type lectin domain (FLD) has also been studied in the bacterial proteins, Streptococcus mitis lectinolysin and Streptococcus pneumoniae SP2159. However, there is little knowledge about the extent of occurrence of FLDs and their domain organization, especially, in bacteria. We have now mined the extensive genomic sequence information available in the public databases with sensitive sequence search techniques in order to exhaustively survey prokaryotic and eukaryotic FLDs. We report 437 FLD sequence clusters (clustered at 80% sequence identity) from eukaryotic, eubacterial and viral proteins. Domain architectures are diverse but mostly conserved in closely related organisms, and domain organizations of bacterial FLD-containing proteins are very different from their eukaryotic counterparts, suggesting unique specialization of FLDs to suit different requirements. Several atypical phylogenetic associations hint at lateral transfer. Among eukaryotes, we observe an expansion of FLDs in terms of occurrence and domain organization diversity in the taxa Mollusca, Hemichordata and Branchiostomi, perhaps coinciding with greater emphasis on innate immune strategies in these organisms. The naturally occurring FLDs with diverse domain organizations that we have identified here will be useful for future studies aimed at creating designer molecular platforms for directing desired biological activities to fucosylated glycoconjugates in target niches.}, }
@article {pmid25940918, year = {2015}, author = {Ravindran, A and Jalan, N and Yuan, JS and Wang, N and Gross, DC}, title = {Comparative genomics of Pseudomonas syringae pv. syringae strains B301D and HS191 and insights into intrapathovar traits associated with plant pathogenesis.}, journal = {MicrobiologyOpen}, volume = {4}, number = {4}, pages = {553-573}, pmid = {25940918}, issn = {2045-8827}, mesh = {DNA, Bacterial/chemistry/genetics ; *Genome, Bacterial ; Molecular Sequence Data ; Plant Diseases/*microbiology ; Pseudomonas syringae/*genetics ; Sequence Analysis, DNA ; Virulence Factors/*genetics ; }, abstract = {Pseudomonas syringae pv. syringae is a common plant-associated bacterium that causes diseases of both monocot and dicot plants worldwide. To help delineate traits critical to adaptation and survival in the plant environment, we generated complete genome sequences of P. syringae pv. syringae strains B301D and HS191, which represent dicot and monocot strains with distinct host specificities. Intrapathovar comparisons of the B301D (6.09 Mb) and HS191 (5.95 Mb plus a 52 kb pCG131 plasmid) genomes to the previously sequenced B728a genome demonstrated that the shared genes encompass about 83% of each genome, and include genes for siderophore biosynthesis, osmotolerance, and extracellular polysaccharide production. Between 7% and 12% of the genes are unique among the genomes, and most of the unique gene regions carry transposons, phage elements, or IS elements associated with horizontal gene transfer. Differences are observed in the type III effector composition for the three strains that likely influences host range. The HS191 genome had the largest number at 25 of effector genes, and seven effector genes are specific to this monocot strain. Toxin production is another major trait associated with virulence of P. syringae pv. syringae, and HS191 is distinguished by genes for production of syringopeptin SP25 and mangotoxin.}, }
@article {pmid25940562, year = {2015}, author = {Dotto, BR and Carvalho, EL and Silva, AF and Duarte Silva, LF and Pinto, PM and Ortiz, MF and Wallau, GL}, title = {HTT-DB: horizontally transferred transposable elements database.}, journal = {Bioinformatics (Oxford, England)}, volume = {31}, number = {17}, pages = {2915-2917}, doi = {10.1093/bioinformatics/btv281}, pmid = {25940562}, issn = {1367-4811}, mesh = {Animals ; DNA Transposable Elements/*genetics ; *Databases, Factual ; Eukaryota/classification/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome ; Humans ; *Software ; Species Specificity ; }, abstract = {MOTIVATION: Horizontal transfer of transposable (HTT) elements among eukaryotes was discovered in the mid-1980s. As then, >300 new cases have been described. New findings about HTT are revealing the evolutionary impact of this phenomenon on host genomes. In order to provide an up to date, interactive and expandable database for such events, we developed the HTT-DB database.<br><br>RESULTS: HTT-DB allows easy access to most of HTT cases reported along with rich information about each case. Moreover, it allows the user to generate tables and graphs based on searches using Transposable elements and/or host species classification and export them in several formats.<br><br>This database is freely available on the web at http://lpa.saogabriel.unipampa.edu.br:8080/httdatabase. HTT-DB was developed based on Java and MySQL with all major browsers supported. Tools and software packages used are free for personal or non-profit projects.<br><br>CONTACT: bdotto82@gmail.com or gabriel.wallau@gmail.com.}, }
@article {pmid25934615, year = {2015}, author = {Shousha, A and Awaiwanont, N and Sofka, D and Smulders, FJ and Paulsen, P and Szostak, MP and Humphrey, T and Hilbert, F}, title = {Bacteriophages Isolated from Chicken Meat and the Horizontal Transfer of Antimicrobial Resistance Genes.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {14}, pages = {4600-4606}, pmid = {25934615}, issn = {1098-5336}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteriophages/*genetics/metabolism ; Chickens ; Drug Resistance, Bacterial ; Escherichia coli/drug effects/*genetics/metabolism/*virology ; Escherichia coli Proteins/genetics/metabolism ; *Gene Transfer, Horizontal ; Humans ; Meat/microbiology/*virology ; Transduction, Genetic ; }, abstract = {Antimicrobial resistance in microbes poses a global and increasing threat to public health. The horizontal transfer of antimicrobial resistance genes was thought to be due largely to conjugative plasmids or transposons, with only a minor part being played by transduction through bacteriophages. However, whole-genome sequencing has recently shown that the latter mechanism could be highly important in the exchange of antimicrobial resistance genes between microorganisms and environments. The transfer of antimicrobial resistance genes by phages could underlie the origin of resistant bacteria found in food. We show that chicken meat carries a number of phages capable of transferring antimicrobial resistance. Of 243 phages randomly isolated from chicken meat, about a quarter (24.7%) were able to transduce resistance to one or more of the five antimicrobials tested into Escherichia coli ATCC 13706 (DSM 12242). Resistance to kanamycin was transduced the most often, followed by that to chloramphenicol, with four phages transducing tetracycline resistance and three transducing ampicillin resistance. Phages able to transduce antimicrobial resistance were isolated from 44% of the samples of chicken meat that we tested. The statistically significant (P = 0.01) relationship between the presence of phages transducing kanamycin resistance and E. coli isolates resistant to this antibiotic suggests that transduction may be an important mechanism for transferring kanamycin resistance to E. coli. It appears that the transduction of resistance to certain antimicrobials, e.g., kanamycin, not only is widely distributed in E. coli isolates found on meat but also could represent a major mechanism for resistance transfer. The result is of high importance for animal and human health.}, }
@article {pmid25933054, year = {2015}, author = {Devarajan, N and Laffite, A and Graham, ND and Meijer, M and Prabakar, K and Mubedi, JI and Elongo, V and Mpiana, PT and Ibelings, BW and Wildi, W and Poté, J}, title = {Accumulation of clinically relevant antibiotic-resistance genes, bacterial load, and metals in freshwater lake sediments in Central Europe.}, journal = {Environmental science &amp; technology}, volume = {49}, number = {11}, pages = {6528-6537}, doi = {10.1021/acs.est.5b01031}, pmid = {25933054}, issn = {1520-5851}, mesh = {Bacteria/genetics ; Bacterial Load/*genetics ; DNA, Ribosomal/genetics ; Drug Resistance, Microbial/*genetics ; Escherichia coli/genetics ; Europe ; *Genes, Bacterial ; Geography ; Geologic Sediments/*microbiology ; Humans ; Lakes/*microbiology ; Metals/*analysis ; Polymerase Chain Reaction ; }, abstract = {Wastewater treatment plants (WWTP) receive the effluents from various sources (communities, industrial, and hospital effluents) and are recognized as reservoir for antibiotic-resistance genes (ARGs) that are associated with clinical pathogens. The aquatic environment is considered a hot-spot for horizontal gene transfer, and lake sediments offer the opportunity for reconstructing the pollution history and evaluating the impacts. In this context, variation with depth and time of the total bacterial load, the abundance of faecal indicator bacteria (FIB; E. coli and Enterococcus spp. (ENT)), Pseudomonas spp., and ARGs (blaTEM, blaSHV, blaCTX-M, blaNDM, and aadA) were quantified in sediment profiles of different parts of Lake Geneva using quantitative PCR. The abundance of bacterial marker genes was identified in sediments contaminated by WWTP following eutrophication of the lake. Additionally, ARGs, including the extended-spectrum ß-lactam- and aminoglycoside-resistance genes, were identified in the surface sediments. The ARG and FIB abundance strongly correlated (r ≥ 0.403, p < 0.05, n = 34) with organic matter and metal concentrations in the sediments, indicating a common and contemporary source of contamination. The contamination of sediments by untreated or partially treated effluent water can affect the quality of ecosystem. Therefore, the reduction of contaminants from the source is recommended for further improvement of water quality.}, }
@article {pmid25926654, year = {2015}, author = {Contreras-Galindo, R and Kaplan, MH and Dube, D and Gonzalez-Hernandez, MJ and Chan, S and Meng, F and Dai, M and Omenn, GS and Gitlin, SD and Markovitz, DM}, title = {Human Endogenous Retrovirus Type K (HERV-K) Particles Package and Transmit HERV-K-Related Sequences.}, journal = {Journal of virology}, volume = {89}, number = {14}, pages = {7187-7201}, pmid = {25926654}, issn = {1098-5514}, support = {T32 AI007528/AI/NIAID NIH HHS/United States ; 1F31CA150523-01/CA/NCI NIH HHS/United States ; 5T32AI007528-13/AI/NIAID NIH HHS/United States ; T32 GM145304/GM/NIGMS NIH HHS/United States ; F31 CA150523/CA/NCI NIH HHS/United States ; 3R01CA144043-03S1/CA/NCI NIH HHS/United States ; U54 DA021519/DA/NIDA NIH HHS/United States ; UL1RR24986/RR/NCRR NIH HHS/United States ; RM-08-029/RM/RMOD NIH HHS/United States ; U54DA021519/DA/NIDA NIH HHS/United States ; K22 CA177824/CA/NCI NIH HHS/United States ; F32 AI106189/AI/NIAID NIH HHS/United States ; P30 ES017885/ES/NIEHS NIH HHS/United States ; UL1 RR024986/RR/NCRR NIH HHS/United States ; P30U54ES017885/ES/NIEHS NIH HHS/United States ; R01 CA144043/CA/NCI NIH HHS/United States ; T32 GM007315/GM/NIGMS NIH HHS/United States ; 1 F32 AI106189-01/AI/NIAID NIH HHS/United States ; }, mesh = {Cell Line ; DNA, Viral/genetics/*metabolism ; Endogenous Retroviruses/*genetics/*physiology ; Gene Transfer, Horizontal ; Genes, Reporter ; Humans ; Reverse Transcription ; Transcription, Genetic ; Transduction, Genetic ; *Virus Assembly ; }, abstract = {UNLABELLED: Human endogenous retroviruses (HERV) make up 8% of the human genome. While the youngest of these retroviruses, HERV-K(HML-2), termed HK2, is able to code for all viral proteins and produce virus-like particles, it is not known if these virus particles package and transmit HK2-related sequences. Here, we analyzed the capacity of HK2 for packaging and transmitting HK2 sequences. We created an HK2 probe, termed Bogota, which can be packaged into HK2 viruses, and transfected it into cells that make HK2 particles. Supernatants of the transfected cells, which contained HK2 viral particles, then were added to target cells, and the transmissibility of the HK2 Bogota reporter was tracked by G418 resistance. Our studies revealed that contemporary HK2 virions produced by some teratocarcinoma and breast cancer cell lines, as well as by peripheral blood lymphocytes from lymphoma patients, can package HK2 Bogota probes, and these viruses transmitted these probes to other cells. After transmission, HK2 Bogota transcripts undergo reverse transcription, a step impaired by antiretroviral agents or by introduction of mutations into the probe sequences required for reverse transcription. HK2 viruses were more efficiently transmitted in the presence of HK2 Rec or HIV-1 Tat and Vif. Transmitted Bogota probes formed episomes but did not integrate into the cellular genome. Resistance to integration might explain the relatively low number of HK2 insertions that were acquired during the last 25 million years of evolution. Whether transient transmission of modern HK2 sequences, which encode two putative oncoproteins, can lead to disease remains to be studied.<br><br>IMPORTANCE: Retroviruses invaded the genome of human ancestors over the course of millions of years, yet these viruses generally have been inactivated during evolution, with only remnants of these infectious sequences remaining in the human genome. One of these viruses, termed HK2, still is capable of producing virus particles, although these particles have been regarded as being noninfectious. Using a genetic probe derived from HK2, we have discovered that HK2 viruses produced in modern humans can package HK2 sequences and transmit them to various other cells. Furthermore, the genetic sequences packaged in HK2 undergo reverse transcription. The transmitted probe circularized in the cell and failed to integrate into the cellular genome. These findings suggest that modern HK2 viruses can package viral RNA and transmit it to other cells. Contrary to previous views, we provide evidence of an extracellular viral phase of modern HK2 viruses. We have no evidence of sustained, spreading infection.}, }
@article {pmid25926236, year = {2015}, author = {Mathers, AJ and Peirano, G and Pitout, JD}, title = {The role of epidemic resistance plasmids and international high-risk clones in the spread of multidrug-resistant Enterobacteriaceae.}, journal = {Clinical microbiology reviews}, volume = {28}, number = {3}, pages = {565-591}, pmid = {25926236}, issn = {1098-6618}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteriological Techniques/standards ; Biological Evolution ; Drug Resistance, Bacterial/*genetics ; Enterobacteriaceae/drug effects/*genetics ; Enterobacteriaceae Infections/epidemiology/*microbiology/transmission ; Gene Transfer, Horizontal ; Plasmids/*genetics ; }, abstract = {Escherichia coli sequence type 131 (ST131) and Klebsiella pneumoniae ST258 emerged in the 2000s as important human pathogens, have spread extensively throughout the world, and are responsible for the rapid increase in antimicrobial resistance among E. coli and K. pneumoniae strains, respectively. E. coli ST131 causes extraintestinal infections and is often fluoroquinolone resistant and associated with extended-spectrum β-lactamase production, especially CTX-M-15. K. pneumoniae ST258 causes urinary and respiratory tract infections and is associated with carbapenemases, most often KPC-2 and KPC-3. The most prevalent lineage within ST131 is named fimH30 because it contains the H30 variant of the type 1 fimbrial adhesin gene, and recent molecular studies have demonstrated that this lineage emerged in the early 2000s and was then followed by the rapid expansion of its sublineages H30-R and H30-Rx. K. pneumoniae ST258 comprises 2 distinct lineages, namely clade I and clade II. Moreover, it seems that ST258 is a hybrid clone that was created by a large recombination event between ST11 and ST442. Epidemic plasmids with blaCTX-M and blaKPC belonging to incompatibility group F have contributed significantly to the success of these clones. E. coli ST131 and K. pneumoniae ST258 are the quintessential examples of international multidrug-resistant high-risk clones.}, }
@article {pmid25922398, year = {2015}, author = {Doron, S and Snydman, DR}, title = {Risk and safety of probiotics.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {60 Suppl 2}, number = {Suppl 2}, pages = {S129-34}, pmid = {25922398}, issn = {1537-6591}, support = {K23 AT003391/AT/NCCIH NIH HHS/United States ; 5K23 AT003391-03/AT/NCCIH NIH HHS/United States ; }, mesh = {Clinical Trials as Topic ; Fungemia/etiology ; Gastrointestinal Tract/physiology ; Gene Transfer, Horizontal ; Humans ; Lactobacillus/pathogenicity ; Probiotics/*adverse effects/standards ; Risk ; Saccharomyces/pathogenicity ; Sepsis/etiology ; United States ; }, abstract = {Probiotics have been used safely for years. Safety outcomes are inconsistently reported in published clinical trials. In 2011, a report released by the Agency for Healthcare Research and Quality concluded that, although the existing probiotic clinical trials reveal no evidence of increased risk, "the current literature is not well equipped to answer questions on the safety of probiotics in intervention studies with confidence." Critics point out that the preponderance of evidence, including the long history of safe probiotic use as well as data from clinical trials, and animal and in vitro studies all support the assumption that probiotics are generally safe for most populations. Theoretical risks have been described in case reports, clinical trial results and experimental models, include systemic infections, deleterious metabolic activities, excessive immune stimulation in susceptible individuals, gene transfer and gastrointestinal side effects. More research is needed to properly describe the incidence and severity of adverse events related to probiotics.}, }
@article {pmid25919787, year = {2015}, author = {Artamonova, II and Lappi, T and Zudina, L and Mushegian, AR}, title = {Prokaryotic genes in eukaryotic genome sequences: when to infer horizontal gene transfer and when to suspect an actual microbe.}, journal = {Environmental microbiology}, volume = {17}, number = {7}, pages = {2203-2208}, doi = {10.1111/1462-2920.12854}, pmid = {25919787}, issn = {1462-2920}, mesh = {Bacteria/*genetics ; Base Sequence ; Biological Evolution ; Computational Biology ; DNA, Bacterial/*genetics ; Eukaryota/*genetics ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Genome, Bacterial/genetics ; Phylogeny ; }, abstract = {Assessment of phylogenetic positions of predicted gene and protein sequences is a routine step in any genome project, useful for validating the species' taxonomic position and for evaluating hypotheses about genome evolution and function. Several recent eukaryotic genome projects have reported multiple gene sequences that were much more similar to homologues in bacteria than to any eukaryotic sequence. In the spirit of the times, horizontal gene transfer from bacteria to eukaryotes has been invoked in some of these cases. Here, we show, using comparative sequence analysis, that some of those bacteria-like genes indeed appear likely to have been horizontally transferred from bacteria to eukaryotes. In other cases, however, the evidence strongly indicates that the eukaryotic DNA sequenced in the genome project contains a sample of non-integrated DNA from the actual bacteria, possibly providing a window into the host microbiome. Recent literature suggests also that common reagents, kits and laboratory equipment may be systematically contaminated with bacterial DNA, which appears to be sampled by metagenome projects non-specifically. We review several bioinformatic criteria that help to distinguish putative horizontal gene transfers from the admixture of genes from autonomously replicating bacteria in their hosts' genome databases or from the reagent contamination.}, }
@article {pmid25918444, year = {2015}, author = {van Schaik, W}, title = {The human gut resistome.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1670}, pages = {20140087}, pmid = {25918444}, issn = {1471-2970}, mesh = {Disease Reservoirs/*microbiology ; Drug Resistance, Microbial/*genetics ; Gastrointestinal Microbiome/*genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/*genetics ; Humans ; Metagenomics/*methods/trends ; }, abstract = {In recent decades, the emergence and spread of antibiotic resistance among bacterial pathogens has become a major threat to public health. Bacteria can acquire antibiotic resistance genes by the mobilization and transfer of resistance genes from a donor strain. The human gut contains a densely populated microbial ecosystem, termed the gut microbiota, which offers ample opportunities for the horizontal transfer of genetic material, including antibiotic resistance genes. Recent technological advances allow microbiota-wide studies into the diversity and dynamics of the antibiotic resistance genes that are harboured by the gut microbiota ('the gut resistome'). Genes conferring resistance to antibiotics are ubiquitously present among the gut microbiota of humans and most resistance genes are harboured by strictly anaerobic gut commensals. The horizontal transfer of genetic material, including antibiotic resistance genes, through conjugation and transduction is a frequent event in the gut microbiota, but mostly involves non-pathogenic gut commensals as these dominate the microbiota of healthy individuals. Resistance gene transfer from commensals to gut-dwelling opportunistic pathogens appears to be a relatively rare event but may contribute to the emergence of multi-drug resistant strains, as is illustrated by the vancomycin resistance determinants that are shared by anaerobic gut commensals and the nosocomial pathogen Enterococcus faecium.}, }
@article {pmid25918442, year = {2015}, author = {Aarestrup, FM}, title = {The livestock reservoir for antimicrobial resistance: a personal view on changing patterns of risks, effects of interventions and the way forward.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1670}, pages = {20140085}, pmid = {25918442}, issn = {1471-2970}, mesh = {Animals ; Anti-Infective Agents/*administration &amp; dosage ; Bacterial Infections/*prevention &amp; control/*veterinary ; Disease Reservoirs/*veterinary ; Drug Resistance, Microbial/*genetics ; Gene Transfer, Horizontal/genetics ; Humans ; Livestock/*genetics/immunology ; }, abstract = {The purpose of this review was to provide an updated overview on the use of antimicrobial agents in livestock, the associated problems for humans and current knowledge on the effects of reducing resistance in the livestock reservoir on both human health and animal production. There is still limiting data on both use of antimicrobial agents, occurrence and spread of resistance as well as impact on human health. However, in recent years, emerging issues related to methicillin-resistant Staphylococcus aureus, Clostridium difficile, Escherichia coli and horizontally transferred genes indicates that the livestock reservoir has a more significant impact on human health than was estimated 10 years ago, where the focus was mainly on resistance in Campylobacter and Salmonella. Studies have indicated that there might only be a marginal if any benefit from the regular use of antibiotics and have shown that it is possible to substantially reduce the use of antimicrobial agents in livestock production without compromising animal welfare or health or production. In some cases, this should be done in combination with other measures such as biosecurity and use of vaccines. To enable better studies on both the global burden and the effect of interventions, there is a need for global harmonized integrated and continuous surveillance of antimicrobial usage and antimicrobial resistance, preferably associated with data on production and animal diseases to determine the positive and negative impact of reducing antimicrobial use in livestock.}, }
@article {pmid25918441, year = {2015}, author = {Woolhouse, M and Ward, M and van Bunnik, B and Farrar, J}, title = {Antimicrobial resistance in humans, livestock and the wider environment.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1670}, pages = {20140083}, pmid = {25918441}, issn = {1471-2970}, support = {095831//Wellcome Trust/United Kingdom ; WT098441MA//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Anti-Infective Agents/*administration &amp; dosage ; *Biological Evolution ; Drug Resistance, Microbial/*genetics ; *Environment ; Gene Transfer, Horizontal/*genetics ; Humans ; *Livestock ; Methicillin-Resistant Staphylococcus aureus/*genetics ; }, abstract = {Antimicrobial resistance (AMR) in humans is inter-linked with AMR in other populations, especially farm animals, and in the wider environment. The relatively few bacterial species that cause disease in humans, and are the targets of antibiotic treatment, constitute a tiny subset of the overall diversity of bacteria that includes the gut microbiota and vast numbers in the soil. However, resistance can pass between these different populations; and homologous resistance genes have been found in pathogens, normal flora and soil bacteria. Farm animals are an important component of this complex system: they are exposed to enormous quantities of antibiotics (despite attempts at reduction) and act as another reservoir of resistance genes. Whole genome sequencing is revealing and beginning to quantify the two-way traffic of AMR bacteria between the farm and the clinic. Surveillance of bacterial disease, drug usage and resistance in livestock is still relatively poor, though improving, but achieving better antimicrobial stewardship on the farm is challenging: antibiotics are an integral part of industrial agriculture and there are very few alternatives. Human production and use of antibiotics either on the farm or in the clinic is but a recent addition to the natural and ancient process of antibiotic production and resistance evolution that occurs on a global scale in the soil. Viewed in this way, AMR is somewhat analogous to climate change, and that suggests that an intergovernmental panel, akin to the Intergovernmental Panel on Climate Change, could be an appropriate vehicle to actively address the problem.}, }
@article {pmid25918141, year = {2015}, author = {Dale, JL and Cagnazzo, J and Phan, CQ and Barnes, AM and Dunny, GM}, title = {Multiple roles for Enterococcus faecalis glycosyltransferases in biofilm-associated antibiotic resistance, cell envelope integrity, and conjugative transfer.}, journal = {Antimicrobial agents and chemotherapy}, volume = {59}, number = {7}, pages = {4094-4105}, pmid = {25918141}, issn = {1098-6596}, support = {R56 AI058134/AI/NIAID NIH HHS/United States ; T32 HL007741/HL/NHLBI NIH HHS/United States ; T90 DE0227232/DE/NIDCR NIH HHS/United States ; R01 AI058134/AI/NIAID NIH HHS/United States ; T90 DE022732/DE/NIDCR NIH HHS/United States ; AI058134/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Bile Acids and Salts/pharmacology ; Biofilms/*drug effects ; Cell Wall/genetics ; Conjugation, Genetic ; DNA Transposable Elements/genetics ; Detergents/pharmacology ; Drug Resistance, Bacterial/*genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Enterococcus faecalis/*enzymology/*genetics ; Glycosyltransferases/*genetics/*metabolism ; Microbial Sensitivity Tests ; Mutation/genetics ; Plasmids/genetics ; Polysaccharides/metabolism ; Quorum Sensing/genetics ; beta-Galactosidase/metabolism ; }, abstract = {The emergence of multidrug-resistant bacteria and the limited availability of new antibiotics are of increasing clinical concern. A compounding factor is the ability of microorganisms to form biofilms (communities of cells encased in a protective extracellular matrix) that are intrinsically resistant to antibiotics. Enterococcus faecalis is an opportunistic pathogen that readily forms biofilms and also has the propensity to acquire resistance determinants via horizontal gene transfer. There is intense interest in the genetic basis for intrinsic and acquired antibiotic resistance in E. faecalis, since clinical isolates exhibiting resistance to multiple antibiotics are not uncommon. We performed a genetic screen using a library of transposon (Tn) mutants to identify E. faecalis biofilm-associated antibiotic resistance determinants. Five Tn mutants formed wild-type biofilms in the absence of antibiotics but produced decreased biofilm biomass in the presence of antibiotic concentrations that were subinhibitory to the parent strain. Genetic determinants responsible for biofilm-associated antibiotic resistance include components of the quorum-sensing system (fsrA, fsrC, and gelE) and two glycosyltransferase (GTF) genes (epaI and epaOX). We also found that the GTFs play additional roles in E. faecalis resistance to detergent and bile salts, maintenance of cell envelope integrity, determination of cell shape, polysaccharide composition, and conjugative transfer of the pheromone-inducible plasmid pCF10. The epaOX gene is located in a variable extended region of the enterococcal polysaccharide antigen (epa) locus. These data illustrate the importance of GTFs in E. faecalis adaptation to diverse growth conditions and suggest new targets for antimicrobial design.}, }
@article {pmid25918135, year = {2015}, author = {Søndergaard, A and Witherden, EA and Nørskov-Lauritsen, N and Tristram, SG}, title = {Interspecies transfer of the penicillin-binding protein 3-encoding gene ftsI between Haemophilus influenzae and Haemophilus haemolyticus can confer reduced susceptibility to β-lactam antimicrobial agents.}, journal = {Antimicrobial agents and chemotherapy}, volume = {59}, number = {7}, pages = {4339-4342}, pmid = {25918135}, issn = {1098-6596}, mesh = {Ampicillin/pharmacology ; Anti-Bacterial Agents/*pharmacology ; Cefotaxime/pharmacology ; Gene Transfer, Horizontal ; Haemophilus/*genetics ; Haemophilus influenzae/*genetics ; Homologous Recombination/genetics ; Microbial Sensitivity Tests ; Penicillin-Binding Proteins/*genetics ; beta-Lactam Resistance/*genetics ; beta-Lactams/*pharmacology ; }, abstract = {Mutations in ftsI, encoding penicillin-binding protein 3, can cause decreased β-lactam susceptibility in Haemophilus influenzae. Sequencing of ftsI from clinical strains has indicated interspecies recombination of ftsI between H. influenzae and Haemophilus haemolyticus. This study documented apparently unrestricted homologous recombination of ftsI between H. influenzae and H. haemolyticus in vitro. Transfer of ftsI from resistant isolates conferred similar but not identical increases in the MICs of susceptible strains of H. influenzae and H. haemolyticus.}, }
@article {pmid25911489, year = {2015}, author = {Zeng, X and Ardeshna, D and Lin, J}, title = {Heat Shock-Enhanced Conjugation Efficiency in Standard Campylobacter jejuni Strains.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {13}, pages = {4546-4552}, pmid = {25911489}, issn = {1098-5336}, mesh = {Campylobacter jejuni/genetics/*physiology/*radiation effects ; Conjugation, Genetic/*radiation effects ; Escherichia coli/genetics ; *Gene Transfer Techniques ; Gene Transfer, Horizontal/*drug effects ; *Hot Temperature ; Transformation, Bacterial/radiation effects ; }, abstract = {Campylobacter jejuni, the leading bacterial cause of human gastroenteritis in the United States, displays significant strain diversity due to horizontal gene transfer. Conjugation is an important horizontal gene transfer mechanism contributing to the evolution of bacterial pathogenesis and antimicrobial resistance. It has been observed that heat shock could increase transformation efficiency in some bacteria. In this study, the effect of heat shock on C. jejuni conjugation efficiency and the underlying mechanisms were examined. With a modified Escherichia coli donor strain, different C. jejuni recipient strains displayed significant variation in conjugation efficiency ranging from 6.2 × 10(-8) to 6.0 × 10(-3) CFU per recipient cell. Despite reduced viability, heat shock of standard C. jejuni NCTC 11168 and 81-176 strains (e.g., 48 to 54°C for 30 to 60 min) could dramatically enhance C. jejuni conjugation efficiency up to 1,000-fold. The phenotype of the heat shock-enhanced conjugation in C. jejuni recipient cells could be sustained for at least 9 h. Filtered supernatant from the heat shock-treated C. jejuni cells could not enhance conjugation efficiency, which suggests that the enhanced conjugation efficiency is independent of secreted substances. Mutagenesis analysis indicated that the clustered regularly interspaced short palindromic repeats system and the selected restriction-modification systems (Cj0030/Cj0031, Cj0139/Cj0140, Cj0690c, and HsdR) were dispensable for heat shock-enhanced conjugation in C. jejuni. Taking all results together, this study demonstrated a heat shock-enhanced conjugation efficiency in standard C. jejuni strains, leading to an optimized conjugation protocol for molecular manipulation of this organism. The findings from this study also represent a significant step toward elucidation of the molecular mechanism of conjugative gene transfer in C. jejuni.}, }
@article {pmid25911229, year = {2015}, author = {Zoller, S and Boskova, V and Anisimova, M}, title = {Maximum-Likelihood Tree Estimation Using Codon Substitution Models with Multiple Partitions.}, journal = {Molecular biology and evolution}, volume = {32}, number = {8}, pages = {2208-2216}, pmid = {25911229}, issn = {1537-1719}, mesh = {Bacterial Proteins/*genetics ; *Codon ; *Models, Genetic ; Ralstonia solanacearum/*genetics ; }, abstract = {Many protein sequences have distinct domains that evolve with different rates, different selective pressures, or may differ in codon bias. Instead of modeling these differences by more and more complex models of molecular evolution, we present a multipartition approach that allows maximum-likelihood phylogeny inference using different codon models at predefined partitions in the data. Partition models can, but do not have to, share free parameters in the estimation process. We test this approach with simulated data as well as in a phylogenetic study of the origin of the leucin-rich repeat regions in the type III effector proteins of the pythopathogenic bacteria Ralstonia solanacearum. Our study does not only show that a simple two-partition model resolves the phylogeny better than a one-partition model but also gives more evidence supporting the hypothesis of lateral gene transfer events between the bacterial pathogens and its eukaryotic hosts.}, }
@article {pmid25910948, year = {2015}, author = {Harmer, CJ and Hall, RM}, title = {The A to Z of A/C plasmids.}, journal = {Plasmid}, volume = {80}, number = {}, pages = {63-82}, doi = {10.1016/j.plasmid.2015.04.003}, pmid = {25910948}, issn = {1095-9890}, mesh = {Animals ; Bacteria/*genetics ; Bacterial Proteins/genetics ; Conjugation, Genetic ; DNA Replication ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Plasmids/*genetics ; }, abstract = {Plasmids belonging to incompatibility groups A and C (now A/C) were among the earliest to be associated with antibiotic resistance in Gram-negative bacteria. A/C plasmids are large, conjugative plasmids with a broad host range. The prevalence of A/C plasmids in collections of clinical isolates has revealed their importance in the dissemination of extended-spectrum β-lactamases and carbapenemases. They also mobilize SGI1-type resistance islands. Revived interest in the family has yielded many complete A/C plasmid sequences, revealing that RA1, designated A/C1, is different from the remainder, designated A/C2. There are two distinct A/C2 lineages. Backbones of 128-130 kb include over 120 genes or ORFs encoding proteins of at least 100 amino acids, but very few have been characterized. Genes potentially required for replication, stability and transfer have been identified, but only the replication system of RA1 and the regulation of transfer have been studied. There is enormous variety in the antibiotic resistance genes carried by A/C2 plasmids but they are usually clustered in larger regions at various locations in the backbone. The ARI-A and ARI-B resistance islands are always at a specific location but have variable content. ARI-A is only found in type 1 A/C2 plasmids, which disseminate blaCMY-2 and blaNDM-1 genes, whereas ARI-B, carrying the sul2 gene, is found in both type 1 and type 2. This review summarizes current knowledge of A/C plasmids, and highlights areas of research to be considered in the future.}, }
@article {pmid25902528, year = {2015}, author = {Archibald, JM}, title = {Genomic perspectives on the birth and spread of plastids.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {33}, pages = {10147-10153}, pmid = {25902528}, issn = {1091-6490}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Cell Nucleus/*genetics ; Chlorophyta/physiology ; Cyanobacteria/genetics ; Gene Transfer, Horizontal ; Genome ; *Genomics ; Mosaicism ; Photosynthesis ; Phylogeny ; Plastids/*physiology ; Symbiosis/*physiology ; }, abstract = {The endosymbiotic origin of plastids from cyanobacteria was a landmark event in the history of eukaryotic life. Subsequent to the evolution of primary plastids, photosynthesis spread from red and green algae to unrelated eukaryotes by secondary and tertiary endosymbiosis. Although the movement of cyanobacterial genes from endosymbiont to host is well studied, less is known about the migration of eukaryotic genes from one nucleus to the other in the context of serial endosymbiosis. Here I explore the magnitude and potential impact of nucleus-to-nucleus endosymbiotic gene transfer in the evolution of complex algae, and the extent to which such transfers compromise our ability to infer the deep structure of the eukaryotic tree of life. In addition to endosymbiotic gene transfer, horizontal gene transfer events occurring before, during, and after endosymbioses further confound our efforts to reconstruct the ancient mergers that forged multiple lines of photosynthetic microbial eukaryotes.}, }
@article {pmid25902487, year = {2015}, author = {Kyndt, T and Quispe, D and Zhai, H and Jarret, R and Ghislain, M and Liu, Q and Gheysen, G and Kreuze, JF}, title = {The genome of cultivated sweet potato contains Agrobacterium T-DNAs with expressed genes: An example of a naturally transgenic food crop.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {18}, pages = {5844-5849}, pmid = {25902487}, issn = {1091-6490}, mesh = {Agrobacterium/*genetics ; DNA, Bacterial/genetics ; DNA, Plant/genetics ; Food Safety ; Gene Transfer, Horizontal ; *Genome, Plant ; Ipomoea batatas/*genetics ; Open Reading Frames ; Phylogeny ; Plant Leaves/metabolism ; Plant Roots/metabolism ; Plant Shoots/metabolism ; Plant Stems/metabolism ; *Plants, Genetically Modified ; RNA, Small Interfering/genetics ; Sequence Analysis, DNA ; }, abstract = {Agrobacterium rhizogenes and Agrobacterium tumefaciens are plant pathogenic bacteria capable of transferring DNA fragments [transfer DNA (T-DNA)] bearing functional genes into the host plant genome. This naturally occurring mechanism has been adapted by plant biotechnologists to develop genetically modified crops that today are grown on more than 10% of the world's arable land, although their use can result in considerable controversy. While assembling small interfering RNAs, or siRNAs, of sweet potato plants for metagenomic analysis, sequences homologous to T-DNA sequences from Agrobacterium spp. were discovered. Simple and quantitative PCR, Southern blotting, genome walking, and bacterial artificial chromosome library screening and sequencing unambiguously demonstrated that two different T-DNA regions (IbT-DNA1 and IbT-DNA2) are present in the cultivated sweet potato (Ipomoea batatas [L.] Lam.) genome and that these foreign genes are expressed at detectable levels in different tissues of the sweet potato plant. IbT-DNA1 was found to contain four open reading frames (ORFs) homologous to the tryptophan-2-monooxygenase (iaaM), indole-3-acetamide hydrolase (iaaH), C-protein (C-prot), and agrocinopine synthase (Acs) genes of Agrobacterium spp. IbT-DNA1 was detected in all 291 cultigens examined, but not in close wild relatives. IbT-DNA2 contained at least five ORFs with significant homology to the ORF14, ORF17n, rooting locus (Rol)B/RolC, ORF13, and ORF18/ORF17n genes of A. rhizogenes. IbT-DNA2 was detected in 45 of 217 genotypes that included both cultivated and wild species. Our finding, that sweet potato is naturally transgenic while being a widely and traditionally consumed food crop, could affect the current consumer distrust of the safety of transgenic food crops.}, }
@article {pmid25901001, year = {2015}, author = {Domingues, S and da Silva, GJ and Nielsen, KM}, title = {Global dissemination patterns of common gene cassette arrays in class 1 integrons.}, journal = {Microbiology (Reading, England)}, volume = {161}, number = {7}, pages = {1313-1337}, doi = {10.1099/mic.0.000099}, pmid = {25901001}, issn = {1465-2080}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/*genetics ; Bacterial Infections/*microbiology ; *Disease Transmission, Infectious ; Drug Resistance, Bacterial ; *Environmental Microbiology ; *Gene Transfer, Horizontal ; Global Health ; Humans ; *Integrons ; *Interspersed Repetitive Sequences ; }, abstract = {Integrons are genetic elements that contain a site-specific recombination system able to capture, express and exchange gene cassettes. Mobile integrons are widespread and often confer resistance to multiple antibiotics, due to the expression of the arrays of gene cassettes they carry. Although >300 cassette arrays have been described, < 10 array compositions prevail in the reports related to class 1 integrons. These common arrays are found in a broad variety of hosts and environments, highlighting the high level of horizontal dissemination of these elements amongst bacterial populations and species. Clonal expansion also contributes to the current prevalence and inter-regional spread of integron-carrying bacterial species. Here, we review the dissemination pattern of common cassette arrays with a focus on the bacterial species, the geographical dispersal pattern and the environments in which they reside. Conserved arrays of gene cassettes are found in at least 74 countries and 72 species present in different environments. The factors governing the further spread and population dynamics of these cassette arrays remain to be determined.}, }
@article {pmid25898829, year = {2015}, author = {Sharma, A and Sangwan, N and Negi, V and Kohli, P and Khurana, JP and Rao, DL and Lal, R}, title = {Pan-genome dynamics of Pseudomonas gene complements enriched across hexachlorocyclohexane dumpsite.}, journal = {BMC genomics}, volume = {16}, number = {1}, pages = {313}, pmid = {25898829}, issn = {1471-2164}, mesh = {Base Sequence ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genotype ; Hexachlorocyclohexane/chemistry/*metabolism ; Integrons/genetics ; Metagenomics ; Phylogeny ; Pseudomonas/classification/*genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, DNA ; Soil Microbiology ; Water Microbiology ; Water Pollutants, Chemical/chemistry/metabolism ; }, abstract = {BACKGROUND: Phylogenetic heterogeneity across Pseudomonas genus is complemented by its diverse genome architecture enriched by accessory genetic elements (plasmids, transposons, and integrons) conferring resistance across this genus. Here, we sequenced a stress tolerant genotype i.e. Pseudomonas sp. strain RL isolated from a hexachlorocyclohexane (HCH) contaminated pond (45 mg of total HCH g(-1) sediment) and further compared its gene repertoire with 17 reference ecotypes belonging to P. stutzeri, P. mendocina, P. aeruginosa, P. psychrotolerans and P. denitrificans, representing metabolically diverse ecosystems (i.e. marine, clinical, and soil/sludge). Metagenomic data from HCH contaminated pond sediment and similar HCH contaminated sites were further used to analyze the pan-genome dynamics of Pseudomonas genotypes enriched across increasing HCH gradient.<br><br>RESULTS: Although strain RL demonstrated clear species demarcation (ANI&#x2009;&#x2264;&#x2009;80.03%) from the rest of its phylogenetic relatives, it was found to be closest to P. stutzeri clade which was further complemented functionally. Comparative functional analysis elucidated strain specific enrichment of metabolic pathways like &#x3b1;-linoleic acid degradation and carbazole degradation in Pseudomonas sp. strain RL and P. stutzeri XLDN-R, respectively. Composition based methods (%codon bias and %G&#x2009;+&#x2009;C difference) further highlighted the significance of horizontal gene transfer (HGT) in evolution of nitrogen metabolism, two-component system (TCS) and methionine metabolism across the Pseudomonas genomes used in this study. An intact mobile class-I integron (3,552&#xa0;bp) with a captured gene cassette encoding for dihydrofolate reductase (dhfra1) was detected in strain RL, distinctly demarcated from other integron harboring species (i.e. P. aeruginosa, P. stutzeri, and P. putida). Mobility of this integron was confirmed by its association with Tnp21-like transposon (95% identity) suggesting stress specific mobilization across HCH contaminated sites. Metagenomics data from pond sediment and recently surveyed HCH adulterated soils revealed the in situ enrichment of integron associated transposase gene (TnpA6100) across increasing HCH contamination (0.7 to 450&#xa0;mg HCH g(-1) of soil).<br><br>CONCLUSIONS: Unlocking the potential of comparative genomics supplemented with metagenomics, we have attempted to resolve the environment and strain specific demarcations across 18 Pseudomonas gene complements. Pan-genome analyses of these strains indicate at astoundingly diverse metabolic strategies and provide genetic basis for the cosmopolitan existence of this taxon.}, }
@article {pmid25897780, year = {2015}, author = {Ho, MH and Chen, CH and Goodwin, JS and Wang, BY and Xie, H}, title = {Functional Advantages of Porphyromonas gingivalis Vesicles.}, journal = {PloS one}, volume = {10}, number = {4}, pages = {e0123448}, pmid = {25897780}, issn = {1932-6203}, support = {UL1 TR000445/TR/NCATS NIH HHS/United States ; U54 CA163069/CA/NCI NIH HHS/United States ; G12 MD007586/MD/NIMHD NIH HHS/United States ; S10 RR025497/RR/NCRR NIH HHS/United States ; U54 MD007586/MD/NIMHD NIH HHS/United States ; R24 DA036420/DA/NIDA NIH HHS/United States ; DE022428/DE/NIDCR NIH HHS/United States ; R21 DE022428/DE/NIDCR NIH HHS/United States ; U54 MD007593/MD/NIMHD NIH HHS/United States ; MD007593/MD/NIMHD NIH HHS/United States ; UL1 RR024975/RR/NCRR NIH HHS/United States ; DE020915/DE/NIDCR NIH HHS/United States ; UL1 RR024975-01/RR/NCRR NIH HHS/United States ; MD007586/MD/NIMHD NIH HHS/United States ; 2 UL1 TR000445-06/TR/NCATS NIH HHS/United States ; R21 DE020915/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacteroidaceae Infections/*microbiology ; *Biofilms ; Cell Membrane ; Cells, Cultured ; Extracellular Vesicles/physiology ; Fibroblasts/microbiology/physiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Host-Pathogen Interactions ; Human Umbilical Vein Endothelial Cells/microbiology/physiology ; Humans ; Keratinocytes/microbiology/physiology ; Periodontitis/microbiology ; Porphyromonas gingivalis/*physiology ; }, abstract = {Porphyromonas gingivalis is a keystone pathogen of periodontitis. Outer membrane vesicles (OMVs) have been considered as both offense and defense components of this bacterium. Previous studies indicated that like their originating cells, P. gingivalis vesicles, are able to invade oral epithelial cells and gingival fibroblasts, in order to promote aggregation of some specific oral bacteria and to induce host immune responses. In the present study, we investigated the invasive efficiency of P. gingivalis OMVs and compared results with that of the originating cells. Results revealed that 70-90% of human primary oral epithelial cells, gingival fibroblasts, and human umbilical vein endothelial cells carried vesicles from P. gingivalis 33277 after being exposed to the vesicles for 1 h, while 20-50% of the host cells had internalized P. gingivalis cells. We also detected vesicle-associated DNA and RNA and a vesicle-mediated horizontal gene transfer in P. gingivalis strains, which represents a novel mechanism for gene transfer between P. gingivalis strains. Moreover, purified vesicles of P. gingivalis appear to have a negative impact on biofilm formation and the maintenance of Streptococcus gordonii. Our results suggest that vesicles are likely the best offence weapon of P. gingivalis for bacterial survival in the oral cavity and for induction of periodontitis.}, }
@article {pmid25897759, year = {2015}, author = {Fournier, GP and Andam, CP and Gogarten, JP}, title = {Ancient horizontal gene transfer and the last common ancestors.}, journal = {BMC evolutionary biology}, volume = {15}, number = {}, pages = {70}, pmid = {25897759}, issn = {1471-2148}, mesh = {Amino Acyl-tRNA Synthetases/*genetics ; Animals ; Archaea/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Phylogeny ; }, abstract = {BACKGROUND: The genomic history of prokaryotic organismal lineages is marked by extensive horizontal gene transfer (HGT) between groups of organisms at all taxonomic levels. These HGT events have played an essential role in the origin and distribution of biological innovations. Analyses of ancient gene families show that HGT existed in the distant past, even at the time of the organismal last universal common ancestor (LUCA). Most gene transfers originated in lineages that have since gone extinct. Therefore, one cannot assume that the last common ancestors of each gene were all present in the same cell representing the cellular ancestor of all extant life.<br><br>RESULTS: Organisms existing as part of a diverse ecosystem at the time of LUCA likely shared genetic material between lineages. If these other lineages persisted for some time, HGT with the descendants of LUCA could have continued into the bacterial and archaeal lineages. Phylogenetic analyses of aminoacyl-tRNA synthetase protein families support the hypothesis that the molecular common ancestors of the most ancient gene families did not all coincide in space and time. This is most apparent in the evolutionary histories of seryl-tRNA synthetase and threonyl-tRNA synthetase protein families, each containing highly divergent "rare" forms, as well as the sparse phylogenetic distributions of pyrrolysyl-tRNA synthetase, and the bacterial heterodimeric form of glycyl-tRNA synthetase. These topologies and phyletic distributions are consistent with horizontal transfers from ancient, likely extinct branches of the tree of life.<br><br>CONCLUSIONS: Of all the organisms that may have existed at the time of LUCA, by definition only one lineage is survived by known progeny; however, this lineage retains a genomic record of heterogeneous genetic origins. The evolutionary histories of aminoacyl-tRNA synthetases (aaRS) are especially informative in detecting this signal, as they perform primordial biological functions, have undergone several ancient HGT events, and contain many sites with low substitution rates allowing deep phylogenetic reconstruction. We conclude that some aaRS families contain groups that diverge before LUCA. We propose that these ancient gene variants be described by the term "hypnologs", reflecting their ancient, reticulate origin from a time in life history that has been all but erased".}, }
@article {pmid25897488, year = {2015}, author = {San Millan, A and Toll-Riera, M and Qi, Q and MacLean, RC}, title = {Interactions between horizontally acquired genes create a fitness cost in Pseudomonas aeruginosa.}, journal = {Nature communications}, volume = {6}, number = {}, pages = {6845}, pmid = {25897488}, issn = {2041-1723}, support = {281591/ERC_/European Research Council/International ; G0900747//Medical Research Council/United Kingdom ; 090532/Z/09/Z//Wellcome Trust/United Kingdom ; }, mesh = {Bacterial Proteins/genetics/*metabolism ; Cloning, Molecular ; Gene Expression Regulation, Bacterial/*physiology ; *Gene Transfer, Horizontal ; *Genetic Fitness ; Plasmids ; *Pseudomonas aeruginosa ; RNA, Bacterial/genetics/metabolism ; }, abstract = {Horizontal gene transfer (HGT) plays a key role in bacterial evolution, especially with respect to antibiotic resistance. Fitness costs associated with mobile genetic elements (MGEs) are thought to constrain HGT, but our understanding of these costs remains fragmentary, making it difficult to predict the success of HGT events. Here we use the interaction between P. aeruginosa and a costly plasmid (pNUK73) to investigate the molecular basis of the cost of HGT. Using RNA-Seq, we show that the acquisition of pNUK73 results in a profound alteration of the transcriptional profile of chromosomal genes. Mutations that inactivate two genes encoded on chromosomally integrated MGEs recover these fitness costs and transcriptional changes by decreasing the expression of the pNUK73 replication gene. Our study demonstrates that interactions between MGEs can compromise bacterial fitness via altered gene expression, and we argue that conflicts between mobile elements impose a general constraint on evolution by HGT.}, }
@article {pmid25896956, year = {2015}, author = {Zhang, Y and Zhang, S and Zhang, G and Liu, X and Wang, C and Xu, J}, title = {Comparison of mitochondrial genomes provides insights into intron dynamics and evolution in the caterpillar fungus Cordyceps militaris.}, journal = {Fungal genetics and biology : FG &amp; B}, volume = {77}, number = {}, pages = {95-107}, doi = {10.1016/j.fgb.2015.04.009}, pmid = {25896956}, issn = {1096-0937}, mesh = {Animals ; Cordyceps/*genetics/pathogenicity/ultrastructure ; *Evolution, Molecular ; Exons ; Gene Transfer, Horizontal ; *Genome, Mitochondrial ; *Introns ; Larva/microbiology ; Mitochondrial Proteins/genetics ; Phylogeny ; }, abstract = {Intra-specific comparison of mitochondrial genomes can help elucidate the evolution of a species, however it has not been performed for hypocrealean fungi that form diverse symbiotic associations with other organisms. In this study, comparative analyses of three completely sequenced mitochondrial genomes of a hypocrealean fungus, Cordyceps militaris, the type species of Cordyceps genus, revealed that the introns were the main contributors to mitochondrial genome size variations among strains. Mitochondrial genes in C. militaris have been invaded by group I introns in at least eight positions. PCR assays of various C. militaris isolates showed abundant variations of intron presence/absence among strains at seven of the eight intronic loci. Although the ancestral intron pattern was inferred to contain all eight introns, loss and/or gain events occurred for seven of the eight introns. These introns invaded the C. militaris mitochondrial genome probably by horizontal transfer from other fungi, and intron insertions into intronless genes in C. militaris were accompanied by co-conversions of upstream exon sequences especially for those introns targeting protein-coding genes. We also detected phylogenetic congruence between the intron and exon trees at each individual locus, consistent with the ancestral mitochondria of C. militaris as having all eight introns. This study helps to explain the evolution of C. militaris mitochondrial genomes and will facilitate population genetic studies of this medicinally important fungus.}, }
@article {pmid25896520, year = {2015}, author = {Atkinson, CT and Kunde, DA and Tristram, SG}, title = {Acquired macrolide resistance genes in Haemophilus influenzae?.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {70}, number = {8}, pages = {2234-2236}, doi = {10.1093/jac/dkv093}, pmid = {25896520}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/*pharmacology ; Cohort Studies ; Disk Diffusion Antimicrobial Tests ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genotype ; Haemophilus Infections/microbiology ; Haemophilus influenzae/*drug effects/*genetics/isolation &amp; purification ; Humans ; Macrolides/*pharmacology ; Phenotype ; Polymerase Chain Reaction ; Respiratory Tract Infections/microbiology ; }, abstract = {OBJECTIVES: The objective of this study was to determine the prevalence of specific acquired macrolide resistance genes previously reported as present in clinical isolates of Haemophilus influenzae.<br><br>METHODS: A collection of 172 clinical respiratory isolates of H. influenzae, including 59 isolates from cystic fibrosis patients and 27 from non-cystic fibrosis bronchiectasis patients with significant prior macrolide use, was established. This collection was tested for azithromycin susceptibility using Etest and screened for the presence of erm(A), erm(B), erm(C), erm(F), mef(A) and mef(E) using locked nucleic acid dual-labelled hydrolysis probes.<br><br>RESULTS: The azithromycin MICs ranged from 0.09 to >256 mg/L, with 2 (1.2%) isolates susceptible, 163 (94.8%) intermediate and 7 (4%) resistant according to EUCAST breakpoints (susceptible, &#x2264;0.12 mg/L; resistant, >4 mg/L). None of the acquired macrolide resistance genes erm(A), erm(B), erm(C), erm(F), mef(A) or mef(E) was detected in any of the isolates.<br><br>CONCLUSIONS: The specific acquired macrolide resistance genes are not widespread in H. influenzae and the high prevalence of these genes previously reported might be unique to the specific circumstances of that study.}, }
@article {pmid25895973, year = {2015}, author = {Valero-Rello, A and Hapeshi, A and Anastasi, E and Alvarez, S and Scortti, M and Meijer, WG and MacArthur, I and Vázquez-Boland, JA}, title = {An Invertron-Like Linear Plasmid Mediates Intracellular Survival and Virulence in Bovine Isolates of Rhodococcus equi.}, journal = {Infection and immunity}, volume = {83}, number = {7}, pages = {2725-2737}, pmid = {25895973}, issn = {1098-5522}, support = {095831/WT_/Wellcome Trust/United Kingdom ; G0900740/MRC_/Medical Research Council/United Kingdom ; MR/K001744/1/MRC_/Medical Research Council/United Kingdom ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Cattle ; Cluster Analysis ; Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Macrophages/*microbiology ; Mice, Inbred BALB C ; *Microbial Viability ; Molecular Sequence Data ; Phylogeny ; *Plasmids ; Rhodococcus equi/genetics/growth &amp; development/isolation &amp; purification/*physiology ; Sequence Analysis, DNA ; Sequence Homology ; Virulence ; Virulence Factors/genetics ; }, abstract = {We report a novel host-associated virulence plasmid in Rhodococcus equi, pVAPN, carried by bovine isolates of this facultative intracellular pathogenic actinomycete. Surprisingly, pVAPN is a 120-kb invertron-like linear replicon unrelated to the circular virulence plasmids associated with equine (pVAPA) and porcine (pVAPB variant) R. equi isolates. pVAPN is similar to the linear plasmid pNSL1 from Rhodococcus sp. NS1 and harbors six new vap multigene family members (vapN to vapS) in a vap pathogenicity locus presumably acquired via en bloc mobilization from a direct predecessor of equine pVAPA. Loss of pVAPN rendered R. equi avirulent in macrophages and mice. Mating experiments using an in vivo transconjugant selection strategy demonstrated that pVAPN transfer is sufficient to confer virulence to a plasmid-cured R. equi recipient. Phylogenetic analyses assigned the vap multigene family complement from pVAPN, pVAPA, and pVAPB to seven monophyletic clades, each containing plasmid type-specific allelic variants of a precursor vap gene carried by the nearest vap island ancestor. Deletion of vapN, the predicted "bovine-type" allelic counterpart of vapA, essential for virulence in pVAPA, abrogated pVAPN-mediated intramacrophage proliferation and virulence in mice. Our findings support a model in which R. equi virulence is conferred by host-adapted plasmids. Their central role is mediating intracellular proliferation in macrophages, promoted by a key vap determinant present in the common ancestor of the plasmid-specific vap islands, with host tropism as a secondary trait selected during coevolution with specific animal species.}, }
@article {pmid25894542, year = {2015}, author = {Koonin, EV}, title = {The Turbulent Network Dynamics of Microbial Evolution and the Statistical Tree of Life.}, journal = {Journal of molecular evolution}, volume = {80}, number = {5-6}, pages = {244-250}, pmid = {25894542}, issn = {1432-1432}, support = {//Intramural NIH HHS/United States ; }, mesh = {Archaea/classification/*genetics ; Bacteria/classification/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Archaeal ; *Genome, Bacterial ; *Models, Genetic ; Mutation Rate ; Phylogeny ; }, abstract = {The wide spread and high rate of gene exchange and loss in the prokaryotic world translate into "network genomics". The rates of gene gain and loss are comparable with the rate of point mutations but are substantially greater than the duplication rate. Thus, evolution of prokaryotes is primarily shaped by gene gain and loss. These processes are essential to prevent mutational meltdown of microbial populations by stopping Muller's ratchet and appear to trigger emergence of major novel clades by opening up new ecological niches. At least some bacteria and archaea seem to have evolved dedicated devices for gene transfer. Despite the dominance of gene gain and loss, evolution of genes is intrinsically tree-like. The significant coherence between the topologies of numerous gene trees, particularly those for (nearly) universal genes, is compatible with the concept of a statistical tree of life, which forms the framework for reconstruction of the evolutionary processes in the prokaryotic world.}, }
@article {pmid25891795, year = {2015}, author = {Moon, BY and Park, JY and Hwang, SY and Robinson, DA and Thomas, JC and Fitzgerald, JR and Park, YH and Seo, KS}, title = {Phage-mediated horizontal transfer of a Staphylococcus aureus virulence-associated genomic island.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {9784}, pmid = {25891795}, issn = {2045-2322}, support = {BB/I013873/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 1P20GM103646-01A1/GM/NIGMS NIH HHS/United States ; GM080602/GM/NIGMS NIH HHS/United States ; P20 GM103646/GM/NIGMS NIH HHS/United States ; BB/1013873/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; R01 GM080602/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics ; Blotting, Southern ; DNA, Bacterial/analysis ; DNA, Viral/analysis ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Genomic Islands/*genetics ; Prophages/genetics/physiology ; Sequence Analysis, DNA ; Staphylococcus aureus/*genetics ; Virulence Factors/*genetics ; }, abstract = {Staphylococcus aureus is a major pathogen of humans and animals. The capacity of S. aureus to adapt to different host species and tissue types is strongly influenced by the acquisition of mobile genetic elements encoding determinants involved in niche adaptation. The genomic islands νSaα and νSaβ are found in almost all S. aureus strains and are characterized by extensive variation in virulence gene content. However the basis for the diversity and the mechanism underlying mobilization of the genomic islands between strains are unexplained. Here, we demonstrated that the genomic island, νSaβ, encoding an array of virulence factors including staphylococcal superantigens, proteases, and leukotoxins, in addition to bacteriocins, was transferrable in vitro to human and animal strains of multiple S. aureus clones via a resident prophage. The transfer of the νSaβ appears to have been accomplished by multiple conversions of transducing phage particles carrying overlapping segments of the νSaβ. Our findings solve a long-standing mystery regarding the diversification and spread of the genomic island νSaβ, highlighting the central role of bacteriophages in the pathogenic evolution of S. aureus.}, }
@article {pmid25890302, year = {2015}, author = {Caballero, ZC and Costa-Martins, AG and Ferreira, RC and P Alves, JM and Serrano, MG and Camargo, EP and Buck, GA and Minoprio, P and G Teixeira, MM}, title = {Phylogenetic and syntenic data support a single horizontal transference to a Trypanosoma ancestor of a prokaryotic proline racemase implicated in parasite evasion from host defences.}, journal = {Parasites &amp; vectors}, volume = {8}, number = {}, pages = {222}, pmid = {25890302}, issn = {1756-3305}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Isomerases/*genetics ; Amino Acid Sequence ; *Evolution, Molecular ; Firmicutes/enzymology/*genetics ; *Gene Transfer, Horizontal ; Immune Evasion ; Molecular Sequence Data ; *Phylogeny ; Protozoan Proteins/*genetics ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Synteny ; Trypanosoma/enzymology/*genetics/immunology ; }, abstract = {BACKGROUND: Proline racemase (PRAC) enzymes of Trypanosoma cruzi (TcPRAC), the agent of Chagas disease, and Trypanosoma vivax (TvPRAC), the agent of livestock trypanosomosis, have been implicated in the B-cells polyclonal activation contributing to immunosuppression and the evasion of host defences. The similarity to prokaryotic PRAC and the absence in Trypanosoma brucei and Trypanosoma congolense have raised many questions about the origin, evolution, and functions of trypanosome PRAC (TryPRAC) enzymes.<br><br>FINDINGS: We identified TryPRAC homologs as single copy genes per haploid genome in 12 of 15 Trypanosoma species, including T. cruzi and T. cruzi marinkellei, T. dionisii, T. erneyi, T. rangeli, T. conorhini and T. lewisi, all parasites of mammals. Polymorphisms in TcPRAC genes matched T. cruzi genotypes: TcI-TcIV and Tcbat have unique genes, while the hybrids TcV and TcVI contain TcPRACA and TcPRACB from parental TcII and TcIII, respectively. PRAC homologs were identified in trypanosomes from anurans, snakes, crocodiles, lizards, and birds. Most trypanosomes have intact PRAC genes. T. rangeli possesses only pseudogenes, maybe in the process of being lost. T. brucei, T. congolense and their allied species, except the more distantly related T. vivax, have completely lost PRAC genes.<br><br>CONCLUSIONS: The genealogy of TryPRAC homologs supports an evolutionary history congruent with the Trypanosoma phylogeny. This finding, together with the synteny of PRAC loci, the relationships with prokaryotic PRAC inferred by taxon-rich phylogenetic analysis, and the absence in trypanosomatids of any other genera or in bodonids or euglenids suggest that a common ancestor of Trypanosoma gained PRAC gene by a single and ancient horizontal gene transfer (HGT) from a Firmicutes bacterium more closely related to Gemella and other species of Bacilli than to Clostridium as previously suggested. Our broad phylogenetic study allowed investigation of TryPRAC evolution over long and short timescales. TryPRAC genes diverged to become species-specific and genotype-specific for T. cruzi and T. rangeli, with resulting genealogies congruent with those obtained using vertically inherited genes. The inventory of TryPRAC genes described here is the first step toward the understanding of the roles of PRAC enzymes in trypanosomes differing in life cycles, virulence, and infection and immune evasion strategies.}, }
@article {pmid25888688, year = {2015}, author = {Méric, G and Miragaia, M and de Been, M and Yahara, K and Pascoe, B and Mageiros, L and Mikhail, J and Harris, LG and Wilkinson, TS and Rolo, J and Lamble, S and Bray, JE and Jolley, KA and Hanage, WP and Bowden, R and Maiden, MC and Mack, D and de Lencastre, H and Feil, EJ and Corander, J and Sheppard, SK}, title = {Ecological Overlap and Horizontal Gene Transfer in Staphylococcus aureus and Staphylococcus epidermidis.}, journal = {Genome biology and evolution}, volume = {7}, number = {5}, pages = {1313-1328}, pmid = {25888688}, issn = {1759-6653}, support = {090532/Z/09/Z/WT_/Wellcome Trust/United Kingdom ; BB/I02464X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 087622/WT_/Wellcome Trust/United Kingdom ; G0801929/MRC_/Medical Research Council/United Kingdom ; MR/M501608/1/MRC_/Medical Research Council/United Kingdom ; MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; U54 GM088558/GM/NIGMS NIH HHS/United States ; U54GM088558/GM/NIGMS NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Ecological and Environmental Phenomena ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Fungal ; Genetic Variation ; Genome, Fungal ; Homologous Recombination ; Staphylococcus aureus/*genetics ; Staphylococcus epidermidis/*genetics ; }, abstract = {The opportunistic pathogens Staphylococcus aureus and Staphylococcus epidermidis represent major causes of severe nosocomial infection, and are associated with high levels of mortality and morbidity worldwide. These species are both common commensals on the human skin and in the nasal pharynx, but are genetically distinct, differing at 24% average nucleotide divergence in 1,478 core genes. To better understand the genome dynamics of these ecologically similar staphylococcal species, we carried out a comparative analysis of 324 S. aureus and S. epidermidis genomes, including 83 novel S. epidermidis sequences. A reference pan-genome approach and whole genome multilocus-sequence typing revealed that around half of the genome was shared between the species. Based on a BratNextGen analysis, homologous recombination was found to have impacted on 40% of the core genes in S. epidermidis, but on only 24% of the core genes in S. aureus. Homologous recombination between the species is rare, with a maximum of nine gene alleles shared between any two S. epidermidis and S. aureus isolates. In contrast, there was considerable interspecies admixture of mobile elements, in particular genes associated with the SaPIn1 pathogenicity island, metal detoxification, and the methicillin-resistance island SCCmec. Our data and analysis provide a context for considering the nature of recombinational boundaries between S. aureus and S. epidermidis and, the selective forces that influence realized recombination between these species.}, }
@article {pmid25888333, year = {2015}, author = {Ailloud, F and Lowe, T and Cellier, G and Roche, D and Allen, C and Prior, P}, title = {Comparative genomic analysis of Ralstonia solanacearum reveals candidate genes for host specificity.}, journal = {BMC genomics}, volume = {16}, number = {1}, pages = {270}, pmid = {25888333}, issn = {1471-2164}, mesh = {Ecotype ; *Genes, Bacterial ; *Genomics ; *Host Specificity ; Musa/microbiology ; Phylogeny ; Plant Diseases/*microbiology ; Plants/microbiology ; Polymorphism, Genetic ; Ralstonia solanacearum/*genetics/pathogenicity ; Virulence Factors/genetics ; }, abstract = {BACKGROUND: Ralstonia solanacearum is a vascular soil-borne plant pathogen with an unusually broad host range. This economically destructive and globally distributed bacterium has thousands of distinct lineages within a heterogeneous and taxonomically disputed species complex. Some lineages include highly host-adapted strains (ecotypes), such as the banana Moko disease-causing strains, the cold-tolerant potato brown rot strains (also known as R3bv2) and the recently emerged Not Pathogenic to Banana (NPB) strains.<br><br>RESULTS: These distinct ecotypes offer a robust model to study host adaptation and the emergence of ecotypes because the polyphyletic Moko strains include lineages that are phylogenetically close to the monophyletic brown rot and NPB strains. Draft genomes of eight new strains belonging to these three model ecotypes were produced to complement the eleven publicly available R. solanacearum genomes. Using a suite of bioinformatics methods, we searched for genetic and evolutionary features that distinguish ecotypes and propose specific hypotheses concerning mechanisms of host adaptation in the R. solanacearum species complex. Genome-wide, few differences were identified, but gene loss events, non-synonymous polymorphisms, and horizontal gene transfer were identified among type III effectors and were associated with host range differences.<br><br>CONCLUSIONS: This extensive comparative genomics analysis uncovered relatively few divergent features among closely related strains with contrasting biological characteristics; however, several virulence factors were associated with the emergence of Moko, NPB and brown rot and could explain host adaptation.}, }
@article {pmid25888315, year = {2015}, author = {Xu, K and Yuan, Z and Rayner, S and Hu, X}, title = {Genome comparison provides molecular insights into the phylogeny of the reassigned new genus Lysinibacillus.}, journal = {BMC genomics}, volume = {16}, number = {1}, pages = {140}, pmid = {25888315}, issn = {1471-2164}, mesh = {Animals ; Bacillus/*genetics ; Bacterial Toxins/genetics ; *Classification ; Culex/genetics ; Culicidae/drug effects/genetics ; *Genome, Bacterial ; Insecticides/pharmacology ; Interspersed Repetitive Sequences/genetics ; *Phylogeny ; }, abstract = {BACKGROUND: Lysinibacillus sphaericus (formerly named Bacillus sphaericus) is incapable of polysaccharide utilization and some isolates produce active insecticidal proteins against mosquito larvae. Its taxonomic status was changed to the genus Lysinibacillus in 2007 with some other organisms previously regarded as members of Bacillus. However, this classification is mainly based on physiology and phenotype and there is limited genomic information to support it.<br><br>RESULTS: In this study, four genomes of L. sphaericus were sequenced and compared with those of 24 representative strains belonging to Lysinibacillus and Bacillus. The results show that Lysinibacillus strains are phylogenetically related based on the genome sequences and composition of core genes. Comparison of gene function indicates the major difference between Lysinibacillus and the two Bacillus species is related to metabolism and cell wall/membrane biogenesis. Although L. sphaericus mosquitocidal isolates are highly conserved, other Lysinibacillus strains display a large heterogeneity. It was observed that mosquitocidal toxin genes in L. sphaericus were in close proximity to genome islands (GIs) and mobile genetic elements (MGEs). Furthermore, different copies and varying genomic location of the GIs containing binA/binB was observed amongst the different isolates. In addition, a plasmid highly similar to pBsph, but lacking the GI containing binA/binB, was found in L. sphaericus SSII-1.<br><br>CONCLUSIONS: Our results confirm the taxonomy of the new genus Lysinibacillus at the genome level and suggest a new species for mosquito-toxic L. sphaericus. Based on our findings, we hypothesize that (1) Lysinibacillus strains evolved from a common ancestor and the mosquitocidal L. sphaericus toxin genes were acquired by horizontal gene transfer (HGT), and (2) capture and loss of plasmids occurs in the population, which plays an important role in the transmission of binA/binB.}, }
@article {pmid25887897, year = {2015}, author = {Krueger, T and Fisher, PL and Becker, S and Pontasch, S and Dove, S and Hoegh-Guldberg, O and Leggat, W and Davy, SK}, title = {Transcriptomic characterization of the enzymatic antioxidants FeSOD, MnSOD, APX and KatG in the dinoflagellate genus Symbiodinium.}, journal = {BMC evolutionary biology}, volume = {15}, number = {}, pages = {48}, pmid = {25887897}, issn = {1471-2148}, mesh = {Amino Acid Sequence ; Animals ; Biological Evolution ; Coral Reefs ; Dinoflagellida/*classification/enzymology/*genetics ; Genetic Variation ; Molecular Sequence Data ; Peroxidases/chemistry/*genetics ; Phylogeny ; Superoxide Dismutase/chemistry/*genetics ; Symbiosis ; Transcriptome ; }, abstract = {BACKGROUND: The diversity of the symbiotic dinoflagellate Symbiodinium sp., as assessed by genetic markers, is well established. To what extent this diversity is reflected on the amino acid level of functional genes such as enzymatic antioxidants that play an important role in thermal stress tolerance of the coral-Symbiodinium symbiosis is, however, unknown. Here we present a predicted structural analysis and phylogenetic characterization of the enzymatic antioxidant repertoire of the genus Symbiodinium. We also report gene expression and enzymatic activity under short-term thermal stress in Symbiodinium of the B1 genotype.<br><br>RESULTS: Based on eight different ITS2 types, covering six clades, multiple protein isoforms for three of the four investigated antioxidants (ascorbate peroxidase [APX], catalase peroxidase [KatG], manganese superoxide dismutase [MnSOD]) are present in the genus Symbiodinium. Amino acid sequences of both SOD metalloforms (Fe/Mn), as well as KatG, exhibited a number of prokaryotic characteristics that were also supported by the protein phylogeny. In contrast to the bacterial form, KatG in Symbiodinium is characterized by extended functionally important loops and a shortened C-terminal domain. Intercladal sequence variations were found to be much higher in both peroxidases, compared to SODs. For APX, these variable residues involve binding sites for substrates and cofactors, and might therefore differentially affect the catalytic properties of this enzyme between clades. While expression of antioxidant genes was successfully measured in Symbiodinium B1, it was not possible to assess the link between gene expression and protein activity due to high variability in expression between replicates, and little response in their enzymatic activity over the three-day experimental period.<br><br>CONCLUSIONS: The genus Symbiodinium has a diverse enzymatic antioxidant repertoire that has similarities to prokaryotes, potentially as a result of horizontal gene transfer or events of secondary endosymbiosis. Different degrees of sequence evolution between SODs and peroxidases might be the result of potential selective pressure on the conserved molecular function of SODs as the first line of defence. In contrast, genetic redundancy of hydrogen peroxide scavenging enzymes might permit the observed variations in peroxidase sequences. Our data and successful measurement of antioxidant gene expression in Symbiodinium will serve as basis for further studies of coral health.}, }
@article {pmid25887467, year = {2015}, author = {Wysocki, WP and Clark, LG and Attigala, L and Ruiz-Sanchez, E and Duvall, MR}, title = {Evolution of the bamboos (Bambusoideae; Poaceae): a full plastome phylogenomic analysis.}, journal = {BMC evolutionary biology}, volume = {15}, number = {}, pages = {50}, pmid = {25887467}, issn = {1471-2148}, mesh = {*Biological Evolution ; Chloroplasts/genetics ; Gene Expression Profiling ; Genome, Chloroplast ; Phylogeny ; Poaceae/classification/cytology/*genetics ; }, abstract = {BACKGROUND: Bambusoideae (Poaceae) comprise three distinct and well-supported lineages: tropical woody bamboos (Bambuseae), temperate woody bamboos (Arundinarieae) and herbaceous bamboos (Olyreae). Phylogenetic studies using chloroplast markers have generally supported a sister relationship between Bambuseae and Olyreae. This suggests either at least two origins of the woody bamboo syndrome in this subfamily or its loss in Olyreae.<br><br>RESULTS: Here a full chloroplast genome (plastome) phylogenomic study is presented using the coding and noncoding regions of 13 complete plastomes from the Bambuseae, eight from Olyreae and 10 from Arundinarieae. Trees generated using full plastome sequences support the previously recovered monophyletic relationship between Bambuseae and Olyreae. In addition to these relationships, several unique plastome features are uncovered including the first mitogenome-to-plastome horizontal gene transfer observed in monocots.<br><br>CONCLUSIONS: Phylogenomic agreement with previous published phylogenies reinforces the validity of these studies. Additionally, this study presents the first published plastomes from Neotropical woody bamboos and the first full plastome phylogenomic study performed within the herbaceous bamboos. Although the phylogenomic tree presented in this study is largely robust, additional studies using nuclear genes support monophyly in woody bamboos as well as hybridization among previous woody bamboo lineages. The evolutionary history of the Bambusoideae could be further clarified using transcriptomic techniques to increase sampling among nuclear orthologues and investigate the molecular genetics underlying the development of woody and floral tissues.}, }
@article {pmid25887237, year = {2015}, author = {Hunsperger, HM and Randhawa, T and Cattolico, RA}, title = {Extensive horizontal gene transfer, duplication, and loss of chlorophyll synthesis genes in the algae.}, journal = {BMC evolutionary biology}, volume = {15}, number = {}, pages = {16}, pmid = {25887237}, issn = {1471-2148}, support = {T32 HG000035/HG/NHGRI NIH HHS/United States ; T32 HG00035/HG/NHGRI NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Cell Nucleus/genetics ; Chlorophyll/genetics ; Chlorophyll A ; Chloroplasts/genetics ; Cyanobacteria/*genetics ; Dinoflagellida/cytology/*genetics ; Eukaryota/classification/cytology/*genetics ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Oxidoreductases Acting on CH-CH Group Donors/genetics ; Phylogeny ; Sequence Alignment ; Stramenopiles/cytology/*genetics ; Symbiosis ; }, abstract = {BACKGROUND: Two non-homologous, isofunctional enzymes catalyze the penultimate step of chlorophyll a synthesis in oxygenic photosynthetic organisms such as cyanobacteria, eukaryotic algae and land plants: the light-independent (LIPOR) and light-dependent (POR) protochlorophyllide oxidoreductases. Whereas the distribution of these enzymes in cyanobacteria and land plants is well understood, the presence, loss, duplication, and replacement of these genes have not been surveyed in the polyphyletic and remarkably diverse eukaryotic algal lineages.<br><br>RESULTS: A phylogenetic reconstruction of the history of the POR enzyme (encoded by the por gene in nuclei) in eukaryotic algae reveals replacement and supplementation of ancestral por genes in several taxa with horizontally transferred por genes from other eukaryotic algae. For example, stramenopiles and haptophytes share por gene duplicates of prasinophytic origin, although their plastid ancestry predicts a rhodophytic por signal. Phylogenetically, stramenopile pors appear ancestral to those found in haptophytes, suggesting transfer from stramenopiles to haptophytes by either horizontal or endosymbiotic gene transfer. In dinoflagellates whose plastids have been replaced by those of a haptophyte or diatom, the ancestral por genes seem to have been lost whereas those of the new symbiotic partner are present. Furthermore, many chlorarachniophytes and peridinin-containing dinoflagellates possess por gene duplicates. In contrast to the retention, gain, and frequent duplication of algal por genes, the LIPOR gene complement (chloroplast-encoded chlL, chlN, and chlB genes) is often absent. LIPOR genes have been lost from haptophytes and potentially from the euglenid and chlorarachniophyte lineages. Within the chlorophytes, rhodophytes, cryptophytes, heterokonts, and chromerids, some taxa possess both POR and LIPOR genes while others lack LIPOR. The gradual process of LIPOR gene loss is evidenced in taxa possessing pseudogenes or partial LIPOR gene compliments. No horizontal transfer of LIPOR genes was detected.<br><br>CONCLUSIONS: We document a pattern of por gene acquisition and expansion as well as loss of LIPOR genes from many algal taxa, paralleling the presence of multiple por genes and lack of LIPOR genes in the angiosperms. These studies present an opportunity to compare the regulation and function of por gene families that have been acquired and expanded in patterns unique to each of various algal taxa.}, }
@article {pmid25886068, year = {2015}, author = {Buchberger, T and Lamparter, T}, title = {Streptophyte phytochromes exhibit an N-terminus of cyanobacterial origin and a C-terminus of proteobacterial origin.}, journal = {BMC research notes}, volume = {8}, number = {}, pages = {144}, pmid = {25886068}, issn = {1756-0500}, mesh = {Algorithms ; Archaea/classification/genetics/metabolism ; Bacteroidetes/classification/genetics/metabolism ; Biological Evolution ; Cyanobacteria/classification/genetics/metabolism ; Fungi/classification/genetics/metabolism ; Gene Duplication ; Gene Expression ; Gene Transfer, Horizontal ; Histidine Kinase ; *Phylogeny ; Phytochrome A/*chemistry/genetics/metabolism ; Phytochrome B/*chemistry/genetics/metabolism ; Plant Proteins/*chemistry/genetics/metabolism ; Protein Kinases/*chemistry/genetics/metabolism ; Protein Structure, Tertiary ; Proteobacteria/classification/genetics/metabolism ; Streptophyta/classification/*genetics/metabolism ; }, abstract = {BACKGROUND: Phytochromes are red light-sensitive photoreceptors that control a variety of developmental processes in plants, algae, bacteria and fungi. Prototypical phytochromes exhibit an N-terminal tridomain (PGP) consisting of PAS, GAF and PHY domains and a C-terminal histidine kinase (HK).<br><br>RESULTS: The mode of evolution of streptophyte, fungal and diatom phytochromes from bacteria is analyzed using two programs for sequence alignment and six programs for tree construction. Our results suggest that Bacteroidetes present the most ancient types of phytochromes. We found many examples of lateral gene transfer and rearrangements of PGP and HK sequences. The PGP and HK of streptophyte phytochromes seem to have different origins. In the most likely scenario, PGP was inherited from cyanobacteria, whereas the C-terminal portion originated from a proteobacterial protein with multiple PAS domains and a C-terminal HK. The plant PhyA and PhyB lineages go back to an early gene duplication event before the diversification of streptophytes. Fungal and diatom PGPs could have a common prokaryotic origin within proteobacteria. Early gene duplication is also obvious in fungal phytochromes.<br><br>CONCLUSIONS: The dominant question of the origin of plant phytochromes is difficult to tackle because the patterns differ among phylogenetic trees. We could partially overcome this problem by combining several alignment and tree construction algorithms and comparing many trees. A rearrangement of PGP and HK can directly explain the insertion of the two PAS domains by which streptophyte phytochromes are distinguished from all other phytochromes.}, }
@article {pmid25885771, year = {2015}, author = {Mikalsen, T and Pedersen, T and Willems, R and Coque, TM and Werner, G and Sadowy, E and van Schaik, W and Jensen, LB and Sundsfjord, A and Hegstad, K}, title = {Investigating the mobilome in clinically important lineages of Enterococcus faecium and Enterococcus faecalis.}, journal = {BMC genomics}, volume = {16}, number = {}, pages = {282}, pmid = {25885771}, issn = {1471-2164}, mesh = {Anti-Bacterial Agents/pharmacology ; Base Sequence ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Drug Resistance, Bacterial/drug effects/genetics ; Enterococcus faecalis/*genetics/isolation &amp; purification ; Enterococcus faecium/*genetics/isolation &amp; purification ; Gene Transfer, Horizontal/genetics ; *Genes, Bacterial ; Genetic Linkage ; Gram-Positive Bacterial Infections/microbiology ; Humans ; Interspersed Repetitive Sequences/*genetics ; Microbial Sensitivity Tests ; Nucleic Acid Hybridization ; Plasmids/genetics/metabolism ; Principal Component Analysis ; Prophages/genetics ; }, abstract = {BACKGROUND: The success of Enterococcus faecium and E. faecalis evolving as multi-resistant nosocomial pathogens is associated with their ability to acquire and share adaptive traits, including antimicrobial resistance genes encoded by mobile genetic elements (MGEs). Here, we investigate this mobilome in successful hospital associated genetic lineages, E. faecium sequence type (ST)17 (n=10) and ST78 (n=10), E. faecalis ST6 (n=10) and ST40 (n=10) by DNA microarray analyses.<br><br>RESULTS: The hybridization patterns of 272 representative targets including plasmid backbones (n=85), transposable elements (n=85), resistance determinants (n=67), prophages (n=29) and clustered regularly interspaced short palindromic repeats (CRISPR)-cas sequences (n=6) separated the strains according to species, and for E. faecalis also according to STs. RCR-, Rep_3-, RepA_N- and Inc18-family plasmids were highly prevalent and with the exception of Rep_3, evenly distributed between the species. There was a considerable difference in the replicon profile, with rep 17/pRUM , rep 2/pRE25 , rep 14/EFNP1 and rep 20/pLG1 dominating in E. faecium and rep 9/pCF10 , rep 2/pRE25 and rep 7 in E. faecalis strains. We observed an overall high correlation between the presence and absence of genes coding for resistance towards antibiotics, metals, biocides and their corresponding MGEs as well as their phenotypic antimicrobial susceptibility pattern. Although most IS families were represented in both E. faecalis and E. faecium, specific IS elements within these families were distributed in only one species. The prevalence of IS256-, IS3-, ISL3-, IS200/IS605-, IS110-, IS982- and IS4-transposases was significantly higher in E. faecium than E. faecalis, and that of IS110-, IS982- and IS1182-transposases in E. faecalis ST6 compared to ST40. Notably, the transposases of IS981, ISEfm1 and IS1678 that have only been reported in few enterococcal isolates were well represented in the E. faecium strains. E. faecalis ST40 strains harboured possible functional CRISPR-Cas systems, and still resistance and prophage sequences were generally well represented.<br><br>CONCLUSIONS: The targeted MGEs were highly prevalent among the selected STs, underlining their potential importance in the evolution of hospital-adapted lineages of enterococci. Although the propensity of inter-species horizontal gene transfer (HGT) must be emphasized, the considerable species-specificity of these MGEs indicates a separate vertical evolution of MGEs within each species, and for E. faecalis within each ST.}, }
@article {pmid25884386, year = {2015}, author = {Pagnier, I and Yutin, N and Croce, O and Makarova, KS and Wolf, YI and Benamar, S and Raoult, D and Koonin, EV and La Scola, B}, title = {Babela massiliensis, a representative of a widespread bacterial phylum with unusual adaptations to parasitism in amoebae.}, journal = {Biology direct}, volume = {10}, number = {}, pages = {13}, pmid = {25884386}, issn = {1745-6150}, mesh = {Acanthamoeba castellanii/*microbiology ; Bacterial Proteins/genetics ; Base Sequence ; Cell Culture Techniques ; Cell Division ; Culture Media ; Cytoplasm/microbiology ; Cytoskeletal Proteins/genetics ; DNA, Bacterial/genetics ; Deltaproteobacteria/*genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal/chemistry ; RNA, Transfer/chemistry ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {BACKGROUND: Only a small fraction of bacteria and archaea that are identifiable by metagenomics can be grown on standard media. Recent efforts on deep metagenomics sequencing, single-cell genomics and the use of specialized culture conditions (culturomics) increasingly yield novel microbes some of which represent previously uncharacterized phyla and possess unusual biological traits.<br><br>RESULTS: We report isolation and genome analysis of Babela massiliensis, an obligate intracellular parasite of Acanthamoeba castellanii. B. massiliensis shows an unusual, fission mode of cell multiplication whereby large, polymorphic bodies accumulate in the cytoplasm of infected amoeba and then split into mature bacterial cells. This unique mechanism of cell division is associated with a deep degradation of the cell division machinery and delayed expression of the ftsZ gene. The genome of B. massiliensis consists of a circular chromosome approximately 1.12 megabase in size that encodes, 981 predicted proteins, 38 tRNAs and one typical rRNA operon. Phylogenetic analysis shows that B. massiliensis belongs to the putative bacterial phylum TM6 that so far was represented by the draft genome of the JCVI TM6SC1 bacterium obtained by single cell genomics and numerous environmental sequences.<br><br>CONCLUSIONS: Currently, B. massiliensis is the only cultivated member of the putative TM6 phylum. Phylogenomic analysis shows diverse taxonomic affinities for B. massiliensis genes, suggestive of multiple gene acquisitions via horizontal transfer from other bacteria and eukaryotes. Horizontal gene transfer is likely to be facilitated by the cohabitation of diverse parasites and symbionts inside amoeba. B. massiliensis encompasses many genes encoding proteins implicated in parasite-host interaction including the greatest number of ankyrin repeats among sequenced bacteria and diverse proteins related to the ubiquitin system. Characterization of B. massiliensis, a representative of a distinct bacterial phylum, thanks to its ability to grow in amoeba, reaffirms the critical role of diverse culture approaches in microbiology.}, }
@article {pmid25882680, year = {2015}, author = {Manna, S}, title = {An overview of pentatricopeptide repeat proteins and their applications.}, journal = {Biochimie}, volume = {113}, number = {}, pages = {93-99}, doi = {10.1016/j.biochi.2015.04.004}, pmid = {25882680}, issn = {1638-6183}, mesh = {Animals ; *Evolution, Molecular ; Humans ; RNA Processing, Post-Transcriptional/*physiology ; RNA-Binding Proteins/*genetics/*metabolism ; }, abstract = {Pentatricopeptide repeat (PPR) proteins are a large family of modular RNA-binding proteins which mediate several aspects of gene expression primarily in organelles but also in the nucleus. These proteins facilitate processing, splicing, editing, stability and translation of RNAs. While major advances in PPR research have been achieved with plant PPR proteins, the significance of non-plant PPR proteins is becoming of increasing importance. PPR proteins are classified into different subclasses based on their domain architecture, which is often a reflection of their function. This review provides an overview of the significant findings regarding the functions, evolution and applications of PPR proteins. Horizontal gene transfer appears to have played a major role in the sporadic phylogenetic distribution of different PPR subclasses in both eukaryotes and prokaryotes. Additionally, the use of synthetic biology and protein engineering to create designer PPR proteins to control gene expression in vivo is discussed. This review also highlights some of the aspects of PPR research that require more attention particularly in non-plant organisms. This includes the lack of research into the recently discovered PPR-TGM subclass, which is not only the first PPR subclass absent from plants but present in economically and clinically-relevant pathogens. Investigation into the structure and function of PPR-TGM proteins in these pathogens presents a novel opportunity for the exploitation of PPR proteins as drug targets to prevent disease.}, }
@article {pmid25881168, year = {2015}, author = {Mano, Y and Saga, T and Ishii, Y and Yoshizumi, A and Bonomo, RA and Yamaguchi, K and Tateda, K}, title = {Molecular analysis of the integrons of metallo-β-lactamase-producing Pseudomonas aeruginosa isolates collected by nationwide surveillance programs across Japan.}, journal = {BMC microbiology}, volume = {15}, number = {}, pages = {41}, pmid = {25881168}, issn = {1471-2180}, support = {R01 AI100560/AI/NIAID NIH HHS/United States ; R01 AI072219/AI/NIAID NIH HHS/United States ; R01 AI063517/AI/NIAID NIH HHS/United States ; I01 BX001974/BX/BLRD VA/United States ; R01AI063517/AI/NIAID NIH HHS/United States ; R01AI072219/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Carbapenems/pharmacology ; DNA, Bacterial/genetics ; Electrophoresis, Gel, Pulsed-Field ; Epidemiological Monitoring ; Gene Expression ; Genotype ; *Integrons ; Japan/epidemiology ; Microbial Sensitivity Tests ; Molecular Epidemiology ; Pseudomonas Infections/drug therapy/*epidemiology/microbiology ; Pseudomonas aeruginosa/drug effects/enzymology/*genetics/isolation &amp; purification ; Urinary Tract Infections/drug therapy/*epidemiology/microbiology ; beta-Lactam Resistance/*genetics ; beta-Lactamases/*genetics/metabolism ; }, abstract = {BACKGROUND: We investigate the evolving molecular epidemiology of metallo-β-lactamase (MBL)-producing Pseudomonas aeruginosa isolates collected in a 100 institution, nationwide surveillance study in Japan from 2004 to 2006.<br><br>RESULTS: MBL-producers were detected in 23/996 isolates (2.3%) in 2004 and 21/992 (2.1%) in 2006. Antimicrobial resistance (specifically, carbapenem resistance) rates between two periods did not differ significantly. MBL-producers were more prevalent in urinary tract isolates. bla IMP-1 group was the most predominant (38 isolates, 80%), followed by 3 bla IMP-7, 2 bla IMP-11 group, and 1 bla VIM-1. All MBL genes were identified in 16 different class 1 integrons, most of which were novel to INTEGRALL database. A total of 17 isolates of sequence type (ST) 235, a recognized worldwide drug-resistant lineage, were distributed in 5 geographic regions across Japan. ST235 isolates included a sublineage associated with In113-like integron. ST357 was identified in 14 isolates, 9 of which harboring a sole bla IMP-1 gene cassette (In994) were recovered from Chugoku region in 2004. ST357 isolates with bla IMP-11 group or ST235 with bla IMP-7 emerged in 2006. We also report for the first time the presence of novel fosI gene cassette in strains other than Mycobacterium spp.<br><br>CONCLUSIONS: Our data give an important "snapshot" of the molecular characteristics and dynamics of MBL-producing lineages in P. aeruginosa in Japan. The significant association of specific genotypes and integrons implies that dissemination and transmission of the preexisting resistant lineage, rather than horizontal gene transfer in situ, might largely explain their endemicity.}, }
@article {pmid25881070, year = {2015}, author = {Li, P and Yang, C and Xie, J and Liu, N and Wang, H and Zhang, L and Wang, X and Wang, Y and Qiu, S and Song, H}, title = {Acinetobacter calcoaceticus from a fatal case of pneumonia harboring bla(NDM-1) on a widely distributed plasmid.}, journal = {BMC infectious diseases}, volume = {15}, number = {}, pages = {131}, pmid = {25881070}, issn = {1471-2334}, mesh = {Acinetobacter/drug effects/genetics/isolation &amp; purification ; Acinetobacter Infections/microbiology ; Acinetobacter calcoaceticus/drug effects/*genetics/isolation &amp; purification ; Anti-Bacterial Agents/pharmacology ; China ; DNA Transposable Elements ; Electrophoresis, Gel, Pulsed-Field ; Fatal Outcome ; Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; Plasmids/genetics ; Pneumonia, Bacterial/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA ; beta-Lactamases/*genetics ; }, abstract = {BACKGROUND: We have recovered one bla(NDM-1)-harboring bacterial strain, designated as XM1570, from a sputum sample obtained from a fatal case of pneumonia in China.<br><br>METHODS: Biochemical profiling, 16S rRNA sequencing and antimicrobial susceptibility testing were performed. Conjugation experiments were conducted to determine transmissibility of resistance. Pulsed-field gel electrophoresis and whole genome sequencing were performed to identify strain-specific features.<br><br>RESULTS: The isolate XM1570 was identified as Acinetobacter calcoaceticus. Whole genome sequencing identified two plasmids, pXM1 and pXM2. Comparative analysis showed >99% similarity between XM1570 and A. calcoaceticus PHEA-2. Plasmid pXM1 carried the carbapenemase gene bla(NDM-1) and displayed high homology with previously described plasmids isolated from different Acinetobacter spp., which were collected from human or livestock distributed in China and worldwide. The bla(NDM-1) gene was located on this conjugative plasmid in a transposon-like region flanked by two copies of the insertion sequence ISAba125; and resistance to all tested &#x3b2;-lactams was observed. Transferability of resistance from pXM1 to the transconjugants was identified. Plasmid pXM2 had an insertion sequence ISAba125 and a -35 region of the bla NDM-1 gene promoter but the bla NDM-1 gene was not present. A chromosomally located carbapenemase-encoding gene bla OXA-75 was detected; however, this gene was interrupted by an insertion sequence ISAba22 belonging to IS3 family.<br><br>CONCLUSIONS: Location of bla(NDM-1) on different self-transmissible plasmids could facilitate geographically broad dissemination and host range expansion of the bla(NDM-1) gene via horizontal gene transfer. Our findings of this normally environmental species A. calcoaceticus XM1570 further underline the significant clinical challenge and the essential need for surveillance including molecular methods and plasmid analyses.}, }
@article {pmid25880192, year = {2015}, author = {Loyola, DE and Navarro, C and Uribe, P and García, K and Mella, C and Díaz, D and Valdes, N and Martínez-Urtaza, J and Espejo, RT}, title = {Genome diversification within a clonal population of pandemic Vibrio parahaemolyticus seems to depend on the life circumstances of each individual bacteria.}, journal = {BMC genomics}, volume = {16}, number = {1}, pages = {176}, pmid = {25880192}, issn = {1471-2164}, mesh = {Animals ; Bivalvia/microbiology ; Diarrhea/epidemiology/microbiology ; Gene Transfer, Horizontal ; *Genetic Variation ; *Genome, Bacterial ; Humans ; Pandemics ; Plasmids/genetics/metabolism ; Polymorphism, Single Nucleotide ; Vibrio Infections/epidemiology/microbiology ; Vibrio parahaemolyticus/classification/*genetics/isolation &amp; purification ; }, abstract = {BACKGROUND: New strains of Vibrio parahaemolyticus that cause diarrhea in humans by seafood ingestion periodically emerge through continuous evolution in the ocean. Influx and expansion in the Southern Chilean ocean of a highly clonal V. parahaemolyticus (serotype O3:K6) population from South East Asia caused one of the largest seafood-related diarrhea outbreaks in the world. Here, genomics analyses of isolates from this rapidly expanding clonal population offered an opportunity to observe the molecular evolutionary changes often obscured in more diverse populations.<br><br>RESULTS: Whole genome sequence comparison of eight independent isolates of this population from mussels or clinical cases (from different years) was performed. Differences of 1366 to 217,729&#xa0;bp genome length and 13 to 164&#xa0;bp single nucleotide variants (SNVs) were found. Most genomic differences corresponded to the presence of regions unique to only one or two isolates, and were probably acquired by horizontal gene transfer (HGT). Some DNA gain was chromosomal but most was in plasmids. One isolate had a large region (8,644&#xa0;bp) missing, which was probably caused by excision of a prophage. Genome innovation by the presence of unique DNA, attributable to HGT from related bacteria, varied greatly among the isolates, with values of 1,366 (ten times the number of highest number of SNVs) to 217,729 (a thousand times more than the number of highest number of SNVs).<br><br>CONCLUSIONS: The evolutionary forces (SNVs, HGT) acting on each isolate of the same population were found to differ to an extent that probably depended on the ecological scenario and life circumstances of each bacterium.}, }
@article {pmid25880171, year = {2015}, author = {Kweon, O and Kim, SJ and Blom, J and Kim, SK and Kim, BS and Baek, DH and Park, SI and Sutherland, JB and Cerniglia, CE}, title = {Comparative functional pan-genome analyses to build connections between genomic dynamics and phenotypic evolution in polycyclic aromatic hydrocarbon metabolism in the genus Mycobacterium.}, journal = {BMC evolutionary biology}, volume = {15}, number = {}, pages = {21}, pmid = {25880171}, issn = {1471-2148}, mesh = {Biodegradation, Environmental ; Biological Evolution ; Epistasis, Genetic ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genomics ; Mycobacterium/classification/*genetics/*metabolism ; Phylogeny ; Polycyclic Aromatic Hydrocarbons/metabolism ; }, abstract = {BACKGROUND: The bacterial genus Mycobacterium is of great interest in the medical and biotechnological fields. Despite a flood of genome sequencing and functional genomics data, significant gaps in knowledge between genome and phenome seriously hinder efforts toward the treatment of mycobacterial diseases and practical biotechnological applications. In this study, we propose the use of systematic, comparative functional pan-genomic analysis to build connections between genomic dynamics and phenotypic evolution in polycyclic aromatic hydrocarbon (PAH) metabolism in the genus Mycobacterium.<br><br>RESULTS: Phylogenetic, phenotypic, and genomic information for 27 completely genome-sequenced mycobacteria was systematically integrated to reconstruct a mycobacterial phenotype network (MPN) with a pan-genomic concept at a network level. In the MPN, mycobacterial phenotypes show typical scale-free relationships. PAH degradation is an isolated phenotype with the lowest connection degree, consistent with phylogenetic and environmental isolation of PAH degraders. A series of functional pan-genomic analyses provide conserved and unique types of genomic evidence for strong epistatic and pleiotropic impacts on evolutionary trajectories of the PAH-degrading phenotype. Under strong natural selection, the detailed gene gain/loss patterns from horizontal gene transfer (HGT)/deletion events hypothesize a plausible evolutionary path, an epistasis-based birth and pleiotropy-dependent death, for PAH metabolism in the genus Mycobacterium. This study generated a practical mycobacterial compendium of phenotypic and genomic changes, focusing on the PAH-degrading phenotype, with a pan-genomic perspective of the evolutionary events and the environmental challenges.<br><br>CONCLUSIONS: Our findings suggest that when selection acts on PAH metabolism, only a small fraction of possible trajectories is likely to be observed, owing mainly to a combination of the ambiguous phenotypic effects of PAHs and the corresponding pleiotropy- and epistasis-dependent evolutionary adaptation. Evolutionary constraints on the selection of trajectories, like those seen in PAH-degrading phenotypes, are likely to apply to the evolution of other phenotypes in the genus Mycobacterium.}, }
@article {pmid25879448, year = {2015}, author = {Ho, WS and Ou, HY and Yeo, CC and Thong, KL}, title = {The dnd operon for DNA phosphorothioation modification system in Escherichia coli is located in diverse genomic islands.}, journal = {BMC genomics}, volume = {16}, number = {1}, pages = {199}, pmid = {25879448}, issn = {1471-2164}, mesh = {DNA, Bacterial/*genetics/*metabolism ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/*genetics ; Escherichia coli Proteins/classification/*genetics ; *Genomic Islands ; Genotype ; Multigene Family ; Operon/*genetics ; Phenotype ; Phylogeny ; Sequence Analysis, DNA ; Thiourea/pharmacology ; }, abstract = {BACKGROUND: Strains of Escherichia coli that are non-typeable by pulsed-field gel electrophoresis (PFGE) due to in-gel degradation can influence their molecular epidemiological data. The DNA degradation phenotype (Dnd(+)) is mediated by the dnd operon that encode enzymes catalyzing the phosphorothioation of DNA, rendering the modified DNA susceptible to oxidative cleavage during a PFGE run. In this study, a PCR assay was developed to detect the presence of the dnd operon in Dnd(+) E. coli strains and to improve their typeability. Investigations into the genetic environments of the dnd operon in various E. coli strains led to the discovery that the dnd operon is harboured in various diverse genomic islands.<br><br>RESULTS: The dndBCDE genes (dnd operon) were detected in all Dnd(+) E. coli strains by PCR. The addition of thiourea improved the typeability of Dnd(+) E. coli strains to 100% using PFGE and the Dnd(+) phenotype can be observed in both clonal and genetically diverse E. coli strains. Genomic analysis of 101 dnd operons from genome sequences of Enterobacteriaceae revealed that the dnd operons of the same bacterial species were generally clustered together in the phylogenetic tree. Further analysis of dnd operons of 52 E. coli genomes together with their respective immediate genetic environments revealed a total of 7 types of genetic organizations, all of which were found to be associated with genomic islands designated dnd-encoding GIs. The dnd-encoding GIs displayed mosaic structure and the genomic context of the 7 islands (with 1 representative genome from each type of genetic organization) were also highly variable, suggesting multiple recombination events. This is also the first report where two dnd operons were found within a strain although the biological implication is unknown. Surprisingly, dnd operons were frequently found in pathogenic E. coli although their link with virulence has not been explored.<br><br>CONCLUSION: Genomic islands likely play an important role in facilitating the horizontal gene transfer of the dnd operons in E. coli with 7 different types of islands discovered so far.}, }
@article {pmid25879186, year = {2015}, author = {Leliaert, F and Lopez-Bautista, JM}, title = {The chloroplast genomes of Bryopsis plumosa and Tydemania expeditiones (Bryopsidales, Chlorophyta): compact genomes and genes of bacterial origin.}, journal = {BMC genomics}, volume = {16}, number = {1}, pages = {204}, pmid = {25879186}, issn = {1471-2164}, mesh = {Chlorophyta/*classification/*genetics ; Chloroplasts/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Chloroplast ; Genomics/methods ; Phylogeny ; }, abstract = {BACKGROUND: Species of Bryopsidales form ecologically important components of seaweed communities worldwide. These siphonous macroalgae are composed of a single giant tubular cell containing millions of nuclei and chloroplasts, and harbor diverse bacterial communities. Little is known about the diversity of chloroplast genomes (cpDNAs) in this group, and about the possible consequences of intracellular bacteria on genome composition of the host. We present the complete cpDNAs of Bryopsis plumosa and Tydemania expeditiones, as well as a re-annotated cpDNA of B. hypnoides, which was shown to contain a higher number of genes than originally published. Chloroplast genomic data were also used to evaluate phylogenetic hypotheses in the Chlorophyta, such as monophyly of the Ulvophyceae (the class in which the order Bryopsidales is currently classified).<br><br>RESULTS: Both DNAs are circular and lack a large inverted repeat. The cpDNA of B. plumosa is 106,859 bp long and contains 115 unique genes. A 13 kb region was identified with several freestanding open reading frames (ORFs) of putative bacterial origin, including a large ORF (>8 kb) closely related to bacterial rhs-family genes. The cpDNA of T. expeditiones is 105,200 bp long and contains 125 unique genes. As in B. plumosa, several regions were identified with ORFs of possible bacterial origin, including genes involved in mobile functions (transposases, integrases, phage/plasmid DNA primases), and ORFs showing close similarity with bacterial DNA methyltransferases. The cpDNA of B. hypnoides differs from that of B. plumosa mainly in the presence of long intergenic spacers, and a large tRNA region. Chloroplast phylogenomic analyses were largely inconclusive with respect to monophyly of the Ulvophyceae, and the relationship of the Bryopsidales within the Chlorophyta.<br><br>CONCLUSIONS: The cpDNAs of B. plumosa and T. expeditiones are amongst the smallest and most gene dense chloroplast genomes in the core Chlorophyta. The presence of bacterial genes, including genes typically found in mobile elements, suggest that these have been acquired through horizontal gene transfer, which may have been facilitated by the occurrence of obligate intracellular bacteria in these siphonous algae.}, }
@article {pmid25876066, year = {2015}, author = {Laurenceau, R and Krasteva, PV and Diallo, A and Ouarti, S and Duchateau, M and Malosse, C and Chamot-Rooke, J and Fronzes, R}, title = {Conserved Streptococcus pneumoniae spirosomes suggest a single type of transformation pilus in competence.}, journal = {PLoS pathogens}, volume = {11}, number = {4}, pages = {e1004835}, pmid = {25876066}, issn = {1553-7374}, mesh = {Fimbriae, Bacterial/*ultrastructure ; Gene Transfer, Horizontal ; Macromolecular Substances/ultrastructure ; Microscopy, Electron, Transmission ; Polymerase Chain Reaction ; Proteomics ; Streptococcus pneumoniae/genetics/*ultrastructure ; Transformation, Bacterial/genetics ; }, abstract = {The success of S. pneumoniae as a major human pathogen is largely due to its remarkable genomic plasticity, allowing efficient escape from antimicrobials action and host immune response. Natural transformation, or the active uptake and chromosomal integration of exogenous DNA during the transitory differentiated state competence, is the main mechanism for horizontal gene transfer and genomic makeover in pneumococci. Although transforming DNA has been proposed to be captured by Type 4 pili (T4P) in Gram-negative bacteria, and a competence-inducible comG operon encoding proteins homologous to T4P-biogenesis components is present in transformable Gram-positive bacteria, a prevailing hypothesis has been that S. pneumoniae assembles only short pseudopili to destabilize the cell wall for DNA entry. We recently identified a micrometer-sized T4P-like pilus on competent pneumococci, which likely serves as initial DNA receptor. A subsequent study, however, visualized a different structure--short, 'plaited' polymers--released in the medium of competent S. pneumoniae. Biochemical observation of concurrent pilin secretion led the authors to propose that the 'plaited' structures correspond to transformation pili acting as peptidoglycan drills that leave DNA entry pores upon secretion. Here we show that the 'plaited' filaments are not related to natural transformation as they are released by non-competent pneumococci, as well as by cells with disrupted pilus biogenesis components. Combining electron microscopy visualization with structural, biochemical and proteomic analyses, we further identify the 'plaited' polymers as spirosomes: macromolecular assemblies of the fermentative acetaldehyde-alcohol dehydrogenase enzyme AdhE that is well conserved in a broad range of Gram-positive and Gram-negative bacteria.}, }
@article {pmid25874009, year = {2015}, author = {Chan, JC}, title = {Hypotheses of cancer weakening and origin.}, journal = {Journal of Cancer}, volume = {6}, number = {5}, pages = {457-463}, pmid = {25874009}, issn = {1837-9664}, abstract = {Approximately 2.7 billion years ago, cyanobacteria began producing oxygen by photosynthesis. Any free oxygen they produced was chemically captured by dissolved iron or organic matter. There was no ozone layer to protect living species against the radiation from space. Eukaryotic cells lived in water, under hypoxic environments, and metabolized glucose by fermentation. The Great Oxygenation Event (GOE) describes the point when oxygen sinks became saturated. This massive oxygenation of the Earth occurred approximately half a billion years ago. Species that evolved after the GOE are characterized by aerobic metabolism. Mammals evolved approximately a few hundred million years ago, with the ancient eukaryotic genes deeply embedded in their genome. Many genes have been exchanged by horizontal gene transfer (HGT) throughout the history of cellular evolution. Mammals have been invaded by viruses, and while viral genetic relics are embedded in mammalian junk genes, not all junk genes are genetic relics of viruses. These viral relics have been inactivated through evolution and have little impact on mammalian life. However, there is evidence to suggest that these viral genetic relics are linked to cancer. This hypothesis states that cancer develops when cell reproduction becomes defective because of the active involvement of viral genes, in a process similar to genetic engineering. Cancer cells are amalgamations of genetically modified organisms (GMOs). There are two main groups in cancer development. One group of cells arises by genetic engineering of a viral genetic relic, such as endogenous retroviruses (ERVs), which evolved after oxygenation of the atmosphere. This group is referred to here as genetically modified organisms from viral genes (GMOV). GMOVs may be inhibited by anticancer drugs. The second group arises by engineering of the genes of ancient eukaryotes, which existed prior to the oxygenation of the Earth. This second group is referred to as genetically modified organisms from ancient eukaryotic genes (GMOE). The GMOE group lives in hypoxic environments and metabolizes glucose by fermentation. GMOEs represent advanced cancer, which proliferate aggressively and are resistant to DNA damage. It has been demonstrated that as an ERV becomes more prevalent in a mammalian genome, the possibility that the mammal will develop cancer increases. The hypothesis also states that most cancers have their origins in GMOV by the incorporation of viral genes from junk genes. As the cancer progresses, further subgroups of cancer GMOs will develop. If the cancer advances even further, the GMOE could eventually develop prior to late-stage cancer. Because the genes of ancient eukaryotes have enhanced innate immunity, GMOE will eventually prevail over the weaker GMOV during cancer subgroup competition. Hence, cancer development is mainly determined by genes in the mammalian genome. An inherent weakness of cancer cells is their dependence on glucose and iron. Furthermore, they cannot tolerate physical disturbance. Ancient gene GMOs can be treated with a combination of mechanical vibration using glucose-coated magnetic nanoparticles and strengthening of the immune system. Herein, I suggest trials for verifying this hypothesis.}, }
@article {pmid25871928, year = {2015}, author = {Thézé, J and Takatsuka, J and Nakai, M and Arif, B and Herniou, EA}, title = {Gene acquisition convergence between entomopoxviruses and baculoviruses.}, journal = {Viruses}, volume = {7}, number = {4}, pages = {1960-1974}, pmid = {25871928}, issn = {1999-4915}, mesh = {Adaptation, Biological ; Animals ; Baculoviridae/*genetics/physiology ; DNA, Viral/chemistry/genetics ; Entomopoxvirinae/*genetics/physiology ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Insecta/*virology ; Molecular Sequence Data ; Selection, Genetic ; Sequence Analysis, DNA ; }, abstract = {Organisms from diverse phylogenetic origins can thrive within the same ecological niches. They might be induced to evolve convergent adaptations in response to a similar landscape of selective pressures. Their genomes should bear the signature of this process. The study of unrelated virus lineages infecting the same host panels guarantees a clear identification of phyletically independent convergent adaptation. Here, we investigate the evolutionary history of genes in the accessory genome shared by unrelated insect large dsDNA viruses: the entomopoxviruses (EPVs, Poxviridae) and the baculoviruses (BVs). EPVs and BVs have overlapping ecological niches and have independently evolved similar infection processes. They are, in theory, subjected to the same selective pressures from their host's immune responses. Their accessory genomes might, therefore, bear analogous genomic signatures of convergent adaption and could point out key genomic mechanisms of adaptation hitherto undetected in viruses. We uncovered 32 homologous, yet independent acquisitions of genes originating from insect hosts, different eukaryotes, bacteria and viruses. We showed different evolutionary levels of gene acquisition convergence in these viruses, underlining a continuous evolutionary process. We found both recent and ancient gene acquisitions possibly involved to the adaptation to both specific and distantly related hosts. Multidirectional and multipartite gene exchange networks appear to constantly drive exogenous gene assimilations, bringing key adaptive innovations and shaping the life histories of large DNA viruses. This evolutionary process might lead to genome level adaptive convergence.}, }
@article {pmid25869320, year = {2015}, author = {Farhadi, T and Nezafat, N and Ghasemi, Y}, title = {In silico phylogenetic analysis of Vibrio cholerae isolates based on three housekeeping genes.}, journal = {International journal of computational biology and drug design}, volume = {8}, number = {1}, pages = {62-74}, doi = {10.1504/IJCBDD.2015.068789}, pmid = {25869320}, issn = {1756-0756}, mesh = {Computational Biology/*methods ; Computer Simulation ; *Genes, Bacterial ; *Genes, Essential ; Phylogeny ; Vibrio cholerae/*classification/*genetics ; }, abstract = {Vibrio cholera, a gram-negative bacterium, has been categorised into clinical and environmental species. Phylogenetic studies have been performed to investigate the relationships of the V. cholerae populations in worldwide. In this study, phylogenetic relationship between V. cholerae isolates from Iran and other regions of the world was determined, based on three housekeeping genes analysis. Results for Iranian strains showed that congruency of asd and hlyA phylogenetic trees were remarkably higher than recA tree. Iranian strains displayed 2-3%, 1-14% and 3-5% deference in asd, hlyA and recA nucleotide sequences, respectively. Sequence similarity degrees were variable between Iranian and other region's strains. Furthermore, the non-congruence in the phylogeny of the pathogenic clones in cladograms is probably due to horizontal gene transfer. Finally, results of this study suggest that monitoring of surface waters for housekeeping genes of V. cholerae in the cholera endemic areas may be valuable for forecasting the expected cholera outbreaks.}, }
@article {pmid25869223, year = {2015}, author = {Koechler, S and Farasin, J and Cleiss-Arnold, J and Arsène-Ploetze, F}, title = {Toxic metal resistance in biofilms: diversity of microbial responses and their evolution.}, journal = {Research in microbiology}, volume = {166}, number = {10}, pages = {764-773}, doi = {10.1016/j.resmic.2015.03.008}, pmid = {25869223}, issn = {1769-7123}, mesh = {Adaptation, Biological/*genetics ; Bacteria/*drug effects/growth &amp; development/metabolism ; Bacterial Adhesion ; *Biofilms/drug effects/growth &amp; development ; *Biological Evolution ; Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Metals, Heavy/metabolism/pharmacology/*toxicity ; }, abstract = {Since biofilms are an important issue in the fields of medicine and health, several recent microbiological studies have focused on their formation and their contribution to toxic compound resistance mechanisms. In this review, we describe how metals impact biofilm formation and resistance, and how biofilms can help cells resist toxic metals. First, the organic matrix acts as a barrier isolating the cells from many environmental stresses. Secondly, the metabolism of the cells changes, and a slowly-growing or non-growing sub-population of cells known as persisters emerges. Thirdly, in the case of multispecies biofilms, metabolic interactions are developed, allowing cells to be more persistent or to have greater capacity to survive than a single species biofilm. Finally, we discuss how the high density of the cells may promote horizontal gene transfer processes, resulting in the acquisition of new features. All these crucial mechanisms enable microorganisms to survive and colonize toxic environments, and probably accelerate ongoing evolutionary processes.}, }
@article {pmid25866821, year = {2015}, author = {Cecagno, R and Fritsch, TE and Schrank, IS}, title = {The plant growth-promoting bacteria Azospirillum amazonense: genomic versatility and phytohormone pathway.}, journal = {BioMed research international}, volume = {2015}, number = {}, pages = {898592}, pmid = {25866821}, issn = {2314-6141}, mesh = {*Azospirillum/genetics/metabolism ; *Gene Transfer, Horizontal ; *Genetic Variation ; Indoleacetic Acids/*metabolism ; *Plant Growth Regulators/biosynthesis/genetics ; *Rhizome/genetics/metabolism ; }, abstract = {The rhizosphere bacterium Azospirillum amazonense associates with plant roots to promote plant growth. Variation in replicon numbers and rearrangements is common among Azospirillum strains, and characterization of these naturally occurring differences can improve our understanding of genome evolution. We performed an in silico comparative genomic analysis to understand the genomic plasticity of A. amazonense. The number of A. amazonense-specific coding sequences was similar when compared with the six closely related bacteria regarding belonging or not to the Azospirillum genus. Our results suggest that the versatile gene repertoire found in A. amazonense genome could have been acquired from distantly related bacteria from horizontal transfer. Furthermore, the identification of coding sequence related to phytohormone production, such as flavin-monooxygenase and aldehyde oxidase, is likely to represent the tryptophan-dependent TAM pathway for auxin production in this bacterium. Moreover, the presence of the coding sequence for nitrilase indicates the presence of the alternative route that uses IAN as an intermediate for auxin synthesis, but it remains to be established whether the IAN pathway is the Trp-independent route. Future investigations are necessary to support the hypothesis that its genomic structure has evolved to meet the requirement for adaptation to the rhizosphere and interaction with host plants.}, }
@article {pmid25865067, year = {2015}, author = {Zhou, T and Zhang, Y and Li, M and Yu, X and Sun, Y and Xu, J}, title = {An outbreak of infections caused by extensively drug-resistant Klebsiella pneumoniae strains during a short period of time in a Chinese teaching hospital: epidemiology study and molecular characteristics.}, journal = {Diagnostic microbiology and infectious disease}, volume = {82}, number = {3}, pages = {240-244}, doi = {10.1016/j.diagmicrobio.2015.03.017}, pmid = {25865067}, issn = {1879-0070}, mesh = {Aged ; China/epidemiology ; Cluster Analysis ; Conjugation, Genetic ; Cross Infection/*epidemiology/microbiology/mortality ; *Disease Outbreaks ; *Drug Resistance, Multiple, Bacterial ; Electrophoresis, Polyacrylamide Gel ; Female ; Gene Transfer, Horizontal ; Genes, Bacterial ; Hospitals, Teaching ; Humans ; Klebsiella Infections/*epidemiology/microbiology/mortality ; Klebsiella pneumoniae/classification/drug effects/genetics/*isolation &amp; purification ; Male ; Membrane Transport Proteins/analysis ; Middle Aged ; Molecular Typing ; Plasmids/analysis ; Retrospective Studies ; Sequence Analysis, DNA ; Survival Analysis ; beta-Lactamases/metabolism ; }, abstract = {In this study, we comprehensively described the clinical risk factors, outcome, epidemiology, and molecular basis associated with an outbreak of extensively drug-resistant KPC-2-producing Klebsiella pneumoniae involving 15 patients in a teaching hospital from May 1 to June 27, 2013. Most of the patients were elderly and received long-term hospital treatment, and 40.0% (6/15) of them were dead. All strains carried bla(KPC-2), rmtB, bla(CTX-M-65), bla(SHV-11), oqxA, oqxB, and aac(6')-Ib-cr and even harbored additional other resistance genes, such as armA, bla(CTX-M-1), bla(TEM-1). bla(KPC-2), rmtB, and bla(CTX-M-65) were located on the same ~54.2-kb plasmid, and conjugation experiments further proved the cotransferable characteristic. Alterations of outer membrane proteins were confirmed by sodium dodecyl sulfate--olyacrylamide gelelectrophoresis and sequencing, which can lead to a drastic change in the permeability of cells. All isolates belonged to the clone complex 258, spreading rapidly across the world. Our study demonstrated that a high degree of awareness and surveillance of those drug resistance determinants is urgently needed.}, }
@article {pmid25863176, year = {2015}, author = {Szydlowski, L and Boschetti, C and Crisp, A and Barbosa, EG and Tunnacliffe, A}, title = {Multiple horizontally acquired genes from fungal and prokaryotic donors encode cellulolytic enzymes in the bdelloid rotifer Adineta ricciae.}, journal = {Gene}, volume = {566}, number = {2}, pages = {125-137}, doi = {10.1016/j.gene.2015.04.007}, pmid = {25863176}, issn = {1879-0038}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cellulase/genetics/*metabolism ; Cellulose/*metabolism ; DNA ; Gene Duplication ; *Gene Transfer, Horizontal ; *Genes, Fungal ; Molecular Sequence Data ; Polymerase Chain Reaction ; Prokaryotic Cells ; Rotifera/*enzymology ; Sequence Homology, Amino Acid ; }, abstract = {The bdelloid rotifer, Adineta ricciae, an anhydrobiotic microinvertebrate, exhibits a high rate of horizontal gene transfer (HGT), with as much as 10% of its transcriptome being of foreign origin. Approximately 80% of these foreign transcripts are involved in metabolic processes, and therefore bdelloids represent a useful model for assessing the contribution of HGT to biochemical diversity. To validate this concept, we focused on cellulose digestion, an unusual activity in animals, which is represented by at least 16 genes encoding cellulolytic enzymes in A. ricciae. These genes have been acquired from a variety of different donor organisms among the bacteria and fungi, demonstrating that bdelloids use diverse genetic resources to construct a novel biochemical pathway. A variable complement of the cellulolytic gene set was found in five other bdelloid species, indicating a dynamic process of gene acquisition, duplication and loss during bdelloid evolution. For example, in A. ricciae, gene duplications have led to the formation of three copies of a gene encoding a GH45 family glycoside hydrolase, at least one of which encodes a functional enzyme; all three of these gene copies are present in a close relative, Adineta vaga, but only one copy was found in each of four Rotaria species. Furthermore, analysis of expression levels of the cellulolytic genes suggests that a bacterial-origin cellobiase is upregulated upon desiccation. In summary, bdelloid rotifers have apparently developed cellulolytic functions by the acquisition and domestication of multiple foreign genes.}, }
@article {pmid25862309, year = {2015}, author = {Dalhoff, AA and Levy, SB}, title = {Does use of the polyene natamycin as a food preservative jeopardise the clinical efficacy of amphotericin B? A word of concern.}, journal = {International journal of antimicrobial agents}, volume = {45}, number = {6}, pages = {564-567}, doi = {10.1016/j.ijantimicag.2015.02.011}, pmid = {25862309}, issn = {1872-7913}, mesh = {Amphotericin B/*pharmacology/therapeutic use ; Antifungal Agents/*administration &amp; dosage/*pharmacology/therapeutic use ; Aspergillus fumigatus/drug effects ; Candida/drug effects ; *Drug Resistance, Fungal ; Food Preservation/*methods ; Food Preservatives/*administration &amp; dosage ; Gene Transfer, Horizontal ; Humans ; Natamycin/*administration &amp; dosage ; Selection, Genetic ; Treatment Outcome ; }, abstract = {Natamycin is a poorly soluble, polyene macrolide antifungal agent used in the food industry for the surface treatment of cheese and sausages. This use is not of safety concern. However, highly soluble natamycin-cyclodextrin inclusion complexes have been developed for the protection of beverages. This practice leads to high drug exposures exceeding the safety level. Apart from the definition of an acceptable daily dietary exposure to natamycin, its effect on the faecal flora as a reservoir for resistance has to be examined. Consumption of food to which natamycin has been added and mixed homogeneously, such as yoghurt, and in particular the addition of cyclodextrin inclusion complexes to beverages and wine generates high faecal natamycin concentrations resulting in high drug exposures of faecal Candida spp. Development of natamycin resistance has been observed in Candida spp. colonising the intestinal tract of patients following natamycin treatment of fungal infections. Horizontal gene transfer among different Candida spp. and within Aspergillus fumigatus spreads resistance. Therefore, it cannot be denied that use of natamycin for preservation of yoghurt and beverages may foster development of resistance to polyenes in Candida spp.}, }
@article {pmid25860840, year = {2015}, author = {, }, title = {Correction: an operon of three transcriptional regulators controls horizontal gene transfer of the integrative and conjugative element ICEclc in Pseudomonas knackmussii B13.}, journal = {PLoS genetics}, volume = {11}, number = {4}, pages = {e1005130}, pmid = {25860840}, issn = {1553-7404}, }
@article {pmid25858273, year = {2015}, author = {Chauhan, N}, title = {Two-component phosphorelays in fungal mitochondria and beyond.}, journal = {Mitochondrion}, volume = {22}, number = {}, pages = {60-65}, doi = {10.1016/j.mito.2015.03.003}, pmid = {25858273}, issn = {1872-8278}, mesh = {Fungi/genetics/metabolism/pathogenicity/*physiology ; *Gene Expression Regulation ; Histidine Kinase ; Mitochondria/genetics/metabolism/*physiology ; Phosphoproteins/*metabolism ; Protein Kinases/*metabolism ; *Signal Transduction ; Virulence ; Virulence Factors/biosynthesis ; }, abstract = {Prokaryotes, eukaryotic microorganisms and plants utilize two-component signal transduction pathways to detect and respond to various environmental cues. These signaling cascades were acquired by eukaryotes via horizontal gene transfer events from ancestral bacteria. Recent exciting discoveries have identified two-component signaling systems in mitochondria and chloroplasts of several eukaryotic microorganisms and plants, therefore providing important clues to the evolutionary transition of these signaling cascades from prokaryotes to eukaryotes. This review will focus on the role of two-component signal transduction pathways in fungal pathogenesis and also discuss key new discoveries of presence of proteins participating in these signaling pathways in mitochondrion. Before addressing these issues, I first briefly describe the magnitude and the economic impact of the healthcare problems caused by fungal pathogens.}, }
@article {pmid25858231, year = {2015}, author = {Grall, N and Barraud, O and Wieder, I and Hua, A and Perrier, M and Babosan, A and Gaschet, M and Clermont, O and Denamur, E and Catzeflis, F and Decré, D and Ploy, MC and Andremont, A}, title = {Lack of dissemination of acquired resistance to β-lactams in small wild mammals around an isolated village in the Amazonian forest.}, journal = {Environmental microbiology reports}, volume = {7}, number = {5}, pages = {698-708}, doi = {10.1111/1758-2229.12289}, pmid = {25858231}, issn = {1758-2229}, mesh = {Animals ; Animals, Wild/*microbiology ; Anti-Bacterial Agents/pharmacology ; Escherichia coli/*drug effects/isolation &amp; purification ; Forests ; French Guiana ; *Gene Transfer, Horizontal ; Klebsiella pneumoniae/*drug effects/isolation &amp; purification ; Marsupialia/microbiology ; Rodentia/microbiology ; Selection, Genetic ; Ticarcillin/pharmacology ; *beta-Lactam Resistance ; }, abstract = {In this study, we quantitatively evaluated the spread of resistance to β-lactams and of integrons in small rodents and marsupials living at various distances from a point of antibiotic's use. Rectal swabs from 114 animals were collected in Trois-Sauts, an isolated village in French Guiana, and along a 3 km transect heading through the non-anthropized primary forest. Prevalence of ticarcillin-resistant enterobacteria was 36% (41/114). Klebsiella spp., naturally resistant to ticarcillin, were found in 31.1% (23/73) of animals from the village and in an equal ratio of 31.7% (13/41) of animals trapped along the transect. By contrast Escherichia coli with acquired resistance to ticarcillin were found in 13.7% (10/73) of animals from the village and in only 2.4% (1/41) of those from the transect (600 m from the village). There was a huge diversity of E. coli and Klebsiella pneumoniae strains with very unique and infrequent sequence types. The overall prevalence of class 1 integrons carriage was 19.3% (22/114) homogenously distributed between animals from the village and the transect, which suggests a co-selection by a non-antibiotic environmental factor. Our results indicate that the anthropogenic acquired antibiotic resistance did not disseminate in the wild far from the point of selective pressure.}, }
@article {pmid25853586, year = {2015}, author = {Guo, MT and Yuan, QB and Yang, J}, title = {Distinguishing effects of ultraviolet exposure and chlorination on the horizontal transfer of antibiotic resistance genes in municipal wastewater.}, journal = {Environmental science &amp; technology}, volume = {49}, number = {9}, pages = {5771-5778}, doi = {10.1021/acs.est.5b00644}, pmid = {25853586}, issn = {1520-5851}, mesh = {Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; Disinfection ; Dose-Response Relationship, Radiation ; Drug Resistance, Microbial/*genetics/radiation effects ; Escherichia coli/*genetics/radiation effects/ultrastructure ; Gene Transfer, Horizontal/*radiation effects ; *Genes, Bacterial ; Halogenation/*radiation effects ; L-Lactate Dehydrogenase/metabolism ; Microbial Viability/radiation effects ; *Ultraviolet Rays ; Wastewater/*microbiology ; }, abstract = {Growing attention has been paid to the dissemination of antibiotic resistance genes (ARGs) in wastewater microbial communities; however, the disinfection processes, as microbial control technologies, have not been evaluated for their impacts on ARGs transfer. In this study, the effects of ultraviolet (UV) disinfection and chlorination on the frequency of ARGs transfer have been explored based on the conjugative transfer model between Gram-negative strains of E. coli. The results indicated that UV disinfection and chlorination exhibit distinct influences on the conjugative transfer. Low UV doses (up to 8 mJ/cm2) had little influence on the frequency of conjugative transfer, and UV exposure only decreased the bacterial number but did not change the cell permeability. By comparison, low chlorine doses (up to 40 mg Cl min/L) significantly promoted the frequency of conjugative transfer by 2-5-fold. The generated chloramine stimulated the bacteria and improved the cell permeability. More pilus were induced on the surface of conjugative cells, which acted as pathways for ARGs transfer. The frequency of ARG transfers was greatly suppressed by high doses of UV (>10 mJ/cm2) or chlorine (>80 mg Cl min/L).}, }
@article {pmid25851957, year = {2015}, author = {De Vooght, L and Caljon, G and Van Hees, J and Van Den Abbeele, J}, title = {Paternal Transmission of a Secondary Symbiont during Mating in the Viviparous Tsetse Fly.}, journal = {Molecular biology and evolution}, volume = {32}, number = {8}, pages = {1977-1980}, pmid = {25851957}, issn = {1537-1719}, mesh = {Animals ; Enterobacteriaceae/*physiology ; *Evolution, Molecular ; Female ; Gene Transfer, Horizontal/*physiology ; Genome, Bacterial/*physiology ; Male ; Reproduction/physiology ; Symbiosis/*physiology ; *Tsetse Flies/microbiology/physiology ; }, abstract = {Sodalis glossinidius, a maternally inherited secondary symbiont of the tsetse fly, is a bacterium in the early/intermediate state of the transition toward symbiosis, representing an important model for investigating establishment and evolution of insect-bacteria symbiosis. The absence of phylogenetic congruence in tsetse-Sodalis coevolution and the existence of Sodalis genotypic diversity in field flies are suggestive for a horizontal transmission route. However, to date no natural mechanism for the horizontal transfer of this symbiont has been identified. Using novel methodologies for the stable fluorescent-labeling and introduction of modified Sodalis in tsetse flies, we unambiguously show that male-borne Sodalis is 1) horizontally transferred to females during mating and 2) subsequently vertically transmitted to the progeny, that is, paternal transmission. This mixed mode of transmission has major consequences regarding Sodalis' genome evolution as it can lead to coinfections creating opportunities for lateral gene transfer which in turn could affect the interaction with the tsetse host.}, }
@article {pmid25849429, year = {2015}, author = {Pardi, F and Scornavacca, C}, title = {Reconstructible phylogenetic networks: do not distinguish the indistinguishable.}, journal = {PLoS computational biology}, volume = {11}, number = {4}, pages = {e1004135}, pmid = {25849429}, issn = {1553-7358}, mesh = {*Biological Evolution ; Computer Simulation ; *Evolution, Molecular ; Gene Expression Regulation/*genetics ; Gene Regulatory Networks/*genetics ; *Models, Genetic ; *Phylogeny ; }, abstract = {Phylogenetic networks represent the evolution of organisms that have undergone reticulate events, such as recombination, hybrid speciation or lateral gene transfer. An important way to interpret a phylogenetic network is in terms of the trees it displays, which represent all the possible histories of the characters carried by the organisms in the network. Interestingly, however, different networks may display exactly the same set of trees, an observation that poses a problem for network reconstruction: from the perspective of many inference methods such networks are "indistinguishable". This is true for all methods that evaluate a phylogenetic network solely on the basis of how well the displayed trees fit the available data, including all methods based on input data consisting of clades, triples, quartets, or trees with any number of taxa, and also sequence-based approaches such as popular formalisations of maximum parsimony and maximum likelihood for networks. This identifiability problem is partially solved by accounting for branch lengths, although this merely reduces the frequency of the problem. Here we propose that network inference methods should only attempt to reconstruct what they can uniquely identify. To this end, we introduce a novel definition of what constitutes a uniquely reconstructible network. For any given set of indistinguishable networks, we define a canonical network that, under mild assumptions, is unique and thus representative of the entire set. Given data that underwent reticulate evolution, only the canonical form of the underlying phylogenetic network can be uniquely reconstructed. While on the methodological side this will imply a drastic reduction of the solution space in network inference, for the study of reticulate evolution this is a fundamental limitation that will require an important change of perspective when interpreting phylogenetic networks.}, }
@article {pmid25849216, year = {2015}, author = {Rinerson, CI and Rabara, RC and Tripathi, P and Shen, QJ and Rushton, PJ}, title = {The evolution of WRKY transcription factors.}, journal = {BMC plant biology}, volume = {15}, number = {}, pages = {66}, pmid = {25849216}, issn = {1471-2229}, mesh = {Amino Acid Sequence ; Bryophyta/genetics ; Chlorophyta/genetics ; Consensus Sequence ; *Evolution, Molecular ; Fungi/genetics ; Genes, Plant ; Magnoliopsida/genetics ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Protein Structure, Tertiary ; Transcription Factors/chemistry/*genetics ; }, abstract = {BACKGROUND: The availability of increasing numbers of sequenced genomes has necessitated a re-evaluation of the evolution of the WRKY transcription factor family. Modern day plants descended from a charophyte green alga that colonized the land between 430 and 470 million years ago. The first charophyte genome sequence from Klebsormidium flaccidum filled a gap in the available genome sequences in the plant kingdom between unicellular green algae that typically have 1-3 WRKY genes and mosses that contain 30-40. WRKY genes have been previously found in non-plant species but their occurrence has been difficult to explain.<br><br>RESULTS: Only two WRKY genes are present in the Klebsormidium flaccidum genome and the presence of a Group IIb gene was unexpected because it had previously been thought that Group IIb WRKY genes first appeared in mosses. We found WRKY transcription factor genes outside of the plant lineage in some diplomonads, social amoebae, fungi incertae sedis, and amoebozoa. This patchy distribution suggests that lateral gene transfer is responsible. These lateral gene transfer events appear to pre-date the formation of the WRKY groups in flowering plants. Flowering plants contain proteins with domains typical for both resistance (R) proteins and WRKY transcription factors. R protein-WRKY genes have evolved numerous times in flowering plants, each type being restricted to specific flowering plant lineages. These chimeric proteins contain not only novel combinations of protein domains but also novel combinations and numbers of WRKY domains. Once formed, R protein WRKY genes may combine different components of signalling pathways that may either create new diversity in signalling or accelerate signalling by short circuiting signalling pathways.<br><br>CONCLUSIONS: We propose that the evolution of WRKY transcription factors includes early lateral gene transfers to non-plant organisms and the occurrence of algal WRKY genes that have no counterparts in flowering plants. We propose two alternative hypotheses of WRKY gene evolution: The "Group I Hypothesis" sees all WRKY genes evolving from Group I C-terminal WRKY domains. The alternative "IIa + b Separate Hypothesis" sees Groups IIa and IIb evolving directly from a single domain algal gene separate from the Group I-derived lineage.}, }
@article {pmid25841490, year = {2015}, author = {Xu, X and Dunn, KA and Field, C}, title = {A Robust ANOVA Approach to Estimating a Phylogeny from Multiple Genes.}, journal = {Molecular biology and evolution}, volume = {32}, number = {8}, pages = {2186-2194}, pmid = {25841490}, issn = {1537-1719}, support = {CMF-108026//Canadian Institutes of Health Research/Canada ; }, mesh = {*Databases, Nucleic Acid ; *Phylogeny ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {In this article, we address the issue of estimating the phylogenetic tree based on sequence data across a set of genes. Recognizing that the individual gene trees may not all share the same evolutionary history due to lateral gene transfer or differences in rates of evolution for instance, we develop a robust algorithm for tree estimation based on pairwise distances computed gene by gene. A robust analysis of variance (ANOVA) is used to combine the distances across all genes giving a summary distance for all genes. The tree can then be constructed using any distance method such as BIONJ. Using the weights from the robust ANOVA, we can then identify the outlying genes and taxa for further examination. As the method is based on distances, computation is much faster than maximum likelihood on the concatenated genes. It is also very straightforward to carry out a bootstrap analysis using standard methods for regression models. We test our methods in a comprehensive simulation study and apply them to three data sets recently analyzed in the literature.}, }
@article {pmid25840414, year = {2015}, author = {Krupovic, M and Zhi, N and Li, J and Hu, G and Koonin, EV and Wong, S and Shevchenko, S and Zhao, K and Young, NS}, title = {Multiple layers of chimerism in a single-stranded DNA virus discovered by deep sequencing.}, journal = {Genome biology and evolution}, volume = {7}, number = {4}, pages = {993-1001}, pmid = {25840414}, issn = {1759-6653}, support = {//Intramural NIH HHS/United States ; }, mesh = {DNA Viruses/*genetics ; DNA, Single-Stranded/chemistry ; DNA, Viral/chemistry ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; RNA Viruses/genetics ; Sequence Analysis, DNA ; }, abstract = {Viruses with single-stranded (ss) DNA genomes infect hosts in all three domains of life and include many medically, ecologically, and economically important pathogens. Recently, a new group of ssDNA viruses with chimeric genomes has been discovered through viral metagenomics. These chimeric viruses combine capsid protein genes and replicative protein genes that, respectively, appear to have been inherited from viruses with positive-strand RNA genomes, such as tombusviruses, and ssDNA genomes, such as circoviruses, nanoviruses or geminiviruses. Here, we describe the genome sequence of a new representative of this virus group and reveal an additional layer of chimerism among ssDNA viruses. We show that not only do these viruses encompass genes for capsid proteins and replicative proteins that have distinct evolutionary histories, but also the replicative genes themselves are chimeras of functional domains inherited from viruses of different families. Our results underscore the importance of horizontal gene transfer in the evolution of ssDNA viruses and the role of genetic recombination in the emergence of novel virus groups.}, }
@article {pmid25838493, year = {2015}, author = {Loftie-Eaton, W and Suzuki, H and Bashford, K and Heuer, H and Stragier, P and De Vos, P and Settles, ML and Top, EM}, title = {Draft Genome Sequence of Pseudomonas sp. nov. H2.}, journal = {Genome announcements}, volume = {3}, number = {2}, pages = {}, pmid = {25838493}, issn = {2169-8287}, support = {P20 RR016448/RR/NCRR NIH HHS/United States ; R01 AI084918/AI/NIAID NIH HHS/United States ; P20 GM103397/GM/NIGMS NIH HHS/United States ; P20 GM103408/GM/NIGMS NIH HHS/United States ; P20 RR016454/RR/NCRR NIH HHS/United States ; }, abstract = {We report the draft genome sequence of Pseudomonas sp. nov. H2, isolated from creek sediment in Moscow, ID, USA. The strain is most closely related to Pseudomonas putida. However, it has a slightly smaller genome that appears to have been impacted by horizontal gene transfer and poorly maintains IncP-1 plasmids.}, }
@article {pmid25838283, year = {2015}, author = {Szathmáry, E}, title = {Toward major evolutionary transitions theory 2.0.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {33}, pages = {10104-10111}, pmid = {25838283}, issn = {1091-6490}, support = {294332/ERC_/European Research Council/International ; }, mesh = {Animals ; Bacteria/genetics ; *Biological Evolution ; Cultural Characteristics ; Ecosystem ; Eukaryotic Cells/cytology ; Female ; Gene Transfer, Horizontal ; Genetic Code ; Humans ; Language ; Male ; Mitochondria/genetics ; Organelle Biogenesis ; Phagocytosis ; Phylogeny ; Plastids/genetics ; Reproducibility of Results ; Stochastic Processes ; }, abstract = {The impressive body of work on the major evolutionary transitions in the last 20 y calls for a reconstruction of the theory although a 2D account (evolution of informational systems and transitions in individuality) remains. Significant advances include the concept of fraternal and egalitarian transitions (lower-level units like and unlike, respectively). Multilevel selection, first without, then with, the collectives in focus is an important explanatory mechanism. Transitions are decomposed into phases of origin, maintenance, and transformation (i.e., further evolution) of the higher level units, which helps reduce the number of transitions in the revised list by two so that it is less top-heavy. After the transition, units show strong cooperation and very limited realized conflict. The origins of cells, the emergence of the genetic code and translation, the evolution of the eukaryotic cell, multicellularity, and the origin of human groups with language are reconsidered in some detail in the light of new data and considerations. Arguments are given why sex is not in the revised list as a separate transition. Some of the transitions can be recursive (e.g., plastids, multicellularity) or limited (transitions that share the usual features of major transitions without a massive phylogenetic impact, such as the micro- and macronuclei in ciliates). During transitions, new units of reproduction emerge, and establishment of such units requires high fidelity of reproduction (as opposed to mere replication).}, }
@article {pmid25825433, year = {2015}, author = {Huo, W and Adams, HM and Zhang, MQ and Palmer, KL}, title = {Genome Modification in Enterococcus faecalis OG1RF Assessed by Bisulfite Sequencing and Single-Molecule Real-Time Sequencing.}, journal = {Journal of bacteriology}, volume = {197}, number = {11}, pages = {1939-1951}, pmid = {25825433}, issn = {1098-5530}, support = {K22 AI099088/AI/NIAID NIH HHS/United States ; U01 ES017166/ES/NIEHS NIH HHS/United States ; K22AI099088/AI/NIAID NIH HHS/United States ; U01ES017166/ES/NIEHS NIH HHS/United States ; }, mesh = {Base Sequence ; Conjugation, Genetic ; DNA Methylation ; Enterococcus faecalis/*genetics/metabolism ; *Genome, Bacterial ; Molecular Sequence Data ; Plasmids/genetics ; Sequence Analysis, DNA ; Sulfites/chemistry ; }, abstract = {UNLABELLED: Enterococcus faecalis is a Gram-positive bacterium that natively colonizes the human gastrointestinal tract and opportunistically causes life-threatening infections. Multidrug-resistant (MDR) E. faecalis strains have emerged, reducing treatment options for these infections. MDR E. faecalis strains have large genomes containing mobile genetic elements (MGEs) that harbor genes for antibiotic resistance and virulence determinants. Bacteria commonly possess genome defense mechanisms to block MGE acquisition, and we hypothesize that these mechanisms have been compromised in MDR E. faecalis. In restriction-modification (R-M) defense, the bacterial genome is methylated at cytosine (C) or adenine (A) residues by a methyltransferase (MTase), such that nonself DNA can be distinguished from self DNA. A cognate restriction endonuclease digests improperly modified nonself DNA. Little is known about R-M in E. faecalis. Here, we use genome resequencing to identify DNA modifications occurring in the oral isolate OG1RF. OG1RF has one of the smallest E. faecalis genomes sequenced to date and possesses few MGEs. Single-molecule real-time (SMRT) and bisulfite sequencing revealed that OG1RF has global 5-methylcytosine (m5C) methylation at 5'-GCWGC-3' motifs. A type II R-M system confers the m5C modification, and disruption of this system impacts OG1RF electrotransformability and conjugative transfer of an antibiotic resistance plasmid. A second DNA MTase was poorly expressed under laboratory conditions but conferred global N(4)-methylcytosine (m4C) methylation at 5'-CCGG-3' motifs when expressed in Escherichia coli. Based on our results, we conclude that R-M can act as a barrier to MGE acquisition and likely influences antibiotic resistance gene dissemination in the E. faecalis species.<br><br>IMPORTANCE: The horizontal transfer of antibiotic resistance genes among bacteria is a critical public health concern. Enterococcus faecalis is an opportunistic pathogen that causes life-threatening infections in humans. Multidrug resistance acquired by horizontal gene transfer limits treatment options for these infections. In this study, we used innovative DNA sequencing methodologies to investigate how a model strain of E. faecalis discriminates its own DNA from foreign DNA, i.e., self versus nonself discrimination. We also assess the role of an E. faecalis genome modification system in modulating conjugative transfer of an antibiotic resistance plasmid. These results are significant because they demonstrate that differential genome modification impacts horizontal gene transfer frequencies in E. faecalis.}, }
@article {pmid25824431, year = {2015}, author = {Han, Y and Lu, N and Chen, Q and Zhan, Y and Liu, W and Lu, W and Zhu, B and Lin, M and Yang, Z and Yan, Y}, title = {Interspecies Transfer and Regulation of Pseudomonas stutzeri A1501 Nitrogen Fixation Island in Escherichia coli.}, journal = {Journal of microbiology and biotechnology}, volume = {25}, number = {8}, pages = {1339-1348}, doi = {10.4014/jmb.1502.02027}, pmid = {25824431}, issn = {1738-8872}, mesh = {Ammonia/metabolism ; Escherichia coli/*genetics/metabolism ; *Gene Expression Regulation, Bacterial ; Gene Regulatory Networks ; *Gene Transfer, Horizontal ; *Genomic Islands ; Metabolic Networks and Pathways/*genetics ; *Nitrogen Fixation ; Oxygen/metabolism ; Pseudomonas stutzeri/*genetics/metabolism ; Temperature ; }, abstract = {Until now, considerable effort has been made to engineer novel nitrogen-fixing organisms through the transfer of nif genes from various diazotrophs to non-nitrogen fixers; however, regulatory coupling of the heterologous nif genes with the regulatory system of the new host is still not well understood. In this work, a 49 kb nitrogen fixation island from P. stutzeri A1501 was transferred into E. coli using a novel and efficient transformation strategy, and a series of recombinant nitrogen-fixing E. coli strains were obtained. We found that the nitrogenase activity of the recombinant E. coli strain EN-01, similar to the parent strain P. stutzeri A1501, was dependent on external ammonia concentration, oxygen tension, and temperature. We further found that there existed a regulatory coupling between the E. coli general nitrogen regulatory system and the heterologous P. stutzeri nif island in the recombinant E. coli strain. We also provided evidence that the E. coli general nitrogen regulator GlnG protein was involved in the activation of the nif-specific regulator NifA via a direct interaction with the NifA promoter. To the best of our knowledge, this work plays a groundbreaking role in increasing understanding of the regulatory coupling of the heterologous nitrogen fixation system with the regulatory system of the recipient host. Furthermore, it will shed light on the structure and functional integrity of the nif island and will be useful for the construction of novel and more robust nitrogen-fixing organisms through biosynthetic engineering.}, }
@article {pmid25822626, year = {2015}, author = {Novovic, K and Mihajlovic, S and Vasiljevic, Z and Filipic, B and Begovic, J and Jovcic, B}, title = {Carbapenem-resistant Acinetobacter baumannii from Serbia: revision of CarO classification.}, journal = {PloS one}, volume = {10}, number = {3}, pages = {e0122793}, pmid = {25822626}, issn = {1932-6203}, mesh = {Acinetobacter baumannii/*drug effects/genetics/isolation &amp; purification ; Bacterial Outer Membrane Proteins/*classification/genetics ; Carbapenems/*pharmacology ; Child ; Genotyping Techniques ; Humans ; Molecular Sequence Data ; Polymorphism, Genetic ; Porins/classification/genetics ; Serbia ; *beta-Lactam Resistance/genetics ; beta-Lactamases/genetics ; }, abstract = {Carbapenem-resistant A. baumannii present a significant therapeutic challenge for the treatment of nosocomial infections in many European countries. Although it is known that the gradient of A. baumannii prevalence increases from northern to southern Europe, this study provides the first data from Serbia. Twenty-eight carbapenem-resistant A. baumannii clinical isolates were collected at a Serbian pediatric hospital during a 2-year period. The majority of isolates (67.68%) belonged to the sequence type Group 1, European clonal complex II. All isolates harbored intrinsic OXA-51 and AmpC cephalosporinase. OXA-23 was detected in 16 isolates (57.14%), OXA-24 in 23 isolates (82.14%) and OXA-58 in 11 isolates (39.29%). Six of the isolates (21.43%) harbored all of the analyzed oxacillinases, except OXA-143 and OXA-235 that were not detected in this study. Production of oxacillinases was detected in different pulsotypes indicating the presence of horizontal gene transfer. NDM-1, VIM and IMP were not detected in analyzed clinical A. baumannii isolates. ISAba1 insertion sequence was present upstream of OXA-51 in one isolate, upstream of AmpC in 13 isolates and upstream of OXA-23 in 10 isolates. In silico analysis of carO sequences from analyzed A. baumannii isolates revealed the existence of two out of six highly polymorphic CarO variants. The phylogenetic analysis of CarO protein among Acinetobacter species revised the previous classification CarO variants into three groups based on strong bootstraps scores in the tree analysis. Group I comprises four variants (I-IV) while Groups II and III contain only one variant each. One half of the Serbian clinical isolates belong to Group I variant I, while the other half belongs to Group I variant III.}, }
@article {pmid25817042, year = {2015}, author = {Siriken, B and Türk, H and Yildirim, T and Durupinar, B and Erol, I}, title = {Prevalence and characterization of Salmonella isolated from chicken meat in Turkey.}, journal = {Journal of food science}, volume = {80}, number = {5}, pages = {M1044-50}, doi = {10.1111/1750-3841.12829}, pmid = {25817042}, issn = {1750-3841}, mesh = {Animals ; Anti-Bacterial Agents ; Chickens/*microbiology ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal/genetics ; Humans ; Integrases/genetics ; Integrons/genetics ; Meat/*microbiology ; Phenotype ; Salmonella/classification/genetics/*isolation &amp; purification ; Turkey ; }, abstract = {This study was conducted in a Turkish province to investigate the presence of Salmonella spp. in 150 chicken meat samples using 2 phenotyping techniques: classic culture technique (CCT) and immunomagnetic separation (IMS). For the confirmation of the isolates at molecular levels, invA gene was detected in these isolates. The presence of invA, class 1 (Cls1) integrons, and integrase (Int1) genes was demonstrated by PCR assay; and the resistance of the isolated Salmonella spp. strains to antibiotics was determined by disk diffusion test. All the cultural and PCR results were evaluated together; Salmonella spp. were detected in a total of 64 (42.66%) chicken meat samples. Contamination rate was higher in carcasses (53.33%, n = 75) than in meat pieces (32%, n = 75). When results of standard culture were compared with IMS technique, IMS (n = 54) showed a clear superiority over the CCT (n = 38). A very high resistance rate (≥ 89.28%) to vancomycin, tetracycline, streptomycin, or nalidixic acid was found. Trimethoprim-sulfamethoxazole resistance was present in 32.14%. Relatively lower incidence of resistance (≤ 8.33%) to gentamicin, chloramphenicol, ampicillin, and ceftriaxone was observed. Concurrent resistance to at least 4 antibiotics was detected in 92.85% of the isolates. Cls1 integrons and Int1 were positive in 80.95% and 95.23% of the isolates, respectively. However, Int1 alone was detected in 15.47% (n = 13). In conclusion, the high prevalence of Salmonella spp. in chicken meat may pose a potential public health risk, and the presence of antibiotic-resistant Salmonella spp. isolate together with Cls1 integron and/or integrase might play an important role in horizontal antibiotic gene transfer.}, }
@article {pmid25816508, year = {2014}, author = {Aleshkin, GI and Smelkova, OI and Timakova, NV and Dobrynina, OIu and Umiarov, AM and Rusina, OIu and Markov, AP and Bol'shakova, TN}, title = {[Role of phage LØ7 lysogeny in genetic variability of Escherichia coli].}, journal = {Zhurnal mikrobiologii, epidemiologii i immunobiologii}, volume = {}, number = {6}, pages = {14-20}, pmid = {25816508}, issn = {0372-9311}, mesh = {Bacterial Proteins/genetics ; Chromosome Mapping ; *Chromosomes, Bacterial ; Coliphages/*genetics/pathogenicity ; DNA, Bacterial/genetics ; DNA, Single-Stranded/genetics ; Escherichia coli K12/genetics/*virology ; Escherichia coli Proteins/genetics ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; *Genetic Variation ; Genotype ; Host-Pathogen Interactions ; Lysogeny/*genetics ; Monosaccharide Transport Proteins/genetics ; Mutation ; Phenotype ; Phosphoenolpyruvate Sugar Phosphotransferase System/genetics ; }, abstract = {AIM: Determine the possibility of Iysogenization of Escherichia coli single strain DNA (ssDNA) by 1ø7 bacteriophage from the Microviridae family and determine the role of phage lø7 lysogeny in genetic variability of these bacteria.<br><br>MATERIALS AND METHODS: A method of E. coli K12 lysogenization by phage l&#xf8;7 was developed. A spot-test for the control of resistance of the obtained lysogens against phage l&#xf8;7 and determination of lysogen l&#xf8;7 spontaneous production was worked out. Criteria for phage l&#xf8;7 identification, that is spontaneously produced by E. coli K12 lysogens, were proposed. A kit of isogenic E. coli strains, that vary by mutations in ptsI, ptsH and fruA genes, that code phosphoenolpyruvate (PEP): carbohydrate phosphotransferase system (PTS) proteins, was constructed.<br><br>RESULTS: The ability of highly virulent bacteriophage l&#xf8;7 to lysogenize E. coli was shown. A reduction of l&#xf8;7 titers in ptsI, ptsH and fruA E. coli K12 mutants was demonstrated compared with titers in wild-type bacteria. Lytic bacteriophage l&#xf8;7 was also able to lysogenize ptsI, ptsH and fruA mutants at a high frequency. Lysogens are resistant to phages l&#xf8;7, phiX174 of Microvirus genus and spontaneously produce l&#xf8;7.<br><br>CONCLUSION: Bacteriophage l&#xf8;7 of the Microviridae family is able to lysogenize E. coli K12 and vertically transfer genome of this lytic phage. As a result, lytic phage l&#xf8;7 takes part in bacterial variability as a factor of lysogen selection in bacteria population corresponding to PTS mutants by phenotype.}, }
@article {pmid25816328, year = {2015}, author = {Mathew, DC and Ho, YN and Gicana, RG and Mathew, GM and Chien, MC and Huang, CC}, title = {A rhizosphere-associated symbiont, Photobacterium spp. strain MELD1, and its targeted synergistic activity for phytoprotection against mercury.}, journal = {PloS one}, volume = {10}, number = {3}, pages = {e0121178}, pmid = {25816328}, issn = {1932-6203}, mesh = {Bacterial Proteins/metabolism ; Biodegradation, Environmental ; Fabaceae/microbiology/*physiology ; Mercury/*metabolism/toxicity ; Oxidoreductases/metabolism ; Photobacterium/enzymology/*isolation &amp; purification/*physiology ; Plant Leaves/growth &amp; development/microbiology ; Plant Roots/growth &amp; development/microbiology ; Rhizosphere ; Soil Pollutants/*metabolism/toxicity ; Symbiosis ; }, abstract = {Though heavy metal such as mercury is toxic to plants and microorganisms, the synergistic activity between them may offer benefit for surviving. In this study, a mercury-reducing bacterium, Photobacterium spp. strain MELD1, with an MIC of 33 mg x kg(-1) mercury was isolated from a severely mercury and dioxin contaminated rhizosphere soil of reed (Phragmites australis). While the whole genome sequencing of MELD1 confirmed the presence of a mer operon, the mercury reductase MerA gene showed 99% sequence identity to Vibrio shilloni AK1 and implicates its route resulted from the event of horizontal gene transfer. The efficiency of MELD1 to vaporize mercury (25 mg x kg(-1), 24 h) and its tolerance to toxic metals and xenobiotics such as lead, cadmium, pentachlorophenol, pentachloroethylene, 3-chlorobenzoic acid, 2,3,7,8-tetrachlorodibenzo-p-dioxin and 1,2,3,7,8,9-hexachlorodibenzo-p-dioxin is promising. Combination of a long yard bean (Vigna unguiculata ssp. Sesquipedalis) and strain MELD1 proved beneficial in the phytoprotection of mercury in vivo. The effect of mercury (Hg) on growth, distribution and tolerance was examined in root, shoot, leaves and pod of yard long bean with and without the inoculation of strain MELD1. The model plant inoculated with MELD1 had significant increases in biomass, root length, seed number, and increased mercury uptake limited to roots. Biolog plate assay were used to assess the sole-carbon source utilization pattern of the isolate and Indole-3-acetic acid (IAA) productivity was analyzed to examine if the strain could contribute to plant growth. The results of this study suggest that, as a rhizosphere-associated symbiont, the synergistic activity between the plant and MELD1 can improve the efficiency for phytoprotection, phytostabilization and phytoremediation of mercury.}, }
@article {pmid25816228, year = {2015}, author = {Gibson, W and Peacock, L and Ferris, V and Fischer, K and Livingstone, J and Thomas, J and Bailey, M}, title = {Genetic recombination between human and animal parasites creates novel strains of human pathogen.}, journal = {PLoS neglected tropical diseases}, volume = {9}, number = {3}, pages = {e0003665}, pmid = {25816228}, issn = {1935-2735}, support = {//Wellcome Trust/United Kingdom ; 088099//Wellcome Trust/United Kingdom ; 079375//Wellcome Trust/United Kingdom ; }, mesh = {Africa, Eastern/epidemiology ; Animals ; Crosses, Genetic ; Fluorescence ; *Gene Transfer, Horizontal ; *Genetic Variation ; Humans ; Membrane Glycoproteins/*genetics ; Protozoan Proteins/*genetics ; Recombination, Genetic/*genetics ; Species Specificity ; Trypanosoma brucei rhodesiense/*genetics ; Trypanosomiasis, African/*epidemiology/*parasitology ; }, abstract = {Genetic recombination between pathogens derived from humans and livestock has the potential to create novel pathogen strains, highlighted by the influenza pandemic H1N1/09, which was derived from a re-assortment of swine, avian and human influenza A viruses. Here we investigated whether genetic recombination between subspecies of the protozoan parasite, Trypanosoma brucei, from humans and animals can generate new strains of human pathogen, T. b. rhodesiense (Tbr) responsible for sleeping sickness (Human African Trypanosomiasis, HAT) in East Africa. The trait of human infectivity in Tbr is conferred by a single gene, SRA, which is potentially transferable to the animal pathogen Tbb by sexual reproduction. We tracked the inheritance of SRA in crosses of Tbr and Tbb set up by co-transmitting genetically-engineered fluorescent parental trypanosome lines through tsetse flies. SRA was readily transferred into new genetic backgrounds by sexual reproduction between Tbr and Tbb, thus creating new strains of the human pathogen, Tbr. There was no evidence of diminished growth or transmissibility of hybrid trypanosomes carrying SRA. Although expression of SRA is critical to survival of Tbr in the human host, we show that the gene exists as a single copy in a representative collection of Tbr strains. SRA was found on one homologue of chromosome IV in the majority of Tbr isolates examined, but some Ugandan Tbr had SRA on both homologues. The mobility of SRA by genetic recombination readily explains the observed genetic variability of Tbr in East Africa. We conclude that new strains of the human pathogen Tbr are being generated continuously by recombination with the much larger pool of animal-infective trypanosomes. Such novel recombinants present a risk for future outbreaks of HAT.}, }
@article {pmid25812464, year = {2015}, author = {Michael, GB and Freitag, C and Wendlandt, S and Eidam, C and Feßler, AT and Lopes, GV and Kadlec, K and Schwarz, S}, title = {Emerging issues in antimicrobial resistance of bacteria from food-producing animals.}, journal = {Future microbiology}, volume = {10}, number = {3}, pages = {427-443}, doi = {10.2217/fmb.14.93}, pmid = {25812464}, issn = {1746-0921}, mesh = {Animals ; Bacteria/*drug effects/genetics ; Bacterial Proteins/genetics ; Cattle ; *Drug Resistance, Multiple, Bacterial/genetics ; Enterobacteriaceae/drug effects/genetics ; Gene Transfer, Horizontal ; Humans ; Interspersed Repetitive Sequences ; Livestock/*microbiology ; Mannheimia haemolytica/drug effects/genetics ; Methicillin-Resistant Staphylococcus aureus/drug effects/genetics ; Pasteurella multocida/drug effects/genetics ; beta-Lactamases/genetics ; }, abstract = {During the last decade, antimicrobial resistance in bacteria from food-producing animals has become a major research topic. In this review, different emerging resistance properties related to bacteria of food-producing animals are highlighted. These include: extended-spectrum β-lactamase-producing Enterobacteriaceae; carbapenemase-producing bacteria; bovine respiratory tract pathogens, such as Pasteurella multocida and Mannheimia haemolytica, which harbor the multiresistance mediating integrative and conjugative element ICEPmu1; Gram-positive and Gram-negative bacteria that carry the multiresistance gene cfr; and the occurrence of numerous novel antimicrobial resistance genes in livestock-associated methicillin-resistant Staphylococcus aureus. The emergence of the aforementioned resistance properties is mainly based on the exchange of mobile genetic elements that carry the respective resistance genes.}, }
@article {pmid25811471, year = {2015}, author = {Baldy-Chudzik, K and Bok, E and Mazurek, J}, title = {[Well-known and new variants of pathogenic Escherichia coli as a consequence of the plastic genome].}, journal = {Postepy higieny i medycyny doswiadczalnej (Online)}, volume = {69}, number = {}, pages = {345-361}, doi = {10.5604/17322693.1145173}, pmid = {25811471}, issn = {1732-2693}, mesh = {Adaptation, Biological/genetics ; Biological Evolution ; Escherichia coli/*classification/*genetics ; *Genetic Variation ; *Genome, Bacterial ; Humans ; Phylogeny ; Plasmids ; Virulence Factors/*genetics ; }, abstract = {E. coli is a diverse bacterial species encompassing commensal as well as intestinal and extraintestinal pathogenic strains. The ability to adapt to so many different niches in the host organism is determined by the extreme genomic plasticity of E. coli. The genetic diversity is due to a complex phylogenetic structure in which besides the well-known main groups A, B1, B2 and D, four new groups, C, E, F and Clad I, have been characterized recently. The mobile gene pool exchanged by horizontal gene transfer (HGT) is another important driving force in the evolution of E. coli. Pathogenicity of strains is conditioned by a specific repertoire of virulence factors located on the mobile genetic elements and transmitted by HGT. The environment changing constantly stimulates the formation of new virulence gene combinations that generate the formation, not observed so far, of new pathogenic clones of higher capacity for virulence and greater expansiveness. The presence of very similar virulence plasmids carrying conserved combinations of the virulence genes (CVP) among extraintestinal pathogenic strains in humans and birds has been observed. It indicates a real possibility of occurrence of common virulence factors. The increase in drug resistance among pathogenic E. coli is also reflected in the prevalence of highly expansive clones exhibiting both high virulence and resistance. The presented data indicate that further studies are required to determine the interdependencies of resistance and virulence at the genetic level to help improve our management of the infectious diseases caused by these bacteria.}, }
@article {pmid25809153, year = {2015}, author = {Martínez, F and Arif, A and Nebauer, SG and Bueso, E and Ali, R and Montesinos, C and Brunaud, V and Muñoz-Bertomeu, J and Serrano, R}, title = {A fungal transcription factor gene is expressed in plants from its own promoter and improves drought tolerance.}, journal = {Planta}, volume = {242}, number = {1}, pages = {39-52}, pmid = {25809153}, issn = {1432-2048}, mesh = {*Adaptation, Physiological ; Arabidopsis/genetics/*physiology ; Candida/*genetics ; Cell Nucleus/metabolism ; *Droughts ; Fungal Proteins/*genetics/metabolism ; Gene Expression Regulation, Plant ; Genes, Fungal ; Green Fluorescent Proteins/metabolism ; Nucleotide Motifs/genetics ; Phloem/genetics ; Photosynthesis ; Plant Stomata/physiology ; Plants, Genetically Modified ; Proline/metabolism ; *Promoter Regions, Genetic ; Nicotiana/metabolism ; Transcription Factors/*genetics/metabolism ; Transcriptome/genetics ; }, abstract = {A fungal gene encoding a transcription factor is expressed from its own promoter in Arabidopsis phloem and improves drought tolerance by reducing transpiration and increasing osmotic potential. Horizontal gene transfer from unrelated organisms has occurred in the course of plant evolution, suggesting that some foreign genes may be useful to plants. The CtHSR1 gene, previously isolated from the halophytic yeast Candida tropicalis, encodes a heat-shock transcription factor-related protein. CtHSR1, with expression driven by its own promoter or by the Arabidopsis UBQ10 promoter, was introduced into the model plant Arabidopsis thaliana by Agrobacterium tumefaciens-mediated transformation and the resulting transgenic plants were more tolerant to drought than controls. Fusions of the CtHSR1 promoter with β-glucuronidase reporter gene indicated that this fungal promoter drives expression to phloem tissues. A chimera of CtHSR1 and green fluorescence protein is localized at the cell nucleus. The physiological mechanism of drought tolerance in transgenic plants is based on reduced transpiration (which correlates with decreased opening of stomata and increased levels of jasmonic acid) and increased osmotic potential (which correlates with increased proline accumulation). Transcriptomic analysis indicates that the CtHSR1 transgenic plants overexpressed a hundred of genes, including many relevant to stress defense such as LOX4 (involved in jasmonic acid synthesis) and P5CS1 (involved in proline biosynthesis). The promoters of the induced genes were enriched in upstream activating sequences for water stress induction. These results demonstrate that genes from unrelated organisms can have functional expression in plants from its own promoter and expand the possibilities of useful transgenes for plant biotechnology.}, }
@article {pmid25801684, year = {2015}, author = {Maslunka, C and Gürtler, V and Seviour, RJ}, title = {The impact of horizontal gene transfer on targeting the internal transcribed spacer region (ITS) to identify Acinetobacter junii strains.}, journal = {Journal of applied microbiology}, volume = {118}, number = {6}, pages = {1435-1443}, doi = {10.1111/jam.12800}, pmid = {25801684}, issn = {1365-2672}, mesh = {Acinetobacter/classification/*genetics/isolation &amp; purification ; Base Sequence ; DNA, Intergenic/*genetics ; *Gene Transfer, Horizontal ; Genetic Variation ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Reproducibility of Results ; }, abstract = {AIMS: Despite electrophoretic patterns of ITS PCR amplicons often suggesting only a single ITS sequence variant is present in strains of Acinetobacter junii, sequence data shows differences in ITS copies between and among them. This paper set out to explain why these ITS variants arise, and whether their presence compromises the reliability of the ITS targeted methods currently available for typing Ac. junii strains.<br><br>METHODS AND RESULTS: ITS sequences from a number of strains of Ac. junii were either downloaded from public databases or generated here by cloning and sequencing ITS PCR amplicons. ITS copies of Ac. junii strain 97338 were all 666 bp long, with identical sequences. In Ac. junii ATCC 17908(T) /BCRC 14854(T)), ITS copies were also all identical in their lengths but now were 706/7 bp long. Two sequence variants of these 707 bp ITS were detected. One was identical in its sequence to the nine ITS copies downloaded from the whole genome sequence of Ac. junii CIP 64&#xb7;5, and those in several other Ac. junii strains. The other 707 bp ITS variant occurred elsewhere only in Ac. junii strain DSM 14968 of those examined. The six ITS copies from the genome sequence of Ac. junii NIPH 182 were all 685 bp, and with identical sequences. Ac. junii strain 178 also possessed this same 685 bp ITS variant, one of six variants detected there. At least five ITS sequence variants were seen in Ac. junii strain 97380, four in strain DSM 14968 and two in the whole genome of strain 107470.<br><br>CONCLUSIONS: As with those of other Acinetobacter species, such ITS variants arise not from intragenomic recombination events but from the presence of different length indels. These arise from horizontal gene transfers involving ITS fragments of other Acinetobacter species.<br><br>The presence of these indels compromises the reliability of the ITS targeted methods available for typing Acinetobacter junii. It also precludes the value of using ITS sequences as phylogenetic markers in members of the genus Acinetobacter, since the outcomes in both cases depends on which copy variant is chosen.}, }
@article {pmid25801683, year = {2015}, author = {Arvand, M and Bettge-Weller, G and Fruth, A and Uphoff, H and Pfeifer, Y}, title = {Extended-spectrum beta-lactamase-producing Shiga toxin gene (stx1)-positive Escherichia coli O91:H14 carrying blaCTX-M-15 on an IncI1-ST31 plasmid isolated from a human patient in Germany.}, journal = {International journal of medical microbiology : IJMM}, volume = {305}, number = {3}, pages = {404-407}, doi = {10.1016/j.ijmm.2015.03.003}, pmid = {25801683}, issn = {1618-0607}, mesh = {DNA, Bacterial/genetics ; Escherichia coli Infections/*microbiology ; Escherichia coli Proteins/genetics/*metabolism ; Feces/*microbiology ; Gene Transfer, Horizontal ; Germany ; Humans ; India ; Molecular Weight ; Plasmids/*analysis ; Restriction Mapping ; Serotyping ; Shiga-Toxigenic Escherichia coli/classification/*enzymology/genetics/*isolation &amp; purification ; Travel ; beta-Lactamases/genetics/*metabolism ; }, abstract = {In 2011, the Shiga toxin- and extended-spectrum β-lactamase (ESBL)-producing Escherichia coli O104:H4 caused a serious outbreak of gastroenteritis in Germany. This strain carried bla(CTX-M-15) and bla(TEM-1) on an IncI1-ST31 plasmid. During screening of individuals at risk for acquisition of the epidemic E. coli O104:H4, we isolated another ESBL-producing and Shiga toxin-positive E. coli belonging to serotype O91:H14 from feces of a human patient. Interestingly, the patient also carried a further ESBL-producing but Shiga toxin-negative E. coli. Both strains harbored bla(CTX-M-15) and bla(TEM-1) on an IncI1-ST31 plasmid, which was indistinguishable regarding size and plasmid restriction pattern from the plasmid of the epidemic E. coli O104:H4 strain. The patient had traveled to India 6 months prior to the isolation of the E. coli strains. This is the first report of an ESBL-producing, Shiga toxin-positive E. coli of serogroup O91. Our data suggest a high propensity of the IncI1-ST31 plasmid to spread in the human and/or animal population.}, }
@article {pmid25794502, year = {2015}, author = {Nielsen, SM and de Gier, C and Dimopoulou, C and Gupta, V and Hansen, LH and Nørskov-Lauritsen, N}, title = {The capsule biosynthesis locus of Haemophilus influenzae shows conspicuous similarity to the corresponding locus in Haemophilus sputorum and may have been recruited from this species by horizontal gene transfer.}, journal = {Microbiology (Reading, England)}, volume = {161}, number = {6}, pages = {1182-1188}, doi = {10.1099/mic.0.000081}, pmid = {25794502}, issn = {1465-2080}, mesh = {Bacterial Capsules/*genetics ; Evolution, Molecular ; *Gene Order ; *Gene Transfer, Horizontal ; Genes, Essential ; *Genetic Loci ; Haemophilus/*genetics ; Haemophilus Infections/microbiology ; Humans ; Metabolic Networks and Pathways/*genetics ; Open Reading Frames ; Phylogeny ; Polymerase Chain Reaction ; Respiratory Tract Infections/microbiology ; Sequence Analysis, DNA ; Sequence Homology ; *Synteny ; }, abstract = {The newly described species Haemophilus sputorum has been cultured from the upper respiratory tract of humans and appears to have little pathogenic potential. The species encodes a capsular biosynthesis locus of approximately 12 kb composed of three distinct regions. Region I and III genes, involved in export and processing of the capsular material, show high similarity to the corresponding genes in capsulate lineages of the pathogenic species Haemophilus influenzae; indeed, standard bexA and bexB PCRs for detection of capsulated strains of H. influenzae give positive results with strains of H. sputorum. Three ORFs are present in region II of the sequenced strain of H. sputorum, of which a putative phosphotransferase showed homology with corresponding genes from H. influenzae serotype c and f. Phylogenetic analysis of housekeeping genes from 24 Pasteurellaceae species showed that H. sputorum was only distantly related to H. influenzae. In contrast to H. influenzae, the capsule locus in H. sputorum is not associated with transposases or other transposable elements. Our data suggest that the capsule locus of capsulate lineages of H. influenzae may have been recruited relatively recently from the commensal species H. sputorum by horizontal gene transfer.}, }
@article {pmid25794152, year = {2015}, author = {Makai, S and Li, X and Hussain, J and Cui, C and Wang, Y and Chen, M and Yang, Z and Ma, C and Guo, AY and Zhou, Y and Chang, J and Yang, G and He, G}, title = {A census of nuclear cyanobacterial recruits in the plant kingdom.}, journal = {PloS one}, volume = {10}, number = {3}, pages = {e0120527}, pmid = {25794152}, issn = {1932-6203}, mesh = {Cyanobacteria/classification/*genetics ; Gene Transfer, Horizontal ; Genetic Variation ; Genome ; Genome, Mitochondrial ; Genome, Plastid ; Plants/*genetics ; Plastids/genetics ; *Symbiosis ; }, abstract = {The plastids and mitochondria of the eukaryotic cell are of endosymbiotic origin. These events occurred ~2 billion years ago and produced significant changes in the genomes of the host and the endosymbiont. Previous studies demonstrated that the invasion of land affected plastids and mitochondria differently and that the paths of mitochondrial integration differed between animals and plants. Other studies examined the reasons why a set of proteins remained encoded in the organelles and were not transferred to the nuclear genome. However, our understanding of the functional relations of the transferred genes is insufficient. In this paper, we report a high-throughput phylogenetic analysis to identify genes of cyanobacterial origin for plants of different levels of complexity: Arabidopsis thaliana, Chlamydomonas reinhardtii, Physcomitrella patens, Populus trichocarpa, Selaginella moellendorffii, Sorghum bicolor, Oryza sativa, and Ostreococcus tauri. Thus, a census of cyanobacterial gene recruits and a study of their function are presented to better understand the functional aspects of plastid symbiogenesis. From algae to angiosperms, the GO terms demonstrated a gradual expansion over functionally related genes in the nuclear genome, beginning with genes related to thylakoids and photosynthesis, followed by genes involved in metabolism, and finally with regulation-related genes, primarily in angiosperms. The results demonstrate that DNA is supplied to the nuclear genome on a permanent basis with no regard to function, and only what is needed is kept, which thereby expands on the GO space along the related genes.}, }
@article {pmid25792310, year = {2015}, author = {Bohannon, J}, title = {Biotechnology. Biologists devise invasion plan for mutations.}, journal = {Science (New York, N.Y.)}, volume = {347}, number = {6228}, pages = {1300}, doi = {10.1126/science.347.6228.1300}, pmid = {25792310}, issn = {1095-9203}, mesh = {Albinism/genetics ; Animals ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Culicidae/genetics ; Drosophila melanogaster/*genetics ; Gene Targeting/*methods ; *Gene Transfer Techniques ; Gene Transfer, Horizontal ; *Genes, Recessive ; *Genes, X-Linked ; Humans ; Malaria/prevention &amp; control ; Mutagenesis ; Mutation ; Pigmentation/genetics ; }, }
@article {pmid25791083, year = {2015}, author = {Baltimore, D and Berg, P and Botchan, M and Carroll, D and Charo, RA and Church, G and Corn, JE and Daley, GQ and Doudna, JA and Fenner, M and Greely, HT and Jinek, M and Martin, GS and Penhoet, E and Puck, J and Sternberg, SH and Weissman, JS and Yamamoto, KR}, title = {Biotechnology. A prudent path forward for genomic engineering and germline gene modification.}, journal = {Science (New York, N.Y.)}, volume = {348}, number = {6230}, pages = {36-38}, pmid = {25791083}, issn = {1095-9203}, support = {/HHMI/Howard Hughes Medical Institute/United States ; P50 HG005550/HG/NHGRI NIH HHS/United States ; R01 GM078571/GM/NIGMS NIH HHS/United States ; T32 GM066698/GM/NIGMS NIH HHS/United States ; }, mesh = {Biotechnology/ethics ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Gene Transfer, Horizontal ; *Genetic Engineering/ethics ; Genetic Predisposition to Disease/*prevention &amp; control ; *Genome, Human ; Genomics ; *Germ Cells ; Humans ; Risk Management ; *Targeted Gene Repair ; }, abstract = {A framework for open discourse on the use of CRISPR-Cas9 technology to manipulate the human genome is urgently needed}, }
@article {pmid25790504, year = {2015}, author = {Ballén, V and Sáez, E and Benmessaoud, R and Houssain, T and Alami, H and Barkat, A and Kabiri, M and Moraleda, C and Bezad, R and Vila, J and Bosch, J and Bassat, Q and Soto, SM}, title = {First report of a Klebsiella pneumoniae ST466 strain causing neonatal sepsis harbouring the blaCTX-M-15 gene in Rabat, Morocco.}, journal = {FEMS microbiology letters}, volume = {362}, number = {1}, pages = {1-4}, doi = {10.1093/femsle/fnu026}, pmid = {25790504}, issn = {1574-6968}, mesh = {Blood/microbiology ; Conjugation, Genetic ; Drug Resistance, Bacterial ; Ear/microbiology ; Female ; Gene Transfer, Horizontal ; Humans ; Infant, Newborn ; Klebsiella Infections/*epidemiology/*microbiology ; Klebsiella pneumoniae/classification/*enzymology/genetics/*isolation &amp; purification ; Microbial Sensitivity Tests ; Morocco/epidemiology ; Multilocus Sequence Typing ; Plasmids/analysis ; Pregnancy ; Pregnancy Complications, Infectious/epidemiology ; Prevalence ; Sepsis/*microbiology ; Urine/microbiology ; Vagina/microbiology ; beta-Lactamases/genetics/*metabolism ; }, abstract = {Klebsiella pneumoniae is one of the Gram-negative bacilli most commonly found in urine of pregnant women and causing neonatal sepsis. The aim of this study was to analyse in terms of epidemiology and antimicrobial resistance of 23 K. pneumoniae isolates collected from vaginal swabs or urine of pregnant women, from pharyngeal and ear swabs of apparently healthy newborns and from peripheral cultures and hemocultures of newborns with suspected invasive neonatal infection in Rabat, Morocco. The prevalence of K. pneumoniae was 0.6 and 0.9% among pregnant women and neonates, respectively. These strains showed lower antimicrobial resistance levels regarding the developed countries. Thus, only one strain from a neonate presented an ESBL. This is the first report of a K. pneumoniae strain causing neonatal sepsis harbouring the blaCTX-M-15 gene in an IncFII plasmid and belonging to ST466 in this area.}, }
@article {pmid25790503, year = {2015}, author = {Monnet, C and Landaud, S and Bonnarme, P and Swennen, D}, title = {Growth and adaptation of microorganisms on the cheese surface.}, journal = {FEMS microbiology letters}, volume = {362}, number = {1}, pages = {1-9}, doi = {10.1093/femsle/fnu025}, pmid = {25790503}, issn = {1574-6968}, mesh = {Adaptation, Biological ; Adaptation, Physiological ; Bacteria/genetics/*growth &amp; development/metabolism ; *Biota ; Cheese/*microbiology ; Energy Metabolism ; Fungi/genetics/*growth &amp; development/metabolism ; Gene Transfer, Horizontal ; Hydrogen-Ion Concentration ; Iron/metabolism ; Salinity ; }, abstract = {Microbial communities living on cheese surfaces are composed of various bacteria, yeasts and molds that interact together, thus generating the typical sensory properties of a cheese. Physiological and genomic investigations have revealed important functions involved in the ability of microorganisms to establish themselves at the cheese surface. These functions include the ability to use the cheese's main energy sources, to acquire iron, to tolerate low pH at the beginning of ripening and to adapt to high salt concentrations and moisture levels. Horizontal gene transfer events involved in the adaptation to the cheese habitat have been described, both for bacteria and fungi. In the future, in situ microbial gene expression profiling and identification of genes that contribute to strain fitness by massive sequencing of transposon libraries will help us to better understand how cheese surface communities function.}, }
@article {pmid25790496, year = {2015}, author = {Zhao, JY and Zhu, YQ and Li, YN and Mu, XD and You, LP and Xu, C and Qin, P and Ma, JL}, title = {Coexistence of SFO-1 and NDM-1 β-lactamase genes and fosfomycin resistance gene fosA3 in an Escherichia coli clinical isolate.}, journal = {FEMS microbiology letters}, volume = {362}, number = {1}, pages = {1-7}, doi = {10.1093/femsle/fnu018}, pmid = {25790496}, issn = {1574-6968}, mesh = {Anti-Bacterial Agents/*pharmacology ; China ; Conjugation, Genetic ; *Drug Resistance, Bacterial ; Escherichia coli/drug effects/*enzymology/genetics/isolation &amp; purification ; Escherichia coli Infections/*microbiology ; Female ; Fosfomycin/*pharmacology ; Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Humans ; Middle Aged ; Plasmids/analysis/classification ; beta-Lactamases/*genetics ; }, abstract = {This study aims to characterize antimicrobial resistance and antimicrobial resistance genetic determinants of an Escherichia coli clinical isolate HD0149 from China in 2012. This strain displayed high-level resistance to cephalosporins, carbapenems, fluoroquinolones, aminoglycosides and fosfomycin. A range of antimicrobial resistance genes was detected responsible for its multiple antimicrobial resistances, involving the blaCMY-2, blaCTX-M-65, blaNDM-1, blaSFO-1, blaTEM-1, fosA3, rmtB, sul1 and sul2 genes. Four amino acid substitutions were detected in the quinolone resistance-determining regions (QRDRs) of GyrA (S83L and D87N), ParC (S80I) and ParE (S458A). Conjugation experiments revealed two multiresistance plasmids present in E. coli HD0149. The blaSFO-1 gene associated with blaNDM-1 gene was located in a 190 kb IncA/C plasmid and the blaCTX-M-65, fosA3 and rmtB genes were located in a 110 kb IncF plasmid. This is the first identification of the blaSFO-1 gene in an E. coli isolate and on a conjugative IncA/C plasmid. This may dramatically enhance the international prevalence and dissemination of blaSFO-1 among Enterobacteriaceae.}, }
@article {pmid25787256, year = {2015}, author = {Ramsay, JP and Tester, LG and Major, AS and Sullivan, JT and Edgar, CD and Kleffmann, T and Patterson-House, JR and Hall, DA and Tate, WP and Hynes, MF and Ronson, CW}, title = {Ribosomal frameshifting and dual-target antiactivation restrict quorum-sensing-activated transfer of a mobile genetic element.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {13}, pages = {4104-4109}, pmid = {25787256}, issn = {1091-6490}, mesh = {Base Sequence ; Binding Sites ; *Frameshifting, Ribosomal ; Gene Transfer Techniques ; Genomic Islands ; *Interspersed Repetitive Sequences ; Mass Spectrometry ; Mesorhizobium/metabolism ; Plants/microbiology ; Plasmids/metabolism ; Promoter Regions, Genetic ; Protein Biosynthesis ; *Quorum Sensing ; Rhizobium/metabolism ; Ribosomes/chemistry/*ultrastructure ; Symbiosis ; Transcription Factors ; Transcription, Genetic ; Two-Hybrid System Techniques ; beta-Galactosidase/metabolism ; }, abstract = {Symbiosis islands are integrative and conjugative mobile genetic elements that convert nonsymbiotic rhizobia into nitrogen-fixing symbionts of leguminous plants. Excision of the Mesorhizobium loti symbiosis island ICEMlSym(R7A) is indirectly activated by quorum sensing through TraR-dependent activation of the excisionase gene rdfS. Here we show that a +1 programmed ribosomal frameshift (PRF) fuses the coding sequences of two TraR-activated genes, msi172 and msi171, producing an activator of rdfS expression named Frameshifted excision activator (FseA). Mass-spectrometry and mutational analyses indicated that the PRF occurred through +1 slippage of the tRNA(phe) from UUU to UUC within a conserved msi172-encoded motif. FseA activated rdfS expression in the absence of ICEMlSym(R7A), suggesting that it directly activated rdfS transcription, despite being unrelated to any characterized DNA-binding proteins. Bacterial two-hybrid and gene-reporter assays demonstrated that FseA was also bound and inhibited by the ICEMlSym(R7A)-encoded quorum-sensing antiactivator QseM. Thus, activation of ICEMlSym(R7A) excision is counteracted by TraR antiactivation, ribosomal frameshifting, and FseA antiactivation. This robust suppression likely dampens the inherent biological noise present in the quorum-sensing autoinduction circuit and ensures that ICEMlSym(R7A) transfer only occurs in a subpopulation of cells in which both qseM expression is repressed and FseA is translated. The architecture of the ICEMlSym(R7A) transfer regulatory system provides an example of how a set of modular components have assembled through evolution to form a robust genetic toggle that regulates gene transcription and translation at both single-cell and cell-population levels.}, }
@article {pmid25786859, year = {2015}, author = {Park, JM and Chen, M and Wang, D and Deem, MW}, title = {Modularity enhances the rate of evolution in a rugged fitness landscape.}, journal = {Physical biology}, volume = {12}, number = {2}, pages = {025001}, pmid = {25786859}, issn = {1478-3975}, support = {R01 GM100468/GM/NIGMS NIH HHS/United States ; 1 R01 GM100468-01/GM/NIGMS NIH HHS/United States ; }, mesh = {*Biological Evolution ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Fitness ; Humans ; Immunity, Innate ; Influenza A virus/genetics/physiology ; Influenza, Human ; *Models, Genetic ; Viral Proteins/metabolism ; }, abstract = {Biological systems are modular, and this modularity affects the evolution of biological systems over time and in different environments. We here develop a theory for the dynamics of evolution in a rugged, modular fitness landscape. We show analytically how horizontal gene transfer couples to the modularity in the system and leads to more rapid rates of evolution at short times. The model, in general, analytically demonstrates a selective pressure for the prevalence of modularity in biology. We use this model to show how the evolution of the influenza virus is affected by the modularity of the proteins that are recognized by the human immune system. Approximately 25% of the observed rate of fitness increase of the virus could be ascribed to a modular viral landscape.}, }
@article {pmid25786308, year = {2014}, author = {Provorov, NA and Tikhonovich, IA}, title = {[Super-species genetic systems].}, journal = {Zhurnal obshchei biologii}, volume = {75}, number = {4}, pages = {247-260}, pmid = {25786308}, issn = {0044-4596}, mesh = {Gene Transfer, Horizontal/*physiology ; Metagenome/*physiology ; Microbial Consortia/*physiology ; *Models, Biological ; Quorum Sensing/physiology ; Symbiosis/physiology ; }, abstract = {Genetic integration of diverse organisms results in generation of three types of the super-species systems of heredity: metagenome (set of genetic factors of the microbial community which occupies a certain ecological niche), symbiogenome (functionally integrated system of the partners' symbiotic genes) and hologenome (entire hereditary system of a symbiotically originated organism). The integrity of metagenome is based on the cross-regulation and horizontal transfer of genes in co-evolving organisms which in the soil microbial communities are accompanied by maintenance of the stable extracellular DNA pool. Formation of symbiogenome is related to the highly specific partners' signaling interactions which are responsible for development of the joint metabolic pathways based on the specialized cellular and tissue structures. Transitions of symbiogenome into hologenome are due to the endosymbiotic gene transfer from microsymbionts to their hosts. In symbiotic bacteria, these transitions are coupled with establishments of multi-component, reduced and rudimentary genomes revealed for the ecologically obligatory symbionts, genetically obligatory symbionts, and cellular organelles, respectively. Their evolution is related to the stringency of transmission of microsymbionts by hosts increased from pseudo-vertical (via environment) to the trans-embryonic (via embryos and the surrounding tissues) and trans-ovarian transmission (via germ cells) which are culminated in the cytoplasmic inheritance of cellular organelles. We suggest the hypothesis about generation of endophytic plant symbiogenome on the basis of soil metagenome subjected to the control of host by its involvement into the quorum sensing auto-regulation of microbial community.}, }
@article {pmid25785885, year = {2015}, author = {Tong, P and Sun, Y and Ji, X and Du, X and Guo, X and Liu, J and Zhu, L and Zhou, B and Zhou, W and Liu, G and Feng, S}, title = {Characterization of antimicrobial resistance and extended-spectrum β-lactamase genes in Escherichia coli isolated from chickens.}, journal = {Foodborne pathogens and disease}, volume = {12}, number = {4}, pages = {345-352}, doi = {10.1089/fpd.2014.1857}, pmid = {25785885}, issn = {1556-7125}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Chickens/*microbiology ; China ; *Drug Resistance, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/drug effects/genetics/*isolation &amp; purification ; Escherichia coli Infections/*veterinary ; Gene Transfer, Horizontal ; Genes, Bacterial ; Microbial Sensitivity Tests ; Plasmids ; beta-Lactamases/classification/*genetics ; }, abstract = {Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli have been frequently isolated from food-producing animals and pose a serious threat to human health. This study collected 195 ESBL-producing E. coli isolates from 20 chicken farms and 3 live-bird markets located in Northeast China (Heilongjiang, Liaoning, Jilin) and Jiangsu province from February 2011 to October 2013. ESBL genes, including blaCTX-M, blaTEM, and blaSHV, were detected and characterized, and the susceptibilities of these strains to various antimicrobial agents were determined. One hundred ninety-one of these isolates carried 1 or more bla genes. blaCTX-M, blaTEM-1, and blaSHV-5 were identified in 183, 121, and 2 isolates, respectively. The most common blaCTX-M genes were blaCTX-M-15 (68 strains), blaCTX-M-65 (41 strains), blaCTX-M-55 (35 strains), blaCTX-M-14 (32 strains), followed by blaCTX-M-3, blaCTX-M-13, blaCTX-M-79, and blaCTX-M-101, as well as the chimeric genes blaCTX-M-64, blaCTX-M-123, and blaCTX-M-132. Fifteen strains (7.7%) co-harboring CTX-M-1 group and CTX-M-9 group genes were detected in 195 ESBL-producing strains. Pulsed-field gel electrophoresis of 45 strains showed that these CTX-M-producing isolates belonged to 34 different types. To our knowledge, this is the first study to report the blaSHV-5 gene in E. coli isolated from chickens in China. Conjugation experiments demonstrated that the blaCTX-M and blaTEM genes could be transferred to E. coli strain J53, while conjugative transfer of the blaSHV-5 gene from two isolates was not detectable. blaCTX-M genes are carried by many kinds of transferable and untypable plasmids. Our findings demonstrate that the CTX-M enzymes are predominant in both type and quantity.}, }
@article {pmid25785303, year = {2015}, author = {Crisp, A and Boschetti, C and Perry, M and Tunnacliffe, A and Micklem, G}, title = {Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes.}, journal = {Genome biology}, volume = {16}, number = {1}, pages = {50}, pmid = {25785303}, issn = {1474-760X}, mesh = {Animals ; Bacteria/genetics ; *Evolution, Molecular ; Gene Expression/*genetics ; Gene Transfer, Horizontal/*genetics ; *Genome ; Humans ; Invertebrates/genetics ; Nematoda ; Phylogeny ; Vertebrates/genetics ; }, abstract = {BACKGROUND: A fundamental concept in biology is that heritable material, DNA, is passed from parent to offspring, a process called vertical gene transfer. An alternative mechanism of gene acquisition is through horizontal gene transfer (HGT), which involves movement of genetic material between different species. HGT is well-known in single-celled organisms such as bacteria, but its existence in higher organisms, including animals, is less well established, and is controversial in humans.<br><br>RESULTS: We have taken advantage of the recent availability of a sufficient number of high-quality genomes and associated transcriptomes to carry out a detailed examination of HGT in 26 animal species (10 primates, 12 flies and four nematodes) and a simplified analysis in a further 14 vertebrates. Genome-wide comparative and phylogenetic analyses show that HGT in animals typically gives rise to tens or hundreds of active 'foreign' genes, largely concerned with metabolism. Our analyses suggest that while fruit flies and nematodes have continued to acquire foreign genes throughout their evolution, humans and other primates have gained relatively few since their common ancestor. We also resolve the controversy surrounding previous evidence of HGT in humans and provide at least 33 new examples of horizontally acquired genes.<br><br>CONCLUSIONS: We argue that HGT has occurred, and continues to occur, on a previously unsuspected scale in metazoans and is likely to have contributed to biochemical diversification during animal evolution.}, }
@article {pmid25784900, year = {2015}, author = {Wisecaver, JH and Rokas, A}, title = {Fungal metabolic gene clusters-caravans traveling across genomes and environments.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {161}, pmid = {25784900}, issn = {1664-302X}, abstract = {Metabolic gene clusters (MGCs), physically co-localized genes participating in the same metabolic pathway, are signature features of fungal genomes. MGCs are most often observed in specialized metabolism, having evolved in individual fungal lineages in response to specific ecological needs, such as the utilization of uncommon nutrients (e.g., galactose and allantoin) or the production of secondary metabolic antimicrobial compounds and virulence factors (e.g., aflatoxin and melanin). A flurry of recent studies has shown that several MGCs, whose functions are often associated with fungal virulence as well as with the evolutionary arms race between fungi and their competitors, have experienced horizontal gene transfer (HGT). In this review, after briefly introducing HGT as a source of gene innovation, we examine the evidence for HGT's involvement on the evolution of MGCs and, more generally of fungal metabolism, enumerate the molecular mechanisms that mediate such transfers and the ecological circumstances that favor them, as well as discuss the types of evidence required for inferring the presence of HGT in MGCs. The currently available examples indicate that transfers of entire MGCs have taken place between closely related fungal species as well as distant ones and that they sometimes involve large chromosomal segments. These results suggest that the HGT-mediated acquisition of novel metabolism is an ongoing and successful ecological strategy for many fungal species.}, }
@article {pmid25779587, year = {2015}, author = {Manageiro, V and Ferreira, E and Almeida, J and Barbosa, S and Simões, C and ,  and Bonomo, RA and Caniça, M}, title = {Predominance of KPC-3 in a survey for carbapenemase-producing Enterobacteriaceae in Portugal.}, journal = {Antimicrobial agents and chemotherapy}, volume = {59}, number = {6}, pages = {3588-3592}, pmid = {25779587}, issn = {1098-6596}, support = {R01 AI063517/AI/NIAID NIH HHS/United States ; R01 AI100560/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/*metabolism ; Enterobacter aerogenes/enzymology ; Enterobacteriaceae/*enzymology ; Escherichia coli/enzymology ; Klebsiella oxytoca/enzymology ; Klebsiella pneumoniae/enzymology ; Microbial Sensitivity Tests ; Plasmids/genetics ; Portugal ; beta-Lactamases/genetics/*metabolism ; }, abstract = {Among the 2,105 Enterobacteriaceae tested in a survey done in Portugal, 165 were nonsusceptible to carbapenems, from which 35 (26 Klebsiella pneumoniae, 3 Escherichia coli, 2 Enterobacter aerogenes, and 3 Enterobacter cloacae isolates and 1 Klebsiella oxytoca isolate) were confirmed to be carbapenemase producers by the presence of 30 Tn4401d-blaKPC-3, 4 intI3-blaGES-5, and one intI1-blaVIM-2 gene, alone or in combination with other bla genes. The dissemination of blaKPC-3 gene carried by an IncF plasmid suggests lateral gene transfer as a major mechanism of dissemination.}, }
@article {pmid25769824, year = {2015}, author = {Johnson, TJ and Singer, RS and Isaacson, RE and Danzeisen, JL and Lang, K and Kobluk, K and Rivet, B and Borewicz, K and Frye, JG and Englen, M and Anderson, J and Davies, PR}, title = {In Vivo Transmission of an IncA/C Plasmid in Escherichia coli Depends on Tetracycline Concentration, and Acquisition of the Plasmid Results in a Variable Cost of Fitness.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {10}, pages = {3561-3570}, pmid = {25769824}, issn = {1098-5336}, mesh = {Animals ; Anti-Bacterial Agents/*administration &amp; dosage/analysis ; Drug Resistance, Bacterial ; Escherichia coli/drug effects/*genetics/metabolism ; Escherichia coli Infections/drug therapy/microbiology/*veterinary ; Gene Transfer, Horizontal/*drug effects ; Plasmids/*genetics/metabolism ; Swine ; Swine Diseases/*drug therapy/microbiology ; Tetracycline/*administration &amp; dosage/analysis ; }, abstract = {IncA/C plasmids are broad-host-range plasmids enabling multidrug resistance that have emerged worldwide among bacterial pathogens of humans and animals. Although antibiotic usage is suspected to be a driving force in the emergence of such strains, few studies have examined the impact of different types of antibiotic administration on the selection of plasmid-containing multidrug resistant isolates. In this study, chlortetracycline treatment at different concentrations in pig feed was examined for its impact on selection and dissemination of an IncA/C plasmid introduced orally via a commensal Escherichia coli host. Continuous low-dose administration of chlortetracycline at 50 g per ton had no observable impact on the proportions of IncA/C plasmid-containing E. coli from pig feces over the course of 35 days. In contrast, high-dose administration of chlortetracycline at 350 g per ton significantly increased IncA/C plasmid-containing E. coli in pig feces (P < 0.001) and increased movement of the IncA/C plasmid to other indigenous E. coli hosts. There was no evidence of conjugal transfer of the IncA/C plasmid to bacterial species other than E. coli. In vitro competition assays demonstrated that bacterial host background substantially impacted the cost of IncA/C plasmid carriage in E. coli and Salmonella. In vitro transfer and selection experiments demonstrated that tetracycline at 32 μg/ml was necessary to enhance IncA/C plasmid conjugative transfer, while subinhibitory concentrations of tetracycline in vitro strongly selected for IncA/C plasmid-containing E. coli. Together, these experiments improve our knowledge on the impact of differing concentrations of tetracycline on the selection of IncA/C-type plasmids.}, }
@article {pmid25769111, year = {2015}, author = {Cavalier-Smith, T}, title = {Mixed heterolobosean and novel gregarine lineage genes from culture ATCC 50646: Long-branch artefacts, not lateral gene transfer, distort α-tubulin phylogeny.}, journal = {European journal of protistology}, volume = {51}, number = {2}, pages = {121-137}, doi = {10.1016/j.ejop.2014.12.001}, pmid = {25769111}, issn = {1618-0429}, mesh = {*Artifacts ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Eukaryota/*classification/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; *Phylogeny ; Tubulin/*genetics ; }, abstract = {Contradictory and confusing results can arise if sequenced 'monoprotist' samples really contain DNA of very different species. Eukaryote-wide phylogenetic analyses using five genes from the amoeboflagellate culture ATCC 50646 previously implied it was an undescribed percolozoan related to percolatean flagellates (Stephanopogon, Percolomonas). Contrastingly, three phylogenetic analyses of 18S rRNA alone, did not place it within Percolozoa, but as an isolated deep-branching excavate. I resolve that contradiction by sequence phylogenies for all five genes individually, using up to 652 taxa. Its 18S rRNA sequence (GQ377652) is near-identical to one from stained-glass windows, somewhat more distant from one from cooling-tower water, all three related to terrestrial actinocephalid gregarines Hoplorhynchus and Pyxinia. All four protein-gene sequences (Hsp90; α-tubulin; β-tubulin; actin) are from an amoeboflagellate heterolobosean percolozoan, not especially deeply branching. Contrary to previous conclusions from trees combining protein and rRNA sequences or rDNA trees including Eozoa only, this culture does not represent a major novel deep-branching eukaryote lineage distinct from Heterolobosea, and thus lacks special significance for deep eukaryote phylogeny, though the rDNA sequence is important for gregarine phylogeny. α-Tubulin trees for over 250 eukaryotes refute earlier suggestions of lateral gene transfer within eukaryotes, being largely congruent with morphology and other gene trees.}, }
@article {pmid25766741, year = {2015}, author = {Coates, BS}, title = {Horizontal transfer of a non-autonomous Helitron among insect and viral genomes.}, journal = {BMC genomics}, volume = {16}, number = {1}, pages = {137}, pmid = {25766741}, issn = {1471-2164}, mesh = {Animals ; Bombyx/genetics/virology ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Insect ; Genome, Viral ; Interspersed Repetitive Sequences/*genetics ; Sequence Alignment ; Viruses/*genetics ; }, abstract = {BACKGROUND: The movement of mobile elements among species by horizontal transposon transfer (HTT) influences the evolution of genomes through the modification of structure and function. Helitrons are a relatively new lineage of DNA-based (class II) transposable elements (TEs) that propagate by rolling-circle replication, and are capable of acquiring host DNA. The rapid spread of Helitrons among animal lineages by HTT is facilitated by shuttling in viral particles or by unknown mechanisms mediated by close organism associations (e.g. between hosts and parasites).<br><br>RESULTS: A non-autonomous Helitron independently annotated as BmHel-2 from Bombyx mori and the MITE01 element from Ostrinia nubilalis was predicted in the genomes of 24 species in the insect Order Lepidoptera. Integrated Helitrons retained&#x2009;&#x2265;&#x2009;65% sequence identity over a 250&#xa0;bp consensus, and were predicted to retain secondary structures inclusive of a 3'-hairpin and a 5'-subterminal inverted repeat. Highly similar Hel-2 copies were predicted in the genomes of insects and associated viruses, which along with a previous documented case of real-time virus-insect cell line transposition suggests that this Helitron has likely propagated by HTT.<br><br>CONCLUSIONS: These findings provide evidence that insect virus may mediate the HTT of Helitron-like TEs. This movement may facilitate the shuttling of DNA elements among insect genomes. Further sampling is required to determine the putative role of HTT in insect genome evolution.}, }
@article {pmid25765920, year = {2015}, author = {Seifert, SN and Khatchikian, CE and Zhou, W and Brisson, D}, title = {Evolution and population genomics of the Lyme borreliosis pathogen, Borrelia burgdorferi.}, journal = {Trends in genetics : TIG}, volume = {31}, number = {4}, pages = {201-207}, pmid = {25765920}, issn = {0168-9525}, support = {AI076342/AI/NIAID NIH HHS/United States ; R01 AI076342/AI/NIAID NIH HHS/United States ; AI097137/AI/NIAID NIH HHS/United States ; T32 AI055400/AI/NIAID NIH HHS/United States ; R01 AI097137/AI/NIAID NIH HHS/United States ; }, mesh = {Borrelia burgdorferi/classification/*genetics ; *Evolution, Molecular ; *Genetics, Population ; *Genomics ; Humans ; Lyme Disease/*microbiology ; Phylogeny ; Phylogeography ; Research ; Selection, Genetic ; }, abstract = {Population genomic studies have the potential to address many unresolved questions about microbial pathogens by facilitating the identification of genes underlying ecologically important traits, such as novel virulence factors and adaptations to humans or other host species. Additionally, this framework improves estimations of population demography and evolutionary history to accurately reconstruct recent epidemics and identify the molecular and environmental factors that resulted in the outbreak. The Lyme disease bacterium, Borrelia burgdorferi, exemplifies the power and promise of the application of population genomics to microbial pathogens. We discuss here the future of evolutionary studies in B. burgdorferi, focusing on the primary evolutionary forces of horizontal gene transfer, natural selection, and migration, as investigations transition from analyses of single genes to genomes.}, }
@article {pmid25765460, year = {2015}, author = {Ruan, Y and Shen, L and Zou, Y and Qi, Z and Yin, J and Jiang, J and Guo, L and He, L and Chen, Z and Tang, Z and Qin, S}, title = {Comparative genome analysis of Prevotella intermedia strain isolated from infected root canal reveals features related to pathogenicity and adaptation.}, journal = {BMC genomics}, volume = {16}, number = {1}, pages = {122}, pmid = {25765460}, issn = {1471-2164}, mesh = {Adult ; Animals ; Bacterial Proteins/genetics ; Bacteriocins/metabolism ; *Comparative Genomic Hybridization ; Contig Mapping ; DNA/chemistry/isolation &amp; purification ; Dental Pulp Cavity/*microbiology ; Drug Resistance, Bacterial/genetics ; Erythrocytes/metabolism ; *Genome, Bacterial ; Hemolysis ; Humans ; Iron/metabolism ; Male ; Models, Theoretical ; Multigene Family ; Open Reading Frames/genetics ; Phylogeny ; Prevotella intermedia/classification/*genetics/pathogenicity ; Sequence Analysis, DNA ; Virulence Factors/genetics ; }, abstract = {BACKGROUND: Many species of the genus Prevotella are pathogens that cause oral diseases. Prevotella intermedia is known to cause various oral disorders e.g. periodontal disease, periapical periodontitis and noma as well as colonize in the respiratory tract and be associated with cystic fibrosis and chronic bronchitis. It is of clinical significance to identify the main drive of its various adaptation and pathogenicity. In order to explore the intra-species genetic differences among strains of Prevotella intermedia of different niches, we isolated a strain Prevotella intermedia ZT from the infected root canal of a Chinese patient with periapical periodontitis and gained a draft genome sequence. We annotated the genome and compared it with the genomes of other taxa in the genus Prevotella.<br><br>RESULTS: The raw data set, consisting of approximately 65X-coverage reads, was trimmed and assembled into contigs from which 2165 ORFs were predicted. The comparison of the Prevotella intermedia ZT genome sequence with the published genome sequence of Prevotella intermedia 17 and Prevotella intermedia ATCC25611 revealed that ~14% of the genes were strain-specific. The Preveotella intermedia strains share a set of conserved genes contributing to its adaptation and pathogenic and possess strain-specific genes especially those involved in adhesion and secreting bacteriocin. The Prevotella intermedia ZT shares similar gene content with other taxa of genus Prevotella. The genomes of the genus Prevotella is highly dynamic with relative conserved parts: on average, about half of the genes in one Prevotella genome were not included in another genome of the different Prevotella species. The degree of conservation varied with different pathways: the ability of amino acid biosynthesis varied greatly with species but the pathway of cell wall components biosynthesis were nearly constant. Phylogenetic tree shows that the taxa from different niches are scarcely distributed among clades.<br><br>CONCLUSIONS: Prevotella intermedia ZT belongs to a genus marked with highly dynamic genomes. The specific genes of Prevotella intermedia indicate that adhesion, competing with surrounding microbes and horizontal gene transfer are the main drive of the evolution of Prevotella intermedia.}, }
@article {pmid25759432, year = {2015}, author = {Göttig, S and Gruber, TM and Stecher, B and Wichelhaus, TA and Kempf, VA}, title = {In vivo horizontal gene transfer of the carbapenemase OXA-48 during a nosocomial outbreak.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {60}, number = {12}, pages = {1808-1815}, doi = {10.1093/cid/civ191}, pmid = {25759432}, issn = {1537-6591}, mesh = {Aged ; Animals ; Cross Infection/*microbiology ; DNA, Bacterial/analysis/genetics ; Escherichia coli/drug effects/genetics ; Female ; Gene Transfer, Horizontal/*genetics ; Humans ; Klebsiella Infections/*microbiology ; Klebsiella pneumoniae/drug effects/genetics ; Male ; Mice ; Middle Aged ; Multilocus Sequence Typing ; Plasmids/genetics ; beta-Lactam Resistance/*genetics ; beta-Lactamases/*genetics ; }, abstract = {BACKGROUND: OXA-48 is a highly prevalent carbapenemase and has been isolated worldwide. Here, we investigate the in vivo horizontal gene transfer (HGT) of blaOXA-48 from Klebsiella pneumoniae to Escherichia coli in an infected patient.<br><br>METHODS: Bacterial isolates were characterized by susceptibility testing, multilocus sequence typing, DiversiLab, and plasmid analyses. Transferability of blaOXA-48 was evaluated by in vitro transconjugation using the outbreak strain and E. coli J53. In vivo transconjugation was investigated using the larvae of the greater wax moth (Galleria mellonella) and low-complexity-microbiota mice.<br><br>RESULTS: OXA-48-harboring K. pneumoniae isolates belonging to ST14 were isolated during a nosocomial outbreak from 6 patients. Molecular and epidemiological analyses revealed the HGT of an approximately 60-kb OXA-48-containing IncL/M-type plasmid from K. pneumoniae to E. coli belonging to the novel ST666 in a patient. In vitro conjugation experiments revealed a transconjugation frequency of 8.7 &#xd7; 10(-7). HGT of OXA-48 in a newly developed in vivo model using G. mellonella larvae revealed a higher transconjugation frequency of 1.3 &#xd7; 10(-4). The conjugation frequency of OXA-48 from K. pneumoniae and E. coli in the gut of low-complexity-microbiota mice was determined to be 2.9 &#xd7; 10(-5).<br><br>CONCLUSIONS: The in vivo intergenus gene transfer of OXA-48 in the gut of an infected patient was verified in vitro and in 2 in vivo models, which both showed even higher transmission frequencies vs in vitro conditions. This implies that the current in vitro protocols might not correctly reflect the HGT of carbapenemase genes in vivo.}, }
@article {pmid25759293, year = {2015}, author = {Zhang, A and Xu, C and Wang, H and Lei, C and Liu, B and Guan, Z and Yang, C and Yang, Y and Peng, L}, title = {Presence and new genetic environment of pleuromutilin-lincosamide-streptogramin A resistance gene lsa(E) in Erysipelothrix rhusiopathiae of swine origin.}, journal = {Veterinary microbiology}, volume = {177}, number = {1-2}, pages = {162-167}, doi = {10.1016/j.vetmic.2015.02.014}, pmid = {25759293}, issn = {1873-2542}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Base Sequence ; China ; Clindamycin/pharmacology ; Diterpenes/pharmacology ; Drug Resistance, Multiple, Bacterial/*genetics ; Erysipelothrix/*drug effects/*genetics ; Genes, MDR/*genetics ; Lincosamides/pharmacology ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Multigene Family/genetics ; Polycyclic Compounds ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Streptogramin A/pharmacology ; Swine/*microbiology ; Pleuromutilins ; }, abstract = {Erysipelothrix rhusiopathiae is a Gram-positive bacillus that causes erysipelas in swine. In recent years, erysipelas infection among swine in China has been increasing. A combined resistance phenotype to pleuromutilins, lincosamides, and streptogramin A (PLSA phenotype) was found in some E. rhusiopathiae isolates. The aim of this study was to identify the resistance genes responsible for the PLSA phenotype in E. rhusiopathiae strains and to map the genetic environment of the identified resistance gene. A total of 46 E. rhusiopathiae isolates from 31 pig farms in China were studied. Minimum inhibitory concentrations (MICs) of 11 antimicrobial agents were determined by broth microdilution method. Seven were highly resistant to tiamulin (MICs 32 μg/ml) and clindamycin (MICs 64 μg/ml). Resistance genes responsible for the PLSA phenotype were screened by PCR. The lsa(E), spw, lnu(B), aadE and aphA3 genes were detected in strains had the PLSA phenotype, whereas none was detected in susceptible strains. The genetic environment of lsa(E) gene was determined by whole-genome sequencing and overlapping PCR assays. A novel multiresistance gene cluster, orf1-aadE-apt-spw-lsa(E)-lnu(B)-rec-orf2-orf1-aadE-sat4-aphA3, was found. Horizontal gene transfer experiments and whole-genome sequencing suggested that the lsa(E)-carrying multiresistance gene cluster was located in the chromosome. This is the first molecular characterization of PLSA resistance in E. rhusiopathiae. The lsa(E), spw and lnu(B) genes were found in E. rhusiopathiae for the first time. A novel lsa(E)-carrying multiresistance gene cluster was found. The location of lsa(E) in different gene cluster facilitates its persistence and dissemination.}, }
@article {pmid27246756, year = {2015}, author = {Iwai, M and Yokono, M and Kono, M and Noguchi, K and Akimoto, S and Nakano, A}, title = {Light-harvesting complex Lhcb9 confers a green alga-type photosystem I supercomplex to the moss Physcomitrella patens.}, journal = {Nature plants}, volume = {1}, number = {}, pages = {14008}, doi = {10.1038/nplants.2014.8}, pmid = {27246756}, issn = {2055-0278}, abstract = {Light-harvesting complex (LHC) proteins in chloroplast thylakoid membranes not only transfer absorbed light energy to the two photosystems but also regulate the rate of energy transfer to avoid photodamage. Here we demonstrate that Lhcb9, a recently discovered LHC protein in the moss Physcomitrella patens, functions to connect LHC proteins with photosystem I (PSI), resulting in the formation of two different types of PSI supercomplexes in thylakoid membranes. We observed that the Lhcb9-containing PSI supercomplex is disassembled in response to excess light conditions. On the basis of our phylogenetic analysis, it appears that P. patens acquired Lhcb9 by horizontal gene transfer from the earlier green algal lineage, leading to the presence of both green alga-type and vascular plant-type PSI supercomplexes, which would have been crucial for conquering the dynamic environmental interface between aquatic and terrestrial conditions it faced during evolution.}, }
@article {pmid26999960, year = {2015}, author = {Piekarska, K and Zacharczuk, K and Rzeczkowska, M and Wołkowicz, T and Januszkiewicz, A and Podsiadły, E and Demkow, U and Gierczyński, R}, title = {Probable Interspecies Transfer of the bla(VIM-4) Gene between Enterobacter cloacae and Klebsiella pneumoniae in a Single Infant Patient.}, journal = {Polish journal of microbiology}, volume = {64}, number = {4}, pages = {387-389}, doi = {10.5604/17331331.1185239}, pmid = {26999960}, issn = {1733-1331}, mesh = {Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Bacterial/genetics ; Enterobacter cloacae/*genetics/physiology ; Gene Expression Regulation, Bacterial ; Gene Expression Regulation, Enzymologic ; Gene Transfer, Horizontal ; Humans ; Infant, Extremely Low Birth Weight ; Infant, Newborn ; Klebsiella pneumoniae/*genetics/physiology ; Male ; beta-Lactamases/genetics/*metabolism ; }, abstract = {We report the interspecies transfer of the bla(VLM-4) gene in MBL-producing Enterobacter cloacae and Klebsiella pneumoniae isolates from a newborn patient who had received meropenem therapy. We show evidence that gene bla(VIM-4) was transmitted as a part of the class-1 integron on a ca. -90 kb conjugative plasmid. High homology of nucleotide sequence was observed between the integron found in VIM-4 producing E. cloacae and K. pneumoniae strains tested and class-1 integrons previously reporteded in Pseudomonas aeruginosa from Hungary and Poland. This finding may suggest P. aeruginosa as a potential source of acquired VIM-4 in Enterobacteriaceae.}, }
@article {pmid26998230, year = {2015}, author = {Sharma, P and Das De, T and Sharma, S and Kumar Mishra, A and Thomas, T and Verma, S and Kumari, V and Lata, S and Singh, N and Valecha, N and Chand Pandey, K and Dixit, R}, title = {Deep sequencing revealed molecular signature of horizontal gene transfer of plant like transcripts in the mosquito Anopheles culicifacies: an evolutionary puzzle.}, journal = {F1000Research}, volume = {4}, number = {}, pages = {1523}, pmid = {26998230}, issn = {2046-1402}, abstract = {In prokaryotes, horizontal gene transfer (HGT) has been regarded as an important evolutionary drive to acquire and retain beneficial genes for their survival in diverse ecologies. However, in eukaryotes, the functional role of HGTs remains questionable, although current genomic tools are providing increased evidence of acquisition of novel traits within non-mating metazoan species. Here, we provide another transcriptomic evidence for the acquisition of massive plant genes in the mosquito, Anopheles culicifacies. Our multiple experimental validations including genomic PCR, RT-PCR, real-time PCR, immuno-blotting and immuno-florescence microscopy, confirmed that plant like transcripts (PLTs) are of mosquito origin and may encode functional proteins. A comprehensive molecular analysis of the PLTs and ongoing metagenomic analysis of salivary microbiome provide initial clues that mosquitoes may have survival benefits through the acquisition of nuclear as well as chloroplast encoded plant genes. Our findings of PLTs further support the similar questionable observation of HGTs in other higher organisms, which is still a controversial and debatable issue in the community of evolutionists. We believe future understanding of the underlying mechanism of the feeding associated molecular responses may shed new insights in the functional role of PLTs in the mosquito.}, }
@article {pmid26958724, year = {2014}, author = {Dy, RL and Richter, C and Salmond, GP and Fineran, PC}, title = {Remarkable Mechanisms in Microbes to Resist Phage Infections.}, journal = {Annual review of virology}, volume = {1}, number = {1}, pages = {307-331}, doi = {10.1146/annurev-virology-031413-085500}, pmid = {26958724}, issn = {2327-056X}, support = {BB/G000298/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/H002677/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {Bacteriophages (phages) specifically infect bacteria and are the most abundant biological entities on Earth. The constant exposure to phage infection imposes a strong selective pressure on bacteria to develop viral resistance strategies that promote prokaryotic survival. Thus, this parasite-host relationship results in an evolutionary arms race of adaptation and counteradaptation between the interacting partners. The evolutionary outcome is a spectrum of remarkable strategies used by the bacteria and phages as they attempt to coexist. These approaches include adsorption inhibition, injection blocking, abortive infection, toxin-antitoxin, and CRISPR-Cas systems. In this review, we highlight the diverse and complementary antiphage systems in bacteria, as well as the evasion mechanisms used by phages to escape these resistance strategies.}, }
@article {pmid26988457, year = {2014}, author = {Piccin-Santos, V and Brandão, MM and Bittencourt-Oliveira, Mdo C}, title = {Phylogenetic study of Geitlerinema and Microcystis (Cyanobacteria) using PC-IGS and 16S-23S ITS as markers: investigation of horizontal gene transfer.}, journal = {Journal of phycology}, volume = {50}, number = {4}, pages = {736-743}, doi = {10.1111/jpy.12204}, pmid = {26988457}, issn = {1529-8817}, abstract = {Selection of genes that have not been horizontally transferred for prokaryote phylogenetic inferences is regarded as a challenging task. The markers internal transcribed spacer of ribosomal genes (16S-23S ITS) and phycocyanin intergenic spacer (PC-IGS), based on the operons of ribosomal and phycocyanin genes respectively, are among the most used markers in cyanobacteria. The region of the ribosomal genes has been considered stable, whereas the phycocyanin operon may have undergone horizontal transfer. To investigate the occurrence of horizontal transfer of PC-IGS, phylogenetic trees of Geitlerinema and Microcystis strains were generated using PC-IGS and 16S-23S ITS and compared. Phylogenetic trees based on the two markers were mostly congruent for Geitlerinema and Microcystis, indicating a common evolutionary history among ribosomal and phycocyanin genes with no evidence for horizontal transfer of PC-IGS. Thus, PC-IGS is a suitable marker, along with 16S-23S ITS for phylogenetic studies of cyanobacteria.}, }
@article {pmid26082110, year = {2014}, author = {Derbyshire, KM and Gray, TA}, title = {Distributive Conjugal Transfer: New Insights into Horizontal Gene Transfer and Genetic Exchange in Mycobacteria.}, journal = {Microbiology spectrum}, volume = {2}, number = {1}, pages = {MGM2-0022-2013}, doi = {10.1128/microbiolspec.MGM2-0022-2013}, pmid = {26082110}, issn = {2165-0497}, mesh = {*Conjugation, Genetic ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Mycobacterium smegmatis/*genetics ; }, abstract = {The past decade has seen an explosion in the application of genomic tools across all biological disciplines. This is also true for mycobacteria, where whole-genome sequences are now available for pathogens and nonpathogens alike. Genomes within the Mycobacterium tuberculosis complex (MTBC) bear the hallmarks of horizontal gene transfer (HGT). Conjugation is the form of HGT with the highest potential capacity and evolutionary influence. Donor and recipient strains of Mycobacterium smegmatis actively conjugate upon coculturing in biofilms and on solid media. Whole-genome sequencing of the transconjugant progeny demonstrated the incredible scale and range of genomic variation that conjugation generates. Transconjugant genomes are complex mosaics of the parental strains. Some transconjugant genomes are up to one-quarter donor-derived, distributed over 30 segments. Transferred segments range from ∼50 bp to ∼225,000 bp in length and are exchanged with their recipient orthologs all around the genome. This unpredictable genome-wide infusion of DNA sequences is called distributive conjugal transfer (DCT), to distinguish it from traditional oriT-based conjugation. The mosaicism generated in a single transfer event resembles that seen from meiotic recombination in sexually reproducing organisms and contrasts with traditional models of HGT. This similarity allowed the application of a genome-wide association study approach to map the donor genes that confer a donor mating identity phenotype. The mating identity genes map to the esx1 locus, expanding the central role of ESX-1 function in conjugation. The potential for DCT to instantaneously blend genomes will affect how we view mycobacterial evolution and provide new tools for the facile manipulation of mycobacterial genomes.}, }
@article {pmid27437481, year = {2014}, author = {Khan, CM}, title = {The Dynamic Interactions between Salmonella and the Microbiota, within the Challenging Niche of the Gastrointestinal Tract.}, journal = {International scholarly research notices}, volume = {2014}, number = {}, pages = {846049}, pmid = {27437481}, issn = {2356-7872}, abstract = {Understanding how Salmonella species establish successful infections remains a foremost research priority. This gastrointestinal pathogen not only faces the hostile defenses of the host's immune system, but also faces fierce competition from the large and diverse community of microbiota for space and nutrients. Salmonella have solved these challenges ingeniously. To jump-start growth, Salmonella steal hydrogen produced by the gastrointestinal microbiota. Type 3 effector proteins are subsequently secreted by Salmonella to trigger potent inflammatory responses, which generate the alternative terminal electron acceptors tetrathionate and nitrate. Salmonella exclusively utilize these electron acceptors for anaerobic respiration, permitting metabolic access to abundant substrates such as ethanolamine to power growth blooms. Chemotaxis and flagella-mediated motility enable the identification of nutritionally beneficial niches. The resulting growth blooms also promote horizontal gene transfer amongst the resident microbes. Within the gastrointestinal tract there are opportunities for chemical signaling between host cells, the microbiota, and Salmonella. Host produced catecholamines and bacterial autoinducers form components of this chemical dialogue leading to dynamic interactions. Thus, Salmonella have developed remarkable strategies to initially shield against host defenses and to transiently compete against the intestinal microbiota leading to successful infections. However, the immunocompetent host is subsequently able to reestablish control and clear the infection.}, }
@article {pmid27433520, year = {2014}, author = {Wan, P and Che, D}, title = {A Computational Framework for Tracing the Origins of Genomic Islands in Prokaryotes.}, journal = {International scholarly research notices}, volume = {2014}, number = {}, pages = {732857}, pmid = {27433520}, issn = {2356-7872}, abstract = {Genomic islands (GIs) are chunks of genomic fragments that are acquired from nongenealogical organisms through horizontal gene transfer (HGT). Current researches on studying donor-recipient relationships for HGT are limited at a gene level. As more GIs have been identified and verified, the way of studying donor-recipient relationships can be better modeled by using GIs rather than individual genes. In this paper, we report the development of a computational framework for detecting origins of GIs. The main idea of our computational framework is to identify GIs in a query genome, search candidate genomes that contain genomic regions similar to those GIs in the query genome by BLAST search, and then filter out some candidate genomes if those similar genomic regions are also alien (detected by GI detection tools). We have applied our framework in finding the GI origins for Mycobacterium tuberculosis H37Rv, Herminiimonas arsenicoxydans, and three Thermoanaerobacter species. The predicted results were used to establish the donor-recipient network relationships and visualized by Gephi. Our studies have shown that donor genomes detected by our computational approach were mainly consistent with previous studies. Our framework was implemented with Perl and executed on Windows operating system.}, }
@article {pmid26713222, year = {2014}, author = {Rosenwald, AG and Murray, B and Toth, T and Madupu, R and Kyrillos, A and Arora, G}, title = {Evidence for horizontal gene transfer between Chlamydophila pneumoniae and Chlamydia phage.}, journal = {Bacteriophage}, volume = {4}, number = {4}, pages = {e965076}, pmid = {26713222}, issn = {2159-7073}, abstract = {Chlamydia-infecting bacteriophages, members of the Microviridae family, specifically the Gokushovirinae subfamily, are small (4.5-5 kb) single-stranded circles with 8-10 open-reading frames similar to E. coli phage ϕX174. Using sequence information found in GenBank, we examined related genes in Chlamydophila pneumoniae and Chlamydia-infecting bacteriophages. The 5 completely sequenced C. pneumoniae strains contain a gene orthologous to a phage gene annotated as the putative replication initiation protein (PRIP, also called VP4), which is not found in any other members of the Chlamydiaceae family sequenced to date. The C. pneumoniae strain infecting koalas, LPCoLN, in addition contains another region orthologous to phage sequences derived from the minor capsid protein gene, VP3. Phylogenetically, the phage PRIP sequences are more diverse than the bacterial PRIP sequences; nevertheless, the bacterial sequences and the phage sequences each cluster together in their own clade. Finally, we found evidence for another Microviridae phage-related gene, the major capsid protein gene, VP1 in a number of other bacterial species and 2 eukaryotes, the woodland strawberry and a nematode. Thus, we find considerable evidence for DNA sequences related to genes found in bacteriophages of the Microviridae family not only in a variety of prokaryotic but also eukaryotic species.}, }
@article {pmid25902698, year = {2014}, author = {Ciszewski, M and Czekaj, T and Szewczyk, EM}, title = {[New insight into bacterial zoonotic pathogens posing health hazards to humans].}, journal = {Medycyna pracy}, volume = {65}, number = {6}, pages = {819-829}, pmid = {25902698}, issn = {0465-5893}, mesh = {Animals ; Consumer Product Safety ; European Union ; *Food Microbiology ; Foodborne Diseases/*epidemiology/microbiology/parasitology/*prevention &amp; control/virology ; Humans ; Poland ; Primary Prevention/*organization &amp; administration ; Risk Factors ; Zoonoses/*epidemiology/microbiology/parasitology/*prevention &amp; control/virology ; }, abstract = {This article presents the problem of evolutionary changes of zoonotic pathogens responsible for human diseases. Everyone is exposed to the risk of zoonotic infection, particularly employees having direct contact with animals, i.e. veterinarians, breeders, butchers and workers of animal products' processing industry. The article focuses on pathogens monitored by the European Centre for Disease Prevention and Control (ECDC), which has been collecting statistical data on zoonoses from all European Union countries for 19 years and publishing collected data in annual epidemiological reports. Currently, the most important 11 pathogens responsible for causing human zoonotic diseases are being monitored, of which seven are bacteria: Salmonella spp., Campylobacter spp., Listeria monocytogenes, Mycobacterium bovis, Brucella spp., Coxiella burnetti and Verotoxin-producing E. coli (VTEC)/Shiga-like toxin producing E. coli (STEC). As particularly important are considered foodborne pathogens. The article also includes new emerging zoonotic bacteria, which are not currently monitored by ECDC but might pose a serious epidemiological problem in a foreseeable future: Streptococcus iniae, S. suis, S. dysgalactiae and staphylococci: Staphylococcus intermedius, S. pseudintermedius. Those species have just crossed the animal-human interspecies barrier. The exact mechanism of this phenomenon remains unknown, it is connected, however, with genetic variability, capability to survive in changing environment. These abilities derive from DNA rearrangement and horizontal gene transfer between bacterial cells. Substantial increase in the number of scientific publications on this subject, observed over the last few years, illustrates the importance of the problem.}, }
@article {pmid25864333, year = {2014}, author = {Van Meervenne, E and De Weirdt, R and Van Coillie, E and Devlieghere, F and Herman, L and Boon, N}, title = {Plasmid transfer in biofilms from a food industry perspective.}, journal = {Communications in agricultural and applied biological sciences}, volume = {79}, number = {1}, pages = {167-171}, pmid = {25864333}, issn = {1379-1176}, mesh = {*Biofilms ; *Food Microbiology ; Food-Processing Industry ; *Gene Transfer, Horizontal ; Plasmids/*genetics ; Pseudomonas putida/*genetics/growth &amp; development/physiology ; }, }
@article {pmid25780496, year = {2014}, author = {Reeve, W and Sullivan, J and Ronson, C and Tian, R and Bräu, L and Davenport, K and Goodwin, L and Chain, P and Woyke, T and Lobos, E and Huntemann, M and Pati, A and Mavromatis, K and Markowitz, V and Ivanova, N and Kyrpides, N}, title = {Genome sequence of the Lotus corniculatus microsymbiont Mesorhizobium loti strain R88B.}, journal = {Standards in genomic sciences}, volume = {9}, number = {}, pages = {3}, pmid = {25780496}, issn = {1944-3277}, abstract = {Mesorhizobium loti strain R88B was isolated in 1993 in the Rocklands range in Otago, New Zealand from a Lotus corniculatus root nodule. R88B is an aerobic, Gram-negative, non-spore-forming rod. This report reveals the genome of M. loti strain R88B contains a single scaffold of size 7,195,110 bp which encodes 6,950 protein-coding genes and 66 RNA-only encoding genes. This genome does not harbor any plasmids but contains the integrative and conjugative element ICEMlSym(R7A), also known as the R7A symbiosis island, acquired by horizontal gene transfer in the field environment from M. loti strain R7A. It also contains a mobilizable genetic element ICEMladh(R88B), that encodes a likely adhesin gene which has integrated downstream of ICEMlSym(R7A), and three acquired loci that together allow the utilization of the siderophore ferrichrome. This rhizobial genome is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.}, }
@article {pmid26184966, year = {2013}, author = {Almagro-Moreno, S and Taylor, RK}, title = {Cholera: Environmental Reservoirs and Impact on Disease Transmission.}, journal = {Microbiology spectrum}, volume = {1}, number = {2}, pages = {}, doi = {10.1128/microbiolspec.OH-0003-2012}, pmid = {26184966}, issn = {2165-0497}, abstract = {Vibrio cholerae is widely known to be the etiological agent of the life-threatening diarrheal disease cholera. Cholera remains a major scourge in many developing countries, infecting hundreds of thousands every year. Remarkably, V. cholerae is a natural inhabitant of brackish riverine, estuarine, and coastal waters, and only a subset of strains are known to be pathogenic to humans. Recent studies have begun to uncover a very complex network of relationships between V. cholerae and other sea dwellers, and the mechanisms associated with the occurrence of seasonal epidemics in regions where cholera is endemic are beginning to be elucidated. Many of the factors required for the organism's survival and persistence in its natural environment have been revealed, as well as the ubiquitous presence of horizontal gene transfer in the emergence of pathogenic strains of V. cholerae. In this article, we will focus on the environmental stage of pathogenic V. cholerae and the interactions of the microorganism with other inhabitants of aquatic environments. We will discuss the impact that its environmental reservoirs have on disease transmission and the distinction between reservoirs of V. cholerae and the vectors that establish cholera as a zoonosis.}, }
@article {pmid27008402, year = {2013}, author = {Bhattacharya, D and Price, DC and Bicep, C and Bapteste, E and Sarwade, M and Rajah, VD and Yoon, HS}, title = {Identification of a Marine Cyanophage in a Protist Single-cell Metagenome Assembly.}, journal = {Journal of phycology}, volume = {49}, number = {1}, pages = {207-212}, doi = {10.1111/jpy.12028}, pmid = {27008402}, issn = {0022-3646}, abstract = {Analysis of microbial biodiversity is hampered by a lack of reference genomes from most bacteria, viruses, and algae. This necessitates either the cultivation of a restricted number of species for standard sequencing projects or the analysis of highly complex environmental DNA metagenome data. Single-cell genomics (SCG) offers a solution to this problem by constraining the studied DNA sample to an individual cell and its associated symbionts, prey, and pathogens. We used SCG to study marine heterotrophic amoebae related to Paulinella ovalis (A. Wulff) P.W. Johnson, P.E. Hargraves &amp; J.M. Sieburth (Rhizaria). The genus Paulinella is best known for its photosynthetic members such as P. chromatophora Lauterborn that is the only case of plastid primary endosymbiosis known outside of algae and plants. Here, we studied the phagotrophic sister taxa of P. chromatophora that are related to P. ovalis and found one SCG assembly to contain α-cyanobacterial DNA. These cyanobacterial contigs are presumably derived from prey. We also uncovered an associated cyanophage lineage (provisionally named phage PoL_MC2). Phylogenomic analysis of the fragmented genome assembly suggested a minimum genome size of 200 Kbp for phage PoL_MC2 that encodes 179 proteins and is most closely related to Synechococcus phage S-SM2. For this phage, gene network analysis demonstrates a highly modular genome structure typical of other cyanophages. Our work demonstrates that SCG is a powerful approach for discovering algal and protist biodiversity and for elucidating biotic interactions in natural samples.}, }
@article {pmid27029305, year = {2013}, author = {Baharoglu, Z and Garriss, G and Mazel, D}, title = {Multiple Pathways of Genome Plasticity Leading to Development of Antibiotic Resistance.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {2}, number = {2}, pages = {288-315}, pmid = {27029305}, issn = {2079-6382}, abstract = {The emergence of multi-resistant bacterial strains is a major source of concern and has been correlated with the widespread use of antibiotics. The origins of resistance are intensively studied and many mechanisms involved in resistance have been identified, such as exogenous gene acquisition by horizontal gene transfer (HGT), mutations in the targeted functions, and more recently, antibiotic tolerance through persistence. In this review, we focus on factors leading to integron rearrangements and gene capture facilitating antibiotic resistance acquisition, maintenance and spread. The role of stress responses, such as the SOS response, is discussed.}, }
@article {pmid27029295, year = {2013}, author = {Laureti, L and Matic, I and Gutierrez, A}, title = {Bacterial Responses and Genome Instability Induced by Subinhibitory Concentrations of Antibiotics.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {2}, number = {1}, pages = {100-114}, pmid = {27029295}, issn = {2079-6382}, abstract = {Nowadays, the emergence and spread of antibiotic resistance have become an utmost medical and economical problem. It has also become evident that subinhibitory concentrations of antibiotics, which pollute all kind of terrestrial and aquatic environments, have a non-negligible effect on the evolution of antibiotic resistance in bacterial populations. Subinhibitory concentrations of antibiotics have a strong effect on mutation rates, horizontal gene transfer and biofilm formation, which may all contribute to the emergence and spread of antibiotic resistance. Therefore, the molecular mechanisms and the evolutionary pressures shaping the bacterial responses to subinhibitory concentrations of antibiotics merit to be extensively studied. Such knowledge is valuable for the development of strategies to increase the efficacy of antibiotic treatments and to extend the lifetime of antibiotics used in therapy by slowing down the emergence of antibiotic resistance.}, }
@article {pmid27009993, year = {2012}, author = {D'Alelio, D and Gandolfi, A}, title = {Recombination Signals In The rpoC1 Gene Indicate Gene-Flow Between Planktothrix (Cyanoprokaryota) Species.}, journal = {Journal of phycology}, volume = {48}, number = {6}, pages = {1424-1432}, doi = {10.1111/j.1529-8817.2012.01225.x}, pmid = {27009993}, issn = {0022-3646}, abstract = {The delineation of species boundaries in the potentially harmful cyanobacterium Planktothrix Anagnostidis et Komárek 1988 is particularly tangled. Genetic recombination has been invoked to explain the occurrence of overlapping biological traits among recognized species. Although horizontal gene transfer is shown as a driver of diversification in this genus, clear evidence for homologous recombination at the single gene level is still lacking. Several Planktothrix strains (n = 244) sampled in eight fresh water lakes in north Italy were characterized by sequencing the rpoC1 gene, a molecular marker previously proposed to discriminate between species. Six haplotypes were detected, four of which are newly described. A relevant number of rpoC1 sequences (n = 54) showed evidence of homologous recombination. By comparing the sequences produced in the work presented here to those available on GenBank for the genus, multiple recombination events were tracked between haplotypes associated to P. rubescens, P. suspensa and P. agardhii, the latter being a species not found in our survey. Recombination signals were in form of (i) a vast mosaic structure present in the alignment of rpoC1 haplotypes, (ii) multiple and statistically significant paths in the split decomposition network connecting these haplotypes and (iii) many individual crossing-over events detected by means of recombination detection tests. Data suggest that the molecular evolution of the rpoC1 gene in the genus Planktothrix appears as strongly influenced by homologous recombination. In addition, rpoC1 diversity effectively tracks recombinational processes among species in the complex made up by P. rubescens, P. agardhii and P. suspensa, which are not isolated in terms of gene-flow.}, }
@article {pmid26038416, year = {2012}, author = {Wong, SS and Yuen, KY}, title = {Streptococcus pyogenes and re-emergence of scarlet fever as a public health problem.}, journal = {Emerging microbes &amp; infections}, volume = {1}, number = {7}, pages = {e2}, pmid = {26038416}, issn = {2222-1751}, abstract = {Explosive outbreaks of infectious diseases occasionally occur without immediately obvious epidemiological or microbiological explanations. Plague, cholera and Streptococcus pyogenes infection are some of the epidemic-prone bacterial infections. Besides epidemiological and conventional microbiological methods, the next-generation gene sequencing technology permits prompt detection of genomic and transcriptomic profiles associated with invasive phenotypes. Horizontal gene transfer due to mobile genetic elements carrying virulence factors and antimicrobial resistance, or mutations associated with the two component CovRS operon are important bacterial factors conferring survival advantage or invasiveness. The high incidence of scarlet fever in children less than 10 years old suggests that the lack of protective immunity is an important host factor. A high population density, overcrowded living environment and a low yearly rainfall are environmental factors contributing to outbreak development. Inappropriate antibiotic use is not only ineffective for treatment, but may actually drive an epidemic caused by drug-resistant strains and worsen patient outcomes by increasing the bacterial density at the site of infection and inducing toxin production. Surveillance of severe S. pyogenes infection is important because it can complicate concurrent chickenpox and influenza. Concomitant outbreaks of these two latter infections with a highly virulent and drug-resistant S. pyogenes strain can be disastrous.}, }
@article {pmid27020015, year = {2011}, author = {Johnson, TL and Palenik, B and Brahamsha, B}, title = {CHARACTERIZATION OF A FUNCTIONAL VANADIUM-DEPENDENT BROMOPEROXIDASE IN THE MARINE CYANOBACTERIUM SYNECHOCOCCUS SP. CC9311(1).}, journal = {Journal of phycology}, volume = {47}, number = {4}, pages = {792-801}, doi = {10.1111/j.1529-8817.2011.01007.x}, pmid = {27020015}, issn = {0022-3646}, abstract = {Vanadium-dependent bromoperoxidases (VBPOs) are characterized by the ability to oxidize halides using hydrogen peroxide. These enzymes are well-studied in eukaryotic macroalgae and are known to produce a variety of brominated secondary metabolites. Though genes have been annotated as VBPO in multiple prokaryotic genomes, they remain uncharacterized. The genome of the coastal marine cyanobacterium Synechococcus sp. CC9311 encodes a predicted VBPO (YP_731869.1, sync_2681), and in this study, we show that protein extracts from axenic cultures of Synechococcus possess bromoperoxidase activity, oxidizing bromide and iodide, but not chloride. In-gel activity assays of Synechococcus proteins separated using PAGE reveal a single band having VBPO activity. When sequenced via liquid chromatography/mass spectrometry/mass spectrometry (LC/MS/MS), peptides from the band aligned to the VBPO sequence predicted by the open reading frame (ORF) sync_2681. We show that a VBPO gene is present in a closely related strain, Synechococcus sp. WH8020, but not other clade I Synechococcus strains, consistent with recent horizontal transfer of the gene into Synechococcus. Diverse cyanobacterial-like VBPO genes were detected in a pelagic environment off the California coast using PCR. Investigation of functional VBPOs in unicellular cyanobacteria may lead to discovery of novel halogenated molecules and a better understanding of these organisms' chemical ecology and physiology.}, }
@article {pmid26443725, year = {2008}, author = {Long, KS and Vester, B}, title = {Antibiotic Resistance Mechanisms, with an Emphasis on Those Related to the Ribosome.}, journal = {EcoSal Plus}, volume = {3}, number = {1}, pages = {}, doi = {10.1128/ecosalplus.2.5.7}, pmid = {26443725}, issn = {2324-6200}, abstract = {Antibiotic resistance is a fundamental aspect of microbiology, but it is also a phenomenon of vital importance in the treatment of diseases caused by pathogenic microorganisms. A resistance mechanism can involve an inherent trait or the acquisition of a new characteristic through either mutation or horizontal gene transfer. The natural susceptibilities of bacteria to a certain drug vary significantly from one species of bacteria to another and even from one strain to another. Once inside the cell, most antibiotics affect all bacteria similarly. The ribosome is a major site of antibiotic action and is targeted by a large and chemically diverse group of antibiotics. A number of these antibiotics have important applications in human and veterinary medicine in the treatment of bacterial infections. The antibiotic binding sites are clustered at functional centers of the ribosome, such as the decoding center, the peptidyl transferase center, the GTPase center, the peptide exit tunnel, and the subunit interface spanning both subunits on the ribosome. Upon binding, the drugs interfere with the positioning and movement of substrates, products, and ribosomal components that are essential for protein synthesis. Ribosomal antibiotic resistance is due to the alteration of the antibiotic binding sites through either mutation or methylation. Our knowledge of antibiotic resistance mechanisms has increased, in particular due to the elucidation of the detailed structures of antibiotic-ribosome complexes and the components of the efflux systems. A number of mutations and methyltransferases conferring antibiotic resistance have been characterized. These developments are important for understanding and approaching the problems associated with antibiotic resistance, including design of antimicrobials that are impervious to known bacterial resistance mechanisms.}, }
@article {pmid27041032, year = {2008}, author = {Bhattacharya, D and Nosenko, T}, title = {ENDOSYMBIOTIC AND HORIZONTAL GENE TRANSFER IN CHROMALVEOLATES(1).}, journal = {Journal of phycology}, volume = {44}, number = {1}, pages = {7-10}, doi = {10.1111/j.1529-8817.2007.00433.x}, pmid = {27041032}, issn = {0022-3646}, abstract = {Chromalveolates include photosynthetic and nonphotosynthetic (some plastid-lacking) algae and protists that define a vast swath of eukaryotic diversity. These taxa are masters of gene acquisition through serial endosymbiosis (endosymbiotic gene transfer, EGT) and horizontal gene transfer (HGT). Understanding the contribution of these sources to nuclear genomes is key to elucidating chromalveolate evolution and to identifying suitable phylogenetic markers to place this lineage in the tree of life. Here we briefly review recent findings in our lab with regard to EGT and HGT in chromalveolates.}, }
@article {pmid25942745, year = {2007}, author = {Shittu, AO and Udo, EE and Lin, J}, title = {Insights on Virulence and Antibiotic Resistance: A Review of the Accessory Genome of Staphylococcus aureus.}, journal = {Wounds : a compendium of clinical research and practice}, volume = {19}, number = {9}, pages = {237-244}, pmid = {25942745}, issn = {1044-7946}, abstract = {Staphylococcus aureus continues to be a serious health problem worldwide due to its intrinsic nature of virulence, ability to cause a wide array of infection, and its capacity to develop resistance to a number of antibiotics. The S aureus genome has continually evolved through both mutation and acquisition of exogenous genes, leading to the emergence of antibiotic-resistant strains with the ability for clonal dissemination across nations and continents. Methicillin-resistant S aureus (MRSA) is one of the most commonly identified antibiotic-resistant pathogens in the hospital and community settings with substantial mortality and morbidity. This review examines the accessory genome of 8 sequenced S aureus strains regarding the variety of virulence factors and mechanisms of antibiotic resistance. The remarkable nature of this organism to acquire and disseminate an array of mobile genetic elements (MBEs) through horizontal gene transfer illustrates the mechanisms for evolution and its fitness level in the face of constant environmental challenges. The relative ease of transfer of genetic materials, especially antibiotic-resistant genes, across staphylococcal species indicates that there is a potential pandemic problem in the hospital and community environment.}, }
@article {pmid25758953, year = {2015}, author = {Domman, D and Horn, M and Embley, TM and Williams, TA}, title = {Plastid establishment did not require a chlamydial partner.}, journal = {Nature communications}, volume = {6}, number = {}, pages = {6421}, pmid = {25758953}, issn = {2041-1723}, support = {281633/ERC_/European Research Council/International ; 089803/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 268701/ERC_/European Research Council/International ; 045404/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacterial Proteins/genetics/metabolism ; Bayes Theorem ; Biological Evolution ; Carbohydrate Metabolism/*physiology ; Chlamydia/classification/*genetics/metabolism ; Cyanobacteria/classification/*genetics/metabolism ; Cyanophora/classification/*genetics/metabolism ; Gene Transfer, Horizontal ; Membrane Transport Proteins/genetics/metabolism ; Phylogeny ; Plastids/genetics/*metabolism ; Symbiosis/physiology ; }, abstract = {Primary plastids descend from the cyanobacterial endosymbiont of an ancient eukaryotic host, but the initial selective drivers that stabilized the association between these two cells are still unclear. One hypothesis that has achieved recent prominence suggests that the first role of the cyanobiont was in energy provision for a host cell whose reserves were being depleted by an intracellular chlamydial pathogen. A pivotal claim is that it was chlamydial proteins themselves that converted otherwise unusable cyanobacterial metabolites into host energy stores. We test this hypothesis by investigating the origins of the key enzymes using sophisticated phylogenetics. Here we show a mosaic origin for the relevant pathway combining genes with host, cyanobacterial or bacterial ancestry, but we detect no strong case for Chlamydiae to host transfer under the best-fitting models. Our conclusion is that there is no compelling evidence from gene trees that Chlamydiae played any role in establishing the primary plastid endosymbiosis.}, }
@article {pmid25756111, year = {2014}, author = {Ma, Y and Allen, LZ and Palenik, B}, title = {Diversity and genome dynamics of marine cyanophages using metagenomic analyses.}, journal = {Environmental microbiology reports}, volume = {6}, number = {6}, pages = {583-594}, doi = {10.1111/1758-2229.12160}, pmid = {25756111}, issn = {1758-2229}, mesh = {Bacteriophages/classification/*genetics/isolation &amp; purification/physiology ; Cyanobacteria/virology ; Gene Transfer, Horizontal ; *Genetic Variation ; Genome, Viral ; Host Specificity ; Maine ; Metagenomics ; Molecular Sequence Data ; Oceans and Seas ; Phylogeny ; Seawater/*virology ; }, abstract = {Cyanophages are abundant in the oceanic environment and directly impact cyanobacterial distributions, physiological processes and evolution. Two samples collected from coastal Maine in July and September 2009 were enriched for Synechococcus cells using flow cytometry and examined through metagenomic sequencing. Homology-based sequence prediction indicated cyanophages, largely myoviruses, accounted for almost half the reads and provided insights into environmental infection events. T4-phage core-gene phylogenetic reconstruction revealed unique diversity among uncultured cyanophages and reference isolates resulting in identification of a new phylogenetic cluster. Genomic comparison of reference cyanophage strains S-SM2 and Syn1 with putative homologous contigs recovered from metagenomes provided evidence that gene insertion, deletion and recombination have occurred among, and are likely important for diversification of, natural populations. Identification of putative genetic exchange between cyanophage and non-cyanophage viruses, i.e. Micromonas virus and Pelagibacter phage, supports hypotheses related to a significant role for viruses in mediating transfer of genetic material between taxonomically diverse organisms with overlapping ecological niches.}, }
@article {pmid25754577, year = {2015}, author = {Chang, TC and Stergiopoulos, I}, title = {Inter- and intra-domain horizontal gene transfer, gain-loss asymmetry and positive selection mark the evolutionary history of the CBM14 family.}, journal = {The FEBS journal}, volume = {282}, number = {10}, pages = {2014-2028}, doi = {10.1111/febs.13256}, pmid = {25754577}, issn = {1742-4658}, mesh = {Chitin/metabolism ; Chitin Synthase/genetics/*metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; }, abstract = {Protein-carbohydrate interactions are ubiquitous in nature and at the core of many physiological processes of profound importance to health and disease. Specificity in protein-carbohydrate interactions is conferred by carbohydrate-binding modules (CBMs) that can accurately discriminate among the multitude of saccharides found in nature, thus targeting proteins to their particular substrates. Family 14 carbohydrate-binding modules (CBM14s), more specifically, are short modules that bind explicitly to chitin, the second most abundant carbohydrate in nature. Although considerable effort has been placed in elucidating protein-carbohydrate interactions at the molecular level for biological and biotechnological applications, in contrast the evolutionary relationships among these modules are minimally understood. Using the CBM14 family as an example, here we describe one of the first global molecular evolutionary analyses of a CBM family across all domains of life, with an emphasis on its origin, taxonomic distribution and pattern of diversification as a result of gene and module duplication, and positive selection. Our genome-wide searches recovered an impressive number of CBM14s from diverse lineages across nearly all domains of life. However, their highly disseminated distribution in taxa outside the Opisthokonta group strongly suggests a later evolutionary origin and elevated rates of inter- and intra-domain horizontal gene transfer. Moreover, accelerated rates of asymmetric gains and losses reveal a dynamic mode of birth-and-death evolution, whereas positive selection acting on paralogous CBM14-containing proteins suggest changes in substrate specificity and an increase in the functional promiscuity of this ancient CBM family. The importance of these results is discussed.}, }
@article {pmid25752202, year = {2015}, author = {Giakkoupi, P and Tryfinopoulou, K and Polemis, M and Pappa, O and Miriagou, V and Vatopoulos, A}, title = {Circulation of a multiresistant, conjugative, IncA/C plasmid within the nosocomial Providencia stuartii population in the Athens area.}, journal = {Diagnostic microbiology and infectious disease}, volume = {82}, number = {1}, pages = {62-64}, doi = {10.1016/j.diagmicrobio.2015.02.009}, pmid = {25752202}, issn = {1879-0070}, mesh = {Cluster Analysis ; Conjugation, Genetic ; Cross Infection/epidemiology/*microbiology ; *Drug Resistance, Multiple, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Enterobacteriaceae Infections/epidemiology/*microbiology ; Gene Transfer, Horizontal ; Genotype ; Greece/epidemiology ; Hospitals ; Humans ; Molecular Epidemiology ; Molecular Typing ; Plasmids/*analysis/classification ; Polymerase Chain Reaction ; Providencia/classification/*drug effects/*genetics/isolation &amp; purification ; }, abstract = {The objective of the study is to report a multidrug-resistant outbreak of Providencia stuartii that occurred in inpatients in the Athens area in 2012 resulting from a very successful transmissible A/C multidrug-resistant plasmid. Thirteen multidrug-resistant P. stuartii clinical isolates from 5 hospitals were studied. Molecular typing was performed by pulsed-field gel electrophoresis. Antibiotic resistance genes and their genetic surround were detected by PCR and sequencing. Plasmid analysis included conjugation experiments using liquid cultures, sizing by S1 digestion, and incompatibility replicon typing by PCR. Isolates were grouped into 2 distinct clonal types A and B, exhibiting similarity less than 70%. Isolates of type A were recovered from patients hospitalized in 4 different hospitals with no obvious epidemiological linkage, while isolates of type B were recovered from patients treated in a single hospital. Both clonal types harbored a conjugative plasmid of 130 bp and IncA/C replicon type carrying 5 β-lactamase genes bla(SHV-5), bla(VEB-1), bla(VIM-1), bla(OXA-10), and bla(TEM-1) and aminoglycosides resistant determinants. All β-lactamase genes were included in stable structures as IS26, IS1999, and In-e541. The current plasmid seemed to have many common determinants with previously reported plasmids derived from P. stuartii and Proteus mirabilis clinical isolates and exhibited the ability to circulate in nosocomial bacterial populations.}, }
@article {pmid25750179, year = {2015}, author = {Marsit, S and Mena, A and Bigey, F and Sauvage, FX and Couloux, A and Guy, J and Legras, JL and Barrio, E and Dequin, S and Galeote, V}, title = {Evolutionary Advantage Conferred by an Eukaryote-to-Eukaryote Gene Transfer Event in Wine Yeasts.}, journal = {Molecular biology and evolution}, volume = {32}, number = {7}, pages = {1695-1707}, pmid = {25750179}, issn = {1537-1719}, mesh = {Amino Acids/metabolism ; Base Sequence ; *Biological Evolution ; Biomass ; Fermentation ; Gene Transfer, Horizontal/*genetics ; *Genes, Fungal ; Glutathione/metabolism ; Homologous Recombination/genetics ; Oligopeptides/metabolism ; Phenotype ; Saccharomyces cerevisiae/*genetics ; Vitis/metabolism ; Wine/*microbiology ; }, abstract = {Although an increasing number of horizontal gene transfers have been reported in eukaryotes, experimental evidence for their adaptive value is lacking. Here, we report the recent transfer of a 158-kb genomic region between Torulaspora microellipsoides and Saccharomyces cerevisiae wine yeasts or closely related strains. This genomic region has undergone several rearrangements in S. cerevisiae strains, including gene loss and gene conversion between two tandemly duplicated FOT genes encoding oligopeptide transporters. We show that FOT genes confer a strong competitive advantage during grape must fermentation by increasing the number and diversity of oligopeptides that yeast can utilize as a source of nitrogen, thereby improving biomass formation, fermentation efficiency, and cell viability. Thus, the acquisition of FOT genes has favored yeast adaptation to the nitrogen-limited wine fermentation environment. This finding indicates that anthropic environments offer substantial ecological opportunity for evolutionary diversification through gene exchange between distant yeast species.}, }
@article {pmid25744779, year = {2015}, author = {Popoff, MR}, title = {From saprophytic to toxigenic clostridia, a complex evolution based on multiple diverse genetic transfers and/or rearrangements.}, journal = {Research in microbiology}, volume = {166}, number = {4}, pages = {221-224}, doi = {10.1016/j.resmic.2015.02.008}, pmid = {25744779}, issn = {1769-7123}, mesh = {*Adaptation, Biological ; Clostridium/*genetics/pathogenicity ; *Evolution, Molecular ; *Gene Rearrangement ; *Gene Transfer, Horizontal ; }, }
@article {pmid25738592, year = {2015}, author = {Löhr, IH and Hülter, N and Bernhoff, E and Johnsen, PJ and Sundsfjord, A and Naseer, U}, title = {Persistence of a pKPN3-like CTX-M-15-encoding IncFIIK plasmid in a Klebsiella pneumonia ST17 host during two years of intestinal colonization.}, journal = {PloS one}, volume = {10}, number = {3}, pages = {e0116516}, pmid = {25738592}, issn = {1932-6203}, mesh = {Child ; Gene Transfer, Horizontal ; Humans ; Intestines/microbiology ; Klebsiella Infections/*microbiology ; Klebsiella pneumoniae/enzymology/*genetics ; Molecular Sequence Data ; Molecular Typing ; Plasmids/*genetics ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: To characterize the CTX-M-15-encoding plasmid in a Klebsiella pneumoniae ST17 strain, responsible for an outbreak at a Norwegian neonatal intensive care unit and subsequent colonization of affected children for up to two years. To identify plasmid-mediated features relevant for the outbreak dynamics, and to investigate the plasmids capability of horizontal transfer, its segregational stability and plasmid-mediated fitness costs.<br><br>METHODS: Plasmid profiling was performed by S1-nuclease PFGE, PCR-based replicon typing and Southern blot-hybridization. The complete sequence of the CTX-M-15-encoding plasmid was obtained by 454 sequencing. Plasmid self-transferability was investigated by broth- and filter mating, segregational stability was explored by serial passage, and plasmid-conferred fitness costs were examined in pairwise head-to-head competitions and by growth rate comparisons.<br><br>RESULTS: CTX-M-15 was encoded by a ~180 kb IncFIIK plasmid in K. pneumoniae ST17. S1-nuclease PFGE profiles of the first and the last CTX-M-15-producing K. pneumoniae isolates, recovered from the four children colonized the longest, suggested that the plasmid was stably maintained during intestinal carriage of up to two years. The DNA sequence of the pKPN3-like plasmid, pKp848CTX, uncovered a Tn3-like antibiotic resistance region and multiple heavy metal- and thermoresistance determinants. Plasmid pKp848CTX could not be transferred to Escherichia coli in vitro and we found no evidence to support horizontal plasmid transfer in vivo. Segregational plasmid loss ranging from 0.83% to 17.5% was demonstrated in evolved populations in vitro, but only minor fitness costs were associated with plasmid-carriage.<br><br>CONCLUSIONS: Plasmid pKp848CTX encodes phenotypic traits, which may have had an impact on the fitness and survival of the K. pneumoniae ST17 strain in the outbreak setting. The antibiotic resistance plasmid pKp848CTX was stably maintained during two years of intestinal colonization, conferring negligible fitness cost to its host, and thus seem well adapted to its K. pneumoniae host.}, }
@article {pmid25733908, year = {2015}, author = {Dhillon, B and Feau, N and Aerts, AL and Beauseigle, S and Bernier, L and Copeland, A and Foster, A and Gill, N and Henrissat, B and Herath, P and LaButti, KM and Levasseur, A and Lindquist, EA and Majoor, E and Ohm, RA and Pangilinan, JL and Pribowo, A and Saddler, JN and Sakalidis, ML and de Vries, RP and Grigoriev, IV and Goodwin, SB and Tanguay, P and Hamelin, RC}, title = {Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {11}, pages = {3451-3456}, pmid = {25733908}, issn = {1091-6490}, mesh = {Adaptation, Physiological/*genetics ; Ascomycota/*genetics/*growth &amp; development/pathogenicity ; Base Sequence ; Colony Count, Microbial ; *Gene Dosage ; Gene Expression Regulation, Fungal ; *Gene Transfer, Horizontal ; Genetic Speciation ; Genome, Fungal/genetics ; Host-Pathogen Interactions/genetics ; Indole Alkaloids/metabolism ; Molecular Sequence Data ; Nitrogen/metabolism ; Phylogeny ; Populus/microbiology ; Proteolysis ; Synteny/genetics ; Time Factors ; Trees/*microbiology ; Wood/*microbiology ; }, abstract = {Some of the most damaging tree pathogens can attack woody stems, causing lesions (cankers) that may be lethal. To identify the genomic determinants of wood colonization leading to canker formation, we sequenced the genomes of the poplar canker pathogen, Mycosphaerella populorum, and the closely related poplar leaf pathogen, M. populicola. A secondary metabolite cluster unique to M. populorum is fully activated following induction by poplar wood and leaves. In addition, genes encoding hemicellulose-degrading enzymes, peptidases, and metabolite transporters were more abundant and were up-regulated in M. populorum growing on poplar wood-chip medium compared with M. populicola. The secondary gene cluster and several of the carbohydrate degradation genes have the signature of horizontal transfer from ascomycete fungi associated with wood decay and from prokaryotes. Acquisition and maintenance of the gene battery necessary for growth in woody tissues and gene dosage resulting in gene expression reconfiguration appear to be responsible for the adaptation of M. populorum to infect, colonize, and cause mortality on poplar woody stems.}, }
@article {pmid25733873, year = {2015}, author = {Ku, C and Nelson-Sathi, S and Roettger, M and Garg, S and Hazkani-Covo, E and Martin, WF}, title = {Endosymbiotic gene transfer from prokaryotic pangenomes: Inherited chimerism in eukaryotes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {33}, pages = {10139-10146}, pmid = {25733873}, issn = {1091-6490}, support = {232975/ERC_/European Research Council/International ; }, mesh = {Alleles ; Animals ; Chloroplasts/genetics ; Computational Biology ; Cyanobacteria/genetics ; DNA, Bacterial/genetics ; Escherichia coli/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome ; Genome, Bacterial ; Humans ; Mitochondria/genetics ; Phylogeny ; Plastids/genetics ; Recombination, Genetic ; Symbiosis/*genetics ; }, abstract = {Endosymbiotic theory in eukaryotic-cell evolution rests upon a foundation of three cornerstone partners--the plastid (a cyanobacterium), the mitochondrion (a proteobacterium), and its host (an archaeon)--and carries a corollary that, over time, the majority of genes once present in the organelle genomes were relinquished to the chromosomes of the host (endosymbiotic gene transfer). However, notwithstanding eukaryote-specific gene inventions, single-gene phylogenies have never traced eukaryotic genes to three single prokaryotic sources, an issue that hinges crucially upon factors influencing phylogenetic inference. In the age of genomes, single-gene trees, once used to test the predictions of endosymbiotic theory, now spawn new theories that stand to eventually replace endosymbiotic theory with descriptive, gene tree-based variants featuring supernumerary symbionts: prokaryotic partners distinct from the cornerstone trio and whose existence is inferred solely from single-gene trees. We reason that the endosymbiotic ancestors of mitochondria and chloroplasts brought into the eukaryotic--and plant and algal--lineage a genome-sized sample of genes from the proteobacterial and cyanobacterial pangenomes of their respective day and that, even if molecular phylogeny were artifact-free, sampling prokaryotic pangenomes through endosymbiotic gene transfer would lead to inherited chimerism. Recombination in prokaryotes (transduction, conjugation, transformation) differs from recombination in eukaryotes (sex). Prokaryotic recombination leads to pangenomes, and eukaryotic recombination leads to vertical inheritance. Viewed from the perspective of endosymbiotic theory, the critical transition at the eukaryote origin that allowed escape from Muller's ratchet--the origin of eukaryotic recombination, or sex--might have required surprisingly little evolutionary innovation.}, }
@article {pmid25728596, year = {2015}, author = {Turrini, A and Sbrana, C and Giovannetti, M}, title = {Belowground environmental effects of transgenic crops: a soil microbial perspective.}, journal = {Research in microbiology}, volume = {166}, number = {3}, pages = {121-131}, doi = {10.1016/j.resmic.2015.02.006}, pmid = {25728596}, issn = {1769-7123}, mesh = {Bacillus thuringiensis/genetics ; Crops, Agricultural/*genetics/*physiology ; Gene Transfer, Horizontal ; Genetic Pleiotropy ; Microbial Consortia/genetics/physiology ; Microbiota/genetics/physiology ; Plants, Genetically Modified/genetics/*physiology ; Rhizosphere ; *Soil Microbiology ; }, abstract = {Experimental studies investigated the effects of transgenic crops on the structure, function and diversity of soil and rhizosphere microbial communities playing key roles in belowground environments. Here we review available data on direct, indirect and pleiotropic effects of engineered plants on soil microbiota, considering both the technology and the genetic construct utilized. Plants modified to express phytopathogen/phytoparasite resistance, or traits beneficial to food industries and consumers, differentially affected soil microorganisms depending on transformation events, experimental conditions and taxa analyzed. Future studies should address the development of harmonized methodologies by taking into account the complex interactions governing soil life.}, }
@article {pmid25726971, year = {2015}, author = {Asnani, M and Kumar, P and Hellen, CU}, title = {Widespread distribution and structural diversity of Type IV IRESs in members of Picornaviridae.}, journal = {Virology}, volume = {478}, number = {}, pages = {61-74}, pmid = {25726971}, issn = {1096-0341}, support = {R01 AI051340/AI/NIAID NIH HHS/United States ; R56 AI051340/AI/NIAID NIH HHS/United States ; AI-51340/AI/NIAID NIH HHS/United States ; }, mesh = {Conserved Sequence ; Evolution, Molecular ; Gene Transfer, Horizontal ; Nucleic Acid Conformation ; Picornaviridae/*genetics ; *Protein Biosynthesis ; RNA, Messenger/*genetics/metabolism ; RNA, Viral/*genetics/metabolism ; Recombination, Genetic ; Ribosomes/*metabolism ; }, abstract = {Picornavirus genomes contain internal ribosomal entry sites (IRESs) that promote end-independent translation initiation. Five structural classes of picornavirus IRES have been identified, but numerous IRESs remain unclassified. Here, previously unrecognized Type IV IRESs were identified in members of three proposed picornavirus genera (Limnipivirus, Pasivirus, Rafivirus) and four recognized genera (Kobuvirus, Megrivirus, Sapelovirus, Parechovirus). These IRESs are ~230-420 nucleotides long, reflecting heterogeneity outside a common structural core. Closer analysis yielded insights into evolutionary processes that have shaped contemporary IRESs. The presence of related IRESs in diverse genera supports the hypothesis that they are heritable genetic elements that spread by horizontal gene transfer. Recombination likely also accounts for the exchange of some peripheral subdomains, suggesting that IRES evolution involves incremental addition of elements to a pre-existing core. Nucleotide conservation is concentrated in ribosome-binding sites, and at the junction of helical domains, likely to ensure orientation of subdomains in an active conformation.}, }
@article {pmid25721219, year = {2015}, author = {Kaur, G and Subramanian, S}, title = {The insertion domain 1 of class IIA dimeric glycyl-tRNA synthetase is a rubredoxin-like zinc ribbon.}, journal = {Journal of structural biology}, volume = {190}, number = {1}, pages = {38-46}, doi = {10.1016/j.jsb.2015.02.004}, pmid = {25721219}, issn = {1095-8657}, mesh = {Amino Acid Sequence ; Conserved Sequence ; Evolution, Molecular ; Glycine-tRNA Ligase/*chemistry ; Humans ; Molecular Sequence Data ; Protein Structure, Tertiary ; }, abstract = {The insertion domain 1 (ID1) of class IIA dimeric glycyl-tRNA synthetase (α2GRS) is an appended domain in the core catalytic region of the enzyme. ID1 has been shown to play a role in tRNA aminoacylation, mediating interaction with the acceptor arm of tRNA and diadenosine tetraphosphate (Ap4A) synthesis. Mutations in α2GRS, including those in the ID1 region, have been implicated in distal hereditary motor neuropathy-V (dHMN-V) and Charcot-Marie-Tooth (CMT) disease. Through sequence and structure based evolutionary analysis, we show that ID1 of α2GRS is a rubredoxin-like zinc ribbon domain. The zinc-chelating cysteines of ID1 are well conserved in all archaeal versions of the enzyme and also in several eukaryotes, which most likely have acquired them via horizontal gene transfer from bacteria; but in all other eukaryotes, the zinc-chelating residues are not preserved. ID1 from bacteria display a selective preservation of zinc-binding residues, ranging from complete conservation to complete loss. The ID1 from different organisms harbor variable-sized non-conserved insertions between the two zinc-binding half-sites of the zinc ribbon. Three of the previously identified CMT-associated mutations in α2GRS, viz., human D146N, mouse C157R and human S211F, are located in the zinc ribbon region of ID1. Interestingly, human Asp146 which is implicated in the synthesis of Ap4A, a molecule known to act during neuronal transmission, has also been reported to be mutated in dHMN-V, suggesting a possible link between hereditary motor neuropathy and Ap4A synthesis.}, }
@article {pmid25713786, year = {2015}, author = {Stevens, RH}, title = {Transduction-mediated horizontal gene transfer in the oral microbiome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {5}, number = {}, pages = {12}, pmid = {25713786}, issn = {2235-2988}, mesh = {Bacteria/*genetics/isolation &amp; purification ; *Gene Transfer, Horizontal ; Humans ; *Microbiota ; Mouth/*microbiology ; *Transduction, Genetic ; }, }
@article {pmid25712422, year = {2015}, author = {Krypotou, E and Evangelidis, T and Bobonis, J and Pittis, AA and Gabaldón, T and Scazzocchio, C and Mikros, E and Diallinas, G}, title = {Origin, diversification and substrate specificity in the family of NCS1/FUR transporters.}, journal = {Molecular microbiology}, volume = {96}, number = {5}, pages = {927-950}, doi = {10.1111/mmi.12982}, pmid = {25712422}, issn = {1365-2958}, mesh = {Amino Acid Sequence ; Aspergillus nidulans/*genetics/metabolism ; Binding Sites/genetics ; Fungal Proteins/chemistry/*genetics/*metabolism ; Gene Duplication ; Gene Transfer, Horizontal ; Membrane Transport Proteins/chemistry/classification/*genetics/*metabolism ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Mutation ; Phylogeny ; Protein Conformation ; Protein Structure, Tertiary ; Pseudogenes ; Sequence Homology, Amino Acid ; Substrate Specificity ; Symporters/genetics ; }, abstract = {NCS1 proteins are H(+)/Na(+) symporters specific for the uptake of purines, pyrimidines and related metabolites. In this article, we study the origin, diversification and substrate specificity of fungal NCS1 transporters. We show that the two fungal NCS1 sub-families, Fur and Fcy, and plant homologues originate through independent horizontal transfers from prokaryotes and that expansion by gene duplication led to the functional diversification of fungal NCS1. We characterised all Fur proteins of the model fungus Aspergillus nidulans and discovered novel functions and specificities. Homology modelling, substrate docking, molecular dynamics and systematic mutational analysis in three Fur transporters with distinct specificities identified residues critical for function and specificity, located within a major substrate binding site, in transmembrane segments TMS1, TMS3, TMS6 and TMS8. Most importantly, we predict and confirm that residues determining substrate specificity are located not only in the major substrate binding site, but also in a putative outward-facing selective gate. Our evolutionary and structure-function analysis contributes in the understanding of the molecular mechanisms underlying the functional diversification of eukaryotic NCS1 transporters, and in particular, forward the concept that selective channel-like gates might contribute to substrate specificity.}, }
@article {pmid25711245, year = {2015}, author = {Yant, L}, title = {When two is a crowd: mitochondrial genome merger and its aftermath.}, journal = {The New phytologist}, volume = {206}, number = {1}, pages = {8-9}, doi = {10.1111/nph.13321}, pmid = {25711245}, issn = {1469-8137}, mesh = {Genome, Mitochondrial/*genetics ; Genome, Plant/*genetics ; *Homologous Recombination ; Magnoliopsida/*genetics ; Solanaceae/*genetics ; }, }
@article {pmid25710183, year = {2015}, author = {Gophna, U and Kristensen, DM and Wolf, YI and Popa, O and Drevet, C and Koonin, EV}, title = {No evidence of inhibition of horizontal gene transfer by CRISPR-Cas on evolutionary timescales.}, journal = {The ISME journal}, volume = {9}, number = {9}, pages = {2021-2027}, pmid = {25710183}, issn = {1751-7370}, support = {281357/ERC_/European Research Council/International ; /ImNIH/Intramural NIH HHS/United States ; }, mesh = {Adaptive Immunity ; Archaea/genetics ; Bacteria/*genetics ; Biological Evolution ; *CRISPR-Cas Systems ; *Clustered Regularly Interspaced Short Palindromic Repeats ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Models, Genetic ; Temperature ; Viruses/genetics ; }, abstract = {The CRISPR (clustered, regularly, interspaced, short, palindromic repeats)-Cas (CRISPR-associated genes) systems of archaea and bacteria provide adaptive immunity against viruses and other selfish elements and are believed to curtail horizontal gene transfer (HGT). Limiting acquisition of new genetic material could be one of the sources of the fitness cost of CRISPR-Cas maintenance and one of the causes of the patchy distribution of CRISPR-Cas among bacteria, and across environments. We sought to test the hypothesis that the activity of CRISPR-Cas in microbes is negatively correlated with the extent of recent HGT. Using three independent measures of HGT, we found no significant dependence between the length of CRISPR arrays, which reflects the activity of the immune system, and the estimated number of recent HGT events. In contrast, we observed a significant negative dependence between the estimated extent of HGT and growth temperature of microbes, which could be explained by the lower genetic diversity in hotter environments. We hypothesize that the relevant events in the evolution of resistance to mobile elements and proclivity for HGT, to which CRISPR-Cas systems seem to substantially contribute, occur on the population scale rather than on the timescale of species evolution.}, }
@article {pmid25709556, year = {2015}, author = {Gudhka, RK and Neilan, BA and Burns, BP}, title = {Adaptation, ecology, and evolution of the halophilic stromatolite archaeon Halococcus hamelinensis inferred through genome analyses.}, journal = {Archaea (Vancouver, B.C.)}, volume = {2015}, number = {}, pages = {241608}, pmid = {25709556}, issn = {1472-3654}, mesh = {*Adaptation, Biological ; Base Composition ; Cyanobacteria/growth &amp; development ; DNA, Archaeal/chemistry/genetics ; Ecosystem ; *Evolution, Molecular ; Genome, Archaeal ; Halococcus/*genetics/growth &amp; development/isolation &amp; purification ; Molecular Sequence Data ; Open Reading Frames ; Sequence Analysis, DNA ; }, abstract = {Halococcus hamelinensis was the first archaeon isolated from stromatolites. These geomicrobial ecosystems are thought to be some of the earliest known on Earth, yet, despite their evolutionary significance, the role of Archaea in these systems is still not well understood. Detailed here is the genome sequencing and analysis of an archaeon isolated from stromatolites. The genome of H. hamelinensis consisted of 3,133,046 base pairs with an average G+C content of 60.08% and contained 3,150 predicted coding sequences or ORFs, 2,196 (68.67%) of which were protein-coding genes with functional assignments and 954 (29.83%) of which were of unknown function. Codon usage of the H. hamelinensis genome was consistent with a highly acidic proteome, a major adaptive mechanism towards high salinity. Amino acid transport and metabolism, inorganic ion transport and metabolism, energy production and conversion, ribosomal structure, and unknown function COG genes were overrepresented. The genome of H. hamelinensis also revealed characteristics reflecting its survival in its extreme environment, including putative genes/pathways involved in osmoprotection, oxidative stress response, and UV damage repair. Finally, genome analyses indicated the presence of putative transposases as well as positive matches of genes of H. hamelinensis against various genomes of Bacteria, Archaea, and viruses, suggesting the potential for horizontal gene transfer.}, }
@article {pmid25708825, year = {2015}, author = {Reva, O and Korotetskiy, I and Ilin, A}, title = {Role of the horizontal gene exchange in evolution of pathogenic Mycobacteria.}, journal = {BMC evolutionary biology}, volume = {15 Suppl 1}, number = {Suppl 1}, pages = {S2}, pmid = {25708825}, issn = {1471-2148}, mesh = {Bacterial Proteins/*genetics ; Biological Evolution ; *Gene Transfer, Horizontal ; Genomic Islands ; Mycobacterium/*genetics ; Mycobacterium tuberculosis/genetics/pathogenicity ; Virulence/genetics ; Virulence Factors/*genetics ; }, abstract = {BACKGROUND: Mycobacterium tuberculosis is one of the most dangerous human pathogens, the causative agent of tuberculosis. While this pathogen is considered as extremely clonal and resistant to horizontal gene exchange, there are many facts supporting the hypothesis that on the early stages of evolution the development of pathogenicity of ancestral Mtb has started with a horizontal acquisition of virulence factors. Episodes of infections caused by non-tuberculosis Mycobacteria reported worldwide may suggest a potential for new pathogens to appear. If so, what is the role of horizontal gene transfer in this process?<br><br>RESULTS: Availing of accessibility of complete genomes sequences of multiple pathogenic, conditionally pathogenic and saprophytic Mycobacteria, a genome comparative study was performed to investigate the distribution of genomic islands among bacteria and identify ontological links between these mobile elements. It was shown that the ancient genomic islands from M. tuberculosis still may be rooted to the pool of mobile genetic vectors distributed among Mycobacteria. A frequent exchange of genes was observed between M. marinum and several saprophytic and conditionally pathogenic species. Among them M. avium was the most promiscuous species acquiring genetic materials from diverse origins.<br><br>CONCLUSIONS: Recent activation of genetic vectors circulating among Mycobacteria potentially may lead to emergence of new pathogens from environmental and conditionally pathogenic Mycobacteria. The species which require monitoring are M. marinum and M. avium as they eagerly acquire genes from different sources and may become donors of virulence gene cassettes to other micro-organisms.}, }
@article {pmid25706180, year = {2015}, author = {Pi, B and Yu, D and Dai, F and Song, X and Zhu, C and Li, H and Yu, Y}, title = {A genomics based discovery of secondary metabolite biosynthetic gene clusters in Aspergillus ustus.}, journal = {PloS one}, volume = {10}, number = {2}, pages = {e0116089}, pmid = {25706180}, issn = {1932-6203}, mesh = {Aspergillus/*genetics ; Biosynthetic Pathways/*genetics ; *Gene Transfer, Horizontal ; *Genes, Fungal ; Genome, Fungal ; Genomics ; Molecular Sequence Data ; *Multigene Family ; }, abstract = {Secondary metabolites (SMs) produced by Aspergillus have been extensively studied for their crucial roles in human health, medicine and industrial production. However, the resulting information is almost exclusively derived from a few model organisms, including A. nidulans and A. fumigatus, but little is known about rare pathogens. In this study, we performed a genomics based discovery of SM biosynthetic gene clusters in Aspergillus ustus, a rare human pathogen. A total of 52 gene clusters were identified in the draft genome of A. ustus 3.3904, such as the sterigmatocystin biosynthesis pathway that was commonly found in Aspergillus species. In addition, several SM biosynthetic gene clusters were firstly identified in Aspergillus that were possibly acquired by horizontal gene transfer, including the vrt cluster that is responsible for viridicatumtoxin production. Comparative genomics revealed that A. ustus shared the largest number of SM biosynthetic gene clusters with A. nidulans, but much fewer with other Aspergilli like A. niger and A. oryzae. These findings would help to understand the diversity and evolution of SM biosynthesis pathways in genus Aspergillus, and we hope they will also promote the development of fungal identification methodology in clinic.}, }
@article {pmid25705361, year = {2014}, author = {Dehghan-Noodeh, A and Nasir, A and Robson, GD}, title = {Effect of phosphatidylcholine on the level expression of plc genes of Aspergillus fumigatus by real time PCR method and investigation of these genes using bioinformatics analysis.}, journal = {Iranian journal of microbiology}, volume = {6}, number = {2}, pages = {104-111}, pmid = {25705361}, issn = {2008-3289}, abstract = {BACKGROUND AND OBJECTIVES: Phosphlipases are a group of enzymes that breakdown phosphatidylcholine (phospholipids) molecules producing second products. These produced products have a divers role in the cell like signal transduction and digestion in humans. In this research the effect of phosphatidylcholine on the expression of plc genes of A. fumigatus was studied. The plc genes of this fungus were also interrogated using bioinformatics studies.<br><br>MATERIALS AND METHODS: Real-time PCR was performed to study the expression of plc genes and these genes were interrogated using bioinformatics studies.<br><br>RESULTS: There was more significant expression for all three plc genes when A. fumigatus was grown on the presence of phosphatidylcholine in the medium. The sequence of plc genes of A. fumigatus was also interrogated using bioinformatics analysis and their relationship with the other microorganisms was investigated.<br><br>CONCLUSION: Real-time PCR revealed that afplc1, afplc2 and afplc3 were up-regulated in the presence of phosphatidylcholine. In this study we suggest either the plc's of A. fumigatus were present in an ancestral genome and have become lost in some lineages, or that they have been acquired from other organisms by horizontal gene transfer. We also found that plc's of this fungus appeared to be more closely related to the plant plc's than the bacterial plc's.}, }
@article {pmid25702524, year = {2015}, author = {Jeong, SH and Lee, KM and Lee, J and Bae, IK and Kim, JS and Kim, HS and Song, W}, title = {Clonal and horizontal spread of the blaOXA-232 gene among Enterobacteriaceae in a Korean hospital.}, journal = {Diagnostic microbiology and infectious disease}, volume = {82}, number = {1}, pages = {70-72}, doi = {10.1016/j.diagmicrobio.2015.02.001}, pmid = {25702524}, issn = {1879-0070}, mesh = {Adult ; Aged ; Aged, 80 and over ; Conjugation, Genetic ; Cross Infection/*microbiology ; Electrophoresis, Gel, Pulsed-Field ; Enterobacteriaceae Infections/epidemiology/*microbiology ; Escherichia coli/*enzymology/genetics/isolation &amp; purification ; Female ; Gene Transfer, Horizontal ; Genotype ; Hospitals ; Humans ; Klebsiella pneumoniae/classification/*enzymology/genetics/isolation &amp; purification ; Korea/epidemiology ; Male ; Middle Aged ; Molecular Epidemiology ; Molecular Typing ; Plasmids/*analysis ; beta-Lactamases/*genetics/metabolism ; }, abstract = {All 16 Klebsiella pneumoniae isolates and both Escherichia coli isolates harbored the bla(OXA-232) and bla(CTX-M-15) genes. Furthermore, all 16 K. pneumoniae isolates belonged to a unique pulsed-field gel electrophoresis clone and were assigned to an identical sequence type (ST14). The 2 E. coli isolates were identified as ST131 and ST457. The bla(OXA-232) gene underwent horizontal transfer to E. coli isolates via a conjugative ColE-type plasmid. The introduction of this K. pneumoniae ST14 strain to the Korean hospital was attributed to an index patient who was likely colonized during a prior hospitalization in India.}, }
@article {pmid25695687, year = {2015}, author = {Balcázar, JL}, title = {Effect of ciliates in transfer of plasmid-mediated quinolone-resistance genes in bacteria.}, journal = {Emerging infectious diseases}, volume = {21}, number = {3}, pages = {547-549}, pmid = {25695687}, issn = {1080-6059}, mesh = {Bacteria/*drug effects/*genetics ; Drug Resistance, Bacterial/*genetics ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Plasmids/*genetics ; Quinolones/*pharmacology ; Tetrahymena thermophila/*physiology ; }, }
@article {pmid25691597, year = {2015}, author = {Ferreira, RM and de Oliveira, AC and Moreira, LM and Belasque, J and Gourbeyre, E and Siguier, P and Ferro, MI and Ferro, JA and Chandler, M and Varani, AM}, title = {A TALE of transposition: Tn3-like transposons play a major role in the spread of pathogenicity determinants of Xanthomonas citri and other xanthomonads.}, journal = {mBio}, volume = {6}, number = {1}, pages = {e02505-14}, pmid = {25691597}, issn = {2150-7511}, mesh = {Citrus/metabolism ; *DNA Transposable Elements ; *Gene Transfer, Horizontal ; Plasmids ; Protein Transport ; Type III Secretion Systems/metabolism ; Virulence Factors/*genetics/metabolism ; Xanthomonas/*genetics/pathogenicity ; }, abstract = {UNLABELLED: Members of the genus Xanthomonas are among the most important phytopathogens. A key feature of Xanthomonas pathogenesis is the translocation of type III secretion system (T3SS) effector proteins (T3SEs) into the plant target cells via a T3SS. Several T3SEs and a murein lytic transglycosylase gene (mlt, required for citrus canker symptoms) are found associated with three transposition-related genes in Xanthomonas citri plasmid pXAC64. These are flanked by short inverted repeats (IRs). The region was identified as a transposon, TnXax1, with typical Tn3 family features, including a transposase and two recombination genes. Two 14-bp palindromic sequences within a 193-bp potential resolution site occur between the recombination genes. Additional derivatives carrying different T3SEs and other passenger genes occur in different Xanthomonas species. The T3SEs include transcription activator-like effectors (TALEs). Certain TALEs are flanked by the same IRs as found in TnXax1 to form mobile insertion cassettes (MICs), suggesting that they may be transmitted horizontally. A significant number of MICs carrying other passenger genes (including a number of TALE genes) were also identified, flanked by the same TnXax1 IRs and delimited by 5-bp target site duplications. We conclude that a large fraction of T3SEs, including individual TALEs and potential pathogenicity determinants, have spread by transposition and that TnXax1, which exhibits all of the essential characteristics of a functional transposon, may be involved in driving MIC transposition. We also propose that TALE genes may diversify by fork slippage during the replicative Tn3 family transposition. These mechanisms may play a crucial role in the emergence of Xanthomonas pathogenicity.<br><br>IMPORTANCE: Xanthomonas genomes carry many insertion sequences (IS) and transposons, which play an important role in their evolution and architecture. This study reveals a key relationship between transposons and pathogenicity determinants in Xanthomonas. We propose that several transposition events mediated by a Tn3-like element carrying different sets of passenger genes, such as different type III secretion system effectors (including transcription activation-like effectors [TALEs]), were determinant in the evolution and emergence of Xanthomonas pathogenicity. TALE genes are DNA-binding effectors that modulate plant transcription. We also present a model for generating TALE gene diversity based on fork slippage associated with the replicative transposition mechanism of Tn3-like transposons. This may provide a mechanism for niche adaptation, specialization, host-switching, and other lifestyle changes. These results will also certainly lead to novel insights into the evolution and emergence of the various diseases caused by different Xanthomonas species and pathovars.}, }
@article {pmid25689519, year = {2015}, author = {Zhang, H and Feng, J and Manolii, VP and Strelkov, SE and Hwang, SF}, title = {Characterization of a Gene Identified in Pathotype 5 of the Clubroot Pathogen Plasmodiophora brassicae.}, journal = {Phytopathology}, volume = {105}, number = {6}, pages = {764-770}, doi = {10.1094/PHYTO-10-14-0270-R}, pmid = {25689519}, issn = {0031-949X}, mesh = {Brassica napus/*parasitology ; Chromosome Mapping ; DNA Primers/genetics ; Disease Resistance ; Gene Transfer, Horizontal ; Plant Diseases/*parasitology ; Plant Roots/parasitology ; Plasmodiophorida/*genetics/pathogenicity ; Protozoan Proteins/*genetics ; Up-Regulation ; Virulence ; }, abstract = {Clubroot caused by Plasmodiophora brassicae is an important disease of crucifers worldwide. Isolates of the pathogen can be classified into pathotypes according to their pathogenicity on differential hosts. In this study, the presence or absence of all database-available nonhousekeeping P. brassicae genes (118 in total) were assessed by polymerase chain reaction (PCR) analysis in isolates belonging to five P. brassicae pathotypes (2, 3, 5, 6, and 8 according to Williams' differential set). One gene, designated Cr811, was present exclusively in the isolate of pathotype 5. This was further confirmed by dot blot hybridization and by PCR using alternative DNA preparations and primers. Reverse transcription quantitative PCR analysis indicated that in planta expression of Cr811 was up-regulated during canola infection, especially in the stage of secondary plasmodia. Primers specific to Cr811 could distinguish a field isolate of P. brassicae belonging to pathotype 5 from two other field isolates representing pathotypes 3 and 8. These findings suggest that Cr811 is a gene that is potentially involved in clubroot pathogenesis and that it also might serve as a molecular marker for differentiation of pathotype 5 from other pathotypes.}, }
@article {pmid25688108, year = {2015}, author = {Degli Esposti, M and Rosas-Pérez, T and Servín-Garcidueñas, LE and Bolaños, LM and Rosenblueth, M and Martínez-Romero, E}, title = {Molecular evolution of cytochrome bd oxidases across proteobacterial genomes.}, journal = {Genome biology and evolution}, volume = {7}, number = {3}, pages = {801-820}, pmid = {25688108}, issn = {1759-6653}, mesh = {Bacterial Proteins/classification/*genetics ; Cytochromes/classification/*genetics ; Electron Transport Complex IV ; *Evolution, Molecular ; Gammaproteobacteria/genetics ; Gene Transfer, Horizontal ; Genome, Bacterial ; Multigene Family ; Oxidoreductases/classification/*genetics ; Phylogeny ; Proteobacteria/classification/*genetics ; }, abstract = {This work is aimed to resolve the complex molecular evolution of cytochrome bd ubiquinol oxidase, a nearly ubiquitous bacterial enzyme that is involved in redox balance and bioenergetics. Previous studies have created an unclear picture of bd oxidases phylogenesis without considering the existence of diverse types of bd oxidases. Integrated approaches of genomic and protein analysis focused on proteobacteria have generated a molecular classification of diverse types of bd oxidases, which produces a new scenario for interpreting their evolution. A duplication of the original gene cluster of bd oxidase might have occurred in the ancestors of extant α-proteobacteria of the Rhodospirillales order, such as Acidocella, from which the bd-I type of the oxidase might have diffused to other proteobacterial lineages. In contrast, the Cyanide-Insensitive Oxidase type may have differentiated into recognizable subtypes after another gene cluster duplication. These subtypes are widespread in the genomes of α-, β-, and γ-proteobacteria, with occasional instances of lateral gene transfer. In resolving the evolutionary pattern of proteobacterial bd oxidases, this work sheds new light on the basal taxa of α-proteobacteria from which the γ-proteobacterial lineage probably emerged.}, }
@article {pmid25688107, year = {2015}, author = {Pierella Karlusich, JJ and Ceccoli, RD and Graña, M and Romero, H and Carrillo, N}, title = {Environmental selection pressures related to iron utilization are involved in the loss of the flavodoxin gene from the plant genome.}, journal = {Genome biology and evolution}, volume = {7}, number = {3}, pages = {750-767}, pmid = {25688107}, issn = {1759-6653}, mesh = {Cyanobacteria/genetics ; Environment ; *Evolution, Molecular ; Flavodoxin/classification/*genetics ; Genes, Plant ; *Genome, Plant ; Iron/metabolism ; Photosystem II Protein Complex/genetics ; Phototrophic Processes/genetics ; Phylogeny ; }, abstract = {Oxidative stress and iron limitation represent the grim side of life in an oxygen-rich atmosphere. The versatile electron transfer shuttle ferredoxin, an iron-sulfur protein, is particularly sensitive to these hardships, and its downregulation under adverse conditions severely compromises survival of phototrophs. Replacement of ferredoxin by a stress-resistant isofunctional carrier, flavin-containing flavodoxin, is a widespread strategy employed by photosynthetic microorganisms to overcome environmental adversities. The flavodoxin gene was lost in the course of plant evolution, but its reintroduction in transgenic plants confers increased tolerance to environmental stress and iron starvation, raising the question as to why a genetic asset with obvious adaptive value was not kept by natural selection. Phylogenetic analyses reveal that the evolutionary history of flavodoxin is intricate, with several horizontal gene transfer events between distant organisms, including Eukarya, Bacteria, and Archaea. The flavodoxin gene is unevenly distributed in most algal lineages, with flavodoxin-containing species being overrepresented in iron-limited regions and scarce or absent in iron-rich environments. Evaluation of cyanobacterial genomic and metagenomic data yielded essentially the same results, indicating that there was little selection pressure to retain flavodoxin in iron-rich coastal/freshwater phototrophs. Our results show a highly dynamic evolution pattern of flavodoxin tightly connected to the bioavailability of iron. Evidence presented here also indicates that the high concentration of iron in coastal and freshwater habitats may have facilitated the loss of flavodoxin in the freshwater ancestor of modern plants during the transition of photosynthetic organisms from the open oceans to the firm land.}, }
@article {pmid25682011, year = {2015}, author = {Thynne, E and McDonald, MC and Solomon, PS}, title = {Phytopathogen emergence in the genomics era.}, journal = {Trends in plant science}, volume = {20}, number = {4}, pages = {246-255}, doi = {10.1016/j.tplants.2015.01.009}, pmid = {25682011}, issn = {1878-4372}, mesh = {*Bacterial Physiological Phenomena/genetics ; Fungi/genetics/*physiology ; Gene Transfer, Horizontal ; Genome, Microbial ; Host Specificity ; *Host-Pathogen Interactions ; Plant Diseases/genetics/*microbiology/virology ; *Virus Physiological Phenomena/genetics ; }, abstract = {Phytopathogens are a global threat to plant agriculture and biodiversity. The genomics era has lead to an exponential rise in comparative gene and genome studies of both economically significant and insignificant microorganisms. In this review we highlight some recent comparisons and discuss how they identify shared genes or genomic regions associated with host virulence. The two major mechanisms of rapid genome adaptation - horizontal gene transfer and hybridisation - are reviewed and we consider how intra-specific pan-genome sequences encode alternative host specificity. We also discuss the power that access to expansive gene databases provides in aiding the study of phytopathogen emergence. These databases can rapidly enable the identification of an unknown pathogen and its origin, as well as genomic adaptations required for emergence.}, }
@article {pmid25681241, year = {2015}, author = {Lemire, BD}, title = {Evolution of FOXRED1, an FAD-dependent oxidoreductase necessary for NADH:ubiquinone oxidoreductase (Complex I) assembly.}, journal = {Biochimica et biophysica acta}, volume = {1847}, number = {4-5}, pages = {451-457}, doi = {10.1016/j.bbabio.2015.01.014}, pmid = {25681241}, issn = {0006-3002}, mesh = {*Biological Evolution ; Electron Transport ; Electron Transport Complex I/*metabolism ; Humans ; Molecular Chaperones/chemistry/genetics/*metabolism ; NADH, NADPH Oxidoreductases/*metabolism ; *Phylogeny ; }, abstract = {Complex I (NADH:ubiquinone oxidoreductase) is the major entry point for electrons into the respiratory chains of bacteria and mitochondria. Mammalian complex I is composed of 45 subunits and harbors FMN and iron-sulfur cluster cofactors. A heterogeneous disease profile is associated with complex I deficiency. In a large fraction of complex I deficiencies, the primary defect is not in any of the genes encoding a subunit. The proper assembly and function of complex I require the participation of at least 12 assembly factors or chaperones. FOXRED1 encodes a complex I-specific assembly factor and mutations in this gene result in complex I deficiency, infantile onset encephalomyopathy and Leigh syndrome. The human FOXRED1 protein is a mitochondria-targeted 486-amino acid FAD-dependent oxidoreductase. It is most closely related to N-methyl amino acid dehydrogenases. FOXRED1 orthologs are present in archaea, bacteria and eukaryotes. Fungal FOXRED1 orthologs were likely acquired from alphaproteobacteria by horizontal gene transfer. The phylogenetic profile of FOXRED1 orthologs does not parallel the phylogenetic profile of complex I, strongly suggesting that, at least in some organisms, FOXRED1 has a function unrelated to complex I. The only large clade where all members investigated contain both FOXRED1 and complex I is the metazoans. Some bacterial FOXRED1 genes are present in metabolic operons related to amino acid metabolism. FOXRED1 phylogenetic distribution and gene organization suggest a metabolic role for FOXRED1 in complex I biogenesis should be considered.}, }
@article {pmid25673284, year = {2015}, author = {Hellberg Lindqvist, M and Nilsson, T and Sundin, P and Rova, M}, title = {Chlorate reductase is cotranscribed with cytochrome c and other downstream genes in the gene cluster for chlorate respiration of Ideonella dechloratans.}, journal = {FEMS microbiology letters}, volume = {362}, number = {6}, pages = {}, doi = {10.1093/femsle/fnv019}, pmid = {25673284}, issn = {1574-6968}, mesh = {Anaerobiosis ; Betaproteobacteria/enzymology/*genetics ; Chlorates/*metabolism ; Cytochromes c/*genetics/metabolism ; *Multigene Family ; Open Reading Frames ; Oxidoreductases/*genetics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Trans-Activators/genetics ; }, abstract = {The chlorate-respiring bacterium Ideonella dechloratans is a facultative anaerobe that can use both oxygen and chlorate as terminal electron acceptors. The genes for the enzymes chlorate reductase (clrABDC) and chlorite dismutase, necessary for chlorate metabolism and probably acquired by lateral gene transfer, are located in a gene cluster that also includes other genes potentially important for chlorate metabolism. Among those are a gene for cytochrome c (cyc) whose gene product may serve as an electron carrier during chlorate reduction, a cofactor biosynthesis gene (mobB) and a predicted transcriptional regulator (arsR). Only chlorate reductase and chlorite dismutase have been shown to be expressed in vivo. Here, we report the in vivo production of a single polycistronic transcript covering eight open reading frames including clrABDC, cyc, mobB and arsR. Transcription levels of the cyc and clrA genes were compared to each other by the use of qRT-PCR in RNA preparations from cells grown under aerobic or chlorate reducing anaerobic conditions. The two genes showed the same mRNA levels under both growth regimes, indicating that no transcription termination occurs between them. Higher transcription levels were observed at growth without external oxygen supply. Implications for electron pathway integration following lateral gene transfer are discussed.}, }
@article {pmid25673050, year = {2015}, author = {Evangelista, DE and de Paula, FF and Rodrigues, A and Henrique-Silva, F}, title = {Pectinases from Sphenophorus levis Vaurie, 1978 (Coleoptera: Curculionidae): putative accessory digestive enzymes.}, journal = {Journal of insect science (Online)}, volume = {15}, number = {1}, pages = {168}, pmid = {25673050}, issn = {1536-2442}, mesh = {Amino Acid Sequence ; Animals ; Bacteria ; Base Sequence ; Carboxylic Ester Hydrolases/*genetics ; Cell Wall/metabolism ; DNA, Complementary ; Fungi ; Gastrointestinal Tract/*enzymology ; Larva/enzymology/genetics ; Pecten/metabolism ; Phylogeny ; Polygalacturonase/*genetics ; RNA, Messenger ; Weevils/*enzymology/*genetics ; }, abstract = {The cell wall in plants offers protection against invading organisms and is mainly composed of the polysaccharides pectin, cellulose, and hemicellulose, which can be degraded by plant cell wall degrading enzymes (PCWDEs). Such enzymes are often synthesized by free living microorganisms or endosymbionts that live in the gut of some animals, including certain phytophagous insects. Thus, the ability of an insect to degrade the cell wall was once thought to be related to endosymbiont enzyme activity. However, recent studies have revealed that some phytophagous insects are able to synthesize their own PCWDEs by endogenous genes, although questions regarding the origin of these genes remain unclear. This study describes two pectinases from the sugarcane weevil, Sphenophorus levis Vaurie, 1978 (Sl-pectinases), which is considered one of the most serious agricultural pests in Brazil. Two cDNA sequences identified in a cDNA library of the insect larvae coding for a pectin methylesterase (PME) and an endo-polygalacturonase (endo-PG)-denominated Sl-PME and Sl-endoPG, respectively-were isolated and characterized. The quantitative real-time reverse transcriptase polymerase chain reaction expression profile for both Sl-pectinases showed mRNA production mainly in the insect feeding stages and exclusively in midgut tissue of the larvae. This analysis, together Western blotting data, suggests that Sl-pectinases have a digestive role. Phylogenetic analyses indicate that Sl-PME and Sl-endoPG sequences are closely related to bacteria and fungi, respectively. Moreover, the partial genomic sequences of the pectinases were amplified from insect fat body DNA, which was certified to be free of endosymbiotic DNA. The analysis of genomic sequences revealed the existence of two small introns with 53 and 166 bp in Sl-endoPG, which is similar to the common pattern in fungal introns. In contrast, no intron was identified in the Sl-PME genomic sequence, as generally observed in bacteria. These data support the theory of horizontal gene transfer proposed for the origin of insect pectinases, reinforcing the acquisition of PME genes from bacteria and endo-PG genes from fungi.}, }
@article {pmid25670735, year = {2015}, author = {Mai-Prochnow, A and Hui, JG and Kjelleberg, S and Rakonjac, J and McDougald, D and Rice, SA}, title = {'Big things in small packages: the genetics of filamentous phage and effects on fitness of their host'.}, journal = {FEMS microbiology reviews}, volume = {39}, number = {4}, pages = {465-487}, doi = {10.1093/femsre/fuu007}, pmid = {25670735}, issn = {1574-6976}, mesh = {Bacteria/pathogenicity/*virology ; Biofilms ; Genes, Viral/genetics ; Host-Pathogen Interactions/*genetics ; Humans ; Inovirus/*genetics ; Microbial Viability ; Phenotype ; }, abstract = {This review synthesizes recent and past observations on filamentous phages and describes how these phages contribute to host phentoypes. For example, the CTXφ phage of Vibrio cholerae encodes the cholera toxin genes, responsible for causing the epidemic disease, cholera. The CTXφ phage can transduce non-toxigenic strains, converting them into toxigenic strains, contributing to the emergence of new pathogenic strains. Other effects of filamentous phage include horizontal gene transfer, biofilm development, motility, metal resistance and the formation of host morphotypic variants, important for the biofilm stress resistance. These phages infect a wide range of Gram-negative bacteria, including deep-sea, pressure-adapted bacteria. Many filamentous phages integrate into the host genome as prophage. In some cases, filamentous phages encode their own integrase genes to facilitate this process, while others rely on host-encoded genes. These differences are mediated by different sets of 'core' and 'accessory' genes, with the latter group accounting for some of the mechanisms that alter the host behaviours in unique ways. It is increasingly clear that despite their relatively small genomes, these phages exert signficant influence on their hosts and ultimately alter the fitness and other behaviours of their hosts.}, }
@article {pmid25663439, year = {2015}, author = {Elmore, MH and McGary, KL and Wisecaver, JH and Slot, JC and Geiser, DM and Sink, S and O'Donnell, K and Rokas, A}, title = {Clustering of two genes putatively involved in cyanate detoxification evolved recently and independently in multiple fungal lineages.}, journal = {Genome biology and evolution}, volume = {7}, number = {3}, pages = {789-800}, pmid = {25663439}, issn = {1759-6653}, mesh = {Ascomycota/genetics ; Carbon-Nitrogen Lyases/*genetics ; Carbonic Anhydrases/*genetics ; Cyanates/metabolism ; *Evolution, Molecular ; Fusarium/classification/*genetics ; Gene Duplication ; Gene Transfer, Horizontal ; *Genes, Fungal ; Multigene Family ; Phylogeny ; }, abstract = {Fungi that have the enzymes cyanase and carbonic anhydrase show a limited capacity to detoxify cyanate, a fungicide employed by both plants and humans. Here, we describe a novel two-gene cluster that comprises duplicated cyanase and carbonic anhydrase copies, which we name the CCA gene cluster, trace its evolution across Ascomycetes, and examine the evolutionary dynamics of its spread among lineages of the Fusarium oxysporum species complex (hereafter referred to as the FOSC), a cosmopolitan clade of purportedly clonal vascular wilt plant pathogens. Phylogenetic analysis of fungal cyanase and carbonic anhydrase genes reveals that the CCA gene cluster arose independently at least twice and is now present in three lineages, namely Cochliobolus lunatus, Oidiodendron maius, and the FOSC. Genome-wide surveys within the FOSC indicate that the CCA gene cluster varies in copy number across isolates, is always located on accessory chromosomes, and is absent in FOSC's closest relatives. Phylogenetic reconstruction of the CCA gene cluster in 163 FOSC strains from a wide variety of hosts suggests a recent history of rampant transfers between isolates. We hypothesize that the independent formation of the CCA gene cluster in different fungal lineages and its spread across FOSC strains may be associated with resistance to plant-produced cyanates or to use of cyanate fungicides in agriculture.}, }
@article {pmid25660375, year = {2015}, author = {Petitjean, C and Deschamps, P and López-García, P and Moreira, D and Brochier-Armanet, C}, title = {Extending the conserved phylogenetic core of archaea disentangles the evolution of the third domain of life.}, journal = {Molecular biology and evolution}, volume = {32}, number = {5}, pages = {1242-1254}, doi = {10.1093/molbev/msv015}, pmid = {25660375}, issn = {1537-1719}, mesh = {Archaea/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Archaeal ; *Phylogeny ; RNA, Ribosomal/*genetics ; Ribosomal Proteins/genetics ; Ribosome Subunits, Small/*genetics ; Ribosomes/genetics ; }, abstract = {Initial studies of the archaeal phylogeny relied mainly on the analysis of the RNA component of the small subunit of the ribosome (SSU rRNA). The resulting phylogenies have provided interesting but partial information on the evolutionary history of the third domain of life because SSU rRNA sequences do not contain enough phylogenetic signal to resolve all nodes of the archaeal tree. Thus, many relationships, and especially the most ancient ones, remained elusive. Moreover, SSU rRNA phylogenies can be heavily biased by tree reconstruction artifacts. The sequencing of complete genomes allows using a variety of protein markers as an alternative to SSU rRNA. Taking advantage of the recent burst of archaeal complete genome sequences, we have carried out an in-depth phylogenomic analysis of this domain. We have identified 200 new protein families that, in addition to the ribosomal proteins and the subunits of the RNA polymerase, form a conserved phylogenetic core of archaeal genes. The accurate analysis of these markers combined with desaturation approaches shed new light on the evolutionary history of Archaea and reveals that several relationships recovered in recent analyses are likely the consequence of tree reconstruction artifacts. Among others, we resolve a number of important relationships, such as those among methanogens Class I, and we propose the definition of two new superclasses within the Euryarchaeota: Methanomada and Diaforarchaea.}, }
@article {pmid25657641, year = {2014}, author = {Jørgensen, TS and Kiil, AS and Hansen, MA and Sørensen, SJ and Hansen, LH}, title = {Current strategies for mobilome research.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {750}, pmid = {25657641}, issn = {1664-302X}, abstract = {Mobile genetic elements (MGEs) are pivotal for bacterial evolution and adaptation, allowing shuffling of genes even between distantly related bacterial species. The study of these elements is biologically interesting as the mode of genetic propagation is kaleidoscopic and important, as MGEs are the main vehicles of the increasing bacterial antibiotic resistance that causes thousands of human deaths each year. The study of MGEs has previously focused on plasmids from individual isolates, but the revolution in sequencing technology has allowed the study of mobile genomic elements of entire communities using metagenomic approaches. The problem in using metagenomic sequencing for the study of MGEs is that plasmids and other mobile elements only comprise a small fraction of the total genetic content that are difficult to separate from chromosomal DNA based on sequence alone. The distinction between plasmid and chromosome is important as the mobility and regulation of genes largely depend on their genetic context. Several different approaches have been proposed that specifically enrich plasmid DNA from community samples. Here, we review recent approaches used to study entire plasmid pools from complex environments, and point out possible future developments for and pitfalls of these approaches. Further, we discuss the use of the PacBio long-read sequencing technology for MGE discovery.}, }
@article {pmid25657162, year = {2015}, author = {Hashem, YA and Yassin, AS and Amin, MA}, title = {Molecular characterization of Enterococcus spp. clinical isolates from Cairo, Egypt.}, journal = {Indian journal of medical microbiology}, volume = {33 Suppl}, number = {}, pages = {80-86}, doi = {10.4103/0255-0857.148836}, pmid = {25657162}, issn = {1998-3646}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; Egypt/epidemiology ; Enterococcus/*classification/drug effects/*genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; Genes, Bacterial ; Gram-Positive Bacterial Infections/epidemiology/*microbiology ; Humans ; Microbial Sensitivity Tests ; Urinary Tract Infections/epidemiology/microbiology ; Virulence/genetics ; Virulence Factors/genetics ; }, abstract = {PURPOSE: Enterococci are responsible for serious diseases such as bacteraemia, endocarditis and urinary tract infections. The ability of enterococci to cause such diseases is due to acquisition of certain virulence factors such as haemolysin, gelatinase and enterococcus surface protein. This study has been conducted to investigate the occurrence of virulence factors and resistance to various antibiotics with emphasis on vancomycin in the Enterococcus spp.<br><br>MATERIALS AND METHODS: Clinical specimens were collected and isolates were identified by proper microscopic, culture and biochemical tests. Susceptibility and degree of resistance of the isolates to various antibiotics were determined. Virulence factors were examined by phenotypic tests followed by molecular methods. Bioinformatics analysis was used to detect regions in the genomes that might have originated from horizontal gene transfer.<br><br>RESULT: The presence or absence of virulence genes did not affect the pattern of antimicrobial resistance in Enterococcus isolates; consequently, no relationship was found between virulence factors and resistance to different antibiotics used. Bioinformatics analysis showed that the virulence genes were mainly transferred by transposons.<br><br>CONCLUSION: Among the enterococci, environmental factors may interfere in the expression of virulence factors. Horizontal gene transfer plays an important role in the spread of resistance and virulence genes.}, }
@article {pmid25654978, year = {2015}, author = {Suzuki, Y and Assad-Garcia, N and Kostylev, M and Noskov, VN and Wise, KS and Karas, BJ and Stam, J and Montague, MG and Hanly, TJ and Enriquez, NJ and Ramon, A and Goldgof, GM and Richter, RA and Vashee, S and Chuang, RY and Winzeler, EA and Hutchison, CA and Gibson, DG and Smith, HO and Glass, JI and Venter, JC}, title = {Bacterial genome reduction using the progressive clustering of deletions via yeast sexual cycling.}, journal = {Genome research}, volume = {25}, number = {3}, pages = {435-444}, pmid = {25654978}, issn = {1549-5469}, support = {T32 GM007198/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; DNA Transposable Elements ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; *Multigene Family ; *Sequence Deletion ; Yeasts/*genetics ; }, abstract = {The availability of genetically tractable organisms with simple genomes is critical for the rapid, systems-level understanding of basic biological processes. Mycoplasma bacteria, with the smallest known genomes among free-living cellular organisms, are ideal models for this purpose, but the natural versions of these cells have genome complexities still too great to offer a comprehensive view of a fundamental life form. Here we describe an efficient method for reducing genomes from these organisms by identifying individually deletable regions using transposon mutagenesis and progressively clustering deleted genomic segments using meiotic recombination between the bacterial genomes harbored in yeast. Mycoplasmal genomes subjected to this process and transplanted into recipient cells yielded two mycoplasma strains. The first simultaneously lacked eight singly deletable regions of the genome, representing a total of 91 genes and ∼ 10% of the original genome. The second strain lacked seven of the eight regions, representing 84 genes. Growth assay data revealed an absence of genetic interactions among the 91 genes under tested conditions. Despite predicted effects of the deletions on sugar metabolism and the proteome, growth rates were unaffected by the gene deletions in the seven-deletion strain. These results support the feasibility of using single-gene disruption data to design and construct viable genomes lacking multiple genes, paving the way toward genome minimization. The progressive clustering method is expected to be effective for the reorganization of any mega-sized DNA molecules cloned in yeast, facilitating the construction of designer genomes in microbes as well as genomic fragments for genetic engineering of higher eukaryotes.}, }
@article {pmid25653446, year = {2015}, author = {Schibler, M and Piuz, I and Hao, W and Tapparel, C}, title = {Chimeric rhinoviruses obtained via genetic engineering or artificially induced recombination are viable only if the polyprotein coding sequence derives from the same species.}, journal = {Journal of virology}, volume = {89}, number = {8}, pages = {4470-4480}, pmid = {25653446}, issn = {1098-5514}, mesh = {5' Untranslated Regions/genetics ; Base Sequence ; Chimera/*genetics ; Chromosome Mapping ; Fluorescent Antibody Technique ; Gene Products, env/*genetics ; Gene Transfer Techniques ; Gene Transfer, Horizontal/*genetics ; Genetic Engineering/*methods ; HeLa Cells ; Humans ; Molecular Sequence Data ; Reverse Transcriptase Polymerase Chain Reaction ; Rhinovirus/*genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {UNLABELLED: Recombination is a widespread phenomenon that ensures both the stability and variation of RNA viruses. This phenomenon occurs with different frequencies within species of the Enterovirus genus. Intraspecies recombination is described frequently among non-rhinovirus enteroviruses but appears to be sporadic in rhinoviruses. Interspecies recombination is even rarer for rhinoviruses and mostly is related to ancient events which contributed to the speciation of these viruses. We reported that artificially engineered 5' untranslated region (UTR) interspecies rhinovirus/rhinovirus or rhinovirus/non-rhinovirus enterovirus recombinants are fully viable. Using a similar approach, we demonstrated in this study that exchanges of the P1-2A polyprotein region between members of the same rhinovirus species, but not between members of different species, give rise to competent chimeras. To further assess the rhinovirus intra- and interspecies recombination potential, we used artificially induced recombination by cotransfection of 5'-end-deleted and 3'-end-deleted and replication-deficient genomes. In this system, intraspecies recombination also resulted in viable viruses with high frequency, whereas no interspecies rhinovirus recombinants could be recovered. Mapping intraspecies recombination sites within the polyprotein highlighted recombinant hotspots in nonstructural genes and at gene boundaries. Notably, all recombinants occurring at gene junctions presented in-frame sequence duplications, whereas most intragenic recombinants were homologous. Taken together, our results suggest that only intraspecies recombination gives rise to viable rhinovirus chimeras in the polyprotein coding region and that recombination hotspots map to nonstructural genes with in-frame duplications at gene boundaries. These data provide new insights regarding the mechanism and limitations of rhinovirus recombination.<br><br>IMPORTANCE: Recombination represents a means to ensure both the stability and the variation of RNA viruses. While intraspecies recombination is described frequently among non-rhinovirus enteroviruses, it seems to occur more rarely in rhinoviruses. Interspecies recombination is even rarer in this virus group and is mostly related to ancient events, which contributed to its speciation. We used engineered chimeric genomes and artificially induced RNA recombination to study experimentally the recombination potential of rhinoviruses and analyze recombination sites. Our results suggest that only intraspecies recombination gives rise to viable chimeras in the polyprotein coding region. Furthermore, characterization of intraspecies chimeras provides new insight into putative recombination hotspots within the polyprotein. In summary, we applied two powerful and complementary experimental approaches to improve current knowledge on rhinovirus recombination.}, }
@article {pmid25653402, year = {2015}, author = {Quesada-Gómez, C and López-Ureña, D and Acuña-Amador, L and Villalobos-Zúñiga, M and Du, T and Freire, R and Guzmán-Verri, C and del Mar Gamboa-Coronado, M and Lawley, TD and Moreno, E and Mulvey, MR and de Castro Brito, GA and Rodríguez-Cavallini, E and Rodríguez, C and Chaves-Olarte, E}, title = {Emergence of an outbreak-associated Clostridium difficile variant with increased virulence.}, journal = {Journal of clinical microbiology}, volume = {53}, number = {4}, pages = {1216-1226}, pmid = {25653402}, issn = {1098-660X}, support = {/WT_/Wellcome Trust/United Kingdom ; 086418/WT_/Wellcome Trust/United Kingdom ; 098051/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Clostridioides difficile/classification/genetics/*isolation &amp; purification/*pathogenicity ; Clostridium Infections/*epidemiology/microbiology/pathology ; Costa Rica/epidemiology ; Cross Infection/chemically induced/epidemiology/microbiology ; DNA, Bacterial/genetics ; Diarrhea/*epidemiology/microbiology/pathology ; Disease Models, Animal ; *Disease Outbreaks ; Electrophoresis, Gel, Pulsed-Field ; Female ; Gene Transfer, Horizontal ; Genotype ; Hospitals ; Humans ; Intestines/pathology ; Male ; Mesocricetus ; Mice ; Molecular Sequence Data ; Molecular Typing ; Retrospective Studies ; Ribotyping ; Sequence Analysis, DNA ; Survival Analysis ; Virulence ; Virulence Factors/genetics ; }, abstract = {The prevalence of Clostridium difficile infections has increased due to the emergence of epidemic variants from diverse genetic lineages. Here we describe the emergence of a novel variant during an outbreak in a Costa Rican hospital that was associated with severe clinical presentations. This C. difficile variant elicited higher white blood cell counts and caused disease in younger patients than did other strains isolated during the outbreak. Furthermore, it had a recurrence rate, a 30-day attributable disease rate, and disease severity as great as those of the epidemic strain NAP1. Pulsed-field gel electrophoresis genotyping indicated that the outbreak strains belong to a previously undescribed variant, designated NAPCR1. Whole-genome sequencing and ribotyping indicated that the NAPCR1 variant belongs to C. difficile ribotype 012 and sequence type 54, as does the reference strain 630. NAPCR1 strains are resistant to fluoroquinolones due to a mutation in gyrA, and they possess an 18-bp deletion in tcdC that is characteristic of the epidemic, evolutionarily distinct, C. difficile NAP1 variant. NAPCR1 genomes contain 10% more predicted genes than strain 630, most of which are of hypothetical function and are present on phages and other mobile genetic elements. The increased virulence of NAPCR1 was confirmed by mortality rates in the hamster model and strong inflammatory responses induced by bacteria-free supernatants in the murine ligated loop model. However, NAPCR1 strains do not synthesize toxin A and toxin B at levels comparable to those in NAP1 strains. Our results suggest that the pathogenic potential of this emerging C. difficile variant is due to the acquisition of hypothetical functions associated with laterally acquired DNA.}, }
@article {pmid25648151, year = {2015}, author = {Rafaï, C and Frank, T and Manirakiza, A and Gaudeuille, A and Mbecko, JR and Nghario, L and Serdouma, E and Tekpa, B and Garin, B and Breurec, S}, title = {Dissemination of IncF-type plasmids in multiresistant CTX-M-15-producing Enterobacteriaceae isolates from surgical-site infections in Bangui, Central African Republic.}, journal = {BMC microbiology}, volume = {15}, number = {1}, pages = {15}, pmid = {25648151}, issn = {1471-2180}, mesh = {Central African Republic/epidemiology ; DNA, Bacterial/chemistry/genetics ; Enterobacteriaceae/*enzymology/*genetics ; Enterobacteriaceae Infections/epidemiology/*microbiology ; *Gene Transfer, Horizontal ; Humans ; *Plasmids ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Surgical Wound Infection/epidemiology/*microbiology ; Tertiary Care Centers ; beta-Lactamases/*metabolism ; }, abstract = {BACKGROUND: Surgical-site infection is the most frequent health care-associated infection in the developing world, with a strikingly higher prevalence than in developed countries We studied the prevalence of resistance to antibiotics in Enterobacteriaceae isolates from surgical-site infections collected in three major tertiary care centres in Bangui, Central African Republic. We also studied the genetic basis for antibiotic resistance and the genetic background of third-generation cephalosporin-resistant (3GC-R) Enterobacteriaceae.<br><br>RESULTS: Between April 2011 and April 2012, 195 patients with nosocomial surgical-site infections were consecutively recruited into the study at five surgical departments in three major tertiary care centres. Of the 165 bacterial isolates collected, most were Enterobacteriaceae (102/165, 61.8%). Of these, 65/102 (63.7%) were 3GC-R, which were characterized for resistance gene determinants and genetic background. The bla CTX-M-15 and aac(6')-Ib-cr genes were detected in all strains, usually associated with qnr genes (98.5%). Escherichia coli, the most commonly recovered species (33/65, 50.8%), occurred in six different sequence types, including the pandemic B2-O25b-ST131 group (12/33, 36.4%). Resistance transfer was studied in one representative strain of the resistance gene content in each repetitive extragenic palindromic and enterobacterial repetitive intergenic consensus sequence-PCR banding pattern. Plasmids were characterized by PCR-based replicon typing and sub-typing schemes. In most isolates (18/27, 66.7%), bla CTX-M-15 genes were found in incompatibility groups F/F31:A4:B1 and F/F36:A4:B1 conjugative plasmids. Horizontal transfer of both plasmids is probably an important mechanism for the spread of bla CTX-M-15 among Enterobacteriaceae species and hospitals. The presence of sets of antibiotic resistance genes in these two plasmids indicates their capacity for gene rearrangement and their evolution into new variants.<br><br>CONCLUSIONS: Diverse modes are involved in transmission of resistance, plasmid dissemination probably playing a major role.}, }
@article {pmid25647243, year = {2015}, author = {Jahan, M and Zhanel, GG and Sparling, R and Holley, RA}, title = {Horizontal transfer of antibiotic resistance from Enterococcus faecium of fermented meat origin to clinical isolates of E. faecium and Enterococcus faecalis.}, journal = {International journal of food microbiology}, volume = {199}, number = {}, pages = {78-85}, doi = {10.1016/j.ijfoodmicro.2015.01.013}, pmid = {25647243}, issn = {1879-3460}, mesh = {Animals ; Drug Resistance, Microbial/*genetics ; Electrophoresis, Gel, Pulsed-Field ; Enterococcus faecalis/*genetics ; Enterococcus faecium/*genetics ; Feces/microbiology ; Food Microbiology ; Gene Transfer, Horizontal ; Gram-Positive Bacterial Infections/*microbiology/transmission ; Humans ; Integrons/genetics ; Meat/*microbiology ; }, abstract = {Enterococcus species are part of the normal intestinal flora of a large number of mammals including humans and consequently, they can be used as indicators of faecal contamination in food and water for human consumption. Their presence in large numbers in foods may indicate a lapse in sanitation and their ability to serve as a genetic reservoir of transferable antibiotic resistance is of concern. In the present study, Enterococcus spp., isolated from commercially fermented meat and human clinical specimen were studied to determine genetic relationships. SmaI pulsed-field gel electrophoresis (PFGE) patterns exhibited genomic heterogeneity within and between both groups of isolates. However, in spite of this heterogeneity there were still substantial phenotypic similarities which suggested that food might be a potential vehicle for distribution of resistant bacteria among humans. In vitro conjugation experiments demonstrated transfer of the tetracycline resistant determinant, tet(M), from Enterococcus faecium S27 isolated from fermented sausage to clinical isolates of both E. faecium and Enterococcus faecalis. The streptomycin resistance of E. faecium S27 was also transferred to a clinical strain, E. faecalis 82916, which was confirmed by the presence of the streptomycin resistance gene, aadA, in the donor and transconjugant strains. Since the aadA gene is associated with a class 1 integron, results also suggested that resistance transfer might have occurred via an integron. It appears this is the first identification of a class 1 integron in E. faecium isolated from food. The importance of food enterococci as a reservoir of antibiotic resistance genes and the potential for their genetic transfer to human strains following consumption of uncooked or undercooked contaminated meat is underlined by this work.}, }
@article {pmid25646541, year = {2014}, author = {Fernández, M and Udaondo, Z and Niqui, JL and Duque, E and Ramos, JL}, title = {Synergic role of the two ars operons in arsenic tolerance in Pseudomonas putida KT2440.}, journal = {Environmental microbiology reports}, volume = {6}, number = {5}, pages = {483-489}, doi = {10.1111/1758-2229.12167}, pmid = {25646541}, issn = {1758-2229}, mesh = {Arsenic/*metabolism ; Bacterial Proteins/genetics/*metabolism ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; *Operon ; Pseudomonas putida/genetics/*metabolism ; }, abstract = {The chromosome of Pseudomonas putida KT2440 carries two clusters of genes, denoted ars1 and ars2, that are annotated as putative arsenic resistance operons. In this work, we present evidence that both operons encode functional arsenic-response regulatory genes as well as arsenic extrusion systems that confer resistance to both arsenite [As(III)] and arsenate [As(V)]. Transcriptional fusions of P(ars1) and P(ars2) to lacZ revealed that expression of both operons was induced by arsenite and arsenate. We generated single mutants in ars1 and ars2, which showed lower resistance to arsenic than the wild-type strain. A double ars1/ars2 was found to be highly sensitive to arsenic. Minimum inhibitory concentrations (MICs) for single mutants decreased two- to fourfold with respect to the parental strain, while in the double mutant the MIC decreased 128-fold for arsenite and 32-fold for arsenate. Bioinformatic analysis revealed that the ars2 resistance operon is part of the core genome of P. putida, while the ars1 operon appears to only occur in the KT2440 strain, suggesting that ars1 was acquired by horizontal gene transfer. The presence of ars1 in KT2440 may explain why it exhibits higher resistance to arsenic than other P. putida strains, which bear only the ars2 operon.}, }
@article {pmid25646426, year = {2015}, author = {Hellmuth, M and Wieseke, N and Lechner, M and Lenhof, HP and Middendorf, M and Stadler, PF}, title = {Phylogenomics with paralogs.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {7}, pages = {2058-2063}, pmid = {25646426}, issn = {1091-6490}, mesh = {*Genomics ; *Phylogeny ; }, abstract = {Phylogenomics heavily relies on well-curated sequence data sets that comprise, for each gene, exclusively 1:1 orthologos. Paralogs are treated as a dangerous nuisance that has to be detected and removed. We show here that this severe restriction of the data sets is not necessary. Building upon recent advances in mathematical phylogenetics, we demonstrate that gene duplications convey meaningful phylogenetic information and allow the inference of plausible phylogenetic trees, provided orthologs and paralogs can be distinguished with a degree of certainty. Starting from tree-free estimates of orthology, cograph editing can sufficiently reduce the noise to find correct event-annotated gene trees. The information of gene trees can then directly be translated into constraints on the species trees. Although the resolution is very poor for individual gene families, we show that genome-wide data sets are sufficient to generate fully resolved phylogenetic trees, even in the presence of horizontal gene transfer.}, }
@article {pmid25644974, year = {2015}, author = {Betrán, E}, title = {The "life histories" of genes.}, journal = {Journal of molecular evolution}, volume = {80}, number = {3-4}, pages = {186-188}, pmid = {25644974}, issn = {1432-1432}, support = {R01 GM071813/GM/NIGMS NIH HHS/United States ; R01GM071813/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Drosophila melanogaster/genetics ; *Gene Duplication ; *Gene Transfer, Horizontal ; Genes, Homeobox ; Humans ; RNA, Untranslated/genetics/*metabolism ; Recombination, Genetic ; Viruses/genetics ; }, }
@article {pmid25644973, year = {2015}, author = {Liu, G and Zhang, M and Chen, X and Zhang, W and Ding, W and Zhang, Q}, title = {Evolution of threonine aldolases, a diverse family involved in the second pathway of glycine biosynthesis.}, journal = {Journal of molecular evolution}, volume = {80}, number = {2}, pages = {102-107}, pmid = {25644973}, issn = {1432-1432}, mesh = {Archaea/enzymology/genetics ; Bacteria/enzymology/genetics ; Eukaryota/enzymology/genetics ; *Evolution, Molecular ; Glycine/biosynthesis/genetics ; Glycine Hydroxymethyltransferase/chemistry/*classification/genetics ; *Phylogeny ; }, abstract = {Threonine aldolases (TAs) catalyze the interconversion of threonine and glycine plus acetaldehyde in a pyridoxal phosphate-dependent manner. This class of enzymes complements the primary glycine biosynthetic pathway catalyzed by serine hydroxymethyltransferase (SHMT), and was shown to be necessary for yeast glycine auxotrophy. Because the reverse reaction of TA involves carbon-carbon bond formation, resulting in a β-hydroxyl-α-amino acid with two adjacent chiral centers, TAs are of high interests in synthetic chemistry and bioengineering studies. Here, we report systematic phylogenetic analysis of TAs. Our results demonstrated that L-TAs and D-TAs that are specific for L- and D-threonine, respectively, are two phylogenetically unique families, and both enzymes are different from their closely related enzymes SHMTs and bacterial alanine racemases (ARs). Interestingly, L-TAs can be further grouped into two evolutionarily distinct families, which share low sequence similarity with each other but likely possess the same structural fold, suggesting a convergent evolution of these enzymes. The first L-TA family contains enzymes of both prokaryotic and eukaryotic origins, and is related to fungal ARs, whereas the second contains only prokaryotic L-TAs. Furthermore, we show that horizontal gene transfer may occur frequently during the evolution of both L-TA families. Our results indicate the complex, dynamic, and convergent evolution process of TAs and suggest an updated classification scheme for L-TAs.}, }
@article {pmid25636836, year = {2015}, author = {Farias, P and Espírito Santo, C and Branco, R and Francisco, R and Santos, S and Hansen, L and Sorensen, S and Morais, PV}, title = {Natural hot spots for gain of multiple resistances: arsenic and antibiotic resistances in heterotrophic, aerobic bacteria from marine hydrothermal vent fields.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {7}, pages = {2534-2543}, pmid = {25636836}, issn = {1098-5336}, mesh = {Anti-Bacterial Agents/*pharmacology ; Antimony/pharmacology ; Arsenic/*pharmacology ; Azores ; Bacteria, Aerobic/*drug effects/isolation &amp; purification ; *Drug Resistance, Multiple, Bacterial ; Genes, Bacterial ; Hydrothermal Vents/*microbiology ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Plasmids/analysis ; Sequence Analysis, DNA ; }, abstract = {Microorganisms are responsible for multiple antibiotic resistances that have been associated with resistance/tolerance to heavy metals, with consequences to public health. Many genes conferring these resistances are located on mobile genetic elements, easily exchanged among phylogenetically distant bacteria. The objective of the present work was to isolate arsenic-, antimonite-, and antibiotic-resistant strains and to determine the existence of plasmids harboring antibiotic/arsenic/antimonite resistance traits in phenotypically resistant strains, in a nonanthropogenically impacted environment. The hydrothermal Lucky Strike field in the Azores archipelago (North Atlantic, between 11°N and 38°N), at the Mid-Atlantic Ridge, protected under the OSPAR Convention, was sampled as a metal-rich pristine environment. A total of 35 strains from 8 different species were isolated in the presence of arsenate, arsenite, and antimonite. ACR3 and arsB genes were amplified from the sediment's total DNA, and 4 isolates also carried ACR3 genes. Phenotypic multiple resistances were found in all strains, and 7 strains had recoverable plasmids. Purified plasmids were sequenced by Illumina and assembled by EDENA V3, and contig annotation was performed using the "Rapid Annotation using the Subsystems Technology" server. Determinants of resistance to copper, zinc, cadmium, cobalt, and chromium as well as to the antibiotics β-lactams and fluoroquinolones were found in the 3 sequenced plasmids. Genes coding for heavy metal resistance and antibiotic resistance in the same mobile element were found, suggesting the possibility of horizontal gene transfer and distribution of theses resistances in the bacterial population.}, }
@article {pmid25634990, year = {2015}, author = {Sabat, AJ and Ilczyszyn, WM and van Rijen, M and Akkerboom, V and Sinha, B and Kluytmans, J and Miedzobrodzki, J and Grundmann, H and Friedrich, AW}, title = {Genome-wide analysis reveals two novel mosaic regions containing an ACME with an identical DNA sequence in the MRSA ST398-t011 and MSSA ST8-t008 isolates.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {70}, number = {5}, pages = {1298-1302}, doi = {10.1093/jac/dku531}, pmid = {25634990}, issn = {1460-2091}, mesh = {Animals ; *Conserved Sequence ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genomic Islands ; Genotype ; Humans ; *Interspersed Repetitive Sequences ; Livestock ; Molecular Typing ; Netherlands ; Poland ; Sequence Analysis, DNA ; Staphylococcal Infections/microbiology/transmission ; Staphylococcus aureus/classification/*genetics/isolation &amp; purification ; }, abstract = {OBJECTIVES: The presence of the arginine catabolic mobile element (ACME) in Staphylococcus aureus has been reported to enhance the colonization of the human host. The aim of this study was to determine the genetic organization of composite islands harbouring ACME.<br><br>METHODS: Two ACME-positive S. aureus isolates obtained during two different surveys conducted in the Netherlands and Poland were characterized in this study. The isolates were analysed by spa typing, DNA microarrays and whole-genome sequencing.<br><br>RESULTS: The two isolates harboured a truncated yet fully functional ACME type II with an identical nucleotide sequence, but differed in their adjacent mobile genetic elements. The first strain was a livestock-associated ST398-t011 MRSA, which had a staphylococcal cassette chromosome mec (SCCmec) composite island composed of SCCpls adjacent to orfX followed by ACME type II and SCCmec type IVa. The second ACME-positive isolate was an ST8-t008 MSSA. Its composite island showed an SCC-like element carrying the ccrC gene followed by ACME II.<br><br>CONCLUSIONS: This is the first report of an ACME in a livestock-associated MRSA ST398. It is also the first presentation of an ACME composite island structure in an MSSA isolate. Our findings indicate an extensive mosaicism of composite islands in S. aureus, which has implications for the transmissibility among humans and thus for public health.}, }
@article {pmid25634949, year = {2015}, author = {Pillonel, T and Bertelli, C and Salamin, N and Greub, G}, title = {Taxogenomics of the order Chlamydiales.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {65}, number = {Pt 4}, pages = {1381-1393}, doi = {10.1099/ijs.0.000090}, pmid = {25634949}, issn = {1466-5034}, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics ; Chlamydiales/*classification ; Conserved Sequence ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Bacterial classification is a long-standing problem for taxonomists and species definition itself is constantly debated among specialists. The classification of strict intracellular bacteria such as members of the order Chlamydiales mainly relies on DNA- or protein-based phylogenetic reconstructions because these organisms exhibit few phenotypic differences and are difficult to culture. The availability of full genome sequences allows the comparison of the performance of conserved protein sequences to reconstruct Chlamydiales phylogeny. This approach permits the identification of markers that maximize the phylogenetic signal and the robustness of the inferred tree. In this study, a set of 424 core proteins was identified and concatenated to reconstruct a reference species tree. Although individual protein trees present variable topologies, we detected only few cases of incongruence with the reference species tree, which were due to horizontal gene transfers. Detailed analysis of the phylogenetic information of individual protein sequences (i) showed that phylogenies based on single randomly chosen core proteins are not reliable and (ii) led to the identification of twenty taxonomically highly reliable proteins, allowing the reconstruction of a robust tree close to the reference species tree. We recommend using these protein sequences to precisely classify newly discovered isolates at the family, genus and species levels.}, }
@article {pmid25633105, year = {2015}, author = {Zhou, Y and Xu, YB and Xu, JX and Zhang, XH and Xu, SH and Du, QP}, title = {Combined toxic effects of heavy metals and antibiotics on a Pseudomonas fluorescens strain ZY2 isolated from swine wastewater.}, journal = {International journal of molecular sciences}, volume = {16}, number = {2}, pages = {2839-2850}, pmid = {25633105}, issn = {1422-0067}, mesh = {Amoxicillin/pharmacology ; Animals ; Anti-Bacterial Agents/*pharmacology ; Cephradine/pharmacology ; Drug Resistance, Bacterial ; Metals, Heavy/*toxicity ; Microbial Sensitivity Tests ; Norfloxacin/pharmacology ; Pseudomonas fluorescens/*drug effects/isolation &amp; purification ; Swine ; Wastewater/*microbiology ; }, abstract = {A Pseudomonas fluorescens strain ZY2, isolated from swine wastewater, was used to investigate the synergistic effects of five heavy metals (Pb, Cu, Zn, Cr(VI) and Hg) on bacterial resistance to antibiotics. Results indicate that the combined effects of antibiotic type, heavy metal type and concentration were significant (p < 0.01). Cross-resistance to Hg and antibiotics was the most noticeable. Moreover, the resistance to Hg and cefradine or amoxicillin, and Cr and amoxicillin were synergistic for low heavy metal concentrations, and turned antagonistic with increasing concentrations, while the resistances to Cr or Cu and cefradine, Pb or Cu and amoxicillin, Cu and norfloxacin showed reverse effects. In addition, resistance to Zn and amoxicillin were always synergetic, while resistance to Pb and cefradine or norfloxacin, Cr or Hg and norfloxacin as well as all the heavy metals and tetracycline were antagonistic. These results indicate that bacterial resistance to antibiotics can be affected by the type and concentration of co-exposed heavy metals and may further threaten people's health and ecological security severely via horizontal gene transfer.}, }
@article {pmid25631811, year = {2015}, author = {Salipante, SJ and SenGupta, DJ and Cummings, LA and Land, TA and Hoogestraat, DR and Cookson, BT}, title = {Application of whole-genome sequencing for bacterial strain typing in molecular epidemiology.}, journal = {Journal of clinical microbiology}, volume = {53}, number = {4}, pages = {1072-1079}, pmid = {25631811}, issn = {1098-660X}, support = {UL1 TR000423/TR/NCATS NIH HHS/United States ; UL1 TR002319/TR/NCATS NIH HHS/United States ; UL1TR000423/TR/NCATS NIH HHS/United States ; }, mesh = {Bacteria/genetics/isolation &amp; purification ; Bacterial Infections/microbiology ; Cross Infection/microbiology ; DNA, Bacterial/analysis/genetics ; Disease Outbreaks ; Genome, Bacterial/*genetics ; Humans ; Molecular Epidemiology/*methods ; Molecular Typing/*methods ; Sequence Analysis, DNA/*methods ; }, abstract = {Nosocomial infections pose a significant threat to patient health; however, the gold standard laboratory method for determining bacterial relatedness (pulsed-field gel electrophoresis [PFGE]) remains essentially unchanged 20 years after its introduction. Here, we explored bacterial whole-genome sequencing (WGS) as an alternative approach for molecular strain typing. We compared WGS to PFGE for investigating presumptive outbreaks involving three important pathogens: vancomycin-resistant Enterococcus faecium (n=19), methicillin-resistant Staphylococcus aureus (n=17), and Acinetobacter baumannii (n=15). WGS was highly reproducible (average≤0.39 differences between technical replicates), which enabled a functional, quantitative definition for determining clonality. Strain relatedness data determined by PFGE and WGS roughly correlated, but the resolution of WGS was superior (P=5.6×10(-8) to 0.016). Several discordant results were noted between the methods. A total of 28.9% of isolates which were indistinguishable by PFGE were nonclonal by WGS. For A. baumannii, a species known to undergo rapid horizontal gene transfer, 16.2% of isolate pairs considered nonidentical by PFGE were clonal by WGS. Sequencing whole bacterial genomes with single-nucleotide resolution demonstrates that PFGE is prone to false-positive and false-negative results and suggests the need for a new gold standard approach for molecular epidemiological strain typing.}, }
@article {pmid25630639, year = {2015}, author = {Gheorghe, I and Novais, &#xc2; and Grosso, F and Rodrigues, C and Chifiriuc, MC and Lazar, V and Peixe, L}, title = {Snapshot on carbapenemase-producing Pseudomonas aeruginosa and Acinetobacter baumannii in Bucharest hospitals reveals unusual clones and novel genetic surroundings for blaOXA-23.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {70}, number = {4}, pages = {1016-1020}, doi = {10.1093/jac/dku527}, pmid = {25630639}, issn = {1460-2091}, mesh = {Acinetobacter Infections/*microbiology ; Acinetobacter baumannii/classification/*enzymology/genetics/isolation &amp; purification ; Bacterial Proteins/genetics/*metabolism ; Conjugation, Genetic ; Cross Infection/*microbiology ; Electrophoresis, Gel, Pulsed-Field ; Gene Transfer, Horizontal ; *Genotype ; Hospitals ; Humans ; Multilocus Sequence Typing ; Nucleic Acid Hybridization ; Plasmids/analysis/classification ; Polymerase Chain Reaction ; Pseudomonas Infections/*microbiology ; Pseudomonas aeruginosa/classification/*enzymology/genetics/isolation &amp; purification ; Romania ; Spectroscopy, Fourier Transform Infrared ; beta-Lactamases/genetics/*metabolism ; }, abstract = {OBJECTIVES: The present study was designed to provide a snapshot on carbapenemase-producing Pseudomonas aeruginosa (n=11) and Acinetobacter baumannii (n=7) isolates in hospitalized patients (November 2011, January-March 2012) from two main hospitals in Bucharest, south Romania.<br><br>METHODS: Clonality among isolates was established by PFGE, MLST and Fourier transform infrared spectroscopy. Carbapenemases were screened by the Blue-Carba test, PCR and sequencing. Transferability of blaOXA-23 was tested by conjugation and plasmid typing (number, size and identity) was assessed by S1-PFGE, replicon typing, hybridization and PCR mapping.<br><br>RESULTS: All P. aeruginosa isolates carried chromosomally located blaVIM-2, associated with a common class 1 integron (aacA7-blaVIM-2) or an atypical configuration (aacA7-blaVIM-2-dfrB5-tniC). These isolates belonged to unusual lineages; mostly ST233 disseminated in one hospital unit, with ST364 and ST1074 also being detected. A. baumannii isolates carried blaOXA-23 in Tn2008, which was found truncating a TnaphA6 transposon located in a common 60 kb GR6 (aci6) pABKp1-like conjugative plasmid in highly related CC92 clones (ST437, ST764 and ST765), where CC stands for clonal complex.<br><br>CONCLUSIONS: Our results show the spread of VIM-2-producing P. aeruginosa and OXA-23-producing A. baumannii clinical isolates in two hospitals from Bucharest and highlight a peculiar population structure in this Eastern European country. Also, we demonstrate the dissemination of a common and conjugative aci6 pABKp1-like plasmid scaffold in different A. baumannii clones and we report the first known identification of Tnaph6-carrying pACICU2-like plasmids in Europe.}, }
@article {pmid25630351, year = {2015}, author = {Lossouarn, J and Nesbø, CL and Mercier, C and Zhaxybayeva, O and Johnson, MS and Charchuck, R and Farasin, J and Bienvenu, N and Baudoux, AC and Michoud, G and Jebbar, M and Geslin, C}, title = {'Ménage à trois': a selfish genetic element uses a virus to propagate within Thermotogales.}, journal = {Environmental microbiology}, volume = {17}, number = {9}, pages = {3278-3288}, doi = {10.1111/1462-2920.12783}, pmid = {25630351}, issn = {1462-2920}, mesh = {Bacteria/genetics/isolation &amp; purification/*virology ; Clustered Regularly Interspaced Short Palindromic Repeats/*genetics ; DNA, Viral/genetics ; Gene Dosage/drug effects/genetics ; Gene Transfer, Horizontal/*genetics ; Hydrothermal Vents/*microbiology/virology ; Mitomycin/pharmacology ; Plasmids/*genetics ; Siphoviridae/*genetics ; }, abstract = {Prokaryotic viruses play a major role in the microbial ecology and evolution. However, the virosphere associated with deep-sea hydrothermal ecosystems remains largely unexplored. Numerous instances of lateral gene transfer have contributed to the complex and incongruent evolutionary history of Thermotogales, an order well represented in deep-sea hydrothermal vents. The presence of clustered regularly interspaced short palindromic repeats (CRISPR) loci has been reported in all Thermotogales genomes, suggesting that these bacteria have been exposed to viral infections that could have mediated gene exchange. In this study, we isolated and characterized the first virus infecting bacteria from the order Thermotogales, Marinitoga piezophila virus 1 (MPV1). The host, Marinitoga piezophila is a thermophilic, anaerobic and piezophilic bacterium isolated from a deep-sea hydrothermal chimney. MPV1 is a temperate Siphoviridae-like virus with a 43.7 kb genome. Surprisingly, we found that MPV1 virions carry not only the viral DNA but preferentially package a plasmid of 13.3 kb (pMP1) also carried by M. piezophila. This 'ménage à trois' highlights potential relevance of selfish genetic elements in facilitating lateral gene transfer in the deep-sea biosphere.}, }
@article {pmid25630302, year = {2015}, author = {Pajuelo, D and Lee, CT and Roig, FJ and Hor, LI and Amaro, C}, title = {Novel host-specific iron acquisition system in the zoonotic pathogen Vibrio vulnificus.}, journal = {Environmental microbiology}, volume = {17}, number = {6}, pages = {2076-2089}, doi = {10.1111/1462-2920.12782}, pmid = {25630302}, issn = {1462-2920}, mesh = {Animals ; Bacterial Proteins/*genetics ; Carrier Proteins/*metabolism ; Eels/blood/microbiology ; Fish Diseases/*microbiology ; Gene Transfer, Horizontal ; Humans ; Immune Evasion/genetics/immunology ; Immunity, Innate/immunology ; Iron/*metabolism ; Membrane Proteins/genetics/metabolism ; Mice ; Photobacterium/genetics/pathogenicity ; Plasmids/genetics ; Receptors, Transferrin/*genetics ; Vibrio Infections/*microbiology ; Vibrio vulnificus/genetics/*metabolism ; }, abstract = {Vibrio vulnificus is a marine bacterium associated with human and fish (mainly farmed eels) diseases globally known as vibriosis. The ability to infect and overcome eel innate immunity relies on a virulence plasmid (pVvbt2) specific for biotype 2 (Bt2) strains. In the present study, we demonstrated that pVvbt2 encodes a host-specific iron acquisition system that depends on an outer membrane receptor for eel transferrin called Vep20. The inactivation of vep20 did not affect either bacterial growth in human plasma or virulence for mice, while bacterial growth in eel blood/plasma was abolished and virulence for eels was significantly impaired. Furthermore, vep20 is an iron-regulated gene overexpressed in eel blood during artificially induced vibriosis both in vitro and in vivo. Interestingly, homologues to vep20 were identified in the transferable plasmids of two fish pathogen species of broad-host range, Vibrio harveyi (pVh1) and Photobacterium damselae subsp. damselae (pPHDD1). These data suggest that Vep20 belongs to a new family of plasmid-encoded fish-specific transferrin receptors, and the acquisition of these plasmids through horizontal gene transfer is likely positively selected in the fish-farming environment. Moreover, we propose Ftbp (fish transferrin binding proteins) as a formal name for this family of proteins.}, }
@article {pmid25628613, year = {2014}, author = {Frisvad, JC}, title = {Taxonomy, chemodiversity, and chemoconsistency of Aspergillus, Penicillium, and Talaromyces species.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {773}, pmid = {25628613}, issn = {1664-302X}, abstract = {Aspergillus, Penicillium, and Talaromyces are among the most chemically inventive of all fungi, producing a wide array of secondary metabolites (exometabolites). The three genera are holophyletic in a cladistic sense and polythetic classes in an anagenetic or functional sense, and contain 344, 354, and 88 species, respectively. New developments in classification, cladification, and nomenclature have meant that the species, series, and sections suggested are natural groups that share many extrolites, including exometabolites, exoproteins, exocarbohydrates, and exolipids in addition to morphological features. The number of exometabolites reported from these species is very large, and genome sequencing projects have shown that a large number of additional exometabolites may be expressed, given the right conditions ("cryptic" gene clusters for exometabolites). The exometabolites are biosynthesized via shikimic acid, tricarboxylic acid cycle members, nucleotides, carbohydrates or as polyketides, non-ribosomal peptides, terpenes, or mixtures of those. The gene clusters coding for these compounds contain genes for the biosynthetic building blocks, the linking of these building blocks, tailoring enzymes, resistance for own products, and exporters. Species within a series or section in Aspergillus, Penicillium, and Talaromyces have many exometabolites in common, seemingly acquired by cladogenesis, but some the gene clusters for autapomorphic exometabolites may have been acquired by horizontal gene transfer. Despite genome sequencing efforts, and the many breakthroughs these will give, it is obvious that epigenetic factors play a large role in evolution and function of chemodiversity, and better methods for characterizing the epigenome are needed. Most of the individual species of the three genera produce a consistent and characteristic profile of exometabolites, but growth medium variations, stimulation by exometabolites from other species, and variations in abiotic intrinsic and extrinsic environmental factors such as pH, temperature, redox potential, and water activity will add significantly to the number of biosynthetic families expressed in anyone species. An example of the shared exometabolites in a natural group such as Aspergillus section Circumdati series Circumdati is that most, but not all species produce penicillic acids, aspyrones, neoaspergillic acids, xanthomegnins, melleins, aspergamides, circumdatins, and ochratoxins, in different combinations.}, }
@article {pmid25624355, year = {2015}, author = {Tan, A and Petty, NK and Hocking, D and Bennett-Wood, V and Wakefield, M and Praszkier, J and Tauschek, M and Yang, J and Robins-Browne, R}, title = {Evolutionary adaptation of an AraC-like regulatory protein in Citrobacter rodentium and Escherichia species.}, journal = {Infection and immunity}, volume = {83}, number = {4}, pages = {1384-1395}, pmid = {25624355}, issn = {1098-5522}, mesh = {Animals ; AraC Transcription Factor/*genetics ; Bacterial Proteins/*genetics ; Biological Evolution ; Citrobacter rodentium/*genetics/*pathogenicity ; Escherichia coli/*genetics/pathogenicity ; Escherichia coli Proteins/*genetics ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Male ; Mice ; Mice, Inbred C57BL ; Phosphoproteins/genetics ; Phylogeny ; Repressor Proteins/genetics ; Virulence Factors/genetics ; }, abstract = {The evolution of pathogenic bacteria is a multifaceted and complex process, which is strongly influenced by the horizontal acquisition of genetic elements and their subsequent expression in their new hosts. A well-studied example is the RegA regulon of the enteric pathogen Citrobacter rodentium. The RegA regulatory protein is a member of the AraC/XylS superfamily, which coordinates the expression of a gene repertoire that is necessary for full pathogenicity of this murine pathogen. Upon stimulation by an exogenous, gut-associated signal, namely, bicarbonate ions, RegA activates the expression of a series of genes, including virulence factors, such as autotransporters, fimbriae, a dispersin-like protein, and the grlRA operon on the locus of enterocyte effacement pathogenicity island. Interestingly, the genes encoding RegA homologues are distributed across the genus Escherichia, encompassing pathogenic and nonpathogenic subtypes. In this study, we carried out a series of bioinformatic, transcriptional, and functional analyses of the RegA regulons of these bacteria. Our results demonstrated that regA has been horizontally transferred to Escherichia spp. and C. rodentium. Comparative studies of two RegA homologues, namely, those from C. rodentium and E. coli SMS-3-5, a multiresistant environmental strain of E. coli, showed that the two regulators acted similarly in vitro but differed in terms of their abilities to activate the virulence of C. rodentium in vivo, which evidently was due to their differential activation of grlRA. Our data indicate that RegA from C. rodentium has strain-specific adaptations that facilitate infection of its murine host. These findings shed new light on the development of virulence by C. rodentium and on the evolution of virulence-regulatory genes of bacterial pathogens in general.}, }
@article {pmid25621459, year = {2015}, author = {Ai, H and Fang, X and Yang, B and Huang, Z and Chen, H and Mao, L and Zhang, F and Zhang, L and Cui, L and He, W and Yang, J and Yao, X and Zhou, L and Han, L and Li, J and Sun, S and Xie, X and Lai, B and Su, Y and Lu, Y and Yang, H and Huang, T and Deng, W and Nielsen, R and Ren, J and Huang, L}, title = {Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing.}, journal = {Nature genetics}, volume = {47}, number = {3}, pages = {217-225}, doi = {10.1038/ng.3199}, pmid = {25621459}, issn = {1546-1718}, mesh = {Acclimatization/genetics ; Adaptation, Physiological/*genetics ; Amino Acid Sequence ; Animals ; China ; Environment ; Evolution, Molecular ; Female ; Gene Transfer, Horizontal/*genetics ; Genetics, Population/methods ; Genome ; Genome-Wide Association Study/methods ; Haplotypes ; Male ; Molecular Sequence Data ; Polymorphism, Single Nucleotide ; Sequence Homology, Amino Acid ; Swine ; X Chromosome ; }, abstract = {Domestic pigs have evolved genetic adaptations to their local environmental conditions, such as cold and hot climates. We sequenced the genomes of 69 pigs from 15 geographically divergent locations in China and detected 41 million variants, of which 21 million were absent from the dbSNP database. In a genome-wide scan, we identified a set of loci that likely have a role in regional adaptations to high- and low-latitude environments within China. Intriguingly, we found an exceptionally large (14-Mb) region with a low recombination rate on the X chromosome that appears to have two distinct haplotypes in the high- and low-latitude populations, possibly underlying their adaptation to cold and hot environments, respectively. Surprisingly, the adaptive sweep in the high-latitude regions has acted on DNA that might have been introgressed from an extinct Sus species. Our findings provide new insights into the evolutionary history of pigs and the role of introgression in adaptation.}, }
@article {pmid25616805, year = {2015}, author = {Winstel, V and Kühner, P and Krismer, B and Peschel, A and Rohde, H}, title = {Transfer of plasmid DNA to clinical coagulase-negative staphylococcal pathogens by using a unique bacteriophage.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {7}, pages = {2481-2488}, pmid = {25616805}, issn = {1098-5336}, mesh = {Bacterial Proteins/genetics ; *Gene Transfer, Horizontal ; Genetic Vectors ; Genetics, Microbial/*methods ; *Plasmids ; Sigma Factor/genetics ; Staphylococcus Phages/*genetics ; Staphylococcus aureus/*genetics ; Staphylococcus epidermidis/*genetics ; *Transduction, Genetic ; }, abstract = {Genetic manipulation of emerging bacterial pathogens, such as coagulase-negative staphylococci (CoNS), is a major hurdle in clinical and basic microbiological research. Strong genetic barriers, such as restriction modification systems or clustered regularly interspaced short palindromic repeats (CRISPR), usually interfere with available techniques for DNA transformation and therefore complicate manipulation of CoNS or render it impossible. Thus, current knowledge of pathogenicity and virulence determinants of CoNS is very limited. Here, a rapid, efficient, and highly reliable technique is presented to transfer plasmid DNA essential for genetic engineering to important CoNS pathogens from a unique Staphylococcus aureus strain via a specific S. aureus bacteriophage, Φ187. Even strains refractory to electroporation can be transduced by this technique once donor and recipient strains share similar Φ187 receptor properties. As a proof of principle, this technique was used to delete the alternative transcription factor sigma B (SigB) via allelic replacement in nasal and clinical Staphylococcus epidermidis isolates at high efficiencies. The described approach will allow the genetic manipulation of a wide range of CoNS pathogens and might inspire research activities to manipulate other important pathogens in a similar fashion.}, }
@article {pmid25615532, year = {2015}, author = {Biedler, JK and Chen, X and Tu, Z}, title = {Horizontal transmission of an R4 clade non-long terminal repeat retrotransposon between the divergent Aedes and Anopheles mosquito genera.}, journal = {Insect molecular biology}, volume = {24}, number = {3}, pages = {331-337}, pmid = {25615532}, issn = {1365-2583}, support = {R01 AI042121/AI/NIAID NIH HHS/United States ; R29 AI042121/AI/NIAID NIH HHS/United States ; AI42121/AI/NIAID NIH HHS/United States ; }, mesh = {Aedes/*genetics ; Animals ; Anopheles/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Open Reading Frames ; *Retroelements ; }, abstract = {AaegR4_1 and AgamR4_1 are the sole R4 clade non-long terminal repeat (non-LTR) retrotransposons in Aedes aegypti and Anopheles gambiae, two species that diverged approximately 145-200 million years ago. Twelve full-length copies were found in Ae. aegypti and have less than 1% nucleotide (nt) divergence, suggesting recent activity on an evolutionary time scale. Five of these copies have intact open reading frames and the 3.6 kb open reading frame of AaegR4_1.1 has 78% nt identity to AgamR4_1.1. No intact copies were found in An. gambiae. Searches of 25 genomic databases for 22 mosquito species from three genera revealed R4 clade representatives in Aedes and Anopheles genera but not in Culex. Interestingly, these elements are present in all six species of the An. gambiae species complex that were searched but not in 13 other anopheline species. These results combined with divergence vs. age analysis suggest that horizontal transfer is the most likely explanation for the low divergence between R4 clade retrotransposon sequences of the divergent mosquito species from the Aedes and Anopheles genera. This is the first report of the horizontal transfer of an R4 clade non-LTR retrotransposon and the first report of the horizontal transfer of a non-LTR retrotransposon in mosquitoes.}, }
@article {pmid25609309, year = {2015}, author = {Cuartas, PE and Barrera, GP and Belaich, MN and Barreto, E and Ghiringhelli, PD and Villamizar, LF}, title = {The complete sequence of the first Spodoptera frugiperda Betabaculovirus genome: a natural multiple recombinant virus.}, journal = {Viruses}, volume = {7}, number = {1}, pages = {394-421}, pmid = {25609309}, issn = {1999-4915}, mesh = {Animals ; Baculoviridae/*genetics/isolation &amp; purification ; Colombia ; DNA/chemistry/genetics ; DNA, Circular/chemistry/genetics ; DNA, Viral/*chemistry/*genetics ; Gene Transfer, Horizontal ; *Genome, Viral ; Molecular Sequence Annotation ; Molecular Sequence Data ; Open Reading Frames ; Recombination, Genetic ; Sequence Analysis, DNA ; Sequence Homology ; Spodoptera/*virology ; Virulence Factors/genetics ; }, abstract = {Spodoptera frugiperda (Lepidoptera: Noctuidae) is a major pest in maize crops in Colombia, and affects several regions in America. A granulovirus isolated from S. frugiperda (SfGV VG008) has potential as an enhancer of insecticidal activity of previously described nucleopolyhedrovirus from the same insect species (SfMNPV). The SfGV VG008 genome was sequenced and analyzed showing circular double stranded DNA of 140,913 bp encoding 146 putative ORFs that include 37 Baculoviridae core genes, 88 shared with betabaculoviruses, two shared only with betabaculoviruses from Noctuide insects, two shared with alphabaculoviruses, three copies of own genes (paralogs) and the other 14 corresponding to unique genes without representation in the other baculovirus species. Particularly, the genome encodes for important virulence factors such as 4 chitinases and 2 enhancins. The sequence analysis revealed the existence of eight homologous regions (hrs) and also suggests processes of gene acquisition by horizontal transfer including the SfGV VG008 ORFs 046/047 (paralogs), 059, 089 and 099. The bioinformatics evidence indicates that the genome donors of mentioned genes could be alpha- and/or betabaculovirus species. The previous reported ability of SfGV VG008 to naturally co-infect the same host with other virus show a possible mechanism to capture genes and thus improve its fitness.}, }
@article {pmid25607991, year = {2015}, author = {Almagro, G and Viale, AM and Montero, M and Rahimpour, M and Muñoz, FJ and Baroja-Fernández, E and Bahaji, A and Zúñiga, M and González-Candelas, F and Pozueta-Romero, J}, title = {Comparative genomic and phylogenetic analyses of Gammaproteobacterial glg genes traced the origin of the Escherichia coli glycogen glgBXCAP operon to the last common ancestor of the sister orders Enterobacteriales and Pasteurellales.}, journal = {PloS one}, volume = {10}, number = {1}, pages = {e0115516}, pmid = {25607991}, issn = {1932-6203}, mesh = {Escherichia coli/*genetics ; *Evolution, Molecular ; Glycogen/*genetics ; *Operon ; Pasteurellaceae/*genetics ; *Phylogeny ; }, abstract = {Production of branched α-glucan, glycogen-like polymers is widely spread in the Bacteria domain. The glycogen pathway of synthesis and degradation has been fairly well characterized in the model enterobacterial species Escherichia coli (order Enterobacteriales, class Gammaproteobacteria), in which the cognate genes (branching enzyme glgB, debranching enzyme glgX, ADP-glucose pyrophosphorylase glgC, glycogen synthase glgA, and glycogen phosphorylase glgP) are clustered in a glgBXCAP operon arrangement. However, the evolutionary origin of this particular arrangement and of its constituent genes is unknown. Here, by using 265 complete gammaproteobacterial genomes we have carried out a comparative analysis of the presence, copy number and arrangement of glg genes in all lineages of the Gammaproteobacteria. These analyses revealed large variations in glg gene presence, copy number and arrangements among different gammaproteobacterial lineages. However, the glgBXCAP arrangement was remarkably conserved in all glg-possessing species of the orders Enterobacteriales and Pasteurellales (the E/P group). Subsequent phylogenetic analyses of glg genes present in the Gammaproteobacteria and in other main bacterial groups indicated that glg genes have undergone a complex evolutionary history in which horizontal gene transfer may have played an important role. These analyses also revealed that the E/P glgBXCAP genes (a) share a common evolutionary origin, (b) were vertically transmitted within the E/P group, and (c) are closely related to glg genes of some phylogenetically distant betaproteobacterial species. The overall data allowed tracing the origin of the E. coli glgBXCAP operon to the last common ancestor of the E/P group, and also to uncover a likely glgBXCAP transfer event from the E/P group to particular lineages of the Betaproteobacteria.}, }
@article {pmid25607366, year = {2015}, author = {Mandell, DJ and Lajoie, MJ and Mee, MT and Takeuchi, R and Kuznetsov, G and Norville, JE and Gregg, CJ and Stoddard, BL and Church, GM}, title = {Biocontainment of genetically modified organisms by synthetic protein design.}, journal = {Nature}, volume = {518}, number = {7537}, pages = {55-60}, pmid = {25607366}, issn = {1476-4687}, support = {R01 GM049857/GM/NIGMS NIH HHS/United States ; //Howard Hughes Medical Institute/United States ; //Canadian Institutes of Health Research/Canada ; }, mesh = {Amino Acids/*chemistry/*metabolism ; Biological Evolution ; Codon/genetics ; Containment of Biohazards/*methods ; Ecosystem ; Escherichia coli/enzymology/*genetics/growth &amp; development/*metabolism ; Escherichia coli Proteins/*biosynthesis/genetics/metabolism ; Gene Transfer, Horizontal/genetics ; Genes, Essential/genetics ; Genetic Code/genetics ; Genetic Engineering/methods ; Microbial Viability/genetics ; Mutation/genetics ; Organisms, Genetically Modified/*genetics/metabolism ; Safety ; Selection, Genetic ; Synthetic Biology/*methods ; }, abstract = {Genetically modified organisms (GMOs) are increasingly deployed at large scales and in open environments. Genetic biocontainment strategies are needed to prevent unintended proliferation of GMOs in natural ecosystems. Existing biocontainment methods are insufficient because they impose evolutionary pressure on the organism to eject the safeguard by spontaneous mutagenesis or horizontal gene transfer, or because they can be circumvented by environmentally available compounds. Here we computationally redesign essential enzymes in the first organism possessing an altered genetic code (Escherichia coli strain C321.ΔA) to confer metabolic dependence on non-standard amino acids for survival. The resulting GMOs cannot metabolically bypass their biocontainment mechanisms using known environmental compounds, and they exhibit unprecedented resistance to evolutionary escape through mutagenesis and horizontal gene transfer. This work provides a foundation for safer GMOs that are isolated from natural ecosystems by a reliance on synthetic metabolites.}, }
@article {pmid25607356, year = {2015}, author = {Rovner, AJ and Haimovich, AD and Katz, SR and Li, Z and Grome, MW and Gassaway, BM and Amiram, M and Patel, JR and Gallagher, RR and Rinehart, J and Isaacs, FJ}, title = {Recoded organisms engineered to depend on synthetic amino acids.}, journal = {Nature}, volume = {518}, number = {7537}, pages = {89-93}, pmid = {25607356}, issn = {1476-4687}, support = {K01 DK089006/DK/NIDDK NIH HHS/United States ; T32 GM007205/GM/NIGMS NIH HHS/United States ; T32GM07205/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acids/*chemical synthesis/chemistry/metabolism/*pharmacology ; Amino Acyl-tRNA Synthetases/genetics/metabolism ; Catalytic Domain/genetics ; Codon/genetics ; Containment of Biohazards/*methods ; Culture Media/chemistry/pharmacology ; Environment ; Escherichia coli/cytology/*drug effects/*genetics/metabolism ; Escherichia coli Proteins/biosynthesis/chemistry/genetics/metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genes, Essential/genetics ; Genetic Code/genetics ; Genetic Engineering/methods ; Genome, Bacterial/genetics ; Microbial Viability/*drug effects/genetics ; Molecular Sequence Data ; Organisms, Genetically Modified/genetics/growth &amp; development/metabolism ; Peptide Termination Factors/genetics ; Phenylalanine/chemistry/metabolism ; Protein Multimerization/genetics ; RNA, Transfer/genetics ; Synthetic Biology/*methods ; }, abstract = {Genetically modified organisms (GMOs) are increasingly used in research and industrial systems to produce high-value pharmaceuticals, fuels and chemicals. Genetic isolation and intrinsic biocontainment would provide essential biosafety measures to secure these closed systems and enable safe applications of GMOs in open systems, which include bioremediation and probiotics. Although safeguards have been designed to control cell growth by essential gene regulation, inducible toxin switches and engineered auxotrophies, these approaches are compromised by cross-feeding of essential metabolites, leaked expression of essential genes, or genetic mutations. Here we describe the construction of a series of genomically recoded organisms (GROs) whose growth is restricted by the expression of multiple essential genes that depend on exogenously supplied synthetic amino acids (sAAs). We introduced a Methanocaldococcus jannaschii tRNA:aminoacyl-tRNA synthetase pair into the chromosome of a GRO derived from Escherichia coli that lacks all TAG codons and release factor 1, endowing this organism with the orthogonal translational components to convert TAG into a dedicated sense codon for sAAs. Using multiplex automated genome engineering, we introduced in-frame TAG codons into 22 essential genes, linking their expression to the incorporation of synthetic phenylalanine-derived amino acids. Of the 60 sAA-dependent variants isolated, a notable strain harbouring three TAG codons in conserved functional residues of MurG, DnaA and SerS and containing targeted tRNA deletions maintained robust growth and exhibited undetectable escape frequencies upon culturing ∼10(11) cells on solid media for 7 days or in liquid media for 20 days. This is a significant improvement over existing biocontainment approaches. We constructed synthetic auxotrophs dependent on sAAs that were not rescued by cross-feeding in environmental growth assays. These auxotrophic GROs possess alternative genetic codes that impart genetic isolation by impeding horizontal gene transfer and now depend on the use of synthetic biochemical building blocks, advancing orthogonal barriers between engineered organisms and the environment.}, }
@article {pmid25606350, year = {2014}, author = {Fernández-López, C and Bravo, A and Ruiz-Cruz, S and Solano-Collado, V and Garsin, DA and Lorenzo-Díaz, F and Espinosa, M}, title = {Mobilizable Rolling-Circle Replicating Plasmids from Gram-Positive Bacteria: A Low-Cost Conjugative Transfer.}, journal = {Microbiology spectrum}, volume = {2}, number = {5}, pages = {8}, pmid = {25606350}, issn = {2165-0497}, support = {R01 AI076406/AI/NIAID NIH HHS/United States ; R56 AI093699/AI/NIAID NIH HHS/United States ; R56 AI110432/AI/NIAID NIH HHS/United States ; }, abstract = {Conjugation is a key mechanism for horizontal gene transfer in bacteria. Some plasmids are not self-transmissible but can be mobilized by functions encoded in trans provided by other auxiliary conjugative elements. Although the transfer efficiency of mobilizable plasmids is usually lower than that of conjugative elements, mobilizable plasmidsare more frequently found in nature. In this sense, replication and mobilization can be considered as important mechanisms influencing plasmid promiscuity. Here we review the present available information on two families of small mobilizable plasmids from Gram-positive bacteria that replicate via the rolling-circle mechanism. One of these families, represented by the streptococcal plasmid pMV158, is an interesting model since it contains a specific mobilization module (MOBV) that is widely distributed among mobilizable plasmids. We discuss a mechanism in which the promiscuity of the pMV158 replicon is based on the presence of two origins of lagging strand synthesis. The current strategies to assess plasmid transfer efficiency as well as to inhibit conjugative plasmid transfer are presented. Some applications of these plasmids as biotechnological tools are also reviewed.}, }
@article {pmid25605357, year = {2015}, author = {Liu, LL and Ji, SJ and Ruan, Z and Fu, Y and Fu, YQ and Wang, YF and Yu, YS}, title = {Dissemination of blaOXA-23 in Acinetobacter spp. in China: main roles of conjugative plasmid pAZJ221 and transposon Tn2009.}, journal = {Antimicrobial agents and chemotherapy}, volume = {59}, number = {4}, pages = {1998-2005}, pmid = {25605357}, issn = {1098-6596}, mesh = {Acinetobacter/*drug effects/*genetics ; Acinetobacter Infections/microbiology ; Bacterial Proteins/*genetics ; China ; Chromosomes, Bacterial/genetics ; Conjugation, Genetic/*genetics ; DNA Transposable Elements/*genetics ; DNA, Bacterial/genetics ; Humans ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Plasmids/*genetics ; beta-Lactamases/*genetics ; }, abstract = {Production of the OXA-23 carbapenemase is the most common reason for the increasing carbapenem resistance in Acinetobacter spp. This study was conducted to reveal the genetic basis of blaOXA-23 dissemination in Acinetobacter spp. in China. A total of 63 carbapenem-resistant OXA-23-producing Acinetobacter sp. isolates, representing different backgrounds, were selected from 28 hospitals in 18 provinces for this study. Generally, two patterns of plasmids carrying blaOXA-23 were detected according to S1-nuclease pulsed-field gel electrophoresis and Southern blot hybridization. A ca. 78-kb plasmid, designated pAZJ221, was found in 23 Acinetobacter baumannii and three Acinetobacter nosocomialis isolates, while a novel ca. 50-kb plasmid was carried by only two other A. baumannii isolates. Three of these isolates had an additional copy of blaOXA-23 on the chromosome. Transformation of the two plasmids succeeded, but only pAZJ221 was conjugative. Plasmid pAZJ221 was sequenced completely and found to carry no previously known resistance genes except blaOXA-23. The blaOXA-23 gene of the remaining 35 isolates was chromosome borne. The blaOXA-23 genetic environments were correlated with Tn2009 in 57 isolates, Tn2008 in 5 isolates, and Tn2006 in 1 isolate. The MIC values for the carbapenems with these isolates were not significantly associated with the genomic locations or the copy numbers of blaOXA-23. Overall, these observations suggest that the plasmid pAZJ221 and Tn2009 have effectively contributed to the wide dissemination of blaOXA-23 in Acinetobacter spp. in China and that horizontal gene transfer may play an important role in dissemination of the blaOXA-23 gene.}, }
@article {pmid25604946, year = {2015}, author = {Wang, B and Climent, J and Wang, XR}, title = {Horizontal gene transfer from a flowering plant to the insular pine Pinus canariensis (Chr. Sm. Ex DC in Buch).}, journal = {Heredity}, volume = {114}, number = {4}, pages = {413-418}, pmid = {25604946}, issn = {1365-2540}, mesh = {Bayes Theorem ; *Biological Evolution ; DNA, Chloroplast/genetics ; DNA, Plant/genetics ; *Gene Transfer, Horizontal ; *Genome, Mitochondrial ; Genome, Plant ; Likelihood Functions ; Magnoliopsida/*genetics ; Markov Chains ; Molecular Sequence Data ; Monte Carlo Method ; *Phylogeny ; Pinus/*genetics ; Sequence Analysis, DNA ; }, abstract = {Horizontal gene transfer (HGT) is viewed as very common in the plant mitochondrial (mt) genome, but, to date, only one case of HGT has been found in gymnosperms. Here we report a new case of HGT, in which a mt nad5-1 fragment was transferred from an angiosperm to Pinus canariensis. Quantitative assay and sequence analyses showed that the foreign nad5-1 is located in the mt genome of P. canariensis and is nonfunctional. An extensive survey in the genus Pinus revealed that the angiosperm-derived nad5-1 is restricted to P. canariensis and present across the species' range. Molecular dating based on chloroplast DNA suggested that the HGT event occurred in the late Miocene after P. canariensis split from its closest relatives, and that the foreign copy became fixed in P. canariensis owing to drift during its colonization of the Canary Islands. The mechanism of this HGT is unclear but it was probably achieved through either direct cell-cell contact or external vectors. Our discovery provides evidence for an important role of HGT in plant mt genome evolution.}, }
@article {pmid25604860, year = {2015}, author = {Goldsmith, CE and Hara, Y and Sato, T and Nakajima, T and Nakanishi, S and Mason, C and Moore, JE and Matsuda, M and Coulter, WA}, title = {Comparison of antibiotic susceptibility in viridans group streptococci in low and high antibiotic-prescribing General Practices.}, journal = {Journal of clinical pharmacy and therapeutics}, volume = {40}, number = {2}, pages = {204-207}, doi = {10.1111/jcpt.12245}, pmid = {25604860}, issn = {1365-2710}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Anti-Bacterial Agents/*pharmacology/*therapeutic use ; Child ; Child, Preschool ; *Drug Resistance, Bacterial ; Female ; Fluoroquinolones/pharmacology ; General Practice/*statistics &amp; numerical data ; Humans ; Infant ; Infant, Newborn ; Macrolides/pharmacology ; Male ; Microbial Sensitivity Tests ; Middle Aged ; Practice Patterns, Physicians' ; Streptococcal Infections/*drug therapy ; Tetracyclines/pharmacology ; *Viridans Streptococci ; Young Adult ; beta-Lactams/pharmacology ; }, abstract = {WHAT IS KNOWN AND OBJECTIVE: Antibiotic resistance has become a global public health issue. Most antibiotics are prescribed in the community, although there is less stewardship of such agents in the community compared to secondary and tertiary care. Few studies have attempted to examine the prescribing practices in General Practice and its impact on antibiotic resistance and, therefore, a study was performed in order to compare antibiotic susceptibilities of commensal viridans group streptococci (VGS) obtained from patient cohorts in General Practices (GP), who were high and low prescribers of oral antibiotics.<br><br>METHOD: Sixty-five patients (<1 month-81 years; 77% female: 23% male) were enrolled onto the study, and viridans group streptococci (n = 5/patient) were collected from each patient's nasal passages and oropharynx region and tested for antibiotic susceptibility against (i) tetracyclines (doxycycline); (ii) macrolides (erythromycin); (iii) &#x3b2;-lactams (penicillin G); and (iv) fluoroquinolones (ofloxacin &amp; levofloxacin).<br><br>RESULTS AND DISCUSSION: There were no significant differences in MICs between high and low GP prescribers with doxycycline (P = 0&#xb7;094), erythromycin (P = 0&#xb7;122), ofloxacin (P = 0&#xb7;193) and levofloxacin (P = 0&#xb7;058). However, there was a significant difference between high and low GP practices with regard to penicillin G (P = 0&#xb7;031). This finding is important as the &#x3b2;-lactams are the most commonly prescribed oral antibiotic in the community.<br><br>WHAT IS NEW AND CONCLUSION: This study demonstrates that high prescribing practices may lead to an altered (higher) level of resistance to these agents in the commensal VGS population, which may be important as reservoirs of antibiotic resistance determinants in subsequent horizontal gene transfer events, particularly with newly colonizing pathogens, including pneumococci. Primary care physicians should be aware that increased prescribing of antibiotics may led to increased level of penicillin resistance.}, }
@article {pmid25601290, year = {2015}, author = {Méheust, R and Lopez, P and Bapteste, E}, title = {Metabolic bacterial genes and the construction of high-level composite lineages of life.}, journal = {Trends in ecology &amp; evolution}, volume = {30}, number = {3}, pages = {127-129}, pmid = {25601290}, issn = {1872-8383}, mesh = {Archaea/*classification/*genetics ; Bacteria/*genetics ; Euryarchaeota/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genes, Archaeal/*genetics ; Genes, Bacterial/*genetics ; }, abstract = {Understanding how major organismal lineages originated is fundamental for understanding processes by which life evolved. Major evolutionary transitions, like eukaryogenesis, merging genetic material from distantly related organisms, are rare events, hence difficult ones to explain causally. If most archaeal lineages emerged after massive acquisitions of bacterial genes, a rule however arises: metabolic bacterial genes contributed to all major evolutionary transitions.}, }
@article {pmid25601101, year = {2015}, author = {Raghavan, R and Kacharia, FR and Millar, JA and Sislak, CD and Ochman, H}, title = {Genome rearrangements can make and break small RNA genes.}, journal = {Genome biology and evolution}, volume = {7}, number = {2}, pages = {557-566}, pmid = {25601101}, issn = {1759-6653}, support = {R01 GM074738/GM/NIGMS NIH HHS/United States ; R01 GM108657/GM/NIGMS NIH HHS/United States ; GM74738/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Sequence ; Biofilms ; DNA, Intergenic/genetics ; Escherichia coli/*genetics/physiology ; Escherichia coli Proteins/metabolism ; Evolution, Molecular ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; Gene Rearrangement/*genetics ; Gene Transfer, Horizontal/genetics ; *Genes, Bacterial ; Molecular Sequence Data ; Promoter Regions, Genetic/genetics ; RNA, Bacterial/*genetics ; Salmonella enterica/*genetics/pathogenicity ; Species Specificity ; Synteny/genetics ; }, abstract = {Small RNAs (sRNAs) are short, transcribed regulatory elements that are typically encoded in the intergenic regions (IGRs) of bacterial genomes. Several sRNAs, first recognized in Escherichia coli, are conserved among enteric bacteria, but because of the regulatory roles of sRNAs, differences in sRNA repertoires might be responsible for features that differentiate closely related species. We scanned the E. coli MG1655 and Salmonella enterica Typhimurium genomes for nonsyntenic IGRs as a potential source of uncharacterized, species-specific sRNAs and found that genome rearrangements have reconfigured several IGRs causing the disruption and formation of sRNAs. Within an IGR that is present in E. coli but was disrupted in Salmonella by a translocation event is an sRNA that is associated with the FNR/CRP global regulators and influences E. coli biofilm formation. A Salmonella-specific sRNA evolved de novo through point mutations that generated a σ(70) promoter sequence in an IGR that arose through genome rearrangement events. The differences in the sRNA pools among bacterial species have previously been ascribed to duplication, deletion, or horizontal acquisition. Here, we show that genomic rearrangements also contribute to this process by either disrupting sRNA-containing IGRs or creating IGRs in which novel sRNAs may evolve.}, }
@article {pmid25599642, year = {2015}, author = {Piepenbrink, KH and Maldarelli, GA and Martinez de la Peña, CF and Dingle, TC and Mulvey, GL and Lee, A and von Rosenvinge, E and Armstrong, GD and Donnenberg, MS and Sundberg, EJ}, title = {Structural and evolutionary analyses show unique stabilization strategies in the type IV pili of Clostridium difficile.}, journal = {Structure (London, England : 1993)}, volume = {23}, number = {2}, pages = {385-396}, pmid = {25599642}, issn = {1878-4186}, support = {F30 DK105539/DK/NIDDK NIH HHS/United States ; F32 AI110045/AI/NIAID NIH HHS/United States ; R21 AI105881/AI/NIAID NIH HHS/United States ; F32AI 110045/AI/NIAID NIH HHS/United States ; R01 AI114902/AI/NIAID NIH HHS/United States ; T32 AI095190/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Clostridioides difficile/*chemistry ; *Evolution, Molecular ; Fimbriae, Bacterial/*chemistry/metabolism/ultrastructure ; Immunohistochemistry ; Microscopy, Electron ; *Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Sequence Alignment ; Species Specificity ; }, abstract = {Type IV pili are produced by many pathogenic Gram-negative bacteria and are important for processes as diverse as twitching motility, biofilm formation, cellular adhesion, and horizontal gene transfer. However, many Gram-positive species, including Clostridium difficile, also produce type IV pili. Here, we identify the major subunit of the type IV pili of C. difficile, PilA1, and describe multiple 3D structures of PilA1, demonstrating the diversity found in three strains of C. difficile. We also model the incorporation of both PilA1 and a minor pilin, PilJ, into the pilus fiber. Although PilA1 contains no cysteine residues, and therefore cannot form the disulfide bonds found in all Gram-negative type IV pilins, it adopts unique strategies to achieve a typical pilin fold. The structures of PilA1 and PilJ exhibit similarities with the type IVb pilins from Gram-negative bacteria that suggest that the type IV pili of C. difficile are involved in microcolony formation.}, }
@article {pmid25599586, year = {2015}, author = {Weetman, D and Clarkson, CS}, title = {Evolving the world's most dangerous animal.}, journal = {Trends in parasitology}, volume = {31}, number = {2}, pages = {39-40}, doi = {10.1016/j.pt.2015.01.001}, pmid = {25599586}, issn = {1471-5007}, mesh = {Adaptation, Physiological/genetics ; Animals ; Anopheles/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genome, Insect/*genetics ; Insect Vectors/genetics ; }, abstract = {The devastating consequences of malaria are well known but many mysteries remain about its key protagonists, a handful of Anopheles species. New work provides a framework for solving such puzzles, by generation and analysis of whole genome assemblies for 16 Anopheles species, with genomic flexibility a key emergent theme.}, }
@article {pmid25597519, year = {2015}, author = {Brown-Jaque, M and Calero-Cáceres, W and Muniesa, M}, title = {Transfer of antibiotic-resistance genes via phage-related mobile elements.}, journal = {Plasmid}, volume = {79}, number = {}, pages = {1-7}, doi = {10.1016/j.plasmid.2015.01.001}, pmid = {25597519}, issn = {1095-9890}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/*drug effects ; Bacteriophages/*genetics ; Drug Resistance, Bacterial/*genetics ; *Environmental Microbiology ; *Gene Transfer, Horizontal ; Interspersed Repetitive Sequences/*genetics ; }, abstract = {Antibiotic resistance is a major concern for society because it threatens the effective prevention of infectious diseases. While some bacterial strains display intrinsic resistance, others achieve antibiotic resistance by mutation, by the recombination of foreign DNA into the chromosome or by horizontal gene acquisition. In many cases, these three mechanisms operate together. Several mobile genetic elements (MGEs) have been reported to mobilize different types of resistance genes and despite sharing common features, they are often considered and studied separately. Bacteriophages and phage-related particles have recently been highlighted as MGEs that transfer antibiotic resistance. This review focuses on phages, phage-related elements and on composite MGEs (phages-MGEs) involved in antibiotic resistance mobility. We review common features of these elements, rather than differences, and provide a broad overview of the antibiotic resistance transfer mechanisms observed in nature, which is a necessary first step to controlling them.}, }
@article {pmid25595742, year = {2015}, author = {Lukac, PJ and Bonomo, RA and Logan, LK}, title = {Extended-spectrum β-lactamase-producing Enterobacteriaceae in children: old foe, emerging threat.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {60}, number = {9}, pages = {1389-1397}, pmid = {25595742}, issn = {1537-6591}, support = {R01 AI100560/AI/NIAID NIH HHS/United States ; R01AI100560/AI/NIAID NIH HHS/United States ; R01 AI072219/AI/NIAID NIH HHS/United States ; R01 AI063517/AI/NIAID NIH HHS/United States ; K08 AI112506/AI/NIAID NIH HHS/United States ; R01AI063517/AI/NIAID NIH HHS/United States ; R01AI072219/AI/NIAID NIH HHS/United States ; 1K08AI112506-01/AI/NIAID NIH HHS/United States ; }, mesh = {Adult ; Anti-Bacterial Agents/therapeutic use ; Child ; Child, Preschool ; Drug Resistance, Multiple, Bacterial ; Enterobacteriaceae/drug effects/*enzymology/genetics/*pathogenicity ; Enterobacteriaceae Infections/drug therapy/*epidemiology/microbiology ; Humans ; Infection Control ; Microbial Sensitivity Tests ; Risk Factors ; beta-Lactamases/*biosynthesis/genetics ; }, abstract = {Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae present an ever-growing burden in the hospital and community settings, across all ages and demographics. Infections due to ESBL-containing pathogens continue to be associated with significant morbidity and mortality worldwide. With widespread empiric broad-spectrum β-lactam use creating selective pressure, and the resultant emergence of stable, rapidly proliferating ESBL-producing clones with continued horizontal gene transfer across genera, addressing this issue remains imperative. Although well characterized in adults, the epidemiology, risk factors, outcomes, therapies, and control measures for ESBL-producing bacteria are less appreciated in children. This analysis provides a brief summary of ESBL-producing Enterobacteriaceae in children, with a focus on recent clinical and molecular data regarding colonization and infection in nonoutbreak settings.}, }
@article {pmid25592263, year = {2015}, author = {Thoma, L and Muth, G}, title = {The conjugative DNA-transfer apparatus of Streptomyces.}, journal = {International journal of medical microbiology : IJMM}, volume = {305}, number = {2}, pages = {224-229}, doi = {10.1016/j.ijmm.2014.12.020}, pmid = {25592263}, issn = {1618-0607}, mesh = {Bacterial Proteins/genetics/*metabolism ; Biological Transport ; *Conjugation, Genetic ; DNA, Bacterial/*metabolism ; DNA-Binding Proteins/genetics/metabolism ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Plasmids ; Protein Multimerization ; Streptomyces/*genetics/*metabolism ; }, abstract = {Conjugation is a major route of horizontal gene transfer, an important driving force in the evolution of bacterial genomes. Since antibiotic producing streptomycetes represent a natural reservoir of antibiotic resistance genes, the Streptomyces conjugation system might have a particular role in the dissemination of the resistance genes. Streptomycetes transfer DNA in a unique process, clearly distinguished from the well-known DNA-transfer by type IV secretion systems. A single plasmid-encoded DNA-translocase, TraB, transfers a double-stranded DNA-molecule to the recipient. Elucidation of the structure, pore forming ability and DNA binding characteristics of TraB indicated that the TraB conjugation system is derived from an FtsK-like ancestor protein suggesting that Streptomyces adapted the FtsK/SpoIIIE chromosome segregation system to transfer DNA between two distinct Streptomyces cells. Following the primary transfer, a multi-protein DNA-translocation apparatus consisting of TraB and several Spd-proteins spreads the newly transferred DNA to the neighbouring mycelial compartments resulting in the rapid colonization of the recipient mycelium by the donor DNA.}, }
@article {pmid25589577, year = {2015}, author = {Kumar, N and Lad, G and Giuntini, E and Kaye, ME and Udomwong, P and Shamsani, NJ and Young, JP and Bailly, X}, title = {Bacterial genospecies that are not ecologically coherent: population genomics of Rhizobium leguminosarum.}, journal = {Open biology}, volume = {5}, number = {1}, pages = {140133}, pmid = {25589577}, issn = {2046-2441}, mesh = {*Ecosystem ; *Genetic Speciation ; *Genome, Bacterial ; Phylogeny ; Rhizobium leguminosarum/classification/*genetics ; }, abstract = {Biological species may remain distinct because of genetic isolation or ecological adaptation, but these two aspects do not always coincide. To establish the nature of the species boundary within a local bacterial population, we characterized a sympatric population of the bacterium Rhizobium leguminosarum by genomic sequencing of 72 isolates. Although all strains have 16S rRNA typical of R. leguminosarum, they fall into five genospecies by the criterion of average nucleotide identity (ANI). Many genes, on plasmids as well as the chromosome, support this division: recombination of core genes has been largely within genospecies. Nevertheless, variation in ecological properties, including symbiotic host range and carbon-source utilization, cuts across these genospecies, so that none of these phenotypes is diagnostic of genospecies. This phenotypic variation is conferred by mobile genes. The genospecies meet the Mayr criteria for biological species in respect of their core genes, but do not correspond to coherent ecological groups, so periodic selection may not be effective in purging variation within them. The population structure is incompatible with traditional 'polyphasic taxonomy' that requires bacterial species to have both phylogenetic coherence and distinctive phenotypes. More generally, genomics has revealed that many bacterial species share adaptive modules by horizontal gene transfer, and we envisage a more consistent taxonomic framework that explicitly recognizes this. Significant phenotypes should be recognized as 'biovars' within species that are defined by core gene phylogeny.}, }
@article {pmid25587991, year = {2015}, author = {Lara, E and Holmfeldt, K and Solonenko, N and Sà, EL and Ignacio-Espinoza, JC and Cornejo-Castillo, FM and Verberkmoes, NC and Vaqué, D and Sullivan, MB and Acinas, SG}, title = {Life-style and genome structure of marine Pseudoalteromonas siphovirus B8b isolated from the northwestern Mediterranean Sea.}, journal = {PloS one}, volume = {10}, number = {1}, pages = {e0114829}, pmid = {25587991}, issn = {1932-6203}, mesh = {Bacteriophages/genetics/*isolation &amp; purification ; DNA, Viral/genetics ; *Genome, Viral ; Mediterranean Sea ; *Metagenome ; Phylogeny ; Pseudoalteromonas/genetics/*isolation &amp; purification ; Seawater/microbiology ; }, abstract = {Marine viruses (phages) alter bacterial diversity and evolution with impacts on marine biogeochemical cycles, and yet few well-developed model systems limit opportunities for hypothesis testing. Here we isolate phage B8b from the Mediterranean Sea using Pseudoalteromonas sp. QC-44 as a host and characterize it using myriad techniques. Morphologically, phage B8b was classified as a member of the Siphoviridae family. One-step growth analyses showed that this siphovirus had a latent period of 70 min and released 172 new viral particles per cell. Host range analysis against 89 bacterial host strains revealed that phage B8b infected 3 Pseudoalteromonas strains (52 tested, >99.9% 16S rRNA gene nucleotide identity) and 1 non-Pseudoaltermonas strain belonging to Alteromonas sp. (37 strains from 6 genera tested), which helps bound the phylogenetic distance possible in a phage-mediated horizontal gene transfer event. The Pseudoalteromonas phage B8b genome size was 42.7 kb, with clear structural and replication modules where the former were delineated leveraging identification of 16 structural genes by virion structural proteomics, only 4 of which had any similarity to known structural proteins. In nature, this phage was common in coastal marine environments in both photic and aphotic layers (found in 26.5% of available viral metagenomes), but not abundant in any sample (average per sample abundance was 0.65% of the reads). Together these data improve our understanding of siphoviruses in nature, and provide foundational information for a new 'rare virosphere' phage-host model system.}, }
@article {pmid25587774, year = {2015}, author = {Ma, Y and Xie, TT and Hu, Q and Qiu, Z and Song, F}, title = {Sequencing analysis and characterization of the plasmid pBIF10 isolated from Bifidobacterium longum.}, journal = {Canadian journal of microbiology}, volume = {61}, number = {2}, pages = {124-130}, doi = {10.1139/cjm-2014-0581}, pmid = {25587774}, issn = {1480-3275}, mesh = {Anti-Bacterial Agents/chemistry ; Bacterial Proteins/*genetics ; Base Sequence ; Bifidobacterium/*genetics ; Feces ; Gene Transfer, Horizontal ; Genetic Vectors ; Humans ; Molecular Sequence Data ; Open Reading Frames ; Plasmids/*genetics ; Sequence Analysis, DNA ; Tetracycline Resistance/*genetics ; }, abstract = {A resident plasmid, pBIF10, was isolated from Bifidobacterium longum B200304, and the full-length sequence of pBIF10 was analyzed. In this sequence, we identified at least 17 major open reading frames longer than 200 bp. A tetracycline resistance gene, tetQ, was identified and verified to confer antibiotic resistance to tetracycline. The plasmid replicon with replication protein B gene (repB) and a typical iteron was identified in pBIF10. An artificial clone vector was constructed with the replicon of pBIF10; the results showed that repB controlled plasmid replication in other bifidobacteria host cells at low transformation frequency. Taken together, the analysis and characterization of pBIF10 provided necessary information for the understanding of antibiotic resistance mediated by a plasmid in a Bifidobacterium strain. GC% and repB sequence analyses indicated that pBIF10 was a molecular hybrid of at least 2 other bacterial genera plasmids.}, }
@article {pmid25587356, year = {2014}, author = {Meinel, DM and Margos, G and Konrad, R and Krebs, S and Blum, H and Sing, A}, title = {Next generation sequencing analysis of nine Corynebacterium ulcerans isolates reveals zoonotic transmission and a novel putative diphtheria toxin-encoding pathogenicity island.}, journal = {Genome medicine}, volume = {6}, number = {11}, pages = {113}, pmid = {25587356}, issn = {1756-994X}, abstract = {BACKGROUND: Toxigenic Corynebacterium ulcerans can cause a diphtheria-like illness in humans and have been found in domestic animals, which were suspected to serve as reservoirs for a zoonotic transmission. Additionally, toxigenic C. ulcerans were reported to take over the leading role in causing diphtheria in the last years in many industrialized countries.<br><br>METHODS: To gain deeper insights into the tox gene locus and to understand the transmission pathway in detail, we analyzed nine isolates derived from human patients and their domestic animals applying next generation sequencing and comparative genomics.<br><br>RESULTS: We provide molecular evidence for zoonotic transmission of C. ulcerans in four cases and demonstrate the superior resolution of next generation sequencing compared to multi-locus sequence typing for epidemiologic research. Additionally, we provide evidence that the virulence of C. ulcerans can change rapidly by acquisition of novel virulence genes. This mechanism is exemplified by an isolate which acquired a prophage not present in the corresponding isolate from the domestic animal. This prophage contains a putative novel virulence factor, which shares high identity with the RhuM virulence factor from Salmonella enterica but which is unknown in Corynebacteria so far. Furthermore, we identified a putative pathogenicity island for C. ulcerans bearing a diphtheria toxin gene.<br><br>CONCLUSION: The novel putative diphtheria toxin pathogenicity island could provide a new and alternative pathway for Corynebacteria to acquire a functional diphtheria toxin-encoding gene by horizontal gene transfer, distinct from the previously well characterized phage infection model. The novel transmission pathway might explain the unexpectedly high number of toxigenic C. ulcerans.}, }
@article {pmid25587016, year = {2015}, author = {Pombert, JF and Haag, KL and Beidas, S and Ebert, D and Keeling, PJ}, title = {The Ordospora colligata genome: Evolution of extreme reduction in microsporidia and host-to-parasite horizontal gene transfer.}, journal = {mBio}, volume = {6}, number = {1}, pages = {}, pmid = {25587016}, issn = {2150-7511}, support = {MOP-42517//Canadian Institutes of Health Research/Canada ; }, mesh = {Animals ; Daphnia/*genetics/*microbiology ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Fungal ; Host-Parasite Interactions ; Microsporidia/classification/*genetics/physiology ; Phylogeny ; }, abstract = {UNLABELLED: Microsporidia are a group of obligate intracellular parasites that are best known for their unique infection mechanism and their unparalleled levels of genomic reduction and compaction. We sequenced the genome of Ordospora colligata, a gut parasite of the microcrustacean Daphnia sp. and the closest known relative to the microsporidia characterized by the most extreme genomic reduction, the model genus Encephalitozoon. We found that the O. colligata genome is as compact as those of Encephalitozoon spp., featuring few introns and a similar complement of about 2,000 genes, altogether showing that the extreme reduction took place before the origin of Encephalitozoon spp. and their adaptation to vertebrate hosts. We also found that the O. colligata genome has acquired by horizontal transfer from its animal host a septin that is structurally analogous to septin 7, a protein that plays a major role in the endocytosis-based invasion mechanism of the fungal pathogen Candida albicans. Microsporidian invasion is most often characterized by injection through a projectile tube, but microsporidia are also known to invade cells by inducing endocytosis. Given the function of septins in other systems, we hypothesize that the acquired septin could help O. colligata induce its uptake by mimicking host receptors.<br><br>IMPORTANCE: The smallest known eukaryotic genomes are found in members of the Encephalitozoon genus of microsporidian parasites. Their extreme compaction, however, is not characteristic of the group, whose genomes can differ by an order of magnitude. The processes and evolutionary forces that led the Encephalitozoon genomes to shed so much of their ancestral baggage are unclear. We sequenced the genome of Ordospora colligata, a parasite of the water flea Daphnia sp. and the closest known relative of Encephalitozoon species, and show that this extreme reduction predated the split between the two lineages. We also found that O. colligata has acquired a septin gene by host-to-parasite horizontal transfer and predicted that the encoded protein folds like a septin 7, which plays a major role in endocytosis. We hypothesize that this acquisition could help O. colligata parasitize its hosts by facilitating endocytic infection, a mechanism that occurs in microsporidia but that is not yet well understood.}, }
@article {pmid25586509, year = {2015}, author = {Nasfi, H and Travers, MA and de Lorgeril, J and Habib, C and Sannie, T and Sorieul, L and Gerard, J and Avarre, JC and Haffner, P and Tourbiez, D and Renault, T and Furones, D and Roque, A and Pruzzo, C and Cheslett, D and Gdoura, R and Vallaeys, T}, title = {A European epidemiological survey of Vibrio splendidus clade shows unexplored diversity and massive exchange of virulence factors.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {31}, number = {3}, pages = {461-475}, pmid = {25586509}, issn = {1573-0972}, mesh = {Animals ; Aquatic Organisms/*microbiology ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Europe ; *Genetic Variation ; Genotype ; Minisatellite Repeats ; *Molecular Typing ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Seafood/*microbiology ; Seawater/microbiology ; Vibrio/classification/*genetics/*isolation &amp; purification ; Virulence Factors/*genetics ; }, abstract = {The Vibrio splendidus clade has previously been associated with epidemic outbreaks of various aquatic animals, as in the case of the cupped oyster, Crassostrea gigas. To investigate whether involved strains could present a clonal origin and to identify possible alternative background carriage animals or zooplankton, a large epidemiological survey was conducted on isolates of the splendidus clade. For this purpose, Vibrio strains were isolated from various samples including oysters, mussels, sediments, zooplankton, and sea water on the basis of a North/South gradient of the European sea water zone (Ireland, The Netherlands, France, Italy, and Spain). A total of 435 isolates were successfully associated to the V. splendidus clade using real time polymerase chain reaction with 16S specific primers and probes. A multiple-locus variable-number tandem-repeat analysis (VNTR) was conducted on all isolates based on a multiplex PCR-VNTR with a set of primer pairs designed from the V. tasmaniensis LGP32 genome. Preliminary validation of the primers on a set of collection strains from the V. splendidus clade confirmed that the former V. splendidus-related LGP32 and relative strains were related to V. tasmaniensis rather than to the type strain V. splendidus LMG 4042. The VNTR analysis was then successfully conducted on 335 isolates which led to the characterization of 87 different profiles. Our results showed that (1) the high diversity of VNTR did not enlighten significant correlation between a specific pattern and the origin of collected samples. However, populations isolated from animal samples tend to differ from those of the background environment; (2) oyster mortality events could not be linked to the clonal proliferation of a particular VNTR type. However, few different patterns seemed successively associated with samples collected during peaks of oyster's mortality. (3) Finally, no correlation could be seen between specific VNTR patterns and sequence phylogeny of the virulence factors vsm and ompU that were detected among strains isolated during as well as outside mortality events. These results, combined with incongruence observed between the ompU and vsm phylogenetic trees, suggested both large diffusion of strains and massive lateral gene transfer within the V. splendidus clade.}, }
@article {pmid25585805, year = {2014}, author = {Sengupta, S and Aggarwal, N and Bandhu, AV}, title = {Two perspectives on the origin of the standard genetic code.}, journal = {Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life}, volume = {44}, number = {4}, pages = {287-291}, pmid = {25585805}, issn = {1573-0875}, mesh = {Amino Acids/chemistry/metabolism ; Amino Acyl-tRNA Synthetases/*chemistry/metabolism ; Codon/*chemistry/metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genes ; *Genetic Code ; Models, Genetic ; *Origin of Life ; Probability ; Protein Biosynthesis ; RNA, Messenger/*chemistry/metabolism ; RNA, Transfer, Amino Acid-Specific/*chemistry/metabolism ; Selection, Genetic ; }, abstract = {The origin of a genetic code made it possible to create ordered sequences of amino acids. In this article we provide two perspectives on code origin by carrying out simulations of code-sequence coevolution in finite populations with the aim of examining how the standard genetic code may have evolved from more primitive code(s) encoding a small number of amino acids. We determine the efficacy of the physico-chemical hypothesis of code origin in the absence and presence of horizontal gene transfer (HGT) by allowing a diverse collection of code-sequence sets to compete with each other. We find that in the absence of horizontal gene transfer, natural selection between competing codes distinguished by differences in the degree of physico-chemical optimization is unable to explain the structure of the standard genetic code. However, for certain probabilities of the horizontal transfer events, a universal code emerges having a structure that is consistent with the standard genetic code.}, }
@article {pmid25584532, year = {2015}, author = {Papadimitriou, K and Anastasiou, R and Maistrou, E and Plakas, T and Papandreou, NC and Hamodrakas, SJ and Ferreira, S and Supply, P and Renault, P and Pot, B and Tsakalidou, E}, title = {Acquisition through horizontal gene transfer of plasmid pSMA198 by Streptococcus macedonicus ACA-DC 198 points towards the dairy origin of the species.}, journal = {PloS one}, volume = {10}, number = {1}, pages = {e0116337}, pmid = {25584532}, issn = {1932-6203}, mesh = {Animals ; Cattle ; Food Microbiology ; *Gene Transfer, Horizontal ; Lactococcus lactis/genetics/*isolation &amp; purification ; Milk/*microbiology ; Plasmids/*genetics ; Streptococcus/genetics/*isolation &amp; purification ; }, abstract = {BACKGROUND: Streptococcus macedonicus is an intriguing streptococcal species whose most frequent source of isolation is fermented foods similarly to Streptococcus thermophilus. However, S. macedonicus is closely related to commensal opportunistic pathogens of the Streptococcus bovis/Streptococcus equinus complex.<br><br>We analyzed the pSMA198 plasmid isolated from the dairy strain Streptococcus macedonicus ACA-DC 198 in order to provide novel clues about the main ecological niche of this bacterium. pSMA198 belongs to the narrow host range pCI305/pWV02 family found primarily in lactococci and to the best of our knowledge it is the first such plasmid to be reported in streptococci. Comparative analysis of the pSMA198 sequence revealed a high degree of similarity with plasmids isolated from Lactococcus lactis strains deriving from milk or its products. Phylogenetic analysis of the pSMA198 Rep showed that the vast majority of closely related proteins derive from lactococcal dairy isolates. Additionally, cloning of the pSMA198 ori in L. lactis revealed a 100% stability of replication over 100 generations. Both pSMA198 and the chromosome of S. macedonicus exhibit a high percentage of potential pseudogenes, indicating that they have co-evolved under the same gene decay processes. We identified chromosomal regions in S. macedonicus that may have originated from pSMA198, also supporting a long co-existence of the two replicons. pSMA198 was also found in divergent biotypes of S. macedonicus and in strains isolated from dispersed geographic locations (e.g. Greece and Switzerland) showing that pSMA198's acquisition is not a recent event.<br><br>CONCLUSIONS/SIGNIFICANCE: Here we propose that S. macedonicus acquired plasmid pSMA198 from L. lactis via an ancestral genetic exchange event that took place most probably in milk or dairy products. We provide important evidence that point towards the dairy origin of this species.}, }
@article {pmid25583337, year = {2015}, author = {Cavanagh, D and Fitzgerald, GF and McAuliffe, O}, title = {From field to fermentation: the origins of Lactococcus lactis and its domestication to the dairy environment.}, journal = {Food microbiology}, volume = {47}, number = {}, pages = {45-61}, doi = {10.1016/j.fm.2014.11.001}, pmid = {25583337}, issn = {1095-9998}, mesh = {Animals ; Dairy Products/microbiology ; Environment ; *Fermentation ; Gene Transfer, Horizontal ; Genetic Variation ; Genome, Bacterial ; Genotype ; Lactococcus lactis/classification/genetics/isolation &amp; purification/*physiology ; Milk/*microbiology ; Phenotype ; Phylogeny ; Plants/*microbiology ; }, abstract = {Lactococcus lactis is an organism of substantial economic importance, used extensively in the production of fermented foods and widely held to have evolved from plant strains. The domestication of this organism to the milk environment is associated with genome reduction and gene decay, and the acquisition of specific genes involved in protein and lactose utilisation by horizontal gene transfer. In recent years, numerous studies have focused on uncovering the physiology and molecular biology of lactococcal strains from the wider environment for exploitation in the dairy industry. This in turn has facilitated comparative genome analysis of lactococci from different environments and provided insight into the natural phenotypic and genetic diversity of L. lactis. This diversity may be exploited in dairy fermentations to develop products with improved quality and sensory attributes. In this review, we discuss the classification of L. lactis and the problems that arise with phenotype/genotype designation. We also discuss the adaptation of non-dairy lactococci to milk, the traits associated with this adaptation and the potential application of non-dairy lactococci to dairy fermentations.}, }
@article {pmid25581459, year = {2015}, author = {Briegel, A and Ortega, DR and Huang, AN and Oikonomou, CM and Gunsalus, RP and Jensen, GJ}, title = {Structural conservation of chemotaxis machinery across Archaea and Bacteria.}, journal = {Environmental microbiology reports}, volume = {7}, number = {3}, pages = {414-419}, pmid = {25581459}, issn = {1758-2229}, support = {R01 GM101425/GM/NIGMS NIH HHS/United States ; GM101425/GM/NIGMS NIH HHS/United States ; }, mesh = {Archaea/*genetics/*physiology ; Bacteria/*genetics ; *Bacterial Physiological Phenomena ; *Chemotaxis ; Conserved Sequence ; Evolution, Molecular ; *Gene Regulatory Networks ; }, abstract = {Chemotaxis allows cells to sense and respond to their environment. In Bacteria, stimuli are detected by arrays of chemoreceptors that relay the signal to a two-component regulatory system. These arrays take the form of highly stereotyped super-lattices comprising hexagonally packed trimers-of-receptor-dimers networked by rings of histidine kinase and coupling proteins. This structure is conserved across chemotactic Bacteria, and between membrane-bound and cytoplasmic arrays, and gives rise to the highly cooperative, dynamic nature of the signalling system. The chemotaxis system, absent in eukaryotes, is also found in Archaea, where its structural details remain uncharacterized. Here we provide evidence that the chemotaxis machinery was not present in the last archaeal common ancestor, but rather was introduced in one of the waves of lateral gene transfer that occurred after the branching of Eukaryota but before the diversification of Euryarchaeota. Unlike in Bacteria, the chemotaxis system then evolved largely vertically in Archaea, with very few subsequent successful lateral gene transfer events. By electron cryotomography, we find that the structure of both membrane-bound and cytoplasmic chemoreceptor arrays is conserved between Bacteria and Archaea, suggesting the fundamental importance of this signalling architecture across diverse prokaryotic lifestyles.}, }
@article {pmid25581302, year = {2015}, author = {Pérez-Cruz, C and Delgado, L and López-Iglesias, C and Mercade, E}, title = {Outer-inner membrane vesicles naturally secreted by gram-negative pathogenic bacteria.}, journal = {PloS one}, volume = {10}, number = {1}, pages = {e0116896}, pmid = {25581302}, issn = {1932-6203}, mesh = {Bacterial Outer Membrane Proteins/*metabolism ; Biological Transport/physiology ; Cell Membrane/metabolism ; Cytoplasm/metabolism ; DNA/metabolism ; Gram-Negative Bacteria/*metabolism ; Secretory Vesicles/*metabolism ; Shewanella/metabolism ; }, abstract = {Outer-inner membrane vesicles (O-IMVs) were recently described as a new type of membrane vesicle secreted by the Antarctic bacterium Shewanella vesiculosa M7T. Their formation is characterized by the protrusion of both outer and plasma membranes, which pulls cytoplasmic components into the vesicles. To demonstrate that this is not a singular phenomenon in a bacterium occurring in an extreme environment, the identification of O-IMVs in pathogenic bacteria was undertaken. With this aim, a structural study by Transmission Electron Microscopy (TEM) and Cryo-transmission electron microscopy (Cryo-TEM) was carried out, confirming that O-IMVs are also secreted by Gram-negative pathogenic bacteria such as Neisseria gonorrhoeae, Pseudomonas aeruginosa PAO1 and Acinetobacter baumannii AB41, in which they represent between 0.23% and 1.2% of total vesicles produced. DNA and ATP, which are components solely found in the cell cytoplasm, were identified within membrane vesicles of these strains. The presence of DNA inside the O-IMVs produced by N. gonorrhoeae was confirmed by gold DNA immunolabeling with a specific monoclonal IgM against double-stranded DNA. A proteomic analysis of N. gonorrhoeae-derived membrane vesicles identified proteins from the cytoplasm and plasma membrane. This confirmation of O-IMV extends the hitherto uniform definition of membrane vesicles in Gram-negative bacteria and explains the presence of components in membrane vesicles such as DNA, cytoplasmic and inner membrane proteins, as well as ATP, detected for the first time. The production of these O-IMVs by pathogenic Gram-negative bacteria opens up new areas of study related to their involvement in lateral gene transfer, the transfer of cytoplasmic proteins, as well as the functionality and role of ATP detected in these new vesicles.}, }
@article {pmid25576774, year = {2015}, author = {Mullany, P and Allan, E and Roberts, AP}, title = {Mobile genetic elements in Clostridium difficile and their role in genome function.}, journal = {Research in microbiology}, volume = {166}, number = {4}, pages = {361-367}, pmid = {25576774}, issn = {1769-7123}, support = {G0601176/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adaptation, Biological ; Bacterial Toxins/genetics/metabolism ; Clostridioides difficile/*genetics ; Gene Transfer, Horizontal ; Genome, Bacterial ; *Interspersed Repetitive Sequences ; }, abstract = {Approximately 11% the Clostridium difficile genome is made up of mobile genetic elements which have a profound effect on the biology of the organism. This includes transfer of antibiotic resistance and other factors that allow the organism to survive challenging environments, modulation of toxin gene expression, transfer of the toxin genes themselves and the conversion of non-toxigenic strains to toxin producers. Mobile genetic elements have also been adapted by investigators to probe the biology of the organism and the various ways in which these have been used are reviewed.}, }
@article {pmid25576529, year = {2015}, author = {Jin, W and Wachino, J and Kimura, K and Yamada, K and Arakawa, Y}, title = {New plasmid-mediated aminoglycoside 6'-N-acetyltransferase, AAC(6')-Ian, and ESBL, TLA-3, from a Serratia marcescens clinical isolate.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {70}, number = {5}, pages = {1331-1337}, doi = {10.1093/jac/dku537}, pmid = {25576529}, issn = {1460-2091}, mesh = {Acetyltransferases/*genetics/isolation &amp; purification ; Chromatography, High Pressure Liquid ; Chromatography, Liquid ; Chromatography, Thin Layer ; Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; Gene Transfer, Horizontal ; High-Throughput Nucleotide Sequencing ; Humans ; Plasmids/*analysis ; Sequence Analysis, DNA ; Serratia Infections/*microbiology ; Serratia marcescens/drug effects/*enzymology/isolation &amp; purification ; beta-Lactamases/*genetics/isolation &amp; purification ; }, abstract = {OBJECTIVES: Enterobacteriaceae clinical isolates showing amikacin resistance (MIC 64 to >256 mg/L) in the absence of 16S rRNA methyltransferase (MTase) genes were found. The aim of this study was to clarify the molecular mechanisms underlying amikacin resistance in Enterobacteriaceae clinical isolates that do not produce 16S rRNA MTases.<br><br>METHODS: PCR was performed to detect already-known amikacin resistance determinants. Cloning experiments and sequence analyses were performed to characterize unknown amikacin resistance determinants. Transfer of amikacin resistance determinants was performed by conjugation and transformation. The complete nucleotide sequence of the plasmids was determined by next-generation sequencing technology. Amikacin resistance enzymes were purified with a column chromatography system. The enzymatic function of the purified protein was investigated by thin-layer chromatography (TLC) and HPLC.<br><br>RESULTS: Among the 14 isolates, 9 were found to carry already-known amikacin resistance determinants such as aac(6')-Ia and aac(6')-Ib. Genetic analyses revealed the presence of a new amikacin acetyltransferase gene, named aac(6')-Ian, located on a 169&#x200a;829 bp transferable plasmid (p11663) of the Serratia marcescens strain NUBL-11663, one of the five strains negative for known aac(6') genes by PCR. Plasmid p11663 also carried a novel ESBL gene, named blaTLA-3. HPLC and TLC analyses demonstrated that AAC(6')-Ian catalysed the transfer of an acetyl group from acetyl coenzyme A onto an amine at the 6'-position of various aminoglycosides.<br><br>CONCLUSIONS: We identified aac(6')-Ian as a novel amikacin resistance determinant together with a new ESBL gene, blaTLA-3, on a transferable plasmid of a S. marcescens clinical isolate.}, }
@article {pmid25574122, year = {2014}, author = {Saeb, AT and David, SK and Al-Brahim, H}, title = {In silico detection of virulence gene homologues in the human pathogen sphingomonas spp.}, journal = {Evolutionary bioinformatics online}, volume = {10}, number = {}, pages = {229-238}, pmid = {25574122}, issn = {1176-9343}, abstract = {There is an ongoing debate about the clinical significance of Sphingomonas paucimobilis as a virulent bacterial pathogen. In the present study, we investigated the presence of different virulence factors and genes in Sphingomonas bacteria. We utilized phylogenetic, comparative genomics and bioinformatics analysis to investigate the potentiality of Sphingomonas bacteria as virulent pathogenic bacteria. The 16S ribosomal RNA gene (16S rDNA) phylogenetic tree showed that the closest bacterial taxon to Sphingomonas is Brucella with a bootstrap value of 87 followed by Helicobacter, Campylobacter, Pseudomonas, and then Legionella. Sphingomonas shared no virulence factors with Helicobacter or Campylobacter, despite their close phylogenic relationship. In spite of the phylogenetic divergence between Sphingomonas and Pseudomonas, they shared many major virulence factors, such as adherence, antiphagocytosis, iron uptake, proteases, and quorum sensing. In conclusion, Sphingomonas spp. contains several major virulence factors resembling Pseudomonas sp., Legionella sp., Brucella sp., and Bordetella sp. virulence factors. Similarity of virulence factors did not match phylogenetic relationships. These findings suggest horizontal gene transfer of virulence factors rather than sharing a common pathogenic ancestor. Sphingomonas spp. is potential virulent bacterial pathogen.}, }
@article {pmid25573905, year = {2015}, author = {Nývltová, E and Stairs, CW and Hrdý, I and Rídl, J and Mach, J and Pačes, J and Roger, AJ and Tachezy, J}, title = {Lateral gene transfer and gene duplication played a key role in the evolution of Mastigamoeba balamuthi hydrogenosomes.}, journal = {Molecular biology and evolution}, volume = {32}, number = {4}, pages = {1039-1055}, pmid = {25573905}, issn = {1537-1719}, support = {MOP-62809//Canadian Institutes of Health Research/Canada ; }, mesh = {Anaerobiosis/genetics ; Archamoebae/enzymology/*genetics/metabolism ; Cell Membrane Structures/genetics/metabolism ; Energy Metabolism/*genetics ; Enzymes/genetics/isolation &amp; purification ; *Evolution, Molecular ; *Gene Duplication ; *Gene Transfer, Horizontal ; Organelles/enzymology/*genetics/metabolism ; }, abstract = {Lateral gene transfer (LGT) is an important mechanism of evolution for protists adapting to oxygen-poor environments. Specifically, modifications of energy metabolism in anaerobic forms of mitochondria (e.g., hydrogenosomes) are likely to have been associated with gene transfer from prokaryotes. An interesting question is whether the products of transferred genes were directly targeted into the ancestral organelle or initially operated in the cytosol and subsequently acquired organelle-targeting sequences. Here, we identified key enzymes of hydrogenosomal metabolism in the free-living anaerobic amoebozoan Mastigamoeba balamuthi and analyzed their cellular localizations, enzymatic activities, and evolutionary histories. Additionally, we characterized 1) several canonical mitochondrial components including respiratory complex II and the glycine cleavage system, 2) enzymes associated with anaerobic energy metabolism, including an unusual D-lactate dehydrogenase and acetyl CoA synthase, and 3) a sulfate activation pathway. Intriguingly, components of anaerobic energy metabolism are present in at least two gene copies. For each component, one copy possesses an mitochondrial targeting sequence (MTS), whereas the other lacks an MTS, yielding parallel cytosolic and hydrogenosomal extended glycolysis pathways. Experimentally, we confirmed that the organelle targeting of several proteins is fully dependent on the MTS. Phylogenetic analysis of all extended glycolysis components suggested that these components were acquired by LGT. We propose that the transformation from an ancestral organelle to a hydrogenosome in the M. balamuthi lineage involved the lateral acquisition of genes encoding extended glycolysis enzymes that initially operated in the cytosol and that established a parallel hydrogenosomal pathway after gene duplication and MTS acquisition.}, }
@article {pmid25572217, year = {2014}, author = {Schwartz, JA and Curtis, NE and Pierce, SK}, title = {FISH labeling reveals a horizontally transferred algal (Vaucheria litorea) nuclear gene on a sea slug (Elysia chlorotica) chromosome.}, journal = {The Biological bulletin}, volume = {227}, number = {3}, pages = {300-312}, doi = {10.1086/BBLv227n3p300}, pmid = {25572217}, issn = {1939-8697}, mesh = {Algal Proteins/*genetics ; Animals ; Chromosomes/genetics ; Gastropoda/*genetics ; Gene Transfer, Horizontal/*genetics ; In Situ Hybridization, Fluorescence ; Stramenopiles/*genetics ; Transcriptome ; }, abstract = {The horizontal transfer of functional nuclear genes, coding for both chloroplast proteins and chlorophyll synthesis, from the food alga Vaucheria litorea to the sea slug Elysia chlorotica has been demonstrated by pharmacological, polymerase chain reaction (PCR), real time PCR (qRT-PCR), and transcriptome sequencing experiments. However, partial genomic sequencing of E. chlorotica larvae failed to find evidence for gene transfer. Here, we have used fluorescent in situ hybridization to localize an algal nuclear gene, prk, found in both larval and adult slug DNA by PCR and in adult RNA by transcriptome sequencing and RT-PCR. The prk probe hybridized with a metaphase chromosome in slug larvae, confirming gene transfer between alga and slug.}, }
@article {pmid25566271, year = {2014}, author = {Suwastika, IN and Denawa, M and Yomogihara, S and Im, CH and Bang, WY and Ohniwa, RL and Bahk, JD and Takeyasu, K and Shiina, T}, title = {Evidence for lateral gene transfer (LGT) in the evolution of eubacteria-derived small GTPases in plant organelles.}, journal = {Frontiers in plant science}, volume = {5}, number = {}, pages = {678}, pmid = {25566271}, issn = {1664-462X}, abstract = {The genomes of free-living bacteria frequently exchange genes via lateral gene transfer (LGT), which has played a major role in bacterial evolution. LGT also played a significant role in the acquisition of genes from non-cyanobacterial bacteria to the lineage of "primary" algae and land plants. Small GTPases are widely distributed among prokaryotes and eukaryotes. In this study, we inferred the evolutionary history of organelle-targeted small GTPases in plants. Arabidopsis thaliana contains at least one ortholog in seven subfamilies of OBG-HflX-like and TrmE-Era-EngA-YihA-Septin-like GTPase superfamilies (together referred to as Era-like GTPases). Subcellular localization analysis of all Era-like GTPases in Arabidopsis revealed that all 30 eubacteria-related GTPases are localized to chloroplasts and/or mitochondria, whereas archaea-related DRG and NOG1 are localized to the cytoplasm and nucleus, respectively, suggesting that chloroplast- and mitochondrion-localized GTPases are derived from the ancestral cyanobacterium and α-proteobacterium, respectively, through endosymbiotic gene transfer (EGT). However, phylogenetic analyses revealed that plant organelle GTPase evolution is rather complex. Among the eubacterium-related GTPases, only four localized to chloroplasts (including one dual targeting GTPase) and two localized to mitochondria were derived from cyanobacteria and α-proteobacteria, respectively. Three other chloroplast-targeted GTPases were related to α-proteobacterial proteins, rather than to cyanobacterial GTPases. Furthermore, we found that four other GTPases showed neither cyanobacterial nor α-proteobacterial affiliation. Instead, these GTPases were closely related to clades from other eubacteria, such as Bacteroides (Era1, EngB-1, and EngB-2) and green non-sulfur bacteria (HflX). This study thus provides novel evidence that LGT significantly contributed to the evolution of organelle-targeted Era-like GTPases in plants.}, }
@article {pmid25566238, year = {2014}, author = {Klümper, U and Droumpali, A and Dechesne, A and Smets, BF}, title = {Novel assay to measure the plasmid mobilizing potential of mixed microbial communities.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {730}, pmid = {25566238}, issn = {1664-302X}, abstract = {Mobilizable plasmids lack necessary genes for complete conjugation and are therefore non-self-transmissible. Instead, they rely on the conjugation system of conjugal plasmids to be horizontally transferred to new recipients. While community permissiveness, the fraction of a mixed microbial community that can receive self-transmissible conjugal plasmids, has been studied, the intrinsic ability of a community to mobilize plasmids that lack conjugation systems is unexplored. Here, we present a novel framework and experimental method to estimate the mobilization potential of mixed communities. We compare the transfer frequency of a mobilizable plasmid to that of a mobilizing and conjugal plasmid measured for a model strain and for the assayed community. With Pseudomonas putida carrying the gfp-tagged mobilizable IncQ plasmid RSF1010 as donor strain, we conducted solid surface mating experiments with either a P. putida strain carrying the mobilizing IncP-1α plasmid RP4 or a model bacterial community that was extracted from the inner walls of a domestic shower conduit. Additionally, we estimated the permissiveness of the same community for RP4 using P. putida as donor strain. The permissiveness of the model community for RP4 [at 1.16 × 10(-4) transconjugants per recipient (T/R)] was similar to that previously measured for soil microbial communities. RSF1010 was mobilized by the model community at a frequency of 1.16 × 10(-5) T/R, only one order of magnitude lower than its permissiveness to RP4. This mobilization frequency is unexpectedly high considering that (i) mobilization requires the presence of mobilizing conjugal plasmids within the permissive fraction of the recipients; (ii) in pure culture experiments with P. putida retromobilization of RSF1010 through RP4 only took place in approximately half of the donors receiving the conjugal plasmid in the first step. Further work is needed to establish how plasmid mobilization potential varies within and across microbial communities. This method has the potential to provide such insights; in addition it allows for the direct isolation of in situ mobilizing plasmids together with their endogenous hosts.}, }
@article {pmid25566202, year = {2014}, author = {McNeilly, CL and McMillan, DJ}, title = {Horizontal gene transfer and recombination in Streptococcus dysgalactiae subsp. equisimilis.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {676}, pmid = {25566202}, issn = {1664-302X}, abstract = {Streptococcus dysgalactiae subsp. equisimilis (SDSE) is a human pathogen that colonizes the skin or throat, and causes a range of diseases from relatively benign pharyngitis to potentially fatal invasive diseases. While not as virulent as the close relative Streptococcus pyogenes the two share a number of virulence factors and are known to coexist in a human host. Both pre- and post-genomic studies have revealed that horizontal gene transfer (HGT) and recombination occurs between these two organisms and plays a major role in shaping the population structure of SDSE. This review summarizes our current knowledge of HGT and recombination in the evolution of SDSE.}, }
@article {pmid25560233, year = {2015}, author = {Hüttener, M and Paytubi, S and Juárez, A}, title = {Success in incorporating horizontally transferred genes: the H-NS protein.}, journal = {Trends in microbiology}, volume = {23}, number = {2}, pages = {67-69}, doi = {10.1016/j.tim.2014.12.009}, pmid = {25560233}, issn = {1878-4380}, mesh = {Bacterial Proteins/*genetics ; DNA-Binding Proteins/*genetics ; Enterobacteriaceae/genetics ; Escherichia coli Proteins/genetics ; *Evolution, Molecular ; *Gene Silencing ; *Gene Transfer, Horizontal ; Genetic Fitness ; Molecular Chaperones/genetics ; Salmonella/*genetics ; }, abstract = {The nucleoid-associated protein H-NS silences unwanted expression of acquired foreign DNA. Ali and colleagues recently identified which horizontally-acquired genes are targeted by H-NS in Salmonella to avoid fitness loss. The reported data strengthen our view about the role of H-NS in bacterial evolution driven by horizontal gene transfer.}, }
@article {pmid25556253, year = {2015}, author = {Wang, X and Shutt, KA and Vuong, JT and Cohn, A and MacNeil, J and Schmink, S and Plikaytis, B and Messonnier, NE and Harrison, LH and Clark, TA and Mayer, LW}, title = {Changes in the Population Structure of Invasive Neisseria meningitidis in the United States After Quadrivalent Meningococcal Conjugate Vaccine Licensure.}, journal = {The Journal of infectious diseases}, volume = {211}, number = {12}, pages = {1887-1894}, doi = {10.1093/infdis/jiu842}, pmid = {25556253}, issn = {1537-6613}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Child ; Child, Preschool ; Female ; Genotype ; Humans ; Infant ; Infant, Newborn ; Male ; Meningococcal Infections/*epidemiology/*microbiology/prevention &amp; control ; Meningococcal Vaccines/*administration &amp; dosage ; Middle Aged ; Neisseria meningitidis/*classification/genetics/immunology/*isolation &amp; purification ; Serogroup ; United States ; Vaccines, Conjugate/administration &amp; dosage ; Young Adult ; }, abstract = {BACKGROUND: Meningococcal conjugate vaccines against serogroups A, C, W, and Y (MenACWY) are recommended for routine use in adolescents aged 11-18 years. The impact of these vaccines on the meningococcal population structure in the United States have yet to be evaluated.<br><br>METHODS: Meningococcal isolates recovered during 2006-2010 (ie, after introduction of MenACWY) collected through Active Bacterial Core surveillance (ABCs) were characterized; serogroup distribution and molecular features of these isolates were compared to previously published data on ABCs isolates recovered from 2000 to 2005 (ie, before introduction of MenACWY). P values were generated using &#x3c7;(2) statistics and exact methods.<br><br>RESULTS: There was a significant change (P < .05) in serogroup distribution among all age groups between the 2 periods. A small proportion of isolates showed evidence of capsular switching in both periods. Between the 2 periods, significant changes were observed in the distribution of porin A, ferric enterobactin transport, and strain genotypes among vaccine and nonvaccine serogroups.<br><br>CONCLUSIONS: The population structure of US meningococcal isolates is dynamic; some changes occurred over time, but the basic structure remained. Vaccine-induced serogroup replacement was not observed, although a small proportion of isolates had undergone capsule switching, possibly driven by non-vaccine-mediated selection. Changes in the distribution of molecular features are likely due to horizontal gene transfer and changes in serogroup distribution.}, }
@article {pmid25555916, year = {2015}, author = {López-Pelegrín, M and Ksiazek, M and Karim, AY and Guevara, T and Arolas, JL and Potempa, J and Gomis-Rüth, FX}, title = {A novel mechanism of latency in matrix metalloproteinases.}, journal = {The Journal of biological chemistry}, volume = {290}, number = {8}, pages = {4728-4740}, pmid = {25555916}, issn = {1083-351X}, support = {R01 DE009761/DE/NIDCR NIH HHS/United States ; R01 DE022597/DE/NIDCR NIH HHS/United States ; DE022597/DE/NIDCR NIH HHS/United States ; DE09761/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacterial Proteins/*chemistry/genetics/metabolism ; Bacteroidaceae/*enzymology/genetics ; Cysteine/chemistry/genetics/metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal ; Humans ; Matrix Metalloproteinases/*chemistry/genetics/metabolism ; Periodontitis/enzymology/genetics/microbiology ; *Protein Folding ; Protein Structure, Tertiary ; }, abstract = {The matrix metalloproteinases (MMPs) are a family of secreted soluble or membrane-anchored multimodular peptidases regularly found in several paralogous copies in animals and plants, where they have multiple functions. The minimal consensus domain architecture comprises a signal peptide, a 60-90-residue globular prodomain with a conserved sequence motif including a cysteine engaged in "cysteine-switch" or "Velcro" mediated latency, and a catalytic domain. Karilysin, from the human periodontopathogen Tannerella forsythia, is the only bacterial MMP to have been characterized biochemically to date. It shares with eukaryotic forms the catalytic domain but none of the flanking domains. Instead of the consensus MMP prodomain, it features a 14-residue propeptide, the shortest reported for a metallopeptidase, which lacks cysteines. Here we determined the structure of a prokarilysin fragment encompassing the propeptide and the catalytic domain, and found that the former runs across the cleft in the opposite direction to a bound substrate and inhibits the latter through an "aspartate-switch" mechanism. This finding is reminiscent of latency maintenance in the otherwise unrelated astacin and fragilysin metallopeptidase families. In addition, in vivo and biochemical assays showed that the propeptide contributes to protein folding and stability. Our analysis of prokarilysin reveals a novel mechanism of latency and activation in MMPs. Finally, our findings support the view that the karilysin catalytic domain was co-opted by competent bacteria through horizontal gene transfer from a eukaryotic source, and later evolved in a specific bacterial environment.}, }
@article {pmid25555398, year = {2015}, author = {Jaramillo, VD and Sukno, SA and Thon, MR}, title = {Identification of horizontally transferred genes in the genus Colletotrichum reveals a steady tempo of bacterial to fungal gene transfer.}, journal = {BMC genomics}, volume = {16}, number = {1}, pages = {2}, pmid = {25555398}, issn = {1471-2164}, mesh = {Bacteria/*genetics ; Colletotrichum/*genetics/physiology ; Databases, Protein ; Gene Deletion ; Gene Duplication ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genes, Fungal ; Phylogeny ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT) is the stable transmission of genetic material between organisms by means other than vertical inheritance. HGT has an important role in the evolution of prokaryotes but is relatively rare in eukaryotes. HGT has been shown to contribute to virulence in eukaryotic pathogens. We studied the importance of HGT in plant pathogenic fungi by identifying horizontally transferred genes in the genomes of three members of the genus Colletotrichum.<br><br>RESULTS: We identified eleven HGT events from bacteria into members of the genus Colletotrichum or their ancestors. The HGT events include genes involved in amino acid, lipid and sugar metabolism as well as lytic enzymes. Additionally, the putative minimal dates of transference were calculated using a time calibrated phylogenetic tree. This analysis reveals a constant flux of genes from bacteria to fungi throughout the evolution of subphylum Pezizomycotina.<br><br>CONCLUSIONS: Genes that are typically transferred by HGT are those that are constantly subject to gene duplication and gene loss. The functions of some of these genes suggest roles in niche adaptation and virulence. We found no evidence of a burst of HGT events coinciding with major geological events. In contrast, HGT appears to be a constant, albeit rare phenomenon in the Pezizomycotina, occurring at a steady rate during their evolution.}, }
@article {pmid25554784, year = {2015}, author = {Borgeaud, S and Metzger, LC and Scrignari, T and Blokesch, M}, title = {The type VI secretion system of Vibrio cholerae fosters horizontal gene transfer.}, journal = {Science (New York, N.Y.)}, volume = {347}, number = {6217}, pages = {63-67}, doi = {10.1126/science.1260064}, pmid = {25554784}, issn = {1095-9203}, mesh = {Bacterial Proteins/genetics/physiology ; Bacterial Secretion Systems/*genetics ; *DNA Transformation Competence ; *Gene Transfer, Horizontal ; Multigene Family ; Trans-Activators/genetics/physiology ; Vibrio cholerae/*genetics/*physiology ; }, abstract = {Natural competence for transformation is a common mode of horizontal gene transfer and contributes to bacterial evolution. Transformation occurs through the uptake of external DNA and its integration into the genome. Here we show that the type VI secretion system (T6SS), which serves as a predatory killing device, is part of the competence regulon in the naturally transformable pathogen Vibrio cholerae. The T6SS-encoding gene cluster is under the positive control of the competence regulators TfoX and QstR and is induced by growth on chitinous surfaces. Live-cell imaging revealed that deliberate killing of nonimmune cells via competence-mediated induction of T6SS releases DNA and makes it accessible for horizontal gene transfer in V. cholerae.}, }
@article {pmid25552925, year = {2015}, author = {Ying, J and Wang, H and Bao, B and Zhang, Y and Zhang, J and Zhang, C and Li, A and Lu, J and Li, P and Ying, J and Liu, Q and Xu, T and Yi, H and Li, J and Zhou, L and Zhou, T and Xu, Z and Ni, L and Bao, Q}, title = {Molecular variation and horizontal gene transfer of the homocysteine methyltransferase gene mmuM and its distribution in clinical pathogens.}, journal = {International journal of biological sciences}, volume = {11}, number = {1}, pages = {11-21}, pmid = {25552925}, issn = {1449-2288}, mesh = {Bacteria/*enzymology ; Base Sequence ; Chromosome Mapping ; Cluster Analysis ; DNA Primers/genetics ; Gene Transfer, Horizontal/*genetics ; Genetic Variation/*genetics ; High-Throughput Nucleotide Sequencing ; Homocysteine S-Methyltransferase/*genetics ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; }, abstract = {The homocysteine methyltransferase encoded by mmuM is widely distributed among microbial organisms. It is the key enzyme that catalyzes the last step in methionine biosynthesis and plays an important role in the metabolism process. It also enables the microbial organisms to tolerate high concentrations of selenium in the environment. In this research, 533 mmuM gene sequences covering 70 genera of the bacteria were selected from GenBank database. The distribution frequency of mmuM is different in the investigated genera of bacteria. The mapping results of 160 mmuM reference sequences showed that the mmuM genes were found in 7 species of pathogen genomes sequenced in this work. The polymerase chain reaction products of one mmuM genotype (NC_013951 as the reference) were sequenced and the sequencing results confirmed the mapping results. Furthermore, 144 representative sequences were chosen for phylogenetic analysis and some mmuM genes from totally different genera (such as the genes between Escherichia and Klebsiella and between Enterobacter and Kosakonia) shared closer phylogenetic relationship than those from the same genus. Comparative genomic analysis of the mmuM encoding regions on plasmids and bacterial chromosomes showed that pKF3-140 and pIP1206 plasmids shared a 21 kb homology region and a 4.9 kb fragment in this region was in fact originated from the Escherichia coli chromosome. These results further suggested that mmuM gene did go through the gene horizontal transfer among different species or genera of bacteria. High-throughput sequencing combined with comparative genomics analysis would explore distribution and dissemination of the mmuM gene among bacteria and its evolution at a molecular level.}, }
@article {pmid25548049, year = {2015}, author = {Puri, AW and Owen, S and Chu, F and Chavkin, T and Beck, DA and Kalyuzhnaya, MG and Lidstrom, ME}, title = {Genetic tools for the industrially promising methanotroph Methylomicrobium buryatense.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {5}, pages = {1775-1781}, pmid = {25548049}, issn = {1098-5336}, mesh = {Conjugation, Genetic ; Gene Deletion ; Gene Transfer, Horizontal ; Genetic Vectors ; Genetics, Microbial/*methods ; Metabolic Engineering ; Metabolic Networks and Pathways/genetics ; Methane/metabolism ; Methylococcaceae/*genetics/growth &amp; development ; Molecular Biology/*methods ; Oxidation-Reduction ; Plasmids ; }, abstract = {Aerobic methanotrophs oxidize methane at ambient temperatures and pressures and are therefore attractive systems for methane-based bioconversions. In this work, we developed and validated genetic tools for Methylomicrobium buryatense, a haloalkaliphilic gammaproteobacterial (type I) methanotroph. M. buryatense was isolated directly on natural gas and grows robustly in pure culture with a 3-h doubling time, enabling rapid genetic manipulation compared to many other methanotrophic species. As a proof of concept, we used a sucrose counterselection system to eliminate glycogen production in M. buryatense by constructing unmarked deletions in two redundant glycogen synthase genes. We also selected for a more genetically tractable variant strain that can be conjugated with small incompatibility group P (IncP)-based broad-host-range vectors and determined that this capability is due to loss of the native plasmid. These tools make M. buryatense a promising model system for studying aerobic methanotroph physiology and enable metabolic engineering in this bacterium for industrial biocatalysis of methane.}, }
@article {pmid25547755, year = {2014}, author = {Thiergart, T and Landan, G and Martin, WF}, title = {Concatenated alignments and the case of the disappearing tree.}, journal = {BMC evolutionary biology}, volume = {14}, number = {}, pages = {266}, pmid = {25547755}, issn = {1471-2148}, support = {281357/ERC_/European Research Council/International ; }, mesh = {Animals ; Archaea/classification/genetics ; Bacteria/classification/genetics ; Conserved Sequence/genetics ; Evolution, Molecular ; Fungi/classification/genetics ; Gene Transfer, Horizontal ; *Genome ; *Phylogeny ; Plants/classification/genetics ; }, abstract = {BACKGROUND: Analyzed individually, gene trees for a given taxon set tend to harbour incongruent or conflicting signals. One popular approach to deal with this circumstance is to use concatenated data. But especially in prokaryotes, where lateral gene transfer (LGT) is a natural mechanism of generating genetic diversity, there are open questions as to whether concatenation amplifies or averages phylogenetic signals residing in individual genes. Here we investigate concatenations of prokaryotic and eukaryotic datasets to investigate possible sources of incongruence in phylogenetic trees and to examine the level of overlap between individual and concatenated alignments.<br><br>RESULTS: We analyzed prokaryotic datasets comprising 248 invidual gene trees from 315 genomes at three taxonomic depths spanning gammaproteobacteria, proteobacteria, and prokaryotes (bacteria plus archaea), and eukaryotic datasets comprising 279 invidual gene trees from 85 genomes at two taxonomic depths: across plants-animals-fungi and within fungi. Consistent with previous findings, the branches in trees made from concatenated alignments are, in general, not supported by any of their underlying individual gene trees, even though the concatenation trees tend to possess high bootstrap proportions values. For the prokaryote data, this observation is independent of phylogenetic depth and sequence conservation. The eukaryotic data show much better agreement between concatenation and single gene trees. LGT frequencies in trees were estimated using established methods. Sequence length in individual alignments, but not sequence divergence, was found to correlate with the generation of branches that correspond to the concatenated tree.<br><br>CONCLUSIONS: The weak correspondence of concatenation trees with single gene trees gives rise to the question where the phylogenetic signal in concatenated trees is coming from. The eukaryote data reveals a better correspondence between individual and concatenation trees than the prokaryote data. The question of whether the lack of correspondence between individual genes and the concatenation tree in the prokaryotic data is due to LGT or phylogenetic artefacts remains unanswered. If LGT is the cause of incongruence between concatenation and individual trees, we would have expected to see greater degrees of incongruence for more divergent prokaryotic data sets, which was not observed, although estimated rates of LGT suggest that LGT is responsible for at least some of the observed incongruence.}, }
@article {pmid25544937, year = {2014}, author = {Van Tyne, D and Gilmore, MS}, title = {Virulence Plasmids of Nonsporulating Gram-Positive Pathogens.}, journal = {Microbiology spectrum}, volume = {2}, number = {5}, pages = {}, pmid = {25544937}, issn = {2165-0497}, support = {EY007145/EY/NEI NIH HHS/United States ; AI083214/AI/NIAID NIH HHS/United States ; R01 AI072360/AI/NIAID NIH HHS/United States ; AI072360/AI/NIAID NIH HHS/United States ; P01 AI083214/AI/NIAID NIH HHS/United States ; T32 EY007145/EY/NEI NIH HHS/United States ; }, mesh = {Animals ; Bacterial Infections/microbiology ; Gene Transfer, Horizontal ; Gram-Positive Bacteria/*genetics/*pathogenicity ; Humans ; *Plasmids ; Virulence ; Virulence Factors/*genetics/*metabolism ; }, abstract = {Gram-positive bacteria are leading causes of many types of human infection, including pneumonia, skin and nasopharyngeal infections, as well as urinary tract and surgical wound infections among hospitalized patients. These infections have become particularly problematic because many of the species causing them have become highly resistant to antibiotics. The role of mobile genetic elements, such as plasmids, in the dissemination of antibiotic resistance among Gram-positive bacteria has been well studied; less well understood is the role of mobile elements in the evolution and spread of virulence traits among these pathogens. While these organisms are leading agents of infection, they are also prominent members of the human commensal ecology. It appears that these bacteria are able to take advantage of the intimate association between host and commensal, via virulence traits that exacerbate infection and cause disease. However, evolution into an obligate pathogen has not occurred, presumably because it would lead to rejection of pathogenic organisms from the host ecology. Instead, in organisms that exist as both commensal and pathogen, selection has favored the development of mechanisms for variability. As a result, many virulence traits are localized on mobile genetic elements, such as virulence plasmids and pathogenicity islands. Virulence traits may occur within a minority of isolates of a given species, but these minority populations have nonetheless emerged as a leading problem in infectious disease. This chapter reviews virulence plasmids in nonsporulating Gram-positive bacteria, and examines their contribution to disease pathogenesis.}, }
@article {pmid25541486, year = {2015}, author = {Mansfield, MJ and Adams, JB and Doxey, AC}, title = {Botulinum neurotoxin homologs in non-Clostridium species.}, journal = {FEBS letters}, volume = {589}, number = {3}, pages = {342-348}, doi = {10.1016/j.febslet.2014.12.018}, pmid = {25541486}, issn = {1873-3468}, mesh = {Botulinum Toxins/*genetics/isolation &amp; purification ; Clostridium/chemistry/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Multigene Family ; Protein Structure, Tertiary ; Tetanus Toxin/*genetics/isolation &amp; purification ; Weissella/chemistry/*genetics ; }, abstract = {Clostridial neurotoxins (CNTs) are the deadliest toxins known and the causative agents of botulism and tetanus. Despite their structural and functional complexity, no CNT homologs are currently known outside Clostridium. Here, we report the first homologs of Clostridium CNTs within the genome of the rice fermentation organism Weissella oryzae SG25. One gene in W. oryzae S25 encodes a protein with a four-domain architecture and HExxH protease motif common to botulinum neurotoxins (BoNTs). An adjacent gene with partial similarity to CNTs is also present, and both genes seem to have been laterally transferred into the W. oryzae genome from an unknown source. Identification of mobile, CNT-related genes outside of Clostridium has implications for our understanding of the evolution of this important toxin family.}, }
@article {pmid25540453, year = {2015}, author = {Tazzyman, SJ and Bonhoeffer, S}, title = {Why There Are No Essential Genes on Plasmids.}, journal = {Molecular biology and evolution}, volume = {32}, number = {12}, pages = {3079-3088}, doi = {10.1093/molbev/msu293}, pmid = {25540453}, issn = {1537-1719}, mesh = {Bacteria/*genetics ; Biological Evolution ; Chromosomes ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, Essential ; Models, Genetic ; Plasmids/*genetics ; }, abstract = {Mobile genetic elements such as plasmids are important for the evolution of prokaryotes. It has been suggested that there are differences between functions coded for by mobile genes and those in the "core" genome and that these differences can be seen between plasmids and chromosomes. In particular, it has been suggested that essential genes, such as those involved in the formation of structural proteins or in basic metabolic functions, are rarely located on plasmids. We model competition between genotypically varying bacteria within a single population to investigate whether selection favors a chromosomal location for essential genes. We find that in general, chromosomal locations for essential genes are indeed favored. This is because the inheritance of chromosomes is more stable than that for plasmids. We define the "degradation" rate as the rate at which chance genetic processes, for example, mutation, deletion, or translocation, render essential genes nonfunctioning. The only way in which plasmids can be a location for functioning essential genes is if chromosomal genes degrade faster than plasmid genes. If the two degradation rates are equal, or if plasmid genes degrade faster than chromosomal genes, functioning essential genes will be found only on chromosomes.}, }
@article {pmid25540374, year = {2015}, author = {Sullivan, MB}, title = {Viromes, not gene markers, for studying double-stranded DNA virus communities.}, journal = {Journal of virology}, volume = {89}, number = {5}, pages = {2459-2461}, pmid = {25540374}, issn = {1098-5514}, mesh = {Biota ; DNA/*genetics ; DNA Viruses/*classification/genetics/*isolation &amp; purification ; Metagenomics/*methods ; }, abstract = {Microbes have recently been recognized as dominant forces in nature, with studies benefiting from gene markers that can be quickly, informatively, and universally surveyed. Viruses, where explored, have proven to be powerful modulators of locally and globally important microbes through mortality, horizontal gene transfer, and metabolic reprogramming. However, community-wide virus studies have been challenged by the lack of a universal marker. Here, I propose that viral metagenomics has advanced to largely take over study of double-stranded DNA viruses.}, }
@article {pmid25537049, year = {2014}, author = {Casane, D and Laurenti, P}, title = {[Compulsive molecular hoarding enables the evolution of protein-coding DNA from non-coding DNA].}, journal = {Medecine sciences : M/S}, volume = {30}, number = {12}, pages = {1177-1183}, doi = {10.1051/medsci/20143012022}, pmid = {25537049}, issn = {0767-0974}, mesh = {Animals ; Biological Evolution ; DNA/*genetics ; Evolution, Molecular ; Genetic Drift ; Genome/genetics ; Humans ; Mutation/genetics ; Proteins/*genetics ; Recombination, Genetic/genetics ; Selection, Genetic ; }, abstract = {It was thought until recently that a new gene could only evolve from a previously existing gene, from recombination of genes, or from horizontal gene transfer. Recently a series of genomic and transcriptomic studies have led to the identification of non-coding DNA as a significant source of protein coding genes. The mechanism, which is probably universal since it has been identified in a wide array of eukaryotes, implies that a gradient of proto-genes, probably established by a balance between selection and genetic drift, exists between coding DNA and non-coding DNA. Therefore genome dynamics could account for the progressive formation of genes "out of the blue" thanks to the interplay of mutation and natural selection.}, }
@article {pmid25535270, year = {2015}, author = {Grace, ED and Gopalkrishnan, S and Girard, ME and Blankschien, MD and Ross, W and Gourse, RL and Herman, C}, title = {Activation of the σE-dependent stress pathway by conjugative TraR may anticipate conjugational stress.}, journal = {Journal of bacteriology}, volume = {197}, number = {5}, pages = {924-931}, pmid = {25535270}, issn = {1098-5530}, support = {P30 CA125123/CA/NCI NIH HHS/United States ; 1R01GM088653/GM/NIGMS NIH HHS/United States ; P30 AI036211/AI/NIAID NIH HHS/United States ; R01 GM088653/GM/NIGMS NIH HHS/United States ; S10 RR024574/RR/NCRR NIH HHS/United States ; R37 GM037048/GM/NIGMS NIH HHS/United States ; R37 GM37048/GM/NIGMS NIH HHS/United States ; }, mesh = {*Conjugation, Genetic ; Escherichia coli/genetics/*physiology ; Escherichia coli Proteins/genetics/*metabolism ; Gene Expression Regulation, Bacterial ; Operon ; Promoter Regions, Genetic ; Sigma Factor/*genetics/metabolism ; Stress, Physiological ; Transcription Factors/genetics/*metabolism ; Transcriptional Activation ; *Up-Regulation ; }, abstract = {Horizontal gene transfer by conjugation plays a major role in bacterial evolution, allowing the acquisition of new traits, such as virulence and resistance to antibacterial agents. With the increased antibiotic resistance in bacterial pathogens, a better understanding of how bacteria modulate conjugation under changing environments and the genetic factors involved is needed. Despite the evolutionary advantages conjugation may confer, the process can be quite stressful for the donor cell. Here, we characterize the ability of TraR, encoded on the episomal F' plasmid, to upregulate the σ(E) extracytoplasmic stress pathway in Escherichia coli. TraR, a DksA homolog, modulates transcription initiation through the secondary channel of RNA polymerase. We show here that TraR activates transcription directly; however, unlike DksA, it does so without using ppGpp as a cofactor. TraR expression can stimulate the σ(E) extracytoplasmic stress response independently of the DegS/RseA signal transduction cascade. In the absence of TraR, bacteria carrying conjugative plasmids become more susceptible to external stress. We propose that TraR increases the concentrations of periplasmic chaperones and proteases by directly activating the transcription of σ(E)-dependent promoters; this increased protein folding capacity may prepare the bacterium to endure the periplasmic stress of sex pilus biosynthesis during mating.}, }
@article {pmid25535106, year = {2015}, author = {Igaz, I and Igaz, P}, title = {Possible role for microRNAs as inter-species mediators of epigenetic information in disease pathogenesis: is the non-coding dark matter of the genome responsible for epigenetic interindividual or interspecies communication?.}, journal = {Medical hypotheses}, volume = {84}, number = {2}, pages = {150-154}, doi = {10.1016/j.mehy.2014.11.021}, pmid = {25535106}, issn = {1532-2777}, mesh = {Body Fluids/*chemistry ; Epigenesis, Genetic/*physiology ; *Food Chain ; Gene Expression Regulation/*physiology ; Gene Transfer, Horizontal/*genetics ; Humans ; MicroRNAs/*genetics ; *Models, Genetic ; }, abstract = {MicroRNAs are short non-coding RNA molecules involved in the posttranscriptional epigenetic regulation of gene expression. Recent data show that microRNAs can be found in body fluids, and these microRNAs might enter cells giving rise to a hormone like way of action. MicroRNAs released in body fluids might affect other individuals, and there are some data of potential cross-species action of microRNAs, as well. Here, the authors discuss hypotheses concerning the potential pathogenic relevance of interindividual and cross-species action of microRNAs including food-derived microRNAs. Supposing that microRNAs might traverse the gastrointestinal tract, microRNAs might wander via the food-chain and even master regulatory microRNAs might be envisaged that could influence gene expression in a wide range of species and might thereby link different species via common gene expression signatures. Since many microRNA genes are located in the non-protein coding "dark matter" of the genome, a novel function of this "dark matter" is raised regarding interindividual and cross-species epigenetic communication via information transfer by gene products coded by the non-protein coding part of the genome.}, }
@article {pmid25534811, year = {2015}, author = {Martínez, JL and Coque, TM and Baquero, F}, title = {What is a resistance gene? Ranking risk in resistomes.}, journal = {Nature reviews. Microbiology}, volume = {13}, number = {2}, pages = {116-123}, pmid = {25534811}, issn = {1740-1534}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/drug effects/*genetics/*metabolism ; Bacterial Infections/epidemiology/microbiology ; Drug Resistance, Bacterial/*genetics ; Environmental Microbiology ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Humans ; }, abstract = {Metagenomic studies have shown that antibiotic resistance genes are ubiquitous in the environment, which has led to the suggestion that there is a high risk that these genes will spread to bacteria that cause human infections. If this is true, estimating the real risk of dissemination of resistance genes from environmental reservoirs to human pathogens is therefore very difficult. In this Opinion article, we analyse the current definitions of antibiotic resistance and antibiotic resistance genes, and we describe the bottlenecks that affect the transfer of antibiotic resistance genes to human pathogens. We propose rules for estimating the risks associated with genes that are present in environmental resistomes by evaluating the likelihood of their introduction into human pathogens, and the consequences of such events for the treatment of infections.}, }
@article {pmid25528295, year = {2015}, author = {Penadés, JR and Chen, J and Quiles-Puchalt, N and Carpena, N and Novick, RP}, title = {Bacteriophage-mediated spread of bacterial virulence genes.}, journal = {Current opinion in microbiology}, volume = {23}, number = {}, pages = {171-178}, doi = {10.1016/j.mib.2014.11.019}, pmid = {25528295}, issn = {1879-0364}, support = {MR/M003876/1/MRC_/Medical Research Council/United Kingdom ; R01AI022159/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/*genetics/*virology ; Bacteriophages/*genetics/*growth &amp; development ; *Gene Transfer, Horizontal ; *Transduction, Genetic ; Virulence Factors/*genetics ; }, abstract = {Bacteriophages are types of viruses that infect bacteria. They are the most abundant and diverse entities in the biosphere, and influence the evolution of most bacterial species by promoting gene transfer, sometimes in unexpected ways. Although pac-type phages can randomly package and transfer bacterial DNA by a process called generalized transduction, some mobile genetic elements have developed elegant and sophisticated strategies to hijack the phage DNA-packaging machinery for their own transfer. Moreover, phage-like particles (gene transfer agents) have also evolved, that can package random pieces of the producing cell's genome. The purpose of this review is to give an overview of some of the various ways by which phages and phage-like particles can transfer bacterial genes, driving bacterial evolution and promoting the emergence of novel pathogens.}, }
@article {pmid25527835, year = {2014}, author = {Urbanczyk, H and Ogura, Y and Hayashi, T}, title = {Contrasting inter- and intraspecies recombination patterns in the "Harveyi clade" vibrio collected over large spatial and temporal scales.}, journal = {Genome biology and evolution}, volume = {7}, number = {1}, pages = {71-80}, pmid = {25527835}, issn = {1759-6653}, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial ; Phylogeny ; *Recombination, Genetic ; Sequence Analysis, DNA ; Vibrio/*genetics ; }, abstract = {Recombination plays an important role in the divergence of bacteria, but the frequency of interspecies and intraspecies recombination events remains poorly understood. We investigated recombination events that occurred within core genomes of 35 Vibrio strains (family Vibrionaceae, Gammaproteobacteria), from six closely related species in the so-called "Harveyi clade." The strains were selected from a collection of strains isolated in the last 90 years, from various environments worldwide. We found a close relationship between the number of interspecies recombination events within core genomes of the 35 strains and the overall genomic identity, as inferred from calculations of the average nucleotide identity. The relationship between the overall nucleotide identity and the number of detected interspecies recombination events was comparable when analyzing strains isolated over 80 years apart, from different hemispheres, or from different ecologies, as well as in strains isolated from the same geographic location within a short time frame. We further applied the same method of detecting recombination events to analyze 11 strains of Vibrio campbellii, and identified disproportionally high number of intraspecies recombination events within the core genomes of some, but not all, strains. The high number of recombination events was detected between V. campbellii strains that have significant temporal (over 18 years) and geographical (over 10,000 km) differences in their origins of isolation. Results of this study reveal a remarkable stability of Harveyi clade species, and give clues about the origins and persistence of species in the clade.}, }
@article {pmid25527550, year = {2015}, author = {Tardy, F and Mick, V and Dordet-Frisoni, E and Marenda, MS and Sirand-Pugnet, P and Blanchard, A and Citti, C}, title = {Integrative conjugative elements are widespread in field isolates of Mycoplasma species pathogenic for ruminants.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {5}, pages = {1634-1643}, pmid = {25527550}, issn = {1098-5336}, mesh = {Animals ; Conserved Sequence ; Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences ; Mycoplasma/*genetics/*isolation &amp; purification ; Mycoplasma Infections/microbiology/*veterinary ; Recombination, Genetic ; *Ruminants ; }, abstract = {Comparative genomics have revealed massive horizontal gene transfer (HGT) between Mycoplasma species sharing common ruminant hosts. Further results pointed toward an integrative conjugative element (ICE) as an important contributor of HGT in the small-ruminant-pathogen Mycoplasma agalactiae. To estimate the prevalence of ICEs in ruminant mycoplasmas, we surveyed their occurrence in a collection of 166 field strains representing 4 (sub)species that are recognized as major pathogens. Based on available sequenced genomes, we first defined the conserved, minimal ICE backbone as composed of 4 coding sequences (CDSs) that are evenly distributed and predicted to be essential for ICE chromosomal integration-excision and horizontal transfer. Screening of the strain collection revealed that these 4 CDSs are well represented in ruminant Mycoplasma species, suggesting widespread occurrence of ICEs. Yet their prevalence varies within and among species, with no correlation found with the individual strain history. Extrachromosomal ICE forms were also often detected, suggesting that ICEs are able to circularize in all species, a first and essential step in ICE horizontal transfer. Examination of the junction of the circular forms and comparative sequence analysis of conserved CDSs clearly pointed toward two types of ICE, the hominis and spiroplasma types, most likely differing in their mechanism of excision-integration. Overall, our data indicate the occurrence and maintenance of functional ICEs in a large number of field isolates of ruminant mycoplasmas. These may contribute to genome plasticity and gene exchanges and, presumably, to the emergence of diverse genotypes within pathogenic mycoplasmas of veterinary importance.}, }
@article {pmid25527273, year = {2015}, author = {McCarthy, AJ and Harrison, EM and Stanczak-Mrozek, K and Leggett, B and Waller, A and Holmes, MA and Lloyd, DH and Lindsay, JA and Loeffler, A}, title = {Genomic insights into the rapid emergence and evolution of MDR in Staphylococcus pseudintermedius.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {70}, number = {4}, pages = {997-1007}, doi = {10.1093/jac/dku496}, pmid = {25527273}, issn = {1460-2091}, support = {G1001787/MRC_/Medical Research Council/United Kingdom ; G1001787/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; *Biological Evolution ; DNA, Bacterial/chemistry/genetics ; *Drug Resistance, Multiple, Bacterial ; Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; Interspersed Repetitive Sequences ; Molecular Sequence Data ; Mutation ; Sequence Analysis, DNA ; Staphylococcus/*drug effects ; }, abstract = {OBJECTIVES: MDR methicillin-resistant Staphylococcus pseudintermedius (MRSP) strains have emerged rapidly as major canine pathogens and present serious treatment issues and concerns to public health due to their, albeit low, zoonotic potential. A further understanding of the genetics of resistance arising from a broadly susceptible background of S. pseudintermedius is needed.<br><br>METHODS: We sequenced the genomes of 12 S. pseudintermedius isolates of varied STs and resistance phenotypes.<br><br>RESULTS: Nine distinct clonal lineages had acquired either staphylococcal cassette chromosome (SCC) mec elements and/or Tn5405-like elements carrying up to five resistance genes [aphA3, sat, aadE, erm(B), dfrG] to generate MRSP, MDR methicillin-susceptible S. pseudintermedius and MDR MRSP populations. The most successful and clinically problematic MDR MRSP clones, ST68 SCCmecV(T) and ST71 SCCmecII-III, have further accumulated mutations in gyrA and grlA conferring resistance to fluoroquinolones. The carriage of additional mobile genetic elements (MGEs) was highly variable, suggesting that horizontal gene transfer is frequent in S. pseudintermedius populations.<br><br>CONCLUSIONS: Importantly, the data suggest that MDR MRSP evolved rapidly by the acquisition of a very limited number of MGEs and mutations, and that the use of many classes of antimicrobials may co-select for the spread and emergence of MDR and XDR strains. Antimicrobial stewardship will need to be comprehensive, encompassing human medicine and veterinary disciplines to successfully preserve antimicrobial efficacy.}, }
@article {pmid25527045, year = {2014}, author = {Misner, I and Blouin, N and Leonard, G and Richards, TA and Lane, CE}, title = {The secreted proteins of Achlya hypogyna and Thraustotheca clavata identify the ancestral oomycete secretome and reveal gene acquisitions by horizontal gene transfer.}, journal = {Genome biology and evolution}, volume = {7}, number = {1}, pages = {120-135}, pmid = {25527045}, issn = {1759-6653}, support = {P20 GM103430/GM/NIGMS NIH HHS/United States ; 8P20GM103430-12/GM/NIGMS NIH HHS/United States ; }, mesh = {Achlya/*genetics ; *Evolution, Molecular ; Fungal Proteins/*genetics/metabolism ; *Gene Transfer, Horizontal ; Genome, Fungal ; Phylogeny ; Proteome ; }, abstract = {Saprotrophic and parasitic microorganisms secrete proteins into the environment to breakdown macromolecules and obtain nutrients. The molecules secreted are collectively termed the "secretome" and the composition and function of this set of proteins varies depending on the ecology, life cycle, and environment of an organism. Beyond the function of nutrient acquisition, parasitic lineages must also secrete molecules to manipulate their host. Here, we use a combination of de novo genome and transcriptome sequencing and bioinformatic identification of signal peptides to identify the putative secreted proteome of two oomycetes, the facultative parasite Achlya hypogyna and free-living Thraustotheca clavata. By comparing the secretomes of these saprolegnialean oomycetes with that of eight other oomycetes, we were able to characterize the evolution of this protein set across the oomycete clade. These species span the last common ancestor of the two major oomycete families allowing us to identify the ancestral secretome. This putative ancestral secretome consists of at least 84 gene families. Only 11 of these gene families are conserved across all 10 secretomes analyzed and the two major branches in the oomycete radiation. Notably, we have identified expressed elicitin-like effector genes in the saprotrophic decomposer, T. clavata. Phylogenetic analyses show six novel horizontal gene transfers to the oomycete secretome from bacterial and fungal donor lineages, four of which are specific to the Saprolegnialeans. Comparisons between free-living and pathogenic taxa highlight the functional changes of oomycete secretomes associated with shifts in lifestyle.}, }
@article {pmid25526263, year = {2014}, author = {Raz, N and Danin-Poleg, Y and Hayman, RB and Bar-On, Y and Linetsky, A and Shmoish, M and Sanjuán, E and Amaro, C and Walt, DR and Kashi, Y}, title = {Genome-wide SNP-genotyping array to study the evolution of the human pathogen Vibrio vulnificus biotype 3.}, journal = {PloS one}, volume = {9}, number = {12}, pages = {e114576}, pmid = {25526263}, issn = {1932-6203}, mesh = {*Evolution, Molecular ; *Genome, Viral ; *Polymorphism, Single Nucleotide ; Vibrio vulnificus/*genetics ; }, abstract = {Vibrio vulnificus is an aquatic bacterium and an important human pathogen. Strains of V. vulnificus are classified into three different biotypes. The newly emerged biotype 3 has been found to be clonal and restricted to Israel. In the family Vibrionaceae, horizontal gene transfer is the main mechanism responsible for the emergence of new pathogen groups. To better understand the evolution of the bacterium, and in particular to trace the evolution of biotype 3, we performed genome-wide SNP genotyping of 254 clinical and environmental V. vulnificus isolates with worldwide distribution recovered over a 30-year period, representing all phylogeny groups. A custom single-nucleotide polymorphism (SNP) array implemented on the Illumina GoldenGate platform was developed based on 570 SNPs randomly distributed throughout the genome. In general, the genotyping results divided the V. vulnificus species into three main phylogenetic lineages and an additional subgroup, clade B, consisting of environmental and clinical isolates from Israel. Data analysis suggested that 69% of biotype 3 SNPs are similar to SNPs from clade B, indicating that biotype 3 and clade B have a common ancestor. The rest of the biotype 3 SNPs were scattered along the biotype 3 genome, probably representing multiple chromosomal segments that may have been horizontally inserted into the clade B recipient core genome from other phylogroups or bacterial species sharing the same ecological niche. Results emphasize the continuous evolution of V. vulnificus and support the emergence of new pathogenic groups within this species as a recurrent phenomenon. Our findings contribute to a broader understanding of the evolution of this human pathogen.}, }
@article {pmid25523226, year = {2015}, author = {Boronat, A and Rodríguez-Concepción, M}, title = {Terpenoid biosynthesis in prokaryotes.}, journal = {Advances in biochemical engineering/biotechnology}, volume = {148}, number = {}, pages = {3-18}, doi = {10.1007/10_2014_285}, pmid = {25523226}, issn = {0724-6145}, mesh = {Archaea/metabolism ; Bacteria/metabolism ; Bacteriochlorophylls/chemistry ; Carotenoids/chemistry ; Cell Membrane/metabolism ; Cell Wall/metabolism ; Chlorophyll/chemistry ; Drug Design ; Fungi/metabolism ; Mitochondria/metabolism ; Plastids/metabolism ; Rhodopsin/chemistry ; Terpenes/chemistry/*metabolism ; Ubiquinone/chemistry ; Vitamin K 2/chemistry ; }, abstract = {Prokaryotic organisms (archaea and eubacteria) are found in all habitats where life exists on our planet. This would not be possible without the astounding biochemical plasticity developed by such organisms. Part of the metabolic diversity of prokaryotes was transferred to eukaryotic cells when endosymbiotic prokaryotes became mitochondria and plastids but also in a large number of horizontal gene transfer episodes. A group of metabolites produced by all free-living organisms is terpenoids (also known as isoprenoids). In prokaryotes, terpenoids play an indispensable role in cell-wall and membrane biosynthesis (bactoprenol, hopanoids), electron transport (ubiquinone, menaquinone), or conversion of light into chemical energy (chlorophylls, bacteriochlorophylls, rhodopsins, carotenoids), among other processes. But despite their remarkable structural and functional diversity, they all derive from the same metabolic precursors. Here we describe the metabolic pathways producing these universal terpenoid units and provide a complete picture of the main terpenoid compounds found in prokaryotic organisms.}, }
@article {pmid25520706, year = {2014}, author = {Bengtsson-Palme, J and Boulund, F and Fick, J and Kristiansson, E and Larsson, DG}, title = {Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {648}, pmid = {25520706}, issn = {1664-302X}, abstract = {There is increasing evidence for an environmental origin of many antibiotic resistance genes. Consequently, it is important to identify environments of particular risk for selecting and maintaining such resistance factors. In this study, we described the diversity of antibiotic resistance genes in an Indian lake subjected to industrial pollution with fluoroquinolone antibiotics. We also assessed the genetic context of the identified resistance genes, to try to predict their genetic transferability. The lake harbored a wide range of resistance genes (81 identified gene types) against essentially every major class of antibiotics, as well as genes responsible for mobilization of genetic material. Resistance genes were estimated to be 7000 times more abundant than in a Swedish lake included for comparison, where only eight resistance genes were found. The sul2 and qnrD genes were the most common resistance genes in the Indian lake. Twenty-six known and 21 putative novel plasmids were recovered in the Indian lake metagenome, which, together with the genes found, indicate a large potential for horizontal gene transfer through conjugation. Interestingly, the microbial community of the lake still included a wide range of taxa, suggesting that, across most phyla, bacteria has adapted relatively well to this highly polluted environment. Based on the wide range and high abundance of known resistance factors we have detected, it is plausible that yet unrecognized resistance genes are also present in the lake. Thus, we conclude that environments polluted with waste from antibiotic manufacturing could be important reservoirs for mobile antibiotic resistance genes.}, }
@article {pmid25516714, year = {2014}, author = {Carletti, G and Nervo, G and Cattivelli, L}, title = {Flavonoids and Melanins: a common strategy across two kingdoms.}, journal = {International journal of biological sciences}, volume = {10}, number = {10}, pages = {1159-1170}, pmid = {25516714}, issn = {1449-2288}, mesh = {Animals ; Antioxidants/*metabolism ; Betalains/chemistry/metabolism ; *Biological Evolution ; Flavonoids/*metabolism ; Free Radical Scavengers/*metabolism ; Genetic Fitness/physiology ; Melanins/*metabolism ; Metabolic Networks and Pathways/*physiology ; Molecular Structure ; Pigmentation/*physiology ; Plants ; Reproduction/physiology ; Ultraviolet Rays/adverse effects ; }, abstract = {Ultraviolet (UV) radiations alter a number of metabolic functions in vivant. They produce damages to lipids, nucleic acids and proteins, generating reactive oxygen species such as singlet oxygen (O2), hydroxyl radical (HO) and superoxide anion (O2 (-)). Plants and animals, after their water emersion, have developed biochemical mechanisms to protect themselves from that environmental threat through a common strategy. Melanins in animals and flavonoids in plants are antioxidant pigments acting as free radical scavenging mechanisms. Both are phenol compounds constitutively synthesized and enhanced after exposure to UV rays, often conferring a red-brown-dark tissue pigmentation. Noteworthy, beside anti-oxidant scavenging activity, melanins and flavonoids have acquired secondary functions that, both in plants and animals, concern reproductions and fitness. Plants highly pigmented are more resistant to biotic and abiotic stresses. Darker wild vertebrates are generally more aggressive, sexually active and resistant to stress than lighter individuals. Flavonoids have been associated with signal attraction between flowers and insects and with plant-plant interaction. Melanin pigmentation has been proposed as trait in bird communication, acting as honest signals of quality. This review shows how the molecular mechanisms leading to tissue pigmentation have many functional analogies between plants and animals and how their origin lies in simpler organisms such as Cyanobacteria. Comparative studies between plant and animal kingdoms can reveal new insight of the antioxidant strategies in vivant.}, }
@article {pmid25505644, year = {2014}, author = {Derbyshire, KM and Gray, TA}, title = {Distributive Conjugal Transfer: New Insights into Horizontal Gene Transfer and Genetic Exchange in Mycobacteria.}, journal = {Microbiology spectrum}, volume = {2}, number = {1}, pages = {}, pmid = {25505644}, issn = {2165-0497}, support = {R01 AI042308/AI/NIAID NIH HHS/United States ; R56 AI080694/AI/NIAID NIH HHS/United States ; }, abstract = {The last decade has seen an explosion in the application of genomic tools across all biological disciplines. This is also true for mycobacteria, where whole genome sequences are now available for pathogens and non-pathogens alike. Genomes within the Mycobacterium tuberculosis Complex (MTBC) bear the hallmarks of horizontal gene transfer (HGT). Conjugation is the form of HGT with the highest potential capacity and evolutionary influence. Donor and recipient strains of Mycobacterium smegmatis actively conjugate upon co-culturing in biofilms and on solid media. Whole genome sequencing of the transconjugant progeny demonstrated the incredible scale and range of genomic variation that conjugation generates. Transconjugant genomes are complex mosaics of the parental strains. Some transconjugant genomes are up to one-quarter donor-derived, distributed over 30 segments. Transferred segments range from ~50 bp to ~225,000 bp in length, and are exchanged with their recipient orthologs all around the genome. This unpredictable genome-wide infusion of DNA sequences is called Distributive Conjugal Transfer (DCT), to distinguish it from traditional oriT-based conjugation. The mosaicism generated in a single transfer event resembles that seen from meiotic recombination in sexually reproducing organisms, and contrasts with traditional models of HGT. This similarity allowed the application of a GWAS-like approach to map the donor genes that confer a donor mating identity phenotype. The mating identity genes map to the esx1 locus, expanding the central role of ESX-1 function in conjugation. The potential for DCT to instantaneously blend genomes will affect how we view mycobacterial evolution, and provide new tools for the facile manipulation of mycobacterial genomes.}, }
@article {pmid25505188, year = {2015}, author = {Maslunka, C and Gürtler, V and Seviour, R}, title = {Unusual features of the sequences of copies of the 16S-23S rRNA internal transcribed spacer regions of Acinetobacter bereziniae, Acinetobacter guillouiae and Acinetobacter baylyi arise from horizontal gene transfer events.}, journal = {Microbiology (Reading, England)}, volume = {161}, number = {Pt 2}, pages = {322-329}, doi = {10.1099/mic.0.083600-0}, pmid = {25505188}, issn = {1465-2080}, mesh = {Acinetobacter/*genetics ; Base Sequence ; DNA, Bacterial/*genetics ; DNA, Ribosomal Spacer/*genetics ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; RNA, Ribosomal, 16S/*genetics ; RNA, Ribosomal, 23S/*genetics ; }, abstract = {The highly variable nature of the internal transcribed spacer region (ITS) has been claimed to represent an ideal target for designing species-specific probes/primers capable of differentiating between closely related Acinetobacter species. However, several Acinetobacter species contain multiple ITS copies of variable lengths, and these include Acinetobacter bereziniae, Acinetobacter guillouiae and Acinetobacter baylyi. This study shows these length variations result from inter-genomic insertion/deletion events (indels) involving horizontal transfer of ITS fragments of other Acinetobacter species and possibly unrelated bacteria, as shown previously by us. In some instances, indel incorporation results in the loss of probe target sites in the recipient cell ITS. In other cases, some indel sequences contain target sites for probes designed from a single ITS sequence to target other Acinetobacter species. Hence, these can generate false positives. The largest of the indels that remove probe sites is 683 bp (labelled bay/i1-0), and it derives from the horizontal transfer of a complete ITS between A. bereziniae BCRC15423(T) and A. baylyi strain ADP1. As a consequence, ITS sequencing or fingerprinting cannot be used to distinguish between the 683 bp ITS in these two strains.}, }
@article {pmid25504421, year = {2015}, author = {Ghoshroy, S and Robertson, DL}, title = {Molecular evolution of nitrogen assimilatory enzymes in marine prasinophytes.}, journal = {Journal of molecular evolution}, volume = {80}, number = {1}, pages = {65-80}, pmid = {25504421}, issn = {1432-1432}, mesh = {Animals ; Chlorophyta/classification/enzymology/*genetics ; *Evolution, Molecular ; Glutamate-Ammonia Ligase/*genetics ; Nitrate Reductase/*genetics ; Nitrogen/*metabolism ; Phylogeny ; }, abstract = {Nitrogen assimilation is a highly regulated process requiring metabolic coordination of enzymes and pathways in the cytosol, chloroplast, and mitochondria. Previous studies of prasinophyte genomes revealed that genes encoding nitrate and ammonium transporters have a complex evolutionary history involving both vertical and horizontal transmission. Here we examine the evolutionary history of well-conserved nitrogen-assimilating enzymes to determine if a similar complex history is observed. Phylogenetic analyses suggest that genes encoding glutamine synthetase (GS) III in the prasinophytes evolved by horizontal gene transfer from a member of the heterokonts. In contrast, genes encoding GSIIE, a canonical vascular plant and green algal enzyme, were found in the Micromonas genomes but have been lost from Ostreococcus. Phylogenetic analyses placed the Micromonas GSIIs in a larger chlorophyte/vascular plant clade; a similar topology was observed for ferredoxin-dependent nitrite reductase (Fd-NiR), indicating the genes encoding GSII and Fd-NiR in these prasinophytes evolved via vertical transmission. Our results show that genes encoding the nitrogen-assimilating enzymes in Micromonas and Ostreococcus have been differentially lost and as well as recruited from different evolutionary lineages, suggesting that the regulation of nitrogen assimilation in prasinophytes will differ from other green algae.}, }
@article {pmid25503461, year = {2014}, author = {Sekizuka, T and Kai, M and Nakanaga, K and Nakata, N and Kazumi, Y and Maeda, S and Makino, M and Hoshino, Y and Kuroda, M}, title = {Complete genome sequence and comparative genomic analysis of Mycobacterium massiliense JCM 15300 in the Mycobacterium abscessus group reveal a conserved genomic island MmGI-1 related to putative lipid metabolism.}, journal = {PloS one}, volume = {9}, number = {12}, pages = {e114848}, pmid = {25503461}, issn = {1932-6203}, mesh = {DNA, Bacterial ; *Genome, Bacterial ; Genomic Islands/*genetics ; Humans ; Lipid Metabolism/genetics ; Mycobacterium/*genetics ; Nontuberculous Mycobacteria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Mycobacterium abscessus group subsp., such as M. massiliense, M. abscessus sensu stricto and M. bolletii, are an environmental organism found in soil, water and other ecological niches, and have been isolated from respiratory tract infection, skin and soft tissue infection, postoperative infection of cosmetic surgery. To determine the unique genetic feature of M. massiliense, we sequenced the complete genome of M. massiliense type strain JCM 15300 (corresponding to CCUG 48898). Comparative genomic analysis was performed among Mycobacterium spp. and among M. abscessus group subspp., showing that additional ß-oxidation-related genes and, notably, the mammalian cell entry (mce) operon were located on a genomic island, M. massiliense Genomic Island 1 (MmGI-1), in M. massiliense. In addition, putative anaerobic respiration system-related genes and additional mycolic acid cyclopropane synthetase-related genes were found uniquely in M. massiliense. Japanese isolates of M. massiliense also frequently possess the MmGI-1 (14/44, approximately 32%) and three unique conserved regions (26/44; approximately 60%, 34/44; approximately 77% and 40/44; approximately 91%), as well as isolates of other countries (Malaysia, France, United Kingdom and United States). The well-conserved genomic island MmGI-1 may play an important role in high growth potential with additional lipid metabolism, extra factors for survival in the environment or synthesis of complex membrane-associated lipids. ORFs on MmGI-1 showed similarities to ORFs of phylogenetically distant M. avium complex (MAC), suggesting that horizontal gene transfer or genetic recombination events might have occurred within MmGI-1 among M. massiliense and MAC.}, }
@article {pmid25502987, year = {2015}, author = {Chan, YB and Ranwez, V and Scornavacca, C}, title = {Exploring the space of gene/species reconciliations with transfers.}, journal = {Journal of mathematical biology}, volume = {71}, number = {5}, pages = {1179-1209}, pmid = {25502987}, issn = {1432-1416}, mesh = {Algorithms ; Computer Simulation ; *Evolution, Molecular ; Gene Deletion ; Gene Duplication ; Gene Transfer, Horizontal ; Genetic Speciation ; Mathematical Concepts ; *Models, Genetic ; Multigene Family ; *Phylogeny ; Species Specificity ; }, abstract = {Reconciliations between gene and species trees have important applications in the study of genome evolution (e.g. sequence orthology prediction or quantification of transfer events). While numerous methods have been proposed to infer them, little has been done to study the underlying reconciliation space. In this paper, we characterise the reconciliation space for two evolutionary models: the [Formula: see text] (duplication, loss and transfer) model and a variant of it-the no-[Formula: see text] model-which does not allow [Formula: see text] events (a transfer immediately followed by a loss). We provide formulae to compute the size of the corresponding spaces and define a set of transformation operators sufficient to explore the entire reconciliation space. We also define a distance between two reconciliations as the minimal number of operations needed to transform one into the other and prove that this distance is easily computable in the no-[Formula: see text] model. Computing this distance in the [Formula: see text] model is more difficult and it is an open question whether it is NP-hard or not. This work constitutes an important step toward reconciliation space characterisation and reconciliation comparison, needed to better assess the performance of reconciliation inference methods through simulations.}, }
@article {pmid25502908, year = {2014}, author = {Li, J and Wong, CF and Wong, MT and Huang, H and Leung, FC}, title = {Modularized evolution in archaeal methanogens phylogenetic forest.}, journal = {Genome biology and evolution}, volume = {6}, number = {12}, pages = {3344-3359}, pmid = {25502908}, issn = {1759-6653}, mesh = {Euryarchaeota/classification/*genetics/metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, Archaeal ; Methane/metabolism ; *Phylogeny ; }, abstract = {Methanogens are methane-producing archaea that plays a key role in the global carbon cycle. To date, the evolutionary history of methanogens and closely related nonmethanogen species remains unresolved among studies conducted upon different genetic markers, attributing to horizontal gene transfers (HGTs). With an effort to decipher both congruent and conflicting evolutionary events, reconstruction of coevolved gene clusters and hierarchical structure in the archaeal methanogen phylogenetic forest, comprehensive evolution, and network analyses were performed upon 3,694 gene families from 41 methanogens and 33 closely related archaea. Our results show that 1) greater than 50% of genes are in topological dissonance with others; 2) the prevalent interorder HGTs, even for core genes, in methanogen genomes led to their scrambled phylogenetic relationships; 3) most methanogenesis-related genes have experienced at least one HGT; 4) greater than 20% of the genes in methanogen genomes were transferred horizontally from other archaea, with genes involved in cell-wall synthesis and defense system having been transferred most frequently; 5) the coevolution network contains seven statistically robust modules, wherein the central module has the highest average node strength and comprises a majority of the core genes; 6) different coevolutionary module genes boomed in different time and evolutionary lineage, constructing diversified pan-genome structures; 7) the modularized evolution is also closely related to the vertical evolution signals and the HGT rate of the genes. Overall, this study presented a modularized phylogenetic forest that describes a combination of complicated vertical and nonvertical evolutionary processes for methanogenic archaeal species.}, }
@article {pmid25500508, year = {2015}, author = {Gillings, MR and Gaze, WH and Pruden, A and Smalla, K and Tiedje, JM and Zhu, YG}, title = {Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution.}, journal = {The ISME journal}, volume = {9}, number = {6}, pages = {1269-1279}, pmid = {25500508}, issn = {1751-7370}, mesh = {Anti-Bacterial Agents/chemistry ; Bacteria/drug effects/*genetics ; DNA Transposable Elements ; Drug Resistance, Bacterial ; Environmental Monitoring/*methods ; *Environmental Pollution ; Gene Transfer, Horizontal ; Genetic Variation ; Integrases/*genetics ; Integrons/*genetics ; Metals, Heavy/*analysis ; }, abstract = {Around all human activity, there are zones of pollution with pesticides, heavy metals, pharmaceuticals, personal care products and the microorganisms associated with human waste streams and agriculture. This diversity of pollutants, whose concentration varies spatially and temporally, is a major challenge for monitoring. Here, we suggest that the relative abundance of the clinical class 1 integron-integrase gene, intI1, is a good proxy for pollution because: (1) intI1 is linked to genes conferring resistance to antibiotics, disinfectants and heavy metals; (2) it is found in a wide variety of pathogenic and nonpathogenic bacteria; (3) its abundance can change rapidly because its host cells can have rapid generation times and it can move between bacteria by horizontal gene transfer; and (4) a single DNA sequence variant of intI1 is now found on a wide diversity of xenogenetic elements, these being complex mosaic DNA elements fixed through the agency of human selection. Here we review the literature examining the relationship between anthropogenic impacts and the abundance of intI1, and outline an approach by which intI1 could serve as a proxy for anthropogenic pollution.}, }
@article {pmid25498339, year = {2014}, author = {Dunning Hotopp, JC and Estes, AM}, title = {Biology wars: the eukaryotes strike back.}, journal = {Cell host &amp; microbe}, volume = {16}, number = {6}, pages = {701-703}, doi = {10.1016/j.chom.2014.11.014}, pmid = {25498339}, issn = {1934-6069}, support = {BB/I020012/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; DP2 OD007372/OD/NIH HHS/United States ; 1-DP2-OD007372/OD/NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*enzymology/*genetics ; Bacterial Toxins/*genetics ; Eukaryota/*genetics/*immunology ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/*genetics ; *Immunity, Innate ; }, abstract = {It is increasingly clear that eukaryotes have acquired bacterial DNA and function through horizontal gene transfer (HGT). In this issue of Cell Host &amp; Microbe, Chou et al. (2014) and Metcalf et al. (2014) report multiple HGTs of bacterial tae and lysozyme genes, respectively, to diverse eukaryotic and archaeal hosts that may complement their response to bacteria.}, }
@article {pmid25498143, year = {2015}, author = {Chen, J and Ram, G and Penadés, JR and Brown, S and Novick, RP}, title = {Pathogenicity island-directed transfer of unlinked chromosomal virulence genes.}, journal = {Molecular cell}, volume = {57}, number = {1}, pages = {138-149}, pmid = {25498143}, issn = {1097-4164}, support = {R01 AI022159/AI/NIAID NIH HHS/United States ; 5R01-AI022159-27/AI/NIAID NIH HHS/United States ; }, mesh = {Base Sequence ; Chromosomes, Bacterial/*chemistry ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genomic Islands ; Humans ; Molecular Sequence Data ; Prophages/genetics ; Staphylococcal Infections/microbiology/pathology/transmission ; Staphylococcus Phages/genetics ; Staphylococcus aureus/*genetics/pathogenicity/virology ; Virulence ; }, abstract = {In recent decades, the notorious pathogen Staphylococcus aureus has become progressively more contagious, more virulent, and more resistant to antibiotics. This implies a rather dynamic evolutionary capability, representing a remarkable level of genomic plasticity, most probably maintained by horizontal gene transfer. Here we report that the staphylococcal pathogenicity islands have a dual role in gene transfer: they not only mediate their own transfer, but they can independently direct the transfer of unlinked chromosomal segments containing virulence genes. While transfer of the island itself requires specific helper phages, transfer of unlinked chromosomal segments does not, so potentially any pac-type phage will serve. These results reveal that SaPIs can increase the horizontal exchange of accessory genes associated with disease and may shape pathogen genomes beyond the confines of their attachment sites.}, }
@article {pmid25496002, year = {2014}, author = {Klasson, L and Kumar, N and Bromley, R and Sieber, K and Flowers, M and Ott, SH and Tallon, LJ and Andersson, SG and Dunning Hotopp, JC}, title = {Extensive duplication of the Wolbachia DNA in chromosome four of Drosophila ananassae.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {1097}, pmid = {25496002}, issn = {1471-2164}, support = {DP2 OD007372/OD/NIH HHS/United States ; T32 DK067872/DK/NIDDK NIH HHS/United States ; 1-DP2-OD007372/OD/NIH HHS/United States ; }, mesh = {Animals ; Chromosome Mapping ; *DNA Replication ; DNA, Bacterial/*biosynthesis/*genetics ; Drosophila/*genetics/*microbiology ; Female ; Gene Dosage ; *Gene Transfer, Horizontal ; Genome, Insect/genetics ; Heterozygote ; Male ; Polytene Chromosomes/genetics ; Sequence Analysis, DNA ; Species Specificity ; Symbiosis ; Wolbachia/*genetics ; }, abstract = {BACKGROUND: Lateral gene transfer (LGT) from bacterial Wolbachia endosymbionts has been detected in ~20% of arthropod and nematode genome sequencing projects. Many of these transfers are large and contain a substantial part of the Wolbachia genome.<br><br>RESULTS: Here, we re-sequenced three D. ananassae genomes from Asia and the Pacific that contain large LGTs from Wolbachia. We find that multiple copies of the Wolbachia genome are transferred to the Drosophila nuclear genome in all three lines. In the D. ananassae line from Indonesia, the copies of Wolbachia DNA in the nuclear genome are nearly identical in size and sequence yielding an even coverage of mapped reads over the Wolbachia genome. In contrast, the D. ananassae lines from Hawaii and India show an uneven coverage of mapped reads over the Wolbachia genome suggesting that different parts of these LGTs are present in different copy numbers. In the Hawaii line, we find that this LGT is underrepresented in third instar larvae indicative of being heterochromatic. Fluorescence in situ hybridization of mitotic chromosomes confirms that the LGT in the Hawaii line is heterochromatic and represents ~20% of the sequence on chromosome 4 (dot chromosome, Muller element F).<br><br>CONCLUSIONS: This collection of related lines contain large lateral gene transfers composed of multiple Wolbachia genomes that constitute >2% of the D. ananassae genome (~5 Mbp) and partially explain the abnormally large size of chromosome 4 in D. ananassae.}, }
@article {pmid25494465, year = {2015}, author = {Bock, R}, title = {Engineering plastid genomes: methods, tools, and applications in basic research and biotechnology.}, journal = {Annual review of plant biology}, volume = {66}, number = {}, pages = {211-241}, doi = {10.1146/annurev-arplant-050213-040212}, pmid = {25494465}, issn = {1545-2123}, mesh = {Biotechnology/methods ; Chloroplasts/*genetics ; *DNA, Chloroplast ; *Genes, Chloroplast ; Genetic Engineering/*methods ; *Genome, Chloroplast ; Plants, Genetically Modified/*genetics ; *Transformation, Genetic ; }, abstract = {The small bacterial-type genome of the plastid (chloroplast) can be engineered by genetic transformation, generating cells and plants with transgenic plastid genomes, also referred to as transplastomic plants. The transformation process relies on homologous recombination, thereby facilitating the site-specific alteration of endogenous plastid genes as well as the precisely targeted insertion of foreign genes into the plastid DNA. The technology has been used extensively to analyze chloroplast gene functions and study plastid gene expression at all levels in vivo. Over the years, a large toolbox has been assembled that is now nearly comparable to the techniques available for plant nuclear transformation and that has enabled new applications of transplastomic technology in basic and applied research. This review describes the state of the art in engineering the plastid genomes of algae and land plants (Embryophyta). It provides an overview of the existing tools for plastid genome engineering, discusses current technological limitations, and highlights selected applications that demonstrate the immense potential of chloroplast transformation in several key areas of plant biotechnology.}, }
@article {pmid25491478, year = {2015}, author = {Akhtar, N and Ghauri, MA and Anwar, MA and Heaphy, S}, title = {Phylogenetic characterization and novelty of organic sulphur metabolizing genes of Rhodococcus spp. (Eu-32).}, journal = {Biotechnology letters}, volume = {37}, number = {4}, pages = {837-847}, doi = {10.1007/s10529-014-1736-6}, pmid = {25491478}, issn = {1573-6776}, mesh = {Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Metabolic Networks and Pathways/*genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhodococcus/*classification/*genetics/metabolism ; Sequence Analysis, DNA ; Sequence Homology ; Thiophenes/*metabolism ; }, abstract = {Rhodococcus spp. (Eu-32) has the unique ability to metabolize organic sulphur containing compounds like dibenzothiophene through an extended sulphur specific pathway (Akhtar et al., in FEMS Microbiol Lett 301:95-102, 2009). Efforts were made to isolate and characterize the presumed desulphurizing genes (dszABC) involved in the sulphur specific pathway of isolate Eu-32 by employing standard and degenerate polymerase chain reaction primers. The partial dszA gene sequence of isolate Eu-32 showed 92% sequence identity with a putative FMNH-2 dependent monooxygenase of Rhodococcus erythropolis PR4. The dszC gene sequence showed 99% homology with the dibenzothiophene monooxygenase desulphurizing enzyme of another Rhodococcus species. The dszB gene was not unambiguously identified. A phylogenetic analysis by maximum likelihood method of the 16S rRNA gene and deduced DszA and C amino acid sequences suggest that horizontal gene transfer events might have taken place during the evolution of desulphurizing genes of Rhodococcus spp. (Eu-32).}, }
@article {pmid25489752, year = {2015}, author = {Smith, TJ and Hill, KK and Xie, G and Foley, BT and Williamson, CHD and Foster, JT and Johnson, SL and Chertkov, O and Teshima, H and Gibbons, HS and Johnsky, LA and Karavis, MA and Smith, LA}, title = {Genomic sequences of six botulinum neurotoxin-producing strains representing three clostridial species illustrate the mobility and diversity of botulinum neurotoxin genes.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {30}, number = {}, pages = {102-113}, pmid = {25489752}, issn = {1567-7257}, support = {U01 AI056493/AI/NIAID NIH HHS/United States ; U01AI056493/AI/NIAID NIH HHS/United States ; }, mesh = {Botulinum Toxins/*genetics ; Clostridium/*genetics/*pathogenicity ; Clostridium Infections/microbiology ; DNA, Bacterial/genetics ; Environmental Microbiology ; Food Microbiology ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial/*genetics ; Humans ; Multigene Family/genetics ; Phylogeny ; Sequence Alignment ; }, abstract = {The whole genomes for six botulinum neurotoxin-producing clostridial strains were sequenced to provide references for under-represented toxin types, bivalent strains or unusual toxin complexes associated with a bont gene. The strains include three Clostridium botulinum Group I strains (CDC 297, CDC 1436, and Prevot 594), a Group II C. botulinum strain (Eklund 202F), a Group IV Clostridium argentinense strain (CDC 2741), and a Group V Clostridium baratii strain (Sullivan). Comparisons of the Group I genomic sequences revealed close relationships and conservation of toxin gene locations with previously published Group I C. botulinum genomes. The bont/F6 gene of strain Eklund 202F was determined to be a chimeric toxin gene composed of bont/F1 and bont/F2. The serotype G strain CDC 2741 remained unfinished in 20 contigs with the bont/G located within a 1.15Mb contig, indicating a possible chromosomal location for this toxin gene. Within the genome of C. baratii Sullivan strain, direct repeats of IS1182 insertion sequence (IS) elements were identified flanking the bont/F7 toxin complex that may be the mechanism of bont insertion into C. baratii. Highlights of the six strains are described and release of their genomic sequences will allow further study of unusual neurotoxin-producing clostridial strains.}, }
@article {pmid25488608, year = {2015}, author = {Njage, PM and Buys, EM}, title = {Pathogenic and commensal Escherichia coli from irrigation water show potential in transmission of extended spectrum and AmpC β-lactamases determinants to isolates from lettuce.}, journal = {Microbial biotechnology}, volume = {8}, number = {3}, pages = {462-473}, pmid = {25488608}, issn = {1751-7915}, mesh = {Agricultural Irrigation ; Anti-Bacterial Agents/pharmacology ; Cluster Analysis ; Conjugation, Genetic ; Escherichia coli/*enzymology/genetics/*isolation &amp; purification ; *Gene Transfer, Horizontal ; Genotype ; Lactuca/*microbiology ; Molecular Typing ; *Water Microbiology ; beta-Lactam Resistance ; beta-Lactamases/*genetics ; beta-Lactams/pharmacology ; }, abstract = {There are few studies on the presence of extended-spectrum β-lactamases and AmpC β-lactamases (ESBL/AmpC) in bacteria that contaminate vegetables. The role of the production environment in ESBL/AmpC gene transmission is poorly understood. The occurrence of ESBL/AmpC in Escherichia coli (n = 46) from lettuce and irrigation water and the role of irrigation water in the transmission of resistant E. coli were studied. The presence of ESBL/AmpC, genetic similarity and phylogeny were typed using genotypic and phenotypic techniques. The frequency of β-lactamase gene transfer was studied in vitro. ESBLs/AmpC were detected in 35 isolates (76%). Fourteen isolates (30%) produced both ESBLs/AmpC. Prevalence was highest in E. coli from lettuce (90%). Twenty-two isolates (48%) were multi-resistant with between two and five ESBL/AmpC genes. The major ESBL determinant was the CTX-M type (34 isolates). DHA (33% of isolates) were the dominant AmpC β lactamases. There was a high conjugation efficiency among the isolates, ranging from 3.5 × 10(-2) to 1 × 10(-2) ± 1.4 × 10(-1) transconjugants per recipient. Water isolates showed a significantly higher conjugation frequency than those from lettuce. A high degree of genetic relatedness between E. coli from irrigation water and lettuce indicated possible common ancestry and pathway of transmission.}, }
@article {pmid25488300, year = {2015}, author = {Wisniewski, JA and Teng, WL and Bannam, TL and Rood, JI}, title = {Two novel membrane proteins, TcpD and TcpE, are essential for conjugative transfer of pCW3 in Clostridium perfringens.}, journal = {Journal of bacteriology}, volume = {197}, number = {4}, pages = {774-781}, pmid = {25488300}, issn = {1098-5530}, mesh = {Bacterial Proteins/genetics/*metabolism ; Clostridium perfringens/genetics/*metabolism ; *Conjugation, Genetic ; *Gene Transfer, Horizontal ; Plasmids/*genetics/metabolism ; }, abstract = {The anaerobic pathogen Clostridium perfringens encodes either toxin genes or antibiotic resistance determinants on a unique family of conjugative plasmids that have a novel conjugation region, the tcp locus. Studies of the paradigm conjugative plasmid from C. perfringens, the 47-kb tetracycline resistance plasmid pCW3, have identified several tcp-encoded proteins that are involved in conjugative transfer and form part of the transfer apparatus. In this study, the role of the conserved hypothetical proteins TcpD, TcpE, and TcpJ was examined. Mutation and complementation analyses showed that TcpD and TcpE were essential for the conjugative transfer of pCW3, whereas TcpJ was not required. To analyze the TcpD and TcpE proteins in C. perfringens, functional hemagglutinin (HA)-tagged derivatives were constructed. Western blots showed that TcpD and TcpE localized to the cell envelope fraction independently of the presence of other pCW3-encoded proteins. Finally, examination of the subcellular localization of TcpD and TcpE by immunofluorescence showed that these proteins were concentrated at both poles of C. perfringens donor cells, where they are postulated to form essential components of the multiprotein complex that comprises the transfer apparatus.}, }
@article {pmid25487115, year = {2015}, author = {Choi, JM and Woo, GJ}, title = {Transfer of tetracycline resistance genes with aggregation substance in food-borne Enterococcus faecalis.}, journal = {Current microbiology}, volume = {70}, number = {4}, pages = {476-484}, pmid = {25487115}, issn = {1432-0991}, mesh = {*Bacterial Adhesion ; Bacterial Proteins/genetics/*metabolism ; *Conjugation, Genetic ; Enterococcus faecalis/*drug effects/*genetics/physiology ; *Gene Transfer, Horizontal ; Korea ; *Tetracycline Resistance ; }, abstract = {Enterococcus faecalis has the ability to conjugate with the aid of aggregation substance (AS) and inducible sex pheromones to exchange genetic elements in food matrix. To evaluate the food safety condition and the transferable factor, 250 tetracycline-resistant food-borne E. faecalis were collected in Korea. Among the isolates, a majority of tetracycline-resistant isolates (49.6 %) harbored both the tet(M) and tet(L) genes together, followed by tet(M) (19.6 %), and tet(L) (6.8 %) alone. Also, we found the combination of tet(L)/tet(M)/tet(O) or tet(M)/tet(O). We identified two tet(S) genes including the isolate carrying tet(M) + tet(S) genes. Additionally, most E. faecalis were positive for cpd and ccf (both 96.8 %) followed by cob (57.2 %). Through mating experiments, we confirmed E. faecalis possessing the Int-Tn gene and/or any AS gene successfully transferred tet genes to JH2-2 E. faecalis, whereas neither E. faecalis carrying AS genes nor the Int-Tn gene showed the conjugation. Pulsed-field gel electrophoresis results supported a distinct pattern, implying transfer of genetic information. Our study revealed a high occurrence of tetracycline resistance genes in E. faecalis from various foods. The widespread dissemination of tetracycline resistance genes would be promoted to transfer tetracycline resistance genes by pheromone-mediated conjugation systems.}, }
@article {pmid25485928, year = {2015}, author = {Song, M and Bai, Y and Xu, J and Carter, MQ and Shi, C and Shi, X}, title = {Genetic diversity and virulence potential of Staphylococcus aureus isolates from raw and processed food commodities in Shanghai.}, journal = {International journal of food microbiology}, volume = {195}, number = {}, pages = {1-8}, doi = {10.1016/j.ijfoodmicro.2014.11.020}, pmid = {25485928}, issn = {1879-3460}, mesh = {Bacterial Toxins/genetics ; China ; Food Handling ; *Food Microbiology ; *Genetic Variation ; Raw Foods/*microbiology ; Staphylococcus aureus/*genetics/isolation &amp; purification/*pathogenicity ; Virulence/*genetics ; Virulence Factors/genetics ; }, abstract = {The risk of zoonotic transmission to humans highlights the need to understand the molecular ecology of Staphylococcus aureus in foods. In this study, 142 S. aureus isolates obtained from various raw and processed foods from Shanghai, China were characterized to determine their genetic diversity and virulence gene content. A total of 16 clonal complexes (CCs), 34 staphylococcal protein A (spa) types, and 6 accessory gene regulator (agr) allelic groups were identified and analyzed among the 142 S. aureus isolates. Among these, the genotype CC188-t189-agr Ι was the most prevalent, constituting 28.2% of all isolates. The presence of virulence genes encoding 20 staphylococcal enterotoxins (se), toxic shock syndrome toxin (tsst1), exfoliative toxins (eta, etb, and etd), Panton-Valentine leukocidin (lukS-PV and lukF-PV), as well as methicillin resistance gene (mecA), was determined by PCR. Of these S. aureus isolates, 72.5% harbored toxin genes, in which the most frequent toxin gene was sep (43.7%), followed by sej (26.1%) and pvl (21.1%). In contrast, see, ses, set, tsst1, etb, and etd were not found in any of the isolates tested. Eight S. aureus isolates (5.6%, 8/142), seven from raw milk and one from frozen food, were mecA positive and resistant to oxacillin, thus were MRSA. The 142 S. aureus isolates displayed 52 different toxin gene profiles. Although no direct association was found between toxin gene profile and the S. aureus genotype, the isolates belonging to CC5, CC9, CC20, CC50, and CC72 clonal lineages in general carried more toxin genes (>5) compared with the isolates in other CCs. It was also revealed that raw milk and raw meat were the major sources of isolates containing multiple toxin genes. S. aureus isolates from food that were genetically highly related, displayed diverse toxin gene profiles, implying the significant role of horizontal gene transfer in the emergence of highly toxigenic S. aureus isolates.}, }
@article {pmid25483352, year = {2015}, author = {Hirt, RP and Alsmark, C and Embley, TM}, title = {Lateral gene transfers and the origins of the eukaryote proteome: a view from microbial parasites.}, journal = {Current opinion in microbiology}, volume = {23}, number = {}, pages = {155-162}, pmid = {25483352}, issn = {1879-0364}, support = {//Wellcome Trust/United Kingdom ; 268701/ERC_/European Research Council/International ; 045404/WT_/Wellcome Trust/United Kingdom ; 075796/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Eukaryota/*chemistry/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Humans ; *Prokaryotic Cells ; Proteome/*analysis ; }, abstract = {Our knowledge of the extent and functional impact of lateral gene transfer (LGT) from prokaryotes to eukaryotes, outside of endosymbiosis, is still rather limited. Here we review the recent literature, focusing mainly on microbial parasites, indicating that LGT from diverse prokaryotes has played a significant role in the evolution of a number of lineages, and by extension throughout eukaryotic evolution. As might be expected, taxonomic biases for donor prokaryotes indicate that shared habitat is a major factor driving transfers. The LGTs identified predominantly affect enzymes from metabolic pathways, but over a third of LGT are genes for putative proteins of unknown function. Finally, we discuss the difficulties in analysing LGT among eukaryotes and suggest that high-throughput methodologies integrating different approaches are needed to achieve a more global understanding of the importance of LGT in eukaryotic evolution.}, }
@article {pmid25482231, year = {2014}, author = {Yang, H and Ma, Y and Wang, Y and Yang, H and Shen, W and Chen, X}, title = {Transcription regulation mechanisms of bacteriophages: recent advances and future prospects.}, journal = {Bioengineered}, volume = {5}, number = {5}, pages = {300-304}, pmid = {25482231}, issn = {2165-5987}, mesh = {Bacteriophages/*genetics ; DNA-Directed RNA Polymerases/genetics ; *Gene Expression Regulation, Viral ; Promoter Regions, Genetic/genetics ; }, abstract = {Phage diversity significantly contributes to ecology and evolution of new bacterial species through horizontal gene transfer. Therefore, it is essential to understand the mechanisms underlying phage-host interactions. After initial infection, the phage utilizes the transcriptional machinery of the host to direct the expression of its own genes. This review presents a view on the transcriptional regulation mechanisms of bacteriophages, and its contribution to phage diversity and classification. Through this review, we aim to broaden the understanding of phage-host interactions while providing a reference source for researchers studying the regulation of phage transcription.}, }
@article {pmid25482188, year = {2014}, author = {Zhao, S and Wan, C and Ke, C and Seto, J and Dehghan, S and Zou, L and Zhou, J and Cheng, Z and Jing, S and Zeng, Z and Zhang, J and Wan, X and Wu, X and Zhao, W and Zhu, L and Seto, D and Zhang, Q}, title = {Re-emergent human adenovirus genome type 7d caused an acute respiratory disease outbreak in Southern China after a twenty-one year absence.}, journal = {Scientific reports}, volume = {4}, number = {}, pages = {7365}, pmid = {25482188}, issn = {2045-2322}, mesh = {Adenovirus Infections, Human/*epidemiology/*virology ; Adenoviruses, Human/classification/*genetics ; China/epidemiology ; *Communicable Diseases, Emerging ; Computational Biology ; Disease Outbreaks ; Gene Order ; Genes, Viral ; Genome, Viral ; Humans ; Molecular Typing ; Mutation ; Phylogeny ; Polymorphism, Single Nucleotide ; Prohibitins ; Recombination, Genetic ; Respiratory Tract Infections/*epidemiology/*virology ; Selection, Genetic ; }, abstract = {Human adenoviruses (HAdVs) are highly contagious pathogens causing acute respiratory disease (ARD), among other illnesses. Of the ARD genotypes, HAdV-7 presents with more severe morbidity and higher mortality than the others. We report the isolation and identification of a genome type HAdV-7d (DG01_2011) from a recent outbreak in Southern China. Genome sequencing, phylogenetic analysis, and restriction endonuclease analysis (REA) comparisons with past pathogens indicate HAdV-7d has re-emerged in Southern China after an absence of twenty-one years. Recombination analysis reveals this genome differs from the 1950s-era prototype and vaccine strains by a lateral gene transfer, substituting the coding region for the L1 52/55 kDa DNA packaging protein from HAdV-16. DG01_2011 descends from both a strain circulating in Southwestern China (2010) and a strain from Shaanxi causing a fatality and outbreak (Northwestern China; 2009). Due to the higher morbidity and mortality rates associated with HAdV-7, the surveillance, identification, and characterization of these strains in population-dense China by REA and/or whole genome sequencing are strongly indicated. With these accurate identifications of specific HAdV types and an epidemiological database of regional HAdV pathogens, along with the HAdV genome stability noted across time and space, the development, availability, and deployment of appropriate vaccines are needed.}, }
@article {pmid25481482, year = {2014}, author = {Goldstone, RJ and Popat, R and Schuberth, HJ and Sandra, O and Sheldon, IM and Smith, DG}, title = {Genomic characterisation of an endometrial pathogenic Escherichia coli strain reveals the acquisition of genetic elements associated with extra-intestinal pathogenicity.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {1075}, pmid = {25481482}, issn = {1471-2164}, support = {095831/WT_/Wellcome Trust/United Kingdom ; BB/I017283/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/1017283/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; BB/1017240/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Cluster Analysis ; Computational Biology ; Endometrium/microbiology ; Escherichia coli/*classification/*genetics/isolation &amp; purification/metabolism ; Escherichia coli Infections/microbiology ; Escherichia coli Proteins/genetics/metabolism ; Female ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genomics ; Humans ; Molecular Sequence Annotation ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; }, abstract = {BACKGROUND: Strains of Escherichia coli cause a wide variety of intestinal and extra-intestinal diseases in both humans and animals, and are also often found in healthy individuals or the environment. Broadly, a strong phylogenetic relationship exists that distinguishes most E. coli causing intestinal disease from those that cause extra-intestinal disease, however, isolates within a recently described subclass of Extra-Intestinal Pathogenic E. coli (ExPEC), termed endometrial pathogenic E. coli, tend to be phylogenetically distant from the vast majority of characterised ExPECs, and more closely related to human intestinal pathogens. In this work, we investigate the genetic basis for ExPEC infection in the prototypic endometrial pathogenic E. coli strain MS499.<br><br>RESULTS: By investigating the genome of MS499 in comparison with a range of other E. coli sequences, we have discovered that this bacterium has acquired substantial lengths of DNA which encode factors more usually associated with ExPECs and less frequently found in the phylogroup relatives of MS499. Many of these acquired factors, including several iron acquisition systems and a virulence plasmid similar to that found in several ExPECs such as APEC O1 and the neonatal meningitis E. coli S88, play characterised roles in a variety of typical ExPEC infections and appear to have been acquired recently by the evolutionary lineage leading to MS499.<br><br>CONCLUSIONS: Taking advantage of the phylogenetic relationship we describe between MS499 and several other closely related E. coli isolates from across the globe, we propose a step-wise evolution of a novel clade of sequence type 453 ExPECs within phylogroup B1, involving the recruitment of ExPEC virulence factors into the genome of an ancestrally non-extraintestinal E. coli, which has repurposed this lineage with the capacity to cause extraintestinal disease. These data reveal the genetic components which may be involved in this phenotype switching, and argue that horizontal gene exchange may be a key factor in the emergence of novel lineages of ExPECs.}, }
@article {pmid25481006, year = {2015}, author = {Bansal, MS and Wu, YC and Alm, EJ and Kellis, M}, title = {Improved gene tree error correction in the presence of horizontal gene transfer.}, journal = {Bioinformatics (Oxford, England)}, volume = {31}, number = {8}, pages = {1211-1218}, pmid = {25481006}, issn = {1367-4811}, support = {RC2 HG005639/HG/NHGRI NIH HHS/United States ; }, mesh = {*Algorithms ; Computational Biology/methods ; Cyanobacteria/*genetics ; *Evolution, Molecular ; Gene Duplication ; *Gene Transfer, Horizontal ; Multigene Family ; Phylogeny ; }, abstract = {MOTIVATION: The accurate inference of gene trees is a necessary step in many evolutionary studies. Although the problem of accurate gene tree inference has received considerable attention, most existing methods are only applicable to gene families unaffected by horizontal gene transfer. As a result, the accurate inference of gene trees affected by horizontal gene transfer remains a largely unaddressed problem.<br><br>RESULTS: In this study, we introduce a new and highly effective method for gene tree error correction in the presence of horizontal gene transfer. Our method efficiently models horizontal gene transfers, gene duplications and losses, and uses a statistical hypothesis testing framework [Shimodaira-Hasegawa (SH) test] to balance sequence likelihood with topological information from a known species tree. Using a thorough simulation study, we show that existing phylogenetic methods yield inaccurate gene trees when applied to horizontally transferred gene families and that our method dramatically improves gene tree accuracy. We apply our method to a dataset of 11 cyanobacterial species and demonstrate the large impact of gene tree accuracy on downstream evolutionary analyses.<br><br>An implementation of our method is available at http://compbio.mit.edu/treefix-dtl/<br><br>CONTACT: : mukul@engr.uconn.edu or manoli@mit.edu<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid25480683, year = {2014}, author = {Wuichet, K and Søgaard-Andersen, L}, title = {Evolution and diversity of the Ras superfamily of small GTPases in prokaryotes.}, journal = {Genome biology and evolution}, volume = {7}, number = {1}, pages = {57-70}, pmid = {25480683}, issn = {1759-6653}, mesh = {Bacteria/*genetics ; *Biological Evolution ; Cell Movement/genetics ; Cell Polarity/genetics ; Computational Biology ; Drug Resistance, Microbial/genetics ; Genomics ; Monomeric GTP-Binding Proteins/*genetics ; Multigene Family ; Phylogeny ; *Prokaryotic Cells ; Signal Transduction/genetics ; }, abstract = {The Ras superfamily of small GTPases are single domain nucleotide-dependent molecular switches that act as highly tuned regulators of complex signal transduction pathways. Originally identified in eukaryotes for their roles in fundamental cellular processes including proliferation, motility, polarity, nuclear transport, and vesicle transport, recent studies have revealed that single domain GTPases also control complex functions such as cell polarity, motility, predation, development and antibiotic resistance in bacteria. Here, we used a computational genomics approach to understand the abundance, diversity, and evolution of small GTPases in prokaryotes. We collected 520 small GTPase sequences present in 17% of 1,611 prokaryotic genomes analyzed that cover diverse lineages. We identified two discrete families of small GTPases in prokaryotes that show evidence of three distinct catalytic mechanisms. The MglA family includes MglA homologs, which are typically associated with the MglB GTPase activating protein, whereas members of the Rup (Ras superfamily GTPase of unknown function in prokaryotes) family are not predicted to interact with MglB homologs. System classification and genome context analyses support the involvement of small GTPases in diverse prokaryotic signal transduction pathways including two component systems, laying the foundation for future experimental characterization of these proteins. Phylogenetic analysis of prokaryotic and eukaryotic GTPases supports that the last universal common ancestor contained ancestral MglA and Rup family members. We propose that the MglA family was lost from the ancestral eukaryote and that the Ras superfamily members in extant eukaryotes are the result of vertical and horizontal gene transfer events of ancestral Rup GTPases.}, }
@article {pmid25480015, year = {2014}, author = {Ojala, T and Kankainen, M and Castro, J and Cerca, N and Edelman, S and Westerlund-Wikström, B and Paulin, L and Holm, L and Auvinen, P}, title = {Comparative genomics of Lactobacillus crispatus suggests novel mechanisms for the competitive exclusion of Gardnerella vaginalis.}, journal = {BMC genomics}, volume = {15}, number = {}, pages = {1070}, pmid = {25480015}, issn = {1471-2164}, mesh = {Antibiosis/*genetics ; Bacterial Adhesion/genetics ; Bacteriophages ; Cell Wall/metabolism ; Clustered Regularly Interspaced Short Palindromic Repeats ; Computational Biology ; Female ; Gardnerella vaginalis/*genetics ; Gene Order ; Gene Transfer, Horizontal ; Genetic Variation ; *Genome, Bacterial ; *Genomics ; HeLa Cells ; Humans ; Lactobacillus/classification/*genetics/metabolism/virology ; Metabolic Networks and Pathways ; Molecular Sequence Annotation ; Multigene Family ; Phylogeny ; Polysaccharides, Bacterial/metabolism ; }, abstract = {BACKGROUND: Lactobacillus crispatus is a ubiquitous micro-organism encountered in a wide range of host-associated habitats. It can be recovered from the gastrointestinal tract of animals and it is a common constituent of the vaginal microbiota of humans. Moreover, L. crispatus can contribute to the urogenital health of the host through competitive exclusion and the production of antimicrobial agents. In order to investigate the genetic diversity of this important urogenital species, we performed a comparative genomic analysis of L. crispatus.<br><br>RESULTS: Utilizing the completed genome sequence of a strain ST1 and the draft genome sequences of nine other L. crispatus isolates, we defined the scale and scope of the pan- and core genomic potential of L. crispatus. Our comparative analysis identified 1,224 and 2,705 ortholog groups present in all or only some of the ten strains, respectively. Based on mathematical modeling, sequencing of additional L. crispatus isolates would result in the identification of new genes and functions, whereas the conserved core of the ten strains was a good representation of the final L. crispatus core genome, estimated to level at about 1,116 ortholog groups. Importantly, the current core was observed to encode bacterial components potentially promoting urogenital health. Using antibody fragments specific for one of the conserved L. crispatus adhesins, we demonstrated that the L. crispatus core proteins have a potential to reduce the ability of Gardnerella vaginalis to adhere to epithelial cells. These findings thereby suggest that L. crispatus core proteins could protect the vagina from G. vaginalis and bacterial vaginosis.<br><br>CONCLUSIONS: Our pan-genome analysis provides insights into the intraspecific genome variability and the collective molecular mechanisms of the species L. crispatus. Using this approach, we described the differences and similarities between the genomes and identified features likely to be important for urogenital health. Notably, the conserved genetic backbone of L. crispatus accounted for close to 60% of the ortholog groups of an average L. crispatus strain and included factors for the competitive exclusion of G. vaginalis, providing an explanation on how this urogenital species could improve vaginal health.}, }
@article {pmid25477875, year = {2014}, author = {Degnan, SM}, title = {Think laterally: horizontal gene transfer from symbiotic microbes may extend the phenotype of marine sessile hosts.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {638}, pmid = {25477875}, issn = {1664-302X}, abstract = {Since the origin of the animal kingdom, marine animals have lived in association with viruses, prokaryotes and unicellular eukaryotes, often as symbionts. This long and continuous interaction has provided ample opportunity not only for the evolution of intimate interactions such as sharing of metabolic pathways, but also for horizontal gene transfer (HGT) of non-metazoan genes into metazoan genomes. The number of demonstrated cases of inter-kingdom HGT is currently small, such that it is not yet widely appreciated as a significant player in animal evolution. Sessile marine invertebrates that vertically inherit bacterial symbionts, that have no dedicated germ line, or that bud or excise pluripotent somatic cells during their life history may be particularly receptive to HGT from their symbionts. Closer scrutiny of the growing number of genomes being accrued for these animals may thus reveal HGT as a regular source of novel variation that can function to extend the host phenotype metabolically, morphologically, or even behaviorally. Taxonomic identification of symbionts will help to address the intriguing question of whether past HGT events may constrain contemporary symbioses.}, }
@article {pmid25477419, year = {2014}, author = {Gillespie, JJ and Driscoll, TP and Verhoeve, VI and Utsuki, T and Husseneder, C and Chouljenko, VN and Azad, AF and Macaluso, KR}, title = {Genomic diversification in strains of Rickettsia felis Isolated from different arthropods.}, journal = {Genome biology and evolution}, volume = {7}, number = {1}, pages = {35-56}, pmid = {25477419}, issn = {1759-6653}, support = {R01 AI043006/AI/NIAID NIH HHS/United States ; R56AI104923/AI/NIAID NIH HHS/United States ; R01 AI017828/AI/NIAID NIH HHS/United States ; R01 AI122672/AI/NIAID NIH HHS/United States ; HHSN272200900040C/AI/NIAID NIH HHS/United States ; HHSN272200900040C//PHS HHS/United States ; R01AI017828/AI/NIAID NIH HHS/United States ; P30GM110760/GM/NIGMS NIH HHS/United States ; R01AI043006/AI/NIAID NIH HHS/United States ; P30 GM110760/GM/NIGMS NIH HHS/United States ; R56 AI104923/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Arthropods/microbiology ; Bacterial Proteins/*genetics ; Cats ; Gene Transfer, Horizontal ; Genomics ; Hemolysin Proteins/*genetics ; Humans ; Phylogeny ; Plasmids/genetics ; Rickettsia felis/*genetics/pathogenicity ; Rickettsiaceae Infections/*genetics/*microbiology/transmission ; Siphonaptera/microbiology ; }, abstract = {Rickettsia felis (Alphaproteobacteria: Rickettsiales) is the causative agent of an emerging flea-borne rickettsiosis with worldwide occurrence. Originally described from the cat flea, Ctenocephalides felis, recent reports have identified R. felis from other flea species, as well as other insects and ticks. This diverse host range for R. felis may indicate an underlying genetic variability associated with host-specific strains. Accordingly, to determine a potential genetic basis for host specialization, we sequenced the genome of R. felis str. LSU-Lb, which is an obligate mutualist of the parthenogenic booklouse Liposcelis bostrychophila (Insecta: Psocoptera). We also sequenced the genome of R. felis str. LSU, the second genome sequence for cat flea-associated strains (cf. R. felis str. URRWXCal2), which are presumably facultative parasites of fleas. Phylogenomics analysis revealed R. felis str. LSU-Lb diverged from the flea-associated strains. Unexpectedly, R. felis str. LSU was found to be divergent from R. felis str. URRWXCal2, despite sharing similar hosts. Although all three R. felis genomes contain the pRF plasmid, R. felis str. LSU-Lb carries an additional unique plasmid, pLbaR (plasmid of L. bostrychophila associated Rickettsia), nearly half of which encodes a unique 23-gene integrative conjugative element. Remarkably, pLbaR also encodes a repeats-in-toxin-like type I secretion system and associated toxin, heretofore unknown from other Rickettsiales genomes, which likely originated from lateral gene transfer with another obligate intracellular parasite of arthropods, Cardinium (Bacteroidetes). Collectively, our study reveals unexpected genomic diversity across three R. felis strains and identifies several diversifying factors that differentiate facultative parasites of fleas from obligate mutualists of booklice.}, }
@article {pmid25477379, year = {2015}, author = {Yamaichi, Y and Chao, MC and Sasabe, J and Clark, L and Davis, BM and Yamamoto, N and Mori, H and Kurokawa, K and Waldor, MK}, title = {High-resolution genetic analysis of the requirements for horizontal transmission of the ESBL plasmid from Escherichia coli O104:H4.}, journal = {Nucleic acids research}, volume = {43}, number = {1}, pages = {348-360}, pmid = {25477379}, issn = {1362-4962}, support = {R37 AI042347/AI/NIAID NIH HHS/United States ; AI-042347//Howard Hughes Medical Institute/United States ; }, mesh = {DNA Transposable Elements ; Escherichia coli/*genetics ; Gene Library ; *Gene Transfer, Horizontal ; Genes, Bacterial ; High-Throughput Nucleotide Sequencing ; Plasmids/*genetics ; Sequence Analysis, DNA ; }, abstract = {Horizontal dissemination of the genes encoding extended spectrum beta-lactamases (ESBLs) via conjugative plasmids is facilitating the increasingly widespread resistance of pathogens to beta-lactam antibiotics. However, there is relatively little known about the regulatory factors and mechanisms that govern the spread of these plasmids. Here, we carried out a high-throughput, transposon insertion site sequencing analysis (TnSeq) to identify genes that enable the maintenance and transmission of pESBL, an R64 (IncI1)-related resistance plasmid that was isolated from Escherichia coli O104:H4 linked to a recent large outbreak of gastroenteritis. With a few exceptions, the majority of the genes identified as required for maintenance and transmission of pESBL matched those of their previously defined R64 counterparts. However, our analyses of the high-density transposon insertion library in pESBL also revealed two very short and linked regions that constitute a previously unrecognized regulatory system controlling spread of IncI1 plasmids. In addition, we investigated the function of the pESBL-encoded M.EcoGIX methyltransferase, which is also encoded by many other IncI1 and IncF plasmids. This enzyme proved to protect pESBL from restriction in new hosts, suggesting it aids in expanding the plasmid's host range. Collectively, our work illustrates the power of the TnSeq approach to enable rapid and comprehensive analyses of plasmid genes and sequences that facilitate the dissemination of determinants of antibiotic resistance.}, }
@article {pmid25476764, year = {2014}, author = {Roberts, AP and Allan, E and Mullany, P}, title = {The impact of horizontal gene transfer on the biology of Clostridium difficile.}, journal = {Advances in microbial physiology}, volume = {65}, number = {}, pages = {63-82}, doi = {10.1016/bs.ampbs.2014.08.002}, pmid = {25476764}, issn = {2162-5468}, mesh = {Bacteriophages ; Clostridioides difficile/*genetics/*pathogenicity ; Clostridium Infections/genetics/*microbiology ; DNA Transposable Elements ; Diarrhea/*etiology ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; Interspersed Repetitive Sequences ; Introns ; Virulence ; }, abstract = {Clostridium difficile infection (CDI) is now recognised as the main cause of healthcare associated diarrhoea. Over the recent years there has been a change in the epidemiology of CDI with certain related strains dominating infection. These strains have been termed hyper-virulent and have successfully spread across the globe. Many C. difficile strains have had their genomes completely sequenced allowing researchers to build up a very detailed picture of the contribution of horizontal gene transfer to the adaptive potential, through the acquisition of mobile DNA, of this organism. Here, we review and discuss the contribution of mobile genetic elements to the biology of this clinically important pathogen.}, }
@article {pmid25475368, year = {2014}, author = {Allen, RJ and Brenner, EP and VanOrsdel, CE and Hobson, JJ and Hearn, DJ and Hemm, MR}, title = {Conservation analysis of the CydX protein yields insights into small protein identification and evolution.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {946}, pmid = {25475368}, issn = {1471-2164}, support = {R15 AI094548/AI/NIAID NIH HHS/United States ; 1R15AI094548-01/AI/NIAID NIH HHS/United States ; }, mesh = {Alleles ; Amino Acid Sequence ; Computational Biology/methods ; Conserved Sequence ; Cytochrome b Group ; Cytochromes/chemistry/*genetics/metabolism ; Electron Transport Chain Complex Proteins/chemistry/*genetics/metabolism ; Escherichia coli Proteins/chemistry/*genetics/metabolism ; *Evolution, Molecular ; Gene Order ; Gene Transfer, Horizontal ; Genetic Complementation Test ; Genome, Bacterial ; Genomics ; Hydrophobic and Hydrophilic Interactions ; Markov Chains ; Molecular Sequence Annotation ; Molecular Sequence Data ; Mutation ; Operon ; Oxidoreductases/chemistry/*genetics/metabolism ; Phylogeny ; Position-Specific Scoring Matrices ; Protein Interaction Domains and Motifs ; Proteobacteria/genetics/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The reliable identification of proteins containing 50 or fewer amino acids is difficult due to the limited information content in short sequences. The 37 amino acid CydX protein in Escherichia coli is a member of the cytochrome bd oxidase complex, an enzyme found throughout Eubacteria. To investigate the extent of CydX conservation and prevalence and evaluate different methods of small protein homologue identification, we surveyed 1095 Eubacteria species for the presence of the small protein.<br><br>RESULTS: Over 300 homologues were identified, including 80 unannotated genes. The ability of both closely-related and divergent homologues to complement the E. coli &#x394;cydX mutant supports our identification techniques, and suggests that CydX homologues retain similar function among divergent species. However, sequence analysis of these proteins shows a great degree of variability, with only a few highly-conserved residues. An analysis of the co-variation between CydX homologues and their corresponding cydA and cydB genes shows a close synteny of the small protein with the CydA long Q-loop. Phylogenetic analysis suggests that the cydABX operon has undergone horizontal gene transfer, although the cydX gene likely evolved in a progenitor of the Alpha, Beta, and Gammaproteobacteria. Further investigation of cydAB operons identified two additional conserved hypothetical small proteins: CydY encoded in CydAQlong operons that lack cydX, and CydZ encoded in more than 150 CydAQshort operons.<br><br>CONCLUSIONS: This study provides a systematic analysis of bioinformatics techniques required for the unique challenges present in small protein identification and phylogenetic analyses. These results elucidate the prevalence of CydX throughout the Proteobacteria, provide insight into the selection pressure and sequence requirements for CydX function, and suggest a potential functional interaction between the small protein and the CydA Q-loop, an enigmatic domain of the cytochrome bd oxidase complex. Finally, these results identify other conserved small proteins encoded in cytochrome bd oxidase operons, suggesting that small protein subunits may be a more common component of these enzymes than previously thought.}, }
@article {pmid25474706, year = {2014}, author = {Novikova, O and Smith, D and Hahn, I and Beauregard, A and Belfort, M}, title = {Interaction between conjugative and retrotransposable elements in horizontal gene transfer.}, journal = {PLoS genetics}, volume = {10}, number = {12}, pages = {e1004853}, pmid = {25474706}, issn = {1553-7404}, support = {GM44844/GM/NIGMS NIH HHS/United States ; R37 GM039422/GM/NIGMS NIH HHS/United States ; GM39422/GM/NIGMS NIH HHS/United States ; R01 GM039422/GM/NIGMS NIH HHS/United States ; R01 GM044844/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Sequence ; Conjugation, Genetic/*physiology ; DNA, Single-Stranded/metabolism ; Endoribonucleases/physiology ; Epistasis, Genetic ; *Gene Transfer, Horizontal ; Introns/genetics ; Lactococcus lactis/*genetics ; Organisms, Genetically Modified ; RNA Splicing/genetics ; Retroelements/*physiology ; }, abstract = {Mobile genetic elements either encode their own mobilization machineries or hijack them from other mobile elements. Multiple classes of mobile elements often coexist within genomes and it is unclear whether they have the capacity to functionally interact and even collaborate. We investigate the possibility that molecular machineries of disparate mobile elements may functionally interact, using the example of a retrotransposon, in the form of a mobile group II intron, found on a conjugative plasmid pRS01 in Lactococcus lactis. This intron resides within the pRS01 ltrB gene encoding relaxase, the enzyme required for nicking the transfer origin (oriT) for conjugal transmission of the plasmid into a recipient cell. Here, we show that relaxase stimulates both the frequency and diversity of retrotransposition events using a retromobility indicator gene (RIG), and by developing a high-throughput genomic retrotransposition detection system called RIG-Seq. We demonstrate that LtrB relaxase not only nicks ssDNA of its cognate oriT in a sequence- and strand-specific manner, but also possesses weak off-target activity. Together, the data support a model in which the two different mobile elements, one using an RNA-based mechanism, the other using DNA-based transfer, do functionally interact. Intron splicing facilitates relaxase expression required for conjugation, whereas relaxase introduces spurious nicks in recipient DNA that stimulate both the frequency of intron mobility and the density of events. We hypothesize that this functional interaction between the mobile elements would promote horizontal conjugal gene transfer while stimulating intron dissemination in the donor and recipient cells.}, }
@article {pmid25474404, year = {2014}, author = {Wisecaver, JH and Slot, JC and Rokas, A}, title = {The evolution of fungal metabolic pathways.}, journal = {PLoS genetics}, volume = {10}, number = {12}, pages = {e1004816}, pmid = {25474404}, issn = {1553-7404}, mesh = {Ascomycota/genetics ; *Evolution, Molecular ; Gene Duplication ; Gene Regulatory Networks ; Gene Transfer, Horizontal ; Genes, Fungal ; *Genome, Fungal ; Metabolic Networks and Pathways/*genetics ; Multigene Family ; Phylogeny ; }, abstract = {Fungi contain a remarkable range of metabolic pathways, sometimes encoded by gene clusters, enabling them to digest most organic matter and synthesize an array of potent small molecules. Although metabolism is fundamental to the fungal lifestyle, we still know little about how major evolutionary processes, such as gene duplication (GD) and horizontal gene transfer (HGT), have interacted with clustered and non-clustered fungal metabolic pathways to give rise to this metabolic versatility. We examined the synteny and evolutionary history of 247,202 fungal genes encoding enzymes that catalyze 875 distinct metabolic reactions from 130 pathways in 208 diverse genomes. We found that gene clustering varied greatly with respect to metabolic category and lineage; for example, clustered genes in Saccharomycotina yeasts were overrepresented in nucleotide metabolism, whereas clustered genes in Pezizomycotina were more common in lipid and amino acid metabolism. The effects of both GD and HGT were more pronounced in clustered genes than in their non-clustered counterparts and were differentially distributed across fungal lineages; specifically, GD, which was an order of magnitude more abundant than HGT, was most frequently observed in Agaricomycetes, whereas HGT was much more prevalent in Pezizomycotina. The effect of HGT in some Pezizomycotina was particularly strong; for example, we identified 111 HGT events associated with the 15 Aspergillus genomes, which sharply contrasts with the 60 HGT events detected for the 48 genomes from the entire Saccharomycotina subphylum. Finally, the impact of GD within a metabolic category was typically consistent across all fungal lineages, whereas the impact of HGT was variable. These results indicate that GD is the dominant process underlying fungal metabolic diversity, whereas HGT is episodic and acts in a category- or lineage-specific manner. Both processes have a greater impact on clustered genes, suggesting that metabolic gene clusters represent hotspots for the generation of fungal metabolic diversity.}, }
@article {pmid25473828, year = {2014}, author = {Jaquiéry, J and Stoeckel, S and Larose, C and Nouhaud, P and Rispe, C and Mieuzet, L and Bonhomme, J and Mahéo, F and Legeai, F and Gauthier, JP and Prunier-Leterme, N and Tagu, D and Simon, JC}, title = {Genetic control of contagious asexuality in the pea aphid.}, journal = {PLoS genetics}, volume = {10}, number = {12}, pages = {e1004838}, pmid = {25473828}, issn = {1553-7404}, mesh = {Animals ; Aphids/*genetics/physiology ; Chromosome Mapping ; Crosses, Genetic ; Female ; *Gene Transfer, Horizontal ; Genetics, Population ; Male ; Parthenogenesis/genetics ; Pisum sativum/*parasitology ; Quantitative Trait Loci ; Reproduction/genetics ; Reproduction, Asexual/*genetics ; }, abstract = {Although evolutionary transitions from sexual to asexual reproduction are frequent in eukaryotes, the genetic bases of such shifts toward asexuality remain largely unknown. We addressed this issue in an aphid species where both sexual and obligate asexual lineages coexist in natural populations. These sexual and asexual lineages may occasionally interbreed because some asexual lineages maintain a residual production of males potentially able to mate with the females produced by sexual lineages. Hence, this species is an ideal model to study the genetic basis of the loss of sexual reproduction with quantitative genetic and population genomic approaches. Our analysis of the co-segregation of ∼ 300 molecular markers and reproductive phenotype in experimental crosses pinpointed an X-linked region controlling obligate asexuality, this state of character being recessive. A population genetic analysis (>400-marker genome scan) on wild sexual and asexual genotypes from geographically distant populations under divergent selection for reproductive strategies detected a strong signature of divergent selection in the genomic region identified by the experimental crosses. These population genetic data confirm the implication of the candidate region in the control of reproductive mode in wild populations originating from 700 km apart. Patterns of genetic differentiation along chromosomes suggest bidirectional gene flow between populations with distinct reproductive modes, supporting contagious asexuality as a prevailing route to permanent parthenogenesis in pea aphids. This genetic system provides new insights into the mechanisms of coexistence of sexual and asexual aphid lineages.}, }
@article {pmid25470067, year = {2015}, author = {Chou, S and Daugherty, MD and Peterson, SB and Biboy, J and Yang, Y and Jutras, BL and Fritz-Laylin, LK and Ferrin, MA and Harding, BN and Jacobs-Wagner, C and Yang, XF and Vollmer, W and Malik, HS and Mougous, JD}, title = {Transferred interbacterial antagonism genes augment eukaryotic innate immune function.}, journal = {Nature}, volume = {518}, number = {7537}, pages = {98-101}, pmid = {25470067}, issn = {1476-4687}, support = {R01 AI083640/AI/NIAID NIH HHS/United States ; BB/I020012/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; AI083640/AI/NIAID NIH HHS/United States ; //Howard Hughes Medical Institute/United States ; AI080609/AI/NIAID NIH HHS/United States ; R01 AI080609/AI/NIAID NIH HHS/United States ; }, mesh = {Amidohydrolases/genetics/metabolism ; Animals ; Bacteria/cytology/*enzymology/*genetics/immunology ; Bacterial Secretion Systems ; Bacterial Toxins/*genetics/metabolism ; Borrelia burgdorferi/cytology/growth &amp; development/immunology ; Cell Wall/metabolism ; Conserved Sequence/genetics ; Eukaryota/*genetics/*immunology/metabolism ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/*genetics ; *Immunity, Innate/genetics ; Ixodes/genetics/immunology/metabolism/microbiology ; Phylogeny ; Substrate Specificity ; }, abstract = {Horizontal gene transfer allows organisms to rapidly acquire adaptive traits. Although documented instances of horizontal gene transfer from bacteria to eukaryotes remain rare, bacteria represent a rich source of new functions potentially available for co-option. One benefit that genes of bacterial origin could provide to eukaryotes is the capacity to produce antibacterials, which have evolved in prokaryotes as the result of eons of interbacterial competition. The type VI secretion amidase effector (Tae) proteins are potent bacteriocidal enzymes that degrade the cell wall when delivered into competing bacterial cells by the type VI secretion system. Here we show that tae genes have been transferred to eukaryotes on at least six occasions, and that the resulting domesticated amidase effector (dae) genes have been preserved for hundreds of millions of years through purifying selection. We show that the dae genes acquired eukaryotic secretion signals, are expressed within recipient organisms, and encode active antibacterial toxins that possess substrate specificity matching extant Tae proteins of the same lineage. Finally, we show that a dae gene in the deer tick Ixodes scapularis limits proliferation of Borrelia burgdorferi, the aetiologic agent of Lyme disease. Our work demonstrates that a family of horizontally acquired toxins honed to mediate interbacterial antagonism confers previously undescribed antibacterial capacity to eukaryotes. We speculate that the selective pressure imposed by competition between bacteria has produced a reservoir of genes encoding diverse antimicrobial functions that are tailored for co-option by eukaryotic innate immune systems.}, }
@article {pmid25468904, year = {2015}, author = {Gruber, TM and Göttig, S and Mark, L and Christ, S and Kempf, VA and Wichelhaus, TA and Hamprecht, A}, title = {Pathogenicity of pan-drug-resistant Serratia marcescens harbouring blaNDM-1.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {70}, number = {4}, pages = {1026-1030}, doi = {10.1093/jac/dku482}, pmid = {25468904}, issn = {1460-2091}, mesh = {Animals ; DNA, Bacterial/chemistry/genetics ; Disease Models, Animal ; *Drug Resistance, Multiple, Bacterial ; Humans ; Lepidoptera ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Plasmids/analysis ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Serratia Infections/*microbiology/pathology ; Serratia marcescens/drug effects/*enzymology/isolation &amp; purification/*pathogenicity ; Virulence ; beta-Lactamases/genetics/*metabolism ; }, abstract = {OBJECTIVES: To characterize a pan-drug-resistant Serratia marcescens clinical isolate carrying the New Delhi metallo-β-lactamase (NDM)-1.<br><br>METHODS: The presence of &#x3b2;-lactamase genes was examined by PCR and sequencing. Antibiotic susceptibility was determined by antibiotic gradient test. Transformation assays, transconjugation assays, PFGE and PCR-based replicon typing were used for plasmid analysis. Horizontal gene transfer was evaluated by liquid mating using Escherichia coli J53 as a recipient. Pathogenicity of NDM-1 expressing S. marcescens was analysed using the Galleria mellonella infection model.<br><br>RESULTS: S. marcescens isolate SM1890 was non-susceptible to all tested antibiotics, with minocycline retaining intermediate activity. blaNDM-1 was located on a 140 kb IncA/C-type plasmid which was transferable to E. coli and Klebsiella pneumoniae by conjugation. The LD50 of the NDM-positive, SM1890 isolate was higher than that of other, NDM-1 negative, S. marcescens strains.<br><br>CONCLUSIONS: The presence of a blaNDM-1-harbouring IncA/C plasmid resulted in marked resistance to &#x3b2;-lactam antibiotics, but had no significant effect on virulence of isogenic strains. Because of the intrinsic resistance of S. marcescens to colistin and reduced susceptibility to tigecycline, treatment options for infections by NDM-1-positive isolates are extremely limited in this species.}, }
@article {pmid25461843, year = {2015}, author = {Andam, CP and Hanage, WP}, title = {Mechanisms of genome evolution of Streptococcus.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {33}, number = {}, pages = {334-342}, pmid = {25461843}, issn = {1567-7257}, support = {R01 AI106786/AI/NIAID NIH HHS/United States ; R01 AI106786-01/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteriophages/physiology ; Biodiversity ; DNA Transposable Elements ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; *Genome, Bacterial ; Humans ; Pneumococcal Infections/*microbiology ; Selection, Genetic ; Streptococcus/*classification/drug effects/*genetics/immunology/virology ; Vaccination ; }, abstract = {The genus Streptococcus contains 104 recognized species, many of which are associated with human or animal hosts. A globally prevalent human pathogen in this group is Streptococcus pneumoniae (the pneumococcus). While being a common resident of the upper respiratory tract, it is also a major cause of otitis media, pneumonia, bacteremia and meningitis, accounting for a high burden of morbidity and mortality worldwide. Recent findings demonstrate the importance of recombination and selection in driving the population dynamics and evolution of different pneumococcal lineages, allowing them to successfully evade the impacts of selective pressures such as vaccination and antibiotic treatment. We highlight the ability of pneumococci to respond to these pressures through processes including serotype replacement, capsular switching and horizontal gene transfer (HGT) of antibiotic resistance genes. The challenge in controlling this pathogen also lies in the exceptional genetic and phenotypic variation among different pneumococcal lineages, particularly in terms of their pathogenicity and resistance to current therapeutic strategies. The widespread use of pneumococcal conjugate vaccines, which target only a small subset of the more than 90 pneumococcal serotypes, provides us with a unique opportunity to elucidate how the processes of selection and recombination interact to generate a remarkable level of plasticity and heterogeneity in the pneumococcal genome. These processes also play an important role in the emergence and spread of multi-resistant strains, which continues to pose a challenge in disease control and/or eradication. The application of population of genomic approaches at different spatial and temporal scales will help improve strategies to control this global pathogen, and potentially other pathogenic streptococci.}, }
@article {pmid25461693, year = {2015}, author = {Rashid, H and Rahman, M}, title = {Possible transfer of plasmid mediated third generation cephalosporin resistance between Escherichia coli and Shigella sonnei in the human gut.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {30}, number = {}, pages = {15-18}, doi = {10.1016/j.meegid.2014.11.023}, pmid = {25461693}, issn = {1567-7257}, mesh = {*Cephalosporin Resistance ; Disk Diffusion Antimicrobial Tests ; Drug Resistance, Multiple, Bacterial ; Dysentery, Bacillary/*microbiology ; *Escherichia coli/drug effects/isolation &amp; purification ; Feces/microbiology ; Gastrointestinal Tract/microbiology ; Gene Transfer, Horizontal ; Humans ; Phenotype ; *Plasmids ; *Shigella sonnei/drug effects/isolation &amp; purification ; }, abstract = {Choice of antibiotic for treatment of serious bacterial infection is rapidly diminishing by plasmid mediated transfer of antibiotic resistance. Here, we report a possible horizontal transfer of plasmid carrying third-generation-cephalosporin (TGC) resistance between Escherichia coli and Shigella sonnei. Two different types of colonies were identified in MacConkey agar plate from a faecal specimen collected from a patient with shigellosis. The colonies were identified as E. coli and S. sonnei. Both of the isolates were resistant to ampicillin, chloramphenicol, co-trimoxazole, erythromycin, azithromycin, nalidixic acid, ceftriaxone, cefixime, ceftazidime, cefotaxime and susceptible to co-amoxiclave, amikacin, imipenam, astreonam, levofloxacin, moxifloxacin, mecillinam. These two strains were positive for extended spectrum β-lactamase. We were able to transfer ESBL producing property from both ceftriaxone-resistant isolates to the ceftriaxone susceptible recipient E. coli K12 and S. sonnei. Plasmid profile analysis revealed that the first-generation E. coli K12 and S. sonnei transconjugants harbored a 50MDa R plasmid, as two-parent ESBL-producing S. sonnei and E. coli strains. Similar patterns of ESBL producing plasmid and transferable antimicrobial phenotype suggests that the ESBL producing plasmid might transferred between E. coli and S. sonnei through conjugation in the human gut.}, }
@article {pmid25461567, year = {2015}, author = {Will, WR and Navarre, WW and Fang, FC}, title = {Integrated circuits: how transcriptional silencing and counter-silencing facilitate bacterial evolution.}, journal = {Current opinion in microbiology}, volume = {23}, number = {}, pages = {8-13}, pmid = {25461567}, issn = {1879-0364}, support = {R01 AI101084/AI/NIAID NIH HHS/United States ; AI101084/AI/NIAID NIH HHS/United States ; MOP-86683//Canadian Institutes of Health Research/Canada ; }, mesh = {Bacteria/*genetics ; *Evolution, Molecular ; *Gene Expression ; *Gene Expression Regulation, Bacterial ; Gene Regulatory Networks ; *Gene Silencing ; *Gene Transfer, Horizontal ; }, abstract = {Horizontal gene transfer is a major contributor to bacterial evolution and diversity. For a bacterial cell to utilize newly-acquired traits such as virulence and antibiotic resistance, new genes must be integrated into the existing regulatory circuitry to allow appropriate expression. Xenogeneic silencing of horizontally-acquired genes by H-NS or other nucleoid-associated proteins avoids adventitious expression and can be relieved by other DNA-binding counter-silencing proteins in an environmentally-responsive and physiologically-responsive manner. Biochemical and genetic analyses have recently demonstrated that counter-silencing can occur at a variety of promoter architectures, in contrast to classical transcriptional activation. Disruption of H-NS nucleoprotein filaments by DNA bending is a suggested mechanism by which silencing can be relieved. This review discusses recent advances in our understanding of the mechanisms and importance of xenogeneic silencing and counter-silencing in the successful integration of horizontally-acquired genes into regulatory networks.}, }
@article {pmid25458609, year = {2014}, author = {Youseif, SH and Abd El-Megeed, FH and Ageez, A and Cocking, EC and Saleh, SA}, title = {Phylogenetic multilocus sequence analysis of native rhizobia nodulating faba bean (Vicia faba L.) in Egypt.}, journal = {Systematic and applied microbiology}, volume = {37}, number = {8}, pages = {560-569}, doi = {10.1016/j.syapm.2014.10.001}, pmid = {25458609}, issn = {1618-0984}, mesh = {Acyltransferases/genetics ; Bacterial Proteins/genetics ; DNA, Bacterial/analysis/genetics ; Egypt ; Multilocus Sequence Typing ; Phylogeny ; RNA, Ribosomal, 16S ; Rhizobium/*classification/*genetics ; Root Nodules, Plant/*microbiology ; Symbiosis ; Vicia faba/*microbiology ; }, abstract = {The taxonomic diversity of forty-two Rhizobium strains, isolated from nodules of faba bean grown in Egypt, was studied using 16S rRNA sequencing, multilocus sequence analyses (MLSA) of three chromosomal housekeeping loci and one nodulation gene (nodA). Based on the 16S rRNA gene sequences, most of the strains were related to Rhizobium leguminosarum, Rhizobium etli, and Rhizobium radiobacter (syn. Agrobacterium tumefaciens). A maximum likelihood (ML) tree built from the concatenated sequences of housekeeping proteins encoded by glnA, gyrB and recA, revealed the existence of three distinct genospecies (I, II and III) affiliated to the defined species within the genus Rhizobium/Agrobacterium. Seventeen strains in genospecies I could be classified as R. leguminosarum sv. viciae. Whereas, a single strain of genospecies II was linked to R. etli. Interestingly, twenty-four strains of genospecies III were identified as A. tumefaciens. Strains of R. etli and A. tumefaciens have been shown to harbor the nodA gene and formed effective symbioses with faba bean plants in Leonard jar assemblies. In the nodA tree, strains belonging to the putative genospecies were closely related to each other and were clustered tightly to R. leguminosarum sv. viciae, supporting the hypothesis that symbiotic and core genome of the species have different evolutionary histories and indicative of horizontal gene transfer among these rhizobia.}, }
@article {pmid25456526, year = {2014}, author = {Young, D}, title = {On the sociology of Mycobacterium tuberculosis.}, journal = {Tuberculosis (Edinburgh, Scotland)}, volume = {94}, number = {6}, pages = {535-537}, doi = {10.1016/j.tube.2014.10.002}, pmid = {25456526}, issn = {1873-281X}, mesh = {Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Mycobacterium tuberculosis/*genetics ; Phylogeny ; *Social Support ; Tuberculosis/*microbiology/transmission ; }, }
@article {pmid25447909, year = {2015}, author = {Eraclio, G and Ricci, G and Fortina, MG}, title = {Insertion sequence elements in Lactococcus garvieae.}, journal = {Gene}, volume = {555}, number = {2}, pages = {291-296}, doi = {10.1016/j.gene.2014.11.019}, pmid = {25447909}, issn = {1879-0038}, mesh = {Base Sequence ; *DNA Transposable Elements ; Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; Lactococcus/*genetics ; Lactococcus lactis/genetics ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Repetitive Sequences, Nucleic Acid ; Sequence Alignment ; Sequence Analysis, DNA ; Streptococcal Infections/*microbiology ; }, abstract = {Insertion sequences are the simplest intracellular Mobile Genetic Elements which can occur in very high numbers in prokaryotic genomes, where they play an important evolutionary role by promoting genome plasticity. As such, the studies on the diversity and distribution of insertion sequences in genomes not yet investigated can contribute to improve the knowledge on a bacterial species and to identify new transposable elements. The present work describes the occurrence of insertion sequences in Lactococcus garvieae, an opportunistic emerging zoonotic and human pathogen, also associated with different food matrices. To date, no insertion elements have been described for L. garvieae in the IS element database. The analysis of the twelve published L. garvieae genomes identified 15 distinct insertion sequences that are members of the IS3, IS982, IS6, IS21 and IS256 families, including five new elements. Most of the insertion sequences in L. garvieae show substantial homology to the Lactococcus lactis elements, suggesting the movement of IS between these two species phylogenetically closely related. ISLL6 elements belonging to IS3 family were most abundant, with several copies distributed in 9 of the 12 genomes analyzed. An alignment analysis of two complete genomes carrying multi-copies of this insertion sequence indicates a possible involvement of ISLL6 in chromosomal rearrangement.}, }
@article {pmid25447812, year = {2015}, author = {Francis, AR and Steel, M}, title = {Tree-like reticulation networks--when do tree-like distances also support reticulate evolution?.}, journal = {Mathematical biosciences}, volume = {259}, number = {}, pages = {12-19}, doi = {10.1016/j.mbs.2014.10.008}, pmid = {25447812}, issn = {1879-3134}, mesh = {*Evolution, Molecular ; *Gene Transfer, Horizontal ; *Models, Theoretical ; *Phylogeny ; }, abstract = {Hybrid evolution and horizontal gene transfer (HGT) are processes where evolutionary relationships may more accurately be described by a reticulated network than by a tree. In such a network, there will often be several paths between any two extant species, reflecting the possible pathways that genetic material may have been passed down from a common ancestor to these species. These paths will typically have different lengths but an 'average distance' can still be calculated between any two taxa. In this article, we ask whether this average distance is able to distinguish reticulate evolution from pure tree-like evolution. We consider two types of reticulation networks: hybridisation networks and HGT networks. For the former, we establish a general result which shows that average distances between extant taxa can appear tree-like, but only under a single hybridisation event near the root; in all other cases, the two forms of evolution can be distinguished by average distances. For HGT networks, we demonstrate some analogous but more intricate results.}, }
@article {pmid25447033, year = {2014}, author = {Pedezzi, R and Fonseca, FP and Santos Júnior, CD and Kishi, LT and Terra, WR and Henrique-Silva, F}, title = {A novel β-fructofuranosidase in Coleoptera: Characterization of a β-fructofuranosidase from the sugarcane weevil, Sphenophorus levis.}, journal = {Insect biochemistry and molecular biology}, volume = {55}, number = {}, pages = {31-38}, doi = {10.1016/j.ibmb.2014.10.005}, pmid = {25447033}, issn = {1879-0240}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Gastrointestinal Tract/enzymology ; Larva/enzymology ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Weevils/*enzymology/genetics ; beta-Fructofuranosidase/genetics/*metabolism ; }, abstract = {β-fructofuranosidases or invertases (EC 3.2.1.26) catalyze the hydrolysis of sucrose into fructose and glucose. β-fructofuranosidases have been widely described in microorganisms, but were not known in the animal kingdom until very recently. There are studies reporting lepidopteran β-fructofuranosidases, but no β-fructofuranosidase gene sequence or encoding transcript has previously been identified in beetles. Considering the scarcity of functional studies on insect β-fructofuranosidases and their apparent non-occurrence among coleopterans, the aim of the present study was to investigate the occurrence and characterize a β-fructofuranosidase transcript identified in a cDNA library from the sugarcane weevil, Sphenophorus levis (Curculionidae). To validate that the β-fructofuranosidase sequence (herein denominated Sl-β-fruct) is indeed encoded by the S. levis genome, PCRs were performed using genomic DNA extracted from the larval fat body as well as DNA from the midgut with microbial content. Amplification of Sl-β-fruct gene using larval fat body DNA indicated its presence in the insect's genomic DNA. The Sl-β-fruct gene was cloned in Pichia pastoris to produce the recombinant enzyme (rSl-β-fruct). Molecular weight of the recombinant protein was about 64 kDa, indicating possible glycosylation, since the theoretical weight was 54.8 kDa. The substrate specificity test revealed that rSl-β-fruct hydrolyzes sucrose and raffinose, but not melibiose or maltose, thereby confirming invertase activity. The pH curve revealed greatest activity at pH 5.0, demonstrating rSl-β-fruct to be an acidic β-fructofuranosidase. Quantitative PCR (qRT-PCR) analyses indicated that the production of mRNA only occurs in the midgut and reaches the greatest expression level in 30-day-old larvae, which is the expected pattern for digestive enzymes. Chromatography of glycosidases from S. levis midguts showed two enzymes acting as β-fructofuranosidase, indicating the presence of a Sl-β-fruct isoform or a β-fructofuranosidase from insect intestinal microbiota. Moreover, it was found that α-glucosidases do not act on sucrose hydrolysis. Phylogenetic analyses indicated this enzyme to be similar to enzymes found in other coleopteran and lepidopteran β-fructofuranosidases, but also closely similar to bacterial enzymes, suggesting potential horizontal gene transfer. Despite this, the enzyme seems to be restricted to different groups of bacteria, which suggests distinct origin events. The present study expands the concept of the occurrence of β-fructofuranosidase in insects. Despite the few descriptions of this gene in the animal kingdom, it is possible to state that β-fructofuranosidase is crucial to the establishment of some insects throughout their evolutionary history, especially members of the Lepidoptera and Coleoptera clades.}, }
@article {pmid25446906, year = {2014}, author = {Kim, JS and Kim, J and Jeon, SE and Kim, SJ and Kim, NO and Hong, S and Kang, YH and Han, S and Chung, GT}, title = {Complete nucleotide sequence of the IncI1 plasmid pSH4469 encoding CTX-M-15 extended-spectrum β-lactamase in a clinical isolate of Shigella sonnei from an outbreak in the Republic of Korea.}, journal = {International journal of antimicrobial agents}, volume = {44}, number = {6}, pages = {533-537}, doi = {10.1016/j.ijantimicag.2014.08.007}, pmid = {25446906}, issn = {1872-7913}, mesh = {Anti-Bacterial Agents/*therapeutic use ; Base Sequence ; Child ; DNA, Bacterial/chemistry/genetics ; *Disease Outbreaks ; Dysentery, Bacillary/*drug therapy ; Electrophoresis, Gel, Pulsed-Field ; Gene Transfer, Horizontal ; Humans ; Male ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Multilocus Sequence Typing ; Plasmids/genetics ; Republic of Korea ; Sequence Analysis, DNA ; Shigella sonnei/drug effects/*enzymology/genetics ; beta-Lactamases/*genetics ; }, abstract = {An outbreak of extended-spectrum β-lactamase (ESBL)-producing Shigella sonnei infections occurred in a school for disabled children in Gyeongbuk Province, Republic of Korea, in 2008. Five students were affected. Pulsed-field gel electrophoresis (PFGE) analysis revealed that all of the ESBL-producing S. sonnei isolates belonged to the same clone, and nucleotide sequence analysis of ESBL genes revealed that they harboured bla(CTX-M-15). This is the first identification of bla(CTX-M-15) in Shigella spp. in South Korea. In this study, a plasmid carrying the bla(CTX-M-15) gene, designated pSH4469, recovered from a S. sonnei isolate responsible for the outbreak was characterised. Replicon typing and plasmid multilocus sequence typing (pMLST) analysis of plasmids in the outbreak strain identified that the bla(CTX-M-15) gene was located on an IncI1 incompatibility group plasmid of sequence type 16 (ST16). The complete nucleotide sequence of pSH4469 revealed that this plasmid is 91109bp and harbours 119 putative genes, including another antibiotic resistance gene (bla(TEM-1b)) that is often associated with the ISEcp1-bla(CTX-M-15)-orf477delta transposable unit. The plasmid consists of a large backbone with considerable homology to the pEK204 plasmid isolated from Escherichia coli in the UK, except for insertion of an IS66 element found in pEK204. These data demonstrate that IncI1 plasmids are used as a successful platform for efficient horizontal gene transfer, thereby resulting in the dissemination of CTX-M-type β-lactamases among Enterobacteriaceae.}, }
@article {pmid25445567, year = {2015}, author = {Hassan, KA and Elbourne, LD and Tetu, SG and Melville, SB and Rood, JI and Paulsen, IT}, title = {Genomic analyses of Clostridium perfringens isolates from five toxinotypes.}, journal = {Research in microbiology}, volume = {166}, number = {4}, pages = {255-263}, doi = {10.1016/j.resmic.2014.10.003}, pmid = {25445567}, issn = {1769-7123}, support = {N01-AI-30071/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacterial Toxins/classification/genetics ; Clostridium Infections/microbiology/veterinary ; Clostridium perfringens/*genetics/isolation &amp; purification ; Gene Order ; *Genome, Bacterial ; Genomics ; Humans ; Plasmids/analysis ; Synteny ; }, abstract = {Clostridium perfringens can be isolated from a range of environments, including soil, marine and fresh water sediments, and the gastrointestinal tracts of animals and humans. Some C. perfringens strains have attractive industrial applications, e.g., in the degradation of waste products or the production of useful chemicals. However, C. perfringens has been most studied as the causative agent of a range of enteric and soft tissue infections of varying severities in humans and animals. Host preference and disease type in C. perfringens are intimately linked to the production of key extracellular toxins and on this basis toxigenic C. perfringens strains have been classified into five toxinotypes (A-E). To date, twelve genome sequences have been generated for a diverse collection of C. perfringens isolates, including strains associated with human and animal infections, a human commensal strain, and a strain with potential industrial utility. Most of the sequenced strains are classified as toxinotype A. However, genome sequences of representative strains from each of the other four toxinotypes have also been determined. Analysis of this collection of sequences has highlighted a lack of features differentiating toxinotype A strains from the other isolates, indicating that the primary defining characteristic of toxinotype A strains is their lack of key plasmid-encoded extracellular toxin genes associated with toxinotype B to E strains. The representative B-E strains sequenced to date each harbour many unique genes. Additional genome sequences are needed to determine if these genes are characteristic of their respective toxinotypes.}, }
@article {pmid25440554, year = {2015}, author = {Mooyottu, S and Flock, G and Kollanoor-Johny, A and Upadhyaya, I and Jayarao, B and Venkitanarayanan, K}, title = {Characterization of a multidrug resistant C. difficile meat isolate.}, journal = {International journal of food microbiology}, volume = {192}, number = {}, pages = {111-116}, doi = {10.1016/j.ijfoodmicro.2014.10.002}, pmid = {25440554}, issn = {1879-3460}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Clostridioides difficile/classification/drug effects/*genetics ; Drug Resistance, Bacterial/*genetics ; Genome, Bacterial/genetics ; Meat/*microbiology ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Phylogeny ; Swine ; }, abstract = {Clostridium difficile is a pathogen of significant public health concern causing a life-threatening, toxin-mediated enteric disease in humans. The incidence and severity of the disease associated with C. difficile have increased in the US with the emergence of hypervirulent strains and community associated outbreaks. The detection of genotypically similar and identical C. difficile strains implicated from human infections in foods and food animals indicates the potential role of food as a source of community associated C. difficile disease. One hundred samples each of ground beef, pork and chicken obtained from geographically distant grocery stores in Connecticut were tested for C. difficile. Positive isolates were characterized by ribotyping, antibiotic susceptibility, toxin production and whole genome sequencing. Of the 300 meat samples, only two pork samples tested positive for C. difficile indicating a very low prevalence of C. difficile in meat. The isolates were non toxigenic; however, genome characterization revealed the presence of several antibiotic resistance genes and mobile elements that can potentially contribute to generation of multidrug resistant toxigenic C. difficile by horizontal gene transfer. Further studies are warranted to investigate potential food-borne transmission of the meat isolates and development of multi-drug resistance in these strains.}, }
@article {pmid25437804, year = {2014}, author = {Yamashita, A and Sekizuka, T and Kuroda, M}, title = {Characterization of Antimicrobial Resistance Dissemination across Plasmid Communities Classified by Network Analysis.}, journal = {Pathogens (Basel, Switzerland)}, volume = {3}, number = {2}, pages = {356-376}, pmid = {25437804}, issn = {2076-0817}, abstract = {The global clustering of gene families through network analysis has been demonstrated in whole genome, plasmid, and microbiome analyses. In this study, we carried out a plasmidome network analysis of all available complete bacterial plasmids to determine plasmid associations. A blastp clustering search at 100% aa identity cut-off and sharing at least one gene between plasmids, followed by a multilevel community network analysis revealed that a surprisingly large number of the plasmids were connected by one largest connected component (LCC), with dozens of community sub-groupings. The LCC consisted mainly of Bacilli and Gammaproteobacteria plasmids. Intriguingly, horizontal gene transfer (HGT) was noted between different phyla (i.e., Staphylococcus and Pasteurellaceae), suggesting that Pasteurellaceae can acquire antimicrobial resistance (AMR) genes from closely contacting Staphylococcus spp., which produce the external supplement of V-factor (NAD). Such community network analysis facilitate displaying possible recent HGTs like a class 1 integron, str and tet resistance markers between communities. Furthermore, the distribution of the Inc replicon type and AMR genes, such as the extended-spectrum ß-lactamase (ESBL) CTX-M or the carbapenemases KPC NDM-1, implies that such genes generally circulate within limited communities belonging to typical bacterial genera. Thus, plasmidome network analysis provides a remarkable discriminatory power for plasmid-related HGT and evolution.}, }
@article {pmid25435831, year = {2014}, author = {Ashraf, S and Chatha, MA and Ejaz, W and Janjua, HA and Hussain, I}, title = {Lysozyme-coated silver nanoparticles for differentiating bacterial strains on the basis of antibacterial activity.}, journal = {Nanoscale research letters}, volume = {9}, number = {1}, pages = {565}, pmid = {25435831}, issn = {1931-7573}, abstract = {Lysozyme, an antibacterial enzyme, was used as a stabilizing ligand for the synthesis of fairly uniform silver nanoparticles adopting various strategies. The synthesized particles were characterized using UV-visible spectroscopy, FTIR, dynamic light scattering (DLS), and TEM to observe their morphology and surface chemistry. The silver nanoparticles were evaluated for their antimicrobial activity against several bacterial species and various bacterial strains within the same species. The cationic silver nanoparticles were found to be more effective against Pseudomonas aeruginosa 3 compared to other bacterial species/strains investigated. Some of the bacterial strains of the same species showed variable antibacterial activity. The difference in antimicrobial activity of these particles has led to the conclusion that antimicrobial products formed from silver nanoparticles may not be equally effective against all the bacteria. This difference in the antibacterial activity of silver nanoparticles for different bacterial strains from the same species may be due to the genome islands that are acquired through horizontal gene transfer (HGT). These genome islands are expected to possess some genes that may encode enzymes to resist the antimicrobial activity of silver nanoparticles. These silver nanoparticles may thus also be used to differentiate some bacterial strains within the same species due to variable silver resistance of these variants, which may not possible by simple biochemical tests.}, }
@article {pmid25433005, year = {2015}, author = {Nigro, SJ and Holt, KE and Pickard, D and Hall, RM}, title = {Carbapenem and amikacin resistance on a large conjugative Acinetobacter baumannii plasmid.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {70}, number = {4}, pages = {1259-1261}, pmid = {25433005}, issn = {1460-2091}, support = {628930//Wellcome Trust/United Kingdom ; }, mesh = {Acinetobacter Infections/microbiology ; Acinetobacter baumannii/*drug effects/*genetics/isolation &amp; purification ; Amikacin/*pharmacology ; Anti-Bacterial Agents/*pharmacology ; Australia ; Carbapenems/*pharmacology ; Conjugation, Genetic ; DNA Transposable Elements ; DNA, Bacterial/chemistry/genetics ; *Drug Resistance, Bacterial ; Gene Order ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Molecular Sequence Data ; *Plasmids ; Sequence Analysis, DNA ; }, }
@article {pmid25431047, year = {2015}, author = {Bhatty, M and Cruz, MR and Frank, KL and Gomez, JA and Andrade, F and Garsin, DA and Dunny, GM and Kaplan, HB and Christie, PJ}, title = {Enterococcus faecalis pCF10-encoded surface proteins PrgA, PrgB (aggregation substance) and PrgC contribute to plasmid transfer, biofilm formation and virulence.}, journal = {Molecular microbiology}, volume = {95}, number = {4}, pages = {660-677}, pmid = {25431047}, issn = {1365-2958}, support = {R01GM48746/GM/NIGMS NIH HHS/United States ; R21AI105454/AI/NIAID NIH HHS/United States ; R01GM49530/GM/NIGMS NIH HHS/United States ; R01 GM049530/GM/NIGMS NIH HHS/United States ; R56 AI110432/AI/NIAID NIH HHS/United States ; R01 GM048746/GM/NIGMS NIH HHS/United States ; R21 AI105454/AI/NIAID NIH HHS/United States ; R01AI076406/AI/NIAID NIH HHS/United States ; R01 AI076406/AI/NIAID NIH HHS/United States ; R56AI110432/AI/NIAID NIH HHS/United States ; R01DE021394/DE/NIDCR NIH HHS/United States ; R01 DE021394/DE/NIDCR NIH HHS/United States ; }, mesh = {Animals ; Bacterial Proteins/genetics/*metabolism ; Biofilms/*growth &amp; development ; Caenorhabditis elegans/*microbiology ; Conjugation, Genetic ; Enterococcus faecalis/*genetics/*pathogenicity/physiology ; Gene Expression Regulation, Bacterial ; Membrane Proteins/genetics/*metabolism ; *Plasmids ; Promoter Regions, Genetic ; Sequence Deletion ; Transcription, Genetic ; Virulence/genetics ; Virulence Factors/metabolism ; }, abstract = {Enterococcus faecalis pCF10 transfers at high frequencies upon pheromone induction of the prgQ transfer operon. This operon codes for three cell wall-anchored proteins - PrgA, PrgB (aggregation substance) and PrgC - and a type IV secretion system through which the plasmid is delivered to recipient cells. Here, we defined the contributions of the Prg surface proteins to plasmid transfer, biofilm formation and virulence using the Caenorhabditis elegans infection model. We report that a combination of PrgB and extracellular DNA (eDNA), but not PrgA or PrgC, was required for extensive cellular aggregation and pCF10 transfer at wild-type frequencies. In addition to PrgB and eDNA, production of PrgA was necessary for extensive binding of enterococci to abiotic surfaces and development of robust biofilms. However, although PrgB is a known virulence factor in mammalian infection models, we determined that PrgA and PrgC, but not PrgB, were required for efficient killing in the worm infection model. We propose that the pheromone-responsive, conjugative plasmids of E. faecalis have retained Prg-like surface functions over evolutionary time for attachment, colonization and robust biofilm development. In natural settings, these biofilms are polymicrobial in composition and constitute optimal environments for signal exchange, mating pair formation and widespread lateral gene transfer.}, }
@article {pmid25430522, year = {2016}, author = {Salvucci, E}, title = {Microbiome, holobiont and the net of life.}, journal = {Critical reviews in microbiology}, volume = {42}, number = {3}, pages = {485-494}, doi = {10.3109/1040841X.2014.962478}, pmid = {25430522}, issn = {1549-7828}, mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification ; *Bacterial Physiological Phenomena ; Biological Evolution ; Humans ; *Microbiota ; *Symbiosis ; }, abstract = {Holistic emerging approaches allow us to understand that every organism is the result of integration mechanisms observed at every level of nature: integration of DNA from virus and bacteria in metazoans, endosymbiotic relationships and holobionts. Horizontal gene transfer events in Bacteria, Archaea and Eukaryotes have resulted in the chimeric nature of genomes. As a continuity of this genomic landscape, the human body contains more bacterial than human cells. Human microbiome has co-evolved with the human being as a unity called holobiont. The loss of part of our microbiome along evolution can explain the continuous increasing incidence of immune and inflammatory-related diseases. Life is a continuous process in which the organism experiences its environment and this interaction impacts in the epigenetic system and the genomic structure. The emerging perspectives restitute the great importance of Lamarck's theoretical contributions (the milieu) and Darwin's pangenesis theory.}, }
@article {pmid25428893, year = {2015}, author = {Iguchi, A and Iyoda, S and Kikuchi, T and Ogura, Y and Katsura, K and Ohnishi, M and Hayashi, T and Thomson, NR}, title = {A complete view of the genetic diversity of the Escherichia coli O-antigen biosynthesis gene cluster.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {22}, number = {1}, pages = {101-107}, pmid = {25428893}, issn = {1756-1663}, mesh = {*Databases, Genetic ; Escherichia coli/*genetics/metabolism ; Escherichia coli Proteins/*genetics/metabolism ; Genome, Bacterial/physiology ; Multigene Family/*physiology ; O Antigens/biosynthesis/*genetics ; *Phylogeny ; }, abstract = {The O antigen constitutes the outermost part of the lipopolysaccharide layer in Gram-negative bacteria. The chemical composition and structure of the O antigen show high levels of variation even within a single species revealing itself as serological diversity. Here, we present a complete sequence set for the O-antigen biosynthesis gene clusters (O-AGCs) from all 184 recognized Escherichia coli O serogroups. By comparing these sequences, we identified 161 well-defined O-AGCs. Based on the wzx/wzy or wzm/wzt gene sequences, in addition to 145 singletons, 37 serogroups were placed into 16 groups. Furthermore, phylogenetic analysis of all the E. coli O-serogroup reference strains revealed that the nearly one-quarter of the 184 serogroups were found in the ST10 lineage, which may have a unique genetic background allowing a more successful exchange of O-AGCs. Our data provide a complete view of the genetic diversity of O-AGCs in E. coli showing a stronger association between host phylogenetic lineage and O-serogroup diversification than previously recognized. These data will be a valuable basis for developing a systematic molecular O-typing scheme that will allow traditional typing approaches to be linked to genomic exploration of E. coli diversity.}, }
@article {pmid25426110, year = {2014}, author = {Dziewit, L and Bartosik, D}, title = {Plasmids of psychrophilic and psychrotolerant bacteria and their role in adaptation to cold environments.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {596}, pmid = {25426110}, issn = {1664-302X}, abstract = {Extremely cold environments are a challenge for all organisms. They are mostly inhabited by psychrophilic and psychrotolerant bacteria, which employ various strategies to cope with the cold. Such harsh environments are often highly vulnerable to the influence of external factors and may undergo frequent dynamic changes. The rapid adjustment of bacteria to changing environmental conditions is crucial for their survival. Such "short-term" evolution is often enabled by plasmids-extrachromosomal replicons that represent major players in horizontal gene transfer. The genomic sequences of thousands of microorganisms, including those of many cold-active bacteria have been obtained over the last decade, but the collected data have yet to be thoroughly analyzed. This report describes the results of a meta-analysis of the NCBI sequence databases to identify and characterize plasmids of psychrophilic and psychrotolerant bacteria. We have performed in-depth analyses of 66 plasmids, almost half of which are cryptic replicons not exceeding 10 kb in size. Our analyses of the larger plasmids revealed the presence of numerous genes, which may increase the phenotypic flexibility of their host strains. These genes encode enzymes possibly involved in (i) protection against cold and ultraviolet radiation, (ii) scavenging of reactive oxygen species, (iii) metabolism of amino acids, carbohydrates, nucleotides and lipids, (iv) energy production and conversion, (v) utilization of toxic organic compounds (e.g., naphthalene), and (vi) resistance to heavy metals, metalloids and antibiotics. Some of the plasmids also contain type II restriction-modification systems, which are involved in both plasmid stabilization and protection against foreign DNA. Moreover, approx. 50% of the analyzed plasmids carry genetic modules responsible for conjugal transfer or mobilization for transfer, which may facilitate the spread of these replicons among various bacteria, including across species boundaries.}, }
@article {pmid25425282, year = {2015}, author = {Minerdi, D and Sadeghi, SJ and Di Nardo, G and Rua, F and Castrignanò, S and Allegra, P and Gilardi, G}, title = {CYP116B5: a new class VII catalytically self-sufficient cytochrome P450 from Acinetobacter radioresistens that enables growth on alkanes.}, journal = {Molecular microbiology}, volume = {95}, number = {3}, pages = {539-554}, doi = {10.1111/mmi.12883}, pmid = {25425282}, issn = {1365-2958}, mesh = {Acinetobacter/*enzymology/*genetics/growth &amp; development ; Alkanes/*metabolism ; Amino Acid Sequence ; Binding Sites ; Biocatalysis ; Biological Evolution ; Cytochrome P-450 Enzyme System/chemistry/genetics/*isolation &amp; purification/*metabolism ; Escherichia coli/genetics/growth &amp; development ; Evolution, Molecular ; Gene Transfer, Horizontal ; Heme/chemistry ; Italy ; Molecular Sequence Data ; NADP/metabolism ; Oxidation-Reduction ; Phylogeny ; Recombinant Proteins/metabolism ; Rhodococcus/genetics ; Sequence Alignment ; Soil Microbiology ; }, abstract = {A gene coding for a class VII cytochrome P450 monooxygenase (CYP116B5) was identified from Acinetobacter radioresistens S13 growing on media with medium (C14, C16) and long (C24, C36) chain alkanes as the sole energy source. Phylogenetic analysis of its N- and C-terminal domains suggests an evolutionary model involving a plasmid-mediated horizontal gene transfer from the donor Rhodococcus jostii RHA1 to the receiving A. radioresistens S13. This event was followed by fusion and integration of the new gene in A. radioresistens chromosome. Heterologous expression of CYP116B5 in Escherichia coli BL21, together with the A. radioresistens Baeyer-Villiger monooxygenase, allowed the recombinant bacteria to grow on long- and medium-chain alkanes, showing that CYP116B5 is involved in the first step of terminal oxidation of medium-chain alkanes overlapping AlkB and in the first step of sub-terminal oxidation of long-chain alkanes. It was also demonstrated that CYP116B5 is a self-sufficient cytochrome P450 consisting of a heme domain (aa 1-392) involved in the oxidation step of n-alkanes degradation, and its reductase domain (aa 444-758) comprising the NADPH-, FMN- and [2Fe2S]-binding sites. To our knowledge, CYP116B5 is the first member of this class to have its natural substrate and function identified.}, }
@article {pmid25425234, year = {2014}, author = {Dordet-Frisoni, E and Sagné, E and Baranowski, E and Breton, M and Nouvel, LX and Blanchard, A and Marenda, MS and Tardy, F and Sirand-Pugnet, P and Citti, C}, title = {Chromosomal transfers in mycoplasmas: when minimal genomes go mobile.}, journal = {mBio}, volume = {5}, number = {6}, pages = {e01958}, pmid = {25425234}, issn = {2150-7511}, mesh = {*Chromosomes, Bacterial ; Conjugation, Genetic ; *Gene Transfer, Horizontal ; Homologous Recombination ; *Interspersed Repetitive Sequences ; Mycoplasma agalactiae/*genetics ; }, abstract = {UNLABELLED: Horizontal gene transfer (HGT) is a main driving force of bacterial evolution and innovation. This phenomenon was long thought to be marginal in mycoplasmas, a large group of self-replicating bacteria characterized by minute genomes as a result of successive gene losses during evolution. Recent comparative genomic analyses challenged this paradigm, but the occurrence of chromosomal exchanges had never been formally addressed in mycoplasmas. Here, we demonstrated the conjugal transfer of large chromosomal regions within and among ruminant mycoplasma species, with the incorporation of the incoming DNA occurring by homologous recombination into the recipient chromosome. By combining classical mating experiments with high-throughput next-generation sequencing, we documented the transfer of almost every position of the mycoplasma chromosome. Mycoplasma conjugation relies on the occurrence of an integrative conjugative element (ICE) in at least one parent cell. While ICE propagates horizontally from ICE-positive to ICE-negative cells, chromosomal transfers (CTs) occurred in the opposite direction, from ICE-negative to ICE-positive cells, independently of ICE movement. These findings challenged the classical mechanisms proposed for other bacteria in which conjugative CTs are driven by conjugative elements, bringing into the spotlight a new means for rapid mycoplasma innovation. Overall, they radically change our current views concerning the evolution of mycoplasmas, with particularly far-reaching implications given that over 50 species are human or animal pathogens.<br><br>IMPORTANCE: Horizontal gene transfers (HGT) shape bacterial genomes and are key contributors to microbial diversity and innovation. One main mechanism involves conjugation, a process that allows the simultaneous transfer of significant amounts of DNA upon cell-to-cell contact. Recognizing and deciphering conjugal mechanisms are thus essential in understanding the impact of gene flux on bacterial evolution. We addressed this issue in mycoplasmas, the smallest and simplest self-replicating bacteria. In these organisms, HGT was long thought to be marginal. We showed here that nearly every position of the Mycoplasma agalactiae chromosome could be transferred via conjugation, using an unconventional mechanism. The transfer involved DNA blocks containing up to 80 genes that were incorporated into the host chromosome by homologous recombination. These findings radically change our views concerning mycoplasma evolution and adaptation with particularly far-reaching implications given that over 50 species are human or animal pathogens.}, }
@article {pmid25425232, year = {2014}, author = {Kang, Y and Gu, C and Yuan, L and Wang, Y and Zhu, Y and Li, X and Luo, Q and Xiao, J and Jiang, D and Qian, M and Ahmed Khan, A and Chen, F and Zhang, Z and Yu, J}, title = {Flexibility and symmetry of prokaryotic genome rearrangement reveal lineage-associated core-gene-defined genome organizational frameworks.}, journal = {mBio}, volume = {5}, number = {6}, pages = {e01867}, pmid = {25425232}, issn = {2150-7511}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Computational Biology ; Gene Rearrangement ; *Genes, Essential ; Genome, Archaeal ; Genome, Bacterial ; Genomic Instability ; *Genomic Structural Variation ; Synteny ; }, abstract = {UNLABELLED: The prokaryotic pangenome partitions genes into core and dispensable genes. The order of core genes, albeit assumed to be stable under selection in general, is frequently interrupted by horizontal gene transfer and rearrangement, but how a core-gene-defined genome maintains its stability or flexibility remains to be investigated. Based on data from 30 species, including 425 genomes from six phyla, we grouped core genes into syntenic blocks in the context of a pangenome according to their stability across multiple isolates. A subset of the core genes, often species specific and lineage associated, formed a core-gene-defined genome organizational framework (cGOF). Such cGOFs are either single segmental (one-third of the species analyzed) or multisegmental (the rest). Multisegment cGOFs were further classified into symmetric or asymmetric according to segment orientations toward the origin-terminus axis. The cGOFs in Gram-positive species are exclusively symmetric and often reversible in orientation, as opposed to those of the Gram-negative bacteria, which are all asymmetric and irreversible. Meanwhile, all species showing strong strand-biased gene distribution contain symmetric cGOFs and often specific DnaE (α subunit of DNA polymerase III) isoforms. Furthermore, functional evaluations revealed that cGOF genes are hub associated with regard to cellular activities, and the stability of cGOF provides efficient indexes for scaffold orientation as demonstrated by assembling virtual and empirical genome drafts. cGOFs show species specificity, and the symmetry of multisegmental cGOFs is conserved among taxa and constrained by DNA polymerase-centric strand-biased gene distribution. The definition of species-specific cGOFs provides powerful guidance for genome assembly and other structure-based analysis.<br><br>IMPORTANCE: Prokaryotic genomes are frequently interrupted by horizontal gene transfer (HGT) and rearrangement. To know whether there is a set of genes not only conserved in position among isolates but also functionally essential for a given species and to further evaluate the stability or flexibility of such genome structures across lineages are of importance. Based on a large number of multi-isolate pangenomic data, our analysis reveals that a subset of core genes is organized into a core-gene-defined genome organizational framework, or cGOF. Furthermore, the lineage-associated cGOFs among Gram-positive and Gram-negative bacteria behave differently: the former, composed of 2 to 4 segments, have their fragments symmetrically rearranged around the origin-terminus axis, whereas the latter show more complex segmentation and are partitioned asymmetrically into chromosomal structures. The definition of cGOFs provides new insights into prokaryotic genome organization and efficient guidance for genome assembly and analysis.}, }
@article {pmid25422937, year = {2014}, author = {Catchpole, RJ and Poole, AM}, title = {Antibiotic genes spread far and wide.}, journal = {eLife}, volume = {3}, number = {}, pages = {}, pmid = {25422937}, issn = {2050-084X}, mesh = {Anti-Bacterial Agents/*metabolism ; Bacteria/*enzymology/*genetics ; Gene Transfer, Horizontal/*genetics ; Muramidase/*genetics ; *Phylogeny ; }, abstract = {The genes responsible for antibiotics can spread between the three domains of life—Archaea, Bacteria and Eukaryotes.}, }
@article {pmid25422936, year = {2014}, author = {Metcalf, JA and Funkhouser-Jones, LJ and Brileya, K and Reysenbach, AL and Bordenstein, SR}, title = {Antibacterial gene transfer across the tree of life.}, journal = {eLife}, volume = {3}, number = {}, pages = {}, pmid = {25422936}, issn = {2050-084X}, support = {R01 GM085163/GM/NIGMS NIH HHS/United States ; T32 GM007347/GM/NIGMS NIH HHS/United States ; T32GM07347/GM/NIGMS NIH HHS/United States ; R01GM085163/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Anti-Bacterial Agents/*metabolism ; Archaea/enzymology ; Bacteria/*enzymology/*genetics ; Coculture Techniques ; Escherichia coli/cytology ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial ; Microbial Viability ; Models, Molecular ; Molecular Sequence Data ; Muramidase/chemistry/*genetics ; *Phylogeny ; RNA, Ribosomal/genetics ; }, abstract = {Though horizontal gene transfer (HGT) is widespread, genes and taxa experience biased rates of transferability. Curiously, independent transmission of homologous DNA to archaea, bacteria, eukaryotes, and viruses is extremely rare and often defies ecological and functional explanations. Here, we demonstrate that a bacterial lysozyme family integrated independently in all domains of life across diverse environments, generating the only glycosyl hydrolase 25 muramidases in plants and archaea. During coculture of a hydrothermal vent archaeon with a bacterial competitor, muramidase transcription is upregulated. Moreover, recombinant lysozyme exhibits broad-spectrum antibacterial action in a dose-dependent manner. Similar to bacterial transfer of antibiotic resistance genes, transfer of a potent antibacterial gene across the universal tree seemingly bestows a niche-transcending adaptation that trumps the barriers against parallel HGT to all domains. The discoveries also comprise the first characterization of an antibacterial gene in archaea and support the pursuit of antibiotics in this underexplored group.}, }
@article {pmid25420718, year = {2014}, author = {Tian, Y and Li, T and Zhu, Y and Wang, B and Zou, X and Li, M}, title = {Mechanisms of linezolid resistance in staphylococci and enterococci isolated from two teaching hospitals in Shanghai, China.}, journal = {BMC microbiology}, volume = {14}, number = {}, pages = {292}, pmid = {25420718}, issn = {1471-2180}, mesh = {Acetamides/*pharmacology ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics ; Cell Wall/ultrastructure ; China ; *Drug Resistance, Bacterial ; Enterococcus/*drug effects/genetics/isolation &amp; purification/ultrastructure ; Gene Transfer, Horizontal ; Gram-Positive Bacterial Infections/microbiology ; Hospitals, Teaching ; Humans ; Linezolid ; Microbial Sensitivity Tests ; Microscopy, Electron, Transmission ; Oxazolidinones/*pharmacology ; *Point Mutation ; RNA, Ribosomal, 23S/genetics ; Ribosomal Proteins/genetics ; Staphylococcus/*drug effects/genetics/isolation &amp; purification/ultrastructure ; }, abstract = {BACKGROUND: Linezolid is one of the most effective treatments against Gram-positive pathogens. However, linezolid-resistant/intermediate strains have recently emerged in worldwide. The purpose of this study was to analyse the prevalence and resistance mechanisms of linezolid-resistant/intermediate staphylococci and enterococci in Shanghai, China.<br><br>RESULTS: Thirty-two linezolid-resistant/intermediate strains, including 14&#x2009;Staphylococcus capitis, three Staphylococcus aureus, 14 Enterococcus faecalis and one Enterococcus faecium clinical isolates, were collected in this study which displayed linezolid MICs of 8 to 512 &#x3bc;g/ml, 8-32 &#x3bc;g/ml, 4-8 &#x3bc;g/ml and 4 &#x3bc;g/ml, respectively. All linezolid-resistant S. capitis isolates had a novel C2131T mutation and a G2603T mutation in the 23S rRNA region, and some had a C316T (Arg106Cys) substitution in protein L4 and/or harboured cfr. Linezolid-resistant S. aureus isolates carried a C389G (Ala130Gly) substitution in protein L3, and/or harboured cfr. The cfr gene was flanked by two copies of the IS256-like element, with a downstream orf1 gene. Linezolid-resistant/intermediate enterococci lacked major resistance mechanisms. The semi-quantitative biofilm assay showed that 14 linezolid-resistant E. faecalis isolates produced a larger biofilm than linezolid-susceptible E. faecalis strains. Transmission electron microscopy showed the cell walls of linezolid-resistant/intermediate strains were thicker than linezolid-susceptible strains.<br><br>CONCLUSION: Our data indicated that major resistance mechanisms, such as mutations in 23S rRNA and ribosomal proteins L3 and L4, along with cfr acquisition, played an important role in linezolid resistance. Secondary resistance mechanisms, such as biofilm formation and cell wall thickness, should also be taken into account.}, }
@article {pmid25420622, year = {2014}, author = {Dobri, N and Candelori, A and Ricci, F and Luporini, P and Vallesi, A}, title = {Evidence for methionine-sulfoxide-reductase gene transfer from Alphaproteobacteria to the transcriptionally active (macro)nucleus of the ciliate, Euplotes raikovi.}, journal = {BMC microbiology}, volume = {14}, number = {}, pages = {288}, pmid = {25420622}, issn = {1471-2180}, mesh = {Alphaproteobacteria/*genetics ; Amino Acid Sequence ; Base Sequence ; Cell Nucleus/*genetics ; Ciliophora/*genetics ; Euplotes/*genetics ; Methionine/analogs &amp; derivatives/genetics ; Methionine Sulfoxide Reductases/*genetics ; Molecular Sequence Data ; Open Reading Frames/genetics ; Oxidation-Reduction ; Protein Isoforms/genetics ; Sequence Alignment ; }, abstract = {BACKGROUND: Deleterious phenomena of protein oxidation affect every aerobic organism and methionine residues are their elective targets. The reduction of methionine sulfoxides back to methionines is catalyzed by methionine-sulfoxide reductases (Msrs), enzymes which are particularly active in microorganisms because of their unique nature of individual cells directly exposed to environmental oxidation.<br><br>RESULTS: From the transcriptionally active somatic genome of a common free-living marine protist ciliate, Euplotes raikovi, we cloned multiple gene isoforms encoding Msr of type A (MsrA) committed to repair methionine-S-sulfoxides. One of these isoforms, in addition to including a MsrA-specific nucleotide sequence, included also a sequence specific for a Msr of type B (MsrB) committed to repair methionine-R-sulfoxides. Analyzed for its structural relationships with MsrA and MsrB coding sequences of other organisms, the coding region of this gene (named msrAB) showed much more significant relationships with Msr gene coding sequences of Rhodobacterales and Rhizobiales (Alphaproteobacteria), than of other eukaryotic organisms.<br><br>CONCLUSIONS: Based on the fact that the msrAB gene is delimited by Euplotes-specific regulatory 5' and 3' regions and telomeric C4A4/G4T4 repeats, it was concluded that E. raikovi inherited the coding region of this gene through a phenomenon of horizontal gene transfer from species of Alphaproteobacteria with which it coexists in nature and on which it likely feeds.}, }
@article {pmid25420550, year = {2015}, author = {Yang, Z and Zhou, Y and Huang, J and Hu, Y and Zhang, E and Xie, Z and Ma, S and Gao, Y and Song, S and Xu, C and Liang, G}, title = {Ancient horizontal transfer of transaldolase-like protein gene and its role in plant vascular development.}, journal = {The New phytologist}, volume = {206}, number = {2}, pages = {807-816}, pmid = {25420550}, issn = {1469-8137}, mesh = {Bacteria/*genetics ; Biological Evolution ; Embryophyta/*genetics/growth &amp; development ; Gene Transfer, Horizontal ; Introns/genetics ; Oryza/*genetics/growth &amp; development ; Phylogeny ; Plant Proteins/genetics ; Plant Vascular Bundle/genetics/growth &amp; development ; Plants, Genetically Modified ; Transaldolase/*genetics ; }, abstract = {A major event in land plant evolution is the origin of vascular tissues, which ensure the long-distance transport of water, nutrients and organic compounds. However, the molecular basis for the origin and evolution of plant vascular tissues remains largely unknown. Here, we investigate the evolution of the land plant TAL-type transaldolase (TAL) gene and its potential function in rice (Oryza sativa) based on phylogenetic analyses and transgenic experiments, respectively. TAL genes are only present in land plants and bacteria. Phylogenetic analyses suggest that land plant TAL genes are derived from Actinobacteria through an ancient horizontal gene transfer (HGT) event. Further evidence reveals that land plant TAL genes have undergone positive selection and gained several introns following its acquisition by the most recent common ancestor of land plants. Transgenic plant experiments show that rice TAL is specifically expressed in vascular tissues and that knockdown of TAL expression leads to changes in both the number and pattern of vascular bundles. Our findings show that the ancient HGT of TAL from bacteria probably plays an important role in plant vascular development and adaptation to land environments.}, }
@article {pmid25420106, year = {2014}, author = {Kovacova, V and Zluvova, J and Janousek, B and Talianova, M and Vyskot, B}, title = {The evolutionary fate of the horizontally transferred agrobacterial mikimopine synthase gene in the genera Nicotiana and Linaria.}, journal = {PloS one}, volume = {9}, number = {11}, pages = {e113872}, pmid = {25420106}, issn = {1932-6203}, mesh = {Agrobacterium/enzymology/*genetics ; Bacterial Proteins/classification/*genetics/metabolism ; Base Sequence ; Evolution, Molecular ; Frameshift Mutation ; Gene Expression Regulation, Enzymologic ; *Gene Transfer, Horizontal ; Host-Pathogen Interactions/genetics ; Imidazoles/metabolism ; Linaria/*genetics/microbiology ; Molecular Sequence Data ; Oxidoreductases Acting on CH-NH Group Donors/classification/*genetics/metabolism ; Phylogeny ; Pyridines/metabolism ; Selection, Genetic ; Species Specificity ; Nicotiana/classification/*genetics/microbiology ; Transformation, Genetic ; }, abstract = {Few cases of spontaneously horizontally transferred bacterial genes into plant genomes have been described to date. The occurrence of horizontally transferred genes from the T-DNA of Agrobacterium rhizogenes into the plant genome has been reported in the genus Nicotiana and in the species Linaria vulgaris. Here we compare patterns of evolution in one of these genes (a gene encoding mikimopine synthase, mis) following three different events of horizontal gene transfer (HGT). As this gene plays an important role in Agrobacterium, and there are known cases showing that genes from pathogens can acquire plant protection function, we hypothesised that in at least some of the studied species we will find signs of selective pressures influencing mis sequence. The mikimopine synthase (mis) gene evolved in a different manner in the branch leading to Nicotiana tabacum and N. tomentosiformis, in the branch leading to N. glauca and in the genus Linaria. Our analyses of the genus Linaria suggest that the mis gene began to degenerate soon after the HGT. In contrast, in the case of N. glauca, the mis gene evolved under significant selective pressures. This suggests a possible role of mikimopine synthase in current N. glauca and its ancestor(s). In N. tabacum and N. tomentosiformis, the mis gene has a common frameshift mutation that disrupted its open reading frame. Interestingly, our results suggest that in spite of the frameshift, the mis gene could evolve under selective pressures. This sequence may still have some regulatory role at the RNA level as suggested by coverage of this sequence by small RNAs in N. tabacum.}, }
@article {pmid25419704, year = {2014}, author = {Mazzei, M and Carrozza, ML and Luisi, E and Forzan, M and Giusti, M and Sagona, S and Tolari, F and Felicioli, A}, title = {Infectivity of DWV associated to flower pollen: experimental evidence of a horizontal transmission route.}, journal = {PloS one}, volume = {9}, number = {11}, pages = {e113448}, pmid = {25419704}, issn = {1932-6203}, mesh = {Animals ; Bees/genetics/physiology/*virology ; Flowers/genetics/parasitology/*virology ; *Gene Transfer, Horizontal ; Host-Parasite Interactions ; Host-Pathogen Interactions ; Insect Viruses/genetics/*physiology ; Pollen/genetics/parasitology/*virology ; Pollination ; Reverse Transcriptase Polymerase Chain Reaction ; Viral Load/genetics ; Virus Replication/genetics ; }, abstract = {Deformed wing virus (DWV) is a honeybee pathogen whose presence is generally associated with infestation of the colony by the mite Varroa destructor, leading to the onset of infections responsible for the collapse of the bee colony. DWV contaminates bee products such as royal jelly, bee-bread and honey stored within the infected hive. Outside the hive, DWV has been found in pollen loads collected directly from infected as well as uninfected forager bees. It has been shown that the introduction of virus-contaminated pollen into a DWV-free hive results in the production of virus-contaminated food, whose role in the development of infected bees from virus-free eggs has been experimentally demonstrated. The aim of this study was twofold: (i) to ascertain the presence of DWV on pollen collected directly from flowers visited by honeybees and then quantify the viral load and (ii) determine whether the virus associated with pollen is infective. The results of our investigation provide evidence that DWV is present on pollen sampled directly from visited flowers and that, following injection in individuals belonging to the pollinator species Apis mellifera, it is able to establish an active infection, as indicated by the presence of replicating virus in the head of the injected bees. We also provide the first indication that the pollinator species Osmia cornuta is susceptible to DWV infection.}, }
@article {pmid25418043, year = {2014}, author = {Michener, JK and Camargo Neves, AA and Vuilleumier, S and Bringel, F and Marx, CJ}, title = {Effective use of a horizontally-transferred pathway for dichloromethane catabolism requires post-transfer refinement.}, journal = {eLife}, volume = {3}, number = {}, pages = {}, pmid = {25418043}, issn = {2050-084X}, support = {P20 RR016448/RR/NCRR NIH HHS/United States ; P20GM103397/GM/NIGMS NIH HHS/United States ; P20 GM103397/GM/NIGMS NIH HHS/United States ; P20RR016448/RR/NCRR NIH HHS/United States ; F32 GM106629/GM/NIGMS NIH HHS/United States ; }, mesh = {Alleles ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Methylene Chloride/*metabolism ; Methylobacterium/genetics/metabolism ; Mutation ; }, abstract = {When microbes acquire new abilities through horizontal gene transfer, the genes and pathways must function under conditions with which they did not coevolve. If newly-acquired genes burden the host, their utility will depend on further evolutionary refinement of the recombinant strain. We used laboratory evolution to recapitulate this process of transfer and refinement, demonstrating that effective use of an introduced dichloromethane degradation pathway required one of several mutations to the bacterial host that are predicted to increase chloride efflux. We then used this knowledge to identify parallel, beneficial mutations that independently evolved in two natural dichloromethane-degrading strains. Finally, we constructed a synthetic mobile genetic element carrying both the degradation pathway and a chloride exporter, which preempted the adaptive process and directly enabled effective dichloromethane degradation across diverse Methylobacterium environmental isolates. Our results demonstrate the importance of post-transfer refinement in horizontal gene transfer, with potential applications in bioremediation and synthetic biology.}, }
@article {pmid25415968, year = {2015}, author = {Knie, N and Polsakiewicz, M and Knoop, V}, title = {Horizontal gene transfer of chlamydial-like tRNA genes into early vascular plant mitochondria.}, journal = {Molecular biology and evolution}, volume = {32}, number = {3}, pages = {629-634}, doi = {10.1093/molbev/msu324}, pmid = {25415968}, issn = {1537-1719}, mesh = {Chlamydiales/*genetics ; Chloroplasts/genetics ; DNA, Plant/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/*genetics ; Genes, Mitochondrial ; Huperzia/*genetics ; Phylogeny ; Plants/classification/genetics ; RNA, Transfer/*genetics ; }, abstract = {Mitochondrial genomes of lycophytes are surprisingly diverse, including strikingly different transfer RNA (tRNA) gene complements: No mitochondrial tRNA genes are present in the spikemoss Selaginella moellendorffii, whereas 26 tRNAs are encoded in the chondrome of the clubmoss Huperzia squarrosa. Reinvestigating the latter we found that trnL(gag) and trnS(gga) had never before been identified in any other land plant mitochondrial DNA. Sensitive sequence comparisons showed these two tRNAs as well as trnN(guu) and trnS(gcu) to be very similar to their respective counterparts in chlamydial bacteria. We identified homologs of these chlamydial-type tRNAs also in other lycophyte, fern, and gymnosperm DNAs, suggesting horizontal gene transfer (HGT) into mitochondria in the early vascular plant stem lineages. These findings extend plant mitochondrial HGT to affect individual tRNA genes, to include bacterial donors, and suggest that Chlamydiae on top of their recently proposed key role in primary chloroplast establishment may also have participated in early tracheophyte genome evolution.}, }
@article {pmid25412680, year = {2014}, author = {Yap, KP and Gan, HM and Teh, CS and Chai, LC and Thong, KL}, title = {Comparative genomics of closely related Salmonella enterica serovar Typhi strains reveals genome dynamics and the acquisition of novel pathogenic elements.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {1007}, pmid = {25412680}, issn = {1471-2164}, mesh = {Bacterial Proteins/chemistry/genetics ; Carrier State ; Clustered Regularly Interspaced Short Palindromic Repeats ; Disease Outbreaks ; Evolution, Molecular ; Gene Order ; *Genome, Bacterial ; Genomic Islands ; *Genomics ; Models, Molecular ; Mutagenesis, Insertional ; Phylogeny ; Polymorphism, Single Nucleotide ; Protein Conformation ; Salmonella Phages ; Salmonella typhi/classification/*genetics/virology ; Typhoid Fever/epidemiology/microbiology ; Virulence Factors/genetics ; }, abstract = {BACKGROUND: Typhoid fever is an infectious disease of global importance that is caused by Salmonella enterica subsp. enterica serovar Typhi (S. Typhi). This disease causes an estimated 200,000 deaths per year and remains a serious global health threat. S. Typhi is strictly a human pathogen, and some recovered individuals become long-term carriers who continue to shed the bacteria in their faeces, thus becoming main reservoirs of infection.<br><br>RESULTS: A comparative genomics analysis combined with a phylogenomic analysis revealed that the strains from the outbreak and carrier were closely related with microvariations and possibly derived from a common ancestor. Additionally, the comparative genomics analysis with all of the other completely sequenced S. Typhi genomes revealed that strains BL196 and CR0044 exhibit unusual genomic variations despite S. Typhi being generally regarded as highly clonal. The two genomes shared distinct chromosomal architectures and uncommon genome features; notably, the presence of a ~10 kb novel genomic island containing uncharacterised virulence-related genes, and zot in particular. Variations were also detected in the T6SS system and genes that were related to SPI-10, insertion sequences, CRISPRs and nsSNPs among the studied genomes. Interestingly, the carrier strain CR0044 harboured far more genetic polymorphisms (83% mutant nsSNPs) compared with the closely related BL196 outbreak strain. Notably, the two highly related virulence-determinant genes, rpoS and tviE, were mutated in strains BL196 and CR0044, respectively, which revealed that the mutation in rpoS is stabilising, while that in tviE is destabilising. These microvariations provide novel insight into the optimisation of genes by the pathogens. However, the sporadic strain was found to be far more conserved compared with the others.<br><br>CONCLUSIONS: The uncommon genomic variations in the two closely related BL196 and CR0044 strains suggests that S. Typhi is more diverse than previously thought. Our study has demonstrated that the pathogen is continually acquiring new genes through horizontal gene transfer in the process of host adaptation, providing novel insight into its unusual genomic dynamics. The understanding of these strains and virulence factors, and particularly the strain that is associated with the large outbreak and the less studied asymptomatic Typhi carrier in the population, will have important impact on disease control.}, }
@article {pmid25411186, year = {2015}, author = {O'Brien, FG and Ramsay, JP and Monecke, S and Coombs, GW and Robinson, OJ and Htet, Z and Alshaikh, FA and Grubb, WB}, title = {Staphylococcus aureus plasmids without mobilization genes are mobilized by a novel conjugative plasmid from community isolates.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {70}, number = {3}, pages = {649-652}, doi = {10.1093/jac/dku454}, pmid = {25411186}, issn = {1460-2091}, mesh = {Community-Acquired Infections/microbiology ; *Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; Gene Order ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Molecular Sequence Data ; *Plasmids ; Sequence Analysis, DNA ; Staphylococcal Infections/microbiology ; Staphylococcus aureus/*genetics/isolation &amp; purification ; }, abstract = {OBJECTIVES: To describe a family of conjugative plasmids isolated from colonizing community Staphylococcus aureus and determine their ability to mobilize unrelated antimicrobial resistance/virulence plasmids, not encoding mobilization functions.<br><br>METHODS: Plasmid pWBG749 was labelled with Tn551 (pWBG749e) to enable laboratory manipulation. Plasmid pWBG749e was conjugated into S. aureus of seven different lineages that harboured unrelated plasmids and mobilization experiments were performed. Plasmids were screened by EcoRI restriction and hybridization with probes prepared from unique pWBG749 conjugation genes.<br><br>RESULTS: Conjugative plasmids pWBG745, pWBG748 and pWBG749 belong to the same conjugative-plasmid family as the vancomycin resistance plasmid pBRZ01. Plasmid pWBG749e mobilized five unrelated plasmids. Mobilized plasmid pWBG744 is a pIB485-family plasmid that was also found in international S. aureus.<br><br>CONCLUSIONS: Plasmid pWBG749e can mobilize unrelated S. aureus plasmids whose means of dissemination have not previously been understood.}, }
@article {pmid25410051, year = {2015}, author = {Shukla, A and Hilgenfeld, R}, title = {Acquisition of new protein domains by coronaviruses: analysis of overlapping genes coding for proteins N and 9b in SARS coronavirus.}, journal = {Virus genes}, volume = {50}, number = {1}, pages = {29-38}, pmid = {25410051}, issn = {1572-994X}, mesh = {Coronavirus Nucleocapsid Proteins ; Genes, Overlapping ; Genes, Viral ; Humans ; Models, Molecular ; Nucleocapsid Proteins/*chemistry/*genetics ; Protein Conformation ; Protein Structure, Tertiary ; Severe acute respiratory syndrome-related coronavirus/*chemistry/*genetics ; Viral Proteins/*chemistry/*genetics ; }, abstract = {Acquisition of new proteins by viruses usually occurs through horizontal gene transfer or through gene duplication, but another, less common mechanism is the usage of completely or partially overlapping reading frames. A case of acquisition of a completely new protein through introduction of a start codon in an alternative reading frame is the protein encoded by open reading frame (orf) 9b of SARS coronavirus. This gene completely overlaps with the nucleocapsid (N) gene (orf9a). Our findings indicate that the orf9b gene features a discordant codon-usage pattern. We analyzed the evolution of orf9b in concert with orf9a using sequence data of betacoronavirus-lineage b and found that orf9b, which encodes the overprinting protein, evolved largely independent of the overprinted orf9a. We also examined the protein products of these genomic sequences for their structural flexibility and found that it is not necessary for a newly acquired, overlapping protein product to be intrinsically disordered, in contrast to earlier suggestions. Our findings contribute to characterizing sequence properties of newly acquired genes making use of overlapping reading frames.}, }
@article {pmid25409531, year = {2014}, author = {Ji, W and Lee, D and Wong, E and Dadlani, P and Dinh, D and Huang, V and Kearns, K and Teng, S and Chen, S and Haliburton, J and Heimberg, G and Heineike, B and Ramasubramanian, A and Stevens, T and Helmke, KJ and Zepeda, V and Qi, LS and Lim, WA}, title = {Specific gene repression by CRISPRi system transferred through bacterial conjugation.}, journal = {ACS synthetic biology}, volume = {3}, number = {12}, pages = {929-931}, pmid = {25409531}, issn = {2161-5063}, support = {P50 GM081879/GM/NIGMS NIH HHS/United States ; T32 EB009383/EB/NIBIB NIH HHS/United States ; DP5 OD017887/OD/NIH HHS/United States ; R01 DA036858/DA/NIDA NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; T32 GM008284/GM/NIGMS NIH HHS/United States ; T32 GM067547/GM/NIGMS NIH HHS/United States ; }, mesh = {CRISPR-Cas Systems/*genetics ; Conjugation, Genetic/*genetics ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Genetic Engineering/*methods ; Models, Genetic ; *RNA Interference ; Synthetic Biology ; }, abstract = {In microbial communities, bacterial populations are commonly controlled using indiscriminate, broad range antibiotics. There are few ways to target specific strains effectively without disrupting the entire microbiome and local environment. Here, we use conjugation, a natural DNA horizontal transfer process among bacterial species, to deliver an engineered CRISPR interference (CRISPRi) system for targeting specific genes in recipient Escherichia coli cells. We show that delivery of the CRISPRi system is successful and can specifically repress a reporter gene in recipient cells, thereby establishing a new tool for gene regulation across bacterial cells and potentially for bacterial population control.}, }
@article {pmid25407899, year = {2015}, author = {Chaib De Mares, M and Hess, J and Floudas, D and Lipzen, A and Choi, C and Kennedy, M and Grigoriev, IV and Pringle, A}, title = {Horizontal transfer of carbohydrate metabolism genes into ectomycorrhizal Amanita.}, journal = {The New phytologist}, volume = {205}, number = {4}, pages = {1552-1564}, doi = {10.1111/nph.13140}, pmid = {25407899}, issn = {1469-8137}, mesh = {Amanita/enzymology/*genetics ; Carbohydrate Metabolism/*genetics ; Fungal Proteins/chemistry/genetics ; *Gene Transfer, Horizontal ; *Genes, Fungal ; Models, Molecular ; Mycorrhizae/*genetics ; Phylogeny ; Physical Chromosome Mapping ; Species Specificity ; }, abstract = {The genus Amanita encompasses both symbiotic, ectomycorrhizal fungi and asymbiotic litter decomposers; all species are derived from asymbiotic ancestors. Symbiotic species are no longer able to degrade plant cell walls. The carbohydrate esterases family 1 (CE1s) is a diverse group of enzymes involved in carbon metabolism, including decomposition and carbon storage. CE1 genes of the ectomycorrhizal A. muscaria appear diverged from all other fungal homologues, and more similar to CE1s of bacteria, suggesting a horizontal gene transfer (HGT) event. In order to test whether AmanitaCE1s were acquired horizontally, we built a phylogeny of CE1s collected from across the tree of life, and describe the evolution of CE1 genes among Amanita and relevant lineages of bacteria. CE1s of symbiotic Amanita were very different from CE1s of asymbiotic Amanita, and are more similar to bacterial CE1s. The protein structure of one CE1 gene of A. muscaria matched a depolymerase that degrades the carbon storage molecule poly((R)-3-hydroxybutyrate) (PHB). Asymbiotic Amanita do not carry sequence or structural homologues of these genes. The CE1s acquired through HGT may enable novel metabolisms, or play roles in signaling or defense. This is the first evidence for the horizontal transfer of carbohydrate metabolism genes into ectomycorrhizal fungi.}, }
@article {pmid25407321, year = {2014}, author = {Kaushik, S and Sowdhamini, R}, title = {Distribution, classification, domain architectures and evolution of prolyl oligopeptidases in prokaryotic lineages.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {985}, pmid = {25407321}, issn = {1471-2164}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Archaea/cytology/*enzymology/genetics ; Bacteria/cytology/*enzymology/genetics ; Cell Membrane/enzymology ; Cluster Analysis ; Conserved Sequence ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial/genetics ; Molecular Sequence Annotation ; Molecular Sequence Data ; *Phylogeny ; Prolyl Oligopeptidases ; Protein Structure, Tertiary ; Protein Transport ; Sequence Homology, Nucleic Acid ; Serine Endopeptidases/*chemistry/classification/*genetics/metabolism ; }, abstract = {BACKGROUND: Prolyl oligopeptidases (POPs) are proteolytic enzymes, widely distributed in all the kingdoms of life. Bacterial POPs are pharmaceutically important enzymes, yet their functional and evolutionary details are not fully explored. Therefore, current analysis is aimed at understanding the distribution, domain architecture, probable biological functions and gene family expansion of POPs in bacterial and archaeal lineages.<br><br>RESULTS: Exhaustive sequence analysis of 1,202 bacterial and 91 archaeal genomes revealed ~3,000 POP homologs, with only 638 annotated POPs. We observed wide distribution of POPs in all the analysed bacterial lineages. Phylogenetic analysis and co-clustering of POPs of different phyla suggested their common functions in all the prokaryotic species. Further, on the basis of unique sequence motifs we could classify bacterial POPs into eight subtypes. Analysis of coexisting domains in POPs highlighted their involvement in protein-protein interactions and cellular signaling. We proposed significant extension of this gene family by characterizing 39 new POPs and 158 new &#x3b1;/&#x3b2; hydrolase members.<br><br>CONCLUSIONS: Our study reflects diversity and functional importance of POPs in bacterial species. Many genomes with multiple POPs were identified with high sequence variations and different cellular localizations. Such anomalous distribution of POP genes in different bacterial genomes shows differential expansion of POP gene family primarily by multiple horizontal gene transfer events.}, }
@article {pmid25406466, year = {2015}, author = {Gilliland, WD and Colwell, EM and Osiecki, DM and Park, S and Lin, D and Rathnam, C and Barbash, DA}, title = {Normal segregation of a foreign-species chromosome during Drosophila female meiosis despite extensive heterochromatin divergence.}, journal = {Genetics}, volume = {199}, number = {1}, pages = {73-83}, pmid = {25406466}, issn = {1943-2631}, support = {R15 GM099054/GM/NIGMS NIH HHS/United States ; GM099054/GM/NIGMS NIH HHS/United States ; P40 OD018537/OD/NIH HHS/United States ; P40OD018537/OD/NIH HHS/United States ; GM074737/GM/NIGMS NIH HHS/United States ; R01 GM074737/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Chromosome Segregation ; Chromosomes, Insect/*genetics ; Drosophila melanogaster/*genetics ; Female ; Gene Transfer, Horizontal ; Heterochromatin/*genetics ; Meiosis/*genetics ; Microsatellite Repeats ; }, abstract = {The abundance and composition of heterochromatin changes rapidly between species and contributes to hybrid incompatibility and reproductive isolation. Heterochromatin differences may also destabilize chromosome segregation and cause meiotic drive, the non-Mendelian segregation of homologous chromosomes. Here we use a range of genetic and cytological assays to examine the meiotic properties of a Drosophila simulans chromosome 4 (sim-IV) introgressed into D. melanogaster. These two species differ by ∼12-13% at synonymous sites and several genes essential for chromosome segregation have experienced recurrent adaptive evolution since their divergence. Furthermore, their chromosome 4s are visibly different due to heterochromatin divergence, including in the AATAT pericentromeric satellite DNA. We find a visible imbalance in the positioning of the two chromosome 4s in sim-IV/mel-IV heterozygote and also replicate this finding with a D. melanogaster 4 containing a heterochromatic deletion. These results demonstrate that heterochromatin abundance can have a visible effect on chromosome positioning during meiosis. Despite this effect, however, we find that sim-IV segregates normally in both diplo and triplo 4 D. melanogaster females and does not experience elevated nondisjunction. We conclude that segregation abnormalities and a high level of meiotic drive are not inevitable byproducts of extensive heterochromatin divergence. Animal chromosomes typically contain large amounts of noncoding repetitive DNA that nevertheless varies widely between species. This variation may potentially induce non-Mendelian transmission of chromosomes. We have examined the meiotic properties and transmission of a highly diverged chromosome 4 from a foreign species within the fruitfly Drosophila melanogaster. This chromosome has substantially less of a simple sequence repeat than does D. melanogaster 4, and we find that this difference results in altered positioning when chromosomes align during meiosis. Yet this foreign chromosome segregates at normal frequencies, demonstrating that chromosome segregation can be robust to major differences in repetitive DNA abundance.}, }
@article {pmid25401060, year = {2014}, author = {Sharma, PK and Fu, J and Zhang, X and Fristensky, B and Sparling, R and Levin, DB}, title = {Genome features of Pseudomonas putida LS46, a novel polyhydroxyalkanoate producer and its comparison with other P. putida strains.}, journal = {AMB Express}, volume = {4}, number = {}, pages = {37}, pmid = {25401060}, issn = {2191-0855}, abstract = {A novel strain of Pseudomonas putida LS46 was isolated from wastewater on the basis of its ability to synthesize medium chain-length polyhydroxyalkanoates (mcl-PHAs). P.putida LS46 was differentiated from other P.putida strains on the basis of cpn60 (UT). The complete genome of P.putida LS46 was sequenced and annotated. Its chromosome is 5,86,2556 bp in size with GC ratio of 61.69. It is encoding 5316 genes, including 7 rRNA genes and 76 tRNA genes. Nucleotide sequence data of the complete P. putida LS46 genome was compared with nine other P. putida strains (KT2440, F1, BIRD-1, S16, ND6, DOT-T1E, UW4, W619 and GB-1) identified either as biocontrol agents or as bioremediation agents and isolated from different geographical region and different environment. BLASTn analysis of whole genome sequences of the ten P. putida strains revealed nucleotide sequence identities of 86.54 to 97.52%. P.putida genome arrangement was LS46 highly similar to P.putida BIRD1 and P.putida ND6 but was markedly different than P.putida DOT-T1E, P.putida UW4 and P.putida W619. Fatty acid biosynthesis (fab), fatty acid degradation (fad) and PHA synthesis genes were highly conserved among biocontrol and bioremediation P.putida strains. Six genes in pha operon of P. putida LS46 showed >98% homology at gene and proteins level. It appears that polyhydroxyalkanoate (PHA) synthesis is an intrinsic property of P. putida and was not affected by its geographic origin. However, all strains, including P. putida LS46, were different from one another on the basis of house keeping genes, and presence of plasmid, prophages, insertion sequence elements and genomic islands. While P. putida LS46 was not selected for plant growth promotion or bioremediation capacity, its genome also encoded genes for root colonization, pyoverdine synthesis, oxidative stress (present in other soil isolates), degradation of aromatic compounds, heavy metal resistance and nicotinic acid degradation, manganese (Mn II) oxidation. Genes for toluene or naphthalene degradation found in the genomes of P. putida F1, DOT-T1E, and ND6 were absent in the P. putida LS46 genome. Heavy metal resistant genes encoded by the P. putida W619 genome were also not present in the P. putida LS46 genome. Despite the overall similarity among genome of P.putida strains isolated for different applications and from different geographical location a number of differences were observed in genome arrangement, occurrence of transposon, genomic islands and prophage. It appears that P.putida strains had a common ancestor and by acquiring some specific genes by horizontal gene transfer it differed from other related strains.}, }
@article {pmid25400622, year = {2014}, author = {Davidson, SK and Dulla, GF and Go, RA and Stahl, DA and Pinel, N}, title = {Earthworm symbiont Verminephrobacter eiseniae mediates natural transformation within host egg capsules using type IV pili.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {546}, pmid = {25400622}, issn = {1664-302X}, abstract = {The dense microbial communities commonly associated with plants and animals should offer many opportunities for horizontal gene transfer through described mechanisms of DNA exchange including natural transformation (NT). However, studies of the significance of NT have focused primarily on pathogens. The study presented here demonstrates highly efficient DNA exchange by NT in a common symbiont of earthworms. The obligate bacterial symbiont Verminephrobacter eiseniae is a member of a microbial consortium of the earthworm Eisenia fetida that is transmitted into the egg capsules to colonize the embryonic worms. In the study presented here, by testing for transformants under different conditions in culture, we demonstrate that V. eiseniae can incorporate free DNA from the environment, that competency is regulated by environmental factors, and that it is sequence specific. Mutations in the type IV pili of V. eiseniae resulted in loss of DNA uptake, implicating the type IV pilus (TFP) apparatus in DNA uptake. Furthermore, injection of DNA carrying antibiotic-resistance genes into egg capsules resulted in transformants within the capsule, demonstrating the relevance of DNA uptake within the earthworm system. The ability to take up species-specific DNA from the environment may explain the maintenance of the relatively large, intact genome of this long-associated obligate symbiont, and provides a mechanism for acquisition of foreign genes within the earthworm system.}, }
@article {pmid25398856, year = {2015}, author = {Bertin, C and Pau-Roblot, C and Courtois, J and Manso-Silván, L and Tardy, F and Poumarat, F and Citti, C and Sirand-Pugnet, P and Gaurivaud, P and Thiaucourt, F}, title = {Highly dynamic genomic loci drive the synthesis of two types of capsular or secreted polysaccharides within the Mycoplasma mycoides cluster.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {2}, pages = {676-687}, pmid = {25398856}, issn = {1098-5336}, mesh = {Animals ; Cattle ; Cluster Analysis ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genetic Loci ; Genome, Bacterial ; Magnetic Resonance Spectroscopy ; Mycoplasma mycoides/*genetics/isolation &amp; purification/*metabolism ; Phylogeny ; Polysaccharides, Bacterial/*biosynthesis/chemistry/isolation &amp; purification ; Sequence Homology ; }, abstract = {Mycoplasmas of the Mycoplasma mycoides cluster are all ruminant pathogens. Mycoplasma mycoides subsp. mycoides is responsible for contagious bovine pleuropneumonia and is known to produce capsular polysaccharide (CPS) and exopolysaccharide (EPS). Previous studies have strongly suggested a role for Mycoplasma mycoides subsp. mycoides polysaccharides in pathogenicity. Mycoplasma mycoides subsp. mycoides-secreted EPS was recently characterized as a β(1→6)-galactofuranose homopolymer (galactan) identical to the capsular product. Here, we extended the characterization of secreted polysaccharides to all other members of the M. mycoides cluster: M. capricolum subsp. capripneumoniae, M. capricolum subsp. capricolum, M. leachii, and M. mycoides subsp. capri (including the LC and Capri serovars). Extracted EPS was characterized by nuclear magnetic resonance, resulting in the identification of a homopolymer of β(1→2)-glucopyranose (glucan) in M. capricolum subsp. capripneumoniae and M. leachii. Monoclonal antibodies specific for this glucan and for the Mycoplasma mycoides subsp. mycoides-secreted galactan were used to detect the two polysaccharides. While M. mycoides subsp. capri strains of serovar LC produced only capsular galactan, no polysaccharide could be detected in strains of serovar Capri. All strains of M. capricolum subsp. capripneumoniae and M. leachii produced glucan CPS and EPS, whereas glucan production and localization varied among M. capricolum subsp. capricolum strains. Genes associated with polysaccharide synthesis and forming a biosynthetic pathway were predicted in all cluster members. These genes were organized in clusters within two loci representing genetic variability hot spots. Phylogenetic analysis showed that some of these genes, notably galE and glf, were acquired via horizontal gene transfer. These findings call for a reassessment of the specificity of the serological tests based on mycoplasma polysaccharides.}, }
@article {pmid25393412, year = {2014}, author = {Becker, EA and Seitzer, PM and Tritt, A and Larsen, D and Krusor, M and Yao, AI and Wu, D and Madern, D and Eisen, JA and Darling, AE and Facciotti, MT}, title = {Phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response.}, journal = {PLoS genetics}, volume = {10}, number = {11}, pages = {e1004784}, pmid = {25393412}, issn = {1553-7404}, mesh = {Adaptation, Physiological/*genetics ; Archaea/*genetics ; Base Sequence ; Evolution, Molecular ; Genome, Archaeal ; Humans ; *Metagenomics ; Molecular Sequence Annotation ; Osmolar Concentration ; Phylogeny ; Salinity ; TATA-Box Binding Protein/*genetics ; }, abstract = {Organisms across the tree of life use a variety of mechanisms to respond to stress-inducing fluctuations in osmotic conditions. Cellular response mechanisms and phenotypes associated with osmoadaptation also play important roles in bacterial virulence, human health, agricultural production and many other biological systems. To improve understanding of osmoadaptive strategies, we have generated 59 high-quality draft genomes for the haloarchaea (a euryarchaeal clade whose members thrive in hypersaline environments and routinely experience drastic changes in environmental salinity) and analyzed these new genomes in combination with those from 21 previously sequenced haloarchaeal isolates. We propose a generalized model for haloarchaeal management of cytoplasmic osmolarity in response to osmotic shifts, where potassium accumulation and sodium expulsion during osmotic upshock are accomplished via secondary transport using the proton gradient as an energy source, and potassium loss during downshock is via a combination of secondary transport and non-specific ion loss through mechanosensitive channels. We also propose new mechanisms for magnesium and chloride accumulation. We describe the expansion and differentiation of haloarchaeal general transcription factor families, including two novel expansions of the TATA-binding protein family, and discuss their potential for enabling rapid adaptation to environmental fluxes. We challenge a recent high-profile proposal regarding the evolutionary origins of the haloarchaea by showing that inclusion of additional genomes significantly reduces support for a proposed large-scale horizontal gene transfer into the ancestral haloarchaeon from the bacterial domain. The combination of broad (17 genera) and deep (≥5 species in four genera) sampling of a phenotypically unified clade has enabled us to uncover both highly conserved and specialized features of osmoadaptation. Finally, we demonstrate the broad utility of such datasets, for metagenomics, improvements to automated gene annotation and investigations of evolutionary processes.}, }
@article {pmid25385643, year = {2014}, author = {Midonet, C and Das, B and Paly, E and Barre, FX}, title = {XerD-mediated FtsK-independent integration of TLCϕ into the Vibrio cholerae genome.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {47}, pages = {16848-16853}, pmid = {25385643}, issn = {1091-6490}, mesh = {Bacterial Proteins/*physiology ; Bacteriophages/*physiology ; Biocatalysis ; Electrophoretic Mobility Shift Assay ; *Genome, Bacterial ; Vibrio cholerae/*genetics/virology ; *Virus Integration ; }, abstract = {As in most bacteria, topological problems arising from the circularity of the two Vibrio cholerae chromosomes, chrI and chrII, are resolved by the addition of a crossover at a specific site of each chromosome, dif, by two tyrosine recombinases, XerC and XerD. The reaction is under the control of a cell division protein, FtsK, which activates the formation of a Holliday Junction (HJ) intermediate by XerD catalysis that is resolved into product by XerC catalysis. Many plasmids and phages exploit Xer recombination for dimer resolution and for integration, respectively. In all cases so far described, they rely on an alternative recombination pathway in which XerC catalyzes the formation of a HJ independently of FtsK. This is notably the case for CTXϕ, the cholera toxin phage. Here, we show that in contrast, integration of TLCϕ, a toxin-linked cryptic satellite phage that is almost always found integrated at the chrI dif site before CTXϕ, depends on the formation of a HJ by XerD catalysis, which is then resolved by XerC catalysis. The reaction nevertheless escapes the normal cellular control exerted by FtsK on XerD. In addition, we show that the same reaction promotes the excision of TLCϕ, along with any CTXϕ copy present between dif and its left attachment site, providing a plausible mechanism for how chrI CTXϕ copies can be eliminated, as occurred in the second wave of the current cholera pandemic.}, }
@article {pmid25382584, year = {2015}, author = {Lin, W and Pan, Y}, title = {A putative greigite-type magnetosome gene cluster from the candidate phylum Latescibacteria.}, journal = {Environmental microbiology reports}, volume = {7}, number = {2}, pages = {237-242}, doi = {10.1111/1758-2229.12234}, pmid = {25382584}, issn = {1758-2229}, mesh = {Bacteria/*genetics/metabolism ; Computational Biology ; Conserved Sequence ; Gene Order ; Gene Transfer, Horizontal ; Iron/metabolism ; Magnetosomes/*genetics ; *Multigene Family ; Sequence Homology ; Sulfides/metabolism ; }, abstract = {The intracellular biomineralization of magnetite and/or greigite magnetosomes in magnetotactic bacteria (MTB) is strictly controlled by a group of conserved genes, termed magnetosome genes, which are organized as clusters (or islands) in MTB genomes. So far, all reported MTB are affiliated within the Proteobacteria phylum, the Nitrospirae phylum and the candidate division OP3. Here, we report the discovery of a putative magnetosome gene cluster structure from the draft genome of an uncultivated bacterium belonging to the candidate phylum Latescibacteria (formerly candidate division WS3) recently recovered by Rinke and colleagues, which contains 10 genes with homology to magnetosome mam genes of magnetotactic Proteobacteria and Nitrospirae. Moreover, these genes are phylogenetically closely related to greigite-type magnetosome genes that were only found from the Deltaproteobacteria MTB before, suggesting that the greigite genes may originate earlier than previously imagined. These findings indicate that some members of Latescibacteria may be capable of forming greigite magnetosomes, and thus may play previously unrecognized roles in environmental iron and sulfur cycles. The conserved genomic structure of magnetosome gene cluster in Latescibacteria phylum supports the hypothesis of horizontal transfer of these genes among distantly related bacterial groups in nature.}, }
@article {pmid25375929, year = {2014}, author = {Staudová, B and Strouhal, M and Zobaníková, M and Cejková, D and Fulton, LL and Chen, L and Giacani, L and Centurion-Lara, A and Bruisten, SM and Sodergren, E and Weinstock, GM and Smajs, D}, title = {Whole genome sequence of the Treponema pallidum subsp. endemicum strain Bosnia A: the genome is related to yaws treponemes but contains few loci similar to syphilis treponemes.}, journal = {PLoS neglected tropical diseases}, volume = {8}, number = {11}, pages = {e3261}, pmid = {25375929}, issn = {1935-2735}, mesh = {Base Sequence ; Bosnia and Herzegovina ; Cluster Analysis ; Gene Transfer, Horizontal ; Genome, Bacterial/*genetics ; Humans ; Molecular Sequence Data ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; Synteny ; Syphilis/*microbiology ; Treponema pallidum/classification/*genetics ; Yaws/*microbiology ; }, abstract = {BACKGROUND: T. pallidum subsp. endemicum (TEN) is the causative agent of bejel (also known as endemic syphilis). Clinical symptoms of syphilis and bejel are overlapping and the epidemiological context is important for correct diagnosis of both diseases. In contrast to syphilis, caused by T. pallidum subsp. pallidum (TPA), TEN infections are usually spread by direct contact or contaminated utensils rather than by sexual contact. Bejel is most often seen in western Africa and in the Middle East. The strain Bosnia A was isolated in 1950 in Bosnia, southern Europe.<br><br>The complete genome of the Bosnia A strain was amplified and sequenced using the pooled segment genome sequencing (PSGS) method and a combination of three next-generation sequencing techniques (SOLiD, Roche 454, and Illumina). Using this approach, a total combined average genome coverage of 513&#xd7; was achieved. The size of the Bosnia A genome was found to be 1,137,653 bp, i.e. 1.6-2.8 kbp shorter than any previously published genomes of uncultivable pathogenic treponemes. Conserved gene synteny was found in the Bosnia A genome compared to other sequenced syphilis and yaws treponemes. The TEN Bosnia A genome was distinct but very similar to the genome of yaws-causing T. pallidum subsp. pertenue (TPE) strains. Interestingly, the TEN Bosnia A genome was found to contain several sequences, which so far, have been uniquely identified only in syphilis treponemes.<br><br>CONCLUSIONS/SIGNIFICANCE: The genome of TEN Bosnia A contains several sequences thought to be unique to TPA strains; these sequences very likely represent remnants of recombination events during the evolution of TEN treponemes. This finding emphasizes a possible role of repeated horizontal gene transfer between treponemal subspecies in shaping the Bosnia A genome.}, }
@article {pmid25374789, year = {2014}, author = {Huang, X}, title = {Horizontal transfer generates genetic variation in an asexual pathogen.}, journal = {PeerJ}, volume = {2}, number = {}, pages = {e650}, pmid = {25374789}, issn = {2167-8359}, abstract = {There are major gaps in the understanding of how genetic variation is generated in the asexual pathogen Verticillium dahliae. On the one hand, V. dahliae is a haploid organism that reproduces clonally. On the other hand, single-nucleotide polymorphisms and chromosomal rearrangements were found between V. dahliae strains. Lineage-specific (LS) regions comprising about 5% of the genome are highly variable between V. dahliae strains. Nonetheless, it is unknown whether horizontal gene transfer plays a major role in generating genetic variation in V. dahliae. Here, we analyzed a previously sequenced V. dahliae population of nine strains from various geographical locations and hosts. We found highly homologous elements in LS regions of each strain; LS regions of V. dahliae strain JR2 are much richer in highly homologous elements than the core genome. In addition, we discovered, in LS regions of JR2, several structural forms of nonhomologous recombination, and two or three homologous sequence types of each form, with almost each sequence type present in an LS region of another strain. A large section of one of the forms is known to be horizontally transferred between V. dahliae strains. We unexpectedly found that 350 kilobases of dynamic LS regions were much more conserved than the core genome between V. dahliae and a closely related species (V. albo-atrum), suggesting that these LS regions were horizontally transferred recently. Our results support the view that genetic variation in LS regions is generated by horizontal transfer between strains, and by chromosomal reshuffling reported previously.}, }
@article {pmid25374564, year = {2014}, author = {Liu, H and Yang, CL and Ge, MY and Ibrahim, M and Li, B and Zhao, WJ and Chen, GY and Zhu, B and Xie, GL}, title = {Regulatory role of tetR gene in a novel gene cluster of Acidovorax avenae subsp. avenae RS-1 under oxidative stress.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {547}, pmid = {25374564}, issn = {1664-302X}, abstract = {Acidovorax avenae subsp. avenae is the causal agent of bacterial brown stripe disease in rice. In this study, we characterized a novel horizontal transfer of a gene cluster, including tetR, on the chromosome of A. avenae subsp. avenae RS-1 by genome-wide analysis. TetR acted as a repressor in this gene cluster and the oxidative stress resistance was enhanced in tetR-deletion mutant strain. Electrophoretic mobility shift assay demonstrated that TetR regulator bound directly to the promoter of this gene cluster. Consistently, the results of quantitative real-time PCR also showed alterations in expression of associated genes. Moreover, the proteins affected by TetR under oxidative stress were revealed by comparing proteomic profiles of wild-type and mutant strains via 1D SDS-PAGE and LC-MS/MS analyses. Taken together, our results demonstrated that tetR gene in this novel gene cluster contributed to cell survival under oxidative stress, and TetR protein played an important regulatory role in growth kinetics, biofilm-forming capability, superoxide dismutase and catalase activity, and oxide detoxicating ability.}, }
@article {pmid25371435, year = {2015}, author = {Groussin, M and Hobbs, JK and Szöllősi, GJ and Gribaldo, S and Arcus, VL and Gouy, M}, title = {Toward more accurate ancestral protein genotype-phenotype reconstructions with the use of species tree-aware gene trees.}, journal = {Molecular biology and evolution}, volume = {32}, number = {1}, pages = {13-22}, pmid = {25371435}, issn = {1537-1719}, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics ; Computational Biology/*methods ; Computer Simulation ; Evolution, Molecular ; Genotype ; Gram-Positive Bacteria/enzymology/genetics ; Phenotype ; Phylogeny ; Proteins/*genetics ; }, abstract = {The resurrection of ancestral proteins provides direct insight into how natural selection has shaped proteins found in nature. By tracing substitutions along a gene phylogeny, ancestral proteins can be reconstructed in silico and subsequently synthesized in vitro. This elegant strategy reveals the complex mechanisms responsible for the evolution of protein functions and structures. However, to date, all protein resurrection studies have used simplistic approaches for ancestral sequence reconstruction (ASR), including the assumption that a single sequence alignment alone is sufficient to accurately reconstruct the history of the gene family. The impact of such shortcuts on conclusions about ancestral functions has not been investigated. Here, we show with simulations that utilizing information on species history using a model that accounts for the duplication, horizontal transfer, and loss (DTL) of genes statistically increases ASR accuracy. This underscores the importance of the tree topology in the inference of putative ancestors. We validate our in silico predictions using in vitro resurrection of the LeuB enzyme for the ancestor of the Firmicutes, a major and ancient bacterial phylum. With this particular protein, our experimental results demonstrate that information on the species phylogeny results in a biochemically more realistic and kinetically more stable ancestral protein. Additional resurrection experiments with different proteins are necessary to statistically quantify the impact of using species tree-aware gene trees on ancestral protein phenotypes. Nonetheless, our results suggest the need for incorporating both sequence and DTL information in future studies of protein resurrections to accurately define the genotype-phenotype space in which proteins diversify.}, }
@article {pmid25370747, year = {2014}, author = {McAdam, PR and Vander Broek, CW and Lindsay, DS and Ward, MJ and Hanson, MF and Gillies, M and Watson, M and Stevens, JM and Edwards, GF and Fitzgerald, JR}, title = {Gene flow in environmental Legionella pneumophila leads to genetic and pathogenic heterogeneity within a Legionnaires' disease outbreak.}, journal = {Genome biology}, volume = {15}, number = {11}, pages = {504}, pmid = {25370747}, issn = {1474-760X}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; //Medical Research Council/United Kingdom ; }, mesh = {Disease Outbreaks ; *Gene Flow ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Host-Pathogen Interactions/genetics/immunology ; Humans ; Legionella pneumophila/*genetics/immunology/pathogenicity ; Legionnaires' Disease/*genetics/immunology/microbiology ; Phylogeny ; }, abstract = {BACKGROUND: Legionnaires' disease is a severe form of pneumonia caused by the environmental bacterium Legionella pneumophila. Outbreaks commonly affect people with known risk factors, but the genetic and pathogenic complexity of L. pneumophila within an outbreak is not well understood. Here, we investigate the etiology of the major Legionnaires' disease outbreak that occurred in Edinburgh, UK, in 2012, by examining the evolutionary history, genome content, and virulence of L. pneumophila clinical isolates.<br><br>RESULTS: Our high resolution genomic approach reveals that the outbreak was caused by multiple genetic subtypes of L. pneumophila, the majority of which had diversified from a single progenitor through mutation, recombination, and horizontal gene transfer within an environmental reservoir prior to release. In addition, we discover that some patients were infected with multiple L. pneumophila subtypes, a finding which can affect the certainty of source attribution. Importantly, variation in the complement of type IV secretion systems encoded by different genetic subtypes correlates with virulence in a Galleria mellonella model of infection, revealing variation in pathogenic potential among the outbreak source population of L. pneumophila.<br><br>CONCLUSIONS: Taken together, our study indicates previously cryptic levels of pathogen heterogeneity within a Legionnaires' disease outbreak, a discovery that impacts on source attribution for future outbreak investigations. Furthermore, our data suggest that in addition to host immune status, pathogen diversity may be an important influence on the clinical outcome of individual outbreak infections.}, }
@article {pmid25370375, year = {2014}, author = {Jheeta, S and Joshi, PC}, title = {Prebiotic RNA synthesis by montmorillonite catalysis.}, journal = {Life (Basel, Switzerland)}, volume = {4}, number = {3}, pages = {318-330}, pmid = {25370375}, issn = {2075-1729}, abstract = {This review summarizes our recent findings on the role of mineral salts in prebiotic RNA synthesis, which is catalyzed by montmorillonite clay minerals. The clay minerals not only catalyze the synthesis of RNA but also facilitate homochiral selection. Preliminary data of these findings have been presented at the "Horizontal Gene Transfer and the Last Universal Common Ancestor (LUCA)" conference at the Open University, Milton Keynes, UK, 5-6 September 2013. The objective of this meeting was to recognize the significance of RNA in LUCA. We believe that the prebiotic RNA synthesis from its monomers must have been a simple process. As a first step, it may have required activation of the 5'-end of the mononucleotide with a leaving group, e.g., imidazole in our model reaction (Figure 1). Wide ranges of activating groups are produced from HCN under plausible prebiotic Earth conditions. The final step is clay mineral catalysis in the presence of mineral salts to facilitate selective production of functional RNA. Both the clay minerals and mineral salts would have been abundant on early Earth. We have demonstrated that while montmorillonite (pH 7) produced only dimers from its monomers in water, addition of sodium chloride (1 M) enhanced the chain length multifold, as detected by HPLC. The effect of monovalent cations on RNA synthesis was of the following order: Li+ > Na+ > K+. A similar effect was observed with the anions, enhancing catalysis in the following order: Cl- > Br- > I-. The montmorillonite-catalyzed RNA synthesis was not affected by hydrophobic or hydrophilic interactions. We thus show that prebiotic synthesis of RNA from its monomers was a simple process requiring only clay minerals and a small amount of salt.}, }
@article {pmid25370194, year = {2014}, author = {Arber, W}, title = {Horizontal Gene Transfer among Bacteria and Its Role in Biological Evolution.}, journal = {Life (Basel, Switzerland)}, volume = {4}, number = {2}, pages = {217-224}, pmid = {25370194}, issn = {2075-1729}, abstract = {This is a contribution to the history of scientific advance in the past 70 years concerning the identification of genetic information, its molecular structure, the identification of its functions and the molecular mechanisms of its evolution. Particular attention is thereby given to horizontal gene transfer among microorganisms, as well as to biosafety considerations with regard to beneficial applications of acquired scientific knowledge.}, }
@article {pmid25368607, year = {2014}, author = {Santoro, F and Vianna, ME and Roberts, AP}, title = {Variation on a theme; an overview of the Tn916/Tn1545 family of mobile genetic elements in the oral and nasopharyngeal streptococci.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {535}, pmid = {25368607}, issn = {1664-302X}, abstract = {The oral and nasopharyngeal streptococci are a major part of the normal microbiota in humans. Most human associated streptococci are considered commensals, however, a small number of them are pathogenic, causing a wide range of diseases including oral infections such as dental caries and periodontitis and diseases at other body sites including sinusitis and endocarditis, and in the case of Streptococcus pneumoniae, meningitis. Both phenotypic and sequence based studies have shown that the human associated streptococci from the mouth and nasopharynx harbor a large number of antibiotic resistance genes and these are often located on mobile genetic elements (MGEs) known as conjugative transposons or integrative and conjugative elements of the Tn916/Tn1545 family. These MGEs are responsible for the spread of the resistance genes between streptococci and also between streptococci and other bacteria. In this review we describe the resistances conferred by, and the genetic variations between the many different Tn916-like elements found in recent studies of oral and nasopharyngeal streptococci and show that Tn916-like elements are important mediators of antibiotic resistance genes within this genus. We will also discuss the role of the oral environment and how this is conducive to the transfer of these elements and discuss the contribution of both transformation and conjugation on the transfer and evolution of these elements in different streptococci.}, }
@article {pmid25368161, year = {2014}, author = {Hu, X and Xiao, G and Zheng, P and Shang, Y and Su, Y and Zhang, X and Liu, X and Zhan, S and St Leger, RJ and Wang, C}, title = {Trajectory and genomic determinants of fungal-pathogen speciation and host adaptation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {47}, pages = {16796-16801}, pmid = {25368161}, issn = {1091-6490}, mesh = {*Adaptation, Physiological ; DNA Transposable Elements ; *Genomics ; *Host-Pathogen Interactions ; Metarhizium/*classification/genetics ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Much remains unknown regarding speciation. Host-pathogen interactions are a major driving force for diversification, but the genomic basis for speciation and host shifting remains unclear. The fungal genus Metarhizium contains species ranging from specialists with very narrow host ranges to generalists that attack a wide range of insects. By genomic analyses of seven species, we demonstrated that generalists evolved from specialists via transitional species with intermediate host ranges and that this shift paralleled insect evolution. We found that specialization was associated with retention of sexuality and rapid evolution of existing protein sequences whereas generalization was associated with protein-family expansion, loss of genome-defense mechanisms, genome restructuring, horizontal gene transfer, and positive selection that accelerated after reinforcement of reproductive isolation. These results advance understanding of speciation and genomic signatures that underlie pathogen adaptation to hosts.}, }
@article {pmid25367272, year = {2014}, author = {Watve, SS and Bernardy, EE and Hammer, BK}, title = {Vibrio cholerae: Measuring Natural Transformation Frequency.}, journal = {Current protocols in microbiology}, volume = {35}, number = {}, pages = {6A.4.1-12}, doi = {10.1002/9780471729259.mc06a04s35}, pmid = {25367272}, issn = {1934-8533}, mesh = {Biological Transport/genetics ; Chitin ; DNA Transformation Competence/*genetics ; DNA, Bacterial/*genetics ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal/genetics ; Transformation, Genetic/*physiology ; Vibrio cholerae/*genetics ; }, abstract = {Many bacteria can become naturally competent to take up extracellular DNA across their outer and inner membranes by a dedicated competence apparatus. Whereas some studies show that the DNA delivered to the cytoplasm may be used for genome repair or for nutrition, it can also be recombined onto the chromosome by homologous recombination: a process called natural transformation. Along with conjugation and transduction, natural transformation represents a mechanism for horizontal transfer of genetic material, e.g., antibiotic resistance genes, which can confer new beneficial characteristics onto the recipient bacteria. Described here are protocols for quantifying the frequency of transformation for the human pathogen Vibrio cholerae, one of several Vibrio species recently shown to be capable of natural transformation.}, }
@article {pmid25367149, year = {2014}, author = {Struchtemeyer, CG and Ranganathan, A and Couger, MB and Liggenstoffer, AS and Youssef, NH and Elshahed, MS}, title = {Survival of the anaerobic fungus Orpinomyces sp. strain C1A after prolonged air exposure.}, journal = {Scientific reports}, volume = {4}, number = {}, pages = {6892}, pmid = {25367149}, issn = {2045-2322}, mesh = {Air ; Anaerobiosis ; Cellobiose/metabolism ; Culture Media ; Fungal Proteins/biosynthesis/genetics ; Gene Expression ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Fungal ; Genes, Fungal ; Microbial Viability ; Neocallimastigales/*physiology ; Oxygen/physiology ; Phylogeny ; Stress, Physiological ; Superoxide Dismutase/biosynthesis/genetics ; }, abstract = {Anaerobic fungi are efficient plant biomass degraders and represent promising agents for a variety of biotechnological applications. We evaluated the tolerance of an anaerobic fungal isolate, Orpinomyces sp. strain C1A, to air exposure in liquid media using soluble (cellobiose) and insoluble (dried switchgrass) substrates. Strain C1A grown on cellobiose survived for 11, and 13.5 hours following air exposure when grown under planktonic, and immobilized conditions, respectively. When grown on switchgrass media, strain C1A exhibited significantly enhanced air tolerance and survived for 168 hours. The genome of strain C1A lacked a catalase gene, but contained superoxide dismutase and glutathione peroxidase genes. Real time PCR analysis indicated that superoxide dismutase, but not glutathione peroxidase, exhibits a transient increase in expression level post aeration. Interestingly, the C1A superoxide dismutase gene of strain C1A appears to be most closely related to bacterial SODs, which implies its acquisition from a bacterial donor via cross kingdom horizontal gene transfer during Neocallimastigomycota evolution. We conclude that strain C1A utilizes multiple mechanisms to minimize the deleterious effects of air exposure such as physical protection and the production of oxidative stress enzymes.}, }
@article {pmid25365877, year = {2014}, author = {Voeĭkova, TA and Tiaglov, BV and Novikova, LM and Krest'ianova, IN and Emel'ianova, LK and Korshunov, DV and Morozova, IuA and Il'in, VK}, title = {[Bion-M1. Biological activities of microorganisms under the conditions of a 30-day space flight].}, journal = {Aviakosmicheskaia i ekologicheskaia meditsina = Aerospace and environmental medicine}, volume = {48}, number = {4}, pages = {46-52}, pmid = {25365877}, issn = {0233-528X}, mesh = {Anthraquinones/metabolism ; Bacteriophages/*physiology ; Crosses, Genetic ; Gene Transfer, Horizontal ; Genetic Markers ; Lysogeny ; Oxidation-Reduction ; Recombination, Genetic ; Shewanella/*genetics/metabolism ; *Space Flight ; Streptomyces coelicolor/*genetics/metabolism/virology ; Streptomyces lividans/*genetics/metabolism/virology ; Tylosin/biosynthesis ; Virus Activation ; Weightlessness ; }, abstract = {It was stated that spaceflight factors (SFF) affect the chromosomal DNA interchange during Streptomyces crossing. Cross polarity and primary input of a parent chromosome fragment in recombinant generation imply a more lasting cells contact in microgravity and a broader horizontal transport of genetic material. SFF had no effect on recombination frequency and mutation in a model of parental auxotrophic markers reversion to prototrophism. It was demonstrated that SFF boosted the fC31 phage exit from S. lividans 66 (fC31) and did not influence phage induction in S. coelicolor A3(2) (fC31). SFF inhibited synthesis of antiobiotic actinorhodin in lisogenic S. coelicolor A3(2), and tylosin and desmicosin in S. fradiae. Survivability of electrogenic bacteria Shewanella oneidensis MR-1 in space flight was higher compared with the synchronous control experiment. The reduction activity of S. oneidensis MR-1 as an indicator of electron generation effectiveness was identical in flight and laboratory samples.}, }
@article {pmid25351426, year = {2014}, author = {Turner, PE and Williams, ES and Okeke, C and Cooper, VS and Duffy, S and Wertz, JE}, title = {Antibiotic resistance correlates with transmission in plasmid evolution.}, journal = {Evolution; international journal of organic evolution}, volume = {68}, number = {12}, pages = {3368-3380}, doi = {10.1111/evo.12537}, pmid = {25351426}, issn = {1558-5646}, mesh = {Anti-Bacterial Agents/pharmacology ; *Conjugation, Genetic ; DNA Transposable Elements ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/drug effects/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Plasmids/*genetics ; Tetracycline/pharmacology ; Virulence/genetics ; }, abstract = {Conjugative (horizontally transmissible) plasmids are autonomous replicators, whose "self-interests" do not necessarily overlap with those of their hosts. This situation causes plasmids and bacteria to sometimes experience differing selection pressures. Escherichia coli plasmid pB15 contains genes for resistance to several antibiotics, including tetracycline. When plasmid-bearing cells were experimentally evolved in the laboratory, changes in resistance level in the unselected tetracycline marker coincided with changes in plasmid rates of vertical versus horizontal transmission. Here, we used minimum inhibitory assays that measure resistance levels as quantitative traits to determine phenotypic correlations among plasmid characters and to estimate divergence among plasmid lineages. Results suggested that plasmid-level evolution led to formation of two phenotypically dissimilar groups: virulent (highly infectious) and avirulent (weakly infectious) plasmids. In contrast, measures of carbon-source utilization, and fitness assays relative to a common competitor revealed that bacterial hosts generally converged in phenotypic performance, despite divergence among their associated plasmids. Preliminary sequence analyses suggested that divergence in plasmid conjugation was due to altered configurations of a shufflon region (a site-specific recombination system), where genetic rearrangements affect conjugative ability. Furthermore, we proposed that correlated resistance and transmission in pB15 derivatives were caused by a tetracycline-resistance transposon inserted into a transfer operon, allowing transcription from its promoter to simultaneously affect both plasmid resistance and transmission.}, }
@article {pmid25350501, year = {2014}, author = {Toby, IT and Widmer, J and Dyer, DW}, title = {Divergence of protein-coding capacity and regulation in the Bacillus cereus sensu lato group.}, journal = {BMC bioinformatics}, volume = {15 Suppl 11}, number = {Suppl 11}, pages = {S8}, pmid = {25350501}, issn = {1471-2105}, support = {P20RR016478/RR/NCRR NIH HHS/United States ; }, mesh = {Bacillus cereus/classification/*genetics/metabolism ; Bacterial Proteins/*genetics ; Cluster Analysis ; Evolution, Molecular ; Genome, Bacterial ; Phenotype ; Phylogeny ; Regulon ; }, abstract = {BACKGROUND: The Bacillus cereus sensu lato group contains ubiquitous facultative anaerobic soil-borne Gram-positive spore-forming bacilli. Molecular phylogeny and comparative genome sequencing have suggested that these organisms should be classified as a single species. While clonal in nature, there do not appear to be species-specific clonal lineages, excepting B. anthracis, in spite of the wide array of phenotypes displayed by these organisms.<br><br>RESULTS: We compared the protein-coding content of 201 B. cereus sensu lato genomes to characterize differences and understand the consequences of these differences on biological function. From this larger group we selected a subset consisting of 25 whole genomes for deeper analysis. Cluster analysis of orthologous proteins grouped these genomes into five distinct clades. Each clade could be characterized by unique genes shared among the group, with consequences for the phenotype of each clade. Surprisingly, this population structure recapitulates our recent observations on the divergence of the generalized stress response (SigB) regulons in these organisms. Divergence of the SigB regulon among these organisms is primarily due to the placement of SigB-dependent promoters that bring genes from a common gene pool into/out of the SigB regulon.<br><br>CONCLUSIONS: Collectively, our observations suggest the hypothesis that the evolution of these closely related bacteria is a consequence of two distinct processes. Horizontal gene transfer, gene duplication/divergence and deletion dictate the underlying coding capacity in these genomes. Regulatory divergence overlays this protein coding reservoir and shapes the expression of both the unique and shared coding capacity of these organisms, resulting in phenotypic divergence. Data from other organisms suggests that this is likely a common pattern in prokaryotic evolution.}, }
@article {pmid25348042, year = {2014}, author = {Will, WR and Bale, DH and Reid, PJ and Libby, SJ and Fang, FC}, title = {Evolutionary expansion of a regulatory network by counter-silencing.}, journal = {Nature communications}, volume = {5}, number = {}, pages = {5270}, pmid = {25348042}, issn = {2041-1723}, support = {R21 AI048622/AI/NIAID NIH HHS/United States ; R01 AI048622/AI/NIAID NIH HHS/United States ; AI101084/AI/NIAID NIH HHS/United States ; AI48622/AI/NIAID NIH HHS/United States ; R01 AI101084/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/metabolism ; *Biological Evolution ; DNA-Binding Proteins/metabolism ; Deoxyribonuclease I/metabolism ; Gene Expression Regulation, Bacterial ; *Gene Regulatory Networks ; *Gene Silencing ; Promoter Regions, Genetic ; Regulon/genetics ; Salmonella typhimurium/*genetics ; Ultraviolet Rays ; }, abstract = {Horizontal gene transfer plays a major role in bacterial evolution. Successful acquisition of new genes requires their incorporation into existing regulatory networks. This study compares the regulation of conserved genes in the PhoPQ regulon of Salmonella enterica serovar Typhimurium with that of PhoPQ-regulated horizontally acquired genes, which are silenced by the histone-like protein H-NS. We demonstrate that PhoP upregulates conserved and horizontally acquired genes by distinct mechanisms. Conserved genes are regulated by classical PhoP-mediated activation and are invariant in promoter architecture, whereas horizontally acquired genes exhibit variable promoter architecture and are regulated by PhoP-mediated counter-silencing. Biochemical analyses show that a horizontally acquired promoter adopts different structures in the silenced and counter-silenced states, implicating the remodelling of the H-NS nucleoprotein filament and the subsequent restoration of open-complex formation as the central mechanism of counter-silencing. Our results indicate that counter-silencing is favoured in the regulatory integration of newly acquired genes because it is able to accommodate multiple promoter architectures.}, }
@article {pmid25340397, year = {2014}, author = {Pachulec, E and Siewering, K and Bender, T and Heller, EM and Salgado-Pabon, W and Schmoller, SK and Woodhams, KL and Dillard, JP and van der Does, C}, title = {Functional analysis of the Gonococcal Genetic Island of Neisseria gonorrhoeae.}, journal = {PloS one}, volume = {9}, number = {10}, pages = {e109613}, pmid = {25340397}, issn = {1932-6203}, support = {R01 AI047958/AI/NIAID NIH HHS/United States ; T32 AI055397/AI/NIAID NIH HHS/United States ; AI047958/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Secretion Systems/genetics ; Chromosome Mapping ; CpG Islands/*genetics ; DNA Mutational Analysis ; DNA, Bacterial/genetics ; Gammaproteobacteria/genetics ; Genes, Bacterial ; Humans ; Neisseria gonorrhoeae/*genetics ; Operon/genetics ; Plasmids/metabolism ; Transcription, Genetic ; }, abstract = {Neisseria gonorrhoeae is an obligate human pathogen that is responsible for the sexually-transmitted disease gonorrhea. N. gonorrhoeae encodes a T4SS within the Gonococcal Genetic Island (GGI), which secretes ssDNA directly into the external milieu. Type IV secretion systems (T4SSs) play a role in horizontal gene transfer and delivery of effector molecules into target cells. We demonstrate that GGI-like T4SSs are present in other β-proteobacteria, as well as in α- and γ-proteobacteria. Sequence comparison of GGI-like T4SSs reveals that the GGI-like T4SSs form a highly conserved unit that can be found located both on chromosomes and on plasmids. To better understand the mechanism of DNA secretion by N. gonorrhoeae, we performed mutagenesis of all genes encoded within the GGI, and studied the effects of these mutations on DNA secretion. We show that genes required for DNA secretion are encoded within the yaa-atlA and parA-parB regions, while genes encoded in the yfeB-exp1 region could be deleted without any effect on DNA secretion. Genes essential for DNA secretion are encoded within at least four different operons.}, }
@article {pmid25338275, year = {2014}, author = {He, LY and Liu, YS and Su, HC and Zhao, JL and Liu, SS and Chen, J and Liu, WR and Ying, GG}, title = {Dissemination of antibiotic resistance genes in representative broiler feedlots environments: identification of indicator ARGs and correlations with environmental variables.}, journal = {Environmental science &amp; technology}, volume = {48}, number = {22}, pages = {13120-13129}, doi = {10.1021/es5041267}, pmid = {25338275}, issn = {1520-5851}, mesh = {*Animal Feed ; Animals ; Anti-Bacterial Agents/analysis/pharmacology ; Chickens/*genetics ; Drug Resistance, Microbial/drug effects/*genetics ; *Environment ; Genes, Bacterial/drug effects ; Manure/analysis ; Soil/chemistry ; Solid Waste/analysis ; }, abstract = {Livestock operations are known to harbor elevated levels of antibiotic resistance genes (ARGs) that may pose a threat to public health. Broiler feedlots may represent an important source of ARGs in the environment. However, the prevalence and dissemination mechanisms of various types of ARGs in the environment of broiler feedlots have not previously been identified. We examined the occurrence, abundance and variation of ARGs conferring resistance to chloramphenicols, sulfonamides and tetracyclines in the environments of two representative types of broiler feedlots (free range and indoor) by quantitative PCR, and assessed their dissemination mechanisms. The results showed the prevalence of various types of ARGs in the environmental samples of the broiler feedlots including manure/litter, soil, sediment, and water samples, with the first report of five chloramphenicol resistance genes (cmlA, floR, fexA, cfr, and fexB) in broiler feedlots. Overall, chloramphenicol resistance genes and sulfonamides sul genes were more abundant than tetracyclines tet genes. The ARG abundances in the samples from indoor boiler feedlots were generally different to the free range feedlots, suggesting the importance of feeding operations in ARG dissemination. Pearson correlation analysis showed significant correlations between ARGs and mobile genetic element genes (int1 and int2), and between the different classes of ARGs themselves, revealing the roles of horizontal gene transfer and coselection for ARG dissemination in the environment. Further regression analysis revealed that fexA, sul1 and tetW could be reliable indicator genes to surrogate anthropogenic sources of ARGs in boiler feedlots (correlations of fexA, sul1 and tetW to all ARGs: R = 0.95, 0.96 and 0.86, p < 0.01). Meanwhile, significant correlations were also identified between indicator ARGs and their corresponding antibiotics. In addition, some ARGs were significantly correlated with typical metals (e.g., Cu, Zn, and As with fexA, fexB, cfr, sul1, tetW, tetO, tetS: R = 0.52-0.71) and some environmental parameters (e.g., TOC, TN, TP, NH3-N with fexA, fexB, cfr, sul1, tetW, tetO, tetQ, tetS: R = 0.53-0.87) (p < 0.01). Further redundancy analysis demonstrated that the distribution and transportation of ARGs from the boiler feedlots to the receiving environments were correlated with environmental variables. The findings highlight the contribution of some chemicals such as antibiotics and metals to the development of ARGs in broiler feedlots environments; and the observed ARG dissemination mechanism in the broiler feedlots facilitates the development of effective mitigation measures.}, }
@article {pmid25336458, year = {2014}, author = {Lamelas, A and Harris, SR and Röltgen, K and Dangy, JP and Hauser, J and Kingsley, RA and Connor, TR and Sie, A and Hodgson, A and Dougan, G and Parkhill, J and Bentley, SD and Pluschke, G}, title = {Emergence of a new epidemic Neisseria meningitidis serogroup A Clone in the African meningitis belt: high-resolution picture of genomic changes that mediate immune evasion.}, journal = {mBio}, volume = {5}, number = {5}, pages = {e01974-14}, pmid = {25336458}, issn = {2150-7511}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Africa/epidemiology ; Antigens, Bacterial/genetics ; *Disease Outbreaks ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genotype ; Homologous Recombination ; Humans ; *Immune Evasion ; Meningitis, Meningococcal/*epidemiology ; Neisseria meningitidis, Serogroup A/*classification/*genetics/immunology/isolation &amp; purification ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {In the African "meningitis belt," outbreaks of meningococcal meningitis occur in cycles, representing a model for the role of host-pathogen interactions in epidemic processes. The periodicity of the epidemics is not well understood, nor is it currently possible to predict them. In our longitudinal colonization and disease surveys, we have observed waves of clonal replacement with the same serogroup, suggesting that immunity to noncapsular antigens plays a significant role in natural herd immunity. Here, through comparative genomic analysis of 100 meningococcal isolates, we provide a high-resolution view of the evolutionary changes that occurred during clonal replacement of a hypervirulent meningococcal clone (ST-7) by a descendant clone (ST-2859). We show that the majority of genetic changes are due to homologous recombination of laterally acquired DNA, with more than 20% of these events involving acquisition of DNA from other species. Signals of adaptation to evade herd immunity were indicated by genomic hot spots of recombination. Most striking is the high frequency of changes involving the pgl locus, which determines the glycosylation patterns of major protein antigens. High-frequency changes were also observed for genes involved in the regulation of pilus expression and the synthesis of Maf3 adhesins, highlighting the importance of these surface features in host-pathogen interaction and immune evasion. Importance: While established meningococcal capsule polysaccharide vaccines are protective through the induction of anticapsular antibodies, findings of our longitudinal studies in the African meningitis belt have indicated that immunity to noncapsular antigens plays a significant role in natural herd immunity. Our results show that meningococci evade herd immunity through the rapid homologous replacement of just a few key genomic loci that affect noncapsular cell surface components. Identification of recombination hot spots thus represents an eminent approach to gain insight into targets of protective natural immune responses. Moreover, our results highlight the role of the dynamics of the protein glycosylation repertoire in immune evasion by Neisseria meningitidis. These results have major implications for the design of next-generation protein-based subunit vaccines.}, }
@article {pmid25336457, year = {2014}, author = {Yoon, EJ and Goussard, S and Touchon, M and Krizova, L and Cerqueira, G and Murphy, C and Lambert, T and Grillot-Courvalin, C and Nemec, A and Courvalin, P}, title = {Origin in Acinetobacter guillouiae and dissemination of the aminoglycoside-modifying enzyme Aph(3')-VI.}, journal = {mBio}, volume = {5}, number = {5}, pages = {e01972-14}, pmid = {25336457}, issn = {2150-7511}, support = {281605/ERC_/European Research Council/International ; HHSN272200900018C/AI/NIAID NIH HHS/United States ; }, mesh = {Acinetobacter/drug effects/*enzymology/*genetics/isolation &amp; purification ; Amino Acid Sequence ; Aminoglycosides/pharmacology ; Anti-Bacterial Agents/pharmacology ; Base Sequence ; Cluster Analysis ; Conjugation, Genetic ; Drug Resistance, Bacterial ; Environmental Microbiology ; Escherichia coli/enzymology/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Interspersed Repetitive Sequences ; Kanamycin Kinase/*genetics ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Phylogeny ; Promoter Regions, Genetic ; Sequence Homology ; }, abstract = {The amikacin resistance gene aphA6 was first detected in the nosocomial pathogen Acinetobacter baumannii and subsequently in other genera. Analysis of 133 whole-genome sequences covering the taxonomic diversity of Acinetobacter spp. detected aphA6 in the chromosome of 2 isolates of A. guillouiae, which is an environmental species, 1 of 8 A. parvus isolates, and 5 of 34 A. baumannii isolates. The gene was also present in 29 out of 36 A. guillouiae isolates screened by PCR, indicating that it is ancestral to this species. The Pnative promoter for aphA6 in A. guillouiae and A. parvus was replaced in A. baumannii by PaphA6, which was generated by use of the insertion sequence ISAba125, which brought a -35 sequence. Study of promoter strength in Escherichia coli and A. baumannii indicated that PaphA6 was four times more potent than Pnative. There was a good correlation between aminoglycoside MICs and aphA6 transcription in A. guillouiae isolates that remained susceptible to amikacin. The marked topology differences of the phylogenetic trees of aphA6 and of the hosts strongly support its recent direct transfer within Acinetobacter spp. and also to evolutionarily remote bacterial genera. Concomitant expression of aphA6 must have occurred because, contrary to the donors, it can confer resistance to the new hosts. Mobilization and expression of aphA6 via composite transposons and the upstream IS-generating hybrid PaphA6, followed by conjugation, seems the most plausible mechanism. This is in agreement with the observation that, in the recipients, aphA6 is carried by conjugative plasmids and flanked by IS that are common in Acinetobacter spp. Our data indicate that resistance genes can also be found in susceptible environmental bacteria. Importance: We speculated that the aphA6 gene for an enzyme that confers resistance to amikacin, the most active aminoglycoside for the treatment of nosocomial infections due to Acinetobacter spp., originated in this genus before disseminating to phylogenetically distant genera pathogenic for humans. Using a combination of whole-genome sequencing of a collection of Acinetobacter spp. covering the breadth of the known taxonomic diversity of the genus, gene cloning, detailed promoter analysis, study of heterologous gene expression, and comparative analysis of the phylogenetic trees of aphA6 and of the bacterial hosts, we found that aphA6 originated in Acinetobacter guillouiae, an amikacin-susceptible environmental species. The gene conferred, upon mobilization, high-level resistance to the new hosts. This work stresses that nonpathogenic bacteria can act as reservoirs of resistance determinants, and it provides an example of the use of a genomic library to study the origin and dissemination of an antibiotic resistance gene to human pathogens.}, }
@article {pmid25336138, year = {2014}, author = {Metzler, S and Kalinina, OV}, title = {Detection of atypical genes in virus families using a one-class SVM.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {913}, pmid = {25336138}, issn = {1471-2164}, mesh = {Gene Transfer, Horizontal ; *Genes, Viral ; Genome Size ; Models, Genetic ; Models, Statistical ; *Support Vector Machine ; Viruses/classification/*genetics ; }, abstract = {BACKGROUND: The diversity of viruses, the absence of universally common genes in them, and their ability to act as carriers of genetic material make assessment of evolutionary paths of viral genes very difficult. One important factor contributing to this complexity is horizontal gene transfer.<br><br>RESULTS: We explore the possibility for the systematic identification of atypical genes within virus families, including viruses whose genome is not encoded by a double-stranded DNA. Our method is based on gene statistical features that differ in genes that were subject of recent horizontal gene transfer from those of the genome in which they are observed. We employ a one-class SVM approach to detect atypical genes within a virus family basing of their statistical signatures and without explicit knowledge of the source species. The simplicity of the statistical features used makes the method applicable to various viruses irrespective of their genome size or type.<br><br>CONCLUSIONS: On simulated data, the method can robustly identify alien genes irrespective of the coding nucleic acid found in a virus. It also compares well to results obtained in related studies for double-stranded DNA viruses. Its value in practice is confirmed by the identification of isolated examples of horizontal gene transfer events that have already been described in the literature. A Python package implementing the method and the results for the analyzed virus families are available at http://svm-agp.bioinf.mpi-inf.mpg.de.}, }
@article {pmid25333987, year = {2014}, author = {Sieber, CM and Lee, W and Wong, P and Münsterkötter, M and Mewes, HW and Schmeitzl, C and Varga, E and Berthiller, F and Adam, G and Güldener, U}, title = {The Fusarium graminearum genome reveals more secondary metabolite gene clusters and hints of horizontal gene transfer.}, journal = {PloS one}, volume = {9}, number = {10}, pages = {e110311}, pmid = {25333987}, issn = {1932-6203}, mesh = {Cluster Analysis ; Evolution, Molecular ; Fusarium/*genetics ; Gene Expression Profiling ; Gene Expression Regulation, Fungal ; *Gene Transfer, Horizontal ; *Genes, Fungal ; *Genome, Fungal ; *Multigene Family ; Nucleotide Motifs ; Promoter Regions, Genetic ; Secondary Metabolism/*genetics ; }, abstract = {Fungal secondary metabolite biosynthesis genes are of major interest due to the pharmacological properties of their products (like mycotoxins and antibiotics). The genome of the plant pathogenic fungus Fusarium graminearum codes for a large number of candidate enzymes involved in secondary metabolite biosynthesis. However, the chemical nature of most enzymatic products of proteins encoded by putative secondary metabolism biosynthetic genes is largely unknown. Based on our analysis we present 67 gene clusters with significant enrichment of predicted secondary metabolism related enzymatic functions. 20 gene clusters with unknown metabolites exhibit strong gene expression correlation in planta and presumably play a role in virulence. Furthermore, the identification of conserved and over-represented putative transcription factor binding sites serves as additional evidence for cluster co-regulation. Orthologous cluster search provided insight into the evolution of secondary metabolism clusters. Some clusters are characteristic for the Fusarium phylum while others show evidence of horizontal gene transfer as orthologs can be found in representatives of the Botrytis or Cochliobolus lineage. The presented candidate clusters provide valuable targets for experimental examination.}, }
@article {pmid25333461, year = {2015}, author = {Klümper, U and Riber, L and Dechesne, A and Sannazzarro, A and Hansen, LH and Sørensen, SJ and Smets, BF}, title = {Broad host range plasmids can invade an unexpectedly diverse fraction of a soil bacterial community.}, journal = {The ISME journal}, volume = {9}, number = {4}, pages = {934-945}, pmid = {25333461}, issn = {1751-7370}, mesh = {Actinobacteria/genetics ; Bacteria/classification/*genetics ; Conjugation, Genetic ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Host Specificity ; Plasmids/*genetics ; Proteobacteria/genetics ; *Soil Microbiology ; }, abstract = {Conjugal plasmids can provide microbes with full complements of new genes and constitute potent vehicles for horizontal gene transfer. Conjugal plasmid transfer is deemed responsible for the rapid spread of antibiotic resistance among microbes. While broad host range plasmids are known to transfer to diverse hosts in pure culture, the extent of their ability to transfer in the complex bacterial communities present in most habitats has not been comprehensively studied. Here, we isolated and characterized transconjugants with a degree of sensitivity not previously realized to investigate the transfer range of IncP- and IncPromA-type broad host range plasmids from three proteobacterial donors to a soil bacterial community. We identified transfer to many different recipients belonging to 11 different bacterial phyla. The prevalence of transconjugants belonging to diverse Gram-positive Firmicutes and Actinobacteria suggests that inter-Gram plasmid transfer of IncP-1 and IncPromA-type plasmids is a frequent phenomenon. While the plasmid receiving fractions of the community were both plasmid- and donor- dependent, we identified a core super-permissive fraction that could take up different plasmids from diverse donor strains. This fraction, comprising 80% of the identified transconjugants, thus has the potential to dominate IncP- and IncPromA-type plasmid transfer in soil. Our results demonstrate that these broad host range plasmids have a hitherto unrecognized potential to transfer readily to very diverse bacteria and can, therefore, directly connect large proportions of the soil bacterial gene pool. This finding reinforces the evolutionary and medical significances of these plasmids.}, }
@article {pmid25331432, year = {2015}, author = {Blesa, A and César, CE and Averhoff, B and Berenguer, J}, title = {Noncanonical cell-to-cell DNA transfer in Thermus spp. is insensitive to argonaute-mediated interference.}, journal = {Journal of bacteriology}, volume = {197}, number = {1}, pages = {138-146}, pmid = {25331432}, issn = {1098-5530}, mesh = {Argonaute Proteins/genetics/*metabolism ; Bacterial Proteins/genetics/*metabolism ; DNA, Bacterial/*physiology ; Gene Expression Regulation, Bacterial/physiology ; Gene Transfer, Horizontal/*physiology ; Plasmids ; Thermus thermophilus/cytology/genetics/*metabolism ; }, abstract = {Horizontal gene transfer drives the rapid evolution of bacterial populations. Classical processes that promote the lateral flow of genetic information are conserved throughout the prokaryotic world. However, some species have nonconserved transfer mechanisms that are not well known. This is the case for the ancient extreme thermophile Thermus thermophilus. In this work, we show that T. thermophilus strains are capable of exchanging large DNA fragments by a novel mechanism that requires cell-to-cell contacts and employs components of the natural transformation machinery. This process facilitates the bidirectional transfer of virtually any DNA locus but favors by 10-fold loci found in the megaplasmid over those in the chromosome. In contrast to naked DNA acquisition by transformation, the system does not activate the recently described DNA-DNA interference mechanism mediated by the prokaryotic Argonaute protein, thus allowing the organism to distinguish between DNA transferred from a mate and exogenous DNA acquired from unknown hosts. This Argonaute-mediated discrimination may be tentatively viewed as a strategy for safe sharing of potentially "useful" traits by the components of a given population of Thermus spp. without increasing the genome sizes of its individuals.}, }
@article {pmid25317564, year = {2015}, author = {Nelson-Sathi, S and Sousa, FL and Roettger, M and Lozada-Chávez, N and Thiergart, T and Janssen, A and Bryant, D and Landan, G and Schönheit, P and Siebers, B and McInerney, JO and Martin, WF}, title = {Origins of major archaeal clades correspond to gene acquisitions from bacteria.}, journal = {Nature}, volume = {517}, number = {7532}, pages = {77-80}, pmid = {25317564}, issn = {1476-4687}, support = {232975/ERC_/European Research Council/International ; 281357/ERC_/European Research Council/International ; }, mesh = {Archaea/*classification/*genetics/metabolism ; Archaeal Proteins/genetics ; Bacteria/*genetics/metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genes, Archaeal/*genetics ; Genes, Bacterial/*genetics ; Genome, Archaeal/genetics ; Phylogeny ; }, abstract = {The mechanisms that underlie the origin of major prokaryotic groups are poorly understood. In principle, the origin of both species and higher taxa among prokaryotes should entail similar mechanisms--ecological interactions with the environment paired with natural genetic variation involving lineage-specific gene innovations and lineage-specific gene acquisitions. To investigate the origin of higher taxa in archaea, we have determined gene distributions and gene phylogenies for the 267,568 protein-coding genes of 134 sequenced archaeal genomes in the context of their homologues from 1,847 reference bacterial genomes. Archaeal-specific gene families define 13 traditionally recognized archaeal higher taxa in our sample. Here we report that the origins of these 13 groups unexpectedly correspond to 2,264 group-specific gene acquisitions from bacteria. Interdomain gene transfer is highly asymmetric, transfers from bacteria to archaea are more than fivefold more frequent than vice versa. Gene transfers identified at major evolutionary transitions among prokaryotes specifically implicate gene acquisitions for metabolic functions from bacteria as key innovations in the origin of higher archaeal taxa.}, }
@article {pmid25314321, year = {2015}, author = {Chen, J and Carpena, N and Quiles-Puchalt, N and Ram, G and Novick, RP and Penadés, JR}, title = {Intra- and inter-generic transfer of pathogenicity island-encoded virulence genes by cos phages.}, journal = {The ISME journal}, volume = {9}, number = {5}, pages = {1260-1263}, pmid = {25314321}, issn = {1751-7370}, support = {R01 AI022159/AI/NIAID NIH HHS/United States ; R01AI022159/AI/NIAID NIH HHS/United States ; }, mesh = {Gene Transfer Techniques ; *Genomic Islands ; Integrases/metabolism ; Mitomycin/chemistry ; Open Reading Frames ; Staphylococcus Phages/*genetics ; Staphylococcus aureus/*genetics/virology ; Virulence/*genetics ; Virulence Factors/genetics ; }, abstract = {Bacteriophage-mediated horizontal gene transfer is one of the primary driving forces of bacterial evolution. The pac-type phages are generally thought to facilitate most of the phage-mediated gene transfer between closely related bacteria, including that of mobile genetic elements-encoded virulence genes. In this study, we report that staphylococcal cos-type phages transferred the Staphylococcus aureus pathogenicity island SaPIbov5 to non-aureus staphylococcal species and also to different genera. Our results describe the first intra- and intergeneric transfer of a pathogenicity island by a cos phage, and highlight a gene transfer mechanism that may have important implications for pathogen evolution.}, }
@article {pmid25314320, year = {2015}, author = {Caro-Quintero, A and Konstantinidis, KT}, title = {Inter-phylum HGT has shaped the metabolism of many mesophilic and anaerobic bacteria.}, journal = {The ISME journal}, volume = {9}, number = {4}, pages = {958-967}, pmid = {25314320}, issn = {1751-7370}, mesh = {Bacteria/classification/*genetics/metabolism ; Bacteria, Anaerobic/*genetics/metabolism ; Computational Biology ; Ecological and Environmental Phenomena ; *Gene Transfer, Horizontal ; Genetic Variation ; Genome, Bacterial ; }, abstract = {Genome sequencing has revealed that horizontal gene transfer (HGT) is a major evolutionary process in bacteria. Although it is generally assumed that closely related organisms engage in genetic exchange more frequently than distantly related ones, the frequency of HGT among distantly related organisms and the effect of ecological relatedness on the frequency has not been rigorously assessed. Here, we devised a novel bioinformatic pipeline, which minimized the effect of over-representation of specific taxa in the available databases and other limitations of homology-based approaches by analyzing genomes in standardized triplets, to quantify gene exchange between bacterial genomes representing different phyla. Our analysis revealed the existence of networks of genetic exchange between organisms with overlapping ecological niches, with mesophilic anaerobic organisms showing the highest frequency of exchange and engaging in HGT twice as frequently as their aerobic counterparts. Examination of individual cases suggested that inter-phylum HGT is more pronounced than previously thought, affecting up to ∼ 16% of the total genes and ∼ 35% of the metabolic genes in some genomes (conservative estimation). In contrast, ribosomal and other universal protein-coding genes were subjected to HGT at least 150 times less frequently than genes encoding the most promiscuous metabolic functions (for example, various dehydrogenases and ABC transport systems), suggesting that the species tree based on the former genes may be reliable. These results indicated that the metabolic diversity of microbial communities within most habitats has been largely assembled from preexisting genetic diversity through HGT and that HGT accounts for the functional redundancy among phyla.}, }
@article {pmid25313075, year = {2014}, author = {Sakowski, EG and Munsell, EV and Hyatt, M and Kress, W and Williamson, SJ and Nasko, DJ and Polson, SW and Wommack, KE}, title = {Ribonucleotide reductases reveal novel viral diversity and predict biological and ecological features of unknown marine viruses.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {44}, pages = {15786-15791}, pmid = {25313075}, issn = {1091-6490}, support = {P20 GM103446/GM/NIGMS NIH HHS/United States ; T32 GM008550/GM/NIGMS NIH HHS/United States ; }, mesh = {Aquatic Organisms/*genetics ; Base Sequence ; Biodiversity ; DNA Viruses/*genetics ; DNA, Single-Stranded/genetics ; DNA, Viral/genetics ; *Genome, Viral ; *Metagenome ; Molecular Sequence Data ; Ribonucleotide Reductases/*genetics ; Viral Proteins/*genetics ; }, abstract = {Virioplankton play a crucial role in aquatic ecosystems as top-down regulators of bacterial populations and agents of horizontal gene transfer and nutrient cycling. However, the biology and ecology of virioplankton populations in the environment remain poorly understood. Ribonucleotide reductases (RNRs) are ancient enzymes that reduce ribonucleotides to deoxyribonucleotides and thus prime DNA synthesis. Composed of three classes according to O2 reactivity, RNRs can be predictive of the physiological conditions surrounding DNA synthesis. RNRs are universal among cellular life, common within viral genomes and virioplankton shotgun metagenomes (viromes), and estimated to occur within >90% of the dsDNA virioplankton sampled in this study. RNRs occur across diverse viral groups, including all three morphological families of tailed phages, making these genes attractive for studies of viral diversity. Differing patterns in virioplankton diversity were clear from RNRs sampled across a broad oceanic transect. The most abundant RNRs belonged to novel lineages of podoviruses infecting α-proteobacteria, a bacterial class critical to oceanic carbon cycling. RNR class was predictive of phage morphology among cyanophages and RNR distribution frequencies among cyanophages were largely consistent with the predictions of the "kill the winner-cost of resistance" model. RNRs were also identified for the first time to our knowledge within ssDNA viromes. These data indicate that RNR polymorphism provides a means of connecting the biological and ecological features of virioplankton populations.}, }
@article {pmid25311532, year = {2015}, author = {Delorme, C and Abraham, AL and Renault, P and Guédon, E}, title = {Genomics of Streptococcus salivarius, a major human commensal.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {33}, number = {}, pages = {381-392}, doi = {10.1016/j.meegid.2014.10.001}, pmid = {25311532}, issn = {1567-7257}, mesh = {Cluster Analysis ; Gene Order ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genes, Essential ; *Genome, Bacterial ; *Genomics/methods ; Humans ; Metabolomics ; Multilocus Sequence Typing ; Phylogeny ; Streptococcal Infections/*microbiology ; Streptococcus/*classification/*genetics/metabolism ; }, abstract = {The salivarius group of streptococci is of particular importance for humans. This group consists of three genetically similar species, Streptococcus salivarius, Streptococcus vestibularis and Streptococcus thermophilus. S. salivarius and S. vestibularis are commensal organisms that may occasionally cause opportunistic infections in humans, whereas S. thermophilus is a food bacterium widely used in dairy production. We developed Multilocus sequence typing (MLST) and comparative genomic analysis to confirm the clear separation of these three species. These analyses also identified a subgroup of four strains, with a core genome diverging by about 10%, in terms of its nucleotide sequence, from that of S. salivarius sensu stricto. S. thermophilus species displays a low level of nucleotide variability, due to its recent emergence with the development of agriculture. By contrast, nucleotide variability is high in the other two species of the salivarius group, reflecting their long-standing association with humans. The species of the salivarius group have genome sizes ranging from the smallest (∼ 1.7 Mb for S. thermophilus) to the largest (∼ 2.3 Mb for S. salivarius) among streptococci, reflecting genome reduction linked to a narrow, nutritionally rich environment for S. thermophilus, and natural, more competitive niches for the other two species. Analyses of genomic content have indicated that the core genes of S. salivarius account for about two thirds of the genome, indicating considerable variability of gene content and differences in potential adaptive features. Furthermore, we showed that the genome of this species is exceptionally rich in genes encoding surface factors, glycosyltransferases and response regulators. Evidence of widespread genetic exchanges was obtained, probably involving a natural competence system and the presence of diverse mobile elements. However, although the S. salivarius strains studied were isolated from several human body-related sites (all levels of the digestive tract, skin, breast milk, and body fluids) and included clinical strains, no genetic or genomic niche-specific features could be identified to discriminate specific group.}, }
@article {pmid25307893, year = {2014}, author = {Dutta, S and Bhawsinghka, N and Das Gupta, SK}, title = {Gp66, a calcineurin family phosphatase encoded by mycobacteriophage D29, is a 2', 3' cyclic nucleotide phosphodiesterase that negatively regulates phage growth.}, journal = {FEMS microbiology letters}, volume = {361}, number = {1}, pages = {84-93}, doi = {10.1111/1574-6968.12625}, pmid = {25307893}, issn = {1574-6968}, mesh = {Amino Acid Sequence ; Calcineurin/genetics/*metabolism ; Mutation ; Mycobacteriophages/*enzymology/genetics/growth &amp; development ; Mycobacterium smegmatis/metabolism/*virology ; Phosphoric Diester Hydrolases/genetics/*metabolism ; Phosphoric Monoester Hydrolases/genetics/*metabolism ; Phylogeny ; Recombinant Proteins ; Sequence Alignment ; Viral Proteins/genetics/metabolism ; }, abstract = {Mycobacteriophage D29 encodes a protein Gp66 which has been predicted to be a calcineurin family phosphoesterase. Phylogenetically Gp66 and related proteins mostly derived from mycobacteriophages form a distinct clade within this family. Interestingly, the presence of gene 66 orthologs can be traced to bacteria of diverse phylogenetic lineages such as Aquifex aeolicus, a deep branching eubacteria and Methanococcus jannaschii, an archaebacteria. The promiscuous nature of gene 66 suggests that it may have been transferred across genus barriers by horizontal gene transfer mechanisms. The biological function of members of this novel clade comprising mostly the mycobacteriophage phosphoesterases have not been elucidated so far. In this investigation, it has been demonstrated for the first time that Gp66, a member of this novel family, is a 2', 3' cyclic phosphodiesterase. The gene is expressed during phage infection and the net result is negative regulation of bacteriophage as well as bacterial growth.}, }
@article {pmid25304505, year = {2014}, author = {Merod, RT and Wuertz, S}, title = {Extracellular polymeric substance architecture influences natural genetic transformation of Acinetobacter baylyi in biofilms.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {24}, pages = {7752-7757}, pmid = {25304505}, issn = {1098-5336}, mesh = {Acinetobacter/*genetics/physiology ; *Biofilms ; Plasmids/genetics ; Polymers/*chemistry ; *Transformation, Bacterial ; }, abstract = {Genetic exchange by natural transformation is an important mechanism of horizontal gene transfer in biofilms. Thirty-two biofilm metrics were quantified in a heavily encapsulated Acinetobacter baylyi strain and a miniencapsulated mutant strain, accounting for cellular architecture, extracellular polymeric substances (EPS) architecture, and their combined biofilm architecture. In general, transformation location, abundance, and frequency were more closely correlated to EPS architecture than to cellular or combined architecture. Transformation frequency and transformant location had the greatest correlation with the EPS metric surface area-to-biovolume ratio. Transformation frequency peaked when EPS surface area-to-biovolume ratio was greater than 3 μm(2)/μm(3) and less than 5 μm(2)/μm(3). Transformant location shifted toward the biofilm-bulk fluid interface as the EPS surface area-to-biovolume ratio increased. Transformant biovolume was most closely correlated with EPS biovolume and peaked when transformation occurred in close proximity to the substratum. This study demonstrates that biofilm architecture influences A. baylyi transformation frequency and transformant location and abundance. The major role of EPS may be to facilitate the binding and stabilization of plasmid DNA for cellular uptake.}, }
@article {pmid25302567, year = {2014}, author = {San Millan, A and Peña-Miller, R and Toll-Riera, M and Halbert, ZV and McLean, AR and Cooper, BS and MacLean, RC}, title = {Positive selection and compensatory adaptation interact to stabilize non-transmissible plasmids.}, journal = {Nature communications}, volume = {5}, number = {}, pages = {5208}, pmid = {25302567}, issn = {2041-1723}, support = {/WT_/Wellcome Trust/United Kingdom ; 281591/ERC_/European Research Council/International ; 089275/Z/09/Z/WT_/Wellcome Trust/United Kingdom ; MR/K006924/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adaptation, Physiological ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; Plasmids/*genetics/metabolism ; Pseudomonas aeruginosa/drug effects/*genetics/physiology ; }, abstract = {Plasmids are important drivers of bacterial evolution, but it is challenging to understand how plasmids persist over the long term because plasmid carriage is costly. Classical models predict that horizontal transfer is necessary for plasmid persistence, but recent work shows that almost half of plasmids are non-transmissible. Here we use a combination of mathematical modelling and experimental evolution to investigate how a costly, non-transmissible plasmid, pNUK73, can be maintained in populations of Pseudomonas aeruginosa. Compensatory adaptation increases plasmid stability by eliminating the cost of plasmid carriage. However, positive selection for plasmid-encoded antibiotic resistance is required to maintain the plasmid by offsetting reductions in plasmid frequency due to segregational loss. Crucially, we show that compensatory adaptation and positive selection reinforce each other's effects. Our study provides a new understanding of how plasmids persist in bacterial populations, and it helps to explain why resistance can be maintained after antibiotic use is stopped.}, }
@article {pmid25302406, year = {2014}, author = {Gibert, M and Juárez, A and Zechner, EL and Madrid, C and Balsalobre, C}, title = {TrhR, TrhY and HtdA, a novel regulatory circuit that modulates conjugation of the IncHI plasmids.}, journal = {Molecular microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mmi.12823}, pmid = {25302406}, issn = {1365-2958}, support = {P 24016/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Bacterial conjugation promotes horizontal gene transfer and, consequently, the acquisition of new capabilities such as resistance to antimicrobial compounds and virulence related traits. Conjugative plasmids belonging to the incompatibility group HI are associated with multidrug resistance in Gram-negative pathogens. IncHI plasmid conjugation is thermodependent and all transfer-related genes are encoded in six operons (tra operons). Using R27, the prototype of IncHI1 plasmids, we reported that the plasmid-encoded factor HtdA represses four of the six tra operons. Moreover, our results indicated that other R27 factors were required for appropriate expression of the tra genes. In this report, using R27 libraries and random mutagenesis assays, two genes - trhR and trhY - have been identified as essential for the transcriptional expression of four tra operons and, accordingly, for the R27 conjugation. TrhR and TrhY are required simultaneously and their stimulatory activity is counteracted by HtdA. Functional and physical interactions between TrhR, TrhY and HtdA suggest that they form a three-element regulatory circuit that controls conjugation of IncHI plasmids. Expression studies suggest that H-NS represses conjugation at high temperature by repressing trhR expression. Remarkably, we show that this regulatory circuit is highly conserved among the IncHI plasmids.}, }
@article {pmid25299187, year = {2014}, author = {Costa, J and Teixeira, PG and d'Avó, AF and Júnior, CS and Veríssimo, A}, title = {Intragenic recombination has a critical role on the evolution of Legionella pneumophila virulence-related effector sidJ.}, journal = {PloS one}, volume = {9}, number = {10}, pages = {e109840}, pmid = {25299187}, issn = {1932-6203}, mesh = {Bacterial Proteins/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Host-Pathogen Interactions/genetics ; Humans ; Legionella pneumophila/*genetics/pathogenicity ; Legionnaires' Disease/*genetics/microbiology ; Membrane Proteins ; Phylogeny ; Protein Transport/genetics ; *Recombination, Genetic ; Selection, Genetic ; Virulence Factors/*genetics ; }, abstract = {SidJ is a Dot/Icm effector involved in the trafficking or retention of ER-derived vesicles to Legionella pneumophila vacuoles whose mutation causes an observable growth defect, both in macrophage and amoeba hosts. Given the crucial role of this effector in L. pneumophila virulence we investigated the mechanisms shaping its molecular evolution. The alignment of SidJ sequences revealed several alleles with amino acid variations that may influence the protein properties. The identification of HGT events and the detection of balancing selection operating on sidJ evolution emerge as a clear result. Evidence suggests that intragenic recombination is an important strategy in the evolutionary adaptive process playing an active role on sidJ genetic plasticity. This pattern of evolution is in accordance with the life style of L. pneumophila as a broad host-range pathogen by preventing host-specialization and contributing to the resilience of the species.}, }
@article {pmid25297974, year = {2014}, author = {Bohlin, J and Brynildsrud, OB and Sekse, C and Snipen, L}, title = {An evolutionary analysis of genome expansion and pathogenicity in Escherichia coli.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {882}, pmid = {25297974}, issn = {1471-2164}, mesh = {Base Composition ; Cluster Analysis ; Entropy ; *Escherichia coli/classification/genetics/pathogenicity ; Escherichia coli Proteins/genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Phylogeny ; Pyrophosphatases/genetics ; Virulence Factors/*genetics ; }, abstract = {BACKGROUND: There are several studies describing loss of genes through reductive evolution in microbes, but how selective forces are associated with genome expansion due to horizontal gene transfer (HGT) has not received similar attention. The aim of this study was therefore to examine how selective pressures influence genome expansion in 53 fully sequenced and assembled Escherichia coli strains. We also explored potential connections between genome expansion and the attainment of virulence factors. This was performed using estimations of several genomic parameters such as AT content, genomic drift (measured using relative entropy), genome size and estimated HGT size, which were subsequently compared to analogous parameters computed from the core genome consisting of 1729 genes common to the 53 E. coli strains. Moreover, we analyzed how selective pressures (quantified using relative entropy and dN/dS), acting on the E. coli core genome, influenced lineage and phylogroup formation.<br><br>RESULTS: Hierarchical clustering of dS and dN estimations from the E. coli core genome resulted in phylogenetic trees with topologies in agreement with known E. coli taxonomy and phylogroups. High values of dS, compared to dN, indicate that the E. coli core genome has been subjected to substantial purifying selection over time; significantly more than the non-core part of the genome (p<0.001). This is further supported by a linear association between strain-wise dS and dN values (&#x3b2; = 26.94 &#xb1; 0.44, R2~0.98, p<0.001). The non-core part of the genome was also significantly more AT-rich (p<0.001) than the core genome and E. coli genome size correlated with estimated HGT size (p<0.001). In addition, genome size (p<0.001), AT content (p<0.001) as well as estimated HGT size (p<0.005) were all associated with the presence of virulence factors, suggesting that pathogenicity traits in E. coli are largely attained through HGT. No associations were found between selective pressures operating on the E. coli core genome, as estimated using relative entropy, and genome size (p~0.98).<br><br>CONCLUSIONS: On a larger time frame, genome expansion in E. coli, which is significantly associated with the acquisition of virulence factors, appears to be independent of selective forces operating on the core genome.}, }
@article {pmid25297844, year = {2015}, author = {Khayi, S and Raoul des Essarts, Y and Quêtu-Laurent, A and Moumni, M and Hélias, V and Faure, D}, title = {Genomic overview of the phytopathogen Pectobacterium wasabiae strain RNS 08.42.1A suggests horizontal acquisition of quorum-sensing genes.}, journal = {Genetica}, volume = {143}, number = {2}, pages = {241-252}, pmid = {25297844}, issn = {1573-6857}, mesh = {DNA, Bacterial/genetics ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Molecular Sequence Data ; Pectobacterium/*genetics/isolation &amp; purification/pathogenicity ; Phylogeny ; Plant Diseases/microbiology ; Quorum Sensing/*genetics ; Sequence Analysis, DNA ; Solanum tuberosum/microbiology ; Synteny ; Virulence/genetics ; }, abstract = {The blackleg and soft-rot diseases caused by pectinolytic enterobacteria such as Pectobacterium and Dickeya are major causes of losses affecting potato crop in the field and upon storage. In this work, we report the isolation, characterization and genome analysis of the Pectobacterium wasabiae (formerly identified as Pectobacterium carotovorum subsp. carotovorum) strain RNS 08.42.1A, that has been isolated from a Solanum tuberosum host plant in France. Comparative genomics with 3 other P. wasabiae strains isolated from potato plants in different areas in North America and Europe, highlighted both a strong similarity at the whole genome level (ANI > 99 %) and a conserved synteny of the virulence genes. In addition, our analyses evidenced a robust separation between these four P. wasabiae strains and the type strain P. wasabiae CFBP 3304(T), isolated from horseradish in Japan. In P. wasabiae RNS 08.42.1A, the expI and expR nucleotidic sequences are more related to those of some Pectobacterium atrosepticum and P. carotovorum strains (90 % of identity) than to those of the other potato P. wasabiae strains (70 to 74 % of identity). This could suggest a recruitment of these genes in the P. wasabiae strain RNS 08.42.1A by an horizontal transfer between pathogens infecting the same potato host plant.}, }
@article {pmid25296163, year = {2014}, author = {Schneider, SE and Thomas, JH}, title = {Accidental genetic engineers: horizontal sequence transfer from parasitoid wasps to their Lepidopteran hosts.}, journal = {PloS one}, volume = {9}, number = {10}, pages = {e109446}, pmid = {25296163}, issn = {1932-6203}, mesh = {Animals ; *Gene Transfer, Horizontal ; Genome, Insect/genetics ; Host-Parasite Interactions/*genetics ; Lepidoptera/*genetics/*parasitology ; Polydnaviridae/genetics/physiology ; Symbiosis/genetics ; Wasps/*genetics/*physiology/virology ; }, abstract = {We show here that 105 regions in two Lepidoptera genomes appear to derive from horizontally transferred wasp DNA. We experimentally verified the presence of two of these sequences in a diverse set of silkworm (Bombyx mori) genomes. We hypothesize that these horizontal transfers are made possible by the unusual strategy many parasitoid wasps employ of injecting hosts with endosymbiotic polydnaviruses to minimize the host's defense response. Because these virus-like particles deliver wasp DNA to the cells of the host, there has been much interest in whether genetic information can be permanently transferred from the wasp to the host. Two transferred sequences code for a BEN domain, known to be associated with polydnaviruses and transcriptional regulation. These findings represent the first documented cases of horizontal transfer of genes between two organisms by a polydnavirus. This presents an interesting evolutionary paradigm in which host species can acquire new sequences from parasitoid wasps that attack them. Hymenoptera and Lepidoptera diverged ∼300 MYA, making this type of event a source of novel sequences for recipient species. Unlike many other cases of horizontal transfer between two eukaryote species, these sequence transfers can be explained without the need to invoke the sequences 'hitchhiking' on a third organism (e.g. retrovirus) capable of independent reproduction. The cellular machinery necessary for the transfer is contained entirely in the wasp genome. The work presented here is the first such discovery of what is likely to be a broader phenomenon among species affected by these wasps.}, }
@article {pmid25286745, year = {2015}, author = {Nesme, J and Simonet, P}, title = {The soil resistome: a critical review on antibiotic resistance origins, ecology and dissemination potential in telluric bacteria.}, journal = {Environmental microbiology}, volume = {17}, number = {4}, pages = {913-930}, doi = {10.1111/1462-2920.12631}, pmid = {25286745}, issn = {1462-2920}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/*genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Ecology ; Fungi/metabolism ; Gene Transfer, Horizontal/*genetics ; Genetic Variation/genetics ; Humans ; Microbiota/drug effects/*genetics ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Soil is a large reservoir of microbial diversity and the majority of antimicrobial compounds used today in human and veterinary health care have been isolated from soil microorganisms. The Darwinian hypothesis of an 'arms-shields race' between antibiotic producers and resistant strains is often cited to explain antibiotic resistance gene determinants (ARGD) origins and diversity. ARGD abundance and antibiotic molecule exposure are, however, not systematically linked, and many other factors can contribute to resistance gene emergence, selection and dissemination in the environment. Soil is a heterogeneous habitat and represents a broad spectrum of different ecological niches. Soil harbours a large genetic diversity at small spatial scale, favouring exchange of genetic materials by means of horizontal gene transfer (HGT) that will contribute to ARGD dissemination between bacteria and eventually acquisition by pathogen genomes, therefore threatening antibiotic therapies. Our current knowledge on the extent of the soil resistome abundance and diversity has been greatly enhanced since the metagenomic revolution and help of high-throughput sequencing technologies. Different ecological hypotheses explaining their high prevalence in soil and questioning their transfer rate to pathogens, in respect to these recent experimental results, will be discussed in the present review.}, }
@article {pmid25283728, year = {2015}, author = {Freedman, JC and Theoret, JR and Wisniewski, JA and Uzal, FA and Rood, JI and McClane, BA}, title = {Clostridium perfringens type A-E toxin plasmids.}, journal = {Research in microbiology}, volume = {166}, number = {4}, pages = {264-279}, pmid = {25283728}, issn = {1769-7123}, support = {T32 AI060525/AI/NIAID NIH HHS/United States ; R01 AI056177/AI/NIAID NIH HHS/United States ; R37 AI019844/AI/NIAID NIH HHS/United States ; R01AI056177-09/AI/NIAID NIH HHS/United States ; R37AI19844-30/AI/NIAID NIH HHS/United States ; U54 AI057168/AI/NIAID NIH HHS/United States ; 2U54AI57168-09/AI/NIAID NIH HHS/United States ; }, mesh = {Adaptation, Biological ; Bacterial Toxins/*genetics ; Clostridium perfringens/*genetics ; Conjugation, Genetic ; DNA Transposable Elements ; Gene Transfer, Horizontal ; *Plasmids ; Virulence Factors/genetics ; }, abstract = {Clostridium perfringens relies upon plasmid-encoded toxin genes to cause intestinal infections. These toxin genes are associated with insertion sequences that may facilitate their mobilization and transfer, giving rise to new toxin plasmids with common backbones. Most toxin plasmids carry a transfer of clostridial plasmids locus mediating conjugation, which likely explains the presence of similar toxin plasmids in otherwise unrelated C. perfringens strains. The association of many toxin genes with insertion sequences and conjugative plasmids provides virulence flexibility when causing intestinal infections. However, incompatibility issues apparently limit the number of toxin plasmids maintained by a single cell.}, }
@article {pmid25283610, year = {2015}, author = {Kozlowska-Makulska, A and Hasiow-Jaroszewska, B and Szyndel, MS and Herrbach, E and Bouzoubaa, S and Lemaire, O and Beuve, M}, title = {Phylogenetic relationships and the occurrence of interspecific recombination between beet chlorosis virus (BChV) and Beet mild yellowing virus (BMYV).}, journal = {Archives of virology}, volume = {160}, number = {2}, pages = {429-433}, doi = {10.1007/s00705-014-2245-6}, pmid = {25283610}, issn = {1432-8798}, mesh = {Amino Acid Sequence ; Base Sequence ; Beta vulgaris/*virology ; Capsid Proteins/genetics ; France ; Gene Transfer, Horizontal/*genetics ; Genetic Variation ; Genome, Viral ; Luteoviridae/*genetics ; Molecular Sequence Data ; Phylogeny ; Plant Diseases/*virology ; Poland ; Recombination, Genetic/*genetics ; Sequence Analysis, RNA ; }, abstract = {Samples containing two viruses belonging to the genus Polerovirus, beet chlorosis virus (BChV) and beet mild yellowing virus (BMYV), were collected from French and Polish sugar beet fields. The molecular properties of 24 isolates of BChV and BMYV were investigated, and their genetic diversity was examined in the coat protein (CP)- and P0-encoding genes. For the first time, we have demonstrated that beet polerovirus populations include recombinants between BChV and BMYV containing breakpoints within the CP gene. Moreover, a partial correlation between geographic origin and phylogenetic clustering was observed for BMYV isolates.}, }
@article {pmid25283338, year = {2014}, author = {Dvořák, P and Casamatta, DA and Poulíčková, A and Hašler, P and Ondřej, V and Sanges, R}, title = {Synechococcus: 3 billion years of global dominance.}, journal = {Molecular ecology}, volume = {23}, number = {22}, pages = {5538-5551}, doi = {10.1111/mec.12948}, pmid = {25283338}, issn = {1365-294X}, mesh = {*Biological Evolution ; DNA, Bacterial/genetics ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Synechococcus/classification/*genetics ; }, abstract = {Cyanobacteria are among the most important primary producers on the Earth. However, the evolutionary forces driving cyanobacterial species diversity remain largely enigmatic due to both their distinction from macro-organisms and an undersampling of sequenced genomes. Thus, we present a new genome of a Synechococcus-like cyanobacterium from a novel evolutionary lineage. Further, we analyse all existing 16S rRNA sequences and genomes of Synechococcus-like cyanobacteria. Chronograms showed extremely polyphyletic relationships in Synechococcus, which has not been observed in any other cyanobacteria. Moreover, most Synechococcus lineages bifurcated after the Great Oxidation Event, including the most abundant marine picoplankton lineage. Quantification of horizontal gene transfer among 70 cyanobacterial genomes revealed significant differences among studied genomes. Horizontal gene transfer levels were not correlated with ecology, genome size or phenotype, but were correlated with the age of divergence. All findings were synthetized into a novel model of cyanobacterial evolution, characterized by serial convergence of the features, that is multicellularity and ecology.}, }
@article {pmid25281847, year = {2016}, author = {De Oliveira Martins, L and Mallo, D and Posada, D}, title = {A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction.}, journal = {Systematic biology}, volume = {65}, number = {3}, pages = {397-416}, pmid = {25281847}, issn = {1076-836X}, support = {203161/ERC_/European Research Council/International ; }, mesh = {Bayes Theorem ; Classification/*methods ; Computer Simulation ; Genome/genetics ; *Models, Genetic ; *Phylogeny ; Software ; }, abstract = {Current phylogenomic data sets highlight the need for species tree methods able to deal with several sources of gene tree/species tree incongruence. At the same time, we need to make most use of all available data. Most species tree methods deal with single processes of phylogenetic discordance, namely, gene duplication and loss, incomplete lineage sorting (ILS) or horizontal gene transfer. In this manuscript, we address the problem of species tree inference from multilocus, genome-wide data sets regardless of the presence of gene duplication and loss and ILS therefore without the need to identify orthologs or to use a single individual per species. We do this by extending the idea of Maximum Likelihood (ML) supertrees to a hierarchical Bayesian model where several sources of gene tree/species tree disagreement can be accounted for in a modular manner. We implemented this model in a computer program called guenomu whose inputs are posterior distributions of unrooted gene tree topologies for multiple gene families, and whose output is the posterior distribution of rooted species tree topologies. We conducted extensive simulations to evaluate the performance of our approach in comparison with other species tree approaches able to deal with more than one leaf from the same species. Our method ranked best under simulated data sets, in spite of ignoring branch lengths, and performed well on empirical data, as well as being fast enough to analyze relatively large data sets. Our Bayesian supertree method was also very successful in obtaining better estimates of gene trees, by reducing the uncertainty in their distributions. In addition, our results show that under complex simulation scenarios, gene tree parsimony is also a competitive approach once we consider its speed, in contrast to more sophisticated models.}, }
@article {pmid25280947, year = {2014}, author = {Ardisson-Araújo, DM and de Melo, FL and Andrade, Mde S and Sihler, W and Báo, SN and Ribeiro, BM and de Souza, ML}, title = {Genome sequence of Erinnyis ello granulovirus (ErelGV), a natural cassava hornworm pesticide and the first sequenced sphingid-infecting betabaculovirus.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {856}, pmid = {25280947}, issn = {1471-2164}, mesh = {Animals ; Databases, Genetic ; *Genome, Viral ; Granulovirus/classification/*genetics/isolation &amp; purification ; Larva/virology ; Lepidoptera/growth &amp; development/*virology ; Manihot/parasitology ; Open Reading Frames/genetics ; Phylogeny ; Pyrophosphatases/genetics ; Sequence Analysis, DNA ; Viral Proteins/classification/genetics ; }, abstract = {BACKGROUND: Cassava (Manihot esculenta) is the basic source for dietary energy of 500 million people in the world. In Brazil, Erinnyis ello ello (Lepidoptera: Sphingidae) is a major pest of cassava crops and a bottleneck for its production. In the 1980s, a naturally occurring baculovirus was isolated from E. ello larva and successfully applied as a bio-pesticide in the field. Here, we described the structure, the complete genome sequence, and the phylogenetic relationships of the first sphingid-infecting betabaculovirus.<br><br>RESULTS: The baculovirus isolated from the cassava hornworm cadavers is a betabaculovirus designated Erinnyis ello granulovirus (ErelGV). The 102,759 bp long genome has a G + C content of 38.7%. We found 130 putative ORFs coding for polypeptides of at least 50 amino acid residues. Only eight genes were found to be unique. ErelGV is closely related to ChocGV and PiraGV isolates. We did not find typical homologous regions and cathepsin and chitinase homologous genes are lacked. The presence of he65 and p43 homologous genes suggests horizontal gene transfer from Alphabaculovirus. Moreover, we found a nucleotide metabolism-related gene and two genes that could be acquired probably from Densovirus.<br><br>CONCLUSIONS: The ErelGV represents a new virus species from the genus Betabaculovirus and is the closest relative of ChocGV. It contains a dUTPase-like, a he65-like, p43-like genes, which are also found in several other alpha- and betabaculovirus genomes, and two Densovirus-related genes. Importantly, recombination events between insect viruses from unrelated families and genera might drive baculovirus genomic evolution.}, }
@article {pmid25280764, year = {2014}, author = {Alegado, RA and King, N}, title = {Bacterial influences on animal origins.}, journal = {Cold Spring Harbor perspectives in biology}, volume = {6}, number = {11}, pages = {a016162}, pmid = {25280764}, issn = {1943-0264}, support = {F32 GM086054/GM/NIGMS NIH HHS/United States ; R01 GM099533/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; 5F32GM086054/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*genetics/metabolism ; *Biological Evolution ; Cell Adhesion ; Choanoflagellata/genetics/*physiology ; Eukaryota/genetics/physiology ; Phagocytosis ; Phylogeny ; Signal Transduction ; }, abstract = {Animals evolved in seas teeming with bacteria, yet the influences of bacteria on animal origins are poorly understood. Comparisons among modern animals and their closest living relatives, the choanoflagellates, suggest that the first animals used flagellated collar cells to capture bacterial prey. The cell biology of prey capture, such as cell adhesion between predator and prey, involves mechanisms that may have been co-opted to mediate intercellular interactions during the evolution of animal multicellularity. Moreover, a history of bacterivory may have influenced the evolution of animal genomes by driving the evolution of genetic pathways for immunity and facilitating lateral gene transfer. Understanding the interactions between bacteria and the progenitors of animals may help to explain the myriad ways in which bacteria shape the biology of modern animals, including ourselves.}, }
@article {pmid25280222, year = {2014}, author = {Perry, JA and Westman, EL and Wright, GD}, title = {The antibiotic resistome: what's new?.}, journal = {Current opinion in microbiology}, volume = {21}, number = {}, pages = {45-50}, doi = {10.1016/j.mib.2014.09.002}, pmid = {25280222}, issn = {1879-0364}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/drug effects/*genetics ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial/physiology ; }, abstract = {The antibiotic resistome is dynamic and ever expanding, yet its foundations were laid long before the introduction of antibiotics into clinical practice. Here, we revisit our theoretical framework for the resistome concept and consider the many factors that influence the evolution of novel resistance genes, the spread of mobile resistance elements, and the ramifications of these processes for clinical practice. Observing the trends and prevalence of genes within the antibiotic resistome is key to maintaining the efficacy of antibiotics in the clinic.}, }
@article {pmid25279954, year = {2014}, author = {Anderson, RE and Sogin, ML and Baross, JA}, title = {Evolutionary strategies of viruses, bacteria and archaea in hydrothermal vent ecosystems revealed through metagenomics.}, journal = {PloS one}, volume = {9}, number = {10}, pages = {e109696}, pmid = {25279954}, issn = {1932-6203}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Biological Evolution ; Ecosystem ; Host-Pathogen Interactions ; Hydrothermal Vents/*microbiology/*virology ; Lysogeny ; Metagenomics/*methods ; Phylogeny ; Seawater/microbiology/virology ; Viruses/*genetics ; }, abstract = {The deep-sea hydrothermal vent habitat hosts a diverse community of archaea and bacteria that withstand extreme fluctuations in environmental conditions. Abundant viruses in these systems, a high proportion of which are lysogenic, must also withstand these environmental extremes. Here, we explore the evolutionary strategies of both microorganisms and viruses in hydrothermal systems through comparative analysis of a cellular and viral metagenome, collected by size fractionation of high temperature fluids from a diffuse flow hydrothermal vent. We detected a high enrichment of mobile elements and proviruses in the cellular fraction relative to microorganisms in other environments. We observed a relatively high abundance of genes related to energy metabolism as well as cofactors and vitamins in the viral fraction compared to the cellular fraction, which suggest encoding of auxiliary metabolic genes on viral genomes. Moreover, the observation of stronger purifying selection in the viral versus cellular gene pool suggests viral strategies that promote prolonged host integration. Our results demonstrate that there is great potential for hydrothermal vent viruses to integrate into hosts, facilitate horizontal gene transfer, and express or transfer genes that manipulate the hosts' functional capabilities.}, }
@article {pmid25279369, year = {2014}, author = {Michael, CA and Dominey-Howes, D and Labbate, M}, title = {The antimicrobial resistance crisis: causes, consequences, and management.}, journal = {Frontiers in public health}, volume = {2}, number = {}, pages = {145}, pmid = {25279369}, issn = {2296-2565}, abstract = {The antimicrobial resistance (AMR) crisis is the increasing global incidence of infectious diseases affecting the human population, which are untreatable with any known antimicrobial agent. This crisis will have a devastating cost on human society as both debilitating and lethal diseases increase in frequency and scope. Three major factors determine this crisis: (1) the increasing frequency of AMR phenotypes among microbes is an evolutionary response to the widespread use of antimicrobials; (2) the large and globally connected human population allows pathogens in any environment access to all of humanity; and (3) the extensive and often unnecessary use of antimicrobials by humanity provides the strong selective pressure that is driving the evolutionary response in the microbial world. Of these factors, the size of the human population is least amenable to rapid change. In contrast, the remaining two factors may be affected, so offering a means of managing the crisis: the rate at which AMR, as well as virulence factors evolve in microbial world may be slowed by reducing the applied selective pressure. This may be accomplished by radically reducing the global use of current and prospective antimicrobials. Current management measures to legislate the use of antimicrobials and to educate the healthcare world in the issues, while useful, have not comprehensively addressed the problem of achieving an overall reduction in the human use of antimicrobials. We propose that in addition to current measures and increased research into new antimicrobials and diagnostics, a comprehensive education program will be required to change the public paradigm of antimicrobial usage from that of a first line treatment to that of a last resort when all other therapeutic options have failed.}, }
@article {pmid25271726, year = {2014}, author = {Modi, SR and Collins, JJ and Relman, DA}, title = {Antibiotics and the gut microbiota.}, journal = {The Journal of clinical investigation}, volume = {124}, number = {10}, pages = {4212-4218}, pmid = {25271726}, issn = {1558-8238}, support = {AI112401/AI/NIAID NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R01 DE023113/DE/NIDCR NIH HHS/United States ; GM099534/GM/NIGMS NIH HHS/United States ; R01 GM099534/GM/NIGMS NIH HHS/United States ; DE023113/DE/NIDCR NIH HHS/United States ; R01 AI112401/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/*therapeutic use ; Bacteria/drug effects ; Drug Resistance, Microbial ; Gastrointestinal Tract/*microbiology ; Gene Transfer, Horizontal ; Humans ; Mice ; *Microbiota ; }, abstract = {Antibiotics have been a cornerstone of innovation in the fields of public health, agriculture, and medicine. However, recent studies have shed new light on the collateral damage they impart on the indigenous host-associated communities. These drugs have been found to alter the taxonomic, genomic, and functional capacity of the human gut microbiota, with effects that are rapid and sometimes persistent. Broad-spectrum antibiotics reduce bacterial diversity while expanding and collapsing membership of specific indigenous taxa. Furthermore, antibiotic treatment selects for resistant bacteria, increases opportunities for horizontal gene transfer, and enables intrusion of pathogenic organisms through depletion of occupied natural niches, with profound implications for the emergence of resistance. Because these pervasive alterations can be viewed as an uncoupling of mutualistic host-microbe relationships, it is valuable to reconsider antimicrobial therapies in the context of an ecological framework. Understanding the biology of competitive exclusion, interspecies protection, and gene flow of adaptive functions in the gut environment may inform the design of new strategies that treat infections while preserving the ecology of our beneficial constituents.}, }
@article {pmid25267667, year = {2014}, author = {Vincent, AT and Trudel, MV and Paquet, VE and Boyle, B and Tanaka, KH and Dallaire-Dufresne, S and Daher, RK and Frenette, M and Derome, N and Charette, SJ}, title = {Detection of variants of the pRAS3, pAB5S9, and pSN254 plasmids in Aeromonas salmonicida subsp. salmonicida: multidrug resistance, interspecies exchanges, and plasmid reshaping.}, journal = {Antimicrobial agents and chemotherapy}, volume = {58}, number = {12}, pages = {7367-7374}, pmid = {25267667}, issn = {1098-6596}, mesh = {Aeromonas salmonicida/drug effects/genetics/isolation &amp; purification ; Animals ; Anti-Bacterial Agents/pharmacology ; Base Sequence ; Canada/epidemiology ; Drug Resistance, Multiple, Bacterial/*genetics ; Fish Diseases/drug therapy/*epidemiology/microbiology/transmission ; Furunculosis/drug therapy/epidemiology/microbiology/transmission ; Gene Transfer, Horizontal ; Gram-Negative Bacterial Infections/drug therapy/epidemiology/transmission/*veterinary ; Molecular Sequence Data ; Plasmids/*chemistry/classification/metabolism ; Salmon/*microbiology ; Sequence Analysis, DNA ; Tetracycline/pharmacology ; }, abstract = {The ubiquitous water-borne Gram-negative bacterium Aeromonas salmonicida subsp. salmonicida is the causative agent of furunculosis, a worldwide disease in fish farms. Plasmids carrying antibiotic resistance genes have already been described for this bacterium. The aim of the present study was to identify and characterize additional multidrug resistance plasmids in A. salmonicida subsp. salmonicida. We sequenced the plasmids present in two multiple antibiotic-resistant isolates using high-throughput technologies. We also investigated 19 other isolates with various multidrug resistance profiles by genotyping PCR and assessed their resistance to tetracycline. We identified variants of the pAB5S9 and pSN254 plasmids that carry several antibiotic resistance genes and that have been previously reported in bacteria other than A. salmonicida subsp. salmonicida, which suggests a high level of interspecies exchange. Genotyping analyses and the antibiotic resistance profiles of the 19 other isolates support the idea that multiple versions of pAB5S9 and pSN254 exist in A. salmonicida subsp. salmonicida. We also identified variants of the pRAS3 plasmid. The present study revealed that A. salmonicida subsp. salmonicida harbors a wide variety of plasmids, which suggests that this ubiquitous bacterium may contribute to the spread of antibiotic resistance genes in the environment.}, }
@article {pmid25266386, year = {2014}, author = {Bleibtreu, A and Clermont, O and Darlu, P and Glodt, J and Branger, C and Picard, B and Denamur, E}, title = {The rpoS gene is predominantly inactivated during laboratory storage and undergoes source-sink evolution in Escherichia coli species.}, journal = {Journal of bacteriology}, volume = {196}, number = {24}, pages = {4276-4284}, pmid = {25266386}, issn = {1098-5530}, mesh = {Alleles ; Bacterial Proteins/*genetics ; Escherichia coli/*genetics ; *Evolution, Molecular ; Humans ; *Laboratories ; Mutation Rate ; Mutation, Missense ; Phylogeny ; Point Mutation ; *Preservation, Biological ; Sigma Factor/*genetics ; }, abstract = {The rpoS gene codes for an alternative RNA polymerase sigma factor, which acts as a general regulator of the stress response. Inactivating alleles of rpoS in collections of natural Escherichia coli isolates have been observed at very variable frequencies, from less than 1% to more than 70% of strains. rpoS is easily inactivated in nutrient-deprived environments such as stab storage, which makes it difficult to determine the true frequency of rpoS inactivation in nature. We studied the evolutionary history of rpoS and compared it to the phylogenetic history of bacteria in two collections of 82 human commensal and extraintestinal E. coli strains. These strains were representative of the phylogenetic diversity of the species and differed only by their storage conditions. In both collections, the phylogenetic histories of rpoS and of the strains were congruent, indicating that horizontal gene transfer had not occurred at the rpoS locus, and rpoS was under strong purifying selection, with a ratio of the nonsynonymous mutation rate (Ka) to the synonymous substitution rate (Ks) substantially smaller than 1. Stab storage was associated with a high frequency of inactivating alleles, whereas almost no amino acid sequence variation was observed in RpoS in the collection studied directly after isolation of the strains from the host. Furthermore, the accumulation of variations in rpoS was typical of source-sink dynamics. In conclusion, rpoS is rarely inactivated in natural E. coli isolates within their mammalian hosts, probably because such strains rapidly become evolutionary dead ends. Our data should encourage bacteriologists to freeze isolates immediately and to avoid the use of stab storage.}, }
@article {pmid25264902, year = {2014}, author = {Pivetal, J and Ciuta, G and Frenea-Robin, M and Haddour, N and Dempsey, NM and Dumas-Bouchiat, F and Simonet, P}, title = {Magnetic nanoparticle DNA labeling for individual bacterial cell detection and recovery.}, journal = {Journal of microbiological methods}, volume = {107}, number = {}, pages = {84-91}, doi = {10.1016/j.mimet.2014.09.006}, pmid = {25264902}, issn = {1872-8359}, mesh = {Bacteria/genetics/isolation &amp; purification ; DNA/*chemistry ; DNA, Bacterial/*chemistry ; Environmental Microbiology ; Escherichia coli/genetics/isolation &amp; purification ; Magnetite Nanoparticles/*chemistry/toxicity ; Plasmids/*chemistry ; Transformation, Bacterial ; }, abstract = {A culture independent approach was developed for recovering individual bacterial cells out of communities from complex environments including soils and sediments where autofluorescent contaminants hinder the use of fluorescence based techniques. For that purpose fifty nanometer sized streptavidin-coated superparamagnetic nanoparticles were used to chemically bond biotin-functionalized plasmid DNA molecules. We show that micromagnets can efficiently trap magnetically labeled transformed Escherichia coli cells after these bacteria were subjected to electro-transformation by these nanoparticle-labeled plasmids. Among other applications, this method could extend the range of approaches developed to study DNA dissemination among environmental bacteria without requiring cultivability of recombinant strains or expression of heterologous genes in the new hosts.}, }
@article {pmid25261942, year = {2014}, author = {Paholcsek, M and Leiter, E and Markovics, A and Biró, S}, title = {Novel and sensitive qPCR assays for the detection and identification of aspergillosis causing species.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {61}, number = {3}, pages = {273-284}, doi = {10.1556/AMicr.61.2014.3.3}, pmid = {25261942}, issn = {1217-8950}, mesh = {Aspergillosis/diagnosis/*microbiology ; Aspergillus/classification/genetics/*isolation &amp; purification ; DNA Primers/genetics ; Fungal Proteins/genetics ; Humans ; Polymerase Chain Reaction/*methods ; Sensitivity and Specificity ; }, abstract = {Despite concerted efforts, diagnosis of aspergillosis is still a great challenge to clinical microbiology laboratories. Along with the requirement for high sensitivity and specificity, species-specific identification is important. We developed rapid, sensitive and species-specific qPCR assays using the TaqMan technology for the detection and identification of Aspergillus fumigatus and Aspergillus terreus. The assays were designed to target orthologs of the Streptomyces factor C gene that are only found in a few species of filamentous fungi. Fungi acquired this gene through horizontal gene transfer and divergence of the gene allows identification of species. The assays have potential as a molecular diagnosis tool for the early detection of fungal infection caused by Aspergillus fumigatus and Aspergillus terreus, which merits future diagnostic studies. The assays were sensitive enough to detect a few genomic equivalents in blood samples.}, }
@article {pmid25261830, year = {2014}, author = {Alonso, R and Girbau, C and Martinez-Malaxetxebarria, I and Fernández-Astorga, A}, title = {Multilocus sequence typing reveals genetic diversity of foodborne Arcobacter butzleri isolates in the North of Spain.}, journal = {International journal of food microbiology}, volume = {191}, number = {}, pages = {125-128}, doi = {10.1016/j.ijfoodmicro.2014.09.012}, pmid = {25261830}, issn = {1879-3460}, mesh = {Alleles ; Animals ; Arcobacter/*genetics ; Bacteriocins/genetics ; *Food Microbiology ; Gene Transfer, Horizontal ; *Genetic Variation ; Glutamate-Ammonia Ligase/genetics ; Humans ; *Multilocus Sequence Typing ; Spain ; }, abstract = {The emerging pathogen Arcobacter butzleri is being increasingly isolated from different animal food products but the routes of its transmission to human are not well established yet. Typing methods would be useful in gaining such knowledge. Here we report the great genetic diversity observed among A. butzleri isolates from different food products. Forty-five isolates were analyzed by Multilocus Sequence Typing (MLST). A total of 157 alleles were identified across all seven loci, ranging from 16 alleles at glnA to 31 at glyA. MLST differentiated the isolates into 34 sequence types (STs), with the majority of isolates containing a unique sequence type. Seventy-four new alleles were identified, which resulted in the assignment of 33 new STs. No association of alleles or STs with food source was observed. For the first time, lateral gene transfer from Arcobacter skirrowii to A. butzleri at the glyA locus is also reported.}, }
@article {pmid25260585, year = {2014}, author = {McCarthy, AJ and Loeffler, A and Witney, AA and Gould, KA and Lloyd, DH and Lindsay, JA}, title = {Extensive horizontal gene transfer during Staphylococcus aureus co-colonization in vivo.}, journal = {Genome biology and evolution}, volume = {6}, number = {10}, pages = {2697-2708}, pmid = {25260585}, issn = {1759-6653}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Bacteriophages/genetics ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial/genetics ; Humans ; Plasmids/genetics ; Population Dynamics ; Staphylococcus aureus/*genetics ; Swine ; Virulence ; }, abstract = {Staphylococcus aureus is a commensal and major pathogen of humans and animals. Comparative genomics of S. aureus populations suggests that colonization of different host species is associated with carriage of mobile genetic elements (MGE), particularly bacteriophages and plasmids capable of encoding virulence, resistance, and immune evasion pathways. Antimicrobial-resistant S. aureus of livestock are a potential zoonotic threat to human health if they adapt to colonize humans efficiently. We utilized the technique of experimental evolution and co-colonized gnotobiotic piglets with both human- and pig-associated variants of the lineage clonal complex 398, and investigated growth and genetic changes over 16 days using whole genome sequencing. The human isolate survived co-colonization on piglets more efficiently than in vitro. During co-colonization, transfer of MGE from the pig to the human isolate was detected within 4 h. Extensive and repeated transfer of two bacteriophages and three plasmids resulted in colonization with isolates carrying a wide variety of mobilomes. Whole genome sequencing of progeny bacteria revealed no acquisition of core genome polymorphisms, highlighting the importance of MGE. Staphylococcus aureus bacteriophage recombination and integration into novel sites was detected experimentally for the first time. During colonization, clones coexisted and diversified rather than a single variant dominating. Unexpectedly, each piglet carried unique populations of bacterial variants, suggesting limited transmission of bacteria between piglets once colonized. Our data show that horizontal gene transfer occurs at very high frequency in vivo and significantly higher than that detectable in vitro.}, }
@article {pmid25257245, year = {2014}, author = {Kumwenda, B and Litthauer, D and Reva, O}, title = {Analysis of genomic rearrangements, horizontal gene transfer and role of plasmids in the evolution of industrial important Thermus species.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {813}, pmid = {25257245}, issn = {1471-2164}, mesh = {Chromosome Mapping ; Chromosomes, Bacterial ; Evolution, Molecular ; Gene Order ; *Gene Rearrangement ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Industrial Microbiology ; Metabolic Networks and Pathways ; Phylogeny ; Plasmids/*genetics ; Thermus/classification/*genetics ; }, abstract = {BACKGROUND: Bacteria of genus Thermus inhabit both man-made and natural thermal environments. Several Thermus species have shown biotechnological potential such as reduction of heavy metals which is essential for eradication of heavy metal pollution; removing of organic contaminants in water; opening clogged pipes, controlling global warming among many others. Enzymes from thermophilic bacteria have exhibited higher activity and stability than synthetic or enzymes from mesophilic organisms.<br><br>RESULTS: Using Meiothermus silvanus DSM 9946 as a reference genome, high level of coordinated rearrangements has been observed in extremely thermophilic Thermus that may imply existence of yet unknown evolutionary forces controlling adaptive re-organization of whole genomes of thermo-extremophiles. However, no remarkable differences were observed across species on distribution of functionally related genes on the chromosome suggesting constraints imposed by metabolic networks. The metabolic network exhibit evolutionary pressures similar to levels of rearrangements as measured by the cross-clustering index. Using stratigraphic analysis of donor-recipient, intensive gene exchanges were observed from Meiothermus species and some unknown sources to Thermus species confirming a well established DNA uptake mechanism as previously proposed.<br><br>CONCLUSION: Global genome rearrangements were found to play an important role in the evolution of Thermus bacteria at both genomic and metabolic network levels. Relatively higher level of rearrangements was observed in extremely thermophilic Thermus strains in comparison to the thermo-tolerant Thermus scotoductus. Rearrangements did not significantly disrupt operons and functionally related genes. Thermus species appeared to have a developed capability for acquiring DNA through horizontal gene transfer as shown by the donor-recipient stratigraphic analysis.}, }
@article {pmid25251852, year = {2014}, author = {Rotman, E and Seifert, HS}, title = {The genetics of Neisseria species.}, journal = {Annual review of genetics}, volume = {48}, number = {}, pages = {405-431}, doi = {10.1146/annurev-genet-120213-092007}, pmid = {25251852}, issn = {1545-2948}, support = {F32 AI0I94945/AI/NIAID NIH HHS/United States ; R01 AI044239/AI/NIAID NIH HHS/United States ; R37 AI033493/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteriophages/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Gene Transfer, Horizontal/genetics ; *Genome, Bacterial ; Gonorrhea/genetics/microbiology ; Meningitis, Bacterial/genetics/microbiology ; Neisseria gonorrhoeae/*genetics/pathogenicity ; Neisseria meningitidis/*genetics/pathogenicity ; *Recombination, Genetic ; Sepsis/genetics/microbiology ; }, abstract = {Neisseria gonorrhoeae and Neisseria meningitidis are closely related organisms that cause the sexually transmitted infection gonorrhea and serious bacterial meningitis and septicemia, respectively. Both species possess multiple mechanisms to alter the expression of surface-exposed proteins through the processes of phase and antigenic variation. This potential for wide variability in surface-exposed structures allows the organisms to always have subpopulations of divergent antigenic types to avoid immune surveillance and to contribute to functional variation. Additionally, the Neisseria are naturally competent for DNA transformation, which is their main means of genetic exchange. Although bacteriophages and plasmids are present in this genus, they are not as effective as DNA transformation for horizontal genetic exchange. There are barriers to genetic transfer, such as restriction-modification systems and CRISPR loci, that limit particular types of exchange. These host-restricted pathogens illustrate the rich complexity of genetics that can help define the similarities and differences of closely related organisms.}, }
@article {pmid25251496, year = {2014}, author = {Venieraki, A and Dimou, M and Vezyri, E and Vamvakas, A and Katinaki, PA and Chatzipavlidis, I and Tampakaki, A and Katinakis, P}, title = {The nitrogen-fixation island insertion site is conserved in diazotrophic Pseudomonas stutzeri and Pseudomonas sp. isolated from distal and close geographical regions.}, journal = {PloS one}, volume = {9}, number = {9}, pages = {e105837}, pmid = {25251496}, issn = {1932-6203}, mesh = {Bacterial Proteins/genetics ; Base Sequence ; China ; DNA, Bacterial/chemistry/genetics ; Evolution, Molecular ; Genetic Variation ; Genomic Islands/*genetics ; Geography ; Germany ; Greece ; Models, Genetic ; Molecular Sequence Data ; Nitrogen Fixation/*genetics ; Phylogeny ; Pseudomonas/classification/*genetics ; Pseudomonas stutzeri/*genetics ; RNA, Ribosomal, 16S/genetics ; Repetitive Sequences, Nucleic Acid/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Species Specificity ; }, abstract = {The presence of nitrogen fixers within the genus Pseudomonas has been established and so far most isolated strains are phylogenetically affiliated to Pseudomonas stutzeri. A gene ortholog neighborhood analysis of the nitrogen fixation island (NFI) in four diazotrophic P. stutzeri strains and Pseudomonas azotifigens revealed that all are flanked by genes coding for cobalamin synthase (cobS) and glutathione peroxidise (gshP). The putative NFIs lack all the features characterizing a mobilizable genomic island. Nevertheless, bioinformatic analysis P. stutzeri DSM 4166 NFI demonstrated the presence of short inverted and/or direct repeats within both flanking regions. The other P. stutzeri strains carry only one set of repeats. The genetic diversity of eleven diazotrophic Pseudomonas isolates was also investigated. Multilocus sequence typing grouped nine isolates along with P. stutzeri and two isolates are grouped in a separate clade. A Rep-PCR fingerprinting analysis grouped the eleven isolates into four distinct genotypes. We also provided evidence that the putative NFI in our diazotrophic Pseudomonas isolates is flanked by cobS and gshP genes. Furthermore, we demonstrated that the putative NFI of Pseudomonas sp. Gr65 is flanked by inverted repeats identical to those found in P. stutzeri DSM 4166 and while the other P. stutzeri isolates harbor the repeats located in the intergenic region between cobS and glutaredoxin genes as in the case of P. stutzeri A1501. Taken together these data suggest that all putative NFIs of diazotrophic Pseudomonas isolates are anchored in an intergenic region between cobS and gshP genes and their flanking regions are designated by distinct repeats patterns. Moreover, the presence of almost identical NFIs in diazotrophic Pseudomonas strains isolated from distal geographical locations around the world suggested that this horizontal gene transfer event may have taken place early in the evolution.}, }
@article {pmid25250243, year = {2014}, author = {Roberts, AP and Kreth, J}, title = {The impact of horizontal gene transfer on the adaptive ability of the human oral microbiome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {4}, number = {}, pages = {124}, pmid = {25250243}, issn = {2235-2988}, support = {R01 DE021726/DE/NIDCR NIH HHS/United States ; R01DE021726/DE/NIDCR NIH HHS/United States ; }, mesh = {*Adaptation, Biological ; Bacteria/genetics/metabolism ; Bacterial Adhesion ; Bacterial Physiological Phenomena ; Biofilms ; DNA Transposable Elements ; Drug Resistance, Bacterial ; Extracellular Space/metabolism ; *Gene Transfer, Horizontal ; Humans ; *Microbiota ; Mouth/*microbiology ; }, abstract = {The oral microbiome is composed of a multitude of different species of bacteria, each capable of occupying one or more of the many different niches found within the human oral cavity. This community exhibits many types of complex interactions which enable it to colonize and rapidly respond to changes in the environment in which they live. One of these interactions is the transfer, or acquisition, of DNA within this environment, either from co-resident bacterial species or from exogenous sources. Horizontal gene transfer in the oral cavity gives some of the resident bacteria the opportunity to sample a truly enormous metagenome affording them considerable adaptive potential which may be key to survival in such a varying environment. In this review the underlying mechanisms of HGT are discussed in relation to the oral microbiome with numerous examples described where the direct acquisition of exogenous DNA has contributed to the fitness of the bacterial host within the human oral cavity.}, }
@article {pmid25249284, year = {2014}, author = {Ummels, R and Abdallah, AM and Kuiper, V and Aâjoud, A and Sparrius, M and Naeem, R and Spaink, HP and van Soolingen, D and Pain, A and Bitter, W}, title = {Identification of a novel conjugative plasmid in mycobacteria that requires both type IV and type VII secretion.}, journal = {mBio}, volume = {5}, number = {5}, pages = {e01744-14}, pmid = {25249284}, issn = {2150-7511}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Secretion Systems/*genetics ; Conjugation, Genetic ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; Genome, Bacterial ; Molecular Sequence Data ; Mutagenesis, Insertional ; Mycobacterium tuberculosis/*genetics ; Plasmids/*genetics ; Sequence Analysis, DNA ; }, abstract = {UNLABELLED: Conjugative plasmids have been identified in a wide variety of different bacteria, ranging from proteobacteria to firmicutes, and conjugation is one of the most efficient routes for horizontal gene transfer. The most widespread mechanism of plasmid conjugation relies on different variants of the type IV secretion pathway. Here, we describe the identification of a novel type of conjugative plasmid that seems to be unique for mycobacteria. Interestingly, while this plasmid is efficiently exchanged between different species of slow-growing mycobacteria, including Mycobacterium tuberculosis, it could not be transferred to any of the fast-growing mycobacteria tested. Genetic analysis of the conjugative plasmid showed the presence of a locus containing homologues of three type IV secretion system components and a relaxase. In addition, a new type VII secretion locus was present. Using transposon insertion mutagenesis, we show that in fact both these secretion systems are essential for conjugation, indicating that this plasmid represents a new class of conjugative plasmids requiring two secretion machineries. This plasmid could form a useful new tool to exchange or introduce DNA in slow-growing mycobacteria.<br><br>IMPORTANCE: Conjugative plasmids play an important role in horizontal gene transfer between different bacteria and, as such, in their adaptation and evolution. This effect is most obvious in the spread of antibiotic resistance genes. Thus far, conjugation of natural plasmids has been described only rarely for mycobacterial species. In fact, it is generally accepted that M. tuberculosis does not show any recent sign of horizontal gene transfer. In this study, we describe the identification of a new widespread conjugative plasmid that can also be efficiently transferred to M. tuberculosis. This plasmid therefore poses both a threat and an opportunity. The threat is that, through the acquisition of antibiotic resistance markers, this plasmid could start a rapid spread of antibiotic resistance genes between pathogenic mycobacteria. The opportunity is that we could use this plasmid to generate new tools for the efficient introduction of foreign DNA in slow-growing mycobacteria.}, }
@article {pmid25249283, year = {2014}, author = {Brown, NF and Rogers, LD and Sanderson, KL and Gouw, JW and Hartland, EL and Foster, LJ}, title = {A horizontally acquired transcription factor coordinates Salmonella adaptations to host microenvironments.}, journal = {mBio}, volume = {5}, number = {5}, pages = {e01727-14}, pmid = {25249283}, issn = {2150-7511}, support = {MOP-77688//Canadian Institutes of Health Research/Canada ; }, mesh = {Adaptation, Physiological/*genetics ; Bacterial Proteins/genetics/*metabolism ; Bacterial Secretion Systems/*genetics ; Computational Biology ; Cytochrome b Group/genetics/metabolism ; Ferritins/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genomic Islands ; Multigene Family ; Phenotype ; Proteomics ; RNA, Messenger/genetics/metabolism ; Regulon ; Salmonella/*genetics/growth &amp; development ; Trans-Activators/genetics/*metabolism ; Transcription Factors/genetics/*metabolism ; Virulence Factors/genetics/metabolism ; }, abstract = {UNLABELLED: The transcription factors HilA and SsrB activate expression of two type III secretion systems (T3SSs) and cognate effectors that reprogram host cell functions to benefit infecting Salmonella in the host. These transcription factors, the secretion systems, and the effectors are all encoded by horizontally acquired genes. Using quantitative proteomics, we quantified the abundance of 2,149 proteins from hilA or ssrB Salmonella in vitro. Our results suggest that the HilA regulon does not extend significantly beyond proteins known to be involved in direct interactions with intestinal epithelium. On the other hand, SsrB influences the expression of a diverse range of proteins, many of which are ancestral to the acquisition of ssrB. In addition to the known regulon of T3SS-related proteins, we show that, through SodCI and bacterioferritin, SsrB controls resistance to reactive oxygen species and that SsrB down-regulates flagella and motility. This indicates that SsrB-controlled proteins not only redirect host cell membrane traffic to establish a supportive niche within host cells but also have adapted to the chemistry and physical constraints of that niche.<br><br>IMPORTANCE: Expression of T3SSs typically requires a transcription factor that is linked in a genomic island. Studies of the targets of HilA and SsrB have focused on almost exclusively on T3SS substrates that are either linked or encoded in distinct genomic islands. By broadening our focus, we found that the regulon of SsrB extended considerably beyond T3SS-2 and its substrates, while that of HilA did not. That at least two SsrB-regulated processes streamline existence in the intracellular niche afforded by T3SS-2 seems to be a predictable outcome of evolution and natural selection. However, and importantly, these are the &#xfb01;rst such functions to be implicated as being SsrB dependent. The concept of T3SS-associated transcription factors coordinating manipulations of host cells together with distinct bacterial processes for increased efficiency has unrealized implications for numerous host-pathogen systems.}, }
@article {pmid25246394, year = {2014}, author = {Matsumoto, Y and Izumiya, H and Sekizuka, T and Kuroda, M and Ohnishi, M}, title = {Characterization of blaTEM-52-carrying plasmids of extended-spectrum-β-lactamase-producing Salmonella enterica isolates from chicken meat with a common supplier in Japan.}, journal = {Antimicrobial agents and chemotherapy}, volume = {58}, number = {12}, pages = {7545-7547}, pmid = {25246394}, issn = {1098-6596}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Cattle ; Chickens ; Denmark ; Drug Resistance, Bacterial/*genetics ; Food Microbiology ; Gene Transfer, Horizontal ; Japan ; Meat/*microbiology ; Microbial Sensitivity Tests ; Plasmids/*chemistry/metabolism ; Salmonella enterica/drug effects/enzymology/*genetics/growth &amp; development ; beta-Lactamases/*genetics/metabolism ; beta-Lactams/pharmacology ; }, abstract = {The acquisition of resistance to cephalosporins among Salmonella spp. is a major public health concern. This study identified clonal plasmids carrying bla(TEM-52) from 10 Salmonella enterica serovar Infantis and Manhattan isolates from retail chicken meats that originated from a common supplier in Japan. Whole-genome analyses of the representative plasmids, including pYM4, revealed that they are 38 kb in size and that pYM4 is identical to pDKX1 from beef in Denmark, suggesting a global dissemination of resistance mediated by the plasmids.}, }
@article {pmid25246232, year = {2014}, author = {Omaleki, L and Browning, GF and Barber, SR and Allen, JL and Srikumaran, S and Markham, PF}, title = {Sequence diversity, cytotoxicity and antigenic similarities of the leukotoxin of isolates of Mannheimia species from mastitis in domestic sheep.}, journal = {Veterinary microbiology}, volume = {174}, number = {1-2}, pages = {172-179}, doi = {10.1016/j.vetmic.2014.08.009}, pmid = {25246232}, issn = {1873-2542}, mesh = {Animals ; Base Sequence ; Blotting, Western/veterinary ; Cluster Analysis ; Cross Reactions/immunology ; Electrophoresis, Gel, Two-Dimensional/veterinary ; Exotoxins/*genetics/toxicity ; Female ; Gene Transfer, Horizontal/genetics ; *Genetic Variation ; Mannheimia/*genetics ; Mannheimia haemolytica/*genetics ; Mastitis/genetics/microbiology/*veterinary ; Molecular Sequence Data ; Neutralization Tests/veterinary ; Pasteurellaceae Infections/genetics/*veterinary ; Phylogeny ; Sequence Analysis, DNA/veterinary ; Sheep ; Sheep Diseases/*microbiology ; Sheep, Domestic ; Species Specificity ; Virulence Factors/genetics/metabolism ; }, abstract = {Species within the genus Mannheimia are among the most important causes of ovine mastitis. Isolates of these species can express leukotoxin A (LktA), a primary virulence factor of these bacteria. To examine the significance of variation in the LktA, the sequences of the lktA genes in a panel of isolates from cases of ovine mastitis were compared. The cross-neutralising capacities of rat antisera raised against LktA of one Mannheimia glucosida, one haemolytic Mannheimia ruminalis, and two Mannheimia haemolytica isolates were also examined to assess the effect that variation in the lktA gene can have on protective immunity against leukotoxins with differing sequences. The lktA nucleotide distance between the M. haemolytica isolates was greater than between the M. glucosida isolates, with the M. haemolytica isolates divisible into two groups based on their lktA sequences. Comparison of the topology of phylogenetic trees of 16S rDNA and lktA sequences revealed differences in the relationships between some isolates, suggesting horizontal gene transfer. Cross neutralisation data obtained with monospecific anti-LktA rat sera were used to derive antigenic similarity coefficients for LktA from the four Mannheimia species isolates. Similarity coefficients indicated that LktA of the two M. haemolytica isolates were least similar, while LktA from M. glucosida was most similar to those for one of the M. haemolytica isolates and the haemolytic M. ruminalis isolate. The results suggested that vaccination with the M. glucosida leukotoxin would generate the greatest cross-protection against ovine mastitis caused by Mannheimia species with these alleles.}, }
@article {pmid25246075, year = {2015}, author = {Nobbs, AH and Jenkinson, HF and Everett, DB}, title = {Generic determinants of Streptococcus colonization and infection.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {33}, number = {}, pages = {361-370}, doi = {10.1016/j.meegid.2014.09.018}, pmid = {25246075}, issn = {1567-7257}, support = {101113//Wellcome Trust/United Kingdom ; R01 DE016690/DE/NIDCR NIH HHS/United States ; }, mesh = {Animals ; Genome, Bacterial ; Genomics ; Humans ; Streptococcal Infections/immunology/*microbiology ; Streptococcus/pathogenicity/*physiology ; Virulence/genetics ; Virulence Factors/genetics/immunology/metabolism ; }, abstract = {Bacteria within the genus Streptococcus have evolved to become exquisitely adapted to the colonization of humans and other animals. These bacteria predominantly live in harmony with their hosts, but all have capacity to cause disease should prevailing conditions allow. Streptococci express a myriad of colonization and virulence attributes that promote their survival at a variety of ecological sites. Many of these factors are surface-expressed adhesins that exhibit conservation at structural or functional levels across the genus. This reflects the importance of adherence interactions with a multitude of host substrata, such as epithelia or extracellular matrix components, to streptococcal survival. Other important factors are more restricted in their distribution, often conferring pathogenic capabilities associated with immune evasion or host tissue destruction. Evidence suggests that dissemination of these streptococcal attributes has frequently been driven by the movement of genetic material via lateral gene transfer, reflecting ecological pressures. Such recombination events have simultaneously facilitated extensive diversification, resulting in distinct tropisms at the species- or strain- level. These generic determinants offer significant potential as targets for combating streptococcal disease. However, this will depend upon better understanding of their mechanistic basis, and refined mapping of their distribution by epidemiological and metagenomic studies.}, }
@article {pmid25245396, year = {2014}, author = {Cordue, P and Linz, S and Semple, C}, title = {Phylogenetic networks that display a tree twice.}, journal = {Bulletin of mathematical biology}, volume = {76}, number = {10}, pages = {2664-2679}, doi = {10.1007/s11538-014-0032-x}, pmid = {25245396}, issn = {1522-9602}, mesh = {Algorithms ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Speciation ; Mathematical Concepts ; *Models, Genetic ; *Phylogeny ; }, abstract = {In the last decade, the use of phylogenetic networks to analyze the evolution of species whose past is likely to include reticulation events, such as horizontal gene transfer or hybridization, has gained popularity among evolutionary biologists. Nevertheless, the evolution of a particular gene can generally be described without reticulation events and therefore be represented by a phylogenetic tree. While this is not in contrast to each other, it places emphasis on the necessity of algorithms that analyze and summarize the tree-like information that is contained in a phylogenetic network. We contribute to the toolbox of such algorithms by investigating the question of whether or not a phylogenetic network embeds a tree twice and give a quadratic-time algorithm to solve this problem for a class of networks that is more general than tree-child networks.}, }
@article {pmid25244307, year = {2015}, author = {Gillan, DC and Roosa, S and Kunath, B and Billon, G and Wattiez, R}, title = {The long-term adaptation of bacterial communities in metal-contaminated sediments: a metaproteogenomic study.}, journal = {Environmental microbiology}, volume = {17}, number = {6}, pages = {1991-2005}, doi = {10.1111/1462-2920.12627}, pmid = {25244307}, issn = {1462-2920}, mesh = {Adaptation, Biological/*genetics ; Betaproteobacteria/classification/*genetics ; Fresh Water ; Geologic Sediments/*microbiology ; Metals/*metabolism ; Phylogeny ; Proteomics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The aim of the study was to understand the effect of a long-term metal exposure (110 years) on sediment microbial communities. Two freshwater sites, Férin and MetalEurop, differing by one order of magnitude in metal levels (MetalEurop: 3218 mg Zn kg(-1) ; 913 mg Pb kg(-1)) were compared by shotgun metaproteogenomics. A total of 69-118 Mpb of DNA and 943-1241 proteins were obtained. PhymmBL analysis of the DNA sequences indicated that the phylogenetic profile was similar in both stations and that β-Proteobacteria were dominant. However, subtle but significant changes were observed for some bacteria: e.g. Pseudomonas (+0.4%), Leptothrix (-0.4%), Thiobacillus (+0.36%) and Acidovorax (+0.48%). Using the stamp software, the two communities were found to be functionally very similar. However, significant genetic differences (10(-6) < P < 10(-3)) were observed for three SEED categories: synthesis of exopolymeric substances, virulence and defence mechanisms (including czcA metal efflux genes), and elements involved in horizontal gene transfer. The CzcA protein was found by metaproteomics in MetalEurop, but the levels were too low to allow comparisons. It is concluded that bacterial communities in freshwater sediments may adapt to high metal levels without broad changes in the structure of the population.}, }
@article {pmid25239467, year = {2015}, author = {Eidam, C and Poehlein, A and Leimbach, A and Michael, GB and Kadlec, K and Liesegang, H and Daniel, R and Sweeney, MT and Murray, RW and Watts, JL and Schwarz, S}, title = {Analysis and comparative genomics of ICEMh1, a novel integrative and conjugative element (ICE) of Mannheimia haemolytica.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {70}, number = {1}, pages = {93-97}, doi = {10.1093/jac/dku361}, pmid = {25239467}, issn = {1460-2091}, mesh = {Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; Drug Resistance, Bacterial ; Gene Order ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; *Interspersed Repetitive Sequences ; Mannheimia haemolytica/*genetics ; Molecular Sequence Data ; Pasteurella multocida ; Sequence Analysis, DNA ; }, abstract = {OBJECTIVES: The aim of this study was to identify and analyse the first integrative and conjugative element (ICE) from Mannheimia haemolytica, the major bacterial component of the bovine respiratory disease (BRD) complex.<br><br>METHODS: The novel ICEMh1 was discovered in the whole-genome sequence of M. haemolytica 42548 by sequence analysis and comparative genomics. Transfer of ICEMh1 was confirmed by conjugation into Pasteurella multocida recipient cells.<br><br>RESULTS: ICEMh1 has a size of 92,345 bp and harbours 107 genes. It integrates into a chromosomal tRNA(Leu) copy. Within two resistance gene regions of &#x223c; 7.4 and 3.3 kb, ICEMh1 harbours five genes, which confer resistance to streptomycin (strA and strB), kanamycin/neomycin (aphA1), tetracycline [tetR-tet(H)] and sulphonamides (sul2). ICEMh1 is related to the recently described ICEPmu1 and both ICEs seem to have evolved from a common ancestor. A region of ICEMh1 that is absent in ICEPmu1 was found in putative ICE regions of other M. haemolytica genomes, suggesting a recombination event between two ICEs. ICEMh1 transfers to P. multocida by conjugation, in which it also uses a tRNA(Leu) as the integration site. PCR assays and susceptibility testing confirmed the presence and activity of the ICEMh1-associated resistance genes in the P. multocida recipient.<br><br>CONCLUSIONS: These findings showed that ICEs, with structurally variable resistance gene regions, are present in BRD-associated Pasteurellaceae, can easily spread across genus borders and enable the acquisition of multidrug resistance via a single horizontal gene transfer event. This poses a threat to efficient antimicrobial chemotherapy of BRD-associated bacterial pathogens.}, }
@article {pmid25236918, year = {2015}, author = {Fontaine, L and Wahl, A and Fléchard, M and Mignolet, J and Hols, P}, title = {Regulation of competence for natural transformation in streptococci.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {33}, number = {}, pages = {343-360}, doi = {10.1016/j.meegid.2014.09.010}, pmid = {25236918}, issn = {1567-7257}, mesh = {Bacterial Proteins/genetics ; *DNA Transformation Competence ; Gene Expression Regulation, Bacterial ; Humans ; Phenotype ; Pheromones/metabolism ; Proteolysis ; Sigma Factor/genetics/metabolism ; Signal Transduction ; Streptococcus/classification/*physiology ; Transcription Factors/genetics ; *Transformation, Bacterial ; }, abstract = {Natural DNA transformation is a lateral gene transfer mechanism during which bacteria take up naked DNA from their environment and stably integrate it in their genome. The proteins required for this process are conserved between species and are produced during a specific physiological state known as competence. Although natural transformation drives genome plasticity and adaptability, it is also likely to cause deleterious effects in the chromosome of the recipient bacteria and negatively impact cell growth. The competence window is thus generally tightly regulated in response to species-specific environmental conditions and limited to a proportion of the cell population. In streptococci species, the entry into competence is dictated by the amount of the competence sigma factor σ(X), the master regulator of natural transformation in those species. The Streptococcus genus includes 7 phylogenetic groups that have evolved different regulatory circuits to govern natural transformation. Here, we review the current knowledge on transcriptional and post-transcriptional mechanisms that control the activity of σ(X) at the whole population and the single-cell level, with an emphasis on growth conditions that modulate their activation. Recent findings regarding competence regulation by the ComCDE and ComRS cell-cell signalling pathways and the Clp proteolytic system are specifically highlighted.}, }
@article {pmid25236617, year = {2015}, author = {Nandi, T and Holden, MT and Didelot, X and Mehershahi, K and Boddey, JA and Beacham, I and Peak, I and Harting, J and Baybayan, P and Guo, Y and Wang, S and How, LC and Sim, B and Essex-Lopresti, A and Sarkar-Tyson, M and Nelson, M and Smither, S and Ong, C and Aw, LT and Hoon, CH and Michell, S and Studholme, DJ and Titball, R and Chen, SL and Parkhill, J and Tan, P}, title = {Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles.}, journal = {Genome research}, volume = {25}, number = {1}, pages = {129-141}, pmid = {25236617}, issn = {1549-5469}, support = {/WT_/Wellcome Trust/United Kingdom ; 098051/WT_/Wellcome Trust/United Kingdom ; MR/K010174/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Burkholderia pseudomallei/*genetics ; DNA Primers ; DNA, Bacterial/genetics ; *Epigenesis, Genetic ; Escherichia coli/genetics ; Female ; Gene Deletion ; Genetic Association Studies ; *Genome, Bacterial ; Genomics ; Haplotypes ; Humans ; Melioidosis/microbiology ; Mice ; Mice, Inbred BALB C ; Multilocus Sequence Typing ; Phylogeny ; Polymorphism, Single Nucleotide ; *Recombination, Genetic ; Sequence Analysis, DNA ; *Transcriptome ; }, abstract = {Burkholderia pseudomallei (Bp) is the causative agent of the infectious disease melioidosis. To investigate population diversity, recombination, and horizontal gene transfer in closely related Bp isolates, we performed whole-genome sequencing (WGS) on 106 clinical, animal, and environmental strains from a restricted Asian locale. Whole-genome phylogenies resolved multiple genomic clades of Bp, largely congruent with multilocus sequence typing (MLST). We discovered widespread recombination in the Bp core genome, involving hundreds of regions associated with multiple haplotypes. Highly recombinant regions exhibited functional enrichments that may contribute to virulence. We observed clade-specific patterns of recombination and accessory gene exchange, and provide evidence that this is likely due to ongoing recombination between clade members. Reciprocally, interclade exchanges were rarely observed, suggesting mechanisms restricting gene flow between clades. Interrogation of accessory elements revealed that each clade harbored a distinct complement of restriction-modification (RM) systems, predicted to cause clade-specific patterns of DNA methylation. Using methylome sequencing, we confirmed that representative strains from separate clades indeed exhibit distinct methylation profiles. Finally, using an E. coli system, we demonstrate that Bp RM systems can inhibit uptake of non-self DNA. Our data suggest that RM systems borne on mobile elements, besides preventing foreign DNA invasion, may also contribute to limiting exchanges of genetic material between individuals of the same species. Genomic clades may thus represent functional units of genetic isolation in Bp, modulating intraspecies genetic diversity.}, }
@article {pmid25233845, year = {2015}, author = {Jans, C and Meile, L and Lacroix, C and Stevens, MJ}, title = {Genomics, evolution, and molecular epidemiology of the Streptococcus bovis/Streptococcus equinus complex (SBSEC).}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {33}, number = {}, pages = {419-436}, doi = {10.1016/j.meegid.2014.09.017}, pmid = {25233845}, issn = {1567-7257}, mesh = {Animal Diseases/epidemiology/microbiology ; Animals ; DNA Barcoding, Taxonomic ; Drug Resistance, Bacterial ; *Evolution, Molecular ; Food Microbiology ; *Genome, Bacterial ; *Genomics ; Global Health ; Humans ; Molecular Epidemiology ; Streptococcal Infections/*epidemiology/*microbiology ; Streptococcus/*classification/drug effects/*genetics/pathogenicity ; Streptococcus bovis/genetics ; Streptococcus equi/genetics ; Virulence/genetics ; Virulence Factors ; }, abstract = {The Streptococcus bovis/Streptococcus equinus complex (SBSEC) is a group of human and animal derived streptococci that are commensals (rumen and gastrointestinal tract), opportunistic pathogens or food fermentation associates. The classification of SBSEC has undergone massive changes and currently comprises 7 (sub)species grouped into four branches based on sequences identities: the Streptococcus gallolyticus, the Streptococcus equinus, the Streptococcus infantarius and the Streptococcus alactolyticus branch. In animals, SBSEC are causative agents for ruminal acidosis, potentially laminitis and infective endocarditis (IE). In humans, a strong association was established between bacteraemia, IE and colorectal cancer. Especially the SBSEC-species S. gallolyticus subsp. gallolyticus is an emerging pathogen for IE and prosthetic joint infections. S. gallolyticus subsp. pasteurianus and the S. infantarius branch are further associated with biliary and urinary tract infections. Knowledge on pathogenic mechanisms is so far limited to colonization factors such as pili and biofilm formation. Certain strain variants of S. gallolyticus subsp. macedonicus and S. infantarius subsp. infantarius are associated with traditional dairy and plant-based food fermentations and display traits suggesting safety. However, due to their close relationship to virulent strains, their use in food fermentation has to be critically assessed. Additionally, implementing accurate and up-to-date taxonomy is critical to enable appropriate treatment of patients and risk assessment of species and strains via recently developed multilocus sequence typing schemes to enable comparative global epidemiology. Comparative genomics revealed that SBSEC strains harbour genomics islands (GI) that seem acquired from other streptococci by horizontal gene transfer. In case of virulent strains these GI frequently encode putative virulence factors, in strains from food fermentation the GI encode functions that are pivotal for strain performance during fermentation. Comparative genomics is a powerful tool to identify acquired pathogenic functions, but there is still an urgent need for more physiological and epidemiological data to understand SBSEC-specific traits.}, }
@article {pmid25232661, year = {2014}, author = {Redrejo-Rodríguez, M and Salas, M}, title = {Multiple roles of genome-attached bacteriophage terminal proteins.}, journal = {Virology}, volume = {468-470}, number = {}, pages = {322-329}, doi = {10.1016/j.virol.2014.08.003}, pmid = {25232661}, issn = {1096-0341}, mesh = {Bacteriophages/*genetics/*physiology ; Gene Expression Regulation, Viral/*physiology ; Genome, Viral/*physiology ; Models, Molecular ; Protein Conformation ; Viral Proteins/genetics/*metabolism ; Virus Replication ; }, abstract = {Protein-primed replication constitutes a generalized mechanism to initiate DNA or RNA synthesis in linear genomes, including viruses, gram-positive bacteria, linear plasmids and mobile elements. By this mechanism a specific amino acid primes replication and becomes covalently linked to the genome ends. Despite the fact that TPs lack sequence homology, they share a similar structural arrangement, with the priming residue in the C-terminal half of the protein and an accumulation of positively charged residues at the N-terminal end. In addition, various bacteriophage TPs have been shown to have DNA-binding capacity that targets TPs and their attached genomes to the host nucleoid. Furthermore, a number of bacteriophage TPs from different viral families and with diverse hosts also contain putative nuclear localization signals and localize in the eukaryotic nucleus, which could lead to the transport of the attached DNA. This suggests a possible role of bacteriophage TPs in prokaryote-to-eukaryote horizontal gene transfer.}, }
@article {pmid25232178, year = {2014}, author = {Conlan, S and Thomas, PJ and Deming, C and Park, M and Lau, AF and Dekker, JP and Snitkin, ES and Clark, TA and Luong, K and Song, Y and Tsai, YC and Boitano, M and Dayal, J and Brooks, SY and Schmidt, B and Young, AC and Thomas, JW and Bouffard, GG and Blakesley, RW and ,  and Mullikin, JC and Korlach, J and Henderson, DK and Frank, KM and Palmore, TN and Segre, JA}, title = {Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae.}, journal = {Science translational medicine}, volume = {6}, number = {254}, pages = {254ra126}, pmid = {25232178}, issn = {1946-6242}, support = {ZIA HG200382-02//Intramural NIH HHS/United States ; ZIA HG200382-03//Intramural NIH HHS/United States ; }, mesh = {Bacterial Proteins/*biosynthesis ; *Cross Infection ; Enterobacteriaceae/classification/*enzymology/genetics ; Hospitals, Public ; Humans ; National Institutes of Health (U.S.) ; *Plasmids ; Population Surveillance ; Real-Time Polymerase Chain Reaction ; United States ; beta-Lactamases/*biosynthesis ; }, abstract = {Public health officials have raised concerns that plasmid transfer between Enterobacteriaceae species may spread resistance to carbapenems, an antibiotic class of last resort, thereby rendering common health care-associated infections nearly impossible to treat. To determine the diversity of carbapenemase-encoding plasmids and assess their mobility among bacterial species, we performed comprehensive surveillance and genomic sequencing of carbapenem-resistant Enterobacteriaceae in the National Institutes of Health (NIH) Clinical Center patient population and hospital environment. We isolated a repertoire of carbapenemase-encoding Enterobacteriaceae, including multiple strains of Klebsiella pneumoniae, Klebsiella oxytoca, Escherichia coli, Enterobacter cloacae, Citrobacter freundii, and Pantoea species. Long-read genome sequencing with full end-to-end assembly revealed that these organisms carry the carbapenem resistance genes on a wide array of plasmids. K. pneumoniae and E. cloacae isolated simultaneously from a single patient harbored two different carbapenemase-encoding plasmids, indicating that plasmid transfer between organisms was unlikely within this patient. We did, however, find evidence of horizontal transfer of carbapenemase-encoding plasmids between K. pneumoniae, E. cloacae, and C. freundii in the hospital environment. Our data, including full plasmid identification, challenge assumptions about horizontal gene transfer events within patients and identify possible connections between patients and the hospital environment. In addition, we identified a new carbapenemase-encoding plasmid of potentially high clinical impact carried by K. pneumoniae, E. coli, E. cloacae, and Pantoea species, in unrelated patients and in the hospital environment.}, }
@article {pmid25229999, year = {2015}, author = {Forlani, G and Bertazzini, M and Barillaro, D and Rippka, R}, title = {Divergent properties and phylogeny of cyanobacterial 5-enol-pyruvyl-shikimate-3-phosphate synthases: evidence for horizontal gene transfer in the Nostocales.}, journal = {The New phytologist}, volume = {205}, number = {1}, pages = {160-171}, doi = {10.1111/nph.13022}, pmid = {25229999}, issn = {1469-8137}, mesh = {3-Phosphoshikimate 1-Carboxyvinyltransferase/chemistry/*genetics ; Cyanobacteria/drug effects/*enzymology/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal/drug effects ; *Genetic Variation ; Glycine/analogs &amp; derivatives/toxicity ; Likelihood Functions ; Molecular Weight ; *Phylogeny ; Protein Multimerization/drug effects ; Protein Structure, Quaternary ; Spirulina/drug effects/enzymology ; Glyphosate ; }, abstract = {As it represents the target of the successful herbicide glyphosate, great attention has been paid to the shikimate pathway enzyme 5-enol-pyruvyl-shikimate-3-phosphate (EPSP) synthase. However, inconsistent results have been reported concerning the sensitivity of the enzyme from cyanobacteria, and consequent inhibitory effects on cyanobacterial growth. The properties of EPSP synthase were investigated in a set of 42 strains representative of the large morphological diversity of these prokaryotes. Publicly available protein sequences were analyzed, and related to enzymatic features. In most cases, the native protein showed an unusual homodimeric composition and a general sensitivity to micromolar doses of glyphosate. By contrast, eight out of 15 Nostocales strains were found to possess a monomeric EPSP synthase, whose activity was inhibited only at concentrations exceeding 1 mM. Sequence analysis showed that these two forms are only distantly related, the latter clustering separately in a clade composed of diverse bacterial phyla. The results are consistent with the occurrence of a horizontal gene transfer event involving an evolutionarily distant organism. Moreover, data suggest that the existence of class I (glyphosate-sensitive) and class II (glyphosate-tolerant) EPSP synthases representing two distinct phylogenetic clades is an oversimplification because of the limited number of analyzed samples.}, }
@article {pmid25228549, year = {2014}, author = {Srinivas, V and Gopal, S}, title = {LmTDRM database: a comprehensive database on thiol metabolic gene/gene products in Listeria monocytogenes EGDe.}, journal = {Journal of integrative bioinformatics}, volume = {11}, number = {1}, pages = {245}, doi = {10.2390/biecoll-jib-2014-245}, pmid = {25228549}, issn = {1613-4516}, mesh = {Animals ; *Bacterial Proteins/genetics/metabolism ; *Databases, Genetic ; Gene Regulatory Networks/*physiology ; Gene Transfer, Horizontal/physiology ; Genes, Bacterial/*physiology ; Humans ; *Listeria monocytogenes/genetics/metabolism ; Listeriosis/genetics/metabolism ; Protein Folding ; Sulfhydryl Compounds/*metabolism ; }, abstract = {There are a number of databases on the Listeria species and about their genome. However, these databases do not specifically address a set of network that is important in defence mechanism of the bacteria. Listeria monocytogenes EGDe is a well-established intracellular model organism to study host pathogenicity because of its versatility in the host environment. Here, we have focused on thiol disulphide redox metabolic network proteins, specifically in L. monocytogenes EGDe. The thiol redox metabolism is involved in oxidative stress mechanism and is found in all living cells. It functions to maintain the thiol disulphide balance required for protein folding by providing reducing power. Nevertheless, they are involved in the reversible oxidation of thiol groups in biomolecules by creating disulphide bonds; therefore, the term thiol disulphide redox metabolism (TDRM). TDRM network genes play an important role in oxidative stress mechanism and during host&amp;ndash;pathogen interaction. Therefore, it is essential to have detailed information on these proteins with regard to other bacteria and its genome analysis to understand the presence of tRNA, transposons, and insertion elements for horizontal gene transfer. LmTDRM database is a new comprehensive web-based database on thiol proteins and their functions. It includes: Description, Search, TDRM analysis, and genome viewer. The quality of these data has been evaluated before they were aggregated to produce a final representation. The web interface allows for various queries to understand the protein function and their annotation with respect to their relationship with other bacteria. LmTDRM is a major step towards the development of databases on thiol disulphide redox proteins; it would definitely help researchers to understand the mechanism of these proteins and their interaction. Database URL: www.lmtdrm.com.}, }
@article {pmid25228513, year = {2014}, author = {Zabłotni, A and Jaworski, A}, title = {[Sources of antibiotics in natural environments and their biological role].}, journal = {Postepy higieny i medycyny doswiadczalnej (Online)}, volume = {68}, number = {}, pages = {1040-1049}, doi = {10.5604/17322693.1119027}, pmid = {25228513}, issn = {1732-2693}, mesh = {Animals ; Anti-Bacterial Agents/*analysis/*pharmacology ; Bacteria/drug effects ; Bacterial Infections/drug therapy ; Biological Evolution ; Drug Resistance, Bacterial/*drug effects ; Drug Resistance, Microbial/*drug effects ; Environmental Exposure/*analysis ; *Environmental Microbiology ; }, abstract = {Nowadays antibiotics are broadly used not only for treatment of bacterial infections but also in nonmedical applications. For many years they have been added as livestock and poultry growth supplements, and they are applied similarly in fish farming. In basically unchanged form they may get into the natural environment and remain there for a long time. Excessive use of antibiotics leads to widespread of antibiotic resistance among clinical and environmental bacterial strains. Subinhibitory concentrations of antibiotics, which do not inhibit growth of bacteria, are often found in soil, water or even in the tissue of different organisms. Such low concentrations affect many bacterial genes through changes in their transcription level and increase of the mutation rate, and as a consequence lead to many bacterial adaptations to environmental stresses. There is also evidence that subinhibitory concentrations of antibiotics induce transfer of mobile genetic elements through horizontal gene transfer pathways, and therefore enhance antibiotic resistance, also among environmental strains. The analyzed data suggest the necessity of restriction and regular monitoring of antibiotics, which may be considered as environmental pollutants.}, }
@article {pmid25225265, year = {2014}, author = {Bao, Y and Liang, Z and Booyjzsen, C and Mayfield, JA and Li, Y and Lee, SW and Ploplis, VA and Song, H and Castellino, FJ}, title = {Unique genomic arrangements in an invasive serotype M23 strain of Streptococcus pyogenes identify genes that induce hypervirulence.}, journal = {Journal of bacteriology}, volume = {196}, number = {23}, pages = {4089-4102}, pmid = {25225265}, issn = {1098-5530}, support = {R01 HL013423/HL/NHLBI NIH HHS/United States ; R37 HL013423/HL/NHLBI NIH HHS/United States ; R56 HL013423/HL/NHLBI NIH HHS/United States ; HL013423/HL/NHLBI NIH HHS/United States ; }, mesh = {Bacterial Adhesion ; Epithelial Cells/microbiology ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; *Gene Order ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Polymerase Chain Reaction ; Prophages/genetics ; Pseudogenes ; Recombination, Genetic ; Serogroup ; Streptococcus pyogenes/*genetics/*growth &amp; development/physiology ; Virulence ; Virulence Factors/genetics ; }, abstract = {The first genome sequence of a group A Streptococcus pyogenes serotype M23 (emm23) strain (M23ND), isolated from an invasive human infection, has been completed. The genome of this opacity factor-negative (SOF(-)) strain is composed of a circular chromosome of 1,846,477 bp. Gene profiling showed that this strain contained six phage-encoded and 24 chromosomally inherited well-known virulence factors, as well as 11 pseudogenes. The bacterium has acquired four large prophage elements, ΦM23ND.1 to ΦM23ND.4, harboring genes encoding streptococcal superantigen (ssa), streptococcal pyrogenic exotoxins (speC, speH, and speI), and DNases (spd1 and spd3), with phage integrase genes being present at one flank of each phage insertion, suggesting that the phages were integrated by horizontal gene transfer. Comparative analyses revealed unique large-scale genomic rearrangements that result in genomic rearrangements that differ from those of previously sequenced GAS strains. These rearrangements resulted in an imbalanced genomic architecture and translocations of chromosomal virulence genes. The covS sensor in M23ND was identified as a pseudogene, resulting in the attenuation of speB function and increased expression of the genes for the chromosomal virulence factors multiple-gene activator (mga), M protein (emm23), C5a peptidase (scpA), fibronectin-binding proteins (sfbI and fbp54), streptolysin O (slo), hyaluronic acid capsule (hasA), streptokinase (ska), and DNases (spd and spd3), which were verified by PCR. These genes are responsible for facilitating host epithelial cell binding and and/or immune evasion, thus further contributing to the virulence of M23ND. In conclusion, strain M23ND has become highly pathogenic as the result of a combination of multiple genetic factors, particularly gene composition and mutations, prophage integrations, unique genomic rearrangements, and regulated expression of critical virulence factors.}, }
@article {pmid25224692, year = {2014}, author = {Sassi, M and Gouret, P and Chabrol, O and Pontarotti, P and Drancourt, M}, title = {Mycobacteriophage-drived diversification of Mycobacterium abscessus.}, journal = {Biology direct}, volume = {9}, number = {}, pages = {19}, pmid = {25224692}, issn = {1745-6150}, mesh = {Bacterial Proteins/genetics ; Chromosome Mapping ; Cluster Analysis ; Gene Transfer, Horizontal/genetics ; *Genetic Variation ; Genome, Bacterial/genetics ; Molecular Sequence Annotation ; Mycobacteriophages/*physiology ; Mycobacterium/*genetics/*virology ; Phylogeny ; Prophages/genetics ; }, abstract = {BACKGROUND: Mycobacterium abscessus is an emerging opportunistic pathogen which diversity was acknowledged by the recent description of two subspecies accommodating M. abscessus, Mycobacterium bolletii and Mycobacterium massiliense isolates.<br><br>RESULTS: Here, genome analysis found 1-8 prophage regions in 47/48 M. abscessus genomes ranging from small prophage-like elements to complete prophages. A total of 20,304 viral and phage proteins clustered into 853 orthologous groups. Phylogenomic and phylogenetic analyses based on prophage region homology found three main clusters corresponding to M. abscessus, M. bolletii and M. massiliense. Analysing 135 annotated Tape Measure Proteins found thirteen clusters and four singletons, suggesting that at least 17 mycobacteriophages had infected M. abscessus during its evolution. The evolutionary history of phages differed from that of their mycobacterial hosts. In particular, 33 phage-related proteins have been horizontally transferred within M. abscessus genomes. They comprise of an integrase, specific mycobacteriophage proteins, hypothetical proteins and DNA replication and metabolism proteins. Gene exchanges, loss and gains which occurred in M. abscessus genomes have been driven by several mycobacteriophages.<br><br>CONCLUSIONS: This analysis of phage-mycobacterium co-evolution suggests that mycobacteriophages are playing a key-role in the on-going diversification of M. abscessus.<br><br>REVIEWERS: This article was reviewed by Eric Bapteste, Patrick Forterre and Eugene Koonin.}, }
@article {pmid25224649, year = {2014}, author = {Zhao, C and Doucet, D and Mittapalli, O}, title = {Characterization of horizontally transferred β-fructofuranosidase (ScrB) genes in Agrilus planipennis.}, journal = {Insect molecular biology}, volume = {23}, number = {6}, pages = {821-832}, doi = {10.1111/imb.12127}, pmid = {25224649}, issn = {1365-2583}, mesh = {Animals ; Bacteria/genetics ; Base Sequence ; Coleoptera/*enzymology/*genetics/metabolism ; Gastrointestinal Tract/*enzymology/metabolism ; Gene Expression ; *Gene Transfer, Horizontal ; Larva/enzymology/genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; Sucrose/metabolism ; Transcriptome ; beta-Fructofuranosidase/*genetics ; }, abstract = {The emerald ash borer (Agrilus planipennis) is an important invasive insect pest of Fraxinus spp. that feeds on host tissues containing high levels of sucrose. However, little is known about how it digests sucrose. Here, using larval midgut transcriptome data and preliminary genome sequence efforts, two β-fructofuranosidase-encoding ScrB genes, AplaScrB-1 and AplaScrB-2, were identified, and proved to reside within the A. planipennis genome. Homology and phylogenetic analysis revealed that they were acquired by A. planipennis via horizontal gene transfer (HGT) from bacteria, possibly an event independent from that reported in bark beetles (eg ScrB genes). Microsynteny between A. planipennis DNA scaffold #2042940, which hosts AplaScrB-1, and a region in the Tribolium castaneum chromosome LG4 suggested that A. planipennis gained this gene after the separation of Buprestidae and Tenebrionidae. Although both of the putative AplaScrB proteins have conserved β-fructofuranosidase motifs, only AplaScrB-2 was predicted to be a secretory protein. Expression of AplaScrB-1 seemed constitutive during development and in all tissues examined, whereas AplaScrB-2 showed a peak expression in adults and in the midgut. We propose that acquisition of these genes by A. planipennis from bacteria is adaptive, and specifically AplaScrB-2 is involved in breaking down dietary sucrose to obtain energy for development.}, }
@article {pmid25222494, year = {2014}, author = {Ochoa de Alda, JA and Esteban, R and Diago, ML and Houmard, J}, title = {The plastid ancestor originated among one of the major cyanobacterial lineages.}, journal = {Nature communications}, volume = {5}, number = {}, pages = {4937}, doi = {10.1038/ncomms5937}, pmid = {25222494}, issn = {2041-1723}, mesh = {Biological Evolution ; *Cyanobacteria/classification/genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Models, Genetic ; Nitrogen Fixation ; *Phylogeny ; Plants/metabolism/microbiology ; Plastids/*genetics ; RNA, Ribosomal, 16S/*genetics ; RNA, Ribosomal, 23S/*genetics ; Symbiosis/genetics ; }, abstract = {The primary endosymbiotic origin of chloroplasts is now well established but the identification of the present cyanobacteria most closely related to the plastid ancestor remains debated. We analyse the evolutionary trajectory of a subset of highly conserved cyanobacterial proteins (core) along the plastid lineage, those which were not lost after the endosymbiosis. We concatenate the sequences of 33 cyanobacterial core proteins that share a congruent evolutionary history, with their eukaryotic counterparts to reconstruct their phylogeny using sophisticated evolutionary models. We perform an independent reconstruction using concatenated 16S and 23S rRNA sequences. These complementary approaches converge to a plastid origin occurring during the divergence of one of the major cyanobacterial lineages that include N2-fixing filamentous cyanobacteria and species able to differentiate heterocysts.}, }
@article {pmid25221566, year = {2014}, author = {Sagy, O and Shamir, R and Rechavi, O}, title = {Examination of exhaustive cloning attempts reveals that C. elegans piRNAs, transposons, and repeat sequences are efficiently cloned in yeast, but not in bacteria.}, journal = {Frontiers in genetics}, volume = {5}, number = {}, pages = {275}, pmid = {25221566}, issn = {1664-8021}, abstract = {Genome sequencing requires insertion of random fragments of the sequenced organism's DNA into a unicellular host, most often Escherichia coli bacteria. This manipulation was found in the past to be analogous to naturally occurring horizontal gene transfer, and moreover has proved valuable to understanding toxicity of foreign genetic elements to E. coli. Sequencing of the Caenorhabditis elegans genome was similarly achieved via DNA transformation into E. coli. However, numerous attempts have proven a significant percentage of the genome unclonable using bacteria, although clonable via yeast. We examined the genomic segments that were not clonable in bacteria but were clonable in yeast, and observed that, in line with previous hypotheses, such sequences are more repetitive on average compared with the entire C. elegans genome. In addition, we found that these gap-sequences encode significantly more for DNA transposons. Surprisingly, we discovered that although the vast majority of the C. elegans genome is clonable in bacteria (77.5%), almost all the thousands of sequences that encode for PIWI-interacting small RNAs, or 21U-RNAs (91.6%) were only clonable in yeast. These results might help understanding why most piRNAs in C. elegans are physically clustered on particular loci on chromosome IV. In worms and in a large number of other organisms, piRNAs serve to distinguish "Self" from "Non-Self" sequences, and thus to protect the integrity of the genome against foreign genetic elements, such as transposons. We discuss the possible implications of these discoveries.}, }
@article {pmid25219519, year = {2014}, author = {Chen, K and Dorlhac de Borne, F and Szegedi, E and Otten, L}, title = {Deep sequencing of the ancestral tobacco species Nicotiana tomentosiformis reveals multiple T-DNA inserts and a complex evolutionary history of natural transformation in the genus Nicotiana.}, journal = {The Plant journal : for cell and molecular biology}, volume = {80}, number = {4}, pages = {669-682}, doi = {10.1111/tpj.12661}, pmid = {25219519}, issn = {1365-313X}, mesh = {*Biological Evolution ; *DNA, Bacterial ; Gene Transfer, Horizontal ; Genes, Plant ; High-Throughput Nucleotide Sequencing ; Open Reading Frames ; Nicotiana/*genetics ; }, abstract = {Nicotiana species carry cellular T-DNA sequences (cT-DNAs), acquired by Agrobacterium-mediated transformation. We characterized the cT-DNA sequences of the ancestral Nicotiana tabacum species Nicotiana tomentosiformis by deep sequencing. N. tomentosiformis contains four cT-DNA inserts derived from different Agrobacterium strains. Each has an incomplete inverted-repeat structure. TA is similar to part of the Agrobacterium rhizogenes 1724 mikimopine-type T-DNA, but has unusual orf14 and mis genes. TB carries a 1724 mikimopine-type orf14-mis fragment and a mannopine-agropine synthesis region (mas2-mas1-ags). The mas2' gene codes for an active enzyme. TC is similar to the left part of the A. rhizogenes A4 T-DNA, but also carries octopine synthase-like (ocl) and c-like genes normally found in A. tumefaciens. TD shows a complex rearrangement of T-DNA fragments similar to the right end of the A4 TL-DNA, and including an orf14-like gene and a gene with unknown function, orf511. The TA, TB, TC and TD insertion sites were identified by alignment with N. tabacum and Nicotiana sylvestris sequences. The divergence values for the TA, TB, TC and TD repeats provide an estimate for their relative introduction times. A large deletion has occurred in the central part of the N. tabacum cv. Basma/Xanthi TA region, and another deletion removed the complete TC region in N. tabacum. Nicotiana otophora lacks TA, TB and TD, but contains TC and another cT-DNA, TE. This analysis, together with that of Nicotiana glauca and other Nicotiana species, indicates multiple sequential insertions of cT-DNAs during the evolution of the genus Nicotiana.}, }
@article {pmid25219384, year = {2014}, author = {Willems, M and Tahiri, N and Makarenkov, V}, title = {A new efficient algorithm for inferring explicit hybridization networks following the Neighbor-Joining principle.}, journal = {Journal of bioinformatics and computational biology}, volume = {12}, number = {5}, pages = {1450024}, doi = {10.1142/S0219720014500243}, pmid = {25219384}, issn = {1757-6334}, mesh = {*Algorithms ; Animals ; Biological Evolution ; Computational Biology ; Computer Simulation ; Culicidae/classification/genetics ; Databases, Genetic ; Diploidy ; *Hybridization, Genetic ; Least-Squares Analysis ; Models, Genetic ; *Phylogeny ; Plants/classification/genetics ; Polyploidy ; Software ; }, abstract = {Several algorithms and software have been developed for inferring phylogenetic trees. However, there exist some biological phenomena such as hybridization, recombination, or horizontal gene transfer which cannot be represented by a tree topology. We need to use phylogenetic networks to adequately represent these important evolutionary mechanisms. In this article, we present a new efficient heuristic algorithm for inferring hybridization networks from evolutionary distance matrices between species. The famous Neighbor-Joining concept and the least-squares criterion are used for building networks. At each step of the algorithm, before joining two given nodes, we check if a hybridization event could be related to one of them or to both of them. The proposed algorithm finds the exact tree solution when the considered distance matrix is a tree metric (i.e. it is representable by a unique phylogenetic tree). It also provides very good hybrids recovery rates for large trees (with 32 and 64 leaves in our simulations) for both distance and sequence types of data. The results yielded by the new algorithm for real and simulated datasets are illustrated and discussed in detail.}, }
@article {pmid25218701, year = {2014}, author = {Krebes, J and Didelot, X and Kennemann, L and Suerbaum, S}, title = {Bidirectional genomic exchange between Helicobacter pylori strains from a family in Coventry, United Kingdom.}, journal = {International journal of medical microbiology : IJMM}, volume = {304}, number = {8}, pages = {1135-1146}, doi = {10.1016/j.ijmm.2014.08.007}, pmid = {25218701}, issn = {1618-0607}, support = {MR/K010174/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adolescent ; Aged ; DNA, Bacterial/chemistry/genetics ; *Family Health ; *Gene Transfer, Horizontal ; Genetic Variation ; Genome, Bacterial ; Genotype ; Helicobacter Infections/*microbiology ; Helicobacter pylori/*genetics/isolation &amp; purification ; Humans ; Male ; Middle Aged ; Molecular Sequence Data ; Recombination, Genetic ; Sequence Analysis, DNA ; United Kingdom ; }, abstract = {The human gastric pathogen Helicobacter pylori is characterised by a high mutation rate and frequent recombination during mixed infection, which result in extensive genetic diversity and rapid allelic diversification. Mixed infections are believed to be much more common in regions with a high H. pylori prevalence than in industrialised countries. To better understand the genomic flexibility of H. pylori in a low prevalence region, we used 454 sequencing technology to investigate whole genome sequences of H. pylori strains isolated from members of three generations of a family living in Coventry, UK. The genomes of four H. pylori strains isolated from a grandfather, two of his sons and one grandson were sequenced. Three of these genomes showed a high overall sequence similarity, suggesting a recent common ancestor. The genomes differed by 316-336 SNPs, and recombination events (imports) resulted in 170-251 clusters of polymorphisms (CNPs). Imports were particularly frequent in genes encoding Helicobacter outer membrane proteins, suggesting an adaptation of the strains to their individual host. The fourth strain differed substantially from these three highly related strains but still shared long fragments of identical sequence, which most likely reflect imports from the highly related family variants. The data show extensive bidirectional exchange of DNA between the strains isolated from the family members, illustrating both the convergence and divergence effect that recombination can lead to. Detailed analysis of the distribution of SNPs and imports permits to draw up a complex scenario of the transmission history involving infection with at least two, and probably more separate strains. This complexity and the resulting high frequency of recombination were unexpected for an industrialised country where the prevalence of H. pylori infection has strongly declined in recent decades.}, }
@article {pmid25217846, year = {2014}, author = {Peng, L and Pei, J and Pang, H and Guo, Y and Lin, L and Huang, R}, title = {Whole genome sequencing reveals a novel CRISPR system in industrial Clostridium acetobutylicum.}, journal = {Journal of industrial microbiology &amp; biotechnology}, volume = {41}, number = {11}, pages = {1677-1685}, pmid = {25217846}, issn = {1476-5535}, mesh = {CRISPR-Cas Systems ; Clostridium acetobutylicum/*genetics ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Genome, Bacterial ; Industrial Microbiology ; Multigene Family ; Sequence Analysis, DNA ; }, abstract = {Clostridium acetobutylicum is an important organism for biobutanol production. Due to frequent exposure to bacteriophages during fermentation, industrial C. acetobutylicum strains require a strong immune response against foreign genetic invaders. In the present study, a novel CRISPR system was reported in a C. acetobutylicum GXAS18-1 strain by whole genome sequencing, and several specific characteristics of the CRISPR system were revealed as follows: (1) multiple CRISPR loci were confirmed within the whole bacterial genome, while only one cluster of CRISPR-associated genes (Cas) was found in the current strain; (2) similar leader sequences at the 5' end of the multiple CRISPR loci were identified as promoter elements by promoter prediction, suggesting that these CRISPR loci were under the control of the same transcriptional factor; (3) homology analysis indicated that the present Cas genes shared only low sequence similarity with the published Cas families; and (4) concerning gene similarity and gene cluster order, these Cas genes belonged to the csm family and originated from the euryarchaeota by horizontal gene transfer.}, }
@article {pmid25217830, year = {2014}, author = {Lahiri, A and Sanchini, A and Semmler, T and Schäfer, H and Lewin, A}, title = {Identification and comparative analysis of a genomic island in Mycobacterium avium subsp. hominissuis.}, journal = {FEBS letters}, volume = {588}, number = {21}, pages = {3906-3911}, doi = {10.1016/j.febslet.2014.08.037}, pmid = {25217830}, issn = {1873-3468}, mesh = {Animals ; Environment ; *Genomic Islands ; *Genomics ; Humans ; Mycobacterium avium/*genetics/isolation &amp; purification ; Species Specificity ; }, abstract = {Mycobacterium avium subsp. hominissuis (MAH) is an environmental bacterium causing opportunistic infections. The objective of this study was to identify flexible genome regions in MAH isolated from different sources. By comparing five complete and draft MAH genomes we identified a genomic island conferring additional flexibility to the MAH genomes. The island was absent in one of the five strains and had sizes between 16.37 and 84.85kb in the four other strains. The genes present in the islands differed among strains and included phage- and plasmid-derived genes, integrase genes, hypothetical genes, and virulence-associated genes like mmpL or mce genes.}, }
@article {pmid25216190, year = {2014}, author = {Mardanov, AV and Beletsky, AV and Kadnikov, VV and Ignatov, AN and Ravin, NV}, title = {The 203 kbp mitochondrial genome of the phytopathogenic fungus Sclerotinia borealis reveals multiple invasions of introns and genomic duplications.}, journal = {PloS one}, volume = {9}, number = {9}, pages = {e107536}, pmid = {25216190}, issn = {1932-6203}, mesh = {Ascomycota/*genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Fungal ; *Genome, Mitochondrial ; Introns/*genetics ; Segmental Duplications, Genomic ; }, abstract = {Here we report the complete sequence of the mitochondrial (mt) genome of the necrotrophic phytopathogenic fungus Sclerotinia borealis, a member of the order Helotiales of Ascomycetes. The 203,051 bp long mtDNA of S. borealis represents one of the largest sequenced fungal mt genomes. The large size is mostly determined by the presence of mobile genetic elements, which include 61 introns. Introns contain a total of 125,394 bp, are scattered throughout the genome, and are found in 12 protein-coding genes and in the ribosomal RNA genes. Most introns contain complete or truncated ORFs that are related to homing endonucleases of the LAGLIDADG and GIY-YIG families. Integrations of mobile elements are also evidenced by the presence of two regions similar to fragments of inverton-like plasmids. Although duplications of some short genome regions, resulting in the appearance of truncated extra copies of genes, did occur, we found no evidences of extensive accumulation of repeat sequences accounting for mitochondrial genome size expansion in some other fungi. Comparisons of mtDNA of S. borealis with other members of the order Helotiales reveal considerable gene order conservation and a dynamic pattern of intron acquisition and loss during evolution. Our data are consistent with the hypothesis that horizontal DNA transfer has played a significant role in the evolution and size expansion of the S. borealis mt genome.}, }
@article {pmid25213620, year = {2014}, author = {Perry, JA and Wright, GD}, title = {Forces shaping the antibiotic resistome.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {36}, number = {12}, pages = {1179-1184}, doi = {10.1002/bies.201400128}, pmid = {25213620}, issn = {1521-1878}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/*genetics ; Drug Resistance, Bacterial/drug effects/*genetics ; Environmental Monitoring ; Environmental Pollution/prevention &amp; control ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Metagenomics ; Microbiota/genetics ; Mutation ; Selection, Genetic ; *Soil Microbiology ; }, abstract = {Antibiotic resistance has become a problem of global scale. Resistance arises through mutation or through the acquisition of resistance gene(s) from other bacteria in a process called horizontal gene transfer (HGT). While HGT is recognized as an important factor in the dissemination of resistance genes in clinical pathogens, its role in the environment has been called into question by a recent study published in Nature. The authors found little evidence of HGT in soil using a culture-independent functional metagenomics approach, which is in contrast to previous work from the same lab showing HGT between the environment and human microbiome. While surprising at face value, these results may be explained by the lack of selective pressure in the environment studied. Importantly, this work suggests the need for careful monitoring of environmental antibiotic pollution and stringent antibiotic stewardship in the fight against resistance.}, }
@article {pmid25206351, year = {2014}, author = {López-Madrigal, S and Beltrà, A and Resurrección, S and Soto, A and Latorre, A and Moya, A and Gil, R}, title = {Molecular evidence for ongoing complementarity and horizontal gene transfer in endosymbiotic systems of mealybugs.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {449}, pmid = {25206351}, issn = {1664-302X}, abstract = {Intracellular bacterial supply of essential amino acids is common among sap-feeding insects, thus complementing the scarcity of nitrogenous compounds in plant phloem. This is also the role of the two mealybug endosymbiotic systems whose genomes have been sequenced. In the nested endosymbiotic system from Planococcus citri (Pseudococcinae), "Candidatus Tremblaya princeps" and "Candidatus Moranella endobia" cooperate to synthesize essential amino acids, while in Phenacoccus avenae (Phenacoccinae) this function is performed by its single endosymbiont "Candidatus Tremblaya phenacola." However, little is known regarding the evolution of essential amino acid supplementation strategies in other mealybug systems. To address this knowledge gap, we screened for the presence of six selected loci involved in essential amino acid biosynthesis in five additional mealybug species. We found evidence of ongoing complementarity among endosymbionts from insects of subfamily Pseudococcinae, as well as horizontal gene transfer affecting endosymbionts from insects of family Phenacoccinae, providing a more comprehensive picture of the evolutionary history of these endosymbiotic systems. Additionally, we report two diagnostic motifs to help identify invasive mealybug species.}, }
@article {pmid25205608, year = {2014}, author = {Govindarajan, G and Satheeja Santhi, V and Jebakumar, SR}, title = {Antimicrobial potential of phylogenetically unique actinomycete, Streptomyces sp. JRG-04 from marine origin.}, journal = {Biologicals : journal of the International Association of Biological Standardization}, volume = {42}, number = {6}, pages = {305-311}, doi = {10.1016/j.biologicals.2014.08.003}, pmid = {25205608}, issn = {1095-8320}, mesh = {3-Oxoacyl-(Acyl-Carrier-Protein) Synthase/chemistry ; Animals ; Anti-Infective Agents/*chemistry ; Biomass ; Chromatography, Liquid ; Drug Resistance, Microbial ; Fermentation ; Gene Transfer, Horizontal ; Magnetic Resonance Spectroscopy ; Methicillin/chemistry ; Microbial Sensitivity Tests ; Microscopy, Confocal ; Microscopy, Electron, Scanning ; Multigene Family ; Phylogeny ; Polyketides/chemistry ; Protein Structure, Tertiary ; RNA, Ribosomal, 16S/metabolism ; Rats ; Spectrometry, Mass, Electrospray Ionization ; Spectroscopy, Fourier Transform Infrared ; Streptomyces/*chemistry/genetics ; }, abstract = {Due to the emergence of severe infectious diseases and thriving antibiotic resistance, there is a need to explore microbial-derived bioactive secondary metabolites from unexplored regions. Present study deals with a mangrove estuary derived strain of Streptomyces sp. with potent antimicrobial activity against various pathogens, including methicillin resistant Staphylococcus aureus. Bioactive compound was effective even at low MIC level, damages the membrane of methicillin resistant S. aureus and causes cell death, however it has no cytotoxic effect on H9C2 cells. 16S rRNA shared 99.5% sequence similarity to Streptomyces longispororuber. Optimum biomass and antimicrobial compound production were observed in production medium supplemented with 1.0% maltose and 0.5% yeast extract. The active compound purified from the chloroform extract of the cell-free supernatant was studied by FT-IR, 1H NMR, 13C NMR and LC ESI-MS and identified as aromatic polyketide. β-ketosynthase (KS) domain of the Streptomyces strain revealed 93.2% sequence similarity to the benzoisochromanequinone, an actinorhodin biosynthetic gene cluster of Streptomyces coelicolor A3(2). However, the region synthesizing the secondary metabolite produced by the S. longispororuber was not related to the KS domain of the strain, due to the phenomenon of horizontal gene transfer over the period of evolutionary process, thus generating metabolic compound diversity.}, }
@article {pmid25199561, year = {2015}, author = {Guo, X and Wang, Y and Duan, G and Xue, Z and Wang, L and Wang, P and Qiu, S and Xi, Y and Yang, H}, title = {Detection and analysis of CRISPRs of Shigella.}, journal = {Current microbiology}, volume = {70}, number = {1}, pages = {85-90}, pmid = {25199561}, issn = {1432-0991}, mesh = {Base Sequence ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Dysentery, Bacillary/*microbiology ; Genetic Variation ; Genotype ; Humans ; Molecular Sequence Data ; Shigella/*genetics/isolation &amp; purification ; }, abstract = {The recently discovered CRISPRs (Clustered regularly interspaced short palindromic repeats) and Cas (CRISPR-associated) proteins are a novel genetic barrier that limits horizontal gene transfer in prokaryotes and the CRISPR loci provide a historical view of the exposure of prokaryotes to a variety of foreign genetic elements. The aim of study was to investigate the occurrence and distribution of the CRISPRs in Shigella. A collection of 61 strains of Shigella were screened for the existence of CRISPRs. Three CRISPR loci were identified among 61 shigella strains. CRISPR1/cas loci are detected in 49 strains of shigella. Yet, IS elements were detected in cas gene in some strains. In the remaining 12 Shigella flexneri strains, the CRISPR1/cas locus is deleted and only a cas3' pseudo gene and a repeat sequence are present. The presence of CRISPR2 is frequently accompanied by the emergence of CRISPR1. CRISPR3 loci were present in almost all strains (52/61). The length of CRISPR arrays varied from 1 to 9 spacers. Sequence analysis of the CRISPR arrays revealed that few spacers had matches in the GenBank databases. However, one spacer in CRISPR3 loci matches the cognate cas3 genes and no cas gene was present around CRISPR3 region. Analysis of CRISPR sequences show that CRISPR have little change which makes CRISPR poor genotyping markers. The present study is the first attempt to determine and analyze CRISPRs of shigella isolated from clinical patients.}, }
@article {pmid25197432, year = {2014}, author = {Nandasena, K and Yates, R and Tiwari, R and O'Hara, G and Howieson, J and Ninawi, M and Chertkov, O and Detter, C and Tapia, R and Han, S and Woyke, T and Pitluck, S and Nolan, M and Land, M and Liolios, K and Pati, A and Copeland, A and Kyrpides, N and Ivanova, N and Goodwin, L and Meenakshi, U and Reeve, W}, title = {Complete genome sequence of Mesorhizobium ciceri bv. biserrulae type strain (WSM1271(T)).}, journal = {Standards in genomic sciences}, volume = {9}, number = {3}, pages = {462-472}, pmid = {25197432}, issn = {1944-3277}, abstract = {Mesorhizobium ciceri bv. biserrulae strain WSM1271(T) was isolated from root nodules of the pasture legume Biserrula pelecinus growing in the Mediterranean basin. Previous studies have shown this aerobic, motile, Gram negative, non-spore-forming rod preferably nodulates B. pelecinus - a legume with many beneficial agronomic attributes for sustainable agriculture in Australia. We describe the genome of Mesorhizobium ciceri bv. biserrulae strain WSM1271(T) consisting of a 6,264,489 bp chromosome and a 425,539 bp plasmid that together encode 6,470 protein-coding genes and 61 RNA-only encoding genes.}, }
@article {pmid25196177, year = {2014}, author = {Miller, JH and Novak, JT and Knocke, WR and Pruden, A}, title = {Elevation of antibiotic resistance genes at cold temperatures: implications for winter storage of sludge and biosolids.}, journal = {Letters in applied microbiology}, volume = {59}, number = {6}, pages = {587-593}, doi = {10.1111/lam.12325}, pmid = {25196177}, issn = {1472-765X}, mesh = {Bacteria/*genetics ; *Cold Temperature ; Drug Resistance, Microbial/*genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Integrases/*genetics ; Integrons/genetics ; Seasons ; Sewage/*microbiology ; Wastewater/*microbiology ; }, abstract = {UNLABELLED: Prior research suggests that cold temperatures may stimulate the proliferation of certain antibiotic resistance genes (ARGs) and gene transfer elements during storage of biosolids. This could have important implications on cold weather storage of biosolids, as often required in northern climates until a time suitable for land application. In this study, levels of an integron-associated gene (intI1) and an ARG (sul1) were monitored in biosolids subject to storage at 4, 10 and 20°C. Both intI1 and sul1 were observed to increase during short-term storage (<2 months), but the concentrations returned to background within 4 months. The increases in concentration were more pronounced at lower temperatures than ambient temperatures. Overall, the results suggest that cold stress may induce horizontal gene transfer of integron-associated ARGs and that biosolids storage conditions should be considered prior to land application.<br><br>Wastewater treatment plants have been identified as the hot spots for the proliferation and dissemination of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) to the environment through discharge of treated effluent to water bodies as well as application of biosolids to land. Identifying critical control points within the treatment process may aid in the development of solutions for the reduction of ARGs and ARB and curbing the spread of antibiotic resistance. This study found increases in ARGs during biosolids storage and identifies changes in operational protocols that could help reduce ARG loading to the environment when biosolids are land-applied.}, }
@article {pmid25195866, year = {2015}, author = {Palenik, B}, title = {Molecular mechanisms by which marine phytoplankton respond to their dynamic chemical environment.}, journal = {Annual review of marine science}, volume = {7}, number = {}, pages = {325-340}, doi = {10.1146/annurev-marine-010814-015639}, pmid = {25195866}, issn = {1941-0611}, mesh = {Acclimatization/genetics/*physiology ; Gene Transfer, Horizontal ; Metabolomics/*methods ; Metals/metabolism ; Nitrogen/metabolism ; Oceanography/*methods ; Phosphorus/metabolism ; Phytoplankton/cytology/genetics/metabolism/*physiology ; Seawater/*chemistry ; Silicon Dioxide/metabolism ; }, abstract = {Marine scientists have long been interested in the interactions of marine phytoplankton with their chemical environments. Nutrient availability clearly controls carbon fixation on a global scale, but the interactions between phytoplankton and nutrients are complex and include both short-term responses (seconds to minutes) and longer-term evolutionary adaptations. This review outlines how genomics and functional genomics approaches are providing a better understanding of these complex interactions, especially for cyanobacteria and diatoms, for which the genome sequences of multiple model organisms are available. Transporters and related genes are emerging as the most likely candidates for biomarkers in stress-specific studies, but other genes are also possible candidates. One surprise has been the important role of horizontal gene transfer in mediating chemical-biological interactions.}, }
@article {pmid25193709, year = {2014}, author = {Walter, F and Albersmeier, A and Kalinowski, J and Rückert, C}, title = {Complete genome sequence of Corynebacterium casei LMG S-19264T (=DSM 44701T), isolated from a smear-ripened cheese.}, journal = {Journal of biotechnology}, volume = {189}, number = {}, pages = {76-77}, doi = {10.1016/j.jbiotec.2014.08.038}, pmid = {25193709}, issn = {1873-4863}, mesh = {Cheese/*microbiology ; Corynebacterium/*genetics ; Genome, Bacterial/*genetics ; Molecular Sequence Data ; }, abstract = {We report the complete genome sequence of Corynebacterium casei LMG S-19264(T) (=DSM 44701(T)) which was isolated from the surface of an Irish farmhouse smear-ripened cheese. The genome of C. casei LMG S-19264(T) consists of three replicons: the chromosome (3,113,488 bp, 55.69% G+C content), the plasmid pCASE1 (2461 bp, 56.77% G+C content) and the plasmid pCASE2 (16,264 bp, 55.08% G+C content), encoding a total of 2908 protein coding genes. Analysis of the sequence data revealed a large region of ∼ 98 kb with an average G+C content of ∼ 65% that was acquired by horizontal gene transfer.}, }
@article {pmid25193310, year = {2014}, author = {Iraola, G and Pérez, R and Naya, H and Paolicchi, F and Pastor, E and Valenzuela, S and Calleros, L and Velilla, A and Hernández, M and Morsella, C}, title = {Genomic evidence for the emergence and evolution of pathogenicity and niche preferences in the genus Campylobacter.}, journal = {Genome biology and evolution}, volume = {6}, number = {9}, pages = {2392-2405}, pmid = {25193310}, issn = {1759-6653}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Bacterial Proteins/*genetics/metabolism ; Campylobacter/classification/*genetics/metabolism/*pathogenicity ; Campylobacter Infections/*microbiology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; *Genome, Bacterial ; Genomics ; Humans ; Molecular Sequence Data ; Phylogeny ; }, abstract = {The genus Campylobacter includes some of the most relevant pathogens for human and animal health; the continuous effort in their characterization has also revealed new species putatively involved in different kind of infections. Nowadays, the available genomic data for the genus comprise a wide variety of species with different pathogenic potential and niche preferences. In this work, we contribute to enlarge this available information presenting the first genome for the species Campylobacter sputorum bv. sputorum and use this and the already sequenced organisms to analyze the emergence and evolution of pathogenicity and niche preferences among Campylobacter species. We found that campylobacters can be unequivocally distinguished in established and putative pathogens depending on their repertory of virulence genes, which have been horizontally acquired from other bacteria because the nonpathogenic Campylobacter ancestor emerged, and posteriorly interchanged between some members of the genus. Additionally, we demonstrated the role of both horizontal gene transfers and diversifying evolution in niche preferences, being able to distinguish genetic features associated to the tropism for oral, genital, and gastrointestinal tissues. In particular, we highlight the role of nonsynonymous evolution of disulphide bond proteins, the invasion antigen B (CiaB), and other secreted proteins in the determination of niche preferences. Our results arise from assessing the previously unmet goal of considering the whole available Campylobacter diversity for genome comparisons, unveiling notorious genetic features that could explain particular phenotypes and set the basis for future research in Campylobacter biology.}, }
@article {pmid25191313, year = {2014}, author = {Lux, TM and Lee, R and Love, J}, title = {Genome-wide phylogenetic analysis of the pathogenic potential of Vibrio furnissii.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {435}, pmid = {25191313}, issn = {1664-302X}, abstract = {We recently reported the genome sequence of a free-living strain of Vibrio furnissii (NCTC 11218) harvested from an estuarine environment. V. furnissii is a widespread, free-living proteobacterium and emerging pathogen that can cause acute gastroenteritis in humans and lethal zoonoses in aquatic invertebrates, including farmed crustaceans and molluscs. Here we present the analyses to assess the potential pathogenic impact of V. furnissii. We compared the complete genome of V. furnissii with 8 other emerging and pathogenic Vibrio species. We selected and analyzed more deeply 10 genomic regions based upon unique or common features, and used 3 of these regions to construct a phylogenetic tree. Thus, we positioned V. furnissii more accurately than before and revealed a closer relationship between V. furnissii and V. cholerae than previously thought. However, V. furnissii lacks several important features normally associated with virulence in the human pathogens V. cholera and V. vulnificus. A striking feature of the V. furnissii genome is the hugely increased Super Integron, compared to the other Vibrio. Analyses of predicted genomic islands resulted in the discovery of a protein sequence that is present only in Vibrio associated with diseases in aquatic animals. We also discovered evidence of high levels horizontal gene transfer in V. furnissii. V. furnissii seems therefore to have a dynamic and fluid genome that could quickly adapt to environmental perturbation or increase its pathogenicity. Taken together, these analyses confirm the potential of V. furnissii as an emerging marine and possible human pathogen, especially in the developing, tropical, coastal regions that are most at risk from climate change.}, }
@article {pmid25190099, year = {2015}, author = {Banerjee, R and Chakraborti, P and Bhowmick, R and Mukhopadhyay, S}, title = {Distinct molecular features facilitating ice-binding mechanisms in hyperactive antifreeze proteins closely related to an Antarctic sea ice bacterium.}, journal = {Journal of biomolecular structure &amp; dynamics}, volume = {33}, number = {7}, pages = {1424-1441}, doi = {10.1080/07391102.2014.952665}, pmid = {25190099}, issn = {1538-0254}, mesh = {Amino Acid Sequence ; Antarctic Regions ; Antifreeze Proteins/*chemistry/*genetics ; Bacteria/classification/genetics/metabolism ; Bacterial Proteins/*chemistry/*genetics ; Cluster Analysis ; Codon ; Evolution, Molecular ; Ice Cover/*microbiology ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Protein Conformation ; Selection, Genetic ; Sequence Alignment ; }, abstract = {Antifreeze proteins or ice-binding proteins (IBPs) facilitate the survival of certain cellular organisms in freezing environment by inhibiting the growth of ice crystals in solution. Present study identifies orthologs of the IBP of Colwellia sp. SLW05, which were obtained from a wide range of taxa. Phylogenetic analysis on the basis of conserved regions (predicted as the 'ice-binding domain' [IBD]) present in all the orthologs, separates the bacterial and archaeal orthologs from that of the eukaryotes'. Correspondence analysis pointed out that the bacterial and archaeal IBDs have relatively higher average hydrophobicity than the eukaryotic members. IBDs belonging to bacterial as well as archaeal AFPs contain comparatively more strands, and therefore are revealed to be under higher evolutionary selection pressure. Molecular docking studies prove that the ice crystals form more stable complex with the bacterial as well as archaeal proteins than the eukaryotic orthologs. Analysis of the docked structures have traced out the ice-binding sites (IBSs) in all the orthologs which continue to facilitate ice-binding activity even after getting mutated with respect to the well-studied IBSs of Typhula ishikariensis and notably, all these mutations performing ice-binding using 'anchored clathrate mechanism' have been found to prefer polar and hydrophilic amino acids. Horizontal gene transfer studies point toward a strong selection pressure favoring independent evolution of the IBPs in some polar organisms including prokaryotes as well as eukaryotes because these proteins facilitate the polar organisms to acclimatize to the adversities in their niche, thus safeguarding their existence.}, }
@article {pmid25188293, year = {2014}, author = {Koumandou, VL and Kossida, S}, title = {Evolution of the F0F1 ATP synthase complex in light of the patchy distribution of different bioenergetic pathways across prokaryotes.}, journal = {PLoS computational biology}, volume = {10}, number = {9}, pages = {e1003821}, pmid = {25188293}, issn = {1553-7358}, mesh = {Archaea/classification/*genetics ; Bacteria/classification/*genetics ; DNA, Archaeal/*analysis/chemistry ; DNA, Bacterial/*analysis/chemistry ; Energy Metabolism/genetics ; Phylogeny ; Proton-Translocating ATPases/*chemistry ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; }, abstract = {Bacteria and archaea are characterized by an amazing metabolic diversity, which allows them to persist in diverse and often extreme habitats. Apart from oxygenic photosynthesis and oxidative phosphorylation, well-studied processes from chloroplasts and mitochondria of plants and animals, prokaryotes utilize various chemo- or lithotrophic modes, such as anoxygenic photosynthesis, iron oxidation and reduction, sulfate reduction, and methanogenesis. Most bioenergetic pathways have a similar general structure, with an electron transport chain composed of protein complexes acting as electron donors and acceptors, as well as a central cytochrome complex, mobile electron carriers, and an ATP synthase. While each pathway has been studied in considerable detail in isolation, not much is known about their relative evolutionary relationships. Wanting to address how this metabolic diversity evolved, we mapped the distribution of nine bioenergetic modes on a phylogenetic tree based on 16S rRNA sequences from 272 species representing the full diversity of prokaryotic lineages. This highlights the patchy distribution of many pathways across different lineages, and suggests either up to 26 independent origins or 17 horizontal gene transfer events. Next, we used comparative genomics and phylogenetic analysis of all subunits of the F0F1 ATP synthase, common to most bacterial lineages regardless of their bioenergetic mode. Our results indicate an ancient origin of this protein complex, and no clustering based on bioenergetic mode, which suggests that no special modifications are needed for the ATP synthase to work with different electron transport chains. Moreover, examination of the ATP synthase genetic locus indicates various gene rearrangements in the different bacterial lineages, ancient duplications of atpI and of the beta subunit of the F0 subcomplex, as well as more recent stochastic lineage-specific and species-specific duplications of all subunits. We discuss the implications of the overall pattern of conservation and flexibility of the F0F1 ATP synthase genetic locus.}, }
@article {pmid25187538, year = {2014}, author = {Dziewit, L and Oscik, K and Bartosik, D and Radlinska, M}, title = {Molecular characterization of a novel temperate sinorhizobium bacteriophage, ФLM21, encoding DNA methyltransferase with CcrM-like specificity.}, journal = {Journal of virology}, volume = {88}, number = {22}, pages = {13111-13124}, pmid = {25187538}, issn = {1098-5514}, mesh = {Bacteriophages/*enzymology/*genetics/isolation &amp; purification/ultrastructure ; DNA, Viral/chemistry/genetics ; Genome, Viral ; Mass Spectrometry ; Molecular Sequence Data ; Open Reading Frames ; Sequence Analysis, DNA ; Sinorhizobium/*virology ; Siphoviridae/enzymology/genetics/isolation &amp; purification/ultrastructure ; Site-Specific DNA-Methyltransferase (Adenine-Specific)/*genetics/*metabolism ; Substrate Specificity ; Viral Proteins/chemistry/isolation &amp; purification ; Virion/ultrastructure ; }, abstract = {UNLABELLED: ΦLM21 is a temperate phage isolated from Sinorhizobium sp. strain LM21 (Alphaproteobacteria). Genomic analysis and electron microscopy suggested that ΦLM21 is a member of the family Siphoviridae. The phage has an isometric head and a long noncontractile tail. The genome of ΦLM21 has 50,827 bp of linear double-stranded DNA encoding 72 putative proteins, including proteins responsible for the assembly of the phage particles, DNA packaging, transcription, replication, and lysis. Virion proteins were characterized using mass spectrometry, leading to the identification of the major capsid and tail components, tape measure, and a putative portal protein. We have confirmed the activity of two gene products, a lytic enzyme (a putative chitinase) and a DNA methyltransferase, sharing sequence specificity with the cell cycle-regulating methyltransferase (CcrM) of the bacterial host. Interestingly, the genome of Sinorhizobium phage ΦLM21 shows very limited similarity to other known phage genome sequences and is thus considered unique.<br><br>IMPORTANCE: Prophages are known to play an important role in the genomic diversification of bacteria via horizontal gene transfer. The influence of prophages on pathogenic bacteria is very well documented. However, our knowledge of the overall impact of prophages on the survival of their lysogenic, nonpathogenic bacterial hosts is still limited. In particular, information on prophages of the agronomically important Sinorhizobium species is scarce. In this study, we describe the isolation and molecular characterization of a novel temperate bacteriophage, &#x3a6;LM21, of Sinorhizobium sp. LM21. Since we have not found any similar sequences, we propose that this bacteriophage is a novel species. We conducted a functional analysis of selected proteins. We have demonstrated that the phage DNA methyltransferase has the same sequence specificity as the cell cycle-regulating methyltransferase CcrM of its host. We point out that this phenomenon of mimicking the host regulatory mechanisms by viruses is quite common in bacteriophages.}, }
@article {pmid25187417, year = {2014}, author = {Godziszewska, J and Kulińska, A and Jagura-Burdzy, G}, title = {MobC of conjugative RA3 plasmid from IncU group autoregulates the expression of bicistronic mobC-nic operon and stimulates conjugative transfer.}, journal = {BMC microbiology}, volume = {14}, number = {}, pages = {235}, pmid = {25187417}, issn = {1471-2180}, mesh = {Amino Acid Motifs ; Bacteria/*genetics ; Cluster Analysis ; *Conjugation, Genetic ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; *Operon ; Phylogeny ; *Plasmids ; Protein Multimerization ; Sequence Homology, Amino Acid ; Transcription Factors/*genetics/metabolism ; }, abstract = {BACKGROUND: The IncU conjugative transfer module represents highly efficient promiscuous system widespread among conjugative plasmids of different incompatibility groups. Despite its frequent occurrence the mechanisms of relaxosome formation/action are far from understood. Here we analyzed the putative transfer auxiliary protein MobC of the conjugative plasmid RA3 from the IncU incompatibility group.<br><br>RESULTS: MobC is a protein of 176 amino acids encoded in the bicistronic operon mobC-nic adjacent to oriT. MobC is homologous to prokaryotic transcription factors of the ribbon-helix-helix (RHH) superfamily. Conserved LxxugxNlNQiaxxLn motif clusters MobC with the clade of conjugative transfer auxilliary proteins of MobP relaxases. MobC forms dimers in solution and autoregulates the expression of mobCp by binding to an imperfect palindromic sequence (OM) located between putative -35 and -10 motifs of the promoter. Medium-copy number test plasmid containing the oriT-mobCp region is mobilized with a high frequency by the RA3 conjugative system. The mutations introduced into OM that abolished MobC binding in vitro decreased 2-3 fold the frequency of mobilization of the test plasmids. The deletion of OM within the RA3 conjugative module had no effect on transfer if the mobC-nic operon was expressed from the heterologous promoter. If only nic was expressed from the heterologous promoter (no mobC) the conjugative transfer frequency of such plasmid was 1000-fold lower.<br><br>CONCLUSION: The MobC is an auxiliary transfer protein of dual function. It autoregulates the expression of mobC-nic operon while its presence significantly stimulates transfer efficiency.}, }
@article {pmid25186768, year = {2014}, author = {Douillard, FP and de Vos, WM}, title = {Functional genomics of lactic acid bacteria: from food to health.}, journal = {Microbial cell factories}, volume = {13 Suppl 1}, number = {Suppl 1}, pages = {S8}, pmid = {25186768}, issn = {1475-2859}, support = {250172/ERC_/European Research Council/International ; }, mesh = {Biological Evolution ; *Food Microbiology ; Gastrointestinal Tract/microbiology ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; Lactobacillaceae/classification/*genetics/growth &amp; development ; Mouth Mucosa/microbiology ; Phylogeny ; }, abstract = {Genome analysis using next generation sequencing technologies has revolutionized the characterization of lactic acid bacteria and complete genomes of all major groups are now available. Comparative genomics has provided new insights into the natural and laboratory evolution of lactic acid bacteria and their environmental interactions. Moreover, functional genomics approaches have been used to understand the response of lactic acid bacteria to their environment. The results have been instrumental in understanding the adaptation of lactic acid bacteria in artisanal and industrial food fermentations as well as their interactions with the human host. Collectively, this has led to a detailed analysis of genes involved in colonization, persistence, interaction and signaling towards to the human host and its health. Finally, massive parallel genome re-sequencing has provided new opportunities in applied genomics, specifically in the characterization of novel non-GMO strains that have potential to be used in the food industry. Here, we provide an overview of the state of the art of these functional genomics approaches and their impact in understanding, applying and designing lactic acid bacteria for food and health.}, }
@article {pmid25186071, year = {2014}, author = {Goris, T and Schubert, T and Gadkari, J and Wubet, T and Tarkka, M and Buscot, F and Adrian, L and Diekert, G}, title = {Insights into organohalide respiration and the versatile catabolism of Sulfurospirillum multivorans gained from comparative genomics and physiological studies.}, journal = {Environmental microbiology}, volume = {16}, number = {11}, pages = {3562-3580}, doi = {10.1111/1462-2920.12589}, pmid = {25186071}, issn = {1462-2920}, mesh = {Citric Acid Cycle ; Corrinoids/biosynthesis ; Epsilonproteobacteria/*genetics/*metabolism ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomics ; Hydrocarbons, Halogenated/*metabolism ; Nitrogen Fixation ; Oxidoreductases/genetics ; Reactive Oxygen Species/metabolism ; }, abstract = {Sulfurospirillum multivorans, a free-living ε-proteobacterium, is among the best studied organisms capable of organohalide respiration. It is able to use several halogenated ethenes as terminal electron acceptor. In this report, the complete genome sequence of S. multivorans including a comparison with genome sequences of two related non-dehalogenating species, Sulfurospirillum deleyianum and Sulfurospirillum barnesii, is described. The 3.2 Mbp genome of S. multivorans revealed a ∼ 50 kbp gene region encoding proteins required for organohalide respiration and corrinoid cofactor biosynthesis. This region includes genes for components not detected before in organohalide-respiring organisms. A transcript analysis of genes coding for some of these proteins indicates the involvement of a putative quinol dehydrogenase in organohalide respiration. The presence of genes encoding a variety of oxidoreductases reflects the organism's metabolic versatility. This was confirmed by growth studies with different electron acceptors including perchlorate and several sulfur-containing compounds. A comparison with other ε-proteobacteria indicates horizontal acquisition of many genes in the S. multivorans genome, which might be the basis of the bacterium's catabolic flexibility.}, }
@article {pmid25184564, year = {2014}, author = {Lebeaux, D and Ghigo, JM and Beloin, C}, title = {Biofilm-related infections: bridging the gap between clinical management and fundamental aspects of recalcitrance toward antibiotics.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {78}, number = {3}, pages = {510-543}, pmid = {25184564}, issn = {1098-5557}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology/therapeutic use ; Bacterial Infections/drug therapy/*microbiology ; *Biofilms ; Catheter-Related Infections/drug therapy/*microbiology ; *Drug Resistance, Bacterial ; Escherichia coli/physiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Microbial Viability ; Pseudomonas aeruginosa/physiology ; }, abstract = {Surface-associated microbial communities, called biofilms, are present in all environments. Although biofilms play an important positive role in a variety of ecosystems, they also have many negative effects, including biofilm-related infections in medical settings. The ability of pathogenic biofilms to survive in the presence of high concentrations of antibiotics is called "recalcitrance" and is a characteristic property of the biofilm lifestyle, leading to treatment failure and infection recurrence. This review presents our current understanding of the molecular mechanisms of biofilm recalcitrance toward antibiotics and describes how recent progress has improved our capacity to design original and efficient strategies to prevent or eradicate biofilm-related infections.}, }
@article {pmid25183653, year = {2015}, author = {Juhas, M}, title = {Type IV secretion systems and genomic islands-mediated horizontal gene transfer in Pseudomonas and Haemophilus.}, journal = {Microbiological research}, volume = {170}, number = {}, pages = {10-17}, doi = {10.1016/j.micres.2014.06.007}, pmid = {25183653}, issn = {1618-0623}, mesh = {*Bacterial Secretion Systems ; Drug Resistance, Neoplasm/genetics ; *Gene Transfer, Horizontal ; *Genomic Islands ; Haemophilus/*genetics/*metabolism ; Pseudomonas/*genetics/*metabolism ; }, abstract = {Bacterial secretion systems, such as type IV secretion systems (T4SSs) are multi-subunit machines transferring macromolecules across membranes. Besides proteins, T4SSs also transfer nucleoprotein complexes, thus having a significant impact on the evolution of bacterial species. By T4SS-mediated horizontal gene transfer bacteria can acquire a broad spectrum of fitness genes allowing them to thrive in the wide variety of environments. Furthermore, acquisition of antibiotic-resistance and virulence genes can lead to the emergence of novel 'superbugs'. This review provides an update on the investigation of T4SSs. It highlights the role T4SSs play in the horizontal gene transfer, particularly in the evolution of catabolic pathways, antibiotic-resistance and virulence in Haemophilus and Pseudomonas.}, }
@article {pmid25182643, year = {2014}, author = {Maurya, AP and Talukdar, AD and Chanda, DD and Chakravarty, A and Bhattacharjee, A}, title = {Integron-borne transmission of VEB-1 extended-spectrum β-lactamase in Pseudomonas aeruginosa in a tertiary care hospital in India.}, journal = {Antimicrobial agents and chemotherapy}, volume = {58}, number = {11}, pages = {6966-6969}, pmid = {25182643}, issn = {1098-6596}, mesh = {Amino Acid Sequence ; Anti-Bacterial Agents/pharmacology ; Cephalosporins/*pharmacology ; DNA, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli Proteins ; Gene Transfer, Horizontal/*genetics ; Humans ; India ; Microbial Sensitivity Tests ; Plasmids/genetics ; Polymyxin B/therapeutic use ; Pseudomonas Infections/drug therapy/microbiology ; Pseudomonas aeruginosa/*drug effects/genetics/isolation &amp; purification ; Tertiary Care Centers ; Tertiary Healthcare ; beta-Lactamases/*genetics ; }, abstract = {A total 14 clinical isolates of Pseudomonas aeruginosa that produced VEB-1 and were susceptible only to polymyxin B were recovered from hospitalized patients. VEB-1 was located within variable regions of the class 1 integron, flanked by resistant genes, and was horizontally transferable as well as carried within the IncP-type plasmid. We conclude that the IncP-type plasmid is responsible for the horizontal transmission of VEB-1-mediated expanded-spectrum cephalosporin resistance in this medical center.}, }
@article {pmid25182641, year = {2014}, author = {Vilacoba, E and Quiroga, C and Pistorio, M and Famiglietti, A and Rodríguez, H and Kovensky, J and Déraspe, M and Raymond, F and Roy, PH and Centrón, D}, title = {A blaVIM-2 plasmid disseminating in extensively drug-resistant clinical Pseudomonas aeruginosa and Serratia marcescens isolates.}, journal = {Antimicrobial agents and chemotherapy}, volume = {58}, number = {11}, pages = {7017-7018}, pmid = {25182641}, issn = {1098-6596}, mesh = {Base Sequence ; Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Plasmids ; Pseudomonas Infections/drug therapy/microbiology ; Pseudomonas aeruginosa/*drug effects/*genetics/isolation &amp; purification ; Sequence Analysis, DNA ; Serratia Infections/drug therapy/microbiology ; Serratia marcescens/*drug effects/*genetics/isolation &amp; purification ; beta-Lactamases/*genetics ; }, }
@article {pmid25181446, year = {2014}, author = {Roberts, RG}, title = {Symbiosis plasmids bring their own mutagen to the wedding party.}, journal = {PLoS biology}, volume = {12}, number = {9}, pages = {e1001943}, doi = {10.1371/journal.pbio.1001943}, pmid = {25181446}, issn = {1545-7885}, mesh = {Cupriavidus/*genetics ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genome, Bacterial ; Plasmids/*metabolism ; Ralstonia solanacearum/*genetics ; }, }
@article {pmid25181317, year = {2014}, author = {Remigi, P and Capela, D and Clerissi, C and Tasse, L and Torchet, R and Bouchez, O and Batut, J and Cruveiller, S and Rocha, EP and Masson-Boivin, C}, title = {Transient hypermutagenesis accelerates the evolution of legume endosymbionts following horizontal gene transfer.}, journal = {PLoS biology}, volume = {12}, number = {9}, pages = {e1001942}, pmid = {25181317}, issn = {1545-7885}, mesh = {ATP-Binding Cassette Transporters/genetics ; Adaptation, Physiological/genetics ; Biological Evolution ; Cupriavidus/*genetics ; Fabaceae/microbiology/physiology ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genome, Bacterial ; Mimosa/microbiology/physiology ; Mutation ; Plasmids/*metabolism ; Ralstonia solanacearum/*genetics ; Symbiosis/genetics ; }, abstract = {Horizontal gene transfer (HGT) is an important mode of adaptation and diversification of prokaryotes and eukaryotes and a major event underlying the emergence of bacterial pathogens and mutualists. Yet it remains unclear how complex phenotypic traits such as the ability to fix nitrogen with legumes have successfully spread over large phylogenetic distances. Here we show, using experimental evolution coupled with whole genome sequencing, that co-transfer of imuABC error-prone DNA polymerase genes with key symbiotic genes accelerates the evolution of a soil bacterium into a legume symbiont. Following introduction of the symbiotic plasmid of Cupriavidus taiwanensis, the Mimosa symbiont, into pathogenic Ralstonia solanacearum we challenged transconjugants to become Mimosa symbionts through serial plant-bacteria co-cultures. We demonstrate that a mutagenesis imuABC cassette encoded on the C. taiwanensis symbiotic plasmid triggered a transient hypermutability stage in R. solanacearum transconjugants that occurred before the cells entered the plant. The generated burst in genetic diversity accelerated symbiotic adaptation of the recipient genome under plant selection pressure, presumably by improving the exploration of the fitness landscape. Finally, we show that plasmid imuABC cassettes are over-represented in rhizobial lineages harboring symbiotic plasmids. Our findings shed light on a mechanism that may have facilitated the dissemination of symbiotic competency among α- and β-proteobacteria in natura and provide evidence for the positive role of environment-induced mutagenesis in the acquisition of a complex lifestyle trait. We speculate that co-transfer of complex phenotypic traits with mutagenesis determinants might frequently enhance the ecological success of HGT.}, }
@article {pmid25180848, year = {2014}, author = {García-Aljaro, C and Riera-Heredia, J and Blanch, AR}, title = {Antimicrobial resistance and presence of the SXT mobile element in Vibrio spp. isolated from aquaculture facilities.}, journal = {The new microbiologica}, volume = {37}, number = {3}, pages = {339-346}, pmid = {25180848}, issn = {1121-7138}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; *DNA Transposable Elements ; *Drug Resistance, Multiple, Bacterial ; Fisheries ; Fishes/*microbiology ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Vibrio/classification/*drug effects/*genetics/isolation &amp; purification ; }, abstract = {The aim of this work was to assess the susceptibility of Vibrio spp. strains isolated from fish cultures against some usually applied antibiotics and the occurrence of the SXT mobile genetic element among them. Antimicrobial resistance was assessed by the standard disk diffusion technique while the presence of the SXT mobile genetic element was determined by conventional PCR. High levels of resistance to ampicillin (70%), cefoxitin (44%), streptomycin (31%), aztreonam (25%) and sulfamethoxazole (21%) were detected, and a high inter-and-intraspecies diversity in the resistance profile was observed for the majority of the analysed isolates. The SXT mobile genetic element was detected in only 4 isolates belonging to the species V. diazotrophicus (1), V. mediterranei (2) and V. vulnificus (1), which showed a variable antibiotic resistance profile. Horizontal antibiotic resistance gene transfer from the V. diazotrophicus SXT-positive strain to a laboratory E. coli strain was demonstrated under laboratory conditions. Our results suggest that the Vibrio spp. isolated from aquaculture facilities analysed in this study, although not being pathogenic, they constitute a source of antimicrobial resistance genes that could be mobilized to other bacterial populations through mobile genetic elements. However, the low occurrence of the SXT element in these isolates supports the hypothesis that this element is not involved in the development of resistance in the majority of Vibrio spp. in the examined aquaculture facilities.}, }
@article {pmid25179686, year = {2014}, author = {Mikhailov, KV and Janouškovec, J and Tikhonenkov, DV and Mirzaeva, GS and Diakin, AY and Simdyanov, TG and Mylnikov, AP and Keeling, PJ and Aleoshin, VV}, title = {A complex distribution of elongation family GTPases EF1A and EFL in basal alveolate lineages.}, journal = {Genome biology and evolution}, volume = {6}, number = {9}, pages = {2361-2367}, pmid = {25179686}, issn = {1759-6653}, support = {MOP-42517//Canadian Institutes of Health Research/Canada ; }, mesh = {Alveolata/classification/*enzymology/*genetics ; Evolution, Molecular ; GTP Phosphohydrolases/*genetics ; Gene Transfer, Horizontal ; Molecular Sequence Data ; *Multigene Family ; Phylogeny ; Protozoan Proteins/*genetics ; }, abstract = {Translation elongation factor-1 alpha (EF1A) and the related GTPase EF-like (EFL) are two proteins with a complex mutually exclusive distribution across the tree of eukaryotes. Recent surveys revealed that the distribution of the two GTPases in even closely related taxa is frequently at odds with their phylogenetic relationships. Here, we investigate the distribution of EF1A and EFL in the alveolate supergroup. Alveolates comprise three major lineages: ciliates and apicomplexans encode EF1A, whereas dinoflagellates encode EFL. We searched transcriptome databases for seven early-diverging alveolate taxa that do not belong to any of these groups: colpodellids, chromerids, and colponemids. Current data suggest all seven are expected to encode EF1A, but we find three genera encode EFL: Colpodella, Voromonas, and the photosynthetic Chromera. Comparing this distribution with the phylogeny of alveolates suggests that EF1A and EFL evolution in alveolates cannot be explained by a simple horizontal gene transfer event or lineage sorting.}, }
@article {pmid25175817, year = {2014}, author = {Hooton, SP and Timms, AR and Cummings, NJ and Moreton, J and Wilson, R and Connerton, IF}, title = {The complete plasmid sequences of Salmonella enterica serovar Typhimurium U288.}, journal = {Plasmid}, volume = {76}, number = {}, pages = {32-39}, doi = {10.1016/j.plasmid.2014.08.002}, pmid = {25175817}, issn = {1095-9890}, mesh = {Conjugation, Genetic ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Integrons ; Plasmids/drug effects/*genetics ; Salmonella typhimurium/*genetics/pathogenicity ; Sequence Analysis, DNA ; }, abstract = {Salmonella enterica Serovar Typhimurium U288 is an emerging pathogen of pigs. The strain contains three plasmids of diverse origin that encode traits that are of concern for food security and safety, these include antibiotic resistant determinants, an array of functions that can modify cell physiology and permit genetic mobility. At 148,711 bp, pSTU288-1 appears to be a hybrid plasmid containing a conglomerate of genes found in pSLT of S. Typhimurium LT2, coupled with a mosaic of horizontally-acquired elements. Class I integron containing gene cassettes conferring resistance against clinically important antibiotics and compounds are present in pSTU288-1. A curious feature of the plasmid involves the deletion of two genes encoded in the Salmonella plasmid virulence operon (spvR and spvA) following the insertion of a tnpA IS26-like element coupled to a blaTEM gene. The spv operon is considered to be a major plasmid-encoded Salmonella virulence factor that is essential for the intracellular lifecycle. The loss of the positive regulator SpvR may impact on the pathogenesis of S. Typhimurium U288. A second 11,067 bp plasmid designated pSTU288-2 contains further antibiotic resistance determinants, as well as replication and mobilization genes. Finally, a small 4675 bp plasmid pSTU288-3 was identified containing mobilization genes and a pleD-like G-G-D/E-E-F conserved domain protein that modulate intracellular levels of cyclic di-GMP, and are associated with motile to sessile transitions in growth.}, }
@article {pmid25173757, year = {2014}, author = {Mortimer, TD and Pepperell, CS}, title = {Genomic signatures of distributive conjugal transfer among mycobacteria.}, journal = {Genome biology and evolution}, volume = {6}, number = {9}, pages = {2489-2500}, pmid = {25173757}, issn = {1759-6653}, support = {T32 GM007215/GM/NIGMS NIH HHS/United States ; T32 GM07215/GM/NIGMS NIH HHS/United States ; }, mesh = {*Conjugation, Genetic ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomics ; Humans ; Mycobacterium/classification/*genetics/isolation &amp; purification ; Mycobacterium Infections/microbiology ; Phylogeny ; Recombination, Genetic ; }, abstract = {Distributive conjugal transfer (DCT) is a newly described mechanism of lateral gene transfer (LGT) that results in a mosaic transconjugant structure, similar to the products of meiosis. We have tested popular LGT detection methods on whole-genome sequence data from experimental DCT transconjugants and used the best performing methods to compare genomic signatures of DCT with those of LGT through natural transformation, conjugative plasmids, and mobile genetic elements (MGE). We found that DCT results in transfer of larger chromosomal segments, that these segments are distributed more broadly around the chromosome, and that a greater proportion of the chromosome is affected by DCT than by other mechanisms of LGT. We used the best performing methods to characterize LGT in Mycobacterium canettii, the mycobacterial species most closely related to Mycobacterium tuberculosis. Patterns of LGT among M. canettii were highly distinctive. Gene flow appeared unidirectional, from lineages with minimal evidence of LGT to isolates with a substantial proportion (6-13%) of sites identified as recombinant. Among M. canettii isolates with evidence of LGT, recombinant fragments were larger and more evenly distributed relative to bacteria that undergo LGT through natural transformation, conjugative plasmids, and MGE. Spatial bias in M. canettii was also unusual in that patterns of recombinant fragment sharing mirrored overall phylogenetic structure. Based on the proportion of recombinant sites, the size of recombinant fragments, their spatial distribution and lack of association with MGE, as well as unidirectionality of DNA transfer, we conclude that DCT is the predominant mechanism of LGT among M. canettii.}, }
@article {pmid25172905, year = {2014}, author = {Parisot, N and Pelin, A and Gasc, C and Polonais, V and Belkorchia, A and Panek, J and El Alaoui, H and Biron, DG and Brasset, E and Vaury, C and Peyret, P and Corradi, N and Peyretaillade, &#xc9; and Lerat, E}, title = {Microsporidian genomes harbor a diverse array of transposable elements that demonstrate an ancestry of horizontal exchange with metazoans.}, journal = {Genome biology and evolution}, volume = {6}, number = {9}, pages = {2289-2300}, pmid = {25172905}, issn = {1759-6653}, mesh = {*DNA Transposable Elements ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Fungal ; Humans ; Microsporidia/classification/*genetics/isolation &amp; purification ; Molecular Sequence Data ; Mycoses/*microbiology ; Phylogeny ; }, abstract = {Microsporidian genomes are the leading models to understand the streamlining in response to a pathogenic lifestyle; they are gene-poor and often possess small genomes. In this study, we show a feature of microsporidian genomes that contrasts this pattern of genome reduction. Specifically, genome investigations targeted at Anncaliia algerae, a human pathogen with a genome size of 23 Mb, revealed the presence of a hitherto undetected diversity in transposable elements (TEs). A total of 240 TE families per genome were identified, exceeding that found in many free-living fungi, and searches of microsporidian species revealed that these mobile elements represent a significant portion of their coding repertoire. Their phylogenetic analysis revealed that many cases of ancestry involve recent and bidirectional horizontal transfers with metazoans. The abundance and horizontal transfer origin of microsporidian TEs highlight a novel dimension of genome evolution in these intracellular pathogens, demonstrating that factors beyond reduction are at play in their diversification.}, }
@article {pmid25169983, year = {2014}, author = {Ternes, CM and Schönknecht, G}, title = {Gene transfers shaped the evolution of de novo NAD+ biosynthesis in eukaryotes.}, journal = {Genome biology and evolution}, volume = {6}, number = {9}, pages = {2335-2349}, pmid = {25169983}, issn = {1759-6653}, mesh = {Animals ; Eukaryota/classification/genetics/*metabolism ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Humans ; Metabolic Networks and Pathways ; NAD/*biosynthesis ; Phylogeny ; }, abstract = {NAD(+) is an essential molecule for life, present in each living cell. It can function as an electron carrier or cofactor in redox biochemistry and energetics, and serves as substrate to generate the secondary messenger cyclic ADP ribose and nicotinic acid adenine dinucleotide phosphate. Although de novo NAD(+) biosynthesis is essential, different metabolic pathways exist in different eukaryotic clades. The kynurenine pathway starting with tryptophan was most likely present in the last common ancestor of all eukaryotes, and is active in fungi and animals. The aspartate pathway, detected in most photosynthetic eukaryotes, was probably acquired from the cyanobacterial endosymbiont that gave rise to chloroplasts. An evolutionary analysis of enzymes catalyzing de novo NAD(+) biosynthesis resulted in evolutionary trees incongruent with established organismal phylogeny, indicating numerous gene transfers. Endosymbiotic gene transfers probably introduced the aspartate pathway into eukaryotes and may have distributed it among different photosynthetic clades. In addition, several horizontal gene transfers substituted eukaryotic genes with bacterial orthologs. Although horizontal gene transfer is accepted as a key mechanism in prokaryotic evolution, it is supposed to be rare in eukaryotic evolution. The essential metabolic pathway of de novo NAD(+) biosynthesis in eukaryotes was shaped by numerous gene transfers.}, }
@article {pmid25168586, year = {2014}, author = {Ioannidis, P and Lu, Y and Kumar, N and Creasy, T and Daugherty, S and Chibucos, MC and Orvis, J and Shetty, A and Ott, S and Flowers, M and Sengamalay, N and Tallon, LJ and Pick, L and Dunning Hotopp, JC}, title = {Rapid transcriptome sequencing of an invasive pest, the brown marmorated stink bug Halyomorpha halys.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {738}, pmid = {25168586}, issn = {1471-2164}, mesh = {Animals ; Bacteria/genetics ; Bacterial Proteins/genetics ; Computational Biology/methods ; Female ; Gene Expression Profiling/*methods ; Gene Transfer, Horizontal ; Heteroptera/*genetics/microbiology ; Insect Proteins/*genetics ; Introduced Species ; Male ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, RNA/*methods ; Symbiosis ; }, abstract = {BACKGROUND: Halyomorpha halys (Stål) (Insecta:Hemiptera;Pentatomidae), commonly known as the Brown Marmorated Stink Bug (BMSB), is an invasive pest of the mid-Atlantic region of the United States, causing economically important damage to a wide range of crops. Native to Asia, BMSB was first observed in Allentown, PA, USA, in 1996, and this pest is now well-established throughout the US mid-Atlantic region and beyond. In addition to the serious threat BMSB poses to agriculture, BMSB has become a nuisance to homeowners, invading home gardens and congregating in large numbers in human-made structures, including homes, to overwinter. Despite its significance as an agricultural pest with limited control options, only 100 bp of BMSB sequence data was available in public databases when this project began.<br><br>RESULTS: Transcriptome sequencing was undertaken to provide a molecular resource to the research community to inform the development of pest control strategies and to provide molecular data for population genetics studies of BMSB. Using normalized, strand-specific libraries, we sequenced pools of all BMSB life stages on the Illumina HiSeq. Trinity was used to assemble 200,000 putative transcripts in >100,000 components. A novel bioinformatic method that analyzed the strand-specificity of the data reduced this to 53,071 putative transcripts from 18,573 components. By integrating multiple other data types, we narrowed this further to 13,211 representative transcripts.<br><br>CONCLUSIONS: Bacterial endosymbiont genes were identified in this dataset, some of which have a copy number consistent with being lateral gene transfers between endosymbiont genomes and Hemiptera, including ankyrin-repeat related proteins, lysozyme, and mannanase. Such genes and endosymbionts may provide novel targets for BMSB-specific biocontrol. This study demonstrates the utility of strand-specific sequencing in generating shotgun transcriptomes and that rapid sequencing shotgun transcriptomes is possible without the need for extensive inbreeding to generate homozygous lines. Such sequencing can provide a rapid response to pest invasions similar to that already described for disease epidemiology.}, }
@article {pmid25165618, year = {2014}, author = {Husain, F and Veeranagouda, Y and Boente, R and Tang, K and Mulato, G and Wexler, HM}, title = {The Ellis Island Effect: A novel mobile element in a multi-drug resistant Bacteroides fragilis clinical isolate includes a mosaic of resistance genes from Gram-positive bacteria.}, journal = {Mobile genetic elements}, volume = {4}, number = {}, pages = {e29801}, pmid = {25165618}, issn = {2159-2543}, support = {R21 AI109545/AI/NIAID NIH HHS/United States ; }, abstract = {Objectives: Bacteroides fragilis, a Gram-negative anaerobic bacterium, is alternately a gut commensal or virulent pathogen and is an important reservoir for horizontal gene transfer (HGT) of bacterial resistance and virulence genes in the human gastrointestinal tract. We identified a unique conjugative transposon (CTn) in a multidrug resistant clinical isolate of B. fragilis (BF-HMW615); we named this element CTnHyb because it included a hybrid mosaic of foreign elements. This study reports the characterization of CTnHyb and discusses the potential impact on horizontal spread of resistance genes. Results: CTnHyb contains several efflux pump genes and several genes that confer or may confer antibiotic resistance to tetracycline, kanamycin, metronidazole and spectinomycin (truncated gene). CTnHyb also contains a mosaic of mobile elements from Gram-positive organisms. CTnHyb is easily transferred from BF-HMW615 (the original isolate) to BF638R (lab strain) and integrated into the BF638R chromosome. The "foreign" (from Gram-positive bacteria) nucleotide sequences within CTnHyb were > 99% preserved indicating that the gene acquisition from the Gram-positive bacteria was very recent. Conclusion: CTnHyb is a novel CTn residing in a multidrug resistant strain of B. fragilis. The global nature and wide phylogenetic reach of HGT means that any gene in any bacterium can potentially be mobilized. Understanding the mechanisms that drive the formation and transfer of these elements and, potentially, ways to limit the transfer are necessary to prevent a devastating spread of resistance elements.}, }
@article {pmid25163544, year = {2014}, author = {Li, X and Deng, Z and Liu, Z and Yan, Y and Wang, T and Xie, J and Lin, M and Cheng, Q and Chen, S}, title = {The genome of Paenibacillus sabinae T27 provides insight into evolution, organization and functional elucidation of nif and nif-like genes.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {723}, pmid = {25163544}, issn = {1471-2164}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/*genetics ; *Evolution, Molecular ; Genes, Bacterial/*genetics ; *Genomics ; Molecular Sequence Data ; Multigene Family/genetics ; Nitrogen Fixation/*genetics ; Nitrogenase/chemistry/genetics/metabolism ; Operon/genetics ; Paenibacillus/*genetics/*metabolism ; Rhizosphere ; }, abstract = {BACKGROUND: Most biological nitrogen fixation is catalyzed by the molybdenum nitrogenase. This enzyme is a complex which contains the MoFe protein encoded by nifDK and the Fe protein encoded by nifH. In addition to nifHDK, nifHDK-like genes were found in some Archaea and Firmicutes, but their function is unclear.<br><br>RESULTS: We sequenced the genome of Paenibacillus sabinae T27. A total of 4,793 open reading frames were predicted from its 5.27 Mb genome. The genome of P. sabinae T27 contains fifteen nitrogen fixation (nif) genes, including three nifH, one nifD, one nifK, four nifB, two nifE, two nifN, one nifX and one nifV. Of the 15 nif genes, eight nif genes (nifB, nifH, nifD, nifK, nifE, nifN, nifX and nifV) and two non-nif genes (orf1 and hesA) form a complete nif gene cluster. In addition to the nif genes, there are nitrogenase-like genes, including two nifH-like genes and five pairs of nifDK-like genes. IS elements on the flanking regions of nif and nif-like genes imply that these genes might have been obtained by horizontal gene transfer. Phylogenies of the concatenated 8 nif gene (nifB, nifH, nifD, nifK, nifE, nifN, nifX and nifV) products suggest that P. sabinae T27 is closely related to Frankia. RT-PCR analysis showed that the complete nif gene cluster is organized as an operon. We demonstrated that the complete nif gene cluster under the control of &#x3c3;70-dependent promoter enabled Escherichia coli JM109 to fix nitrogen. Also, here for the first time we demonstrated that unlike nif genes, the transcriptions of nifHDK-like genes were not regulated by ammonium and oxygen, and nifH-like or nifD-like gene could not restore the nitrogenase activity of Klebsiella pneumonia nifH- and nifD- mutant strains, respectively, suggesting that nifHDK-like genes were not involved in nitrogen fixation.<br><br>CONCLUSIONS: Our data and analysis reveal the contents and distribution of nif and nif-like genes and contribute to the study of evolutionary history of nitrogen fixation in Paenibacillus. For the first time we demonstrated that the transcriptions of nifHDK-like genes were not regulated by ammonium and oxygen and nifHDK-like genes were not involved in nitrogen fixation.}, }
@article {pmid25161648, year = {2014}, author = {Roy Chowdhury, P and McKinnon, J and Wyrsch, E and Hammond, JM and Charles, IG and Djordjevic, SP}, title = {Genomic interplay in bacterial communities: implications for growth promoting practices in animal husbandry.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {394}, pmid = {25161648}, issn = {1664-302X}, abstract = {The discovery of antibiotics heralded the start of a "Golden Age" in the history of medicine. Over the years, the use of antibiotics extended beyond medical practice into animal husbandry, aquaculture and agriculture. Now, however, we face the worldwide threat of diseases caused by pathogenic bacteria that are resistant to all existing major classes of antibiotic, reflecting the possibility of an end to the antibiotic era. The seriousness of the threat is underscored by the severely limited production of new classes of antibiotics. Evolution of bacteria resistant to multiple antibiotics results from the inherent genetic capability that bacteria have to adapt rapidly to changing environmental conditions. Consequently, under antibiotic selection pressures, bacteria have acquired resistance to all classes of antibiotics, sometimes very shortly after their introduction. Arguably, the evolution and rapid dissemination of multiple drug resistant genes en-masse across microbial pathogens is one of the most serious threats to human health. In this context, effective surveillance strategies to track the development of resistance to multiple antibiotics are vital to managing global infection control. These surveillance strategies are necessary for not only human health but also for animal health, aquaculture and plant production. Shortfalls in the present surveillance strategies need to be identified. Raising awareness of the genetic events that promote co-selection of resistance to multiple antimicrobials is an important prerequisite to the design and implementation of molecular surveillance strategies. In this review we will discuss how lateral gene transfer (LGT), driven by the use of low-dose antibiotics in animal husbandry, has likely played a significant role in the evolution of multiple drug resistance (MDR) in Gram-negative bacteria and has complicated molecular surveillance strategies adopted for predicting imminent resistance threats.}, }
@article {pmid25160847, year = {2014}, author = {Hao, J and Jia, X and Yu, J and Deng, S}, title = {Direct visualization of horizontal gene transfer in cotton plants.}, journal = {The Journal of heredity}, volume = {105}, number = {6}, pages = {834-836}, doi = {10.1093/jhered/esu052}, pmid = {25160847}, issn = {1465-7333}, mesh = {DNA, Chloroplast/genetics ; DNA, Plant/genetics ; Flowers/*anatomy &amp; histology ; *Gene Transfer, Horizontal ; Gossypium/*genetics ; Inheritance Patterns ; Phenotype ; Seeds/*anatomy &amp; histology ; }, abstract = {Plant mitochondrial and chloroplast genes that underwent horizontal transfer have been identified by parasite and grafting systems, respectively. Here, we directly observed 3 horizontal gene transfer (HGT) events in the 45 second axillary shoots of grafted cotton plants (Gossypium barbadense and Gossypium hirsutum) after extirpating the first axillary bud. The second axillary shoots showed phenotypic variations in cotton flowers and seeds that were evidence of spontaneous development from cells in the grafting site. As the progeny segregated and did not show stable inheritance across 3 generations, inheritance of traits in our study differed from the stable heredity of HGT plants in previous studies. In those studies, plants were artificially regenerated from the graft junctions, and inheritance involved only the movement of chloroplast DNA or genomic material between cells. Our findings may provide a feasible method to enhance plant breeding and the study of HGT.}, }
@article {pmid25159222, year = {2014}, author = {Zhu, Q and Kosoy, M and Dittmar, K}, title = {HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {717}, pmid = {25159222}, issn = {1471-2164}, mesh = {Computer Simulation ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Genomics ; Models, Genetic ; Rickettsia/genetics ; Search Engine ; *Software ; }, abstract = {BACKGROUND: First pass methods based on BLAST match are commonly used as an initial step to separate the different phylogenetic histories of genes in microbial genomes, and target putative horizontal gene transfer (HGT) events. This will continue to be necessary given the rapid growth of genomic data and the technical difficulties in conducting large-scale explicit phylogenetic analyses. However, these methods often produce misleading results due to their inability to resolve indirect phylogenetic links and their vulnerability to stochastic events.<br><br>RESULTS: A new computational method of rapid, exhaustive and genome-wide detection of HGT was developed, featuring the systematic analysis of BLAST hit distribution patterns in the context of a priori defined hierarchical evolutionary categories. Genes that fall beyond a series of statistically determined thresholds are identified as not adhering to the typical vertical history of the organisms in question, but instead having a putative horizontal origin. Tests on simulated genomic data suggest that this approach effectively targets atypically distributed genes that are highly likely to be HGT-derived, and exhibits robust performance compared to conventional BLAST-based approaches. This method was further tested on real genomic datasets, including Rickettsia genomes, and was compared to previous studies. Results show consistency with currently employed categories of HGT prediction methods. In-depth analysis of both simulated and real genomic data suggests that the method is notably insensitive to stochastic events such as gene loss, rate variation and database error, which are common challenges to the current methodology. An automated pipeline was created to implement this approach and was made publicly available at: https://github.com/DittmarLab/HGTector. The program is versatile, easily deployed, has a low requirement for computational resources.<br><br>CONCLUSIONS: HGTector is an effective tool for initial or standalone large-scale discovery of candidate HGT-derived genes.}, }
@article {pmid25158906, year = {2014}, author = {Kumar, D and Mondal, AK and Yadav, AK and Dash, D}, title = {Discovery of rare protein-coding genes in model methylotroph Methylobacterium extorquens AM1.}, journal = {Proteomics}, volume = {14}, number = {23-24}, pages = {2790-2794}, doi = {10.1002/pmic.201400153}, pmid = {25158906}, issn = {1615-9861}, mesh = {Bacterial Proteins/genetics/*metabolism ; Computational Biology/*methods ; Genome, Bacterial/*genetics ; Methylobacterium extorquens/genetics/*metabolism ; }, abstract = {Proteogenomics involves the use of MS to refine annotation of protein-coding genes and discover genes in a genome. We carried out comprehensive proteogenomic analysis of Methylobacterium extorquens AM1 (ME-AM1) from publicly available proteomics data with a motive to improve annotation for methylotrophs; organisms capable of surviving in reduced carbon compounds such as methanol. Besides identifying 2482(50%) proteins, 29 new genes were discovered and 66 annotated gene models were revised in ME-AM1 genome. One such novel gene is identified with 75 peptides, lacks homolog in other methylobacteria but has glycosyl transferase and lipopolysaccharide biosynthesis protein domains, indicating its potential role in outer membrane synthesis. Many novel genes are present only in ME-AM1 among methylobacteria. Distant homologs of these genes in unrelated taxonomic classes and low GC-content of few genes suggest lateral gene transfer as a potential mode of their origin. Annotations of methylotrophy related genes were also improved by the discovery of a short gene in methylotrophy gene island and redefining a gene important for pyrroquinoline quinone synthesis, essential for methylotrophy. The combined use of proteogenomics and rigorous bioinformatics analysis greatly enhanced the annotation of protein-coding genes in model methylotroph ME-AM1 genome.}, }
@article {pmid25157257, year = {2014}, author = {Matveeva, TV and Lutova, LA}, title = {Horizontal gene transfer from Agrobacterium to plants.}, journal = {Frontiers in plant science}, volume = {5}, number = {}, pages = {326}, pmid = {25157257}, issn = {1664-462X}, abstract = {Most genetic engineering of plants uses Agrobacterium mediated transformation to introduce novel gene content. In nature, insertion of T-DNA in the plant genome and its subsequent transfer via sexual reproduction has been shown in several species in the genera Nicotiana and Linaria. In these natural examples of horizontal gene transfer from Agrobacterium to plants, the T-DNA donor is assumed to be a mikimopine strain of A. rhizogenes. A sequence homologous to the T-DNA of the Ri plasmid of Agrobacterium rhizogenes was found in the genome of untransformed Nicotiana glauca about 30 years ago, and was named "cellular T-DNA" (cT-DNA). It represents an imperfect inverted repeat and contains homologs of several T-DNA oncogenes (NgrolB, NgrolC, NgORF13, NgORF14) and an opine synthesis gene (Ngmis). A similar cT-DNA has also been found in other species of the genus Nicotiana. These presumably ancient homologs of T-DNA genes are still expressed, indicating that they may play a role in the evolution of these plants. Recently T-DNA has been detected and characterized in Linaria vulgaris and L. dalmatica. In Linaria vulgaris the cT-DNA is present in two copies and organized as a tandem imperfect direct repeat, containing LvORF2, LvORF3, LvORF8, LvrolA, LvrolB, LvrolC, LvORF13, LvORF14, and the Lvmis genes. All L. vulgaris and L. dalmatica plants screened contained the same T-DNA oncogenes and the mis gene. Evidence suggests that there were several independent T-DNA integration events into the genomes of these plant genera. We speculate that ancient plants transformed by A. rhizogenes might have acquired a selective advantage in competition with the parental species. Thus, the events of T-DNA insertion in the plant genome might have affected their evolution, resulting in the creation of new plant species. In this review we focus on the structure and functions of cT-DNA in Linaria and Nicotiana and discuss their possible evolutionary role.}, }
@article {pmid25156377, year = {2014}, author = {Muniesa, M and Jofre, J}, title = {Identifying and analyzing bacteriophages in human fecal samples: what could we discover?.}, journal = {Future microbiology}, volume = {9}, number = {7}, pages = {879-886}, doi = {10.2217/fmb.14.47}, pmid = {25156377}, issn = {1746-0921}, mesh = {Bacteria/chemistry/cytology/isolation &amp; purification ; Bacteriophages/classification/genetics/*isolation &amp; purification ; Feces/microbiology/*virology ; Humans ; Intestines/microbiology/virology ; Microbiota ; }, abstract = {The human gut is a complex ecosystem, densely populated with microbes including enormous amounts of phages. Metagenomic studies indicate a great diversity of bacteriophages, and because of the variety of gut bacterial species, the human or animal gut is probably a perfect ecological niche for phages that can infect and propagate in their bacterial communities. In addition, some phages have the capacity to mobilize genes, as demonstrated by the enormous fraction of phage particles in feces that contain bacterial DNA. All these facts indicate that, through predation and horizontal gene transfer, bacteriophages play a key role in shaping the size, structure and function of intestinal microbiomes, although our understanding of their effects on gut bacterial populations is only just beginning.}, }
@article {pmid25155269, year = {2014}, author = {Fagerlund, A and Granum, PE and Håvarstein, LS}, title = {Staphylococcus aureus competence genes: mapping of the SigH, ComK1 and ComK2 regulons by transcriptome sequencing.}, journal = {Molecular microbiology}, volume = {94}, number = {3}, pages = {557-579}, doi = {10.1111/mmi.12767}, pmid = {25155269}, issn = {1365-2958}, mesh = {Bacterial Proteins ; *DNA Transformation Competence ; Gene Expression Profiling ; *Gene Expression Regulation, Bacterial ; *Regulon ; Sequence Analysis, DNA ; Sigma Factor ; Staphylococcus aureus/*genetics ; Transcription Factors/*genetics/metabolism ; Transformation, Bacterial ; }, abstract = {Staphylococcus aureus is a major human pathogen. Hospital infections caused by methicillin-resistant strains (MRSA), which have acquired resistance to a broad spectrum of antibiotics through horizontal gene transfer (HGT), are of particular concern. In S. aureus, virulence and antibiotic resistance genes are often encoded on mobile genetic elements that are disseminated by HGT. Conjugation and phage transduction have long been known to mediate HGT in this species, but it is unclear whether natural genetic transformation contributes significantly to the process. Recently, it was reported that expression of the alternative sigma factor SigH induces the competent state in S. aureus. The transformation efficiency obtained, however, was extremely low, indicating that the optimal conditions for competence development had not been found. We therefore used transcriptome sequencing to determine whether the full set of genes known to be required for competence in other naturally transformable bacteria is part of the SigH regulon. Our results show that several essential competence genes are not controlled by SigH. This presumably explains the low transformation efficiency previously reported, and demonstrates that additional regulating mechanisms must be involved. We found that one such mechanism involves ComK1, a transcriptional activator that acts synergistically with SigH.}, }
@article {pmid25154632, year = {2015}, author = {Cabezón, E and Ripoll-Rozada, J and Peña, A and de la Cruz, F and Arechaga, I}, title = {Towards an integrated model of bacterial conjugation.}, journal = {FEMS microbiology reviews}, volume = {39}, number = {1}, pages = {81-95}, doi = {10.1111/1574-6976.12085}, pmid = {25154632}, issn = {1574-6976}, mesh = {Bacteria/*genetics/*metabolism ; Bacterial Proteins/metabolism ; Bacterial Secretion Systems/physiology ; Conjugation, Genetic/genetics/*physiology ; DNA, Bacterial/genetics ; Models, Biological ; Protein Transport ; }, abstract = {Bacterial conjugation is one of the main mechanisms for horizontal gene transfer. It constitutes a key element in the dissemination of antibiotic resistance and virulence genes to human pathogenic bacteria. DNA transfer is mediated by a membrane-associated macromolecular machinery called Type IV secretion system (T4SS). T4SSs are involved not only in bacterial conjugation but also in the transport of virulence factors by pathogenic bacteria. Thus, the search for specific inhibitors of different T4SS components opens a novel approach to restrict plasmid dissemination. This review highlights recent biochemical and structural findings that shed new light on the molecular mechanisms of DNA and protein transport by T4SS. Based on these data, a model for pilus biogenesis and substrate transfer in conjugative systems is proposed. This model provides a renewed view of the mechanism that might help to envisage new strategies to curb the threating expansion of antibiotic resistance.}, }
@article {pmid25152272, year = {2014}, author = {Sherrard, LJ and Tunney, MM and Elborn, JS}, title = {Antimicrobial resistance in the respiratory microbiota of people with cystic fibrosis.}, journal = {Lancet (London, England)}, volume = {384}, number = {9944}, pages = {703-713}, doi = {10.1016/S0140-6736(14)61137-5}, pmid = {25152272}, issn = {1474-547X}, mesh = {Anti-Bacterial Agents/*pharmacology ; Chronic Disease ; Cystic Fibrosis/*drug therapy/*microbiology ; Disease Progression ; Drug Resistance, Multiple, Bacterial ; Humans ; Microbiota/*drug effects ; Respiratory System/*drug effects/*microbiology/pathology ; Respiratory Tract Infections/*drug therapy/*microbiology ; }, abstract = {Cystic fibrosis is characterised by chronic polymicrobial infection and inflammation in the airways of patients. Antibiotic treatment regimens, targeting recognised pathogens, have substantially contributed to increased life expectancy of patients with this disease. Although the emergence of antimicrobial resistance and selection of highly antibiotic-resistant bacterial strains is of major concern, the clinical relevance in cystic fibrosis is yet to be defined. Resistance has been identified in recognised cystic fibrosis pathogens and in other bacteria (eg, Prevotella and Streptococcus spp) detected in the airway microbiota, but their role in the pathophysiology of infection and inflammation in chronic lung disease is unclear. Increased antibiotic resistance in cystic fibrosis might be attributed to a range of complex factors including horizontal gene transfer, hypoxia, and biofilm formation. Strategies to manage antimicrobial resistance consist of new antibiotics or localised delivery of antimicrobial agents, iron sequestration, inhibition of quorum-sensing, and resistome analysis. Determination of the contributions of every bacterial species to lung health or disease in cystic fibrosis might also have an important role in the management of antibiotic resistance.}, }
@article {pmid25151044, year = {2014}, author = {Cox, DG and Oh, J and Keasling, A and Colson, KL and Hamann, MT}, title = {The utility of metabolomics in natural product and biomarker characterization.}, journal = {Biochimica et biophysica acta}, volume = {1840}, number = {12}, pages = {3460-3474}, pmid = {25151044}, issn = {0006-3002}, support = {R01 AT007318/AT/NCCIH NIH HHS/United States ; }, abstract = {BACKGROUND: Metabolomics is a well-established rapidly developing research field involving quantitative and qualitative metabolite assessment within biological systems. Recent improvements in metabolomics technologies reveal the unequivocal value of metabolomics tools in natural products discovery, gene-function analysis, systems biology and diagnostic platforms.<br><br>SCOPE OF REVIEW: We review here some of the prominent metabolomics methodologies employed in data acquisition and analysis of natural products and disease-related biomarkers.<br><br>MAJOR CONCLUSIONS: This review demonstrates that metabolomics represents a highly adaptable technology with diverse applications ranging from environmental toxicology to disease diagnosis. Metabolomic analysis is shown to provide a unique snapshot of the functional genetic status of an organism by examining its biochemical profile, with relevance toward resolving phylogenetic associations involving horizontal gene transfer and distinguishing subgroups of genera possessing high genetic homology, as well as an increasing role in both elucidating biosynthetic transformations of natural products and detecting preclinical biomarkers of numerous disease states.<br><br>GENERAL SIGNIFICANCE: This review expands the interest in multiplatform combinatorial metabolomic analysis. The applications reviewed range from phylogenetic assignment, biosynthetic transformations of natural products, and the detection of preclinical biomarkers.}, }
@article {pmid25149284, year = {2015}, author = {Zhang, M and Visser, S and Pereira e Silva, MC and van Elsas, JD}, title = {IncP-1 and PromA group plasmids are major providers of horizontal gene transfer capacities across bacteria in the mycosphere of different soil fungi.}, journal = {Microbial ecology}, volume = {69}, number = {1}, pages = {169-179}, pmid = {25149284}, issn = {1432-184X}, mesh = {Bacteria/*genetics ; Fungi/*genetics ; Gene Transfer, Horizontal/*genetics ; Plasmids/*genetics ; Soil Microbiology ; }, abstract = {Plasmids of the IncP-1β group have been found to be important carriers of accessory genes that enhance the ecological fitness of bacteria, whereas plasmids of the PromA group are key agents of horizontal gene transfer in particular soil settings. However, there is still a paucity of knowledge with respect to the diversity, abundance, and involvement in horizontal gene transfer of plasmids of both groups in the mycosphere. Using triparental exogenous isolation based on the IncQ tracer plasmid pSUP104 as well as direct molecular detection, we analyzed the pool of mobilizer and self-transferable plasmids in mycosphere soil. Replicate mushroom types that were related to Russula, Inocybe, Ampulloclitocybe, and Galerina spp. were sampled from a forest soil area, and bulk soil was used as the control. The data showed that the levels of IncP-1β plasmids are significantly raised across several of the mycospheres analyzed, whereas those of PromA group plasmids were similar across the mycospheres and corresponding bulk soil. Moreover, the frequencies of triparental exogenous isolation of mobilizer plasmids into a Pseudomonas fluorescens recipient strain were significantly elevated in communities from several mycospheres as compared with those from bulk soil. Molecular analysis of selected transconjugants, as well as from directly isolated strains, revealed the presence of plasmids of three size groups, i.e., (1) 40-45, (2) 50-60, and (3) ≥60 kb, across all isolations. Replicon typing using IncN, IncW and IncA/C proxies revealed no positive signals. In contrast, a suite of plasmids produced signals with IncP-1β as well as PromA type replicon typing systems. Moreover, a selected subset of plasmids, obtained from the Inocybe and Galerina isolates, was transferred out further, revealing their capacities to transfer and mobilize across a broad host range.}, }
@article {pmid25148779, year = {2014}, author = {Travisany, D and Cortés, MP and Latorre, M and Di Genova, A and Budinich, M and Bobadilla-Fazzini, RA and Parada, P and González, M and Maass, A}, title = {A new genome of Acidithiobacillus thiooxidans provides insights into adaptation to a bioleaching environment.}, journal = {Research in microbiology}, volume = {165}, number = {9}, pages = {743-752}, doi = {10.1016/j.resmic.2014.08.004}, pmid = {25148779}, issn = {1769-7123}, mesh = {Acidithiobacillus thiooxidans/*genetics/isolation &amp; purification/physiology ; Adaptation, Biological ; DNA, Bacterial/*chemistry/*genetics ; Drug Tolerance ; Environmental Microbiology ; Genes, Bacterial ; *Genome, Bacterial ; Industrial Microbiology ; Interspersed Repetitive Sequences ; Metabolic Networks and Pathways ; Metals/toxicity ; Molecular Sequence Data ; *Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {Acidithiobacillus thiooxidans is a sulfur oxidizing acidophilic bacterium found in many sulfur-rich environments. It is particularly interesting due to its role in bioleaching of sulphide minerals. In this work, we report the genome sequence of At. thiooxidans Licanantay, the first strain from a copper mine to be sequenced and currently used in bioleaching industrial processes. Through comparative genomic analysis with two other At. thiooxidans non-metal mining strains (ATCC 19377 and A01) we determined that these strains share a large core genome of 2109 coding sequences and a high average nucleotide identity over 98%. Nevertheless, the presence of 841 strain-specific genes (absent in other At. thiooxidans strains) suggests a particular adaptation of Licanantay to its specific biomining environment. Among this group, we highlight genes encoding for proteins involved in heavy metal tolerance, mineral cell attachment and cysteine biosynthesis. Several of these genes were located near genetic motility genes (e.g. transposases and integrases) in genomic regions of over 10 kbp absent in the other strains, suggesting the presence of genomic islands in the Licanantay genome probably produced by horizontal gene transfer in mining environments.}, }
@article {pmid25147720, year = {2014}, author = {Bakhshi, B and Eftekhari, N and Pourshafie, MR}, title = {Genetic elements associated with antimicrobial resistance among intestinal bacteria.}, journal = {Jundishapur journal of microbiology}, volume = {7}, number = {5}, pages = {e9924}, pmid = {25147720}, issn = {2008-3645}, abstract = {BACKGROUND: Integrons are the major reasons of multidrug resistance (MDR) among enteropathogenic bacteria. Occurrence of horizontal gene transfer between integron-carrying microorganisms and other enteric bacteria may increase the rate of emergence of integron-associated antibiotic resistance.<br><br>OBJECTIVES: The objective of this study was to investigate class 1 integrons among members of enteropathogenic bacteria isolated from patients in Iran.<br><br>MATERIALS AND METHODS: A total of 120 enteropathogenic bacterial isolates from diarrhoeal patients were included in this study. Identities of the isolates were investigated by biochemical tests and confirmed by genus or species specific PCRs. Antimicrobial susceptibility testing was performed according to the Clinical and Laboratory Standards Institute (CLSI) guidelines. Presence of class 1 integron among the isolates was investigated using primers specific for the integrase gene conserved region.<br><br>RESULTS: The result of this study showed the highest resistance to trimethoprim and cotrimoxazole, especially in enteropathogenic Escherichia coli (EPEC) (100%), Shigella sonnei (93.7%) and Vibrio cholerae (95%). The results showed that 16 (57.1%) of the 28 EPEC, 9 (25%) of the 36 Salmonella enterica, 32 of the 13 (40.6%) Sh. sonnei, and only 1 (4.2%) of the 24 V. cholerae isolate harbored class 1 integron.<br><br>CONCLUSIONS: The data obtained in the present study suggested that class 1 integrons are widely distributed among members of Enterobacteriaceae. The resistance patterns of our E. coli, S. sonnei, and S. enterica isolates were nearly identical, suggesting the same genetic elements involved in attainment of multi-drug resistance.}, }
@article {pmid25147547, year = {2014}, author = {Cua, LS and Stein, LY}, title = {Characterization of denitrifying activity by the alphaproteobacterium, Sphingomonas wittichii RW1.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {404}, pmid = {25147547}, issn = {1664-302X}, abstract = {Sphingomonas wittichii RW1 has no reported denitrifying activity yet encodes nitrite and nitric oxide reductases. The aims of this study were to determine conditions under which S. wittichii RW1 consumes nitrite (NO(-) 2) and produces nitrous oxide (N2O), examine expression of putative genes for N-oxide metabolism, and determine the functionality of chromosomal (ch) and plasmid (p) encoded quinol-dependent nitric oxide reductases (NorZ). Batch cultures of wildtype (WT) and a norZ ch mutant of S. wittichii RW1 consumed NO(-) 2 and produced N2O during stationary phase. The norZ ch mutant produced N2O, although at significantly lower levels (c.a. 66-87%) relative to the WT. Rates of N2O production were 2-3 times higher in cultures initiated at low relative to atmospheric O2 per unit biomass, although rates of NO(-) 2 consumption were elevated in cultures initiated with atmospheric O2 and 1 mM NaNO2. Levels of mRNA encoding nitrite reductase (nirK), plasmid-encoded nitric oxide dioxygenase (hmp p) and plasmid-encoded nitric oxide reductase (norZ p) were significantly higher in the norZ ch mutant over a growth curve relative to WT. The presence of NO(-) 2 further increased levels of nirK and hmp p mRNA in both the WT and norZ ch mutant; levels of norZ p mRNA compensated for the loss of norZ ch expression in the norZ ch mutant. Together, the results suggest that S. wittichii RW1 denitrifies NO(-) 2 to N2O and expresses gene products predicted to detoxify N-oxides. So far, only S. wittichii strains within four closely related taxa have been observed to encode both nirK and norZ genes, indicating a species-specific lateral gene transfer that may be relevant to the niche preference of S. wittichii.}, }
@article {pmid25146840, year = {2015}, author = {Ortiz, MF and Wallau, GL and Graichen, D&#xc2; and Loreto, EL}, title = {An evaluation of the ecological relationship between Drosophila species and their parasitoid wasps as an opportunity for horizontal transposon transfer.}, journal = {Molecular genetics and genomics : MGG}, volume = {290}, number = {1}, pages = {67-78}, pmid = {25146840}, issn = {1617-4623}, mesh = {Animals ; Base Sequence ; DNA Transposable Elements/*genetics ; Drosophila/microbiology/*parasitology ; Gene Transfer, Horizontal/*genetics ; Genes, Mitochondrial ; Genome, Insect/genetics ; *Host-Parasite Interactions ; Phylogeny ; Reproducibility of Results ; Species Specificity ; Wasps/*physiology/virology ; Wolbachia/physiology ; }, abstract = {Evidences of horizontal transfer, the exchange of genetic material between reproductively isolated species, have accumulated over the last decades, including for multicellular eukaryotic organisms. However, the mechanisms and ecological relationships that promote such phenomenon is still poorly known. Host-parasite interaction is one type of relationship usually pointed in the literature that could potentially increase the probability of the horizontal transfer between species, because the species involved in such relationships are generally in close contact. Transposable elements, which are well-known genomic parasites, are DNA entities that tend to be involved in horizontal transfer due to their ability to mobilize between different genomic locations. Using Drosophila species and their parasitoid wasps as a host-parasite model, we evaluated the hypothesis that horizontal transposon transfers (HTTs) are more frequent in this set of species than in species that do not exhibit a close ecological and phylogenetic relationship. For this purpose, we sequenced two sets of species using a metagenomic and single-species genomic sampling approach through next-generation DNA sequencing. The first set was composed of five generalist Drosophila (D. maculifrons, D. bandeirantorum, D. polymorpha, D. mercatorum and D. willistoni) species and their associated parasitoid wasps, whereas the second set was composed of D. incompta, which is a flower specialist species, and its parasitoid wasp. We did not find strong evidence of HTT in the two sets of Drosophila and wasp parasites. However, at least five cases of HTT were observed between the generalist and specialist Drosophila species. Moreover, we detected an HT event involving a Wolbachia lineage between generalist and specialist species, indicating that these endosymbiotic bacteria could play a role as HTT vectors. In summary, our results do not support the hypothesis of prevalent HTT between species with a host-parasite relationship, at least for the studied wasp-Drosophila pairs. Moreover, it suggests that other mechanisms or parasites are involved in promoting HTT between Drosophila species as the Wolbachia endosymbiotic bacteria.}, }
@article {pmid25146649, year = {2014}, author = {Grant, JR and Katz, LA}, title = {Phylogenomic study indicates widespread lateral gene transfer in Entamoeba and suggests a past intimate relationship with parabasalids.}, journal = {Genome biology and evolution}, volume = {6}, number = {9}, pages = {2350-2360}, pmid = {25146649}, issn = {1759-6653}, support = {R15 GM097722/GM/NIGMS NIH HHS/United States ; 1R15GM097722-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Archaea/genetics ; Bacteria/genetics ; Entamoeba/*classification/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome ; Parabasalidea/*classification/*genetics ; *Phylogeny ; }, abstract = {Lateral gene transfer (LGT) has impacted the evolutionary history of eukaryotes, though to a lesser extent than in bacteria and archaea. Detecting LGT and distinguishing it from single gene tree artifacts is difficult, particularly when considering very ancient events (i.e., over hundreds of millions of years). Here, we use two independent lines of evidence--a taxon-rich phylogenetic approach and an assessment of the patterns of gene presence/absence--to evaluate the extent of LGT in the parasitic amoebozoan genus Entamoeba. Previous work has suggested that a number of genes in the genome of Entamoeba spp. were acquired by LGT. Our approach, using an automated phylogenomic pipeline to build taxon-rich gene trees, suggests that LGT is more extensive than previously thought. Our analyses reveal that genes have frequently entered the Entamoeba genome via nonvertical events, including at least 116 genes acquired directly from bacteria or archaea, plus an additional 22 genes in which Entamoeba plus one other eukaryote are nested among bacteria and/or archaea. These genes may make good candidates for novel therapeutics, as drugs targeting these genes are less likely to impact the human host. Although we recognize the challenges of inferring intradomain transfers given systematic errors in gene trees, we find 109 genes supporting LGT from a eukaryote to Entamoeba spp., and 178 genes unique to Entamoeba spp. and one other eukaryotic taxon (i.e., presence/absence data). Inspection of these intradomain LGTs provide evidence of a common sister relationship between genes of Entamoeba (Amoebozoa) and parabasalids (Excavata). We speculate that this indicates a past close relationship (e.g., symbiosis) between ancestors of these extant lineages.}, }
@article {pmid25146648, year = {2014}, author = {Fu, CJ and Sheikh, S and Miao, W and Andersson, SG and Baldauf, SL}, title = {Missing genes, multiple ORFs, and C-to-U type RNA editing in Acrasis kona (Heterolobosea, Excavata) mitochondrial DNA.}, journal = {Genome biology and evolution}, volume = {6}, number = {9}, pages = {2240-2257}, pmid = {25146648}, issn = {1759-6653}, mesh = {Base Sequence ; Codon ; DNA, Mitochondrial/*genetics ; Eukaryota/classification/*genetics ; Gene Transfer, Horizontal ; *Genome, Mitochondrial ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; *RNA Editing ; }, abstract = {Discoba (Excavata) is an ancient group of eukaryotes with great morphological and ecological diversity. Unlike the other major divisions of Discoba (Jakobida and Euglenozoa), little is known about the mitochondrial DNAs (mtDNAs) of Heterolobosea. We have assembled a complete mtDNA genome from the aggregating heterolobosean amoeba, Acrasis kona, which consists of a single circular highly AT-rich (83.3%) molecule of 51.5 kb. Unexpectedly, A. kona mtDNA is missing roughly 40% of the protein-coding genes and nearly half of the transfer RNAs found in the only other sequenced heterolobosean mtDNAs, those of Naegleria spp. Instead, over a quarter of A. kona mtDNA consists of novel open reading frames. Eleven of the 16 protein-coding genes missing from A. kona mtDNA were identified in its nuclear DNA and polyA RNA, and phylogenetic analyses indicate that at least 10 of these 11 putative nuclear-encoded mitochondrial (NcMt) proteins arose by direct transfer from the mitochondrion. Acrasis kona mtDNA also employs C-to-U type RNA editing, and 12 homologs of DYW-type pentatricopeptide repeat (PPR) proteins implicated in plant organellar RNA editing are found in A. kona nuclear DNA. A mapping of mitochondrial gene content onto a consensus phylogeny reveals a sporadic pattern of relative stasis and rampant gene loss in Discoba. Rampant loss occurred independently in the unique common lineage leading to Heterolobosea + Tsukubamonadida and later in the unique lineage leading to Acrasis. Meanwhile, mtDNA gene content appears to be remarkably stable in the Acrasis sister lineage leading to Naegleria and in their distant relatives Jakobida.}, }
@article {pmid25143190, year = {2014}, author = {Overballe-Petersen, S and Willerslev, E}, title = {Horizontal transfer of short and degraded DNA has evolutionary implications for microbes and eukaryotic sexual reproduction.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {36}, number = {10}, pages = {1005-1010}, pmid = {25143190}, issn = {1521-1878}, mesh = {Animals ; Bacteria/*genetics ; *Biological Evolution ; DNA/*genetics ; DNA Damage/*genetics ; Eukaryota/*genetics ; *Gene Transfer, Horizontal ; Humans ; Reproduction/*genetics ; }, abstract = {Horizontal gene transfer in the form of long DNA fragments has changed our view of bacterial evolution. Recently, we discovered that such processes may also occur with the massive amounts of short and damaged DNA in the environment, and even with truly ancient DNA. Although it presently remains unclear how often it takes place in nature, horizontal gene transfer of short and damaged DNA opens up the possibility for genetic exchange across distinct species in both time and space. In this essay, we speculate on the potential evolutionary consequences of this phenomenon. We argue that it may challenge basic assumptions in evolutionary theory; that it may have distant origins in life's history; and that horizontal gene transfer should be viewed as an evolutionary strategy not only preceding but causally underpinning the evolution of sexual reproduction.}, }
@article {pmid25141959, year = {2014}, author = {Puigbò, P and Lobkovsky, AE and Kristensen, DM and Wolf, YI and Koonin, EV}, title = {Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes.}, journal = {BMC biology}, volume = {12}, number = {}, pages = {66}, pmid = {25141959}, issn = {1741-7007}, support = {//Intramural NIH HHS/United States ; }, mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; *Genome, Archaeal ; *Genome, Bacterial ; Likelihood Functions ; Phylogeny ; }, abstract = {BACKGROUND: Genomes of bacteria and archaea (collectively, prokaryotes) appear to exist in incessant flux, expanding via horizontal gene transfer and gene duplication, and contracting via gene loss. However, the actual rates of genome dynamics and relative contributions of different types of event across the diversity of prokaryotes are largely unknown, as are the sizes of microbial supergenomes, i.e. pools of genes that are accessible to the given microbial species.<br><br>RESULTS: We performed a comprehensive analysis of the genome dynamics in 35 groups (34 bacterial and one archaeal) of closely related microbial genomes using a phylogenetic birth-and-death maximum likelihood model to quantify the rates of gene family gain and loss, as well as expansion and reduction. The results show that loss of gene families dominates the evolution of prokaryotes, occurring at approximately three times the rate of gain. The rates of gene family expansion and reduction are typically seven and twenty times less than the gain and loss rates, respectively. Thus, the prevailing mode of evolution in bacteria and archaea is genome contraction, which is partially compensated by the gain of new gene families via horizontal gene transfer. However, the rates of gene family gain, loss, expansion and reduction vary within wide ranges, with the most stable genomes showing rates about 25 times lower than the most dynamic genomes. For many groups, the supergenome estimated from the fraction of repetitive gene family gains includes about tenfold more gene families than the typical genome in the group although some groups appear to have vast, 'open' supergenomes.<br><br>CONCLUSIONS: Reconstruction of evolution for groups of closely related bacteria and archaea reveals an extremely rapid and highly variable flux of genes in evolving microbial genomes, demonstrates that extensive gene loss and horizontal gene transfer leading to innovation are the two dominant evolutionary processes, and yields robust estimates of the supergenome size.}, }
@article {pmid25141005, year = {2014}, author = {Maslunka, C and Gifford, B and Tucci, J and Gürtler, V and Seviour, RJ}, title = {Insertions or deletions (Indels) in the rrn 16S-23S rRNA gene internal transcribed spacer region (ITS) compromise the typing and identification of strains within the Acinetobacter calcoaceticus-baumannii (Acb) complex and closely related members.}, journal = {PloS one}, volume = {9}, number = {8}, pages = {e105390}, pmid = {25141005}, issn = {1932-6203}, mesh = {Acinetobacter baumannii/classification/*genetics ; Acinetobacter calcoaceticus/classification/*genetics ; DNA, Ribosomal Spacer/*genetics ; *INDEL Mutation ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; RNA, Ribosomal, 23S/*genetics ; }, abstract = {To determine whether ITS sequences in the rrn operon are suitable for identifying individual Acinetobacter Acb complex members, we analysed length and sequence differences between multiple ITS copies within the genomes of individual strains. Length differences in ITS reported previously between A. nosocomialis BCRC15417T (615 bp) and other strains (607 bp) can be explained by presence of an insertion (indel 13i/1) in the longer ITS variant. The same Indel 13i/1 was also found in ITS sequences of ten strains of A. calcoaceticus, all 639 bp long, and the 628 bp ITS of Acinetobacter strain BENAB127. Four additional indels (13i/2-13i/5) were detected in Acinetobacter strain c/t13TU 10090 ITS length variants (608, 609, 620, 621 and 630 bp). These ITS variants appear to have resulted from horizontal gene transfer involving other Acinetobacter species or in some cases unrelated bacteria. Although some ITS copies in strain c/t13TU 10090 are of the same length (620 bp) as those in Acinetobacter strains b/n1&amp;3, A. pittii (10 strains), A. calcoaceticus and A. oleivorans (not currently acknowledged as an Acb member), their individual ITS sequences differ. Thus ITS length by itself can not by itself be used to identify Acb complex strains. A shared indel in ITS copies in two separate Acinetobacter species compromises the specificity of ITS targeted probes, as shown with the Aun-3 probe designed to target the ITS in A. pitti. The presence of indel 13i/5 in the ITS of Acinetobacter strain c/t13TU means it too responded positively to this probe. Thus, neither ITS sequencing nor the currently available ITS targeted probes can distinguish reliably between Acb member species.}, }
@article {pmid25140821, year = {2014}, author = {Zhou, Z and Li, Y and Sun, N and Sun, Z and Lv, L and Wang, Y and Shen, L and Li, YQ}, title = {Function and evolution of two forms of SecDF homologs in Streptomyces coelicolor.}, journal = {PloS one}, volume = {9}, number = {8}, pages = {e105237}, pmid = {25140821}, issn = {1932-6203}, support = {G12MD007591/MD/NIMHD NIH HHS/United States ; SC1 GM081068/GM/NIGMS NIH HHS/United States ; GM100806/GM/NIGMS NIH HHS/United States ; G12 MD007591/MD/NIMHD NIH HHS/United States ; SC1 GM100806/GM/NIGMS NIH HHS/United States ; AI080579/AI/NIAID NIH HHS/United States ; SC1 AI080579/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/*genetics/*metabolism ; Biological Evolution ; Genome, Bacterial/genetics ; Membrane Proteins/*genetics/*metabolism ; Membrane Transport Proteins/*genetics/*metabolism ; Protein Transport/genetics ; Streptomyces coelicolor/*genetics/*metabolism ; Transcription, Genetic/genetics ; }, abstract = {The general secretion (Sec) pathway plays a prominent role in bacterial protein export, and the accessory component SecDF has been shown to improve transportation efficiency. Inspection of Streptomyces coelicolor genome reveals the unexpected presence of two different forms of secDF homologous genes: one in fused form (secDF) and the other in separated form (secD and secF). However, the functional role of two SecDF homologs in S. coelicolor has not yet been determined. Transcriptional analysis of secDF homologs reveals that these genes are constitutively expressed. However, the transcript levels of secD and secF are much higher than that of secDF in S. coelicolor. Deletion of secDF or/and secD/secF in S. coelicolor did result in reduced secretion efficiency of Xylanase A and Amylase C, suggesting that they may have redundant functions for Sec-dependent translocation pathway. Moreover, our results also indicate that SecD/SecF plays a more prominent role than SecDF in protein translocation. Evolutionary analysis suggests that the fused and separated SecDF homologs in Streptomyces may have disparate evolutionary ancestries. SecD/SecF may be originated from vertical transmission of existing components from ancestor of Streptomyces species. However, SecDF may be derived from bacterial ancestors through horizontal gene transfer. Alternately, it is also plausible that SecDF may have arisen through additional gene duplication and fusion events. The acquisition of a second copy may confer a selective benefit to Streptomyces by enhancing protein transport capacity. Taken together, our results provide new insights into the potential biological function and evolutionary aspects of the prokaryotic SecDF complex.}, }
@article {pmid25139903, year = {2014}, author = {Seitz, P and Blokesch, M}, title = {DNA transport across the outer and inner membranes of naturally transformable Vibrio cholerae is spatially but not temporally coupled.}, journal = {mBio}, volume = {5}, number = {4}, pages = {}, pmid = {25139903}, issn = {2150-7511}, support = {309064/ERC_/European Research Council/International ; }, mesh = {Cytoplasm/metabolism ; DNA, Bacterial/genetics/*metabolism ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Periplasm/metabolism ; *Transformation, Bacterial ; Vibrio cholerae/*genetics ; }, abstract = {UNLABELLED: The physiological state of natural competence for transformation allows certain bacteria to take up free DNA from the environment and to recombine such newly acquired DNA into their chromosomes. However, even though conserved components that are required to undergo natural transformation have been identified in several naturally competent bacteria, our knowledge of the underlying mechanisms of the DNA uptake process remains very limited. To better understand these mechanisms, we investigated the competence-mediated DNA transport in the naturally transformable pathogen Vibrio cholerae. Previously, we used a cell biology-based approach to experimentally address an existing hypothesis, which suggested the competence protein ComEA plays a role in the DNA uptake process across the outer membrane of Gram-negative bacteria. Here, we extended this knowledge by investigating the dynamics of DNA translocation across both membranes. More precisely, we indirectly visualized the transfer of the external DNA from outside the cell into the periplasm followed by the shuttling of the DNA into the cytoplasm. Based on these data, we conclude that for V. cholerae, the DNA translocation across the outer and inner membranes is spatially but not temporally coupled.<br><br>IMPORTANCE: As a mode of horizontal gene transfer, natural competence for transformation has contributed substantially to the plasticity of genomes and to bacterial evolution. Natural competence is often a tightly regulated process and is induced by diverse environmental cues. This is in contrast to the mechanistic aspects of the DNA translocation event, which are most likely conserved among naturally transformable bacteria. However, the DNA uptake process is still not well understood. We therefore investigated how external DNA reaches the cytosol of the naturally transformable bacterium V.&#xa0;cholerae. More specifically, we provide evidence that the DNA translocation across the membranes is spatially but not temporally coupled. We hypothesize that this model also applies to other competent Gram-negative bacteria and that our study contributes to the general understanding of this important biological process.}, }
@article {pmid25139901, year = {2014}, author = {Spagnoletti, M and Ceccarelli, D and Rieux, A and Fondi, M and Taviani, E and Fani, R and Colombo, MM and Colwell, RR and Balloux, F}, title = {Acquisition and evolution of SXT-R391 integrative conjugative elements in the seventh-pandemic Vibrio cholerae lineage.}, journal = {mBio}, volume = {5}, number = {4}, pages = {}, pmid = {25139901}, issn = {2150-7511}, support = {260801/ERC_/European Research Council/International ; 2R01 AI039129-11A2/AI/NIAID NIH HHS/United States ; }, mesh = {Bayes Theorem ; *Conjugation, Genetic ; *DNA Transposable Elements ; Databases, Genetic ; Drug Resistance, Multiple ; Evolution, Molecular ; Gammaproteobacteria/genetics ; Gene Transfer, Horizontal ; Genetic Variation ; Genome ; Genomics ; *Homologous Recombination ; Pandemics ; Phenotype ; Phylogeny ; Polymorphism, Single Nucleotide ; Vibrio cholerae/*genetics ; }, abstract = {UNLABELLED: SXT-R391 Integrative conjugative elements (ICEs) are self-transmissible mobile genetic elements able to confer multidrug resistance and other adaptive features to bacterial hosts, including Vibrio cholerae, the causative agent of cholera. ICEs are arranged in a mosaic genetic structure composed of a conserved backbone interspersed with variable DNA clusters located in conserved hot spots. In this study, we investigated ICE acquisition and subsequent microevolution in pandemic V. cholerae. Ninety-six ICEs were retrieved from publicly available sequence databases from V. cholerae clinical strains and were compared to a set of reference ICEs. Comparative genomics highlighted the existence of five main ICE groups with a distinct genetic makeup, exemplified by ICEVchInd5, ICEVchMoz10, SXT, ICEVchInd6, and ICEVchBan11. ICEVchInd5 (the most frequent element, represented by 70 of 96 elements analyzed) displayed no sequence rearrangements and was characterized by 46 single nucleotide polymorphisms (SNPs). SNP analysis revealed that recent inter-ICE homologous recombination between ICEVchInd5 and other ICEs circulating in gammaproteobacteria generated ICEVchMoz10, ICEVchInd6, and ICEVchBan11. Bayesian phylogenetic analyses indicated that ICEVchInd5 and SXT were independently acquired by the current pandemic V. cholerae O1 and O139 lineages, respectively, within a period of only a few years.<br><br>IMPORTANCE: SXT-R391 ICEs have been recognized as key vectors of antibiotic resistance in the seventh-pandemic lineage of V.&#xa0;cholerae, which remains a major cause of mortality and morbidity on a global scale. ICEs were acquired only recently in this clade and are acknowledged to be major contributors to horizontal gene transfer and the acquisition of new traits in bacterial species. We have reconstructed the temporal dynamics of SXT-R391 ICE acquisition and spread and have identified subsequent recombination events generating significant diversity in ICEs currently circulating among V.&#xa0;cholerae clinical strains. Our results showed that acquisition of SXT-R391 ICEs provided the V.&#xa0;cholerae seventh-pandemic lineage not only with a multidrug resistance phenotype but also with a powerful molecular tool for rapidly accessing the pan-genome of a large number of gammaproteobacteria.}, }
@article {pmid25131403, year = {2014}, author = {Haq, IU and Zhang, M and Yang, P and van Elsas, JD}, title = {The interactions of bacteria with fungi in soil: emerging concepts.}, journal = {Advances in applied microbiology}, volume = {89}, number = {}, pages = {185-215}, doi = {10.1016/B978-0-12-800259-9.00005-6}, pmid = {25131403}, issn = {0065-2164}, mesh = {Bacteria/genetics ; *Bacterial Physiological Phenomena ; Ecosystem ; Fungi/genetics/*physiology ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {In this chapter, we review the existing literature on bacterial-fungal interactions in soil, exploring the role fungi may play for soil bacteria as providers of hospitable niches. A focus is placed on the mycosphere, i.e., the narrow zone of influence of fungal hyphae on the external soil milieu, in which hypha-associated bacterial cells dwell. Evidence is brought forward for the contention that the hyphae of both mycorrhizal and saprotrophic fungi serve as providers of ecological opportunities in a grossly carbon-limited soil, as a result of their release of carbonaceous compounds next to the provision of a colonizable surface. Soil bacteria of particular nature are postulated to have adapted to such selection pressures, evolving to the extent that they acquired capabilities that allow them to thrive in the novel habitat created by the emerging fungal hyphae. The mechanisms involved in the interactions and the modes of genetic adaptation of the mycosphere dwellers are discussed, with an emphasis on one key mycosphere-adapted bacterium, Burkholderia terrae BS001. In this discussion, we interrogate the positive interactions between soil fungi and bacteria, and refrain from considering negative interactions.}, }
@article {pmid25129418, year = {2014}, author = {Yue, J and Hu, X and Huang, J}, title = {Origin of plant auxin biosynthesis.}, journal = {Trends in plant science}, volume = {19}, number = {12}, pages = {764-770}, doi = {10.1016/j.tplants.2014.07.004}, pmid = {25129418}, issn = {1878-4372}, mesh = {Biological Evolution ; Gene Transfer, Horizontal/genetics ; Indoleacetic Acids/*metabolism ; Plants/*metabolism ; }, abstract = {The recent finding of the tryptophan aminotransferase (TAA)/flavin monooxygenase (YUC) pathway as the principal route of auxin production in plants provides an opportunity to revisit the origin of plant auxin biosynthesis. Phylogenetic analyses of the TAA and YUC gene families provide very little evidence for the production of indole-3-acetic acid (IAA) in algae. Instead, horizontal gene transfer of YUCs from bacteria to the ancestral land plant suggests that the TAA/YUC pathway is a land plant innovation. In this Opinion article we postulate that the origin of tryptophan-dependent IAA biosynthesis in land plants might have evolved in response to interactions with microbes, particularly bacteria, allowing plants to counteract bacterial activities and control their own auxin signaling.}, }
@article {pmid25128982, year = {2014}, author = {Kim, KM and Nasir, A and Hwang, K and Caetano-Anollés, G}, title = {A tree of cellular life inferred from a genomic census of molecular functions.}, journal = {Journal of molecular evolution}, volume = {79}, number = {5-6}, pages = {240-262}, pmid = {25128982}, issn = {1432-1432}, mesh = {Archaea/*chemistry/classification/cytology ; *Biological Evolution ; Eukaryota/*chemistry/classification/metabolism ; Gene Ontology ; Molecular Sequence Annotation ; *Origin of Life ; Phylogeny ; Prokaryotic Cells/*chemistry/classification/metabolism ; RNA, Ribosomal/genetics/metabolism ; Time Factors ; }, abstract = {Phylogenomics aims to describe evolutionary relatedness between organisms by analyzing genomic data. The common practice is to produce phylogenomic trees from molecular information in the sequence, order, and content of genes in genomes. These phylogenies describe the evolution of life and become valuable tools for taxonomy. The recent availability of structural and functional data for hundreds of genomes now offers the opportunity to study evolution using more deep, conserved, and reliable sets of molecular features. Here, we reconstruct trees of life from the functions of proteins. We start by inferring rooted phylogenomic trees and networks of organisms directly from Gene Ontology annotations. Phylogenies and networks yield novel insights into the emergence and evolution of cellular life. The ancestor of Archaea originated earlier than the ancestors of Bacteria and Eukarya and was thermophilic. In contrast, basal bacterial lineages were non-thermophilic. A close relationship between Plants and Metazoa was also identified that disagrees with the traditional Fungi-Metazoa grouping. While measures of evolutionary reticulation were minimum in Eukarya and maximum in Bacteria, the massive role of horizontal gene transfer in microbes did not materialize in phylogenomic networks. Phylogenies and networks also showed that the best reconstructions were recovered when problematic taxa (i.e., parasitic/symbiotic organisms) and horizontally transferred characters were excluded from analysis. Our results indicate that functionomic data represent a useful addition to the set of molecular characters used for tree reconstruction and that trees of cellular life carry in deep branches considerable predictive power to explain the evolution of living organisms.}, }
@article {pmid25128344, year = {2014}, author = {Hansen, KH and Bortolaia, V and Damborg, P and Guardabassi, L}, title = {Strain diversity of CTX-M-producing Enterobacteriaceae in individual pigs: insights into the dynamics of shedding during the production cycle.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {21}, pages = {6620-6626}, pmid = {25128344}, issn = {1098-5336}, mesh = {Animals ; *Biodiversity ; DNA, Bacterial/chemistry/genetics ; Electrophoresis, Gel, Pulsed-Field ; Enterobacteriaceae/*classification/enzymology/genetics/*isolation &amp; purification ; Feces/*microbiology ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Plasmids ; Sequence Analysis, DNA ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Swine ; beta-Lactamases/*metabolism ; }, abstract = {The aim of this study was to evaluate the population dynamics of CTX-M-producing Enterobacteriaceae in individual pigs on a farm positive for CTX-M-14-producing Escherichia coli. Fecal samples were collected once around the farrowing time from five sows and four times along the production cycle from two of their respective offspring. Multiple colonies per sample were isolated on cefotaxime-supplemented MacConkey agar with or without prior enrichment, resulting in 98 isolates identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry and tested for blaCTX-M. CTX-M-positive isolates (n = 86) were typed by pulsed-field gel electrophoresis (PFGE). Plasmids harboring blaCTX-M were characterized in 22 representative isolates by replicon typing and restriction fragment length polymorphism. Based on the PFGE results, all individuals shed unrelated CTX-M-14-producing E. coli strains during the course of life. Concomitant shedding of CTX-M-2/97-producing Proteus mirabilis or Providencia rettgeri was observed in two sows and two offspring. At least two genetically unrelated CTX-M-producing E. coli strains were isolated from approximately one-fourth of the samples, with remarkable differences between isolates obtained by enrichment and direct plating. A clear decrease in strain diversity was observed after weaning. Dissemination of blaCTX-M-14 within the farm was attributed to horizontal transfer of an IncK plasmid that did not carry additional resistance genes and persisted in the absence of antimicrobial selective pressure. Assessment of strain diversity was shown to be influenced by the production stage from which samples were collected, as well as by the isolation method, providing useful information for the design and interpretation of future epidemiological studies of CTX-M-producing Enterobacteriaceae in pig farms.}, }
@article {pmid25124934, year = {2014}, author = {Chimileski, S and Franklin, MJ and Papke, RT}, title = {Biofilms formed by the archaeon Haloferax volcanii exhibit cellular differentiation and social motility, and facilitate horizontal gene transfer.}, journal = {BMC biology}, volume = {12}, number = {}, pages = {65}, pmid = {25124934}, issn = {1741-7007}, mesh = {*Biofilms ; *Gene Transfer, Horizontal ; Haloferax volcanii/genetics/*physiology ; *Microbial Interactions ; Microscopy, Confocal ; }, abstract = {BACKGROUND: Archaea share a similar microbial lifestyle with bacteria, and not surprisingly then, also exist within matrix-enclosed communities known as biofilms. Advances in biofilm biology have been made over decades for model bacterial species, and include characterizations of social behaviors and cellular differentiation during biofilm development. Like bacteria, archaea impact ecological and biogeochemical systems. However, the biology of archaeal biofilms is only now being explored. Here, we investigated the development, composition and dynamics of biofilms formed by the haloarchaeon Haloferax volcanii DS2.<br><br>RESULTS: Biofilms were cultured in static liquid and visualized with fluorescent cell membrane dyes and by engineering cells to express green fluorescent protein (GFP). Analysis by confocal scanning laser microscopy showed that H. volcanii cells formed microcolonies within 24 h, which developed into larger clusters by 48 h and matured into flake-like towers often greater than 100 &#x3bc;m in height after 7 days. To visualize the extracellular matrix, biofilms formed by GFP-expressing cells were stained with concanavalin A, DAPI, Congo red and thioflavin T. Stains colocalized with larger cellular structures and indicated that the extracellular matrix may contain a combination of polysaccharides, extracellular DNA and amyloid protein. Following a switch to biofilm growth conditions, a sub-population of cells differentiated into chains of long rods sometimes exceeding 25 &#x3bc;m in length, compared to their planktonic disk-shaped morphology. Time-lapse photography of static liquid biofilms also revealed wave-like social motility. Finally, we quantified gene exchange between biofilm cells, and found that it was equivalent to the mating frequency of a classic filter-based experimental method.<br><br>CONCLUSIONS: The developmental processes, functional properties and dynamics of H. volcanii biofilms provide insight on how haloarchaeal species might persist, interact and exchange DNA in natural communities. H. volcanii demonstrates some biofilm phenotypes similar to bacterial biofilms, but also has interesting phenotypes that may be unique to this organism or to this class of organisms, including changes in cellular morphology and an unusual form of social motility. Because H. volcanii has one of the most advanced genetic systems for any archaeon, the phenotypes reported here may promote the study of genetic and developmental processes in archaeal biofilms.}, }
@article {pmid25124438, year = {2014}, author = {Kim, G and LeBlanc, ML and Wafula, EK and dePamphilis, CW and Westwood, JH}, title = {Plant science. Genomic-scale exchange of mRNA between a parasitic plant and its hosts.}, journal = {Science (New York, N.Y.)}, volume = {345}, number = {6198}, pages = {808-811}, doi = {10.1126/science.1253122}, pmid = {25124438}, issn = {1095-9203}, mesh = {Arabidopsis/*genetics/parasitology ; Cuscuta/*genetics/physiology ; DNA, Complementary ; Gene Transfer, Horizontal ; Genes, Plant ; Genome, Plant ; Host-Parasite Interactions ; Solanum lycopersicum/*genetics/parasitology ; RNA, Messenger/*genetics/metabolism ; RNA, Plant/*genetics/metabolism ; *Transcriptome ; }, abstract = {Movement of RNAs between cells of a single plant is well documented, but cross-species RNA transfer is largely unexplored. Cuscuta pentagona (dodder) is a parasitic plant that forms symplastic connections with its hosts and takes up host messenger RNAs (mRNAs). We sequenced transcriptomes of Cuscuta growing on Arabidopsis and tomato hosts to characterize mRNA transfer between species and found that mRNAs move in high numbers and in a bidirectional manner. The mobile transcripts represented thousands of different genes, and nearly half the expressed transcriptome of Arabidopsis was identified in Cuscuta. These findings demonstrate that parasitic plants can exchange large proportions of their transcriptomes with hosts, providing potential mechanisms for RNA-based interactions between species and horizontal gene transfer.}, }
@article {pmid25123114, year = {2014}, author = {Eves-van den Akker, S and Lilley, CJ and Danchin, EG and Rancurel, C and Cock, PJ and Urwin, PE and Jones, JT}, title = {The transcriptome of Nacobbus aberrans reveals insights into the evolution of sedentary endoparasitism in plant-parasitic nematodes.}, journal = {Genome biology and evolution}, volume = {6}, number = {9}, pages = {2181-2194}, pmid = {25123114}, issn = {1759-6653}, support = {BB/F000642/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/H000801/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *Biological Evolution ; Female ; Helminth Proteins/*genetics/metabolism ; Host Specificity ; *Host-Parasite Interactions ; Molecular Sequence Data ; Phylogeny ; Plant Diseases/*parasitology ; Sequence Alignment ; Nicotiana/parasitology ; *Transcriptome ; Tylenchoidea/classification/*genetics/growth &amp; development/physiology ; }, abstract = {Within the phylum Nematoda, plant-parasitism is hypothesized to have arisen independently on at least four occasions. The most economically damaging plant-parasitic nematode species, and consequently the most widely studied, are those that feed as they migrate destructively through host roots causing necrotic lesions (migratory endoparasites) and those that modify host root tissue to create a nutrient sink from which they feed (sedentary endoparasites). The false root-knot nematode Nacobbus aberrans is the only known species to have both migratory endoparasitic and sedentary endoparasitic stages within its life cycle. Moreover, its sedentary stage appears to have characteristics of both the root-knot and the cyst nematodes. We present the first large-scale genetic resource of any false-root knot nematode species. We use RNAseq to describe relative abundance changes in all expressed genes across the life cycle to provide interesting insights into the biology of this nematode as it transitions between modes of parasitism. A multigene phylogenetic analysis of N. aberrans with respect to plant-parasitic nematodes of all groups confirms its proximity to both cyst and root-knot nematodes. We present a transcriptome-wide analysis of both lateral gene transfer events and the effector complement. Comparing parasitism genes of typical root-knot and cyst nematodes to those of N. aberrans has revealed interesting similarities. Importantly, genes that were believed to be either cyst nematode, or root-knot nematode, "specific" have both been identified in N. aberrans. Our results provide insights into the characteristics of a common ancestor and the evolution of sedentary endoparasitism of plants by nematodes.}, }
@article {pmid25121584, year = {2014}, author = {Wacholder, AC and Cox, C and Meyer, TJ and Ruggiero, RP and Vemulapalli, V and Damert, A and Carbone, L and Pollock, DD}, title = {Inference of transposable element ancestry.}, journal = {PLoS genetics}, volume = {10}, number = {8}, pages = {e1004482}, pmid = {25121584}, issn = {1553-7404}, support = {R01 GM083127/GM/NIGMS NIH HHS/United States ; R01 GM097251/GM/NIGMS NIH HHS/United States ; GM083127/GM/NIGMS NIH HHS/United States ; }, mesh = {Bayes Theorem ; DNA Transposable Elements/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Humans ; Mutation ; *Phylogeny ; }, abstract = {Most common methods for inferring transposable element (TE) evolutionary relationships are based on dividing TEs into subfamilies using shared diagnostic nucleotides. Although originally justified based on the "master gene" model of TE evolution, computational and experimental work indicates that many of the subfamilies generated by these methods contain multiple source elements. This implies that subfamily-based methods give an incomplete picture of TE relationships. Studies on selection, functional exaptation, and predictions of horizontal transfer may all be affected. Here, we develop a Bayesian method for inferring TE ancestry that gives the probability that each sequence was replicative, its frequency of replication, and the probability that each extant TE sequence came from each possible ancestral sequence. Applying our method to 986 members of the newly-discovered LAVA family of TEs, we show that there were far more source elements in the history of LAVA expansion than subfamilies identified using the CoSeg subfamily-classification program. We also identify multiple replicative elements in the AluSc subfamily in humans. Our results strongly indicate that a reassessment of subfamily structures is necessary to obtain accurate estimates of mutation processes, phylogenetic relationships and historical times of activity.}, }
@article {pmid25120263, year = {2014}, author = {Oliveira, PH and Touchon, M and Rocha, EP}, title = {The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts.}, journal = {Nucleic acids research}, volume = {42}, number = {16}, pages = {10618-10631}, pmid = {25120263}, issn = {1362-4962}, support = {281605/ERC_/European Research Council/International ; }, mesh = {CRISPR-Cas Systems ; DNA Restriction-Modification Enzymes/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Archaeal ; *Genome, Bacterial ; *Interspersed Repetitive Sequences ; Prophages/genetics ; }, abstract = {The roles of restriction-modification (R-M) systems in providing immunity against horizontal gene transfer (HGT) and in stabilizing mobile genetic elements (MGEs) have been much debated. However, few studies have precisely addressed the distribution of these systems in light of HGT, its mechanisms and its vectors. We analyzed the distribution of R-M systems in 2261 prokaryote genomes and found their frequency to be strongly dependent on the presence of MGEs, CRISPR-Cas systems, integrons and natural transformation. Yet R-M systems are rare in plasmids, in prophages and nearly absent from other phages. Their abundance depends on genome size for small genomes where it relates with HGT but saturates at two occurrences per genome. Chromosomal R-M systems might evolve under cycles of purifying and relaxed selection, where sequence conservation depends on the biochemical activity and complexity of the system and total gene loss is frequent. Surprisingly, analysis of 43 pan-genomes suggests that solitary R-M genes rarely arise from the degradation of R-M systems. Solitary genes are transferred by large MGEs, whereas complete systems are more frequently transferred autonomously or in small MGEs. Our results suggest means of testing the roles for R-M systems and their associations with MGEs.}, }
@article {pmid25118883, year = {2014}, author = {Wash, R and Soria, CD}, title = {Voyage to the bottom of the 'seaquence'.}, journal = {Nature reviews. Microbiology}, volume = {12}, number = {9}, pages = {597}, pmid = {25118883}, issn = {1740-1534}, mesh = {Bacterial Proteins/genetics ; Bacteriophages/enzymology/*genetics ; Gammaproteobacteria/enzymology/*genetics/virology ; Gene Transfer, Horizontal ; Genome, Bacterial/*genetics ; Genome, Viral/*genetics ; High-Throughput Nucleotide Sequencing ; Host-Pathogen Interactions ; Hot Temperature ; Hydrogen Sulfide/metabolism ; Hydrogensulfite Reductase/*genetics ; Hydrothermal Vents/microbiology ; *Metagenomics ; Oxidation-Reduction ; Sequence Analysis, DNA ; Sulfur/metabolism ; Viral Proteins/genetics ; }, }
@article {pmid25118075, year = {2014}, author = {Matilla, MA and Fang, X and Salmond, GP}, title = {Viunalikeviruses are environmentally common agents of horizontal gene transfer in pathogens and biocontrol bacteria.}, journal = {The ISME journal}, volume = {8}, number = {10}, pages = {2143-2147}, pmid = {25118075}, issn = {1751-7370}, support = {BB/G000298/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/H002677/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteria/genetics/virology ; Bacteriophages/genetics ; Biological Control Agents ; *Gene Transfer, Horizontal ; Myoviridae/*genetics/ultrastructure ; Plasmids/genetics ; Transduction, Genetic ; Virulence/genetics ; }, abstract = {Bacteriophages have been used as natural biocontrol and therapeutic agents, but also as biotechnological tools for bacterial engineering. We showed recently that the transducing bacteriophage ϕMAM1 is a ViI-like phage and a member of the new genus, 'Viunalikevirus'. Here, we show that four additional ViI-like phages and three new environmentally isolated viunalikeviruses, all infecting plant and human pathogens, are very efficient generalised transducers capable of transducing chromosomal markers at frequencies of up to 10(-4) transductants per plaque-forming unit. We also demonstrate the interstrain transduction of plasmids and chromosomal markers, including genes involved in anabolism, genes for virulence and genes encoding secondary metabolites involved in biocontrol. We propose that all viunalikeviruses are likely to perform efficient horizontal gene transfer. Viunalikeviruses therefore represent useful agents for functional genomics and bacterial engineering, and for chemical and synthetic biology studies, but could be viewed as inappropriate choices for phage therapy.}, }
@article {pmid25115940, year = {2014}, author = {Dagan, T and Bapteste, E and McInerney, JO and Martin, WF}, title = {SMBE Satellite meeting on reticulated microbial evolution 2014--meeting report.}, journal = {Genome biology and evolution}, volume = {6}, number = {9}, pages = {2206-2209}, pmid = {25115940}, issn = {1759-6653}, mesh = {Bacteria/classification/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial ; }, }
@article {pmid25115242, year = {2014}, author = {Smyth, DJ and Shera, J and Bauer, MJ and Cameron, A and McNeilly, CL and Sriprakash, KS and McMillan, DJ}, title = {Conjugative transfer of ICESde3396 between three β-hemolytic streptococcal species.}, journal = {BMC research notes}, volume = {7}, number = {}, pages = {521}, pmid = {25115242}, issn = {1756-0500}, mesh = {*Conjugation, Genetic ; Hemolysis ; *Interspersed Repetitive Sequences ; Species Specificity ; Streptococcus/classification/*genetics ; }, abstract = {BACKGROUND: Integrative conjugative elements (ICEs) are mobile genetic elements (MGEs) that possess all genes necessary for excision, transfer and integration into recipient genome. They also carry accessory genes that impart new phenotypic features to recipient strains. ICEs therefore play an important role in genomic plasticity and population structure. We previously characterised ICESde3396, the first ICE identified in the β-hemolytic Streptococcus dysgalactiae subsp equisimilis (SDSE) and demonstrated its transfer to single isolates of Streptococcus pyogenes (group A streptococcus, GAS) and Streptococcus agalactiae (group B streptococcus, GBS). While molecular studies found the ICE in multiple SDSE and GBS isolates, it was absent in all GAS isolates examined.<br><br>RESULTS: Here we demonstrate that ICESde3396:km is transferable from SDSE to multiple SDSE, GAS and GBS isolates. However not all strains of these species were successful recipients under the same growth conditions. To address the role that host factors may have in conjugation we also undertook conjugation experiments in the presence of A549 epithelial cells and DMEM. While Horizontal Gene Transfer (HGT) occurred, conjugation efficiencies were no greater than when similar experiments were conducted in DMEM. Additionally transfer to GAS NS235 was successful in the presence of DMEM but not in Todd Hewitt Broth suggesting that nutritional factors may also influence HGT. The GAS and GBS transconjugants produced in this study are also able to act as donors of the ICE.<br><br>CONCLUSION: We conclude that ICEs are major sources of interspecies HGT between &#x3b2;-hemolytic streptococci, and by introducing accessory genes imparting novel phenotypic characteristics, have the potential to alter the population structure of these species.}, }
@article {pmid25110129, year = {2014}, author = {Bettini, PP and Frascella, A and Kolařík, M and Comparini, C and Pepori, AL and Santini, A and Scala, F and Scala, A}, title = {Widespread horizontal transfer of the cerato-ulmin gene between Ophiostoma novo-ulmi and Geosmithia species.}, journal = {Fungal biology}, volume = {118}, number = {8}, pages = {663-674}, doi = {10.1016/j.funbio.2014.04.007}, pmid = {25110129}, issn = {1878-6146}, mesh = {Ascomycota/*genetics/isolation &amp; purification ; Fungal Proteins/*genetics ; Gene Expression Profiling ; *Gene Transfer, Horizontal ; Genes, Fungal ; Molecular Sequence Data ; Mycotoxins/*genetics ; Plant Diseases/microbiology ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Ulmus/microbiology ; }, abstract = {Previous work had shown that a sequence homologous to the gene encoding class II hydrophobin cerato-ulmin from the fungus Ophiostoma novo-ulmi, the causal agent of Dutch Elm Disease (DED), was present in a strain of the unrelated species Geosmithia species 5 (Ascomycota: Hypocreales) isolated from Ulmus minor affected by DED. As both fungi occupy the same habitat, even if different ecological niches, the occurrence of horizontal gene transfer was proposed. In the present work we have analysed for the presence of the cerato-ulmin gene 70 Geosmithia strains representing 29 species, isolated from different host plants and geographic locations. The gene was found in 52.1 % of the strains derived from elm trees, while none of those isolated from nonelms possessed it. The expression of the gene in Geosmithia was also assessed by real time PCR in different growth conditions (liquid culture, solid culture, elm sawdust, dual culture with O. novo-ulmi), and was found to be extremely low in all conditions tested. On the basis of these results we propose that the cerato-ulmin gene is not functional in Geosmithia, but can be considered instead a marker of more extensive transfers of genetic material as shown in other fungi.}, }
@article {pmid25108459, year = {2014}, author = {Shanker, A and Pardasani, KR}, title = {Insilico model for prediction of lateral gene transfer in Rhodopseudomonas paulistris.}, journal = {Interdisciplinary sciences, computational life sciences}, volume = {6}, number = {4}, pages = {323-330}, doi = {10.1007/s12539-012-0071-7}, pmid = {25108459}, issn = {1867-1462}, mesh = {Alphaproteobacteria/genetics ; Bacterial Proteins/*genetics ; Bradyrhizobium/genetics ; Computer Simulation ; Cyanobacteria/genetics ; DNA, Ribosomal/analysis ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Least-Squares Analysis ; Models, Biological ; Oxidoreductases/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhodobacter/genetics ; Rhodopseudomonas/*genetics ; Sequence Analysis, DNA ; }, abstract = {Study of evolutionary phenomenon is of great interest to biologists in discovering the secrets of life. The presence of reticulation events due to lateral gene transfer (LGT) among species poses new challenges for such evolutionary studies. In this paper an attempt has been made to develop an insilico model to predict LGT in the Rhodopseudomonas paulistris. Neighbour Joining method is employed to generate phylogenetic tree of 26 sequences of Alphaproteobacteria and one sequence of Cyanobacteria used as an out group. Then Least Squares approach is employed to predict the reticulation branches. Three reticulation branches were detected among these 27 sequences. The lateral gene transfer was predicted between Rhodopseudomonas paulistris 99 D and Rhodobacter sphaeroides, Rhodopseudomonas paulistris HMD 88 and Bradyrhizobium japonicum USDA and Bradyrhizobium japonicum USDA and Rhodobacter blasticus. The results obtained are in agreement with the results obtained by earlier research workers.}, }
@article {pmid25107968, year = {2014}, author = {Matilla, MA and Salmond, GP}, title = {Bacteriophage ϕMAM1, a viunalikevirus, is a broad-host-range, high-efficiency generalized transducer that infects environmental and clinical isolates of the enterobacterial genera Serratia and Kluyvera.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {20}, pages = {6446-6457}, pmid = {25107968}, issn = {1098-5336}, support = {BB/G000298/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/H002677/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteriophages/chemistry/*genetics/*isolation &amp; purification/pathogenicity ; Gene Expression Regulation, Viral ; Gene Transfer, Horizontal ; *Genome, Viral ; Host Specificity ; Humans ; Kluyvera/isolation &amp; purification/*virology ; Lactones ; Microscopy, Electron ; Multigene Family ; Mutation ; Myoviridae/isolation &amp; purification/pathogenicity ; Phylogeny ; Plasmids ; Regulatory Sequences, Nucleic Acid ; Rhizosphere ; Serratia/genetics/isolation &amp; purification/*virology ; Transduction, Genetic ; Viral Structural Proteins/analysis/chemistry ; }, abstract = {Members of the enterobacterial genus Serratia are ecologically widespread, and some strains are opportunistic human pathogens. Bacteriophage ϕMAM1 was isolated on Serratia plymuthica A153, a biocontrol rhizosphere strain that produces the potently bioactive antifungal and anticancer haterumalide oocydin A. The ϕMAM1 phage is a generalized transducing phage that infects multiple environmental and clinical isolates of Serratia spp. and a rhizosphere strain of Kluyvera cryocrescens. Electron microscopy allowed classification of ϕMAM1 in the family Myoviridae. Bacteriophage ϕMAM1 is virulent, uses capsular polysaccharides as a receptor, and can transduce chromosomal markers at frequencies of up to 7 × 10(-6) transductants per PFU. We also demonstrated transduction of the complete 77-kb oocydin A gene cluster and heterogeneric transduction of a plasmid carrying a type III toxin-antitoxin system. These results support the notion of the potential ecological importance of transducing phages in the acquisition of genes by horizontal gene transfer. Phylogenetic analyses grouped ϕMAM1 within the ViI-like bacteriophages, and genomic analyses revealed that the major differences between ϕMAM1 and other ViI-like phages arise in a region encoding the host recognition determinants. Our results predict that the wider genus of ViI-like phages could be efficient transducing phages, and this possibility has obvious implications for the ecology of horizontal gene transfer, bacterial functional genomics, and synthetic biology.}, }
@article {pmid25106622, year = {2014}, author = {Zhu, Q and Kosoy, M and Olival, KJ and Dittmar, K}, title = {Horizontal transfers and gene losses in the phospholipid pathway of bartonella reveal clues about early ecological niches.}, journal = {Genome biology and evolution}, volume = {6}, number = {8}, pages = {2156-2169}, pmid = {25106622}, issn = {1759-6653}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Animals ; Arthropods/microbiology ; Bacterial Proteins/chemistry/genetics/metabolism ; Bartonella/chemistry/*genetics/physiology ; Bartonella Infections/*microbiology ; Biosynthetic Pathways ; Gene Deletion ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Glycerol-3-Phosphate Dehydrogenase (NAD+)/chemistry/genetics/metabolism ; Humans ; Molecular Sequence Data ; Phospholipids/*genetics/metabolism ; Phylogeny ; Sequence Alignment ; }, abstract = {Bartonellae are mammalian pathogens vectored by blood-feeding arthropods. Although of increasing medical importance, little is known about their ecological past, and host associations are underexplored. Previous studies suggest an influence of horizontal gene transfers in ecological niche colonization by acquisition of host pathogenicity genes. We here expand these analyses to metabolic pathways of 28 Bartonella genomes, and experimentally explore the distribution of bartonellae in 21 species of blood-feeding arthropods. Across genomes, repeated gene losses and horizontal gains in the phospholipid pathway were found. The evolutionary timing of these patterns suggests functional consequences likely leading to an early intracellular lifestyle for stem bartonellae. Comparative phylogenomic analyses discover three independent lineage-specific reacquisitions of a core metabolic gene-NAD(P)H-dependent glycerol-3-phosphate dehydrogenase (gpsA)-from Gammaproteobacteria and Epsilonproteobacteria. Transferred genes are significantly closely related to invertebrate Arsenophonus-, and Serratia-like endosymbionts, and mammalian Helicobacter-like pathogens, supporting a cellular association with arthropods and mammals at the base of extant Bartonella spp. Our studies suggest that the horizontal reacquisitions had a key impact on bartonellae lineage specific ecological and functional evolution.}, }
@article {pmid25105197, year = {2014}, author = {Hespeels, B and Knapen, M and Hanot-Mambres, D and Heuskin, AC and Pineux, F and LUCAS, S and Koszul, R and Van Doninck, K}, title = {Gateway to genetic exchange? DNA double-strand breaks in the bdelloid rotifer Adineta vaga submitted to desiccation.}, journal = {Journal of evolutionary biology}, volume = {27}, number = {7}, pages = {1334-1345}, doi = {10.1111/jeb.12326}, pmid = {25105197}, issn = {1420-9101}, mesh = {Animals ; *Biological Evolution ; *DNA Breaks, Double-Stranded ; DNA Repair ; Desiccation ; *Gene Transfer, Horizontal ; Genome, Helminth ; Reproduction ; Rotifera/*genetics/physiology/radiation effects ; Ultraviolet Rays ; }, abstract = {The bdelloid rotifer lineage Adineta vaga inhabits temporary habitats subjected to frequent episodes of drought. The recently published draft sequence of the genome of A. vaga revealed a peculiar genomic structure incompatible with meiosis and suggesting that DNA damage induced by desiccation may have reshaped the genomic structure of these organisms. However, the causative link between DNA damage and desiccation has never been proven to date in rotifers. To test for the hypothesis that desiccation induces DNA double-strand breaks (DSBs), we developed a protocol allowing a high survival rate of desiccated A. vaga. Using pulsed-field gel electrophoresis to monitor genomic integrity, we followed the occurrence of DSBs in dried bdelloids and observed an accumulation of these breaks with time spent in dehydrated state. These DSBs are gradually repaired upon rehydration. Even when the genome was entirely shattered into small DNA fragments by proton radiation, A. vaga individuals were able to efficiently recover from desiccation and repair a large amount of DSBs. Interestingly, when investigating the influence of UV-A and UV-B exposure on the genomic integrity of desiccated bdelloids, we observed that these natural radiations also caused important DNA DSBs, suggesting that the genome is not protected during the desiccated stage but that the repair mechanisms are extremely efficient in these intriguing organisms.}, }
@article {pmid25093636, year = {2015}, author = {Hurwitz, BL and Brum, JR and Sullivan, MB}, title = {Depth-stratified functional and taxonomic niche specialization in the 'core' and 'flexible' Pacific Ocean Virome.}, journal = {The ISME journal}, volume = {9}, number = {2}, pages = {472-484}, pmid = {25093636}, issn = {1751-7370}, mesh = {Bacteriophages/classification/genetics/isolation &amp; purification ; DNA, Viral/metabolism ; Ecosystem ; Evolution, Molecular ; Genes, Viral ; Iron-Sulfur Proteins/genetics ; *Metagenome ; Metagenomics ; Pacific Ocean ; Seawater/*virology ; Viral Proteins/genetics ; Viruses/*classification/genetics/isolation &amp; purification/metabolism ; }, abstract = {Microbes drive myriad ecosystem processes, and their viruses modulate microbial-driven processes through mortality, horizontal gene transfer, and metabolic reprogramming by viral-encoded auxiliary metabolic genes (AMGs). However, our knowledge of viral roles in the oceans is primarily limited to surface waters. Here we assess the depth distribution of protein clusters (PCs) in the first large-scale quantitative viral metagenomic data set that spans much of the pelagic depth continuum (the Pacific Ocean Virome; POV). This established 'core' (180 PCs; one-third new to science) and 'flexible' (423K PCs) community gene sets, including niche-defining genes in the latter (385 and 170 PCs are exclusive and core to the photic and aphotic zones, respectively). Taxonomic annotation suggested that tailed phages are ubiquitous, but not abundant (<5% of PCs) and revealed depth-related taxonomic patterns. Functional annotation, coupled with extensive analyses to document non-viral DNA contamination, uncovered 32 new AMGs (9 core, 20 photic and 3 aphotic) that introduce ways in which viruses manipulate infected host metabolism, and parallel depth-stratified host adaptations (for example, photic zone genes for iron-sulphur cluster modulation for phage production, and aphotic zone genes for high-pressure deep-sea survival). Finally, significant vertical flux of photic zone viruses to the deep sea was detected, which is critical for interpreting depth-related patterns in nature. Beyond the ecological advances outlined here, this catalog of viral core, flexible and niche-defining genes provides a resource for future investigation into the organization, function and evolution of microbial molecular networks to mechanistically understand and model viral roles in the biosphere.}, }
@article {pmid25091277, year = {2014}, author = {Miller, EW and Cao, TN and Pflughoeft, KJ and Sumby, P}, title = {RNA-mediated regulation in Gram-positive pathogens: an overview punctuated with examples from the group A Streptococcus.}, journal = {Molecular microbiology}, volume = {94}, number = {1}, pages = {9-20}, pmid = {25091277}, issn = {1365-2958}, support = {R01 AI087747/AI/NIAID NIH HHS/United States ; AI087747/AI/NIAID NIH HHS/United States ; }, mesh = {*Gene Expression Regulation, Bacterial ; Gram-Positive Bacteria/genetics/metabolism ; RNA, Bacterial/*genetics/metabolism ; RNA, Small Untranslated/*genetics/metabolism ; Streptococcus pyogenes/*genetics/metabolism ; }, abstract = {RNA-based mechanisms of regulation represent a ubiquitous class of regulators that are associated with diverse processes including nutrient sensing, stress response, modulation of horizontal gene transfer, and virulence factor expression. While better studied in Gram-negative bacteria, the literature is replete with examples of the importance of RNA-mediated regulatory mechanisms to the virulence and fitness of Gram-positives. Regulatory RNAs are classified as cis-acting, e.g. riboswitches, which modulate the transcription, translation, or stability of co-transcribed RNA, or trans-acting, e.g. small regulatory RNAs, which target separate mRNAs or proteins. The group A Streptococcus (GAS, Streptococcus pyogenes) is a Gram-positive bacterial pathogen from which several regulatory RNA mechanisms have been characterized. The study of RNA-mediated regulation in GAS has uncovered novel concepts with respect to how small regulatory RNAs may positively regulate target mRNA stability, and to how CRISPR RNAs are processed from longer precursors. This review provides an overview of RNA-mediated regulation in Gram-positive bacteria, and is highlighted with specific examples from GAS research. The key roles that these systems play in regulating bacterial virulence are discussed and future perspectives outlined.}, }
@article {pmid25091146, year = {2014}, author = {McNally, L and Viana, M and Brown, SP}, title = {Cooperative secretions facilitate host range expansion in bacteria.}, journal = {Nature communications}, volume = {5}, number = {}, pages = {4594}, pmid = {25091146}, issn = {2041-1723}, support = {//Wellcome Trust/United Kingdom ; 095831//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Bacteria/*metabolism ; Gene Transfer, Horizontal ; *Host Specificity ; Host-Pathogen Interactions ; Humans ; Phylogeny ; Population Dynamics ; Species Specificity ; Virulence/genetics ; Zoonoses ; }, abstract = {The majority of emergent human pathogens are zoonotic in origin, that is, they can transmit to humans from other animals. Understanding the factors underlying the evolution of pathogen host range is therefore of critical importance in protecting human health. There are two main evolutionary routes to generalism: organisms can tolerate multiple environments or they can modify their environments to forms to which they are adapted. Here we use a combination of theory and a phylogenetic comparative analysis of 191 pathogenic bacterial species to show that bacteria use cooperative secretions that modify their environment to extend their host range and infect multiple host species. Our results suggest that cooperative secretions are key determinants of host range in bacteria, and that monitoring for the acquisition of secreted proteins by horizontal gene transfer can help predict emerging zoonoses.}, }
@article {pmid25090942, year = {2015}, author = {Koblížek, M and Moulisová, V and Muroňová, M and Oborník, M}, title = {Horizontal transfers of two types of puf operons among phototrophic members of the Roseobacter clade.}, journal = {Folia microbiologica}, volume = {60}, number = {1}, pages = {37-43}, pmid = {25090942}, issn = {1874-9356}, mesh = {Bacterial Proteins/*genetics/metabolism ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; *Operon ; Phototrophic Processes ; Phylogeny ; Roseobacter/classification/*genetics/metabolism ; }, abstract = {The Roseobacter clade represents one of the most important bacterial groups in marine environments. While some of its members are heterotrophs, many Roseobacter clade members contain bacterial photosynthetic reaction centers. We investigated the phylogeny of pufL and pufM genes encoding the L and M subunits of reaction centers using available genomic data and our own cultured species. Interestingly, phylogeny of pufL and pufM genes largely deviated from 16S rRNA-based phylogeny. The sequences split into two clearly distinct clades. While most of the studied species contained pufL and pufM sequences related to those found in Roseobacter litoralis, some of the marine species contained sequences related to the freshwater Rhodobacter species. In addition, genomic data documents that Roseobacter-type centers contain cytochrome c subunits (pufC gene product), whereas Rhodobacter-type centers incorporate PufX proteins. This indicates that the two forms of the reaction centers are not only distinct phylogenetically, but also structurally. The large deviation of pufL and pufM phylogeny from 16S phylogeny indicates multiple horizontal transfers of the puf operon among members of the order Rhodobacterales.}, }
@article {pmid25090479, year = {2014}, author = {Soanes, D and Richards, TA}, title = {Horizontal gene transfer in eukaryotic plant pathogens.}, journal = {Annual review of phytopathology}, volume = {52}, number = {}, pages = {583-614}, doi = {10.1146/annurev-phyto-102313-050127}, pmid = {25090479}, issn = {1545-2107}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteria/*pathogenicity ; Fungi/*pathogenicity ; *Gene Transfer, Horizontal ; Plants/*microbiology ; }, abstract = {Gene transfer has been identified as a prevalent and pervasive phenomenon and an important source of genomic innovation in bacteria. The role of gene transfer in microbial eukaryotes seems to be of a reduced magnitude but in some cases can drive important evolutionary innovations, such as new functions that underpin the colonization of different niches. The aim of this review is to summarize published cases that support the hypothesis that horizontal gene transfer (HGT) has played a role in the evolution of phytopathogenic traits in fungi and oomycetes. Our survey of the literature identifies 46 proposed cases of transfer of genes that have a putative or experimentally demonstrable phytopathogenic function. When considering the life-cycle steps through which a pathogen must progress, the majority of the HGTs identified are associated with invading, degrading, and manipulating the host. Taken together, these data suggest HGT has played a role in shaping how fungi and oomycetes colonize plant hosts.}, }
@article {pmid25087596, year = {2014}, author = {Riber, L and Poulsen, PH and Al-Soud, WA and Skov Hansen, LB and Bergmark, L and Brejnrod, A and Norman, A and Hansen, LH and Magid, J and Sørensen, SJ}, title = {Exploring the immediate and long-term impact on bacterial communities in soil amended with animal and urban organic waste fertilizers using pyrosequencing and screening for horizontal transfer of antibiotic resistance.}, journal = {FEMS microbiology ecology}, volume = {90}, number = {1}, pages = {206-224}, doi = {10.1111/1574-6941.12403}, pmid = {25087596}, issn = {1574-6941}, mesh = {Animals ; Bacteria/*classification/genetics/isolation &amp; purification ; Biodiversity ; Cattle ; Drug Resistance, Microbial/*genetics ; *Fertilizers ; Gene Transfer, Horizontal ; Manure ; Pseudomonas/drug effects/*genetics/isolation &amp; purification ; Recycling ; Sequence Analysis, DNA ; Sewage ; *Soil Microbiology ; }, abstract = {We investigated immediate and long-term effects on bacterial populations of soil amended with cattle manure, sewage sludge or municipal solid waste compost in an ongoing agricultural field trial. Soils were sampled in weeks 0, 3, 9 and 29 after fertilizer application. Pseudomonas isolates were enumerated, and the impact on soil bacterial community structure was investigated using 16S rRNA amplicon pyrosequencing. Bacterial community structure at phylum level remained mostly unaffected. Actinobacteria, Proteobacteria and Chloroflexi were the most prevalent phyla significantly responding to sampling time. Seasonal changes seemed to prevail with decreasing bacterial richness in week 9 followed by a significant increase in week 29 (springtime). The Pseudomonas population richness seemed temporarily affected by fertilizer treatments, especially in sludge- and compost-amended soils. To explain these changes, prevalence of antibiotic- and mercury-resistant pseudomonads was investigated. Fertilizer amendment had a transient impact on the resistance profile of the soil community; abundance of resistant isolates decreased with time after fertilizer application, but persistent strains appeared multiresistant, also in unfertilized soil. Finally, the ability of a P. putida strain to take up resistance genes from indigenous soil bacteria by horizontal gene transfer was present only in week 0, indicating a temporary increase in prevalence of transferable antibiotic resistance genes.}, }
@article {pmid25083931, year = {2015}, author = {Youssef, NH and Rinke, C and Stepanauskas, R and Farag, I and Woyke, T and Elshahed, MS}, title = {Insights into the metabolism, lifestyle and putative evolutionary history of the novel archaeal phylum 'Diapherotrites'.}, journal = {The ISME journal}, volume = {9}, number = {2}, pages = {447-460}, pmid = {25083931}, issn = {1751-7370}, mesh = {Archaea/classification/*genetics/metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Archaeal ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The archaeal phylum 'Diapherotrites' was recently proposed based on phylogenomic analysis of genomes recovered from an underground water seep in an abandoned gold mine (Homestake mine in Lead, SD, USA). Here we present a detailed analysis of the metabolic capabilities and genomic features of three single amplified genomes (SAGs) belonging to the 'Diapherotrites'. The most complete of the SAGs, Candidatus 'Iainarchaeum andersonii' (Cand. IA), had a small genome (∼1.24 Mb), short average gene length (822 bp), one ribosomal RNA operon, high coding density (∼90.4%), high percentage of overlapping genes (27.6%) and low incidence of gene duplication (2.16%). Cand. IA genome possesses limited catabolic capacities that, nevertheless, could theoretically support a free-living lifestyle by channeling a narrow range of substrates such as ribose, polyhydroxybutyrate and several amino acids to acetyl-coenzyme A. On the other hand, Cand. IA possesses relatively well-developed anabolic capabilities, although it remains auxotrophic for several amino acids and cofactors. Phylogenetic analysis suggests that the majority of Cand. IA anabolic genes were acquired from bacterial donors via horizontal gene transfer. We thus propose that members of the 'Diapherotrites' have evolved from an obligate symbiotic ancestor by acquiring anabolic genes from bacteria that enabled independent biosynthesis of biological molecules previously acquired from symbiotic hosts. 'Diapherotrites' 16S rRNA genes exhibit multiple mismatches with the majority of archaeal 16S rRNA primers, a fact that could be responsible for their observed rarity in amplicon-generated data sets. The limited substrate range, complex growth requirements and slow growth rate predicted could be responsible for its refraction to isolation.}, }
@article {pmid25081867, year = {2014}, author = {Thapa, K and Oja, T and Metsä-Ketelä, M}, title = {Molecular evolution of the bacterial pseudouridine-5'-phosphate glycosidase protein family.}, journal = {The FEBS journal}, volume = {281}, number = {19}, pages = {4439-4449}, doi = {10.1111/febs.12950}, pmid = {25081867}, issn = {1742-4658}, mesh = {Amino Acid Sequence ; Burkholderia/enzymology/genetics ; Conserved Sequence ; Escherichia coli/enzymology/genetics ; Escherichia coli Proteins/chemistry/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; Glycoside Hydrolases/chemistry/*genetics ; Naphthoquinones/chemistry ; Phylogeny ; Streptomyces/enzymology/genetics ; Uracil/chemistry ; }, abstract = {Pseudouridine is a noncanonical C-nucleoside commonly present in RNA, which is not metabolized in mammals, but can be recycled by the unique enzyme family of bacterial pseudouridine glycosidases such as YeiN from Escherichia coli. Here, we present rigorous bioinformatic and biochemical analyses of the protein family in order to find sequences that might code for nonpseudouridine glycosidase activities. To date, the only other function reported for the enzyme family occurs during the biosynthesis of the antibiotic alnumycin A in Streptomyces species, where AlnA functions as an unusual C-glycosynthase. Bioinformatics analysis of 755 protein sequences identified one group of sequences that were unlikely to harbour pseudouridine glycosidase activities. This observation was confirmed in vitro with one representative protein, IdgA from Streptomyces albus, which was unable to synthesize pseudouridine monophosphate, but was able to attach d-ribose-5-phosphate to juglone. Furthermore, our analyses provide evidence for horizontal gene transfer of pseudouridine glycosidases that may have occurred in Streptomyces and Doria species. Inspection of the genomic loci in the vicinity of pseudouridine glycosidases revealed that in 77% of the strains a kinase gene putatively involved in the phosphorylation of pseudouridine was found nearby, whereas the sequences encoding nonpseudouridine glycosidases coexisted with a phosphatase of the haloacid dehalogenase enzyme family. The investigation suggested that these unknown sequences might be involved in the biosynthesis of soluble blue pigments because of the presence of genes homologous to nonribosomal peptide synthetases.}, }
@article {pmid25081506, year = {2014}, author = {Raymond, JA}, title = {The ice-binding proteins of a snow alga, Chloromonas brevispina: probable acquisition by horizontal gene transfer.}, journal = {Extremophiles : life under extreme conditions}, volume = {18}, number = {6}, pages = {987-994}, pmid = {25081506}, issn = {1433-4909}, support = {P20GM103440/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Chlamydomonas/*genetics/metabolism ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/chemistry/*genetics/metabolism ; Protein Binding ; Protein Isoforms/chemistry/genetics/metabolism ; Protein Structure, Tertiary ; Snow/*microbiology ; }, abstract = {All ice-and snow-related unicellular algae examined so far secrete ice-binding proteins (IBPs) to mitigate freezing damage. Two types of IBP have been identified in chlorophytes. Type 1 IBPs are members of a large family of proteins that share a large domain of unknown function (DUF3494). Previous studies have suggested that the type 1 algal IBP genes were acquired by horizontal gene transfer. To test this hypothesis I sequenced the IBP genes of a snow alga, Chloromonas brevispina. The IBPs were identified by ice affinity purification, de novo sequencing of a tryptic peptide and large-scale sequencing of the transcriptome and genome. C. brevispina has genes for over 20 IBP isoforms, which strongly indicates their importance. The IBPs are all of type 1 and match fungal and bacterial proteins more closely than they match known algal IBPs, providing further evidence that the genes were acquired by horizontal transfer. Modeling of the 3D structures of the IBPs based on the known structure of a homologous protein suggests that the ice-binding site has characteristics that are shared by all DUF3494 proteins.}, }
@article {pmid25080366, year = {2014}, author = {Nagashima, KV and Verméglio, A and Fusada, N and Nagashima, S and Shimada, K and Inoue, K}, title = {Exchange and complementation of genes coding for photosynthetic reaction center core subunits among purple bacteria.}, journal = {Journal of molecular evolution}, volume = {79}, number = {1-2}, pages = {52-62}, pmid = {25080366}, issn = {1432-1432}, mesh = {Bacterial Proteins/*genetics ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; Genetic Complementation Test ; Mutation ; Photosynthesis/genetics ; Photosynthetic Reaction Center Complex Proteins/*genetics ; Phylogeny ; Proteobacteria/*genetics/growth &amp; development ; }, abstract = {A mutant of the phototrophic species belonging to the β-proteobacteria, Rubrivivax gelatinosus, lacking the photosynthetic growth ability was constructed by the removal of genes coding for the L, M, and cytochrome subunits of the photosynthetic reaction center complex. The L, M, and cytochrome genes derived from five other species of proteobacteria, Acidiphilium rubrum, Allochromatium vinosum, Blastochloris viridis, Pheospirillum molischianum, and Roseateles depolymerans, and the L and M subunits from two other species, Rhodobacter sphaeroides and Rhodopseudomonas palustris, respectively, have been introduced into this mutant. Introduction of the genes from three of these seven species, Rte. depolymerans, Ach. vinosum, and Psp. molischianum, restored the photosynthetic growth ability of the mutant of Rvi. gelatinosus, although the growth rates were 1.5, 9.4, and 10.7 times slower, respectively, than that of the parent strain. Flash-induced kinetic measurements for the intact cells of these three mutants showed that the photo-oxidized cytochrome c bound to the introduced reaction center complex could be rereduced by electron donor proteins of Rvi. gelatinosus with a t1/2 of less than 10 ms. The reaction center core subunits of photosynthetic proteobacteria appear to be exchangeable if the sequence identities of the LM core subunits between donor and acceptor species are high enough, i.e., 70% or more.}, }
@article {pmid25076031, year = {2014}, author = {Wang, Z and Xie, Z and Cai, Y and Shu, K and Huang, F}, title = {Advances in phylogenomics.}, journal = {Yi chuan = Hereditas}, volume = {36}, number = {7}, pages = {669-678}, doi = {10.3724/SP.J.1005.2014.0669}, pmid = {25076031}, issn = {0253-9772}, mesh = {Animals ; Eukaryota/*genetics ; Genome ; Genomics/instrumentation/methods/*trends ; Humans ; *Phylogeny ; }, abstract = {Phylogenomics is a new phylogenetic field that aims to rebuild phylogenetic relationship of organisms using whole genome data. It can effectively eliminate the impact of horizontal gene transfer and variant evolutionary rates on phylogeny. According to the genome data type they are based on, these methods can be classified into five groups: multi-gene based, gene content based, gene order based, K-string based, and metabolic pathway based. The mechanism, speed, accuracy, applicable range and their application of these methods are summarized. The prospects of phylogenomics and challenges that it is faced with are also discussed.}, }
@article {pmid25074823, year = {2014}, author = {Trubitsyn, IV and Belousova, EV and Tutukina, MN and Merkel, AY and Dubinina, GA and Grabovich, MY}, title = {Expansion of ability of denitrification within the filamentous colorless sulfur bacteria of the genus Thiothrix.}, journal = {FEMS microbiology letters}, volume = {358}, number = {1}, pages = {72-80}, doi = {10.1111/1574-6968.12548}, pmid = {25074823}, issn = {1574-6968}, mesh = {Anaerobiosis ; Cluster Analysis ; *Denitrification ; Evolution, Molecular ; Gene Transfer, Horizontal ; Metabolic Networks and Pathways/*genetics ; Molecular Sequence Data ; Nitrates/*metabolism ; Nitrite Reductases/analysis/genetics ; Nitrites/*metabolism ; Oxidation-Reduction ; Phylogeny ; Sequence Analysis, DNA ; Sulfur/metabolism ; Thiothrix/*genetics/*metabolism ; }, abstract = {Filamentous sulfur bacteria of the genus Thiothrix are able to respire nitrate (NO3-→NO2-) under anaerobic growth. Here, Thiothrix caldifontis (G1(T), G3), Thiothrix unzii (A1(T), TN) and Thiothrix lacustris AS were shown to be capable of further reduction of nitrite and/or nitrous oxides (denitrification). In particular, in the genomes of these strains, excluding T. unzii TN, the nirS gene encoding periplasmic respiratory nitrite reductase was detected, and for T. lacustris AS the nirS expression was confirmed during anaerobic growth. The nirK gene, coding for an alternative nitrite reductase, and the nrfA gene, encoding nitrite reduction to ammonia, were not found in any investigated strains. All Thiothrix species capable of denitrification possess the cnorB gene encoding cytochrome c-dependent NO reductase but not the qnorB gene coding for quinol-dependent NO reductase. Denitrifying capacity ('full' or 'truncated') can vary between strains belonging to the same species and correlates with physical-chemical parameters of the environment such as nitrate, hydrogen sulfide and oxygen concentrations. Phylogenetic analysis revealed the absence of recent horizontal transfer events for narG and nirS; however, cnorB was subjected to gene transfer before the separation of modern species from a last common ancestor of the Thiothrix species.}, }
@article {pmid25071736, year = {2014}, author = {Gardiner, M and Hoke, DE and Egan, S}, title = {An ortholog of the Leptospira interrogans lipoprotein LipL32 aids in the colonization of Pseudoalteromonas tunicata to host surfaces.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {323}, pmid = {25071736}, issn = {1664-302X}, abstract = {The bacterium Pseudoalteromonas tunicata is a common surface colonizer of marine eukaryotes, including the macroalga Ulva australis.Genomic analysis of P. tunicata identified genes potentially involved in surface colonization, including genes with homology to bacterial virulence factors that mediate attachment. Of particular interest is the presence of a gene, designated ptlL32, encoding an ortholog to the Leptospira lipoprotein LipL32, which has been shown to facilitate the interaction of Leptospira sp. with host extracellular matrix (ECM) structures and is thought to be an important virulence trait for pathogenic Leptospira. To investigate the role of PtlL32 in the colonization by P. tunicata we constructed and characterized a ΔptlL32 mutant strain. Whilst P. tunicata ΔptlL32 bound to an abiotic surface with the same capacity as the wild type strain, it had a marked effect on the ability of P. tunicata to bind to ECM, suggesting a specific role in attachment to biological surfaces. Loss of PtlL32 also significantly reduced the capacity for P. tunciata to colonize the host algal surface demonstrating a clear role for this protein as a host-colonization factor. PtlL32 appears to have a patchy distribution across specific groups of environmental bacteria and phylogenetic analysis of PtlL32 orthologous proteins from non-Leptospira species suggests it may have been acquired via horizontal gene transfer between distantly related lineages. This study provides the first evidence for an attachment function for a LipL32-like protein outside the Leptospira and thereby contributes to the understanding of host colonization in ecologically distinct bacterial species.}, }
@article {pmid25069588, year = {2014}, author = {Johnson, CM and Grossman, AD}, title = {Identification of host genes that affect acquisition of an integrative and conjugative element in Bacillus subtilis.}, journal = {Molecular microbiology}, volume = {93}, number = {6}, pages = {1284-1301}, pmid = {25069588}, issn = {1365-2958}, support = {R01 GM050895/GM/NIGMS NIH HHS/United States ; R01GM050895/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacillus subtilis/*genetics ; Bacterial Proteins/*genetics ; Conjugation, Genetic ; *DNA Transposable Elements ; Gene Expression Regulation, Bacterial ; Gene Library ; Mutation ; }, abstract = {Conjugation, a major type of horizontal gene transfer in bacteria, involves transfer of DNA from a donor to a recipient using donor-encoded conjugation machinery. Using a high-throughput screen (Tn-seq), we identified genes in recipients that contribute to acquisition of the integrative and conjugative element ICEBs1 by Bacillus subtilis. We found that null mutations in some genes caused an increase, and others a decrease in conjugation efficiency. Some mutations affected conjugation only when present in recipients. Other mutations affected conjugation when present in donors or recipients. Most of the genes identified are known or predicted to affect the cell envelope. Several encode enzymes involved in phospholipid biosynthesis and one encodes a homologue of penicillin-binding proteins. Two of the genes identified also affected conjugation of Tn916, indicating that their roles in conjugation may be general. We did not identify any genes in recipients that were essential for ICEBs1 conjugation, indicating that if there are such genes, then these are either essential for cell growth or redundant. Our results indicate that acquisition of ICEBs1, and perhaps other conjugative elements, is robust and not easily avoided by mutation and that several membrane-related functions affect the efficiency of conjugation.}, }
@article {pmid25069453, year = {2014}, author = {Kulkarni, HM and Jagannadham, MV}, title = {Biogenesis and multifaceted roles of outer membrane vesicles from Gram-negative bacteria.}, journal = {Microbiology (Reading, England)}, volume = {160}, number = {Pt 10}, pages = {2109-2121}, doi = {10.1099/mic.0.079400-0}, pmid = {25069453}, issn = {1465-2080}, mesh = {Cell Membrane/chemistry/*metabolism ; Exosomes/*metabolism ; Gram-Negative Bacteria/chemistry/cytology/*metabolism ; }, abstract = {Outer membrane vesicles (OMVs) released from Gram-negative bacteria consist of lipids, proteins, lipopolysaccharides and other molecules. OMVs are associated with several biological functions such as horizontal gene transfer, intracellular and intercellular communication, transfer of contents to host cells, and eliciting an immune response in host cells. Although hypotheses have been made concerning the mechanism of biogenesis of these vesicles, research on OMV formation is far from complete. The roles of outer membrane components, bacterial quorum sensing molecules and some specific proteins in OMV biogenesis have been studied. This review discusses the different models that have been proposed for OMV biogenesis, along with details of the biological functions of OMVs and the likely scope of future research.}, }
@article {pmid25068406, year = {2014}, author = {Jones, GW and Doyle, S and Fitzpatrick, DA}, title = {The evolutionary history of the genes involved in the biosynthesis of the antioxidant ergothioneine.}, journal = {Gene}, volume = {549}, number = {1}, pages = {161-170}, doi = {10.1016/j.gene.2014.07.065}, pmid = {25068406}, issn = {1879-0038}, mesh = {Bacteria/*classification/genetics/metabolism ; Bacterial Proteins/*genetics/metabolism ; Ergothioneine/*biosynthesis ; Evolution, Molecular ; Fungal Proteins/*genetics/metabolism ; Fungi/*classification/genetics/metabolism ; Gene Fusion ; Gene Transfer, Horizontal ; Genome, Bacterial ; Genome, Fungal ; Multigene Family ; Phylogeny ; }, abstract = {Ergothioneine (EGT) is a histidine betaine derivative that exhibits antioxidant action in humans. EGT is primarily synthesized by fungal species and a number of bacterial species. A five-gene cluster (egtA, egtB, egtC, egtD &amp;egtE) responsible for EGT production in Mycobacteria smegmatis has recently been identified. The first fungal biosynthetic EGT gene (NcEgt-1) has also been identified in Neurospora crassa. NcEgt-1 contains domains similar to those found in M. smegmatis egtB and egtD. EGT is biomembrane impermeable. Here we inferred the evolutionary history of the EGT cluster in prokaryotes as well as examining the phyletic distribution of Egt-1 in the fungal kingdom. A genomic survey of 2509 prokaryotes showed that the five-gene EGT cluster is only found in the Actinobacteria. Our survey identified more than 400 diverse prokaryotes that contain genetically linked orthologs of egtB and egtD. Phylogenetic analyses of Egt proteins show a complex evolutionary history and multiple incidences of horizontal gene transfer. Our analysis also identified two independent incidences of a fusion event of egtB and egtD in bacterial species. A genomic survey of over 100 fungal genomes shows that Egt-1 is found in all fungal phyla, except species that belong to the Saccharomycotina subphylum. This analysis provides a comprehensive analysis of the distribution of the key genes involved in the synthesis of EGT in prokaryotes and fungi. Our phylogenetic inferences illuminate the complex evolutionary history of the genes involved in EGT synthesis in prokaryotes. The potential to synthesize EGT is a fungal trait except for species belonging to the Saccharomycotina subphylum.}, }
@article {pmid25065645, year = {2014}, author = {Prigent, S and Collet, G and Dittami, SM and Delage, L and Ethis de Corny, F and Dameron, O and Eveillard, D and Thiele, S and Cambefort, J and Boyen, C and Siegel, A and Tonon, T}, title = {The genome-scale metabolic network of Ectocarpus siliculosus (EctoGEM): a resource to study brown algal physiology and beyond.}, journal = {The Plant journal : for cell and molecular biology}, volume = {80}, number = {2}, pages = {367-381}, doi = {10.1111/tpj.12627}, pmid = {25065645}, issn = {1365-313X}, mesh = {*Genome, Plant ; Molecular Sequence Data ; Phaeophyceae/genetics/metabolism/*physiology ; }, abstract = {Brown algae (stramenopiles) are key players in intertidal ecosystems, and represent a source of biomass with several industrial applications. Ectocarpus siliculosus is a model to study the biology of these organisms. Its genome has been sequenced and a number of post-genomic tools have been implemented. Based on this knowledge, we report the reconstruction and analysis of a genome-scale metabolic network for E. siliculosus, EctoGEM (http://ectogem.irisa.fr). This atlas of metabolic pathways consists of 1866 reactions and 2020 metabolites, and its construction was performed by means of an integrative computational approach for identifying metabolic pathways, gap filling and manual refinement. The capability of the network to produce biomass was validated by flux balance analysis. EctoGEM enabled the reannotation of 56 genes within the E. siliculosus genome, and shed light on the evolution of metabolic processes. For example, E. siliculosus has the potential to produce phenylalanine and tyrosine from prephenate and arogenate, but does not possess a phenylalanine hydroxylase, as is found in other stramenopiles. It also possesses the complete eukaryote molybdenum co-factor biosynthesis pathway, as well as a second molybdopterin synthase that was most likely acquired via horizontal gene transfer from cyanobacteria by a common ancestor of stramenopiles. EctoGEM represents an evolving community resource to gain deeper understanding of the biology of brown algae and the diversification of physiological processes. The integrative computational method applied for its reconstruction will be valuable to set up similar approaches for other organisms distant from biological benchmark models.}, }
@article {pmid25063440, year = {2014}, author = {Mönttinen, HA and Ravantti, JJ and Stuart, DI and Poranen, MM}, title = {Automated structural comparisons clarify the phylogeny of the right-hand-shaped polymerases.}, journal = {Molecular biology and evolution}, volume = {31}, number = {10}, pages = {2741-2752}, doi = {10.1093/molbev/msu219}, pmid = {25063440}, issn = {1537-1719}, support = {G1000099/MRC_/Medical Research Council/United Kingdom ; G19/3/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Aspartic Acid/*genetics ; Automation, Laboratory/methods ; Bacteria/*enzymology/genetics ; Bacterial Proteins/*chemistry/genetics ; Catalytic Domain ; Computational Biology/*methods ; Conserved Sequence ; DNA-Directed DNA Polymerase/*chemistry/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Models, Molecular ; Phylogeny ; Viral Proteins/chemistry/metabolism ; Viruses/enzymology ; }, abstract = {Polymerases are essential for life, being responsible for replication, transcription, and the repair of nucleic acid molecules. Those that share a right-hand-shaped fold and catalytic site structurally similar to the DNA polymerase I of Escherichia coli may catalyze RNA- or DNA-dependent RNA polymerization, reverse transcription, or DNA replication in eukarya, archaea, bacteria, and their viruses. We have applied novel computational methods for structure-based clustering and phylogenetic analyses of this functionally diverse polymerase superfamily, which currently comprises six families. We identified a structural core common to all right-handed polymerases, composed of 57 amino acid residues, harboring two positionally and chemically conserved residues, the catalytic aspartates. The structural conservation within each of the six families is considerable, for example, the structural core shared by family Y DNA polymerases covers over 90% of the polymerase domain of the Sulfolobus solfataricus Dpo4. Our phylogenetic analyses propose an early separation of RNA-dependent polymerases that use primers from those that are primer-independent. Furthermore, the exchange of polymerase genes between viruses and their hosts is evident. Because of this horizontal gene transfer, the phylogeny of polymerases does not always reflect the evolutionary history of the corresponding organisms.}, }
@article {pmid25061474, year = {2014}, author = {Deepak, A and Fernández-Baca, D}, title = {Enumerating all maximal frequent subtrees in collections of phylogenetic trees.}, journal = {Algorithms for molecular biology : AMB}, volume = {9}, number = {}, pages = {16}, pmid = {25061474}, issn = {1748-7188}, abstract = {BACKGROUND: A common problem in phylogenetic analysis is to identify frequent patterns in a collection of phylogenetic trees. The goal is, roughly, to find a subset of the species (taxa) on which all or some significant subset of the trees agree. One popular method to do so is through maximum agreement subtrees (MASTs). MASTs are also used, among other things, as a metric for comparing phylogenetic trees, computing congruence indices and to identify horizontal gene transfer events.<br><br>RESULTS: We give algorithms and experimental results for two approaches to identify common patterns in a collection of phylogenetic trees, one based on agreement subtrees, called maximal agreement subtrees, the other on frequent subtrees, called maximal frequent subtrees. These approaches can return subtrees on larger sets of taxa than MASTs, and can reveal new common phylogenetic relationships not present in either MASTs or the majority rule tree (a popular consensus method). Our current implementation is available on the web at https://code.google.com/p/mfst-miner/.<br><br>CONCLUSIONS: Our computational results confirm that maximal agreement subtrees and all maximal frequent subtrees can reveal a more complete phylogenetic picture of the common patterns in collections of phylogenetic trees than maximum agreement subtrees; they are also often more resolved than the majority rule tree. Further, our experiments show that enumerating maximal frequent subtrees is considerably more practical than enumerating ordinary (not necessarily maximal) frequent subtrees.}, }
@article {pmid25056334, year = {2014}, author = {Sidjabat, HE and Heney, C and George, NM and Nimmo, GR and Paterson, DL}, title = {Interspecies transfer of blaIMP-4 in a patient with prolonged colonization by IMP-4-producing Enterobacteriaceae.}, journal = {Journal of clinical microbiology}, volume = {52}, number = {10}, pages = {3816-3818}, pmid = {25056334}, issn = {1098-660X}, mesh = {Enterobacter cloacae/*enzymology/*genetics ; Enterobacteriaceae Infections/*microbiology ; Escherichia coli/*enzymology/*genetics ; Female ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genotype ; Humans ; Middle Aged ; Plasmids/analysis ; Time Factors ; beta-Lactamases/*genetics ; }, abstract = {A patient was colonized by IMP-4-producing Enterobacter cloacae and Escherichia coli strains for 7 months. IMP-4-producing E. cloacae strains were first and last isolated at day 33 and at 8 months after admission, respectively. IMP-4-producing E. coli strains were first and last isolated at days 88 and 181 after admission, respectively. The E. cloacae and E. coli isolates shared identical genetic features in terms of blaIMP-4, blaTEM-1, qnrB2, aacA4, HI2 plasmids, and ISCR1. This study shows the first prolonged colonization with in vivo interspecies transfer of blaIMP-4.}, }
@article {pmid25053814, year = {2014}, author = {Kwong, WK and Engel, P and Koch, H and Moran, NA}, title = {Genomics and host specialization of honey bee and bumble bee gut symbionts.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {31}, pages = {11509-11514}, pmid = {25053814}, issn = {1091-6490}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Bees/*genetics/metabolism/*microbiology ; Evolution, Molecular ; Gastrointestinal Tract/*microbiology ; Gene Transfer, Horizontal/genetics ; Genes, Insect/genetics ; *Genomics ; Host Specificity/*genetics ; Microbiota/genetics ; Molecular Sequence Data ; Sequence Homology, Nucleic Acid ; Symbiosis/*genetics ; }, abstract = {Gilliamella apicola and Snodgrassella alvi are dominant members of the honey bee (Apis spp.) and bumble bee (Bombus spp.) gut microbiota. We generated complete genomes of the type strains G. apicola wkB1(T) and S. alvi wkB2(T) (isolated from Apis), as well as draft genomes for four other strains from Bombus. G. apicola and S. alvi were found to occupy very different metabolic niches: The former is a saccharolytic fermenter, whereas the latter is an oxidizer of carboxylic acids. Together, they may form a syntrophic network for partitioning of metabolic resources. Both species possessed numerous genes [type 6 secretion systems, repeats in toxin (RTX) toxins, RHS proteins, adhesins, and type IV pili] that likely mediate cell-cell interactions and gut colonization. Variation in these genes could account for the host fidelity of strains observed in previous phylogenetic studies. Here, we also show the first experimental evidence, to our knowledge, for this specificity in vivo: Strains of S. alvi were able to colonize their native bee host but not bees of another genus. Consistent with specific, long-term host association, comparative genomic analysis revealed a deep divergence and little or no gene flow between Apis and Bombus gut symbionts. However, within a host type (Apis or Bombus), we detected signs of horizontal gene transfer between G. apicola and S. alvi, demonstrating the importance of the broader gut community in shaping the evolution of any one member. Our results show that host specificity is likely driven by multiple factors, including direct host-microbe interactions, microbe-microbe interactions, and social transmission.}, }
@article {pmid25053789, year = {2014}, author = {Kilian, M and Riley, DR and Jensen, A and Brüggemann, H and Tettelin, H}, title = {Parallel evolution of Streptococcus pneumoniae and Streptococcus mitis to pathogenic and mutualistic lifestyles.}, journal = {mBio}, volume = {5}, number = {4}, pages = {e01490-14}, pmid = {25053789}, issn = {2150-7511}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Biological Evolution ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/genetics ; Molecular Sequence Data ; Phylogeny ; Streptococcus mitis/*genetics/pathogenicity/physiology ; Streptococcus pneumoniae/*genetics/pathogenicity/physiology ; }, abstract = {The bacterium Streptococcus pneumoniae is one of the leading causes of fatal infections affecting humans. Intriguingly, phylogenetic analysis shows that the species constitutes one evolutionary lineage in a cluster of the otherwise commensal Streptococcus mitis strains, with which humans live in harmony. In a comparative analysis of 35 genomes, including phylogenetic analyses of all predicted genes, we have shown that the pathogenic pneumococcus has evolved into a master of genomic flexibility while lineages that evolved into the nonpathogenic S. mitis secured harmonious coexistence with their host by stabilizing an approximately 15%-reduced genome devoid of many virulence genes. Our data further provide evidence that interspecies gene transfer between S. pneumoniae and S. mitis occurs in a unidirectional manner, i.e., from S. mitis to S. pneumoniae. Import of genes from S. mitis and other mitis, anginosus, and salivarius group streptococci ensured allelic replacements and antigenic diversification and has been driving the evolution of the remarkable structural diversity of capsular polysaccharides of S. pneumoniae. Our study explains how the unique structural diversity of the pneumococcal capsule emerged and conceivably will continue to increase and reveals a striking example of the fragile border between the commensal and pathogenic lifestyles. While genomic plasticity enabling quick adaptation to environmental stress is a necessity for the pathogenic streptococci, the commensal lifestyle benefits from stability. Importance: One of the leading causes of fatal infections affecting humans, Streptococcus pneumoniae, and the commensal Streptococcus mitis are closely related obligate symbionts associated with hominids. Faced with a shortage of accessible hosts, the two opposing lifestyles evolved in parallel. We have shown that the nonpathogenic S. mitis secured harmonious coexistence with its host by stabilizing a reduced genome devoid of many virulence genes. Meanwhile, the pathogenic pneumococcus evolved into a master of genomic flexibility and imports genes from S. mitis and other related streptococci. This process ensured antigenic diversification and has been driving the evolution of the remarkable structural diversity of capsular polysaccharides of S. pneumoniae, which conceivably will continue to increase and present a challenge to disease prevention.}, }
@article {pmid25052868, year = {2014}, author = {Sidjabat, HE and Seah, KY and Coleman, L and Sartor, A and Derrington, P and Heney, C and Faoagali, J and Nimmo, GR and Paterson, DL}, title = {Expansive spread of IncI1 plasmids carrying blaCMY-2 amongst Escherichia coli.}, journal = {International journal of antimicrobial agents}, volume = {44}, number = {3}, pages = {203-208}, doi = {10.1016/j.ijantimicag.2014.04.016}, pmid = {25052868}, issn = {1872-7913}, mesh = {DNA Transposable Elements ; Escherichia coli/classification/*enzymology/*genetics ; Escherichia coli Infections/*microbiology ; Gene Order ; Gene Transfer, Horizontal ; Humans ; Molecular Typing ; Phylogeny ; Plasmids/*analysis ; Sequence Analysis, DNA ; Synteny ; Urinary Tract Infections/*microbiology ; beta-Lactamases/*genetics/*metabolism ; }, abstract = {Escherichia coli is a leading cause of urinary tract infections. One of the most common antibiotic classes used to treat such infections is the β-lactams, including cephalosporins. Resistance to the third-generation cephalosporins can be caused by production of extended-spectrum β-lactamases (ESBLs) or plasmid-mediated AmpC β-lactamases. The most commonly reported AmpC β-lactamase in E. coli is CMY-2. Plasmid-mediated CMY-2 has been frequently reported in E. coli and Salmonella sp. from food-producing animals. This study aimed to elucidate the molecular characteristics of clinical E. coli isolates carrying plasmids encoding CMY-2. A total of 67 CMY-2-producing E. coli were characterised by clonal analysis and phylogenetic typing. Characterisation of the plasmids carrying blaCMY-2 included replicon typing, plasmid profiling, plasmid transferability and sequencing of the blaCMY-2 genetic environment. As a result, E. coli producing CMY-2 was found to be highly polyclonal. The majority of CMY-2-producing E. coli belonged to phylogenetic group D. IncI1 plasmids were predominant among those carrying blaCMY-2 (96%). Restriction analysis revealed a single IncI1 plasmid carrying blaCMY-2 to be predominant and present in different clones of E. coli. IS1294-ISEcp1 complex or ISEcp1 that was truncated by IS1294 was the predominant insertion sequence upstream of blaCMY-2. The homogeneous genetic environment of blaCMY-2 observed among different strains of E. coli strongly suggests horizontal transfer of this IncI1, blaCMY-2-carrying plasmid. In summary, horizontal plasmid transfer plays a major role in the spread of blaCMY-2 in E. coli.}, }
@article {pmid25051707, year = {2014}, author = {Shamsutdinov, AF and Tiurin, IuA}, title = {[Protein toxins of Staphylococcus aureus].}, journal = {Zhurnal mikrobiologii, epidemiologii i immunobiologii}, volume = {}, number = {2}, pages = {113-120}, pmid = {25051707}, issn = {0372-9311}, mesh = {Bacterial Proteins/genetics/immunology ; Bacterial Toxins/biosynthesis/classification/genetics/*immunology ; Clonal Anergy ; Gene Expression Regulation, Bacterial/*immunology ; Gene Transfer, Horizontal ; Host-Pathogen Interactions ; Humans ; Lymphocyte Activation ; Monomeric GTP-Binding Proteins/genetics/immunology ; Staphylococcal Infections/*immunology/microbiology/pathology ; Staphylococcus aureus/genetics/*immunology/pathogenicity ; Superantigens/genetics/immunology ; T-Lymphocytes/*immunology/microbiology/pathology ; Trans-Activators/genetics/immunology ; Virulence ; }, abstract = {Main scientific-research studies regarding protein bacterial toxins of the most widespread bacteria that belong to Staphylococcus spp. genus and in particular the most pathogenic species for humans--Staphylococcus aureus, are analyzed. Structural and biological properties of protein toxins that have received the name of staphylococcus pyrogenic toxins (PTSAg) are presented. Data regarding genetic regulation of secretion and synthesis of these toxins and 3 main regulatory genetic systems (agr--accessory gene regulator, xpr--extracellular protein regulator, sar--staphylococcal accessory regulator) that coordinate synthesis of the most important protein toxins and enzymes for virulence of S. aureus, are presented.}, }
@article {pmid25051706, year = {2014}, author = {Blinov, VM and Gaĭsler, V and Krasnov, GS and Shargunov, AV and Shurdov, MA and Zverev, VV}, title = {[Cell analogs of viral proteins].}, journal = {Zhurnal mikrobiologii, epidemiologii i immunobiologii}, volume = {}, number = {2}, pages = {101-113}, pmid = {25051706}, issn = {0372-9311}, mesh = {Animals ; Biological Evolution ; Female ; Gene Products, env/genetics ; Gene Transfer, Horizontal/*immunology ; *Genome, Human ; *Genome, Viral ; Herpesviridae/*genetics ; Host-Pathogen Interactions ; Humans ; Immune Tolerance ; Placenta/immunology/metabolism/virology ; Pregnancy ; Pregnancy Proteins/genetics ; Retroelements ; Retroviridae/*genetics ; }, abstract = {Horizontal transfer of genes between viruses and their hosts played an important role in the evolution of various eukaryotes including contemporary mammals as well as the pathogens themselves. Elements of viruses of various types can be found in the genome of animals. Endogenous retroviral elements composing up to 8% of human genome length not only determine its high flexibility and rapid adaptation potential. Many of virus genes such as Fv1, Lv1, Lv2 being analogues of capsid and other proteins determine effective suppression of viral replication after cell penetration by the causative agent. Introduction of these elements into genome of a wide variety of animals from fish to primates could have taken place against the background of global natural cataclysms of viral origin. Integration of retrovirus genes coding surface glycoproteins with immunosuppressing domains into genetic apparatus of animals served as an impetus to the development of viviparity and spread ofplacental mammals. Their cell analogs syncytins perform a dual function: take direct part in the formation of syncytiotrophoblast layer of placenta and ensure tolerance of immune system of mother to embryo. The acquisition of cell genes by viruses also played an important role in their evolution: various interleukins and other modulators of immune response introduced into viral genome from cell genetic apparatus became one of the most important factors of pathogenicity of a wide variety of causative agents including poxviruses, cytomegalovirus, Epstein-Barr virus and many others. Evolutionary pathways of the virus and host are thus inseparable from each other, and character of one of these directions is largely dictated by the vector of another.}, }
@article {pmid25050964, year = {2014}, author = {McCutcheon, JP and Keeling, PJ}, title = {Endosymbiosis: protein targeting further erodes the organelle/symbiont distinction.}, journal = {Current biology : CB}, volume = {24}, number = {14}, pages = {R654-R655}, doi = {10.1016/j.cub.2014.05.073}, pmid = {25050964}, issn = {1879-0445}, mesh = {Animals ; Aphids/*genetics ; Bacteria/*genetics ; Genes, Bacterial/*genetics ; Symbiosis/*genetics ; }, abstract = {New work in aphids shows that a nuclear-encoded protein resulting from a horizontal gene transfer is targeted to a bacterial symbiont, further blurring the distinction between organelle and symbiont.}, }
@article {pmid25050957, year = {2014}, author = {Nakabachi, A and Ishida, K and Hongoh, Y and Ohkuma, M and Miyagishima, SY}, title = {Aphid gene of bacterial origin encodes a protein transported to an obligate endosymbiont.}, journal = {Current biology : CB}, volume = {24}, number = {14}, pages = {R640-R641}, doi = {10.1016/j.cub.2014.06.038}, pmid = {25050957}, issn = {1879-0445}, mesh = {Animals ; Aphids/*genetics ; Bacteria/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Symbiosis/*genetics ; }, }
@article {pmid25048697, year = {2014}, author = {Dougherty, K and Smith, BA and Moore, AF and Maitland, S and Fanger, C and Murillo, R and Baltrus, DA}, title = {Multiple phenotypic changes associated with large-scale horizontal gene transfer.}, journal = {PloS one}, volume = {9}, number = {7}, pages = {e102170}, pmid = {25048697}, issn = {1932-6203}, mesh = {Biofilms ; Drug Resistance, Microbial ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; Phenotype ; Pseudomonas Infections/*microbiology ; Pseudomonas stutzeri/cytology/drug effects/*genetics/physiology ; }, abstract = {Horizontal gene transfer often leads to phenotypic changes within recipient organisms independent of any immediate evolutionary benefits. While secondary phenotypic effects of horizontal transfer (i.e., changes in growth rates) have been demonstrated and studied across a variety of systems using relatively small plasmids and phage, little is known about the magnitude or number of such costs after the transfer of larger regions. Here we describe numerous phenotypic changes that occur after a large-scale horizontal transfer event (∼1 Mb megaplasmid) within Pseudomonas stutzeri including sensitization to various stresses as well as changes in bacterial behavior. These results highlight the power of horizontal transfer to shift pleiotropic relationships and cellular networks within bacterial genomes. They also provide an important context for how secondary effects of transfer can bias evolutionary trajectories and interactions between species. Lastly, these results and system provide a foundation to investigate evolutionary consequences in real time as newly acquired regions are ameliorated and integrated into new genomic contexts.}, }
@article {pmid25042042, year = {2014}, author = {Kruse, T and Levisson, M and de Vos, WM and Smidt, H}, title = {vanI: a novel D-Ala-D-Lac vancomycin resistance gene cluster found in Desulfitobacterium hafniense.}, journal = {Microbial biotechnology}, volume = {7}, number = {5}, pages = {456-466}, pmid = {25042042}, issn = {1751-7915}, mesh = {Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; Desulfitobacterium/*drug effects/*genetics ; Molecular Sequence Data ; *Multigene Family ; Phylogeny ; Sequence Analysis, DNA ; *Vancomycin Resistance ; }, abstract = {The glycopeptide vancomycin was until recently considered a drug of last resort against Gram-positive bacteria. Increasing numbers of bacteria, however, are found to carry genes that confer resistance to this antibiotic. So far, 10 different vancomycin resistance clusters have been described. A chromosomal vancomycin resistance gene cluster was previously described for the anaerobic Desulfitobacterium hafniense Y51. We demonstrate that this gene cluster, characterized by its d-Ala-d-Lac ligase-encoding vanI gene, is present in all strains of D. hafniense, D. chlororespirans and some strains of Desulfosporosinus spp. This gene cluster was not found in vancomycin-sensitive Desulfitobacterium or Desulfosporosinus spp., and we show that this antibiotic resistance can be exploited as an intrinsic selection marker for Desulfitobacterium hafniense and D. chlororespirans. The gene cluster containing vanI is phylogenetically only distantly related with those described from soil and gut bacteria, but clusters instead with vancomycin resistance genes found within the phylum Actinobacteria that include several vancomycin-producing bacteria. It lacks a vanH homologue, encoding a D-lactate dehydrogenase, previously thought to always be present within vancomycin resistance gene clusters. The location of vanH outside the resistance gene cluster likely hinders horizontal gene transfer. Hence, the vancomycin resistance cluster in D. hafniense should be regarded a novel one that we here designated vanI after its unique d-Ala-d-Lac ligase.}, }
@article {pmid25040107, year = {2014}, author = {Ma, LJ}, title = {Horizontal chromosome transfer and rational strategies to manage Fusarium vascular wilt diseases.}, journal = {Molecular plant pathology}, volume = {15}, number = {8}, pages = {763-766}, pmid = {25040107}, issn = {1364-3703}, mesh = {Chromosomes, Plant/*genetics ; Food Supply ; Fusarium/pathogenicity/*physiology ; Gene Transfer, Horizontal/*genetics ; Host-Pathogen Interactions/genetics ; Plant Diseases/*genetics/immunology/*microbiology ; Virulence Factors/metabolism ; }, }
@article {pmid25039682, year = {2014}, author = {Boritsch, EC and Supply, P and Honoré, N and Seemann, T and Stinear, TP and Brosch, R}, title = {A glimpse into the past and predictions for the future: the molecular evolution of the tuberculosis agent.}, journal = {Molecular microbiology}, volume = {93}, number = {5}, pages = {835-852}, doi = {10.1111/mmi.12720}, pmid = {25039682}, issn = {1365-2958}, mesh = {*Evolution, Molecular ; Genome, Bacterial ; Humans ; Mycobacterium/classification/*genetics/isolation &amp; purification ; Phylogeny ; Tuberculosis/*microbiology ; }, abstract = {Recent advances in genomics and molecular biology are providing an excellent opportunity to get a glimpse into the past, to examine the present, and to predict the future evolution of pathogenic mycobacteria, and in particular that of Mycobacterium tuberculosis, the agent of human tuberculosis. The recent availability of genome sequences of several Mycobacterium canettii strains, representing evolutionary early-branching tubercle bacilli, has allowed the genomic and molecular features of the putative ancestor of the M. tuberculosis complex (MTBC) to be reconstituted. Analyses have identified extensive lateral gene transfer and recombination events in M. canettii and/or the MTBC, leading to suggestions of a past environmental reservoir where the ancestor(s) of the tubercle bacilli might have adapted to an intracellular lifestyle. The daily increases in M. tuberculosis genome data and the remaining urgent Public Health problem of tuberculosis make it more important than ever to try and understand the origins and the future evolution of the MTBC. Here we critically discuss a series of questions on gene-loss, acquisition, recombination, mutation and conservation that have recently arisen and which are key to better understand the outstanding evolutionary success of one of the most widespread and most deadly bacterial pathogens in the history of humankind.}, }
@article {pmid25039543, year = {2014}, author = {Kaschner, M and Loeschcke, A and Krause, J and Minh, BQ and Heck, A and Endres, S and Svensson, V and Wirtz, A and von Haeseler, A and Jaeger, KE and Drepper, T and Krauss, U}, title = {Discovery of the first light-dependent protochlorophyllide oxidoreductase in anoxygenic phototrophic bacteria.}, journal = {Molecular microbiology}, volume = {93}, number = {5}, pages = {1066-1078}, doi = {10.1111/mmi.12719}, pmid = {25039543}, issn = {1365-2958}, mesh = {Alphaproteobacteria/classification/*enzymology/genetics/isolation &amp; purification ; Amino Acid Sequence ; Bacterial Proteins/chemistry/genetics/*metabolism ; Biocatalysis/radiation effects ; Light ; Molecular Sequence Data ; Oxidoreductases Acting on CH-CH Group Donors/chemistry/genetics/*metabolism ; Oxygen/metabolism ; Phototrophic Processes/radiation effects ; Phylogeny ; Protochlorophyllide/metabolism ; Sequence Alignment ; Triticum/microbiology ; }, abstract = {In all photosynthetic organisms, chlorophylls function as light-absorbing photopigments allowing the efficient harvesting of light energy. Chlorophyll biosynthesis recurs in similar ways in anoxygenic phototrophic proteobacteria as well as oxygenic phototrophic cyanobacteria and plants. Here, the biocatalytic conversion of protochlorophyllide to chlorophyllide is catalysed by evolutionary and structurally distinct protochlorophyllide reductases (PORs) in anoxygenic and oxygenic phototrophs. It is commonly assumed that anoxygenic phototrophs only contain oxygen-sensitive dark-operative PORs (DPORs), which catalyse protochlorophyllide reduction independent of the presence of light. In contrast, oxygenic phototrophs additionally (or exclusively) possess oxygen-insensitive but light-dependent PORs (LPORs). Based on this observation it was suggested that light-dependent protochlorophyllide reduction first emerged as a consequence of increased atmospheric oxygen levels caused by oxygenic photosynthesis in cyanobacteria. Here, we provide experimental evidence for the presence of an LPOR in the anoxygenic phototrophic α-proteobacterium Dinoroseobacter shibae DFL12(T). In vitro and in vivo functional assays unequivocally prove light-dependent protochlorophyllide reduction by this enzyme and reveal that LPORs are not restricted to cyanobacteria and plants. Sequence-based phylogenetic analyses reconcile our findings with current hypotheses about the evolution of LPORs by suggesting that the light-dependent enzyme of D. shibae DFL12(T) might have been obtained from cyanobacteria by horizontal gene transfer.}, }
@article {pmid25038297, year = {2014}, author = {Liang, J and Bi, Z and Shi, G and Xiao, Y and Qiu, H and Kou, Z and Hu, B and Jing, H and Wang, X}, title = {Two novel ail-positive biotype 1A strains of Yersinia enterocolitica isolated in China with unequal adhesion and invasion properties.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {27}, number = {}, pages = {83-88}, doi = {10.1016/j.meegid.2014.07.009}, pmid = {25038297}, issn = {1567-7257}, mesh = {Animals ; Bacterial Adhesion/*genetics ; China ; Cluster Analysis ; Epithelial Cells/microbiology ; *Genes, Bacterial ; Molecular Sequence Data ; Mutation ; Open Reading Frames ; Phylogeny ; Polymorphism, Genetic ; Sheep ; Virulence/genetics ; Virulence Factors ; Yersinia enterocolitica/*classification/isolation &amp; purification/pathogenicity/*physiology ; }, abstract = {Yersinia enterocolitica is an enteric pathogen having six biotypes: 1A, 1B, 2, 3, 4, and 5. Different bioserotypes have been associated with varying pathogenicity, and the strains of biotype 1A lack the virulence-associated pYV-bearing genes and were once considered to be avirulent. However, there is growing epidemiological, clinical, and experimental evidence to suggest some biotype 1A isolates are virulent and can cause gastrointestinal disease. Here, we describe two biotype 1A strains discovered from 3807 isolates that carry the ail (attachment and invasion locus) gene. The two strains showed unique PFGE patterns compared to all other isolates in the Chinese Y. enterocolitica isolate PFGE database. Strain SDWL-003 isolated from a sheep shared ail sequence identical to A1 pattern, and the foxA (ferrioxamine receptor) sequence was identical to the pathogenic F5 pattern, besides, the PFGE patterns of SDWL-003 was also cluster to pathogenic branch; however it does not attach to or invade Hep-2 cells. The ail sequence of strain 2006RAT isolated from a Microtus fortis showed several mutations compared to other published genomes, and therefore formed an entirely new pathogenic pattern. Though it clustered to non-pathogenic block with foxA sequence polymorphism analysis or PFGE assay, the strain 2006RAT showed adhesion properties. The data here bring new insights into the molecular genetics of Y. enterocolitica biotype 1A, show some isolates of 1A biotype gaining potential pathogenicity using the function of the virulence gene - ail, and indicate the lateral gene transfer of ail virulence genes proceeded between pathogenic and nonpathogenic Y. enterocolitica.}, }
@article {pmid25036863, year = {2014}, author = {Wang, YY and Li, YD and Liu, JB and Ran, XX and Guo, YY and Ren, NN and Chen, X and Jiang, H and Li, YQ}, title = {Characterization and evolutionary implications of the triad Asp-Xxx-Glu in group II phosphopantetheinyl transferases.}, journal = {PloS one}, volume = {9}, number = {7}, pages = {e103031}, pmid = {25036863}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Bacterial Proteins/*genetics/metabolism ; Binding Sites/genetics ; Biological Evolution ; Dipeptides/*genetics ; Magnesium/metabolism ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Transferases (Other Substituted Phosphate Groups)/*genetics/metabolism ; }, abstract = {Phosphopantetheinyl transferases (PPTases), which play an essential role in both primary and secondary metabolism, are magnesium binding enzymes. In this study, we characterized the magnesium binding residues of all known group II PPTases by biochemical and evolutionary analysis. Our results suggested that group II PPTases could be classified into two subgroups, two-magnesium-binding-residue-PPTases containing the triad Asp-Xxx-Glu and three-magnesium-binding-residue-PPTases containing the triad Asp-Glu-Glu. Mutations of two three-magnesium-binding-residue-PPTases and one two-magnesium-binding-residue-PPTase indicate that the first and the third residues in the triads are essential to activities; the second residues in the triads are non-essential. Although variations of the second residues in the triad Asp-Xxx-Glu exist throughout the whole phylogenetic tree, the second residues are conserved in animals, plants, algae, and most prokaryotes, respectively. Evolutionary analysis suggests that: the animal group II PPTases may originate from one common ancestor; the plant two-magnesium-binding-residue-PPTases may originate from one common ancestor; the plant three-magnesium-binding-residue-PPTases may derive from horizontal gene transfer from prokaryotes.}, }
@article {pmid25036029, year = {2014}, author = {Deng, H and Sun, J and Ma, J and Li, L and Fang, LX and Zhang, Q and Liu, YH and Liao, XP}, title = {Identification of the multi-resistance gene cfr in Escherichia coli isolates of animal origin.}, journal = {PloS one}, volume = {9}, number = {7}, pages = {e102378}, pmid = {25036029}, issn = {1932-6203}, mesh = {Animals ; Drug Resistance, Multiple/*genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/*drug effects/*genetics/isolation &amp; purification ; Escherichia coli Proteins/*genetics ; Gene Transfer, Horizontal ; Homologous Recombination ; Methyltransferases/*genetics ; Molecular Sequence Data ; Plasmids/genetics ; Swine/*microbiology ; }, abstract = {Previous study indicated that the multi-resistance gene cfr was mainly found in gram-positive bacteria, such as Staphylococcus and Enterococcus, and was sporadically detected in Escherichia coli. Little is known about the prevalence and transmission mechanism of cfr in E. coli. In this study, the presence of cfr in E. coli isolates collected during 2010-2012 from food-producing animals in Guangdong Province of China was investigated, and the cfr-positive E. coli isolates were characterized by PFGE, plasmid profiling, and genetic environment analysis. Of the 839 E. coli isolates, 10 isolates from pig were cfr positive. All the cfr-positive isolates presented a multi-resistance phenotype and were genetically divergent as determined by PFGE. In 8 out of the 10 strains, the cfr gene was located on plasmids of ∼30 kb. Restriction digestion of the plasmids with EcoRI and sequence hybridization with a cfr-specific probe revealed that the cfr-harboring fragments ranged from 6 to 23 kb and a ∼18 kb cfr-carrying fragment was common for the plasmids that were ∼30 kb. Four different genetic environments of cfr were detected, in which cfr is flanked by two identical copies of IS26, which may loop out the intervening sequence through homologous recombination. Among the 8 plasmids of ∼30 kb, 7 plasmids shared the same genetic environment. These results demonstrate plasmid-carried cfr in E. coli and suggest that transposition and homologous recombination mediated by IS26 might have played a rule in the transfer of the cfr gene in E. coli.}, }
@article {pmid25035954, year = {2014}, author = {Okoye, IS and Coomes, SM and Pelly, VS and Czieso, S and Papayannopoulos, V and Tolmachova, T and Seabra, MC and Wilson, MS}, title = {MicroRNA-containing T-regulatory-cell-derived exosomes suppress pathogenic T helper 1 cells.}, journal = {Immunity}, volume = {41}, number = {1}, pages = {89-103}, pmid = {25035954}, issn = {1097-4180}, support = {MC_UP_A253_1028//Medical Research Council/United Kingdom ; }, mesh = {Animals ; Antigens, CD19/immunology ; B-Lymphocytes/immunology ; Cell Proliferation ; Cytokines/metabolism ; DEAD-box RNA Helicases/genetics ; Exosomes/*genetics/immunology/metabolism ; Female ; Forkhead Transcription Factors/immunology ; Gene Transfer, Horizontal/genetics ; Inflammation/immunology ; Lymphocyte Activation/genetics/immunology ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; MicroRNAs/biosynthesis/genetics/*immunology ; RNA Interference ; Ribonuclease III/genetics ; T-Lymphocytes, Regulatory/*immunology ; Th1 Cells/*immunology ; Th17 Cells/immunology ; rab GTP-Binding Proteins/genetics ; rab27 GTP-Binding Proteins ; }, abstract = {Foxp3(+) T regulatory (Treg) cells prevent inflammatory disease but the mechanistic basis of suppression is not understood completely. Gene silencing by RNA interference can act in a cell-autonomous and non-cell-autonomous manner, providing mechanisms of intercellular regulation. Here, we demonstrate that non-cell-autonomous gene silencing, mediated by miRNA-containing exosomes, is a mechanism employed by Treg cells to suppress T-cell-mediated disease. Treg cells transferred microRNAs (miRNA) to various immune cells, including T helper 1 (Th1) cells, suppressing Th1 cell proliferation and cytokine secretion. Use of Dicer-deficient or Rab27a and Rab27b double-deficient Treg cells to disrupt miRNA biogenesis or the exosomal pathway, respectively, established a requirement for miRNAs and exosomes for Treg-cell-mediated suppression. Transcriptional analysis and miRNA inhibitor studies showed that exosome-mediated transfer of Let-7d from Treg cell to Th1 cells contributed to suppression and prevention of systemic disease. These studies reveal a mechanism of Treg-cell-mediated suppression mediated by miRNA-containing exosomes.}, }
@article {pmid25034814, year = {2014}, author = {Hovde, BT and Starkenburg, SR and Hunsperger, HM and Mercer, LD and Deodato, CR and Jha, RK and Chertkov, O and Monnat, RJ and Cattolico, RA}, title = {The mitochondrial and chloroplast genomes of the haptophyte Chrysochromulina tobin contain unique repeat structures and gene profiles.}, journal = {BMC genomics}, volume = {15}, number = {}, pages = {604}, pmid = {25034814}, issn = {1471-2164}, support = {RL1 CA133831/CA/NCI NIH HHS/United States ; T32 HG000035/HG/NHGRI NIH HHS/United States ; T32 HG00035/HG/NHGRI NIH HHS/United States ; }, mesh = {Chromosome Mapping ; Conserved Sequence ; *Genome, Chloroplast ; *Genome, Mitochondrial ; Haptophyta/*genetics ; Membrane Transport Proteins/genetics ; Models, Molecular ; Open Reading Frames ; Operon ; Phylogeny ; Repetitive Sequences, Nucleic Acid ; Ribosomal Proteins/genetics ; Sequence Analysis, DNA ; Signal Transduction ; Structural Homology, Protein ; }, abstract = {BACKGROUND: Haptophytes are widely and abundantly distributed in both marine and freshwater ecosystems. Few genomic analyses of representatives within this taxon have been reported, despite their early evolutionary origins and their prominent role in global carbon fixation.<br><br>RESULTS: The complete mitochondrial and chloroplast genome sequences of the haptophyte Chrysochromulina tobin (Prymnesiales) provide insight into the architecture and gene content of haptophyte organellar genomes. The mitochondrial genome (~34 kb) encodes 21 protein coding genes and contains a complex, 9 kb tandem repeat region. Similar to other haptophytes and rhodophytes, but not cryptophytes or stramenopiles, the mitochondrial genome has lost the nad7, nad9 and nad11 genes. The ~105 kb chloroplast genome encodes 112 protein coding genes, including ycf39 which has strong structural homology to NADP-binding nitrate transcriptional regulators; a divergent 'CheY-like' two-component response regulator (ycf55) and Tic/Toc (ycf60 and ycf80) membrane transporters. Notably, a zinc finger domain has been identified in the rpl36 ribosomal protein gene of all chloroplasts sequenced to date with the exception of haptophytes and cryptophytes--algae that have gained (via lateral gene transfer) an alternative rpl36 lacking the zinc finger motif. The two C. tobin chloroplast ribosomal RNA operon spacer regions differ in tRNA content. Additionally, each ribosomal operon contains multiple single nucleotide polymorphisms (SNPs)--a pattern observed in rhodophytes and cryptophytes, but few stramenopiles. Analysis of small (<200 bp) chloroplast encoded tandem and inverted repeats in C. tobin and 78 other algal chloroplast genomes show that repeat type, size and location are correlated with gene identity and taxonomic clade.<br><br>CONCLUSION: The Chrysochromulina tobin organellar genomes provide new insight into organellar function and evolution. These are the first organellar genomes to be determined for the prymnesiales, a taxon that is present in both oceanic and freshwater systems and represents major primary photosynthetic producers and contributors to global ecosystem stability.}, }
@article {pmid25026064, year = {2014}, author = {Martens, EC and Kelly, AG and Tauzin, AS and Brumer, H}, title = {The devil lies in the details: how variations in polysaccharide fine-structure impact the physiology and evolution of gut microbes.}, journal = {Journal of molecular biology}, volume = {426}, number = {23}, pages = {3851-3865}, pmid = {25026064}, issn = {1089-8638}, support = {K01 DK084214/DK/NIDDK NIH HHS/United States ; R01 GM099513/GM/NIGMS NIH HHS/United States ; DK084214/DK/NIDDK NIH HHS/United States ; GM099513/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*drug effects/growth &amp; development/*metabolism ; Diet/*methods ; Gastrointestinal Tract/*microbiology ; Humans ; Microbiota/*drug effects ; Polysaccharides/*chemistry/*metabolism ; }, abstract = {The critical importance of gastrointestinal microbes to digestion of dietary fiber in humans and other mammals has been appreciated for decades. Symbiotic microorganisms expand mammalian digestive physiology by providing an armament of diverse polysaccharide-degrading enzymes, which are largely absent in mammalian genomes. By out-sourcing this aspect of digestive physiology to our gut microbes, we maximize our ability to adapt to different carbohydrate nutrients on timescales as short as several hours due to the ability of the gut microbial community to rapidly alter its physiology from meal to meal. Because of their ability to pick up new traits by lateral gene transfer, our gut microbes also enable adaption over time periods as long as centuries and millennia by adjusting their gene content to reflect cultural dietary trends. Despite a vast amount of sequence-based insight into the metabolic potential of gut microbes, the specific mechanisms by which symbiotic gut microorganisms recognize and attack complex carbohydrates remain largely undefined. Here, we review the recent literature on this topic and posit that numerous, subtle variations in polysaccharides diversify the spectrum of available nutrient niches, each of which may be best filled by a subset of microorganisms that possess the corresponding proteins to recognize and degrade different carbohydrates. Understanding these relationships at precise mechanistic levels will be essential to obtain a complete understanding of the forces shaping gut microbial ecology and genomic evolution, as well as devising strategies to intentionally manipulate the composition and physiology of the gut microbial community to improve health.}, }
@article {pmid25024219, year = {2014}, author = {Dimitriu, T and Lotton, C and Bénard-Capelle, J and Misevic, D and Brown, SP and Lindner, AB and Taddei, F}, title = {Genetic information transfer promotes cooperation in bacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {30}, pages = {11103-11108}, pmid = {25024219}, issn = {1091-6490}, support = {095831//Wellcome Trust/United Kingdom ; }, mesh = {Bacteria/*genetics/pathogenicity ; Gene Transfer, Horizontal/*physiology ; Genes, Bacterial/*physiology ; Plasmids/*genetics ; }, abstract = {Many bacterial species are social, producing costly secreted "public good" molecules that enhance the growth of neighboring cells. The genes coding for these cooperative traits are often propagated via mobile genetic elements and can be virulence factors from a biomedical perspective. Here, we present an experimental framework that links genetic information exchange and the selection of cooperative traits. Using simulations and experiments based on a synthetic bacterial system to control public good secretion and plasmid conjugation, we demonstrate that horizontal gene transfer can favor cooperation. In a well-mixed environment, horizontal transfer brings a direct infectious advantage to any gene, regardless of its cooperation properties. However, in a structured population transfer selects specifically for cooperation by increasing the assortment among cooperative alleles. Conjugation allows cooperative alleles to overcome rarity thresholds and invade bacterial populations structured purely by stochastic dilution effects. Our results provide an explanation for the prevalence of cooperative genes on mobile elements, and suggest a previously unidentified benefit of horizontal gene transfer for bacteria.}, }
@article {pmid25022856, year = {2014}, author = {Nagy, CI and Vass, I and Rákhely, G and Vass, IZ and Tóth, A and Duzs, A and Peca, L and Kruk, J and Kós, PB}, title = {Coregulated genes link sulfide:quinone oxidoreductase and arsenic metabolism in Synechocystis sp. strain PCC6803.}, journal = {Journal of bacteriology}, volume = {196}, number = {19}, pages = {3430-3440}, pmid = {25022856}, issn = {1098-5530}, mesh = {Arsenic/*metabolism ; Bacterial Proteins/*genetics/metabolism ; *Gene Expression Regulation, Bacterial ; Gene Expression Regulation, Enzymologic ; Quinone Reductases/*genetics/metabolism ; Quinones/metabolism ; Sulfides/metabolism ; Synechocystis/enzymology/genetics/*metabolism ; }, abstract = {Although the biogeochemistry of the two environmentally hazardous compounds arsenic and sulfide has been extensively investigated, the biological interference of these two toxic but potentially energy-rich compounds has only been hypothesized and indirectly proven. Here we provide direct evidence for the first time that in the photosynthetic model organism Synechocystis sp. strain PCC6803 the two metabolic pathways are linked by coregulated genes that are involved in arsenic transport, sulfide oxidation, and probably in sulfide-based alternative photosynthesis. Although Synechocystis sp. strain PCC6803 is an obligate photoautotrophic cyanobacterium that grows via oxygenic photosynthesis, we discovered that specific genes are activated in the presence of sulfide or arsenite to exploit the energy potentials of these chemicals. These genes form an operon that we termed suoRSCT, located on a transposable element of type IS4 on the plasmid pSYSM of the cyanobacterium. suoS (sll5036) encodes a light-dependent, type I sulfide:quinone oxidoreductase. The suoR (sll5035) gene downstream of suoS encodes a regulatory protein that belongs to the ArsR-type repressors that are normally involved in arsenic resistance. We found that this repressor has dual specificity, resulting in 200-fold induction of the operon upon either arsenite or sulfide exposure. The suoT gene encodes a transmembrane protein similar to chromate transporters but in fact functioning as an arsenite importer at permissive concentrations. We propose that the proteins encoded by the suoRSCT operon might have played an important role under anaerobic, reducing conditions on primordial Earth and that the operon was acquired by the cyanobacterium via horizontal gene transfer.}, }
@article {pmid25018750, year = {2014}, author = {Soucy, SM and Fullmer, MS and Papke, RT and Gogarten, JP}, title = {Inteins as indicators of gene flow in the halobacteria.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {299}, pmid = {25018750}, issn = {1664-302X}, abstract = {This research uses inteins, a type of mobile genetic element, to infer patterns of gene transfer within the Halobacteria. We surveyed 118 genomes representing 26 genera of Halobacteria for intein sequences. We then used the presence-absence profile, sequence similarity and phylogenies from the inteins recovered to explore how intein distribution can provide insight on the dynamics of gene flow between closely related and divergent organisms. We identified 24 proteins in the Halobacteria that have been invaded by inteins at some point in their evolutionary history, including two proteins not previously reported to contain an intein. Furthermore, the size of an intein is used as a heuristic for the phase of the intein's life cycle. Larger size inteins are assumed to be the canonical two domain inteins, consisting of self-splicing and homing endonuclease domains (HEN); smaller sizes are assumed to have lost the HEN domain. For many halobacterial groups the consensus phylogenetic signal derived from intein sequences is compatible with vertical inheritance or with a strong gene transfer bias creating these clusters. Regardless, the coexistence of intein-free and intein-containing alleles reveal ongoing transfer and loss of inteins within these groups. Inteins were frequently shared with other Euryarchaeota and among the Bacteria, with members of the Cyanobacteria (Cyanothece, Anabaena), Bacteriodetes (Salinibacter), Betaproteobacteria (Delftia, Acidovorax), Firmicutes (Halanaerobium), Actinobacteria (Longispora), and Deinococcus-Thermus-group.}, }
@article {pmid25018641, year = {2014}, author = {Huddleston, JR}, title = {Horizontal gene transfer in the human gastrointestinal tract: potential spread of antibiotic resistance genes.}, journal = {Infection and drug resistance}, volume = {7}, number = {}, pages = {167-176}, pmid = {25018641}, issn = {1178-6973}, abstract = {Bacterial infections are becoming increasingly difficult to treat due to widespread antibiotic resistance among pathogens. This review aims to give an overview of the major horizontal transfer mechanisms and their evolution and then demonstrate the human lower gastrointestinal tract as an environment in which horizontal gene transfer of resistance determinants occurs. Finally, implications for antibiotic usage and the development of resistant infections and persistence of antibiotic resistance genes in populations as a result of horizontal gene transfer in the large intestine will be discussed.}, }
@article {pmid25016824, year = {2014}, author = {Baranov, IuO and Slishchuk, HI and Volkova, NE and Syvolap, IuM}, title = {[Bioinformatic analysis of maize granule-bound starch synthase gene].}, journal = {TSitologiia i genetika}, volume = {48}, number = {3}, pages = {18-23}, pmid = {25016824}, issn = {0564-3783}, mesh = {Base Sequence ; Computational Biology/*methods ; Exons ; Gene Transfer, Horizontal ; *Genes, Plant ; *Phylogeny ; Plant Proteins/*genetics ; Polymerase Chain Reaction ; *Polymorphism, Genetic ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Starch Synthase/*genetics ; Zea mays/*enzymology/genetics ; }, abstract = {Local alignment of Wx gene and its homolog sequences has been conducted. Phylogenetic dendrogram displaying evolutionary relationship between Poaceae members has been built basing on results of the alignment. Ancient Wx gene transfer from Zea mays to Dimeria lawsonii has been assumed. Primers for the exons 8-10 polymorphic region have been designed. In silico PCR has been conducted.}, }
@article {pmid25014185, year = {2014}, author = {Canfora, L and Sbrana, C and Avio, L and Felici, B and Scatà, MC and Neri, U and Benedetti, A}, title = {Risk management tools and the case study Brassica napus: evaluating possible effects of genetically modified plants on soil microbial diversity.}, journal = {The Science of the total environment}, volume = {493}, number = {}, pages = {983-994}, doi = {10.1016/j.scitotenv.2014.06.086}, pmid = {25014185}, issn = {1879-1026}, mesh = {Brassica napus/*genetics ; Europe ; Gene Transfer, Horizontal ; Mycorrhizae ; *Plants, Genetically Modified ; Risk Management ; *Soil Microbiology ; }, abstract = {The cultivation of GMPs in Europe raises many questions about the environmental risks, in particular about their ecological impact on non-target organisms and on soil properties. The aim of a multidisciplinary group engaged in a LIFE+project (MAN-GMP-ITA) was to validate and improve an existing environmental risk assessment (ERA) methodology on GMPs within the European legislative framework on GMOs. Given the impossibility of evaluating GMO impact directly, as GMPs are banned in Italy, GMPs have not been used at any stage of the project. The project thus specifically focused on the conditions for the implementation of ERA in different areas of Italy, with an emphasis on some sensitive and protected areas located in the North, Centre, and South of the country, in order to lay the necessary baseline for evaluating the possible effects of a GMP on soil communities. Our sub-group carried out soil analyses in order to obtain soil health and fertility indicators to be used as baselines in the ERA model. Using various methods of chemical, biochemical, functional and genetic analysis, our study assessed the changes in diversity and functionality of bacterial populations, and arbuscular mycorrhizal fungi. The results show that plant identity and growth, soil characteristics, and field site climatic parameters are key factors in contributing to variation in microbial community structure and diversity, thus validating our methodological approach. Our project has come to the conclusion that the uneven composition and biological-agronomical quality of soils need to be taken into consideration in a risk analysis within the framework of ERA for the release of genetically modified plants.}, }
@article {pmid25013378, year = {2014}, author = {Dröge, J and Buczek, D and Suzuki, Y and Makałowski, W}, title = {Amoebozoa possess lineage-specific globin gene repertoires gained by individual horizontal gene transfers.}, journal = {International journal of biological sciences}, volume = {10}, number = {7}, pages = {689-701}, pmid = {25013378}, issn = {1449-2288}, mesh = {Amino Acid Sequence ; Amoebozoa/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genes, Protozoan ; Genome, Protozoan ; Globins/chemistry/*genetics ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, Protein ; }, abstract = {The Amoebozoa represent a clade of unicellular amoeboid organisms that display a wide variety of lifestyles, including free-living and parasitic species. For example, the social amoeba Dictyostelium discoideum has the ability to aggregate into a multicellular fruiting body upon starvation, while the pathogenic amoeba Entamoeba histolytica is a parasite of humans. Globins are small heme proteins that are present in almost all extant organisms. Although several genomes of amoebozoan species have been sequenced, little is known about the phyletic distribution of globin genes within this phylum. Only two flavohemoglobins (FHbs) of D. discoideum have been reported and characterized previously while the genomes of Entamoeba species are apparently devoid of globin genes. We investigated eleven amoebozoan species for the presence of globin genes by genomic and phylogenetic in silico analyses. Additional FHb genes were identified in the genomes of four social amoebas and the true slime mold Physarum polycephalum. Moreover, a single-domain globin (SDFgb) of Hartmannella vermiformis, as well as two truncated hemoglobins (trHbs) of Acanthamoeba castellanii were identified. Phylogenetic evidence suggests that these globin genes were independently acquired via horizontal gene transfer from some ancestral bacteria. Furthermore, the phylogenetic tree of amoebozoan FHbs indicates that they do not share a common ancestry and that a transfer of FHbs from bacteria to amoeba occurred multiple times.}, }
@article {pmid25011666, year = {2014}, author = {Piccirillo, A and Giovanardi, D and Dotto, G and Grilli, G and Montesissa, C and Boldrin, C and Salata, C and Giacomelli, M}, title = {Antimicrobial resistance and class 1 and 2 integrons in Escherichia coli from meat turkeys in Northern Italy.}, journal = {Avian pathology : journal of the W.V.P.A}, volume = {43}, number = {5}, pages = {396-405}, doi = {10.1080/03079457.2014.943690}, pmid = {25011666}, issn = {1465-3338}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Bacterial ; Escherichia coli/*drug effects/genetics ; Escherichia coli Infections/epidemiology/*veterinary ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Integrons/*genetics ; Italy/epidemiology ; Male ; Poultry Diseases/epidemiology/*microbiology ; *Turkeys ; }, abstract = {This study is aimed at determining the antimicrobial resistance (AMR) and the presence of class 1 and 2 integrons in 48 avian pathogenic Escherichia coli (APEC) strains isolated from meat turkeys during three sequential production cycles. Thirty avian faecal E. coli (AFEC) strains from the first cycle were also analysed. Strains were tested for AMR against 25 antimicrobials by disk diffusion test and were screened for the presence of integrons and associated gene cassettes by polymerase chain reaction followed by sequencing. Genetic relatedness of isolates was established by pulsed-field gel electrophoresis. High levels of resistance were detected to tetracyclines, penicillins and sulphonamides in APEC and AFEC. Resistance to aminoglycosides, fluoroquinolones, cephalosporins and phenicols was variable, based on the antimicrobial drug and the isolate (APEC vs. AFEC). Full susceptibility to colistin was detected. Multidrug resistance of up to seven antimicrobial classes was exhibited by APEC (93.8%) and AFEC (100%). Nearly 44% of strains tested positive for class 1 and/or class 2 integrons containing the dfrA, aadA and sat2 genes, alone or in combination, coding for streptomycin/spectinomycin, trimethoprim and streptothricin resistance, respectively. The estX and orfF genes of unknown function were also detected. A significant association was found between the presence of integrons and the resistance to aminoglycosides and potentiated sulphonamides. The results of this study showed that AMR, multidrug resistance and class 1 and 2 integrons are widespread among pathogenic and commensal E. coli from Italian turkeys. More attention should be addressed to limit the use of antimicrobials in turkeys and the AMR of turkey E. coli.}, }
@article {pmid25010934, year = {2014}, author = {Creason, AL and Vandeputte, OM and Savory, EA and Davis, EW and Putnam, ML and Hu, E and Swader-Hines, D and Mol, A and Baucher, M and Prinsen, E and Zdanowska, M and Givan, SA and El Jaziri, M and Loper, JE and Mahmud, T and Chang, JH}, title = {Analysis of genome sequences from plant pathogenic Rhodococcus reveals genetic novelties in virulence loci.}, journal = {PloS one}, volume = {9}, number = {7}, pages = {e101996}, pmid = {25010934}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/genetics/metabolism ; Conserved Sequence ; Evolution, Molecular ; Gene Fusion ; Gene Transfer, Horizontal/genetics ; Genetic Loci/*genetics ; Genome, Bacterial/genetics ; *Genomics ; Isopentenyladenosine/metabolism ; Molecular Sequence Data ; Operon/genetics ; Plants/*microbiology ; Plasmids/genetics ; Polymorphism, Genetic ; Rhodococcus/*genetics/metabolism/*pathogenicity/physiology ; *Sequence Analysis ; }, abstract = {Members of Gram-positive Actinobacteria cause economically important diseases to plants. Within the Rhodococcus genus, some members can cause growth deformities and persist as pathogens on a wide range of host plants. The current model predicts that phytopathogenic isolates require a cluster of three loci present on a linear plasmid, with the fas operon central to virulence. The Fas proteins synthesize, modify, and activate a mixture of growth regulating cytokinins, which cause a hormonal imbalance in plants, resulting in abnormal growth. We sequenced and compared the genomes of 20 isolates of Rhodococcus to gain insights into the mechanisms and evolution of virulence in these bacteria. Horizontal gene transfer was identified as critical but limited in the scale of virulence evolution, as few loci are conserved and exclusive to phytopathogenic isolates. Although the fas operon is present in most phytopathogenic isolates, it is absent from phytopathogenic isolate A21d2. Instead, this isolate has a horizontally acquired gene chimera that encodes a novel fusion protein with isopentyltransferase and phosphoribohydrolase domains, predicted to be capable of catalyzing and activating cytokinins, respectively. Cytokinin profiling of the archetypal D188 isolate revealed only one activate cytokinin type that was specifically synthesized in a fas-dependent manner. These results suggest that only the isopentenyladenine cytokinin type is synthesized and necessary for Rhodococcus phytopathogenicity, which is not consistent with the extant model stating that a mixture of cytokinins is necessary for Rhodococcus to cause leafy gall symptoms. In all, data indicate that only four horizontally acquired functions are sufficient to confer the trait of phytopathogenicity to members of the genetically diverse clade of Rhodococcus.}, }
@article {pmid25009843, year = {2014}, author = {Qin, QL and Xie, BB and Yu, Y and Shu, YL and Rong, JC and Zhang, YJ and Zhao, DL and Chen, XL and Zhang, XY and Chen, B and Zhou, BC and Zhang, YZ}, title = {Comparative genomics of the marine bacterial genus Glaciecola reveals the high degree of genomic diversity and genomic characteristic for cold adaptation.}, journal = {Environmental microbiology}, volume = {16}, number = {6}, pages = {1642-1653}, doi = {10.1111/1462-2920.12318}, pmid = {25009843}, issn = {1462-2920}, mesh = {Adaptation, Physiological/genetics ; Alteromonadaceae/*genetics ; Base Sequence ; Clustered Regularly Interspaced Short Palindromic Repeats ; Gene Transfer, Horizontal ; Genetic Variation ; *Genome, Bacterial ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {To what extent the genomes of different species belonging to one genus can be diverse and the relationship between genomic differentiation and environmental factor remain unclear for oceanic bacteria. With many new bacterial genera and species being isolated from marine environments, this question warrants attention. In this study, we sequenced all the type strains of the published species of Glaciecola, a recently defined cold-adapted genus with species from diverse marine locations, to study the genomic diversity and cold-adaptation strategy in this genus.The genome size diverged widely from 3.08 to 5.96 Mb, which can be explained by massive gene gain and loss events. Horizontal gene transfer and new gene emergence contributed substantially to the genome size expansion. The genus Glaciecola had an open pan-genome. Comparative genomic research indicated that species of the genus Glaciecola had high diversity in genome size, gene content and genetic relatedness. This may be prevalent in marine bacterial genera considering the dynamic and complex environments of the ocean. Species of Glaciecola had some common genomic features related to cold adaptation, which enable them to thrive and play a role in biogeochemical cycle in the cold marine environments.}, }
@article {pmid25008981, year = {2014}, author = {Cinelli, T and Moscetti, I and Marchi, G}, title = {PsasM2I, a type II restriction-modification system in Pseudomonas savastanoi pv. savastanoi: differential distribution of carrier strains in the environment and the evolutionary history of homologous RM systems in the Pseudomonas syringae complex.}, journal = {Microbial ecology}, volume = {68}, number = {4}, pages = {842-858}, pmid = {25008981}, issn = {1432-184X}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/*genetics/metabolism ; *Biological Evolution ; DNA Restriction-Modification Enzymes/chemistry/*genetics/metabolism ; DNA Transposable Elements ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Nerium/microbiology ; Olea/microbiology ; Organisms, Genetically Modified/genetics ; Phylogeny ; Pseudomonas/*enzymology/*genetics ; }, abstract = {A type II restriction-modification system was found in a native plasmid of Pseudomonas savastanoi pv. savastanoi MLLI2. Functional analysis of the methyltransferase showed that the enzyme acts by protecting the DNA sequence CTGCAG from cleavage. Restriction endonuclease expression in recombinant Escherichia coli cells resulted in mutations in the REase sequence or transposition of insertion sequence 1A in the coding sequence, preventing lethal gene expression. Population screening detected homologous RM systems in other P. savastanoi strains and in the Pseudomonas syringae complex. An epidemiological survey carried out by sampling olive and oleander knots in two Italian regions showed an uneven diffusion of carrier strains, whose presence could be related to a selective advantage in maintaining the RM system in particular environments or subpopulations. Moreover, carrier strains can coexist in the same orchards, plants, and knot tissues with non-carriers, revealing unexpected genetic variability on a very small spatial scale. Phylogenetic analysis of the RM system and housekeeping gene sequences in the P. syringae complex demonstrated the ancient acquisition of the RM systems. However, the evolutionary history of the gene complex also showed the involvement of horizontal gene transfer between related strains and recombination events.}, }
@article {pmid25008817, year = {2014}, author = {Wang, J and Liang, F and Wu, XM and Qi, W}, title = {Transfer patterns of integron-associated and antibiotic resistance genes in S. flexneri during different time intervals in Tianjin, China.}, journal = {Indian journal of medical microbiology}, volume = {32}, number = {3}, pages = {256-260}, doi = {10.4103/0255-0857.136556}, pmid = {25008817}, issn = {1998-3646}, mesh = {Adolescent ; Adult ; Aged ; Child ; Child, Preschool ; China ; *Drug Resistance, Bacterial ; Dysentery, Bacillary/*microbiology ; Evolution, Molecular ; Female ; *Gene Transfer, Horizontal ; Humans ; *Integrons ; Male ; Middle Aged ; Shigella flexneri/*drug effects/*genetics/isolation &amp; purification ; Young Adult ; }, abstract = {BACKGROUND: Shigella is one of the common genera of pathogens responsible for bacterial diarrhoea in humans. According to World Health Organisation (WHO), 800,000-1,700,000 patients in China were infected with Shigella spp. in 2000, and Shigella flexneri is the most common serotype (86%).<br><br>OBJECTIVES: We investigated the transfer patterns of integron-associated and antibiotic resistance genes in S. flexneri during different time intervals in the city of Tianjin in the People's Republic of China.<br><br>MATERIALS AND METHODS: The integrase-encoding and variable regions of the integrons of the bacterial strains were amplified by polymerase chain reaction (PCR), followed by gene sequencing. Fifty-six S. flexneri strains, 32 of which were stored in our laboratory and the other 24 were isolated from tertiary hospitals in Tianjin during different time intervals, were tested for their sensitivity to 12 antibiotics by using the Kirby-Bauer antibiotic testing method (K-B method).<br><br>RESULTS AND CONCLUSION: Of the 32 strains of S. flexneri isolated from 1981 to 1983 and stored in our laboratory, class 1 integron was detected in 28 strains (87.50%), while 27 strains (84.37%) harboured an aminoglycoside resistance gene, aadA, in the variable region of their integrons. Class 1 integron was identified in 22 (91.67%) of the 24 S. flexneri strains isolated from 2009 to 2010, whereas the variable region and 3'-end amplification were not present in any of the strains. Class 2 integron was not found in the 1981-1983 group (group A) of strains; although 19 (79.17%) of the 24 strains in the 2009-2010 group (group B) possessed class 2 integron, and the variable region of the integron harboured dfrA1+sat1+aadA1 genes, which, respectively, mediate antibiotic resistance to trimethoprim, streptothricin and streptomycin. Seventeen strains of the total 56 possessed both class 1 and 2 integrons. Strains belonging to group A were highly resistant to tetracycline, chloramphenicol and a combination of trimethoprim-sulfamethoxazole; 65.63% of the strains were multi-resistant to three or more antibiotics. In group B, the strains showed high resistance to ampicillin, trimethoprim-sulfamethoxazole, piperacillin and tetracycline; 83.33% of the strains were multi-resistant to three or more antibiotics. Class 1 and 2 integrons exist extensively in S. flexneri, and the 3'-conserved segments of class 1 integron may have deletion or other types of mutations. Comparing the antibiotic and multi-drug resistance of group A with that of group B, it is apparent that the antibiotic resistance and the incidence of genes that confer multi-drug resistance have increased over the years in S. flexneri.}, }
@article {pmid25006233, year = {2014}, author = {Sacco, E and Cortes, M and Josseaume, N and Rice, LB and Mainardi, JL and Arthur, M}, title = {Serine/threonine protein phosphatase-mediated control of the peptidoglycan cross-linking L,D-transpeptidase pathway in Enterococcus faecium.}, journal = {mBio}, volume = {5}, number = {4}, pages = {e01446-14}, pmid = {25006233}, issn = {2150-7511}, support = {R01 AI046626/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/*metabolism ; Enterococcus faecium/*enzymology/*metabolism ; Peptidoglycan/*metabolism ; Peptidoglycan Glycosyltransferase/*metabolism ; Phosphoprotein Phosphatases/*metabolism ; }, abstract = {The last step of peptidoglycan polymerization involves two families of unrelated transpeptidases that are the essential targets of β-lactam antibiotics. D,D-transpeptidases of the penicillin-binding protein (PBP) family are active-site serine enzymes that use pentapeptide precursors and are the main or exclusive cross-linking enzymes in nearly all bacteria. However, peptidoglycan cross-linking is performed mainly by active-site cysteine L,D-transpeptidases that use tetrapeptides in Mycobacterium tuberculosis, Clostridium difficile, and β-lactam-resistant mutants of Enterococcus faecium. We have investigated reprogramming of the E. faecium peptidoglycan assembly pathway by a switch from pentapeptide to tetrapeptide precursors and bypass of PBPs by L,D-transpeptidase Ldtfm. Mutational alterations of two signal transduction systems were necessary and sufficient for activation of the L,D-transpeptidation pathway, which is essentially cryptic in wild-type strains. The first one is a classical two-component regulatory system, DdcRS, that controls the activity of Ldtfm at the substrate level. As previously described, loss of DdcS phosphatase activity leads to production of the D,D-carboxypeptidase DdcY and conversion of the pentapeptide into the tetrapeptide substrate of Ldtfm. Here we show that full bypass of PBPs by Ldtfm also requires increased Ser/Thr protein phosphorylation resulting from impaired activity of phosphoprotein phosphatase StpA. This enzyme negatively controlled the level of protein phosphorylation both by direct dephosphorylation of target proteins and by dephosphorylation of its cognate kinase Stk. In combination with production of DdcY, increased protein phosphorylation by this eukaryotic-enzyme-like Ser/Thr protein kinase was sufficient for activation of the L,D-transpeptidation pathway in the absence of mutational alteration of peptidoglycan synthesis enzymes. Importance: The mechanism of acquisition of high-level ampicillin resistance involving bypass of the penicillin-binding proteins (PBPs) by L,D-transpeptidase Ldtfm was incompletely understood, as production of tetrapeptide precursors following transcriptional activation of the ddc locus by the DdcRS two-component regulatory system was necessary but not sufficient for full activation of the L,D-transpeptidation pathway. Here, we identified the release of a negative control of Ser/Thr protein phosphorylation mediated by phosphatase StpA as the additional factor essential for ampicillin resistance. Thus, bypass of PBPs by Ldtfm requires the modification of signal transduction regulatory systems without any gain of function by mutational alteration of peptidoglycan biosynthetic enzymes. In contrast, previously characterized mechanisms of antibiotic resistance involve horizontal gene transfer and mutational alteration of drug targets. Activation of the L,D-transpeptidation pathway reported in this study is an unprecedented mechanism of emergence of a new metabolic pathway since it involved the recruitment of preexisting functions following modifications of regulatory circuits.}, }
@article {pmid25000583, year = {2014}, author = {Bellanger, X and Guilloteau, H and Bonot, S and Merlin, C}, title = {Demonstrating plasmid-based horizontal gene transfer in complex environmental matrices: a practical approach for a critical review.}, journal = {The Science of the total environment}, volume = {493}, number = {}, pages = {872-882}, doi = {10.1016/j.scitotenv.2014.06.070}, pmid = {25000583}, issn = {1879-1026}, mesh = {Bacteria/*genetics ; *DNA, Bacterial ; Drug Resistance, Microbial/*genetics ; Environment ; *Gene Transfer, Horizontal ; Plasmids ; }, abstract = {Plasmid-based dissemination of antibiotic resistance genes in environmental microbial communities is a matter of concern for public health, but it remains difficult to study for methodological reasons. In this study, we used the broad host range plasmid pB10 to compare and to point out the main drawbacks of the three different approaches currently used to evaluate plasmid transfer in natural communities. Culture-based selection of transconjugants appeared to be compromised by high prevalence of antibiotic resistances among natural communities, unless high loads of initial pB10-donor inocula were used. Fluorescence-based detection of transconjugants reached a dead-end consequently to the narrow host range of bacteria expressing fluorescent proteins from a genetically modified pB10 plasmid, in addition to the relatively high background level of fluorescence exhibited by some environmental matrices. The molecular-based approach was the only one to provide a mean to detect rare plasmid transfer events following a low but realistic initial pB10-donor inoculation. Whatever the method, culture-based or molecular-based, the detection of successful transfer events in a given environmental matrix seemed to be linked to the initial stability of the donor inoculum. Depending on the matrix considered, eukaryotic predation plays a significant role in either limiting or promoting the plasmid transfer events.}, }
@article {pmid24999047, year = {2014}, author = {Zhang, T and Jiang, Y and Dong, W}, title = {A novel monopartite dsRNA virus isolated from the phytopathogenic fungus Ustilaginoidea virens and ancestrally related to a mitochondria-associated dsRNA in the green alga Bryopsis.}, journal = {Virology}, volume = {462-463}, number = {}, pages = {227-235}, doi = {10.1016/j.virol.2014.06.003}, pmid = {24999047}, issn = {1096-0341}, mesh = {China ; Chlorophyta/genetics ; Cluster Analysis ; Genome, Viral ; Hypocreales/*virology ; Mitochondria/genetics ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; RNA Viruses/*classification/genetics/*isolation &amp; purification ; RNA, Double-Stranded/*genetics ; RNA, Viral/*genetics ; Saccharomycetales/genetics ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {In this study, we describe a novel mycovirus isolated from Ustilaginoidea virens, which was designated Ustilaginoidea virens nonsegmented virus 1 (UvNV-1). The sequence analysis revealed that UvNV-1 has two open reading frames (ORFs). ORF1 encodes an unknown protein, which is similar to the hypothetical protein BN7_5177 of Wickerhamomyces ciferrii. ORF2 encodes a putative RNA-dependent RNA polymerase (RdRp), which is most closely related to Bryopsis mitochondria-associated dsRNA (BDRM) and is likely expressed by a +1 ribosomal frameshift within the sequence CCC_UUU_CGA. The phylogenetic analysis of the RdRp of UvNV-1 showed that UvNV-1 represents a new virus taxon of mycoviruses with a partitivirus-like lineage that is classified into the family of picorna-like viruses. Based on northern hybridization, UvNV-1 was found to be common to U. virens from different geographic locations in China. The biological comparison of virus-free and infected fungal strains revealed that UvNV-1 is likely to be cryptic to its host.}, }
@article {pmid24998348, year = {2014}, author = {Filée, J}, title = {Multiple occurrences of giant virus core genes acquired by eukaryotic genomes: the visible part of the iceberg?.}, journal = {Virology}, volume = {466-467}, number = {}, pages = {53-59}, doi = {10.1016/j.virol.2014.06.004}, pmid = {24998348}, issn = {1096-0341}, mesh = {Chromosomes/genetics ; Cryptophyta/genetics/virology ; DNA Primase/genetics ; DNA Viruses/classification/*genetics ; DNA, Viral/genetics ; Eukaryota/*genetics/virology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome/*genetics ; Genome, Viral/*genetics ; Genomics ; Host-Pathogen Interactions ; Phylogeny ; Viral Proteins/*genetics ; }, abstract = {Giant Viruses are a widespread group of viruses, characterized by huge genomes composed of a small subset of ancestral, vertically inherited core genes along with a large body of highly variable genes. In this study, I report the acquisition of 23 core ancestral Giant Virus genes by diverse eukaryotic species including various protists, a moss and a cnidarian. The viral genes are inserted in large scaffolds or chromosomes with intron-rich, eukaryotic-like genomic contexts, refuting the possibility of DNA contaminations. Some of these genes are expressed and in the cryptophyte alga Guillardia theta, a possible non-homologous displacement of the eukaryotic DNA primase by a viral D5 helicase/primase is documented. As core Giant Virus genes represent only a tiny fraction of the total genomic repertoire of these viruses, these results suggest that Giant Viruses represent an underestimated source of new genes and functions for their hosts.}, }
@article {pmid24998344, year = {2014}, author = {Dorman, CJ}, title = {H-NS-like nucleoid-associated proteins, mobile genetic elements and horizontal gene transfer in bacteria.}, journal = {Plasmid}, volume = {75}, number = {}, pages = {1-11}, doi = {10.1016/j.plasmid.2014.06.004}, pmid = {24998344}, issn = {1095-9890}, mesh = {Amino Acid Sequence ; Bacteria/*genetics ; Bacterial Proteins/*genetics ; Chromosomes, Bacterial/genetics ; DNA, Bacterial/genetics ; Evolution, Molecular ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal/*genetics ; Interspersed Repetitive Sequences/*genetics ; Molecular Sequence Data ; Plasmids/*genetics ; }, abstract = {Horizontal gene transfer plays an important role in the evolution of bacterial species, conferring new genetic traits on the recipient bacterium that extend its range of phenotypes and plasmids make important contributions to this process. However, the inappropriate expression of newly acquired genes may lead to a loss of competitive fitness, resulting in the elimination of the new gene-bacterium combination. It is thought that transcriptional silencing of horizontally acquired genes offers a route out of this dilemma and that nucleoid-associated proteins, especially those related to the H-NS protein, play a particularly important role in the silencing process. The discovery that many plasmids express orthologues of nucleoid-associated proteins adds an interesting dimension to current models of regulatory integration following lateral transfer of DNA. Other horizontally acquired genetic elements, such as genomic islands, also express nucleoid-associated proteins of their own. Here the interactions of H-NS-like nucleoid-associated proteins encoded by the core genome, genomic islands and plasmids are described.}, }
@article {pmid24997027, year = {2014}, author = {Lyte, M}, title = {Microbial endocrinology and the microbiota-gut-brain axis.}, journal = {Advances in experimental medicine and biology}, volume = {817}, number = {}, pages = {3-24}, doi = {10.1007/978-1-4939-0897-4_1}, pmid = {24997027}, issn = {0065-2598}, mesh = {Animals ; Behavior ; Brain/*physiology ; Diet ; *Endocrinology ; Host-Pathogen Interactions/*physiology ; Humans ; Intestines/*microbiology ; Microbiota/*physiology ; }, abstract = {Microbial endocrinology is defined as the study of the ability of microorganisms to both produce and recognize neurochemicals that originate either within the microorganisms themselves or within the host they inhabit. As such, microbial endocrinology represents the intersection of the fields of microbiology and neurobiology. The acquisition of neurochemical-based cell-to-cell signaling mechanisms in eukaryotic organisms is believed to have been acquired due to late horizontal gene transfer from prokaryotic microorganisms. When considered in the context of the microbiota's ability to influence host behavior, microbial endocrinology with its theoretical basis rooted in shared neuroendocrine signaling mechanisms provides for testable experiments with which to understand the role of the microbiota in host behavior and as importantly the ability of the host to influence the microbiota through neuroendocrine-based mechanisms.}, }
@article {pmid24995588, year = {2014}, author = {Singh, PK and Meijer, WJ}, title = {Diverse regulatory circuits for transfer of conjugative elements.}, journal = {FEMS microbiology letters}, volume = {358}, number = {2}, pages = {119-128}, doi = {10.1111/1574-6968.12526}, pmid = {24995588}, issn = {1574-6968}, mesh = {Bacillus subtilis/*genetics ; *Conjugation, Genetic ; *Gene Regulatory Networks ; *Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences ; }, abstract = {Conjugation systems are present on many plasmids as well as on chromosomally integrated elements. Conjugation, which is a major route by which bacteria exchange genetic material, is a complex and energy-consuming process. Hence, a shared feature of conjugation systems is that expression of the genes involved is strictly controlled in such a way that conjugation is kept in a default 'OFF' state and that the process is switched on only under conditions that favor the transfer of the conjugative element into a recipient cell. However, there is a remarkable diversity in the way by which conjugation genes present on different transferable elements are regulated. Here, we review these diverse regulatory circuits on the basis of several prototypes with a special focus on the recently discovered regulation of the conjugation genes present on the native Bacillus subtilis plasmid pLS20.}, }
@article {pmid24994022, year = {2015}, author = {Chen, B and Liang, X and Nie, X and Huang, X and Zou, S and Li, X}, title = {The role of class I integrons in the dissemination of sulfonamide resistance genes in the Pearl River and Pearl River Estuary, South China.}, journal = {Journal of hazardous materials}, volume = {282}, number = {}, pages = {61-67}, doi = {10.1016/j.jhazmat.2014.06.010}, pmid = {24994022}, issn = {1873-3336}, mesh = {Anti-Bacterial Agents/*analysis ; Bacterial Proteins/genetics ; China ; DNA, Bacterial/analysis ; Drug Resistance, Microbial/*genetics ; Estuaries ; *Genes, Bacterial ; Geologic Sediments/analysis ; *Integrons ; RNA, Ribosomal, 16S/analysis ; Rivers ; Sulfonamides/*analysis ; Water Pollutants/*analysis ; }, abstract = {Antibiotic resistance genes (ARGs), as a newly emerging contaminant, are unique because they are disseminated through horizontal gene transfer in the environment. In the present study, a class 1 integron gene (int1) and various ARGs (sul1, sul2, sul3, qnrS, and ermB) were measured in water and sediment samples from the Pearl River (PR) to the Pearl River Estuary (PRE), where there is a distinct gradient in anthropogenic impact. The int1, sul1, and sul2 genes were detected in all samples, and their concentrations exhibited a clear trend of decline consistent with anthropogenic impact. Both the int1 and sul genes had dynamically migrated between water and sediments. The relative abundance of the int1 gene normalized to the 16S rRNA gene correlated significantly with the total concentrations of antibiotics in water and sediments. Good correlations were also observed between the abundance of int1 and each type of sul gene in the samples. However, the sul1 gene showed a much stronger relationship with int1 in different seasons, probably due to the presence of sul1 in the conserved region of class 1 integron. Our results strongly support that integrons play an important role in the dissemination of ARGs in human-impacted aquatic environments.}, }
@article {pmid24992884, year = {2015}, author = {Uecker, H and Setter, D and Hermisson, J}, title = {Adaptive gene introgression after secondary contact.}, journal = {Journal of mathematical biology}, volume = {70}, number = {7}, pages = {1523-1580}, pmid = {24992884}, issn = {1432-1416}, support = {W 1225/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Adaptation, Biological/*genetics ; Alleles ; Computer Simulation ; Evolution, Molecular ; Gene Flow ; Gene Transfer, Horizontal ; Genetic Linkage ; Genetics, Population ; Haplotypes ; Hybridization, Genetic ; Mathematical Concepts ; *Models, Genetic ; Probability ; Selection, Genetic ; Stochastic Processes ; }, abstract = {By hybridization and backcrossing, alleles can surmount species boundaries and be incorporated into the genome of a related species. This introgression of genes is of particular evolutionary relevance if it involves the transfer of adaptations between populations. However, any beneficial allele will typically be associated with other alien alleles that are often deleterious and hamper the introgression process. In order to describe the introgression of an adaptive allele, we set up a stochastic model with an explicit genetic makeup of linked and unlinked deleterious alleles. Based on the theory of reducible multitype branching processes, we derive a recursive expression for the establishment probability of the beneficial allele after a single hybridization event. We furthermore study the probability that slightly deleterious alleles hitchhike to fixation. The key to the analysis is a split of the process into a stochastic phase in which the advantageous alleles establishes and a deterministic phase in which it sweeps to fixation. We thereafter apply the theory to a set of biologically relevant scenarios such as introgression in the presence of many unlinked or few closely linked deleterious alleles. A comparison to computer simulations shows that the approximations work well over a large parameter range.}, }
@article {pmid24990771, year = {2014}, author = {Ambrose, KV and Koppenhöfer, AM and Belanger, FC}, title = {Horizontal gene transfer of a bacterial insect toxin gene into the Epichloë fungal symbionts of grasses.}, journal = {Scientific reports}, volume = {4}, number = {}, pages = {5562}, pmid = {24990771}, issn = {2045-2322}, mesh = {Animals ; Bacterial Toxins/*genetics/metabolism ; Endophytes/*genetics/metabolism ; Epichloe/*genetics/metabolism ; Evolution, Molecular ; Gene Expression ; Gene Transfer, Horizontal ; Genes, Fungal ; Herbivory ; Larva/physiology ; Molecular Sequence Data ; Moths/physiology ; Photorhabdus/genetics ; Phylogeny ; Poaceae/microbiology ; }, abstract = {Horizontal gene transfer is recognized as an important factor in genome evolution, particularly when the newly acquired gene confers a new capability to the recipient species. We identified a gene similar to the makes caterpillars floppy (mcf1 and mcf2) insect toxin genes in Photorhabdus, bacterial symbionts of nematodes, in the genomes of the Epichloë fungi, which are intercellular symbionts of grasses. Infection by Epichloë spp. often confers insect resistance to the grass hosts, largely due to the production of fungal alkaloids. A mcf-like gene is present in all of the Epichloë genome sequences currently available but in no other fungal genomes. This suggests the Epichloë genes were derived from a single lineage-specific HGT event. Molecular dating was used to estimate the time of the HGT event at between 7.2 and 58.8 million years ago. The mcf-like coding sequence from Epichloë typhina subsp. poae was cloned and expressed in Escherichia coli. E. coli cells expressing the Mcf protein were toxic to black cutworms (Agrotis ipsilon), whereas E. coli cells containing the vector only were non-toxic. These results suggest that the Epichloë mcf-like genes may be a component, in addition to the fungal alkaloids, of the insect resistance observed in Epichloë-infected grasses.}, }
@article {pmid24990676, year = {2014}, author = {Bruto, M and Prigent-Combaret, C and Luis, P and Moënne-Loccoz, Y and Muller, D}, title = {Frequent, independent transfers of a catabolic gene from bacteria to contrasted filamentous eukaryotes.}, journal = {Proceedings. Biological sciences}, volume = {281}, number = {1789}, pages = {20140848}, pmid = {24990676}, issn = {1471-2954}, mesh = {Biological Evolution ; Carbon-Carbon Lyases/*genetics ; Eukaryota/*genetics ; *Evolution, Molecular ; Fungi/genetics ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Introns ; Phylogeny ; Pseudomonas fluorescens/genetics ; Selection, Genetic ; Stramenopiles/genetics ; }, abstract = {Even genetically distant prokaryotes can exchange genes between them, and these horizontal gene transfer events play a central role in adaptation and evolution. While this was long thought to be restricted to prokaryotes, certain eukaryotes have acquired genes of bacterial origin. However, gene acquisitions in eukaryotes are thought to be much less important in magnitude than in prokaryotes. Here, we describe the complex evolutionary history of a bacterial catabolic gene that has been transferred repeatedly from different bacterial phyla to stramenopiles and fungi. Indeed, phylogenomic analysis pointed to multiple acquisitions of the gene in these filamentous eukaryotes-as many as 15 different events for 65 microeukaryotes. Furthermore, once transferred, this gene acquired introns and was found expressed in mRNA databases for most recipients. Our results show that effective inter-domain transfers and subsequent adaptation of a prokaryotic gene in eukaryotic cells can happen at an unprecedented magnitude.}, }
@article {pmid24986220, year = {2014}, author = {Berezovskaya, FS and Wolf, YI and Koonin, EV and Karev, GP}, title = {Pseudo-chaotic oscillations in CRISPR-virus coevolution predicted by bifurcation analysis.}, journal = {Biology direct}, volume = {9}, number = {}, pages = {13}, pmid = {24986220}, issn = {1745-6150}, support = {//Intramural NIH HHS/United States ; }, mesh = {Archaea/genetics/virology ; Bacteria/genetics/virology ; Clustered Regularly Interspaced Short Palindromic Repeats/*genetics ; *Evolution, Molecular ; Logistic Models ; *Models, Genetic ; *Nonlinear Dynamics ; Viruses/genetics ; }, abstract = {BACKGROUND: The CRISPR-Cas systems of adaptive antivirus immunity are present in most archaea and many bacteria, and provide resistance to specific viruses or plasmids by inserting fragments of foreign DNA into the host genome and then utilizing transcripts of these spacers to inactivate the cognate foreign genome. The recent development of powerful genome engineering tools on the basis of CRISPR-Cas has sharply increased the interest in the diversity and evolution of these systems. Comparative genomic data indicate that during evolution of prokaryotes CRISPR-Cas loci are lost and acquired via horizontal gene transfer at high rates. Mathematical modeling and initial experimental studies of CRISPR-carrying microbes and viruses reveal complex coevolutionary dynamics.<br><br>RESULTS: We performed a bifurcation analysis of models of coevolution of viruses and microbial host that possess CRISPR-Cas hereditary adaptive immunity systems. The analyzed Malthusian and logistic models display complex, and in particular, quasi-chaotic oscillation regimes that have not been previously observed experimentally or in agent-based models of the CRISPR-mediated immunity. The key factors for the appearance of the quasi-chaotic oscillations are the non-linear dependence of the host immunity on the virus load and the partitioning of the hosts into the immune and susceptible populations, so that the system consists of three components.<br><br>CONCLUSIONS: Bifurcation analysis of CRISPR-host coevolution model predicts complex regimes including quasi-chaotic oscillations. The quasi-chaotic regimes of virus-host coevolution are likely to be biologically relevant given the evolutionary instability of the CRISPR-Cas loci revealed by comparative genomics. The results of this analysis might have implications beyond the CRISPR-Cas systems, i.e. could describe the behavior of any adaptive immunity system with a heritable component, be it genetic or epigenetic. These predictions are experimentally testable.<br><br>REVIEWERS' REPORTS: This manuscript was reviewed by Sandor Pongor, Sergei Maslov and Marek Kimmel. For the complete reports, go to the Reviewers' Reports section.}, }
@article {pmid24985194, year = {2014}, author = {Xu, L and Zhang, Y and Wang, L and Chen, W and Wei, G}, title = {Diversity of endophytic bacteria associated with nodules of two indigenous legumes at different altitudes of the Qilian Mountains in China.}, journal = {Systematic and applied microbiology}, volume = {37}, number = {6}, pages = {457-465}, doi = {10.1016/j.syapm.2014.05.009}, pmid = {24985194}, issn = {1618-0984}, mesh = {*Altitude ; Bacteria/*classification/genetics ; China ; Endophytes/*classification ; Fabaceae/*microbiology ; Genes, Bacterial ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S ; Root Nodules, Plant/*microbiology ; }, abstract = {A total of 201 endophytic root nodule-associated bacteria collected from two legumes indigenous to different Qilian Mountain altitudes (Hexi Corridor) were characterized through 16S rDNA polymerase chain reaction (PCR)-restriction fragment length polymorphism, 16S rRNA gene sequence analysis, and enterobacterial repetitive intergenic consensus-PCR clustering. The isolates phylogenetically belonged to 35 species in the Phyllobacterium, Ensifer, Rhizobium, Microvirga, Sphingomonas, Paracoccus, Mycobacterium, Paenibacillus, Cohnella, Sporosarcina, Bacillus, Staphylococcus, Brevibacterium, Xenophilus, Erwinia, Leclercia, Acinetobacter, and Pseudomonas genera. Phylogenetic nodA sequence analysis showed higher similarity to Sinorhizobium meliloti with strains related to the Rhizobium, Sinorhizobium, and Acinetobacter genera. Sequence analysis of the nifH gene revealed that the strains belonging to Xenophilus, Acinetobacter, Phyllobacterium, and Rhizobium had genes similar to those of Mesorhizobium and Sinorhizobium. The results indicated that horizontal gene transfer could have occurred between rhizobia and non-rhizobial endophytes. Canonical correspondence analysis revealed that altitude and host plant species contributed more to the bacterial endosymbiont separation than other ecological factors. This study provided valuable information on the interactions between symbiotic bacteria, non-symbiotic bacteria and their habitats, and thus provided knowledge on their genetic diversity and ecology.}, }
@article {pmid24984774, year = {2014}, author = {Moreira, D and Deschamps, P}, title = {What was the real contribution of endosymbionts to the eukaryotic nucleus? Insights from photosynthetic eukaryotes.}, journal = {Cold Spring Harbor perspectives in biology}, volume = {6}, number = {7}, pages = {a016014}, pmid = {24984774}, issn = {1943-0264}, mesh = {Alveolata/genetics ; Cell Nucleus/*genetics/physiology ; Chlorophyta/genetics ; Diatoms/genetics ; Eukaryota/*genetics/physiology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Plastid ; Photosynthesis/*genetics ; Phylogeny ; Plastids/genetics ; Symbiosis/*genetics ; }, abstract = {Eukaryotic genomes are composed of genes of different evolutionary origins. This is especially true in the case of photosynthetic eukaryotes, which, in addition to typical eukaryotic genes and genes of mitochondrial origin, also contain genes coming from the primary plastids and, in the case of secondary photosynthetic eukaryotes, many genes provided by the nuclei of red or green algal endosymbionts. Phylogenomic analyses have been applied to detect those genes and, in some cases, have led to proposing the existence of cryptic, no longer visible endosymbionts. However, detecting them is a very difficult task because, most often, those genes were acquired a long time ago and their phylogenetic signal has been heavily erased. We revisit here two examples, the putative cryptic endosymbiosis of green algae in diatoms and chromerids and of Chlamydiae in the first photosynthetic eukaryotes. We show that the evidence sustaining them has been largely overestimated, and we insist on the necessity of careful, accurate phylogenetic analyses to obtain reliable results.}, }
@article {pmid24982308, year = {2014}, author = {Heckel, BC and Tomlinson, AD and Morton, ER and Choi, JH and Fuqua, C}, title = {Agrobacterium tumefaciens exoR controls acid response genes and impacts exopolysaccharide synthesis, horizontal gene transfer, and virulence gene expression.}, journal = {Journal of bacteriology}, volume = {196}, number = {18}, pages = {3221-3233}, pmid = {24982308}, issn = {1098-5530}, support = {R01 GM080546/GM/NIGMS NIH HHS/United States ; T32 GM007757/GM/NIGMS NIH HHS/United States ; GM080546/GM/NIGMS NIH HHS/United States ; T32-GM007757/GM/NIGMS NIH HHS/United States ; }, mesh = {Agrobacterium tumefaciens/genetics/*metabolism/*pathogenicity ; Bacterial Proteins/genetics/*metabolism ; Gene Expression Regulation, Bacterial/*physiology ; Gene Transfer, Horizontal/*physiology ; Mutation ; Polysaccharides, Bacterial/*biosynthesis/genetics/metabolism ; Virulence/genetics ; }, abstract = {Agrobacterium tumefaciens is a facultative plant pathogen and the causative agent of crown gall disease. The initial stage of infection involves attachment to plant tissues, and subsequently, biofilms may form at these sites. This study focuses on the periplasmic ExoR regulator, which was identified based on the severe biofilm deficiency of A. tumefaciens exoR mutants. Genome-wide expression analysis was performed to elucidate the complete ExoR regulon. Overproduction of the exopolysaccharide succinoglycan is a dramatic phenotype of exoR mutants. Comparative expression analyses revealed that the core ExoR regulon is unaffected by succinoglycan synthesis. Several findings are consistent with previous observations: genes involved in succinoglycan biosynthesis, motility, and type VI secretion are differentially expressed in the ΔexoR mutant. In addition, these studies revealed new functional categories regulated by ExoR, including genes related to virulence, conjugation of the pAtC58 megaplasmid, ABC transporters, and cell envelope architecture. To address how ExoR exerts a broad impact on gene expression from its periplasmic location, a genetic screen was performed to isolate suppressor mutants that mitigate the exoR motility phenotype and identify downstream components of the ExoR regulatory pathway. This suppression analysis identified the acid-sensing two-component system ChvG-ChvI, and the suppressor mutant phenotypes suggest that all or most of the characteristic exoR properties are mediated through ChvG-ChvI. Subsequent analysis indicates that exoR mutants are simulating a response to acidic conditions, even in neutral media. This work expands the model for ExoR regulation in A. tumefaciens and underscores the global role that this regulator plays on gene expression.}, }
@article {pmid24982177, year = {2014}, author = {Nikoh, N and Hosokawa, T and Moriyama, M and Oshima, K and Hattori, M and Fukatsu, T}, title = {Evolutionary origin of insect-Wolbachia nutritional mutualism.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {28}, pages = {10257-10262}, pmid = {24982177}, issn = {1091-6490}, mesh = {Animals ; Base Sequence ; *Bedbugs/metabolism/microbiology ; Biotin/biosynthesis/genetics ; Feeding Behavior/*physiology ; Genes, Bacterial/*physiology ; Genome, Bacterial/*physiology ; Molecular Sequence Data ; Symbiosis/*physiology ; Vitamin B Complex/biosynthesis/genetics ; *Wolbachia/genetics/metabolism ; }, abstract = {Obligate insect-bacterium nutritional mutualism is among the most sophisticated forms of symbiosis, wherein the host and the symbiont are integrated into a coherent biological entity and unable to survive without the partnership. Originally, however, such obligate symbiotic bacteria must have been derived from free-living bacteria. How highly specialized obligate mutualisms have arisen from less specialized associations is of interest. Here we address this evolutionary issue by focusing on an exceptional insect-Wolbachia nutritional mutualism. Although Wolbachia endosymbionts are ubiquitously found in diverse insects and generally regarded as facultative/parasitic associates for their insect hosts, a Wolbachia strain associated with the bedbug Cimex lectularius, designated as wCle, was shown to be essential for host's growth and reproduction via provisioning of B vitamins. We determined the 1,250,060-bp genome of wCle, which was generally similar to the genomes of insect-associated facultative Wolbachia strains, except for the presence of an operon encoding the complete biotin synthetic pathway that was acquired via lateral gene transfer presumably from a coinfecting endosymbiont Cardinium or Rickettsia. Nutritional and physiological experiments, in which wCle-infected and wCle-cured bedbugs of the same genetic background were fed on B-vitamin-manipulated blood meals via an artificial feeding system, demonstrated that wCle certainly synthesizes biotin, and the wCle-provisioned biotin significantly contributes to the host fitness. These findings strongly suggest that acquisition of a single gene cluster consisting of biotin synthesis genes underlies the bedbug-Wolbachia nutritional mutualism, uncovering an evolutionary transition from facultative symbiosis to obligate mutualism facilitated by lateral gene transfer in an endosymbiont lineage.}, }
@article {pmid24982175, year = {2014}, author = {Strachan, CR and Singh, R and VanInsberghe, D and Ievdokymenko, K and Budwill, K and Mohn, WW and Eltis, LD and Hallam, SJ}, title = {Metagenomic scaffolds enable combinatorial lignin transformation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {28}, pages = {10143-10148}, pmid = {24982175}, issn = {1091-6490}, mesh = {Base Sequence ; Biotransformation ; *Escherichia coli K12/genetics/metabolism ; Lignin/*metabolism ; *Metabolic Engineering ; *Metagenomics ; Molecular Sequence Data ; Pseudomonas stutzeri/genetics ; }, abstract = {Engineering the microbial transformation of lignocellulosic biomass is essential to developing modern biorefining processes that alleviate reliance on petroleum-derived energy and chemicals. Many current bioprocess streams depend on the genetic tractability of Escherichia coli with a primary emphasis on engineering cellulose/hemicellulose catabolism, small molecule production, and resistance to product inhibition. Conversely, bioprocess streams for lignin transformation remain embryonic, with relatively few environmental strains or enzymes implicated. Here we develop a biosensor responsive to monoaromatic lignin transformation products compatible with functional screening in E. coli. We use this biosensor to retrieve metagenomic scaffolds sourced from coal bed bacterial communities conferring an array of lignin transformation phenotypes that synergize in combination. Transposon mutagenesis and comparative sequence analysis of active clones identified genes encoding six functional classes mediating lignin transformation phenotypes that appear to be rearrayed in nature via horizontal gene transfer. Lignin transformation activity was then demonstrated for one of the predicted gene products encoding a multicopper oxidase to validate the screen. These results illuminate cellular and community-wide networks acting on aromatic polymers and expand the toolkit for engineering recombinant lignin transformation based on ecological design principles.}, }
@article {pmid24982156, year = {2014}, author = {Kelly, LW and Williams, GJ and Barott, KL and Carlson, CA and Dinsdale, EA and Edwards, RA and Haas, AF and Haynes, M and Lim, YW and McDole, T and Nelson, CE and Sala, E and Sandin, SA and Smith, JE and Vermeij, MJ and Youle, M and Rohwer, F}, title = {Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressors.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {28}, pages = {10227-10232}, pmid = {24982156}, issn = {1091-6490}, mesh = {*Adaptation, Physiological ; *Bacteria/genetics/metabolism ; *Coral Reefs ; *Gene Transfer, Horizontal ; *Metagenome ; *Microbiota ; Pacific Ocean ; *Water Pollution ; }, abstract = {Holobionts are species-specific associations between macro- and microorganisms. On coral reefs, the benthic coverage of coral and algal holobionts varies due to natural and anthropogenic forcings. Different benthic macroorganisms are predicted to have specific microbiomes. In contrast, local environmental factors are predicted to select for specific metabolic pathways in microbes. To reconcile these two predictions, we hypothesized that adaptation of microbiomes to local conditions is facilitated by the horizontal transfer of genes responsible for specific metabolic capabilities. To test this hypothesis, microbial metagenomes were sequenced from 22 coral reefs at 11 Line Islands in the central Pacific that together span a wide range of biogeochemical and anthropogenic influences. Consistent with our hypothesis, the percent cover of major benthic functional groups significantly correlated with particular microbial taxa. Reefs with higher coral cover had a coral microbiome with higher abundances of Alphaproteobacteria (such as Rhodobacterales and Sphingomonadales), whereas microbiomes of algae-dominated reefs had higher abundances of Gammaproteobacteria (such as Alteromonadales, Pseudomonadales, and Vibrionales), Betaproteobacteria, and Bacteriodetes. In contrast to taxa, geography was the strongest predictor of microbial community metabolism. Microbial communities on reefs with higher nutrient availability (e.g., equatorial upwelling zones) were enriched in genes involved in nutrient-related metabolisms (e.g., nitrate and nitrite ammonification, Ton/Tol transport, etc.). On reefs further from the equator, microbes had more genes encoding chlorophyll biosynthesis and photosystems I/II. These results support the hypothesis that core microbiomes are determined by holobiont macroorganisms, and that those core taxa adapt to local conditions by selecting for advantageous metabolic genes.}, }
@article {pmid24978610, year = {2014}, author = {Kirsch, R and Gramzow, L and Theißen, G and Siegfried, BD and Ffrench-Constant, RH and Heckel, DG and Pauchet, Y}, title = {Horizontal gene transfer and functional diversification of plant cell wall degrading polygalacturonases: Key events in the evolution of herbivory in beetles.}, journal = {Insect biochemistry and molecular biology}, volume = {52}, number = {}, pages = {33-50}, doi = {10.1016/j.ibmb.2014.06.008}, pmid = {24978610}, issn = {1879-0240}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Ascomycota/enzymology/genetics ; Base Sequence ; *Biological Evolution ; Cell Wall ; Coleoptera/*enzymology/*genetics ; *Gene Transfer, Horizontal ; Herbivory/*genetics ; Molecular Sequence Data ; Pectins/metabolism ; Phylogeny ; Plants/parasitology ; Polygalacturonase/*genetics ; Transcriptome ; }, abstract = {Plant cell walls are the largest reservoir of organic carbon on earth. To breach and utilize this carbohydrate-rich protective barrier, microbes secrete plant cell wall degrading enzymes (PCWDEs) targeting pectin, cellulose and hemicelluloses. There is a growing body of evidence that genomes of some herbivorous insects also encode PCWDEs, raising questions about their evolutionary origins and functions. Among herbivorous beetles, pectin-degrading polygalacturonases (PGs) are found in the diverse superfamilies Chrysomeloidea (leaf beetles, long-horn beetles) and Curculionoidea (weevils). Here our aim was to test whether these arose from a common ancestor of beetles or via horizontal gene transfer (HGT), and whether PGs kept their ancestral function in degrading pectin or evolved novel functions. Transcriptome data derived from 10 beetle species were screened for PG-encoding sequences and used for phylogenetic comparisons with their bacterial, fungal and plant counterparts. These analyses revealed a large family of PG-encoding genes of Chrysomeloidea and Curculionoidea sharing a common ancestor, most similar to PG genes of ascomycete fungi. In addition, 50 PGs from beetle digestive systems were heterologously expressed and functionally characterized, showing a set of lineage-specific consecutively pectin-degrading enzymes, as well as conserved but enzymatically inactive PG proteins. The evidence indicates that a PG gene was horizontally transferred ∼200 million years ago from an ascomycete fungus to a common ancestor of Chrysomeloidea and Curculionoidea. This has been followed by independent duplications in these two lineages, as well as independent replacement in two sublineages of Chrysomeloidea by two other subsequent HGTs. This origin, leading to subsequent functional diversification of the PG gene family within its new hosts, was a key event promoting the evolution of herbivory in these beetles.}, }
@article {pmid24976890, year = {2013}, author = {Dogs, M and Voget, S and Teshima, H and Petersen, J and Davenport, K and Dalingault, H and Chen, A and Pati, A and Ivanova, N and Goodwin, LA and Chain, P and Detter, JC and Standfest, S and Rohde, M and Gronow, S and Kyrpides, NC and Woyke, T and Simon, M and Klenk, HP and Göker, M and Brinkhoff, T}, title = {Genome sequence of Phaeobacter inhibens type strain (T5(T)), a secondary metabolite producing representative of the marine Roseobacter clade, and emendation of the species description of Phaeobacter inhibens.}, journal = {Standards in genomic sciences}, volume = {9}, number = {2}, pages = {334-350}, pmid = {24976890}, issn = {1944-3277}, abstract = {Strain T5(T) is the type strain of the species Phaeobacter inhibens Martens et al. 2006, a secondary metabolite producing bacterium affiliated to the Roseobacter clade. Strain T5(T) was isolated from a water sample taken at the German Wadden Sea, southern North Sea. Here we describe the complete genome sequence and annotation of this bacterium with a special focus on the secondary metabolism and compare it with the genomes of the Phaeobacter inhibens strains DSM 17395 and DSM 24588 (2.10), selected because of the close phylogenetic relationship based on the 16S rRNA gene sequences of these three strains. The genome of strain T5(T) comprises 4,130,897 bp with 3.923 protein-coding genes and shows high similarities in genetic and genomic characteristics compared to P. inhibens DSM 17395 and DSM 24588 (2.10). Besides the chromosome, strain T5(T) possesses four plasmids, three of which show a high similarity to the plasmids of the strains DSM 17395 and DSM 24588 (2.10). Analysis of the fourth plasmid suggested horizontal gene transfer. Most of the genes on this plasmid are not present in the strains DSM 17395 and DSM 24588 (2.10) including a nitrous oxide reductase, which allows strain T5(T) a facultative anaerobic lifestyle. The G+C content was calculated from the genome sequence and differs significantly from the previously published value, thus warranting an emendation of the species description.}, }
@article {pmid24976886, year = {2013}, author = {Reeve, W and Nandasena, K and Yates, R and Tiwari, R and O'Hara, G and Ninawi, M and Chertkov, O and Goodwin, L and Bruce, D and Detter, C and Tapia, R and Han, S and Woyke, T and Pitluck, S and Nolan, M and Land, M and Copeland, A and Liolios, K and Pati, A and Mavromatis, K and Markowitz, V and Kyrpides, N and Ivanova, N and Goodwin, L and Meenakshi, U and Howieson, J}, title = {Complete genome sequence of Mesorhizobium opportunistum type strain WSM2075(T.).}, journal = {Standards in genomic sciences}, volume = {9}, number = {2}, pages = {294-303}, pmid = {24976886}, issn = {1944-3277}, abstract = {Mesorhizobium opportunistum strain WSM2075(T) was isolated in Western Australia in 2000 from root nodules of the pasture legume Biserrula pelecinus that had been inoculated with M. ciceri bv. biserrulae WSM1271. WSM2075(T) is an aerobic, motile, Gram negative, non-spore-forming rod that has gained the ability to nodulate B. pelecinus but is completely ineffective in N2 fixation with this host. This report reveals that the genome of M. opportunistum strain WSM2075(T) contains a chromosome of size 6,884,444 bp, encoding 6,685 protein-coding genes and 62 RNA-only encoding genes. The genome contains no plasmids, but does harbor a 455.7 kb genomic island from Mesorhizobium ciceri bv. biserrulae WSM1271 that has been integrated into a phenylalanine-tRNA gene.}, }
@article {pmid24974201, year = {2014}, author = {Behnam, E and Smith, AD}, title = {The Amordad database engine for metagenomics.}, journal = {Bioinformatics (Oxford, England)}, volume = {30}, number = {20}, pages = {2949-2955}, pmid = {24974201}, issn = {1367-4811}, support = {P50 HG002790/HG/NHGRI NIH HHS/United States ; }, mesh = {*Databases, Genetic ; Information Storage and Retrieval/*methods ; Metagenomics/*methods ; *Software ; }, abstract = {MOTIVATION: Several technical challenges in metagenomic data analysis, including assembling metagenomic sequence data or identifying operational taxonomic units, are both significant and well known. These forms of analysis are increasingly cited as conceptually flawed, given the extreme variation within traditionally defined species and rampant horizontal gene transfer. Furthermore, computational requirements of such analysis have hindered content-based organization of metagenomic data at large scale.<br><br>RESULTS: In this article, we introduce the Amordad database engine for alignment-free, content-based indexing of metagenomic datasets. Amordad places the metagenome comparison problem in a geometric context, and uses an indexing strategy that combines random hashing with a regular nearest neighbor graph. This framework allows refinement of the database over time by continual application of random hash functions, with the effect of each hash function encoded in the nearest neighbor graph. This eliminates the need to explicitly maintain the hash functions in order for query efficiency to benefit from the accumulated randomness. Results on real and simulated data show that Amordad can support logarithmic query time for identifying similar metagenomes even as the database size reaches into the millions.<br><br>Source code, licensed under the GNU general public license (version 3) is freely available for download from http://smithlabresearch.org/amordad<br><br>CONTACT: andrewds@usc.edu<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid24972019, year = {2014}, author = {Yang, Y and Matsuzaki, M and Takahashi, F and Qu, L and Nozaki, H}, title = {Phylogenomic analysis of "red" genes from two divergent species of the "green" secondary phototrophs, the chlorarachniophytes, suggests multiple horizontal gene transfers from the red lineage before the divergence of extant chlorarachniophytes.}, journal = {PloS one}, volume = {9}, number = {6}, pages = {e101158}, pmid = {24972019}, issn = {1932-6203}, mesh = {Cyanobacteria/classification/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genes, Protozoan ; Genetic Speciation ; Photosynthesis/genetics ; Phototrophic Processes/*genetics ; *Phylogeny ; Rhizaria/classification/*genetics ; }, abstract = {The plastids of chlorarachniophytes were derived from an ancestral green alga via secondary endosymbiosis. Thus, genes from the "green" lineage via secondary endosymbiotic gene transfer (EGT) are expected in the nuclear genomes of the Chlorarachniophyta. However, several recent studies have revealed the presence of "red" genes in their nuclear genomes. To elucidate the origin of such "red" genes in chlorarachniophyte nuclear genomes, we carried out exhaustive single-gene phylogenetic analyses, including two operational taxonomic units (OTUs) that represent two divergent sister lineages of the Chlorarachniophyta, Amorphochlora amoeboformis (= Lotharella amoeboformis; based on RNA sequences newly determined here) and Bigelowiella natans (based on the published genome sequence). We identified 10 genes of cyanobacterial origin, phylogenetic analysis of which showed the chlorarachniophytes to branch with the red lineage (red algae and/or red algal secondary or tertiary plastid-containing eukaryotes). Of the 10 genes, 7 demonstrated robust monophyly of the two chlorarachniophyte OTUs. Thus, the common ancestor of the extant chlorarachniophytes likely experienced multiple horizontal gene transfers from the red lineage. Because 4 of the 10 genes are obviously photosynthesis- and/or plastid-related, and almost all of the eukaryotic OTUs in the 10 trees possess plastids, such red genes most likely originated directly from photosynthetic eukaryotes. This situation could be explained by a possible cryptic endosymbiosis of a red algal plastid before the secondary endosymbiosis of the green algal plastid, or a long-term feeding on a single (or multiple closely related) red algal plastid-containing eukaryote(s) after the green secondary endosymbiosis.}, }
@article {pmid24969138, year = {2014}, author = {Maumus, F and Epert, A and Nogué, F and Blanc, G}, title = {Plant genomes enclose footprints of past infections by giant virus relatives.}, journal = {Nature communications}, volume = {5}, number = {}, pages = {4268}, pmid = {24969138}, issn = {2041-1723}, mesh = {Bryopsida/*genetics/virology ; DNA Methylation ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Plant/*genetics ; Mimiviridae/*genetics ; Open Reading Frames/*genetics ; Plant Diseases/*genetics ; *Plant Viruses ; Selaginellaceae/*genetics/virology ; *Sequence Homology, Nucleic Acid ; }, abstract = {Nucleocytoplasmic large DNA viruses (NCLDVs) are eukaryotic viruses with large genomes (100 kb-2.5 Mb), which include giant Mimivirus, Megavirus and Pandoravirus. NCLDVs are known to infect animals, protists and phytoplankton but were never described as pathogens of land plants. Here, we show that the bryophyte Physcomitrella patens and the lycophyte Selaginella moellendorffii have open reading frames (ORFs) with high phylogenetic affinities to NCLDV homologues. The P. patens genes are clustered in DNA stretches (up to 13 kb) containing up to 16 NCLDV-like ORFs. Molecular evolution analysis suggests that the NCLDV-like regions were acquired by horizontal gene transfer from distinct but closely related viruses that possibly define a new family of NCLDVs. Transcriptomics and DNA methylation data indicate that the NCLDV-like regions are transcriptionally inactive and are highly cytosine methylated through a mechanism not relying on small RNAs. Altogether, our data show that members of NCLDV have infected land plants.}, }
@article {pmid24967627, year = {2014}, author = {Iranzo, J and Gómez, MJ and López de Saro, FJ and Manrubia, S}, title = {Large-scale genomic analysis suggests a neutral punctuated dynamics of transposable elements in bacterial genomes.}, journal = {PLoS computational biology}, volume = {10}, number = {6}, pages = {e1003680}, pmid = {24967627}, issn = {1553-7358}, mesh = {DNA Transposable Elements/*genetics ; Evolution, Molecular ; Gene Duplication/genetics ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/*genetics ; Genomics/*methods ; *Models, Genetic ; }, abstract = {Insertion sequences (IS) are the simplest and most abundant form of transposable DNA found in bacterial genomes. When present in multiple copies, it is thought that they can promote genomic plasticity and genetic exchange, thus being a major force of evolutionary change. The main processes that determine IS content in genomes are, though, a matter of debate. In this work, we take advantage of the large amount of genomic data currently available and study the abundance distributions of 33 IS families in 1811 bacterial chromosomes. This allows us to test simple models of IS dynamics and estimate their key parameters by means of a maximum likelihood approach. We evaluate the roles played by duplication, lateral gene transfer, deletion and purifying selection. We find that the observed IS abundances are compatible with a neutral scenario where IS proliferation is controlled by deletions instead of purifying selection. Even if there may be some cases driven by selection, neutral behavior dominates over large evolutionary scales. According to this view, IS and hosts tend to coexist in a dynamic equilibrium state for most of the time. Our approach also allows for a detection of recent IS expansions, and supports the hypothesis that rapid expansions constitute transient events-punctuations-during which the state of coexistence of IS and host becomes perturbated.}, }
@article {pmid24966539, year = {2014}, author = {Salahuddin, P and Khan, AU}, title = {Studies on structure-based sequence alignment and phylogenies of beta-lactamases.}, journal = {Bioinformation}, volume = {10}, number = {5}, pages = {308-313}, pmid = {24966539}, issn = {0973-2063}, abstract = {The β-lactamases enzymes cleave the amide bond in β-lactam ring, rendering β-lactam antibiotics harmless to bacteria. In this communication we have studied structure-function relationship and phylogenies of class A, B and D beta-lactamases using structure-based sequence alignment and phylip programs respectively. The data of structure-based sequence alignment suggests that in different isolates of TEM-1, mutations did not occur at or near sequence motifs. Since deletions are reported to be lethal to structure and function of enzyme. Therefore, in these variants antibiotic hydrolysis profile and specificity will be affected. The alignment data of class A enzyme SHV-1, CTX-M-15, class D enzyme, OXA-10, and class B enzyme VIM-2 and SIM-1 show sequence motifs along with other part of polypeptide are essentially conserved. These results imply that conformations of betalactamases are close to native state and possess normal hydrolytic activities towards beta-lactam antibiotics. However, class B enzyme such as IMP-1 and NDM-1 are less conserved than other class A and D studied here because mutation and deletions occurred at critically important region such as active site. Therefore, the structure of these beta-lactamases will be altered and antibiotic hydrolysis profile will be affected. Phylogenetic studies suggest that class A and D beta-lactamases including TOHO-1 and OXA-10 respectively evolved by horizontal gene transfer (HGT) whereas other member of class A such as TEM-1 evolved by gene duplication mechanism. Taken together, these studies justify structure-function relationship of beta-lactamases and phylogenetic studies suggest these enzymes evolved by different mechanisms.}, }
@article {pmid24966179, year = {2014}, author = {Chen, W and Lee, MK and Jefcoate, C and Kim, SC and Chen, F and Yu, JH}, title = {Fungal cytochrome p450 monooxygenases: their distribution, structure, functions, family expansion, and evolutionary origin.}, journal = {Genome biology and evolution}, volume = {6}, number = {7}, pages = {1620-1634}, pmid = {24966179}, issn = {1759-6653}, mesh = {Animals ; Conserved Sequence ; *Cytochrome P-450 Enzyme System/chemistry/genetics/metabolism ; *Evolution, Molecular ; Fungi/chemistry/classification/*enzymology/*genetics ; Humans ; Phylogeny ; }, abstract = {Cytochrome P450 (CYP) monooxygenase superfamily contributes a broad array of biological functions in living organisms. In fungi, CYPs play diverse and pivotal roles in versatile metabolism and fungal adaptation to specific ecological niches. In this report, CYPomes in the 47 genomes of fungi belong to the phyla Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota have been studied. The comparison of fungal CYPomes suggests that generally fungi possess abundant CYPs belonging to a variety of families with the two global families CYP51 and CYP61, indicating individuation of CYPomes during the evolution of fungi. Fungal CYPs show highly conserved characteristic motifs, but very low overall sequence similarities. The characteristic motifs of fungal CYPs are distinguishable from those of CYPs in animals, plants, and especially archaea and bacteria. The four representative motifs contribute to the general function of CYPs. Fungal CYP51s and CYP61s can be used as the models for the substrate recognition sites analysis. The CYP proteins are clustered into 15 clades and the phylogenetic analyses suggest that the wide variety of fungal CYPs has mainly arisen from gene duplication. Two large duplication events might have been associated with the booming of Ascomycota and Basidiomycota. In addition, horizontal gene transfer also contributes to the diversification of fungal CYPs. Finally, a possible evolutionary scenario for fungal CYPs along with fungal divergences is proposed. Our results provide the fundamental information for a better understanding of CYP distribution, structure and function, and new insights into the evolutionary events of fungal CYPs along with the evolution of fungi.}, }
@article {pmid24966114, year = {2014}, author = {Pelchovich, G and Nadejda, S and Dana, A and Tuller, T and Bravo, IG and Gophna, U}, title = {Ribosomal mutations affecting the translation of genes that use non-optimal codons.}, journal = {The FEBS journal}, volume = {281}, number = {16}, pages = {3701-3718}, doi = {10.1111/febs.12892}, pmid = {24966114}, issn = {1742-4658}, mesh = {AT Rich Sequence ; Chloramphenicol O-Acetyltransferase/genetics/metabolism ; *Codon ; Drug Resistance, Bacterial ; Escherichia coli/*genetics/metabolism ; Escherichia coli Proteins/*genetics/metabolism ; Gene Expression Regulation, Bacterial ; Mutation, Missense ; *Protein Biosynthesis ; RNA, Bacterial/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Ribosomal Protein S9 ; Ribosomal Proteins/*genetics/metabolism ; Ribosomes/*physiology ; }, abstract = {Genes that are laterally acquired by a new host species often contain codons that are non-optimal to the tRNA repertoire of the new host, which may lead to insufficient translational levels. Inefficient translation can be overcome by different mechanisms, such as incremental amelioration of the coding sequence, compensatory mutations in the regulatory sequences leading to increased transcription or increase in gene copy number. However, there is also a possibility that ribosomal mutations can improve the expression of such genes. To test this hypothesis, we examined the effects of point mutations in the endogenous ribosomal proteins S12 and S5 in Escherichia coli, which are known to be involved in the decoding of the mRNA, on the efficiency of translation of exogenous genes that use non-optimal codons, in vivo. We show that an S12 mutant in E. coli is able to express exogenous genes, with non-optimal codons, to higher levels than the wild-type, and explore the mechanisms underlying this phenomenon in this mutant. Our results suggest that the transient emergence of mutants that allow efficient expression of exogenous genes with non-optimal codons could also increase the chances of fixation of laterally transferred genes.}, }
@article {pmid24965277, year = {2015}, author = {Foflonker, F and Price, DC and Qiu, H and Palenik, B and Wang, S and Bhattacharya, D}, title = {Genome of the halotolerant green alga Picochlorum sp. reveals strategies for thriving under fluctuating environmental conditions.}, journal = {Environmental microbiology}, volume = {17}, number = {2}, pages = {412-426}, doi = {10.1111/1462-2920.12541}, pmid = {24965277}, issn = {1462-2920}, mesh = {Bacteria/genetics ; Base Sequence ; Chlorophyta/*enzymology/*genetics/metabolism ; Climate Change ; DNA, Plant/genetics ; Environment ; Gene Transfer, Horizontal ; Genome, Plant ; Microalgae ; Salinity ; Salt Tolerance/*genetics/physiology ; Salts ; Sequence Analysis, DNA ; }, abstract = {An expected outcome of climate change is intensification of the global water cycle, which magnifies surface water fluxes, and consequently alters salinity patterns. It is therefore important to understand the adaptations and limits of microalgae to survive changing salinities. To this end, we sequenced the 13.5 Mbp genome of the halotolerant green alga Picochlorum SENEW3 (SE3) that was isolated from a brackish water pond subject to large seasonal salinity fluctuations. Picochlorum SE3 encodes 7367 genes, making it one of the smallest and most gene dense eukaryotic genomes known. Comparison with the pico-prasinophyte Ostreococcus tauri, a species with a limited range of salt tolerance, reveals the enrichment of transporters putatively involved in the salt stress response in Picochlorum SE3. Analysis of cultures and the protein complement highlight the metabolic flexibility of Picochlorum SE3 that encodes genes involved in urea metabolism, acetate assimilation and fermentation, acetoin production and glucose uptake, many of which form functional gene clusters. Twenty-four cases of horizontal gene transfer from bacterial sources were found in Picochlorum SE3 with these genes involved in stress adaptation including osmolyte production and growth promotion. Our results identify Picochlorum SE3 as a model for understanding microalgal adaptation to stressful, fluctuating environments.}, }
@article {pmid24963920, year = {2014}, author = {Niu, YD and McAllister, TA and Nash, JH and Kropinski, AM and Stanford, K}, title = {Four Escherichia coli O157:H7 phages: a new bacteriophage genus and taxonomic classification of T1-like phages.}, journal = {PloS one}, volume = {9}, number = {6}, pages = {e100426}, pmid = {24963920}, issn = {1932-6203}, mesh = {Bacteriophages/*classification/genetics/*physiology ; Escherichia coli O157/*virology ; Phylogeny ; Proteomics ; }, abstract = {The T1-like bacteriophages vB_EcoS_AHP24, AHS24, AHP42 and AKS96 of the family Siphoviridae were shown to lyse common phage types of Shiga toxin-producing Escherichia coli O157:H7 (STEC O157:H7), but not non-O157 E. coli. All contained circularly permuted genomes of 45.7-46.8 kb (43.8-44 mol% G+C) encoding 74-81 open reading frames and 1 arginyl-tRNA. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed that the structural proteins were identical among the four phages. Further proteomic analysis identified seven structural proteins responsible for tail fiber, tail tape measure protein, major capsid, portal protein as well as major and minor tail proteins. Bioinformatic analyses on the proteins revealed that genomes of AHP24, AHS24, AHP42 and AKS96 did not encode for bacterial virulence factors, integration-related proteins or antibiotic resistance determinants. All four phages were highly lytic to STEC O157:H7 with considerable potential as biocontrol agents. Comparative genomic, proteomic and phylogenetic analysis suggested that the four phages along with 17 T1-like phage genomes from database of National Center for Biotechnology Information (NCBI) can be assigned into a proposed subfamily "Tunavirinae" with further classification into five genera, namely "Tlslikevirus" (TLS, FSL SP-126), "Kp36likevirus" (KP36, F20), Tunalikevirus (T1, ADB-2 and Shf1), "Rtplikevirus" (RTP, vB_EcoS_ACG-M12) and "Jk06likevirus" (JK06, vB_EcoS_Rogue1, AHP24, AHS24, AHP42, AKS96, phiJLA23, phiKP26, phiEB49). The fact that the viruses related to JK06 have been isolated independently in Israel (JK06) (GenBank Assession #, NC_007291), Canada (vB_EcoS_Rogue1, AHP24, AHS24, AHP42, AKS96) and Mexico (phiKP26, phiJLA23) (between 2005 and 2011) indicates that these similar phages are widely distributed, and that horizontal gene transfer does not always prevent the characterization of bacteriophage evolution. With this new scheme, any new discovered phages with same type can be more properly identified. Genomic- and proteomic-based taxonomic classification of phages would facilitate better understanding phages diversity and genetic traits involved in phage evolution.}, }
@article {pmid24963913, year = {2014}, author = {Utter, B and Deutsch, DR and Schuch, R and Winer, BY and Verratti, K and Bishop-Lilly, K and Sozhamannan, S and Fischetti, VA}, title = {Beyond the chromosome: the prevalence of unique extra-chromosomal bacteriophages with integrated virulence genes in pathogenic Staphylococcus aureus.}, journal = {PloS one}, volume = {9}, number = {6}, pages = {e100502}, pmid = {24963913}, issn = {1932-6203}, support = {R01 AI057472/AI/NIAID NIH HHS/United States ; T32 AI070084/AI/NIAID NIH HHS/United States ; AI-057472/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteriophages/genetics/*physiology ; Chromosomes, Bacterial/*genetics/virology ; DNA, Viral/genetics ; Genetic Variation ; Genome, Viral/genetics ; Sequence Analysis, DNA ; Staphylococcus aureus/cytology/genetics/*pathogenicity/*virology ; Virulence/genetics ; }, abstract = {In Staphylococcus aureus, the disease impact of chromosomally integrated prophages on virulence is well described. However, the existence of extra-chromosomal prophages, both plasmidial and episomal, remains obscure. Despite the recent explosion in bacterial and bacteriophage genomic sequencing, studies have failed to specifically focus on extra-chromosomal elements. We selectively enriched and sequenced extra-chromosomal DNA from S. aureus isolates using Roche-454 technology and uncovered evidence for the widespread distribution of multiple extra-chromosomal prophages (ExPΦs) throughout both antibiotic-sensitive and -resistant strains. We completely sequenced one such element comprised of a 43.8 kbp, circular ExPΦ (designated ФBU01) from a vancomycin-intermediate S. aureus (VISA) strain. Assembly and annotation of ФBU01 revealed a number of putative virulence determinants encoded within a bacteriophage immune evasion cluster (IEC). Our identification of several potential ExPΦs and mobile genetic elements (MGEs) also revealed numerous putative virulence factors and antibiotic resistance genes. We describe here a previously unidentified level of genetic diversity of stealth extra-chromosomal elements in S. aureus, including phages with a larger presence outside the chromosome that likely play a prominent role in pathogenesis and strain diversity driven by horizontal gene transfer (HGT).}, }
@article {pmid24963797, year = {2015}, author = {Blaxter, M and Koutsovoulos, G}, title = {The evolution of parasitism in Nematoda.}, journal = {Parasitology}, volume = {142 Suppl 1}, number = {Suppl 1}, pages = {S26-39}, pmid = {24963797}, issn = {1469-8161}, support = {//Wellcome Trust/United Kingdom ; 095831//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Bacteria/growth &amp; development ; Biological Evolution ; Gene Transfer, Horizontal ; Genome, Helminth/*genetics ; Invertebrates/*parasitology ; Nematoda/*genetics/microbiology ; Nematode Infections/*parasitology ; Phylogeny ; Plants/*parasitology ; Symbiosis ; }, abstract = {Nematodes are abundant and diverse, and include many parasitic species. Molecular phylogenetic analyses have shown that parasitism of plants and animals has arisen at least 15 times independently. Extant nematode species also display lifestyles that are proposed to be on the evolutionary trajectory to parasitism. Recent advances have permitted the determination of the genomes and transcriptomes of many nematode species. These new data can be used to further resolve the phylogeny of Nematoda, and identify possible genetic patterns associated with parasitism. Plant-parasitic nematode genomes show evidence of horizontal gene transfer from other members of the rhizosphere, and these genes play important roles in the parasite-host interface. Similar horizontal transfer is not evident in animal parasitic groups. Many nematodes have bacterial symbionts that can be essential for survival. Horizontal transfer from symbionts to the nematode is also common, but its biological importance is unclear. Over 100 nematode species are currently targeted for sequencing, and these data will yield important insights into the biology and evolutionary history of parasitism. It is important that these new technologies are also applied to free-living taxa, so that the pre-parasitic ground state can be inferred, and the novelties associated with parasitism isolated.}, }
@article {pmid24962815, year = {2014}, author = {Benson, MA and Ohneck, EA and Ryan, C and Alonzo, F and Smith, H and Narechania, A and Kolokotronis, SO and Satola, SW and Uhlemann, AC and Sebra, R and Deikus, G and Shopsin, B and Planet, PJ and Torres, VJ}, title = {Evolution of hypervirulence by a MRSA clone through acquisition of a transposable element.}, journal = {Molecular microbiology}, volume = {93}, number = {4}, pages = {664-681}, pmid = {24962815}, issn = {1365-2958}, support = {R21 AI101533/AI/NIAID NIH HHS/United States ; R01 AI099394/AI/NIAID NIH HHS/United States ; K08AI090013/AI/NIAID NIH HHS/United States ; R01 AI103268/AI/NIAID NIH HHS/United States ; T32 AI007180/AI/NIAID NIH HHS/United States ; K08AI101005/AI/NIAID NIH HHS/United States ; T32-AI007180/AI/NIAID NIH HHS/United States ; R01AI099394/AI/NIAID NIH HHS/United States ; R01AI105129/AI/NIAID NIH HHS/United States ; F32-AI098395/AI/NIAID NIH HHS/United States ; R01 AI105129/AI/NIAID NIH HHS/United States ; K08 AI090013/AI/NIAID NIH HHS/United States ; K08 AI101005/AI/NIAID NIH HHS/United States ; F32 AI098395/AI/NIAID NIH HHS/United States ; R01AI103268/AI/NIAID NIH HHS/United States ; R21AI101533/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/biosynthesis/genetics ; Bacterial Toxins/biosynthesis/genetics ; *DNA Transposable Elements ; DNA, Bacterial/chemistry/genetics ; *Evolution, Molecular ; *Gene Expression Regulation, Bacterial ; Humans ; Methicillin-Resistant Staphylococcus aureus/*genetics/*growth &amp; development ; Molecular Sequence Data ; Mutagenesis, Insertional ; *Recombination, Genetic ; Repressor Proteins/biosynthesis/genetics ; Sequence Analysis, DNA ; Virulence ; Virulence Factors/biosynthesis/genetics ; }, abstract = {Staphylococcus aureus has evolved as a pathogen that causes a range of diseases in humans. There are two dominant modes of evolution thought to explain most of the virulence differences between strains. First, virulence genes may be acquired from other organisms. Second, mutations may cause changes in the regulation and expression of genes. Here we describe an evolutionary event in which transposition of an IS element has a direct impact on virulence gene regulation resulting in hypervirulence. Whole-genome analysis of a methicillin-resistant S. aureus (MRSA) strain USA500 revealed acquisition of a transposable element (IS256) that is absent from close relatives of this strain. Of the multiple copies of IS256 found in the USA500 genome, one was inserted in the promoter sequence of repressor of toxins (Rot), a master transcriptional regulator responsible for the expression of virulence factors in S. aureus. We show that insertion into the rot promoter by IS256 results in the derepression of cytotoxin expression and increased virulence. Taken together, this work provides new insight into evolutionary strategies by which S. aureus is able to modify its virulence properties and demonstrates a novel mechanism by which horizontal gene transfer directly impacts virulence through altering toxin regulation.}, }
@article {pmid24961694, year = {2014}, author = {Chen, L and Mathema, B and Pitout, JD and DeLeo, FR and Kreiswirth, BN}, title = {Epidemic Klebsiella pneumoniae ST258 is a hybrid strain.}, journal = {mBio}, volume = {5}, number = {3}, pages = {e01355-14}, pmid = {24961694}, issn = {2150-7511}, support = {R01 AI090155/AI/NIAID NIH HHS/United States ; /ImNIH/Intramural NIH HHS/United States ; 1R01AI090155/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/metabolism ; Epidemics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial ; Klebsiella Infections/epidemiology/*microbiology ; Klebsiella pneumoniae/classification/*genetics/*isolation &amp; purification/metabolism ; Molecular Sequence Data ; Phylogeny ; *Recombination, Genetic ; United States/epidemiology ; }, abstract = {UNLABELLED: Carbapenem-resistant Enterobacteriaceae (CRE), especially Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae, pose an urgent threat in health facilities in the United States and worldwide. K. pneumoniae isolates classified as sequence type 258 (ST258) by multilocus sequence typing are largely responsible for the global spread of KPC. A recent comparative genome study revealed that ST258 K. pneumoniae strains are two distinct genetic clades; however, the molecular origin of ST258 largely remains unknown, and our understanding of the evolution of the two genetic clades is incomplete. Here we compared the genetic structures and single-nucleotide polymorphism (SNP) distributions in the core genomes of strains from two ST258 clades and other STs (ST11, ST442, and ST42). We identified an ~1.1-Mbp region on ST258 genomes that is homogeneous to that of ST442, while the rest of the ST258 genome resembles that of ST11. Our results suggest ST258 is a hybrid clone--80% of the genome originated from ST11-like strains and 20% from ST442-like strains. Meanwhile, we sequenced an ST42 strain that carries the same K-antigen-encoding capsule polysaccharide biosynthesis gene (cps) region as ST258 clade I strains. Comparison of the cps-harboring regions between the ST42 and ST258 strains (clades I and II) suggests the ST258 clade I strains evolved from a clade II strain as a result of cps region replacement. Our findings unravel the molecular evolution history of ST258 strains, an important first step toward the development of diagnostic, therapeutic, and vaccine strategies to combat infections caused by multidrug-resistant K. pneumoniae.<br><br>IMPORTANCE: Recombination events and replacement of chromosomal regions have been documented in various bacteria, and these events have given rise to successful pathogenic clones. Here we used comparative genomic analyses to discover that the ST258 K. pneumoniae genome is a hybrid--80% of the chromosome is homologous to ST11 strains, while the remaining 20% is homologous to that of ST442. Meanwhile, a recent study indicated that ST258 strains can be segregated into two ST258 clades, with distinct capsule polysaccharide gene (cps) regions. Our analysis suggests ST258 clade I strains evolved from clade II through homologous recombination of cps region. Horizontal transfer of the cps region appears to be a key element driving the molecular diversification in K. pneumoniae strains. These findings not only extend our understanding of the molecular evolution of ST258 but are an important step toward the development of effective control and treatment strategies for multidrug-resistant K. pneumoniae.}, }
@article {pmid24961279, year = {2014}, author = {Cottell, JL and Saw, HT and Webber, MA and Piddock, LJ}, title = {Functional genomics to identify the factors contributing to successful persistence and global spread of an antibiotic resistance plasmid.}, journal = {BMC microbiology}, volume = {14}, number = {}, pages = {168}, pmid = {24961279}, issn = {1471-2180}, mesh = {Bacteria/*genetics ; Conjugation, Genetic ; *Evolution, Molecular ; Gene Knockout Techniques ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Genomic Instability ; *Genomics ; Humans ; *Plasmids ; *beta-Lactam Resistance ; }, abstract = {BACKGROUND: The spread of bacterial plasmids is an increasing global problem contributing to the widespread dissemination of antibiotic resistance genes including β-lactamases. Our understanding of the details of the biological mechanisms by which these natural plasmids are able to persist in bacterial populations and are able to establish themselves in new hosts via conjugative transfer is very poor. We recently identified and sequenced a globally successful plasmid, pCT, conferring β-lactam resistance.<br><br>RESULTS: Here, we investigated six plasmid encoded factors (tra and pil loci; rci shufflon recombinase, a putative sigma factor, a putative parB partitioning gene and a pndACB toxin-antitoxin system) hypothesised to contribute to the 'evolutionary success' of plasmid pCT. Using a functional genomics approach, the role of these loci was investigated by systematically inactivating each region and examining the impact on plasmid persistence, conjugation and bacterial host biology. While the tra locus was found to be essential for all pCT conjugative transfer, the second conjugation (pil) locus was found to increase conjugation frequencies in liquid media to particular bacterial host recipients (determined in part by the rci shufflon recombinase). Inactivation of the pCT pndACB system and parB did not reduce the stability of this plasmid.<br><br>CONCLUSIONS: Our findings suggest the success of pCT may be due to a combination of factors including plasmid stability within a range of bacterial hosts, a lack of a fitness burden and efficient transfer rates to new bacterial hosts rather than the presence of a particular gene or phenotype transferred to the host. The methodology used in our study could be applied to other 'successful' globally distributed plasmids to discover the role of currently unknown plasmid backbone genes or to investigate other factors which allow these elements to persist and spread.}, }
@article {pmid24960293, year = {2014}, author = {Perin, LM and Miranda, RO and Todorov, SD and Franco, BD and Nero, LA}, title = {Virulence, antibiotic resistance and biogenic amines of bacteriocinogenic lactococci and enterococci isolated from goat milk.}, journal = {International journal of food microbiology}, volume = {185}, number = {}, pages = {121-126}, doi = {10.1016/j.ijfoodmicro.2014.06.001}, pmid = {24960293}, issn = {1879-3460}, mesh = {Animals ; Biogenic Amines/*analysis ; Drug Resistance, Microbial/*genetics ; *Enterococcus/chemistry/genetics/isolation &amp; purification/pathogenicity ; Gene Expression Profiling ; Goats ; *Lactococcus/chemistry/genetics/isolation &amp; purification/pathogenicity ; Milk/*microbiology ; Polymerase Chain Reaction ; Virulence Factors/*genetics ; }, abstract = {The present study aimed to investigate the virulence, antibiotic resistance and biogenic amine production in bacteriocinogenic lactococci and enterococci isolated from goat milk in order to evaluate their safety. Twenty-nine bacteriocinogenic lactic acid bacteria (LAB: 11 Lactococcus spp., and 18 Enterococcus spp.) isolated from raw goat milk were selected and subjected to PCR to identify gelE, cylA, hyl, asa1, esp, efaA, ace, vanA, vanB, hdc1, hdc2, tdc and odc genes. The expression of virulence factors (gelatinase, hemolysis, lipase, DNAse, tyramine, histamine, putrescine) in different incubation temperatures was assessed by phenotypic methods, as well as the resistance to vancomycin, gentamicin, chloramphenicol, ampicillin and rifampicin (using Etest®). The tested isolates presented distinct combinations of virulence related genes, but not necessarily the expression of such factors. The relevance of identifying virulence-related genes in bacteriocinogenic LAB was highlighted, demanding for care in their usage as starter cultures or biopreservatives due to the possibility of horizontal gene transfer to other bacteria in food systems.}, }
@article {pmid24958798, year = {2014}, author = {Du, P and Cao, B and Wang, J and Li, W and Jia, H and Zhang, W and Lu, J and Li, Z and Yu, H and Chen, C and Cheng, Y}, title = {Sequence variation in tcdA and tcdB of Clostridium difficile: ST37 with truncated tcdA is a potential epidemic strain in China.}, journal = {Journal of clinical microbiology}, volume = {52}, number = {9}, pages = {3264-3270}, pmid = {24958798}, issn = {1098-660X}, mesh = {Bacterial Proteins/*genetics ; Bacterial Toxins/*genetics ; China/epidemiology ; Clostridioides difficile/classification/*genetics/*isolation &amp; purification ; Clostridium Infections/epidemiology/*microbiology ; Cluster Analysis ; Cross Infection/epidemiology/microbiology ; DNA, Bacterial/chemistry/genetics ; Diarrhea/epidemiology/*microbiology ; Enterotoxins/*genetics ; Epidemics ; Genotype ; Humans ; Multilocus Sequence Typing ; Phylogeny ; *Polymorphism, Single Nucleotide ; Sequence Homology ; }, abstract = {Clostridium difficile is a well-known nosocomial infectious pathogen. Research on C. difficile infection has primarily focused on strains such as the hypervirulent PCR ribotype 027 (sequence type 1 [ST1]) emerging in Europe and North America. However, other new emerging ribotypes in some countries have attracted attention, such as PCR ribotype 17 (ST37) in Asia and Latin America. We collected 70 strains and sequenced their toxin genes, tcdA and tcdB. Multilocus sequence typing (MLST) was used to study their population structure. In addition, tcdA and/or tcdB sequences of 25 other isolates were obtained from GenBank. Single nucleotide polymorphisms (SNPs) were identified and analyzed. Phylogenetic analyses were performed to study toxin gene evolution. All tcdA and tcdB sequences were divided into 1 of 16 types (denoted A01 to -16 and B01 to -16, respectively). Hypervirulent strain RT027 is A13B12, and RT078 is A14B10, whereas the newly epidemic strain RT017 is A15B13. SNP analysis suggests the possibility of recombination in tcdB, perhaps through horizontal gene transfer. SNPs were also found in the sequences corresponding to the PCR primers widely used for toxin detection. Our study shows that ST037 shares a few genotypic features in its tcdA and tcdB genes with some known hypervirulent strains, indicating that they fall into a unique clade. Our findings can be used to map the relationships among C. difficile strains more finely than can be done with less sensitive methods, such as toxinotyping or even MLST, to reveal their inherent epidemiological characteristics.}, }
@article {pmid24958439, year = {2014}, author = {Jones, B}, title = {Plant genetics: joining forces - asexual genome merger creates new allopolyploid species.}, journal = {Nature reviews. Genetics}, volume = {15}, number = {8}, pages = {515}, pmid = {24958439}, issn = {1471-0064}, mesh = {*Gene Transfer, Horizontal ; *Genetic Speciation ; Genome, Plant/*genetics ; Nicotiana/*genetics ; }, }
@article {pmid24957089, year = {2014}, author = {Jolley, KA and Maiden, MC}, title = {Using multilocus sequence typing to study bacterial variation: prospects in the genomic era.}, journal = {Future microbiology}, volume = {9}, number = {5}, pages = {623-630}, doi = {10.2217/fmb.14.24}, pmid = {24957089}, issn = {1746-0921}, support = {087622//Wellcome Trust/United Kingdom ; }, mesh = {Bacillus anthracis/genetics ; Bacterial Typing Techniques/*methods ; Base Sequence ; Biodiversity ; Genetic Variation ; Genome, Bacterial/*genetics ; Microbial Sensitivity Tests ; Multilocus Sequence Typing/*methods ; Neisseria meningitidis/drug effects/genetics/isolation &amp; purification ; Pseudomonas aeruginosa/drug effects/genetics ; Sequence Analysis, DNA ; }, abstract = {Multilocus sequence typing (MLST) indexes the sequence variation present in a small number (usually seven) of housekeeping gene fragments located around the bacterial genome. Unique alleles at these loci are assigned arbitrary integer identifiers, which effectively summarizes the variation present in several thousand base pairs of genome sequence information as a series of numbers. Comparing bacterial isolates using allele-based methods efficiently corrects for the effects of lateral gene transfer present in many bacterial populations and is computationally efficient. This 'gene-by-gene' approach can be applied to larger collections of loci, such as the ribosomal protein genes used in ribosomal MLST (rMLST), up to and including the complete set of coding sequences present in a genome, whole-genome MLST (wgMLST), providing scalable, efficient and readily interpreted genome analysis.}, }
@article {pmid24956175, year = {2014}, author = {Robinson, KM and Dunning Hotopp, JC}, title = {Mobile elements and viral integrations prompt considerations for bacterial DNA integration as a novel carcinogen.}, journal = {Cancer letters}, volume = {352}, number = {2}, pages = {137-144}, pmid = {24956175}, issn = {1872-7980}, support = {DP2 OD007372/OD/NIH HHS/United States ; DP2-OD007372/OD/NIH HHS/United States ; }, mesh = {Animals ; Bacterial Infections/*genetics/microbiology ; *Cell Transformation, Viral ; DNA, Bacterial/*genetics ; Gene Expression Regulation, Neoplastic ; Genetic Predisposition to Disease ; Humans ; *Interspersed Repetitive Sequences ; *Mutagenesis, Insertional ; Neoplasms/*genetics/microbiology/pathology/virology ; Phenotype ; Risk Factors ; Tumor Virus Infections/*genetics/virology ; *Virus Integration ; }, abstract = {Insertional mutagenesis has been repeatedly demonstrated in cancer genomes and has a role in oncogenesis. Mobile genetic elements can induce cancer development by random insertion into cancer related genes or by inducing translocations. L1s are typically implicated in cancers of an epithelial cell origin, while Alu elements have been implicated in leukemia as well as epithelial cell cancers. Likewise, viral infections have a significant role in cancer development predominantly through integration into the human genome and mutating or deregulating cancer related genes. Human papilloma virus is the best-known example of viral integrations contributing to carcinogenesis. However, hepatitis B virus, Epstein-Barr virus, and Merkel cell polyomavirus also integrate into the human genome and disrupt cancer related genes. Thus far, the role of microbes in cancer has primarily been attributed to mutations induced through chronic inflammation or toxins, as is the case with Helicobacter pylori and enterotoxigenic Bacteroides fragilis. We hypothesize that like mobile elements and viral DNA, bacterial and parasitic DNA may also integrate into the human somatic genome and be oncogenic. Until recently it was believed that bacterial DNA could not integrate into the human genome, but new evidence demonstrates that bacterial insertional mutagenesis may occur in cancer cells. Although this work does not show causation between bacterial insertions and cancer, it prompts more research in this area. Promising new sequencing technologies may reduce the risk of artifactual chimeric sequences, thus diminishing some of the challenges of identifying novel insertions in the somatic human genome.}, }
@article {pmid24955890, year = {2014}, author = {Alawi, M and Schneider, B and Kallmeyer, J}, title = {A procedure for separate recovery of extra- and intracellular DNA from a single marine sediment sample.}, journal = {Journal of microbiological methods}, volume = {104}, number = {}, pages = {36-42}, doi = {10.1016/j.mimet.2014.06.009}, pmid = {24955890}, issn = {1872-8359}, mesh = {Analytic Sample Preparation Methods/*methods ; DNA/genetics/*isolation &amp; purification ; Geologic Sediments/*chemistry ; Oceans and Seas ; Polymerase Chain Reaction ; Soil/chemistry ; }, abstract = {Extracellular DNA (eDNA) is a ubiquitous biological compound in aquatic sediment and soil. Previous studies suggested that eDNA plays an important role in biogeochemical element cycling, horizontal gene transfer and stabilization of biofilm structures. Previous methods for eDNA extraction were either not suitable for oligotrophic sediments or only allowed quantification but no genetic analyses. Our procedure is based on cell detachment and eDNA liberation from sediment particles by sequential washing with an alkaline sodium phosphate buffer followed by a separation of cells and eDNA. The separated eDNA is then bound onto silica particles and purified, whereas the intracellular DNA from the separated cells is extracted using a commercial kit. The method provides extra- and intracellular DNA of high purity that is suitable for downstream applications like PCR. Extracellular DNA was extracted from organic-rich shallow sediment of the Baltic Sea, glacially influenced sediment of the Barents Sea and from the oligotrophic South Pacific Gyre. The eDNA concentration in these samples varied from 23 to 626ngg(-1) wet weight sediment. A number of experiments were performed to verify each processing step. Although extraction efficiency is higher than other published methods, it is not fully quantitative.}, }
@article {pmid24951809, year = {2014}, author = {Fernández, J and Montero, I and Fleites, A and Rodicio, MR}, title = {Cluster of Escherichia coli isolates producing a plasmid-mediated OXA-48 β-lactamase in a Spanish hospital in 2012.}, journal = {Journal of clinical microbiology}, volume = {52}, number = {9}, pages = {3414-3417}, pmid = {24951809}, issn = {1098-660X}, mesh = {Aged ; Anti-Bacterial Agents/*pharmacology ; Conjugation, Genetic ; Ertapenem ; Escherichia coli/classification/*enzymology/genetics/isolation &amp; purification ; Escherichia coli Infections/*microbiology ; Escherichia coli Proteins ; Female ; Gene Transfer, Horizontal ; Genotype ; Hospitals ; Humans ; Imipenem/pharmacology ; Male ; Middle Aged ; Plasmids/analysis ; Spain/epidemiology ; beta-Lactamases/*genetics ; beta-Lactams/pharmacology ; }, abstract = {Three unrelated sequence type 131 (ST131), ST58, and ST83 Escherichia coli isolates with low-level resistance to imipenem and resistance to ertapenem were recovered in a Spanish hospital from July to October 2012. They were positive for blaOXA-48 carried by an IncL/M conjugative plasmid, which may have been acquired from Klebsiella pneumoniae.}, }
@article {pmid24951673, year = {2014}, author = {Bello-Ortí, B and Aragon, V and Pina-Pedrero, S and Bensaid, A}, title = {Genome comparison of three serovar 5 pathogenic strains of Haemophilus parasuis: insights into an evolving swine pathogen.}, journal = {Microbiology (Reading, England)}, volume = {160}, number = {Pt 9}, pages = {1974-1984}, doi = {10.1099/mic.0.079483-0}, pmid = {24951673}, issn = {1465-2080}, mesh = {Animals ; DNA, Bacterial/chemistry/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; *Genome, Bacterial ; Haemophilus Infections/microbiology/veterinary ; Haemophilus parasuis/classification/*genetics/isolation &amp; purification ; Molecular Sequence Data ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; *Serogroup ; Swine ; Swine Diseases/microbiology ; }, abstract = {Haemophilus parasuis is the causative agent of Glässer's disease, a systemic disorder characterized by polyarthritis, polyserositis and meningitis in pigs. Although it is well known that H. parasuis serovar 5 is the most prevalent serovar associated with the disease, the genetic differences among strains are only now being discovered. Genomes from two serovar 5 strains, SH0165 and 29755, are already available. Here, we present the draft genome of a third H. parasuis serovar 5 strain, the formal serovar 5 reference strain Nagasaki. An in silico genome subtractive analysis with full-length predicted genes of the three H. parasuis serovar 5 strains detected 95, 127 and 95 strain-specific genes (SSGs) for Nagasaki, SH0165 and 29755, respectively. We found that the genomic diversity within these three strains was high, in part because of a high number of mobile elements. Furthermore, a detailed analysis of large sequence polymorphisms (LSPs), encompassing regions ranging from 2 to 16 kb, revealed LSPs in virulence-related elements, such as a Toll-IL receptor, the AcrA multidrug efflux protein, an ATP-binding cassette (ABC) transporter, lipopolysaccharide-synthetizing enzymes and a tripartite ATP-independent periplasmic (TRAP) transporter. The whole-genome codon adaptation index (CAI) was also calculated and revealed values similar to other well-known bacterial pathogens. In addition, whole-genome SNP analysis indicated that nucleotide changes tended to be increased in membrane-related genes. This analysis provides further evidence that the genome of H. parasuis has been subjected to multiple lateral gene transfers (LGTs) and to fine-tuning of virulence factors, and has the potential for accelerated genome evolution.}, }
@article {pmid24950802, year = {2014}, author = {Jechalke, S and Heuer, H and Siemens, J and Amelung, W and Smalla, K}, title = {Fate and effects of veterinary antibiotics in soil.}, journal = {Trends in microbiology}, volume = {22}, number = {9}, pages = {536-545}, doi = {10.1016/j.tim.2014.05.005}, pmid = {24950802}, issn = {1878-4380}, mesh = {Agriculture/methods ; Animals ; Anti-Bacterial Agents/*analysis/pharmacology/therapeutic use ; Bacteria/*drug effects ; *Drug Resistance, Bacterial ; Environmental Monitoring ; Humans ; Manure/microbiology ; Rhizosphere ; *Soil Microbiology ; Soil Pollutants/*analysis ; Veterinary Medicine/trends ; }, abstract = {Large amounts of veterinary antibiotics are applied worldwide to farm animals and reach agricultural fields by manure fertilization, where they might lead to an increased abundance and transferability of antibiotic-resistance determinants. In this review we discuss recent advances, limitations, and research needs in determining the fate of veterinary antibiotics and resistant bacteria applied with manure to soil, and their effects on the structure and function of soil microbial communities in bulk soils and the rhizosphere. The increased abundance and mobilization of antibiotic-resistance genes (ARGs) might contribute to the emergence of multi-resistant human pathogens that increasingly threaten the successful antibiotic treatment of bacterial infections.}, }
@article {pmid24945944, year = {2014}, author = {Pradervand, N and Sulser, S and Delavat, F and Miyazaki, R and Lamas, I and van der Meer, JR}, title = {An operon of three transcriptional regulators controls horizontal gene transfer of the integrative and conjugative element ICEclc in Pseudomonas knackmussii B13.}, journal = {PLoS genetics}, volume = {10}, number = {6}, pages = {e1004441}, pmid = {24945944}, issn = {1553-7404}, mesh = {Bacterial Proteins/genetics ; Conjugation, Genetic ; DNA Transposable Elements/*genetics ; Gene Expression Regulation, Bacterial ; Gene Knockout Techniques ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Promoter Regions, Genetic ; Pseudomonas/*genetics ; Regulatory Elements, Transcriptional/*genetics ; Repressor Proteins/genetics ; Trans-Activators/genetics ; Transcription, Genetic/genetics ; }, abstract = {The integrative and conjugative element ICEclc is a mobile genetic element in Pseudomonas knackmussii B13, and an experimental model for a widely distributed group of elements in Proteobacteria. ICEclc is transferred from specialized transfer competent cells, which arise at a frequency of 3-5% in a population at stationary phase. Very little is known about the different factors that control the transfer frequency of this ICE family. Here we report the discovery of a three-gene operon encoded by ICEclc, which exerts global control on transfer initiation. The operon consists of three consecutive regulatory genes, encoding a TetR-type repressor MfsR, a MarR-type regulator and a LysR-type activator TciR. We show that MfsR autoregulates expression of the operon, whereas TciR is a global activator of ICEclc gene expression, but no clear role was yet found for MarR. Deletion of mfsR increases expression of tciR and marR, causing the proportion of transfer competent cells to reach almost 100% and transfer frequencies to approach 1 per donor. mfsR deletion also caused a two orders of magnitude loss in population viability, individual cell growth arrest and loss of ICEclc. This indicates that autoregulation is an important feature maintaining ICE transfer but avoiding fitness loss. Bioinformatic analysis showed that the mfsR-marR-tciR operon is unique for ICEclc and a few highly related ICE, whereas tciR orthologues occur more widely in a large variety of suspected ICE among Proteobacteria.}, }
@article {pmid24942651, year = {2014}, author = {Repizo, GD and Espariz, M and Blancato, VS and Suárez, CA and Esteban, L and Magni, C}, title = {Genomic comparative analysis of the environmental Enterococcus mundtii against enterococcal representative species.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {489}, pmid = {24942651}, issn = {1471-2164}, mesh = {Antibiosis/*genetics ; Bacteriocins/genetics ; Comparative Genomic Hybridization ; Drug Resistance, Bacterial/genetics ; Enterococcus/classification/*genetics/pathogenicity ; Environmental Microbiology ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomic Islands ; *Genomics ; Humans ; Phylogeny ; Pigments, Biological/genetics ; Stress, Physiological/genetics ; Virulence/genetics ; Virulence Factors/genetics ; }, abstract = {BACKGROUND: Enterococcus mundtii is a yellow-pigmented microorganism rarely found in human infections. The draft genome sequence of E. mundtii was recently announced. Its genome encodes at least 2,589 genes and 57 RNAs, and 4 putative genomic islands have been detected. The objective of this study was to compare the genetic content of E. mundtii with respect to other enterococcal species and, more specifically, to identify genes coding for putative virulence traits present in enterococcal opportunistic pathogens.<br><br>RESULTS: An in-depth mining of the annotated genome was performed in order to uncover the unique properties of this microorganism, which allowed us to detect a gene encoding the antimicrobial peptide mundticin among other relevant features. Moreover, in this study a comparative genomic analysis against commensal and pathogenic enterococcal species, for which genomic sequences have been released, was conducted for the first time. Furthermore, our study reveals significant similarities in gene content between this environmental isolate and the selected enterococci strains (sharing an "enterococcal gene core" of 805 CDS), which contributes to understand the persistence of this genus in different niches and also improves our knowledge about the genetics of this diverse group of microorganisms that includes environmental, commensal and opportunistic pathogens.<br><br>CONCLUSION: Although E. mundtii CRL1656 is phylogenetically closer to E. faecium, frequently responsible of nosocomial infections, this strain does not encode the most relevant relevant virulence factors found in the enterococcal clinical isolates and bioinformatic predictions indicate that it possesses the lowest number of putative pathogenic genes among the most representative enterococcal species. Accordingly, infection assays using the Galleria mellonella model confirmed its low virulence.}, }
@article {pmid24939888, year = {2014}, author = {Coyne, MJ and Zitomersky, NL and McGuire, AM and Earl, AM and Comstock, LE}, title = {Evidence of extensive DNA transfer between bacteroidales species within the human gut.}, journal = {mBio}, volume = {5}, number = {3}, pages = {e01305-14}, pmid = {24939888}, issn = {2150-7511}, support = {HHSN272200900018C/AI/NIAID NIH HHS/United States ; U54-HG004969/HG/NHGRI NIH HHS/United States ; AI093771/AI/NIAID NIH HHS/United States ; R01 AI081843/AI/NIAID NIH HHS/United States ; AI081843/AI/NIAID NIH HHS/United States ; R01 AI093771/AI/NIAID NIH HHS/United States ; U54 HG004969/HG/NHGRI NIH HHS/United States ; U19 AI110818/AI/NIAID NIH HHS/United States ; }, mesh = {Adult ; Bacterial Proteins/genetics/metabolism ; Bacteroidetes/classification/*genetics/isolation &amp; purification/metabolism ; Conjugation, Genetic ; DNA, Bacterial/*genetics/metabolism ; Feces/microbiology ; Female ; *Gene Transfer, Horizontal ; Humans ; Intestines/*microbiology ; Male ; Molecular Sequence Data ; Young Adult ; }, abstract = {UNLABELLED: The genome sequences of intestinal Bacteroidales strains reveal evidence of extensive horizontal gene transfer. In vitro studies of Bacteroides and other bacteria have addressed mechanisms of conjugative transfer and some phenotypic outcomes of these DNA acquisitions in the recipient, such as the acquisition of antibiotic resistance. However, few studies have addressed the horizontal transfer of genetic elements between bacterial species coresident in natural microbial communities, especially microbial ecosystems of humans. Here, we examine the genomes of Bacteroidales species from two human adults to identify genetic elements that were likely transferred among these Bacteroidales while they were coresident in the intestine. Using seven coresident Bacteroidales species from one individual and eight from another, we identified five large chromosomal regions, each present in a minimum of three of the coresident strains at near 100% DNA identity. These five regions are not found in any other sequenced Bacteroidetes genome at this level of identity and are likely all integrative conjugative elements (ICEs). Such highly similar and unique regions occur in only 0.4% of phylogenetically representative mock communities, providing strong evidence that these five regions were transferred between coresident strains in these subjects. In addition to the requisite proteins necessary for transfer, these elements encode proteins predicted to increase fitness, including orphan DNA methylases that may alter gene expression, fimbriae synthesis proteins that may facilitate attachment and the utilization of new substrates, putative secreted antimicrobial molecules, and a predicted type VI secretion system (T6SS), which may confer a competitive ecological advantage to these strains in their complex microbial ecosystem.<br><br>IMPORTANCE: By analyzing Bacteroidales strains coresident in the gut microbiota of two human adults, we provide strong evidence for extensive interspecies and interfamily transfer of integrative conjugative elements within the intestinal microbiota of individual humans. In the recipient strain, we show that the conjugative elements themselves can be modified by the transposition of insertion sequences and retroelements from the recipient's genome, with subsequent transfer of these modified elements to other members of the microbiota. These data suggest that the genomes of our gut bacteria are substantially modified by other, coresident members of the ecosystem, resulting in highly personalized Bacteroidales strains likely unique to that individual. The genetic content of these ICEs suggests that their transfer from successful adapted members of an ecosystem confers beneficial properties to the recipient, increasing its fitness and allowing it to better compete within its particular personalized gut microbial ecosystem.}, }
@article {pmid24939392, year = {2014}, author = {Krupovic, M and Koonin, EV}, title = {Evolution of eukaryotic single-stranded DNA viruses of the Bidnaviridae family from genes of four other groups of widely different viruses.}, journal = {Scientific reports}, volume = {4}, number = {}, pages = {5347}, pmid = {24939392}, issn = {2045-2322}, support = {//Intramural NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Bombyx/virology ; Capsid Proteins/classification/genetics ; DNA Viruses/classification/*genetics ; DNA, Single-Stranded/*genetics ; DNA, Viral/*genetics ; Eukaryotic Cells/*virology ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Viral/*genetics ; Genome, Viral/genetics ; Molecular Sequence Data ; Parvovirus/classification/genetics ; Phylogeny ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Viral Nonstructural Proteins/classification/genetics ; }, abstract = {Single-stranded (ss)DNA viruses are extremely widespread, infect diverse hosts from all three domains of life and include important pathogens. Most ssDNA viruses possess small genomes that replicate by the rolling-circle-like mechanism initiated by a distinct virus-encoded endonuclease. However, viruses of the family Bidnaviridae, instead of the endonuclease, encode a protein-primed type B DNA polymerase (PolB) and hence break this pattern. We investigated the provenance of all bidnavirus genes and uncover an unexpected turbulent evolutionary history of these unique viruses. Our analysis strongly suggests that bidnaviruses evolved from a parvovirus ancestor from which they inherit a jelly-roll capsid protein and a superfamily 3 helicase. The radiation of bidnaviruses from parvoviruses was probably triggered by integration of the ancestral parvovirus genome into a large virus-derived DNA transposon of the Polinton (polintovirus) family resulting in the acquisition of the polintovirus PolB gene along with terminal inverted repeats. Bidnavirus genes for a receptor-binding protein and a potential novel antiviral defense modulator are derived from dsRNA viruses (Reoviridae) and dsDNA viruses (Baculoviridae), respectively. The unusual evolutionary history of bidnaviruses emphasizes the key role of horizontal gene transfer, sometimes between viruses with completely different genomes but occupying the same niche, in the emergence of new viral types.}, }
@article {pmid24939150, year = {2014}, author = {Kim, Y and Liesack, W}, title = {DAFGA: diversity analysis of functional gene amplicons.}, journal = {Bioinformatics (Oxford, England)}, volume = {30}, number = {19}, pages = {2820-2821}, doi = {10.1093/bioinformatics/btu394}, pmid = {24939150}, issn = {1367-4811}, mesh = {*Cluster Analysis ; Computational Biology/*methods ; Evolution, Molecular ; *Genes, rRNA ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Software ; }, abstract = {SUMMARY: Diversity analysis of functional marker genes provides physiological insights into microbial guilds that perform an ecologically relevant process. However, it is challenging to group functional gene sequences to valid taxonomic units, primarily because of differences in the evolutionary rates of individual genes and possible horizontal gene transfer events. We developed a python script package named DAFGA, which estimates the evolutionary rate of a particular functional gene in a standardized manner by relating its sequence divergence to that of the 16S rRNA gene. As a result, DAFGA provides gene-specific parameter sets for operational taxonomic unit clustering and taxonomic assignment at desired rank, and it can be implemented into the diversity measurements offered by QIIME.<br><br>DAFGA is freely available with a manual and test data from https://github.com/outbig/DAFGA.}, }
@article {pmid24938123, year = {2014}, author = {Rigden, DJ and Eberhardt, RY and Gilbert, HJ and Xu, Q and Chang, Y and Godzik, A}, title = {Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of glycoside hydrolase.}, journal = {BMC bioinformatics}, volume = {15}, number = {}, pages = {196}, pmid = {24938123}, issn = {1471-2105}, support = {P41GM103393/GM/NIGMS NIH HHS/United States ; U54 GM094586-03/GM/NIGMS NIH HHS/United States ; WT077044/Z/05/Z//Wellcome Trust/United Kingdom ; //Howard Hughes Medical Institute/United States ; }, mesh = {Bacteroides/chemistry/enzymology ; Biocatalysis ; Glycoside Hydrolases/*chemistry/genetics/metabolism ; Models, Molecular ; Phylogeny ; Protein Structure, Tertiary ; Structural Homology, Protein ; }, abstract = {BACKGROUND: Gut microbiome metagenomics has revealed many protein families and domains found largely or exclusively in that environment. Proteins containing the GxGYxYP domain are over-represented in the gut microbiota, and are found in Polysaccharide Utilization Loci in the gut symbiont Bacteroides thetaiotaomicron, suggesting their involvement in polysaccharide metabolism, but little else is known of the function of this domain.<br><br>RESULTS: Genomic context and domain architecture analyses support a role for the GxGYxYP domain in carbohydrate metabolism. Sparse occurrences in eukaryotes are the result of lateral gene transfer. The structure of the GxGYxYP domain-containing protein encoded by the BT2193 locus reveals two structural domains, the first composed of three divergent repeats with no recognisable homology to previously solved structures, the second a more familiar seven-stranded &#x3b2;/&#x3b1; barrel. Structure-based analyses including conservation mapping localise a presumed functional site to a cleft between the two domains of BT2193. Matching to a catalytic site template from a GH9 cellulase and other analyses point to a putative catalytic triad composed of Glu272, Asp331 and Asp333.<br><br>CONCLUSIONS: We suggest that GxGYxYP-containing proteins constitute a novel glycoside hydrolase family of as yet unknown specificity.}, }
@article {pmid24937281, year = {2014}, author = {Cooper, ED}, title = {Horizontal gene transfer: accidental inheritance drives adaptation.}, journal = {Current biology : CB}, volume = {24}, number = {12}, pages = {R562-R564}, doi = {10.1016/j.cub.2014.04.042}, pmid = {24937281}, issn = {1879-0445}, mesh = {Bryophyta/*genetics ; Ferns/*genetics ; *Gene Transfer, Horizontal ; Photoreceptors, Plant/*genetics ; }, abstract = {Few facts in biology are more certain than offspring inheriting genetic material from their parents, but not all genes are acquired this way. A new report documents the horizontal transfer of a potentially adaptive gene between distantly related plants.}, }
@article {pmid24929742, year = {2014}, author = {Rossi, F and Rizzotti, L and Felis, GE and Torriani, S}, title = {Horizontal gene transfer among microorganisms in food: current knowledge and future perspectives.}, journal = {Food microbiology}, volume = {42}, number = {}, pages = {232-243}, doi = {10.1016/j.fm.2014.04.004}, pmid = {24929742}, issn = {1095-9998}, mesh = {Bacteria/*genetics/metabolism ; *Food Microbiology ; *Gene Transfer, Horizontal ; }, abstract = {The possibility of horizontal gene transfer (HGT) among microorganisms in food matrices has been specifically targeted in a few investigations, though most current knowledge has been obtained indirectly or derived from genome sequence analyses. In this review, we have assembled reported examples of the HGT events that probably occurred in food matrices since the bacterial partners involved are commonly found in association in a food matrix or are specifically adapted to it. Exchanged genes include those encoding for substrate utilization, bacteriocin, exopolysaccharide and biogenic amine (BA) production, immunity to bacteriophages and antibiotic resistance (AR). While the acquisition of new traits involved in substrate utilization led to the natural genetic improvement of the microbial cultures for food production, the acquisition of hazardous traits, e.g., AR, virulence or BA production genes, can give rise to health concerns in otherwise innocuous species. Available evidence suggests that it would be opportune to determine what conditions favour HGT among bacteria in food ecosystems in order to naturally obtain improved starter or adjunct cultures, and also to prevent the propagation of hazardous traits.}, }
@article {pmid24929711, year = {2014}, author = {Yang, B and Wang, Q and Cui, S and Wang, Y and Shi, C and Xia, X and Xi, M and Wang, X and Shi, X and Wang, D and Zhang, Z and Meng, J}, title = {Characterization of extended-spectrum beta-lactamases-producing Salmonella strains isolated from retail foods in Shaanxi and Henan Province, China.}, journal = {Food microbiology}, volume = {42}, number = {}, pages = {14-18}, doi = {10.1016/j.fm.2014.02.003}, pmid = {24929711}, issn = {1095-9998}, mesh = {Animals ; Bacterial Proteins/genetics/*metabolism ; Cattle ; Chickens ; China ; Conjugation, Genetic ; Electrophoresis, Gel, Pulsed-Field ; Fishes ; Food Contamination/analysis ; Gene Transfer, Horizontal ; Meat/*microbiology ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Phylogeny ; Plasmids/genetics/metabolism ; Salmonella/classification/*enzymology/genetics/*isolation &amp; purification ; Swine ; beta-Lactamases/genetics/*metabolism ; }, abstract = {Extended-spectrum beta-lactamases (ESBL)-producing Salmonella enterica have been reported worldwide. However, research on foodborne ESBL-producing Salmonella has been rarely conducted. One hundred and thirty eight ceftriaxone or/and cefoperazone-resistant Salmonella strains recovered from retail foods in Shaanxi and Henan Province, China, were screened for ESBL. The ESBL-producing strains were further characterized for antimicrobial resistance, pulse field gel electrophoresis (PFGE) profiles, and the presence of blaTEM, blaSHV, blaOXA, blaCTX-M, and blaPSE. The transferability of ESBL encoding genes to a susceptible Escherichia coli strain was also investigated. Thirty (21.7%) isolates were identified as ESBL positive and belonged to S. enterica serovars Indiana, Shubra, Typhimurium, and Enteritidis. S. Indiana and S. Shubra isolates were firstly identified in ESBL-producing strains. Great genetic diversity was seen among these ESBL-producing strains. Nucleotide sequence analysis revealed that blaTEM-1B was the only ESBL-encoding gene among the genes tested and was detected in 26 of 30 strains and was carried in the conjugative plasmids. The blaTEM-1B gene was transferable through conjugation at rates ranging from 4.71 × 10(-7) to 7.55 × 10(-6) transconjugant per recipient cell. This study provides the evidence of foodborne ESBL-producing Salmonella, and the transferability of plasmid harboring ESBL-encoding genes could possibly contribute to the dissemination of ESBL.}, }
@article {pmid24927540, year = {2014}, author = {Wang, H and Fewer, DP and Holm, L and Rouhiainen, L and Sivonen, K}, title = {Atlas of nonribosomal peptide and polyketide biosynthetic pathways reveals common occurrence of nonmodular enzymes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {25}, pages = {9259-9264}, pmid = {24927540}, issn = {1091-6490}, mesh = {Bacteria/*genetics ; *Evolution, Molecular ; *Genome, Bacterial ; Multigene Family/physiology ; Polyketide Synthases/*genetics ; *Polyketides ; Protein Structure, Tertiary ; Sequence Analysis, Protein/methods ; Siderophores/*genetics ; }, abstract = {Nonribosomal peptides and polyketides are a diverse group of natural products with complex chemical structures and enormous pharmaceutical potential. They are synthesized on modular nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) enzyme complexes by a conserved thiotemplate mechanism. Here, we report the widespread occurrence of NRPS and PKS genetic machinery across the three domains of life with the discovery of 3,339 gene clusters from 991 organisms, by examining a total of 2,699 genomes. These gene clusters display extraordinarily diverse organizations, and a total of 1,147 hybrid NRPS/PKS clusters were found. Surprisingly, 10% of bacterial gene clusters lacked modular organization, and instead catalytic domains were mostly encoded as separate proteins. The finding of common occurrence of nonmodular NRPS differs substantially from the current classification. Sequence analysis indicates that the evolution of NRPS machineries was driven by a combination of common descent and horizontal gene transfer. We identified related siderophore NRPS gene clusters that encoded modular and nonmodular NRPS enzymes organized in a gradient. A higher frequency of the NRPS and PKS gene clusters was detected from bacteria compared with archaea or eukarya. They commonly occurred in the phyla of Proteobacteria, Actinobacteria, Firmicutes, and Cyanobacteria in bacteria and the phylum of Ascomycota in fungi. The majority of these NRPS and PKS gene clusters have unknown end products highlighting the power of genome mining in identifying novel genetic machinery for the biosynthesis of secondary metabolites.}, }
@article {pmid24923325, year = {2014}, author = {Haq, IU and Graupner, K and Nazir, R and van Elsas, JD}, title = {The genome of the fungal-interactive soil bacterium Burkholderia terrae BS001-a plethora of outstanding interactive capabilities unveiled.}, journal = {Genome biology and evolution}, volume = {6}, number = {7}, pages = {1652-1668}, pmid = {24923325}, issn = {1759-6653}, mesh = {Burkholderia/*genetics ; Computational Biology ; *Evolution, Molecular ; Fungi/*genetics ; Genome, Fungal/*genetics ; Phylogeny ; Sequence Alignment ; *Soil Microbiology ; }, abstract = {Burkholderia terrae strain BS001, obtained as an inhabitant of the mycosphere of Laccaria proxima (a close relative of Lyophyllum sp. strain Karsten), actively interacts with Lyophyllum sp. strain Karsten. We here summarize the remarkable ecological behavior of B. terrae BS001 in the mycosphere and add key data to this. Moreover, we extensively analyze the approximately 11.5-Mb five-replicon genome of B. terrae BS001 and highlight its remarkable features. Seventy-nine regions of genomic plasticity (RGP), that is, 16.48% of the total genome size, were found. One 70.42-kb RGP, RGP76, revealed a typical conjugal element structure, including a full type 4 secretion system. Comparative analyses across 24 related Burkholderia genomes revealed that 95.66% of the total BS001 genome belongs to the variable part, whereas the remaining 4.34% constitutes the core genome. Genes for biofilm formation and several secretion systems, under which a type 3 secretion system (T3SS), were found, which is consistent with the hypothesis that T3SSs play a role in the interaction with Lyophyllum sp. strain Karsten. The high number of predicted metabolic pathways and membrane transporters suggested that strain BS001 can take up and utilize a range of sugars, amino acids and organic acids. In particular, a unique glycerol uptake system was found. The BS001 genome further contains genetic systems for the degradation of complex organic compounds. Moreover, gene clusters encoding nonribosomal peptide synthetases (NRPS) and hybrid polyketide synthases/NRPS were found, highlighting the potential role of secondary metabolites in the ecology of strain BS001. The patchwork of genetic features observed in the genome is consistent with the notion that 1) horizontal gene transfer is a main driver of B. terrae BS001 adaptation and 2) the organism is very flexible in its ecological behavior in soil.}, }
@article {pmid24923324, year = {2014}, author = {Deschamps, P and Zivanovic, Y and Moreira, D and Rodriguez-Valera, F and López-García, P}, title = {Pangenome evidence for extensive interdomain horizontal transfer affecting lineage core and shell genes in uncultured planktonic thaumarchaeota and euryarchaeota.}, journal = {Genome biology and evolution}, volume = {6}, number = {7}, pages = {1549-1563}, pmid = {24923324}, issn = {1759-6653}, mesh = {Archaea/*genetics ; Euryarchaeota/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; *Genome ; Genomic Library ; *Phylogeny ; }, abstract = {Horizontal gene transfer (HGT) is an important force in evolution, which may lead, among other things, to the adaptation to new environments by the import of new metabolic functions. Recent studies based on phylogenetic analyses of a few genome fragments containing archaeal 16S rRNA genes and fosmid-end sequences from deep-sea metagenomic libraries have suggested that marine planktonic archaea could be affected by high HGT frequency. Likewise, a composite genome of an uncultured marine euryarchaeote showed high levels of gene sequence similarity to bacterial genes. In this work, we ask whether HGT is frequent and widespread in genomes of these marine archaea, and whether HGT is an ancient and/or recurrent phenomenon. To answer these questions, we sequenced 997 fosmid archaeal clones from metagenomic libraries of deep-Mediterranean waters (1,000 and 3,000 m depth) and built comprehensive pangenomes for planktonic Thaumarchaeota (Group I archaea) and Euryarchaeota belonging to the uncultured Groups II and III Euryarchaeota (GII/III-Euryarchaeota). Comparison with available reference genomes of Thaumarchaeota and a composite marine surface euryarchaeote genome allowed us to define sets of core, lineage-specific core, and shell gene ortholog clusters for the two archaeal lineages. Molecular phylogenetic analyses of all gene clusters showed that 23.9% of marine Thaumarchaeota genes and 29.7% of GII/III-Euryarchaeota genes had been horizontally acquired from bacteria. HGT is not only extensive and directional but also ongoing, with high HGT levels in lineage-specific core (ancient transfers) and shell (recent transfers) genes. Many of the acquired genes are related to metabolism and membrane biogenesis, suggesting an adaptive value for life in cold, oligotrophic oceans. We hypothesize that the acquisition of an important amount of foreign genes by the ancestors of these archaeal groups significantly contributed to their divergence and ecological success.}, }
@article {pmid24923323, year = {2014}, author = {Nowell, RW and Green, S and Laue, BE and Sharp, PM}, title = {The extent of genome flux and its role in the differentiation of bacterial lineages.}, journal = {Genome biology and evolution}, volume = {6}, number = {6}, pages = {1514-1529}, pmid = {24923323}, issn = {1759-6653}, support = {095831//Wellcome Trust/United Kingdom ; }, mesh = {Bacterial Proteins/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Phylogeny ; Pseudomonas syringae/*genetics ; }, abstract = {Horizontal gene transfer (HGT) and gene loss are key processes in bacterial evolution. However, the role of gene gain and loss in the emergence and maintenance of ecologically differentiated bacterial populations remains an open question. Here, we use whole-genome sequence data to quantify gene gain and loss for 27 lineages of the plant-associated bacterium Pseudomonas syringae. We apply an extensive error-control procedure that accounts for errors in draft genome data and greatly improves the accuracy of patterns of gene occurrence among these genomes. We demonstrate a history of extensive genome fluctuation for this species and show that individual lineages could have acquired thousands of genes in the same period in which a 1% amino acid divergence accrues in the core genome. Elucidating the dynamics of genome fluctuation reveals the rapid turnover of gained genes, such that the majority of recently gained genes are quickly lost. Despite high observed rates of fluctuation, a phylogeny inferred from patterns of gene occurrence is similar to a phylogeny based on amino acid replacements within the core genome. Furthermore, the core genome phylogeny suggests that P. syringae should be considered a number of distinct species, with levels of divergence at least equivalent to those between recognized bacterial species. Gained genes are transferred from a variety of sources, reflecting the depth and diversity of the potential gene pool available via HGT. Overall, our results provide further insights into the evolutionary dynamics of genome fluctuation and implicate HGT as a major factor contributing to the diversification of P. syringae lineages.}, }
@article {pmid24917581, year = {2014}, author = {Hamidian, M and Hall, RM}, title = {Resistance to third-generation cephalosporins in Acinetobacter baumannii due to horizontal transfer of a chromosomal segment containing ISAba1-ampC.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {69}, number = {10}, pages = {2865-2866}, doi = {10.1093/jac/dku202}, pmid = {24917581}, issn = {1460-2091}, mesh = {Acinetobacter Infections/drug therapy/*microbiology ; Acinetobacter baumannii/*drug effects/*genetics ; Bacterial Proteins/*genetics ; Cephalosporin Resistance/*genetics ; *Chromosomes, Bacterial ; *Gene Transfer, Horizontal ; Humans ; beta-Lactamases/*genetics ; }, }
@article {pmid24916868, year = {2014}, author = {Yu, T and Jiang, X and Zhou, Q and Wu, J and Wu, Z}, title = {Antimicrobial resistance, class 1 integrons, and horizontal transfer in Salmonella isolated from retail food in Henan, China.}, journal = {Journal of infection in developing countries}, volume = {8}, number = {6}, pages = {705-711}, doi = {10.3855/jidc.4190}, pmid = {24916868}, issn = {1972-2680}, mesh = {Animals ; China ; Developing Countries ; Drug Resistance, Bacterial/genetics ; *Food Microbiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Integrons ; Meat/microbiology ; Salmonella/drug effects/genetics/*isolation &amp; purification ; Salmonella Food Poisoning/*microbiology ; Serogroup ; }, abstract = {INTRODUCTION: Salmonellosis remains one of the most frequently occurring foodborne diseases worldwide, especially in developing countries. The increasing prevalence of multidrug resistance among Salmonella isolates from food has been an emerging problem in China.<br><br>METHODOLOGY: In this study, a total of 638 food samples including raw meat, seafood, vegetables, and cooked meat were collected in Henan province of China between July 2007 and August 2008 to determine the prevalence of Salmonella. These isolates were subjected to serotyping, antimicrobial susceptibility, presence of class 1 integrons, and horizontal transfer of integrons.<br><br>RESULTS: The overall percentage of Salmonella prevalence was 9.7% (n = 62). Among these isolates, S. Anatum and S. Senftenberg were most common, and high rates of antimicrobial resistance were observed to sulfamethoxazole (90.3%), trimethoprim/sulfamethoxazole (87.1%), streptomycin (29.0%), and ciprofloxacin (25.8%). Class 1 integrons were detected in 16.1% of these isolates, and contained gene cassettes dfrA12-aadA2, dfrA1-aadA1, and dfrA1. Three Salmonella isolates could transfer their integrons and resistance genes to Escherichia coli by conjugation.<br><br>CONCLUSIONS: Our findings indicate that the mobile DNA elements could play an important role in the dissemination of resistance determinants among those Salmonella isolates.}, }
@article {pmid24911101, year = {2014}, author = {Zallot, R and Brochier-Armanet, C and Gaston, KW and Forouhar, F and Limbach, PA and Hunt, JF and de Crécy-Lagard, V}, title = {Plant, animal, and fungal micronutrient queuosine is salvaged by members of the DUF2419 protein family.}, journal = {ACS chemical biology}, volume = {9}, number = {8}, pages = {1812-1825}, pmid = {24911101}, issn = {1554-8937}, support = {U54 GM075026/GM/NIGMS NIH HHS/United States ; U54 GM094597/GM/NIGMS NIH HHS/United States ; 2U54GM75026/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Fungi/*metabolism ; Models, Molecular ; Nucleoside Q/chemistry/*metabolism ; Phylogeny ; Plants/*metabolism ; Proteins/*metabolism ; }, abstract = {Queuosine (Q) is a modification found at the wobble position of tRNAs with GUN anticodons. Although Q is present in most eukaryotes and bacteria, only bacteria can synthesize Q de novo. Eukaryotes acquire queuine (q), the free base of Q, from diet and/or microflora, making q an important but under-recognized micronutrient for plants, animals, and fungi. Eukaryotic type tRNA-guanine transglycosylases (eTGTs) are composed of a catalytic subunit (QTRT1) and a homologous accessory subunit (QTRTD1) forming a complex that catalyzes q insertion into target tRNAs. Phylogenetic analysis of eTGT subunits revealed a patchy distribution pattern in which gene losses occurred independently in different clades. Searches for genes co-distributing with eTGT family members identified DUF2419 as a potential Q salvage protein family. This prediction was experimentally validated in Schizosaccharomyces pombe by confirming that Q was present by analyzing tRNA(Asp) with anticodon GUC purified from wild-type cells and by showing that Q was absent from strains carrying deletions in the QTRT1 or DUF2419 encoding genes. DUF2419 proteins occur in most Eukarya with a few possible cases of horizontal gene transfer to bacteria. The universality of the DUF2419 function was confirmed by complementing the S. pombe mutant with the Zea mays (maize), human, and Sphaerobacter thermophilus homologues. The enzymatic function of this family is yet to be determined, but structural similarity with DNA glycosidases suggests a ribonucleoside hydrolase activity.}, }
@article {pmid24909992, year = {2014}, author = {Fuentes, I and Stegemann, S and Golczyk, H and Karcher, D and Bock, R}, title = {Horizontal genome transfer as an asexual path to the formation of new species.}, journal = {Nature}, volume = {511}, number = {7508}, pages = {232-235}, pmid = {24909992}, issn = {1476-4687}, mesh = {Drug Resistance, Bacterial/genetics ; *Gene Transfer, Horizontal ; *Genetic Speciation ; Genome, Plant/*genetics ; Kanamycin Resistance/genetics ; Karyotype ; Phenotype ; Plants, Genetically Modified ; Reproduction, Asexual ; Species Specificity ; Nicotiana/*genetics ; }, abstract = {Allopolyploidization, the combination of the genomes from two different species, has been a major source of evolutionary innovation and a driver of speciation and environmental adaptation. In plants, it has also contributed greatly to crop domestication, as the superior properties of many modern crop plants were conferred by ancient allopolyploidization events. It is generally thought that allopolyploidization occurred through hybridization events between species, accompanied or followed by genome duplication. Although many allopolyploids arose from closely related species (congeners), there are also allopolyploid species that were formed from more distantly related progenitor species belonging to different genera or even different tribes. Here we have examined the possibility that allopolyploidization can also occur by asexual mechanisms. We show that upon grafting--a mechanism of plant-plant interaction that is widespread in nature--entire nuclear genomes can be transferred between plant cells. We provide direct evidence for this process resulting in speciation by creating a new allopolyploid plant species from a herbaceous species and a woody species in the nightshade family. The new species is fertile and produces fertile progeny. Our data highlight natural grafting as a potential asexual mechanism of speciation and also provide a method for the generation of novel allopolyploid crop species.}, }
@article {pmid24905353, year = {2014}, author = {Nascimento, FX and Rossi, MJ and Soares, CR and McConkey, BJ and Glick, BR}, title = {New insights into 1-aminocyclopropane-1-carboxylate (ACC) deaminase phylogeny, evolution and ecological significance.}, journal = {PloS one}, volume = {9}, number = {6}, pages = {e99168}, pmid = {24905353}, issn = {1932-6203}, mesh = {*Bacteria/enzymology/genetics ; Bacterial Proteins/*genetics ; Carbon-Carbon Lyases/*genetics ; *Ecosystem ; *Evolution, Molecular ; Fungal Proteins/*genetics ; *Fungi/enzymology/genetics ; *Phylogeny ; *Stramenopiles/enzymology/genetics ; }, abstract = {The main objective of this work is the study of the phylogeny, evolution and ecological importance of the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase, the activity of which represents one of the most important and studied mechanisms used by plant growth-promoting microorganisms. The ACC deaminase gene and its regulatory elements presence in completely sequenced organisms was verified by multiple searches in diverse databases, and based on the data obtained a comprehensive analysis was conducted. Strain habitat, origin and ACC deaminase activity were taken into account when analyzing the results. In order to unveil ACC deaminase origin, evolution and relationships with other closely related pyridoxal phosphate (PLP) dependent enzymes a phylogenetic analysis was also performed. The data obtained show that ACC deaminase is mostly prevalent in some Bacteria, Fungi and members of Stramenopiles. Contrary to previous reports, we show that ACC deaminase genes are predominantly vertically inherited in various bacterial and fungal classes. Still, results suggest a considerable degree of horizontal gene transfer events, including interkingdom transfer events. A model for ACC deaminase origin and evolution is also proposed. This study also confirms the previous reports suggesting that the Lrp-like regulatory protein AcdR is a common mechanism regulating ACC deaminase expression in Proteobacteria, however, we also show that other regulatory mechanisms may be present in some Proteobacteria and other bacterial phyla. In this study we provide a more complete view of the role for ACC deaminase than was previously available. The results show that ACC deaminase may not only be related to plant growth promotion abilities, but may also play multiple roles in microorganism's developmental processes. Hence, exploring the origin and functioning of this enzyme may be the key in a variety of important agricultural and biotechnological applications.}, }
@article {pmid24898731, year = {2014}, author = {Strese, A and Backlund, A and Alsmark, C}, title = {A recently transferred cluster of bacterial genes in Trichomonas vaginalis--lateral gene transfer and the fate of acquired genes.}, journal = {BMC evolutionary biology}, volume = {14}, number = {}, pages = {119}, pmid = {24898731}, issn = {1471-2148}, mesh = {Bacteria/classification/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Protozoan ; Multigene Family ; Phylogeny ; Trichomonas vaginalis/*genetics ; }, abstract = {BACKGROUND: Lateral Gene Transfer (LGT) has recently gained recognition as an important contributor to some eukaryote proteomes, but the mechanisms of acquisition and fixation in eukaryotic genomes are still uncertain. A previously defined norm for LGTs in microbial eukaryotes states that the majority are genes involved in metabolism, the LGTs are typically localized one by one, surrounded by vertically inherited genes on the chromosome, and phylogenetics shows that a broad collection of bacterial lineages have contributed to the transferome.<br><br>RESULTS: A unique 34 kbp long fragment with 27 clustered genes (TvLF) of prokaryote origin was identified in the sequenced genome of the protozoan parasite Trichomonas vaginalis. Using a PCR based approach we confirmed the presence of the orthologous fragment in four additional T. vaginalis strains. Detailed sequence analyses unambiguously suggest that TvLF is the result of one single, recent LGT event. The proposed donor is a close relative to the firmicute bacterium Peptoniphilus harei. High nucleotide sequence similarity between T. vaginalis strains, as well as to P. harei, and the absence of homologs in other Trichomonas species, suggests that the transfer event took place after the radiation of the genus Trichomonas. Some genes have undergone pseudogenization and degradation, indicating that they may not be retained in the future. Functional annotations reveal that genes involved in informational processes are particularly prone to degradation.<br><br>CONCLUSIONS: We conclude that, although the majority of eukaryote LGTs are single gene occurrences, they may be acquired in clusters of several genes that are subsequently cleansed of evolutionarily less advantageous genes.}, }
@article {pmid24892935, year = {2014}, author = {Zhou, C and Mao, F and Yin, Y and Huang, J and Gogarten, JP and Xu, Y}, title = {AST: an automated sequence-sampling method for improving the taxonomic diversity of gene phylogenetic trees.}, journal = {PloS one}, volume = {9}, number = {6}, pages = {e98844}, pmid = {24892935}, issn = {1932-6203}, mesh = {Computational Biology/*methods ; *Phylogeny ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA ; }, abstract = {A challenge in phylogenetic inference of gene trees is how to properly sample a large pool of homologous sequences to derive a good representative subset of sequences. Such a need arises in various applications, e.g. when (1) accuracy-oriented phylogenetic reconstruction methods may not be able to deal with a large pool of sequences due to their high demand in computing resources; (2) applications analyzing a collection of gene trees may prefer to use trees with fewer operational taxonomic units (OTUs), for instance for the detection of horizontal gene transfer events by identifying phylogenetic conflicts; and (3) the pool of available sequences is biased towards extensively studied species. In the past, the creation of subsamples often relied on manual selection. Here we present an Automated sequence-Sampling method for improving the Taxonomic diversity of gene phylogenetic trees, AST, to obtain representative sequences that maximize the taxonomic diversity of the sampled sequences. To demonstrate the effectiveness of AST, we have tested it to solve four problems, namely, inference of the evolutionary histories of the small ribosomal subunit protein S5 of E. coli, 16 S ribosomal RNAs and glycosyl-transferase gene family 8, and a study of ancient horizontal gene transfers from bacteria to plants. Our results show that the resolution of our computational results is almost as good as that of manual inference by domain experts, hence making the tool generally useful to phylogenetic studies by non-phylogeny specialists. The program is available at http://csbl.bmb.uga.edu/~zhouchan/AST.php.}, }
@article {pmid24892910, year = {2014}, author = {Maguire, F and Richards, TA}, title = {Organelle evolution: a mosaic of 'mitochondrial' functions.}, journal = {Current biology : CB}, volume = {24}, number = {11}, pages = {R518-20}, doi = {10.1016/j.cub.2014.03.075}, pmid = {24892910}, issn = {1879-0445}, mesh = {Eukaryota/*genetics/*metabolism ; Organelles/*metabolism ; *Proteome ; Sulfur/*metabolism ; }, abstract = {An ancient endosymbiosis of an α-proteobacterium produced a diverse range of organelles including mitochondria. Reconstruction of the Pygsuia biforma proteome adds to the mosaic of functional systems present in mitochondrial-related organelles and demonstrates the role of horizontal gene transfer.}, }
@article {pmid24889424, year = {2015}, author = {Rapa, RA and Islam, A and Monahan, LG and Mutreja, A and Thomson, N and Charles, IG and Stokes, HW and Labbate, M}, title = {A genomic island integrated into recA of Vibrio cholerae contains a divergent recA and provides multi-pathway protection from DNA damage.}, journal = {Environmental microbiology}, volume = {17}, number = {4}, pages = {1090-1102}, pmid = {24889424}, issn = {1462-2920}, support = {/WT_/Wellcome Trust/United Kingdom ; 098051/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Sequence ; Bacterial Adhesion/genetics ; Base Sequence ; Cholera/*microbiology ; Cholera Toxin/genetics ; DNA Damage/genetics/*radiation effects ; DNA Repair/*genetics ; DNA-Directed DNA Polymerase/genetics ; Escherichia coli/genetics ; Escherichia coli Proteins/genetics ; Gene Transfer, Horizontal ; Genomic Islands/*genetics ; Humans ; Molecular Sequence Data ; Rec A Recombinases/*genetics ; Recombination, Genetic ; Ultraviolet Rays/adverse effects ; Vibrio cholerae/genetics/*pathogenicity ; Virulence Factors/genetics ; }, abstract = {Lateral gene transfer (LGT) has been crucial in the evolution of the cholera pathogen, Vibrio cholerae. The two major virulence factors are present on two different mobile genetic elements, a bacteriophage containing the cholera toxin genes and a genomic island (GI) containing the intestinal adhesin genes. Non-toxigenic V. cholerae in the aquatic environment are a major source of novel DNA that allows the pathogen to morph via LGT. In this study, we report a novel GI from a non-toxigenic V. cholerae strain containing multiple genes involved in DNA repair including the recombination repair gene recA that is 23% divergent from the indigenous recA and genes involved in the translesion synthesis pathway. This is the first report of a GI containing the critical gene recA and the first report of a GI that targets insertion into a specific site within recA. We show that possession of the island in Escherichia coli is protective against DNA damage induced by UV-irradiation and DNA targeting antibiotics. This study highlights the importance of genetic elements such as GIs in the evolution of V. cholerae and emphasizes the importance of environmental strains as a source of novel DNA that can influence the pathogenicity of toxigenic strains.}, }
@article {pmid24889250, year = {2014}, author = {Megens, S and Vaira, D and De Baets, G and Dekeersmaeker, N and Schrooten, Y and Li, G and Schymkowitz, J and Rousseau, F and Vandamme, AM and Moutschen, M and Van Laethem, K}, title = {Horizontal gene transfer from human host to HIV-1 reverse transcriptase confers drug resistance and partly compensates for replication deficits.}, journal = {Virology}, volume = {456-457}, number = {}, pages = {310-318}, doi = {10.1016/j.virol.2014.03.023}, pmid = {24889250}, issn = {1096-0341}, mesh = {Chromosomes, Human ; *Drug Resistance, Viral ; *Gene Transfer, Horizontal ; HIV Infections/virology ; HIV Reverse Transcriptase/*genetics ; HIV-1/drug effects/*enzymology/*genetics/isolation &amp; purification/physiology ; Humans ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Insertional ; Phylogeny ; Protein Conformation ; RNA, Viral/genetics ; Sequence Analysis, DNA ; Sequence Homology ; *Virus Replication ; }, abstract = {We investigated the origin and the effect of insertion D67D-THGERDLGPA within HIV-1 RT from a patient failing antiviral therapy. The insertion developed within the context of pre-existing NRTI and NNRTI mutations (M41L, L210W, T215Y and N348I). Concurrently, the NRTI mutations T69I and V118I and the NNRTI mutations K103N and Y181C were detected for the first time. High-level drug resistance (fold-changes≥50) and a good replication capacity (87% of wild-type) were observed, significantly higher than for the previous virus without insertion. The insertion was very similar to a region within human chromosome 17 (31/34 nucleotide identity), and had already been detected independently in a Japanese HIV-1 isolate. These results suggest that a particular sequence within human chromosome 17 is prone to horizontal gene transfer into the HIV-1 RT finger subdomain. This insertion confers selective advantage to HIV-1 by its contribution to multi-drug resistance and restoration of impaired replication capacity.}, }
@article {pmid24888871, year = {2014}, author = {Heang, V and Hout, B and Prouty, MG and Supraprom, C and Ford, GW and Newell, SW and Leski, TA and Vora, GJ and Taitt, CR}, title = {Detection of qnrVC and rmtB genes from a multidrug-resistant Ralstonia pickettii wound infection isolate in Cambodia.}, journal = {International journal of antimicrobial agents}, volume = {44}, number = {1}, pages = {84-85}, doi = {10.1016/j.ijantimicag.2014.04.003}, pmid = {24888871}, issn = {1872-7913}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics/metabolism ; Cambodia ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal ; Gram-Negative Bacterial Infections/drug therapy/microbiology ; Humans ; Methyltransferases/*genetics/metabolism ; Microbial Sensitivity Tests ; Plasmids ; Quinolones/pharmacology ; Ralstonia pickettii/*drug effects/*genetics/isolation &amp; purification/metabolism ; Wound Infection/drug therapy/microbiology ; }, }
@article {pmid24887088, year = {2014}, author = {Catone, MV and Ruiz, JA and Castellanos, M and Segura, D and Espin, G and López, NI}, title = {High polyhydroxybutyrate production in Pseudomonas extremaustralis is associated with differential expression of horizontally acquired and core genome polyhydroxyalkanoate synthase genes.}, journal = {PloS one}, volume = {9}, number = {6}, pages = {e98873}, pmid = {24887088}, issn = {1932-6203}, mesh = {Acyltransferases/*genetics ; Bacterial Proteins/*genetics ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Hydroxybutyrates/*metabolism ; Pseudomonas/*genetics/metabolism ; }, abstract = {Pseudomonas extremaustralis produces mainly polyhydroxybutyrate (PHB), a short chain length polyhydroxyalkanoate (sclPHA) infrequently found in Pseudomonas species. Previous studies with this strain demonstrated that PHB genes are located in a genomic island. In this work, the analysis of the genome of P. extremaustralis revealed the presence of another PHB cluster phbFPX, with high similarity to genes belonging to Burkholderiales, and also a cluster, phaC1ZC2D, coding for medium chain length PHA production (mclPHA). All mclPHA genes showed high similarity to genes from Pseudomonas species and interestingly, this cluster also showed a natural insertion of seven ORFs not related to mclPHA metabolism. Besides PHB, P. extremaustralis is able to produce mclPHA although in minor amounts. Complementation analysis demonstrated that both mclPHA synthases, PhaC1 and PhaC2, were functional. RT-qPCR analysis showed different levels of expression for the PHB synthase, phbC, and the mclPHA synthases. The expression level of phbC, was significantly higher than the obtained for phaC1 and phaC2, in late exponential phase cultures. The analysis of the proteins bound to the PHA granules showed the presence of PhbC and PhaC1, whilst PhaC2 could not be detected. In addition, two phasin like proteins (PhbP and PhaI) associated with the production of scl and mcl PHAs, respectively, were detected. The results of this work show the high efficiency of a foreign gene (phbC) in comparison with the mclPHA core genome genes (phaC1 and phaC2) indicating that the ability of P. extremaustralis to produce high amounts of PHB could be explained by the different expression levels of the genes encoding the scl and mcl PHA synthases.}, }
@article {pmid24885784, year = {2014}, author = {Wang, J and Pritchard, JR and Kreitmann, L and Montpetit, A and Behr, MA}, title = {Disruption of Mycobacterium avium subsp. paratuberculosis-specific genes impairs in vivo fitness.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {415}, pmid = {24885784}, issn = {1471-2164}, support = {MOP-97813//Canadian Institutes of Health Research/Canada ; }, mesh = {Animals ; Bacterial Proteins/*genetics/metabolism ; *DNA Transposable Elements ; DNA, Bacterial/metabolism ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genes, Essential ; Genetic Fitness ; High-Throughput Nucleotide Sequencing ; Mice ; Mice, Inbred C57BL ; Mycobacterium avium subsp. paratuberculosis/*genetics/physiology ; Paratuberculosis/*microbiology ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Mycobacterium avium subsp. paratuberculosis (MAP) is an obligate intracellular pathogen that infects many ruminant species. The acquisition of foreign genes via horizontal gene transfer has been postulated to contribute to its pathogenesis, as these genetic elements are absent from its putative ancestor, M. avium subsp. hominissuis (MAH), an environmental organism with lesser pathogenicity. In this study, high-throughput sequencing of MAP transposon libraries were analyzed to qualitatively and quantitatively determine the contribution of individual genes to bacterial survival during infection.<br><br>RESULTS: Out of 52384 TA dinucleotides present in the MAP K-10 genome, 12607 had a MycoMarT7 transposon in the input pool, interrupting 2443 of the 4350 genes in the MAP genome (56%). Of 96 genes situated in MAP-specific genomic islands, 82 were disrupted in the input pool, indicating that MAP-specific genomic regions are dispensable for in vitro growth (odds ratio&#x2009;=&#x2009;0.21). Following 5 independent in vivo infections with this pool of mutants, the correlation between output pools was high for 4 of 5 (R&#x2009;=&#x2009;0.49 to 0.61) enabling us to define genes whose disruption reproducibly reduced bacterial fitness in vivo. At three different thresholds for reduced fitness in vivo, MAP-specific genes were over-represented in the list of predicted essential genes. We also identified additional genes that were severely depleted after infection, and several of them have orthologues that are essential genes in M. tuberculosis.<br><br>CONCLUSIONS: This work indicates that the genetic elements required for the in vivo survival of MAP represent a combination of conserved mycobacterial virulence genes and MAP-specific genes acquired via horizontal gene transfer. In addition, the in vitro and in vivo essential genes identified in this study may be further characterized to offer a better understanding of MAP pathogenesis, and potentially contribute to the discovery of novel therapeutic and vaccine targets.}, }
@article {pmid24884896, year = {2014}, author = {El Kafsi, H and Binesse, J and Loux, V and Buratti, J and Boudebbouze, S and Dervyn, R and Kennedy, S and Galleron, N and Quinquis, B and Batto, JM and Moumen, B and Maguin, E and van de Guchte, M}, title = {Lactobacillus delbrueckii ssp. lactis and ssp. bulgaricus: a chronicle of evolution in action.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {407}, pmid = {24884896}, issn = {1471-2164}, mesh = {Amino Acids/biosynthesis ; Bacterial Proteins/genetics ; Carbohydrate Metabolism ; *Evolution, Molecular ; Fermentation ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genome, Bacterial ; Lactobacillus delbrueckii/*genetics ; Multilocus Sequence Typing ; Proteome/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Lactobacillus delbrueckii ssp. lactis and ssp. bulgaricus are lactic acid producing bacteria that are largely used in dairy industries, notably in cheese-making and yogurt production. An earlier in-depth study of the first completely sequenced ssp. bulgaricus genome revealed the characteristics of a genome in an active phase of rapid evolution, in what appears to be an adaptation to the milk environment. Here we examine for the first time if the same conclusions apply to the ssp. lactis, and discuss intra- and inter-subspecies genomic diversity in the context of evolutionary adaptation.<br><br>RESULTS: Both L. delbrueckii ssp. show the signs of reductive evolution through the elimination of superfluous genes, thereby limiting their carbohydrate metabolic capacities and amino acid biosynthesis potential. In the ssp. lactis this reductive evolution has gone less far than in the ssp. bulgaricus. Consequently, the ssp. lactis retained more extended carbohydrate metabolizing capabilities than the ssp. bulgaricus but, due to high intra-subspecies diversity, very few carbohydrate substrates, if any, allow a reliable distinction of the two ssp. We further show that one of the most important traits, lactose fermentation, of one of the economically most important dairy bacteria, L. delbruecki ssp. bulgaricus, relies on horizontally acquired rather than deep ancestral genes. In this sense this bacterium may thus be regarded as a natural GMO avant la lettre.<br><br>CONCLUSIONS: The dairy lactic acid producing bacteria L. delbrueckii ssp. lactis and ssp. bulgaricus appear to represent different points on the same evolutionary track of adaptation to the milk environment through the loss of superfluous functions and the acquisition of functions that allow an optimized utilization of milk resources, where the ssp. bulgaricus has progressed further away from the common ancestor.}, }
@article {pmid24884625, year = {2014}, author = {Park, S and Ruhlman, TA and Sabir, JS and Mutwakil, MH and Baeshen, MN and Sabir, MJ and Baeshen, NA and Jansen, RK}, title = {Complete sequences of organelle genomes from the medicinal plant Rhazya stricta (Apocynaceae) and contrasting patterns of mitochondrial genome evolution across asterids.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {405}, pmid = {24884625}, issn = {1471-2164}, mesh = {Apocynaceae/classification/*genetics ; Base Sequence ; Biological Evolution ; DNA Transposable Elements ; Gene Transfer, Horizontal ; *Genome, Mitochondrial ; *Genome, Plant ; Genome, Plastid ; Molecular Sequence Data ; Open Reading Frames/genetics ; Phylogeny ; Plant Proteins/classification/genetics ; Plants, Medicinal/genetics ; Plastids/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Rhazya stricta is native to arid regions in South Asia and the Middle East and is used extensively in folk medicine to treat a wide range of diseases. In addition to generating genomic resources for this medicinally important plant, analyses of the complete plastid and mitochondrial genomes and a nuclear transcriptome from Rhazya provide insights into inter-compartmental transfers between genomes and the patterns of evolution among eight asterid mitochondrial genomes.<br><br>RESULTS: The 154,841&#xa0;bp plastid genome is highly conserved with gene content and order identical to the ancestral organization of angiosperms. The 548,608&#xa0;bp mitochondrial genome exhibits a number of phenomena including the presence of recombinogenic repeats that generate a multipartite organization, transferred DNA from the plastid and nuclear genomes, and bidirectional DNA transfers between the mitochondrion and the nucleus. The mitochondrial genes sdh3 and rps14 have been transferred to the nucleus and have acquired targeting presequences. In the case of rps14, two copies are present in the nucleus; only one has a mitochondrial targeting presequence and may be functional. Phylogenetic analyses of both nuclear and mitochondrial copies of rps14 across angiosperms suggests Rhazya has experienced a single transfer of this gene to the nucleus, followed by a duplication event. Furthermore, the phylogenetic distribution of gene losses and the high level of sequence divergence in targeting presequences suggest multiple, independent transfers of both sdh3 and rps14 across asterids. Comparative analyses of mitochondrial genomes of eight sequenced asterids indicates a complicated evolutionary history in this large angiosperm clade with considerable diversity in genome organization and size, repeat, gene and intron content, and amount of foreign DNA from the plastid and nuclear genomes.<br><br>CONCLUSIONS: Organelle genomes of Rhazya stricta provide valuable information for improving the understanding of mitochondrial genome evolution among angiosperms. The genomic data have enabled a rigorous examination of the gene transfer events. Rhazya is unique among the eight sequenced asterids in the types of events that have shaped the evolution of its mitochondrial genome. Furthermore, the organelle genomes of R. stricta provide valuable genomic resources for utilizing this important medicinal plant in biotechnology applications.}, }
@article {pmid24884411, year = {2014}, author = {Matari, NH and Blair, JE}, title = {A multilocus timescale for oomycete evolution estimated under three distinct molecular clock models.}, journal = {BMC evolutionary biology}, volume = {14}, number = {}, pages = {101}, pmid = {24884411}, issn = {1471-2148}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {Bayes Theorem ; *Biological Evolution ; Fossils ; Gene Transfer, Horizontal ; *Models, Genetic ; Oomycetes/*classification/*genetics ; Phylogeny ; Transcription Factors/genetics ; }, abstract = {BACKGROUND: Molecular clock methodologies allow for the estimation of divergence times across a variety of organisms; this can be particularly useful for groups lacking robust fossil histories, such as microbial eukaryotes with few distinguishing morphological traits. Here we have used a Bayesian molecular clock method under three distinct clock models to estimate divergence times within oomycetes, a group of fungal-like eukaryotes that are ubiquitous in the environment and include a number of devastating pathogenic species. The earliest fossil evidence for oomycetes comes from the Lower Devonian (~400 Ma), however the taxonomic affinities of these fossils are unclear.<br><br>RESULTS: Complete genome sequences were used to identify orthologous proteins among oomycetes, diatoms, and a brown alga, with a focus on conserved regulators of gene expression such as DNA and histone modifiers and transcription factors. Our molecular clock estimates place the origin of oomycetes by at least the mid-Paleozoic (~430-400&#xa0;Ma), with the divergence between two major lineages, the peronosporaleans and saprolegnialeans, in the early Mesozoic (~225-190&#xa0;Ma). Divergence times estimated under the three clock models were similar, although only the strict and random local clock models produced reliable estimates for most parameters.<br><br>CONCLUSIONS: Our molecular timescale suggests that modern pathogenic oomycetes diverged well after the origin of their respective hosts, indicating that environmental conditions or perhaps horizontal gene transfer events, rather than host availability, may have driven lineage diversification. Our findings also suggest that the last common ancestor of oomycetes possessed a full complement of eukaryotic regulatory proteins, including those involved in histone modification, RNA interference, and tRNA and rRNA methylation; interestingly no match to canonical DNA methyltransferases could be identified in the oomycete genomes studied here.}, }
@article {pmid24884375, year = {2014}, author = {Skaare, D and Anthonisen, IL and Caugant, DA and Jenkins, A and Steinbakk, M and Strand, L and Sundsfjord, A and Tveten, Y and Kristiansen, BE}, title = {Multilocus sequence typing and ftsI sequencing: a powerful tool for surveillance of penicillin-binding protein 3-mediated beta-lactam resistance in nontypeable Haemophilus influenzae.}, journal = {BMC microbiology}, volume = {14}, number = {}, pages = {131}, pmid = {24884375}, issn = {1471-2180}, mesh = {Aged ; Aged, 80 and over ; Child, Preschool ; Epidemiological Monitoring ; Female ; Gene Transfer, Horizontal ; *Genetic Variation ; Haemophilus Infections/*epidemiology/microbiology ; Haemophilus influenzae/*classification/drug effects/*genetics ; Humans ; Infant ; Japan ; Male ; Middle Aged ; Molecular Epidemiology ; Multilocus Sequence Typing/*methods ; Norway/epidemiology ; Penicillin-Binding Proteins/*genetics ; *beta-Lactam Resistance ; }, abstract = {BACKGROUND: Beta-lactam resistance in Haemophilus influenzae due to ftsI mutations causing altered penicillin-binding protein 3 (PBP3) is increasing worldwide. Low-level resistant isolates with the N526K substitution (group II low-rPBP3) predominate in most geographical regions, while high-level resistant isolates with the additional S385T substitution (group III high-rPBP3) are common in Japan and South Korea.Knowledge about the molecular epidemiology of rPBP3 strains is limited. We combined multilocus sequence typing (MLST) and ftsI/PBP3 typing to study the emergence and spread of rPBP3 in nontypeable H. influenzae (NTHi) in Norway.<br><br>RESULTS: The prevalence of rPBP3 in a population of 795 eye, ear and respiratory isolates (99% NTHi) from 2007 was 15%. The prevalence of clinical PBP3-mediated resistance to ampicillin was 9%, compared to 2.5% three years earlier. Group II low-rPBP3 predominated (96%), with significant proportions of isolates non-susceptible to cefotaxime (6%) and meropenem (20%). Group III high-rPBP3 was identified for the first time in Northern Europe.Four MLST sequence types (ST) with characteristic, highly diverging ftsI alleles accounted for 61% of the rPBP3 isolates. The most prevalent substitution pattern (PBP3 type A) was present in 41% of rPBP3 isolates, mainly carried by ST367 and ST14. Several unrelated STs possessed identical copies of the ftsI allele encoding PBP3 type A.Infection sites, age groups, hospitalization rates and rPBP3 frequencies differed between STs and phylogenetic groups.<br><br>CONCLUSIONS: This study is the first to link ftsI alleles to STs in H. influenzae. The results indicate that horizontal gene transfer contributes to the emergence of rPBP3 by phylogeny restricted transformation.Clonally related virulent rPBP3 strains are widely disseminated and high-level resistant isolates emerge in new geographical regions, threatening current empiric antibiotic treatment. The need of continuous monitoring of beta-lactam susceptibility and a global system for molecular surveillance of rPBP3 strains is underlined. Combining MLST and ftsI/PBP3 typing is a powerful tool for this purpose.}, }
@article {pmid24879667, year = {2014}, author = {Huijbers, PM and Graat, EA and Haenen, AP and van Santen, MG and van Essen-Zandbergen, A and Mevius, DJ and van Duijkeren, E and van Hoek, AH}, title = {Extended-spectrum and AmpC β-lactamase-producing Escherichia coli in broilers and people living and/or working on broiler farms: prevalence, risk factors and molecular characteristics.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {69}, number = {10}, pages = {2669-2675}, doi = {10.1093/jac/dku178}, pmid = {24879667}, issn = {1460-2091}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Agriculture ; Animals ; Bacterial Proteins/*genetics ; Chickens ; Child ; Child, Preschool ; Cross-Sectional Studies ; Escherichia coli/classification/*genetics/isolation &amp; purification ; Escherichia coli Infections/*epidemiology/*microbiology ; Female ; Humans ; Infant ; Infant, Newborn ; Male ; Middle Aged ; Multilocus Sequence Typing ; Netherlands ; Phylogeny ; Poultry Diseases/*epidemiology/*microbiology ; Prevalence ; Risk Factors ; Young Adult ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: The objectives of this study were to: estimate the prevalence of extended-spectrum β-lactamase (ESBL)- and AmpC β-lactamase-producing Escherichia coli carriage among broiler farmers, their family members and employees; identify and quantify risk factors for carriage, with an emphasis on contact with live broilers; and compare isolates from humans and broilers within farms with respect to molecular characteristics to gain insight into transmission routes.<br><br>METHODS: A cross-sectional prevalence study was conducted on 50 randomly selected Dutch broiler farms. Cloacal swabs were taken from 20 randomly chosen broilers. Faecal swabs were returned by 141 individuals living and/or working on 47 farms. ESBL/AmpC-producing E. coli were isolated and, for selected isolates, phylogenetic groups, plasmids and sequence types were determined. Questionnaires were used for risk factor analysis.<br><br>RESULTS: All sampled farms were positive, with 96.4% positive pooled broiler samples. The human prevalence was 19.1%, with 14.3% and 27.1% among individuals having a low and a high degree of contact with live broilers, respectively. Five pairs of human-broiler isolates had identical genes, plasmid families and E. coli sequence types, showing clonal transmission. Furthermore, similar ESBL/AmpC genes on the same plasmid families in different E. coli sequence types in humans and broilers hinted at horizontal gene transfer.<br><br>CONCLUSIONS: The prevalence among people on broiler farms was higher than in previous studies involving patients and the general population. Furthermore, an increased risk of carriage was shown among individuals having a high degree of contact with live broilers. The (relative) contribution of transmission routes that might play a role in the dissemination of ESBL/AmpC-encoding resistance genes to humans on broiler farms should be pursued in future studies.}, }
@article {pmid24874102, year = {2014}, author = {Guo, X and Gao, J and Li, F and Wang, J}, title = {Evidence of horizontal transfer of non-autonomous Lep1 Helitrons facilitated by host-parasite interactions.}, journal = {Scientific reports}, volume = {4}, number = {}, pages = {5119}, pmid = {24874102}, issn = {2045-2322}, mesh = {Animals ; Base Sequence ; Chromosome Mapping ; DNA Transposable Elements/*genetics ; Gene Transfer, Horizontal/*genetics ; Genetic Variation/*genetics ; Host-Parasite Interactions/*genetics ; Models, Genetic ; Molecular Sequence Data ; Moths/classification/*genetics ; Wasps/*genetics ; }, abstract = {Horizontal transfer (HT) of transposable elements has been recognized to be a major force driving genomic variation and biological innovation of eukaryotic organisms. However, the mechanisms of HT in eukaryotes remain poorly appreciated. The non-autonomous Helitron family, Lep1, has been found to be widespread in lepidopteran species, and showed little interspecific sequence similarity of acquired sequences at 3' end, which makes Lep1 a good candidate for the study of HT. In this study, we describe the Lep1-like elements in multiple non-lepidopteran species, including two aphids, Acyrthosiphon pisum and Aphis gossypii, two parasitoid wasps, Cotesia vestalis, and Copidosoma floridanum, one beetle, Anoplophora glabripennis, as well as two bracoviruses in parasitoid wasps, and one intracellular microsporidia parasite, Nosema bombycis. The patchy distribution and high sequence similarity of Lep1-like elements among distantly related lineages as well as incongruence of Lep1-like elements and host phylogeny suggest the occurrence of HT. Remarkably, the acquired sequences of both NbLep1 from N. bombycis and CfLep1 from C. floridanum showed over 90% identity with their lepidopteran host Lep1. Thus, our study provides evidence of HT facilitated by host-parasite interactions. Furthermore, in the context of these data, we discuss the putative directions and vectors of HT of Lep1 Helitrons.}, }
@article {pmid24868016, year = {2014}, author = {Zhang, HH and Feschotte, C and Han, MJ and Zhang, Z}, title = {Recurrent horizontal transfers of Chapaev transposons in diverse invertebrate and vertebrate animals.}, journal = {Genome biology and evolution}, volume = {6}, number = {6}, pages = {1375-1386}, pmid = {24868016}, issn = {1759-6653}, support = {R01 GM077582/GM/NIGMS NIH HHS/United States ; R01-GM077582/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; *DNA Transposable Elements ; Gene Dosage ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; }, abstract = {Horizontal transfer (HT) of a transposable element (TE) into a new genome is regarded as an important force to drive genome variation and biological innovation. In addition, HT also plays an important role in the persistence of TEs in eukaryotic genomes. Here, we provide the first documented example for the repeated HT of three families of Chapaev transposons in a wide range of animal species, including mammals, reptiles, jawed fishes, lampreys, insects, and in an insect bracovirus. Multiple alignments of the Chapaev transposons identified in these species revealed extremely high levels of nucleotide sequence identity (79-99%), which are inconsistent with vertical evolution given the deep divergence time separating these host species. Rather, the discontinuous distribution amongst species and lack of purifying selection acting on these transposons strongly suggest that they were independently and horizontally transferred into these species lineages. The detection of Chapaev transposons in an insect bracovirus indicated that these viruses might act as a possible vector for the horizontal spread of Chapaev transposons. One of the Chapaev families was also shared by lampreys and some of their common hosts (such as sturgeon and paddlefish), which suggested that parasite-host interaction might facilitate HTs.}, }
@article {pmid24865146, year = {2014}, author = {Perina, D and Mikoč, A and Ahel, J and Ćetković, H and Žaja, R and Ahel, I}, title = {Distribution of protein poly(ADP-ribosyl)ation systems across all domains of life.}, journal = {DNA repair}, volume = {23}, number = {}, pages = {4-16}, pmid = {24865146}, issn = {1568-7856}, support = {//Wellcome Trust/United Kingdom ; 101794//Wellcome Trust/United Kingdom ; 281739/ERC_/European Research Council/International ; }, mesh = {Animals ; Archaeal Proteins/genetics/metabolism ; Catalytic Domain ; DNA Repair ; DNA Repair Enzymes/chemistry/metabolism ; Eukaryotic Cells/metabolism ; Evolution, Molecular ; Fishes ; Humans ; Hydrolases/chemistry/metabolism ; Insect Proteins/chemistry/metabolism ; Phylogeny ; Plant Proteins/chemistry/metabolism ; Poly Adenosine Diphosphate Ribose/*chemistry/*metabolism ; Poly(ADP-ribose) Polymerases/chemistry/*metabolism ; Prokaryotic Cells/metabolism ; Protein Structure, Tertiary ; Proto-Oncogene Proteins/chemistry/metabolism ; Signal Transduction ; Tankyrases/chemistry/metabolism ; Viruses/genetics/metabolism ; }, abstract = {Poly(ADP-ribosyl)ation is a post-translational modification of proteins involved in regulation of many cellular pathways. Poly(ADP-ribose) (PAR) consists of chains of repeating ADP-ribose nucleotide units and is synthesized by the family of enzymes called poly(ADP-ribose) polymerases (PARPs). This modification can be removed by the hydrolytic action of poly(ADP-ribose) glycohydrolase (PARG) and ADP-ribosylhydrolase 3 (ARH3). Hydrolytic activity of macrodomain proteins (MacroD1, MacroD2 and TARG1) is responsible for the removal of terminal ADP-ribose unit and for complete reversion of protein ADP-ribosylation. Poly(ADP-ribosyl)ation is widely utilized in eukaryotes and PARPs are present in representatives from all six major eukaryotic supergroups, with only a small number of eukaryotic species that do not possess PARP genes. The last common ancestor of all eukaryotes possessed at least five types of PARP proteins that include both mono and poly(ADP-ribosyl) transferases. Distribution of PARGs strictly follows the distribution of PARP proteins in eukaryotic species. At least one of the macrodomain proteins that hydrolyse terminal ADP-ribose is also always present. Therefore, we can presume that the last common ancestor of all eukaryotes possessed a fully functional and reversible PAR metabolism and that PAR signalling provided the conditions essential for survival of the ancestral eukaryote in its ancient environment. PARP proteins are far less prevalent in bacteria and were probably gained through horizontal gene transfer. Only eleven bacterial species possess all proteins essential for a functional PAR metabolism, although it is not known whether PAR metabolism is truly functional in bacteria. Several dsDNA viruses also possess PARP homologues, while no PARP proteins have been identified in any archaeal genome. Our analysis of the distribution of enzymes involved in PAR metabolism provides insight into the evolution of these important signalling systems, as well as providing the basis for selection of the appropriate genetic model organisms to study the physiology of the specific human PARP proteins.}, }
@article {pmid24864033, year = {2014}, author = {Zhang, GQ and Yao, YH and Yu, XL and Niu, JJ}, title = {A survey of five broad-host-range plasmids in gram-negative bacilli isolated from patients.}, journal = {Plasmid}, volume = {74}, number = {}, pages = {9-14}, doi = {10.1016/j.plasmid.2014.05.002}, pmid = {24864033}, issn = {1095-9890}, mesh = {Acinetobacter baumannii/genetics/isolation &amp; purification ; Adolescent ; Adult ; Aged ; Aged, 80 and over ; Bacillus/*genetics/*isolation &amp; purification ; Bacterial Typing Techniques/methods ; Child ; Child, Preschool ; Drug Resistance, Bacterial ; Enterobacter cloacae/genetics/isolation &amp; purification ; Escherichia coli/genetics/isolation &amp; purification ; Female ; Host Specificity/*genetics ; Humans ; Infant ; Klebsiella pneumoniae/genetics/isolation &amp; purification ; Logistic Models ; Male ; Middle Aged ; Multiplex Polymerase Chain Reaction ; Plasmids/*genetics ; Proteus mirabilis/genetics/isolation &amp; purification ; Pseudomonas aeruginosa/genetics/isolation &amp; purification ; Replicon/genetics ; Sensitivity and Specificity ; Specimen Handling ; Young Adult ; }, abstract = {OBJECTIVES: To learn the prevalence of the primary classical broad-host-range (BHR) IncA/C, IncN, IncP, IncQ, and IncW plasmids in dominant gram-negative bacilli from inpatients in a teaching hospital in southern China.<br><br>METHODS: A multiplex polymerase chain reaction based on the replicons of BHR IncA/C, IncN, IncP, IncQ, and IncW plasmids was developed and used to determine these BHR plasmids. The difference in prevalence rates among the different species from three specimens was evaluated by a binary logistic regression model and the differences between multidrug-resistant organisms (MDRO) and non-MDRO were assessed using a chi-square test.<br><br>RESULTS: The average positive detection percentages of the replicons were 4.3%, 3.7%, 3.0%, 2.6%, and 1.9%, respectively, for IncN, IncP, IncQ, IncW, and IncA/C in descending order. The distribution of all five BHR plasmids did not differ significantly between specimens collected from wounds and urine, although both were significantly higher than those of sputum. The prevalence rates of all five BHR plasmids in MDROs were significantly higher than those in non-MDRO for Enterobacteriaceae; however, no significant difference was seen in non-fermenting gram-negative bacilli (NFGNB).<br><br>CONCLUSIONS: BHR IncA/C, IncN, IncP, IncQ, and IncW plasmids, which occur more often in bacilli from wound and urine specimens than those of sputum, are widespread in Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Enterobacter cloacae, Pseudomonas aeruginosa, and Acinetobacter baumannii strains isolated from inpatients. The prevalence rates in MDRO are higher than those in non-MDRO for Enterobacteriaceae but not significantly different for NFGNB.}, }
@article {pmid24862920, year = {2014}, author = {Matsutani, M and Fukushima, K and Kayama, C and Arimitsu, M and Hirakawa, H and Toyama, H and Adachi, O and Yakushi, T and Matsushita, K}, title = {Replacement of a terminal cytochrome c oxidase by ubiquinol oxidase during the evolution of acetic acid bacteria.}, journal = {Biochimica et biophysica acta}, volume = {1837}, number = {10}, pages = {1810-1820}, doi = {10.1016/j.bbabio.2014.05.355}, pmid = {24862920}, issn = {0006-3002}, mesh = {Acetobacter/enzymology/genetics/*metabolism ; *Biological Evolution ; Electron Transport Complex IV/*metabolism ; Escherichia coli/genetics ; Genes, Bacterial ; Oxidoreductases/*metabolism ; Phylogeny ; }, abstract = {The bacterial aerobic respiratory chain has a terminal oxidase of the heme-copper oxidase superfamily, comprised of cytochrome c oxidase (COX) and ubiquinol oxidase (UOX); UOX evolved from COX. Acetobacter pasteurianus, an α-Proteobacterial acetic acid bacterium (AAB), produces UOX but not COX, although it has a partial COX gene cluster, ctaBD and ctaA, in addition to the UOX operon cyaBACD. We expressed ctaB and ctaA genes of A. pasteurianus in Escherichia coli and demonstrated their function as heme O and heme A synthases. We also found that the absence of ctaD function is likely due to accumulated mutations. These COX genes are closely related to other α-Proteobacterial COX proteins. However, the UOX operons of AAB are closely related to those of the β/γ-Proteobacteria (γ-type UOX), distinct from the α/β-Proteobacterial proteins (α-type UOX), but different from the other γ-type UOX proteins by the absence of the cyoE heme O synthase. Thus, we suggest that A. pasteurianus has a functional γ-type UOX but has lost the COX genes, with the exception of ctaB and ctaA, which supply the heme O and A moieties for UOX. Our results suggest that, in AAB, COX was replaced by β/γ-Proteobacterial UOX via horizontal gene transfer, while the COX genes, except for the heme O/A synthase genes, were lost.}, }
@article {pmid24862457, year = {2014}, author = {Jung, CM}, title = {Dissemination of bacterial fluoroquinolone resistance in two multidrug-resistant enterobacteriaceae.}, journal = {Journal of molecular microbiology and biotechnology}, volume = {24}, number = {2}, pages = {130-134}, doi = {10.1159/000362278}, pmid = {24862457}, issn = {1660-2412}, mesh = {Anti-Bacterial Agents/*pharmacology ; *Conjugation, Genetic ; *Drug Resistance, Multiple, Bacterial ; Enterobacter aerogenes/*drug effects/genetics/isolation &amp; purification ; Escherichia coli/*drug effects/genetics/isolation &amp; purification ; Fluoroquinolones/*pharmacology ; *Gene Transfer, Horizontal ; Plasmids ; }, abstract = {Bacterial resistance to antimicrobials has become one of the greatest challenges for clinical microbiologists and healthcare practitioners worldwide. Acquisition of resistance genes has proven to be difficult to characterize and is largely uncontrollable in the environment. Here we sought to characterize conjugal horizontal gene transfer of plasmid-encoded fluoroquinolone resistance genes from two strains of Enterobacteriaceae, one clinical and one from a municipal wastewater treatment plant environment. Conjugation was dissimilar between the two strains. Escherichia coli strain LR09, containing a plasmid with the aac(6')-Ib-cr fluoroquinolone resistance gene, did not conjugate with any of the 15 strains tested, while Enterobacter aerogenes strain YS11 conjugated with two strains of E. coli. The resultant transconjugants were also dissimilar in their stability and potential persistence. The observations presented herein exemplify the difficulties in understanding and controlling the spread of antimicrobial resistance. Thus, it may be prudent to address drug disposal and destruction, incorporating a life-cycle assessment plan 'from cradle to grave', treating antimicrobials as chemical or environmental contaminants.}, }
@article {pmid24856215, year = {2014}, author = {Stairs, CW and Eme, L and Brown, MW and Mutsaers, C and Susko, E and Dellaire, G and Soanes, DM and van der Giezen, M and Roger, AJ}, title = {A SUF Fe-S cluster biogenesis system in the mitochondrion-related organelles of the anaerobic protist Pygsuia.}, journal = {Current biology : CB}, volume = {24}, number = {11}, pages = {1176-1186}, doi = {10.1016/j.cub.2014.04.033}, pmid = {24856215}, issn = {1879-0445}, support = {MOP-82809//Canadian Institutes of Health Research/Canada ; MOP-84260//Canadian Institutes of Health Research/Canada ; }, mesh = {Anaerobiosis ; Eukaryota/*genetics/*metabolism ; Molecular Sequence Data ; Organelles/*metabolism ; Phylogeny ; *Proteome ; Saccharomyces cerevisiae/metabolism ; Sequence Analysis, RNA ; Sulfur/*metabolism ; }, abstract = {BACKGROUND: Many microbial eukaryotes have evolved anaerobic alternatives to mitochondria known as mitochondrion-related organelles (MROs). Yet, only a few of these have been experimentally investigated. Here we report an RNA-seq-based reconstruction of the MRO proteome of Pygsuia biforma, an anaerobic representative of an unexplored deep-branching eukaryotic lineage.<br><br>RESULTS: Pygsuia's MRO has a completely novel suite of functions, defying existing "function-based" organelle classifications. Most notable is the replacement of the mitochondrial iron-sulfur cluster machinery by an archaeal sulfur mobilization (SUF) system acquired via lateral gene transfer (LGT). Using immunolocalization in Pygsuia and heterologous expression in yeast, we show that the SUF system does indeed localize to the MRO. The Pygsuia MRO also possesses a unique assemblage of features, including: cardiolipin, phosphonolipid, amino acid, and fatty acid metabolism; a partial Kreb's cycle; a reduced respiratory chain; and a laterally acquired rhodoquinone (RQ) biosynthesis enzyme. The latter observation suggests that RQ is an electron carrier of a fumarate reductase-type complex II in this MRO.<br><br>CONCLUSIONS: The unique functional profile of this MRO underscores the tremendous plasticity of mitochondrial function within eukaryotes and showcases the role of LGT in forging metabolic mosaics of ancestral and newly acquired organellar pathways.}, }
@article {pmid24856193, year = {2014}, author = {Hong, SK and Kim, EC}, title = {Possible misidentification of Mycobacterium yongonense.}, journal = {Emerging infectious diseases}, volume = {20}, number = {6}, pages = {1089-1090}, pmid = {24856193}, issn = {1080-6059}, mesh = {*Diagnostic Errors ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Mycobacterium/genetics/*isolation &amp; purification ; Mycobacterium Infections/*diagnosis/microbiology ; RNA, Ribosomal, 16S/genetics ; }, }
@article {pmid24853639, year = {2014}, author = {Everitt, RG and Didelot, X and Batty, EM and Miller, RR and Knox, K and Young, BC and Bowden, R and Auton, A and Votintseva, A and Larner-Svensson, H and Charlesworth, J and Golubchik, T and Ip, CL and Godwin, H and Fung, R and Peto, TE and Walker, AS and Crook, DW and Wilson, DJ}, title = {Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus.}, journal = {Nature communications}, volume = {5}, number = {}, pages = {3956}, pmid = {24853639}, issn = {2041-1723}, support = {MR/K010174/1/MRC_/Medical Research Council/United Kingdom ; 087646/Z/08/Z/WT_/Wellcome Trust/United Kingdom ; G0800778/MRC_/Medical Research Council/United Kingdom ; 101237/Z/13/Z/WT_/Wellcome Trust/United Kingdom ; 090532/Z/09/Z/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; G0800778/DH_/Department of Health/United Kingdom ; 087646/WT_/Wellcome Trust/United Kingdom ; 101237/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Chromosomes, Bacterial/genetics ; DNA Transposable Elements/*genetics ; Gene Transfer, Horizontal/genetics ; Genetic Variation ; Genome, Bacterial/*genetics ; Likelihood Functions ; Linkage Disequilibrium/genetics ; Phylogeny ; *Recombination, Genetic ; Species Specificity ; Staphylococcus aureus/*genetics/isolation &amp; purification ; }, abstract = {Horizontal gene transfer is an important driver of bacterial evolution, but genetic exchange in the core genome of clonal species, including the major pathogen Staphylococcus aureus, is incompletely understood. Here we reveal widespread homologous recombination in S. aureus at the species level, in contrast to its near-complete absence between closely related strains. We discover a patchwork of hotspots and coldspots at fine scales falling against a backdrop of broad-scale trends in rate variation. Over megabases, homoplasy rates fluctuate 1.9-fold, peaking towards the origin-of-replication. Over kilobases, we find core recombination hotspots of up to 2.5-fold enrichment situated near fault lines in the genome associated with mobile elements. The strongest hotspots include regions flanking conjugative transposon ICE6013, the staphylococcal cassette chromosome (SCC) and genomic island νSaα. Mobile element-driven core genome transfer represents an opportunity for adaptation and challenges our understanding of the recombination landscape in predominantly clonal pathogens, with important implications for genotype-phenotype mapping.}, }
@article {pmid24852141, year = {2014}, author = {Butaye, P and van Duijkeren, E and Prescott, JF and Schwarz, S}, title = {Antimicrobial resistance in bacteria from animals and the environment.}, journal = {Veterinary microbiology}, volume = {171}, number = {3-4}, pages = {269-272}, doi = {10.1016/j.vetmic.2014.04.009}, pmid = {24852141}, issn = {1873-2542}, mesh = {Animals ; Anti-Infective Agents/*adverse effects ; Bacteria/drug effects/genetics/*growth &amp; development ; Drug Resistance, Bacterial/drug effects/*physiology ; Environment ; Gene Transfer, Horizontal/genetics ; *Selection, Genetic ; }, }
@article {pmid24848275, year = {2014}, author = {Eckshtain-Levi, N and Munitz, T and Živanović, M and Traore, SM and Spröer, C and Zhao, B and Welbaum, G and Walcott, R and Sikorski, J and Burdman, S}, title = {Comparative Analysis of Type III Secreted Effector Genes Reflects Divergence of Acidovorax citrulli Strains into Three Distinct Lineages.}, journal = {Phytopathology}, volume = {104}, number = {11}, pages = {1152-1162}, doi = {10.1094/PHYTO-12-13-0350-R}, pmid = {24848275}, issn = {0031-949X}, mesh = {Base Sequence ; Citrullus/*microbiology ; Comamonadaceae/*genetics/metabolism/pathogenicity ; Cucumis melo/*microbiology ; Fruit/microbiology ; Molecular Sequence Data ; Phenotype ; Phylogeny ; Plant Diseases/*microbiology ; *Polymorphism, Single Nucleotide ; Seedlings/microbiology ; Sequence Analysis, DNA ; Type III Secretion Systems/*genetics/metabolism ; Virulence ; }, abstract = {Acidovorax citrulli causes bacterial fruit blotch of cucurbits, a serious economic threat to watermelon (Citrullus lanatus) and melon (Cucumis melo) production worldwide. Based on genetic and biochemical traits, A. citrulli strains have been divided into two distinct groups: group I strains have been mainly isolated from various non-watermelon hosts, while group II strains have been generally isolated from and are highly virulent on watermelon. The pathogen depends on a functional type III secretion system for pathogenicity. Annotation of the genome of the group II strain AAC00-1 revealed 11 genes encoding putative type III secreted (T3S) effectors. Due to the crucial role of type III secretion for A. citrulli pathogenicity, we hypothesized that group I and II strains differ in their T3S effector repertoire. Comparative analysis of the 11 effector genes from a collection of 22 A. citrulli strains confirmed this hypothesis. Moreover, this analysis led to the identification of a third A. citrulli group, which was supported by DNA:DNA hybridization, DNA fingerprinting, multilocus sequence analysis of conserved genes, and virulence assays. The effector genes assessed in this study are homologous to effectors from other plant-pathogenic bacteria, mainly belonging to Xanthomonas spp. and Ralstonia solanacearum. Analyses of the effective number of codons and gas chromatography content of effector genes relative to a representative set of housekeeping genes support the idea that these effector genes were acquired by lateral gene transfer. Further investigation is required to identify new T3S effectors of A. citrulli and to determine their contribution to virulence and host preferential association.}, }
@article {pmid24847957, year = {2014}, author = {Dennehy, JJ}, title = {What ecologists can tell virologists.}, journal = {Annual review of microbiology}, volume = {68}, number = {}, pages = {117-135}, doi = {10.1146/annurev-micro-091313-103436}, pmid = {24847957}, issn = {1545-3251}, mesh = {Animals ; Biodiversity ; *Ecosystem ; Host-Pathogen Interactions ; Humans ; Virus Diseases/virology ; *Virus Physiological Phenomena ; Viruses/genetics ; }, abstract = {I pictured myself as a virus…and tried to sense what it would be like. --Jonas Salk. Ecology as a science evolved from natural history, the observational study of the interactions of plants and animals with each other and their environments. As natural history matured, it became increasingly quantitative, experimental, and taxonomically broad. Focus diversified beyond the Eukarya to include the hidden world of microbial life. Microbes, particularly viruses, were shown to exist in unfathomable numbers, affecting every living organism. Slowly viruses came to be viewed in an ecological context rather than as abstract, disease-causing agents. This shift is exemplified by an increasing tendency to refer to viruses as living organisms instead of inert particles. In recent years, researchers have recognized the critical contributions of viruses to fundamental ecological processes such as biogeochemical cycling, competition, community structuring, and horizontal gene transfer. This review describes virus ecology from a virus's perspective. If we are, like Jonas Salk, to imagine ourselves as a virus, what kind of world would we experience?}, }
@article {pmid24847883, year = {2014}, author = {Forsberg, KJ and Patel, S and Gibson, MK and Lauber, CL and Knight, R and Fierer, N and Dantas, G}, title = {Bacterial phylogeny structures soil resistomes across habitats.}, journal = {Nature}, volume = {509}, number = {7502}, pages = {612-616}, pmid = {24847883}, issn = {1476-4687}, support = {DP2 DK098089/DK/NIDDK NIH HHS/United States ; DP2-DK-098089/DK/NIDDK NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; GM 007067/GM/NIGMS NIH HHS/United States ; T32 HG000045/HG/NHGRI NIH HHS/United States ; T32 GM007067/GM/NIGMS NIH HHS/United States ; }, mesh = {Agriculture ; Anti-Bacterial Agents/pharmacology ; Bacteria/classification/drug effects/*genetics/*isolation &amp; purification ; Drug Resistance, Microbial/drug effects/*genetics ; *Ecosystem ; Fertilizers ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/drug effects/genetics ; Genome, Bacterial/drug effects/genetics ; Integrases/genetics ; Metagenome/drug effects/*genetics ; Metagenomics ; Models, Genetic ; Molecular Sequence Data ; Nitrogen/metabolism/pharmacology ; Open Reading Frames/genetics ; *Phylogeny ; Poaceae/growth &amp; development ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Synteny/genetics ; Transposases/genetics ; }, abstract = {Ancient and diverse antibiotic resistance genes (ARGs) have previously been identified from soil, including genes identical to those in human pathogens. Despite the apparent overlap between soil and clinical resistomes, factors influencing ARG composition in soil and their movement between genomes and habitats remain largely unknown. General metagenome functions often correlate with the underlying structure of bacterial communities. However, ARGs are proposed to be highly mobile, prompting speculation that resistomes may not correlate with phylogenetic signatures or ecological divisions. To investigate these relationships, we performed functional metagenomic selections for resistance to 18 antibiotics from 18 agricultural and grassland soils. The 2,895 ARGs we discovered were mostly new, and represent all major resistance mechanisms. We demonstrate that distinct soil types harbour distinct resistomes, and that the addition of nitrogen fertilizer strongly influenced soil ARG content. Resistome composition also correlated with microbial phylogenetic and taxonomic structure, both across and within soil types. Consistent with this strong correlation, mobility elements (genes responsible for horizontal gene transfer between bacteria such as transposases and integrases) syntenic with ARGs were rare in soil by comparison with sequenced pathogens, suggesting that ARGs may not transfer between soil bacteria as readily as is observed between human pathogens. Together, our results indicate that bacterial community composition is the primary determinant of soil ARG content, challenging previous hypotheses that horizontal gene transfer effectively decouples resistomes from phylogeny.}, }
@article {pmid24847673, year = {2015}, author = {Wright, O and Delmans, M and Stan, GB and Ellis, T}, title = {GeneGuard: A modular plasmid system designed for biosafety.}, journal = {ACS synthetic biology}, volume = {4}, number = {3}, pages = {307-316}, doi = {10.1021/sb500234s}, pmid = {24847673}, issn = {2161-5063}, support = {BB/J019720/1//Medical Research Council/United Kingdom ; //Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Biotechnology/methods/*standards ; Escherichia coli ; Genetic Vectors/*genetics ; Models, Genetic ; Molecular Biology/methods/*standards ; Plasmids/*genetics ; *Safety ; Synthetic Biology/methods/*standards ; }, abstract = {Synthetic biology applications in biosensing, bioremediation, and biomining envision the use of engineered microbes beyond a contained laboratory. Deployment of such microbes in the environment raises concerns of unchecked cellular proliferation or unwanted spread of synthetic genes. While antibiotic-resistant plasmids are the most utilized vectors for introducing synthetic genes into bacteria, they are also inherently insecure, acting naturally to propagate DNA from one cell to another. To introduce security into bacterial synthetic biology, we here took on the task of completely reformatting plasmids to be dependent on their intended host strain and inherently disadvantageous for others. Using conditional origins of replication, rich-media compatible auxotrophies, and toxin-antitoxin pairs we constructed a mutually dependent host-plasmid platform, called GeneGuard. In this, replication initiators for the R6K or ColE2-P9 origins are provided in trans by a specified host, whose essential thyA or dapA gene is translocated from a genomic to a plasmid location. This reciprocal arrangement is stable for at least 100 generations without antibiotic selection and is compatible for use in LB medium and soil. Toxin genes ζ or Kid are also employed in an auxiliary manner to make the vector disadvantageous for strains not expressing their antitoxins. These devices, in isolation and in concert, severely reduce unintentional plasmid propagation in E. coli and B. subtilis and do not disrupt the intended E. coli host's growth dynamics. Our GeneGuard system comprises several versions of modular cargo-ready vectors, along with their requisite genomic integration cassettes, and is demonstrated here as an efficient vector for heavy-metal biosensors.}, }
@article {pmid24845577, year = {2014}, author = {Kemen, E}, title = {Microbe-microbe interactions determine oomycete and fungal host colonization.}, journal = {Current opinion in plant biology}, volume = {20}, number = {}, pages = {75-81}, doi = {10.1016/j.pbi.2014.04.005}, pmid = {24845577}, issn = {1879-0356}, mesh = {Fungi/*physiology ; *Microbial Interactions ; Oomycetes/*physiology ; Plant Diseases/*microbiology ; Plants/*microbiology ; *Symbiosis ; }, abstract = {Microbial organisms sharing habitats aim for maximum fitness that they can only reach by collaboration. Developing stable networks within communities are crucial and can be achieved by exchanging common goods and genes that benefit the community. Only recently was it shown that horizontal gene transfer is not only common between prokaryotes but also into eukaryotic organisms such as fungi and oomycetes benefiting communal stability. Eukaryotic plant symbionts and pathogens coevolve with the plant microbiome and can acquire the ability to communicate or even collaborate, facilitating communal host colonization. Understanding communal infection will lead to a mechanistic understanding in how new hosts can be colonized under natural conditions and how we can counteract.}, }
@article {pmid24843024, year = {2014}, author = {Wybouw, N and Dermauw, W and Tirry, L and Stevens, C and Grbić, M and Feyereisen, R and Van Leeuwen, T}, title = {A gene horizontally transferred from bacteria protects arthropods from host plant cyanide poisoning.}, journal = {eLife}, volume = {3}, number = {}, pages = {e02365}, pmid = {24843024}, issn = {2050-084X}, mesh = {Alanine/analogs &amp; derivatives/metabolism ; Animals ; *Animals, Genetically Modified ; Bacteria/*genetics ; Cysteine Synthase/genetics/metabolism ; Gene Expression Profiling ; *Gene Transfer, Horizontal ; Glycosides/*metabolism ; Hydrogen Cyanide/toxicity ; Lyases/genetics/metabolism ; Phylogeny ; Tetranychidae/*genetics ; Transcription, Genetic ; }, abstract = {Cyanogenic glucosides are among the most widespread defense chemicals of plants. Upon plant tissue disruption, these glucosides are hydrolyzed to a reactive hydroxynitrile that releases toxic hydrogen cyanide (HCN). Yet many mite and lepidopteran species can thrive on plants defended by cyanogenic glucosides. The nature of the enzyme known to detoxify HCN to β-cyanoalanine in arthropods has remained enigmatic. Here we identify this enzyme by transcriptome analysis and functional expression. Phylogenetic analysis showed that the gene is a member of the cysteine synthase family horizontally transferred from bacteria to phytophagous mites and Lepidoptera. The recombinant mite enzyme had both β-cyanoalanine synthase and cysteine synthase activity but enzyme kinetics showed that cyanide detoxification activity was strongly favored. Our results therefore suggest that an ancient horizontal transfer of a gene originally involved in sulfur amino acid biosynthesis in bacteria was co-opted by herbivorous arthropods to detoxify plant produced cyanide.DOI: http://dx.doi.org/10.7554/eLife.02365.001.}, }
@article {pmid24841263, year = {2014}, author = {Händel, N and Schuurmans, JM and Feng, Y and Brul, S and ter Kuile, BH}, title = {Interaction between mutations and regulation of gene expression during development of de novo antibiotic resistance.}, journal = {Antimicrobial agents and chemotherapy}, volume = {58}, number = {8}, pages = {4371-4379}, pmid = {24841263}, issn = {1098-6596}, mesh = {Adaptation, Physiological ; Amoxicillin/pharmacology ; Anti-Bacterial Agents/*pharmacology ; Base Sequence ; Drug Resistance, Microbial/*drug effects/genetics ; Enrofloxacin ; Escherichia coli/*drug effects/genetics/metabolism ; Escherichia coli Proteins/*genetics/metabolism ; Fluoroquinolones/pharmacology ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial/*drug effects ; Membrane Transport Proteins/*genetics/metabolism ; Molecular Sequence Data ; Mutation ; SOS Response, Genetics/drug effects ; Sequence Analysis, DNA ; Tetracycline/pharmacology ; Time Factors ; }, abstract = {Bacteria can become resistant not only by horizontal gene transfer or other forms of exchange of genetic information but also by de novo by adaptation at the gene expression level and through DNA mutations. The interrelationship between changes in gene expression and DNA mutations during acquisition of resistance is not well documented. In addition, it is not known whether the DNA mutations leading to resistance always occur in the same order and whether the final result is always identical. The expression of >4,000 genes in Escherichia coli was compared upon adaptation to amoxicillin, tetracycline, and enrofloxacin. During adaptation, known resistance genes were sequenced for mutations that cause resistance. The order of mutations varied within two sets of strains adapted in parallel to amoxicillin and enrofloxacin, respectively, whereas the buildup of resistance was very similar. No specific mutations were related to the rather modest increase in tetracycline resistance. Ribosome-sensed induction and efflux pump activation initially protected the cell through induction of expression and allowed it to survive low levels of antibiotics. Subsequently, mutations were promoted by the stress-induced SOS response that stimulated modulation of genetic instability, and these mutations resulted in resistance to even higher antibiotic concentrations. The initial adaptation at the expression level enabled a subsequent trial and error search for the optimal mutations. The quantitative adjustment of cellular processes at different levels accelerated the acquisition of antibiotic resistance.}, }
@article {pmid24831027, year = {2014}, author = {Campanaro, S and Treu, L and Vendramin, V and Bovo, B and Giacomini, A and Corich, V}, title = {Metagenomic analysis of the microbial community in fermented grape marc reveals that Lactobacillus fabifermentans is one of the dominant species: insights into its genome structure.}, journal = {Applied microbiology and biotechnology}, volume = {98}, number = {13}, pages = {6015-6037}, doi = {10.1007/s00253-014-5795-3}, pmid = {24831027}, issn = {1432-0614}, mesh = {Alcoholic Beverages/*microbiology ; *Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genome, Bacterial ; Lactobacillus/*genetics/isolation &amp; purification ; Metagenomics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Vitis/microbiology ; }, abstract = {Grape marc used for the production of distilled beverages undergoes prolonged storage which allows alcoholic fermentation to occur. Harsh conditions including low pH, limited oxygen and nutrients, temperature fluctuations, and high ethanol concentrations imposed by that environment create a strong selective pressure on microorganisms. A detailed characterization of the bacterial community during two time points of the fermentation process was performed using high-throughput sequencing of the V3-V6 16S rDNA hypervariable regions. The results revealed a marked reduction in the number of bacterial species after 30 days of incubation and made it possible to identify those species that are able to grow in that extreme environment. The genome sequence of Lactobacillus fabifermentans, one of the dominant species identified, was then analyzed using shotgun sequencing and comparative genomics. The results revealed that it is one of the largest genomes among the Lactobacillus sequenced and is characterized by a large number of genes involved in carbohydrate utilization and in the regulation of gene expression. The genome was shaped through a large number of gene duplication events, while lateral gene transfer contributed to a lesser extent with respect to other Lactobacillus species. According to genomic analysis, its carbohydrate utilization pattern and ability to form biofilm are the main genetic traits linked to the adaptation the species underwent permitting it to grow in fermenting grape marc.}, }
@article {pmid24830763, year = {2014}, author = {Shao, Z and Zhang, P and Li, Q and Wang, X and Duan, D}, title = {Characterization of mannitol-2-dehydrogenase in Saccharina japonica: evidence for a new polyol-specific long-chain dehydrogenases/reductase.}, journal = {PloS one}, volume = {9}, number = {5}, pages = {e97935}, pmid = {24830763}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Catalytic Domain ; Fructose/chemistry ; Gene Expression Regulation, Enzymologic ; Hydrogen Peroxide/pharmacology ; Laminaria/*enzymology ; Mannitol Dehydrogenases/biosynthesis/chemistry/*genetics ; Models, Molecular ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Protein Structure, Secondary ; Salinity ; Structural Homology, Protein ; Substrate Specificity ; Transcription, Genetic ; }, abstract = {Mannitol plays a crucial role in brown algae, acting as carbon storage, organic osmolytes and antioxidant. Transcriptomic analysis of Saccharina japonica revealed that the relative genes involved in the mannitol cycle are existent. Full-length sequence of mannitol-2-dehydrogenase (M2DH) gene was obtained, with one open reading frame of 2,007 bp which encodes 668 amino acids. Cis-regulatory elements for response to methyl jasmonic acid, light and drought existed in the 5'-upstream region. Phylogenetic analysis indicated that SjM2DH has an ancient prokaryotic origin, and is probably acquired by horizontal gene transfer event. Multiple alignment and spatial structure prediction displayed a series of conserved functional residues, motifs and domains, which favored that SjM2DH belongs to the polyol-specific long-chain dehydrogenases/reductase (PSLDR) family. Expressional profiles of SjM2DH in the juvenile sporophytes showed that it was influenced by saline, oxidative and desiccative factors. SjM2DH was over-expressed in Escherichia coli, and the cell-free extracts with recombinant SjM2DH displayed high activity on D-fructose reduction reaction. The analysis on SjM2DH gene structure and biochemical parameters reached a consensus that activity of SjM2DH is NADH-dependent and metal ion-independent. The characterization of SjM2DH showed that M2DH is a new member of PSLDR family and play an important role in mannitol metabolism in S. japonica.}, }
@article {pmid24829449, year = {2014}, author = {Grilli, J and Romano, M and Bassetti, F and Cosentino Lagomarsino, M}, title = {Cross-species gene-family fluctuations reveal the dynamics of horizontal transfers.}, journal = {Nucleic acids research}, volume = {42}, number = {11}, pages = {6850-6860}, pmid = {24829449}, issn = {1362-4962}, mesh = {Evolution, Molecular ; Gene Duplication ; *Gene Transfer, Horizontal ; Models, Genetic ; *Multigene Family ; }, abstract = {Prokaryotes vary their protein repertoire mainly through horizontal transfer and gene loss. To elucidate the links between these processes and the cross-species gene-family statistics, we perform a large-scale data analysis of the cross-species variability of gene-family abundance (the number of members of the family found on a given genome). We find that abundance fluctuations are related to the rate of horizontal transfers. This is rationalized by a minimal theoretical model, which predicts this link. The families that are not captured by the model show abundance profiles that are markedly peaked around a mean value, possibly because of specific abundance selection. Based on these results, we define an abundance variability index that captures a family's evolutionary behavior (and thus some of its relevant functional properties) purely based on its cross-species abundance fluctuations. Analysis and model, combined, show a quantitative link between cross-species family abundance statistics and horizontal transfer dynamics, which can be used to analyze genome 'flux'. Groups of families with different values of the abundance variability index correspond to genome sub-parts having different plasticity in terms of the level of horizontal exchange allowed by natural selection.}, }
@article {pmid24829093, year = {2014}, author = {Nie, Y and Chi, CQ and Fang, H and Liang, JL and Lu, SL and Lai, GL and Tang, YQ and Wu, XL}, title = {Diverse alkane hydroxylase genes in microorganisms and environments.}, journal = {Scientific reports}, volume = {4}, number = {}, pages = {4968}, pmid = {24829093}, issn = {2045-2322}, support = {R01 AA021505/AA/NIAAA NIH HHS/United States ; }, mesh = {Alkanes/metabolism ; Cytochrome P-450 CYP4A/*genetics/metabolism ; Cytochrome P-450 Enzyme System/*genetics/metabolism ; DNA, Bacterial/*genetics ; Environment ; Fresh Water/microbiology ; Genome, Bacterial/*genetics ; Metagenome/genetics ; Phylogeny ; }, abstract = {AlkB and CYP153 are important alkane hydroxylases responsible for aerobic alkane degradation in bioremediation of oil-polluted environments and microbial enhanced oil recovery. Since their distribution in nature is not clear, we made the investigation among thus-far sequenced 3,979 microbial genomes and 137 metagenomes from terrestrial, freshwater, and marine environments. Hundreds of diverse alkB and CYP153 genes including many novel ones were found in bacterial genomes, whereas none were found in archaeal genomes. Moreover, these genes were detected with different distributional patterns in the terrestrial, freshwater, and marine metagenomes. Hints for horizontal gene transfer, gene duplication, and gene fusion were found, which together are likely responsible for diversifying the alkB and CYP153 genes adapt to the ubiquitous distribution of different alkanes in nature. In addition, different distributions of these genes between bacterial genomes and metagenomes suggested the potentially important roles of unknown or less common alkane degraders in nature.}, }
@article {pmid24824929, year = {2014}, author = {Hainova, K and Adamcikova, Z and Ciernikova, S and Stevurkova, V and Tyciakova, S and Zajac, V}, title = {Intestinal flora of FAP patients containing APC-like sequences.}, journal = {Neoplasma}, volume = {61}, number = {3}, pages = {283-290}, doi = {10.4149/neo_2014_036}, pmid = {24824929}, issn = {0028-2685}, mesh = {Adenomatous Polyposis Coli/genetics/*microbiology ; Bacteria/*genetics ; Base Sequence ; Gene Transfer, Horizontal ; Genes, APC/*physiology ; Germ-Line Mutation ; Humans ; Molecular Sequence Data ; Rectum/*microbiology ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {Colorectal cancer mortality is one of the most common cause of cancer-related mortality. A multiple risk factors are associated with colorectal cancer, including hereditary, enviromental and inflammatory syndromes affecting the gastrointestinal tract. Familial adenomatous polyposis (FAP) is characterized by the emergence of hundreds to thousands of colorectal adenomatous polyps and FAP syndrome is caused by mutations within the adenomatous polyposis coli (APC) tumor suppressor gene. We analyzed 21 rectal bacterial subclones isolated from FAP patient 41-1 with confirmed 5bp ACAAA deletion within codons 1060-1063 for the presence of APC-like sequences in longest exon 15. The studied section was defined by primers 15Efor-15Erev, what correlates with mutation cluster region (MCR) in which the 75% of all APC germline mutations were detected. More than 90% homology was showed by sequencing and subsequent software comparison. The expression of APC-like sequences was demostrated by Western blot analysis using monoclonal and polyclonal antibodies against APC protein. To study missing link between the DNA analysis (PCR, DNA sequencing) and protein expresion experiments (Western blotting) we analyzed bacterial transcripts containing the 15Efor-15Erev sequence of APC gene by reverse transcription-PCR, what indicated that an APC gene derived fragment may be produced. We observed 97-100 % homology after computer comparison of cDNA PCR products. Our results suggest that presence of APC-like sequences in intestinal/rectal bacteria is enrichment of bacterial genetic information in which horizontal gene transfer between humans and microflora play an important role.}, }
@article {pmid24824441, year = {2014}, author = {Lauro, FM and Eloe-Fadrosh, EA and Richter, TK and Vitulo, N and Ferriera, S and Johnson, JH and Bartlett, DH}, title = {Ecotype diversity and conversion in Photobacterium profundum strains.}, journal = {PloS one}, volume = {9}, number = {5}, pages = {e96953}, pmid = {24824441}, issn = {1932-6203}, mesh = {*Ecotype ; *Gene Expression Regulation, Bacterial ; *Genetic Variation ; *Genome, Bacterial ; Photobacterium/*genetics ; }, abstract = {Photobacterium profundum is a cosmopolitan marine bacterium capable of growth at low temperature and high hydrostatic pressure. Multiple strains of P. profundum have been isolated from different depths of the ocean and display remarkable differences in their physiological responses to pressure. The genome sequence of the deep-sea piezopsychrophilic strain Photobacterium profundum SS9 has provided some clues regarding the genetic features required for growth in the deep sea. The sequenced genome of Photobacterium profundum strain 3TCK, a non-piezophilic strain isolated from a shallow-water environment, is now available and its analysis expands the identification of unique genomic features that correlate to environmental differences and define the Hutchinsonian niche of each strain. These differences range from variations in gene content to specific gene sequences under positive selection. Genome plasticity between Photobacterium bathytypes was investigated when strain 3TCK-specific genes involved in photorepair were introduced to SS9, demonstrating that horizontal gene transfer can provide a mechanism for rapid colonisation of new environments.}, }
@article {pmid24821787, year = {2014}, author = {Zeng, Y and Feng, F and Medová, H and Dean, J and Koblížek, M}, title = {Functional type 2 photosynthetic reaction centers found in the rare bacterial phylum Gemmatimonadetes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {21}, pages = {7795-7800}, pmid = {24821787}, issn = {1091-6490}, mesh = {Bacteria/*cytology/*genetics/metabolism ; Base Sequence ; China ; Cluster Analysis ; Fluorometry ; Lakes/*microbiology ; Likelihood Functions ; Microscopy, Fluorescence ; Models, Genetic ; Molecular Sequence Data ; Photosystem II Protein Complex/*genetics/metabolism ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; Spectrum Analysis ; }, abstract = {Photosynthetic bacteria emerged on Earth more than 3 Gyr ago. To date, despite a long evolutionary history, species containing (bacterio)chlorophyll-based reaction centers have been reported in only 6 out of more than 30 formally described bacterial phyla: Cyanobacteria, Proteobacteria, Chlorobi, Chloroflexi, Firmicutes, and Acidobacteria. Here we describe a bacteriochlorophyll a-producing isolate AP64 that belongs to the poorly characterized phylum Gemmatimonadetes. This red-pigmented semiaerobic strain was isolated from a freshwater lake in the western Gobi Desert. It contains fully functional type 2 (pheophytin-quinone) photosynthetic reaction centers but does not assimilate inorganic carbon, suggesting that it performs a photoheterotrophic lifestyle. Full genome sequencing revealed the presence of a 42.3-kb-long photosynthesis gene cluster (PGC) in its genome. The organization and phylogeny of its photosynthesis genes suggests an ancient acquisition of PGC via horizontal transfer from purple phototrophic bacteria. The data presented here document that Gemmatimonadetes is the seventh bacterial phylum containing (bacterio)chlorophyll-based phototrophic species. To our knowledge, these data provide the first evidence that (bacterio)chlorophyll-based phototrophy can be transferred between distant bacterial phyla, providing new insights into the evolution of bacterial photosynthesis.}, }
@article {pmid24818695, year = {2014}, author = {Li, X and Ding, P and Han, C and Fan, H and Wang, Y and Mi, Z and Feng, F and Tong, Y}, title = {Genome analysis of Enterococcus faecalis bacteriophage IME-EF3 harboring a putative metallo-beta-lactamase gene.}, journal = {Virus genes}, volume = {49}, number = {1}, pages = {145-151}, pmid = {24818695}, issn = {1572-994X}, mesh = {Amino Acid Sequence ; Bacteriophages/enzymology/*genetics/isolation &amp; purification/ultrastructure ; DNA, Viral/*chemistry/*genetics ; Enterococcus faecalis/*virology ; *Genome, Viral ; Hospitals ; Microscopy, Electron, Transmission ; Molecular Sequence Data ; Sequence Alignment ; Sequence Analysis, DNA ; Sewage/virology ; Siphoviridae/enzymology/genetics/isolation &amp; purification/ultrastructure ; Virion/ultrastructure ; beta-Lactamases/*genetics ; }, abstract = {Lytic Enterococcus faecalis bacteriophage IME-EF3 was isolated from hospital sewage, and its genome was sequenced using high-throughput sequencing. Genomic analysis and electron microscopy suggested that IME-EF3 was a member of the family Siphoviridae. The phage has an isometric head and a long non-contractile tail with a 41 kb linear double-stranded DNA genome. The genome encodes 69 putative proteins, with 32 annotated functionally, including proteins related to phage structure, packaging, transcription, replication, and a lysis module. Interestingly, a metallo-beta-lactamase gene responsible for multi-drug resistance was found in the genome of IME-EF3. The possibility of horizontal gene transfer of the metallo-beta-lactamase gene suggests that phage IME-EF3, although lytic, might not be suitable for phage therapy unless one would devise a way to delete the metallo-beta-lactamase gene. Hence, whole genome sequencing should always be a prerequisite for identifying a phage therapy candidate.}, }
@article {pmid24818264, year = {2014}, author = {Dibrova, DV and Galperin, MY and Mulkidjanian, AY}, title = {Phylogenomic reconstruction of archaeal fatty acid metabolism.}, journal = {Environmental microbiology}, volume = {16}, number = {4}, pages = {907-918}, pmid = {24818264}, issn = {1462-2920}, support = {Z99 LM999999//Intramural NIH HHS/United States ; ZIA LM000073-14//Intramural NIH HHS/United States ; }, mesh = {3-Hydroxyacyl CoA Dehydrogenases/genetics/*metabolism ; Acyl-CoA Dehydrogenase/*metabolism ; Archaea/genetics/*metabolism ; Enoyl-CoA Hydratase/genetics/*metabolism ; Fatty Acids/*metabolism ; Gene Transfer, Horizontal ; Genomics ; Multienzyme Complexes/metabolism ; Oxidation-Reduction ; Phylogeny ; }, abstract = {While certain archaea appear to synthesize and/or metabolize fatty acids, the respective pathways still remain obscure. By analysing the genomic distribution of the key lipid-related enzymes, we were able to identify the likely components of the archaeal pathway of fatty acid metabolism, namely, a combination of the enzymes of bacterial-type β-oxidation of fatty acids [acyl-coenzyme A (CoA) dehydrogenase, enoyl-CoA hydratase and 3-hydroxyacyl-CoA dehydrogenase] with paralogs of the archaeal acetyl-CoA C-acetyltransferase, an enzyme of the mevalonate biosynthesis pathway. These three β-oxidation enzymes working in the reverse direction could potentially catalyse biosynthesis of fatty acids, with paralogs of acetyl-CoA C-acetyltransferase performing addition of C2 fragments. The presence in archaea of the genes for energy-transducing membrane enzyme complexes, such as cytochrome bc complex, cytochrome c oxidase and diverse rhodopsins, was found to correlate with the presence of the proposed system of fatty acid biosynthesis. We speculate that because these membrane complexes functionally depend on fatty acid chains, their genes could have been acquired via lateral gene transfer from bacteria only by those archaea that already possessed a system of fatty acid biosynthesis. The proposed pathway of archaeal fatty acid metabolism operates in extreme conditions and therefore might be of interest in the context of biofuel production and other industrial applications.}, }
@article {pmid24818127, year = {2014}, author = {Cerezer, VG and Bando, SY and Pasternak, J and Franzolin, MR and Moreira-Filho, CA}, title = {Phylogenetic analysis of Stenotrophomonas spp. isolates contributes to the identification of nosocomial and community-acquired infections.}, journal = {BioMed research international}, volume = {2014}, number = {}, pages = {151405}, pmid = {24818127}, issn = {2314-6141}, mesh = {Community-Acquired Infections/*microbiology ; Cross Infection/*microbiology ; Drug Resistance, Bacterial ; Environmental Microbiology ; Genetic Variation ; Humans ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Nucleotides/genetics ; *Phylogeny ; Stenotrophomonas/*classification/genetics/*isolation &amp; purification ; }, abstract = {Stenotrophomonas ssp. has a wide environmental distribution and is also found as an opportunistic pathogen, causing nosocomial or community-acquired infections. One species, S. maltophilia, presents multidrug resistance and has been associated with serious infections in pediatric and immunocompromised patients. Therefore, it is relevant to conduct resistance profile and phylogenetic studies in clinical isolates for identifying infection origins and isolates with augmented pathogenic potential. Here, multilocus sequence typing was performed for phylogenetic analysis of nosocomial isolates of Stenotrophomonas spp. and, environmental and clinical strains of S. maltophilia. Biochemical and multidrug resistance profiles of nosocomial and clinical strains were determined. The inferred phylogenetic profile showed high clonal variability, what correlates with the adaptability process of Stenotrophomonas to different habitats. Two clinical isolates subgroups of S. maltophilia sharing high phylogenetic homogeneity presented intergroup recombination, thus indicating the high permittivity to horizontal gene transfer, a mechanism involved in the acquisition of antibiotic resistance and expression of virulence factors. For most of the clinical strains, phylogenetic inference was made using only partial ppsA gene sequence. Therefore, the sequencing of just one specific fragment of this gene would allow, in many cases, determining whether the infection with S. maltophilia was nosocomial or community-acquired.}, }
@article {pmid24814286, year = {2014}, author = {Sharma, A and Presting, GG}, title = {Evolution of centromeric retrotransposons in grasses.}, journal = {Genome biology and evolution}, volume = {6}, number = {6}, pages = {1335-1352}, pmid = {24814286}, issn = {1759-6653}, mesh = {Centromere/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Plant ; Oryza/genetics ; Phylogeny ; Poaceae/*genetics ; *Retroelements ; Sorghum/genetics ; Terminal Repeat Sequences ; Zea mays/genetics ; }, abstract = {Centromeric retrotransposons (CRs) constitute a family of plant retroelements, some of which have the ability to target their insertion almost exclusively to the functional centromeres. Our exhaustive analysis of CR family members in four grass genomes revealed not only horizontal transfer (HT) of CR elements between the oryzoid and panicoid grass lineages but also their subsequent recombination with endogenous elements that in some cases created prolific recombinants in foxtail millet and sorghum. HT events are easily identifiable only in cases where host genome divergence significantly predates HT, thus documented HT events likely represent only a fraction of the total. If the more difficult to detect ancient HT events occurred at frequencies similar to those observable in present day grasses, the extant long terminal repeat retrotransposons represent the mosaic products of HT and recombination that are optimized for retrotransposition in their host genomes. This complicates not only phylogenetic analysis but also the establishment of a meaningful retrotransposon nomenclature, which we have nevertheless attempted to implement here. In contrast to the plant-centric naming convention used currently for CR elements, we classify elements primarily based on their phylogenetic relationships regardless of host plant, using the exhaustively studied maize elements assigned to six different subfamilies as a standard. The CR2 subfamily is the most widely distributed of the six CR subfamilies discovered in grass genomes to date and thus the most likely to play a functional role at grass centromeres.}, }
@article {pmid24813762, year = {2014}, author = {Rivas, AJ and Labella, AM and Borrego, JJ and Lemos, ML and Osorio, CR}, title = {Evidence for horizontal gene transfer, gene duplication and genetic variation as driving forces of the diversity of haemolytic phenotypes in Photobacterium damselae subsp. damselae.}, journal = {FEMS microbiology letters}, volume = {355}, number = {2}, pages = {152-162}, doi = {10.1111/1574-6968.12464}, pmid = {24813762}, issn = {1574-6968}, mesh = {Chromosomes, Bacterial/genetics ; DNA, Bacterial/genetics ; *Gene Duplication ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genetic Variation ; Hemolysin Proteins/genetics ; Phenotype ; Photobacterium/classification/*genetics ; Phylogeny ; Plasmids/genetics ; Sequence Analysis, DNA ; }, abstract = {Photobacterium damselae subsp. damselae, a marine bacterium that causes infections in marine animals and in humans, produces up to three different haemolysins involved in virulence, which include the pPHDD1 plasmid-encoded damselysin (Dly) and HlyApl , and the chromosome-encoded HlyAch . We screened 45 isolates from different origins, and found a correlation between their haemolytic phenotypes and the differential haemolysin gene content. All highly and medium haemolytic strains harboured pPHDD1, with amino acid substitutions in HlyApl and HlyAch being the cause of the medium haemolytic phenotypes in some pPHDD1-harbouring strains. Weakly haemolytic strains contained only hlyAch , whereas nonhaemolytic isolates, in addition to lacking pPHDD1, either lacked hlyAch or contained a hlyAch pseudogene. Sequence analysis of the genomic context of hlyAch uncovered an unexpected genetic diversity, suggesting that hlyAch is located in an unstable chromosomal region. Phylogenetic analysis suggested that hlyApl and hlyAch originated by gene duplication within P. damselae subsp. damselae following acquisition by horizontal transfer. These observations together with the differential distribution of pPHDD1 plasmid among strains suggest that horizontal gene transfer has played a main role in shaping the haemolysin gene baggage in this pathogen.}, }
@article {pmid24812591, year = {2014}, author = {Hou, Q and He, J and Yu, J and Ye, Y and Zhou, D and Sun, Y and Zhang, D and Ma, L and Shen, B and Zhu, C}, title = {A case of horizontal gene transfer from Wolbachia to Aedes albopictus C6/36 cell line.}, journal = {Mobile genetic elements}, volume = {4}, number = {1}, pages = {e28914}, pmid = {24812591}, issn = {2159-2543}, support = {R01 AI075746/AI/NIAID NIH HHS/United States ; }, abstract = {Horizontal gene transfer plays an essential role in evolution and ecological adaptation, yet this phenomenon has remained controversial, particularly where it occurs between prokaryotes and eukaryotes. There are a handful of reported examples of horizontal gene transfer occurring between prokaryotes and eukaryotes in the literature, with most of these documented cases pertaining to invertebrates and endosymbionts. However, the vast majority of these horizontally transferred genes were either eventually excluded or rapidly became nonfunctional in the recipient genome. In this study, we report the discovery of a horizontal gene transfer from the endosymbiont Wolbachia in the C6/36 cell line derived from the mosquito Aedes albopictus. Moreover, we report that this horizontally transferred gene displayed high transcription level. This finding and the results of further experimentation strongly suggest this gene is functional and has been expressed and translated into a protein in the mosquito host cells.}, }
@article {pmid24811122, year = {2014}, author = {Atsmon-Raz, Y and Tannenbaum, ED}, title = {Repression/depression of conjugative plasmids and their influence on the mutation-selection balance in static environments.}, journal = {PloS one}, volume = {9}, number = {5}, pages = {e96839}, pmid = {24811122}, issn = {1932-6203}, mesh = {*Environment ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Models, Genetic ; *Mutation ; Plasmids/*genetics ; *Selection, Genetic ; }, abstract = {We study the effect that conjugation-mediated Horizontal Gene Transfer (HGT) has on the mutation-selection balance of a population in a static environment. We consider a model whereby a population of unicellular organisms, capable of conjugation, comes to mutation-selection balance in the presence of an antibiotic, which induces a first-order death rate constant [Formula: see text] for genomes that are not resistant. We explicitly take into consideration the repression/de-repression dynamics of the conjugative plasmid, and assume that a de-repressed plasmid remains temporarily de-repressed after copying itself into another cell. We assume that both repression and de-repression are characterized by first-order rate constants [Formula: see text]and [Formula: see text], respectively. We find that conjugation has a deleterious effect on the mean fitness of the population, suggesting that HGT does not provide a selective advantage in a static environment, but is rather only useful for adapting to new environments. This effect can be ameliorated by repression, suggesting that while HGT is not necessarily advantageous for a population in a static environment, its deleterious effect on the mean fitness can be negated via repression. Therefore, it is likely that HGT is much more advantageous in a dynamic landscape. Furthermore, in the limiting case of a vanishing spontaneous de-repression rate constant, we find that the fraction of conjugators in the population undergoes a phase transition as a function of population density. Below a critical population density, the fraction of conjugators is zero, while above this critical population density the fraction of conjugators rises continuously to one. Our model for conjugation-mediated HGT is related to models of infectious disease dynamics, where the conjugators play the role of the infected (I) class, and the non-conjugators play the role of the susceptible (S) class.}, }
@article {pmid24809820, year = {2014}, author = {Grosjean, H and Breton, M and Sirand-Pugnet, P and Tardy, F and Thiaucourt, F and Citti, C and Barré, A and Yoshizawa, S and Fourmy, D and de Crécy-Lagard, V and Blanchard, A}, title = {Predicting the minimal translation apparatus: lessons from the reductive evolution of mollicutes.}, journal = {PLoS genetics}, volume = {10}, number = {5}, pages = {e1004363}, pmid = {24809820}, issn = {1553-7404}, mesh = {*Biological Evolution ; Genes, Bacterial ; *Protein Biosynthesis ; Tenericutes/*genetics ; }, abstract = {Mollicutes is a class of parasitic bacteria that have evolved from a common Firmicutes ancestor mostly by massive genome reduction. With genomes under 1 Mbp in size, most Mollicutes species retain the capacity to replicate and grow autonomously. The major goal of this work was to identify the minimal set of proteins that can sustain ribosome biogenesis and translation of the genetic code in these bacteria. Using the experimentally validated genes from the model bacteria Escherichia coli and Bacillus subtilis as input, genes encoding proteins of the core translation machinery were predicted in 39 distinct Mollicutes species, 33 of which are culturable. The set of 260 input genes encodes proteins involved in ribosome biogenesis, tRNA maturation and aminoacylation, as well as proteins cofactors required for mRNA translation and RNA decay. A core set of 104 of these proteins is found in all species analyzed. Genes encoding proteins involved in post-translational modifications of ribosomal proteins and translation cofactors, post-transcriptional modifications of t+rRNA, in ribosome assembly and RNA degradation are the most frequently lost. As expected, genes coding for aminoacyl-tRNA synthetases, ribosomal proteins and initiation, elongation and termination factors are the most persistent (i.e. conserved in a majority of genomes). Enzymes introducing nucleotides modifications in the anticodon loop of tRNA, in helix 44 of 16S rRNA and in helices 69 and 80 of 23S rRNA, all essential for decoding and facilitating peptidyl transfer, are maintained in all species. Reconstruction of genome evolution in Mollicutes revealed that, beside many gene losses, occasional gains by horizontal gene transfer also occurred. This analysis not only showed that slightly different solutions for preserving a functional, albeit minimal, protein synthetizing machinery have emerged in these successive rounds of reductive evolution but also has broad implications in guiding the reconstruction of a minimal cell by synthetic biology approaches.}, }
@article {pmid24809511, year = {2014}, author = {Pombert, JF and Blouin, NA and Lane, C and Boucias, D and Keeling, PJ}, title = {A lack of parasitic reduction in the obligate parasitic green alga Helicosporidium.}, journal = {PLoS genetics}, volume = {10}, number = {5}, pages = {e1004355}, pmid = {24809511}, issn = {1553-7404}, support = {MOP-42517//Canadian Institutes of Health Research/Canada ; }, mesh = {Chitinases/genetics ; Chlorophyta/enzymology/genetics/*virology ; Gene Transfer, Horizontal ; Genome, Plant ; Plant Viruses/classification ; }, abstract = {The evolution of an obligate parasitic lifestyle is often associated with genomic reduction, in particular with the loss of functions associated with increasing host-dependence. This is evident in many parasites, but perhaps the most extreme transitions are from free-living autotrophic algae to obligate parasites. The best-known examples of this are the apicomplexans such as Plasmodium, which evolved from algae with red secondary plastids. However, an analogous transition also took place independently in the Helicosporidia, where an obligate parasite of animals with an intracellular infection mechanism evolved from algae with green primary plastids. We characterised the nuclear genome of Helicosporidium to compare its transition to parasitism with that of apicomplexans. The Helicosporidium genome is small and compact, even by comparison with the relatively small genomes of the closely related green algae Chlorella and Coccomyxa, but at the functional level we find almost no evidence for reduction. Nearly all ancestral metabolic functions are retained, with the single major exception of photosynthesis, and even here reduction is not complete. The great majority of genes for light-harvesting complexes, photosystems, and pigment biosynthesis have been lost, but those for other photosynthesis-related functions, such as Calvin cycle, are retained. Rather than loss of whole function categories, the predominant reductive force in the Helicosporidium genome is a contraction of gene family complexity, but even here most losses affect families associated with genome maintenance and expression, not functions associated with host-dependence. Other gene families appear to have expanded in response to parasitism, in particular chitinases, including those predicted to digest the chitinous barriers of the insect host or remodel the cell wall of Helicosporidium. Overall, the Helicosporidium genome presents a fascinating picture of the early stages of a transition from free-living autotroph to parasitic heterotroph where host-independence has been unexpectedly preserved.}, }
@article {pmid24809444, year = {2014}, author = {Reyes-Prieto, A and Barquera, B and Juárez, O}, title = {Origin and evolution of the sodium -pumping NADH: ubiquinone oxidoreductase.}, journal = {PloS one}, volume = {9}, number = {5}, pages = {e96696}, pmid = {24809444}, issn = {1932-6203}, mesh = {Bacteria/enzymology/genetics ; Electron Transport Complex I/genetics/*metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Operon/genetics ; Phylogeny ; Sodium-Potassium-Exchanging ATPase/*metabolism ; }, abstract = {The sodium -pumping NADH: ubiquinone oxidoreductase (Na+-NQR) is the main ion pump and the primary entry site for electrons into the respiratory chain of many different types of pathogenic bacteria. This enzymatic complex creates a transmembrane gradient of sodium that is used by the cell to sustain ionic homeostasis, nutrient transport, ATP synthesis, flagellum rotation and other essential processes. Comparative genomics data demonstrate that the nqr operon, which encodes all Na+-NQR subunits, is found in a large variety of bacterial lineages with different habitats and metabolic strategies. Here we studied the distribution, origin and evolution of this enzymatic complex. The molecular phylogenetic analyses and the organizations of the nqr operon indicate that Na+-NQR evolved within the Chlorobi/Bacteroidetes group, after the duplication and subsequent neofunctionalization of the operon that encodes the homolog RNF complex. Subsequently, the nqr operon dispersed through multiple horizontal transfer events to other bacterial lineages such as Chlamydiae, Planctomyces and α, β, γ and δ -proteobacteria. Considering the biochemical properties of the Na+-NQR complex and its physiological role in different bacteria, we propose a detailed scenario to explain the molecular mechanisms that gave rise to its novel redox- dependent sodium -pumping activity. Our model postulates that the evolution of the Na+-NQR complex involved a functional divergence from its RNF homolog, following the duplication of the rnf operon, the loss of the rnfB gene and the recruitment of the reductase subunit of an aromatic monooxygenase.}, }
@article {pmid24809232, year = {2014}, author = {Zhu, Y and Yi, Y and Liu, F and Lv, N and Yang, X and Li, J and Hu, Y and Zhu, B}, title = {Distribution and molecular profiling of class 1 integrons in MDR Acinetobacter baumannii isolates and whole genome-based analysis of antibiotic resistance mechanisms in a representative strain.}, journal = {Microbiological research}, volume = {169}, number = {11}, pages = {811-816}, doi = {10.1016/j.micres.2014.04.002}, pmid = {24809232}, issn = {1618-0623}, mesh = {Acinetobacter Infections/microbiology ; Acinetobacter baumannii/drug effects/*genetics/isolation &amp; purification ; Anti-Bacterial Agents/*pharmacology ; Cross Infection/microbiology ; *Drug Resistance, Bacterial ; Genome, Bacterial ; *Integrons ; Microbial Sensitivity Tests ; }, abstract = {The class 1 integron is an important driver of the nosocomial dissemination of multidrug-resistant (MDR) bacteria, such as Acinetobacters. In this study, we characterized the gene cassette arrays of class 1 integrons in Acinetobacter baumannii, where the detailed structure of these integrons for 38 clinical strains was analyzed. The results showed that there are three types of gene cassette arrays that are carried by different class 1 integrons, among them the aac(6')-IId-catB8-aadA1 array was the most prevalent. For detailed analysis of the integron structure, whole genome sequencing was carried out on strain AB16, and it was found that a single integron on its chromosome has a partial Tn21 transposon in its 5' flanking region and two complete copies of the insertion element IS26 in both the 5' and 3' flanking regions, indicating that the integron could be acquired by horizontal gene transfer. Furthermore, there is one resistance island AbaR22, one bla gene containing a transposon, four intrinsic resistant genes and one efflux pump that together confer six types of antibiotic resistance.}, }
@article {pmid24809026, year = {2014}, author = {Koraimann, G and Wagner, MA}, title = {Social behavior and decision making in bacterial conjugation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {4}, number = {}, pages = {54}, pmid = {24809026}, issn = {2235-2988}, mesh = {*Bacterial Physiological Phenomena ; Biofilms ; Biological Evolution ; *Conjugation, Genetic ; DNA Transposable Elements ; DNA, Bacterial ; DNA, Single-Stranded ; Gene Transfer, Horizontal ; Gram-Negative Bacteria/physiology ; Gram-Positive Bacteria/physiology ; Host-Pathogen Interactions ; Plasmids/genetics ; Quorum Sensing/*physiology ; }, abstract = {Bacteria frequently acquire novel genes by horizontal gene transfer (HGT). HGT through the process of bacterial conjugation is highly efficient and depends on the presence of conjugative plasmids (CPs) or integrated conjugative elements (ICEs) that provide the necessary genes for DNA transmission. This review focuses on recent advancements in our understanding of ssDNA transfer systems and regulatory networks ensuring timely and spatially controlled DNA transfer (tra) gene expression. As will become obvious by comparing different systems, by default, tra genes are shut off in cells in which conjugative elements are present. Only when conditions are optimal, donor cells-through epigenetic alleviation of negatively acting roadblocks and direct stimulation of DNA transfer genes-become transfer competent. These transfer competent cells have developmentally transformed into specialized cells capable of secreting ssDNA via a T4S (type IV secretion) complex directly into recipient cells. Intriguingly, even under optimal conditions, only a fraction of the population undergoes this transition, a finding that indicates specialization and cooperative, social behavior. Thereby, at the population level, the metabolic burden and other negative consequences of tra gene expression are greatly reduced without compromising the ability to horizontally transfer genes to novel bacterial hosts. This undoubtedly intelligent strategy may explain why conjugative elements-CPs and ICEs-have been successfully kept in and evolved with bacteria to constitute a major driving force of bacterial evolution.}, }
@article {pmid24807742, year = {2014}, author = {Zhang, M and Pereira e Silva, Mde C and Chaib De Mares, M and van Elsas, JD}, title = {The mycosphere constitutes an arena for horizontal gene transfer with strong evolutionary implications for bacterial-fungal interactions.}, journal = {FEMS microbiology ecology}, volume = {89}, number = {3}, pages = {516-526}, doi = {10.1111/1574-6941.12350}, pmid = {24807742}, issn = {1574-6941}, mesh = {Bacteria/*genetics ; *Evolution, Molecular ; Fungi/*genetics ; *Gene Transfer, Horizontal ; Microbial Interactions/genetics ; Plasmids/genetics ; *Soil Microbiology ; }, abstract = {In the microhabitat that surrounds fungal hyphae in soil, coined the mycosphere, carbonaceous compounds that are released from the hyphae stimulate the growth of heterotrophic bacteria, and thus activate organism-to-organism contacts through genetic interactions. Therefore, the mycosphere is postulated to constitute a gene transfer arena, in which a plethora of genes, including locally adaptive ones, are swapped across the resident microbial communities. Such genetic transfers may have plasmids, in particular ones with broad host ranges, as the basis. Indeed, evidence is increasing for the contention that plasmids play crucial roles as accelerators of evolution in the mycosphere, serving as a horizontal gene pool and, therefore, providing competence factors to local bacteria as well as fungi. The evidence so far points at mycosphere roles for two major plasmid classes, the IncP-1 and PromA groups. Moreover, recent data indicate that bacterium-to-fungus gene transfers are detectable and have been evolutionarily important. The large gene pool present in the mycosphere, coupled with the chances for cell-to-cell contact between mycosphere dwellers allows enhanced recombination frequencies, and as such, organisms are selected locally for enhanced fitness.}, }
@article {pmid24803571, year = {2014}, author = {Epstein, B and Sadowsky, MJ and Tiffin, P}, title = {Selection on horizontally transferred and duplicated genes in sinorhizobium (ensifer), the root-nodule symbionts of medicago.}, journal = {Genome biology and evolution}, volume = {6}, number = {5}, pages = {1199-1209}, pmid = {24803571}, issn = {1759-6653}, mesh = {Gene Frequency ; *Gene Transfer, Horizontal ; *Genes, Duplicate ; Genetic Fitness ; Genetic Variation ; Genome, Bacterial ; Medicago/*microbiology ; Polymorphism, Single Nucleotide ; Root Nodules, Plant/*microbiology ; *Selection, Genetic ; Sinorhizobium meliloti/*genetics ; Symbiosis/genetics ; }, abstract = {Structural variation, including variation in gene copy number and presence or absence of genes, is a widespread and important source of genomic variation. We used whole-genome DNA sequences from 48 strains of Sinorhizobium (recently renamed Ensifer), including 20 strains of Sinorhizobium meliloti and 12 strains of S. medicae that were the focus of the analyses, to study the fitness effects of new structural variants created by duplication and horizontal gene transfer. We find that derived duplicated and horizontally transferred (HT) genes segregate at lower frequency than synonymous and nonsynonymous nucleotide variants in S. meliloti and S. medicae. Furthermore, the relative frequencies of different types of variants are more similar in S. medicae than in S. meliloti, the species with the larger effective population size. These results are consistent with the hypothesis that most duplications and HT genes have deleterious effects. Diversity of duplications, as measured by segregating duplicated genes per gene, is greater than nucleotide diversity, consistent with a high rate of duplication. Our results suggest that the vast majority of structural variants found among closely related bacterial strains are short-lived and unlikely to be involved in species-wide adaptation.}, }
@article {pmid24800245, year = {2014}, author = {Rusin, LY and Lyubetskaya, EV and Gorbunov, KY and Lyubetsky, VA}, title = {Reconciliation of gene and species trees.}, journal = {BioMed research international}, volume = {2014}, number = {}, pages = {642089}, pmid = {24800245}, issn = {2314-6141}, mesh = {*Algorithms ; Computational Biology/*methods ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Models, Genetic ; Mutation ; *Phylogeny ; }, abstract = {The first part of the paper briefly overviews the problem of gene and species trees reconciliation with the focus on defining and algorithmic construction of the evolutionary scenario. Basic ideas are discussed for the aspects of mapping definitions, costs of the mapping and evolutionary scenario, imposing time scales on a scenario, incorporating horizontal gene transfers, binarization and reconciliation of polytomous trees, and construction of species trees and scenarios. The review does not intend to cover the vast diversity of literature published on these subjects. Instead, the authors strived to overview the problem of the evolutionary scenario as a central concept in many areas of evolutionary research. The second part provides detailed mathematical proofs for the solutions of two problems: (i) inferring a gene evolution along a species tree accounting for various types of evolutionary events and (ii) trees reconciliation into a single species tree when only gene duplications and losses are allowed. All proposed algorithms have a cubic time complexity and are mathematically proved to find exact solutions. Solving algorithms for problem (ii) can be naturally extended to incorporate horizontal transfers, other evolutionary events, and time scales on the species tree.}, }
@article {pmid24799672, year = {2014}, author = {Tal, A and Arbel-Goren, R and Costantino, N and Court, DL and Stavans, J}, title = {Location of the unique integration site on an Escherichia coli chromosome by bacteriophage lambda DNA in vivo.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {20}, pages = {7308-7312}, pmid = {24799672}, issn = {1091-6490}, support = {//Intramural NIH HHS/United States ; }, mesh = {Bacteriophage lambda/*genetics ; Binding Sites ; Chromosome Mapping ; Chromosomes, Bacterial/*ultrastructure ; DNA, Viral/*genetics ; Diffusion ; Escherichia coli/metabolism/*virology ; Genome, Viral ; Luminescent Proteins/metabolism ; Lysogeny ; Recombination, Genetic ; Viral Proteins/genetics ; Virus Integration ; Red Fluorescent Protein ; }, abstract = {The search for specific sequences on long genomes is a key process in many biological contexts. How can specific target sequences be located with high efficiency, within physiologically relevant times? We addressed this question for viral integration, a fundamental mechanism of horizontal gene transfer driving prokaryotic evolution, using the infection of Escherichia coli bacteria with bacteriophage λ and following the establishment of a lysogenic state. Following the targeting process in individual live E. coli cells in real time revealed that λ DNA remains confined near the entry point of a cell following infection. The encounter between the 15-bp-long target sequence on the chromosome and the recombination site on the viral genome is facilitated by the directed motion of bacterial DNA generated during chromosome replication, in conjunction with constrained diffusion of phage DNA. Moving the native bacterial integration site to different locations on the genome and measuring the integration frequency in these strains reveals that the frequencies of the native site and a site symmetric to it relative to the origin are similar, whereas both are significantly higher than when the integration site is moved near the terminus, consistent with the replication-driven mechanism we propose. This novel search mechanism is yet another example of the exquisite coevolution of λ with its host.}, }
@article {pmid24797710, year = {2014}, author = {Krause, S and van Bodegom, PM and Cornwell, WK and Bodelier, PL}, title = {Weak phylogenetic signal in physiological traits of methane-oxidizing bacteria.}, journal = {Journal of evolutionary biology}, volume = {27}, number = {6}, pages = {1240-1247}, doi = {10.1111/jeb.12401}, pmid = {24797710}, issn = {1420-9101}, mesh = {Genetic Markers ; Methylococcaceae/*genetics/physiology ; *Phylogeny ; Temperature ; }, abstract = {The presence of phylogenetic signal is assumed to be ubiquitous. However, for microorganisms, this may not be true given that they display high physiological flexibility and have fast regeneration. This may result in fundamentally different patterns of resemblance, that is, in variable strength of phylogenetic signal. However, in microbiological inferences, trait similarities and therewith microbial interactions with its environment are mostly assumed to follow evolutionary relatedness. Here, we tested whether indeed a straightforward relationship between relatedness and physiological traits exists for aerobic methane-oxidizing bacteria (MOB). We generated a comprehensive data set that included 30 MOB strains with quantitative physiological trait information. Phylogenetic trees were built from the 16S rRNA gene, a common phylogenetic marker, and the pmoA gene which encodes a subunit of the key enzyme involved in the first step of methane oxidation. We used a Blomberg's K from comparative biology to quantify the strength of phylogenetic signal of physiological traits. Phylogenetic signal was strongest for physiological traits associated with optimal growth pH and temperature indicating that adaptations to habitat are very strongly conserved in MOB. However, those physiological traits that are associated with kinetics of methane oxidation had only weak phylogenetic signals and were more pronounced with the pmoA than with the 16S rRNA gene phylogeny. In conclusion, our results give evidence that approaches based solely on taxonomical information will not yield further advancement on microbial eco-evolutionary interactions with its environment. This is a novel insight on the connection between function and phylogeny within microbes and adds new understanding on the evolution of physiological traits across microbes, plants and animals.}, }
@article {pmid24797064, year = {2014}, author = {Amos, GC and Hawkey, PM and Gaze, WH and Wellington, EM}, title = {Waste water effluent contributes to the dissemination of CTX-M-15 in the natural environment.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {69}, number = {7}, pages = {1785-1791}, pmid = {24797064}, issn = {1460-2091}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacterial Load ; Conjugation, Genetic ; DNA, Bacterial/genetics ; Enterobacteriaceae/*enzymology/genetics/*isolation &amp; purification ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Plasmids/analysis/classification ; Polymerase Chain Reaction ; Rivers ; Sequence Analysis, DNA ; Sewage/*microbiology ; United Kingdom ; Wastewater/*microbiology ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: Multidrug-resistant Enterobacteriaceae pose a significant threat to public health. We aimed to study the impact of sewage treatment effluent on antibiotic resistance reservoirs in a river.<br><br>METHODS: River sediment samples were taken from downstream and upstream of a waste water treatment plant (WWTP) in 2009 and 2011. Third-generation cephalosporin (3GC)-resistant Enterobacteriaceae were enumerated. PCR-based techniques were used to elucidate mechanisms of resistance, with a new two-step PCR-based assay developed to investigate bla(CTX-M-15) mobilization. Conjugation experiments and incompatibility replicon typing were used to investigate plasmid ecology.<br><br>RESULTS: We report the first examples of bla(CTX-M-15) in UK river sediment; the prevalence of bla(CTX-M-15) was dramatically increased downstream of the WWTP. Ten novel genetic contexts for this gene were identified, carried in pathogens such as Escherichia coli ST131 as well as indigenous aquatic bacteria such as Aeromonas media. The bla(CTX-M-15) -gene was readily transferable to other Gram-negative bacteria. We also report the first finding of an imipenem-resistant E. coli in a UK river.<br><br>CONCLUSIONS: The high diversity and host range of novel genetic contexts proves that evolution of novel combinations of resistance genes is occurring at high frequency and has to date been significantly underestimated. We have identified a worrying reservoir of highly resistant enteric bacteria in the environment that poses a threat to human and animal health.}, }
@article {pmid24793903, year = {2014}, author = {Wendlandt, S and Li, J and Ho, J and Porta, MA and Feßler, AT and Wang, Y and Kadlec, K and Monecke, S and Ehricht, R and Boost, M and Schwarz, S}, title = {Enterococcal multiresistance gene cluster in methicillin-resistant Staphylococcus aureus from various origins and geographical locations.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {69}, number = {9}, pages = {2573-2575}, doi = {10.1093/jac/dku137}, pmid = {24793903}, issn = {1460-2091}, mesh = {Animals ; *Drug Resistance, Multiple, Bacterial ; Enterococcus/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genotype ; Humans ; Methicillin-Resistant Staphylococcus aureus/*drug effects/*genetics/isolation &amp; purification ; *Multigene Family ; Staphylococcal Infections/*microbiology/*veterinary ; }, }
@article {pmid24793159, year = {2014}, author = {Yu, D and Pi, B and Yu, M and Wang, Y and Ruan, Z and Feng, Y and Yu, Y}, title = {Diversity and evolution of oligopeptide permease systems in staphylococcal species.}, journal = {Genomics}, volume = {104}, number = {1}, pages = {8-13}, doi = {10.1016/j.ygeno.2014.04.003}, pmid = {24793159}, issn = {1089-8646}, mesh = {Bacterial Proteins/*genetics ; Coagulase/genetics ; *Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; Genetic Speciation ; Genome, Bacterial ; Hydrolases/genetics ; Interspersed Repetitive Sequences ; Membrane Transport Proteins/*genetics ; Operon ; Phylogeny ; Staphylococcus/classification/enzymology/*genetics ; }, abstract = {Several oligopeptide permease (Opp) systems have been found in staphylococcal species, including Opp1-4, Opp3' and the arginine catabolic mobile element (ACME)-encoded Opp system (ACME-Opp). They confer upon bacteria the increasing fitness, but their evolutionary histories remain unclear. In this work, we performed a genome-wide identification of Opp systems in staphylococcal species. Novel Opp systems were identified, including the duplicate of Opp4 in Staphylococcus pseudintermedius and the ACME-Opp-like systems in coagulase-negative staphylococci (CoNS). Phylogenetic analysis revealed that all of the identified Opp systems were derived from Opp3 system by operon duplication during species divergence, while lateral gene transfer might also confer to the dissemination of Opp in staphylococci. In addition, we proposed an improved theory on evolution of ACME: the Opp and arginine-deiminase systems were firstly transferred from Staphylococcus haemolyticus to Staphylococcus epidermidis independently; in S. epidermidis they were assembled together and then transferred to Staphylococcus aureus.}, }
@article {pmid24792221, year = {2014}, author = {Romanchuk, A and Jones, CD and Karkare, K and Moore, A and Smith, BA and Jones, C and Dougherty, K and Baltrus, DA}, title = {Bigger is not always better: transmission and fitness burden of ∼1MB Pseudomonas syringae megaplasmid pMPPla107.}, journal = {Plasmid}, volume = {73}, number = {}, pages = {16-25}, doi = {10.1016/j.plasmid.2014.04.002}, pmid = {24792221}, issn = {1095-9890}, mesh = {*Biological Evolution ; Conjugation, Genetic ; Plant Diseases/*genetics/microbiology ; Plasmids/*genetics ; Pseudomonas/classification/*genetics/pathogenicity ; Pseudomonas Infections/genetics/*transmission ; Pseudomonas syringae/*genetics/pathogenicity ; Virulence/*genetics ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT) is a widespread process that enables the acquisition of genes and metabolic pathways in single evolutionary steps. Previous reports have described fitness costs of HGT, but have largely focused on the acquisition of relatively small plasmids. We have previously shown that a Pseudomonas syringae pv. lachrymans strain recently acquired a cryptic megaplasmid, pMPPla107. This extrachromosomal element contributes hundreds of new genes to P. syringae and increases total genomic content by approximately 18%. However, this early work did not directly explore transmissibility, stability, or fitness costs associated with acquisition of pMPPla107.<br><br>RESULTS: Here, we show that pMPPla107 is self-transmissible across a variety of diverse pseudomonad strains, on both solid agar and within shaking liquid cultures, with conjugation dependent on a type IV secretion system. To the best of our knowledge, this is the largest self-transmissible megaplasmid known outside of Sinorhizobium. This megaplasmid can be lost from all novel hosts although the rate of loss depends on medium type and genomic background. However, in contrast, pMPPla107 is faithfully maintained within the original parent strain (Pla107) even under direct negative selection during laboratory assays. These results suggest that Pla107 specific stabilizing mutations have occurred either on this strain's chromosome or within the megaplasmid. Lastly, we demonstrate that acquisition of pMPPla107 by strains other than Pla107 imparts severe (20%) fitness costs under competitive conditions in vitro.<br><br>CONCLUSIONS: We show that pMPPla107 is capable of transmitting and maintaining itself across multiple Pseudomonas species, rendering it one of the largest conjugative elements discovered to date. The relative stability of pMPPla107, coupled with extensive fitness costs, makes it a tractable model system for investigating evolutionary and genetic mechanisms of megaplasmid maintenance and a unique testing ground to explore evolutionary dynamics after HGT of large secondary elements.}, }
@article {pmid24784901, year = {2014}, author = {Brimacombe, CA and Ding, H and Beatty, JT}, title = {Rhodobacter capsulatus DprA is essential for RecA-mediated gene transfer agent (RcGTA) recipient capability regulated by quorum-sensing and the CtrA response regulator.}, journal = {Molecular microbiology}, volume = {92}, number = {6}, pages = {1260-1278}, doi = {10.1111/mmi.12628}, pmid = {24784901}, issn = {1365-2958}, support = {93779//Canadian Institutes of Health Research/Canada ; }, mesh = {Bacterial Proteins/chemistry/*metabolism ; DNA-Binding Proteins/*metabolism ; *Gene Transfer, Horizontal ; Homologous Recombination ; Membrane Proteins/chemistry/*metabolism ; Models, Molecular ; Protein Conformation ; *Quorum Sensing ; Rec A Recombinases/*metabolism ; Rhodobacter capsulatus/*enzymology/genetics/metabolism/*physiology ; }, abstract = {Gene transfer agents (GTAs) are genetic exchange elements that resemble small DNA bacteriophages that transfer random pieces of the producing cell's genome to recipient cells. The best-studied GTA is that of Rhodobacter capsulatus, termed RcGTA. We discovered that the putative response regulator CtrA, which is essential for RcGTA production, is required for RcGTA-mediated gene acquisition, and confirmed that a RecA homologue is required. It was also discovered that a DprA (DNA-protecting protein A) homologue is essential for RcGTA-mediated gene acquisition, and that dprA expression is induced by gtaI-dependent quorum-sensing and non-phosphorylated CtrA. Modelling of the R. capsulatus DprA structure indicated the presence of a C-terminal region that resembles a dsDNA-binding protein domain. Purified His-tagged R. capsulatus DprA protein bound to both single-stranded (ss)DNA and double-stranded (ds)DNA, but with a greater affinity for ssDNA. Additionally, DprA protected dsDNA from endonuclease digestion, and increased the rate of nucleation of Escherichia coli RecA onto ssDNA. Single-cell expression analyses revealed that dprA is expressed in the majority of cells throughout a population. Overall, the results suggest that incorporation of RcGTA DNA into the recipient cell genome proceeds through a homologous recombination pathway resembling DNA recombination in natural transformation.}, }
@article {pmid24782530, year = {2014}, author = {Lisboa, J and Andreani, J and Sanchez, D and Boudes, M and Collinet, B and Liger, D and van Tilbeurgh, H and Guérois, R and Quevillon-Cheruel, S}, title = {Molecular determinants of the DprA-RecA interaction for nucleation on ssDNA.}, journal = {Nucleic acids research}, volume = {42}, number = {11}, pages = {7395-7408}, pmid = {24782530}, issn = {1362-4962}, mesh = {Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; DNA, Single-Stranded/*metabolism ; Evolution, Molecular ; Membrane Proteins/*chemistry/metabolism ; Models, Molecular ; Molecular Docking Simulation ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Rec A Recombinases/*chemistry/metabolism ; Streptococcus pneumoniae ; }, abstract = {Natural transformation is a major mechanism of horizontal gene transfer in bacteria that depends on DNA recombination. RecA is central to the homologous recombination pathway, catalyzing DNA strand invasion and homology search. DprA was shown to be a key binding partner of RecA acting as a specific mediator for its loading on the incoming exogenous ssDNA. Although the 3D structures of both RecA and DprA have been solved, the mechanisms underlying their cross-talk remained elusive. By combining molecular docking simulations and experimental validation, we identified a region on RecA, buried at its self-assembly interface and involving three basic residues that contact an acidic triad of DprA previously shown to be crucial for the interaction. At the core of these patches, (DprA)M238 and (RecA)F230 are involved in the interaction. The other DprA binding regions of RecA could involve the N-terminal α-helix and a DNA-binding region. Our data favor a model of DprA acting as a cap of the RecA filament, involving a DprA-RecA interplay at two levels: their own oligomeric states and their respective interaction with DNA. Our model forms the basis for a mechanistic explanation of how DprA can act as a mediator for the loading of RecA on ssDNA.}, }
@article {pmid24782525, year = {2014}, author = {Wald, N and Margalit, H}, title = {Auxiliary tRNAs: large-scale analysis of tRNA genes reveals patterns of tRNA repertoire dynamics.}, journal = {Nucleic acids research}, volume = {42}, number = {10}, pages = {6552-6566}, pmid = {24782525}, issn = {1362-4962}, mesh = {Anticodon ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genome, Bacterial ; Mutation ; Operon ; RNA, Transfer/*genetics ; }, abstract = {Decoding of all codons can be achieved by a subset of tRNAs. In bacteria, certain tRNA species are mandatory, while others are auxiliary and are variably used. It is currently unknown how this variability has evolved and whether it provides an adaptive advantage. Here we shed light on the subset of auxiliary tRNAs, using genomic data from 319 bacteria. By reconstructing the evolution of tRNAs we show that the auxiliary tRNAs are highly dynamic, being frequently gained and lost along the phylogenetic tree, with a clear dominance of loss events for most auxiliary tRNA species. We reveal distinct co-gain and co-loss patterns for subsets of the auxiliary tRNAs, suggesting that they are subjected to the same selection forces. Controlling for phylogenetic dependencies, we find that the usage of these tRNA species is positively correlated with GC content and may derive directly from nucleotide bias or from preference of Watson-Crick codon-anticodon interactions. Our results highlight the highly dynamic nature of these tRNAs and their complicated balance with codon usage.}, }
@article {pmid24781744, year = {2014}, author = {Flynn, KJ and Swanson, MS}, title = {Integrative conjugative element ICE-βox confers oxidative stress resistance to Legionella pneumophila in vitro and in macrophages.}, journal = {mBio}, volume = {5}, number = {3}, pages = {e01091-14}, pmid = {24781744}, issn = {2150-7511}, support = {T32 AI007528/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *DNA Transposable Elements ; Female ; Gene Order ; Genes, Bacterial ; Genetic Fitness ; Genetic Loci ; Legionella pneumophila/*physiology ; Macrophages/metabolism/*microbiology ; Mice ; Mutagenesis, Insertional ; NADPH Oxidases/metabolism ; Oxidants/pharmacology ; Oxidative Stress/*genetics ; beta-Lactam Resistance/genetics ; }, abstract = {Integrative conjugative elements (ICEs) are mobile blocks of DNA that can contribute to bacterial evolution by self-directed transmission of advantageous traits. Here, we analyze the activity of a putative 65-kb ICE harbored by Legionella pneumophila using molecular genetics, conjugation assays, a phenotype microarray screen, and macrophage infections. The element transferred to a naive L. pneumophila strain, integrated site-specifically, and conferred increased resistance to oxacillin, penicillin, hydrogen peroxide, and bleach. Furthermore, the element increased survival of L. pneumophila within restrictive mouse macrophages. In particular, this ICE protects L. pneumophila from phagocyte oxidase activity, since mutation of the macrophage NADPH oxidase eliminated the fitness difference between strains that carried and those that lacked the mobile element. Renamed ICE-βox (for β-lactam antibiotics and oxidative stress), this transposable element is predicted to contribute to the emergence of L. pneumophila strains that are more fit in natural and engineered water systems and in macrophages. IMPORTANCE Bacteria evolve rapidly by acquiring new traits via horizontal gene transfer. Integrative conjugative elements (ICEs) are mobile blocks of DNA that encode the machinery necessary to spread among bacterial populations. ICEs transfer antibiotic resistance and other bacterial survival factors as cargo genes carried within the element. Here, we show that Legionella pneumophila, the causative agent of Legionnaires' disease, carries ICE-βox, which enhances the resistance of this opportunistic pathogen to bleach and β-lactam antibiotics. Moreover, L. pneumophila strains encoding ICE-βox are more resistant to macrophages that carry phagocyte oxidase. Accordingly, ICE-βox is predicted to increase the fitness of L. pneumophila in natural and engineered waters and in humans. To our knowledge, this is the first description of an ICE that confers oxidative stress resistance to a nosocomial pathogen.}, }
@article {pmid24776772, year = {2014}, author = {Jones, B}, title = {Evolution: Planting genes.}, journal = {Nature reviews. Genetics}, volume = {15}, number = {6}, pages = {362}, pmid = {24776772}, issn = {1471-0064}, mesh = {Bryophyta/*genetics ; Ferns/*genetics ; *Gene Transfer, Horizontal ; Photoreceptors, Plant/*genetics ; }, }
@article {pmid24770645, year = {2014}, author = {Takabayashi, S and Seto, S and Katoh, H}, title = {A new Enpp1 allele, Enpp1(ttw-Ham), identified in an ICR closed colony.}, journal = {Experimental animals}, volume = {63}, number = {2}, pages = {193-204}, pmid = {24770645}, issn = {1881-7122}, mesh = {*Alleles ; Animals ; Ankylosis/genetics ; Base Sequence ; Chromosomes, Mammalian/genetics ; Disease Models, Animal ; Female ; Gene Transfer, Horizontal ; Humans ; Male ; Malnutrition/genetics ; Mice ; Mice, Inbred ICR ; *Mice, Mutant Strains ; Molecular Sequence Data ; Mutation ; Osteochondrodysplasias/genetics ; Phosphoric Diester Hydrolases/*genetics/*isolation &amp; purification ; Pyrophosphatases/*genetics/*isolation &amp; purification ; }, abstract = {We recently have reported on a novel ankylosis gene that is closely linked to the Enpp1 (ectonucleotide pyrophosphatase/phosphodiesterase 1) gene on chromosome 10. Here, we have discovered novel mutant mice in a Jcl:ICR closed colony with ankylosis in the toes of the forelimbs at about 3 weeks of age. The mutant mice exhibited rigidity in almost all joints, including the vertebral column, which increased with age. These mice also showed hypogrowth with age after 16 weeks due to a loss of visceral fat, which may have been caused by poor nutrition. Histological examination and soft X-ray imaging demonstrated the ectopic ossification of various joints in the mutant mice. In particular, increased calcium deposits were observed in the joints of the toes, the carpal bones and the vertebral column. We sequenced all exons and exon/intron boundaries of Enpp1 in the normal and mutant mice, and identified a G-to-T substitution (c.259+1G>T) in the 5' splice donor site of intron 2 in the Enpp1 gene of the mutant mice. This substitution led to the skipping of exon 2 (73 bp), which generated a stop codon at position 354 bp (amino acid 62) of the cDNA (p.V63Xfs). Nucleotide pyrophosphohydrolase (NPPH) activity of ENPP1 in the mutant mice was also decreased, suggesting that Enpp1 gene function is disrupted in this novel mutant. The mutant mice reported in this study will be a valuable animal model for future studies of human osteochondral diseases and malnutrition.}, }
@article {pmid24768721, year = {2014}, author = {Liu, CC and Tang, CY and Chang, KC and Kuo, HY and Liou, ML}, title = {A comparative study of class 1 integrons in Acinetobacter baumannii.}, journal = {Gene}, volume = {544}, number = {1}, pages = {75-82}, doi = {10.1016/j.gene.2014.04.047}, pmid = {24768721}, issn = {1879-0038}, mesh = {Acinetobacter baumannii/*genetics ; Amino Acid Sequence ; Anti-Bacterial Agents/pharmacology ; Bacteria/classification/genetics ; Bacterial Proteins/classification/genetics ; DNA, Bacterial/classification/*genetics ; Drug Resistance, Multiple, Bacterial/drug effects/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial/genetics ; Genomics/methods ; Integrases/classification/genetics ; Integrons/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Amino Acid ; Soil Microbiology ; }, abstract = {Multidrug resistance (MDR) in Acinetobacter baumannii is increasingly reported and has become a significant public concern. The method responsible for the acquisition of resistance genes via integrons from the environment or intra-species in A. baumannii remains to be understood. This study was performed to investigate the transmission route of these integrons using a comparative analysis of published A. baumannii complete genomes. The phylogenetic analysis of A. baumannii type 1 integrases (IntI1) showed that the integrons could be transferred across the two evolutionary lineages, the international clone I (IC I) and clone II (IC II) strains. In addition, the integrons in A. baumannii strains were mainly responsible for the transfer of resistance genes for two types of long-term usage antibiotics and antiseptics, such as aminoglycosides, chloramphenicol and the quaternary-ammonium-compound family. The in silico comparative analysis of known integron integrases revealed that the intI genes were phylogenetically related among A. baumannii strains and some microorganisms living in a sediment community, implicating that the integrons of A. baumannii might have originated from those microorganisms belonging to the β-preoteobacterial class in the sediment environment. The data suggest that the gain of class 1 integrons in A. baumannii strains may have started before the antibiotic era. This report shows that the origins of A. baumannii class 1 integrons may be the soil environment and that the resistance genes included in integrons are horizontally transferred across all the A. baumannii genomes, including IC I and IC II.}, }
@article {pmid24767410, year = {2014}, author = {Fischer, W and Breithaupt, U and Kern, B and Smith, SI and Spicher, C and Haas, R}, title = {A comprehensive analysis of Helicobacter pylori plasticity zones reveals that they are integrating conjugative elements with intermediate integration specificity.}, journal = {BMC genomics}, volume = {15}, number = {}, pages = {310}, pmid = {24767410}, issn = {1471-2164}, mesh = {Gene Transfer, Horizontal ; Genes, Bacterial ; Geography ; Helicobacter pylori/classification/genetics/*physiology ; Molecular Sequence Data ; Phylogeny ; }, abstract = {BACKGROUND: The human gastric pathogen Helicobacter pylori is a paradigm for chronic bacterial infections. Its persistence in the stomach mucosa is facilitated by several mechanisms of immune evasion and immune modulation, but also by an unusual genetic variability which might account for the capability to adapt to changing environmental conditions during long-term colonization. This variability is reflected by the fact that almost each infected individual is colonized by a genetically unique strain. Strain-specific genes are dispersed throughout the genome, but clusters of genes organized as genomic islands may also collectively be present or absent.<br><br>RESULTS: We have comparatively analysed such clusters, which are commonly termed plasticity zones, in a high number of H. pylori strains of varying geographical origin. We show that these regions contain fixed gene sets, rather than being true regions of genome plasticity, but two different types and several subtypes with partly diverging gene content can be distinguished. Their genetic diversity is incongruent with variations in the rest of the genome, suggesting that they are subject to horizontal gene transfer within H. pylori populations. We identified 40 distinct integration sites in 45 genome sequences, with a conserved heptanucleotide motif that seems to be the minimal requirement for integration.<br><br>CONCLUSIONS: The significant number of possible integration sites, together with the requirement for a short conserved integration motif and the high level of gene conservation, indicates that these elements are best described as integrating conjugative elements (ICEs) with an intermediate integration site specificity.}, }
@article {pmid24766488, year = {2014}, author = {Arioli, S and Guglielmetti, S and Amalfitano, S and Viti, C and Marchi, E and Decorosi, F and Giovannetti, L and Mora, D}, title = {Characterization of tetA-like gene encoding for a major facilitator superfamily efflux pump in Streptococcus thermophilus.}, journal = {FEMS microbiology letters}, volume = {355}, number = {1}, pages = {61-70}, doi = {10.1111/1574-6968.12449}, pmid = {24766488}, issn = {1574-6968}, mesh = {Antiporters/*genetics/*metabolism ; Bacterial Proteins/*genetics/*metabolism ; DNA, Bacterial/chemistry/genetics ; Drug Resistance ; Ethidium/toxicity ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Sequence Analysis, DNA ; Streptococcus thermophilus/drug effects/*enzymology/genetics ; Tetracycline/toxicity ; }, abstract = {Efflux pumps are membrane proteins involved in the active extrusion of a wide range of structurally dissimilar substrates from cells. A multidrug efflux pump named TetA belonging to the major facilitator superfamily (MFS) of transporters was identified in the Streptococcus thermophilus DSM 20617(T) genome. The tetA-like gene was found in the genomes of a number of S. thermophilus strains sequenced to date and in Streptococcus macedonicus ACA-DC 198, suggesting a possible horizontal gene transfer event between these two Streptococcus species, which are both adapted to the milk environment. Flow cytometry (single-cell) analysis revealed bistable TetA activity in the S. thermophilus population, and tetA-like gene over-expression resulted in a reduced susceptibility to ethidium bromide, tetracycline, and other toxic compounds even when the efflux pump was over-expressed in a strain naturally lacking tetA-like gene.}, }
@article {pmid24766399, year = {2014}, author = {Pohl, S and Klockgether, J and Eckweiler, D and Khaledi, A and Schniederjans, M and Chouvarine, P and Tümmler, B and Häussler, S}, title = {The extensive set of accessory Pseudomonas aeruginosa genomic components.}, journal = {FEMS microbiology letters}, volume = {356}, number = {2}, pages = {235-241}, doi = {10.1111/1574-6968.12445}, pmid = {24766399}, issn = {1574-6968}, mesh = {Gene Expression Profiling ; Gene Transfer, Horizontal ; Genetic Variation ; *Genome, Bacterial ; *Interspersed Repetitive Sequences ; Pseudomonas Infections/microbiology ; Pseudomonas aeruginosa/classification/*genetics/isolation &amp; purification ; }, abstract = {Up to 20% of the chromosomal Pseudomonas aeruginosa DNA belong to the so-called accessory genome. Its elements are specific for subgroups or even single strains and are likely acquired by horizontal gene transfer (HGT). Similarities of the accessory genomic elements to DNA from other bacterial species, mainly the DNA of γ- and β-proteobacteria, indicate a role of interspecies HGT. In this study, we analysed the expression of the accessory genome in 150 clinical P. aeruginosa isolates as uncovered by transcriptome sequencing and the presence of accessory genes in eleven additional isolates. Remarkably, despite the large number of P. aeruginosa strains that have been sequenced to date, we found new strain-specific compositions of accessory genomic elements and a high portion (10-20%) of genes without P. aeruginosa homologues. Although some genes were detected to be expressed/present in several isolates, individual patterns regarding the genes, their functions and the possible origin of the DNA were widespread among the tested strains. Our results demonstrate the unaltered potential to discover new traits within the P. aeruginosa population and underline that the P. aeruginosa pangenome is likely to increase with increasing sequence information.}, }
@article {pmid24765662, year = {2014}, author = {Altamia, MA and Wood, N and Fung, JM and Dedrick, S and Linton, EW and Concepcion, GP and Haygood, MG and Distel, DL}, title = {Genetic differentiation among isolates of Teredinibacter turnerae, a widely occurring intracellular endosymbiont of shipworms.}, journal = {Molecular ecology}, volume = {23}, number = {6}, pages = {1418-1432}, pmid = {24765662}, issn = {1365-294X}, support = {U01 TW008163/TW/FIC NIH HHS/United States ; U19 TW008163/TW/FIC NIH HHS/United States ; U01TW008163/TW/FIC NIH HHS/United States ; }, mesh = {Animals ; Atlantic Ocean ; Bivalvia/*microbiology ; DNA, Bacterial/genetics ; Gammaproteobacteria/*classification/genetics/isolation &amp; purification ; Genes, Bacterial ; Genetic Variation ; Indian Ocean ; Pacific Ocean ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {Teredinibacter turnerae is a cultivable intracellular endosymbiont of xylotrophic (woodfeeding)bivalves of the Family Teredinidae (shipworms). Although T. turnerae has been isolated from many shipworm taxa collected in many locations, no systematic effort has been made to explore genetic diversity within this symbiont species across the taxonomic and geographical range of its hosts. The mode of symbiont transmission is unknown. Here, we examine sequence diversity in fragments of six genes (16S rRNA, gyrB, sseA, recA, rpoB and celAB) among 25 isolates of T. turnerae cultured from 13 shipworm species collected in 15 locations in the Atlantic, Pacific and Indian Oceans. While 16S rRNA sequences are nearly invariant between all examined isolates (maximum pairwise difference <0.26%), variation between examined protein-coding loci is greater (mean pairwise difference 2.2–5.9%). Phylogenetic analyses based on each protein-coding locus differentiate the 25 isolates into two distinct and well-supported clades. With five exceptions, clade assignments for each isolate were supported by analysis of alleles of each of the five protein-coding loci. These exceptions include (i) putative recombinant alleles of the celAB and gyrB loci in two isolates (PMS-535T.S.1b.3 and T8510), suggesting homologous recombination between members of the two clades; and (ii) evidence for a putative lateral gene transfer event affecting a second locus (recA) in three isolates (T8412, T8503 and T8513). These results demonstrate that T. turnerae isolates do not represent a homogeneous global population. Instead, they indicate the emergence of two lineages that, although distinct, likely experience some level of genetic exchange with each other and with other bacterial species.}, }
@article {pmid24765574, year = {2014}, author = {Pettengill, JB and Timme, RE and Barrangou, R and Toro, M and Allard, MW and Strain, E and Musser, SM and Brown, EW}, title = {The evolutionary history and diagnostic utility of the CRISPR-Cas system within Salmonella enterica ssp. enterica.}, journal = {PeerJ}, volume = {2}, number = {}, pages = {e340}, pmid = {24765574}, issn = {2167-8359}, abstract = {Evolutionary studies of clustered regularly interspaced short palindromic repeats (CRISPRs) and their associated (cas) genes can provide insights into host-pathogen co-evolutionary dynamics and the frequency at which different genomic events (e.g., horizontal vs. vertical transmission) occur. Within this study, we used whole genome sequence (WGS) data to determine the evolutionary history and genetic diversity of CRISPR loci and cas genes among a diverse set of 427 Salmonella enterica ssp. enterica isolates representing 64 different serovars. We also evaluated the performance of CRISPR loci for typing when compared to whole genome and multilocus sequence typing (MLST) approaches. We found that there was high diversity in array length within both CRISPR1 (median = 22; min = 3; max = 79) and CRISPR2 (median = 27; min = 2; max = 221). There was also much diversity within serovars (e.g., arrays differed by as many as 50 repeat-spacer units among Salmonella ser. Senftenberg isolates). Interestingly, we found that there are two general cas gene profiles that do not track phylogenetic relationships, which suggests that non-vertical transmission events have occurred frequently throughout the evolutionary history of the sampled isolates. There is also considerable variation among the ranges of pairwise distances estimated within each cas gene, which may be indicative of the strength of natural selection acting on those genes. We developed a novel clustering approach based on CRISPR spacer content, but found that typing based on CRISPRs was less accurate than the MLST-based alternative; typing based on WGS data was the most accurate. Notwithstanding cost and accessibility, we anticipate that draft genome sequencing, due to its greater discriminatory power, will eventually become routine for traceback investigations.}, }
@article {pmid24765091, year = {2014}, author = {Wang, J and Behr, MA}, title = {Building a better bacillus: the emergence of Mycobacterium tuberculosis.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {139}, pmid = {24765091}, issn = {1664-302X}, abstract = {The genus Mycobacterium is comprised of more than 150 species that reside in a wide variety of habitats. Most mycobacteria are environmental organisms that are either not associated with disease or are opportunistic pathogens that cause non-transmissible disease in immunocompromised individuals. In contrast, a small number of species, such as the tubercle bacillus, Mycobacterium tuberculosis, are host-adapted pathogens for which there is no known environmental reservoir. In recent years, gene disruption studies using the host-adapted pathogen have uncovered a number of "virulence factors," yet genomic data indicate that many of these elements are present in non-pathogenic mycobacteria. This suggests that much of the genetic make-up that enables virulence in the host-adapted pathogen is already present in environmental members of the genus. In addition to these generic factors, we hypothesize that molecules elaborated exclusively by professional pathogens may be particularly implicated in the ability of M. tuberculosis to infect, persist, and cause transmissible pathology in its host species, Homo sapiens. One approach to identify these molecules is to employ comparative analysis of mycobacterial genomes, to define evolutionary events such as horizontal gene transfer (HGT) that contributed M. tuberculosis-specific genetic elements. Independent studies have now revealed the presence of HGT genes in the M. tuberculosis genome and their role in the pathogenesis of disease is the subject of ongoing investigations. Here we review these studies, focusing on the hypothesized role played by HGT loci in the emergence of M. tuberculosis from a related environmental species into a highly specialized human-adapted pathogen.}, }
@article {pmid24764459, year = {2014}, author = {Weyenberg, G and Huggins, PM and Schardl, CL and Howe, DK and Yoshida, R}, title = {kdetrees: Non-parametric estimation of phylogenetic tree distributions.}, journal = {Bioinformatics (Oxford, England)}, volume = {30}, number = {16}, pages = {2280-2287}, pmid = {24764459}, issn = {1367-4811}, support = {R01 GM086888/GM/NIGMS NIH HHS/United States ; R01GM086888/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Apicomplexa/genetics ; Epichloe/genetics ; Gene Transfer, Horizontal ; Genes ; *Phylogeny ; Sequence Alignment ; Software ; Statistics, Nonparametric ; }, abstract = {MOTIVATION: Although the majority of gene histories found in a clade of organisms are expected to be generated by a common process (e.g. the coalescent process), it is well known that numerous other coexisting processes (e.g. horizontal gene transfers, gene duplication and subsequent neofunctionalization) will cause some genes to exhibit a history distinct from those of the majority of genes. Such 'outlying' gene trees are considered to be biologically interesting, and identifying these genes has become an important problem in phylogenetics.<br><br>RESULTS: We propose and implement kdetrees, a non-parametric method for estimating distributions of phylogenetic trees, with the goal of identifying trees that are significantly different from the rest of the trees in the sample. Our method compares favorably with a similar recently published method, featuring an improvement of one polynomial order of computational complexity (to quadratic in the number of trees analyzed), with simulation studies suggesting only a small penalty to classification accuracy. Application of kdetrees to a set of Apicomplexa genes identified several unreliable sequence alignments that had escaped previous detection, as well as a gene independently reported as a possible case of horizontal gene transfer. We also analyze a set of Epichlo&#xeb; genes, fungi symbiotic with grasses, successfully identifying a contrived instance of paralogy.<br><br>Our method for estimating tree distributions and identifying outlying trees is implemented as the R package kdetrees and is available for download from CRAN.}, }
@article {pmid24764001, year = {2014}, author = {Sarkar, A and Kazy, SK and Sar, P}, title = {Studies on arsenic transforming groundwater bacteria and their role in arsenic release from subsurface sediment.}, journal = {Environmental science and pollution research international}, volume = {21}, number = {14}, pages = {8645-8662}, pmid = {24764001}, issn = {1614-7499}, mesh = {Arsenic/*metabolism ; Bacteria/genetics/*metabolism ; Electron Transport ; Genes, rRNA ; Groundwater ; Oxidation-Reduction ; Oxidoreductases/metabolism ; Phenotype ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Rhizobium/genetics/metabolism ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Ten different Gram-negative arsenic (As)-resistant and As-transforming bacteria isolated from As-rich groundwater of West Bengal were characterized to assess their role in As mobilization. 16S rRNA gene analysis confirmed the affiliation of these bacteria to genera Achromobacter, Brevundimonas, Rhizobium, Ochrobactrum, and Pseudoxanthomonas. Along with superior As-resistance and As-transformation abilities, the isolates showed broad metabolic capacity in terms of utilizing a variety of electron donors and acceptors (including As) under aerobic and anaerobic conditions, respectively. Arsenic transformation studies performed under various conditions indicated highly efficient As(3+) oxidation or As(5+) reduction kinetics. Genes encoding As(3+) oxidase (aioA), cytosolic As(5+) reductase (arsC), and As(3+) efflux pump (arsB and acr3) were detected within the test isolates. Sequence analyses suggested that As homeostasis genes (particularly arsC, arsB, and acr3) were acquired by most of the bacteria through horizontal gene transfer. A strong correlation between As resistance phenotype and the presence of As(3+) transporter genes was observed. Microcosm study showed that bacterial strain having cytosolic As(5+) reductase property could play important role in mobilizing As (as As(3+)) from subsurface sediment.}, }
@article {pmid24763368, year = {2014}, author = {Khelifi, N and Amin Ali, O and Roche, P and Grossi, V and Brochier-Armanet, C and Valette, O and Ollivier, B and Dolla, A and Hirschler-Réa, A}, title = {Anaerobic oxidation of long-chain n-alkanes by the hyperthermophilic sulfate-reducing archaeon, Archaeoglobus fulgidus.}, journal = {The ISME journal}, volume = {8}, number = {11}, pages = {2153-2166}, pmid = {24763368}, issn = {1751-7370}, mesh = {Alkanes/*metabolism ; Anaerobiosis ; Archaeal Proteins/chemistry/classification/genetics/metabolism ; Archaeoglobus fulgidus/enzymology/genetics/growth &amp; development/*metabolism ; Fatty Acids/metabolism ; Hot Temperature ; Oxidation-Reduction ; Phylogeny ; Sulfates/metabolism ; }, abstract = {The thermophilic sulfate-reducing archaeon Archaeoglobus fulgidus strain VC-16 (DSM 4304), which is known to oxidize fatty acids and n-alkenes, was shown to oxidize saturated hydrocarbons (n-alkanes in the range C10-C21) with thiosulfate or sulfate as a terminal electron acceptor. The amount of n-hexadecane degradation observed was in stoichiometric agreement with the theoretically expected amount of thiosulfate reduction. One of the pathways used by anaerobic microorganisms to activate alkanes is addition to fumarate that involves alkylsuccinate synthase as a key enzyme. A search for genes encoding homologous enzymes in A. fulgidus identified the pflD gene (locus-tag AF1449) that was previously annotated as a pyruvate formate lyase. A phylogenetic analysis revealed that this gene is of bacterial origin and was likely acquired by A. fulgidus from a bacterial donor through a horizontal gene transfer. Based on three-dimensional modeling of the corresponding protein and molecular dynamic simulations, we hypothesize an alkylsuccinate synthase activity for this gene product. The pflD gene expression was upregulated during the growth of A. fulgidus on an n-alkane (C16) compared with growth on a fatty acid. Our results suggest that anaerobic alkane degradation in A. fulgidus may involve the gene pflD in alkane activation through addition to fumarate. These findings highlight the possible importance of hydrocarbon oxidation at high temperatures by A. fulgidus in hydrothermal vents and the deep biosphere.}, }
@article {pmid24763283, year = {2014}, author = {Brelsfoard, C and Tsiamis, G and Falchetto, M and Gomulski, LM and Telleria, E and Alam, U and Doudoumis, V and Scolari, F and Benoit, JB and Swain, M and Takac, P and Malacrida, AR and Bourtzis, K and Aksoy, S}, title = {Presence of extensive Wolbachia symbiont insertions discovered in the genome of its host Glossina morsitans morsitans.}, journal = {PLoS neglected tropical diseases}, volume = {8}, number = {4}, pages = {e2728}, pmid = {24763283}, issn = {1935-2735}, support = {R01 AI051584/AI/NIAID NIH HHS/United States ; R01 AI068932/AI/NIAID NIH HHS/United States ; AI068932/AI/NIAID NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Blotting, Southern ; *Genome, Bacterial ; *Genome, Insect ; In Situ Hybridization, Fluorescence ; Molecular Sequence Data ; *Mutagenesis, Insertional ; *Recombination, Genetic ; Sequence Analysis, DNA ; Tsetse Flies/*genetics ; Wolbachia/*genetics ; }, abstract = {Tsetse flies (Glossina spp.) are the cyclical vectors of Trypanosoma spp., which are unicellular parasites responsible for multiple diseases, including nagana in livestock and sleeping sickness in humans in Africa. Glossina species, including Glossina morsitans morsitans (Gmm), for which the Whole Genome Sequence (WGS) is now available, have established symbiotic associations with three endosymbionts: Wigglesworthia glossinidia, Sodalis glossinidius and Wolbachia pipientis (Wolbachia). The presence of Wolbachia in both natural and laboratory populations of Glossina species, including the presence of horizontal gene transfer (HGT) events in a laboratory colony of Gmm, has already been shown. We herein report on the draft genome sequence of the cytoplasmic Wolbachia endosymbiont (cytWol) associated with Gmm. By in silico and molecular and cytogenetic analysis, we discovered and validated the presence of multiple insertions of Wolbachia (chrWol) in the host Gmm genome. We identified at least two large insertions of chrWol, 527,507 and 484,123 bp in size, from Gmm WGS data. Southern hybridizations confirmed the presence of Wolbachia insertions in Gmm genome, and FISH revealed multiple insertions located on the two sex chromosomes (X and Y), as well as on the supernumerary B-chromosomes. We compare the chrWol insertions to the cytWol draft genome in an attempt to clarify the evolutionary history of the HGT events. We discuss our findings in light of the evolution of Wolbachia infections in the tsetse fly and their potential impacts on the control of tsetse populations and trypanosomiasis.}, }
@article {pmid24762028, year = {2015}, author = {Martínez-García, E and Jatsenko, T and Kivisaar, M and de Lorenzo, V}, title = {Freeing Pseudomonas putida KT2440 of its proviral load strengthens endurance to environmental stresses.}, journal = {Environmental microbiology}, volume = {17}, number = {1}, pages = {76-90}, doi = {10.1111/1462-2920.12492}, pmid = {24762028}, issn = {1462-2920}, mesh = {DNA Damage ; Genome, Bacterial ; Plasmids/genetics ; Prophages/genetics ; Proviruses/*genetics ; Pseudomonas putida/*genetics/metabolism/radiation effects ; Sequence Deletion ; Stress, Physiological/*genetics ; Ultraviolet Rays ; }, abstract = {2.6% of the genome of the soil bacterium Pseudomonas putida KT2440 encodes phage-related functions, but the burden of such opportunistic DNA on the host physiology is unknown. Each of the four apparently complete prophages borne by this strain was tested for stability, spontaneous excision and ability to cause lysis under various stressing conditions. While prophages P3 (PP2266-PP2297) and P4 (PP1532-1584) were discharged from the genome at a detectable rate, their induction failed otherwise to yield infective viruses. Isogenic P. putida KT2440 derivatives bearing single and multiple deletions of each of the prophages were then subjected to thorough phenotypic analyses, which generally associated the loss of proviral DNA with an increase of physiological vigour. The most conspicuous benefit acquired by prophage-less cells was a remarkable improvement in tolerance to UV light and other insults to DNA. This was not accompanied, however, with an upgrade of recA-mediated homologous recombination. The range of tolerance to DNA damage gained by the prophage-free strain was equivalent to the UV resistance endowed by the TOL plasmid pWW0 to the wild-type bacterium. While the P. putida's prophages are therefore genuinely parasitic, their detrimental effects can be offset by acquisition of compensatory traits through horizontal gene transfer.}, }
@article {pmid24759094, year = {2014}, author = {Roy, RS and Price, DC and Schliep, A and Cai, G and Korobeynikov, A and Yoon, HS and Yang, EC and Bhattacharya, D}, title = {Single cell genome analysis of an uncultured heterotrophic stramenopile.}, journal = {Scientific reports}, volume = {4}, number = {}, pages = {4780}, pmid = {24759094}, issn = {2045-2322}, mesh = {Biodiversity ; Computational Biology ; *Genomics ; Phylogeny ; Proteome ; Proteomics ; RNA, Ribosomal, 18S/genetics ; Seawater ; *Single-Cell Analysis ; Stramenopiles/classification/*genetics/metabolism ; }, abstract = {A broad swath of eukaryotic microbial biodiversity cannot be cultivated in the lab and is therefore inaccessible to conventional genome-wide comparative methods. One promising approach to study these lineages is single cell genomics (SCG), whereby an individual cell is captured from nature and genome data are produced from the amplified total DNA. Here we tested the efficacy of SCG to generate a draft genome assembly from a single sample, in this case a cell belonging to the broadly distributed MAST-4 uncultured marine stramenopiles. Using de novo gene prediction, we identified 6,996 protein-encoding genes in the MAST-4 genome. This genetic inventory was sufficient to place the cell within the ToL using multigene phylogenetics and provided preliminary insights into the complex evolutionary history of horizontal gene transfer (HGT) in the MAST-4 lineage.}, }
@article {pmid24758311, year = {2014}, author = {Barve, A and Hosseini, SR and Martin, OC and Wagner, A}, title = {Historical contingency and the gradual evolution of metabolic properties in central carbon and genome-scale metabolisms.}, journal = {BMC systems biology}, volume = {8}, number = {}, pages = {48}, pmid = {24758311}, issn = {1752-0509}, mesh = {Carbon/*metabolism ; *Evolution, Molecular ; *Genomics ; Genotype ; Phenotype ; }, abstract = {BACKGROUND: A metabolism can evolve through changes in its biochemical reactions that are caused by processes such as horizontal gene transfer and gene deletion. While such changes need to preserve an organism's viability in its environment, they can modify other important properties, such as a metabolism's maximal biomass synthesis rate and its robustness to genetic and environmental change. Whether such properties can be modulated in evolution depends on whether all or most viable metabolisms - those that can synthesize all essential biomass precursors - are connected in a space of all possible metabolisms. Connectedness means that any two viable metabolisms can be converted into one another through a sequence of single reaction changes that leave viability intact. If the set of viable metabolisms is disconnected and highly fragmented, then historical contingency becomes important and restricts the alteration of metabolic properties, as well as the number of novel metabolic phenotypes accessible in evolution.<br><br>RESULTS: We here computationally explore two vast spaces of possible metabolisms to ask whether viable metabolisms are connected. We find that for all but the simplest metabolisms, most viable metabolisms can be transformed into one another by single viability-preserving reaction changes. Where this is not the case, alternative essential metabolic pathways consisting of multiple reactions are responsible, but such pathways are not common.<br><br>CONCLUSIONS: Metabolism is thus highly evolvable, in the sense that its properties could be fine-tuned by successively altering individual reactions. Historical contingency does not strongly restrict the origin of novel metabolic phenotypes.}, }
@article {pmid24757839, year = {2014}, author = {Smirnova, NI and Agafonov, DA and Shchelkanova, EY and Zadnova, SP and Cherkasov, AV and Kutyrev, VV}, title = {[Genovariants of the cholera agent biovar El Tor: construction, molecular-genetic, and proteomic analysis].}, journal = {Molekuliarnaia genetika, mikrobiologiia i virusologiia}, volume = {}, number = {1}, pages = {21-31}, pmid = {24757839}, issn = {0208-0613}, mesh = {Base Sequence ; Chromosomes, Bacterial/virology ; DNA, Bacterial/chemistry/genetics ; Molecular Sequence Data ; Polymorphism, Genetic ; Prophages/genetics ; Proteome/*genetics/metabolism ; Vibrio cholerae/*genetics/metabolism/virology ; }, abstract = {Experimental modeling of origination of the virulent Vibrio cholerae El Tor genovariants is presented. It was demonstrated that the genovariants obtained did not differ from the natural genetically modified strains emerged in a natural population of the agent, either in phenotypical or genotypic properties. Using the PCR assay and sequencing techniques it was proved that the constructed genovariants carried a CTX(Class phi) prophage genome region with ctxBl gene of the V. cholerae classical biovar in the chromosome. It is shown that the prophage structure alterations lead to the increase in the toxigenicity and virulence in the genovariants compared to the typical strain-recipient. Moreover, as regards proteomics, changes in the expression of 26 proteins that perform various functions in the cell, such as metabolism, energy exchange, transportation, etc., were demonstrated. The data are indicative of the impact that a new DNA region in the genome of the genovariants has on the expression level of different house-keeping genes. The results obtained testify to the fact that one of the mechanisms of the genovariant emergence in the natural populations of the agent can be horizontal gene transfer.}, }
@article {pmid24755769, year = {2014}, author = {Juhász, J and Kertész-Farkas, A and Szabó, D and Pongor, S}, title = {Emergence of collective territorial defense in bacterial communities: horizontal gene transfer can stabilize microbiomes.}, journal = {PloS one}, volume = {9}, number = {4}, pages = {e95511}, pmid = {24755769}, issn = {1932-6203}, mesh = {Bacteria/*genetics/*immunology ; Computer Simulation ; *Gene Transfer, Horizontal ; Genetic Variation ; Genotype ; Microbiota/*genetics ; Models, Biological ; }, abstract = {Multispecies bacterial communities such as the microbiota of the gastrointestinal tract can be remarkably stable and resilient even though they consist of cells and species that compete for resources and also produce a large number of antimicrobial agents. Computational modeling suggests that horizontal transfer of resistance genes may greatly contribute to the formation of stable and diverse communities capable of protecting themselves with a battery of antimicrobial agents while preserving a varied metabolic repertoire of the constituent species. In other words horizontal transfer of resistance genes makes a community compatible in terms of exoproducts and capable to maintain a varied and mature metagenome. The same property may allow microbiota to protect a host organism, or if used as a microbial therapy, to purge pathogens and restore a protective environment.}, }
@article {pmid24749717, year = {2014}, author = {Tazzyman, SJ and Bonhoeffer, S}, title = {Plasmids and evolutionary rescue by drug resistance.}, journal = {Evolution; international journal of organic evolution}, volume = {68}, number = {7}, pages = {2066-2078}, doi = {10.1111/evo.12423}, pmid = {24749717}, issn = {1558-5646}, mesh = {Bacteria/genetics ; Drug Resistance, Bacterial/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Models, Genetic ; Mutation ; Plasmids/*genetics ; }, abstract = {Antibiotic resistance provides evolutionary rescue for bacterial populations under the threat of extinction through antibiotics. It can arise de novo through mutation in the population, or be obtained from other bacterial populations via the transfer of a resistance-conferring plasmid. We use stochastic modeling methods to establish whether the most likely source of rescue is via a plasmid or via the chromosome, and show that contrary to what is assumed plasmids are not necessarily beneficial locations for resistance genes. Competition at the plasmid level of selection is of great importance-the spread of a resistant plasmid in the population can be slowed or entirely stopped by a nonresistant version of the same plasmid. We suggest that future studies on antibiotic-resistant plasmids should explicitly consider competition at this level of selection.}, }
@article {pmid24747127, year = {2014}, author = {Parker, MA and Rousteau, A}, title = {Mosaic origins of Bradyrhizobium legume symbionts on the Caribbean island of Guadeloupe.}, journal = {Molecular phylogenetics and evolution}, volume = {77}, number = {}, pages = {110-115}, doi = {10.1016/j.ympev.2014.04.011}, pmid = {24747127}, issn = {1095-9513}, mesh = {Bayes Theorem ; Bradyrhizobium/classification/*genetics/isolation &amp; purification ; Fabaceae/*microbiology ; Gene Transfer, Horizontal ; Guadeloupe ; *Phylogeny ; Sequence Analysis, DNA ; *Symbiosis/genetics ; }, abstract = {To analyze geographic affinities of Bradyrhizobium sp. symbionts associated with the diverse legume flora on the Caribbean island of Guadeloupe, 39 isolates from 18 legume genera were compared to a reference set of 269 Bradyrhizobium strains from North America, Central America, Puerto Rico and the Philippines. A multilocus sequence analysis (4192 bp) showed that nucleotide diversity in Guadeloupe equaled or exceeded that found in all other regional Bradyrhizobium populations examined. Bayesian phylogenetic tree analysis grouped the Guadeloupe Bradyrhizobium strains into clades with at least 20 distinct sets of non-Guadeloupe relatives, implying that the island was colonized numerous times from multiple source regions. However, for 18% of the Guadeloupe isolates, inferred geographic affinities for the nifD locus, in the symbiosis island region of the Bradyrhizobium chromosome, conflicted with the source region deduced from a tree based on six concatenated housekeeping genes. Geographic mosaic ancestry was therefore evident among Guadeloupe bradyrhizobia. Horizontal gene transfer subsequent to island colonization appears to have generated strains that carry combinations of genes from disparate source regions.}, }
@article {pmid24740277, year = {2014}, author = {San Martin-Uriz, P and Mirete, S and Alcolea, PJ and Gomez, MJ and Amils, R and Gonzalez-Pastor, JE}, title = {Nickel-resistance determinants in Acidiphilium sp. PM identified by genome-wide functional screening.}, journal = {PloS one}, volume = {9}, number = {4}, pages = {e95041}, pmid = {24740277}, issn = {1932-6203}, mesh = {ATP-Dependent Proteases/genetics ; Acidiphilium/*genetics/metabolism ; Bacteria/classification/genetics ; Bacterial Proteins/genetics/metabolism ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genome, Bacterial/*genetics ; Genomic Library ; Lipopolysaccharides/biosynthesis ; Microbial Viability/drug effects/genetics ; Molecular Sequence Data ; Nickel/metabolism/*pharmacology ; Open Reading Frames/genetics ; Operon ; Phylogeny ; Rivers/microbiology ; Sequence Analysis, DNA ; Spain ; }, abstract = {Acidiphilium spp. are conspicuous dwellers of acidic, metal-rich environments. Indeed, they are among the most metal-resistant organisms; yet little is known about the mechanisms behind the metal tolerance in this genus. Acidiphilium sp. PM is an environmental isolate from Rio Tinto, an acidic, metal-laden river located in southwestern Spain. The characterization of its metal resistance revealed a remarkable ability to tolerate high Ni concentrations. Here we report the screening of a genomic library of Acidiphilium sp. PM to identify genes involved in Ni resistance. This approach revealed seven different genes conferring Ni resistance to E. coli, two of which form an operon encoding the ATP-dependent protease HslVU (ClpQY). This protease was found to enhance resistance to both Ni and Co in E. coli, a function not previously reported. Other Ni-resistance determinants include genes involved in lipopolysaccharide biosynthesis and the synthesis of branched amino acids. The diversity of molecular functions of the genes recovered in the screening suggests that Ni resistance in Acidiphilium sp. PM probably relies on different molecular mechanisms.}, }
@article {pmid24738669, year = {2014}, author = {Rossi, F and Diaz, L and Wollam, A and Panesso, D and Zhou, Y and Rincon, S and Narechania, A and Xing, G and Di Gioia, TS and Doi, A and Tran, TT and Reyes, J and Munita, JM and Carvajal, LP and Hernandez-Roldan, A and Brandão, D and van der Heijden, IM and Murray, BE and Planet, PJ and Weinstock, GM and Arias, CA}, title = {Transferable vancomycin resistance in a community-associated MRSA lineage.}, journal = {The New England journal of medicine}, volume = {370}, number = {16}, pages = {1524-1531}, pmid = {24738669}, issn = {1533-4406}, support = {U54 HG004968/HG/NHGRI NIH HHS/United States ; 1U54 HG004968/HG/NHGRI NIH HHS/United States ; U54 HG003079/HG/NHGRI NIH HHS/United States ; R01 AI093749/AI/NIAID NIH HHS/United States ; K08 AI101005/AI/NIAID NIH HHS/United States ; }, mesh = {Adult ; Bacteremia/*microbiology ; Brazil ; Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; Male ; Methicillin-Resistant Staphylococcus aureus/*genetics ; Microbial Sensitivity Tests ; Multigene Family ; Mycosis Fungoides/complications ; Plasmids/genetics ; Sequence Analysis, DNA ; Vancomycin Resistance/*genetics ; }, abstract = {We report the case of a patient from Brazil with a bloodstream infection caused by a strain of methicillin-resistant Staphylococcus aureus (MRSA) that was susceptible to vancomycin (designated BR-VSSA) but that acquired the vanA gene cluster during antibiotic therapy and became resistant to vancomycin (designated BR-VRSA). Both strains belong to the sequence type (ST) 8 community-associated genetic lineage that carries the staphylococcal chromosomal cassette mec (SCCmec) type IVa and the S. aureus protein A gene (spa) type t292 and are phylogenetically related to MRSA lineage USA300. A conjugative plasmid of 55,706 bp (pBRZ01) carrying the vanA cluster was identified and readily transferred to other staphylococci. The pBRZ01 plasmid harbors DNA sequences that are typical of the plasmid-associated replication genes rep24 or rep21 described in community-associated MRSA strains from Australia (pWBG745). The presence and dissemination of community-associated MRSA containing vanA could become a serious public health concern.}, }
@article {pmid24736967, year = {2014}, author = {Stazi, MA and Toccaceli, V}, title = {[Genome and microbiome: hologenome. Is epigenetics their link?].}, journal = {Epidemiologia e prevenzione}, volume = {38}, number = {1}, pages = {67-68}, pmid = {24736967}, issn = {1120-9763}, mesh = {Animals ; *Epigenomics ; Gene Transfer, Horizontal ; *Genome ; Germ-Free Life ; Humans ; Intestines/microbiology ; Mice ; MicroRNAs/genetics ; *Microbiota ; }, }
@article {pmid24736222, year = {2014}, author = {Pawluk, A and Bondy-Denomy, J and Cheung, VH and Maxwell, KL and Davidson, AR}, title = {A new group of phage anti-CRISPR genes inhibits the type I-E CRISPR-Cas system of Pseudomonas aeruginosa.}, journal = {mBio}, volume = {5}, number = {2}, pages = {e00896}, pmid = {24736222}, issn = {2150-7511}, support = {MOP-130482//Canadian Institutes of Health Research/Canada ; MOP-62796//Canadian Institutes of Health Research/Canada ; }, mesh = {*CRISPR-Cas Systems ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Host-Parasite Interactions ; Pseudomonas Phages/*genetics/*growth &amp; development ; Pseudomonas aeruginosa/*genetics/*virology ; Viral Proteins/*metabolism ; }, abstract = {CRISPR-Cas systems are one of the most widespread phage resistance mechanisms in prokaryotes. Our lab recently identified the first examples of phage-borne anti-CRISPR genes that encode protein inhibitors of the type I-F CRISPR-Cas system of Pseudomonas aeruginosa. A key question arising from this work was whether there are other types of anti-CRISPR genes. In the current work, we address this question by demonstrating that some of the same phages carrying type I-F anti-CRISPR genes also possess genes that mediate inhibition of the type I-E CRISPR-Cas system of P. aeruginosa. We have discovered four distinct families of these type I-E anti-CRISPR genes. These genes do not inhibit the type I-F CRISPR-Cas system of P. aeruginosa or the type I-E system of Escherichia coli. Type I-E and I-F anti-CRISPR genes are located at the same position in the genomes of a large group of related P. aeruginosa phages, yet they are found in a variety of combinations and arrangements. We have also identified functional anti-CRISPR genes within nonprophage Pseudomonas genomic regions that are likely mobile genetic elements. This work emphasizes the potential importance of anti-CRISPR genes in phage evolution and lateral gene transfer and supports the hypothesis that more undiscovered families of anti-CRISPR genes exist. Finally, we provide the first demonstration that the type I-E CRISPR-Cas system of P. aeruginosa is naturally active without genetic manipulation, which contrasts with E. coli and other previously characterized I-E systems. IMPORTANCE The CRISPR-Cas system is an adaptive immune system possessed by the majority of prokaryotic organisms to combat potentially harmful foreign genetic elements. This study reports the discovery of bacteriophage-encoded anti-CRISPR genes that mediate inhibition of a well-studied subtype of CRISPR-Cas system. The four families of anti-CRISPR genes described here, which comprise only the second group of anti-CRISPR genes to be identified, encode small proteins that bear no sequence similarity to previously studied phage or bacterial proteins. Anti-CRISPR genes represent a newly discovered and intriguing facet of the ongoing evolutionary competition between phages and their bacterial hosts.}, }
@article {pmid24735463, year = {2014}, author = {Ettensohn, CA}, title = {Horizontal transfer of the msp130 gene supported the evolution of metazoan biomineralization.}, journal = {Evolution &amp; development}, volume = {16}, number = {3}, pages = {139-148}, doi = {10.1111/ede.12074}, pmid = {24735463}, issn = {1525-142X}, mesh = {Amino Acid Sequence ; Animal Shells/physiology ; Animals ; *Calcification, Physiologic ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; Sea Urchins/genetics/*physiology ; Sequence Alignment ; }, abstract = {It is widely accepted that biomineralized structures appeared independently in many metazoan clades during the Cambrian. How this occurred, and whether it involved the parallel co-option of a common set of biochemical and developmental pathways (i.e., a shared biomineralization "toolkit"), are questions that remain unanswered. Here, I provide evidence that horizontal gene transfer supported the evolution of biomineralization in some metazoans. I show that Msp130 proteins, first described as proteins expressed selectively by the biomineral-forming primary mesenchyme cells of the sea urchin embryo, have a much wider taxonomic distribution than was previously appreciated. Msp130 proteins are present in several invertebrate deuterostomes and in one protostome clade (molluscs). Surprisingly, closely related proteins are also present in many bacteria and several algae, and I propose that msp130 genes were introduced into metazoan lineages via multiple, independent horizontal gene transfer events. Phylogenetic analysis shows that the introduction of an ancestral msp130 gene occurred in the sea urchin lineage more than 250 million years ago and that msp130 genes underwent independent, parallel duplications in each of the metazoan phyla in which these genes are found.}, }
@article {pmid24733898, year = {2014}, author = {Li, FW and Villarreal, JC and Kelly, S and Rothfels, CJ and Melkonian, M and Frangedakis, E and Ruhsam, M and Sigel, EM and Der, JP and Pittermann, J and Burge, DO and Pokorny, L and Larsson, A and Chen, T and Weststrand, S and Thomas, P and Carpenter, E and Zhang, Y and Tian, Z and Chen, L and Yan, Z and Zhu, Y and Sun, X and Wang, J and Stevenson, DW and Crandall-Stotler, BJ and Shaw, AJ and Deyholos, MK and Soltis, DE and Graham, SW and Windham, MD and Langdale, JA and Wong, GK and Mathews, S and Pryer, KM}, title = {Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {18}, pages = {6672-6677}, pmid = {24733898}, issn = {1091-6490}, mesh = {Algal Proteins/genetics ; Anthocerotophyta/genetics ; Base Sequence ; Bryophyta/*genetics ; DNA, Plant/genetics ; Evolution, Molecular ; Ferns/*genetics ; *Gene Transfer, Horizontal ; Genes, Plant ; Molecular Sequence Data ; Photoreceptors, Plant/*genetics ; Phototropins/genetics ; Phylogeny ; Phytochrome/genetics ; Recombinant Fusion Proteins/genetics ; Transcriptome ; Xanthophylls/genetics ; }, abstract = {Ferns are well known for their shade-dwelling habits. Their ability to thrive under low-light conditions has been linked to the evolution of a novel chimeric photoreceptor--neochrome--that fuses red-sensing phytochrome and blue-sensing phototropin modules into a single gene, thereby optimizing phototropic responses. Despite being implicated in facilitating the diversification of modern ferns, the origin of neochrome has remained a mystery. We present evidence for neochrome in hornworts (a bryophyte lineage) and demonstrate that ferns acquired neochrome from hornworts via horizontal gene transfer (HGT). Fern neochromes are nested within hornwort neochromes in our large-scale phylogenetic reconstructions of phototropin and phytochrome gene families. Divergence date estimates further support the HGT hypothesis, with fern and hornwort neochromes diverging 179 Mya, long after the split between the two plant lineages (at least 400 Mya). By analyzing the draft genome of the hornwort Anthoceros punctatus, we also discovered a previously unidentified phototropin gene that likely represents the ancestral lineage of the neochrome phototropin module. Thus, a neochrome originating in hornworts was transferred horizontally to ferns, where it may have played a significant role in the diversification of modern ferns.}, }
@article {pmid24733896, year = {2014}, author = {Nasser, W and Beres, SB and Olsen, RJ and Dean, MA and Rice, KA and Long, SW and Kristinsson, KG and Gottfredsson, M and Vuopio, J and Raisanen, K and Caugant, DA and Steinbakk, M and Low, DE and McGeer, A and Darenberg, J and Henriques-Normark, B and Van Beneden, CA and Hoffmann, S and Musser, JM}, title = {Evolutionary pathway to increased virulence and epidemic group A Streptococcus disease derived from 3,615 genome sequences.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {17}, pages = {E1768-76}, pmid = {24733896}, issn = {1091-6490}, mesh = {Animals ; Base Sequence ; Disease Models, Animal ; *Epidemics ; *Evolution, Molecular ; Fasciitis, Necrotizing/epidemiology/genetics/microbiology ; Finland/epidemiology ; Genes, Bacterial/genetics ; Genome, Bacterial/*genetics ; Genomics ; Humans ; INDEL Mutation/genetics ; Pharyngitis/epidemiology/genetics/microbiology ; Polymorphism, Single Nucleotide/genetics ; Primates/microbiology ; Selection, Genetic ; Serotyping ; Streptococcal Infections/*epidemiology/*genetics/microbiology ; Streptococcus pyogenes/*genetics/isolation &amp; purification/*pathogenicity ; Time Factors ; Virulence/genetics ; }, abstract = {We sequenced the genomes of 3,615 strains of serotype Emm protein 1 (M1) group A Streptococcus to unravel the nature and timing of molecular events contributing to the emergence, dissemination, and genetic diversification of an unusually virulent clone that now causes epidemic human infections worldwide. We discovered that the contemporary epidemic clone emerged in stepwise fashion from a precursor cell that first contained the phage encoding an extracellular DNase virulence factor (streptococcal DNase D2, SdaD2) and subsequently acquired the phage encoding the SpeA1 variant of the streptococcal pyrogenic exotoxin A superantigen. The SpeA2 toxin variant evolved from SpeA1 by a single-nucleotide change in the M1 progenitor strain before acquisition by horizontal gene transfer of a large chromosomal region encoding secreted toxins NAD(+)-glycohydrolase and streptolysin O. Acquisition of this 36-kb region in the early 1980s into just one cell containing the phage-encoded sdaD2 and speA2 genes was the final major molecular event preceding the emergence and rapid intercontinental spread of the contemporary epidemic clone. Thus, we resolve a decades-old controversy about the type and sequence of genomic alterations that produced this explosive epidemic. Analysis of comprehensive, population-based contemporary invasive strains from seven countries identified strong patterns of temporal population structure. Compared with a preepidemic reference strain, the contemporary clone is significantly more virulent in nonhuman primate models of pharyngitis and necrotizing fasciitis. A key finding is that the molecular evolutionary events transpiring in just one bacterial cell ultimately have produced millions of human infections worldwide.}, }
@article {pmid24732957, year = {2014}, author = {Hawkins, NJ and Cools, HJ and Sierotzki, H and Shaw, MW and Knogge, W and Kelly, SL and Kelly, DE and Fraaije, BA}, title = {Paralog re-emergence: a novel, historically contingent mechanism in the evolution of antimicrobial resistance.}, journal = {Molecular biology and evolution}, volume = {31}, number = {7}, pages = {1793-1802}, pmid = {24732957}, issn = {1537-1719}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Ascomycota/classification/drug effects/*genetics ; Azoles/pharmacology ; Cytochrome P-450 Enzyme System/*genetics ; *Drug Resistance, Fungal ; Evolution, Molecular ; Fungal Proteins/*genetics ; Fungicides, Industrial/pharmacology ; Hordeum/microbiology ; Phylogeny ; Selection, Genetic ; Sequence Analysis, DNA ; }, abstract = {Evolution of resistance to drugs and pesticides poses a serious threat to human health and agricultural production. CYP51 encodes the target site of azole fungicides, widely used clinically and in agriculture. Azole resistance can evolve due to point mutations or overexpression of CYP51, and previous studies have shown that fungicide-resistant alleles have arisen by de novo mutation. Paralogs CYP51A and CYP51B are found in filamentous ascomycetes, but CYP51A has been lost from multiple lineages. Here, we show that in the barley pathogen Rhynchosporium commune, re-emergence of CYP51A constitutes a novel mechanism for the evolution of resistance to azoles. Pyrosequencing analysis of historical barley leaf samples from a unique long-term experiment from 1892 to 2008 indicates that the majority of the R. commune population lacked CYP51A until 1985, after which the frequency of CYP51A rapidly increased. Functional analysis demonstrates that CYP51A retains the same substrate as CYP51B, but with different transcriptional regulation. Phylogenetic analyses show that the origin of CYP51A far predates azole use, and newly sequenced Rhynchosporium genomes show CYP51A persisting in the R. commune lineage rather than being regained by horizontal gene transfer; therefore, CYP51A re-emergence provides an example of adaptation to novel compounds by selection from standing genetic variation.}, }
@article {pmid24729584, year = {2014}, author = {Freire Martín, I and AbuOun, M and Reichel, R and La Ragione, RM and Woodward, MJ}, title = {Sequence analysis of a CTX-M-1 IncI1 plasmid found in Salmonella 4,5,12:i:-, Escherichia coli and Klebsiella pneumoniae on a UK pig farm.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {69}, number = {8}, pages = {2098-2101}, doi = {10.1093/jac/dku098}, pmid = {24729584}, issn = {1460-2091}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Base Sequence ; Cefotaxime/pharmacology ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/drug effects/*genetics/isolation &amp; purification ; Escherichia coli Infections/drug therapy/veterinary ; Gene Transfer, Horizontal ; Klebsiella Infections/drug therapy/veterinary ; Klebsiella pneumoniae/drug effects/*genetics/isolation &amp; purification ; Microbial Sensitivity Tests ; Mutation ; Plasmids/genetics ; Salmonella Infections, Animal/drug therapy ; Salmonella enterica/drug effects/*genetics/isolation &amp; purification ; Sequence Analysis, DNA ; Swine ; United Kingdom ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: In 2009, CTX-M Enterobacteriaceae and Salmonella isolates were recovered from a UK pig farm, prompting studies into the dissemination of the resistance and to establish any relationships between the isolates.<br><br>METHODS: PFGE was used to elucidate clonal relationships between isolates whilst plasmid profiling, restriction analysis, sequencing and PCR were used to characterize the CTX-M-harbouring plasmids.<br><br>RESULTS: Escherichia coli, Klebsiella pneumoniae and Salmonella 4,5,12:i:- and Bovismorbificans resistant to cefotaxime (n&#x200a;=&#x200a;65) were recovered and 63 were shown by PCR to harbour a group 1 CTX-M gene. The harbouring hosts were diverse, but the group 1 CTX-M plasmids were common. Three sequenced CTX-M plasmids from E. coli, K. pneumoniae and Salmonella enterica serotype 4,5,12:i:- were identical except for seven mutations and highly similar to IncI1 plasmid ColIb-P9. Two antimicrobial resistance regions were identified: one inserted upstream of yacABC harbouring ISCR2 transposases, sul2 and floR; and the other inserted within shfB of the pilV shufflon harbouring the ISEcp1 transposase followed by blaCTX-M-1.<br><br>CONCLUSIONS: These data suggest that an ST108 IncI1 plasmid encoding a blaCTX-M-1 gene had disseminated across multiple genera on this farm, an example of horizontal gene transfer of the blaCTX-M-1 gene.}, }
@article {pmid24728941, year = {2014}, author = {Shi, L and Ji, B and Kolar-Znika, L and Boskovic, A and Jadeau, F and Combet, C and Grangeasse, C and Franjevic, D and Talla, E and Mijakovic, I}, title = {Evolution of bacterial protein-tyrosine kinases and their relaxed specificity toward substrates.}, journal = {Genome biology and evolution}, volume = {6}, number = {4}, pages = {800-817}, pmid = {24728941}, issn = {1759-6653}, mesh = {Bacillus subtilis/enzymology/*genetics ; Bacterial Proteins/*genetics/metabolism ; *Evolution, Molecular ; Protein-Tyrosine Kinases/*genetics/metabolism ; Substrate Specificity/physiology ; }, abstract = {It has often been speculated that bacterial protein-tyrosine kinases (BY-kinases) evolve rapidly and maintain relaxed substrate specificity to quickly adopt new substrates when evolutionary pressure in that direction arises. Here, we report a phylogenomic and biochemical analysis of BY-kinases, and their relationship to substrates aimed to validate this hypothesis. Our results suggest that BY-kinases are ubiquitously distributed in bacterial phyla and underwent a complex evolutionary history, affected considerably by gene duplications and horizontal gene transfer events. This is consistent with the fact that the BY-kinase sequences represent a high level of substitution saturation and have a higher evolutionary rate compared with other bacterial genes. On the basis of similarity networks, we could classify BY kinases into three main groups with 14 subgroups. Extensive sequence conservation was observed only around the three canonical Walker motifs, whereas unique signatures proposed the functional speciation and diversification within some subgroups. The relationship between BY-kinases and their substrates was analyzed using a ubiquitous substrate (Ugd) and some Firmicute-specific substrates (YvyG and YjoA) from Bacillus subtilis. No evidence of coevolution between kinases and substrates at the sequence level was found. Seven BY-kinases, including well-characterized and previously uncharacterized ones, were used for experimental studies. Most of the tested kinases were able to phosphorylate substrates from B. subtilis (Ugd, YvyG, and YjoA), despite originating from very distant bacteria. Our results are consistent with the hypothesis that BY-kinases have evolved relaxed substrate specificity and are probably maintained as rapidly evolving platforms for adopting new substrates.}, }
@article {pmid24728610, year = {2014}, author = {Alibayov, B and Baba-Moussa, L and Sina, H and Zdeňková, K and Demnerová, K}, title = {Staphylococcus aureus mobile genetic elements.}, journal = {Molecular biology reports}, volume = {41}, number = {8}, pages = {5005-5018}, pmid = {24728610}, issn = {1573-4978}, mesh = {Bacteriophages/*genetics ; Chromosomes, Bacterial/*genetics ; DNA Transposable Elements/*genetics ; Gene Transfer, Horizontal/*genetics ; Genomic Islands/*genetics ; Humans ; Interspersed Repetitive Sequences/*genetics ; Staphylococcus aureus/*genetics ; }, abstract = {Among the bacteria groups, most of them are known to be beneficial to human being whereas only a minority is being recognized as harmful. The pathogenicity of bacteria is due, in part, to their rapid adaptation in the presence of selective pressures exerted by the human host. In addition, through their genomes, bacteria are subject to mutations, various rearrangements or horizontal gene transfer among and/or within bacterial species. Bacteria's essential metabolic functions are generally encoding by the core genes. Apart of the core genes, there are several number of mobile genetic elements (MGE) acquired by horizontal gene transfer that might be beneficial under certain environmental conditions. These MGE namely bacteriophages, transposons, plasmids, and pathogenicity islands represent about 15% Staphylococcus aureus genomes. The acquisition of most of the MGE is made by horizontal genomic islands (GEI), recognized as discrete DNA segments between closely related strains, transfer. The GEI contributes to the wide spread of microorganisms with an important effect on their genome plasticity and evolution. The GEI are also involve in the antibiotics resistance and virulence genes dissemination. In this review, we summarize the mobile genetic elements of S. aureus.}, }
@article {pmid24727645, year = {2014}, author = {Oliveira, P and Lima, FM and Cruz, MC and Ferreira, RC and Sanchez-Flores, A and Cordero, EM and Cortez, DR and Ferreira, &#xc9;R and Briones, MR and Mortara, RA and da Silveira, JF and Bahia, D}, title = {Trypanosoma cruzi: Genome characterization of phosphatidylinositol kinase gene family (PIK and PIK-related) and identification of a novel PIK gene.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {25}, number = {}, pages = {157-165}, doi = {10.1016/j.meegid.2014.03.022}, pmid = {24727645}, issn = {1567-7257}, mesh = {Bayes Theorem ; Chagas Disease/epidemiology ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Protozoan ; Humans ; Phosphatidylinositol 3-Kinases/*genetics/metabolism ; Phylogeny ; Protozoan Proteins/*genetics/metabolism ; Trypanosoma cruzi/*classification/*enzymology/genetics ; }, abstract = {Chagas disease is caused by the protozoan Trypanosoma cruzi which affects 10 million people worldwide. Very few kinases have been characterized in this parasite, including the phosphatidylinositol kinases (PIKs) that are at the heart of one of the major pathways of intracellular signal transduction. Recently, we have classified the PIK family in T. cruzi using five different models based on the presence of PIK conserved domains. In this study, we have mapped PIK genes to the chromosomes of two different T. cruzi lineages (G and CL Brener) and determined the cellular localization of two PIK members. The kinases have crucial roles in metabolism and are assumed to be conserved throughout evolution. For this reason, they should display a conserved localization within the same eukaryotic species. In spite of this, there is an extensive polymorphism regarding PIK localization at both genomic and cellular levels, among different T. cruzi isolates and between T. cruzi and Trypanosomabrucei, respectively. We showed in this study that the cellular localization of two PIK-related proteins (TOR1 and 2) in the T. cruzi lineage is distinct from that previously observed in T. brucei. In addition, we identified a new PIK gene with peculiar feature, that is, it codes for a FYVE domain at N-terminal position. FYVE-PIK genes are phylogenetically distant from the groups containing exclusively the FYVE or PIK domain. The FYVE-PIK architecture is only present in trypanosomatids and in virus such as Acanthamoeba mimivirus, suggesting a horizontal acquisition. Our Bayesian phylogenetic inference supports this hypothesis. The exact functions of this FYVE-PIK gene are unknown, but the presence of FYVE domain suggests a role in membranous compartments, such as endosome. Taken together, the data presented here strengthen the possibility that trypanosomatids are characterized by extensive genomic plasticity that may be considered in designing drugs and vaccines for prevention of Chagas disease.}, }
@article {pmid24727276, year = {2014}, author = {Beimgraben, C and Gutekunst, K and Opitz, F and Appel, J}, title = {hypD as a marker for [NiFe]-hydrogenases in microbial communities of surface waters.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {12}, pages = {3776-3782}, pmid = {24727276}, issn = {1098-5336}, mesh = {Bacteria/classification/*enzymology/genetics/isolation &amp; purification ; Ecosystem ; Hydrogen/metabolism ; Hydrogenase/*genetics/metabolism ; Lakes/*microbiology ; Molecular Sequence Data ; Phylogeny ; Proteins/*genetics/metabolism ; }, abstract = {Hydrogen is an important trace gas in the atmosphere. Soil microorganisms are known to be an important part of the biogeochemical H2 cycle, contributing 80 to 90% of the annual hydrogen uptake. Different aquatic ecosystems act as either sources or sinks of hydrogen, but the contribution of their microbial communities is unknown. [NiFe]-hydrogenases are the best candidates for hydrogen turnover in these environments since they are able to cope with oxygen. As they lack sufficiently conserved sequence motifs, reliable markers for these enzymes are missing, and consequently, little is known about their environmental distribution. We analyzed the essential maturation genes of [NiFe]-hydrogenases, including their frequency of horizontal gene transfer, and found hypD to be an applicable marker for the detection of the different known hydrogenase groups. Investigation of two freshwater lakes showed that [NiFe]-hydrogenases occur in many prokaryotic orders. We found that the respective hypD genes cooccur with oxygen-tolerant [NiFe]-hydrogenases (groups 1 and 5) mainly of Actinobacteria, Acidobacteria, and Burkholderiales; cyanobacterial uptake hydrogenases (group 2a) of cyanobacteria; H2-sensing hydrogenases (group 2b) of Burkholderiales, Rhizobiales, and Rhodobacterales; and two groups of multimeric soluble hydrogenases (groups 3b and 3d) of Legionellales and cyanobacteria. These findings support and expand a previous analysis of metagenomic data (M. Barz et al., PLoS One 5:e13846, 2010, http://dx.doi.org/10.1371/journal.pone.0013846) and further identify [NiFe]-hydrogenases that could be involved in hydrogen cycling in aquatic surface waters.}, }
@article {pmid24727020, year = {2014}, author = {Ahn, SJ and Dermauw, W and Wybouw, N and Heckel, DG and Van Leeuwen, T}, title = {Bacterial origin of a diverse family of UDP-glycosyltransferase genes in the Tetranychus urticae genome.}, journal = {Insect biochemistry and molecular biology}, volume = {50}, number = {}, pages = {43-57}, doi = {10.1016/j.ibmb.2014.04.003}, pmid = {24727020}, issn = {1879-0240}, mesh = {Animals ; Arthropods/enzymology/genetics ; Astacoidea/enzymology/genetics ; Cladocera/enzymology/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome ; Glycosyltransferases/*genetics/metabolism ; Introns ; Phylogeny ; Tetranychidae/*enzymology/*genetics ; Xenobiotics/metabolism/toxicity ; }, abstract = {UDP-glycosyltransferases (UGTs) catalyze the conjugation of a variety of small lipophilic molecules with uridine diphosphate (UDP) sugars, altering them into more water-soluble metabolites. Thereby, UGTs play an important role in the detoxification of xenobiotics and in the regulation of endobiotics. Recently, the genome sequence was reported for the two-spotted spider mite, Tetranychus urticae, a polyphagous herbivore damaging a number of agricultural crops. Although various gene families implicated in xenobiotic metabolism have been documented in T. urticae, UGTs so far have not. We identified 80 UGT genes in the T. urticae genome, the largest number of UGT genes in a metazoan species reported so far. Phylogenetic analysis revealed that lineage-specific gene expansions increased the diversity of the T. urticae UGT repertoire. Genomic distribution, intron-exon structure and structural motifs in the T. urticae UGTs were also described. In addition, expression profiling after host-plant shifts and in acaricide resistant lines supported an important role for UGT genes in xenobiotic metabolism. Expanded searches of UGTs in other arachnid species (Subphylum Chelicerata), including a spider, a scorpion, two ticks and two predatory mites, unexpectedly revealed the complete absence of UGT genes. However, a centipede (Subphylum Myriapoda) and a water flea and a crayfish (Subphylum Crustacea) contain UGT genes in their genomes similar to insect UGTs, suggesting that the UGT gene family might have been lost early in the Chelicerata lineage and subsequently re-gained in the tetranychid mites. Sequence similarity of T. urticae UGTs and bacterial UGTs and their phylogenetic reconstruction suggest that spider mites acquired UGT genes from bacteria by horizontal gene transfer. Our findings show a unique evolutionary history of the T. urticae UGT gene family among other arthropods and provide important clues to its functions in relation to detoxification and thereby host adaptation.}, }
@article {pmid24371153, year = {2014}, author = {Jaron, KS and Moravec, JC and Martínková, N}, title = {SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes.}, journal = {Bioinformatics (Oxford, England)}, volume = {30}, number = {8}, pages = {1081-1086}, doi = {10.1093/bioinformatics/btt727}, pmid = {24371153}, issn = {1367-4811}, mesh = {Base Composition ; Computational Biology ; Eukaryota/*genetics ; *Gene Transfer, Horizontal ; *Genomic Islands ; Genomics/methods ; *Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {MOTIVATION: Genomic islands (GIs) are DNA fragments incorporated into a genome through horizontal gene transfer (also called lateral gene transfer), often with functions novel for a given organism. While methods for their detection are well researched in prokaryotes, the complexity of eukaryotic genomes makes direct utilization of these methods unreliable, and so labour-intensive phylogenetic searches are used instead.<br><br>RESULTS: We present a surrogate method that investigates nucleotide base composition of the DNA sequence in a eukaryotic genome and identifies putative GIs. We calculate a genomic signature as a vector of tetranucleotide (4-mer) frequencies using a sliding window approach. Extending the neighbourhood of the sliding window, we establish a local kernel density estimate of the 4-mer frequency. We score the number of 4-mer frequencies in the sliding window that deviate from the credibility interval of their local genomic density using a newly developed discrete interval accumulative score (DIAS). To further improve the effectiveness of DIAS, we select informative 4-mers in a range of organisms using the tetranucleotide quality score developed herein. We show that the SigHunt method is computationally efficient and able to detect GIs in eukaryotic genomes that represent non-ameliorated integration. Thus, it is suited to scanning for change in organisms with different DNA composition.<br><br>Source code and scripts freely available for download at http://www.iba.muni.cz/index-en.php?pg=research-data-analysis-tools-sighunt are implemented in C and R and are platform-independent.<br><br>CONTACT: 376090@mail.muni.cz or martinkova@ivb.cz.}, }
@article {pmid24723149, year = {2014}, author = {Yamada, K and Kawanishi, Y and Yamada, A and Tokuda, G and Gurung, RD and Sasaki, T and Nakajima, Y and Maekawa, H}, title = {A novel cluster of mariner-like elements belonging to mellifera subfamily from spiders and insects: implications of recent horizontal transfer on the South-West Islands of Japan.}, journal = {Genetica}, volume = {142}, number = {2}, pages = {149-160}, pmid = {24723149}, issn = {1573-6857}, mesh = {Amino Acid Sequence ; Animals ; DNA Transposable Elements/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Insect ; Hymenoptera/*classification/*genetics ; Insect Proteins/genetics ; Japan ; Lepidoptera/*classification/*genetics ; Phylogeny ; Sequence Alignment ; Transposases/genetics ; }, abstract = {Mariner-like elements (MLEs) have been isolated from various eukaryotic genomes and they are divided into 15 subfamilies, including main five subfamilies: mauritiana, cecropia, mellifera/capitata, irritans, and elegans/briggsae. In the present study, MLEs belonging to mellifera subfamily were isolated from various spiders and insects (Hymenoptera and Lepidoptera) inhabiting the South-West Islands of Japan and neighboring regions. MLEs isolated from 15 different species formed a distinct novel cluster in mellifera subfamily. MLEs obtained from three different species [i.e., the bee Amegilla senahai subflavescens (Amsmar1), the wasp Campsomeris sp. (Casmar1), and the swallowtail butterfly Pachliopta aristolochiae (Paamar1)] contained an intact open reading frame that encoded a putative transposase. These transposases exhibited high similarity of 97.9% among themselves. In case of Casmar1, the presence of an intact ORF was found in high frequencies (i.e., 11 out of 12 clones). In addition, these transposases also showed the presence of a terminal inverted repeat-binding motif, DD(34)D and two highly conserved amino acid motifs, (W/L)(I/L)PHQL and YSP(D/N)L(A/S)P. These two motifs differed from previously known motifs, WVPHEL and YSPDLAP. MLEs isolated from these three different species may have been inserted into their genomes by horizontal transfer. Furthermore, the presence of an intact ORF suggests that they are still active in habitats along these isolated islands.}, }
@article {pmid24722668, year = {2014}, author = {Zhao, H and Xu, C and Lu, HL and Chen, X and St Leger, RJ and Fang, W}, title = {Host-to-pathogen gene transfer facilitated infection of insects by a pathogenic fungus.}, journal = {PLoS pathogens}, volume = {10}, number = {4}, pages = {e1004009}, pmid = {24722668}, issn = {1553-7374}, mesh = {Animals ; Beauveria/genetics/metabolism ; Carrier Proteins/*biosynthesis/genetics ; Cholesterol/metabolism ; *Fungal Proteins/biosynthesis/genetics ; Gene Transfer, Horizontal/*physiology ; Host-Pathogen Interactions/*physiology ; Metarhizium/*physiology ; Moths/metabolism/*microbiology ; *Phylogeny ; }, abstract = {Metarhizium robertsii is a plant root colonizing fungus that is also an insect pathogen. Its entomopathogenicity is a characteristic that was acquired during evolution from a plant endophyte ancestor. This transition provides a novel perspective on how new functional mechanisms important for host switching and virulence have evolved. From a random T-DNA insertion library, we obtained a pathogenicity defective mutant that resulted from the disruption of a sterol carrier gene (Mr-npc2a). Phylogenetic analysis revealed that Metarhizium acquired Mr-npc2a from an insect by horizontal gene transfer (HGT). Mr-NPC2a binds to cholesterol, an animal sterol, rather than the fungal sterol ergosterol, indicating it retains the specificity of insect NPC2 proteins. Mr-NPC2a is an intracellular protein and is exclusively expressed in the hemolymph of living insects. The disruption of Mr-npc2a reduced the amount of sterol in cell membranes of the yeast-like hyphal bodies that facilitate dispersal in the host body. These were consequently more susceptible to insect immune responses than the wild type. Transgenic expression of Mr-NPC2a increased the virulence of Beauveria bassiana, an endophytic insect-pathogenic fungus that lacks a Mr-NPC2a homolog.}, }
@article {pmid24718603, year = {2014}, author = {Eyun, SI and Wang, H and Pauchet, Y and Ffrench-Constant, RH and Benson, AK and Valencia-Jiménez, A and Moriyama, EN and Siegfried, BD}, title = {Molecular evolution of glycoside hydrolase genes in the Western corn rootworm (Diabrotica virgifera virgifera).}, journal = {PloS one}, volume = {9}, number = {4}, pages = {e94052}, pmid = {24718603}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Animals ; Coleoptera/*genetics ; Evolution, Molecular ; Gene Expression Regulation, Developmental ; *Genes, Insect ; Glycoside Hydrolases/biosynthesis/classification/*genetics ; Insect Proteins/biosynthesis/classification/*genetics ; Larva/enzymology ; Molecular Sequence Data ; Ovum/enzymology ; Phylogeny ; RNA Interference ; Sequence Alignment ; Sequence Analysis, RNA ; Sequence Homology, Amino Acid ; Transcriptome ; }, abstract = {Cellulose is an important nutritional resource for a number of insect herbivores. Digestion of cellulose and other polysaccharides in plant-based diets requires several types of enzymes including a number of glycoside hydrolase (GH) families. In a previous study, we showed that a single GH45 gene is present in the midgut tissue of the western corn rootworm, Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae). However, the presence of multiple enzymes was also suggested by the lack of a significant biological response when the expression of the gene was silenced by RNA interference. In order to clarify the repertoire of cellulose-degrading enzymes and related GH family proteins in D. v. virgifera, we performed next-generation sequencing and assembled transcriptomes from the tissue of three different developmental stages (eggs, neonates, and third instar larvae). Results of this study revealed the presence of seventy-eight genes that potentially encode GH enzymes belonging to eight families (GH45, GH48, GH28, GH16, GH31, GH27, GH5, and GH1). The numbers of GH45 and GH28 genes identified in D. v. virgifera are among the largest in insects where these genes have been identified. Three GH family genes (GH45, GH48, and GH28) are found almost exclusively in two coleopteran superfamilies (Chrysomeloidea and Curculionoidea) among insects, indicating the possibility of their acquisitions by horizontal gene transfer rather than simple vertical transmission from ancestral lineages of insects. Acquisition of GH genes by horizontal gene transfers and subsequent lineage-specific GH gene expansion appear to have played important roles for phytophagous beetles in specializing on particular groups of host plants and in the case of D. v. virgifera, its close association with maize.}, }
@article {pmid24717845, year = {2014}, author = {Dunkle, JA and Vinal, K and Desai, PM and Zelinskaya, N and Savic, M and West, DM and Conn, GL and Dunham, CM}, title = {Molecular recognition and modification of the 30S ribosome by the aminoglycoside-resistance methyltransferase NpmA.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {17}, pages = {6275-6280}, pmid = {24717845}, issn = {1091-6490}, support = {R01 AI088025/AI/NIAID NIH HHS/United States ; P41 RR015301/RR/NCRR NIH HHS/United States ; RR-15301/RR/NCRR NIH HHS/United States ; R01 GM093278/GM/NIGMS NIH HHS/United States ; R01-GM093279/GM/NIGMS NIH HHS/United States ; R01-AI088025/AI/NIAID NIH HHS/United States ; R01 GM093279/GM/NIGMS NIH HHS/United States ; }, mesh = {Adenosine/analogs &amp; derivatives/chemistry/pharmacology ; Amino Acids/metabolism ; Aminoglycosides/*pharmacology ; Biocatalysis/drug effects ; Catalytic Domain ; Conserved Sequence ; Crystallography, X-Ray ; Drug Resistance, Bacterial/drug effects ; Escherichia coli/drug effects/*enzymology ; Escherichia coli Proteins/*chemistry/*metabolism ; Gene Transfer, Horizontal/drug effects ; Methylation/drug effects ; Methyltransferases/*chemistry/*metabolism ; *Models, Molecular ; Nucleotides/metabolism ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA, Ribosomal, 16S/chemistry ; Ribosome Subunits, Small, Bacterial/*chemistry/*metabolism ; Structure-Activity Relationship ; }, abstract = {Aminoglycosides are potent, broad spectrum, ribosome-targeting antibacterials whose clinical efficacy is seriously threatened by multiple resistance mechanisms. Here, we report the structural basis for 30S recognition by the novel plasmid-mediated aminoglycoside-resistance rRNA methyltransferase A (NpmA). These studies are supported by biochemical and functional assays that define the molecular features necessary for NpmA to catalyze m(1)A1408 modification and confer resistance. The requirement for the mature 30S as a substrate for NpmA is clearly explained by its recognition of four disparate 16S rRNA helices brought into proximity by 30S assembly. Our structure captures a "precatalytic state" in which multiple structural reorganizations orient functionally critical residues to flip A1408 from helix 44 and position it precisely in a remodeled active site for methylation. Our findings provide a new molecular framework for the activity of aminoglycoside-resistance rRNA methyltransferases that may serve as a functional paradigm for other modification enzymes acting late in 30S biogenesis.}, }
@article {pmid24713320, year = {2014}, author = {Winstel, V and Sanchez-Carballo, P and Holst, O and Xia, G and Peschel, A}, title = {Biosynthesis of the unique wall teichoic acid of Staphylococcus aureus lineage ST395.}, journal = {mBio}, volume = {5}, number = {2}, pages = {e00869}, pmid = {24713320}, issn = {2150-7511}, mesh = {Biosynthetic Pathways/genetics ; Cell Wall/*metabolism ; Gene Transfer, Horizontal ; Staphylococcus Phages/physiology ; Staphylococcus aureus/genetics/*metabolism ; Teichoic Acids/*biosynthesis ; Transduction, Genetic ; Virus Attachment ; }, abstract = {The major clonal lineages of the human pathogen Staphylococcus aureus produce cell wall-anchored anionic poly-ribitol-phosphate (RboP) wall teichoic acids (WTA) substituted with d-Alanine and N-acetyl-d-glucosamine. The phylogenetically isolated S. aureus ST395 lineage has recently been found to produce a unique poly-glycerol-phosphate (GroP) WTA glycosylated with N-acetyl-d-galactosamine (GalNAc). ST395 clones bear putative WTA biosynthesis genes on a novel genetic element probably acquired from coagulase-negative staphylococci (CoNS). We elucidated the ST395 WTA biosynthesis pathway and identified three novel WTA biosynthetic genes, including those encoding an α-O-GalNAc transferase TagN, a nucleotide sugar epimerase TagV probably required for generation of the activated sugar donor substrate for TagN, and an unusually short GroP WTA polymerase TagF. By using a panel of mutants derived from ST395, the GalNAc residues carried by GroP WTA were found to be required for infection by the ST395-specific bacteriophage Φ187 and to play a crucial role in horizontal gene transfer of S. aureus pathogenicity islands (SaPIs). Notably, ectopic expression of ST395 WTA biosynthesis genes rendered normal S. aureus susceptible to Φ187 and enabled Φ187-mediated SaPI transfer from ST395 to regular S. aureus. We provide evidence that exchange of WTA genes and their combination in variable, mosaic-like gene clusters have shaped the evolution of staphylococci and their capacities to undergo horizontal gene transfer events. IMPORTANCE The structural highly diverse wall teichoic acids (WTA) are cell wall-anchored glycopolymers produced by most Gram-positive bacteria. While most of the dominant Staphylococcus aureus lineages produce poly-ribitol-phosphate WTA, the recently described ST395 lineage produces a distinct poly-glycerol-phosphate WTA type resembling the WTA backbone of coagulase-negative staphylococci (CoNS). Here, we analyzed the ST395 WTA biosynthesis pathway and found new types of WTA biosynthesis genes along with an evolutionary link between ST395 and CoNS, from which the ST395 WTA genes probably originate. The elucidation of ST395 WTA biosynthesis will help to understand how Gram-positive bacteria produce highly variable WTA types and elucidate functional consequences of WTA variation.}, }
@article {pmid24713045, year = {2014}, author = {Papadimitriou, K and Anastasiou, R and Mavrogonatou, E and Blom, J and Papandreou, NC and Hamodrakas, SJ and Ferreira, S and Renault, P and Supply, P and Pot, B and Tsakalidou, E}, title = {Comparative genomics of the dairy isolate Streptococcus macedonicus ACA-DC 198 against related members of the Streptococcus bovis/Streptococcus equinus complex.}, journal = {BMC genomics}, volume = {15}, number = {}, pages = {272}, pmid = {24713045}, issn = {1471-2164}, mesh = {Adaptation, Biological/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats ; Dairy Products/*microbiology ; Energy Metabolism/genetics ; *Food Microbiology ; Gastrointestinal Tract/microbiology ; Gene Order ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; Genomic Islands ; *Genomics ; Humans ; Phylogeny ; Proteolysis ; Streptococcus/classification/*genetics/isolation &amp; purification/metabolism ; Streptococcus bovis/genetics/isolation &amp; purification/metabolism ; Virulence Factors/genetics ; Vitamins/biosynthesis ; }, abstract = {BACKGROUND: Within the genus Streptococcus, only Streptococcus thermophilus is used as a starter culture in food fermentations. Streptococcus macedonicus though, which belongs to the Streptococcus bovis/Streptococcus equinus complex (SBSEC), is also frequently isolated from fermented foods mainly of dairy origin. Members of the SBSEC have been implicated in human endocarditis and colon cancer. Here we compare the genome sequence of the dairy isolate S. macedonicus ACA-DC 198 to the other SBSEC genomes in order to assess in silico its potential adaptation to milk and its pathogenicity status.<br><br>RESULTS: Despite the fact that the SBSEC species were found tightly related based on whole genome phylogeny of streptococci, two distinct patterns of evolution were identified among them. Streptococcus macedonicus, Streptococcus infantarius CJ18 and Streptococcus pasteurianus ATCC 43144 seem to have undergone reductive evolution resulting in significantly diminished genome sizes and increased percentages of potential pseudogenes when compared to Streptococcus gallolyticus subsp. gallolyticus. In addition, the three species seem to have lost genes for catabolizing complex plant carbohydrates and for detoxifying toxic substances previously linked to the ability of S. gallolyticus to survive in the rumen. Analysis of the S. macedonicus genome revealed features that could support adaptation to milk, including an extra gene cluster for lactose and galactose metabolism, a proteolytic system for casein hydrolysis, auxotrophy for several vitamins, an increased ability to resist bacteriophages and horizontal gene transfer events with the dairy Lactococcus lactis and S. thermophilus as potential donors. In addition, S. macedonicus lacks several pathogenicity-related genes found in S. gallolyticus. For example, S. macedonicus has retained only one (i.e. the pil3) of the three pilus gene clusters which may mediate the binding of S. gallolyticus to the extracellular matrix. Unexpectedly, similar findings were obtained not only for the dairy S. infantarius CJ18, but also for the blood isolate S. pasteurianus ATCC 43144.<br><br>CONCLUSIONS: Our whole genome analyses suggest traits of adaptation of S. macedonicus to the nutrient-rich dairy environment. During this process the bacterium gained genes presumably important for this new ecological niche. Finally, S. macedonicus carries a reduced number of putative SBSEC virulence factors, which suggests a diminished pathogenic potential.}, }
@article {pmid24712882, year = {2014}, author = {Horn, K and Parker, IM and Malek, W and Rodríguez-Echeverría, S and Parker, MA}, title = {Disparate origins of Bradyrhizobium symbionts for invasive populations of Cytisus scoparius (Leguminosae) in North America.}, journal = {FEMS microbiology ecology}, volume = {89}, number = {1}, pages = {89-98}, doi = {10.1111/1574-6941.12335}, pmid = {24712882}, issn = {1574-6941}, mesh = {Base Sequence ; Bayes Theorem ; Bradyrhizobium/classification/*genetics ; Cytisus/*microbiology ; Europe ; Genes, Bacterial ; Genes, Essential ; Genomic Islands ; Introduced Species ; Multilocus Sequence Typing ; Phenotype ; Phylogeny ; Phylogeography ; RNA, Ribosomal/genetics ; Symbiosis/genetics ; United States ; }, abstract = {To identify the geographic origin of nodule bacteria associated with invasion of the European legume Cytisus scoparius in the United States, isolates from 15 sites in six states were compared to > 200 Bradyrhizobium strains from indigenous legumes in the U.S., Mexico, Europe (six countries), Morocco, and Australia. Portions of five housekeeping loci (2849 bp) were sequenced, along with the nifD locus in the symbiosis island (SI) portion of the Bradyrhizobium chromosome. Bayesian phylogenetic analysis showed that North American C. scoparius symbionts had highly heterogeneous ancestry. Some were grouped into three distinct clades of European C. scoparius symbionts. One isolate had both housekeeping and SI genes belonging to a Bradyrhizobium clade from native legumes in western North America. Two other clades had mosaic ancestry: sequences for nifD as well as two other SI genes (nifH, nodC) were highly similar or identical to a C. scoparius strain from Spain, while their housekeeping loci belonged to American Bradyrhizobium clades. Thus, it appears that bacteria ancestrally associated with other North American legumes have evolved to utilize C. scoparius, by acquiring SI-region genes from European C. scoparius symbionts. Inoculation assays indicated that North American isolates were as competent as European strains in promoting plant growth, consistent with the findings on symbiont ancestry.}, }
@article {pmid24711427, year = {2014}, author = {Fineran, PC and Gerritzen, MJ and Suárez-Diez, M and Künne, T and Boekhorst, J and van Hijum, SA and Staals, RH and Brouns, SJ}, title = {Degenerate target sites mediate rapid primed CRISPR adaptation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {16}, pages = {E1629-38}, pmid = {24711427}, issn = {1091-6490}, mesh = {Base Pair Mismatch/genetics ; Base Sequence ; Clustered Regularly Interspaced Short Palindromic Repeats/*genetics ; Databases, Genetic ; Escherichia coli K12/*genetics/*immunology ; High-Throughput Screening Assays ; Molecular Sequence Data ; Mutation/genetics ; Nucleotide Motifs/genetics ; Plasmids/genetics ; RNA, Bacterial/genetics ; }, abstract = {Prokaryotes encode adaptive immune systems, called CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated), to provide resistance against mobile invaders, such as viruses and plasmids. Host immunity is based on incorporation of invader DNA sequences in a memory locus (CRISPR), the formation of guide RNAs from this locus, and the degradation of cognate invader DNA (protospacer). Invaders can escape type I-E CRISPR-Cas immunity in Escherichia coli K12 by making point mutations in the seed region of the protospacer or its adjacent motif (PAM), but hosts quickly restore immunity by integrating new spacers in a positive-feedback process termed "priming." Here, by using a randomized protospacer and PAM library and high-throughput plasmid loss assays, we provide a systematic analysis of the constraints of both direct interference and subsequent priming in E. coli. We have defined a high-resolution genetic map of direct interference by Cascade and Cas3, which includes five positions of the protospacer at 6-nt intervals that readily tolerate mutations. Importantly, we show that priming is an extremely robust process capable of using degenerate target regions, with up to 13 mutations throughout the PAM and protospacer region. Priming is influenced by the number of mismatches, their position, and is nucleotide dependent. Our findings imply that even outdated spacers containing many mismatches can induce a rapid primed CRISPR response against diversified or related invaders, giving microbes an advantage in the coevolutionary arms race with their invaders.}, }
@article {pmid24711396, year = {2014}, author = {Quiles-Puchalt, N and Carpena, N and Alonso, JC and Novick, RP and Marina, A and Penadés, JR}, title = {Staphylococcal pathogenicity island DNA packaging system involving cos-site packaging and phage-encoded HNH endonucleases.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {16}, pages = {6016-6021}, pmid = {24711396}, issn = {1091-6490}, support = {R01 AI022159/AI/NIAID NIH HHS/United States ; R01AI022159/AI/NIAID NIH HHS/United States ; }, mesh = {Attachment Sites, Microbiological/*genetics ; *DNA Packaging ; DNA Replication ; Endonucleases/*metabolism ; Genomic Islands/*genetics ; Mutation/genetics ; Staphylococcus/*genetics/*virology ; Staphylococcus Phages/*enzymology/genetics/ultrastructure ; Viral Proteins/metabolism ; Virus Assembly ; }, abstract = {Staphylococcal pathogenicity islands (SaPIs) are the prototypical members of a widespread family of chromosomally located mobile genetic elements that contribute substantially to intra- and interspecies gene transfer, host adaptation, and virulence. The key feature of their mobility is the induction of SaPI excision and replication by certain helper phages and their efficient encapsidation into phage-like infectious particles. Most SaPIs use the headful packaging mechanism and encode small terminase subunit (TerS) homologs that recognize the SaPI-specific pac site and determine SaPI packaging specificity. Several of the known SaPIs do not encode a recognizable TerS homolog but are nevertheless packaged efficiently by helper phages and transferred at high frequencies. In this report, we have characterized one of the non-terS-coding SaPIs, SaPIbov5, and found that it uses two different, undescribed packaging strategies. SaPIbov5 is packaged in full-sized phage-like particles either by typical pac-type helper phages, or by cos-type phages--i.e., it has both pac and cos sites--a configuration that has not hitherto been described for any mobile element, phages included--and uses the two different phage-coded TerSs. To our knowledge, this is the first example of SaPI packaging by a cos phage, and in this, it resembles the P4 plasmid of Escherichia coli. Cos-site packaging in Staphylococcus aureus is additionally unique in that it requires the HNH nuclease, carried only by cos phages, in addition to the large terminase subunit, for cos-site cleavage and melting.}, }
@article {pmid24709563, year = {2014}, author = {Soo, RM and Skennerton, CT and Sekiguchi, Y and Imelfort, M and Paech, SJ and Dennis, PG and Steen, JA and Parks, DH and Tyson, GW and Hugenholtz, P}, title = {An expanded genomic representation of the phylum cyanobacteria.}, journal = {Genome biology and evolution}, volume = {6}, number = {5}, pages = {1031-1045}, pmid = {24709563}, issn = {1759-6653}, mesh = {Animals ; Biological Evolution ; Bioreactors/*microbiology ; Cyanobacteria/classification/*genetics/isolation &amp; purification/metabolism ; Feces/microbiology ; Genetics, Population ; *Genome, Bacterial ; Male ; Phascolarctidae/*microbiology ; Photosynthesis ; *Phylogeny ; RNA, Ribosomal, 16S ; Waste Disposal, Fluid/instrumentation/methods ; }, abstract = {Molecular surveys of aphotic habitats have indicated the presence of major uncultured lineages phylogenetically classified as members of the Cyanobacteria. One of these lineages has recently been proposed as a nonphotosynthetic sister phylum to the Cyanobacteria, the Melainabacteria, based on recovery of population genomes from human gut and groundwater samples. Here, we expand the phylogenomic representation of the Melainabacteria through sequencing of six diverse population genomes from gut and bioreactor samples supporting the inference that this lineage is nonphotosynthetic, but not the assertion that they are strictly fermentative. We propose that the Melainabacteria is a class within the phylogenetically defined Cyanobacteria based on robust monophyly and shared ancestral traits with photosynthetic representatives. Our findings are consistent with theories that photosynthesis occurred late in the Cyanobacteria and involved extensive lateral gene transfer and extends the recognized functionality of members of this phylum.}, }
@article {pmid24708309, year = {2014}, author = {Rudder, S and Doohan, F and Creevey, CJ and Wendt, T and Mullins, E}, title = {Genome sequence of Ensifer adhaerens OV14 provides insights into its ability as a novel vector for the genetic transformation of plant genomes.}, journal = {BMC genomics}, volume = {15}, number = {}, pages = {268}, pmid = {24708309}, issn = {1471-2164}, mesh = {Agrobacterium tumefaciens/genetics ; Bacterial Secretion Systems ; *Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; *Genome, Plant ; Host-Pathogen Interactions ; Phylogeny ; Plant Tumor-Inducing Plasmids/genetics ; Rhizobiaceae/classification/*physiology ; *Transformation, Genetic ; Virulence/genetics ; }, abstract = {BACKGROUND: Recently it has been shown that Ensifer adhaerens can be used as a plant transformation technology, transferring genes into several plant genomes when equipped with a Ti plasmid. For this study, we have sequenced the genome of Ensifer adhaerens OV14 (OV14) and compared it with those of Agrobacterium tumefaciens C58 (C58) and Sinorhizobium meliloti 1021 (1021); the latter of which has also demonstrated a capacity to genetically transform crop genomes, albeit at significantly reduced frequencies.<br><br>RESULTS: The 7.7 Mb OV14 genome comprises two chromosomes and two plasmids. All protein coding regions in the OV14 genome were functionally grouped based on an eggNOG database. No genes homologous to the A. tumefaciens Ti plasmid vir genes appeared to be present in the OV14 genome. Unexpectedly, OV14 and 1021 were found to possess homologs to chromosomal based genes cited as essential to A. tumefaciens T-DNA transfer. Of significance, genes that are non-essential but exert a positive influence on virulence and the ability to genetically transform host genomes were identified in OV14 but were absent from the 1021 genome.<br><br>CONCLUSIONS: This study reveals the presence of homologs to chromosomally based Agrobacterium genes that support T-DNA transfer within the genome of OV14 and other alphaproteobacteria. The sequencing and analysis of the OV14 genome increases our understanding of T-DNA transfer by non-Agrobacterium species and creates a platform for the continued improvement of Ensifer-mediated transformation (EMT).}, }
@article {pmid24707447, year = {2014}, author = {Grant, JR and Katz, LA}, title = {Building a phylogenomic pipeline for the eukaryotic tree of life - addressing deep phylogenies with genome-scale data.}, journal = {PLoS currents}, volume = {6}, number = {}, pages = {}, pmid = {24707447}, issn = {2157-3999}, support = {R15 GM097722/GM/NIGMS NIH HHS/United States ; }, abstract = {Background Understanding the evolutionary relationships of all eukaryotes on Earth remains a paramount goal of modern biology, yet analyzing homologous sequences across 1.8 billion years of eukaryotic evolution is challenging. Many existing tools for identifying gene orthologs are inadequate when working with heterogeneous rates of evolution and endosymbiotic/lateral gene transfer. Moreover, genomic-scale sequencing, which was once the domain of large sequencing centers, has advanced to the point where small laboratories can now generate the data needed for phylogenomic studies. This has opened the door for increased taxonomic sampling as individual research groups have the ability to conduct genome-scale projects on their favorite non-model organism. Results Here we present some of the tools developed, and insights gained, as we created a pipeline that combines data-mining from public databases and our own transcriptome data to study the eukaryotic tree of life. The first steps of a phylogenomic pipeline involve choosing taxa and loci, and making decisions about how to handle alleles, paralogs and non-overlapping sequences. Next, orthologs are aligned for analyses including gene tree reconstruction and concatenation for supermatrix approaches. To build our pipeline, we created scripts written in Python that integrate third-party tools with custom methods. As a test case, we present the placement of five amoebae on the eukaryotic tree of life based on analyses of transcriptome data. Our scripts available on GitHUb and may be used as-is for automated analyses of large scale phylogenomics, or adapted for use in other types of studies. Conclusion Analyses on the scale of all eukaryotes present challenges not necessarily found in studies of more closely related organisms. Our approach will be of relevance to others for whom existing third-party tools fail to fully answer desired phylogenetic questions.}, }
@article {pmid24706803, year = {2014}, author = {Rowland, MA and Deeds, EJ}, title = {Crosstalk and the evolution of specificity in two-component signaling.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {15}, pages = {5550-5555}, pmid = {24706803}, issn = {1091-6490}, mesh = {Amino Acid Sequence ; Bacteria/*genetics/metabolism ; *Biological Evolution ; Cluster Analysis ; Gene Transfer, Horizontal ; Histidine Kinase ; *Models, Biological ; Molecular Sequence Data ; Phosphorylation ; Phylogeny ; Protein Kinases/genetics/metabolism ; Receptor Cross-Talk/*physiology ; Regression Analysis ; Sequence Alignment ; Signal Transduction/*physiology ; Species Specificity ; }, abstract = {Two-component signaling (TCS) serves as the dominant signaling modality in bacteria. A typical pathway includes a sensor histidine kinase (HK) that phosphorylates a response regulator (RR), modulating its activity in response to an incoming signal. Most HKs are bifunctional, acting as both kinase and phosphatase for their substrates. Unlike eukaryotic signaling networks, there is very little crosstalk between bacterial TCS pathways; indeed, adding crosstalk to a pathway can have disastrous consequences for cell fitness. It is currently unclear exactly what feature of TCS necessitates this degree of pathway isolation. In this work we used mathematical models to show that, in the case of bifunctional HKs, adding a competing substrate to a TCS pathway will always reduce response of that pathway to incoming signals. We found that the pressure to maintain cognate signaling is sufficient to explain the experimentally observed "kinetic preference" of HKs for their cognate RRs. These findings imply a barrier to the evolution of new HK-RR pairs, because crosstalk is unavoidable immediately after the duplication of an existing pathway. We characterized a set of "near-neutral" evolutionary trajectories that minimize the impact of crosstalk on the function of the parental pathway. These trajectories predicted that crosstalk interactions should be removed before new input/output functionalities evolve. Analysis of HK sequences in bacterial genomes provided evidence that the selective pressures on the HK-RR interface are different from those experienced by the input domain immediately after duplication. This work thus provides a unifying explanation for the evolution of specificity in TCS networks.}, }
@article {pmid24706773, year = {2014}, author = {Rothman, DH and Fournier, GP and French, KL and Alm, EJ and Boyle, EA and Cao, C and Summons, RE}, title = {Methanogenic burst in the end-Permian carbon cycle.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {15}, pages = {5462-5467}, pmid = {24706773}, issn = {1091-6490}, mesh = {*Biological Evolution ; Carbon Cycle/physiology ; Carbon Isotopes/analysis ; China ; *Extinction, Biological ; Geologic Sediments/*chemistry ; History, Ancient ; Metabolic Networks and Pathways/*physiology ; Methane/*biosynthesis ; Methanosarcina/*genetics/physiology ; Nickel/analysis ; Oceans and Seas ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Volcanic Eruptions/adverse effects/*history ; }, abstract = {The end-Permian extinction is associated with a mysterious disruption to Earth's carbon cycle. Here we identify causal mechanisms via three observations. First, we show that geochemical signals indicate superexponential growth of the marine inorganic carbon reservoir, coincident with the extinction and consistent with the expansion of a new microbial metabolic pathway. Second, we show that the efficient acetoclastic pathway in Methanosarcina emerged at a time statistically indistinguishable from the extinction. Finally, we show that nickel concentrations in South China sediments increased sharply at the extinction, probably as a consequence of massive Siberian volcanism, enabling a methanogenic expansion by removal of nickel limitation. Collectively, these results are consistent with the instigation of Earth's greatest mass extinction by a specific microbial innovation.}, }
@article {pmid24696435, year = {2014}, author = {Evans, BA and Amyes, SG}, title = {OXA β-lactamases.}, journal = {Clinical microbiology reviews}, volume = {27}, number = {2}, pages = {241-263}, pmid = {24696435}, issn = {1098-6618}, mesh = {Acinetobacter/*enzymology/genetics/isolation &amp; purification ; Acinetobacter Infections/microbiology ; Anti-Bacterial Agents/*pharmacology ; Enterobacteriaceae/*enzymology/genetics/isolation &amp; purification ; Enterobacteriaceae Infections/microbiology ; Gene Transfer, Horizontal ; Humans ; *beta-Lactam Resistance ; beta-Lactamases/genetics/*metabolism ; }, abstract = {The OXA β-lactamases were among the earliest β-lactamases detected; however, these molecular class D β-lactamases were originally relatively rare and always plasmid mediated. They had a substrate profile limited to the penicillins, but some became able to confer resistance to cephalosporins. From the 1980s onwards, isolates of Acinetobacter baumannii that were resistant to the carbapenems emerged, manifested by plasmid-encoded β-lactamases (OXA-23, OXA-40, and OXA-58) categorized as OXA enzymes because of their sequence similarity to earlier OXA β-lactamases. It was soon found that every A. baumannii strain possessed a chromosomally encoded OXA β-lactamase (OXA-51-like), some of which could confer resistance to carbapenems when the genetic environment around the gene promoted its expression. Similarly, Acinetobacter species closely related to A. baumannii also possessed their own chromosomally encoded OXA β-lactamases; some could be transferred to A. baumannii, and they formed the basis of transferable carbapenem resistance in this species. In some cases, the carbapenem-resistant OXA β-lactamases (OXA-48) have migrated into the Enterobacteriaceae and are becoming a significant cause of carbapenem resistance. The emergence of OXA enzymes that can confer resistance to carbapenems, particularly in A. baumannii, has transformed these β-lactamases from a minor hindrance into a major problem set to demote the clinical efficacy of the carbapenems.}, }
@article {pmid24695589, year = {2014}, author = {Whidden, C and Zeh, N and Beiko, RG}, title = {Supertrees Based on the Subtree Prune-and-Regraft Distance.}, journal = {Systematic biology}, volume = {63}, number = {4}, pages = {566-581}, pmid = {24695589}, issn = {1076-836X}, mesh = {Algorithms ; Bacteria/*classification/genetics ; Classification/*methods ; *Computer Simulation ; Gene Transfer, Horizontal ; Genome, Bacterial/genetics ; *Phylogeny ; Reproducibility of Results ; }, abstract = {Supertree methods reconcile a set of phylogenetic trees into a single structure that is often interpreted as a branching history of species. A key challenge is combining conflicting evolutionary histories that are due to artifacts of phylogenetic reconstruction and phenomena such as lateral gene transfer (LGT). Many supertree approaches use optimality criteria that do not reflect underlying processes, have known biases, and may be unduly influenced by LGT. We present the first method to construct supertrees by using the subtree prune-and-regraft (SPR) distance as an optimality criterion. Although calculating the rooted SPR distance between a pair of trees is NP-hard, our new maximum agreement forest-based methods can reconcile trees with hundreds of taxa and>50 transfers in fractions of a second, which enables repeated calculations during the course of an iterative search. Our approach can accommodate trees in which uncertain relationships have been collapsed to multifurcating nodes. Using a series of benchmark datasets simulated under plausible rates of LGT, we show that SPR supertrees are more similar to correct species histories than supertrees based on parsimony or Robinson-Foulds distance criteria. We successfully constructed an SPR supertree from a phylogenomic dataset of 40,631 gene trees that covered 244 genomes representing several major bacterial phyla. Our SPR-based approach also allowed direct inference of highways of gene transfer between bacterial classes and genera. A Small number of these highways connect genera in different phyla and can highlight specific genes implicated in long-distance LGT. [Lateral gene transfer; matrix representation with parsimony; phylogenomics; prokaryotic phylogeny; Robinson-Foulds; subtree prune-and-regraft; supertrees.].}, }
@article {pmid24690293, year = {2014}, author = {Palomares-Rius, JE and Hirooka, Y and Tsai, IJ and Masuya, H and Hino, A and Kanzaki, N and Jones, JT and Kikuchi, T}, title = {Distribution and evolution of glycoside hydrolase family 45 cellulases in nematodes and fungi.}, journal = {BMC evolutionary biology}, volume = {14}, number = {}, pages = {69}, pmid = {24690293}, issn = {1471-2148}, mesh = {Animals ; Ascomycota/enzymology/*genetics ; Cellulase/chemistry/*genetics/metabolism ; *Evolution, Molecular ; Exons ; Introns ; Nematoda/enzymology/*genetics ; *Phylogeny ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT) has been suggested as the mechanism by which various plant parasitic nematode species have obtained genes important in parasitism. In particular, cellulase genes have been acquired by plant parasitic nematodes that allow them to digest plant cell walls. Unlike the typical glycoside hydrolase (GH) family 5 cellulase genes which are found in several nematode species from the order Tylenchida, members of the GH45 cellulase have only been identified in a cluster including the families Parasitaphelenchidae (with the pinewood nematode Bursaphelenchus xylophilus) and Aphelenchoididae, and their origins remain unknown.<br><br>RESULTS: In order to investigate the distribution and evolution of GH45 cellulase genes in nematodes and fungi we performed a wide ranging screen for novel putative GH45 sequences. This revealed that the sequences are widespread mainly in Ascomycetous fungi and have so far been found in a single major nematode lineage. Close relationships between the sequences from nematodes and fungi were found through our phylogenetic analyses. An intron position is shared by sequences from Bursaphelenchus nematodes and several Ascomycetous fungal species.<br><br>CONCLUSIONS: The close phylogenetic relationships and conserved gene structure between the sequences from nematodes and fungi strongly supports the hypothesis that nematode GH45 cellulase genes were acquired via HGT from fungi. The rapid duplication and turnover of these genes within Bursaphelenchus genomes demonstrate that useful sequences acquired via HGT can become established in the genomes of recipient organisms and may open novel niches for these organisms to exploit.}, }
@article {pmid24684786, year = {2014}, author = {Paz, A and Frenkel, S and Snir, S and Kirzhner, V and Korol, AB}, title = {Implications of human genome structural heterogeneity: functionally related genes tend to reside in organizationally similar genomic regions.}, journal = {BMC genomics}, volume = {15}, number = {}, pages = {252}, pmid = {24684786}, issn = {1471-2164}, mesh = {Animals ; Base Composition ; Evolution, Molecular ; Genes ; *Genetic Heterogeneity ; Genetic Variation ; *Genome, Human ; Genome, Mitochondrial ; *Genomics ; Humans ; Multigene Family ; Segmental Duplications, Genomic ; }, abstract = {BACKGROUND: In an earlier study, we hypothesized that genomic segments with different sequence organization patterns (OPs) might display functional specificity despite their similar GC content. Here we tested this hypothesis by dividing the human genome into 100 kb segments, classifying these segments into five compositional groups according to GC content, and then characterizing each segment within the five groups by oligonucleotide counting (k-mer analysis; also referred to as compositional spectrum analysis, or CSA), to examine the distribution of sequence OPs in the segments. We performed the CSA on the entire DNA, i.e., its coding and non-coding parts the latter being much more abundant in the genome than the former.<br><br>RESULTS: We identified 38 OP-type clusters of segments that differ in their compositional spectrum (CS) organization. Many of the segments that shared the same OP type were enriched with genes related to the same biological processes (developmental, signaling, etc.), components of biochemical complexes, or organelles. Thirteen OP-type clusters showed significant enrichment in genes connected to specific gene-ontology terms. Some of these clusters seemed to reflect certain events during periods of horizontal gene transfer and genome expansion, and subsequent evolution of genomic regions requiring coordinated regulation.<br><br>CONCLUSIONS: There may be a tendency for genes that are involved in the same biological process, complex or organelle to use the same OP, even at a distance of ~ 100 kb from the genes. Although the intergenic DNA is non-coding, the general pattern of sequence organization (e.g., reflected in over-represented oligonucleotide "words") may be important and were protected, to some extent, in the course of evolution.}, }
@article {pmid24682326, year = {2014}, author = {Michener, JK and Vuilleumier, S and Bringel, F and Marx, CJ}, title = {Phylogeny poorly predicts the utility of a challenging horizontally transferred gene in Methylobacterium strains.}, journal = {Journal of bacteriology}, volume = {196}, number = {11}, pages = {2101-2107}, pmid = {24682326}, issn = {1098-5530}, support = {F32 GM106629/GM/NIGMS NIH HHS/United States ; }, mesh = {Gene Expression Regulation, Bacterial/*physiology ; Gene Expression Regulation, Enzymologic/physiology ; Gene Transfer, Horizontal/*physiology ; Hydrogen-Ion Concentration ; Lyases/genetics/*metabolism ; Methylene Chloride/metabolism ; Methylobacterium/*classification/*genetics ; *Phylogeny ; }, abstract = {Horizontal gene transfer plays a crucial role in microbial evolution. While much is known about the mechanisms that determine whether physical DNA can be transferred into a new host, the factors determining the utility of the transferred genes are less clear. We have explored this issue using dichloromethane consumption in Methylobacterium strains. Methylobacterium extorquens DM4 expresses a dichloromethane dehalogenase (DcmA) that has been acquired through horizontal gene transfer and allows the strain to grow on dichloromethane as the sole carbon and energy source. We transferred the dcmA gene into six Methylobacterium strains that include both close and distant evolutionary relatives. The transconjugants varied in their ability to grow on dichloromethane, but their fitness on dichloromethane did not correlate with the phylogeny of the parental strains or with any single tested physiological factor. This work highlights an important limiting factor in horizontal gene transfer, namely, the capacity of the recipient strain to accommodate the stress and metabolic disruption resulting from the acquisition of a new enzyme or pathway. Understanding these limitations may help to rationalize historical examples of horizontal transfer and aid deliberate genetic transfers in biotechnology for metabolic engineering.}, }
@article {pmid24682298, year = {2014}, author = {Baugher, JL and Durmaz, E and Klaenhammer, TR}, title = {Spontaneously induced prophages in Lactobacillus gasseri contribute to horizontal gene transfer.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {11}, pages = {3508-3517}, pmid = {24682298}, issn = {1098-5336}, mesh = {Bacteriophages/*genetics/isolation &amp; purification/physiology ; DNA, Viral/chemistry/genetics ; *Gene Transfer, Horizontal ; Host Specificity ; Lactobacillus/*virology ; Molecular Sequence Data ; Plasmids ; Prophages/*genetics/isolation &amp; purification/physiology ; Sequence Analysis, DNA ; Transduction, Genetic ; *Virus Activation ; }, abstract = {Lactobacillus gasseri is an endogenous species of the human gastrointestinal tract and vagina. With recent advances in microbial taxonomy, phylogenetics, and genomics, L. gasseri is recognized as an important commensal and is increasingly being used in probiotic formulations. L. gasseri strain ADH is lysogenic and harbors two inducible prophages. In this study, prophage adh was found to spontaneously induce in broth cultures to populations of ∼ 10(7) PFU/ml by stationary phase. The adh prophage-cured ADH derivative NCK102 was found to harbor a new, second inducible phage, vB_Lga_jlb1 (jlb1). Phage jlb1 was sequenced and found to be highly similar to the closely related phage LgaI, which resides as two tandem prophages in the neotype strain L. gasseri ATCC 33323. The common occurrence of multiple prophages in L. gasseri genomes, their propensity for spontaneous induction, and the high degree of homology among phages within multiple species of Lactobacillus suggest that temperate bacteriophages likely contribute to horizontal gene transfer (HGT) in commensal lactobacilli. In this study, the host ranges of phages adh and jlb1 were determined against 16 L. gasseri strains. The transduction range and the rate of spontaneous transduction were investigated in coculture experiments to ascertain the degree to which prophages can promote HGT among a variety of commensal and probiotic lactobacilli. Both adh and jlb1 particles were confirmed to mediate plasmid transfer. As many as ∼10(3) spontaneous transductants/ml were obtained. HGT by transducing phages of commensal lactobacilli may have a significant impact on the evolution of bacteria within the human microbiota.}, }
@article {pmid24680835, year = {2014}, author = {Yin, LF and Wang, F and Zhang, Y and Kuang, H and Schnabel, G and Li, GQ and Luo, CX}, title = {Evolutionary analysis revealed the horizontal transfer of the Cyt b gene from Fungi to Chromista.}, journal = {Molecular phylogenetics and evolution}, volume = {76}, number = {}, pages = {155-161}, doi = {10.1016/j.ympev.2014.03.016}, pmid = {24680835}, issn = {1095-9513}, mesh = {Amino Acid Sequence ; Base Sequence ; Conserved Sequence ; Cytochromes b/chemistry/*genetics ; *Evolution, Molecular ; Fungi/chemistry/*genetics ; *Gene Transfer, Horizontal ; Genes, Essential/genetics ; Introns/genetics ; Molecular Sequence Data ; Oomycetes/chemistry/*genetics ; Phylogeny ; Prokaryotic Cells/metabolism ; Sequence Analysis, DNA ; Symbiosis/genetics ; }, abstract = {In this study, the cytochrome b (Cyt b) amino acid sequences were analyzed in 50 organisms covering all 5 kingdoms of eukaryotes. Six conserved domains, i.e., heme bL binding sites, heme bH binding sites, Qo binding sites, Qi binding sites, the interchain domain interface, and the intrachain domain interface were found in all investigated sequences. The topology of the phylogenetic trees was largely consistent with the well recognized taxonomic relationships, indicating that the Cyt b genes originated from a common ancestral gene before the divergence of eukaryotic kingdoms. The eukaryotic Cyt b genes likely originated from an ancient prokaryotic gene in Alphaproteobacteria based on shared conserved domains. We provide evidence that the Cyt b gene of oomycete Pseudoperonospora cubensis was horizontally transferred from a fungus in the order Hypocreales. To our knowledge, this is the first reported evidence of Horizontal gene transfer (HGT) from Fungi to Chromista involving an essential house-keeping gene. Our data suggest that HGT events must be considered when evolutionary trees are constructed only based on Cyt b genes. Additional analysis of thousands of Cyt b sequences from Genbank revealed that introns in mitochondrial Cyt b genes were acquired after the endosymbiosis of alphaproteobacteria in eukaryotic cells.}, }
@article {pmid24679252, year = {2014}, author = {Bock, R}, title = {Genetic engineering of the chloroplast: novel tools and new applications.}, journal = {Current opinion in biotechnology}, volume = {26}, number = {}, pages = {7-13}, doi = {10.1016/j.copbio.2013.06.004}, pmid = {24679252}, issn = {1879-0429}, mesh = {Biotechnology/*methods ; Chloroplasts/*genetics ; Gene Transfer, Horizontal/genetics ; *Genetic Engineering ; Metabolic Engineering ; Operon/genetics ; Plants/genetics ; Plants, Genetically Modified/*genetics ; Plastids/genetics ; Transformation, Genetic ; Transgenes/genetics ; }, abstract = {The plastid genome represents an attractive target of genetic engineering in crop plants. Plastid transgenes often give high expression levels, can be stacked in operons and are largely excluded from pollen transmission. Recent research has greatly expanded our toolbox for plastid genome engineering and many new proof-of-principle applications have highlighted the enormous potential of the transplastomic technology in both crop improvement and the development of plants as bioreactors for the sustainable and cost-effective production of biopharmaceuticals, enzymes and raw materials for the chemical industry. This review describes recent technological advances with plastid transformation in seed plants. It focuses on novel tools for plastid genome engineering and transgene expression and summarizes progress with harnessing the potential of plastid transformation in biotechnology.}, }
@article {pmid24678768, year = {2014}, author = {Martínez, JL and Baquero, F}, title = {Emergence and spread of antibiotic resistance: setting a parameter space.}, journal = {Upsala journal of medical sciences}, volume = {119}, number = {2}, pages = {68-77}, pmid = {24678768}, issn = {2000-1967}, support = {L60 MD002414/MD/NIMHD NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; Humans ; }, abstract = {The emergence and spread of antibiotic resistance among human pathogens is a relevant problem for human health and one of the few evolution processes amenable to experimental studies. In the present review, we discuss some basic aspects of antibiotic resistance, including mechanisms of resistance, origin of resistance genes, and bottlenecks that modulate the acquisition and spread of antibiotic resistance among human pathogens. In addition, we analyse several parameters that modulate the evolution landscape of antibiotic resistance. Learning why some resistance mechanisms emerge but do not evolve after a first burst, whereas others can spread over the entire world very rapidly, mimicking a chain reaction, is important for predicting the evolution, and relevance for human health, of a given mechanism of resistance. Because of this, we propose that the emergence and spread of antibiotic resistance can only be understood in a multi-parameter space. Measuring the effect on antibiotic resistance of parameters such as contact rates, transfer rates, integration rates, replication rates, diversification rates, and selection rates, for different genes and organisms, growing under different conditions in distinct ecosystems, will allow for a better prediction of antibiotic resistance and possibilities of focused interventions.}, }
@article {pmid24675865, year = {2014}, author = {Oberto, J and Gaudin, M and Cossu, M and Gorlas, A and Slesarev, A and Marguet, E and Forterre, P}, title = {Genome Sequence of a Hyperthermophilic Archaeon, Thermococcus nautili 30-1, That Produces Viral Vesicles.}, journal = {Genome announcements}, volume = {2}, number = {2}, pages = {}, pmid = {24675865}, issn = {2169-8287}, abstract = {Thermococcus nautili 30-1 (formerly Thermococcus nautilus), an anaerobic hyperthermophilic marine archaeon, was isolated in 1999 from a deep-sea hydrothermal vent during the Amistad campaign. Here, we present the complete sequence of T. nautili, which is able to produce membrane vesicles containing plasmid DNA. This property makes T. nautili a model organism to study horizontal gene transfer.}, }
@article {pmid24675805, year = {2014}, author = {Pradel, E and Lemaître, N and Merchez, M and Ricard, I and Reboul, A and Dewitte, A and Sebbane, F}, title = {New insights into how Yersinia pestis adapts to its mammalian host during bubonic plague.}, journal = {PLoS pathogens}, volume = {10}, number = {3}, pages = {e1004029}, pmid = {24675805}, issn = {1553-7374}, mesh = {Animals ; Disease Models, Animal ; Female ; Host-Parasite Interactions/*genetics ; Humans ; Macrophages/microbiology ; Plague/*genetics ; Rats ; Virulence ; Yersinia pestis/*genetics/*pathogenicity ; }, abstract = {Bubonic plague (a fatal, flea-transmitted disease) remains an international public health concern. Although our understanding of the pathogenesis of bubonic plague has improved significantly over the last few decades, researchers have still not been able to define the complete set of Y. pestis genes needed for disease or to characterize the mechanisms that enable infection. Here, we generated a library of Y. pestis mutants, each lacking one or more of the genes previously identified as being up-regulated in vivo. We then screened the library for attenuated virulence in rodent models of bubonic plague. Importantly, we tested mutants both individually and using a novel, "per-pool" screening method that we have developed. Our data showed that in addition to genes involved in physiological adaptation and resistance to the stress generated by the host, several previously uncharacterized genes are required for virulence. One of these genes (ympt1.66c, which encodes a putative helicase) has been acquired by horizontal gene transfer. Deletion of ympt1.66c reduced Y. pestis' ability to spread to the lymph nodes draining the dermal inoculation site--probably because loss of this gene decreased the bacteria's ability to survive inside macrophages. Our results suggest that (i) intracellular survival during the early stage of infection is important for plague and (ii) horizontal gene transfer was crucial in the acquisition of this ability.}, }
@article {pmid24675169, year = {2013}, author = {Picossi, S and Flores, E and Ekman, M}, title = {Diverse roles of the GlcP glucose permease in free-living and symbiotic cyanobacteria.}, journal = {Plant signaling &amp; behavior}, volume = {8}, number = {12}, pages = {e27416}, pmid = {24675169}, issn = {1559-2324}, mesh = {Chemotaxis/drug effects ; Evolution, Molecular ; Glucose/pharmacology ; Nostoc/cytology/drug effects/*enzymology/growth &amp; development ; Phosphoenolpyruvate Sugar Phosphotransferase System/*metabolism ; Phylogeny ; *Symbiosis/drug effects ; }, abstract = {Certain cyanobacteria can form symbiotic associations with plants, where the symbiont supplies the plant partner with nitrogen and in return obtains sugars. We recently showed that in the symbiotic cyanobacterium Nostoc punctiforme, a glucose specific permease, GlcP, is necessary for the symbiosis to be formed. Results presented here from growth yield measurements of mutant strains with inactivated or overexpressing sugar transporters suggest that GlcP could be induced by a symbiosis specific substance. We also discuss that the transporter may have a role other than nutritional once the symbiosis is established, i.e., during infection, and more specifically in the chemotaxis of the symbiont. Phylogenetic analysis shows that the distribution of GlcP among cyanobacteria is likely influenced by horizontal gene transfer, but also that it is not correlated with symbiotic competence. Instead, regulatory patterns of the transporter in Nostoc punctiforme likely constitute symbiosis specific adaptations.}, }
@article {pmid24670243, year = {2014}, author = {DuBuc, TQ and Traylor-Knowles, N and Martindale, MQ}, title = {Initiating a regenerative response; cellular and molecular features of wound healing in the cnidarian Nematostella vectensis.}, journal = {BMC biology}, volume = {12}, number = {}, pages = {24}, pmid = {24670243}, issn = {1741-7007}, support = {R01 GM093116/GM/NIGMS NIH HHS/United States ; GM093116/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Apoptosis ; Cnidaria/*cytology/enzymology/genetics/*physiology ; Down-Regulation/genetics ; Extracellular Signal-Regulated MAP Kinases/metabolism ; MAP Kinase Signaling System ; Models, Biological ; Mucins/metabolism ; Oligonucleotide Array Sequence Analysis ; RNA, Messenger/genetics/metabolism ; Real-Time Polymerase Chain Reaction ; Receptors, Notch/metabolism ; *Regeneration/genetics ; Time-Lapse Imaging ; Transcription, Genetic ; Up-Regulation/genetics ; *Wound Healing/genetics ; }, abstract = {BACKGROUND: Wound healing is the first stage of a series of cellular events that are necessary to initiate a regenerative response. Defective wound healing can block regeneration even in animals with a high regenerative capacity. Understanding how signals generated during wound healing promote regeneration of lost structures is highly important, considering that virtually all animals have the ability to heal but many lack the ability to regenerate missing structures. Cnidarians are the phylogenetic sister taxa to bilaterians and are highly regenerative animals. To gain a greater understanding of how early animals generate a regenerative response, we examined the cellular and molecular components involved during wound healing in the anthozoan cnidarian Nematostella vectensis.<br><br>RESULTS: Pharmacological inhibition of extracellular signal-regulated kinases (ERK) signaling blocks regeneration and wound healing in Nematostella. We characterized early and late wound healing events through genome-wide microarray analysis, quantitative PCR, and in situ hybridization to identify potential wound healing targets. We identified a number of genes directly related to the wound healing response in other animals (metalloproteinases, growth factors, transcription factors) and suggest that glycoproteins (mucins and uromodulin) play a key role in early wound healing events. This study also identified a novel cnidarian-specific gene, for a thiamine biosynthesis enzyme (vitamin B synthesis), that may have been incorporated into the genome by lateral gene transfer from bacteria and now functions during wound healing. Lastly, we suggest that ERK signaling is a shared element of the early wound response for animals with a high regenerative capacity.<br><br>CONCLUSIONS: This research describes the temporal events involved during Nematostella wound healing, and provides a foundation for comparative analysis with other regenerative and non-regenerative species. We have shown that the same genes that heal puncture wounds are also activated after oral-aboral bisection, indicating a clear link with the initiation of regenerative healing. This study demonstrates the strength of using a forward approach (microarray) to characterize a developmental phenomenon (wound healing) at a phylogenetically important crossroad of animal evolution (cnidarian-bilaterian ancestor). Accumulation of data on the early wound healing events across numerous systems may provide clues as to why some animals have limited regenerative abilities.}, }
@article {pmid24669202, year = {2014}, author = {Borrel, G and Gaci, N and Peyret, P and O'Toole, PW and Gribaldo, S and Brugère, JF}, title = {Unique characteristics of the pyrrolysine system in the 7th order of methanogens: implications for the evolution of a genetic code expansion cassette.}, journal = {Archaea (Vancouver, B.C.)}, volume = {2014}, number = {}, pages = {374146}, pmid = {24669202}, issn = {1472-3654}, mesh = {Amino Acyl-tRNA Synthetases/genetics ; Bacteria/genetics ; Biosynthetic Pathways/*genetics ; Euryarchaeota/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Code ; Lysine/*analogs &amp; derivatives/biosynthesis ; Phylogeny ; RNA, Transfer/genetics ; Sequence Homology ; }, abstract = {Pyrrolysine (Pyl), the 22nd proteogenic amino acid, was restricted until recently to few organisms. Its translational use necessitates the presence of enzymes for synthesizing it from lysine, a dedicated amber stop codon suppressor tRNA, and a specific amino-acyl tRNA synthetase. The three genomes of the recently proposed Thermoplasmata-related 7th order of methanogens contain the complete genetic set for Pyl synthesis and its translational use. Here, we have analyzed the genomic features of the Pyl-coding system in these three genomes with those previously known from Bacteria and Archaea and analyzed the phylogeny of each component. This shows unique peculiarities, notably an amber tRNA(Pyl) with an imperfect anticodon stem and a shortened tRNA(Pyl) synthetase. Phylogenetic analysis indicates that a Pyl-coding system was present in the ancestor of the seventh order of methanogens and appears more closely related to Bacteria than to Methanosarcinaceae, suggesting the involvement of lateral gene transfer in the spreading of pyrrolysine between the two prokaryotic domains. We propose that the Pyl-coding system likely emerged once in Archaea, in a hydrogenotrophic and methanol-H2-dependent methylotrophic methanogen. The close relationship between methanogenesis and the Pyl system provides a possible example of expansion of a still evolving genetic code, shaped by metabolic requirements.}, }
@article {pmid24667156, year = {2014}, author = {Goldenfeld, N}, title = {Looking in the right direction: Carl Woese and evolutionary biology.}, journal = {RNA biology}, volume = {11}, number = {3}, pages = {248-253}, doi = {10.4161/rna.28640}, pmid = {24667156}, issn = {1555-8584}, mesh = {*Biological Evolution ; Genetics, Population ; Origin of Life ; Phylogeny ; RNA, Ribosomal/*genetics ; }, abstract = {Carl Woese is known to the scientific community primarily through his landmark contributions to microbiology, in particular, his discovery of the third Domain of Life, which came to be known as the Archaea. While it is well known how he made this discovery, through the techniques he developed based on his studies of rRNA, the reasons why he was driven in this scientific direction, and what he saw as the principle outcome of his discovery--it was not the Archaea!--are not so widely appreciated. In this essay, I discuss his vision of evolution, one which transcends population genetics, and which has ramifications not only for our understanding of the origin of life on Earth and elsewhere, but also for our understanding of biology as a novel class of complex dynamical systems.}, }
@article {pmid24664508, year = {2014}, author = {Yonogi, S and Matsuda, S and Kawai, T and Yoda, T and Harada, T and Kumeda, Y and Gotoh, K and Hiyoshi, H and Nakamura, S and Kodama, T and Iida, T}, title = {BEC, a novel enterotoxin of Clostridium perfringens found in human clinical isolates from acute gastroenteritis outbreaks.}, journal = {Infection and immunity}, volume = {82}, number = {6}, pages = {2390-2399}, pmid = {24664508}, issn = {1098-5522}, mesh = {ADP Ribose Transferases/genetics ; Acute Disease ; Analysis of Variance ; Animals ; Clostridium perfringens/*metabolism ; Disease Models, Animal ; Disease Outbreaks ; Enterotoxins/genetics/*metabolism ; Gastroenteritis/*microbiology ; Humans ; Mice ; Molecular Weight ; Rabbits ; Recombinant Proteins/metabolism ; Sequence Analysis, DNA ; }, abstract = {Clostridium perfringens is a causative agent of food-borne gastroenteritis for which C. perfringens enterotoxin (CPE) has been considered an essential factor. Recently, we experienced two outbreaks of food-borne gastroenteritis in which non-CPE producers of C. perfringens were strongly suspected to be the cause. Here, we report a novel enterotoxin produced by C. perfringens isolates, BEC (binary enterotoxin of C. perfringens). Culture supernatants of the C. perfringens strains showed fluid-accumulating activity in rabbit ileal loop and suckling mouse assays. Purification of the enterotoxic substance in the supernatants and high-throughput sequencing of genomic DNA of the strains revealed BEC, composed of BECa and BECb. BECa and BECb displayed limited amino acid sequence similarity to other binary toxin family members, such as the C. perfringens iota toxin. The becAB genes were located on 54.5-kb pCP13-like plasmids. Recombinant BECb (rBECb) alone had fluid-accumulating activity in the suckling mouse assay. Although rBECa alone did not show enterotoxic activity, rBECa enhanced the enterotoxicity of rBECb when simultaneously administered in suckling mice. The entertoxicity of the mutant in which the becB gene was disrupted was dramatically decreased compared to that of the parental strain. rBECa showed an ADP-ribosylating activity on purified actin. Although we have not directly evaluated whether BECb delivers BECa into cells, rounding of Vero cells occurred only when cells were treated with both rBECa and rBECb. These results suggest that BEC is a novel enterotoxin of C. perfringens distinct from CPE, and that BEC-producing C. perfringens strains can be causative agents of acute gastroenteritis in humans. Additionally, the presence of becAB on nearly identical plasmids in distinct lineages of C. perfringens isolates suggests the involvement of horizontal gene transfer in the acquisition of the toxin genes.}, }
@article {pmid24659751, year = {2014}, author = {Mataseje, LF and Boyd, DA and Delport, J and Hoang, L and Imperial, M and Lefebvre, B and Kuhn, M and Van Caeseele, P and Willey, BM and Mulvey, MR}, title = {Serratia marcescens harbouring SME-type class A carbapenemases in Canada and the presence of blaSME on a novel genomic island, SmarGI1-1.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {69}, number = {7}, pages = {1825-1829}, doi = {10.1093/jac/dku040}, pmid = {24659751}, issn = {1460-2091}, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacterial Proteins/*analysis/*genetics ; Canada ; DNA, Bacterial/genetics ; Electrophoresis, Gel, Pulsed-Field ; Female ; Gene Transfer, Horizontal ; Genetic Variation ; *Genomic Islands ; Humans ; Interspersed Repetitive Sequences ; Male ; Microbial Sensitivity Tests ; Middle Aged ; Molecular Sequence Data ; Molecular Typing ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Serratia Infections/*microbiology ; Serratia marcescens/*enzymology/*genetics/isolation &amp; purification ; beta-Lactamases/*analysis/*genetics ; }, abstract = {OBJECTIVES: An increasing prevalence since 2010 of Serratia marcescens harbouring the Ambler class A carbapenemase SME prompted us to further characterize these isolates.<br><br>METHODS: Isolates harbouring bla(SME) were identified by PCR and sequencing. Phenotypic analysis for carbapenemase activity was carried out by a modified Hodge test and a modified Carba NP test. Antimicrobial susceptibilities were determined by Etest and Vitek 2. Typing was by PFGE of macrorestriction digests. Whole-genome sequencing of three isolates was carried out to characterize the genomic region harbouring the bla(SME)-type genes.<br><br>RESULTS: All S. marcescens harbouring SME-type enzymes could be detected using a modified Carba NP test. Isolates harbouring bla(SME) were resistant to penicillins and carbapenems, but remained susceptible to third-generation cephalosporins, as well as fluoroquinolones and trimethoprim/sulfamethoxazole. Isolates exhibited diverse genetic backgrounds, though 57% of isolates were found in three clusters. Analysis of whole-genome sequence data from three isolates revealed that the bla(SME) gene occurred in a novel cryptic prophage genomic island, SmarGI1-1.<br><br>CONCLUSIONS: There has been an increasing occurrence of S. marcescens harbouring bla(SME) in Canada since 2010. The bla(SME) gene was found on a genomic island, SmarGI1-1, that can be excised and circularized, which probably contributes to its dissemination amongst S. marcescens.}, }
@article {pmid24657872, year = {2014}, author = {Fulsundar, S and Harms, K and Flaten, GE and Johnsen, PJ and Chopade, BA and Nielsen, KM}, title = {Gene transfer potential of outer membrane vesicles of Acinetobacter baylyi and effects of stress on vesiculation.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {11}, pages = {3469-3483}, pmid = {24657872}, issn = {1098-5336}, mesh = {Acinetobacter/*genetics ; DNA, Bacterial/*analysis/genetics ; Escherichia coli/genetics ; *Gene Transfer, Horizontal ; Plasmids/analysis ; Secretory Vesicles/*chemistry ; *Transformation, Bacterial ; }, abstract = {Outer membrane vesicles (OMVs) are continually released from a range of bacterial species. Numerous functions of OMVs, including the facilitation of horizontal gene transfer (HGT) processes, have been proposed. In this study, we investigated whether OMVs contribute to the transfer of plasmids between bacterial cells and species using Gram-negative Acinetobacter baylyi as a model system. OMVs were extracted from bacterial cultures and tested for the ability to vector gene transfer into populations of Escherichia coli and A. baylyi, including naturally transformation-deficient mutants of A. baylyi. Anti-double-stranded DNA (anti-dsDNA) antibodies were used to determine the movement of DNA into OMVs. We also determined how stress affected the level of vesiculation and the amount of DNA in vesicles. OMVs were further characterized by measuring particle size distribution (PSD) and zeta potential. Transmission electron microscopy (TEM) and immunogold labeling were performed using anti-fluorescein isothiocyanate (anti-FITC)-conjugated antibodies and anti-dsDNA antibodies to track the movement of FITC-labeled and DNA-containing OMVs. Exposure to OMVs isolated from plasmid-containing donor cells resulted in HGT to A. baylyi and E. coli at transfer frequencies ranging from 10(-6) to 10(-8), with transfer efficiencies of approximately 10(3) and 10(2) per μg of vesicular DNA, respectively. Antibiotic stress was shown to affect the DNA content of OMVs as well as their hydrodynamic diameter and zeta potential. Morphological observations suggest that OMVs from A. baylyi interact with recipient cells in different ways, depending on the recipient species. Interestingly, the PSD measurements suggest that distinct size ranges of OMVs are released from A. baylyi.}, }
@article {pmid24657069, year = {2016}, author = {Yang, WC and Chan, OW and Wu, TL and Chen, CL and Su, LH and Chiu, CH}, title = {Development of ceftriaxone resistance in Salmonella enterica serotype Oranienburg during therapy for bacteremia.}, journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi}, volume = {49}, number = {1}, pages = {41-45}, doi = {10.1016/j.jmii.2014.01.011}, pmid = {24657069}, issn = {1995-9133}, mesh = {Anti-Bacterial Agents/*therapeutic use ; Bacteremia/*drug therapy/microbiology ; Ceftriaxone/*therapeutic use ; *Drug Resistance, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Female ; Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; Molecular Typing ; Recurrence ; Salmonella Infections/*drug therapy/microbiology ; Salmonella enterica/classification/*drug effects/genetics/isolation &amp; purification ; Treatment Failure ; }, abstract = {BACKGROUND: The majority of nontyphoid Salmonella infection is identified in children. When an invasive or severe Salmonella infection is encountered, ceftriaxone is recommended for such patients. A 2-year-old girl was hospitalized for the treatment of Salmonella bacteremia and discharged with standard ceftriaxone treatment. She was readmitted to the hospital after 2 days due to the recurrence of the Salmonella bacteremia. The study aimed to unveil the mechanism for the relapse.<br><br>METHODS: Six isolates (4 blood and 2 stool) were recovered from the patient, with the last two blood isolates being ceftriaxone-resistant. Pulsed-field gel electrophoresis was used for genotyping. Ceftriaxone resistance genes and transferability of the resistance plasmid were examined by molecular methods.<br><br>RESULTS: All isolates were identified as Salmonella enterica serotype Oranienburg. Five isolates demonstrated almost identical electrophoresis patterns, except that in the two ceftriaxone-resistant isolates an extra band (>100&#xa0;kb) was noted. A blaCMY-2 gene, carried by a 120-kb conjugative IncI1 plasmid of the sequence type 53, was identified in the two ceftriaxone-resistant isolates. Transfer of the resistance plasmid from one blood isolate to Escherichia coli J53 resulted in the increase of ceftriaxone minimum inhibitory concentration from 0.125&#xa0;&#x3bc;g/mL to 32&#xa0;&#x3bc;g/mL in the recipient.<br><br>CONCLUSION: Ceftriaxone is the standard therapeutic choice for invasive or serious Salmonella infections in children. Pediatricians should be aware of the possibility of resistance development during therapy, especially in areas with a widespread of ceftriaxone resistance genes that are carried by a self-transferrable plasmid, such as the blaCMY-2-carrying IncI1 plasmid identified herein.}, }
@article {pmid24655382, year = {2014}, author = {Veremeichik, GN and Shkryl, YN and Pinkus, SA and Bulgakov, VP}, title = {Expression profiles of calcium-dependent protein kinase genes (CDPK1-14) in Agrobacterium rhizogenes pRiA4-transformed calli of Rubia cordifolia under temperature- and salt-induced stresses.}, journal = {Journal of plant physiology}, volume = {171}, number = {7}, pages = {467-474}, doi = {10.1016/j.jplph.2013.12.010}, pmid = {24655382}, issn = {1618-1328}, mesh = {Agrobacterium/genetics ; Amino Acid Sequence ; Bacterial Proteins/chemistry/*genetics/metabolism ; *Gene Expression Regulation, Plant ; Molecular Sequence Data ; Phylogeny ; Plants, Genetically Modified/genetics/metabolism ; Plasmids/genetics ; Protein Kinases/chemistry/*genetics/metabolism ; Rubia/drug effects/*genetics/metabolism ; Sequence Alignment ; Sodium Chloride/pharmacology ; *Stress, Physiological ; Temperature ; Transcriptome ; }, abstract = {Agrobacterium rhizogenes genetically transform plant cells naturally via horizontal gene transfer by the introduction of T-DNA from the Ri plasmid into genomic DNA to create favorable conditions for successful colonization. An intriguing feature of pRiA4-transformed cells is their recently discovered enhanced tolerance to abiotic stress stimuli and activation of antioxidant enzyme expression. The mechanism by which A. rhizogenes modulates the defense responses of transformed cells remains unclear. It has been established that calcium-dependent protein kinase (CDPK) genes mediate crosstalk of signaling pathways in plants, and these genes have been implicated in biotic and abiotic stress signaling. In this study, we identified fourteen CDPK genes from Rubia cordifolia and examined their expression in aerial plant organs as well as in non-transformed and A. rhizogenes A4-transformed calli. Expression of RcCDPK4, RcCDPK5, RcCDPK7, and RcCDPK10 was 1.2- to 3.9-fold higher in pRiA4-transformed cells than in non-transformed cells, whereas expression of RcCDPK1, RcCDPK9, RcCDPK11, and RcCDPK14 was 1.2- to 1.9-fold lower. Agrobacterium transformation substantially modified the transcriptional responses of specific RcCDPK isoforms in pRiA4-transformed cells under conditions of temperature- and salinity-induced stress. On the basis of the results, we suggest that A. rhizogenes T-DNA genes exert their diverse biological functions by altering the expression of various CDPK genes.}, }
@article {pmid24652760, year = {2014}, author = {Avila-Adame, C}, title = {Transmission of the G143A QoI-resistance point mutation through anastomosis in Magnaporthe grisea.}, journal = {Pest management science}, volume = {70}, number = {12}, pages = {1918-1823}, doi = {10.1002/ps.3758}, pmid = {24652760}, issn = {1526-4998}, mesh = {Cinnamates/pharmacology ; Cytochromes b/genetics ; Drug Resistance, Fungal/*genetics ; Fungicides, Industrial/*pharmacology ; *Gene Transfer, Horizontal ; Hordeum/microbiology ; Hygromycin B/analogs &amp; derivatives/pharmacology ; Hyphae ; Magnaporthe/drug effects/*genetics ; Methacrylates/pharmacology ; *Point Mutation ; Pyrimidines/pharmacology ; Strobilurins ; }, abstract = {BACKGROUND: Soon after the introduction of Qo inhibitor fungicides in 1996, the point mutation leading to the amino acid exchange glycine to alanine at the 143 position of the mitochondrial cytochrome b gene was identified as the main cause of resistance. The present study describes the role of anastomosis in the transmission of the G143A mutation in Magnaporthe grisea.<br><br>RESULTS: Two M. grisea mutants were co-cultivated on oatmeal agar and also co-inoculated on barley leaves. The mutants differed by the presence of the G143A mutation in one isolate and a disrupted AOX gene by insertion of a hygromycin gene in the other (M-145). Specific resistant (r) or sensitive (s) phenotypes of 409 monosporic cultures were determined on media amended with either hygromycin (H) or azoxystrobin (S) plus SHAM. The phenotypes identified reflected not only the phenotypes of mutants M-145 and G143A but also the wild-type parent phenotype HsSs and a new HrSr isolate.<br><br>CONCLUSION: Identification of the M. grisea phenotypes HrSr and HsSs suggests that anastomosis occurred during co-cultivation and co-inoculation of the mutants M-145 and G143A, allowing the transfer of the G143A point mutation from the QoI-resistant isolate to the susceptible isolate.}, }
@article {pmid24652253, year = {2013}, author = {Caldera, SM and Jaramillo, MC and Cochero, S and Pérez-Doria, A and Bejarano, EE}, title = {[Genetic differences between populations of Aedes aegypti from municipalities in northern Colombia, with high and low dengue incidence].}, journal = {Biomedica : revista del Instituto Nacional de Salud}, volume = {33 Suppl 1}, number = {}, pages = {89-98}, pmid = {24652253}, issn = {2590-7379}, mesh = {Aedes/classification/*genetics ; Animals ; Colombia/epidemiology ; DNA, Mitochondrial/genetics ; Dengue/*epidemiology/transmission ; Ecosystem ; Female ; Gene Transfer, Horizontal ; Genes, Insect ; Genetic Variation ; Haplotypes ; Incidence ; Insect Proteins/genetics ; Insect Vectors/*genetics ; NADH Dehydrogenase/genetics ; Polymorphism, Genetic ; Sequence Analysis, DNA ; Species Specificity ; Urban Health ; }, abstract = {INTRODUCTION: Aedes aegypti is the principal vector of dengue in urban areas. Despite its epidemiological importance, the genetic variability of Colombian populations of this species is unknown.<br><br>OBJETIVE: To determine the genetic variability of mitocondrial gene ND4, which codes for subunit 4 of the enzyme NADH deshydrogenase, between populations of Ae. aegypti from municipalities of Sincelejo and Guaranda. The incidences of dengue reported from these two localities are high and low, respectively.<br><br>MATERIALS AND METHODS: Genetic material extracted from 36 females of Ae. aegypti was used to determine the partial sequence of the mitocondrial gene ND4 as well as to estimate the parameters of nucleotidic and haplotypic diversities, genetic structure and gene flow between the Sincelejo and Guaranda populations. The molecular variance was also analysed and a haplotypic network constructed.<br><br>RESULTS: In all 36 nucleotide sequences of 282 pb were obtained. These presented 12 polymorphic sites and could grouped into 10 haplotypes, two of them present in both populations, three exclusive to the Sincelejo population and five to that of Guaranda. The estimators of genetic structure (FST = 0.15) and gene flow (Nm = 1.40) are both indicative of genetic differentiation and a limited exchange of genes between the populations.<br><br>CONCLUSIONS: The Sincelejo and Guaranda populations of Ae. aegypti are genetically divergent.}, }
@article {pmid24651770, year = {2014}, author = {Muziasari, WI and Managaki, S and Pärnänen, K and Karkman, A and Lyra, C and Tamminen, M and Suzuki, S and Virta, M}, title = {Sulphonamide and trimethoprim resistance genes persist in sediments at Baltic Sea aquaculture farms but are not detected in the surrounding environment.}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e92702}, pmid = {24651770}, issn = {1932-6203}, mesh = {Aquaculture ; Drug Resistance, Microbial/*genetics ; *Environmental Microbiology ; Finland ; Gene Transfer, Horizontal ; Genes, Bacterial ; Geologic Sediments/*microbiology ; Humans ; Integrons ; *Microbiota ; Sulfanilamide ; Sulfanilamides/*pharmacology ; Trimethoprim/*pharmacology ; }, abstract = {Persistence and dispersal of antibiotic resistance genes (ARGs) are important factors for assessing ARG risk in aquaculture environments. Here, we quantitatively detected ARGs for sulphonamides (sul1 and sul2) and trimethoprim (dfrA1) and an integrase gene for a class 1 integron (intI1) at aquaculture facilities in the northern Baltic Sea, Finland. The ARGs persisted in sediments below fish farms at very low antibiotic concentrations during the 6-year observation period from 2006 to 2012. Although the ARGs persisted in the farm sediments, they were less prevalent in the surrounding sediments. The copy numbers between the sul1 and intI1 genes were significantly correlated suggesting that class 1 integrons may play a role in the prevalence of sul1 in the farm sediments through horizontal gene transfer. In conclusion, the presence of ARGs may limit the effectiveness of antibiotics in treating fish illnesses, thereby causing a potential risk to the aquaculture industry. However, the restricted presence of ARGs at the farms is unlikely to cause serious effects in the northern Baltic Sea sediment environments around the farms.}, }
@article {pmid24651173, year = {2014}, author = {Xie, JB and Du, Z and Bai, L and Tian, C and Zhang, Y and Xie, JY and Wang, T and Liu, X and Chen, X and Cheng, Q and Chen, S and Li, J}, title = {Comparative genomic analysis of N2-fixing and non-N2-fixing Paenibacillus spp.: organization, evolution and expression of the nitrogen fixation genes.}, journal = {PLoS genetics}, volume = {10}, number = {3}, pages = {e1004231}, pmid = {24651173}, issn = {1553-7404}, mesh = {Binding Sites ; Escherichia coli/*genetics/metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; *Genomics ; Multigene Family ; Nitrogen Fixation/*genetics/physiology ; Nitrogenase/genetics ; Paenibacillus/genetics/*metabolism ; Phylogeny ; Promoter Regions, Genetic ; }, abstract = {We provide here a comparative genome analysis of 31 strains within the genus Paenibacillus including 11 new genomic sequences of N2-fixing strains. The heterogeneity of the 31 genomes (15 N2-fixing and 16 non-N2-fixing Paenibacillus strains) was reflected in the large size of the shell genome, which makes up approximately 65.2% of the genes in pan genome. Large numbers of transposable elements might be related to the heterogeneity. We discovered that a minimal and compact nif cluster comprising nine genes nifB, nifH, nifD, nifK, nifE, nifN, nifX, hesA and nifV encoding Mo-nitrogenase is conserved in the 15 N2-fixing strains. The nif cluster is under control of a σ(70)-depedent promoter and possesses a GlnR/TnrA-binding site in the promoter. Suf system encoding [Fe-S] cluster is highly conserved in N2-fixing and non-N2-fixing strains. Furthermore, we demonstrate that the nif cluster enabled Escherichia coli JM109 to fix nitrogen. Phylogeny of the concatenated NifHDK sequences indicates that Paenibacillus and Frankia are sister groups. Phylogeny of the concatenated 275 single-copy core genes suggests that the ancestral Paenibacillus did not fix nitrogen. The N2-fixing Paenibacillus strains were generated by acquiring the nif cluster via horizontal gene transfer (HGT) from a source related to Frankia. During the history of evolution, the nif cluster was lost, producing some non-N2-fixing strains, and vnf encoding V-nitrogenase or anf encoding Fe-nitrogenase was acquired, causing further diversification of some strains. In addition, some N2-fixing strains have additional nif and nif-like genes which may result from gene duplications. The evolution of nitrogen fixation in Paenibacillus involves a mix of gain, loss, HGT and duplication of nif/anf/vnf genes. This study not only reveals the organization and distribution of nitrogen fixation genes in Paenibacillus, but also provides insight into the complex evolutionary history of nitrogen fixation.}, }
@article {pmid24648508, year = {2014}, author = {Wendlandt, S and Feßler, AT and Kadlec, K and van Duijkeren, E and Schwarz, S}, title = {Identification of the novel spectinomycin resistance gene spd in a different plasmid background among methicillin-resistant Staphylococcus aureus CC398 and methicillin-susceptible S. aureus ST433.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {69}, number = {7}, pages = {2000-2003}, doi = {10.1093/jac/dku067}, pmid = {24648508}, issn = {1460-2091}, mesh = {Animals ; Humans ; Methicillin-Resistant Staphylococcus aureus/*enzymology/*isolation &amp; purification ; Nucleotidyltransferases/*genetics ; Plasmids/*isolation &amp; purification ; Staphylococcal Infections/*microbiology/*veterinary ; }, }
@article {pmid24646299, year = {2014}, author = {Torres Tejerizo, G and Pistorio, M and Althabegoiti, MJ and Cervantes, L and Wibberg, D and Schlüter, A and Pühler, A and Lagares, A and Romero, D and Brom, S}, title = {Rhizobial plasmid pLPU83a is able to switch between different transfer machineries depending on its genomic background.}, journal = {FEMS microbiology ecology}, volume = {88}, number = {3}, pages = {565-578}, doi = {10.1111/1574-6941.12325}, pmid = {24646299}, issn = {1574-6941}, mesh = {Bacterial Proteins/genetics ; *Conjugation, Genetic ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Phylogeny ; Plasmids/classification/*genetics ; Rhizobium/*genetics ; Sinorhizobium/genetics ; Transcription Factors/genetics ; }, abstract = {Plasmids have played a major role in bacterial evolution, mainly by their capacity to perform horizontal gene transfer (HGT). Their conjugative transfer (CT) properties are usually described in terms of the plasmid itself. In this work, we analyzed structural and functional aspects of the CT of pLPU83a, an accessory replicon from Rhizobium sp. LPU83, able to transfer from its parental strain, from Ensifer meliloti, or from Rhizobium etli. pLPU83a contains a complete set of transfer genes, featuring a particular organization, shared with only two other rhizobial plasmids. These plasmids contain a TraR quorum-sensing (QS) transcriptional regulator, but lack an acyl-homoserine lactone (AHL) synthase gene. We also determined that the ability of pLPU83a to transfer from R. etli CFN42 genomic background was mainly achieved through mobilization, employing the machinery of the endogenous plasmid pRetCFN42a, falling under control of the QS regulators from pRetCFN42a. In contrast, from its native or from the E. meliloti background, pLPU83a utilized its own machinery for conjugation, requiring the plasmid-encoded traR. Activation of TraR seemed to be AHL independent. The results obtained indicate that the CT phenotype of a plasmid is dictated not only by the genes it carries, but by their interaction with its genomic context.}, }
@article {pmid24642917, year = {2014}, author = {Guimaraes, AM and Santos, AP and do Nascimento, NC and Timenetsky, J and Messick, JB}, title = {Comparative genomics and phylogenomics of hemotrophic mycoplasmas.}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e91445}, pmid = {24642917}, issn = {1932-6203}, mesh = {Codon ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome Size ; *Genome, Bacterial ; *Genomics ; Metabolic Networks and Pathways/genetics ; Mycoplasma/classification/*genetics/metabolism ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Synteny ; }, abstract = {Hemotrophic mycoplasmas (hemoplasmas) are a group of animal pathogens of the Mollicutes class. Recently, the genomes of 8 hemoplasmas have been completely sequenced. The aim of this study was to gain a better understanding of their genomic features and relationship to other Mycoplasma species. The genome structure and dynamics of hemoplasmas were analyzed by evaluating gene synteny, adaptive evolution of paralogous gene families (PGF) and horizontal gene transfer (HGT). The Mollicutes class was then phylogenetically analyzed by constructing a distance matrix of the 16S rRNA genes and a phylogenetic tree with 32 conserved, concatenated proteins. Our results suggest that the hemoplasmas have dynamic genomes. The genome size variation (from 547 to 1,545 genes) indicates substantial gene gain/loss throughout evolution. Poorly conserved gene syntenies among hemoplasmas, positional shuffling of paralogous genes between strains, HGT, and codons under positive selection in PGFs were also observed. When compared to other Mollicutes species, the hemoplasmas experienced further metabolic reduction, and the 16S rRNA gene distance matrix of the available mollicutes suggests that these organisms presently constitute the most divergent clade within its class. Our phylogenetic tree of concatenated proteins showed some differences when compared to the 16S rRNA gene tree, but non-mycoplasma organisms, such as Ureaplasma spp. and Mesoplasma spp., continue to branch within Mycoplasma clades. In conclusion, while the hemoplasmas experienced further metabolic shrinkage through gene loss, PGFs with positively selected codons are likely beneficial to these species. Phylogeny of the mollicutes based on 16S rRNA genes or concatenated proteins do not obey the current taxonomy. The metabolism and genetic diversity of the mollicutes, the presence of HGT, and lack of standard for genus circumscription are likely to hinder attempts to classify these organisms based on phylogenetic analyses.}, }
@article {pmid24637724, year = {2014}, author = {Herman, RA and Raybould, A}, title = {Expert opinion vs. empirical evidence: the precautionary principle applied to GM crops.}, journal = {GM crops &amp; food}, volume = {5}, number = {1}, pages = {8-10}, pmid = {24637724}, issn = {2164-5701}, mesh = {Crops, Agricultural/*genetics ; *Empirical Research ; Gene Transfer, Horizontal/genetics ; Plants, Genetically Modified/*genetics ; Risk Assessment ; }, abstract = {Expert opinion is often sought by government regulatory agencies when there is insufficient empirical evidence to judge the safety implications of a course of action. However, it can be reckless to continue following expert opinion when a preponderance of evidence is amassed that conflicts with this opinion. Factual evidence should always trump opinion in prioritizing the information that is used to guide regulatory policy. Evidence-based medicine has seen a dramatic upturn in recent years spurred by examples where evidence indicated that certain treatments recommended by expert opinions increased death rates. We suggest that scientific evidence should also take priority over expert opinion in the regulation of genetically modified crops (GM). Examples of regulatory data requirements that are not justified based on the mass of evidence are described, and it is suggested that expertise in risk assessment should guide evidence-based regulation of GM crops.}, }
@article {pmid24637153, year = {2014}, author = {Hsu, JT and Chen, CY and Young, CW and Chao, WL and Li, MH and Liu, YH and Lin, CM and Ying, C}, title = {Prevalence of sulfonamide-resistant bacteria, resistance genes and integron-associated horizontal gene transfer in natural water bodies and soils adjacent to a swine feedlot in northern Taiwan.}, journal = {Journal of hazardous materials}, volume = {277}, number = {}, pages = {34-43}, doi = {10.1016/j.jhazmat.2014.02.016}, pmid = {24637153}, issn = {1873-3336}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal/*drug effects ; *Genes, Bacterial ; Integrons/drug effects/*genetics ; Manure/*microbiology ; Microbial Sensitivity Tests ; Phylogeny ; *Soil Microbiology/standards ; Sulfonamides/*pharmacology ; Sus scrofa ; Taiwan ; *Water Microbiology/standards ; }, abstract = {Antibiotics are commonly used in swine feed to treat and prevent disease, as well as to promote growth. Antibiotics released into the environment via wastewater could accelerate the emergence of antibiotic-resistant bacteria and resistance genes in the surrounding environment. In this study, we quantified the occurrence of sulfonamides, sulfonamide-resistant microorganisms and resistance genes in the wastewater from a swine farm in northern Taiwan and its surrounding natural water bodies and soils. Sulfonamide levels were similar in the receiving downstream and upstream river water. However, the prevalence of sulfonamide-resistant bacteria and resistance genes, as analyzed by cultivation-dependent and -independent molecular approaches, was significantly greater in the downstream compared to the upstream river water samples. Barcoded-pyrosequencing revealed a highly diverse bacterial community structure in each sample. However, the sequence identity of the sulfonamide resistance gene sul1 in the wastewater and downstream environment samples was nearly identical (99-100%). The sul1 gene, which is genetically linked to class 1 integrons, was dominant in the downstream water bodies and soils. In conclusion, the increased prevalence of sulfonamide resistance genes in the wastewater from a swine farm, independent of the persistent presence of sulfonamides, could be a potential source of resistant gene pools in the surrounding environment.}, }
@article {pmid24634779, year = {2014}, author = {Castagnola, A and Stock, SP}, title = {Common Virulence Factors and Tissue Targets of Entomopathogenic Bacteria for Biological Control of Lepidopteran Pests.}, journal = {Insects}, volume = {5}, number = {1}, pages = {139-166}, pmid = {24634779}, issn = {2075-4450}, support = {K12 GM000708/GM/NIGMS NIH HHS/United States ; }, abstract = {This review focuses on common insecticidal virulence factors from entomopathogenic bacteria with special emphasis on two insect pathogenic bacteria Photorhabdus (Proteobacteria: Enterobacteriaceae) and Bacillus (Firmicutes: Bacillaceae). Insect pathogenic bacteria of diverse taxonomic groups and phylogenetic origin have been shown to have striking similarities in the virulence factors they produce. It has been suggested that the detection of phage elements surrounding toxin genes, horizontal and lateral gene transfer events, and plasmid shuffling occurrences may be some of the reasons that virulence factor genes have so many analogs throughout the bacterial kingdom. Comparison of virulence factors of Photorhabdus, and Bacillus, two bacteria with dissimilar life styles opens the possibility of re-examining newly discovered toxins for novel tissue targets. For example, nematodes residing in the hemolymph may release bacteria with virulence factors targeting neurons or neuromuscular junctions. The first section of this review focuses on toxins and their context in agriculture. The second describes the mode of action of toxins from common entomopathogens and the third draws comparisons between Gram positive and Gram negative bacteria. The fourth section reviews the implications of the nervous system in biocontrol.}, }
@article {pmid24632261, year = {2014}, author = {Kim, SJ and Park, SJ and Jung, MY and Kim, JG and Madsen, EL and Rhee, SK}, title = {An uncultivated nitrate-reducing member of the genus Herminiimonas degrades toluene.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {10}, pages = {3233-3243}, pmid = {24632261}, issn = {1098-5336}, mesh = {Bacterial Proteins/genetics ; Betaproteobacteria/classification/genetics/isolation &amp; purification/*metabolism ; Gene Expression Regulation, Bacterial ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Molecular Structure ; Nitrates/*metabolism ; Oxidation-Reduction ; Phylogeny ; Toluene/chemistry/*metabolism ; }, abstract = {Stable isotope probing (SIP) is a cultivation-free methodology that provides information about the identity of microorganisms participating in assimilatory processes in complex communities. In this study, a Herminiimonas-related bacterium was identified as the dominant member of a denitrifying microcosm fed [(13)C]toluene. The genome of the uncultivated toluene-degrading bacterium was obtained by applying pyrosequencing to the heavy DNA fraction. The draft genome comprised ~3.8 Mb, in 131 assembled contigs. Metabolic reconstruction of aromatic hydrocarbon (toluene, benzoate, p-cresol, 4-hydroxybenzoate, phenylacetate, and cyclohexane carboxylate) degradation indicated that the bacterium might specialize in anaerobic hydrocarbon degradation. This characteristic is novel for the order Burkholderiales within the class Betaproteobacteria. Under aerobic conditions, the benzoate oxidation gene cluster (BOX) system is likely involved in the degradation of benzoate via benzoyl coenzyme A. Many putative genes for aromatic hydrocarbon degradation were closely related to those in the Rhodocyclaceae (particularly Aromatoleum aromaticum EbN1) with respect to organization and sequence similarity. Putative mobile genetic elements associated with these catabolic genes were highly abundant, suggesting gene acquisition by Herminiimonas via horizontal gene transfer.}, }
@article {pmid24631858, year = {2014}, author = {Scheel, BM and Hausdorf, B}, title = {Dynamic evolution of mitochondrial ribosomal proteins in Holozoa.}, journal = {Molecular phylogenetics and evolution}, volume = {76}, number = {}, pages = {67-74}, doi = {10.1016/j.ympev.2014.03.005}, pmid = {24631858}, issn = {1095-9513}, mesh = {Amoeba/genetics/metabolism ; Animals ; Bacterial Proteins/genetics/metabolism ; Ctenophora/genetics/metabolism ; DNA, Mitochondrial/genetics/metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genome, Mitochondrial/genetics ; Genomics ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/*genetics/metabolism ; *Phylogeny ; RNA, Ribosomal/genetics/metabolism ; Ribosomal Proteins/*genetics/metabolism ; Ribosomes/genetics/metabolism ; Sequence Analysis, DNA ; }, abstract = {We studied the highly dynamic evolution of mitochondrial ribosomal proteins (MRPs) in Holozoa. Most major clades within Holozoa are characterized by gains and/or losses of MRPs. The usefulness of gains of MRPs as rare genomic changes in phylogenetics is undermined by the high frequency of secondary losses. However, phylogenetic analyses of the MRP sequences provide evidence for the Acrosomata hypothesis, a sister group relationship between Ctenophora and Bilateria. An extensive restructuring of the mitochondrial genome and, as a consequence, of the mitochondrial ribosomes occurred in the ancestor of metazoans. The last MRP genes encoded in the mitochondrial genome were either moved to the nuclear genome or were lost. The strong decrease in size of the mitochondrial genome was probably caused by selection for rapid replication of mitochondrial DNA during oogenesis in the metazoan ancestor. A phylogenetic analysis of MRPL56 sequences provided evidence for a horizontal gene transfer of the corresponding MRP gene between metazoans and Dictyostelidae (Amoebozoa). The hypothesis that the requisition of additional MRPs compensated for a loss of rRNA segments in the mitochondrial ribosomes is corroborated by a significant negative correlation between the number of MRPs and length of the rRNA. Newly acquired MRPs evolved faster than bacterial MRPs and positions in eukaryote-specific MRPs were more strongly affected by coevolution than positions in prokaryotic MRPs in accordance with the necessity to fit these proteins into the pre-existing structure of the mitoribosome.}, }
@article {pmid24630527, year = {2014}, author = {Shapiro, BJ and Polz, MF}, title = {Ordering microbial diversity into ecologically and genetically cohesive units.}, journal = {Trends in microbiology}, volume = {22}, number = {5}, pages = {235-247}, pmid = {24630527}, issn = {1878-4380}, support = {P30 ES002109/ES/NIEHS NIH HHS/United States ; P30-ES002109/ES/NIEHS NIH HHS/United States ; }, mesh = {*Biota ; Gene Transfer, Horizontal ; *Genetic Variation ; Mutation ; Phylogeography ; Recombination, Genetic ; Selection, Genetic ; }, abstract = {We propose that microbial diversity must be viewed in light of gene flow and selection, which define units of genetic similarity, and of phenotype and ecological function, respectively. We discuss to what extent ecological and genetic units overlap to form cohesive populations in the wild, based on recent evolutionary modeling and on evidence from some of the first microbial populations studied with genomics. These show that if recombination is frequent and selection moderate, ecologically adaptive mutations or genes can spread within populations independently of their original genomic background (gene-specific sweeps). Alternatively, if the effect of recombination is smaller than selection, genome-wide selective sweeps should occur. In both cases, however, distinct units of overlapping ecological and genotypic similarity will form if microgeographic separation, likely involving ecological tradeoffs, induces barriers to gene flow. These predictions are supported by (meta)genomic data, which suggest that a 'reverse ecology' approach, in which genomic and gene flow information is used to make predictions about the nature of ecological units, is a powerful approach to ordering microbial diversity.}, }
@article {pmid24629778, year = {2014}, author = {Nguyen, HN and Van, TT and Nguyen, HT and Smooker, PM and Shimeta, J and Coloe, PJ}, title = {Molecular characterization of antibiotic resistance in Pseudomonas and Aeromonas isolates from catfish of the Mekong Delta, Vietnam.}, journal = {Veterinary microbiology}, volume = {171}, number = {3-4}, pages = {397-405}, doi = {10.1016/j.vetmic.2014.01.028}, pmid = {24629778}, issn = {1873-2542}, mesh = {Aeromonas/drug effects/*genetics ; Animals ; Anti-Bacterial Agents/*pharmacology ; Aquaculture ; Catfishes/*microbiology ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal/*genetics ; Integrons/genetics ; Microbial Sensitivity Tests ; Plasmids/genetics ; Pseudomonas/drug effects/*genetics ; Species Specificity ; Vietnam ; }, abstract = {A collection of 116 motile Pseudomonas spp. and 92 Aeromonas spp. isolated from 15 Vietnamese intensive catfish farms was analyzed to examine the molecular antibiotic resistance characteristics and the transferability of resistance markers within and between species. High levels of resistance to ampicillin, trimethoprim/sulfamethoxazole, nalidixic acid, chloramphenicol, and nitrofurantoin were observed. The percentage of multiple drug resistance of Pseudomonas spp. and Aeromonas spp. isolates was 96.6% and 61.9%, respectively. The multiple antibiotic resistance (MAR) index mean values of 0.457 and 0.293 of Pseudomonas and Aeromonas isolates, respectively, indicated that these isolates were exposed to high risk sources of contamination where antibiotics were commonly used. Approximately 33% of Pseudomonas spp. and 28% of Aeromonas spp. isolates from catfish contained class 1 integrons, but no class 2 integrons were detected. Several common resistance genes including aadA, dfrA and catB were harbored in class 1 integrons. Large plasmids (>55 kb) were frequently detected in 50% and 71.4% of the plasmids extracted from Pseudomonas and Aeromonas isolates, respectively. Conjugation and transformation experiments demonstrated the successful transfer of all or part of the resistance phenotypes of catfish isolates to the recipient strains, including laboratory strains and strains isolated from this study. These results highlight the likely role of catfish bacteria as a reservoir of antibiotic resistant, Gram-negative bacteria harboring a pool of mobile genetic elements that can readily be transferred intra- and interspecies. To our knowledge, this is the first report on molecular characterization of antibiotic resistance of bacteria isolated from catfish in Vietnam.}, }
@article {pmid24626479, year = {2014}, author = {Kerr, JE and Abramian, JR and Dao, DH and Rigney, TW and Fritz, J and Pham, T and Gay, I and Parthasarathy, K and Wang, BY and Zhang, W and Tribble, GD}, title = {Genetic exchange of fimbrial alleles exemplifies the adaptive virulence strategy of Porphyromonas gingivalis.}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e91696}, pmid = {24626479}, issn = {1932-6203}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; R01 DE019634/DE/NIDCR NIH HHS/United States ; UL1 TR000371/TR/NCATS NIH HHS/United States ; DE-019634/DE/NIDCR NIH HHS/United States ; }, mesh = {Alleles ; Fimbriae Proteins/genetics/metabolism ; Fimbriae, Bacterial/*genetics ; *Gene Transfer, Horizontal ; Genetic Variation ; Genotype ; Humans ; Periodontitis/*genetics/microbiology/pathology ; Phenotype ; Porphyromonas gingivalis/*genetics/pathogenicity ; Virulence/genetics ; }, abstract = {Porphyromonas gingivalis is a gram-negative anaerobic bacterium, a member of the human oral microbiome, and a proposed "keystone" pathogen in the development of chronic periodontitis, an inflammatory disease of the gingiva. P. gingivalis is a genetically diverse species, and is able to exchange chromosomal DNA between strains by natural competence and conjugation. In this study, we investigate the role of horizontal DNA transfer as an adaptive process to modify behavior, using the major fimbriae as our model system, due to their critical role in mediating interactions with the host environment. We show that P. gingivalis is able to exchange fimbrial allele types I and IV into four distinct strain backgrounds via natural competence. In all recombinants, we detected a complete exchange of the entire fimA allele, and the rate of exchange varies between the different strain backgrounds. In addition, gene exchange within other regions of the fimbrial genetic locus was identified. To measure the biological implications of these allele swaps we compared three genotypes of fimA in an isogenic background, strain ATCC 33277. We demonstrate that exchange of fimbrial allele type results in profound phenotypic changes, including the quantity of fimbriae elaborated, membrane blebbing, auto-aggregation and other virulence-associated phenotypes. Replacement of the type I allele with either the type III or IV allele resulted in increased invasion of gingival fibroblast cells relative to the isogenic parent strain. While genetic variability is known to impact host-microbiome interactions, this is the first study to quantitatively assess the adaptive effect of exchanging genes within the pan genome cloud. This is significant as it presents a potential mechanism by which opportunistic pathogens may acquire the traits necessary to modify host-microbial interactions.}, }
@article {pmid24625962, year = {2014}, author = {Richards, VP and Palmer, SR and Pavinski Bitar, PD and Qin, X and Weinstock, GM and Highlander, SK and Town, CD and Burne, RA and Stanhope, MJ}, title = {Phylogenomics and the dynamic genome evolution of the genus Streptococcus.}, journal = {Genome biology and evolution}, volume = {6}, number = {4}, pages = {741-753}, pmid = {24625962}, issn = {1759-6653}, support = {T90 DE021990/DE/NIDCR NIH HHS/United States ; R01 AI073368/AI/NIAID NIH HHS/United States ; AI073368/AI/NIAID NIH HHS/United States ; HHSN272200900007C/AI/NIAID NIH HHS/United States ; 272200900007C//PHS HHS/United States ; }, mesh = {Base Sequence ; *Evolution, Molecular ; Gene Transfer, Horizontal/*physiology ; Genome, Bacterial/*physiology ; Humans ; Molecular Sequence Data ; *Phylogeny ; Streptococcus/*genetics ; }, abstract = {The genus Streptococcus comprises important pathogens that have a severe impact on human health and are responsible for substantial economic losses to agriculture. Here, we utilize 46 Streptococcus genome sequences (44 species), including eight species sequenced here, to provide the first genomic level insight into the evolutionary history and genetic basis underlying the functional diversity of all major groups of this genus. Gene gain/loss analysis revealed a dynamic pattern of genome evolution characterized by an initial period of gene gain followed by a period of loss, as the major groups within the genus diversified. This was followed by a period of genome expansion associated with the origins of the present extant species. The pattern is concordant with an emerging view that genomes evolve through a dynamic process of expansion and streamlining. A large proportion of the pan-genome has experienced lateral gene transfer (LGT) with causative factors, such as relatedness and shared environment, operating over different evolutionary scales. Multiple gene ontology terms were significantly enriched for each group, and mapping terms onto the phylogeny showed that those corresponding to genes born on branches leading to the major groups represented approximately one-fifth of those enriched. Furthermore, despite the extensive LGT, several biochemical characteristics have been retained since group formation, suggesting genomic cohesiveness through time, and that these characteristics may be fundamental to each group. For example, proteolysis: mitis group; urea metabolism: salivarius group; carbohydrate metabolism: pyogenic group; and transcription regulation: bovis group.}, }
@article {pmid24625961, year = {2014}, author = {Meehan, CJ and Beiko, RG}, title = {A phylogenomic view of ecological specialization in the Lachnospiraceae, a family of digestive tract-associated bacteria.}, journal = {Genome biology and evolution}, volume = {6}, number = {3}, pages = {703-713}, pmid = {24625961}, issn = {1759-6653}, support = {CMF-108026//Canadian Institutes of Health Research/Canada ; }, mesh = {Animals ; Bacteria/*genetics/isolation &amp; purification ; Butyric Acid/metabolism ; Ecosystem ; Evolution, Molecular ; Gastrointestinal Tract/*microbiology ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; Mammals/microbiology ; *Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Several bacterial families are known to be highly abundant within the human microbiome, but their ecological roles and evolutionary histories have yet to be investigated in depth. One such family, Lachnospiraceae (phylum Firmicutes, class Clostridia) is abundant in the digestive tracts of many mammals and relatively rare elsewhere. Members of this family have been linked to obesity and protection from colon cancer in humans, mainly due to the association of many species within the group with the production of butyric acid, a substance that is important for both microbial and host epithelial cell growth. We examined the genomes of 30 Lachnospiraceae isolates to better understand the origin of butyric acid capabilities and other ecological adaptations within this group. Butyric acid production-related genes were detected in fewer than half of the examined genomes with the distribution of this function likely arising in part from lateral gene transfer (LGT). An investigation of environment-specific functional signatures indicated that human gut-associated Lachnospiraceae possess genes for endospore formation, whereas other members of this family lack key sporulation-associated genes, an observation supported by analysis of metagenomes from the human gut, oral cavity, and bovine rumen. Our analysis demonstrates that adaptation to an ecological niche and acquisition of defining functional roles within a microbiome can arise through a combination of both habitat-specific gene loss and LGT.}, }
@article {pmid24625193, year = {2014}, author = {Mærk, M and Johansen, J and Ertesvåg, H and Drabløs, F and Valla, S}, title = {Safety in numbers: multiple occurrences of highly similar homologs among Azotobacter vinelandii carbohydrate metabolism proteins probably confer adaptive benefits.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {192}, pmid = {24625193}, issn = {1471-2164}, mesh = {Adaptation, Physiological ; Archaeal Proteins/genetics ; Azotobacter vinelandii/*genetics ; Bacterial Proteins/*genetics ; Carbohydrate Metabolism/*genetics ; Conserved Sequence ; Genome, Bacterial ; Proteome/genetics ; Pseudomonas/genetics ; Sequence Homology, Amino Acid ; }, abstract = {BACKGROUND: Gene duplication and horizontal gene transfer are common processes in bacterial and archaeal genomes, and are generally assumed to result in either diversification or loss of the redundant gene copies. However, a recent analysis of the genome of the soil bacterium Azotobacter vinelandii DJ revealed an abundance of highly similar homologs among carbohydrate metabolism genes. In many cases these multiple genes did not appear to be the result of recent duplications, or to function only as a means of stimulating expression by increasing gene dosage, as the homologs were located in varying functional genetic contexts. Based on these initial findings we here report in-depth bioinformatic analyses focusing specifically on highly similar intra-genome homologs, or synologs, among carbohydrate metabolism genes, as well as an analysis of the general occurrence of very similar synologs in prokaryotes.<br><br>RESULTS: Approximately 900 bacterial and archaeal genomes were analysed for the occurrence of synologs, both in general and among carbohydrate metabolism genes specifically. This showed that large numbers of highly similar synologs among carbohydrate metabolism genes are very rare in bacterial and archaeal genomes, and that the A. vinelandii DJ genome contains an unusually large amount of such synologs. The majority of these synologs were found to be non-tandemly organized and localized in varying but metabolically relevant genomic contexts. The same observation was made for other genomes harbouring high levels of such synologs. It was also shown that highly similar synologs generally constitute a very small fraction of the protein-coding genes in prokaryotic genomes. The overall synolog fraction of the A. vinelandii DJ genome was well above the data set average, but not nearly as remarkable as the levels observed when only carbohydrate metabolism synologs were considered.<br><br>CONCLUSIONS: Large numbers of highly similar synologs are rare in bacterial and archaeal genomes, both in general and among carbohydrate metabolism genes. However, A. vinelandii and several other soil bacteria harbour large numbers of highly similar carbohydrate metabolism synologs which seem not to result from recent duplication or transfer events. These genes may confer adaptive benefits with respect to certain lifestyles and environmental factors, most likely due to increased regulatory flexibility and/or increased gene dosage.}, }
@article {pmid24624128, year = {2014}, author = {Bapteste, E}, title = {The origins of microbial adaptations: how introgressive descent, egalitarian evolutionary transitions and expanded kin selection shape the network of life.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {83}, pmid = {24624128}, issn = {1664-302X}, }
@article {pmid24623814, year = {2014}, author = {Guglielmini, J and Néron, B and Abby, SS and Garcillán-Barcia, MP and de la Cruz, F and Rocha, EP}, title = {Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion.}, journal = {Nucleic acids research}, volume = {42}, number = {9}, pages = {5715-5727}, pmid = {24623814}, issn = {1362-4962}, support = {281605/ERC_/European Research Council/International ; }, mesh = {Bacteria/*genetics ; Bacterial Proteins/*metabolism ; Bacterial Secretion Systems/*genetics ; *Conjugation, Genetic ; Databases, Genetic ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Plasmids/genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {Conjugation of DNA through a type IV secretion system (T4SS) drives horizontal gene transfer. Yet little is known on the diversity of these nanomachines. We previously found that T4SS can be divided in eight classes based on the phylogeny of the only ubiquitous protein of T4SS (VirB4). Here, we use an ab initio approach to identify protein families systematically and specifically associated with VirB4 in each class. We built profiles for these proteins and used them to scan 2262 genomes for the presence of T4SS. Our analysis led to the identification of thousands of occurrences of 116 protein families for a total of 1623 T4SS. Importantly, we could identify almost always in our profiles the essential genes of well-studied T4SS. This allowed us to build a database with the largest number of T4SS described to date. Using profile-profile alignments, we reveal many new cases of homology between components of distant classes of T4SS. We mapped these similarities on the T4SS phylogenetic tree and thus obtained the patterns of acquisition and loss of these protein families in the history of T4SS. The identification of the key VirB4-associated proteins paves the way toward experimental analysis of poorly characterized T4SS classes.}, }
@article {pmid24621524, year = {2014}, author = {Larsson, J and Celepli, N and Ininbergs, K and Dupont, CL and Yooseph, S and Bergman, B and Ekman, M}, title = {Picocyanobacteria containing a novel pigment gene cluster dominate the brackish water Baltic Sea.}, journal = {The ISME journal}, volume = {8}, number = {9}, pages = {1892-1903}, pmid = {24621524}, issn = {1751-7370}, mesh = {Cyanobacteria/classification/*genetics/isolation &amp; purification ; Genes, Bacterial ; *Multigene Family ; Oceans and Seas ; Phycocyanin/classification/*genetics ; Phycoerythrin/classification/*genetics ; Phylogeny ; Seawater/*microbiology ; }, abstract = {Photoautotrophic picocyanobacteria harvest light via phycobilisomes (PBS) consisting of the pigments phycocyanin (PC) and phycoerythrin (PE), encoded by genes in conserved gene clusters. The presence and arrangement of these gene clusters give picocyanobacteria characteristic light absorption properties and allow the colonization of specific ecological niches. To date, a full understanding of the evolution and distribution of the PBS gene cluster in picocyanobacteria has been hampered by the scarcity of genome sequences from fresh- and brackish water-adapted strains. To remediate this, we analysed genomes assembled from metagenomic samples collected along a natural salinity gradient, and over the course of a growth season, in the Baltic Sea. We found that while PBS gene clusters in picocyanobacteria sampled in marine habitats were highly similar to known references, brackish-adapted genotypes harboured a novel type not seen in previously sequenced genomes. Phylogenetic analyses showed that the novel gene cluster belonged to a clade of uncultivated picocyanobacteria that dominate the brackish Baltic Sea throughout the summer season, but are uncommon in other examined aquatic ecosystems. Further, our data suggest that the PE genes were lost in the ancestor of PC-containing coastal picocyanobacteria and that multiple horizontal gene transfer events have re-introduced PE genes into brackish-adapted strains, including the novel clade discovered here.}, }
@article {pmid24616526, year = {2014}, author = {Ziemert, N and Lechner, A and Wietz, M and Millán-Aguiñaga, N and Chavarria, KL and Jensen, PR}, title = {Diversity and evolution of secondary metabolism in the marine actinomycete genus Salinispora.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {12}, pages = {E1130-9}, pmid = {24616526}, issn = {1091-6490}, support = {R01 GM086261/GM/NIGMS NIH HHS/United States ; R01 GM085770/GM/NIGMS NIH HHS/United States ; U01 TW007401/TW/FIC NIH HHS/United States ; U01-TW0007401/TW/FIC NIH HHS/United States ; GM086261/GM/NIGMS NIH HHS/United States ; GM085770/GM/NIGMS NIH HHS/United States ; }, mesh = {Actinobacteria/genetics/*metabolism ; Cluster Analysis ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Marine Biology ; Phylogeny ; }, abstract = {Access to genome sequence data has challenged traditional natural product discovery paradigms by revealing that the products of most bacterial biosynthetic pathways have yet to be discovered. Despite the insight afforded by this technology, little is known about the diversity and distributions of natural product biosynthetic pathways among bacteria and how they evolve to generate structural diversity. Here we analyze genome sequence data derived from 75 strains of the marine actinomycete genus Salinispora for pathways associated with polyketide and nonribosomal peptide biosynthesis, the products of which account for some of today's most important medicines. The results reveal high levels of diversity, with a total of 124 pathways identified and 229 predicted with continued sequencing. Recent horizontal gene transfer accounts for the majority of pathways, which occur in only one or two strains. Acquired pathways are incorporated into genomic islands and are commonly exchanged within and between species. Acquisition and transfer events largely involve complete pathways, which subsequently evolve by gene gain, loss, and duplication followed by divergence. The exchange of similar pathway types at the precise chromosomal locations in different strains suggests that the mechanisms of integration include pathway-level homologous recombination. Despite extensive horizontal gene transfer there is clear evidence of species-level vertical inheritance, supporting the concept that secondary metabolites represent functional traits that help define Salinispora species. The plasticity of the Salinispora secondary metabolome provides an effective mechanism to maximize population-level secondary metabolite diversity while limiting the number of pathways maintained within any individual genome.}, }
@article {pmid24603854, year = {2014}, author = {De Paepe, M and Hutinet, G and Son, O and Amarir-Bouhram, J and Schbath, S and Petit, MA}, title = {Temperate phages acquire DNA from defective prophages by relaxed homologous recombination: the role of Rad52-like recombinases.}, journal = {PLoS genetics}, volume = {10}, number = {3}, pages = {e1004181}, pmid = {24603854}, issn = {1553-7404}, mesh = {Bacteriophage lambda/genetics ; Escherichia coli/genetics ; *Evolution, Molecular ; Genetic Variation ; *Homologous Recombination ; *Mosaicism ; Rad52 DNA Repair and Recombination Protein/*genetics ; Recombinases/genetics ; }, abstract = {Bacteriophages (or phages) dominate the biosphere both numerically and in terms of genetic diversity. In particular, genomic comparisons suggest a remarkable level of horizontal gene transfer among temperate phages, favoring a high evolution rate. Molecular mechanisms of this pervasive mosaicism are mostly unknown. One hypothesis is that phage encoded recombinases are key players in these horizontal transfers, thanks to their high efficiency and low fidelity. Here, we associate two complementary in vivo assays and a bioinformatics analysis to address the role of phage encoded recombinases in genomic mosaicism. The first assay allowed determining the genetic determinants of mosaic formation between lambdoid phages and Escherichia coli prophage remnants. In the second assay, recombination was monitored between sequences on phage λ, and allowed to compare the performance of three different Rad52-like recombinases on the same substrate. We also addressed the importance of homologous recombination in phage evolution by a genomic comparison of 84 E. coli virulent and temperate phages or prophages. We demonstrate that mosaics are mainly generated by homology-driven mechanisms that tolerate high substrate divergence. We show that phage encoded Rad52-like recombinases act independently of RecA, and that they are relatively more efficient when the exchanged fragments are divergent. We also show that accessory phage genes orf and rap contribute to mosaicism. A bioinformatics analysis strengthens our experimental results by showing that homologous recombination left traces in temperate phage genomes at the borders of recently exchanged fragments. We found no evidence of exchanges between virulent and temperate phages of E. coli. Altogether, our results demonstrate that Rad52-like recombinases promote gene shuffling among temperate phages, accelerating their evolution. This mechanism may prove to be more general, as other mobile genetic elements such as ICE encode Rad52-like functions, and play an important role in bacterial evolution itself.}, }
@article {pmid24603481, year = {2014}, author = {Goh, KM and Gan, HM and Chan, KG and Chan, GF and Shahar, S and Chong, CS and Kahar, UM and Chai, KP}, title = {Analysis of anoxybacillus genomes from the aspects of lifestyle adaptations, prophage diversity, and carbohydrate metabolism.}, journal = {PloS one}, volume = {9}, number = {6}, pages = {e90549}, pmid = {24603481}, issn = {1932-6203}, mesh = {*Adaptation, Physiological ; Anoxybacillus/enzymology/*genetics ; Bacterial Proteins/genetics ; Carbohydrate Metabolism/*genetics ; DNA Repair ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; Genetic Variation ; Genome, Bacterial ; Genomic Instability ; Glycoside Hydrolases/genetics ; Hot Springs/microbiology ; Molecular Sequence Annotation ; Multigene Family ; Phylogeny ; Prophages/*genetics ; Sequence Analysis, DNA ; Viral Proteins/genetics ; Water Microbiology ; }, abstract = {Species of Anoxybacillus are widespread in geothermal springs, manure, and milk-processing plants. The genus is composed of 22 species and two subspecies, but the relationship between its lifestyle and genome is little understood. In this study, two high-quality draft genomes were generated from Anoxybacillus spp. SK3-4 and DT3-1, isolated from Malaysian hot springs. De novo assembly and annotation were performed, followed by comparative genome analysis with the complete genome of Anoxybacillus flavithermus WK1 and two additional draft genomes, of A. flavithermus TNO-09.006 and A. kamchatkensis G10. The genomes of Anoxybacillus spp. are among the smaller of the family Bacillaceae. Despite having smaller genomes, their essential genes related to lifestyle adaptations at elevated temperature, extreme pH, and protection against ultraviolet are complete. Due to the presence of various competence proteins, Anoxybacillus spp. SK3-4 and DT3-1 are able to take up foreign DNA fragments, and some of these transferred genes are important for the survival of the cells. The analysis of intact putative prophage genomes shows that they are highly diversified. Based on the genome analysis using SEED, many of the annotated sequences are involved in carbohydrate metabolism. The presence of glycosyl hydrolases among the Anoxybacillus spp. was compared, and the potential applications of these unexplored enzymes are suggested here. This is the first study that compares Anoxybacillus genomes from the aspect of lifestyle adaptations, the capacity for horizontal gene transfer, and carbohydrate metabolism.}, }
@article {pmid24602988, year = {2014}, author = {Zhi, XY and Yao, JC and Li, HW and Huang, Y and Li, WJ}, title = {Genome-wide identification, domain architectures and phylogenetic analysis provide new insights into the early evolution of shikimate pathway in prokaryotes.}, journal = {Molecular phylogenetics and evolution}, volume = {75}, number = {}, pages = {154-164}, doi = {10.1016/j.ympev.2014.02.015}, pmid = {24602988}, issn = {1095-9513}, mesh = {3-Phosphoshikimate 1-Carboxyvinyltransferase/genetics ; Aldehyde-Ketone Transferases/genetics ; Archaea/enzymology/*genetics ; Bacteria/enzymology/*genetics ; *Biological Evolution ; Computational Biology ; Gene Transfer, Horizontal ; Markov Chains ; Metabolic Networks and Pathways/genetics ; Multigene Family ; Phosphorus-Oxygen Lyases/genetics ; Phosphotransferases (Alcohol Group Acceptor)/genetics ; *Phylogeny ; Proteome/analysis ; Sequence Analysis, DNA ; Shikimic Acid/*metabolism ; }, abstract = {Despite intense scrutiny from researchers in the fields of biochemistry and metabolism, our understanding of the evolutionary history of the key anabolic shikimate pathway remains limited. To shed light on the early evolutionary events leading to the assembly of the pathway, we investigated the distributions, domain architectures and phylogenies of component enzymes using a bioinformatic procedure based on Hidden Markov Model profiles. The aro genes for the canonical shikimate pathway had most wider distribution in prokaryotes; and the variant pathway coordinated by 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonic acid (ADH) synthase and type II 3-dehydroquinate (DHQ) synthase could be identified in most of archaeal species. In addition, the ancient bidirectional horizontal gene transfer events had happened between two prokaryotic domains: Bacteria and Archaea. Besides 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase, the phylogenetically distinct subfamilies of 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase and chorismate synthase had ever emerged in the evolutionary history of shikimate pathway. These findings provide new insight into the early evolution of the shikimate pathway and advance our understanding of the evolution of metabolic pathways.}, }
@article {pmid24600039, year = {2014}, author = {Darmon, E and Leach, DR}, title = {Bacterial genome instability.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {78}, number = {1}, pages = {1-39}, pmid = {24600039}, issn = {1098-5557}, support = {G0901622/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Antigenic Variation ; Biological Evolution ; DNA Transposable Elements ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genomic Instability ; Homologous Recombination ; Inteins/genetics ; Inverted Repeat Sequences ; }, abstract = {Bacterial genomes are remarkably stable from one generation to the next but are plastic on an evolutionary time scale, substantially shaped by horizontal gene transfer, genome rearrangement, and the activities of mobile DNA elements. This implies the existence of a delicate balance between the maintenance of genome stability and the tolerance of genome instability. In this review, we describe the specialized genetic elements and the endogenous processes that contribute to genome instability. We then discuss the consequences of genome instability at the physiological level, where cells have harnessed instability to mediate phase and antigenic variation, and at the evolutionary level, where horizontal gene transfer has played an important role. Indeed, this ability to share DNA sequences has played a major part in the evolution of life on Earth. The evolutionary plasticity of bacterial genomes, coupled with the vast numbers of bacteria on the planet, substantially limits our ability to control disease.}, }
@article {pmid24599066, year = {2014}, author = {Djukic, M and Brzuszkiewicz, E and Fünfhaus, A and Voss, J and Gollnow, K and Poppinga, L and Liesegang, H and Garcia-Gonzalez, E and Genersch, E and Daniel, R}, title = {How to kill the honey bee larva: genomic potential and virulence mechanisms of Paenibacillus larvae.}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e90914}, pmid = {24599066}, issn = {1932-6203}, mesh = {Animals ; Bacterial Proteins/metabolism ; Bacterial Toxins/genetics ; Base Composition/genetics ; Bees/*microbiology ; Biosynthetic Pathways/genetics ; Chromosomes, Bacterial/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Genetic Loci ; Genome, Bacterial/genetics ; Genomic Islands/genetics ; *Genomics ; Larva/microbiology ; Models, Biological ; Multigene Family ; Paenibacillus/*genetics/*pathogenicity ; Virulence/genetics ; }, abstract = {Paenibacillus larvae, a Gram positive bacterial pathogen, causes American Foulbrood (AFB), which is the most serious infectious disease of honey bees. In order to investigate the genomic potential of P. larvae, two strains belonging to two different genotypes were sequenced and used for comparative genome analysis. The complete genome sequence of P. larvae strain DSM 25430 (genotype ERIC II) consisted of 4,056,006 bp and harbored 3,928 predicted protein-encoding genes. The draft genome sequence of P. larvae strain DSM 25719 (genotype ERIC I) comprised 4,579,589 bp and contained 4,868 protein-encoding genes. Both strains harbored a 9.7 kb plasmid and encoded a large number of virulence-associated proteins such as toxins and collagenases. In addition, genes encoding large multimodular enzymes producing nonribosomally peptides or polyketides were identified. In the genome of strain DSM 25719 seven toxin associated loci were identified and analyzed. Five of them encoded putatively functional toxins. The genome of strain DSM 25430 harbored several toxin loci that showed similarity to corresponding loci in the genome of strain DSM 25719, but were non-functional due to point mutations or disruption by transposases. Although both strains cause AFB, significant differences between the genomes were observed including genome size, number and composition of transposases, insertion elements, predicted phage regions, and strain-specific island-like regions. Transposases, integrases and recombinases are important drivers for genome plasticity. A total of 390 and 273 mobile elements were found in strain DSM 25430 and strain DSM 25719, respectively. Comparative genomics of both strains revealed acquisition of virulence factors by horizontal gene transfer and provided insights into evolution and pathogenicity.}, }
@article {pmid24597605, year = {2014}, author = {Frenkel, J and Vyverman, W and Pohnert, G}, title = {Pheromone signaling during sexual reproduction in algae.}, journal = {The Plant journal : for cell and molecular biology}, volume = {79}, number = {4}, pages = {632-644}, doi = {10.1111/tpj.12496}, pmid = {24597605}, issn = {1365-313X}, mesh = {Chlorophyta/*metabolism ; Pheromones/*metabolism ; Reproduction ; Stramenopiles/metabolism ; }, abstract = {Algae are found in all aquatic and many terrestrial habitats. They are dominant in phytoplankton and biofilms thereby contributing massively to global primary production. Since algae comprise photosynthetic representatives of the various protoctist groups their physiology and appearance is highly diverse. This diversity is also mirrored in their characteristic life cycles that exhibit various facets of ploidy and duration of the asexual phase as well as gamete morphology. Nevertheless, sexual reproduction in unicellular and colonial algae usually has as common motive that two specialized, sexually compatible haploid gametes establish physical contact and fuse. To guarantee mating success, processes during sexual reproduction are highly synchronized and regulated. This review focuses on sex pheromones of algae that play a key role in these processes. Especially, the diversity of sexual strategies as well as of the compounds involved are the focus of this contribution. Discoveries connected to algal pheromone chemistry shed light on the role of key evolutionary processes, including endosymbiotic events and lateral gene transfer, speciation and adaptation at all phylogenetic levels. But progress in this field might also in the future provide valid tools for the manipulation of aquaculture and environmental processes.}, }
@article {pmid24596284, year = {2014}, author = {Musovic, S and Klümper, U and Dechesne, A and Magid, J and Smets, BF}, title = {Long-term manure exposure increases soil bacterial community potential for plasmid uptake.}, journal = {Environmental microbiology reports}, volume = {6}, number = {2}, pages = {125-130}, doi = {10.1111/1758-2229.12138}, pmid = {24596284}, issn = {1758-2229}, mesh = {Agrochemicals/*pharmacology ; Bacteria/*drug effects/*genetics/metabolism ; Biodiversity ; *Gene Transfer, Horizontal ; Manure/analysis/*microbiology ; Plasmids/*genetics/metabolism ; Soil Microbiology ; }, abstract = {Microbial communities derived from soils subject to different agronomic treatments were challenged with three broad host range plasmids, RP4, pIPO2tet and pRO101, via solid surface filter matings to assess their permissiveness. Approximately 1 in 10 000 soil bacterial cells could receive and maintain the plasmids. The community permissiveness increased up to 100% in communities derived from manured soil. While the plasmid transfer frequency was significantly influenced by both the type of plasmid and the agronomic treatment, the diversity of the transconjugal pools was purely plasmid dependent and was dominated by β- and γ-Proteobacteria.}, }
@article {pmid24594007, year = {2013}, author = {Jansen, G and Barbosa, C and Schulenburg, H}, title = {Experimental evolution as an efficient tool to dissect adaptive paths to antibiotic resistance.}, journal = {Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy}, volume = {16}, number = {6}, pages = {96-107}, doi = {10.1016/j.drup.2014.02.002}, pmid = {24594007}, issn = {1532-2084}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Humans ; Mutation ; }, abstract = {Antibiotic treatments increasingly fail due to rapid dissemination of drug resistance. Comparative genomics of clinical isolates highlights the role of de novo adaptive mutations and horizontal gene transfer (HGT) in the acquisition of resistance. Yet it cannot fully describe the selective pressures and evolutionary trajectories that yielded today's problematic strains. Experimental evolution offers a compelling addition to such studies because the combination of replicated experiments under tightly controlled conditions with genomics of intermediate time points allows real-time reconstruction of evolutionary trajectories. Recent studies thus established causal links between antibiotic deployment therapies and the course and timing of mutations, the cost of resistance and the likelihood of compensating mutations. They particularly underscored the importance of long-term effects. Similar investigations incorporating horizontal gene transfer (HGT) are wanting, likely because of difficulties associated with its integration into experiments. In this review, we describe current advances in experimental evolution of antibiotic resistance and reflect on ways to incorporate horizontal gene transfer into the approach. We contend it provides a powerful tool for systematic and highly controlled dissection of evolutionary paths to antibiotic resistance that needs to be taken into account for the development of sustainable anti-bacterial treatment strategies.}, }
@article {pmid24589583, year = {2014}, author = {Luo, C and Rodriguez-R, LM and Konstantinidis, KT}, title = {MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences.}, journal = {Nucleic acids research}, volume = {42}, number = {8}, pages = {e73}, pmid = {24589583}, issn = {1362-4962}, mesh = {Algorithms ; Classification/methods ; Genes ; Genomics/*methods ; Humans ; Metagenomics/*methods ; Microbiota ; *Phylogeny ; Software ; }, abstract = {Determining the taxonomic affiliation of sequences assembled from metagenomes remains a major bottleneck that affects research across the fields of environmental, clinical and evolutionary microbiology. Here, we introduce MyTaxa, a homology-based bioinformatics framework to classify metagenomic and genomic sequences with unprecedented accuracy. The distinguishing aspect of MyTaxa is that it employs all genes present in an unknown sequence as classifiers, weighting each gene based on its (predetermined) classifying power at a given taxonomic level and frequency of horizontal gene transfer. MyTaxa also implements a novel classification scheme based on the genome-aggregate average amino acid identity concept to determine the degree of novelty of sequences representing uncharacterized taxa, i.e. whether they represent novel species, genera or phyla. Application of MyTaxa on in silico generated (mock) and real metagenomes of varied read length (100-2000 bp) revealed that it correctly classified at least 5% more sequences than any other tool. The analysis also showed that ∼10% of the assembled sequences from human gut metagenomes represent novel species with no sequenced representatives, several of which were highly abundant in situ such as members of the Prevotella genus. Thus, MyTaxa can find several important applications in microbial identification and diversity studies.}, }
@article {pmid24586200, year = {2014}, author = {Fernandez-Lopez, R and Del Campo, I and Revilla, C and Cuevas, A and de la Cruz, F}, title = {Negative feedback and transcriptional overshooting in a regulatory network for horizontal gene transfer.}, journal = {PLoS genetics}, volume = {10}, number = {2}, pages = {e1004171}, pmid = {24586200}, issn = {1553-7404}, mesh = {Computer Simulation ; Evolution, Molecular ; Gene Regulatory Networks ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Plasmids/*genetics ; Proteobacteria/*genetics ; Selection, Genetic/*genetics ; }, abstract = {Horizontal gene transfer (HGT) is a major force driving bacterial evolution. Because of their ability to cross inter-species barriers, bacterial plasmids are essential agents for HGT. This ability, however, poses specific requisites on plasmid physiology, in particular the need to overcome a multilevel selection process with opposing demands. We analyzed the transcriptional network of plasmid R388, one of the most promiscuous plasmids in Proteobacteria. Transcriptional analysis by fluorescence expression profiling and quantitative PCR revealed a regulatory network controlled by six transcriptional repressors. The regulatory network relied on strong promoters, which were tightly repressed in negative feedback loops. Computational simulations and theoretical analysis indicated that this architecture would show a transcriptional burst after plasmid conjugation, linking the magnitude of the feedback gain with the intensity of the transcriptional burst. Experimental analysis showed that transcriptional overshooting occurred when the plasmid invaded a new population of susceptible cells. We propose that transcriptional overshooting allows genome rebooting after horizontal gene transfer, and might have an adaptive role in overcoming the opposing demands of multilevel selection.}, }
@article {pmid24586126, year = {2014}, author = {Amrine, KC and Swingley, WD and Ardell, DH}, title = {tRNA signatures reveal a polyphyletic origin of SAR11 strains among alphaproteobacteria.}, journal = {PLoS computational biology}, volume = {10}, number = {2}, pages = {e1003454}, pmid = {24586126}, issn = {1553-7358}, mesh = {Alphaproteobacteria/*classification/*genetics ; Bacterial Proteins/genetics ; Computational Biology ; Evolution, Molecular ; Gene Regulatory Networks ; Gene Transfer, Horizontal ; Genome, Bacterial ; Models, Genetic ; Phylogeny ; RNA, Bacterial/*genetics ; RNA, Transfer/*genetics ; Rhodospirillales/classification/genetics ; }, abstract = {Molecular phylogenetics and phylogenomics are subject to noise from horizontal gene transfer (HGT) and bias from convergence in macromolecular compositions. Extensive variation in size, structure and base composition of alphaproteobacterial genomes has complicated their phylogenomics, sparking controversy over the origins and closest relatives of the SAR11 strains. SAR11 are highly abundant, cosmopolitan aquatic Alphaproteobacteria with streamlined, A+T-biased genomes. A dominant view holds that SAR11 are monophyletic and related to both Rickettsiales and the ancestor of mitochondria. Other studies dispute this, finding evidence of a polyphyletic origin of SAR11 with most strains distantly related to Rickettsiales. Although careful evolutionary modeling can reduce bias and noise in phylogenomic inference, entirely different approaches may be useful to extract robust phylogenetic signals from genomes. Here we develop simple phyloclassifiers from bioinformatically derived tRNA Class-Informative Features (CIFs), features predicted to target tRNAs for specific interactions within the tRNA interaction network. Our tRNA CIF-based model robustly and accurately classifies alphaproteobacterial genomes into one of seven undisputed monophyletic orders or families, despite great variability in tRNA gene complement sizes and base compositions. Our model robustly rejects monophyly of SAR11, classifying all but one strain as Rhizobiales with strong statistical support. Yet remarkably, conventional phylogenetic analysis of tRNAs classifies all SAR11 strains identically as Rickettsiales. We attribute this discrepancy to convergence of SAR11 and Rickettsiales tRNA base compositions. Thus, tRNA CIFs appear more robust to compositional convergence than tRNA sequences generally. Our results suggest that tRNA-CIF-based phyloclassification is robust to HGT of components of the tRNA interaction network, such as aminoacyl-tRNA synthetases. We explain why tRNAs are especially advantageous for prediction of traits governing macromolecular interactions from genomic data, and why such traits may be advantageous in the search for robust signals to address difficult problems in classification and phylogeny.}, }
@article {pmid24583362, year = {2014}, author = {Porres-Osante, N and Azcona-Gutiérrez, JM and Rojo-Bezares, B and Undabeitia, E and Torres, C and Sáenz, Y}, title = {Emergence of a multiresistant KPC-3 and VIM-1 carbapenemase-producing Escherichia coli strain in Spain.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {69}, number = {7}, pages = {1792-1795}, doi = {10.1093/jac/dku055}, pmid = {24583362}, issn = {1460-2091}, mesh = {Aged ; Bacterial Proteins/*genetics/*metabolism ; DNA, Bacterial/chemistry/genetics ; *Drug Resistance, Multiple, Bacterial ; Escherichia coli/*drug effects/*enzymology/genetics/isolation &amp; purification ; Escherichia coli Infections/*microbiology ; Fatal Outcome ; Female ; Gene Transfer, Horizontal ; Humans ; Interspersed Repetitive Sequences ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Spain ; Urinary Tract Infections/microbiology ; beta-Lactamases/*genetics/*metabolism ; }, abstract = {OBJECTIVES: To characterize the mechanisms involved in carbapenem resistance, as well as the genetic elements supporting their mobilization, in a multidrug-resistant Escherichia coli isolate.<br><br>METHODS: The E. coli isolate was obtained from a patient with fatal urinary sepsis. Antimicrobial susceptibility testing was performed by the disc diffusion and agar dilution methods. The E. coli molecular type and phylogroup were determined using multilocus sequence typing and the triple PCR technique, respectively. PCR and sequencing were used for virulence and resistance genotype characterization. Plasmid content and gene location were analysed by S1-PFGE, I-Ceu1-PFGE and hybridization experiments. Transformation assays were performed.<br><br>RESULTS: The E. coli strain, typed as ST448 and phylogroup B1, was resistant to all tested antibiotics except fosfomycin, tigecycline and tetracycline. The following resistance and virulence genetic structures were obtained: ISKpn7&#x200a;+&#x200a;bla(KPC-3)&#x200a;+&#x200a;ISKpn6 linked to Tn4401; tnpR&#x200a;+&#x200a;aac(6')-Ib'-9&#x200a;+&#x200a;aadA1&#x200a;+&#x200a;bla(OXA-9)&#x200a;+&#x200a;tnpR&#x200a;+&#x200a;bla(TEM-1a)&#x200a;+&#x200a;tnpB&#x200a;+&#x200a;strB&#x200a;+&#x200a;strA&#x200a;+&#x200a;sul2; intI1&#x200a;+&#x200a;bla(VIM-1)&#x200a;+&#x200a;aac(6')-Ib'&#x200a;+&#x200a;aphA15&#x200a;+&#x200a;aadA1&#x200a;+&#x200a;catB2&#x200a;+&#x200a;qacE&#x394;1-sul1&#x200a;+&#x200a;orf5; ISEcp1&#x200a;+&#x200a;bla(CMY-2); IS26&#x200a;+&#x200a;bla(SHV-12); aph(3')-I; aac(3)-IV; floR; catA; and fimA. Mutations in the ampC promoter (-18, -1 and +58) and substitutions in the GyrA (Ser-83&#x2192;Leu and Asp-87&#x2192;Asn) and ParC (Ser-80&#x2192;Ile) proteins were observed. IncFII (ST2), IncA/C and ColE(TP) plasmids of 145.5, 87 and <2 kb, respectively, were found. The bla(VIM-1) gene was located in a non-typeable plasmid of >300 kb, and the bla(KPC-3) gene in the 145.5 kb IncFII plasmid. Transformant strains carried the IncFII and ColE(TP) plasmids, and the bla(KPC-3), bla(TEM-1a), bla(OXA-9), aadA1, aac(6')-Ib'-9, aac(3)-IV and floR genes.<br><br>CONCLUSIONS: This is the first report of the co-production of KPC-3, VIM-1, SHV-12, OXA-9 and CMY-2 in a unique clinical multiresistant E. coli isolate. The dissemination of these genes on mobile genetic elements is alarming and complicates antimicrobial therapies.}, }
@article {pmid24583288, year = {2014}, author = {Ramulu, HG and Groussin, M and Talla, E and Planel, R and Daubin, V and Brochier-Armanet, C}, title = {Ribosomal proteins: toward a next generation standard for prokaryotic systematics?.}, journal = {Molecular phylogenetics and evolution}, volume = {75}, number = {}, pages = {103-117}, doi = {10.1016/j.ympev.2014.02.013}, pmid = {24583288}, issn = {1095-9513}, mesh = {Bayes Theorem ; Biological Evolution ; DNA, Bacterial/genetics ; Epsilonproteobacteria/classification/genetics ; Gene Transfer, Horizontal ; Likelihood Functions ; Models, Genetic ; *Phylogeny ; Proteobacteria/*classification/genetics ; Ribosomal Proteins/*genetics ; Ribosome Subunits, Small, Bacterial/genetics ; Sequence Analysis, DNA ; }, abstract = {The seminal work of Carl Woese and co-workers has contributed to promote the RNA component of the small subunit of the ribosome (SSU rRNA) as a "gold standard" of modern prokaryotic taxonomy and systematics, and an essential tool to explore microbial diversity. Yet, this marker has a limited resolving power, especially at deep phylogenetic depth and can lead to strongly biased trees. The ever-larger number of available complete genomes now calls for a novel standard dataset of robust protein markers that may complement SSU rRNA. In this respect, concatenation of ribosomal proteins (r-proteins) is being growingly used to reconstruct large-scale prokaryotic phylogenies, but their suitability for systematic and/or taxonomic purposes has not been specifically addressed. Using Proteobacteria as a case study, we show that amino acid and nucleic acid r-protein sequences contain a reliable phylogenetic signal at a wide range of taxonomic depths, which has not been totally blurred by mutational saturation or horizontal gene transfer. The use of accurate evolutionary models and reconstruction methods allows overcoming most tree reconstruction artefacts resulting from compositional biases and/or fast evolutionary rates. The inferred phylogenies allow clarifying the relationships among most proteobacterial orders and families, along with the position of several unclassified lineages, suggesting some possible revisions of the current classification. In addition, we investigate the root of the Proteobacteria by considering the time-variation of nucleic acid composition of r-protein sequences and the information carried by horizontal gene transfers, two approaches that do not require the use of an outgroup and limit tree reconstruction artefacts. Altogether, our analyses indicate that r-proteins may represent a promising standard for prokaryotic taxonomy and systematics.}, }
@article {pmid24582794, year = {2014}, author = {Boycheva, S and Daviet, L and Wolfender, JL and Fitzpatrick, TB}, title = {The rise of operon-like gene clusters in plants.}, journal = {Trends in plant science}, volume = {19}, number = {7}, pages = {447-459}, doi = {10.1016/j.tplants.2014.01.013}, pmid = {24582794}, issn = {1878-4372}, mesh = {Biosynthetic Pathways/genetics ; Evolution, Molecular ; *Gene Duplication ; *Gene Expression Regulation, Plant ; Genome, Plant/*genetics ; Models, Genetic ; Multigene Family/*genetics ; Operon/genetics ; Phylogeny ; Plants/chemistry/*genetics/metabolism ; Secondary Metabolism/genetics ; Translocation, Genetic ; }, abstract = {Gene clusters are common features of prokaryotic genomes also present in eukaryotes. Most clustered genes known are involved in the biosynthesis of secondary metabolites. Although horizontal gene transfer is a primary source of prokaryotic gene cluster (operon) formation and has been reported to occur in eukaryotes, the predominant source of cluster formation in eukaryotes appears to arise de novo or through gene duplication followed by neo- and sub-functionalization or translocation. Here we aim to provide an overview of the current knowledge and open questions related to plant gene cluster functioning, assembly, and regulation. We also present potential research approaches and point out the benefits of a better understanding of gene clusters in plants for both fundamental and applied plant science.}, }
@article {pmid24582529, year = {2014}, author = {Bondy-Denomy, J and Davidson, AR}, title = {To acquire or resist: the complex biological effects of CRISPR-Cas systems.}, journal = {Trends in microbiology}, volume = {22}, number = {4}, pages = {218-225}, doi = {10.1016/j.tim.2014.01.007}, pmid = {24582529}, issn = {1878-4380}, support = {MOP-130482//Canadian Institutes of Health Research/Canada ; XNE86943//Canadian Institutes of Health Research/Canada ; }, mesh = {*Adaptation, Biological ; *CRISPR-Cas Systems ; Evolution, Molecular ; Prokaryotic Cells/*physiology ; Recombination, Genetic ; }, abstract = {Prokaryotic CRISPR-Cas (clustered regularly interspaced short palindromic repeat-CRISPR associated) systems provide a sophisticated adaptive immune system that offers protection against foreign DNA. These systems are widely distributed in prokaryotes and exert an important influence on bacterial behavior and evolution. However, interpreting the biological effects of a CRISPR-Cas system within a given species can be complicated because the outcome of rejecting foreign DNA does not always provide a fitness advantage, as foreign DNA uptake is sometimes beneficial. To address these issues, here we review data pertaining to the potential in vivo costs and benefits of CRISPR-Cas systems, novel functions for these systems, and how they may be inactivated.}, }
@article {pmid24581697, year = {2014}, author = {Hatoum-Aslan, A and Marraffini, LA}, title = {Impact of CRISPR immunity on the emergence and virulence of bacterial pathogens.}, journal = {Current opinion in microbiology}, volume = {17}, number = {}, pages = {82-90}, pmid = {24581697}, issn = {1879-0364}, support = {DP2 AI104556/AI/NIAID NIH HHS/United States ; 1DP2AI104556-01/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Bacteria/immunology/pathogenicity ; Bacterial Infections ; *CRISPR-Cas Systems/immunology/physiology ; Humans ; Mice ; }, abstract = {CRISPR-Cas systems protect prokaryotes from viruses and plasmids and function primarily as an adaptive immune system in these organisms. Recent discoveries, however, revealed unexpected roles for CRISPR loci as barriers to horizontal gene transfer and as modulators of gene expression. We review how both of these functions of CRISPR-Cas systems can affect the emergence and virulence of human bacterial pathogens.}, }
@article {pmid24581597, year = {2014}, author = {Jiang, HX and Song, L and Liu, J and Zhang, XH and Ren, YN and Zhang, WH and Zhang, JY and Liu, YH and Webber, MA and Ogbolu, DO and Zeng, ZL and Piddock, LJ}, title = {Multiple transmissible genes encoding fluoroquinolone and third-generation cephalosporin resistance co-located in non-typhoidal Salmonella isolated from food-producing animals in China.}, journal = {International journal of antimicrobial agents}, volume = {43}, number = {3}, pages = {242-247}, doi = {10.1016/j.ijantimicag.2013.12.005}, pmid = {24581597}, issn = {1872-7913}, mesh = {Animals ; Animals, Domestic ; Cephalosporins/*pharmacology ; China ; Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; *Drug Resistance, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Fluoroquinolones/*pharmacology ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Molecular Typing ; *Plasmids ; Polymerase Chain Reaction ; Salmonella/classification/*drug effects/genetics/isolation &amp; purification ; Salmonella Infections, Animal/*microbiology ; Sequence Analysis, DNA ; Serotyping ; }, abstract = {The aim of this study was to identify genes conferring resistance to fluoroquinolones and extended-spectrum β-lactams in non-typhoidal Salmonella (NTS) from food-producing animals in China. In total, 31 non-duplicate NTS were obtained from food-producing animals that were sick. Isolates were identified and serotyped and the genetic relatedness of the isolates was determined by pulsed-field gel electrophoresis of XbaI-digested chromosomal DNA. Antimicrobial susceptibility was determined using Clinical and Laboratory Standards Institute methodology. The presence of extended-spectrum β-lactamase (ESBL) and fluoroquinolone resistance genes was established by PCR and sequencing. Genes encoded on transmissible elements were identified by conjugation and transformation. Plasmids were typed by PCR-based replicon typing. The occurrence and diversity of numerous different transmissible genes conferring fluoroquinolone resistance [qnrA, qnrD, oqxA and aac(6')-Ib-cr] and ESBLs (CTX-M-27 and CTX-M-14), and which co-resided in different isolates and serovars of Salmonella, were much higher than in European countries. Furthermore, different plasmids encoded fluoroquinolone resistance (ca. 6 kb) and β-lactam resistance (ca. 63 kb) and these co-resided in isolates with mutations in topoisomerase genes (gyrA and parC) giving very resistant Salmonella. The presence of multidrug-resistant bacteria in food-producing animals in countries that export foodstuffs suggests that global transfer of antibiotic resistances from country to country on food is possible.}, }
@article {pmid24578351, year = {2014}, author = {van Passel, MW and Nijveen, H and Wahl, LM}, title = {Birth, death, and diversification of mobile promoters in prokaryotes.}, journal = {Genetics}, volume = {197}, number = {1}, pages = {291-299}, pmid = {24578351}, issn = {1943-2631}, mesh = {Chromosome Mapping ; Gene Duplication/genetics ; Gene Transfer, Horizontal ; Genetic Variation/*genetics ; *Genomics ; Interspersed Repetitive Sequences/*genetics ; *Models, Genetic ; *Prokaryotic Cells ; Promoter Regions, Genetic/*genetics ; }, abstract = {A previous study of prokaryotic genomes identified large reservoirs of putative mobile promoters (PMPs), that is, homologous promoter sequences associated with nonhomologous coding sequences. Here we extend this data set to identify the full complement of mobile promoters in sequenced prokaryotic genomes. The expanded search identifies nearly 40,000 PMP sequences, 90% of which occur in noncoding regions of the genome. To gain further insight from this data set, we develop a birth-death-diversification model for mobile genetic elements subject to sequence diversification; applying the model to PMPs we are able to quantify the relative importance of duplication, loss, horizontal gene transfer (HGT), and diversification to the maintenance of the PMP reservoir. The model predicts low rates of HGT relative to the duplication and loss of PMP copies, rapid dynamics of PMP families, and a pool of PMPs that exist as a single copy in a genome at any given time, despite their mobility. We report evidence of these "singletons" at high frequencies in prokaryotic genomes. We also demonstrate that including selection, either for or against PMPs, was not necessary to describe the observed data.}, }
@article {pmid24575358, year = {2014}, author = {Kleinheinz, KA and Joensen, KG and Larsen, MV}, title = {Applying the ResFinder and VirulenceFinder web-services for easy identification of acquired antibiotic resistance and E. coli virulence genes in bacteriophage and prophage nucleotide sequences.}, journal = {Bacteriophage}, volume = {4}, number = {1}, pages = {e27943}, pmid = {24575358}, issn = {2159-7073}, abstract = {Extensive research is currently being conducted on the use of bacteriophages for applications in human medicine, agriculture and food manufacturing. However, phages are important vehicles of horisontal gene transfer and play a significant role in bacterial evolution. As a result, concern has been raised that this increased use and dissemination of phages could result in spread of deleterious genes, e.g., antibiotic resistance and virulence genes. Meanwhile, in the wake of the genomic era, several tools have been developed for characterization of bacterial genomes. Here we describe how two of these tools, ResFinder and VirulenceFinder, can be used to identify acquired antibiotic resistance and virulence genes in phage genomes of interest. The general applicability of the tools is demonstrated on data sets of 1,642 phage genomes and 1,442 predicted prophages.}, }
@article {pmid24575089, year = {2014}, author = {Bearson, BL and Allen, HK and Brunelle, BW and Lee, IS and Casjens, SR and Stanton, TB}, title = {The agricultural antibiotic carbadox induces phage-mediated gene transfer in Salmonella.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {52}, pmid = {24575089}, issn = {1664-302X}, abstract = {Antibiotics are used for disease therapeutic or preventative effects in humans and animals, as well as for enhanced feed conversion efficiency in livestock. Antibiotics can also cause undesirable effects in microbial populations, including selection for antibiotic resistance, enhanced pathogen invasion, and stimulation of horizontal gene transfer. Carbadox is a veterinary antibiotic used in the US during the starter phase of swine production for improved feed efficiency and control of swine dysentery and bacterial swine enteritis. Carbadox has been shown in vitro to induce phage-encoded Shiga toxin in Shiga toxin-producing Escherichia coli (STEC) and a phage-like element transferring antibiotic resistance genes in Brachyspira hyodysenteriae, but the effect of carbadox on prophages in other bacteria is unknown. This study examined carbadox exposure on prophage induction and genetic transfer in Salmonella enterica serovar Typhimurium, a human foodborne pathogen that frequently colonizes swine without causing disease. S. Typhimurium LT2 exposed to carbadox induced prophage production, resulting in bacterial cell lysis and release of virions that were visible by electron microscopy. Carbadox induction of phage-mediated gene transfer was confirmed by monitoring the transduction of a sodCIII::neo cassette in the Fels-1 prophage from LT2 to a recipient Salmonella strain. Furthermore, carbadox frequently induced generalized transducing phages in multidrug-resistant phage type DT104 and DT120 isolates, resulting in the transfer of chromosomal and plasmid DNA that included antibiotic resistance genes. Our research indicates that exposure of Salmonella to carbadox induces prophages that can transfer virulence and antibiotic resistance genes to susceptible bacterial hosts. Carbadox-induced, phage-mediated gene transfer could serve as a contributing factor in bacterial evolution during animal production, with prophages being a reservoir for bacterial fitness genes in the environment.}, }
@article {pmid24572738, year = {2014}, author = {Sarkar, S}, title = {Woese on the received view of evolution.}, journal = {RNA biology}, volume = {11}, number = {3}, pages = {220-224}, pmid = {24572738}, issn = {1555-8584}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Biological Evolution ; Gene Transfer, Horizontal ; Genetic Code ; Humans ; Origin of Life ; }, abstract = {As part of his attempt to reconstruct the earliest phase of the evolution of life on Earth, Woese produced a compelling critique of the received view of evolution from the 20th century. This paper explicitly articulates two related features of that critique that are fundamental but the first of which has not been sufficiently clearly recognized in the context of evolutionary theorizing: (1) according to Woese's scenario of communal evolution during life's earliest phase (roughly, the first billion years of life on Earth), well-defined biological individuals (and, thus, individual lineages) did not exist; and (2) during that phase, evolutionary change took place through ubiquitous horizontal gene transfer (HGT) rather than through vertical transmission of features (including genes) and the combinatorics of HGT was the dominant mechanism of evolutionary change. Both factors present serious challenges to the received view of evolution and that framework would have to be radically altered to incorporate these factors. The extent to which this will be necessary will depend on whether Woese's scenario of collective early evolution is correct.}, }
@article {pmid24572480, year = {2014}, author = {Koonin, EV}, title = {Carl Woese's vision of cellular evolution and the domains of life.}, journal = {RNA biology}, volume = {11}, number = {3}, pages = {197-204}, pmid = {24572480}, issn = {1555-8584}, support = {//Intramural NIH HHS/United States ; }, mesh = {*Biological Evolution ; Gene Transfer, Horizontal ; Genomics ; Phylogeny ; RNA, Ribosomal ; }, abstract = {In a series of conceptual articles published around the millennium, Carl Woese emphasized that evolution of cells is the central problem of evolutionary biology, that the three-domain ribosomal tree of life is an essential framework for reconstructing cellular evolution, and that the evolutionary dynamics of functionally distinct cellular systems are fundamentally different, with the information processing systems "crystallizing" earlier than operational systems. The advances of evolutionary genomics over the last decade vindicate major aspects of Woese's vision. Despite the observations of pervasive horizontal gene transfer among bacteria and archaea, the ribosomal tree of life comes across as a central statistical trend in the "forest" of phylogenetic trees of individual genes, and hence, an appropriate scaffold for evolutionary reconstruction. The evolutionary stability of information processing systems, primarily translation, becomes ever more striking with the accumulation of comparative genomic data indicating that nearly all of the few universal genes encode translation system components. Woese's view on the fundamental distinctions between the three domains of cellular life also withstand the test of comparative genomics, although his non-acceptance of symbiogenetic scenarios for the origin of eukaryotes might not. Above all, Woese's key prediction that understanding evolution of microbes will be the core of the new evolutionary biology appears to be materializing.}, }
@article {pmid24572460, year = {2014}, author = {Shapiro, JA}, title = {Constraint and opportunity in genome innovation.}, journal = {RNA biology}, volume = {11}, number = {3}, pages = {186-196}, pmid = {24572460}, issn = {1555-8584}, mesh = {DNA/*genetics ; DNA Transposable Elements ; Evolution, Molecular ; Gene Transfer, Horizontal ; Phylogeny ; Symbiosis ; }, abstract = {The development of rigorous molecular taxonomy pioneered by Carl Woese has freed evolution science to explore numerous cellular activities that lead to genome change in evolution. These activities include symbiogenesis, inter- and intracellular horizontal DNA transfer, incorporation of DNA from infectious agents, and natural genetic engineering, especially the activity of mobile elements. This article reviews documented examples of all these processes and proposes experiments to extend our understanding of cell-mediated genome change.}, }
@article {pmid24569295, year = {2014}, author = {Li, Y and Modis, Y}, title = {A novel membrane fusion protein family in Flaviviridae?.}, journal = {Trends in microbiology}, volume = {22}, number = {4}, pages = {176-182}, pmid = {24569295}, issn = {1878-4380}, support = {R01 GM102869/GM/NIGMS NIH HHS/United States ; }, mesh = {Hepacivirus/chemistry/*physiology ; Membrane Fusion ; Models, Molecular ; Pestivirus/chemistry/*physiology ; Protein Conformation ; Viral Fusion Proteins/chemistry/*metabolism ; *Virus Internalization ; }, abstract = {Enveloped viruses must fuse their lipid membrane to a cellular membrane to deliver their genome into the cytoplasm for replication. Viral envelope proteins catalyze this critical membrane fusion event. They fall into three distinct structural classes. In 2013, envelope proteins from a pestivirus and hepatitis C virus were found to have two distinct novel folds. This was unexpected because these viruses are in the same family as flaviviruses, which have class II fusion proteins. We propose that the membrane fusion machinery of the closely related pestiviruses and hepatitis C virus defines a new structural class. This and other recently identified structural relationships between viral fusion proteins shift the paradigm for how these proteins evolved.}, }
@article {pmid24569039, year = {2014}, author = {Mell, JC and Lee, JY and Firme, M and Sinha, S and Redfield, RJ}, title = {Extensive cotransformation of natural variation into chromosomes of naturally competent Haemophilus influenzae.}, journal = {G3 (Bethesda, Md.)}, volume = {4}, number = {4}, pages = {717-731}, pmid = {24569039}, issn = {2160-1836}, mesh = {Chromosomes, Bacterial/*genetics ; Cluster Analysis ; *Genetic Variation ; *Genome, Bacterial ; Genotype ; Haemophilus influenzae/*genetics ; High-Throughput Nucleotide Sequencing ; Polymorphism, Single Nucleotide ; Recombination, Genetic ; Sequence Analysis, DNA ; Transformation, Bacterial ; }, abstract = {Naturally competent bacterial species actively take up environmental DNA and can incorporate it into their chromosomes by homologous recombination. This can bring genetic variation from environmental DNA to recipient chromosomes, often in multiple long "donor" segments. Here, we report the results of genome sequencing 96 colonies of a laboratory Haemophilus influenzae strain, which had been experimentally transformed by DNA from a diverged clinical isolate. Donor segments averaged 6.9 kb (spanning several genes) and were clustered into recombination tracts of ~19.5 kb. Individual colonies had replaced from 0.1 to 3.2% of their chromosomes, and ~1/3 of all donor-specific single-nucleotide variants were present in at least one recombinant. We found that nucleotide divergence did not obviously limit the locations of recombination tracts, although there were small but significant reductions in divergence at recombination breakpoints. Although indels occasionally transformed as parts of longer recombination tracts, they were common at breakpoints, suggesting that indels typically block progression of strand exchange. Some colonies had recombination tracts in which variant positions contained mixtures of both donor and recipient alleles. These tracts were clustered around the origin of replication and were interpreted as the result of heteroduplex segregation in the original transformed cell. Finally, a pilot experiment demonstrated the utility of natural transformation for genetically dissecting natural phenotypic variation. We discuss our results in the context of the potential to merge experimental and population genetic approaches, giving a more holistic understanding of bacterial gene transfer.}, }
@article {pmid24567731, year = {2014}, author = {Carraro, N and Sauvé, M and Matteau, D and Lauzon, G and Rodrigue, S and Burrus, V}, title = {Development of pVCR94ΔX from Vibrio cholerae, a prototype for studying multidrug resistant IncA/C conjugative plasmids.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {44}, pmid = {24567731}, issn = {1664-302X}, abstract = {Antibiotic resistance has grown steadily in Vibrio cholerae over the last few decades to become a major threat in countries affected by cholera. Multi-drug resistance (MDR) spreads among clinical and environmental V. cholerae strains by lateral gene transfer often mediated by integrative and conjugative elements (ICEs) of the SXT/R391 family. However, in a few reported but seemingly isolated cases, MDR in V. cholerae was shown to be associated with other self-transmissible genetic elements such as conjugative plasmids. IncA/C conjugative plasmids are often found associated with MDR in isolates of Enterobacteriaceae. To date, IncA/C plasmids have not been commonly found in V. cholerae or other species of Vibrio. Here we present a detailed analysis of pVCR94ΔX derived from pVCR94, a novel IncA/C conjugative plasmid identified in a V. cholerae clinical strain isolated during the 1994 Rwandan cholera outbreak. pVCR94 was found to confer resistance to sulfamethoxazole, trimethoprim, ampicillin, streptomycin, tetracycline, and chloramphenicol and to transfer at very high frequency. Sequence analysis revealed its mosaic nature as well as high similarity of the core genes responsible for transfer and maintenance with other IncA/C plasmids and ICEs of the SXT/R391 family. Although IncA/C plasmids are considered a major threat in antibiotics resistance, their basic biology has received little attention, mostly because of the difficulty to genetically manipulate these MDR conferring elements. Therefore, we developed a convenient derivative from pVCR94, pVCR94Δ X, a 120.5-kb conjugative plasmid which only codes for sulfamethoxazole resistance. Using pVCR94Δ X, we identified the origin of transfer (oriT) and discovered an essential gene for transfer, both located within the shared backbone, allowing for an annotation update of all IncA/C plasmids. pVCR94Δ X may be a useful model that will provide new insights on the basic biology of IncA/C conjugative plasmids.}, }
@article {pmid24567305, year = {2014}, author = {Ruck, EC and Nakov, T and Jansen, RK and Theriot, EC and Alverson, AJ}, title = {Serial gene losses and foreign DNA underlie size and sequence variation in the plastid genomes of diatoms.}, journal = {Genome biology and evolution}, volume = {6}, number = {3}, pages = {644-654}, pmid = {24567305}, issn = {1759-6653}, mesh = {Chromosome Mapping ; DNA/genetics/*isolation &amp; purification ; DNA, Intergenic ; Diatoms/classification/*genetics ; Evolution, Molecular ; *Gene Deletion ; Gene Duplication ; Gene Order ; Gene Rearrangement ; *Genome, Plastid ; Open Reading Frames ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Photosynthesis by diatoms accounts for roughly one-fifth of global primary production, but despite this, relatively little is known about their plastid genomes. We report the completely sequenced plastid genomes for eight phylogenetically diverse diatoms and show them to be variable in size, gene and foreign sequence content, and gene order. The genomes contain a core set of 122 protein-coding genes, with 15 additional genes exhibiting complex patterns of 1) gene losses at varying phylogenetic scales, 2) functional transfers to the nucleus, 3) gene duplication, divergence, and differential retention of paralogs, and 4) acquisitions of putatively functional recombinase genes from resident plasmids. The newly sequenced genomes also contain several previously unreported genes, highlighting how poorly characterized diatom plastid genomes are overall. Genome size variation reflects major expansions of the inverted repeat region in some cases but, more commonly, large-scale expansions of intergenic regions, many of which contain unique open reading frames of likely foreign origin. Although many gene clusters are conserved across species, rearrangements appear to be frequent in most lineages.}, }
@article {pmid24564645, year = {2014}, author = {Faria, NA and Conceição, T and Miragaia, M and Bartels, MD and de Lencastre, H and Westh, H}, title = {Nasal carriage of methicillin resistant staphylococci.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {20}, number = {2}, pages = {108-117}, doi = {10.1089/mdr.2013.0197}, pmid = {24564645}, issn = {1931-8448}, mesh = {Adult ; Bacterial Typing Techniques ; Carrier State/*epidemiology/microbiology ; *Chromosomes, Bacterial ; DNA, Intergenic/genetics ; Denmark/epidemiology ; Gene Transfer, Horizontal ; Humans ; Infant ; Infant, Newborn ; Methicillin-Resistant Staphylococcus aureus/*genetics/isolation &amp; purification ; Middle Aged ; Nose/microbiology ; RNA, Ribosomal, 16S/*genetics ; Staphylococcal Infections/*epidemiology/microbiology ; Staphylococcus epidermidis/genetics/isolation &amp; purification ; Staphylococcus haemolyticus/genetics/isolation &amp; purification ; Staphylococcus hominis/genetics/isolation &amp; purification ; }, abstract = {Coagulase-negative staphylococci (CoNS) are believed to function as reservoirs, as well as possible sources of staphylococcal chromosome cassette mec (SCCmec) to Staphylococcus aureus, but the frequency, preferred partners, and factors promoting SCCmec transfer are not known. Such postulated in vivo genetic transfer events are likely to occur at anatomical sites such as the normal nasal mucosa, which is known to be colonized by both CoNS and coagulase positive staphylococci. In this study, we characterized S. aureus and CoNS strains colonizing the anterior nares of 67 patients in Denmark. A total of 54 patients (80%) were colonized with staphylococci that included nine different species identified by internal transcribed spacer PCR (ITS-PCR) and 16S RNA sequencing. The highest rates of colonization were found for S. epidermidis (58%) and S. aureus (39%). Methicillin resistance was present in S. aureus (53%), S. epidermidis (53%), S. haemolyticus (33%), and S. hominis (62%). Genetic backgrounds were characterized by spa typing for S. aureus and by pulsed-field gel electrophoresis for CoNS. SCCmec typing showed that SCCmec type IV (2B) was the most common in the entire collection (65%). Carriage of multiple species was detected in 20 patients (30%), 16 of whom were colonized with both S. aureus and S. epidermidis. In two cases, simultaneous carriage of different methicillin resistant species was detected. However, the strains carried different SCCmec types. Additional studies in the same epidemiological settings are warranted to identify interspecific genetic events that involve the acquisition of SCCmec by S. aureus.}, }
@article {pmid24564205, year = {2013}, author = {Patterson, M and Szöllősi, G and Daubin, V and Tannier, E}, title = {Lateral gene transfer, rearrangement, reconciliation.}, journal = {BMC bioinformatics}, volume = {14 Suppl 15}, number = {Suppl 15}, pages = {S4}, pmid = {24564205}, issn = {1471-2105}, mesh = {Algorithms ; Cyanobacteria/genetics ; *Evolution, Molecular ; Gene Duplication ; *Gene Transfer, Horizontal ; *Genome ; Software ; }, abstract = {BACKGROUND: Models of ancestral gene order reconstruction have progressively integrated different evolutionary patterns and processes such as unequal gene content, gene duplications, and implicitly sequence evolution via reconciled gene trees. These models have so far ignored lateral gene transfer, even though in unicellular organisms it can have an important confounding effect, and can be a rich source of information on the function of genes through the detection of transfers of clusters of genes.<br><br>RESULT: We report an algorithm together with its implementation, DeCoLT, that reconstructs ancestral genome organization based on reconciled gene trees which summarize information on sequence evolution, gene origination, duplication, loss, and lateral transfer. DeCoLT optimizes in polynomial time on the number of rearrangements, computed as the number of gains and breakages of adjacencies between pairs of genes. We apply DeCoLT to 1099 gene families from 36 cyanobacteria genomes.<br><br>CONCLUSION: DeCoLT is able to reconstruct adjacencies in 35 ancestral bacterial genomes with a thousand gene families in a few hours, and detects clusters of co-transferred genes. DeCoLT may also be used with any relationship between genes instead of adjacencies, to reconstruct ancestral interactions, functions or complexes.<br><br>AVAILABILITY: http://pbil.univ-lyon1.fr/software/DeCoLT/}, }
@article {pmid24563701, year = {2013}, author = {Armijos Jaramillo, VD and Vargas, WA and Sukno, SA and Thon, MR}, title = {New insights into the evolution and structure of Colletotrichum plant-like subtilisins (CPLSs).}, journal = {Communicative &amp; integrative biology}, volume = {6}, number = {6}, pages = {e25727}, pmid = {24563701}, issn = {1942-0889}, abstract = {The Colletotrichum plant-like subtilisins (CPLSs) are a family of proteins found only in species of the phytopathogenic fungus Colletotrichum. CPLSs have high similarity to plant subtilisins and our previous work has shown that they were acquired by an ancient horizontal gene transfer event from plants. The rapid growth of sequence data in public databases enabled us to reexamine the structure and evolution of the CPLSs. A new plant subtilisin structural model aided us in refining the tertiary structure of CPLSs. Also, new information about protein interactions of plant subtilisin has provided new insights into the putative function of CPLSs. The availability of new genome sequences of members of the genus Colletotrichum gave us the opportunity to further validate our hypothesis that the CPLSs are unique to the Colletotrichum lineage. Together, this information furthers our knowledge of the potential role of the CPLSs in pathogenicity and the role of HGT in the genome evolution of plant pathogenic fungi.}, }
@article {pmid24562812, year = {2014}, author = {Sjöstrand, J and Tofigh, A and Daubin, V and Arvestad, L and Sennblad, B and Lagergren, J}, title = {A Bayesian method for analyzing lateral gene transfer.}, journal = {Systematic biology}, volume = {63}, number = {3}, pages = {409-420}, doi = {10.1093/sysbio/syu007}, pmid = {24562812}, issn = {1076-836X}, mesh = {Bayes Theorem ; Classification/*methods ; Cyanobacteria/classification/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Models, Theoretical ; Phylogeny ; Tenericutes/classification/genetics ; }, abstract = {Lateral gene transfer (LGT)--which transfers DNA between two non-vertically related individuals belonging to the same or different species--is recognized as a major force in prokaryotic evolution, and evidence of its impact on eukaryotic evolution is ever increasing. LGT has attracted much public attention for its potential to transfer pathogenic elements and antibiotic resistance in bacteria, and to transfer pesticide resistance from genetically modified crops to other plants. In a wider perspective, there is a growing body of studies highlighting the role of LGT in enabling organisms to occupy new niches or adapt to environmental changes. The challenge LGT poses to the standard tree-based conception of evolution is also being debated. Studies of LGT have, however, been severely limited by a lack of computational tools. The best currently available LGT algorithms are parsimony-based phylogenetic methods, which require a pre-computed gene tree and cannot choose between sometimes wildly differing most parsimonious solutions. Moreover, in many studies, simple heuristics are applied that can only handle putative orthologs and completely disregard gene duplications (GDs). Consequently, proposed LGT among specific gene families, and the rate of LGT in general, remain debated. We present a Bayesian Markov-chain Monte Carlo-based method that integrates GD, gene loss, LGT, and sequence evolution, and apply the method in a genome-wide analysis of two groups of bacteria: Mollicutes and Cyanobacteria. Our analyses show that although the LGT rate between distant species is high, the net combined rate of duplication and close-species LGT is on average higher. We also show that the common practice of disregarding reconcilability in gene tree inference overestimates the number of LGT and duplication events.}, }
@article {pmid24562614, year = {2014}, author = {Witherden, EA and Bajanca-Lavado, MP and Tristram, SG and Nunes, A}, title = {Role of inter-species recombination of the ftsI gene in the dissemination of altered penicillin-binding-protein-3-mediated resistance in Haemophilus influenzae and Haemophilus haemolyticus.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {69}, number = {6}, pages = {1501-1509}, doi = {10.1093/jac/dku022}, pmid = {24562614}, issn = {1460-2091}, mesh = {Haemophilus/*drug effects/*genetics ; Haemophilus Infections/microbiology ; Haemophilus influenzae/*drug effects/*genetics ; Humans ; Penicillin Resistance/*genetics ; Penicillin-Binding Proteins/*genetics ; *Recombination, Genetic ; }, abstract = {OBJECTIVES: To screen the ftsI gene sequences obtained from clinical isolates of non-typeable Haemophilus influenzae (NTHi) and Haemophilus haemolyticus for the presence of mosaic ftsI gene structures, and to evaluate the role of inter-species recombination of the ftsI gene in the formation and distribution of resistant ftsI genes.<br><br>METHODS: The ftsI genes of 100 Haemophilus isolates comprising genetically defined &#x3b2;-lactamase-negative ampicillin-susceptible (gBLNAS), &#x3b2;-lactamase-positive ampicillin-resistant (gBLPAR), &#x3b2;-lactamase-negative ampicillin-resistant (gBLNAR) and &#x3b2;-lactamase-positive amoxicillin/clavulanate-resistant (gBLPACR) isolates of NTHi (n&#x200a;=&#x200a;50) and H. haemolyticus (n&#x200a;=&#x200a;50) were analysed in this study. Both the flanking regions and the full-length ftsI gene sequences of all study isolates were screened for mosaic structures using H. influenzae Rd and H. haemolyticus ATCC 33390 as reference parental sequences, and bioinformatics methods were used for recombination analysis using SimPlot.<br><br>RESULTS: Of the 100 clinical isolates analysed 34% (34/100) harboured mosaic ftsI gene structures containing distinct ftsI gene fragments similar to both reference parental sequences. The inter-species recombination events were exclusively encountered in the ftsI gene of gBLNAR/gBLPACR isolates of both NTHi and H. haemolyticus, and were always associated with the formation of a mosaic fragment at the 3' end of the ftsI gene. There was no evidence supporting horizontal gene transfer (HGT) involving the entire ftsI gene among the clinical isolates in vivo.<br><br>CONCLUSIONS: We provide evidence for the HGT and inter-species recombination of the ftsI gene among gBLNAR/gBLPACR isolates of NTHi and H. haemolyticus in a clinical setting, highlighting the importance of recombination of the ftsI gene in the emergence of altered penicillin-binding protein 3 and BLNAR-mediated resistance.}, }
@article {pmid24559997, year = {2014}, author = {Freese, PD and Korolev, KS and Jiménez, JI and Chen, IA}, title = {Genetic drift suppresses bacterial conjugation in spatially structured populations.}, journal = {Biophysical journal}, volume = {106}, number = {4}, pages = {944-954}, pmid = {24559997}, issn = {1542-0086}, support = {P50 GM068763/GM/NIGMS NIH HHS/United States ; GM068763/GM/NIGMS NIH HHS/United States ; }, mesh = {*Conjugation, Genetic ; Escherichia coli/*genetics/physiology ; F Factor/genetics ; *Genetic Drift ; *Models, Genetic ; }, abstract = {Conjugation is the primary mechanism of horizontal gene transfer that spreads antibiotic resistance among bacteria. Although conjugation normally occurs in surface-associated growth (e.g., biofilms), it has been traditionally studied in well-mixed liquid cultures lacking spatial structure, which is known to affect many evolutionary and ecological processes. Here we visualize spatial patterns of gene transfer mediated by F plasmid conjugation in a colony of Escherichia coli growing on solid agar, and we develop a quantitative understanding by spatial extension of traditional mass-action models. We found that spatial structure suppresses conjugation in surface-associated growth because strong genetic drift leads to spatial isolation of donor and recipient cells, restricting conjugation to rare boundaries between donor and recipient strains. These results suggest that ecological strategies, such as enforcement of spatial structure and enhancement of genetic drift, could complement molecular strategies in slowing the spread of antibiotic resistance genes.}, }
@article {pmid24558639, year = {2014}, author = {Metzger, LC and Blokesch, M}, title = {Composition of the DNA-uptake complex of Vibrio cholerae.}, journal = {Mobile genetic elements}, volume = {4}, number = {1}, pages = {e28142}, pmid = {24558639}, issn = {2159-2543}, support = {309064/ERC_/European Research Council/International ; }, abstract = {Natural competence for transformation is a developmental program that allows certain bacteria to take up free extracellular DNA from the environment and integrate this DNA into their genome. Thereby, natural transformation acts as mode of horizontal gene transfer and impacts bacterial evolution. The number of genes induced upon competence induction varies significantly between organisms. However, all of the naturally competent bacteria possess competence genes that encode so-called DNA-uptake machineries. Some components of these multi-protein complexes resemble subunits of type IV pili and type II secretion systems. However, knowledge on the mechanistic aspects of such DNA-uptake complexes is still very limited. Here, we discuss some new findings regarding the DNA-uptake machinery of the naturally transformable human pathogen Vibrio cholerae. The potential of this organism to initiate the competence program was discovered less than a decade ago. However, recent studies have provided new insight into both the regulatory pathways of competence induction and into the DNA uptake dynamics.}, }
@article {pmid24556716, year = {2014}, author = {Iwanaga, S and Isawa, H and Yuda, M}, title = {Horizontal gene transfer of a vertebrate vasodilatory hormone into ticks.}, journal = {Nature communications}, volume = {5}, number = {}, pages = {3373}, doi = {10.1038/ncomms4373}, pmid = {24556716}, issn = {2041-1723}, mesh = {Adrenomedullin/genetics ; Animals ; Gene Transfer, Horizontal/*genetics ; Insect Hormones/*genetics ; Ornithodoros/*genetics ; Vertebrates/*genetics ; }, abstract = {The horizontal gene transfer (HGT) of functional molecules is found in higher eukaryotes, but its influence on their evolution has not been fully evaluated. Here we describe the HGT of a vertebrate vasodilator, adrenomedullin (ADM), into ticks of the genus Ornithodoros and hypothesize its involvement in tick evolution. The salivary glands of Ornithodoros ticks contain ADM-like vasodilators, tick-adrenomedullin (TAM). ADM-like molecules, including TAM, are conserved in all vertebrates and Ornithodoros ticks but not in any other invertebrates, including Argas ticks, which share a common ancestor with Ornithodoros ticks. In addition, the close evolutionarily relationship between TAM and ADM is supported through genomic sequence and phylogenetic relatedness analyses. Ornithodoros ticks horizontally acquired vertebrate ADM and currently employ it to facilitate blood feeding. The acquisition of TAM might result in a beneficial change in feeding behaviour and influence the divergence of Ornithodoros ticks.}, }
@article {pmid24556639, year = {2014}, author = {Gilbert, C and Chateigner, A and Ernenwein, L and Barbe, V and Bézier, A and Herniou, EA and Cordaux, R}, title = {Population genomics supports baculoviruses as vectors of horizontal transfer of insect transposons.}, journal = {Nature communications}, volume = {5}, number = {}, pages = {3348}, pmid = {24556639}, issn = {2041-1723}, mesh = {Animals ; Baculoviridae/*genetics ; DNA Transposable Elements/*genetics ; Gene Transfer, Horizontal/*genetics ; Genetic Vectors/*genetics ; Insecta/*genetics ; Metagenomics/*methods ; Nucleopolyhedroviruses/genetics ; }, abstract = {Horizontal transfer (HT) of DNA is an important factor shaping eukaryote evolution. Although several hundreds of eukaryote-to-eukaryote HTs of transposable elements (TEs) have been reported, the vectors underlying these transfers remain elusive. Here, we show that multiple copies of two TEs from the cabbage looper (Trichoplusia ni) transposed in vivo into genomes of the baculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV) during caterpillar infection. We further demonstrate that both TEs underwent recent HT between several sympatric moth species (T. ni, Manduca sexta, Helicoverpa spp.) showing different degrees of susceptibility to AcMNPV. Based on two independent population genomics data sets (reaching a total coverage >330,000X), we report a frequency of one moth TE in ~8,500 AcMNPV genomes. Together, our results provide strong support for the role of viruses as vectors of TE HT between animals, and they call for a systematic evaluation of the frequency and impact of virus-mediated HT on the evolution of host genomes.}, }
@article {pmid24555518, year = {2014}, author = {Yang, J and Grünewald, S and Xu, Y and Wan, XF}, title = {Quartet-based methods to reconstruct phylogenetic networks.}, journal = {BMC systems biology}, volume = {8}, number = {}, pages = {21}, pmid = {24555518}, issn = {1752-0509}, support = {RC1 AI086830/AI/NIAID NIH HHS/United States ; RC1AI086830/AI/NIAID NIH HHS/United States ; }, mesh = {Computational Biology/*methods ; Evolution, Molecular ; *Phylogeny ; }, abstract = {BACKGROUND: Phylogenetic networks are employed to visualize evolutionary relationships among a group of nucleotide sequences, genes or species when reticulate events like hybridization, recombination, reassortant and horizontal gene transfer are believed to be involved. In comparison to traditional distance-based methods, quartet-based methods consider more information in the reconstruction process and thus have the potential to be more accurate.<br><br>RESULTS: We introduce QuartetSuite, which includes a set of new quartet-based methods, namely QuartetS, QuartetA, and QuartetM, to reconstruct phylogenetic networks from nucleotide sequences. We tested their performances and compared them with other popular methods on two simulated nucleotide sequence data sets: one generated from a tree topology and the other from a complicated evolutionary history containing three reticulate events. We further validated these methods to two real data sets: a bacterial data set consisting of seven concatenated genes of 36 bacterial species and an influenza data set related to recently emerging H7N9 low pathogenic avian influenza viruses in China.<br><br>CONCLUSION: QuartetS, QuartetA, and QuartetM have the potential to accurately reconstruct evolutionary scenarios from simple branching trees to complicated networks containing many reticulate events. These methods could provide insights into the understanding of complicated biological evolutionary processes such as bacterial taxonomy and reassortant of influenza viruses.}, }
@article {pmid24553412, year = {2014}, author = {Wendlandt, S and Kadlec, K and Feßler, AT and van Duijkeren, E and Schwarz, S}, title = {Two different erm(C)-carrying plasmids in the same methicillin-resistant Staphylococcus aureus CC398 isolate from a broiler farm.}, journal = {Veterinary microbiology}, volume = {171}, number = {3-4}, pages = {382-387}, doi = {10.1016/j.vetmic.2014.01.009}, pmid = {24553412}, issn = {1873-2542}, mesh = {Animals ; Base Sequence ; Chickens/microbiology ; DNA Primers/genetics ; Gene Deletion ; Lincosamides/genetics ; Methicillin-Resistant Staphylococcus aureus/*genetics ; Methyltransferases/*genetics/metabolism ; Molecular Sequence Data ; Plasmids/*genetics ; Poultry Diseases/*microbiology ; Sequence Analysis, DNA ; Staphylococcal Infections/*veterinary ; }, abstract = {During a study on plasmid-borne antimicrobial resistance among methicillin-resistant Staphylococcus aureus (MRSA) isolates from broiler farms, an MRSA isolate was identified which carried multiple plasmids. This MRSA isolate belonged to CC398 and exhibited spa type t3015 and dru type dt11a. Plasmid profiling revealed the presence of one large and two small plasmids. The resistance genes tet(L) (tetracycline resistance), dfrK (trimethoprim resistance) and aadD (kanamycin/neomycin resistance) were located on the large plasmid. Both small plasmids, designated pSWS371 and pSWS372, carried only an erm(C) gene for macrolide/lincosamide resistance. Sequence analysis revealed that the 2458-bp plasmid pSWS371 carried only a repL gene for plasmid replication in addition to the erm(C) gene. In contrast, the 3882-bp plasmid pSWS372 harbored - in addition to the erm(C) gene - three more genes: a repF gene for plasmid replication, a cop-6 gene for a small protein potentially involved in copy number control of the plasmid and a novel pre/mob gene for a protein involved in plasmid recombination and mobilization. The erm(C) genes of both small plasmids exhibited constitutive erm(C) gene expression and analysis of the respective translational attenuators identified deletions of 16 bp and 74 bp which explain the constitutive expression. The simultaneous presence of two small plasmids that carry the same resistance gene in the same MRSA isolate is a rare observation. The fact that both plasmids belong to different incompatibility groups as specified by the different rep genes, repL and repF, explains why they can stably coexist in the same bacterial cell.}, }
@article {pmid24552593, year = {2014}, author = {Marti, E and Variatza, E and Balcázar, JL}, title = {Bacteriophages as a reservoir of extended-spectrum β-lactamase and fluoroquinolone resistance genes in the environment.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {20}, number = {7}, pages = {O456-9}, doi = {10.1111/1469-0691.12446}, pmid = {24552593}, issn = {1469-0691}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteriophages/*genetics/*isolation &amp; purification ; DNA, Bacterial/genetics/isolation &amp; purification ; DNA, Viral/genetics/isolation &amp; purification ; *Drug Resistance, Bacterial ; Fluoroquinolones/pharmacology ; *Genes, Bacterial ; Humans ; *Water Microbiology ; beta-Lactamases/*genetics ; beta-Lactams/pharmacology ; }, abstract = {Six antibiotic resistance genes (blaCTX-M , blaSHV , blaTEM , qnrA, qnrB and qnrS) were quantified by qPCR in both phage and bacterial DNA fractions of environmental water samples in order to determine the contribution of phages to the dissemination of antibiotic resistance genes (ARGs) in the environment. Although the highest copy numbers (p <0.05) of ARGs were detected in the bacterial DNA fraction, qnrS and blaSHV genes were found in the phage DNA from all samples analysed, reaching up to 4 log10 copy numbers/mL in hospital samples. These results indicate that bacteriophages are a potential reservoir of resistance genes and may act as efficient vehicles for horizontal gene transfer.}, }
@article {pmid24551624, year = {2013}, author = {Basu, S and Mukherjee, SK and Hazra, A and Mukherjee, M}, title = {Molecular Characterization of Uropathogenic Escherichia coli: Nalidixic Acid and Ciprofloxacin Resistance, Virulent Factors and Phylogenetic Background.}, journal = {Journal of clinical and diagnostic research : JCDR}, volume = {7}, number = {12}, pages = {2727-2731}, pmid = {24551624}, issn = {2249-782X}, abstract = {BACKGROUND AND OBJECTIVE: A proficient pathogen should be virulent, resistant to antibiotics, and epidemic. However, the interplay between resistance and virulence is poorly understood. Perhaps, the most commonly accepted view is that resistance to quinolones is linked to a loss of virulence factors. However, the low virulent phylogenetic groups may be more prone to acquire resistance to quinolones. The aim of this study was to identify and characterise the Nalidixic Acid (NA) and ciprofloxacin (CIP) resistant uropathogenic Escherichia coli (UPEC) isolates with respect to virulence and phylogenetic background, from hospital settings in Kolkata, an eastern region in India. Research based on these bacterial populations will help in understanding the molecular mechanisms underlying the association between resistance and virulence, that in turn, may help in managing the future disseminations of UTIs in their entirety.<br><br>MATERIAL AND METHODS: One hundred and ten E. coli isolates were screened against NA and CIP using Kirby-Bauer disk diffusion technique, following CLSI guidelines. Prevalence of virulent factor genes and distribution of phylogenetic groups amongst the isolates was determined by PCR, using gene specific primers against the different virulent factors and DNA markers (chuA, yjaA and DNA fragment, TSPE4.C2) respectively. Statistical analysis of the data was performed using SPSS software.<br><br>RESULTS: Resistance to both NA and CIP was reported in 75.5 % of the isolates which were analysed. The virulent determinants, papC, pap GII, papEF, afa, cnf1, hlyA and iroN were significantly predominant in the drug susceptible than the resistant isolates. A significant reduction of phylogroup B2 in NA (85.7% versus 64.6%, &#x3c7;(2)P<0.001) and CIP (85.2 % versus 61.4%, &#x3c7;(2)P<0.001) resistant UPEC isolates, followed by increase in predominance of non-B2 phylotypes (group D and group B1), were observed.<br><br>CONCLUSION: This is the first report from India that has indicated possible evidence on horizontal gene transfer from pathogenic to commensal strains and selection of the latter, on extensive usage of this group of antimicrobials in hospital settings, where these drugs were routinely prescribed for treating urinary tract infection. Therefore, this information necessitates surveillance programs and administration of effective strategies, to put an end to random prescription policies involving this group of antimicrobials.}, }
@article {pmid24549803, year = {2014}, author = {Jiang, Q and Zhou, C and Wang, Y and Si, F and Zhou, Y and Chen, B and Zhao, Y and Chen, J and Xiao, M}, title = {Pseudomonas stutzeri strain possessing a self-transmissible TOL-like plasmid degrades phenol and promotes maize growth in contaminated environments.}, journal = {Applied biochemistry and biotechnology}, volume = {172}, number = {7}, pages = {3461-3475}, doi = {10.1007/s12010-014-0785-6}, pmid = {24549803}, issn = {1559-0291}, mesh = {Biodegradation, Environmental ; *Gene Transfer, Horizontal ; Phenol/*metabolism ; Plasmids/*genetics/metabolism ; Pseudomonas stutzeri/*genetics/*metabolism ; Soil Microbiology ; Soil Pollutants/*metabolism ; Zea mays/growth &amp; development/*microbiology ; }, abstract = {Phenol is volatile organic pollutant that plants can little degrade. For complete degradation of volatile pollutants, we introduced Pseudomonas stutzeri strain P7 to phenol-contaminated soils. The strain effectively degraded phenol and even promoted plant growth. A TOL-like plasmid was detected in the strain and found to be responsible for phenol degradation and self-transmissible. In addition, phenol degradation by strain P7 was more rapid in the contaminated soils with than without plants over the full course of the experiment; especially by 5 days, the phenol concentration was reduced by about 30 % in soil without plants and reduced by about 50-65 % in soil with plants. This situation also occurred when inoculated with different transconjugants. Furthermore, transfer frequencies of TOL-like plasmid were significantly higher in soil with than without plants. Populations of rifampin-resistant P7 strain remained relatively constant for 20 days, while the number of rhizosphere bacteria that contained the degradative plasmids gradually increased at the later stages, suggesting that plants might stimulate plasmid transfer from strain P7 to indigenous bacteria, one possible reason for plant enhancing microbial degradation. This is attractive for implementation of combinations of phytoremediation and bioaugmentation in degradation of volatile pollutants that plants can little degrade.}, }
@article {pmid24536043, year = {2014}, author = {Knöppel, A and Lind, PA and Lustig, U and Näsvall, J and Andersson, DI}, title = {Minor fitness costs in an experimental model of horizontal gene transfer in bacteria.}, journal = {Molecular biology and evolution}, volume = {31}, number = {5}, pages = {1220-1227}, doi = {10.1093/molbev/msu076}, pmid = {24536043}, issn = {1537-1719}, mesh = {Bacteria/*genetics/metabolism ; DNA, Bacterial/genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Fitness ; Humans ; *Models, Genetic ; Mutagenesis, Insertional ; Salmonella typhimurium/genetics/metabolism ; Selection, Genetic ; }, abstract = {Genes introduced by horizontal gene transfer (HGT) from other species constitute a significant portion of many bacterial genomes, and the evolutionary dynamics of HGTs are important for understanding the spread of antibiotic resistance and the emergence of new pathogenic strains of bacteria. The fitness effects of the transferred genes largely determine the fixation rates and the amount of neutral diversity of newly acquired genes in bacterial populations. Comparative analysis of bacterial genomes provides insight into what genes are commonly transferred, but direct experimental tests of the fitness constraints on HGT are scarce. Here, we address this paucity of experimental studies by introducing 98 random DNA fragments varying in size from 0.45 to 5 kb from Bacteroides, Proteus, and human intestinal phage into a defined position in the Salmonella chromosome and measuring the effects on fitness. Using highly sensitive competition assays, we found that eight inserts were deleterious with selection coefficients (s) ranging from ≈ -0.007 to -0.02 and 90 did not have significant fitness effects. When inducing transcription from a PBAD promoter located at one end of the insert, 16 transfers were deleterious and 82 were not significantly different from the control. In conclusion, a major fraction of the inserts had minor effects on fitness implying that extra DNA transferred by HGT, even though it does not confer an immediate selective advantage, could be maintained at selection-transfer balance and serve as raw material for the evolution of novel beneficial functions.}, }
@article {pmid24532767, year = {2014}, author = {DeWitt, T and Grossman, AD}, title = {The bifunctional cell wall hydrolase CwlT is needed for conjugation of the integrative and conjugative element ICEBs1 in Bacillus subtilis and B. anthracis.}, journal = {Journal of bacteriology}, volume = {196}, number = {8}, pages = {1588-1596}, pmid = {24532767}, issn = {1098-5530}, support = {R01 GM050895/GM/NIGMS NIH HHS/United States ; R01GM050895/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacillus anthracis/*enzymology/*genetics ; Bacillus subtilis/*enzymology/*genetics ; Bacterial Proteins/genetics/*metabolism ; Cell Wall ; *Conjugation, Genetic ; Gene Transfer, Horizontal ; Hydrolases/genetics/*metabolism ; Protein Sorting Signals ; Protein Structure, Tertiary ; }, abstract = {The mobile genetic element ICEBs1 is an integrative and conjugative element (ICE) found in Bacillus subtilis. One of the ICEBs1 genes, cwlT, encodes a cell wall hydrolase with two catalytic domains, a muramidase and a peptidase. We found that cwlT is required for ICEBs1 conjugation. We examined the role of each of the two catalytic domains and found that the muramidase is essential, whereas the peptidase is partially dispensable for transfer of ICEBs1. We also found that the putative signal peptide in CwlT is required for CwlT to function in conjugation, consistent with the notion that CwlT is normally secreted from the cytoplasm. We found that alteration of the putative lipid attachment site on CwlT had no effect on its role in conjugation, indicating that if CwlT is a lipoprotein, the lipid attachment is not required for conjugation. Finally, we found conditions supporting efficient transfer of ICEBs1 into and out of Bacillus anthracis and that cwlT was needed for ICEBs1 to function in B. anthracis. The mature cell wall of B. anthracis is resistant to digestion by CwlT, indicating that CwlT might act during cell wall synthesis, before modifications of the peptidoglycan are complete.}, }
@article {pmid24526637, year = {2014}, author = {Ding, H and Moksa, MM and Hirst, M and Beatty, JT}, title = {Draft Genome Sequences of Six Rhodobacter capsulatus Strains, YW1, YW2, B6, Y262, R121, and DE442.}, journal = {Genome announcements}, volume = {2}, number = {1}, pages = {}, pmid = {24526637}, issn = {2169-8287}, abstract = {Rhodobacter capsulatus is a model organism for studying a novel type of horizontal gene transfer mediated by a phage-like gene transfer agent (RcGTA). Here we report the draft genome sequences of six R. capsulatus strains that exhibit different RcGTA properties, including RcGTA overproducers, RcGTA nonproducers, and/or RcGTA nonreceivers.}, }
@article {pmid24525238, year = {2014}, author = {Schuurmans, JM and van Hijum, SA and Piet, JR and Händel, N and Smelt, J and Brul, S and ter Kuile, BH}, title = {Effect of growth rate and selection pressure on rates of transfer of an antibiotic resistance plasmid between E. coli strains.}, journal = {Plasmid}, volume = {72}, number = {}, pages = {1-8}, doi = {10.1016/j.plasmid.2014.01.002}, pmid = {24525238}, issn = {1095-9890}, mesh = {Anti-Bacterial Agents/pharmacology ; DNA Mutational Analysis ; Drug Resistance, Bacterial/genetics ; Escherichia coli/drug effects/*genetics/growth &amp; development ; *Gene Transfer, Horizontal ; INDEL Mutation ; Microbial Sensitivity Tests ; Polymorphism, Single Nucleotide ; R Factors/*genetics ; Selection, Genetic ; Tetracycline/pharmacology ; }, abstract = {Antibiotic resistance increases costs for health care and causes therapy failure. An important mechanism for spreading resistance is transfer of plasmids containing resistance genes and subsequent selection. Yet the factors that influence the rate of transfer are poorly known. Rates of plasmid transfer were measured in co-cultures in chemostats of a donor and a acceptor strain under various selective pressures. To document whether specific mutations in either plasmid or acceptor genome are associated with the plasmid transfer, whole genome sequencing was performed. The DM0133 TetR tetracycline resistance plasmid was transferred between Escherichia coli K-12 strains during co-culture at frequencies that seemed higher at increased growth rate. Modeling of the take-over of the culture by the transformed strain suggests that in reality more transfer events occurred at low growth rates. At moderate selection pressure due to an antibiotic concentration that still allowed growth, a maximum transfer frequency was determined of once per 10(11) cell divisions. In the absence of tetracycline or in the presence of high concentrations the frequency of transfer was sometimes zero, but otherwise reduced by at least a factor of 5. Whole genome sequencing showed that the plasmid was transferred without mutations, but two functional mutations in the genome of the recipient strain accompanied this transfer. Exposure to concentrations of antibiotics that fall within the mutant selection window stimulated transfer of the resistance plasmid most.}, }
@article {pmid24524824, year = {2014}, author = {Skarp-de Haan, CP and Culebro, A and Schott, T and Revez, J and Schweda, EK and Hänninen, ML and Rossi, M}, title = {Comparative genomics of unintrogressed Campylobacter coli clades 2 and 3.}, journal = {BMC genomics}, volume = {15}, number = {}, pages = {129}, pmid = {24524824}, issn = {1471-2164}, mesh = {Bacterial Proteins/classification/genetics/metabolism ; Bayes Theorem ; Campylobacter coli/*classification/*genetics ; Campylobacter jejuni/classification/genetics ; *Genome, Bacterial ; *Phylogeny ; Sialyltransferases/classification/genetics/metabolism ; gamma-Glutamyltransferase/classification/genetics/metabolism ; }, abstract = {BACKGROUND: Campylobacter jejuni and C. coli share a multitude of risk factors associated with human gastrointestinal disease, yet their phylogeny differs significantly. C. jejuni is scattered into several lineages, with no apparent linkage, whereas C. coli clusters into three distinct phylogenetic groups (clades) of which clade 1 has shown extensive genome-wide introgression with C. jejuni, yet the other two clades (2 and 3) have less than 2% of C. jejuni ancestry. We characterized a C. coli strain (76339) with four novel multilocus sequence type alleles (ST-5088) and having the capability to express gamma-glutamyltranspeptidase (GGT); an accessory feature in C. jejuni. Our aim was to further characterize unintrogressed C. coli clades 2 and 3, using comparative genomics and with additional genome sequences available, to investigate the impact of horizontal gene transfer in shaping the accessory and core gene pools in unintrogressed C. coli.<br><br>RESULTS: Here, we present the first fully closed C. coli clade 3 genome (76339). The phylogenomic analysis of strain 76339, revealed that it belonged to clade 3 of unintrogressed C. coli. A more extensive respiratory metabolism among unintrogressed C. coli strains was found compared to introgressed C. coli (clade 1). We also identified other genes, such as serine proteases and an active sialyltransferase in the lipooligosaccharide locus, not present in C. coli clade 1 and we further propose a unique scenario for the evolution of Campylobacter ggt.<br><br>CONCLUSIONS: We propose new insights into the evolution of the accessory genome of C. coli clade 3 and C. jejuni. Also, in silico analysis of the gene content revealed that C. coli clades 2 and 3 have genes associated with infection, suggesting they are a potent human pathogen, and may currently be underreported in human infections due to niche separation.}, }
@article {pmid24521860, year = {2014}, author = {Enoki, S and Shimizu, A and Hayashi, C and Imanishi, H and Hashizume, O and Mekada, K and Suzuki, H and Hashimoto, T and Nakada, K and Hayashi, J}, title = {Selection of rodent species appropriate for mtDNA transfer to generate transmitochondrial mito-mice expressing mitochondrial respiration defects.}, journal = {Experimental animals}, volume = {63}, number = {1}, pages = {21-30}, pmid = {24521860}, issn = {1881-7122}, mesh = {Animals ; Cells, Cultured ; DNA, Mitochondrial/*genetics/metabolism ; Embryonic Stem Cells ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Mice/*genetics ; Mice, Inbred BALB C ; Mice, Nude ; Mitochondrial Diseases/*genetics ; *Mutation ; Oxygen Consumption ; Phylogeny ; Rats/*genetics ; }, abstract = {Previous reports have shown that transmitochondrial mito-mice with nuclear DNA from Mus musculus and mtDNA from M. spretus do not express respiration defects, whereas those with mtDNA from Rattus norvegicus cannot be generated from ES cybrids with mtDNA from R. norvegicus due to inducing significant respiration defects and resultant losing multipotency. Here, we isolated transmitochondrial cybrids with mtDNA from various rodent species classified between M. spretus and R. norvegicus, and compared the O2 consumption rates. The results showed a strong negative correlation between phylogenetic distance and reduction of O2 consumption rates, which would be due to the coevolution of nuclear and mitochondrial genomes and the resultant incompatibility between the nuclear genome from M. musculus and the mitochondrial genome from the other rodent species. These observations suggested that M. caroli was an appropriate mtDNA donor to generate transmitochondrial mito-mice with nuclear DNA from M. musculus. Then, we generated ES cybrids with M. caroli mtDNA, and found that these ES cybrids expressed respiration defects without losing multipotency and can be used to generate transmitochondrial mito-mice expressing mitochondrial disorders.}, }
@article {pmid24521160, year = {2014}, author = {Dasgupta, S and Basu, G}, title = {Evolutionary insights about bacterial GlxRS from whole genome analyses: is GluRS2 a chimera?.}, journal = {BMC evolutionary biology}, volume = {14}, number = {}, pages = {26}, pmid = {24521160}, issn = {1471-2148}, mesh = {Amino Acyl-tRNA Synthetases/chemistry/*genetics/metabolism ; Animals ; Bacteria/classification/*enzymology/genetics/metabolism ; Bacterial Proteins/chemistry/*genetics/metabolism ; Chimera/*genetics ; Eukaryota/*enzymology/genetics/metabolism ; *Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Glutamate-tRNA Ligase/chemistry/*genetics/metabolism ; Phylogeny ; RNA, Transfer, Gln/metabolism ; }, abstract = {BACKGROUND: Evolutionary histories of glutamyl-tRNA synthetase (GluRS) and glutaminyl-tRNA synthetase (GlnRS) in bacteria are convoluted. After the divergence of eubacteria and eukarya, bacterial GluRS glutamylated both tRNAGln and tRNAGlu until GlnRS appeared by horizontal gene transfer (HGT) from eukaryotes or a duplicate copy of GluRS (GluRS2) that only glutamylates tRNAGln appeared. The current understanding is based on limited sequence data and not always compatible with available experimental results. In particular, the origin of GluRS2 is poorly understood.<br><br>RESULTS: A large database of bacterial GluRS, GlnRS, tRNAGln and the trimeric aminoacyl-tRNA-dependent amidotransferase (gatCAB), constructed from whole genomes by functionally annotating and classifying these enzymes according to their mutual presence and absence in the genome, was analyzed. Phylogenetic analyses showed that the catalytic and the anticodon-binding domains of functional GluRS2 (as in Helicobacter pylori) were independently acquired from evolutionarily distant hosts by HGT. Non-functional GluRS2 (as in Thermotoga maritima), on the other hand, was found to contain an anticodon-binding domain appended to a gene-duplicated catalytic domain. Several genomes were found to possess both GluRS2 and GlnRS, even though they share the common function of aminoacylating tRNAGln. GlnRS was widely distributed among bacterial phyla and although phylogenetic analyses confirmed the origin of most bacterial GlnRS to be through a single HGT from eukarya, many GlnRS sequences also appeared with evolutionarily distant phyla in phylogenetic tree. A GlnRS pseudogene could be identified in Sorangium cellulosum.<br><br>CONCLUSIONS: Our analysis broadens the current understanding of bacterial GlxRS evolution and highlights the idiosyncratic evolution of GluRS2. Specifically we show that: i) GluRS2 is a chimera of mismatching catalytic and anticodon-binding domains, ii) the appearance of GlnRS and GluRS2 in a single bacterial genome indicating that the evolutionary histories of the two enzymes are distinct, iii) GlnRS is more widespread in bacteria than is believed, iv) bacterial GlnRS appeared both by HGT from eukarya and intra-bacterial HGT, v) presence of GlnRS pseudogene shows that many bacteria could not retain the newly acquired eukaryal GlnRS. The functional annotation of GluRS, without recourse to experiments, performed in this work, demonstrates the inherent and unique advantages of using whole genome over isolated sequence databases.}, }
@article {pmid24518071, year = {2014}, author = {El Baidouri, M and Carpentier, MC and Cooke, R and Gao, D and Lasserre, E and Llauro, C and Mirouze, M and Picault, N and Jackson, SA and Panaud, O}, title = {Widespread and frequent horizontal transfers of transposable elements in plants.}, journal = {Genome research}, volume = {24}, number = {5}, pages = {831-838}, pmid = {24518071}, issn = {1549-5469}, mesh = {DNA Transposable Elements/*genetics ; *Gene Transfer, Horizontal ; *Genome, Plant ; Magnoliopsida/*genetics ; Retroelements/*genetics ; Species Specificity ; }, abstract = {Vertical, transgenerational transmission of genetic material occurs through reproduction of living organisms. In addition to vertical inheritance, horizontal gene transfer between reproductively isolated species has recently been shown to be an important, if not dominant, mechanism in the evolution of prokaryotic genomes. In contrast, only a few horizontal transfer (HT) events have been characterized so far in eukaryotes and mainly concern transposable elements (TEs). Whether these are frequent and have a significant impact on genome evolution remains largely unknown. We performed a computational search for highly conserved LTR retrotransposons among 40 sequenced eukaryotic genomes representing the major plant families. We found that 26 genomes (65%) harbor at least one case of horizontal TE transfer (HTT). These transfers concern species as distantly related as palm and grapevine, tomato and bean, or poplar and peach. In total, we identified 32 cases of HTTs, which could translate into more than 2 million among the 13,551 monocot and dicot genera. Moreover, we show that these TEs have remained functional after their transfer, occasionally causing a transpositional burst. This suggests that plants can frequently exchange genetic material through horizontal transfers and that this mechanism may be important in TE-driven genome evolution.}, }
@article {pmid24517416, year = {2014}, author = {Szabová, J and Yubuki, N and Leander, BS and Triemer, RE and Hampl, V}, title = {The evolution of paralogous enzymes MAT and MATX within the Euglenida and beyond.}, journal = {BMC evolutionary biology}, volume = {14}, number = {}, pages = {25}, pmid = {24517416}, issn = {1471-2148}, mesh = {Chlorophyta/*enzymology/genetics/physiology ; Chloroplasts/genetics ; Euglenida/classification/*enzymology/genetics/physiology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Methionine Adenosyltransferase/*genetics ; Molecular Sequence Data ; Phylogeny ; Protozoan Proteins/*genetics ; Symbiosis ; }, abstract = {BACKGROUND: Methionine adenosyltransferase (MAT) is a ubiquitous essential enzyme that, in eukaryotes, occurs in two relatively divergent paralogues: MAT and MATX. MATX has a punctate distribution across the tree of eukaryotes and, except for a few cases, is mutually exclusive with MAT. This phylogenetic pattern could have arisen by either differential loss of old paralogues or the spread of one of these paralogues by horizontal gene transfer. Our aim was to map the distribution of MAT/MATX genes within the Euglenida in order to more comprehensively characterize the evolutionary history of MATX.<br><br>RESULTS: We generated 26 new sequences from 23 different lineages of euglenids and one prasinophyte alga Pyramimonas parkeae. MATX was present only in photoautotrophic euglenids. The mixotroph Rapaza viridis and the prasinophyte alga Pyramimonas parkeae, which harbors chloroplasts that are most closely related to the chloroplasts in photoautotrophic euglenids, both possessed only the MAT paralogue. We found both the MAT and MATX paralogues in two photoautotrophic species (Phacus orbicularis and Monomorphina pyrum). The significant conflict between eukaryotic phylogenies inferred from MATX and SSU rDNA data represents strong evidence that MATX paralogues have undergone horizontal gene transfer across the tree of eukaryotes.<br><br>CONCLUSIONS: Our results suggest that MATX entered the euglenid lineage in a single horizontal gene transfer event that took place after the secondary endosymbiotic origin of the euglenid chloroplast. The origin of the MATX paralogue is unclear, and it cannot be excluded that it arose by a gene duplication event before the most recent common ancestor of eukaryotes.}, }
@article {pmid24516448, year = {2013}, author = {Alam, MZ and Aqil, F and Ahmad, I and Ahmad, S}, title = {Incidence and transferability of antibiotic resistance in the enteric bacteria isolated from hospital wastewater.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {44}, number = {3}, pages = {799-806}, pmid = {24516448}, issn = {1678-4405}, mesh = {Anti-Bacterial Agents/*pharmacology ; Conjugation, Genetic ; *Drug Resistance, Bacterial ; Enterobacteriaceae/drug effects/*genetics/*isolation &amp; purification ; Escherichia coli K12/genetics ; *Gene Transfer, Horizontal ; Hospitals ; Humans ; Incidence ; Microbial Sensitivity Tests ; R Factors ; Wastewater/*microbiology ; beta-Lactamases/metabolism ; }, abstract = {This study reports the occurrence of antibiotic resistance and production of β-lactamases including extended spectrum beta-lactamases (ESβL) in enteric bacteria isolated from hospital wastewater. Among sixty-nine isolates, tested for antibiotic sensitivity, 73.9% strains were resistant to ampicillin followed by nalidixic acid (72.5%), penicillin (63.8%), co-trimoxazole (55.1%), norfloxacin (53.6%), methicillin (52.7%), cefuroxime (39.1%), cefotaxime (23.2%) and cefixime (20.3%). Resistance to streptomycin, chloramphenicol, nitrofurantoin, tetracycline, and doxycycline was recorded in less than 13% of the strains. The minimum inhibitory concentration (MIC) showed a high level of resistance (800-1600 μg/mL) to one or more antibiotics. Sixty three (91%) isolates produced β-lactamases as determined by rapid iodometric test. Multiple antibiotic resistances were noted in both among ESβL and non-ESβL producers. The β-lactamases hydrolyzed multiple substrates including penicillin (78.8% isolates), ampicillin (62.3%), cefodroxil (52.2%), cefotoxime (21.7%) and cefuroxime (18.8%). Fifteen isolates producing ESβLs were found multidrug resistant. Four ESβL producing isolates could transfer their R-plasmid to the recipient strain E. coli K-12 with conjugation frequency ranging from 7.0 × 10(-3) to 8.8 × 10(-4). The findings indicated that ESβL producing enteric bacteria are common in the waste water. Such isolates may disseminate the multiple antibiotic resistance traits among bacterial community through genetic exchange mechanisms and thus requires immediate attention.}, }
@article {pmid24515309, year = {2014}, author = {Fernandez-Gonzalez, E and Backert, S}, title = {DNA transfer in the gastric pathogen Helicobacter pylori.}, journal = {Journal of gastroenterology}, volume = {49}, number = {4}, pages = {594-604}, pmid = {24515309}, issn = {1435-5922}, mesh = {Bacterial Proteins/genetics ; Bacterial Secretion Systems/*genetics ; Conjugation, Genetic ; *Gene Transfer, Horizontal ; Helicobacter Infections/*genetics ; Helicobacter pylori/*genetics/pathogenicity ; Humans ; Plasmids/*genetics ; *Recombination, Genetic ; Transformation, Bacterial ; }, abstract = {The gastric pathogen Helicobacter pylori is one of the most genetically diverse bacteria. Recombination and DNA transfer contribute to its genetic variability and enhance host adaptation. Among the strategies described to increase genetic diversity in bacteria, DNA transfer by conjugation is one of the best characterized. Using this mechanism, a fragment of DNA from a donor cell can be transferred to a recipient, always mediated by a conjugative nucleoprotein complex, which is evolutionarily related to type IV secretion systems (T4SSs). Interestingly, the H. pylori chromosomes can encode up to four T4SSs, including the cagPAI, comB, tfs3, and tfs4 genes, some of which are known to promote chronic H. pylori infection. The T4SS encoded by the cagPAI mediates the injection of the effector protein CagA and proinflammatory signaling, and the comB system is involved in DNA uptake from the environment. However, the role of tfs3 and tfs4 is not yet clear. The presence of a functional XerD tyrosine recombinase and 5'AAAGAATG-3' border sequences as well as two putative conjugative relaxases (Rlx1 and Rlx2), a coupling protein (TraG), and a chromosomal region carrying a putative origin of transfer (oriT) suggest the existence of a DNA transfer apparatus in tfs4. Moreover, a conjugation-like DNA transfer mechanism in H. pylori has already been described in vitro, but whether this occurs in vivo is still unknown. Some extrachromosomal plasmids and phages are also present in various H. pylori strains. Genetic exchange among plasmids and chromosomes, and involved DNA mobilization events, could explain part of H. pylori's genetic diversity. Here, we review our knowledge about the possible DNA transfer mechanisms in H. pylori and its implications in bacterial adaptation to the host environment.}, }
@article {pmid24515269, year = {2014}, author = {Wu, B and Hao, W}, title = {Horizontal transfer and gene conversion as an important driving force in shaping the landscape of mitochondrial introns.}, journal = {G3 (Bethesda, Md.)}, volume = {4}, number = {4}, pages = {605-612}, pmid = {24515269}, issn = {2160-1836}, mesh = {Deoxyribonucleases, Type II Site-Specific/genetics ; Exons ; Gene Conversion/*genetics ; Gene Transfer, Horizontal/*genetics ; *Genome, Mitochondrial ; Introns/*genetics ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; Saccharomyces/classification/genetics ; Saccharomyces cerevisiae Proteins/genetics ; Sequence Analysis, DNA ; }, abstract = {Group I introns are highly dynamic and mobile, featuring extensive presence-absence variation and widespread horizontal transfer. Group I introns can invade intron-lacking alleles via intron homing powered by their own encoded homing endonuclease gene (HEG) after horizontal transfer or via reverse splicing through an RNA intermediate. After successful invasion, the intron and HEG are subject to degeneration and sequential loss. It remains unclear whether these mechanisms can fully address the high dynamics and mobility of group I introns. Here, we found that HEGs undergo a fast gain-and-loss turnover comparable with introns in the yeast mitochondrial 21S-rRNA gene, which is unexpected, as the intron and HEG are generally believed to move together as a unit. We further observed extensively mosaic sequences in both the introns and HEGs, and evidence of gene conversion between HEG-containing and HEG-lacking introns. Our findings suggest horizontal transfer and gene conversion can accelerate HEG/intron degeneration and loss, or rescue and propagate HEG/introns, and ultimately result in high HEG/intron turnover rate. Given that up to 25% of the yeast mitochondrial genome is composed of introns and most mitochondrial introns are group I introns, horizontal transfer and gene conversion could have served as an important mechanism in introducing mitochondrial intron diversity, promoting intron mobility and consequently shaping mitochondrial genome architecture.}, }
@article {pmid24512041, year = {2014}, author = {Lee, R and Lai, H and Malik, SB and Saldarriaga, JF and Keeling, PJ and Slamovits, CH}, title = {Analysis of EST data of the marine protist Oxyrrhis marina, an emerging model for alveolate biology and evolution.}, journal = {BMC genomics}, volume = {15}, number = {}, pages = {122}, pmid = {24512041}, issn = {1471-2164}, mesh = {Biological Evolution ; Cluster Analysis ; DNA Repair/genetics ; Dinoflagellida/classification/*genetics ; *Expressed Sequence Tags ; Gene Library ; Gene Transfer, Horizontal ; Genome, Protozoan ; Meiosis/genetics ; *Models, Biological ; Phylogeny ; Retroelements ; }, abstract = {BACKGROUND: The alveolates include a large number of important lineages of protists and algae, among which are three major eukaryotic groups: ciliates, apicomplexans and dinoflagellates. Collectively alveolates are present in virtually every environment and include a vast diversity of cell shapes, molecular and cellular features and feeding modes including lifestyles such as phototrophy, phagotrophy/predation and intracellular parasitism, in addition to a variety of symbiotic associations. Oxyrrhis marina is a well-known model for heterotrophic protist biology, and is now emerging as a useful organism to explore the many changes that occurred during the origin and diversification of dinoflagellates by virtue of its phylogenetic position at the base of the dinoflagellate tree.<br><br>RESULTS: We have generated and analysed expressed sequence tag (EST) sequences from the alveolate Oxyrrhis marina in order to shed light on the evolution of a number of dinoflagellate characteristics, especially regarding the emergence of highly unusual genomic features. We found that O. marina harbours extensive gene redundancy, indicating high rates of gene duplication and transcription from multiple genomic loci. In addition, we observed a correlation between expression level and copy number in several genes, suggesting that copy number may contribute to determining transcript levels for some genes. Finally, we analyze the genes and predicted products of the recently discovered Dinoflagellate Viral Nuclear Protein, and several cases of horizontally acquired genes.<br><br>CONCLUSION: The dataset presented here has proven very valuable for studying this important group of protists. Our analysis indicates that gene redundancy is a pervasive feature of dinoflagellate genomes, thus the mechanisms involved in its generation must have arisen early in the evolution of the group.}, }
@article {pmid24510140, year = {2013}, author = {Stucken, K and Koch, R and Dagan, T}, title = {Cyanobacterial defense mechanisms against foreign DNA transfer and their impact on genetic engineering.}, journal = {Biological research}, volume = {46}, number = {4}, pages = {373-382}, doi = {10.4067/S0716-97602013000400009}, pmid = {24510140}, issn = {0717-6287}, mesh = {Amino Acid Sequence ; Bacterial Proteins/*genetics ; Base Sequence ; Cyanobacteria/*genetics ; DNA, Bacterial/*genetics ; Gene Transfer Techniques ; Phylogeny ; }, abstract = {Cyanobacteria display a large diversity of cellular forms ranging from unicellular to complex multicellular filaments or aggregates. Species in the group present a wide range of metabolic characteristics including the fixation of atmospheric nitrogen, resistance to extreme environments, production of hydrogen, secondary metabolites and exopolysaccharides. These characteristics led to the growing interest in cyanobacteria across the fields of ecology, evolution, cell biology and biotechnology. The number of available cyanobacterial genome sequences has increased considerably in recent years, with more than 140 fully sequenced genomes to date. Genetic engineering of cyanobacteria is widely applied to the model unicellular strains Synechocystis sp. PCC 6803 and Synechococcus elongatus PCC 7942. However the establishment of transformation protocols in many other cyanobacterial strains is challenging. One obstacle to the development of these novel model organisms is that many species have doubling times of 48 h or more, much longer than the bacterial models E. coli or B. subtilis. Furthermore, cyanobacterial defense mechanisms against foreign DNA pose a physical and biochemical barrier to DNA insertion in most strains. Here we review the various barriers to DNA uptake in the context of lateral gene transfer among microbes and the various mechanisms for DNA acquisition within the prokaryotic domain. Understanding the cyanobacterial defense mechanisms is expected to assist in the development and establishment of novel transformation protocols that are specifically suitable for this group.}, }
@article {pmid24510139, year = {2013}, author = {Navarro, CA and von Bernath, D and Jerez, CA}, title = {Heavy metal resistance strategies of acidophilic bacteria and their acquisition: importance for biomining and bioremediation.}, journal = {Biological research}, volume = {46}, number = {4}, pages = {363-371}, doi = {10.4067/S0716-97602013000400008}, pmid = {24510139}, issn = {0717-6287}, mesh = {Acidithiobacillus/*drug effects/genetics ; Adaptation, Physiological ; Betaproteobacteria/*drug effects/genetics ; *Biodegradation, Environmental ; *Gene Expression Regulation, Bacterial ; Genomic Islands ; Homeostasis ; Metals, Heavy/*pharmacology ; }, abstract = {Microbial solubilizing of metals in acid environments is successfully used in industrial bioleaching of ores or biomining to extract metals such as copper, gold, uranium and others. This is done mainly by acidophilic and other microorganisms that mobilize metals and generate acid mine drainage or AMD, causing serious environmental problems. However, bioremediation or removal of the toxic metals from contaminated soils can be achieved by using the specific properties of the acidophilic microorganisms interacting with these elements. These bacteria resist high levels of metals by using a few "canonical" systems such as active efflux or trapping of the metal ions by metal chaperones. Nonetheless, gene duplications, the presence of genomic islands, the existence of additional mechanisms such as passive instruments for pH and cation homeostasis in acidophiles and an inorganic polyphosphate-driven metal resistance mechanism have also been proposed. Horizontal gene transfer in environmental microorganisms present in natural ecosystems is considered to be an important mechanism in their adaptive evolution. This process is carried out by different mobile genetic elements, including genomic islands (GI), which increase the adaptability and versatility of the microorganism. This mini-review also describes the possible role of GIs in metal resistance of some environmental microorganisms of importance in biomining and bioremediation of metal polluted environments such as Thiomonas arsenitoxydans, a moderate acidophilic microorganism, Acidithiobacillus caldus and Acidithiobacillus ferrooxidans strains ATCC 23270 and ATCC 53993, all extreme acidophiles able to tolerate exceptionally high levels of heavy metals. Some of these bacteria contain variable numbers of GIs, most of which code for high numbers of genes related to metal resistance. In some cases there is an apparent correlation between the number of metal resistance genes and the metal tolerance of each of these microorganisms. It is expected that a detailed knowledge of the mechanisms that these environmental microorganisms use to adapt to their harsh niche will help to improve biomining and metal bioremediation in industrial processes.}, }
@article {pmid24509315, year = {2014}, author = {Encinas, D and Garcillán-Barcia, MP and Santos-Merino, M and Delaye, L and Moya, A and de la Cruz, F}, title = {Plasmid conjugation from proteobacteria as evidence for the origin of xenologous genes in cyanobacteria.}, journal = {Journal of bacteriology}, volume = {196}, number = {8}, pages = {1551-1559}, pmid = {24509315}, issn = {1098-5530}, mesh = {*Conjugation, Genetic ; Electroporation ; Escherichia coli/*genetics ; Gene Transfer, Horizontal ; Genetic Vectors ; *Plasmids ; Synechococcus/*genetics ; }, abstract = {Comparative genomics have shown that 5% of Synechococcus elongatus PCC 7942 genes are of probable proteobacterial origin. To investigate the role of interphylum conjugation in cyanobacterial gene acquisition, we tested the ability of a set of prototype proteobacterial conjugative plasmids (RP4, pKM101, R388, R64, and F) to transfer DNA from Escherichia coli to S. elongatus. A series of BioBrick-compatible, mobilizable shuttle vectors was developed. These vectors were based on the putative origin of replication of the Synechococcus resident plasmid pANL. Not only broad-host-range plasmids, such as RP4 and R388, but also narrower-host-range plasmids, such as pKM101, all encoding MPFT-type IV secretion systems, were able to transfer plasmid DNA from E. coli to S. elongatus by conjugation. Neither MPFF nor MPFI could be used as interphylum DNA delivery agents. Reciprocally, pANL-derived cointegrates could be introduced in E. coli by electroporation, where they conferred a functional phenotype. These results suggest the existence of potentially ample channels of gene flow between proteobacteria and cyanobacteria and point to MPFT-based interphylum conjugation as a potential mechanism to explain the proteobacterial origin of a majority of S. elongatus xenologous genes.}, }
@article {pmid24508048, year = {2014}, author = {Johnston, C and Campo, N and Bergé, MJ and Polard, P and Claverys, JP}, title = {Streptococcus pneumoniae, le transformiste.}, journal = {Trends in microbiology}, volume = {22}, number = {3}, pages = {113-119}, doi = {10.1016/j.tim.2014.01.002}, pmid = {24508048}, issn = {1878-4380}, mesh = {Adaptation, Biological ; *Gene Transfer, Horizontal ; Streptococcus pneumoniae/*genetics ; *Transformation, Bacterial ; }, abstract = {Streptococcus pneumoniae (the pneumococcus) is an important human pathogen. Natural genetic transformation, which was discovered in this species, involves internalization of exogenous single-stranded DNA and its incorporation into the chromosome. It allows acquisition of pathogenicity islands and antibiotic resistance and promotes vaccine escape via capsule switching. This opinion article discusses how recent advances regarding several facets of pneumococcal transformation support the view that the process has evolved to maximize plasticity potential in this species, making the pneumococcus le transformiste of the bacterial kingdom and providing an advantage in the constant struggle between this pathogen and its host.}, }
@article {pmid24504266, year = {2014}, author = {Choi, HY and Moon, SJ and Ratliff, BB and Ahn, SH and Jung, A and Lee, M and Lee, S and Lim, BJ and Kim, BS and Plotkin, MD and Ha, SK and Park, HC}, title = {Microparticles from kidney-derived mesenchymal stem cells act as carriers of proangiogenic signals and contribute to recovery from acute kidney injury.}, journal = {PloS one}, volume = {9}, number = {2}, pages = {e87853}, pmid = {24504266}, issn = {1932-6203}, mesh = {Acute Kidney Injury/genetics/*metabolism/pathology ; Animals ; Apoptosis ; Biological Transport ; Cell Proliferation ; Cell-Derived Microparticles/*metabolism/ultrastructure ; Disease Models, Animal ; Endothelial Cells/*metabolism ; Gene Expression Profiling ; Gene Transfer, Horizontal ; Human Umbilical Vein Endothelial Cells ; Humans ; Male ; Mesenchymal Stem Cells/*metabolism ; Mice ; Neovascularization, Physiologic ; Reperfusion Injury/genetics/metabolism/pathology ; *Signal Transduction ; }, abstract = {We recently demonstrated the use of in vitro expanded kidney-derived mesenchymal stem cells (KMSC) protected peritubular capillary endothelial cells in acute renal ischemia-reperfusion injury. Herein, we isolated and characterized microparticles (MPs) from KMSC. We investigated their in vitro biologic effects on human endothelial cells and in vivo renoprotective effects in acute ischemia-reperfusion renal injury. MPs were isolated from the supernatants of KMSC cultured in anoxic conditions in serum-deprived media for 24 hours. KMSC-derived MPs demonstrated the presence of several adhesion molecules normally expressed on KMSC membranes, such as CD29, CD44, CD73, α4, 5, and 6 integrins. Quantitative real time PCR confirmed the presence of 3 splicing variants of VEGF-A (120, 164, 188), bFGF and IGF-1 in isolated MPs. MPs labeled with PKH26 red fluorescence dye were incorporated by cultured human umbilical vein endothelial cells (HUVEC) via surface molecules such as CD44, CD29, and α4, 5, and 6 integrins. MP dose dependently improved in vitro HUVEC proliferation and promoted endothelial tube formation on growth factor reduced Matrigel. Moreover, apoptosis of human microvascular endothelial cell was inhibited by MPs. Administration of KMSC-derived MPs into mice with acute renal ischemia was followed by selective engraftment in ischemic kidneys and significant improvement in renal function. This was achieved by improving proliferation, of peritubular capillary endothelial cell and amelioration of peritubular microvascular rarefaction. Our results support the hypothesis that KMSC-derived MPs may act as a source of proangiogenic signals and confer renoprotective effects in ischemic kidneys.}, }
@article {pmid24502835, year = {2014}, author = {Sharma, P and Gupta, SK and Rolain, JM}, title = {Whole genome sequencing of bacteria in cystic fibrosis as a model for bacterial genome adaptation and evolution.}, journal = {Expert review of anti-infective therapy}, volume = {12}, number = {3}, pages = {343-355}, doi = {10.1586/14787210.2014.887441}, pmid = {24502835}, issn = {1744-8336}, mesh = {Burkholderia cepacia complex/genetics ; Cystic Fibrosis/*microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome Size ; *Genome, Bacterial ; Humans ; Pseudomonas aeruginosa/genetics ; Sequence Analysis, DNA ; Staphylococcus aureus/genetics ; }, abstract = {Cystic fibrosis (CF) airways harbor a wide variety of new and/or emerging multidrug resistant bacteria which impose a heavy burden on patients. These bacteria live in close proximity with one another, which increases the frequency of lateral gene transfer. The exchange and movement of mobile genetic elements and genomic islands facilitate the spread of genes between genetically diverse bacteria, which seem to be advantageous to the bacterium as it allows adaptation to the new niches of the CF lungs. Niche adaptation is one of the major evolutionary forces shaping bacterial genome composition and in CF the chronic strains adapt and become less virulent. The purpose of this review is to shed light on CF bacterial genome alterations. Next-generation sequencing technology is an exciting tool that may help us to decipher the genome architecture and the evolution of bacteria colonizing CF lungs.}, }
@article {pmid24501396, year = {2014}, author = {Gaby, JC and Buckley, DH}, title = {A comprehensive aligned nifH gene database: a multipurpose tool for studies of nitrogen-fixing bacteria.}, journal = {Database : the journal of biological databases and curation}, volume = {2014}, number = {}, pages = {bau001}, pmid = {24501396}, issn = {1758-0463}, mesh = {Base Composition/genetics ; Base Sequence ; Computational Biology/*methods ; *Databases, Genetic ; Genes, Bacterial/*genetics ; Multigene Family ; Nitrogen Fixation/*genetics ; Oxidoreductases/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment/*methods ; }, abstract = {We describe a nitrogenase gene sequence database that facilitates analysis of the evolution and ecology of nitrogen-fixing organisms. The database contains 32 954 aligned nitrogenase nifH sequences linked to phylogenetic trees and associated sequence metadata. The database includes 185 linked multigene entries including full-length nifH, nifD, nifK and 16S ribosomal RNA (rRNA) gene sequences. Evolutionary analyses enabled by the multigene entries support an ancient horizontal transfer of nitrogenase genes between Archaea and Bacteria and provide evidence that nifH has a different history of horizontal gene transfer from the nifDK enzyme core. Further analyses show that lineages in nitrogenase cluster I and cluster III have different rates of substitution within nifD, suggesting that nifD is under different selection pressure in these two lineages. Finally, we find that that the genetic divergence of nifH and 16S rRNA genes does not correlate well at sequence dissimilarity values used commonly to define microbial species, as stains having <3% sequence dissimilarity in their 16S rRNA genes can have up to 23% dissimilarity in nifH. The nifH database has a number of uses including phylogenetic and evolutionary analyses, the design and assessment of primers/probes and the evaluation of nitrogenase sequence diversity. Database URL: http://www.css.cornell.edu/faculty/buckley/nifh.htm.}, }
@article {pmid24499790, year = {2014}, author = {Chandraprakash, D and Seshasayee, AS}, title = {Inhibition of factor-dependent transcription termination in Escherichia coli might relieve xenogene silencing by abrogating H-NS-DNA interactions in vivo.}, journal = {Journal of biosciences}, volume = {39}, number = {1}, pages = {53-61}, pmid = {24499790}, issn = {0973-7138}, mesh = {Bridged Bicyclo Compounds, Heterocyclic/pharmacology ; Chromatin Immunoprecipitation ; Escherichia coli/*physiology ; Escherichia coli Proteins/antagonists &amp; inhibitors/*genetics/physiology ; Fimbriae Proteins/*genetics ; Gene Expression Regulation, Bacterial/*physiology ; Gene Silencing/*physiology ; Gene Transfer, Horizontal/*physiology ; High-Throughput Nucleotide Sequencing ; Transcription Termination, Genetic/*physiology ; }, abstract = {Many horizontally acquired genes (xenogenes) in the bacterium Escherichia coli are maintained in a silent transcriptional state by the nucleoid-associated transcription regulatory protein H-NS. Recent evidence has shown that antibiotic-mediated inhibition of the transcription terminator protein Rho leads to de-repression of horizontally acquired genes, akin to a deletion of hns. The mechanism behind this similarity in outcomes between the perturbations of two distinct processes remains unclear. Using ChIP-seq of H-NS in wild-type cells, in addition to that in cells treated with bicyclomycin--a specific inhibitor of Rho, we show that bicyclomycin treatment leads to a decrease in binding signal for H-NS to the E. coli chromosome. Rho inhibition leads to RNA polymerase readthrough, which in principle could displace H-NS from the DNA, thus leading to transcriptional derepression of H-NS-silenced genes. Other possible mediators of the effect of Rho on H-NS are discussed. A possible positive feedback between Rho and H-NS might help reinforce xenogene silencing.}, }
@article {pmid24497602, year = {2014}, author = {Modolo, L and Picard, F and Lerat, E}, title = {A new genome-wide method to track horizontally transferred sequences: application to Drosophila.}, journal = {Genome biology and evolution}, volume = {6}, number = {2}, pages = {416-432}, pmid = {24497602}, issn = {1759-6653}, mesh = {Animals ; DNA Transposable Elements ; Drosophila/classification/*genetics ; *Gene Transfer, Horizontal ; *Genetic Techniques ; Genome ; Phylogeny ; }, abstract = {Because of methodological breakthroughs and the availability of an increasing amount of whole-genome sequence data, horizontal transfers (HTs) in eukaryotes have received much attention recently. Contrary to similar analyses in prokaryotes, most studies in eukaryotes usually investigate particular sequences corresponding to transposable elements (TEs), neglecting the other components of the genome. We present a new methodological framework for the genome-wide detection of all putative horizontally transferred sequences between two species that requires no prior knowledge of the transferred sequences. This method provides a broader picture of HTs in eukaryotes by fully exploiting complete-genome sequence data. In contrast to previous genome-wide approaches, we used a well-defined statistical framework to control for the number of false positives in the results, and we propose two new validation procedures to control for confounding factors. The first validation procedure relies on a comparative analysis with other species of the phylogeny to validate HTs for the nonrepeated sequences detected, whereas the second one built upon the study of the dynamics of the detected TEs. We applied our method to two closely related Drosophila species, Drosophila melanogaster and D. simulans, in which we discovered 10 new HTs in addition to all the HTs previously detected in different studies, which underscores our method's high sensitivity and specificity. Our results favor the hypothesis of multiple independent HTs of TEs while unraveling a small portion of the network of HTs in the Drosophila phylogeny.}, }
@article {pmid24496724, year = {2014}, author = {Chen, Z and Martinez, DA and Gujja, S and Sykes, SM and Zeng, Q and Szaniszlo, PJ and Wang, Z and Cuomo, CA}, title = {Comparative genomic and transcriptomic analysis of wangiella dermatitidis, a major cause of phaeohyphomycosis and a model black yeast human pathogen.}, journal = {G3 (Bethesda, Md.)}, volume = {4}, number = {4}, pages = {561-578}, pmid = {24496724}, issn = {2160-1836}, support = {U54 HG003067/HG/NHGRI NIH HHS/United States ; U54 HG004969/HG/NHGRI NIH HHS/United States ; U54HG003067/HG/NHGRI NIH HHS/United States ; U54HG004969/HG/NHGRI NIH HHS/United States ; }, mesh = {Cell Wall/metabolism ; Chitin Synthase/genetics/metabolism ; Comparative Genomic Hybridization ; Exophiala/classification/*genetics/isolation &amp; purification ; Fungal Proteins/chemistry/metabolism ; Gene Expression Profiling ; *Gene Expression Regulation, Fungal ; Genetic Linkage ; *Genome, Fungal ; Genomics ; Humans ; Hydrogen-Ion Concentration ; Melanins/biosynthesis ; Multigene Family ; Oxidative Stress ; Phaeohyphomycosis/*microbiology ; Phylogeny ; Sequence Analysis, RNA ; }, abstract = {Black or dark brown (phaeoid) fungi cause cutaneous, subcutaneous, and systemic infections in humans. Black fungi thrive in stressful conditions such as intense light, high radiation, and very low pH. Wangiella (Exophiala) dermatitidis is arguably the most studied phaeoid fungal pathogen of humans. Here, we report our comparative analysis of the genome of W. dermatitidis and the transcriptional response to low pH stress. This revealed that W. dermatitidis has lost the ability to synthesize alpha-glucan, a cell wall compound many pathogenic fungi use to evade the host immune system. In contrast, W. dermatitidis contains a similar profile of chitin synthase genes as related fungi and strongly induces genes involved in cell wall synthesis in response to pH stress. The large portfolio of transporters may provide W. dermatitidis with an enhanced ability to remove harmful products as well as to survive on diverse nutrient sources. The genome encodes three independent pathways for producing melanin, an ability linked to pathogenesis; these are active during pH stress, potentially to produce a barrier to accumulated oxidative damage that might occur under stress conditions. In addition, a full set of fungal light-sensing genes is present, including as part of a carotenoid biosynthesis gene cluster. Finally, we identify a two-gene cluster involved in nucleotide sugar metabolism conserved with a subset of fungi and characterize a horizontal transfer event of this cluster between fungi and algal viruses. This work reveals how W. dermatitidis has adapted to stress and survives in diverse environments, including during human infections.}, }
@article {pmid24495587, year = {2014}, author = {Romano, A and Ladero, V and Alvarez, MA and Lucas, PM}, title = {Putrescine production via the ornithine decarboxylation pathway improves the acid stress survival of Lactobacillus brevis and is part of a horizontally transferred acid resistance locus.}, journal = {International journal of food microbiology}, volume = {175}, number = {}, pages = {14-19}, doi = {10.1016/j.ijfoodmicro.2014.01.009}, pmid = {24495587}, issn = {1879-3460}, mesh = {Acids/toxicity ; Beverages/microbiology ; Biogenic Amines/metabolism ; Cytosol/chemistry ; Decarboxylation ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal/*genetics ; Levilactobacillus brevis/*genetics/*metabolism ; Molecular Sequence Data ; Ornithine Decarboxylase/genetics/metabolism ; Putrescine/*biosynthesis/metabolism ; }, abstract = {Decarboxylation pathways are widespread among lactic acid bacteria; their physiological role is related to acid resistance through the regulation of the intracellular pH and to the production of metabolic energy via the generation of a proton motive force and its conversion into ATP. These pathways include, among others, biogenic amine (BA) production pathways. BA accumulation in foodstuffs is a health risk; thus, the study of the factors involved in their production is of major concern. The analysis of several lactic acid bacterial strains isolated from different environments, including fermented foods and beverages, revealed that the genes encoding these pathways are clustered on the chromosome, which suggests that these genes are part of a genetic hotspot related to acid stress resistance. Further attention was devoted to the ornithine decarboxylase pathway, which affords putrescine from ornithine. Studies were performed on three lactic acid bacteria belonging to different species. The ODC pathway was always shown to be involved in cytosolic pH alkalinisation and acid shock survival, which were observed to occur with a concomitant increase in putrescine production.}, }
@article {pmid24495094, year = {2016}, author = {Woappi, Y and Gabani, P and Singh, A and Singh, OV}, title = {Antibiotrophs: The complexity of antibiotic-subsisting and antibiotic-resistant microorganisms.}, journal = {Critical reviews in microbiology}, volume = {42}, number = {1}, pages = {17-30}, doi = {10.3109/1040841X.2013.875982}, pmid = {24495094}, issn = {1549-7828}, mesh = {Anti-Infective Agents/*metabolism/*pharmacology ; Bacteria/drug effects/genetics/metabolism ; Computational Biology/methods ; *Drug Resistance, Microbial ; Fungi/drug effects/genetics/metabolism ; Gene Transfer, Horizontal ; Genes, MDR ; Humans ; Mutation ; Web Browser ; }, abstract = {Widespread overuse of antibiotics has led to the emergence of numerous antibiotic-resistant bacteria; among these are antibiotic-subsisting strains capable of surviving in environments with antibiotics as the sole carbon source. This unparalleled expansion of antibiotic resistance reveals the potent and diversified resistance abilities of certain bacterial strains. Moreover, these strains often possess hypermutator phenotypes and virulence transmissibility competent for genomic and proteomic propagation and pathogenicity. Pragmatic and prospicient approaches will be necessary to develop efficient therapeutic methods against such bacteria and to understand the extent of their genomic adaptability. This review aims to reveal the niches of these antibiotic-catabolizing microbes and assesses the underlying factors linking natural microbial antibiotic production, multidrug resistance, and antibiotic-subsistence.}, }
@article {pmid24488316, year = {2014}, author = {Mell, JC and Redfield, RJ}, title = {Natural competence and the evolution of DNA uptake specificity.}, journal = {Journal of bacteriology}, volume = {196}, number = {8}, pages = {1471-1483}, pmid = {24488316}, issn = {1098-5530}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Bacteria/*genetics/*metabolism ; Biological Evolution ; Biological Transport ; Carbon/metabolism ; DNA/genetics/*metabolism ; *DNA Transformation Competence ; Nitrogen/metabolism ; Recombination, Genetic ; }, abstract = {Many bacteria are naturally competent, able to actively transport environmental DNA fragments across their cell envelope and into their cytoplasm. Because incoming DNA fragments can recombine with and replace homologous segments of the chromosome, competence provides cells with a potent mechanism of horizontal gene transfer as well as access to the nutrients in extracellular DNA. This review starts with an introductory overview of competence and continues with a detailed consideration of the DNA uptake specificity of competent proteobacteria in the Pasteurellaceae and Neisseriaceae. Species in these distantly related families exhibit strong preferences for genomic DNA from close relatives, a self-specificity arising from the combined effects of biases in the uptake machinery and genomic overrepresentation of the sequences this machinery prefers. Other competent species tested lack obvious uptake bias or uptake sequences, suggesting that strong convergent evolutionary forces have acted on these two families. Recent results show that uptake sequences have multiple "dialects," with clades within each family preferring distinct sequence variants and having corresponding variants enriched in their genomes. Although the genomic consensus uptake sequences are 12 and 29 to 34 bp, uptake assays have found that only central cores of 3 to 4 bp, conserved across dialects, are crucial for uptake. The other bases, which differ between dialects, make weaker individual contributions but have important cooperative interactions. Together, these results make predictions about the mechanism of DNA uptake across the outer membrane, supporting a model for the evolutionary accumulation and stability of uptake sequences and suggesting that uptake biases may be more widespread than currently thought.}, }
@article {pmid24483241, year = {2014}, author = {Fahrenfeld, N and Knowlton, K and Krometis, LA and Hession, WC and Xia, K and Lipscomb, E and Libuit, K and Green, BL and Pruden, A}, title = {Effect of manure application on abundance of antibiotic resistance genes and their attenuation rates in soil: field-scale mass balance approach.}, journal = {Environmental science &amp; technology}, volume = {48}, number = {5}, pages = {2643-2650}, doi = {10.1021/es404988k}, pmid = {24483241}, issn = {1520-5851}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/*genetics/*isolation &amp; purification ; Cattle ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial/drug effects/*genetics ; Geologic Sediments/*microbiology ; Horses ; Manure/analysis/*microbiology ; Seasons ; Sheep ; *Soil Microbiology ; Virginia ; }, abstract = {The development of models for understanding antibiotic resistance gene (ARG) persistence and transport is a critical next step toward informing mitigation strategies to prevent the spread of antibiotic resistance in the environment. A field study was performed that used a mass balance approach to gain insight into the transport and dissipation of ARGs following land application of manure. Soil from a small drainage plot including a manure application site, an unmanured control site, and an adjacent stream and buffer zone were sampled for ARGs and metals before and after application of dairy manure slurry and a dry stack mixture of equine, bovine, and ovine manure. Results of mass balance suggest growth of bacterial hosts containing ARGs and/or horizontal gene transfer immediately following slurry application with respect to ermF, sul1, and sul2 and following a lag (13 days) for dry-stack-amended soils. Generally no effects on tet(G), tet(O), or tet(W) soil concentrations were observed despite the presence of these genes in applied manure. Dissipation rates were fastest for ermF in slurry-treated soils (logarithmic decay coefficient of -3.5) and for sul1 and sul2 in dry-stack-amended soils (logarithmic decay coefficients of -0.54 and -0.48, respectively), and evidence for surface and subsurface transport was not observed. Results provide a mass balance approach for tracking ARG fate and insights to inform modeling and limiting the transport of manure-borne ARGs to neighboring surface water.}, }
@article {pmid24483098, year = {2013}, author = {Yang, FX and Mao, DQ and Luo, Y and Wang, Q and Mu, QH}, title = {[Horizontal transfer of antibiotic resistance genes in the environment].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {24}, number = {10}, pages = {2993-3002}, pmid = {24483098}, issn = {1001-9332}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/*genetics ; Environmental Pollutants/*analysis ; *Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; }, abstract = {The transfer of antibiotic resistance genes (ARGs), a new type of environmental pollutants, could have more adverse effects on the environment than the ARGs themselves, while the horizontal gene transfer (HGT) could be the most important propagation pathways of the ARGs, being one of the reasons for the growing pollution of ARGs in the environment. This paper systematically elaborated the molecular elements of the horizontal transfer of ARGs and the related affecting factors, which was of significance for investigating the molecular mechanisms of the horizontal transfer of the ARGs. In combining with the phylogenetic mechanisms of multiple antibiotic resistances, this paper also provided effective strategies to reduce the transfer and proliferation of ARGs in the environment. Based on the present contamination situations, the further researches on the horizontal transfer of ARGs in the environment were prospected.}, }
@article {pmid24480987, year = {2014}, author = {Zhu, X and You, Y and Li, Q and Zeng, C and Fu, F and Guo, A and Zhang, H and Zou, P and Zhong, Z and Wang, H and Wu, Y and Li, Q and Kong, F and Chen, Z}, title = {BCR-ABL1-positive microvesicles transform normal hematopoietic transplants through genomic instability: implications for donor cell leukemia.}, journal = {Leukemia}, volume = {28}, number = {8}, pages = {1666-1675}, pmid = {24480987}, issn = {1476-5551}, mesh = {*Cell Transformation, Neoplastic ; Cytidine Deaminase/metabolism ; Fusion Proteins, bcr-abl/genetics ; Gene Transfer, Horizontal ; *Genomic Instability ; Hematopoietic Stem Cell Transplantation/*adverse effects ; Hematopoietic Stem Cells/*pathology ; Humans ; K562 Cells ; Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology/*therapy ; Reactive Oxygen Species/metabolism ; AICDA (Activation-Induced Cytidine Deaminase) ; }, abstract = {Malignant transformation of normal hematopoietic transplants induced by residual leukemia cells is considered as a pivotal mechanism of donor cell leukemia (DCL). The effects of leukemia cell-derived microvesicles (MVs) in this transformation were examined. We found that MVs derived from K562 leukemia cells contained the breakpoint cluster region-Abelson leukemia gene human homolog 1 (BCR-ABL1) mRNA. Following incubation with BCR-ABL1-positive MVs, mononuclear cells derived from normal transplants exhibited a leukemia-like malignant phenotype both in vitro and in vivo. Horizontal transfer of BCR-ABL1 mRNA from MVs into the recipient cells was critical to the transformation. Relative genomic instability was observed and considered the main mechanism in the recipient cells. MVs contributed to genomic instability by two distinct pathways: via consequent overexpression of activation-induced cytidine deaminase and reactive oxygen species, which mediated DNA breakage and recombination; and via upregulation of methyltransferases and global DNA hypermethylation. We demonstrated that BCR-ABL1-positive MVs could initiate malignant transformation of normal hematopoietic transplants through genomic instability, which might serve as a convenient and operable model for investigating leukemogenesis, especially for DCL. Furthermore, MVs themselves could act as an early warning indicator and a novel tool to detect and prevent the occurrence of DCL.}, }
@article {pmid24477196, year = {2014}, author = {Lee, KC and Morgan, XC and Dunfield, PF and Tamas, I and McDonald, IR and Stott, MB}, title = {Genomic analysis of Chthonomonas calidirosea, the first sequenced isolate of the phylum Armatimonadetes.}, journal = {The ISME journal}, volume = {8}, number = {7}, pages = {1522-1533}, pmid = {24477196}, issn = {1751-7370}, mesh = {ATP-Binding Cassette Transporters/*genetics/metabolism ; Bacterial Proteins/*genetics/metabolism ; Biological Transport ; Cellulose/metabolism ; Chloroflexi/classification/*genetics/metabolism ; *Gene Expression Regulation, Bacterial ; *Genome, Bacterial ; Genomics ; Operon ; Phylogeny ; Sigma Factor/drug effects/*genetics/metabolism ; Transcription, Genetic ; }, abstract = {Most of the lineages of bacteria have remained unknown beyond environmental surveys using molecular markers. Until the recent characterisation of several strains, the phylum Armatimonadetes (formerly known as 'candidate division OP10') was a dominant and globally-distributed lineage within this 'uncultured majority'. Here we report the first Armatimonadetes genome from the thermophile Chthonomonas calidirosea T49(T) and its role as a saccharide scavenger in a geothermal steam-affected soil environment. Phylogenomic analysis indicates T49(T) to be related closely to the phylum Chloroflexi. The predicted genes encoding for carbohydrate transporters (27 carbohydrate ATP-binding cassette transporter-related genes) and carbohydrate-metabolising enzymes (including at least 55 putative enzymes with glycosyl hydrolase domains) within the 3.43 Mb genome help explain its ability to utilise a wide range of carbohydrates as well as its inability to break down extracellular cellulose. The presence of only a single class of branched amino acid transporter appears to be the causative step for the requirement of isoleucine for growth. The genome lacks many commonly conserved operons (for example, lac and trp). Potential causes for this, such as dispersion of functionally related genes via horizontal gene transfer from distant taxa or recent genome recombination, were rejected. Evidence suggests T49(T) relies on the relatively abundant σ-factors, instead of operonic organisation, as the primary means of transcriptional regulation. Examination of the genome with physiological data and environmental dynamics (including interspecific interactions) reveals ecological factors behind the apparent elusiveness of T49(T) to cultivation and, by extension, the remaining 'uncultured majority' that have so far evaded conventional microbiological techniques.}, }
@article {pmid24476498, year = {2014}, author = {Gona, F and Barbera, F and Pasquariello, AC and Grossi, P and Gridelli, B and Mezzatesta, ML and Caio, C and Stefani, S and Conaldi, PG}, title = {In vivo multiclonal transfer of bla(KPC-3) from Klebsiella pneumoniae to Escherichia coli in surgery patients.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {20}, number = {10}, pages = {O633-5}, doi = {10.1111/1469-0691.12577}, pmid = {24476498}, issn = {1469-0691}, mesh = {Bacterial Proteins/*genetics/metabolism ; Cross Infection/microbiology ; Enterobacteriaceae Infections/classification/*microbiology ; Escherichia coli/enzymology/genetics/*isolation &amp; purification ; Gene Transfer, Horizontal ; Humans ; Italy ; Klebsiella pneumoniae/enzymology/genetics/*isolation &amp; purification ; Multilocus Sequence Typing ; beta-Lactamases/*genetics/metabolism ; }, abstract = {During active surveillance at the Mediterranean Institute for Transplantation and Advanced Specialized Therapies (ISMETT, Palermo, Italy) with the CARBA screening medium, five pairs of Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae and Escherichia coli strains were isolated in each of five colonized patients. In each patient, lateral gene transfer was demonstrated by comparing K. pneumoniae and E. coli strains, both possessing KPC-3, Tn4401a and pKpQIL-IT elements. The isolates were found to be multiclonal by multilocus sequence typing (sequence type (ST) 512 related to ST258, and ST307 belonging to a clonal complex different from the habitual sequence clone ST258 isolated in Italy) and pulsed-field gel electrophoresis. The results of our study highlight the easy transfer of KPC among Enterobacteriaceae colonizing the human intestine, and the active and careful surveillance required to identify and prevent the spread of these multidrug-resistant microorganisms.}, }
@article {pmid24475038, year = {2014}, author = {Coates, RC and Podell, S and Korobeynikov, A and Lapidus, A and Pevzner, P and Sherman, DH and Allen, EE and Gerwick, L and Gerwick, WH}, title = {Characterization of cyanobacterial hydrocarbon composition and distribution of biosynthetic pathways.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e85140}, pmid = {24475038}, issn = {1932-6203}, support = {TW007404/TW/FIC NIH HHS/United States ; U01 TW007404/TW/FIC NIH HHS/United States ; R01 CA108874/CA/NCI NIH HHS/United States ; GM067550/GM/NIGMS NIH HHS/United States ; CA108874/CA/NCI NIH HHS/United States ; T32 GM067550/GM/NIGMS NIH HHS/United States ; }, mesh = {Aldehyde Oxidoreductases/metabolism ; Bayes Theorem ; Biosynthetic Pathways/*physiology ; Computational Biology ; Cyanobacteria/*chemistry/physiology ; Fatty Acids/metabolism ; Gas Chromatography-Mass Spectrometry ; Hydrocarbons/*analysis ; Models, Genetic ; Phylogeny ; Species Specificity ; }, abstract = {Cyanobacteria possess the unique capacity to naturally produce hydrocarbons from fatty acids. Hydrocarbon compositions of thirty-two strains of cyanobacteria were characterized to reveal novel structural features and insights into hydrocarbon biosynthesis in cyanobacteria. This investigation revealed new double bond (2- and 3-heptadecene) and methyl group positions (3-, 4- and 5-methylheptadecane) for a variety of strains. Additionally, results from this study and literature reports indicate that hydrocarbon production is a universal phenomenon in cyanobacteria. All cyanobacteria possess the capacity to produce hydrocarbons from fatty acids yet not all accomplish this through the same metabolic pathway. One pathway comprises a two-step conversion of fatty acids first to fatty aldehydes and then alkanes that involves a fatty acyl ACP reductase (FAAR) and aldehyde deformylating oxygenase (ADO). The second involves a polyketide synthase (PKS) pathway that first elongates the acyl chain followed by decarboxylation to produce a terminal alkene (olefin synthase, OLS). Sixty-one strains possessing the FAAR/ADO pathway and twelve strains possessing the OLS pathway were newly identified through bioinformatic analyses. Strains possessing the OLS pathway formed a cohesive phylogenetic clade with the exception of three Moorea strains and Leptolyngbya sp. PCC 6406 which may have acquired the OLS pathway via horizontal gene transfer. Hydrocarbon pathways were identified in one-hundred-forty-two strains of cyanobacteria over a broad phylogenetic range and there were no instances where both the FAAR/ADO and the OLS pathways were found together in the same genome, suggesting an unknown selective pressure maintains one or the other pathway, but not both.}, }
@article {pmid24475037, year = {2014}, author = {Hargreaves, KR and Kropinski, AM and Clokie, MR}, title = {What does the talking?: quorum sensing signalling genes discovered in a bacteriophage genome.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e85131}, pmid = {24475037}, issn = {1932-6203}, support = {G0700855//Medical Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Bacteriophages/classification/*physiology/ultrastructure ; Clostridioides difficile/virology ; Evolution, Molecular ; Gene Order ; Gene Transfer, Horizontal ; *Genes, Viral ; Genetic Variation ; *Genome, Viral ; Host-Pathogen Interactions ; Molecular Sequence Data ; Phylogeny ; Quorum Sensing/*genetics ; Sequence Alignment ; *Signal Transduction ; Transcription, Genetic ; }, abstract = {The transfer of novel genetic material into the genomes of bacterial viruses (phages) has been widely documented in several host-phage systems. Bacterial genes are incorporated into the phage genome and, if retained, subsequently evolve within them. The expression of these phage genes can subvert or bolster bacterial processes, including altering bacterial pathogenicity. The phage phiCDHM1 infects Clostridium difficile, a pathogenic bacterium that causes nosocomial infections and is associated with antibiotic treatment. Genome sequencing and annotation of phiCDHM1 shows that despite being closely related to other C. difficile myoviruses, it has several genes that have not been previously reported in any phage genomes. Notably, these include three homologs of bacterial genes from the accessory gene regulator (agr) quorum sensing (QS) system. These are; a pre-peptide (AgrD) of an autoinducing peptide (AIP), an enzyme which processes the pre-peptide (AgrB) and a histidine kinase (AgrC) that detects the AIP to activate a response regulator. Phylogenetic analysis of the phage and C. difficile agr genes revealed that there are three types of agr loci in this species. We propose that the phage genes belonging to a third type, agr3, and have been horizontally transferred from the host. AgrB and AgrC are transcribed during the infection of two different strains. In addition, the phage agrC appears not to be confined to the phiCDHM1 genome as it was detected in genetically distinct C. difficile strains. The discovery of QS gene homologs in a phage genome presents a novel way in which phages could influence their bacterial hosts, or neighbouring bacterial populations. This is the first time that these QS genes have been reported in a phage genome and their distribution both in C. difficile and phage genomes suggests that the agr3 locus undergoes horizontal gene transfer within this species.}, }
@article {pmid24475028, year = {2014}, author = {Paliwal, V and Raju, SC and Modak, A and Phale, PS and Purohit, HJ}, title = {Pseudomonas putida CSV86: a candidate genome for genetic bioaugmentation.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e84000}, pmid = {24475028}, issn = {1932-6203}, mesh = {Biodegradation, Environmental ; Computational Biology ; Gene Expression Regulation, Bacterial ; Gene Order ; *Genome, Bacterial ; Genomics ; Genotype ; Hydrocarbons, Aromatic/metabolism ; Metabolic Networks and Pathways ; Metals, Heavy/metabolism ; Molecular Sequence Annotation ; Operon ; Phylogeny ; Pseudomonas putida/classification/*genetics/*metabolism ; }, abstract = {Pseudomonas putida CSV86, a plasmid-free strain possessing capability to transfer the naphthalene degradation property, has been explored for its metabolic diversity through genome sequencing. The analysis of draft genome sequence of CSV86 (6.4 Mb) revealed the presence of genes involved in the degradation of naphthalene, salicylate, benzoate, benzylalcohol, p-hydroxybenzoate, phenylacetate and p-hydroxyphenylacetate on the chromosome thus ensuring the stability of the catabolic potential. Moreover, genes involved in the metabolism of phenylpropanoid and homogentisate, as well as heavy metal resistance, were additionally identified. Ability to grow on vanillin, veratraldehyde and ferulic acid, detection of inducible homogentisate dioxygenase and growth on aromatic compounds in the presence of heavy metals like copper, cadmium, cobalt and arsenic confirm in silico observations reflecting the metabolic versatility. In silico analysis revealed the arrangement of genes in the order: tRNA(Gly), integrase followed by nah operon, supporting earlier hypothesis of existence of a genomic island (GI) for naphthalene degradation. Deciphering the genomic architecture of CSV86 for aromatic degradation pathways and identification of elements responsible for horizontal gene transfer (HGT) suggests that genetic bioaugmentation strategies could be planned using CSV86 for effective bioremediation.}, }
@article {pmid24472137, year = {2014}, author = {Lee, CN and Tseng, TT and Chang, HC and Lin, JW and Weng, SF}, title = {Genomic sequence of temperate phage Smp131 of Stenotrophomonas maltophilia that has similar prophages in xanthomonads.}, journal = {BMC microbiology}, volume = {14}, number = {}, pages = {17}, pmid = {24472137}, issn = {1471-2180}, mesh = {DNA, Viral/*chemistry/*genetics ; Gene Order ; *Genome, Viral ; Microscopy, Electron, Transmission ; Molecular Sequence Data ; Myoviridae/genetics/isolation &amp; purification/ultrastructure ; Open Reading Frames ; Prophages/*genetics/*isolation &amp; purification/ultrastructure ; Sequence Analysis, DNA ; Stenotrophomonas maltophilia/*virology ; Synteny ; Viral Proteins/genetics ; Virion/ultrastructure ; }, abstract = {BACKGROUND: Stenotrophomonas maltophilia is a ubiquitous Gram-negative bacterium previously named as Xanthomonas maltophilia. This organism is an important nosocomial pathogen associated with infections in immunocompromised patients. Clinical isolates of S. maltophilia are mostly resistant to multiple antibiotics and treatment of its infections is becoming problematic. Several virulent bacteriophages, but not temperate phage, of S. maltophilia have been characterized.<br><br>RESULTS: In this study, a temperate myophage of S. maltophilia (Smp131) was isolated and characterized. Sequence analysis showed that its genome is 33,525-bp long with 47 open reading frames (ORFs). Its similarity to P2-like phages and prophages in S. maltophilia and several Xanthomonas pathovars includes genomic organization, arrangement of several operons, and possession of a slippery sequence T&#x2087;G for translational frameshifting in tail assembly genes. Smp131 encodes a tyrosine family integrase that shares low degrees of similarity with those of other phages and a lysin belonging to family 19 chitinase that is observed in plants and some bacteria, although not in phages. tRNA are the preferred sites for host integration of Smp131 and the related phages: tRNA-Thr for Smp131 and prophage of S. maltophilia K279a; tRNA-Lys for prophages of X. campestris pv. campestris ATCC33913, X. oryzae pv. oryzae strains MAFF311018, and KACC10331; and tRNA-Asn for prophage of X. oryzae pv. oryzae PXO99A and remnant of X. axonopodis pv. citri 306. Regions flanking the prophages are varied highly in nucleotide sequence and rich in transposase genes, suggesting that frequent insertion/excision had occurred.<br><br>CONCLUSIONS: Prevalence of closely related prophages in Stenotrophomonas and Xanthomonads may have contributed to the diversity of these closely related species owing to possible horizontal gene transfer mediated by the phages.}, }
@article {pmid24467930, year = {2014}, author = {Marosevic, D and Cervinkova, D and Vlkova, H and Videnska, P and Babak, V and Jaglic, Z}, title = {In vivo spread of macrolide-lincosamide-streptogramin B (MLSB) resistance--a model study in chickens.}, journal = {Veterinary microbiology}, volume = {171}, number = {3-4}, pages = {388-396}, doi = {10.1016/j.vetmic.2013.12.017}, pmid = {24467930}, issn = {1873-2542}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Base Sequence ; *Chickens ; Chlortetracycline/pharmacology ; DNA Primers/genetics ; Drug Resistance, Bacterial/*genetics ; Electrophoresis, Gel, Pulsed-Field/veterinary ; Enterococcus faecalis/drug effects/*genetics ; Feces/microbiology ; Gene Transfer, Horizontal/genetics ; Gram-Positive Bacterial Infections/*veterinary ; Lincosamides/*pharmacology ; Macrolides/*pharmacology ; Methyltransferases/genetics ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Plasmids/genetics ; Polymerase Chain Reaction/veterinary ; Poultry Diseases/*microbiology ; Sequence Analysis, DNA ; Species Specificity ; Statistics, Nonparametric ; Streptogramin B/*pharmacology ; Tylosin/pharmacology ; }, abstract = {The influence of specific and non-specific antibiotic pressure on in vivo spread of macrolide-lincosamide-streptogramin B (MLSB) resistance was evaluated in this study. Chickens repeatedly inoculated with Enterococcus faecalis harbouring the plasmid pAMβ1 carrying the erm(B) gene were perorally treated for one week with tylosin, lincomycin (both specific antibiotic pressure) and chlortetracycline (non-specific antibiotic pressure). Antibiotic non-treated but E. faecalis inoculated chickens served as a control. To quantify the erm(B) gene and characterise intestinal microflora, faecal DNA was analysed by qPCR and 454-pyrosequencing. Under the pressure of antibiotics, a significant increase in erm(B) was observed by qPCR. However, at the final stage of the experiment, an increase in erm(B) was also observed in two out of five non-treated chickens. In chickens treated with tylosin and chlortetracycline, the increase in erm(B) was accompanied by an increase in enterococci. However, E. faecalis was at the limit of detection in all animals. This suggests that the erm(B) gene spread among the gut microbiota other than E. faecalis. Pyrosequencing results indicated that, depending on the particular antibiotic pressure, different bacteria could be responsible for the spread of MLSB resistance. Different species of MLSB-resistant enterococci and streptococci were isolated from cloacal swabs during and after the treatment. PFGE analysis of MLSB-resistant enterococci revealed four clones, all differing from the challenge strain. All of the MLSB-resistant isolates harboured a plasmid of the same size as pAMβ1. This study has shown that MLSB resistance may spread within the gut microbiota under specific and non-specific pressure and even in the absence of any antimicrobial pressure. Finally, depending on the particular antibiotic pressure, different bacterial species seems to be involved in the spread of MLSB resistance.}, }
@article {pmid24467712, year = {2014}, author = {Smith, DR}, title = {Mitochondrion-to-plastid DNA transfer: it happens.}, journal = {The New phytologist}, volume = {202}, number = {3}, pages = {736-738}, doi = {10.1111/nph.12704}, pmid = {24467712}, issn = {1469-8137}, mesh = {Asclepias/metabolism ; DNA, Plant/*metabolism ; Daucus carota/metabolism ; Mitochondria/*metabolism ; Plastids/*metabolism ; }, }
@article {pmid24465485, year = {2014}, author = {Matzke, NJ and Shih, PM and Kerfeld, CA}, title = {Bayesian analysis of congruence of core genes in Prochlorococcus and Synechococcus and implications on horizontal gene transfer.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e85103}, pmid = {24465485}, issn = {1932-6203}, mesh = {Aquatic Organisms ; Bayes Theorem ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genes, Essential ; *Models, Genetic ; *Phylogeny ; Prochlorococcus/classification/*genetics ; Synechococcus/classification/*genetics ; }, abstract = {It is often suggested that horizontal gene transfer is so ubiquitous in microbes that the concept of a phylogenetic tree representing the pattern of vertical inheritance is oversimplified or even positively misleading. "Universal proteins" have been used to infer the organismal phylogeny, but have been criticized as being only the "tree of one percent." Currently, few options exist for those wishing to rigorously assess how well a universal protein phylogeny, based on a relative handful of well-conserved genes, represents the phylogenetic histories of hundreds of genes. Here, we address this problem by proposing a visualization method and a statistical test within a Bayesian framework. We use the genomes of marine cyanobacteria, a group thought to exhibit substantial amounts of HGT, as a test case. We take 379 orthologous gene families from 28 cyanobacteria genomes and estimate the Bayesian posterior distributions of trees - a "treecloud" - for each, as well as for a concatenated dataset based on putative "universal proteins." We then calculate the average distance between trees within and between all treeclouds on various metrics and visualize this high-dimensional space with non-metric multidimensional scaling (NMMDS). We show that the tree space is strongly clustered and that the universal protein treecloud is statistically significantly closer to the center of this tree space than any individual gene treecloud. We apply several commonly-used tests for incongruence/HGT and show that they agree HGT is rare in this dataset, but make different choices about which genes were subject to HGT. Our results show that the question of the representativeness of the "tree of one percent" is a quantitative empirical question, and that the phylogenetic central tendency is a meaningful observation even if many individual genes disagree due to the various sources of incongruence.}, }
@article {pmid24465371, year = {2014}, author = {Molina, L and Udaondo, Z and Duque, E and Fernández, M and Molina-Santiago, C and Roca, A and Porcel, M and de la Torre, J and Segura, A and Plesiat, P and Jeannot, K and Ramos, JL}, title = {Antibiotic resistance determinants in a Pseudomonas putida strain isolated from a hospital.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e81604}, pmid = {24465371}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/chemistry ; Chromosomes, Bacterial/genetics ; Drug Resistance, Microbial/drug effects/*genetics ; Genome, Bacterial/genetics ; Genomic Islands/genetics ; *Hospitals ; Humans ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Plasmids/genetics ; Pseudomonas putida/drug effects/*genetics/*isolation &amp; purification ; Sequence Analysis, DNA ; }, abstract = {Environmental microbes harbor an enormous pool of antibiotic and biocide resistance genes that can impact the resistance profiles of animal and human pathogens via horizontal gene transfer. Pseudomonas putida strains are ubiquitous in soil and water but have been seldom isolated from humans. We have established a collection of P. putida strains isolated from in-patients in different hospitals in France. One of the isolated strains (HB3267) kills insects and is resistant to the majority of the antibiotics used in laboratories and hospitals, including aminoglycosides, ß-lactams, cationic peptides, chromoprotein enediyne antibiotics, dihydrofolate reductase inhibitors, fluoroquinolones and quinolones, glycopeptide antibiotics, macrolides, polyketides and sulfonamides. Similar to other P. putida clinical isolates the strain was sensitive to amikacin. To shed light on the broad pattern of antibiotic resistance, which is rarely found in clinical isolates of this species, the genome of this strain was sequenced and analysed. The study revealed that the determinants of multiple resistance are both chromosomally-borne as well as located on the pPC9 plasmid. Further analysis indicated that pPC9 has recruited antibiotic and biocide resistance genes from environmental microorganisms as well as from opportunistic and true human pathogens. The pPC9 plasmid is not self-transmissible, but can be mobilized by other bacterial plasmids making it capable of spreading antibiotic resistant determinants to new hosts.}, }
@article {pmid24465015, year = {2014}, author = {Marks, LR and Mashburn-Warren, L and Federle, MJ and Hakansson, AP}, title = {Streptococcus pyogenes biofilm growth in vitro and in vivo and its role in colonization, virulence, and genetic exchange.}, journal = {The Journal of infectious diseases}, volume = {210}, number = {1}, pages = {25-34}, pmid = {24465015}, issn = {1537-6613}, support = {R01 AI091779/AI/NIAID NIH HHS/United States ; AI091779/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Biofilms/*growth &amp; development ; Cells, Cultured ; *Gene Transfer, Horizontal ; Humans ; Keratinocytes/microbiology ; Lymphoid Tissue/microbiology ; Mice ; Mice, Inbred BALB C ; Nasal Cavity/microbiology ; Streptococcus pyogenes/genetics/growth &amp; development/pathogenicity/*physiology ; }, abstract = {BACKGROUND: Group A streptococcus (GAS) commonly colonizes the oropharynx and nonintact skin. However, colonization has been little studied and the role of biofilm formation is unclear, as biofilm experiments to date have not been conducted under conditions that mimic the host environment.<br><br>METHODS: In this study we grew GAS biofilms on human keratinocytes under various environmental conditions and used this model to evaluate colonization, invasive disease and natural transformation.<br><br>RESULTS: GAS grown on epithelial cells, but not biofilms grown on abiotic surfaces, produced biofilms with characteristics similar to in vivo colonization. These biofilm bacteria showed a 100-fold higher bacterial burden of nasal-associated lymphoid tissue in mice than broth-grown bacteria, and were not virulent during septic infection, which was attributed in part to down-regulation of genes typically involved in localized and invasive disease. We also showed for the first time that GAS were naturally transformable when grown in biofilms and during colonization of NALT in vivo.<br><br>CONCLUSIONS: These findings provide novel model systems to study biofilm formation of GAS in vitro and in vivo, suggest an important role for biofilm formation during GAS colonization, and provide an explanation for the known genome diversity within the GAS population.}, }
@article {pmid24464463, year = {2014}, author = {Reinhard, F and van der Meer, JR}, title = {Life history analysis of integrative and conjugative element activation in growing microcolonies of Pseudomonas.}, journal = {Journal of bacteriology}, volume = {196}, number = {7}, pages = {1425-1434}, pmid = {24464463}, issn = {1098-5530}, mesh = {*Conjugation, Genetic ; *DNA Transposable Elements ; Gene Transfer, Horizontal ; Pseudomonas/*genetics/*growth &amp; development/metabolism ; Reactive Oxygen Species/metabolism ; }, abstract = {Integrative and conjugative elements (ICE) are in some ways parasitic mobile DNA that propagate vertically through replication with the bacterial host chromosome but at low frequencies can excise and invade new recipient cells through conjugation and reintegration (horizontal propagation). The factors that contribute to successful horizontal propagation are not very well understood. Here, we study the influence of host cell life history on the initiation of transfer of a model ICE named ICEclc in bacteria of the genus Pseudomonas. We use time-lapse microscopy of growing and stationary-phase microcolonies of ICEclc bearing cells in combination with physiological staining and gene reporter analysis in stationary-phase suspended cells. We provide evidence that cell age and cell lineage are unlikely to play a role in the decision to initiate the ICEclc transfer program. In contrast, cells activating ICEclc show more often increased levels of reactive oxygen species and membrane damage than nonactivating cells, suggesting that some form of biochemical damage may make cells more prone to ICEclc induction. Finally, we find that ICEclc active cells appear spatially at random in a microcolony, which may have been a selective advantage for maximizing ICEclc horizontal transmission to new recipient species.}, }
@article {pmid24461455, year = {2014}, author = {Le, PT and Pontarotti, P and Raoult, D}, title = {Alphaproteobacteria species as a source and target of lateral sequence transfers.}, journal = {Trends in microbiology}, volume = {22}, number = {3}, pages = {147-156}, doi = {10.1016/j.tim.2013.12.006}, pmid = {24461455}, issn = {1878-4380}, mesh = {Alphaproteobacteria/*genetics ; Bacterial Secretion Systems ; Biological Evolution ; *Gene Transfer, Horizontal ; }, abstract = {Alphaproteobacterial genomes show a remarkable genome plasticity linked with different lifestyles (intracellular, facultative, and free-living). They represent the major source of the genome repertoire of mitochondria, and their genes (specifically those of Wolbachia) have been massively transferred into their modern eukaryotic hosts, such as arthropods and nematodes. Conversely, other organisms (bacteria, viruses, archaea, and eukaryotes) and selfish DNA have contributed to their genomes. This bidirectional lateral sequence transfer explains the mosaic nature of their genomes. In contrast to those living in allopatry, alphaproteobacteria living in sympatry (in protist cells such as in the environment) favor lateral sequence transfer. Evidence shows that intracellular transfer of the type IV secretion system might have played a critical role in the evolution of these alphaproteobacteria.}, }
@article {pmid24460966, year = {2013}, author = {Chumakov, MI}, title = {Protein apparatus for horizontal transfer of agrobacterial T-DNA to eukaryotic cells.}, journal = {Biochemistry. Biokhimiia}, volume = {78}, number = {12}, pages = {1321-1332}, doi = {10.1134/S000629791312002X}, pmid = {24460966}, issn = {1608-3040}, mesh = {Agrobacterium tumefaciens/*genetics ; Bacterial Proteins/chemistry/metabolism ; DNA, Bacterial/*metabolism ; DNA-Binding Proteins/chemistry/metabolism ; Eukaryotic Cells/*metabolism ; Fimbriae Proteins/chemistry/metabolism ; *Gene Transfer, Horizontal ; Genome, Plant ; Ion Channels/chemistry/metabolism ; Plants/genetics ; Virulence Factors/chemistry/metabolism ; }, abstract = {This review analyzes agrobacterial virulence proteins and recipient cell proteins involved in horizontal transfer of a T-DNA-protein complex. Specifically, it considers the early stages of the interactions of partners (signal exchange, attachment, close contact); T-DNA release from bacterial cells; channel formation for the transfer of ssDNA between the partners; transfer of agrobacterial T-DNA through the membrane, cytoplasm, and nuclear membrane of the recipient cell and its incorporation into the recipient cell genome. It further discusses possible pathways of agrobacterial ssDNA transfer to the recipient cells. In particular, the possible role of T-pili and VirE2 protein during conjugative transfer of agrobacterial ssDNA between donor and recipient cells is discussed.}, }
@article {pmid24460898, year = {2014}, author = {Yang, Y and Zhao, H and Barrero, RA and Zhang, B and Sun, G and Wilson, IW and Xie, F and Walker, KD and Parks, JW and Bruce, R and Guo, G and Chen, L and Zhang, Y and Huang, X and Tang, Q and Liu, H and Bellgard, MI and Qiu, D and Lai, J and Hoffman, A}, title = {Genome sequencing and analysis of the paclitaxel-producing endophytic fungus Penicillium aurantiogriseum NRRL 62431.}, journal = {BMC genomics}, volume = {15}, number = {}, pages = {69}, pmid = {24460898}, issn = {1471-2164}, mesh = {Acyltransferases/classification/genetics/metabolism ; Base Sequence ; Chromatography, High Pressure Liquid ; Farnesyltranstransferase/classification/genetics/metabolism ; Fungal Proteins/classification/genetics/metabolism ; Fungi/genetics ; Gene Transfer, Horizontal ; *Genome, Fungal ; Mass Spectrometry ; Mixed Function Oxygenases/classification/genetics/metabolism ; Molecular Sequence Data ; Paclitaxel/analysis/*biosynthesis ; Penicillium/classification/*genetics ; Phylogeny ; Sequence Analysis, RNA ; }, abstract = {BACKGROUND: Paclitaxel (Taxol™) is an important anticancer drug with a unique mode of action. The biosynthesis of paclitaxel had been considered restricted to the Taxus species until it was discovered in Taxomyces andreanae, an endophytic fungus of T. brevifolia. Subsequently, paclitaxel was found in hazel (Corylus avellana L.) and in several other endophytic fungi. The distribution of paclitaxel in plants and endophytic fungi and the reported sequence homology of key genes in paclitaxel biosynthesis between plant and fungi species raises the question about whether the origin of this pathway in these two physically associated groups could have been facilitated by horizontal gene transfer.<br><br>RESULTS: The ability of the endophytic fungus of hazel Penicillium aurantiogriseum NRRL 62431 to independently synthesize paclitaxel was established by liquid chromatography-mass spectrometry and proton nuclear magnetic resonance. The genome of Penicillium aurantiogriseum NRRL 62431 was sequenced and gene candidates that may be involved in paclitaxel biosynthesis were identified by comparison with the 13 known paclitaxel biosynthetic genes in Taxus. We found that paclitaxel biosynthetic gene candidates in P. aurantiogriseum NRRL 62431 have evolved independently and that horizontal gene transfer between this endophytic fungus and its plant host is unlikely.<br><br>CONCLUSIONS: Our findings shed new light on how paclitaxel-producing endophytic fungi synthesize paclitaxel, and will facilitate metabolic engineering for the industrial production of paclitaxel from fungi.}, }
@article {pmid24460813, year = {2014}, author = {Rokicki, J and Knox, D and Dowell, RD and Copley, SD}, title = {CodaChrome: a tool for the visualization of proteome conservation across all fully sequenced bacterial genomes.}, journal = {BMC genomics}, volume = {15}, number = {}, pages = {65}, pmid = {24460813}, issn = {1471-2164}, support = {R01 GM078554/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Bacteria/*genetics ; Databases, Genetic ; Enterococcus/genetics ; *Genome, Bacterial ; Helicobacter pylori/genetics ; Internet ; Proteome/*analysis/genetics ; Proteomics/*instrumentation ; RNA, Ribosomal, 16S/genetics ; *Software ; User-Computer Interface ; }, abstract = {BACKGROUND: The relationships between bacterial genomes are complicated by rampant horizontal gene transfer, varied selection pressures, acquisition of new genes, loss of genes, and divergence of genes, even in closely related lineages. As more and more bacterial genomes are sequenced, organizing and interpreting the incredible amount of relational information that connects them becomes increasingly difficult.<br><br>RESULTS: We have developed CodaChrome (http://www.sourceforge.com/p/codachrome), a one-versus-all proteome comparison tool that allows the user to visually investigate the relationship between a bacterial proteome of interest and the proteomes encoded by every other bacterial genome recorded in GenBank in a massive interactive heat map. This tool has allowed us to rapidly identify the most highly conserved proteins encoded in the bacterial pan-genome, fast-clock genes useful for subtyping of bacterial species, the evolutionary history of an indel in the Sphingobium lineage, and an example of horizontal gene transfer from a member of the genus Enterococcus to a recent ancestor of Helicobacter pylori.<br><br>CONCLUSION: CodaChrome is a user-friendly and powerful tool for simultaneously visualizing relationships between thousands of proteomes.}, }
@article {pmid24459831, year = {2013}, author = {Mechri, B and Medhioub, A and Medhioub, MN and Aouni, M}, title = {Genotypic diversity, antimicrobial resistance and screening of Vibrio cholerae molecular virulence markers in Vibrio alginolyticus strains recovered from a Tunisian Ruditapes decussatus hatchery.}, journal = {Polish journal of microbiology}, volume = {62}, number = {3}, pages = {263-272}, pmid = {24459831}, issn = {1733-1331}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics ; Bivalvia/growth &amp; development/*microbiology ; Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Genetic Markers ; *Genetic Variation ; Genotype ; HeLa Cells ; Humans ; Molecular Sequence Data ; Phylogeny ; Shellfish/*microbiology ; Tunisia ; Vibrio alginolyticus/classification/drug effects/*genetics/isolation &amp; purification ; Vibrio cholerae/*genetics ; Virulence Factors/genetics ; }, abstract = {In this study, a total of 54 Vibrio alginolyticus strains were analyzed. The isolates were recovered from different compartments of the Ruditapes decussatus hatchery in the National Institute of Marine Sciences and Technologies, Monastir, Tunisia. All isolates were biochemically identified (API 20E and API ZYM strips), characterized by amplification of the Hsp-40 gene polymerase chain reaction (PCR) and analyzed by enterobacterial repetitive intergenic consensus (ERIC)-based genotyping to evaluate genetic relationship between the isolated strains. We also looked for the presence of ten V cholera virulence genes (toxRS, toxR, toxT toxS, tcpP, tcpA, ace, vpi, zot and ctxA) in the genomes of Vibrio isolates. The antibiotics susceptibility, exoenzymes production and in vitro cytotoxic activitiy against HeLa cell line were also carried out for all tested bacteria. Most of V alginolyticus isolates showed significant antimicrobial resistance rates to at least ten antibacterial agents. For most isolates, the minimum inhibitory concentration (MIC) data showed that tetracydclin and streptomycin were the most effective antibiotics. Construction of the phylogenetic dendogram showed that studied isolates were in general genetically heterogeneous; however some Vibrio strains were present in different structures of the R. decussatus hatchery. The V cholerae virulence genes investigation showed a wild distribution of toxS (49/54), toxaR (45/54) and toxT (22/54) genes among V alginolyticus strains isolated from the R. decussatus rearing system. Cytotoxic effects of several Vibrio extracellular products (28154) were also observed on HeLa cells.}, }
@article {pmid24459285, year = {2014}, author = {Rossato, DO and Ludwig, A and Deprá, M and Loreto, EL and Ruiz, A and Valente, VL}, title = {BuT2 is a member of the third major group of hAT transposons and is involved in horizontal transfer events in the genus Drosophila.}, journal = {Genome biology and evolution}, volume = {6}, number = {2}, pages = {352-365}, pmid = {24459285}, issn = {1759-6653}, mesh = {Animals ; *DNA Transposable Elements ; Drosophila/classification/enzymology/*genetics ; Drosophila Proteins/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Phylogeny ; Transposases/genetics ; }, abstract = {The hAT superfamily comprises a large and diverse array of DNA transposons found in all supergroups of eukaryotes. Here we characterized the Drosophila buzzatii BuT2 element and found that it harbors a five-exon gene encoding a 643-aa putatively functional transposase. A phylogeny built with 85 hAT transposases yielded, in addition to the two major groups already described, Ac and Buster, a third one comprising 20 sequences that includes BuT2, Tip100, hAT-4_BM, and RP-hAT1. This third group is here named Tip. In addition, we studied the phylogenetic distribution and evolution of BuT2 by in silico searches and molecular approaches. Our data revealed BuT2 was, most often, vertically transmitted during the evolution of genus Drosophila being lost independently in several species. Nevertheless, we propose the occurrence of three horizontal transfer events to explain its distribution and conservation among species. Another aspect of BuT2 evolution and life cycle is the presence of short related sequences, which contain similar 5' and 3' regions, including the terminal inverted repeats. These sequences that can be considered as miniature inverted repeat transposable elements probably originated by internal deletion of complete copies and show evidences of recent mobilization.}, }
@article {pmid24458509, year = {2014}, author = {Colomer-Lluch, M and Jofre, J and Muniesa, M}, title = {Quinolone resistance genes (qnrA and qnrS) in bacteriophage particles from wastewater samples and the effect of inducing agents on packaged antibiotic resistance genes.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {69}, number = {5}, pages = {1265-1274}, doi = {10.1093/jac/dkt528}, pmid = {24458509}, issn = {1460-2091}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteriophages/*genetics/*isolation &amp; purification ; DNA, Viral/genetics ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Quinolones/*pharmacology ; Real-Time Polymerase Chain Reaction ; Wastewater/*virology ; }, abstract = {OBJECTIVES: This study quantifies quinolone antibiotic resistance genes (qnrA and qnrS) in DNA of phage particles isolated from faecally polluted waters and evaluates the influence of phage inducers on the abundance of antibiotic resistance genes in packaged DNA.<br><br>METHODS: qnrA and qnrS were quantified by qPCR in DNA of phage particles isolated from 18 raw urban wastewater samples, 18 river samples and 28 archived samples of animal wastewater. The bacterial fraction of the samples was treated with mitomycin C, ciprofloxacin, EDTA or sodium citrate under different conditions, and the number of resistance genes in DNA of phage particles was compared with the non-induced samples.<br><br>RESULTS: qnrA was more prevalent than qnrS, with 100% of positive samples in urban wastewater and river and 71.4% of positive samples in animal wastewater. Densities of qnrA ranged from 2.3&#x200a;&#xd7;&#x200a;10(2) gene copies (GC)/mL in urban wastewater to 7.4&#x200a;&#xd7;&#x200a;10(1) GC/mL in animal wastewater. qnrS was detected in 38.9% of urban wastewater samples, in 22.2% of river samples and only in one animal wastewater sample (3.6%). Despite the lower prevalence, qnrS densities reached values of 10(3) GC/mL. Both qnr genes and other resistance genes assayed (blaTEM and blaCTX-M) showed a significant increase in DNA of phage particles when treated with EDTA or sodium citrate, while mitomycin C and ciprofloxacin showed no effect under the different conditions assayed.<br><br>CONCLUSIONS: This study confirms the contribution of phages to the mobilization of resistance genes and the role of the environment and certain inducers in the spread of antibiotic resistance genes by means of phages.}, }
@article {pmid24458431, year = {2014}, author = {Molina, J and Hazzouri, KM and Nickrent, D and Geisler, M and Meyer, RS and Pentony, MM and Flowers, JM and Pelser, P and Barcelona, J and Inovejas, SA and Uy, I and Yuan, W and Wilkins, O and Michel, CI and Locklear, S and Concepcion, GP and Purugganan, MD}, title = {Possible loss of the chloroplast genome in the parasitic flowering plant Rafflesia lagascae (Rafflesiaceae).}, journal = {Molecular biology and evolution}, volume = {31}, number = {4}, pages = {793-803}, pmid = {24458431}, issn = {1537-1719}, mesh = {Evolution, Molecular ; *Genome, Chloroplast ; Magnoliopsida/*genetics ; Mitochondria/genetics ; Photosynthesis/genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Rafflesia is a genus of holoparasitic plants endemic to Southeast Asia that has lost the ability to undertake photosynthesis. With short-read sequencing technology, we assembled a draft sequence of the mitochondrial genome of Rafflesia lagascae Blanco, a species endemic to the Philippine island of Luzon, with ∼350× sequencing depth coverage. Using multiple approaches, however, we were only able to identify small fragments of plastid sequences at low coverage depth (<2×) and could not recover any substantial portion of a chloroplast genome. The gene fragments we identified included photosynthesis and energy production genes (atp, ndh, pet, psa, psb, rbcL), ribosomal RNA genes (rrn16, rrn23), ribosomal protein genes (rps7, rps11, rps16), transfer RNA genes, as well as matK, accD, ycf2, and multiple nongenic regions from the inverted repeats. None of the identified plastid gene sequences had intact reading frames. Phylogenetic analysis suggests that ∼33% of these remnant plastid genes may have been horizontally transferred from the host plant genus Tetrastigma with the rest having ambiguous phylogenetic positions (<50% bootstrap support), except for psaB that was strongly allied with the plastid homolog in Nicotiana. Our inability to identify substantial plastid genome sequences from R. lagascae using multiple approaches--despite success in identifying and developing a draft assembly of the much larger mitochondrial genome--suggests that the parasitic plant genus Rafflesia may be the first plant group for which there is no recognizable plastid genome, or if present is found in cryptic form at very low levels.}, }
@article {pmid24458378, year = {2014}, author = {Nguyen, AN and Jacq, A}, title = {Small RNAs in the Vibrionaceae: an ocean still to be explored.}, journal = {Wiley interdisciplinary reviews. RNA}, volume = {5}, number = {3}, pages = {381-392}, doi = {10.1002/wrna.1218}, pmid = {24458378}, issn = {1757-7012}, mesh = {Animals ; Evolution, Molecular ; *Gene Expression Regulation, Bacterial ; Gram-Negative Bacterial Infections/microbiology ; Humans ; Iron/metabolism ; Quorum Sensing ; RNA, Bacterial/*genetics/metabolism ; RNA, Small Untranslated/*genetics/metabolism ; Vibrionaceae/*genetics/pathogenicity/physiology ; }, abstract = {In bacteria, the discovery of noncoding small RNAs (sRNAs) as modulators of gene expression in response to environmental signals has brought new insights into bacterial gene regulation, including control of pathogenicity. The Vibrionaceae constitute a family of marine bacteria of which many are responsible for infections affecting not only humans, such as Vibrio cholerae but also fish and marine invertebrates, representing the major cause of mortality in farmed marine species. They are able to colonize many habitats, existing as planktonic forms, in biofilms or associated with various hosts. This high adaptability is linked to their capacity to generate genetic diversity, in part through lateral gene transfer, but also by varying gene expression control. In the recent years, several major studies have illustrated the importance of small regulatory sRNAs in the Vibrionaceae for the control of pathogenicity and adaptation to environment and nutrient sources such as chitin, especially in V. cholerae and Vibrio harveyi. The existence of a complex regulatory network controlled by quorum sensing has been demonstrated in which sRNAs play central roles. This review covers major advances made in the discovery and elucidation of functions of Vibrionaceae sRNAs within the last 10 years.}, }
@article {pmid24454864, year = {2014}, author = {Kodavali, PK and Dudkiewicz, M and Pikuła, S and Pawłowski, K}, title = {Bioinformatics analysis of bacterial annexins--putative ancestral relatives of eukaryotic annexins.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e85428}, pmid = {24454864}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Animals ; Annexins/chemistry/*genetics ; Bacteria/genetics ; Bacterial Proteins/chemistry/*genetics ; Computational Biology ; Conserved Sequence ; Humans ; Molecular Sequence Annotation ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Tertiary ; }, abstract = {Annexins are Ca(2+)-binding, membrane-interacting proteins, widespread among eukaryotes, consisting usually of four structurally similar repeated domains. It is accepted that vertebrate annexins derive from a double genome duplication event. It has been postulated that a single domain annexin, if found, might represent a molecule related to the hypothetical ancestral annexin. The recent discovery of a single-domain annexin in a bacterium, Cytophaga hutchinsonii, apparently confirmed this hypothesis. Here, we present a more complex picture. Using remote sequence similarity detection tools, a survey of bacterial genomes was performed in search of annexin-like proteins. In total, we identified about thirty annexin homologues, including single-domain and multi-domain annexins, in seventeen bacterial species. The thorough search yielded, besides the known annexin homologue from C. hutchinsonii, homologues from the Bacteroidetes/Chlorobi phylum, from Gemmatimonadetes, from beta- and delta-Proteobacteria, and from Actinobacteria. The sequences of bacterial annexins exhibited remote but statistically significant similarity to sequence profiles built of the eukaryotic ones. Some bacterial annexins are equipped with additional, different domains, for example those characteristic for toxins. The variation in bacterial annexin sequences, much wider than that observed in eukaryotes, and different domain architectures suggest that annexins found in bacteria may actually descend from an ancestral bacterial annexin, from which eukaryotic annexins also originate. The hypothesis of an ancient origin of bacterial annexins has to be reconciled with the fact that remarkably few bacterial strains possess annexin genes compared to the thousands of known bacterial genomes and with the patchy, anomalous phylogenetic distribution of bacterial annexins. Thus, a massive annexin gene loss in several bacterial lineages or very divergent evolution would appear a likely explanation. Alternative evolutionary scenarios, involving horizontal gene transfer between bacteria and protozoan eukaryotes, in either direction, appear much less likely. Altogether, current evidence does not allow unequivocal judgement as to the origin of bacterial annexins.}, }
@article {pmid24454682, year = {2014}, author = {Bingle, LE and Constantinidou, C and Shaw, RK and Islam, MS and Patel, M and Snyder, LA and Lee, DJ and Penn, CW and Busby, SJ and Pallen, MJ}, title = {Microarray analysis of the Ler regulon in enteropathogenic and enterohaemorrhagic Escherichia coli strains.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e80160}, pmid = {24454682}, issn = {1932-6203}, support = {BB/C516701/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/E020860/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Adaptation, Physiological/genetics ; Enterohemorrhagic Escherichia coli/*genetics/physiology ; Enteropathogenic Escherichia coli/*genetics/physiology ; Escherichia coli Proteins/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/genetics ; *Oligonucleotide Array Sequence Analysis ; Regulon/*genetics ; Trans-Activators/*genetics ; Transcription, Genetic/genetics ; }, abstract = {The type III protein secretion system is an important pathogenicity factor of enteropathogenic and enterohaemorrhagic Escherichia coli pathotypes. The genes encoding this apparatus are located on a pathogenicity island (the locus of enterocyte effacement) and are transcriptionally activated by the master regulator Ler. In each pathotype Ler is also known to regulate genes located elsewhere on the chromosome, but the full extent of the Ler regulon is unclear, especially for enteropathogenic E. coli. The Ler regulon was defined for two strains of E. coli: E2348/69 (enteropathogenic) and EDL933 (enterohaemorrhagic) in mid and late log phases of growth by DNA microarray analysis of the transcriptomes of wild-type and ler mutant versions of each strain. In both strains the Ler regulon is focused on the locus of enterocyte effacement - all major transcriptional units of which are activated by Ler, with the sole exception of the LEE1 operon during mid-log phase growth in E2348/69. However, the Ler regulon does extend more widely and also includes unlinked pathogenicity genes: in E2348/69 more than 50 genes outside of this locus were regulated, including a number of known or potential pathogenicity determinants; in EDL933 only 4 extra-LEE genes, again including known pathogenicity factors, were activated. In E2348/69, where the Ler regulon is clearly growth phase dependent, a number of genes including the plasmid-encoded regulator operon perABC, were found to be negatively regulated by Ler. Negative regulation by Ler of PerC, itself a positive regulator of the ler promoter, suggests a negative feedback loop involving these proteins.}, }
@article {pmid24454310, year = {2014}, author = {Yue, M and Schifferli, DM}, title = {Allelic variation in Salmonella: an underappreciated driver of adaptation and virulence.}, journal = {Frontiers in microbiology}, volume = {4}, number = {}, pages = {419}, pmid = {24454310}, issn = {1664-302X}, support = {R21 AI098041/AI/NIAID NIH HHS/United States ; }, abstract = {Salmonella enterica causes substantial morbidity and mortality in humans and animals. Infection and intestinal colonization by S. enterica require virulence factors that mediate bacterial binding and invasion of enterocytes and innate immune cells. Some S. enterica colonization factors and their alleles are host restricted, suggesting a potential role in regulation of host specificity. Recent data also suggest that colonization factors promote horizontal gene transfer of antimicrobial resistance genes by increasing the local density of Salmonella in colonized intestines. Although a profusion of genes are involved in Salmonella pathogenesis, the relative importance of their allelic variation has only been studied intensely in the type 1 fimbrial adhesin FimH. Although other Salmonella virulence factors demonstrate allelic variation, their association with specific metadata (e.g., host species, disease or carrier state, time and geographic place of isolation, antibiotic resistance profile, etc.) remains to be interrogated. To date, genome-wide association studies (GWAS) in bacteriology have been limited by the paucity of relevant metadata. In addition, due to the many variables amid metadata categories, a very large number of strains must be assessed to attain statistically significant results. However, targeted approaches in which genes of interest (e.g., virulence factors) are specifically sequenced alleviates the time-consuming and costly statistical GWAS analysis and increases statistical power, as larger numbers of strains can be screened for non-synonymous single nucleotide polymorphisms (SNPs) that are associated with available metadata. Congruence of specific allelic variants with specific metadata from strains that have a relevant clinical and epidemiological history will help to prioritize functional wet-lab and animal studies aimed at determining cause-effect relationships. Such an approach should be applicable to other pathogens that are being collected in well-curated repositories.}, }
@article {pmid24451210, year = {2014}, author = {Yabuki, A and Toyofuku, T and Takishita, K}, title = {Lateral transfer of eukaryotic ribosomal RNA genes: an emerging concern for molecular ecology of microbial eukaryotes.}, journal = {The ISME journal}, volume = {8}, number = {7}, pages = {1544-1547}, pmid = {24451210}, issn = {1751-7370}, mesh = {Alveolata/classification/genetics ; Ecosystem ; *Gene Transfer, Horizontal ; *Genes, rRNA ; Phylogeny ; RNA, Ribosomal, 18S/*genetics ; Stramenopiles/classification/*genetics ; }, abstract = {Ribosomal RNA (rRNA) genes are widely utilized in depicting organismal diversity and distribution in a wide range of environments. Although a few cases of lateral transfer of rRNA genes between closely related prokaryotes have been reported, it remains to be reported from eukaryotes. Here, we report the first case of lateral transfer of eukaryotic rRNA genes. Two distinct sequences of the 18S rRNA gene were detected from a clonal culture of the stramenopile, Ciliophrys infusionum. One was clearly derived from Ciliophrys, but the other gene originated from a perkinsid alveolate. Genome-walking analyses revealed that this alveolate-type rRNA gene is immediately adjacent to two protein-coding genes (ubc12 and usp39), and the origin of both genes was shown to be a stramenopile (that is, Ciliophrys) in our phylogenetic analyses. These findings indicate that the alveolate-type rRNA gene is encoded on the Ciliophrys genome and that eukaryotic rRNA genes can be transferred laterally.}, }
@article {pmid24451209, year = {2014}, author = {Wu, H and Fang, Y and Yu, J and Zhang, Z}, title = {The quest for a unified view of bacterial land colonization.}, journal = {The ISME journal}, volume = {8}, number = {7}, pages = {1358-1369}, pmid = {24451209}, issn = {1751-7370}, mesh = {Adaptation, Physiological ; Animals ; Aquatic Organisms/genetics/pathogenicity ; Bacteria/classification/*genetics ; Base Composition ; Biological Evolution ; DNA Polymerase III/*genetics ; *Ecosystem ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Metagenome ; *Phylogeny ; Plants/microbiology ; }, abstract = {Exploring molecular mechanisms underlying bacterial water-to-land transition represents a critical start toward a better understanding of the functioning and stability of the terrestrial ecosystems. Here, we perform comprehensive analyses based on a large variety of bacteria by integrating taxonomic, phylogenetic and metagenomic data, in the quest for a unified view that elucidates genomic, evolutionary and ecological dynamics of the marine progenitors in adapting to nonaquatic environments. We hypothesize that bacterial land colonization is dominated by a single-gene sweep, that is, the emergence of dnaE2 derived from an early duplication event of the primordial dnaE, followed by a series of niche-specific genomic adaptations, including GC content increase, intensive horizontal gene transfer and constant genome expansion. In addition, early bacterial radiation may be stimulated by an explosion of land-borne hosts (for example, plants and animals) after initial land colonization events.}, }
@article {pmid24448981, year = {2014}, author = {Imanian, B and Keeling, PJ}, title = {Horizontal gene transfer and redundancy of tryptophan biosynthetic enzymes in dinotoms.}, journal = {Genome biology and evolution}, volume = {6}, number = {2}, pages = {333-343}, pmid = {24448981}, issn = {1759-6653}, mesh = {Biosynthetic Pathways ; Dinoflagellida/chemistry/classification/*enzymology/*genetics/metabolism ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; Protozoan Proteins/chemistry/*genetics ; Tryptophan/*biosynthesis ; }, abstract = {A tertiary endosymbiosis between a dinoflagellate host and diatom endosymbiont gave rise to "dinotoms," cells with a unique nuclear and mitochondrial redundancy derived from two evolutionarily distinct eukaryotic lineages. To examine how this unique redundancy might have affected the evolution of metabolic systems, we investigated the transcription of genes involved in biosynthesis of the amino acid tryptophan in three species, Durinskia baltica, Kryptoperidinium foliaceum, and Glenodinium foliaceum. From transcriptome sequence data, we recovered two distinct sets of protein-coding transcripts covering the entire tryptophan biosynthetic pathway. Phylogenetic analyses suggest a diatom origin for one set of the proteins, which we infer to be expressed in the endosymbiont, and that the other arose from multiple horizontal gene transfer events to the dinoflagellate ancestor of the host lineage. This is the first indication that these cells retain redundant sets of transcripts and likely metabolic pathways for the biosynthesis of small molecules and extend their redundancy to their two distinct nuclear genomes.}, }
@article {pmid24441525, year = {2014}, author = {Su, HC and Ying, GG and He, LY and Liu, YS and Zhang, RQ and Tao, R}, title = {Antibiotic resistance, plasmid-mediated quinolone resistance (PMQR) genes and ampC gene in two typical municipal wastewater treatment plants.}, journal = {Environmental science. Processes &amp; impacts}, volume = {16}, number = {2}, pages = {324-332}, doi = {10.1039/c3em00555k}, pmid = {24441525}, issn = {2050-7895}, mesh = {Bacterial Proteins/analysis ; Drug Resistance, Microbial/*genetics ; *Genes, Bacterial ; Waste Disposal Facilities ; *Waste Disposal, Fluid ; Wastewater/*microbiology ; *Water Microbiology ; beta-Lactamases/analysis ; }, abstract = {Antibiotic resistant bacteria and plasmid-mediated quinolone resistance genes and ampC gene were investigated for Escherichia coli isolates from two typical municipal wastewater treatment plants in both dry and wet seasons by using the antibiotic susceptibility test and PCR assay, respectively. The results showed that 98.4% of the isolates (1056) were found resistant to antibiotic(s) tested and 90.6% showed multiple resistances to at least three antibiotics. Tetracycline was found to have the highest resistance frequency (70.8%), followed by ampicillin (65.1%), whereas ceftazidime had the lowest resistance frequency of 9.0%. Moreover, 39.2% of the E. coli isolates were carrying plasmids. intI1 had the highest detection rate in the plasmids (38.1%), followed by qnrS, ampC, qnrB, intI2 and aac(6')-Ib-cr. The disinfection process (UV and chlorination) could significantly reduce the number of bacteria, but percentage of the resistant bacteria, resistance frequency for each antibiotic, MAR index and detection rate of the plasmid-mediated resistance genes were all found increasing in the effluents of biological units. The results of this study showed that a more frequent horizontal gene transfer occurred in the biological units. Wastewater treatment plants were an important medium for the recombination and dissemination of antibiotic resistance genes in the environment.}, }
@article {pmid24439196, year = {2014}, author = {Lindsay, JA}, title = {Staphylococcus aureus genomics and the impact of horizontal gene transfer.}, journal = {International journal of medical microbiology : IJMM}, volume = {304}, number = {2}, pages = {103-109}, doi = {10.1016/j.ijmm.2013.11.010}, pmid = {24439196}, issn = {1618-0607}, mesh = {*Adaptation, Biological ; Animals ; DNA Restriction-Modification Enzymes ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genetic Variation ; *Genomics ; Humans ; Selection, Genetic ; Staphylococcal Infections/microbiology ; Staphylococcus aureus/classification/*genetics ; }, abstract = {Whole genome sequencing and microarrays have revealed the population structure of Staphylococcus aureus, and identified epidemiological shifts, transmission routes, and adaptation of major clones. S. aureus genomes are highly diverse. This is partly due to a population structure of conserved lineages, each with unique combinations of genes encoding surface proteins, regulators, immune evasion and virulence pathways. Even more variable are the mobile genetic elements (MGE), which encode key proteins for antibiotic resistance, virulence and host-adaptation. MGEs can transfer at high frequency between isolates of the same lineage by horizontal gene transfer (HGT). There is increasing evidence that HGT is key to bacterial adaptation and success. Recent studies have shed light on new mechanisms of DNA transfer such as transformation, the identification of receptors for transduction, on integration of DNA pathways, mechanisms blocking transfer including CRISPR and new restriction systems, strategies for evasion of restriction barriers, as well as factors influencing MGE selection and stability. These studies have also lead to new tools enabling construction of genetically modified clinical S. aureus isolates. This review will focus on HGT mechanisms and their importance in shaping the evolution of new clones adapted to antibiotic resistance, healthcare, communities and livestock.}, }
@article {pmid24432015, year = {2014}, author = {Nielsen, KM and Bøhn, T and Townsend, JP}, title = {Detecting rare gene transfer events in bacterial populations.}, journal = {Frontiers in microbiology}, volume = {4}, number = {}, pages = {415}, pmid = {24432015}, issn = {1664-302X}, abstract = {Horizontal gene transfer (HGT) enables bacteria to access, share, and recombine genetic variation, resulting in genetic diversity that cannot be obtained through mutational processes alone. In most cases, the observation of evolutionary successful HGT events relies on the outcome of initially rare events that lead to novel functions in the new host, and that exhibit a positive effect on host fitness. Conversely, the large majority of HGT events occurring in bacterial populations will go undetected due to lack of replication success of transformants. Moreover, other HGT events that would be highly beneficial to new hosts can fail to ensue due to lack of physical proximity to the donor organism, lack of a suitable gene transfer mechanism, genetic compatibility, and stochasticity in tempo-spatial occurrence. Experimental attempts to detect HGT events in bacterial populations have typically focused on the transformed cells or their immediate offspring. However, rare HGT events occurring in large and structured populations are unlikely to reach relative population sizes that will allow their immediate identification; the exception being the unusually strong positive selection conferred by antibiotics. Most HGT events are not expected to alter the likelihood of host survival to such an extreme extent, and will confer only minor changes in host fitness. Due to the large population sizes of bacteria and the time scales involved, the process and outcome of HGT are often not amenable to experimental investigation. Population genetic modeling of the growth dynamics of bacteria with differing HGT rates and resulting fitness changes is therefore necessary to guide sampling design and predict realistic time frames for detection of HGT, as it occurs in laboratory or natural settings. Here we review the key population genetic parameters, consider their complexity and highlight knowledge gaps for further research.}, }
@article {pmid24428587, year = {2014}, author = {Fontanez, KM and Cavanaugh, CM}, title = {Evidence for horizontal transmission from multilocus phylogeny of deep-sea mussel (Mytilidae) symbionts.}, journal = {Environmental microbiology}, volume = {16}, number = {12}, pages = {3608-3621}, doi = {10.1111/1462-2920.12379}, pmid = {24428587}, issn = {1462-2920}, mesh = {Animals ; Bacteria/*genetics ; Bacterial Physiological Phenomena ; Biofilms ; Environment ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, rRNA ; Genome, Bacterial ; *Hydrothermal Vents ; Mytilidae/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Symbiosis/*genetics ; }, abstract = {Many invertebrates at deep-sea hydrothermal vents depend upon bacterial symbionts for nutrition, and thus the mechanism of symbiont transmission, vertical (via the egg or sperm) or horizontal (from environment or contemporary hosts) is critically important. Under a strict maternal transmission model, symbiont and host mitochondrial genomes pass through the same individuals leading to congruent host-symbiont phylogenies. In contrast, horizontally transmitted symbionts are environmentally acquired, leading to incongruent host-symbiont phylogenies. Each of these transmission strategies is predicted to have different consequences for symbiont ecology and genome evolution. Deep-sea mussels (Bathymodiolinae) are globally distributed at deep-sea hydrothermal vents, depend upon chemoautotrophic symbionts for their survival, and are hypothesized to transmit their symbionts horizontally. This study explored bathymodioline symbiont ecology through quantification of symbionts at two hydrothermal vent sites and symbiont evolution using functional gene phylogenies. These phylogenies revealed a dramatically more complex evolutionary history than 16S ribosomal RNA phylogenies, suggesting that horizontal gene transfer may have played an important role in symbiont gene evolution. Tests of the strict maternal transmission hypothesis found that host-symbiont lineages were significantly decoupled across multiple genes. These findings expand our understanding of symbiont ecology and evolution, and provide the strongest evidence yet for horizontal transmission of bathymodioline symbionts.}, }
@article {pmid24426125, year = {2013}, author = {Lalzampuia, H and Dutta, TK and Warjri, I and Chandra, R}, title = {PCR-Based Detection of Extended-Spectrum β-Lactamases (bla CTX-M-1 and bla TEM) in Escherichia coli, Salmonella spp. and Klebsiella pneumoniae Isolated from Pigs in North Eastern India (Mizoram).}, journal = {Indian journal of microbiology}, volume = {53}, number = {3}, pages = {291-296}, pmid = {24426125}, issn = {0046-8991}, abstract = {Cephalosporins are major antimicrobials used to treat serious infections. However, their effectiveness is being compromised by the emergence of extended-spectrum β-lactamases (ESBLs). A total of 138 enteric bacteria were isolated from 53 faecal samples of pigs collected from different districts of Mizoram, of which 102 (73.91 %) were Escherichia coli, 26 (18.84 %) were Salmonella spp. and 10 (7.25 %) were Klebsiella pneumoniae. Phenotypic confirmatory test (Double Discs Synergy Test) showed that 8 (5.80 %) E. coli isolates were ESBLs producer. PCR analysis confirmed that out of the eight isolate, 7 (5.07 %) harboured bla CTX-M-1 gene and/or bla TEM gene. Of the eight positive isolates, 7 (5.07 %) and 3 (2.17 %) were found to be positive for bla CTX-M-1 gene and bla TEM gene, respectively, of which 3 (2.17 %) isolates were positive for both the genes. Only 4 (2.90 %) E. coli isolates carried bla CTX-M-1 gene alone. Agarose gel electrophoresis showed that all the isolates were carrying plasmids ranging between 0.9 and ~30 kb. Out of the seven isolates positive for bla CTX-M-1 and/or bla TEM , 2 (1.84 %) isolates were confirmed for bla CTX-M-1 gene in their plasmid. Only one E. coli isolate was found to be positive for both the genes in its plasmid. The resistance plasmid could not be transferred to a recipient by in vitro horizontal gene transfer method.}, }
@article {pmid24416416, year = {2014}, author = {Kienesberger, S and Sprenger, H and Wolfgruber, S and Halwachs, B and Thallinger, GG and Perez-Perez, GI and Blaser, MJ and Zechner, EL and Gorkiewicz, G}, title = {Comparative genome analysis of Campylobacter fetus subspecies revealed horizontally acquired genetic elements important for virulence and niche specificity.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e85491}, pmid = {24416416}, issn = {1932-6203}, support = {P 20479/FWF_/Austrian Science Fund FWF/Austria ; R01 GM063270/GM/NIGMS NIH HHS/United States ; GM63270/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacterial Secretion Systems/genetics ; Base Sequence ; Campylobacter Infections/microbiology ; Campylobacter fetus/classification/*genetics/*pathogenicity ; Cattle ; Chromosome Mapping ; Chromosomes, Bacterial/*chemistry ; DNA, Bacterial/*genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Host Specificity ; Humans ; Lipopolysaccharides/biosynthesis/genetics ; Molecular Sequence Data ; Sequence Analysis, DNA ; Species Specificity ; Synteny ; Virulence ; }, abstract = {Campylobacter fetus are important animal and human pathogens and the two major subspecies differ strikingly in pathogenicity. C. fetus subsp. venerealis is highly niche-adapted, mainly infecting the genital tract of cattle. C. fetus subsp. fetus has a wider host-range, colonizing the genital- and intestinal-tract of animals and humans. We report the complete genomic sequence of C. fetus subsp. venerealis 84-112 and comparisons to the genome of C. fetus subsp. fetus 82-40. Functional analysis of genes predicted to be involved in C. fetus virulence was performed. The two subspecies are highly syntenic with 92% sequence identity but C. fetus subsp. venerealis has a larger genome and an extra-chromosomal element. Aside from apparent gene transfer agents and hypothetical proteins, the unique genes in both subspecies comprise two known functional groups: lipopolysaccharide production, and type IV secretion machineries. Analyses of lipopolysaccharide-biosynthesis genes in C. fetus isolates showed linkage to particular pathotypes, and mutational inactivation demonstrated their roles in regulating virulence and host range. The comparative analysis presented here broadens knowledge of the genomic basis of C. fetus pathogenesis and host specificity. It further highlights the importance of surface-exposed structures to C. fetus pathogenicity and demonstrates how evolutionary forces optimize the fitness and host-adaptation of these pathogens.}, }
@article {pmid24416331, year = {2014}, author = {Gardiner, DM and Upadhyaya, NM and Stiller, J and Ellis, JG and Dodds, PN and Kazan, K and Manners, JM}, title = {Genomic analysis of Xanthomonas translucens pathogenic on wheat and barley reveals cross-kingdom gene transfer events and diverse protein delivery systems.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e84995}, pmid = {24416331}, issn = {1932-6203}, mesh = {Adenylyl Cyclases/genetics/metabolism ; Amino Acid Sequence ; Bacterial Proteins/genetics/metabolism ; Bacterial Secretion Systems ; Fusarium/genetics ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Genes, Reporter ; *Genome, Bacterial ; Genomic Islands ; Hordeum/*microbiology ; Mitochondrial Proton-Translocating ATPases/genetics/metabolism ; Molecular Sequence Data ; Multigene Family ; Oryza/microbiology ; Phylogeny ; Plant Diseases/microbiology ; Protein Subunits/genetics/metabolism ; Protein Transport ; Species Specificity ; Triticum/*microbiology ; Virulence ; Xanthomonas/classification/*genetics/*pathogenicity ; }, abstract = {In comparison to dicot-infecting bacteria, only limited numbers of genome sequences are available for monocot-infecting and in particular cereal-infecting bacteria. Herein we report the characterisation and genome sequence of Xanthomonas translucens isolate DAR61454 pathogenic on wheat and barley. Based on phylogenetic analysis of the ATP synthase beta subunit (atpD) gene, DAR61454 is most closely related to other X. translucens strains and the sugarcane- and banana- infecting Xanthomonas strains, but shares a type III secretion system (T3SS) with X. translucens pv. graminis and more distantly related xanthomonads. Assays with an adenylate cyclase reporter protein demonstrate that DAR61454's T3SS is functional in delivering proteins to wheat cells. X. translucens DAR61454 also encodes two type VI secretion systems with one most closely related to those found in some strains of the rice infecting strain X. oryzae pv. oryzae but not other xanthomonads. Comparative analysis of 18 different Xanthomonas isolates revealed 84 proteins unique to cereal (i.e. rice) infecting isolates and the wheat/barley infecting DAR61454. Genes encoding 60 of these proteins are found in gene clusters in the X. translucens DAR61454 genome, suggesting cereal-specific pathogenicity islands. However, none of the cereal pathogen specific proteins were homologous to known Xanthomonas spp. effectors. Comparative analysis outside of the bacterial kingdom revealed a nucleoside triphosphate pyrophosphohydrolase encoding gene in DAR61454 also present in other bacteria as well as a number of pathogenic Fusarium species, suggesting that this gene may have been transmitted horizontally from bacteria to the Fusarium lineage of pathogenic fungi. This example further highlights the importance of horizontal gene acquisition from bacteria in the evolution of fungi.}, }
@article {pmid24415958, year = {2014}, author = {Wang, D and Ning, K and Li, J and Hu, J and Han, D and Wang, H and Zeng, X and Jing, X and Zhou, Q and Su, X and Chang, X and Wang, A and Wang, W and Jia, J and Wei, L and Xin, Y and Qiao, Y and Huang, R and Chen, J and Han, B and Yoon, K and Hill, RT and Zohar, Y and Chen, F and Hu, Q and Xu, J}, title = {Nannochloropsis genomes reveal evolution of microalgal oleaginous traits.}, journal = {PLoS genetics}, volume = {10}, number = {1}, pages = {e1004094}, pmid = {24415958}, issn = {1553-7404}, mesh = {Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; *Genome ; Microalgae/*genetics ; Molecular Sequence Annotation ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Transcriptome ; Triglycerides/biosynthesis/*genetics ; }, abstract = {Oleaginous microalgae are promising feedstock for biofuels, yet the genetic diversity, origin and evolution of oleaginous traits remain largely unknown. Here we present a detailed phylogenomic analysis of five oleaginous Nannochloropsis species (a total of six strains) and one time-series transcriptome dataset for triacylglycerol (TAG) synthesis on one representative strain. Despite small genome sizes, high coding potential and relative paucity of mobile elements, the genomes feature small cores of ca. 2,700 protein-coding genes and a large pan-genome of >38,000 genes. The six genomes share key oleaginous traits, such as the enrichment of selected lipid biosynthesis genes and certain glycoside hydrolase genes that potentially shift carbon flux from chrysolaminaran to TAG synthesis. The eleven type II diacylglycerol acyltransferase genes (DGAT-2) in every strain, each expressed during TAG synthesis, likely originated from three ancient genomes, including the secondary endosymbiosis host and the engulfed green and red algae. Horizontal gene transfers were inferred in most lipid synthesis nodes with expanded gene doses and many glycoside hydrolase genes. Thus multiple genome pooling and horizontal genetic exchange, together with selective inheritance of lipid synthesis genes and species-specific gene loss, have led to the enormous genetic apparatus for oleaginousness and the wide genomic divergence among present-day Nannochloropsis. These findings have important implications in the screening and genetic engineering of microalgae for biofuels.}, }
@article {pmid24411460, year = {2014}, author = {Yang, CW and Chang, YT and Chao, WL and Shiung, II and Lin, HS and Chen, H and Ho, SH and Lu, MJ and Lee, PH and Fan, SN}, title = {An investigation of total bacterial communities, culturable antibiotic-resistant bacterial communities and integrons in the river water environments of Taipei city.}, journal = {Journal of hazardous materials}, volume = {277}, number = {}, pages = {159-168}, doi = {10.1016/j.jhazmat.2013.12.046}, pmid = {24411460}, issn = {1873-3336}, mesh = {Anti-Bacterial Agents/*toxicity ; Bacteria/*drug effects/genetics ; Cities ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal/drug effects ; Genes, Bacterial/drug effects ; Integrons/drug effects/genetics ; RNA, Ribosomal, 16S ; *Rivers/chemistry/microbiology ; Taiwan ; *Water Microbiology ; Water Pollutants, Chemical/*toxicity ; }, abstract = {The intensive use of antibiotics may accelerate the development of antibiotic-resistant bacteria (ARB). The global geographical distribution of environmental ARB has been indicated by many studies. However, the ARB in the water environments of Taiwan has not been extensively investigated. The objective of this study was to investigate the communities of ARB in Huanghsi Stream, which presents a natural acidic (pH 4) water environment. Waishuanghsi Stream provides a neutral (pH 7) water environment and was thus also monitored to allow comparison. The plate counts of culturable bacteria in eight antibiotics indicate that the numbers of culturable carbenicillin- and vancomycin-resistant bacteria in both Huanghsi and Waishuanghsi Streams are greater than the numbers of culturable bacteria resistant to the other antibiotics tested. Using a 16S rDNA sequencing approach, both the antibiotic-resistant bacterial communities (culture-based) and the total bacterial communities (metagenome-based) in Waishuanghsi Stream exhibit a higher diversity than those in Huanghsi Stream were observed. Of the three classes of integron, only class I integrons were identified in Waishuanghsi Stream. Our results suggest that an acidic (pH 4) water environment may not only affect the community composition of antibiotic-resistant bacteria but also the horizontal gene transfer mediated by integrons.}, }
@article {pmid24411025, year = {2014}, author = {Zhang, D and Qi, J and Yue, J and Huang, J and Sun, T and Li, S and Wen, JF and Hettenhausen, C and Wu, J and Wang, L and Zhuang, H and Wu, J and Sun, G}, title = {Root parasitic plant Orobanche aegyptiaca and shoot parasitic plant Cuscuta australis obtained Brassicaceae-specific strictosidine synthase-like genes by horizontal gene transfer.}, journal = {BMC plant biology}, volume = {14}, number = {}, pages = {19}, pmid = {24411025}, issn = {1471-2229}, mesh = {Brassicaceae/*genetics/parasitology ; Carbon-Nitrogen Lyases/genetics/metabolism ; Cuscuta/*genetics ; Gene Transfer, Horizontal/*genetics ; Orobanche/*genetics ; Plant Proteins/genetics/metabolism ; Plant Roots/genetics/*parasitology ; }, abstract = {BACKGROUND: Besides gene duplication and de novo gene generation, horizontal gene transfer (HGT) is another important way of acquiring new genes. HGT may endow the recipients with novel phenotypic traits that are important for species evolution and adaption to new ecological niches. Parasitic systems expectedly allow the occurrence of HGT at relatively high frequencies due to their long-term physical contact. In plants, a number of HGT events have been reported between the organelles of parasites and the hosts, but HGT between host and parasite nuclear genomes has rarely been found.<br><br>RESULTS: A thorough transcriptome screening revealed that a strictosidine synthase-like (SSL) gene in the root parasitic plant Orobanche aegyptiaca and the shoot parasitic plant Cuscuta australis showed much higher sequence similarities with those in Brassicaceae than with those in their close relatives, suggesting independent gene horizontal transfer events from Brassicaceae to these parasites. These findings were strongly supported by phylogenetic analysis and their identical unique amino acid residues and deletions. Intriguingly, the nucleus-located SSL genes in Brassicaceae belonged to a new member of SSL gene family, which were originated from gene duplication. The presence of introns indicated that the transfer occurred directly by DNA integration in both parasites. Furthermore, positive selection was detected in the foreign SSL gene in O. aegyptiaca but not in C. australis. The expression of the foreign SSL genes in these two parasitic plants was detected in multiple development stages and tissues, and the foreign SSL gene was induced after wounding treatment in C. australis stems. These data imply that the foreign genes may still retain certain functions in the recipient species.<br><br>CONCLUSIONS: Our study strongly supports that parasitic plants can gain novel nuclear genes from distantly related host species by HGT and the foreign genes may execute certain functions in the new hosts.}, }
@article {pmid24410921, year = {2014}, author = {Cooper, KK and Mandrell, RE and Louie, JW and Korlach, J and Clark, TA and Parker, CT and Huynh, S and Chain, PS and Ahmed, S and Carter, MQ}, title = {Comparative genomics of enterohemorrhagic Escherichia coli O145:H28 demonstrates a common evolutionary lineage with Escherichia coli O157:H7.}, journal = {BMC genomics}, volume = {15}, number = {}, pages = {17}, pmid = {24410921}, issn = {1471-2164}, mesh = {*Biological Evolution ; Enterohemorrhagic Escherichia coli/classification/genetics/virology ; Escherichia coli/*classification/*genetics/virology ; Escherichia coli O157/*classification/genetics/virology ; Escherichia coli Proteins/genetics/metabolism ; *Genome, Bacterial ; Genomics ; Methyltransferases/genetics/metabolism ; Phylogeny ; Prophages/metabolism ; Serotyping ; Shiga Toxin/genetics ; Shigella/classification/genetics ; Virulence Factors/genetics ; }, abstract = {BACKGROUND: Although serotype O157:H7 is the predominant enterohemorrhagic Escherichia coli (EHEC), outbreaks of non-O157 EHEC that cause severe foodborne illness, including hemolytic uremic syndrome have increased worldwide. In fact, non-O157 serotypes are now estimated to cause over half of all the Shiga toxin-producing Escherichia coli (STEC) cases, and outbreaks of non-O157 EHEC infections are frequently associated with serotypes O26, O45, O103, O111, O121, and O145. Currently, there are no complete genomes for O145 in public databases.<br><br>RESULTS: We determined the complete genome sequences of two O145 strains (EcO145), one linked to a US lettuce-associated outbreak (RM13514) and one to a Belgium ice-cream-associated outbreak (RM13516). Both strains contain one chromosome and two large plasmids, with genome sizes of 5,737,294 bp for RM13514 and 5,559,008 bp for RM13516. Comparative analysis of the two EcO145 genomes revealed a large core (5,173 genes) and a considerable amount of strain-specific genes. Additionally, the two EcO145 genomes display distinct chromosomal architecture, virulence gene profile, phylogenetic origin of Stx2a prophage, and methylation profile (methylome). Comparative analysis of EcO145 genomes to other completely sequenced STEC and other E. coli and Shigella genomes revealed that, unlike any other known non-O157 EHEC strain, EcO145 ascended from a common lineage with EcO157/EcO55. This evolutionary relationship was further supported by the pangenome analysis of the 10 EHEC str ains. Of the 4,192 EHEC core genes, EcO145 shares more genes with EcO157 than with the any other non-O157 EHEC strains.<br><br>CONCLUSIONS: Our data provide evidence that EcO145 and EcO157 evolved from a common lineage, but ultimately each serotype evolves via a lineage-independent nature to EHEC by acquisition of the core set of EHEC virulence factors, including the genes encoding Shiga toxin and the large virulence plasmid. The large variation between the two EcO145 genomes suggests a distinctive evolutionary path between the two outbreak strains. The distinct methylome between the two EcO145 strains is likely due to the presence of a BsuBI/PstI methyltransferase gene cassette in the Stx2a prophage of the strain RM13514, suggesting a role of horizontal gene transfer-mediated epigenetic alteration in the evolution of individual EHEC strains.}, }
@article {pmid24409764, year = {2013}, author = {Chen, X and Zhang, W and Yin, J and Zhang, N and Chen, C and Yang, S and Jiao, X}, title = {[Prevalence and transmission of plasmid-mediated quinolone resistance qnrS gene among Escherichia coli isolates in a poultry farm].}, journal = {Wei sheng wu xue bao = Acta microbiologica Sinica}, volume = {53}, number = {10}, pages = {1080-1086}, pmid = {24409764}, issn = {0001-6209}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Chickens ; China/epidemiology ; *Drug Resistance, Bacterial ; Ducks ; Environmental Microbiology ; Escherichia coli/classification/drug effects/*genetics/isolation &amp; purification ; Escherichia coli Infections/epidemiology/microbiology/transmission/*veterinary ; Escherichia coli Proteins/*genetics/metabolism ; Geese ; *Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Phylogeny ; Plasmids/genetics ; Poultry Diseases/epidemiology/*microbiology/transmission ; Quinolones/*pharmacology ; }, abstract = {OBJECTIVE: To investigate the prevalence and transmission of plasmid-mediated quinolone resistance qnrS gene among Escherichia coli isolates in a poultry farm and its environment.<br><br>METHODS: E. coli isolates from fecal samples in a poultry farm and its environment from February to June 2010 were screened for the prevalence and dynamic changes of qnrS gene. Susceptibility testing, conjugant experiments, and pulsed field gel electrophoresis of qnrS-positive isolates were also performed.<br><br>RESULTS: A total of 379 isolates were randomly obtained from feces samples of chickens, ducks and geese in a poultry farm and its environment. The qnrS positive strains were detected in all sources of isolates and two alleles of qnrS were prevalent on this farm. The positive rate of qnrS gene in environmental strains was 29.2%, which was significantly higher than that in the avian strains (13.4%). Chicken can quickly acquire qnrS gene after they live on this farm. Transconjugants of the qnrS gene can elevate ciprofloxacin Minimun inhibitory concentrations (MICs) by 16 - 32 fold compared with the recipient. Various determinants for resistance to other antimicrobial agents were also transferred with the qnrS plasmid. The Xba I PFGE analysis of the qnrS positive strains showed that the dissemination of qnrS was not mainly due to the clonal dissemination of positive strains. However, qnrS-positive strains with indistinguishable PFGE patterns were found in ducks and environment.<br><br>CONCLUSION: Both horizontal gene transfer and clonal spread could be responsible for the dissemination of the qnrS gene in the poultry farm and its environment, but it is mainly disseminated by horizontal transmission.}, }
@article {pmid24408912, year = {2014}, author = {Esser, C and Kuhn, A and Groth, G and Lercher, MJ and Maurino, VG}, title = {Plant and animal glycolate oxidases have a common eukaryotic ancestor and convergently duplicated to evolve long-chain 2-hydroxy acid oxidases.}, journal = {Molecular biology and evolution}, volume = {31}, number = {5}, pages = {1089-1101}, doi = {10.1093/molbev/msu041}, pmid = {24408912}, issn = {1537-1719}, mesh = {Alcohol Oxidoreductases/chemistry/*genetics/*metabolism ; Animals ; Arabidopsis Proteins/chemistry/genetics/metabolism ; *Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; Genes, Plant ; Genetic Speciation ; Models, Molecular ; Phylogeny ; Plants/*enzymology/*genetics ; Protein Conformation ; Structural Homology, Protein ; Substrate Specificity ; Symbiosis/genetics ; }, abstract = {Glycolate oxidase (GOX) is a crucial enzyme of plant photorespiration. The encoding gene is thought to have originated from endosymbiotic gene transfer between the eukaryotic host and the cyanobacterial endosymbiont at the base of plantae. However, animals also possess GOX activities. Plant and animal GOX belong to the gene family of (L)-2-hydroxyacid-oxidases ((L)-2-HAOX). We find that all (L)-2-HAOX proteins in animals and archaeplastida go back to one ancestral eukaryotic sequence; the sole exceptions are green algae of the chlorophyta lineage. Chlorophyta replaced the ancestral eukaryotic (L)-2-HAOX with a bacterial ortholog, a lactate oxidase that may have been obtained through the primary endosymbiosis at the base of plantae; independent losses of this gene may explain its absence in other algal lineages (glaucophyta, rhodophyta, and charophyta). We also show that in addition to GOX, plants possess (L)-2-HAOX proteins with different specificities for medium- and long-chain hydroxyacids (lHAOX), likely involved in fatty acid and protein catabolism. Vertebrates possess lHAOX proteins acting on similar substrates as plant lHAOX; however, the existence of GOX and lHAOX subfamilies in both plants and animals is not due to shared ancestry but is the result of convergent evolution in the two most complex eukaryotic lineages. On the basis of targeting sequences and predicted substrate specificities, we conclude that the biological role of plantae (L)-2-HAOX in photorespiration evolved by co-opting an existing peroxisomal protein.}, }
@article {pmid24407037, year = {2014}, author = {Cheeseman, K and Ropars, J and Renault, P and Dupont, J and Gouzy, J and Branca, A and Abraham, AL and Ceppi, M and Conseiller, E and Debuchy, R and Malagnac, F and Goarin, A and Silar, P and Lacoste, S and Sallet, E and Bensimon, A and Giraud, T and Brygoo, Y}, title = {Multiple recent horizontal transfers of a large genomic region in cheese making fungi.}, journal = {Nature communications}, volume = {5}, number = {}, pages = {2876}, pmid = {24407037}, issn = {2041-1723}, support = {309403/ERC_/European Research Council/International ; }, mesh = {Base Sequence ; Cheese ; DNA, Fungal/*genetics ; Gene Transfer, Horizontal/*genetics ; Genomic Islands/*genetics ; Molecular Sequence Data ; Penicillium/*genetics ; }, abstract = {While the extent and impact of horizontal transfers in prokaryotes are widely acknowledged, their importance to the eukaryotic kingdom is unclear and thought by many to be anecdotal. Here we report multiple recent transfers of a huge genomic island between Penicillium spp. found in the food environment. Sequencing of the two leading filamentous fungi used in cheese making, P. roqueforti and P. camemberti, and comparison with the penicillin producer P. rubens reveals a 575 kb long genomic island in P. roqueforti--called Wallaby--present as identical fragments at non-homologous loci in P. camemberti and P. rubens. Wallaby is detected in Penicillium collections exclusively in strains from food environments. Wallaby encompasses about 250 predicted genes, some of which are probably involved in competition with microorganisms. The occurrence of multiple recent eukaryotic transfers in the food environment provides strong evidence for the importance of this understudied and probably underestimated phenomenon in eukaryotes.}, }
@article {pmid24404416, year = {2013}, author = {Chan, CX and Baglivi, FL and Jenkins, CE and Bhattacharya, D}, title = {Foreign gene recruitment to the fatty acid biosynthesis pathway in diatoms.}, journal = {Mobile genetic elements}, volume = {3}, number = {5}, pages = {e27313}, pmid = {24404416}, issn = {2159-2543}, abstract = {Diatoms are highly successful marine and freshwater algae that contribute up to 20% of global carbon fixation. These species are leading candidates for biofuel production owing to ease of culturing and high fatty acid content. To assist in strain improvement and downstream applications for potential use as a biofuel, it is important to understand the evolution of lipid biosynthesis in diatoms. The evolutionary history of diatoms is however complicated by likely multiple endosymbioses involving the capture of foreign cells and horizontal gene transfer into the host genome. Using a phylogenomic approach, we assessed the evolutionary history of 12 diatom genes putatively encoding functions related to lipid biosynthesis. We found evidence of gene transfer likely from a green algal source for seven of these genes, with the remaining showing either vertical inheritance or evolutionary histories too complicated to interpret given current genome data. The functions of horizontally transferred genes encompass all aspects of lipid biosynthesis (initiation, biosynthesis, and desaturation of fatty acids) as well as fatty acid elongation, and are not restricted to plastid-targeted proteins. Our findings demonstrate that the transfer, duplication, and subfunctionalization of genes were key steps in the evolution of lipid biosynthesis in diatoms and other photosynthetic eukaryotes. This target pathway for biofuel research is highly chimeric and surprisingly, our results suggest that research done on related genes in green algae may have application to diatom models.}, }
@article {pmid24403327, year = {2014}, author = {Boto, L}, title = {Horizontal gene transfer in the acquisition of novel traits by metazoans.}, journal = {Proceedings. Biological sciences}, volume = {281}, number = {1777}, pages = {20132450}, pmid = {24403327}, issn = {1471-2954}, mesh = {Animals ; *Biological Evolution ; Chordata/*genetics ; *Gene Transfer, Horizontal ; Invertebrates/*genetics ; Symbiosis ; }, abstract = {Horizontal gene transfer is accepted as an important evolutionary force modulating the evolution of prokaryote genomes. However, it is thought that horizontal gene transfer plays only a minor role in metazoan evolution. In this paper, I critically review the rising evidence on horizontally transferred genes and on the acquisition of novel traits in metazoans. In particular, I discuss suspected examples in sponges, cnidarians, rotifers, nematodes, molluscs and arthropods which suggest that horizontal gene transfer in metazoans is not simply a curiosity. In addition, I stress the scarcity of studies in vertebrates and other animal groups and the importance of forthcoming studies to understand the importance and extent of horizontal gene transfer in animals.}, }
@article {pmid24402501, year = {2014}, author = {Jamrozy, DM and Coldham, NG and Butaye, P and Fielder, MD}, title = {Identification of a novel plasmid-associated spectinomycin adenyltransferase gene spd in methicillin-resistant Staphylococcus aureus ST398 isolated from animal and human sources.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {69}, number = {5}, pages = {1193-1196}, doi = {10.1093/jac/dkt510}, pmid = {24402501}, issn = {1460-2091}, mesh = {Animals ; DNA, Bacterial/chemistry/genetics ; Gene Transfer, Horizontal ; Genotype ; Humans ; Methicillin-Resistant Staphylococcus aureus/classification/*enzymology/genetics/*isolation &amp; purification ; Molecular Sequence Data ; Molecular Typing ; Nucleotidyltransferases/*genetics ; Plasmids/*isolation &amp; purification ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Staphylococcal Infections/*microbiology/*veterinary ; Transformation, Bacterial ; }, abstract = {OBJECTIVES: Previously described methicillin-resistant Staphylococcus aureus (MRSA) ST398 strains revealed a high frequency of phenotypic resistance to spectinomycin. However, only a few were found to carry the spc resistance determinant. The aim of this study was to identify the genetic mechanism of spectinomycin resistance among spc-negative MRSA ST398 strains.<br><br>METHODS: Nine spectinomycin-resistant, but spc-negative, MRSA ST398 strains were analysed. The strains were screened for carriage of the spw gene and tested for the presence of transferrable spectinomycin resistance. Plasmid DNA was isolated from all strains and used in transformation assays. The plasmid identified as mediating resistance to spectinomycin was fully sequenced. The function of the novel spectinomycin resistance gene was confirmed by restriction digest inactivation and its distribution was determined using a PCR assay.<br><br>RESULTS: A single MRSA ST398 strain was spw positive. The remaining strains carried a plasmid that mediated resistance to spectinomycin. Sequence analysis of a single plasmid, termed pDJ91S, revealed that it was 3928 bp in size and contained three open reading frames: a novel spectinomycin resistance gene, designated spd, as well as a repN gene and a rec gene. The XmnI digest inactivation of the spd gene resulted in a 4-fold decrease in spectinomycin MIC. The spd gene was detected in seven other spectinomycin-resistant MRSA ST398 strains that carried a plasmid comparable in size to pDJ91S.<br><br>CONCLUSIONS: A novel gene, designated spd, that confers resistance to spectinomycin has been identified on a small plasmid in MRSA ST398.}, }
@article {pmid24400851, year = {2014}, author = {Jalasvuori, M and Lehtonen, J}, title = {Virus epidemics can lead to a population-wide spread of intragenomic parasites in a previously parasite-free asexual population.}, journal = {Molecular ecology}, volume = {23}, number = {5}, pages = {987-991}, doi = {10.1111/mec.12662}, pmid = {24400851}, issn = {1365-294X}, mesh = {Computer Simulation ; Endogenous Retroviruses/*genetics ; Gene Transfer, Horizontal ; Genetics, Population ; *Models, Biological ; *Reproduction, Asexual ; Retroelements ; }, abstract = {Sexual reproduction is problematic to explain due to its costs, most notably the twofold cost of sex. Yet, sex has been suggested to be favourable in the presence of proliferating intragenomic parasites given that sexual recombination provides a mechanism to confine the accumulation of deleterious mutations. Kraaijeveld et al. compared recently the accumulation of transposons in sexually and asexually reproducing lines of the same species, the parasitoid wasp Leptopilina clavipes. They discovered that within asexually reproducing wasps, the number of gypsy-like retrotransposons was increased fourfold, whereas other retrotransposons were not. Interestingly, gypsy-like retrotransposons are closely related to retroviruses. Endogenous retroviruses are retroviruses that have integrated to the germ line cells and are inherited thereafter vertically. They can also replicate within the genome similarly to retrotransposons as well as form virus particles and infect previously uninfected cells. This highlights the possibility that endogenous retroviruses could play a role in the evolution of sexual reproduction. Here, we show with an individual-based computational model that a virus epidemic within a previously parasite-free asexual population may establish a new intragenomic parasite to the population. Moreover and in contrast to other transposons, the possibility of endogenous viruses to maintain a virus epidemic and simultaneously provide resistance to individuals carrying active endogenous viruses selects for the presence of active intragenomic parasites in the population despite their deleterious effects. Our results suggest that the viral nature of certain intragenomic parasites should be taken into account when sex and its benefits are being considered.}, }
@article {pmid24398376, year = {2014}, author = {Zhi, XY and Yao, JC and Tang, SK and Huang, Y and Li, HW and Li, WJ}, title = {The futalosine pathway played an important role in menaquinone biosynthesis during early prokaryote evolution.}, journal = {Genome biology and evolution}, volume = {6}, number = {1}, pages = {149-160}, pmid = {24398376}, issn = {1759-6653}, mesh = {Archaea/enzymology/*genetics/metabolism ; Bacteria/enzymology/*genetics/metabolism ; *Evolution, Molecular ; Genome, Archaeal ; Genome, Bacterial ; Nucleosides/*metabolism ; Proteome/genetics/metabolism ; Vitamin K 2/*metabolism ; }, abstract = {Menaquinone (MK) is an important component of the electron-transfer system in prokaryotes. One of its precursors, 1,4-dihydroxy-2-naphthoate, can be synthesized from chorismate by the classical MK pathway. Interestingly, in some bacteria, chorismate can also be converted to 1,4-dihydroxy-6-naphthoate by four enzymes encoded by mqnABCD in an alternative futalosine pathway. In this study, six crucial enzymes belonging to these two independent nonhomologous pathways were identified in the predicted proteomes of prokaryotes representing a broad phylogenetic distribution. Although the classical MK pathway was found in 32.1% of the proteomes, more than twice the proportion containing the futalosine pathway, the latter was found in a broader taxonomic range of organisms (18 of 31 phyla). The prokaryotes equipped with the classical MK pathway were almost all aerobic or facultatively anaerobic, but those with the futalosine pathway were not only aerobic or facultatively anaerobic but also anaerobic. Phylogenies of enzymes of the classical MK pathway indicated that its genes in archaea were probably acquired by an ancient horizontal gene transfer from bacterial donors. Therefore, the organization of the futalosine pathway likely predated that of the classical MK pathway in the evolutionary history of prokaryotes.}, }
@article {pmid24398374, year = {2014}, author = {Raymann, K and Forterre, P and Brochier-Armanet, C and Gribaldo, S}, title = {Global phylogenomic analysis disentangles the complex evolutionary history of DNA replication in archaea.}, journal = {Genome biology and evolution}, volume = {6}, number = {1}, pages = {192-212}, pmid = {24398374}, issn = {1759-6653}, mesh = {Archaea/*genetics/metabolism ; Archaeal Proteins/genetics/metabolism ; *DNA Replication ; DNA, Archaeal/*genetics/metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Archaeal ; *Phylogeny ; }, abstract = {The archaeal machinery responsible for DNA replication is largely homologous to that of eukaryotes and is clearly distinct from its bacterial counterpart. Moreover, it shows high diversity in the various archaeal lineages, including different sets of components, heterogeneous taxonomic distribution, and a large number of additional copies that are sometimes highly divergent. This has made the evolutionary history of this cellular system particularly challenging to dissect. Here, we have carried out an exhaustive identification of homologs of all major replication components in over 140 complete archaeal genomes. Phylogenomic analysis allowed assigning them to either a conserved and probably essential core of replication components that were mainly vertically inherited, or to a variable and highly divergent shell of extra copies that have likely arisen from integrative elements. This suggests that replication proteins are frequently exchanged between extrachromosomal elements and cellular genomes. Our study allowed clarifying the history that shaped this key cellular process (ancestral components, horizontal gene transfers, and gene losses), providing important evolutionary and functional information. Finally, our precise identification of core components permitted to show that the phylogenetic signal carried by DNA replication is highly consistent with that harbored by two other key informational machineries (translation and transcription), strengthening the existence of a robust organismal tree for the Archaea.}, }
@article {pmid24398322, year = {2014}, author = {Sloan, DB and Nakabachi, A and Richards, S and Qu, J and Murali, SC and Gibbs, RA and Moran, NA}, title = {Parallel histories of horizontal gene transfer facilitated extreme reduction of endosymbiont genomes in sap-feeding insects.}, journal = {Molecular biology and evolution}, volume = {31}, number = {4}, pages = {857-871}, pmid = {24398322}, issn = {1537-1719}, support = {S10 RR029676/RR/NCRR NIH HHS/United States ; RR19895/RR/NCRR NIH HHS/United States ; F32 GM099334/GM/NIGMS NIH HHS/United States ; U54 HG003273/HG/NHGRI NIH HHS/United States ; S10 RR019895/RR/NCRR NIH HHS/United States ; 1F32GM099334/GM/NIGMS NIH HHS/United States ; RR029676-01/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; *Evolution, Molecular ; Gammaproteobacteria/*genetics ; Gene Expression ; *Gene Transfer, Horizontal ; Genes, Insect ; Genome, Bacterial ; Hemiptera/*genetics ; Metabolic Networks and Pathways/genetics ; Phylogeny ; RNA, Messenger/genetics ; Sequence Analysis, RNA ; Symbiosis/*genetics ; }, abstract = {Bacteria confined to intracellular environments experience extensive genome reduction. In extreme cases, insect endosymbionts have evolved genomes that are so gene-poor that they blur the distinction between bacteria and endosymbiotically derived organelles such as mitochondria and plastids. To understand the host's role in this extreme gene loss, we analyzed gene content and expression in the nuclear genome of the psyllid Pachypsylla venusta, a sap-feeding insect that harbors an ancient endosymbiont (Carsonella) with one of the most reduced bacterial genomes ever identified. Carsonella retains many genes required for synthesis of essential amino acids that are scarce in plant sap, but most of these biosynthetic pathways have been disrupted by gene loss. Host genes that are upregulated in psyllid cells housing Carsonella appear to compensate for endosymbiont gene losses, resulting in highly integrated metabolic pathways that mirror those observed in other sap-feeding insects. The host contribution to these pathways is mediated by a combination of native eukaryotic genes and bacterial genes that were horizontally transferred from multiple donor lineages early in the evolution of psyllids, including one gene that appears to have been directly acquired from Carsonella. By comparing the psyllid genome to a recent analysis of mealybugs, we found that a remarkably similar set of functional pathways have been shaped by independent transfers of bacterial genes to the two hosts. These results show that horizontal gene transfer is an important and recurring mechanism driving coevolution between insects and their bacterial endosymbionts and highlight interesting similarities and contrasts with the evolutionary history of mitochondria and plastids.}, }
@article {pmid24398320, year = {2014}, author = {Rochette, NC and Brochier-Armanet, C and Gouy, M}, title = {Phylogenomic test of the hypotheses for the evolutionary origin of eukaryotes.}, journal = {Molecular biology and evolution}, volume = {31}, number = {4}, pages = {832-845}, pmid = {24398320}, issn = {1537-1719}, mesh = {Archaea/genetics ; Bacteria/genetics ; Biological Evolution ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Speciation ; Genome, Human ; Humans ; *Models, Genetic ; Phylogeny ; Symbiosis/genetics ; Yeasts/genetics ; }, abstract = {The evolutionary origin of eukaryotes is a question of great interest for which many different hypotheses have been proposed. These hypotheses predict distinct patterns of evolutionary relationships for individual genes of the ancestral eukaryotic genome. The availability of numerous completely sequenced genomes covering the three domains of life makes it possible to contrast these predictions with empirical data. We performed a systematic analysis of the phylogenetic relationships of ancestral eukaryotic genes with archaeal and bacterial genes. In contrast with previous studies, we emphasize the critical importance of methods accounting for statistical support, horizontal gene transfer, and gene loss, and we disentangle the processes underlying the phylogenomic pattern we observe. We first recover a clear signal indicating that a fraction of the bacteria-like eukaryotic genes are of alphaproteobacterial origin. Then, we show that the majority of bacteria-related eukaryotic genes actually do not point to a relationship with a specific bacterial taxonomic group. We also provide evidence that eukaryotes branch close to the last archaeal common ancestor. Our results demonstrate that there is no phylogenetic support for hypotheses involving a fusion with a bacterium other than the ancestor of mitochondria. Overall, they leave only two possible interpretations, respectively, based on the early-mitochondria hypotheses, which suppose an early endosymbiosis of an alphaproteobacterium in an archaeal host and on the slow-drip autogenous hypothesis, in which early eukaryotic ancestors were particularly prone to horizontal gene transfers.}, }
@article {pmid24397311, year = {2014}, author = {Althabegoiti, MJ and Ormeño-Orrillo, E and Lozano, L and Torres Tejerizo, G and Rogel, MA and Mora, J and Martínez-Romero, E}, title = {Characterization of Rhizobium grahamii extrachromosomal replicons and their transfer among rhizobia.}, journal = {BMC microbiology}, volume = {14}, number = {}, pages = {6}, pmid = {24397311}, issn = {1471-2180}, mesh = {Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; *Extrachromosomal Inheritance ; Fabaceae/microbiology ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Mexico ; Molecular Sequence Data ; Plant Roots/microbiology ; *Plasmids ; Rhizobium/*genetics/isolation &amp; purification ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Rhizobium grahamii belongs to a new phylogenetic group of rhizobia together with Rhizobium mesoamericanum and other species. R. grahamii has a broad-host-range that includes Leucaena leucocephala and Phaseolus vulgaris, although it is a poor competitor for P. vulgaris nodulation in the presence of Rhizobium etli or Rhizobium phaseoli strains. This work analyzed the genome sequence and transfer properties of R. grahamii plasmids.<br><br>RESULTS: Genome sequence was obtained from R. grahamii CCGE502 type strain isolated from Dalea leporina in Mexico. The CCGE502 genome comprises one chromosome and two extrachromosomal replicons (ERs), pRgrCCGE502a and pRgrCCGE502b. Additionally, a plasmid integrated in the CCGE502 chromosome was found. The genomic comparison of ERs from this group showed that gene content is more variable than average nucleotide identity (ANI). Well conserved nod and nif genes were found in R. grahamii and R. mesoamericanum with some differences. R. phaseoli Ch24-10 genes expressed in bacterial cells in roots were found to be conserved in pRgrCCGE502b. Regarding conjugative transfer we were unable to transfer the R. grahamii CCGE502 symbiotic plasmid and its megaplasmid to other rhizobial hosts but we could transfer the symbiotic plasmid to Agrobacterium tumefaciens with transfer dependent on homoserine lactones.<br><br>CONCLUSION: Variable degrees of nucleotide identity and gene content conservation were found among the different R. grahamii CCGE502 replicons in comparison to R. mesoamericanum genomes. The extrachromosomal replicons from R. grahamii were more similar to those found in phylogenetically related Rhizobium species. However, limited similarities of R. grahamii CCGE502 symbiotic plasmid and megaplasmid were observed in other more distant Rhizobium species. The set of conserved genes in R. grahamii comprises some of those that are highly expressed in R. phaseoli on plant roots, suggesting that they play an important role in root colonization.}, }
@article {pmid24396307, year = {2013}, author = {Mahajan, A and Singh, B and Kashyap, D and Kumar, A and Mahajan, P}, title = {Interspecies communication and periodontal disease.}, journal = {TheScientificWorldJournal}, volume = {2013}, number = {}, pages = {765434}, pmid = {24396307}, issn = {1537-744X}, mesh = {Bacteria/genetics ; *Bacterial Physiological Phenomena ; Bacterial Proteins/physiology ; Bacterial Secretion Systems ; Biofilms ; Dental Plaque/*microbiology ; Extracellular Matrix/microbiology ; Gene Transfer, Horizontal ; Humans ; *Microbial Consortia ; Periodontitis/*microbiology ; Quorum Sensing ; Species Specificity ; }, abstract = {More than 500 bacterial strains may be found in dental plaque. In the beginning, the emphasis was laid on the isolation of bacteria in pure culture to define their properties. However, now, it has been well established that in nature the bacteria exist as a member of polymicrobial community or consortium of interacting species. Interactions among human oral bacteria are integral to the development and maturation of the plaque. These interactions occur at several levels including physical contact, metabolic exchange, small-signal molecule-mediated communication, and exchange of genetic material. This high level of interspecies interaction benefits the microorganism by providing a broader habitat range, effective metabolism, increasing the resistance to host defence, and enhancing their virulence. This generally has a detrimental effect on the host and is attributed to many chronic infections which poses a therapeutic challenge.}, }
@article {pmid24391933, year = {2013}, author = {Butzin, NC and Lapierre, P and Green, AG and Swithers, KS and Gogarten, JP and Noll, KM}, title = {Reconstructed ancestral Myo-inositol-3-phosphate synthases indicate that ancestors of the Thermococcales and Thermotoga species were more thermophilic than their descendants.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e84300}, pmid = {24391933}, issn = {1932-6203}, mesh = {Adaptation, Biological/*genetics ; Archaea/enzymology/genetics ; Computational Biology/*methods ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; *Hot Temperature ; Intramolecular Lyases/*genetics ; Likelihood Functions ; Models, Genetic ; Phylogeny ; Species Specificity ; Thermococcales/*enzymology/genetics ; Thermotoga maritima/*enzymology/genetics ; }, abstract = {The bacterial genomes of Thermotoga species show evidence of significant interdomain horizontal gene transfer from the Archaea. Members of this genus acquired many genes from the Thermococcales, which grow at higher temperatures than Thermotoga species. In order to study the functional history of an interdomain horizontally acquired gene we used ancestral sequence reconstruction to examine the thermal characteristics of reconstructed ancestral proteins of the Thermotoga lineage and its archaeal donors. Several ancestral sequence reconstruction methods were used to determine the possible sequences of the ancestral Thermotoga and Archaea myo-inositol-3-phosphate synthase (MIPS). These sequences were predicted to be more thermostable than the extant proteins using an established sequence composition method. We verified these computational predictions by measuring the activities and thermostabilities of purified proteins from the Thermotoga and the Thermococcales species, and eight ancestral reconstructed proteins. We found that the ancestral proteins from both the archaeal donor and the Thermotoga most recent common ancestor recipient were more thermostable than their descendants. We show that there is a correlation between the thermostability of MIPS protein and the optimal growth temperature (OGT) of its host, which suggests that the OGT of the ancestors of these species of Archaea and the Thermotoga grew at higher OGTs than their descendants.}, }
@article {pmid24391155, year = {2014}, author = {Feng, S and Powell, SM and Wilson, R and Bowman, JP}, title = {Extensive gene acquisition in the extremely psychrophilic bacterial species Psychroflexus torquis and the link to sea-ice ecosystem specialism.}, journal = {Genome biology and evolution}, volume = {6}, number = {1}, pages = {133-148}, pmid = {24391155}, issn = {1759-6653}, mesh = {Adaptation, Physiological ; Antarctic Regions ; Arctic Regions ; Cold Temperature ; *Ecosystem ; *Evolution, Molecular ; Fatty Acids/biosynthesis/genetics ; Flavobacteriaceae/classification/*genetics/metabolism ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Ice Cover/*microbiology ; Oceans and Seas ; Phylogeny ; Polysaccharides, Bacterial/biosynthesis/genetics ; Proteome/genetics/metabolism ; Pseudogenes ; }, abstract = {Sea ice is a highly dynamic and productive environment that includes a diverse array of psychrophilic prokaryotic and eukaryotic taxa distinct from the underlying water column. Because sea ice has only been extensive on Earth since the mid-Eocene, it has been hypothesized that bacteria highly adapted to inhabit sea ice have traits that have been acquired through horizontal gene transfer (HGT). Here we compared the genomes of the psychrophilic bacterium Psychroflexus torquis ATCC 700755(T), associated with both Antarctic and Arctic sea ice, and its closely related nonpsychrophilic sister species, P. gondwanensis ACAM 44(T). Results show that HGT has occurred much more extensively in P. torquis in comparison to P. gondwanensis. Genetic features that can be linked to the psychrophilic and sea ice-specific lifestyle of P. torquis include genes for exopolysaccharide (EPS) and polyunsaturated fatty acid (PUFA) biosynthesis, numerous specific modes of nutrient acquisition, and proteins putatively associated with ice-binding, light-sensing (bacteriophytochromes), and programmed cell death (metacaspases). Proteomic analysis showed that several genes associated with these traits are highly translated, especially those involved with EPS and PUFA production. Because most of the genes relating to the ability of P. torquis to dwell in sea-ice ecosystems occur on genomic islands that are absent in closely related P. gondwanensis, its adaptation to the sea-ice environment appears driven mainly by HGT. The genomic islands are rich in pseudogenes, insertional elements, and addiction modules, suggesting that gene acquisition is being followed by a process of genome reduction potentially indicative of evolving ecosystem specialism.}, }
@article {pmid24391152, year = {2014}, author = {Greene, GH and McGary, KL and Rokas, A and Slot, JC}, title = {Ecology drives the distribution of specialized tyrosine metabolism modules in fungi.}, journal = {Genome biology and evolution}, volume = {6}, number = {1}, pages = {121-132}, pmid = {24391152}, issn = {1759-6653}, mesh = {Ascomycota/*genetics/metabolism ; *Ecosystem ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, Fungal ; Gentisates/metabolism ; *Multigene Family ; Stilbenes/metabolism ; Tyrosine/genetics/*metabolism ; }, abstract = {Gene clusters encoding accessory or environmentally specialized metabolic pathways likely play a significant role in the evolution of fungal genomes. Two such gene clusters encoding enzymes associated with the tyrosine metabolism pathway (KEGG #00350) have been identified in the filamentous fungus Aspergillus fumigatus. The l-tyrosine degradation (TD) gene cluster encodes a functional module that facilitates breakdown of the phenolic amino acid, l-tyrosine through a homogentisate intermediate, but is also involved in the production of pyomelanin, a fungal pathogenicity factor. The gentisate catabolism (GC) gene cluster encodes a functional module likely involved in phenolic compound degradation, which may enable metabolism of biphenolic stilbenes in multiple lineages. Our investigation of the evolution of the TD and GC gene clusters in 214 fungal genomes revealed spotty distributions partially shaped by gene cluster loss and horizontal gene transfer (HGT). Specifically, a TD gene cluster shows evidence of HGT between the extremophilic, melanized fungi Exophiala dermatitidis and Baudoinia compniacensis, and a GC gene cluster shows evidence of HGT between Sordariomycete and Dothideomycete grass pathogens. These results suggest that the distribution of specialized tyrosine metabolism modules is influenced by both the ecology and phylogeny of fungal species.}, }
@article {pmid24385974, year = {2013}, author = {Efimov, V and Danin-Poleg, Y and Raz, N and Elgavish, S and Linetsky, A and Kashi, Y}, title = {Insight into the evolution of Vibrio vulnificus biotype 3's genome.}, journal = {Frontiers in microbiology}, volume = {4}, number = {}, pages = {393}, pmid = {24385974}, issn = {1664-302X}, abstract = {Vibrio vulnificus is an aquatic bacterium and an important human pathogen. Strains of V. vulnificus are biochemically classified into three biotypes. The newly emerged biotype 3 appears to be rather clonal and geographically restricted to Israel, where it caused an outbreak of wound infections and bacteremia. To understand the evolution of the bacterium's genome, we sequenced and analyzed the genome of biotype 3 strain VVyb1(BT3), and then conducted a microbial environmental survey of the hypothesized niche from which it probably evolved. The genome of this environmental isolate revealed higher similarity to the published biotype 1 genomes of clinical strains (90%) than to the environmental strains (87%), supporting the virulence of the biotype 3 group. Moreover, 214 of the total 5361 genes were found to be unique to strain VVyb1(BT3), having no sequence similarity to any of the known genomes of V. vulnificus; 35 of them function in DNA mobility and rearrangement, supporting the role of horizontal gene transfer in genome evolution. Interestingly, 29 of the "unique" genes had homologies among Shewanella species. In a survey conducted in aquaculture ponds in Israel, we successfully co-isolated Shewanella and V. vulnificus from the same niche, further supporting the probable contribution of Shewanella to the genome evolution of biotype 3. Indeed, one gene was found in a S. algae isolate. Surprisingly, molecular analysis revealed that some of the considered unique genes are harbored by non-sequenced biotype 1 strains isolated from the same environment. Finally, analyses of the biotype 3 genome together with the environmental survey suggested that its genome originated from a biotype 1 Israeli strain that acquired a rather small number of genes from other bacterial species in the niche, such as Shewanella. Therefore, aquaculture is likely to play a major role as a man-made ecological niche in bacterial evolution, leading the emergence of new pathogenic groups in V. vulnificus.}, }
@article {pmid24385921, year = {2013}, author = {Berry, JL and Cehovin, A and McDowell, MA and Lea, SM and Pelicic, V}, title = {Functional analysis of the interdependence between DNA uptake sequence and its cognate ComP receptor during natural transformation in Neisseria species.}, journal = {PLoS genetics}, volume = {9}, number = {12}, pages = {e1004014}, pmid = {24385921}, issn = {1553-7404}, support = {100298/WT_/Wellcome Trust/United Kingdom ; MR/J006874/1/MRC_/Medical Research Council/United Kingdom ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacterial Proteins/genetics ; Base Sequence/*genetics ; DNA, Bacterial/genetics ; DNA-Binding Proteins/*genetics ; Gene Transfer, Horizontal/*genetics ; Humans ; Neisseria meningitidis/*genetics/growth &amp; development ; Transformation, Bacterial/*genetics ; }, abstract = {Natural transformation is the widespread biological process by which "competent" bacteria take up free DNA, incorporate it into their genomes, and become genetically altered or "transformed". To curb often deleterious transformation by foreign DNA, several competent species preferentially take up their own DNA that contains specific DUS (DNA uptake sequence) watermarks. Our recent finding that ComP is the long sought DUS receptor in Neisseria species paves the way for the functional analysis of the DUS-ComP interdependence which is reported here. By abolishing/modulating ComP levels in Neisseria meningitidis, we show that the enhancement of transformation seen in the presence of DUS is entirely dependent on ComP, which also controls transformation in the absence of DUS. While peripheral bases in the DUS were found to be less important, inner bases are essential since single base mutations led to dramatically impaired interaction with ComP and transformation. Strikingly, naturally occurring DUS variants in the genomes of human Neisseria commensals differing from DUS by only one or two bases were found to be similarly impaired for transformation of N. meningitidis. By showing that ComPsub from the N. subflava commensal specifically binds its cognate DUS variant and mediates DUS-enhanced transformation when expressed in a comP mutant of N. meningitidis, we confirm that a similar mechanism is used by all Neisseria species to promote transformation by their own, or closely related DNA. Together, these findings shed new light on the molecular events involved in the earliest step in natural transformation, and reveal an elegant mechanism for modulating horizontal gene transfer between competent species sharing the same niche.}, }
@article {pmid24383794, year = {2014}, author = {Hadjirin, NF and Harrison, EM and Holmes, MA and Paterson, GK}, title = {Conjugative transfer frequencies of mef(A)-containing Tn1207.3 to macrolide-susceptible Streptococcus pyogenes belonging to different emm types.}, journal = {Letters in applied microbiology}, volume = {58}, number = {4}, pages = {299-302}, pmid = {24383794}, issn = {1472-765X}, support = {//Medical Research Council/United Kingdom ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/*genetics ; *Conjugation, Genetic ; DNA Transposable Elements ; Drug Resistance, Bacterial/genetics ; *Gene Transfer, Horizontal ; Macrolides/*pharmacology ; Membrane Proteins/*genetics ; Streptococcus pyogenes/classification/drug effects/*genetics ; }, abstract = {UNLABELLED: The aim of this study was to examine the gene transfer potential of mef(A)-containing Tn120.3 to macrolide-susceptible Streptococcus pyogenes belonging to different emm types. Using the filter mating technique, Tn1207.3 was transferred by conjugation to 23 macrolide-susceptible recipients representing 11 emm types. PCR analysis confirmed the presence of the mef(A) gene and the comEC junction regions of the Tn1207.3 insertion in resultant transconjugants. Significant variation was found in the transfer frequency of Tn1207.3 to different Strep. pyogenes strains, and this phenomenon may contribute to the differences in mef(A) frequency observed among clinical isolates.<br><br>The spread of antimicrobial resistance among pathogenic bacteria is an important problem, but the mechanisms of horizontal transfer between strains and species are often poorly understood. For instance, little is known on how macrolide resistance spreads between strains of the human pathogen Strep. pyogenes and why certain strains more commonly display resistance than others. Here, we show that Strep. pyogenes strains vary greatly in their ability to acquire a transposon encoding macrolide resistance by horizontal gene transfer in vitro. These data provide a novel insight into the transfer of antibiotic resistance between bacterial strains and offer an explanation for the differences in the frequency of resistance determinates and resistance seen among clinical isolates.}, }
@article {pmid24382842, year = {2014}, author = {Bertsch, D and Muelli, M and Weller, M and Uruty, A and Lacroix, C and Meile, L}, title = {Antimicrobial susceptibility and antibiotic resistance gene transfer analysis of foodborne, clinical, and environmental Listeria spp. isolates including Listeria monocytogenes.}, journal = {MicrobiologyOpen}, volume = {3}, number = {1}, pages = {118-127}, pmid = {24382842}, issn = {2045-8827}, mesh = {Animals ; Dairy Products/microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; *Food Microbiology ; Genotype ; Humans ; Listeria/*drug effects/genetics/isolation &amp; purification ; Listeria monocytogenes/drug effects/genetics/isolation &amp; purification ; Listeriosis/*microbiology ; Meat/microbiology ; Phenotype ; R Factors ; Seafood/microbiology ; Transformation, Bacterial ; Vegetables/microbiology ; *Water Microbiology ; }, abstract = {The aims of this study were to assess antibiotic resistance pheno- and genotypes in foodborne, clinical, and environmental Listeria isolates, as well as to elucidate the horizontal gene transfer potential of detected resistance genes. A small fraction of in total 524 Listeria spp. isolates (3.1%) displayed acquired antibiotic resistance mainly to tetracycline (n = 11), but also to clindamycin (n = 4) and trimethoprim (n = 3), which was genotypically confirmed. In two cases, a tetracycline resistance phenotype was observed together with a trimethoprim resistance phenotype, namely in a clinical L. monocytogenes strain and in a foodborne L. innocua isolate. Depending on the applied guidelines, a differing number of isolates (n = 2 or n = 20) showed values for ampicillin that are on the edge between intermediate susceptibility and resistance. Transferability of the antibiotic resistance genes from the Listeria donors, elucidated in vitro by filter matings, was demonstrated for genes located on transposons of the Tn916 family and for an unknown clindamycin resistance determinant. Transfer rates of up to 10(-5) transconjugants per donor were obtained with a L. monocytogenes recipient and up to 10(-7) with an Enterococcus faecalis recipient, respectively. Although the prevalence of acquired antibiotic resistance in Listeria isolates from this study was rather low, the transferability of these resistances enables further spread in the future. This endorses the importance of surveillance of L. monocytogenes and other Listeria spp. in terms of antibiotic susceptibility.}, }
@article {pmid24382125, year = {2014}, author = {Flood, BE and Bailey, JV and Biddle, JF}, title = {Horizontal gene transfer and the rock record: comparative genomics of phylogenetically distant bacteria that induce wrinkle structure formation in modern sediments.}, journal = {Geobiology}, volume = {12}, number = {2}, pages = {119-132}, doi = {10.1111/gbi.12072}, pmid = {24382125}, issn = {1472-4669}, mesh = {Beggiatoa/*genetics ; Cyanobacteria/*genetics ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; }, abstract = {Wrinkle structures are sedimentary features that are produced primarily through the trapping and binding of siliciclastic sediments by mat-forming micro-organisms. Wrinkle structures and related sedimentary structures in the rock record are commonly interpreted to represent the stabilizing influence of cyanobacteria on sediments because cyanobacteria are known to produce similar textures and structures in modern tidal flat settings. However, other extant bacteria such as filamentous representatives of the family Beggiatoaceae can also interact with sediments to produce sedimentary features that morphologically resemble many of those associated with cyanobacteria-dominated mats. While Beggiatoa spp. and cyanobacteria are metabolically and phylogenetically distant, genomic analyses show that the two groups share hundreds of homologous genes, likely as the result of horizontal gene transfer. The comparative genomics results described here suggest that some horizontally transferred genes may code for phenotypic traits such as filament formation, chemotaxis, and the production of extracellular polymeric substances that potentially underlie the similar biostabilizing influences of these organisms on sediments. We suggest that the ecological utility of certain basic life modes such as the construction of mats and biofilms, coupled with the lateral mobility of genes in the microbial world, introduces an element of uncertainty into the inference of specific phylogenetic origins from gross morphological features preserved in the ancient rock record.}, }
@article {pmid24381073, year = {2014}, author = {Fleury, C and Resman, F and Rau, J and Riesbeck, K}, title = {Prevalence, distribution and transfer of small β-lactamase-containing plasmids in Swedish Haemophilus influenzae.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {69}, number = {5}, pages = {1238-1242}, doi = {10.1093/jac/dkt511}, pmid = {24381073}, issn = {1460-2091}, mesh = {Adult ; Child ; Child, Preschool ; DNA, Bacterial/genetics ; Haemophilus Infections/*microbiology ; Haemophilus influenzae/*enzymology/*genetics/isolation &amp; purification ; Humans ; Multilocus Sequence Typing ; Plasmids/*analysis ; Polymerase Chain Reaction ; Prevalence ; Sweden ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: The β-lactamase genes of Haemophilus influenzae are commonly positioned on large integrative and conjugative elements, but a group of blaTEM-carrying small plasmids (4000-6000 bp) with a common structural backbone have recently been characterized. In this study we investigated the epidemiological significance and potential for transfer of this group of small plasmids.<br><br>METHODS: We developed a two-step PCR assay to screen for and type this group of resistance plasmids in H. influenzae. A large collection of respiratory isolates (n = 2845) from south Sweden, obtained from 2009 to 2011, as well as a collection of invasive Swedish H. influenzae from 1997 to 2010 (n = 310) was screened. The distribution of plasmid types among clinical isolates was investigated using multilocus sequence typing (MLST).<br><br>RESULTS: In the collection, 15.8% of &#x3b2;-lactamase-producing isolates and 1.4% of total isolates possessed a small plasmid with the signature structure. The plasmids were genetically conserved and widely spread geographically. MLST revealed that the spread of small plasmids occurred by both clonal expansion and horizontal transfer. In vitro experiments suggested that one plasmid type, pN223, can transfer ampicillin resistance to susceptible Escherichia coli.<br><br>CONCLUSIONS: Small &#x3b2;-lactamase-encoding plasmids constitute a significant mechanism for &#x3b2;-lactam resistance in H. influenzae and can spread through clonal expansion of resistant clones as well as through horizontal plasmid transfer.}, }
@article {pmid24379303, year = {2014}, author = {Doublet, B and Praud, K and Nguyen-Ho-Bao, T and Argudín, MA and Bertrand, S and Butaye, P and Cloeckaert, A}, title = {Extended-spectrum β-lactamase- and AmpC β-lactamase-producing D-tartrate-positive Salmonella enterica serovar Paratyphi B from broilers and human patients in Belgium, 2008-10.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {69}, number = {5}, pages = {1257-1264}, doi = {10.1093/jac/dkt504}, pmid = {24379303}, issn = {1460-2091}, mesh = {Animals ; Belgium ; Conjugation, Genetic ; Electrophoresis, Gel, Pulsed-Field ; Gene Transfer, Horizontal ; Humans ; Paratyphoid Fever/*microbiology/*veterinary ; Polymerase Chain Reaction ; Poultry ; Salmonella paratyphi B/*enzymology/genetics/*isolation &amp; purification/metabolism ; Sequence Analysis, DNA ; Tartrates/*metabolism ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: To characterize the genetic determinants responsible for extended-spectrum cephalosporin (ESC) resistance of d-tartrate-positive Salmonella enterica subsp. enterica serovar Paratyphi B (serovar Paratyphi B dT+) strains that have emerged in poultry and humans in Belgium during 2008-10.<br><br>METHODS: The ESC resistance genes among non-redundant serovar Paratyphi B dT+ strains were determined using PCR and sequencing. ESC phenotypes were horizontally transferred by conjugation. Extended-spectrum &#x3b2;-lactamase (ESBL)- or AmpC-carrying plasmids were typed by PCR-based replicon typing, plasmid multilocus sequence typing and restriction fragment length polymorphism. The genetic relationship of ESC-resistant strains was assessed by XbaI PFGE and multilocus sequence typing.<br><br>RESULTS: Since 2008, the proportion of serovar Paratyphi B dT+ strains from broiler origin has increased significantly to reach 36.5% in 2010. Among 95 non-duplicate serovar Paratyphi B dT+ strains, 35% were resistant to ESCs. At the same time, a few ESC-resistant serovar Paratyphi B dT+ strains from humans were also detected in Belgium. The most prevalent ESBL gene, blaCTX-M-1, and the AmpC cephalosporinase gene blaCMY-2 were identified on various conjugative IncI1 plasmids of different sequence types and with different additional non-&#x3b2;-lactam phenotypes. Interestingly, the blaCTX-M-2 gene was located on large multireplicon IncHI2/P plasmids. In addition, highly ESC-resistant strains contained both the ESBL CTX-M-2 and the AmpC CMY-2 encoded by the IncHI2/P and IncI1 plasmids, respectively. All ESC-resistant serovar Paratyphi B dT+ strains belonged to sequence type 28 and showed the common PFGE pattern X8, as well as the chromosomal class 2 integron cassette array dfrA1-sat2-aadA1 previously described in the European poultry-associated serovar Paratyphi B dT+ clonal population.<br><br>CONCLUSIONS: This study showed that the clonal population of multidrug-resistant serovar Paratyphi B dT+, persisting in broilers in Belgium for the last decade, recently acquired various plasmid-borne ESC resistance determinants, constituting a major concern for public health. Further surveillance programmes and research are an absolute necessity to understand their epidemiology and to propose interventions to limit the spread of ESC- and multidrug-resistant Salmonella spp.}, }
@article {pmid24376718, year = {2013}, author = {Beury-Cirou, A and Tannières, M and Minard, C and Soulère, L and Rasamiravaka, T and Dodd, RH and Queneau, Y and Dessaux, Y and Guillou, C and Vandeputte, OM and Faure, D}, title = {At a supra-physiological concentration, human sexual hormones act as quorum-sensing inhibitors.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e83564}, pmid = {24376718}, issn = {1932-6203}, mesh = {Agrobacterium tumefaciens/cytology/drug effects/genetics ; Bacterial Proteins/chemistry/genetics/metabolism ; Dose-Response Relationship, Drug ; Drug Evaluation, Preclinical ; Gene Transfer, Horizontal/drug effects ; Gonadal Steroid Hormones/chemistry/metabolism/*pharmacology ; Humans ; Indoles/chemistry/pharmacology ; Inhibitory Concentration 50 ; Models, Molecular ; Plasmids/genetics ; Protein Conformation ; Pseudomonas aeruginosa/cytology/drug effects ; Quorum Sensing/*drug effects ; Tyramine/analogs &amp; derivatives/pharmacology ; }, abstract = {N-acylhomoserine lactone (AHL)-mediated quorum-sensing (QS) regulates virulence functions in plant and animal pathogens such as Agrobacterium tumefaciens and Pseudomonas aeruginosa. A chemolibrary of more than 3500 compounds was screened using two bacterial AHL-biosensors to identify QS-inhibitors (QSIs). The purity and structure of 15 QSIs selected through this screening were verified using HPLC MS/MS tools and their activity tested on the A. tumefaciens and P. aeruginosa bacterial models. The IC50 value of the identified QSIs ranged from 2.5 to 90 µg/ml, values that are in the same range as those reported for the previously identified QSI 4-nitropyridine-N-oxide (IC50 24 µg/ml). Under the tested culture conditions, most of the identified QSIs did not exhibit bacteriostatic or bactericidal activities. One third of the tested QSIs, including the plant compound hordenine and the human sexual hormone estrone, decreased the frequency of the QS-regulated horizontal transfer of the tumor-inducing (Ti) plasmid in A. tumefaciens. Hordenine, estrone as well as its structural relatives estriol and estradiol, also decreased AHL accumulation and the expression of six QS-regulated genes (lasI, lasR, lasB, rhlI, rhlR, and rhlA) in cultures of the opportunist pathogen P. aeruginosa. Moreover, the ectopic expression of the AHL-receptors RhlR and LasR of P. aeruginosa in E. coli showed that their gene-regulatory activity was affected by the QSIs. Finally, modeling of the structural interactions between the human hormones and AHL-receptors LasR of P. aeruginosa and TraR of A. tumefaciens confirmed the competitive binding capability of the human sexual hormones. This work indicates potential interferences between bacterial and eukaryotic hormonal communications.}, }
@article {pmid24375688, year = {2014}, author = {List, JM and Nelson-Sathi, S and Geisler, H and Martin, W}, title = {Networks of lexical borrowing and lateral gene transfer in language and genome evolution.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {36}, number = {2}, pages = {141-150}, pmid = {24375688}, issn = {1521-1878}, mesh = {Biological Evolution ; Gene Transfer, Horizontal/*genetics ; Prokaryotic Cells/metabolism ; }, abstract = {Like biological species, languages change over time. As noted by Darwin, there are many parallels between language evolution and biological evolution. Insights into these parallels have also undergone change in the past 150 years. Just like genes, words change over time, and language evolution can be likened to genome evolution accordingly, but what kind of evolution? There are fundamental differences between eukaryotic and prokaryotic evolution. In the former, natural variation entails the gradual accumulation of minor mutations in alleles. In the latter, lateral gene transfer is an integral mechanism of natural variation. The study of language evolution using biological methods has attracted much interest of late, most approaches focusing on language tree construction. These approaches may underestimate the important role that borrowing plays in language evolution. Network approaches that were originally designed to study lateral gene transfer may provide more realistic insights into the complexities of language evolution.}, }
@article {pmid24373130, year = {2014}, author = {Scheublin, TR and Deusch, S and Moreno-Forero, SK and Müller, JA and van der Meer, JR and Leveau, JH}, title = {Transcriptional profiling of Gram-positive Arthrobacter in the phyllosphere: induction of pollutant degradation genes by natural plant phenolic compounds.}, journal = {Environmental microbiology}, volume = {16}, number = {7}, pages = {2212-2225}, doi = {10.1111/1462-2920.12375}, pmid = {24373130}, issn = {1462-2920}, mesh = {Agar ; Arbutin/biosynthesis ; Arthrobacter/*genetics/metabolism ; Biodegradation, Environmental ; Chlorophenols/metabolism ; *Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; *Genome, Bacterial ; Hydroquinones/metabolism ; Molecular Sequence Annotation ; Phaseolus/metabolism/*microbiology ; Phenol/metabolism ; Plant Leaves/metabolism/*microbiology ; Transcriptome ; }, abstract = {Arthrobacter chlorophenolicus A6 is a Gram-positive, 4-chlorophenol-degrading soil bacterium that was recently shown to be an effective colonizer of plant leaf surfaces. The genetic basis for this phyllosphere competency is unknown. In this paper, we describe the genome-wide expression profile of A.chlorophenolicus on leaves of common bean (Phaseolus vulgaris) compared with growth on agar surfaces. In phyllosphere-grown cells, we found elevated expression of several genes known to contribute to epiphytic fitness, for example those involved in nutrient acquisition, attachment, stress response and horizontal gene transfer. A surprising result was the leaf-induced expression of a subset of the so-called cph genes for the degradation of 4-chlorophenol. This subset encodes the conversion of the phenolic compound hydroquinone to 3-oxoadipate, and was shown to be induced not only by 4-chlorophenol but also hydroquinone, its glycosylated derivative arbutin, and phenol. Small amounts of hydroquinone, but not arbutin or phenol, were detected in leaf surface washes of P.vulgaris by gas chromatography-mass spectrometry. Our findings illustrate the utility of genomics approaches for exploration and improved understanding of a microbial habitat. Also, they highlight the potential for phyllosphere-based priming of bacteria to stimulate pollutant degradation, which holds promise for the application of phylloremediation.}, }
@article {pmid24372031, year = {2013}, author = {Taniguchi, Y and Yamada, Y and Maruyama, O and Kuhara, S and Ikeda, D}, title = {The purity measure for genomic regions leads to horizontally transferred genes.}, journal = {Journal of bioinformatics and computational biology}, volume = {11}, number = {6}, pages = {1343002}, doi = {10.1142/S0219720013430026}, pmid = {24372031}, issn = {1757-6334}, mesh = {*DNA Transposable Elements ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; *Models, Genetic ; *RNA, Bacterial ; }, abstract = {Sequence analysis is important to understand a genome, and a number of approaches such as sequence alignments and hidden Markov models have been employed. In the field of text mining, the purity measure is developed to detect unusual regions of a string without any domain knowledge. It is reported in that work that only RNAs and transposons are shown to have high purity values. In this work, the purity values of regions of various bacterial genome sequences are computed, and those regions are analyzed extensively. It is found that mobile elements and phages as well as RNAs and transposons have high purity values. It is interesting that they are all classified into a group of horizontally transferred genes. This means that the purity measure is useful to predict horizontally transferred genes.}, }
@article {pmid24369756, year = {2013}, author = {Richards, VP and Choi, SC and Pavinski Bitar, PD and Gurjar, AA and Stanhope, MJ}, title = {Transcriptomic and genomic evidence for Streptococcus agalactiae adaptation to the bovine environment.}, journal = {BMC genomics}, volume = {14}, number = {}, pages = {920}, pmid = {24369756}, issn = {1471-2164}, support = {AI073368/AI/NIAID NIH HHS/United States ; }, mesh = {Adaptation, Physiological/*genetics ; Animals ; Cattle/microbiology ; *Ecotype ; Female ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; Lactose/metabolism ; Mammary Glands, Animal/microbiology ; Mastitis, Bovine/microbiology ; Milk/microbiology ; Operon ; Phylogeny ; Streptococcus agalactiae/*genetics ; Transcriptome ; }, abstract = {BACKGROUND: Streptococcus agalactiae is a major cause of bovine mastitis, which is the dominant health disorder affecting milk production within the dairy industry and is responsible for substantial financial losses to the industry worldwide. However, there is considerable evidence for host adaptation (ecotypes) within S. agalactiae, with both bovine and human sourced isolates showing a high degree of distinctiveness, suggesting differing ability to cause mastitis. Here, we (i) generate RNAseq data from three S. agalactiae isolates (two putative bovine adapted and one human) and (ii) compare publicly available whole genome shotgun sequence data from an additional 202 isolates, obtained from six host species, to elucidate possible genetic factors/adaptations likely important for S. agalactiae growth and survival in the bovine mammary gland.<br><br>RESULTS: Tests for differential expression showed distinct expression profiles for the three isolates when grown in bovine milk. A key finding for the two putatively bovine adapted isolates was the up regulation of a lactose metabolism operon (Lac.2) that was strongly correlated with the bovine environment (all 36 bovine sourced isolates on GenBank possessed the operon, in contrast to only 8/151 human sourced isolates). Multi locus sequence typing of all genome sequences and phylogenetic analysis using conserved operon genes from 44&#x2009;S. agalactiae isolates and 16 additional Streptococcus species provided strong evidence for acquisition of the operon via multiple lateral gene transfer events, with all Streptococcus species known to be major causes of mastitis, identified as possible donors. Furthermore, lactose fermentation tests were only positive for isolates possessing Lac.2. Combined, these findings suggest that lactose metabolism is likely an important adaptation to the bovine environment. Additional up regulation in the bovine adapted isolates included genes involved in copper homeostasis, metabolism of purine, pyrimidine, glycerol and glucose, and possibly aminoglycoside antibiotic resistance.<br><br>CONCLUSION: We detected several genetic factors likely important in S. agalactiae's adaptation to the bovine environment, in particular lactose metabolism. Of concern is the up regulation of a putative antibiotic resistance gene (GCN5-related N-acetyltransferase) that might reflect an adaptation to the use of aminoglycoside antibiotics within this environment.}, }
@article {pmid24369123, year = {2014}, author = {Ng, V and Lin, WJ}, title = {Comparison of assembled Clostridium botulinum A1 genomes revealed their evolutionary relationship.}, journal = {Genomics}, volume = {103}, number = {1}, pages = {94-106}, pmid = {24369123}, issn = {1089-8646}, support = {SC3 GM086303/GM/NIGMS NIH HHS/United States ; 1SC3 GM086303/GM/NIGMS NIH HHS/United States ; }, mesh = {Chromosome Mapping ; Clostridium botulinum/*genetics ; Comparative Genomic Hybridization ; DNA, Bacterial/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Microarray Analysis ; Multigene Family ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Clostridium botulinum encompasses bacteria that produce at least one of the seven serotypes of botulinum neurotoxin (BoNT/A-G). The availability of genome sequences of four closely related Type A1 or A1(B) strains, as well as the A1-specific microarray, allowed the analysis of their genomic organizations and evolutionary relationship. The four genomes share >90% core genes and >96% functional groups. Phylogenetic analysis based on COG shows closer relations of the A1(B) strain, NCTC 2916, to B1 and F1 than A1 strains. Alignment of the genomes of the three A1 strains revealed a highly similar chromosomal structure with three small gaps in the genome of ATCC 19397 and one additional gap in the genome of Hall A, suggesting ATCC 19379 as an evolutionary intermediate between Hall A and ATCC 3502. Analyses of the four gap regions indicated potential horizontal gene transfer and recombination events important for the evolution of A1 strains.}, }
@article {pmid24368349, year = {2014}, author = {Chen, K and Reuter, M and Sanghvi, B and Roberts, GA and Cooper, LP and Tilling, M and Blakely, GW and Dryden, DT}, title = {ArdA proteins from different mobile genetic elements can bind to the EcoKI Type I DNA methyltransferase of E. coli K12.}, journal = {Biochimica et biophysica acta}, volume = {1844}, number = {3}, pages = {505-511}, pmid = {24368349}, issn = {0006-3002}, support = {090288/Z/09/ZA/WT_/Wellcome Trust/United Kingdom ; BB/D001870/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; GR080463MA/WT_/Wellcome Trust/United Kingdom ; BB/C511599/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Chromatography, Gel ; Circular Dichroism ; Escherichia coli K12/enzymology/*metabolism ; Escherichia coli Proteins/chemistry/*metabolism ; *Interspersed Repetitive Sequences ; Models, Molecular ; Protein Binding ; Protein Denaturation ; Protein Structure, Secondary ; Repressor Proteins/chemistry/*metabolism ; Site-Specific DNA-Methyltransferase (Adenine-Specific)/*metabolism ; }, abstract = {Anti-restriction and anti-modification (anti-RM) is the ability to prevent cleavage by DNA restriction-modification (RM) systems of foreign DNA entering a new bacterial host. The evolutionary consequence of anti-RM is the enhanced dissemination of mobile genetic elements. Homologues of ArdA anti-RM proteins are encoded by genes present in many mobile genetic elements such as conjugative plasmids and transposons within bacterial genomes. The ArdA proteins cause anti-RM by mimicking the DNA structure bound by Type I RM enzymes. We have investigated ArdA proteins from the genomes of Enterococcus faecalis V583, Staphylococcus aureus Mu50 and Bacteroides fragilis NCTC 9343, and compared them to the ArdA protein expressed by the conjugative transposon Tn916. We find that despite having very different structural stability and secondary structure content, they can all bind to the EcoKI methyltransferase, a core component of the EcoKI Type I RM system. This finding indicates that the less structured ArdA proteins become fully folded upon binding. The ability of ArdA from diverse mobile elements to inhibit Type I RM systems from other bacteria suggests that they are an advantage for transfer not only between closely-related bacteria but also between more distantly related bacterial species.}, }
@article {pmid24367362, year = {2013}, author = {Rapa, RA and Labbate, M}, title = {The function of integron-associated gene cassettes in Vibrio species: the tip of the iceberg.}, journal = {Frontiers in microbiology}, volume = {4}, number = {}, pages = {385}, pmid = {24367362}, issn = {1664-302X}, abstract = {The integron is a genetic element that incorporates mobile genes termed gene cassettes into a reserved genetic site via site-specific recombination. It is best known for its role in antibiotic resistance with one type of integron, the class 1 integron, a major player in the dissemination of antibiotic resistance genes across Gram negative pathogens and commensals. However, integrons are ancient structures with over 100 classes (including class 1) present in bacteria from the broader environment. While, the class 1 integron is only one example of an integron being mobilized into the clinical environment, it is by far the most successful. Unlike clinical class 1 integrons which are largely found on plasmids, other integron classes are found on the chromosomes of bacteria and carry diverse gene cassettes indicating a non-antibiotic resistance role(s). However, there is very limited knowledge on what these alternative roles are. This is particularly relevant to Vibrio species where gene cassettes make up approximately 1-3% of their entire genome. In this review, we discuss how emphasis on class 1 integron research has resulted in a limited understanding by the wider research community on the role of integrons in the broader environment. This has the capacity to be counterproductive in solving or improving the antibiotic resistance problem into the future. Furthermore, there is still a significant lack of knowledge on how gene cassettes in Vibrio species drive adaptation and evolution. From research in Vibrio rotiferianus DAT722, new insight into how gene cassettes affect cellular physiology offers new alternative roles for the gene cassette resource. At least a subset of gene cassettes are involved in host surface polysaccharide modification suggesting that gene cassettes may be important in processes such as bacteriophage resistance, adhesion/biofilm formation, protection from grazers and bacterial aggregation.}, }
@article {pmid24365712, year = {2014}, author = {Brembu, T and Winge, P and Tooming-Klunderud, A and Nederbragt, AJ and Jakobsen, KS and Bones, AM}, title = {The chloroplast genome of the diatom Seminavis robusta: new features introduced through multiple mechanisms of horizontal gene transfer.}, journal = {Marine genomics}, volume = {16}, number = {}, pages = {17-27}, doi = {10.1016/j.margen.2013.12.002}, pmid = {24365712}, issn = {1876-7478}, mesh = {Diatoms/classification/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Chloroplast/*genetics ; Phylogeny ; Plasmids/genetics ; }, abstract = {The chloroplasts of heterokont algae such as diatoms are the result of a secondary endosymbiosis event, in which a red alga was engulfed by a non-photosynthetic eukaryote. The diatom chloroplast genomes sequenced to date show a high degree of similarity, but some examples of gene replacement or introduction of genes through horizontal gene transfer are known. The evolutionary origin of the gene transfers is unclear. We have sequenced and characterised the complete chloroplast genome and a putatively chloroplast-associated plasmid of the pennate diatom Seminavis robusta. The chloroplast genome contains two introns, a feature that has not previously been found in diatoms. The group II intron of atpB appears to be recently transferred from a Volvox-like green alga. The S. robusta chloroplast genome (150,905 bp) is the largest diatom chloroplast genome characterised to date, mainly due to the presence of four large gene-poor regions. Open reading frames (ORFs) encoded by the gene-poor regions show similarity to putative proteins encoded by the chloroplast genomes of different heterokonts, as well as the plasmids pCf1 and pCf2 found in the diatom Cylindrotheca fusiformis. A tyrosine recombinase and a serine recombinase are encoded by the S. robusta chloroplast genome, indicating a possible mechanism for the introduction of novel genes. A plasmid with similarity to pCf2 was also identified. Phylogenetic analyses of three ORFs identified on pCf2 suggest that two of them are part of an operon-like gene cluster conserved in bacteria. Several genetic elements have moved through horizontal gene transfer between the chloroplast genomes of different heterokonts. Two recombinases are likely to promote such gene insertion events, and the plasmid identified may act as vectors in this process. The copy number of the plasmid was similar to that of the plastid genome indicating a plastid localization.}, }
@article {pmid24364333, year = {2013}, author = {Liang, XM and Nie, XP and Shi, Z}, title = {[Preliminary studies on the occurrence of antibiotic resistance genes in typical aquaculture area of the Pearl River Estuary].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {34}, number = {10}, pages = {4073-4080}, pmid = {24364333}, issn = {0250-3301}, mesh = {Anti-Bacterial Agents ; *Aquaculture ; China ; Drug Resistance, Microbial/*genetics ; Estuaries ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Polymerase Chain Reaction ; Rivers ; *Water Microbiology ; }, abstract = {Traditional and quantitative PCR techniques were used to determine the occurrence and quantities of ARGs, including three types of genes resistant to sulfonamide, seven for tetracycline resistance and one for quinolone resistance, as well as one integron gene in typical aquaculture of the Pearl River Estuary. The results showed that all genes except for tetW were detectable in the aquaculture environment, and sull, sul2 and int1 were the most frequently detected genes (detectable percentage, 100%). Relative abundances of ARGs increased with the prolongation of rearing time under the same aquaculture pattern, suggesting a cumulative effect. Moreover, the occurrences of ARGs in the ponds were different with different aquaculture patterns, indicating that the aquaculture pattern might play an important role in the abundances and distributions of ARGs. Relative abundances of intl, as a horizontal mobile genetic element, were significantly correlated to the levels of sull and the total ARGs (P < 0. 05). The total concentration of antibiotics exhibited a good positive correlation with the total concentration of ARGs in sediments (P <0. 05). All results elucidated that extensive residues of antibiotics in the aquaculture substantially increased the abundances of ARGs probably owning to the induction of horizontal gene transfer of ARGs among bacteria.}, }
@article {pmid24361902, year = {2014}, author = {Sabharwal, V and Stevenson, A and Figueira, M and Orthopoulos, G and Trzciński, K and Pelton, SI}, title = {Capsular switching as a strategy to increase pneumococcal virulence in experimental otitis media model.}, journal = {Microbes and infection}, volume = {16}, number = {4}, pages = {292-299}, doi = {10.1016/j.micinf.2013.12.002}, pmid = {24361902}, issn = {1769-714X}, support = {KL2RR025770/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Bacterial Capsules/*chemistry/*immunology ; Chinchilla ; Complement C3/immunology/metabolism ; Disease Models, Animal ; Humans ; Otitis Media/*immunology/*microbiology/pathology ; Pneumococcal Infections/immunology/microbiology ; Recombination, Genetic ; Streptococcus pneumoniae/*chemistry/*immunology/isolation &amp; purification ; Virulence ; }, abstract = {We hypothesized that capsular switch event, in which pneumococcus acquires a new capsule operon by horizontal gene transfer, may result in emergence of strains with increased virulence in acute otitis media. Using serotype 6A strain from a patient with invasive pneumococcal disease and clonally distant serotype 6C strain isolated from asymptomatic carrier we created 6A:6C (6A background with 6C capsule) capsular transformants and applied whole genome macro-restriction analysis to assess conservation of the 6A chassis. Next, we assessed complement (C3) and antibodies deposition on surface of pneumococcal cells and tested capsule recipient, capsule donor and two 6A:6C transformants for virulence in chinchilla experimental otitis media model. Both 6A:6C(1 or 2) transformants bound less C3 compared to 6C capsule-donor strain but more compared to serotype 6A capsule-recipient strain. Pneumococci were present in significantly higher proportion of ears among animals challenged with either of two 6A:6C(1 or 2) transformants compared to chinchillas infected with 6C capsule-donor strain [p < 0.001] whereas a significantly decreased proportion of ears were infected with 6A:6C(1 or 2) transformants as compared to 6A capsule-recipient strain. Our observations though limited to two serotypes demonstrate that capsular switch events can result in Streptococcus pneumoniae strains of enhanced virulence for respiratory tract infection.}, }
@article {pmid24361203, year = {2014}, author = {García-Bayona, L and Garavito, MF and Lozano, GL and Vasquez, JJ and Myers, K and Fry, WE and Bernal, A and Zimmermann, BH and Restrepo, S}, title = {De novo pyrimidine biosynthesis in the oomycete plant pathogen Phytophthora infestans.}, journal = {Gene}, volume = {537}, number = {2}, pages = {312-321}, doi = {10.1016/j.gene.2013.12.009}, pmid = {24361203}, issn = {1879-0038}, mesh = {Alternative Splicing ; Cloning, Molecular ; Dihydroorotase/genetics/metabolism ; Orotate Phosphoribosyltransferase/genetics/metabolism ; Orotidine-5'-Phosphate Decarboxylase/genetics/metabolism ; Phylogeny ; Phytophthora infestans/*genetics/*metabolism/*pathogenicity ; Pyrimidines/*biosynthesis/metabolism ; Solanum/microbiology ; }, abstract = {The oomycete Phytophthora infestans, causal agent of the tomato and potato late blight, generates important economic and environmental losses worldwide. As current control strategies are becoming less effective, there is a need for studies on oomycete metabolism to help identify promising and more effective targets for chemical control. The pyrimidine pathways are attractive metabolic targets to combat tumors, virus and parasitic diseases but have not yet been studied in Phytophthora. Pyrimidines are involved in several critical cellular processes and play structural, metabolic and regulatory functions. Here, we used genomic and transcriptomic information to survey the pyrimidine metabolism during the P. infestans life cycle. After assessing the putative gene machinery for pyrimidine salvage and de novo synthesis, we inferred genealogies for each enzymatic domain in the latter pathway, which displayed a mosaic origin. The last two enzymes of the pathway, orotate phosphoribosyltransferase and orotidine-5-monophosphate decarboxylase, are fused in a multi-domain enzyme and are duplicated in some P. infestans strains. Two splice variants of the third gene (dihydroorotase) were identified, one of them encoding a premature stop codon generating a non-functional truncated protein. Relative expression profiles of pyrimidine biosynthesis genes were evaluated by qRT-PCR during infection in Solanum phureja. The third and fifth genes involved in this pathway showed high up-regulation during biotrophic stages and down-regulation during necrotrophy, whereas the uracil phosphoribosyl transferase gene involved in pyrimidine salvage showed the inverse behavior. These findings suggest the importance of de novo pyrimidine biosynthesis during the fast replicative early infection stages and highlight the dynamics of the metabolism associated with the hemibiotrophic life style of pathogen.}, }
@article {pmid24359207, year = {2013}, author = {Layeghifard, M and Peres-Neto, PR and Makarenkov, V}, title = {Inferring explicit weighted consensus networks to represent alternative evolutionary histories.}, journal = {BMC evolutionary biology}, volume = {13}, number = {}, pages = {274}, pmid = {24359207}, issn = {1471-2148}, mesh = {*Algorithms ; *Biological Evolution ; Evolution, Molecular ; Gene Transfer, Horizontal ; Hybridization, Genetic ; *Phylogeny ; }, abstract = {BACKGROUND: The advent of molecular biology techniques and constant increase in availability of genetic material have triggered the development of many phylogenetic tree inference methods. However, several reticulate evolution processes, such as horizontal gene transfer and hybridization, have been shown to blur the species evolutionary history by causing discordance among phylogenies inferred from different genes.<br><br>METHODS: To tackle this problem, we hereby describe a new method for inferring and representing alternative (reticulate) evolutionary histories of species as an explicit weighted consensus network which can be constructed from a collection of gene trees with or without prior knowledge of the species phylogeny.<br><br>RESULTS: We provide a way of building a weighted phylogenetic network for each of the following reticulation mechanisms: diploid hybridization, intragenic recombination and complete or partial horizontal gene transfer. We successfully tested our method on some synthetic and real datasets to infer the above-mentioned evolutionary events which may have influenced the evolution of many species.<br><br>CONCLUSIONS: Our weighted consensus network inference method allows one to infer, visualize and validate statistically major conflicting signals induced by the mechanisms of reticulate evolution. The results provided by the new method can be used to represent the inferred conflicting signals by means of explicit and easy-to-interpret phylogenetic networks.}, }
@article {pmid24357311, year = {2013}, author = {Rice, DW and Alverson, AJ and Richardson, AO and Young, GJ and Sanchez-Puerta, MV and Munzinger, J and Barry, K and Boore, JL and Zhang, Y and dePamphilis, CW and Knox, EB and Palmer, JD}, title = {Horizontal transfer of entire genomes via mitochondrial fusion in the angiosperm Amborella.}, journal = {Science (New York, N.Y.)}, volume = {342}, number = {6165}, pages = {1468-1473}, doi = {10.1126/science.1246275}, pmid = {24357311}, issn = {1095-9203}, support = {R01-GM-76012/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Sequence ; Bryophyta/classification/genetics ; Chlorophyta/classification/genetics ; DNA, Mitochondrial/*genetics ; *Gene Transfer, Horizontal ; *Genome, Plant ; Membrane Fusion ; *Mitochondrial Dynamics ; Molecular Sequence Data ; Phylogeny ; Tracheophyta/classification/*genetics ; }, abstract = {We report the complete mitochondrial genome sequence of the flowering plant Amborella trichopoda. This enormous, 3.9-megabase genome contains six genome equivalents of foreign mitochondrial DNA, acquired from green algae, mosses, and other angiosperms. Many of these horizontal transfers were large, including acquisition of entire mitochondrial genomes from three green algae and one moss. We propose a fusion-compatibility model to explain these findings, with Amborella capturing whole mitochondria from diverse eukaryotes, followed by mitochondrial fusion (limited mechanistically to green plant mitochondria) and then genome recombination. Amborella's epiphyte load, propensity to produce suckers from wounds, and low rate of mitochondrial DNA loss probably all contribute to the high level of foreign DNA in its mitochondrial genome.}, }
@article {pmid24357306, year = {2013}, author = {Adams, K}, title = {Genomics. Genomic clues to the ancestral flowering plant.}, journal = {Science (New York, N.Y.)}, volume = {342}, number = {6165}, pages = {1456-1457}, doi = {10.1126/science.1248709}, pmid = {24357306}, issn = {1095-9203}, mesh = {Contig Mapping/*methods ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Flowers/*genetics ; *Gene Transfer, Horizontal ; *Genome, Plant ; *Mitochondrial Dynamics ; Sequence Analysis, DNA/*methods ; Tracheophyta/*genetics/*growth &amp; development ; }, }
@article {pmid24349398, year = {2013}, author = {Urbanczyk, H and Urbanczyk, Y and Hayashi, T and Ogura, Y}, title = {Diversification of two lineages of symbiotic Photobacterium.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e82917}, pmid = {24349398}, issn = {1932-6203}, mesh = {Animals ; DNA, Bacterial/*genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial/*physiology ; Nucleic Acid Hybridization ; *Photobacterium/classification/genetics ; *Phylogeny ; Symbiosis/*genetics ; }, abstract = {Understanding of processes driving bacterial speciation requires examination of closely related, recently diversified lineages. To gain an insight into diversification of bacteria, we conducted comparative genomic analysis of two lineages of bioluminescent symbionts, Photobacterium leiognathi and 'P. mandapamensis'. The two lineages are evolutionary and ecologically closely related. Based on the methods used in bacterial taxonomy for classification of new species (DNA-DNA hybridization and ANI), genetic relatedness of the two lineages is at a cut-off point for species delineation. In this study, we obtained the whole genome sequence of a representative P. leiognathi strain lrivu.4.1, and compared it to the whole genome sequence of 'P. mandapamensis' svers.1.1. Results of the comparative genomic analysis suggest that P. leiognathi has a more plastic genome and acquired genes horizontally more frequently than 'P. mandapamensis'. We predict that different rates of recombination and gene acquisition contributed to diversification of the two lineages. Analysis of lineage-specific sequences in 25 strains of P. leiognathi and 'P. mandapamensis' found no evidence that bioluminescent symbioses with specific host animals have played a role in diversification of the two lineages.}, }
@article {pmid24349319, year = {2013}, author = {Nakabachi, A and Nikoh, N and Oshima, K and Inoue, H and Ohkuma, M and Hongoh, Y and Miyagishima, SY and Hattori, M and Fukatsu, T}, title = {Horizontal gene acquisition of Liberibacter plant pathogens from a bacteriome-confined endosymbiont of their psyllid vector.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e82612}, pmid = {24349319}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Amino Acid Transport Systems/chemistry/genetics ; Animals ; Bacterial Proteins/chemistry/genetics ; Gene Order ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Hemiptera/*microbiology ; *Host-Pathogen Interactions ; Insect Vectors/*microbiology ; Molecular Sequence Data ; Phylogeny ; Rhizobiaceae/classification/*genetics ; Sequence Alignment ; }, abstract = {he Asian citrus psyllid Diaphorina citri is a notorious agricultural pest that transmits the phloem-inhabiting alphaproteobacterial 'Candidatus Liberibacter asiaticus' and allied plant pathogens, which cause the devastating citrus disease called Huanglongbing or greening disease. D. citri harbors two distinct bacterial mutualists in the symbiotic organ called bacteriome: the betaproteobacterium 'Candidatus Profftella armatura' in the syncytial cytoplasm at the center of the bacteriome, and the gammaproteobacterium 'Candidatus Carsonella ruddii' in uninucleate bacteriocytes. Here we report that a putative amino acid transporter LysE of Profftella forms a highly supported clade with proteins of L. asiaticus, L. americanus, and L. solanacearum. L. crescens, the most basal Liberibacter lineage currently known, lacked the corresponding gene. The Profftella-Liberibacter subclade of LysE formed a clade with proteins from betaproteobacteria of the order Burkholderiales, to which Profftella belongs. This phylogenetic pattern favors the hypothesis that the Liberibacter lineage acquired the gene from the Profftella lineage via horizontal gene transfer (HGT) after L. crescens diverged from other Liberibacter lineages. K A/K S analyses further supported the hypothesis that the genes encoded in the Liberibacter genomes are functional. These findings highlight the possible evolutionary importance of HGT between plant pathogens and their insect vector's symbionts that are confined in the symbiotic organ and seemingly sequestered from external microbial populations.}, }
@article {pmid24348465, year = {2013}, author = {Valia, R and Taviani, E and Spagnoletti, M and Ceccarelli, D and Cappuccinelli, P and Colombo, MM}, title = {Vibrio cholerae O1 epidemic variants in Angola: a retrospective study between 1992 and 2006.}, journal = {Frontiers in microbiology}, volume = {4}, number = {}, pages = {354}, pmid = {24348465}, issn = {1664-302X}, abstract = {Cholera is still a major public health concern in many African countries. In Angola, after a decade of absence, cholera reemerged in 1987, spreading throughout the country until 1996, with outbreaks recurring in a seasonal pattern. In 2006 Angola was hit by one of the most severe outbreaks of the last decade, with ca. 240,000 cases reported. We analyzed 21 clinical strains isolated between 1992 and 2006 from several provinces throughout the country: Benguela, Bengo, Luanda, Cuando Cubango, and Cabinda. We used two multiplex PCR assays to investigate discriminatory mobile genetic elements (MGE) [Integrative Conjugative Elements (ICEs), VSP-II, GI12, GI14, GI15, K, and TLC phages] and we compared the profiles obtained with those of different reference V. cholerae O1 variants (prototypical, altered, and hybrid), responsible for the ongoing 7th pandemic. We also tested the strains for the presence of specific VSP-II variants and for the presence of a genomic island (GI) (WASA-1), correlated with the transmission of seventh pandemic cholera from Africa to South America. Based on the presence/absence of the analyzed genetic elements, five novel profiles were detected in the epidemic strains circulating in the 1990s. The most frequent profiles, F and G, were characterized by the absence of ICEs and the three GIs tested, and the presence of GI WASA-1 and the WASA variant of the VSP-II island. Our results identified unexpected variability within the 1990s epidemic, showing different rearrangements in a dynamic part of the genome not present in the prototypical V. cholerae O1 N16961. Moreover the 2006 strains differed from the current pandemic V. cholerae O1 strain. Taken together, our results highlight the role of horizontal gene transfer (HGT) in diversifying the genetic background of V. cholerae within a single epidemic.}, }
@article {pmid24347631, year = {2014}, author = {Takeuchi, N and Kaneko, K and Koonin, EV}, title = {Horizontal gene transfer can rescue prokaryotes from Muller's ratchet: benefit of DNA from dead cells and population subdivision.}, journal = {G3 (Bethesda, Md.)}, volume = {4}, number = {2}, pages = {325-339}, pmid = {24347631}, issn = {2160-1836}, support = {//Intramural NIH HHS/United States ; }, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Cell Death ; *Gene Transfer, Horizontal ; Homologous Recombination ; *Models, Genetic ; }, abstract = {Horizontal gene transfer (HGT) is a major factor in the evolution of prokaryotes. An intriguing question is whether HGT is maintained during evolution of prokaryotes owing to its adaptive value or is a byproduct of selection driven by other factors such as consumption of extracellular DNA (eDNA) as a nutrient. One hypothesis posits that HGT can restore genes inactivated by mutations and thereby prevent stochastic, irreversible deterioration of genomes in finite populations known as Muller's ratchet. To examine this hypothesis, we developed a population genetic model of prokaryotes undergoing HGT via homologous recombination. Analysis of this model indicates that HGT can prevent the operation of Muller's ratchet even when the source of transferred genes is eDNA that comes from dead cells and on average carries more deleterious mutations than the DNA of recipient live cells. Moreover, if HGT is sufficiently frequent and eDNA diffusion sufficiently rapid, a subdivided population is shown to be more resistant to Muller's ratchet than an undivided population of an equal overall size. Thus, to maintain genomic information in the face of Muller's ratchet, it is more advantageous to partition individuals into multiple subpopulations and let them "cross-reference" each other's genetic information through HGT than to collect all individuals in one population and thereby maximize the efficacy of natural selection. Taken together, the results suggest that HGT could be an important condition for the long-term maintenance of genomic information in prokaryotes through the prevention of Muller's ratchet.}, }
@article {pmid24346234, year = {2014}, author = {Ching, TH and Yoza, BA and Li, QX}, title = {Quartet analysis of putative horizontal gene transfer in Crenarchaeota.}, journal = {Journal of molecular evolution}, volume = {78}, number = {2}, pages = {163-170}, pmid = {24346234}, issn = {1432-1432}, support = {5P20RR016467-11/RR/NCRR NIH HHS/United States ; 8 P20 GM103466-11/GM/NIGMS NIH HHS/United States ; }, mesh = {Computational Biology ; Crenarchaeota/classification/*genetics ; Ferredoxins/genetics ; *Gene Transfer, Horizontal ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Horizontal gene transfers (HGT) between four Crenarchaeota species (Metallosphaera cuprina Ar-4T, Acidianus hospitalis W1T, Vulcanisaeta moutnovskia 768-28T, and Pyrobaculum islandicum DSM 4184T) were investigated with quartet analysis. Strong support was found for individual genes that disagree with the phylogeny of the majority, implying genomic mosaicism. One such gene, a ferredoxin-related gene, was investigated further and incorporated into a larger phylogeny, which provided evidence for HGT of this gene from the Vulcanisaeta lineage to the Acidianus lineage. This is the first application of quartet analysis of HGT for the phylum Crenarchaeota. The results have shown that quartet analysis is a powerful technique to screen homologous sequences for putative HGTs and is useful in visually describing genomic mosaicism and HGT within four taxa.}, }
@article {pmid24345744, year = {2013}, author = {Planet, PJ and LaRussa, SJ and Dana, A and Smith, H and Xu, A and Ryan, C and Uhlemann, AC and Boundy, S and Goldberg, J and Narechania, A and Kulkarni, R and Ratner, AJ and Geoghegan, JA and Kolokotronis, SO and Prince, A}, title = {Emergence of the epidemic methicillin-resistant Staphylococcus aureus strain USA300 coincides with horizontal transfer of the arginine catabolic mobile element and speG-mediated adaptations for survival on skin.}, journal = {mBio}, volume = {4}, number = {6}, pages = {e00889-13}, pmid = {24345744}, issn = {2150-7511}, support = {K08 AI090013/AI/NIAID NIH HHS/United States ; R01 HL079395/HL/NHLBI NIH HHS/United States ; UL1 TR000040/TR/NCATS NIH HHS/United States ; K08 AI101005/AI/NIAID NIH HHS/United States ; R01 AI 103854/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/metabolism ; Biotransformation ; DNA, Bacterial/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Humans ; Interspersed Repetitive Sequences ; Methicillin-Resistant Staphylococcus aureus/*genetics/*physiology ; *Microbial Viability ; Phylogeny ; Polyamines/*metabolism ; Skin/*microbiology ; Staphylococcus epidermidis/*genetics ; }, abstract = {UNLABELLED: The arginine catabolic mobile element (ACME) is the largest genomic region distinguishing epidemic USA300 strains of methicillin-resistant Staphylococcus aureus (MRSA) from other S. aureus strains. However, the functional relevance of ACME to infection and disease has remained unclear. Using phylogenetic analysis, we have shown that the modular segments of ACME were assembled into a single genetic locus in Staphylococcus epidermidis and then horizontally transferred to the common ancestor of USA300 strains in an extremely recent event. Acquisition of one ACME gene, speG, allowed USA300 strains to withstand levels of polyamines (e.g., spermidine) produced in skin that are toxic to other closely related S. aureus strains. speG-mediated polyamine tolerance also enhanced biofilm formation, adherence to fibrinogen/fibronectin, and resistance to antibiotic and keratinocyte-mediated killing. We suggest that these properties gave USA300 a major selective advantage during skin infection and colonization, contributing to the extraordinary evolutionary success of this clone.<br><br>IMPORTANCE: Over the past 15 years, methicillin-resistant Staphylococcus aureus (MRSA) has become a major public health problem. It is likely that adaptations in specific MRSA lineages (e.g., USA300) drove the spread of MRSA across the United States and allowed it to replace other, less-virulent S. aureus strains. We suggest that one major factor in the evolutionary success of MRSA may have been the acquisition of a gene (speG) that allows S. aureus to evade the toxicity of polyamines (e.g., spermidine and spermine) that are produced in human skin. Polyamine tolerance likely gave MRSA multiple fitness advantages, including the formation of more-robust biofilms, increased adherence to host tissues, and resistance to antibiotics and killing by human skin cells.}, }
@article {pmid24343895, year = {2014}, author = {Silveira, E and Freitas, AR and Antunes, P and Barros, M and Campos, J and Coque, TM and Peixe, L and Novais, C}, title = {Co-transfer of resistance to high concentrations of copper and first-line antibiotics among Enterococcus from different origins (humans, animals, the environment and foods) and clonal lineages.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {69}, number = {4}, pages = {899-906}, doi = {10.1093/jac/dkt479}, pmid = {24343895}, issn = {1460-2091}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Conjugation, Genetic ; Copper/*pharmacology ; DNA, Bacterial/genetics ; *Drug Resistance, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Enterococcus/classification/*drug effects/genetics/isolation &amp; purification ; *Environmental Microbiology ; *Food Microbiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Gram-Positive Bacterial Infections/*microbiology/veterinary ; Humans ; Multilocus Sequence Typing ; Polymerase Chain Reaction ; }, abstract = {OBJECTIVES: We studied the occurrence of diverse copper (Cu) tolerance genes from Gram-positive bacteria and their co-transfer with antibiotic resistance genes among Enterococcus from diverse sources.<br><br>METHODS: Enterococcus (n = 922) of several species and from human, animal, environment and food samples were included. Antimicrobial and CuSO4 susceptibility and conjugation assays were performed by standard procedures, bacterial screening of Cu and antibiotic resistance genes by PCR, and clonality by PFGE/multilocus sequence typing.<br><br>RESULTS: tcrB and cueO genes occurred in 15% (n = 137/922) and 14% (n = 128/922) of isolates, respectively, with the highest occurrence in piggeries (P < 0.05). They were more frequent among Enterococcus faecium (tcrB: 23% versus 8% in Enterococcus faecalis and 12% in other species; cueO: 25% versus 5% and 9%, respectively; P < 0.05). A correlation between phenotypic and genotypic assays was observed for most E. faecium (CuSO4 MIC50 = 24 mM in tcrB/cueO(+) versus CuSO4 MIC50 = 12 mM in tcrB/cueO(-)), but not for other species. Co-transfer of Cu tolerance (associated with tcrB, cueO or an unknown mechanism) with erythromycin, tetracycline, vancomycin, aminoglycosides or ampicillin resistance was demonstrated. A variety of PFGE types was detected among isolates carrying Cu tolerance mechanisms, some identified in sequence types (STs) often linked to human infections (E. faecium from ST18 and ST78 clonal lineages and E. faecalis clonal complex 2).<br><br>CONCLUSIONS: Cu tolerance might contribute to the selection/maintenance of multidrug-resistant Enterococcus (including resistance to first-line antibiotics used to treat enterococcal infections) due to the use of Cu compounds (e.g. antiseptics/animal feed supplements). The distribution of the multicopper oxidase cueO and the co-transfer of ampicillin resistance along with Cu tolerance genes are described for the first time.}, }
@article {pmid24343830, year = {2014}, author = {Locke, JB and Zurenko, GE and Shaw, KJ and Bartizal, K}, title = {Tedizolid for the management of human infections: in vitro characteristics.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {58 Suppl 1}, number = {}, pages = {S35-42}, doi = {10.1093/cid/cit616}, pmid = {24343830}, issn = {1537-6591}, mesh = {Acetamides/pharmacology/therapeutic use ; Anti-Bacterial Agents/*pharmacology/*therapeutic use ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Humans ; Linezolid ; Organophosphates/*pharmacology/*therapeutic use ; Oxazoles/*pharmacology/*therapeutic use ; Oxazolidinones/pharmacology/therapeutic use ; Point Mutation ; RNA, Ribosomal, 23S/genetics/metabolism ; Ribosomal Protein L3 ; Ribosomal Proteins/genetics ; Staphylococcal Infections/*drug therapy/microbiology ; Staphylococcus aureus/*drug effects/genetics ; tRNA Methyltransferases/metabolism ; }, abstract = {The emerging antibiotic resistance of Gram-positive pathogens represents a significant challenge to the management of human infections. The novel oxazolidinone tedizolid demonstrates antimicrobial activity across a broad range of Gram-positive pathogens and greater potency than linezolid against wild-type and drug-resistant pathogens, including linezolid-resistant Staphylococcus aureus strains possessing mutations in chromosomal genes encoding 23S rRNA or ribosomal proteins L3 or L4. Strains harboring such mutations are also selected for much less frequently with tedizolid than with linezolid. In addition, tedizolid has a significant potency advantage over linezolid-resistant strains carrying the horizontally transferable cfr gene. Methylation of A2503 of 23S rRNA by the Cfr methyltransferase confers resistance to linezolid (and a variety of other 50S ribosomal subunit-targeted antibiotics) but not to tedizolid because of structural differences in A-ring C5 substituents between the 2 drugs. The greater potency and improved resistance profile of tedizolid provides the microbiologic basis for considering this molecule as an alternative to linezolid for the treatment of serious infections caused by Gram-positive pathogens.}, }
@article {pmid24343827, year = {2014}, author = {Stryjewski, ME and Corey, GR}, title = {Methicillin-resistant Staphylococcus aureus: an evolving pathogen.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {58 Suppl 1}, number = {}, pages = {S10-9}, doi = {10.1093/cid/cit613}, pmid = {24343827}, issn = {1537-6591}, mesh = {Anti-Bacterial Agents/*pharmacology ; *Biological Evolution ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Glycopeptides/*pharmacology ; Humans ; Methicillin-Resistant Staphylococcus aureus/*drug effects/genetics/physiology ; Point Mutation ; Staphylococcal Infections/epidemiology/*microbiology ; }, abstract = {The horizontal transmission of methicillin resistance to Staphylococcus aureus (MRSA) in hospital and community settings, and growing prevalence of these strains, presents a significant clinical challenge to the management of serious infections worldwide. While infection control initiatives have stemmed the rising prevalence, MRSA remains a significant pathogen. More recently, evidence that MRSA is becoming resistant to glycopeptides and newer therapies raises concern about the use of these therapies in clinical practice. Vancomycin resistance has become evident in select clinical settings through rising MICs, growing awareness of heteroresistance, and emergence of intermediate-resistant and fully resistant strains. While resistance to linezolid and daptomycin remains low overall, point mutations leading to resistance have been described for linezolid, and horizontal transmission of cfr-mediated resistance to linezolid has been reported in clinical isolates. These resistance trends for newer therapies highlight the ongoing need for new and more potent antimicrobial therapies.}, }
@article {pmid24341913, year = {2014}, author = {Gladieux, P and Ropars, J and Badouin, H and Branca, A and Aguileta, G and de Vienne, DM and Rodríguez de la Vega, RC and Branco, S and Giraud, T}, title = {Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes.}, journal = {Molecular ecology}, volume = {23}, number = {4}, pages = {753-773}, doi = {10.1111/mec.12631}, pmid = {24341913}, issn = {1365-294X}, mesh = {*Adaptation, Biological ; *Biological Evolution ; DNA Transposable Elements ; Eukaryota/genetics ; Fungi/*genetics ; Gene Transfer, Horizontal ; *Genetic Speciation ; Genomics ; Hybridization, Genetic ; Reproductive Isolation ; }, abstract = {Fungi are ideal model organisms for dissecting the genomic bases of adaptive divergence in eukaryotes. They have simple morphologies and small genomes, occupy contrasting, well-identified ecological niches and tend to have short generation times, and many are amenable to experimental approaches. Fungi also display diverse lifestyles, from saprotrophs to pathogens or mutualists, and they play extremely important roles in both ecosystems and human activities, as wood decayers, mycorrhizal fungi, lichens, endophytes, plant and animal pathogens, and in fermentation or drug production. We review here recent insights into the patterns and mechanisms of adaptive divergence in fungi, including sources of divergence, genomic variation and, ultimately, speciation. We outline the various ecological sources of divergent selection and genomic changes, showing that gene loss and changes in gene expression and in genomic architecture are important adaptation processes, in addition to the more widely recognized processes of amino acid substitution and gene duplication. We also review recent findings regarding the interspecific acquisition of genomic variation and suggesting an important role for introgression, hybridization and horizontal gene transfers (HGTs). We show that transposable elements can mediate several of these genomic changes, thus constituting important factors for adaptation. Finally, we review the consequences of divergent selection in terms of speciation, arguing that genetic incompatibilities may not be as widespread as generally thought and that pleiotropy between adaptation and reproductive isolation is an important route of speciation in fungal pathogens.}, }
@article {pmid24341328, year = {2013}, author = {Olson, AB and Kent, H and Sibley, CD and Grinwis, ME and Mabon, P and Ouellette, C and Tyson, S and Graham, M and Tyler, SD and Van Domselaar, G and Surette, MG and Corbett, CR}, title = {Phylogenetic relationship and virulence inference of Streptococcus Anginosus Group: curated annotation and whole-genome comparative analysis support distinct species designation.}, journal = {BMC genomics}, volume = {14}, number = {}, pages = {895}, pmid = {24341328}, issn = {1471-2164}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Clustered Regularly Interspaced Short Palindromic Repeats ; Gene Order ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Loci ; *Genome, Bacterial ; Genomics ; Histidine Kinase ; Minisatellite Repeats ; Molecular Sequence Data ; *Phylogeny ; Polymorphism, Single Nucleotide ; Protein Kinases/genetics ; Repetitive Sequences, Nucleic Acid ; Streptococcus anginosus/*classification/*genetics/pathogenicity ; Virulence/genetics ; Virulence Factors/genetics ; }, abstract = {BACKGROUND: The Streptococcus Anginosus Group (SAG) represents three closely related species of the viridans group streptococci recognized as commensal bacteria of the oral, gastrointestinal and urogenital tracts. The SAG also cause severe invasive infections, and are pathogens during cystic fibrosis (CF) pulmonary exacerbation. Little genomic information or description of virulence mechanisms is currently available for SAG. We conducted intra and inter species whole-genome comparative analyses with 59 publically available Streptococcus genomes and seven in-house closed high quality finished SAG genomes; S. constellatus (3), S. intermedius (2), and S. anginosus (2). For each SAG species, we sequenced at least one numerically dominant strain from CF airways recovered during acute exacerbation and an invasive, non-lung isolate. We also evaluated microevolution that occurred within two isolates that were cultured from one individual one year apart.<br><br>RESULTS: The SAG genomes were most closely related to S. gordonii and S. sanguinis, based on shared orthologs and harbor a similar number of proteins within each COG category as other Streptococcus species. Numerous characterized streptococcus virulence factor homologs were identified within the SAG genomes including; adherence, invasion, spreading factors, LPxTG cell wall proteins, and two component histidine kinases known to be involved in virulence gene regulation. Mobile elements, primarily integrative conjugative elements and bacteriophage, account for greater than 10% of the SAG genomes. S. anginosus was the most variable species sequenced in this study, yielding both the smallest and the largest SAG genomes containing multiple genomic rearrangements, insertions and deletions. In contrast, within the S. constellatus and S. intermedius species, there was extensive continuous synteny, with only slight differences in genome size between strains. Within S. constellatus we were able to determine important SNPs and changes in VNTR numbers that occurred over the course of one year.<br><br>CONCLUSIONS: The comparative genomic analysis of the SAG clarifies the phylogenetics of these bacteria and supports the distinct species classification. Numerous potential virulence determinants were identified and provide a foundation for further studies into SAG pathogenesis. Furthermore, the data may be used to enable the development of rapid diagnostic assays and therapeutics for these pathogens.}, }
@article {pmid24337108, year = {2014}, author = {Hong, H and Ko, HJ and Choi, IG and Park, W}, title = {Previously undescribed plasmids recovered from activated sludge confer tetracycline resistance and phenotypic changes to Acinetobacter oleivorans DR1.}, journal = {Microbial ecology}, volume = {67}, number = {2}, pages = {369-379}, pmid = {24337108}, issn = {1432-184X}, mesh = {Acinetobacter/*genetics/isolation &amp; purification ; Alkanes/chemistry ; Anti-Bacterial Agents/pharmacology ; Biodegradation, Environmental ; Biofilms ; DNA, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Oxidative Stress ; Phenotype ; Plasmids/*isolation &amp; purification ; Polymorphism, Restriction Fragment Length ; Quorum Sensing ; Salts/metabolism ; Sequence Analysis, DNA ; Sewage/*microbiology ; Tetracycline/pharmacology ; Tetracycline Resistance/*genetics ; }, abstract = {We used culture-dependent and culture-independent methods to extract previously undescribed plasmids harboring tetracycline (TC) resistance genes from activated sludge. The extracted plasmids were transformed into naturally competent Acinetobacter oleivorans DR1 to recover a non-Escherichia coli-based plasmid. The transformed cells showed 80-100-fold higher TC resistance than the wild-type strain. Restriction length polymorphism performed using 30 transformed cells showed four different types of plasmids. Illumina-based whole sequencing of the four plasmids identified three previously unreported plasmids and one previously reported plasmid. All plasmids carried TC resistance-related genes (tetL, tetH), tetracycline transcriptional regulators (tetR), and mobilization-related genes. As per expression analysis, TC resistance genes were functional in the presence of TC. The recovered plasmids showed mosaic gene acquisition through horizontal gene transfer. Membrane fluidity, hydrophobicity, biofilm formation, motility, growth rate, sensitivity to stresses, and quorum sensing signals of the transformed cells were different from those of the wild-type cells. Plasmid-bearing cells seemed to have an energy burden for maintaining and expressing plasmid genes. Our data showed that acquisition of TC resistance through plasmid uptake is related to loss of biological fitness. Thus, cells acquiring antibiotic resistance plasmids can survive in the presence of antibiotics, but must pay ecological costs.}, }
@article {pmid24336939, year = {2014}, author = {Wattam, AR and Foster, JT and Mane, SP and Beckstrom-Sternberg, SM and Beckstrom-Sternberg, JM and Dickerman, AW and Keim, P and Pearson, T and Shukla, M and Ward, DV and Williams, KP and Sobral, BW and Tsolis, RM and Whatmore, AM and O'Callaghan, D}, title = {Comparative phylogenomics and evolution of the Brucellae reveal a path to virulence.}, journal = {Journal of bacteriology}, volume = {196}, number = {5}, pages = {920-930}, pmid = {24336939}, issn = {1098-5530}, support = {HHSN272200900040C/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/metabolism ; *Biological Evolution ; Brucellaceae/*genetics/*pathogenicity ; Gene Expression Regulation, Bacterial/physiology ; *Genome, Bacterial ; Genomics/*methods ; *Phylogeny ; Virulence ; }, abstract = {Brucella species include important zoonotic pathogens that have a substantial impact on both agriculture and human health throughout the world. Brucellae are thought of as "stealth pathogens" that escape recognition by the host innate immune response, modulate the acquired immune response, and evade intracellular destruction. We analyzed the genome sequences of members of the family Brucellaceae to assess its evolutionary history from likely free-living soil-based progenitors into highly successful intracellular pathogens. Phylogenetic analysis split the genus into two groups: recently identified and early-dividing "atypical" strains and a highly conserved "classical" core clade containing the major pathogenic species. Lateral gene transfer events brought unique genomic regions into Brucella that differentiated them from Ochrobactrum and allowed the stepwise acquisition of virulence factors that include a type IV secretion system, a perosamine-based O antigen, and systems for sequestering metal ions that are absent in progenitors. Subsequent radiation within the core Brucella resulted in lineages that appear to have evolved within their preferred mammalian hosts, restricting their virulence to become stealth pathogens capable of causing long-term chronic infections.}, }
@article {pmid24336424, year = {2013}, author = {de Vries, J and Habicht, J and Woehle, C and Huang, C and Christa, G and Wägele, H and Nickelsen, J and Martin, WF and Gould, SB}, title = {Is ftsH the key to plastid longevity in sacoglossan slugs?.}, journal = {Genome biology and evolution}, volume = {5}, number = {12}, pages = {2540-2548}, pmid = {24336424}, issn = {1759-6653}, mesh = {Acetabularia/*genetics ; Algal Proteins ; Animals ; Carboxypeptidases/genetics/*physiology ; Chloroplasts/genetics ; Gastropoda/*physiology ; Genome, Plastid ; Plant Proteins/genetics/*physiology ; Plastids/*genetics ; Proprotein Convertases/genetics/*physiology ; }, abstract = {Plastids sequestered by sacoglossan sea slugs have long been a puzzle. Some sacoglossans feed on siphonaceous algae and can retain the plastids in the cytosol of their digestive gland cells. There, the stolen plastids (kleptoplasts) can remain photosynthetically active in some cases for months. Kleptoplast longevity itself challenges current paradigms concerning photosystem turnover, because kleptoplast photosystems remain active in the absence of nuclear algal genes. In higher plants, nuclear genes are essential for plastid maintenance, in particular, for the constant repair of the D1 protein of photosystem II. Lateral gene transfer was long suspected to underpin slug kleptoplast longevity, but recent transcriptomic and genomic analyses show that no algal nuclear genes are expressed from the slug nucleus. Kleptoplast genomes themselves, however, appear expressed in the sequestered state. Here we present sequence data for the chloroplast genome of Acetabularia acetabulum, the food source of the sacoglossan Elysia timida, which can maintain Acetabularia kleptoplasts in an active state for months. The data reveal what might be the key to sacoglossan kleptoplast longevity: plastids that remain photosynthetically active within slugs for periods of months share the property of encoding ftsH, a D1 quality control protease that is essential for photosystem II repair. In land plants, ftsH is always nuclear encoded, it was transferred to the nucleus from the plastid genome when Charophyta and Embryophyta split. A replenishable supply of ftsH could, in principle, rescue kleptoplasts from D1 photodamage, thereby influencing plastid longevity in sacoglossan slugs.}, }
@article {pmid24335826, year = {2014}, author = {Sato, T and Kuwahara, H and Fujita, K and Noda, S and Kihara, K and Yamada, A and Ohkuma, M and Hongoh, Y}, title = {Intranuclear verrucomicrobial symbionts and evidence of lateral gene transfer to the host protist in the termite gut.}, journal = {The ISME journal}, volume = {8}, number = {5}, pages = {1008-1019}, pmid = {24335826}, issn = {1751-7370}, mesh = {Animals ; Biological Evolution ; DNA, Bacterial/genetics ; Gastrointestinal Tract/microbiology ; *Gene Transfer, Horizontal ; In Situ Hybridization, Fluorescence ; Isoptera/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Symbiosis ; Verrucomicrobia/*physiology ; }, abstract = {In 1944, Harold Kirby described microorganisms living within nuclei of the protists Trichonympha in guts of termites; however, their taxonomic assignment remains to be accomplished. Here, we identified intranuclear symbionts of Trichonympha agilis in the gut of the termite Reticulitermes speratus. We isolated single nuclei of T. agilis, performed whole-genome amplification, and obtained bacterial 16S rRNA genes by PCR. Unexpectedly, however, all of the analyzed clones were from pseudogenes of 16S rRNA with large deletions and numerous sequence variations even within a single-nucleus sample. Authentic 16S rRNA gene sequences were finally recovered by digesting the nuclear DNA; these pseudogenes were present on the host Trichonympha genome. The authentic sequences represented two distinct bacterial species belonging to the phylum Verrucomicrobia, and the pseudogenes have originated from each of the two species. Fluorescence in situ hybridization confirmed that both species are specifically localized, and occasionally co-localized, within nuclei of T. agilis. Transmission electron microscopy revealed that they are distorted cocci with characteristic electron-dense and lucent regions, which resemble the intranuclear symbionts illustrated by Kirby. For these symbionts, we propose a novel genus and species, 'Candidatus Nucleococcus trichonymphae' and 'Candidatus Nucleococcus kirbyi'. These formed a termite-specific cluster with database sequences, other members of which were also detected within nuclei of various gut protists, including both parabasalids and oxymonads. We suggest that this group is widely distributed as intranuclear symbionts of diverse protists in termite guts and that they might have affected the evolution of the host genome through lateral gene transfer.}, }
@article {pmid24335515, year = {2014}, author = {Qin, S and Wang, Y and Zhang, Q and Zhang, M and Deng, F and Shen, Z and Wu, C and Wang, S and Zhang, J and Shen, J}, title = {Report of ribosomal RNA methylase gene erm(B) in multidrug-resistant Campylobacter coli.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {69}, number = {4}, pages = {964-968}, doi = {10.1093/jac/dkt492}, pmid = {24335515}, issn = {1460-2091}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Campylobacter coli/*drug effects/*enzymology/genetics/isolation &amp; purification ; Campylobacter jejuni/genetics ; Cloning, Molecular ; DNA, Bacterial/chemistry/genetics ; *Drug Resistance, Multiple, Bacterial ; Gene Transfer, Horizontal ; Macrolides/*pharmacology ; Methyltransferases/*genetics ; Molecular Sequence Data ; Sequence Analysis, DNA ; Swine ; }, abstract = {OBJECTIVES: Campylobacter is a major foodborne enteric pathogen and macrolides are the drug of choice for the clinical therapy of campylobacteriosis. Macrolide resistance among Campylobacter compromises clinical treatment, is associated with adverse health events and is a significant public health concern. Here, we report the first identification of a horizontally transferrable macrolide resistance mechanism in porcine Campylobacter coli ZC113 that is mediated by a ribosomal RNA methylase, Erm(B).<br><br>METHODS: Horizontal transfer of a macrolide resistance determinant between C. coli and Campylobacter jejuni was performed by natural transformation. Whole-genome sequencing was initially used to identify the ribosomal methylase-encoding gene erm(B) in Campylobacter. Cloning of erm(B) into C. jejuni NCTC 11168 was performed to evaluate whether the erm(B) gene is responsible for high-level macrolide resistance in Campylobacter.<br><br>RESULTS: The erm(B) gene was identified in ZC113, conferred high-level resistance to macrolides and was associated with a chromosomal multidrug-resistant genomic island (MDRGI). The MDRGI probably originated from Gram-positive bacteria and was horizontally transferred between C. coli and C. jejuni via natural transformation. Furthermore, the erm(B)-positive isolate ZC113 was resistant to all clinically important antibiotics used for treating campylobacteriosis and is essentially multidrug-resistant Campylobacter.<br><br>CONCLUSIONS: To the best of our knowledge, this is the first report of a horizontally transferable macrolide resistance mechanism in thermophilic Campylobacter. Surveillance of erm(B) and its associated MDRGI in both C. coli and C. jejuni is urgently warranted.}, }
@article {pmid24335352, year = {2014}, author = {Hamidian, M and Hall, RM}, title = {pACICU2 is a conjugative plasmid of Acinetobacter carrying the aminoglycoside resistance transposon TnaphA6.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {69}, number = {4}, pages = {1146-1148}, doi = {10.1093/jac/dkt488}, pmid = {24335352}, issn = {1460-2091}, mesh = {Acinetobacter/*genetics ; Acinetobacter Infections/*microbiology ; Aminoglycosides/*pharmacology ; Anti-Bacterial Agents/*pharmacology ; *Conjugation, Genetic ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; *Plasmids ; }, }
@article {pmid24332546, year = {2014}, author = {Glöckner, G and Hülsmann, N and Schleicher, M and Noegel, AA and Eichinger, L and Gallinger, C and Pawlowski, J and Sierra, R and Euteneuer, U and Pillet, L and Moustafa, A and Platzer, M and Groth, M and Szafranski, K and Schliwa, M}, title = {The genome of the foraminiferan Reticulomyxa filosa.}, journal = {Current biology : CB}, volume = {24}, number = {1}, pages = {11-18}, doi = {10.1016/j.cub.2013.11.027}, pmid = {24332546}, issn = {1879-0445}, mesh = {Cytoskeleton/genetics ; Gene Transfer, Horizontal ; *Genome, Protozoan ; Meiosis ; Molecular Sequence Data ; Rhizaria/cytology/*genetics ; Transcription Factors/genetics ; }, abstract = {BACKGROUND: Rhizaria are a major branch of eukaryote evolution with an extensive microfossil record, but only scarce molecular data are available. The rhizarian species Reticulomyxa filosa, belonging to the Foraminifera, is free-living in freshwater environments. In culture, it thrives only as a plasmodium with thousands of haploid nuclei in one cell. The R. filosa genome is the first foraminiferal genome to be deciphered.<br><br>RESULTS: The genome is extremely repetitive, and the large amounts of identical sequences hint at frequent amplifications and homologous recombination events. Presumably, these mechanisms are employed to provide more gene copies for higher transcriptional activity and to build up a reservoir of gene diversification in certain gene families, such as the kinesin family. The gene repertoire indicates that it is able to switch to a single-celled, flagellated sexual state never observed in culture. Comparison to another rhizarian, the chlorarachniophyte alga Bigelowiella natans, reveals that proteins involved in signaling were likely drivers in establishing the Rhizaria lineage. Compared to some other protists, horizontal gene transfer is limited, but we found evidence of bacterial-to-eukaryote and eukaryote-to-eukaryote transfer events.<br><br>CONCLUSIONS: The R. filosa genome exhibits a unique architecture with extensive repeat homogenization and gene amplification, which highlights its potential for diverse life-cycle stages. The ability of R. filosa to rapidly transport matter from the pseudopodia to the cell body may be supported by the high diversification of actin and kinesin gene family members.}, }
@article {pmid24329755, year = {2014}, author = {Gandon, S and Vale, PF}, title = {The evolution of resistance against good and bad infections.}, journal = {Journal of evolutionary biology}, volume = {27}, number = {2}, pages = {303-312}, doi = {10.1111/jeb.12291}, pmid = {24329755}, issn = {1420-9101}, mesh = {Bacteria/drug effects/*genetics ; Bacteriophages/genetics ; Biological Evolution ; Drug Resistance, Bacterial/genetics ; Evolution, Molecular ; Plasmids ; }, abstract = {Opportunities for genetic exchange are abundant between bacteria and foreign genetic elements (FGEs) such as conjugative plasmids, transposable elements and bacteriophages. The genetic novelty that may arise from these forms of genetic exchange is potentially beneficial to bacterial hosts, but there are also potential costs, which may be considerable in the case of phage infection. Some bacterial resistance mechanisms target both beneficial and deleterious forms of genetic exchange. Using a general epidemiological model, we explored under which conditions such resistance mechanisms may evolve. We considered a population of hosts that may be infected by FGEs that either confer a benefit or are deleterious to host fitness, and we analysed the epidemiological and evolutionary outcomes of resistance evolving under different cost/benefit scenarios. We show that the degree of co-infection between these two types of infection is particularly important in determining the evolutionarily stable level of host resistance. We explore these results using the example of CRISPR-Cas, a form of bacterial immunity that targets a variety of FGEs, and we show the potential role of bacteriophage infection in selecting for resistance mechanisms that in turn limit the acquisition of plasmid-borne antibiotic resistance. Finally, beyond microbes, we discuss how endosymbiotic associations may have shaped the evolution of host immune responses to pathogens.}, }
@article {pmid24329527, year = {2014}, author = {Ueki, M and Kimura-Kataoka, K and Fujihara, J and Takeshita, H and Iida, R and Yasuda, T}, title = {Evaluation of all nonsynonymous single-nucleotide polymorphisms in the gene encoding human deoxyribonuclease I-like 1, possibly implicated in the blocking of endocytosis-mediated foreign gene transfer.}, journal = {DNA and cell biology}, volume = {33}, number = {2}, pages = {79-87}, pmid = {24329527}, issn = {1557-7430}, mesh = {Amino Acid Sequence ; Base Sequence ; Catalysis ; Computational Biology ; DNA Primers/genetics ; Deoxyribonuclease I/*genetics ; Endocytosis/*genetics ; Ethnicity/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genetic Vectors ; Genotype ; Humans ; Molecular Sequence Data ; Muscle Proteins/*genetics ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Polymorphism, Single Nucleotide/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Many nonsynonymous single-nucleotide polymorphisms (SNPs) in the human deoxyribonuclease I-like 1 (DNase 1L1) gene, possibly implicated in the blocking of endocytosis-mediated foreign gene transfer, have been identified, but only limited population data are available and no studies have evaluated whether such SNPs are functional. Genotyping of all 21 nonsynonymous human DNase 1L1 SNPs was performed in 16 different populations representing three ethnic groups using the PCR-restriction fragment length polymorphism technique. All of the nonsynonymous SNPs, except for SNP p.Val122Ile in Caucasian populations, exhibited a monoallelic distribution in all of the populations. On the basis of alterations in the activity levels resulting from the corresponding amino acid substitutions, two activity-abolishing and four activity-reducing SNPs were confirmed to be functional. Although all of the nonsynonymous SNPs that affected the catalytic activity showed extremely low genetic heterogeneity, it seems plausible that a minor allele of six SNPs producing a loss-of-function or extremely low-activity variant could serve directly as a genetic risk factor for diseases. Especially, the amino acid residues in activity-abolishing SNPs were conserved in animal DNases 1L1. Furthermore, results of phylogenetic analysis suggest that DNase 1L1 might have appeared latest among the DNase I family during the course of molecular evolution.}, }
@article {pmid24329306, year = {2013}, author = {Saakian, DB and Hu, CK}, title = {Evolutionary advantage via common action of recombination and neutrality.}, journal = {Physical review. E, Statistical, nonlinear, and soft matter physics}, volume = {88}, number = {5}, pages = {052717}, doi = {10.1103/PhysRevE.88.052717}, pmid = {24329306}, issn = {1550-2376}, mesh = {*Evolution, Molecular ; HIV/genetics/physiology ; *Models, Genetic ; *Recombination, Genetic ; Selection, Genetic ; }, abstract = {We investigate evolution models with recombination and neutrality. We consider the Crow-Kimura (parallel) mutation-selection model with the neutral fitness landscape, in which there is a central peak with high fitness A, and some of 1-point mutants have the same high fitness A, while the fitness of other sequences is 0. We find that the effect of recombination and neutrality depends on the concrete version of both neutrality and recombination. We consider three versions of neutrality: (a) all the nearest neighbor sequences of the peak sequence have the same high fitness A; (b) all the l-point mutations in a piece of genome of length l≥1 are neutral; (c) the neutral sequences are randomly distributed among the nearest neighbors of the peak sequences. We also consider three versions of recombination: (I) the simple horizontal gene transfer (HGT) of one nucleotide; (II) the exchange of a piece of genome of length l, HGT-l; (III) two-point crossover recombination (2CR). For the case of (a), the 2CR gives a rather strong contribution to the mean fitness, much stronger than that of HGT for a large genome length L. For the random distribution of neutral sequences there is a critical degree of neutrality ν(c), and for μ<μ(c) and (μ(c)-μ) is not large, the 2CR suppresses the mean fitness while HGT increases it; for ν much larger than ν(c), the 2CR and HGT-l increase the mean fitness larger than that of the HGT. We also consider the recombination in the case of smooth fitness landscapes. The recombination gives some advantage in the evolutionary dynamics, where recombination distinguishes clearly the mean-field-like evolutionary factors from the fluctuation-like ones. By contrast, mutations affect the mean-field-like and fluctuation-like factors similarly. Consequently, recombination can accelerate the non-mean-field (fluctuation) type dynamics without considerably affecting the mean-field-like factors.}, }
@article {pmid24328379, year = {2014}, author = {Bonnin, RA and Poirel, L and Nordmann, P}, title = {New Delhi metallo-β-lactamase-producing Acinetobacter baumannii: a novel paradigm for spreading antibiotic resistance genes.}, journal = {Future microbiology}, volume = {9}, number = {1}, pages = {33-41}, doi = {10.2217/fmb.13.69}, pmid = {24328379}, issn = {1746-0921}, mesh = {Acinetobacter baumannii/*enzymology/*genetics ; DNA Transposable Elements ; *Drug Resistance, Bacterial ; Evolution, Molecular ; Gene Order ; *Gene Transfer, Horizontal ; Recombination, Genetic ; Synteny ; beta-Lactamases/*genetics ; }, abstract = {The impact of carbapenemase production among clinically significant Gram-negative rods is becoming a major medical issue. To date, Acinetobacter baumannii has been considered as a final recipient of carbapenemase genes (imipenemase, Verona metallo-β-lactamase, Guiana extended-spectrum β-lactamase and Klebsiella pneumonia carbapenemase types) from Enterobacteriaceae and Pseudomonas aeruginosa. However, recent findings regarding the spread of the blaNDM carbapenemase genes revealed that A. baumannii likely acts as a source of emerging antibiotic resistance genes. The analysis of genetic structure surrounding the blaNDM-1 gene revealed that the genetic structure (Tn125) responsible for its dissemination most probably originates from Acinetobacter. Moreover, analysis of the blaNDM-1 gene itself demonstrated that it might be constructed in Acinetobacter through a recombination event with another resistance gene found in A. baumannii (aphA6). This novel paradigm highlights a novel and unexpected role played by A. baumannii.}, }
@article {pmid24324684, year = {2013}, author = {Graham, LA and Hobbs, RS and Fletcher, GL and Davies, PL}, title = {Helical antifreeze proteins have independently evolved in fishes on four occasions.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e81285}, pmid = {24324684}, issn = {1932-6203}, support = {106612//Canadian Institutes of Health Research/Canada ; }, mesh = {Alanine/genetics ; Amino Acid Sequence ; Animals ; Antifreeze Proteins/*chemistry/*genetics ; Codon/genetics ; DNA, Complementary/genetics ; DNA, Intergenic/genetics ; Databases, Protein ; *Evolution, Molecular ; Fish Proteins/chemistry/genetics ; Fishes/*genetics ; Molecular Sequence Data ; Open Reading Frames/genetics ; Protein Structure, Secondary ; Species Specificity ; }, abstract = {Alanine-rich α-helical (type I) antifreeze proteins (AFPs) are produced by a variety of fish species from three different orders to protect against freezing in icy seawater. Interspersed amongst and within these orders are fishes making AFPs that are completely different in both sequence and structure. The origin of this variety of types I, II, III and antifreeze glycoproteins (AFGPs) has been attributed to adaptation following sea-level glaciations that occurred after the divergence of most of the extant families of fish. The presence of similar types of AFPs in distantly related fishes has been ascribed to lateral gene transfer in the case of the structurally complex globular type II lectin-like AFPs and to convergent evolution for the AFGPs, which consist of a well-conserved tripeptide repeat. In this paper, we examine the genesis of the type I AFPs, which are intermediate in complexity. These predominantly α-helical peptides share many features, such as putative capping structures, Ala-richness and amphipathic character. We have added to the type I repertoire by cloning additional sequences from sculpin and have found that the similarities between the type I AFPs of the four distinct groups of fishes are not borne out at the nucleotide level. Both the non-coding sequences and the codon usage patterns are strikingly different. We propose that these AFPs arose via convergence from different progenitor helices with a weak affinity for ice and that their similarity is dictated by the propensity of specific amino acids to form helices and to align water on one side of the helix into an ice-like pattern.}, }
@article {pmid24324624, year = {2013}, author = {Yu, X and Li, Y and Wang, X}, title = {Molecular evolution of threonine dehydratase in bacteria.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e80750}, pmid = {24324624}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Bacillus subtilis/*enzymology/genetics ; Bacterial Proteins/chemistry/*classification/genetics/metabolism ; Base Sequence ; Butyrates/metabolism ; Catalytic Domain ; Escherichia coli/*enzymology/genetics ; Evolution, Molecular ; Gene Duplication ; Gene Expression ; Gene Fusion ; Gene Transfer, Horizontal ; Isoenzymes/chemistry/classification/genetics/metabolism ; Models, Molecular ; Molecular Sequence Data ; *Phylogeny ; Salmonella typhimurium/*enzymology/genetics ; Sequence Alignment ; Threonine/metabolism ; Threonine Dehydratase/chemistry/*classification/genetics/metabolism ; }, abstract = {Threonine dehydratase converts L-threonine to 2-ketobutyrate. Several threonine dehydratases exist in bacteria, but their origins and evolutionary pathway are unknown. Here we analyzed all the available threonine dehydratases in bacteria and proposed an evolutionary pathway leading to the genes encoding three different threonine dehydratases CTD, BTD1 and BTD2. The ancestral threonine dehydratase might contain only a catalytic domain, but one or two ACT-like subdomains were fused during the evolution, resulting BTD1 and BTD2, respectively. Horizontal gene transfer, gene fusion, gene duplication, and gene deletion may occur during the evolution of this enzyme. The results are important for understanding the functions of various threonine dehydratases found in bacteria.}, }
@article {pmid24323918, year = {2014}, author = {Schönknecht, G and Weber, AP and Lercher, MJ}, title = {Horizontal gene acquisitions by eukaryotes as drivers of adaptive evolution.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {36}, number = {1}, pages = {9-20}, doi = {10.1002/bies.201300095}, pmid = {24323918}, issn = {1521-1878}, mesh = {Adaptation, Physiological/*genetics ; Animals ; Biological Evolution ; Eukaryota/*genetics ; Gene Transfer, Horizontal/*genetics ; Humans ; Phylogeny ; }, abstract = {In contrast to vertical gene transfer from parent to offspring, horizontal (or lateral) gene transfer moves genetic information between different species. Bacteria and archaea often adapt through horizontal gene transfer. Recent analyses indicate that eukaryotic genomes, too, have acquired numerous genes via horizontal transfer from prokaryotes and other lineages. Based on this we raise the hypothesis that horizontally acquired genes may have contributed more to adaptive evolution of eukaryotes than previously assumed. Current candidate sets of horizontally acquired eukaryotic genes may just be the tip of an iceberg. We have recently shown that adaptation of the thermoacidophilic red alga Galdieria sulphuraria to its hot, acid, toxic-metal laden, volcanic environment was facilitated by the acquisition of numerous genes from extremophile bacteria and archaea. Other recently published examples of horizontal acquisitions involved in adaptation include ice-binding proteins in marine algae, enzymes for carotenoid biosynthesis in aphids, and genes involved in fungal metabolism. Editor's suggested further reading in BioEssays Jumping the fine LINE between species: Horizontal transfer of transposable elements in animals catalyses genome evolution Abstract.}, }
@article {pmid24323917, year = {2014}, author = {Koonin, EV}, title = {Bacterial genes in eukaryotes: relatively rare but real and important (Comment on DOI 10.1002/bies.201300095).}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {36}, number = {1}, pages = {8}, doi = {10.1002/bies.201300158}, pmid = {24323917}, issn = {1521-1878}, mesh = {Adaptation, Physiological/*genetics ; Animals ; Eukaryota/*genetics ; Gene Transfer, Horizontal/*genetics ; Humans ; }, }
@article {pmid24321593, year = {2014}, author = {Wisecaver, JH and Hackett, JD}, title = {The impact of automated filtering of BLAST-determined homologs in the phylogenetic detection of horizontal gene transfer from a transcriptome assembly.}, journal = {Molecular phylogenetics and evolution}, volume = {71}, number = {}, pages = {184-192}, doi = {10.1016/j.ympev.2013.11.016}, pmid = {24321593}, issn = {1095-9513}, mesh = {Alveolata/*genetics ; *Gene Transfer, Horizontal ; Humans ; *Phylogeny ; Sequence Analysis, DNA ; *Transcriptome ; }, abstract = {Phylomes (comprehensive sets of gene phylogenies for organisms) are built to investigate fundamental questions in genomics and evolutionary biology, such as those pertaining to the detection and characterization of horizontal gene transfer in microbes. To address these questions, phylome construction demands rigorous yet efficient phylogenetic methods. Currently, many sequence alignment and tree-building models can analyze several thousands of genes in a high-throughput manner. However, the phylogenetics is complicated by variability in sequence divergence and different taxon sampling among genes. In addition, homolog selection for automated approaches often relies on arbitrary sequence similarity thresholds that are likely inappropriate for all genes in a genome. To investigate the effects of automated homolog selection on the detection of horizontal gene transfer using phylogenomics, we constructed the phylome of a transcriptome assembly of Alexandrium tamarense, a microbial eukaryote with a history of horizontal and endosymbiotic gene transfer, using seven sequence similarity thresholds for selecting putative homologs to be included in phylogenetic analyses. We show that no single threshold recovered informative trees for the majority of A. tamarense unigenes compared to the pooled results from all pipeline iterations. As much as 29% of trees built could have misleading phylogenetic relationships that appear biased in favor of those otherwise indicative of horizontal gene transfer. Perhaps worse, nearly half of the unigenes were represented by a single tree built at just one threshold, making it difficult to assess the validity of phylogenetic relationships recovered in these cases. However, combining the results from several pipeline iterations maximizes the number of informative phylogenies. Moreover, when the same phylogenetic relationship for a given unigene is recovered in multiple pipeline iterations, conclusions regarding gene origin are more robust to methodological artifact. Using these methods, the majority of A. tamarense unigenes showed evolutionary relationships indicative of vertical inheritance. Nevertheless, many other unigenes revealed diverse phylogenetic associations, suggestive of possible gene transfer. This analysis suggests that caution should be used when interpreting the results from phylogenetic pipelines implementing a single similarity threshold. Our approach is a practical method to mitigate the problems associated with automated sequence selection in phylogenomics.}, }
@article {pmid24321137, year = {2013}, author = {Manna, S and Barth, C}, title = {Identification of a novel pentatricopeptide repeat subfamily with a C-terminal domain of bacterial origin acquired via ancient horizontal gene transfer.}, journal = {BMC research notes}, volume = {6}, number = {}, pages = {525}, pmid = {24321137}, issn = {1756-0500}, mesh = {*Gene Transfer, Horizontal ; Phylogeny ; *Repetitive Sequences, Amino Acid ; }, abstract = {BACKGROUND: Pentatricopeptide repeat (PPR) proteins are a large family of sequence-specific RNA binding proteins involved in organelle RNA metabolism. Very little is known about the origin and evolution of these proteins, particularly outside of plants. Here, we report the identification of a novel subfamily of PPR proteins not found in plants and explore their evolution.<br><br>RESULTS: We identified a novel subfamily of PPR proteins, which all contain a C-terminal tRNA guanine methyltransferase (TGM) domain, suggesting a predicted function not previously associated with PPR proteins. This group of proteins, which we have named the PPR-TGM subfamily, is found in distantly related eukaryotic lineages including cellular slime moulds, entamoebae, algae and diatoms, but appears to be the first PPR subfamily absent from plants. Each PPR-TGM protein identified is predicted to have different subcellular locations, thus we propose that these proteins have roles in tRNA metabolism in all subcellular locations, not just organelles. We demonstrate that the TGM domain is not only similar to bacterial TGM proteins, but that it is most similar to chlamydial TGMs in particular, despite the absence of PPR proteins in bacteria. Based on our data, we postulate that this subfamily of PPR proteins evolved from a TGM-encoding gene of a member of the Chlamydiae, which was obtained via ancient prokaryote-to-eukaryote horizontal gene transfer. Following its acquisition, the N-terminus of the encoded TGM protein must have been extended to include PPR motifs, possibly to confer additional functions to the protein, giving rise to the PPR-TGM subfamily.<br><br>CONCLUSIONS: The identification of a unique PPR subfamily which originated from the Chlamydiae group of bacteria offers novel insight into the origin and evolution of PPR proteins not previously considered. It also provides further understanding into their roles in non-organellar RNA metabolism.}, }
@article {pmid24319064, year = {2014}, author = {Caspermeyer, J}, title = {Plants found to aid their enemies.}, journal = {Molecular biology and evolution}, volume = {31}, number = {2}, pages = {498}, doi = {10.1093/molbev/mst236}, pmid = {24319064}, issn = {1537-1719}, mesh = {Amoebozoa/*genetics ; Bacteria/*genetics ; Cellulase/*metabolism ; Fungi/*genetics ; *Gene Transfer, Horizontal ; Plant Proteins/*chemistry/*genetics ; Plants/*genetics ; }, }
@article {pmid24318976, year = {2014}, author = {Gyles, C and Boerlin, P}, title = {Horizontally transferred genetic elements and their role in pathogenesis of bacterial disease.}, journal = {Veterinary pathology}, volume = {51}, number = {2}, pages = {328-340}, doi = {10.1177/0300985813511131}, pmid = {24318976}, issn = {1544-2217}, mesh = {Animal Diseases/microbiology/*pathology ; Animals ; Bacteria/*genetics/pathogenicity ; Bacterial Adhesion/genetics ; Bacterial Infections/microbiology/*pathology ; Bacterial Secretion Systems/genetics ; Bacterial Toxins ; Clostridium perfringens/genetics/pathogenicity ; DNA, Bacterial/*genetics ; Drug Resistance, Microbial/genetics ; Escherichia coli/genetics/pathogenicity ; *Gene Transfer, Horizontal ; Interspersed Repetitive Sequences/genetics ; Iron/metabolism ; Plasmids/genetics ; Salmonella/genetics/pathogenicity ; Streptococcus/genetics/pathogenicity ; Virulence ; Virulence Factors/genetics ; }, abstract = {This article reviews the roles that laterally transferred genes (LTG) play in the virulence of bacterial pathogens. The features of LTG that allow them to be recognized in bacterial genomes are described, and the mechanisms by which LTG are transferred between and within bacteria are reviewed. Genes on plasmids, integrative and conjugative elements, prophages, and pathogenicity islands are highlighted. Virulence genes that are frequently laterally transferred include genes for bacterial adherence to host cells, type 3 secretion systems, toxins, iron acquisition, and antimicrobial resistance. The specific roles of LTG in pathogenesis are illustrated by specific reference to Escherichia coli, Salmonella, pyogenic streptococci, and Clostridium perfringens.}, }
@article {pmid24317973, year = {2013}, author = {Morales, L and Noel, B and Porcel, B and Marcet-Houben, M and Hullo, MF and Sacerdot, C and Tekaia, F and Leh-Louis, V and Despons, L and Khanna, V and Aury, JM and Barbe, V and Couloux, A and Labadie, K and Pelletier, E and Souciet, JL and Boekhout, T and Gabaldon, T and Wincker, P and Dujon, B}, title = {Complete DNA sequence of Kuraishia capsulata illustrates novel genomic features among budding yeasts (Saccharomycotina).}, journal = {Genome biology and evolution}, volume = {5}, number = {12}, pages = {2524-2539}, pmid = {24317973}, issn = {1759-6653}, support = {310325/ERC_/European Research Council/International ; }, mesh = {Animals ; Base Composition/genetics ; Base Sequence ; Centromere/genetics ; DNA, Fungal/*analysis ; Gene Transfer, Horizontal ; Genome, Fungal/*genetics ; Insecta/microbiology ; Larva/microbiology ; Meiosis/genetics ; Nitrates/metabolism ; Phylogeny ; RNA, Transfer ; RNA, Untranslated/genetics ; Saccharomycetales/*genetics/isolation &amp; purification ; Sequence Analysis, DNA ; }, abstract = {The numerous yeast genome sequences presently available provide a rich source of information for functional as well as evolutionary genomics but unequally cover the large phylogenetic diversity of extant yeasts. We present here the complete sequence of the nuclear genome of the haploid-type strain of Kuraishia capsulata (CBS1993(T)), a nitrate-assimilating Saccharomycetales of uncertain taxonomy, isolated from tunnels of insect larvae underneath coniferous barks and characterized by its copious production of extracellular polysaccharides. The sequence is composed of seven scaffolds, one per chromosome, totaling 11.4 Mb and containing 6,029 protein-coding genes, ~13.5% of which being interrupted by introns. This GC-rich yeast genome (45.7%) appears phylogenetically related with the few other nitrate-assimilating yeasts sequenced so far, Ogataea polymorpha, O. parapolymorpha, and Dekkera bruxellensis, with which it shares a very reduced number of tRNA genes, a novel tRNA sparing strategy, and a common nitrate assimilation cluster, three specific features to this group of yeasts. Centromeres were recognized in GC-poor troughs of each scaffold. The strain bears MAT alpha genes at a single MAT locus and presents a significant degree of conservation with Saccharomyces cerevisiae genes, suggesting that it can perform sexual cycles in nature, although genes involved in meiosis were not all recognized. The complete absence of conservation of synteny between K. capsulata and any other yeast genome described so far, including the three other nitrate-assimilating species, validates the interest of this species for long-range evolutionary genomic studies among Saccharomycotina yeasts.}, }
@article {pmid24317084, year = {2014}, author = {Guo, HJ and Wang, ET and Zhang, XX and Li, QQ and Zhang, YM and Tian, CF and Chen, WX}, title = {Replicon-dependent differentiation of symbiosis-related genes in Sinorhizobium strains nodulating Glycine max.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {4}, pages = {1245-1255}, pmid = {24317084}, issn = {1098-5336}, mesh = {Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genetic Variation ; Molecular Sequence Data ; Phylogeny ; *Plant Root Nodulation ; Recombination, Genetic ; Sequence Analysis, DNA ; Sinorhizobium/*genetics/*physiology ; Glycine max/*microbiology ; *Symbiosis ; }, abstract = {In order to investigate the genetic differentiation of Sinorhizobium strains nodulating Glycine max and related microevolutionary mechanisms, three housekeeping genes (SMc00019, truA, and thrA) and 16 symbiosis-related genes on the chromosome (7 genes), pSymA (6 genes), and pSymB (3 genes) were analyzed. Five distinct species were identified among the test strains by calculating the average nucleotide identity (ANI) of SMc00019-truA-thrA: Sinorhizobium fredii, Sinorhizobium sojae, Sinorhizobium sp. I, Sinorhizobium sp. II, and Sinorhizobium sp. III. These species assignments were also supported by population genetics and phylogenetic analyses of housekeeping genes and symbiosis-related genes on the chromosome and pSymB. Different levels of genetic differentiation were observed among these species or different replicons. S. sojae was the most divergent from the other test species and was characterized by its low intraspecies diversity and limited geographic distribution. Intergenic recombination dominated the evolution of 19 genes from different replicons. Intraspecies recombination happened frequently in housekeeping genes and symbiosis-related genes on the chromosome and pSymB, whereas pSymA genes showed a clear pattern of lateral-transfer events between different species. Moreover, pSymA genes were characterized by a lower level of polymorphism and recombination than those on the chromosome and pSymB. Taken together, genes from different replicons of rhizobia might be involved in the establishment of symbiosis with legumes, but these symbiosis-related genes might have evolved differently according to their corresponding replicons.}, }
@article {pmid24314259, year = {2013}, author = {Peeters, N and Carrère, S and Anisimova, M and Plener, L and Cazalé, AC and Genin, S}, title = {Repertoire, unified nomenclature and evolution of the Type III effector gene set in the Ralstonia solanacearum species complex.}, journal = {BMC genomics}, volume = {14}, number = {}, pages = {859}, pmid = {24314259}, issn = {1471-2164}, mesh = {Bacterial Proteins/*genetics/metabolism ; Computational Biology/methods ; Databases, Genetic ; *Evolution, Molecular ; Gene Order ; Gene Transfer, Horizontal ; Genomics ; Open Reading Frames ; Phylogeny ; Ralstonia solanacearum/classification/*genetics ; Recombination, Genetic ; Selection, Genetic ; *Terminology as Topic ; }, abstract = {BACKGROUND: Ralstonia solanacearum is a soil-borne beta-proteobacterium that causes bacterial wilt disease in many food crops and is a major problem for agriculture in intertropical regions. R. solanacearum is a heterogeneous species, both phenotypically and genetically, and is considered as a species complex. Pathogenicity of R. solanacearum relies on the Type III secretion system that injects Type III effector (T3E) proteins into plant cells. T3E collectively perturb host cell processes and modulate plant immunity to enable bacterial infection.<br><br>RESULTS: We provide the catalogue of T3E in the R. solanacearum species complex, as well as candidates in newly sequenced strains. 94 T3E orthologous groups were defined on phylogenetic bases and ordered using a uniform nomenclature. This curated T3E catalog is available on a public website and a bioinformatic pipeline has been designed to rapidly predict T3E genes in newly sequenced strains. Systematical analyses were performed to detect lateral T3E gene transfer events and identify T3E genes under positive selection. Our analyses also pinpoint the RipF translocon proteins as major discriminating determinants among the phylogenetic lineages.<br><br>CONCLUSIONS: Establishment of T3E repertoires in strains representatives of the R. solanacearum biodiversity allowed determining a set of 22 T3E present in all the strains but provided no clues on host specificity determinants. The definition of a standardized nomenclature and the optimization of predictive tools will pave the way to understanding how variation of these repertoires is correlated to the diversification of this species complex and how they contribute to the different strain pathotypes.}, }
@article {pmid24312089, year = {2013}, author = {Li, H and Li, M and Huang, Y and Rensing, C and Wang, G}, title = {In silico analysis of bacterial arsenic islands reveals remarkable synteny and functional relatedness between arsenate and phosphate.}, journal = {Frontiers in microbiology}, volume = {4}, number = {}, pages = {347}, pmid = {24312089}, issn = {1664-302X}, abstract = {In order to construct a more universal model for understanding the genetic requirements for bacterial AsIII oxidation, an in silico examination of the available sequences in the GenBank was assessed and revealed 21 conserved 5-71 kb arsenic islands within phylogenetically diverse bacterial genomes. The arsenic islands included the AsIII oxidase structural genes aioBA, ars operons (e.g., arsRCB) which code for arsenic resistance, and pho, pst, and phn genes known to be part of the classical phosphate stress response and that encode functions associated with regulating and acquiring organic and inorganic phosphorus. The regulatory genes aioXSR were also an island component, but only in Proteobacteria and orientated differently depending on whether they were in α-Proteobacteria or β-/γ-Proteobacteria. Curiously though, while these regulatory genes have been shown to be essential to AsIII oxidation in the Proteobacteria, they are absent in most other organisms examined, inferring different regulatory mechanism(s) yet to be discovered. Phylogenetic analysis of the aio, ars, pst, and phn genes revealed evidence of both vertical inheritance and horizontal gene transfer (HGT). It is therefore likely the arsenic islands did not evolve as a whole unit but formed independently by acquisition of functionally related genes and operons in respective strains. Considering gene synteny and structural analogies between arsenate and phosphate, we presumed that these genes function together in helping these microbes to be able to use even low concentrations of phosphorus needed for vital functions under high concentrations of arsenic, and defined these sequences as the arsenic islands.}, }
@article {pmid24311786, year = {2014}, author = {Premkumar, L and Kurth, F and Neyer, S and Schembri, MA and Martin, JL}, title = {The multidrug resistance IncA/C transferable plasmid encodes a novel domain-swapped dimeric protein-disulfide isomerase.}, journal = {The Journal of biological chemistry}, volume = {289}, number = {5}, pages = {2563-2576}, pmid = {24311786}, issn = {1083-351X}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/*genetics/metabolism ; Catalytic Domain ; Conjugation, Genetic/genetics ; Dimerization ; Drug Resistance, Multiple/*genetics ; Escherichia coli/enzymology/*genetics ; Escherichia coli Proteins/chemistry/*genetics/metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Phosphoproteins/chemistry/*genetics/metabolism ; Plasmids/*genetics ; Protein Disulfide-Isomerases/chemistry/*genetics/metabolism ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Ribonuclease, Pancreatic/metabolism ; }, abstract = {The multidrug resistance-encoding IncA/C conjugative plasmids disseminate antibiotic resistance genes among clinically relevant enteric bacteria. A plasmid-encoded disulfide isomerase is associated with conjugation. Sequence analysis of several IncA/C plasmids and IncA/C-related integrative and conjugative elements (ICE) from commensal and pathogenic bacteria identified a conserved DsbC/DsbG homolog (DsbP). The crystal structure of DsbP reveals an N-terminal domain, a linker region, and a C-terminal catalytic domain. A DsbP homodimer is formed through domain swapping of two DsbP N-terminal domains. The catalytic domain incorporates a thioredoxin-fold with characteristic CXXC and cis-Pro motifs. Overall, the structure and redox properties of DsbP diverge from the Escherichia coli DsbC and DsbG disulfide isomerases. Specifically, the V-shaped dimer of DsbP is inverted compared with EcDsbC and EcDsbG. In addition, the redox potential of DsbP (-161 mV) is more reducing than EcDsbC (-130 mV) and EcDsbG (-126 mV). Other catalytic properties of DsbP more closely resemble those of EcDsbG than EcDsbC. These catalytic differences are in part a consequence of the unusual active site motif of DsbP (CAVC); substitution to the EcDsbC-like (CGYC) motif converts the catalytic properties to those of EcDsbC. Structural comparison of the 12 independent subunit structures of DsbP that we determined revealed that conformational changes in the linker region contribute to mobility of the catalytic domain, providing mechanistic insight into DsbP function. In summary, our data reveal that the conserved plasmid-encoded DsbP protein is a bona fide disulfide isomerase and suggest that a dedicated oxidative folding enzyme is important for conjugative plasmid transfer.}, }
@article {pmid24310000, year = {2014}, author = {Wu, YC and Rasmussen, MD and Bansal, MS and Kellis, M}, title = {Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees.}, journal = {Genome research}, volume = {24}, number = {3}, pages = {475-486}, pmid = {24310000}, issn = {1549-5469}, mesh = {Algorithms ; Animals ; Diptera/*genetics ; *Evolution, Molecular ; Fungi/*genetics ; *Gene Deletion ; *Gene Duplication ; Gene Transfer, Horizontal ; Genes ; Genome ; Models, Genetic ; Multigene Family ; Phylogeny ; Primates/*genetics ; Species Specificity ; }, abstract = {Accurate gene tree-species tree reconciliation is fundamental to inferring the evolutionary history of a gene family. However, although it has long been appreciated that population-related effects such as incomplete lineage sorting (ILS) can dramatically affect the gene tree, many of the most popular reconciliation methods consider discordance only due to gene duplication and loss (and sometimes horizontal gene transfer). Methods that do model ILS are either highly parameterized or consider a restricted set of histories, thus limiting their applicability and accuracy. To address these challenges, we present a novel algorithm DLCpar for inferring a most parsimonious (MP) history of a gene family in the presence of duplications, losses, and ILS. Our algorithm relies on a new reconciliation structure, the labeled coalescent tree (LCT), that simultaneously describes coalescent and duplication-loss history. We show that the LCT representation enables an exhaustive and efficient search over the space of reconciliations, and, for most gene families, the least common ancestor (LCA) mapping is an optimal solution for the species mapping between the gene tree and species tree in an MP LCT. Applying our algorithm to a variety of clades, including flies, fungi, and primates, as well as to simulated phylogenies, we achieve high accuracy, comparable to sophisticated probabilistic reconciliation methods, at reduced run time and with far fewer parameters. These properties enable inferences of the complex evolution of gene families across a broad range of species and large data sets.}, }
@article {pmid24308710, year = {2014}, author = {Wailan, AM and Paterson, DL}, title = {The spread and acquisition of NDM-1: a multifactorial problem.}, journal = {Expert review of anti-infective therapy}, volume = {12}, number = {1}, pages = {91-115}, doi = {10.1586/14787210.2014.856756}, pmid = {24308710}, issn = {1744-8336}, mesh = {Anti-Bacterial Agents/therapeutic use ; Cross Infection/drug therapy/prevention &amp; control ; Drug Resistance, Bacterial/*genetics ; Gram-Negative Bacteria/*drug effects ; Gram-Negative Bacterial Infections/drug therapy/prevention &amp; control ; beta-Lactamases/*genetics ; }, abstract = {bla NDM is a major mechanism of resistance of Gram-negative bacteria to β-lactam antibiotics including the carbapenems. bla NDM has been acquired by a large range of Gram-negative bacilli, especially by the Enterobacteriaceae and Acinetobacter spp. The combination of human factors (suboptimal antibiotic stewardship and infection control, movement of people between countries) plus bacterial factors (hospital adapted clones, environmental persistence and prolific horizontal gene transfer) have led to global spread of bla NDM at a rapid pace. Treatment options for New Delhi metallo-β-lactamase (NDM) producers are very limited. For serious infections, combination therapy including a polymyxin is preferred. However, resistance to polymyxins is emerging. Clearly, substantial international efforts must be made to control the spread of NDM producers or else many of the advances of modern medicine may be undermined by untreatable infections.}, }
@article {pmid24306098, year = {2014}, author = {Zhang, R and Hu, YY and Yang, XF and Gu, DX and Zhou, HW and Hu, QF and Zhao, K and Yu, SF and Chen, GX}, title = {Emergence of NDM-producing non-baumannii Acinetobacter spp. isolated from China.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {33}, number = {5}, pages = {853-860}, pmid = {24306098}, issn = {1435-4373}, mesh = {Acinetobacter/classification/*enzymology/genetics/*isolation &amp; purification ; Acinetobacter Infections/*microbiology ; Adult ; Aged ; Aged, 80 and over ; China ; Cluster Analysis ; Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; DNA, Intergenic/chemistry/genetics ; DNA-Directed RNA Polymerases ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/drug effects/genetics ; Female ; Gene Transfer, Horizontal ; Hospitals ; Humans ; Male ; Molecular Sequence Data ; Molecular Typing ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; beta-Lactamases/genetics/*metabolism ; }, abstract = {One hundred and thirty-six bla OXA-51-negative strains were identified from 1,067 Acinetobacter calcoaceticus-A. baumannii complex (ACB complex) isolates, which were collected during October 2010 to March 2013 from 15 general hospitals in 10 cities throughout Zhejiang Province, China. Seven of the 136 bla OXA-51-negative ACB complex isolates were New Delhi metallo-β-lactamase-1 (NDM-1)-positive, among which three were identified as A. nosocomialis and four were identified as A. pittii strains using 16S-23S rRNA gene intergenic spacer (ITS) sequencing and partial RNA polymerase β-subunit (rpoB) sequencing. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) analysis showed that the seven NDM-positive isolates belonged to three clonal strains with three novel sequence types (STs). Polymerase chain reaction (PCR) assays and DNA sequence analysis of the carbapenemase and other β-lactamase genes indicated that all the isolates harbored the bla NDM-1 gene, and that only one strain of A. nosocomialis isolates harbored both bla NDM-1 and bla OXA-23. All of them were positive for bla ADC, from which three novel bla ADC genes (designated as bla ADC-69, bla ADC-70, and bla ADC-71) were detected for the first time. The presence of ISAba125 upstream of bla NDM-1 was identified through genetic environment analysis. Carbapenem resistance can be transferred from A. nosocomialis and A. pittii to Escherichia coli EC600 by the conjugation experiment. Plasmid analysis, DNA hybridization, and extraction experiments indicated that bla NDM-1 was located on a plasmid of approximately 50 kb. In conclusion, we characterized the dissemination of NDM-1-positive A. pittii strains in Zhejiang Province, China, and reported the NDM-producing A. nosocomialis for the first time.}, }
@article {pmid24305740, year = {2014}, author = {Yuan, J and Yang, M and Ren, J and Fu, B and Jiang, F and Zhang, X}, title = {Analysis of genomic characters reveals that four distinct gene clusters are correlated with different functions in Burkholderia cenocepacia AU 1054.}, journal = {Applied microbiology and biotechnology}, volume = {98}, number = {1}, pages = {361-372}, doi = {10.1007/s00253-013-5415-7}, pmid = {24305740}, issn = {1432-0614}, mesh = {Burkholderia cenocepacia/*genetics ; Chromosomes, Bacterial ; Codon ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; *Multigene Family ; Mutation ; Selection, Genetic ; }, abstract = {Possessing three circular chromosomes is a distinct genomic characteristic of Burkholderia cenocepacia AU 1054, a clinically important pathogen in cystic fibrosis. In this study, base composition, codon usage and functional role category were analyzed in the B. cenocepacia AU 1054 genome. Although no bias in the base and codon usage was detected between any two chromosomes, function differences did exist in the genes of each chromosome. Similar base composition and differential functional role categories indicated that genes on these three chromosomes were relatively stable and that a proper division of labor was established. Based on variations in the base or codon usage, four small gene clusters were observed in all of the genes. Multivariate analysis revealed that protein hydrophobicity played a predominant role in shaping base usage bias, while horizontal gene transfer and the gene expression level were the two most important factors that affected the codon usage bias. Interestingly, we also found that these gene clusters were correlated with different biological functions: (i) 45 pyrimidine-leading-codon preferred genes were predominantly involved in regulatory function; (ii) most drug resistance-related genes involved in 826 genes that coding for hydrophobic proteins; (iii) most of the 111 horizontal transfer genes were responsible for genomic plasticity; and (iv) 73 highly expressed genes (predicted by their codon adaptation index values) showed environmental adaptation to cystic fibrosis. Our results showed that genes with base or codon usage bias were affected by mutational pressure and natural selection, and their functions could contribute to drug assistance and transmissible activity in B. cenocepacia.}, }
@article {pmid24303798, year = {2015}, author = {Okshevsky, M and Meyer, RL}, title = {The role of extracellular DNA in the establishment, maintenance and perpetuation of bacterial biofilms.}, journal = {Critical reviews in microbiology}, volume = {41}, number = {3}, pages = {341-352}, doi = {10.3109/1040841X.2013.841639}, pmid = {24303798}, issn = {1549-7828}, mesh = {Bacteria/genetics/growth &amp; development/immunology ; Bacterial Adhesion/*genetics ; Bacterial Physiological Phenomena/genetics ; Biofilms/*growth &amp; development ; DNA, Bacterial/*genetics/metabolism ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal/genetics ; Immune Evasion/*genetics/immunology ; }, abstract = {The significance of extracellular DNA (eDNA) in biofilms was overlooked until researchers added DNAse to a Pseudomonas aeruginosa biofilm and watched the biofilm disappear. Now, a decade later, the widespread importance of eDNA in biofilm formation is undisputed, but detailed knowledge about how it promotes biofilm formation and conveys antimicrobial resistance is only just starting to emerge. In this review, we discuss how eDNA is produced, how it aids bacterial adhesion, secures the structural stability of biofilms and contributes to antimicrobial resistance. The appearance of eDNA in biofilms is no accident: It is produced by active secretion or controlled cell lysis - sometimes linked to competence development. eDNA adsorbs to and extends from the cell surface, promoting adhesion to abiotic surfaces through acid-base interactions. In the biofilm, is it less clear how eDNA interacts with cells and matrix components. A few eDNA-binding biomolecules have been identified, revealing new concepts in biofilm formation. Being anionic, eDNA chelates cations and restricts diffusion of cationic antimicrobials. Furthermore, chelation of Mg(2+) triggers a genetic response that further increases resistance. The multifaceted role of eDNA makes it an attractive target to sensitize biofilms to conventional antimicrobial treatment or development of new strategies to combat biofilms.}, }
@article {pmid24301919, year = {2013}, author = {Kang, JH and Yang, SG and Moon, TS and Park, JY and Choi, TJ}, title = {Development of microsatellite markers for the kelp grouper Epinephelus bruneus by 454 pyrosequencing and transfer to related species.}, journal = {Genetics and molecular research : GMR}, volume = {12}, number = {4}, pages = {5485-5493}, doi = {10.4238/2013.November.13.1}, pmid = {24301919}, issn = {1676-5680}, mesh = {Animals ; Gene Frequency ; *Gene Transfer, Horizontal ; Genetic Markers ; Microsatellite Repeats/*genetics ; Perciformes/*genetics ; }, abstract = {The kelp or longtooth grouper (Epinephelus bruneus), which inhabits Eastern Asia, is the most economically important of 11 grouper species that inhabit the Southern Sea near Jeju Island in Korea. This species is listed as vulnerable by the International Union for the Conservation of Nature and Natural Resources because of a rapid decrease in its resources. We developed microsatellite markers for E. bruneus using the pyrosequencing technique for applications in resource management and aquaculture. In addition, we tested the cross-species transferability of the microsatellite markers in four species belonging to the Epinephelus genus. Among 66,452 simple sequence repeats, 64 loci containing more than eight CA or TG repeats were randomly selected for primer synthesis; 45 primer sets (75.0%) produced polymerase chain reaction (PCR) products of 100-300 bp and were selected as candidates. After primary testing with four E. bruneus fish, 28 polymorphic loci were selected as the final microsatellite markers, and 23 sets showing clear amplification of polymorphic loci were used to analyze 71 fish. These loci have allele numbers ranging from 2 to 23. Null alleles were detected at three loci, and three loci showed an excess of homozygotes in the Hardy-Weinberg equilibrium test. Of the three species used for cross-species transfer of these markers, Epinephelus moara showed the highest transferability (92.9%) and polymorphism (67.9%), followed by Epinephelus fuscoguttatus (75.0 and 67.9%, respectively) and Epinephelus septemfasciatus (57.1 and 46.4%, respectively). These results suggested that these microsatellite loci should be valuable tools for population genetic studies of the species Epinephelus.}, }
@article {pmid24298062, year = {2014}, author = {Venegas-Ortiz, J and Allen, RJ and Evans, MR}, title = {Speed of invasion of an expanding population by a horizontally transmitted trait.}, journal = {Genetics}, volume = {196}, number = {2}, pages = {497-507}, pmid = {24298062}, issn = {1943-2631}, mesh = {Algorithms ; Computer Simulation ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genetics, Population ; *Models, Genetic ; *Quantitative Trait, Heritable ; Selection, Genetic ; }, abstract = {Range expansions are a ubiquitous phenomenon, leading to the spatial spread of genetic, ecological, and cultural traits. While some of these traits are advantageous (and hence selected), other, nonselected traits can also spread by hitchhiking on the wave of population expansion. This requires us to understand how the spread of a hitchhiking trait is coupled to the wave of advance of its host population. Here, we use a system of coupled Fisher-Kolmogorov-Petrovsky-Piskunov (F-KPP) equations to describe the spread of a horizontally transmitted hitchhiking trait within a population as it expands. We extend F-KPP wave theory to the system of coupled equations to predict how the hitchhiking trait spreads as a wave within the expanding population. We show that the speed of this trait wave is controlled by an intricate coupling between the tip of the population and trait waves. Our analysis yields a new speed selection mechanism for coupled waves of advance and reveals the existence of previously unexpected speed transitions.}, }
@article {pmid24297445, year = {2014}, author = {Burki, F and Imanian, B and Hehenberger, E and Hirakawa, Y and Maruyama, S and Keeling, PJ}, title = {Endosymbiotic gene transfer in tertiary plastid-containing dinoflagellates.}, journal = {Eukaryotic cell}, volume = {13}, number = {2}, pages = {246-255}, pmid = {24297445}, issn = {1535-9786}, mesh = {Cell Nucleus/genetics ; Dinoflagellida/*genetics/physiology ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Plastid ; Plastids/genetics ; Symbiosis/*genetics ; Transcriptome ; }, abstract = {Plastid establishment involves the transfer of endosymbiotic genes to the host nucleus, a process known as endosymbiotic gene transfer (EGT). Large amounts of EGT have been shown in several photosynthetic lineages but also in present-day plastid-lacking organisms, supporting the notion that endosymbiotic genes leave a substantial genetic footprint in the host nucleus. Yet the extent of this genetic relocation remains debated, largely because the long period that has passed since most plastids originated has erased many of the clues to how this process unfolded. Among the dinoflagellates, however, the ancestral peridinin-containing plastid has been replaced by tertiary plastids on several more recent occasions, giving us a less ancient window to examine plastid origins. In this study, we evaluated the endosymbiotic contribution to the host genome in two dinoflagellate lineages with tertiary plastids. We generated the first nuclear transcriptome data sets for the "dinotoms," which harbor diatom-derived plastids, and analyzed these data in combination with the available transcriptomes for kareniaceans, which harbor haptophyte-derived plastids. We found low level of detectable EGT in both dinoflagellate lineages, with only 9 genes and 90 genes of possible tertiary endosymbiotic origin in dinotoms and kareniaceans, respectively, suggesting that tertiary endosymbioses did not heavily impact the host dinoflagellate genomes.}, }
@article {pmid24296573, year = {2013}, author = {Foley, SL and Johnson, TJ and Ricke, SC and Nayak, R and Danzeisen, J}, title = {Salmonella pathogenicity and host adaptation in chicken-associated serovars.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {77}, number = {4}, pages = {582-607}, pmid = {24296573}, issn = {1098-5557}, mesh = {Animals ; Chickens ; Salmonella/genetics/metabolism/*pathogenicity ; Salmonella enterica/genetics/metabolism/pathogenicity ; Virulence/physiology ; }, abstract = {Enteric pathogens such as Salmonella enterica cause significant morbidity and mortality. S. enterica serovars are a diverse group of pathogens that have evolved to survive in a wide range of environments and across multiple hosts. S. enterica serovars such as S. Typhi, S. Dublin, and S. Gallinarum have a restricted host range, in which they are typically associated with one or a few host species, while S. Enteritidis and S. Typhimurium have broad host ranges. This review examines how S. enterica has evolved through adaptation to different host environments, especially as related to the chicken host, and continues to be an important human pathogen. Several factors impact host range, and these include the acquisition of genes via horizontal gene transfer with plasmids, transposons, and phages, which can potentially expand host range, and the loss of genes or their function, which would reduce the range of hosts that the organism can infect. S. Gallinarum, with a limited host range, has a large number of pseudogenes in its genome compared to broader-host-range serovars. S. enterica serovars such as S. Kentucky and S. Heidelberg also often have plasmids that may help them colonize poultry more efficiently. The ability to colonize different hosts also involves interactions with the host's immune system and commensal organisms that are present. Thus, the factors that impact the ability of Salmonella to colonize a particular host species, such as chickens, are complex and multifactorial, involving the host, the pathogen, and extrinsic pressures. It is the interplay of these factors which leads to the differences in host ranges that we observe today.}, }
@article {pmid24296570, year = {2013}, author = {Sapp, J and Fox, GE}, title = {The singular quest for a universal tree of life.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {77}, number = {4}, pages = {541-550}, pmid = {24296570}, issn = {1098-5557}, mesh = {*Biological Evolution ; Gene Transfer, Horizontal/genetics ; RNA, Ribosomal/*genetics ; }, abstract = {Carl Woese developed a unique research program, based on rRNA, for discerning bacterial relationships and constructing a universal tree of life. Woese's interest in the evolution of the genetic code led to him to investigate the deep roots of evolution, develop the concept of the progenote, and conceive of the Archaea. In so doing, he and his colleagues at the University of Illinois in Urbana revolutionized microbiology and brought the classification of microbes into an evolutionary framework. Woese also provided definitive evidence for the role of symbiosis in the evolution of the eukaryotic cell while underscoring the importance of lateral gene transfer in microbial evolution. Woese and colleagues' proposal of three fundamental domains of life was brought forward in direct conflict with the prokaryote-eukaryote dichotomy. Together with several colleagues and associates, he brought together diverse evidence to support the rRNA evidence for the fundamentally tripartite nature of life. This paper aims to provide insight into his accomplishments, how he achieved them, and his place in the history of biology.}, }
@article {pmid24295128, year = {2013}, author = {Zheng, J and Peng, D and Ruan, L and Sun, M}, title = {Evolution and dynamics of megaplasmids with genome sizes larger than 100 kb in the Bacillus cereus group.}, journal = {BMC evolutionary biology}, volume = {13}, number = {}, pages = {262}, pmid = {24295128}, issn = {1471-2148}, mesh = {Bacillus cereus/classification/*genetics ; *Biological Evolution ; DNA Replication ; *Genome Size ; *Genome, Bacterial ; Phylogeny ; Plasmids/*genetics ; }, abstract = {BACKGROUND: Plasmids play a crucial role in the evolution of bacterial genomes by mediating horizontal gene transfer. However, the origin and evolution of most plasmids remains unclear, especially for megaplasmids. Strains of the Bacillus cereus group contain up to 13 plasmids with genome sizes ranging from 2 kb to 600 kb, and thus can be used to study plasmid dynamics and evolution.<br><br>RESULTS: This work studied the origin and evolution of 31 B. cereus group megaplasmids (>100 kb) focusing on the most conserved regions on plasmids, minireplicons. Sixty-five putative minireplicons were identified and classified to six types on the basis of proteins that are essential for replication. Twenty-nine of the 31 megaplasmids contained two or more minireplicons. Phylogenetic analysis of the protein sequences showed that different minireplicons on the same megaplasmid have different evolutionary histories. Therefore, we speculated that these megaplasmids are the results of fusion of smaller plasmids. All plasmids of a bacterial strain must be compatible. In megaplasmids of the B. cereus group, individual minireplicons of different megaplasmids in the same strain belong to different types or subtypes. Thus, the subtypes of each minireplicon they contain may determine the incompatibilities of megaplasmids. A broader analysis of all 1285 bacterial plasmids with putative known minireplicons whose complete genome sequences were available from GenBank revealed that 34% (443 plasmids) of the plasmids have two or more minireplicons. This indicates that plasmid fusion events are general among bacterial plasmids.<br><br>CONCLUSIONS: Megaplasmids of B. cereus group are fusion of smaller plasmids, and the fusion of plasmids likely occurs frequently in the B. cereus group and in other bacterial taxa. Plasmid fusion may be one of the major mechanisms for formation of novel megaplasmids in the evolution of bacteria.}, }
@article {pmid24289955, year = {2014}, author = {Marti, E and Variatza, E and Balcazar, JL}, title = {The role of aquatic ecosystems as reservoirs of antibiotic resistance.}, journal = {Trends in microbiology}, volume = {22}, number = {1}, pages = {36-41}, doi = {10.1016/j.tim.2013.11.001}, pmid = {24289955}, issn = {1878-4380}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/*genetics ; *Drug Resistance, Bacterial ; *Ecosystem ; *Gene Transfer, Horizontal ; Humans ; *Water Microbiology ; }, abstract = {Although antibiotic resistance has become a major threat to human health worldwide, this phenomenon has been largely overlooked in studies in environmental settings. Aquatic environments may provide an ideal setting for the acquisition and dissemination of antibiotic resistance, because they are frequently impacted by anthropogenic activities. This review focuses primarily on the emergence and dissemination of antibiotic resistance in the aquatic environment, with a special emphasis on the role of antibiotic resistance genes.}, }
@article {pmid25674360, year = {2013}, author = {Almagro-Moreno, S and Taylor, RK}, title = {Cholera: Environmental Reservoirs and Impact on Disease Transmission.}, journal = {Microbiology spectrum}, volume = {1}, number = {2}, pages = {}, pmid = {25674360}, issn = {2165-0497}, support = {R01 AI025096/AI/NIAID NIH HHS/United States ; R01 AI039654/AI/NIAID NIH HHS/United States ; R37 AI025096/AI/NIAID NIH HHS/United States ; R56 AI039654/AI/NIAID NIH HHS/United States ; }, abstract = {Vibrio cholerae is widely known to be the etiological agent of the life-threatening diarrheal disease cholera. Cholera remains a major scourge in many developing countries, infecting hundreds of thousands every year. Remarkably, V. cholerae is a natural inhabitant of brackish riverine, estuarine, and coastal waters, and only a subset of strains are known to be pathogenic to humans. Recent studies have begun to uncover a very complex network of relationships between V. cholerae and other sea dwellers, and the mechanisms associated with the occurrence of seasonal epidemics in regions where cholera is endemic are beginning to be elucidated. Many of the factors required for the organism's survival and persistence in its natural environment have been revealed, as well as the ubiquitous presence of horizontal gene transfer in the emergence of pathogenic strains of V. cholerae. In this article, we will focus on the environmental stage of pathogenic V. cholerae and the interactions of the microorganism with other inhabitants of aquatic environments. We will discuss the impact that its environmental reservoirs have on disease transmission and the distinction between reservoirs of V. cholerae and the vectors that establish cholera as a zoonosis.}, }
@article {pmid24285199, year = {2014}, author = {Engelstädter, J and Moradigaravand, D}, title = {Adaptation through genetic time travel? Fluctuating selection can drive the evolution of bacterial transformation.}, journal = {Proceedings. Biological sciences}, volume = {281}, number = {1775}, pages = {20132609}, pmid = {24285199}, issn = {1471-2954}, mesh = {Adaptation, Biological/genetics ; Genome, Bacterial ; *Models, Theoretical ; *Selection, Genetic ; Transformation, Bacterial/*genetics ; }, abstract = {Natural transformation is a process whereby bacteria actively take up DNA from the surrounding environment and incorporate it into their genome. Natural transformation is widespread in bacteria, but its evolutionary significance is still debated. Here, we hypothesize that transformation may confer a fitness advantage in changing environments through a process we term 'genetic time travel': by taking up old genes that were retained in the environment, the bacteria may revert to a past genotypic state that proves advantageous in the present or a future environment. We scrutinize our hypothesis by means of a mathematical model involving two bacterial types (transforming and non-transforming), a single locus under natural selection and a free DNA pool. The two bacterial types were competed in environments with changing selection regimes. We demonstrate that for a wide range of parameter values for the DNA turnover rate, the transformation rate and the frequency of environmental change, the transforming type outcompetes the non-transforming type. We discuss the empirical plausibility of our hypothesis, as well as its relationship to other hypotheses for the evolution of transformation in bacteria and sex more generally, speculating that 'genetic time travel' may also be relevant in eukaryotes that undergo horizontal gene transfer.}, }
@article {pmid24281402, year = {2014}, author = {Feng, Y and Chiu, CH}, title = {Predicting genetic and ecological characteristics of bacterial species by comparing the trajectories of dN/dS and dI/dS in bacterial genomes.}, journal = {Molecular bioSystems}, volume = {10}, number = {2}, pages = {266-272}, doi = {10.1039/c3mb70476a}, pmid = {24281402}, issn = {1742-2051}, mesh = {Bacteria/*genetics ; Ecosystem ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; *Genome, Bacterial ; *INDEL Mutation ; Models, Genetic ; Mutation ; Phylogeny ; Selection, Genetic ; Species Specificity ; }, abstract = {Indel (insertion/deletion) causes gene disruption and is considered to be deleterious like non-synonymous mutation during the evolution of bacterial genomes. The trajectory of dN/dS (the ratio of non-synonymous to synonymous mutation) has been found to decrease exponentially over time, but the trajectory of dI/dS (the ratio of indel to synonymous mutation) has not been thoroughly explored yet. Here we compared the patterns of dN/dS and dI/dS for several bacterial species. The majority of them showed a much steeper dI/dS trajectory than the dN/dS trajectory, suggesting that indel was more deleterious than non-synonymous mutation and therefore was more difficult to fix in genomes. However, the naturally competent bacteria, or those with a much lower genetic barrier for DNA exchange, presented a reverse relationship between dI/dS and dN/dS, indicative of an exceptional ability to tolerate horizontal genetic transfer. The result suggests that plotting of dN/dS and dI/dS trajectories can help to predict the genetic and ecological characteristics of bacterial species.}, }
@article {pmid24281050, year = {2013}, author = {Eveleigh, RJ and Meehan, CJ and Archibald, JM and Beiko, RG}, title = {Being Aquifex aeolicus: Untangling a hyperthermophile's checkered past.}, journal = {Genome biology and evolution}, volume = {5}, number = {12}, pages = {2478-2497}, pmid = {24281050}, issn = {1759-6653}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Archaea/genetics ; Bacteria/*classification/*genetics ; Base Sequence ; Cell Wall/genetics ; Clostridium/genetics ; Deltaproteobacteria/genetics ; Energy Metabolism/genetics/physiology ; Epsilonproteobacteria/genetics ; *Evolution, Molecular ; Flagella/genetics ; Flagellin/genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Lipopolysaccharides/genetics ; Oxidative Phosphorylation ; Peptidoglycan/genetics ; Phylogeny ; Ribosomes/genetics ; }, abstract = {Lateral gene transfer (LGT) is an important factor contributing to the evolution of prokaryotic genomes. The Aquificae are a hyperthermophilic bacterial group whose genes show affiliations to many other lineages, including the hyperthermophilic Thermotogae, the Proteobacteria, and the Archaea. Previous phylogenomic analyses focused on Aquifex aeolicus identified Thermotogae and Aquificae either as successive early branches or sisters in a rooted bacterial phylogeny, but many phylogenies and cellular traits have suggested a stronger affiliation with the Epsilonproteobacteria. Different scenarios for the evolution of the Aquificae yield different phylogenetic predictions. Here, we outline these scenarios and consider the fit of the available data, including three sequenced Aquificae genomes, to different sets of predictions. Evidence from phylogenetic profiles and trees suggests that the Epsilonproteobacteria have the strongest affinities with the three Aquificae analyzed. However, this pattern is shown by only a minority of encoded proteins, and the Archaea, many lineages of thermophilic bacteria, and members of genus Clostridium and class Deltaproteobacteria also show strong connections to the Aquificae. The phylogenetic affiliations of different functional subsystems showed strong biases: Most but not all genes implicated in the core translational apparatus tended to group Aquificae with Thermotogae, whereas a wide range of metabolic and cellular processes strongly supported the link between Aquificae and Epsilonproteobacteria. Depending on which sets of genes are privileged, either Thermotogae or Epsilonproteobacteria is the most plausible adjacent lineage to the Aquificae. Both scenarios require massive sharing of genes to explain the history of this enigmatic group, whose history is further complicated by specific affinities of different members of Aquificae to different partner lineages.}, }
@article {pmid24278351, year = {2013}, author = {Hossain, MJ and Waldbieser, GC and Sun, D and Capps, NK and Hemstreet, WB and Carlisle, K and Griffin, MJ and Khoo, L and Goodwin, AE and Sonstegard, TS and Schroeder, S and Hayden, K and Newton, JC and Terhune, JS and Liles, MR}, title = {Implication of lateral genetic transfer in the emergence of Aeromonas hydrophila isolates of epidemic outbreaks in channel catfish.}, journal = {PloS one}, volume = {8}, number = {11}, pages = {e80943}, pmid = {24278351}, issn = {1932-6203}, mesh = {Aeromonas hydrophila/classification/*genetics/isolation &amp; purification/metabolism/virology ; Animals ; Computational Biology ; *Disease Outbreaks ; Fish Diseases/*epidemiology/microbiology/transmission ; Gene Order ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Genotype ; Ictaluridae/*microbiology ; Metabolic Networks and Pathways ; Molecular Sequence Data ; Multigene Family ; O Antigens/genetics ; Phenotype ; Phylogeny ; Prophages/genetics ; Virulence Factors/genetics ; }, abstract = {To investigate the molecular basis of the emergence of Aeromonas hydrophila responsible for an epidemic outbreak of motile aeromonad septicemia of catfish in the Southeastern United States, we sequenced 11 A. hydrophila isolates that includes five reference and six recent epidemic isolates. Comparative genomics revealed that recent epidemic A. hydrophila isolates are highly clonal, whereas reference isolates are greatly diverse. We identified 55 epidemic-associated genetic regions with 313 predicted genes that are present in epidemic isolates but absent from reference isolates and 35% of these regions are located within genomic islands, suggesting their acquisition through lateral gene transfer. The epidemic-associated regions encode predicted prophage elements, pathogenicity islands, metabolic islands, fitness islands and genes of unknown functions, and 34 of the genes encoded in these regions were predicted as virulence factors. We found two pilus biogenesis gene clusters encoded within predicted pathogenicity islands. A functional metabolic island that encodes a complete pathway for myo-inositol catabolism was evident by the ability of epidemic A. hydrophila isolates to use myo-inositol as a sole carbon source. Testing of A. hydrophila field isolates found a consistent correlation between myo-inositol utilization as a sole carbon source and the presence of an epidemic-specific genetic marker. All epidemic isolates and one reference isolate shared a novel O-antigen cluster. Altogether we identified four different O-antigen biosynthesis gene clusters within the 11 sequenced A. hydrophila genomes. Our study reveals new insights into the evolutionary changes that have resulted in the emergence of recent epidemic A. hydrophila strains.}, }
@article {pmid24277980, year = {2013}, author = {Yang, Y and Luo, D}, title = {The origin of parasitism gene in nematodes: evolutionary analysis through the construction of domain trees.}, journal = {Evolutionary bioinformatics online}, volume = {9}, number = {}, pages = {453-466}, pmid = {24277980}, issn = {1176-9343}, abstract = {Inferring evolutionary history of parasitism genes is important to understand how evolutionary mechanisms affect the occurrences of parasitism genes. In this study, we constructed multiple domain trees for parasitism genes and genes under free-living conditions. Further analyses of horizontal gene transfer (HGT)-like phylogenetic incongruences, duplications, and speciations were performed based on these trees. By comparing these analyses, the contributions of pre-adaptations were found to be more important to the evolution of parasitism genes than those of duplications, and pre-adaptations are as crucial as previously reported HGTs to parasitism. Furthermore, speciation may also affect the evolution of parasitism genes. In addition, Pristionchus pacificus was suggested to be a common model organism for studies of parasitic nematodes, including root-knot species. These analyses provided information regarding mechanisms that may have contributed to the evolution of parasitism genes.}, }
@article {pmid24277046, year = {2014}, author = {Guan, J and Liu, S and Lin, Z and Li, W and Liu, X and Chen, D}, title = {Severe sepsis facilitates intestinal colonization by extended-spectrum-β-lactamase-producing Klebsiella pneumoniae and transfer of the SHV-18 resistance gene to Escherichia coli during antimicrobial treatment.}, journal = {Antimicrobial agents and chemotherapy}, volume = {58}, number = {2}, pages = {1039-1046}, pmid = {24277046}, issn = {1098-6596}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Burns/drug therapy/*microbiology/pathology ; Ceftriaxone/pharmacology ; Drug Resistance, Multiple, Bacterial ; Endotoxins ; Escherichia coli/enzymology/*genetics ; *Gene Transfer, Horizontal ; Hot Temperature ; Intestines/microbiology/pathology ; Klebsiella Infections/drug therapy/*microbiology/pathology ; Klebsiella pneumoniae/drug effects/enzymology/*genetics ; Male ; Rats ; Rats, Sprague-Dawley ; Sepsis/chemically induced/drug therapy/*microbiology/pathology ; beta-Lactamases/*genetics/metabolism ; }, abstract = {Infections caused by multidrug-resistant pathogens are frequent and life threatening in critically ill patients. To investigate whether severe sepsis affects gut colonization by resistant pathogens and genetic exchange between opportunistic pathogens, we tested the intestinal-colonization ability of an extended-spectrum beta-lactamase-producing Klebsiella pneumoniae strain carrying the SHV-18 resistance gene and the transfer ability of the resistance gene to endogenous Escherichia coli under ceftriaxone treatment in rats with burn injury only or severe sepsis induced by burns plus endotoxin exposure. Without ceftriaxone treatment, the K. pneumoniae strain colonized the intestine in both septic and burned rats for a short time, with clearance occurring earlier in burn-only rats but never in sham burn rats. In both burned and septic rats, the colonization level of the challenge strain dropped at the beginning and then later increased during ceftriaxone treatment, after which it declined gradually. This pattern coincided with the change in resistance of K. pneumoniae to ceftriaxone during and after ceftriaxone treatment. Compared with burn-only injury, severe sepsis had a more significant effect on the change in antimicrobial resistance to ceftriaxone. Only in septic rats was the resistance gene successfully transferred from the challenge strain to endogenous E. coli during ceftriaxone treatment; the gene persisted for at least 4 weeks after ceftriaxone treatment. We concluded that severe sepsis can facilitate intestinal colonization by an exogenous resistant pathogen and the transfer of the resistance gene to a potential endogenous pathogen during antimicrobial treatment.}, }
@article {pmid24275491, year = {2014}, author = {Huerta-Cepas, J and Capella-Gutiérrez, S and Pryszcz, LP and Marcet-Houben, M and Gabaldón, T}, title = {PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome.}, journal = {Nucleic acids research}, volume = {42}, number = {Database issue}, pages = {D897-902}, pmid = {24275491}, issn = {1362-4962}, support = {310325/ERC_/European Research Council/International ; }, mesh = {*Databases, Genetic ; Gene Expression Profiling ; *Genome ; Humans ; Internet ; *Phylogeny ; Proteins/classification/genetics ; Proteome ; }, abstract = {Phylogenetic trees representing the evolutionary relationships of homologous genes are the entry point for many evolutionary analyses. For instance, the use of a phylogenetic tree can aid in the inference of orthology and paralogy relationships, and in the detection of relevant evolutionary events such as gene family expansions and contractions, horizontal gene transfer, recombination or incomplete lineage sorting. Similarly, given the plurality of evolutionary histories among genes encoded in a given genome, there is a need for the combined analysis of genome-wide collections of phylogenetic trees (phylomes). Here, we introduce a new release of PhylomeDB (http://phylomedb.org), a public repository of phylomes. Currently, PhylomeDB hosts 120 public phylomes, comprising >1.5 million maximum likelihood trees and multiple sequence alignments. In the current release, phylogenetic trees are annotated with taxonomic, protein-domain arrangement, functional and evolutionary information. PhylomeDB is also a major source for phylogeny-based predictions of orthology and paralogy, covering >10 million proteins across 1059 sequenced species. Here we describe newly implemented PhylomeDB features, and discuss a benchmark of the orthology predictions provided by the database, the impact of proteome updates and the use of the phylome approach in the analysis of newly sequenced genomes and transcriptomes.}, }
@article {pmid24267588, year = {2013}, author = {Liu, Z and Müller, J and Li, T and Alvey, RM and Vogl, K and Frigaard, NU and Rockwell, NC and Boyd, ES and Tomsho, LP and Schuster, SC and Henke, P and Rohde, M and Overmann, J and Bryant, DA}, title = {Genomic analysis reveals key aspects of prokaryotic symbiosis in the phototrophic consortium "Chlorochromatium aggregatum".}, journal = {Genome biology}, volume = {14}, number = {11}, pages = {R127}, pmid = {24267588}, issn = {1474-760X}, mesh = {Bacteria/classification/*genetics ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomics ; Microbial Consortia/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Symbiosis/*genetics ; }, abstract = {BACKGROUND: 'Chlorochromatium aggregatum' is a phototrophic consortium, a symbiosis that may represent the highest degree of mutual interdependence between two unrelated bacteria not associated with a eukaryotic host. 'Chlorochromatium aggregatum' is a motile, barrel-shaped aggregate formed from a single cell of 'Candidatus Symbiobacter mobilis", a polarly flagellated, non-pigmented, heterotrophic bacterium, which is surrounded by approximately 15 epibiont cells of Chlorobium chlorochromatii, a non-motile photolithoautotrophic green sulfur bacterium.<br><br>RESULTS: We analyzed the complete genome sequences of both organisms to understand the basis for this symbiosis. Chl. chlorochromatii has acquired relatively few symbiosis-specific genes; most acquired genes are predicted to modify the cell wall or function in cell-cell adhesion. In striking contrast, 'Ca. S. mobilis' appears to have undergone massive gene loss, is probably no longer capable of independent growth, and thus may only reproduce when consortia divide. A detailed model for the energetic and metabolic bases of the dependency of 'Ca. S. mobilis' on Chl. chlorochromatii is described.<br><br>CONCLUSIONS: Genomic analyses suggest that three types of interactions lead to a highly sophisticated relationship between these two organisms. Firstly, extensive metabolic exchange, involving carbon, nitrogen, and sulfur sources as well as vitamins, occurs from the epibiont to the central bacterium. Secondly, 'Ca. S. mobilis' can sense and move towards light and sulfide, resources that only directly benefit the epibiont. Thirdly, electron cycling mechanisms, particularly those mediated by quinones and potentially involving shared protonmotive force, could provide an important basis for energy exchange in this and other symbiotic relationships.}, }
@article {pmid24265503, year = {2013}, author = {Chopra, N and Saumitra,  and Pathak, A and Bhatnagar, R and Bhatnagar, S}, title = {Linkage, mobility, and selfishness in the MazF family of bacterial toxins: a snapshot of bacterial evolution.}, journal = {Genome biology and evolution}, volume = {5}, number = {12}, pages = {2268-2284}, pmid = {24265503}, issn = {1759-6653}, mesh = {Bacillus anthracis/genetics ; Bacterial Proteins/genetics ; *Bacterial Toxins/chemistry/classification/genetics ; Base Sequence ; Binding Sites ; *DNA-Binding Proteins/chemistry/classification/genetics ; *Endoribonucleases/chemistry/classification/genetics ; *Escherichia coli Proteins/chemistry/classification/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Linkage ; Genome, Bacterial ; Models, Molecular ; Phylogeny ; Protein Binding ; Protein Structure, Tertiary ; Sequence Analysis, DNA ; }, abstract = {Prokaryotic MazF family toxins cooccur with cognate antitoxins having divergent DNA-binding folds and can be of chromosomal or plasmid origin. Sequence similarity search was carried out to identify the Toxin-Antitoxin (TA) operons of MazF family followed by sequence analysis and phylogenetic studies. The genomic DNA upstream of the TA operons was searched for the presence of regulatory motifs. The MazF family toxins showed a conserved hydrophobic pocket in a multibinding site and are present in pathogenic bacteria. The toxins of the MazF family are associated with four main types of cognate antitoxin partners and cluster as a subfamily on the branches of the phylogenetic tree. This indicates that transmission of the entire operon is the dominant mode of inheritance. The plasmid borne TA modules were interspersed between the chromosomal TA modules of the same subfamily, compatible with a frequent interchange of TA genes between the chromosome and the plasmid akin to that observed for antibiotic resistance gens. The split network of the MazF family toxins showed the AbrB-linked toxins as a hub of horizontal gene transfer. Distinct motifs are present in the upstream region of each subfamily. The presence of MazF family TA modules in pathogenic bacteria and identification of a conserved binding pocket are significant for the development of novel antibacterials to disrupt the TA interaction. However, the role of TAs in stress resistance needs to be established. Phylogenetic studies provide insight into the evolution of MazF family TAs and effect on the bacterial genome.}, }
@article {pmid24263112, year = {2014}, author = {Velineni, S and Breathnach, CC and Timoney, JF}, title = {Evidence of lateral gene transfer among strains of Streptococcus zooepidemicus in weanling horses with respiratory disease.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {21}, number = {}, pages = {157-160}, doi = {10.1016/j.meegid.2013.11.006}, pmid = {24263112}, issn = {1567-7257}, mesh = {Animals ; Bacterial Proteins/*genetics ; Dogs ; Gene Transfer, Horizontal ; Herpesviridae Infections/*veterinary/virology ; Herpesvirus 1, Equid/physiology ; Horse Diseases/*microbiology/virology ; Horses ; Multilocus Sequence Typing ; Recombination, Genetic ; Respiratory Tract Infections/microbiology/*veterinary/virology ; Streptococcal Infections/complications/microbiology/*veterinary ; Streptococcus equi/classification/*genetics ; }, abstract = {Streptococcus zooepidemicus (Sz) is a tonsillar commensal of healthy horses but with potential to opportunistically invade the lower respiratory tract. Sz is genetically variable and recombinogenic based on analysis of gene sequences including szp, szm and MLST data. Although a variety of serovars of the protective SzP are commonly harbored in the tonsils of the same horse, lower respiratory infections usually involve a single clone. Nevertheless, isolation of specific clones from epizootics of respiratory disease has been recently reported in horses and dogs in N. America, Europe and Asia. In this report, we provide evidence suggestive of lateral gene exchange and recombination between strains of Sz from cases of respiratory disease secondary to experimental equine herpes 1 virus infection in an isolated group of weanling horses and ponies. Nasal swabs of 13 of 18 weanlings with respiratory disease yielded mucoid colonies of Sz following culture. Comparison of arcC, nrdE, proS, spi, tdk, tpi and yqiL of these Sz revealed 3 Clades. Clade-1 (ST-212) and 2 (ST-24) were composed of 7 and 3 isolates, respectively. ST-24 and 212 differed in all 7 housekeeping as well as szp and szm alleles. Two isolates of Clade-1 were assigned to ST-308, a single locus variant of ST-212 that contained the proS-16 allele sequenced in ST-24. One isolate of ST-308 contained szm-2, the same allele sequenced in Clade 2 isolates; the other was positive for the szp-N2HV2 allele of Clade 2. These observations are consistent with gene transfer between Sz in the natural host and may explain formation of novel clones that invade the lower respiratory tract or cause epizootics of respiratory disease in dogs and horses.}, }
@article {pmid24262067, year = {2013}, author = {Wiesner, M and Fernández-Mora, M and Cevallos, MA and Zavala-Alvarado, C and Zaidi, MB and Calva, E and Silva, C}, title = {Conjugative transfer of an IncA/C plasmid-borne blaCMY-2 gene through genetic re-arrangements with an IncX1 plasmid.}, journal = {BMC microbiology}, volume = {13}, number = {}, pages = {264}, pmid = {24262067}, issn = {1471-2180}, mesh = {Animals ; *Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; Escherichia coli/genetics ; Gene Rearrangement ; *Gene Transfer, Horizontal ; Humans ; Mexico ; Molecular Sequence Data ; *Plasmids ; Recombination, Genetic ; Salmonella Infections/microbiology ; Salmonella Infections, Animal/microbiology ; Salmonella typhimurium/*enzymology/*genetics/isolation &amp; purification ; Sequence Analysis, DNA ; beta-Lactamases/*genetics ; }, abstract = {BACKGROUND: Our observation that in the Mexican Salmonella Typhimurium population none of the ST19 and ST213 strains harbored both the Salmonella virulence plasmid (pSTV) and the prevalent IncA/C plasmid (pA/C) led us to hypothesize that restriction to horizontal transfer of these plasmids existed. We designed a conjugation scheme using ST213 strain YU39 as donor of the blaCMY-2 gene (conferring resistance to ceftriaxone; CRO) carried by pA/C, and two E. coli lab strains (DH5α and HB101) and two Typhimurium ST19 strains (SO1 and LT2) carrying pSTV as recipients. The aim of this study was to determine if the genetic background of the different recipient strains affected the transfer frequencies of pA/C.<br><br>RESULTS: YU39 was able to transfer CRO resistance, via a novel conjugative mechanism, to all the recipient strains although at low frequencies (10-7 to 10-10). The presence of pSTV in the recipients had little effect on the conjugation frequency. The analysis of the transconjugants showed that three different phenomena were occurring associated to the transfer of blaCMY-2: 1) the co-integration of pA/C and pX1; 2) the transposition of the CMY region from pA/C to pX1; or 3) the rearrangement of pA/C. In addition, the co-lateral mobilization of a small (5 kb) ColE1-like plasmid was observed. The transconjugant plasmids involving pX1 re-arrangements (either via co-integration or ISEcp1-mediated transposition) obtained the capacity to conjugate at very high levels, similar to those found for pX1 (10-1). Two versions of the region containing blaCMY-2 were found to transpose to pX1: the large version was inserted into an intergenic region located where the "genetic load" operons are frequently inserted into pX1, while the short version was inserted into the stbDE operon involved in plasmid addiction system. This is the first study to report the acquisition of an extended spectrum cephalosporin (ESC)-resistance gene by an IncX1 plasmid.<br><br>CONCLUSIONS: We showed that the transfer of the YU39 blaCMY-2 gene harbored on a non- conjugative pA/C requires the machinery of a highly conjugative pX1 plasmid. Our experiments demonstrate the complex interactions a single strain can exploit to contend with the challenge of horizontal transfer and antibiotic selective pressure.}, }
@article {pmid24260361, year = {2013}, author = {Maj, A and Dziewit, L and Czarnecki, J and Wlodarczyk, M and Baj, J and Skrzypczyk, G and Giersz, D and Bartosik, D}, title = {Plasmids of carotenoid-producing Paracoccus spp. (Alphaproteobacteria) - structure, diversity and evolution.}, journal = {PloS one}, volume = {8}, number = {11}, pages = {e80258}, pmid = {24260361}, issn = {1932-6203}, mesh = {Alphaproteobacteria/*genetics/*metabolism ; Biological Evolution ; Carotenoids/*genetics/*metabolism ; Conjugation, Genetic/genetics ; DNA Replication/genetics ; Gene Transfer, Horizontal/genetics ; Genetic Variation/genetics ; Genetic Vectors/genetics ; Genome, Bacterial/genetics ; Paracoccus/*genetics/*metabolism ; Plasmids/*genetics ; }, abstract = {Plasmids are components of many bacterial genomes. They enable the spread of a large pool of genetic information via lateral gene transfer. Many bacterial strains contain mega-sized replicons and these are particularly common in Alphaproteobacteria. Considerably less is known about smaller alphaproteobacterial plasmids. We analyzed the genomes of 14 such plasmids residing in 4 multireplicon carotenoid-producing strains of the genus Paracoccus (Alphaproteobacteria): P. aestuarii DSM 19484, P. haeundaensis LG P-21903, P. marcusii DSM 11574 and P. marcusii OS22. Comparative analyses revealed mosaic structures of the plasmids and recombinational shuffling of diverse genetic modules involved in (i) plasmid replication, (ii) stabilization (including toxin-antitoxin systems of the relBE/parDE, tad-ata, higBA, mazEF and toxBA families) and (iii) mobilization for conjugal transfer (encoding relaxases of the MobQ, MobP or MobV families). A common feature of the majority of the plasmids is the presence of AT-rich sequence islets (located downstream of exc1-like genes) containing genes, whose homologs are conserved in the chromosomes of many bacteria (encoding e.g. RelA/SpoT, SMC-like proteins and a retron-type reverse transcriptase). The results of this study have provided insight into the diversity and plasticity of plasmids of Paracoccus spp., and of the entire Alphaproteobacteria. Some of the identified plasmids contain replication systems not described previously in this class of bacteria. The composition of the plasmid genomes revealed frequent transfer of chromosomal genes into plasmids, which significantly enriches the pool of mobile DNA that can participate in lateral transfer. Many strains of Paracoccus spp. have great biotechnological potential, and the plasmid vectors constructed in this study will facilitate genetic studies of these bacteria.}, }
@article {pmid24260300, year = {2013}, author = {Klein, CC and Alves, JM and Serrano, MG and Buck, GA and Vasconcelos, AT and Sagot, MF and Teixeira, MM and Camargo, EP and Motta, MC}, title = {Biosynthesis of vitamins and cofactors in bacterium-harbouring trypanosomatids depends on the symbiotic association as revealed by genomic analyses.}, journal = {PloS one}, volume = {8}, number = {11}, pages = {e79786}, pmid = {24260300}, issn = {1932-6203}, mesh = {Betaproteobacteria/*genetics/metabolism ; Biological Factors/*biosynthesis/genetics/metabolism ; Biosynthetic Pathways/*genetics ; Genome, Protozoan/genetics ; Genomics/methods ; Phylogeny ; Symbiosis/*genetics ; Trypanosoma/*genetics/metabolism/*microbiology ; Vitamins/*biosynthesis/genetics/metabolism ; }, abstract = {Some non-pathogenic trypanosomatids maintain a mutualistic relationship with a betaproteobacterium of the Alcaligenaceae family. Intensive nutritional exchanges have been reported between the two partners, indicating that these protozoa are excellent biological models to study metabolic co-evolution. We previously sequenced and herein investigate the entire genomes of five trypanosomatids which harbor a symbiotic bacterium (SHTs for Symbiont-Haboring Trypanosomatids) and the respective bacteria (TPEs for Trypanosomatid Proteobacterial Endosymbiont), as well as two trypanosomatids without symbionts (RTs for Regular Trypanosomatids), for the presence of genes of the classical pathways for vitamin biosynthesis. Our data show that genes for the biosynthetic pathways of thiamine, biotin, and nicotinic acid are absent from all trypanosomatid genomes. This is in agreement with the absolute growth requirement for these vitamins in all protozoa of the family. Also absent from the genomes of RTs are the genes for the synthesis of pantothenic acid, folic acid, riboflavin, and vitamin B6. This is also in agreement with the available data showing that RTs are auxotrophic for these essential vitamins. On the other hand, SHTs are autotrophic for such vitamins. Indeed, all the genes of the corresponding biosynthetic pathways were identified, most of them in the symbiont genomes, while a few genes, mostly of eukaryotic origin, were found in the host genomes. The only exceptions to the latter are: the gene coding for the enzyme ketopantoate reductase (EC:1.1.1.169) which is related instead to the Firmicutes bacteria; and two other genes, one involved in the salvage pathway of pantothenic acid and the other in the synthesis of ubiquinone, that are related to Gammaproteobacteria. Their presence in trypanosomatids may result from lateral gene transfer. Taken together, our results reinforce the idea that the low nutritional requirement of SHTs is associated with the presence of the symbiotic bacterium, which contains most genes for vitamin production.}, }
@article {pmid24259313, year = {2013}, author = {Wisecaver, JH and Brosnahan, ML and Hackett, JD}, title = {Horizontal gene transfer is a significant driver of gene innovation in dinoflagellates.}, journal = {Genome biology and evolution}, volume = {5}, number = {12}, pages = {2368-2381}, pmid = {24259313}, issn = {1759-6653}, mesh = {Cells, Cultured ; Databases, Nucleic Acid ; Dinoflagellida/*genetics/metabolism ; Evolution, Molecular ; Gene Deletion ; *Gene Transfer, Horizontal ; Genetic Variation ; Genome, Protozoan/genetics ; Isocitrate Dehydrogenase/genetics ; Ketone Oxidoreductases/genetics ; Mitochondria/*genetics/metabolism ; Molecular Sequence Data ; NADH Dehydrogenase/genetics ; Oxidative Phosphorylation ; Pentose Phosphate Pathway/genetics ; Phylogeny ; Sequence Analysis, DNA ; Transcriptome/genetics ; }, abstract = {The dinoflagellates are an evolutionarily and ecologically important group of microbial eukaryotes. Previous work suggests that horizontal gene transfer (HGT) is an important source of gene innovation in these organisms. However, dinoflagellate genomes are notoriously large and complex, making genomic investigation of this phenomenon impractical with currently available sequencing technology. Fortunately, de novo transcriptome sequencing and assembly provides an alternative approach for investigating HGT. We sequenced the transcriptome of the dinoflagellate Alexandrium tamarense Group IV to investigate how HGT has contributed to gene innovation in this group. Our comprehensive A. tamarense Group IV gene set was compared with those of 16 other eukaryotic genomes. Ancestral gene content reconstruction of ortholog groups shows that A. tamarense Group IV has the largest number of gene families gained (314-1,563 depending on inference method) relative to all other organisms in the analysis (0-782). Phylogenomic analysis indicates that genes horizontally acquired from bacteria are a significant proportion of this gene influx, as are genes transferred from other eukaryotes either through HGT or endosymbiosis. The dinoflagellates also display curious cases of gene loss associated with mitochondrial metabolism including the entire Complex I of oxidative phosphorylation. Some of these missing genes have been functionally replaced by bacterial and eukaryotic xenologs. The transcriptome of A. tamarense Group IV lends strong support to a growing body of evidence that dinoflagellate genomes are extraordinarily impacted by HGT.}, }
@article {pmid24259310, year = {2013}, author = {Hernández-López, A and Chabrol, O and Royer-Carenzi, M and Merhej, V and Pontarotti, P and Raoult, D}, title = {To tree or not to tree? Genome-wide quantification of recombination and reticulate evolution during the diversification of strict intracellular bacteria.}, journal = {Genome biology and evolution}, volume = {5}, number = {12}, pages = {2305-2317}, pmid = {24259310}, issn = {1759-6653}, mesh = {Base Sequence ; Computational Biology/methods ; Databases, Nucleic Acid ; *Evolution, Molecular ; Gene Regulatory Networks/*genetics ; Gene Transfer, Horizontal/*genetics ; Genetic Speciation ; Genetic Variation ; Genome, Bacterial/genetics ; Phylogeny ; Proteome/genetics ; Recombination, Genetic ; Rickettsia/*classification/*genetics ; Sequence Alignment ; }, abstract = {It is well known that horizontal gene transfer (HGT) is a major force in the evolution of prokaryotes. During the adaptation of a bacterial population to a new ecological niche, and particularly for intracellular bacteria, selective pressures are shifted and ecological niches reduced, resulting in a lower rate of genetic connectivity. HGT and positive selection are therefore two important evolutionary forces in microbial pathogens that drive adaptation to new hosts. In this study, we use genomic distance analyses, phylogenomic networks, tree topology comparisons, and Bayesian inference methods to investigate to what extent HGT has occurred during the evolution of the genus Rickettsia, the effect of the use of different genomic regions in estimating reticulate evolution and HGT events, and the link of these to host range. We show that ecological specialization restricts recombination occurrence in Rickettsia, but other evolutionary processes and genome architecture are also important for the occurrence of HGT. We found that recombination, genomic rearrangements, and genome conservation all show evidence of network-like evolution at whole-genome scale. We show that reticulation occurred mainly, but not only, during the early Rickettsia radiation, and that core proteome genes of every major functional category have experienced reticulated evolution and possibly HGT. Overall, the evolution of Rickettsia bacteria has been tree-like, with evidence of HGT and reticulated evolution for around 10-25% of the core Rickettsia genome. We present evidence of extensive recombination/incomplete lineage sorting (ILS) during the radiation of the genus, probably linked with the emergence of intracellularity in a wide range of hosts.}, }
@article {pmid24259309, year = {2013}, author = {Nakjang, S and Williams, TA and Heinz, E and Watson, AK and Foster, PG and Sendra, KM and Heaps, SE and Hirt, RP and Martin Embley, T}, title = {Reduction and expansion in microsporidian genome evolution: new insights from comparative genomics.}, journal = {Genome biology and evolution}, volume = {5}, number = {12}, pages = {2285-2303}, pmid = {24259309}, issn = {1759-6653}, support = {/WT_/Wellcome Trust/United Kingdom ; 268701/ERC_/European Research Council/International ; 045404/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Bacteria/genetics ; Cell Lineage ; Chromosome Mapping ; Databases, Genetic ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genetic Variation ; *Genome, Fungal ; Genomics ; HSP90 Heat-Shock Proteins/genetics ; Hexokinase/genetics ; Host-Parasite Interactions/genetics ; Humans ; Metalloproteases/genetics ; Microsporidia/*genetics ; Peptidoglycan Glycosyltransferase/genetics ; }, abstract = {Microsporidia are an abundant group of obligate intracellular parasites of other eukaryotes, including immunocompromised humans, but the molecular basis of their intracellular lifestyle and pathobiology are poorly understood. New genomes from a taxonomically broad range of microsporidians, complemented by published expression data, provide an opportunity for comparative analyses to identify conserved and lineage-specific patterns of microsporidian genome evolution that have underpinned this success. In this study, we infer that a dramatic bottleneck in the last common microsporidian ancestor (LCMA) left a small conserved core of genes that was subsequently embellished by gene family expansion driven by gene acquisition in different lineages. Novel expressed protein families represent a substantial fraction of sequenced microsporidian genomes and are significantly enriched for signals consistent with secretion or membrane location. Further evidence of selection is inferred from the gain and reciprocal loss of functional domains between paralogous genes, for example, affecting transport proteins. Gene expansions among transporter families preferentially affect those that are located on the plasma membrane of model organisms, consistent with recruitment to plug conserved gaps in microsporidian biosynthesis and metabolism. Core microsporidian genes shared with other eukaryotes are enriched in orthologs that, in yeast, are highly expressed, highly connected, and often essential, consistent with strong negative selection against further reduction of the conserved gene set since the LCMA. Our study reveals that microsporidian genome evolution is a highly dynamic process that has balanced constraint, reductive evolution, and genome expansion during adaptation to an extraordinarily successful obligate intracellular lifestyle.}, }
@article {pmid24257443, year = {2014}, author = {Meyer, JL and Huber, JA}, title = {Strain-level genomic variation in natural populations of Lebetimonas from an erupting deep-sea volcano.}, journal = {The ISME journal}, volume = {8}, number = {4}, pages = {867-880}, pmid = {24257443}, issn = {1751-7370}, mesh = {Epsilonproteobacteria/classification/enzymology/*genetics/isolation &amp; purification ; Gene Flow ; *Genetic Variation ; Genome, Bacterial/*genetics ; Genomic Islands ; Hydrothermal Vents/*microbiology ; Metagenomics ; Nitrogen Fixation/genetics ; Nitrogenase/genetics ; Operon/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Recombination, Genetic ; }, abstract = {Chemolithoautotrophic Epsilonproteobacteria are ubiquitous in sulfidic, oxygen-poor habitats, including hydrothermal vents, marine oxygen minimum zones, marine sediments and sulfidic caves and have a significant role in cycling carbon, hydrogen, nitrogen and sulfur in these environments. The isolation of diverse strains of Epsilonproteobacteria and the sequencing of their genomes have revealed that this group has the metabolic potential to occupy a wide range of niches, particularly at dynamic deep-sea hydrothermal vents. We expand on this body of work by examining the population genomics of six strains of Lebetimonas, a vent-endemic, thermophilic, hydrogen-oxidizing Epsilonproteobacterium, from a single seamount in the Mariana Arc. Using Lebetimonas as a model for anaerobic, moderately thermophilic organisms in the warm, anoxic subseafloor environment, we show that genomic content is highly conserved and that recombination is limited between closely related strains. The Lebetimonas genomes are shaped by mobile genetic elements and gene loss as well as the acquisition of novel functional genes by horizontal gene transfer, which provide the potential for adaptation and microbial speciation in the deep sea. In addition, these Lebetimonas genomes contain two operons of nitrogenase genes with different evolutionary origins. Lebetimonas expressed nifH during growth with nitrogen gas as the sole nitrogen source, thus providing the first evidence of nitrogen fixation in any Epsilonproteobacteria from deep-sea hydrothermal vents. In this study, we provide a comparative overview of the genomic potential within the Nautiliaceae as well as among more distantly related hydrothermal vent Epsilonproteobacteria to broaden our understanding of microbial adaptation and diversity in the deep sea.}, }
@article {pmid24257316, year = {2014}, author = {Shin, J and Soo Ko, K}, title = {Single origin of three plasmids bearing blaCTX-M-15 from different Klebsiella pneumoniae clones.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {69}, number = {4}, pages = {969-972}, doi = {10.1093/jac/dkt464}, pmid = {24257316}, issn = {1460-2091}, mesh = {DNA, Bacterial/chemistry/genetics ; Gene Order ; Gene Transfer, Horizontal ; Genotype ; Humans ; Klebsiella Infections/microbiology ; Klebsiella pneumoniae/*enzymology/*genetics ; Korea ; Molecular Sequence Data ; *Plasmids ; Sequence Analysis, DNA ; Synteny ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: To determine and compare the complete nucleotide sequences of plasmids carrying blaCTX-M-15 from three different Klebsiella pneumoniae clones.<br><br>METHODS: IncFII-type plasmids pKP02022, pKP09085 and pKP007 were extracted from three K. pneumoniae strains. These strains belong to sequence types (STs) ST15, ST48 and ST23, respectively, and were isolated in Korea. Plasmids were sequenced using the 454 Genome Sequencer FLX system.<br><br>RESULTS: The three plasmids, pKP02022 (203577 bp), pKP09085 (213019 bp) and pKP007 (246&#x200a;176 bp), all exhibited a very similar structure, with a pKPN3-like backbone and a resistance region including blaOXA-1, aac(6')-Ib-cr and cat genes as well as blaCTX-M-15. They were also very similar to pUUH239.2, previously isolated in Sweden. Iron (III) uptake-related genes were found in pKP007 from the ST23 strain, which has been reported to be associated with liver abscesses. The resistance region contained several insertion sequences, such as IS26, which may play an important role in structural rearrangements of plasmids.<br><br>CONCLUSIONS: The very similar structure of the three plasmids, extracted from different clones, suggests that the spread of CTX-M-producing K. pneumoniae isolates might result from the horizontal transfer of plasmids and subsequent integration and recombination.}, }
@article {pmid24251073, year = {2013}, author = {Dy, RL and Pitman, AR and Fineran, PC}, title = {Chromosomal targeting by CRISPR-Cas systems can contribute to genome plasticity in bacteria.}, journal = {Mobile genetic elements}, volume = {3}, number = {5}, pages = {e26831}, pmid = {24251073}, issn = {2159-2543}, abstract = {The clustered regularly interspaced short palindromic repeats (CRISPR) and their associated (Cas) proteins form adaptive immune systems in bacteria to combat phage and other foreign genetic elements. Typically, short spacer sequences are acquired from the invader DNA and incorporated into CRISPR arrays in the bacterial genome. Small RNAs are generated that contain these spacer sequences and enable sequence-specific destruction of the foreign nucleic acids. Occasionally, spacers are acquired from the chromosome, which instead leads to targeting of the host genome. Chromosomal targeting is highly toxic to the bacterium, providing a strong selective pressure for a variety of evolutionary routes that enable host cell survival. Mutations that inactivate the CRISPR-Cas functionality, such as within the cas genes, CRISPR repeat, protospacer adjacent motifs (PAM), and target sequence, mediate escape from toxicity. This self-targeting might provide some explanation for the incomplete distribution of CRISPR-Cas systems in less than half of sequenced bacterial genomes. More importantly, self-genome targeting can cause large-scale genomic alterations, including remodeling or deletion of pathogenicity islands and other non-mobile chromosomal regions. While control of horizontal gene transfer is perceived as their main function, our recent work illuminates an alternative role of CRISPR-Cas systems in causing host genomic changes and influencing bacterial evolution.}, }
@article {pmid24251070, year = {2013}, author = {Noda-García, L and Barona-Gómez, F}, title = {Enzyme evolution beyond gene duplication: A model for incorporating horizontal gene transfer.}, journal = {Mobile genetic elements}, volume = {3}, number = {5}, pages = {e26439}, pmid = {24251070}, issn = {2159-2543}, abstract = {Understanding the evolution of enzyme function after gene duplication has been a major goal of molecular biologists, biochemists and evolutionary biologists alike, for almost half a century. In contrast, the impact that horizontal gene transfer (HGT) has had on the evolution of enzyme specialization and the assembly of metabolic networks has just started to being investigated. Traditionally, evolutionary studies of enzymes have been limited to either the function of enzymes in vitro, or to sequence variability at the population level, where in almost all cases the starting conceptual framework embraces gene duplication as the mechanism responsible for the appearance of genetic redundancy. Very recently, we merged comparative phylogenomics, detection of selection signals, enzyme kinetics, X-ray crystallography and computational molecular dynamics, to characterize the sub-functionalization process of an amino acid biosynthetic enzyme prompted by an episode of HGT in bacteria. Some of the evolutionary implications of these functional studies, including a proposed model of enzyme specialization independent of gene duplication, are developed in this commentary.}, }
@article {pmid24251068, year = {2013}, author = {Ku, C and Lo, WS and Kuo, CH}, title = {Horizontal transfer of potential mobile units in phytoplasmas.}, journal = {Mobile genetic elements}, volume = {3}, number = {5}, pages = {e26145}, pmid = {24251068}, issn = {2159-2543}, abstract = {Phytoplasmas are uncultivated phytopathogenic bacteria that cause diseases in a wide range of economically important plants. Through secretion of effector proteins, they are able to manipulate their plant hosts to facilitate their multiplication and dispersal by insect vectors. The genome sequences of several phytoplasmas have been characterized to date and a group of putative composite transposons called potential mobile units (PMUs) are found in these highly reduced genomes. Recently, our team reported the genome sequence and comparative analysis of a peanut witches' broom (PnWB) phytoplasma, the first representative of the phytoplasma 16SrII group. Comparisons between the species phylogeny and the phylogenies of the PMU genes revealed that the PnWB PMU is likely to have been transferred from the 16SrI group. This indicates that PMUs are not only the DNA unit for transposition within a genome, but also for horizontal transfer among divergent phytoplasma lineages. Given the association of PMUs with effector genes, the mobility of PMUs across genomes has important implications for phytoplasma ecology and evolution.}, }
@article {pmid24248389, year = {2013}, author = {Zanni, V and Eymery, A and Coiffet, M and Zytnicki, M and Luyten, I and Quesneville, H and Vaury, C and Jensen, S}, title = {Distribution, evolution, and diversity of retrotransposons at the flamenco locus reflect the regulatory properties of piRNA clusters.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {49}, pages = {19842-19847}, pmid = {24248389}, issn = {1091-6490}, mesh = {Animals ; Base Sequence ; Cadherins/*genetics ; Computational Biology ; Drosophila Proteins/*genetics ; Drosophila melanogaster/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; *Genetic Variation ; Heterochromatin/*genetics ; Molecular Sequence Data ; Oligonucleotides/genetics ; RNA Interference ; RNA, Small Interfering/*genetics ; Retroelements/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Most of our understanding of Drosophila heterochromatin structure and evolution has come from the annotation of heterochromatin from the isogenic y; cn bw sp strain. However, almost nothing is known about the heterochromatin's structural dynamics and evolution. Here, we focus on a 180-kb heterochromatic locus producing Piwi-interacting RNAs (piRNA cluster), the flamenco (flam) locus, known to be responsible for the control of at least three transposable elements (TEs). We report its detailed structure in three different Drosophila lines chosen according to their capacity to repress or not to repress the expression of two retrotransposons named ZAM and Idefix, and we show that they display high structural diversity. Numerous rearrangements due to homologous and nonhomologous recombination, deletions and segmental duplications, and loss and gain of TEs are diverse sources of active genomic variation at this locus. Notably, we evidence a correlation between the presence of ZAM and Idefix in this piRNA cluster and their silencing. They are absent from flam in the strain where they are derepressed. We show that, unexpectedly, more than half of the flam locus results from recent TE insertions and that most of the elements concerned are prone to horizontal transfer between species of the melanogaster subgroup. We build a model showing how such high and constant dynamics of a piRNA master locus open the way to continual emergence of new patterns of piRNA biogenesis leading to changes in the level of transposition control.}, }
@article {pmid24248361, year = {2013}, author = {Overballe-Petersen, S and Harms, K and Orlando, LA and Mayar, JV and Rasmussen, S and Dahl, TW and Rosing, MT and Poole, AM and Sicheritz-Ponten, T and Brunak, S and Inselmann, S and de Vries, J and Wackernagel, W and Pybus, OG and Nielsen, R and Johnsen, PJ and Nielsen, KM and Willerslev, E}, title = {Bacterial natural transformation by highly fragmented and damaged DNA.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {49}, pages = {19860-19865}, pmid = {24248361}, issn = {1091-6490}, mesh = {Acinetobacter/*genetics ; Animals ; Base Sequence ; DNA/genetics/*metabolism ; DNA Damage/*genetics ; DNA Primers/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Mammoths/genetics ; Molecular Sequence Data ; Sequence Analysis, DNA ; Transformation, Bacterial/*genetics ; }, abstract = {DNA molecules are continuously released through decomposition of organic matter and are ubiquitous in most environments. Such DNA becomes fragmented and damaged (often <100 bp) and may persist in the environment for more than half a million years. Fragmented DNA is recognized as nutrient source for microbes, but not as potential substrate for bacterial evolution. Here, we show that fragmented DNA molecules (≥ 20 bp) that additionally may contain abasic sites, cross-links, or miscoding lesions are acquired by the environmental bacterium Acinetobacter baylyi through natural transformation. With uptake of DNA from a 43,000-y-old woolly mammoth bone, we further demonstrate that such natural transformation events include ancient DNA molecules. We find that the DNA recombination is RecA recombinase independent and is directly linked to DNA replication. We show that the adjacent nucleotide variations generated by uptake of short DNA fragments escape mismatch repair. Moreover, double-nucleotide polymorphisms appear more common among genomes of transformable than nontransformable bacteria. Our findings reveal that short and damaged, including truly ancient, DNA molecules, which are present in large quantities in the environment, can be acquired by bacteria through natural transformation. Our findings open for the possibility that natural genetic exchange can occur with DNA up to several hundreds of thousands years old.}, }
@article {pmid24243847, year = {2014}, author = {Shifman, A and Ninyo, N and Gophna, U and Snir, S}, title = {Phylo SI: a new genome-wide approach for prokaryotic phylogeny.}, journal = {Nucleic acids research}, volume = {42}, number = {4}, pages = {2391-2404}, pmid = {24243847}, issn = {1362-4962}, mesh = {Archaea/*classification ; Bacteria/*classification ; Genome, Archaeal ; Genome, Bacterial ; Genomics/methods ; *Phylogeny ; *Software ; Synteny ; }, abstract = {The evolutionary history of all life forms is usually represented as a vertical tree-like process. In prokaryotes, however, the vertical signal is partly obscured by the massive influence of horizontal gene transfer (HGT). The HGT creates widespread discordance between evolutionary histories of different genes as genomes become mosaics of gene histories. Thus, the Tree of Life (TOL) has been questioned as an appropriate representation of the evolution of prokaryotes. Nevertheless a common hypothesis is that prokaryotic evolution is primarily tree-like, and a routine effort is made to place new isolates in their appropriate location in the TOL. Moreover, it appears desirable to exploit non-tree-like evolutionary processes for the task of microbial classification. In this work, we present a novel technique that builds on the straightforward observation that gene order conservation ('synteny') decreases in time as a result of gene mobility. This is particularly true in prokaryotes, mainly due to HGT. Using a 'synteny index' (SI) that measures the average synteny between a pair of genomes, we developed the phylogenetic reconstruction tool 'Phylo SI'. Phylo SI offers several attractive properties such as easy bootstrapping, high sensitivity in cases where phylogenetic signal is weak and computational efficiency. Phylo SI was tested both on simulated data and on two bacterial data sets and compared with two well-established phylogenetic methods. Phylo SI is particularly efficient on short evolutionary distances where synteny footprints remain detectable, whereas the nucleotide substitution signal is too weak for reliable sequence-based phylogenetic reconstruction. The method is publicly available at http://research.haifa.ac.il/ssagi/software/PhyloSI.zip.}, }
@article {pmid24240317, year = {2013}, author = {Yin, Q and Yue, D and Peng, Y and Liu, Y and Xiao, L}, title = {Occurrence and distribution of antibiotic-resistant bacteria and transfer of resistance genes in Lake Taihu.}, journal = {Microbes and environments}, volume = {28}, number = {4}, pages = {479-486}, pmid = {24240317}, issn = {1347-4405}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/*drug effects/genetics/*isolation &amp; purification ; *Drug Resistance, Multiple, Bacterial ; *Gene Transfer, Horizontal ; Humans ; Lakes/*microbiology ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Phylogeny ; }, abstract = {The overuse of antibiotics has accelerated antibiotic resistance in the natural environment, especially fresh water, generating a potential risk for public health around the world. In this study, antibiotic resistance in Lake Taihu was investigated and this was the first thorough data obtained through culture-dependent methods. High percentages of resistance to streptomycin and ampicillin among bacterial isolates were detected, followed by tetracycline and chloramphenicol. Especially high levels of ampicillin resistance in the western and northern regions were illustrated. Bacterial identification of the isolates selected for further study indicated the prevalence of some opportunistic pathogens and 62.0% of the 78 isolates exhibited multiple antibiotic resistance. The presence of ESBLs genes was in the following sequence: bla(TEM) > bla(SHV) > bla(CTMX) and 38.5% of the isolates had a class I integrase gene. Of all tested strains, 80.8% were able to transfer antibiotic resistance through conjugation. We also concluded that some new families of human-associated ESBLs and AmpC genes can be found in natural environmental isolates. The prevalence of antibiotic resistance and the dissemination of transferable antibiotic resistance in bacterial isolates (especially in opportunistic pathogens) was alarming and clearly indicated the urgency of realizing the health risks of antibiotic resistance to human and animal populations who are dependent on Lake Taihu for water consumption.}, }
@article {pmid24236045, year = {2013}, author = {Simone, D and Bay, DC and Leach, T and Turner, RJ}, title = {Diversity and evolution of bacterial twin arginine translocase protein, TatC, reveals a protein secretion system that is evolving to fit its environmental niche.}, journal = {PloS one}, volume = {8}, number = {11}, pages = {e78742}, pmid = {24236045}, issn = {1932-6203}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Amino Acid Sequence ; Bacteria/enzymology/genetics ; Bacterial Proteins/chemistry/genetics ; Conserved Sequence ; Environmental Microbiology ; Escherichia coli Proteins/chemistry/*genetics ; *Evolution, Molecular ; Genetic Variation ; Membrane Transport Proteins/chemistry/*genetics ; Molecular Sequence Data ; Operon ; Phylogeny ; Selection, Genetic ; Sequence Analysis, Protein ; }, abstract = {BACKGROUND: The twin-arginine translocation (Tat) protein export system enables the transport of fully folded proteins across a membrane. This system is composed of two integral membrane proteins belonging to TatA and TatC protein families and in some systems a third component, TatB, a homolog of TatA. TatC participates in substrate protein recognition through its interaction with a twin arginine leader peptide sequence.<br><br>The aim of this study was to explore TatC diversity, evolution and sequence conservation in bacteria to identify how TatC is evolving and diversifying in various bacterial phyla. Surveying bacterial genomes revealed that 77% of all species possess one or more tatC loci and half of these classes possessed only tatC and tatA genes. Phylogenetic analysis of diverse TatC homologues showed that they were primarily inherited but identified a small subset of taxonomically unrelated bacteria that exhibited evidence supporting lateral gene transfer within an ecological niche. Examination of bacilli tatCd/tatCy isoform operons identified a number of known and potentially new Tat substrate genes based on their frequent association to tatC loci. Evolutionary analysis of these Bacilli isoforms determined that TatCy was the progenitor of TatCd. A bacterial TatC consensus sequence was determined and highlighted conserved and variable regions within a three dimensional model of the Escherichia coli TatC protein. Comparative analysis between the TatC consensus sequence and Bacilli TatCd/y isoform consensus sequences revealed unique sites that may contribute to isoform substrate specificity or make TatA specific contacts. Synonymous to non-synonymous nucleotide substitution analyses of bacterial tatC homologues determined that tatC sequence variation differs dramatically between various classes and suggests TatC specialization in these species.<br><br>CONCLUSIONS/SIGNIFICANCE: TatC proteins appear to be diversifying within particular bacterial classes and its specialization may be driven by the substrates it transports and the environment of its host.}, }
@article {pmid24235093, year = {2014}, author = {Wei, Q and Hu, Q and Li, S and Lu, H and Chen, G and Shen, B and Zhang, P and Zhou, Y}, title = {A novel functional class 2 integron in clinical Proteus mirabilis isolates.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {69}, number = {4}, pages = {973-976}, doi = {10.1093/jac/dkt456}, pmid = {24235093}, issn = {1460-2091}, mesh = {Codon, Terminator ; DNA, Bacterial/chemistry/genetics ; Genotype ; Humans ; *Integrons ; Molecular Sequence Data ; Molecular Typing ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Promoter Regions, Genetic ; Proteus Infections/*microbiology ; Proteus mirabilis/classification/*genetics/isolation &amp; purification ; Sequence Analysis, DNA ; }, abstract = {OBJECTIVES: To describe a novel functional class 2 integron that was found in clinical Proteus mirabilis isolates.<br><br>METHODS: Class 1 and 2 integrons were screened by PCR in 153 clinical Proteus isolates. The variable regions of class 1 and 2 integrons were determined by restriction analysis and sequencing. The mutations of internal stop codons in class 2 integrons and their common promoters were also determined by sequencing. Enterobacterial repetitive intergenic consensus (ERIC)-PCR was used to analyse the phylogenetic relations of class 2 integron-positive P. mirabilis isolates.<br><br>RESULTS: Class 1 integrons were detected in 96 (63%) of 153 Proteus isolates: eight different gene cassette arrays were detected, including dfrA32-ereA1-aadA2, which was detected for the first time in P. mirabilis. Class 2 integrons were detected in 101 (66%) of 153 Proteus isolates: four different gene cassette arrays were detected, including dfrA1-catB2-sat2-aadA1, which was detected for the first time in a class 2 integron. A novel functional class 2 integron was detected in 38 P. mirabilis isolates with a common promoter (-35 TTTAAT|16 bp|-10 TAAAGT). The variable region of this functional class 2 integron contained dfrA14 and three novel open reading frames with unknown functions. Very similar ERIC-PCR fingerprinting patterns were detected in these 38 P. mirabilis isolates and were different from other class 2 integron-positive isolates.<br><br>CONCLUSIONS: A novel functional class 2 integron was found for the first time in P. mirabilis. These functional class 2 integron-harbouring P. mirabilis isolates were likely to be clonally spread in our hospital.}, }
@article {pmid24232571, year = {2013}, author = {Shu, CC and Chatterjee, A and Hu, WS and Ramkrishna, D}, title = {Role of intracellular stochasticity in biofilm growth. Insights from population balance modeling.}, journal = {PloS one}, volume = {8}, number = {11}, pages = {e79196}, pmid = {24232571}, issn = {1932-6203}, support = {R01 GM081388/GM/NIGMS NIH HHS/United States ; GM081888/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Biofilms/*growth &amp; development ; Conjugation, Genetic/physiology ; Enterococcus faecalis/*physiology ; Gene Expression Regulation, Bacterial ; Intracellular Space/metabolism/microbiology ; *Models, Biological ; Plankton/microbiology ; }, abstract = {There is increasing recognition that stochasticity involved in gene regulatory processes may help cells enhance the signal or synchronize expression for a group of genes. Thus the validity of the traditional deterministic approach to modeling the foregoing processes cannot be without exception. In this study, we identify a frequently encountered situation, i.e., the biofilm, which has in the past been persistently investigated with intracellular deterministic models in the literature. We show in this paper circumstances in which use of the intracellular deterministic model appears distinctly inappropriate. In Enterococcus faecalis, the horizontal gene transfer of plasmid spreads drug resistance. The induction of conjugation in planktonic and biofilm circumstances is examined here with stochastic as well as deterministic models. The stochastic model is formulated with the Chemical Master Equation (CME) for planktonic cells and Reaction-Diffusion Master Equation (RDME) for biofilm. The results show that although the deterministic model works well for the perfectly-mixed planktonic circumstance, it fails to predict the averaged behavior in the biofilm, a behavior that has come to be known as stochastic focusing. A notable finding from this work is that the interception of antagonistic feedback loops to signaling, accentuates stochastic focusing. Moreover, interestingly, increasing particle number of a control variable could lead to an even larger deviation. Intracellular stochasticity plays an important role in biofilm and we surmise by implications from the model, that cell populations may use it to minimize the influence from environmental fluctuation.}, }
@article {pmid24223296, year = {2013}, author = {Letarov, AV and Krisch, HM}, title = {The episodic evolution of fibritin: traces of ancient global environmental alterations may remain in the genomes of T4-like phages.}, journal = {Ecology and evolution}, volume = {3}, number = {10}, pages = {3628-3635}, pmid = {24223296}, issn = {2045-7758}, abstract = {The evolutionary adaptation of bacteriophages to their environment is achieved by alterations of their genomes involving a combination of both point mutations and lateral gene transfer. A phylogenetic analysis of a large set of collar fiber protein (fibritin) loci from diverse T4-like phages indicates that nearly all the modular swapping involving the C-terminal domain of this gene occurred in the distant past and has since ceased. In phage T4, this fibritin domain encodes the sequence that mediates both the attachment of the long tail fibers to the virion and also controls, in an environmentally sensitive way, the phage's ability to infect its host bacteria. Subsequent to its distant period of modular exchange, the evolution of fibritin has proceeded primarily by the slow vertical divergence mechanism. We suggest that ancient and sudden changes in the environment forced the T4-like phages to alter fibritin's mode of action or function. The genome's response to such episodes of rapid environmental change could presumably only be achieved quickly enough by employing the modular evolution mechanism. A phylogenetic analysis of the fibritin locus reveals the possible traces of such events within the T4 superfamily's genomes.}, }
@article {pmid24220130, year = {2013}, author = {Kaur, C and Vishnoi, A and Ariyadasa, TU and Bhattacharya, A and Singla-Pareek, SL and Sopory, SK}, title = {Episodes of horizontal gene-transfer and gene-fusion led to co-existence of different metal-ion specific glyoxalase I.}, journal = {Scientific reports}, volume = {3}, number = {}, pages = {3076}, pmid = {24220130}, issn = {2045-2322}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Bacteria/genetics/metabolism ; Catalysis ; Cluster Analysis ; Evolution, Molecular ; *Gene Fusion ; *Gene Transfer, Horizontal ; Ions/*metabolism ; Lactoylglutathione Lyase/chemistry/classification/genetics/*metabolism ; Metals/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Protein Binding ; Protein Conformation ; Protein Transport ; Sequence Alignment ; Stress, Physiological ; Substrate Specificity ; }, abstract = {Glyoxalase pathway plays an important role in stress adaptation and many clinical disorders. The first enzyme of this pathway, glyoxalase I (GlxI), uses methylglyoxal as a substrate and requires either Ni(II)/Co(II) or Zn(II) for activity. Here we have investigated the origin of different metal ion specificities of GlxI and subsequent pattern of inheritance during evolution. Our results suggest a primitive origin of single-domain Ni dependent GlxI [Ni-GlxI]. This subsequently evolved into Zn activated GlxI [Zn-GlxI] in deltaproteobacteria. However, origin of eukaryotic Zn-GlxI is different and can be traced to GlxI from Candidatus pelagibacter and Sphingomonas. In eukaryotes GlxI has evolved as two-domain protein but the corresponding Zn form is lost in plants/higher eukaryotes. In plants gene expansion has given rise to multiple two-domain Ni-GlxI which are differentially regulated under abiotic stress conditions. Our results suggest that different forms of GlxI have evolved to help plants adapt to stress.}, }
@article {pmid24214488, year = {2014}, author = {Song, L and Carlson, JH and Zhou, B and Virtaneva, K and Whitmire, WM and Sturdevant, GL and Porcella, SF and McClarty, G and Caldwell, HD}, title = {Plasmid-mediated transformation tropism of chlamydial biovars.}, journal = {Pathogens and disease}, volume = {70}, number = {2}, pages = {189-193}, pmid = {24214488}, issn = {2049-632X}, support = {ZIA AI000845-15//Intramural NIH HHS/United States ; }, mesh = {Animals ; Chlamydia muridarum/*genetics ; Chlamydia trachomatis/*genetics ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Genetic Vectors ; *Host Specificity ; Humans ; Mice ; *Plasmids ; *Transformation, Bacterial ; Virulence Factors/biosynthesis ; }, abstract = {Chlamydia trachomatis and C. muridarum are human and mouse pathogens, respectively, which show high conservation of gene order and content. Both species contain a common 7.5-kb plasmid that is an important virulence factor. Recently described transformation systems have been used to characterize C. trachomatis L2 plasmid gene functions; however, similar studies have not been reported for C. trachomatis ocular tropic serovar A or the mouse strain, C. muridarum. Here, we have conducted genetic experiments with C. trachomatis serovar A and C. muridarum and report the following: (1) successful transformation of C. muridarum and C. trachomatis serovar A is restricted to a shuttle vector with a C. muridarum or C. trachomatis serovar A plasmid backbone, respectively; (2) transformation of plasmid-deficient C. muridarum with the C. muridarum-based shuttle vector complement glycogen accumulation and inclusion morphology; and (3) C. muridarum plasmid-encoded Pgp4 is a regulator of chromosomal (glgA) and plasmid (pgp3) virulence genes. In summary, our findings show a previously unrecognized and unexpected role for the chlamydial plasmid in its transformation tropism and confirm the plasmids regulatory role of virulence genes in C. muridarum.}, }
@article {pmid24204801, year = {2013}, author = {Marathe, NP and Regina, VR and Walujkar, SA and Charan, SS and Moore, ER and Larsson, DG and Shouche, YS}, title = {A treatment plant receiving waste water from multiple bulk drug manufacturers is a reservoir for highly multi-drug resistant integron-bearing bacteria.}, journal = {PloS one}, volume = {8}, number = {10}, pages = {e77310}, pmid = {24204801}, issn = {1932-6203}, mesh = {Anti-Bacterial Agents/classification/pharmacology ; Bacteria/classification/drug effects/*genetics ; Conjugation, Genetic ; Drug Resistance, Multiple, Bacterial/drug effects/*genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; Integrons/*genetics ; Microbial Sensitivity Tests ; RNA, Ribosomal, 16S/classification/genetics/isolation &amp; purification ; Wastewater/*microbiology ; *Water Microbiology ; }, abstract = {The arenas and detailed mechanisms for transfer of antibiotic resistance genes between environmental bacteria and pathogens are largely unclear. Selection pressures from antibiotics in situations where environmental bacteria and human pathogens meet are expected to increase the risks for such gene transfer events. We hypothesize that waste-water treatment plants (WWTPs) serving antibiotic manufacturing industries may provide such spawning grounds, given the high bacterial densities present there together with exceptionally strong and persistent selection pressures from the antibiotic-contaminated waste. Previous analyses of effluent from an Indian industrial WWTP that processes waste from bulk drug production revealed the presence of a range of drugs, including broad spectrum antibiotics at extremely high concentrations (mg/L range). In this study, we have characterized the antibiotic resistance profiles of 93 bacterial strains sampled at different stages of the treatment process from the WWTP against 39 antibiotics belonging to 12 different classes. A large majority (86%) of the strains were resistant to 20 or more antibiotics. Although there were no classically-recognized human pathogens among the 93 isolated strains, opportunistic pathogens such as Ochrobactrum intermedium, Providencia rettgeri, vancomycin resistant Enterococci (VRE), Aerococcus sp. and Citrobacter freundii were found to be highly resistant. One of the O. intermedium strains (ER1) was resistant to 36 antibiotics, while P. rettgeri (OSR3) was resistant to 35 antibiotics. Class 1 and 2 integrons were detected in 74/93 (80%) strains each, and 88/93 (95%) strains harbored at least one type of integron. The qPCR analysis of community DNA also showed an unprecedented high prevalence of integrons, suggesting that the bacteria living under such high selective pressure have an appreciable potential for genetic exchange of resistance genes via mobile gene cassettes. The present study provides insight into the mechanisms behind and the extent of multi-drug resistance among bacteria living under an extreme antibiotic selection pressure.}, }
@article {pmid24204305, year = {2013}, author = {Singh, PK and Ramachandran, G and Ramos-Ruiz, R and Peiró-Pastor, R and Abia, D and Wu, LJ and Meijer, WJ}, title = {Mobility of the native Bacillus subtilis conjugative plasmid pLS20 is regulated by intercellular signaling.}, journal = {PLoS genetics}, volume = {9}, number = {10}, pages = {e1003892}, pmid = {24204305}, issn = {1553-7404}, support = {//Wellcome Trust/United Kingdom ; 098374//Wellcome Trust/United Kingdom ; 098374/Z/12/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacillus subtilis/genetics ; Cell Movement/*genetics ; Drug Resistance, Microbial/genetics ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; High-Throughput Nucleotide Sequencing ; Intercellular Signaling Peptides and Proteins/*genetics/physiology ; Molecular Sequence Data ; Plasmids/*genetics/physiology ; Signal Transduction/genetics ; }, abstract = {Horizontal gene transfer mediated by plasmid conjugation plays a significant role in the evolution of bacterial species, as well as in the dissemination of antibiotic resistance and pathogenicity determinants. Characterization of their regulation is important for gaining insights into these features. Relatively little is known about how conjugation of Gram-positive plasmids is regulated. We have characterized conjugation of the native Bacillus subtilis plasmid pLS20. Contrary to the enterococcal plasmids, conjugation of pLS20 is not activated by recipient-produced pheromones but by pLS20-encoded proteins that regulate expression of the conjugation genes. We show that conjugation is kept in the default "OFF" state and identified the master repressor responsible for this. Activation of the conjugation genes requires relief of repression, which is mediated by an anti-repressor that belongs to the Rap family of proteins. Using both RNA sequencing methodology and genetic approaches, we have determined the regulatory effects of the repressor and anti-repressor on expression of the pLS20 genes. We also show that the activity of the anti-repressor is in turn regulated by an intercellular signaling peptide. Ultimately, this peptide dictates the timing of conjugation. The implications of this regulatory mechanism and comparison with other mobile systems are discussed.}, }
@article {pmid24198337, year = {2013}, author = {Wagner, A and Zarecki, R and Reshef, L and Gochev, C and Sorek, R and Gophna, U and Ruppin, E}, title = {Computational evaluation of cellular metabolic costs successfully predicts genes whose expression is deleterious.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {47}, pages = {19166-19171}, pmid = {24198337}, issn = {1091-6490}, support = {260432/ERC_/European Research Council/International ; R01 AI082376/AI/NIAID NIH HHS/United States ; R01AI082376-01/AI/NIAID NIH HHS/United States ; }, mesh = {*Algorithms ; Computational Biology/*methods ; Gene Expression/*genetics ; Gene Expression Profiling/methods ; Gene Expression Regulation, Neoplastic/genetics ; Humans ; Metabolic Networks and Pathways/*genetics ; *Models, Genetic ; }, abstract = {Gene suppression and overexpression are both fundamental tools in linking genotype to phenotype in model organisms. Computational methods have proven invaluable in studying and predicting the deleterious effects of gene deletions, and yet parallel computational methods for overexpression are still lacking. Here, we present Expression-Dependent Gene Effects (EDGE), an in silico method that can predict the deleterious effects resulting from overexpression of either native or foreign metabolic genes. We first test and validate EDGE's predictive power in bacteria through a combination of small-scale growth experiments that we performed and analysis of extant large-scale datasets. Second, a broad cross-species analysis, ranging from microorganisms to multiple plant and human tissues, shows that genes that EDGE predicts to be deleterious when overexpressed are indeed typically down-regulated. This reflects a universal selection force keeping the expression of potentially deleterious genes in check. Third, EDGE-based analysis shows that cancer genetic reprogramming specifically suppresses genes whose overexpression impedes proliferation. The magnitude of this suppression is large enough to enable an almost perfect distinction between normal and cancerous tissues based solely on EDGE results. We expect EDGE to advance our understanding of human pathologies associated with up-regulation of particular transcripts and to facilitate the utilization of gene overexpression in metabolic engineering.}, }
@article {pmid24196581, year = {2013}, author = {Aserse, AA and Räsänen, LA and Aseffa, F and Hailemariam, A and Lindström, K}, title = {Diversity of sporadic symbionts and nonsymbiotic endophytic bacteria isolated from nodules of woody, shrub, and food legumes in Ethiopia.}, journal = {Applied microbiology and biotechnology}, volume = {97}, number = {23}, pages = {10117-10134}, doi = {10.1007/s00253-013-5248-4}, pmid = {24196581}, issn = {1432-0614}, mesh = {Amplified Fragment Length Polymorphism Analysis ; Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; Endophytes/classification/genetics/*isolation &amp; purification/physiology ; Ethiopia ; Fabaceae/*microbiology ; Molecular Sequence Data ; Phylogeny ; Root Nodules, Plant/*microbiology ; Symbiosis ; Trees/*microbiology ; Wood/*microbiology ; }, abstract = {Fifty-five bacterial isolates were obtained from surface-sterilized nodules of woody and shrub legumes growing in Ethiopia: Crotalaria spp., Indigofera spp., and Erythrina brucei, and the food legumes soybean and common bean. Based on partial 16S rRNA gene sequence analysis, the majority of the isolates were identified as Gram-negative bacteria belonging to the genera Achromobacter, Agrobacterium, Burkholderia, Cronobacter, Enterobacter, Mesorhizobium, Novosphingobium, Pantoea, Pseudomonas, Rahnella, Rhizobium, Serratia, and Variovorax. Seven isolates were Gram-positive bacteria belonging to the genera Bacillus, Paenibacillus, Planomicrobium, and Rhodococcus. Amplified fragment length polymorphism (AFLP) fingerprinting showed that each strain was genetically distinct. According to phylogenetic analysis of recA, glnII, rpoB, and 16S rRNA gene sequences, Rhizobium, Mesorhizobium, and Agrobacterium were further classified into six different genospecies: Agrobacterium spp., Agrobacterium radiobacter, Rhizobium sp., Rhizobium phaseoli, Mesorhizobium sp., and putative new Rhizobium species. The strains from R. phaseoli, Rhizobium sp. IAR30, and Mesorhizobium sp. ERR6 induced nodules on their host plants. The other strains did not form nodules on their original host. Nine endophytic bacterial strains representing seven genera, Agrobacterium, Burkholderia, Paenibacillus, Pantoea, Pseudomonas, Rhizobium, and Serratia, were found to colonize nodules of Crotalaria incana and common bean on co-inoculation with symbiotic rhizobia. Four endophytic Rhizobium and two Agrobacterium strains had identical nifH gene sequences with symbiotic Rhizobium strains, suggesting horizontal gene transfer. Most symbiotic and nonsymbiotic endophytic bacteria showed plant growth-promoting properties in vitro, which indicate their potential role in the promotion of plant growth when colonizing plant roots and the rhizosphere.}, }
@article {pmid24195016, year = {2013}, author = {Muniesa, M and Colomer-Lluch, M and Jofre, J}, title = {Could bacteriophages transfer antibiotic resistance genes from environmental bacteria to human-body associated bacterial populations?.}, journal = {Mobile genetic elements}, volume = {3}, number = {4}, pages = {e25847}, pmid = {24195016}, issn = {2159-2543}, abstract = {Environments without any contact with anthropogenic antibiotics show a great abundance of antibiotic resistance genes that use to be chromosomal and are part of the core genes of the species that harbor them. Some of these genes are shared with human pathogens where they appear in mobile genetic elements. Diversity of antibiotic resistance genes in non-contaminated environments is much greater than in human and animal pathogens, and in environments contaminated with antibiotic from anthropogenic activities. This suggests the existence of some bottleneck effect for the mobilization of antibiotic resistance genes among different biomes. Bacteriophages have characteristics that make them suitable vectors between different biomes, and as well for transferring genes from biome to biome. Recent metagenomic studies and detection of bacterial genes by genomic techniques in the bacteriophage fraction of different microbiota provide indirect evidences that the mobilization of genes mediated by phages, including antibiotic resistance genes, is far more relevant than previously thought. Our hypothesis is that bacteriophages might be of critical importance for evading one of the bottlenecks, the lack of ecological connectivity that modulates the pass of antibiotic resistance genes from natural environments such as waters and soils, to animal and human microbiomes. This commentary concentrates on the potential importance of bacteriophages in transferring resistance genes from the environment to human and animal body microbiomes, but there is no doubt that transduction occurs also in body microbiomes.}, }
@article {pmid24195014, year = {2013}, author = {Mackiewicz, P and Bodył, A and Moszczyński, K}, title = {The case of horizontal gene transfer from bacteria to the peculiar dinoflagellate plastid genome.}, journal = {Mobile genetic elements}, volume = {3}, number = {4}, pages = {e25845}, pmid = {24195014}, issn = {2159-2543}, abstract = {Organelle genomes lose their genes by transfer to host nuclear genomes, but only occasionally are enriched by foreign genes from other sources. In contrast to mitochondria, plastid genomes are especially resistant to such horizontal gene transfer (HGT), and thus every gene acquired in this way is notable. An exceptional case of HGT was recently recognized in the peculiar peridinin plastid genome of dinoflagellates, which is organized in plasmid-like minicircles. Genomic and phylogenetic analyses of Ceratium horridum and Pyrocystis lunula minicircles revealed four genes and one unannotated open reading frame that probably were gained from bacteria belonging to the Bacteroidetes. Such bacteria seem to be a good source of genes because close endosymbiotic associations between them and dinoflagellates have been observed. The HGT-acquired genes are involved in plastid functions characteristic of other photosynthetic eukaryotes, and their arrangement resembles bacterial operons. These studies indicate that the peridinin plastid genome, usually regarded as having resulted from reduction and fragmentation of a typical plastid genome derived from red algae, may have a chimeric origin that includes bacterial contributions. Potential contamination of the Ceratium and Pyrocystis plastid genomes by bacterial sequences and the controversial localization of their minicircles in the nucleus are also discussed.}, }
@article {pmid24187086, year = {2014}, author = {Hatoum-Aslan, A and Maniv, I and Samai, P and Marraffini, LA}, title = {Genetic characterization of antiplasmid immunity through a type III-A CRISPR-Cas system.}, journal = {Journal of bacteriology}, volume = {196}, number = {2}, pages = {310-317}, pmid = {24187086}, issn = {1098-5530}, support = {DP2 AI104556/AI/NIAID NIH HHS/United States ; 1DP2AI104556-01/AI/NIAID NIH HHS/United States ; }, mesh = {*CRISPR-Cas Systems ; DNA Mutational Analysis ; *Gene Transfer, Horizontal ; Genes, Bacterial ; *Plasmids ; RNA, Small Interfering/genetics/metabolism ; Ribonucleoproteins/genetics/metabolism ; Sequence Deletion ; Staphylococcus epidermidis/*genetics ; }, abstract = {Many prokaryotes possess an adaptive immune system encoded by clustered regularly interspaced short palindromic repeats (CRISPRs). CRISPR loci produce small guide RNAs (crRNAs) that, in conjunction with flanking CRISPR-associated (cas) genes, combat viruses and block plasmid transfer by an antisense targeting mechanism. CRISPR-Cas systems have been classified into three types (I to III) that employ distinct mechanisms of crRNA biogenesis and targeting. The type III-A system in Staphylococcus epidermidis RP62a blocks the transfer of staphylococcal conjugative plasmids and harbors nine cas-csm genes. Previous biochemical analysis indicated that Cas10, Csm2, Csm3, Csm4, and Csm5 form a crRNA-containing ribonucleoprotein complex; however, the roles of these genes toward antiplasmid targeting remain unknown. Here, we determined the cas-csm genes that are required for antiplasmid immunity and used genetic and biochemical analyses to investigate the functions of predicted motifs and domains within these genes. We found that many mutations affected immunity by impacting the formation of the Cas10-Csm complex or crRNA biogenesis. Surprisingly, mutations in the predicted nuclease domains of the members of the Cas10-Csm complex had no detectable effect on antiplasmid immunity or crRNA biogenesis. In contrast, the deletion of csm6 and mutations in the cas10 Palm polymerase domain prevented CRISPR immunity without affecting either complex formation or crRNA production, suggesting their involvement in target destruction. By delineating the genetic requirements of this system, our findings further contribute to the mechanistic understanding of type III CRISPR-Cas systems.}, }
@article {pmid24180377, year = {2013}, author = {Chaudhary, R and Burleigh, JG and Fernández-Baca, D}, title = {Inferring species trees from incongruent multi-copy gene trees using the Robinson-Foulds distance.}, journal = {Algorithms for molecular biology : AMB}, volume = {8}, number = {1}, pages = {28}, pmid = {24180377}, issn = {1748-7188}, abstract = {BACKGROUND: Constructing species trees from multi-copy gene trees remains a challenging problem in phylogenetics. One difficulty is that the underlying genes can be incongruent due to evolutionary processes such as gene duplication and loss, deep coalescence, or lateral gene transfer. Gene tree estimation errors may further exacerbate the difficulties of species tree estimation.<br><br>RESULTS: We present a new approach for inferring species trees from incongruent multi-copy gene trees that is based on a generalization of the Robinson-Foulds (RF) distance measure to multi-labeled trees (mul-trees). We prove that it is NP-hard to compute the RF distance between two mul-trees; however, it is easy to calculate this distance between a mul-tree and a singly-labeled species tree. Motivated by this, we formulate the RF problem for mul-trees (MulRF) as follows: Given a collection of multi-copy gene trees, find a singly-labeled species tree that minimizes the total RF distance from the input mul-trees. We develop and implement a fast SPR-based heuristic algorithm for the NP-hard MulRF problem.We compare the performance of the MulRF method (available at http://genome.cs.iastate.edu/CBL/MulRF/) with several gene tree parsimony approaches using gene tree simulations that incorporate gene tree error, gene duplications and losses, and/or lateral transfer. The MulRF method produces more accurate species trees than gene tree parsimony approaches. We also demonstrate that the MulRF method infers in minutes a credible plant species tree from a collection of nearly 2,000 gene trees.<br><br>CONCLUSIONS: Our new phylogenetic inference method, based on a generalized RF distance, makes it possible to quickly estimate species trees from large genomic data sets. Since the MulRF method, unlike gene tree parsimony, is based on a generic tree distance measure, it is appealing for analyses of genomic data sets, in which many processes such as deep coalescence, recombination, gene duplication and losses as well as phylogenetic error may contribute to gene tree discord. In experiments, the MulRF method estimated species trees accurately and quickly, demonstrating MulRF as an efficient alternative approach for phylogenetic inference from large-scale genomic data sets.}, }
@article {pmid24179178, year = {2014}, author = {Radl, V and Simões-Araújo, JL and Leite, J and Passos, SR and Martins, LMV and Xavier, GR and Rumjanek, NG and Baldani, JI and Zilli, JE}, title = {Microvirga vignae sp. nov., a root nodule symbiotic bacterium isolated from cowpea grown in semi-arid Brazil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {64}, number = {Pt 3}, pages = {725-730}, doi = {10.1099/ijs.0.053082-0}, pmid = {24179178}, issn = {1466-5034}, mesh = {Amplified Fragment Length Polymorphism Analysis ; Bacterial Typing Techniques ; Brazil ; DNA, Bacterial/genetics ; Fabaceae/*microbiology ; Genes, Bacterial ; Methylobacteriaceae/*classification/genetics/isolation &amp; purification ; Molecular Sequence Data ; Nucleic Acid Hybridization ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Root Nodules, Plant/*microbiology ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {16S rRNA gene sequence analysis of eight strains (BR 3299(T), BR 3296, BR 10192, BR 10193, BR 10194, BR 10195, BR 10196 and BR 10197) isolated from nodules of cowpea collected from a semi-arid region of Brazil showed 97 % similarity to sequences of recently described rhizobial species of the genus Microvirga. Phylogenetic analyses of four housekeeping genes (gyrB, recA, dnaK and rpoB), DNA-DNA relatedness and AFLP further indicated that these strains belong to a novel species within the genus Microvirga. Our data support the hypothesis that genes related to nitrogen fixation were obtained via horizontal gene transfer, as sequences of nifH genes were very similar to those found in members of the genera Rhizobium and Mesorhizobium, which are not immediate relatives of the genus Microvirga, as shown by 16S rRNA gene sequence analysis. Phenotypic traits, such as host range and carbon utilization, differentiate the novel strains from the most closely related species, Microvirga lotononidis, Microvirga zambiensis and Microvirga lupini. Therefore, these symbiotic nitrogen-fixing bacteria are proposed to be representatives of a novel species, for which the name Microvirga vignae sp. nov. is suggested. The type strain is BR3299(T) (= HAMBI 3457(T)).}, }
@article {pmid24173426, year = {2014}, author = {Kim, SY and Rhee, JY and Shin, SY and Ko, KS}, title = {Characteristics of community-onset NDM-1-producing Klebsiella pneumoniae isolates.}, journal = {Journal of medical microbiology}, volume = {63}, number = {Pt 1}, pages = {86-89}, doi = {10.1099/jmm.0.067744-0}, pmid = {24173426}, issn = {1473-5644}, mesh = {Adult ; Aged ; Anti-Bacterial Agents/pharmacology ; Community-Acquired Infections/*microbiology ; Conjugation, Genetic ; Gene Order ; Genotype ; Humans ; Klebsiella Infections/*microbiology ; Klebsiella pneumoniae/classification/*enzymology/genetics/*isolation &amp; purification ; Korea ; Male ; Molecular Typing ; Plasmids ; beta-Lactam Resistance ; beta-Lactamases/genetics/*metabolism ; beta-Lactams/pharmacology ; }, abstract = {Multilocus sequence typing and in vitro antimicrobial susceptibility testing were performed for three community-onset New Delhi metallo-β-lactamase-1 (NDM-1)-producing Klebsiella pneumoniae isolates from Korea. The genetic structure surrounding the blaNDM-1 gene was determined in blaNDM-1-harbouring plasmids. Three NDM-1-producing K. pneumoniae isolates were found to belong to the same clone (sequence type 340). Each of these isolates showed the same genetic structure surrounding the blaNDM-1 gene. The genes blaNDM-1, bleMBL, trpF and dsbC were flanked by two intact insertion sequences, ISAba125 and IS26, which may promote horizontal gene transfer. The blaNDM-1-harbouring plasmids conferred antimicrobial resistance to carbapenems, cephalosporins, aminoglycosides and aztreonam in transconjugants. It can be speculated that either the entire blaNDM-1-harbouring plasmids or just the part of the plasmid containing the blaNDM-1 gene may have transferred between K. pneumoniae and Escherichia coli. Following the transfer, the isolate disseminated throughout Korea. This study suggests the need for monitoring the dissemination of NDM-1-producing isolates across countries or continents due to their potential transferability via ISAba125- and IS26-associated transposons.}, }
@article {pmid24170857, year = {2013}, author = {Chan, JM and Carlsson, G and Rabadan, R}, title = {Topology of viral evolution.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {46}, pages = {18566-18571}, pmid = {24170857}, issn = {1091-6490}, support = {U54 CA121852/CA/NCI NIH HHS/United States ; I-U54-CA149145-01/CA/NCI NIH HHS/United States ; U54 CA121852-05/CA/NCI NIH HHS/United States ; }, mesh = {Base Sequence ; Classification/*methods ; Computational Biology ; Computer Simulation ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; HIV-1/genetics ; Influenza A Virus, H1N1 Subtype/genetics ; Influenza A Virus, H7N9 Subtype/genetics ; *Models, Genetic ; Molecular Sequence Annotation ; *Phylogeny ; Principal Component Analysis ; Reassortant Viruses/*genetics ; Sequence Homology ; }, abstract = {The tree structure is currently the accepted paradigm to represent evolutionary relationships between organisms, species or other taxa. However, horizontal, or reticulate, genomic exchanges are pervasive in nature and confound characterization of phylogenetic trees. Drawing from algebraic topology, we present a unique evolutionary framework that comprehensively captures both clonal and reticulate evolution. We show that whereas clonal evolution can be summarized as a tree, reticulate evolution exhibits nontrivial topology of dimension greater than zero. Our method effectively characterizes clonal evolution, reassortment, and recombination in RNA viruses. Beyond detecting reticulate evolution, we succinctly recapitulate the history of complex genetic exchanges involving more than two parental strains, such as the triple reassortment of H7N9 avian influenza and the formation of circulating HIV-1 recombinants. In addition, we identify recurrent, large-scale patterns of reticulate evolution, including frequent PB2-PB1-PA-NP cosegregation during avian influenza reassortment. Finally, we bound the rate of reticulate events (i.e., 20 reassortments per year in avian influenza). Our method provides an evolutionary perspective that not only captures reticulate events precluding phylogeny, but also indicates the evolutionary scales where phylogenetic inference could be accurate.}, }
@article {pmid24169574, year = {2013}, author = {Waters, JL and Salyers, AA}, title = {Regulation of CTnDOT conjugative transfer is a complex and highly coordinated series of events.}, journal = {mBio}, volume = {4}, number = {6}, pages = {e00569-13}, pmid = {24169574}, issn = {2150-7511}, mesh = {Bacteroides/drug effects/*genetics ; *Conjugation, Genetic ; *DNA Transposable Elements ; Drug Resistance, Bacterial ; Gastrointestinal Tract/microbiology ; Gene Expression Regulation, Bacterial/drug effects ; *Gene Transfer, Horizontal ; Humans ; Tetracycline/metabolism ; }, abstract = {UNLABELLED: CTnDOT is a 65-kb conjugative transposon that is found in Bacteroides spp., which are one of the more abundant members within the lower human gastrointestinal tract. CTnDOT encodes resistance to the antibiotics erythromycin and tetracycline (Tc). An interesting feature of CTnDOT is that exposure to low levels of Tc induces a cascade of events that ultimately results in CTnDOT conjugative transfer. However, Tc is apparently not a switch that activates transfer but rather a signal that appears to override a series of negative regulators that inhibit premature excision and transfer of CTnDOT. In this minireview, we summarize over 20 years of research that focused on elucidating the highly coordinated regulation of excision, mobilization, and transfer of CTnDOT.<br><br>IMPORTANCE: Bacteroides spp. are abundant commensals in the human colon, but they are also considered opportunistic pathogens, as they can cause life-threatening infections if they should escape the colon. Bacteroides spp. are the most common cause of anaerobic infections and are rather difficult to treat due to the prevalence of antibiotic resistance within this genus. Today over 80% of Bacteroides are resistant to tetracycline (Tc), and a study looking at both clinical and community isolates demonstrated that this resistance was specifically due to the conjugative transposon CTnDOT.}, }
@article {pmid24167782, year = {2013}, author = {Newton, RR and Newton, IL}, title = {PhyBin: binning trees by topology.}, journal = {PeerJ}, volume = {1}, number = {}, pages = {e187}, pmid = {24167782}, issn = {2167-8359}, abstract = {A major goal of many evolutionary analyses is to determine the true evolutionary history of an organism. Molecular methods that rely on the phylogenetic signal generated by a few to a handful of loci can be used to approximate the evolution of the entire organism but fall short of providing a global, genome-wide, perspective on evolutionary processes. Indeed, individual genes in a genome may have different evolutionary histories. Therefore, it is informative to analyze the number and kind of phylogenetic topologies found within an orthologous set of genes across a genome. Here we present PhyBin: a flexible program for clustering gene trees based on topological structure. PhyBin can generate bins of topologies corresponding to exactly identical trees or can utilize Robinson-Fould's distance matrices to generate clusters of similar trees, using a user-defined threshold. Additionally, PhyBin allows the user to adjust for potential noise in the dataset (as may be produced when comparing very closely related organisms) by pre-processing trees to collapse very short branches or those nodes not meeting a defined bootstrap threshold. As a test case, we generated individual trees based on an orthologous gene set from 10 Wolbachia species across four different supergroups (A-D) and utilized PhyBin to categorize the complete set of topologies produced from this dataset. Using this approach, we were able to show that although a single topology generally dominated the analysis, confirming the separation of the supergroups, many genes supported alternative evolutionary histories. Because PhyBin's output provides the user with lists of gene trees in each topological cluster, it can be used to explore potential reasons for discrepancies between phylogenies including homoplasies, long-branch attraction, or horizontal gene transfer events.}, }
@article {pmid24158624, year = {2013}, author = {Timme, RE and Pettengill, JB and Allard, MW and Strain, E and Barrangou, R and Wehnes, C and Van Kessel, JS and Karns, JS and Musser, SM and Brown, EW}, title = {Phylogenetic diversity of the enteric pathogen Salmonella enterica subsp. enterica inferred from genome-wide reference-free SNP characters.}, journal = {Genome biology and evolution}, volume = {5}, number = {11}, pages = {2109-2123}, pmid = {24158624}, issn = {1759-6653}, mesh = {Base Sequence ; Clustered Regularly Interspaced Short Palindromic Repeats ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Molecular Sequence Data ; O Antigens/genetics ; *Phylogeny ; *Polymorphism, Single Nucleotide ; Salmonella enterica/classification/*genetics ; }, abstract = {The enteric pathogen Salmonella enterica is one of the leading causes of foodborne illness in the world. The species is extremely diverse, containing more than 2,500 named serovars that are designated for their unique antigen characters and pathogenicity profiles-some are known to be virulent pathogens, while others are not. Questions regarding the evolution of pathogenicity, significance of antigen characters, diversity of clustered regularly interspaced short palindromic repeat (CRISPR) loci, among others, will remain elusive until a strong evolutionary framework is established. We present the first large-scale S. enterica subsp. enterica phylogeny inferred from a new reference-free k-mer approach of gathering single nucleotide polymorphisms (SNPs) from whole genomes. The phylogeny of 156 isolates representing 78 serovars (102 were newly sequenced) reveals two major lineages, each with many strongly supported sublineages. One of these lineages is the S. Typhi group; well nested within the phylogeny. Lineage-through-time analyses suggest there have been two instances of accelerated rates of diversification within the subspecies. We also found that antigen characters and CRISPR loci reveal different evolutionary patterns than that of the phylogeny, suggesting that a horizontal gene transfer or possibly a shared environmental acquisition might have influenced the present character distribution. Our study also shows the ability to extract reference-free SNPs from a large set of genomes and then to use these SNPs for phylogenetic reconstruction. This automated, annotation-free approach is an important step forward for bacterial disease tracking and in efficiently elucidating the evolutionary history of highly clonal organisms.}, }
@article {pmid24158527, year = {2013}, author = {Bernardo, LP and Loreto, EL}, title = {hobo-brothers elements and their time and place for horizontal transfer.}, journal = {Genetica}, volume = {141}, number = {10-12}, pages = {471-478}, pmid = {24158527}, issn = {1573-6857}, mesh = {Animals ; *DNA Transposable Elements ; Drosophila/*classification/*genetics ; Drosophila Proteins/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Insect ; Phylogeny ; Phylogeography ; Sequence Alignment ; Sequence Homology ; Species Specificity ; Transposases/genetics ; }, abstract = {Transposable elements (TEs) are ubiquitous components of nearly all genomes studied. These elements are highly variable in copy number, molecular structure and transposition strategies. They can move within and between genomes, thus increasing their copy numbers and avoiding being eliminated by stochastic and deterministic processes. hobo is a class II element isolated from Drosophila melanogaster. Previous phylogenetic analyses have shown that the canonical hobo element from D. melanogaster has a sister group formed by sequences found in D. willistoni (called howilli2) and D. mojavensis (called homo1). In the present study, we investigated 36 Drosophilidae species for sequences similar to howilli2 and homo1 using degenerate primers. Additionally, in silico searches were performed in 21 available Drosophila genomes. The obtained sequences formed a monophyletic sister group with the canonical hobo element; we termed these sequences 'hobo-brothers' elements. These elements showed a patch distribution and incongruities with the TE and host species phylogenies, suggesting possible cases of horizontal transfer (HT). Species that possess hobo-brothers sequences are from the New World, mainly Neotropical areas. In addition, the estimated divergence of the sequences found showed that these elements are or were recently active; the large number of HT events observed suggests that these elements could be experiencing an expansion process in Neotropical genomes. A comparison of these results with the literature is discussed with regard to the importance of the time and location of horizontal transposon transfer events.}, }
@article {pmid24157885, year = {2013}, author = {Boughalmi, M and Pagnier, I and Aherfi, S and Colson, P and Raoult, D and La Scola, B}, title = {First isolation of a Marseillevirus in the Diptera Syrphidae Eristalis tenax.}, journal = {Intervirology}, volume = {56}, number = {6}, pages = {386-394}, doi = {10.1159/000354560}, pmid = {24157885}, issn = {1423-0100}, mesh = {Animals ; DNA Viruses/*classification/genetics/*isolation &amp; purification ; DNA, Viral/chemistry/*genetics ; Diptera/*virology ; *Genome, Viral ; Larva/virology ; Molecular Sequence Data ; Sequence Analysis, DNA ; Tunisia ; Viruses, Unclassified/*classification/genetics/*isolation &amp; purification ; }, abstract = {OBJECTIVE: Giant viruses and amoebae are common in freshwater, where they can coexist with various insects. We screened insect larvae to detect giant viruses using a high-throughput method.<br><br>METHODS: We analyzed 86 Eristalis tenax larvae obtained from stagnant water reservoirs in Tunisia. The larvae were decontaminated and then dissected to remove internal parts for coculture with Acanthamoeba polyphaga. Genome sequencing of isolated viruses was performed on a 454 Roche instrument, and comparative genomics were performed.<br><br>RESULTS: One Marseillevirus, named Insectomime virus, was isolated. The genome assembly generated two scaffolds, which were 382,776 and 3,855 bp in length. Among the 477 identified predicted proteins, the best hit for 435 of the identified proteins was a Marseillevirus or Lausannevirus protein. Tunisvirus was the most closely related to Insectomime, with 446 orthologs. One Insectomime protein shared with Lausannevirus and Tunisvirus showed the highest similarity with a protein from an aphid.<br><br>CONCLUSION: The isolation of a Marseillevirus from an insect expands the diversity of environments in which giant viruses have been isolated. The coexistence of larvae and giant viruses in stagnant water may explain the presence of the giant virus in the larva internal structures. This study illustrates the putative role of amoeba in lateral gene transfer not only between the organisms it phagocytoses, but also between organisms living in the same environment. &#xa9; 2013 S. Karger AG, Basel.}, }
@article {pmid24157054, year = {2014}, author = {Laranjo, M and Alexandre, A and Oliveira, S}, title = {Legume growth-promoting rhizobia: an overview on the Mesorhizobium genus.}, journal = {Microbiological research}, volume = {169}, number = {1}, pages = {2-17}, doi = {10.1016/j.micres.2013.09.012}, pmid = {24157054}, issn = {1618-0623}, mesh = {Evolution, Molecular ; Fabaceae/*growth &amp; development/*microbiology/physiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Mesorhizobium/*physiology ; *Plant Development ; Plant Root Nodulation ; *Symbiosis ; }, abstract = {The need for sustainable agricultural practices is revitalizing the interest in biological nitrogen fixation and rhizobia-legumes symbioses, particularly those involving economically important legume crops in terms of food and forage. The genus Mesorhizobium includes species with high geographical dispersion and able to nodulate a wide variety of legumes, including important crop species, like chickpea or biserrula. Some cases of legume-mesorhizobia inoculant introduction represent exceptional opportunities to study the rhizobia genomes evolution and the evolutionary relationships among species. Complete genome sequences revealed that mesorhizobia typically harbour chromosomal symbiosis islands. The phylogenies of symbiosis genes, such as nodC, are not congruent with the phylogenies based on core genes, reflecting rhizobial host range, rather than species affiliation. This agrees with studies showing that Mesorhizobium species are able to exchange symbiosis genes through lateral transfer of chromosomal symbiosis islands, thus acquiring the ability to nodulate new hosts. Phylogenetic analyses of the Mesorhizobium genus based on core and accessory genes reveal complex evolutionary relationships and a high genomic plasticity, rendering the Mesorhizobium genus as a good model to investigate rhizobia genome evolution and adaptation to different host plants. Further investigation of symbiosis genes as well as stress response genes will certainly contribute to understand mesorhizobia-legume symbiosis and to develop more effective mesorhizobia inoculants.}, }
@article {pmid24156600, year = {2013}, author = {Yue, J and Sun, G and Hu, X and Huang, J}, title = {The scale and evolutionary significance of horizontal gene transfer in the choanoflagellate Monosiga brevicollis.}, journal = {BMC genomics}, volume = {14}, number = {1}, pages = {729}, pmid = {24156600}, issn = {1471-2164}, mesh = {Bacteria/genetics ; Biological Evolution ; Chlorophyta/genetics ; Choanoflagellata/classification/*genetics ; Databases, Genetic ; *Gene Transfer, Horizontal ; *Genome, Protozoan ; Phylogeny ; }, abstract = {BACKGROUND: It is generally agreed that horizontal gene transfer (HGT) is common in phagotrophic protists. However, the overall scale of HGT and the cumulative impact of acquired genes on the evolution of these organisms remain largely unknown.<br><br>RESULTS: Choanoflagellates are phagotrophs and the closest living relatives of animals. In this study, we performed phylogenomic analyses to investigate the scale of HGT and the evolutionary importance of horizontally acquired genes in the choanoflagellate Monosiga brevicollis. Our analyses identified 405 genes that are likely derived from algae and prokaryotes, accounting for approximately 4.4% of the Monosiga nuclear genome. Many of the horizontally acquired genes identified in Monosiga were probably acquired from food sources, rather than by endosymbiotic gene transfer (EGT) from obsolete endosymbionts or plastids. Of 193 genes identified in our analyses with functional information, 84 (43.5%) are involved in carbohydrate or amino acid metabolism, and 45 (23.3%) are transporters and/or involved in response to oxidative, osmotic, antibiotic, or heavy metal stresses. Some identified genes may also participate in biosynthesis of important metabolites such as vitamins C and K12, porphyrins and phospholipids.<br><br>CONCLUSIONS: Our results suggest that HGT is frequent in Monosiga brevicollis and might have contributed substantially to its adaptation and evolution. This finding also highlights the importance of HGT in the genome and organismal evolution of phagotrophic eukaryotes.}, }
@article {pmid24150040, year = {2014}, author = {Nikolaidis, N and Doran, N and Cosgrove, DJ}, title = {Plant expansins in bacteria and fungi: evolution by horizontal gene transfer and independent domain fusion.}, journal = {Molecular biology and evolution}, volume = {31}, number = {2}, pages = {376-386}, doi = {10.1093/molbev/mst206}, pmid = {24150040}, issn = {1537-1719}, mesh = {Adaptation, Biological ; Amoebozoa/*genetics ; Bacteria/*genetics ; Cellulase/*metabolism ; Evolution, Molecular ; Fungi/*genetics ; *Gene Transfer, Horizontal ; Models, Molecular ; Phylogeny ; Plant Proteins/*chemistry/*genetics/metabolism ; Plants/*genetics/microbiology/parasitology ; Protein Conformation ; Protein Structure, Tertiary ; }, abstract = {Horizontal gene transfer (HGT) has been described as a common mechanism of transferring genetic material between prokaryotes, whereas genetic transfers from eukaryotes to prokaryotes have been rarely documented. Here we report a rare case of HGT in which plant expansin genes that code for plant cell-wall loosening proteins were transferred from plants to bacteria, fungi, and amoebozoa. In several cases, the species in which the expansin gene was found is either in intimate association with plants or is a known plant pathogen. Our analyses suggest that at least two independent genetic transfers occurred from plants to bacteria and fungi. These events were followed by multiple HGT events within bacteria and fungi. We have also observed that in bacteria expansin genes have been independently fused to DNA fragments that code for an endoglucanase domain or for a carbohydrate binding module, pointing to functional convergence at the molecular level. Furthermore, the functional similarities between microbial expansins and their plant xenologs suggest that these proteins mediate microbial-plant interactions by altering the plant cell wall and therefore may provide adaptive advantages to these species. The evolution of these nonplant expansins represents a unique case in which bacteria and fungi have found innovative and adaptive ways to interact with and infect plants by acquiring genes from their host. This evolutionary paradigm suggests that despite their low frequency such HGT events may have significantly contributed to the evolution of prokaryotic and eukaryotic species.}, }
@article {pmid24149707, year = {2014}, author = {Kung, SH and Almeida, RPP}, title = {Biological and genetic factors regulating natural competence in a bacterial plant pathogen.}, journal = {Microbiology (Reading, England)}, volume = {160}, number = {Pt 1}, pages = {37-46}, doi = {10.1099/mic.0.070581-0}, pmid = {24149707}, issn = {1465-2080}, mesh = {*DNA Transformation Competence ; Gene Transfer, Horizontal ; Plant Diseases/microbiology ; Plants/microbiology ; Recombination, Genetic ; *Transformation, Bacterial ; Xylella/*genetics/*growth &amp; development ; }, abstract = {For naturally competent bacteria, spatially structured growth can provide an environment for enhanced horizontal gene transfer through transformation and recombination. DNA is often present in the extracellular environment, such as in the extracellular matrix of biofilms, and the lysis of a single cell can result in high local DNA concentrations. Xylella fastidiosa is a naturally competent plant pathogen that typically lives in a surface-attached state, yet previous work characterizing the competence of this organism was conducted with planktonic cells in liquid environments. Here, we show that transformation and recombination efficiencies are two to three orders of magnitude higher for cells grown on solid compared with liquid media, with maximum recombination efficiencies of about 10(-3). Cells were highly competent throughout their exponential growth phase, with no significant change in recombination efficiencies until population growth rates began to slow. Mutations in type IV pili, competency-related, and cell-cell signalling genes significantly impacted the ability of X. fastidiosa to acquire and incorporate DNA. Because X. fastidiosa is highly competent when growing in a surface-attached state, as it does within its insect vectors and host plants, recombination of naturally transformed DNA could be a significant route by which horizontal gene transfer occurs in natural environments.}, }
@article {pmid24149625, year = {2014}, author = {Gherardi, G and Imperi, M and Palmieri, C and Magi, G and Facinelli, B and Baldassarri, L and Pataracchia, M and Creti, R}, title = {Genetic diversity and virulence properties of Streptococcus dysgalactiae subsp. equisimilis from different sources.}, journal = {Journal of medical microbiology}, volume = {63}, number = {Pt 1}, pages = {90-98}, doi = {10.1099/jmm.0.062109-0}, pmid = {24149625}, issn = {1473-5644}, mesh = {Anti-Bacterial Agents/pharmacology ; Antigens, Bacterial/genetics ; Bacterial Outer Membrane Proteins/genetics ; Carrier Proteins/genetics ; Carrier State/*microbiology ; Cell Line ; Drug Resistance, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Endocytosis ; Epithelial Cells/microbiology ; *Genetic Variation ; Genotype ; Humans ; Italy/epidemiology ; Molecular Epidemiology ; Molecular Typing ; Polymerase Chain Reaction ; Streptococcal Infections/epidemiology/*microbiology ; Streptococcus/*classification/*genetics/isolation &amp; purification/pathogenicity ; Virulence Factors/genetics ; }, abstract = {A recent increase in virulence of pathogenic Streptococcus dysgalactiae subsp. equisimilis (SDSE) has been widely proposed. Such an increase may be partly explained by the acquisition of new virulence traits by horizontal gene transfer from related streptococci such as Streptococcus pyogenes (GAS) and Streptococcus agalactiae (GBS). A collection of 54 SDSE strains isolated in Italy in the years 2000-2010 from different sources (paediatric throat carriage, invasive and non-invasive diseases) was characterized by emm typing and pulsed-field gel electrophoresis (PFGE) analysis. The virulence repertoire was evaluated by PCR for the presence of GAS superantigen (spe) genes, the streptolysin S (sagA) gene, the group G fibronectin-binding protein (gfbA) gene and GAS-GBS alpha-like protein family (alp) genes; moreover, the ability to invade human epithelial cells was investigated. Resistance to tetracycline, erythromycin and clindamycin was assessed. The combined use of emm typing and PFGE proved to be a reliable strategy for the epidemiological analysis of SDSE isolates. The most frequent emm types were the same as those more frequently reported in other studies, thus indicating the diffusion of a limited number of a few successful emm types fit to disseminate in humans. The speG gene was detected in SDSE strains of different genetic backgrounds. Erythromycin resistance determined by the erm(T) gene, and the unusual, foggy MLSB phenotype, observed in one and seven strains, respectively, have never previously, to our knowledge, been reported in SDSE. Moreover, a new member of the alp family was identified. The identification of new antibiotic and virulence determinants, despite the small size of the sample analysed, shows the importance of constant attention to monitoring the extent of lateral gene transfer in this emerging pathogen.}, }
@article {pmid24146634, year = {2013}, author = {Robinson, KM and Sieber, KB and Dunning Hotopp, JC}, title = {A review of bacteria-animal lateral gene transfer may inform our understanding of diseases like cancer.}, journal = {PLoS genetics}, volume = {9}, number = {10}, pages = {e1003877}, pmid = {24146634}, issn = {1553-7404}, support = {DP2 OD007372/OD/NIH HHS/United States ; 1-DP2-OD007372/OD/NIH HHS/United States ; }, mesh = {Animals ; Chromosomes/genetics/microbiology ; DNA, Bacterial/*genetics ; Gene Transfer, Horizontal/*genetics ; Humans ; Interspersed Repetitive Sequences ; Neoplasms/*genetics/microbiology/virology ; Phylogeny ; Symbiosis/genetics ; Wolbachia/*genetics ; }, abstract = {Lateral gene transfer (LGT) from bacteria to animals occurs more frequently than was appreciated prior to the advent of genome sequencing. In 2007, LGT from bacterial Wolbachia endosymbionts was detected in ~33% of the sequenced arthropod genomes using a bioinformatic approach. Today, Wolbachia/host LGT is thought to be widespread and many other cases of bacteria-animal LGT have been described. In insects, LGT may be more frequently associated with endosymbionts that colonize germ cells and germ stem cells, like Wolbachia endosymbionts. We speculate that LGT may occur from bacteria to a wide variety of eukaryotes, but only becomes vertically inherited when it occurs in germ cells. As such, LGT may happen routinely in somatic cells but never become inherited or fixed in the population. Lack of inheritance of such mutations greatly decreases our ability to detect them. In this review, we propose that such noninherited bacterial DNA integration into chromosomes in human somatic cells could induce mutations leading to cancer or autoimmune diseases in a manner analogous to mobile elements and viral integrations.}, }
@article {pmid24142247, year = {2014}, author = {Hershey, DM and Lu, X and Zi, J and Peters, RJ}, title = {Functional conservation of the capacity for ent-kaurene biosynthesis and an associated operon in certain rhizobia.}, journal = {Journal of bacteriology}, volume = {196}, number = {1}, pages = {100-106}, pmid = {24142247}, issn = {1098-5530}, mesh = {Biosynthetic Pathways/*genetics ; Bradyrhizobium/genetics/*metabolism ; Conserved Sequence ; Diterpenes, Kaurane/*biosynthesis ; Mesorhizobium/genetics/*metabolism ; *Operon ; Polyisoprenyl Phosphates/metabolism ; Rhizobiaceae/genetics/*metabolism ; Soil Microbiology ; Synteny ; }, abstract = {Bacterial interactions with plants are accompanied by complex signal exchange processes. Previously, the nitrogen-fixing symbiotic (rhizo)bacterium Bradyrhizobium japonicum was found to carry adjacent genes encoding two sequentially acting diterpene cyclases that together transform geranylgeranyl diphosphate to ent-kaurene, the olefin precursor to the gibberellin plant hormones. Species from the three other major genera of rhizobia were found to have homologous terpene synthase genes. Cloning and functional characterization of a representative set of these enzymes confirmed the capacity of each genus to produce ent-kaurene. Moreover, comparison of their genomic context revealed that these diterpene synthases are found in a conserved operon which includes an adjacent isoprenyl diphosphate synthase, shown here to produce the geranylgeranyl diphosphate precursor, providing a critical link to central metabolism. In addition, the rest of the operon consists of enzymatic genes that presumably lead to a more elaborated diterpenoid, although the production of gibberellins was not observed. Nevertheless, it has previously been shown that the operon is selectively expressed during nodulation, and the scattered distribution of the operon via independent horizontal gene transfer within the symbiotic plasmid or genomic island shown here suggests that such diterpenoid production may modulate the interaction of these particular symbionts with their host plants.}, }
@article {pmid24141123, year = {2014}, author = {Alvarez, L and Bricio, C and Blesa, A and Hidalgo, A and Berenguer, J}, title = {Transferable denitrification capability of Thermus thermophilus.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {1}, pages = {19-28}, pmid = {24141123}, issn = {1098-5336}, mesh = {Conjugation, Genetic ; *Denitrification ; Electron Transport ; *Gene Transfer, Horizontal ; Metabolic Networks and Pathways/*genetics ; Nitrates/metabolism ; Nitric Oxide/metabolism ; Nitrites/metabolism ; Nitrogen Oxides/metabolism ; *Plasmids ; Thermus thermophilus/*genetics/*metabolism ; }, abstract = {Laboratory-adapted strains of Thermus spp. have been shown to require oxygen for growth, including the model strains T. thermophilus HB27 and HB8. In contrast, many isolates of this species that have not been intensively grown under laboratory conditions keep the capability to grow anaerobically with one or more electron acceptors. The use of nitrogen oxides, especially nitrate, as electron acceptors is one of the most widespread capabilities among these facultative strains. In this process, nitrate is reduced to nitrite by a reductase (Nar) that also functions as electron transporter toward nitrite and nitric oxide reductases when nitrate is scarce, effectively replacing respiratory complex III. In many T. thermophilus denitrificant strains, most electrons for Nar are provided by a new class of NADH dehydrogenase (Nrc). The ability to reduce nitrite to NO and subsequently to N2O by the corresponding Nir and Nor reductases is also strain specific. The genes encoding the capabilities for nitrate (nar) and nitrite (nir and nor) respiration are easily transferred between T. thermophilus strains by natural competence or by a conjugation-like process and may be easily lost upon continuous growth under aerobic conditions. The reason for this instability is apparently related to the fact that these metabolic capabilities are encoded in gene cluster islands, which are delimited by insertion sequences and integrated within highly variable regions of easily transferable extrachromosomal elements. Together with the chromosomal genes, these plasmid-associated genetic islands constitute the extended pangenome of T. thermophilus that provides this species with an enhanced capability to adapt to changing environments.}, }
@article {pmid24141122, year = {2014}, author = {Shintani, M and Matsui, K and Inoue, J and Hosoyama, A and Ohji, S and Yamazoe, A and Nojiri, H and Kimbara, K and Ohkuma, M}, title = {Single-cell analyses revealed transfer ranges of IncP-1, IncP-7, and IncP-9 plasmids in a soil bacterial community.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {1}, pages = {138-145}, pmid = {24141122}, issn = {1098-5336}, mesh = {Bacteria/*classification/*genetics ; *Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Flow Cytometry ; *Gene Transfer, Horizontal ; Genes, Reporter ; Green Fluorescent Proteins/analysis ; Molecular Sequence Data ; *Plasmids ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Single-Cell Analysis ; *Soil Microbiology ; }, abstract = {The conjugative transfer ranges of three different plasmids of the incompatibility groups IncP-1 (pBP136), IncP-7 (pCAR1), and IncP-9 (NAH7) were investigated in soil bacterial communities by culture-dependent and culture-independent methods. Pseudomonas putida, a donor of each plasmid, was mated with soil bacteria, and green fluorescent protein (GFP), encoded on the plasmid, was used as a reporter protein for successful transfer. GFP-expressing transconjugants were detected and separated at the single-cell level by flow cytometry. Each cell was then analyzed by PCR and sequencing of its 16S rRNA gene following either whole-genome amplification or cultivation. A large number of bacteria within the phylum Proteobacteria was identified as transconjugants for pBP136 by both culture-dependent and culture-independent methods. Transconjugants belonging to the phyla Actinobacteria, Bacteroidetes, and Firmicutes were detected only by the culture-independent method. Members of the genus Pseudomonas (class Gammaproteobacteria) were identified as major transconjugants of pCAR1 and NAH7 by both methods, whereas Delftia species (class Betaproteobacteria) were detected only by the culture-independent method. The transconjugants represented a minority of the soil bacteria. Although pCAR1-containing Delftia strains could not be cultivated after a one-to-one filter mating assay between the donor and cultivable Delftia strains as recipients, fluorescence in situ hybridization detected pCAR1-containing Delftia cells, suggesting that Delftia was a "transient" host of pCAR1.}, }
@article {pmid24139901, year = {2013}, author = {Qiu, H and Price, DC and Weber, AP and Facchinelli, F and Yoon, HS and Bhattacharya, D}, title = {Assessing the bacterial contribution to the plastid proteome.}, journal = {Trends in plant science}, volume = {18}, number = {12}, pages = {680-687}, doi = {10.1016/j.tplants.2013.09.007}, pmid = {24139901}, issn = {1878-4372}, mesh = {Biological Evolution ; Chlorophyta/*metabolism ; Cyanobacteria/*metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal ; Photosynthesis ; Phylogeny ; Plastids/metabolism ; *Proteome ; Symbiosis ; }, abstract = {Plastids fulfill a variety of different functions (e.g., photosynthesis and amino acid biosynthesis) that rely on proteins of cyanobacterial (i.e., endosymbiont), noncyanobacterial, and 'host' (eukaryotic) origins. Analysis of plastid proteome data from glaucophytes and green algae allows robust inference of protein origins and organelle protein sharing across the >1 billion years of Archaeplastida evolution. Here, we show that more than one-third of genes encoding plastid proteins lack detectable homologs in Cyanobacteria, underlining the taxonomically broad contributions to plastid functions. Chlamydiae and Proteobacteria are the most significant other bacterial sources of plastid proteins. Mapping of plastid proteins to metabolic pathways shows a core set of anciently derived proteins in Archaeplastida, with many others being lineage specific and derived from independent horizontal gene transfer (HGT) events.}, }
@article {pmid24136884, year = {2013}, author = {Ingram, PR and Rogers, BA and Sidjabat, HE and Gibson, JS and Inglis, TJJ}, title = {Co-selection may explain high rates of ciprofloxacin non-susceptible Escherichia coli from retail poultry reared without prior fluoroquinolone exposure.}, journal = {Journal of medical microbiology}, volume = {62}, number = {Pt 11}, pages = {1743-1746}, doi = {10.1099/jmm.0.062729-0}, pmid = {24136884}, issn = {1473-5644}, mesh = {Acetyltransferases/genetics ; Animals ; Anti-Bacterial Agents/*pharmacology ; Australia ; Chromosomes, Bacterial ; Ciprofloxacin/*pharmacology ; Cluster Analysis ; *Drug Resistance, Bacterial ; Escherichia coli/classification/*drug effects/genetics/*isolation &amp; purification ; Gene Transfer, Horizontal ; Genes, Bacterial ; Molecular Typing ; Phylogeny ; Plasmids ; Poultry/*microbiology ; *Selection, Genetic ; Transformation, Bacterial ; }, abstract = {Australia has never permitted fluoroquinolone use in food-producing animals. We examined local retail poultry for contamination with fluoroquinolone non-susceptible Escherichia coli, then explored the hypothesis that their presence may be due to co-selection of resistance determinants. Between August and November 2010, samples from 30 locally produced, uncooked retail poultry carcasses from four different processing centres underwent selective enrichment culture for ciprofloxacin non-susceptible E. coli. Their chromosomal- and plasmid-mediated resistance determinants were characterized, and phylogenetic analysis and transformation experiments were performed. Unexpectedly, we found nine (30 %) of our small collection of poultry samples carried fluoroquinolone non-susceptible E. coli of which nearly half possessed aac(6')-Ib-cr, a novel plasmid-mediated gene encoding an aminoglycoside acetylating enzyme that also confers fluoroquinolone resistance. All nine isolates were co-resistant to amoxicillin, gentamicin, tetracycline and trimethoprim/sulfamethoxazole--all antibiotic classes that are registered for use in poultry reared for food production within Australia. Their unique phylogenetic relatedness suggested clonal dissemination driven by non-fluoroquinolone selective pressures. aac(6')-Ib-cr was successfully transformed and selected for using non-fluoroquinolone antibiotic pressure. Vertical and perhaps horizontal co-selection may be contributing to the emergence of fluoroquinolone resistance in poultry and could play a similar role in the human setting. This suggests that preservation of the usefulness of fluoroquinolones may require more than just restriction of their use in isolation from other interventions.}, }
@article {pmid24136405, year = {2014}, author = {Hagemann, S and Stöger, L and Kappelmann, M and Hassl, I and Ellinger, A and Velimirov, B}, title = {DNA-bearing membrane vesicles produced by Ahrensia kielensis and Pseudoalteromonas marina.}, journal = {Journal of basic microbiology}, volume = {54}, number = {10}, pages = {1062-1072}, doi = {10.1002/jobm.201300376}, pmid = {24136405}, issn = {1521-4028}, mesh = {Alphaproteobacteria/genetics/*physiology/ultrastructure ; Bacterial Outer Membrane Proteins/chemistry ; Cell Membrane Structures/genetics/physiology/*ultrastructure ; DNA, Bacterial/*analysis ; Pseudoalteromonas/genetics/*physiology/ultrastructure ; }, abstract = {Outer membrane vesicles (OMVs) derived from the alphaproteobacterium Ahrensia kielensis and from Pseudoalteromonas marina, a gammaproteobacterium, were sampled from liquid cultures in order to extract the MV-associated DNA, establish a shotgun library, and sequence randomly chosen clones to determine the origins of their DNA. We show that OMVs from A. kielensis and from P. marina both harbour DNA larger than 20 or 30 kbp. Transmission electron microscopical inspection of OMVs of A. kielensis and P. marina showed two types of vesicles: bilayered OMVs with a diameter between 30 and 250 nm and double bilayered OMVs ranging between 80 and 200 nm. Bilayered OMVs are either characterized by the presence of a large electron-dense substance or are elctron translucent. Double bilayered OMVs contained an electron dense substance in the core region surrounded by the second bilayer. 30,094 bp of the genome from OMV of A. kielensis and 45,981 bp of that from P. marina were sequenced. The results indicated that all sequences were single copy and that all sequences, with one exception, were similar to prokaryotic sequences, inserted viral sequences were not detected.}, }
@article {pmid24133656, year = {2013}, author = {Liu, M and Yan, M and Liu, L and Chen, S}, title = {Characterization of a novel zinc transporter ZnuA acquired by Vibrio parahaemolyticus through horizontal gene transfer.}, journal = {Frontiers in cellular and infection microbiology}, volume = {3}, number = {}, pages = {61}, pmid = {24133656}, issn = {2235-2988}, mesh = {ATP-Binding Cassette Transporters/*genetics/*metabolism ; Amino Acid Sequence ; Animals ; Carrier Proteins/*genetics/*metabolism ; Cluster Analysis ; DNA Mutational Analysis ; Disease Models, Animal ; Epithelial Cells/microbiology ; Gene Deletion ; Gene Expression Profiling ; Gene Order ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Complementation Test ; Genomic Islands ; HeLa Cells ; Humans ; Mice ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Amino Acid ; Vibrio Infections/microbiology/pathology ; Vibrio parahaemolyticus/*genetics/*metabolism ; Virulence ; }, abstract = {Vibrio parahaemolyticus is a clinically important foodborne pathogen that causes acute gastroenteritis worldwide. It has been shown that horizontal gene transfer (HGT) contributes significantly to virulence development of V. parahaemolyticus. In this study, we identified a novel znuA homolog (vpa1307) that belongs to a novel subfamily of ZnuA, a bacterial zinc transporter. The vpa1307 gene is located upstream of the V. parahaemolyticus pathogenicity island (Vp-PAIs) in both tdh-positive and trh-positive V. parahaemolyticus strains. Phylogenetic analysis revealed the exogenous origin of vpa1307 with 40% of V. parahaemolyticus clinical isolates possessing this gene. The expression of vpa1307 gene in V. parahaemolyticus clinical strain VP3218 is induced under zinc limitation condition. Gene deletion and complementation assays confirmed that vpa1307 contributes to the growth of VP3218 under zinc depletion condition and that conserved histidine residues of Vpa1307 contribute to its activity. Importantly, vpa1307 contributes to the cytotoxicity of VP3218 in HeLa cells and a certain degree of virulence in murine model. These results suggest that the horizontally acquired znuA subfamily gene, vpa1307, contributes to the fitness and virulence of Vibrio species.}, }
@article {pmid24132513, year = {2014}, author = {Gao, C and Ren, X and Mason, AS and Liu, H and Xiao, M and Li, J and Fu, D}, title = {Horizontal gene transfer in plants.}, journal = {Functional &amp; integrative genomics}, volume = {14}, number = {1}, pages = {23-29}, pmid = {24132513}, issn = {1438-7948}, mesh = {Animals ; Bacteria/genetics ; DNA Transposable Elements ; Fungi/genetics ; *Gene Transfer, Horizontal ; Host-Pathogen Interactions/genetics ; Insecta/genetics ; Plants/*genetics/microbiology/parasitology/virology ; Plastids/genetics ; Viruses/genetics ; }, abstract = {Horizontal gene transfer (HGT) describes the transmission of genetic material across species boundaries. HGT often occurs in microbic and eukaryotic genomes. However, the pathways by which HGTs occur in multicellular eukaryotes, especially in plants, are not well understood. We systematically summarized more than ten possible pathways for HGT. The intimate contact which frequently occurs in parasitism, symbiosis, pathogen, epiphyte, entophyte, and grafting interactions could promote HGTs between two species. Besides these direct transfer methods, genes can be exchanged with a vector as a bridge: possible vectors include pollen, fungi, bacteria, viruses, viroids, plasmids, transposons, and insects. HGT, especially when involving horizontal transfer of transposable elements, is recognized as a significant force propelling genomic variation and biological innovation, playing an important functional and evolutionary role in both eukaryotic and prokaryotic genomes. We proposed possible mechanisms by which HGTs can occur, which is useful in understanding the genetic information exchange among distant species or distant cellular components.}, }
@article {pmid24131955, year = {2013}, author = {Brouwer, MS and Roberts, AP and Hussain, H and Williams, RJ and Allan, E and Mullany, P}, title = {Horizontal gene transfer converts non-toxigenic Clostridium difficile strains into toxin producers.}, journal = {Nature communications}, volume = {4}, number = {}, pages = {2601}, pmid = {24131955}, issn = {2041-1723}, support = {G0601176/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Bacterial Proteins/*genetics/metabolism ; Bacterial Toxins/*genetics/metabolism ; Cell Line ; Cell Survival ; Clostridioides difficile/*genetics/metabolism ; Conjugation, Genetic ; Enterotoxins/*genetics/metabolism ; Fibroblasts/cytology/microbiology ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; }, abstract = {Clostridium difficile is a major nosocomial pathogen and the main causative agent of antibiotic-associated diarrhoea. The organism produces two potent toxins, A and B, which are its major virulence factors. These are chromosomally encoded on a region termed the pathogenicity locus (PaLoc), which also contains regulatory genes, and is absent in non-toxigenic strains. Here we show that the PaLoc can be transferred from the toxin-producing strain, 630Δerm, to three non-toxigenic strains of different ribotypes. One of the transconjugants is shown by cytotoxicity assay to produce toxin B at a similar level to the donor strain, demonstrating that a toxigenic C. difficile strain is capable of converting a non-toxigenic strain to a toxin producer by horizontal gene transfer. This has implications for the treatment of C. difficile infections, as non-toxigenic strains are being tested as treatments in clinical trials.}, }
@article {pmid24129283, year = {2013}, author = {Cantón, R and Horcajada, JP and Oliver, A and Garbajosa, PR and Vila, J}, title = {Inappropriate use of antibiotics in hospitals: the complex relationship between antibiotic use and antimicrobial resistance.}, journal = {Enfermedades infecciosas y microbiologia clinica}, volume = {31 Suppl 4}, number = {}, pages = {3-11}, doi = {10.1016/S0213-005X(13)70126-5}, pmid = {24129283}, issn = {1578-1852}, mesh = {Anti-Bacterial Agents/*therapeutic use ; *Drug Resistance, Bacterial ; *Hospitals ; Humans ; *Inappropriate Prescribing ; }, abstract = {Hospitals are considered an excellent compartment for the selection of resistant and multi-drug resistant (MDR) bacteria. The overuse and misuse of antimicrobial agents are considered key points fuelling this situation. Antimicrobial stewardship programs have been designed for better use of these compounds to prevent the emergence of resistant microorganisms and to diminish the upward trend in resistance. Nevertheless, the relationship between antibiotic use and antimicrobial resistance is complex, and the desired objectives are difficult to reach. Various factors affecting this relationship have been advocated including, among others, antibiotic exposure and mutant selection windows, antimicrobial pharmacodynamics, the nature of the resistance (natural or acquired, including mutational and that associated with horizontal gene transfer) and the definition of resistance. Moreover, antimicrobial policies to promote better use of these drugs should be implemented not only in the hospital setting coupled with infection control programs, but also in the community, which should also include animal and environmental compartments. Within hospitals, the restriction of antimicrobials, cycling and mixing strategies and the use of combination therapies have been used to avoid resistance. Nevertheless, the results have not always been favorable and resistant bacteria have persisted despite the theoretical benefits of these strategies. Mathematical models as well as microbiological knowledge can explain this failure, which is mainly related to the current scenario involving MDR bacteria and overcoming the fitness associated with resistance. New antimicrobials, rapid diagnostic and antimicrobial susceptibility testing and biomarkers will be useful for future antimicrobial stewardship interventions.}, }
@article {pmid24129002, year = {2013}, author = {Goessweiner-Mohr, N and Arends, K and Keller, W and Grohmann, E}, title = {Conjugative type IV secretion systems in Gram-positive bacteria.}, journal = {Plasmid}, volume = {70}, number = {3}, pages = {289-302}, pmid = {24129002}, issn = {1095-9890}, mesh = {Bacterial Proteins/*genetics/metabolism ; Bacterial Secretion Systems/*genetics ; Biological Transport ; Cell Wall/metabolism ; Clostridium/*genetics/metabolism ; *Conjugation, Genetic ; DNA/genetics/metabolism ; DNA, Single-Stranded/genetics/metabolism ; Enterococcus faecalis/*genetics/metabolism ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Operon ; Plasmids/metabolism ; Streptomycetaceae/*genetics/metabolism ; }, abstract = {Bacterial conjugation presents the most important means to spread antibiotic resistance and virulence factors among closely and distantly related bacteria. Conjugative plasmids are the mobile genetic elements mainly responsible for this task. All the genetic information required for the horizontal transmission is encoded on the conjugative plasmids themselves. Two distinct concepts for horizontal plasmid transfer in Gram-positive bacteria exist, the most prominent one transports single stranded plasmid DNA via a multi-protein complex, termed type IV secretion system, across the Gram-positive cell envelope. Type IV secretion systems have been found in virtually all unicellular Gram-positive bacteria, whereas multicellular Streptomycetes seem to have developed a specialized system more closely related to the machinery involved in bacterial cell division and sporulation, which transports double stranded DNA from donor to recipient cells. This review intends to summarize the state of the art of prototype systems belonging to the two distinct concepts; it focuses on protein key players identified so far and gives future directions for research in this emerging field of promiscuous interbacterial transport.}, }
@article {pmid24127573, year = {2013}, author = {Seitz, P and Blokesch, M}, title = {DNA-uptake machinery of naturally competent Vibrio cholerae.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {44}, pages = {17987-17992}, pmid = {24127573}, issn = {1091-6490}, mesh = {Biological Transport/physiology ; DNA/*pharmacokinetics ; Fimbriae Proteins/metabolism ; Fimbriae, Bacterial/metabolism/ultrastructure ; Microscopy, Fluorescence ; Polymerase Chain Reaction ; Transformation, Bacterial/*physiology ; Vibrio cholerae/*metabolism ; }, abstract = {Natural competence for transformation is a mode of horizontal gene transfer that is commonly used by bacteria to take up DNA from their environment. As part of this developmental program, so-called competence genes, which encode the components of a DNA-uptake machinery, are expressed. Several models have been proposed for the DNA-uptake complexes of competent bacteria, and most include a type IV (pseudo)pilus as a core component. However, cell-biology-based approaches to visualizing competence proteins have so far been restricted to Gram-positive bacteria. Here, we report the visualization of a competence-induced pilus in the Gram-negative bacterium Vibrio cholerae. We show that piliated cells mostly contain a single pilus that is not biased toward a polar localization and that this pilus colocalizes with the outer membrane secretin PilQ. PilQ, on the other hand, forms several foci around the cell and occasionally colocalizes with the dynamic cytoplasmic-traffic ATPase PilB, which is required for pilus extension. We also determined the minimum competence regulon of V. cholerae, which includes at least 19 genes. Bacteria with mutations in those genes were characterized with respect to the presence of surface-exposed pili, DNA uptake, and natural transformability. Based on these phenotypes, we propose that DNA uptake in naturally competent V. cholerae cells occurs in at least two steps: a pilus-dependent translocation of the incoming DNA across the outer membrane and a pilus-independent shuttling of the DNA through the periplasm and into the cytoplasm.}, }
@article {pmid24123430, year = {2014}, author = {Chen, YT and Lin, JC and Fung, CP and Lu, PL and Chuang, YC and Wu, TL and Siu, LK}, title = {KPC-2-encoding plasmids from Escherichia coli and Klebsiella pneumoniae in Taiwan.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {69}, number = {3}, pages = {628-631}, doi = {10.1093/jac/dkt409}, pmid = {24123430}, issn = {1460-2091}, mesh = {DNA, Bacterial/chemistry/genetics ; Disease Outbreaks ; Escherichia coli/classification/*enzymology/*genetics/isolation &amp; purification ; Escherichia coli Infections/epidemiology/microbiology ; Gene Transfer, Horizontal ; Genotype ; Humans ; Klebsiella Infections/epidemiology/microbiology ; Klebsiella pneumoniae/classification/*enzymology/*genetics/isolation &amp; purification ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Multilocus Sequence Typing ; *Plasmids ; Taiwan/epidemiology ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: Two plasmids carrying bla(KPC-2) isolated from carbapenem-resistant Escherichia coli (CR-EC) and carbapenem-resistant Klebsiella pneumoniae (CR-KP), respectively, were completely sequenced. The CR-KP strain was selected from an outbreak in 2012, and the CR-EC strain was the first blaKPC-2-carrying E. coli identified in the same carbapenem resistance monitoring programme in Taiwan.<br><br>METHODS: Antimicrobial susceptibility tests, multilocus sequence typing (MLST) and the conjugal transfer of plasmids were performed. Complete sequencing of the plasmids was performed using a shotgun approach.<br><br>RESULTS: The CR-EC and CR-KP strains in this study were determined to be ST410 and ST11, respectively, by MLST. From CR-EC, we identified a 145 kb conjugative plasmid that carries bla(KPC-2), bla(CMY-2), bla(CTX-M-3) and bla(TEM-1). The plasmid is a chimera composed of three regions related to IncI, IncN and RepFIC replicons. From CR-KP, we identified an 86.5 kb plasmid, pKPC-LK30, which carries bla(KPC-2) and bla(SHV-11). The plasmid is very similar to two bla(KPC-2)-carrying IncFII(K) plasmids, but lacks one of the replication origins and cannot conjugate.<br><br>CONCLUSIONS: The differences in cross-species transferability of the two plasmids can be explained by genetic differences between their backbones and could have resulted in the confined bla(KPC-2)-carrying CR-KP outbreak in Taiwan. Plasmid pKPC-LKEc is the first bla(KPC-2)-carrying plasmid identified from CR-EC in Taiwan. With relatively high transferability it should be closely monitored.}, }
@article {pmid24118435, year = {2013}, author = {Gerth, M and Röthe, J and Bleidorn, C}, title = {Tracing horizontal Wolbachia movements among bees (Anthophila): a combined approach using multilocus sequence typing data and host phylogeny.}, journal = {Molecular ecology}, volume = {22}, number = {24}, pages = {6149-6162}, doi = {10.1111/mec.12549}, pmid = {24118435}, issn = {1365-294X}, mesh = {Animals ; Bayes Theorem ; Bees/genetics/*microbiology ; *Biological Evolution ; *Gene Transfer, Horizontal ; Models, Genetic ; Molecular Sequence Data ; Multilocus Sequence Typing ; *Phylogeny ; Symbiosis/genetics ; Wolbachia/classification/*genetics ; }, abstract = {The endosymbiotic bacterium Wolbachia enhances its spread via vertical transmission by generating reproductive effects in its hosts, most notably cytoplasmic incompatibility (CI). Additionally, frequent interspecific horizontal transfer is evident from a lack of phylogenetic congruence between Wolbachia and its hosts. The mechanisms of this lateral transfer are largely unclear. To identify potential pathways of Wolbachia movements, we performed multilocus sequence typing of Wolbachia strains from bees (Anthophila). Using a host phylogeny and ecological data, we tested various models of horizontal endosymbiont transmission. In general, Wolbachia strains seem to be randomly distributed among bee hosts. Kleptoparasite-host associations among bees as well as other ecological links could not be supported as sole basis for the spread of Wolbachia. However, cophylogenetic analyses and divergence time estimations suggest that Wolbachia may persist within a host lineage over considerable timescales and that strictly vertical transmission and subsequent random loss of infections across lineages may have had a greater impact on Wolbachia strain distribution than previously estimated. Although general conclusions about Wolbachia movements among arthropod hosts cannot be made, we present a framework by which precise assumptions about shared evolutionary histories of Wolbachia and a host taxon can be modelled and tested.}, }
@article {pmid24116129, year = {2013}, author = {Dueholm, MS and Otzen, D and Nielsen, PH}, title = {Evolutionary insight into the functional amyloids of the pseudomonads.}, journal = {PloS one}, volume = {8}, number = {10}, pages = {e76630}, pmid = {24116129}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Amyloid/classification/*genetics/metabolism ; Bacterial Proteins/*genetics/metabolism ; Biofilms/growth &amp; development ; *Evolution, Molecular ; Genetic Variation ; Genome, Bacterial/genetics ; Markov Chains ; Metagenome/genetics ; Molecular Sequence Data ; Operon ; Phylogeny ; Proteobacteria/classification/genetics/metabolism ; Pseudomonas/classification/*genetics/physiology ; Sequence Homology, Amino Acid ; Species Specificity ; }, abstract = {Functional bacterial amyloids (FuBA) are important components in many environmental biofilms where they provide structural integrity to the biofilm, mediate bacterial aggregation and may function as virulence factor by binding specifically to host cell molecules. A novel FuBA system, the Fap system, was previously characterized in the genus Pseudomonas, however, very little is known about the phylogenetic diversity of bacteria with the genetic capacity to apply this system. Studies of genomes and public metagenomes from a diverse range of habitats showed that the Fap system is restricted to only three classes in the phylum Proteobacteria, the Beta-, Gamma- and Deltaproteobacteria. The structural organization of the fap genes into a single fapABCDEF operon is well conserved with minor variations such as a frequent deletion of fapA. A high degree of variation was seen within the primary structure of the major Fap fibril monomers, FapC, whereas the minor monomers, FapB, showed less sequence variation. Comparison of phylogenetic trees based on Fap proteins and the 16S rRNA gene of the corresponding bacteria showed remarkably similar overall topology. This indicates, that horizontal gene transfer is an infrequent event in the evolution of the Fap system.}, }
@article {pmid24115946, year = {2013}, author = {Devirgiliis, C and Zinno, P and Perozzi, G}, title = {Update on antibiotic resistance in foodborne Lactobacillus and Lactococcus species.}, journal = {Frontiers in microbiology}, volume = {4}, number = {}, pages = {301}, pmid = {24115946}, issn = {1664-302X}, abstract = {Lactobacilli represent a major Lactic Acid Bacteria (LAB) component within the complex microbiota of fermented foods obtained from meat, dairy, and vegetable sources. Lactococci, on the other hand, are typical of milk and fermented dairy products, which in turn represent the vast majority of fermented foods. As is the case for all species originating from the environment, foodborne lactobacilli and lactococci consist of natural, uncharacterized strains, whose biodiversity depends on geographical origin, seasonality, animal feeding/plant growth conditions. Although a few species of opportunistic pathogens have been described, lactobacilli and lactococci are mostly non-pathogenic, Gram-positive bacteria displaying probiotic features. Since antibiotic resistant (AR) strains do not constitute an immediate threat to human health, scientific interest for detailed studies on AR genes in these species has been greatly hindered. However, increasing evidence points at a crucial role for foodborne LAB as reservoir of potentially transmissible AR genes, underlining the need for further, more detailed studies aimed at identifying possible strategies to avoid AR spread to pathogens through fermented food consumption. The availability of a growing number of sequenced bacterial genomes has been very helpful in identifying the presence/distribution of mobile elements associated with AR genes, but open questions and knowledge gaps still need to be filled, highlighting the need for systematic and datasharing approaches to implement both surveillance and mechanistic studies on transferability of AR genes. In the present review we report an update of the recent literature on AR in lactobacilli and lactococci following the 2006 EU-wide ban of the use of antibiotics as feed additives in animal farming, and we discuss the limits of the present knowledge in evaluating possible risks for human health.}, }
@article {pmid24115603, year = {2013}, author = {Zhang, HH and Xu, HE and Shen, YH and Han, MJ and Zhang, Z}, title = {The origin and evolution of six miniature inverted-repeat transposable elements in Bombyx mori and Rhodnius prolixus.}, journal = {Genome biology and evolution}, volume = {5}, number = {11}, pages = {2020-2031}, pmid = {24115603}, issn = {1759-6653}, mesh = {Animals ; Base Sequence ; Bombyx/*genetics ; *DNA Transposable Elements ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Inverted Repeat Sequences ; Molecular Sequence Data ; Rhodnius/*genetics ; }, abstract = {Miniature inverted-repeat transposable elements (MITEs) are a specific group of nonautonomous DNA transposons, and they are distributed in a wide range of hosts. However, the origin and evolutionary history of MITEs in eukaryotic genomes remain unclear. In this study, six MITEs were identified in the silkworm (Bombyx mori). Five elements are grouped into four known superfamilies of DNA transposons, and one represents a novel class of MITEs. Unexpectedly, six similar MITEs are also present in the triatomine bug (Rhodnius prolixus) that diverged from the common ancestor with the silkworm about 370 Ma. However, they show different lengths in two species, suggesting that they are different derivatives of progenitor transposons. Three direct progenitor transposons (Sola1, hobo/Ac/Tam [hAT], and Ginger2) are also identified in some other organisms, and several lines of evidence suggested that these autonomous elements might have been independently and horizontally transferred into their hosts. Furthermore, it is speculated that the twisted-wing parasites may be the candidate vectors for these horizontal transfers. The data presented in this study provide some new insights into the origin and evolutionary history of MITEs in the silkworm and triatomine bug.}, }
@article {pmid24115441, year = {2013}, author = {Ho, BT and Basler, M and Mekalanos, JJ}, title = {Type 6 secretion system-mediated immunity to type 4 secretion system-mediated gene transfer.}, journal = {Science (New York, N.Y.)}, volume = {342}, number = {6155}, pages = {250-253}, pmid = {24115441}, issn = {1095-9203}, support = {R01 AI026289/AI/NIAID NIH HHS/United States ; R37 AI018045/AI/NIAID NIH HHS/United States ; R01 AI018045/AI/NIAID NIH HHS/United States ; AI-26289/AI/NIAID NIH HHS/United States ; AI-018045/AI/NIAID NIH HHS/United States ; }, mesh = {*Antibiosis ; Bacterial Secretion Systems/drug effects/*physiology ; *Conjugation, Genetic ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal/drug effects/*physiology ; Plasmids/genetics ; Polymyxin B/pharmacology ; Pseudomonas aeruginosa/drug effects/*genetics/*physiology ; }, abstract = {Gram-negative bacteria use the type VI secretion system (T6SS) to translocate toxic effector proteins into adjacent cells. The Pseudomonas aeruginosa H1-locus T6SS assembles in response to exogenous T6SS attack by other bacteria. We found that this lethal T6SS counterattack also occurs in response to the mating pair formation (Mpf) system encoded by broad-host-range IncPα conjugative plasmid RP4 present in adjacent donor cells. This T6SS response was eliminated by disruption of Mpf structural genes but not components required only for DNA transfer. Because T6SS activity was also strongly induced by membrane-disrupting natural product polymyxin B, we conclude that RP4 induces "donor-directed T6SS attacks" at sites corresponding to Mpf-mediated membrane perturbations in recipient P. aeruginosa cells to potentially block acquisition of parasitic foreign DNA.}, }
@article {pmid24115208, year = {2015}, author = {Chen, W and Sun, L and Lu, J and Bi, L and Wang, E and Wei, G}, title = {Diverse nodule bacteria were associated with Astragalus species in arid region of northwestern China.}, journal = {Journal of basic microbiology}, volume = {55}, number = {1}, pages = {121-128}, doi = {10.1002/jobm.201300209}, pmid = {24115208}, issn = {1521-4028}, mesh = {Agrobacterium/genetics/isolation &amp; purification/physiology ; Astragalus Plant/*microbiology ; China ; Endophytes/classification/*isolation &amp; purification/*physiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genes, rRNA ; Genetic Variation ; Mesorhizobium/genetics/isolation &amp; purification/physiology ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Rhizobiaceae/genetics/*isolation &amp; purification/*physiology ; Rhizobium/genetics/isolation &amp; purification/physiology ; Root Nodules, Plant/*microbiology ; Sequence Analysis, DNA ; Symbiosis/genetics ; }, abstract = {The legume species of Astragalus as traditional Chinese medicine source and environmental protection plants showed an extensive distribution in the arid region of northwestern China. However, few rhizobia associating with Astragalus have been investigated in this region so far. In this study, 78 endophytic bacteria were isolated from root nodules of 12 Astragalus species and characterized by the PCR-RFLP of 16S rRNA gene and symbiotic genes together with the phylogenetic analysis. Results showed that the majority (53%) of isolates are non-nodulating Agrobacterium sp. and the rest are Mesorhizobium genomic species (41%), Ensifer spp. and Rhizobium gallicum (6%), respectively. Mesorhizobium genomic species are broadly distributed in the Astragalus symbioses and most of them share similar symbiotic genes. It seems that horizontal gene transfer occurred frequently among different genomic species independent of their original hosts and sites. Astragalus adsurgens is nodulated by a widely range of rhizobial species in the nodulation test, revealing that it could play an important role in diversification of Astragalus symbionts and that might be a reason for its wide adaptation to diverse environments.}, }
@article {pmid24112977, year = {2013}, author = {Qiu, H and Price, DC and Weber, AP and Reeb, V and Yang, EC and Lee, JM and Kim, SY and Yoon, HS and Bhattacharya, D}, title = {Adaptation through horizontal gene transfer in the cryptoendolithic red alga Galdieria phlegrea.}, journal = {Current biology : CB}, volume = {23}, number = {19}, pages = {R865-6}, doi = {10.1016/j.cub.2013.08.046}, pmid = {24112977}, issn = {1879-0445}, mesh = {Adaptation, Physiological/*genetics ; Chlamydomonas reinhardtii/genetics ; Gene Deletion ; Gene Transfer, Horizontal/*genetics ; Genome, Plant/genetics ; Rhodophyta/*genetics ; Volvox/genetics ; }, }
@article {pmid24109604, year = {2014}, author = {Zwart, MP and Willemsen, A and Daròs, JA and Elena, SF}, title = {Experimental evolution of pseudogenization and gene loss in a plant RNA virus.}, journal = {Molecular biology and evolution}, volume = {31}, number = {1}, pages = {121-134}, pmid = {24109604}, issn = {1537-1719}, mesh = {Chromosome Mapping ; Cloning, Molecular ; *Evolution, Molecular ; *Gene Deletion ; Gene Transfer, Horizontal ; *Genome, Viral ; Plant Viruses/*genetics/physiology ; Polymorphism, Single Nucleotide ; *Pseudogenes ; RNA Viruses/*genetics/physiology ; RNA, Viral/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Selection, Genetic ; Nicotiana/virology ; Virus Replication ; }, abstract = {Viruses have evolved highly streamlined genomes and a variety of mechanisms to compress them, suggesting that genome size is under strong selection. Horizontal gene transfer has, on the other hand, played an important role in virus evolution. However, evolution cannot integrate initially nonfunctional sequences into the viral genome if they are rapidly purged by selection. Here we report on the experimental evolution of pseudogenization in virus genomes using a plant RNA virus expressing a heterologous gene. When long 9-week passages were performed, the added gene was lost in all lineages, whereas viruses with large genomic deletions were fixed in only two out of ten 3-week lineages and none in 1-week lineages. Illumina next-generation sequencing revealed considerable convergent evolution in the 9- and 3-week lineages with genomic deletions. Genome size was correlated to within-host competitive fitness, although there was no correlation with virus accumulation or virulence. Within-host competitive fitness of the 3-week virus lineages without genomic deletions was higher than for the 1-week lineages. Our results show that the strength of selection for a reduced genome size and the rate of pseudogenization depend on demographic conditions. Moreover, for the 3-week passage condition, we observed increases in within-host fitness, whereas selection was not strong enough to quickly remove the nonfunctional heterologous gene. These results suggest a demographically determined "sweet spot" might exist, where heterologous insertions are not immediately lost while evolution can act to integrate them into the viral genome.}, }
@article {pmid24108212, year = {2013}, author = {Uhrig, RG and Kerk, D and Moorhead, GB}, title = {Evolution of bacterial-like phosphoprotein phosphatases in photosynthetic eukaryotes features ancestral mitochondrial or archaeal origin and possible lateral gene transfer.}, journal = {Plant physiology}, volume = {163}, number = {4}, pages = {1829-1843}, pmid = {24108212}, issn = {1532-2548}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Archaea/*metabolism ; Bacteria/*enzymology ; Eukaryota/*enzymology ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phosphoprotein Phosphatases/chemistry/*genetics ; Photosynthesis ; *Phylogeny ; Protein Transport ; Subcellular Fractions/enzymology ; }, abstract = {Protein phosphorylation is a reversible regulatory process catalyzed by the opposing reactions of protein kinases and phosphatases, which are central to the proper functioning of the cell. Dysfunction of members in either the protein kinase or phosphatase family can have wide-ranging deleterious effects in both metazoans and plants alike. Previously, three bacterial-like phosphoprotein phosphatase classes were uncovered in eukaryotes and named according to the bacterial sequences with which they have the greatest similarity: Shewanella-like (SLP), Rhizobiales-like (RLPH), and ApaH-like (ALPH) phosphatases. Utilizing the wealth of data resulting from recently sequenced complete eukaryotic genomes, we conducted database searching by hidden Markov models, multiple sequence alignment, and phylogenetic tree inference with Bayesian and maximum likelihood methods to elucidate the pattern of evolution of eukaryotic bacterial-like phosphoprotein phosphatase sequences, which are predominantly distributed in photosynthetic eukaryotes. We uncovered a pattern of ancestral mitochondrial (SLP and RLPH) or archaeal (ALPH) gene entry into eukaryotes, supplemented by possible instances of lateral gene transfer between bacteria and eukaryotes. In addition to the previously known green algal and plant SLP1 and SLP2 protein forms, a more ancestral third form (SLP3) was found in green algae. Data from in silico subcellular localization predictions revealed class-specific differences in plants likely to result in distinct functions, and for SLP sequences, distinctive and possibly functionally significant differences between plants and nonphotosynthetic eukaryotes. Conserved carboxyl-terminal sequence motifs with class-specific patterns of residue substitutions, most prominent in photosynthetic organisms, raise the possibility of complex interactions with regulatory proteins.}, }
@article {pmid24107993, year = {2013}, author = {Dai, W and Fu, C and Raytcheva, D and Flanagan, J and Khant, HA and Liu, X and Rochat, RH and Haase-Pettingell, C and Piret, J and Ludtke, SJ and Nagayama, K and Schmid, MF and King, JA and Chiu, W}, title = {Visualizing virus assembly intermediates inside marine cyanobacteria.}, journal = {Nature}, volume = {502}, number = {7473}, pages = {707-710}, pmid = {24107993}, issn = {1476-4687}, support = {R01 GM080139/GM/NIGMS NIH HHS/United States ; P41 GM103832/GM/NIGMS NIH HHS/United States ; R56 AI075208/AI/NIAID NIH HHS/United States ; P41GM123832/GM/NIGMS NIH HHS/United States ; GM080139/GM/NIGMS NIH HHS/United States ; PN2 EY016525/EY/NEI NIH HHS/United States ; T15 LM007093/LM/NLM NIH HHS/United States ; T32 GM007330/GM/NIGMS NIH HHS/United States ; AI0175208/AI/NIAID NIH HHS/United States ; PN2EY016525/EY/NEI NIH HHS/United States ; T15LM007093/LM/NLM NIH HHS/United States ; T32GM007330/GM/NIGMS NIH HHS/United States ; }, mesh = {Aquatic Organisms/cytology/ultrastructure/virology ; Bacteriophages/*growth &amp; development/*ultrastructure ; Cryoelectron Microscopy/*methods ; Electron Microscope Tomography/*methods ; Models, Biological ; Synechococcus/cytology/*ultrastructure/*virology ; *Virus Assembly ; }, abstract = {Cyanobacteria are photosynthetic organisms responsible for ∼25% of organic carbon fixation on the Earth. These bacteria began to convert solar energy and carbon dioxide into bioenergy and oxygen more than two billion years ago. Cyanophages, which infect these bacteria, have an important role in regulating the marine ecosystem by controlling cyanobacteria community organization and mediating lateral gene transfer. Here we visualize the maturation process of cyanophage Syn5 inside its host cell, Synechococcus, using Zernike phase contrast electron cryo-tomography (cryoET). This imaging modality yields dramatic enhancement of image contrast over conventional cryoET and thus facilitates the direct identification of subcellular components, including thylakoid membranes, carboxysomes and polyribosomes, as well as phages, inside the congested cytosol of the infected cell. By correlating the structural features and relative abundance of viral progeny within cells at different stages of infection, we identify distinct Syn5 assembly intermediates. Our results indicate that the procapsid releases scaffolding proteins and expands its volume at an early stage of genome packaging. Later in the assembly process, we detected full particles with a tail either with or without an additional horn. The morphogenetic pathway we describe here is highly conserved and was probably established long before that of double-stranded DNA viruses infecting more complex organisms.}, }
@article {pmid24107487, year = {2014}, author = {Piacente, F and Bernardi, C and Marin, M and Blanc, G and Abergel, C and Tonetti, MG}, title = {Characterization of a UDP-N-acetylglucosamine biosynthetic pathway encoded by the giant DNA virus Mimivirus.}, journal = {Glycobiology}, volume = {24}, number = {1}, pages = {51-61}, doi = {10.1093/glycob/cwt089}, pmid = {24107487}, issn = {1460-2423}, mesh = {Acanthamoeba/virology ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Mimiviridae/*enzymology/genetics ; *Phylogeny ; Uridine Diphosphate N-Acetylmuramic Acid/*biosynthesis/genetics ; Viral Proteins/genetics/*metabolism ; }, abstract = {Mimivirus is a giant DNA virus belonging to the Megaviridae family and infecting unicellular Eukaryotes of the genus Acanthamoeba. The viral particles are characterized by heavily glycosylated surface fibers. Several experiments suggest that Mimivirus and other related viruses encode an autonomous glycosylation system, forming viral glycoproteins independently of their host. In this study, we have characterized three Mimivirus proteins involved in the de novo uridine diphosphate-N-acetylglucosamine (UDP-GlcNAc) production: a glutamine-fructose-6-phosphate transaminase (CDS L619), a glucosamine-6-phosphate N-acetyltransferase (CDS L316) and a UDP-GlcNAc pyrophosphorylase (CDS R689). Sequence and enzymatic analyses have revealed some unique features of the viral pathway. While it follows the eukaryotic-like strategy, it also shares some properties of the prokaryotic pathway. Phylogenetic analyses revealed that the Megaviridae enzymes cluster in monophyletic groups, indicating that they share common ancestors, but did not support the hypothesis of recent acquisitions from one of the known hosts. Rather, viral clades branched at deep nodes in phylogenetic trees, forming independent clades outside sequenced cellular organisms. The intermediate properties between the eukaryotic and prokaryotic pathways, the phylogenetic analyses and the fact that these enzymes are shared between most of the known members of the Megaviridae family altogether suggest that the viral pathway has an ancient origin, resulting from lateral transfers of cellular genes early in the Megaviridae evolution, or from vertical inheritance from a more complex cellular ancestor (reductive evolution hypothesis). The identification of a virus-encoded UDP-GlcNAc pathway reinforces the concept that GlcNAc is a ubiquitous sugar representing a universal and fundamental process in all organisms.}, }
@article {pmid24105273, year = {2013}, author = {Stern, DL}, title = {The genetic causes of convergent evolution.}, journal = {Nature reviews. Genetics}, volume = {14}, number = {11}, pages = {751-764}, pmid = {24105273}, issn = {1471-0064}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {Adaptation, Physiological/*genetics ; Alleles ; Animals ; Bacteria/*genetics ; *Biological Evolution ; Butterflies/*genetics ; Fishes/*genetics ; Gene Transfer, Horizontal ; Humans ; Linkage Disequilibrium ; *Models, Genetic ; Mutation ; Phenotype ; Viruses/*genetics ; }, abstract = {The evolution of phenotypic similarities between species, known as convergence, illustrates that populations can respond predictably to ecological challenges. Convergence often results from similar genetic changes, which can emerge in two ways: the evolution of similar or identical mutations in independent lineages, which is termed parallel evolution; and the evolution in independent lineages of alleles that are shared among populations, which I call collateral genetic evolution. Evidence for parallel and collateral evolution has been found in many taxa, and an emerging hypothesis is that they result from the fact that mutations in some genetic targets minimize pleiotropic effects while simultaneously maximizing adaptation. If this proves correct, then the molecular changes underlying adaptation might be more predictable than has been appreciated previously.}, }
@article {pmid24102722, year = {2014}, author = {Pereira, SG and Cardoso, O}, title = {Mobile genetic elements of Pseudomonas aeruginosa isolates from hydrotherapy facility and respiratory infections.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {20}, number = {3}, pages = {O203-6}, doi = {10.1111/1469-0691.12359}, pmid = {24102722}, issn = {1469-0691}, mesh = {Cross Infection/*microbiology ; *DNA Transposable Elements ; *DNA, Bacterial ; Genome, Bacterial ; Hospital Units ; Humans ; Hydrotherapy/adverse effects ; Pseudomonas Infections/*microbiology ; Pseudomonas aeruginosa/classification/*genetics/isolation &amp; purification ; Respiratory Tract Infections/*microbiology ; }, abstract = {The content of mobile genetic elements in Pseudomonas aeruginosa isolates of a pristine natural mineral water system associated with healthcare was compared with clinical isolates from respiratory infections. One isolate, from the therapy pool circuit, presented a class 1 integron, with 100% similarity to a class 1 integron contained in plasmid p4800 of the Klebsiella pneumoniae Kp4800 strain, which is the first time it has been reported in P. aeruginosa. Class 1 integrons were found in 25.6% of the clinical isolates. PAGI1 orf3 was more prevalent in environmental isolates, while PAGI2 c105 and PAGI3 sg100 were more prevalent in clinical isolates. Plasmids were not observed in either population.}, }
@article {pmid24101916, year = {2013}, author = {Fish, JA and Chai, B and Wang, Q and Sun, Y and Brown, CT and Tiedje, JM and Cole, JR}, title = {FunGene: the functional gene pipeline and repository.}, journal = {Frontiers in microbiology}, volume = {4}, number = {}, pages = {291}, pmid = {24101916}, issn = {1664-302X}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; UH3 DK083993/DK/NIDDK NIH HHS/United States ; }, abstract = {Ribosomal RNA genes have become the standard molecular markers for microbial community analysis for good reasons, including universal occurrence in cellular organisms, availability of large databases, and ease of rRNA gene region amplification and analysis. As markers, however, rRNA genes have some significant limitations. The rRNA genes are often present in multiple copies, unlike most protein-coding genes. The slow rate of change in rRNA genes means that multiple species sometimes share identical 16S rRNA gene sequences, while many more species share identical sequences in the short 16S rRNA regions commonly analyzed. In addition, the genes involved in many important processes are not distributed in a phylogenetically coherent manner, potentially due to gene loss or horizontal gene transfer. While rRNA genes remain the most commonly used markers, key genes in ecologically important pathways, e.g., those involved in carbon and nitrogen cycling, can provide important insights into community composition and function not obtainable through rRNA analysis. However, working with ecofunctional gene data requires some tools beyond those required for rRNA analysis. To address this, our Functional Gene Pipeline and Repository (FunGene; http://fungene.cme.msu.edu/) offers databases of many common ecofunctional genes and proteins, as well as integrated tools that allow researchers to browse these collections and choose subsets for further analysis, build phylogenetic trees, test primers and probes for coverage, and download aligned sequences. Additional FunGene tools are specialized to process coding gene amplicon data. For example, FrameBot produces frameshift-corrected protein and DNA sequences from raw reads while finding the most closely related protein reference sequence. These tools can help provide better insight into microbial communities by directly studying key genes involved in important ecological processes.}, }
@article {pmid24100224, year = {2013}, author = {Sampson, TR and Weiss, DS}, title = {Degeneration of a CRISPR/Cas system and its regulatory target during the evolution of a pathogen.}, journal = {RNA biology}, volume = {10}, number = {10}, pages = {1618-1622}, pmid = {24100224}, issn = {1555-8584}, support = {R56 AI087673/AI/NIAID NIH HHS/United States ; U54 AI057157/AI/NIAID NIH HHS/United States ; U54-AI057157/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/genetics ; Base Sequence ; *Biological Evolution ; *CRISPR-Cas Systems ; Francisella/classification/genetics/*pathogenicity ; Francisella tularensis/*genetics/*pathogenicity ; Gene Transfer, Horizontal ; Lipoproteins/chemistry/genetics ; Sequence Alignment ; Virulence ; }, abstract = {CRISPR/Cas systems are bacterial RNA-guided endonuclease machineries that target foreign nucleic acids. Recently, we demonstrated that the Cas protein Cas9 controls gene expression and virulence in Francisella novicida by altering the stability of the mRNA for an immunostimulatory bacterial lipoprotein (BLP). Genomic analyses, however, revealed that Francisella species with increased virulence harbor degenerated CRISPR/Cas systems. We hypothesize that CRISPR/Cas degeneration removed a barrier against genome alterations, which resulted in enhanced virulence. Importantly, the BLP locus was also lost; likely a necessary adaptation in the absence of Cas9-mediated repression. CRISPR/Cas systems likely play regulatory roles in numerous bacteria, and these data suggest additional genomic changes may be required to maintain fitness after CRISPR/Cas loss in such bacteria, having important evolutionary implications.}, }
@article {pmid24100138, year = {2013}, author = {Reid, EL and Weynberg, KD and Love, J and Isupov, MN and Littlechild, JA and Wilson, WH and Kelly, SL and Lamb, DC and Allen, MJ}, title = {Functional and structural characterisation of a viral cytochrome b5.}, journal = {FEBS letters}, volume = {587}, number = {22}, pages = {3633-3639}, doi = {10.1016/j.febslet.2013.09.035}, pmid = {24100138}, issn = {1873-3468}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; //Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Sequence ; Chlorophyta/virology ; Conserved Sequence ; Crystallography, X-Ray ; Cytochromes b5/*chemistry ; Models, Molecular ; Molecular Sequence Data ; Oxidation-Reduction ; *Plant Viruses ; Protein Structure, Tertiary ; Surface Properties ; Viral Proteins/*chemistry ; }, abstract = {Cytochrome b5 is a ubiquitous electron transport protein. The sequenced viral OtV-2 genome, which infects Ostreococcus tauri, was predicted to encode a putative cytochrome b5 enzyme. Using purified OtV-2 cytochrome b5 we confirm this protein has identical spectral properties to purified human cytochrome b5 and additionally that the viral enzyme can substitute for yeast cytochrome b5 in yeast cytochrome P450 51 mediated sterol 14α-demethylation. The crystal structure of the OtV-2 cytochrome b5 enzyme reveals a single domain, comprising four β sheets, four α helices and a haem moiety, which is similar to that found in larger eukaryotic cytochrome proteins. As a product of a horizontal gene transfer event involving a subdomain of the host fumarate reductase-like protein, OtV-2 cytochrome b5 appears to have diverged in function and is likely to have evolved an entirely new role for the virus during infection. Indeed, lacking a hydrophobic C-terminal anchor, OtV-2 encodes the first cytosolic cytochrome b5 characterised. The lack of requirement for membrane attachment (in contrast to all other microsomal cytochrome b5s) may be a reflection of the small size of the host cell, further emphasizes the unique nature of this virus gene product and draws attention to the potential importance of cytochrome b5 metabolic activity at the extremes of cellular scale.}, }
@article {pmid24098496, year = {2013}, author = {Fonseca, LS and da Silva, JB and Milanez, JS and Monteiro-Vitorello, CB and Momo, L and de Morais, ZM and Vasconcellos, SA and Marques, MV and Ho, PL and da Costa, RM}, title = {Leptospira interrogans serovar copenhageni harbors two lexA genes involved in SOS response.}, journal = {PloS one}, volume = {8}, number = {10}, pages = {e76419}, pmid = {24098496}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/*genetics/*metabolism ; Binding Sites ; DNA Repair/genetics ; *Gene Dosage ; Gene Expression Regulation, Bacterial/radiation effects ; Gene Order ; Genome, Bacterial ; Leptospira interrogans/classification/*genetics/*metabolism/radiation effects ; Molecular Sequence Data ; Nucleotide Motifs ; Open Reading Frames ; Phenotype ; Phylogeny ; Promoter Regions, Genetic ; Protein Binding ; *SOS Response, Genetics ; Sequence Alignment ; Serine Endopeptidases/chemistry/*genetics/*metabolism ; Ultraviolet Rays/adverse effects ; }, abstract = {Bacteria activate a regulatory network in response to the challenges imposed by DNA damage to genetic material, known as the SOS response. This system is regulated by the RecA recombinase and by the transcriptional repressor lexA. Leptospira interrogans is a pathogen capable of surviving in the environment for weeks, being exposed to a great variety of stress agents and yet retaining its ability to infect the host. This study aims to investigate the behavior of L. interrogans serovar Copenhageni after the stress induced by DNA damage. We show that L. interrogans serovar Copenhageni genome contains two genes encoding putative LexA proteins (lexA1 and lexA2) one of them being potentially acquired by lateral gene transfer. Both genes are induced after DNA damage, but the steady state levels of both LexA proteins drop, probably due to auto-proteolytic activity triggered in this condition. In addition, seven other genes were up-regulated following UV-C irradiation, recA, recN, dinP, and four genes encoding hypothetical proteins. This set of genes is potentially regulated by LexA1, as it showed binding to their promoter regions. All these regions contain degenerated sequences in relation to the previously described SOS box, TTTGN 5CAAA. On the other hand, LexA2 was able to bind to the palindrome TTGTAN10TACAA, found in its own promoter region, but not in the others. Therefore, the L. interrogans serovar Copenhageni SOS regulon may be even more complex, as a result of LexA1 and LexA2 binding to divergent motifs. New possibilities for DNA damage response in Leptospira are expected, with potential influence in other biological responses such as virulence.}, }
@article {pmid24097899, year = {2013}, author = {Kreuzer, KN}, title = {DNA damage responses in prokaryotes: regulating gene expression, modulating growth patterns, and manipulating replication forks.}, journal = {Cold Spring Harbor perspectives in biology}, volume = {5}, number = {11}, pages = {a012674}, pmid = {24097899}, issn = {1943-0264}, support = {R01 GM066934/GM/NIGMS NIH HHS/United States ; R01 GM072089/GM/NIGMS NIH HHS/United States ; GM072089/GM/NIGMS NIH HHS/United States ; GM066934/GM/NIGMS NIH HHS/United States ; }, mesh = {Apoptosis ; Bacteria/*genetics ; Bacterial Proteins/metabolism ; Cell Survival ; *DNA Damage ; DNA Repair ; *DNA Replication ; Deinococcus/genetics/physiology ; Drug Resistance, Bacterial ; Escherichia coli/genetics/physiology ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Mycobacterium/genetics/physiology ; Rec A Recombinases/metabolism ; *SOS Response, Genetics ; Serine Endopeptidases/metabolism ; }, abstract = {Recent advances in the area of bacterial DNA damage responses are reviewed here. The SOS pathway is still the major paradigm of bacterial DNA damage response, and recent studies have clarified the mechanisms of SOS induction and key physiological roles of SOS including a very major role in genetic exchange and variation. When considering diverse bacteria, it is clear that SOS is not a uniform pathway with one purpose, but rather a platform that has evolved for differing functions in different bacteria. Relating in part to the SOS response, the field has uncovered multiple apparent cell-cycle checkpoints that assist cell survival after DNA damage and remarkable pathways that induce programmed cell death in bacteria. Bacterial DNA damage responses are also much broader than SOS, and several important examples of LexA-independent regulation will be reviewed. Finally, some recent advances that relate to the replication and repair of damaged DNA will be summarized.}, }
@article {pmid24094336, year = {2013}, author = {Chaverri, P and Samuels, GJ}, title = {Evolution of habitat preference and nutrition mode in a cosmopolitan fungal genus with evidence of interkingdom host jumps and major shifts in ecology.}, journal = {Evolution; international journal of organic evolution}, volume = {67}, number = {10}, pages = {2823-2837}, doi = {10.1111/evo.12169}, pmid = {24094336}, issn = {1558-5646}, mesh = {Base Sequence ; Bayes Theorem ; *Biological Evolution ; DNA Primers/genetics ; *Ecosystem ; Fruiting Bodies, Fungal/cytology/physiology ; *Genetic Speciation ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; Nutritional Physiological Phenomena/*physiology ; Phylogeny ; Selection, Genetic ; Sequence Analysis, DNA ; *Soil Microbiology ; *Symbiosis ; Trichoderma/genetics/*physiology ; }, abstract = {Host jumps by microbial symbionts are often associated with bursts of species diversification driven by the exploitation of new adaptive zones. The objective of this study was to infer the evolution of habitat preference (decaying plants, soil, living fungi, and living plants), and nutrition mode (saprotrophy and mycoparasitism) in the fungal genus Trichoderma to elucidate possible interkingdom host jumps and shifts in ecology. Host and ecological role shifts were inferred by phylogenetic analyses and ancestral character reconstructions. The results support several interkingdom host jumps and also show that the preference for a particular habitat was gained or lost multiple times. Diversification analysis revealed that mycoparasitism is associated with accelerated speciation rates, which then suggests that this trait may be linked to the high number of species in Trichoderma. In this study it was also possible to infer the cryptic roles that endophytes or soil inhabitants play in their hosts by evaluating their closest relatives and determining their most recent ancestors. Findings from this study may have implications for understanding certain evolutionary processes such as species radiations in some hyperdiverse groups of fungi, and for more applied fields such as the discovery and development of novel biological control strategies.}, }
@article {pmid24086164, year = {2013}, author = {Jiang, W and Maniv, I and Arain, F and Wang, Y and Levin, BR and Marraffini, LA}, title = {Dealing with the evolutionary downside of CRISPR immunity: bacteria and beneficial plasmids.}, journal = {PLoS genetics}, volume = {9}, number = {9}, pages = {e1003844}, pmid = {24086164}, issn = {1553-7404}, support = {DP2 AI104556/AI/NIAID NIH HHS/United States ; R01 GM091875/GM/NIGMS NIH HHS/United States ; 1DP2AI104556-01/AI/NIAID NIH HHS/United States ; GM 091875/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteriophages/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/*genetics/immunology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Fitness ; Host-Parasite Interactions/genetics ; Immunity/*genetics ; Plasmids/genetics/physiology ; Sequence Deletion/genetics ; Staphylococcus epidermidis/*genetics/immunology ; }, abstract = {The immune systems that protect organisms from infectious agents invariably have a cost for the host. In bacteria and archaea CRISPR-Cas loci can serve as adaptive immune systems that protect these microbes from infectiously transmitted DNAs. When those DNAs are borne by lytic viruses (phages), this protection can provide a considerable advantage. CRISPR-Cas immunity can also prevent cells from acquiring plasmids and free DNA bearing genes that increase their fitness. Here, we use a combination of experiments and mathematical-computer simulation models to explore this downside of CRISPR-Cas immunity and its implications for the maintenance of CRISPR-Cas loci in microbial populations. We analyzed the conjugational transfer of the staphylococcal plasmid pG0400 into Staphylococcus epidermidis RP62a recipients that bear a CRISPR-Cas locus targeting this plasmid. Contrary to what is anticipated for lytic phages, which evade CRISPR by mutations in the target region, the evasion of CRISPR immunity by plasmids occurs at the level of the host through loss of functional CRISPR-Cas immunity. The results of our experiments and models indicate that more than 10(-4) of the cells in CRISPR-Cas positive populations are defective or deleted for the CRISPR-Cas region and thereby able to receive and carry the plasmid. Most intriguingly, the loss of CRISPR function even by large deletions can have little or no fitness cost in vitro. These theoretical and experimental results can account for the considerable variation in the existence, number and function of CRISPR-Cas loci within and between bacterial species. We postulate that as a consequence of the opposing positive and negative selection for immunity, CRISPR-Cas systems are in a continuous state of flux. They are lost when they bear immunity to laterally transferred beneficial genes, re-acquired by horizontal gene transfer, and ascend in environments where phage are a major source of mortality.}, }
@article {pmid24086118, year = {2013}, author = {Smith, SA and Brown, JW and Hinchliff, CE}, title = {Analyzing and synthesizing phylogenies using tree alignment graphs.}, journal = {PLoS computational biology}, volume = {9}, number = {9}, pages = {e1003223}, pmid = {24086118}, issn = {1553-7358}, mesh = {*Phylogeny ; *Sequence Homology, Nucleic Acid ; }, abstract = {Phylogenetic trees are used to analyze and visualize evolution. However, trees can be imperfect datatypes when summarizing multiple trees. This is especially problematic when accommodating for biological phenomena such as horizontal gene transfer, incomplete lineage sorting, and hybridization, as well as topological conflict between datasets. Additionally, researchers may want to combine information from sets of trees that have partially overlapping taxon sets. To address the problem of analyzing sets of trees with conflicting relationships and partially overlapping taxon sets, we introduce methods for aligning, synthesizing and analyzing rooted phylogenetic trees within a graph, called a tree alignment graph (TAG). The TAG can be queried and analyzed to explore uncertainty and conflict. It can also be synthesized to construct trees, presenting an alternative to supertrees approaches. We demonstrate these methods with two empirical datasets. In order to explore uncertainty, we constructed a TAG of the bootstrap trees from the Angiosperm Tree of Life project. Analysis of the resulting graph demonstrates that areas of the dataset that are unresolved in majority-rule consensus tree analyses can be understood in more detail within the context of a graph structure, using measures incorporating node degree and adjacency support. As an exercise in synthesis (i.e., summarization of a TAG constructed from the alignment trees), we also construct a TAG consisting of the taxonomy and source trees from a recent comprehensive bird study. We synthesized this graph into a tree that can be reconstructed in a repeatable fashion and where the underlying source information can be updated. The methods presented here are tractable for large scale analyses and serve as a basis for an alternative to consensus tree and supertree methods. Furthermore, the exploration of these graphs can expose structures and patterns within the dataset that are otherwise difficult to observe.}, }
@article {pmid24085835, year = {2013}, author = {Wagner, MA and Bischof, K and Kati, D and Koraimann, G}, title = {Silencing and activating type IV secretion genes of the F-like conjugative resistance plasmid R1.}, journal = {Microbiology (Reading, England)}, volume = {159}, number = {Pt 12}, pages = {2481-2491}, doi = {10.1099/mic.0.071738-0}, pmid = {24085835}, issn = {1465-2080}, mesh = {Bacterial Outer Membrane Proteins/metabolism ; Bacterial Proteins/metabolism ; Bacterial Secretion Systems/*genetics ; DNA-Binding Proteins/metabolism ; *Drug Resistance, Bacterial ; *F Factor ; *Gene Silencing ; Gene Transfer, Horizontal ; Promoter Regions, Genetic ; *R Factors ; Salmonella/*genetics ; *Transcriptional Activation ; }, abstract = {Expression of DNA transfer (tra) genes of F-type conjugative plasmids is required for the assembly of a functional type IV secretion machinery and subsequent plasmid DNA transfer from donor to recipient cells. Transcription of tra genes depends on the activation of a single promoter, designated PY, by the plasmid encoded TraJ protein. We here determine plasmid specificity of TraJ proteins from various subgroups of F-like plasmids and find that plasmid R1 conjugation and PY promoter activation can be achieved only by its cognate activator and by TraJ of the Salmonella plasmid pSLT and not by F or R100 TraJ proteins. In addition, we characterize the PY promoter of plasmid R1. We show that TraJ binds to PY DNA in vivo and that H-NS acts as a silencer of the PY promoter. In the natural plasmid context, H-NS silences transfer gene expression and horizontal plasmid DNA transfer. In contrast to what was found for the F plasmid, lack of H-NS did not abolish the requirement for ArcA and TraJ to reach full tra gene expression and DNA transfer activity. We propose that, besides a passive de-silencing activity, both ArcA and TraJ play a direct role in synergistically stimulating tra operon transcription and subsequent DNA transfer.}, }
@article {pmid24082106, year = {2013}, author = {DeMaere, MZ and Williams, TJ and Allen, MA and Brown, MV and Gibson, JA and Rich, J and Lauro, FM and Dyall-Smith, M and Davenport, KW and Woyke, T and Kyrpides, NC and Tringe, SG and Cavicchioli, R}, title = {High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {42}, pages = {16939-16944}, pmid = {24082106}, issn = {1091-6490}, mesh = {Antarctic Regions ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Archaeal/*physiology ; Halobacteriaceae/*genetics ; Lakes/*microbiology ; Metagenome ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; *Water Microbiology ; }, abstract = {Deep Lake in Antarctica is a globally isolated, hypersaline system that remains liquid at temperatures down to -20 °C. By analyzing metagenome data and genomes of four isolates we assessed genome variation and patterns of gene exchange to learn how the lake community evolved. The lake is completely and uniformly dominated by haloarchaea, comprising a hierarchically structured, low-complexity community that differs greatly to temperate and tropical hypersaline environments. The four Deep Lake isolates represent distinct genera (∼85% 16S rRNA gene similarity and ∼73% genome average nucleotide identity) with genomic characteristics indicative of niche adaptation, and collectively account for ∼72% of the cellular community. Network analysis revealed a remarkable level of intergenera gene exchange, including the sharing of long contiguous regions (up to 35 kb) of high identity (∼100%). Although the genomes of closely related Halobacterium, Haloquadratum, and Haloarcula (>90% average nucleotide identity) shared regions of high identity between species or strains, the four Deep Lake isolates were the only distantly related haloarchaea to share long high-identity regions. Moreover, the Deep Lake high-identity regions did not match to any other hypersaline environment metagenome data. The most abundant species, tADL, appears to play a central role in the exchange of insertion sequences, but not the exchange of high-identity regions. The genomic characteristics of the four haloarchaea are consistent with a lake ecosystem that sustains a high level of intergenera gene exchange while selecting for ecotypes that maintain sympatric speciation. The peculiarities of this polar system restrict which species can grow and provide a tempo and mode for accentuating gene exchange.}, }
@article {pmid24080312, year = {2013}, author = {Tazzyman, SJ and Bonhoeffer, S}, title = {Fixation probability of mobile genetic elements such as plasmids.}, journal = {Theoretical population biology}, volume = {90}, number = {}, pages = {49-55}, doi = {10.1016/j.tpb.2013.09.012}, pmid = {24080312}, issn = {1096-0325}, mesh = {Bacteria/genetics ; Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences ; Models, Theoretical ; *Plasmids ; *Probability ; }, abstract = {Mobile genetic elements such as plasmids are increasingly becoming thought of as evolutionarily important. Being horizontally transmissible is generally assumed to be beneficial for a gene. Using several simple modelling approaches we show that in fact being horizontally transferable is just as important for fixation as being beneficial to the host, in line with other results. We find fixation probability is approximately 2(s+β), where s is the increased (vertical) fitness provided by the gene, and β the rate of horizontal transfer when rare. This result comes about because when the gene is rare, almost all individuals in the population are possible recipients of horizontal transfer. The ability to horizontally transfer could thus cause a deleterious gene to become fixed in a population even without hitchhiking. Our findings provide further evidence for the importance and ubiquity of mobile genetic elements, particularly in microorganisms.}, }
@article {pmid24078614, year = {2013}, author = {Waters, JL and Wang, GR and Salyers, AA}, title = {Tetracycline-related transcriptional regulation of the CTnDOT mobilization region.}, journal = {Journal of bacteriology}, volume = {195}, number = {24}, pages = {5431-5438}, pmid = {24078614}, issn = {1098-5530}, support = {R01 AI022383/AI/NIAID NIH HHS/United States ; R56 AI022383/AI/NIAID NIH HHS/United States ; AI 22383/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteroides/*drug effects/genetics ; Conjugation, Genetic/*drug effects ; DNA Transposable Elements/*drug effects ; Gene Expression Regulation, Bacterial/*drug effects ; Gene Transfer, Horizontal/*drug effects ; Tetracycline/*metabolism ; Transcription, Genetic/*drug effects ; }, abstract = {CTnDOT is a 65-kb conjugative transposon (CTn) in Bacteroides spp. that confers resistance to the antibiotics erythromycin and tetracycline (Tc). Conjugative transfer of CTnDOT is regulated upon exposure of cells to Tc. In the absence of Tc, no transfer is detectable; however, a cascade of regulatory events results in the conjugative transfer of CTnDOT upon Tc induction. Previous studies addressing regulation of CTnDOT conjugative transfer focused primarily on the 13-kb transfer (tra) operon, which encodes the proteins required for assembly of the mating apparatus. We report here that the mob operon that encodes the relaxase and coupling proteins required for mobilization of CTnDOT are regulated at the transcriptional level upon Tc induction. The Xis2d and Exc excision proteins are required for the upregulation of mob transcription upon Tc induction, and yet a deletion of xis2c has no effect. We also show preliminary evidence suggesting that the integrase, IntDOT, may play a regulatory role, as pLYL72 transfer is not detectable when intDOT is provided in trans.}, }
@article {pmid24076502, year = {2014}, author = {Kim, S and Yun, Z and Ha, UH and Lee, S and Park, H and Kwon, EE and Cho, Y and Choung, S and Oh, J and Medriano, CA and Chandran, K}, title = {Transfer of antibiotic resistance plasmids in pure and activated sludge cultures in the presence of environmentally representative micro-contaminant concentrations.}, journal = {The Science of the total environment}, volume = {468-469}, number = {}, pages = {813-820}, doi = {10.1016/j.scitotenv.2013.08.100}, pmid = {24076502}, issn = {1879-1026}, mesh = {Analysis of Variance ; Anti-Bacterial Agents/*analysis ; Drug Resistance, Bacterial/*genetics ; Escherichia coli ; Gene Transfer, Horizontal/*genetics ; Plasmids/*genetics ; Pseudomonas aeruginosa ; Sewage/*microbiology ; Sulfamethoxazole ; Tetracycline ; }, abstract = {The presence of antibiotics in the natural environment has been a growing issue. This presence could also account for the influence that affects microorganisms in such a way that they develop resistance against these antibiotics. The aim of this study was to evaluate whether the antibiotic resistant gene (ARG) plasmid transfer can be facilitated by the impact of 1) environmentally representative micro-contaminant concentrations in ppb (part per billion) levels and 2) donor-recipient microbial complexity (pure vs. mixed). For this purpose, the multidrug resistant plasmid, pB10, and Escherichia coli DH5α were used as a model plasmid and a model donor, respectively. Based on conjugation experiments with pure (Pseudomonas aeruginosa PAKexoT) and mixed (activated sludge) cultures as recipients, increased relative plasmid transfer frequencies were observed at ppb (μg/L) levels of tetracycline and sulfamethoxazole micro-contaminant exposure. When sludge, a more complex community, was used as a recipient, the increases of the plasmid transfer rate were always statistically significant but not always in P. aeruginosa. The low concentration (10 ppb) of tetracycline exposure led to the pB10 transfer to enteric bacteria, which are clinically important pathogens.}, }
@article {pmid24076419, year = {2013}, author = {Lovejoy, DA and de Lannoy, L}, title = {Evolution and phylogeny of the corticotropin-releasing factor (CRF) family of peptides: expansion and specialization in the vertebrates.}, journal = {Journal of chemical neuroanatomy}, volume = {54}, number = {}, pages = {50-56}, doi = {10.1016/j.jchemneu.2013.09.006}, pmid = {24076419}, issn = {1873-6300}, mesh = {Animals ; Corticotropin-Releasing Hormone/*genetics ; *Evolution, Molecular ; Humans ; Phylogeny ; Vertebrates ; }, abstract = {New sequence data on CRF family members from a number of genomes has led to the modification of our understanding of CRF evolution in the Metazoa. The corticotropin-releasing factor (CRF) family of peptides include four paralogous lineages in jawed vertebrates; CRF, urotensin-I/urocortin/sauvagine, urocortin 2 (Ucn2) and urocortin 3 (Ucn3). CRF and the urotensin-I/urocortin/sauvagine group represent a gene duplication from one lineage, whereas Ucns 2 and 3 are the result of a gene duplication in the other paralogous lineage. Both paralogous lineages are the result of a gene duplication from a single ancestral peptide that occurred after the divergence of the tunicates from the ancestor that led to the evolution of chordates and vertebrates. The presence of a single CRF-like peptide in tunicates and insects suggests that a single CRF-like ancestor was present before the separation of deuterostomes and protostomes. Currently there is no strong evidence that indicates that CRF-like peptides were present in metazoan taxa that evolved before this time although the structural similarity between some CRF peptides in insects, tunicates and vertebrates with the calcitonin family of peptides hints that prior to the formation of deuterostomes and protostomes the ancestral peptide possessed both CRF and calcitonin-like structural attributes. Here, we show evidences of conservation of CRF-like function dating back to early prokaryotes. This ancestral CRF-calcitonin-like peptide may have initially resulted from a horizontal gene transfer event from prokaryotes to a protistan species that later gave rise to the metazoans.}, }
@article {pmid24074349, year = {2013}, author = {Song, Y and Yu, P and Li, B and Pan, Y and Zhang, X and Cong, J and Zhao, Y and Wang, H and Chen, L}, title = {The mosaic accessory gene structures of the SXT/R391-like integrative and conjugative elements derived from Vibrio spp. isolated from aquatic products and environment in the Yangtze River Estuary, China.}, journal = {BMC microbiology}, volume = {13}, number = {}, pages = {214}, pmid = {24074349}, issn = {1471-2180}, mesh = {Anti-Bacterial Agents/pharmacology ; China ; Cluster Analysis ; Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; Drug Resistance, Bacterial ; *Environmental Microbiology ; Estuaries ; *Food Microbiology ; *Gene Order ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genetic Variation ; *Interspersed Repetitive Sequences ; Phylogeny ; Rivers ; Sequence Analysis, DNA ; Vibrio/*genetics/isolation &amp; purification ; }, abstract = {BACKGROUND: The emergence, resurgence and spread of human food-borne pathogenic Vibrios are one of the major contributors to disease burden and mortality particularly in developing countries with disputable sanitary conditions. Previous research on pathogenic Vibrio cholerae and Vibrio parahaemolitycus derived from clinical samples has proposed links between acquisition of virulence and multiple drug resistance traits and intercellular transmissibility of mobile genetic elements in the environment. To date, very few information is available on environmental Vibrio isolates. In this study, we characterized eleven Vibrio strains bearing the SXT/R391-like integrative and conjugative elements (ICEs) derived from aquatic products and environment in the Yangtze River Estuary, China.<br><br>RESULTS: The eleven Vibrio strains were isolated in 2010 to 2011, and taxonomically identified, which included six Vibrio cholerae, three Vibrio parahaemolyticus, one Vibrio alginolyticus and one Vibrio natriegens. Most of the strains displayed strong resistance phenotypes to ampicillin, mercury and chromium. The majority of their ICEs, which belong to S and R exclusion system groups, contain ICEs-chromosome junction sequences and highly conserved core-genes required for ICE transfer. However, comparative sequence analysis uncovered interesting diversity in their mosaic accessory gene structures, which carry many novel genes that have not been described in any known ICEs to date. In addition, antibiotic resistance was transmitted by ICEVchChn6 and ICEVpaChn1 from V. cholerae, V. parahaemolyticus to E. coli MG1655 via conjugation, respectively. Our data also revealed that the ICEs characterized in this study are phylogenetically distant from most of the SXT/R391 ICEs reported previously, which may represent a novel cluster likely shaped by the ecological environment in the Yangtze River Estuary, China.<br><br>CONCLUSIONS: This study constitutes the first investigation of ICEs-positive Vibrio spp. in the Yangze River Estuary, China. The newly identified ICEs were characterized with mosaic accessory gene structures and many novel genes. The results demonstrated self-transmissibility of antibiotic resistance mediated by two of the ICEs from V. cholerae, V. parahaemolyticus to E. coli via conjugation, respectively. Our results also revealed that the ICEs examined in this study may represent a novel cluster in the SXT/R391 family.}, }
@article {pmid24071635, year = {2014}, author = {Wang, FH and Qiao, M and Lv, ZE and Guo, GX and Jia, Y and Su, YH and Zhu, YG}, title = {Impact of reclaimed water irrigation on antibiotic resistance in public parks, Beijing, China.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {184}, number = {}, pages = {247-253}, doi = {10.1016/j.envpol.2013.08.038}, pmid = {24071635}, issn = {1873-6424}, mesh = {*Agricultural Irrigation ; Anti-Bacterial Agents/*analysis ; Bacteria/drug effects/genetics/pathogenicity ; China ; Drug Resistance, Microbial/*genetics ; Environmental Monitoring ; Genes, Bacterial ; Polymerase Chain Reaction ; Soil/*chemistry ; Soil Pollutants/*analysis ; Tandem Mass Spectrometry ; Tetracyclines ; Waste Disposal, Fluid ; Water Pollutants, Chemical/*analysis ; }, abstract = {The abundance and distribution of antibiotics and antibiotic resistance genes (ARGs) in soils from six parks using reclaimed water in Beijing, China, were characterized. Three classes of commonly used antibiotics (tetracycles, quinolones, and sulfonamides) were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The highest concentrations of tetracyclines and quinolones were 145.2 μg kg(-1) and 79.2 μg kg(-1), respectively. Detected tetG, tetW, sulI, and sulII genes were quantified by quantitative PCR. ARGs exhibited various abundances for different park soils. The integrase gene (intI1) as an indicator of horizontal gene transfer potential was also detected in high abundance, and had significant positive correlation with tetG, sulI, and sulII genes, suggesting that intI1 may be involved in ARGs dissemination. Both sulII and intI1 clones had high homology with some classes of pathogenic bacteria, such as Klebsiella oxytoca, Acinetobacter baumannii, Shigella flexneri, which could trigger potential public health concern.}, }
@article {pmid24067113, year = {2013}, author = {Hester, SE and Park, J and Goodfield, LL and Feaga, HA and Preston, A and Harvill, ET}, title = {Horizontally acquired divergent O-antigen contributes to escape from cross-immunity in the classical bordetellae.}, journal = {BMC evolutionary biology}, volume = {13}, number = {}, pages = {209}, pmid = {24067113}, issn = {1471-2148}, support = {R01 AI053075/AI/NIAID NIH HHS/United States ; R01 GM083113/GM/NIGMS NIH HHS/United States ; GM083113/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bordetella/*genetics/immunology ; Bordetella Infections/immunology/microbiology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genetic Variation ; Mice ; Mice, Inbred C57BL ; O Antigens/*genetics/immunology ; Phylogeny ; Recombination, Genetic ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT) allows for rapid spread of genetic material between species, increasing genetic and phenotypic diversity. Although HGT contributes to adaptation and is widespread in many bacteria, others show little HGT. This study builds on previous work to analyze the evolutionary mechanisms contributing to variation within the locus encoding a prominent antigen of the classical bordetellae.<br><br>RESULTS: We observed amongst classical bordetellae discrete regions of the lipopolysaccharide O-antigen locus with higher sequence diversity than the genome average. Regions of this locus had less than 50% sequence similarity, low dN/dS ratios and lower GC content compared to the genome average. Additionally, phylogenetic tree topologies based on genome-wide SNPs were incongruent with those based on genes within these variable regions, suggesting portions of the O-antigen locus may have been horizontally transferred. Furthermore, several predicted recombination breakpoints correspond with the ends of these variable regions. To examine the evolutionary forces that might have selected for this rare example of HGT in bordetellae, we compared in vitro and in vivo phenotypes associated with different O-antigen types. Antibodies against O1- and O2-serotypes were poorly cross-reactive, and did not efficiently kill or mediate clearance of alternative O-type bacteria, while a distinct and poorly immunogenic O-antigen offered no protection against colonization.<br><br>CONCLUSIONS: This study suggests that O-antigen variation was introduced to the classical bordetellae via HGT through recombination. Additionally, genetic variation may be maintained within the O-antigen locus because it can provide escape from immunity to different O-antigen types, potentially allowing for the circulation of different Bordetella strains within the same host population.}, }
@article {pmid24065973, year = {2013}, author = {Qiu, H and Yoon, HS and Bhattacharya, D}, title = {Algal endosymbionts as vectors of horizontal gene transfer in photosynthetic eukaryotes.}, journal = {Frontiers in plant science}, volume = {4}, number = {}, pages = {366}, pmid = {24065973}, issn = {1664-462X}, abstract = {Photosynthesis in eukaryotes occurs in the plastid, an organelle that is derived from a single cyanobacterial primary endosymbiosis in the common ancestor of the supergroup Plantae (or Archaeplastida) that includes green, red, and glaucophyte algae and plants. However a variety of other phytoplankton such as the chlorophyll c-containing diatoms, dinoflagellates, and haptophytes contain a red alga-derived plastid that traces its origin to secondary or tertiary (eukaryote engulfs eukaryote) endosymbiosis. The hypothesis of Plantae monophyly has only recently been substantiated, however the extent and role of endosymbiotic and horizontal gene transfer (EGT and HGT) in algal genome evolution still remain to be fully understood. What is becoming clear from analysis of complete genome data is that algal gene complements can no longer be considered essentially eukaryotic in provenance; i.e., with the expected addition of several hundred cyanobacterial genes derived from EGT and a similar number derived from the mitochondrial ancestor. For example, we now know that foreign cells such as Chlamydiae and other prokaryotes have made significant contributions to plastid functions in Plantae. Perhaps more surprising is the recent finding of extensive bacterium-derived HGT in the nuclear genome of the unicellular red alga Porphyridium purpureum that does not relate to plastid functions. These non-endosymbiont gene transfers not only shaped the evolutionary history of Plantae but also were propagated via secondary endosymbiosis to a multitude of other phytoplankton. Here we discuss the idea that Plantae (in particular red algae) are one of the major players in eukaryote genome evolution by virtue of their ability to act as "sinks" and "sources" of foreign genes through HGT and endosymbiosis, respectively. This hypothesis recognizes the often under-appreciated Rhodophyta as major sources of genetic novelty among photosynthetic eukaryotes.}, }
@article {pmid24064419, year = {2013}, author = {Haubold, B and Krause, L and Horn, T and Pfaffelhuber, P}, title = {An alignment-free test for recombination.}, journal = {Bioinformatics (Oxford, England)}, volume = {29}, number = {24}, pages = {3121-3127}, pmid = {24064419}, issn = {1367-4811}, mesh = {*Algorithms ; *Computational Biology ; Computer Simulation ; Escherichia coli/genetics ; *Genome, Bacterial ; Phylogeny ; *Recombination, Genetic ; Sequence Alignment/*methods ; }, abstract = {MOTIVATION: Why recombination? is one of the central questions in biology. This has led to a host of methods for quantifying recombination from sequence data. These methods are usually based on aligned DNA sequences. Here, we propose an efficient alignment-free alternative.<br><br>RESULTS: Our method is based on the distribution of match lengths, which we look up using enhanced suffix arrays. By eliminating the alignment step, the test becomes fast enough for application to whole bacterial genomes. Using simulations we show that our test has similar power as established tests when applied to long pairs of sequences. When applied to 58 genomes of Escherichia coli, we pick up the strongest recombination signal from a 125 kb horizontal gene transfer engineered 20 years ago.<br><br>We have implemented our method in the command-line program rush. Its C sources and documentation are available under the GNU General Public License from http://guanine.evolbio.mpg.de/rush/.}, }
@article {pmid24062636, year = {2013}, author = {Chen, Y and Xu, M and De Almeida, R and Lovejoy, DA}, title = {Teneurin C-terminal associated peptides (TCAP): modulators of corticotropin-releasing factor (CRF) physiology and behavior.}, journal = {Frontiers in neuroscience}, volume = {7}, number = {}, pages = {166}, pmid = {24062636}, issn = {1662-4548}, abstract = {The existence of the teneurin C-terminal associated peptides (TCAP) was reported in 2004 after screening a rainbow trout hypothalamic cDNA for corticotropin-releasing factor (CRF)-related homologs. In vertebrates, there are four TCAP paralogs, where each peptide is associated with a teneurin transmembrane protein. The TCAPs are 40 or 41 amino acids in length and possess less than 20% residue identity with the CRF family of paralogs. Orthologs of TCAP are found in all metazoans with the possible exception of poriferans and cnidarians. Recent evidence indicates that TCAP and the teneurins may have been introduced into the Metazoa via horizontal gene transfer from prokaryotes into a basal protistan. Thus, the origin of the TCAPs likely predated that of the CRF family. In the mammalian brain, TCAP-1 is transcribed independently from teneurin-1. Moreover, TCAP-1 acts on neurons by a CRF-receptor independent signal transduction pathway to regulate cellular cytoskeletal function to stimulate cell activity. Administration of synthetic TCAP-1 to rodents inhibits a number of CRF- and stress-associated behaviors via a hypothalamic-pituitary-adrenal (HPA) axis-independent mechanism.}, }
@article {pmid24060120, year = {2013}, author = {Solonenko, SA and Sullivan, MB}, title = {Preparation of metagenomic libraries from naturally occurring marine viruses.}, journal = {Methods in enzymology}, volume = {531}, number = {}, pages = {143-165}, doi = {10.1016/B978-0-12-407863-5.00008-3}, pmid = {24060120}, issn = {1557-7988}, mesh = {Aquatic Organisms/*virology ; Bacteriophages/genetics ; DNA, Single-Stranded ; *Gene Library ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Viruses/genetics ; }, abstract = {Microbes are now well recognized as major drivers of the biogeochemical cycling that fuels the Earth, and their viruses (phages) are known to be abundant and important in microbial mortality, horizontal gene transfer, and modulating microbial metabolic output. Investigation of environmental phages has been frustrated by an inability to culture the vast majority of naturally occurring diversity coupled with the lack of robust, quantitative, culture-independent methods for studying this uncultured majority. However, for double-stranded DNA phages, a quantitative viral metagenomic sample-to-sequence workflow now exists. Here, we review these advances with special emphasis on the technical details of preparing DNA sequencing libraries for metagenomic sequencing from environmentally relevant low-input DNA samples. Library preparation steps broadly involve manipulating the sample DNA by fragmentation, end repair and adaptor ligation, size fractionation, and amplification. One critical area of future research and development is parallel advances for alternate nucleic acid types such as single-stranded DNA and RNA viruses that are also abundant in nature. Combinations of recent advances in fragmentation (e.g., acoustic shearing and tagmentation), ligation reactions (adaptor-to-template ratio reference table availability), size fractionation (non-gel-sizing), and amplification (linear amplification for deep sequencing and linker amplification protocols) enhance our ability to generate quantitatively representative metagenomic datasets from low-input DNA samples. Such datasets are already providing new insights into the role of viruses in marine systems and will continue to do so as new environments are explored and synergies and paradigms emerge from large-scale comparative analyses.}, }
@article {pmid24058593, year = {2013}, author = {Moriguchi, K and Yamamoto, S and Tanaka, K and Kurata, N and Suzuki, K}, title = {Trans-kingdom horizontal DNA transfer from bacteria to yeast is highly plastic due to natural polymorphisms in auxiliary nonessential recipient genes.}, journal = {PloS one}, volume = {8}, number = {9}, pages = {e74590}, pmid = {24058593}, issn = {1932-6203}, mesh = {Conjugation, Genetic/genetics ; DNA, Bacterial/genetics ; Escherichia coli/*genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/*genetics ; Genetic Complementation Test ; Genetic Loci/genetics ; Genetic Testing ; Mitochondria/metabolism ; Models, Genetic ; Mutation/genetics ; Phenotype ; *Polymorphism, Genetic ; Saccharomyces cerevisiae/*genetics ; }, abstract = {With the rapid accumulation of genomic information from various eukaryotes in the last decade, genes proposed to have been derived from recent horizontal gene transfer (HGT) events have been reported even in non-phagotrophic unicellular and multicellular organisms, but the molecular pathways underlying HGT remain to be explained. The development of in vitro HGT detection systems, which permit the molecular and genetic analyses of donor and recipient organisms and quantify HGT, are helpful in order to gain insight into mechanisms that may contribute to contemporary HGT events or may have contributed to past HGT events. We applied a horizontal DNA transfer system model based on conjugal gene transfer called trans-kingdom conjugation (TKC) from the prokaryote Escherichia coli to the eukaryote Saccharomyces cerevisiae, and assessed whether and to what extent genetic variations in the eukaryotic recipient affect its receptivity to TKC. Strains from a collection of 4,823 knock-out mutants of S. cerevisiae MAT-α haploids were tested for their individual TKC receptivity. Two types of mutants, an ssd1 mutant and respiratory mutants, which are also found in experimental strains and in nature widely, were identified as highly receptive mutants. The TKC efficiency for spontaneously accrued petite (rho (-/0)) mutants of the functional allele (SSD1-V) strain showed increased receptivity. The TKC efficiency of the ssd1Δ mutant was 36% for bacterial conjugation, while that of the petite/ssd1Δ double mutants was even higher (220% in average) compared to bacterial conjugation. This increased TKC receptivity was also observed when other conjugal transfer systems were applied and the donor bacterium was changed to Agrobacterium tumefaciens. These results support the idea that the genomes of certain eukaryotes have been exposed to exogenous DNA more frequently and continuously than previously thought.}, }
@article {pmid24055388, year = {2013}, author = {Brown Kav, A and Benhar, I and Mizrahi, I}, title = {A method for purifying high quality and high yield plasmid DNA for metagenomic and deep sequencing approaches.}, journal = {Journal of microbiological methods}, volume = {95}, number = {2}, pages = {272-279}, doi = {10.1016/j.mimet.2013.09.008}, pmid = {24055388}, issn = {1872-8359}, mesh = {Animals ; Cattle ; DNA, Bacterial/genetics/*isolation &amp; purification ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/*methods ; Plasmids/genetics/*isolation &amp; purification ; Polymerase Chain Reaction ; Rumen/microbiology ; Sequence Analysis, DNA/methods ; }, abstract = {Deep sequencing techniques used in metagenomic approaches have greatly advanced the study of microbial communities in various environments. However, one microbial segment that has remained largely unexplored is the natural plasmids residing within microbial environments. Plasmids are perceived as mobile genetic elements that exist extra-chromosomally and occasionally carry accessory genes that confer an advantage to their host in its ecological niche. They are thus thought to play an important evolutionary role in microbial communities by laterally introducing genes and traits into microbial genomes. Despite their importance, technical obstacles still limit the metagenomic study of natural plasmids using deep sequencing techniques. These include low copy number of the plasmids and heterogeneity of microbes in environmental samples, reflected in the low abundance of each individual plasmid. Furthermore, the extracted plasmids usually contain remnants of chromosomal DNA that can potentially interfere with the analysis of unique plasmid traits. We have recently studied the rumen metagenomic plasmid population using a newly developed procedure that successfully overcomes these obstacles. This procedure enables extraction of pure plasmid DNA suited for deep sequencing studies. Here we present a detailed description and characterization of this procedure which could potentially allow the study of plasmids in other environmental niches.}, }
@article {pmid24053667, year = {2013}, author = {Nakamura, Y and Takano, T and Yasuike, M and Sakai, T and Matsuyama, T and Sano, M}, title = {Comparative genomics reveals that a fish pathogenic bacterium Edwardsiella tarda has acquired the locus of enterocyte effacement (LEE) through horizontal gene transfer.}, journal = {BMC genomics}, volume = {14}, number = {}, pages = {642}, pmid = {24053667}, issn = {1471-2164}, mesh = {Animals ; Bacterial Proteins/*genetics ; Cluster Analysis ; Computational Biology ; Edwardsiella tarda/classification/*genetics/pathogenicity ; Fishes/*microbiology ; Gene Order ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomic Islands/*genetics ; *Genomics ; Molecular Sequence Annotation ; Mutation ; Phylogeny ; Polymorphism, Single Nucleotide ; Reproducibility of Results ; Sequence Analysis, DNA ; Virulence/genetics ; }, abstract = {BACKGROUND: Edwardsiella tarda is an enterobacterium which causes edwardsiellosis, a fatal disease of cultured fishes such as red sea bream, eel, and flounder. Preventing the occurrence of E. tarda infection has thus been an important issue in aquaculture. E. tarda has been isolated from other animals and from many environments; however, the relationship between the genotype and evolutionary process of this pathogen is not fully understood. To clarify this relationship, we sequenced and compared the genomes of pathogenic and non-pathogenic E. tarda strains isolated from fish, human, and eel pond using next-generation sequencing technology.<br><br>RESULTS: Eight strains of E. tarda were sequenced with high accuracy (>99.9%) with coverages from 50- to 400-fold. The obtained reads were mapped to a public reference genome. By comparing single nucleotide and insertion/deletion polymorphisms, we found that an attenuated strain of E. tarda had a loss-of-function mutation in a gene related to the type III secretion system (T3SS), suggesting that this gene is involved in the virulence of E. tarda. A comprehensive gene comparison indicated that fish pathogenic strains possessed a type VI secretion system (T6SS) and pilus assembly genes in addition to the T3SS. Moreover, we found that an E. tarda strain isolated from red sea bream harbored two pathogenicity islands of T3SS and T6SS, which were absent in other strains. In particular, this T3SS was homologous to the locus of enterocyte effacement (LEE) in enteropathogenic and enterohemorrhagic Escherichia coli. Evolutionary analysis suggested that this locus, here named Et-LEE (E. tarda LEE), was introgressed into the E. tarda genome through horizontal transfer.<br><br>CONCLUSIONS: We found significant differences in the presence/absence of virulence-related genes among E. tarda strains, reflecting their evolutionary relationship. In particular, a single genotype previously proposed for fish-pathogenic strains may be further divided into two subgroups. Furthermore, the current study demonstrated, for the first time, that a fish pathogenic bacterium carried a LEE-like pathogenicity island which was previously reported only in zoonotic pathogenic enterobacteria. These findings will contribute to the exploration of strain-specific drug targets against E. tarda in aquafarms, while also shedding light on the evolution of pathogenesis in enterobacteria.}, }
@article {pmid24053607, year = {2013}, author = {Ioannidis, P and Johnston, KL and Riley, DR and Kumar, N and White, JR and Olarte, KT and Ott, S and Tallon, LJ and Foster, JM and Taylor, MJ and Dunning Hotopp, JC}, title = {Extensively duplicated and transcriptionally active recent lateral gene transfer from a bacterial Wolbachia endosymbiont to its host filarial nematode Brugia malayi.}, journal = {BMC genomics}, volume = {14}, number = {}, pages = {639}, pmid = {24053607}, issn = {1471-2164}, support = {DP2 OD007372/OD/NIH HHS/United States ; 1-DP2-OD007372/OD/NIH HHS/United States ; }, mesh = {Animals ; Brugia malayi/*genetics ; DNA, Bacterial/genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Genome, Helminth ; Open Reading Frames ; Sequence Analysis, DNA ; Wolbachia/*genetics ; }, abstract = {BACKGROUND: Lymphatic filariasis is a neglected tropical disease afflicting more than 120 million people, while another 1.3 billion people are at risk of infection. The nematode worm Brugia malayi is one of the causative agents of the disease and exists in a mutualistic symbiosis with Wolbachia bacteria. Since extensive lateral gene transfer occurs frequently between Wolbachia and its hosts, we sought to measure the extent of such LGT in B. malayi by whole genome sequencing of Wolbachia-depleted worms.<br><br>RESULTS: A considerable fraction (at least 115.4-kbp, or 10.6%) of the 1.08-Mbp Wolbachia wBm genome has been transferred to its nematode host and retains high levels of similarity, including 227 wBm genes and gene fragments. Complete open reading frames were transferred for 32 of these genes, meaning they have the potential to produce functional proteins. Moreover, four transfers have evidence of life stage-specific regulation of transcription at levels similar to other nematode transcripts, strengthening the possibility that they are functional.<br><br>CONCLUSIONS: There is extensive and ongoing transfer of Wolbachia DNA to the worm genome and some transfers are transcribed in a stage-specific manner at biologically relevant levels.}, }
@article {pmid24050390, year = {2013}, author = {Maldonado-Contreras, A and Mane, SP and Zhang, XS and Pericchi, L and Alarcón, T and Contreras, M and Linz, B and Blaser, MJ and Domínguez-Bello, MG}, title = {Phylogeographic evidence of cognate recognition site patterns and transformation efficiency differences in H. pylori: theory of strain dominance.}, journal = {BMC microbiology}, volume = {13}, number = {}, pages = {211}, pmid = {24050390}, issn = {1471-2180}, support = {R01GM63270/GM/NIGMS NIH HHS/United States ; }, mesh = {*DNA Restriction-Modification Enzymes ; Evolution, Molecular ; Gene Flow ; Gene Transfer, Horizontal ; Helicobacter Infections/*microbiology ; Helicobacter pylori/classification/*genetics/*pathogenicity ; Humans ; Latin America ; *Phylogeography ; Transformation, Bacterial ; }, abstract = {BACKGROUND: Helicobacter pylori has diverged in parallel to its human host, leading to distinct phylogeographic populations. Recent evidence suggests that in the current human mixing in Latin America, European H. pylori (hpEurope) are increasingly dominant at the expense of Amerindian haplotypes (hspAmerind). This phenomenon might occur via DNA recombination, modulated by restriction-modification systems (RMS), in which differences in cognate recognition sites (CRS) and in active methylases will determine direction and frequency of gene flow. We hypothesized that genomes from hspAmerind strains that evolved from a small founder population have lost CRS for RMS and active methylases, promoting hpEurope's DNA invasion. We determined the observed and expected frequencies of CRS for RMS in DNA from 7 H. pylori whole genomes and 110 multilocus sequences. We also measured the number of active methylases by resistance to in vitro digestion by 16 restriction enzymes of genomic DNA from 9 hpEurope and 9 hspAmerind strains, and determined the direction of DNA uptake in co-culture experiments of hspAmerind and hpEurope strains.<br><br>RESULTS: Most of the CRS were underrepresented with consistency between whole genomes and multilocus sequences. Although neither the frequency of CRS nor the number of active methylases differ among the bacterial populations (average 8.6 &#xb1; 2.6), hspAmerind strains had a restriction profile distinct from that in hpEurope strains, with 15 recognition sites accounting for the differences. Amerindians strains also exhibited higher transformation rates than European strains, and were more susceptible to be subverted by larger DNA hpEurope-fragments than vice versa.<br><br>CONCLUSIONS: The geographical variation in the pattern of CRS provides evidence for ancestral differences in RMS representation and function, and the transformation findings support the hypothesis of Europeanization of the Amerindian strains in Latin America via DNA recombination.}, }
@article {pmid24050177, year = {2013}, author = {Long, M and VanKuren, NW and Chen, S and Vibranovski, MD}, title = {New gene evolution: little did we know.}, journal = {Annual review of genetics}, volume = {47}, number = {}, pages = {307-333}, pmid = {24050177}, issn = {1545-2948}, support = {R01 GM100768/GM/NIGMS NIH HHS/United States ; T32 GM007197/GM/NIGMS NIH HHS/United States ; 1R01GM100768-01A1/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Brain/embryology ; Drosophila melanogaster/genetics ; *Evolution, Molecular ; Forecasting ; Gene Dosage ; Gene Duplication ; Gene Expression Regulation ; Gene Regulatory Networks ; Gene Transfer, Horizontal ; *Genes ; Genes, Insect ; Genes, Plant ; Genetic Structures ; Humans ; Mammals/genetics ; Models, Genetic ; Phenotype ; Phylogeny ; RNA, Untranslated/physiology ; Recombination, Genetic ; Selection, Genetic ; Sex Characteristics ; Transcription, Genetic ; }, abstract = {Genes are perpetually added to and deleted from genomes during evolution. Thus, it is important to understand how new genes are formed and how they evolve to be critical components of the genetic systems that determine the biological diversity of life. Two decades of effort have shed light on the process of new gene origination and have contributed to an emerging comprehensive picture of how new genes are added to genomes, ranging from the mechanisms that generate new gene structures to the presence of new genes in different organisms to the rates and patterns of new gene origination and the roles of new genes in phenotypic evolution. We review each of these aspects of new gene evolution, summarizing the main evidence for the origination and importance of new genes in evolution. We highlight findings showing that new genes rapidly change existing genetic systems that govern various molecular, cellular, and phenotypic functions.}, }
@article {pmid24048585, year = {2013}, author = {Swithers, KS and Soucy, SM and Lasek-Nesselquist, E and Lapierre, P and Gogarten, JP}, title = {Distribution and evolution of the mobile vma-1b intein.}, journal = {Molecular biology and evolution}, volume = {30}, number = {12}, pages = {2676-2687}, doi = {10.1093/molbev/mst164}, pmid = {24048585}, issn = {1537-1719}, mesh = {Amino Acid Substitution ; Archaea/classification/enzymology/*genetics ; Bacteria/enzymology/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; Inteins/*genetics ; Phylogeny ; Ribosomes/genetics ; Vacuolar Proton-Translocating ATPases/*genetics ; }, abstract = {Inteins are self-splicing parasitic genetic elements found in all domains of life. These genetic elements are found in highly conserved positions in conserved proteins. One protein family that has been invaded by inteins is the vacuolar and archaeal catalytic ATPase subunits (vma-1). There are two intein insertion sites in this protein, "a" and "b." The b site was previously thought to be only invaded in archaeal lineages. Here we survey the distribution and evolutionary histories of the b site inteins and show that the intein is present in more lineages than previously annotated, including a bacterial lineage, Mahella australiensis 50-1 BON. We present evidence, through ancestral character state reconstruction and substitution ratios between host genes and inteins, for several transfers of this intein between divergent species, including an interdomain transfer between the archaea and bacteria. Although inteins may persist within a single population or species for long periods of time, transfer of the vma-1b intein between divergent species contributed to the distribution of this intein.}, }
@article {pmid24047744, year = {2013}, author = {Pasom, W and Chanawong, A and Lulitanond, A and Wilailuckana, C and Kenprom, S and Puang-Ngern, P}, title = {Plasmid-mediated quinolone resistance genes, aac(6')-Ib-cr, qnrS, qnrB, and qnrA, in urinary isolates of Escherichia coli and Klebsiella pneumoniae at a teaching hospital, Thailand.}, journal = {Japanese journal of infectious diseases}, volume = {66}, number = {5}, pages = {428-432}, doi = {10.7883/yoken.66.428}, pmid = {24047744}, issn = {1884-2836}, mesh = {Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; *Drug Resistance, Bacterial ; Escherichia coli/classification/*drug effects/*genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; Genes, Bacterial ; Hospitals, Teaching ; Humans ; Klebsiella pneumoniae/classification/*drug effects/*genetics/isolation &amp; purification ; Molecular Typing ; *Plasmids ; Quinolones/*pharmacology ; Thailand ; Urinary Tract Infections/microbiology ; Urine/microbiology ; }, abstract = {A total of 121 Escherichia coli (47 extended-spectrum β-lactamase [ESBL] and 74 non-ESBL producers) and 75 Klebsiella pneumoniae isolates (49 ESBL and 26 non-ESBL producers) were collected from urine samples between October 2010 and April 2011 at a university hospital and assessed for the presence of plasmid-mediated quinolone resistance (PMQR) genes. Twenty-seven E. coli (22.3%) and 49 K. pneumoniae (65.3%) isolates harbored PMQR genes, which mostly consisted of aac(6')-Ib-cr and qnrS, followed by qnrB and qnrA. Among the 76 PMQR-positive isolates, 15 (19.7%) and 2 (2.6%) carried 2 and 3 different PMQR genes, respectively. However, qnrC, qnrD, and qepA were not found in any isolate. The PMQR genes were more prevalent in ESBL producers than in non-ESBL producers (42.6% versus 9.5% in E. coli and 81.6% versus 34.6% in K. pneumoniae). Approximately 35%-60% of the PMQR-positive isolates were susceptible or intermediately susceptible to fluoroquinolones. The enterobacterial repetitive intergenic consensus-PCR method revealed that most PMQR-positive isolates belonged to different strains, indicating the spread of these resistance determinants. PMQR gene transfer by conjugation was successful in 10%-25% of the test donors. This study showed a high prevalence of PMQR genes among both organisms. Clinical use of fluoroquinolones for the treatment of infections caused by fluoroquinolone-susceptible strains harboring PMQR genes may lead to decreased therapeutic efficacy.}, }
@article {pmid24043788, year = {2013}, author = {Essere, B and Yver, M and Gavazzi, C and Terrier, O and Isel, C and Fournier, E and Giroux, F and Textoris, J and Julien, T and Socratous, C and Rosa-Calatrava, M and Lina, B and Marquet, R and Moules, V}, title = {Critical role of segment-specific packaging signals in genetic reassortment of influenza A viruses.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {40}, pages = {E3840-8}, pmid = {24043788}, issn = {1091-6490}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Birds/*virology ; Coinfection/*virology ; DNA Primers/genetics ; Dogs ; Gene Transfer, Horizontal/*genetics ; Genotype ; HEK293 Cells ; Hemagglutinins, Viral/*genetics ; Humans ; Influenza A Virus, H3N2 Subtype/*genetics ; Influenza A Virus, H5N2 Subtype/*genetics ; Madin Darby Canine Kidney Cells ; Molecular Sequence Data ; Mutation/genetics ; Sequence Analysis, DNA ; Signal Transduction/genetics ; Species Specificity ; Virus Assembly/*genetics ; }, abstract = {The fragmented nature of the influenza A genome allows the exchange of gene segments when two or more influenza viruses infect the same cell, but little is known about the rules underlying this process. Here, we studied genetic reassortment between the A/Moscow/10/99 (H3N2, MO) virus originally isolated from human and the avian A/Finch/England/2051/91 (H5N2, EN) virus and found that this process is strongly biased. Importantly, the avian HA segment never entered the MO genetic background alone but always was accompanied by the avian PA and M fragments. Introduction of the 5' and 3' packaging sequences of HA(MO) into an otherwise HA(EN) backbone allowed efficient incorporation of the chimerical viral RNA (vRNA) into the MO genetic background. Furthermore, forcing the incorporation of the avian M segment or introducing five silent mutations into the human M segment was sufficient to drive coincorporation of the avian HA segment into the MO genetic background. These silent mutations also strongly affected the genotype of reassortant viruses. Taken together, our results indicate that packaging signals are crucial for genetic reassortment and that suboptimal compatibility between the vRNA packaging signals, which are detected only when vRNAs compete for packaging, limit this process.}, }
@article {pmid24039805, year = {2013}, author = {Lapadula, WJ and Sánchez Puerta, MV and Juri Ayub, M}, title = {Revising the taxonomic distribution, origin and evolution of ribosome inactivating protein genes.}, journal = {PloS one}, volume = {8}, number = {9}, pages = {e72825}, pmid = {24039805}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Animals ; Bacteria/classification/genetics ; Databases, Genetic ; Eukaryota/classification/genetics ; *Evolution, Molecular ; Fungi/classification/genetics ; Gene Order ; Genome ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Ribosome Inactivating Proteins/chemistry/*genetics ; Sequence Alignment ; }, abstract = {Ribosome inactivating proteins are enzymes that depurinate a specific adenine residue in the alpha-sarcin-ricin loop of the large ribosomal RNA, being ricin and Shiga toxins the most renowned examples. They are widely distributed in plants and their presence has also been confirmed in a few bacterial species. According to this taxonomic distribution, the current model about the origin and evolution of RIP genes postulates that an ancestral RIP domain was originated in flowering plants, and later acquired by some bacteria via horizontal gene transfer. Here, we unequivocally detected the presence of RIP genes in fungi and metazoa. These findings, along with sequence and phylogenetic analyses, led us to propose an alternative, more parsimonious, hypothesis about the origin and evolutionary history of the RIP domain, where several paralogous RIP genes were already present before the three domains of life evolved. This model is in agreement with the current idea of the Last Universal Common Ancestor (LUCA) as a complex, genetically redundant organism. Differential loss of paralogous genes in descendants of LUCA, rather than multiple horizontal gene transfer events, could account for the complex pattern of RIP genes across extant species, as it has been observed for other genes.}, }
@article {pmid24038701, year = {2013}, author = {Johnning, A and Moore, ER and Svensson-Stadler, L and Shouche, YS and Larsson, DG and Kristiansson, E}, title = {Acquired genetic mechanisms of a multiresistant bacterium isolated from a treatment plant receiving wastewater from antibiotic production.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {23}, pages = {7256-7263}, pmid = {24038701}, issn = {1098-5336}, mesh = {Anti-Bacterial Agents/*pharmacology ; DNA Mutational Analysis ; DNA Transposable Elements ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Genome, Bacterial ; India ; *Industrial Waste ; Microbial Sensitivity Tests ; Mutation, Missense ; Ochrobactrum/*drug effects/*genetics/isolation &amp; purification ; Sequence Analysis, DNA ; Wastewater/*microbiology ; }, abstract = {The external environment, particularly wastewater treatment plants (WWTPs), where environmental bacteria meet human commensals and pathogens in large numbers, has been highlighted as a potential breeding ground for antibiotic resistance. We have isolated the extensively drug-resistant Ochrobactrum intermedium CCUG 57381 from an Indian WWTP receiving industrial wastewater from pharmaceutical production contaminated with high levels of quinolones. Antibiotic susceptibility testing against 47 antibiotics showed that the strain was 4 to >500 times more resistant to sulfonamides, quinolones, tetracyclines, macrolides, and the aminoglycoside streptomycin than the type strain O. intermedium LMG 3301T. Whole-genome sequencing identified mutations in the Indian strain causing amino acid substitutions in the target enzymes of quinolones. We also characterized three acquired regions containing resistance genes to sulfonamides (sul1), tetracyclines [tet(G) and tetR], and chloramphenicol/florfenicol (floR). Furthermore, the Indian strain harbored acquired mechanisms for horizontal gene transfer, including a type I mating pair-forming system (MPFI), a MOBP relaxase, and insertion sequence transposons. Our results highlight that WWTPs serving antibiotic manufacturing may provide nearly ideal conditions for the recruitment of resistance genes into human commensal and pathogenic bacteria.}, }
@article {pmid24037739, year = {2013}, author = {Huang, J}, title = {Horizontal gene transfer in eukaryotes: the weak-link model.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {35}, number = {10}, pages = {868-875}, pmid = {24037739}, issn = {1521-1878}, mesh = {Animals ; Eukaryota/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Mitochondria/genetics ; *Models, Genetic ; Phylogeny ; Plastids/genetics ; Symbiosis/genetics ; }, abstract = {The significance of horizontal gene transfer (HGT) in eukaryotic evolution remains controversial. Although many eukaryotic genes are of bacterial origin, they are often interpreted as being derived from mitochondria or plastids. Because of their fixed gene pool and gene loss, however, mitochondria and plastids alone cannot adequately explain the presence of all, or even the majority, of bacterial genes in eukaryotes. Available data indicate that no insurmountable barrier to HGT exists, even in complex multicellular eukaryotes. In addition, the discovery of both recent and ancient HGT events in all major eukaryotic groups suggests that HGT has been a regular occurrence throughout the history of eukaryotic evolution. A model of HGT is proposed that suggests both unicellular and early developmental stages as likely entry points for foreign genes into multicellular eukaryotes.}, }
@article {pmid24036222, year = {2013}, author = {Balderrama-Subieta, A and Quillaguamán, J}, title = {Genomic studies on nitrogen metabolism in Halomonas boliviensis: metabolic pathway, biochemistry and evolution.}, journal = {Computational biology and chemistry}, volume = {47}, number = {}, pages = {96-104}, doi = {10.1016/j.compbiolchem.2013.08.002}, pmid = {24036222}, issn = {1476-928X}, mesh = {Biological Evolution ; *Genomics ; Glutamate Dehydrogenase/genetics/metabolism ; Glutamate-Ammonia Ligase/genetics/metabolism ; Glutamic Acid/genetics/metabolism ; Halomonas/chemistry/*genetics/*metabolism ; Metabolic Networks and Pathways/*genetics ; Nitrogen/*metabolism ; Phylogeny ; }, abstract = {Halomonas boliviensis LC1(T)=DSM 15516(T) is a halophilic bacterium that copiously produces osmolytes and polyesters. The growth of H. boliviensis is restricted when glutamate or glutamine is not included in its culture medium. The concentration of glutamate in the medium can regulate the production of either osmolytes or polyesters. However, genomic studies on the nitrogen assimilation have not been performed on H. boliviensis and other members of the family Halomonadaceae. Glutamate metabolism in H. boliviensis was discerned based on genome sequence analysis. The genome sequences of other Halomonadaceae members revealed similar enzymes to those found in H. boliviensis. H. boliviensis and H. elongata DSM 2581(T) acquired distinct glutamate dehydrogenase genes through horizontal gene transfer from a different bacterium. Two alleles of glutamine synthetase could be found in H. boliviensis, one of which was obtained from a thermophilic archaeon via horizontal gene transfer. Two subunits of glutamate synthase were also present in H. boliviensis. The small β-subunit had a molecular weight of 52 kDa and was phylogenetically closely affiliated to proteins of other halomonads and Gammaproteobacteria. The large (161 kDa) α-subunit of the halomonads gathered in a separate phylogenetic group, hence glutamate synthase α-subunits of halomonads may be included a novel group of enzymes. Furthermore, putative enzymes obtained from the genome of H. boliviensis should permit complete glutamate metabolism. A similar metabolism should be followed by other halomonads. However, some phenotypic differences between halomonads, such as the ability to assimilate ammonia, resulted as a consequence of horizontal gene transfer. Each enzyme that forms part of the glutamate metabolism in prokaryotes evolved following a different pattern. Yet, most enzymes of halomonads diverged in phylogenetic clusters composed of Proteobacteria, as might be expected.}, }
@article {pmid24035465, year = {2013}, author = {McInerney, JO}, title = {More than tree dimensions: inter-lineage evolution's ecological importance.}, journal = {Trends in ecology &amp; evolution}, volume = {28}, number = {11}, pages = {624-625}, doi = {10.1016/j.tree.2013.09.002}, pmid = {24035465}, issn = {1872-8383}, mesh = {Adaptation, Biological/*genetics/physiology ; *Biological Evolution ; Campylobacter/genetics ; Gene Transfer, Horizontal/*genetics ; *Models, Genetic ; *Phylogeny ; *Selection, Genetic ; Species Specificity ; Symbiosis/*genetics ; }, abstract = {Horizontal transfer of genes has sometimes been viewed as a nuisance for the work of understanding the evolutionary history of lineages. Recent work has shown that clever analysis of inter-lineage gene transfer is productive and has tremendous explanatory power, in particular, for niche adaptation. These studies alter our perception of what are the fundamental units of evolution and selection.}, }
@article {pmid24033385, year = {2013}, author = {Caporale, LH and Doyle, J}, title = {In Darwinian evolution, feedback from natural selection leads to biased mutations.}, journal = {Annals of the New York Academy of Sciences}, volume = {1305}, number = {}, pages = {18-28}, doi = {10.1111/nyas.12235}, pmid = {24033385}, issn = {1749-6632}, mesh = {Animals ; *Biological Evolution ; Gene-Environment Interaction ; Genetic Fitness ; Genetic Variation ; Humans ; *Mutation ; *Selection, Genetic ; }, abstract = {Natural selection provides feedback through which information about the environment and its recurring challenges is captured, inherited, and accumulated within genomes in the form of variations that contribute to survival. The variation upon which natural selection acts is generally described as "random." Yet evidence has been mounting for decades, from such phenomena as mutation hotspots, horizontal gene transfer, and highly mutable repetitive sequences, that variation is far from the simplifying idealization of random processes as white (uniform in space and time and independent of the environment or context). This paper focuses on what is known about the generation and control of mutational variation, emphasizing that it is not uniform across the genome or in time, not unstructured with respect to survival, and is neither memoryless nor independent of the (also far from white) environment. We suggest that, as opposed to frequentist methods, Bayesian analysis could capture the evolution of nonuniform probabilities of distinct classes of mutation, and argue not only that the locations, styles, and timing of real mutations are not correctly modeled as generated by a white noise random process, but that such a process would be inconsistent with evolutionary theory.}, }
@article {pmid24033262, year = {2013}, author = {Bansal, MS and Alm, EJ and Kellis, M}, title = {Reconciliation revisited: handling multiple optima when reconciling with duplication, transfer, and loss.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {20}, number = {10}, pages = {738-754}, pmid = {24033262}, issn = {1557-8666}, support = {RC2 HG005639/HG/NHGRI NIH HHS/United States ; }, mesh = {Algorithms ; Chromosome Mapping/*methods ; Evolution, Molecular ; *Gene Deletion ; *Gene Duplication ; *Gene Transfer, Horizontal ; Models, Genetic ; }, abstract = {Phylogenetic tree reconciliation is a powerful approach for inferring evolutionary events like gene duplication, horizontal gene transfer, and gene loss, which are fundamental to our understanding of molecular evolution. While duplication-loss (DL) reconciliation leads to a unique maximum-parsimony solution, duplication-transfer-loss (DTL) reconciliation yields a multitude of optimal solutions, making it difficult to infer the true evolutionary history of the gene family. This problem is further exacerbated by the fact that different event cost assignments yield different sets of optimal reconciliations. Here, we present an effective, efficient, and scalable method for dealing with these fundamental problems in DTL reconciliation. Our approach works by sampling the space of optimal reconciliations uniformly at random and aggregating the results. We show that even gene trees with only a few dozen genes often have millions of optimal reconciliations and present an algorithm to efficiently sample the space of optimal reconciliations uniformly at random in O(mn(2)) time per sample, where m and n denote the number of genes and species, respectively. We use these samples to understand how different optimal reconciliations vary in their node mappings and event assignments and to investigate the impact of varying event costs. We apply our method to a biological dataset of approximately 4700 gene trees from 100 taxa and observe that 93% of event assignments and 73% of mappings remain consistent across different multiple optima. Our analysis represents the first systematic investigation of the space of optimal DTL reconciliations and has many important implications for the study of gene family evolution.}, }
@article {pmid24032108, year = {2013}, author = {Barteneva, NS and Maltsev, N and Vorobjev, IA}, title = {Microvesicles and intercellular communication in the context of parasitism.}, journal = {Frontiers in cellular and infection microbiology}, volume = {3}, number = {}, pages = {49}, pmid = {24032108}, issn = {2235-2988}, mesh = {Animals ; *Cell Communication ; Exosomes/*metabolism ; *Host-Parasite Interactions ; Humans ; Parasites/*physiology ; }, abstract = {There is a rapidly growing body of evidence that production of microvesicles (MVs) is a universal feature of cellular life. MVs can incorporate microRNA (miRNA), mRNA, mtDNA, DNA and retrotransposons, camouflage viruses/viral components from immune surveillance, and transfer cargo between cells. These properties make MVs an essential player in intercellular communication. Increasing evidence supports the notion that MVs can also act as long-distance vehicles for RNA molecules and participate in metabolic synchronization and reprogramming eukaryotic cells including stem and germinal cells. MV ability to carry on DNA and their general distribution makes them attractive candidates for horizontal gene transfer, particularly between multi-cellular organisms and their parasites; this suggests important implications for the co-evolution of parasites and their hosts. In this review, we provide current understanding of the roles played by MVs in intracellular pathogens and parasitic infections. We also discuss the possible role of MVs in co-infection and host shifting.}, }
@article {pmid24030592, year = {2014}, author = {Sangwan, N and Verma, H and Kumar, R and Negi, V and Lax, S and Khurana, P and Khurana, JP and Gilbert, JA and Lal, R}, title = {Reconstructing an ancestral genotype of two hexachlorocyclohexane-degrading Sphingobium species using metagenomic sequence data.}, journal = {The ISME journal}, volume = {8}, number = {2}, pages = {398-408}, pmid = {24030592}, issn = {1751-7370}, mesh = {Biodegradation, Environmental ; Environmental Pollutants/metabolism ; Gene Transfer, Horizontal ; Genotype ; Hexachlorocyclohexane/metabolism ; India ; Japan ; *Metagenomics ; Molecular Sequence Data ; Plasmids/genetics ; Sphingomonadaceae/*classification/*genetics/metabolism ; }, abstract = {Over the last 60 years, the use of hexachlorocyclohexane (HCH) as a pesticide has resulted in the production of >4 million tons of HCH waste, which has been dumped in open sinks across the globe. Here, the combination of the genomes of two genetic subspecies (Sphingobium japonicum UT26 and Sphingobium indicum B90A; isolated from two discrete geographical locations, Japan and India, respectively) capable of degrading HCH, with metagenomic data from an HCH dumpsite (∼450 mg HCH per g soil), enabled the reconstruction and validation of the last-common ancestor (LCA) genotype. Mapping the LCA genotype (3128 genes) to the subspecies genomes demonstrated that >20% of the genes in each subspecies were absent in the LCA. This includes two enzymes from the 'upper' HCH degradation pathway, suggesting that the ancestor was unable to degrade HCH isomers, but descendants acquired lin genes by transposon-mediated lateral gene transfer. In addition, anthranilate and homogentisate degradation traits were found to be strain (selectively retained only by UT26) and environment (absent in the LCA and subspecies, but prevalent in the metagenome) specific, respectively. One draft secondary chromosome, two near complete plasmids and eight complete lin transposons were assembled from the metagenomic DNA. Collectively, these results reinforce the elastic nature of the genus Sphingobium, and describe the evolutionary acquisition mechanism of a xenobiotic degradation phenotype in response to environmental pollution. This also demonstrates for the first time the use of metagenomic data in ancestral genotype reconstruction, highlighting its potential to provide significant insight into the development of such phenotypes.}, }
@article {pmid24030554, year = {2013}, author = {Aoki, S and Ito, M and Iwasaki, W}, title = {From β- to α-proteobacteria: the origin and evolution of rhizobial nodulation genes nodIJ.}, journal = {Molecular biology and evolution}, volume = {30}, number = {11}, pages = {2494-2508}, doi = {10.1093/molbev/mst153}, pmid = {24030554}, issn = {1537-1719}, mesh = {ATP-Binding Cassette Transporters/*genetics ; Adaptation, Biological ; Alphaproteobacteria/classification/*genetics ; Bacterial Proteins/*genetics ; Base Composition ; Betaproteobacteria/classification/*genetics ; Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genome, Bacterial ; Mimosa/microbiology ; Phylogeny ; Plant Root Nodulation/genetics ; Rhizobium/classification/*genetics ; }, abstract = {Although many α- and some β-proteobacterial species are symbiotic with legumes, the evolutionary origin of nitrogen-fixing nodulation remains unclear. We examined α- and β-proteobacteria whose genomes were sequenced using large-scale phylogenetic profiling and revealed the evolutionary origin of two nodulation genes. These genes, nodI and nodJ (nodIJ), play key roles in the secretion of Nod factors, which are recognized by legumes during nodulation. We found that only the nodulating β-proteobacteria, including the novel strains isolated in this study, possess both nodIJ and their paralogous genes (DRA-ATPase/permease genes). Contrary to the widely accepted scenario of the α-proteobacterial origin of rhizobia, our exhaustive phylogenetic analysis showed that the entire nodIJ clade is included in the clade of Burkholderiaceae DRA-ATPase/permease genes, that is, the nodIJ genes originated from gene duplication in a lineage of the β-proteobacterial family. After duplication, the evolutionary rates of nodIJ were significantly accelerated relative to those of homologous genes, which is consistent with their novel function in nodulation. The likelihood analyses suggest that this accelerated evolution is not associated with changes in either nonsynonymous/synonymous substitution rates or transition/transversion rates, but rather, in the GC content. Although the low GC content of the nodulation genes has been assumed to reflect past horizontal transfer events from donor rhizobial genomes with low GC content, no rhizobial genome with such low GC content has yet been found. Our results encourage a reconsideration of the origin of nodulation and suggest new perspectives on the role of the GC content of bacterial genes in functional adaptation.}, }
@article {pmid24029811, year = {2013}, author = {Straub, SC and Cronn, RC and Edwards, C and Fishbein, M and Liston, A}, title = {Horizontal transfer of DNA from the mitochondrial to the plastid genome and its subsequent evolution in milkweeds (apocynaceae).}, journal = {Genome biology and evolution}, volume = {5}, number = {10}, pages = {1872-1885}, pmid = {24029811}, issn = {1759-6653}, mesh = {Apocynaceae/genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Gene Conversion ; *Gene Transfer, Horizontal ; *Genome, Mitochondrial ; *Genome, Plastid ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Pseudogenes/genetics ; }, abstract = {Horizontal gene transfer (HGT) of DNA from the plastid to the nuclear and mitochondrial genomes of higher plants is a common phenomenon; however, plastid genomes (plastomes) are highly conserved and have generally been regarded as impervious to HGT. We sequenced the 158 kb plastome and the 690 kb mitochondrial genome of common milkweed (Asclepias syriaca [Apocynaceae]) and found evidence of intracellular HGT for a 2.4-kb segment of mitochondrial DNA to the rps2-rpoC2 intergenic spacer of the plastome. The transferred region contains an rpl2 pseudogene and is flanked by plastid sequence in the mitochondrial genome, including an rpoC2 pseudogene, which likely provided the mechanism for HGT back to the plastome through double-strand break repair involving homologous recombination. The plastome insertion is restricted to tribe Asclepiadeae of subfamily Asclepiadoideae, whereas the mitochondrial rpoC2 pseudogene is present throughout the subfamily, which confirms that the plastid to mitochondrial HGT event preceded the HGT to the plastome. Although the plastome insertion has been maintained in all lineages of Asclepiadoideae, it shows minimal evidence of transcription in A. syriaca and is likely nonfunctional. Furthermore, we found recent gene conversion of the mitochondrial rpoC2 pseudogene in Asclepias by the plastid gene, which reflects continued interaction of these genomes.}, }
@article {pmid24028952, year = {2013}, author = {White, JA}, title = {Evolution: a bacterially mediated swap meet for adaptive traits.}, journal = {Current biology : CB}, volume = {23}, number = {17}, pages = {R723-5}, doi = {10.1016/j.cub.2013.07.069}, pmid = {24028952}, issn = {1879-0445}, mesh = {*Ecosystem ; *Gene Transfer, Horizontal ; *Symbiosis ; }, abstract = {New research suggests that secondary bacterial symbionts in insects act as a mechanism for horizontal genetic exchange among hosts, facilitating adaptation to new ecological niches.}, }
@article {pmid24028687, year = {2013}, author = {Porcelli, I and Reuter, M and Pearson, BM and Wilhelm, T and van Vliet, AH}, title = {Parallel evolution of genome structure and transcriptional landscape in the Epsilonproteobacteria.}, journal = {BMC genomics}, volume = {14}, number = {}, pages = {616}, pmid = {24028687}, issn = {1471-2164}, support = {BB/J004529/1.//Arthritis Research UK/United Kingdom ; IFR/08/3//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {5' Untranslated Regions ; Base Sequence ; Campylobacter jejuni/*genetics ; Comparative Genomic Hybridization ; Conserved Sequence ; Epsilonproteobacteria/genetics ; *Evolution, Molecular ; Gene Library ; Gene Order ; *Genome, Bacterial ; Promoter Regions, Genetic ; Protein Sorting Signals ; RNA, Bacterial/genetics ; RNA, Untranslated/genetics ; Sequence Analysis, RNA ; Transcription Initiation Site ; Transcription, Genetic ; *Transcriptome ; }, abstract = {BACKGROUND: Gene reshuffling, point mutations and horizontal gene transfer contribute to bacterial genome variation, but require the genome to rewire its transcriptional circuitry to ensure that inserted, mutated or reshuffled genes are transcribed at appropriate levels. The genomes of Epsilonproteobacteria display very low synteny, due to high levels of reshuffling and reorganisation of gene order, but still share a significant number of gene orthologs allowing comparison. Here we present the primary transcriptome of the pathogenic Epsilonproteobacterium Campylobacter jejuni, and have used this for comparative and predictive transcriptomics in the Epsilonproteobacteria.<br><br>RESULTS: Differential RNA-sequencing using 454 sequencing technology was used to determine the primary transcriptome of C. jejuni NCTC 11168, which consists of 992 transcription start sites (TSS), which included 29 putative non-coding and stable RNAs, 266 intragenic (internal) TSS, and 206 antisense TSS. Several previously unknown features were identified in the C. jejuni transcriptional landscape, like leaderless mRNAs and potential leader peptides upstream of amino acid biosynthesis genes. A cross-species comparison of the primary transcriptomes of C. jejuni and the related Epsilonproteobacterium Helicobacter pylori highlighted a lack of conservation of operon organisation, position of intragenic and antisense promoters or leaderless mRNAs. Predictive comparisons using 40 other Epsilonproteobacterial genomes suggests that this lack of conservation of transcriptional features is common to all Epsilonproteobacterial genomes, and is associated with the absence of genome synteny in this subdivision of the Proteobacteria.<br><br>CONCLUSIONS: Both the genomes and transcriptomes of Epsilonproteobacteria are highly variable, both at the genome level by combining and division of multicistronic operons, but also on the gene level by generation or deletion of promoter sequences and 5' untranslated regions. Regulatory features may have evolved after these species split from a common ancestor, with transcriptome rewiring compensating for changes introduced by genomic reshuffling and horizontal gene transfer.}, }
@article {pmid24018670, year = {2013}, author = {Shimizu-Kadota, M and Kato, H and Shiwa, Y and Oshima, K and Machii, M and Araya-Kojima, T and Zendo, T and Hattori, M and Sonomoto, K and Yoshikawa, H}, title = {Genomic features of Lactococcus lactis IO-1, a lactic acid bacterium that utilizes xylose and produces high levels of L-lactic acid.}, journal = {Bioscience, biotechnology, and biochemistry}, volume = {77}, number = {9}, pages = {1804-1808}, doi = {10.1271/bbb.130080}, pmid = {24018670}, issn = {1347-6947}, mesh = {Amino Acids/biosynthesis ; Base Sequence ; DNA Transposable Elements/genetics ; Gene Transfer, Horizontal ; Genome, Bacterial/genetics ; *Genomics ; Lactic Acid/*biosynthesis/*metabolism ; Lactococcus lactis/*genetics/*metabolism/virology ; Molecular Sequence Data ; Nisin/metabolism ; Prophages/genetics ; Sucrose/metabolism ; Vitamins/biosynthesis ; Xylose/*metabolism ; }, abstract = {Lactococcus lactis IO-1 (JCM7638) produces L-lactic acid predominantly when grown at high xylose concentrations, and its utilization is highly desired in the green plastics industry. Therefore it is worthwhile studying its genomic traits. In this study, we focused on (i) genes of possible horizontal transfer derivation (prophages, the nisin-sucrose transposon, and several restriction-modification systems), and (ii) genes for the synthetic pathways of amino acids and vitamins in the IO-1 genome. In view of the results of this analysis, we consider their meanings in strain IO-1.}, }
@article {pmid24018383, year = {2013}, author = {Richards, TA and Talbot, NJ}, title = {Horizontal gene transfer in osmotrophs: playing with public goods.}, journal = {Nature reviews. Microbiology}, volume = {11}, number = {10}, pages = {720-727}, pmid = {24018383}, issn = {1740-1534}, support = {BB/G00885X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Carbohydrate Metabolism ; Environment ; Evolution, Molecular ; Fungal Proteins/genetics/metabolism ; *Gene Transfer, Horizontal ; *Genes, Fungal ; Oomycetes/classification/*genetics/metabolism ; Phenotype ; Phylogeny ; Protein Interaction Mapping ; Saccharomyces cerevisiae/classification/*genetics/metabolism ; Species Specificity ; Symbiosis ; }, abstract = {Osmotrophic microorganisms, such as fungi and oomycetes, feed by secreting depolymerizing enzymes to process complex food sources in the extracellular environment, and taking up the resulting simple sugars, micronutrients and amino acids. As a consequence of this lifestyle, osmotrophs engage in the acquisition and protection of public goods. In this Opinion article, we propose that horizontal gene transfer (HGT) has played a key part in shaping both the repertoire of proteins required for osmotrophy and the nature of public goods interactions in which eukaryotic microorganisms engage.}, }
@article {pmid24016550, year = {2014}, author = {Segura, RL and Aguila-Arcos, S and Ugarte-Uribe, B and Vecino, AJ and de la Cruz, F and Goñi, FM and Alkorta, I}, title = {Subcellular location of the coupling protein TrwB and the role of its transmembrane domain.}, journal = {Biochimica et biophysica acta}, volume = {1838}, number = {1 Pt B}, pages = {223-230}, doi = {10.1016/j.bbamem.2013.08.016}, pmid = {24016550}, issn = {0006-3002}, mesh = {Adenosine Triphosphate/metabolism ; Binding Sites ; Cell Membrane/genetics/*metabolism/ultrastructure ; *Conjugation, Genetic ; DNA-Binding Proteins/deficiency/*genetics ; Escherichia coli/genetics/*metabolism/ultrastructure ; Escherichia coli Proteins/*genetics ; *Gene Expression Regulation, Bacterial ; Genes, Reporter ; Green Fluorescent Proteins/genetics/metabolism ; Protein Binding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Time Factors ; }, abstract = {Conjugation is the most important mechanism for horizontal gene transfer and it is the main responsible for the successful adaptation of bacteria to the environment. Conjugative plasmids are the DNA molecules transferred and a multiprotein system encoded by the conjugative plasmid itself is necessary. The high number of proteins involved in the process suggests that they should have a defined location in the cell and therefore, they should be recruited to that specific point. One of these proteins is the coupling protein that plays an essential role in bacterial conjugation. TrwB is the coupling protein of R388 plasmid that is divided in two domains: i) The N-terminal domain referred as transmembrane domain and ii) a large cytosolic domain that contains a nucleotide-binding motif similar to other ATPases. To investigate the role of these domains in the subcellular location of TrwB, we constructed two mutant proteins that comprised the transmembrane (TrwBTM) or the cytoplasmic (TrwBΔN70) domain of TrwB. By immunofluorescence and GFP-fusion proteins we demonstrate that TrwB and TrwBTM mutant protein were localized to the cell pole independently of the remaining R388 proteins. On the contrary, a soluble mutant protein (TrwBΔN70) was localized to the cytoplasm in the absence of R388 proteins. However, in the presence of other R388-encoded proteins, TrwBΔN70 localizes uniformly to the cell membrane, suggesting that interactions between the cytosolic domain of TrwB and other membrane proteins of R388 plasmid may happen. Our results suggest that the transmembrane domain of TrwB leads the protein to the cell pole.}, }
@article {pmid24016192, year = {2013}, author = {Mitri, S and Foster, KR}, title = {The genotypic view of social interactions in microbial communities.}, journal = {Annual review of genetics}, volume = {47}, number = {}, pages = {247-273}, doi = {10.1146/annurev-genet-111212-133307}, pmid = {24016192}, issn = {1545-2948}, mesh = {Bacterial Proteins/genetics/physiology ; Bacterial Secretion Systems/physiology ; Bacterial Toxins/metabolism ; Ecology ; Genetic Fitness ; Genome, Bacterial ; Genotype ; Microbial Consortia/*physiology ; Microbial Interactions/*genetics ; Models, Biological ; Phenotype ; Selection, Genetic ; Species Specificity ; }, abstract = {Dense and diverse microbial communities are found in many environments. Disentangling the social interactions between strains and species is central to understanding microbes and how they respond to perturbations. However, the study of social evolution in microbes tends to focus on single species. Here, we broaden this perspective and review evolutionary and ecological theory relevant to microbial interactions across all phylogenetic scales. Despite increased complexity, we reduce the theory to a simple null model that we call the genotypic view. This states that cooperation will occur when cells are surrounded by identical genotypes at the loci that drive interactions, with genetic identity coming from recent clonal growth or horizontal gene transfer (HGT). In contrast, because cooperation is only expected to evolve between different genotypes under restrictive ecological conditions, different genotypes will typically compete. Competition between two genotypes includes mutual harm but, importantly, also many interactions that are beneficial to one of the two genotypes, such as predation. The literature offers support for the genotypic view with relatively few examples of cooperation between genotypes. However, the study of microbial interactions is still at an early stage. We outline the logic and methods that help to better evaluate our perspective and move us toward rationally engineering microbial communities to our own advantage.}, }
@article {pmid24015778, year = {2013}, author = {Alves, JM and Klein, CC and da Silva, FM and Costa-Martins, AG and Serrano, MG and Buck, GA and Vasconcelos, AT and Sagot, MF and Teixeira, MM and Motta, MC and Camargo, EP}, title = {Endosymbiosis in trypanosomatids: the genomic cooperation between bacterium and host in the synthesis of essential amino acids is heavily influenced by multiple horizontal gene transfers.}, journal = {BMC evolutionary biology}, volume = {13}, number = {}, pages = {190}, pmid = {24015778}, issn = {1471-2148}, mesh = {Amino Acids, Essential/*biosynthesis ; Betaproteobacteria/*genetics/physiology ; Biological Evolution ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Phylogeny ; *Symbiosis ; Trypanosomatina/classification/*genetics/metabolism/*microbiology ; }, abstract = {BACKGROUND: Trypanosomatids of the genera Angomonas and Strigomonas live in a mutualistic association characterized by extensive metabolic cooperation with obligate endosymbiotic Betaproteobacteria. However, the role played by the symbiont has been more guessed by indirect means than evidenced. Symbiont-harboring trypanosomatids, in contrast to their counterparts lacking symbionts, exhibit lower nutritional requirements and are autotrophic for essential amino acids. To evidence the symbiont's contributions to this autotrophy, entire genomes of symbionts and trypanosomatids with and without symbionts were sequenced here.<br><br>RESULTS: Analyses of the essential amino acid pathways revealed that most biosynthetic routes are in the symbiont genome. By contrast, the host trypanosomatid genome contains fewer genes, about half of which originated from different bacterial groups, perhaps only one of which (ornithine cyclodeaminase, EC:4.3.1.12) derived from the symbiont. Nutritional, enzymatic, and genomic data were jointly analyzed to construct an integrated view of essential amino acid metabolism in symbiont-harboring trypanosomatids. This comprehensive analysis showed perfect concordance among all these data, and revealed that the symbiont contains genes for enzymes that complete essential biosynthetic routes for the host amino acid production, thus explaining the low requirement for these elements in symbiont-harboring trypanosomatids. Phylogenetic analyses show that the cooperation between symbionts and their hosts is complemented by multiple horizontal gene transfers, from bacterial lineages to trypanosomatids, that occurred several times in the course of their evolution. Transfers occur preferentially in parts of the pathways that are missing from other eukaryotes.<br><br>CONCLUSION: We have herein uncovered the genetic and evolutionary bases of essential amino acid biosynthesis in several trypanosomatids with and without endosymbionts, explaining and complementing decades of experimental results. We uncovered the remarkable plasticity in essential amino acid biosynthesis pathway evolution in these protozoans, demonstrating heavy influence of horizontal gene transfer events, from Bacteria to trypanosomatid nuclei, in the evolution of these pathways.}, }
@article {pmid24014662, year = {2013}, author = {Hong, Y and Duda, KA and Cunneen, MM and Holst, O and Reeves, PR}, title = {The WbaK acetyltransferase of Salmonella enterica group E gives insights into O antigen evolution.}, journal = {Microbiology (Reading, England)}, volume = {159}, number = {Pt 11}, pages = {2316-2322}, doi = {10.1099/mic.0.069823-0}, pmid = {24014662}, issn = {1465-2080}, mesh = {Acetylation ; Acetyltransferases/*genetics/*metabolism ; *Evolution, Molecular ; Gene Order ; Gene Transfer, Horizontal ; Multigene Family ; O Antigens/*metabolism ; Recombination, Genetic ; Salmonella enterica/*enzymology/*genetics ; }, abstract = {O antigens are polysaccharides consisting of repeat units of three to eight sugars, generally assembled by genes in a discrete O antigen gene cluster. Salmonella enterica produces 46 forms of O antigen, and most of the variation is determined by genes in the gene cluster. However in some cases the structures are modified by enzymes encoded outside of the gene cluster, and several such modifications have been reported for Salmonella enterica group E, some with the genes on bacteriophages and one gene at a distant chromosomal site. We identified the enzyme, WbaK, that is responsible for O-acetylating the subgroup E1 O antigen, and found that the gene is located just downstream of the gene cluster as currently known. The wbaK gene appears to have been imported by a recombination event that also replaced the last 37 bp of the wbaP gene, indicating that homologous recombination was involved. Some of the group E strains we studied must have the original gene cluster, as they lack wbaK and the sequence downstream of wbaP is very similar to that in several other S. enterica O antigen gene clusters. In effect the gene cluster was extended by one gene in subgroup E1. It appears that a function that is usually encoded by a gene outside of the gene cluster has been added to the gene cluster, in this case giving an example of how such gene clusters can evolve.}, }
@article {pmid24014288, year = {2013}, author = {Madsen, JS and Burmølle, M and Sørensen, SJ}, title = {A spatiotemporal view of plasmid loss in biofilms and planktonic cultures.}, journal = {Biotechnology and bioengineering}, volume = {110}, number = {12}, pages = {3071-3074}, doi = {10.1002/bit.25109}, pmid = {24014288}, issn = {1097-0290}, mesh = {Biofilms/*growth &amp; development ; *Genomic Instability ; Plasmids/*analysis ; Pseudomonas putida/*genetics/*physiology ; }, abstract = {This Commentary by Madsen, Burmølle, and Sørensen discusses the article Non-invasive in situ monitoring and quantification of TOL plasmid segregational loss within Pseudomonas putida biofilms by Ma, Katzenmeyer, and Bryers. (2013. Biotechnol Bioeng. 110(11):2949-2958. DOI: 10.1002/bit.24953).}, }
@article {pmid24013706, year = {2013}, author = {Niewiadomska, AM and Gifford, RJ}, title = {The extraordinary evolutionary history of the reticuloendotheliosis viruses.}, journal = {PLoS biology}, volume = {11}, number = {8}, pages = {e1001642}, pmid = {24013706}, issn = {1545-7885}, mesh = {Animals ; Biological Evolution ; Birds/virology ; Chickens/virology ; Genome, Viral/genetics ; Reticuloendotheliosis virus/classification/*genetics ; }, abstract = {The reticuloendotheliosis viruses (REVs) comprise several closely related amphotropic retroviruses isolated from birds. These viruses exhibit several highly unusual characteristics that have not so far been adequately explained, including their extremely close relationship to mammalian retroviruses, and their presence as endogenous sequences within the genomes of certain large DNA viruses. We present evidence for an iatrogenic origin of REVs that accounts for these phenomena. Firstly, we identify endogenous retroviral fossils in mammalian genomes that share a unique recombinant structure with REVs-unequivocally demonstrating that REVs derive directly from mammalian retroviruses. Secondly, through sequencing of archived REV isolates, we confirm that contaminated Plasmodium lophurae stocks have been the source of multiple REV outbreaks in experimentally infected birds. Finally, we show that both phylogenetic and historical evidence support a scenario wherein REVs originated as mammalian retroviruses that were accidentally introduced into avian hosts in the late 1930s, during experimental studies of P. lophurae, and subsequently integrated into the fowlpox virus (FWPV) and gallid herpesvirus type 2 (GHV-2) genomes, generating recombinant DNA viruses that now circulate in wild birds and poultry. Our findings provide a novel perspective on the origin and evolution of REV, and indicate that horizontal gene transfer between virus families can expand the impact of iatrogenic transmission events.}, }
@article {pmid24006473, year = {2013}, author = {Lefèvre, CT and Bazylinski, DA}, title = {Ecology, diversity, and evolution of magnetotactic bacteria.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {77}, number = {3}, pages = {497-526}, pmid = {24006473}, issn = {1098-5557}, mesh = {Bacteria/*metabolism ; Bacterial Proteins/metabolism ; Gene Transfer, Horizontal/genetics/physiology ; Magnetosomes/*metabolism ; }, abstract = {Magnetotactic bacteria (MTB) are widespread, motile, diverse prokaryotes that biomineralize a unique organelle called the magnetosome. Magnetosomes consist of a nano-sized crystal of a magnetic iron mineral that is enveloped by a lipid bilayer membrane. In cells of almost all MTB, magnetosomes are organized as a well-ordered chain. The magnetosome chain causes the cell to behave like a motile, miniature compass needle where the cell aligns and swims parallel to magnetic field lines. MTB are found in almost all types of aquatic environments, where they can account for an important part of the bacterial biomass. The genes responsible for magnetosome biomineralization are organized as clusters in the genomes of MTB, in some as a magnetosome genomic island. The functions of a number of magnetosome genes and their associated proteins in magnetosome synthesis and construction of the magnetosome chain have now been elucidated. The origin of magnetotaxis appears to be monophyletic; that is, it developed in a common ancestor to all MTB, although horizontal gene transfer of magnetosome genes also appears to play a role in their distribution. The purpose of this review, based on recent progress in this field, is focused on the diversity and the ecology of the MTB and also the evolution and transfer of the molecular determinants involved in magnetosome formation.}, }
@article {pmid24004839, year = {2013}, author = {Carretero-Paulet, L and Lipska, A and Pérez-Gil, J and Sangari, FJ and Albert, VA and Rodríguez-Concepción, M}, title = {Evolutionary diversification and characterization of the eubacterial gene family encoding DXR type II, an alternative isoprenoid biosynthetic enzyme.}, journal = {BMC evolutionary biology}, volume = {13}, number = {}, pages = {180}, pmid = {24004839}, issn = {1471-2148}, mesh = {Aldose-Ketose Isomerases/*genetics/metabolism ; Bacteria/classification/*enzymology/*genetics/metabolism ; Biological Evolution ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Multienzyme Complexes/genetics/metabolism ; Oxidoreductases/chemistry/genetics/metabolism ; *Phylogeny ; Terpenes/*metabolism ; }, abstract = {BACKGROUND: Isoprenoids constitute a vast family of natural compounds performing diverse and essential functions in all domains of life. In most eubacteria, isoprenoids are synthesized through the methylerythritol 4-phosphate (MEP) pathway. The production of MEP is usually catalyzed by deoxyxylulose 5-phosphate reductoisomerase (DXR-I) but a few organisms use an alternative DXR-like enzyme (DXR-II).<br><br>RESULTS: Searches through 1498 bacterial complete proteomes detected 130 sequences with similarity to DXR-II. Phylogenetic analysis identified three well-resolved clades: the DXR-II family (clustering 53 sequences including eleven experimentally verified as functional enzymes able to produce MEP), and two previously uncharacterized NAD(P)-dependent oxidoreductase families (designated DLO1 and DLO2 for DXR-II-like oxidoreductases 1 and 2). Our analyses identified amino acid changes critical for the acquisition of DXR-II biochemical function through type-I functional divergence, two of them mapping onto key residues for DXR-II activity. DXR-II showed a markedly discontinuous distribution, which was verified at several levels: taxonomic (being predominantly found in Alphaproteobacteria and Firmicutes), metabolic (being mostly found in bacteria with complete functional MEP pathways with or without DXR-I), and phenotypic (as no biological/phenotypic property was found to be preferentially distributed among DXR-II-containing strains, apart from pathogenicity in animals). By performing a thorough comparative sequence analysis of GC content, 3:1 dinucleotide frequencies, codon usage and codon adaptation indexes (CAI) between DXR-II sequences and their corresponding genomes, we examined the role of horizontal gene transfer (HGT), as opposed to an scenario of massive gene loss, in the evolutionary origin and diversification of the DXR-II subfamily in bacteria.<br><br>CONCLUSIONS: Our analyses support a single origin of the DXR-II family through functional divergence, in which constitutes an exceptional model of acquisition and maintenance of redundant gene functions between non-homologous genes as a result of convergent evolution. Subsequently, although old episodic events of HGT could not be excluded, the results supported a prevalent role of gene loss in explaining the distribution of DXR-II in specific pathogenic eubacteria. Our results highlight the importance of the functional characterization of evolutionary shortcuts in isoprenoid biosynthesis for screening specific antibacterial drugs and for regulating the production of isoprenoids of human interest.}, }
@article {pmid24003001, year = {2013}, author = {Ivancevic, AM and Walsh, AM and Kortschak, RD and Adelson, DL}, title = {Jumping the fine LINE between species: horizontal transfer of transposable elements in animals catalyses genome evolution.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {35}, number = {12}, pages = {1071-1082}, doi = {10.1002/bies.201300072}, pmid = {24003001}, issn = {1521-1878}, mesh = {Animals ; DNA Transposable Elements/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome/*genetics ; Retroelements/*genetics ; }, abstract = {Horizontal transfer (HT) is the transmission of genetic material between non-mating species, a phenomenon thought to occur rarely in multicellular eukaryotes. However, many transposable elements (TEs) are not only capable of HT, but have frequently jumped between widely divergent species. Here we review and integrate reported cases of HT in retrotransposons of the BovB family, and DNA transposons, over a broad range of animals spanning all continents. Our conclusions challenge the paradigm that HT in vertebrates is restricted to infective long terminal repeat (LTR) retrotransposons or retroviruses. This raises the possibility that other non-LTR retrotransposons, such as L1 or CR1 elements, believed to be only vertically transmitted, can horizontally transfer between species. Growing evidence indicates that the process of HT is much more general across different TEs and species than previously believed, and that it likely shapes eukaryotic genomes and catalyses genome evolution.}, }
@article {pmid24002094, year = {2013}, author = {Sabat, AJ and Köck, R and Akkerboom, V and Hendrix, R and Skov, RL and Becker, K and Friedrich, AW}, title = {Novel organization of the arginine catabolic mobile element and staphylococcal cassette chromosome mec composite island and its horizontal transfer between distinct Staphylococcus aureus genotypes.}, journal = {Antimicrobial agents and chemotherapy}, volume = {57}, number = {11}, pages = {5774-5777}, pmid = {24002094}, issn = {1098-6596}, mesh = {Arginine/genetics/*metabolism ; Base Sequence ; Chromosome Mapping ; *Chromosomes, Bacterial ; *DNA Transposable Elements ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Genotype ; High-Throughput Nucleotide Sequencing ; Humans ; Methicillin Resistance/*genetics ; Methicillin-Resistant Staphylococcus aureus/*genetics/isolation &amp; purification ; Molecular Sequence Data ; Mutagenesis, Insertional ; Staphylococcal Infections/microbiology ; }, abstract = {In this study, 425 methicillin-resistant Staphylococcus aureus (MRSA) isolates recovered in the Dutch-German Euregio were investigated for the presence of the arginine catabolic mobile element (ACME). Sequence analysis by whole-genome sequencing revealed an entirely new organization of the ACME-staphylococcal cassette chromosome mec composite island (SCCmec-CI), with truncated ACME type II located downstream of SCCmec. An identical nucleotide sequence of ACME-SCCmec-CI was found in two distinct MRSA lineages (t064-ST8 and t002-ST5), which has not been reported previously in S. aureus.}, }
@article {pmid23998923, year = {2013}, author = {Kotnik, T}, title = {Prokaryotic diversity, electrified DNA, lightning waveforms, abiotic gene transfer, and the Drake equation: assessing the hypothesis of lightning-driven evolution.}, journal = {Physics of life reviews}, volume = {10}, number = {3}, pages = {384-388}, doi = {10.1016/j.plrev.2013.07.027}, pmid = {23998923}, issn = {1873-1457}, mesh = {Animals ; *Electroporation ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Humans ; *Lightning ; }, }
@article {pmid23995927, year = {2013}, author = {Tooming-Klunderud, A and Sogge, H and Rounge, TB and Nederbragt, AJ and Lagesen, K and Glöckner, G and Hayes, PK and Rohrlack, T and Jakobsen, KS}, title = {From green to red: horizontal gene transfer of the phycoerythrin gene cluster between Planktothrix strains.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {21}, pages = {6803-6812}, pmid = {23995927}, issn = {1098-5336}, mesh = {Base Sequence ; Cluster Analysis ; Color ; Cyanobacteria/*genetics ; Gene Transfer, Horizontal/*genetics ; Homologous Recombination/genetics ; Lakes/microbiology ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Annotation ; Molecular Sequence Data ; Multigene Family/*genetics ; Norway ; *Phenotype ; Phycoerythrin/*genetics ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Horizontal gene transfer is common in cyanobacteria, and transfer of large gene clusters may lead to acquisition of new functions and conceivably niche adaption. In the present study, we demonstrate that horizontal gene transfer between closely related Planktothrix strains can explain the production of the same oligopeptide isoforms by strains of different colors. Comparison of the genomes of eight Planktothrix strains revealed that strains producing the same oligopeptide isoforms are closely related, regardless of color. We have investigated genes involved in the synthesis of the photosynthetic pigments phycocyanin and phycoerythrin, which are responsible for green and red appearance, respectively. Sequence comparisons suggest the transfer of a functional phycoerythrin gene cluster generating a red phenotype in a strain that is otherwise more closely related to green strains. Our data show that the insertion of a DNA fragment containing the 19.7-kb phycoerythrin gene cluster has been facilitated by homologous recombination, also replacing a region of the phycocyanin operon. These findings demonstrate that large DNA fragments spanning entire functional gene clusters can be effectively transferred between closely related cyanobacterial strains and result in a changed phenotype. Further, the results shed new light on the discussion of the role of horizontal gene transfer in the sporadic distribution of large gene clusters in cyanobacteria, as well as the appearance of red and green strains.}, }
@article {pmid23995641, year = {2013}, author = {Westbye, AB and Leung, MM and Florizone, SM and Taylor, TA and Johnson, JA and Fogg, PC and Beatty, JT}, title = {Phosphate concentration and the putative sensor kinase protein CckA modulate cell lysis and release of the Rhodobacter capsulatus gene transfer agent.}, journal = {Journal of bacteriology}, volume = {195}, number = {22}, pages = {5025-5040}, pmid = {23995641}, issn = {1098-5530}, support = {93779-1//Canadian Institutes of Health Research/Canada ; 93779/CAPMC/CIHR/Canada ; }, mesh = {Bacteriophages/genetics/*physiology ; Culture Media/chemistry ; Gene Expression Regulation/drug effects ; Gene Expression Regulation, Viral ; Histidine Kinase ; Host-Parasite Interactions ; Phosphates/*metabolism ; Protein Kinases/*metabolism ; Rhodobacter capsulatus/metabolism/*virology ; *Transduction, Genetic ; *Virus Release ; }, abstract = {The gene transfer agent of Rhodobacter capsulatus (RcGTA) is a bacteriophage-like genetic element with the sole known function of horizontal gene transfer. Homologues of RcGTA genes are present in many members of the alphaproteobacteria and may serve an important role in microbial evolution. Transcription of RcGTA genes is induced as cultures enter the stationary phase; however, little is known about cis-active sequences. In this work, we identify the promoter of the first gene in the RcGTA structural gene cluster. Additionally, gene transduction frequency depends on the growth medium, and the reason for this is not known. We report that millimolar concentrations of phosphate posttranslationally inhibit the lysis-dependent release of RcGTA from cells in both a complex medium and a defined medium. Furthermore, we found that cell lysis requires the genes rcc00555 and rcc00556, which were expressed and studied in Escherichia coli to determine their predicted functions as an endolysin and holin, respectively. Production of RcGTA is regulated by host systems, including a putative histidine kinase, CckA, and we found that CckA is required for maximal expression of rcc00555 and for maturation of RcGTA to yield gene transduction-functional particles.}, }
@article {pmid23995634, year = {2013}, author = {Barton, MD and Petronio, M and Giarrizzo, JG and Bowling, BV and Barton, HA}, title = {The genome of Pseudomonas fluorescens strain R124 demonstrates phenotypic adaptation to the mineral environment.}, journal = {Journal of bacteriology}, volume = {195}, number = {21}, pages = {4793-4803}, pmid = {23995634}, issn = {1098-5530}, support = {P20 RR016481/RR/NCRR NIH HHS/United States ; 5P20RR016481/RR/NCRR NIH HHS/United States ; }, mesh = {*Adaptation, Physiological ; Bacteriological Techniques ; Caves ; Ecosystem ; Gene Expression Regulation, Bacterial/*physiology ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Metals/metabolism ; Minerals/*metabolism ; Nitrogen/metabolism ; Phylogeny ; Pseudomonas fluorescens/genetics/*metabolism ; Silicon Dioxide ; }, abstract = {Microbial adaptation to environmental conditions is a complex process, including acquisition of positive traits through horizontal gene transfer or the modification of existing genes through duplication and/or mutation. In this study, we examined the adaptation of a Pseudomonas fluorescens isolate (R124) from the nutrient-limited mineral environment of a silica cave in comparison with P. fluorescens isolates from surface soil and the rhizosphere. Examination of metal homeostasis gene pathways demonstrated a high degree of conservation, suggesting that such systems remain functionally similar across chemical environments. The examination of genomic islands unique to our strain revealed the presence of genes involved in carbohydrate metabolism, aromatic carbon metabolism, and carbon turnover, confirmed through phenotypic assays, suggesting the acquisition of potentially novel mechanisms for energy metabolism in this strain. We also identified a twitching motility phenotype active at low-nutrient concentrations that may allow alternative exploratory mechanisms for this organism in a geochemical environment. Two sets of candidate twitching motility genes are present within the genome, one on the chromosome and one on a plasmid; however, a plasmid knockout identified the functional gene as being present on the chromosome. This work highlights the plasticity of the Pseudomonas genome, allowing the acquisition of novel nutrient-scavenging pathways across diverse geochemical environments while maintaining a core of functional stress response genes.}, }
@article {pmid23994344, year = {2013}, author = {Elmer, JJ and Christensen, MD and Rege, K}, title = {Applying horizontal gene transfer phenomena to enhance non-viral gene therapy.}, journal = {Journal of controlled release : official journal of the Controlled Release Society}, volume = {172}, number = {1}, pages = {246-257}, pmid = {23994344}, issn = {1873-4995}, support = {R01 GM093229/GM/NIGMS NIH HHS/United States ; 1R01GM093229-01A1/GM/NIGMS NIH HHS/United States ; }, mesh = {Agrobacterium tumefaciens/genetics/physiology ; Animals ; Bartonella henselae/genetics/physiology ; *Gene Transfer, Horizontal ; Genetic Therapy/*methods ; Host-Pathogen Interactions ; Humans ; Plants/microbiology ; Transgenes ; Trypanosoma cruzi/genetics/physiology ; Virus Physiological Phenomena ; Viruses/genetics ; }, abstract = {Horizontal gene transfer (HGT) is widespread amongst prokaryotes, but eukaryotes tend to be far less promiscuous with their genetic information. However, several examples of HGT from pathogens into eukaryotic cells have been discovered and mimicked to improve non-viral gene delivery techniques. For example, several viral proteins and DNA sequences have been used to significantly increase cytoplasmic and nuclear gene delivery. Plant genetic engineering is routinely performed with the pathogenic bacterium Agrobacterium tumefaciens and similar pathogens (e.g. Bartonella henselae) may also be able to transform human cells. Intracellular parasites like Trypanosoma cruzi may also provide new insights into overcoming cellular barriers to gene delivery. Finally, intercellular nucleic acid transfer between host cells will also be briefly discussed. This article will review the unique characteristics of several different viruses and microbes and discuss how their traits have been successfully applied to improve non-viral gene delivery techniques. Consequently, pathogenic traits that originally caused diseases may eventually be used to treat many genetic diseases.}, }
@article {pmid23993843, year = {2013}, author = {Henry, LM and Peccoud, J and Simon, JC and Hadfield, JD and Maiden, MJ and Ferrari, J and Godfray, HC}, title = {Horizontally transmitted symbionts and host colonization of ecological niches.}, journal = {Current biology : CB}, volume = {23}, number = {17}, pages = {1713-1717}, pmid = {23993843}, issn = {1879-0445}, support = {087622//Wellcome Trust/United Kingdom ; }, mesh = {*Ecosystem ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; *Symbiosis ; }, abstract = {Facultative or "secondary" symbionts are common in eukaryotes, particularly insects. While not essential for host survival, they often provide significant fitness benefits. It has been hypothesized that secondary symbionts form a "horizontal gene pool" shuttling adaptive genes among host lineages in an analogous manner to plasmids and other mobile genetic elements in bacteria. However, we do not know whether the distributions of symbionts across host populations reflect random acquisitions followed by vertical inheritance or whether the associations have occurred repeatedly in a manner consistent with a dynamic horizontal gene pool. Here we explore these questions using the phylogenetic and ecological distributions of secondary symbionts carried by 1,104 pea aphids, Acyrthosiphon pisum. We find that not only is horizontal transfer common, but it is also associated with aphid lineages colonizing new ecological niches, including novel plant species and climatic regions. Moreover, aphids that share the same ecologies worldwide have independently acquired related symbiont genotypes, suggesting significant involvement of symbionts in their host's adaptation to different niches. We conclude that the secondary symbiont community forms a horizontal gene pool that influences the adaptation and distribution of their insect hosts. These findings highlight the importance of symbiotic microorganisms in the radiation of eukaryotes.}, }
@article {pmid23988880, year = {2013}, author = {Rubinsky, B}, title = {Mechanisms of abiotic horizontal gene transfer: comment on "Lightning-triggered electroporation and electrofusion as possible contributors to natural horizontal gene transfer" by Tadej Kotnik.}, journal = {Physics of life reviews}, volume = {10}, number = {3}, pages = {377-379}, doi = {10.1016/j.plrev.2013.07.031}, pmid = {23988880}, issn = {1873-1457}, mesh = {Animals ; *Electroporation ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Humans ; *Lightning ; }, }
@article {pmid23985741, year = {2014}, author = {Tamas, I and Smirnova, AV and He, Z and Dunfield, PF}, title = {The (d)evolution of methanotrophy in the Beijerinckiaceae--a comparative genomics analysis.}, journal = {The ISME journal}, volume = {8}, number = {2}, pages = {369-382}, pmid = {23985741}, issn = {1751-7370}, mesh = {Beijerinckiaceae/*classification/enzymology/*genetics ; Gene Transfer, Horizontal/genetics ; Genome ; Genome, Bacterial/*genetics ; *Genomics ; Membrane Transport Proteins/genetics ; Metabolic Networks and Pathways ; Methane/metabolism ; Oxygenases/genetics ; *Phylogeny ; }, abstract = {The alphaproteobacterial family Beijerinckiaceae contains generalists that grow on a wide range of substrates, and specialists that grow only on methane and methanol. We investigated the evolution of this family by comparing the genomes of the generalist organotroph Beijerinckia indica, the facultative methanotroph Methylocella silvestris and the obligate methanotroph Methylocapsa acidiphila. Highly resolved phylogenetic construction based on universally conserved genes demonstrated that the Beijerinckiaceae forms a monophyletic cluster with the Methylocystaceae, the only other family of alphaproteobacterial methanotrophs. Phylogenetic analyses also demonstrated a vertical inheritance pattern of methanotrophy and methylotrophy genes within these families. Conversely, many lateral gene transfer (LGT) events were detected for genes encoding carbohydrate transport and metabolism, energy production and conversion, and transcriptional regulation in the genome of B. indica, suggesting that it has recently acquired these genes. A key difference between the generalist B. indica and its specialist methanotrophic relatives was an abundance of transporter elements, particularly periplasmic-binding proteins and major facilitator transporters. The most parsimonious scenario for the evolution of methanotrophy in the Alphaproteobacteria is that it occurred only once, when a methylotroph acquired methane monooxygenases (MMOs) via LGT. This was supported by a compositional analysis suggesting that all MMOs in Alphaproteobacteria methanotrophs are foreign in origin. Some members of the Beijerinckiaceae subsequently lost methanotrophic functions and regained the ability to grow on multicarbon energy substrates. We conclude that B. indica is a recidivist multitroph, the only known example of a bacterium having completely abandoned an evolved lifestyle of specialized methanotrophy.}, }
@article {pmid23983220, year = {2013}, author = {Meslet-Cladière, L and Delage, L and Leroux, CJ and Goulitquer, S and Leblanc, C and Creis, E and Gall, EA and Stiger-Pouvreau, V and Czjzek, M and Potin, P}, title = {Structure/function analysis of a type iii polyketide synthase in the brown alga Ectocarpus siliculosus reveals a biochemical pathway in phlorotannin monomer biosynthesis.}, journal = {The Plant cell}, volume = {25}, number = {8}, pages = {3089-3103}, pmid = {23983220}, issn = {1532-298X}, mesh = {Acclimatization ; Amino Acid Sequence ; *Biosynthetic Pathways ; Catalytic Domain ; Crystallography, X-Ray ; Fresh Water ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Plant ; Models, Molecular ; Molecular Sequence Data ; Phaeophyceae/*enzymology/genetics ; Phloroglucinol/chemistry/metabolism ; Phylogeny ; Polyketide Synthases/*chemistry/genetics/*metabolism ; RNA, Messenger/genetics/metabolism ; Recombinant Proteins/metabolism ; Seawater ; Sequence Alignment ; Structure-Activity Relationship ; Tannins/*biosynthesis/chemistry ; }, abstract = {Brown algal phlorotannins are structural analogs of condensed tannins in terrestrial plants and, like plant phenols, they have numerous biological functions. Despite their importance in brown algae, phlorotannin biosynthetic pathways have been poorly characterized at the molecular level. We found that a predicted type III polyketide synthase in the genome of the brown alga Ectocarpus siliculosus, PKS1, catalyzes a major step in the biosynthetic pathway of phlorotannins (i.e., the synthesis of phloroglucinol monomers from malonyl-CoA). The crystal structure of PKS1 at 2.85-Å resolution provided a good quality electron density map showing a modified Cys residue, likely connected to a long chain acyl group. An additional pocket not found in other known type III PKSs contains a reaction product that might correspond to a phloroglucinol precursor. In vivo, we also found a positive correlation between the phloroglucinol content and the PKS III gene expression level in cells of a strain of Ectocarpus adapted to freshwater during its reacclimation to seawater. The evolution of the type III PKS gene family in Stramenopiles suggests a lateral gene transfer event from an actinobacterium.}, }
@article {pmid23980812, year = {2014}, author = {Nguyen, MTHD and Liu, M and Thomas, T}, title = {Ankyrin-repeat proteins from sponge symbionts modulate amoebal phagocytosis.}, journal = {Molecular ecology}, volume = {23}, number = {6}, pages = {1635-1645}, doi = {10.1111/mec.12384}, pmid = {23980812}, issn = {1365-294X}, mesh = {Acanthamoeba/physiology ; Animals ; *Ankyrin Repeat ; Bacterial Proteins/genetics/*metabolism ; Gammaproteobacteria/*genetics/physiology ; Molecular Sequence Data ; *Phagocytosis ; Phagosomes/physiology ; Phylogeny ; Porifera/*microbiology ; *Symbiosis ; Vacuoles/physiology ; }, abstract = {Bacteria-eukaryote symbiosis occurs in all stages of evolution, from simple amoebae to mammals, and from facultative to obligate associations. Sponges are ancient metazoans that form intimate symbiotic interactions with complex communities of bacteria. The basic nutritional requirements of the sponge are in part satisfied by the phagocytosis of bacterial food particles from the surrounding water. How bacterial symbionts, which are permanently associated with the sponge, survive in the presence of phagocytic cells is largely unknown. Here, we present the discovery of a genomic fragment from an uncultured gamma-proteobacterial sponge symbiont that encodes for four proteins, whose closest known relatives are found in a sponge genome. Through recombinant approaches, we show that these four eukaryotic-like, ankyrin-repeat proteins (ARP) when expressed in Eschericha coli can modulate phagocytosis of amoebal cells and lead to accumulation of bacteria in the phagosome. Mechanistically, two ARPs appear to interfere with phagosome development in a similar way to reduced vacuole acidification, by blocking the fusion of the early phagosome with the lysosome and its digestive enzymes. Our results show that ARP from sponge symbionts can function to interfere with phagocytosis, and we postulate that this might be one mechanism by which symbionts can escape digestion in a sponge host.}, }
@article {pmid23977007, year = {2013}, author = {Svartström, O and Mushtaq, M and Pringle, M and Segerman, B}, title = {Genome-wide relatedness of Treponema pedis, from gingiva and necrotic skin lesions of pigs, with the human oral pathogen Treponema denticola.}, journal = {PloS one}, volume = {8}, number = {8}, pages = {e71281}, pmid = {23977007}, issn = {1932-6203}, mesh = {Animals ; Base Composition ; Gene Transfer, Horizontal ; Genetic Variation ; Genome Size ; *Genome, Bacterial ; Gingiva/*microbiology ; Humans ; *Phylogeny ; Sequence Homology, Nucleic Acid ; Swine/microbiology ; Treponema/*classification/genetics/isolation &amp; purification ; Treponema denticola/*classification/genetics/isolation &amp; purification ; }, abstract = {Treponema pedis and T. denticola are two genetically related species with different origins of isolation. Treponema denticola is part of the human oral microbiota and is associated with periodontitis while T. pedis has been isolated from skin lesions in animals, e.g., digital dermatitis in cattle and necrotic ulcers in pigs. Although multiple Treponema phylotypes may exist in ulcerative lesions in pigs, T. pedis appears to be a predominant spirochete in these lesions. Treponema pedis can also be present in pig gingiva. In this study, we determined the complete genome sequence of T. pedis strain T A4, isolated from a porcine necrotic ear lesion, and compared its genome with that of T. denticola. Most genes in T. pedis were homologous to those in T. denticola and the two species were similar in general genomic features such as size, G+C content, and number of genes. In addition, many homologues of specific virulence-related genes in T. denticola were found in T. pedis. Comparing a selected pair of strains will usually not give a complete picture of the relatedness between two species. We therefore complemented the analysis with draft genomes from six T. pedis isolates, originating from gingiva and necrotic ulcers in pigs, and from twelve T. denticola strains. Each strain carried a considerable amount of accessory genetic material, of which a large part was strain specific. There was also extensive sequence variability in putative virulence-related genes between strains belonging to the same species. Signs of lateral gene-transfer events from bacteria known to colonize oral environments were found. This suggests that the oral cavity is an important habitat for T. pedis. In summary, we found extensive genomic similarities between T. pedis and T. denticola but also large variability within each species.}, }
@article {pmid23973006, year = {2013}, author = {Liberti, M and Apollonio, F and Merla, C and d'Inzeo, G}, title = {Proving lightning role in the evolution of life: comment on "Lightning-triggered electroporation and electrofusion as possible contributors to natural horizontal gene transfer" by Tadej Kotnik.}, journal = {Physics of life reviews}, volume = {10}, number = {3}, pages = {380-381}, doi = {10.1016/j.plrev.2013.07.026}, pmid = {23973006}, issn = {1873-1457}, mesh = {Animals ; *Electroporation ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Humans ; *Lightning ; }, }
@article {pmid23972949, year = {2013}, author = {Boerlin, P and Poljak, Z and Gallant, J and Chalmers, G and Nicholson, V and Soltes, GA and MacInnes, JI}, title = {Genetic diversity of Haemophilus parasuis from sick and healthy pigs.}, journal = {Veterinary microbiology}, volume = {167}, number = {3-4}, pages = {459-467}, doi = {10.1016/j.vetmic.2013.07.028}, pmid = {23972949}, issn = {1873-2542}, mesh = {Animals ; Cluster Analysis ; Gene Frequency ; Genetic Linkage ; *Genetic Variation ; Haemophilus Infections/microbiology/*veterinary ; Haemophilus parasuis/classification/*genetics/isolation &amp; purification ; *Molecular Typing ; Multigene Family ; Sus scrofa ; Swine ; Swine Diseases/*microbiology ; Virulence/genetics ; }, abstract = {A collection of 94 Haemophilus parasuis isolates was used for this study. It consisted of isolates from organs of pigs with Glässer's disease and pneumonia (n=54), from nasal swabs of healthy pigs in farms without Glässer's disease problems (n=25), and 15 reference strains. These isolates were typed using a new multilocus variable number of tandem repeats analysis (MLVA) protocol and investigated for the presence of nine putative virulence genes. The new MLVA protocol was highly discriminatory (54 types identified and discrimination index of 97.4%) and reproducible. Similar to previous investigations done with other methods, two major genetic clusters were identified by MLVA, which partially correlated with serotype and virulence gene distributions. Gene linkage analysis suggested that lateral gene transfer occurs within each of these clusters, but rarely between them. Although one single MLVA type included more than 20% of the clinical isolates, no significant correlation was detected between a specific MLVA type, the major genetic clusters, or the presence of any of the virulence genes investigated or the source of the isolates (clinical infection vs. healthy pig). The MLVA typing protocol described in this study is a promising new tool for future investigations into the epidemiology of Glässer's disease and could help us to better understand interacting microbial, host and environmental factors that lead to the development of H. parasuis disease.}, }
@article {pmid23972581, year = {2013}, author = {Weaver, JC}, title = {Estimating the contribution of lightning to microbial evolution: guidance from the Drake equation: comment on "Lightning-triggered electroporation and electrofusion as possible contributors to natural horizontal gene transfer" by Tadej Kotnik.}, journal = {Physics of life reviews}, volume = {10}, number = {3}, pages = {373-376}, doi = {10.1016/j.plrev.2013.07.030}, pmid = {23972581}, issn = {1873-1457}, support = {GM063857/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Electroporation ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Humans ; *Lightning ; }, }
@article {pmid23967454, year = {2013}, author = {Stencel, A and Crespi, B}, title = {What is a genome?.}, journal = {Molecular ecology}, volume = {22}, number = {13}, pages = {3437-3443}, doi = {10.1111/mec.12355}, pmid = {23967454}, issn = {1365-294X}, mesh = {Cell Lineage ; DNA/genetics ; Empirical Research ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome ; *Genomics ; *Terminology as Topic ; }, abstract = {The field of genomics is expanding rapidly, yet the meanings of the word ‘genome’ have yet to be conceptualized in explicit, coherent and useful frameworks. We develop and apply an evolutionary conceptualization of the genome,which represents a logical extension of the evolutionary definition of a gene developed by George C.Williams. An evolutionary genome thus represents a set of genetic material, in a lineage, that due to common interests tends to favour the same or similar phenotypes.This conceptualization provides novel perspectives on genome functions, boundaries and evolution, which should help to guide theoretical and empirical genomics research.}, }
@article {pmid23967008, year = {2013}, author = {Silva, DC and Silva, RC and Ferreira, RC and Briones, MR}, title = {Examining marginal sequence similarities between bacterial type III secretion system components and Trypanosoma cruzi surface proteins: horizontal gene transfer or convergent evolution?.}, journal = {Frontiers in genetics}, volume = {4}, number = {}, pages = {143}, pmid = {23967008}, issn = {1664-8021}, abstract = {The cell invasion mechanism of Trypanosoma cruzi has similarities with some intracellular bacterial taxa especially regarding calcium mobilization. This mechanism is not observed in other trypanosomatids, suggesting that the molecules involved in this type of cell invasion were a product of (1) acquisition by horizontal gene transfer (HGT); (2) secondary loss in the other trypanosomatid lineages of the mechanism inherited since the bifurcation Bacteria-Neomura (1.9 billion to 900 million years ago); or (3) de novo evolution from non-homologous proteins via convergent evolution. Similar to T. cruzi, several bacterial genera require increased host cell cytosolic calcium for intracellular invasion. Among intracellular bacteria, the mechanism of host cell invasion of genus Salmonella is the most similar to T. cruzi. The invasion of Salmonella occurs by contact with the host's cell surface and is mediated by the type III secretion system (T3SS) that promotes the contact-dependent translocation of effector proteins directly into host's cell cytoplasm. Here we provide evidence of distant sequence similarities and structurally conserved domains between T. cruzi and Salmonella spp T3SS proteins. Exhaustive database searches were directed to a wide range of intracellular bacteria and trypanosomatids, exploring sequence patterns for comparison of structural similarities and Bayesian phylogenies. Based on our data we hypothesize that T. cruzi acquired genes for calcium mobilization mediated invasion by ancient HGT from ancestral Salmonella lineages.}, }
@article {pmid23966031, year = {2013}, author = {Orr, RJ and Stüken, A and Murray, SA and Jakobsen, KS}, title = {Evolution and distribution of saxitoxin biosynthesis in dinoflagellates.}, journal = {Marine drugs}, volume = {11}, number = {8}, pages = {2814-2828}, pmid = {23966031}, issn = {1660-3397}, mesh = {Animals ; Cyanobacteria/genetics/metabolism ; Dinoflagellida/genetics/*metabolism ; Gene Transfer, Horizontal ; Humans ; Neurotoxins/*biosynthesis/genetics/toxicity ; Saxitoxin/*biosynthesis/genetics/toxicity ; Shellfish Poisoning/etiology ; }, abstract = {Numerous species of marine dinoflagellates synthesize the potent environmental neurotoxic alkaloid, saxitoxin, the agent of the human illness, paralytic shellfish poisoning. In addition, certain freshwater species of cyanobacteria also synthesize the same toxic compound, with the biosynthetic pathway and genes responsible being recently reported. Three theories have been postulated to explain the origin of saxitoxin in dinoflagellates: The production of saxitoxin by co-cultured bacteria rather than the dinoflagellates themselves, convergent evolution within both dinoflagellates and bacteria and horizontal gene transfer between dinoflagellates and bacteria. The discovery of cyanobacterial saxitoxin homologs in dinoflagellates has enabled us for the first time to evaluate these theories. Here, we review the distribution of saxitoxin within the dinoflagellates and our knowledge of its genetic basis to determine the likely evolutionary origins of this potent neurotoxin.}, }
@article {pmid23965785, year = {2013}, author = {Winstel, V and Liang, C and Sanchez-Carballo, P and Steglich, M and Munar, M and Bröker, BM and Penadés, JR and Nübel, U and Holst, O and Dandekar, T and Peschel, A and Xia, G}, title = {Wall teichoic acid structure governs horizontal gene transfer between major bacterial pathogens.}, journal = {Nature communications}, volume = {4}, number = {}, pages = {2345}, pmid = {23965785}, issn = {2041-1723}, mesh = {Amino Acid Sequence ; Bacteriophages/genetics ; Cell Wall/metabolism ; Escherichia coli/genetics ; Gene Transfer, Horizontal/*genetics ; Genomic Islands/*genetics ; Listeria monocytogenes/genetics ; Molecular Sequence Data ; Sequence Alignment ; Staphylococcus aureus/*genetics ; Staphylococcus epidermidis/genetics ; Teichoic Acids/biosynthesis/chemistry/*metabolism ; }, abstract = {Mobile genetic elements (MGEs) encoding virulence and resistance genes are widespread in bacterial pathogens, but it has remained unclear how they occasionally jump to new host species. Staphylococcus aureus clones exchange MGEs such as S. aureus pathogenicity islands (SaPIs) with high frequency via helper phages. Here we report that the S. aureus ST395 lineage is refractory to horizontal gene transfer (HGT) with typical S. aureus but exchanges SaPIs with other species and genera including Staphylococcus epidermidis and Listeria monocytogenes. ST395 produces an unusual wall teichoic acid (WTA) resembling that of its HGT partner species. Notably, distantly related bacterial species and genera undergo efficient HGT with typical S. aureus upon ectopic expression of S. aureus WTA. Combined with genomic analyses, these results indicate that a 'glycocode' of WTA structures and WTA-binding helper phages permits HGT even across long phylogenetic distances thereby shaping the evolution of Gram-positive pathogens.}, }
@article {pmid23956949, year = {2013}, author = {Al-Assil, B and Mahfoud, M and Hamzeh, AR}, title = {First report on class 1 integrons and Trimethoprim-resistance genes from dfrA group in uropathogenic E. coli (UPEC) from the Aleppo area in Syria.}, journal = {Mobile genetic elements}, volume = {3}, number = {3}, pages = {e25204}, pmid = {23956949}, issn = {2159-2543}, abstract = {Horizontal gene transfer (HGT) introduces advantageous genetic elements into pathogenic bacteria using tools such as class1 integrons. This study aimed at investigating the distribution of these integrons among uropathogenic E. coli (UPEC) isolated from patients in Aleppo, Syria. It also set to uncover the frequencies of the clinically relevant DfrA1 and DfrA17,7, as well as various associations leading to reduced susceptibility. This study involved 75 Trimethoprim-resistant E. coli isolates from in- and outpatients with urinary tract infections (UTIs) from 3 major hospitals in Aleppo. Bacterial identification, resistance and extended-spectrum-β-lactamase (ESBL) production testing were performed according to Clinical Laboratory Standards Institute guidelines. Detection of integrons and DfrA genes was done using PCR and statistical significance was inferred through χ2 (Fisher's) test. Class1 integrons were detected in 54.6% of isolates while DfrA1 and DfrA17,7 were found in 16% and 70.6% of tested samples respectively. Furthermore, only DfrA17,7 were strongly associated with class1 integrons, as were reduced susceptibility to the majority of individual antibiotics, multidrug resistance and ESBL production. This study demonstrated the high prevalence of class1 integrons among UPEC strains in Aleppo, Syria, as well as their significant associations with MDR. This data give information for local healthcare provision using antibiotic chemotherapy.}, }
@article {pmid23953027, year = {2013}, author = {Wendlandt, S and Li, B and Ma, Z and Schwarz, S}, title = {Complete sequence of the multi-resistance plasmid pV7037 from a porcine methicillin-resistant Staphylococcus aureus.}, journal = {Veterinary microbiology}, volume = {166}, number = {3-4}, pages = {650-654}, doi = {10.1016/j.vetmic.2013.07.017}, pmid = {23953027}, issn = {1873-2542}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Methicillin-Resistant Staphylococcus aureus/drug effects/*genetics/isolation &amp; purification ; Plasmids/*genetics ; Sequence Analysis, DNA ; Staphylococcal Infections/microbiology/*veterinary ; Swine ; Swine Diseases/*microbiology ; beta-Lactamases/genetics ; }, abstract = {The aim of this study was to determine the complete sequence of the multi-resistance plasmid pV7037 to gain insight into the structure and organization of this plasmid. Of the four XbaI clones of pV7037, one clone of 17,577 bp has already been sequenced and shown to carry a multi-resistance gene cluster. The remaining three clones of approximately 12.5, 6.5 and 4.5 kb were sequenced, the entire plasmid sequence correctly assembled and investigated for reading frames. In addition, two reading frames one coding for an ABC transporter and the other coding for an rRNA methylase were cloned and expressed in a S. aureus host to see whether they confer antimicrobial resistance properties. Plasmid pV7037 proved to be 40,971 bp in size. Besides the previously determined resistance gene cluster, it carried a functionally active tet(L) gene for tetracycline resistance, a complete cadDX operon for cadmium resistance and also a variant of the β-lactamase transposon Tn552. Two single bp deletions, which resulted in frame shifts, functionally deleted the genes for the BlaZ β-lactamase and the signal transducer protein BlaR1 in this Tn552 variant of pV7037. Plasmid pV7037 seems to be composed of various parts previously known from plasmids and transposons of staphylococci and other Gram-positive bacteria. However, there are also parts of the plasmid which do not show any homology to so far known sequences deposited in the databases. The novel ABC transporter and rRNA methylase genes identified on pV7037 do not seem to play a role in antimicrobial resistance. The co-location of numerous antimicrobial resistance genes bears the risk of co-transfer and co-selection of resistance genes, but also persistence of resistance genes even if no direct selective pressure by the use of the respective antimicrobial agents is applied.}, }
@article {pmid23950996, year = {2013}, author = {Humbert, JF and Barbe, V and Latifi, A and Gugger, M and Calteau, A and Coursin, T and Lajus, A and Castelli, V and Oztas, S and Samson, G and Longin, C and Medigue, C and de Marsac, NT}, title = {A tribute to disorder in the genome of the bloom-forming freshwater cyanobacterium Microcystis aeruginosa.}, journal = {PloS one}, volume = {8}, number = {8}, pages = {e70747}, pmid = {23950996}, issn = {1932-6203}, mesh = {Base Composition ; Computational Biology/methods ; Ecosystem ; Fresh Water/*microbiology ; Gene Order ; Gene Transfer, Horizontal ; Genome Size ; *Genome, Bacterial ; Microcystis/classification/*genetics/metabolism ; Multigene Family ; Phylogeny ; Repetitive Sequences, Nucleic Acid ; *Water Microbiology ; }, abstract = {Microcystis aeruginosa is one of the most common bloom-forming cyanobacteria in freshwater ecosystems worldwide. This species produces numerous secondary metabolites, including microcystins, which are harmful to human health. We sequenced the genomes of ten strains of M. aeruginosa in order to explore the genomic basis of their ability to occupy varied environments and proliferate. Our findings show that M. aeruginosa genomes are characterized by having a large open pangenome, and that each genome contains similar proportions of core and flexible genes. By comparing the GC content of each gene to the mean value of the whole genome, we estimated that in each genome, around 11% of the genes seem to result from recent horizontal gene transfer events. Moreover, several large gene clusters resulting from HGT (up to 19 kb) have been found, illustrating the ability of this species to integrate such large DNA molecules. It appeared also that all M. aeruginosa displays a large genomic plasticity, which is characterized by a high proportion of repeat sequences and by low synteny values between the strains. Finally, we identified 13 secondary metabolite gene clusters, including three new putative clusters. When comparing the genomes of Microcystis and Prochlorococcus, one of the dominant picocyanobacteria living in marine ecosystems, our findings show that they are characterized by having almost opposite evolutionary strategies, both of which have led to ecological success in their respective environments.}, }
@article {pmid23949298, year = {2013}, author = {Hassan, MI and Alkharsah, KR and Alzahrani, AJ and Obeid, OE and Khamis, AH and Diab, A}, title = {Detection of extended spectrum beta-lactamases-producing isolates and effect of AmpC overlapping.}, journal = {Journal of infection in developing countries}, volume = {7}, number = {8}, pages = {618-629}, doi = {10.3855/jidc.2919}, pmid = {23949298}, issn = {1972-2680}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Conjugation, Genetic ; DNA, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial ; Enterobacteriaceae/*enzymology/genetics/isolation &amp; purification ; Enterobacteriaceae Infections/*epidemiology/*microbiology ; Gene Transfer, Horizontal ; Genotype ; Humans ; Male ; Microbial Sensitivity Tests ; Middle Aged ; Phenotype ; Prevalence ; Saudi Arabia/epidemiology ; Young Adult ; beta-Lactamases/analysis/*genetics ; }, abstract = {INTRODUCTION: Few reports about the prevalence and genetic basis of extended spectrum beta-lactamases (ESBLs) are available from Saudi Arabia. We sought to determine the prevalence of ESBL-producing Enterobacteriaceae in a university hospital in eastern Saudi Arabia and to characterize the ESBLs produced by these isolates at the molecular level.<br><br>METHODOLOGY: All clinical isolates of Escherichia coli, Klebsiella spp., and Proteus spp. collected over two years were evaluated for susceptibility to a panel of antimicrobials and were analyzed for the ESBL phenotype using screening and confirmatory tests. ESBL-positive isolates were then screened for the presence of genes encoding CTX-M, SHV, and TEM beta-lactamases by PCR.<br><br>RESULTS AND CONCLUSIONS: The overall prevalence of ESBL-producing isolates was 4.8% (253/5256). Most isolates (80%) were from the inpatient department. The ESBL phenotype was more frequently detected in K. pneumonia. CTX-M genes were the most prevalent ESBL genes, detected in 82% of the studied isolates. The ESBL producers demonstrated a high multidrug resistance rate (96.6%). In transconjugation assay, the same ESBL gene pattern was transmitted from 29.7% of K. pneumoniae donors to the recipient strain, and the latter exhibited concomitant decreased aminoglycosides and co-trimoxazole susceptibility. We observed the presence of ESBL screen-positive but confirmatory-negative isolates (8.9%). Phenotypic tests for the production of AmpC &#x3b2;-lactamase tested positive in 52% of these isolates. Further studies are needed for appropriate detection of concomitant ESBL and AmpC enzyme production among such isolates. Continued surveillance and judicious antibiotic usage together with the implementation of efficient infection control measures are absolutely required.}, }
@article {pmid23948139, year = {2013}, author = {Golberg, A}, title = {The impact of pulsed electric fields on cells and biomolecules: comment on "Lightning-triggered electroporation and electrofusion as possible contributors to natural horizontal gene transfer" by Tadej Kotnik.}, journal = {Physics of life reviews}, volume = {10}, number = {3}, pages = {382-383}, doi = {10.1016/j.plrev.2013.07.025}, pmid = {23948139}, issn = {1873-1457}, mesh = {Animals ; *Electroporation ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Humans ; *Lightning ; }, }
@article {pmid23943757, year = {2013}, author = {Spoor, LE and McAdam, PR and Weinert, LA and Rambaut, A and Hasman, H and Aarestrup, FM and Kearns, AM and Larsen, AR and Skov, RL and Fitzgerald, JR}, title = {Livestock origin for a human pandemic clone of community-associated methicillin-resistant Staphylococcus aureus.}, journal = {mBio}, volume = {4}, number = {4}, pages = {}, pmid = {23943757}, issn = {2150-7511}, support = {095831/WT_/Wellcome Trust/United Kingdom ; BB/I013873/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Cluster Analysis ; Community-Acquired Infections/epidemiology/*microbiology ; Gene Transfer, Horizontal ; Humans ; Interspersed Repetitive Sequences ; Livestock/*microbiology ; Methicillin-Resistant Staphylococcus aureus/*classification/*genetics/isolation &amp; purification ; Molecular Epidemiology ; Molecular Typing ; *Pandemics ; Phylogeny ; Staphylococcal Infections/epidemiology/*microbiology ; Zoonoses/epidemiology/*microbiology ; }, abstract = {UNLABELLED: The importance of livestock as a source of bacterial pathogens with the potential for epidemic spread in human populations is unclear. In recent years, there has been a global increase in community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) infections of healthy humans, but an understanding of the different evolutionary origins of CA-MRSA clones and the basis for their recent expansion is lacking. Here, using a high-resolution phylogenetic approach, we report the discovery of two emergent clones of human epidemic CA-MRSA which resulted from independent livestock-to-human host jumps by the major bovine S. aureus complex, CC97. Of note, one of the new clones was isolated from human infections on four continents, demonstrating its global dissemination since the host jump occurred over 40 years ago. The emergence of both human S. aureus clones coincided with the independent acquisition of mobile genetic elements encoding antimicrobial resistance and human-specific mediators of immune evasion, consistent with an important role for these genetic events in the capacity to survive and transmit among human populations. In conclusion, we provide evidence that livestock represent a reservoir for the emergence of new human-pathogenic S. aureus clones with the capacity for pandemic spread. These findings have major public health implications highlighting the importance of surveillance for early identification of emergent clones and improved transmission control measures at the human-livestock interface.<br><br>IMPORTANCE: Animals are the major source of new pathogens affecting humans. However, the potential for pathogenic bacteria that originally were found in animals to switch hosts and become widely established in human populations is not clear. Here, we report the discovery of emergent clones of methicillin-resistant Staphylococcus aureus (MRSA) that originated in livestock and switched to humans, followed by host-adaptive evolution and epidemic spread in global human populations. Our findings demonstrate that livestock can act as a reservoir for the emergence of new human bacterial clones with potential for pandemic spread, highlighting the potential role of surveillance and biosecurity measures in the agricultural setting for preventing the emergence of new human pathogens.}, }
@article {pmid23943635, year = {2013}, author = {Danishuddin, M and Hassan Baig, M and Kaushal, L and Khan, AU}, title = {BLAD: a comprehensive database of widely circulated beta-lactamases.}, journal = {Bioinformatics (Oxford, England)}, volume = {29}, number = {19}, pages = {2515-2516}, doi = {10.1093/bioinformatics/btt417}, pmid = {23943635}, issn = {1367-4811}, mesh = {*Databases, Nucleic Acid ; Internet ; *Software ; beta-Lactamases/*analysis/*genetics ; }, abstract = {MOTIVATION: Beta-lactamases confer resistance to a broad range of antibiotics and inhibitors by accumulating mutations. The number of beta-lactamases and their variants is steadily increasing. The horizontal gene transfer likely plays a major role in dissemination of these markers to new environments and hosts. Moreover, information about the beta-lactamase classes and their variants was scattered. Categorizing all these classes and their associated variants along with their epidemiology and resistance pattern information on one platform could be helpful to the researcher working on multidrug-resistant bacteria. Thus, the beta-lactamase database (BLAD) has been developed to provide comprehensive information (epidemiology and resistance pattern) on beta-lactamases. Beta-lactamase gene sequences in BLAD are linked with structural data, phenotypic data (i.e. antibiotic resistance) and literature references to experimental studies. In summary, BLAD integrates information that may provide insight into the epidemiology of multidrug resistance and enable the designing of novel drug candidates.<br><br>AVAILABILITY: The database can be accessed from the website www.blad.co.in.}, }
@article {pmid23942379, year = {2013}, author = {Yang, D and Wang, J and Qiu, Z and Jin, M and Shen, Z and Chen, Z and Wang, X and Zhang, B and Li, JW}, title = {Horizontal transfer of antibiotic resistance genes in a membrane bioreactor.}, journal = {Journal of biotechnology}, volume = {167}, number = {4}, pages = {441-447}, doi = {10.1016/j.jbiotec.2013.08.004}, pmid = {23942379}, issn = {1873-4863}, mesh = {Bacteria/*genetics ; Biofilms/growth &amp; development ; *Bioreactors ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Photobacterium/genetics ; Proteus/genetics ; Pseudomonas/genetics ; R Factors/*genetics ; Sewage/microbiology ; Shewanella/genetics ; Vibrio/genetics ; }, abstract = {Growing attention has been paid to the dissemination of antibiotic resistance genes (ARGs) in wastewater microbial communities. The application of membrane bioreactors (MBRs) in wastewater treatment is becoming increasingly widespread. We hypothesized that the transfer of ARGs among bacteria could occur in MBRs, which combine a high density of bacterial cells, biofilms, and antibiotic resistance bacteria or ARGs. In this study, the transfer discipline and dissemination of the RP4 plasmid in MBRs were investigated by the counting plate method, the MIDI microorganism identification system, and quantitative polymerase chain reaction (qPCR) techniques. The results showed that the average transfer frequency of the RP4 plasmid from the donor strain to cultivable bacteria in activated sludge was 2.76×10[-5] per recipient, which was greater than the transfer frequency in wastewater and bacterial sludge reported previously. In addition, many bacterial species in the activated sludge had received RP4 by horizontal transfer, while the genera of Shewanella spp., Photobacterium spp., Pseudomonas spp., Proteus spp., and Vibrio spp. were more likely to acquire this plasmid. Interestingly, the abundance of the RP4 plasmid in total DNA remained at high levels and relatively stable at 10[4] copies/mg of biosolids, suggesting that ARGs were transferred from donor strains to activated sludge bacteria in our study. Thus, the presence of ARGs in sewage sludge poses a potential health threat.}, }
@article {pmid23940551, year = {2013}, author = {Zhou, Y and Bu, L and Guo, M and Zhou, C and Wang, Y and Chen, L and Liu, J}, title = {Comprehensive genomic characterization of campylobacter genus reveals some underlying mechanisms for its genomic diversification.}, journal = {PloS one}, volume = {8}, number = {8}, pages = {e70241}, pmid = {23940551}, issn = {1932-6203}, mesh = {Campylobacter jejuni/*genetics ; Gene Transfer, Horizontal/genetics ; Genetic Variation/genetics ; Genome, Bacterial/*genetics ; Phylogeny ; }, abstract = {Campylobacter species.are phenotypically diverse in many aspects including host habitats and pathogenicities, which demands comprehensive characterization of the entire Campylobacter genus to study their underlying genetic diversification. Up to now, 34 Campylobacter strains have been sequenced and published in public databases, providing good opportunity to systemically analyze their genomic diversities. In this study, we first conducted genomic characterization, which includes genome-wide alignments, pan-genome analysis, and phylogenetic identification, to depict the genetic diversity of Campylobacter genus. Afterward, we improved the tetranucleotide usage pattern-based naïve Bayesian classifier to identify the abnormal composition fragments (ACFs, fragments with significantly different tetranucleotide frequency profiles from its genomic tetranucleotide frequency profiles) including horizontal gene transfers (HGTs) to explore the mechanisms for the genetic diversity of this organism. Finally, we analyzed the HGTs transferred via bacteriophage transductions. To our knowledge, this study is the first to use single nucleotide polymorphism information to construct liable microevolution phylogeny of 21 Campylobacter jejuni strains. Combined with the phylogeny of all the collected Campylobacter species based on genome-wide core gene information, comprehensive phylogenetic inference of all 34 Campylobacter organisms was determined. It was found that C. jejuni harbors a high fraction of ACFs possibly through intraspecies recombination, whereas other Campylobacter members possess numerous ACFs possibly via intragenus recombination. Furthermore, some Campylobacter strains have undergone significant ancient viral integration during their evolution process. The improved method is a powerful tool for bacterial genomic analysis. Moreover, the findings would provide useful information for future research on Campylobacter genus.}, }
@article {pmid23937442, year = {2013}, author = {Proctor, RH and Van Hove, F and Susca, A and Stea, G and Busman, M and van der Lee, T and Waalwijk, C and Moretti, A and Ward, TJ}, title = {Birth, death and horizontal transfer of the fumonisin biosynthetic gene cluster during the evolutionary diversification of Fusarium.}, journal = {Molecular microbiology}, volume = {90}, number = {2}, pages = {290-306}, doi = {10.1111/mmi.12362}, pmid = {23937442}, issn = {1365-2958}, mesh = {Amino Acid Sequence ; *Evolution, Molecular ; Fumonisins/chemistry/*metabolism ; Fusarium/classification/*genetics/metabolism ; Gene Duplication ; Gene Expression Regulation, Fungal ; *Gene Transfer, Horizontal ; *Genes, Fungal ; Multigene Family ; Phylogeny ; }, abstract = {Fumonisins are a family of carcinogenic secondary metabolites produced by members of the Fusarium fujikuroi species complex (FFSC) and rare strains of Fusarium oxysporum. In Fusarium, fumonisin biosynthetic genes (FUM) are clustered, and the cluster is uniform in gene organization. Here, sequence analyses indicated that the cluster exists in five different genomic contexts, defining five cluster types. In FUM gene genealogies, evolutionary relationships between fusaria with different cluster types were largely incongruent with species relationships inferred from primary-metabolism (PM) gene genealogies, and FUM cluster types are not trans-specific. In addition, synonymous site divergence analyses indicated that three FUM cluster types predate diversification of FFSC. The data are not consistent with balancing selection or interspecific hybridization, but they are consistent with two competing hypotheses: (i) multiple horizontal transfers of the cluster from unknown donors to FFSC recipients and (ii) cluster duplication and loss (birth and death). Furthermore, low levels of FUM gene divergence in F. bulbicola, an FFSC species, and F. oxysporum provide evidence for horizontal transfer of the cluster from the former, or a closely related species, to the latter. Thus, uniform gene organization within the FUM cluster belies a complex evolutionary history that has not always paralleled the evolution of Fusarium.}, }
@article {pmid23934491, year = {2013}, author = {Jung, J and Park, W}, title = {Comparative genomic and transcriptomic analyses reveal habitat differentiation and different transcriptional responses during pectin metabolism in Alishewanella species.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {20}, pages = {6351-6361}, pmid = {23934491}, issn = {1098-5336}, mesh = {Adaptation, Biological ; Alteromonadaceae/*genetics/*metabolism ; *Ecosystem ; *Environmental Microbiology ; *Gene Expression Profiling ; Gene Transfer, Horizontal ; Genome, Bacterial ; Genomic Islands ; Metabolic Networks and Pathways/genetics ; Pectins/*metabolism ; Prophages/genetics ; Recombination, Genetic ; }, abstract = {Alishewanella species are expected to have high adaptability to diverse environments because they are isolated from different natural habitats. To investigate how the evolutionary history of Alishewanella species is reflected in their genomes, we performed comparative genomic and transcriptomic analyses of A. jeotgali, A. aestuarii, and A. agri, which were isolated from fermented seafood, tidal flat sediment, and soil, respectively. Genomic islands with variable GC contents indicated that invasion of prophage and transposition events occurred in A. jeotgali and A. agri but not in A. aestuarii. Habitat differentiation of A. agri from a marine environment to a terrestrial environment was proposed because the species-specific genes of A. agri were similar to those of soil bacteria, whereas those of A. jeotgali and A. aestuarii were more closely related to marine bacteria. Comparative transcriptomic analysis with pectin as a sole carbon source revealed different transcriptional responses in Alishewanella species, especially in oxidative stress-, methylglyoxal detoxification-, membrane maintenance-, and protease/chaperone activity-related genes. Transcriptomic and experimental data demonstrated that A. agri had a higher pectin degradation rate and more resistance to oxidative stress under pectin-amended conditions than the other 2 Alishewanella species. However, expression patterns of genes in the pectin metabolic pathway and of glyoxylate bypass genes were similar among all 3 Alishewanella species. Our comparative genomic and transcriptomic data revealed that Alishewanella species have evolved through horizontal gene transfer and habitat differentiation and that pectin degradation pathways in Alishewanella species are highly conserved, although stress responses of each Alishewanella species differed under pectin culture conditions.}, }
@article {pmid23932912, year = {2013}, author = {Friães, A and Lopes, JP and Melo-Cristino, J and Ramirez, M and , }, title = {Changes in Streptococcus pyogenes causing invasive disease in Portugal: evidence for superantigen gene loss and acquisition.}, journal = {International journal of medical microbiology : IJMM}, volume = {303}, number = {8}, pages = {505-513}, doi = {10.1016/j.ijmm.2013.07.004}, pmid = {23932912}, issn = {1618-0607}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Antigens, Bacterial/genetics ; Bacterial Outer Membrane Proteins/genetics ; Carrier Proteins/genetics ; Child ; Child, Preschool ; Electrophoresis, Gel, Pulsed-Field ; Female ; Gene Deletion ; Gene Transfer, Horizontal ; Genetic Variation ; Genotype ; Humans ; Infant ; Male ; Middle Aged ; Molecular Epidemiology ; Molecular Typing ; Portugal/epidemiology ; Prevalence ; Streptococcal Infections/*epidemiology/*microbiology ; Streptococcus pyogenes/*genetics/*isolation &amp; purification ; Superantigens/*genetics ; Young Adult ; }, abstract = {The emergence of highly virulent and successful Streptococcus pyogenes (group A streptococci - GAS) clones has been attributed to the exchange of virulence factors by lateral gene transfer mechanisms, which strongly contribute to genomic diversity. We characterized a collection of 191 GAS isolates recovered from normally sterile sites in Portugal during 2006-2009 and compared them to invasive isolates obtained during 2000-2005. Antimicrobial resistance rates did not change significantly between the two periods and were generally low. In 2006-2009, emm1, emm89, emm3, and emm6 represented 60% of the isolates. The chromosomally encoded superantigen (SAg) genes speG and smeZ were present in the majority (>90%) of the isolates, while speJ was found in only 45%. The phage encoded SAgs varied greatly in prevalence (2-53%). The distribution of emm types, pulsed-field gel electrophoresis profiling (PFGE) clusters, and SAg profiles changed significantly between the periods, although there were no statistically supported changes in the prevalence of individual types. While the macrolide susceptible clone emm1-T1-ST28 remained dominant (28%), there was a significant decrease in clonal diversity as indicated by both PFGE profiling and emm typing. This was accompanied by intra-clonal divergence of SAg profiles, which was statistically confirmed for isolates representing emm1, emm28, and emm44. This diversification was associated with the loss and acquisition of SAg genes, carried by phages and of chromosomal origin. These data suggest an ongoing genomic diversification of GAS invasive isolates in Portugal that may contribute to the persistence of clones with improved fitness or virulence.}, }
@article {pmid23922968, year = {2013}, author = {Satoh, S and Mimuro, M and Tanaka, A}, title = {Construction of a phylogenetic tree of photosynthetic prokaryotes based on average similarities of whole genome sequences.}, journal = {PloS one}, volume = {8}, number = {7}, pages = {e70290}, pmid = {23922968}, issn = {1932-6203}, mesh = {Archaea/classification/*genetics ; Cyanobacteria/classification/*genetics ; Genome, Archaeal ; Genome, Bacterial ; *Phylogeny ; Proteobacteria/classification/*genetics ; }, abstract = {Phylogenetic trees have been constructed for a wide range of organisms using gene sequence information, especially through the identification of orthologous genes that have been vertically inherited. The number of available complete genome sequences is rapidly increasing, and many tools for construction of genome trees based on whole genome sequences have been proposed. However, development of a reasonable method of using complete genome sequences for construction of phylogenetic trees has not been established. We have developed a method for construction of phylogenetic trees based on the average sequence similarities of whole genome sequences. We used this method to examine the phylogeny of 115 photosynthetic prokaryotes, i.e., cyanobacteria, Chlorobi, proteobacteria, Chloroflexi, Firmicutes and nonphotosynthetic organisms including Archaea. Although the bootstrap values for the branching order of phyla were low, probably due to lateral gene transfer and saturated mutation, the obtained tree was largely consistent with the previously reported phylogenetic trees, indicating that this method is a robust alternative to traditional phylogenetic methods.}, }
@article {pmid23921237, year = {2013}, author = {Campbell, MA and Staats, M and van Kan, JA and Rokas, A and Slot, JC}, title = {Repeated loss of an anciently horizontally transferred gene cluster in Botrytis.}, journal = {Mycologia}, volume = {105}, number = {5}, pages = {1126-1134}, doi = {10.3852/12-390}, pmid = {23921237}, issn = {0027-5514}, mesh = {Botrytis/*genetics ; *Evolution, Molecular ; Fusarium/genetics ; Gene Transfer, Horizontal/*genetics ; Genome, Fungal/*genetics ; Models, Biological ; Multigene Family/*genetics ; Phylogeny ; Pseudogenes/genetics ; RNA, Fungal/genetics ; RNA, Messenger/genetics ; Species Specificity ; Xanthones/metabolism ; }, abstract = {At least five of the six genes of the bikaverin secondary metabolic gene cluster were shown to have undergone horizontal transfer (HGT) from a Fusarium donor to the Botrytis lineage. Of these five, two enzyme-encoding genes are found as pseudogenes in B. cinerea whereas two regulatory genes and the transporter remain intact. To reconstruct the evolutionary events leading to decay of this gene cluster and infer a more precise timing of its transfer, we examined the genomes of nine additional broadly sampled Botrytis species. We found evidence that a Botrytis ancestor acquired the entire gene cluster through an ancient HGT that occurred before the diversification of the genus. During the subsequent evolution and diversification of the genus, four of the 10 genomes appear to have lost the gene cluster, while in the other six the cluster is in various stages of degeneration. Across the Botrytis genomes, the modes of gene decay in the cluster differed between enzyme-encoding genes, which had higher rates of transition to or retention of pseudogenes and were universally inactivated, and regulatory genes (particularly the non-pathway-specific regulator bik4), which more frequently appeared intact. Consistent with these results, the regulatory genes bik4 and bik5 showed stronger evidence of transcriptional expression than other bikaverin genes under multiple conditions in B. cinerea. These results could be explained by pleiotropy in the bikaverin regulatory genes either through rewiring or their interaction with more central pathways or by constraints on the order of gene loss driven by the intrinsic toxicity of the pathway. Our finding that most of the bikaverin pathway genes have been lost or pseudogenized in these Botrytis genomes suggests that the incidence of HGT of gene cluster-encoded metabolic pathways might be higher than what is possible to be inferred from isolated genome analyses.}, }
@article {pmid23919480, year = {2014}, author = {Oravcova, V and Zurek, L and Townsend, A and Clark, AB and Ellis, JC and Cizek, A and Literak, I}, title = {American crows as carriers of vancomycin-resistant enterococci with vanA gene.}, journal = {Environmental microbiology}, volume = {16}, number = {4}, pages = {939-949}, doi = {10.1111/1462-2920.12213}, pmid = {23919480}, issn = {1462-2920}, mesh = {Animals ; Bacterial Proteins/*genetics ; Carbon-Oxygen Ligases/*genetics ; Crows/*microbiology ; Enterococcus faecalis/*genetics/isolation &amp; purification ; Enterococcus faecium/*genetics/isolation &amp; purification ; Feces/microbiology ; Gene Transfer, Horizontal ; Multilocus Sequence Typing ; United States ; Vancomycin Resistance/*genetics ; }, abstract = {We studied the vanA-carrying vancomycin-resistant enterococci (VRE) isolated from American crows in the United States during the winter 2011/2012. Faecal samples from crows were cultured selectively for VRE and characterized. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) were used to examine epidemiological relationships of vanA-containing VRE. Isolates were tested in vitro for their ability to horizontally transfer the vancomycin resistance trait. VRE with the vanA gene were found in 15 (2.5%) of 590 crows samples, from which we obtained 22 different isolates. Enterococcal species were Enterococcus faecium (14) and E. faecalis (8). One, two and 19 isolates originated from Kansas, New York State and Massachusetts, respectively. Based on MLST analysis, E. faecium isolates were grouped as ST18 (6 isolates), ST555 (2), and novel types ST749 (1), ST750 (3), ST751 (1), ST752 (1). Enterococcus faecalis isolates belonged to ST6 (1), ST16 (3) and ST179 (4). All isolates were able to transfer the vancomycin resistance trait via filter mating with very high transfer range. Clinically important enterococci with the vanA gene occur in faeces of wild American crows throughout the United States. These migrating birds may contribute to the dissemination of VRE in environment over large distances. [Correction added after first online publication on 06 August 2013: The number of E. faecium ST752 isolate is now amended to '1', consistent with that shown in the 'Results' section and Figure 2.].}, }
@article {pmid23918348, year = {2013}, author = {Arcas, A and Cases, I and Rojas, AM}, title = {Serine/threonine kinases and E2-ubiquitin conjugating enzymes in Planctomycetes: unexpected findings.}, journal = {Antonie van Leeuwenhoek}, volume = {104}, number = {4}, pages = {509-520}, doi = {10.1007/s10482-013-9993-2}, pmid = {23918348}, issn = {1572-9699}, mesh = {Bacteria/*classification/*genetics ; Eukaryota/genetics ; Genome, Bacterial ; Phylogeny ; Protein Serine-Threonine Kinases/*genetics ; RNA, Ribosomal, 16S/genetics ; Ubiquitin-Conjugating Enzymes/*genetics ; }, abstract = {The regulation of signal transduction by phosphorylation and ubiquitination is essential to ensure the correct behavior of eukaryotic cells. We searched for protein families involved in such signaling in several eukaryotic species and in a limited set of prokaryotes, where two members of the Planctomycetes phylum were included as they exhibit eukaryote-like features (Gemmata obscuriglobus and Pirellula staleyi). We identified sequences homologous to eukaryotic serine/threonine kinases (STKs) and E2-ubiquitin conjugating enzymes in the two Planctomycetes species. To extend these analyses to the Planctomycetes/Verrucomicrobia/Chlamydia super-phylum, we performed comparative analyses using domains from kinases, phosphatases and GTPases that serve as signaling signatures, and we analyzed their distributions. We found substantial differences in kinome densities with regards to other prokaryote clades and among the groups in the Planctomycetes/Verrucomicrobia/Chlamydia super-phylum. In addition, we identified the presence of classic eukaryotic E2-conjugating ubiquitin proteins in prokaryotes, these having previously believed to exist only in eukaryotes. Our phylogenetic analyses of the STKs signature domains and E2-enzymes suggest the existence of horizontal gene transfer.}, }
@article {pmid23917989, year = {2013}, author = {Yurtsev, EA and Chao, HX and Datta, MS and Artemova, T and Gore, J}, title = {Bacterial cheating drives the population dynamics of cooperative antibiotic resistance plasmids.}, journal = {Molecular systems biology}, volume = {9}, number = {}, pages = {683}, pmid = {23917989}, issn = {1744-4292}, support = {R01 GM102311/GM/NIGMS NIH HHS/United States ; DP2AG04279/AG/NIA NIH HHS/United States ; T32 GM087237/GM/NIGMS NIH HHS/United States ; R00 GM085279-02/GM/NIGMS NIH HHS/United States ; R00 GM085279/GM/NIGMS NIH HHS/United States ; K99 GM085279/GM/NIGMS NIH HHS/United States ; R01 GM102311-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Ampicillin/pharmacology ; Anti-Bacterial Agents/pharmacology ; Bacterial Load/drug effects ; Escherichia coli/*drug effects/enzymology/genetics ; Gene Transfer, Horizontal/*drug effects ; Models, Genetic ; Plasmids/agonists/*metabolism ; Quorum Sensing/*genetics ; beta-Lactam Resistance/*drug effects/genetics ; beta-Lactamase Inhibitors ; beta-Lactamases/genetics/metabolism ; }, abstract = {Inactivation of β-lactam antibiotics by resistant bacteria is a 'cooperative' behavior that may allow sensitive bacteria to survive antibiotic treatment. However, the factors that determine the fraction of resistant cells in the bacterial population remain unclear, indicating a fundamental gap in our understanding of how antibiotic resistance evolves. Here, we experimentally track the spread of a plasmid that encodes a β-lactamase enzyme through the bacterial population. We find that independent of the initial fraction of resistant cells, the population settles to an equilibrium fraction proportional to the antibiotic concentration divided by the cell density. A simple model explains this behavior, successfully predicting a data collapse over two orders of magnitude in antibiotic concentration. This model also successfully predicts that adding a commonly used β-lactamase inhibitor will lead to the spread of resistance, highlighting the need to incorporate social dynamics into the study of antibiotic resistance.}, }
@article {pmid23915186, year = {2013}, author = {Andersen, MT and Liefting, LW and Havukkala, I and Beever, RE}, title = {Comparison of the complete genome sequence of two closely related isolates of 'Candidatus Phytoplasma australiense' reveals genome plasticity.}, journal = {BMC genomics}, volume = {14}, number = {}, pages = {529}, pmid = {23915186}, issn = {1471-2164}, mesh = {Base Sequence ; Evolution, Molecular ; Fragaria/microbiology ; Genes, Bacterial/genetics ; *Genomics ; Molecular Sequence Data ; *Phylogeny ; Phytoplasma/*genetics/*isolation &amp; purification ; Plant Diseases/microbiology ; }, abstract = {BACKGROUND: 'Candidatus Phytoplasma australiense' is associated with at least nine diseases in Australia and New Zealand. The impact of this phytoplasma is considerable, both economically and environmentally. The genome of a NZ isolate was sequenced in an effort to understand its pathogenicity and ecology. Comparison with a closely related Australian isolate enabled us to examine mechanisms of genomic rearrangement.<br><br>RESULTS: The complete genome sequence of a strawberry lethal yellows (SLY) isolate of 'Candidatus Phytoplasma australiense' was determined. It is a circular genome of 959,779 base pairs with 1126 predicted open reading frames. Despite being 80 kbp larger than another 'Ca. Phytoplasma australiense' isolate PAa, the variation between housekeeping genes was generally less than 1% at a nucleotide level. The difference in size between the two isolates was largely due to the number and size of potential mobile units (PMUs), which contributed to some changes in gene order. Comparison of the genomes of the two isolates revealed that the highly conserved 5' UTR of a putative DNA-directed RNA polymerase seems to be associated with insertion and rearrangement events. Two types of PMUs have been identified on the basis of the order of three to four conserved genes, with both PMUs appearing to have been present in the last common ancestor of 'Ca. Phytoplasma asteris' and 'Ca. Phytoplasma australiense'. Comparison with other phytoplasma genomes showed that modification methylases were, in general, species-specific. A putative methylase (xorIIM) found in 'Ca. Phytoplasma australiense' appeared to have no analogue in any other firmicute, and we believe has been introduced by way of lateral gene transfer. A putative retrostransposon (ltrA) analogous to that found in OY-M was present in both isolates, although all examples in PAa appear to be fragments. Comparative analysis identified highly conserved 5' and 3' UTR regions of ltrA, which may indicate how the gene is excised and inserted.<br><br>CONCLUSIONS: Comparison of two assembled 'Ca. Phytoplasma australiense' genomes has shown they possess a high level of plasticity. This comparative analysis has yielded clues as to how rearrangements occur, and the identification of sets of genes that appear to be associated with these events.}, }
@article {pmid23914989, year = {2013}, author = {Yuan, JB and Zhang, XJ and Liu, CZ and Wei, JK and Li, FH and Xiang, JH}, title = {Horizontally transferred genes in the genome of Pacific white shrimp, Litopenaeus vannamei.}, journal = {BMC evolutionary biology}, volume = {13}, number = {}, pages = {165}, pmid = {23914989}, issn = {1471-2148}, mesh = {Animals ; Bacteria/*genetics ; Fungi/*genetics ; *Gene Transfer, Horizontal ; *Genome ; Introns ; Penaeidae/classification/*genetics/*microbiology ; Phylogeny ; }, abstract = {BACKGROUND: In recent years, as the development of next-generation sequencing technology, a growing number of genes have been reported as being horizontally transferred from prokaryotes to eukaryotes, most of them involving arthropods. As a member of the phylum Arthropoda, the Pacific white shrimp Litopenaeus vannamei has to adapt to the complex water environments with various symbiotic or parasitic microorganisms, which provide a platform for horizontal gene transfer (HGT).<br><br>RESULTS: In this study, we analyzed the genome-wide HGT events in L. vannamei. Through homology search and phylogenetic analysis, followed by experimental PCR confirmation, 14 genes with HGT event were identified: 12 of them were transferred from bacteria and two from fungi. Structure analysis of these genes showed that the introns of the two fungi-originated genes were substituted by shrimp DNA fragment, two genes transferred from bacteria had shrimp specific introns inserted in them. Furthermore, around other three bacteria-originated genes, there were three large DNA segments inserted into the shrimp genome. One segment was a transposon that fully transferred, and the other two segments contained only coding regions of bacteria. Functional prediction of these 14 genes showed that 6 of them might be related to energy metabolism, and 4 others related to defense of the organism.<br><br>CONCLUSIONS: HGT events from bacteria or fungi were happened in the genome of L. vannamei, and these horizontally transferred genes can be transcribed in shrimp. This is the first time to report the existence of horizontally transferred genes in shrimp. Importantly, most of these genes are exposed to a negative selection pressure and appeared to be functional.}, }
@article {pmid23914312, year = {2013}, author = {Pillet, L}, title = {The role of horizontal gene transfer in kleptoplastidy and the establishment of photosynthesis in the eukaryotes.}, journal = {Mobile genetic elements}, volume = {3}, number = {2}, pages = {e24773}, pmid = {23914312}, issn = {2159-2543}, abstract = {Found in different eukaryotic lineages, kleptoplastidy is the ability to sequester chloroplasts from algal preys that are ingested and partially digested. While most of the genetic information required for the activity and maintenance of the kleptoplastids disappeared with the digestion of the algal nuclei, the photosynthetic organelles remain active during extended period of time. Many different hypotheses have been proposed to explain the longevity of the kleptoplastids within their host. The most popular one involves Horizontal Gene Transfer (HGT) from the algal genome to the host nucleus. In order to test this hypothesis, transcriptome-based analyses have been performed on different kleptoplastidic organisms during the past few years. However, the variability of the results obtained does not allow drawing a convincing conclusion regarding the precise role of HGT in kleptoplastidy. Understanding the mechanism that allow persistence of the plastids is crucial, not only for the characterization of kleptoplastidy, but also for important evolutionary questions surrounding endosymbiotic events and the emergence and spread of photosynthesis in the eukaryotes. Here, I discuss alternative theories that could explain the longevity of sequestered plastids in their host, with special focus on the simplest chloroplast stability hypothesis.}, }
@article {pmid23911585, year = {2013}, author = {Leikoski, N and Liu, L and Jokela, J and Wahlsten, M and Gugger, M and Calteau, A and Permi, P and Kerfeld, CA and Sivonen, K and Fewer, DP}, title = {Genome mining expands the chemical diversity of the cyanobactin family to include highly modified linear peptides.}, journal = {Chemistry &amp; biology}, volume = {20}, number = {8}, pages = {1033-1043}, doi = {10.1016/j.chembiol.2013.06.015}, pmid = {23911585}, issn = {1879-1301}, mesh = {Amino Acid Sequence ; Cyanobacteria/chemistry/*genetics/metabolism ; Evolution, Molecular ; *Genome, Bacterial ; Molecular Sequence Data ; Multigene Family ; Peptides/*chemistry/*genetics/metabolism ; Protein Processing, Post-Translational ; Ribosomes/genetics/metabolism ; }, abstract = {Ribosomal peptides are produced through the posttranslational modification of short precursor peptides. Cyanobactins are a growing family of cyclic ribosomal peptides produced by cyanobacteria. However, a broad systematic survey of the genetic capacity to produce cyanobactins is lacking. Here we report the identification of 31 cyanobactin gene clusters from 126 genomes of cyanobacteria. Genome mining suggested a complex evolutionary history defined by horizontal gene transfer and rapid diversification of precursor genes. Extensive chemical analyses demonstrated that some cyanobacteria produce short linear cyanobactins with a chain length ranging from three to five amino acids. The linear peptides were N-prenylated and O-methylated on the N and C termini, respectively, and named aeruginosamide and viridisamide. These findings broaden the structural diversity of the cyanobactin family to include highly modified linear peptides with rare posttranslational modifications.}, }
@article {pmid23910724, year = {2013}, author = {Roberts, GA and Chen, K and Bower, EK and Madrzak, J and Woods, A and Barker, AM and Cooper, LP and White, JH and Blakely, GW and Manfield, I and Dryden, DT}, title = {Mutations of the domain forming the dimeric interface of the ArdA protein affect dimerization and antimodification activity but not antirestriction activity.}, journal = {The FEBS journal}, volume = {280}, number = {19}, pages = {4903-4914}, pmid = {23910724}, issn = {1742-4658}, support = {090288/Z/09/ZA//Wellcome Trust/United Kingdom ; BB/C511599/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; GR080463MA//Wellcome Trust/United Kingdom ; }, mesh = {DNA Restriction Enzymes/chemistry/genetics/metabolism ; Escherichia coli Proteins/*chemistry/*genetics/metabolism ; Gene Transfer, Horizontal/genetics ; Mutation ; Protein Multimerization/genetics/physiology ; Protein Structure, Secondary ; Repressor Proteins/*chemistry/*genetics/metabolism ; }, abstract = {ArdA antirestriction proteins are encoded by genes present in many conjugative plasmids and transposons within bacterial genomes. Antirestriction is the ability to prevent cleavage of foreign incoming DNA by restriction-modification (RM) systems. Antimodification, the ability to inhibit modification by the RM system, can also be observed with some antirestriction proteins. As these mobile genetic elements can transfer antibiotic resistance genes, the ArdA proteins assist their spread. The consequence of antirestriction is therefore the enhanced dissemination of mobile genetic elements. ArdA proteins cause antirestriction by mimicking the DNA structure bound by Type I RM enzymes. The crystal structure of ArdA showed it to be a dimeric protein with a highly elongated curved cylindrical shape [McMahon SA et al. (2009) Nucleic Acids Res 37, 4887-4897]. Each monomer has three domains covered with negatively charged side chains and a very small interface with the other monomer. We investigated the role of the domain forming the dimer interface for ArdA activity via site-directed mutagenesis. The antirestriction activity of ArdA was maintained when up to seven mutations per monomer were made or the interface was disrupted such that the protein could only exist as a monomer. The antimodification activity of ArdA was lost upon mutation of this domain. The ability of the monomeric form of ArdA to function in antirestriction suggests, first, that it can bind independently to the restriction subunit or the modification subunits of the RM enzyme, and second, that the many ArdA homologues with long amino acid extensions, present in sequence databases, may be active in antirestriction.}, }
@article {pmid23904149, year = {2013}, author = {Sangal, V and Fineran, PC and Hoskisson, PA}, title = {Novel configurations of type I and II CRISPR-Cas systems in Corynebacterium diphtheriae.}, journal = {Microbiology (Reading, England)}, volume = {159}, number = {Pt 10}, pages = {2118-2126}, doi = {10.1099/mic.0.070235-0}, pmid = {23904149}, issn = {1465-2080}, mesh = {Base Composition ; *CRISPR-Cas Systems ; Corynebacterium diphtheriae/*genetics ; *Genomic Structural Variation ; Interspersed Repetitive Sequences ; Neisseria meningitidis/genetics ; Phylogeny ; }, abstract = {Clustered regularly interspaced short palindromic repeats (CRISPRs) are major barriers to recombination through recognition of invading nucleic acids, such as phage and plasmids, and promoting their degredation through the action of CRISPR associated (Cas) proteins. The genomic comparison of 17 Corynebacterium diphtheriae strains led to the identification of three novel CRISPR-Cas system variants, based on the Type II (Type II-C) or type I-E systems. The type II-C system was the most common (11/17 isolates) but it lacked the csn2 and cas4 genes that are involved in spacer acquisition. We also identified that this variant type II-C CRISPR-Cas system is present in other bacteria, and the first system was recently characterized in Neisseria meningitidis. In the remaining isolates, the type II-C system was replaced by a variant of type I-E (I-E-a), where the repeat arrays are inserted between the cas3 and cse1 genes. Three isolates with the type II-C system also possess an additional variant of type I-E (I-E-b), elsewhere in the genome, that exhibits a novel divergent gene organization within the cas operon. The nucleotide sequences of the palindromic repeats and the cas1 gene were phylogenetically incongruent to the core genome. The G+C content of the systems is lower (46.0-49.5 mol%) than the overall DNA G+C content (53 mol%), and they are flanked by mobile genetic elements, providing evidence that they were acquired in three independent horizontal gene transfer events. The majority of spacers lack identity with known phage or plasmid sequences, indicating that there is an unexplored reservoir of corynebacteriophages and plasmids. These novel CRISPR-Cas systems may represent a unique mechanism for spacer acquisitions and defence against invading DNA.}, }
@article {pmid23898467, year = {2013}, author = {Korhonen, TK and Haiko, J and Laakkonen, L and Järvinen, HM and Westerlund-Wikström, B}, title = {Fibrinolytic and coagulative activities of Yersinia pestis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {3}, number = {}, pages = {35}, pmid = {23898467}, issn = {2235-2988}, mesh = {Animals ; Bacterial Proteins/*metabolism ; *Blood Coagulation ; Endotoxins/metabolism ; *Fibrinolysis ; Humans ; Lipopolysaccharides/metabolism ; Mice ; Plasminogen Activators/*metabolism ; Virulence Factors/*metabolism ; Yersinia pestis/*enzymology/*pathogenicity ; }, abstract = {The outer membrane protease Pla belongs to the omptin protease family spread by horizontal gene transfer into Gram-negative bacteria that infect animals or plants. Pla has adapted to support the life style of the plague bacterium Yersinia pestis. Pla has a β-barrel fold with 10 membrane-spanning β strands and five surface loops, and the barrel surface contains bound lipopolysaccharide (LPS) that is critical for the conformation and the activity of Pla. The biological activity of Pla is influenced by the structure of the surface loops around the active site groove and by temperature-induced LPS modifications. Several of the putative virulence-related functions documented for Pla in vitro address control of the human hemostatic system, i.e., coagulation and fibrinolysis. Pla activates human plasminogen to the serine protease plasmin and activates the physiological plasminogen activator urokinase. Pla also inactivates the protease inhibitors alpha-2-antiplasmin and plasminogen activator inhibitor 1 (PAI-1) and prevents the activation of thrombin-activatable fibrinolysis inhibitor (TAFI). These functions enhance uncontrolled fibrinolysis which is thought to improve Y. pestis dissemination and survival in the mammalian host, and lowered fibrin(ogen) deposition has indeed been observed in mice infected with Pla-positive Y. pestis. However, Pla also inactivates an anticoagulant, the tissue factor (TF) pathway inhibitor, which should increase fibrin formation and clotting. Thus, Pla and Y. pestis have complex interactions with the hemostatic system. Y. pestis modifies its LPS upon transfer to the mammalian host and we hypothesize that the contrasting biological activities of Pla in coagulation and fibrinolysis are influenced by LPS changes during infection.}, }
@article {pmid23894381, year = {2013}, author = {Buffet, JP and Pisanu, B and Brisse, S and Roussel, S and Félix, B and Halos, L and Chapuis, JL and Vayssier-Taussat, M}, title = {Deciphering bartonella diversity, recombination, and host specificity in a rodent community.}, journal = {PloS one}, volume = {8}, number = {7}, pages = {e68956}, pmid = {23894381}, issn = {1932-6203}, mesh = {Animals ; Bartonella/classification/*genetics/pathogenicity ; Bartonella Infections/genetics ; Genotype ; Host Specificity/*physiology ; Mice ; Phylogeny ; Polymorphism, Genetic/genetics ; }, abstract = {Host-specificity is an intrinsic feature of many bacterial pathogens, resulting from a long history of co-adaptation between bacteria and their hosts. Alpha-proteobacteria belonging to the genus Bartonella infect the erythrocytes of a wide range of mammal orders, including rodents. In this study, we performed genetic analysis of Bartonella colonizing a rodent community dominated by bank voles (Myodes glareolus) and wood mice (Apodemus sylvaticus) in a French suburban forest to evaluate their diversity, their capacity to recombine and their level of host specificity. Following the analysis of 550 rodents, we detected 63 distinct genotypes related to B. taylorii, B. grahamii, B. doshiae and a new B. rochalimae-like species. Investigating the most highly represented species, we showed that B. taylorii strain diversity was markedly higher than that of B. grahamii, suggesting a possible severe bottleneck for the latter species. The majority of recovered genotypes presented a strong association with either bank voles or wood mice, with the exception of three B. taylorii genotypes which had a broader host range. Despite the physical barriers created by host specificity, we observed lateral gene transfer between Bartonella genotypes associated with wood mice and Bartonella adapted to bank voles, suggesting that those genotypes might co-habit during their life cycle.}, }
@article {pmid23894338, year = {2013}, author = {Smokvina, T and Wels, M and Polka, J and Chervaux, C and Brisse, S and Boekhorst, J and van Hylckama Vlieg, JE and Siezen, RJ}, title = {Lactobacillus paracasei comparative genomics: towards species pan-genome definition and exploitation of diversity.}, journal = {PloS one}, volume = {8}, number = {7}, pages = {e68731}, pmid = {23894338}, issn = {1932-6203}, mesh = {Carbohydrate Metabolism/genetics ; Cluster Analysis ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Fatty Acids/metabolism ; Gene Order ; Gene Transfer, Horizontal ; *Genetic Variation ; *Genome, Bacterial ; *Genomics ; Lactobacillus/classification/*genetics/metabolism ; Molecular Sequence Annotation ; Phylogeny ; Plasmids/genetics ; }, abstract = {Lactobacillus paracasei is a member of the normal human and animal gut microbiota and is used extensively in the food industry in starter cultures for dairy products or as probiotics. With the development of low-cost, high-throughput sequencing techniques it has become feasible to sequence many different strains of one species and to determine its "pan-genome". We have sequenced the genomes of 34 different L. paracasei strains, and performed a comparative genomics analysis. We analysed genome synteny and content, focussing on the pan-genome, core genome and variable genome. Each genome was shown to contain around 2800-3100 protein-coding genes, and comparative analysis identified over 4200 ortholog groups that comprise the pan-genome of this species, of which about 1800 ortholog groups make up the conserved core. Several factors previously associated with host-microbe interactions such as pili, cell-envelope proteinase, hydrolases p40 and p75 or the capacity to produce short branched-chain fatty acids (bkd operon) are part of the L. paracasei core genome present in all analysed strains. The variome consists mainly of hypothetical proteins, phages, plasmids, transposon/conjugative elements, and known functions such as sugar metabolism, cell-surface proteins, transporters, CRISPR-associated proteins, and EPS biosynthesis proteins. An enormous variety and variability of sugar utilization gene cassettes were identified, with each strain harbouring between 25-53 cassettes, reflecting the high adaptability of L. paracasei to different niches. A phylogenomic tree was constructed based on total genome contents, and together with an analysis of horizontal gene transfer events we conclude that evolution of these L. paracasei strains is complex and not always related to niche adaptation. The results of this genome content comparison was used, together with high-throughput growth experiments on various carbohydrates, to perform gene-trait matching analysis, in order to link the distribution pattern of a specific phenotype to the presence/absence of specific sets of genes.}, }
@article {pmid23892748, year = {2013}, author = {Dutta, V and Elhanafi, D and Kathariou, S}, title = {Conservation and distribution of the benzalkonium chloride resistance cassette bcrABC in Listeria monocytogenes.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {19}, pages = {6067-6074}, pmid = {23892748}, issn = {1098-5336}, mesh = {Benzalkonium Compounds/*pharmacology ; Chromosomes, Bacterial ; Conserved Sequence ; DNA, Bacterial/chemistry/genetics ; Disinfectants/*pharmacology ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Listeria monocytogenes/*drug effects/*genetics ; Molecular Sequence Data ; *Multigene Family ; Plasmids ; Sequence Analysis, DNA ; Transcription, Genetic ; }, abstract = {Analysis of a panel of 116 Listeria monocytogenes strains of diverse serotypes and sources (clinical, environment of food processing plants, and food) revealed that all but one of the 71 benzalkonium chloride-resistant (BC(r)) isolates harbored bcrABC, previously identified on a large plasmid (pLM80) of the 1998-1999 hot dog outbreak strain H7858. In contrast, bcrABC was not detected among BC-susceptible (BC(s)) isolates. The bcrABC sequences were highly conserved among strains of different serotypes, but variability was noted in sequences flanking bcrABC. The majority of the BC(r) isolates had either the pLM80-type of organization of the bcrABC region or appeared to harbor bcrABC on the chromosome, adjacent to novel sequences. Transcription of bcrABC was induced by BC (10 μg/ml) in strains of different serotypes and diverse bcrABC region organization. These findings reveal widespread dissemination of bcrABC across BC(r) L. monocytogenes strains regardless of serotype and source, while also suggesting possible mechanisms of bcrABC dissemination across L. monocytogenes genomes.}, }
@article {pmid23891663, year = {2013}, author = {Marmon, L}, title = {Elucidating the origin of the ExbBD components of the TonB system through Bayesian inference and maximum-likelihood phylogenies.}, journal = {Molecular phylogenetics and evolution}, volume = {69}, number = {3}, pages = {674-686}, doi = {10.1016/j.ympev.2013.07.010}, pmid = {23891663}, issn = {1095-9513}, mesh = {Bacterial Proteins/*genetics ; Bayes Theorem ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Likelihood Functions ; Membrane Proteins/*genetics ; *Phylogeny ; }, abstract = {Uptake of ferric siderophores, vitamin B12, and other molecules in gram-negative bacteria is mediated by a multi-protein complex known as the TonB system. The ExbB and ExbD protein components of the TonB system play key energizing roles and are homologous with the flagellar motor proteins MotA and MotB. Here, the phylogenetic relationships of ExbBD and MotAB were investigated using Bayesian inference and the maximum-likelihood method. Phylogenetic trees of these proteins suggest that they are separated into distinct monophyletic groups and have originated from a common ancestral system. Several horizontal gene transfer events for ExbB-ExbD are also inferred, and a model for the evolution of the TonB system is proposed.}, }
@article {pmid25509375, year = {2013}, author = {Naumov, DG}, title = {[Multiple horizontal gene transfers and duplication as the source of genetic variation of alpha-l-rhamnosidases in Clostridium methylpentosum DSM5476 ].}, journal = {Mikrobiologiia}, volume = {82}, number = {4}, pages = {408-416}, pmid = {25509375}, issn = {0026-3656}, mesh = {Clostridium/enzymology/*genetics ; Gene Duplication/*physiology ; Gene Transfer, Horizontal/*physiology ; Genetic Variation/*physiology ; Glycoside Hydrolases/*genetics ; }, }
@article {pmid25437336, year = {2013}, author = {Zhou, Y and Call, DR and Broschat, SL}, title = {Whole-proteome analysis of twelve species of alphaproteobacteria links four pathogens.}, journal = {Pathogens (Basel, Switzerland)}, volume = {2}, number = {4}, pages = {627-635}, pmid = {25437336}, issn = {2076-0817}, abstract = {Thousands of whole-genome and whole-proteome sequences have been made available through advances in sequencing technology, and sequences of millions more organisms will become available in the coming years. This wealth of genetic information will provide numerous opportunities to enhance our understanding of these organisms including a greater understanding of relationships among species. Researchers have used 16S rRNA and other gene sequences to study the evolutionary origins of bacteria, but these strategies do not provide insight into the sharing of genes among bacteria via horizontal transfer. In this work we use an open source software program called pClust to cluster proteins from the complete proteomes of twelve species of Alphaproteobacteria and generate a dendrogram from the resulting orthologous protein clusters. We compare the results with dendrograms constructed using the 16S rRNA gene and multiple sequence alignment of seven housekeeping genes. Analysis of the whole proteomes of these pathogens grouped Rickettsia typhi with three other animal pathogens whereas conventional sequence analysis failed to group these pathogens together. We conclude that whole-proteome analysis can give insight into relationships among species beyond their phylogeny, perhaps reflecting the effects of horizontal gene transfer and potentially providing insight into the functions of shared genes by means of shared phenotypes.}, }
@article {pmid25371342, year = {2013}, author = {Legat, A and Denner, EB and Dornmayr-Pfaffenhuemer, M and Pfeiffer, P and Knopf, B and Claus, H and Gruber, C and König, H and Wanner, G and Stan-Lotter, H}, title = {Properties of Halococcus salifodinae, an Isolate from Permian Rock Salt Deposits, Compared with Halococci from Surface Waters.}, journal = {Life (Basel, Switzerland)}, volume = {3}, number = {1}, pages = {244-259}, pmid = {25371342}, issn = {2075-1729}, abstract = {Halococcus salifodinae BIpT DSM 8989T, an extremely halophilic archaeal isolate from an Austrian salt deposit (Bad Ischl), whose origin was dated to the Permian period, was described in 1994. Subsequently, several strains of the species have been isolated, some from similar but geographically separated salt deposits. Hcc. salifodinae may be regarded as one of the most ancient culturable species which existed already about 250 million years ago. Since its habitat probably did not change during this long period, its properties were presumably not subjected to the needs of mutational adaptation. Hcc. salifodinae and other isolates from ancient deposits would be suitable candidates for testing hypotheses on prokaryotic evolution, such as the molecular clock concept, or the net-like history of genome evolution. A comparison of available taxonomic characteristics from strains of Hcc. salifodinae and other Halococcus species, most of them originating from surface waters, is presented. The cell wall polymer of Hcc. salifodinae was examined and found to be a heteropolysaccharide, similar to that of Hcc. morrhuae. Polyhydroxyalkanoate granules were present in Hcc. salifodinae, suggesting a possible lateral gene transfer before Permian times.}, }
@article {pmid25369883, year = {2013}, author = {Jheeta, S}, title = {Horizontal Gene Transfer and Its Part in the Reorganisation of Genetics during the LUCA Epoch.}, journal = {Life (Basel, Switzerland)}, volume = {3}, number = {4}, pages = {518-523}, pmid = {25369883}, issn = {2075-1729}, abstract = {Currently there are five known mechanisms of horizontal gene transfer (HGT): transduction, conjugation, transformation, gene transfer agents and membrane vesicle transfer. The question here is: what part did HGT play in the reorganisation of genetics during the last universal common ancestor (LUCA) epoch? LUCA is a construct to explain the origin of the three domains of life; namely Archaea, Bacteria and Eukarya. This editorial offers a general introduction to the relevance and ultimate significance of HGT in relation to the LUCA. [...].}, }
@article {pmid24957995, year = {2013}, author = {Obata, T and Fernie, AR and Nunes-Nesi, A}, title = {The central carbon and energy metabolism of marine diatoms.}, journal = {Metabolites}, volume = {3}, number = {2}, pages = {325-346}, pmid = {24957995}, issn = {2218-1989}, abstract = {Diatoms are heterokont algae derived from a secondary symbiotic event in which a eukaryotic host cell acquired an eukaryotic red alga as plastid. The multiple endosymbiosis and horizontal gene transfer processes provide diatoms unusual opportunities for gene mixing to establish distinctive biosynthetic pathways and metabolic control structures. Diatoms are also known to have significant impact on global ecosystems as one of the most dominant phytoplankton species in the contemporary ocean. As such their metabolism and growth regulating factors have been of particular interest for many years. The publication of the genomic sequences of two independent species of diatoms and the advent of an enhanced experimental toolbox for molecular biological investigations have afforded far greater opportunities than were previously apparent for these species and re-invigorated studies regarding the central carbon metabolism of diatoms. In this review we discuss distinctive features of the central carbon metabolism of diatoms and its response to forthcoming environmental changes and recent advances facilitating the possibility of industrial use of diatoms for oil production. Although the operation and importance of several key pathways of diatom metabolism have already been demonstrated and determined, we will also highlight other potentially important pathways wherein this has yet to be achieved.}, }
@article {pmid24834437, year = {2013}, author = {Hughes, AL}, title = {Origin of Ecdysosteroid UDP-glycosyltransferases of Baculoviruses through Horizontal Gene Transfer from Lepidoptera.}, journal = {Coevolution}, volume = {1}, number = {1}, pages = {1-7}, pmid = {24834437}, issn = {2325-6214}, support = {R01 GM043940/GM/NIGMS NIH HHS/United States ; }, abstract = {Baculoviruses infecting Lepidoptera (butterflies and moths) encodes an enzyme known as ecdysosteroid UDP-glycosyltransferase (EGT), which inactivates insect host ecdysosteroid hormones, thereby preventing molt and pupation and permitting a build-up of the viral population within the host. Baculovirus EGT shows evidence of homology to insect UDP-glycosyltransferases, and a phylogenetic analysis supported the closest relative of baculovirus EGT are the UGT33 and UGT34 families of lepidopteran UDP-glycosyltransferases. The phylogenetic analysis thus supported that baculovirus EGT arose by horizontal gene transfer of a UDP-glycosyltransferase from a lepidopteran host, an event that occurred 70 million years ago at the earliest but possibly much more recently. Three amino acid replacements unique to baculovirus EGTs and conserved in all available baculovirus sequences were identified in the N-terminal region of the molecule. Because of their conservation, these amino acids are candidates for playing an important functional role in baculovirus EGT function.}, }
@article {pmid24757824, year = {2013}, author = {Vinogradova, KA and Bulgakova, VG and Polin, AN and Kozhevin, PA}, title = {[Microbial antibiotic resistance: resistome, its volume, diversity and development].}, journal = {Antibiotiki i khimioterapiia = Antibiotics and chemoterapy [sic]}, volume = {58}, number = {5-6}, pages = {38-48}, pmid = {24757824}, issn = {0235-2990}, mesh = {ATP-Binding Cassette Transporters/genetics/metabolism ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/drug effects/*genetics ; *Gene Expression Regulation, Bacterial ; *Gene Expression Regulation, Fungal ; Gene Transfer, Horizontal ; Humans ; Microbial Consortia/drug effects/*genetics ; Microbiota/drug effects/*genetics ; beta-Lactamases/genetics/metabolism ; }, abstract = {The known conceptions of resistome as a complex of all the antibiotic resistance genes in the genomes of all the microorganisms, pathogenic and nonpathogenic ones, in nature are considered. The data on the origin, evolution and distribution of antibiotic resistance genes and possible approaches to the resistance distribution control are presented.}, }
@article {pmid25114551, year = {2012}, author = {Jin, H and Squier, TC and Long, PE}, title = {Dying for Good: Virus-Bacterium Biofilm Co-evolution Enhances Environmental Fitness.}, journal = {Biochemistry insights}, volume = {5}, number = {}, pages = {1-9}, pmid = {25114551}, issn = {1178-6264}, abstract = {Commonly used in biotechnology applications, filamentous M13 phage are non-lytic viruses that infect E. coli and other bacteria, with the potential to promote horizontal gene transfer in natural populations with synthetic biology implications for engineering community systems. Using the E. coli strain TG1, we have investigated how a selective pressure involving elevated levels of toxic chromate, mimicking that found in some superfund sites, alters population dynamics following infection with either wild-type M13 phage or an M13-phage encoding a chromate reductase (Gh-ChrR) capable of the reductive immobilization of chromate (ie, M13-phageGh-ChrR). In the absence of a selective pressure, M13-phage infection results in a reduction in bacterial growth rate; in comparison, in the presence of chromate there are substantial increases in both cellular killing and biomass formation following infection of E. coli strain TG1with M13-phageGh-ChrR that is dependent on chromate-reductase activity. These results are discussed in terms of community structures that facilitate lateral gene transfer of beneficial traits that enhance phage replication, infectivity, and stability against environmental change.}, }
@article {pmid24957641, year = {2012}, author = {Takemoto, K}, title = {Current understanding of the formation and adaptation of metabolic systems based on network theory.}, journal = {Metabolites}, volume = {2}, number = {3}, pages = {429-457}, pmid = {24957641}, issn = {2218-1989}, abstract = {Formation and adaptation of metabolic networks has been a long-standing question in biology. With recent developments in biotechnology and bioinformatics, the understanding of metabolism is progressively becoming clearer from a network perspective. This review introduces the comprehensive metabolic world that has been revealed by a wide range of data analyses and theoretical studies; in particular, it illustrates the role of evolutionary events, such as gene duplication and horizontal gene transfer, and environmental factors, such as nutrient availability and growth conditions, in evolution of the metabolic network. Furthermore, the mathematical models for the formation and adaptation of metabolic networks have also been described, according to the current understanding from a perspective of metabolic networks. These recent findings are helpful in not only understanding the formation of metabolic networks and their adaptation, but also metabolic engineering.}, }
@article {pmid24704847, year = {2012}, author = {Black, M and Moolhuijzen, P and Chapman, B and Barrero, R and Howieson, J and Hungria, M and Bellgard, M}, title = {The genetics of symbiotic nitrogen fixation: comparative genomics of 14 rhizobia strains by resolution of protein clusters.}, journal = {Genes}, volume = {3}, number = {1}, pages = {138-166}, pmid = {24704847}, issn = {2073-4425}, abstract = {The symbiotic relationship between legumes and nitrogen fixing bacteria is critical for agriculture, as it may have profound impacts on lowering costs for farmers, on land sustainability, on soil quality, and on mitigation of greenhouse gas emissions. However, despite the importance of the symbioses to the global nitrogen cycling balance, very few rhizobial genomes have been sequenced so far, although there are some ongoing efforts in sequencing elite strains. In this study, the genomes of fourteen selected strains of the order Rhizobiales, all previously fully sequenced and annotated, were compared to assess differences between the strains and to investigate the feasibility of defining a core 'symbiome'-the essential genes required by all rhizobia for nodulation and nitrogen fixation. Comparison of these whole genomes has revealed valuable information, such as several events of lateral gene transfer, particularly in the symbiotic plasmids and genomic islands that have contributed to a better understanding of the evolution of contrasting symbioses. Unique genes were also identified, as well as omissions of symbiotic genes that were expected to be found. Protein comparisons have also allowed the identification of a variety of similarities and differences in several groups of genes, including those involved in nodulation, nitrogen fixation, production of exopolysaccharides, Type I to Type VI secretion systems, among others, and identifying some key genes that could be related to host specificity and/or a better saprophytic ability. However, while several significant differences in the type and number of proteins were observed, the evidence presented suggests no simple core symbiome exists. A more abstract systems biology concept of nitrogen fixing symbiosis may be required. The results have also highlighted that comparative genomics represents a valuable tool for capturing specificities and generalities of each genome.}, }
@article {pmid25567970, year = {2011}, author = {Russell, RJ and Scott, C and Jackson, CJ and Pandey, R and Pandey, G and Taylor, MC and Coppin, CW and Liu, JW and Oakeshott, JG}, title = {The evolution of new enzyme function: lessons from xenobiotic metabolizing bacteria versus insecticide-resistant insects.}, journal = {Evolutionary applications}, volume = {4}, number = {2}, pages = {225-248}, pmid = {25567970}, issn = {1752-4571}, abstract = {Here, we compare the evolutionary routes by which bacteria and insects have evolved enzymatic processes for the degradation of four classes of synthetic chemical insecticide. For insects, the selective advantage of such degradative activities is survival on exposure to the insecticide, whereas for the bacteria the advantage is simply a matter of access to additional sources of nutrients. Nevertheless, bacteria have evolved highly efficient enzymes from a wide variety of enzyme families, whereas insects have relied upon generalist esterase-, cytochrome P450- and glutathione-S-transferase-dependent detoxification systems. Moreover, the mutant insect enzymes are less efficient kinetically and less diverged in sequence from their putative ancestors than their bacterial counterparts. This presumably reflects several advantages that bacteria have over insects in the acquisition of new enzymatic functions, such as a broad biochemical repertoire from which new functions can be evolved, large population sizes, high effective mutation rates, very short generation times and access to genetic diversity through horizontal gene transfer. Both the insect and bacterial systems support recent theory proposing that new biochemical functions often evolve from 'promiscuous' activities in existing enzymes, with subsequent mutations then enhancing those activities. Study of the insect enzymes will help in resistance management, while the bacterial enzymes are potential bioremediants of insecticide residues in a range of contaminated environments.}, }
@article {pmid24318922, year = {1993}, author = {Nagashima, KV and Shimada, K and Matsuura, K}, title = {Phylogenetic analysis of photosynthetic genes of Rhodocyclus gelatinosus: Possibility of horizontal gene transfer in purple bacteria.}, journal = {Photosynthesis research}, volume = {36}, number = {3}, pages = {185-191}, pmid = {24318922}, issn = {0166-8595}, abstract = {Nucleotide sequences of the genes coding for the M and cytochrome subunits of the photosynthetic reaction center of Rhodocyclus gelatinosus, a purple bacterium in the β subdivision, were determined. The deduced amino acid sequences of these proteins were compared with those of other photosynthetic bacteria. Based on the homology of these two photosynthetic proteins, Rc. gelatinosus was placed in the α subdivision of purple bacteria, which disagrees with the phylogenetic trees based on 16S rRNA and soluble cytochrome c 2. Horizontal transfer of the genes which code for the photosynthetic apparatus in purple bacteria can be postulated if the phylogenetic trees based on 16S rRNA and soluble cytochrome c 2 reflect the real history of purple bacteria.}, }
@article {pmid23889491, year = {2013}, author = {Zhang, HH and Shen, YH and Xu, HE and Liang, HY and Han, MJ and Zhang, Z}, title = {A novel hAT element in Bombyx mori and Rhodnius prolixus: its relationship with miniature inverted repeat transposable elements (MITEs) and horizontal transfer.}, journal = {Insect molecular biology}, volume = {22}, number = {5}, pages = {584-596}, doi = {10.1111/imb.12047}, pmid = {23889491}, issn = {1365-2583}, mesh = {Animals ; Base Sequence ; Bombyx/enzymology/*genetics ; Consensus Sequence ; DNA Transposable Elements/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome, Insect ; Microsatellite Repeats/*genetics ; Molecular Sequence Data ; Rhodnius/enzymology/*genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {Comparative analysis of transposable elements (TEs) from different species can make it possible to reconstruct their history over evolutionary time. In this study, we identified a novel hAT element in Bombyx mori and Rhodnius prolixus with characteristic GGGCGGCA repeats in its subterminal region. Meanwhile, phylogenetic analysis demonstrated that the elements in these two species might represent a separate cluster of the hAT superfamily. Strikingly, a previously identified miniature inverted repeat transposable element (MITE) shared high identity with this autonomous element across the entire length, supporting the hypothesis that MITEs are derived from the internal deletion of DNA transposons. Interestingly, identity of the consensus sequences of this novel hAT element between B. mori and R. prolixus, which diverged about 370 million years ago, was as high as 96.5% over their full length (about 3.6 kb) at the nucleotide level. The patchy distribution amongst species, coupled with overall lack of intense purifying selection acting on this element, suggest that this novel hAT element might have experienced horizontal transfer between the ancestors of B. mori and R. prolixus. Our results highlight that this novel hAT element could be used as a potential tool for germline transformation of R. prolixus to control the transmission of Trypanosoma cruzi, which causes Chagas disease.}, }
@article {pmid23888872, year = {2013}, author = {Dordet Frisoni, E and Marenda, MS and Sagné, E and Nouvel, LX and Guérillot, R and Glaser, P and Blanchard, A and Tardy, F and Sirand-Pugnet, P and Baranowski, E and Citti, C}, title = {ICEA of Mycoplasma agalactiae: a new family of self-transmissible integrative elements that confers conjugative properties to the recipient strain.}, journal = {Molecular microbiology}, volume = {89}, number = {6}, pages = {1226-1239}, doi = {10.1111/mmi.12341}, pmid = {23888872}, issn = {1365-2958}, mesh = {Bacterial Proteins/genetics/metabolism ; *Conjugation, Genetic ; Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences ; Lipoproteins/genetics/metabolism ; Mycoplasma agalactiae/*genetics ; }, abstract = {Horizontal gene transfer (HGT) is a major force of microbial evolution but was long thought to be marginal in mycoplasmas. In silico detection of exchanged regions and of loci encoding putative Integrative Conjugative Elements (ICE) in several mycoplasma genomes challenged this view, raising the prospect of these simple bacteria being able to conjugate. Using the model pathogen Mycoplasma agalactiae, we demonstrated for the first time that one of these elements, ICEA, is indeed self-transmissible. As a hallmark of conjugative processes, ICEA transfers were DNase resistant and required viable cells. ICEA acquisition conferred ICE-negative strains with the new ability to conjugate, allowing the spread of ICEA. Analysis of transfer-deficient mutants indicated that this process requires an ICEA-encoded lipoprotein of unknown function, CDS14. Formation of a circular extrachromosomal intermediate and the subsequent chromosomal integration of ICEA involved CDS22, an ICEA-encoded product distantly related to the ISLre2 transposase family. Remarkably, ICEA has no specific or no preferential integration site, often resulting in gene disruptions. Occurrence of functional mycoplasma ICE offers these bacteria with a means for HGT, a phenomenon with far-reaching implications given their minute-size genome and the number of species that are pathogenic for a broad host-range.}, }
@article {pmid23886578, year = {2013}, author = {Korzeniewska, E and Harnisz, M}, title = {Extended-spectrum beta-lactamase (ESBL)-positive Enterobacteriaceae in municipal sewage and their emission to the environment.}, journal = {Journal of environmental management}, volume = {128}, number = {}, pages = {904-911}, doi = {10.1016/j.jenvman.2013.06.051}, pmid = {23886578}, issn = {1095-8630}, mesh = {Cephalosporin Resistance/genetics ; Cephalosporins/pharmacology ; Drug Resistance, Bacterial/genetics ; Enterobacteriaceae/drug effects/*genetics/*isolation &amp; purification ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Poland ; RNA, Ribosomal, 16S ; Rivers/*microbiology ; Sewage/*microbiology ; Waste Disposal, Fluid ; Water Microbiology ; beta-Lactamases/*genetics ; }, abstract = {The spread of Gram-negative bacteria with plasmid-borne extended-spectrum beta-lactamases (ESBLs) has become a worldwide problem. Their prevalence is increasing, both in hospitals and in the environment. The aim of this study was to investigate the presence of ESBL-positive Enterobacteriaceae in municipal sewage and their emission to the ambient air and the river receiving effluent from wastewater treatment plant (WWTP). In the group of 455 isolated strains, up to 19.8% (90 isolates) were phenotypic ESBL-producers. They were detected in the 63 (100%) of sewage samples analyzed, 7 (33.3%) of river water and in 10 (23.8%) of air samples collected at the WWTP area. The plasmid-mediated genes encoding beta-lactams resistance were detected in almost 10% out of bacteria of the WWTP's final effluents and in above 32% out of bacteria of air at the WWTP area. It confirms that those genes are released into the environment, which might facilitate further dissemination among environmental bacteria. Moreover, genes encoding antibiotic resistance were shown to be transferrable to an Escherichia coli recipient strain, which indicates a high possibility of horizontal gene transfer among strains of different genera within the sewage and environmental samples. This study demonstrated that despite the treatment, the municipal sewage may be a reservoir of antibiotic-resistant microorganisms and plasmid-mediated antibiotic resistance genes. This may pose a public health risk, which requires future evaluation and control.}, }
@article {pmid23884627, year = {2013}, author = {Mihasan, M and Brandsch, R}, title = {pAO1 of Arthrobacter nicotinovorans and the spread of catabolic traits by horizontal gene transfer in gram-positive soil bacteria.}, journal = {Journal of molecular evolution}, volume = {77}, number = {1-2}, pages = {22-30}, pmid = {23884627}, issn = {1432-1432}, mesh = {Arthrobacter/classification/*genetics/metabolism ; Bacterial Proteins/chemistry/*genetics/metabolism ; Chromosomes, Bacterial ; Gene Order ; *Gene Transfer, Horizontal ; Multigene Family ; Phenotype ; Phylogeny ; Plasmids/genetics ; *Quantitative Trait, Heritable ; Soil Microbiology ; }, abstract = {The 165-kb megaplasmid pAO1 of Arthrobacter nicotinovorans carries two large gene clusters, one involved in nicotine catabolism (nic-gene cluster) and one in carbohydrate utilization (ch-gene cluster). Here, we propose that both gene clusters were acquired by A. nicotinovorans by horizontal gene transfer mediated by pAO1. Protein-protein blast search showed that none of the published Arthrobacter genomes contains nic-genes, but Rhodococcus opacus carries on its chromosome a nic-gene cluster highly similar to that of pAO1. Analysis of the nic-genes in the two species suggested a recombination event between their nic-gene clusters. Apparently, there was a gene exchange between pAO1, or a precursor plasmid, and a nic-gene cluster of an as yet unidentified Arthrobacter specie or other soil bacterium, possibly related to Rhodococcus, leading to the transfer by pAO1 of this catabolic trait to A. nicotinovorans. Analysis of the pAO1 ch-gene cluster revealed a virtually identical counterpart on the chromosome of Arthrobacter phenanthrenivorans. Moreover, the sequence analysis of the genes flanking the ch-gene cluster suggested that it was acquired by pAO1 by Xer-related site directed recombination and transferred via the plasmid to A. nicotinovorans. The G+C content, the level of sequence identity, gene co-linearity of nic- and ch-gene clusters as well as the signs of recombination events clearly supports the notion of pAO1 and its precursor plasmids as vehicles in HGT among Gram + soil bacteria.}, }
@article {pmid23877221, year = {2013}, author = {Kube, M and Chernikova, TN and Al-Ramahi, Y and Beloqui, A and Lopez-Cortez, N and Guazzaroni, ME and Heipieper, HJ and Klages, S and Kotsyurbenko, OR and Langer, I and Nechitaylo, TY and Lünsdorf, H and Fernández, M and Juárez, S and Ciordia, S and Singer, A and Kagan, O and Egorova, O and Petit, PA and Stogios, P and Kim, Y and Tchigvintsev, A and Flick, R and Denaro, R and Genovese, M and Albar, JP and Reva, ON and Martínez-Gomariz, M and Tran, H and Ferrer, M and Savchenko, A and Yakunin, AF and Yakimov, MM and Golyshina, OV and Reinhardt, R and Golyshin, PN}, title = {Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica.}, journal = {Nature communications}, volume = {4}, number = {}, pages = {2156}, pmid = {23877221}, issn = {2041-1723}, support = {U54 GM074942/GM/NIGMS NIH HHS/United States ; U54 GM094585/GM/NIGMS NIH HHS/United States ; GM074942/GM/NIGMS NIH HHS/United States ; GM094585/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Physiological/*genetics ; Alcanivoraceae/genetics/metabolism ; Amino Acid Sequence ; Bacterial Proteins/*chemistry/genetics ; Biodegradation, Environmental ; Chromosome Mapping ; Cold Temperature ; Gammaproteobacteria/classification/*genetics/metabolism ; Gene Transfer, Horizontal ; Genome Size ; *Genome, Bacterial ; Industrial Oils ; Molecular Chaperones/*chemistry/genetics ; Molecular Sequence Data ; Phylogeny ; Protein Folding ; Salinity ; Sequence Analysis, DNA ; }, abstract = {Ubiquitous bacteria from the genus Oleispira drive oil degradation in the largest environment on Earth, the cold and deep sea. Here we report the genome sequence of Oleispira antarctica and show that compared with Alcanivorax borkumensis--the paradigm of mesophilic hydrocarbonoclastic bacteria--O. antarctica has a larger genome that has witnessed massive gene-transfer events. We identify an array of alkane monooxygenases, osmoprotectants, siderophores and micronutrient-scavenging pathways. We also show that at low temperatures, the main protein-folding machine Cpn60 functions as a single heptameric barrel that uses larger proteins as substrates compared with the classical double-barrel structure observed at higher temperatures. With 11 protein crystal structures, we further report the largest set of structures from one psychrotolerant organism. The most common structural feature is an increased content of surface-exposed negatively charged residues compared to their mesophilic counterparts. Our findings are relevant in the context of microbial cold-adaptation mechanisms and the development of strategies for oil-spill mitigation in cold environments.}, }
@article {pmid23877005, year = {2013}, author = {Dallman, T and Cross, L and Bishop, C and Perry, N and Olesen, B and Grant, KA and Jenkins, C}, title = {Whole genome sequencing of an unusual serotype of Shiga toxin-producing Escherichia coli.}, journal = {Emerging infectious diseases}, volume = {19}, number = {8}, pages = {1302-1304}, pmid = {23877005}, issn = {1080-6059}, mesh = {*Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Humans ; Likelihood Functions ; Multilocus Sequence Typing ; Phylogeny ; Polymorphism, Single Nucleotide ; Serotyping ; Shiga-Toxigenic Escherichia coli/classification/*genetics ; }, abstract = {Shiga toxin-producing Escherichia coli serotype O117:K1:H7 is a cause of persistent diarrhea in travelers to tropical locations. Whole genome sequencing identified genetic mechanisms involved in the pathoadaptive phenotype. Sequencing also identified toxin and putative adherence genes flanked by sequences indicating horizontal gene transfer from Shigella dysenteriae and Salmonella spp., respectively.}, }
@article {pmid23874940, year = {2013}, author = {Reeves, PR and Cunneen, MM and Liu, B and Wang, L}, title = {Genetics and evolution of the Salmonella galactose-initiated set of o antigens.}, journal = {PloS one}, volume = {8}, number = {7}, pages = {e69306}, pmid = {23874940}, issn = {1932-6203}, mesh = {Base Composition ; Base Sequence ; Cloning, Molecular ; DNA Primers/genetics ; *Evolution, Molecular ; Galactose/analysis ; *Genetic Variation ; Models, Genetic ; Molecular Sequence Data ; Multigene Family/*genetics ; O Antigens/*biosynthesis/chemistry/*genetics ; *Phylogeny ; Salmonella enterica/*genetics ; Sequence Analysis, DNA ; Serotyping ; Species Specificity ; }, abstract = {This paper covers eight Salmonella serogroups, that are defined by O antigens with related structures and gene clusters. They include the serovars that are now most frequently isolated. Serogroups A, B1, B2, C2-C3, D1, D2, D3 and E have O antigens that are distinguished by having galactose as first sugar, and not N-acetyl glucosamine or N-acetyl galactosamine as in the other 38 serogroups, and indeed in most Enterobacteriaceae. The gene clusters for these galactose-initiated appear to have entered S. enterica since its divergence from E. coli, but sequence comparisons show that much of the diversification occurred long before this. We conclude that the gene clusters must have entered S. enterica in a series of parallel events. The individual gene clusters are discussed, followed by analysis of the divergence for those genes shared by two or more gene clusters, and a putative phylogenic tree for the gene clusters is presented. This set of O antigens provides a rare case where it is possible to examine in detail the relationships of a significant number of O antigens. In contrast the more common pattern of O-antigen diversity within a species is for there to be only a few cases of strains having related gene clusters, suggesting that diversity arose through gain of individual O-antigen gene clusters by lateral gene transfer, and under these circumstances the evolution of the diversity is not accessible. This paper on the galactose-initiated set of gene clusters gives new insights into the origins of O-antigen diversity generally.}, }
@article {pmid23874611, year = {2013}, author = {Beukes, CW and Venter, SN and Law, IJ and Phalane, FL and Steenkamp, ET}, title = {South african papilionoid legumes are nodulated by diverse burkholderia with unique nodulation and nitrogen-fixation Loci.}, journal = {PloS one}, volume = {8}, number = {7}, pages = {e68406}, pmid = {23874611}, issn = {1932-6203}, mesh = {Acyltransferases/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Biological Evolution ; Burkholderia/*genetics/metabolism ; Fabaceae/*genetics/metabolism/*microbiology ; Gene Transfer, Horizontal ; *Genetic Loci ; Nitrogen/metabolism ; Nitrogen Fixation/*genetics ; Oxidoreductases/genetics/metabolism ; Phylogeny ; Plant Roots/genetics/metabolism/microbiology ; RNA, Ribosomal, 16S/genetics ; Rhizobium/genetics/metabolism ; South Africa ; Symbiosis ; }, abstract = {The root-nodule bacteria of legumes endemic to the Cape Floristic Region are largely understudied, even though recent reports suggest the occurrence of nodulating Burkholderia species unique to the region. In this study, we considered the diversity and evolution of nodulating Burkholderia associated with the endemic papilionoid tribes Hypocalypteae and Podalyrieae. We identified distinct groups from verified rhizobial isolates by phylogenetic analyses of the 16S rRNA and recA housekeeping gene regions. In order to gain insight into the evolution of the nodulation and diazotrophy of these rhizobia we analysed the genes encoding NifH and NodA. The majority of these 69 isolates appeared to be unique, potentially representing novel species. Evidence of horizontal gene transfer determining the symbiotic ability of these Cape Floristic Region isolates indicate evolutionary origins distinct from those of nodulating Burkholderia from elsewhere in the world. Overall, our findings suggest that Burkholderia species associated with fynbos legumes are highly diverse and their symbiotic abilities have unique ancestries. It is therefore possible that the evolution of these bacteria is closely linked to the diversification and establishment of legumes characteristic of the Cape Floristic Region.}, }
@article {pmid23874325, year = {2013}, author = {Wang, J and Stephan, R and Karczmarczyk, M and Yan, Q and Hächler, H and Fanning, S}, title = {Molecular characterization of bla ESBL-harboring conjugative plasmids identified in multi-drug resistant Escherichia coli isolated from food-producing animals and healthy humans.}, journal = {Frontiers in microbiology}, volume = {4}, number = {}, pages = {188}, pmid = {23874325}, issn = {1664-302X}, abstract = {BACKGROUND: Extended-spectrum β-lactamase (ESBL)-encoding genes are frequently mapped to plasmids, yet few of these structures have been characterized at the molecular level, to date.<br><br>METHODS: Eighty-seven ESBL-producing Escherichia coli were isolated from fecal samples of food-producing animals and healthy humans in Switzerland from 2009 to 2011. Plasmid DNA of all isolates was purified. Broth mating assays were carried out individually for 32 isolates to determine if the ESBL marker could be transferred by conjugation. The plasmid sizes were determined by S1-nuclease pulsed-field gel electrophoresis (PFGE) and the plasmids were typed by PCR-based replicon typing. Susceptibility tests by disk diffusion followed with a re-analysis S1-nuclease PFGE and PCRs were performed to confirm plasmid transfer. Microarray was performed to detect additional antibiotic resistance markers and multi-locus sequence typing was also performed in selected donor strains. The phylotypes were identified by triplex PCR.<br><br>RESULTS: About half (n = 46) of the 87 isolates carried small (<20-kb) plasmids. All selected 32 isolates contained large plasmids (ranging in sizes from 20- to 600-kb). Eleven plasmid replicon types were detected. Of these, IncFIA (n = 5), IncFIB (n = 9), and IncK/B (n = 4) were common. Nine isolates demonstrated the ability to transfer their cefotaxime resistance marker at high transfer rates. Plasmid profile re-analysis of these transconjugants identified 16 plasmids. IncFIB and IncI1 were the most prevalent replicon types. Phylogenetic grouping showed that five of the nine donor strains belonged to phylogroup B1. Nine different sequence types were identified in nine tested donor strains.<br><br>CONCLUSION: Characterization of these ESBL-encoding conjugative plasmids extends our understanding on these resistance markers in multi-drug resistant E. coli cultured from healthy human and animal sources.}, }
@article {pmid23874222, year = {2013}, author = {Menard, KL and Grossman, AD}, title = {Selective pressures to maintain attachment site specificity of integrative and conjugative elements.}, journal = {PLoS genetics}, volume = {9}, number = {7}, pages = {e1003623}, pmid = {23874222}, issn = {1553-7404}, support = {R01 GM050895/GM/NIGMS NIH HHS/United States ; GM050895/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacillus subtilis/*genetics ; *Chromosomes, Bacterial ; DNA Replication/genetics ; Drug Resistance, Microbial/*genetics ; Gene Transfer, Horizontal ; Genome, Bacterial ; Interspersed Repetitive Sequences/*genetics ; }, abstract = {Integrative and conjugative elements (ICEs) are widespread mobile genetic elements that are usually found integrated in bacterial chromosomes. They are important agents of evolution and contribute to the acquisition of new traits, including antibiotic resistances. ICEs can excise from the chromosome and transfer to recipients by conjugation. Many ICEs are site-specific in that they integrate preferentially into a primary attachment site in the bacterial genome. Site-specific ICEs can also integrate into secondary locations, particularly if the primary site is absent. However, little is known about the consequences of integration of ICEs into alternative attachment sites or what drives the apparent maintenance and prevalence of the many ICEs that use a single attachment site. Using ICEBs1, a site-specific ICE from Bacillus subtilis that integrates into a tRNA gene, we found that integration into secondary sites was detrimental to both ICEBs1 and the host cell. Excision of ICEBs1 from secondary sites was impaired either partially or completely, limiting the spread of ICEBs1. Furthermore, induction of ICEBs1 gene expression caused a substantial drop in proliferation and cell viability within three hours. This drop was dependent on rolling circle replication of ICEBs1 that was unable to excise from the chromosome. Together, these detrimental effects provide selective pressure against the survival and dissemination of ICEs that have integrated into alternative sites and may explain the maintenance of site-specific integration for many ICEs.}, }
@article {pmid23874149, year = {2013}, author = {Gray, TA and Krywy, JA and Harold, J and Palumbo, MJ and Derbyshire, KM}, title = {Distributive conjugal transfer in mycobacteria generates progeny with meiotic-like genome-wide mosaicism, allowing mapping of a mating identity locus.}, journal = {PLoS biology}, volume = {11}, number = {7}, pages = {e1001602}, pmid = {23874149}, issn = {1545-7885}, support = {R56 AI080694/AI/NIAID NIH HHS/United States ; AI042308/AI/NIAID NIH HHS/United States ; R56AI080694/AI/NIAID NIH HHS/United States ; T32 AI055429/AI/NIAID NIH HHS/United States ; R01 AI042308/AI/NIAID NIH HHS/United States ; }, mesh = {Conjugation, Genetic/*genetics ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/*genetics ; Mosaicism ; Mycobacterium/*genetics ; Mycobacterium tuberculosis/genetics ; }, abstract = {Horizontal gene transfer (HGT) in bacteria generates variation and drives evolution, and conjugation is considered a major contributor as it can mediate transfer of large segments of DNA between strains and species. We previously described a novel form of chromosomal conjugation in mycobacteria that does not conform to classic oriT-based conjugation models, and whose potential evolutionary significance has not been evaluated. Here, we determined the genome sequences of 22 F1-generation transconjugants, providing the first genome-wide view of conjugal HGT in bacteria at the nucleotide level. Remarkably, mycobacterial recipients acquired multiple, large, unlinked segments of donor DNA, far exceeding expectations for any bacterial HGT event. Consequently, conjugal DNA transfer created extensive genome-wide mosaicism within individual transconjugants, which generated large-scale sibling diversity approaching that seen in meiotic recombination. We exploited these attributes to perform genome-wide mapping and introgression analyses to map a locus that determines conjugal mating identity in M. smegmatis. Distributive conjugal transfer offers a plausible mechanism for the predicted HGT events that created the genome mosaicism observed among extant Mycobacterium tuberculosis and Mycobacterium canettii species. Mycobacterial distributive conjugal transfer permits innovative genetic approaches to map phenotypic traits and confers the evolutionary benefits of sexual reproduction in an asexual organism.}, }
@article {pmid23873078, year = {2013}, author = {Ho, CC and Lau, SK and Woo, PC}, title = {Romance of the three domains: how cladistics transformed the classification of cellular organisms.}, journal = {Protein &amp; cell}, volume = {4}, number = {9}, pages = {664-676}, pmid = {23873078}, issn = {1674-8018}, mesh = {Animals ; Biological Evolution ; Classification/methods ; Humans ; Pedigree ; *Phylogeny ; }, abstract = {Cladistics is a biological philosophy that uses genealogical relationship among species and an inferred sequence of divergence as the basis of classification. This review critically surveys the chronological development of biological classification from Aristotle through our postgenomic era with a central focus on cladistics. In 1957, Julian Huxley coined cladogenesis to denote splitting from subspeciation. In 1960, the English translation of Willi Hennig's 1950 work, Systematic Phylogenetics, was published, which received strong opposition from pheneticists, such as numerical taxonomists Peter Sneath and Robert Sokal, and evolutionary taxonomist, Ernst Mayr, and sparked acrimonious debates in 1960-1980. In 1977-1990, Carl Woese pioneered in using small subunit rRNA gene sequences to delimitate the three domains of cellular life and established major prokaryotic phyla. Cladistics has since dominated taxonomy. Despite being compatible with modern microbiological observations, i.e. organisms with unusual phenotypes, restricted expression of characteristics and occasionally being uncultivable, increasing recognition of pervasiveness and abundance of horizontal gene transfer has challenged relevance and validity of cladistics. The mosaic nature of eukaryotic and prokaryotic genomes was also gradually discovered. In the mid-2000s, high-throughput and whole-genome sequencing became routine and complex geneologies of organisms have led to the proposal of a reticulated web of life. While genomics only indirectly leads to understanding of functional adaptations to ecological niches, computational modeling of entire organisms is underway and the gap between genomics and phenetics may soon be bridged. Controversies are not expected to settle as taxonomic classifications shall remain subjective to serve the human scientist, not the classified.}, }
@article {pmid23873043, year = {2013}, author = {Flot, JF and Hespeels, B and Li, X and Noel, B and Arkhipova, I and Danchin, EG and Hejnol, A and Henrissat, B and Koszul, R and Aury, JM and Barbe, V and Barthélémy, RM and Bast, J and Bazykin, GA and Chabrol, O and Couloux, A and Da Rocha, M and Da Silva, C and Gladyshev, E and Gouret, P and Hallatschek, O and Hecox-Lea, B and Labadie, K and Lejeune, B and Piskurek, O and Poulain, J and Rodriguez, F and Ryan, JF and Vakhrusheva, OA and Wajnberg, E and Wirth, B and Yushenova, I and Kellis, M and Kondrashov, AS and Mark Welch, DB and Pontarotti, P and Weissenbach, J and Wincker, P and Jaillon, O and Van Doninck, K}, title = {Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga.}, journal = {Nature}, volume = {500}, number = {7463}, pages = {453-457}, pmid = {23873043}, issn = {1476-4687}, mesh = {Animals ; *Biological Evolution ; Gene Conversion/*genetics ; Gene Transfer, Horizontal/genetics ; Genome/*genetics ; Genomics ; Meiosis/genetics ; Models, Biological ; Reproduction, Asexual/*genetics ; Rotifera/*genetics ; Tetraploidy ; }, abstract = {Loss of sexual reproduction is considered an evolutionary dead end for metazoans, but bdelloid rotifers challenge this view as they appear to have persisted asexually for millions of years. Neither male sex organs nor meiosis have ever been observed in these microscopic animals: oocytes are formed through mitotic divisions, with no reduction of chromosome number and no indication of chromosome pairing. However, current evidence does not exclude that they may engage in sex on rare, cryptic occasions. Here we report the genome of a bdelloid rotifer, Adineta vaga (Davis, 1873), and show that its structure is incompatible with conventional meiosis. At gene scale, the genome of A. vaga is tetraploid and comprises both anciently duplicated segments and less divergent allelic regions. However, in contrast to sexual species, the allelic regions are rearranged and sometimes even found on the same chromosome. Such structure does not allow meiotic pairing; instead, we find abundant evidence of gene conversion, which may limit the accumulation of deleterious mutations in the absence of meiosis. Gene families involved in resistance to oxidation, carbohydrate metabolism and defence against transposons are significantly expanded, which may explain why transposable elements cover only 3% of the assembled sequence. Furthermore, 8% of the genes are likely to be of non-metazoan origin and were probably acquired horizontally. This apparent convergence between bdelloids and prokaryotes sheds new light on the evolutionary significance of sex.}, }
@article {pmid23871432, year = {2013}, author = {Teissié, J}, title = {Was Zeus responsible for horizontal gene transfer: a comment on "Lightning-triggered electroporation and electrofusion as possible contributors to natural horizontal gene transfer" by Tadej Kotnik.}, journal = {Physics of life reviews}, volume = {10}, number = {3}, pages = {371-372}, doi = {10.1016/j.plrev.2013.07.008}, pmid = {23871432}, issn = {1873-1457}, mesh = {Animals ; *Electroporation ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Humans ; *Lightning ; }, }
@article {pmid23871297, year = {2013}, author = {Gubry-Rangin, C and Béna, G and Cleyet-Marel, JC and Brunel, B}, title = {Definition and evolution of a new symbiovar, sv. rigiduloides, among Ensifer meliloti efficiently nodulating Medicago species.}, journal = {Systematic and applied microbiology}, volume = {36}, number = {7}, pages = {490-496}, doi = {10.1016/j.syapm.2013.06.004}, pmid = {23871297}, issn = {1618-0984}, mesh = {Bacterial Proteins/genetics ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; *Genetic Variation ; Genotype ; Medicago/*microbiology ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Phylogeny ; Plant Root Nodulation ; Root Nodules, Plant/*microbiology ; Sequence Analysis, DNA ; Sinorhizobium meliloti/*classification/genetics/*isolation &amp; purification/physiology ; }, abstract = {Understanding functional diversity is one of the main goals of microbial ecology, and definition of new bacterial ecotypes contributes significantly to this objective. Nitrogen-fixing bacteria provide a good system for investigation of ecotypes/biovars/symbiovars, as they present different specific associations with several host plants. This specific symbiosis is reflected both in the nodulation and fixation efficiency and in genetic characters of the bacteria, and several biovars have already been described in the bacterial species Ensifer meliloti. In the present study, the species affiliation of E. meliloti strains trapped from nodules sampled from Medicago rigiduloïdes roots was analyzed using housekeeping recA genes and DNA-DNA hybridization. The genetic diversity of these isolates was also investigated using several symbiotic markers: nodulation (nodA, nodB, nodC) and nitrogen fixation (nifH) genes, as well as the performance of phenotypic tests of nodulation capacity and nitrogen fixation efficiency. These analyses led to the proposal of a new bacterial symbiovar, E. meliloti sv. rigiduloides, that fixed nitrogen efficiently on M. rigiduloïdes, but not on Medicago truncatula. Using phylogenetic reconstructions, including the different described symbiovars, several hypotheses of lateral gene transfer and gene loss are proposed to explain the emergence of symbiovars within this species. The widespread geographical distribution of this symbiovar around the Mediterranean Basin, in contrast to restriction of M. rigiduloïdes to Eastern European countries, suggests that these isolates might also be associated with other plant species. The description of a new symbiovar within E. meliloti confirms the need for accurate bacterial ecological classification, especially for analysis of bacterial populations.}, }
@article {pmid23870305, year = {2013}, author = {Gerardo, NM}, title = {The give and take of host-microbe symbioses.}, journal = {Cell host &amp; microbe}, volume = {14}, number = {1}, pages = {1-3}, doi = {10.1016/j.chom.2013.07.001}, pmid = {23870305}, issn = {1934-6069}, mesh = {Animals ; Bacteria/*genetics ; Betaproteobacteria/*genetics ; *Gene Transfer, Horizontal ; Hemiptera/*genetics/*microbiology ; *Symbiosis ; }, abstract = {Studying the association between mealybugs and two bacterial symbionts, Husnik et al. (2013) demonstrated that both integration of metabolic pathways across the partners' genomes and horizontal gene transfer from diverse bacteria into the insect host genome are integral to symbiosis.}, }
@article {pmid23870163, year = {2013}, author = {Davolos, D and Pietrangeli, B}, title = {A molecular study on bacterial resistance to arsenic-toxicity in surface and underground waters of Latium (Italy).}, journal = {Ecotoxicology and environmental safety}, volume = {96}, number = {}, pages = {1-9}, doi = {10.1016/j.ecoenv.2013.05.039}, pmid = {23870163}, issn = {1090-2414}, mesh = {Arsenic/*toxicity ; Bacteria/classification/*drug effects/*genetics/isolation &amp; purification ; Biodiversity ; Drinking Water/microbiology ; Drug Resistance, Bacterial/genetics ; Fresh Water/*microbiology ; Groundwater/*microbiology ; Ion Pumps/genetics ; Italy ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; *Water Microbiology ; Water Pollutants, Chemical/toxicity ; }, abstract = {Latium, a region in central Italy, is known for its extensive volcanic areas that make a significant contribution to the arsenic (As) contamination of freshwater environments, even though some degree of As water pollution may be caused by human activities. The information available on indigenous As-resistant prokaryotes in aquatic environments of Latium is, however, still limited. In this study, we describe new bacteria that are resistant to arsenic toxicity and were isolated from the surface waters of Lake Vico and the Sacco River, two groundwater systems in Latium, as well as from bottled natural mineral water from the same region. The 16S rRNA gene sequence analysis for the As-resistant strains in lake and river waters points to a prevalence of β- and γ-Proteobacteria, while α-Proteobacteria, Firmicutes and Bacteroidetes are represented to a lesser extent. By contrast, solely γ-Proteobacteria were isolated from groundwater samples. The presence of Actinobacteria was documented exclusively in bottled mineral water. In addition, we conducted a DNA sequence-based study on the gene codifying arsB, an As(III) efflux membrane protein pump related to arsenic resistance, for all the As-resistant bacterial isolates. A phylogenetic analysis was carried out on the newly sequenced 16S rRNA genes and arsB in the present study as well as on an additional 16S rRNA/arsB dataset we obtained previously from Lake Albano, from the Tiber and from a well in Bassano Romano located in Latium (Davolos and Pietrangeli, 2011). Overall, the phylogenetic diversity of As-resistant bacteria in underground water was very limited if compared with lentic and lotic waters. Lastly, our molecular data support the hypothesis that the horizontal gene transfer of ars in As-containing freshwater environments is not limited to closely-related genomes, but also occurs between bacteria that are distant from an evolutionary viewpoint, thereby indicating that such genetic events may be considered a source of microbial resistance to arsenic-toxicity.}, }
@article {pmid23865952, year = {2013}, author = {Schulte, RD and Makus, C and Schulenburg, H}, title = {Host-parasite coevolution favours parasite genetic diversity and horizontal gene transfer.}, journal = {Journal of evolutionary biology}, volume = {26}, number = {8}, pages = {1836-1840}, doi = {10.1111/jeb.12174}, pmid = {23865952}, issn = {1420-9101}, mesh = {Animals ; Bacillus thuringiensis/*genetics ; *Biological Evolution ; Caenorhabditis elegans/genetics/*microbiology ; Chromosomes, Bacterial/genetics ; *Gene Transfer, Horizontal ; Genetic Variation ; Genotype ; *Host-Parasite Interactions/genetics ; }, abstract = {Host-parasite coevolution is predicted to favour genetic diversity and the underlying mechanisms (e.g. sexual reproduction and, more generally, genetic exchange), because diversity enhances the antagonists' potential for rapid adaptation. To date, this prediction has mainly been tested and confirmed for the host. It should similarly apply to the parasite. Indeed, our previous work demonstrated that experimental coevolution between the nematode Caenorhabditis elegans and its microparasite Bacillus thuringiensis selects for genetic diversity in both antagonists. For the parasite, the previous analysis was based on plasmid-encoded toxin gene markers. Thus, it was restricted to a very small part of the bacterial genome and did not cover the main chromosome, which harbours a large variety of virulence factors. Here, we present new data for chromosomal gene markers of B. thuringiensis and combine this information with the previous results on plasmid-encoded toxins. Our new results demonstrate that, in comparison with the control treatment, coevolution with a host similarly leads to higher levels of genetic diversity in the bacterial chromosome, thus indicating the relevance of chromosomal genes for coevolution. Furthermore, the frequency of toxin gene gain is significantly elevated during coevolution, highlighting the importance of horizontal gene transfer as a diversity-generating mechanism. In conclusion, our study emphasizes the strong influence of antagonistic coevolution on parasite genetic diversity and gene exchange.}, }
@article {pmid23865862, year = {2013}, author = {Liu, Y and Li, XY and Wan, LG and Jiang, WY and Li, FQ and Yang, JH}, title = {Efflux system overexpression and decreased OprD contribute to the carbapenem resistance among extended-spectrum beta-lactamase-producing Pseudomonas aeruginosa isolates from a Chinese university hospital.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {19}, number = {6}, pages = {463-468}, doi = {10.1089/mdr.2013.0010}, pmid = {23865862}, issn = {1931-8448}, mesh = {Anti-Bacterial Agents/therapeutic use ; Bacterial Outer Membrane Proteins/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Carbapenems/therapeutic use ; China ; Clone Cells ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; *Genes, MDR ; Hospitals, University ; Humans ; Membrane Proteins/genetics/metabolism ; Membrane Transport Proteins/genetics/metabolism ; Multilocus Sequence Typing ; Plasmids ; Porins/*genetics/metabolism ; Pseudomonas Infections/drug therapy/microbiology ; Pseudomonas aeruginosa/drug effects/*genetics/isolation &amp; purification ; beta-Lactam Resistance/*genetics ; beta-Lactamases/*genetics/metabolism ; }, abstract = {The aim of this study was to investigate, for the first time, the combinations of carbapenem resistance mechanisms in clinical isolates of extended-spectrum beta-lactamase (ESBL)-producing Pseudomonas aeruginosa in a Chinese hospital. Pulsed-field gel electrophoresis revealed the presence of eight clonal types among the 15 ESBL producers. Multilocus sequence typing of two isolates harboured blaIMP-1 identified the clonal strain as ST325. All these genes were found either alone or simultaneously in the strains in the following five different arrangements:<blaOXA-10>; <blaOXA-10, blaIMP-1>; <blaPER-1, blaOXA-10>; <blaPER-1, blaPSE-1>; <blaOXA-10, blaTEM-1>. Regarding mutation-driven resistance, all, but four of the isolates had a relevant decrease of oprD expression. In addition, 73.3% of the isolates overexpressed mexB, 40% mexD, and 33.3% mexY. A specific combination of overexpressed mexB or mexY and alteration in loop L710 of OprD were significantly associated with meropenem resistance. In conclusion, combination of several mutation-driven mechanisms leading to OprD inactivation and overexpression of efflux systems was the main carbapenem resistance mechanism among the ESBL-producing P. aeruginosa isolates, but acquisition of a transferable resistance determinant such as metallo-β-lactamase could be problematic in clinical settings in China.}, }
@article {pmid23865633, year = {2013}, author = {Moriconi, V and Sellaro, R and Ayub, N and Soto, G and Rugnone, M and Shah, R and Pathak, GP and Gärtner, W and Casal, JJ}, title = {LOV-domain photoreceptor, encoded in a genomic island, attenuates the virulence of Pseudomonas syringae in light-exposed Arabidopsis leaves.}, journal = {The Plant journal : for cell and molecular biology}, volume = {76}, number = {2}, pages = {322-331}, doi = {10.1111/tpj.12289}, pmid = {23865633}, issn = {1365-313X}, mesh = {Arabidopsis/microbiology/radiation effects ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; *Genomic Islands ; *Light ; Open Reading Frames ; Operon ; Photoreceptors, Microbial/*genetics/radiation effects ; Plant Diseases/microbiology ; Plant Leaves/*microbiology/radiation effects ; Pseudomonas syringae/genetics/*pathogenicity ; Quorum Sensing ; Sigma Factor/metabolism ; *Virulence ; }, abstract = {In Arabidopsis thaliana, light signals modulate the defences against bacteria. Here we show that light perceived by the LOV domain-regulated two-component system (Pst-Lov) of Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) modulates virulence against A. thaliana. Bioinformatic analysis and the existence of an episomal circular intermediate indicate that the locus encoding Pst-Lov is present in an active genomic island acquired by horizontal transfer. Strains mutated at Pst-Lov showed enhanced growth on minimal medium and in leaves of A. thaliana exposed to light, but not in leaves incubated in darkness or buried in the soil. Pst-Lov repressed the expression of principal and alternative sigma factor genes and their downstream targets linked to bacterial growth, virulence and quorum sensing, in a strictly light-dependent manner. We propose that the function of Pst-Lov is to distinguish between soil (dark) and leaf (light) environments, attenuating the damage caused to host tissues while releasing growth out of the host. Therefore, in addition to its direct actions via photosynthesis and plant sensory receptors, light may affect plants indirectly via the sensory receptors of bacterial pathogens.}, }
@article {pmid23865498, year = {2013}, author = {Moreno Switt, AI and Orsi, RH and den Bakker, HC and Vongkamjan, K and Altier, C and Wiedmann, M}, title = {Genomic characterization provides new insight into Salmonella phage diversity.}, journal = {BMC genomics}, volume = {14}, number = {}, pages = {481}, pmid = {23865498}, issn = {1471-2164}, mesh = {Amino Acid Sequence ; Anti-Infective Agents/pharmacology ; Bacteriophages/drug effects/*genetics/pathogenicity ; Cluster Analysis ; DNA, Viral/metabolism ; Drug Resistance, Viral/genetics ; Environment ; *Genetic Variation ; *Genomics ; Molecular Sequence Data ; Polymorphism, Single Nucleotide/genetics ; Salmonella/*virology ; Viral Proteins/chemistry/genetics ; }, abstract = {BACKGROUND: Salmonella is a widely distributed foodborne pathogen that causes tens of millions of salmonellosis cases globally every year. While the genomic diversity of Salmonella is increasingly well studied, our knowledge of Salmonella phage genomic diversity is still rather limited, despite the contributions of both lysogenic and lytic phages to Salmonella virulence, diversity and ecology (e.g., through horizontal gene transfer and Salmonella lysis). To gain a better understanding of phage diversity in a specific ecological niche, we sequenced 22 Salmonella phages isolated from a number of dairy farms from New York State (United States) and analyzed them using a comparative genomics approach.<br><br>RESULTS: Classification of the 22 phages according to the presence/absence of orthologous genes allowed for classification into 8 well supported clusters. In addition to two phage clusters that represent novel virulent Salmonella phages, we also identified four phage clusters that each contained previously characterized phages from multiple continents. Our analyses also identified two clusters of phages that carry putative virulence (e.g., adhesins) and antimicrobial resistance (tellurite and bicyclomycin) genes as well as virulent and temperate transducing phages. Insights into phage evolution from our analyses include (i) identification of DNA metabolism genes that may facilitate nucleotide synthesis in phages with a G+C % distinct from Salmonella, and (ii) evidence of Salmonella phage tailspike and fiber diversity due to both single nucleotide polymorphisms and major re-arrangements, which may affect the host specificity of Salmonella phages.<br><br>CONCLUSIONS: Genomics-based characterization of 22 Salmonella phages isolated from dairy farms allowed for identification of a number of novel Salmonella phages. While the comparative genomics analyses of these phages provide a number of new insights in the evolution and diversity of Salmonella phages, they only represent a first glimpse into the diversity of Salmonella phages that is likely to be discovered when phages from different environments are characterized.}, }
@article {pmid23863837, year = {2013}, author = {Lange, SJ and Alkhnbashi, OS and Rose, D and Will, S and Backofen, R}, title = {CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems.}, journal = {Nucleic acids research}, volume = {41}, number = {17}, pages = {8034-8044}, pmid = {23863837}, issn = {1362-4962}, mesh = {Adaptive Immunity/genetics ; Archaea/genetics/immunology ; Archaeal Proteins/chemistry/classification ; Bacteria/genetics/immunology ; Bacterial Proteins/chemistry/classification ; Cluster Analysis ; Conserved Sequence ; Crenarchaeota/genetics ; Euryarchaeota/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Internet ; *Inverted Repeat Sequences ; Nucleotide Motifs ; RNA Cleavage ; RNA, Archaeal/*chemistry/classification ; RNA, Bacterial/*chemistry/classification ; Software ; }, abstract = {Central to Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-Cas systems are repeated RNA sequences that serve as Cas-protein-binding templates. Classification is based on the architectural composition of associated Cas proteins, considering repeat evolution is essential to complete the picture. We compiled the largest data set of CRISPRs to date, performed comprehensive, independent clustering analyses and identified a novel set of 40 conserved sequence families and 33 potential structure motifs for Cas-endoribonucleases with some distinct conservation patterns. Evolutionary relationships are presented as a hierarchical map of sequence and structure similarities for both a quick and detailed insight into the diversity of CRISPR-Cas systems. In a comparison with Cas-subtypes, I-C, I-E, I-F and type II were strongly coupled and the remaining type I and type III subtypes were loosely coupled to repeat and Cas1 evolution, respectively. Subtypes with a strong link to CRISPR evolution were almost exclusive to bacteria; nevertheless, we identified rare examples of potential horizontal transfer of I-C and I-E systems into archaeal organisms. Our easy-to-use web server provides an automated assignment of newly sequenced CRISPRs to our classification system and enables more informed choices on future hypotheses in CRISPR-Cas research: http://rna.informatik.uni-freiburg.de/CRISPRmap.}, }
@article {pmid23862575, year = {2015}, author = {Juhas, M}, title = {Horizontal gene transfer in human pathogens.}, journal = {Critical reviews in microbiology}, volume = {41}, number = {1}, pages = {101-108}, doi = {10.3109/1040841X.2013.804031}, pmid = {23862575}, issn = {1549-7828}, mesh = {Bacterial Infections/*microbiology ; *Bacterial Physiological Phenomena ; Clostridioides difficile/genetics/pathogenicity ; Escherichia coli/genetics/pathogenicity ; *Gene Transfer, Horizontal ; Humans ; *Virulence ; }, abstract = {Horizontal gene transfer has a tremendous impact on the genome plasticity, adaptation and evolution of bacteria. Horizontally transferred mobile genetic elements are involved in the dissemination of antibiotic resistance and virulence genes, thus contributing to the emergence of novel "superbugs". This review provides update on various mechanisms of horizontal gene transfer and examines how horizontal gene transfer contributes to the evolution of pathogenic bacteria. Special focus is paid to the role horizontal gene transfer plays in pathogenicity of the emerging human pathogens: hypervirulent Clostridium difficile and Escherichia coli (including the most recent haemolytic uraemic syndrome outbreak strain) and methicillin-resistant Staphylococcus aureus (MRSA), which have been associated with largest outbreaks of infection recently.}, }
@article {pmid23861954, year = {2013}, author = {Thumbi, DK and Béliveau, C and Cusson, M and Lapointe, R and Lucarotti, CJ}, title = {Comparative genome sequence analysis of Choristoneura occidentalis Freeman and C. rosaceana Harris (Lepidoptera: Tortricidae) alphabaculoviruses.}, journal = {PloS one}, volume = {8}, number = {7}, pages = {e68968}, pmid = {23861954}, issn = {1932-6203}, mesh = {Animals ; Computational Biology ; Gene Order ; Genes, Viral ; *Genome, Viral ; Moths/*virology ; Nucleopolyhedroviruses/classification/*genetics/physiology ; Open Reading Frames ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology ; Virus Replication ; }, abstract = {The complete genome sequences of Choristoneura occidentalis and C. rosaceana nucleopolyhedroviruses (ChocNPV and ChroNPV, respectively) (Baculoviridae: Alphabaculovirus) were determined and compared with each other and with those of other baculoviruses, including the genome of the closely related C. fumiferana NPV (CfMNPV). The ChocNPV genome was 128,446 bp in length (1147 bp smaller than that of CfMNPV), had a G+C content of 50.1%, and contained 148 open reading frames (ORFs). In comparison, the ChroNPV genome was 129,052 bp in length, had a G+C content of 48.6% and contained 149 ORFs. ChocNPV and ChroNPV shared 144 ORFs in common, and had a 77% sequence identity with each other and 96.5% and 77.8% sequence identity, respectively, with CfMNPV. Five homologous regions (hrs), with sequence similarities to those of CfMNPV, were identified in ChocNPV, whereas the ChroNPV genome contained three hrs featuring up to 14 repeats. Both genomes encoded three inhibitors of apoptosis (IAP-1, IAP-2, and IAP-3), as reported for CfMNPV, and the ChocNPV IAP-3 gene represented the most divergent functional region of this genome relative to CfMNPV. Two ORFs were unique to ChocNPV, and four were unique to ChroNPV. ChroNPV ORF chronpv38 is a eukaryotic initiation factor 5 (eIF-5) homolog that has also been identified in the C. occidentalis granulovirus (ChocGV) and is believed to be the product of horizontal gene transfer from the host. Based on levels of sequence identity and phylogenetic analysis, both ChocNPV and ChroNPV fall within group I alphabaculoviruses, where ChocNPV appears to be more closely related to CfMNPV than does ChroNPV. Our analyses suggest that it may be appropriate to consider ChocNPV and CfMNPV as variants of the same virus species.}, }
@article {pmid23861490, year = {2013}, author = {Roper, M and Simonin, A and Hickey, PC and Leeder, A and Glass, NL}, title = {Nuclear dynamics in a fungal chimera.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {32}, pages = {12875-12880}, pmid = {23861490}, issn = {1091-6490}, mesh = {Algorithms ; Cell Nucleus/genetics/metabolism/*physiology ; Cell Physiological Phenomena ; Cytoplasm/metabolism/physiology ; Fungal Proteins/genetics/metabolism ; Histones/genetics/metabolism ; Hyphae/genetics/metabolism/*physiology ; Kinetics ; Luminescent Proteins/genetics/metabolism ; Microscopy, Confocal ; Models, Biological ; Neurospora crassa/genetics/metabolism/*physiology ; Recombinant Fusion Proteins/genetics/metabolism ; Spores, Fungal/genetics/metabolism/*physiology ; }, abstract = {A fungal colony is a syncytium composed of a branched and interconnected network of cells. Chimerism endows colonies with increased virulence and ability to exploit nutritionally complex substrates. Moreover, chimera formation may be a driver for diversification at the species level by allowing lateral gene transfer between strains that are too distantly related to hybridize sexually. However, the processes by which genomic diversity develops and is maintained within a single colony are little understood. In particular, both theory and experiments show that genetically diverse colonies may be unstable and spontaneously segregate into genetically homogenous sectors. By directly measuring patterns of nuclear movement in the model ascomycete fungus Neurospora crassa, we show that genetic diversity is maintained by complex mixing flows of nuclei at all length scales within the hyphal network. Mathematical modeling and experiments in a morphological mutant reveal some of the exquisite hydraulic engineering necessary to create the mixing flows. In addition to illuminating multinucleate and multigenomic lifestyles, the adaptation of a hyphal network for mixing nuclear material provides a previously unexamined organizing principle for understanding morphological diversity in the more-than-a-million species of filamentous fungi.}, }
@article {pmid23861308, year = {2013}, author = {Roth, AL and Lister, PD and Hanson, ND}, title = {Effect of drug treatment options on the mobility and expression of blaKPC.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {68}, number = {12}, pages = {2779-2785}, doi = {10.1093/jac/dkt280}, pmid = {23861308}, issn = {1460-2091}, mesh = {Blotting, Southern ; DNA Transposable Elements ; DNA, Bacterial/chemistry/genetics ; Enterobacteriaceae/*drug effects/genetics ; Gene Expression/*drug effects ; Gene Transfer, Horizontal/*drug effects ; Humans ; Molecular Sequence Data ; Plasmids/analysis ; Pseudomonas aeruginosa/*drug effects/genetics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; beta-Lactamases/*biosynthesis/*genetics ; }, abstract = {OBJECTIVES: Both transposition and increases in gene expression have been implicated in the success of KPC-producing pathogens, but the stimulus required for these phenomena are unknown. It is possible that exposure to antimicrobials during patient treatment increases bla(KPC) expression or induces Tn4401 transposition. The purpose of this study was to determine if exposure to carbapenems or other antimicrobial drug classes could stimulate expression of bla(KPC) or the in vitro transposition of Tn4401.<br><br>METHODS: Five KPC-producing clinical isolates were evaluated in this study. Gene expression of RNA from each isolate exposed to subinhibitory, MIC or suprainhibitory levels of antibiotics was evaluated using real-time RT-PCR. Southern blots were performed on plasmids from isolates exposed to subinhibitory levels of antibiotics.<br><br>RESULTS: There were subtle changes in bla(KPC) RNA expression following antibiotic exposure that were both strain and drug dependent. Multiple plasmids ranging from ~8 to >200 kb were observed for the Enterobacteriaceae isolates, whereas the Pseudomonas aeruginosa isolate had one ~55 kb plasmid. No changes in hybridization patterns or binding intensity for the bla(KPC) probe were observed after antibiotic exposure.<br><br>CONCLUSIONS: While the changes in bla(KPC) RNA expression are subtle, the different responses observed suggest both strain- and genera-specific variations in response to different antibiotic treatments.}, }
@article {pmid23860765, year = {2013}, author = {Crawford, RW and Wangdi, T and Spees, AM and Xavier, MN and Tsolis, RM and Bäumler, AJ}, title = {Loss of very-long O-antigen chains optimizes capsule-mediated immune evasion by Salmonella enterica serovar Typhi.}, journal = {mBio}, volume = {4}, number = {4}, pages = {}, pmid = {23860765}, issn = {2150-7511}, support = {R01 AI044170/AI/NIAID NIH HHS/United States ; AI044170/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Colitis/microbiology/pathology ; Complement System Proteins/immunology ; Disease Models, Animal ; Female ; *Immune Evasion ; Mice ; Mice, Inbred C57BL ; O Antigens/genetics/*metabolism ; Polysaccharides, Bacterial/genetics/*immunology/*metabolism ; Salmonella typhi/genetics/*immunology/*metabolism/pathogenicity ; Salmonella typhimurium/genetics/immunology/pathogenicity ; Typhoid Fever/microbiology/*pathology ; Virulence ; }, abstract = {UNLABELLED: Expression of capsular polysaccharides is a variable trait often associated with more-virulent forms of a bacterial species. For example, typhoid fever is caused by the capsulated Salmonella enterica serovar Typhi, while nontyphoidal Salmonella serovars associated with gastroenteritis are noncapsulated. Here we show that optimization of the immune evasive properties conferred by the virulence-associated (Vi) capsular polysaccharide involved an additional alteration to the cell envelope of S. Typhi, namely inactivation of the fepE gene, encoding the regulator of very-long O-antigen chains. Introduction of the capsule-encoding viaB locus into the nontyphoidal S. enterica serovar Typhimurium reduced complement deposition in vitro and intestinal inflammation in a mouse colitis model. However, both phenotypes were markedly enhanced when the viaB locus was introduced into an S. Typhimurium fepE mutant, which lacks very-long O-antigen chains. Collectively, these data suggest that during the evolution of the S. Typhi lineage, loss of very-long O-antigen chains by pseudogene formation was an adaptation to maximize the anti-inflammatory properties of the Vi capsular polysaccharide.<br><br>IMPORTANCE: Genomic comparison illustrates that acquisition of virulence factors by horizontal gene transfer is an important contributor to the evolution of enteric pathogens. Acquisition of complex virulence traits commonly involves horizontal transfer of a large gene cluster, and integration of the gene cluster into the host genome results in the formation of a pathogenicity island. Acquisition of the virulence-associated (Vi) capsular polysaccharide encoded by SPI7 (Salmonella pathogenicity island 7) was accompanied in the human-adapted Salmonella enterica serovar Typhi by inactivation of the fepE gene, encoding the regulator of very-long O-antigen chains. We show that the resulting loss of very-long O-antigen chains was an important mechanism for maximizing immune evasion mediated by the Vi capsular polysaccharide. These data suggest that successful incorporation of a capsular polysaccharide requires changes in the cell envelope of the hosting pathogen.}, }
@article {pmid23859822, year = {2013}, author = {Sand, A and Steel, M}, title = {The standard lateral gene transfer model is statistically consistent for pectinate four-taxon trees.}, journal = {Journal of theoretical biology}, volume = {335}, number = {}, pages = {295-298}, doi = {10.1016/j.jtbi.2013.07.002}, pmid = {23859822}, issn = {1095-8541}, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal/*physiology ; *Models, Genetic ; *Phylogeny ; }, abstract = {Evolutionary events such as incomplete lineage sorting and lateral gene transfers constitute major problems for inferring species trees from gene trees, as they can sometimes lead to gene trees which conflict with the underlying species tree. One particularly simple and efficient way to infer species trees from gene trees under such conditions is to combine three-taxon analyses for several genes using a majority vote approach. For incomplete lineage sorting this method is known to be statistically consistent; however, for lateral gene transfers it was recently shown that a zone of inconsistency exists for a specific four-taxon tree topology, and it was posed as an open question whether inconsistencies could exist for other four-taxon tree topologies? In this letter we analyze all remaining four-taxon topologies and show that no other inconsistencies exist.}, }
@article {pmid23859214, year = {2013}, author = {Chen, K and Huang, L and Xu, C and Liu, X and He, J and Zinder, SH and Li, S and Jiang, J}, title = {Molecular characterization of the enzymes involved in the degradation of a brominated aromatic herbicide.}, journal = {Molecular microbiology}, volume = {89}, number = {6}, pages = {1121-1139}, doi = {10.1111/mmi.12332}, pmid = {23859214}, issn = {1365-2958}, mesh = {Aerobiosis ; Biotransformation ; Bromides/metabolism ; Comamonas/*enzymology/genetics/*metabolism ; DNA, Bacterial/chemistry/genetics ; Enzymes/*genetics/metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal ; Herbicides/*metabolism ; Metabolic Networks and Pathways/*genetics ; Molecular Sequence Data ; Nitriles/*metabolism ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; }, abstract = {Dehalogenation is the key step in the degradation of halogenated aromatics, while reductive dehalogenation is originally thought to rarely occur in aerobes. In this study, an aerobic strain of Comamonas sp. 7D-2 was shown to degrade the brominated aromatic herbicide bromoxynil completely and release two equivalents of bromides under aerobic conditions. The enzymes involved in the degradation of bromoxynil to 4-carboxy-2-hydroxymuconate-6-semialdehyde, including nitrilase, reductive dehalogenase (BhbA), 4-hydroxybenzoate 3-monooxygenase and protocatechuate 4,5-dioxygenase, were molecularly characterized. The novel dehalogenase BhbA was shown to be a complex of a respiration-linked reductive dehalogenase (RdhA) domain and a NAD(P)H-dependent oxidoreductase domain and to have key features of anaerobic respiratory RdhAs, including two predicted binding motifs for [4Fe-4S] clusters and a close association with a hydrophobic membrane protein (BhbB). BhbB was confirmed to anchor BhbA to the membrane. BhbA was partially purified and found to use NAD(P)H as electron donors. Full-length bhbA homologues were found almost exclusively in marine aerobic proteobacteria, suggesting that reductive dehalogenation occurs extensively in aerobes and that bhbA is horizontally transferred from marine microorganisms. The discovery of a functional reductive dehalogenase and ring-cleavage oxygenases in an aerobe opens up possibilities for basic research as well as the potential application for bioremediation.}, }
@article {pmid23857509, year = {2013}, author = {Spence, E and Bryan, SJ and Lisfi, M and Cullum, J and Dunlap, WC and Shick, JM and Mullineaux, CW and Long, PF}, title = {2-epi-5-epi-Valiolone synthase activity is essential for maintaining phycobilisome composition in the cyanobacterium Anabaena variabilis ATCC 29413 when grown in the presence of a carbon source.}, journal = {Photosynthesis research}, volume = {116}, number = {1}, pages = {33-43}, pmid = {23857509}, issn = {1573-5079}, support = {BB/H010009/2//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Absorption ; Anabaena variabilis/drug effects/*enzymology/genetics/*growth &amp; development ; Carbon/*pharmacology ; Chromatography, Liquid ; Inositol/*analogs &amp; derivatives/metabolism ; Lyases/*metabolism ; Mass Spectrometry ; Mutation/genetics ; Phycobilisomes/*metabolism ; Phylogeny ; Real-Time Polymerase Chain Reaction ; Spectrometry, Fluorescence ; Sugar Phosphates/analysis/chemistry ; Transcription, Genetic/drug effects ; }, abstract = {The cyclase 2-epi-5-epi-valiolone synthase (EVS) is reported to be a key enzyme for biosynthesis of the mycosporine-like amino acid shinorine in the cyanobacterium Anabaena variabilis ATCC 29413. Subsequently, we demonstrated that an in-frame complete deletion of the EVS gene had little effect on in vivo production of shinorine. Complete segregation of the EVS gene deletion mutant proved difficult and was achieved only when the mutant was grown in the dark and in a medium supplemented with fructose. The segregated mutant showed a striking colour change from native blue-green to pale yellow-green, corresponding to substantial loss of the photosynthetic pigment phycocyanin, as evinced by combinations of absorbance and emission spectra. Transcriptional analysis of the mutant grown in the presence of fructose under dark or light conditions revealed downregulation of the cpcA gene that encodes the alpha subunit of phycocyanin, whereas the gene encoding nblA, a protease chaperone essential for phycobilisome degradation, was not expressed. We propose that the substrate of EVS (sedoheptulose 7-phosphate) or possibly lack of its EVS-downstream products, represses transcription of cpcA to exert a hitherto unknown control over photosynthesis in this cyanobacterium. The significance of this finding is enhanced by phylogenetic analyses revealing horizontal gene transfer of the EVS gene of cyanobacteria to fungi and dinoflagellates. It is also conceivable that the EVS gene has been transferred from dinoflagellates, as evident in the host genome of symbiotic corals. A role of EVS in regulating sedoheptulose 7-phosphate concentrations in the photophysiology of coral symbiosis is yet to be determined.}, }
@article {pmid23857385, year = {2013}, author = {Kumar, Y and Sood, S and Sharma, A and Mani, KR}, title = {Antibiogram and characterization of resistance markers among Escherichia coli Isolates from urinary tract infections.}, journal = {Journal of infection in developing countries}, volume = {7}, number = {7}, pages = {513-519}, doi = {10.3855/jidc.2706}, pmid = {23857385}, issn = {1972-2680}, mesh = {Adolescent ; Adult ; Aged ; Anti-Bacterial Agents/*pharmacology ; Child ; Child, Preschool ; Conjugation, Genetic ; *Drug Resistance, Bacterial ; Escherichia coli/*drug effects/isolation &amp; purification ; Escherichia coli Infections/*microbiology ; Female ; Gene Transfer, Horizontal ; Genomic Instability ; Humans ; Infant ; Male ; Microbial Sensitivity Tests ; Middle Aged ; Plasmids/analysis ; Urinary Tract Infections/*microbiology ; Young Adult ; }, abstract = {INTRODUCTION: Urinary tract infection is the most frequently diagnosed kidney and urologic disease, and Escherichia coli is by far its most common etiological agent. Uropathogenic E. coli are responsible for approximately 90% of urinary tract infections seen in individuals with ordinary anatomy therefore, it is essential to review the antibiogram of uropathogenic E. coli periodically to help clinicians decide on the appropriate therapy.<br><br>METHODOLOGY: We evaluated E. coli isolated from urinary tract infections at the National Salmonella and Escherichia Centre for antibiogram, plasmid transferability and stability of resistance markers.<br><br>RESULTS: In total, 90.9% of the isolates were found to be sensitive to nitrofurantoin while the highest proportion of the isolates was found to be resistant to nalidixic acid. Minimum inhibitory concentrations of all antimicrobials for different isolates were well within the limits specified by the Clinical and Laboratory Standards Institute.&#xa0; Resistance against tetracycline was not transferred either by conjugation and transformation. Streptomycin resistance was found to be lost in the maximum number of tested isolates showing loss at the 10th, 15th and 20th passages.<br><br>CONCLUSION: Changing trends in antibiotic resistance necessitates the periodic generation of antibiogram data to help health authorities revise treatment strategies for urinary tract infections caused by E. coli.}, }
@article {pmid23856962, year = {2013}, author = {Molloy, S}, title = {Symbiosis: a symbiotic mosaic.}, journal = {Nature reviews. Microbiology}, volume = {11}, number = {8}, pages = {510}, pmid = {23856962}, issn = {1740-1534}, mesh = {Animals ; Bacteria/*genetics ; Betaproteobacteria/*genetics ; *Gene Transfer, Horizontal ; Hemiptera/*genetics/*microbiology ; *Symbiosis ; }, }
@article {pmid23856721, year = {2013}, author = {Hunter, P}, title = {The secret garden's gardeners. Research increasingly appreciates the crucial role of gut viruses for human health and disease.}, journal = {EMBO reports}, volume = {14}, number = {8}, pages = {683-685}, pmid = {23856721}, issn = {1469-3178}, mesh = {Bacteriophages/genetics/*immunology/pathogenicity ; Escherichia coli O157/genetics/virology ; Gastrointestinal Tract/*immunology/microbiology/virology ; Gene Transfer, Horizontal ; Humans ; Metagenome/physiology ; *Microbial Interactions ; }, }
@article {pmid23855904, year = {2013}, author = {Wimalarathna, HM and Richardson, JF and Lawson, AJ and Elson, R and Meldrum, R and Little, CL and Maiden, MC and McCarthy, ND and Sheppard, SK}, title = {Widespread acquisition of antimicrobial resistance among Campylobacter isolates from UK retail poultry and evidence for clonal expansion of resistant lineages.}, journal = {BMC microbiology}, volume = {13}, number = {}, pages = {160}, pmid = {23855904}, issn = {1471-2180}, support = {087622//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Campylobacter/*classification/*drug effects/genetics/isolation &amp; purification ; Campylobacter Infections/epidemiology/microbiology/*veterinary ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; *Drug Resistance, Bacterial ; Genotype ; Humans ; Molecular Epidemiology ; Multilocus Sequence Typing ; Poultry ; Poultry Diseases/*epidemiology/*microbiology ; United Kingdom/epidemiology ; }, abstract = {BACKGROUND: Antimicrobial resistance is increasing among clinical Campylobacter cases and is common among isolates from other sources, specifically retail poultry - a major source of human infection. In this study the antimicrobial susceptibility of isolates from a UK-wide survey of Campylobacter in retail poultry in 2001 and 2004-5 was investigated. The occurrence of phenotypes resistant to tetracycline, quinolones (ciprofloxacin and naladixic acid), erythromycin, chloramphenicol and aminoglycosides was quantified. This was compared with a phylogeny for these isolates based upon Multi Locus Sequence Typing (MLST) to investigate the pattern of antimicrobial resistance acquisition.<br><br>RESULTS: Antimicrobial resistance was present in all lineage clusters, but statistical testing showed a non-random distribution. Erythromycin resistance was associated with Campylobacter coli. For all antimicrobials tested, resistant isolates were distributed among relatively distant lineages indicative of widespread acquisition. There was also evidence of clustering of resistance phenotypes within lineages; indicative of local expansion of resistant strains.<br><br>CONCLUSIONS: These results are consistent with the widespread acquisition of antimicrobial resistance among chicken associated Campylobacter isolates, either through mutation or horizontal gene transfer, and the expansion of these lineages as a proportion of the population. As Campylobacter are not known to multiply outside of the host and long-term carriage in humans is extremely infrequent in industrialized countries, the most likely location for the proliferation of resistant lineages is in farmed chickens.}, }
@article {pmid23852865, year = {2013}, author = {Wilharm, G and Piesker, J and Laue, M and Skiebe, E}, title = {DNA uptake by the nosocomial pathogen Acinetobacter baumannii occurs during movement along wet surfaces.}, journal = {Journal of bacteriology}, volume = {195}, number = {18}, pages = {4146-4153}, pmid = {23852865}, issn = {1098-5530}, mesh = {Acinetobacter Infections/microbiology ; Acinetobacter baumannii/genetics/metabolism/pathogenicity/*physiology ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics/metabolism ; Cross Infection/*microbiology ; DNA, Bacterial/*genetics/metabolism ; DNA-Binding Proteins/*genetics/metabolism ; Drug Resistance, Multiple, Bacterial/genetics ; Fimbriae, Bacterial/drug effects ; Humans ; Moths/microbiology ; Movement ; Surface Properties ; *Transformation, Bacterial ; }, abstract = {The emergence of Acinetobacter baumannii as an increasingly multidrug-resistant nosocomial pathogen largely relies on acquisition of resistance genes via horizontal gene transfer. Here, we demonstrate that many clinical isolates of A. baumannii take up DNA while they move along wet surfaces. We show that both motility and DNA uptake are abolished after inactivation of pilT, which putatively encodes the type 4 pilus (T4P) retraction ATPase, and comEC, which putatively encodes the DNA uptake channel, respectively. Inactivation of pilT correlates with an increase in the number and length of pili with an average diameter of 7.2 nm. In the Galleria mellonella infection model, the comEC mutant is significantly attenuated, whereas the pilT mutant is not, dissecting biologically distinct roles of T4P and the DNA uptake channel. Collectively, these findings promote our understanding of the mechanisms of DNA uptake and resistance development in A. baumannii, which may also apply to other important pathogens.}, }
@article {pmid23852286, year = {2013}, author = {Kumar, CS and Qureshi, SF and Ali, A and Satyanarayana, ML and Rangaraju, A and Venkateshwari, A and Nallari, P}, title = {Hidden magicians of genome evolution.}, journal = {The Indian journal of medical research}, volume = {137}, number = {6}, pages = {1052-1060}, pmid = {23852286}, issn = {0975-9174}, mesh = {Animals ; Cell Cycle ; DNA/genetics ; DNA Transposable Elements/*genetics ; Enhancer Elements, Genetic ; *Evolution, Molecular ; Gene Silencing ; Gene Transfer, Horizontal ; *Genome ; *Genome, Human ; Humans ; Models, Genetic ; Promoter Regions, Genetic ; Terminal Repeat Sequences ; Transcription, Genetic ; }, abstract = {Transposable elements (TEs) represent genome's dynamic component, causing mutations and genetic variations. Transposable elements can invade eukaryotic genomes in a short span; these are silenced by homology-dependent gene silencing and some functional parts of silenced elements are utilized to perform novel cellular functions. However, during the past two decades, major interest has been focused on the positive contribution of these elements in the evolution of genomes. The interaction between mobile DNAs and their host genomes are quite diverse, ranging from modifications of gene structure to alterations in general genome architecture and can be regarded as hidden magicians in shaping evolution of genomes. Some of the prominent examples that impressively demonstrate the beneficial impact of TEs on host biology over evolutionary time include their role in structure and functions of eukaryotic genomes.}, }
@article {pmid23850282, year = {2013}, author = {Nakabachi, A and Ueoka, R and Oshima, K and Teta, R and Mangoni, A and Gurgui, M and Oldham, NJ and van Echten-Deckert, G and Okamura, K and Yamamoto, K and Inoue, H and Ohkuma, M and Hongoh, Y and Miyagishima, SY and Hattori, M and Piel, J and Fukatsu, T}, title = {Defensive bacteriome symbiont with a drastically reduced genome.}, journal = {Current biology : CB}, volume = {23}, number = {15}, pages = {1478-1484}, doi = {10.1016/j.cub.2013.06.027}, pmid = {23850282}, issn = {1879-0445}, mesh = {Animals ; Bacterial Toxins/chemistry/genetics/metabolism/toxicity ; Betaproteobacteria/*genetics ; Biological Evolution ; Cell Line/drug effects ; Citrus ; Gammaproteobacteria/*genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Hemiptera/*microbiology ; Molecular Sequence Data ; Polyketides/metabolism ; RNA, Ribosomal, 16S ; Rats ; Symbiosis/*genetics ; Toxicity Tests ; }, abstract = {Diverse insect species harbor symbiotic bacteria, which play important roles such as provisioning nutrients and providing defense against natural enemies [1-6]. Whereas nutritional symbioses are often indispensable for both partners, defensive symbioses tend to be of a facultative nature [1-12]. The Asian citrus psyllid Diaphorina citri is a notorious agricultural pest that transmits Liberibacter spp. (Alphaproteobacteria), causing the devastating citrus greening disease or Huanglongbing [13, 14]. In a symbiotic organ called the bacteriome, D. citri harbors two distinct intracellular symbionts: a putative nutrition provider, Carsonella_DC (Gammaproteobacteria), and an unnamed betaproteobacterium with unknown function [15], for which we propose the name "Candidatus Profftella armatura." Here we report that Profftella is a defensive symbiont presumably of an obligate nature with an extremely streamlined genome. The genomes of Profftella and Carsonella_DC were drastically reduced to 464,857 bp and 174,014 bp, respectively, suggesting their ancient and mutually indispensible association with the host. Strikingly, 15% of the small Profftella genome encoded horizontally acquired genes for synthesizing a novel polyketide toxin. The toxin was extracted, pharmacologically and structurally characterized, and designated diaphorin. The presence of Profftella and its diaphorin-biosynthetic genes was perfectly conserved in the world's D. citri populations.}, }
@article {pmid23849122, year = {2013}, author = {Gardiner, DM and Kazan, K and Manners, JM}, title = {Cross-kingdom gene transfer facilitates the evolution of virulence in fungal pathogens.}, journal = {Plant science : an international journal of experimental plant biology}, volume = {210}, number = {}, pages = {151-158}, doi = {10.1016/j.plantsci.2013.06.002}, pmid = {23849122}, issn = {1873-2259}, mesh = {Biological Evolution ; Fungal Proteins/*genetics ; Fungi/*genetics/pathogenicity ; *Gene Transfer, Horizontal ; Plant Diseases/*microbiology ; Plants/*microbiology ; Virulence/genetics ; }, abstract = {The constant interaction between plants and their pathogens has resulted in the evolution of a diverse array of microbial infection strategies. It is increasingly evident that horizontal acquisition of new virulence functions in fungi is one of the evolutionary processes that maintain pathogens' competitive edge over host plants. Genome analyses of fungi are pointing towards this phenomenon being particularly prevalent in the subphylum Pezizomycota. While the extent of cross-kingdom gene transfer can be determined with existing genomic tools and databases, so far very few horizontally transmitted genes have been functionally characterised, and an understanding of their physiological roles in virulence has been determined for even fewer genes. Understanding the evolutionary selection pressures that drive the retention of acquired genes in particular fungal lineages is important, as it will undoubtedly reveal new insights into both fungal virulence mechanisms and corresponding plant defence processes in the future.}, }
@article {pmid23847609, year = {2013}, author = {Ilina, EN and Malakhova, MV and Bodoev, IN and Oparina, NY and Filimonova, AV and Govorun, VM}, title = {Mutation in ribosomal protein S5 leads to spectinomycin resistance in Neisseria gonorrhoeae.}, journal = {Frontiers in microbiology}, volume = {4}, number = {}, pages = {186}, pmid = {23847609}, issn = {1664-302X}, abstract = {Spectinomycin remains a useful reserve option for therapy of gonorrhea. The emergence of multidrug-resistant Neisseria gonorrhoeae strains with decreased susceptibility to cefixime and to ceftriaxone makes it the only medicine still effective for treatment of gonorrhea infection in analogous cases. However, adoption of spectinomycin as a routinely used drug of choice was soon followed by reports of spectinomycin resistance. The main molecular mechanism of spectinomycin resistance in N. gonorrhoeae was C1192T substitution in 16S rRNA genes. Here we reported a Thr-24→Pro mutation in ribosomal protein S5 (RPS5) found in spectinomycin resistant clinical N. gonorrhoeae strain, which carried no changes in 16S rRNA. In a series of experiments, the transfer of rpsE gene allele encoding the mutant RPS5 to the recipient N. gonorrhoeae strains was analyzed. The relatively high rate of transformation [ca. 10(-5) colony-forming units (CFUs)] indicates the possibility of spread of spectinonycin resistance within gonococcal population due to the horizontal gene transfer (HGT).}, }
@article {pmid23846774, year = {2013}, author = {Wang, C and Gu, X and Zhang, S and Wang, P and Guo, C and Gu, J and Hou, J}, title = {Characterization of antibiotic-resistance genes in antibiotic resistance Escherichia coli isolates from a lake.}, journal = {Archives of environmental contamination and toxicology}, volume = {65}, number = {4}, pages = {635-641}, doi = {10.1007/s00244-013-9932-2}, pmid = {23846774}, issn = {1432-0703}, mesh = {Drug Resistance, Bacterial/*genetics ; Environmental Monitoring ; Escherichia coli/classification/*genetics/isolation &amp; purification ; Genes, Bacterial ; Lakes/*microbiology ; Phylogeny ; Water Pollution ; }, abstract = {The spread of antibiotic-resistance bacteria and antibiotic-resistance genes (ARGs) has been of concern worldwide. In this study, 114 Escherichia coli isolates were isolated from surface water samples of a lake to identify their susceptibility to antibiotics, including tetracycline (TC), gentamicin (GN), ampicillin (AMP), streptomycin (ST), oxytetracycline (OC), levofloxacin (LEV), nalidixic acid (NA), and sulfamethoxazole/trimethoprim (SFT). Isolates showing resistance to TC, GN, AMP, ST, OC, LEV, NA, and SFT occurred in 50, 76, 68, 71, 55, 32, 82, and 85 % of the total isolates, respectively. Thirty-seven different resistance patterns were identified, and the most abundant resistance profile (28 of 104) was TC/GN/AMP/ST/OC/LEV/NA/SFT. The occurrence of 29 ARGs were detected in their corresponding resistance clones, and 88 % of TC-resistance, 94 % of SFT-resistance, 90 % of AMP-resistance, 78 % of ST-resistance, and 72 % of quinolone-resistance clones can be described by their corresponding ARGs. It should be noted that most of these antibiotic-resistance clones harbored at least two corresponding ARGs, indicating that high frequencies of combined ARGs occurred in these isolates. In addition, 9 new types of DNA sequence of qnr(B) gene were obtained and were clustered into the same group as showed by phylogenetic trees analysis. These results suggest that the development of antibiotic resistance can be ascribed to the high frequency in the recombination of ARGs through horizontal gene transfer.}, }
@article {pmid23845503, year = {2013}, author = {Kiddee, A and Henghiranyawong, K and Yimsabai, J and Tiloklurs, M and Niumsup, PR}, title = {Nosocomial spread of class 1 integron-carrying extensively drug-resistant Pseudomonas aeruginosa isolates in a Thai hospital.}, journal = {International journal of antimicrobial agents}, volume = {42}, number = {4}, pages = {301-306}, doi = {10.1016/j.ijantimicag.2013.05.009}, pmid = {23845503}, issn = {1872-7913}, mesh = {Anti-Bacterial Agents/pharmacology ; Cross Infection/*epidemiology/microbiology ; DNA Fingerprinting ; DNA, Bacterial/genetics ; *Drug Resistance, Multiple, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Gene Transfer, Horizontal ; Genes, Bacterial ; Hospitals ; Humans ; *Integrons ; Microbial Sensitivity Tests ; Molecular Epidemiology ; Pseudomonas Infections/*epidemiology/microbiology ; Pseudomonas aeruginosa/*drug effects/*genetics/isolation &amp; purification ; Sequence Analysis, DNA ; Thailand/epidemiology ; }, abstract = {Fifty non-duplicate multiresistant isolates of Pseudomonas aeruginosa from a regional hospital in Northern Thailand were investigated for their antimicrobial susceptibility, presence of class 1 integrons and arrangement of gene cassettes as well as their genetic relationships. All but one isolate were classified as extensively drug-resistant P. aeruginosa (XDR-PA). Forty-one isolates (82%) were found to carry class 1 integrons. Amplification of the variable regions of class 1 integrons revealed seven diverse bands ranging in size from 0.7 kb to 7.0 kb. Sequence analysis of class 1 integron variable regions revealed the presence of several gene cassettes associated with resistance to aminoglycosides (aac, aad and aph), including the aac(3)-Ic cassette reported for the first time in Thailand. Gene cassettes encoding resistance to chloramphenicol (cmlA), β-lactams (bla(PSE), bla(OXA) and bla(VEB)) and rifampicin (arr) were found. The putative small multidrug resistance protein (smr) and an open-reading frame with unknown function (orfD) were also detected. The aadA6-orfD cassette array was the most common integron found in this study. Integron-positive isolates had higher frequencies of antimicrobial resistance than isolates lacking integrons. Pulsed-field gel electrophoresis (PFGE) demonstrated the occurrence of horizontal gene transfer. Interestingly, a large number of XDR-PA isolates carrying identical integrons clearly exhibited the same PFGE pattern, indicating nosocomial spread of these isolates. The presence of XDR-PA carrying class 1 integrons is implicated in the possible spread of drug-resistant organisms, therefore screening for integron-positive P. aeruginosa might be necessary for protection against nosocomial infection.}, }
@article {pmid23844895, year = {2013}, author = {Goss, EM and Potnis, N and Jones, JB}, title = {Grudgingly sharing their secrets: new insight into the evolution of plant pathogenic bacteria.}, journal = {The New phytologist}, volume = {199}, number = {3}, pages = {630-632}, doi = {10.1111/nph.12397}, pmid = {23844895}, issn = {1469-8137}, mesh = {*Agriculture ; *Biological Evolution ; Crops, Agricultural/*microbiology ; Disease Reservoirs/*microbiology ; Humans ; Pseudomonas syringae/*physiology ; }, }
@article {pmid23844849, year = {2013}, author = {Xia, R and Ren, Y and Xu, H}, title = {Identification of plasmid-mediated quinolone resistance qnr genes in multidrug-resistant Gram-negative bacteria from hospital wastewaters and receiving waters in the Jinan area, China.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {19}, number = {6}, pages = {446-456}, doi = {10.1089/mdr.2012.0210}, pmid = {23844849}, issn = {1931-8448}, mesh = {China ; Conjugation, Genetic ; Drug Resistance, Multiple, Bacterial/*genetics ; Enterobacteriaceae/*genetics/isolation &amp; purification ; Escherichia coli Proteins/*genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Hospitals, Urban ; Humans ; Integrons ; *Plasmids ; Wastewater/*microbiology ; beta-Lactamases/genetics ; }, abstract = {We investigated the prevalence of plasmid-mediated quinolone resistance (PMQR) qnr genes by the polymerase chain reaction (PCR) in antibiotic-resistant bacteria isolates collected from aquatic environments in Jinan during 2 years (2008.3-2009.11). Genes were identified to variant level by PCR restriction fragment length polymorphism analysis or sequencing. qnrA1, qnrB2, qnrB4, qnrB6, qnrB9, qnrS1, and the new qnrB variant qnrB26 were detected in 31 strains from six genera (Klebsiella spp., Escherichia coli, Enterobacter spp., Proteus spp., Shigella spp., and Citrobacter spp.), four of which contained double qnr genes. Other PMQR genes, aac(6')-Ib-cr and qepA, were found in 12 (38.7%) and 5 (16.1%) of 31 isolates, respectively; while qepA was found in Shigella spp. for the first time. Eight types of β-lactamase genes and eight other types of resistance genes were also present in the 31 qnr-positive isolates. The detection rate for five β-lactamase genes (blaTEM, blaCTX, ampR, blaDHA, and blaSHV) was >45%. Class 1 integrons and complex class 1 integrons were prevalent in these strains, which contained 15 different gene cassette arrays and 5 different insertion sequence common region 1 (ISCR1)-mediated downstream structures. qnrA1, qnrB2, and qnrB6 were present in three ISCR1-mediated downstream structures: qnrA1-ampR, sapA-like-qnrB2, and sdr-qnrB6. We also analyzed the horizontal transferability of PMQR genes and other resistance determinants. The qnr genes and some integrons and resistance genes from 18 (58.1%) of the 31 qnr-positive strains could be transferred to E. coli J53 Azi(R) or E. coli DH5α recipient strains using conjugation or transformation methods. The results showed that a high number of qnr genes were associated with other resistance genes in aquatic environments in Jinan. This suggests that we should avoid over-using antibiotics and monitor aquatic environments to control the spread of antibiotic resistance genes.}, }
@article {pmid23844479, year = {2012}, author = {Luo, P and Jiang, H and Wang, Y and Su, T and Hu, C and Ren, C and Jiang, X}, title = {Prevalence of mobile genetic elements and transposase genes in Vibrio alginolyticus from the southern coastal region of China and their role in horizontal gene transfer.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {15}, number = {4}, pages = {201-210}, doi = {10.2436/20.1501.01.172}, pmid = {23844479}, issn = {1139-6709}, mesh = {China ; *DNA Transposable Elements ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Phylogeny ; Prevalence ; Transposases/*genetics ; Vibrio alginolyticus/*enzymology/*genetics ; }, abstract = {Vibrio alginolyticus has high genetic diversity, but little is known about the means by which it has been acquired. In this study, the distributions of mobile genetic elements (MGEs), including integrating conjugative elements (ICEs), superintegron-like cassettes (SICs), insertion sequences (ISs), and two types of transposase genes (valT1 and valT2), in 192 strains of V. alginolyticus were investigated. ICE, SIC, and IS elements, valT1, and valT2 were detected in 8.9%, 13.0%, 4.7%, 9.4%, and 2.6% of the strains, respectively. Blast searches and phylogenetic analysis of the acquired sequences of the ICE, SIC, IS elements and transposase genes showed that the corresponding homologues were bacterial and derived from extensive sources. The high prevalences of these MGEs in V. alginolyticus implied the extensive and frequent exchange of genes with environmental bacteria and that these elements strongly contribute to the genetic and phenotypic diversity of the bacterium. To our knowledge, this is the first report of V. alginolyticus harboring ICE and SIC elements.}, }
@article {pmid23843190, year = {2013}, author = {Martín-Durán, JM and de Mendoza, A and Sebé-Pedrós, A and Ruiz-Trillo, I and Hejnol, A}, title = {A broad genomic survey reveals multiple origins and frequent losses in the evolution of respiratory hemerythrins and hemocyanins.}, journal = {Genome biology and evolution}, volume = {5}, number = {7}, pages = {1435-1442}, pmid = {23843190}, issn = {1759-6653}, support = {206883/ERC_/European Research Council/International ; }, mesh = {Animals ; Eukaryota ; Evolution, Molecular ; Genome ; Hemerythrin/chemistry/*genetics/physiology ; Hemocyanins/chemistry/*genetics/physiology ; Phylogeny ; Protein Structure, Tertiary ; Transcriptome ; }, abstract = {Hemerythrins and hemocyanins are respiratory proteins present in some of the most ecologically diverse animal lineages; however, the precise evolutionary history of their enzymatic domains (hemerythrin, hemocyanin M, and tyrosinase) is still not well understood. We survey a wide dataset of prokaryote and eukaryote genomes and RNAseq data to reconstruct the phylogenetic origins of these proteins. We identify new species with hemerythrin, hemocyanin M, and tyrosinase domains in their genomes, particularly within animals, and demonstrate that the current distribution of respiratory proteins is due to several events of lateral gene transfer and/or massive gene loss. We conclude that the last common metazoan ancestor had at least two hemerythrin domains, one hemocyanin M domain, and six tyrosinase domains. The patchy distribution of these proteins among animal lineages can be partially explained by physiological adaptations, making these genes good targets for investigations into the interplay between genomic evolution and physiological constraints.}, }
@article {pmid23841635, year = {2013}, author = {Elliott, KT and Cuff, LE and Neidle, EL}, title = {Copy number change: evolving views on gene amplification.}, journal = {Future microbiology}, volume = {8}, number = {7}, pages = {887-899}, doi = {10.2217/fmb.13.53}, pmid = {23841635}, issn = {1746-0921}, mesh = {Animals ; Bacteria/enzymology/*genetics/metabolism ; Bacterial Infections/*microbiology ; Bacterial Proteins/genetics/metabolism ; Evolution, Molecular ; *Gene Amplification ; *Gene Dosage ; Gene Transfer, Horizontal ; Humans ; }, abstract = {The rapid pace of genomic sequence analysis is increasing the awareness of intrinsically dynamic genetic landscapes. Gene duplication and amplification (GDA) contribute to adaptation and evolution by allowing DNA regions to expand and contract in an accordion-like fashion. This process affects diverse aspects of bacterial infection, including antibiotic resistance and host-pathogen interactions. In this review, microbial GDA is discussed, primarily using recent bacterial examples that demonstrate medical and evolutionary consequences. Interplay between GDA and horizontal gene transfer further impact evolutionary trajectories. Complementing the discovery of gene duplication in clinical and environmental settings, experimental evolution provides a powerful method to document genetic change over time. New methods for GDA detection highlight both its importance and its potential application for genetic engineering, synthetic biology and biotechnology.}, }
@article {pmid23841456, year = {2013}, author = {Halary, S and McInerney, JO and Lopez, P and Bapteste, E}, title = {EGN: a wizard for construction of gene and genome similarity networks.}, journal = {BMC evolutionary biology}, volume = {13}, number = {}, pages = {146}, pmid = {23841456}, issn = {1471-2148}, mesh = {Borrelia/*genetics ; Evolution, Molecular ; *Gene Regulatory Networks ; Gene Transfer, Horizontal ; Genetic Variation ; *Genome, Bacterial ; Plasmids/genetics ; *Software ; }, abstract = {BACKGROUND: Increasingly, similarity networks are being used for evolutionary analyses of molecular datasets. These networks are very useful, in particular for the analysis of gene sharing, lateral gene transfer and for the detection of distant homologs. Currently, such analyses require some computer programming skills due to the limited availability of user-friendly freely distributed software. Consequently, although appealing, the construction and analyses of these networks remain less familiar to biologists than do phylogenetic approaches.<br><br>RESULTS: In order to ease the use of similarity networks in the community of evolutionary biologists, we introduce a software program, EGN, that runs under Linux or MacOSX. EGN automates the reconstruction of gene and genome networks from nucleic and proteic sequences. EGN also implements statistics describing genetic diversity in these samples, for various user-defined thresholds of similarities. In the interest of studying the complexity of evolutionary processes affecting microbial evolution, we applied EGN to a dataset of 571,044 proteic sequences from the three domains of life and from mobile elements. We observed that, in Borrelia, plasmids play a different role than in most other eubacteria. Rather than being genetic couriers involved in lateral gene transfer, Borrelia's plasmids and their genes act as private genetic goods, that contribute to the creation of genetic diversity within their parasitic hosts.<br><br>CONCLUSION: EGN can be used for constructing, analyzing, and mining molecular datasets in evolutionary studies. The program can help increase our knowledge of the processes through which genes from distinct sources and/or from multiple genomes co-evolve in lineages of cellular organisms.}, }
@article {pmid23840704, year = {2013}, author = {Geng, L and Gao, Y and Chen, X and Hou, S and Zhan, CG and Radic, Z and Parks, RJ and Russell, SJ and Pham, L and Brimijoin, S}, title = {Gene transfer of mutant mouse cholinesterase provides high lifetime expression and reduced cocaine responses with no evident toxicity.}, journal = {PloS one}, volume = {8}, number = {6}, pages = {e67446}, pmid = {23840704}, issn = {1932-6203}, support = {R01 DA023979 S1/DA/NIDA NIH HHS/United States ; DP1 DA031340/DA/NIDA NIH HHS/United States ; R01 DA032910/DA/NIDA NIH HHS/United States ; R01 DA13930/DA/NIDA NIH HHS/United States ; R01 GM018360/GM/NIGMS NIH HHS/United States ; R01 DA023979/DA/NIDA NIH HHS/United States ; R01 DA013930/DA/NIDA NIH HHS/United States ; DP1DA031340/DA/NIDA NIH HHS/United States ; NIGMS RO1-GM18360//PHS HHS/United States ; }, mesh = {Adenoviridae ; Animals ; Apolipoproteins E ; Butyrylcholinesterase/genetics ; Cholinesterases/*genetics ; Cocaine/*adverse effects ; Cocaine-Related Disorders/*therapy ; Gene Expression/*genetics ; Gene Transfer, Horizontal/*genetics ; Genetic Vectors/genetics ; HEK293 Cells ; Humans ; Hydrolases/blood ; Kinetics ; Male ; Mice ; Mice, Inbred BALB C ; Mutation/*genetics ; Promoter Regions, Genetic/genetics ; Substrate Specificity/genetics ; }, abstract = {Gene transfer of a human cocaine hydrolase (hCocH) derived from butyrylcholinesterase (BChE) by 5 mutations (A199S/F227A/S287G/A328W/Y332G) has shown promise in animal studies for treatment of cocaine addiction. To predict the physiological fate and immunogenicity of this enzyme in humans, a comparable enzyme was created and tested in a conspecific host. Thus, similar mutations (A199S/S227A/S287G/A328W/Y332G) were introduced into mouse BChE to obtain a mouse CocH (mCocH). The cDNA was incorporated into viral vectors based on: a) serotype-5 helper-dependent adenovirus (hdAD) with ApoE promoter, and b) serotype-8 adeno-associated virus with CMV promoter (AAV-CMV) or multiple promoter and enhancer elements (AAV-VIP). Experiments on substrate kinetics of purified mCocH expressed in HEK293T cells showed 30-fold higher activity (U/mg) with (3)H-cocaine and 25% lower activity with butyrylthiocholine, compared with wild type BChE. In mice given modest doses of AAV-CMV-mCocH vector (0.7 or 3 × 10(11) particles) plasma hydrolase activity rose 10-fold above control for over one year with no observed immune response. Under the same conditions, transduction of the human counterpart continued less than 2 months and antibodies to hCocH were readily detected. The advanced AAV-VIP-mCocH vector generated a dose-dependent rise in plasma cocaine hydrolase activity from 20-fold (10(10) particles) to 20,000 fold (10(13) particles), while the hdAD vector (1.7 × 10(12) particles) yielded a 300,000-fold increase. Neither vector caused adverse reactions such as motor weakness, elevated liver enzymes, or disturbance in spontaneous activity. Furthermore, treatment with high dose hdAD-ApoE-mCocH vector (1.7 × 10(12) particles) prevented locomotor abnormalities, other behavioral signs, and release of hepatic alanine amino transferase after a cocaine dose fatal to most control mice (120 mg/kg). This outcome suggests that viral gene transfer can yield clinically effective cocaine hydrolase expression for lengthy periods without immune reactions or cholinergic dysfunction, while blocking toxicity from drug overdose.}, }
@article {pmid23840181, year = {2013}, author = {Riley, DR and Sieber, KB and Robinson, KM and White, JR and Ganesan, A and Nourbakhsh, S and Dunning Hotopp, JC}, title = {Bacteria-human somatic cell lateral gene transfer is enriched in cancer samples.}, journal = {PLoS computational biology}, volume = {9}, number = {6}, pages = {e1003107}, pmid = {23840181}, issn = {1553-7358}, support = {DP2 OD007372/OD/NIH HHS/United States ; 1-DP2-OD007372/OD/NIH HHS/United States ; }, mesh = {Bacteria/genetics/*isolation &amp; purification ; Base Sequence ; DNA, Bacterial/genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Human ; Humans ; Molecular Sequence Data ; Neoplasms/*genetics/metabolism ; Sequence Homology, Nucleic Acid ; }, abstract = {There are 10× more bacterial cells in our bodies from the microbiome than human cells. Viral DNA is known to integrate in the human genome, but the integration of bacterial DNA has not been described. Using publicly available sequence data from the human genome project, the 1000 Genomes Project, and The Cancer Genome Atlas (TCGA), we examined bacterial DNA integration into the human somatic genome. Here we present evidence that bacterial DNA integrates into the human somatic genome through an RNA intermediate, and that such integrations are detected more frequently in (a) tumors than normal samples, (b) RNA than DNA samples, and (c) the mitochondrial genome than the nuclear genome. Hundreds of thousands of paired reads support random integration of Acinetobacter-like DNA in the human mitochondrial genome in acute myeloid leukemia samples. Numerous read pairs across multiple stomach adenocarcinoma samples support specific integration of Pseudomonas-like DNA in the 5'-UTR and 3'-UTR of four proto-oncogenes that are up-regulated in their transcription, consistent with conversion to an oncogene. These data support our hypothesis that bacterial integrations occur in the human somatic genome and may play a role in carcinogenesis. We anticipate that the application of our approach to additional cancer genome projects will lead to the more frequent detection of bacterial DNA integrations in tumors that are in close proximity to the human microbiome.}, }
@article {pmid23838256, year = {2013}, author = {Ashbolt, NJ and Amézquita, A and Backhaus, T and Borriello, P and Brandt, KK and Collignon, P and Coors, A and Finley, R and Gaze, WH and Heberer, T and Lawrence, JR and Larsson, DG and McEwen, SA and Ryan, JJ and Schönfeld, J and Silley, P and Snape, JR and Van den Eede, C and Topp, E}, title = {Human Health Risk Assessment (HHRA) for environmental development and transfer of antibiotic resistance.}, journal = {Environmental health perspectives}, volume = {121}, number = {9}, pages = {993-1001}, pmid = {23838256}, issn = {1552-9924}, mesh = {Dose-Response Relationship, Drug ; *Drug Resistance, Microbial ; Education ; *Environment ; *Health Status Indicators ; Humans ; Models, Theoretical ; Risk Assessment/*methods ; }, abstract = {BACKGROUND: Only recently has the environment been clearly implicated in the risk of antibiotic resistance to clinical outcome, but to date there have been few documented approaches to formally assess these risks.<br><br>OBJECTIVE: We examined possible approaches and sought to identify research needs to enable human health risk assessments (HHRA) that focus on the role of the environment in the failure of antibiotic treatment caused by antibiotic-resistant pathogens.<br><br>METHODS: The authors participated in a workshop held 4-8 March 2012 in Qu&#xe9;bec, Canada, to define the scope and objectives of an environmental assessment of antibiotic-resistance risks to human health. We focused on key elements of environmental-resistance-development "hot spots," exposure assessment (unrelated to food), and dose response to characterize risks that may improve antibiotic-resistance management options.<br><br>DISCUSSION: Various novel aspects to traditional risk assessments were identified to enable an assessment of environmental antibiotic resistance. These include a) accounting for an added selective pressure on the environmental resistome that, over time, allows for development of antibiotic-resistant bacteria (ARB); b) identifying and describing rates of horizontal gene transfer (HGT) in the relevant environmental "hot spot" compartments; and c) modifying traditional dose-response approaches to address doses of ARB for various health outcomes and pathways.<br><br>CONCLUSIONS: We propose that environmental aspects of antibiotic-resistance development be included in the processes of any HHRA addressing ARB. Because of limited available data, a multicriteria decision analysis approach would be a useful way to undertake an HHRA of environmental antibiotic resistance that informs risk managers.}, }
@article {pmid23833178, year = {2013}, author = {Starikova, I and Al-Haroni, M and Werner, G and Roberts, AP and Sørum, V and Nielsen, KM and Johnsen, PJ}, title = {Fitness costs of various mobile genetic elements in Enterococcus faecium and Enterococcus faecalis.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {68}, number = {12}, pages = {2755-2765}, pmid = {23833178}, issn = {1460-2091}, mesh = {Conjugation, Genetic ; *Energy Metabolism ; Enterococcus faecalis/*genetics/*growth &amp; development ; Enterococcus faecium/*genetics/*growth &amp; development ; Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences ; }, abstract = {OBJECTIVES: To determine the fitness effects of various mobile genetic elements (MGEs) in Enterococcus faecium and Enterococcus faecalis when newly acquired. We also tested the hypothesis that the biological cost of vancomycin resistance plasmids could be mitigated during continuous growth in the laboratory.<br><br>METHODS: Different MGEs, including two conjugative transposons (CTns) of the Tn916 family (18 and 33 kb), a pathogenicity island (PAI) of 200 kb and vancomycin-resistance (vanA) plasmids (80-200 kb) of various origins and classes, were transferred into common ancestral E. faecium and E. faecalis strains by conjugation assays and experimentally evolved (vanA plasmids only). Transconjugants were characterized by PFGE, S1 nuclease assays and Southern blotting hybridization analyses. Single specific primer PCR was performed to determine the target sites for the insertion of the CTns. The fitness costs of various MGEs in E. faecium and E. faecalis were estimated in head-to-head competition experiments, and evolved populations were generated in serial transfer assays.<br><br>RESULTS: The biological cost of a newly acquired PAI and two CTns were both host- and insertion-locus-dependent. Newly acquired vanA plasmids may severely reduce host fitness (25%-27%), but these costs were rapidly mitigated after only 400 generations of continuous growth in the absence of antibiotic selection.<br><br>CONCLUSIONS: Newly acquired MGEs may impose an immediate biological cost in E. faecium. However, as demonstrated for vanA plasmids, the initial costs of MGE carriage may be mitigated during growth and beneficial plasmid-host association can rapidly emerge.}, }
@article {pmid23831767, year = {2013}, author = {Ramírez, DG and Nicola, F and Zarate, S and Relloso, S and Smayevsky, J and Arduino, S}, title = {Emergence of Pseudomonas aeruginosa with KPC-type carbapenemase in a teaching hospital: an 8-year study.}, journal = {Journal of medical microbiology}, volume = {62}, number = {Pt 10}, pages = {1565-1570}, doi = {10.1099/jmm.0.059923-0}, pmid = {23831767}, issn = {1473-5644}, mesh = {Argentina/epidemiology ; Bacterial Proteins/*genetics ; Disease Outbreaks ; Gene Transfer, Horizontal ; Hospitals, Teaching ; Humans ; Klebsiella Infections/epidemiology ; Pseudomonas Infections/*microbiology ; Pseudomonas aeruginosa/drug effects/*enzymology/*isolation &amp; purification ; *beta-Lactam Resistance ; beta-Lactamases/*genetics ; }, abstract = {An outbreak of Klebsiella pneumoniae carbapenamase (KPC)-producing K. pneumoniae occurred at our institution. Multiresistant Pseudomonas aeruginosa could have acquired this transmissible resistance mechanism, going unnoticed because its phenotypic detection in this species is difficult. We compared P. aeruginosa isolates obtained before and after the KPC-producing K. pneumoniae outbreak. No bla(KPC) genes were detected in the isolates obtained before the outbreak, whereas 33/76 (43%) of the isolates obtained after the outbreak harboured the bla(KPC) gene. P. aeruginosa may thus become a reservoir of this transmissible resistance mechanism. It is very important to understand the epidemiology of these multiresistant isolates, in order to achieve early implementation of adequate control measures to contain and reduce their dissemination in the hospital environment.}, }
@article {pmid23826337, year = {2013}, author = {Kurre, R and Kouzel, N and Ramakrishnan, K and Oldewurtel, ER and Maier, B}, title = {Speed switching of gonococcal surface motility correlates with proton motive force.}, journal = {PloS one}, volume = {8}, number = {6}, pages = {e67718}, pmid = {23826337}, issn = {1932-6203}, mesh = {ATP Synthetase Complexes/antagonists &amp; inhibitors/metabolism ; Adenosine Triphosphate/deficiency ; Cell Membrane/metabolism ; Fimbriae, Bacterial/metabolism ; Humans ; Hydrogen-Ion Concentration ; Movement ; Myxococcus xanthus/physiology ; Neisseria gonorrhoeae/*physiology ; Nitrites/metabolism ; Oxygen/metabolism ; *Proton-Motive Force ; }, abstract = {Bacterial type IV pili are essential for adhesion to surfaces, motility, microcolony formation, and horizontal gene transfer in many bacterial species. These polymers are strong molecular motors that can retract at two different speeds. In the human pathogen Neisseria gonorrhoeae speed switching of single pili from 2 µm/s to 1 µm/s can be triggered by oxygen depletion. Here, we address the question how proton motive force (PMF) influences motor speed. Using pHluorin expression in combination with dyes that are sensitive to transmembrane ΔpH gradient or transmembrane potential ΔΨ, we measured both components of the PMF at varying external pH. Depletion of PMF using uncouplers reversibly triggered switching into the low speed mode. Reduction of the PMF by ≈ 35 mV was enough to trigger speed switching. Reducing ATP levels by inhibition of the ATP synthase did not induce speed switching. Furthermore, we showed that the strictly aerobic Myxococcus xanthus failed to move upon depletion of PMF or oxygen, indicating that although the mechanical properties of the motor are conserved, its regulatory inputs have evolved differently. We conclude that depletion of PMF triggers speed switching of gonococcal pili. Although ATP is required for gonococcal pilus retraction, our data indicate that PMF is an independent additional energy source driving the high speed mode.}, }
@article {pmid23825666, year = {2013}, author = {den Bakker, HC and Desjardins, CA and Griggs, AD and Peters, JE and Zeng, Q and Young, SK and Kodira, CD and Yandava, C and Hepburn, TA and Haas, BJ and Birren, BW and Wiedmann, M}, title = {Evolutionary dynamics of the accessory genome of Listeria monocytogenes.}, journal = {PloS one}, volume = {8}, number = {6}, pages = {e67511}, pmid = {23825666}, issn = {1932-6203}, support = {HHSN272200900018C/AI/NIAID NIH HHS/United States ; }, mesh = {Conserved Sequence ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial/*genetics ; Genomics ; Listeria monocytogenes/*genetics/physiology/virology ; O Antigens/genetics ; Phosphotransferases/genetics ; Phylogeny ; Prophages/physiology ; }, abstract = {Listeria monocytogenes, a foodborne bacterial pathogen, is comprised of four phylogenetic lineages that vary with regard to their serotypes and distribution among sources. In order to characterize lineage-specific genomic diversity within L. monocytogenes, we sequenced the genomes of eight strains from several lineages and serotypes, and characterized the accessory genome, which was hypothesized to contribute to phenotypic differences across lineages. The eight L. monocytogenes genomes sequenced range in size from 2.85-3.14 Mb, encode 2,822-3,187 genes, and include the first publicly available sequenced representatives of serotypes 1/2c, 3a and 4c. Mapping of the distribution of accessory genes revealed two distinct regions of the L. monocytogenes chromosome: an accessory-rich region in the first 65° adjacent to the origin of replication and a more stable region in the remaining 295°. This pattern of genome organization is distinct from that of related bacteria Staphylococcus aureus and Bacillus cereus. The accessory genome of all lineages is enriched for cell surface-related genes and phosphotransferase systems, and transcriptional regulators, highlighting the selective pressures faced by contemporary strains from their hosts, other microbes, and their environment. Phylogenetic analysis of O-antigen genes and gene clusters predicts that serotype 4 was ancestral in L. monocytogenes and serotype 1/2 associated gene clusters were putatively introduced through horizontal gene transfer in the ancestral population of L. monocytogenes lineage I and II.}, }
@article {pmid23820394, year = {2013}, author = {Katz, LS and Petkau, A and Beaulaurier, J and Tyler, S and Antonova, ES and Turnsek, MA and Guo, Y and Wang, S and Paxinos, EE and Orata, F and Gladney, LM and Stroika, S and Folster, JP and Rowe, L and Freeman, MM and Knox, N and Frace, M and Boncy, J and Graham, M and Hammer, BK and Boucher, Y and Bashir, A and Hanage, WP and Van Domselaar, G and Tarr, CL}, title = {Evolutionary dynamics of Vibrio cholerae O1 following a single-source introduction to Haiti.}, journal = {mBio}, volume = {4}, number = {4}, pages = {}, pmid = {23820394}, issn = {2150-7511}, support = {T32 AI007610/AI/NIAID NIH HHS/United States ; U54 GM088558/GM/NIGMS NIH HHS/United States ; U54GM088558/GM/NIGMS NIH HHS/United States ; }, mesh = {Cholera/*epidemiology/*microbiology ; DNA, Bacterial/chemistry/genetics ; *Epidemics ; *Evolution, Molecular ; Gene Order ; *Genome, Bacterial ; Haiti/epidemiology ; Humans ; Mutation ; Sequence Analysis, DNA ; Vibrio cholerae O1/classification/*genetics/*isolation &amp; purification ; }, abstract = {UNLABELLED: Prior to the epidemic that emerged in Haiti in October of 2010, cholera had not been documented in this country. After its introduction, a strain of Vibrio cholerae O1 spread rapidly throughout Haiti, where it caused over 600,000 cases of disease and >7,500 deaths in the first two years of the epidemic. We applied whole-genome sequencing to a temporal series of V. cholerae isolates from Haiti to gain insight into the mode and tempo of evolution in this isolated population of V. cholerae O1. Phylogenetic and Bayesian analyses supported the hypothesis that all isolates in the sample set diverged from a common ancestor within a time frame that is consistent with epidemiological observations. A pangenome analysis showed nearly homogeneous genomic content, with no evidence of gene acquisition among Haiti isolates. Nine nearly closed genomes assembled from continuous-long-read data showed evidence of genome rearrangements and supported the observation of no gene acquisition among isolates. Thus, intrinsic mutational processes can account for virtually all of the observed genetic polymorphism, with no demonstrable contribution from horizontal gene transfer (HGT). Consistent with this, the 12 Haiti isolates tested by laboratory HGT assays were severely impaired for transformation, although unlike previously characterized noncompetent V. cholerae isolates, each expressed hapR and possessed a functional quorum-sensing system. Continued monitoring of V. cholerae in Haiti will illuminate the processes influencing the origin and fate of genome variants, which will facilitate interpretation of genetic variation in future epidemics.<br><br>IMPORTANCE: Vibrio cholerae is the cause of substantial morbidity and mortality worldwide, with over three million cases of disease each year. An understanding of the mode and rate of evolutionary change is critical for proper interpretation of genome sequence data and attribution of outbreak sources. The Haiti epidemic provides an unprecedented opportunity to study an isolated, single-source outbreak of Vibrio cholerae O1 over an established time frame. By using multiple approaches to assay genetic variation, we found no evidence that the Haiti strain has acquired any genes by horizontal gene transfer, an observation that led us to discover that it is also poorly transformable. We have found no evidence that environmental strains have played a role in the evolution of the outbreak strain.}, }
@article {pmid23820199, year = {2013}, author = {Park, YK and Paik, YH and Yoon, JW and Fox, LK and Hwang, SY and Park, YH}, title = {Dissimilarity of ccrAB gene sequences between methicillin-resistant Staphylococcus epidermidis and methicillin-resistant Staphylococcus aureus among bovine isolates in Korea.}, journal = {Journal of veterinary science}, volume = {14}, number = {3}, pages = {299-305}, pmid = {23820199}, issn = {1976-555X}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/*genetics/metabolism ; Bacterial Typing Techniques/veterinary ; Cattle ; Cattle Diseases/epidemiology/metabolism ; Chickens ; Dog Diseases/epidemiology/metabolism ; Dogs ; *Drug Resistance, Bacterial ; *Gene Transfer, Horizontal ; Methicillin/*pharmacology ; Methicillin-Resistant Staphylococcus aureus/genetics/isolation &amp; purification ; Milk/microbiology ; Multilocus Sequence Typing/veterinary ; Poultry Diseases/epidemiology/metabolism ; Prevalence ; Republic of Korea/epidemiology ; Staphylococcal Infections/epidemiology/microbiology/*veterinary ; Staphylococcus epidermidis/genetics/isolation &amp; purification ; }, abstract = {The sequences of the ccrAB genes from bovine-, canine- and chicken-originating methicillin-resistant Staphylococcus (S.) epidermidis (MRSE) and bovine methicillin-resistant Staphylococcus (S.) aureus (MRSA) were compared to investigate the frequency of intra-species horizontal transfer of the staphylococcal cassette chromosome mec (SCCmec) complex. Nineteen MRSE strains were isolated from bovine milk, chickens, and dogs, and their genetic characteristics were investigated by multilocus sequence typing and SCCmec typing. Among the animal MRSE strains, the most frequent SCCmec type was type IV, which consisted of the type B mec complex and ccrAB type 2. The ccrA2 and ccrB2 genes were sequenced from the bovine, chicken and canine MRSE strains and compared with those of the bovine MRSA strains. The sequences generally clustered as MRSA and MRSE groups, regardless of the animal source. Additionally, no bovine MRSE sequence was associated with the bovine MRSA groups. Although most of the bovine MRSE and MRSA isolates possessed SCCmec type IV sequences, our results suggest that the intra-species gene transfer of the SCCmec complex between bovine S. aureus and bovine S. epidermidis strains is not a frequent event.}, }
@article {pmid23818872, year = {2013}, author = {Coelho, MA and Gonçalves, C and Sampaio, JP and Gonçalves, P}, title = {Extensive intra-kingdom horizontal gene transfer converging on a fungal fructose transporter gene.}, journal = {PLoS genetics}, volume = {9}, number = {6}, pages = {e1003587}, pmid = {23818872}, issn = {1553-7404}, mesh = {Ascomycota/*genetics ; Databases, Genetic ; *Evolution, Molecular ; Fungal Proteins/*genetics ; Gene Transfer, Horizontal/*genetics ; Genome, Fungal ; Membrane Transport Proteins/*genetics ; Phylogeny ; Sequence Homology, Amino Acid ; }, abstract = {Comparative genomics revealed in the last decade a scenario of rampant horizontal gene transfer (HGT) among prokaryotes, but for fungi a clearly dominant pattern of vertical inheritance still stands, punctuated however by an increasing number of exceptions. In the present work, we studied the phylogenetic distribution and pattern of inheritance of a fungal gene encoding a fructose transporter (FSY1) with unique substrate selectivity. 109 FSY1 homologues were identified in two sub-phyla of the Ascomycota, in a survey that included 241 available fungal genomes. At least 10 independent inter-species instances of horizontal gene transfer (HGT) involving FSY1 were identified, supported by strong phylogenetic evidence and synteny analyses. The acquisition of FSY1 through HGT was sometimes suggestive of xenolog gene displacement, but several cases of pseudoparalogy were also uncovered. Moreover, evidence was found for successive HGT events, possibly including those responsible for transmission of the gene among yeast lineages. These occurrences do not seem to be driven by functional diversification of the Fsy1 proteins because Fsy1 homologues from widely distant lineages, including at least one acquired by HGT, appear to have similar biochemical properties. In summary, retracing the evolutionary path of the FSY1 gene brought to light an unparalleled number of independent HGT events involving a single fungal gene. We propose that the turbulent evolutionary history of the gene may be linked to the unique biochemical properties of the encoded transporter, whose predictable effect on fitness may be highly variable. In general, our results support the most recent views suggesting that inter-species HGT may have contributed much more substantially to shape fungal genomes than heretofore assumed.}, }
@article {pmid23818865, year = {2013}, author = {Davies, MR and Broadbent, SE and Harris, SR and Thomson, NR and van der Woude, MW}, title = {Horizontally acquired glycosyltransferase operons drive salmonellae lipopolysaccharide diversity.}, journal = {PLoS genetics}, volume = {9}, number = {6}, pages = {e1003568}, pmid = {23818865}, issn = {1553-7404}, support = {/WT_/Wellcome Trust/United Kingdom ; 076964/WT_/Wellcome Trust/United Kingdom ; 080086MA/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Antigens, Bacterial/*genetics/metabolism ; Gene Transfer, Horizontal/*genetics ; Genetic Variation ; Genome, Bacterial ; Glycosyltransferases/*genetics ; Gram-Negative Bacteria/genetics ; Host-Pathogen Interactions/genetics/*immunology ; Humans ; Lipopolysaccharides/genetics ; Salmonella enterica/genetics/*pathogenicity ; }, abstract = {The immunodominant lipopolysaccharide is a key antigenic factor for Gram-negative pathogens such as salmonellae where it plays key roles in host adaptation, virulence, immune evasion, and persistence. Variation in the lipopolysaccharide is also the major differentiating factor that is used to classify Salmonella into over 2600 serovars as part of the Kaufmann-White scheme. While lipopolysaccharide diversity is generally associated with sequence variation in the lipopolysaccharide biosynthesis operon, extraneous genetic factors such as those encoded by the glucosyltransferase (gtr) operons provide further structural heterogeneity by adding additional sugars onto the O-antigen component of the lipopolysaccharide. Here we identify and examine the O-antigen modifying glucosyltransferase genes from the genomes of Salmonella enterica and Salmonella bongori serovars. We show that Salmonella generally carries between 1 and 4 gtr operons that we have classified into 10 families on the basis of gtrC sequence with apparent O-antigen modification detected for five of these families. The gtr operons localize to bacteriophage-associated genomic regions and exhibit a dynamic evolutionary history driven by recombination and gene shuffling events leading to new gene combinations. Furthermore, evidence of Dam- and OxyR-dependent phase variation of gtr gene expression was identified within eight gtr families. Thus, as O-antigen modification generates significant intra- and inter-strain phenotypic diversity, gtr-mediated modification is fundamental in assessing Salmonella strain variability. This will inform appropriate vaccine and diagnostic approaches, in addition to contributing to our understanding of host-pathogen interactions.}, }
@article {pmid23818858, year = {2013}, author = {Bushley, KE and Raja, R and Jaiswal, P and Cumbie, JS and Nonogaki, M and Boyd, AE and Owensby, CA and Knaus, BJ and Elser, J and Miller, D and Di, Y and McPhail, KL and Spatafora, JW}, title = {The genome of tolypocladium inflatum: evolution, organization, and expression of the cyclosporin biosynthetic gene cluster.}, journal = {PLoS genetics}, volume = {9}, number = {6}, pages = {e1003496}, pmid = {23818858}, issn = {1553-7404}, support = {R01 GM104977/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Coleoptera/*microbiology ; Cyclosporine/*metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome ; Hypocreales/enzymology/*genetics ; Multienzyme Complexes/*genetics/metabolism ; Multigene Family ; Peptide Synthases/*genetics/metabolism ; Phylogeny ; Sequence Analysis, RNA ; }, abstract = {The ascomycete fungus Tolypocladium inflatum, a pathogen of beetle larvae, is best known as the producer of the immunosuppressant drug cyclosporin. The draft genome of T. inflatum strain NRRL 8044 (ATCC 34921), the isolate from which cyclosporin was first isolated, is presented along with comparative analyses of the biosynthesis of cyclosporin and other secondary metabolites in T. inflatum and related taxa. Phylogenomic analyses reveal previously undetected and complex patterns of homology between the nonribosomal peptide synthetase (NRPS) that encodes for cyclosporin synthetase (simA) and those of other secondary metabolites with activities against insects (e.g., beauvericin, destruxins, etc.), and demonstrate the roles of module duplication and gene fusion in diversification of NRPSs. The secondary metabolite gene cluster responsible for cyclosporin biosynthesis is described. In addition to genes necessary for cyclosporin biosynthesis, it harbors a gene for a cyclophilin, which is a member of a family of immunophilins known to bind cyclosporin. Comparative analyses support a lineage specific origin of the cyclosporin gene cluster rather than horizontal gene transfer from bacteria or other fungi. RNA-Seq transcriptome analyses in a cyclosporin-inducing medium delineate the boundaries of the cyclosporin cluster and reveal high levels of expression of the gene cluster cyclophilin. In medium containing insect hemolymph, weaker but significant upregulation of several genes within the cyclosporin cluster, including the highly expressed cyclophilin gene, was observed. T. inflatum also represents the first reference draft genome of Ophiocordycipitaceae, a third family of insect pathogenic fungi within the fungal order Hypocreales, and supports parallel and qualitatively distinct radiations of insect pathogens. The T. inflatum genome provides additional insight into the evolution and biosynthesis of cyclosporin and lays a foundation for further investigations of the role of secondary metabolite gene clusters and their metabolites in fungal biology.}, }
@article {pmid23818639, year = {2013}, author = {Paz-Yepes, J and Brahamsha, B and Palenik, B}, title = {Role of a microcin-C-like biosynthetic gene cluster in allelopathic interactions in marine Synechococcus.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {29}, pages = {12030-12035}, pmid = {23818639}, issn = {1091-6490}, mesh = {Bacteriocins/*biosynthesis/metabolism ; Biosynthetic Pathways/*genetics ; Cloning, Molecular ; Computational Biology ; DNA Primers/genetics ; Escherichia coli/chemistry ; Molecular Structure ; Multigene Family/genetics ; Pheromones/chemistry/*metabolism ; Phytoplankton/*genetics/*growth &amp; development ; Real-Time Polymerase Chain Reaction ; Reverse Transcriptase Polymerase Chain Reaction ; Species Specificity ; Synechococcus/*genetics/*growth &amp; development ; }, abstract = {Competition between phytoplankton species for nutrients and light has been studied for many years, but allelopathic interactions between them have been more difficult to characterize. We used liquid and plate assays to determine whether these interactions occur between marine unicellular cyanobacteria of the genus Synechococcus. We have found a clear growth impairment of Synechococcus sp. CC9311 and Synechococcus sp. WH8102 when they are cultured in the presence of Synechococcus sp. CC9605. The genome of CC9605 contains a region showing homology to genes of the Escherichia coli Microcin C (McC) biosynthetic pathway. McC is a ribosome-synthesized peptide that inhibits translation in susceptible strains. We show that the CC9605 McC gene cluster is expressed and that three genes (mccD, mccA, and mccB) are further induced by coculture with CC9311. CC9605 was resistant to McC purified from E. coli, whereas strains CC9311 and WH8102 were sensitive. Cloning the CC9605 McC biosynthetic gene cluster into sensitive CC9311 led this strain to become resistant to both purified E. coli McC and Synechococcus sp. CC9605. A CC9605 mutant lacking mccA1, mccA2, and the N-terminal domain of mccB did not inhibit CC9311 growth, whereas the inhibition of WH8102 was reduced. Our results suggest that an McC-like molecule is involved in the allelopathic interactions with CC9605.}, }
@article {pmid23813735, year = {2013}, author = {Wang, X and Tan, J and Bai, Z and Deng, X and Li, Z and Zhou, C and Chen, J}, title = {Detection and characterization of miniature inverted-repeat transposable elements in “Candidatus Liberibacter asiaticus”.}, journal = {Journal of bacteriology}, volume = {195}, number = {17}, pages = {3979-3986}, pmid = {23813735}, issn = {1098-5530}, mesh = {Base Sequence ; China ; *DNA Transposable Elements ; DNA, Bacterial/chemistry/genetics ; Florida ; Gene Transfer, Horizontal ; Genetic Variation ; *Inverted Repeat Sequences ; Molecular Sequence Data ; Open Reading Frames ; Phylogeography ; Prophages/genetics ; Rhizobiaceae/*genetics/isolation &amp; purification ; Sequence Analysis, DNA ; }, abstract = {Miniature inverted-repeat transposable elements (MITEs) are nonautonomous transposons (devoid of the transposase gene tps) that affect gene functions through insertion/deletion events. No transposon has yet been reported to occur in “Candidatus Liberibacter asiaticus,” an alphaproteobacterium associated with citrus Huanglongbing (HLB, yellow shoot disease). In this study, two MITEs, MCLas-A and MCLas-B, in “Ca. Liberibacter asiaticus” were detected, and the genome was characterized using 326 isolates collected in China and Florida. MCLas-A had three variants, ranging from 237 to 325 bp, and was inserted into a TTTAGG site of a prophage region. MCLas-A had a pair of 54-bp terminal inverted repeats (TIRs), which contained three tandem repeats of TGGTAACCAC. Both “filled” (with MITE) and “empty” (without MITE) states were detected, suggesting the MITE mobility. The empty sites of all bacterial isolates had TIR tandem repeat remnants (TRR). Frequencies of TRR types varied according to geographical origins. MCLas-B had four variants, ranging from 238 to 250 bp, and was inserted into a TA site of another “Ca. Liberibacter” prophage. The MITE, MCLas-B, had a pair of 23-bp TIRs containing no tandem repeats. No evidence of MCLas-B mobility was found. An identical open reading frame was found upstream of MCLas-A (229 bp) and MCLas-B (232 bp) and was predicted to be a putative tps, suggesting an in cis tps-MITE configuration. MCLas-A and MCLas-B were predominantly copresent in Florida isolates, whereas MCLas-A alone or MCLas-B alone was found in Chinese isolates.}, }
@article {pmid23812683, year = {2013}, author = {Gravey, F and Galopin, S and Grall, N and Auzou, M and Andremont, A and Leclercq, R and Cattoir, V}, title = {Lincosamide resistance mediated by lnu(C) (L phenotype) in a Streptococcus anginosus clinical isolate.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {68}, number = {11}, pages = {2464-2467}, doi = {10.1093/jac/dkt255}, pmid = {23812683}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/*genetics ; Conjugation, Genetic ; DNA, Bacterial/genetics ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Humans ; Infant, Newborn ; Lincosamides/*pharmacology ; Microbial Sensitivity Tests ; Mothers ; Phenotype ; Polymerase Chain Reaction ; Streptococcal Infections/*microbiology ; Streptococcus anginosus/*drug effects/*genetics/isolation &amp; purification ; }, abstract = {OBJECTIVES: Unique resistance to lincosamides (L phenotype) due to the production of nucleotidyltransferases (Lnu) is uncommon among Gram-positive bacteria. The aim of the study was to characterize the L phenotype in a clinical isolate of the Streptococcus milleri group.<br><br>METHODS: The strain UCN93 was recovered from neonatal specimens and from the mother's vaginal swab. Identification was confirmed by sequencing of the sodA gene. Antimicrobial susceptibility testing was carried out by the disc diffusion method, while MICs were determined using the agar dilution method. Screening for lnu(A), lnu(B), lnu(C) and lnu(D) genes was performed by PCR. Genetic environment and support were determined by thermal asymmetric interlaced PCR and PCR mapping. The transfer of lincomycin resistance was also attempted by conjugation.<br><br>RESULTS: UCN93 was unambiguously identified as Streptococcus anginosus. It was susceptible to all tested antibiotics, except lincomycin (MIC, 8 mg/L) and tetracycline (2 mg/L). The lnu(C) gene was found to be responsible for the L phenotype. It was shown that lnu(C) was associated with a gene coding for a transposase within a structure similar to the transposon MTnSag1, described once in Streptococcus agalactiae. Since MTnSag1 was found to be mobilized by Tn916 and S. anginosus UCN93 harboured a Tn916 transposon, several attempts at transfer were performed but they all failed. The lnu(C)-containing genetic element was inserted into a chromosomal intergenic sequence of S. anginosus.<br><br>CONCLUSIONS: Since lnu(C) has been detected in only one S. agalactiae clinical isolate so far, this is its second description among clinically relevant streptococci.}, }
@article {pmid23811504, year = {2013}, author = {Stockwell, VO and Davis, EW and Carey, A and Shaffer, BT and Mavrodi, DV and Hassan, KA and Hockett, K and Thomashow, LS and Paulsen, IT and Loper, JE}, title = {pA506, a conjugative plasmid of the plant epiphyte Pseudomonas fluorescens A506.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {17}, pages = {5272-5282}, pmid = {23811504}, issn = {1098-5336}, mesh = {Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; Enterobacteriaceae/genetics ; Gene Transfer, Horizontal ; Malus/microbiology ; Molecular Sequence Data ; Open Reading Frames ; Plant Diseases/microbiology ; *Plasmids ; Pseudomonas fluorescens/*genetics ; Pseudomonas syringae/genetics ; Pyrus/microbiology ; Sequence Analysis, DNA ; United States ; }, abstract = {Conjugative plasmids are known to facilitate the acquisition and dispersal of genes contributing to the fitness of Pseudomonas spp. Here, we report the characterization of pA506, the 57-kb conjugative plasmid of Pseudomonas fluorescens A506, a plant epiphyte used in the United States for the biological control of fire blight disease of pear and apple. Twenty-nine of the 67 open reading frames (ORFs) of pA506 have putative functions in conjugation, including a type IV secretion system related to that of MOBP6 family plasmids and a gene cluster for type IV pili. We demonstrate that pA506 is self-transmissible via conjugation between A506 and strains of Pseudomonas spp. or the Enterobacteriaceae. The origin of vegetative replication (oriV) of pA506 is typical of those in pPT23A family plasmids, which are present in many pathovars of Pseudomonas syringae, but pA506 lacks repA, a defining locus for pPT23A plasmids, and has a novel partitioning region. We selected a plasmid-cured derivative of A506 and compared it to the wild type to identify plasmid-encoded phenotypes. pA506 conferred UV resistance, presumably due to the plasmid-borne rulAB genes, but did not influence epiphytic fitness of A506 on pear or apple blossoms in the field. pA506 does not appear to confer resistance to antibiotics or other toxic elements. Based on the conjugative nature of pA506 and the large number of its genes that are shared with plasmids from diverse groups of environmental bacteria, the plasmid is likely to serve as a vehicle for genetic exchange between A506 and its coinhabitants on plant surfaces.}, }
@article {pmid23811095, year = {2013}, author = {Wang, J and Guo, M and Liu, X and Liu, Y and Wang, C and Xing, L and Che, K}, title = {LNETWORK: an efficient and effective method for constructing phylogenetic networks.}, journal = {Bioinformatics (Oxford, England)}, volume = {29}, number = {18}, pages = {2269-2276}, doi = {10.1093/bioinformatics/btt378}, pmid = {23811095}, issn = {1367-4811}, mesh = {Algorithms ; Cluster Analysis ; *Phylogeny ; *Software ; }, abstract = {MOTIVATION: The evolutionary history of species is traditionally represented with a rooted phylogenetic tree. Each tree comprises a set of clusters, i.e. subsets of the species that are descended from a common ancestor. When rooted phylogenetic trees are built from several different datasets (e.g. from different genes), the clusters are often conflicting. These conflicting clusters cannot be expressed as a simple phylogenetic tree; however, they can be expressed in a phylogenetic network. Phylogenetic networks are a generalization of phylogenetic trees that can account for processes such as hybridization, horizontal gene transfer and recombination, which are difficult to represent in standard tree-like models of evolutionary histories. There is currently a large body of research aimed at developing appropriate methods for constructing phylogenetic networks from cluster sets. The Cass algorithm can construct a much simpler network than other available methods, but is extremely slow for large datasets or for datasets that need lots of reticulate nodes. The networks constructed by Cass are also greatly dependent on the order of input data, i.e. it generally derives different phylogenetic networks for the same dataset when different input orders are used.<br><br>RESULTS: In this study, we introduce an improved Cass algorithm, Lnetwork, which can construct a phylogenetic network for a given set of clusters. We show that Lnetwork is significantly faster than Cass and effectively weakens the influence of input data order. Moreover, we show that Lnetwork can construct a much simpler network than most of the other available methods.<br><br>AVAILABILITY: Lnetwork has been built as a Java software package and is freely available at http://nclab.hit.edu.cn/&#x223c;wangjuan/Lnetwork/.<br><br>CONTACT: maozuguo@hit.edu.cn<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid23809012, year = {2013}, author = {Gan, HM and Hudson, AO and Rahman, AY and Chan, KG and Savka, MA}, title = {Comparative genomic analysis of six bacteria belonging to the genus Novosphingobium: insights into marine adaptation, cell-cell signaling and bioremediation.}, journal = {BMC genomics}, volume = {14}, number = {}, pages = {431}, pmid = {23809012}, issn = {1471-2164}, mesh = {Adaptation, Physiological/drug effects/*genetics ; Alphaproteobacteria/classification/*cytology/genetics/*physiology ; Amino Acid Sequence ; Bacterial Proteins/chemistry/genetics ; Biodegradation, Environmental ; Conserved Sequence ; Dioxygenases/genetics ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/genetics ; *Genomics ; Molecular Sequence Data ; *Oceans and Seas ; Phenotype ; Phylogeny ; Quorum Sensing/genetics ; Salts/pharmacology ; Sequence Homology, Nucleic Acid ; Signal Transduction/*genetics ; Species Specificity ; }, abstract = {BACKGROUND: Bacteria belonging to the genus Novosphingobium are known to be metabolically versatile and occupy different ecological niches. In the absence of genomic data and/or analysis, knowledge of the bacteria that belong to this genus is currently limited to biochemical characteristics. In this study, we analyzed the whole genome sequencing data of six bacteria in the Novosphingobium genus and provide evidence to show the presence of genes that are associated with salt tolerance, cell-cell signaling and aromatic compound biodegradation phenotypes. Additionally, we show the taxonomic relationship between the sequenced bacteria based on phylogenomic analysis, average amino acid identity (AAI) and genomic signatures.<br><br>RESULTS: The taxonomic clustering of Novosphingobium strains is generally influenced by their isolation source. AAI and genomic signature provide strong support the classification of Novosphingobium sp. PP1Y as Novosphingobium pentaromaticivorans PP1Y. The identification and subsequent functional annotation of the unique core genome in the marine Novosphingobium bacteria show that ectoine synthesis may be the main contributing factor in salt water adaptation. Genes coding for the synthesis and receptor of the cell-cell signaling molecules, of the N-acyl-homoserine lactones (AHL) class are identified. Notably, a solo luxR homolog was found in strain PP1Y that may have been recently acquired via horizontal gene transfer as evident by the presence of multiple mobile elements upstream of the gene. Additionally, phylogenetic tree analysis and sequence comparison with functionally validated aromatic ring hydroxylating dioxygenases (ARDO) revealed the presence of several ARDOs (oxygenase) in Novosphingobium bacteria with the majority of them belonging to the Groups II and III of the enzyme.<br><br>CONCLUSIONS: The combination of prior knowledge on the distinctive phenotypes of Novosphingobium strains and meta-analysis of their whole genomes enables the identification of several genes that are relevant in industrial applications and bioremediation. The results from such targeted but comprehensive comparative genomics analysis have the potential to contribute to the understanding of adaptation, cell-cell communication and bioremediation properties of bacteria belonging to the genus Novosphingobium.}, }
@article {pmid23808959, year = {2013}, author = {Lafeuille, E and Decré, D and Mahjoub-Messai, F and Bidet, P and Arlet, G and Bingen, E}, title = {OXA-48 carbapenemase-producing Klebsiella pneumoniae isolated from Libyan patients.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {19}, number = {6}, pages = {491-497}, doi = {10.1089/mdr.2012.0219}, pmid = {23808959}, issn = {1931-8448}, mesh = {Anti-Bacterial Agents/therapeutic use ; Bacterial Typing Techniques ; Carbapenems/therapeutic use ; DNA Transposable Elements ; Gene Expression ; Gene Transfer, Horizontal ; Humans ; Klebsiella Infections/drug therapy/*epidemiology/microbiology ; Klebsiella pneumoniae ; Libya/epidemiology ; Microbial Sensitivity Tests ; Penicillins/therapeutic use ; *Plasmids ; beta-Lactam Resistance/*genetics ; beta-Lactamases/*genetics/metabolism ; }, abstract = {Six multidrug-resistant Klebsiella pneumoniae isolates were recovered from injured Libyan combatants. Production of carbapenemase was screened by using commercial combination tablets from Rosco combined with a temocillin disk. Polymerase chain reaction (PCR) and sequencing were used to detect several carbapenemase genes and to characterize their genetic environment. Genetic support was studied by mating-out assays. Plasmid size was identified by the KADO method. PCR and sequencing allowed characterization of plasmid scaffold. Genotyping was performed by pulse-field gel electrophoresis (PFGE) and multilocus sequence typing. PCR was used to check for the presence of nine genes linked to virulence in K. pneumoniae. No carbapenemase was identified by Rosco disks, but all isolates showed high-level temocillin resistance. All of them harbored blaOXA-48 in the transposon Tn1999.2, on a self-conjugative plasmid of about 60 kb, similar to pOXA-48. PFGE revealed three clusters in which isolates were genetically related: The first comprised FM9 and FM10, and the second comprised FM1, FM4, and FM5. FM2 formed a third distinct clone. Sequence types ST101, ST11, and ST147 were identified in keeping with PFGE results. The entB, ycfM, ybtS, and mrkD genes were detected in all isolates, and kfu gene was present in the three ST101 strains. This work confirms the current and successful spread of blaOXA-48 by horizontal dissemination of a single IncL/M plasmid through different genetic backbones with strong epidemic potential. It also highlights the need for rapid and reliable phenotypic detection methods. Attempts to link virulence factors and the production of this carbapenemase deserve further studies.}, }
@article {pmid23805310, year = {2013}, author = {Shinya, R and Morisaka, H and Kikuchi, T and Takeuchi, Y and Ueda, M and Futai, K}, title = {Secretome Analysis of the Pine Wood Nematode Bursaphelenchus xylophilus Reveals the Tangled Roots of Parasitism and Its Potential for Molecular Mimicry.}, journal = {PloS one}, volume = {8}, number = {6}, pages = {e67377}, pmid = {23805310}, issn = {1932-6203}, mesh = {Animals ; *Evolution, Molecular ; *Gene Duplication ; *Gene Transfer, Horizontal ; *Helminth Proteins/genetics/metabolism ; *Molecular Mimicry ; *Nematoda/genetics/metabolism ; Plant Diseases/parasitology ; }, abstract = {Since it was first introduced into Asia from North America in the early 20(th) century, the pine wood nematode Bursaphelenchus xylophilus has caused the devastating forest disease called pine wilt. The emerging pathogen spread to parts of Europe and has since been found as the causal agent of pine wilt disease in Portugal and Spain. In 2011, the entire genome sequence of B. xylophilus was determined, and it allowed us to perform a more detailed analysis of B. xylophilus parasitism. Here, we identified 1,515 proteins secreted by B. xylophilus using a highly sensitive proteomics method combined with the available genomic sequence. The catalogue of secreted proteins contained proteins involved in nutrient uptake, migration, and evasion from host defenses. A comparative functional analysis of the secretome profiles among parasitic nematodes revealed a marked expansion of secreted peptidases and peptidase inhibitors in B. xylophilus via gene duplication and horizontal gene transfer from fungi and bacteria. Furthermore, we showed that B. xylophilus secreted the potential host mimicry proteins that closely resemble the host pine's proteins. These proteins could have been acquired by host-parasite co-evolution and might mimic the host defense systems in susceptible pine trees during infection. This study contributes to an understanding of their unique parasitism and its tangled roots, and provides new perspectives on the evolution of plant parasitism among nematodes.}, }
@article {pmid23803158, year = {2013}, author = {Sun, Y and Bernardy, EE and Hammer, BK and Miyashiro, T}, title = {Competence and natural transformation in vibrios.}, journal = {Molecular microbiology}, volume = {89}, number = {4}, pages = {583-595}, pmid = {23803158}, issn = {1365-2958}, support = {R00 GM097032/GM/NIGMS NIH HHS/United States ; RC1 GM090732/GM/NIGMS NIH HHS/United States ; 4R00GM090732/GM/NIGMS NIH HHS/United States ; }, mesh = {*DNA Transformation Competence ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Interspersed Repetitive Sequences ; Recombination, Genetic ; Transformation, Bacterial ; Vibrionaceae/*genetics ; }, abstract = {Natural transformation is a major mechanism of horizontal gene transfer in bacteria. By incorporating exogenous DNA elements into chromosomes, bacteria are able to acquire new traits that can enhance their fitness in different environments. Within the past decade, numerous studies have revealed that natural transformation is prevalent among members of the Vibrionaceae, including the pathogen Vibrio cholerae. Four environmental factors: (i) nutrient limitation, (ii) availability of extracellular nucleosides, (iii) high cell density and (iv) the presence of chitin, promote genetic competence and natural transformation in Vibrio cholerae by co-ordinating expression of the regulators CRP, CytR, HapR and TfoX respectively. Studies of other Vibrionaceae members highlight the general importance of natural transformation within this bacterial family.}, }
@article {pmid23803001, year = {2013}, author = {Sjöstrand, J and Arvestad, L and Lagergren, J and Sennblad, B}, title = {GenPhyloData: realistic simulation of gene family evolution.}, journal = {BMC bioinformatics}, volume = {14}, number = {}, pages = {209}, pmid = {23803001}, issn = {1471-2105}, mesh = {Biological Clocks/genetics ; Computer Simulation ; Evolution, Molecular ; Gene Duplication/*genetics ; Gene Transfer Techniques ; Humans ; Models, Biological ; Multigene Family/*genetics ; *Phylogeny ; Species Specificity ; }, abstract = {BACKGROUND: PrIME-GenPhyloData is a suite of tools for creating realistic simulated phylogenetic trees, in particular for families of homologous genes. It supports generation of trees based on a birth-death process and--perhaps more interestingly--also supports generation of gene family trees guided by a known (synthetic or biological) species tree while accounting for events such as gene duplication, gene loss, and lateral gene transfer (LGT). The suite also supports a wide range of branch rate models enabling relaxation of the molecular clock.<br><br>RESULT: Simulated data created with PrIME-GenPhyloData can be used for benchmarking phylogenetic approaches, or for characterizing models or model parameters with respect to biological data.<br><br>CONCLUSION: The concept of tree-in-tree evolution can also be used to model, for instance, biogeography or host-parasite co-evolution.}, }
@article {pmid23801028, year = {2013}, author = {Wolf, YI and Koonin, EV}, title = {Genome reduction as the dominant mode of evolution.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {35}, number = {9}, pages = {829-837}, pmid = {23801028}, issn = {1521-1878}, support = {//Intramural NIH HHS/United States ; }, mesh = {Archaea/genetics ; Conserved Sequence/genetics ; Eukaryota/genetics ; *Evolution, Molecular ; *Genome ; Genomics ; Introns ; Likelihood Functions ; *Models, Genetic ; }, abstract = {A common belief is that evolution generally proceeds towards greater complexity at both the organismal and the genomic level, numerous examples of reductive evolution of parasites and symbionts notwithstanding. However, recent evolutionary reconstructions challenge this notion. Two notable examples are the reconstruction of the complex archaeal ancestor and the intron-rich ancestor of eukaryotes. In both cases, evolution in most of the lineages was apparently dominated by extensive loss of genes and introns, respectively. These and many other cases of reductive evolution are consistent with a general model composed of two distinct evolutionary phases: the short, explosive, innovation phase that leads to an abrupt increase in genome complexity, followed by a much longer reductive phase, which encompasses either a neutral ratchet of genetic material loss or adaptive genome streamlining. Quantitatively, the evolution of genomes appears to be dominated by reduction and simplification, punctuated by episodes of complexification.}, }
@article {pmid23800623, year = {2013}, author = {Noda-García, L and Camacho-Zarco, AR and Medina-Ruíz, S and Gaytán, P and Carrillo-Tripp, M and Fülöp, V and Barona-Gómez, F}, title = {Evolution of substrate specificity in a recipient's enzyme following horizontal gene transfer.}, journal = {Molecular biology and evolution}, volume = {30}, number = {9}, pages = {2024-2034}, doi = {10.1093/molbev/mst115}, pmid = {23800623}, issn = {1537-1719}, mesh = {Aldose-Ketose Isomerases/chemistry/*genetics/metabolism ; Amino Acid Sequence ; Bacterial Proteins/chemistry/*genetics/metabolism ; Catalytic Domain ; Corynebacterium/classification/enzymology/*genetics ; Crystallography, X-Ray ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Histidine/biosynthesis/genetics ; Kinetics ; Models, Molecular ; Molecular Sequence Data ; Mycobacterium/classification/enzymology/*genetics ; Operon ; Phylogeny ; Protein Structure, Secondary ; Sequence Alignment ; Substrate Specificity ; Tryptophan/biosynthesis/genetics ; }, abstract = {Despite the prominent role of horizontal gene transfer (HGT) in shaping bacterial metabolism, little is known about the impact of HGT on the evolution of enzyme function. Specifically, what is the influence of a recently acquired gene on the function of an existing gene? For example, certain members of the genus Corynebacterium have horizontally acquired a whole l-tryptophan biosynthetic operon, whereas in certain closely related actinobacteria, for example, Mycobacterium, the trpF gene is missing. In Mycobacterium, the function of the trpF gene is performed by a dual-substrate (βα)8 phosphoribosyl isomerase (priA gene) also involved in l-histidine (hisA gene) biosynthesis. We investigated the effect of a HGT-acquired TrpF enzyme upon PriA's substrate specificity in Corynebacterium through comparative genomics and phylogenetic reconstructions. After comprehensive in vivo and enzyme kinetic analyses of selected PriA homologs, a novel (βα)8 isomerase subfamily with a specialized function in l-histidine biosynthesis, termed subHisA, was confirmed. X-ray crystallography was used to reveal active-site mutations in subHisA important for narrowing of substrate specificity, which when mutated to the naturally occurring amino acid in PriA led to gain of function. Moreover, in silico molecular dynamic analyses demonstrated that the narrowing of substrate specificity of subHisA is concomitant with loss of ancestral protein conformational states. Our results show the importance of HGT in shaping enzyme evolution and metabolism.}, }
@article {pmid23800277, year = {2013}, author = {Mnif, B and Harhour, H and Jdidi, J and Mahjoubi, F and Genel, N and Arlet, G and Hammami, A}, title = {Molecular epidemiology of extended-spectrum beta-lactamase-producing Escherichia coli in Tunisia and characterization of their virulence factors and plasmid addiction systems.}, journal = {BMC microbiology}, volume = {13}, number = {}, pages = {147}, pmid = {23800277}, issn = {1471-2180}, mesh = {Cluster Analysis ; Conjugation, Genetic ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/*classification/*enzymology/genetics/isolation &amp; purification ; Escherichia coli Infections/*epidemiology/microbiology ; Gene Transfer, Horizontal ; Hospitals, University ; Humans ; Molecular Epidemiology ; Molecular Typing ; Plasmids/*analysis/classification ; Tunisia/epidemiology ; Virulence Factors/*genetics ; beta-Lactamases/genetics/*metabolism ; }, abstract = {BACKGROUND: Extended-spectrum β-lactamases (ESBLs), particularly CTX-M- type ESBLs, are among the most important resistance determinants spreading worldwide in Enterobacteriaceae. The aim of this study was to characterize a collection of 163 ESBL-producing Escherichia coli collected in Tunisia, their ESBL-encoding plasmids and plasmid associated addiction systems.<br><br>RESULTS: The collection comprised 163 ESBL producers collected from two university hospitals of Sfax between 1989 and 2009. 118 isolates harbored blaCTX-M gene (101 blaCTX-M-15 gene and 17 blaCTX-M-14 gene). 49 isolates carried blaSHV-12 gene, 9 blaSHV-2a gene and only 3 blaTEM-26 gene. 16 isolates produced both CTX-M and SHV-12. The 101 CTX-M-15-producing isolates were significantly associated to phylogroup B2 and exhibiting a high number of virulence factors. 24 (23.7%) of the group B2 isolates belonged to clonal complex ST131. Pulsed-field gel electrophoresis (PFGE) typing revealed a genetic diversity of the isolates. 144 ESBL determinants were transferable mostly by conjugation. The majority of plasmid carrying blaCTX-M-15 genes (72/88) were assigned to various single replicon or multireplicon IncF types and had significantly a higher frequency of addiction systems, notably the VagCD module.<br><br>CONCLUSION: This study demonstrates that the dissemination of CTX-M-15 producing E. coli in our setting was due to the spread of various IncF-type plasmids harboring multiple addiction systems, into related clones with high frequency of virulence determinants.}, }
@article {pmid23800169, year = {2013}, author = {Nilsen, E and Haldorsen, BC and Sundsfjord, A and Simonsen, GS and Ingebretsen, A and Naseer, U and Samuelsen, O and , }, title = {Large IncHI2-plasmids encode extended-spectrum β-lactamases (ESBLs) in Enterobacter spp. bloodstream isolates, and support ESBL-transfer to Escherichia coli.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {19}, number = {11}, pages = {E516-8}, doi = {10.1111/1469-0691.12274}, pmid = {23800169}, issn = {1469-0691}, mesh = {Bacteremia/epidemiology/*microbiology ; Conjugation, Genetic ; Drug Resistance, Multiple ; Enterobacter/*enzymology/*genetics/isolation &amp; purification ; Enterobacteriaceae Infections/epidemiology/microbiology ; Escherichia coli/*genetics ; *Gene Transfer, Horizontal ; Humans ; Norway/epidemiology ; Plasmids/*analysis ; beta-Lactamases/*genetics ; }, abstract = {We investigated the prevalence of extended-spectrum β-lactamases (ESBLs) in Enterobacter spp. bloodstream isolates from 19 hospital laboratories in Norway during 2011. A total of 62/230 (27%) isolates were resistant to third-generation cephalosporins and four (1.7%) were ESBL-positive; blaCTX -M-15 (n = 3) and blaSHV -12 (n = 1). This is comparable to the prevalence of ESBLs in clinical isolates of Escherichia coli and Klebsiella pneumoniae in Norway during the same period. All ESBL-positive isolates were multidrug resistant (MDR) and harboured plasmid-mediated quinolone resistance. Three isolates supported transfer of large IncHI2-plasmids harbouring ESBL- and MDR-encoding genes to E. coli recipients by in vitro conjugation.}, }
@article {pmid23796800, year = {2013}, author = {Garcia-Gonzalez, A and Vicens, L and Alicea, M and Massey, SE}, title = {The distribution of recombination repair genes is linked to information content in bacteria.}, journal = {Gene}, volume = {528}, number = {2}, pages = {295-303}, doi = {10.1016/j.gene.2013.05.082}, pmid = {23796800}, issn = {1879-0038}, mesh = {Bacteria/*genetics ; Bacterial Proteins/genetics ; Base Composition ; Cluster Analysis ; DNA Repair Enzymes/genetics ; Genome, Bacterial ; Models, Genetic ; Proteome/genetics ; Recombinational DNA Repair/*genetics ; }, abstract = {The concept of a 'proteomic constraint' proposes that the information content of the proteome exerts a selective pressure to reduce mutation rates, implying that larger proteomes produce a greater selective pressure to evolve or maintain DNA repair, resulting in a decrease in mutational load. Here, the distribution of 21 recombination repair genes was characterized across 900 bacterial genomes. Consistent with prediction, the presence of 17 genes correlated with proteome size. Intracellular bacteria were marked by a pervasive absence of recombination repair genes, consistent with their small proteome sizes, but also consistent with alternative explanations that reduced effective population size or lack of recombination may decrease selection pressure. However, when only non-intracellular bacteria were examined, the relationship between proteome size and gene presence was maintained. In addition, the more widely distributed (i.e. conserved) a gene, the smaller the average size of the proteomes from which it was absent. Together, these observations are consistent with the operation of a proteomic constraint on DNA repair. Lastly, a correlation between gene absence and genome AT content was shown, indicating a link between absence of DNA repair and elevated genome AT content.}, }
@article {pmid23796697, year = {2013}, author = {Sóki, J and Eitel, Z and Terhes, G and Nagy, E and Urbán, E and , }, title = {Occurrence and analysis of rare cfiA-bft doubly positive Bacteroides fragilis strains.}, journal = {Anaerobe}, volume = {23}, number = {}, pages = {70-73}, doi = {10.1016/j.anaerobe.2013.06.008}, pmid = {23796697}, issn = {1095-8274}, mesh = {Animals ; Bacterial Proteins/*genetics ; Bacterial Toxins/*genetics ; Bacteroides Infections/*microbiology ; Bacteroides fragilis/*genetics/isolation &amp; purification ; Conjugation, Genetic ; DNA Transposable Elements ; DNA, Bacterial/chemistry/genetics ; Europe ; Gene Transfer, Horizontal ; Humans ; Metalloendopeptidases/*genetics ; Molecular Sequence Data ; Sequence Analysis, DNA ; beta-Lactamases/*genetics ; }, abstract = {We detected four cfiA-bft1 doubly positive Bacteroides fragilis strains out of 486 B. fragilis isolates analyzed for antibiotic susceptibilities and antibiotic resistance genes from a recent pan-European survey. The prevalence of the enterotoxin bft genes was roughly equal among cfiA-negative and -positive B. fragilis strains. We also demonstrated that the cfiA-bft doubly positive strains had the most common B. fragilis genomic pattern (I.1.). Thus we concluded that the bft-carrying CTn86 conjugative transposons are mobile accounting for this unexpected simultaneous occurrence of the cfiA and bft genes.}, }
@article {pmid23791183, year = {2013}, author = {Husnik, F and Nikoh, N and Koga, R and Ross, L and Duncan, RP and Fujie, M and Tanaka, M and Satoh, N and Bachtrog, D and Wilson, AC and von Dohlen, CD and Fukatsu, T and McCutcheon, JP}, title = {Horizontal gene transfer from diverse bacteria to an insect genome enables a tripartite nested mealybug symbiosis.}, journal = {Cell}, volume = {153}, number = {7}, pages = {1567-1578}, doi = {10.1016/j.cell.2013.05.040}, pmid = {23791183}, issn = {1097-4172}, support = {R01GM076007/GM/NIGMS NIH HHS/United States ; R01GM093182/GM/NIGMS NIH HHS/United States ; R01 GM076007/GM/NIGMS NIH HHS/United States ; R01 GM093182/GM/NIGMS NIH HHS/United States ; R01 GM101255/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acids/biosynthesis ; Animals ; Bacteria/classification/*genetics ; Betaproteobacteria/*genetics ; Gene Expression Profiling ; *Gene Transfer, Horizontal ; Hemiptera/*genetics/*microbiology/physiology ; Molecular Sequence Data ; Phylogeny ; *Symbiosis ; }, abstract = {The smallest reported bacterial genome belongs to Tremblaya princeps, a symbiont of Planococcus citri mealybugs (PCIT). Tremblaya PCIT not only has a 139 kb genome, but possesses its own bacterial endosymbiont, Moranella endobia. Genome and transcriptome sequencing, including genome sequencing from a Tremblaya lineage lacking intracellular bacteria, reveals that the extreme genomic degeneracy of Tremblaya PCIT likely resulted from acquiring Moranella as an endosymbiont. In addition, at least 22 expressed horizontally transferred genes from multiple diverse bacteria to the mealybug genome likely complement missing symbiont genes. However, none of these horizontally transferred genes are from Tremblaya, showing that genome reduction in this symbiont has not been enabled by gene transfer to the host nucleus. Our results thus indicate that the functioning of this three-way symbiosis is dependent on genes from at least six lineages of organisms and reveal a path to intimate endosymbiosis distinct from that followed by organelles.}, }
@article {pmid23788478, year = {2013}, author = {Piccirillo, A and Dotto, G and Salata, C and Giacomelli, M}, title = {Absence of class 1 and class 2 integrons among Campylobacter jejuni and Campylobacter coli isolated from poultry in Italy.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {68}, number = {11}, pages = {2683-2685}, doi = {10.1093/jac/dkt242}, pmid = {23788478}, issn = {1460-2091}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Campylobacter Infections/microbiology/*veterinary ; Campylobacter coli/drug effects/*genetics/isolation &amp; purification ; Campylobacter jejuni/drug effects/*genetics/isolation &amp; purification ; DNA, Bacterial/*genetics ; *Drug Resistance, Bacterial ; *Integrons ; Italy ; Microbial Sensitivity Tests ; Poultry/*microbiology ; }, }
@article {pmid23787374, year = {2013}, author = {Kotnik, T}, title = {Lightning-triggered electroporation and electrofusion as possible contributors to natural horizontal gene transfer.}, journal = {Physics of life reviews}, volume = {10}, number = {3}, pages = {351-370}, doi = {10.1016/j.plrev.2013.05.001}, pmid = {23787374}, issn = {1873-1457}, mesh = {Animals ; *Electroporation ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Humans ; *Lightning ; }, abstract = {Phylogenetic studies show that horizontal gene transfer (HGT) is a significant contributor to genetic variability of prokaryotes, and was perhaps even more abundant during the early evolution. Hitherto, research of natural HGT has mainly focused on three mechanisms of DNA transfer: conjugation, natural competence, and viral transduction. This paper discusses the feasibility of a fourth such mechanism--cell electroporation and/or electrofusion triggered by atmospheric electrostatic discharges (lightnings). A description of electroporation as a phenomenon is followed by a review of experimental evidence that electroporation of prokaryotes in aqueous environments can result in release of non-denatured DNA, as well as uptake of DNA from the surroundings and transformation. Similarly, a description of electrofusion is followed by a review of experiments showing that prokaryotes devoid of cell wall can electrofuse into hybrids expressing the genes of their both precursors. Under sufficiently fine-tuned conditions, electroporation and electrofusion are efficient tools for artificial transformation and hybridization, respectively, but the quantitative analysis developed here shows that conditions for electroporation-based DNA release, DNA uptake and transformation, as well as for electrofusion are also present in many natural aqueous environments exposed to lightnings. Electroporation is thus a plausible contributor to natural HGT among prokaryotes, and could have been particularly important during the early evolution, when the other mechanisms might have been scarcer or nonexistent. In modern prokaryotes, natural absence of the cell wall is rare, but it is reasonable to assume that the wall has formed during a certain stage of evolution, and at least prior to this, electrofusion could also have contributed to natural HGT. The concluding section outlines several guidelines for assessment of the feasibility of lightning-triggered HGT.}, }
@article {pmid23785357, year = {2013}, author = {He, Y and Xiao, X and Wang, F}, title = {Metagenome reveals potential microbial degradation of hydrocarbon coupled with sulfate reduction in an oil-immersed chimney from Guaymas Basin.}, journal = {Frontiers in microbiology}, volume = {4}, number = {}, pages = {148}, pmid = {23785357}, issn = {1664-302X}, abstract = {Deep-sea hydrothermal vent chimneys contain a high diversity of microorganisms, yet the metabolic activity and the ecological functions of the microbial communities remain largely unexplored. In this study, a metagenomic approach was applied to characterize the metabolic potential in a Guaymas hydrothermal vent chimney and to conduct comparative genomic analysis among a variety of environments with sequenced metagenomes. Complete clustering of functional gene categories with a comparative metagenomic approach showed that this Guaymas chimney metagenome was clustered most closely with a chimney metagenome from Juan de Fuca. All chimney samples were enriched with genes involved in recombination and repair, chemotaxis and flagellar assembly, highlighting their roles in coping with the fluctuating extreme deep-sea environments. A high proportion of transposases was observed in all the metagenomes from deep-sea chimneys, supporting the previous hypothesis that horizontal gene transfer may be common in the deep-sea vent chimney biosphere. In the Guaymas chimney metagenome, thermophilic sulfate reducing microorganisms including bacteria and archaea were found predominant, and genes coding for the degradation of refractory organic compounds such as cellulose, lipid, pullullan, as well as a few hydrocarbons including toluene, ethylbenzene and o-xylene were identified. Therefore, this oil-immersed chimney supported a thermophilic microbial community capable of oxidizing a range of hydrocarbons that served as electron donors for sulphate reduction under anaerobic conditions.}, }
@article {pmid23785293, year = {2013}, author = {Jiang, RH and de Bruijn, I and Haas, BJ and Belmonte, R and Löbach, L and Christie, J and van den Ackerveken, G and Bottin, A and Bulone, V and Díaz-Moreno, SM and Dumas, B and Fan, L and Gaulin, E and Govers, F and Grenville-Briggs, LJ and Horner, NR and Levin, JZ and Mammella, M and Meijer, HJ and Morris, P and Nusbaum, C and Oome, S and Phillips, AJ and van Rooyen, D and Rzeszutek, E and Saraiva, M and Secombes, CJ and Seidl, MF and Snel, B and Stassen, JH and Sykes, S and Tripathy, S and van den Berg, H and Vega-Arreguin, JC and Wawra, S and Young, SK and Zeng, Q and Dieguez-Uribeondo, J and Russ, C and Tyler, BM and van West, P}, title = {Distinctive expansion of potential virulence genes in the genome of the oomycete fish pathogen Saprolegnia parasitica.}, journal = {PLoS genetics}, volume = {9}, number = {6}, pages = {e1003272}, pmid = {23785293}, issn = {1553-7404}, support = {BB/C518457/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/G012075/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Evolution, Molecular ; Fishes/genetics/parasitology ; *Gene Transfer, Horizontal ; Genome ; Host-Parasite Interactions/*genetics ; Oomycetes/classification/*genetics/pathogenicity ; Phylogeny ; Plants/parasitology ; Saprolegnia/classification/*genetics/pathogenicity ; Virulence/*genetics ; }, abstract = {Oomycetes in the class Saprolegniomycetidae of the Eukaryotic kingdom Stramenopila have evolved as severe pathogens of amphibians, crustaceans, fish and insects, resulting in major losses in aquaculture and damage to aquatic ecosystems. We have sequenced the 63 Mb genome of the fresh water fish pathogen, Saprolegnia parasitica. Approximately 1/3 of the assembled genome exhibits loss of heterozygosity, indicating an efficient mechanism for revealing new variation. Comparison of S. parasitica with plant pathogenic oomycetes suggests that during evolution the host cellular environment has driven distinct patterns of gene expansion and loss in the genomes of plant and animal pathogens. S. parasitica possesses one of the largest repertoires of proteases (270) among eukaryotes that are deployed in waves at different points during infection as determined from RNA-Seq data. In contrast, despite being capable of living saprotrophically, parasitism has led to loss of inorganic nitrogen and sulfur assimilation pathways, strikingly similar to losses in obligate plant pathogenic oomycetes and fungi. The large gene families that are hallmarks of plant pathogenic oomycetes such as Phytophthora appear to be lacking in S. parasitica, including those encoding RXLR effectors, Crinkler's, and Necrosis Inducing-Like Proteins (NLP). S. parasitica also has a very large kinome of 543 kinases, 10% of which is induced upon infection. Moreover, S. parasitica encodes several genes typical of animals or animal-pathogens and lacking from other oomycetes, including disintegrins and galactose-binding lectins, whose expression and evolutionary origins implicate horizontal gene transfer in the evolution of animal pathogenesis in S. parasitica.}, }
@article {pmid23771140, year = {2013}, author = {Roberts, GA and Houston, PJ and White, JH and Chen, K and Stephanou, AS and Cooper, LP and Dryden, DT and Lindsay, JA}, title = {Impact of target site distribution for Type I restriction enzymes on the evolution of methicillin-resistant Staphylococcus aureus (MRSA) populations.}, journal = {Nucleic acids research}, volume = {41}, number = {15}, pages = {7472-7484}, pmid = {23771140}, issn = {1362-4962}, support = {090869MA//Wellcome Trust/United Kingdom ; GR080463MA//Wellcome Trust/United Kingdom ; }, mesh = {Bacterial Proteins/genetics/metabolism ; Base Sequence ; Computational Biology/methods ; DNA Cleavage ; DNA Restriction-Modification Enzymes/genetics/*metabolism ; DNA, Bacterial/genetics ; Deoxyribonucleases, Type I Site-Specific/genetics/*metabolism ; *Evolution, Molecular ; Gene Library ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Methicillin-Resistant Staphylococcus aureus/enzymology/*genetics ; Open Reading Frames ; Plasmids/genetics/metabolism ; }, abstract = {A limited number of Methicillin-resistant Staphylococcus aureus (MRSA) clones are responsible for MRSA infections worldwide, and those of different lineages carry unique Type I restriction-modification (RM) variants. We have identified the specific DNA sequence targets for the dominant MRSA lineages CC1, CC5, CC8 and ST239. We experimentally demonstrate that this RM system is sufficient to block horizontal gene transfer between clinically important MRSA, confirming the bioinformatic evidence that each lineage is evolving independently. Target sites are distributed randomly in S. aureus genomes, except in a set of large conjugative plasmids encoding resistance genes that show evidence of spreading between two successful MRSA lineages. This analysis of the identification and distribution of target sites explains evolutionary patterns in a pathogenic bacterium. We show that a lack of specific target sites enables plasmids to evade the Type I RM system thereby contributing to the evolution of increasingly resistant community and hospital MRSA.}, }
@article {pmid23770768, year = {2013}, author = {Bhattacharya, D and Price, DC and Chan, CX and Qiu, H and Rose, N and Ball, S and Weber, AP and Arias, MC and Henrissat, B and Coutinho, PM and Krishnan, A and Zäuner, S and Morath, S and Hilliou, F and Egizi, A and Perrineau, MM and Yoon, HS}, title = {Genome of the red alga Porphyridium purpureum.}, journal = {Nature communications}, volume = {4}, number = {}, pages = {1941}, pmid = {23770768}, issn = {2041-1723}, mesh = {Algal Proteins/genetics ; Carbohydrate Metabolism/genetics ; Cytochrome P-450 Enzyme System/metabolism ; Gene Ontology ; Gene Transfer, Horizontal ; Genome/*genetics ; Glycolipids/biosynthesis ; Light-Harvesting Protein Complexes/metabolism ; Meiosis/genetics ; Membrane Transport Proteins/metabolism ; Molecular Weight ; Phylogeny ; Porphyridium/cytology/enzymology/*genetics ; Reproduction/genetics ; Sphingolipids/metabolism ; Starch/biosynthesis ; }, abstract = {The limited knowledge we have about red algal genomes comes from the highly specialized extremophiles, Cyanidiophyceae. Here, we describe the first genome sequence from a mesophilic, unicellular red alga, Porphyridium purpureum. The 8,355 predicted genes in P. purpureum, hundreds of which are likely to be implicated in a history of horizontal gene transfer, reside in a genome of 19.7 Mbp with 235 spliceosomal introns. Analysis of light-harvesting complex proteins reveals a nuclear-encoded phycobiliprotein in the alga. We uncover a complex set of carbohydrate-active enzymes, identify the genes required for the methylerythritol phosphate pathway of isoprenoid biosynthesis, and find evidence of sexual reproduction. Analysis of the compact, function-rich genome of P. purpureum suggests that ancestral lineages of red algae acted as mediators of horizontal gene transfer between prokaryotes and photosynthetic eukaryotes, thereby significantly enriching genomes across the tree of photosynthetic life.}, }
@article {pmid23769954, year = {2013}, author = {Li, X and Xing, J and Li, B and Yu, F and Lan, X and Liu, J}, title = {Phylogenetic analysis reveals the coexistence of interfamily and interspecies horizontal gene transfer in Streptococcus thermophilus strains isolated from the same yoghurt.}, journal = {Molecular phylogenetics and evolution}, volume = {69}, number = {1}, pages = {286-292}, doi = {10.1016/j.ympev.2013.06.002}, pmid = {23769954}, issn = {1095-9513}, mesh = {Bacterial Proteins/*genetics ; Biological Evolution ; DNA, Bacterial/*classification/genetics ; Enterococcus/enzymology/genetics ; *Gene Transfer, Horizontal ; IMP Dehydrogenase/genetics ; Isoenzymes/genetics ; Phosphopyruvate Hydratase/genetics ; *Phylogeny ; Sequence Analysis, DNA ; Streptococcus thermophilus/*classification/enzymology/genetics ; Yogurt/*microbiology ; }, abstract = {Horizontal gene transfer (HGT) is an important evolutionary mechanism that has shaped prokaryotic genomes. For Streptococcus thermophilus, there is no direct evidence that the bacteria might acquire a second paralog from a different origin in the same niche. In this study, we found that four isolates of S. thermophilus (B, C, E and F) from the same yoghurt contained two putative homologs of the eno genes (eno-1 and eno-2) and two putative homologs of the guaB genes (guaB-1 and guaB-2). Both eno-1 and guaB-1 shared 100% nucleotide identity among the four isolates, and with isolate A and S. thermophilus ND03. Phylogenetic and nucleotide divergence analyses indicated that guaB-2 of these isolates may have been acquired from species in the genus Streptococcus, while eno-2 of isolates B and C may have been acquired from a donor in the genus Streptococcus. The eno-2 genes of isolates E and F may have been acquired from a donor in the Enterococcus genera. Relative synonymous codon usage analysis confirmed the eno-2 genes of isolates E and F as being acquired from a donor in genus Enterococcus. This study provides evidence that interfamily and interspecies HGT occur in S. thermophilus strains isolated from the same niche.}, }
@article {pmid23768140, year = {2013}, author = {Maillard, JY and Bloomfield, S and Coelho, JR and Collier, P and Cookson, B and Fanning, S and Hill, A and Hartemann, P and McBain, AJ and Oggioni, M and Sattar, S and Schweizer, HP and Threlfall, J}, title = {Does microbicide use in consumer products promote antimicrobial resistance? A critical review and recommendations for a cohesive approach to risk assessment.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {19}, number = {5}, pages = {344-354}, doi = {10.1089/mdr.2013.0039}, pmid = {23768140}, issn = {1931-8448}, mesh = {Adaptation, Physiological/drug effects ; Anti-Infective Agents/*pharmacology ; Biofilms/*drug effects/growth &amp; development ; Biological Transport ; Drug Resistance, Multiple, Bacterial/*drug effects/genetics ; Gene Transfer, Horizontal ; Gram-Negative Bacteria/*drug effects/genetics/growth &amp; development ; Gram-Positive Bacteria/*drug effects/genetics/growth &amp; development ; Household Products/analysis ; Humans ; Microbial Sensitivity Tests ; Mutation ; Risk Assessment ; Terminology as Topic ; }, abstract = {The increasing use of microbicides in consumer products is raising concerns related to enhanced microbicide resistance in bacteria and potential cross resistance to antibiotics. The recently published documents on this topic from the European Commission have spawned much interest to better understand the true extent of the putative links for the benefit of the manufacturers, regulators, and consumers alike. This white paper is based on a 2-day workshop (SEAC-Unilever, Bedford, United Kingdom; June 2012) in the fields of microbicide usage and resistance. It identifies gaps in our knowledge and also makes specific recommendations for harmonization of key terms and refinement/standardization of methods for testing microbicide resistance to better assess the impact and possible links with cross resistance to antibiotics. It also calls for a better cohesion in research in this field. Such information is crucial to developing any risk assessment framework on microbicide use notably in consumer products. The article also identifies key research questions where there are inadequate data, which, if addressed, could promote improved knowledge and understanding to assess any related risks for consumer and environmental safety.}, }
@article {pmid23766026, year = {2013}, author = {Yan, HW and Hong, L and Zhou, YQ and Jiang, HY and Zhu, SW and Fan, J and Cheng, BJ}, title = {A genome-wide analysis of the ERF gene family in sorghum.}, journal = {Genetics and molecular research : GMR}, volume = {12}, number = {2}, pages = {2038-2055}, doi = {10.4238/2013.May.13.1}, pmid = {23766026}, issn = {1676-5680}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Arabidopsis/genetics ; Chromosomes, Plant/genetics ; Conserved Sequence ; Ethylenes/*metabolism ; Gene Expression Regulation, Plant ; Genes, Plant/*genetics ; *Genome-Wide Association Study ; Molecular Sequence Data ; Multigene Family/*genetics ; Oryza/genetics ; Phylogeny ; Plant Proteins/chemistry/*genetics/metabolism ; Protein Structure, Tertiary ; Sorghum/*genetics ; Transcription Factors/chemistry/*genetics/metabolism ; Zea mays/genetics ; }, abstract = {The ethylene response factor (ERF) family are members of the APETALA2 (AP2)/ERF transcription factor superfamily; they are known to play an important role in plant adaptation to biotic and abiotic stress. ERF genes have been studied in Arabidopsis, rice, grape, and maize; however, there are few reports of ERF genes in sorghum. We identified 105 sorghum ERF (SbERF) genes, which were categorized into 12 groups (A-1 to A-6 and B-1 to B-6) based on their sequence similarity, and this new method of classification for ERF genes was then further characterized. A comprehensive bioinformatic analysis of SbERF genes was performed using a sorghum genomic database, to analyze the phylogeny of SbERF genes, identify other conserved motifs apart from the AP2/ERF domain, map SbERF genes to the 10 sorghum chromosomes, and determine the tissue-specific expression patterns of SbERF genes. Gene clustering indicates that SbERF genes were generated by tandem duplications. Comparison of SbERF genes with maize ERF homologs suggests lateral gene transfer between monocot species. These results can contribute to our understanting of the evolution of the ERF gene family.}, }
@article {pmid23764294, year = {2013}, author = {Gaze, WH and Krone, SM and Larsson, DG and Li, XZ and Robinson, JA and Simonet, P and Smalla, K and Timinouni, M and Topp, E and Wellington, EM and Wright, GD and Zhu, YG}, title = {Influence of humans on evolution and mobilization of environmental antibiotic resistome.}, journal = {Emerging infectious diseases}, volume = {19}, number = {7}, pages = {}, pmid = {23764294}, issn = {1080-6059}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/drug effects/*genetics ; Drug Resistance, Bacterial/*genetics ; Environmental Pollutants/*pharmacology ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Soil Microbiology ; }, abstract = {The clinical failure of antimicrobial drugs that were previously effective in controlling infectious disease is a tragedy of increasing magnitude that gravely affects human health. This resistance by pathogens is often the endpoint of an evolutionary process that began billions of years ago in non-disease-causing microorganisms. This environmental resistome, its mobilization, and the conditions that facilitate its entry into human pathogens are at the heart of the current public health crisis in antibiotic resistance. Understanding the origins, evolution, and mechanisms of transfer of resistance elements is vital to our ability to adequately address this public health issue.}, }
@article {pmid23764277, year = {2013}, author = {Juhas, M and Dimopoulou, I and Robinson, E and Elamin, A and Harding, R and Hood, D and Crook, D}, title = {Identification of another module involved in the horizontal transfer of the Haemophilus genomic island ICEHin1056.}, journal = {Plasmid}, volume = {70}, number = {2}, pages = {277-283}, pmid = {23764277}, issn = {1095-9890}, support = {G0400039/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Base Sequence ; Computational Biology ; Conjugation, Genetic/*genetics ; DNA Replication/genetics ; Gene Regulatory Networks/*genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/*genetics ; Genomic Instability/genetics ; Genomic Islands/*genetics ; Haemophilus/*genetics ; Haemophilus influenzae/genetics ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Sequence Analysis, DNA ; }, abstract = {A significant part of horizontal gene transfer is facilitated by genomic islands. Haemophilus influenzae genomic island ICEHin1056 is an archetype of a genomic island that accounts for pandemic spread of antibiotics resistance. ICEHin1056 has modular structure and harbors modules involved in type IV secretion and integration. Previous studies have shown that ICEHin1056 encodes a functional type IV secretion system; however, other modules have not been characterized yet. Here we show that the module on the 5' extremity of ICEHin1056 consists of 15 genes that are well conserved in a number of related genomic islands. Furthermore by disrupting six genes of the investigated module of ICEHin1056 by site-specific mutagenesis we demonstrate that in addition to type IV secretion system module, the investigated module is also important for the successful conjugal transfer of ICEHin1056 from donor to recipient cells.}, }
@article {pmid23763770, year = {2013}, author = {Dehghan, S and Seto, J and Liu, EB and Walsh, MP and Dyer, DW and Chodosh, J and Seto, D}, title = {Computational analysis of four human adenovirus type 4 genomes reveals molecular evolution through two interspecies recombination events.}, journal = {Virology}, volume = {443}, number = {2}, pages = {197-207}, pmid = {23763770}, issn = {1096-0341}, support = {R01 EY013124/EY/NEI NIH HHS/United States ; EY013124/EY/NEI NIH HHS/United States ; }, mesh = {Adenovirus Infections, Human/virology ; Adenoviruses, Human/*genetics ; Adenoviruses, Simian/*genetics ; Animals ; Base Sequence ; Computational Biology/*methods ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Viral/*genetics ; Humans ; Molecular Sequence Data ; Pan troglodytes/virology ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Viral Proteins/genetics ; Zoonoses ; }, abstract = {Computational analysis of human adenovirus type 4 (HAdV-E4), a pathogen that is the only HAdV member of species E, provides insights into its zoonotic origin and molecular adaptation. Its genome encodes a domain of the major capsid protein, hexon, from HAdV-B16 recombined into the genome chassis of a simian adenovirus. Genomes of two recent field strains provide a clue to its adaptation to the new host: recombination of a NF-I binding site motif, which is required for efficient viral replication, from another HAdV genome. This motif is absent in the chimpanzee adenoviruses and the HAdV-E4 prototype, but is conserved amongst other HAdVs. This is the first report of an interspecies recombination event for HAdVs, and the first documentation of a lateral partial gene transfer from a chimpanzee AdV. The potential for such recombination events are important when considering chimpanzee adenoviruses as candidate gene delivery vectors for human patients.}, }
@article {pmid23760639, year = {2013}, author = {Mc Ginty, S&#xc9; and Lehmann, L and Brown, SP and Rankin, DJ}, title = {The interplay between relatedness and horizontal gene transfer drives the evolution of plasmid-carried public goods.}, journal = {Proceedings. Biological sciences}, volume = {280}, number = {1761}, pages = {20130400}, pmid = {23760639}, issn = {1471-2954}, support = {/WT_/Wellcome Trust/United Kingdom ; 095831/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacteria/*genetics/pathogenicity ; *Biological Evolution ; *Gene Transfer, Horizontal ; Genetics, Population ; Host-Pathogen Interactions/genetics ; *Models, Genetic ; Plasmids/*genetics ; Selection, Genetic ; Virulence Factors/genetics ; }, abstract = {Plasmids carry a wide range of genes that are often involved in bacterial social behaviour. The question of why such genes are frequently mobile has received increasing attention. Here, we use an explicit population genetic approach to model the evolution of plasmid-borne bacterial public goods production. Our findings highlight the importance of both transmission and relatedness as factors driving the evolution of plasmid-borne public goods production. We partition the effects of plasmid transfer of social traits into those of infectivity and the effect of increased relatedness. Our results demonstrate that, owing to its effect on relatedness, plasmid mobility increases the invasion and stability of public goods, in a way not seen in individually beneficial traits. In addition, we show that plasmid transfer increases relatedness when public goods production is rare but this effect declines when production is common, with both scenarios leading to an increase in the frequency of plasmid-borne public goods. Plasmids remain important vectors for the spread of social genes involved in bacterial virulence thus an understanding of their dynamics is highly relevant from a public health perspective.}, }
@article {pmid23760531, year = {2013}, author = {Trček, J and Matsushita, K}, title = {A unique enzyme of acetic acid bacteria, PQQ-dependent alcohol dehydrogenase, is also present in Frateuria aurantia.}, journal = {Applied microbiology and biotechnology}, volume = {97}, number = {16}, pages = {7369-7376}, doi = {10.1007/s00253-013-5007-6}, pmid = {23760531}, issn = {1432-0614}, mesh = {Alcohol Oxidoreductases/chemistry/genetics/isolation &amp; purification/*metabolism ; Amino Acid Sequence ; Chromatography, Affinity ; Chromatography, Ion Exchange ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; Gluconacetobacter/enzymology/genetics ; Molecular Sequence Data ; Molecular Weight ; Phylogeny ; Protein Multimerization ; Protein Subunits ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Substrate Specificity ; Xanthomonadaceae/*enzymology/genetics ; }, abstract = {A membrane-bound, pyrroloquinoline quinone (PQQ)-dependent alcohol dehydrogenase (ADH) was purified from Frateuria aurantia LMG 1558(T). Although F. aurantia belongs to a group of γ-Proteobacteria, the characteristics of its PQQ-ADH were similar to the enzyme characteristics of the typical high-acetic acid-resistant bacterium Gluconacetobacter europaeus from the group of α-Proteobacteria. The PQQ-dependent ADH was solubilized from the membranes and purified after anionic, cationic, and affinity chromatography with specific activity of 117 U/mg. The purified enzyme was estimated to be composed of two subunits of ca. 72 and 45 kDa, as judged by SDS-polyacrylamide gel electrophoresis. The purified enzyme had maximum activity at pH 4.5 and showed the highest substrate specificity to ethanol, isoamyl alcohol, 1-butanol, and 1-propanol. The deduced sequences of cloned genes adhA and adhB encoding subunits I and II of PQQ-ADH showed 80 % amino acid (AA) identity to AdhA and 68 % AA identity to AdhB of Ga. europaeus V3 (LMG 18494). Because of the high similarity between genes encoding subunits I and II of PQQ-ADH and its homologous genes found in a distantly related taxonomic group of acetic acid bacteria, the results suggest the possibility of horizontal gene transfer between these two groups of genera.}, }
@article {pmid23759724, year = {2013}, author = {Duron, O}, title = {Lateral transfers of insertion sequences between Wolbachia, Cardinium and Rickettsia bacterial endosymbionts.}, journal = {Heredity}, volume = {111}, number = {4}, pages = {330-337}, pmid = {23759724}, issn = {1365-2540}, mesh = {Animals ; Arthropods/genetics/microbiology ; Bacteria/genetics ; DNA Transposable Elements/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Molecular Sequence Data ; Phylogeny ; Rickettsia/*genetics ; Symbiosis/genetics ; Wolbachia/*genetics ; }, abstract = {Various bacteria live exclusively within arthropod cells and collectively act as an important driver of arthropod evolutionary ecology. Whereas rampant intra-generic DNA transfers were recently shown to have a pivotal role in the evolution of the most common of these endosymbionts, Wolbachia, the present study show that inter-generic DNA transfers also commonly take place, constituting a potent source of rapid genomic change. Bioinformatic, molecular and phylogenetic data provide evidence that a selfish genetic element, the insertion sequence ISRpe1, is widespread in the Wolbachia, Cardinium and Rickettsia endosymbionts and experiences recent (and likely ongoing) transfers over long evolutionary distances. Although many ISRpe1 copies were clearly expanding and leading to rapid endosymbiont diversification, degraded copies are also frequently found, constituting an unusual genomic fossil record suggestive of ancient ISRpe1 expansions. Overall, the present data highlight how ecological connections within the arthropod intracellular environment facilitate lateral DNA transfers between distantly related bacterial lineages.}, }
@article {pmid23759418, year = {2013}, author = {Wijayawardena, BK and Minchella, DJ and DeWoody, JA}, title = {Hosts, parasites, and horizontal gene transfer.}, journal = {Trends in parasitology}, volume = {29}, number = {7}, pages = {329-338}, doi = {10.1016/j.pt.2013.05.001}, pmid = {23759418}, issn = {1471-5007}, mesh = {Animals ; Biological Evolution ; *Gene Transfer, Horizontal ; Genome/*genetics ; Host-Parasite Interactions ; Humans ; Life Cycle Stages ; Parasites/*genetics/physiology ; Parasitic Diseases/*parasitology ; Phylogeny ; Schistosomatidae/*genetics/physiology ; Trematode Infections/*parasitology ; }, abstract = {Mendelian inheritance transfers genes vertically within lineages, whereas horizontal gene transfer (HGT) moves genetic material between or among lineages. Herein, we explore possible mechanisms of HGT between parasites and their hosts, as their intimate contact affords substantial opportunities for HGT. We review studies of host-parasite HGT, discussing their merits, their shortcomings, and the multiple lines of evidence needed to conclusively document HGT while avoiding false positives. We focus mainly on schistosomes and other parasites with complex life cycles as they provide numerous opportunities for HGT among the parasite, intermediate, and definitive host genomes. We also highlight future research directions that could prove illuminating with regard to the occurrence, prevalence, and overall importance of HGT in host-parasite coevolution.}, }
@article {pmid23758589, year = {2013}, author = {Pereira, SG and Reis, T and Mendez, IP and Cardoso, O}, title = {Prevalence and molecular epidemiology of imipenem-resistant Pseudomonas aeruginosa carrying metallo-beta-lactamases from two central hospitals in Portugal.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {19}, number = {5}, pages = {392-396}, doi = {10.1089/mdr.2013.0029}, pmid = {23758589}, issn = {1931-8448}, mesh = {Anti-Bacterial Agents/*therapeutic use ; Cross Infection/drug therapy/*epidemiology/microbiology ; Gene Transfer, Horizontal ; Hospitals, Urban ; Humans ; Imipenem/*therapeutic use ; Integrons ; Microbial Sensitivity Tests ; Molecular Epidemiology ; Portugal/epidemiology ; Prevalence ; Pseudomonas Infections/drug therapy/*epidemiology/microbiology ; Pseudomonas aeruginosa/drug effects/enzymology/*genetics/isolation &amp; purification ; beta-Lactam Resistance/drug effects/*genetics ; beta-Lactamases/*genetics/metabolism ; }, abstract = {Metallo-beta-lactamases (MBLs) can confer broad-spectrum beta-lactam resistance, including carbapenems. The aim of this work was to document the occurrence of MBLs in 122 imipenem-resistant Pseudomonas aeruginosa isolates collected in two Portuguese central hospitals, to determine their antimicrobial susceptibility, and to observe if there were intra- and interhospital epidemic spread. About 20.5% of these isolates presented blaVIM-2, which was found to be widespread in both hospitals. Clonal diversity was observed within hospitals, and no interhospital spread was observed. Ten of the blaVIM-2-positive isolates (44%), from both hospitals, presented one or two class 1 integrons. Two of those contained a VIM-2 gene, one from each hospital, which is indicative for the possibility of MBL gene transfer. No interhospital spread of integrons was observed. Regular screening and surveillance is needed to prevent spread of this worrisome resistance determinant.}, }
@article {pmid23757132, year = {2013}, author = {Mašlaňová, I and Doškař, J and Varga, M and Kuntová, L and Mužík, J and Malúšková, D and Růžičková, V and Pantůček, R}, title = {Bacteriophages of Staphylococcus aureus efficiently package various bacterial genes and mobile genetic elements including SCCmec with different frequencies.}, journal = {Environmental microbiology reports}, volume = {5}, number = {1}, pages = {66-73}, doi = {10.1111/j.1758-2229.2012.00378.x}, pmid = {23757132}, issn = {1758-2229}, mesh = {Bacterial Proteins/genetics ; Bacteriophages/*genetics/metabolism ; Chromosomes, Bacterial/*genetics ; Cloning, Molecular ; DNA, Bacterial/genetics ; Gene Frequency ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genetic Loci ; *Interspersed Repetitive Sequences ; Methicillin Resistance/genetics ; Penicillin-Binding Proteins ; Penicillinase/genetics ; Plasmids/genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Staphylococcus aureus/genetics/physiology/*virology ; Virus Assembly ; }, abstract = {Staphylococcus aureus is a serious human and veterinary pathogen in which new strains with increasing virulence and antimicrobial resistance occur due to acquiring new genes by horizontal transfer. It is generally accepted that temperate bacteriophages play a major role in gene transfer. In this study, we proved the presence of various bacterial genes of the S. aureus COL strain directly within the phage particles via qPCR and quantified their packaging frequency. Non-parametric statistical analysis showed that transducing bacteriophages φ11, φ80 and φ80α of serogroup B, in contrast to serogroup A bacteriophage φ81, efficiently package selected chromosomal genes localized in 4 various loci of the chromosome and 8 genes carried on variable elements, such as staphylococcal cassette chromosome SCCmec, staphylococcal pathogenicity island SaPI1, genomic islands vSaα and vSaβ, and plasmids with various frequency. Bacterial gene copy number per ng of DNA isolated from phage particles ranged between 1.05 × 10(2) for the tetK plasmid gene and 3.86 × 10(5) for the SaPI1 integrase gene. The new and crucial finding that serogroup B bacteriophages can package concurrently ccrA1 (1.16 × 10(4)) and mecA (1.26 × 10(4)) located at SCCmec type I into their capsids indicates that generalized transduction plays an important role in the evolution and emergence of new methicillin-resistant clones.}, }
@article {pmid23755230, year = {2013}, author = {Vera-Cabrera, L and Ortiz-Lopez, R and Elizondo-Gonzalez, R and Ocampo-Candiani, J}, title = {Complete genome sequence analysis of Nocardia brasiliensis HUJEG-1 reveals a saprobic lifestyle and the genes needed for human pathogenesis.}, journal = {PloS one}, volume = {8}, number = {6}, pages = {e65425}, pmid = {23755230}, issn = {1932-6203}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics/metabolism ; Chromosome Mapping ; Chromosomes, Bacterial/*chemistry/metabolism ; DNA Transposable Elements ; Drug Resistance, Multiple, Bacterial/drug effects/genetics ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; Metabolic Networks and Pathways/genetics ; Molecular Sequence Annotation ; Mycetoma/microbiology/pathology ; Nocardia/drug effects/*genetics/metabolism/pathogenicity ; Nocardia Infections/microbiology/pathology ; Sequence Analysis, DNA ; *Soil Microbiology ; Virulence Factors/*genetics/metabolism ; }, abstract = {Nocardia brasiliensis is an important etiologic agent of mycetoma. These bacteria live as a saprobe in soil or organic material and enter the tissue via minor trauma. Mycetoma is characterized by tumefaction and the production of fistula and abscesses, with no spontaneous cure. By using mass sequencing, we determined the complete genomic nucleotide sequence of the bacteria. According to our data, the genome is a circular chromosome 9,436,348-bp long with 68% G+C content that encodes 8,414 proteins. We observed orthologs for virulence factors, a higher number of genes involved in lipid biosynthesis and catabolism, and gene clusters for the synthesis of bioactive compounds, such as antibiotics, terpenes, and polyketides. An in silico analysis of the sequence supports the conclusion that the bacteria acquired diverse genes by horizontal transfer from other soil bacteria, even from eukaryotic organisms. The genome composition reflects the evolution of bacteria via the acquisition of a large amount of DNA, which allows it to survive in new ecological niches, including humans.}, }
@article {pmid23755047, year = {2013}, author = {Perry, JA and Wright, GD}, title = {The antibiotic resistance "mobilome": searching for the link between environment and clinic.}, journal = {Frontiers in microbiology}, volume = {4}, number = {}, pages = {138}, pmid = {23755047}, issn = {1664-302X}, abstract = {Antibiotic resistance is an ancient problem, owing to the co-evolution of antibiotic-producing and target organisms in the soil and other environments over millennia. The environmental "resistome" is the collection of all genes that directly or indirectly contribute to antibiotic resistance. Many of these resistance determinants originate in antibiotic-producing organisms (where they serve to mediate self-immunity), while others become resistance determinants only when mobilized and over-expressed in non-native hosts (like plasmid-encoded β-lactamases). The modern environmental resistome is under selective pressure from human activities such as agriculture, which may influence the composition of the local resistome and lead to gene transfer events. Beyond the environment, we are challenged in the clinic by the rise in both frequency and diversity of antibiotic resistant pathogens. We assume that clinical resistance originated in the environment, but few examples of direct gene exchange between the environmental resistome and the clinical resistome have been documented. Strong evidence exists to suggest that clinical aminoglycoside and vancomycin resistance enzymes, the extended-spectrum β-lactamase CTX-M and the quinolone resistance gene qnr have direct links to the environmental resistome. In this review, we highlight recent advances in our understanding of horizontal gene transfer of antibiotic resistance genes from the environment to the clinic. Improvements in sequencing technologies coupled with functional metagenomic studies have revealed previously underappreciated diversity in the environmental resistome, and also established novel genetic links to the clinic. Understanding mechanisms of gene exchange becomes vital in controlling the future dissemination of antibiotic resistance.}, }
@article {pmid23754810, year = {2013}, author = {Kim, JD and Senn, S and Harel, A and Jelen, BI and Falkowski, PG}, title = {Discovering the electronic circuit diagram of life: structural relationships among transition metal binding sites in oxidoreductases.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {368}, number = {1622}, pages = {20120257}, pmid = {23754810}, issn = {1471-2970}, mesh = {Amino Acid Sequence ; Animals ; Binding Sites ; *Biological Evolution ; Ecological and Environmental Phenomena ; Metals/chemistry/*metabolism ; Oceans and Seas ; Oxidation-Reduction ; Oxidoreductases/chemistry/genetics/*metabolism ; Protein Binding ; Protein Conformation ; Protein Folding ; }, abstract = {Oxidoreductases play a central role in catalysing enzymatic electron-transfer reactions across the tree of life. To first order, the equilibrium thermodynamic properties of these proteins are governed by protein folds associated with specific transition metals and ligands at the active site. A global analysis of holoenzyme structures and functions suggests that there are fewer than approximately 500 fundamental oxidoreductases, which can be further clustered into 35 unique groups. These catalysts evolved in prokaryotes early in the Earth's history and are largely responsible for the emergence of non-equilibrium biogeochemical cycles on the planet's surface. Although the evolutionary history of the amino acid sequences in the oxidoreductases is very difficult to reconstruct due to gene duplication and horizontal gene transfer, the evolution of the folds in the catalytic sites can potentially be used to infer the history of these enzymes. Using a novel, yet simple analysis of the secondary structures associated with the ligands in oxidoreductases, we developed a structural phylogeny of these enzymes. The results of this 'composome' analysis suggest an early split from a basal set of a small group of proteins dominated by loop structures into two families of oxidoreductases, one dominated by α-helices and the second by β-sheets. The structural evolutionary patterns in both clades trace redox gradients and increased hydrogen bond energy in the active sites. The overall pattern suggests that the evolution of the oxidoreductases led to decreased entropy in the transition metal folds over approximately 2.5 billion years, allowing the enzymes to use increasingly oxidized substrates with high specificity.}, }
@article {pmid23754393, year = {2013}, author = {Santini, S and Jeudy, S and Bartoli, J and Poirot, O and Lescot, M and Abergel, C and Barbe, V and Wommack, KE and Noordeloos, AA and Brussaard, CP and Claverie, JM}, title = {Genome of Phaeocystis globosa virus PgV-16T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {26}, pages = {10800-10805}, pmid = {23754393}, issn = {1091-6490}, mesh = {Chromosome Mapping ; Gene Duplication ; *Genome, Viral ; Haptophyta/ultrastructure/*virology ; Molecular Sequence Data ; Phycodnaviridae/classification/*genetics/ultrastructure ; Phylogeny ; Phytoplankton/ultrastructure/virology ; Proteome ; Retroelements ; Satellite Viruses/genetics ; Viral Proteins/genetics ; }, abstract = {Large dsDNA viruses are involved in the population control of many globally distributed species of eukaryotic phytoplankton and have a prominent role in bloom termination. The genus Phaeocystis (Haptophyta, Prymnesiophyceae) includes several high-biomass-forming phytoplankton species, such as Phaeocystis globosa, the blooms of which occur mostly in the coastal zone of the North Atlantic and the North Sea. Here, we report the 459,984-bp-long genome sequence of P. globosa virus strain PgV-16T, encoding 434 proteins and eight tRNAs and, thus, the largest fully sequenced genome to date among viruses infecting algae. Surprisingly, PgV-16T exhibits no phylogenetic affinity with other viruses infecting microalgae (e.g., phycodnaviruses), including those infecting Emiliania huxleyi, another ubiquitous bloom-forming haptophyte. Rather, PgV-16T belongs to an emerging clade (the Megaviridae) clustering the viruses endowed with the largest known genomes, including Megavirus, Mimivirus (both infecting acanthamoeba), and a virus infecting the marine microflagellate grazer Cafeteria roenbergensis. Seventy-five percent of the best matches of PgV-16T-predicted proteins correspond to two viruses [Organic Lake phycodnavirus (OLPV)1 and OLPV2] from a hypersaline lake in Antarctica (Organic Lake), the hosts of which are unknown. As for OLPVs and other Megaviridae, the PgV-16T sequence data revealed the presence of a virophage-like genome. However, no virophage particle was detected in infected P. globosa cultures. The presence of many genes found only in Megaviridae in its genome and the presence of an associated virophage strongly suggest that PgV-16T shares a common ancestry with the largest known dsDNA viruses, the host range of which already encompasses the earliest diverging branches of domain Eukarya.}, }
@article {pmid23752350, year = {2013}, author = {Yuan, Y and Xu, W and He, X and Liu, H and Cao, S and Qi, X and Huang, K and Luo, Y}, title = {Effects of genetically modified T2A-1 rice on the GI health of rats after 90-day supplement.}, journal = {Scientific reports}, volume = {3}, number = {}, pages = {1962}, pmid = {23752350}, issn = {2045-2322}, mesh = {Animals ; Electrophoresis, Polyacrylamide Gel ; Gastrointestinal Tract/*drug effects/microbiology ; Gene Transfer, Horizontal ; Immunity, Mucosal ; *Oryza/toxicity ; Permeability ; *Plants, Genetically Modified/toxicity ; Rats ; }, abstract = {Bacillus thuringiensis insecticidal toxin (Bt) rice will be commercialized as a main food source. Traditional safety assessments on genetically modified products pay little attention on gastrointestinal (GI) health. More data about GI health of Bt rice must be provided to dispel public' doubts about the potential effects on human health. We constructed an improved safety assessment animal model using a basic subchronic toxicity experiment, measuring a range of parameters including microflora composition, intestinal permeability, epithelial structure, fecal enzymes, bacterial activity, and intestinal immunity. Significant differences were found between rice-fed groups and AIN93G-fed control groups in several parameters, whereas no differences were observed between genetically modified and non-genetically modified groups. No adverse effects were found on GI health resulting from genetically modified T2A-1 rice. In conclusion, this study may offer a systematic safety assessment model for GM material with respect to the effects on GI health.}, }
@article {pmid23750949, year = {2013}, author = {Coombes, BK}, title = {Regulatory evolution at the host-pathogen interface.}, journal = {Canadian journal of microbiology}, volume = {59}, number = {6}, pages = {365-367}, doi = {10.1139/cjm-2013-0300}, pmid = {23750949}, issn = {1480-3275}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Awards and Prizes ; Bacteria/*genetics/*pathogenicity ; Biological Evolution ; DNA, Bacterial/genetics ; *Evolution, Molecular ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Variation ; Genome, Bacterial ; *Host-Pathogen Interactions ; Mutation ; Regulatory Sequences, Nucleic Acid ; }, abstract = {Horizontal gene transfer plays a major role in microbial evolution by innovating the bacterial genome with new genetic blueprints to adapt to previously unexploited niches. However, to benefit from these genetic acquisitions, the bacterium must integrate the expression of these new genes into existing regulatory nodes and deploy them at the right time. There is much to gain from uncovering the genetic diversity in noncoding DNA that is selective during host infection because of the beneficial effect it has on bacterial gene expression. By identifying genes that have undergone regulatory evolution, a deeper understanding of the arms race between host and pathogen is gained.}, }
@article {pmid23750729, year = {2013}, author = {Bonnin, RA and Nordmann, P and Poirel, L}, title = {Screening and deciphering antibiotic resistance in Acinetobacter baumannii: a state of the art.}, journal = {Expert review of anti-infective therapy}, volume = {11}, number = {6}, pages = {571-583}, doi = {10.1586/eri.13.38}, pmid = {23750729}, issn = {1744-8336}, mesh = {Acinetobacter Infections/diagnosis/drug therapy/microbiology ; Acinetobacter baumannii/drug effects/enzymology/*genetics ; Aminoglycosides/pharmacology ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/*genetics/metabolism ; Bacterial Typing Techniques ; Carbapenems/*pharmacology ; Cephalosporins/pharmacology ; Colistin/pharmacology ; Drug Resistance, Multiple, Bacterial/drug effects/*genetics ; Gene Expression ; Gene Transfer, Horizontal ; Humans ; Minocycline/analogs &amp; derivatives/pharmacology ; Mutation ; Tigecycline ; beta-Lactam Resistance/drug effects/*genetics ; beta-Lactamases/*genetics/metabolism ; }, abstract = {Acinetobacter baumannii, recognized as a serious threat in healthcare facilities, has the ability to develop resistance to antibiotics quite easily. This resistance is related to either gene acquisition (horizontal gene transfer) or mutations in the genome, leading to gene disruption, over- or down-expression of genes. The clinically relevant antibiotic resistances in A. baumannii include resistance to aminoglycosides, broad-spectrum cephalosporins, carbapenems, tigecycline and colistin, which are the last resort antibiotics. The intrinsic and acquired resistance mechanisms of A. baumannii are presented here, with special focus on β-lactam resistance. The most up-to-date techniques for identification, including phenotypical and molecular tests, and screening of those emerging resistance traits are also highlighted. The implementation of early detection and identification of multidrug-resistant A. baumannii is crucial to control their spread.}, }
@article {pmid23750294, year = {2013}, author = {Redrejo-Rodríguez, M and Muñoz-Espín, D and Holguera, I and Mencía, M and Salas, M}, title = {Nuclear localization signals in phage terminal proteins provide a novel gene delivery tool in mammalian cells.}, journal = {Communicative &amp; integrative biology}, volume = {6}, number = {2}, pages = {e22829}, pmid = {23750294}, issn = {1942-0889}, abstract = {Terminal proteins (TPs) of bacteriophages prime DNA replication and become covalently linked to the genome ends. Unexpectedly, we have found functional eukaryotic nuclear localization signals (NLSs) within the TP sequences of bacteriophages from diverse families and hosts. Given the role of bacteriophages as vehicles for horizontal gene transfer (HGT), we postulated that viral genomes that have covalently linked NLS-containing terminal proteins might behave as vectors for HGT between bacteria and the eukaryotic nucleus. To validate this hypothesis, we profited from the in vitro Φ29 amplification system that allows the amplification of heterologous DNAs producing linear molecules of DNA with TP covalently attached to both 5' ends. Interestingly, these in vitro-generated TP-DNA molecules showed enhanced gene delivery in mammalian cells, supporting a possible role in HGT by transferring genes between prokaryotes and eukaryotes. Moreover, these TP-DNA molecules are a useful tool to amplify and subsequently deliver genes efficiently into the eukaryotic nucleus. Here, we suggest various possible applications and further developments of the technique with biotechnological and therapeutic purposes.}, }
@article {pmid23749975, year = {2013}, author = {Borziak, K and Fleetwood, AD and Zhulin, IB}, title = {Chemoreceptor gene loss and acquisition via horizontal gene transfer in Escherichia coli.}, journal = {Journal of bacteriology}, volume = {195}, number = {16}, pages = {3596-3602}, pmid = {23749975}, issn = {1098-5530}, support = {R01 GM072285/GM/NIGMS NIH HHS/United States ; GM072295/GM/NIGMS NIH HHS/United States ; }, mesh = {Chemotaxis/*physiology ; Databases, Factual ; Escherichia coli/genetics/*metabolism ; Escherichia coli Proteins/genetics/*metabolism ; Gene Deletion ; Gene Expression Regulation, Bacterial/*physiology ; Gene Transfer, Horizontal/*physiology ; Genome, Bacterial ; Phylogeny ; }, abstract = {Chemotaxis allows bacteria to more efficiently colonize optimal microhabitats within their larger environment. Chemotaxis in Escherichia coli is the best-studied model system, and a large number of E. coli strains have been sequenced. The Escherichia/Shigella genus encompasses a great variety of commensal and pathogenic strains, but the role of chemotaxis in their association with the host remains poorly understood. Here we show that the core chemotaxis genes are lost in many, but not all, nonmotile strains but are well preserved in all motile strains. The genes encoding the Tar, Tsr, and Aer chemoreceptors, which mediate chemotaxis to a broad spectrum of chemical and physical cues, are also nearly uniformly conserved in motile strains. In contrast, the clade of extraintestinal pathogenic E. coli strains apparently underwent an ancestral loss of Trg and Tap chemoreceptors, which sense sugars, dipeptides, and pyrimidines. The broad range of time estimated for the loss of these genes (1 to 3 million years ago) corresponds to the appearance of the genus Homo.}, }
@article {pmid23748443, year = {2013}, author = {Modi, SR and Lee, HH and Spina, CS and Collins, JJ}, title = {Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome.}, journal = {Nature}, volume = {499}, number = {7457}, pages = {219-222}, pmid = {23748443}, issn = {1476-4687}, support = {DP1 OD003644/OD/NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Aerobiosis ; Ampicillin/pharmacology ; Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteriophages/*drug effects/genetics/isolation &amp; purification ; Ciprofloxacin/pharmacology ; Drug Resistance, Microbial/*drug effects/genetics ; Feces/*microbiology/*virology ; Female ; Gene Transfer, Horizontal/drug effects/genetics ; Genes, Viral/drug effects/genetics ; Genome, Viral/*genetics ; Host Specificity/drug effects ; Metagenome/drug effects/*genetics ; Mice ; Symbiosis/drug effects/genetics ; }, abstract = {The mammalian gut ecosystem has considerable influence on host physiology, but the mechanisms that sustain this complex environment in the face of different stresses remain obscure. Perturbations to the gut ecosystem, such as through antibiotic treatment or diet, are at present interpreted at the level of bacterial phylogeny. Less is known about the contributions of the abundant population of phages to this ecological network. Here we explore the phageome as a potential genetic reservoir for bacterial adaptation by sequencing murine faecal phage populations following antibiotic perturbation. We show that antibiotic treatment leads to the enrichment of phage-encoded genes that confer resistance via disparate mechanisms to the administered drug, as well as genes that confer resistance to antibiotics unrelated to the administered drug, and we demonstrate experimentally that phages from treated mice provide aerobically cultured naive microbiota with increased resistance. Systems-wide analyses uncovered post-treatment phage-encoded processes related to host colonization and growth adaptation, indicating that the phageome becomes broadly enriched for functionally beneficial genes under stress-related conditions. We also show that antibiotic treatment expands the interactions between phage and bacterial species, leading to a more highly connected phage-bacterial network for gene exchange. Our work implicates the phageome in the emergence of multidrug resistance, and indicates that the adaptive capacity of the phageome may represent a community-based mechanism for protecting the gut microflora, preserving its functional robustness during antibiotic stress.}, }
@article {pmid23747695, year = {2013}, author = {Meinersmann, RJ and Lindsey, RL and Bono, JL and Smith, TP and Oakley, BB}, title = {Proposed model for the high rate of rearrangement and rapid migration observed in some IncA/C plasmid lineages.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {16}, pages = {4806-4814}, pmid = {23747695}, issn = {1098-5336}, mesh = {Bacteria/*genetics/metabolism ; DNA, Bacterial/*genetics/metabolism ; Evolution, Molecular ; Molecular Sequence Data ; *Open Reading Frames ; Phylogeny ; Plasmids/*genetics/metabolism ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {IncA/C plasmids are a class of plasmids from the Enterobacteriaceae that are relatively large (49 to >180 kbp), that are readily transferred by conjugation, and that carry multiple antimicrobial resistance genes. Reconstruction of the phylogeny of these plasmids has been difficult because of the high rate of remodeling by recombination-mediated horizontal gene transfer (HGT). We hypothesized that evaluation of nucleotide polymorphisms relative to the rate of HGT would help to develop a clock to show whether anthropic practices have had significant influences on the lineages of the plasmid. A system was developed to rapidly sequence up to 191 known open reading frames from each of 39 recently isolated IncA/C plasmids from a diverse panel of Salmonella enterica and Escherichia coli strains. With these data plus sequences from GenBank, we were able to distinguish six distinct lineages that had extremely low numbers of polymorphisms within each lineage, especially among the largest group designated as group 1. Two regions, each about half the plasmid in size, could be distinguished with a separate lineal pattern. The distribution of group 1 showed that it has migrated extremely rapidly with fewer polymorphisms than can be expected in 2,000 years. Remodeling by frequent HGT was evident, with a pattern that appeared to have the highest rate just upstream of the putative conjugation origin of transfer (oriT). It seems likely that when an IncA/C plasmid is transferred by conjugation there is an opportunity for plasmid remodeling adjacent to the oriT, which was also adjacent to a multiple antimicrobial resistance gene cassette.}, }
@article {pmid23746269, year = {2013}, author = {Kandiba, L and Eichler, J}, title = {Analysis of putative nonulosonic acid biosynthesis pathways in Archaea reveals a complex evolutionary history.}, journal = {FEMS microbiology letters}, volume = {345}, number = {2}, pages = {110-120}, doi = {10.1111/1574-6968.12193}, pmid = {23746269}, issn = {1574-6968}, mesh = {Archaea/classification/enzymology/genetics/*metabolism ; Archaeal Proteins/genetics/*metabolism ; *Biological Evolution ; *Biosynthetic Pathways ; Glycosylation ; Phylogeny ; Sugar Acids/*metabolism ; }, abstract = {Sialic acids and the other nonulosonic acid sugars, legionaminic acid and pseudaminic acid, are nine carbon-containing sugars that can be detected as components of the glycans decorating proteins and other molecules in Eukarya and Bacteria. Yet, despite the prevalence of N-glycosylation in Archaea and the variety of sugars recruited for the archaeal version of this post-translational modification, only a single report of a nonulosonic acid sugar in an archaeal N-linked glycan has appeared. Hence, to obtain a clearer picture of nonulosonic acid sugar biosynthesis capability in Archaea, 122 sequenced genomes were scanned for the presence of genes involved in the biogenesis of these sugars. The results reveal that while Archaea and Bacteria share a common route of sialic acid biosynthesis, numerous archaeal nonulosonic acid sugar biosynthesis pathway components were acquired from elsewhere via various routes. Still, the limited number of Archaea encoding components involved in the synthesis of nonulosonic acid sugars implies that such saccharides are not major components of glycans in this domain.}, }
@article {pmid23742619, year = {2013}, author = {Ma, Z and Geng, J and Yi, L and Xu, B and Jia, R and Li, Y and Meng, Q and Fan, H and Hu, S}, title = {Insight into the specific virulence related genes and toxin-antitoxin virulent pathogenicity islands in swine streptococcosis pathogen Streptococcus equi ssp. zooepidemicus strain ATCC35246.}, journal = {BMC genomics}, volume = {14}, number = {}, pages = {377}, pmid = {23742619}, issn = {1471-2164}, mesh = {Animals ; Bacterial Proteins/*genetics/metabolism ; Bacterial Toxins/*genetics ; Genome, Bacterial/genetics ; Genomic Islands/*genetics ; Genomics ; Streptococcal Infections/*microbiology ; Streptococcus equi/*genetics/*pathogenicity ; Swine/*microbiology ; Swine Diseases/microbiology ; Transcriptome ; }, abstract = {BACKGROUND: Streptococcus equi ssp. zooepidemicus (S. zooepidemicus) is an important pathogen causing swine streptococcosis in China. Pathogenicity islands (PAIs) of S. zooepidemicus have been transferred among bacteria through horizontal gene transfer (HGT) and play important roles in the adaptation and increased virulence of S. zooepidemicus. The present study used comparative genomics to examine the different pathogenicities of S. zooepidemicus.<br><br>RESULTS: Genome of S. zooepidemicus ATCC35246 (Sz35246) comprises 2,167,264-bp of a single circular chromosome, with a GC content of 41.65%. Comparative genome analysis of Sz35246, S. zooepidemicus MGCS10565 (Sz10565), Streptococcus equi. ssp. equi. 4047 (Se4047) and S. zooepidemicus H70 (Sz70) identified 320 Sz35246-specific genes, clustered into three toxin-antitoxin (TA) systems PAIs and one restriction modification system (RM system) PAI. These four acquired PAIs encode proteins that may contribute to the overall pathogenic capacity and fitness of this bacterium to adapt to different hosts. Analysis of the in vivo and in vitro transcriptomes of this bacterium revealed differentially expressed PAI genes and non-PAI genes, suggesting that Sz35246 possess mechanisms for infecting animals and adapting to a wide range of host environments. Analysis of the genome identified potential Sz35246 virulence genes. Genes of the Fim III operon were presumed to be involved in breaking the host-restriction of Sz35246.<br><br>CONCLUSION: Genome wide comparisons of Sz35246 with three other strains and transcriptome analysis revealed novel genes related to bacterial virulence and breaking the host-restriction. Four specific PAIs, which were judged to have been transferred into Sz35246 genome through HGT, were identified for the first time. Further analysis of the TA and RM systems in the PAIs will improve our understanding of the pathogenicity of this bacterium and could lead to the development of diagnostics and vaccines.}, }
@article {pmid23741559, year = {2013}, author = {Olsen, I and Tribble, GD and Fiehn, NE and Wang, BY}, title = {Bacterial sex in dental plaque.}, journal = {Journal of oral microbiology}, volume = {5}, number = {}, pages = {}, pmid = {23741559}, issn = {2000-2297}, support = {R01 DE019634/DE/NIDCR NIH HHS/United States ; }, abstract = {Genes are transferred between bacteria in dental plaque by transduction, conjugation, and transformation. Membrane vesicles can also provide a mechanism for horizontal gene transfer. DNA transfer is considered bacterial sex, but the transfer is not parallel to processes that we associate with sex in higher organisms. Several examples of bacterial gene transfer in the oral cavity are given in this review. How frequently this occurs in dental plaque is not clear, but evidence suggests that it affects a number of the major genera present. It has been estimated that new sequences in genomes established through horizontal gene transfer can constitute up to 30% of bacterial genomes. Gene transfer can be both inter- and intrageneric, and it can also affect transient organisms. The transferred DNA can be integrated or recombined in the recipient's chromosome or remain as an extrachromosomal inheritable element. This can make dental plaque a reservoir for antimicrobial resistance genes. The ability to transfer DNA is important for bacteria, making them better adapted to the harsh environment of the human mouth, and promoting their survival, virulence, and pathogenicity.}, }
@article {pmid23741407, year = {2013}, author = {Ghosh, W and Alam, M and Roy, C and Pyne, P and George, A and Chakraborty, R and Majumder, S and Agarwal, A and Chakraborty, S and Majumdar, S and Gupta, SK}, title = {Genome implosion elicits host-confinement in Alcaligenaceae: evidence from the comparative genomics of Tetrathiobacter kashmirensis, a pathogen in the making.}, journal = {PloS one}, volume = {8}, number = {5}, pages = {e64856}, pmid = {23741407}, issn = {1932-6203}, mesh = {Alcaligenaceae/*genetics/pathogenicity ; Bacterial Adhesion ; Base Composition ; Betaproteobacteria/genetics/pathogenicity ; Biological Evolution ; Cell Line ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; Genomics ; Hemolysis ; *Host-Pathogen Interactions ; Humans ; Molecular Sequence Annotation ; Open Reading Frames ; Recombination, Genetic ; Virulence Factors/genetics ; }, abstract = {This study elucidates the genomic basis of the evolution of pathogens alongside free-living organisms within the family Alcaligenaceae of Betaproteobacteria. Towards that end, the complete genome sequence of the sulfur-chemolithoautotroph Tetrathiobacter kashmirensis WT001(T) was determined and compared with the soil isolate Achromobacter xylosoxidans A8 and the two pathogens Bordetella bronchiseptica RB50 and Taylorella equigenitalis MCE9. All analyses comprehensively indicated that the RB50 and MCE9 genomes were almost the subsets of A8 and WT001(T), respectively. In the immediate evolutionary past Achromobacter and Bordetella shared a common ancestor, which was distinct from the other contemporary stock that gave rise to Tetrathiobacter and Taylorella. The Achromobacter-Bordetella precursor, after diverging from the family ancestor, evolved through extensive genome inflation, subsequent to which the two genera separated via differential gene losses and acquisitions. Tetrathiobacter, meanwhile, retained the core characteristics of the family ancestor, and Taylorella underwent massive genome degeneration to reach an evolutionary dead-end. Interestingly, the WT001(T) genome, despite its conserved architecture, had only 85% coding density, besides which 578 out of its 4452 protein-coding sequences were found to be pseudogenized. Translational impairment of several DNA repair-recombination genes in the first place seemed to have ushered the rampant and indiscriminate frame-shift mutations across the WT001(T) genome. Presumably, this strain has just come out of a recent evolutionary bottleneck, representing a unique transition state where genome self-degeneration has started comprehensively but selective host-confinement has not yet set in. In the light of this evolutionary link, host-adaptation of Taylorella clearly appears to be the aftereffect of genome implosion in another member of the same bottleneck. Remarkably again, potent virulence factors were found widespread in Alcaligenaceae, corroborating which hemolytic and mammalian cell-adhering abilities were discovered in WT001(T). So, while WT001(T) relatives/derivatives in nature could be going the Taylorella way, the lineage as such was well-prepared for imminent host-confinement.}, }
@article {pmid23741025, year = {2013}, author = {Du, XX and Wang, JF and Fu, Y and Zhao, F and Chen, Y and Wang, HP and Yu, YS}, title = {Genetic characteristics of blaNDM-1-positive plasmid in Citrobacter freundii isolate separated from a clinical infectious patient.}, journal = {Journal of medical microbiology}, volume = {62}, number = {Pt 9}, pages = {1332-1337}, doi = {10.1099/jmm.0.057091-0}, pmid = {23741025}, issn = {1473-5644}, mesh = {Acinetobacter/genetics ; Anti-Bacterial Agents/pharmacology ; Base Sequence ; Citrobacter freundii/enzymology/*genetics/isolation &amp; purification ; Conjugation, Genetic ; DNA Transposable Elements ; Enterobacteriaceae Infections/diagnosis ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Variation ; Humans ; Male ; Middle Aged ; Plasmids/*genetics/metabolism ; Urinary Tract Infections/microbiology ; beta-Lactamases/*genetics/metabolism ; }, abstract = {This study reports an infectious case involving an (NDM-1)-producing Citrobacter freundii and further explored the potential threat of the bla(NDM-1) gene by analysing the characteristics of the (NDM-1)-encoding plasmid sequence. A bla(NDM-1)-positive C. freundii with high resistance to carbapenems was separated from a clinical patient suffering from a urinary tract infection. S1 nuclease-based plasmid analysis followed by Southern blot hybridization, a conjugation experiment and electrotransformation confirmed that the bla(NDM-1) gene was located on a plasmid. High-throughput sequencing of the bla(NDM-1)-positive plasmid (pCFNDM-CN) showed that it was a 54 kb IncX-type plasmid and contained a backbone region and a variable region with two β-lactamase genes (bla(NDM-1) and bla(SHV-12)). The NDM-1 composite transposon in the variable region was surrounded by IS26 and IS5-truncated ISAba125, and shared a high sequence similarity to the bla(NDM-1) surrounding structure in Acinetobacter spp. Our research suggested that the NDM-1 composite transposon might play an essential role in mobilization of the bla(NDM-1) gene from Acinetobacter spp. to Enterobacteriaceae.}, }
@article {pmid23739538, year = {2013}, author = {Skovgaard, S and Larsen, MH and Nielsen, LN and Skov, RL and Wong, C and Westh, H and Ingmer, H}, title = {Recently introduced qacA/B genes in Staphylococcus epidermidis do not increase chlorhexidine MIC/MBC.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {68}, number = {10}, pages = {2226-2233}, doi = {10.1093/jac/dkt182}, pmid = {23739538}, issn = {1460-2091}, mesh = {Bacterial Proteins/*genetics ; Chlorhexidine/*pharmacology ; Disinfectants/*pharmacology ; *Drug Tolerance ; *Gene Transfer, Horizontal ; Hand Disinfection/methods ; Humans ; Infection Control/methods ; Membrane Transport Proteins/*genetics ; Microbial Sensitivity Tests ; Nurses ; Staphylococcus epidermidis/*drug effects/genetics/isolation &amp; purification ; }, abstract = {OBJECTIVES: Chlorhexidine is used as a disinfectant to prevent surgical infections. Recently, studies have indicated that chlorhexidine usage has selected methicillin-resistant Staphylococcus aureus strains that are tolerant to chlorhexidine and that this may be related to the presence of the qacA/B-encoded efflux pumps. Here, we evaluated if high-level exposure to chlorhexidine selects for tolerant colonizing Staphylococcus epidermidis and we addressed the consequences of long-term exposure to chlorhexidine.<br><br>METHODS: Chlorhexidine susceptibility and carriage of qacA/B was determined for colonizing S. epidermidis isolated from scrub nurses heavily exposed to chlorhexidine and were compared with isolates from non-users of chlorhexidine hand rubs. S. epidermidis blood isolates from the 1960s, before the wider introduction of chlorhexidine to the market, were also tested and compared with recently collected S. epidermidis blood isolates.<br><br>RESULTS: There was no correlation between the use of chlorhexidine in scrub nurses and the presence of qacA/B genes in S. epidermidis isolates or increased MICs/MBCs of chlorhexidine for S. epidermidis isolates. While 55% of current blood isolates harboured the qacA/B genes, none of the 33 historical S. epidermidis isolates did, although their MICs and MBCs of chlorhexidine were comparable to those for current isolates.<br><br>CONCLUSIONS: Chlorhexidine used as a hand rub does not select for S. epidermidis isolates with increased MICs or MBCs of chlorhexidine. However, the absence of qacA/B genes in S. epidermidis isolates obtained in the 1960s suggests that long-term use of biocides like chlorhexidine or related compounds may select for the presence of qacA/B genes.}, }
@article {pmid23739268, year = {2012}, author = {Cumby, N and Davidson, AR and Maxwell, KL}, title = {The moron comes of age.}, journal = {Bacteriophage}, volume = {2}, number = {4}, pages = {225-228}, pmid = {23739268}, issn = {2159-7073}, abstract = {Prophage-encoded genes can provide a variety of benefits for their bacterial hosts. These beneficial genes are often contained within "moron" elements. Morons, thus termed as the insertion of the DNA encoding them adds "more on" the genome in which they are found, are independent transcriptional units disseminated among phage genomes through horizontal gene transfer. Morons have been identified in the majority of phage genomes and they have been found to play diverse roles in bacterial physiology. At present, we are only beginning to ascribe functions to the many proteins encoded within these ubiquitous genetic elements. Recently, we discovered that the first described moron-encoded protein, gp15 of phage HK97, is expressed from the HK97 prophage and functions as a superinfection exclusion protein, protecting its host from genome injection by other phages. This work and the growing body of data pertaining to other morons challenges the traditional view of phages as purely parasites of bacteria and emphasizes the symbiotic relationship between bacteria and prophages.}, }
@article {pmid23739050, year = {2013}, author = {Goudenège, D and Labreuche, Y and Krin, E and Ansquer, D and Mangenot, S and Calteau, A and Médigue, C and Mazel, D and Polz, MF and Le Roux, F}, title = {Comparative genomics of pathogenic lineages of Vibrio nigripulchritudo identifies virulence-associated traits.}, journal = {The ISME journal}, volume = {7}, number = {10}, pages = {1985-1996}, pmid = {23739050}, issn = {1751-7370}, mesh = {Animals ; Bacterial Toxins/genetics/pharmacology ; Gene Transfer, Horizontal ; Genetic Variation ; Genome, Bacterial/*genetics ; Genomics ; Madagascar ; Microscopy, Electron, Transmission ; New Caledonia ; Penaeidae/drug effects/*microbiology ; Phylogeny ; Plasmids/genetics ; Vibrio/classification/*genetics/isolation &amp; purification/physiology/ultrastructure ; Virulence/*genetics ; }, abstract = {Vibrio nigripulchritudo is an emerging pathogen of farmed shrimp in New Caledonia and other regions in the Indo-Pacific. The molecular determinants of V. nigripulchritudo pathogenicity are unknown; however, molecular epidemiological studies have suggested that pathogenicity is linked to particular lineages. Here, we performed high-throughput sequencing-based comparative genome analysis of 16 V. nigripulchritudo strains to explore the genomic diversity and evolutionary history of pathogen-containing lineages and to identify pathogen-specific genetic elements. Our phylogenetic analysis revealed three pathogen-containing V. nigripulchritudo clades, including two clades previously identified from New Caledonia and one novel clade comprising putatively pathogenic isolates from septicemic shrimp in Madagascar. The similar genetic distance between the three clades indicates that they have diverged from an ancestral population roughly at the same time and recombination analysis indicates that these genomes have, in the past, shared a common gene pool and exchanged genes. As each contemporary lineage is comprised of nearly identical strains, comparative genomics allowed differentiation of genetic elements specific to shrimp pathogenesis of varying severity. Notably, only a large plasmid present in all highly pathogenic (HP) strains encodes a toxin. Although less/non-pathogenic strains contain related plasmids, these are differentiated by a putative toxin locus. Expression of this gene by a non-pathogenic V. nigripulchritudo strain resulted in production of toxic culture supernatant, normally an exclusive feature of HP strains. Thus, this protein, here termed 'nigritoxin', is implicated to an extent that remains to be precisely determined in the toxicity of V. nigripulchritudo.}, }
@article {pmid23738841, year = {2013}, author = {Whitehead, MP and Hooley, P and W Brown, MR}, title = {Horizontal transfer of bacterial polyphosphate kinases to eukaryotes: implications for the ice age and land colonisation.}, journal = {BMC research notes}, volume = {6}, number = {}, pages = {221}, pmid = {23738841}, issn = {1756-0500}, mesh = {Amino Acid Sequence ; Bacteria/*enzymology ; *Gene Transfer, Horizontal ; *Ice ; Molecular Sequence Data ; Phosphotransferases (Phosphate Group Acceptor)/chemistry/genetics/*metabolism ; Phylogeny ; Sequence Homology, Amino Acid ; }, abstract = {BACKGROUND: Studies of online database(s) showed that convincing examples of eukaryote PPKs derived from bacteria type PPK1 and PPK2 enzymes are rare and currently confined to a few simple eukaryotes. These enzymes probably represent several separate horizontal transfer events. Retention of such sequences may be an advantage for tolerance to stresses such as desiccation or nutrient depletion for simple eukaryotes that lack more sophisticated adaptations available to multicellular organisms. We propose that the acquisition of encoding sequences for these enzymes by horizontal transfer enhanced the ability of early plants to colonise the land. The improved ability to sequester and release inorganic phosphate for carbon fixation by photosynthetic algae in the ocean may have accelerated or even triggered global glaciation events. There is some evidence for DNA sequences encoding PPKs in a wider range of eukaryotes, notably some invertebrates, though it is unclear that these represent functional genes.Polyphosphate (poly P) is found in all cells, carrying out a wide range of essential roles. Studied mainly in prokaryotes, the enzymes responsible for synthesis of poly P in eukaryotes (polyphosphate kinases PPKs) are not well understood. The best characterised enzyme from bacteria known to catalyse the formation of high molecular weight polyphosphate from ATP is PPK1 which shows some structural similarity to phospholipase D. A second bacterial PPK (PPK2) resembles thymidylate kinase. Recent reports have suggested a widespread distribution of these bacteria type enzymes in eukaryotes.<br><br>RESULTS: On - line databases show evidence for the presence of genes encoding PPK1 in only a limited number of eukaryotes. These include the photosynthetic eukaryotes Ostreococcus tauri, O. lucimarinus, Porphyra yezoensis, Cyanidioschyzon merolae and the moss Physcomitrella patens, as well as the amoeboid symbiont Capsaspora owczarzaki and the non-photosynthetic eukaryotes Dictyostelium (3 species), Polysphondylium pallidum and Thecamonas trahens. A second bacterial PPK (PPK2) is found in just two eukaryotes (O. tauri and the sea anemone Nematostella vectensis). There is some evidence for PPK1 and PPK2 encoding sequences in other eukaryotes but some of these may be artefacts of bacterial contamination of gene libraries.<br><br>CONCLUSIONS: Evidence for the possible origins of these eukaryote PPK1s and PPK2s and potential prokaryote donors via horizontal gene transfer is presented. The selective advantage of acquiring and maintaining a prokaryote PPK in a eukaryote is proposed to enhance stress tolerance in a changing environment related to the capture and metabolism of inorganic phosphate compounds. Bacterial PPKs may also have enhanced the abilities of marine phytoplankton to sequester phosphate, hence accelerating global carbon fixation.}, }
@article {pmid23738437, year = {2013}, author = {Ji, Y and Lei, T}, title = {Antisense RNA regulation and application in the development of novel antibiotics to combat multidrug resistant bacteria.}, journal = {Science progress}, volume = {96}, number = {Pt 1}, pages = {43-60}, pmid = {23738437}, issn = {0036-8504}, support = {AI057451/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/chemistry/*pharmacology ; Bacteria/*drug effects/genetics/metabolism ; Bacterial Infections/drug therapy/microbiology ; Drug Design ; Drug Resistance, Multiple, Bacterial/drug effects/genetics ; Gene Transfer, Horizontal ; High-Throughput Screening Assays ; Humans ; Mice ; Molecular Targeted Therapy ; Peptide Nucleic Acids/genetics/*pharmacology ; RNA, Antisense/genetics/*pharmacology ; }, abstract = {Despite the availability of antibiotics and vaccines, infectious diseases remain one of most dangerous threats to humans and animals. The overuse and misuse of antibacterial agents have led to the emergence of multidrug resistant bacterial pathogens. Bacterial cells are often resilient enough to survive in even the most extreme environments. To do so, the organisms have evolved different mechanisms, including a variety of two-component signal transduction systems, which allow the bacteria to sense the surrounding environment and regulate gene expression in order to adapt and respond to environmental stimuli. In addition, some bacteria evolve resistance to antibacterial agents while many bacterial cells are able to acquire resistance genes from other bacterial species to enable them to survive in the presence of toxic antimicrobial agents. The crisis of antimicrobial resistance is an unremitting menace to human health and a burden on public health. The rapid increase in antimicrobial resistant organisms and limited options for development of new classes of antibiotics heighten the urgent need to develop novel potent antibacterial therapeutics in order to combat multidrug resistant infections. In this review, we introduce the regulatory mechanisms of antisense RNA and significant applications of regulated antisense RNA interference technology in early drug discovery. This includes the identification and evaluation of drug targets in vitro and in vivo, the determination of mode of action for antibiotics and new antibacterial agents, as well as the development of peptide-nucleic acid conjugates as novel antibacterials.}, }
@article {pmid23737490, year = {2013}, author = {Li, L and Liao, X and Yang, Y and Sun, J and Li, L and Liu, B and Yang, S and Ma, J and Li, X and Zhang, Q and Liu, Y}, title = {Spread of oqxAB in Salmonella enterica serotype Typhimurium predominantly by IncHI2 plasmids.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {68}, number = {10}, pages = {2263-2268}, doi = {10.1093/jac/dkt209}, pmid = {23737490}, issn = {1460-2091}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics ; Blotting, Southern ; China ; DNA, Bacterial/chemistry/genetics ; *Drug Resistance, Multiple, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; *Gene Transfer, Horizontal ; Genotype ; Humans ; Molecular Typing ; Plasmids/*classification ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Quinolones/pharmacology ; Salmonella typhimurium/classification/*genetics ; Sequence Analysis, DNA ; }, abstract = {OBJECTIVES: To investigate the prevalence and genetic environment of the multiresistance gene oqxAB in Salmonella enterica serotype Typhimurium isolated from food-producing animals.<br><br>METHODS: In this study, 63 Salmonella enterica serotype Typhimurium isolates were analysed for the presence of plasmid-mediated quinolone resistance determinants and mutations in the quinolone resistance-determining region by molecular methods (PCR/sequencing). The oqxAB-positive isolates were typed by pulsed-field gel electrophoresis (PFGE). Plasmids carrying oqxAB were studied by conjugation/transformation, replicon typing, Southern hybridization, long-range PCR and restriction fragment length polymorphism (RFLP).<br><br>RESULTS: The oqxAB, aac(6')-Ib-cr and qnrS1 genes were present alone or in combination in 20 (31.7%), 23 (36.5%) and 1 (1.6%) isolate, respectively. The oqxAB-positive isolates were clonally related, as determined by PFGE. All of the oqxAB-aac(6')-Ib-cr-positive isolates carried transferable IncHI2-type plasmids containing an oqxAB cassette and an incomplete class 1 integron harbouring aac(6')-Ib-cr, blaOXA-1, catB3, arr3, qacE&#x394;1 and sul1. Meanwhile, 6 of 15 plasmids carrying both oqxAB and aac(6')-Ib-cr showed identical RFLP patterns.<br><br>CONCLUSIONS: The results suggest that both clonal expansion and horizontal transmission of IncHI2-type plasmids containing oqxAB and aac(6')-Ib-cr may be involved in the spread of oqxAB in Salmonella Typhimurium isolates in food-producing animals in China. There is a great need to monitor the potential dissemination of this multiresistance gene.}, }
@article {pmid23734299, year = {2013}, author = {Kitahara, K and Miyazaki, K}, title = {Revisiting bacterial phylogeny: Natural and experimental evidence for horizontal gene transfer of 16S rRNA.}, journal = {Mobile genetic elements}, volume = {3}, number = {1}, pages = {e24210}, pmid = {23734299}, issn = {2159-2543}, abstract = {Current methods used for phylogenetic classification of prokaryotes largely rely on the sequences of 16S rRNA genes that are ubiquitously present in the cell. Theoretical basis of this methodology is based on the assumption that 16S rRNA genes are only vertically inherited and are thus indigenous to each species. However, microbial genomic analysis has revealed the existence of prokaryotic species containing two types of rRNA (rrn) operons of seemingly different origins. It has also been reported that some bacteria contain 16S rRNA that are mosaics of sequences from multiple species. This suggests that horizontal gene transfer (HGT) occurred for 16S rRNA genes. In addition, a recent HGT experiment mimicking the natural HGT process has shown that a wide range of foreign 16S rRNA genes can be transferred into Escherichia coli, including those from different phylogenetic classes (with a minimum sequence identity of 80.9% to the Escherichia coli 16S rRNA gene). Thus, in contrast to the complexity hypothesis that states informational genes are rarely horizontally transferred between species, 16S rRNA is occasionally amenable to HGT. Results of the current method for rapid identification and classification of prokaryotes based on the 16S rRNA gene should thus be carefully analyzed and interpreted.}, }
@article {pmid23734294, year = {2013}, author = {Hao, W}, title = {Extensive genomic variation within clonal bacterial groups resulted from homologous recombination.}, journal = {Mobile genetic elements}, volume = {3}, number = {1}, pages = {e23463}, pmid = {23734294}, issn = {2159-2543}, abstract = {Due to divergence, genetic variation is generally believed to be high among distantly related strains, low among closely related ones and little or none within the same classified clonal groups. Several recent genome-wide studies, however, revealed that significant genetic variation resides in a considerable number of genes among strains with identical MLST (Multilocus sequence typing) types and much of the variation was introduced by homologous recombination. Recognizing and understanding genomic variation within clonal bacterial groups could shed new light on the evolutionary path of infectious agents and the emergence of particularly pathogenic or virulent variants. This commentary presents our recent contributions to this line of work.}, }
@article {pmid23732852, year = {2013}, author = {Gomez-Valero, L and Buchrieser, C}, title = {Genome dynamics in Legionella: the basis of versatility and adaptation to intracellular replication.}, journal = {Cold Spring Harbor perspectives in medicine}, volume = {3}, number = {6}, pages = {}, pmid = {23732852}, issn = {2157-1422}, mesh = {*Adaptation, Physiological ; Eukaryotic Cells ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; Genetic Variation ; Genetics, Microbial ; *Genome, Bacterial ; Humans ; Legionella/*genetics/*pathogenicity ; Molecular Mimicry ; Phylogeny ; Plasmids/genetics ; Virulence ; Virulence Factors ; }, abstract = {Legionella pneumophila is a bacterial pathogen present in aquatic environments that can cause a severe pneumonia called Legionnaires' disease. Soon after its recognition, it was shown that Legionella replicates inside amoeba, suggesting that bacteria replicating in environmental protozoa are able to exploit conserved signaling pathways in human phagocytic cells. Comparative, evolutionary, and functional genomics suggests that the Legionella-amoeba interaction has shaped this pathogen more than previously thought. A complex evolutionary scenario involving mobile genetic elements, type IV secretion systems, and horizontal gene transfer among Legionella, amoeba, and other organisms seems to take place. This long-lasting coevolution led to the development of very sophisticated virulence strategies and a high level of temporal and spatial fine-tuning of bacteria host-cell interactions. We will discuss current knowledge of the evolution of virulence of Legionella from a genomics perspective and propose our vision of the emergence of this human pathogen from the environment.}, }
@article {pmid23732698, year = {2013}, author = {Bogaerts, P and Huang, TD and Rezende de Castro, R and Bouchahrouf, W and Glupczynski, Y}, title = {Could Acinetobacter pittii act as an NDM-1 reservoir for Enterobacteriaceae?.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {68}, number = {10}, pages = {2414-2415}, doi = {10.1093/jac/dkt201}, pmid = {23732698}, issn = {1460-2091}, mesh = {Acinetobacter/*enzymology/*genetics ; Anti-Bacterial Agents/pharmacology ; DNA Transposable Elements ; Enterobacteriaceae/*enzymology/*genetics ; Gene Order ; *Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; beta-Lactam Resistance ; beta-Lactamases/*genetics/*metabolism ; beta-Lactams/pharmacology ; }, }
@article {pmid23732273, year = {2013}, author = {Porter, MS and Beiko, RG}, title = {SPANNER: taxonomic assignment of sequences using pyramid matching of similarity profiles.}, journal = {Bioinformatics (Oxford, England)}, volume = {29}, number = {15}, pages = {1858-1864}, pmid = {23732273}, issn = {1367-4811}, mesh = {*Algorithms ; *Genome, Microbial ; Genomics/methods ; Metagenome ; Phylogeny ; Sequence Alignment/*methods ; }, abstract = {BACKGROUND: Homology-based taxonomic assignment is impeded by differences between the unassigned read and reference database, forcing a rank-specific classification to the closest (and possibly incorrect) reference lineage. This assignment may be correct only to a general rank (e.g. order) and incorrect below that rank (e.g. family and genus). Algorithms like LCA avoid this by varying the predicted taxonomic rank based on matches to a set of taxonomic references. LCA and related approaches can be conservative, especially if best matches are taxonomically widespread because of events such as lateral gene transfer (LGT).<br><br>RESULTS: Our extension to LCA called SPANNER (similarity profile annotater) uses the set of best homology matches (the LCA Profile) for a given sequence and compares this profile with a set of profiles inferred from taxonomic reference organisms. SPANNER provides an assignment that is less sensitive to LGT and other confounding phenomena. In a series of trials on real and artificial datasets, SPANNER outperformed LCA-style algorithms in terms of taxonomic precision and outperformed best BLAST at certain levels of taxonomic novelty in the dataset. We identify examples where LCA made an overly conservative prediction, but SPANNER produced a more precise and correct prediction.<br><br>CONCLUSIONS: By using profiles of homology matches to represent patterns of genomic similarity that arise because of vertical and lateral inheritance, SPANNER offers an effective compromise between taxonomic assignment based on best BLAST scores, and the conservative approach of LCA and similar approaches.<br><br>AVAILABILITY: C++ source code and binaries are freely available at http://kiwi.cs.dal.ca/Software/SPANNER.<br><br>CONTACT: beiko@cs.dal.ca<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid23729651, year = {2013}, author = {Rusconi, B and Greub, G}, title = {Discovery of catalases in members of the Chlamydiales order.}, journal = {Journal of bacteriology}, volume = {195}, number = {16}, pages = {3543-3551}, pmid = {23729651}, issn = {1098-5530}, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics/*metabolism ; Binding Sites ; Catalase/*classification/genetics/*metabolism ; Chlamydiales/*enzymology/genetics/*metabolism ; Cloning, Molecular ; Epitopes ; Gene Expression Regulation, Bacterial/*physiology ; Gene Expression Regulation, Enzymologic/*physiology ; Heme/genetics/metabolism ; Models, Molecular ; Phylogeny ; Protein Binding ; Protein Conformation ; }, abstract = {Catalase is an important virulence factor for survival in macrophages and other phagocytic cells. In Chlamydiaceae, no catalase had been described so far. With the sequencing and annotation of the full genomes of Chlamydia-related bacteria, the presence of different catalase-encoding genes has been documented. However, their distribution in the Chlamydiales order and the functionality of these catalases remain unknown. Phylogeny of chlamydial catalases was inferred using MrBayes, maximum likelihood, and maximum parsimony algorithms, allowing the description of three clade 3 and two clade 2 catalases. Only monofunctional catalases were found (no catalase-peroxidase or Mn-catalase). All presented a conserved catalytic domain and tertiary structure. Enzymatic activity of cloned chlamydial catalases was assessed by measuring hydrogen peroxide degradation. The catalases are enzymatically active with different efficiencies. The catalase of Parachlamydia acanthamoebae is the least efficient of all (its catalytic activity was 2 logs lower than that of Pseudomonas aeruginosa). Based on the phylogenetic analysis, we hypothesize that an ancestral class 2 catalase probably was present in the common ancestor of all current Chlamydiales but was retained only in Criblamydia sequanensis and Neochlamydia hartmannellae. The catalases of class 3, present in Estrella lausannensis and Parachlamydia acanthamoebae, probably were acquired by lateral gene transfer from Rhizobiales, whereas for Waddlia chondrophila they likely originated from Legionellales or Actinomycetales. The acquisition of catalases on several occasions in the Chlamydiales suggests the importance of this enzyme for the bacteria in their host environment.}, }
@article {pmid23729633, year = {2013}, author = {López-Pérez, M and Gonzaga, A and Rodriguez-Valera, F}, title = {Genomic diversity of "deep ecotype" Alteromonas macleodii isolates: evidence for Pan-Mediterranean clonal frames.}, journal = {Genome biology and evolution}, volume = {5}, number = {6}, pages = {1220-1232}, pmid = {23729633}, issn = {1759-6653}, mesh = {Alteromonas/*genetics ; Base Sequence ; Ecotype ; Gene Transfer, Horizontal ; *Genetic Variation ; Genome, Bacterial ; Genomic Islands ; Mediterranean Region ; Molecular Sequence Data ; Polymorphism, Single Nucleotide ; Recombination, Genetic ; }, abstract = {We have compared genomes of Alteromonas macleodii "deep ecotype" isolates from two deep Mediterranean sites and two surface samples from the Aegean and the English Channel. A total of nine different genomes were analyzed. They belong to five clonal frames (CFs) that differ among them by approximately 30,000 single-nucleotide polymorphisms (SNPs) over their core genomes. Two of the CFs contain three strains each with nearly identical genomes (~100 SNPs over the core genome). One of the CFs had representatives that were isolated from samples taken more than 1,000 km away, 2,500 m deeper, and 5 years apart. These data mark the longest proven persistence of a CF in nature (outside of clinical settings). We have found evidence for frequent recombination events between or within CFs and even with the distantly related A. macleodii surface ecotype. The different CFs had different flexible genomic islands. They can be classified into two groups; one type is additive, that is, containing different numbers of gene cassettes, and is very variable in short time periods (they often varied even within a single CF). The other type was more stable and produced the complete replacement of a genomic fragment by another with different genes. Although this type was more conserved within each CF, we found examples of recombination among distantly related CFs including English Channel and Mediterranean isolates.}, }
@article {pmid23723974, year = {2013}, author = {Lefeuvre, P and Cellier, G and Remenant, B and Chiroleu, F and Prior, P}, title = {Constraints on genome dynamics revealed from gene distribution among the Ralstonia solanacearum species.}, journal = {PloS one}, volume = {8}, number = {5}, pages = {e63155}, pmid = {23723974}, issn = {1932-6203}, mesh = {Base Sequence ; DNA Probes/metabolism ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/*genetics ; Phylogeny ; Ralstonia solanacearum/*genetics ; }, abstract = {Because it is suspected that gene content may partly explain host adaptation and ecology of pathogenic bacteria, it is important to study factors affecting genome composition and its evolution. While recent genomic advances have revealed extremely large pan-genomes for some bacterial species, it remains difficult to predict to what extent gene pool is accessible within or transferable between populations. As genomes bear imprints of the history of the organisms, gene distribution pattern analyses should provide insights into the forces and factors at play in the shaping and maintaining of bacterial genomes. In this study, we revisited the data obtained from a previous CGH microarrays analysis in order to assess the genomic plasticity of the R. solanacearum species complex. Gene distribution analyses demonstrated the remarkably dispersed genome of R. solanacearum with more than half of the genes being accessory. From the reconstruction of the ancestral genomes compositions, we were able to infer the number of gene gain and loss events along the phylogeny. Analyses of gene movement patterns reveal that factors associated with gene function, genomic localization and ecology delineate gene flow patterns. While the chromosome displayed lower rates of movement, the megaplasmid was clearly associated with hot-spots of gene gain and loss. Gene function was also confirmed to be an essential factor in gene gain and loss dynamics with significant differences in movement patterns between different COG categories. Finally, analyses of gene distribution highlighted possible highways of horizontal gene transfer. Due to sampling and design bias, we can only speculate on factors at play in this gene movement dynamic. Further studies examining precise conditions that favor gene transfer would provide invaluable insights in the fate of bacteria, species delineation and the emergence of successful pathogens.}, }
@article {pmid23723195, year = {2013}, author = {Finley, RL and Collignon, P and Larsson, DG and McEwen, SA and Li, XZ and Gaze, WH and Reid-Smith, R and Timinouni, M and Graham, DW and Topp, E}, title = {The scourge of antibiotic resistance: the important role of the environment.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {57}, number = {5}, pages = {704-710}, doi = {10.1093/cid/cit355}, pmid = {23723195}, issn = {1537-6591}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects ; Bacterial Infections/*epidemiology/microbiology/*veterinary ; *Drug Resistance, Bacterial ; Drug Utilization/standards ; Gene Transfer, Horizontal ; Humans ; Selection, Genetic ; Water Purification/methods ; }, abstract = {Antibiotic resistance and associated genes are ubiquitous and ancient, with most genes that encode resistance in human pathogens having originated in bacteria from the natural environment (eg, β-lactamases and fluoroquinolones resistance genes, such as qnr). The rapid evolution and spread of "new" antibiotic resistance genes has been enhanced by modern human activity and its influence on the environmental resistome. This highlights the importance of including the role of the environmental vectors, such as bacterial genetic diversity within soil and water, in resistance risk management. We need to take more steps to decrease the spread of resistance genes in environmental bacteria into human pathogens, to decrease the spread of resistant bacteria to people and animals via foodstuffs, wastes and water, and to minimize the levels of antibiotics and antibiotic-resistant bacteria introduced into the environment. Reducing this risk must include improved management of waste containing antibiotic residues and antibiotic-resistant microorganisms.}, }
@article {pmid23721858, year = {2013}, author = {Dziewit, L and Grzesiak, J and Ciok, A and Nieckarz, M and Zdanowski, MK and Bartosik, D}, title = {Sequence determination and analysis of three plasmids of Pseudomonas sp. GLE121, a psychrophile isolated from surface ice of Ecology Glacier (Antarctica).}, journal = {Plasmid}, volume = {70}, number = {2}, pages = {254-262}, doi = {10.1016/j.plasmid.2013.05.007}, pmid = {23721858}, issn = {1095-9890}, mesh = {Antarctic Regions ; Base Sequence ; Computational Biology ; Disk Diffusion Antimicrobial Tests ; Gene Transfer, Horizontal/genetics ; Ice Cover/*microbiology ; Molecular Sequence Data ; Pili, Sex/genetics ; Plasmids/*genetics ; Pseudomonas/*genetics ; Sequence Analysis, DNA ; }, abstract = {Pseudomonas sp. GLE121 (a psychrophilic Antarctic strain) carries three plasmids: pGLE121P1 (6899 bp), pGLE121P2 (8330 bp) and pGLE121P3 (39,583 bp). Plasmids pGLE121P1 and pGLE121P2 show significant sequence similarity to members of the IncP-9 and IncP-7 incompatibility groups, respectively, while the largest replicon, pGLE121P3, is highly related to plasmid pNCPPB880-40 of Pseudomonas syringae pathovar tomato NCPPB880. All three plasmids have a narrow host range, limited to members of the genus Pseudomonas. Plasmid pGLE121P3 encodes a conjugal transfer system, while pGLE121P1 carries only a putative MOB module, conserved in many mobilizable plasmids. Plasmid pGLE121P3 contains an additional load of genetic information, including a pair of genes with homology to the rulAB operon, responsible for ultraviolet radiation (UVR) tolerance. Given the increasing UV exposure in Antarctic regions, the expression of these genes is likely to be an important adaptive response.}, }
@article {pmid23719233, year = {2013}, author = {Rodrigues, C and Machado, E and Peixe, L and Novais, A}, title = {IncI1/ST3 and IncN/ST1 plasmids drive the spread of blaTEM-52 and blaCTX-M-1/-32 in diverse Escherichia coli clones from different piggeries.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {68}, number = {10}, pages = {2245-2248}, doi = {10.1093/jac/dkt187}, pmid = {23719233}, issn = {1460-2091}, mesh = {Animals ; Electrophoresis, Gel, Pulsed-Field ; Environmental Microbiology ; Escherichia coli/classification/*genetics/isolation &amp; purification ; Escherichia coli Infections/microbiology/*veterinary ; *Gene Transfer, Horizontal ; Genotype ; Multilocus Sequence Typing ; *Plasmids ; Polymorphism, Restriction Fragment Length ; Portugal ; Swine ; beta-Lactam Resistance ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: The spread of ESBL-producing Enterobacteriaceae among food animals/products has raised concerns about their possible transmission through the food chain. We aimed to characterize piggeries (pigs, piggery environments) as reservoirs of TEM-52- and CTX-M-encoding plasmids and clones.<br><br>METHODS: Forty-three samples from five Portuguese intensive production farms were studied (2006-07). Twenty-two ESBL-producing (13 TEM-52, 6 CTX-M-32, 3 CTX-M-1) Escherichia coli isolates from healthy pigs, feed and liquid manure were further characterized. Standard methods were used for clonal (PFGE, MLST) and plasmid (S1-PFGE, replicon typing, pMLST, RFLP) analysis. PCR and sequencing were used for analysis of blaCTX-M genetic context and plasmid-mediated quinolone resistance genes.<br><br>RESULTS: TEM-52 (n = 13/22; 59%), CTX-M-32 (n = 6/22; 27%) and CTX-M-1 (n = 3/22; 14%) were identified in feed (36%), swine faeces (36%), swine hide (9%) and liquid manure (18%) at different farms. Diverse phylogenetic groups and clones were identified among TEM-52 (7 A, 3 B1, 2 B2, 1 D; 8 clones)-producing, CTX-M-1 (1 A, 1 B1, 1 D; 3 clones)-producing and CTX-M-32 (4 A, 2 B1; 4 clones)-producing isolates. However, the ST10 clonal complex was frequent among TEM-52 (n = 6) and CTX-M-32 (n = 3) producers. blaTEM-52 and blaCTX-M-1/-32 genes were identified within epidemic IncI1/ST3 and IncN/ST1 plasmid variants, respectively.<br><br>CONCLUSIONS: We report for the first time a piggery reservoir for blaTEM-52. The spread of blaTEM-52 and blaCTX-M-1/-32 within and/or between different piggeries was mostly associated with epidemic plasmids and clones previously identified in humans and other animal hosts in different EU countries, highlighting possible distribution along the food chain.}, }
@article {pmid23716048, year = {2013}, author = {Xiong, J and Alexander, DC and Ma, JH and Déraspe, M and Low, DE and Jamieson, FB and Roy, PH}, title = {Complete sequence of pOZ176, a 500-kilobase IncP-2 plasmid encoding IMP-9-mediated carbapenem resistance, from outbreak isolate Pseudomonas aeruginosa 96.}, journal = {Antimicrobial agents and chemotherapy}, volume = {57}, number = {8}, pages = {3775-3782}, pmid = {23716048}, issn = {1098-6596}, mesh = {Bacterial Proteins/chemistry/genetics ; Base Composition ; Base Sequence ; Carbapenems/*pharmacology ; DNA Transposable Elements ; Drug Resistance, Multiple, Bacterial ; Evolution, Molecular ; Genome, Bacterial ; Genomic Islands ; Humans ; Microbial Sensitivity Tests ; Multigene Family ; Operon ; Plasmids/*genetics ; Pseudomonas Infections/microbiology ; Pseudomonas aeruginosa/classification/drug effects/*genetics/isolation &amp; purification ; Sputum/microbiology ; beta-Lactamases/chemistry/*genetics ; }, abstract = {Pseudomonas aeruginosa 96 (PA96) was isolated during a multicenter surveillance study in Guangzhou, China, in 2000. Whole-genome sequencing of this outbreak strain facilitated analysis of its IncP-2 carbapenem-resistant plasmid, pOZ176. The plasmid had a length of 500,839 bp and an average percent G+C content of 57%. Of the 618 predicted open reading frames, 65% encode hypothetical proteins. The pOZ176 backbone is not closely related to any plasmids thus far sequenced, but some similarity to pQBR103 of Pseudomonas fluorescens SBW25 was observed. Two multiresistant class 1 integrons and several insertion sequences were identified. The blaIMP-9-carrying integron contained aacA4 → bla(IMP-9) → aacA4, flanked upstream by Tn21 tnpMRA and downstream by a complete tni operon of Tn402 and a mer module, named Tn6016. The second integron carried aacA4 → catB8a → bla(OXA-10) and was flanked by Tn1403-like tnpRA and a sul1-type 3' conserved sequence (3'-CS), named Tn6217. Other features include three resistance genes similar to those of Tn5, a tellurite resistance operon, and two pil operons. The replication and maintenance systems exhibit similarity to a genomic island of Ralstonia solanacearum GM1000. Codon usage analysis suggests the recent acquisition of bla(IMP-9). The origins of the integrons on pOZ176 indicated separate horizontal gene transfer events driven by antibiotic selection. The novel mosaic structure of pOZ176 suggests that it is derived from environmental bacteria.}, }
@article {pmid23712907, year = {2013}, author = {van Wolferen, M and Ajon, M and Driessen, AJ and Albers, SV}, title = {How hyperthermophiles adapt to change their lives: DNA exchange in extreme conditions.}, journal = {Extremophiles : life under extreme conditions}, volume = {17}, number = {4}, pages = {545-563}, pmid = {23712907}, issn = {1433-4909}, mesh = {*Adaptation, Physiological ; Archaea/*genetics/physiology ; Bacteria/*genetics ; Conjugation, Genetic ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Hot Temperature ; Transformation, Bacterial/*genetics ; }, abstract = {Transfer of DNA has been shown to be involved in genome evolution. In particular with respect to the adaptation of bacterial species to high temperatures, DNA transfer between the domains of bacteria and archaea seems to have played a major role. In addition, DNA exchange between similar species likely plays a role in repair of DNA via homologous recombination, a process that is crucial under DNA damaging conditions such as high temperatures. Several mechanisms for the transfer of DNA have been described in prokaryotes, emphasizing its general importance. However, until recently, not much was known about this process in prokaryotes growing in highly thermophilic environments. This review describes the different mechanisms of DNA transfer in hyperthermophiles, and how this may contribute to the survival and adaptation of hyperthermophilic archaea and bacteria to extreme environments.}, }
@article {pmid23707703, year = {2013}, author = {Lasek-Nesselquist, E and Gogarten, JP}, title = {The effects of model choice and mitigating bias on the ribosomal tree of life.}, journal = {Molecular phylogenetics and evolution}, volume = {69}, number = {1}, pages = {17-38}, doi = {10.1016/j.ympev.2013.05.006}, pmid = {23707703}, issn = {1095-9513}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Biological Evolution ; Databases, Genetic ; Eukaryota/*genetics ; *Genome ; *Models, Genetic ; *Phylogeny ; Ribosomal Proteins/*classification/genetics ; Ribosomes/genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Deep-level relationships within Bacteria, Archaea, and Eukarya as well as the relationships of these three domains to each other require resolution. The ribosomal machinery, universal to all cellular life, represents a protein repertoire resistant to horizontal gene transfer, which provides a largely congruent signal necessary for reconstructing a tree suitable as a backbone for life's reticulate history. Here, we generate a ribosomal tree of life from a robust taxonomic sampling of Bacteria, Archaea, and Eukarya to elucidate deep-level intra-domain and inter-domain relationships. Lack of phylogenetic information and systematic errors caused by inadequate models (that cannot account for substitution rate or compositional heterogeneities) or improper model selection compound conflicting phylogenetic signals from HGT and/or paralogy. Thus, we tested several models of varying sophistication on three different datasets, performed removal of fast-evolving or long-branched Archaea and Eukarya, and employed three different strategies to remove compositional heterogeneity to examine their effects on the topological outcome. Our results support a two-domain topology for the tree of life, where Eukarya emerges from within Archaea as sister to a Korarchaeota/Thaumarchaeota (KT) or Crenarchaeota/KT clade for all models under all or at least one of the strategies employed. Taxonomic manipulation allows single-matrix and certain mixture models to vacillate between two-domain and three-domain phylogenies. We find that models vary in their ability to resolve different areas of the tree of life, which does not necessarily correlate with model complexity. For example, both single-matrix and some mixture models recover monophyletic Crenarchaeota and Euryarchaeota archaeal phyla. In contrast, the most sophisticated model recovers a paraphyletic Euryarchaeota but detects two large clades that comprise the Bacteria, which were recovered separately but never together in the other models. Overall, models recovered consistent topologies despite dataset modifications due to the removal of compositional bias, which reflects either ineffective bias reduction or robust datasets that allow models to overcome reconstruction artifacts. We recommend a comparative approach for evolutionary models to identify model weaknesses as well as consensus relationships.}, }
@article {pmid23707611, year = {2013}, author = {Popoff, MR and Bouvet, P}, title = {Genetic characteristics of toxigenic Clostridia and toxin gene evolution.}, journal = {Toxicon : official journal of the International Society on Toxinology}, volume = {75}, number = {}, pages = {63-89}, doi = {10.1016/j.toxicon.2013.05.003}, pmid = {23707611}, issn = {1879-3150}, mesh = {Bacterial Toxins/*genetics ; Botulinum Toxins/genetics ; Calcium-Binding Proteins/genetics ; Chromosomes, Bacterial ; Clostridioides difficile/classification/genetics ; Clostridium/classification/*genetics/isolation &amp; purification ; Clostridium botulinum/classification/genetics ; Clostridium perfringens/classification/genetics ; DNA Transposable Elements ; DNA, Bacterial/genetics ; Enterotoxins/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Loci ; Genetic Variation ; Plasmids/genetics ; Pore Forming Cytotoxic Proteins/genetics ; Protein Conformation ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Type C Phospholipases/genetics ; }, abstract = {Clostridia comprise a heterogenous group of environmental bacteria containing 15 pathogenic species, which produce the most potent toxins. The origin of toxins is still enigmatic. It is hypothesized that toxins exhibiting an enzymatic activity have derived from hydrolytic enzymes, which are abundantly secreted by these bacteria, and that pore-forming toxins have evolved from an ancestor transmembrane protein. The presence of related toxin genes in distinct Clostridium species and the variability of some toxin genes support horizontal toxin gene transfer and subsequent independent evolution from strain to strain. Clostridium perfringens toxin genes involved in myonecrosis, mainly alpha toxin and perfringolysin genes, are chromosomally located, whereas toxin genes responsible for intestinal and food borne diseases are localized on plasmids except the enterotoxin gene which can be located either on the chromosome or plasmids. The distribution of these plasmids containing one or several toxin genes accounts for the diverse C. perfringens toxinotypes. Clostridium difficile strains show a high genetic variability. But in contrast to C. perfringens, toxin genes are clustered in pathogenicity locus located on chromosome. The presence of related toxin genes in distinct clostridial species like Clostridium sordellii, Clostridium novyi, and C. perfringens supports interspecies mobilization of this locus. The multiple C. difficile toxinotypes based on toxin gene variants possibly reflect strain adaptation to the intestinal environment. Botulinum toxin genes also show a high level of genetic variation. They have a diverse genetic localization including chromosome, plasmid or phage, and are spread in various Clostridium species (Clostridium botulinum groups, Clostridium argentinense, Clostridium butyricum, Clostridium baratii). Exchange of toxin genes not only include transfers between Clostridium species but also between Clostridium and other bacterial species as well as eukaryotic cells as supported by the wide distribution of related pore-forming toxins of the aerolysin family in various clostridial and non-clostridial species, animal, mushroom and plant.}, }
@article {pmid23706977, year = {2013}, author = {de Toro, M and García, P and Rodríguez, I and Rojo-Bezares, B and Helmuth, R and Sáenz, Y and Rodicio, MR and Guerra, B and Torres, C}, title = {Characterisation of plasmids implicated in the mobilisation of extended-spectrum and AmpC β-lactamase genes in clinical Salmonella enterica isolates and temporal stability of the resistance genotype.}, journal = {International journal of antimicrobial agents}, volume = {42}, number = {2}, pages = {167-172}, doi = {10.1016/j.ijantimicag.2013.04.016}, pmid = {23706977}, issn = {1872-7913}, mesh = {Blotting, Southern ; Conjugation, Genetic ; *Drug Resistance, Bacterial ; *Gene Transfer, Horizontal ; Genomic Instability ; Genotype ; Hospitals ; Humans ; *Plasmids ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Salmonella Infections/microbiology ; Salmonella enterica/*drug effects/*genetics ; Sequence Analysis, DNA ; Spain ; beta-Lactamases/*genetics ; }, abstract = {Plasmids implicated in the mobilisation of β-lactamase genes in extended-spectrum β-lactamase (ESBL)- and AmpC-producing Salmonella enterica isolates recovered from three Spanish hospitals were characterised. The temporal stability of these plasmids and of the resistance phenotype without antimicrobial pressure was also assessed in the laboratory setting. The resistance determinants and their genetic environments were characterised by PCR sequencing, and their genomic location was analysed by S1 nuclease pulsed-field gel electrophoresis (PFGE) and I-CeuI PFGE, followed by Southern blot hybridisation. The 11 S. enterica studied strains carried blaCTX-M-9 (serovar Virchow, 2 isolates), blaCTX-M-10 (Virchow, 2), blaCTX-M-14 (Enteritidis, 1), blaCTX-M-15 (Gnesta and S. enterica group C, 2), blaSHV-2 (Livingstone, 1), blaSHV-12 (Enteritidis, 1) and blaCMY-2 (Bredeney, 2). The ISEcp1-blaCTX-M-14-IS903 and ISEcp1-blaCTX-M-15-orf477 genetic structures were detected. IncI1 and IncA/C plasmids carried blaCTX-M-14, blaCTX-M-15, blaSHV-2, blaSHV-12 and blaCMY-2 genes. blaCTX-M-9 included in an In60 complex integron and blaCTX-M-10 linked to a phage-related element were found in non-typeable plasmids. Conjugation and temporal stability experiments were performed in vitro through daily passages (100 days) in the absence of antimicrobial pressure. In the stability experiments, 5 of the 11 tested isolates lost the ESBL or AmpC plasmidic genes and this was associated with concomitant loss of the whole or partial plasmid. In conclusion, successful plasmids belonging to different Inc groups mobilise ESBL- and AmpC-encoding genes in S. enterica. Loss of ESBL/AmpC genes in the absence of antimicrobial pressure might explain the low prevalence of these β-lactamases among Salmonella isolates.}, }
@article {pmid23706556, year = {2013}, author = {Baltrus, DA}, title = {Exploring the costs of horizontal gene transfer.}, journal = {Trends in ecology &amp; evolution}, volume = {28}, number = {8}, pages = {489-495}, doi = {10.1016/j.tree.2013.04.002}, pmid = {23706556}, issn = {1872-8383}, mesh = {Adaptation, Biological/*genetics ; DNA, Bacterial/chemistry/metabolism ; *Evolution, Molecular ; Gene Regulatory Networks ; *Gene Transfer, Horizontal ; Genetic Variation ; Genome, Bacterial ; Models, Genetic ; Phenotype ; }, abstract = {Horizontal gene transfer (HGT) is one of the most important evolutionary forces within microbial populations. Although evidence for beneficial fitness effects of HGT is overwhelming, recently acquired regions often function inefficiently within new genomic backgrounds so that each transfer event has the potential to disrupt existing regulatory and physiological networks. Identifying and exploring costs is essential for guiding general discussions about the interplay between selection and HGT, as well as generating hypotheses to explain how HGT affects evolutionary potential through, for example, changing adaptive trajectories. Focusing on costs of HGT as foundations for future studies will enhance exploration at the interface between acquired regions and recipient genomes, including the process of amelioration, and enable experimental evaluation of the role of HGT in structuring genetic diversity across populations.}, }
@article {pmid23706302, year = {2013}, author = {Samuels, J}, title = {Transgene flow from Bt brinjal: a real risk?.}, journal = {Trends in biotechnology}, volume = {31}, number = {6}, pages = {332-334}, doi = {10.1016/j.tibtech.2013.03.007}, pmid = {23706302}, issn = {1879-3096}, mesh = {*Gene Transfer, Horizontal ; Plants, Genetically Modified/*genetics ; Risk Assessment ; Solanum melongena/*genetics ; *Transgenes ; }, }
@article {pmid23706082, year = {2013}, author = {Joseph, S and Hariri, S and Masood, N and Forsythe, S}, title = {Sialic acid utilization by Cronobacter sakazakii.}, journal = {Microbial informatics and experimentation}, volume = {3}, number = {1}, pages = {3}, pmid = {23706082}, issn = {2042-5783}, abstract = {BACKGROUND: The Cronobacter genus is composed of seven species, and can cause infections in all age groups. Of particular concern is C. sakazakii, as this species is strongly associated with severe and often fatal cases of necrotizing enterocolitis and meningitis in neonates and infants. Whole genome sequencing has revealed that the nanAKT gene cluster required for the utilisation of exogenous sialic acid is unique to the C. sakazakii species (ESA_03609-13).Sialic acid is found in breast milk, infant formula, intestinal mucin, and gangliosides in the brain, hence its metabolism by C. sakazakii is of particular interest. Therefore its metabolism could be an important virulence factor. To date, no laboratory studies demonstrating the growth of C. sakazakii on sialic acid have been published nor have there been reports of sialidase activity. The phylogenetic analysis of the nan genes is of interest to determine whether the genes have been acquired by horizontal gene transfer.<br><br>RESULTS: Phylogenetic analysis of 19 Cronobacter strains from 7 recognised species revealed the nanAKTR genes formed a unique cluster, separate from other Enterobacteriaceae such as E. coli K1 and Citrobacter koseri, which are also associated with neonatal meningitis. The gene organisation was similar to Edwardsiella tarda in that nanE gene (N-acetylmannosamine-6-phosphate-2epimerase) was not located within the nanATK cluster. Laboratory studies confirmed that only C. sakazakii, and not the other six Cronobacter species, was able to use sialic acid as a carbon source for growth. Although the ganglioside GM1 was also used as carbon source, no candidate sialidase genes were found in the genome, instead the substrate degradation is probably due to &#x3b2;-galactosidase activity.<br><br>CONCLUSIONS: Given the relatively recent evolution of both C. sakazakii (15-23 million years ago) and sialic acid synthesis in vertebrates, sialic acid utilization may be an example of co-evolution by one species of the Cronobacter genus with the mammalian host. This has possibly resulted in additional virulence factors contributing to severe life-threatening infections in neonates due to the utilization of sialic acid from breast milk, infant formula, milk (oligosaccharides), mucins lining the intestinal wall, and even gangliosides in the brain after passing through the blood-brain barrier.}, }
@article {pmid23706020, year = {2013}, author = {Zamani, N and Russell, P and Lantz, H and Hoeppner, MP and Meadows, JR and Vijay, N and Mauceli, E and di Palma, F and Lindblad-Toh, K and Jern, P and Grabherr, MG}, title = {Unsupervised genome-wide recognition of local relationship patterns.}, journal = {BMC genomics}, volume = {14}, number = {}, pages = {347}, pmid = {23706020}, issn = {1471-2164}, support = {1 U54 HG03067/HG/NHGRI NIH HHS/United States ; }, mesh = {Algorithms ; Animals ; Dengue Virus/genetics ; Disease Outbreaks ; Genomics/*methods ; Humans ; Immunity/genetics ; Markov Chains ; Models, Genetic ; Phylogeny ; Primates/genetics/immunology ; Software ; Species Specificity ; }, abstract = {BACKGROUND: Phenomena such as incomplete lineage sorting, horizontal gene transfer, gene duplication and subsequent sub- and neo-functionalisation can result in distinct local phylogenetic relationships that are discordant with species phylogeny. In order to assess the possible biological roles for these subdivisions, they must first be identified and characterised, preferably on a large scale and in an automated fashion.<br><br>RESULTS: We developed Saguaro, a combination of a Hidden Markov Model (HMM) and a Self Organising Map (SOM), to characterise local phylogenetic relationships among aligned sequences using cacti, matrices of pair-wise distance measures. While the HMM determines the genomic boundaries from aligned sequences, the SOM hypothesises new cacti in an unsupervised and iterative fashion based on the regions that were modelled least well by existing cacti. After testing the software on simulated data, we demonstrate the utility of Saguaro by testing two different data sets: (i) 181 Dengue virus strains, and (ii) 5 primate genomes. Saguaro identifies regions under lineage-specific constraint for the first set, and genomic segments that we attribute to incomplete lineage sorting in the second dataset. Intriguingly for the primate data, Saguaro also classified an additional ~3% of the genome as most incompatible with the expected species phylogeny. A substantial fraction of these regions was found to overlap genes associated with both the innate and adaptive immune systems.<br><br>CONCLUSIONS: Saguaro detects distinct cacti describing local phylogenetic relationships without requiring any a priori hypotheses. We have successfully demonstrated Saguaro's utility with two contrasting data sets, one containing many members with short sequences (Dengue viral strains: n = 181, genome size = 10,700 nt), and the other with few members but complex genomes (related primate species: n = 5, genome size = 3 Gb), suggesting that the software is applicable to a wide variety of experimental populations. Saguaro is written in C++, runs on the Linux operating system, and can be downloaded from http://saguarogw.sourceforge.net/.}, }
@article {pmid23705883, year = {2013}, author = {Spring, S and Riedel, T and Spröer, C and Yan, S and Harder, J and Fuchs, BM}, title = {Taxonomy and evolution of bacteriochlorophyll a-containing members of the OM60/NOR5 clade of marine gammaproteobacteria: description of Luminiphilus syltensis gen. nov., sp. nov., reclassification of Haliea rubra as Pseudohaliea rubra gen. nov., comb. nov., and emendation of Chromatocurvus halotolerans.}, journal = {BMC microbiology}, volume = {13}, number = {}, pages = {118}, pmid = {23705883}, issn = {1471-2180}, mesh = {Aerobiosis ; Aquatic Organisms/chemistry/*classification/*genetics/isolation &amp; purification ; Bacteriochlorophyll A/*analysis ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Gammaproteobacteria/chemistry/*classification/*genetics/isolation &amp; purification ; Genetic Variation ; Germany ; Metabolic Networks and Pathways/genetics ; Molecular Sequence Data ; North Sea ; Photosynthesis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Aerobic gammaproteobacteria affiliated to the OM60/NOR5 clade are widespread in saline environments and of ecological importance in several marine ecosystems, especially the euphotic zone of coastal areas. Within this group a close relationship between aerobic anoxygenic photoheterotrophs and non-phototrophic members has been found.<br><br>RESULTS: Several strains of aerobic red-pigmented bacteria affiliated to the OM60/NOR5 clade were obtained from tidal flat sediment samples at the island of Sylt (North Sea, Germany). Two of the novel isolates, Rap1red and Ivo14(T), were chosen for an analysis in detail. Strain Rap1red shared a 16S rRNA sequence identity of 99% with the type strain of Congregibacter litoralis and was genome-sequenced to reveal the extent of genetic microheterogeneity among closely related strains within this clade. In addition, a draft genome sequence was obtained from the isolate Ivo14(T), which belongs to the environmental important NOR5-1 lineage that contains so far no cultured representative with a comprehensive description. Strain Ivo14(T) was characterized using a polyphasic approach and compared with other red-pigmented members of the OM60/NOR5 clade, including Congregibacter litoralis DSM 17192(T), Haliea rubra DSM 19751(T) and Chromatocurvus halotolerans DSM 23344(T). All analyzed strains contained bacteriochlorophyll a and spirilloxanthin as photosynthetic pigments. Besides a detailed phenotypic characterization including physiological and chemotaxonomic traits, sequence information based on protein-coding genes and a comparison of draft genome data sets were used to identify possible features characteristic for distinct taxa within this clade.<br><br>CONCLUSIONS: Comparative sequence analyses of the pufLM genes of genome-sequenced representatives of the OM60/NOR5 clade indicated that the photosynthetic apparatus of these species was derived from a common ancestor and not acquired by multiple horizontal gene transfer from phylogenetically distant species. An affiliation of the characterized bacteriochlorophyll a-containing strains to different genera was indicated by significant phenotypic differences and pufLM nucleotide sequence identity values below 82%. The revealed high genotypic and phenotypic diversity of closely related strains within this phylogenetic group reflects a rapid evolution and frequent niche separation in the OM60/NOR5 clade, which is possibly driven by the necessities of an adaptation to oligotrophic marine habitats.}, }
@article {pmid23704789, year = {2013}, author = {Burmester, A and Karimi, S and Wetzel, J and Wöstemeyer, J}, title = {Complementation of a stable Met2-1 mutant of the zygomycete Absidia glauca by the corresponding wild-type allele of the mycoparasite Parasitella parasitica, transferred during infection.}, journal = {Microbiology (Reading, England)}, volume = {159}, number = {Pt 8}, pages = {1639-1648}, doi = {10.1099/mic.0.066910-0}, pmid = {23704789}, issn = {1465-2080}, mesh = {DNA, Fungal/chemistry/genetics ; *Gene Knockout Techniques ; *Genetic Complementation Test ; Metabolic Networks and Pathways ; Methionine/*metabolism ; Molecular Sequence Data ; Mucorales/*genetics/*metabolism ; Replicon ; Sequence Analysis, DNA ; }, abstract = {Compared with prokaryotes, where horizontal gene transfer events are frequently found and can be studied in the laboratory at the mechanistic level, few systems are known that allow direct experimental access to parasexual phenomena in eukaryotes. In zygomycetes, a basal lineage of fungi, several mycoparasitic fungi are known that inevitably form a cytoplasmic continuum with their hosts during infection. We provide evidence that, corresponding to the expectation suggested by the morphology of the infection process, gene transfer occurs from the parasite to the host. For analysing this parasexual system at the DNA level, we characterized interspecific recombinants obtained by infecting a stable methionine-auxotrophic Absidia glauca mutant with heavy rearrangements at the Met2-1 locus, which encodes homoserine acetyltransferase. Recipients were shown to be complemented by part of the corresponding gene from Parasitella parasitica. This foreign DNA is neither integrated at the putative Met2-2 locus in the recipient strain nor integrated at Met2-1, a locus encoding a hypothetical protein with amino acid similarity but with unknown function. Based on hybridization studies and on the phenotype of recipients that bear some mitotic instability of the acquired prototrophy, we propose that P. parasitica DNA is established in A. glauca recipients as extrachromosomally located replicons.}, }
@article {pmid23701331, year = {2013}, author = {Muniesa, M and Colomer-Lluch, M and Jofre, J}, title = {Potential impact of environmental bacteriophages in spreading antibiotic resistance genes.}, journal = {Future microbiology}, volume = {8}, number = {6}, pages = {739-751}, doi = {10.2217/fmb.13.32}, pmid = {23701331}, issn = {1746-0921}, mesh = {Bacteria/*drug effects ; Bacteriophages/*genetics ; *Drug Resistance, Bacterial ; *Environmental Microbiology ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Interspersed Repetitive Sequences ; *Transduction, Genetic ; }, abstract = {The idea that bacteriophage transduction plays a role in the horizontal transfer of antibiotic resistance genes is gaining momentum. Such transduction might be vital in horizontal transfer from environmental to human body-associated biomes and here we review many lines of evidence supporting this notion. It is well accepted that bacteriophages are the most abundant entities in most environments, where they have been shown to be quite persistent. This fact, together with the ability of many phages to infect bacteria belonging to different taxa, makes them suitable vehicles for gene transfer. Metagenomic studies confirm that substantial percentages of the bacteriophage particles present in most environments contain bacterial genes, including mobile genetic elements and antibiotic resistance genes. When specific genes of resistance to antibiotics are detected by real-time PCR in the bacteriophage populations of different environments, only tenfold lower numbers of these genes are observed, compared with those found in the corresponding bacterial populations. In addition, the antibiotic resistance genes from these bacteriophages are functional and generate resistance to the bacteria when these genes are transfected. Finally, reports about the transduction of antibiotic resistance genes are on the increase.}, }
@article {pmid23701169, year = {2013}, author = {Held, NL and Herrera, A and Whitaker, RJ}, title = {Reassortment of CRISPR repeat-spacer loci in Sulfolobus islandicus.}, journal = {Environmental microbiology}, volume = {15}, number = {11}, pages = {3065-3076}, doi = {10.1111/1462-2920.12146}, pmid = {23701169}, issn = {1462-2920}, mesh = {Archaeal Viruses/*genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/*genetics ; DNA, Bacterial/analysis/genetics ; Gene Frequency/genetics ; Gene Transfer, Horizontal/*genetics ; Genetic Variation ; Molecular Sequence Data ; Russia ; Sequence Analysis, DNA ; Sulfolobus/*genetics/*virology ; }, abstract = {Virus-host interactions are a key factor shaping population dynamics of microbial species. The CRISPR-Cas adaptive immune system confers sequence-specific immunity to viral infection and has the potential to dramatically shape coevolutionary interactions between viruses and their microbial hosts. To assess evolutionary dynamics of CRISPR loci, we have sampled a population of closely related Sulfolobus islandicus strains from Kamchatka, Russia at two time points, 10 years apart. Sequence analysis of the conserved trailer sequences reveals that alleles are reassorted among three CRISPR spacer loci into combinatorial genotypes. Reassortment provides the evolutionary independence of CRISPR loci from one another as demonstrated by the differential change in allele frequencies between two time points. Genome sequences of 12 strains from this population also reveal very recent horizontal gene transfer of novel, divergent cas gene cassettes. The evolutionary independence of CRISPR loci from each other and of the cas genes that control their function are consistent with the evolutionary expectation that reassortment increases the efficiency of adaptation at these loci that are likely under strong selection by lytic viruses.}, }
@article {pmid23698014, year = {2013}, author = {Pauchet, Y and Heckel, DG}, title = {The genome of the mustard leaf beetle encodes two active xylanases originally acquired from bacteria through horizontal gene transfer.}, journal = {Proceedings. Biological sciences}, volume = {280}, number = {1763}, pages = {20131021}, pmid = {23698014}, issn = {1471-2954}, mesh = {Animals ; Coleoptera/*enzymology/genetics ; Endo-1,4-beta Xylanases/*genetics/metabolism ; Gammaproteobacteria/*enzymology/genetics ; *Gene Transfer, Horizontal ; Genome, Insect/*genetics ; Molecular Sequence Data ; Mustard Plant/*parasitology ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The primary plant cell wall comprises the most abundant polysaccharides on the Earth and represents a rich source of energy for organisms which have evolved the ability to digest them. Enzymes able to degrade plant cell wall polysaccharides are widely distributed in micro-organisms but are generally absent in animals, although their presence in insects, especially phytophagous beetles from the superfamilies Chrysomeloidea and Curculionoidea, has recently begun to be appreciated. The observed patchy distribution of endogenous genes encoding these enzymes in animals has raised questions about their evolutionary origins. Recent evidence suggests that endogenous plant cell wall degrading enzymes-encoding genes have been acquired by animals through a mechanism known as horizontal gene transfer (HGT). HGT describes how genetic material is moved by means other than vertical inheritance from a parent to an offspring. Here, we provide evidence that the mustard leaf beetle, Phaedon cochleariae, possesses in its genome genes encoding active xylanases from the glycoside hydrolase family 11 (GH11). We also provide evidence that these genes were originally acquired by P. cochleariae from a species of gammaproteobacteria through HGT. This represents the first example of the presence of genes from the GH11 family in animals.}, }
@article {pmid23695557, year = {2013}, author = {Guevara, T and Ksiazek, M and Skottrup, PD and Cerdà-Costa, N and Trillo-Muyo, S and de Diego, I and Riise, E and Potempa, J and Gomis-Rüth, FX}, title = {Structure of the catalytic domain of the Tannerella forsythia matrix metallopeptidase karilysin in complex with a tetrapeptidic inhibitor.}, journal = {Acta crystallographica. Section F, Structural biology and crystallization communications}, volume = {69}, number = {Pt 5}, pages = {472-476}, pmid = {23695557}, issn = {1744-3091}, support = {R01 DE009761/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacterial Proteins/*chemistry/metabolism ; Bacteroidetes/*enzymology ; *Catalytic Domain/physiology ; Crystallography, X-Ray ; Matrix Metalloproteinases/*chemistry/metabolism ; Oligopeptides/*chemistry/metabolism ; Protein Binding ; }, abstract = {Karilysin is the only metallopeptidase identified as a virulence factor in the odontopathogen Tannerella forsythia owing to its deleterious effect on the host immune response during bacterial infection. The very close structural and sequence-based similarity of its catalytic domain (Kly18) to matrix metalloproteinases suggests that karilysin was acquired by horizontal gene transfer from an animal host. Previous studies by phage display identified peptides with the consensus sequence XWFPXXXGGG (single-letter amino-acid codes; X represents any residue) as karilysin inhibitors with low-micromolar binding affinities. Subsequent refinement revealed that inhibition comparable to that of longer peptides could be achieved using the tetrapeptide SWFP. To analyze its binding, the high-resolution crystal structure of the complex between Kly18 and SWFP was determined and it was found that the peptide binds to the primed side of the active-site cleft in a substrate-like manner. The catalytic zinc ion is clamped by the α-amino group and the carbonyl O atom of the serine, thus distantly mimicking the general manner of binding of hydroxamate inhibitors to metallopeptidases and contributing, together with three zinc-binding histidines from the protein scaffold, to an octahedral-minus-one metal-coordination sphere. The tryptophan side chain penetrates the deep partially water-filled specificity pocket of Kly18. Together with previous serendipitous product complexes of Kly18, the present results provide the structural determinants of inhibition of karilysin and open the field for the design of novel inhibitory strategies aimed at the treatment of human periodontal disease based on a peptidic hit molecule.}, }
@article {pmid23685468, year = {2013}, author = {Tsai, SE and Jong, KJ and Tey, YH and Yu, WT and Chiou, CS and Lee, YS and Wong, HC}, title = {Molecular characterization of clinical and environmental Vibrio parahaemolyticus isolates in Taiwan.}, journal = {International journal of food microbiology}, volume = {165}, number = {1}, pages = {18-26}, doi = {10.1016/j.ijfoodmicro.2013.04.017}, pmid = {23685468}, issn = {1879-3460}, mesh = {Animals ; Electrophoresis, Gel, Pulsed-Field ; *Environmental Microbiology ; Gene Transfer, Horizontal ; Humans ; Phylogeny ; Polymerase Chain Reaction ; Taiwan ; Vibrio Infections/*microbiology ; Vibrio parahaemolyticus/classification/*genetics/isolation &amp; purification ; Virulence Factors/genetics ; }, abstract = {Vibrio parahaemolyticus is the most prevalent foodborne pathogen in Taiwan and it is frequently recovered from seafood. In this study, V. parahaemolyticus that was isolated in recent years from aquacultural environments and clinical specimens were comparatively analyzed by NotI-restricted pulsed-field gel electrophoresis (PFGE) and polymerase chain reaction, targeting common toxin genes (tdh, trh, ureC), MTase gene, toxR regulator, markers for pandemic strains (ORF8, group-specific toxRS) and representative genes of type three secretion systems T3SS1 (vcrD1, VP1680, vopD) and T3SS2α (vcrD2, vopD2, vopB2, vopP, vopC, vopT). Among the 48 clinical isolates and 93 environmental isolates that were analyzed by PFGE, a total of 26 and 76 pulsetypes were identified and grouped into six and nine clusters, respectively, at 80% similarity. The pandemic O3:K6 clones and other clinical and environmental isolates were further characterized according to the distribution of these examined target genes. The MTase gene and the vopB2, vopP, vopC and vopT genes of T3SS2α were present at a significantly higher frequency (>90%) in the pandemic clones than in other clinical isolates. The MTase gene and some other virulence-associated genes were also present in a few of the environmental isolates, and these results suggest the horizontal transfer of these genes in the clinical and environmental isolates of this species.}, }
@article {pmid23685062, year = {2013}, author = {Pillon, Y and Johansen, JB and Sakishima, T and Roalson, EH and Price, DK and Stacy, EA}, title = {Gene discordance in phylogenomics of recent plant radiations, an example from Hawaiian Cyrtandra (Gesneriaceae).}, journal = {Molecular phylogenetics and evolution}, volume = {69}, number = {1}, pages = {293-298}, doi = {10.1016/j.ympev.2013.05.003}, pmid = {23685062}, issn = {1095-9513}, mesh = {Bayes Theorem ; Cell Nucleus/genetics ; DNA Primers/genetics ; DNA, Plant/*classification/genetics ; Gene Transfer, Horizontal ; *Genetic Speciation ; Hawaii ; Hybridization, Genetic ; Magnoliopsida/*classification/genetics ; *Phylogeny ; Phylogeography ; Plant Dispersal ; Plastids/genetics ; Sample Size ; Sequence Analysis, DNA ; }, abstract = {Resolving species relationships within recent radiations requires analysis at the interface of phylogenetics and population genetics, where coalescence and hybridization may confound our understanding of relationships. We developed 18 new primer pairs for nuclear loci in Cyrtandra (Gesneriaceae), one of the largest plant radiations in the Pacific Islands, and tested the concordance of 14 loci in establishing the phylogenetic relationships of a small number of Hawaiian species. Four genes yielded tree topologies conflicting with the primary concordance tree, suggesting plastid capture and horizontal transfer via hybridization. Combining all concordant genes yielded a tree with stronger support and a different topology from the total-evidence tree. We conclude that a small number of genes may be insufficient for accurate reconstruction of the phylogenetic relationships among closely related species. Further, the combination of genes for phylogenetic analysis without preliminary concordance tests can yield an erroneous tree topology. It seems that the number of genes needed for phylogenetic analysis of closely related species is significantly greater than the small numbers commonly used, which fail to isolate coalescence, introgression and hybridization.}, }
@article {pmid23682915, year = {2013}, author = {Castagnone-Sereno, P and Danchin, EG and Perfus-Barbeoch, L and Abad, P}, title = {Diversity and evolution of root-knot nematodes, genus Meloidogyne: new insights from the genomic era.}, journal = {Annual review of phytopathology}, volume = {51}, number = {}, pages = {203-220}, doi = {10.1146/annurev-phyto-082712-102300}, pmid = {23682915}, issn = {1545-2107}, mesh = {Animals ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Variation ; Genome, Helminth/*genetics ; *Genomics ; Host Specificity ; Hybridization, Genetic ; Parthenogenesis ; Phylogeny ; Plant Diseases/parasitology ; Plant Roots/parasitology ; Plants/parasitology ; Reproduction ; Species Specificity ; Tylenchoidea/*genetics/physiology ; }, abstract = {Root-knot nematodes (RKNs) (Meloidogyne spp.) are obligate endoparasites of major worldwide economic importance. They exhibit a wide continuum of variation in their reproductive strategies, ranging from amphimixis to obligatory mitotic parthenogenesis. Molecular phylogenetic studies have highlighted divergence between mitotic and meiotic parthenogenetic RKN species and probable interspecific hybridization as critical steps in their speciation and diversification process. The recent completion of the genomes of two RKNs, Meloidogyne hapla and Meloidogyne incognita, that exhibit striking differences in their mode of reproduction (with and without sex, respectively), their geographic distribution, and their host range has opened the way for deciphering the evolutionary significance of (a)sexual reproduction in these parasites. Accumulating evidence suggests that whole-genome duplication (in M. incognita) and horizontal gene transfers (HGTs) represent major forces that have shaped the genome of current RKN species and may account for the extreme adaptive capacities and parasitic success of these nematodes.}, }
@article {pmid23680992, year = {2014}, author = {van Iersel, L and Moulton, V}, title = {Trinets encode tree-child and level-2 phylogenetic networks.}, journal = {Journal of mathematical biology}, volume = {68}, number = {7}, pages = {1707-1729}, pmid = {23680992}, issn = {1432-1416}, mesh = {Algorithms ; Biological Evolution ; Gene Regulatory Networks ; Genetic Speciation ; Mathematical Concepts ; *Models, Genetic ; *Phylogeny ; }, abstract = {Phylogenetic networks generalize evolutionary trees, and are commonly used to represent evolutionary histories of species that undergo reticulate evolutionary processes such as hybridization, recombination and lateral gene transfer. Recently, there has been great interest in trying to develop methods to construct rooted phylogenetic networks from triplets, that is rooted trees on three species. However, although triplets determine or encode rooted phylogenetic trees, they do not in general encode rooted phylogenetic networks, which is a potential issue for any such method. Motivated by this fact, Huber and Moulton recently introduced trinets as a natural extension of rooted triplets to networks. In particular, they showed that [Formula: see text] phylogenetic networks are encoded by their trinets, and also conjectured that all "recoverable" rooted phylogenetic networks are encoded by their trinets. Here we prove that recoverable binary level-2 networks and binary tree-child networks are also encoded by their trinets. To do this we prove two decomposition theorems based on trinets which hold for all recoverable binary rooted phylogenetic networks. Our results provide some additional evidence in support of the conjecture that trinets encode all recoverable rooted phylogenetic networks, and could also lead to new approaches to construct phylogenetic networks from trinets.}, }
@article {pmid23680975, year = {2013}, author = {Spaková, T and Fecskeová, LK and Javorský, P and Pristas, P}, title = {Two rep genes in small cryptic plasmid pKST21 of Escherichia coli.}, journal = {Current microbiology}, volume = {67}, number = {4}, pages = {437-441}, pmid = {23680975}, issn = {1432-0991}, mesh = {Amino Acid Sequence ; Base Sequence ; DNA Helicases/chemistry/*genetics ; Escherichia coli/chemistry/*enzymology/genetics ; Escherichia coli Proteins/chemistry/*genetics ; Molecular Sequence Data ; Open Reading Frames ; Plasmids/chemistry/*genetics ; Sequence Homology, Amino Acid ; }, abstract = {The complete nucleotide sequence of a small cryptic plasmid pKST21 from Escherichia coli was determined. This plasmid is 1,460 bp long with an overall GC content of 51 %. Based on sequence analysis, the presence of two segments with different average GC density was observed. The segment with higher GC content revealed 98-90 % similarity to several small plasmids of E. coli and to pCR1 from Gram-positive Corynebacterium renale. Plasmid pKST21 possesses two conversely oriented open reading frames encoding proteins with a high degree of amino acid identity to Rep proteins involved in replication. ORF1 encodes replication protein similar to RepA protein of Bartonella tribocorum or Bacillus cereus plasmids or to the putative plasmid Rep protein from ecologically close Selenomonas ruminantium. ORF2 similarly encodes a replication protein, which shares 97 % homology with Rep protein from C. renale. Genetic diversity observed in plasmid pKST21 indicates a mosaic structure of the plasmid with different segments acquired from different sources. Deletion analysis showed that both fragments carrying the repA and repB genes are necessary for the replication of pKST21 in E. coli. The presence of plasmid with the same gene composition was revealed in 14 % of tested E. coli isolates from the rumen of sheep. All these strains produced identical ERIC-PCR profiles indicating isogenic origin of the strain and lack of horizontal gene transfer of pKST21 plasmid.}, }
@article {pmid23680304, year = {2013}, author = {O'Donnell, MM and O'Toole, PW and Ross, RP}, title = {Catabolic flexibility of mammalian-associated lactobacilli.}, journal = {Microbial cell factories}, volume = {12}, number = {}, pages = {48}, pmid = {23680304}, issn = {1475-2859}, mesh = {Animals ; Bacterial Proteins/genetics/metabolism ; Carbon/metabolism ; Gastrointestinal Tract/microbiology ; Gene Transfer, Horizontal ; Humans ; Lactobacillus/classification/*metabolism ; Phylogeny ; Plasmids/genetics/metabolism ; }, abstract = {Metabolic flexibility may be generally defined as "the capacity for the organism to adapt fuel oxidation to fuel availability". The metabolic diversification strategies used by individual bacteria vary greatly from the use of novel or acquired enzymes to the use of plasmid-localised genes and transporters. In this review, we describe the ability of lactobacilli to utilise a variety of carbon sources from their current or new environments in order to grow and survive. The genus Lactobacillus now includes more than 150 species, many with adaptive capabilities, broad metabolic capacity and species/strain variance. They are therefore, an informative example of a cell factory capable of adapting to new niches with differing nutritional landscapes. Indeed, lactobacilli naturally colonise and grow in a wide variety of environmental niches which include the roots and foliage of plants, silage, various fermented foods and beverages, the human vagina and the mammalian gastrointestinal tract (GIT; including the mouth, stomach, small intestine and large intestine). Here we primarily describe the metabolic flexibility of some lactobacilli isolated from the mammalian gastrointestinal tract, and we also describe some of the food-associated species with a proven ability to adapt to the GIT. As examples this review concentrates on the following species - Lb. plantarum, Lb. acidophilus, Lb. ruminis, Lb. salivarius, Lb. reuteri and Lb. sakei, to highlight the diversity and inter-relationships between the catabolic nature of species within the genus.}, }
@article {pmid23676925, year = {2013}, author = {Jasser, I and Królicka, A and Jakubiec, K and Chróst, RJ}, title = {Seasonal and spatial diversity of picocyanobacteria community in the Great Mazurian Lakes derived from DGGE analyses of ITS region of rDNA and cpcBAIGS [corrected] markers.}, journal = {Journal of microbiology and biotechnology}, volume = {23}, number = {6}, pages = {739-749}, doi = {10.4014/jmb.1208.08002}, pmid = {23676925}, issn = {1738-8872}, mesh = {*Biota ; Cyanobacteria/*genetics/*growth &amp; development ; DNA Fingerprinting/methods ; DNA, Bacterial/genetics ; DNA, Ribosomal Spacer/*genetics ; *Genetic Variation ; Lakes/*microbiology ; *Phylogeography ; Poland ; Seasons ; }, abstract = {The seasonal and spatial diversity of picocyanobacteria (Pcy) in lakes of the Great Mazurian Lakes (GLM) system was examined by DGGE analysis of molecular markers derived from the 16S-23S internal transcribed spacer (ITS) of the ribosomal operon and the phycocyanin operon (cpcBA-IGS). The study of nine lakes, ranging from mesotrophy to hypereutrophy, demonstrated seasonal variance of Pcy. The richness and Shannon diversity index calculated on the basis of both markers were higher in spring and lower in early and late summer. No statistically significant relationships were found between the markers and trophic status of the studied lakes or Pcy abundance. There were, however, statistically significant relationships between the diversity indices and sampling time. The analysis pointed to a different distribution of the two markers. The ITS marker exhibited more unique sequences in time and space, whereas a greater role for common and ubiquitous sequences was indicated by the cpcBA-IGS data. Examination of the Pcy community structure demonstrated that communities were grouped in highly similar clusters according to sampling season/time rather than to the trophic status of the lake. Our results suggest that time is more important than trophic status in shaping the diversity and structure of Pcy communities. The seasonal changes in picocyanobacteria and differences in diversity and community structures are discussed in the context of well-established ecological hypotheses: the PEG model, intermediate disturbance hypothesis (IDH), and horizontal gene transfer (HGT).}, }
@article {pmid23674765, year = {2013}, author = {Eller, C and Simon, S and Miller, T and Frick, JS and Prager, R and Rabsch, W and Guerra, B and Werner, G and Pfeifer, Y}, title = {Presence of β-lactamases in extended-spectrum-cephalosporin-resistant Salmonella enterica of 30 different serovars in Germany 2005-11.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {68}, number = {9}, pages = {1978-1981}, doi = {10.1093/jac/dkt163}, pmid = {23674765}, issn = {1460-2091}, mesh = {Animals ; Cephalosporins/*pharmacology ; Conjugation, Genetic ; DNA, Bacterial/genetics ; Electrophoresis, Gel, Pulsed-Field ; Gene Transfer, Horizontal ; Germany/epidemiology ; Humans ; Microbial Sensitivity Tests ; Molecular Epidemiology ; Molecular Typing ; Plasmids ; Polymerase Chain Reaction ; Salmonella Infections/epidemiology/*microbiology/transmission ; Salmonella enterica/*classification/drug effects/*enzymology/isolation &amp; purification ; Sequence Analysis, DNA ; Serotyping ; *beta-Lactam Resistance ; beta-Lactamases/*genetics/metabolism ; }, abstract = {OBJECTIVES: Between 20 000 and 35 000 cases of salmonellosis are detected annually in Germany, but only a few Salmonella are resistant to third-generation cephalosporins. The German National Reference Centre for Salmonella and other Enterics obtained 150 Salmonella enterica isolates from human infections between 2005 and 2011. In the present study we identified the β-lactamase genes causing resistance to third-generation cephalosporins in these isolates.<br><br>METHODS: For all isolates serotyping and antimicrobial susceptibility testing were performed. The presence of &#x3b2;-lactamase genes was detected by PCR amplification and sequencing. Isolates with identical serovar and &#x3b2;-lactamase genes were typed by XbaI macrorestriction followed by PFGE. Broth mate conjugation assays and plasmid analysis using S1 nuclease restriction of genomic DNA and subsequent PFGE as well as PCR-based replicon typing were performed for selected isolates.<br><br>RESULTS: The 150 isolates were assigned to 30 different serovars, with S. enterica serovar Typhimurium (n&#x200a;=&#x200a;73; 48.7%) as the most prevalent. Two different AmpC &#x3b2;-lactamase genes (blaCMY-2, n&#x200a;=&#x200a;8; blaACC-1, n&#x200a;=&#x200a;6) and various extended-spectrum &#x3b2;-lactamase (ESBL) genes were identified. The majority harboured the blaCTX-M-1 gene (n&#x200a;=&#x200a;91; 60.7%) followed by blaCTX-M-14 (n&#x200a;=&#x200a;12; 8.0%) and blaSHV-12 (n&#x200a;=&#x200a;11; 7.3%). Typing of strains and subsequent comparison with selected Salmonella isolates from livestock revealed the presence of several clones in both humans and livestock.<br><br>CONCLUSIONS: The wide spread of ESBL and AmpC genes in Salmonella of various serovars is most probably due to transfer of conjugative plasmids. Furthermore, our data indicate the clonal spread of distinct cephalosporin-resistant Salmonella strains from livestock to humans.}, }
@article {pmid23674353, year = {2013}, author = {Collins, RE and Deming, JW}, title = {An inter-order horizontal gene transfer event enables the catabolism of compatible solutes by Colwellia psychrerythraea 34H.}, journal = {Extremophiles : life under extreme conditions}, volume = {17}, number = {4}, pages = {601-610}, pmid = {23674353}, issn = {1433-4909}, mesh = {Adaptation, Physiological/genetics ; Alteromonadaceae/*genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Betaine/metabolism ; Choline/metabolism ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Methylation ; Operon/genetics ; Oxidation-Reduction ; Phylogeny ; Sarcosine/analogs &amp; derivatives/metabolism ; Sarcosine Oxidase/genetics/metabolism ; }, abstract = {Colwellia is a genus of mostly psychrophilic halophilic Gammaproteobacteria frequently isolated from polar marine sediments and sea ice. In exploring the capacity of Colwellia psychrerythraea 34H to survive and grow in the liquid brines of sea ice, we detected a duplicated 37 kbp genomic island in its genome based on the abnormally high G + C content. This island contains an operon encoding for heterotetrameric sarcosine oxidase and is located adjacent to several genes used in the serial demethylation of glycine betaine, a compatible solute commonly used for osmoregulation, to dimethylglycine, sarcosine, and glycine. Molecular clock inferences of important events in the adaptation of C. psychrerythraea 34H to compatible solute utilization reflect the geological evolution of the polar regions. Validating genomic predictions, C. psychrerythraea 34H was shown to grow on defined media containing either choline or glycine betaine, and on a medium with sarcosine as the sole organic source of carbon and nitrogen. Growth by 8 of 9 tested Colwellia species on a newly developed sarcosine-based defined medium suggested that the ability to catabolize glycine betaine (the catabolic precursor of sarcosine) is likely widespread in the genus Colwellia. This capacity likely provides a selective advantage to Colwellia species in cold, salty environments like sea ice, and may have contributed to the ability of Colwellia to invade these extreme niches.}, }
@article {pmid23672494, year = {2013}, author = {Pistorio, M and Torres Tejerizo, GA and Del Papa, MF and Giusti, Mde L and Lozano, M and Lagares, A}, title = {rptA, a novel gene from Ensifer (Sinorhizobium) meliloti involved in conjugal transfer.}, journal = {FEMS microbiology letters}, volume = {345}, number = {1}, pages = {22-30}, doi = {10.1111/1574-6968.12177}, pmid = {23672494}, issn = {1574-6968}, mesh = {Bacterial Proteins/genetics/*metabolism ; *Conjugation, Genetic ; Gene Transfer, Horizontal ; Open Reading Frames ; Plasmids/genetics/metabolism ; Sinorhizobium meliloti/*genetics/*metabolism ; }, abstract = {We approached the identification of Ensifer (Sinorhizobium) meliloti conjugal functions by random Tn5-B13 mutagenesis of the pSmeLPU88a plasmid of E. meliloti strain LPU88 and the subsequent selection of those mutants that had lost the ability to mobilize the small plasmid pSmeLPU88b. The Tn5-B13-insertion site of one of the mutants was cloned as an EcoRI-restricted DNA fragment that after subsequent isolation and sequencing demonstrated that a small open reading frame of 522 bp (designated rptA, for rhizobium plasmid transfer A) had been disrupted. The predicted gene product encoded by the rptA sequence shows a significant similarity to two hypothetical proteins of the plasmid pSmed03 of Ensifer medicae WSM419 and other rhizobia plasmids. No significant similarity was found to any protein sequence of known function registered in the databases. Although the rptA gene was required for pSmeLPU88b-plasmid mobilization in the strain 2011 background, it was not required in the original strain LPU88 background.}, }
@article {pmid23671678, year = {2013}, author = {Vollmers, J and Voget, S and Dietrich, S and Gollnow, K and Smits, M and Meyer, K and Brinkhoff, T and Simon, M and Daniel, R}, title = {Poles apart: Arctic and Antarctic Octadecabacter strains share high genome plasticity and a new type of xanthorhodopsin.}, journal = {PloS one}, volume = {8}, number = {5}, pages = {e63422}, pmid = {23671678}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Antarctic Regions ; Arctic Regions ; Conserved Sequence ; DNA Transposable Elements ; *Genome, Bacterial ; Metagenome ; Molecular Sequence Annotation ; Molecular Sequence Data ; Molecular Typing ; Phylogeny ; Phylogeography ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Rhodobacteraceae/classification/*genetics ; Rhodopsins, Microbial/*genetics ; Sequence Analysis, DNA ; Synteny ; }, abstract = {The genus Octadecabacter is a member of the ubiquitous marine Roseobacter clade. The two described species of this genus, Octadecabacter arcticus and Octadecabacter antarcticus, are psychrophilic and display a bipolar distribution. Here we provide the manually annotated and finished genome sequences of the type strains O. arcticus 238 and O. antarcticus 307, isolated from sea ice of the Arctic and Antarctic, respectively. Both genomes exhibit a high genome plasticity caused by an unusually high density and diversity of transposable elements. This could explain the discrepancy between the low genome synteny and high 16S rRNA gene sequence similarity between both strains. Numerous characteristic features were identified in the Octadecabacter genomes, which show indications of horizontal gene transfer and may represent specific adaptations to the habitats of the strains. These include a gene cluster encoding the synthesis and degradation of cyanophycin in O. arcticus 238, which is absent in O. antarcticus 307 and unique among the Roseobacter clade. Furthermore, genes representing a new subgroup of xanthorhodopsins as an adaptation to icy environments are present in both Octadecabacter strains. This new xanthorhodopsin subgroup differs from the previously characterized xanthorhodopsins of Salinibacter ruber and Gloeobacter violaceus in phylogeny, biogeography and the potential to bind 4-keto-carotenoids. Biochemical characterization of the Octadecabacter xanthorhodopsins revealed that they function as light-driven proton pumps.}, }
@article {pmid23671590, year = {2013}, author = {Lenart, A and Dudkiewicz, M and Grynberg, M and Pawłowski, K}, title = {CLCAs - a family of metalloproteases of intriguing phylogenetic distribution and with cases of substituted catalytic sites.}, journal = {PloS one}, volume = {8}, number = {5}, pages = {e62272}, pmid = {23671590}, issn = {1932-6203}, mesh = {Amino Acid Motifs/genetics ; Amino Acid Sequence ; Archaeal Proteins/genetics ; Bacterial Proteins/genetics ; Databases, Protein ; Genome, Human/*genetics ; Humans ; Metalloproteases/classification/*genetics ; Molecular Sequence Data ; Multigene Family/*genetics ; *Phylogeny ; Sequence Homology, Amino Acid ; }, abstract = {The zinc-dependent metalloproteases with His-Glu-x-x-His (HExxH) active site motif, zincins, are a broad group of proteins involved in many metabolic and regulatory functions, and found in all forms of life. Human genome contains more than 100 genes encoding proteins with known zincin-like domains. A survey of all proteins containing the HExxH motif shows that approximately 52% of HExxH occurrences fall within known protein structural domains (as defined in the Pfam database). Domain families with majority of members possessing a conserved HExxH motif include, not surprisingly, many known and putative metalloproteases. Furthermore, several HExxH-containing protein domains thus identified can be confidently predicted to be putative peptidases of zincin fold. Thus, we predict zincin-like fold for eight uncharacterised Pfam families. Besides the domains with the HExxH motif strictly conserved, and those with sporadic occurrences, intermediate families are identified that contain some members with a conserved HExxH motif, but also many homologues with substitutions at the conserved positions. Such substitutions can be evolutionarily conserved and non-random, yet functional roles of these inactive zincins are not known. The CLCAs are a novel zincin-like protease family with many cases of substituted active sites. We show that this allegedly metazoan family has a number of bacterial and archaeal members. An extremely patchy phylogenetic distribution of CLCAs in prokaryotes and their conserved protein domain composition strongly suggests an evolutionary scenario of horizontal gene transfer (HGT) from multicellular eukaryotes to bacteria, providing an example of eukaryote-derived xenologues in bacterial genomes. Additionally, in a protein family identified here as closely homologous to CLCA, the CLCA_X (CLCA-like) family, a number of proteins is found in phages and plasmids, supporting the HGT scenario.}, }
@article {pmid23669427, year = {2013}, author = {Ogbolu, DO and Daini, OA and Ogunledun, A and Terry Alli, OA and Webber, MA}, title = {Dissemination of IncF plasmids carrying beta-lactamase genes in Gram-negative bacteria from Nigerian hospitals.}, journal = {Journal of infection in developing countries}, volume = {7}, number = {5}, pages = {382-390}, doi = {10.3855/jidc.2613}, pmid = {23669427}, issn = {1972-2680}, mesh = {Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; Cross Infection/*epidemiology ; DNA, Bacterial/genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Variation ; Gram-Negative Bacteria/drug effects/*enzymology/*genetics/isolation &amp; purification ; Gram-Negative Bacterial Infections/*epidemiology ; Hospitals ; Humans ; Microbial Sensitivity Tests ; Multiplex Polymerase Chain Reaction ; Nigeria ; Plasmids/classification/*isolation &amp; purification ; beta-Lactamases/*genetics ; }, abstract = {INTRODUCTION: Production of beta-lactamases is the predominant cause of resistance to beta-lactam antibiotics in Gram-negative bacteria. We investigated the diversity of plasmid-borne beta-lactamase genes and replicon type of the plasmids carrying the respective genes in Gram-negative bacteria recovered from clinical infection in Nigerian hospitals.<br><br>METHODOLOGY: A total of 134 Gram-negative bacteria of 13 species were analyzed for antimicrobial susceptibility, phenotypic and genotypic detection of various beta-lactamases, and plasmid analysis, including replicon typing.<br><br>RESULTS: Of the 134 isolates, 111 (82.8%) contained beta-lactamases, while 28 (20.9%) carried extended-spectrum beta-lactamases. PCR and sequencing identified TEM-1 in 109 isolates (81.3%), SHV-1 in 33 isolates (24.6%), OXA-1 in 15 isolates (11.2%) and CTX-M enzymes (24 CTX-M-15 and 1 CTX-M-3) in 25 isolates (18.7%). Multiplex PCR showed that 6 isolates carried plasmidic AmpCs (ACT-1, DHA-1 and CMY-2); these enzymes were detected only in isolates possessing CTX-M beta-lactamases. Of 13 (76.9%) representative plasmids investigated in detail, 9 (69.2%) were self-transferable when selected by a beta-lactam and the plasmids once transferred coded for beta-lactam resistance. Replicon typing indicated IncF as the common vector encoding for beta-lactamases.<br><br>CONCLUSIONS: The study showed a diversity of beta-lactamase genes disseminated by conjugative IncF plasmids in Gram-negative bacteria; TEM-1, SHV-1, OXA-1, CTX-M-15, CTX-M-3 and plasmidic AmpC enzymes are in common circulation in Nigeria.}, }
@article {pmid23668604, year = {2013}, author = {Morita, M and Yamamoto, S and Hiyoshi, H and Kodama, T and Okura, M and Arakawa, E and Alam, M and Ohnishi, M and Izumiya, H and Watanabe, H}, title = {Horizontal gene transfer of a genetic island encoding a type III secretion system distributed in Vibrio cholerae.}, journal = {Microbiology and immunology}, volume = {57}, number = {5}, pages = {334-339}, doi = {10.1111/1348-0421.12039}, pmid = {23668604}, issn = {1348-0421}, mesh = {Cholera/microbiology ; Chromosomes, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Environmental Microbiology ; *Gene Transfer, Horizontal ; Genetic Variation ; *Genomic Islands ; Genotype ; Humans ; Membrane Transport Proteins/*genetics ; Molecular Typing ; Multigene Family ; Polymorphism, Restriction Fragment Length ; Vibrio cholerae/classification/*genetics/isolation &amp; purification/pathogenicity ; Virulence Factors/*genetics ; }, abstract = {Twelve Vibrio cholerae isolates with genes for a type III secretion system (T3SS) were detected among 110 environmental and 14 clinical isolates. T3SS-related genes were distributed among the various serogroups and pulsed-field gel electrophoresis of NotI-digested genomes showed genetic diversity in these strains. However, the restriction fragment length polymorphism profiles of the T3SS-related genes had similar patterns. Additionally, naturally competent T3SS-negative V. cholerae incorporated the ca. 47 kb gene cluster of T3SS, which had been integrated into a site on the chromosome by recombination. Therefore, it is suggested that horizontal gene transfer of T3SS-related genes occurs among V. cholerae in natural ecosystems.}, }
@article {pmid23667703, year = {2013}, author = {Song, D and Cho, WK and Park, SH and Jo, Y and Kim, KH}, title = {Evolution of and horizontal gene transfer in the Endornavirus genus.}, journal = {PloS one}, volume = {8}, number = {5}, pages = {e64270}, pmid = {23667703}, issn = {1932-6203}, mesh = {Base Sequence ; *Biological Evolution ; Capsicum/virology ; Conserved Sequence ; Gene Transfer, Horizontal/*genetics ; Genome, Plant/genetics ; Phylogeny ; Plant Proteins/chemistry ; Plants/genetics/virology ; Protein Structure, Tertiary ; RNA Viruses/*genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {The transfer of genetic information between unrelated species is referred to as horizontal gene transfer. Previous studies have demonstrated that both retroviral and non-retroviral sequences have been integrated into eukaryotic genomes. Recently, we identified many non-retroviral sequences in plant genomes. In this study, we investigated the evolutionary origin and gene transfer of domains present in endornaviruses which are double-stranded RNA viruses. Using the available sequences for endornaviruses, we found that Bell pepper endornavirus-like sequences homologous to the glycosyltransferase 28 domain are present in plants, fungi, and bacteria. The phylogenetic analysis revealed the glycosyltransferase 28 domain of Bell pepper endornavirus may have originated from bacteria. In addition, two domains of Oryza sativa endornavirus, a glycosyltransferase sugar-binding domain and a capsular polysaccharide synthesis protein, also exhibited high similarity to those of bacteria. We found evidence that at least four independent horizontal gene transfer events for the glycosyltransferase 28 domain have occurred among plants, fungi, and bacteria. The glycosyltransferase sugar-binding domains of two proteobacteria may have been horizontally transferred to the genome of Thalassiosira pseudonana. Our study is the first to show that three glycome-related viral genes in the genus Endornavirus have been acquired from marine bacteria by horizontal gene transfer.}, }
@article {pmid23666328, year = {2013}, author = {Amachawadi, RG and Scott, HM and Alvarado, CA and Mainini, TR and Vinasco, J and Drouillard, JS and Nagaraja, TG}, title = {Occurrence of the transferable copper resistance gene tcrB among fecal enterococci of U.S. feedlot cattle fed copper-supplemented diets.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {14}, pages = {4369-4375}, pmid = {23666328}, issn = {1098-5336}, mesh = {Animal Feed/analysis ; Animals ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/*genetics/metabolism ; Blotting, Southern/veterinary ; Cattle ; Copper/administration &amp; dosage/*pharmacology ; Dietary Supplements ; *Drug Resistance, Bacterial ; Drug Resistance, Multiple, Bacterial ; Enterococcus faecium/drug effects/*genetics/metabolism/pathogenicity ; Feces/microbiology ; Female ; Gene Transfer, Horizontal ; Methyltransferases/*genetics/metabolism ; Minisatellite Repeats ; Molecular Sequence Data ; Multilocus Sequence Typing/veterinary ; Multiplex Polymerase Chain Reaction/veterinary ; Sequence Analysis, DNA/veterinary ; Tetracycline/pharmacology ; Tylosin/pharmacology ; Vancomycin/pharmacology ; Virulence Factors/genetics/metabolism ; }, abstract = {Copper, an essential micronutrient, is supplemented in the diet at elevated levels to reduce morbidity and mortality and to promote growth in feedlot cattle. Gut bacteria exposed to copper can acquire resistance, which among enterococci is conferred by a transferable copper resistance gene (tcrB) borne on a plasmid. The present study was undertaken to investigate whether the feeding of copper at levels sufficient to promote growth increases the prevalence of the tcrB gene among the fecal enterococci of feedlot cattle. The study was performed with 261 crossbred yearling heifers housed in 24 pens, with pens assigned randomly to a 2×2 factorial arrangement of treatments consisting of dietary copper and a commercial linseed meal-based energy protein supplement. A total of 22 isolates, each identified as Enterococcus faecium, were positive for tcrB with an overall prevalence of 3.8% (22/576). The prevalence was higher among the cattle fed diets supplemented with copper (6.9%) compared to normal copper levels (0.7%). The tcrB-positive isolates always contained both erm(B) and tet(M) genes. Median copper MICs for tcrB-positive and tcrB-negative enterococci were 22 and 4 mM, respectively. The transferability of the tcrB gene was demonstrated via a filter-mating assay. Multilocus variable number tandem repeat analysis revealed a genetically diverse population of enterococci. The finding of a strong association between the copper resistance gene and other antibiotic (tetracycline and tylosin) resistance determinants is significant because enterococci remain potential pathogens and have the propensity to transfer resistance genes to other bacteria in the gut.}, }
@article {pmid23666077, year = {2014}, author = {Dewan, V and Reader, J and Forsyth, KM}, title = {Role of aminoacyl-tRNA synthetases in infectious diseases and targets for therapeutic development.}, journal = {Topics in current chemistry}, volume = {344}, number = {}, pages = {293-329}, doi = {10.1007/128_2013_425}, pmid = {23666077}, issn = {0340-1022}, support = {AI077387/AI/NIAID NIH HHS/United States ; GM049928/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acyl-tRNA Synthetases/antagonists &amp; inhibitors/chemistry/genetics/*metabolism ; Bacterial Infections/drug therapy/enzymology ; Base Sequence ; Communicable Diseases/*drug therapy/*enzymology ; Drug Discovery/*methods ; Humans ; Molecular Targeted Therapy/*methods ; Virus Diseases/drug therapy/enzymology ; }, abstract = {Aminoacyl-tRNA synthetases (AARSs) play a pivotal role in protein synthesis and cell viability. These 22 "housekeeping" enzymes (1 for each standard amino acid plus pyrrolysine and o-phosphoserine) are specifically involved in recognizing and aminoacylating their cognate tRNAs in the cellular pool with the correct amino acid prior to delivery of the charged tRNA to the protein synthesis machinery. Besides serving this canonical function, higher eukaryotic AARSs, some of which are organized in the cytoplasm as a multisynthetase complex of nine enzymes plus additional cellular factors, have also been implicated in a variety of non-canonical roles. AARSs are involved in the regulation of transcription, translation, and various signaling pathways, thereby ensuring cell survival. Based in part on their versatility, AARSs have been recruited by viruses to perform essential functions. For example, host synthetases are packaged into some retroviruses and are required for their replication. Other viruses mimic tRNA-like structures in their genomes, and these motifs are aminoacylated by the host synthetase as part of the viral replication cycle. More recently, it has been shown that certain large DNA viruses infecting animals and other diverse unicellular eukaryotes encode tRNAs, AARSs, and additional components of the protein-synthesis machinery. This chapter will review our current understanding of the role of host AARSs and tRNA-like structures in viruses and discuss their potential as anti-viral drug targets. The identification and development of compounds that target bacterial AARSs, thereby serving as novel antibiotics, will also be discussed. Particular attention will be given to recent work on a number of tRNA-dependent AARS inhibitors and to advances in a new class of natural "pro-drug" antibiotics called Trojan Horse inhibitors. Finally, we will explore how bacteria that naturally produce AARS-targeting antibiotics must protect themselves against cell suicide using naturally antibiotic resistant AARSs, and how horizontal gene transfer of these AARS genes to pathogens may threaten the future use of this class of antibiotics.}, }
@article {pmid23663384, year = {2013}, author = {Solonenko, SA and Ignacio-Espinoza, JC and Alberti, A and Cruaud, C and Hallam, S and Konstantinidis, K and Tyson, G and Wincker, P and Sullivan, MB}, title = {Sequencing platform and library preparation choices impact viral metagenomes.}, journal = {BMC genomics}, volume = {14}, number = {}, pages = {320}, pmid = {23663384}, issn = {1471-2164}, mesh = {Base Composition ; DNA, Viral/genetics ; *Gene Library ; Genome, Viral/*genetics ; High-Throughput Nucleotide Sequencing ; Metagenome/*genetics ; Nucleic Acid Amplification Techniques ; *Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Microbes drive the biogeochemistry that fuels the planet. Microbial viruses modulate their hosts directly through mortality and horizontal gene transfer, and indirectly by re-programming host metabolisms during infection. However, our ability to study these virus-host interactions is limited by methods that are low-throughput and heavily reliant upon the subset of organisms that are in culture. One way forward are culture-independent metagenomic approaches, but these novel methods are rarely rigorously tested, especially for studies of environmental viruses, air microbiomes, extreme environment microbiology and other areas with constrained sample amounts. Here we perform replicated experiments to evaluate Roche 454, Illumina HiSeq, and Ion Torrent PGM sequencing and library preparation protocols on virus metagenomes generated from as little as 10 pg of DNA.<br><br>RESULTS: Using %G+C content to compare metagenomes, we find that (i) metagenomes are highly replicable, (ii) some treatment effects are minimal, e.g., sequencing technology choice has 6-fold less impact than varying input DNA amount, and (iii) when restricted to a limited DNA concentration (<1 &#x3bc;g), changing the amount of amplification produces little variation. These trends were also observed when examining the metagenomes for gene function and assembly performance, although the latter more closely aligned to sequencing effort and read length than preparation steps tested. Among Illumina library preparation options, transposon-based libraries diverged from all others and adaptor ligation was a critical step for optimizing sequencing yields.<br><br>CONCLUSIONS: These data guide researchers in generating systematic, comparative datasets to understand complex ecosystems, and suggest that neither varied amplification nor sequencing platforms will deter such efforts.}, }
@article {pmid23661089, year = {2013}, author = {Srinivasan, R and Chandraprakash, D and Krishnamurthi, R and Singh, P and Scolari, VF and Krishna, S and Seshasayee, AS}, title = {Genomic analysis reveals epistatic silencing of "expensive" genes in Escherichia coli K-12.}, journal = {Molecular bioSystems}, volume = {9}, number = {8}, pages = {2021-2033}, doi = {10.1039/c3mb70035f}, pmid = {23661089}, issn = {1742-2051}, mesh = {Binding Sites ; DNA-Binding Proteins/*genetics/metabolism ; *Epistasis, Genetic ; Escherichia coli K12/*genetics/metabolism ; Escherichia coli Proteins/*genetics/metabolism ; Fimbriae Proteins/*genetics/metabolism ; *Gene Expression Regulation, Bacterial ; *Gene Silencing ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Molecular Chaperones/*genetics/metabolism ; Protein Binding ; Repressor Proteins/genetics/metabolism ; Sequence Analysis, DNA ; Transcription, Genetic ; Transcriptome ; }, abstract = {A barrier for horizontal gene transfer is high gene expression, which is metabolically expensive. Silencing of horizontally-acquired genes in the bacterium Escherichia coli is caused by the global transcriptional repressor H-NS. The activity of H-NS is enhanced or diminished by other proteins including its homologue StpA, and Hha and YdgT. The interconnections of H-NS with these regulators and their role in silencing gene expression in E. coli are not well understood on a genomic scale. In this study, we use transcriptome sequencing to show that there is a bi-layered gene silencing system - involving the homologous H-NS and StpA - operating on horizontally-acquired genes among others. We show that H-NS-repressed genes belong to two types, termed "epistatic" and "unilateral". In the absence of H-NS, the expression of "epistatically controlled genes" is repressed by StpA, whereas that of "unilaterally controlled genes" is not. Epistatic genes show a higher tendency to be non-essential and recently acquired, when compared to unilateral genes. Epistatic genes reach much higher expression levels than unilateral genes in the absence of the silencing system. Finally, epistatic genes contain more high affinity H-NS binding motifs than unilateral genes. Therefore, both the DNA binding sites of H-NS as well as the function of StpA as a backup system might be selected for silencing highly transcribable genes.}, }
@article {pmid23660485, year = {2014}, author = {Xia, G and Wolz, C}, title = {Phages of Staphylococcus aureus and their impact on host evolution.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {21}, number = {}, pages = {593-601}, doi = {10.1016/j.meegid.2013.04.022}, pmid = {23660485}, issn = {1567-7257}, mesh = {Adsorption ; Animals ; *Biological Evolution ; Gene Transfer, Horizontal ; Genome, Viral ; Humans ; Phylogeny ; Staphylococcus Phages/*classification/*genetics ; Staphylococcus aureus/*genetics/*virology ; }, abstract = {Most of the dissimilarity between Staphylococcus aureus strains is due to the presence of mobile genetic elements such as bacteriophages or pathogenicity islands. These elements provide the bacteria with additional genes that enable them to establish a new lifestyle that is often accompanied by a shift to increased pathogenicity or a jump to a new host. S. aureus phages may carry genes coding for diverse virulence factors such as Panton-Valentine leukocidin, staphylokinase, enterotoxins, chemotaxis-inhibitory proteins, or exfoliative toxins. Phages also mediate the transfer of pathogenicity islands in a highly coordinated manner and are the primary vehicle for the horizontal transfer of chromosomal and extra-chromosomal genes. Here, we summarise recent advances regarding phage classification, genome organisation and function of S. aureus phages with a particular emphasis on their role in the evolution of the bacterial host.}, }
@article {pmid23659602, year = {2013}, author = {Usui, M and Iwasa, T and Fukuda, A and Sato, T and Okubo, T and Tamura, Y}, title = {The role of flies in spreading the extended-spectrum β-lactamase gene from cattle.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {19}, number = {5}, pages = {415-420}, doi = {10.1089/mdr.2012.0251}, pmid = {23659602}, issn = {1931-8448}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacterial Typing Techniques ; Cattle ; Cattle Diseases/*epidemiology/microbiology ; Cephalosporin Resistance/drug effects/genetics ; Cephalosporins/pharmacology ; Diptera/*microbiology ; Disease Reservoirs/*microbiology ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/enzymology/*genetics/isolation &amp; purification ; Escherichia coli Infections/epidemiology/microbiology/*veterinary ; Feces/microbiology ; Gene Transfer, Horizontal ; Humans ; Japan/epidemiology ; Microbial Sensitivity Tests ; Plasmids ; Prevalence ; beta-Lactamases/*genetics/metabolism ; }, abstract = {The spreading of antimicrobial-resistant bacteria and genes from food-producing animals to humans has been a subject of increasing concern. To clarify the role of flies in spreading the extended-spectrum β-lactamase (ESBL) gene from food-producing animals to humans, we isolated and characterized a third-generation cephalosporin-resistant Escherichia coli strain from flies and cattle feces from a cattle barn. Cephalosporin-resistant strains were isolated from 14.3% (13/91) of houseflies, 10.3% (7/68) of false stable flies, and 7.5% (7/93) of cattle feces. Twenty-seven cephalosporin-resistant strains were tested for the presence of antimicrobial resistance genes. Of the 27 samples, 22 isolates from 11 houseflies, 5 false stable flies, and 6 cattle feces samples harbored the blaCTX-M-15 gene. All blaCTX-M-15-harboring isolates belonged to phylogenetic group D and the ST38 clonal group. Analysis of pulsed-field gel electrophoresis showed that these isolates were divided into two clusters, indicating that flies carried several of the same clones that were detected in cattle feces. All blaCTX-M-15 gene-harboring plasmids were transferable and were members of incompatibility group FIB. These results suggest that transferable plasmids encoding ESBL were prevalent among flies and cattle. As vectors, flies may play an important role in spreading ESBL-producing bacteria from food-producing animals to humans.}, }
@article {pmid23659318, year = {2013}, author = {Røder, HL and Hansen, LH and Sørensen, SJ and Burmølle, M}, title = {The impact of the conjugative IncP-1 plasmid pKJK5 on multispecies biofilm formation is dependent on the plasmid host.}, journal = {FEMS microbiology letters}, volume = {344}, number = {2}, pages = {186-192}, doi = {10.1111/1574-6968.12175}, pmid = {23659318}, issn = {1574-6968}, mesh = {*Biofilms ; *Conjugation, Genetic ; Escherichia coli/genetics/*physiology ; Kluyvera/genetics/*physiology ; Plasmids/*genetics/metabolism ; Pseudomonas putida/genetics/*physiology ; Species Specificity ; }, abstract = {Horizontal gene transfer by conjugation has been reported to increase overall biofilm formation. Biofilm is considered a hot spot for plasmid transfer, and it has been found that social interactions during biofilm formation can increase the biomass. In this study, we demonstrate a contrast to previous studies by showing that the conjugative IncP-1 plasmid pKJK5 influences biofilm formation negatively. The results showed that a co-culture (Pseudomonas putida, Kluyvera sp., and Escherichia coli) formed significantly more biofilm than the strains did individually. When pKJK5 was inserted into P. putida, biofilm formation was significantly reduced compared with the co-culture without plasmid. A nonconjugative version of pKJK5 was also used, and the biofilm formation was restored. Visualization with the BioFlux 1000 facility showed that the presence of pKJK5-containing P. putida in the co-culture led to a changed biofilm structure, where the cells showed a higher tendency to attach to other cells rather than surfaces. This study thus indicates that the presence of conjugative plasmids in some species may decrease the surface-associated biofilm formation of a mixed co-culture by facilitating cell-cell attachment with reduced surface attachment as the consequence.}, }
@article {pmid23653265, year = {2013}, author = {Khan, A and Asif, H and Studholme, DJ and Khan, IA and Azim, MK}, title = {Genome characterization of a novel Burkholderia cepacia complex genomovar isolated from dieback affected mango orchards.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {29}, number = {11}, pages = {2033-2044}, pmid = {23653265}, issn = {1573-0972}, mesh = {Bacterial Outer Membrane Proteins/chemistry ; Bacterial Proteins/chemistry ; Bacterial Typing Techniques ; Burkholderia cepacia complex/*genetics/*isolation &amp; purification/metabolism ; Evolution, Molecular ; *Genome, Bacterial ; Genomics/methods ; Gram-Negative Bacteria/genetics/isolation &amp; purification ; Haemophilus influenzae/genetics/metabolism ; High-Throughput Nucleotide Sequencing ; Mangifera/*microbiology ; Models, Molecular ; Molecular Sequence Annotation ; Phylogeny ; Plant Diseases/*microbiology ; Protein Structure, Secondary ; Sequence Alignment ; Serine Endopeptidases/chemistry ; Virulence Factors/genetics/metabolism ; }, abstract = {We characterized the genome of the antibiotic resistant, caseinolytic and non-hemolytic Burkholderia sp. strain TJI49, isolated from mango trees (Mangifera indica L.) with dieback disease. This isolate produced severe disease symptoms on the indicator plants. Next generation DNA sequencing and short-read assembly generated the 60X deep 7,631,934 nucleotide draft genome of Burkholderia sp. TJI49 which comprised three chromosomes and at least one mega plasmid. Genome annotation studies revealed a total 8,992 genes, out of which 8,940 were protein coding genes. Comparative genomics and phylogenetics identified Burkholderia sp. TJI49 as a distinct species of Burkholderia cepacia complex (BCC), closely related to B. multivorans ATCC17616. Genome-wide sequence alignment of this isolate with replicons of BCC members showed conservation of core function genes but considerable variations in accessory genes. Subsystem-based gene annotation identified the active presence of wide spread colonization island and type VI secretion system in Burkholderia sp. TJI49. Sequence comparisons revealed (a) 28 novel ORFs that have no database matches and (b) 23 ORFs with orthologues in species other than Burkholderia, indicating horizontal gene transfer events. Fold recognition of novel ORFs identified genes encoding pertactin autotransporter-like proteins (a constituent of type V secretion system) and Hap adhesion-like proteins (involved in cell-cell adhesion) in the genome of Burkholderia sp. TJI49. The genomic characterization of this isolate provided additional information related to the 'pan-genome' of Burkholderia species.}, }
@article {pmid23651955, year = {2013}, author = {Broaders, E and Gahan, CG and Marchesi, JR}, title = {Mobile genetic elements of the human gastrointestinal tract: potential for spread of antibiotic resistance genes.}, journal = {Gut microbes}, volume = {4}, number = {4}, pages = {271-280}, pmid = {23651955}, issn = {1949-0984}, mesh = {Drug Resistance, Bacterial ; Gastrointestinal Tract/*microbiology ; Gene Transfer, Horizontal ; Humans ; *Interspersed Repetitive Sequences ; *Microbiota ; }, abstract = {The human intestine is an important location for horizontal gene transfer (HGT) due to the presence of a densely populated community of microorganisms which are essential to the health of the human superorganism. HGT in this niche has the potential to influence the evolution of members of this microbial community and to mediate the spread of antibiotic resistance genes from commensal organisms to potential pathogens. Recent culture-independent techniques and metagenomic studies have provided an insight into the distribution of mobile genetic elements (MGEs) and the extent of HGT in the human gastrointestinal tract. In this mini-review, we explore the current knowledge of mobile genetic elements in the gastrointestinal tract, the progress of research into the distribution of antibiotic resistance genes in the gut and the potential role of MGEs in the spread of antibiotic resistance. In the face of reduced treatment options for many clinical infections, understanding environmental and commensal antibiotic resistance and spread is critical to the future development of meaningful and long lasting anti-microbial therapies.}, }
@article {pmid23645598, year = {2013}, author = {Carter, AT and Stringer, SC and Webb, MD and Peck, MW}, title = {The type F6 neurotoxin gene cluster locus of group II clostridium botulinum has evolved by successive disruption of two different ancestral precursors.}, journal = {Genome biology and evolution}, volume = {5}, number = {5}, pages = {1032-1037}, pmid = {23645598}, issn = {1759-6653}, support = {BB/J004529/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Base Sequence ; Botulinum Toxins/*genetics ; Botulinum Toxins, Type A ; Botulism/genetics/microbiology ; Clostridium botulinum/*genetics/pathogenicity ; Clostridium botulinum type E/genetics ; DNA Topoisomerases, Type I/*genetics ; DNA Transposable Elements ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Humans ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; }, abstract = {Genome sequences of five different Group II (nonproteolytic) Clostridium botulinum type F6 strains were compared at a 50-kb locus containing the neurotoxin gene cluster. A clonal origin for these strains is indicated by the fact that sequences were identical except for strain Eklund 202F, with 10 single-nucleotide polymorphisms and a 15-bp deletion. The essential topB gene encoding topoisomerase III was found to have been split by the apparent insertion of 34.4 kb of foreign DNA (in a similar manner to that in Group II C. botulinum type E where the rarA gene has been disrupted by a neurotoxin gene cluster). The foreign DNA, which includes the intact 13.6-kb type F6 neurotoxin gene cluster, bears not only a newly introduced topB gene but also two nonfunctional botulinum neurotoxin gene remnants, a type B and a type E. This observation combined with the discovery of bacteriophage integrase genes and IS4 elements suggest that several rounds of recombination/horizontal gene transfer have occurred at this locus. The simplest explanation for the current genotype is that the ancestral bacterium, a Group II C. botulinum type B strain, received DNA firstly from a strain containing a type E neurotoxin gene cluster, then from a strain containing a type F6 neurotoxin gene cluster. Each event disrupted the previously functional neurotoxin gene. This degree of successive recombination at one hot spot is without precedent in C. botulinum, and it is also the first description of a Group II C. botulinum genome containing more than one neurotoxin gene sequence.}, }
@article {pmid23645554, year = {2013}, author = {Bhattacharya, D and Pelletreau, KN and Price, DC and Sarver, KE and Rumpho, ME}, title = {Genome analysis of Elysia chlorotica Egg DNA provides no evidence for horizontal gene transfer into the germ line of this Kleptoplastic Mollusc.}, journal = {Molecular biology and evolution}, volume = {30}, number = {8}, pages = {1843-1852}, pmid = {23645554}, issn = {1537-1719}, mesh = {Animals ; Computational Biology/methods ; *DNA ; Databases, Nucleic Acid ; Gastropoda/*genetics/metabolism ; *Gene Transfer, Horizontal ; *Genomics ; Germ Cells/*metabolism ; Transcription, Genetic ; }, abstract = {The sea slug Elysia chlorotica offers a unique opportunity to study the evolution of a novel function (photosynthesis) in a complex multicellular host. Elysia chlorotica harvests plastids (absent of nuclei) from its heterokont algal prey, Vaucheria litorea. The "stolen" plastids are maintained for several months in cells of the digestive tract and are essential for animal development. The basis of long-term maintenance of photosynthesis in this sea slug was thought to be explained by extensive horizontal gene transfer (HGT) from the nucleus of the alga to the animal nucleus, followed by expression of algal genes in the gut to provide essential plastid-destined proteins. Early studies of target genes and proteins supported the HGT hypothesis, but more recent genome-wide data provide conflicting results. Here, we generated significant genome data from the E. chlorotica germ line (egg DNA) and from V. litorea to test the HGT hypothesis. Our comprehensive analyses fail to provide evidence for alga-derived HGT into the germ line of the sea slug. Polymerase chain reaction analyses of genomic DNA and cDNA from different individual E. chlorotica suggest, however, that algal nuclear genes (or gene fragments) are present in the adult slug. We suggest that these nucleic acids may derive from and/or reside in extrachromosomal DNAs that are made available to the animal through contact with the alga. These data resolve a long-standing issue and suggest that HGT is not the primary reason underlying long-term maintenance of photosynthesis in E. chlorotica. Therefore, sea slug photosynthesis is sustained in as yet unexplained ways that do not appear to endanger the animal germ line through the introduction of dozens of foreign genes.}, }
@article {pmid23641238, year = {2013}, author = {Djordjevic, SP and Stokes, HW and Roy Chowdhury, P}, title = {Mobile elements, zoonotic pathogens and commensal bacteria: conduits for the delivery of resistance genes into humans, production animals and soil microbiota.}, journal = {Frontiers in microbiology}, volume = {4}, number = {}, pages = {86}, pmid = {23641238}, issn = {1664-302X}, abstract = {Multiple antibiotic resistant pathogens represent a major clinical challenge in both human and veterinary context. It is now well-understood that the genes that encode resistance are context independent. That is, the same gene is commonly present in otherwise very disparate pathogens in both humans and production and companion animals, and among bacteria that proliferate in an agricultural context. This can be true even for pathogenic species or clonal types that are otherwise confined to a single host or ecological niche. It therefore follows that mechanisms of gene flow must exist to move genes from one part of the microbial biosphere to another. It is widely accepted that lateral (or horizontal) gene transfer (L(H)GT) drives this gene flow. LGT is relatively well-understood mechanistically but much of this knowledge is derived from a reductionist perspective. We believe that this is impeding our ability to deal with the medical ramifications of LGT. Resistance genes and the genetic scaffolds that mobilize them in multiply drug resistant bacteria of clinical significance are likely to have their origins in completely unrelated parts of the microbial biosphere. Resistance genes are increasingly polluting the microbial biosphere by contaminating environmental niches where previously they were not detected. More attention needs to be paid to the way that humans have, through the widespread application of antibiotics, selected for combinations of mobile elements that enhance the flow of resistance genes between remotely linked parts of the microbial biosphere. Attention also needs to be paid to those bacteria that link human and animal ecosystems. We argue that multiply antibiotic resistant commensal bacteria are especially important in this regard. More generally, the post genomics era offers the opportunity for understanding how resistance genes are mobilized from a one health perspective. In the long term, this holistic approach offers the best opportunity to better manage what is an enormous problem to humans both in terms of health and food security.}, }
@article {pmid23637766, year = {2013}, author = {Beaudet, D and Nadimi, M and Iffis, B and Hijri, M}, title = {Rapid mitochondrial genome evolution through invasion of mobile elements in two closely related species of arbuscular mycorrhizal fungi.}, journal = {PloS one}, volume = {8}, number = {4}, pages = {e60768}, pmid = {23637766}, issn = {1932-6203}, mesh = {Base Sequence ; Biological Evolution ; DNA, Fungal/genetics ; DNA, Mitochondrial/genetics ; Gene Transfer, Horizontal ; Genetic Variation ; Genome, Mitochondrial/*genetics ; Glomeromycota/*genetics ; Introns ; Mycorrhizae/*genetics ; Open Reading Frames ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) are common and important plant symbionts. They have coenocytic hyphae and form multinucleated spores. The nuclear genome of AMF is polymorphic and its organization is not well understood, which makes the development of reliable molecular markers challenging. In stark contrast, their mitochondrial genome (mtDNA) is homogeneous. To assess the intra- and inter-specific mitochondrial variability in closely related Glomus species, we performed 454 sequencing on total genomic DNA of Glomus sp. isolate DAOM-229456 and we compared its mtDNA with two G. irregulare isolates. We found that the mtDNA of Glomus sp. is homogeneous, identical in gene order and, with respect to the sequences of coding regions, almost identical to G. irregulare. However, certain genomic regions vary substantially, due to insertions/deletions of elements such as introns, mitochondrial plasmid-like DNA polymerase genes and mobile open reading frames. We found no evidence of mitochondrial or cytoplasmic plasmids in Glomus species, and mobile ORFs in Glomus are responsible for the formation of four gene hybrids in atp6, atp9, cox2, and nad3, which are most probably the result of horizontal gene transfer and are expressed at the mRNA level. We found evidence for substantial sequence variation in defined regions of mtDNA, even among closely related isolates with otherwise identical coding gene sequences. This variation makes it possible to design reliable intra- and inter-specific markers.}, }
@article {pmid23636378, year = {2013}, author = {Gilbert, N}, title = {Case studies: A hard look at GM crops.}, journal = {Nature}, volume = {497}, number = {7447}, pages = {24-26}, pmid = {23636378}, issn = {1476-4687}, mesh = {*Food, Genetically Modified/adverse effects/statistics &amp; numerical data ; Gene Transfer, Horizontal ; Glycine/administration &amp; dosage/analogs &amp; derivatives/pharmacology ; Gossypium/genetics/physiology ; Herbicide Resistance/genetics ; India/epidemiology ; Mexico ; Plant Weeds/drug effects/genetics/growth &amp; development ; *Plants, Genetically Modified/drug effects/genetics/physiology ; Transgenes/genetics ; Zea mays/genetics ; Glyphosate ; }, }
@article {pmid23635867, year = {2013}, author = {Brum, JR and Schenck, RO and Sullivan, MB}, title = {Global morphological analysis of marine viruses shows minimal regional variation and dominance of non-tailed viruses.}, journal = {The ISME journal}, volume = {7}, number = {9}, pages = {1738-1751}, pmid = {23635867}, issn = {1751-7370}, mesh = {*Biodiversity ; Capsid/ultrastructure ; Environment ; Geography ; Microscopy, Electron, Transmission ; Oceans and Seas ; Salinity ; Seawater/*virology ; Viruses/classification/*ultrastructure ; *Water Microbiology ; }, abstract = {Viruses influence oceanic ecosystems by causing mortality of microorganisms, altering nutrient and organic matter flux via lysis and auxiliary metabolic gene expression and changing the trajectory of microbial evolution through horizontal gene transfer. Limited host range and differing genetic potential of individual virus types mean that investigations into the types of viruses that exist in the ocean and their spatial distribution throughout the world's oceans are critical to understanding the global impacts of marine viruses. Here we evaluate viral morphological characteristics (morphotype, capsid diameter and tail length) using a quantitative transmission electron microscopy (qTEM) method across six of the world's oceans and seas sampled through the Tara Oceans Expedition. Extensive experimental validation of the qTEM method shows that neither sample preservation nor preparation significantly alters natural viral morphological characteristics. The global sampling analysis demonstrated that morphological characteristics did not vary consistently with depth (surface versus deep chlorophyll maximum waters) or oceanic region. Instead, temperature, salinity and oxygen concentration, but not chlorophyll a concentration, were more explanatory in evaluating differences in viral assemblage morphological characteristics. Surprisingly, given that the majority of cultivated bacterial viruses are tailed, non-tailed viruses appear to numerically dominate the upper oceans as they comprised 51-92% of the viral particles observed. Together, these results document global marine viral morphological characteristics, show that their minimal variability is more explained by environmental conditions than geography and suggest that non-tailed viruses might represent the most ecologically important targets for future research.}, }
@article {pmid23634808, year = {2013}, author = {Luis, P and Gauthier, A and Trouvelot, S and Poinssot, B and Frettinger, P}, title = {Identification of Plasmopara viticola genes potentially involved in pathogenesis on grapevine suggests new similarities between oomycetes and true fungi.}, journal = {Phytopathology}, volume = {103}, number = {10}, pages = {1035-1044}, doi = {10.1094/PHYTO-06-12-0121-R}, pmid = {23634808}, issn = {0031-949X}, mesh = {Fungi ; Gene Expression Regulation, Plant ; Oomycetes ; *Phylogeny ; *Plant Diseases/microbiology ; Plant Leaves ; Vitis/microbiology ; }, abstract = {Plant diseases caused by fungi and oomycetes result in significant economic losses every year. Although phylogenetically distant, these organisms share many common features during infection. We identified genes in the oomycete Plasmopara viticola that are potentially involved in pathogenesis in grapevine by using fungal databases and degenerate primers. Fragments of P. viticola genes encoding NADH-ubiquinone oxidoreductase (PvNuo), laccase (PvLac), and invertase (PvInv) were obtained. PvNuo was overexpressed at 2 days postinoculation (dpi), during the development of the first hyphal structures and haustoria. PvLac was overexpressed at 5 dpi when genes related to pterostilbene biosynthesis were induced in grapevine. Transcript level for PvInv increased between 1 and 4 dpi before reaching a plateau. These results might suggest a finely tuned strategy of infection depending on nutrition and plant response. Phylogenetic analyses of PvNuo showed that P. viticola clustered with other oomycetes and was associated with brown algae and diatoms, forming a typical Straminipila clade. Based on the comparison of available sequences for laccases and invertases, the group formed by P. viticola and other oomycetes tended to be more closely related to Opisthokonta than to Straminipila. Convergent evolution or horizontal gene transfer could explain the presence of fungus-like genes in P. viticola.}, }
@article {pmid23628638, year = {2014}, author = {Chua, KY and Howden, BP and Jiang, JH and Stinear, T and Peleg, AY}, title = {Population genetics and the evolution of virulence in Staphylococcus aureus.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {21}, number = {}, pages = {554-562}, doi = {10.1016/j.meegid.2013.04.026}, pmid = {23628638}, issn = {1567-7257}, mesh = {Drug Resistance, Bacterial ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; Molecular Typing ; Sequence Analysis, DNA ; Staphylococcal Infections/microbiology ; Staphylococcus aureus/classification/*genetics/isolation &amp; purification/*pathogenicity ; Virulence Factors/*genetics/metabolism ; }, abstract = {Staphylococcus aureus is one of the most important human pathogens, causing life-threatening infection in the community and hospital setting. The population genetics of S. aureus and the evolution of virulence is the focus of this review. We describe the various techniques in determining S. aureus population structure and discuss the insights gained from whole genome sequencing of various S. aureus strains. The emergence of community-acquired, methicillin-resistant S. aureus provides a framework for the discussion on evolution of virulence, and the role of horizontal gene transfer in the development of virulence and antibiotic resistance is explored. The knowledge generated from population genetics has the potential to inform strategies to assist in the prevention or treatment of this highly successful human pathogen.}, }
@article {pmid23626855, year = {2013}, author = {Chung, WC and Chen, LL and Lo, WS and Lin, CP and Kuo, CH}, title = {Comparative analysis of the peanut witches'-broom phytoplasma genome reveals horizontal transfer of potential mobile units and effectors.}, journal = {PloS one}, volume = {8}, number = {4}, pages = {e62770}, pmid = {23626855}, issn = {1932-6203}, mesh = {Arachis/microbiology ; Cluster Analysis ; *DNA Transposable Elements ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Metabolic Networks and Pathways ; Molecular Sequence Annotation ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Phytoplasma/classification/*genetics/metabolism ; Plant Diseases/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Phytoplasmas are a group of bacteria that are associated with hundreds of plant diseases. Due to their economical importance and the difficulties involved in the experimental study of these obligate pathogens, genome sequencing and comparative analysis have been utilized as powerful tools to understand phytoplasma biology. To date four complete phytoplasma genome sequences have been published. However, these four strains represent limited phylogenetic diversity. In this study, we report the shotgun sequencing and evolutionary analysis of a peanut witches'-broom (PnWB) phytoplasma genome. The availability of this genome provides the first representative of the 16SrII group and substantially improves the taxon sampling to investigate genome evolution. The draft genome assembly contains 13 chromosomal contigs with a total size of 562,473 bp, covering ∼90% of the chromosome. Additionally, a complete plasmid sequence is included. Comparisons among the five available phytoplasma genomes reveal the differentiations in gene content and metabolic capacity. Notably, phylogenetic inferences of the potential mobile units (PMUs) in these genomes indicate that horizontal transfer may have occurred between divergent phytoplasma lineages. Because many effectors are associated with PMUs, the horizontal transfer of these transposon-like elements can contribute to the adaptation and diversification of these pathogens. In summary, the findings from this study highlight the importance of improving taxon sampling when investigating genome evolution. Moreover, the currently available sequences are inadequate to fully characterize the pan-genome of phytoplasmas. Future genome sequencing efforts to expand phylogenetic diversity are essential in improving our understanding of phytoplasma evolution.}, }
@article {pmid23626675, year = {2013}, author = {Zaparty, M and Hagemann, A and Bräsen, C and Hensel, R and Lupas, AN and Brinkmann, H and Siebers, B}, title = {The first prokaryotic trehalose synthase complex identified in the hyperthermophilic crenarchaeon Thermoproteus tenax.}, journal = {PloS one}, volume = {8}, number = {4}, pages = {e61354}, pmid = {23626675}, issn = {1932-6203}, mesh = {Archaeal Proteins/*genetics/metabolism ; Base Sequence ; Enzyme Activation ; Escherichia coli/genetics/metabolism ; Evolution, Molecular ; *Gene Expression Regulation, Archaeal ; Gene Transfer, Horizontal ; Glucosyltransferases/*genetics/metabolism ; Hot Temperature ; Molecular Sequence Data ; Operon ; Phosphoric Monoester Hydrolases/*genetics/metabolism ; Phylogeny ; Protein Structure, Tertiary ; Recombinant Proteins/genetics/metabolism ; Thermoproteus/chemistry/enzymology/*genetics ; Two-Hybrid System Techniques ; }, abstract = {The role of the disaccharide trehalose, its biosynthesis pathways and their regulation in Archaea are still ambiguous. In Thermoproteus tenax a fused trehalose-6-phosphate synthase/phosphatase (TPSP), consisting of an N-terminal trehalose-6-phosphate synthase (TPS) and a C-terminal trehalose-6-phosphate phosphatase (TPP) domain, was identified. The tpsp gene is organized in an operon with a putative glycosyltransferase (GT) and a putative mechanosensitive channel (MSC). The T. tenax TPSP exhibits high phosphatase activity, but requires activation by the co-expressed GT for bifunctional synthase-phosphatase activity. The GT mediated activation of TPS activity relies on the fusion of both, TPS and TPP domain, in the TPSP enzyme. Activation is mediated by complex-formation in vivo as indicated by yeast two-hybrid and crude extract analysis. In combination with first evidence for MSC activity the results suggest a sophisticated stress response involving TPSP, GT and MSC in T. tenax and probably in other Thermoproteales species. The monophyletic prokaryotic TPSP proteins likely originated via a single fusion event in the Bacteroidetes with subsequent horizontal gene transfers to other Bacteria and Archaea. Furthermore, evidence for the origin of eukaryotic TPSP fusions via HGT from prokaryotes and therefore a monophyletic origin of eukaryotic and prokaryotic fused TPSPs is presented. This is the first report of a prokaryotic, archaeal trehalose synthase complex exhibiting a much more simple composition than the eukaryotic complex described in yeast. Thus, complex formation and a complex-associated regulatory potential might represent a more general feature of trehalose synthesizing proteins.}, }
@article {pmid23615305, year = {2013}, author = {Yamanaka, H and Arita, M and Oi, R and Ohsawa, M and Mizushima, M and Takagi, T and Kubo, N and Yamamoto, N and Takemoto, T and Ohsawa, K}, title = {Prevalence of an unidentified Helicobacter species in laboratory mice and its distribution in the hepatobiliary system and gastrointestinal tract.}, journal = {Experimental animals}, volume = {62}, number = {2}, pages = {109-116}, doi = {10.1538/expanim.62.109}, pmid = {23615305}, issn = {1881-7122}, mesh = {Animals ; Biliary Tract/*microbiology ; Female ; Gastrointestinal Tract/*microbiology ; Helicobacter/genetics/*isolation &amp; purification ; Helicobacter Infections/epidemiology/*microbiology/veterinary ; Liver/*microbiology ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic ; Polymerase Chain Reaction ; Prevalence ; RNA, Ribosomal, 16S ; Rodent Diseases/*epidemiology/*microbiology ; Specific Pathogen-Free Organisms ; }, abstract = {An unidentified Helicobacter species, strain MIT 01-6451, was frequently detected in mice obtained from domestic commercial and academic institutions in Japan. To partially characterize this strain, its distributions in the gastrointestinal tract and hepatobiliary system of mice were investigated. In gastrointestinal tissues, this strain was detected in all cecum, colon, and feces samples tested, whereas fewer mice were positive in the ileum, jejunum, and duodenum. Interestingly, strain MIT 01-6451 was also detected in most stomach samples and in 33% of gallbladder samples. One mouse was found to be infected with multiple Helicobacter species. Fourteen copies of 16S rRNA genes were cloned from the tissues of this mouse. One had the highest level of sequence homology with H. canadensis, while 13 had the highest level of homology with the H. ganmani type strain or strain MIT 01-6451. Twelve of these 13 16S rRNA genes were mosaic sequences, being partially derived from H. ganmani and strain MIT 01-6451. These results suggest that H. ganmani and Helicobacter sp. MIT 01-6451 are prevalent in specific-pathogen-free mouse colonies in Japan and that lateral gene transfer probably occurs among Helicobacter species during coinfection.}, }
@article {pmid23611873, year = {2013}, author = {Fortier, LC and Sekulovic, O}, title = {Importance of prophages to evolution and virulence of bacterial pathogens.}, journal = {Virulence}, volume = {4}, number = {5}, pages = {354-365}, pmid = {23611873}, issn = {2150-5608}, mesh = {Bacteria/genetics/*pathogenicity/*virology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Lysogeny ; Prophages/*genetics ; Transduction, Genetic ; Virulence Factors/*genetics ; }, abstract = {Bacteriophages, or simply phages, are viruses infecting bacteria. With an estimated 10 (31) particles in the biosphere, phages outnumber bacteria by a factor of at least 10 and not surprisingly, they influence the evolution of most bacterial species, sometimes in unexpected ways. "Temperate" phages have the ability to integrate into the chromosome of their host upon infection, where they can reside as "quiescent" prophages until conditions favor their reactivation. Lysogenic conversion resulting from the integration of prophages encoding powerful toxins is probably the most determinant contribution of prophages to the evolution of pathogenic bacteria. We currently grasp only a small fraction of the total phage diversity. Phage biologists keep unraveling novel mechanisms developed by phages to parasitize their host. The purpose of this review is to give an overview of some of the various ways by which prophages change the lifestyle and boost virulence of some of the most dangerous bacterial pathogens.}, }
@article {pmid23611629, year = {2013}, author = {Pérez-Roth, E and Potel-Alvarellos, C and Espartero, X and Constela-Caramés, L and Méndez-Álvarez, S and Alvarez-Fernández, M}, title = {Molecular epidemiology of plasmid-mediated high-level mupirocin resistance in methicillin-resistant Staphylococcus aureus in four Spanish health care settings.}, journal = {International journal of medical microbiology : IJMM}, volume = {303}, number = {4}, pages = {201-204}, doi = {10.1016/j.ijmm.2013.03.003}, pmid = {23611629}, issn = {1618-0607}, mesh = {Anti-Bacterial Agents/*pharmacology ; Community Health Centers ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genotype ; Humans ; Methicillin-Resistant Staphylococcus aureus/*classification/*drug effects/genetics/isolation &amp; purification ; Microbial Sensitivity Tests ; Molecular Epidemiology ; Molecular Typing ; Mupirocin/*pharmacology ; Plasmids/*analysis ; Spain/epidemiology ; Staphylococcal Infections/*epidemiology/microbiology ; }, abstract = {Mupirocin is used for the decolonization of methicillin-resistant Staphylococcus aureus (MRSA). High-level mupirocin resistance (Hi-Mup(R)) is of concern, having been associated with therapeutic failure. Our main objective was to assess the emergence and mode/s of spread of Hi-Mup(R) in the MRSA population recovered between 2002 and 2009 in four health care settings in the Pontevedra province, northwest Spain. Five hundred and fifty consecutive clinical MRSA isolates were obtained and screened for antimicrobial susceptibility. Isolates were stratified into multidrug-resistant (MDR) and non-MDR. High-level mupirocin resistant MRSA were characterized by genotyping and plasmid analysis. Thirty-one MRSA (5.6%) exhibited Hi-Mup(R). No association was detected between Hi-Mup(R) and MDR but isolates displaying Hi-Mup(R) were more likely to be resistant to gentamicin and tobramycin. Four main MRSA clones were identified: ST125/t067/PFGE A, ST36/t018/PFGE D, ST8/t008/PFGE B, and ST72/t148 or t3092/PFGE B. Each isolate carried the Hi-Mup(R)ileS2-encoding gene on plasmids and ten plasmid types were distinguished based on unique IS257-ileS2 configurations. Some plasmid types were successfully disseminated among the MRSA clones. Remarkably, six plasmid types were acquired by the predominant genotype ST125/t067/PFGE A. In conclusion, molecular characterization of MRSA isolates combined with the rapid typing of ileS2-encoding plasmids through determination of IS257-ileS2 configurations have proved to be a powerful strategy to address the molecular epidemiology of Hi-Mup(R). The transmission of a diverse set of ileS2-carrying plasmids promoted the emergence of the resistance, with a limited role of clonal expansion in its dispersion.}, }
@article {pmid23610627, year = {2013}, author = {Rosic, NN and Leggat, W and Kaniewska, P and Dove, S and Hoegh-Guldberg, O}, title = {New-old hemoglobin-like proteins of symbiotic dinoflagellates.}, journal = {Ecology and evolution}, volume = {3}, number = {4}, pages = {822-834}, pmid = {23610627}, issn = {2045-7758}, abstract = {Symbiotic dinoflagellates are unicellular photosynthetic algae that live in mutualistic symbioses with many marine organisms. Within the transcriptome of coral endosymbionts Symbiodinium sp. (type C3), we discovered the sequences of two novel and highly polymorphic hemoglobin-like genes and proposed their 3D protein structures. At the protein level, four isoforms shared between 87 and 97% sequence identity for Hb-1 and 78-99% for Hb-2, whereas between Hb-1 and Hb-2 proteins, only 15-21% sequence homology has been preserved. Phylogenetic analyses of the dinoflagellate encoding Hb sequences have revealed a separate evolutionary origin of the discovered globin genes and indicated the possibility of horizontal gene transfer. Transcriptional regulation of the Hb-like genes was studied in the reef-building coral Acropora aspera exposed to elevated temperatures (6-7°C above average sea temperature) over a 24-h period and a 72-h period, as well as to nutrient stress. Exposure to elevated temperatures resulted in an increased Hb-1 gene expression of 31% after 72 h only, whereas transcript abundance of the Hb-2 gene was enhanced by up to 59% by both 1-day and 3-day thermal stress conditions. Nutrient stress also increased gene expression of Hb-2 gene by 70%. Our findings describe the differential expression patterns of two novel Hb genes from symbiotic dinoflagellates and their polymorphic nature. Furthermore, the inducible nature of Hb-2 gene by both thermal and nutrient stressors indicates a prospective role of this form of hemoglobin in the initial coral-algal responses to changes in environmental conditions. This novel hemoglobin has potential use as a stress biomarker.}, }
@article {pmid23610429, year = {2013}, author = {Wu, B and Novelli, J and Jiang, D and Dailey, HA and Landmann, F and Ford, L and Taylor, MJ and Carlow, CK and Kumar, S and Foster, JM and Slatko, BE}, title = {Interdomain lateral gene transfer of an essential ferrochelatase gene in human parasitic nematodes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {19}, pages = {7748-7753}, pmid = {23610429}, issn = {1091-6490}, support = {L30 DK096501/DK/NIDDK NIH HHS/United States ; R01 DK096051/DK/NIDDK NIH HHS/United States ; DK96501/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Animals, Genetically Modified ; Bayes Theorem ; Brugia malayi/*enzymology/genetics ; Caenorhabditis elegans/genetics ; Cloning, Molecular ; Escherichia coli/metabolism ; Exons ; Female ; Ferrochelatase/*genetics ; *Gene Transfer, Horizontal ; Genetic Complementation Test ; Genome ; Green Fluorescent Proteins/metabolism ; In Situ Hybridization ; Male ; Microscopy, Confocal ; Mitochondria/metabolism ; Molecular Sequence Data ; Phylogeny ; RNA Interference ; }, abstract = {Lateral gene transfer events between bacteria and animals highlight an avenue for evolutionary genomic loss/gain of function. Herein, we report functional lateral gene transfer in animal parasitic nematodes. Members of the Nematoda are heme auxotrophs, lacking the ability to synthesize heme; however, the human filarial parasite Brugia malayi has acquired a bacterial gene encoding ferrochelatase (BmFeCH), the terminal step in heme biosynthesis. BmFeCH, encoded by a 9-exon gene, is a mitochondrial-targeted, functional ferrochelatase based on enzyme assays, complementation, and inhibitor studies. Homologs have been identified in several filariae and a nonfilarial nematode. RNAi and ex vivo inhibitor experiments indicate that BmFeCH is essential for viability, validating it as a potential target for filariasis control.}, }
@article {pmid23608703, year = {2013}, author = {Schoenfeld, TW and Murugapiran, SK and Dodsworth, JA and Floyd, S and Lodes, M and Mead, DA and Hedlund, BP}, title = {Lateral gene transfer of family A DNA polymerases between thermophilic viruses, aquificae, and apicomplexa.}, journal = {Molecular biology and evolution}, volume = {30}, number = {7}, pages = {1653-1664}, pmid = {23608703}, issn = {1537-1719}, support = {R43HG002714/HG/NHGRI NIH HHS/United States ; R44HG002714/HG/NHGRI NIH HHS/United States ; R43HG006078/HG/NHGRI NIH HHS/United States ; R43 HG002714/HG/NHGRI NIH HHS/United States ; R44 HG002714/HG/NHGRI NIH HHS/United States ; R43 HG006078/HG/NHGRI NIH HHS/United States ; }, mesh = {Alveolata/enzymology/genetics ; Amino Acid Sequence ; Animals ; Bacteria/*enzymology/genetics ; Computational Biology ; DNA-Directed DNA Polymerase/*genetics ; Gene Transfer, Horizontal/*genetics ; Hot Springs/virology ; Phylogeny ; Sequence Homology, Amino Acid ; Viruses/*enzymology/genetics ; }, abstract = {Bioinformatics and functional screens identified a group of Family A-type DNA Polymerase (polA) genes encoded by viruses inhabiting circumneutral and alkaline hot springs in Yellowstone National Park and the US Great Basin. The proteins encoded by these viral polA genes (PolAs) shared no significant sequence similarity with any known viral proteins but were remarkably similar to PolAs encoded by two of three families of the bacterial phylum Aquificae and by several apicoplast-targeted PolA-like proteins found in the eukaryotic phylum Apicomplexa, which includes the obligate parasites Plasmodium, Babesia, and Toxoplasma. The viral gene products share signature elements previously associated only with Aquificae and Apicomplexa PolA-like proteins and were similar to proteins encoded by prophage elements of a variety of otherwise unrelated Bacteria, each of which additionally encoded a prototypical bacterial PolA. Unique among known viral DNA polymerases, the viral PolA proteins of this study share with the Apicomplexa proteins large amino-terminal domains with putative helicase/primase elements but low primary sequence similarity. The genomic context and distribution, phylogeny, and biochemistry of these PolA proteins suggest that thermophilic viruses transferred polA genes to the Apicomplexa, likely through secondary endosymbiosis of a virus-infected proto-apicoplast, and to the common ancestor of two of three Aquificae families, where they displaced the orthologous cellular polA gene. On the basis of biochemical activity, gene structure, and sequence similarity, we speculate that the xenologous viral-type polA genes may have functions associated with diversity-generating recombination in both Bacteria and Apicomplexa.}, }
@article {pmid23608360, year = {2013}, author = {Azizgolshani, O and Garmann, RF and Cadena-Nava, R and Knobler, CM and Gelbart, WM}, title = {Reconstituted plant viral capsids can release genes to mammalian cells.}, journal = {Virology}, volume = {441}, number = {1}, pages = {12-17}, doi = {10.1016/j.virol.2013.03.001}, pmid = {23608360}, issn = {1096-0341}, support = {1S10RR23057/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Bromovirus/*genetics ; Capsid/*metabolism ; Cell Line ; Cricetinae ; *Gene Transfer Techniques ; *Gene Transfer, Horizontal ; RNA/genetics/*metabolism ; Sindbis Virus/genetics ; Virus Assembly ; }, abstract = {The nucleocapsids of many plant viruses are significantly more robust and protective of their RNA contents than those of enveloped animal viruses. In particular, the capsid protein (CP) of the plant virus Cowpea Chlorotic Mottle Virus (CCMV) is of special interest because it has been shown to spontaneously package, with high efficiency, a large range of lengths and sequences of single-stranded RNA molecules. In this work we demonstrate that hybrid virus-like particles, assembled in vitro from CCMV CP and a heterologous RNA derived from a mammalian virus (Sindbis), are capable of releasing their RNA in the cytoplasm of mammalian cells. This result establishes the first step in the use of plant viral capsids as vectors for gene delivery and expression in mammalian cells. Furthermore, the CCMV capsid protects the packaged RNA against nuclease degradation and serves as a robust external scaffold with many possibilities for further functionalization and cell targeting.}, }
@article {pmid23607509, year = {2013}, author = {Kim, JH and Cho, JK and Kim, KS}, title = {Prevalence and characterization of plasmid-mediated quinolone resistance genes in Salmonella isolated from poultry in Korea.}, journal = {Avian pathology : journal of the W.V.P.A}, volume = {42}, number = {3}, pages = {221-229}, doi = {10.1080/03079457.2013.779636}, pmid = {23607509}, issn = {1465-3338}, mesh = {Animals ; Blotting, Southern/veterinary ; Ciprofloxacin ; DNA Primers/genetics ; Drug Resistance, Bacterial/*genetics ; Electrophoresis, Gel, Pulsed-Field/veterinary ; Escherichia coli ; Gene Transfer, Horizontal/physiology ; Levofloxacin ; Microbial Sensitivity Tests ; Nalidixic Acid ; Plasmids/genetics ; Polymerase Chain Reaction/veterinary ; Poultry ; Poultry Diseases/*epidemiology/*microbiology ; *Quinolones ; Republic of Korea/epidemiology ; Salmonella/*genetics ; Salmonella Infections, Animal/*epidemiology ; }, abstract = {The purpose of this study was to investigate the prevalence and characteristics of plasmid-mediated quinolone resistance (PMQR) genes qnr, aac(6')-Ib-cr, and qepA in a total of 185 non-duplicate Salmonella spp. isolated from hatcheries, poultry farms, and poultry slaughterhouses during the period 2001 to 2010 in Korea. Additionally, mutation analysis of quinolone resistance determining regions (QRDRs), conjugation experiments, and plasmid analysis were performed in the PMQR-positive isolates. Among the 185 isolates, six (3.2%) contained qnr genes (two qnrB4 and four qnrS1) but none carried the aac(6')-Ib-cr or qepA genes. Among the six PMQR-positive isolates, one showed a single mutation (Ser83-Phe substitution) in the QRDRs of gyrA. Among them, three were non-susceptible (intermediate or resistant) to nalidixic acid (minimum inhibitory concentration [MIC] ≥256 µg/ml), ciprofloxacin (MIC 2 µg/ml), and levofloxacin (MIC 4 µg/ml), but others were susceptible to all of the three fluoroquinolones. They were resistant to six or more antimicrobial agents tested and were able to transfer quinolone resistance to recipient Escherichia coli J53 by conjugation. By performing a hybridization test, plasmids harbouring qnrB4 and qnrS1 genes were less than 8 kb and about 70 kb in size, respectively. The horizontal dissemination of qnrS1 gene was mediated by IncN plasmid. Compared with the recipient strain, MICs of the transconjugants increased two-fold to four-fold for nalidixic acid, and eight-fold to 16-fold for ciprofloxacin and levofloxacin. This report is the first to describe the detection of qnr genes in Salmonella spp. isolated from poultry in Korea. Widespread horizontal transfer of these genes among bacteria may be a serious public health concern because these can rapidly increase fluoroquinolone resistance. To ensure the public health, it is essential to continuously survey and carefully monitor the spread of PMQR genes in Salmonella from poultry.}, }
@article {pmid23603937, year = {2013}, author = {Najle, SR and Nusblat, AD and Nudel, CB and Uttaro, AD}, title = {The Sterol-C7 desaturase from the ciliate Tetrahymena thermophila is a Rieske Oxygenase, which is highly conserved in animals.}, journal = {Molecular biology and evolution}, volume = {30}, number = {7}, pages = {1630-1643}, doi = {10.1093/molbev/mst076}, pmid = {23603937}, issn = {1537-1719}, mesh = {Animals ; Cholestenes/metabolism ; Cholesterol/chemistry/*metabolism ; *Conserved Sequence ; Cytochromes b5/metabolism ; Ecdysteroids/biosynthesis ; Fatty Acid Desaturases/chemistry/classification/*metabolism ; *Oxidation-Reduction ; Phytosterols/metabolism ; Sterols/metabolism ; Tetrahymena thermophila/*enzymology ; }, abstract = {The ciliate Tetrahymena thermophila incorporates sterols from its environment that desaturates at positions C5(6), C7(8), and C22(23). Phytosterols are additionally modified by removal of the ethyl group at carbon 24 (C24). The enzymes involved are oxygen-, NAD(P)H-, and cytochrome b5 dependent, reason why they were classified as members of the hydroxylases/desaturases superfamily. The ciliate's genome revealed the presence of seven putative sterol desaturases belonging to this family, two of which we have previously characterized as the C24-de-ethylase and C5(6)-desaturase. A Rieske oxygenase was also identified; this type of enzyme, with sterol C7(8)-desaturase activity, was observed only in animals, called Neverland in insects and DAF-36 in nematodes. They perform the conversion of cholesterol into 7-dehydrocholesterol, first step in the synthesis of the essential hormones ecdysteroids and dafachronic acids. By adapting an RNA interference-by-feeding protocol, we easily screened six of the eight genes described earlier, allowing the characterization of the Rieske-like oxygenase as the ciliate's C7(8)-desaturase (Des7p). This characterization was confirmed by obtaining the corresponding knockout mutant, making Des7p the first nonanimal Rieske-sterol desaturase described. To our knowledge, this is the first time that the feeding-RNAi technique was successfully applied in T. thermophila, enabling to consider such methodology for future reverse genetics high-throughput screenings in this ciliate. Bioinformatics analyses revealed the presence of Des7p orthologs in other Oligohymenophorean ciliates and in nonanimal Opisthokonts, like the protists Salpingoeca rosetta and Capsaspora owczarzaki. A horizontal gene transfer event from a unicellular Opisthokont to an ancient phagotrophic Oligohymenophorean could explain the acquisition of the Rieske oxygenase by Tetrahymena.}, }
@article {pmid23603674, year = {2013}, author = {MacGregor, BJ and Biddle, JF and Teske, A}, title = {Mobile elements in a single-filament orange Guaymas Basin Beggiatoa ("Candidatus Maribeggiatoa") sp. draft genome: evidence for genetic exchange with cyanobacteria.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {13}, pages = {3974-3985}, pmid = {23603674}, issn = {1098-5336}, support = {HHSN266200400042C//PHS HHS/United States ; }, mesh = {Amino Acid Sequence ; Base Sequence ; Beggiatoa/*genetics ; Cluster Analysis ; Cyanobacteria/*genetics ; Endonucleases/genetics ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial/*genetics ; Hydrothermal Vents/*microbiology ; Likelihood Functions ; Mexico ; Models, Genetic ; Molecular Sequence Annotation ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 23S/genetics ; Sequence Analysis, DNA ; Sequence Homology ; Signal Transduction/genetics ; }, abstract = {The draft genome sequence of a single orange Beggiatoa ("Candidatus Maribeggiatoa") filament collected from a microbial mat at a hydrothermal site in Guaymas Basin (Gulf of California, Mexico) shows evidence of extensive genetic exchange with cyanobacteria, in particular for sensory and signal transduction genes. A putative homing endonuclease gene and group I intron within the 23S rRNA gene; several group II catalytic introns; GyrB and DnaE inteins, also encoding homing endonucleases; multiple copies of sequences similar to the fdxN excision elements XisH and XisI (required for heterocyst differentiation in some cyanobacteria); and multiple sequences related to an open reading frame (ORF) (00024_0693) of unknown function all have close non-Beggiatoaceae matches with cyanobacterial sequences. Sequences similar to the uncharacterized ORF and Xis elements are found in other Beggiatoaceae genomes, a variety of cyanobacteria, and a few phylogenetically dispersed pleiomorphic or filamentous bacteria. We speculate that elements shared among filamentous bacterial species may have been exchanged in microbial mats and that some of them may be involved in cell differentiation.}, }
@article {pmid23602560, year = {2013}, author = {del Castillo, CS and Jang, HB and Hikima, J and Jung, TS and Morii, H and Hirono, I and Kondo, H and Kurosaka, C and Aoki, T}, title = {Comparative analysis and distribution of pP9014, a novel drug resistance IncP-1 plasmid from Photobacterium damselae subsp. piscicida.}, journal = {International journal of antimicrobial agents}, volume = {42}, number = {1}, pages = {10-18}, doi = {10.1016/j.ijantimicag.2013.02.027}, pmid = {23602560}, issn = {1872-7913}, mesh = {Animals ; Base Composition ; Cluster Analysis ; *Drug Resistance, Bacterial ; Genes, Bacterial ; Humans ; Japan ; Molecular Sequence Data ; Open Reading Frames ; Perciformes/microbiology ; Photobacterium/drug effects/*genetics/*isolation &amp; purification ; Phylogeny ; Plasmids/*isolation &amp; purification ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {Photobacterium damselae subsp. piscicida, a causative agent of pseudotuberculosis, often harbours resistance plasmids (R plasmids) that facilitate horizontal gene transfer of drug resistance genes. R plasmid pP9014 was isolated from P. damselae subsp. piscicida and its complete nucleotide sequence was determined using Next Generation Sequencing technology. A protein network analysis was conducted to determine the relatedness of protein coding sequences, and ClustalW was used for the full nucleotide sequences. The occurrence of pP9014-like plasmids compared with pP99-018-like plasmids in a specific region was determined using probes for their transfer regions. pP9014 is 55851bp long with an overall GC content of 44.4% encoding 61 open reading frames (ORFs) including antimicrobial resistance genes and two conjugative transfer regions (Tra and Trb). The backbone showed highest similarity to Marinobacter adhaerens pHP-42 and Methylophaga sp. JAM7. pP9014 is similar to several IncP plasmids but forms a different subgroup. pP9014 is a unique plasmid in P. damselae subsp. piscicida and was not commonly found in drug-resistant P. damselae subsp. piscicida isolated from different areas and years in Japan. Plasmids similar to the previously reported pP99-018 are more widely distributed. This rarity suggests that plasmids similar to pP99-018 are more compatible with γ-proteobacteria. pP9014 is the first reported IncP-1 plasmid from fish pathogens. Its similarity to other IncP plasmids isolated from soil and human pathogens suggests that plasmids of the IncP-1 incompatibility group are vectors for the transfer of drug resistance genes among diverse environments.}, }
@article {pmid23601235, year = {2013}, author = {Bondarev, V and Richter, M and Romano, S and Piel, J and Schwedt, A and Schulz-Vogt, HN}, title = {The genus Pseudovibrio contains metabolically versatile bacteria adapted for symbiosis.}, journal = {Environmental microbiology}, volume = {15}, number = {7}, pages = {2095-2113}, pmid = {23601235}, issn = {1462-2920}, mesh = {Animals ; Carbon/metabolism ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/*genetics ; Nitrogen/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhodobacteraceae/classification/genetics/metabolism/*physiology ; *Symbiosis ; }, abstract = {The majority of strains belonging to the genus Pseudovibrio have been isolated from marine invertebrates such as tunicates, corals and particularly sponges, but the physiology of these bacteria is poorly understood. In this study, we analyse for the first time the genomes of two Pseudovibrio strains - FO-BEG1 and JE062. The strain FO-BEG1 is a required symbiont of a cultivated Beggiatoa strain, a sulfide-oxidizing, autotrophic bacterium, which was initially isolated from a coral. Strain JE062 was isolated from a sponge. The presented data show that both strains are generalistic bacteria capable of importing and oxidizing a wide range of organic and inorganic compounds to meet their carbon, nitrogen, phosphorous and energy requirements under both, oxic and anoxic conditions. Several physiological traits encoded in the analysed genomes were verified in laboratory experiments with both isolates. Besides the versatile metabolic abilities of both Pseudovibrio strains, our study reveals a number of open reading frames and gene clusters in the genomes that seem to be involved in symbiont-host interactions. Both Pseudovibrio strains have the genomic potential to attach to host cells, interact with the eukaryotic cell machinery, produce secondary metabolites and supply the host with cofactors.}, }
@article {pmid23599362, year = {2013}, author = {Fluit, AC and Carpaij, N and Majoor, EA and Bonten, MJ and Willems, RJ}, title = {Shared reservoir of ccrB gene sequences between coagulase-negative staphylococci and methicillin-resistant Staphylococcus aureus.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {68}, number = {8}, pages = {1707-1713}, doi = {10.1093/jac/dkt121}, pmid = {23599362}, issn = {1460-2091}, mesh = {Alleles ; Bacterial Proteins/*genetics ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; Gene Transfer, Horizontal ; *Genetic Variation ; Humans ; *Methicillin Resistance ; Molecular Epidemiology ; Molecular Sequence Data ; Phylogeny ; Recombinases/*genetics ; Sequence Analysis, DNA ; Sequence Homology ; Staphylococcus/*genetics/isolation &amp; purification ; }, abstract = {OBJECTIVES: Methicillin resistance in Staphylococcus aureus and coagulase-negative staphylococci (CoNS) is caused by expression of the low-affinity penicillin-binding protein (PBP) 2a encoded by the mecA gene. This gene is carried on the staphylococcal cassette chromosome mec (SCCmec) of which several types and subtypes have been described. CoNS and S. aureus share SCCmec types and it has been suggested that CoNS are a potential reservoir of mecA for S. aureus. Evidence for this is mainly based on PCR typing of SCCmec or on sequence-based methods including only a limited number of strains. In this study, we determined the genetic relatedness of ccrB sequences contained in SCCmec elements of a spatio-temporally diverse and comprehensive collection of methicillin-resistant CoNS and S. aureus.<br><br>METHODS: Part of the ccrB genes of 367 methicillin-resistant CoNS and 94 methicillin-resistant S. aureus (MRSA) were sequenced and compared.<br><br>RESULTS: The data revealed that 92 of 94 (98%) MRSA isolates carried ccrB genes, involving different ccrB alleles, which were indistinguishable from ccrB genes of methicillin-resistant CoNS. In total, 273 of 367 (74%) CoNS shared ccrB gene sequences with MRSA.<br><br>CONCLUSIONS: The high rate of identical ccrB sequences in a geographically, temporally and genotypically diverse set of S. aureus and CoNS isolates indicates frequent horizontal transfer of SCCmec between CoNS and S. aureus, which may have contributed to the emergence of MRSA.}, }
@article {pmid23599361, year = {2013}, author = {Schink, AK and Kadlec, K and Kaspar, H and Mankertz, J and Schwarz, S}, title = {Analysis of extended-spectrum-β-lactamase-producing Escherichia coli isolates collected in the GERM-Vet monitoring programme.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {68}, number = {8}, pages = {1741-1749}, doi = {10.1093/jac/dkt123}, pmid = {23599361}, issn = {1460-2091}, mesh = {Animals ; Animals, Domestic ; Cluster Analysis ; Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; Escherichia coli/*enzymology/isolation &amp; purification ; Escherichia coli Infections/microbiology/*veterinary ; Gene Transfer, Horizontal ; Germany ; Molecular Sequence Data ; Multilocus Sequence Typing ; Pets ; Phylogeny ; Plasmids ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sequence Homology ; Transformation, Bacterial ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: The aims of this study were (i) to detect extended-spectrum β-lactamase (ESBL) genes among 1378 Escherichia coli isolates from defined disease conditions of companion and farm animals and (ii) to determine the localization and organization of ESBL genes.<br><br>METHODS: E. coli isolates from the German resistance monitoring programme GERM-Vet were included in the study. Plasmids were transferred by conjugation or transformation and typed by PCR-based replicon typing. ESBL genes were detected by PCR; the complete ESBL genes and their flanking regions were sequenced by primer walking. Phylogenetic grouping and multilocus sequence typing (MLST) were performed for all ESBL-producing E. coli isolates.<br><br>RESULTS: Of the 27 ESBL-producing E. coli isolates detected, 22 carried blaCTX-M-1 genes on IncN (n&#x200a;=&#x200a;16), IncF (n&#x200a;=&#x200a;3), IncI1 (n&#x200a;=&#x200a;2) or multireplicon (n&#x200a;=&#x200a;1) plasmids. A blaCTX-M-3 gene was located on an IncN plasmid and a blaCTX-M-15 gene was located on an IncF plasmid. A multireplicon plasmid and an IncHI1 plasmid harboured blaCTX-M-2. A blaTEM-52c gene was identified within Tn2 on an IncI1 plasmid. The blaCTX-M genes located within the same or related genetic contexts showed differences due to the integration of insertion sequences. Various MLST types were detected, with ST10 (n&#x200a;=&#x200a;7), ST167 (n&#x200a;=&#x200a;4) and ST100 (n&#x200a;=&#x200a;3) being the most common.<br><br>CONCLUSIONS: This study showed that the blaCTX-M-1 gene is the predominant ESBL gene among E. coli isolates from diseased animals in Germany and a considerable structural heterogeneity was found in the regions flanking the blaCTX-M-1 gene. Insertion sequences, transposons and recombination events are likely to be involved in alterations of the ESBL gene regions.}, }
@article {pmid23596242, year = {2013}, author = {Domingues, S and Toleman, MA and Nielsen, KM and da Silva, GJ}, title = {Identical miniature inverted repeat transposable elements flank class 1 integrons in clinical isolates of Acinetobacter spp.}, journal = {Journal of clinical microbiology}, volume = {51}, number = {7}, pages = {2382-2384}, pmid = {23596242}, issn = {1098-660X}, mesh = {Acinetobacter/*genetics/isolation &amp; purification ; Acinetobacter Infections/*microbiology ; Brazil ; *DNA Transposable Elements ; DNA, Bacterial/chemistry/genetics ; Gene Transfer, Horizontal ; Humans ; *Integrons ; *Inverted Repeat Sequences ; Molecular Sequence Data ; Portugal ; Sequence Analysis, DNA ; }, abstract = {Miniature inverted repeat transposable elements (MITEs) have been identified flanking class 1 integrons. We have identified and characterized a 439-bp MITE-like structure in seven Acinetobacter species isolates from Portugal and Brazil. The complete sequence similarity of the elements and flanking regions suggests that MITEs may act as mobilizable vectors for the dissemination of integrons.}, }
@article {pmid23595824, year = {2013}, author = {You, Y and Hilpert, M and Ward, MJ}, title = {Identification of Tet45, a tetracycline efflux pump, from a poultry-litter-exposed soil isolate and persistence of tet(45) in the soil.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {68}, number = {9}, pages = {1962-1969}, doi = {10.1093/jac/dkt127}, pmid = {23595824}, issn = {1460-2091}, mesh = {Animals ; Anti-Bacterial Agents/metabolism ; Bacterial Proteins/*genetics/metabolism ; Cloning, Molecular ; DNA, Bacterial/chemistry/*genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; Membrane Transport Proteins/*genetics/metabolism ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Planococcaceae/*genetics/isolation &amp; purification ; Poultry ; Sequence Analysis, DNA ; *Soil Microbiology ; Tetracycline/metabolism ; *Tetracycline Resistance ; }, abstract = {OBJECTIVES: To characterize a tetracycline resistance (Tc(R)) determinant, closely related to the TetL efflux pump, in a Bhargavaea cecembensis strain previously isolated from a poultry-litter-impacted soil.<br><br>METHODS: Genomic DNA of B. cecembensis DMV42A was shotgun cloned and expressed in Escherichia coli. Antimicrobial susceptibility testing and a [(3)H]tetracycline uptake assay were used to confirm the function of the target gene. Transferability of the gene was examined using filter matings and confirmed by PCR and sequencing. Real-time quantitative PCR was performed on soil metagenomic DNA to evaluate the prevalence of the gene in the soil from which B. cecembensis DMV42A was isolated and in more pristine local soils.<br><br>RESULTS: The Tc(R) determinant from B. cecembensis DMV42A, designated Tet45, was identified as a tetracycline efflux pump sharing 78% amino acid identity with certain TetL proteins. In B. cecembensis DMV42A, tet(45) was adjacent to truncated and non-functional arsenic resistance genes with high sequence similarities to genes from staphylococcal plasmids. After filter matings, the tet(45) gene could be found in E. coli transconjugants, although the transfer mechanism was unknown. Tet45 homologues are also present in the genomes of several Bacillus cereus strains and a Bacillus thuringiensis strain. tet(45) was detected in the poultry-litter-impacted soil, and persisted at a similar level 2 years after removal of the chicken waste, although it was not detected in several more pristine soils.<br><br>CONCLUSIONS: Tet45 is a tetracycline efflux pump closely related to TetL. Horizontal gene transfer may have contributed to the dissemination and persistence of tet(45) in a poultry-litter-impacted soil.}, }
@article {pmid23594878, year = {2013}, author = {Jaubert, C and Danioux, C and Oberto, J and Cortez, D and Bize, A and Krupovic, M and She, Q and Forterre, P and Prangishvili, D and Sezonov, G}, title = {Genomics and genetics of Sulfolobus islandicus LAL14/1, a model hyperthermophilic archaeon.}, journal = {Open biology}, volume = {3}, number = {4}, pages = {130010}, pmid = {23594878}, issn = {2046-2441}, mesh = {Antitoxins/metabolism ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; DNA Transposable Elements/genetics ; Gene Transfer, Horizontal ; *Genes, Archaeal ; Genomics ; Models, Genetic ; Phylogeny ; RNA, Transfer/genetics/metabolism ; Replication Origin/genetics ; Sequence Analysis, DNA ; Sulfolobus/classification/*genetics ; Toxins, Biological/metabolism ; }, abstract = {The 2 465 177 bp genome of Sulfolobus islandicus LAL14/1, host of the model rudivirus SIRV2, was sequenced. Exhaustive comparative genomic analysis of S. islandicus LAL14/1 and the nine other completely sequenced S. islandicus strains isolated from Iceland, Russia and USA revealed a highly syntenic common core genome of approximately 2 Mb and a long hyperplastic region containing most of the strain-specific genes. In LAL14/1, the latter region is enriched in insertion sequences, CRISPR (clustered regularly interspaced short palindromic repeats), glycosyl transferase genes, toxin-antitoxin genes and MITE (miniature inverted-repeat transposable elements). The tRNA genes of LAL14/1 are preferential targets for the integration of mobile elements but clusters of atypical genes (CAG) are also integrated elsewhere in the genome. LAL14/1 carries five CRISPR loci with 10 per cent of spacers matching perfectly or imperfectly the genomes of archaeal viruses and plasmids found in the Icelandic hot springs. Strikingly, the CRISPR_2 region of LAL14/1 carries an unusually long 1.9 kb spacer interspersed between two repeat regions and displays a high similarity to pING1-like conjugative plasmids. Finally, we have developed a genetic system for S. islandicus LAL14/1 and created ΔpyrEF and ΔCRISPR_1 mutants using double cross-over and pop-in/pop-out approaches, respectively. Thus, LAL14/1 is a promising model to study virus-host interactions and the CRISPR/Cas defence mechanism in Archaea.}, }
@article {pmid23593470, year = {2013}, author = {Takemoto, K}, title = {Does habitat variability really promote metabolic network modularity?.}, journal = {PloS one}, volume = {8}, number = {4}, pages = {e61348}, pmid = {23593470}, issn = {1932-6203}, mesh = {Databases as Topic ; *Ecosystem ; Gene Transfer, Horizontal ; *Metabolic Networks and Pathways ; Species Specificity ; }, abstract = {The hypothesis that variability in natural habitats promotes modular organization is widely accepted for cellular networks. However, results of some data analyses and theoretical studies have begun to cast doubt on the impact of habitat variability on modularity in metabolic networks. Therefore, we re-evaluated this hypothesis using statistical data analysis and current metabolic information. We were unable to conclude that an increase in modularity was the result of habitat variability. Although horizontal gene transfer was also considered because it may contribute for survival in a variety of environments, closely related to habitat variability, and is known to be positively correlated with network modularity, such a positive correlation was not concluded in the latest version of metabolic networks. Furthermore, we demonstrated that the previously observed increase in network modularity due to habitat variability and horizontal gene transfer was probably due to a lack of available data on metabolic reactions. Instead, we determined that modularity in metabolic networks is dependent on species growth conditions. These results may not entirely discount the impact of habitat variability and horizontal gene transfer. Rather, they highlight the need for a more suitable definition of habitat variability and a more careful examination of relationships of the network modularity with horizontal gene transfer, habitats, and environments.}, }
@article {pmid23593179, year = {2013}, author = {Le Clec'h, W and Chevalier, FD and Genty, L and Bertaux, J and Bouchon, D and Sicard, M}, title = {Cannibalism and predation as paths for horizontal passage of Wolbachia between terrestrial isopods.}, journal = {PloS one}, volume = {8}, number = {4}, pages = {e60232}, pmid = {23593179}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; *Cannibalism ; DNA Primers ; *Gene Transfer, Horizontal ; In Situ Hybridization, Fluorescence ; Phylogeny ; Polymerase Chain Reaction ; *Predatory Behavior ; Wolbachia/classification/genetics/*physiology ; }, abstract = {The alpha-proteobacteria Wolbachia are the most widespread endosymbionts in arthropods and nematodes. Mainly maternally inherited, these so-called sex parasites have selected several strategies that increase their vertical dispersion in host populations. However, the lack of congruence between the Wolbachia and their host phylogenies suggests frequent horizontal transfers. One way that could be used for horizontal Wolbachia transfers between individuals is predation. The aim of this study was to test whether horizontal passage of Wolbachia is possible when an uninfected terrestrial isopod eats an infected one. After having eaten Armadillidium vulgare harbouring Wolbachia, the predator-recipients (the two woodlice A. vulgare and Porcellio dilatatus dilatatus) that were initially Wolbachia-free were tested positive for the presence of Wolbachia both by quantitative PCR and Fluorescence in situ Hybridization (FISH). Even if the titers were low compared to vertically infected individuals, this constitutes the first demonstration of Wolbachia occurrence in various organs of an initially uninfected host after eating an infected one.}, }
@article {pmid23588684, year = {2013}, author = {Bouzat, JL and Hoostal, MJ}, title = {Evolutionary analysis and lateral gene transfer of two-component regulatory systems associated with heavy-metal tolerance in bacteria.}, journal = {Journal of molecular evolution}, volume = {76}, number = {5}, pages = {267-279}, pmid = {23588684}, issn = {1432-1432}, mesh = {Bacterial Proteins/*genetics/metabolism ; Base Composition ; Biological Evolution ; Cadmium/*metabolism ; Copper/*metabolism ; Escherichia coli/genetics/metabolism ; Gene Duplication ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Gram-Negative Bacteria/*genetics/metabolism ; Models, Molecular ; Operon ; Phylogeny ; Plasmids ; Pseudomonas syringae/genetics/metabolism ; Ralstonia/genetics/metabolism ; Salmonella typhimurium/genetics/metabolism ; Structural Homology, Protein ; Zinc/*metabolism ; }, abstract = {Microorganisms have adapted intricate signal transduction mechanisms to coordinate tolerance to toxic levels of metals, including two-component regulatory systems (TCRS). In particular, both cop and czc operons are regulated by TCRS; the cop operon plays a key role in bacterial tolerance to copper, whereas the czc operon is involved in the efflux of cadmium, zinc, and cobalt from the cell. Although the molecular physiology of heavy metal tolerance genes has been extensively studied, their evolutionary relationships are not well-understood. Phylogenetic relationships among heavy-metal efflux proteins and their corresponding two-component regulatory proteins revealed orthologous and paralogous relationships from species divergences and ancient gene duplications. The presence of heavy metal tolerance genes on bacterial plasmids suggests these genes may be prone to spread through horizontal gene transfer. Phylogenetic inferences revealed nine potential examples of lateral gene transfer associated with metal efflux proteins and two examples for regulatory proteins. Notably, four of the examples suggest lateral transfer across major evolutionary domains. In most cases, differences in GC content in metal tolerance genes and their corresponding host genomes confirmed lateral gene transfer events. Three-dimensional protein structures predicted for the response regulators encoded by cop and czc operons showed a high degree of structural similarity with other known proteins involved in TCRS signal transduction, which suggests common evolutionary origins of functional phenotypes and similar mechanisms of action for these response regulators.}, }
@article {pmid23587960, year = {2013}, author = {Yoon, EJ and Courvalin, P and Grillot-Courvalin, C}, title = {RND-type efflux pumps in multidrug-resistant clinical isolates of Acinetobacter baumannii: major role for AdeABC overexpression and AdeRS mutations.}, journal = {Antimicrobial agents and chemotherapy}, volume = {57}, number = {7}, pages = {2989-2995}, pmid = {23587960}, issn = {1098-6596}, mesh = {Acinetobacter baumannii/drug effects/*genetics/isolation &amp; purification/metabolism ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*biosynthesis/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Electrophoresis, Gel, Pulsed-Field ; Humans ; Membrane Transport Proteins/*biosynthesis/genetics ; Microbial Sensitivity Tests ; Minocycline/analogs &amp; derivatives/pharmacology ; Multilocus Sequence Typing ; Mutation ; Tigecycline ; Transcription Factors/genetics ; }, abstract = {Increased expression of chromosomal genes for resistance-nodulation-cell division (RND)-type efflux systems plays a major role in the multidrug resistance (MDR) of Acinetobacter baumannii. However, the relative contributions of the three most prevalent pumps, AdeABC, AdeFGH, and AdeIJK, have not been evaluated in clinical settings. We have screened 14 MDR clinical isolates shown to be distinct on the basis of multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) for the presence and overexpression of the three Ade efflux systems and analyzed the sequences of the regulators AdeRS, a two-component system, for AdeABC and AdeL, a LysR-type regulator, for AdeFGH. Gene adeB was detected in 13 of 14 isolates, and adeG and the intrinsic adeJ gene were detected in all strains. Significant overexpression of adeB was observed in 10 strains, whereas only 7 had moderately increased levels of expression of AdeFGH, and none overexpressed AdeIJK. Thirteen strains had reduced susceptibility to tigecycline, but there was no correlation between tigecycline MICs and the levels of AdeABC expression, suggesting the presence of other mechanisms for tigecycline resistance. No mutations were found in the highly conserved LysR regulator of the nine strains expressing AdeFGH. In contrast, functional mutations were found in conserved domains of AdeRS in all the strains that overexpressed AdeABC with two mutational hot spots, one in AdeS near histidine 149 suggesting convergent evolution and the other in the DNA binding domain of AdeR compatible with horizontal gene transfer. This report outlines the high incidence of AdeABC efflux pump overexpression in MDR A. baumannii as a result of a variety of single mutations in the corresponding two-component regulatory system.}, }
@article {pmid23587361, year = {2013}, author = {Puigbò, P and Wolf, YI and Koonin, EV}, title = {Seeing the Tree of Life behind the phylogenetic forest.}, journal = {BMC biology}, volume = {11}, number = {}, pages = {46}, pmid = {23587361}, issn = {1741-7007}, mesh = {Gene Transfer, Horizontal ; Genomics ; *Phylogeny ; Sequence Analysis, DNA ; Statistics as Topic ; }, }
@article {pmid23587344, year = {2013}, author = {Duron, O and Hurst, GD}, title = {Arthropods and inherited bacteria: from counting the symbionts to understanding how symbionts count.}, journal = {BMC biology}, volume = {11}, number = {}, pages = {45}, pmid = {23587344}, issn = {1741-7007}, mesh = {Animals ; Arthropods/genetics/*microbiology ; Bacteria/*metabolism ; Biological Evolution ; Gene Transfer, Horizontal/genetics ; Host-Pathogen Interactions/genetics ; *Symbiosis/genetics ; }, }
@article {pmid23587287, year = {2013}, author = {Simková, A and Dávidová, M and Papoušek, I and Vetešník, L}, title = {Does interspecies hybridization affect the host specificity of parasites in cyprinid fish?.}, journal = {Parasites &amp; vectors}, volume = {6}, number = {}, pages = {95}, pmid = {23587287}, issn = {1756-3305}, mesh = {Animals ; Cyprinidae/immunology/*parasitology ; *Gene Transfer, Horizontal ; Genotype ; *Host Specificity ; Parasites/genetics/*physiology ; }, abstract = {BACKGROUND: Host specificity varies among parasite species. Some parasites are strictly host-specific, others show a specificity for congeneric or non-congeneric phylogenetically related host species, whilst some others are non-specific (generalists). Two cyprinids, Cyprinus carpio and Carassius gibelio, plus their respective hybrids were investigated for metazoan parasites. The aim of this study was to analyze whether interspecies hybridization affects host specificity. The different degrees of host specificity within a phylogenetic framework were taken into consideration (i.e. strict specialist, intermediate specialist, and intermediate generalist).<br><br>METHODS: Fish were collected during harvesting the pond and identified using meristic traits and molecular markers. Metazoan parasite species were collected. Host specificity of parasites was determined using the following classification: strict specialist, intermediate specialist, intermediate generalist and generalist. Parasite species richness was compared between parental species and their hybrids. The effect of host species on abundance of parasites differing in host specificity was tested.<br><br>RESULTS: Hybrids harbored more different parasite species but their total parasite abundance was lower in comparison with parental species. Interspecies hybridization affected the host specificity of ecto- and endoparasites. Parasite species exhibiting different degrees of host specificity for C. carpio and C. gibelio were also present in hybrids. The abundance of strict specialists of C. carpio was significantly higher in parental species than in hybrids. Intermediate generalists parasitizing C. carpio and C. gibelio as two phylogenetically closely related host species preferentially infected C. gibelio when compared to C. carpio, based on prevalence and maximum intensity of infection. Hybrids were less infected by intermediate generalists when compared to C. gibelio.<br><br>CONCLUSIONS: This finding does not support strict co-adaptation between host and parasite genotypes resulting in narrow host specificity, and showed that hybrid genotypes are susceptible to parasites exhibiting host specificity. The immune mechanisms specific to parental species might represent potential mechanisms explaining the low abundance of parasites in C. gibelio x C. carpio hybrids.}, }
@article {pmid23584995, year = {2013}, author = {Mavrianos, J and Berkow, EL and Desai, C and Pandey, A and Batish, M and Rabadi, MJ and Barker, KS and Pain, D and Rogers, PD and Eugenin, EA and Chauhan, N}, title = {Mitochondrial two-component signaling systems in Candida albicans.}, journal = {Eukaryotic cell}, volume = {12}, number = {6}, pages = {913-922}, pmid = {23584995}, issn = {1535-9786}, support = {R01AI058145/AI/NIAID NIH HHS/United States ; R01 MH096625/MH/NIMH NIH HHS/United States ; AG030504/AG/NIA NIH HHS/United States ; MH076679/MH/NIMH NIH HHS/United States ; K01 MH076679/MH/NIMH NIH HHS/United States ; R01 AG030504/AG/NIA NIH HHS/United States ; R01 AI058145/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Apoptosis ; Bacterial Proteins/*genetics/metabolism ; Biological Evolution ; Candida albicans/*genetics/metabolism/ultrastructure ; Fungal Proteins/*genetics/metabolism ; Gene Deletion ; Gene Expression Regulation, Fungal ; Heat-Shock Proteins/deficiency/*genetics ; Histidine Kinase ; Mitochondria/*metabolism/ultrastructure ; Molecular Sequence Data ; Phylogeny ; Protein Kinases/deficiency/*genetics ; Protein Transport ; Recombinant Fusion Proteins/genetics/metabolism ; Sequence Homology, Amino Acid ; *Signal Transduction ; }, abstract = {Two-component signal transduction pathways are one of the primary means by which microorganisms respond to environmental signals. These signaling cascades originated in prokaryotes and were inherited by eukaryotes via endosymbiotic lateral gene transfer from ancestral cyanobacteria. We report here that the nuclear genome of the pathogenic fungus Candida albicans contains elements of a two-component signaling pathway that seem to be targeted to the mitochondria. The C. albicans two-component response regulator protein Srr1 (stress response regulator 1) contains a mitochondrial targeting sequence at the N terminus, and fluorescence microscopy reveals mitochondrial localization of green fluorescent protein-tagged Srr1. Moreover, phylogenetic analysis indicates that C. albicans Srr1 is more closely related to histidine kinases and response regulators found in marine bacteria than are other two-component proteins present in the fungi. These data suggest conservation of this protein during the evolutionary transition from endosymbiont to a subcellular organelle. We used microarray analysis to determine whether the phenotypes observed with a srr1Δ/Δ mutant could be correlated with gene transcriptional changes. The expression of mitochondrial genes was altered in the srr1Δ/Δ null mutant in comparison to their expression in the wild type. Furthermore, apoptosis increased significantly in the srr1Δ/Δ mutant strain compared to the level of apoptosis in the wild type, suggesting the activation of a mitochondrion-dependent apoptotic cell death pathway in the srr1Δ/Δ mutant. Collectively, this study shows for the first time that a lower eukaryote like C. albicans possesses a two-component response regulator protein that has survived in mitochondria and regulates a subset of genes whose functions are associated with the oxidative stress response and programmed cell death (apoptosis).}, }
@article {pmid23584970, year = {2013}, author = {Dahle, H and Roalkvam, I and Thorseth, IH and Pedersen, RB and Steen, IH}, title = {The versatile in situ gene expression of an Epsilonproteobacteria-dominated biofilm from a hydrothermal chimney.}, journal = {Environmental microbiology reports}, volume = {5}, number = {2}, pages = {282-290}, doi = {10.1111/1758-2229.12016}, pmid = {23584970}, issn = {1758-2229}, mesh = {Arctic Regions ; Bacterial Proteins/*genetics/metabolism ; *Biofilms ; Construction Materials/*microbiology ; DNA, Bacterial/genetics ; Ecosystem ; Epsilonproteobacteria/classification/genetics/*isolation &amp; purification/*physiology ; *Gene Expression Regulation, Bacterial ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The Epsilonproteobacteria, including members of the genus Sulfurovum, are regarded as important primary producers in hydrothermal systems. However, their in situ gene expression in this habitat has so far not been investigated. We report a metatranscriptomic analysis of a Sulfurovum-dominated biofilm from one of the chimneys at the Loki's Castle hydrothermal system, located at the Arctic Mid Ocean Ridge. Transcripts involved in hydrogen oxidation, oxidation of sulfur species, aerobic respiration and denitrification were abundant and mostly assigned to Sulfurovum, indicating that members of this genus utilize multiple chemical energy sources simultaneously for primary production. Sulfurovum also seemed to have a diverse expression of transposases, potentially involved in horizontal gene transfer. Other transcripts were involved in CO2 fixation by the reverse TCA cycle, the CRISPR-Cas system, heavy metal resistance, and sensing and responding to changing environmental conditions. Through pyrosequencing of PCR amplified 16S rRNA genes, the Sulfurovum-dominated biofilm was compared with another biofilm from the same chimney, revealing a large shift in the community structure of Epsilonproteobacteria-dominated biofilms over a few metres.}, }
@article {pmid23579690, year = {2013}, author = {Lederer, FL and Weinert, U and Günther, TJ and Raff, J and Weiß, S and Pollmann, K}, title = {Identification of multiple putative S-layer genes partly expressed by Lysinibacillus sphaericus JG-B53.}, journal = {Microbiology (Reading, England)}, volume = {159}, number = {Pt 6}, pages = {1097-1108}, doi = {10.1099/mic.0.065763-0}, pmid = {23579690}, issn = {1465-2080}, mesh = {Bacillaceae/classification/*genetics/isolation &amp; purification ; Computational Biology ; DNA, Bacterial/chemistry/genetics ; Environmental Microbiology ; *Gene Expression ; Gene Expression Profiling ; Germany ; High-Throughput Nucleotide Sequencing ; Membrane Glycoproteins/biosynthesis/chemistry/*genetics ; Molecular Sequence Data ; Molecular Weight ; Sequence Homology, Amino Acid ; }, abstract = {Lysinibacillus sphaericus JG-B53 was isolated from the uranium mining waste pile Haberland near Johanngeorgenstadt, Germany. Previous studies have shown that many bacteria that have been isolated from these heavy metal contaminated environments possess surface layer (S-layer) proteins that enable the bacteria to survive by binding metals with high affinity. Conversely, essential trace elements are able to cross the filter layer and reach the interior of the cell. This is especially true of the S-layer of L. sphaericus JG-B53, which possesses outstanding recrystallization and metal-binding properties. In this study, S-layer protein gene sequences encoded in the genome of L. sphaericus JG-B53 were identified using next-generation sequencing technology followed by bioinformatic analyses. The genome of L. sphaericus JG-B53 encodes at least eight putative S-layer protein genes with distinct differences. Using mRNA analysis the expression of the putative S-layer protein genes was studied. The functional S-layer protein B53 Slp1 was identified as the dominantly expressed S-layer protein in L. sphaericus JG-B53 by mRNA studies, SDS-PAGE and N-terminal sequencing. B53 Slp1 is characterized by square lattice symmetry and a molecular mass of 116 kDa. The S-layer protein B53 Slp1 shows a high similarity to the functional S-layer protein of L. sphaericus JG-A12, which was isolated from the same uranium mining waste pile Haberland and has been described by previous research. These similarities indicate horizontal gene transfer and DNA rearrangements between these bacteria. The presence of multiple S-layer gene copies may enable the bacterial strains to quickly adapt to changing environments.}, }
@article {pmid23576569, year = {2013}, author = {Netti, F and Malgieri, G and Esposito, S and Palmieri, M and Baglivo, I and Isernia, C and Omichinski, JG and Pedone, PV and Lartillot, N and Fattorusso, R}, title = {An experimentally tested scenario for the structural evolution of eukaryotic Cys2His2 zinc fingers from eubacterial ros homologs.}, journal = {Molecular biology and evolution}, volume = {30}, number = {7}, pages = {1504-1513}, doi = {10.1093/molbev/mst068}, pmid = {23576569}, issn = {1537-1719}, mesh = {Agrobacterium tumefaciens/*chemistry/genetics ; Amino Acid Sequence ; Bacteria/chemistry/genetics ; Bacterial Proteins/*chemistry/genetics ; Binding Sites ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sequence Alignment ; *Zinc Fingers ; }, abstract = {The exact evolutionary origin of the zinc finger (ZF) domain is unknown, as it is still not clear from which organisms it was first derived. However, the unique features of the ZF domains have made it very easy for evolution to tinker with them in a number of different manners, including their combination, variation of their number by unequal crossing-over or tandem duplication and tuning of their affinity for specific DNA sequence motifs through point substitutions. Classical Cys2His2 ZF domains as structurally autonomous motifs arranged in multiple copies are known only in eukaryotes. Nonetheless, a single prokaryotic Cys2His2 ZF domain has been identified in the transcriptional regulator Ros from Agrobacterium tumefaciens and recently characterized. The present work focuses on the evolution of the classical ZF domains with the goal of trying to determine whether eukaryotic ZFs have evolved from the prokaryotic Ros-like proteins. Our results, based on computational and experimental data, indicate that a single insertion of three amino acids in the short loop that separates the β-sheet from the α-helix of the Ros protein is sufficient to induce a structural transition from a Ros like to an eukaryotic-ZF like structure. This observation provides evidence for a structurally plausible and parsimonious scenario of fold evolution, giving a structural basis to the hypothesis of a horizontal gene transfer (HGT) from bacteria to eukaryotes.}, }
@article {pmid23575371, year = {2013}, author = {Hingamp, P and Grimsley, N and Acinas, SG and Clerissi, C and Subirana, L and Poulain, J and Ferrera, I and Sarmento, H and Villar, E and Lima-Mendez, G and Faust, K and Sunagawa, S and Claverie, JM and Moreau, H and Desdevises, Y and Bork, P and Raes, J and de Vargas, C and Karsenti, E and Kandels-Lewis, S and Jaillon, O and Not, F and Pesant, S and Wincker, P and Ogata, H}, title = {Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes.}, journal = {The ISME journal}, volume = {7}, number = {9}, pages = {1678-1695}, pmid = {23575371}, issn = {1751-7370}, mesh = {Animals ; *Biodiversity ; Cell Nucleus/virology ; Cytoplasm/virology ; DNA Viruses/*classification/genetics/*physiology ; Eukaryota/virology ; Gene Transfer, Horizontal ; Genes, Viral/genetics ; Genome, Viral/genetics ; Indian Ocean ; *Metagenome ; Oceans and Seas ; Oomycetes/virology ; Phycodnaviridae/classification/genetics/physiology ; Phylogeny ; Population Density ; Prokaryotic Cells/physiology ; }, abstract = {Nucleo-cytoplasmic large DNA viruses (NCLDVs) constitute a group of eukaryotic viruses that can have crucial ecological roles in the sea by accelerating the turnover of their unicellular hosts or by causing diseases in animals. To better characterize the diversity, abundance and biogeography of marine NCLDVs, we analyzed 17 metagenomes derived from microbial samples (0.2-1.6 μm size range) collected during the Tara Oceans Expedition. The sample set includes ecosystems under-represented in previous studies, such as the Arabian Sea oxygen minimum zone (OMZ) and Indian Ocean lagoons. By combining computationally derived relative abundance and direct prokaryote cell counts, the abundance of NCLDVs was found to be in the order of 10(4)-10(5) genomes ml(-1) for the samples from the photic zone and 10(2)-10(3) genomes ml(-1) for the OMZ. The Megaviridae and Phycodnaviridae dominated the NCLDV populations in the metagenomes, although most of the reads classified in these families showed large divergence from known viral genomes. Our taxon co-occurrence analysis revealed a potential association between viruses of the Megaviridae family and eukaryotes related to oomycetes. In support of this predicted association, we identified six cases of lateral gene transfer between Megaviridae and oomycetes. Our results suggest that marine NCLDVs probably outnumber eukaryotic organisms in the photic layer (per given water mass) and that metagenomic sequence analyses promise to shed new light on the biodiversity of marine viruses and their interactions with potential hosts.}, }
@article {pmid23572252, year = {2013}, author = {Michalska, K and Brown, RN and Li, H and Jedrzejczak, R and Niemann, GS and Heffron, F and Cort, JR and Adkins, JN and Babnigg, G and Joachimiak, A}, title = {New sub-family of lysozyme-like proteins shows no catalytic activity: crystallographic and biochemical study of STM3605 protein from Salmonella Typhimurium.}, journal = {Journal of structural and functional genomics}, volume = {14}, number = {1}, pages = {1-10}, pmid = {23572252}, issn = {1570-0267}, support = {U01 GM094623/GM/NIGMS NIH HHS/United States ; U54 GM094585/GM/NIGMS NIH HHS/United States ; GM094585/GM/NIGMS NIH HHS/United States ; GM094623/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacillus/drug effects ; Bacterial Proteins/*chemistry/genetics/metabolism ; Bacteriophages/*genetics/metabolism ; Crystallography, X-Ray ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Kinetics ; Micelles ; Micrococcus luteus/drug effects ; Molecular Sequence Data ; Muramidase/*chemistry/genetics/metabolism/pharmacology ; Protein Folding ; Protein Isoforms/chemistry/genetics/metabolism/pharmacology ; Recombinant Proteins/chemistry/genetics/metabolism ; Salmonella typhimurium/chemistry/genetics/*metabolism ; Sequence Homology, Amino Acid ; }, abstract = {Phage viruses that infect prokaryotes integrate their genome into the host chromosome; thus, microbial genomes typically contain genetic remnants of both recent and ancient phage infections. Often phage genes occur in clusters of atypical G+C content that reflect integration of the foreign DNA. However, some phage genes occur in isolation without other phage gene neighbors, probably resulting from horizontal gene transfer. In these cases, the phage gene product is unlikely to function as a component of a mature phage particle, and instead may have been co-opted by the host for its own benefit. The product of one such gene from Salmonella enterica serovar Typhimurium, STM3605, encodes a protein with modest sequence similarity to phage-like lysozyme (N-acetylmuramidase) but appears to lack essential catalytic residues that are strictly conserved in all lysozymes. Close homologs in other bacteria share this characteristic. The structure of the STM3605 protein was characterized by X-ray crystallography, and functional assays showed that it is a stable, folded protein whose structure closely resembles lysozyme. However, this protein is unlikely to hydrolyze peptidoglycan. Instead, STM3605 is presumed to have evolved an alternative function because it shows some lytic activity and partitions to micelles.}, }
@article {pmid23567024, year = {2013}, author = {Kaminski, L and Lurie-Weinberger, MN and Allers, T and Gophna, U and Eichler, J}, title = {Phylogenetic- and genome-derived insight into the evolution of N-glycosylation in Archaea.}, journal = {Molecular phylogenetics and evolution}, volume = {68}, number = {2}, pages = {327-339}, doi = {10.1016/j.ympev.2013.03.024}, pmid = {23567024}, issn = {1095-9513}, mesh = {Archaea/enzymology/genetics ; Archaeal Proteins/*genetics/metabolism ; Codon ; Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; *Genome, Archaeal ; Glycoproteins/*genetics/metabolism ; Glycosylation ; Haloferax/enzymology/*genetics ; Hexosyltransferases/genetics ; Membrane Proteins/genetics ; Multigene Family ; Phylogeny ; Protein Processing, Post-Translational/*genetics ; }, abstract = {N-glycosylation, the covalent attachment of oligosaccharides to target protein Asn residues, is a post-translational modification that occurs in all three domains of life. In Archaea, the N-linked glycans that decorate experimentally characterized glycoproteins reveal a diversity in composition and content unequaled by their bacterial or eukaryal counterparts. At the same time, relatively little is known of archaeal N-glycosylation pathways outside of a handful of model strains. To gain insight into the distribution and evolutionary history of the archaeal version of this universal protein-processing event, 168 archaeal genome sequences were scanned for the presence of aglB, encoding the known archaeal oligosaccharyltransferase, an enzyme key to N-glycosylation. Such analysis predicts the presence of AglB in 166 species, with some species seemingly containing multiple versions of the protein. Phylogenetic analysis reveals that the events leading to aglB duplication occurred at various points during archaeal evolution. In many cases, aglB is found as part of a cluster of putative N-glycosylation genes. The presence, arrangement and nucleotide composition of genes in aglB-based clusters in five species of the halophilic archaeon Haloferax points to lateral gene transfer as contributing to the evolution of archaeal N-glycosylation.}, }
@article {pmid23563966, year = {2013}, author = {Gilbert, C and Cordaux, R}, title = {Horizontal transfer and evolution of prokaryote transposable elements in eukaryotes.}, journal = {Genome biology and evolution}, volume = {5}, number = {5}, pages = {822-832}, pmid = {23563966}, issn = {1759-6653}, mesh = {Bacteria/genetics ; Base Sequence ; DNA Transposable Elements/*genetics ; Eukaryota/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome ; Phylogeny ; Prokaryotic Cells ; }, abstract = {Horizontal transfer (HT) of transposable elements (TEs) plays a key role in prokaryotic evolution, and mounting evidence suggests that it has also had an important impact on eukaryotic evolution. Although many prokaryote-to-prokaryote and eukaryote-to-eukaryote HTs of TEs have been characterized, only few cases have been reported between prokaryotes and eukaryotes. Here, we carried out a comprehensive search for all major groups of prokaryotic insertion sequences (ISs) in 430 eukaryote genomes. We uncovered a total of 80 sequences, all deriving from the IS607 family, integrated in the genomes of 14 eukaryote species belonging to four distinct phyla (Amoebozoa, Ascomycetes, Basidiomycetes, and Stramenopiles). Given that eukaryote IS607-like sequences are most closely related to cyanobacterial IS607 and that their phylogeny is incongruent with that of their hosts, we conclude that the presence of IS607-like sequences in eukaryotic genomes is the result of several HT events. Selection analyses further suggest that our ability to detect these prokaryote TEs today in eukaryotes is because HT of these sequences occurred recently and/or some IS607 elements were domesticated after HT, giving rise to new eukaryote genes. Supporting the recent age of some of these HTs, we uncovered intact full-length, potentially active IS607 copies in the amoeba Acanthamoeba castellani. Overall, our study shows that prokaryote-to-eukaryote HT of TEs occurred at relatively low frequency during recent eukaryote evolution and it sets IS607 as the most widespread TE (being present in prokaryotes, eukaryotes, and viruses).}, }
@article {pmid23563106, year = {2013}, author = {Bennett, HM}, title = {Microbial genomes as cheat sheets.}, journal = {Nature reviews. Microbiology}, volume = {11}, number = {5}, pages = {302}, pmid = {23563106}, issn = {1740-1534}, mesh = {Adenosine Triphosphatases/genetics/metabolism ; *Gene Transfer, Horizontal ; *Genome, Archaeal ; *Genome, Bacterial ; Methyltransferases/genetics/metabolism ; Rhodophyta/enzymology/*genetics/metabolism ; }, }
@article {pmid23557360, year = {2013}, author = {McDonald, TR and Mueller, O and Dietrich, FS and Lutzoni, F}, title = {High-throughput genome sequencing of lichenizing fungi to assess gene loss in the ammonium transporter/ammonia permease gene family.}, journal = {BMC genomics}, volume = {14}, number = {}, pages = {225}, pmid = {23557360}, issn = {1471-2164}, mesh = {Ecosystem ; Gene Transfer, Horizontal ; Genes, Fungal/*genetics ; *High-Throughput Nucleotide Sequencing ; Lichens/drug effects/*genetics/growth &amp; development/physiology ; Membrane Transport Proteins/*genetics/*metabolism ; Nitrogen/pharmacology ; Quaternary Ammonium Compounds/*metabolism ; Species Specificity ; Symbiosis ; }, abstract = {BACKGROUND: Horizontal gene transfer has shaped the evolution of the ammonium transporter/ammonia permease gene family. Horizontal transfers of ammonium transporter/ammonia permease genes into the fungi include one transfer from archaea to the filamentous ascomycetes associated with the adaptive radiation of the leotiomyceta. The horizontally transferred gene has subsequently been lost in most of the group but has been selectively retained in lichenizing fungi. However, some groups of lichens appear to have secondarily lost the archaeal ammonium transporter. Definitive assessment of gene loss can only be made via whole genome sequencing.<br><br>RESULTS: Ammonium transporter/ammonia permease gene sequences were recovered from the assembled genomes of eight lichenizing fungi in key clades including the Caliciales, the Peltigerales, the Ostropomycetidae, the Acarosporomycetidae, the Verrucariales, the Arthoniomycetidae and the Lichinales. The genes recovered were included in a refined phylogenetic analysis. The hypothesis that lichens symbiotic with a nitrogen-fixing cyanobacterium as a primary photobiont or lichens living in high nitrogen environments lose the plant-like ammonium transporters was upheld, but did not account for additional losses of ammonium transporters/ammonia permeases in the lichens from the Acarosporomycetidae, Chaetotheriomycetes and Arthoniomycetes. In addition, the four ammonium transporter/ammonia permease genes from Cladonia grayi were shown to be functional by expressing the lichen genes in a strain of Saccharomyces cerevisiae in which all three native ammonium transporters were deleted, and assaying for growth on limiting ammonia as a sole nitrogen source.<br><br>CONCLUSIONS: Given sufficient coverage, next-generation sequencing technology can definitively address the loss of a gene in a genome when using environmental DNA isolated from lichen thalli collected from their natural habitats. Lichen-forming fungi have been losing ammonium transporters/ammonia permease genes at a slower rate than the most closely related non-lichenized lineages. These horizontally transferred genes in the Cladonia grayi genome encode functional ammonium transporters/ammonia permeases.}, }
@article {pmid23555871, year = {2013}, author = {Sun, BF and Xiao, JH and He, S and Liu, L and Murphy, RW and Huang, DW}, title = {Multiple interkingdom horizontal gene transfers in Pyrenophora and closely related species and their contributions to phytopathogenic lifestyles.}, journal = {PloS one}, volume = {8}, number = {3}, pages = {e60029}, pmid = {23555871}, issn = {1932-6203}, mesh = {Ascomycota/classification/*genetics ; Biological Evolution ; Gene Transfer, Horizontal/*genetics ; Phylogeny ; }, abstract = {Many studies have reported horizontal gene transfer (HGT) events from eukaryotes, especially fungi. However, only a few investigations summarized multiple interkingdom HGTs involving important phytopathogenic species of Pyrenophora and few have investigated the genetic contributions of HGTs to fungi. We investigated HGT events in P. teres and P. tritici-repentis and discovered that both species harbored 14 HGT genes derived from bacteria and plants, including 12 HGT genes that occurred in both species. One gene coding a leucine-rich repeat protein was present in both species of Pyrenophora and it may have been transferred from a host plant. The transfer of genes from a host plant to pathogenic fungi has been reported rarely and we discovered the first evidence for this transfer in phytopathogenic Pyrenophora. Two HGTs in Pyrenophora underwent subsequent duplications. Some HGT genes had homologs in a few other fungi, indicating relatively ancient transfer events. Functional analyses indicated that half of the HGT genes encoded extracellular proteins and these may have facilitated the infection of plants by Pyrenophora via interference with plant defense-response and the degradation of plant cell walls. Some other HGT genes appeared to participate in carbohydrate metabolism. Together, these functions implied that HGTs may have led to highly efficient mechanisms of infection as well as the utilization of host carbohydrates. Evolutionary analyses indicated that HGT genes experienced amelioration, purifying selection, and accelerated evolution. These appeared to constitute adaptations to the background genome of the recipient. The discovery of multiple interkingdom HGTs in Pyrenophora, their significance to infection, and their adaptive evolution, provided valuable insights into the evolutionary significance of interkingdom HGTs from multiple donors.}, }
@article {pmid23555299, year = {2013}, author = {Guy, L and Nystedt, B and Toft, C and Zaremba-Niedzwiedzka, K and Berglund, EC and Granberg, F and Näslund, K and Eriksson, AS and Andersson, SG}, title = {A gene transfer agent and a dynamic repertoire of secretion systems hold the keys to the explosive radiation of the emerging pathogen Bartonella.}, journal = {PLoS genetics}, volume = {9}, number = {3}, pages = {e1003393}, pmid = {23555299}, issn = {1553-7404}, mesh = {Animals ; *Bartonella/genetics/pathogenicity ; *Biological Evolution ; Cats ; Dogs ; Electromagnetic Radiation ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; Macropodidae/genetics/microbiology ; Mice ; Multigene Family ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Gene transfer agents (GTAs) randomly transfer short fragments of a bacterial genome. A novel putative GTA was recently discovered in the mouse-infecting bacterium Bartonella grahamii. Although GTAs are widespread in phylogenetically diverse bacteria, their role in evolution is largely unknown. Here, we present a comparative analysis of 16 Bartonella genomes ranging from 1.4 to 2.6 Mb in size, including six novel genomes from Bartonella isolated from a cow, two moose, two dogs, and a kangaroo. A phylogenetic tree inferred from 428 orthologous core genes indicates that the deadly human pathogen B. bacilliformis is related to the ruminant-adapted clade, rather than being the earliest diverging species in the genus as previously thought. A gene flux analysis identified 12 genes for a GTA and a phage-derived origin of replication as the most conserved innovations. These are located in a region of a few hundred kb that also contains 8 insertions of gene clusters for type III, IV, and V secretion systems, and genes for putatively secreted molecules such as cholera-like toxins. The phylogenies indicate a recent transfer of seven genes in the virB gene cluster for a type IV secretion system from a cat-adapted B. henselae to a dog-adapted B. vinsonii strain. We show that the B. henselae GTA is functional and can transfer genes in vitro. We suggest that the maintenance of the GTA is driven by selection to increase the likelihood of horizontal gene transfer and argue that this process is beneficial at the population level, by facilitating adaptive evolution of the host-adaptation systems and thereby expansion of the host range size. The process counters gene loss and forces all cells to contribute to the production of the GTA and the secreted molecules. The results advance our understanding of the role that GTAs play for the evolution of bacterial genomes.}, }
@article {pmid23554975, year = {2013}, author = {Armijos Jaramillo, VD and Vargas, WA and Sukno, SA and Thon, MR}, title = {Horizontal transfer of a subtilisin gene from plants into an ancestor of the plant pathogenic fungal genus Colletotrichum.}, journal = {PloS one}, volume = {8}, number = {3}, pages = {e59078}, pmid = {23554975}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Colletotrichum/*genetics ; Gene Expression ; *Gene Transfer, Horizontal ; Host-Pathogen Interactions ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Plant Diseases/genetics/microbiology ; Plants/*genetics/*microbiology ; Protein Conformation ; Protein Interaction Domains and Motifs ; Sequence Alignment ; Subtilisin/chemistry/*genetics ; }, abstract = {The genus Colletotrichum contains a large number of phytopathogenic fungi that produce enormous economic losses around the world. The effect of horizontal gene transfer (HGT) has not been studied yet in these organisms. Inter-Kingdom HGT into fungal genomes has been reported in the past but knowledge about the HGT between plants and fungi is particularly limited. We describe a gene in the genome of several species of the genus Colletotrichum with a strong resemblance to subtilisins typically found in plant genomes. Subtilisins are an important group of serine proteases, widely distributed in all of the kingdoms of life. Our hypothesis is that the gene was acquired by Colletotrichum spp. through (HGT) from plants to a Colletotrichum ancestor. We provide evidence to support this hypothesis in the form of phylogenetic analyses as well as a characterization of the similarity of the subtilisin at the primary, secondary and tertiary structural levels. The remarkable level of structural conservation of Colletotrichum plant-like subtilisin (CPLS) with plant subtilisins and the differences with the rest of Colletotrichum subtilisins suggests the possibility of molecular mimicry. Our phylogenetic analysis indicates that the HGT event would have occurred approximately 150-155 million years ago, after the divergence of the Colletotrichum lineage from other fungi. Gene expression analysis shows that the gene is modulated during the infection of maize by C. graminicola suggesting that it has a role in plant disease. Furthermore, the upregulation of the CPLS coincides with the downregulation of several plant genes encoding subtilisins. Based on the known roles of subtilisins in plant pathogenic fungi and the gene expression pattern that we observed, we postulate that the CPLSs have an important role in plant infection.}, }
@article {pmid23554920, year = {2013}, author = {Li, X and Zhang, TC and Qiao, Q and Ren, Z and Zhao, J and Yonezawa, T and Hasegawa, M and Crabbe, MJ and Li, J and Zhong, Y}, title = {Complete chloroplast genome sequence of holoparasite Cistanche deserticola (Orobanchaceae) reveals gene loss and horizontal gene transfer from its host Haloxylon ammodendron (Chenopodiaceae).}, journal = {PloS one}, volume = {8}, number = {3}, pages = {e58747}, pmid = {23554920}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Base Sequence ; Chenopodiaceae/*genetics ; Cistanche/*genetics ; *Gene Deletion ; Gene Order ; *Gene Transfer, Horizontal ; Genes, Plant ; *Genome, Chloroplast ; Genomics ; Molecular Sequence Data ; Phylogeny ; Physical Chromosome Mapping ; Plastids/genetics ; Sequence Alignment ; }, abstract = {The central function of chloroplasts is to carry out photosynthesis, and its gene content and structure are highly conserved across land plants. Parasitic plants, which have reduced photosynthetic ability, suffer gene losses from the chloroplast (cp) genome accompanied by the relaxation of selective constraints. Compared with the rapid rise in the number of cp genome sequences of photosynthetic organisms, there are limited data sets from parasitic plants. PRINCIPAL FINDINGS/SIGNIFICANCE: Here we report the complete sequence of the cp genome of Cistanche deserticola, a holoparasitic desert species belonging to the family Orobanchaceae. The cp genome of C. deserticola is greatly reduced both in size (102,657 bp) and in gene content, indicating that all genes required for photosynthesis suffer from gene loss and pseudogenization, except for psbM. The striking difference from other holoparasitic plants is that it retains almost a full set of tRNA genes, and it has lower dN/dS for most genes than another close holoparasitic plant, E. virginiana, suggesting that Cistanche deserticola has undergone fewer losses, either due to a reduced level of holoparasitism, or to a recent switch to this life history. We also found that the rpoC2 gene was present in two copies within C. deserticola. Its own copy has much shortened and turned out to be a pseudogene. Another copy, which was not located in its cp genome, was a homolog of the host plant, Haloxylon ammodendron (Chenopodiaceae), suggesting that it was acquired from its host via a horizontal gene transfer.}, }
@article {pmid23550063, year = {2012}, author = {Domingues, S and da Silva, GJ and Nielsen, KM}, title = {Integrons: Vehicles and pathways for horizontal dissemination in bacteria.}, journal = {Mobile genetic elements}, volume = {2}, number = {5}, pages = {211-223}, pmid = {23550063}, issn = {2159-2543}, abstract = {Integrons are genetic elements first described at the end of the 1980s. Although most integrons were initially described in human clinical isolates, they have now been identified in many non-clinical environments, such as water and soil. Integrons are present in ≈10% of the sequenced bacterial genomes and are frequently linked to mobile genetic elements (MGEs); particularly the class 1 integrons. Genetic linkage to a diverse set of MGEs facilitates horizontal transfer of class 1 integrons within and between bacterial populations and species. The mechanistic aspects limiting transfer of MGEs will therefore limit the transfer of class 1 integrons. However, horizontal movement due to genes provided in trans and homologous recombination can result in class 1 integron dynamics independent of MGEs. A key determinant for continued dissemination of class 1 integrons is the probability that transferred MGEs will be vertically inherited in the recipient bacterial population. Heritability depends both on genetic stability as well as the fitness costs conferred to the host. Here we review the factors known to govern the dissemination of class 1 integrons in bacteria.}, }
@article {pmid23543711, year = {2013}, author = {Goeders, N and Drèze, PL and Van Melderen, L}, title = {Relaxed cleavage specificity within the RelE toxin family.}, journal = {Journal of bacteriology}, volume = {195}, number = {11}, pages = {2541-2549}, pmid = {23543711}, issn = {1098-5530}, mesh = {Amino Acid Sequence ; Bacterial Toxins/genetics/isolation &amp; purification/*metabolism ; Codon ; Consensus Sequence ; Escherichia coli K12/genetics/growth &amp; development/*metabolism ; Escherichia coli Proteins/genetics/isolation &amp; purification/*metabolism ; Genome, Bacterial/*genetics ; RNA Cleavage ; RNA, Bacterial/genetics/metabolism ; RNA, Messenger/genetics/*metabolism ; Sequence Alignment ; Substrate Specificity ; }, abstract = {Bacterial type II toxin-antitoxin systems are widespread in bacteria. Among them, the RelE toxin family is one of the most abundant. The RelE(K-12) toxin of Escherichia coli K-12 represents the paradigm for this family and has been extensively studied, both in vivo and in vitro. RelE(K-12) is an endoribonuclease that cleaves mRNAs that are translated by the ribosome machinery as these transcripts enter the A site. Earlier in vivo reports showed that RelE(K-12) cleaves preferentially in the 5'-end coding region of the transcripts in a codon-independent manner. To investigate whether the molecular activity as well as the cleavage pattern are conserved within the members of this toxin family, RelE-like sequences were selected in Proteobacteria, Cyanobacteria, Actinobacteria, and Spirochaetes and tested in E. coli. Our results show that these RelE-like sequences are part of toxin-antitoxin gene pairs, and that they inhibit translation in E. coli by cleaving transcripts that are being translated. Primer extension analyses show that these toxins exhibit specific cleavage patterns in vivo, both in terms of frequency and location of cleavage sites. We did not observe codon-dependent cleavage but rather a trend to cleave upstream purines and between the second and third positions of codons, except for the actinobacterial toxin. Our results suggest that RelE-like toxins have evolved to rapidly and efficiently shut down translation in a large spectrum of bacterial species, which correlates with the observation that toxin-antitoxin systems are spreading by horizontal gene transfer.}, }
@article {pmid23543608, year = {2013}, author = {Shen, J and Wang, Y and Schwarz, S}, title = {Presence and dissemination of the multiresistance gene cfr in Gram-positive and Gram-negative bacteria.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {68}, number = {8}, pages = {1697-1706}, doi = {10.1093/jac/dkt092}, pmid = {23543608}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Multiple, Bacterial ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Gram-Negative Bacteria/*drug effects/genetics ; Gram-Positive Bacteria/*drug effects/genetics ; Humans ; Plasmids ; tRNA Methyltransferases/*genetics ; }, abstract = {The emergence of the multiresistance gene cfr in staphylococci is of global concern. In addition to conferring resistance to phenicols, lincosamides, pleuromutilins, streptogramin A antibiotics and selected 16-membered macrolides, the cfr gene also confers resistance to the oxazolidinone linezolid. Linezolid is a last-resort antimicrobial agent for the treatment of serious infections in humans caused by resistant Gram-positive bacteria. The cfr gene is often located on plasmids and several cfr-carrying plasmids have been described, which differ in their structure, their size and the presence of additional resistance genes. These plasmids are important vehicles that promote the spread of the cfr gene not only among bacteria of the same species, but also among those of different species and genera. Moreover, the cfr gene has been identified in close proximity to different insertion sequences, which most probably also play an important role in its dissemination. This review summarizes current knowledge on the genetic environment of the multiresistance gene cfr with particular reference to mobile genetic elements and co-located resistance genes that may support its emergence.}, }
@article {pmid23542649, year = {2013}, author = {Cobbs, C and Heath, J and Stireman, JO and Abbot, P}, title = {Carotenoids in unexpected places: gall midges, lateral gene transfer, and carotenoid biosynthesis in animals.}, journal = {Molecular phylogenetics and evolution}, volume = {68}, number = {2}, pages = {221-228}, doi = {10.1016/j.ympev.2013.03.012}, pmid = {23542649}, issn = {1095-9513}, mesh = {Animals ; Carotenoids/*biosynthesis/genetics ; Diptera/enzymology/*genetics ; Evolution, Molecular ; Gene Dosage ; *Gene Transfer, Horizontal ; Genes, Fungal ; Geranylgeranyl-Diphosphate Geranylgeranyltransferase/genetics ; Insect Proteins/*genetics ; Intramolecular Lyases/genetics ; Likelihood Functions ; Molecular Sequence Annotation ; Molecular Sequence Data ; Oxidoreductases/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Carotenoids are conjugated isoprenoid molecules with many important physiological functions in organisms, including roles in photosynthesis, oxidative stress reduction, vision, diapause, photoperiodism, and immunity. Until recently, it was believed that only plants, microorganisms, and fungi were capable of synthesizing carotenoids and that animals acquired them from their diet, but recent studies have demonstrated that two arthropods (pea aphid and spider mite) possess a pair of genes homologous to those required for the first step of carotenoid biosynthesis. Absent in all other known animal genomes, these genes appear to have been acquired by aphids and spider mites in one or several lateral gene transfer events from a fungal donor. We report the third case of fungal carotenoid biosynthesis gene homologs in an arthropod: flies from the family Cecidomyiidae, commonly known as gall midges. Using phylogenetic analyses we show that it is unlikely that lycopene cyclase/phytoene synthase and phytoene desaturase homologs were transferred singly to an ancient arthropod ancestor; instead we propose that genes were transferred independently from related fungal donors after divergence of the major arthropod lineages. We also examine variation in intron placement and copy number of the carotenoid genes that may underlie function in the midges. This trans-kingdom transfer of carotenoid genes may represent a key innovation, underlying the evolution of phytophagy and plant-galling in gall midges and facilitating their extensive diversification across plant lineages.}, }
@article {pmid23541529, year = {2013}, author = {Vinogradov, SN and Tinajero-Trejo, M and Poole, RK and Hoogewijs, D}, title = {Bacterial and archaeal globins - a revised perspective.}, journal = {Biochimica et biophysica acta}, volume = {1834}, number = {9}, pages = {1789-1800}, doi = {10.1016/j.bbapap.2013.03.021}, pmid = {23541529}, issn = {0006-3002}, support = {BB/H016805/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Evolution, Molecular ; Genome, Archaeal/*genetics ; Genome, Bacterial/*genetics ; Globins/*genetics ; Phylogeny ; }, abstract = {A bioinformatics survey of putative globins in over 2200 bacterial and some 140 archaeal genomes revealed that over half the bacterial and approximately one fifth of archaeal genomes contain genes encoding globins that were classified into three families: the M (myoglobin-like), and S (sensor) families all exhibiting the canonical 3/3 myoglobin fold, and the T family (truncated myoglobin fold). Although the M family comprises 2 subfamilies, flavohemoglobins (FHbs) and single domain globins (SDgbs), the S family encompasses chimeric globin-coupled sensors (GCSs), single domain Pgbs (protoglobins) and SSDgbs (sensor single domain globins). The T family comprises three classes TrHb1s, TrHb2s and TrHb3s, characterized by the abbreviated 2/2 myoglobin fold. The Archaea contain only Pgbs, GCSs and TrHb1s. The smallest globin-bearing genomes are the streamlined genomes (~1.3Mbp) of the SAR11 clade of alphaproteobacteria and the slightly larger (ca. 1.7Mbp) genomes of Aquificae. The smallest genome with members of all three families is the 2.3Mbp genome of the extremophile Methylacidiphilum infernorum (Verrumicrobia). Of the 147 possible combinations of the eight globin subfamilies, only 83 are observed. Although binary combinations are infrequent and ternary combinations are rare, the FHb+TrHb2 combination is the most commonly observed. Of the possible functions of bacterial globins we discuss the two principal ones - nitric oxide detoxification via the NO dioxygenase or denitrosylase activities and the sensing of oxygen concentration in the environmental niche. In only few cases has a physiological role been demonstrated in vivo. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.}, }
@article {pmid23541366, year = {2013}, author = {Huddleston, JR and Brokaw, JM and Zak, JC and Jeter, RM}, title = {Natural transformation as a mechanism of horizontal gene transfer among environmental Aeromonas species.}, journal = {Systematic and applied microbiology}, volume = {36}, number = {4}, pages = {224-234}, doi = {10.1016/j.syapm.2013.01.004}, pmid = {23541366}, issn = {1618-0984}, mesh = {Aeromonas/*genetics/physiology ; Culture Media/chemistry ; DNA Transformation Competence ; *Environmental Microbiology ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Sequence Analysis, DNA ; *Transformation, Bacterial ; }, abstract = {Aeromonas species are common inhabitants of aquatic environments and relevant as human pathogens. Their potential as pathogens may be related in part to lateral transfer of genes associated with toxin production, biofilm formation, antibiotic resistance, and other virulence determinants. Natural transformation has not been characterized in aeromonads. DNA from wild-type, prototrophic strains that had been isolated from environmental sources was used as donor DNA in transformation assays with auxotrophs as the recipients. Competence was induced in 20% nutrient broth during the stationary phase of growth. Optimal transformation assay conditions for one chosen isolate were in Tris buffer with magnesium or calcium, pH 5-8, and a saturating concentration of 0.5 μg of DNA per assay (3.3 ng of DNA μl[-1]) at 30°C. Sodium was also required and could not be replaced with ammonium, potassium, or lithium. The maximal transformation frequency observed was 1.95 × 10[-3] transformants (recipient cell)[-1]. A survey of environmental Aeromonas auxotrophic recipients (n=37), assayed with donor DNA from other wild-type environmental aeromonads under optimal assay conditions, demonstrated that 73% were able to act as recipients, and 100% were able to act as donors to at least some other aeromonads. Three different transformation groups were identified based on each isolates' ability to transform other strains with its DNA. The transformation groups roughly corresponded to phylogenetic groups. These results demonstrate that natural transformation is a general property of Aeromonas environmental isolates with implications for the genetic structures of coincident Aeromonas populations.}, }
@article {pmid23537181, year = {2013}, author = {Xiong, ZQ and Yang, YY and Zhao, N and Wang, Y}, title = {Diversity of endophytic fungi and screening of fungal paclitaxel producer from Anglojap yew, Taxus x media.}, journal = {BMC microbiology}, volume = {13}, number = {}, pages = {71}, pmid = {23537181}, issn = {1471-2180}, mesh = {*Biodiversity ; Chromatography, High Pressure Liquid ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Endophytes/*classification/genetics/*isolation &amp; purification/metabolism ; Fungi/*classification/genetics/*isolation &amp; purification/metabolism ; Mass Spectrometry ; Molecular Sequence Data ; Paclitaxel/*metabolism ; Phylogeny ; Sequence Analysis, DNA ; Taxus/*microbiology ; }, abstract = {BACKGROUND: Endophytic fungi represent underexplored resource of novel lead compounds and have a capacity to produce diverse class of plant secondary metabolites. Here we investigated endophytic fungi diversity and screening of paclitaxel-producing fungi from Taxus x media.<br><br>RESULTS: Eighty-one endophytic fungi isolated from T. media were grouped into 8 genera based on the morphological and molecular identification. Guignardia and Colletotrichum were the dominant genera, whereas the remaining genera were infrequent groups. The genera Glomerella and Gibberella were first reported in Taxus. Three representative species of the distinct genera gave positive hits by molecular marker screening and were capable of producing taxol which were validated by HPLC-MS. Among these 3 taxol-producing fungi, the highest yield of taxol was 720 ng/l by Guignardia mangiferae HAA11 compared with those of Fusarium proliferatum HBA29 (240 ng/l) and Colletotrichum gloeosporioides TA67 (120 ng/l). This is the first report of taxol producer from Guignardia. Moreover, the lower similarities of ts and bapt between microbial and plant origin suggested that fungal taxol biosynthetic cluster might be repeatedly invented during evolution, nor horizontal gene transfer from Taxus species.<br><br>CONCLUSIONS: Taxol-producing endophytic fungi could be a fascinating reservoir to generate taxol-related drug lead and to elucidate the remained 5 unknown genes or the potential regulation mechanism in the taxol biosynthesis pathway.}, }
@article {pmid23537049, year = {2013}, author = {Keeling, CI and Yuen, MM and Liao, NY and Docking, TR and Chan, SK and Taylor, GA and Palmquist, DL and Jackman, SD and Nguyen, A and Li, M and Henderson, H and Janes, JK and Zhao, Y and Pandoh, P and Moore, R and Sperling, FA and Huber, DP and Birol, I and Jones, SJ and Bohlmann, J}, title = {Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest.}, journal = {Genome biology}, volume = {14}, number = {3}, pages = {R27}, pmid = {23537049}, issn = {1474-760X}, mesh = {Animals ; Cell Wall/metabolism ; Coleoptera/enzymology/*genetics ; *Ecosystem ; Female ; *Forests ; Gene Transfer, Horizontal/genetics ; Genetic Linkage ; Genome, Insect/*genetics ; Heterozygote ; Male ; Multigene Family ; Phylogeny ; Plant Cells/metabolism ; Polymorphism, Single Nucleotide/genetics ; Repetitive Sequences, Nucleic Acid/genetics ; Sequence Homology, Nucleic Acid ; Sex Chromosomes/genetics ; Synteny/genetics ; }, abstract = {BACKGROUND: The mountain pine beetle, Dendroctonus ponderosae Hopkins, is the most serious insect pest of western North American pine forests. A recent outbreak destroyed more than 15 million hectares of pine forests, with major environmental effects on forest health, and economic effects on the forest industry. The outbreak has in part been driven by climate change, and will contribute to increased carbon emissions through decaying forests.<br><br>RESULTS: We developed a genome sequence resource for the mountain pine beetle to better understand the unique aspects of this insect's biology. A draft de novo genome sequence was assembled from paired-end, short-read sequences from an individual field-collected male pupa, and scaffolded using mate-paired, short-read genomic sequences from pooled field-collected pupae, paired-end short-insert whole-transcriptome shotgun sequencing reads of mRNA from adult beetle tissues, and paired-end Sanger EST sequences from various life stages. We describe the cytochrome P450, glutathione S-transferase, and plant cell wall-degrading enzyme gene families important to the survival of the mountain pine beetle in its harsh and nutrient-poor host environment, and examine genome-wide single-nucleotide polymorphism variation. A horizontally transferred bacterial sucrose-6-phosphate hydrolase was evident in the genome, and its tissue-specific transcription suggests a functional role for this beetle.<br><br>CONCLUSIONS: Despite Coleoptera being the largest insect order with over 400,000 described species, including many agricultural and forest pest species, this is only the second genome sequence reported in Coleoptera, and will provide an important resource for the Curculionoidea and other insects.}, }
@article {pmid23536846, year = {2013}, author = {Janouškovec, J and Liu, SL and Martone, PT and Carré, W and Leblanc, C and Collén, J and Keeling, PJ}, title = {Evolution of red algal plastid genomes: ancient architectures, introns, horizontal gene transfer, and taxonomic utility of plastid markers.}, journal = {PloS one}, volume = {8}, number = {3}, pages = {e59001}, pmid = {23536846}, issn = {1932-6203}, support = {MOP-42517//Canadian Institutes of Health Research/Canada ; }, mesh = {Amino Acid Sequence ; DNA Barcoding, Taxonomic ; Endoribonucleases/metabolism ; *Evolution, Molecular ; Gene Order ; Gene Transfer, Horizontal ; Genes, Plant ; Genetic Markers ; *Genome, Plastid ; Introns ; Molecular Sequence Data ; Nucleic Acid Conformation ; Nucleotidyltransferases/metabolism ; Operon/genetics ; Phylogeny ; RNA, Transfer/chemistry/genetics ; Rhodophyta/*classification/*genetics ; Sequence Alignment ; Species Specificity ; }, abstract = {Red algae have the most gene-rich plastid genomes known, but despite their evolutionary importance these genomes remain poorly sampled. Here we characterize three complete and one partial plastid genome from a diverse range of florideophytes. By unifying annotations across all available red algal plastid genomes we show they all share a highly compact and slowly-evolving architecture and uniquely rich gene complements. Both chromosome structure and gene content have changed very little during red algal diversification, and suggest that plastid-to nucleus gene transfers have been rare. Despite their ancient character, however, the red algal plastids also contain several unprecedented features, including a group II intron in a tRNA-Met gene that encodes the first example of red algal plastid intron maturase - a feature uniquely shared among florideophytes. We also identify a rare case of a horizontally-acquired proteobacterial operon, and propose this operon may have been recruited for plastid function and potentially replaced a nucleus-encoded plastid-targeted paralogue. Plastid genome phylogenies yield a fully resolved tree and suggest that plastid DNA is a useful tool for resolving red algal relationships. Lastly, we estimate the evolutionary rates among more than 200 plastid genes, and assess their usefulness for species and subspecies taxonomy by comparison to well-established barcoding markers such as cox1 and rbcL. Overall, these data demonstrates that red algal plastid genomes are easily obtainable using high-throughput sequencing of total genomic DNA, interesting from evolutionary perspectives, and promising in resolving red algal relationships at evolutionarily-deep and species/subspecies levels.}, }
@article {pmid23535283, year = {2013}, author = {Richards, AM and Von Dwingelo, JE and Price, CT and Abu Kwaik, Y}, title = {Cellular microbiology and molecular ecology of Legionella-amoeba interaction.}, journal = {Virulence}, volume = {4}, number = {4}, pages = {307-314}, pmid = {23535283}, issn = {2150-5608}, mesh = {Amoeba/*microbiology ; *Ecology ; *Host-Parasite Interactions ; Legionella pneumophila/*physiology ; Models, Biological ; }, abstract = {Legionella pneumophila is an aquatic organism that interacts with amoebae and ciliated protozoa as the natural hosts, and this interaction plays a central role in bacterial ecology and infectivity. Upon transmission to humans, L. pneumophila infect and replicate within alveolar macrophages causing pneumonia. Intracellular proliferation of L. pneumophila within the two evolutionarily distant hosts is facilitated by bacterial exploitation of evolutionarily conserved host processes that are targeted by bacterial protein effectors injected into the host cell by the Dot/Icm type VIB translocation system. Although cysteine is semi-essential for humans and essential for amoeba, it is a metabolically favorable source of carbon and energy generation by L. pneumophila. To counteract host limitation of cysteine, L. pneumophila utilizes the AnkB Dot/Icm-translocated F-box effector to promote host proteasomal degradation of polyubiquitinated proteins within amoebae and human cells. Evidence indicates ankB and other Dot/Icm-translocated effector genes have been acquired through inter-kingdom horizontal gene transfer.}, }
@article {pmid23533610, year = {2013}, author = {Wheeler, D and Redding, AJ and Werren, JH}, title = {Characterization of an ancient lepidopteran lateral gene transfer.}, journal = {PloS one}, volume = {8}, number = {3}, pages = {e59262}, pmid = {23533610}, issn = {1932-6203}, support = {R24 GM084917/GM/NIGMS NIH HHS/United States ; GM084917/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Enterococcus/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Lepidoptera/*genetics ; }, abstract = {Bacteria to eukaryote lateral gene transfers (LGT) are an important potential source of material for the evolution of novel genetic traits. The explosion in the number of newly sequenced genomes provides opportunities to identify and characterize examples of these lateral gene transfer events, and to assess their role in the evolution of new genes. In this paper, we describe an ancient lepidopteran LGT of a glycosyl hydrolase family 31 gene (GH31) from an Enterococcus bacteria. PCR amplification between the LGT and a flanking insect gene confirmed that the GH31 was integrated into the Bombyx mori genome and was not a result of an assembly error. Database searches in combination with degenerate PCR on a panel of 7 lepidopteran families confirmed that the GH31 LGT event occurred deep within the Order approximately 65-145 million years ago. The most basal species in which the LGT was found is Plutella xylostella (superfamily: Yponomeutoidea). Array data from Bombyx mori shows that GH31 is expressed, and low dN/dS ratios indicates the LGT coding sequence is under strong stabilizing selection. These findings provide further support for the proposition that bacterial LGTs are relatively common in insects and likely to be an underappreciated source of adaptive genetic material.}, }
@article {pmid23532069, year = {2013}, author = {Mugford, ST and Louveau, T and Melton, R and Qi, X and Bakht, S and Hill, L and Tsurushima, T and Honkanen, S and Rosser, SJ and Lomonossoff, GP and Osbourn, A}, title = {Modularity of plant metabolic gene clusters: a trio of linked genes that are collectively required for acylation of triterpenes in oat.}, journal = {The Plant cell}, volume = {25}, number = {3}, pages = {1078-1092}, pmid = {23532069}, issn = {1532-298X}, support = {BB/E009913/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/J/00000614/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004561/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/E009912/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Acylation ; Acyltransferases/classification/genetics/metabolism ; Amino Acid Sequence ; Antifungal Agents/metabolism/pharmacology ; Ascomycota/pathogenicity ; Avena/enzymology/*genetics/metabolism ; Gene Expression Regulation, Plant ; *Genes, Plant ; Methylation ; Methyltransferases/classification/genetics/metabolism ; Molecular Sequence Data ; *Multigene Family ; Mutation ; Phylogeny ; Plant Diseases/microbiology ; Plant Proteins/classification/genetics/metabolism ; Plant Roots/genetics/metabolism ; Saponins/genetics/*metabolism ; Structure-Activity Relationship ; Nicotiana/genetics/metabolism ; Triterpenes/*metabolism ; }, abstract = {Operon-like gene clusters are an emerging phenomenon in the field of plant natural products. The genes encoding some of the best-characterized plant secondary metabolite biosynthetic pathways are scattered across plant genomes. However, an increasing number of gene clusters encoding the synthesis of diverse natural products have recently been reported in plant genomes. These clusters have arisen through the neo-functionalization and relocation of existing genes within the genome, and not by horizontal gene transfer from microbes. The reasons for clustering are not yet clear, although this form of gene organization is likely to facilitate co-inheritance and co-regulation. Oats (Avena spp) synthesize antimicrobial triterpenoids (avenacins) that provide protection against disease. The synthesis of these compounds is encoded by a gene cluster. Here we show that a module of three adjacent genes within the wider biosynthetic gene cluster is required for avenacin acylation. Through the characterization of these genes and their encoded proteins we present a model of the subcellular organization of triterpenoid biosynthesis.}, }
@article {pmid23529735, year = {2013}, author = {Rodríguez-Beltrán, J and Rodríguez-Rojas, A and Yubero, E and Blázquez, J}, title = {The animal food supplement sepiolite promotes a direct horizontal transfer of antibiotic resistance plasmids between bacterial species.}, journal = {Antimicrobial agents and chemotherapy}, volume = {57}, number = {6}, pages = {2651-2653}, pmid = {23529735}, issn = {1098-6596}, mesh = {*Animal Feed ; Animals ; Animals, Domestic/genetics/microbiology ; Anti-Bacterial Agents/pharmacology ; Bacteria/classification/*drug effects/*genetics ; Drug Resistance, Microbial/*genetics ; Food Additives/*pharmacology ; Gene Transfer, Horizontal/*drug effects ; Magnesium Silicates/*pharmacology ; Microbial Sensitivity Tests ; Plasmids/*genetics ; Transformation, Bacterial/*drug effects/genetics ; }, abstract = {Animal fodder is routinely complemented with antibiotics together with other food supplements to improve growth. For instance, sepiolite is currently used as a dietary coadjuvant in animal feed, as it increases animal growth parameters and improves meat and derived final product quality. This type of food additive has so far been considered innocuous for the development and spread of antibiotic resistance. In this study, we demonstrate that sepiolite promotes the direct horizontal transfer of antibiotic resistance plasmids between bacterial species. The conditions needed for plasmid transfer (sepiolite and friction forces) occur in the digestive tracts of farm animals, which routinely receive sepiolite as a food additive. Furthermore, this effect may be aggravated by the use of antibiotics supplied as growth promoters.}, }
@article {pmid23529618, year = {2013}, author = {Venturini, C and Ong, CL and Gillen, CM and Ben-Zakour, NL and Maamary, PG and Nizet, V and Beatson, SA and Walker, MJ}, title = {Acquisition of the Sda1-encoding bacteriophage does not enhance virulence of the serotype M1 Streptococcus pyogenes strain SF370.}, journal = {Infection and immunity}, volume = {81}, number = {6}, pages = {2062-2069}, pmid = {23529618}, issn = {1098-5522}, support = {R01 AI077780/AI/NIAID NIH HHS/United States ; R01 AR052728/AR/NIAMS NIH HHS/United States ; }, mesh = {Alleles ; Animals ; Base Sequence ; DNA, Bacterial/genetics ; Deoxyribonuclease I/genetics/*metabolism ; Humans ; Mice ; Mice, Inbred C57BL ; Molecular Sequence Data ; Streptococcus Phages/genetics/*metabolism ; Streptococcus pyogenes/*pathogenicity/*virology ; Virulence ; }, abstract = {The resurgence of invasive disease caused by Streptococcus pyogenes (group A Streptococcus [GAS]) in the past 30 years has paralleled the emergence and global dissemination of the highly virulent M1T1 clone. The GAS M1T1 clone has diverged from the ancestral M1 serotype by horizontal acquisition of two unique bacteriophages, encoding the potent DNase Sda1/SdaD2 and the superantigen SpeA, respectively. The phage-encoded DNase promotes escape from neutrophil extracellular traps and is linked to enhanced virulence of the M1T1 clone. In this study, we successfully used in vitro lysogenic conversion to transfer the Sda1-encoding phage from the M1T1 clonal strain 5448 to the nonclonal M1 isolate SF370 and determined the impact of this horizontal gene transfer event on virulence. Although Sda1 was expressed in SF370 lysogens, no capacity of the phage-converted strain to survive human neutrophil killing, switch to a hyperinvasive covRS mutant form, or cause invasive lethal infection in a humanized plasminogen mouse model was observed. This work suggests that the hypervirulence of the M1T1 clone is due to the unique synergic effect of the M1T1 clone bacteriophage-specific virulence factor Sda1 acting in concert with the M1T1 clone-specific genetic scaffold.}, }
@article {pmid23528645, year = {2013}, author = {Fondi, M and Rizzi, E and Emiliani, G and Orlandini, V and Berna, L and Papaleo, MC and Perrin, E and Maida, I and Corti, G and De Bellis, G and Baldi, F and Dijkshoorn, L and Vaneechoutte, M and Fani, R}, title = {The genome sequence of the hydrocarbon-degrading Acinetobacter venetianus VE-C3.}, journal = {Research in microbiology}, volume = {164}, number = {5}, pages = {439-449}, doi = {10.1016/j.resmic.2013.03.003}, pmid = {23528645}, issn = {1769-7123}, mesh = {Acinetobacter/classification/*genetics/isolation &amp; purification/metabolism ; Cluster Analysis ; DNA, Bacterial/*chemistry/*genetics ; Gene Order ; *Genome, Bacterial ; Hydrocarbons/metabolism ; Italy ; Metabolic Networks and Pathways/genetics ; Molecular Sequence Data ; Phylogeny ; Seawater/microbiology ; *Sequence Analysis, DNA ; }, abstract = {Here we report the genome sequence of Acinetobacter venetianus VE-C3, a strain isolated from the Venice Lagoon and known to be able to degrade n-alkanes. Post sequencing analyses revealed that this strain is relatively distantly related to the other Acinetobacter strains completely sequenced so far as shown by phylogenetic analysis and pangenome analysis (1285 genes shared with all the other Acinetobacter genomes sequenced so far). A. venetianus VE-C3 possesses a wide range of determinants whose molecular functions are probably related to the survival in a strongly impacted ecological niche. Among them, genes probably involved in the metabolism of long-chain n-alkanes and in the resistance to toxic metals (e.g. arsenic, cadmium, cobalt and zinc) were found. Genes belonging to these processes were found both on the chromosome and on plasmids. Also, our analysis documented one of the possible genetic bases underlying the strategy adopted by A. venetianus VE-C3 for the adhesion to oil fuel droplets, which could account for the differences existing in this process with other A. venetianus strains. Finally, the presence of a number of DNA mobilization-related genes (i.e. transposases, integrases, resolvases) strongly suggests an important role played by horizontal gene transfer in shaping the genome of A. venetianus VE-C3 and in its adaptation to its special ecological niche.}, }
@article {pmid23527231, year = {2013}, author = {Shi, C and Liu, Y and Huang, H and Xia, EH and Zhang, HB and Gao, LZ}, title = {Contradiction between plastid gene transcription and function due to complex posttranscriptional splicing: an exemplary study of ycf15 function and evolution in angiosperms.}, journal = {PloS one}, volume = {8}, number = {3}, pages = {e59620}, pmid = {23527231}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Base Sequence ; Camellia/*genetics ; *Evolution, Molecular ; Gene Expression Profiling ; Genes, Plant/*genetics ; Genome, Chloroplast/*genetics ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Pseudogenes/genetics ; RNA Processing, Post-Transcriptional/genetics/*physiology ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Plant chloroplast genes are usually co-transcribed while its posttranscriptional splicing is fairly complex and remains largely unsolved. On basis of sequencing the three complete Camellia (Theaceae) chloroplast genomes for the first time, we comprehensively analyzed the evolutionary patterns of ycf15, a plastid gene quite paradoxical in terms of its function and evolution, along the inferred angiosperm phylogeny. Although many species in separate lineages including the three species reported here contained an intact ycf15 gene in their chloroplast genomes, the phylogenetic mixture of both intact and obviously disabled ycf15 genes imply that they are all non-functional. Both intracellular gene transfer (IGT) and horizontal gene transfer (HGT) failed to explain such distributional anomalies. While, transcriptome analyses revealed that ycf15 was transcribed as precursor polycistronic transcript which contained ycf2, ycf15 and antisense trnL-CAA. The transcriptome assembly was surprisingly found to cover near the complete Camellia chloroplast genome. Many non-coding regions including pseudogenes were mapped by multiple transcripts, indicating the generality of pseudogene transcriptions. Our results suggest that plastid DNA posttranscriptional splicing may involve complex cleavage of non-functional genes.}, }
@article {pmid23527145, year = {2013}, author = {Anukam, KC and Macklaim, JM and Gloor, GB and Reid, G and Boekhorst, J and Renckens, B and van Hijum, SA and Siezen, RJ}, title = {Genome sequence of Lactobacillus pentosus KCA1: vaginal isolate from a healthy premenopausal woman.}, journal = {PloS one}, volume = {8}, number = {3}, pages = {e59239}, pmid = {23527145}, issn = {1932-6203}, mesh = {Amino Acids/biosynthesis ; Bacteriocins/genetics ; Base Composition ; Base Sequence ; Female ; Gene Expression Regulation, Bacterial/*genetics ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/*genetics ; Humans ; Lactobacillus plantarum/*genetics ; Membrane Proteins/genetics ; Molecular Sequence Data ; Multigene Family/genetics ; Nigeria ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; Vagina/*microbiology ; }, abstract = {The vaginal microbiota, in particular Lactobacillus species, play an important role in female health through modulation of immunity, countering pathogens and maintaining a pH below 4.7. We report the isolation and genome sequence of Lactobacillus pentosus strain KCA1 (formally known as L. plantarum) from the vagina of a healthy Nigerian woman. The genome was sequenced using Illumina GA II technology. The resulting 16,920,226 paired-end reads were assembled with the Velvet tool. Contigs were annotated using the RAST server, and manually curated. A comparative analysis with the available genomes of L. pentosus IG1 and L. plantarum WCFS1 showed that over 15% of the predicted functional activities are found only in this strain. The strain has a chromosome sequence of 3,418,159 bp with a G+C content of 46.4%, and is devoid of plasmids. Novel gene clusters or variants of known genes relative to the reference genomes were found. In particular, the strain has loci encoding additional putative mannose phosphotransferase systems. Clusters of genes include those for utilization of hydantoin, isopropylmalate, malonate, rhamnosides, and genes for assimilation of polyglycans, suggesting the metabolic versatility of L. pentosus KCA1. Loci encoding putative phage defense systems were also found including clustered regularly interspaced short palindromic repeats (CRISPRs), abortive infection (Abi) systems and toxin-antitoxin systems (TA). A putative cluster of genes for biosynthesis of a cyclic bacteriocin precursor, here designated as pentocin KCA1 (penA) were identified. These findings add crucial information for understanding the genomic and geographic diversity of vaginal lactobacilli.}, }
@article {pmid23526944, year = {2013}, author = {Riedel, T and Gómez-Consarnau, L and Tomasch, J and Martin, M and Jarek, M and González, JM and Spring, S and Rohlfs, M and Brinkhoff, T and Cypionka, H and Göker, M and Fiebig, A and Klein, J and Goesmann, A and Fuhrman, JA and Wagner-Döbler, I}, title = {Genomics and physiology of a marine flavobacterium encoding a proteorhodopsin and a xanthorhodopsin-like protein.}, journal = {PloS one}, volume = {8}, number = {3}, pages = {e57487}, pmid = {23526944}, issn = {1932-6203}, mesh = {Bacterial Proteins/*genetics ; Carotenoids/biosynthesis/genetics ; Flavobacteriaceae/classification/*genetics/*physiology ; Gene Transfer, Horizontal ; Genome, Bacterial ; Phylogeny ; Retinaldehyde/biosynthesis/genetics ; Rhodopsin/*genetics ; Rhodopsins, Microbial/*genetics ; Seawater/microbiology ; Species Specificity ; }, abstract = {Proteorhodopsin (PR) photoheterotrophy in the marine flavobacterium Dokdonia sp. PRO95 has previously been investigated, showing no growth stimulation in the light at intermediate carbon concentrations. Here we report the genome sequence of strain PRO95 and compare it to two other PR encoding Dokdonia genomes: that of strain 4H-3-7-5 which shows the most similar genome, and that of strain MED134 which grows better in the light under oligotrophic conditions. Our genome analysis revealed that the PRO95 genome as well as the 4H-3-7-5 genome encode a protein related to xanthorhodopsins. The genomic environment and phylogenetic distribution of this gene suggest that it may have frequently been recruited by lateral gene transfer. Expression analyses by RT-PCR and direct mRNA-sequencing showed that both rhodopsins and the complete β-carotene pathway necessary for retinal production are transcribed in PRO95. Proton translocation measurements showed enhanced proton pump activity in response to light, supporting that one or both rhodopsins are functional. Genomic information and carbon source respiration data were used to develop a defined cultivation medium for PRO95, but reproducible growth always required small amounts of yeast extract. Although PRO95 contains and expresses two rhodopsin genes, light did not stimulate its growth as determined by cell numbers in a nutrient poor seawater medium that mimics its natural environment, confirming previous experiments at intermediate carbon concentrations. Starvation or stress conditions might be needed to observe the physiological effect of light induced energy acquisition.}, }
@article {pmid23526394, year = {2013}, author = {Li, D and Chu, Y and Ren, L and Li, X and Yuan, L and Kang, Y and Zhang, W and Yang, Y and Wang, X and Baillie, JK and Yu, J and Gao, Z}, title = {Complete genome sequence of methicillin-sensitive Staphylococcus aureus containing a heterogeneic staphylococcal cassette chromosome element.}, journal = {Science China. Life sciences}, volume = {56}, number = {3}, pages = {268-274}, doi = {10.1007/s11427-013-4453-9}, pmid = {23526394}, issn = {1869-1889}, mesh = {Aged ; Bacterial Proteins/genetics ; Bacteriophages/genetics ; Chromosomes, Bacterial/*genetics ; DNA Transposable Elements/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Viral/genetics ; Genes, Bacterial/genetics ; *Genome, Bacterial ; Genomic Islands/genetics ; Humans ; Methicillin Resistance/*genetics ; Open Reading Frames ; Penicillin-Binding Proteins ; Phylogeny ; Repressor Proteins/genetics ; Sequence Analysis, DNA ; Species Specificity ; Staphylococcal Infections/microbiology ; Staphylococcus aureus/classification/*genetics/pathogenicity ; Virulence/genetics ; }, abstract = {Staphylococcus aureus is a common human bacterium that sometimes becomes pathogenic, causing serious infections. A key feature of S. aureus is its ability to acquire resistance to antibiotics. The presence of the staphylococcal cassette chromosome (SCC) element in serotypes of S. aureus has been confirmed using multiplex PCR assays. The SCC element is the only vector known to carry the mecA gene, which encodes methicillin resistance in S. aureus infections. Here, we report the genome sequence of a novel methicillin-sensitive S. aureus (MSSA) strain: SCC-like MSSA463. This strain was originally erroneously serotyped as methicillin-resistant S. aureus in a clinical laboratory using multiplex PCR methods. We sequenced the genome of SCC-like MSSA463 using pyrosequencing techniques and compared it with known genome sequences of other S. aureus isolates. An open reading frame (CZ049; AB037671) was identified downstream of attL and attR inverted repeat sequences. Our results suggest that a lateral gene transfer occurred between S. aureus and other organisms, partially changing S. aureus infectivity. We propose that attL and attR inverted repeats in S. aureus serve as frequent insertion sites for exogenous genes.}, }
@article {pmid23524676, year = {2013}, author = {Jamal, Z and Miot-Sertier, C and Thibau, F and Dutilh, L and Lonvaud-Funel, A and Ballestra, P and Le Marrec, C and Dols-Lafargue, M}, title = {Distribution and functions of phosphotransferase system genes in the genome of the lactic acid bacterium Oenococcus oeni.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {11}, pages = {3371-3379}, pmid = {23524676}, issn = {1098-5336}, mesh = {Adaptation, Biological/*genetics ; Analysis of Variance ; Bacterial Proteins/*genetics ; Base Sequence ; Genome, Bacterial/*genetics ; Membrane Transport Proteins/*genetics ; Molecular Sequence Data ; Oenococcus/*enzymology/genetics ; Phosphotransferases/*genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Wine/*microbiology ; }, abstract = {Oenococcus oeni, the lactic acid bacterium primarily responsible for malolactic fermentation in wine, is able to grow on a large variety of carbohydrates, but the pathways by which substrates are transported and phosphorylated in this species have been poorly studied. We show that the genes encoding the general phosphotransferase proteins, enzyme I (EI) and histidine protein (HPr), as well as 21 permease genes (3 isolated ones and 18 clustered into 6 distinct loci), are highly conserved among the strains studied and may form part of the O. oeni core genome. Additional permease genes differentiate the strains and may have been acquired or lost by horizontal gene transfer events. The core pts genes are expressed, and permease gene expression is modulated by the nature of the bacterial growth substrate. Decryptified O. oeni cells are able to phosphorylate glucose, cellobiose, trehalose, and mannose at the expense of phosphoenolpyruvate. These substrates are present at low concentrations in wine at the end of alcoholic fermentation. The phosphotransferase system (PTS) may contribute to the perfect adaptation of O. oeni to its singular ecological niche.}, }
@article {pmid23523720, year = {2013}, author = {Suzuki, T and Soga, S and Inoue, M and Uda, K}, title = {Characterization and origin of bacterial arginine kinases.}, journal = {International journal of biological macromolecules}, volume = {57}, number = {}, pages = {273-277}, doi = {10.1016/j.ijbiomac.2013.02.023}, pmid = {23523720}, issn = {1879-0003}, mesh = {Arginine Kinase/*genetics/metabolism ; Bacteria/enzymology/*genetics ; Bacterial Proteins/*genetics/metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal/physiology ; Genome, Bacterial/*physiology ; *Phylogeny ; }, abstract = {Arginine kinase (AK) plays a key role in ATP buffering systems of tissues and nerves that display high and variable rates of ATP turnover and is widely distributed in invertebrate animals. The enzyme is also found in unicellular organisms, protists and bacteria, but its occurrence is intermittent among species. The AK sequence is structurally divided into two domains, N- and C-terminal domains. The purpose of this study is to clarify the origin of bacterial AK. A search of over 1700 bacterial genomic sequences revealed eight species from Deinococcus-Thermus (Oceanithermus profundus) and Proteobacteria (Ahrensia sp., Nitratifractor salsuginis, Desulfobacterium autotrophicum, Desulfotalea psychrophila, Myxococcus xanthus, Moritella sp. and Sulfurovum sp.) possessing a complete AK sequence homologue. In addition, we searched another key protein that is homologous with that of the C-terminal domain of AK (mcsB). The mcsB is more widely distributed in about 150 species across at least nine bacterial genera. In agreement with the report by other authors, a phylogenetic tree of AK homologues shows that the eight species are separated into two clusters: cluster-A with AKs from ciliates Tetrahymena and Sterkiella and a porifera and the larger cluster-B, including most of the invertebrate AKs. We cloned and expressed the AK from Sulfurovum lithotrophicum in cluster-A and determined its enzymatic properties. Bacterial AKs were characterized as having the highest catalytic efficiency among known AKs, although there was a marked difference in kcat values for cluster-A and -B bacterial AKs. These observations suggest that bacterial AKs in cluster-B may be the prototype of invertebrate AKs. On the other hand, it appears that bacterial AKs in cluster-A diverged at an early stage of bacterial evolution after the appearance of AK, or introduced by horizontal gene transfer.}, }
@article {pmid23520178, year = {2013}, author = {Klumpp, J and Fouts, DE and Sozhamannan, S}, title = {Bacteriophage functional genomics and its role in bacterial pathogen detection.}, journal = {Briefings in functional genomics}, volume = {12}, number = {4}, pages = {354-365}, doi = {10.1093/bfgp/elt009}, pmid = {23520178}, issn = {2041-2657}, mesh = {Bacteriophages/*genetics ; Genomics/*methods ; High-Throughput Nucleotide Sequencing/*methods ; }, abstract = {Emerging and reemerging bacterial infectious diseases are a major public health concern worldwide. The role of bacteriophages in the emergence of novel bacterial pathogens by horizontal gene transfer was highlighted by the May 2011 Escherichia coli O104:H4 outbreaks that originated in Germany and spread to other European countries. This outbreak also highlighted the pivotal role played by recent advances in functional genomics in rapidly deciphering the virulence mechanism elicited by this novel pathogen and developing rapid diagnostics and therapeutics. However, despite a steady increase in the number of phage sequences in the public databases, boosted by the next-generation sequencing technologies, few functional genomics studies of bacteriophages have been conducted. Our definition of 'functional genomics' encompasses a range of aspects: phage genome sequencing, annotation and ascribing functions to phage genes, prophage identification in bacterial sequences, elucidating the events in various stages of phage life cycle using genomic, transcriptomic and proteomic approaches, defining the mechanisms of host takeover including specific bacterial-phage protein interactions and identifying virulence and other adaptive features encoded by phages and finally, using prophage genomic information for bacterial detection/diagnostics. Given the breadth and depth of this definition and the fact that some of these aspects (especially phage-encoded virulence/adaptive features) have been treated extensively in other reviews, we restrict our focus only on certain aspects. These include phage genome sequencing and annotation, identification of prophages in bacterial sequences and genetic characterization of phages, functional genomics of the infection process and finally, bacterial identification using genomic information.}, }
@article {pmid23520078, year = {2013}, author = {Barrangou, R}, title = {CRISPR-Cas systems and RNA-guided interference.}, journal = {Wiley interdisciplinary reviews. RNA}, volume = {4}, number = {3}, pages = {267-278}, doi = {10.1002/wrna.1159}, pmid = {23520078}, issn = {1757-7012}, mesh = {Archaea/*genetics/*virology ; Bacteria/*genetics/*virology ; Gene Transfer, Horizontal ; Interspersed Repetitive Sequences ; *Plasmids ; RNA, Small Interfering/genetics/metabolism ; RNA, Untranslated/genetics/*metabolism ; Recombination, Genetic ; Repetitive Sequences, Nucleic Acid ; Viruses/*genetics ; }, abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR) together with associated sequences (cas) form the CRISPR-Cas system, which provides adaptive immunity against viruses and plasmids in bacteria and archaea. Immunity is built through acquisition of short stretches of invasive nucleic acids into CRISPR loci as 'spacers'. These immune markers are transcribed and processed into small noncoding interfering CRISPR RNAs (crRNAs) that guide Cas proteins toward target nucleic acids for specific cleavage of homologous sequences. Mechanistically, CRISPR-Cas systems function in three distinct stages, namely: (1) adaptation, where new spacers are acquired from invasive elements for immunization; (2) crRNA biogenesis, where CRISPR loci are transcribed and processed into small interfering crRNAs; and (3) interference, where crRNAs guide the Cas machinery to specifically cleave homologous invasive nucleic acids. A number of studies have shown that CRISPR-mediated immunity can readily increase the breadth and depth of virus resistance in bacteria and archaea. CRISPR interference can also target plasmid sequences and provide a barrier against the uptake of undesirable mobile genetic elements. These inheritable hypervariable loci provide phylogenetic information that can be insightful for typing purposes, epidemiological studies, and ecological surveys of natural habitats and environmental samples. More recently, the ability to reprogram CRISPR-directed endonuclease activity using customizable small noncoding interfering RNAs has set the stage for novel genome editing and engineering avenues. This review highlights recent studies that revealed the molecular basis of CRISPR-mediated immunity, and discusses applications of crRNA-guided interference.}, }
@article {pmid23519158, year = {2013}, author = {Wright, O and Stan, GB and Ellis, T}, title = {Building-in biosafety for synthetic biology.}, journal = {Microbiology (Reading, England)}, volume = {159}, number = {Pt 7}, pages = {1221-1235}, doi = {10.1099/mic.0.066308-0}, pmid = {23519158}, issn = {1465-2080}, support = {BB/J019720/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; //Medical Research Council/United Kingdom ; }, mesh = {Bacteria/*genetics ; Genetic Engineering/*adverse effects/methods ; Organisms, Genetically Modified/genetics ; Synthetic Biology/*methods ; Xenobiotics/adverse effects ; }, abstract = {As the field of synthetic biology develops, real-world applications are moving from the realms of ideas and laboratory-confined research towards implementation. A pressing concern, particularly with microbial systems, is that self-replicating re-engineered cells may produce undesired consequences if they escape or overwhelm their intended environment. To address this biosafety issue, multiple mechanisms for constraining microbial replication and horizontal gene transfer have been proposed. These include the use of host-construct dependencies such as toxin-antitoxin pairs, conditional plasmid replication or the requirement for a specific metabolite to be present for cellular function. While refactoring of the existing genetic code or tailoring of orthogonal systems, e.g. xeno nucleic acids, offers future promise of more stringent 'firewalls' between natural and synthetic cells, here we focus on what can be achieved using existing technology. The state-of-the-art in designing for biosafety is summarized and general recommendations are made (e.g. short environmental retention times) for current synthetic biology projects to better isolate themselves against potentially negative impacts.}, }
@article {pmid23518445, year = {2013}, author = {Labella, A and Gennari, M and Ghidini, V and Trento, I and Manfrin, A and Borrego, JJ and Lleo, MM}, title = {High incidence of antibiotic multi-resistant bacteria in coastal areas dedicated to fish farming.}, journal = {Marine pollution bulletin}, volume = {70}, number = {1-2}, pages = {197-203}, doi = {10.1016/j.marpolbul.2013.02.037}, pmid = {23518445}, issn = {1879-3363}, mesh = {Animals ; *Aquaculture ; Bacteria/*genetics/growth &amp; development ; *Drug Resistance, Microbial ; *Water Microbiology ; *Water Pollution ; }, abstract = {Marine bacteria exposed to antibiotics in fish farms can acquire antimicrobial resistance by mobile genetic elements and horizontal gene transfer. A total of 872 autochthonous marine bacterial strains was isolated from samples collected from four different fish farms located at northern and southern Italian Adriatic Sea. Resistance to only tetracycline (17%) and to trimethoprim-sulfadiazine (7%) were the most frequent patterns obtained, while flumequine resistance has recorded in only 0.3% of the strains. Comparing strains isolated from coastal areas and fish farms, a significant higher incidence (4% versus 10%) of multi-resistant strains in aquaculture centers was found. Significant differences in antibiotic resistance incidence were also detected among the four fish farms due probably to different approaches in farm management and the more or less frequent use of antibiotics. Antibiotic-resistant and multi-resistant strains isolated constitute an environmental reservoir directly involved in the seafood chain and might represent a public health concern.}, }
@article {pmid23518183, year = {2013}, author = {Liu, Y and Li, XY and Wan, LG and Jiang, WY and Yang, JH and Li, FQ}, title = {Acquisition of carbapenem resistance in multiresistant Klebsiella pneumoniae isolates of sequence type 11 at a university hospital in China.}, journal = {Diagnostic microbiology and infectious disease}, volume = {76}, number = {2}, pages = {241-243}, doi = {10.1016/j.diagmicrobio.2013.02.002}, pmid = {23518183}, issn = {1879-0070}, mesh = {Anti-Bacterial Agents/pharmacology ; Carbapenems/*pharmacology ; China ; DNA, Bacterial/isolation &amp; purification ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Hospitals, University ; Humans ; Infant ; Integrons ; Klebsiella pneumoniae/*drug effects/genetics/isolation &amp; purification ; Multilocus Sequence Typing ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/isolation &amp; purification ; Sepsis/microbiology/pathology ; Sequence Analysis, DNA ; }, abstract = {Four closely related KPC-producing Klebsiella pneumoniae strains, which were isolated from the patients with neonatal sepsis, harbored bla(CTX-M-14), bla(TEM-1), bla(CTX-M-15), bla(SHV-11),bla(SHV-12), class 1 integron, qnrS1, acc(6')-Ib-cr, and rmtB genes. Multilocus sequence typing experiments showed that all isolates but Kp122 were proven to share the same sequence type (ST), ST11. These isolates have not yet been previously reported in a university-affiliated children's hospital or in the city of Wenzhou.}, }
@article {pmid23517688, year = {2013}, author = {Rodríguez-Rojas, A and Rodríguez-Beltrán, J and Couce, A and Blázquez, J}, title = {Antibiotics and antibiotic resistance: a bitter fight against evolution.}, journal = {International journal of medical microbiology : IJMM}, volume = {303}, number = {6-7}, pages = {293-297}, doi = {10.1016/j.ijmm.2013.02.004}, pmid = {23517688}, issn = {1618-0607}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Humans ; Mutagens/*pharmacology ; *Mutation ; Recombination, Genetic ; *Selection, Genetic ; }, abstract = {One of the most terrible consequences of Darwinian evolution is arguably the emergence and spread of antibiotic resistance, which is becoming a serious menace to modern societies. While spontaneous mutation, recombination and horizontal gene transfer are recognized as the main causes of this notorious phenomenon; recent research has raised awareness that sub-lethal concentrations of antibiotics can also foster resistance as an undesirable side-effect. They can produce genetic changes by different ways, including a raise of free radicals within the cell, induction of error-prone DNA-polymerases mediated by SOS response, imbalanced nucleotide metabolism or affect directly DNA. In addition to certain environmental conditions, subinhibitory concentrations of antimicrobials may increase, even more, the mutagenic effect of antibiotics. Here, we review the state of knowledge on antibiotics as promoters of antibiotic resistance.}, }
@article {pmid23515315, year = {2013}, author = {Ali, SS and Whitney, JC and Stevenson, J and Robinson, H and Howell, PL and Navarre, WW}, title = {Structural insights into the regulation of foreign genes in Salmonella by the Hha/H-NS complex.}, journal = {The Journal of biological chemistry}, volume = {288}, number = {19}, pages = {13356-13369}, pmid = {23515315}, issn = {1083-351X}, support = {13337//Canadian Institutes of Health Research/Canada ; }, mesh = {Amino Acid Sequence ; Amino Acid Substitution ; Bacterial Proteins/*chemistry/genetics/metabolism ; Conserved Sequence ; Crystallography, X-Ray ; DNA, Bacterial/chemistry/metabolism ; DNA-Binding Proteins/*chemistry/genetics/metabolism ; *Gene Expression Regulation, Bacterial ; Gene Silencing ; Gene Transfer, Horizontal ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Salmonella typhimurium/*genetics/metabolism ; Surface Properties ; Transcriptome ; }, abstract = {BACKGROUND: Hha facilitates H-NS-mediated silencing of foreign genes in bacteria.<br><br>RESULTS: Two Hha monomers bind opposing faces of the H-NS N-terminal dimerization domain.<br><br>CONCLUSION: Hha binds the dimerization domain of H-NS and may contact DNA via positively charged surface residues.<br><br>SIGNIFICANCE: The structure of Hha and H-NS in complex provides a mechanistic model of how Hha may affect gene regulation. The bacterial nucleoid-associated proteins Hha and H-NS jointly repress horizontally acquired genes in Salmonella, including essential virulence loci encoded within Salmonella pathogenicity islands. Hha is known to interact with the N-terminal dimerization domain of H-NS; however, the manner in which this interaction enhances transcriptional silencing is not understood. To further understand this process, we solved the x-ray crystal structure of Hha in complex with the N-terminal dimerization domain of H-NS (H-NS(1-46)) to 3.2 &#xc5; resolution. Two monomers of Hha bind to symmetrical sites on either side of the H-NS(1-46) dimer. Disruption of the Hha/H-NS interaction by the H-NS site-specific mutation I11A results in increased expression of the Hha/H-NS co-regulated gene hilA without affecting the expression levels of proV, a target gene repressed by H-NS in an Hha-independent fashion. Examination of the structure revealed a cluster of conserved basic amino acids that protrude from the surface of Hha on the opposite side of the Hha/H-NS(1-46) interface. Hha mutants with a diminished positively charged surface maintain the ability to interact with H-NS but can no longer regulate hilA. Increased expression of the hilA locus did not correspond to significant depletion of H-NS at the promoter region in chromatin immunoprecipitation assays. However, in vitro, we find Hha improves H-NS binding to target DNA fragments. Taken together, our results show for the first time how Hha and H-NS interact to direct transcriptional repression and reveal that a positively charged surface of Hha enhances the silencing activity of H-NS nucleoprotein filaments.}, }
@article {pmid23514904, year = {2013}, author = {Zhou, T and Zhang, X and Guo, M and Ye, J and Lu, Y and Bao, Q and Chi, W}, title = {Phenotypic and molecular characteristics of carbapenem-non-susceptible Enterobacteriaceae from a teaching hospital in Wenzhou, southern China.}, journal = {Japanese journal of infectious diseases}, volume = {66}, number = {2}, pages = {96-102}, doi = {10.7883/yoken.66.96}, pmid = {23514904}, issn = {1884-2836}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Outer Membrane Proteins/analysis ; Carbapenems/*pharmacology ; China ; Conjugation, Genetic ; Electrophoresis, Gel, Pulsed-Field ; Electrophoresis, Polyacrylamide Gel ; Enterobacteriaceae/*drug effects/*genetics/isolation &amp; purification ; Enterobacteriaceae Infections/*microbiology ; Gene Transfer, Horizontal ; Hospitals, Teaching ; Humans ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Polymerase Chain Reaction ; *beta-Lactam Resistance ; beta-Lactamases/genetics ; }, abstract = {Carbapenem resistance in Enterobacteriaceae is increasing and has become a matter of great concern. The aim of this study was to characterize carbapenem-non-susceptible Enterobacteriaceae from a teaching hospital. A total of 49 carbapenem-non-susceptible Enterobacteriaceae clinical isolates recovered in 2007-2010 from the First Affiliated Hospital of Wenzhou Medical College were analyzed by antimicrobial susceptibility testing. The carbapenemase phenotype, outer membrane protein profiles, and clonal relatedness were investigated using the modified Hodge test, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and pulsed-field gel electrophoresis (PFGE). Multilocus sequence typing (MLST) of Klebsiella pneumoniae was also performed. β-Lactamase genes were examined by PCR and sequencing, and the transferability of carbapenemase genes was determined by a conjugation experiment. The rates of imipenem, meropenem, and ertapenem resistance were 59.2%, 40.8%, and 96.0%, respectively. Thirty isolates exhibited carbapenemase activity, and 32 isolates carried carbapenemase genes. Furthermore, 10 and 9 clinical isolates posessed AmpC β-lactamase and extended-spectrum β-lactamase (ESBL) genes, respectively. Eight of 32 carbapenemase-producing isolates were proved to be carried by conjugative plasmids, and there was porin loss in 34.7% (17/49) of the isolates. PFGE analysis demonstrated that 9 KPC-2-producing Serratia marcescens belonged to a clonal strain, suggesting the clonal dissemination of these KPC-2-bearing isolates among different wards. The MLST of K. pneumoniae revealed that two KPC-2 producers were ST11. This study suggests that KPC-2-type carbapenemase is the main contributor to carbapenems resistance in carbapenemase-producing Enterobacteriaceae, and that ESBL, AmpC β-lactamase overproduction, and porin loss contribute to the resistance level among these isolates; in carbapenemase-non-producing Enterobacteriaceae, ESBL, AmpC enzyme, and porin loss contribute to the carbapenems resistance of Enterobacteriaceae, especially the ertapenem resistance of Enterobacter cloacae.}, }
@article {pmid23509275, year = {2013}, author = {Campbell, JH and O'Donoghue, P and Campbell, AG and Schwientek, P and Sczyrba, A and Woyke, T and Söll, D and Podar, M}, title = {UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {14}, pages = {5540-5545}, pmid = {23509275}, issn = {1091-6490}, support = {R01 GM022854/GM/NIGMS NIH HHS/United States ; R01 HG004857/HG/NHGRI NIH HHS/United States ; R37 GM022854/GM/NIGMS NIH HHS/United States ; GM22854/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; Base Sequence ; Codon, Terminator/*genetics ; Flow Cytometry ; Genetic Code/*genetics ; Genetic Variation ; Glycine/*genetics ; Humans ; Metagenome/*genetics ; Molecular Sequence Data ; Mouth/*microbiology ; Nucleic Acid Amplification Techniques ; Sequence Analysis, DNA ; }, abstract = {The composition of the human microbiota is recognized as an important factor in human health and disease. Many of our cohabitating microbes belong to phylum-level divisions for which there are no cultivated representatives and are only represented by small subunit rRNA sequences. For one such taxon (SR1), which includes bacteria with elevated abundance in periodontitis, we provide a single-cell genome sequence from a healthy oral sample. SR1 bacteria use a unique genetic code. In-frame TGA (opal) codons are found in most genes (85%), often at loci normally encoding conserved glycine residues. UGA appears not to function as a stop codon and is in equilibrium with the canonical GGN glycine codons, displaying strain-specific variation across the human population. SR1 encodes a divergent tRNA(Gly)UCA with an opal-decoding anticodon. SR1 glycyl-tRNA synthetase acylates tRNA(Gly)UCA with glycine in vitro with similar activity compared with normal tRNA(Gly)UCC. Coexpression of SR1 glycyl-tRNA synthetase and tRNA(Gly)UCA in Escherichia coli yields significant β-galactosidase activity in vivo from a lacZ gene containing an in-frame TGA codon. Comparative genomic analysis with Human Microbiome Project data revealed that the human body harbors a striking diversity of SR1 bacteria. This is a surprising finding because SR1 is most closely related to bacteria that live in anoxic and thermal environments. Some of these bacteria share common genetic and metabolic features with SR1, including UGA to glycine reassignment and an archaeal-type ribulose-1,5-bisphosphate carboxylase (RubisCO) involved in AMP recycling. UGA codon reassignment renders SR1 genes untranslatable by other bacteria, which impacts horizontal gene transfer within the human microbiota.}, }
@article {pmid23505460, year = {2013}, author = {Zhang, X and Krause, KH and Xenarios, I and Soldati, T and Boeckmann, B}, title = {Evolution of the ferric reductase domain (FRD) superfamily: modularity, functional diversification, and signature motifs.}, journal = {PloS one}, volume = {8}, number = {3}, pages = {e58126}, pmid = {23505460}, issn = {1932-6203}, mesh = {Amino Acid Motifs ; *Biological Evolution ; Cluster Analysis ; Conserved Sequence ; FMN Reductase/*chemistry/classification/genetics/*metabolism ; Heme/chemistry/metabolism ; Models, Biological ; Multigene Family ; NADH, NADPH Oxidoreductases/chemistry/metabolism ; Phylogeny ; Position-Specific Scoring Matrices ; *Protein Interaction Domains and Motifs ; Reactive Oxygen Species/metabolism ; }, abstract = {A heme-containing transmembrane ferric reductase domain (FRD) is found in bacterial and eukaryotic protein families, including ferric reductases (FRE), and NADPH oxidases (NOX). The aim of this study was to understand the phylogeny of the FRD superfamily. Bacteria contain FRD proteins consisting only of the ferric reductase domain, such as YedZ and short bFRE proteins. Full length FRE and NOX enzymes are mostly found in eukaryotic cells and all possess a dehydrogenase domain, allowing them to catalyze electron transfer from cytosolic NADPH to extracellular metal ions (FRE) or oxygen (NOX). Metazoa possess YedZ-related STEAP proteins, possibly derived from bacteria through horizontal gene transfer. Phylogenetic analyses suggests that FRE enzymes appeared early in evolution, followed by a transition towards EF-hand containing NOX enzymes (NOX5- and DUOX-like). An ancestral gene of the NOX(1-4) family probably lost the EF-hands and new regulatory mechanisms of increasing complexity evolved in this clade. Two signature motifs were identified: NOX enzymes are distinguished from FRE enzymes through a four amino acid motif spanning from transmembrane domain 3 (TM3) to TM4, and YedZ/STEAP proteins are identified by the replacement of the first canonical heme-spanning histidine by a highly conserved arginine. The FRD superfamily most likely originated in bacteria.}, }
@article {pmid23504079, year = {2014}, author = {Nie, Y and Liang, JL and Fang, H and Tang, YQ and Wu, XL}, title = {Characterization of a CYP153 alkane hydroxylase gene in a Gram-positive Dietzia sp. DQ12-45-1b and its "team role" with alkW1 in alkane degradation.}, journal = {Applied microbiology and biotechnology}, volume = {98}, number = {1}, pages = {163-173}, doi = {10.1007/s00253-013-4821-1}, pmid = {23504079}, issn = {1432-0614}, mesh = {Actinomycetales/*enzymology ; Alkanes/*metabolism ; Biotransformation ; Cloning, Molecular ; Cluster Analysis ; Cytochrome P-450 CYP4A/*metabolism ; Cytochrome P-450 Enzyme System/*metabolism ; DNA, Bacterial/chemistry/genetics ; Molecular Sequence Data ; Phylogeny ; Protein Binding ; Pseudomonas fluorescens/genetics ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; }, abstract = {CYP153 and AlkB-like hydroxylases were recently discovered in Gram-positive alkane-degrading bacteria. However, it is unclear whether they cooperate with each other in alkane degradation as they do in Gram-negative bacteria. In this paper, we cloned the CYP153 gene from a representative Gram-positive alkane-degrading bacterium, Dietzia sp. DQ12-45-1b. The CYP153 gene transcription in Dietzia sp. DQ12-45-1b and heterologous expression in alkB gene knockout mutant strain Pseudomonas fluorescens KOB2∆1 both confirmed the functions of CYP153 on C6-C10 n-alkanes degradation, but not on longer chain-length n-alkanes. In addition, substrate-binding analysis of the purified CYP153 protein revealed different substrate affinities to C6-C16 n-alkanes, confirming n-alkanes binding to CYP153 protein. Along with AlkW1, an AlkB-like alkane hydroxylase in Dietzia sp. DQ12-45-1b, a teamwork pattern was found in n-alkane degradation, i.e. CYP153 was responsible for hydroxylating n-alkanes shorter than C10 while AlkW1 was responsible for those longer than C14. Further sequence analysis suggested that the high horizontal gene transfer (HGT) potential of CYP153 genes may be universal in Gram-positive alkane-degrading actinomycetes that contain both alkB and CYP153 genes.}, }
@article {pmid23499306, year = {2013}, author = {Wendlandt, S and Feßler, AT and Monecke, S and Ehricht, R and Schwarz, S and Kadlec, K}, title = {The diversity of antimicrobial resistance genes among staphylococci of animal origin.}, journal = {International journal of medical microbiology : IJMM}, volume = {303}, number = {6-7}, pages = {338-349}, doi = {10.1016/j.ijmm.2013.02.006}, pmid = {23499306}, issn = {1618-0607}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; *Genetic Variation ; Interspersed Repetitive Sequences ; Recombination, Genetic ; Staphylococcal Infections/microbiology/*veterinary ; Staphylococcus/*drug effects/*isolation &amp; purification ; }, abstract = {Staphylococci of animal origin harbor a wide variety of resistance genes. So far, more than 40 different resistance genes have been identified in staphylococci from animals. This includes genes that confer resistance to virtually all classes of antimicrobial agents approved for use in animals, such as penicillins, cephalosporins, tetracyclines, macrolides, lincosamides, phenicols, aminoglycosides, aminocyclitols, pleuromutilins, and diaminopyrimidines. The gene products of some of these resistance genes confer resistance to only specific members of a class of antimicrobial agents, whereas others confer resistance to the entire class or even to members of different classes of antimicrobial agents. The resistance mechanisms specified by the resistance genes fall into three major categories: (i) enzymatic inactivation, (ii) active efflux, or (iii) protection/modification/replacement of the cellular target sites of the antimicrobial agents. Mobile genetic elements, in particular plasmids and transposons, play a major role as carriers of antimicrobial resistance genes in animal staphylococci. They facilitate the exchange of resistance genes with staphylococci of human origin but also with other Gram-positive bacteria.}, }
@article {pmid23499304, year = {2013}, author = {Carattoli, A}, title = {Plasmids and the spread of resistance.}, journal = {International journal of medical microbiology : IJMM}, volume = {303}, number = {6-7}, pages = {298-304}, doi = {10.1016/j.ijmm.2013.02.001}, pmid = {23499304}, issn = {1618-0607}, mesh = {Anti-Bacterial Agents/*pharmacology ; Carbapenems/pharmacology ; *Drug Resistance, Bacterial ; Enterobacteriaceae/*drug effects/*genetics/isolation &amp; purification ; Enterobacteriaceae Infections/microbiology ; *Gene Transfer, Horizontal ; Humans ; *R Factors ; }, abstract = {Plasmids represent one of the most difficult challenge for counteracting the dissemination of antimicrobial resistance. They contribute to the spread of relevant resistance determinants, promoting horizontal gene transfer among unrelated bacteria. Undistinguishable plasmids were identified in unrelated bacterial strains isolated at huge geographically distant area, with no apparent epidemiological links. These plasmids belong to families that are largely prevalent in naturally occurring bacteria, usually carry multiple physically linked genetic determinants, conferring resistance to different classes of antibiotics simultaneously. Plasmids also harbour virulence factors and addiction systems, promoting their stability and maintenance in the bacterial host, in different environmental conditions. The characteristics of the most successful plasmids that were at the origin of the spread of carbapenemase, expanded-spectrum β-lactamase, and plasmid-mediated quinolone resistance genes are discussed in this review.}, }
@article {pmid23497343, year = {2013}, author = {Jeanniard, A and Dunigan, DD and Gurnon, JR and Agarkova, IV and Kang, M and Vitek, J and Duncan, G and McClung, OW and Larsen, M and Claverie, JM and Van Etten, JL and Blanc, G}, title = {Towards defining the chloroviruses: a genomic journey through a genus of large DNA viruses.}, journal = {BMC genomics}, volume = {14}, number = {}, pages = {158}, pmid = {23497343}, issn = {1471-2164}, support = {5P20RR016469/RR/NCRR NIH HHS/United States ; 8P20GM103427/GM/NIGMS NIH HHS/United States ; P20 RR15635/RR/NCRR NIH HHS/United States ; }, mesh = {*Biological Evolution ; Chlorophyta/*genetics/virology ; DNA Viruses/classification/*genetics ; Gene Transfer, Horizontal ; Genome, Viral ; Phycodnaviridae/classification/*genetics ; Phylogeny ; Viral Proteins ; }, abstract = {BACKGROUND: Giant viruses in the genus Chlorovirus (family Phycodnaviridae) infect eukaryotic green microalgae. The prototype member of the genus, Paramecium bursaria chlorella virus 1, was sequenced more than 15 years ago, and to date there are only 6 fully sequenced chloroviruses in public databases. Presented here are the draft genome sequences of 35 additional chloroviruses (287 - 348 Kb/319 - 381 predicted protein encoding genes) collected across the globe; they infect one of three different green algal species. These new data allowed us to analyze the genomic landscape of 41 chloroviruses, which revealed some remarkable features about these viruses.<br><br>RESULTS: Genome colinearity, nucleotide conservation and phylogenetic affinity were limited to chloroviruses infecting the same host, confirming the validity of the three previously known subgenera. Clues for the existence of a fourth new subgenus indicate that the boundaries of chlorovirus diversity are not completely determined. Comparison of the chlorovirus phylogeny with that of the algal hosts indicates that chloroviruses have changed hosts in their evolutionary history. Reconstruction of the ancestral genome suggests that the last common chlorovirus ancestor had a slightly more diverse protein repertoire than modern chloroviruses. However, more than half of the defined chlorovirus gene families have a potential recent origin (after Chlorovirus divergence), among which a portion shows compositional evidence for horizontal gene transfer. Only a few of the putative acquired proteins had close homologs in databases raising the question of the true donor organism(s). Phylogenomic analysis identified only seven proteins whose genes were potentially exchanged between the algal host and the chloroviruses.<br><br>CONCLUSION: The present evaluation of the genomic evolution pattern suggests that chloroviruses differ from that described in the related Poxviridae and Mimiviridae. Our study shows that the fixation of algal host genes has been anecdotal in the evolutionary history of chloroviruses. We finally discuss the incongruence between compositional evidence of horizontal gene transfer and lack of close relative sequences in the databases, which suggests that the recently acquired genes originate from a still largely un-sequenced reservoir of genomes, possibly other unknown viruses that infect the same hosts.}, }
@article {pmid23497212, year = {2013}, author = {Dziewit, L and Pyzik, A and Matlakowska, R and Baj, J and Szuplewska, M and Bartosik, D}, title = {Characterization of Halomonas sp. ZM3 isolated from the Zelazny Most post-flotation waste reservoir, with a special focus on its mobile DNA.}, journal = {BMC microbiology}, volume = {13}, number = {}, pages = {59}, pmid = {23497212}, issn = {1471-2180}, mesh = {DNA Transposable Elements ; DNA, Bacterial/chemistry/*genetics ; *Environmental Microbiology ; Halomonas/*classification/genetics/*isolation &amp; purification ; *Interspersed Repetitive Sequences ; Molecular Sequence Data ; Plasmids/analysis ; Poland ; Sequence Analysis, DNA ; *Solid Waste ; }, abstract = {BACKGROUND: Halomonas sp. ZM3 was isolated from Zelazny Most post-flotation mineral waste repository (Poland), which is highly contaminated with heavy metals and various organic compounds. Mobile DNA of the strain (i.e. plasmids and transposons) were analyzed in order to identify genetic information enabling adaptation of the bacterium to the harsh environmental conditions.<br><br>RESULTS: The analysis revealed that ZM3 carries plasmid pZM3H1 (31,370 bp), whose replication system may be considered as an archetype of a novel subgroup of IncU-like replicons. pZM3H1 is a narrow host range, mobilizable plasmid (encodes a relaxase of the MOBV family) containing mercury resistance operon (mer) and czcD genes (mediate resistance to zinc and cobalt), which are part of a large truncated Tn3 family transposon. Further analysis demonstrated that the phenotypes determined by the pZM3H1 resistance cassette are highly dependent on the host strain. In another strand of the study, the trap plasmid pMAT1 was employed to identify functional transposable elements of Halomonas sp. ZM3. Using the sacB positive selection strategy two insertion sequences were identified: ISHsp1 - representing IS5 group of IS5 family and ISHsp2 - a distinct member of the IS630 family.<br><br>CONCLUSIONS: This study provides the first detailed description of mobile DNA in a member of the family Halomonadaceae. The identified IncU plasmid pZM3H1 confers resistance phenotypes enabling adaptation of the host strain to the Zelazny Most environment. The extended comparative analysis has shed light on the distribution of related IncU plasmids among bacteria, which, in many cases, reflects the frequency and direction of horizontal gene transfer events. Our results also identify plasmid-encoded modules, which may form the basis of novel shuttle vectors, specific for this group of halophilic bacteria.}, }
@article {pmid23497205, year = {2013}, author = {Siqueira, FM and Thompson, CE and Virginio, VG and Gonchoroski, T and Reolon, L and Almeida, LG and da Fonsêca, MM and de Souza, R and Prosdocimi, F and Schrank, IS and Ferreira, HB and de Vasconcelos, AT and Zaha, A}, title = {New insights on the biology of swine respiratory tract mycoplasmas from a comparative genome analysis.}, journal = {BMC genomics}, volume = {14}, number = {}, pages = {175}, pmid = {23497205}, issn = {1471-2164}, mesh = {Animals ; Chromosome Mapping ; Genome ; Mycoplasma/*classification/*genetics/pathogenicity ; Phylogeny ; Pneumonia of Swine, Mycoplasmal/genetics/*microbiology/pathology ; Respiratory System/*microbiology/pathology ; Swine ; }, abstract = {BACKGROUND: Mycoplasma hyopneumoniae, Mycoplasma flocculare and Mycoplasma hyorhinis live in swine respiratory tracts. M. flocculare, a commensal bacterium, is genetically closely related to M. hyopneumoniae, the causative agent of enzootic porcine pneumonia. M. hyorhinis is also pathogenic, causing polyserositis and arthritis. In this work, we present the genome sequences of M. flocculare and M. hyopneumoniae strain 7422, and we compare these genomes with the genomes of other M. hyoponeumoniae strain and to the a M. hyorhinis genome. These analyses were performed to identify possible characteristics that may help to explain the different behaviors of these species in swine respiratory tracts.<br><br>RESULTS: The overall genome organization of three species was analyzed, revealing that the ORF clusters (OCs) differ considerably and that inversions and rearrangements are common. Although M. flocculare and M. hyopneumoniae display a high degree of similarity with respect to the gene content, only some genomic regions display considerable synteny. Genes encoding proteins that may be involved in host-cell adhesion in M. hyopneumoniae and M. flocculare display differences in genomic structure and organization. Some genes encoding adhesins of the P97 family are absent in M. flocculare and some contain sequence differences or lack of domains that are considered to be important for adhesion to host cells. The phylogenetic relationship of the three species was confirmed by a phylogenomic approach. The set of genes involved in metabolism, especially in the uptake of precursors for nucleic acids synthesis and nucleotide metabolism, display some differences in copy number and the presence/absence in the three species.<br><br>CONCLUSIONS: The comparative analyses of three mycoplasma species that inhabit the swine respiratory tract facilitated the identification of some characteristics that may be related to their different behaviors. M. hyopneumoniae and M. flocculare display many differences that may help to explain why one species is pathogenic and the other is considered to be commensal. However, it was not possible to identify specific virulence determinant factors that could explain the differences in the pathogenicity of the analyzed species. The M. hyorhinis genome contains differences in some components involved in metabolism and evasion of the host's immune system that may contribute to its growth aggressiveness. Several horizontal gene transfer events were identified. The phylogenomic analysis places M. hyopneumoniae, M. flocculare and M. hyorhinis in the hyopneumoniae clade.}, }
@article {pmid23496955, year = {2013}, author = {Pan, G and Xu, J and Li, T and Xia, Q and Liu, SL and Zhang, G and Li, S and Li, C and Liu, H and Yang, L and Liu, T and Zhang, X and Wu, Z and Fan, W and Dang, X and Xiang, H and Tao, M and Li, Y and Hu, J and Li, Z and Lin, L and Luo, J and Geng, L and Wang, L and Long, M and Wan, Y and He, N and Zhang, Z and Lu, C and Keeling, PJ and Wang, J and Xiang, Z and Zhou, Z}, title = {Comparative genomics of parasitic silkworm microsporidia reveal an association between genome expansion and host adaptation.}, journal = {BMC genomics}, volume = {14}, number = {}, pages = {186}, pmid = {23496955}, issn = {1471-2164}, mesh = {Animals ; Base Sequence ; Bombyx/*genetics/parasitology ; DNA Transposable Elements ; *Gene Duplication ; Gene Transfer, Horizontal ; Genomics ; Host-Parasite Interactions/*genetics ; Microsporidia/*genetics/pathogenicity ; Molecular Sequence Annotation ; Molecular Sequence Data ; }, abstract = {BACKGROUND: Microsporidian Nosema bombycis has received much attention because the pébrine disease of domesticated silkworms results in great economic losses in the silkworm industry. So far, no effective treatment could be found for pébrine. Compared to other known Nosema parasites, N. bombycis can unusually parasitize a broad range of hosts. To gain some insights into the underlying genetic mechanism of pathological ability and host range expansion in this parasite, a comparative genomic approach is conducted. The genome of two Nosema parasites, N. bombycis and N. antheraeae (an obligatory parasite to undomesticated silkworms Antheraea pernyi), were sequenced and compared with their distantly related species, N. ceranae (an obligatory parasite to honey bees).<br><br>RESULTS: Our comparative genomics analysis show that the N. bombycis genome has greatly expanded due to the following three molecular mechanisms: 1) the proliferation of host-derived transposable elements, 2) the acquisition of many horizontally transferred genes from bacteria, and 3) the production of abundnant gene duplications. To our knowledge, duplicated genes derived not only from small-scale events (e.g., tandem duplications) but also from large-scale events (e.g., segmental duplications) have never been seen so abundant in any reported microsporidia genomes. Our relative dating analysis further indicated that these duplication events have arisen recently over very short evolutionary time. Furthermore, several duplicated genes involving in the cytotoxic metabolic pathway were found to undergo positive selection, suggestive of the role of duplicated genes on the adaptive evolution of pathogenic ability.<br><br>CONCLUSIONS: Genome expansion is rarely considered as the evolutionary outcome acting on those highly reduced and compact parasitic microsporidian genomes. This study, for the first time, demonstrates that the parasitic genomes can expand, instead of shrink, through several common molecular mechanisms such as gene duplication, horizontal gene transfer, and transposable element expansion. We also showed that the duplicated genes can serve as raw materials for evolutionary innovations possibly contributing to the increase of pathologenic ability. Based on our research, we propose that duplicated genes of N. bombycis should be treated as primary targets for treatment designs against p&#xe9;brine. The genome data and annotation information of N. bombycis and N.antheraeae were submitted to GenBank (Accession numbers ACJZ01000001 -ACJZ01003558).}, }
@article {pmid23494301, year = {2013}, author = {Loomis, WF}, title = {Comparative genomics of the dictyostelids.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {983}, number = {}, pages = {39-58}, doi = {10.1007/978-1-62703-302-2_3}, pmid = {23494301}, issn = {1940-6029}, mesh = {Amino Acid Sequence ; Base Composition ; Chemotaxis ; Conserved Sequence ; DNA, Protozoan/genetics ; Dictyostelium/*genetics/physiology ; Gene Expression ; Gene Transfer, Horizontal ; Genetic Speciation ; Genome, Protozoan ; Molecular Sequence Annotation ; Phylogeny ; Proteomics ; Protozoan Proteins/chemistry/genetics/metabolism ; Signal Transduction/genetics ; }, abstract = {The complete genomes of Dictyostelium discoideum, Dictyostelium purpureum, Polysphondylium pallidum and Dictyostelium fasciculatum have been sequenced. The proteins predicted to be encoded by the genes in each species have been compared to each other as well as to the complete compilation of nonredundant proteins from bacteria, plants, fungi, and animals. Likely functions have been assigned to about half of the proteins on the basis of sequence similarity to proteins with experimentally defined functions or properties. Even when the sequence similarity is not sufficiently high to have much confidence in the predicted function of the dictyostelid proteins, the shared ancestry of the proteins can often be clearly recognized. The degree of divergence within such clusters of orthologous proteins can then be used to establish the evolutionary pathways leading to each species and estimate the approximate time of divergence. This approach has established that the dictyostelids are a monophyletic group with four major groups that diverged from the line leading to animals shortly before the fungi. D. fasciculatum and P. pallidum are representatives of group 1 and group 2 dictyostelids, respectively. Their common ancestor diverged about 600-800 million years ago from the line leading to D. discoideum and D. purpureum which are group 4 dictyostelids. Each of these species encodes about 11,000-12,000 proteins which is almost twice that in the yeasts. Most of the genes known to be involved in specific signal transduction pathways that mediate intercellular communication are present in each of the sequenced species but both P. pallidum and D. fasciculatum appear to be missing the gene responsible for synthesis of GABA, gadA, suggesting that release of the SDF-2 precursor AcbA is not regulated by GABA in these species as it is in D. discoideum. Likewise, the gene responsible for making cytokinins, iptA, appears to have entered by horizontal gene transfer from bacteria into the genome of the common ancestor of group 4 dictyostelids after they diverged from the group 1 and 2 species. Therefore, it is unlikely that P. pallidum or D. fasciculatum has the ability to make or respond to the cytokinin discadenine which induces rapid encapsulation of spores and maintains their dormancy in D. discoideum. Other predictions from comparative genomics among the dictyostelids are reviewed and evaluated.}, }
@article {pmid23493256, year = {2013}, author = {Yang, J and Grünewald, S and Wan, XF}, title = {Quartet-net: a quartet-based method to reconstruct phylogenetic networks.}, journal = {Molecular biology and evolution}, volume = {30}, number = {5}, pages = {1206-1217}, pmid = {23493256}, issn = {1537-1719}, support = {I01 BX000596/BX/BLRD VA/United States ; RC1 AI086830/AI/NIAID NIH HHS/United States ; NIAID RC1AI086830/RC/CCR NIH HHS/United States ; }, mesh = {*Evolution, Molecular ; *Models, Genetic ; Models, Theoretical ; Phylogeny ; *Software ; }, abstract = {Phylogenetic networks can model reticulate evolutionary events such as hybridization, recombination, and horizontal gene transfer. However, reconstructing such networks is not trivial. Popular character-based methods are computationally inefficient, whereas distance-based methods cannot guarantee reconstruction accuracy because pairwise genetic distances only reflect partial information about a reticulate phylogeny. To balance accuracy and computational efficiency, here we introduce a quartet-based method to construct a phylogenetic network from a multiple sequence alignment. Unlike distances that only reflect the relationship between a pair of taxa, quartets contain information on the relationships among four taxa; these quartets provide adequate capacity to infer a more accurate phylogenetic network. In applications to simulated and biological data sets, we demonstrate that this novel method is robust and effective in reconstructing reticulate evolutionary events and it has the potential to infer more accurate phylogenetic distances than other conventional phylogenetic network construction methods such as Neighbor-Joining, Neighbor-Net, and Split Decomposition. This method can be used in constructing phylogenetic networks from simple evolutionary events involving a few reticulate events to complex evolutionary histories involving a large number of reticulate events. A software called "Quartet-Net" is implemented and available at http://sysbio.cvm.msstate.edu/QuartetNet/.}, }
@article {pmid23492433, year = {2013}, author = {Biswas, A and Gagnon, JN and Brouns, SJ and Fineran, PC and Brown, CM}, title = {CRISPRTarget: bioinformatic prediction and analysis of crRNA targets.}, journal = {RNA biology}, volume = {10}, number = {5}, pages = {817-827}, pmid = {23492433}, issn = {1555-8584}, mesh = {Archaeal Proteins/genetics/metabolism ; Archaeal Viruses/*genetics ; Bacteria/*genetics/metabolism/virology ; Bacterial Proteins/genetics/metabolism ; Bacteriophages/*genetics ; Base Pairing ; Base Sequence ; CRISPR-Associated Proteins/*genetics/metabolism ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Computational Biology/*methods ; DNA, Intergenic/genetics ; Evolution, Molecular ; Molecular Sequence Data ; RNA, Bacterial/genetics ; Sequence Alignment ; Streptococcus Phages/genetics ; Streptococcus thermophilus/genetics/virology ; Sulfolobus solfataricus/genetics/*metabolism ; }, abstract = {The bacterial and archaeal CRISPR/Cas adaptive immune system targets specific protospacer nucleotide sequences in invading organisms. This requires base pairing between processed CRISPR RNA and the target protospacer. For type I and II CRISPR/Cas systems, protospacer adjacent motifs (PAM) are essential for target recognition, and for type III, mismatches in the flanking sequences are important in the antiviral response. In this study, we examine the properties of each class of CRISPR. We use this information to provide a tool (CRISPRTarget) that predicts the most likely targets of CRISPR RNAs (http://bioanalysis.otago.ac.nz/CRISPRTarget). This can be used to discover targets in newly sequenced genomic or metagenomic data. To test its utility, we discover features and targets of well-characterized Streptococcus thermophilus and Sulfolobus solfataricus type II and III CRISPR/Cas systems. Finally, in Pectobacterium species, we identify new CRISPR targets and propose a model of temperate phage exposure and subsequent inhibition by the type I CRISPR/Cas systems.}, }
@article {pmid23490927, year = {2013}, author = {D'Andrea, MM and Arena, F and Pallecchi, L and Rossolini, GM}, title = {CTX-M-type β-lactamases: a successful story of antibiotic resistance.}, journal = {International journal of medical microbiology : IJMM}, volume = {303}, number = {6-7}, pages = {305-317}, doi = {10.1016/j.ijmm.2013.02.008}, pmid = {23490927}, issn = {1618-0607}, mesh = {Enterobacteriaceae/*enzymology/*genetics ; Enterobacteriaceae Infections/epidemiology/*microbiology ; Gene Transfer, Horizontal ; Genetic Variation ; Humans ; Interspersed Repetitive Sequences ; *beta-Lactam Resistance ; beta-Lactamases/*genetics/*metabolism ; }, abstract = {Production of extended-spectrum β-lactamases (ESBLs) is the principal mechanism of resistance to oxyimino-cephalosporins evolved by members of the family Enterobacteriaceae. Among the several ESBLs emerged among clinical pathogens, the CTX-M-type enzymes have proved the most successful in terms of promiscuity and diffusion in different epidemiological settings, where they have largely replaced and outnumbered other types of ESBLs. Originated by the capture and mobilization of chromosomal β-lactamase genes of strains of Kluyvera species, the blaCTX-M genes have become associated with a variety of mobile genetic elements that have mediated rapid and efficient inter-replicon and cell-to-cell dissemination involving highly successful enterobacterial lineages (e.g. Escherichia coli ST131 and ST405, or Klebsiella pneumoniae CC11 and ST147) to yield high-risk multiresistant clones that have spread on a global scale. The CTX-Mβ-lactamase lineage exhibits a striking plasticity, with a large number of allelic variants belonging in several sublineages, which can be associated with functional heterogeneity of clinical relevance. This review article provides an update on CTX-M-type ESBLs, with focus on structural and functional diversity, epidemiology and clinical significance.}, }
@article {pmid23490446, year = {2013}, author = {Richardson, RE}, title = {Genomic insights into organohalide respiration.}, journal = {Current opinion in biotechnology}, volume = {24}, number = {3}, pages = {498-505}, doi = {10.1016/j.copbio.2013.02.014}, pmid = {23490446}, issn = {1879-0429}, mesh = {Biodegradation, Environmental ; Chloroflexi/classification/enzymology/genetics/metabolism ; Desulfitobacterium/enzymology/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genome, Bacterial/*genetics ; Geobacter/genetics/metabolism ; Halogenation/*genetics ; Hydrolases/*genetics/*metabolism ; Peptococcaceae/enzymology/genetics/metabolism ; Phylogeny ; }, abstract = {In the last few years there has been a burst of genomes released for organohalide respiring bacteria (referred to as OHRB herein though the process is otherwise known as dehalorespiration, reductive dechlorination, or halorespiration). The microorganisms are employed in bioremediation of sites contaminated with chlorinated ethene, ethane, and methanes, as well as chlorinated aromatics. Of particular note are the releases of the first Dehalogenimonas genome (a Dehalococcoides-related Chloroflexi) and not one but seven Dehalobacter (meta)genomes. Collectively, genomes from these three genera (Dehalococcoides, Dehalogenimonas, and Dehalobacter) clearly support their niche as obligate OHRB, while other genera with sequenced genomes (Desulfitobacterium, Geobacter, and Anaeromyxobacter) maintain organohalide respiration (OHR) as one of many possible energy conserving respiration strategies. The obligate OHRB genomes consistently harbor 10-39 unique reductive dehalogenase (RDase) genes and they are flanked with not only transcriptional regulators but also transposition related genes. Active transposition likely plays a key role in the accumulation of such a broad and tightly regulated dehalogenase repertoire. Functional assays are now the bottleneck for genome-informed discovery of dehalogenase substrate ranges.}, }
@article {pmid23486178, year = {2012}, author = {Bustamante, P and Covarrubias, PC and Levicán, G and Katz, A and Tapia, P and Holmes, D and Quatrini, R and Orellana, O}, title = {ICE Afe 1, an actively excising genetic element from the biomining bacterium Acidithiobacillus ferrooxidans.}, journal = {Journal of molecular microbiology and biotechnology}, volume = {22}, number = {6}, pages = {399-407}, doi = {10.1159/000346669}, pmid = {23486178}, issn = {1660-2412}, mesh = {Acidithiobacillus/drug effects/*genetics ; Computational Biology ; Gene Expression ; *Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences ; Mitomycin/metabolism ; Recombination, Genetic ; Transcriptional Activation/drug effects ; }, abstract = {Integrative conjugative elements (ICEs) are self-transferred mobile genetic elements that contribute to horizontal gene transfer. An ICE (ICEAfe1) was identified in the genome of Acidithiobacillus ferrooxidans ATCC 23270. Excision of the element and expression of relevant genes under normal and DNA-damaging growth conditions was analyzed. Bioinformatic tools and DNA amplification methods were used to identify and to assess the excision and expression of genes related to the mobility of the element. Both basal and mitomycin C-inducible excision as well as expression and induction of the genes for integration/excision are demonstrated, suggesting that ICEAfe1 is an actively excising SOS-regulated mobile genetic element. The presence of a complete set of genes encoding self-transfer functions that are induced in response to DNA damage caused by mitomycin C additionally suggests that this element is capable of conjugative transfer to suitable recipient strains. Transfer of ICEAfe1 may provide selective advantages to other acidophiles in this ecological niche through dissemination of gene clusters expressing transfer RNAs, CRISPRs, and exopolysaccharide biosynthesis enzymes, probably by modification of translation efficiency, resistance to bacteriophage infection and biofilm formation, respectively. These data open novel avenues of research on conjugative transformation of biotechnologically relevant microorganisms recalcitrant to genetic manipulation.}, }
@article {pmid23481313, year = {2012}, author = {Nijveen, H and Matus-Garcia, M and van Passel, MW}, title = {Promoter reuse in prokaryotes.}, journal = {Mobile genetic elements}, volume = {2}, number = {6}, pages = {279-281}, pmid = {23481313}, issn = {2159-2543}, abstract = {Anecdotal evidence shows promoters being reused separate from their downstream gene, thus providing a mechanism for the efficient and rapid rewiring of a gene's transcriptional regulation. We have identified over 4000 groups of highly similar promoters using a conservative sequence similarity search in all fully sequenced prokaryotic genomes. About 6% of those groups are shared between bacteria from different taxonomic depth, including different genera, families, orders, classes and even phyla. Database searches against known mobile elements and RNA motifs have indicated that regulatory motifs such as riboswitches could be moved around on putative mobile promoters.}, }
@article {pmid23481263, year = {2012}, author = {Siefert, JL}, title = {Man and his spaceships: Vehicles for extraterrestrial colonization?.}, journal = {Mobile genetic elements}, volume = {2}, number = {6}, pages = {272-278}, pmid = {23481263}, issn = {2159-2543}, abstract = {The resiliency and adaptive ability of microbial life in real time on Earth relies heavily upon horizontal gene transfer. Based on that knowledge, how likely is earth based microbial life to colonize extraterrestrial targets such as Mars? To address this question, we consider manned and unmanned space exploration, the resident microbiota that is likely to inhabit those vehicles, the adaptive potential of that microbiota in an extraterrestrial setting especially with regards to mobile genetic elements, and the likelihood that Mars like environments could initiate and sustain colonization.}, }
@article {pmid23479749, year = {2013}, author = {Villemur, R}, title = {The pentachlorophenol-dehalogenating Desulfitobacterium hafniense strain PCP-1.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {368}, number = {1616}, pages = {20120319}, pmid = {23479749}, issn = {1471-2970}, mesh = {Biodegradation, Environmental ; Chlorophenols/metabolism ; Desulfitobacterium/classification/enzymology/genetics/*metabolism ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genetic Loci ; *Halogenation ; Pentachlorophenol/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; Species Specificity ; Transcription, Genetic ; }, abstract = {In this report, a complete description of Desulfitobacterium hafniense strain PCP-1 is presented. The D. hafniense strain PCP-1 was isolated from a methanogenic consortium for its capacity to dehalogenate pentachlorophenol (PCP) into 3-chlorophenol. This strain is also capable of dehalogenating several other chloroaromatic compounds and tetrachloroethene into trichloroethene. Four gene loci encoding putative chlorophenol-reductive dehalogenases (CprA2 to CprA5) were detected, and the products of two of these loci have been demonstrated to dechlorinate different chlorinated phenols. Strain PCP-1 was used in laboratory-scale bioprocesses to degrade PCP present in contaminated environments. Desulfitobacterium hafniense PCP-1 is an excellent candidate for the development of efficient bioprocesses to degrade organohalide compounds.}, }
@article {pmid23479249, year = {2013}, author = {Dziewit, L and Cegielski, A and Romaniuk, K and Uhrynowski, W and Szych, A and Niesiobedzki, P and Zmuda-Baranowska, MJ and Zdanowski, MK and Bartosik, D}, title = {Plasmid diversity in arctic strains of Psychrobacter spp.}, journal = {Extremophiles : life under extreme conditions}, volume = {17}, number = {3}, pages = {433-444}, pmid = {23479249}, issn = {1433-4909}, mesh = {Arctic Regions ; Bacterial Proteins/genetics ; Conjugation, Genetic/genetics ; DNA Restriction-Modification Enzymes/genetics ; *Genetic Variation ; Peroxiredoxins/genetics ; Plasmids/*genetics ; Psychrobacter/*genetics ; Replicon/genetics ; }, abstract = {Six strains of Psychrobacter spp. isolated from guano of little auks collected on Spitsbergen island (Arctic) carried nine plasmids that were fully sequenced. These replicons (ranging in size from 2917 to 14924 bp) contained either repA (ColE2-type) or repB (iteron-type) replication systems of a relatively narrow host range, limited to Psychrobacter spp. All but one of the plasmids carried predicted mobilization for conjugal transfer systems, encoding relaxases of the MOBQ, MOBV or MOBP families. The plasmids also contained diverse additional genetic load, including a type II restriction-modification system and a gene encoding a putative subunit C of alkyl hydroperoxide reductase (AhpC)-an antioxidant enzyme and major scavenger of reactive oxygen species. Detailed comparative sequence analyses, extended to all plasmids identified so far in psychrophilic bacteria, distinguished groups of the most ubiquitous replicons, which play a key role in horizontal gene transfer in cold environments.}, }
@article {pmid23475938, year = {2013}, author = {Driscoll, T and Gillespie, JJ and Nordberg, EK and Azad, AF and Sobral, BW}, title = {Bacterial DNA sifted from the Trichoplax adhaerens (Animalia: Placozoa) genome project reveals a putative rickettsial endosymbiont.}, journal = {Genome biology and evolution}, volume = {5}, number = {4}, pages = {621-645}, pmid = {23475938}, issn = {1759-6653}, support = {R01 AI017828/AI/NIAID NIH HHS/United States ; R01 AI059118/AI/NIAID NIH HHS/United States ; HHSN272200900040C/AI/NIAID NIH HHS/United States ; R01AI017828/AI/NIAID NIH HHS/United States ; R01AI59118/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; DNA, Bacterial/*genetics ; *Gene Transfer, Horizontal ; Genome ; Gram-Negative Bacteria/classification/genetics/isolation &amp; purification/physiology ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Placozoa/*genetics/*microbiology/physiology ; Rickettsiaceae/classification/*genetics/isolation &amp; purification/physiology ; *Symbiosis ; }, abstract = {Eukaryotic genome sequencing projects often yield bacterial DNA sequences, data typically considered as microbial contamination. However, these sequences may also indicate either symbiont genes or lateral gene transfer (LGT) to host genomes. These bacterial sequences can provide clues about eukaryote-microbe interactions. Here, we used the genome of the primitive animal Trichoplax adhaerens (Metazoa: Placozoa), which is known to harbor an uncharacterized Gram-negative endosymbiont, to search for the presence of bacterial DNA sequences. Bioinformatic and phylogenomic analyses of extracted data from the genome assembly (181 bacterial coding sequences [CDS]) and trace read archive (16S rDNA) revealed a dominant proteobacterial profile strongly skewed to Rickettsiales (Alphaproteobacteria) genomes. By way of phylogenetic analysis of 16S rDNA and 113 proteins conserved across proteobacterial genomes, as well as identification of 27 rickettsial signature genes, we propose a Rickettsiales endosymbiont of T. adhaerens (RETA). The majority (93%) of the identified bacterial CDS belongs to small scaffolds containing prokaryotic-like genes; however, 12 CDS were identified on large scaffolds comprised of eukaryotic-like genes, suggesting that T. adhaerens might have recently acquired bacterial genes. These putative LGTs may coincide with the placozoan's aquatic niche and symbiosis with RETA. This work underscores the rich, and relatively untapped, resource of eukaryotic genome projects for harboring data pertinent to host-microbial interactions. The nature of unknown (or poorly characterized) bacterial species may only emerge via analysis of host genome sequencing projects, particularly if these species are resistant to cell culturing, as are many obligate intracellular microbes. Our work provides methodological insight for such an approach.}, }
@article {pmid23474681, year = {2013}, author = {Stecher, B and Maier, L and Hardt, WD}, title = {'Blooming' in the gut: how dysbiosis might contribute to pathogen evolution.}, journal = {Nature reviews. Microbiology}, volume = {11}, number = {4}, pages = {277-284}, pmid = {23474681}, issn = {1740-1534}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/*growth &amp; development ; *Biological Evolution ; Diet ; Drug Resistance, Microbial/genetics ; Gastrointestinal Tract/drug effects/*microbiology ; Gene Transfer, Horizontal ; Immunity ; Intestines/microbiology ; Mammals ; Metagenome/drug effects/genetics/*physiology ; Virulence Factors/genetics ; }, abstract = {Hundreds of bacterial species make up the mammalian intestinal microbiota. Following perturbations by antibiotics, diet, immune deficiency or infection, this ecosystem can shift to a state of dysbiosis. This can involve overgrowth (blooming) of otherwise under-represented or potentially harmful bacteria (for example, pathobionts). Here, we present evidence suggesting that dysbiosis fuels horizontal gene transfer between members of this ecosystem, facilitating the transfer of virulence and antibiotic resistance genes and thereby promoting pathogen evolution.}, }
@article {pmid23471408, year = {2013}, author = {Schönknecht, G and Chen, WH and Ternes, CM and Barbier, GG and Shrestha, RP and Stanke, M and Bräutigam, A and Baker, BJ and Banfield, JF and Garavito, RM and Carr, K and Wilkerson, C and Rensing, SA and Gagneul, D and Dickenson, NE and Oesterhelt, C and Lercher, MJ and Weber, AP}, title = {Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote.}, journal = {Science (New York, N.Y.)}, volume = {339}, number = {6124}, pages = {1207-1210}, doi = {10.1126/science.1231707}, pmid = {23471408}, issn = {1095-9203}, mesh = {Adaptation, Physiological/*genetics ; Adenosine Triphosphatases/genetics ; Archaea/classification/genetics ; Bacteria/classification/genetics ; DNA, Algal ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Archaeal ; *Genes, Bacterial ; Genome, Plant/*genetics ; Phylogeny ; Rhodophyta/*genetics/*microbiology/physiology ; }, abstract = {Some microbial eukaryotes, such as the extremophilic red alga Galdieria sulphuraria, live in hot, toxic metal-rich, acidic environments. To elucidate the underlying molecular mechanisms of adaptation, we sequenced the 13.7-megabase genome of G. sulphuraria. This alga shows an enormous metabolic flexibility, growing either photoautotrophically or heterotrophically on more than 50 carbon sources. Environmental adaptation seems to have been facilitated by horizontal gene transfer from various bacteria and archaea, often followed by gene family expansion. At least 5% of protein-coding genes of G. sulphuraria were probably acquired horizontally. These proteins are involved in ecologically important processes ranging from heavy-metal detoxification to glycerol uptake and metabolism. Thus, our findings show that a pan-domain gene pool has facilitated environmental adaptation in this unicellular eukaryote.}, }
@article {pmid23471390, year = {2013}, author = {Rocha, EP}, title = {Evolution. With a little help from prokaryotes.}, journal = {Science (New York, N.Y.)}, volume = {339}, number = {6124}, pages = {1154-1155}, doi = {10.1126/science.1234938}, pmid = {23471390}, issn = {1095-9203}, mesh = {Adaptation, Physiological/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Archaeal ; *Genes, Bacterial ; Genome, Plant/*genetics ; Rhodophyta/*genetics/*microbiology ; }, }
@article {pmid23471189, year = {2013}, author = {Popowska, M and Krawczyk-Balska, A}, title = {Broad-host-range IncP-1 plasmids and their resistance potential.}, journal = {Frontiers in microbiology}, volume = {4}, number = {}, pages = {44}, pmid = {23471189}, issn = {1664-302X}, abstract = {The plasmids of the incompatibility (Inc) group IncP-1, also called IncP, as extrachromosomal genetic elements can transfer and replicate virtually in all Gram-negative bacteria. They are composed of backbone genes that encode a variety of essential functions and accessory genes that have implications for human health and environmental bioremediation. Broad-host-range IncP plasmids are known to spread genes between distinct phylogenetic groups of bacteria. These genes often code for resistances to a broad spectrum of antibiotics, heavy metals, and quaternary ammonium compounds used as disinfectants. The backbone of these plasmids carries modules that enable them to effectively replicate, move to a new host via conjugative transfer and to be stably maintained in bacterial cells. The adaptive, resistance, and virulence genes are mainly located on mobile genetic elements integrated between the functional plasmid backbone modules. Environmental studies have demonstrated the wide distribution of IncP-like replicons in manure, soils and wastewater treatment plants. They also are present in strains of pathogenic or opportunistic bacteria, which can be a cause for concern, because they may encode multiresistance. Their broad distribution suggests that IncP plasmids play a crucial role in bacterial adaptation by utilizing horizontal gene transfer. This review summarizes the variety of genetic information and physiological functions carried by IncP plasmids, which can contribute to the spread of antibiotic and heavy metal resistance while also mediating the process of bioremediation of pollutants. Due to the location of the resistance genes on plasmids with a broad-host-range and the presence of transposons carrying these genes it seems that the spread of these genes would be possible and quite hazardous in infection control. Future studies are required to determine the level of risk of the spread of resistance genes located on these plasmids.}, }
@article {pmid23470724, year = {2013}, author = {Yue, J and Hu, X and Huang, J}, title = {Horizontal gene transfer in the innovation and adaptation of land plants.}, journal = {Plant signaling &amp; behavior}, volume = {8}, number = {5}, pages = {e24130}, pmid = {23470724}, issn = {1559-2324}, mesh = {Adaptation, Physiological/*genetics ; Bryopsida/genetics ; Embryophyta/*genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Plant ; }, abstract = {Horizontal gene transfer (HGT) has been well documented in prokaryotes and unicellular eukaryotes, but its role in plants and animals remains elusive. In a recent study, we showed that at least 57 families of nuclear genes in the moss Physcomitrella patens were acquired from prokaryotes, fungi or viruses and that HGT played a critical role in plant colonization of land. In this paper, we categorize all acquired genes based on their putative functions and biological processes, and further address the importance of HGT in plant innovation and evolution.}, }
@article {pmid23469919, year = {2013}, author = {Jia, Y and Huang, H and Zhong, M and Wang, FH and Zhang, LM and Zhu, YG}, title = {Microbial arsenic methylation in soil and rice rhizosphere.}, journal = {Environmental science &amp; technology}, volume = {47}, number = {7}, pages = {3141-3148}, doi = {10.1021/es303649v}, pmid = {23469919}, issn = {1520-5851}, mesh = {Arsenic/*metabolism ; Bacteria/genetics/*metabolism ; Base Sequence ; Biodiversity ; DNA Primers/metabolism ; Gene Dosage/genetics ; Genes, Bacterial/genetics ; Methylation ; Oryza/*metabolism/*microbiology ; Phylogeny ; Plant Roots/microbiology ; *Rhizosphere ; Soil/*chemistry ; *Soil Microbiology ; Solutions ; }, abstract = {Methylated arsenic (As) species are a common constituent of rice grains accounting for 10-90% of the total As. Recent studies have shown that higher plants are unlikely to methylate As in vivo suggesting that As methylation is a microbial mediated process that occurs in soils prior to plant uptake. In this study, we designed primers according to the conserved essential amino acids and structural motifs of arsenite S-adenosylmethionine methyltransferase (ArsM). We report for the first time the successful amplification of the prokaryotic arsM gene in 14 tested soils with wide ranging As concentrations. The abundance and diversity of the arsM gene in the rice rhizosphere soil and roots were analyzed using the designed primers. Results showed that microbes containing arsM genes were phylogenetically diverse, as revealed by the clone library and terminal restriction fragment length polymorphism (T-RFLP) analysis, and were branched into various phyla. Concentration of methylated As species in the soil solution was elevated in the rhizosphere soil and also by the addition of rice straw into the paddy soil, corresponding to the elevated abundance of the arsM gene in the soil. These results, together with evidence of horizontal gene transfer (HGT) of the arsM gene, suggest the genes encoding ArsM in soils are widespread. These findings demonstrate why most rice, when compared with other cereals, contains unusually high concentrations of methylated As species.}, }
@article {pmid23468974, year = {2013}, author = {Hurwitz, BL and Sullivan, MB}, title = {The Pacific Ocean virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology.}, journal = {PloS one}, volume = {8}, number = {2}, pages = {e57355}, pmid = {23468974}, issn = {1932-6203}, mesh = {*Ecology ; *Marine Biology ; *Metagenomics ; Pacific Ocean ; Viruses/*genetics/isolation &amp; purification ; *Water Microbiology ; }, abstract = {Bacteria and their viruses (phage) are fundamental drivers of many ecosystem processes including global biogeochemistry and horizontal gene transfer. While databases and resources for studying function in uncultured bacterial communities are relatively advanced, many fewer exist for their viral counterparts. The issue is largely technical in that the majority (often 90%) of viral sequences are functionally 'unknown' making viruses a virtually untapped resource of functional and physiological information. Here, we provide a community resource that organizes this unknown sequence space into 27 K high confidence protein clusters using 32 viral metagenomes from four biogeographic regions in the Pacific Ocean that vary by season, depth, and proximity to land, and include some of the first deep pelagic ocean viral metagenomes. These protein clusters more than double currently available viral protein clusters, including those from environmental datasets. Further, a protein cluster guided analysis of functional diversity revealed that richness decreased (i) from deep to surface waters, (ii) from winter to summer, (iii) and with distance from shore in surface waters only. These data provide a framework from which to draw on for future metadata-enabled functional inquiries of the vast viral unknown.}, }
@article {pmid23468104, year = {2013}, author = {Behr, MA}, title = {Evolution of Mycobacterium tuberculosis.}, journal = {Advances in experimental medicine and biology}, volume = {783}, number = {}, pages = {81-91}, doi = {10.1007/978-1-4614-6111-1_4}, pmid = {23468104}, issn = {0065-2598}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Animals ; Cattle ; DNA, Bacterial/*genetics ; *Evolution, Molecular ; Gene Deletion ; Gene Transfer, Horizontal ; Genes, Bacterial ; Host Specificity/genetics ; Host-Pathogen Interactions/genetics/immunology ; Humans ; Mutation ; Mycobacterium/classification/genetics ; Mycobacterium Infections, Nontuberculous/microbiology ; Mycobacterium bovis/genetics ; Mycobacterium tuberculosis/*genetics/growth &amp; development/immunology ; Phylogeny ; Polymorphism, Single Nucleotide ; Species Specificity ; Tuberculosis/epidemiology/microbiology ; Tuberculosis, Bovine/epidemiology/microbiology ; Virulence/genetics ; }, abstract = {Genomic studies have provided a refined understanding of the genetic diversity within the Mycobacterium genus, and more specifically within Mycobacterium tuberculosis. These results have informed a new perspective on the macro- and micro-evolution of the tubercle bacillus. In the first step, a M. kansasii-like opportunistic pathogen acquired new genes, through horizontal gene transfer, that enabled it to better exploit an intracellular niche and ultimately evolve into a professional pathogen. In the second step, different subspecies and strains of the M. tuberculosis complex emerged through mutation and deletion of unnecessary DNA. Understanding the differences between M. tuberculosis and related less pathogenic mycobacteria is expected to reveal key bacterial virulence mechanisms and provide opportunities to understand host resistance to mycobacterial infection. Understanding differences within the M. tuberculosis complex and the evolutionary forces shaping these differences is important for investigating the basis of its success as both a symbiont and a pathogen.}, }
@article {pmid23461567, year = {2013}, author = {Lassak, K and Peeters, E and Wróbel, S and Albers, SV}, title = {The one-component system ArnR: a membrane-bound activator of the crenarchaeal archaellum.}, journal = {Molecular microbiology}, volume = {88}, number = {1}, pages = {125-139}, doi = {10.1111/mmi.12173}, pmid = {23461567}, issn = {1365-2958}, mesh = {Archaeal Proteins/chemistry/genetics/*metabolism ; Base Sequence ; Binding Sites/genetics ; Cell Membrane/*metabolism ; Gene Expression Regulation, Archaeal ; Molecular Sequence Data ; Movement ; Multigene Family/genetics ; Mutation/genetics ; Phenotype ; Protein Binding ; Protein Structure, Tertiary ; *Signal Transduction ; Sulfolobus acidocaldarius/genetics/*metabolism ; Trans-Activators/*metabolism ; Transcription, Genetic ; }, abstract = {Linking the motility apparatus to signal transduction systems enables microbes to precisely control their swimming behaviour according to environmental conditions. Bacteria have therefore evolved a complex chemotaxis machinery, which has presumably spread through lateral gene transfer into the euryarchaeal subkingdom. By contrast Crenarchaeota encode no chemotaxis-like proteins but are nevertheless able to connect external stimuli to archaellar derived motility. This raises fundamental questions about the underlying regulatory mechanisms. Recently, we reported that the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius becomes motile upon nutrient starvation by promoting transcription of flaB encoding the filament forming subunits. Here we describe two transcriptional activators as paralogous one-component-systems Saci_1180 and Saci_1171 (ArnR and ArnR1). Deletions of arnR and arnR1 resulted in diminished flaB expression and accordingly the deletion mutants revealed impaired swimming motility. We further identified two inverted repeat sequences located upstream of the flaB core promoter of S. acidocaldarius. These cis-regulatory elements were shown to be critical for ArnR and ArnR1 mediated flaB gene expression in vivo. Finally, bioinformatic analysis revealed ArnR to be conserved not only in Sulfolobales but also in the crenarchaeal order of Desulfurococcales and thus might represent a more general control mechanism of archaeal motility.}, }
@article {pmid23459037, year = {2013}, author = {Xi, Z and Wang, Y and Bradley, RK and Sugumaran, M and Marx, CJ and Rest, JS and Davis, CC}, title = {Massive mitochondrial gene transfer in a parasitic flowering plant clade.}, journal = {PLoS genetics}, volume = {9}, number = {2}, pages = {e1003265}, pmid = {23459037}, issn = {1553-7404}, mesh = {DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Flowers/genetics ; Gene Transfer, Horizontal/*genetics ; Genome, Mitochondrial ; Genome, Plant ; Host-Parasite Interactions/*genetics ; Phylogeny ; Plants/*genetics/parasitology ; RNA, Ribosomal/genetics ; Symbiosis ; }, abstract = {Recent studies have suggested that plant genomes have undergone potentially rampant horizontal gene transfer (HGT), especially in the mitochondrial genome. Parasitic plants have provided the strongest evidence of HGT, which appears to be facilitated by the intimate physical association between the parasites and their hosts. A recent phylogenomic study demonstrated that in the holoparasite Rafflesia cantleyi (Rafflesiaceae), whose close relatives possess the world's largest flowers, about 2.1% of nuclear gene transcripts were likely acquired from its obligate host. Here, we used next-generation sequencing to obtain the 38 protein-coding and ribosomal RNA genes common to the mitochondrial genomes of angiosperms from R. cantleyi and five additional species, including two of its closest relatives and two host species. Strikingly, our phylogenetic analyses conservatively indicate that 24%-41% of these gene sequences show evidence of HGT in Rafflesiaceae, depending on the species. Most of these transgenic sequences possess intact reading frames and are actively transcribed, indicating that they are potentially functional. Additionally, some of these transgenes maintain synteny with their donor and recipient lineages, suggesting that native genes have likely been displaced via homologous recombination. Our study is the first to comprehensively assess the magnitude of HGT in plants involving a genome (i.e., mitochondria) and a species interaction (i.e., parasitism) where it has been hypothesized to be potentially rampant. Our results establish for the first time that, although the magnitude of HGT involving nuclear genes is appreciable in these parasitic plants, HGT involving mitochondrial genes is substantially higher. This may represent a more general pattern for other parasitic plant clades and perhaps more broadly for angiosperms.}, }
@article {pmid23458762, year = {2013}, author = {Zhu, L and Lau, GW}, title = {Therapeutic potential of the Streptococcus pneumoniae competence regulon.}, journal = {Expert review of anti-infective therapy}, volume = {11}, number = {3}, pages = {227-229}, doi = {10.1586/eri.13.10}, pmid = {23458762}, issn = {1744-8336}, support = {R01 HL090699/HL/NHLBI NIH HHS/United States ; R01-HL-090699/HL/NHLBI NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology/*therapeutic use ; Bacterial Proteins/*antagonists &amp; inhibitors/genetics/metabolism ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Humans ; Pneumococcal Infections/drug therapy ; Regulon/*drug effects ; Streptococcus pneumoniae/drug effects/*genetics/*pathogenicity ; *Transformation, Bacterial ; Virulence/genetics ; }, }
@article {pmid23457984, year = {2012}, author = {Onishchenko, GG and Sheveleva, SA and Khotimchenko, SA}, title = {[Hygienic substantiation of the permissible levels for tetracycline-group antibiotics in food].}, journal = {Gigiena i sanitariia}, volume = {}, number = {6}, pages = {4-14}, pmid = {23457984}, issn = {0016-9900}, mesh = {Animals ; Anti-Bacterial Agents/*analysis/toxicity ; Drug Resistance, Bacterial ; Food Contamination/*analysis/legislation &amp; jurisprudence/*prevention &amp; control ; Government Regulation ; Humans ; Hygiene/*legislation &amp; jurisprudence ; Maximum Allowable Concentration ; Russia ; Tetracyclines/*analysis/toxicity ; Toxicity Tests ; World Health Organization ; }, abstract = {For the purpose of justification of the hygienic standard for tetracycline-group antibiotics in the food production established in the Russian Federation at more rigid level, than maximum and admissible levels (MAL) of the Codex Alimentarius Commission, the analysis of data of literature on negative nature of impact of low concentration of these antibiotics on an organism and the environmental conditions and risk for health has been performed. Inadequacy of the accepted admissible daily dose (ADD) accepted by The Joint FAO/WHO Expert Committee on Food Additives (JECFA) on action on selection of resistant E. coli in intestines, for the wide contingent of consumers in connection with ignoring of obvious factors of uncertainty (gastrointestinal dysbiosis, age and individual variations in the microbiota of people synergy with other antibiotics residues in food and indirect impact on an organism through microflora from the natural habitat (resistance genes, modified causative organisms with altered properties).. By the analysis of information received with the use of modern molecular and genetic methods, the role of Subinhibitory concentrations (sub-MICs) of tetracyclines as biologically active substances, signaling molecules which, without causing obvious negative consequences in a macroorganism, serve as a major factor of regulation of a transcription in microorganisms and activation of a horizontal gene transfer coding resistance, transferred on conjugative transposons of Tn916-Tn1545 family. Reasonable scientific data on a dominating contribution of minor levels of tetracyclines in globalization in the nature of the most adverse transmissive type of the antibiotic resistance interfaced to formation new bacterial pathotypes, as consequences of irrationally high scales of application in agriculture and strengthened impact on microbic ecosystems of live organisms and objects of habitat are presented. For minimization of this mediated risk for health the need of preservation of operating level of the tetracyclines residues (by < or = 0,01 mg/kg of a product), MAL which were unlike Codex MAL (< or = 0,1-1,2 mg/kg) in a zone of concentrations below 0,1 Misc not capable to initiation of the above described changes has been proved, till up to receipt of new scientific data on influence on macro - or microorganisms of the doses equal or below this value on macro - or microorganisms.}, }
@article {pmid23454063, year = {2013}, author = {Drewniak, L and Dziewit, L and Ciezkowska, M and Gawor, J and Gromadka, R and Sklodowska, A}, title = {Structural and functional genomics of plasmid pSinA of Sinorhizobium sp. M14 encoding genes for the arsenite oxidation and arsenic resistance.}, journal = {Journal of biotechnology}, volume = {164}, number = {4}, pages = {479-488}, doi = {10.1016/j.jbiotec.2013.01.017}, pmid = {23454063}, issn = {1873-4863}, mesh = {Arsenic/*pharmacology ; Arsenites/*metabolism ; Bacteria/genetics ; Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Models, Genetic ; Oxidation-Reduction ; Plasmids/chemistry/*genetics ; Sinorhizobium/drug effects/*genetics ; }, abstract = {Plasmid pSinA of Sinorhizobium sp. M14 (Alphaproteobacteria) is the first described, natural, self-transferable plasmid harboring a complete set of genes for oxidation of arsenite. Removal of this plasmid from cells of the host strain caused the loss of resistance to arsenic and heavy metals (Cd, Co, Zn and Hg) and abolished the ability to grow on minimal salt medium supplemented with sodium arsenite as the sole energy source. Plasmid pSinA was introduced into other representatives of Alphaproteobacteria which resulted in acquisition of new abilities concerning arsenic resistance and oxidation, as well as heavy metals resistance. Microcosm experiments revealed that plasmid pSinA can also be transferred via conjugation into other indigenous bacteria from microbial community of As-contaminated soils, including representatives of Alpha- and Gammaproteobacteria. Analysis of "natural" transconjugants showed that pSinA is functional (expresses arsenite oxidase) and is stably maintained in their cells after approximately 60 generations of growth under nonselective conditions. This work clearly demonstrates that pSinA is a self-transferable, broad-host-range plasmid, which plays an important role in horizontal transfer of arsenic metabolism genes.}, }
@article {pmid23453965, year = {2013}, author = {Chand, D and de Lannoy, L and Tucker, R and Lovejoy, DA}, title = {Origin of chordate peptides by horizontal protozoan gene transfer in early metazoans and protists: evolution of the teneurin C-terminal associated peptides (TCAP).}, journal = {General and comparative endocrinology}, volume = {188}, number = {}, pages = {144-150}, doi = {10.1016/j.ygcen.2013.02.006}, pmid = {23453965}, issn = {1095-6840}, mesh = {Animals ; Choanoflagellata/genetics ; Gene Transfer, Horizontal/*genetics ; Peptides/classification/*genetics ; Phylogeny ; Prokaryotic Cells/*enzymology ; Tenascin/genetics ; }, abstract = {The teneurin C-terminal associated peptides (TCAP) are found at the extracellular face in C-terminal region of the teneurin transmembrane proteins. One of these peptides, TCAP-1 is independently transcribed as a smaller bioactive peptide that possesses a number of stress response-attenuating activities. The teneurin-TCAP system appears to be the result of a horizontal gene transfer from a prokaryotic proteinaceous polymorphic toxin to a choanoflagellate. In a basal metazoan, the TCAP region has been modified from a toxin to a soluble intercellular signaling system. New studies indicate that the teneurin-TCAP system form a complex signaling system associated with adhesion, cytoskeletal regulation and intracellular signaling. TCAP-1 is highly conserved in all vertebrates and in mammals, inhibits corticotropin-releasing factor (CRF)-associated stress. Using the TCAP-teneurin system as a model, it is likely that numerous peptide systems in the Chordata began as a result of horizontal gene transfer from prokaryotes early in metazoan ancestry.}, }
@article {pmid23453788, year = {2013}, author = {Hu, L and Zhong, Q and Tu, J and Xu, Y and Qin, Z and Parsons, C and Zhang, B and Hu, X and Wang, L and Yu, F and Pan, J}, title = {Emergence of blaNDM-1 among Klebsiella pneumoniae ST15 and novel ST1031 clinical isolates in China.}, journal = {Diagnostic microbiology and infectious disease}, volume = {75}, number = {4}, pages = {373-376}, doi = {10.1016/j.diagmicrobio.2013.01.006}, pmid = {23453788}, issn = {1879-0070}, mesh = {Aged, 80 and over ; Anti-Bacterial Agents/pharmacology ; Carbapenems/pharmacology ; China/epidemiology ; Conjugation, Genetic ; Gene Transfer, Horizontal ; Genotype ; Hospitals, Teaching ; Humans ; Klebsiella Infections/epidemiology/*microbiology ; Klebsiella pneumoniae/*classification/*enzymology/genetics/isolation &amp; purification ; Male ; *Molecular Typing ; Transformation, Bacterial ; Young Adult ; beta-Lactam Resistance ; beta-Lactamases/*metabolism ; }, abstract = {The emergence of NDM-1 has become established as a major public health threat and represents a new and major challenge in the treatment of infectious diseases. A total of 39 carbapenem-resistant Enterobacteriaceae isolates collected from patients receiving care at 5 teaching hospitals in Jiangxi province, central China, were analyzed for carriage of resistance genes, including bla(NDM-1). Two carbapenem-resistant Klebsiella pneumoniae isolates (NC12 and NC18) were found to harbor bla(NDM-1). In addition to bla(NDM-1), NC12 also carried bla(SHV-1), while NC18 harbored additional resistance genes, including bla(SHV-12), bla(CTX-M-14), armA and bla(TEM-1). NC12 and NC18 belonged to ST15 and novel ST1031 and were clonally unrelated. Carbapenem resistance for NC12 could be transferred to Escherichia coli recipients through conjugation and chemical transformation, while carbapenem resistance for NC18 was only transferred to E. coli recipients by chemical transformation. The EcoR1-digested DNA pattern of plasmids from the transformants of NC12 was identical to that for NC18. Taken together, this is the first report of bla(NDM-1) carriage by K. pneumoniae clinical isolates in mainland China, indicating that bla(NDM-1) is disseminated among Enterobacteriaceae in China. Systemic surveillance should focus on the dissemination of bla(NDM-1) among Gram-negative clinical isolates, especially some major clones, such as K. pneumoniae ST15 which is a major clone among CTX-M-15-producing isolates.}, }
@article {pmid23453618, year = {2013}, author = {Jain, P and Roy, S and Viswanathan, R and Basu, S and Singh, AK and Dutta, S}, title = {Concurrent and transferable resistance to extended-spectrum cephalosporins, monobactam and fluoroquinolone in a Salmonella enterica serovar Worthington blood isolate from a neonate in Kolkata, India.}, journal = {International journal of antimicrobial agents}, volume = {41}, number = {5}, pages = {494-495}, doi = {10.1016/j.ijantimicag.2013.01.011}, pmid = {23453618}, issn = {1872-7913}, mesh = {Anti-Bacterial Agents/*pharmacology ; Cephalosporins/*pharmacology ; Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; *Drug Resistance, Multiple, Bacterial ; Fluoroquinolones/*pharmacology ; Gene Transfer, Horizontal ; Humans ; India ; Infant, Newborn ; Molecular Sequence Data ; Monobactams/*pharmacology ; Plasmids/analysis ; Salmonella Infections/*microbiology ; Salmonella enterica/*drug effects/genetics/isolation &amp; purification ; Sequence Analysis, DNA ; }, }
@article {pmid23452519, year = {2013}, author = {Yang, Z and Wang, Y and Zhou, Y and Gao, Q and Zhang, E and Zhu, L and Hu, Y and Xu, C}, title = {Evolution of land plant genes encoding L-Ala-D/L-Glu epimerases (AEEs) via horizontal gene transfer and positive selection.}, journal = {BMC plant biology}, volume = {13}, number = {}, pages = {34}, pmid = {23452519}, issn = {1471-2229}, mesh = {Bryophyta/genetics ; *Evolution, Molecular ; Exons/genetics ; Gene Transfer, Horizontal/*genetics ; Introns/genetics ; Magnoliopsida/genetics ; Phylogeny ; Racemases and Epimerases/*genetics ; }, abstract = {BACKGROUND: The L-Ala-D/L-Glu epimerases (AEEs), a subgroup of the enolase superfamily, catalyze the epimerization of L-Ala-D/L-Glu and other dipeptides in bacteria and contribute to the metabolism of the murein peptide of peptidoglycan. Although lacking in peptidoglycan, land plants possess AEE genes that show high similarity to those in bacteria.<br><br>RESULTS: Similarity searches revealed that the AEE gene is ubiquitous in land plants, from bryophytas to angiosperms. However, other eukaryotes, including green and red algae, do not contain genes encoding proteins with an L-Ala-D/L-Glu_epimerase domain. Homologs of land plant AEE genes were found to only be present in prokaryotes, especially in bacteria. Phylogenetic analysis revealed that the land plant AEE genes formed a monophyletic group with some bacterial homologs. In addition, land plant AEE proteins showed the highest similarity with these bacterial homologs and shared motifs only conserved in land plant and these bacterial AEEs. Integrated information on the taxonomic distribution, phylogenetic relationships and sequence similarity of the AEE proteins revealed that the land plant AEE genes were acquired from bacteria through an ancient horizontal gene transfer (HGT) event. Further evidence revealed that land plant AEE genes had undergone positive selection and formed the main characteristics of exon/intron structures through gaining some introns during the initially evolutionary period in the ancestor of land plants.<br><br>CONCLUSIONS: The results of this study clearly demonstrated that the ancestor of land plants acquired an AEE gene from bacteria via an ancient HGT event. Other findings illustrated that adaptive evolution through positive selection has contributed to the functional adaptation and fixation of this gene in land plants.}, }
@article {pmid23451112, year = {2013}, author = {Dalquen, DA and Altenhoff, AM and Gonnet, GH and Dessimoz, C}, title = {The impact of gene duplication, insertion, deletion, lateral gene transfer and sequencing error on orthology inference: a simulation study.}, journal = {PloS one}, volume = {8}, number = {2}, pages = {e56925}, pmid = {23451112}, issn = {1932-6203}, mesh = {Gene Duplication/*genetics ; Gene Transfer, Horizontal/*genetics ; Genomics/methods ; Mutagenesis, Insertional/*genetics ; }, abstract = {The identification of orthologous genes, a prerequisite for numerous analyses in comparative and functional genomics, is commonly performed computationally from protein sequences. Several previous studies have compared the accuracy of orthology inference methods, but simulated data has not typically been considered in cross-method assessment studies. Yet, while dependent on model assumptions, simulation-based benchmarking offers unique advantages: contrary to empirical data, all aspects of simulated data are known with certainty. Furthermore, the flexibility of simulation makes it possible to investigate performance factors in isolation of one another.Here, we use simulated data to dissect the performance of six methods for orthology inference available as standalone software packages (Inparanoid, OMA, OrthoInspector, OrthoMCL, QuartetS, SPIMAP) as well as two generic approaches (bidirectional best hit and reciprocal smallest distance). We investigate the impact of various evolutionary forces (gene duplication, insertion, deletion, and lateral gene transfer) and technological artefacts (ambiguous sequences) on orthology inference. We show that while gene duplication/loss and insertion/deletion are well handled by most methods (albeit for different trade-offs of precision and recall), lateral gene transfer disrupts all methods. As for ambiguous sequences, which might result from poor sequencing, assembly, or genome annotation, we show that they affect alignment score-based orthology methods more strongly than their distance-based counterparts.}, }
@article {pmid23446800, year = {2012}, author = {Blokesch, M}, title = {A quorum sensing-mediated switch contributes to natural transformation of Vibrio cholerae.}, journal = {Mobile genetic elements}, volume = {2}, number = {5}, pages = {224-227}, pmid = {23446800}, issn = {2159-2543}, abstract = {There is a fundamental gap in our understanding of how horizontal gene transfer contributes to the enormous range of genetic variations that are observed among bacteria. The objective of our study was to better understand how the acquisition of genetic material by natural transformation is regulated within a population of Vibrio cholerae cells. V. cholerae is an aquatic bacterium and a facultative human pathogen. It acquires natural competence for transformation in response to changing environmental signals, such as the presence of chitinous surfaces, the absence of monomeric sugars and quorum sensing-linked autoinducers. The latter play a distinctive role in V. cholerae as they fine-tune a switch from the degradation of extracellular DNA toward the uptake of intact DNA strands in competence-induced cells. The link between quorum sensing and natural competence for transformation will be discussed. Furthermore, we speculate on the overrepresentation of transformation-negative strains of V. cholerae in patient-derived culture collections, which might be the result of a biased sampling strategy as virulence and natural transformation are contrarily regulated by the quorum sensing network.}, }
@article {pmid23445260, year = {2013}, author = {Gilbert, C and Waters, P and Feschotte, C and Schaack, S}, title = {Horizontal transfer of OC1 transposons in the Tasmanian devil.}, journal = {BMC genomics}, volume = {14}, number = {}, pages = {134}, pmid = {23445260}, issn = {1471-2164}, support = {R01 GM077582/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Computational Biology ; DNA Transposable Elements/*genetics ; *Gene Transfer, Horizontal ; Genome ; Interspersed Repetitive Sequences ; Marsupialia/classification/*genetics ; Phylogeny ; }, abstract = {BACKGROUND: There is growing recognition that horizontal DNA transfer, a process known to be common in prokaryotes, is also a significant source of genomic variation in eukaryotes. Horizontal transfer of transposable elements (HTT) may be especially prevalent in eukaryotes given the inherent mobility, widespread occurrence, and prolific abundance of these elements in many eukaryotic genomes.<br><br>RESULTS: Here, we provide evidence for a new case of HTT of the transposon family OposCharlie1 (OC1) in the Tasmanian devil, Sarcophilus harrisii. Bioinformatic analyses of OC1 sequences in the Tasmanian devil genome suggest that this transposon infiltrated the common ancestor of the Dasyuridae family ~17 million years ago. This estimate is corroborated by a PCR-based screen for the presence/absence of this family in Tasmanian devils and closely-related species.<br><br>CONCLUSIONS: This case of HTT is the first to be reported in dasyurids. It brings the number of animal lineages independently invaded by OC1 to 12, and adds a fourth continent to the pandemic-like pattern of invasion of this transposon. In the context of these data, we discuss the evolutionary history of this transposon family and its potential impact on the diversification of marsupials.}, }
@article {pmid23445243, year = {2013}, author = {Corradi, N and Selman, M}, title = {Latest progress in microsporidian genome research.}, journal = {The Journal of eukaryotic microbiology}, volume = {60}, number = {3}, pages = {309-312}, doi = {10.1111/jeu.12030}, pmid = {23445243}, issn = {1550-7408}, mesh = {Gene Transfer, Horizontal/genetics ; Genome, Fungal/genetics ; Microsporidia/classification/*genetics ; Phylogeny ; }, abstract = {Microsporidia are obligate intracellular pathogens of medical and ecological importance whose genomes have been studied extensively over the last decade. Such studies have focused on the remarkably reduced gene content that characterizes all known species, and some have unraveled the mechanisms that are involved in their extreme genome compaction. In the last year, a large number of new genome sequences from several divergent members of the group have been finally released and analyzed, and these have revealed the presence of many features that were previously unsuspected to exist within the group. This study aims to shortly review the most recent progress in the field of microsporidian genomics, highlighting the importance of the most recently released genome data for our understanding of the biology and evolution of this important group of parasites.}, }
@article {pmid23442822, year = {2013}, author = {Alsmark, C and Foster, PG and Sicheritz-Ponten, T and Nakjang, S and Martin Embley, T and Hirt, RP}, title = {Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes.}, journal = {Genome biology}, volume = {14}, number = {2}, pages = {R19}, pmid = {23442822}, issn = {1474-760X}, support = {268701/ERC_/European Research Council/International ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Eukaryota/genetics ; *Gene Transfer, Horizontal ; *Genome, Protozoan ; Molecular Sequence Annotation ; Parasites/*genetics ; }, abstract = {BACKGROUND: The influence of lateral gene transfer on gene origins and biology in eukaryotes is poorly understood compared with those of prokaryotes. A number of independent investigations focusing on specific genes, individual genomes, or specific functional categories from various eukaryotes have indicated that lateral gene transfer does indeed affect eukaryotic genomes. However, the lack of common methodology and criteria in these studies makes it difficult to assess the general importance and influence of lateral gene transfer on eukaryotic genome evolution.<br><br>RESULTS: We used a phylogenomic approach to systematically investigate lateral gene transfer affecting the proteomes of thirteen, mainly parasitic, microbial eukaryotes, representing four of the six eukaryotic super-groups. All of the genomes investigated have been significantly affected by prokaryote-to-eukaryote lateral gene transfers, dramatically affecting the enzymes of core pathways, particularly amino acid and sugar metabolism, but also providing new genes of potential adaptive significance in the life of parasites. A broad range of prokaryotic donors is involved in such transfers, but there is clear and significant enrichment for bacterial groups that share the same habitats, including the human microbiota, as the parasites investigated.<br><br>CONCLUSIONS: Our data show that ecology and lifestyle strongly influence gene origins and opportunities for gene transfer and reveal that, although the outlines of the core eukaryotic metabolism are conserved among lineages, the genes making up those pathways can have very different origins in different eukaryotes. Thus, from the perspective of the effects of lateral gene transfer on individual gene ancestries in different lineages, eukaryotic metabolism appears to be chimeric.}, }
@article {pmid23438345, year = {2013}, author = {Lefèvre, CT and Trubitsyn, D and Abreu, F and Kolinko, S and de Almeida, LG and de Vasconcelos, AT and Lins, U and Schüler, D and Ginet, N and Pignol, D and Bazylinski, DA}, title = {Monophyletic origin of magnetotaxis and the first magnetosomes.}, journal = {Environmental microbiology}, volume = {15}, number = {8}, pages = {2267-2274}, doi = {10.1111/1462-2920.12097}, pmid = {23438345}, issn = {1462-2920}, mesh = {Bacteria/*classification/*genetics/metabolism ; Base Sequence ; DNA Transposable Elements/genetics ; Gene Transfer, Horizontal/genetics ; Genomics ; Magnetosomes/*genetics ; *Phylogeny ; Proteobacteria/classification/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Horizontal gene transfer (HGT), the transfer of genetic material other than by descent, is thought to have played significant roles in the evolution and distribution of genes in prokaryotes. These include those responsible for the ability of motile, aquatic magnetotactic bacteria (MTB) to align and swim along magnetic field lines and the biomineralization of magnetosomes that are responsible for this behaviour. There is some genomic evidence that HGT might be responsible for the distribution of magnetosome genes in different phylogenetic groups of bacteria. For example, in the genomes of a number of MTB, magnetosome genes are present as clusters within a larger structure known as the magnetosome genomic island surrounded by mobile elements such as insertion sequences and transposases as well as tRNA genes. Despite this, there is no strong direct proof of HGT between these organisms. Here we show that a phylogenetic tree based on magnetosome protein amino acid sequences from a number of MTB was congruent with the tree based on the organisms' 16S rRNA gene sequences. This shows that evolution and divergence of these proteins and the 16S rRNA gene occurred similarly. This suggests that magnetotaxis originated monophyletically in the Proteobacteria phylum and implies that the common ancestor of all Proteobacteria was magnetotactic.}, }
@article {pmid23437976, year = {2013}, author = {Escalon, A and Javegny, S and Vernière, C and Noël, LD and Vital, K and Poussier, S and Hajri, A and Boureau, T and Pruvost, O and Arlat, M and Gagnevin, L}, title = {Variations in type III effector repertoires, pathological phenotypes and host range of Xanthomonas citri pv. citri pathotypes.}, journal = {Molecular plant pathology}, volume = {14}, number = {5}, pages = {483-496}, pmid = {23437976}, issn = {1364-3703}, mesh = {Amplified Fragment Length Polymorphism Analysis ; Bacterial Proteins/metabolism ; Bacterial Secretion Systems/*genetics ; Cluster Analysis ; Colony Count, Microbial ; Gene Deletion ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/genetics ; Genetic Variation ; Geography ; Host Specificity/*genetics ; Host-Pathogen Interactions ; Molecular Sequence Data ; Phenotype ; Phylogeny ; Plant Diseases/microbiology ; Plant Immunity/genetics ; Plant Leaves/microbiology ; Plants/microbiology ; Sequence Analysis, DNA ; Xanthomonas/*classification/*genetics/growth &amp; development/pathogenicity ; }, abstract = {The mechanisms determining the host range of Xanthomonas are still undeciphered, despite much interest in their potential roles in the evolution and emergence of plant pathogenic bacteria. Xanthomonas citri pv. citri (Xci) is an interesting model of host specialization because of its pathogenic variants: pathotype A strains infect a wide range of Rutaceous species, whereas pathotype A*/A(W) strains have a host range restricted to Mexican lime (Citrus aurantifolia) and alemow (Citrus macrophylla). Based on a collection of 55 strains representative of Xci worldwide diversity assessed by amplified fragment length polymorphism (AFLP), we investigated the distribution of type III effectors (T3Es) in relation to host range. We examined the presence of 66 T3Es from xanthomonads in Xci and identified a repertoire of 28 effectors, 26 of which were shared by all Xci strains, whereas two (xopAG and xopC1) were present only in some A*/A(W) strains. We found that xopAG (=avrGf1) was present in all A(W) strains, but also in three A* strains genetically distant from A(W) , and that all xopAG-containing strains induced the hypersensitive response (HR) on grapefruit and sweet orange. The analysis of xopAD and xopAG suggested horizontal transfer between X. citri pv. bilvae, another citrus pathogen, and some Xci strains. A strains were genetically less diverse, induced identical phenotypic responses and possessed indistinguishable T3E repertoires. Conversely, A*/A(W) strains exhibited a wider genetic diversity in which clades correlated with geographical origin and T3E repertoire, but not with pathogenicity, according to T3E deletion experiments. Our data outline the importance of taking into account the heterogeneity of Xci A*/A(W) strains when analysing the mechanisms of host specialization.}, }
@article {pmid23435978, year = {2013}, author = {Guérillot, R and Da Cunha, V and Sauvage, E and Bouchier, C and Glaser, P}, title = {Modular evolution of TnGBSs, a new family of integrative and conjugative elements associating insertion sequence transposition, plasmid replication, and conjugation for their spreading.}, journal = {Journal of bacteriology}, volume = {195}, number = {9}, pages = {1979-1990}, pmid = {23435978}, issn = {1098-5530}, mesh = {Bacteria/classification/*genetics ; *Conjugation, Genetic ; *DNA Transposable Elements ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; Plasmids/*genetics ; Streptococcus/classification/genetics ; }, abstract = {Integrative and conjugative elements (ICEs) have a major impact on gene flow and genome dynamics in bacteria. The ICEs TnGBS1 and TnGBS2, first identified in Streptococcus agalactiae, use a DDE transposase, unlike most characterized ICEs, which depend on a phage-like integrase for their mobility. Here we identified 56 additional TnGBS-related ICEs by systematic genome analysis. Interestingly, all except one are inserted in streptococcal genomes. Sequence comparison of the proteins conserved among these ICEs defined two subtypes related to TnGBS1 or TnGBS2. We showed that both types encode different conjugation modules: a type IV secretion system, a VirD4 coupling protein, and a relaxase and its cognate oriT site, shared with distinct lineages of conjugative elements of Firmicutes. Phylogenetic analysis suggested that TnGBSs evolved from two conjugative elements of different origins by the successive recruitment of a transposition module derived from insertion sequences (ISs). Furthermore, TnGBSs share replication modules with different plasmids. Mutational analyses and conjugation experiments showed that TnGBS1 and TnGBS2 combine replication and transposition upstream promoters for their transfer and stabilization. Despite an evolutionarily successful horizontal dissemination within the genus Streptococcus, these ICEs have a restricted host range. However, we reveal that for TnGBS1 and TnGBS2, this host restriction is not due to a transfer incompatibility linked to the conjugation machineries but most likely to their ability for transient maintenance through replication after their transfer.}, }
@article {pmid23435940, year = {2013}, author = {Petersen, J and Frank, O and Göker, M and Pradella, S}, title = {Extrachromosomal, extraordinary and essential--the plasmids of the Roseobacter clade.}, journal = {Applied microbiology and biotechnology}, volume = {97}, number = {7}, pages = {2805-2815}, doi = {10.1007/s00253-013-4746-8}, pmid = {23435940}, issn = {1432-0614}, mesh = {Adaptation, Biological ; Conjugation, Genetic ; Evolution, Molecular ; Gene Deletion ; Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genes, Essential ; Genetics, Microbial/methods ; Genomic Instability ; Molecular Biology/methods ; *Plasmids ; Roseobacter/*genetics ; }, abstract = {The alphaproteobacterial Roseobacter clade (Rhodobacterales) is one of the most important global players in carbon and sulfur cycles of marine ecosystems. The remarkable metabolic versatility of this bacterial lineage provides access to diverse habitats and correlates with a multitude of extrachromosomal elements. Four non-homologous replication systems and additional subsets of individual compatibility groups ensure the stable maintenance of up to a dozen replicons representing up to one third of the bacterial genome. This complexity presents the challenge of successful partitioning of all low copy number replicons. Based on the phenomenon of plasmid incompatibility, we developed molecular tools for target-oriented plasmid curing and could generate customized mutants lacking hundreds of genes. This approach allows one to analyze the relevance of specific replicons including so-called chromids that are known as lifestyle determinants of bacteria. Chromids are extrachromosomal elements with a chromosome-like genetic imprint (codon usage, GC content) that are essential for competitive survival in the natural habitat, whereas classical dispensable plasmids exhibit a deviating codon usage and typically contain type IV secretion systems for conjugation. The impact of horizontal plasmid transfer is exemplified by the scattered occurrence of the characteristic aerobic anoxygenic photosynthesis among the Roseobacter clade and the recently reported transfer of the 45-kb photosynthesis gene cluster to extrachromosomal elements. Conjugative transmission may be the crucial driving force for rapid adaptations and hence the ecological prosperousness of this lineage of pink bacteria.}, }
@article {pmid23435891, year = {2013}, author = {Romano, C and D'Imperio, S and Woyke, T and Mavromatis, K and Lasken, R and Shock, EL and McDermott, TR}, title = {Comparative genomic analysis of phylogenetically closely related Hydrogenobaculum sp. isolates from Yellowstone National Park.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {9}, pages = {2932-2943}, pmid = {23435891}, issn = {1098-5336}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; Bacterial Proteins/genetics ; Base Sequence ; Conserved Sequence ; DNA, Bacterial/genetics/metabolism ; DNA, Ribosomal/chemistry/genetics ; Gene Transfer, Horizontal ; Genetic Loci ; Genome Size ; Genome, Bacterial/*genetics ; Hot Springs/*microbiology ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; Sequence Analysis, DNA ; Species Specificity ; Synteny ; Wyoming ; }, abstract = {We describe the complete genome sequences of four closely related Hydrogenobaculum sp. isolates (≥ 99.7% 16S rRNA gene identity) that were isolated from the outflow channel of Dragon Spring (DS), Norris Geyser Basin, in Yellowstone National Park (YNP), WY. The genomes range in size from 1,552,607 to 1,552,931 bp, contain 1,667 to 1,676 predicted genes, and are highly syntenic. There are subtle differences among the DS isolates, which as a group are different from Hydrogenobaculum sp. strain Y04AAS1 that was previously isolated from a geographically distinct YNP geothermal feature. Genes unique to the DS genomes encode arsenite [As(III)] oxidation, NADH-ubiquinone-plastoquinone (complex I), NADH-ubiquinone oxidoreductase chain, a DNA photolyase, and elements of a type II secretion system. Functions unique to strain Y04AAS1 include thiosulfate metabolism, nitrate respiration, and mercury resistance determinants. DS genomes contain seven CRISPR loci that are almost identical but are different from the single CRISPR locus in strain Y04AAS1. Other differences between the DS and Y04AAS1 genomes include average nucleotide identity (94.764%) and percentage conserved DNA (80.552%). Approximately half of the genes unique to Y04AAS1 are predicted to have been acquired via horizontal gene transfer. Fragment recruitment analysis and marker gene searches demonstrated that the DS metagenome was more similar to the DS genomes than to the Y04AAS1 genome, but that the DS community is likely comprised of a continuum of Hydrogenobaculum genotypes that span from the DS genomes described here to an Y04AAS1-like organism, which appears to represent a distinct ecotype relative to the DS genomes characterized.}, }
@article {pmid23435694, year = {2013}, author = {Rousseau-Gueutin, M and Huang, X and Higginson, E and Ayliffe, M and Day, A and Timmis, JN}, title = {Potential functional replacement of the plastidic acetyl-CoA carboxylase subunit (accD) gene by recent transfers to the nucleus in some angiosperm lineages.}, journal = {Plant physiology}, volume = {161}, number = {4}, pages = {1918-1929}, pmid = {23435694}, issn = {1532-2548}, mesh = {Acetyl-CoA Carboxylase/chemistry/*genetics/metabolism ; Amino Acid Sequence ; Campanulaceae/enzymology/genetics ; Cell Nucleus/*genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Plant/genetics ; Introns/genetics ; Magnoliopsida/*enzymology/*genetics ; Molecular Sequence Data ; Plastids/*genetics ; Protein Subunits/chemistry/*genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Regulatory Sequences, Nucleic Acid/genetics ; Sequence Alignment ; }, abstract = {Eukaryotic cells originated when an ancestor of the nucleated cell engulfed bacterial endosymbionts that gradually evolved into the mitochondrion and the chloroplast. Soon after these endosymbiotic events, thousands of ancestral prokaryotic genes were functionally transferred from the endosymbionts to the nucleus. This process of functional gene relocation, now rare in eukaryotes, continues in angiosperms. In this article, we show that the chloroplastic acetyl-CoA carboxylase subunit (accD) gene that is present in the plastome of most angiosperms has been functionally relocated to the nucleus in the Campanulaceae. Surprisingly, the nucleus-encoded accD transcript is considerably smaller than the plastidic version, consisting of little more than the carboxylase domain of the plastidic accD gene fused to a coding region encoding a plastid targeting peptide. We verified experimentally the presence of a chloroplastic transit peptide by showing that the product of the nuclear accD fused to green fluorescent protein was imported in the chloroplasts. The nuclear gene regulatory elements that enabled the erstwhile plastidic gene to become functional in the nuclear genome were identified, and the evolution of the intronic and exonic sequences in the nucleus is described. Relocation and truncation of the accD gene is a remarkable example of the processes underpinning endosymbiotic evolution.}, }
@article {pmid23434534, year = {2013}, author = {Mishra, S and Sen, MR and Upadhyay, S and Bhattacharjee, A}, title = {Genetic linkage of blaNDM among nosocomial isolates of Acinetobacter baumannii from a tertiary referral hospital in northern India.}, journal = {International journal of antimicrobial agents}, volume = {41}, number = {5}, pages = {452-456}, doi = {10.1016/j.ijantimicag.2013.01.007}, pmid = {23434534}, issn = {1872-7913}, mesh = {Acinetobacter Infections/*epidemiology/microbiology ; Acinetobacter baumannii/classification/*enzymology/genetics/isolation &amp; purification ; Adolescent ; Adult ; Aged ; Aged, 80 and over ; Anti-Bacterial Agents/*pharmacology ; Child ; Child, Preschool ; Cross Infection/*epidemiology/microbiology ; *Drug Resistance, Bacterial ; Female ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; India/epidemiology ; Infant ; Infant, Newborn ; Male ; Microbial Sensitivity Tests ; Middle Aged ; Molecular Epidemiology ; Molecular Typing ; Polymerase Chain Reaction ; Tertiary Care Centers ; Transformation, Bacterial ; Young Adult ; beta-Lactamases/genetics/*metabolism ; }, abstract = {The aim of this study was to evaluate the emergence of blaNDM-1 among clinical isolates of Acinetobacter baumannii isolated from a north Indian tertiary care hospital and to assess the gene cassettes and resistance determinants located within them. In total, 74 A. baumannii were screened for MBL production by the imipenem-EDTA method and were characterised for antibiotic sensitivity. PCR was performed to detect the presence of blaNDM and the co-existence of ESBL and AmpC genes. NDM-producing isolates were typed by ERIC-PCR, and the association of integrons with blaNDM-1 and the presence of gene cassettes were determined using specific primers. The genetic location of blaNDM in ISAba125 was also determined. Transformation was performed using a heat-shock method. Three isolates were found to harbour blaNDM, all of which co-produced blaEBC, blaDHA and blaCIT AmpC β-lactamases. All MBL-producers showed resistance to cephalosporins, carbapenems, aminoglycosides, fluoroquinolones and tigecycline but were susceptible to polymyxin B. Presence of class 1 integrons was demonstrated in all three blaNDM-harbouring isolates, whilst linkage between the integron and blaNDM could not be established. Detection of gene cassettes revealed the presence of dihydrofolate reductase (dhfr) and aminoglycoside 6'-N-acetyltransferase [aac(6')] genes. Presence of blaNDM in ISAba125 was also observed. These findings suggest that ISAba125 appears to be the main genetic component for dissemination of blaNDM in A. baumannii. The association of blaNDM-1 with ISAba125 and the mobility of other multiresistance region (gene cassette)-carrying integrons provide an easy way to cross species barriers and reach a level that places the patients at risk.}, }
@article {pmid23431381, year = {2013}, author = {Chang, S and Wang, Y and Lu, J and Gai, J and Li, J and Chu, P and Guan, R and Zhao, T}, title = {The mitochondrial genome of soybean reveals complex genome structures and gene evolution at intercellular and phylogenetic levels.}, journal = {PloS one}, volume = {8}, number = {2}, pages = {e56502}, pmid = {23431381}, issn = {1932-6203}, mesh = {Cell Nucleus/metabolism ; Chloroplasts/genetics ; Chromosome Mapping ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, Mitochondrial ; *Genes, Plant ; Genome, Mitochondrial ; Models, Genetic ; Phylogeny ; Repetitive Sequences, Nucleic Acid ; Sequence Analysis, DNA ; Glycine max/cytology/*genetics ; }, abstract = {Determining mitochondrial genomes is important for elucidating vital activities of seed plants. Mitochondrial genomes are specific to each plant species because of their variable size, complex structures and patterns of gene losses and gains during evolution. This complexity has made research on the soybean mitochondrial genome difficult compared with its nuclear and chloroplast genomes. The present study helps to solve a 30-year mystery regarding the most complex mitochondrial genome structure, showing that pairwise rearrangements among the many large repeats may produce an enriched molecular pool of 760 circles in seed plants. The soybean mitochondrial genome harbors 58 genes of known function in addition to 52 predicted open reading frames of unknown function. The genome contains sequences of multiple identifiable origins, including 6.8 kb and 7.1 kb DNA fragments that have been transferred from the nuclear and chloroplast genomes, respectively, and some horizontal DNA transfers. The soybean mitochondrial genome has lost 16 genes, including nine protein-coding genes and seven tRNA genes; however, it has acquired five chloroplast-derived genes during evolution. Four tRNA genes, common among the three genomes, are derived from the chloroplast. Sizeable DNA transfers to the nucleus, with pericentromeric regions as hotspots, are observed, including DNA transfers of 125.0 kb and 151.6 kb identified unambiguously from the soybean mitochondrial and chloroplast genomes, respectively. The soybean nuclear genome has acquired five genes from its mitochondrial genome. These results provide biological insights into the mitochondrial genome of seed plants, and are especially helpful for deciphering vital activities in soybean.}, }
@article {pmid23425243, year = {2013}, author = {Zhang, Y and Fernandez-Aparicio, M and Wafula, EK and Das, M and Jiao, Y and Wickett, NJ and Honaas, LA and Ralph, PE and Wojciechowski, MF and Timko, MP and Yoder, JI and Westwood, JH and Depamphilis, CW}, title = {Evolution of a horizontally acquired legume gene, albumin 1, in the parasitic plant Phelipanche aegyptiaca and related species.}, journal = {BMC evolutionary biology}, volume = {13}, number = {}, pages = {48}, pmid = {23425243}, issn = {1471-2148}, mesh = {Amino Acid Sequence ; Bayes Theorem ; Cystine-Knot Miniproteins/*genetics ; DNA, Plant/genetics ; *Evolution, Molecular ; Fabaceae/genetics ; Gene Duplication ; *Gene Transfer, Horizontal ; *Genes, Plant ; Likelihood Functions ; Molecular Sequence Data ; Orobanchaceae/*genetics ; Phylogeny ; Protein Structure, Tertiary ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Parasitic plants, represented by several thousand species of angiosperms, use modified structures known as haustoria to tap into photosynthetic host plants and extract nutrients and water. As a result of their direct plant-plant connections with their host plant, parasitic plants have special opportunities for horizontal gene transfer, the nonsexual transmission of genetic material across species boundaries. There is increasing evidence that parasitic plants have served as recipients and donors of horizontal gene transfer (HGT), but the long-term impacts of eukaryotic HGT in parasitic plants are largely unknown.<br><br>RESULTS: Here we show that a gene encoding albumin 1 KNOTTIN-like protein, closely related to the albumin 1 genes only known from papilionoid legumes, where they serve dual roles as food storage and insect toxin, was found in Phelipanche aegyptiaca and related parasitic species of family Orobanchaceae, and was likely acquired by a Phelipanche ancestor via HGT from a legume host based on phylogenetic analyses. The KNOTTINs are well known for their unique "disulfide through disulfide knot" structure and have been extensively studied in various contexts, including drug design. Genomic sequences from nine related parasite species were obtained, and 3D protein structure simulation tests and evolutionary constraint analyses were performed. The parasite gene we identified here retains the intron structure, six highly conserved cysteine residues necessary to form a KNOTTIN protein, and displays levels of purifying selection like those seen in legumes. The albumin 1 xenogene has evolved through >150 speciation events over ca. 16 million years, forming a small family of differentially expressed genes that may confer novel functions in the parasites. Moreover, further data show that a distantly related parasitic plant, Cuscuta, obtained two copies of albumin 1 KNOTTIN-like genes from legumes through a separate HGT event, suggesting that legume KNOTTIN structures have been repeatedly co-opted by parasitic plants.<br><br>CONCLUSIONS: The HGT-derived albumins in Phelipanche represent a novel example of how plants can acquire genes from other plants via HGT that then go on to duplicate, evolve, and retain the specialized features required to perform a unique host-derived function.}, }
@article {pmid23422322, year = {2013}, author = {Norais, C and Moisan, A and Gaspin, C and Clouet-d'Orval, B}, title = {Diversity of CRISPR systems in the euryarchaeal Pyrococcales.}, journal = {RNA biology}, volume = {10}, number = {5}, pages = {659-670}, pmid = {23422322}, issn = {1555-8584}, mesh = {Archaeal Viruses/genetics/physiology ; *CRISPR-Cas Systems ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Gene Expression Regulation, Archaeal ; Gene Transfer, Horizontal ; Genome, Archaeal ; Phylogeny ; Pyrococcus abyssi/*genetics/*virology ; Thermococcales/*genetics/*virology ; }, abstract = {Pyrococcales are members of the order Thermococcales, a group of hyperthermophilic euryarchaea that are frequently found in deep sea hydrothermal vents. Infectious genetic elements, such as plasmids and viruses, remain a threat even in this remote environment and these microorganisms have developed several ways to fight their genetic invaders. Among these are the recently discovered CRISPR systems. In this review, we have combined and condensed available information on genetic elements infecting the Thermococcales and on the multiple CRISPR systems found in the Pyrococcales to fight them. Their organization and mode of action will be presented with emphasis on the Type III-B system that is the only CRISPR system known to target RNA molecules in a process reminiscent of RNA interference. The intriguing case of Pyrococcus abyssi, which is among the rare strains to present a CRISPR system devoid of the universal cas1 and cas2 genes, is also discussed.}, }
@article {pmid23416362, year = {2013}, author = {Villarreal, JC and Forrest, LL and Wickett, N and Goffinet, B}, title = {The plastid genome of the hornwort Nothoceros aenigmaticus (Dendrocerotaceae): phylogenetic signal in inverted repeat expansion, pseudogenization, and intron gain.}, journal = {American journal of botany}, volume = {100}, number = {3}, pages = {467-477}, doi = {10.3732/ajb.1200429}, pmid = {23416362}, issn = {1537-2197}, mesh = {Anthocerotophyta/*genetics ; Base Sequence ; Genes, Plant/genetics ; Genome, Plastid/*genetics ; Introns/*genetics ; Inverted Repeat Sequences/*genetics ; Molecular Sequence Data ; *Phylogeny ; Plant Proteins/genetics/metabolism ; Pseudogenes/*genetics ; Sequence Alignment ; }, abstract = {PREMISE OF THE STUDY: The previously sequenced plastome of the hornwort Anthoceros angustus differs from that of other bryophytes by an expanded inverted repeat (IR) and the presence of a type I intron in the 23S ribosomal RNA (rrn23) gene. We assembled the plastome of the hornwort Nothoceros aenigmaticus, contrasted its architecture to that of other bryophytes, and assessed the phylogenetic significance of genomic characters in hornwort evolution. •<br><br>METHODS: The Nothoceros plastome was reconstructed from shotgun sequencing of genomic DNA. Comparison with the Anthoceros plastome revealed three structural differences. We sequenced these regions in taxa spanning the hornwort phylogeny. &#x2022;<br><br>KEY RESULTS: The Nothoceros plastome is colinear with other bryophyte plastomes, but differs from the Anthoceros plastome by several gene regions located within the IR in Anthoceros being in the large single-copy region in Nothoceros, by the rrn23 gene lacking an intron, and by the rpl2 being a pseudogene. Comparisons across the hornwort phylogeny indicate that the first two characters are restricted to Anthocerotaceae, while rpl2 pseudogenization diagnoses the sister lineage to Anthocerotaceae. &#x2022;<br><br>CONCLUSIONS: The Nothoceros plastome is structurally similar to that of most bryophytes. However, we identified more structural differences within hornworts than have been described within either the mosses or the liverworts. The distribution of the gene duplication involving the IR and an intron in the rrn23 gene are restricted to Anthocerotaceae. Occurrence of the intron and the conserved intron sequence between Anthoceros and distantly related chlorophyte algae may be due to horizontal gene transfer.}, }
@article {pmid23412141, year = {2013}, author = {Zarei, M and Sclavi, B and Cosentino Lagomarsino, M}, title = {Gene silencing and large-scale domain structure of the E. coli genome.}, journal = {Molecular bioSystems}, volume = {9}, number = {4}, pages = {758-767}, doi = {10.1039/c3mb25364c}, pmid = {23412141}, issn = {1742-2051}, mesh = {Bacterial Proteins/metabolism ; Binding Sites ; Chromosome Mapping ; DNA-Binding Proteins/metabolism ; Escherichia coli/*genetics/metabolism ; Gene Expression Regulation, Bacterial ; *Gene Silencing ; *Genome, Bacterial ; Protein Binding ; }, abstract = {The H-NS chromosome-organizing protein in E. coli can stabilize genomic DNA loops, and form oligomeric structures connected to repression of gene expression. Motivated by the link between chromosome organization, protein binding and gene expression, we analyzed publicly available genomic data sets of various origins, from genome-wide protein binding profiles to evolutionary information, exploring the connections between chromosomal organization, gene-silencing, pseudo-gene localization and horizontal gene transfer. We report the existence of transcriptionally silent contiguous areas corresponding to large regions of H-NS protein binding along the genome, their position indicates a possible relationship with the known large-scale features of chromosome organization.}, }
@article {pmid23408797, year = {2013}, author = {Cheng, L and Connor, TR and Sirén, J and Aanensen, DM and Corander, J}, title = {Hierarchical and spatially explicit clustering of DNA sequences with BAPS software.}, journal = {Molecular biology and evolution}, volume = {30}, number = {5}, pages = {1224-1228}, pmid = {23408797}, issn = {1537-1719}, mesh = {Bayes Theorem ; Borrelia burgdorferi/classification/genetics ; *Evolution, Molecular ; Genetics, Population ; Sequence Analysis, DNA/methods ; *Software ; }, abstract = {Phylogeographical analyses have become commonplace for a myriad of organisms with the advent of cheap DNA sequencing technologies. Bayesian model-based clustering is a powerful tool for detecting important patterns in such data and can be used to decipher even quite subtle signals of systematic differences in molecular variation. Here, we introduce two upgrades to the Bayesian Analysis of Population Structure (BAPS) software, which enable 1) spatially explicit modeling of variation in DNA sequences and 2) hierarchical clustering of DNA sequence data to reveal nested genetic population structures. We provide a direct interface to map the results from spatial clustering with Google Maps using the portal http://www.spatialepidemiology.net/ and illustrate this approach using sequence data from Borrelia burgdorferi. The usefulness of hierarchical clustering is demonstrated through an analysis of the metapopulation structure within a bacterial population experiencing a high level of local horizontal gene transfer. The tools that are introduced are freely available at http://www.helsinki.fi/bsg/software/BAPS/.}, }
@article {pmid23407828, year = {2013}, author = {Marron, AO and Alston, MJ and Heavens, D and Akam, M and Caccamo, M and Holland, PW and Walker, G}, title = {A family of diatom-like silicon transporters in the siliceous loricate choanoflagellates.}, journal = {Proceedings. Biological sciences}, volume = {280}, number = {1756}, pages = {20122543}, pmid = {23407828}, issn = {1471-2954}, support = {BB/E527604/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; CCC-1-10//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Biological Transport/genetics ; Carrier Proteins/*genetics/*metabolism ; Choanoflagellata/genetics/*metabolism ; Conserved Sequence ; Diatoms/metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Amino Acid ; Silicon/*metabolism ; }, abstract = {Biosilicification is widespread across the eukaryotes and requires concentration of silicon in intracellular vesicles. Knowledge of the molecular mechanisms underlying this process remains limited, with unrelated silicon-transporting proteins found in the eukaryotic clades previously studied. Here, we report the identification of silicon transporter (SIT)-type genes from the siliceous loricate choanoflagellates Stephanoeca diplocostata and Diaphanoeca grandis. Until now, the SIT gene family has been identified only in diatoms and other siliceous stramenopiles, which are distantly related to choanoflagellates among the eukaryotes. This is the first evidence of similarity between SITs from different eukaryotic supergroups. Phylogenetic analysis indicates that choanoflagellate and stramenopile SITs form distinct monophyletic groups. The absence of putative SIT genes in any other eukaryotic groups, including non-siliceous choanoflagellates, leads us to propose that SIT genes underwent a lateral gene transfer event between stramenopiles and loricate choanoflagellates. We suggest that the incorporation of a foreign SIT gene into the stramenopile or choanoflagellate genome resulted in a major metabolic change: the acquisition of biomineralized silica structures. This hypothesis implies that biosilicification has evolved multiple times independently in the eukaryotes, and paves the way for a better understanding of the biochemical basis of silicon transport through identification of conserved sequence motifs.}, }
@article {pmid23405862, year = {2013}, author = {Da Lage, JL and Binder, M and Hua-Van, A and Janeček, S and Casane, D}, title = {Gene make-up: rapid and massive intron gains after horizontal transfer of a bacterial α-amylase gene to Basidiomycetes.}, journal = {BMC evolutionary biology}, volume = {13}, number = {}, pages = {40}, pmid = {23405862}, issn = {1471-2148}, mesh = {Basidiomycota/*genetics ; Bayes Theorem ; Consensus Sequence ; DNA, Fungal/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Genome, Fungal ; *Introns ; RNA Splicing ; Sequence Analysis, DNA ; alpha-Amylases/*genetics ; }, abstract = {BACKGROUND: Increasing genome data show that introns, a hallmark of eukaryotes, already existed at a high density in the last common ancestor of extant eukaryotes. However, intron content is highly variable among species. The tempo of intron gains and losses has been irregular and several factors may explain why some genomes are intron-poor whereas other are intron-rich.<br><br>RESULTS: We studied the dynamics of intron gains and losses in an &#x3b1;-amylase gene, whose product breaks down starch and other polysaccharides. It was transferred from an Actinobacterium to an ancestor of Agaricomycotina. This gene underwent further duplications in several species. The results indicate a high rate of intron insertions soon after the gene settled in the fungal genome. A number of these oldest introns, regularly scattered along the gene, remained conserved. Subsequent gains and losses were lineage dependent, with a majority of losses. Moreover, a few species exhibited a high number of both specific intron gains and losses in recent periods. There was little sequence conservation around insertion sites, then probably little information for splicing, whereas splicing sites, inside introns, showed typical and conserved patterns. There was little variation of intron size.<br><br>CONCLUSIONS: Since most Basidiomycetes have intron-rich genomes and this richness was ancestral in Fungi, long before the transfer event, we suggest that the new gene was shaped to comply with requirements of the splicing machinery, such as short exon and intron sizes, in order to be correctly processed.}, }
@article {pmid23405135, year = {2013}, author = {Goldenberg, DM and Gold, DV and Loo, M and Liu, D and Chang, CH and Jaffe, ES}, title = {Horizontal transmission of malignancy: in-vivo fusion of human lymphomas with hamster stroma produces tumors retaining human genes and lymphoid pathology.}, journal = {PloS one}, volume = {8}, number = {2}, pages = {e55324}, pmid = {23405135}, issn = {1932-6203}, support = {CA11327/CA/NCI NIH HHS/United States ; //Intramural NIH HHS/United States ; }, mesh = {Animals ; B-Lymphocytes/metabolism ; Cell Fusion/methods ; Cell Line, Tumor ; Cricetinae ; Disease Models, Animal ; Disease Progression ; Gene Transfer Techniques ; *Gene Transfer, Horizontal ; Hodgkin Disease/*genetics/metabolism ; Humans ; Mesocricetus ; Stromal Cells/metabolism ; }, abstract = {We report the in-vivo fusion of two Hodgkin lymphomas with golden hamster cheek pouch cells, resulting in serially-transplanted (over 5-6 years) GW-532 and GW-584 heterosynkaryon tumor cells displaying both human and hamster DNA (by FISH), lymphoma-like morphology, aggressive metastasis, and retention of 7 human genes (CD74, CXCR4, CD19, CD20, CD71, CD79b, and VIM) out of 24 tested by PCR. The prevalence of B-cell restricted genes (CD19, CD20, and CD79b) suggests that this uniform population may be the clonal initiating (malignant) cells of Hodgkin lymphoma, despite their not showing translation to their respective proteins by immunohistochemical analysis. This is believed to be the first report of in-vivo cell-cell fusion of human lymphoma and rodent host cells, and may be a method to disclose genes regulating both organoid and metastasis signatures, suggesting that the horizontal transfer of tumor DNA to adjacent stromal cells may be implicated in tumor heterogeneity and progression. The B-cell gene signature of the hybrid xenografts suggests that Hodgkin lymphoma, or its initiating cells, is a B-cell malignancy.}, }
@article {pmid23402892, year = {2013}, author = {Bai, J and Liu, Q and Yang, Y and Wang, J and Yang, Y and Li, J and Li, P and Li, X and Xi, Y and Ying, J and Ren, P and Yang, L and Ni, L and Wu, J and Bao, Q and Zhou, T}, title = {Insights into the evolution of gene organization and multidrug resistance from Klebsiella pneumoniae plasmid pKF3-140.}, journal = {Gene}, volume = {519}, number = {1}, pages = {60-66}, doi = {10.1016/j.gene.2013.01.050}, pmid = {23402892}, issn = {1879-0038}, mesh = {Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/drug effects/genetics ; *Evolution, Molecular ; Genes, Bacterial ; Klebsiella pneumoniae/*drug effects/*genetics ; Microbial Sensitivity Tests ; Plasmids/*genetics ; Salmonella enterica/drug effects/genetics ; Tetracycline/pharmacology ; }, abstract = {Plasmid-mediated transfer of drug-resistance genes among various bacterial species is considered one of the most important mechanisms for the spread of multidrug resistance. To gain insights into the evolution of gene organization and antimicrobial resistance in clinical bacterial samples, a complete plasmid genome of Klebsiella pneumoniae pKF3-140 is determined, which has a circular chromosome of 147,416bp in length. Among the 203 predicted genes, 142 have function assignment and about 50 appear to be involved in plasmid replication, maintenance, conjugative transfer, iron acquisition and transport, and drug resistance. Extensive comparative genomic analyses revealed that pKF3-140 exhibits a rather low sequence similarity and structural conservation with other reported K. pneumoniae plasmids. In contrast, the overall organization of pKF3-140 is highly similar to Escherichia coli plasmids p1ESCUM and pUTI89, which indicates the possibility that K. pneumoniae pKF3-140 may have a potential origin in E. coli. Meanwhile, interestingly, several drug resistant genes show high similarity to the plasmid pU302L in Salmonella enterica serovar Typhimurium U302 strain G8430 and the plasmid pK245 in K. pneumoniae. This mosaic pattern of sequence similarities suggests that pKF3-140 might have arisen from E. coli and acquired the resistance genes from a variety of enteric bacteria and underscores the importance of a further understanding of horizontal gene transfer among enteric bacteria.}, }
@article {pmid23398820, year = {2013}, author = {Kishore, SP and Stiller, JW and Deitsch, KW}, title = {Horizontal gene transfer of epigenetic machinery and evolution of parasitism in the malaria parasite Plasmodium falciparum and other apicomplexans.}, journal = {BMC evolutionary biology}, volume = {13}, number = {}, pages = {37}, pmid = {23398820}, issn = {1471-2148}, support = {R01 AI052390/AI/NIAID NIH HHS/United States ; T32 GM007739/GM/NIGMS NIH HHS/United States ; AI 52390/AI/NIAID NIH HHS/United States ; GM07739/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Apicomplexa/*genetics ; Bayes Theorem ; *Biological Evolution ; DNA, Protozoan/genetics ; Dictyostelium/genetics ; *Gene Transfer, Horizontal ; Histone Methyltransferases ; Histone-Lysine N-Methyltransferase/genetics ; Likelihood Functions ; Nematoda/genetics ; Parasites/genetics ; Phylogeny ; Plasmodium falciparum/*genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The acquisition of complex transcriptional regulatory abilities and epigenetic machinery facilitated the transition of the ancestor of apicomplexans from a free-living organism to an obligate parasite. The ability to control sophisticated gene expression patterns enabled these ancient organisms to evolve several differentiated forms, invade multiple hosts and evade host immunity. How these abilities were acquired remains an outstanding question in protistan biology.<br><br>RESULTS: In this work, we study SET domain bearing genes that are implicated in mediating immune evasion, invasion and cytoadhesion pathways of modern apicomplexans, including malaria parasites. We provide the first conclusive evidence of a horizontal gene transfer of a Histone H4 Lysine 20 (H4K20) modifier, Set8, from an animal host to the ancestor of apicomplexans. Set8 is known to contribute to the coordinated expression of genes involved in immune evasion in modern apicomplexans. We also show the likely transfer of a H3K36 methyltransferase (Ashr3 from plants), possibly derived from algal endosymbionts. These transfers appear to date to the transition from free-living organisms to parasitism and coincide with the proposed horizontal acquisition of cytoadhesion domains, the O-glycosyltransferase that modifies these domains, and the primary family of transcription factors found in apicomplexan parasites. Notably, phylogenetic support for these conclusions is robust and the genes clearly are dissimilar to SET sequences found in the closely related parasite Perkinsus marinus, and in ciliates, the nearest free-living organisms with complete genome sequences available.<br><br>CONCLUSIONS: Animal and plant sources of epigenetic machinery provide new insights into the evolution of parasitism in apicomplexans. Along with the horizontal transfer of cytoadhesive domains, O-linked glycosylation and key transcription factors, the acquisition of SET domain methyltransferases marks a key transitional event in the evolution to parasitism in this important protozoan lineage.}, }
@article {pmid23397242, year = {2013}, author = {Gabriško, M}, title = {Evolutionary history of eukaryotic α-glucosidases from the α-amylase family.}, journal = {Journal of molecular evolution}, volume = {76}, number = {3}, pages = {129-145}, pmid = {23397242}, issn = {1432-1432}, mesh = {Aedes/enzymology/genetics ; Animals ; Anopheles/enzymology/genetics ; Culex/enzymology/genetics ; Eukaryota/enzymology/*genetics ; *Evolution, Molecular ; Fungi/enzymology/genetics ; Hymenoptera/enzymology/genetics ; Multigene Family/genetics ; Phylogeny ; Sequence Analysis, DNA ; alpha-Amylases/*genetics ; alpha-Glucosidases/*genetics ; }, abstract = {Although some α-glucosidases from the α-amylase family (glycoside hydrolase family GH13) have been studied extensively, their exact number, organization on the chromosome, and orthology/paralogy relationship were unknown. This was true even for important disease vectors where gut α-glucosidase is known to be receptor for the Bin toxin used to control the population of some mosquito species. In some cases orthologs from related species were studied intensively, while potentially important paralogs were omitted. We have, therefore, used a bioinformatics approach to identify all family GH13 α-glucosidases from the selected species from Metazoa (including three mosquito species: Aedes aegypti, Anopheles gambiae, and Culex quinquefasciatus) as well as from Fungi in an effort to characterize their arrangement on the chromosome and evolutionary relationships among orthologs and among paralogs. We also searched for pseudogenes and genes coding for enzymatically inactive proteins with a possible new function. We have found GH13 α-glucosidases mostly in Arthropoda and Fungi where they form gene families, as a result of multiple lineage-specific gene duplications. In mosquito species we have identified 14 α-glucosidase (Aglu) genes of which only five have been biochemically characterized so far, two are putative pseudogenes and the rest remains uncharacterized. We also revealed quite a complex evolutionary history of the eukaryotic α-glucosidases probably involving multiple losses of genes or horizontal gene transfer from bacteria.}, }
@article {pmid23397241, year = {2013}, author = {Ramírez, MS and Vilacoba, E and Stietz, MS and Merkier, AK and Jeric, P and Limansky, AS and Márquez, C and Bello, H and Catalano, M and Centrón, D}, title = {Spreading of AbaR-type genomic islands in multidrug resistance Acinetobacter baumannii strains belonging to different clonal complexes.}, journal = {Current microbiology}, volume = {67}, number = {1}, pages = {9-14}, pmid = {23397241}, issn = {1432-0991}, mesh = {Acinetobacter baumannii/*classification/drug effects/*genetics/isolation &amp; purification ; Anti-Bacterial Agents/*pharmacology ; Argentina ; Chile ; Cluster Analysis ; Cross Infection/microbiology ; Drug Resistance, Multiple, Bacterial ; Gene Transfer, Horizontal ; *Genomic Islands ; Genotype ; Hospitals ; Humans ; Multilocus Sequence Typing ; Uruguay ; }, abstract = {In order to determine the occurrence of AbaR-type genomic island in multidrug resistant Acinetobacter baumannii (MDRAb) strains circulating in Argentina, Uruguay, and Chile, we studied 51 MDRAb isolates recovered from several hospitals over 30 years. AbaR-type genomic resistance islands were found in 36 MDRAb isolates since 1986 till now. MLST technique allowed us to identify the presence of four different Clonal Complexes (109, 104, 119, 113) among the positive AbaR-type island positive strains. This is the first description of AbaR-type islands in the CC104 and CC113 that are the most widespread Clonal Complexes in Argentina. In addition, PCR mapping exposed different arrays to those previously described, evidencing the plasticity of this island. Our results evidence a widespread distribution of the AbaR-type genomic islands along the time in the MDRAb population, including the epidemic global clone 1 (GC1) as well as different clonal complexes to those already described in the literature.}, }
@article {pmid23396335, year = {2013}, author = {Boldareva-Nuianzina, EN and Bláhová, Z and Sobotka, R and Koblízek, M}, title = {Distribution and origin of oxygen-dependent and oxygen-independent forms of Mg-protoporphyrin monomethylester cyclase among phototrophic proteobacteria.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {8}, pages = {2596-2604}, pmid = {23396335}, issn = {1098-5336}, mesh = {Bacterial Proteins/analysis/chemistry/*genetics ; Cyanobacteria/enzymology/genetics ; Genome, Bacterial ; Oxygen/metabolism ; Oxygenases/*analysis/chemistry/*genetics ; Photosynthesis/genetics ; Phylogeny ; Protein Isoforms/analysis/chemistry/genetics ; Proteobacteria/*enzymology/genetics/metabolism ; }, abstract = {Magnesium-protoporphyrin IX monomethylester cyclase is one of the key enzymes of the bacteriochlorophyll biosynthesis pathway. There exist two fundamentally different forms of this enzyme. The oxygen-dependent form, encoded by the gene acsF, catalyzes the formation of the bacteriochlorophyll fifth ring using oxygen, whereas the oxygen-independent form encoded by the gene bchE utilizes an oxygen atom extracted from water. The presence of acsF and bchE genes was surveyed in various phototrophic Proteobacteria using the available genomic data and newly designed degenerated primers. It was found that while the majority of purple nonsulfur bacteria contained both forms of the cyclase, the purple sulfur bacteria contained only the oxygen-independent form. All tested species of aerobic anoxygenic phototrophs contained acsF genes, but some of them also retained the bchE gene. In contrast to bchE phylogeny, the acsF phylogeny was in good agreement with 16S inferred phylogeny. Moreover, the survey of the genome data documented that the acsF gene occupies a conserved position inside the photosynthesis gene cluster, whereas the bchE location in the genome varied largely between the species. This suggests that the oxygen-dependent cyclase was recruited by purple phototrophic bacteria very early during their evolution. The primary sequence and immunochemical similarity with its cyanobacterial counterparts suggests that acsF may have been acquired by Proteobacteria via horizontal gene transfer from cyanobacteria. The acquisition of the gene allowed purple nonsulfur phototrophic bacteria to proliferate in the mildly oxygenated conditions of the Proterozoic era.}, }
@article {pmid23396083, year = {2013}, author = {Rizzo, L and Manaia, C and Merlin, C and Schwartz, T and Dagot, C and Ploy, MC and Michael, I and Fatta-Kassinos, D}, title = {Urban wastewater treatment plants as hotspots for antibiotic resistant bacteria and genes spread into the environment: a review.}, journal = {The Science of the total environment}, volume = {447}, number = {}, pages = {345-360}, doi = {10.1016/j.scitotenv.2013.01.032}, pmid = {23396083}, issn = {1879-1026}, mesh = {Animals ; Bacteria/*drug effects/*genetics ; Disinfection/methods ; Drug Resistance, Bacterial/*genetics ; Drug Resistance, Microbial/*genetics ; Environment ; Environmental Monitoring ; Gene Transfer, Horizontal ; *Genes, Bacterial/drug effects ; Humans ; Risk Factors ; Urbanization ; Waste Disposal, Fluid/*methods ; Wastewater/*microbiology ; }, abstract = {Urban wastewater treatment plants (UWTPs) are among the main sources of antibiotics' release into the environment. The occurrence of antibiotics may promote the selection of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB), which shade health risks to humans and animals. In this paper the fate of ARB and ARGs in UWTPs, focusing on different processes/technologies (i.e., biological processes, advanced treatment technologies and disinfection), was critically reviewed. The mechanisms by which biological processes influence the development/selection of ARB and ARGs transfer are still poorly understood. Advanced treatment technologies and disinfection process are regarded as a major tool to control the spread of ARB into the environment. In spite of intense efforts made over the last years to bring solutions to control antibiotic resistance spread in the environment, there are still important gaps to fill in. In particular, it is important to: (i) improve risk assessment studies in order to allow accurate estimates about the maximal abundance of ARB in UWTPs effluents that would not pose risks for human and environmental health; (ii) understand the factors and mechanisms that drive antibiotic resistance maintenance and selection in wastewater habitats. The final objective is to implement wastewater treatment technologies capable of assuring the production of UWTPs effluents with an acceptable level of ARB.}, }
@article {pmid23395351, year = {2013}, author = {Gilmore, MS and Lebreton, F and van Schaik, W}, title = {Genomic transition of enterococci from gut commensals to leading causes of multidrug-resistant hospital infection in the antibiotic era.}, journal = {Current opinion in microbiology}, volume = {16}, number = {1}, pages = {10-16}, pmid = {23395351}, issn = {1879-0364}, support = {P01 AI083214/AI/NIAID NIH HHS/United States ; R01 AI072360/AI/NIAID NIH HHS/United States ; AI072360/AI/NIAID NIH HHS/United States ; AI083214/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Carrier State/*microbiology ; Cross Infection/*microbiology ; *Drug Resistance, Multiple, Bacterial ; Enterococcus/genetics/*pathogenicity/*physiology ; Evolution, Molecular ; Gastrointestinal Tract/*microbiology ; Gene Transfer, Horizontal ; Gram-Positive Bacterial Infections/*microbiology ; Humans ; Interspersed Repetitive Sequences ; Virulence Factors/genetics ; }, abstract = {The enterococci evolved over eons as highly adapted members of gastrointestinal consortia of a wide variety of hosts, but for reasons that are not entirely clear, emerged in the 1970s as leading causes of multidrug resistant hospital infection. Hospital-adapted pathogenic isolates are characterized by the presence of multiple mobile elements conferring antibiotic resistance, as well as pathogenicity islands, capsule loci and other variable traits. Enterococci may have been primed to emerge among the vanguard of antibiotic resistant strains because of their occurrence in the GI tracts of insects and simple organisms living and feeding on organic matter that is colonized by antibiotic resistant, antibiotic producing micro-organisms. In response to the opportunity to inhabit a new niche--the antibiotic treated hospital patient--the enterococcal genome is evolving in a pattern characteristic of other bacteria that have emerged as pathogens because of opportunities stemming from anthropogenic change.}, }
@article {pmid23395305, year = {2013}, author = {Seiffert, SN and Hilty, M and Perreten, V and Endimiani, A}, title = {Extended-spectrum cephalosporin-resistant Gram-negative organisms in livestock: an emerging problem for human health?.}, journal = {Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy}, volume = {16}, number = {1-2}, pages = {22-45}, doi = {10.1016/j.drup.2012.12.001}, pmid = {23395305}, issn = {1532-2084}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Cattle ; Cephalosporins/*pharmacology ; Disease Reservoirs/microbiology/*veterinary ; Europe/epidemiology ; Gene Transfer, Horizontal ; Gram-Negative Bacteria/drug effects/enzymology/genetics ; Gram-Negative Bacterial Infections/drug therapy/epidemiology/transmission/*veterinary ; Humans ; Poultry/microbiology ; Prevalence ; Swine/microbiology ; beta-Lactam Resistance/drug effects/*genetics ; beta-Lactamases/*genetics/metabolism ; }, abstract = {Escherichia coli, Salmonella spp. and Acinetobacter spp. are important human pathogens. Serious infections due to these organisms are usually treated with extended-spectrum cephalosporins (ESCs). However, in the past two decades we have faced a rapid increasing of infections and colonization caused by ESC-resistant (ESC-R) isolates due to production of extended-spectrum-β-lactamases (ESBLs), plasmid-mediated AmpCs (pAmpCs) and/or carbapenemase enzymes. This situation limits drastically our therapeutic armamentarium and puts under peril the human health. Animals are considered as potential reservoirs of multidrug-resistant (MDR) Gram-negative organisms. The massive and indiscriminate use of antibiotics in veterinary medicine has contributed to the selection of ESC-R E. coli, ESC-R Salmonella spp. and, to less extent, MDR Acinetobacter spp. among animals, food, and environment. This complex scenario is responsible for the expansion of these MDR organisms which may have life-threatening clinical significance. Nowadays, the prevalence of food-producing animals carrying ESC-R E. coli and ESC-R Salmonella (especially those producing CTX-M-type ESBLs and the CMY-2 pAmpC) has reached worryingly high values. More recently, the appearance of carbapenem-resistant isolates (i.e., VIM-1-producing Enterobacteriaceae and NDM-1 or OXA-23-producing Acinetobacter spp.) in livestock has even drawn greater concerns. In this review, we describe the aspects related to the spread of the above MDR organisms among pigs, cattle, and poultry, focusing on epidemiology, molecular mechanisms of resistance, impact of antibiotic use, and strategies to contain the overall problem. The link and the impact of ESC-R organisms of livestock origin for the human scenario are also discussed.}, }
@article {pmid23391387, year = {2013}, author = {Davis, BM and Waldor, MK}, title = {Horizontal gene transfer: linking sex and cell fate.}, journal = {Current biology : CB}, volume = {23}, number = {3}, pages = {R118-9}, doi = {10.1016/j.cub.2012.12.035}, pmid = {23391387}, issn = {1879-0445}, mesh = {DNA, Bacterial/*physiology ; *Gene Transfer, Horizontal ; Pseudomonas aeruginosa/*physiology ; }, abstract = {Integrative conjugative elements (ICEs) enable horizontal gene transfer among bacteria. In Pseudomonas, only a phenotypically distinct subpopulation of ICE-bearing cells can mobilize ICE DNA to new hosts. Transfer competence is a terminal state; division is limited, and many cells lyse.}, }
@article {pmid23391036, year = {2013}, author = {Dwivedi, B and Xue, B and Lundin, D and Edwards, RA and Breitbart, M}, title = {A bioinformatic analysis of ribonucleotide reductase genes in phage genomes and metagenomes.}, journal = {BMC evolutionary biology}, volume = {13}, number = {}, pages = {33}, pmid = {23391036}, issn = {1471-2148}, mesh = {Bacteria/virology ; Bacteriophages/classification/*enzymology/genetics ; Base Sequence ; Databases, Genetic ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Viral ; Genomics ; *Metagenome ; Phylogeny ; Ribonucleotide Reductases/*genetics ; Viral Proteins/*genetics ; }, abstract = {BACKGROUND: Ribonucleotide reductase (RNR), the enzyme responsible for the formation of deoxyribonucleotides from ribonucleotides, is found in all domains of life and many viral genomes. RNRs are also amongst the most abundant genes identified in environmental metagenomes. This study focused on understanding the distribution, diversity, and evolution of RNRs in phages (viruses that infect bacteria). Hidden Markov Model profiles were used to analyze the proteins encoded by 685 completely sequenced double-stranded DNA phages and 22 environmental viral metagenomes to identify RNR homologs in cultured phages and uncultured viral communities, respectively.<br><br>RESULTS: RNRs were identified in 128 phage genomes, nearly tripling the number of phages known to encode RNRs. Class I RNR was the most common RNR class observed in phages (70%), followed by class II (29%) and class III (28%). Twenty-eight percent of the phages contained genes belonging to multiple RNR classes. RNR class distribution varied according to phage type, isolation environment, and the host's ability to utilize oxygen. The majority of the phages containing RNRs are Myoviridae (65%), followed by Siphoviridae (30%) and Podoviridae (3%). The phylogeny and genomic organization of phage and host RNRs reveal several distinct evolutionary scenarios involving horizontal gene transfer, co-evolution, and differential selection pressure. Several putative split RNR genes interrupted by self-splicing introns or inteins were identified, providing further evidence for the role of frequent genetic exchange. Finally, viral metagenomic data indicate that RNRs are prevalent and highly dynamic in uncultured viral communities, necessitating future research to determine the environmental conditions under which RNRs provide a selective advantage.<br><br>CONCLUSIONS: This comprehensive study describes the distribution, diversity, and evolution of RNRs in phage genomes and environmental viral metagenomes. The distinct distributions of specific RNR classes amongst phages, combined with the various evolutionary scenarios predicted from RNR phylogenies suggest multiple inheritance sources and different selective forces for RNRs in phages. This study significantly improves our understanding of phage RNRs, providing insight into the diversity and evolution of this important auxiliary metabolic gene as well as the evolution of phages in response to their bacterial hosts and environments.}, }
@article {pmid23390917, year = {2013}, author = {Sırıken, B}, title = {[Salmonella pathogenicity islands].}, journal = {Mikrobiyoloji bulteni}, volume = {47}, number = {1}, pages = {181-188}, doi = {10.5578/mb.4138}, pmid = {23390917}, issn = {0374-9096}, mesh = {*Genomic Islands ; *Salmonella/classification ; Salmonella Infections/microbiology ; Virulence/genetics ; Virulence Factors/genetics ; }, abstract = {Salmonella species are facultative intracellular pathogenic bacteria. They can invade macrophages, dendritic and epithelial cells. The responsible virulence genes for invasion, survival, and extraintestinal spread are located in Salmonella pathogenicity islands (SPIs). SPIs are thought to be acquired by horizontal gene transfer. Some of the SPIs are conserved throughout the Salmonella genus, and some of them are specific for certain serovars. There are differences between Salmonella serotypes in terms of adaptation to host cell, virulence factors and the resulting infection according to SPA presence and characteristics. The most important Salmonella virulence gene clusters are located in 12 pathogenicity islands. Virulence genes that are involved in the intestinal phase of infection are located in SPI-1 and SPI-2 and the remaining SPIs are required for intracellular survival, fimbrial expression, magnesium and iron uptake, multiple antibiotic resistance and the development of systemic infections. In addition SPIs, Sigma ss (RpoS) factors and adaptive acid tolerance response (ATR) are the other two important virulence factors. RpoS and ATR found in virulent Salmonella strains help the bacteria to survive under inappropriate conditions such as gastric acidity, bile salts, inadequate oxygen concentration, lack of nutrients, antimicrobial peptides, mucus and natural microbiota and also to live in phagosomes or phagolysosomes. This review article summarizes the data related to pathogenicity islands in Salmonella serotypes and some factors which play role in the regulation of virulence genes.}, }
@article {pmid23390535, year = {2013}, author = {Siozios, S and Ioannidis, P and Klasson, L and Andersson, SG and Braig, HR and Bourtzis, K}, title = {The diversity and evolution of Wolbachia ankyrin repeat domain genes.}, journal = {PloS one}, volume = {8}, number = {2}, pages = {e55390}, pmid = {23390535}, issn = {1932-6203}, mesh = {Animals ; Ankyrin Repeat/*genetics ; Ankyrins/chemistry/*genetics ; Bacterial Proteins/chemistry/*genetics ; Bacteriophages/genetics ; Base Sequence ; Drosophila/classification/microbiology ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Variation ; *Genome, Bacterial ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Symbiosis/*genetics ; Wolbachia/classification/*genetics/metabolism ; }, abstract = {Ankyrin repeat domain-encoding genes are common in the eukaryotic and viral domains of life, but they are rare in bacteria, the exception being a few obligate or facultative intracellular Proteobacteria species. Despite having a reduced genome, the arthropod strains of the alphaproteobacterium Wolbachia contain an unusually high number of ankyrin repeat domain-encoding genes ranging from 23 in wMel to 60 in wPip strain. This group of genes has attracted considerable attention for their astonishing large number as well as for the fact that ankyrin proteins are known to participate in protein-protein interactions, suggesting that they play a critical role in the molecular mechanism that determines host-Wolbachia symbiotic interactions. We present a comparative evolutionary analysis of the wMel-related ankyrin repeat domain-encoding genes present in different Drosophila-Wolbachia associations. Our results show that the ankyrin repeat domain-encoding genes change in size by expansion and contraction mediated by short directly repeated sequences. We provide examples of intra-genic recombination events and show that these genes are likely to be horizontally transferred between strains with the aid of bacteriophages. These results confirm previous findings that the Wolbachia genomes are evolutionary mosaics and illustrate the potential that these bacteria have to generate diversity in proteins potentially involved in the symbiotic interactions.}, }
@article {pmid23386843, year = {2013}, author = {Gillings, MR}, title = {Evolutionary consequences of antibiotic use for the resistome, mobilome and microbial pangenome.}, journal = {Frontiers in microbiology}, volume = {4}, number = {}, pages = {4}, pmid = {23386843}, issn = {1664-302X}, abstract = {The widespread use and abuse of antibiotic therapy has evolutionary and ecological consequences, some of which are only just beginning to be examined. One well known consequence is the fixation of mutations and lateral gene transfer (LGT) events that confer antibiotic resistance. Sequential selection events, driven by different classes of antibiotics, have resulted in the assembly of diverse resistance determinants and mobile DNAs into novel genetic elements of ever-growing complexity and flexibility. These novel plasmids, integrons, and genomic islands have now become fixed at high frequency in diverse cell lineages by human antibiotic use. Consequently they can be regarded as xenogenetic pollutants, analogous to xenobiotic compounds, but with the critical distinction that they replicate rather than degrade when released to pollute natural environments. Antibiotics themselves must also be regarded as pollutants, since human production overwhelms natural synthesis, and a major proportion of ingested antibiotic is excreted unchanged into waste streams. Such antibiotic pollutants have non-target effects, raising the general rates of mutation, recombination, and LGT in all the microbiome, and simultaneously providing the selective force to fix such changes. This has the consequence of recruiting more genes into the resistome and mobilome, and of increasing the overlap between these two components of microbial genomes. Thus the human use and environmental release of antibiotics is having second order effects on the microbial world, because these small molecules act as drivers of bacterial evolution. Continued pollution with both xenogenetic elements and the selective agents that fix such elements in populations has potentially adverse consequences for human welfare.}, }
@article {pmid23386723, year = {2013}, author = {Cehovin, A and Simpson, PJ and McDowell, MA and Brown, DR and Noschese, R and Pallett, M and Brady, J and Baldwin, GS and Lea, SM and Matthews, SJ and Pelicic, V}, title = {Specific DNA recognition mediated by a type IV pilin.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {8}, pages = {3065-3070}, pmid = {23386723}, issn = {1091-6490}, support = {100280/WT_/Wellcome Trust/United Kingdom ; MR/J006874/1/MRC_/Medical Research Council/United Kingdom ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Blotting, Western ; Chromatography, Affinity ; DNA, Bacterial/*metabolism ; Electrophoresis, Polyacrylamide Gel ; Fimbriae Proteins/isolation &amp; purification/*metabolism ; Neisseria meningitidis/*genetics ; Nuclear Magnetic Resonance, Biomolecular ; Protein Binding ; }, abstract = {Natural transformation is a dominant force in bacterial evolution by promoting horizontal gene transfer. This process may have devastating consequences, such as the spread of antibiotic resistance or the emergence of highly virulent clones. However, uptake and recombination of foreign DNA are most often deleterious to competent species. Therefore, model naturally transformable gram-negative bacteria, including the human pathogen Neisseria meningitidis, have evolved means to preferentially take up homotypic DNA containing short and genus-specific sequence motifs. Despite decades of intense investigations, the DNA uptake sequence receptor in Neisseria species has remained elusive. We show here, using a multidisciplinary approach combining biochemistry, molecular genetics, and structural biology, that meningococcal type IV pili bind DNA through the minor pilin ComP via an electropositive stripe that is predicted to be exposed on the filaments surface and that ComP displays an exquisite binding preference for DNA uptake sequence. Our findings illuminate the earliest step in natural transformation, reveal an unconventional mechanism for DNA binding, and suggest that selective DNA uptake is more widespread than previously thought.}, }
@article {pmid23383996, year = {2013}, author = {Roch, S and Snir, S}, title = {Recovering the treelike trend of evolution despite extensive lateral genetic transfer: a probabilistic analysis.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {20}, number = {2}, pages = {93-112}, pmid = {23383996}, issn = {1557-8666}, mesh = {Bacteria/*classification/*genetics ; Biological Evolution ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Models, Genetic ; *Models, Statistical ; *Phylogeny ; }, abstract = {Lateral gene transfer (LGT) is a common mechanism of nonvertical evolution, during which genetic material is transferred between two more or less distantly related organisms. It is particularly common in bacteria where it contributes to adaptive evolution with important medical implications. In evolutionary studies, LGT has been shown to create widespread discordance between gene trees as genomes become mosaics of gene histories. In particular, the Tree of Life has been questioned as an appropriate representation of bacterial evolutionary history. Nevertheless a common hypothesis is that prokaryotic evolution is primarily treelike, but that the underlying trend is obscured by LGT. Extensive empirical work has sought to extract a common treelike signal from conflicting gene trees. Here we give a probabilistic perspective on the problem of recovering the treelike trend despite LGT. Under a model of randomly distributed LGT, we show that the species phylogeny can be reconstructed even in the presence of surprisingly many (almost linear number of) LGT events per gene tree. Our results, which are optimal up to logarithmic factors, are based on the analysis of a robust, computationally efficient reconstruction method and provides insight into the design of such methods. Finally, we show that our results have implications for the discovery of highways of gene sharing.}, }
@article {pmid23383142, year = {2013}, author = {Cázares-García, SV and Vázquez-Garcidueñas, S and Vázquez-Marrufo, G}, title = {Structural and phylogenetic analysis of laccases from Trichoderma: a bioinformatic approach.}, journal = {PloS one}, volume = {8}, number = {1}, pages = {e55295}, pmid = {23383142}, issn = {1932-6203}, mesh = {Amino Acid Motifs/genetics ; Computational Biology ; *Evolution, Molecular ; Gene Components ; Laccase/chemistry/*genetics/metabolism ; Molecular Sequence Data ; *Phylogeny ; Selection, Genetic ; Sequence Alignment ; Species Specificity ; Trichoderma/*enzymology ; }, abstract = {The genus Trichoderma includes species of great biotechnological value, both for their mycoparasitic activities and for their ability to produce extracellular hydrolytic enzymes. Although activity of extracellular laccase has previously been reported in Trichoderma spp., the possible number of isoenzymes is still unknown, as are the structural and functional characteristics of both the genes and the putative proteins. In this study, the system of laccases sensu stricto in the Trichoderma species, the genomes of which are publicly available, were analyzed using bioinformatic tools. The intron/exon structure of the genes and the identification of specific motifs in the sequence of amino acids of the proteins generated in silico allow for clear differentiation between extracellular and intracellular enzymes. Phylogenetic analysis suggests that the common ancestor of the genus possessed a functional gene for each one of these enzymes, which is a characteristic preserved in T. atroviride and T. virens. This analysis also reveals that T. harzianum and T. reesei only retained the intracellular activity, whereas T. asperellum added an extracellular isoenzyme acquired through horizontal gene transfer during the mycoparasitic process. The evolutionary analysis shows that in general, extracellular laccases are subjected to purifying selection, and intracellular laccases show neutral evolution. The data provided by the present study will enable the generation of experimental approximations to better understand the physiological role of laccases in the genus Trichoderma and to increase their biotechnological potential.}, }
@article {pmid23382815, year = {2013}, author = {Zhuo, C and Li, XQ and Zong, ZY and Zhong, NS}, title = {Epidemic plasmid carrying bla(CTX-M-15) in Klebsiella penumoniae in China.}, journal = {PloS one}, volume = {8}, number = {1}, pages = {e52222}, pmid = {23382815}, issn = {1932-6203}, mesh = {Base Sequence ; China ; Drug Resistance, Multiple, Bacterial/genetics ; *Gene Transfer, Horizontal ; Humans ; Klebsiella Infections/epidemiology/*genetics/microbiology ; Klebsiella pneumoniae/*genetics/isolation &amp; purification/pathogenicity ; Phylogeny ; Plasmids/genetics/isolation &amp; purification ; Sequence Analysis, DNA ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVE: To investigate the local epidemiology of Klebsiella penumoniae carrying bla(CTX-M-15) in southern China and to characterize the genetic environment of bla(CTX-M-15).<br><br>METHODS: PCR and DNA sequencing were used to detect and characterize the genetic contexts of bla(CTX-M-15). The clonal relatedness of isolates carrying bla(CTX-M-15) was determined by pulse-field gel electrophoresis. Conjugative plasmids carrying bla(CTX-M-15) were obtained by mating and were further subject to restriction analysis and replicon typing.<br><br>RESULTS: A total of 47CTX-M-15 ESBL-producing isolates of K. pneumoniae were collected from nine hospitals in China from October 2007 to October 2008. Isolates were clustered into various clonal groups. The local spread of bla(CTX-M-15) was mainly mediated by one major conjugative plasmid as determined by S1-PFGE and restriction analysis. A 90-kb plasmid belonging to incompatible group FII was the major carrier of bla(CTX-M-15) in K. pneumoniae. Except bla(TEM-1), the resistance genes such as bla(SHV), bla(DHA-1), bla(OXA-1), qnrB, qnrS, aac(3)-II, and aac(6')-Ib were not found in the plasmid. In the comparing of conjugative gene sequence, it is 100% identical with the plasmid pKF3-94, which was found in K. pneumonia from Zhejiang province of china previously.<br><br>CONCLUSIONS: bla(CTX-M-15) was prevalent in K. pneumonia of southern China. The dissemination of bla(CTX-M-15) appeared to be due to the horizontal transfer of a 90-kb epidemic plasmid.}, }
@article {pmid23382812, year = {2013}, author = {Kim, BJ and Hong, SH and Kook, YH and Kim, BJ}, title = {Molecular evidence of lateral gene transfer in rpoB gene of Mycobacterium yongonense strains via multilocus sequence analysis.}, journal = {PloS one}, volume = {8}, number = {1}, pages = {e51846}, pmid = {23382812}, issn = {1932-6203}, mesh = {Bacterial Proteins/*genetics ; DNA-Directed RNA Polymerases ; *Gene Transfer, Horizontal ; Humans ; Multilocus Sequence Typing ; Mycobacterium avium Complex/*genetics ; Nontuberculous Mycobacteria/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Sequence Analysis, DNA ; }, abstract = {Recently, a novel species, Mycobacterium yongonense (DSM 45126(T)), was introduced and while it is phylogenetically related to Mycobacterium intracellulare, it has a distinct RNA polymerase β-subunit gene (rpoB) sequence that is identical to that of Mycobacterium parascrofulaceum, which is a distantly related scotochromogen, which suggests the acquisition of the rpoB gene via a potential lateral gene transfer (LGT) event. The aims of this study are to prove the presence of the LGT event in the rpoB gene of the M. yongonense strains via multilocus sequence analysis (MLSA). In order to determine the potential of an LGT event in the rpoB gene of the M. yongonense, the MLSA based on full rpoB sequences (3447 or 3450 bp) and on partial sequences of five other targets [16S rRNA (1383 or 1395 bp), hsp65 (603 bp), dnaJ (192 bp), recA (1053 bp), and sodA (501 bp)] were conducted. Incongruences between the phylogenetic analysis of the full rpoB and the five other genes in a total of three M. yongonense strains [two clinical strains (MOTT-12 and MOTT-27) and one type strain (DSM 45126(T))] were observed, suggesting that rpoB gene of three M. yongonense strains may have been acquired very recently via an LGT event from M. parascrofulaceum, which is a distantly related scotochromogen.}, }
@article {pmid23382424, year = {2013}, author = {Croucher, NJ and Harris, SR and Grad, YH and Hanage, WP}, title = {Bacterial genomes in epidemiology--present and future.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {368}, number = {1614}, pages = {20120202}, pmid = {23382424}, issn = {1471-2970}, support = {T32 AI007061/AI/NIAID NIH HHS/United States ; U54 GM088558/GM/NIGMS NIH HHS/United States ; GM088558-01/GM/NIGMS NIH HHS/United States ; 098051/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacteria/*genetics ; Bacterial Infections/*epidemiology/*microbiology ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/*genetics ; Genomics/*methods ; High-Throughput Nucleotide Sequencing/methods ; Models, Genetic ; Molecular Epidemiology/*methods/trends ; }, abstract = {Sequence data are well established in the reconstruction of the phylogenetic and demographic scenarios that have given rise to outbreaks of viral pathogens. The application of similar methods to bacteria has been hindered in the main by the lack of high-resolution nucleotide sequence data from quality samples. Developing and already available genomic methods have greatly increased the amount of data that can be used to characterize an isolate and its relationship to others. However, differences in sequencing platforms and data analysis mean that these enhanced data come with a cost in terms of portability: results from one laboratory may not be directly comparable with those from another. Moreover, genomic data for many bacteria bear the mark of a history including extensive recombination, which has the potential to greatly confound phylogenetic and coalescent analyses. Here, we discuss the exacting requirements of genomic epidemiology, and means by which the distorting signal of recombination can be minimized to permit the leverage of growing datasets of genomic data from bacterial pathogens.}, }
@article {pmid23382234, year = {2013}, author = {Weyand, NJ and Wertheimer, AM and Hobbs, TR and Sisko, JL and Taku, NA and Gregston, LD and Clary, S and Higashi, DL and Biais, N and Brown, LM and Planer, SL and Legasse, AW and Axthelm, MK and Wong, SW and So, M}, title = {Neisseria infection of rhesus macaques as a model to study colonization, transmission, persistence, and horizontal gene transfer.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {8}, pages = {3059-3064}, pmid = {23382234}, issn = {1091-6490}, mesh = {Animals ; *Gene Transfer, Horizontal ; Genetic Markers ; Gram-Negative Bacterial Infections/genetics/*microbiology/transmission ; Host-Pathogen Interactions ; Macaca mulatta ; Molecular Sequence Data ; Neisseria/classification/genetics/*pathogenicity ; Phylogeny ; Virulence ; }, abstract = {The strict tropism of many pathogens for man hampers the development of animal models that recapitulate important microbe-host interactions. We developed a rhesus macaque model for studying Neisseria-host interactions using Neisseria species indigenous to the animal. We report that Neisseria are common inhabitants of the rhesus macaque. Neisseria isolated from the rhesus macaque recolonize animals after laboratory passage, persist in the animals for at least 72 d, and are transmitted between animals. Neisseria are naturally competent and acquire genetic markers from each other in vivo, in the absence of selection, within 44 d after colonization. Neisseria macacae encodes orthologs of known or presumed virulence factors of human-adapted Neisseria, as well as current or candidate vaccine antigens. We conclude that the rhesus macaque model will allow studies of the molecular mechanisms of Neisseria colonization, transmission, persistence, and horizontal gene transfer. The model can potentially be developed further for preclinical testing of vaccine candidates.}, }
@article {pmid23382174, year = {2013}, author = {Lo Scrudato, M and Blokesch, M}, title = {A transcriptional regulator linking quorum sensing and chitin induction to render Vibrio cholerae naturally transformable.}, journal = {Nucleic acids research}, volume = {41}, number = {6}, pages = {3644-3658}, pmid = {23382174}, issn = {1362-4962}, mesh = {Bacterial Proteins/genetics/metabolism/physiology ; Binding Sites ; *Chitin ; DNA Transformation Competence ; DNA-Binding Proteins/genetics/metabolism ; *Gene Expression Regulation, Bacterial ; Promoter Regions, Genetic ; Quorum Sensing/*genetics ; Trans-Activators/metabolism ; *Transformation, Bacterial ; Vibrio cholerae/*genetics ; }, abstract = {The human pathogen Vibrio cholerae is an aquatic bacterium associated with zooplankton and their chitinous exoskeletons. On chitinous surfaces, V. cholerae initiates a developmental programme, known as natural competence, to mediate transformation, which is a mode of horizontal gene transfer. Competence facilitates the uptake of free DNA and recombination into the bacterial genome. Recent studies have indicated that chitin surfaces are required, but not sufficient to induce competence. Two additional regulatory pathways, i.e. catabolite repression and quorum sensing (QS), are components of the regulatory network that controls natural competence in V. cholerae. In this study, we investigated the link between chitin induction and QS. We show that the major regulators of these two pathways, TfoX and HapR, are both involved in the activation of a gene encoding a transcriptional regulator of the LuxR-type family, which we named QS and TfoX-dependent regulator (QstR). We demonstrate that HapR binds the promoter of qstR in a site-specific manner, indicating a role for HapR as an activator of qstR. In addition, epistasis experiments indicate that QstR compensates for the absence of HapR. We also provide evidence that QstR is required for the proper expression of a small but essential subset of competence genes and propose a new regulatory model in which QstR links chitin-induced TfoX activity with QS.}, }
@article {pmid23381940, year = {2013}, author = {Bakkali, M}, title = {Could DNA uptake be a side effect of bacterial adhesion and twitching motility?.}, journal = {Archives of microbiology}, volume = {195}, number = {4}, pages = {279-289}, pmid = {23381940}, issn = {1432-072X}, mesh = {Anti-Bacterial Agents/*pharmacology/therapeutic use ; Bacteria/cytology/drug effects/*genetics/*metabolism ; *Bacterial Adhesion ; Bacterial Infections/drug therapy/microbiology ; Drug Resistance, Bacterial ; Fimbriae, Bacterial/metabolism ; *Gene Transfer, Horizontal ; *Movement ; Stress, Physiological ; *Transformation, Genetic ; }, abstract = {DNA acquisition promotes the spread of resistance to antibiotics and virulence among bacteria. It is also linked to several natural phenomena including recombination, genome dynamics, adaptation and speciation. Horizontal DNA transfer between bacteria occurs via conjugation, transduction or competence for natural transformation by DNA uptake. Among these, competence is the only mechanism of transformation initiated and entirely controlled by the chromosome of the recipient bacteria. While the molecular mechanisms allowing the uptake of extracellular DNA are increasingly characterized, the function of competence for natural transformation by DNA uptake, the selective advantage maintaining it and the reasons why bacteria take up DNA in the first place are still debated. In this synthesis, I review some of the literature and discuss the four hypotheses on how and why do bacteria take up DNA. I argue that DNA uptake by bacteria is an accidental by-product of bacterial adhesion and twitching motility. Adhesion and motility are generally increased in stressful conditions, which may explain why bacteria increase DNA uptake in these conditions. In addition to its fundamental scientific relevance, the new hypothesis suggested here has significant clinical implications and finds further support from the fact that antibiotics sometimes fail to eliminate the targeted bacterium while inevitably causing stress to others. The widespread misuse of antibiotics may thus not only be selecting for resistant strains, but may also be causing bacteria to take up more DNA with the consequent increase in the chances of acquiring drug resistance and virulence-a scenario in full concordance with the previously reported induction of competence genes by antibiotics in Streptococcus pneumoniae and Legionella pneumophila.}, }
@article {pmid23378260, year = {2013}, author = {Gatica, J and Cytryn, E}, title = {Impact of treated wastewater irrigation on antibiotic resistance in the soil microbiome.}, journal = {Environmental science and pollution research international}, volume = {20}, number = {6}, pages = {3529-3538}, pmid = {23378260}, issn = {1614-7499}, mesh = {Agricultural Irrigation ; Drug Resistance, Bacterial/*drug effects ; Environmental Monitoring/*methods ; Genes, Bacterial ; Metagenome/*drug effects ; *Soil Microbiology ; Waste Disposal, Fluid ; Wastewater/*analysis/chemistry ; Water Pollutants, Chemical/adverse effects/analysis ; }, abstract = {The reuse of treated wastewater (TWW) for irrigation is a practical solution for overcoming water scarcity, especially in arid and semiarid regions of the world. However, there are several potential environmental and health-related risks associated with this practice. One such risk stems from the fact that TWW irrigation may increase antibiotic resistance (AR) levels in soil bacteria, potentially contributing to the global propagation of clinical AR. Wastewater treatment plant (WWTP) effluents have been recognized as significant environmental AR reservoirs due to selective pressure generated by antibiotics and other compounds that are frequently detected in effluents. This review summarizes a myriad of recent studies that have assessed the impact of anthropogenic practices on AR in environmental bacterial communities, with specific emphasis on elucidating the potential effects of TWW irrigation on AR in the soil microbiome. Based on the current state of the art, we conclude that contradictory to freshwater environments where WWTP effluent influx tends to expand antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes levels, TWW irrigation does not seem to impact AR levels in the soil microbiome. Although this conclusion is a cause for cautious optimism regarding the future implementation of TWW irrigation, we conclude that further studies aimed at assessing the scope of horizontal gene transfer between effluent-associated ARB and soil bacteria need to be further conducted before ruling out the possible contribution of TWW irrigation to antibiotic-resistant reservoirs in irrigated soils.}, }
@article {pmid23377932, year = {2013}, author = {Theethakaew, C and Feil, EJ and Castillo-Ramírez, S and Aanensen, DM and Suthienkul, O and Neil, DM and Davies, RL}, title = {Genetic relationships of Vibrio parahaemolyticus isolates from clinical, human carrier, and environmental sources in Thailand, determined by multilocus sequence analysis.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {7}, pages = {2358-2370}, pmid = {23377932}, issn = {1098-5336}, mesh = {Carrier State/epidemiology/*microbiology ; Cluster Analysis ; Genetic Variation ; Humans ; Molecular Epidemiology ; *Multilocus Sequence Typing ; Seafood/*microbiology ; Serotyping ; Thailand/epidemiology ; Vibrio Infections/epidemiology/*microbiology ; Vibrio parahaemolyticus/*classification/*genetics/isolation &amp; purification ; *Water Microbiology ; }, abstract = {Vibrio parahaemolyticus is a seafood-borne pathogenic bacterium that is a major cause of gastroenteritis worldwide. We investigated the genetic and evolutionary relationships of 101 V. parahaemolyticus isolates originating from clinical, human carrier, and various environmental and seafood production sources in Thailand using multilocus sequence analysis. The isolates were recovered from clinical samples (n = 15), healthy human carriers (n = 18), various types of fresh seafood (n = 18), frozen shrimp (n = 16), fresh-farmed shrimp tissue (n = 18), and shrimp farm water (n = 16). Phylogenetic analysis revealed a high degree of genetic diversity within the V. parahaemolyticus population, although isolates recovered from clinical samples and from farmed shrimp and water samples represented distinct clusters. The tight clustering of the clinical isolates suggests that disease-causing isolates are not a random sample of the environmental reservoir, although the source of infection remains unclear. Extensive serotypic diversity occurred among isolates representing the same sequence types and recovered from the same source at the same time. These findings suggest that the O- and K-antigen-encoding loci are subject to exceptionally high rates of recombination. There was also strong evidence of interspecies horizontal gene transfer and intragenic recombination involving the recA locus in a large proportion of isolates. As the majority of the intragenic recombinational exchanges involving recA occurred among clinical and carrier isolates, it is possible that the human intestinal tract serves as a potential reservoir of donor and recipient strains that is promoting horizontal DNA transfer, driving evolutionary change, and leading to the emergence of new, potentially pathogenic strains.}, }
@article {pmid23376595, year = {2013}, author = {Mattozzi, Md and Ziesack, M and Voges, MJ and Silver, PA and Way, JC}, title = {Expression of the sub-pathways of the Chloroflexus aurantiacus 3-hydroxypropionate carbon fixation bicycle in E. coli: Toward horizontal transfer of autotrophic growth.}, journal = {Metabolic engineering}, volume = {16}, number = {}, pages = {130-139}, doi = {10.1016/j.ymben.2013.01.005}, pmid = {23376595}, issn = {1096-7184}, mesh = {Bacterial Proteins/*biosynthesis/genetics ; Chloroflexus/enzymology/*genetics ; Enzymes/*biosynthesis/genetics ; Escherichia coli K12/genetics/*metabolism ; *Gene Expression ; Lactic Acid/*analogs &amp; derivatives/biosynthesis ; Recombinant Proteins/biosynthesis/genetics ; }, abstract = {The 3-hydroxypropionate (3-HPA) bicycle is unique among CO2-fixing systems in that none of its enzymes appear to be affected by oxygen. Moreover, the bicycle includes a number of enzymes that produce novel intermediates of biotechnological interest, and the CO2-fixing steps in this pathway are relatively rapid. We expressed portions of the 3-HPA bicycle in a heterologous organism, E. coli K12. We subdivided the 3-HPA bicycle into four sub-pathways: (1) synthesis of propionyl-CoA from acetyl-CoA, (2) synthesis of succinate from propionyl-CoA, (3) glyoxylate production and regeneration of acetyl-CoA, and (4) assimilation of glyoxylate and propionyl-CoA to form pyruvate and regenerate acetyl-CoA. We expressed the novel enzymes of the 3-HPA bicycle in operon form and used phenotypic tests for activity. Sub-pathway 1 activated a propionate-specific biosensor. Sub-pathway 2, found in non-CO2-fixing bacteria, was reassembled in E. coli using genes from diverse sources. Sub-pathway 3, operating in reverse, generated succinyl-CoA sufficient to rescue a sucAD(-) double mutant of its diaminopimelic acid (DAP) auxotrophy. Sub-pathway 4 was able to reduce the toxicity of propionate and allow propionate to contribute to cell biomass in a prpC(-)(2 methylcitrate synthase) mutant strain. These results indicate that all of the sub-pathways of the 3-HPA bicycle can function to some extent in vivo in a heterologous organism, as indicated by growth tests. Overexpression of certain enzymes was deleterious to cell growth, and, in particular, expression of MMC-CoA lyase caused a mucoid phenotype. These results have implications for metabolic engineering and for bacterial evolution through horizontal gene transfer.}, }
@article {pmid23376541, year = {2013}, author = {Tuntufye, HN and Gwakisa, PS and Goddeeris, BM}, title = {In silico analysis of tkt1 from avian pathogenic Escherichia coli and its virulence evaluation in chickens.}, journal = {Research in microbiology}, volume = {164}, number = {4}, pages = {310-318}, doi = {10.1016/j.resmic.2013.01.003}, pmid = {23376541}, issn = {1769-7123}, mesh = {Animals ; Chickens ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; Escherichia coli/*enzymology/genetics/*pathogenicity ; Escherichia coli Infections/microbiology/mortality/pathology ; Escherichia coli Proteins/genetics/*metabolism ; Genomic Islands ; Lethal Dose 50 ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Survival Analysis ; Transketolase/genetics/*metabolism ; Virulence ; Virulence Factors/genetics/*metabolism ; }, abstract = {Extraintestinal pathogenic Escherichia coli (ExPEC) contain tktA and tktB which code for transketolases involved in the pentose phosphate pathway. Recent studies demonstrated that a third gene coding for transketolase 1 (tkt1) was located in a pathogenicity island of avian and human ExPEC belonging to phylogenetic group B2. In the present study, in silico analysis of tkt1 revealed 68% and 69% identity with tktA and tktB, respectively, of ExPEC and 68% identity with tktA and tktB of E. coli MG1655. The translated tkt1 shared 69% and 68% identity with TktA and TktB proteins, respectively, of ExPEC and E. coli MG1655. Phylogenetically, it is shown that the three genes (tktA, tktB and tkt1) cluster in three different clades. Further analysis suggests that tkt1 has been acquired though horizontal gene transfer from plant-associated bacteria within the family Enterobacteriaceae. Virulence studies were performed in order to evaluate whether tkt1 played a role in avian pathogenic E. coli CH2 virulence in chickens. The evaluation revealed that mutant virulence was slightly lower based on LD50 when compared to the wild type during infection of chickens, but there were no significant differences when the two strains were compared based on the number of deaths and lesion scores.}, }
@article {pmid23375108, year = {2013}, author = {Clarke, M and Lohan, AJ and Liu, B and Lagkouvardos, I and Roy, S and Zafar, N and Bertelli, C and Schilde, C and Kianianmomeni, A and Bürglin, TR and Frech, C and Turcotte, B and Kopec, KO and Synnott, JM and Choo, C and Paponov, I and Finkler, A and Heng Tan, CS and Hutchins, AP and Weinmeier, T and Rattei, T and Chu, JS and Gimenez, G and Irimia, M and Rigden, DJ and Fitzpatrick, DA and Lorenzo-Morales, J and Bateman, A and Chiu, CH and Tang, P and Hegemann, P and Fromm, H and Raoult, D and Greub, G and Miranda-Saavedra, D and Chen, N and Nash, P and Ginger, ML and Horn, M and Schaap, P and Caler, L and Loftus, BJ}, title = {Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling.}, journal = {Genome biology}, volume = {14}, number = {2}, pages = {R11}, pmid = {23375108}, issn = {1474-760X}, support = {281633/ERC_/European Research Council/International ; BB/E016308/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Acanthamoeba castellanii/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Protozoan ; Introns ; Protein-Tyrosine Kinases/*genetics/metabolism ; Protozoan Proteins/*genetics/metabolism ; *Signal Transduction ; }, abstract = {BACKGROUND: The Amoebozoa constitute one of the primary divisions of eukaryotes, encompassing taxa of both biomedical and evolutionary importance, yet its genomic diversity remains largely unsampled. Here we present an analysis of a whole genome assembly of Acanthamoeba castellanii (Ac) the first representative from a solitary free-living amoebozoan.<br><br>RESULTS: Ac encodes 15,455 compact intron-rich genes, a significant number of which are predicted to have arisen through inter-kingdom lateral gene transfer (LGT). A majority of the LGT candidates have undergone a substantial degree of intronization and Ac appears to have incorporated them into established transcriptional programs. Ac manifests a complex signaling and cell communication repertoire, including a complete tyrosine kinase signaling toolkit and a comparable diversity of predicted extracellular receptors to that found in the facultatively multicellular dictyostelids. An important environmental host of a diverse range of bacteria and viruses, Ac utilizes a diverse repertoire of predicted pattern recognition receptors, many with predicted orthologous functions in the innate immune systems of higher organisms.<br><br>CONCLUSIONS: Our analysis highlights the important role of LGT in the biology of Ac and in the diversification of microbial eukaryotes. The early evolution of a key signaling facility implicated in the evolution of metazoan multicellularity strongly argues for its emergence early in the Unikont lineage. Overall, the availability of an Ac genome should aid in deciphering the biology of the Amoebozoa and facilitate functional genomic studies in this important model organism and environmental host.}, }
@article {pmid23365769, year = {2012}, author = {Murphy, C and Inverarity, D and McGoldrick, C and Mitchell, L and Paterson, P and Thom, L and Edwards, G}, title = {Treated follicular lymphoma, recurrent invasive pneumococcal disease, nonresponsiveness to vaccination, and a unique pneumococcus.}, journal = {Case reports in hematology}, volume = {2012}, number = {}, pages = {386372}, pmid = {23365769}, issn = {2090-6579}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {A nonneutropenic patient with treated low-grade non-Hodgkin's (Follicular) lymphoma and secondary hypogammaglobulinemia recovered from pneumococcal pneumonia and septicemia (serotype 7F; ST191) subsequent to influenza A H1N1 (2009). Both infections were potentially vaccine preventable. The patient then developed pneumococcal meningitis due to a serotype 35F pneumococcus with a unique Multilocus Sequence Type (ST7004) which was not vaccine preventable. Patient management was influenced by host predisposition to pneumococcal infection, antibiotic intolerance, and poor response to polysaccharide pneumococcal vaccine. Indirect immunofluorescence with anti-human immunoglobulin confirmed a poor or intermediate response to Pneumovax II. Prophylactic erythromycin was initiated, and immunoglobulin transfusions were also commenced as a preventive strategy. ST7004 is a single locus variant of ST1635 which has been associated with the serotype 35F capsule in England. The spi gene in ST7004, which differentiates it from ST1635, is the same as the spi gene present in ST191 which could have arisen from the first disease episode suggesting that horizontal gene transfer may have occurred between different populations of pneumococci present within the patient in an attempt to evade vaccination selection pressure.}, }
@article {pmid23364352, year = {2013}, author = {Liang, H and Zen, K and Zhang, J and Zhang, CY and Chen, X}, title = {New roles for microRNAs in cross-species communication.}, journal = {RNA biology}, volume = {10}, number = {3}, pages = {367-370}, pmid = {23364352}, issn = {1555-8584}, mesh = {Cell Communication ; *Gene Expression Regulation ; Gene Expression Regulation, Viral ; Gene Transfer, Horizontal ; Host-Parasite Interactions ; *Host-Pathogen Interactions ; Humans ; MicroRNAs/*genetics ; Plants/genetics ; Plasmodium falciparum/genetics ; Viruses/genetics/growth &amp; development ; }, abstract = {Communication between cells ensures coordinated behavior. In prokaryotes, this signaling is typically referred to as quorum sensing, whereas in eukaryotic cells, communication occurs through hormones. In recent years, reports have shown that small noncoding RNAs, called microRNAs (miRNAs), can be transmitted from one species to another, inducing signal interference in distant species, even in a cross-kingdom manner. This new mode of cross-species communication might mediate symbiotic and pathogenic relationships between various organisms (e.g., microorganisms and their hosts). Here, we discuss several recent studies concerning miRNA-mediated cross-species gene regulation.}, }
@article {pmid23364192, year = {2013}, author = {Dayaram, A and Goldstien, S and Zawar-Reza, P and Gomez, C and Harding, JS and Varsani, A}, title = {Novel ssDNA virus recovered from estuarine Mollusc (Amphibola crenata) whose replication associated protein (Rep) shares similarities with Rep-like sequences of bacterial origin.}, journal = {The Journal of general virology}, volume = {94}, number = {Pt 5}, pages = {1104-1110}, doi = {10.1099/vir.0.050088-0}, pmid = {23364192}, issn = {1465-2099}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Bacterial Proteins/genetics ; Base Sequence ; DNA Viruses/classification/genetics/*isolation &amp; purification ; DNA, Single-Stranded/*genetics ; DNA, Viral/*genetics ; Estuaries ; Gastropoda/*virology ; Genome, Viral/*genetics ; Humans ; Molecular Sequence Data ; Open Reading Frames/genetics ; Phylogeny ; Sequence Analysis, DNA ; Soil Pollutants ; Viral Proteins/*genetics ; Virus Replication/genetics ; Wetlands ; }, abstract = {Over the past couple of years highly diverse novel ssDNA viruses have been discovered. Here, we present the first ssDNA virus, Gastropod-associated circular ssDNA virus (GaCSV), recovered from a mollusc Amphibola crenata Martyn 1784, which is a deposit feeder that grazes micro-organisms and organic detritus on the surface of tidal mudflats. The GaCSV (2351 nt) genome contains two large bidirectionally transcribed ORFs. The smaller ORF (874 nt) has similarities to viral replication-associated protein (Rep) sequences of some bacteria and circoviruses, whereas the larger ORF (955 nt) does not relate to any sequences in public databases and we presume it potentially encodes the capsid protein. Phylogenetic analysis shows that the GaCSV Rep clusters with Rep-like sequences of bacterial origin, highlighting the role of ssDNA viruses in horizontal gene transfer. The occurrence of previously unknown viruses in organisms associated with human pollution is a relatively unexplored field.}, }
@article {pmid23360999, year = {2013}, author = {Ringrose, JH and van den Toorn, HW and Eitel, M and Post, H and Neerincx, P and Schierwater, B and Altelaar, AF and Heck, AJ}, title = {Deep proteome profiling of Trichoplax adhaerens reveals remarkable features at the origin of metazoan multicellularity.}, journal = {Nature communications}, volume = {4}, number = {}, pages = {1408}, pmid = {23360999}, issn = {2041-1723}, mesh = {Animals ; *Biological Evolution ; Databases, Protein ; Ion Exchange ; Phosphorylation ; Phosphotransferases/metabolism ; Phosphotyrosine/metabolism ; Placozoa/*cytology/*metabolism ; Protein Processing, Post-Translational ; Proteome/*metabolism ; Proteomics/*methods ; Receptors, Notch/metabolism ; Signal Transduction ; }, abstract = {Genome sequencing of arguably the simplest known animal, Trichoplax adhaerens, uncovered a rich array of transcription factor and signalling pathway genes. Although the existence of such genes allows speculation about the presence of complex regulatory events, it does not reveal the level of actual protein expression and functionalization through posttranslational modifications. Using high-resolution mass spectrometry, we here semi-quantify 6,516 predicted proteins, revealing evidence of horizontal gene transfer and the presence at the protein level of nodes important in animal signalling pathways. Moreover, our data demonstrate a remarkably high activity of tyrosine phosphorylation, in line with the hypothesized burst of tyrosine-regulated signalling at the instance of animal multicellularity. Together, this Trichoplax proteomics data set offers significant new insight into the mechanisms underlying the emergence of metazoan multicellularity and provides a resource for interested researchers.}, }
@article {pmid23360210, year = {2013}, author = {Herman, EK and Greninger, AL and Visvesvara, GS and Marciano-Cabral, F and Dacks, JB and Chiu, CY}, title = {The mitochondrial genome and a 60-kb nuclear DNA segment from Naegleria fowleri, the causative agent of primary amoebic meningoencephalitis.}, journal = {The Journal of eukaryotic microbiology}, volume = {60}, number = {2}, pages = {179-191}, pmid = {23360210}, issn = {1550-7408}, support = {R56 AI089532/AI/NIAID NIH HHS/United States ; T32 GM007618/GM/NIGMS NIH HHS/United States ; R56-AI08953/AI/NIAID NIH HHS/United States ; }, mesh = {Amebiasis/parasitology ; Australia ; Central Nervous System Protozoal Infections/parasitology ; DNA, Protozoan/chemistry/*genetics ; Gene Order ; Gene Transfer, Horizontal ; *Genome, Mitochondrial ; Molecular Sequence Data ; Naegleria fowleri/*genetics/isolation &amp; purification ; Protozoan Proteins/genetics ; Sequence Analysis, DNA ; Sequence Homology ; Synteny ; United States ; }, abstract = {Naegleria fowleri is a unicellular eukaryote causing primary amoebic meningoencephalitis, a neuropathic disease killing 99% of those infected, usually within 7-14 days. Naegleria fowleri is found globally in regions including the US and Australia. The genome of the related nonpathogenic species Naegleria gruberi has been sequenced, but the genetic basis for N. fowleri pathogenicity is unclear. To generate such insight, we sequenced and assembled the mitochondrial genome and a 60-kb segment of nuclear genome from N. fowleri. The mitochondrial genome is highly similar to its counterpart in N. gruberi in gene complement and organization, while distinct lack of synteny is observed for the nuclear segments. Even in this short (60-kb) segment, we identified examples of potential factors for pathogenesis, including ten novel N. fowleri-specific genes. We also identified a homolog of cathepsin B; proteases proposed to be involved in the pathogenesis of diverse eukaryotic pathogens, including N. fowleri. Finally, we demonstrate a likely case of horizontal gene transfer between N. fowleri and two unrelated amoebae, one of which causes granulomatous amoebic encephalitis. This initial look into the N. fowleri nuclear genome has revealed several examples of potential pathogenesis factors, improving our understanding of a neglected pathogen of increasing global importance.}, }
@article {pmid23357771, year = {2013}, author = {Savage, VJ and Chopra, I and O'Neill, AJ}, title = {Staphylococcus aureus biofilms promote horizontal transfer of antibiotic resistance.}, journal = {Antimicrobial agents and chemotherapy}, volume = {57}, number = {4}, pages = {1968-1970}, pmid = {23357771}, issn = {1098-6596}, mesh = {Anti-Bacterial Agents/*pharmacology ; Biofilms/*drug effects ; Gene Transfer, Horizontal/genetics/*physiology ; Microbial Sensitivity Tests ; Plasmids/*genetics ; Staphylococcus aureus/*drug effects/*genetics ; }, abstract = {Growth as a biofilm facilitates the emergence of antibiotic resistance by mutation in Staphylococcus aureus. Here we demonstrate that biofilm growth of this species also dramatically increases horizontal transfer of plasmid-borne antibiotic resistance determinants by conjugation/mobilization and that standard laboratory practices to induce conjugation in staphylococci achieve optimal efficiency owing to the presence of a biofilm.}, }
@article {pmid23356413, year = {2014}, author = {Mebrhatu, MT and Cenens, W and Aertsen, A}, title = {An overview of the domestication and impact of the Salmonella mobilome.}, journal = {Critical reviews in microbiology}, volume = {40}, number = {1}, pages = {63-75}, doi = {10.3109/1040841X.2012.755949}, pmid = {23356413}, issn = {1549-7828}, mesh = {*Adaptation, Biological ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Salmonella/*genetics/pathogenicity/physiology ; Virulence ; }, abstract = {Salmonella spp. are accountable for a large fraction of the global infectious disease burden, with most of their infections being food- or water-borne. The phenotypic features and adaptive potential of Salmonella spp. appear to be driven to a large extent by mobile or laterally acquired genetic elements. A better understanding of the conduct and diversification of these important pathogens consequently requires a more profound insight into the different mechanisms by which these pivotal elements establish themselves in the cell and affect its behavior. This review, therefore, provides an overview of the physiological impact and domestication of the Salmonella mobilome.}, }
@article {pmid23355531, year = {2013}, author = {Szöllosi, GJ and Tannier, E and Lartillot, N and Daubin, V}, title = {Lateral gene transfer from the dead.}, journal = {Systematic biology}, volume = {62}, number = {3}, pages = {386-397}, pmid = {23355531}, issn = {1076-836X}, mesh = {Algorithms ; Biodiversity ; Biological Evolution ; Cyanobacteria/*genetics ; DNA, Bacterial/*analysis ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Genetic Speciation ; Models, Genetic ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {In phylogenetic studies, the evolution of molecular sequences is assumed to have taken place along the phylogeny traced by the ancestors of extant species. In the presence of lateral gene transfer, however, this may not be the case, because the species lineage from which a gene was transferred may have gone extinct or not have been sampled. Because it is not feasible to specify or reconstruct the complete phylogeny of all species, we must describe the evolution of genes outside the represented phylogeny by modeling the speciation dynamics that gave rise to the complete phylogeny. We demonstrate that if the number of sampled species is small compared with the total number of existing species, the overwhelming majority of gene transfers involve speciation to and evolution along extinct or unsampled lineages. We show that the evolution of genes along extinct or unsampled lineages can to good approximation be treated as those of independently evolving lineages described by a few global parameters. Using this result, we derive an algorithm to calculate the probability of a gene tree and recover the maximum-likelihood reconciliation given the phylogeny of the sampled species. Examining 473 near-universal gene families from 36 cyanobacteria, we find that nearly a third of transfer events (28%) appear to have topological signatures of evolution along extinct species, but only approximately 6% of transfers trace their ancestry to before the common ancestor of the sampled cyanobacteria.}, }
@article {pmid23354744, year = {2013}, author = {Lautner, M and Schunder, E and Herrmann, V and Heuner, K}, title = {Regulation, integrase-dependent excision, and horizontal transfer of genomic islands in Legionella pneumophila.}, journal = {Journal of bacteriology}, volume = {195}, number = {7}, pages = {1583-1597}, pmid = {23354744}, issn = {1098-5530}, mesh = {Acanthamoeba castellanii/microbiology ; Bacterial Secretion Systems/*genetics ; Chromosomes, Bacterial ; Conjugation, Genetic ; *Gene Transfer, Horizontal ; *Genomic Islands ; Humans ; Integrases/metabolism ; Legionella pneumophila/*genetics/*metabolism ; Plasmids ; *Recombination, Genetic ; }, abstract = {Legionella pneumophila is a Gram-negative freshwater agent which multiplies in specialized nutrient-rich vacuoles of amoebae. When replicating in human alveolar macrophages, Legionella can cause Legionnaires' disease. Recently, we identified a new type of conjugation/type IVA secretion system (T4ASS) in L. pneumophila Corby (named trb-tra). Analogous versions of trb-tra are localized on the genomic islands Trb-1 and Trb-2. Both can exist as an episomal circular form, and Trb-1 can be transferred horizontally to other Legionella strains by conjugation. In our current work, we discovered the importance of a site-specific integrase (Int-1, lpc2818) for the excision and conjugation process of Trb-1. Furthermore, we identified the genes lvrRABC (lpc2813 to lpc2816) to be involved in the regulation of Trb-1 excision. In addition, we demonstrated for the first time that a Legionella genomic island (LGI) of L. pneumophila Corby (LpcGI-2) encodes a functional type IV secretion system. The island can be transferred horizontally by conjugation and is integrated site specifically into the genome of the transconjugants. LpcGI-2 generates three different episomal forms. The predominant episomal form, form A, is generated integrase dependently (Lpc1833) and transferred by conjugation in a pilT-dependent manner. Therefore, the genomic islands Trb-1 and LpcGI-2 should be classified as integrative and conjugative elements (ICEs). Coculture studies of L. pneumophila wild-type and mutant strains revealed that the int-1 and lvrRABC genes (located on Trb-1) as well as lpc1833 and pilT (located on LpcGI-2) do not influence the in vivo fitness of L. pneumophila in Acanthamoeba castellanii.}, }
@article {pmid23354281, year = {2013}, author = {Bonnin, RA and Poirel, L and Nordmann, P and Eikmeyer, FG and Wibberg, D and Pühler, A and Schlüter, A}, title = {Complete sequence of broad-host-range plasmid pNOR-2000 harbouring the metallo-β-lactamase gene blaVIM-2 from Pseudomonas aeruginosa.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {68}, number = {5}, pages = {1060-1065}, doi = {10.1093/jac/dks526}, pmid = {23354281}, issn = {1460-2091}, mesh = {Bacteremia/microbiology ; Computational Biology ; Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; Gene Transfer Techniques ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Host Specificity ; Humans ; Molecular Sequence Data ; Plasmids/*isolation &amp; purification ; Pseudomonas Infections/microbiology ; Pseudomonas aeruginosa/*enzymology/*genetics/physiology ; Sequence Analysis, DNA ; Transformation, Bacterial ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: Metallo-β-lactamases (MBLs) are increasingly reported not only in Enterobacteriaceae but also in Pseudomonas spp. These enzymes hydrolyse all β-lactams, including carbapenems, and are not inhibited by β-lactamase inhibitors. The aim of this study was to fully characterize a plasmid bearing the blaVIM-2 MBL gene identified in a Pseudomonas aeruginosa isolate.<br><br>METHODS: This plasmid was fully sequenced by high-density pyrosequencing and annotated using the GenDB version 2.0 annotation tool. The evaluation of the broad-host-range replication of the pNOR-2000 replication initiation gene was assessed using electro-transformation and conjugation assays and the distribution of this replicase gene was evaluated using an international collection of VIM-producing Pseudomonas spp.<br><br>RESULTS: Analysis of the 21&#x200a;880 bp sequence of pNOR-2000 revealed a truncated and non-functional transfer operon, in addition to novel genes encoding a serine protease and toxin/antitoxin addiction systems. This broad-host-range plasmid shares high gene synteny with part of the mobile genomic island pKLC102 identified in P. aeruginosa strain C.<br><br>CONCLUSIONS: We report here the complete nucleotide sequence of plasmid pNOR-2000 from a P. aeruginosa clinical isolate harbouring the integron-located MBL gene blaVIM-2.}, }
@article {pmid23349695, year = {2013}, author = {Sureshan, V and Deshpande, CN and Boucher, Y and Koenig, JE and ,  and Stokes, HW and Harrop, SJ and Curmi, PM and Mabbutt, BC}, title = {Integron gene cassettes: a repository of novel protein folds with distinct interaction sites.}, journal = {PloS one}, volume = {8}, number = {1}, pages = {e52934}, pmid = {23349695}, issn = {1932-6203}, support = {GM094568/GM/NIGMS NIH HHS/United States ; GM074942/GM/NIGMS NIH HHS/United States ; U01 GM094568/GM/NIGMS NIH HHS/United States ; U54 GM094585/GM/NIGMS NIH HHS/United States ; U54 GM074942/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/*genetics/*metabolism ; Binding Sites ; Crystallography, X-Ray ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/*genetics ; Integrons/*genetics ; Metagenome/genetics ; Models, Molecular ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Protein Binding ; Protein Structure, Secondary ; Vibrio cholerae/genetics/metabolism ; }, abstract = {Mobile gene cassettes captured within integron arrays encompass a vast and diverse pool of genetic novelty. In most cases, functional annotation of gene cassettes directly recovered by cassette-PCR is obscured by their characteristically high sequence novelty. This inhibits identification of those specific functions or biological features that might constitute preferential factors for lateral gene transfer via the integron system. A structural genomics approach incorporating x-ray crystallography has been utilised on a selection of cassettes to investigate evolutionary relationships hidden at the sequence level. Gene cassettes were accessed from marine sediments (pristine and contaminated sites), as well as a range of Vibrio spp. We present six crystal structures, a remarkably high proportion of our survey of soluble proteins, which were found to possess novel folds. These entirely new structures are diverse, encompassing all-α, α+β and α/β fold classes, and many contain clear binding pocket features for small molecule substrates. The new structures emphasise the large repertoire of protein families encoded within the integron cassette metagenome and which remain to be characterised. Oligomeric association is a notable recurring property common to these new integron-derived proteins. In some cases, the protein-protein contact sites utilised in homomeric assembly could instead form suitable contact points for heterogeneous regulator/activator proteins or domains. Such functional features are ideal for a flexible molecular componentry needed to ensure responsive and adaptive bacterial functions.}, }
@article {pmid23348040, year = {2013}, author = {Wissler, L and Gadau, J and Simola, DF and Helmkampf, M and Bornberg-Bauer, E}, title = {Mechanisms and dynamics of orphan gene emergence in insect genomes.}, journal = {Genome biology and evolution}, volume = {5}, number = {2}, pages = {439-455}, pmid = {23348040}, issn = {1759-6653}, mesh = {Animals ; DNA Transposable Elements/*genetics ; Diptera/*genetics ; *Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; Genome, Insect ; Genomics ; Hymenoptera/*genetics ; Phylogeny ; }, abstract = {Orphan genes are defined as genes that lack detectable similarity to genes in other species and therefore no clear signals of common descent (i.e., homology) can be inferred. Orphans are an enigmatic portion of the genome because their origin and function are mostly unknown and they typically make up 10% to 30% of all genes in a genome. Several case studies demonstrated that orphans can contribute to lineage-specific adaptation. Here, we study orphan genes by comparing 30 arthropod genomes, focusing in particular on seven recently sequenced ant genomes. This setup allows analyzing a major metazoan taxon and a comparison between social Hymenoptera (ants and bees) and nonsocial Diptera (flies and mosquitoes). First, we find that recently split lineages undergo accelerated genomic reorganization, including the rapid gain of many orphan genes. Second, between the two insect orders Hymenoptera and Diptera, orphan genes are more abundant and emerge more rapidly in Hymenoptera, in particular, in leaf-cutter ants. With respect to intragenomic localization, we find that ant orphan genes show little clustering, which suggests that orphan genes in ants are scattered uniformly over the genome and between nonorphan genes. Finally, our results indicate that the genetic mechanisms creating orphan genes-such as gene duplication, frame-shift fixation, creation of overlapping genes, horizontal gene transfer, and exaptation of transposable elements-act at different rates in insects, primates, and plants. In Formicidae, the majority of orphan genes has their origin in intergenic regions, pointing to a high rate of de novo gene formation or generalized gene loss, and support a recently proposed dynamic model of frequent gene birth and death.}, }
@article {pmid23347101, year = {2013}, author = {Lehti, TA and Bauchart, P and Kukkonen, M and Dobrindt, U and Korhonen, TK and Westerlund-Wikström, B}, title = {Phylogenetic group-associated differences in regulation of the common colonization factor Mat fimbria in Escherichia coli.}, journal = {Molecular microbiology}, volume = {87}, number = {6}, pages = {1200-1222}, doi = {10.1111/mmi.12161}, pmid = {23347101}, issn = {1365-2958}, mesh = {Adhesins, Bacterial/genetics/*metabolism ; DNA, Bacterial/chemistry/genetics ; Escherichia coli/*genetics/*metabolism ; Escherichia coli Proteins/genetics/*metabolism ; Fimbriae, Bacterial/*metabolism ; *Gene Expression Regulation, Bacterial ; Molecular Sequence Data ; Operon ; Polymorphism, Genetic ; Promoter Regions, Genetic ; Sequence Analysis, DNA ; }, abstract = {Heterogeneity of cell population is a key component behind the evolutionary success of Escherichia coli. The heterogeneity supports species adaptation and mainly results from lateral gene transfer. Adaptation may also involve genomic alterations that affect regulation of conserved genes. Here we analysed regulation of the mat (or ecp) genes that encode a conserved fimbrial adhesin of E. coli. We found that the differential and temperature-sensitive expression control of the mat operon is dependent on mat promoter polymorphism and closely linked to phylogenetic grouping of E. coli. In the mat promoter lineage favouring fimbriae expression, the mat operon-encoded regulator MatA forms a positive feedback loop that overcomes the repression by H-NS and stabilizes the fimbrillin mRNA under low growth temperature, acidic pH or elevated levels of acetate. The study exemplifies phylogenetic group-associated expression of a highly common surface organelle in E. coli.}, }
@article {pmid23344576, year = {2013}, author = {Bertsch, D and Uruty, A and Anderegg, J and Lacroix, C and Perreten, V and Meile, L}, title = {Tn6198, a novel transposon containing the trimethoprim resistance gene dfrG embedded into a Tn916 element in Listeria monocytogenes.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {68}, number = {5}, pages = {986-991}, doi = {10.1093/jac/dks531}, pmid = {23344576}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/pharmacology ; *DNA Transposable Elements ; DNA, Bacterial/chemistry/genetics ; Gene Transfer, Horizontal ; Listeria monocytogenes/*drug effects/*genetics ; Microarray Analysis ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Tetracycline Resistance ; *Trimethoprim Resistance ; }, abstract = {OBJECTIVES: To characterize Tn6198, a novel conjugative transposon from the clinical Listeria monocytogenes strain TTH-2007, which contains the tetracycline and trimethoprim resistance genes tet(M) and dfrG, respectively, and to assess its transferability in vitro and in situ.<br><br>METHODS: The complete sequence of Tn6198 was determined using a primer walking strategy. Horizontal gene transfer studies were performed by filter matings, as well as on the surface of smear-ripened cheese and smoked salmon. The presence of Tn916-like circular intermediates was determined by PCR. Antibiotic resistance was determined by the broth microdilution method and microarray hybridization.<br><br>RESULTS: Sequencing of Tn6198 revealed that a 3.3 kb fragment containing dfrG was integrated between open reading frames 23 and 24 of Tn916. Furthermore, an additional copy of Tn916 was present in L. monocytogenes TTH-2007. Both elements were transferred simultaneously and separately in vitro to recipients L. monocytogenes 10403S and Enterococcus faecalis JH2-2 by conjugation, resulting in either tetracycline- and trimethoprim-resistant or solely tetracycline-resistant transconjugants. On the surface of cheese and salmon, only L. monocytogenes 10403S transconjugants were detected.<br><br>CONCLUSIONS: This study reports the first Tn916-like element associated with a trimethoprim resistance gene, as well as the first fully characterized transposon conferring multidrug resistance in L. monocytogenes. This is of concern, as trimethoprim is administered to listeriosis patients with &#x3b2;-lactam allergy and as Tn6198 has a large potential for dissemination, indicated by both intra-species and inter-genus transfer.}, }
@article {pmid23344559, year = {2012}, author = {Krylov, V and Shaburova, O and Krylov, S and Pleteneva, E}, title = {A genetic approach to the development of new therapeutic phages to fight pseudomonas aeruginosa in wound infections.}, journal = {Viruses}, volume = {5}, number = {1}, pages = {15-53}, pmid = {23344559}, issn = {1999-4915}, mesh = {Biological Therapy/*methods ; Humans ; Molecular Biology/methods ; Pseudomonas Infections/*therapy ; Pseudomonas Phages/*genetics/growth &amp; development ; Pseudomonas aeruginosa/*virology ; Wound Infection/*therapy ; }, abstract = {Pseudomonas aeruginosa is a frequent participant in wound infections. Emergence of multiple antibiotic resistant strains has created significant problems in the treatment of infected wounds. Phage therapy (PT) has been proposed as a possible alternative approach. Infected wounds are the perfect place for PT applications, since the basic condition for PT is ensured; namely, the direct contact of bacteria and their viruses. Plenty of virulent ("lytic") and temperate ("lysogenic") bacteriophages are known in P. aeruginosa. However, the number of virulent phage species acceptable for PT and their mutability are limited. Besides, there are different deviations in the behavior of virulent (and temperate) phages from their expected canonical models of development. We consider some examples of non-canonical phage-bacterium interactions and the possibility of their use in PT. In addition, some optimal approaches to the development of phage therapy will be discussed from the point of view of a biologist, considering the danger of phage-assisted horizontal gene transfer (HGT), and from the point of view of a surgeon who has accepted the Hippocrates Oath to cure patients by all possible means. It is also time now to discuss the possible approaches in international cooperation for the development of PT. We think it would be advantageous to make phage therapy a kind of personalized medicine.}, }
@article {pmid23342011, year = {2013}, author = {Soares, SC and Silva, A and Trost, E and Blom, J and Ramos, R and Carneiro, A and Ali, A and Santos, AR and Pinto, AC and Diniz, C and Barbosa, EG and Dorella, FA and Aburjaile, F and Rocha, FS and Nascimento, KK and Guimarães, LC and Almeida, S and Hassan, SS and Bakhtiar, SM and Pereira, UP and Abreu, VA and Schneider, MP and Miyoshi, A and Tauch, A and Azevedo, V}, title = {The pan-genome of the animal pathogen Corynebacterium pseudotuberculosis reveals differences in genome plasticity between the biovar ovis and equi strains.}, journal = {PloS one}, volume = {8}, number = {1}, pages = {e53818}, pmid = {23342011}, issn = {1932-6203}, mesh = {Animals ; Corynebacterium/*genetics ; Gene Deletion ; Genes, Bacterial/genetics ; Genetic Variation ; Genome, Bacterial/*genetics ; Genomic Islands/genetics ; Multigene Family/genetics ; Species Specificity ; Virulence Factors/genetics ; }, abstract = {Corynebacterium pseudotuberculosis is a facultative intracellular pathogen and the causative agent of several infectious and contagious chronic diseases, including caseous lymphadenitis, ulcerative lymphangitis, mastitis, and edematous skin disease, in a broad spectrum of hosts. In addition, Corynebacterium pseudotuberculosis infections pose a rising worldwide economic problem in ruminants. The complete genome sequences of 15 C. pseudotuberculosis strains isolated from different hosts and countries were comparatively analyzed using a pan-genomic strategy. Phylogenomic, pan-genomic, core genomic, and singleton analyses revealed close relationships among pathogenic corynebacteria, the clonal-like behavior of C. pseudotuberculosis and slow increases in the sizes of pan-genomes. According to extrapolations based on the pan-genomes, core genomes and singletons, the C. pseudotuberculosis biovar ovis shows a more clonal-like behavior than the C. pseudotuberculosis biovar equi. Most of the variable genes of the biovar ovis strains were acquired in a block through horizontal gene transfer and are highly conserved, whereas the biovar equi strains contain great variability, both intra- and inter-biovar, in the 16 detected pathogenicity islands (PAIs). With respect to the gene content of the PAIs, the most interesting finding is the high similarity of the pilus genes in the biovar ovis strains compared with the great variability of these genes in the biovar equi strains. Concluding, the polymerization of complete pilus structures in biovar ovis could be responsible for a remarkable ability of these strains to spread throughout host tissues and penetrate cells to live intracellularly, in contrast with the biovar equi, which rarely attacks visceral organs. Intracellularly, the biovar ovis strains are expected to have less contact with other organisms than the biovar equi strains, thereby explaining the significant clonal-like behavior of the biovar ovis strains.}, }
@article {pmid23340801, year = {2013}, author = {Leimbach, A and Hacker, J and Dobrindt, U}, title = {E. coli as an all-rounder: the thin line between commensalism and pathogenicity.}, journal = {Current topics in microbiology and immunology}, volume = {358}, number = {}, pages = {3-32}, doi = {10.1007/82_2012_303}, pmid = {23340801}, issn = {0070-217X}, mesh = {Animals ; Escherichia coli/classification/genetics/*pathogenicity/*physiology ; Escherichia coli Infections/metabolism/*microbiology ; Genomics ; Humans ; Intestinal Mucosa/metabolism ; Intestines/*microbiology ; Phylogeny ; *Symbiosis ; }, abstract = {Escherichia coli is a paradigm for a versatile bacterial species which comprises harmless commensal as well as different pathogenic variants with the ability to either cause intestinal or extraintestinal diseases in humans and many animal hosts. Because of this broad spectrum of lifestyles and phenotypes, E. coli is a well-suited model organism to study bacterial evolution and adaptation to different growth conditions and niches. The geno- and phenotypic diversity, however, also hampers risk assessment and strain typing. A marked genome plasticity is the key to the great variability seen in this species. Acquisition of genetic information by horizontal gene transfer, gene loss as well as other genomic modifications, like DNA rearrangements and point mutations, can constantly alter the genome content and thus the fitness and competitiveness of individual variants in certain niches. Specific gene subsets and traits have been correlated with an increased potential of E. coli strains to cause intestinal or extraintestinal disease. Intestinal pathogenic E. coli strains can be reliably discriminated from non-pathogenic, commensal, or from extraintestinal E. coli pathogens based on genome content and phenotypic traits. An unambiguous distinction of extraintestinal pathogenic E. coli and commensals is, nevertheless, not so easy, as strains with the ability to cause extraintestinal infection are facultative pathogens and belong to the normal flora of many healthy individuals. Here, we compare insights into phylogeny, geno-, and phenotypic traits of commensal and pathogenic E. coli. We demonstrate that the borderline between extraintestinal virulence and intestinal fitness can be blurred as improved adaptability and competitiveness may promote intestinal colonization as well as extraintestinal infection by E. coli.}, }
@article {pmid23340439, year = {2013}, author = {Steel, M and Linz, S and Huson, DH and Sanderson, MJ}, title = {Identifying a species tree subject to random lateral gene transfer.}, journal = {Journal of theoretical biology}, volume = {322}, number = {}, pages = {81-93}, doi = {10.1016/j.jtbi.2013.01.009}, pmid = {23340439}, issn = {1095-8541}, mesh = {Animals ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Models, Genetic ; Phylogeny ; Poisson Distribution ; }, abstract = {A major problem for inferring species trees from gene trees is that evolutionary processes can sometimes favor gene tree topologies that conflict with an underlying species tree. In the case of incomplete lineage sorting, this phenomenon has recently been well-studied, and some elegant solutions for species tree reconstruction have been proposed. One particularly simple and statistically consistent estimator of the species tree under incomplete lineage sorting is to combine three-taxon analyses, which are phylogenetically robust to incomplete lineage sorting. In this paper, we consider whether such an approach will also work under lateral gene transfer (LGT). By providing an exact analysis of some cases of this model, we show that there is a zone of inconsistency when majority-rule three-taxon gene trees are used to reconstruct species trees under LGT. However, a triplet-based approach will consistently reconstruct a species tree under models of LGT, provided that the expected number of LGT transfers is not too high. Our analysis involves a novel connection between the LGT problem and random walks on cyclic graphs. We have implemented a procedure for reconstructing trees subject to LGT or lineage sorting in settings where taxon coverage may be patchy and illustrate its use on two sample data sets.}, }
@article {pmid23337592, year = {2013}, author = {Hao, W}, title = {Unrecognized fine-scale recombination can mimic the effects of adaptive radiation.}, journal = {Gene}, volume = {518}, number = {2}, pages = {483-488}, doi = {10.1016/j.gene.2012.12.107}, pmid = {23337592}, issn = {1879-0038}, mesh = {Bacterial Proteins/*genetics ; Biological Evolution ; Gene Transfer, Horizontal ; *Phylogeny ; Pseudomonas/*genetics ; Pseudomonas fluorescens/genetics ; *Recombination, Genetic ; }, abstract = {Gene sequences can undergo accelerated nucleotide changes and rapid diversification. The rapid sequence changes can then potentially lead to phylogenetic incongruence. Recently, Bodilis et al. (2011) observed artificial phylogenetic incongruence using the Pseudomonas surface protein gene oprF, and hypothesized that it was the result of a long-branch attraction artifact ultimately caused by adaptive radiation. In this study, an alternative hypothesis, namely fine-scale recombination, was tested on the same dataset. The results reveal that regions in oprF are of different evolutionary origins, and the mosaic gene structure resulted in confounding phylogenetic signals. These findings demonstrate that unrecognized fine-scale recombination can confound the phylogenetic interpretation and emphasize the limitation of using whole genes as the unit of phylogenetic analysis.}, }
@article {pmid23337100, year = {2013}, author = {Wang, Y and He, T and Schwarz, S and Zhao, Q and Shen, Z and Wu, C and Shen, J}, title = {Multidrug resistance gene cfr in methicillin-resistant coagulase-negative staphylococci from chickens, ducks, and pigs in China.}, journal = {International journal of medical microbiology : IJMM}, volume = {303}, number = {2}, pages = {84-87}, doi = {10.1016/j.ijmm.2012.12.004}, pmid = {23337100}, issn = {1618-0607}, mesh = {*Abattoirs ; Animals ; Animals, Domestic/*microbiology ; Chickens ; China ; *Drug Resistance, Multiple, Bacterial ; Ducks ; Electrophoresis, Gel, Pulsed-Field ; Gene Transfer, Horizontal ; Molecular Typing ; Plasmids ; Staphylococcal Infections/microbiology/*veterinary ; Staphylococcus/drug effects/genetics/*isolation &amp; purification ; Swine ; }, abstract = {The multidrug-resistance gene cfr was detected in coagulase-negative staphylococci from 3/401 pigs, 15/305 chickens, and 3/78 ducks from 31 different farms and one slaughterhouse in 2 provinces of China. Twenty of the 21 cfr-positive isolates were methicillin-resistant. Various SmaI-PFGE patterns were observed among the isolates of the same staphylococcal species and suggested horizontal transfer of cfr rather than clonal expansion. The detection of cfr on plasmids in the majority of the isolates supported this assumption. Analysis of the drug usage records of the farms strongly correlated with the resistance patterns of the cfr-positive isolates and suggested that antimicrobial use on farms supports the spread of the cfr gene.}, }
@article {pmid23335767, year = {2013}, author = {Orr, RJ and Stüken, A and Murray, SA and Jakobsen, KS}, title = {Evolutionary acquisition and loss of saxitoxin biosynthesis in dinoflagellates: the second "core" gene, sxtG.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {7}, pages = {2128-2136}, pmid = {23335767}, issn = {1098-5336}, mesh = {Amidinotransferases/*genetics/*metabolism ; Biosynthetic Pathways/*genetics ; Cluster Analysis ; Dinoflagellida/*genetics/*metabolism ; Evolution, Molecular ; Gene Deletion ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; Saxitoxin/*biosynthesis/*genetics ; Sequence Analysis, DNA ; }, abstract = {Saxitoxin and its derivatives are potent neurotoxins produced by several cyanobacteria and dinoflagellate species. SxtA is the initial enzyme in the biosynthesis of saxitoxin. The dinoflagellate full mRNA and partial genomic sequences have previously been characterized, and it appears that sxtA originated in dinoflagellates through a horizontal gene transfer from a bacterium. So far, little is known about the remaining genes involved in this pathway in dinoflagellates. Here we characterize sxtG, an amidinotransferase enzyme gene that putatively encodes the second step in saxitoxin biosynthesis. In this study, the entire sxtG transcripts from Alexandrium fundyense CCMP1719 and Alexandrium minutum CCMP113 were amplified and sequenced. The transcripts contained typical dinoflagellate spliced leader sequences and eukaryotic poly(A) tails. In addition, partial sxtG transcript fragments were amplified from four additional Alexandrium species and Gymnodinium catenatum. The phylogenetic inference of dinoflagellate sxtG, congruent with sxtA, revealed a bacterial origin. However, it is not known if sxtG was acquired independently of sxtA. Amplification and sequencing of the corresponding genomic sxtG region revealed noncanonical introns. These introns show a high interspecies and low intraspecies variance, suggesting multiple independent acquisitions and losses. Unlike sxtA, sxtG was also amplified from Alexandrium species not known to synthesize saxitoxin. However, amplification was not observed for 22 non-saxitoxin-producing dinoflagellate species other than those of the genus Alexandrium or G. catenatum. This result strengthens our hypothesis that saxitoxin synthesis has been secondarily lost in conjunction with sxtA for some descendant species.}, }
@article {pmid23335015, year = {2013}, author = {Bansal, MS and Banay, G and Harlow, TJ and Gogarten, JP and Shamir, R}, title = {Systematic inference of highways of horizontal gene transfer in prokaryotes.}, journal = {Bioinformatics (Oxford, England)}, volume = {29}, number = {5}, pages = {571-579}, doi = {10.1093/bioinformatics/btt021}, pmid = {23335015}, issn = {1367-4811}, mesh = {*Algorithms ; Bacteria/classification/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; *Phylogeny ; }, abstract = {MOTIVATION: Horizontal gene transfer (HGT) plays a crucial role in the evolution of prokaryotic species. Typically, no more than a few genes are horizontally transferred between any two species. However, several studies identified pairs of species (or linages) between which many different genes were horizontally transferred. Such a pair is said to be linked by a highway of gene sharing. Inferring such highways is crucial to understanding the evolution of prokaryotes and for inferring past symbiotic and ecological associations among different species.<br><br>RESULTS: We present a new improved method for systematically detecting highways of gene sharing. As we demonstrate using a variety of simulated datasets, our method is highly accurate and efficient, and robust to noise and high rates of HGT. We further validate our method by applying it to a published dataset of >22 000 gene trees from 144 prokaryotic species. Our method makes it practical, for the first time, to perform accurate highway analysis quickly and easily even on large datasets with high rates of HGT.<br><br>An implementation of the method can be freely downloaded from: http://acgt.cs.tau.ac.il/hide.}, }
@article {pmid23333318, year = {2013}, author = {Reinhard, F and Miyazaki, R and Pradervand, N and van der Meer, JR}, title = {Cell differentiation to "mating bodies" induced by an integrating and conjugative element in free-living bacteria.}, journal = {Current biology : CB}, volume = {23}, number = {3}, pages = {255-259}, doi = {10.1016/j.cub.2012.12.025}, pmid = {23333318}, issn = {1879-0445}, mesh = {Conjugation, Genetic ; DNA, Bacterial/*physiology ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Pseudomonas aeruginosa/*physiology ; }, abstract = {Lateral gene transfer (LGT) is one of the most important processes leading to prokaryotic genome innovation. LGT is typically associated with conjugative plasmids and bacteriophages, but recently, a new class of mobile DNA known as integrating and conjugative elements (ICE) was discovered, which is abundant and widespread among bacterial genomes. By studying at the single-cell level the behavior of a prevalent ICE type in the genus Pseudomonas, we uncover the remarkable way in which the ICE orchestrates host cell differentiation to ensure horizontal transmission. We find that the ICE induces a state of transfer competence (tc) in 3%-5% of cells in a population under nongrowing conditions. ICE factors control the development of tc cells into specific assemblies that we name "mating bodies." Interestingly, cells in mating bodies undergo fewer and slower division than non-tc cells and eventually lyse. Mutations in ICE genes disrupting mating-body formation lead to 5-fold decreased ICE transfer rates. Hence, by confining the tc state to a small proportion of the population, ICE horizontal transmission is achieved with little cost in terms of vertical transmission. Given the low transfer frequencies of most ICE, we anticipate regulation by subpopulation differentiation to be widespread.}, }
@article {pmid23333146, year = {2013}, author = {Yap, JM and Goldsmith, CE and Moore, JE}, title = {Integrity of bacterial genomic DNA after autoclaving: possible implications for horizontal gene transfer and clinical waste management.}, journal = {The Journal of hospital infection}, volume = {83}, number = {3}, pages = {247-249}, doi = {10.1016/j.jhin.2012.11.016}, pmid = {23333146}, issn = {1532-2939}, mesh = {DNA, Bacterial/genetics/*radiation effects ; Escherichia coli/*genetics/radiation effects ; Gene Transfer, Horizontal/*radiation effects ; Hot Temperature ; Humans ; Medical Waste Disposal/*methods ; Polymerase Chain Reaction ; Pseudomonas aeruginosa/*genetics/radiation effects ; Salmonella/*genetics/radiation effects ; Sterilization/*methods ; Time Factors ; }, abstract = {Current autoclaving practices are designed to kill bacteria. Little is known about the effect of autoclaving on the integrity of bacterial genomic DNA. An experiment was performed to examine the effect of standard autoclaving on the integrity of bacterial DNA, employing polymerase chain reaction (PCR) as an indicator of DNA integrity. Amplifiable PCR signal was observed at t = 10, 20 and 30 min autoclaving time for Pseudomonas aeruginosa NCTC 10662; at t = 10, 20, 30 and 40 min for Salmonella Nottingham NCTC 7832; and at t = 10 and 20 min for Escherichia coli NCTC 9001. Careful consideration should therefore be given to residual molecular artefacts in future risk and environmental impact assessments, where the legacy of residual genomic DNA from dead bacterial and higher organisms may act as a potential reservoir, thereby feeding horizontal gene transfer scenarios in viable cells with potential hazardous genes of virulence, persistence or antibiotic resistance characteristics.}, }
@article {pmid23332119, year = {2013}, author = {Polz, MF and Alm, EJ and Hanage, WP}, title = {Horizontal gene transfer and the evolution of bacterial and archaeal population structure.}, journal = {Trends in genetics : TIG}, volume = {29}, number = {3}, pages = {170-175}, pmid = {23332119}, issn = {0168-9525}, support = {U54 GM088558/GM/NIGMS NIH HHS/United States ; GM088558-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Ecosystem ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genotype ; Multigene Family ; }, abstract = {Many bacterial and archaeal lineages have a history of extensive and ongoing horizontal gene transfer and loss, as evidenced by the large differences in genome content even among otherwise closely related isolates. How ecologically cohesive populations might evolve and be maintained under such conditions of rapid gene turnover has remained controversial. Here we synthesize recent literature demonstrating the importance of habitat and niche in structuring horizontal gene transfer. This leads to a model of ecological speciation via gradual genetic isolation triggered by differential habitat-association of nascent populations. Further, we hypothesize that subpopulations can evolve through local gene-exchange networks by tapping into a gene pool that is adaptive towards local, continuously changing organismic interactions and is, to a large degree, responsible for the observed rapid gene turnover. Overall, these insights help to explain how bacteria and archaea form populations that display both ecological cohesion and high genomic diversity.}, }
@article {pmid23330059, year = {2013}, author = {Chadha, T and Trindade, AA}, title = {Phylogenetic analysis of pbp genes in treponemes.}, journal = {Infection ecology &amp; epidemiology}, volume = {3}, number = {}, pages = {}, pmid = {23330059}, issn = {2000-8686}, abstract = {BACKGROUND: β-Lactamases are the main cause of bacterial resistance to penicillin, cephalosporins, and related β-lactam compounds. The presence of the novel penicillin-binding protein (pbp) Tp47 in Treponema pallidum has been reported to be a well-known mechanism for turnover of b-lactam antibiotics. Although, T. pallidum remains sensitive to penicillin, clinically significant resistance to macrolides has emerged in many developing countries. The genome sequence of T. pallidum has shown the presence of genes encoding pbp, but there are no current reports of the presence of mobile plasmids.<br><br>METHODS: The phylogenetic analysis is used to study the diversity of chromosomal pbp genes and its relatedness to Tp47 in Treponema species.<br><br>RESULTS: In our study, genes encoding penicillin-binding proteins that showed significant similarity to each other appeared in separate clusters.<br><br>CONCLUSION: Tp47 showed no substantial similarity to other &#x3b2;-lactamases in treponemes. The relatedness of Treponema denticola to other treponemes, including T. pallidum, and the reported presence of natural mobile antibiotic determinants highlight the importance of investigating the diversity of pbp genes in Treponema species. This will lead to a greater understanding of its potential to develop additional antibiotic resistance via horizontal gene transfer that could seriously compromise the treatment and control of syphilis.}, }
@article {pmid23329317, year = {2013}, author = {Johnson, AP and Woodford, N}, title = {Global spread of antibiotic resistance: the example of New Delhi metallo-β-lactamase (NDM)-mediated carbapenem resistance.}, journal = {Journal of medical microbiology}, volume = {62}, number = {Pt 4}, pages = {499-513}, doi = {10.1099/jmm.0.052555-0}, pmid = {23329317}, issn = {1473-5644}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics/*metabolism ; Carbapenems/*pharmacology ; Gene Transfer, Horizontal ; Global Health ; Gram-Negative Bacteria/*drug effects/*enzymology/genetics ; Gram-Negative Bacterial Infections/*epidemiology/*microbiology ; Humans ; Plasmids ; *beta-Lactam Resistance ; beta-Lactamases/genetics/*metabolism ; }, abstract = {The rapidity with which new types of antibiotic resistance can disseminate globally following their initial emergence or recognition is exemplified by the novel carbapenemase New Delhi metallo-β-lactamase (NDM). The first documented case of infection caused by bacteria producing NDM occurred in 2008, although retrospective analyses of stored cultures have identified the gene encoding this enzyme (blaNDM) in Enterobacteriaceae isolated in 2006. Since its first description, NDM carbapenemase has been reported from 40 countries worldwide, encompassing all continents except South America and Antarctica. The spread of NDM has a complex epidemiology involving the spread of a variety of species of NDM-positive bacteria and the inter-strain, inter-species and inter-genus transmission of diverse plasmids containing blaNDM, with the latter mechanism having played a more prominent role to date. The spread of NDM illustrates that antibiotic resistance is a public health problem that transcends national borders and will require international cooperation between health authorities if it is to be controlled.}, }
@article {pmid23326581, year = {2013}, author = {Liman, R and Facey, PD and van Keulen, G and Dyson, PJ and Del Sol, R}, title = {A laterally acquired galactose oxidase-like gene is required for aerial development during osmotic stress in Streptomyces coelicolor.}, journal = {PloS one}, volume = {8}, number = {1}, pages = {e54112}, pmid = {23326581}, issn = {1932-6203}, support = {BB/E019242/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Actinobacteria/genetics/metabolism ; Aerobiosis/genetics/physiology ; Bacterial Proteins/genetics/metabolism ; Galactose Oxidase/*genetics/metabolism ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Mutation ; Osmosis ; *Osmotic Pressure ; Phylogeny ; Promoter Regions, Genetic ; Sigma Factor/genetics/metabolism ; *Streptomyces coelicolor/genetics/metabolism ; }, abstract = {Phylogenetic reconstruction revealed that most Actinobacterial orthologs of S. coelicolor SCO2837, encoding a metal-dependent galactose oxidase-like protein, are found within Streptomyces and were probably acquired by horizontal gene transfer from fungi. Disruption of SCO2837 (glxA) caused a conditional bld phenotype that could not be reversed by extracellular complementation. Studies aimed at characterising the regulation of expression of glxA showed that it is not a target for other bld genes. We provide evidence that glxA is required for osmotic adaptation, although independently from the known osmotic stress response element SigB. glxA has been predicted to be part of an operon with the transcription unit comprising the upstream cslA gene and glxA. However, both phenotypic and expression studies indicate that it is also expressed from an independent promoter region internal to cslA. GlxA displays an in situ localisation pattern similar to that one observed for CslA at hyphal tips, but localisation of the former is independent of the latter. The functional role of GlxA in relation to CslA is discussed.}, }
@article {pmid23326305, year = {2013}, author = {Krupovic, M and Gonnet, M and Hania, WB and Forterre, P and Erauso, G}, title = {Insights into dynamics of mobile genetic elements in hyperthermophilic environments from five new Thermococcus plasmids.}, journal = {PloS one}, volume = {8}, number = {1}, pages = {e49044}, pmid = {23326305}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Archaeal Proteins/genetics ; Archaeal Viruses/genetics ; DNA Transposable Elements/*genetics ; DNA, Archaeal/chemistry/genetics ; Gene Order ; Gene Transfer, Horizontal ; Genes, Archaeal/genetics ; Hydrothermal Vents/*microbiology ; Methanococcales/classification/genetics ; Molecular Sequence Data ; Phylogeny ; Plasmids/chemistry/classification/*genetics ; Pyrococcus abyssi/virology ; RNA, Ribosomal, 16S/genetics ; Replication Origin/genetics ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Temperature ; Thermococcales/classification/*genetics ; Thermococcus ; }, abstract = {Mobilome of hyperthermophilic archaea dwelling in deep-sea hydrothermal vents is poorly characterized. To gain insight into genetic diversity and dynamics of mobile genetic elements in these environments we have sequenced five new plasmids from different Thermococcus strains that have been isolated from geographically remote hydrothermal vents. The plasmids were ascribed to two subfamilies, pTN2-like and pEXT9a-like. Gene content and phylogenetic analyses illuminated a robust connection between pTN2-like plasmids and Pyrococcus abyssi virus 1 (PAV1), with roughly half of the viral genome being composed of genes that have homologues in plasmids. Unexpectedly, pEXT9a-like plasmids were found to be closely related to the previously sequenced plasmid pMETVU01 from Methanocaldococcus vulcanius M7. Our data suggests that the latter observation is most compatible with an unprecedented horizontal transfer of a pEXT9a-like plasmid from Thermococcales to Methanococcales. Gene content analysis revealed that thermococcal plasmids encode Hfq-like proteins and toxin-antitoxin (TA) systems of two different families, VapBC and RelBE. Notably, although abundant in archaeal genomes, to our knowledge, TA and hfq-like genes have not been previously found in archaeal plasmids or viruses. Finally, the plasmids described here might prove to be useful in developing new genetic tools for hyperthermophiles.}, }
@article {pmid23326247, year = {2013}, author = {Thomas, J and Lee, CA and Grossman, AD}, title = {A conserved helicase processivity factor is needed for conjugation and replication of an integrative and conjugative element.}, journal = {PLoS genetics}, volume = {9}, number = {1}, pages = {e1003198}, pmid = {23326247}, issn = {1553-7404}, support = {R01 GM050895/GM/NIGMS NIH HHS/United States ; GM50895/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacillus subtilis/*genetics ; *Bacterial Proteins/genetics/metabolism ; Conjugation, Genetic ; *DNA Helicases/genetics/metabolism ; DNA Replication/*genetics ; DNA-Binding Proteins/genetics/metabolism ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Interspersed Repetitive Sequences/*genetics ; }, abstract = {Integrative and conjugative elements (ICEs) are agents of horizontal gene transfer and have major roles in evolution and acquisition of new traits, including antibiotic resistances. ICEs are found integrated in a host chromosome and can excise and transfer to recipient bacteria via conjugation. Conjugation involves nicking of the ICE origin of transfer (oriT) by the ICE-encoded relaxase and transfer of the nicked single strand of ICE DNA. For ICEBs1 of Bacillus subtilis, nicking of oriT by the ICEBs1 relaxase NicK also initiates rolling circle replication. This autonomous replication of ICEBs1 is critical for stability of the excised element in growing cells. We found a conserved and previously uncharacterized ICE gene that is required for conjugation and replication of ICEBs1. Our results indicate that this gene, helP (formerly ydcP), encodes a helicase processivity factor that enables the host-encoded helicase PcrA to unwind the double-stranded ICEBs1 DNA. HelP was required for both conjugation and replication of ICEBs1, and HelP and NicK were the only ICEBs1 proteins needed for replication from ICEBs1 oriT. Using chromatin immunoprecipitation, we measured association of HelP, NicK, PcrA, and the host-encoded single-strand DNA binding protein Ssb with ICEBs1. We found that NicK was required for association of HelP and PcrA with ICEBs1 DNA. HelP was required for association of PcrA and Ssb with ICEBs1 regions distal, but not proximal, to oriT, indicating that PcrA needs HelP to progress beyond nicked oriT and unwind ICEBs1. In vitro, HelP directly stimulated the helicase activity of the PcrA homologue UvrD. Our findings demonstrate that HelP is a helicase processivity factor needed for efficient unwinding of ICEBs1 for conjugation and replication. Homologues of HelP and PcrA-type helicases are encoded on many known and putative ICEs. We propose that these factors are essential for ICE conjugation, replication, and genetic stability.}, }
@article {pmid23324436, year = {2013}, author = {Lo, WS and Chen, LL and Chung, WC and Gasparich, GE and Kuo, CH}, title = {Comparative genome analysis of Spiroplasma melliferum IPMB4A, a honeybee-associated bacterium.}, journal = {BMC genomics}, volume = {14}, number = {}, pages = {22}, pmid = {23324436}, issn = {1471-2164}, mesh = {Animals ; Bees/*microbiology ; Evolution, Molecular ; Genetic Variation/genetics ; Genome, Bacterial/genetics ; Genomics/*methods ; Molecular Sequence Annotation ; Mycoplasma/genetics ; Phylogeny ; Phytoplasma/genetics ; Sequence Analysis ; Species Specificity ; Spiroplasma/*genetics/isolation &amp; purification/physiology ; }, abstract = {BACKGROUND: The genus Spiroplasma contains a group of helical, motile, and wall-less bacteria in the class Mollicutes. Similar to other members of this class, such as the animal-pathogenic Mycoplasma and the plant-pathogenic 'Candidatus Phytoplasma', all characterized Spiroplasma species were found to be associated with eukaryotic hosts. While most of the Spiroplasma species appeared to be harmless commensals of insects, a small number of species have evolved pathogenicity toward various arthropods and plants. In this study, we isolated a novel strain of honeybee-associated S. melliferum and investigated its genetic composition and evolutionary history by whole-genome shotgun sequencing and comparative analysis with other Mollicutes genomes.<br><br>RESULTS: The whole-genome shotgun sequencing of S. melliferum IPMB4A produced a draft assembly that was ~1.1 Mb in size and covered ~80% of the chromosome. Similar to other Spiroplasma genomes that have been studied to date, we found that this genome contains abundant repetitive sequences that originated from plectrovirus insertions. These phage fragments represented a major obstacle in obtaining a complete genome sequence of Spiroplasma with the current sequencing technology. Comparative analysis of S. melliferum IPMB4A with other Spiroplasma genomes revealed that these phages may have facilitated extensive genome rearrangements in these bacteria and contributed to horizontal gene transfers that led to species-specific adaptation to different eukaryotic hosts. In addition, comparison of gene content with other Mollicutes suggested that the common ancestor of the SEM (Spiroplasma, Entomoplasma, and Mycoplasma) clade may have had a relatively large genome and flexible metabolic capacity; the extremely reduced genomes of present day Mycoplasma and 'Candidatus Phytoplasma' species are likely to be the result of independent gene losses in these lineages.<br><br>CONCLUSIONS: The findings in this study highlighted the significance of phage insertions and horizontal gene transfer in the evolution of bacterial genomes and acquisition of pathogenicity. Furthermore, the inclusion of Spiroplasma in comparative analysis has improved our understanding of genome evolution in Mollicutes. Future improvements in the taxon sampling of available genome sequences in this group are required to provide further insights into the evolution of these important pathogens of humans, animals, and plants.}, }
@article {pmid23324387, year = {2013}, author = {Duplouy, A and Iturbe-Ormaetxe, I and Beatson, SA and Szubert, JM and Brownlie, JC and McMeniman, CJ and McGraw, EA and Hurst, GD and Charlat, S and O'Neill, SL and Woolfit, M}, title = {Draft genome sequence of the male-killing Wolbachia strain wBol1 reveals recent horizontal gene transfers from diverse sources.}, journal = {BMC genomics}, volume = {14}, number = {}, pages = {20}, pmid = {23324387}, issn = {1471-2164}, mesh = {Adenosine Triphosphatases/genetics ; Animals ; Bacterial Proteins/genetics ; Butterflies/microbiology ; *Gene Transfer, Horizontal ; Genome, Bacterial/*genetics ; Male ; Membrane Transport Proteins/genetics ; Molecular Sequence Annotation ; Phylogeny ; SEC Translocation Channels ; SecA Proteins ; Symbiosis/genetics ; Wolbachia/*genetics ; }, abstract = {BACKGROUND: The endosymbiont Wolbachia pipientis causes diverse and sometimes dramatic phenotypes in its invertebrate hosts. Four Wolbachia strains sequenced to date indicate that the constitution of the genome is dynamic, but these strains are quite divergent and do not allow resolution of genome diversification over shorter time periods. We have sequenced the genome of the strain wBol1-b, found in the butterfly Hypolimnas bolina, which kills the male offspring of infected hosts during embyronic development and is closely related to the non-male-killing strain wPip from Culex pipiens.<br><br>RESULTS: The genomes of wBol1-b and wPip are similar in genomic organisation, sequence and gene content, but show substantial differences at some rapidly evolving regions of the genome, primarily associated with prophage and repetitive elements. We identified 44 genes in wBol1-b that do not have homologs in any previously sequenced strains, indicating that Wolbachia's non-core genome diversifies rapidly. These wBol1-b specific genes include a number that have been recently horizontally transferred from phylogenetically distant bacterial taxa. We further report a second possible case of horizontal gene transfer from a eukaryote into Wolbachia.<br><br>CONCLUSIONS: Our analyses support the developing view that many endosymbiotic genomes are highly dynamic, and are exposed and receptive to exogenous genetic material from a wide range of sources. These data also suggest either that this bacterial species is particularly permissive for eukaryote-to-prokaryote gene transfers, or that these transfers may be more common than previously believed. The wBol1-b-specific genes we have identified provide candidates for further investigations of the genomic bases of phenotypic differences between closely-related Wolbachia strains.}, }
@article {pmid23324080, year = {2013}, author = {Seitzer, P and Huynh, TA and Facciotti, MT}, title = {JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison.}, journal = {BMC bioinformatics}, volume = {14}, number = {}, pages = {18}, pmid = {23324080}, issn = {1471-2105}, mesh = {Algorithms ; Alphaproteobacteria/genetics ; Cluster Analysis ; Gammaproteobacteria/genetics ; Genes, Bacterial ; Genomics/*methods ; Sequence Analysis, DNA ; *Software ; }, abstract = {BACKGROUND: Cross-species comparisons of gene neighborhoods (also called genomic contexts) in microbes may provide insight into determining functionally related or co-regulated sets of genes, suggest annotations of previously un-annotated genes, and help to identify horizontal gene transfer events across microbial species. Existing tools to investigate genomic contexts, however, lack features for dynamically comparing and exploring genomic regions from multiple species. As DNA sequencing technologies improve and the number of whole sequenced microbial genomes increases, a user-friendly genome context comparison platform designed for use by a broad range of users promises to satisfy a growing need in the biological community.<br><br>RESULTS: Here we present JContextExplorer: a tool that organizes genomic contexts into branching diagrams. We implement several alternative context-comparison and tree rendering algorithms, and allow for easy transitioning between different clustering algorithms. To facilitate genomic context analysis, our tool implements GUI features, such as text search filtering, point-and-click interrogation of individual contexts, and genomic visualization via a multi-genome browser. We demonstrate a use case of our tool by attempting to resolve annotation ambiguities between two highly homologous yet functionally distinct genes in a set of 22 alpha and gamma proteobacteria.<br><br>CONCLUSIONS: JContextExplorer should enable a broad range of users to analyze and explore genomic contexts. The program has been tested on Windows, Mac, and Linux operating systems, and is implemented both as an executable JAR file and java WebStart. Program executables, source code, and documentation is available at http://www.bme.ucdavis.edu/facciotti/resources_data/software/.}, }
@article {pmid23321705, year = {2013}, author = {King, J and Armstead, I and Harper, J and Ramsey, L and Snape, J and Waugh, R and James, C and Thomas, A and Gasior, D and Kelly, R and Roberts, L and Gustafson, P and King, I}, title = {Exploitation of interspecific diversity for monocot crop improvement.}, journal = {Heredity}, volume = {110}, number = {5}, pages = {475-483}, pmid = {23321705}, issn = {1365-2540}, support = {BB/E006736/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/E00654X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Brachypodium/genetics ; Chromosome Mapping/methods ; Chromosomes, Plant ; Crops, Agricultural/*genetics ; Festuca/*genetics ; Gene Transfer, Horizontal ; Genetic Engineering/*methods ; Genetic Linkage ; Genetic Variation ; *Genome, Plant ; Hordeum/genetics ; Lolium/*genetics ; Meiosis ; Microsatellite Repeats ; Polymorphism, Single Nucleotide ; Sorghum/genetics ; Synteny ; Triticum/genetics ; }, abstract = {In many cultivated crop species there is limited genetic variation available for the development of new higher yielding varieties adapted to climate change and sustainable farming practises. The distant relatives of crop species provide a vast and largely untapped reservoir of genetic variation for a wide range of agronomically important traits that can be exploited by breeders for crop improvement. In this paper, in what we believe to be the largest introgression programme undertaken in the monocots, we describe the transfer of the entire genome of Festuca pratensis into Lolium perenne in overlapping chromosome segments. The L. perenne/F. pratensis introgressions were identified and characterised via 131 simple sequence repeats and 1612 SNPs anchored to the rice genome. Comparative analyses were undertaken to determine the syntenic relationship between L. perenne/F. pratensis and rice, wheat, barley, sorghum and Brachypodium distachyon. Analyses comparing recombination frequency and gene distribution indicated that a large proportion of the genes within the genome are located in the proximal regions of chromosomes which undergo low/very low frequencies of recombination. Thus, it is proposed that past breeding efforts to produce improved varieties have centred on the subset of genes located in the distal regions of chromosomes where recombination is highest. The use of alien introgression for crop improvement is important for meeting the challenges of global food supply and the monocots such as the forage grasses and cereals, together with recent technological advances in molecular biology, can help meet these challenges.}, }
@article {pmid23316568, year = {2012}, author = {López-García, P}, title = {The place of viruses in biology in light of the metabolism- versus-replication-first debate.}, journal = {History and philosophy of the life sciences}, volume = {34}, number = {3}, pages = {391-406}, pmid = {23316568}, issn = {0391-9714}, mesh = {Animals ; *Biological Evolution ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genes, Viral/*genetics ; History, 20th Century ; History, 21st Century ; Humans ; *Origin of Life ; *Phylogeny ; Virus Replication/*genetics ; Viruses/*genetics/*metabolism ; }, abstract = {The last decade has seen a revival of old virocentric ideas. These concepts are heterogeneous, extending from proposals that consider viruses functionally as living beings and/or as descendants of viral lineages that preceded cell evolution to other claims that consider viruses and/or some viral families a fourth domain of life. While the debates about whether viruses are alive or not and whether some virus-like replicators preceded the first cells fall under the long-lasting dichotomous view on the nature and origin of life (metabolism- versus replication-first), the claim that some giant viruses form a fourth domain in an organismal tree of life is not consistent with current evidence and can be falsified.}, }
@article {pmid23316438, year = {2013}, author = {Manning, VA and Pandelova, I and Dhillon, B and Wilhelm, LJ and Goodwin, SB and Berlin, AM and Figueroa, M and Freitag, M and Hane, JK and Henrissat, B and Holman, WH and Kodira, CD and Martin, J and Oliver, RP and Robbertse, B and Schackwitz, W and Schwartz, DC and Spatafora, JW and Turgeon, BG and Yandava, C and Young, S and Zhou, S and Zeng, Q and Grigoriev, IV and Ma, LJ and Ciuffetti, LM}, title = {Comparative genomics of a plant-pathogenic fungus, Pyrenophora tritici-repentis, reveals transduplication and the impact of repeat elements on pathogenicity and population divergence.}, journal = {G3 (Bethesda, Md.)}, volume = {3}, number = {1}, pages = {41-63}, pmid = {23316438}, issn = {2160-1836}, support = {R01 HG000225/HG/NHGRI NIH HHS/United States ; }, mesh = {Ascomycota/*genetics/*pathogenicity ; Base Sequence ; Chromosome Mapping ; Cytogenetic Analysis ; DNA Primers/genetics ; DNA Transposable Elements/genetics ; *Evolution, Molecular ; Gene Duplication/genetics ; *Genetic Variation ; Genome, Fungal/*genetics ; Genomics ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Annotation ; Molecular Sequence Data ; Mycotoxins/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Triticum/*microbiology ; }, abstract = {Pyrenophora tritici-repentis is a necrotrophic fungus causal to the disease tan spot of wheat, whose contribution to crop loss has increased significantly during the last few decades. Pathogenicity by this fungus is attributed to the production of host-selective toxins (HST), which are recognized by their host in a genotype-specific manner. To better understand the mechanisms that have led to the increase in disease incidence related to this pathogen, we sequenced the genomes of three P. tritici-repentis isolates. A pathogenic isolate that produces two known HSTs was used to assemble a reference nuclear genome of approximately 40 Mb composed of 11 chromosomes that encode 12,141 predicted genes. Comparison of the reference genome with those of a pathogenic isolate that produces a third HST, and a nonpathogenic isolate, showed the nonpathogen genome to be more diverged than those of the two pathogens. Examination of gene-coding regions has provided candidate pathogen-specific proteins and revealed gene families that may play a role in a necrotrophic lifestyle. Analysis of transposable elements suggests that their presence in the genome of pathogenic isolates contributes to the creation of novel genes, effector diversification, possible horizontal gene transfer events, identified copy number variation, and the first example of transduplication by DNA transposable elements in fungi. Overall, comparative analysis of these genomes provides evidence that pathogenicity in this species arose through an influx of transposable elements, which created a genetically flexible landscape that can easily respond to environmental changes.}, }
@article {pmid23315733, year = {2013}, author = {Jechalke, S and Kopmann, C and Rosendahl, I and Groeneweg, J and Weichelt, V and Krögerrecklenfort, E and Brandes, N and Nordwig, M and Ding, GC and Siemens, J and Heuer, H and Smalla, K}, title = {Increased abundance and transferability of resistance genes after field application of manure from sulfadiazine-treated pigs.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {5}, pages = {1704-1711}, pmid = {23315733}, issn = {1098-5336}, mesh = {Animals ; Anti-Bacterial Agents/*therapeutic use ; *Drug Resistance, Bacterial ; Escherichia coli/genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; *Manure ; Plant Roots/microbiology ; Plasmids/isolation &amp; purification ; Poaceae/microbiology ; *Soil Microbiology ; Sulfadiazine/*therapeutic use ; Swine ; Zea mays/microbiology ; }, abstract = {Spreading manure containing antibiotics in agriculture is assumed to stimulate the dissemination of antibiotic resistance in soil bacterial populations. Plant roots influencing the soil environment and its microflora by exudation of growth substrates might considerably increase this effect. In this study, the effects of manure from pigs treated with sulfadiazine (SDZ), here called SDZ manure, on the abundance and transferability of sulfonamide resistance genes sul1 and sul2 in the rhizosphere of maize and grass were compared to the effects in bulk soil in a field experiment. In plots that repeatedly received SDZ manure, a significantly higher abundance of both sul genes was detected compared to that in plots where manure from untreated pigs was applied. Significantly lower abundances of sul genes relative to bacterial ribosomal genes were encountered in the rhizosphere than in bulk soil. However, in contrast to results for bulk soil, the sul gene abundance in the SDZ manure-treated rhizosphere constantly deviated from control treatments over a period of 6 weeks after manuring, suggesting ongoing antibiotic selection over this period. Transferability of sulfonamide resistance was analyzed by capturing resistance plasmids from soil communities into Escherichia coli. Increased rates of plasmid capture were observed in samples from SDZ manure-treated bulk soil and the rhizosphere of maize and grass. More than 97% of the captured plasmids belonged to the LowGC type (having low G+C content), giving further evidence for their important contribution to the environmental spread of antibiotic resistance. In conclusion, differences between bulk soil and rhizosphere need to be considered when assessing the risks associated with the spreading of antibiotic resistance.}, }
@article {pmid23313535, year = {2013}, author = {Drago, L and Mattina, R and De Vecchi, E and Toscano, M}, title = {Phenotypic and genotypic antibiotic resistance in some probiotics proposed for medical use.}, journal = {International journal of antimicrobial agents}, volume = {41}, number = {4}, pages = {396-397}, doi = {10.1016/j.ijantimicag.2012.11.015}, pmid = {23313535}, issn = {1872-7913}, mesh = {Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Bacterial/*genetics/physiology ; Erythromycin/pharmacology ; Europe ; Gastrointestinal Tract/microbiology ; Gene Transfer, Horizontal/genetics ; Genotype ; Gentamicins/pharmacology ; Humans ; Italy ; Lactobacillus/genetics ; Microbial Sensitivity Tests ; Penicillins/pharmacology ; Phenotype ; *Probiotics ; Tetracycline/pharmacology ; }, }
@article {pmid23308280, year = {2013}, author = {Schumacher, J and Gautier, A and Morgant, G and Studt, L and Ducrot, PH and Le Pêcheur, P and Azeddine, S and Fillinger, S and Leroux, P and Tudzynski, B and Viaud, M}, title = {A functional bikaverin biosynthesis gene cluster in rare strains of Botrytis cinerea is positively controlled by VELVET.}, journal = {PloS one}, volume = {8}, number = {1}, pages = {e53729}, pmid = {23308280}, issn = {1932-6203}, mesh = {Amides/pharmacology ; Botrytis/classification/drug effects/*genetics ; Drug Resistance, Fungal/drug effects ; Fungal Proteins/*genetics/metabolism ; Fusarium/classification/genetics ; *Gene Expression Regulation, Fungal ; Gene Transfer, Horizontal ; Genetic Complementation Test ; Genetic Loci ; Melanins/*biosynthesis/genetics ; *Multigene Family ; Mutation ; Phylogeny ; Sequence Homology, Nucleic Acid ; Transcription Factors/*genetics/metabolism ; Xanthones/*metabolism ; }, abstract = {The gene cluster responsible for the biosynthesis of the red polyketidic pigment bikaverin has only been characterized in Fusarium ssp. so far. Recently, a highly homologous but incomplete and nonfunctional bikaverin cluster has been found in the genome of the unrelated phytopathogenic fungus Botrytis cinerea. In this study, we provided evidence that rare B. cinerea strains such as 1750 have a complete and functional cluster comprising the six genes orthologous to Fusarium fujikuroi ffbik1-ffbik6 and do produce bikaverin. Phylogenetic analysis confirmed that the whole cluster was acquired from Fusarium through a horizontal gene transfer (HGT). In the bikaverin-nonproducing strain B05.10, the genes encoding bikaverin biosynthesis enzymes are nonfunctional due to deleterious mutations (bcbik2-3) or missing (bcbik1) but interestingly, the genes encoding the regulatory proteins BcBIK4 and BcBIK5 do not harbor deleterious mutations which suggests that they may still be functional. Heterologous complementation of the F. fujikuroi Δffbik4 mutant confirmed that bcbik4 of strain B05.10 is indeed fully functional. Deletion of bcvel1 in the pink strain 1750 resulted in loss of bikaverin and overproduction of melanin indicating that the VELVET protein BcVEL1 regulates the biosynthesis of the two pigments in an opposite manner. Although strain 1750 itself expresses a truncated BcVEL1 protein (100 instead of 575 aa) that is nonfunctional with regard to sclerotia formation, virulence and oxalic acid formation, it is sufficient to regulate pigment biosynthesis (bikaverin and melanin) and fenhexamid HydR2 type of resistance. Finally, a genetic cross between strain 1750 and a bikaverin-nonproducing strain sensitive to fenhexamid revealed that the functional bikaverin cluster is genetically linked to the HydR2 locus.}, }
@article {pmid23308197, year = {2013}, author = {Li, H and Zhao, C and Chen, H and Zhang, F and He, W and Wang, X and Wang, Q and Yang, R and Zhou, D and Wang, H}, title = {Identification of gene clusters associated with host adaptation and antibiotic resistance in Chinese Staphylococcus aureus isolates by microarray-based comparative genomics.}, journal = {PloS one}, volume = {8}, number = {1}, pages = {e53341}, pmid = {23308197}, issn = {1932-6203}, mesh = {Adaptation, Physiological/*genetics ; Animals ; China ; Clone Cells ; Comparative Genomic Hybridization ; Drug Resistance, Multiple, Bacterial/drug effects/*genetics ; Gene Transfer, Horizontal ; Genomics ; Host Specificity ; Methicillin-Resistant Staphylococcus aureus/*classification/drug effects/*genetics/isolation &amp; purification ; Multigene Family ; Phylogeny ; Phylogeography ; Plasmids ; Species Specificity ; Staphylococcal Infections/drug therapy/microbiology ; Staphylococcus aureus/*classification/drug effects/*genetics/isolation &amp; purification ; Staphylococcus epidermidis/genetics ; Swine/microbiology ; }, abstract = {A comparative genomic microarray comprising 2,457 genes from two whole genomes of S. aureus was employed for the comparative genome hybridization analysis of 50 strains of divergent clonal lineages, including methicillin-resistant S. aureus (MRSA), methicillin-susceptible S. aureus (MSSA), and swine strains in China. Large-scale validation was confirmed via polymerase chain reaction in 160 representative clinical strains. All of the 50 strains were clustered into seven different complexes by phylogenetic tree analysis. Thirteen gene clusters were specific to different S. aureus clones. Ten gene clusters, including seven known (vSa3, vSa4, vSaα, vSaβ, Tn5801, and phage ϕSa3) and three novel (C8, C9, and C10) gene clusters, were specific to human MRSA. Notably, two global regulators, sarH2 and sarH3, at cluster C9 were specific to human MRSA, and plasmid pUB110 at cluster C10 was specific to swine MRSA. Three clusters known to be part of SCCmec, vSa4 or Tn5801, and vSaα as well as one novel gene cluster C12 with homology with Tn554 of S. epidermidis were identified as MRSA-specific gene clusters. The replacement of ST239-spa t037 with ST239-spa t030 in Beijing may be a result of its acquisition of vSa4, phage ϕSa1, and ϕSa3. In summary, thirteen critical gene clusters were identified to be contributors to the evolution of host specificity and antibiotic resistance in Chinese S. aureus.}, }
@article {pmid23303373, year = {2013}, author = {Nakao, R and Abe, T and Nijhof, AM and Yamamoto, S and Jongejan, F and Ikemura, T and Sugimoto, C}, title = {A novel approach, based on BLSOMs (Batch Learning Self-Organizing Maps), to the microbiome analysis of ticks.}, journal = {The ISME journal}, volume = {7}, number = {5}, pages = {1003-1015}, pmid = {23303373}, issn = {1751-7370}, mesh = {Animals ; Archaea/classification/genetics/isolation &amp; purification ; Bacteria/classification/genetics/isolation &amp; purification ; Eukaryota/classification/genetics/isolation &amp; purification ; Humans ; Metagenomics/*methods ; *Microbiota ; Phylogeny ; Tick-Borne Diseases/microbiology/parasitology/virology ; Ticks/classification/*microbiology/*parasitology/virology ; Viruses/classification/genetics/isolation &amp; purification ; }, abstract = {Ticks transmit a variety of viral, bacterial and protozoal pathogens, which are often zoonotic. The aim of this study was to identify diverse tick microbiomes, which may contain as-yet unidentified pathogens, using a metagenomic approach. DNA prepared from bacteria/archaea-enriched fractions obtained from seven tick species, namely Amblyomma testudinarium, Amblyomma variegatum, Haemaphysalis formosensis, Haemaphysalis longicornis, Ixodes ovatus, Ixodes persulcatus and Ixodes ricinus, was subjected to pyrosequencing after whole-genome amplification. The resulting sequence reads were phylotyped using a Batch Learning Self-Organizing Map (BLSOM) program, which allowed phylogenetic estimation based on similarity of oligonucleotide frequencies, and functional annotation by BLASTX similarity searches. In addition to bacteria previously associated with human/animal diseases, such as Anaplasma, Bartonella, Borrelia, Ehrlichia, Francisella and Rickettsia, BLSOM analysis detected microorganisms belonging to the phylum Chlamydiae in some tick species. This was confirmed by pan-Chlamydia PCR and sequencing analysis. Gene sequences associated with bacterial pathogenesis were also identified, some of which were suspected to originate from horizontal gene transfer. These efforts to construct a database of tick microbes may lead to the ability to predict emerging tick-borne diseases. Furthermore, a comprehensive understanding of tick microbiomes will be useful for understanding tick biology, including vector competency and interactions with pathogens and symbionts.}, }
@article {pmid23300632, year = {2012}, author = {Böttger, A and Doxey, AC and Hess, MW and Pfaller, K and Salvenmoser, W and Deutzmann, R and Geissner, A and Pauly, B and Altstätter, J and Münder, S and Heim, A and Gabius, HJ and McConkey, BJ and David, CN}, title = {Horizontal gene transfer contributed to the evolution of extracellular surface structures: the freshwater polyp Hydra is covered by a complex fibrous cuticle containing glycosaminoglycans and proteins of the PPOD and SWT (sweet tooth) families.}, journal = {PloS one}, volume = {7}, number = {12}, pages = {e52278}, pmid = {23300632}, issn = {1932-6203}, mesh = {Animals ; Chondroitin Sulfates/metabolism ; *Evolution, Molecular ; Extracellular Space/genetics/*metabolism ; *Gene Transfer, Horizontal ; Glycocalyx/metabolism ; Glycosaminoglycans/*metabolism ; Hydra/anatomy &amp; histology/*cytology/*genetics/metabolism ; Protein Structure, Tertiary ; Receptor Protein-Tyrosine Kinases/chemistry/*metabolism ; }, abstract = {The single-cell layered ectoderm of the fresh water polyp Hydra fulfills the function of an epidermis by protecting the animals from the surrounding medium. Its outer surface is covered by a fibrous structure termed the cuticle layer, with similarity to the extracellular surface coats of mammalian epithelia. In this paper we have identified molecular components of the cuticle. We show that its outermost layer contains glycoproteins and glycosaminoglycans and we have identified chondroitin and chondroitin-6-sulfate chains. In a search for proteins that could be involved in organising this structure we found PPOD proteins and several members of a protein family containing only SWT (sweet tooth) domains. Structural analyses indicate that PPODs consist of two tandem β-trefoil domains with similarity to carbohydrate-binding sites found in lectins. Experimental evidence confirmed that PPODs can bind sulfated glycans and are secreted into the cuticle layer from granules localized under the apical surface of the ectodermal epithelial cells. PPODs are taxon-specific proteins which appear to have entered the Hydra genome by horizontal gene transfer from bacteria. Their acquisition at the time Hydra evolved from a marine ancestor may have been critical for the transition to the freshwater environment.}, }
@article {pmid23300460, year = {2012}, author = {Chen, HD and Jewett, MW and Groisman, EA}, title = {An allele of an ancestral transcription factor dependent on a horizontally acquired gene product.}, journal = {PLoS genetics}, volume = {8}, number = {12}, pages = {e1003060}, pmid = {23300460}, issn = {1553-7404}, support = {R01 AI042236/AI/NIAID NIH HHS/United States ; R56 AI042236/AI/NIAID NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; AI042236/AI/NIAID NIH HHS/United States ; }, mesh = {Alleles ; *Bacterial Proteins/genetics/metabolism ; *Drug Resistance, Bacterial ; Gene Expression Regulation, Bacterial/drug effects ; *Gene Transfer, Horizontal ; Humans ; Polymyxin B/pharmacology ; Promoter Regions, Genetic ; Salmonella enterica/drug effects/genetics ; Salmonella typhimurium/drug effects/genetics ; }, abstract = {Changes in gene regulatory circuits often give rise to phenotypic differences among closely related organisms. In bacteria, these changes can result from alterations in the ancestral genome and/or be brought about by genes acquired by horizontal transfer. Here, we identify an allele of the ancestral transcription factor PmrA that requires the horizontally acquired pmrD gene product to promote gene expression. We determined that a single amino acid difference between the PmrA proteins from the human adapted Salmonella enterica serovar Paratyphi B and the broad host range S. enterica serovar Typhimurium rendered transcription of PmrA-activated genes dependent on the PmrD protein in the former but not the latter serovar. Bacteria harboring the serovar Typhimurium allele exhibited polymyxin B resistance under PmrA- or under PmrA- and PmrD-inducing conditions. By contrast, isogenic strains with the serovar Paratyphi B allele displayed PmrA-regulated polymyxin B resistance only when experiencing activating conditions for both PmrA and PmrD. We establish that the two PmrA orthologs display quantitative differences in several biochemical properties. Strains harboring the serovar Paratyphi B allele showed enhanced biofilm formation, a property that might promote serovar Paratyphi B's chronic infection of the gallbladder. Our findings illustrate how subtle differences in ancestral genes can impact the ability of horizontally acquired genes to confer new properties.}, }
@article {pmid23300421, year = {2012}, author = {Mannige, RV and Brooks, CL and Shakhnovich, EI}, title = {A universal trend among proteomes indicates an oily last common ancestor.}, journal = {PLoS computational biology}, volume = {8}, number = {12}, pages = {e1002839}, pmid = {23300421}, issn = {1553-7358}, support = {P41 RR012255/RR/NCRR NIH HHS/United States ; R01 GM068670/GM/NIGMS NIH HHS/United States ; GM068670/GM/NIGMS NIH HHS/United States ; }, mesh = {Evolution, Molecular ; Gene Transfer, Horizontal ; *Oils ; Phylogeny ; *Proteome ; Recombination, Genetic ; }, abstract = {Despite progresses in ancestral protein sequence reconstruction, much needs to be unraveled about the nature of the putative last common ancestral proteome that served as the prototype of all extant lifeforms. Here, we present data that indicate a steady decline (oil escape) in proteome hydrophobicity over species evolvedness (node number) evident in 272 diverse proteomes, which indicates a highly hydrophobic (oily) last common ancestor (LCA). This trend, obtained from simple considerations (free from sequence reconstruction methods), was corroborated by regression studies within homologous and orthologous protein clusters as well as phylogenetic estimates of the ancestral oil content. While indicating an inherent irreversibility in molecular evolution, oil escape also serves as a rare and universal reaction-coordinate for evolution (reinforcing Darwin's principle of Common Descent), and may prove important in matters such as (i) explaining the emergence of intrinsically disordered proteins, (ii) developing composition- and speciation-based "global" molecular clocks, and (iii) improving the statistical methods for ancestral sequence reconstruction.}, }
@article {pmid23291652, year = {2013}, author = {Adachi, F and Yamamoto, A and Takakura, K and Kawahara, R}, title = {Occurrence of fluoroquinolones and fluoroquinolone-resistance genes in the aquatic environment.}, journal = {The Science of the total environment}, volume = {444}, number = {}, pages = {508-514}, doi = {10.1016/j.scitotenv.2012.11.077}, pmid = {23291652}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents/*analysis/pharmacology ; Ciprofloxacin/analysis/pharmacology ; DNA Gyrase/genetics ; DNA Topoisomerase IV/genetics ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/*drug effects/*genetics ; Fluoroquinolones/*analysis/pharmacology ; Japan ; Microbial Sensitivity Tests ; Nalidixic Acid/analysis/pharmacology ; Plasmids/genetics ; *Water Microbiology ; }, abstract = {Fluoroquinolones (FQs) have been detected in aquatic environments in several countries. Long-term exposure to low levels of antimicrobial agents provides selective pressure, which might alter the sensitivity of bacteria to antimicrobial agents in the environment. Here, we examined FQ levels and the resistance of Escherichia coli (E. coli) to FQs by phenotyping and genotyping. In the aquatic environment in Osaka, Japan, ciprofloxacin, enoxacin, enfloxacin, lomefloxacin, norfloxacin, and ofloxacin were detected in concentrations ranging from 0.1 to 570 ng L(-1). FQ-resistant E. coli were also found. Although no obvious correlation was detected between the concentration of FQs and the presence of FQ-resistant E. coli, FQ-resistant E. coli were detected in samples along with FQs, particularly ciprofloxacin and ofloxacin. Most FQ-resistant E. coli carried mutations in gyrA, parC, and parE in quinolone resistance-determining regions. No mutations in gyrB were detected in any isolates. Amino acid changes in these isolates were quite similar to those in clinical isolates. Six strains carried the plasmid-mediated quinolone resistance determinant qnrS1 and expressed low susceptibility to ciprofloxacin and nalidixic acid: the minimum inhibitory concentrations ranged from 0.25 μg mL(-1) for ciprofloxacin, and from 8 to 16 μg mL(-1) for nalidixic acid. This finding confirmed that plasmids containing qnr genes themselves did not confer full resistance to quinolones. Because plasmids are responsible for much of the horizontal gene transfer, these genes may transfer and spread in the environment. To our knowledge, this is the first report of plasmid-mediated quinolone resistance determinant qnrS1 in the aquatic environment, and this investigation provides baseline data on antimicrobial resistance profiles in the Osaka area.}, }
@article {pmid23289559, year = {2013}, author = {Clerissi, C and Grimsley, N and Desdevises, Y}, title = {Genetic exchanges of inteins between prasinoviruses (phycodnaviridae).}, journal = {Evolution; international journal of organic evolution}, volume = {67}, number = {1}, pages = {18-33}, doi = {10.1111/j.1558-5646.2012.01738.x}, pmid = {23289559}, issn = {1558-5646}, mesh = {Chlorophyta/virology ; DNA, Viral ; Evolution, Molecular ; Gene Transfer, Horizontal ; Inteins/*genetics ; Phycodnaviridae/*genetics ; Phylogeny ; Recombination, Genetic ; Sequence Analysis, DNA ; }, abstract = {Phylogenetic diversity in the Phycodnaviridae (double-stranded DNA viruses infecting photosynthetic eukaryotes) is most often studied using their DNA polymerase gene (PolB). This gene and its translated protein product can harbor a selfish genetic element called an "intein" that disrupts the sequence of the host gene without affecting its activity. After translation, the intein peptide sequence self-excises precisely, producing a functional ligated host protein. In addition, inteins can encode homing endonuclease (HEN) domains that permit the possibility of lateral transfers to intein-free alleles. However, no clear evidence for their transfer between viruses has previously been shown. The objective of this paper was to determine whether recent transfers of inteins have occurred between prasinoviruses (Phycodnaviridae) that infect the Mamiellophyceae, an abundant and widespread class of unicellular green algae, by using DNA sequence analyses and cophylogenetic methods. Our results suggest that transfer among prasinoviruses is a dynamic ongoing process and, for the first time in the Phycodnaviridae family, we showed a recombination event within an intein.}, }
@article {pmid23289504, year = {2013}, author = {Blädel, I and Wagner, K and Beck, A and Schilling, J and Alexander Schmidt, M and Heusipp, G}, title = {The H-NS protein silences the pyp regulatory network of Yersinia enterocolitica and is involved in controlling biofilm formation.}, journal = {FEMS microbiology letters}, volume = {340}, number = {1}, pages = {41-48}, doi = {10.1111/1574-6968.12073}, pmid = {23289504}, issn = {1574-6968}, mesh = {Artificial Gene Fusion ; Bacterial Proteins/biosynthesis/*metabolism ; Biofilms/*growth &amp; development ; DNA-Binding Proteins/*metabolism ; Electrophoretic Mobility Shift Assay ; *Gene Expression Regulation, Bacterial ; Genes, Reporter ; Protein Binding ; Subtilisins/biosynthesis ; Yersinia enterocolitica/*genetics/physiology ; }, abstract = {Horizontal gene transfer plays an important role in bacterial evolution. DNA acquired by horizontal gene transfer has to be incorporated into existing regulatory networks. The histone-like nucleoid structuring protein H-NS acts as a silencer of horizontally acquired genes to avoid potential damage. However, specific regulators can overcome H-NS repression, resulting in the integration of newly acquired genes into existing regulatory networks. Here, we analyzed the influence of H-NS on the transcription of the Yersinia enterocolitica hreP gene and its regulators pypA, pypB, and pypC by establishing a dominant-negative H-NS version. Using transcriptional fusions and electrophoretic mobility shift assays, we show that H-NS silences hreP, pypA, pypB, and pypC by direct interactions. While the H-NS antagonist RovA activates pypC, it has no effect on pypA and pypB. Furthermore, H-NS affects biofilm formation in Y. enterocolitica.}, }
@article {pmid23288403, year = {2013}, author = {Zong, Z and Zhang, X}, title = {blaNDM-1-carrying Acinetobacter johnsonii detected in hospital sewage.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {68}, number = {5}, pages = {1007-1010}, doi = {10.1093/jac/dks505}, pmid = {23288403}, issn = {1460-2091}, mesh = {Acinetobacter/*enzymology/isolation &amp; purification ; China ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Electrophoresis, Gel, Pulsed-Field ; Gene Transfer, Horizontal ; Hospitals ; Humans ; Molecular Sequence Data ; Molecular Typing ; *Plasmids ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Rec A Recombinases/genetics ; Sequence Analysis, DNA ; Sewage/*microbiology ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: This study screened hospital sewage for the presence of blaNDM.<br><br>METHODS: Colonies grown from plates containing meropenem streaked with hospital sewage were screened for blaNDM by PCR. Species identification was performed by sequencing 16S rRNA genes. Clonal relatedness of isolates was determined by Enterobacterial repetitive intergenic consensus sequence-PCR, sequencing recA and PFGE. Mating was attempted to obtain self-transmissible plasmids carrying blaNDM. The genetic context of blaNDM was investigated by PCR mapping using pNDM-BJ01, a blaNDM-1-carrying plasmid from Acinetobacter lwoffii as the reference.<br><br>RESULTS: Two Acinetobacter johnsonii isolates, designated XBB1 and XBC1, from sewage were found carrying blaNDM-1, but were of different clonal origins. In both cases, blaNDM-1 was carried by a self-transmissible plasmid. PCR mapping and sequencing revealed that the blaNDM-1-carrying plasmid of XBB1, pXBB1, was the same as pNDM-BJ01, whereas that of XBC1, pXBC1, was a variant of pNDM-BJ01. A large region downstream of blaNDM-1, including groES/groEL, ISCR27 and ISAba125, was absent from pXBC1. On pXBB1, blaNDM-1 was carried by Tn125, an ISAba125-formed composite transposon, which was inserted into a sequence downstream of aphA6.<br><br>CONCLUSIONS: Sewage of a hospital in China was found to contain blaNDM-1, suggesting that hospital sewage is an important but often overlooked reservoir of antimicrobial resistance determinants. A variety of Acinetobacter species in different locations have been found to harbour blaNDM-1, so the introduction of blaNDM-1 into Acinetobacter is unlikely to be a single event. The identification of blaNDM-1-carrying plasmid pNDM-BJ01/pXBB1 and its variants suggests that a common plasmid has been transferred among different host species at different locations.}, }
@article {pmid23285175, year = {2012}, author = {Trejo-Becerril, C and Pérez-Cárdenas, E and Taja-Chayeb, L and Anker, P and Herrera-Goepfert, R and Medina-Velázquez, LA and Hidalgo-Miranda, A and Pérez-Montiel, D and Chávez-Blanco, A and Cruz-Velázquez, J and Díaz-Chávez, J and Gaxiola, M and Dueñas-González, A}, title = {Cancer progression mediated by horizontal gene transfer in an in vivo model.}, journal = {PloS one}, volume = {7}, number = {12}, pages = {e52754}, pmid = {23285175}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; Cell Line, Tumor ; Cell Transformation, Neoplastic/*genetics ; Colonic Neoplasms/*genetics/*pathology ; Culture Media, Conditioned/chemistry ; Disease Models, Animal ; Female ; Gene Dosage ; *Gene Transfer, Horizontal ; Genes, ras ; Humans ; Mice ; NIH 3T3 Cells ; Rats ; rab GTP-Binding Proteins/chemistry/genetics ; }, abstract = {It is known that cancer progresses by vertical gene transfer, but this paradigm ignores that DNA circulates in higher organisms and that it is biologically active upon its uptake by recipient cells. Here we confirm previous observations on the ability of cell-free DNA to induce in vitro cell transformation and tumorigenesis by treating NIH3T3 recipient murine cells with serum of colon cancer patients and supernatant of SW480 human cancer cells. Cell transformation and tumorigenesis of recipient cells did not occur if serum and supernatants were depleted of DNA. It is also demonstrated that horizontal cancer progression mediated by circulating DNA occurs via its uptake by recipient cells in an in vivo model where immunocompetent rats subjected to colon carcinogenesis with 1,2-dimethylhydrazine had increased rate of colonic tumors when injected in the dorsum with human SW480 colon carcinoma cells as a source of circulating oncogenic DNA, which could be offset by treating these animals with DNAse I and proteases. Though the contribution of biologically active molecules other than DNA for this phenomenon to occur cannot be ruled out, our results support the fact that cancer cells emit into the circulation biologically active DNA to foster tumor progression. Further exploration of the horizontal tumor progression phenomenon mediated by circulating DNA is clearly needed to determine whether its manipulation could have a role in cancer therapy.}, }
@article {pmid23281896, year = {2013}, author = {McNulty, SN and Fischer, K and Curtis, KC and Weil, GJ and Brattig, NW and Fischer, PU}, title = {Localization of Wolbachia-like gene transcripts and peptides in adult Onchocerca flexuosa worms indicates tissue specific expression.}, journal = {Parasites &amp; vectors}, volume = {6}, number = {}, pages = {2}, pmid = {23281896}, issn = {1756-3305}, mesh = {Animals ; Bacterial Proteins/*biosynthesis ; Gene Expression Profiling ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Immunohistochemistry ; In Situ Hybridization ; Onchocerca/*microbiology ; *Transcription, Genetic ; Wolbachia/*genetics ; }, abstract = {BACKGROUND: Most filarial species in the genus Onchocerca depend on Wolbachia endobacteria to successfully carry out their life cycle. O. flexuosa is a Wolbachia-free species, but its genome contains Wolbachia-like sequences presumably obtained from Wolbachia via horizontal gene transfer. Proteogenomic studies have shown that many of these Wolbachia-like sequences are expressed in adult worms.<br><br>METHODS: Six Wolbachia-like sequences in O. flexuosa were chosen for further study based on their sequence conservation with Wolbachia genes, length of predicted open reading frames, and expression at the RNA and/or protein levels. In situ hybridization and immunohistochemical labeling were used to localize Wolbachia-like transcripts and peptides in adult worm tissues.<br><br>RESULTS: RNA probes representing three of the six target sequences produced hybridization signals in worm tissues. These probes bound to transcripts in the intestine and lateral chords of both sexes, in the hypodermis, median chords and uteri in females, and in sperm precursor cells in males. Antibodies raised to three peptides corresponding to these transcripts bound to specific bands in a soluble extract of adult O. flexuosa by Western blot that were not labeled by control antibodies in pre-immune serum. Two of the three antibodies produced labeling patterns in adult worm sections that were similar to those of the RNA probes, while the third produced a different pattern.<br><br>CONCLUSIONS: A subset of the Wolbachia-like sequences present in the genome of the Wolbachia-free filarial species O. flexuosa are transcribed in tissues where Wolbachia reside in infected filarial species. Some of the peptides and/or proteins derived from these transcripts appear to be concentrated in the same tissues while others may be exported to other regions of the worm. These results suggest that horizontally transferred Wolbachia genes and gene products may replicate important Wolbachia functions in uninfected filarial worms.}, }
@article {pmid23279335, year = {2013}, author = {Limenitakis, J and Oppenheim, RD and Creek, DJ and Foth, BJ and Barrett, MP and Soldati-Favre, D}, title = {The 2-methylcitrate cycle is implicated in the detoxification of propionate in Toxoplasma gondii.}, journal = {Molecular microbiology}, volume = {87}, number = {4}, pages = {894-908}, pmid = {23279335}, issn = {1365-2958}, support = {/WT_/Wellcome Trust/United Kingdom ; 085349/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Acyl Coenzyme A/metabolism/toxicity ; Animals ; Carbon-Carbon Lyases/genetics/metabolism ; Citrates/*metabolism ; Humans ; Mice ; Mitochondria/genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; Propionates/*metabolism/toxicity ; Protozoan Proteins/genetics/metabolism ; Toxoplasma/classification/enzymology/genetics/*metabolism ; Toxoplasmosis/*parasitology ; }, abstract = {Toxoplasma gondii belongs to the coccidian subgroup of the Apicomplexa phylum. The Coccidia are obligate intracellular pathogens that establish infection in their mammalian host via the enteric route. These parasites lack a mitochondrial pyruvate dehydrogenase complex but have preserved the degradation of branched-chain amino acids (BCAA) as a possible pathway to generate acetyl-CoA. Importantly, degradation of leucine, isoleucine and valine could lead to concomitant accumulation of propionyl-CoA, a toxic metabolite that inhibits cell growth. Like fungi and bacteria, the Coccidia possess the complete set of enzymes necessary to metabolize and detoxify propionate by oxidation to pyruvate via the 2-methylcitrate cycle (2-MCC). Phylogenetic analysis provides evidence that the 2-MCC was acquired via horizontal gene transfer. In T. gondii tachyzoites, this pathway is split between the cytosol and the mitochondrion. Although the rate-limiting enzyme 2-methylisocitrate lyase is dispensable for parasite survival, its substrates accumulate in parasites deficient in the enzyme and its absence confers increased sensitivity to propionic acid. BCAA is also dispensable in tachyzoites, leaving unresolved the source of mitochondrial acetyl-CoA.}, }
@article {pmid23277587, year = {2013}, author = {Walsh, AM and Kortschak, RD and Gardner, MG and Bertozzi, T and Adelson, DL}, title = {Widespread horizontal transfer of retrotransposons.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {3}, pages = {1012-1016}, pmid = {23277587}, issn = {1091-6490}, mesh = {Animals ; Base Sequence ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Long Interspersed Nucleotide Elements ; Molecular Sequence Data ; Phylogeny ; *Retroelements ; Sequence Alignment ; Vertebrates/classification/genetics ; }, abstract = {In higher organisms such as vertebrates, it is generally believed that lateral transfer of genetic information does not readily occur, with the exception of retroviral infection. However, horizontal transfer (HT) of protein coding repetitive elements is the simplest way to explain the patchy distribution of BovB, a long interspersed element (LINE) about 3.2 kb long, that has been found in ruminants, marsupials, squamates, monotremes, and African mammals. BovB sequences are a major component of some of these genomes. Here we show that HT of BovB is significantly more widespread than believed, and we demonstrate the existence of two plausible arthropod vectors, specifically reptile ticks. A phylogenetic tree built from BovB sequences from species in all of these groups does not conform to expected evolutionary relationships of the species, and our analysis indicates that at least nine HT events are required to explain the observed topology. Our results provide compelling evidence for HT of genetic material that has transformed vertebrate genomes.}, }
@article {pmid23275950, year = {2013}, author = {Karch, H and Müthing, J and Dobrindt, U and Mellmann, A}, title = {[Evolution and infection biology of hemolytic-uremic syndrome (HUS) associated E. coli (HUSEC)].}, journal = {Bundesgesundheitsblatt, Gesundheitsforschung, Gesundheitsschutz}, volume = {56}, number = {1}, pages = {8-14}, doi = {10.1007/s00103-012-1586-0}, pmid = {23275950}, issn = {1437-1588}, mesh = {Escherichia coli Infections/epidemiology/*genetics/*microbiology ; *Evolution, Molecular ; Genetic Predisposition to Disease/epidemiology/genetics ; Hemolytic-Uremic Syndrome/epidemiology/*genetics/*microbiology ; Humans ; Models, Genetic ; Prevalence ; Risk Factors ; Shiga-Toxigenic Escherichia coli/*genetics/*pathogenicity ; Virulence Factors/genetics ; }, abstract = {Shiga toxin (Stx)-producing Escherichia coli (STEC), which cause hemolytic-uremic syndrome (HUS), are designated as HUSEC. Their exceptional genome variability driven by evolutionary diversification permits fast adaptation to changed environmental conditions. The HUSEC collection (http://www.ehec.org), which has been established at the Institute for Hygiene in Münster, contains 42 EHEC reference strains (HUSEC001-HUSEC042). It represents a unique repository collection of pathogens and is extremely helpful for the analysis of evolutionary changes and fixed properties in the STEC that cause the most severe host injury. Such genomic attributes include slowly evolving loci, mobile genetic elements that often encode virulence factors and are assimilated via horizontal gene transfer. Current evolutionary models indicate that numerous outbreak strains evolved recently and that highly pathogenic HUSEC descend from less pathogenic progenitors. However, additional data suggest that HUSEC have small effective population sizes. The HUSEC collection is also a valuable resource with which to study important non-Shiga toxin virulence factors.}, }
@article {pmid23275877, year = {2012}, author = {Pandeeti, EV and Longkumer, T and Chakka, D and Muthyala, VR and Parthasarathy, S and Madugundu, AK and Ghanta, S and Medipally, SR and Pantula, SC and Yekkala, H and Siddavattam, D}, title = {Multiple mechanisms contribute to lateral transfer of an organophosphate degradation (opd) island in Sphingobium fuliginis ATCC 27551.}, journal = {G3 (Bethesda, Md.)}, volume = {2}, number = {12}, pages = {1541-1554}, pmid = {23275877}, issn = {2160-1836}, mesh = {Attachment Sites, Microbiological ; Bacterial Proteins/genetics/metabolism ; Base Sequence ; Cloning, Molecular ; Escherichia coli/metabolism ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Integrases/genetics/metabolism ; Molecular Sequence Data ; Multigene Family ; Organophosphates/chemistry/*metabolism ; Plasmids/genetics/metabolism ; Recombination, Genetic ; Replication Origin/genetics ; Serine-tRNA Ligase/genetics ; Sphingomonadaceae/*genetics ; }, abstract = {The complete sequence of pPDL2 (37,317 bp), an indigenous plasmid of Sphingobium fuliginis ATCC 27551 that encodes genes for organophosphate degradation (opd), revealed the existence of a site-specific integrase (int) gene with an attachment site attP, typically seen in integrative mobilizable elements (IME). In agreement with this sequence information, site-specific recombination was observed between pPDL2 and an artificial plasmid having a temperature-sensitive replicon and a cloned attB site at the 3' end of the seryl tRNA gene of Sphingobium japonicum. The opd gene cluster on pPDL2 was found to be part of an active catabolic transposon with mobile elements y4qE and Tn3 at its flanking ends. Besides the previously reported opd cluster, this transposon contains genes coding for protocatechuate dioxygenase and for two transport proteins from the major facilitator family that are predicted to be involved in transport and metabolism of aromatic compounds. A pPDL2 derivative, pPDL2-K, was horizontally transferred into Escherichia coli and Acinetobacter strains, suggesting that the oriT identified in pPDL2 is functional. A well-defined replicative origin (oriV), repA was identified along with a plasmid addiction module relB/relE that would support stable maintenance of pPDL2 in Sphingobium fuliginis ATCC 27551. However, if pPDL2 is laterally transferred into hosts that do not support its replication, the opd cluster appears to integrate into the host chromosome, either through transposition or through site-specific integration. The data presented in this study help to explain the existence of identical opd genes among soil bacteria.}, }
@article {pmid23275243, year = {2013}, author = {Puymège, A and Bertin, S and Chuzeville, S and Guédon, G and Payot, S}, title = {Conjugative transfer and cis-mobilization of a genomic island by an integrative and conjugative element of Streptococcus agalactiae.}, journal = {Journal of bacteriology}, volume = {195}, number = {6}, pages = {1142-1151}, pmid = {23275243}, issn = {1098-5530}, mesh = {3' Untranslated Regions/genetics ; Base Sequence ; *Conjugation, Genetic ; *Gene Transfer, Horizontal ; *Genomic Islands ; Open Reading Frames ; RNA, Transfer, Lys/*genetics ; Recombination, Genetic ; Sequence Analysis, DNA ; Streptococcus agalactiae/*genetics ; Streptococcus pyogenes/genetics ; }, abstract = {Putative integrative and conjugative elements (ICEs), i.e., genomic islands which could excise, self-transfer by conjugation, and integrate into the chromosome of the bacterial host strain, were previously identified by in silico analysis in the sequenced genomes of Streptococcus agalactiae (M. Brochet et al., J. Bacteriol. 190:6913-6917, 2008). We investigated here the mobility of the elements integrated into the 3' end of a tRNA(Lys) gene. Three of the four putative ICEs tested were found to excise but only one (ICE_515_tRNA(Lys)) was found to transfer by conjugation not only to S. agalactiae strains but also to a Streptococcus pyogenes strain. Transfer was observed even if recipient cell already carries a related resident ICE or a genomic island flanked by attL and attR recombination sites but devoid of conjugation or recombination genes (CIs-Mobilizable Element [CIME]). The incoming ICE preferentially integrates into the 3' end of the tRNA(Lys) gene (i.e., the attR site of the resident element), leading to a CIME-ICE structure. Transfer of the whole composite element CIME-ICE was obtained, showing that the CIME is mobilizable in cis by the ICE. Therefore, genomic islands carrying putative virulence genes but lacking the mobility gene can be mobilized by a related ICE after site-specific accretion.}, }
@article {pmid23275162, year = {2013}, author = {Nishiyama, T and Noguchi, H and Yoshida, H and Park, SY and Tame, JR}, title = {The structure of the deacetylase domain of Escherichia coli PgaB, an enzyme required for biofilm formation: a circularly permuted member of the carbohydrate esterase 4 family.}, journal = {Acta crystallographica. Section D, Biological crystallography}, volume = {69}, number = {Pt 1}, pages = {44-51}, doi = {10.1107/S0907444912042059}, pmid = {23275162}, issn = {1399-0047}, mesh = {Acetylesterase/*chemistry/genetics ; Amidohydrolases/antagonists &amp; inhibitors/*chemistry/genetics ; Biofilms/*growth &amp; development ; Carboxylesterase/*chemistry/genetics/physiology ; Catalytic Domain/genetics ; Crystallography, X-Ray ; Escherichia coli Proteins/antagonists &amp; inhibitors/*chemistry/genetics ; Histone Deacetylases/*chemistry/genetics/*physiology ; Models, Chemical ; Operon/genetics ; Protein Structure, Tertiary/genetics ; }, abstract = {Bacterial biofilm formation is an extremely widespread phenomenon involving the secretion of a protective exopolysaccharide matrix which helps the bacteria to attach to surfaces and to overcome a variety of stresses in different environments. This matrix may also include proteins, lipids, DNA and metal ions. Its composition depends on the bacterial species and growth conditions, but one of the most widely found components is polymeric β-1,6-N-acetyl-D-glucosamine (PGA). Several studies have suggested that PGA is an essential component of biofilm and it is produced by numerous bacteria, including Escherichia coli, Staphylococcus epidermis, Yersinia pestis, Bordetella spp. and Actinobacillus spp. In E. coli, PGA production and export are dependent on four genes that form a single operon, pgaABCD, which appears to have been transferred between various species. Biofilms themselves are recognized as environments in which such horizontal gene transfer may occur. The pga operon of E. coli, which is even found in innocuous laboratory strains, is highly homologous to that from the plague bacterium Yersinia pestis, and biofilm is believed to play an important role in the transmission of Yersinia. The crystal structure of the N-terminal domain of PgaB, which has deacetylase activity, is described and compared with models of other deacetylases.}, }
@article {pmid23274217, year = {2013}, author = {Reen, FJ and Barret, M and Fargier, E and O'Muinneacháin, M and O'Gara, F}, title = {Molecular evolution of LysR-type transcriptional regulation in Pseudomonas aeruginosa.}, journal = {Molecular phylogenetics and evolution}, volume = {66}, number = {3}, pages = {1041-1049}, doi = {10.1016/j.ympev.2012.12.014}, pmid = {23274217}, issn = {1095-9513}, mesh = {Bacterial Proteins/*genetics ; Base Composition/genetics ; Cluster Analysis ; Computational Biology ; *Evolution, Molecular ; Likelihood Functions ; Models, Genetic ; Multigene Family/*genetics ; *Phylogeny ; Pseudomonas aeruginosa/*genetics ; Regulatory Elements, Transcriptional/*genetics ; Transcription Factors/*genetics ; }, abstract = {Signal perception and transduction through tightly coordinated circuits is integral to the survival and persistence of microbes in diverse ecological niches. The capacity to adapt to changes in the environment is central to their ability to thrive under adverse circumstances. Signal dependent transcriptional regulators are a key mechanism through which microbes assimilate environmental cues and mediate the appropriate adaptive response. By far the largest class of transcriptional regulator is the LysR-class, which is universally distributed among bacteria, archaea, and even eukaryotic organisms. The number of LysR-Type Transcriptional Regulators (LTTRs) varies among species with one of the largest repertoires encoded in the genome of the nosocomial pathogen Pseudomonas aeruginosa. To understand the evolutionary basis for this, we undertook to analyse the relationship between the LTTRs, both at the species and genus level. Phylogenetic analysis of the complete Pseudomonas LTTR dataset revealed significant cluster patterns based on full length and domain analysis. Interestingly, evidence of acquisition through horizontal gene transfer was rare, with divergent evolution apparently favoured. Furthermore, genes that appear to have been acquired, as well as those with a non-classical topological arrangement were clustered in distinct groups in the phylogenetic trees, indicating some ancestral association. The conservation within clusters identified in this study will provide a useful platform for future molecular analyses.}, }
@article {pmid23265929, year = {2013}, author = {Tang, MX and Zheng, XM and Hou, J and Qian, LL and Jiang, SW and Cui, WT and Li, K}, title = {Horizontal gene transfer does not occur between sFat-1 transgenic pigs and nontransgenic pigs.}, journal = {Theriogenology}, volume = {79}, number = {4}, pages = {667-672}, doi = {10.1016/j.theriogenology.2012.11.022}, pmid = {23265929}, issn = {1879-3231}, mesh = {Animals ; Animals, Genetically Modified/*genetics ; Animals, Suckling ; Breeding ; DNA/analysis ; Fatty Acid Desaturases/*genetics ; Fatty Acids, Omega-3/analysis ; Female ; Gene Transfer, Horizontal/*genetics ; Male ; Meat/analysis ; Polymerase Chain Reaction/veterinary ; Sus scrofa/*genetics ; }, abstract = {We previously generated and characterized synthesized fatty acid desaturase-1 (sFat-1) transgenic pigs that had increased concentrations of ω-3 unsaturated fatty acid in their meat. The objective was to assess whether the inserted foreign gene in sFat-1 transgenic pigs was able to transfer and integrate into the genome of nontransgenic pigs by suckling or mating. Tests for suckling-mediated horizontal gene transfer (HGT) included sFat-1 transgenic sows nursing nontransgenic piglets and sFat-1 transgenic piglets suckling nontransgenic sows. Tests for mating-mediated HGT were performed by male sFat-1 transgenic pigs mated with nontransgenic females and female sFat-1 transgenic pigs mated with nontransgenic males. Polymerase chain reaction was used to detect the sFat-1 gene fragment in various tissues sampled from nontransgenic pigs. The foreign target gene sFat-1 was not detected in the genomic DNA of various tissues and organs sampled from nontransgenic pigs. Therefore, we concluded that HGT from transgenic pigs to wild type pigs via suckling or mating was unlikely.}, }
@article {pmid23264229, year = {2013}, author = {Sala, A and Calderon, V and Bordes, P and Genevaux, P}, title = {TAC from Mycobacterium tuberculosis: a paradigm for stress-responsive toxin-antitoxin systems controlled by SecB-like chaperones.}, journal = {Cell stress &amp; chaperones}, volume = {18}, number = {2}, pages = {129-135}, pmid = {23264229}, issn = {1466-1268}, mesh = {Antitoxins/*metabolism ; Bacterial Proteins/*metabolism ; Bacterial Toxins/*metabolism ; Biological Evolution ; Genome, Bacterial ; Markov Chains ; Molecular Chaperones/*metabolism ; Mycobacterium tuberculosis/genetics/*physiology ; }, abstract = {Bacterial type II toxin-antitoxins (TAs) are two-component systems that modulate growth in response to specific stress conditions, thus promoting adaptation and persistence. The major human pathogen Mycobacterium tuberculosis potentially encodes 75 TAs and it has been proposed that persistence induced by active toxins might be relevant for its pathogenesis. In this work, we focus on the newly discovered toxin-antitoxin-chaperone (TAC) system of M. tuberculosis, an atypical stress-responsive TA system tightly controlled by a molecular chaperone that shows similarity to the canonical SecB chaperone involved in Sec-dependent protein export in Gram-negative bacteria. We performed a large-scale genome screening to reconstruct the evolutionary history of TAC systems and found that TAC is not restricted to mycobacteria and seems to have disseminated in diverse taxonomic groups by horizontal gene transfer. Our results suggest that TAC chaperones are evolutionary related to the solitary chaperone SecB and have diverged to become specialized toward their cognate antitoxins.}, }
@article {pmid23259572, year = {2012}, author = {Chan, JZ and Halachev, MR and Loman, NJ and Constantinidou, C and Pallen, MJ}, title = {Defining bacterial species in the genomic era: insights from the genus Acinetobacter.}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {302}, pmid = {23259572}, issn = {1471-2180}, support = {BB/E011179/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/J014370/1/MRC_/Medical Research Council/United Kingdom ; G0901717/MRC_/Medical Research Council/United Kingdom ; BBE0111791/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Acinetobacter/*classification/*genetics/physiology ; Bacterial Typing Techniques ; Classification/*methods ; Genes, Bacterial ; Genes, rRNA ; Genome, Bacterial ; Genomics/*methods ; Nucleic Acid Hybridization ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Microbial taxonomy remains a conservative discipline, relying on phenotypic information derived from growth in pure culture and techniques that are time-consuming and difficult to standardize, particularly when compared to the ease of modern high-throughput genome sequencing. Here, drawing on the genus Acinetobacter as a test case, we examine whether bacterial taxonomy could abandon phenotypic approaches and DNA-DNA hybridization and, instead, rely exclusively on analyses of genome sequence data.<br><br>RESULTS: In pursuit of this goal, we generated a set of thirteen new draft genome sequences, representing ten species, combined them with other publically available genome sequences and analyzed these 38 strains belonging to the genus. We found that analyses based on 16S rRNA gene sequences were not capable of delineating accepted species. However, a core genome phylogenetic tree proved consistent with the currently accepted taxonomy of the genus, while also identifying three misclassifications of strains in collections or databases. Among rapid distance-based methods, we found average-nucleotide identity (ANI) analyses delivered results consistent with traditional and phylogenetic classifications, whereas gene content based approaches appear to be too strongly influenced by the effects of horizontal gene transfer to agree with previously accepted species.<br><br>CONCLUSION: We believe a combination of core genome phylogenetic analysis and ANI provides an appropriate method for bacterial species delineation, whereby bacterial species are defined as monophyletic groups of isolates with genomes that exhibit at least 95% pair-wise ANI. The proposed method is backwards compatible; it provides a scalable and uniform approach that works for both culturable and non-culturable species; is faster and cheaper than traditional taxonomic methods; is easily replicable and transferable among research institutions; and lastly, falls in line with Darwin's vision of classification becoming, as far as is possible, genealogical.}, }
@article {pmid23259527, year = {2012}, author = {Pleckaityte, M and Zilnyte, M and Zvirbliene, A}, title = {Insights into the CRISPR/Cas system of Gardnerella vaginalis.}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {301}, pmid = {23259527}, issn = {1471-2180}, mesh = {DNA, Bacterial/chemistry/genetics ; DNA, Intergenic/chemistry/genetics ; Female ; Gardnerella vaginalis/*genetics/pathogenicity ; *Gene Transfer, Horizontal ; Genetic Loci ; Genetic Variation ; Genome, Bacterial ; Humans ; Molecular Sequence Data ; *Recombination, Genetic ; Sequence Analysis, DNA ; Virulence ; }, abstract = {BACKGROUND: Gardnerella vaginalis is identified as the predominant colonist of the vaginal tracts of women diagnosed with bacterial vaginosis (BV). G. vaginalis can be isolated from healthy women, and an asymptomatic BV state is also recognised. The association of G. vaginalis with different clinical phenotypes could be explained by different cytotoxicity of the strains, presumably based on disparate gene content. The contribution of horizontal gene transfer to shaping the genomes of G. vaginalis is acknowledged. The CRISPR loci of the recently discovered CRISPR/Cas microbial defence system provide a historical view of the exposure of prokaryotes to a variety of foreign genetic elements.<br><br>RESULTS: The CRISPR/Cas loci were analysed using available sequence data from three G. vaginalis complete genomes and 18&#x2009;G. vaginalis draft genomes in the NCBI database, as well as PCR amplicons of the genomic DNA of 17 clinical isolates. The cas genes in the CRISPR/Cas loci of G. vaginalis belong to the E. coli subtype. Approximately 20% of the spacers had matches in the GenBank database. Sequence analysis of the CRISPR arrays revealed that nearly half of the spacers matched G. vaginalis chromosomal sequences. The spacers that matched G. vaginalis chromosomal sequences were determined to not be self-targeting and were presumably neither constituents of mobile-element-associated genes nor derived from plasmids/viruses. The protospacers targeted by these spacers displayed conserved protospacer-adjacent motifs.<br><br>CONCLUSIONS: The CRISPR/Cas system has been identified in about one half of the analysed G. vaginalis strains. Our analysis of CRISPR sequences did not reveal a potential link between their presence and the virulence of the G. vaginalis strains. Based on the origins of the spacers found in the G. vaginalis CRISPR arrays, we hypothesise that the transfer of genetic material among G. vaginalis strains could be regulated by the CRISPR/Cas mechanism. The present study is the first attempt to determine and analyse the CRISPR loci of bacteria isolated from the human vaginal tract.}, }
@article {pmid23258841, year = {2013}, author = {Sousa, FL and Shavit-Grievink, L and Allen, JF and Martin, WF}, title = {Chlorophyll biosynthesis gene evolution indicates photosystem gene duplication, not photosystem merger, at the origin of oxygenic photosynthesis.}, journal = {Genome biology and evolution}, volume = {5}, number = {1}, pages = {200-216}, pmid = {23258841}, issn = {1759-6653}, mesh = {Bacterial Proteins/genetics ; Bacteriochlorophylls/*biosynthesis ; Chlorophyllides/biosynthesis ; Cyanobacteria/*genetics/metabolism ; *Evolution, Molecular ; *Gene Duplication ; Photosynthesis/*genetics ; Photosystem I Protein Complex/*genetics ; Photosystem II Protein Complex/*genetics ; Phylogeny ; Protoporphyrins/genetics ; }, abstract = {An open question regarding the evolution of photosynthesis is how cyanobacteria came to possess the two reaction center (RC) types, Type I reaction center (RCI) and Type II reaction center (RCII). The two main competing theories in the foreground of current thinking on this issue are that either 1) RCI and RCII are related via lineage divergence among anoxygenic photosynthetic bacteria and became merged in cyanobacteria via an event of large-scale lateral gene transfer (also called "fusion" theories) or 2) the two RC types are related via gene duplication in an ancestral, anoxygenic but protocyanobacterial phototroph that possessed both RC types before making the transition to using water as an electron donor. To distinguish between these possibilities, we studied the evolution of the core (bacterio)chlorophyll biosynthetic pathway from protoporphyrin IX (Proto IX) up to (bacterio)chlorophyllide a. The results show no dichotomy of chlorophyll biosynthesis genes into RCI- and RCII-specific chlorophyll biosynthetic clades, thereby excluding models of fusion at the origin of cyanobacteria and supporting the selective-loss hypothesis. By considering the cofactor demands of the pathway and the source genes from which several steps in chlorophyll biosynthesis are derived, we infer that the cell that first synthesized chlorophyll was a cobalamin-dependent, heme-synthesizing, diazotrophic anaerobe.}, }
@article {pmid23258263, year = {2013}, author = {Aznar, S and Paytubi, S and Juárez, A}, title = {The Hha protein facilitates incorporation of horizontally acquired DNA in enteric bacteria.}, journal = {Microbiology (Reading, England)}, volume = {159}, number = {Pt 3}, pages = {545-554}, doi = {10.1099/mic.0.062448-0}, pmid = {23258263}, issn = {1465-2080}, mesh = {Bacterial Proteins/genetics ; DNA, Bacterial/*genetics/*metabolism ; DNA-Binding Proteins/genetics/*metabolism ; Escherichia coli/*genetics/metabolism ; Gene Knockout Techniques ; *Gene Transfer, Horizontal ; Plasmids ; *Recombination, Genetic ; Salmonella/*genetics/metabolism ; }, abstract = {Hha-like proteins are an evolutive trait of members of the family Enterobacteriaceae. These proteins mimic the oligomerization domain of the nucleoid-associated protein H-NS and interact with this latter protein to modulate gene expression. In this report, we provide evidence that, as has been shown for H-NS, Hha-like proteins play an essential role facilitating acquisition of horizontally transferred DNA in both Escherichia coli and Salmonella. Incorporation of conjugative plasmids such as pHly152 or R27 results in a fitness cost in E. coli or Salmonella strains that lack Hha-like proteins. E. coli spontaneous derivatives from double hha ydgT mutants that showed an increased growth rate and a restored fitness overexpressed the H-NS protein. In addition to reinforcing the role of H-NS/Hha-modulating xenogeneic DNA, the results obtained demonstrate that the Enterobacteriaceae display regulatory features not found in other bacteria that facilitate incorporation of horizontally transferred DNA.}, }
@article {pmid23252970, year = {2013}, author = {Behlau, F and Hong, JC and Jones, JB and Graham, JH}, title = {Evidence for acquisition of copper resistance genes from different sources in citrus-associated xanthomonads.}, journal = {Phytopathology}, volume = {103}, number = {5}, pages = {409-418}, doi = {10.1094/PHYTO-06-12-0134-R}, pmid = {23252970}, issn = {0031-949X}, mesh = {Argentina ; Bacterial Proteins/genetics ; Base Sequence ; Citrus/*microbiology ; Copper/*pharmacology ; DNA Primers/genetics ; Drug Resistance, Bacterial/*genetics ; Florida ; *Gene Transfer, Horizontal ; *Multigene Family ; Phylogeny ; Plant Diseases/microbiology ; Plasmids ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Xanthomonas/drug effects/*genetics/physiology ; }, abstract = {We determined that multiple and independent introductions of copper resistance genes have taken place for strains of Xanthomonas citri subsp. citri from Argentina and strains of X. alfalfae subsp. citrumelonis from Florida. This study compared the partial nucleotide sequences of principal copper resistance genes copL, copA, and copB from X. citri subsp. citri and X. alfalfae subsp. citrumelonis to strains of other Xanthomonas spp. resistant to copper that were isolated from 12 different countries or territories. The survey confirmed that the copLAB gene cluster is present in many species of Xanthomonas from different parts of the world. Alignment of partial nucleotide sequences of copper resistance genes among the copper-resistant (Cu(R)) strains of Xanthomonas detected homology of ≥92, ≥96, and ≥91% for copL, copA, and copB, respectively. Grouping of strains based on branching patterns of phylogenetic trees was similar for copL and copA but differed for copB. When the three genes were concatenated and analyzed using various phylogenetic methods, it appeared that the plasmid had been horizontally transferred and various populations were mutating based on selection pressure unique to geographic regions. Although high homology of the genes among the strains indicated that the copper resistance in xanthomonads has a common origin, the slight differences in nucleotide sequences within groups of strains indicated that Cu(R) genes have been independently exchanged among species of Xanthomonas throughout the world.}, }
@article {pmid23251705, year = {2012}, author = {Leclercq, S and Cordaux, R}, title = {Selection-driven extinction dynamics for group II introns in Enterobacteriales.}, journal = {PloS one}, volume = {7}, number = {12}, pages = {e52268}, pmid = {23251705}, issn = {1932-6203}, mesh = {DNA Transposable Elements/genetics ; Enterobacteriaceae/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Introns ; }, abstract = {Transposable elements (TEs) are one of the major driving forces of genome evolution, raising the question of the long-term dynamics underlying their evolutionary success. Some TEs were proposed to evolve under a pattern of periodic extinctions-recolonizations, in which elements recurrently invade and quickly proliferate within their host genomes, then start to disappear until total extinction. Depending on the model, TE extinction is assumed to be driven by purifying selection against colonized host genomes (Sel-DE model) or by saturation of host genomes (Sat-DE model). Bacterial group II introns are suspected to follow an extinction-recolonization model of evolution, but whether they follow Sel-DE or Sat-DE dynamics is not known. Our analysis of almost 200 group II intron copies from 90 sequenced Enterobacteriales genomes confirms their extinction-recolonization dynamics: patchy element distributions among genera and even among strains within genera, acquisition of new group II introns through plasmids or other mobile genetic elements, and evidence for recent proliferations in some genomes. Distributions of recent and past proliferations and of their respective homing sites further provide strong support for the Sel-DE model, suggesting that group II introns are deleterious to their hosts. Overall, our observations emphasize the critical impact of host properties on TE dynamics.}, }
@article {pmid23251687, year = {2012}, author = {Jiménez, DJ and Andreote, FD and Chaves, D and Montaña, JS and Osorio-Forero, C and Junca, H and Zambrano, MM and Baena, S}, title = {Structural and functional insights from the metagenome of an acidic hot spring microbial planktonic community in the Colombian Andes.}, journal = {PloS one}, volume = {7}, number = {12}, pages = {e52069}, pmid = {23251687}, issn = {1932-6203}, mesh = {Bacteria/*classification/genetics ; Chloroplasts/genetics ; Ecosystem ; Gene Transfer, Horizontal ; Hot Springs/*microbiology ; *Metagenome ; Microalgae/genetics ; Nitrogen ; Plankton/*classification/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; Sulfur ; }, abstract = {A taxonomic and annotated functional description of microbial life was deduced from 53 Mb of metagenomic sequence retrieved from a planktonic fraction of the Neotropical high Andean (3,973 meters above sea level) acidic hot spring El Coquito (EC). A classification of unassembled metagenomic reads using different databases showed a high proportion of Gammaproteobacteria and Alphaproteobacteria (in total read affiliation), and through taxonomic affiliation of 16S rRNA gene fragments we observed the presence of Proteobacteria, micro-algae chloroplast and Firmicutes. Reads mapped against the genomes Acidiphilium cryptum JF-5, Legionella pneumophila str. Corby and Acidithiobacillus caldus revealed the presence of transposase-like sequences, potentially involved in horizontal gene transfer. Functional annotation and hierarchical comparison with different datasets obtained by pyrosequencing in different ecosystems showed that the microbial community also contained extensive DNA repair systems, possibly to cope with ultraviolet radiation at such high altitudes. Analysis of genes involved in the nitrogen cycle indicated the presence of dissimilatory nitrate reduction to N2 (narGHI, nirS, norBCDQ and nosZ), associated with Proteobacteria-like sequences. Genes involved in the sulfur cycle (cysDN, cysNC and aprA) indicated adenylsulfate and sulfite production that were affiliated to several bacterial species. In summary, metagenomic sequence data provided insight regarding the structure and possible functions of this hot spring microbial community, describing some groups potentially involved in the nitrogen and sulfur cycling in this environment.}, }
@article {pmid23251478, year = {2012}, author = {Dueholm, MS and Albertsen, M and Otzen, D and Nielsen, PH}, title = {Curli functional amyloid systems are phylogenetically widespread and display large diversity in operon and protein structure.}, journal = {PloS one}, volume = {7}, number = {12}, pages = {e51274}, pmid = {23251478}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Amyloid/chemistry/*classification ; Bacterial Proteins/chemistry/classification/*metabolism ; Escherichia coli/*metabolism/pathogenicity ; Metagenome ; Molecular Sequence Data ; *Operon ; *Phylogeny ; *Protein Conformation ; Sequence Homology, Amino Acid ; Virulence ; }, abstract = {Escherichia coli and a few other members of the Enterobacteriales can produce functional amyloids known as curli. These extracellular fibrils are involved in biofilm formation and studies have shown that they may act as virulence factors during infections. It is not known whether curli fibrils are restricted to the Enterobacteriales or if they are phylogenetically widespread. The growing number of genome-sequenced bacteria spanning many phylogenetic groups allows a reliable bioinformatic investigation of the phylogenetic diversity of the curli system. Here we show that the curli system is phylogenetically much more widespread than initially assumed, spanning at least four phyla. Curli fibrils may consequently be encountered frequently in environmental as well as pathogenic biofilms, which was supported by identification of curli genes in public metagenomes from a diverse range of habitats. Identification and comparison of curli subunit (CsgA/B) homologs show that these proteins allow a high degree of freedom in their primary protein structure, although a modular structure of tightly spaced repeat regions containing conserved glutamine, asparagine and glycine residues has to be preserved. In addition, a high degree of variability within the operon structure of curli subunits between bacterial taxa suggests that the curli fibrils might have evolved to fulfill specific functions. Variations in the genetic organization of curli genes are also seen among different bacterial genera. This suggests that some genera may utilize alternative regulatory pathways for curli expression. Comparison of phylogenetic trees of Csg proteins and the 16S rRNA genes of the corresponding bacteria showed remarkably similar overall topography, suggesting that horizontal gene transfer is a minor player in the spreading of the curli system.}, }
@article {pmid23251445, year = {2012}, author = {Peng, Y and Cai, J and Wang, W and Su, B}, title = {Multiple inter-kingdom horizontal gene transfers in the evolution of the phosphoenolpyruvate carboxylase gene family.}, journal = {PloS one}, volume = {7}, number = {12}, pages = {e51159}, pmid = {23251445}, issn = {1932-6203}, mesh = {Archaea/*enzymology ; Bacteria/*enzymology ; *Gene Transfer, Horizontal ; Likelihood Functions ; Phosphoenolpyruvate Carboxykinase (ATP)/*genetics ; Phosphoenolpyruvate Carboxykinase (GTP)/*genetics ; Phylogeny ; Plants/*enzymology ; }, abstract = {Pepcase is a gene encoding phosphoenolpyruvate carboxylase that exists in bacteria, archaea and plants,playing an important role in plant metabolism and development. Most plants have two or more pepcase genes belonging to two gene sub-families, while only one gene exists in other organisms. Previous research categorized one plant pepcase gene as plant-type pepcase (PTPC) while the other as bacteria-type pepcase (BTPC) because of its similarity with the pepcase gene found in bacteria. Phylogenetic reconstruction showed that PTPC is the ancestral lineage of plant pepcase, and that all bacteria, protistpepcase and BTPC in plants are derived from a lineage of pepcase closely related with PTPC in algae. However, their phylogeny contradicts the species tree and traditional chronology of organism evolution. Because the diversification of bacteria occurred much earlier than the origin of plants, presumably all bacterialpepcase derived from the ancestral PTPC of algal plants after divergingfrom the ancestor of vascular plant PTPC. To solve this contradiction, we reconstructed the phylogeny of pepcase gene family. Our result showed that both PTPC and BTPC are derived from an ancestral lineage of gamma-proteobacteriapepcases, possibly via an ancient inter-kingdom horizontal gene transfer (HGT) from bacteria to the eukaryotic common ancestor of plants, protists and cellular slime mold. Our phylogenetic analysis also found 48other pepcase genes originated from inter-kingdom HGTs. These results imply that inter-kingdom HGTs played important roles in the evolution of the pepcase gene family and furthermore that HGTsare a more frequent evolutionary event than previouslythought.}, }
@article {pmid23249905, year = {2013}, author = {Vandevoorde, A and Ascenzo, S and Miendje Deyi, VY and Mascart, G and Mansbach, AL and Landsberg, M and Dreze, P and Steer, AC and Van Melderen, L and Smeesters, PR}, title = {Group A streptococcus colonies from a single throat swab can have heterogeneous antimicrobial susceptibility patterns.}, journal = {The Pediatric infectious disease journal}, volume = {32}, number = {3}, pages = {296-298}, doi = {10.1097/INF.0b013e31827c9796}, pmid = {23249905}, issn = {1532-0987}, mesh = {Anti-Bacterial Agents/*pharmacology ; Child ; Child, Preschool ; Female ; Genetic Heterogeneity ; Genotype ; Humans ; Male ; Microbial Sensitivity Tests ; Pharyngitis/*microbiology ; Pharynx/*microbiology ; Phenotype ; Streptococcal Infections/*microbiology ; Streptococcus pyogenes/classification/*drug effects/genetics/*isolation &amp; purification ; }, abstract = {This study describes for the first time heterogeneity of antibiotic resistance profiles among group A Streptococcus isolates originating from a single throat swab in patients with acute pharyngitis. For each throat swab, 10 group A Streptococcus colonies were randomly selected from the primary plate and subcultured to a secondary plate. These isolates were characterized by various phenotypic and genotypic methods. Our results demonstrated that differing antibiotic resistance profiles were present in 19% of pediatric patients with acute pharyngitis before antimicrobial treatment. This heterogeneity likely resulted from horizontal gene transfer among streptococcal isolates sharing the same genetic background. As only a minority of colonies displayed antibiotic resistance among these heterogeneous samples, a classical diagnostic antibiogram would have classified them in most instances as "susceptible," although therapeutic failure could be caused by the proliferation of resistant strains after initiation of antibiotic treatment.}, }
@article {pmid23248780, year = {2012}, author = {Keen, EC}, title = {Paradigms of pathogenesis: targeting the mobile genetic elements of disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {2}, number = {}, pages = {161}, pmid = {23248780}, issn = {2235-2988}, mesh = {Bacteria/*genetics/*pathogenicity ; Bacterial Infections/*microbiology ; Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences ; Virulence Factors/*genetics/*metabolism ; }, }
@article {pmid23248300, year = {2013}, author = {Dermauw, W and Wybouw, N and Rombauts, S and Menten, B and Vontas, J and Grbic, M and Clark, RM and Feyereisen, R and Van Leeuwen, T}, title = {A link between host plant adaptation and pesticide resistance in the polyphagous spider mite Tetranychus urticae.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {2}, pages = {E113-22}, pmid = {23248300}, issn = {1091-6490}, mesh = {Adaptation, Biological/genetics/*physiology ; Animals ; Base Sequence ; Cluster Analysis ; Computational Biology ; Gene Expression Profiling ; Gene Expression Regulation/*physiology ; Herbivory/*physiology ; Host-Pathogen Interactions ; Insect Proteins/*genetics ; Insecticide Resistance/genetics/*physiology ; Likelihood Functions ; Lipocalins/chemistry ; Solanum lycopersicum/chemistry/parasitology ; Microarray Analysis ; Models, Genetic ; Molecular Sequence Data ; Multigene Family/genetics ; Phaseolus/chemistry/parasitology ; Phylogeny ; Tetranychidae/genetics/*physiology ; Time Factors ; Toxicity Tests ; }, abstract = {Plants produce a wide range of allelochemicals to defend against herbivore attack, and generalist herbivores have evolved mechanisms to avoid, sequester, or detoxify a broad spectrum of natural defense compounds. Successful arthropod pests have also developed resistance to diverse classes of pesticides and this adaptation is of critical importance to agriculture. To test whether mechanisms to overcome plant defenses predispose the development of pesticide resistance, we examined adaptation of the generalist two-spotted spider mite, Tetranychus urticae, to host plant transfer and pesticides. T. urticae is an extreme polyphagous pest with more than 1,100 documented hosts and has an extraordinary ability to develop pesticide resistance. When mites from a pesticide-susceptible strain propagated on bean were adapted to a challenging host (tomato), transcriptional responses increased over time with ~7.5% of genes differentially expressed after five generations. Whereas many genes with altered expression belonged to known detoxification families (like P450 monooxygenases), new gene families not previously associated with detoxification in other herbivores showed a striking response, including ring-splitting dioxygenase genes acquired by horizontal gene transfer. Strikingly, transcriptional profiles of tomato-adapted mites resembled those of multipesticide-resistant strains, and adaptation to tomato decreased the susceptibility to unrelated pesticide classes. Our findings suggest key roles for both an expanded environmental response gene repertoire and transcriptional regulation in the life history of generalist herbivores. They also support a model whereby selection for the ability to mount a broad response to the diverse defense chemistry of plants predisposes the evolution of pesticide resistance in generalists.}, }
@article {pmid23247295, year = {2013}, author = {Farkas, A and Butiuc-Keul, A and Ciatarâş, D and Neamţu, C and Crăciunaş, C and Podar, D and Drăgan-Bularda, M}, title = {Microbiological contamination and resistance genes in biofilms occurring during the drinking water treatment process.}, journal = {The Science of the total environment}, volume = {443}, number = {}, pages = {932-938}, doi = {10.1016/j.scitotenv.2012.11.068}, pmid = {23247295}, issn = {1879-1026}, mesh = {Bacteria/genetics ; *Biofilms ; Drinking Water/*microbiology ; Drug Resistance, Microbial/*genetics ; Gene Transfer, Horizontal ; Integrons ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; *Water Microbiology ; }, abstract = {Biofilms are the predominant mode of microbial growth in drinking water systems. A dynamic exchange of individuals occurs between the attached and planktonic populations, while lateral gene transfer mediates genetic exchange in these bacterial communities. Integrons are important vectors for the spread of antimicrobial resistance. The presence of class 1 integrons (intI1, qac and sul genes) was assessed in biofilms occurring throughout the drinking water treatment process. Isolates from general and specific culture media, covering a wide range of environmental bacteria, fecal indicators and opportunistic pathogens were tested. From 96 isolates tested, 9.37% were found to possess genetic determinants of putative antimicrobial resistance, and these occurred in both Gram-positive and Gram-negative bacteria. Class 1 integron integrase gene was present in 8.33% of bacteria, all positive for the qacEΔ1 gene. The sul1 gene was present in 3.12% of total isolates, representing 37.5% of the class 1 integron positive cells. The present study shows that biofilm communities in a drinking water treatment plant are a reservoir of class 1 integrons, mainly in bacteria that may be associated with microbiological contamination. Eight out of nine integron bearing strains (88.8%) were identified based on 16S rRNA gene sequencing as either enteric bacteria or species that may be connected to animal and anthropogenic disturbance.}, }
@article {pmid23247042, year = {2013}, author = {Prasad, AB and Mullikin, JC and ,  and Green, ED}, title = {A scalable and flexible approach for investigating the genomic landscapes of phylogenetic incongruence.}, journal = {Molecular phylogenetics and evolution}, volume = {66}, number = {3}, pages = {1067-1074}, doi = {10.1016/j.ympev.2012.11.023}, pmid = {23247042}, issn = {1095-9513}, support = {//Intramural NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; Chromosomes, Artificial, Bacterial/genetics ; Classification/*methods ; Computer Simulation ; Data Interpretation, Statistical ; Genome/*genetics ; Humans ; Likelihood Functions ; Molecular Sequence Data ; *Phylogeny ; Primates/genetics ; *Research Design ; Sequence Alignment/methods ; Sequence Analysis, DNA ; *Software ; }, abstract = {Analyses of DNA sequence datasets have repeatedly revealed inconsistencies in phylogenetic trees derived with different data. This is termed phylogenetic incongruence, and may arise from a methodological failure of the inference process or from biological processes, such as horizontal gene transfer, incomplete lineage sorting, and introgression. To better understand patterns of incongruence, we developed a method (PartFinder) that uses likelihood ratios applied to sliding windows for visualizing tree-support changes across genome-sequence alignments, allowing the comparative examination of complex phylogenetic scenarios among many species. As a pilot, we used PartFinder to investigate incongruence in the Homo-Pan-Gorilla group as well as Platyrrhini using high-quality bacterial artificial chromosome (BAC)-derived sequences as well as assembled whole-genome shotgun sequences. Our simulations verified the sensitivity of PartFinder, and our results were comparable to other studies of the Homo-Pan-Gorilla group. Analyses of the whole-genome alignments reveal significant associations between support for the accepted species relationship and specific characteristics of the genomic regions, such as GC-content, alignment score, exon content, and conservation. Finally, we analyzed sequence data generated for five platyrrhine species, and found incongruence that suggests a polytomy within Cebidae, in particular. Together, these studies demonstrate the utility of PartFinder for investigating the patterns of phylogenetic incongruence.}, }
@article {pmid23244770, year = {2012}, author = {Richards, VP and Zadoks, RN and Pavinski Bitar, PD and Lefébure, T and Lang, P and Werner, B and Tikofsky, L and Moroni, P and Stanhope, MJ}, title = {Genome characterization and population genetic structure of the zoonotic pathogen, Streptococcus canis.}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {293}, pmid = {23244770}, issn = {1471-2180}, support = {AI073368/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Cattle ; Computational Biology ; DNA, Bacterial/*chemistry/*genetics ; Evolution, Molecular ; *Genome, Bacterial ; Interspersed Repetitive Sequences ; Milk/microbiology ; Molecular Sequence Data ; Phylogeny ; *Sequence Analysis, DNA ; Streptococcus/*genetics/isolation &amp; purification ; Virulence Factors/genetics ; }, abstract = {BACKGROUND: Streptococcus canis is an important opportunistic pathogen of dogs and cats that can also infect a wide range of additional mammals including cows where it can cause mastitis. It is also an emerging human pathogen.<br><br>RESULTS: Here we provide characterization of the first genome sequence for this species, strain FSL S3-227 (milk isolate from a cow with an intra-mammary infection). A diverse array of putative virulence factors was encoded by the S. canis FSL S3-227 genome. Approximately 75% of these gene sequences were homologous to known Streptococcal virulence factors involved in invasion, evasion, and colonization. Present in the genome are multiple potentially mobile genetic elements (MGEs) [plasmid, phage, integrative conjugative element (ICE)] and comparison to other species provided convincing evidence for lateral gene transfer (LGT) between S. canis and two additional bovine mastitis causing pathogens (Streptococcus agalactiae, and Streptococcus dysgalactiae subsp. dysgalactiae), with this transfer possibly contributing to host adaptation. Population structure among isolates obtained from Europe and USA [bovine&#x2009;=&#x2009;56, canine&#x2009;=&#x2009;26, and feline&#x2009;=&#x2009;1] was explored. Ribotyping of all isolates and multi locus sequence typing (MLST) of a subset of the isolates (n&#x2009;=&#x2009;45) detected significant differentiation between bovine and canine isolates (Fisher exact test: P&#x2009;=&#x2009;0.0000 [ribotypes], P&#x2009;=&#x2009;0.0030 [sequence types]), suggesting possible host adaptation of some genotypes. Concurrently, the ancestral clonal complex (54% of isolates) occurred in many tissue types, all hosts, and all geographic locations suggesting the possibility of a wide and diverse niche.<br><br>CONCLUSION: This study provides evidence highlighting the importance of LGT in the evolution of the bacteria S. canis, specifically, its possible role in host adaptation and acquisition of virulence factors. Furthermore, recent LGT detected between S. canis and human bacteria (Streptococcus urinalis) is cause for concern, as it highlights the possibility for continued acquisition of human virulence factors for this emerging zoonotic pathogen.}, }
@article {pmid23241446, year = {2012}, author = {Wolf, YI and Makarova, KS and Yutin, N and Koonin, EV}, title = {Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer.}, journal = {Biology direct}, volume = {7}, number = {}, pages = {46}, pmid = {23241446}, issn = {1745-6150}, support = {//Intramural NIH HHS/United States ; }, mesh = {Archaea/*genetics ; Archaeal Proteins/genetics ; Cluster Analysis ; Databases, Protein ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Archaeal ; *Genome, Archaeal ; Genomics ; Multigene Family ; Phylogeny ; Sequence Alignment ; }, abstract = {BACKGROUND: Collections of Clusters of Orthologous Genes (COGs) provide indispensable tools for comparative genomic analysis, evolutionary reconstruction and functional annotation of new genomes. Initially, COGs were made for all complete genomes of cellular life forms that were available at the time. However, with the accumulation of thousands of complete genomes, construction of a comprehensive COG set has become extremely computationally demanding and prone to error propagation, necessitating the switch to taxon-specific COG collections. Previously, we reported the collection of COGs for 41 genomes of Archaea (arCOGs). Here we present a major update of the arCOGs and describe evolutionary reconstructions to reveal general trends in the evolution of Archaea.<br><br>RESULTS: The updated version of the arCOG database incorporates 91% of the pangenome of 120 archaea (251,032 protein-coding genes altogether) into 10,335 arCOGs. Using this new set of arCOGs, we performed maximum likelihood reconstruction of the genome content of archaeal ancestral forms and gene gain and loss events in archaeal evolution. This reconstruction shows that the last Common Ancestor of the extant Archaea was an organism of greater complexity than most of the extant archaea, probably with over 2,500 protein-coding genes. The subsequent evolution of almost all archaeal lineages was apparently dominated by gene loss resulting in genome streamlining. Overall, in the evolution of Archaea as well as a representative set of bacteria that was similarly analyzed for comparison, gene losses are estimated to outnumber gene gains at least 4 to 1. Analysis of specific patterns of gene gain in Archaea shows that, although some groups, in particular Halobacteria, acquire substantially more genes than others, on the whole, gene exchange between major groups of Archaea appears to be largely random, with no major 'highways' of horizontal gene transfer.<br><br>CONCLUSIONS: The updated collection of arCOGs is expected to become a key resource for comparative genomics, evolutionary reconstruction and functional annotation of new archaeal genomes. Given that, in spite of the major increase in the number of genomes, the conserved core of archaeal genes appears to be stabilizing, the major evolutionary trends revealed here have a chance to stand the test of time.<br><br>REVIEWERS: This article was reviewed by (for complete reviews see the Reviewers' Reports section): Dr. PLG, Prof. PF, Dr. PL (nominated by Prof. JPG).}, }
@article {pmid23240107, year = {2012}, author = {Bloch, SK and Felczykowska, A and Nejman-Faleńczyk, B}, title = {Escherichia coli O104:H4 outbreak--have we learnt a lesson from it?.}, journal = {Acta biochimica Polonica}, volume = {59}, number = {4}, pages = {483-488}, pmid = {23240107}, issn = {1734-154X}, mesh = {*Chromosomes, Bacterial/genetics/metabolism ; Disease Outbreaks/prevention &amp; control ; *Escherichia coli Infections/diagnosis/epidemiology/genetics/pathology ; Foodborne Diseases/diagnosis/epidemiology/genetics/pathology ; Germany ; Humans ; *Shiga-Toxigenic Escherichia coli/genetics/isolation &amp; purification/pathogenicity ; }, abstract = {Shiga toxin-producing Escherichia coli (STEC) strains belong to the group of pathogens that cause bloody diarrhea and hemorrhagic colitis with often severe complications. The main problem with human pathogenic E. coli strains, including STEC, is a wide spectrum of phenotypes and clinical manifestations. It is related to a variety of exchangeable genetic elements, like plasmids, bacteriophages, transposons and pathogenicity islands, that take part in horizontal gene transfer which influences creation of new dangerous bacterial strains. A good example of this phenomenon is a novel Shiga toxin-producing E. coli O104:H4 serotype that was associated with a widespread and severe foodborne disease outbreak in Germany in 2011. The O104:H4 strain was created by a number of horizontal gene transfer events between two distinct pathogens, resulting in the emergence of the new, atypical strain. That outbreak proved that also rare and unusual serotypes of STEC may be a significant risk factor and that the procedures recommended for STEC detection were not suitable to deal with this kind of pathogens. With respect to new combinations of chromosomal and extrachromosomal elements in susceptible bacterial hosts, epidemics and frequent human infections caused by STEC strains, we suggest that more attention should be paid to the development and improvement of diagnostic methods. It is difficult to determine STEC bacteria by general microbiological, biochemical and immunological assays, because strains can vary dramatically in their phenotypic and serotypic properties. It is postulated that standardized genetic tests, based on detection of features most frequently presented by STEC, particularly those located on easily exchangeable elements (such as Shiga toxin-encoding phages), can be more adequate for STEC detection.}, }
@article {pmid23240053, year = {2012}, author = {Millen, AM and Horvath, P and Boyaval, P and Romero, DA}, title = {Mobile CRISPR/Cas-mediated bacteriophage resistance in Lactococcus lactis.}, journal = {PloS one}, volume = {7}, number = {12}, pages = {e51663}, pmid = {23240053}, issn = {1932-6203}, mesh = {Bacteriophages/genetics/*pathogenicity ; Dairy Products/microbiology ; Fermentation ; *Inverted Repeat Sequences/genetics/immunology ; *Lactococcus lactis/genetics/immunology/virology ; *Plasmids/genetics/immunology ; }, abstract = {Lactococcus lactis is a biotechnological workhorse for food fermentations and potentially therapeutic products and is therefore widely consumed by humans. It is predominantly used as a starter microbe for fermented dairy products, and specialized strains have adapted from a plant environment through reductive evolution and horizontal gene transfer as evidenced by the association of adventitious traits with mobile elements. Specifically, L. lactis has armed itself with a myriad of plasmid-encoded bacteriophage defensive systems to protect against viral predation. This known arsenal had not included CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins), which forms a remarkable microbial immunity system against invading DNA. Although CRISPR/Cas systems are common in the genomes of closely related lactic acid bacteria (LAB), none was identified within the eight published lactococcal genomes. Furthermore, a PCR-based search of the common LAB CRISPR/Cas systems (Types I and II) in 383 industrial L. lactis strains proved unsuccessful. Here we describe a novel, Type III, self-transmissible, plasmid-encoded, phage-interfering CRISPR/Cas discovered in L. lactis. The native CRISPR spacers confer resistance based on sequence identity to corresponding lactococcal phage. The interference is directed at phages problematic to the dairy industry, indicative of a responsive system. Moreover, targeting could be modified by engineering the spacer content. The 62.8-kb plasmid was shown to be conjugally transferrable to various strains. Its mobility should facilitate dissemination within microbial communities and provide a readily applicable system to naturally introduce CRISPR/Cas to industrially relevant strains for enhanced phage resistance and prevention against acquisition of undesirable genes.}, }
@article {pmid23239346, year = {2013}, author = {Hill, KK and Smith, TJ}, title = {Genetic diversity within Clostridium botulinum serotypes, botulinum neurotoxin gene clusters and toxin subtypes.}, journal = {Current topics in microbiology and immunology}, volume = {364}, number = {}, pages = {1-20}, doi = {10.1007/978-3-642-33570-9_1}, pmid = {23239346}, issn = {0070-217X}, mesh = {Base Sequence ; Botulinum Toxins/*classification/genetics ; Chromosome Mapping ; Chromosomes, Bacterial/genetics ; Clostridium botulinum/classification/*genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genetic Variation ; *Multigene Family ; Mutagenesis, Insertional ; Mutation ; Neurotoxins/classification/genetics ; Open Reading Frames ; Operon ; Phylogeny ; Plasmids/genetics ; Recombination, Genetic ; Species Specificity ; }, abstract = {Clostridium botulinum is a species of spore-forming anaerobic bacteria defined by the expression of any one or two of seven serologically distinct botulinum neurotoxins (BoNTs) designated BoNT/A-G. This Gram-positive bacterium was first identified in 1897 and since then the paralyzing and lethal effects of its toxin have resulted in the recognition of different forms of the intoxication known as food-borne, infant, or wound botulism. Early microbiological and biochemical characterization of C. botulinum isolates revealed that the bacteria within the species had different characteristics and expressed different toxin types. To organize the variable bacterial traits within the species, Group I-IV designations were created. Interestingly, it was observed that isolates within different Groups could express the same toxin type and conversely a single Group could express different toxin types. This discordant phylogeny between the toxin and the host bacteria indicated that horizontal gene transfer of the toxin was responsible for the variation observed within the species. The recent availability of multiple C. botulinum genomic sequences has offered the ability to bioinformatically analyze the locations of the bont genes, the composition of their toxin gene clusters, and the genes flanking these regions to understand their variation. Comparison of the genomic sequences representing multiple serotypes indicates that the bont genes are not in random locations. Instead the analyses revealed specific regions where the toxin genes occur within the genomes representing serotype A, B, C, E, and F C. botulinum strains and C. butyricum type E strains. The genomic analyses have provided evidence of horizontal gene transfer, site-specific insertion, and recombination events. These events have contributed to the variation observed among the neurotoxins, the toxin gene clusters and the bacteria that contain them, and has supported the historical microbiological, and biochemical characterization of the Group classification within the species.}, }
@article {pmid23238642, year = {2013}, author = {Sarkar, A and Kazy, SK and Sar, P}, title = {Characterization of arsenic resistant bacteria from arsenic rich groundwater of West Bengal, India.}, journal = {Ecotoxicology (London, England)}, volume = {22}, number = {2}, pages = {363-376}, pmid = {23238642}, issn = {1573-3017}, mesh = {Achromobacter/drug effects/growth &amp; development/metabolism ; Agrobacterium/drug effects/growth &amp; development/metabolism ; Arsenate Reductases/metabolism ; Arsenicals/*adverse effects/analysis/metabolism ; Bacteria/classification/*drug effects/genetics/growth &amp; development/metabolism ; Bacterial Proteins/metabolism ; Colony Count, Microbial ; DNA, Bacterial/analysis ; Dose-Response Relationship, Drug ; *Drug Resistance, Bacterial ; Groundwater/*chemistry/*microbiology ; India ; Ochrobactrum/drug effects/growth &amp; development/metabolism ; Oxidoreductases/metabolism ; Phosphoric Monoester Hydrolases/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhizobium/drug effects/growth &amp; development/metabolism ; Ribotyping ; Time Factors ; *Water Microbiology ; Water Pollutants, Chemical/analysis/metabolism/*toxicity ; }, abstract = {Sixty-four arsenic (As) resistant bacteria isolated from an arsenic rich groundwater sample of West Bengal were characterized to investigate their potential role in subsurface arsenic mobilization. Among the isolated strains predominance of genera Agrobacterium/Rhizobium, Ochrobactrum and Achromobacter which could grow chemolitrophically and utilize arsenic as electron donor were detected. Higher tolerance to As(3+) [maximum tolerable concentration (MTC): ≥10 mM], As(5+) (MTC: ≥100 mM) and other heavy metals like Cu(2+), Cr(2+), Ni(2+) etc. (MTC: ≥10 mM), presence of arsenate reductase and siderophore was frequently observed among the isolates. Ability to produce arsenite oxidase and phosphatase enzyme was detected in 50 and 34 % of the isolates, respectively. Although no direct correlation among taxonomic identity of bacterial strains and their metabolic abilities as mentioned above was apparent, several isolates affiliated to genera Ochrobactrum, Achromobacter and unclassified Rhizobiaceae members were found to be highly resistant to As(3+) and As(5+) and positive for all the test properties. Arsenate reductase activity was found to be conferred by arsC gene, which in many strains was coupled with arsenite efflux gene arsB as well. Phylogenetic incongruence between the 16S rRNA and ars genes lineages indicated possible incidence of horizontal gene transfer for ars genes. Based on the results we propose that under the prevailing low nutrient condition inhabitant bacteria capable of using inorganic electron donors play a synergistic role wherein siderophores and phosphatase activities facilitate the release of sediment bound As(5+), which is subsequently reduced by arsenate reductase resulting into the mobilization of As(3+) in groundwater.}, }
@article {pmid23236161, year = {2012}, author = {Leonard, G and Richards, TA}, title = {Genome-scale comparative analysis of gene fusions, gene fissions, and the fungal tree of life.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {52}, pages = {21402-21407}, pmid = {23236161}, issn = {1091-6490}, support = {BB/G00885X/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Fungi/*genetics ; Gene Fusion/*genetics ; Genes, Fungal/*genetics ; Genome, Fungal/*genetics ; Genomic Instability ; *Phylogeny ; }, abstract = {During the course of evolution genes undergo both fusion and fission by which ORFs are joined or separated. These processes can amend gene function and represent an important factor in the evolution of protein interaction networks. Gene fusions have been suggested to be useful characters for identifying evolutionary relationships because they constitute synapomorphies or cladistic characters. To investigate the fidelity of gene-fusion characters, we developed an approach for identifying differentially distributed gene fusions among whole-genome datasets: fdfBLAST. Applying this tool to the Fungi, we identified 63 gene fusions present in two or more genomes. Using a combination of phylogenetic and comparative genomic analyses, we then investigated the evolution of these genes across 115 fungal genomes, testing each gene fusion for evidence of homoplasy, including gene fission, convergence, and horizontal gene transfer. These analyses demonstrated 110 gene-fission events. We then identified a minimum of three mechanisms that drive gene fission: separation, degeneration, and duplication. These data suggest that gene fission plays an important and hitherto underestimated role in gene evolution. Gene fusions therefore are highly labile characters, and their use for polarizing evolutionary relationships, without reference to gene and species phylogenies, is limited. Accounting for these considerable sources of homoplasy, we identified fusion characters that provide support for multiple nodes in the phylogeny of the Fungi, including relationships within the deeply derived flagellum-forming fungi (i.e., the chytrids).}, }
@article {pmid23235290, year = {2013}, author = {Martiny, AC and Treseder, K and Pusch, G}, title = {Phylogenetic conservatism of functional traits in microorganisms.}, journal = {The ISME journal}, volume = {7}, number = {4}, pages = {830-838}, pmid = {23235290}, issn = {1751-7370}, mesh = {Archaea/*classification/genetics/*physiology ; Bacteria/*classification/genetics ; *Bacterial Physiological Phenomena ; *Biodiversity ; Biological Evolution ; Carbon ; Ecosystem ; *Environmental Microbiology ; Phenotype ; *Phylogeny ; }, abstract = {A central question in biology is how biodiversity influences ecosystem functioning. Underlying this is the relationship between organismal phylogeny and the presence of specific functional traits. The relationship is complicated by gene loss and convergent evolution, resulting in the polyphyletic distribution of many traits. In microorganisms, lateral gene transfer can further distort the linkage between phylogeny and the presence of specific functional traits. To identify the phylogenetic conservation of specific traits in microorganisms, we developed a new phylogenetic metric-consenTRAIT-to estimate the clade depth where organisms share a trait. We then analyzed the distribution of 89 functional traits across a broad range of Bacteria and Archaea using genotypic and phenotypic data. A total of 93% of the traits were significantly non-randomly distributed, which suggested that vertical inheritance was generally important for the phylogenetic dispersion of functional traits in microorganisms. Further, traits in microbes were associated with a continuum of trait depths (τD), ranging from a few deep to many shallow clades (average τD: 0.101-0.0011 rRNA sequence dissimilarity). Next, we demonstrated that the dispersion and the depth of clades that contain a trait is correlated with the trait's complexity. Specifically, complex traits encoded by many genes like photosynthesis and methanogenesis were found in a few deep clusters, whereas the ability to use simple carbon substrates was highly phylogenetically dispersed. On the basis of these results, we propose a framework for predicting the phylogenetic conservatism of functional traits depending on the complexity of the trait. This framework enables predicting how variation in microbial composition may affect microbially-mediated ecosystem processes as well as linking phylogenetic and trait-based patterns of biogeography.}, }
@article {pmid23234643, year = {2012}, author = {Le, PT and Ramulu, HG and Guijarro, L and Paganini, J and Gouret, P and Chabrol, O and Raoult, D and Pontarotti, P}, title = {An automated approach for the identification of horizontal gene transfers from complete genomes reveals the rhizome of Rickettsiales.}, journal = {BMC evolutionary biology}, volume = {12}, number = {}, pages = {243}, pmid = {23234643}, issn = {1471-2148}, mesh = {Alphaproteobacteria/*genetics ; Bayes Theorem ; Electronic Data Processing ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomics/methods ; Phylogeny ; Proteome/analysis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT) is considered to be a major force driving the evolutionary history of prokaryotes. HGT is widespread in prokaryotes, contributing to the genomic repertoire of prokaryotic organisms, and is particularly apparent in Rickettsiales genomes. Gene gains from both distantly and closely related organisms play crucial roles in the evolution of bacterial genomes. In this work, we focus on genes transferred from distantly related species into Rickettsiales species.<br><br>RESULTS: We developed an automated approach for the detection of HGT from other organisms (excluding alphaproteobacteria) into Rickettsiales genomes. Our systematic approach consisted of several specialized features including the application of a parsimony method for inferring phyletic patterns followed by blast filter, automated phylogenetic reconstruction and the application of patterns for HGT detection. We identified 42 instances of HGT in 31 complete Rickettsiales genomes, of which 38 were previously unidentified instances of HGT from Anaplasma, Wolbachia, Candidatus Pelagibacter ubique and Rickettsia genomes. Additionally, putative cases with no phylogenetic support were assigned gene ontology terms. Overall, these transfers could be characterized as "rhizome-like".<br><br>CONCLUSIONS: Our analysis provides a comprehensive, systematic approach for the automated detection of HGTs from several complete proteome sequences that can be applied to detect instances of HGT within other genomes of interest.}, }
@article {pmid23234273, year = {2012}, author = {Joardar, V and Abrams, NF and Hostetler, J and Paukstelis, PJ and Pakala, S and Pakala, SB and Zafar, N and Abolude, OO and Payne, G and Andrianopoulos, A and Denning, DW and Nierman, WC}, title = {Sequencing of mitochondrial genomes of nine Aspergillus and Penicillium species identifies mobile introns and accessory genes as main sources of genome size variability.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {698}, pmid = {23234273}, issn = {1471-2164}, support = {HHSN272200900007C//PHS HHS/United States ; N01-AI-30071/AI/NIAID NIH HHS/United States ; }, mesh = {Aspergillus/*genetics ; Base Sequence ; Evolution, Molecular ; Genes, Fungal/*genetics ; Genes, Mitochondrial/genetics ; Genetic Variation/genetics ; Genome Size/*genetics ; Genome, Mitochondrial/*genetics ; Introns/*genetics ; Molecular Sequence Annotation ; Mutagenesis, Insertional/genetics ; Penicillium/*genetics ; Phylogeny ; Plasmids/genetics ; *Sequence Analysis ; }, abstract = {BACKGROUND: The genera Aspergillus and Penicillium include some of the most beneficial as well as the most harmful fungal species such as the penicillin-producer Penicillium chrysogenum and the human pathogen Aspergillus fumigatus, respectively. Their mitochondrial genomic sequences may hold vital clues into the mechanisms of their evolution, population genetics, and biology, yet only a handful of these genomes have been fully sequenced and annotated.<br><br>RESULTS: Here we report the complete sequence and annotation of the mitochondrial genomes of six Aspergillus and three Penicillium species: A. fumigatus, A. clavatus, A. oryzae, A. flavus, Neosartorya fischeri (A. fischerianus), A. terreus, P. chrysogenum, P. marneffei, and Talaromyces stipitatus (P. stipitatum). The accompanying comparative analysis of these and related publicly available mitochondrial genomes reveals wide variation in size (25-36 Kb) among these closely related fungi. The sources of genome expansion include group I introns and accessory genes encoding putative homing endonucleases, DNA and RNA polymerases (presumed to be of plasmid origin) and hypothetical proteins. The two smallest sequenced genomes (A. terreus and P. chrysogenum) do not contain introns in protein-coding genes, whereas the largest genome (T. stipitatus), contains a total of eleven introns. All of the sequenced genomes have a group I intron in the large ribosomal subunit RNA gene, suggesting that this intron is fixed in these species. Subsequent analysis of several A. fumigatus strains showed low intraspecies variation. This study also includes a phylogenetic analysis based on 14 concatenated core mitochondrial proteins. The phylogenetic tree has a different topology from published multilocus trees, highlighting the challenges still facing the Aspergillus systematics.<br><br>CONCLUSIONS: The study expands the genomic resources available to fungal biologists by providing mitochondrial genomes with consistent annotations for future genetic, evolutionary and population studies. Despite the conservation of the core genes, the mitochondrial genomes of Aspergillus and Penicillium species examined here exhibit significant amount of interspecies variation. Most of this variation can be attributed to accessory genes and mobile introns, presumably acquired by horizontal gene transfer of mitochondrial plasmids and intron homing.}, }
@article {pmid23231464, year = {2012}, author = {Boulund, F and Johnning, A and Pereira, MB and Larsson, DG and Kristiansson, E}, title = {A novel method to discover fluoroquinolone antibiotic resistance (qnr) genes in fragmented nucleotide sequences.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {695}, pmid = {23231464}, issn = {1471-2164}, mesh = {Anti-Bacterial Agents/*pharmacology ; Base Sequence ; Drug Resistance, Bacterial/*genetics ; Escherichia coli Proteins/*genetics ; Fluoroquinolones/*pharmacology ; High-Throughput Nucleotide Sequencing ; Markov Chains ; Metagenome/*genetics ; Models, Genetic ; Multigene Family/*genetics ; Sequence Alignment ; }, abstract = {BACKGROUND: Broad-spectrum fluoroquinolone antibiotics are central in modern health care and are used to treat and prevent a wide range of bacterial infections. The recently discovered qnr genes provide a mechanism of resistance with the potential to rapidly spread between bacteria using horizontal gene transfer. As for many antibiotic resistance genes present in pathogens today, qnr genes are hypothesized to originate from environmental bacteria. The vast amount of data generated by shotgun metagenomics can therefore be used to explore the diversity of qnr genes in more detail.<br><br>RESULTS: In this paper we describe a new method to identify qnr genes in nucleotide sequence data. We show, using cross-validation, that the method has a high statistical power of correctly classifying sequences from novel classes of qnr genes, even for fragments as short as 100 nucleotides. Based on sequences from public repositories, the method was able to identify all previously reported plasmid-mediated qnr genes. In addition, several fragments from novel putative qnr genes were identified in metagenomes. The method was also able to annotate 39 chromosomal variants of which 11 have previously not been reported in literature.<br><br>CONCLUSIONS: The method described in this paper significantly improves the sensitivity and specificity of identification and annotation of qnr genes in nucleotide sequence data. The predicted novel putative qnr genes in the metagenomic data support the hypothesis of a large and uncharacterized diversity within this family of resistance genes in environmental bacterial communities. An implementation of the method is freely available at http://bioinformatics.math.chalmers.se/qnr/.}, }
@article {pmid23227424, year = {2012}, author = {de la Casa-Esperón, E}, title = {Horizontal transfer and the evolution of host-pathogen interactions.}, journal = {International journal of evolutionary biology}, volume = {2012}, number = {}, pages = {679045}, pmid = {23227424}, issn = {2090-052X}, abstract = {Horizontal gene transfer has been long known in viruses and prokaryotes, but its importance in eukaryotes has been only acknowledged recently. Close contact between organisms, as it occurs between pathogens and their hosts, facilitates the occurrence of DNA transfer events. Once inserted in a foreign genome, DNA sequences have sometimes been coopted by pathogens to improve their survival or infectivity, or by hosts to protect themselves against the harm of pathogens. Hence, horizontal transfer constitutes a source of novel sequences that can be adopted to change the host-pathogen interactions. Therefore, horizontal transfer can have an important impact on the coevolution of pathogens and their hosts.}, }
@article {pmid23226971, year = {2012}, author = {Blank, CE}, title = {Low rates of lateral gene transfer among metabolic genes define the evolving biogeochemical niches of archaea through deep time.}, journal = {Archaea (Vancouver, B.C.)}, volume = {2012}, number = {}, pages = {843539}, pmid = {23226971}, issn = {1472-3654}, mesh = {Archaea/*genetics ; Archaeal Proteins/genetics ; Cluster Analysis ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Metabolic Networks and Pathways/*genetics ; Phylogeny ; Sequence Homology ; }, abstract = {Phylogenomic analyses of archaeal genome sequences are providing windows into the group's evolutionary past, even though most archaeal taxa lack a conventional fossil record. Here, phylogenetic analyses were performed using key metabolic genes that define the metabolic niche of microorganisms. Such genes are generally considered to have undergone high rates of lateral gene transfer. Many gene sequences formed clades that were identical, or similar, to the tree constructed using large numbers of genes from the stable core of the genome. Surprisingly, such lateral transfer events were readily identified and quantifiable, occurring only a relatively small number of times in the archaeal domain of life. By placing gene acquisition events into a temporal framework, the rates by which new metabolic genes were acquired can be quantified. The highest lateral transfer rates were among cytochrome oxidase genes that use oxygen as a terminal electron acceptor (with a total of 12-14 lateral transfer events, or 3.4-4.0 events per billion years, across the entire archaeal domain). Genes involved in sulfur or nitrogen metabolism had much lower rates, on the order of one lateral transfer event per billion years. This suggests that lateral transfer rates of key metabolic proteins are rare and not rampant.}, }
@article {pmid23226439, year = {2012}, author = {Carr, M and Bensasson, D and Bergman, CM}, title = {Evolutionary genomics of transposable elements in Saccharomyces cerevisiae.}, journal = {PloS one}, volume = {7}, number = {11}, pages = {e50978}, pmid = {23226439}, issn = {1932-6203}, mesh = {Base Sequence ; DNA Transposable Elements/*genetics ; *Evolution, Molecular ; Gene Dosage/genetics ; Gene Transfer, Horizontal/genetics ; Genetic Variation ; Genome, Fungal/genetics ; *Genomics ; Likelihood Functions ; Molecular Sequence Annotation ; Nucleotides/genetics ; Saccharomyces cerevisiae/*genetics ; Sequence Homology, Nucleic Acid ; Terminal Repeat Sequences/genetics ; }, abstract = {Saccharomyces cerevisiae is one of the premier model systems for studying the genomics and evolution of transposable elements. The availability of the S. cerevisiae genome led to unprecedented insights into its five known transposable element families (the LTR retrotransposons Ty1-Ty5) in the years shortly after its completion. However, subsequent advances in bioinformatics tools for analysing transposable elements and the recent availability of genome sequences for multiple strains and species of yeast motivates new investigations into Ty evolution in S. cerevisiae. Here we provide a comprehensive phylogenetic and population genetic analysis of all Ty families in S. cerevisiae based on a systematic re-annotation of Ty elements in the S288c reference genome. We show that previous annotation efforts have underestimated the total copy number of Ty elements for all known families. In addition, we identify a new family of Ty3-like elements related to the S. paradoxus Ty3p which is composed entirely of degenerate solo LTRs. Phylogenetic analyses of LTR sequences identified three families with short-branch, recently active clades nested among long branch, inactive insertions (Ty1, Ty3, Ty4), one family with essentially all recently active elements (Ty2) and two families with only inactive elements (Ty3p and Ty5). Population genomic data from 38 additional strains of S. cerevisiae show that the majority of Ty insertions in the S288c reference genome are fixed in the species, with insertions in active clades being predominantly polymorphic and insertions in inactive clades being predominantly fixed. Finally, we use comparative genomic data to provide evidence that the Ty2 and Ty3p families have arisen in the S. cerevisiae genome by horizontal transfer. Our results demonstrate that the genome of a single individual contains important information about the state of TE population dynamics within a species and suggest that horizontal transfer may play an important role in shaping the genomic diversity of transposable elements in unicellular eukaryotes.}, }
@article {pmid23226415, year = {2012}, author = {Paganini, J and Campan-Fournier, A and Da Rocha, M and Gouret, P and Pontarotti, P and Wajnberg, E and Abad, P and Danchin, EG}, title = {Contribution of lateral gene transfers to the genome composition and parasitic ability of root-knot nematodes.}, journal = {PloS one}, volume = {7}, number = {11}, pages = {e50875}, pmid = {23226415}, issn = {1932-6203}, mesh = {Animals ; Bacteria/genetics ; Base Composition/genetics ; Codon/genetics ; DNA Transposable Elements/genetics ; Gene Duplication ; Gene Transfer, Horizontal/*genetics ; Genes, Protozoan/genetics ; Genetic Association Studies ; Genome/*genetics ; Open Reading Frames/genetics ; Parasites/*genetics ; Phylogeny ; Plant Diseases/*parasitology ; Plant Roots/*parasitology ; Plasmids/genetics ; Protozoan Proteins/genetics ; Sequence Homology, Nucleic Acid ; Soil Microbiology ; Tylenchoidea/*genetics ; }, abstract = {Lateral gene transfers (LGT), species to species transmission of genes by means other than direct inheritance from a common ancestor, have played significant role in shaping prokaryotic genomes and are involved in gain or transfer of important biological processes. Whether LGT significantly contributed to the composition of an animal genome is currently unclear. In nematodes, multiple LGT are suspected to have favored emergence of plant-parasitism. With the availability of whole genome sequences it is now possible to assess whether LGT have significantly contributed to the composition of an animal genome and to establish a comprehensive list of these events. We generated clusters of homologous genes and automated phylogenetic inference, to detect LGT in the genomes of root-knot nematodes and found that up to 3.34% of the genes originate from LGT of non-metazoan origin. After their acquisition, the majority of genes underwent series of duplications. Compared to the rest of the genes in these species, several predicted functional categories showed a skewed distribution in the set of genes acquired via LGT. Interestingly, functions related to metabolism, degradation or modification of carbohydrates or proteins were substantially more frequent. This suggests that genes involved in these processes, related to a parasitic lifestyle, have been more frequently fixed in these parasites after their acquisition. Genes from soil bacteria, including plant-pathogens were the most frequent closest relatives, suggesting donors were preferentially bacteria from the rhizosphere. Several of these bacterial genes are plasmid-borne, pointing to a possible role of these mobile genetic elements in the transfer mechanism. Our analysis provides the first comprehensive description of the ensemble of genes of non-metazoan origin in an animal genome. Besides being involved in important processes regarding plant-parasitism, genes acquired via LGT now constitute a substantial proportion of protein-coding genes in these nematode genomes.}, }
@article {pmid23224296, year = {2013}, author = {Ishihara, S and Bitner, JJ and Farley, GH and Gillock, ET}, title = {Vancomycin-resistant gram-positive cocci isolated from the saliva of wild songbirds.}, journal = {Current microbiology}, volume = {66}, number = {4}, pages = {337-343}, pmid = {23224296}, issn = {1432-0991}, support = {P20 GM103418/GM/NIGMS NIH HHS/United States ; P20 RR016475/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Enterococcus/classification/*drug effects/genetics/*isolation &amp; purification ; Kansas ; Saliva/*microbiology ; Songbirds/*microbiology ; Staphylococcus/classification/*drug effects/genetics/*isolation &amp; purification ; Vancomycin/pharmacology ; *Vancomycin Resistance ; }, abstract = {We analyzed highly vancomycin-resistant Gram-positive bacteria isolated from the saliva of migratory songbirds captured, sampled, and released from a bird-banding station in western Kansas. Individual bacterial isolates were identified by partial 16S rRNA sequencing. Most of the bacteria in this study were shown to be Staphylococcus succinus with the majority being isolated from the American Robin. Some of these bacteria were shown to carry vanA, vanB, and vanC vancomycin-resistance genes and have the ability to form biofilms. One of the van gene-carrying isolates is also coagulase positive, which is normally considered a virulence factor. Other organisms isolated included Staphylococcus saprophyticus as well as Enterococcus gallinarum. Given the wide range of the American Robin and ease of horizontal gene transfer between Gram-positive cocci, we postulate that these organisms could serve as a reservoir of vancomycin-resistance genes capable of transferring to human pathogens.}, }
@article {pmid23221676, year = {2013}, author = {Dagan, T and Roettger, M and Stucken, K and Landan, G and Koch, R and Major, P and Gould, SB and Goremykin, VV and Rippka, R and Tandeau de Marsac, N and Gugger, M and Lockhart, PJ and Allen, JF and Brune, I and Maus, I and Pühler, A and Martin, WF}, title = {Genomes of Stigonematalean cyanobacteria (subsection V) and the evolution of oxygenic photosynthesis from prokaryotes to plastids.}, journal = {Genome biology and evolution}, volume = {5}, number = {1}, pages = {31-44}, pmid = {23221676}, issn = {1759-6653}, support = {232975/ERC_/European Research Council/International ; 281357/ERC_/European Research Council/International ; }, mesh = {Cyanobacteria/*genetics/metabolism ; Ecosystem ; *Evolution, Molecular ; Fresh Water ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genome, Plastid ; Multigene Family ; Photosynthesis/*genetics ; Phylogeny ; Plants/genetics ; Symbiosis/genetics ; Water/metabolism ; }, abstract = {Cyanobacteria forged two major evolutionary transitions with the invention of oxygenic photosynthesis and the bestowal of photosynthetic lifestyle upon eukaryotes through endosymbiosis. Information germane to understanding those transitions is imprinted in cyanobacterial genomes, but deciphering it is complicated by lateral gene transfer (LGT). Here, we report genome sequences for the morphologically most complex true-branching cyanobacteria, and for Scytonema hofmanni PCC 7110, which with 12,356 proteins is the most gene-rich prokaryote currently known. We investigated components of cyanobacterial evolution that have been vertically inherited, horizontally transferred, and donated to eukaryotes at plastid origin. The vertical component indicates a freshwater origin for water-splitting photosynthesis. Networks of the horizontal component reveal that 60% of cyanobacterial gene families have been affected by LGT. Plant nuclear genes acquired from cyanobacteria define a lower bound frequency of 611 multigene families that, in turn, specify diazotrophic cyanobacterial lineages as having a gene collection most similar to that possessed by the plastid ancestor.}, }
@article {pmid23221609, year = {2012}, author = {Yoosuf, N and Yutin, N and Colson, P and Shabalina, SA and Pagnier, I and Robert, C and Azza, S and Klose, T and Wong, J and Rossmann, MG and La Scola, B and Raoult, D and Koonin, EV}, title = {Related giant viruses in distant locations and different habitats: Acanthamoeba polyphaga moumouvirus represents a third lineage of the Mimiviridae that is close to the megavirus lineage.}, journal = {Genome biology and evolution}, volume = {4}, number = {12}, pages = {1324-1330}, pmid = {23221609}, issn = {1759-6653}, support = {R37 AI011219/AI/NIAID NIH HHS/United States ; }, mesh = {Acanthamoeba/virology ; Ecosystem ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Viral ; Mimiviridae/*classification/*genetics/ultrastructure ; *Phylogeny ; Viral Proteins/genetics ; }, abstract = {The 1,021,348 base pair genome sequence of the Acanthamoeba polyphaga moumouvirus, a new member of the Mimiviridae family infecting Acanthamoeba polyphaga, is reported. The moumouvirus represents a third lineage beside mimivirus and megavirus. Thereby, it is a new member of the recently proposed Megavirales order. This giant virus was isolated from a cooling tower water in southeastern France but is most closely related to Megavirus chiliensis, which was isolated from ocean water off the coast of Chile. The moumouvirus is predicted to encode 930 proteins, of which 879 have detectable homologs. Among these predicted proteins, for 702 the closest homolog was detected in Megavirus chiliensis, with the median amino acid sequence identity of 62%. The evolutionary affinity of moumouvirus and megavirus was further supported by phylogenetic tree analysis of conserved genes. The moumouvirus and megavirus genomes share near perfect orthologous gene collinearity in the central part of the genome, with the variations concentrated in the terminal regions. In addition, genomic comparisons of the Mimiviridae reveal substantial gene loss in the moumouvirus lineage. The majority of the remaining moumouvirus proteins are most similar to homologs from other Mimiviridae members, and for 27 genes the closest homolog was found in bacteria. Phylogenetic analysis of these genes supported gene acquisition from diverse bacteria after the separation of the moumouvirus and megavirus lineages. Comparative genome analysis of the three lineages of the Mimiviridae revealed significant mobility of Group I self-splicing introns, with the highest intron content observed in the moumouvirus genome.}, }
@article {pmid23221607, year = {2012}, author = {Kamneva, OK and Knight, SJ and Liberles, DA and Ward, NL}, title = {Analysis of genome content evolution in pvc bacterial super-phylum: assessment of candidate genes associated with cellular organization and lifestyle.}, journal = {Genome biology and evolution}, volume = {4}, number = {12}, pages = {1375-1390}, pmid = {23221607}, issn = {1759-6653}, support = {P20 RR016474/RR/NCRR NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics ; DNA Repeat Expansion ; Ecosystem ; *Evolution, Molecular ; Gene Deletion ; Gene Duplication ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome Size ; *Genome, Bacterial ; Gram-Negative Bacteria/*genetics ; Phylogeny ; }, abstract = {The Planctomycetes, Verrucomicrobia, Chlamydiae (PVC) super-phylum contains bacteria with either complex cellular organization or simple cell structure; it also includes organisms of different lifestyles (pathogens, mutualists, commensal, and free-living). Genome content evolution of this group has not been studied in a systematic fashion, which would reveal genes underlying the emergence of PVC-specific phenotypes. Here, we analyzed the evolutionary dynamics of 26 PVC genomes and several outgroup species. We inferred HGT, duplications, and losses by reconciliation of 27,123 gene trees with the species phylogeny. We showed that genome expansion and contraction have driven evolution within Planctomycetes and Chlamydiae, respectively, and balanced each other in Verrucomicrobia and Lentisphaerae. We also found that for a large number of genes in PVC genomes the most similar sequences are present in Acidobacteria, suggesting past and/or current ecological interaction between organisms from these groups. We also found evidence of shared ancestry between carbohydrate degradation genes in the mucin-degrading human intestinal commensal Akkermansia muciniphila and sequences from Acidobacteria and Bacteroidetes, suggesting that glycoside hydrolases are transferred laterally between gut microbes and that the process of carbohydrate degradation is crucial for microbial survival within the human digestive system. Further, we identified a highly conserved genetic module preferentially present in compartmentalized PVC species and possibly associated with the complex cell plan in these organisms. This conserved machinery is likely to be membrane targeted and involved in electron transport, although its exact function is unknown. These genes represent good candidates for future functional studies.}, }
@article {pmid23215733, year = {2013}, author = {Gnanadhas, DP and Marathe, SA and Chakravortty, D}, title = {Biocides--resistance, cross-resistance mechanisms and assessment.}, journal = {Expert opinion on investigational drugs}, volume = {22}, number = {2}, pages = {191-206}, doi = {10.1517/13543784.2013.748035}, pmid = {23215733}, issn = {1744-7658}, mesh = {Animals ; Anti-Bacterial Agents/administration &amp; dosage/classification/*pharmacology ; Bacteria/drug effects/genetics/ultrastructure ; Biofilms/drug effects/growth &amp; development ; Disinfectants/administration &amp; dosage/classification/*pharmacology ; *Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Humans ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Structure-Activity Relationship ; }, abstract = {IMPORTANCE OF THE FIELD: Antibiotic resistance in bacterial pathogens has increased worldwide leading to treatment failures. Concerns have been raised about the use of biocides as a contributing factor to the risk of antimicrobial resistance (AMR) development. In vitro studies demonstrating increase in resistance have often been cited as evidence for increased risks. It is therefore important to understand the mechanisms of resistance employed by bacteria toward biocides used in consumer products and their potential to impart cross-resistance to therapeutic antibiotics.<br><br>AREAS COVERED: In this review, the mechanisms of resistance and cross-resistance reported in the literature toward biocides commonly used in consumer products are summarized. The physiological and molecular techniques used in describing and examining these mechanisms are reviewed and application of these techniques for systematic assessment of biocides for their potential to develop resistance and/or cross-resistance is discussed.<br><br>EXPERT OPINION: The guidelines in the usage of biocides in household or industrial purpose should be monitored and regulated to avoid the emergence of any MDR strains. The genetic and molecular methods to monitor the resistance development to biocides should be developed and included in preclinical and clinical studies.}, }
@article {pmid23211014, year = {2013}, author = {Sun, BF and Xiao, JH and He, SM and Liu, L and Murphy, RW and Huang, DW}, title = {Multiple ancient horizontal gene transfers and duplications in lepidopteran species.}, journal = {Insect molecular biology}, volume = {22}, number = {1}, pages = {72-87}, doi = {10.1111/imb.12004}, pmid = {23211014}, issn = {1365-2583}, mesh = {Animals ; Biological Evolution ; Bombyx/genetics ; Expressed Sequence Tags ; *Gene Transfer, Horizontal ; Genome, Insect ; Lepidoptera/*genetics/metabolism ; Phylogeny ; Selection, Genetic ; }, abstract = {Eukaryotic horizontal gene transfer (HGT) events are increasingly being discovered yet few reports have summarized multiple occurrences in a wide range of species. We systematically investigated HGT events in the order Lepidoptera by employing a series of filters. Bombyx mori, Danaus plexippus and Heliconius melpomene had 13, 12 and 12 HGTs, respectively, from bacteria and fungi. These HGTs contributed a total of 64 predicted genes: 22 to B. mori, 22 to D. plexippus and 20 to H. melpomene. Several new genes were generated by post-transfer duplications. Post-transfer duplication of a suite of functional HGTs has rarely been reported in higher organisms. The distributional patterns of paralogues for certain genes differed in the three species, indicating potential independent duplication or loss events. All of these HGTs had homologues expressed in some other lepidopterans, indicating ancient transfer events. Most HGTs were involved in the metabolism of sugar and amino acids. These HGTs appeared to have experienced amelioration, purifying selection and accelerated evolution to adapt to the background genome of the recipient. The discovery of ancient, massive HGTs and duplications in lepidopterans and their adaptive evolution provides further insights into the evolutionary significance of the events from donors to multicellular host recipients.}, }
@article {pmid23210906, year = {2013}, author = {Adler, A and Baraniak, A and Izdebski, R and Fiett, J and Gniadkowski, M and Hryniewicz, W and Salvia, A and Rossini, A and Goossens, H and Malhotra, S and Lerman, Y and Elenbogen, M and Carmeli, Y and , }, title = {A binational cohort study of intestinal colonization with extended-spectrum β-lactamase-producing Proteus mirabilis in patients admitted to rehabilitation centres.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {19}, number = {2}, pages = {E51-8}, doi = {10.1111/1469-0691.12072}, pmid = {23210906}, issn = {1469-0691}, mesh = {Aged ; Aged, 80 and over ; Carrier State/*epidemiology/microbiology ; Case-Control Studies ; Cohort Studies ; Electrophoresis, Gel, Pulsed-Field ; Female ; Genotype ; Humans ; Israel/epidemiology ; Male ; Middle Aged ; Molecular Typing ; Polymerase Chain Reaction ; Prospective Studies ; Proteus Infections/*epidemiology/microbiology ; Proteus mirabilis/classification/enzymology/genetics/*isolation &amp; purification ; Rectum/*microbiology ; *Rehabilitation Centers ; Risk Factors ; Rome/epidemiology ; Sequence Analysis, DNA ; beta-Lactamases/*metabolism ; }, abstract = {The aims of our study were to analyse the risk factors for colonization by Extended-spectrum β-lactamases (ESBL)-producing Proteus mirabilis (ESBL-PM) in rehabilitation patients and to characterize the molecular features of these strains. The study was conducted in two rehabilitation centres located in Rome, Italy (Fondazione Santa Lucia IRCCS (FSL)), and Tel-Aviv, Israel (Tel-Aviv Sourasky Medical Center (TASMC)). Carriage of ESBL-PM was surveyed by rectal swabs. Strain typing was performed by pulsed-field gel electrophoresis (PFGE). Identification of ESBL genes was done by PCR and sequencing. Patients admitted to the same institutions without ESBL carriage were included as controls. The study group included 70 and 41 patients from FSL and TASMC, respectively. In FSL, the multivariate analysis identified severe acute brain injury (OR = 15, 95% CI = 3.2-69.5, p 0.001), decubitus ulcer (OR = 3.5, 95% CI = 1.2-9.8, p 0.018) and recent treatment with quinolones (OR = 5.7, 95% CI = 1.07-30.1, p 0.042) as independent risk factors. ESBL-PM carriers stayed longer in the hospital on average and were less likely to be discharged home. No significant risk factor was identified in TASMC. There were no similarities in PFGE types or ESBL genes between the ESBL-PM isolates from the two institutions. In both hospitals, a variety of PFGE types existed but a single ESBL type predominated, namely TEM-92 in FSL (n = 64/70; 91%) and CTX-M-2 in TASMC (n = 37/41; 90%). A new TEM ESBL variant, TEM-177 was identified in FSL. The clonal diversity and the predominance of a single ESBL type suggested that horizontal gene transfer played an important role in dissemination of resistance. The development of a population analysis tool that would allow tracing deeper genetic relationships is required.}, }
@article {pmid23209414, year = {2012}, author = {Starikova, I and Harms, K and Haugen, P and Lunde, TT and Primicerio, R and Samuelsen, &#xd8; and Nielsen, KM and Johnsen, PJ}, title = {A trade-off between the fitness cost of functional integrases and long-term stability of integrons.}, journal = {PLoS pathogens}, volume = {8}, number = {11}, pages = {e1003043}, pmid = {23209414}, issn = {1553-7374}, mesh = {Acinetobacter baumannii/*enzymology/genetics ; Bacterial Proteins/genetics/*metabolism ; Base Sequence ; Genomic Instability/*physiology ; Integrases/genetics/*metabolism ; Integrons/*physiology ; Molecular Sequence Data ; Salmonella typhimurium/*enzymology/genetics ; }, abstract = {Horizontal gene transfer (HGT) plays a major role in bacterial microevolution as evident from the rapid emergence and spread of antimicrobial drug resistance. Few studies have however addressed the population dynamics of newly imported genetic elements after HGT. Here, we show that newly acquired class-1 integrons from Salmonella enterica serovar Typhimurium and Acinetobacter baumannii, free of associated transposable elements, strongly reduce host fitness in Acinetobacter baylyi. Insertional inactivation of the integron intI1 restored fitness, demonstrating that the observed fitness costs were due to the presence of an active integrase. The biological cost of harboring class-1 integrons was rapidly reduced during serial transfers due to intI1 frameshift mutations leading to inactivated integrases. We use a mathematical model to explore the conditions where integrons with functional integrases are maintained and conclude that environmental fluctuations and episodic selection is necessary for the maintenance of functional integrases. Taken together, the presented data suggest a trade-off between the ability to capture gene cassettes and long-term stability of integrons and provide an explanation for the frequent observation of inactive integron-integrases in bacterial populations.}, }
@article {pmid23204388, year = {2013}, author = {Roelofs, D and Timmermans, MJ and Hensbergen, P and van Leeuwen, H and Koopman, J and Faddeeva, A and Suring, W and de Boer, TE and Mariën, J and Boer, R and Bovenberg, R and van Straalen, NM}, title = {A functional isopenicillin N synthase in an animal genome.}, journal = {Molecular biology and evolution}, volume = {30}, number = {3}, pages = {541-548}, doi = {10.1093/molbev/mss269}, pmid = {23204388}, issn = {1537-1719}, mesh = {Amino Acid Sequence ; Animals ; Catalytic Domain ; Genome, Insect ; Insect Proteins/chemistry/*genetics ; Insecta/*enzymology/genetics ; Models, Molecular ; Molecular Sequence Data ; Oligopeptides/chemistry ; Oxidoreductases/chemistry/*genetics ; Penicillins/biosynthesis ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Horizontal transfer of genes is widespread among prokaryotes, but is less common between microorganisms and animals. Here, we present evidence for the presence of a gene encoding functional isopenicillin N synthase, an enzyme in the β-lactam antibiotics biosynthesis pathway, in the genome of the soil-living collembolan species, Folsomia candida (FcIPNS). At present, this gene is only known from bacteria and fungi, as is the capacity to produce β-lactam antibiotics. The FcIPNS gene was located on two genomic contigs, was physically linked to a predicted insect ATP-binding cassette transporter gene, and contained three introns each flanked by eukaryotic splicing recognition sites (GT/AG). Homology searches revealed no similarity between these introns and the FcIPNS regions of bacteria or fungi. All amino acids conserved across bacteria and fungi were also conserved in F. candida. Recombinant FcIPNS was able to convert its substrate amino δ-(l-α-aminoadipyl)-l-cysteinyl-d-valine into isopenicillin N, providing strong evidence that FcIPNS is functional. Phylogenetic analysis clustered FcIPNS outside the bacterial IPNS clade, and also outside the fungal IPNS clade, suggesting an ancient gene transfer followed by divergence in the F. candida genome. In conclusion, the data suggest that the soil-living collembolan F. candida has assimilated the capacity for antibacterial activity by horizontal gene transfer, which may be an important adaptive trait in the microbe-dominated soil ecosystem.}, }
@article {pmid23202379, year = {2013}, author = {Maal-Bared, R and Bartlett, KH and Bowie, WR and Hall, ER}, title = {Phenotypic antibiotic resistance of Escherichia coli and E. coli O157 isolated from water, sediment and biofilms in an agricultural watershed in British Columbia.}, journal = {The Science of the total environment}, volume = {443}, number = {}, pages = {315-323}, doi = {10.1016/j.scitotenv.2012.10.106}, pmid = {23202379}, issn = {1879-1026}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {*Agriculture ; *Biofilms ; British Columbia ; *Drug Resistance, Microbial ; Escherichia coli/drug effects/*isolation &amp; purification ; Geologic Sediments/*microbiology ; Microbial Sensitivity Tests ; *Water Microbiology ; }, abstract = {This study examined the distribution of antibiotic resistant Escherichia coli and E. coli O157 isolated from water, sediment and biofilms in an intensive agricultural watershed (Elk Creek, British Columbia) between 2005 and 2007. It also examined physical and chemical water parameters associated with antibiotic resistance. Broth microdilution techniques were used to determine minimum inhibitory concentrations (MIC) for E. coli (n=214) and E. coli O157 (n=27) recovered isolates for ampicillin, cefotaxime, ciprofloxacin, nalidixic acid, streptomycin and tetracycline. Both E. coli and E. coli O157 isolates showed highest frequency of resistance to tetracycline, ampicillin, streptomycin and nalidixic acid; respectively. For E. coli, the highest frequency of resistance was observed at the most agriculturally-impacted site, while the lowest frequency of resistance was found at the headwaters. Sediment and river rock biofilms were the most likely to be associated with resistant E. coli, while water was the least likely. While seasonality (wet versus dry) had no relationship with resistance frequency, length of biofilm colonization of the substratum in the aquatic environment only affected resistance frequency to nalidixic acid and tetracycline. Multivariate logistic regressions showed that water depth, nutrient concentrations, temperature, dissolved oxygen and salinity had statistically significant associations with frequency of E. coli resistance to nalidixic acid, streptomycin, ampicillin and tetracycline. The results indicate that antibiotic resistant E. coli and E. coli O157 were prevalent in an agricultural stream. Since E. coli is adept at horizontal gene transfer and prevalent in biofilms and sediment, where ample opportunities for genetic exchange with potential environmental pathogens present themselves, resistant isolates may present a risk to ecosystem, wildlife and public health.}, }
@article {pmid23201678, year = {2012}, author = {Curtis, BA and Tanifuji, G and Burki, F and Gruber, A and Irimia, M and Maruyama, S and Arias, MC and Ball, SG and Gile, GH and Hirakawa, Y and Hopkins, JF and Kuo, A and Rensing, SA and Schmutz, J and Symeonidi, A and Elias, M and Eveleigh, RJ and Herman, EK and Klute, MJ and Nakayama, T and Oborník, M and Reyes-Prieto, A and Armbrust, EV and Aves, SJ and Beiko, RG and Coutinho, P and Dacks, JB and Durnford, DG and Fast, NM and Green, BR and Grisdale, CJ and Hempel, F and Henrissat, B and Höppner, MP and Ishida, K and Kim, E and Kořený, L and Kroth, PG and Liu, Y and Malik, SB and Maier, UG and McRose, D and Mock, T and Neilson, JA and Onodera, NT and Poole, AM and Pritham, EJ and Richards, TA and Rocap, G and Roy, SW and Sarai, C and Schaack, S and Shirato, S and Slamovits, CH and Spencer, DF and Suzuki, S and Worden, AZ and Zauner, S and Barry, K and Bell, C and Bharti, AK and Crow, JA and Grimwood, J and Kramer, R and Lindquist, E and Lucas, S and Salamov, A and McFadden, GI and Lane, CE and Keeling, PJ and Gray, MW and Grigoriev, IV and Archibald, JM}, title = {Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs.}, journal = {Nature}, volume = {492}, number = {7427}, pages = {59-65}, pmid = {23201678}, issn = {1476-4687}, support = {BB/G00885X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Algal Proteins/genetics/metabolism ; Alternative Splicing/genetics ; Cell Nucleus/*genetics ; Cercozoa/cytology/*genetics/metabolism ; Cryptophyta/cytology/*genetics/metabolism ; Cytosol/metabolism ; *Evolution, Molecular ; Gene Duplication/genetics ; Gene Transfer, Horizontal/genetics ; Genes, Essential/genetics ; Genome/*genetics ; Genome, Mitochondrial/genetics ; Genome, Plant/genetics ; Genome, Plastid/genetics ; Molecular Sequence Data ; *Mosaicism ; Phylogeny ; Protein Transport ; Proteome/genetics/metabolism ; Symbiosis/*genetics ; Transcriptome/genetics ; }, abstract = {Cryptophyte and chlorarachniophyte algae are transitional forms in the widespread secondary endosymbiotic acquisition of photosynthesis by engulfment of eukaryotic algae. Unlike most secondary plastid-bearing algae, miniaturized versions of the endosymbiont nuclei (nucleomorphs) persist in cryptophytes and chlorarachniophytes. To determine why, and to address other fundamental questions about eukaryote-eukaryote endosymbiosis, we sequenced the nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. Both genomes have >21,000 protein genes and are intron rich, and B. natans exhibits unprecedented alternative splicing for a single-celled organism. Phylogenomic analyses and subcellular targeting predictions reveal extensive genetic and biochemical mosaicism, with both host- and endosymbiont-derived genes servicing the mitochondrion, the host cell cytosol, the plastid and the remnant endosymbiont cytosol of both algae. Mitochondrion-to-nucleus gene transfer still occurs in both organisms but plastid-to-nucleus and nucleomorph-to-nucleus transfers do not, which explains why a small residue of essential genes remains locked in each nucleomorph.}, }
@article {pmid23201291, year = {2013}, author = {Brusini, J and Robin, C}, title = {Mycovirus transmission revisited by in situ pairings of vegetatively incompatible isolates of Cryphonectria parasitica.}, journal = {Journal of virological methods}, volume = {187}, number = {2}, pages = {435-442}, doi = {10.1016/j.jviromet.2012.11.025}, pmid = {23201291}, issn = {1879-0984}, mesh = {Ascomycota/genetics/isolation &amp; purification/*virology ; Biological Assay/methods ; Crosses, Genetic ; Fagaceae/microbiology ; Gene Transfer, Horizontal ; Mycelium/genetics/growth &amp; development ; Mycology/*methods ; Plant Diseases/microbiology ; Spores, Fungal/genetics/growth &amp; development ; Viruses/genetics/*isolation &amp; purification ; }, abstract = {In disease ecology, parasite transmission is a key parameter important at both epidemiological and evolutionary scales. Mycoviruses can be transmitted both horizontally and vertically. Their horizontal transmission is strongly restricted by the host vegetative compatibility system, which controls the outcome of somatic fusion in fungi, and by the same way, may limit mycovirus transmission. However, most of current knowledge and predictive capabilities regarding these host/pathogen systems are derived from studies pairing fungal mycelia on artificial medium. An original bioassay method, using infected mycelia as well as asexual spores, had been developed to assess in situ transmission of Cryphonectria Hypovirus-1 (CHV1), a mycovirus of Cryphonectria parasitica that causes chestnut blight. For every pair of different vegetative compatibility types tested, rates of CHV1 transmission were always superior in situ than in vitro. This study supports the hypothesis that the natural ability of CHV1 to migrate within a fungal population composed of different vegetative compatible types may have been underestimated by in vitro essays. This result offers opportunities for a biological control of fungal diseases with mycoviruses.}, }
@article {pmid23200944, year = {2013}, author = {Jörnvall, H and Hedlund, J and Bergman, T and Kallberg, Y and Cederlund, E and Persson, B}, title = {Origin and evolution of medium chain alcohol dehydrogenases.}, journal = {Chemico-biological interactions}, volume = {202}, number = {1-3}, pages = {91-96}, doi = {10.1016/j.cbi.2012.11.008}, pmid = {23200944}, issn = {1872-7786}, mesh = {Alcohol Dehydrogenase/*genetics ; Animals ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Humans ; Isoenzymes/genetics ; Liver/enzymology/metabolism ; Oxidation-Reduction ; Prokaryotic Cells/enzymology/metabolism ; }, abstract = {Different lines of alcohol dehydrogenases (ADHs) have separate superfamily origins, already recognized but now extended and re-evaluated by re-screening of the latest databank update. The short-chain form (SDR) is still the superfamily with most abundant occurrence, most multiple divergence, most prokaryotic emphasis, and most non-complicated architecture. This pattern is compatible with an early appearance at the time of the emergence of prokaryotic cellular life. The medium-chain form (MDR) is also old but second in terms of all the parameters above, and therefore compatible with a second emergence. However, this step appears seemingly earlier than previously considered, and may indicate sub-stages of early emergences at the increased resolution available from the now greater number of data entries. The Zn-MDR origin constitutes a third stage, possibly compatible with the transition to oxidative conditions on earth. Within all these three lines, repeated enzymogeneses gave the present divergence. MDR-ADH origin(s), at a fourth stage, may also be further resolved in multiple or extended modes, but the classical liver MDR-ADH of the liver type can still be traced to a gene duplication ~550 MYA (million years ago), at the early vertebrate radiation, compatible with the post-eon-shift, "Cambrian explosion". Classes and isozymes correspond to subsequent and recent duplicatory events, respectively. They illustrate a peculiar pattern with functional and emerging evolutionary distinctions between parent and emerging lines, suggesting a parallelism between duplicatory and mutational events, now also visible at separate sub-stages. Combined, all forms show distinctive patterns at different levels and illustrate correlations with global events. They further show that simple molecular observations on patterns, multiplicities and occurrence give much information, suggesting common divergence rules not much disturbed by horizontal gene transfers after the initial origins.}, }
@article {pmid23200465, year = {2013}, author = {Gilchrist, TL and Smith, DG and Fitzpatrick, JL and Zadoks, RN and Fontaine, MC}, title = {Comparative molecular analysis of ovine and bovine Streptococcus uberis isolates.}, journal = {Journal of dairy science}, volume = {96}, number = {2}, pages = {962-970}, doi = {10.3168/jds.2012-5705}, pmid = {23200465}, issn = {1525-3198}, mesh = {Animals ; Cattle/microbiology ; DNA, Bacterial/genetics ; Female ; Mastitis/microbiology/veterinary ; Mastitis, Bovine/microbiology ; Multilocus Sequence Typing/veterinary ; Polymerase Chain Reaction/veterinary ; Sequence Analysis, DNA/veterinary ; Sheep/microbiology ; Sheep Diseases/microbiology ; Streptococcal Infections/microbiology/veterinary ; Streptococcus/*genetics/isolation &amp; purification ; }, abstract = {Streptococcus uberis causes clinical and subclinical mastitis in cattle and sheep, but it is unknown whether the composition of Strep. uberis populations differs between host species. To address this, we characterized a collection of bovine and ovine Strep. uberis isolates with shared geographical and temporal origins by means of an expanded multilocus sequence typing scheme. Among 14 ovine and 35 bovine isolates, 35 allelic profiles were detected. Each allelic profile was associated with a single host species and all but one were new to the multilocus sequence typing database. The median number of new alleles per isolate was higher for ovine isolates than for bovine isolates. None of the ovine isolates belonged to the global clonal complexes 5 or 143, which are commonly associated with bovine mastitis and which have a wide geographical distribution. Ovine isolates also differed from bovine isolates in carriage of plasminogen activator genes, with significantly higher prevalence of pauB in ovine isolates. Isolates that were negative for yqiL, one of the targets of multilocus sequence typing, were found among ovine and bovine isolates and were not associated with a specific sequence type or global clonal complex. One bovine isolate carried a gapC allele that was probably acquired through lateral gene transfer, most likely from Streptococcus salivarius. We conclude that ovine isolates are distinct from bovine isolates of Strep. uberis, and that recombination between isolates from different host species or bacterial species could contribute to changes in virulence gene profiles with relevance for vaccine development.}, }
@article {pmid23193285, year = {2013}, author = {Felder, M and Romualdi, A and Petzold, A and Platzer, M and Sühnel, J and Glöckner, G}, title = {GenColors-based comparative genome databases for small eukaryotic genomes.}, journal = {Nucleic acids research}, volume = {41}, number = {Database issue}, pages = {D692-9}, pmid = {23193285}, issn = {1362-4962}, mesh = {Amoebozoa/genetics ; *Databases, Genetic ; Eukaryota/*genetics ; Genome, Fungal ; *Genomics ; Internet ; Molecular Sequence Annotation ; }, abstract = {Many sequence data repositories can give a quick and easily accessible overview on genomes and their annotations. Less widespread is the possibility to compare related genomes with each other in a common database environment. We have previously described the GenColors database system (http://gencolors.fli-leibniz.de) and its applications to a number of bacterial genomes such as Borrelia, Legionella, Leptospira and Treponema. This system has an emphasis on genome comparison. It combines data from related genomes and provides the user with an extensive set of visualization and analysis tools. Eukaryote genomes are normally larger than prokaryote genomes and thus pose additional challenges for such a system. We have, therefore, adapted GenColors to also handle larger datasets of small eukaryotic genomes and to display eukaryotic gene structures. Further recent developments include whole genome views, genome list options and, for bacterial genome browsers, the display of horizontal gene transfer predictions. Two new GenColors-based databases for two fungal species (http://fgb.fli-leibniz.de) and for four social amoebas (http://sacgb.fli-leibniz.de) were set up. Both new resources open up a single entry point for related genomes for the amoebozoa and fungal research communities and other interested users. Comparative genomics approaches are greatly facilitated by these resources.}, }
@article {pmid23189077, year = {2012}, author = {Budd, A and Devos, DP}, title = {Evaluating the Evolutionary Origins of Unexpected Character Distributions within the Bacterial Planctomycetes-Verrucomicrobia-Chlamydiae Superphylum.}, journal = {Frontiers in microbiology}, volume = {3}, number = {}, pages = {401}, pmid = {23189077}, issn = {1664-302X}, abstract = {Recently, several characters that are absent from most bacteria, but which are found in many eukaryotes or archaea, have been identified within the bacterial Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) superphylum. Hypotheses of the evolutionary history of such characters are commonly based on the inference of phylogenies of gene or protein families associated with the traits, estimated from multiple sequence alignments (MSAs). So far, studies of this kind have focused on the distribution of (i) two genes involved in the synthesis of sterol, (ii) tubulin genes, and (iii) c1 transfer genes. In many cases, these analyses have concluded that horizontal gene transfer (HGT) is likely to have played a role in shaping the taxonomic distribution of these gene families. In this article, we describe several issues with the inference of HGT from such analyses, in particular concerning the considerable uncertainty associated with our estimation of both gene family phylogenies (especially those containing ancient lineage divergences) and the Tree of Life (ToL), and the need for wider use and further development of explicit probabilistic models to compare hypotheses of vertical and horizontal genetic transmission. We suggest that data which is often taken as evidence for the occurrence of ancient HGT events may not be as convincing as is commonly described, and consideration of alternative theories is recommended. While focusing on analyses including PVCs, this discussion is also relevant for inferences of HGT involving other groups of organisms.}, }
@article {pmid23188508, year = {2012}, author = {Warnes, SL and Highmore, CJ and Keevil, CW}, title = {Horizontal transfer of antibiotic resistance genes on abiotic touch surfaces: implications for public health.}, journal = {mBio}, volume = {3}, number = {6}, pages = {}, pmid = {23188508}, issn = {2150-7511}, mesh = {Bacterial Adhesion/*genetics ; Copper ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/drug effects/*genetics/metabolism ; Gene Dosage ; *Gene Transfer, Horizontal ; Klebsiella pneumoniae/drug effects/*genetics/metabolism ; Plasmids/genetics/metabolism ; Stainless Steel ; Surface Properties ; Temperature ; beta-Lactamases/*genetics/metabolism ; }, abstract = {UNLABELLED: Horizontal gene transfer (HGT) is largely responsible for increasing the incidence of antibiotic-resistant infections worldwide. While studies have focused on HGT in vivo, this work investigates whether the ability of pathogens to persist in the environment, particularly on touch surfaces, may also play an important role. Escherichia coli, virulent clone ST131, and Klebsiella pneumoniae harboring extended-spectrum-β-lactamase (ESBL) bla(CTX-M-15) and metallo-β-lactamase bla(NDM-1), respectively, exhibited prolonged survival on stainless steel, with approximately 10(4) viable cells remaining from an inoculum of 10(7) CFU per cm(2) after 1 month at 21°C. HGT of bla to an antibiotic-sensitive but azide-resistant recipient E. coli strain occurred on stainless steel dry touch surfaces and in suspension but not on dry copper. The conjugation frequency was approximately 10 to 50 times greater and occurred immediately, and resulting transconjugants were more stable with ESBL E. coli as the donor cell than with K. pneumoniae, but bla(NDM-1) transfer increased with time. Transconjugants also exhibited the same resistance profile as the donor, suggesting multiple gene transfer. Rapid death, inhibition of respiration, and destruction of genomic and plasmid DNA of both pathogens occurred on copper alloys accompanied by a reduction in bla copy number. Naked E. coli DNA degraded on copper at 21°C and 37°C but slowly at 4°C, suggesting a direct role for the metal. Persistence of viable pathogenic bacteria on touch surfaces may not only increase the risk of infection transmission but may also contribute to the spread of antibiotic resistance by HGT. The use of copper alloys as antimicrobial touch surfaces may help reduce infection and HGT.<br><br>IMPORTANCE: Horizontal gene transfer (HGT) conferring resistance to many classes of antimicrobials has resulted in a worldwide epidemic of nosocomial and community infections caused by multidrug-resistant microorganisms, leading to suggestions that we are in effect returning to the preantibiotic era. While studies have focused on HGT in vivo, this work investigates whether the ability of pathogens to persist in the environment, particularly on touch surfaces, may also play an important role. Here we show prolonged (several-week) survival of multidrug-resistant Escherichia coli and Klebsiella pneumoniae on stainless steel surfaces. Plasmid-mediated HGT of &#x3b2;-lactamase genes to an azide-resistant recipient E. coli strain occurred when the donor and recipient cells were mixed together on stainless steel and in suspension but not on copper surfaces. In addition, rapid death of both antibiotic-resistant strains and destruction of plasmid and genomic DNA were observed on copper and copper alloy surfaces, which could be useful in the prevention of infection spread and gene transfer.}, }
@article {pmid23184964, year = {2012}, author = {Nelson-Sathi, S and Dagan, T and Landan, G and Janssen, A and Steel, M and McInerney, JO and Deppenmeier, U and Martin, WF}, title = {Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {50}, pages = {20537-20542}, pmid = {23184964}, issn = {1091-6490}, mesh = {Archaeal Proteins/genetics ; Bacteria/*genetics ; Euryarchaeota/classification/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Genome, Archaeal ; Genome, Bacterial ; Models, Genetic ; Phylogeny ; }, abstract = {Archaebacterial halophiles (Haloarchaea) are oxygen-respiring heterotrophs that derive from methanogens--strictly anaerobic, hydrogen-dependent autotrophs. Haloarchaeal genomes are known to have acquired, via lateral gene transfer (LGT), several genes from eubacteria, but it is yet unknown how many genes the Haloarchaea acquired in total and, more importantly, whether independent haloarchaeal lineages acquired their genes in parallel, or as a single acquisition at the origin of the group. Here we have studied 10 haloarchaeal and 1,143 reference genomes and have identified 1,089 haloarchaeal gene families that were acquired by a methanogenic recipient from eubacteria. The data suggest that these genes were acquired in the haloarchaeal common ancestor, not in parallel in independent haloarchaeal lineages, nor in the common ancestor of haloarchaeans and methanosarcinales. The 1,089 acquisitions include genes for catabolic carbon metabolism, membrane transporters, menaquinone biosynthesis, and complexes I-IV of the eubacterial respiratory chain that functions in the haloarchaeal membrane consisting of diphytanyl isoprene ether lipids. LGT on a massive scale transformed a strictly anaerobic, chemolithoautotrophic methanogen into the heterotrophic, oxygen-respiring, and bacteriorhodopsin-photosynthetic haloarchaeal common ancestor.}, }
@article {pmid23183983, year = {2013}, author = {Solheim, HT and Sekse, C and Urdahl, AM and Wasteson, Y and Nesse, LL}, title = {Biofilm as an environment for dissemination of stx genes by transduction.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {3}, pages = {896-900}, pmid = {23183983}, issn = {1098-5336}, mesh = {Bacteriophages/*genetics/*growth &amp; development ; Biofilms/*growth &amp; development ; Escherichia coli/genetics/*physiology/virology ; Gene Transfer, Horizontal ; Shiga Toxin/*genetics ; Temperature ; *Transduction, Genetic ; }, abstract = {Dissemination of Shiga toxin (Stx)-encoding bacteriophages is the most likely mechanism for the spread of Stx-encoding genes and the emergence of new Stx-producing Escherichia coli (STEC). Biofilm has been reported to be a place where horizontal gene transfer by plasmid conjugation and DNA transformation may occur, and in this study, horizontal gene transfer by transduction has been demonstrated. Transfer of Stx-encoding bacteriophages to potentially pathogenic E. coli in biofilm was observed at both 20°C and 37°C. The infection rates were higher at 37°C than at 20°C. To our knowledge, this study is the first to show lateral gene transfer in biofilm mediated by a temperate bacteriophage. The study shows that the biofilm environment can be suitable for transduction events and can thereby be an environment for the emergence of new pathogenic E. coli.}, }
@article {pmid23183460, year = {2012}, author = {Choudhury, R and Panda, S and Singh, DV}, title = {Emergence and dissemination of antibiotic resistance: a global problem.}, journal = {Indian journal of medical microbiology}, volume = {30}, number = {4}, pages = {384-390}, doi = {10.4103/0255-0857.103756}, pmid = {23183460}, issn = {1998-3646}, mesh = {Anti-Bacterial Agents/*pharmacology/*therapeutic use ; Bacteria/*drug effects ; Bacterial Infections/*drug therapy/microbiology ; *Drug Resistance, Bacterial ; Emigration and Immigration ; Gene Transfer, Horizontal ; Humans ; Travel ; }, abstract = {Antibiotic resistance is a major problem in clinical health settings. Interestingly the origin of many of antibiotic resistance mechanisms can be traced back to non-pathogenic environmental organisms. Important factors leading to the emergence and spread of antibiotic resistance include absence of regulation in the use of antibiotics, improper waste disposal and associated transmission of antibiotic resistance genes in the community through commensals. In this review, we discussed the impact of globalisation on the transmission of antibiotic resistance genes in bacteria through immigration and export/import of foodstuff. The significance of surveillance to define appropriate use of antibiotics in the clinic has been included as an important preventive measure.}, }
@article {pmid23182842, year = {2013}, author = {Rodríguez-Avial, C and Alvarez-Novoa, A and Losa, A and Picazo, JJ}, title = {[Significant increase in the colonisation of Staphylococcus aureus among medical students during their hospital practices].}, journal = {Enfermedades infecciosas y microbiologia clinica}, volume = {31}, number = {8}, pages = {516-519}, doi = {10.1016/j.eimc.2012.09.017}, pmid = {23182842}, issn = {1578-1852}, mesh = {Adult ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Carrier State/*epidemiology/microbiology ; Cross Infection/epidemiology/transmission ; Cross-Sectional Studies ; Disease Reservoirs ; Drug Resistance, Multiple, Bacterial ; Female ; Follow-Up Studies ; Gene Transfer, Horizontal ; Hand Disinfection ; Hospitals, Urban ; Humans ; Infectious Disease Transmission, Professional-to-Patient ; Male ; Methicillin Resistance ; Morbidity/trends ; Nasal Cavity/*microbiology ; Penicillin-Binding Proteins ; Spain ; Staphylococcal Infections/*epidemiology/microbiology/prevention &amp; control/transmission ; Staphylococcus aureus/drug effects/genetics/*isolation &amp; purification ; *Students, Medical/psychology ; Surveys and Questionnaires ; Young Adult ; }, abstract = {INTRODUCTION: Staphylococcus aureus is a pathogen of major concern. The emergence of methicillin-resistant S. aureus (MRSA) has increasingly complicated the therapeutic approach of hospital-acquired infections. Surveillance of MRSA and control measures must be implemented in different healthcare settings, including screening programs for carriers. Our first aim was to determine the prevalence of methicillin-susceptible S. aureus (MSSA) and MRSA nasal carriage in medical students from the Clínico San Carlos Hospital (Madrid). As the MRSA carrier rate in healthcare workers is higher than in the general population, we hypothesised that carrier rate could be increased during their clinical practice in their last three years.<br><br>METHODS: We performed an epidemiologic al study of the prevalence of S. aureus colonisation among a group of medical students, who were sampled in 2008 in their third-year, and in 2012 when this class was in its sixth year.<br><br>RESULTS: We have found a significant increase in MSSA carriage, from 27% to 46%. There were no MRSA colonisations in the third-year, but one was found in the sixth-year group. The large majority of strains (89%) of strains were resistant to penicillin, and 27% to erythromycin and clindamycin. As 19 coagulase-negative Staphylococcus MR were also identified, a horizontal transfer of genes, such as mecA gene to S. aureus, could have occurred.<br><br>CONCLUSIONS: Medical students are both, at risk for acquiring, and a potential source of nosocomial pathogens, mainly MSSA. Therefore, they should take special care for hygienic precautions, such as frequent and proper hand washing, while working in the hospital.}, }
@article {pmid23181807, year = {2012}, author = {Hobley, L and Lerner, TR and Williams, LE and Lambert, C and Till, R and Milner, DS and Basford, SM and Capeness, MJ and Fenton, AK and Atterbury, RJ and Harris, MA and Sockett, RE}, title = {Genome analysis of a simultaneously predatory and prey-independent, novel Bdellovibrio bacteriovorus from the River Tiber, supports in silico predictions of both ancient and recent lateral gene transfer from diverse bacteria.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {670}, pmid = {23181807}, issn = {1471-2164}, support = {BB/G003092/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/G013632/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; G003092/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; G01362/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Antibiosis ; Bacterial Proteins/*genetics ; Bdellovibrio/*genetics/*growth &amp; development/pathogenicity ; Escherichia coli/*genetics/growth &amp; development ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Mutation ; Rivers/microbiology ; Symbiosis ; Synteny ; }, abstract = {BACKGROUND: Evolution equipped Bdellovibrio bacteriovorus predatory bacteria to invade other bacteria, digesting and replicating, sealed within them thus preventing nutrient-sharing with organisms in the surrounding environment. Bdellovibrio were previously described as "obligate predators" because only by mutations, often in gene bd0108, are 1 in ~1x10(7) of predatory lab strains of Bdellovibrio converted to prey-independent growth. A previous genomic analysis of B. bacteriovorus strain HD100 suggested that predatory consumption of prey DNA by lytic enzymes made Bdellovibrio less likely than other bacteria to acquire DNA by lateral gene transfer (LGT). However the Doolittle and Pan groups predicted, in silico, both ancient and recent lateral gene transfer into the B. bacteriovorus HD100 genome.<br><br>RESULTS: To test these predictions, we isolated a predatory bacterium from the River Tiber- a good potential source of LGT as it is rich in diverse bacteria and organic pollutants- by enrichment culturing with E. coli prey cells. The isolate was identified as B. bacteriovorus and named as strain Tiberius. Unusually, this Tiberius strain showed simultaneous prey-independent growth on organic nutrients and predatory growth on live prey. Despite the prey-independent growth, the homolog of bd0108 did not have typical prey-independent-type mutations. The dual growth mode may reflect the high carbon content of the river, and gives B. bacteriovorus Tiberius extended non-predatory contact with the other bacteria present. The HD100 and Tiberius genomes were extensively syntenic despite their different cultured-terrestrial/freshly-isolated aquatic histories; but there were significant differences in gene content indicative of genomic flux and LGT. Gene content comparisons support previously published in silico predictions for LGT in strain HD100 with substantial conservation of genes predicted to have ancient LGT origins but little conservation of AT-rich genes predicted to be recently acquired.<br><br>CONCLUSIONS: The natural niche and dual predatory, and prey-independent growth of the B. bacteriovorus Tiberius strain afforded it extensive non-predatory contact with other marine and freshwater bacteria from which LGT is evident in its genome. Thus despite their arsenal of DNA-lytic enzymes; Bdellovibrio are not always predatory in natural niches and their genomes are shaped by acquiring whole genes from other bacteria.}, }
@article {pmid23181628, year = {2012}, author = {Petitjean, C and Moreira, D and López-García, P and Brochier-Armanet, C}, title = {Horizontal gene transfer of a chloroplast DnaJ-Fer protein to Thaumarchaeota and the evolutionary history of the DnaK chaperone system in Archaea.}, journal = {BMC evolutionary biology}, volume = {12}, number = {}, pages = {226}, pmid = {23181628}, issn = {1471-2148}, mesh = {Archaea/*genetics ; Binding Sites/genetics ; Chlorophyta/genetics ; Chloroplast Proteins/*genetics ; Cyanobacteria/genetics ; Databases, Nucleic Acid ; Evolution, Molecular ; Ferredoxins/classification/*genetics ; *Gene Transfer, Horizontal ; Genome, Archaeal/genetics ; Genomics/methods ; HSP40 Heat-Shock Proteins/classification/*genetics ; HSP70 Heat-Shock Proteins/*genetics ; Molecular Chaperones/genetics ; Phylogeny ; Plants/genetics ; Recombinant Fusion Proteins/genetics ; }, abstract = {BACKGROUND: In 2004, we discovered an atypical protein in metagenomic data from marine thaumarchaeotal species. This protein, referred as DnaJ-Fer, is composed of a J domain fused to a Ferredoxin (Fer) domain. Surprisingly, the same protein was also found in Viridiplantae (green algae and land plants). Because J domain-containing proteins are known to interact with the major chaperone DnaK/Hsp70, this suggested that a DnaK protein was present in Thaumarchaeota. DnaK/Hsp70, its co-chaperone DnaJ and the nucleotide exchange factor GrpE are involved, among others, in heat shocks and heavy metal cellular stress responses.<br><br>RESULTS: Using phylogenomic approaches we have investigated the evolutionary history of the DnaJ-Fer protein and of interacting proteins DnaK, DnaJ and GrpE in Thaumarchaeota. These proteins have very complex histories, involving several inter-domain horizontal gene transfers (HGTs) to explain the contemporary distribution of these proteins in archaea. These transfers include one from Cyanobacteria to Viridiplantae and one from Viridiplantae to Thaumarchaeota for the DnaJ-Fer protein, as well as independent HGTs from Bacteria to mesophilic archaea for the DnaK/DnaJ/GrpE system, followed by HGTs among mesophilic and thermophilic archaea.<br><br>CONCLUSIONS: We highlight the chimerical origin of the set of proteins DnaK, DnaJ, GrpE and DnaJ-Fer in Thaumarchaeota and suggest that the HGT of these proteins has played an important role in the adaptation of several archaeal groups to mesophilic and thermophilic environments from hyperthermophilic ancestors. Finally, the evolutionary history of DnaJ-Fer provides information useful for the relative dating of the diversification of Archaeplastida and Thaumarchaeota.}, }
@article {pmid23176117, year = {2012}, author = {Power, PM and Bentley, SD and Parkhill, J and Moxon, ER and Hood, DW}, title = {Investigations into genome diversity of Haemophilus influenzae using whole genome sequencing of clinical isolates and laboratory transformants.}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {273}, pmid = {23176117}, issn = {1471-2180}, support = {//Medical Research Council/United Kingdom ; //Wellcome Trust/United Kingdom ; }, mesh = {Cluster Analysis ; Gene Transfer, Horizontal ; *Genetic Variation ; *Genome, Bacterial ; Genotype ; Haemophilus Infections/microbiology ; Haemophilus influenzae/*classification/*genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Humans ; Phylogeny ; }, abstract = {BACKGROUND: Haemophilus influenzae is an important human commensal pathogen associated with significant levels of disease. High-throughput DNA sequencing was used to investigate differences in genome content within this species.<br><br>RESULTS: Genomic DNA sequence was obtained from 85 strains of H. influenzae and from other related species, selected based on geographical site of isolation, disease association and documented genotypic and phenotypic differences. When compared by Mauve alignment these indicated groupings of H. influenzae that were consistent with previously published analyses; capsule expressing strains fell into two distinct groups and those of serotype b (Hib) were found in two closely positioned lineages. For 18 Hib strains representing both lineages we found many discrete regions (up to 40% of the total genome) displaying sequence variation when compared to a common reference strain. Evidence that this naturally occurring pattern of inter-strain variation in H. influenzae can be mediated by transformation was obtained through sequencing DNA obtained from a pool of 200 independent transformants of a recipient (strain Rd) using donor DNA from a heterologous Hib strain (Eagan).<br><br>CONCLUSION: Much of the inter-strain variation in genome sequence in H. influenzae is likely the result of inter-strain exchanges of DNA, most plausibly through transformation.}, }
@article {pmid23171342, year = {2012}, author = {Marcet-Houben, M and Ballester, AR and de la Fuente, B and Harries, E and Marcos, JF and González-Candelas, L and Gabaldón, T}, title = {Genome sequence of the necrotrophic fungus Penicillium digitatum, the main postharvest pathogen of citrus.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {646}, pmid = {23171342}, issn = {1471-2164}, mesh = {Base Sequence ; Citrus/drug effects/*microbiology ; *DNA, Fungal ; Drug Resistance, Fungal/genetics ; Fungicides, Industrial/pharmacology ; *Genome, Fungal ; Genome, Mitochondrial ; Molecular Sequence Data ; Multigene Family ; Mutation ; Penicillium/drug effects/*genetics/metabolism/*pathogenicity ; Plant Diseases/*microbiology/therapy ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Virulence ; }, abstract = {BACKGROUND: Penicillium digitatum is a fungal necrotroph causing a common citrus postharvest disease known as green mold. In order to gain insight into the genetic bases of its virulence mechanisms and its high degree of host-specificity, the genomes of two P. digitatum strains that differ in their antifungal resistance traits have been sequenced and compared with those of 28 other Pezizomycotina.<br><br>RESULTS: The two sequenced genomes are highly similar, but important differences between them include the presence of a unique gene cluster in the resistant strain, and mutations previously shown to confer fungicide resistance. The two strains, which were isolated in Spain, and another isolated in China have identical mitochondrial genome sequences suggesting a recent worldwide expansion of the species. Comparison with the closely-related but non-phytopathogenic P. chrysogenum reveals a much smaller gene content in P. digitatum, consistent with a more specialized lifestyle. We show that large regions of the P. chrysogenum genome, including entire supercontigs, are absent from P. digitatum, and that this is the result of large gene family expansions rather than acquisition through horizontal gene transfer. Our analysis of the P. digitatum genome is indicative of heterothallic sexual reproduction and reveals the molecular basis for the inability of this species to assimilate nitrate or produce the metabolites patulin and penicillin. Finally, we identify the predicted secretome, which provides a first approximation to the protein repertoire used during invasive growth.<br><br>CONCLUSIONS: The complete genome of P. digitatum, the first of a phytopathogenic Penicillium species, is a valuable tool for understanding the virulence mechanisms and host-specificity of this economically important pest.}, }
@article {pmid23171084, year = {2012}, author = {Rybarczyk-Mydłowska, K and Maboreke, HR and van Megen, H and van den Elsen, S and Mooyman, P and Smant, G and Bakker, J and Helder, J}, title = {Rather than by direct acquisition via lateral gene transfer, GHF5 cellulases were passed on from early Pratylenchidae to root-knot and cyst nematodes.}, journal = {BMC evolutionary biology}, volume = {12}, number = {}, pages = {221}, pmid = {23171084}, issn = {1471-2148}, mesh = {Amino Acid Sequence ; Animals ; Bayes Theorem ; Cellulases/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Introns ; Likelihood Functions ; Phylogeny ; Plant Roots/parasitology ; Protein Interaction Domains and Motifs ; Sequence Alignment ; Sequence Analysis, DNA ; Tylenchida/enzymology/*genetics ; }, abstract = {BACKGROUND: Plant parasitic nematodes are unusual Metazoans as they are equipped with genes that allow for symbiont-independent degradation of plant cell walls. Among the cell wall-degrading enzymes, glycoside hydrolase family 5 (GHF5) cellulases are relatively well characterized, especially for high impact parasites such as root-knot and cyst nematodes. Interestingly, ancestors of extant nematodes most likely acquired these GHF5 cellulases from a prokaryote donor by one or multiple lateral gene transfer events. To obtain insight into the origin of GHF5 cellulases among evolutionary advanced members of the order Tylenchida, cellulase biodiversity data from less distal family members were collected and analyzed.<br><br>RESULTS: Single nematodes were used to obtain (partial) genomic sequences of cellulases from representatives of the genera Meloidogyne, Pratylenchus, Hirschmanniella and Globodera. Combined Bayesian analysis of &#x2248; 100 cellulase sequences revealed three types of catalytic domains (A, B, and C). Represented by 84 sequences, type B is numerically dominant, and the overall topology of the catalytic domain type shows remarkable resemblance with trees based on neutral (= pathogenicity-unrelated) small subunit ribosomal DNA sequences. Bayesian analysis further suggested a sister relationship between the lesion nematode Pratylenchus thornei and all type B cellulases from root-knot nematodes. Yet, the relationship between the three catalytic domain types remained unclear. Superposition of intron data onto the cellulase tree suggests that types B and C are related, and together distinct from type A that is characterized by two unique introns.<br><br>CONCLUSIONS: All Tylenchida members investigated here harbored one or multiple GHF5 cellulases. Three types of catalytic domains are distinguished, and the presence of at least two types is relatively common among plant parasitic Tylenchida. Analysis of coding sequences of cellulases suggests that root-knot and cyst nematodes did not acquire this gene directly by lateral genes transfer. More likely, these genes were passed on by ancestors of a family nowadays known as the Pratylenchidae.}, }
@article {pmid23166747, year = {2012}, author = {Chen, W and Xie, T and Shao, Y and Chen, F}, title = {Phylogenomic relationships between amylolytic enzymes from 85 strains of fungi.}, journal = {PloS one}, volume = {7}, number = {11}, pages = {e49679}, pmid = {23166747}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Amylases/chemistry/*genetics ; Evolution, Molecular ; Fungi/classification/enzymology/*genetics ; Gene Transfer, Horizontal ; Genome, Fungal ; Glucan 1,4-alpha-Glucosidase/genetics ; Molecular Sequence Data ; *Phylogeny ; Protein Binding ; Protein Interaction Domains and Motifs ; Sequence Alignment ; Starch/metabolism ; alpha-Glucosidases/genetics ; }, abstract = {Fungal amylolytic enzymes, including α-amylase, gluocoamylase and α-glucosidase, have been extensively exploited in diverse industrial applications such as high fructose syrup production, paper making, food processing and ethanol production. In this paper, amylolytic genes of 85 strains of fungi from the phyla Ascomycota, Basidiomycota, Chytridiomycota and Zygomycota were annotated on the genomic scale according to the classification of glycoside hydrolase (GH) from the Carbohydrate-Active enZymes (CAZy) Database. Comparisons of gene abundance in the fungi suggested that the repertoire of amylolytic genes adapted to their respective lifestyles. Amylolytic enzymes in family GH13 were divided into four distinct clades identified as heterologous α-amylases, eukaryotic α-amylases, bacterial and fungal α-amylases and GH13 α-glucosidases. Family GH15 had two branches, one for gluocoamylases, and the other with currently unknown function. GH31 α-glucosidases showed diverse branches consisting of neutral α-glucosidases, lysosomal acid α-glucosidases and a new clade phylogenetically related to the bacterial counterparts. Distribution of starch-binding domains in above fungal amylolytic enzymes was related to the enzyme source and phylogeny. Finally, likely scenarios for the evolution of amylolytic enzymes in fungi based on phylogenetic analyses were proposed. Our results provide new insights into evolutionary relationships among subgroups of fungal amylolytic enzymes and fungal evolutionary adaptation to ecological conditions.}, }
@article {pmid23166508, year = {2012}, author = {Boschetti, C and Carr, A and Crisp, A and Eyres, I and Wang-Koh, Y and Lubzens, E and Barraclough, TG and Micklem, G and Tunnacliffe, A}, title = {Biochemical diversification through foreign gene expression in bdelloid rotifers.}, journal = {PLoS genetics}, volume = {8}, number = {11}, pages = {e1003035}, pmid = {23166508}, issn = {1553-7404}, support = {BB/F020562/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/F020856/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Desiccation ; *Gene Expression ; Gene Library ; *Gene Transfer, Horizontal ; Metabolic Networks and Pathways/*genetics ; Phylogeny ; Radiation, Ionizing ; *Rotifera/genetics/physiology ; Transcriptome ; }, abstract = {Bdelloid rotifers are microinvertebrates with unique characteristics: they have survived tens of millions of years without sexual reproduction; they withstand extreme desiccation by undergoing anhydrobiosis; and they tolerate very high levels of ionizing radiation. Recent evidence suggests that subtelomeric regions of the bdelloid genome contain sequences originating from other organisms by horizontal gene transfer (HGT), of which some are known to be transcribed. However, the extent to which foreign gene expression plays a role in bdelloid physiology is unknown. We address this in the first large scale analysis of the transcriptome of the bdelloid Adineta ricciae: cDNA libraries from hydrated and desiccated bdelloids were subjected to massively parallel sequencing and assembled transcripts compared against the UniProtKB database by blastx to identify their putative products. Of ~29,000 matched transcripts, ~10% were inferred from blastx matches to be horizontally acquired, mainly from eubacteria but also from fungi, protists, and algae. After allowing for possible sources of error, the rate of HGT is at least 8%-9%, a level significantly higher than other invertebrates. We verified their foreign nature by phylogenetic analysis and by demonstrating linkage of foreign genes with metazoan genes in the bdelloid genome. Approximately 80% of horizontally acquired genes expressed in bdelloids code for enzymes, and these represent 39% of enzymes in identified pathways. Many enzymes encoded by foreign genes enhance biochemistry in bdelloids compared to other metazoans, for example, by potentiating toxin degradation or generation of antioxidants and key metabolites. They also supplement, and occasionally potentially replace, existing metazoan functions. Bdelloid rotifers therefore express horizontally acquired genes on a scale unprecedented in animals, and foreign genes make a profound contribution to their metabolism. This represents a potential mechanism for ancient asexuals to adapt rapidly to changing environments and thereby persist over long evolutionary time periods in the absence of sex.}, }
@article {pmid23165978, year = {2013}, author = {Otto, M}, title = {Coagulase-negative staphylococci as reservoirs of genes facilitating MRSA infection: Staphylococcal commensal species such as Staphylococcus epidermidis are being recognized as important sources of genes promoting MRSA colonization and virulence.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {35}, number = {1}, pages = {4-11}, pmid = {23165978}, issn = {1521-1878}, support = {ZIA AI000904/ImNIH/Intramural NIH HHS/United States ; ZIA AI000904-11/ImNIH/Intramural NIH HHS/United States ; ZIA AI001080-05/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Coagulase/metabolism ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Interspersed Repetitive Sequences/*genetics ; Methicillin-Resistant Staphylococcus aureus/drug effects/*genetics ; Microbial Sensitivity Tests ; Staphylococcal Infections/drug therapy ; Staphylococcus epidermidis/*genetics ; }, abstract = {Recent research has suggested that Staphylococcus epidermidis is a reservoir of genes that, after horizontal transfer, facilitate the potential of Staphylococcus aureus to colonize, survive during infection, or resist antibiotic treatment, traits that are notably manifest in methicillin-resistant S. aureus (MRSA). S. aureus is a dangerous human pathogen and notorious for acquiring antibiotic resistance. MRSA in particular is one of the most frequent causes of morbidity and death in hospitalized patients. S. aureus is an extremely versatile pathogen with a multitude of mechanisms to cause disease and circumvent immune defenses. In contrast, most other staphylococci, such as S. epidermidis, are commonly benign commensals and only occasionally cause disease. Recent findings highlight the key importance of efforts to better understand how genes of staphylococci other than S. aureus contribute to survival in the human host, how they are transferred to S. aureus, and why this exchange appears to be uni-directional.}, }
@article {pmid23163032, year = {2012}, author = {Monakhova, EV and Shalu, OA and Mazrukho, AB and Smolikova, LM and Nepomniashchaia, NB}, title = {[Study of possibility of formation of Vibrio parahaemolyticus pandemic clones based on retrospective PCR-screening of clinical strains].}, journal = {Zhurnal mikrobiologii, epidemiologii i immunobiologii}, volume = {}, number = {5}, pages = {28-32}, pmid = {23163032}, issn = {0372-9311}, mesh = {Clone Cells ; *Disease Outbreaks ; Gastroenteritis/*epidemiology/microbiology ; Gene Transfer, Horizontal ; *Genes, Viral ; Genetic Markers ; Genomic Islands/genetics ; Humans ; Interspersed Repetitive Sequences ; Japan/epidemiology ; Molecular Typing ; Phylogeography ; Polymerase Chain Reaction ; Retrospective Studies ; Russia/epidemiology ; Vibrio Infections/*epidemiology/microbiology/transmission ; Vibrio parahaemolyticus/*genetics/isolation &amp; purification/pathogenicity ; }, abstract = {AIM: PCR-genotyping of Vibrio parahaemolyticus strains that had caused sporadic diseases in Novorossiysk from 1973 to 1976.<br><br>MATERIALS AND METHODS: 24 clinical strains of V. parahaemolyticus isolated in Novorossiysk, most of which belonged to serogroups O4:K12 and O4:K8; 10 O3:K6 strains--causative agents of gastroenteritis outbreak in Vladivostok (1997) and 3 from Japan (1971) were used. PCR genotyping was performed by a set of marker genes of 7 pathogenicity islands (VPaI-1 - VPaI-7) and a number of other pathogenicity factors.<br><br>RESULTS: All the strains isolated in 1970s differed significantly by sets of VPaI marker genes. In contrast to causative agents of outbreak in Vladivostok that contain all 7 VPaI genes (that is, members of the pandemic group that had spread globally since 1996) none of the O4:K12 and O4:K8 Novorossiysk strains contained the full set of all the VPaI genes. However this set was distributed among the members of the group.<br><br>CONCLUSION: Taking into account that O4:K12 and O4:K8 serogroups are considered by a number of authors as O3:K6 serovariants, PCR-screening data obtained by us allows to assume that horizontal transfer of mobile elements (VPaI) between strains circulating in the region could have led to the formation of pandemic clones already in the 1970s. This implies that in several coastal regions in certain periods of time conditions that favor these process may form, and risk of infection with pandemic clones is associated not only with import of seafood.}, }
@article {pmid23160063, year = {2012}, author = {Williams, D and Gogarten, JP and Papke, RT}, title = {Quantifying homologous replacement of loci between haloarchaeal species.}, journal = {Genome biology and evolution}, volume = {4}, number = {12}, pages = {1223-1244}, pmid = {23160063}, issn = {1759-6653}, mesh = {Algorithms ; Evolution, Molecular ; Gene Order ; Gene Transfer, Horizontal ; Genome, Archaeal ; Halobacteriaceae/*genetics ; *Homologous Recombination ; *Phylogeny ; Ribosomal Proteins/genetics ; }, abstract = {In vitro studies of the haloarchaeal genus Haloferax have demonstrated their ability to frequently exchange DNA between species, whereas rates of homologous recombination estimated from natural populations in the genus Halorubrum are high enough to maintain random association of alleles between five loci. To quantify the effects of gene transfer and recombination of commonly held (relaxed core) genes during the evolution of the class Halobacteria (haloarchaea), we reconstructed the history of 21 genomes representing all major groups. Using a novel algorithm and a concatenated ribosomal protein phylogeny as a reference, we created a directed horizontal genetic transfer (HGT) network of contemporary and ancestral genomes. Gene order analysis revealed that 90% of testable HGTs were by direct homologous replacement, rather than nonhomologous integration followed by a loss. Network analysis revealed an inverse log-linear relationship between HGT frequency and ribosomal protein evolutionary distance that is maintained across the deepest divergences in Halobacteria. We use this mathematical relationship to estimate the total transfers and amino acid substitutions delivered by HGTs in each genome, providing a measure of chimerism. For the relaxed core genes of each genome, we conservatively estimate that 11-20% of their evolution occurred in other haloarchaea. Our findings are unexpected, because the transfer and homologous recombination of relaxed core genes between members of the class Halobacteria disrupts the coevolution of genes; however, the generation of new combinations of divergent but functionally related genes may lead to adaptive phenotypes not available through cumulative mutations and recombination within a single population.}, }
@article {pmid23158461, year = {2012}, author = {Wyres, KL and Lambertsen, LM and Croucher, NJ and McGee, L and von Gottberg, A and Liñares, J and Jacobs, MR and Kristinsson, KG and Beall, BW and Klugman, KP and Parkhill, J and Hakenbeck, R and Bentley, SD and Brueggemann, AB}, title = {The multidrug-resistant PMEN1 pneumococcus is a paradigm for genetic success.}, journal = {Genome biology}, volume = {13}, number = {11}, pages = {R103}, pmid = {23158461}, issn = {1474-760X}, mesh = {Evolution, Molecular ; Genome, Bacterial ; *Penicillin Resistance ; Penicillins/*metabolism ; Phylogeny ; Recombination, Genetic ; Sequence Analysis, DNA ; Streptococcus pneumoniae/*drug effects/*genetics/isolation &amp; purification ; }, abstract = {BACKGROUND: Streptococcus pneumoniae, also called the pneumococcus, is a major bacterial pathogen. Since its introduction in the 1940s, penicillin has been the primary treatment for pneumococcal diseases. Penicillin resistance rapidly increased among pneumococci over the past 30 years, and one particular multidrug-resistant clone, PMEN1, became highly prevalent globally. We studied a collection of 426 pneumococci isolated between 1937 and 2007 to better understand the evolution of penicillin resistance within this species.<br><br>RESULTS: We discovered that one of the earliest known penicillin-nonsusceptible pneumococci, recovered in 1967 from Australia, was the likely ancestor of PMEN1, since approximately 95% of coding sequences identified within its genome were highly similar to those of PMEN1. The regions of the PMEN1 genome that differed from the ancestor contained genes associated with antibiotic resistance, transmission and virulence. We also revealed that PMEN1 was uniquely promiscuous with its DNA, donating penicillin-resistance genes and sometimes many other genes associated with antibiotic resistance, virulence and cell adherence to many genotypically diverse pneumococci. In particular, we describe two strains in which up to 10% of the PMEN1 genome was acquired in multiple fragments, some as long as 32 kb, distributed around the recipient genomes. This type of directional genetic promiscuity from a single clone to numerous unrelated clones has, to our knowledge, never before been described.<br><br>CONCLUSIONS: These findings suggest that PMEN1 is a paradigm of genetic success both through its epidemiology and promiscuity. These findings also challenge the existing views about horizontal gene transfer among pneumococci.}, }
@article {pmid23153396, year = {2012}, author = {McKinney, CW and Pruden, A}, title = {Ultraviolet disinfection of antibiotic resistant bacteria and their antibiotic resistance genes in water and wastewater.}, journal = {Environmental science &amp; technology}, volume = {46}, number = {24}, pages = {13393-13400}, doi = {10.1021/es303652q}, pmid = {23153396}, issn = {1520-5851}, mesh = {Bacteria/*genetics/radiation effects ; Dimerization ; Disinfection/*methods ; Drug Resistance, Microbial/*genetics ; Extracellular Space/metabolism ; Genes, Bacterial/*genetics ; Intracellular Space/metabolism ; Polymerase Chain Reaction ; Pyrimidines/metabolism ; Reference Standards ; *Ultraviolet Rays ; Wastewater/*microbiology ; *Water Microbiology ; }, abstract = {Disinfection of wastewater treatment plant effluent may be an important barrier for limiting the spread of antibiotic-resistant bacteria (ARBs) and antibiotic resistance genes (ARGs). While ideally disinfection should destroy ARGs, to prevent horizontal gene transfer to downstream bacteria, little is known about the effect of conventional water disinfection technologies on ARGs. This study examined the potential of UV disinfection to damage four ARGs, mec(A), van(A), tet(A), and amp(C), both in extracellular form and present within a host ARBs: methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus faecium (VRE), Escherichia coli SMS-3-5, and Pseudomonas aeruginosa 01, respectively. An extended amplicon-length quantitative polymerase chain reaction assay was developed to enhance capture of ARG damage events and also to normalize to an equivalent length of target DNA (∼1000 bp) for comparison. It was found that the two Gram-positive ARBs (MRSA and VRE) were more resistant to UV disinfection than the two Gram-negative ARBs (E. coli and P. aeruginosa). The two Gram-positive organisms also possessed smaller total genome sizes, which could also have reduced their susceptibility to UV because of fewer potential pyrimidine dimer targets. An effect of cell type on damage to ARGs was only observed in VRE and P. aeruginosa, the latter potentially because of extracellular polymeric substances. In general, damage of ARGs required much greater UV doses (200-400 mJ/cm[2] for 3- to 4-log reduction) than ARB inactivation (10-20 mJ/cm[2] for 4- to 5-log reduction). The proportion of amplifiable ARGs following UV treatment exhibited a strong negative correlation with the number of adjacent thymines (Pearson r < -0.9; p < 0.0001). ARBs surviving UV treatment were negatively correlated with total genome size (Pearson r < -0.9; p < 0.0001) and adjacent cytosines (Pearson r < -0.88; p < 0.0001) but positively correlated with adjacent thymines (Pearson r > 0.85; p < 0.0001). This suggests that formation of thymine dimers is not the sole mechanism of ARB inactivation. Overall, the results indicate that UV is limited in its potential to damage ARGs and other disinfection technologies should be explored.}, }
@article {pmid23150581, year = {2012}, author = {Hehemann, JH and Kelly, AG and Pudlo, NA and Martens, EC and Boraston, AB}, title = {Bacteria of the human gut microbiome catabolize red seaweed glycans with carbohydrate-active enzyme updates from extrinsic microbes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {48}, pages = {19786-19791}, pmid = {23150581}, issn = {1091-6490}, support = {K01 DK084214/DK/NIDDK NIH HHS/United States ; /CAPMC/CIHR/Canada ; K01DK084214/DK/NIDDK NIH HHS/United States ; }, mesh = {Biocatalysis ; Catalytic Domain ; Enzymes/*metabolism ; Humans ; Intestines/*microbiology ; *Metagenome ; Models, Molecular ; Polysaccharides/*metabolism ; Rhodophyta/*metabolism ; Seaweed/*metabolism ; }, abstract = {Humans host an intestinal population of microbes--collectively referred to as the gut microbiome--which encode the carbohydrate active enzymes, or CAZymes, that are absent from the human genome. These CAZymes help to extract energy from recalcitrant polysaccharides. The question then arises as to if and how the microbiome adapts to new carbohydrate sources when modern humans change eating habits. Recent metagenome analysis of microbiomes from healthy American, Japanese, and Spanish populations identified putative CAZymes obtained by horizontal gene transfer from marine bacteria, which suggested that human gut bacteria evolved to degrade algal carbohydrates-for example, consumed in form of sushi. We approached this hypothesis by studying such a polysaccharide utilization locus (PUL) obtained by horizontal gene transfer by the gut bacterium Bacteroides plebeius. Transcriptomic and growth experiments revealed that the PUL responds to the polysaccharide porphyran from red algae, enabling growth on this carbohydrate but not related substrates like agarose and carrageenan. The X-ray crystallographic and biochemical analysis of two proteins encoded by this PUL, BACPLE_01689 and BACPLE_01693, showed that they are β-porphyranases belonging to glycoside hydrolase families 16 and 86, respectively. The product complex of the GH86 at 1.3 Å resolution highlights the molecular details of porphyran hydrolysis by this new porphyranase. Combined, these data establish experimental support for the argument that CAZymes and associated genes obtained from extrinsic microbes add new catabolic functions to the human gut microbiome.}, }
@article {pmid23150395, year = {2013}, author = {Buchrieser, C and Charpentier, X}, title = {Induction of competence for natural transformation in Legionella pneumophila and exploitation for mutant construction.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {954}, number = {}, pages = {183-195}, doi = {10.1007/978-1-62703-161-5_9}, pmid = {23150395}, issn = {1940-6029}, mesh = {Culture Media ; DNA Damage/radiation effects ; Legionella pneumophila/*genetics/*metabolism/radiation effects ; *Mutation ; Plasmids/genetics/metabolism ; *Transformation, Bacterial ; }, abstract = {Many Gram-positive and Gram-negative bacteria possess natural competence mechanisms for DNA -capture and internalization that play an important role in diversifying adaptation of bacteria through horizontal gene transfer. Natural transformation and other mechanisms of horizontal gene transfer are dependent on DNA recombination. Natural competence can be exploited both for studying adaptation and horizontal gene transfer as well as for genetic engineering of a strain. We report here different approaches to measure competence on solid and in liquid media by using a reporter plasmid where GFP is fused to the comEA gene or by inducing competence and measuring transformability induced by DNA-damaging stress. Finally we describe a method where competence is induced through a combined temperature and aeration shift, which may be exploited for the construction of mutants in Legionella pneumophila. This approach seems to be less prone to the appearance of secondary mutations during mutant construction as compared to procedures using electroporation.}, }
@article {pmid23145983, year = {2012}, author = {Westra, ER and Swarts, DC and Staals, RH and Jore, MM and Brouns, SJ and van der Oost, J}, title = {The CRISPRs, they are a-changin': how prokaryotes generate adaptive immunity.}, journal = {Annual review of genetics}, volume = {46}, number = {}, pages = {311-339}, doi = {10.1146/annurev-genet-110711-155447}, pmid = {23145983}, issn = {1545-2948}, mesh = {Amino Acid Motifs ; Bacteriophages/genetics/immunology/pathogenicity ; CRISPR-Associated Proteins ; DNA Helicases/genetics/*metabolism ; DNA, Viral/genetics/metabolism ; Deoxyribonucleases, Type I Site-Specific/genetics/metabolism ; Endodeoxyribonucleases/genetics/*metabolism ; Escherichia coli K12/genetics/*immunology/metabolism/virology ; Escherichia coli Proteins/genetics/*metabolism ; *Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Lysogeny ; Prophages/genetics/metabolism ; Species Specificity ; Virus Internalization ; }, abstract = {All organisms need to continuously adapt to changes in their environment. Through horizontal gene transfer, bacteria and archaea can rapidly acquire new traits that may contribute to their survival. However, because new DNA may also cause damage, removal of imported DNA and protection against selfish invading DNA elements are also important. Hence, there should be a delicate balance between DNA uptake and DNA degradation. Here, we describe prokaryotic antiviral defense systems, such as receptor masking or mutagenesis, blocking of phage DNA injection, restriction/modification, and abortive infection. The main focus of this review is on CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated), a prokaryotic adaptive immune system. Since its recent discovery, our biochemical understanding of this defense system has made a major leap forward. Three highly diverse CRISPR/Cas types exist that display major structural and functional differences in their mode of generating resistance against invading nucleic acids. Because several excellent recent reviews cover all CRISPR subtypes, we mainly focus on a detailed description of the type I-E CRISPR/Cas system of the model bacterium Escherichia coli K12.}, }
@article {pmid23145826, year = {2012}, author = {Aly, SA and Debavalya, N and Suh, SJ and Oryazabal, OA and Boothe, DM}, title = {Molecular mechanisms of antimicrobial resistance in fecal Escherichia coli of healthy dogs after enrofloxacin or amoxicillin administration.}, journal = {Canadian journal of microbiology}, volume = {58}, number = {11}, pages = {1288-1294}, doi = {10.1139/w2012-105}, pmid = {23145826}, issn = {1480-3275}, mesh = {Amoxicillin/administration &amp; dosage/*pharmacology ; Animals ; Anti-Bacterial Agents/*pharmacology ; DNA Gyrase/genetics ; DNA Topoisomerase IV/genetics ; Dogs ; Drug Resistance, Microbial/drug effects/*genetics ; Enrofloxacin ; Escherichia coli/drug effects/genetics/isolation &amp; purification ; Escherichia coli Proteins/genetics ; Feces/*microbiology ; Fluoroquinolones/administration &amp; dosage/*pharmacology ; Gene Transfer, Horizontal ; Mutation ; Plasmids/genetics ; Polymerase Chain Reaction ; beta-Lactamases/genetics ; beta-Lactams/pharmacology ; }, abstract = {Escherichia coli respond to selective pressure of antimicrobial therapy by developing resistance through a variety of mechanisms. The purpose of this study was to characterize the genetic mechanisms of antimicrobial resistance in fecal E. coli after the routine use of 2 popular antimicrobials. Fourteen resistant E. coli isolates, representing predominant clones that emerged in healthy dogs' feces after treatment with either amoxicillin (11 E. coli isolates) or enrofloxacin (3 E. coli isolates), were tested for mutations in DNA gyrase (gyrA and gyrB) and in topoisomerase IV (parC) and for the presence of β-lactamases (bla(TEM), bla(SHV), bla(PSE-1) and bla(CTX-M)) and plasmid-mediated quinolone resistance (qnrA, qnrB, qnrS, aac(6')-Ib, and qepA), by polymerase chain reaction. Escherichia coli isolates cultured following amoxicillin therapy only expressed single-drug resistance to β-lactams, while the isolates cultured from dogs receiving enrofloxacin therapy expressed multidrug resistance (MDR). The use of RND efflux pump inhibitors increased the susceptibility of the 3 MDR E. coli isolates to doxycycline, chloramphenicol, enrofloxacin, and ciprofloxacin, which indicates a role of the efflux pump in the acquisition of the MDR phenotype. Amplification and sequencing of AcrAB efflux pump regulators (soxR, soxS, marR, and acrR) revealed only the presence of a single mutation in soxS in the 3 MDR isolates.}, }
@article {pmid23145790, year = {2012}, author = {Breton, M and Tardy, F and Dordet-Frisoni, E and Sagne, E and Mick, V and Renaudin, J and Sirand-Pugnet, P and Citti, C and Blanchard, A}, title = {Distribution and diversity of mycoplasma plasmids: lessons from cryptic genetic elements.}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {257}, pmid = {23145790}, issn = {1471-2180}, mesh = {Animals ; Cluster Analysis ; DNA, Bacterial/chemistry/*genetics ; Gene Order ; Gene Transfer, Horizontal ; *Genetic Variation ; Molecular Sequence Data ; Mycoplasma Infections/microbiology/veterinary ; Mycoplasma mycoides/*genetics/isolation &amp; purification ; Phylogeny ; *Plasmids ; Recombination, Genetic ; Ruminants ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The evolution of mycoplasmas from a common ancestor with Firmicutes has been characterized not only by genome down-sizing but also by horizontal gene transfer between mycoplasma species sharing a common host. The mechanisms of these gene transfers remain unclear because our knowledge of the mycoplasma mobile genetic elements is limited. In particular, only a few plasmids have been described within the Mycoplasma genus.<br><br>RESULTS: We have shown that several species of ruminant mycoplasmas carry plasmids that are members of a large family of elements and replicate via a rolling-circle mechanism. All plasmids were isolated from species that either belonged or were closely related to the Mycoplasma mycoides cluster; none was from the Mycoplasma bovis-Mycoplasma agalactiae group. Twenty one plasmids were completely sequenced, named and compared with each other and with the five mycoplasma plasmids previously reported. All plasmids share similar size and genetic organization, and present a mosaic structure. A peculiar case is that of the plasmid pMyBK1 from M. yeatsii; it is larger in size and is predicted to be mobilizable. Its origin of replication and replication protein were identified. In addition, pMyBK1 derivatives were shown to replicate in various species of the M. mycoides cluster, and therefore hold considerable promise for developing gene vectors. The phylogenetic analysis of these plasmids confirms the uniqueness of pMyBK1 and indicates that the other mycoplasma plasmids cluster together, apart from the related replicons found in phytoplasmas and in species of the clade Firmicutes.<br><br>CONCLUSIONS: Our results unraveled a totally new picture of mycoplasma plasmids. Although they probably play a limited role in the gene exchanges that participate in mycoplasma evolution, they are abundant in some species. Evidence for the occurrence of frequent genetic recombination strongly suggests they are transmitted between species sharing a common host or niche.}, }
@article {pmid23145189, year = {2012}, author = {Ricaldi, JN and Fouts, DE and Selengut, JD and Harkins, DM and Patra, KP and Moreno, A and Lehmann, JS and Purushe, J and Sanka, R and Torres, M and Webster, NJ and Vinetz, JM and Matthias, MA}, title = {Whole genome analysis of Leptospira licerasiae provides insight into leptospiral evolution and pathogenicity.}, journal = {PLoS neglected tropical diseases}, volume = {6}, number = {10}, pages = {e1853}, pmid = {23145189}, issn = {1935-2735}, support = {D43TW007120/TW/FIC NIH HHS/United States ; R01TW05860/TW/FIC NIH HHS/United States ; K24AI068903/AI/NIAID NIH HHS/United States ; HHSN272200900007C/AI/NIAID NIH HHS/United States ; R01 TW005860/TW/FIC NIH HHS/United States ; T32 GM008666/GM/NIGMS NIH HHS/United States ; D43 TW007120/TW/FIC NIH HHS/United States ; K24 AI068903/AI/NIAID NIH HHS/United States ; }, mesh = {DNA, Bacterial/chemistry/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomic Islands ; Humans ; Leptospira/*genetics/*pathogenicity ; Molecular Sequence Data ; Multigene Family ; Prophages/genetics ; Sequence Analysis, DNA ; Virulence Factors/*genetics ; }, abstract = {The whole genome analysis of two strains of the first intermediately pathogenic leptospiral species to be sequenced (Leptospira licerasiae strains VAR010 and MMD0835) provides insight into their pathogenic potential and deepens our understanding of leptospiral evolution. Comparative analysis of eight leptospiral genomes shows the existence of a core leptospiral genome comprising 1547 genes and 452 conserved genes restricted to infectious species (including L. licerasiae) that are likely to be pathogenicity-related. Comparisons of the functional content of the genomes suggests that L. licerasiae retains several proteins related to nitrogen, amino acid and carbohydrate metabolism which might help to explain why these Leptospira grow well in artificial media compared with pathogenic species. L. licerasiae strains VAR010(T) and MMD0835 possess two prophage elements. While one element is circular and shares homology with LE1 of L. biflexa, the second is cryptic and homologous to a previously identified but unnamed region in L. interrogans serovars Copenhageni and Lai. We also report a unique O-antigen locus in L. licerasiae comprised of a 6-gene cluster that is unexpectedly short compared with L. interrogans in which analogous regions may include >90 such genes. Sequence homology searches suggest that these genes were acquired by lateral gene transfer (LGT). Furthermore, seven putative genomic islands ranging in size from 5 to 36 kb are present also suggestive of antecedent LGT. How Leptospira become naturally competent remains to be determined, but considering the phylogenetic origins of the genes comprising the O-antigen cluster and other putative laterally transferred genes, L. licerasiae must be able to exchange genetic material with non-invasive environmental bacteria. The data presented here demonstrate that L. licerasiae is genetically more closely related to pathogenic than to saprophytic Leptospira and provide insight into the genomic bases for its infectiousness and its unique antigenic characteristics.}, }
@article {pmid23144395, year = {2012}, author = {Brunet-Galmés, I and Busquets, A and Peña, A and Gomila, M and Nogales, B and García-Valdés, E and Lalucat, J and Bennasar, A and Bosch, R}, title = {Complete genome sequence of the naphthalene-degrading bacterium Pseudomonas stutzeri AN10 (CCUG 29243).}, journal = {Journal of bacteriology}, volume = {194}, number = {23}, pages = {6642-6643}, pmid = {23144395}, issn = {1098-5530}, mesh = {Aerobiosis ; DNA, Bacterial/*chemistry/*genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Metabolic Networks and Pathways/genetics ; Molecular Sequence Data ; Naphthalenes/metabolism ; Pseudomonas stutzeri/*genetics/metabolism ; *Sequence Analysis, DNA ; }, abstract = {Pseudomonas stutzeri AN10 (CCUG 29243) can be considered a model strain for aerobic naphthalene degradation. We report the complete genome sequence of this bacterium. Its 4.71-Mb chromosome provides insights into other biodegradative capabilities of strain AN10 (i.e., benzoate catabolism) and suggests a high number of horizontal gene transfer events.}, }
@article {pmid23144138, year = {2013}, author = {Carrión, VJ and Gutiérrez-Barranquero, JA and Arrebola, E and Bardaji, L and Codina, JC and de Vicente, A and Cazorla, FM and Murillo, J}, title = {The mangotoxin biosynthetic operon (mbo) is specifically distributed within Pseudomonas syringae genomospecies 1 and was acquired only once during evolution.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {3}, pages = {756-767}, pmid = {23144138}, issn = {1098-5336}, mesh = {Bacterial Toxins/*genetics ; *Biosynthetic Pathways ; Cluster Analysis ; DNA Primers/genetics ; DNA, Bacterial/chemistry/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genotype ; Molecular Sequence Data ; *Operon ; Phylogeny ; Polymerase Chain Reaction ; Pseudomonas syringae/classification/*genetics ; Sequence Analysis, DNA ; }, abstract = {Mangotoxin production was first described in Pseudomonas syringae pv. syringae strains. A phenotypic characterization of 94 P. syringae strains was carried out to determine the genetic evolution of the mangotoxin biosynthetic operon (mbo). We designed a PCR primer pair specific for the mbo operon to examine its distribution within the P. syringae complex. These primers amplified a 692-bp DNA fragment from 52 mangotoxin-producing strains and from 7 non-mangotoxin-producing strains that harbor the mbo operon, whereas 35 non-mangotoxin-producing strains did not yield any amplification. This, together with the analysis of draft genomes, allowed the identification of the mbo operon in five pathovars (pathovars aptata, avellanae, japonica, pisi, and syringae), all of which belong to genomospecies 1, suggesting a limited distribution of the mbo genes in the P. syringae complex. Phylogenetic analyses using partial sequences from housekeeping genes differentiated three groups within genomospecies 1. All of the strains containing the mbo operon clustered in groups I and II, whereas those lacking the operon clustered in group III; however, the relative branching order of these three groups is dependent on the genes used to construct the phylogeny. The mbo operon maintains synteny and is inserted in the same genomic location, with high sequence conservation around the insertion point, for all the strains in groups I and II. These data support the idea that the mbo operon was acquired horizontally and only once by the ancestor of groups I and II from genomospecies 1 within the P. syringae complex.}, }
@article {pmid23134518, year = {2012}, author = {Matveeva, TV and Bogomaz, DI and Pavlova, OA and Nester, EW and Lutova, LA}, title = {Horizontal gene transfer from genus agrobacterium to the plant linaria in nature.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {25}, number = {12}, pages = {1542-1551}, doi = {10.1094/MPMI-07-12-0169-R}, pmid = {23134518}, issn = {0894-0282}, mesh = {Agrobacterium/*genetics/isolation &amp; purification ; Base Sequence ; DNA, Bacterial/genetics ; DNA, Plant/genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Linaria/*genetics/microbiology ; Molecular Sequence Data ; Real-Time Polymerase Chain Reaction ; Regeneration ; Russia ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Genes can be transferred horizontally between prokaryotes and eukaryotes in nature. The best-studied examples occur between Agrobacterium rhizogenes and certain Nicotiana spp. To investigate possible additional cases of horizontal gene transfer in nature between Agrobacterium and plants, a real-time polymerase chain reaction-based approach was employed to screen 127 plant species, belonging to 38 families of Dicotyledones, for the presence of oncogenes homologous to the transfer DNA fragments (T-DNA) from both A. tumefaciens and A. rhizogenes. Among all of the analyzed plant species, we found that only Linaria vulgaris contained sequences homologous to the T-DNA of A. rhizogenes. All screened L. vulgaris plants from various parts of Russia contained the same homologous sequences, including rolB, rolC, ORF13, ORF14, and mis genes. The same opine gene is found in the species of Nicotiana which contain genes of A. rhizogenes. In L. vulgaris, there are two copies of T-DNA organized as a single tandem imperfect direct repeat. The plant DNA sequence of the site of integration shows similarity to a retrotransposon. This site is most likely silent, suggesting that the T-DNA is not expressed. Attempts to demonstrate expression of the T-DNA genes were negative. Our study indicates that the frequency of gene transfer and fixation in the germline from Agrobacterium to plant hosts is rare in the natural environment.}, }
@article {pmid23133654, year = {2012}, author = {Zafra, O and Lamprecht-Grandío, M and de Figueras, CG and González-Pastor, JE}, title = {Extracellular DNA release by undomesticated Bacillus subtilis is regulated by early competence.}, journal = {PloS one}, volume = {7}, number = {11}, pages = {e48716}, pmid = {23133654}, issn = {1932-6203}, mesh = {Bacillus subtilis/*genetics ; Bacterial Proteins/genetics ; Biofilms ; Cloning, Molecular ; DNA/metabolism ; DNA Transposable Elements/genetics ; DNA, Bacterial/genetics ; Deoxyribonuclease I/metabolism ; Escherichia coli Proteins/metabolism ; Flow Cytometry/methods ; Gene Library ; Gene Transfer, Horizontal ; Mutagenesis ; Mutation ; Phenotype ; Plasmids/metabolism ; Ribosomal Proteins/metabolism ; Temperature ; }, abstract = {Extracellular DNA (eDNA) release is a widespread capacity described in many microorganisms. We identified and characterized lysis-independent eDNA production in an undomesticated strain of Bacillus subtilis. DNA fragments are released during a short time in late-exponential phase. The released eDNA corresponds to whole genome DNA, and does not harbour mutations suggesting that is not the result of error prone DNA synthesis. The absence of eDNA was linked to a spread colony morphology, which allowed a visual screening of a transposon library to search for genes involved in its production. Transposon insertions in genes related to quorum sensing and competence (oppA, oppF and comXP) and to DNA metabolism (mfd and topA) were impaired in eDNA release. Mutants in early competence genes such as comA and srfAA were also defective in eDNA while in contrast mutations in late competence genes as those for the DNA uptake machinery had no effect. A subpopulation of cells containing more DNA is present in the eDNA producing strains but absent from the eDNA defective strain. Finally, competent B. subtilis cells can be transformed by eDNA suggesting it could be used in horizontal gene transfer and providing a rationale for the molecular link between eDNA release and early-competence in B. subtilis that we report.}, }
@article {pmid23133569, year = {2012}, author = {Nongkhlaw, M and Kumar, R and Acharya, C and Joshi, SR}, title = {Occurrence of horizontal gene transfer of P(IB)-type ATPase genes among bacteria isolated from the uranium rich deposit of Domiasiat in North East India.}, journal = {PloS one}, volume = {7}, number = {10}, pages = {e48199}, pmid = {23133569}, issn = {1932-6203}, mesh = {Adenosine Triphosphatases/chemistry/*genetics/metabolism ; Cluster Analysis ; Environmental Monitoring/methods ; *Gene Transfer, Horizontal ; Genomics ; India ; Metals, Heavy ; *Mining ; Models, Genetic ; Phylogeny ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/metabolism ; Sequence Analysis, DNA ; *Soil Microbiology ; Uranium/chemistry ; }, abstract = {Uranium (U) tolerant aerobic heterotrophs were isolated from the subsurface soils of one of the pre-mined U-rich deposits at Domiasiat located in the north-eastern part of India. On screening of genomic DNA from 62 isolates exhibiting superior U and heavy metal tolerance, 32 isolates were found to be positive for P(IB)-type ATPase genes. Phylogenetic incongruence and anomalous DNA base compositions revealed the acquisition of P(IB)-type ATPase genes by six isolates through horizontal gene transfer (HGT). Three of these instances of HGT appeared to have occurred at inter-phylum level and the other three instances indicated to have taken place at intra-phylum level. This study provides an insight into one of the possible survival strategies that bacteria might employ to adapt to environments rich in uranium and heavy metals.}, }
@article {pmid23133391, year = {2012}, author = {Nykyri, J and Niemi, O and Koskinen, P and Nokso-Koivisto, J and Pasanen, M and Broberg, M and Plyusnin, I and Törönen, P and Holm, L and Pirhonen, M and Palva, ET}, title = {Revised phylogeny and novel horizontally acquired virulence determinants of the model soft rot phytopathogen Pectobacterium wasabiae SCC3193.}, journal = {PLoS pathogens}, volume = {8}, number = {11}, pages = {e1003013}, pmid = {23133391}, issn = {1553-7374}, mesh = {*Gene Transfer, Horizontal ; *Multigene Family ; Pectobacterium/*genetics/*pathogenicity ; *Phylogeny ; Plant Diseases/*genetics/microbiology ; Plant Roots/microbiology ; Solanum tuberosum/microbiology ; Virulence Factors/*genetics/metabolism ; }, abstract = {Soft rot disease is economically one of the most devastating bacterial diseases affecting plants worldwide. In this study, we present novel insights into the phylogeny and virulence of the soft rot model Pectobacterium sp. SCC3193, which was isolated from a diseased potato stem in Finland in the early 1980s. Genomic approaches, including proteome and genome comparisons of all sequenced soft rot bacteria, revealed that SCC3193, previously included in the species Pectobacterium carotovorum, can now be more accurately classified as Pectobacterium wasabiae. Together with the recently revised phylogeny of a few P. carotovorum strains and an increasing number of studies on P. wasabiae, our work indicates that P. wasabiae has been unnoticed but present in potato fields worldwide. A combination of genomic approaches and in planta experiments identified features that separate SCC3193 and other P. wasabiae strains from the rest of soft rot bacteria, such as the absence of a type III secretion system that contributes to virulence of other soft rot species. Experimentally established virulence determinants include the putative transcriptional regulator SirB, two partially redundant type VI secretion systems and two horizontally acquired clusters (Vic1 and Vic2), which contain predicted virulence genes. Genome comparison also revealed other interesting traits that may be related to life in planta or other specific environmental conditions. These traits include a predicted benzoic acid/salicylic acid carboxyl methyltransferase of eukaryotic origin. The novelties found in this work indicate that soft rot bacteria have a reservoir of unknown traits that may be utilized in the poorly understood latent stage in planta. The genomic approaches and the comparison of the model strain SCC3193 to other sequenced Pectobacterium strains, including the type strain of P. wasabiae, provides a solid basis for further investigation of the virulence, distribution and phylogeny of soft rot bacteria and, potentially, other bacteria as well.}, }
@article {pmid23133387, year = {2012}, author = {Morikawa, K and Takemura, AJ and Inose, Y and Tsai, M and Nguyen Thi, le T and Ohta, T and Msadek, T}, title = {Expression of a cryptic secondary sigma factor gene unveils natural competence for DNA transformation in Staphylococcus aureus.}, journal = {PLoS pathogens}, volume = {8}, number = {11}, pages = {e1003003}, pmid = {23133387}, issn = {1553-7374}, mesh = {Bacterial Proteins/biosynthesis/*genetics ; Chromosomes, Bacterial/*genetics/metabolism ; DNA, Bacterial/*genetics/metabolism ; *Gene Duplication ; Humans ; Sigma Factor/biosynthesis/*genetics ; Staphylococcus aureus/*genetics/metabolism ; *Transformation, Bacterial ; }, abstract = {It has long been a question whether Staphylococcus aureus, a major human pathogen, is able to develop natural competence for transformation by DNA. We previously showed that a novel staphylococcal secondary sigma factor, SigH, was a likely key component for competence development, but the corresponding gene appeared to be cryptic as its expression could not be detected during growth under standard laboratory conditions. Here, we have uncovered two distinct mechanisms allowing activation of SigH production in a minor fraction of the bacterial cell population. The first is a chromosomal gene duplication rearrangement occurring spontaneously at a low frequency [≤10(-5)], generating expression of a new chimeric sigH gene. The second involves post-transcriptional regulation through an upstream inverted repeat sequence, effectively suppressing expression of the sigH gene. Importantly, we have demonstrated for the first time that S. aureus cells producing active SigH become competent for transformation by plasmid or chromosomal DNA, which requires the expression of SigH-controlled competence genes. Additionally, using DNA from the N315 MRSA strain, we successfully transferred the full length SCCmecII element through natural transformation to a methicillin-sensitive strain, conferring methicillin resistance to the resulting S. aureus transformants. Taken together, we propose a unique model for staphylococcal competence regulation by SigH that could help explain the acquisition of antibiotic resistance genes through horizontal gene transfer in this important pathogen.}, }
@article {pmid23133357, year = {2012}, author = {Hoeppner, MP and Gardner, PP and Poole, AM}, title = {Comparative analysis of RNA families reveals distinct repertoires for each domain of life.}, journal = {PLoS computational biology}, volume = {8}, number = {11}, pages = {e1002752}, pmid = {23133357}, issn = {1553-7358}, support = {/WT_/Wellcome Trust/United Kingdom ; WT077044/Z/05/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Databases, Nucleic Acid ; Eukaryota/*genetics ; *Evolution, Molecular ; Genome ; Genomics ; Phylogeny ; RNA/*genetics ; }, abstract = {The RNA world hypothesis, that RNA genomes and catalysts preceded DNA genomes and genetically-encoded protein catalysts, has been central to models for the early evolution of life on Earth. A key part of such models is continuity between the earliest stages in the evolution of life and the RNA repertoires of extant lineages. Some assessments seem consistent with a diverse RNA world, yet direct continuity between modern RNAs and an RNA world has not been demonstrated for the majority of RNA families, and, anecdotally, many RNA functions appear restricted in their distribution. Despite much discussion of the possible antiquity of RNA families, no systematic analyses of RNA family distribution have been performed. To chart the broad evolutionary history of known RNA families, we performed comparative genomic analysis of over 3 million RNA annotations spanning 1446 families from the Rfam 10 database. We report that 99% of known RNA families are restricted to a single domain of life, revealing discrete repertoires for each domain. For the 1% of RNA families/clans present in more than one domain, over half show evidence of horizontal gene transfer (HGT), and the rest show a vertical trace, indicating the presence of a complex protein synthesis machinery in the Last Universal Common Ancestor (LUCA) and consistent with the evolutionary history of the most ancient protein-coding genes. However, with limited interdomain transfer and few RNA families exhibiting demonstrable antiquity as predicted under RNA world continuity, our results indicate that the majority of modern cellular RNA repertoires have primarily evolved in a domain-specific manner.}, }
@article {pmid23131563, year = {2012}, author = {Matsuda, A and Kurono, N and Kawano, C and Shirota, K and Hirabayashi, A and Horino, M and Etchuya, R and Sobue, R and Sasaki, Y and Miyaue, S and Sekoguchi, A and Sugiura, C and Shibata, Y and Ito, M and Ando, T and Maeda, S}, title = {Genome-wide screen for Escherichia coli genes involved in repressing cell-to-cell transfer of non-conjugative plasmids.}, journal = {Biochemical and biophysical research communications}, volume = {428}, number = {4}, pages = {445-450}, doi = {10.1016/j.bbrc.2012.10.098}, pmid = {23131563}, issn = {1090-2104}, mesh = {Conjugation, Genetic/*genetics ; Escherichia coli/*genetics ; Gene Knockout Techniques ; Gene Transfer, Horizontal/*genetics ; Mutation ; Plasmids/*genetics ; Sequence Analysis, DNA ; Transformation, Genetic ; }, abstract = {Acquiring new genetic traits by lateral gene transfer is a bacterial strategy for environment adaptation. We previously showed that Escherichia coli could laterally transmit non-conjugative plasmids in co-cultures containing strains with and without the plasmid. In this study, using the Keio collection, a comprehensive library of E. coli knock-out mutants for non-essential genes, we screened for genes responsible for repressing cell-to-cell plasmid transfer in recipient cells. By stepwise screening, we identified 55 'transfer-up' mutants that exhibited approximately 2- to 30-fold increased activities. We confirmed plasmid acquisition by these 'up' mutants and revealed that there were no significant changes in antibiotic resistance in the original Keio strains. The presumed functions of these gene products covered a wide range of activities, including metabolism and synthesis, transport, transcription or translation and others. Two competence-gene homologues (ybaV and yhiR) were identified from among these genes. The presumed localizations of these 55 gene products were estimated to be 34 cytoplasmic proteins, 20 in or around the cell surface and 1 unknown location. Our results suggest that these 55 genes may be involved in repressing plasmid uptake during cell-to-cell plasmid transfer.}, }
@article {pmid23131096, year = {2012}, author = {Sridhar, S and Sharma, A and Kongshaug, H and Nilsen, F and Jonassen, I}, title = {Whole genome sequencing of the fish pathogen Francisella noatunensis subsp. orientalis Toba04 gives novel insights into Francisella evolution and pathogenecity.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {598}, pmid = {23131096}, issn = {1471-2164}, mesh = {Animals ; Biological Evolution ; Fish Diseases/*microbiology ; Francisella/classification/*genetics/*pathogenicity ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Gram-Negative Bacterial Infections/microbiology/*veterinary ; Host-Pathogen Interactions ; Humans ; Metabolic Networks and Pathways/*genetics ; Mutation ; Open Reading Frames ; Phylogeny ; Pseudogenes ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Tilapia/*microbiology ; Virulence ; }, abstract = {BACKGROUND: Francisella is a genus of gram-negative bacterium highly virulent in fishes and human where F. tularensis is causing the serious disease tularaemia in human. Recently Francisella species have been reported to cause mortality in aquaculture species like Atlantic cod and tilapia. We have completed the sequencing and draft assembly of the Francisella noatunensis subsp. orientalisToba04 strain isolated from farmed Tilapia. Compared to other available Francisella genomes, it is most similar to the genome of Francisella philomiragia subsp. philomiragia, a free-living bacterium not virulent to human.<br><br>RESULTS: The genome is rearranged compared to the available Francisella genomes even though we found no IS-elements in the genome. Nearly 16% percent of the predicted ORFs are pseudogenes. Computational pathway analysis indicates that a number of the metabolic pathways are disrupted due to pseudogenes. Comparing the novel genome with other available Francisella genomes, we found around 2.5% of unique genes present in Francisella noatunensis subsp. orientalis Toba04 and a list of genes uniquely present in the human-pathogenic Francisella subspecies. Most of these genes might have transferred from bacterial species through horizontal gene transfer. Comparative analysis between human and fish pathogen also provide insights into genes responsible for pathogenecity. Our analysis of pseudogenes indicates that the evolution of Francisella subspecies's pseudogenes from Tilapia is old with large number of pseudogenes having more than one inactivating mutation.<br><br>CONCLUSIONS: The fish pathogen has lost non-essential genes some time ago. Evolutionary analysis of the Francisella genomes, strongly suggests that human and fish pathogenic Francisella species have evolved independently from free-living metabolically competent Francisella species. These findings will contribute to understanding the evolution of Francisella species and pathogenesis.}, }
@article {pmid23128628, year = {2013}, author = {Schreiber, C and Kistemann, T}, title = {Antibiotic resistance among autochthonous aquatic environmental bacteria.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {67}, number = {1}, pages = {117-123}, doi = {10.2166/wst.2012.539}, pmid = {23128628}, issn = {0273-1223}, mesh = {Anti-Bacterial Agents/*pharmacology ; *Drug Resistance, Multiple, Bacterial ; Rhodospirillaceae/*drug effects ; Waste Disposal, Fluid ; Water Microbiology ; Water Pollutants, Chemical ; }, abstract = {Antibiotics are widely used in both human and veterinary medicine and antibiotic-resistant bacteria cause problems in antibiotic therapy. The current study was conducted in the catchment area of the river Swist (Germany) and focuses on the resistance of environmental Rhodospirillaceae to antibiotics used in human medicine. The samples collected reflect different levels of human impact on the environment. In total, 614 isolates were tested for antibiotic susceptibility. About half of these isolates were susceptible to all substances tested. Oxacillin resistance was observed most frequently (41%). Resistant Rhodospirillaceae were detected in wastewater effluent from a municipal sewage treatment plant, as well as in non-polluted upper reaches. The highest multi-resistance level was detected in small tributaries and it surprisingly decreased with an increasing influence of municipal wastewater. It could be shown that the detected resistances were acquired rather than intrinsic. Besides natural occurrence of multi-resistance among non-sulphur purple bacteria, horizontal gene transfer and acquired cross-resistance against veterinary antibiotics are assumed to be important factors. To the authors' knowledge, this is the first study investigating the potential of Rhodospirillaceae as a reservoir for resistance to antibiotics used in human medicine. The consequence for resistance prevalence in human pathogens and for their antibiotic therapy needs evaluation.}, }
@article {pmid23124749, year = {2012}, author = {Dai, M and Lu, J and Wang, Y and Liu, Z and Yuan, Z}, title = {In vitro development and transfer of resistance to chlortetracycline in Bacillus subtilis.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {50}, number = {5}, pages = {807-812}, pmid = {23124749}, issn = {1976-3794}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacillus subtilis/*drug effects/genetics ; Chlortetracycline/*pharmacology ; Conjugation, Genetic ; Enterococcus faecalis/drug effects/genetics ; Escherichia coli/drug effects/genetics ; *Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; }, abstract = {The present criteria and rules controlling the approval of the use of probiotics are limited to antibiotic resistance patterns and the presence of antibiotic resistance genes in bacteria. There is little information available in the literature regarding the risk of the usage of probiotics in the presence of antibiotic pressure. In this study we investigated the development and transfer of antibiotic resistance in Bacillus subtilis selected in vitro by chlortetracycline in a stepwise manner. Bacillus subtilis was exposed to increasing concentrations of chlortetracyclineto induce in vitro resistance to chlortetracycline, and the minimal inhibitory concentrations were determinedfor the mutants. Resistant B. subtilis were conjugated with Escherichia coli NK5449 and Enterococcus faecalis JH2-2 using the filter mating. Three B. subtilis tetracycline resistant mutants (namely, BS-1, BS-2, and BS-3) were derived in vitro. A tetracycline resistant gene, tet (K), was found in the plasmids of BS-1 and BS-2. Three conjugates (BS-1N, BS-2N, and BS-3N) were obtained when the resistant B. subtilis was conjugated with E. coli NK5449. The conjugation frequencies for the BS-1N, BS-2N, and BS-3N conjugates were 4.57×10(-7), 1.4×10(-7), and 1.3×10(-8), respectively. The tet(K) gene was found only in the plasmids of BS-1N. These results indicate that long-term use of probiotics under antibiotic selection pressure could cause antibiotic resistance, and the resistance gene could be transferred to other bacteria. The risk arising from the use of probiotics under antibiotic pressure should be considered in the criteria and rules for the safety assessment of probiotics.}, }
@article {pmid23123908, year = {2013}, author = {Paul, S and Linardopoulou, EV and Billig, M and Tchesnokova, V and Price, LB and Johnson, JR and Chattopadhyay, S and Sokurenko, EV}, title = {Role of homologous recombination in adaptive diversification of extraintestinal Escherichia coli.}, journal = {Journal of bacteriology}, volume = {195}, number = {2}, pages = {231-242}, pmid = {23123908}, issn = {1098-5530}, mesh = {*Adaptation, Biological ; Adhesins, Escherichia coli/genetics ; Anti-Bacterial Agents/pharmacology ; DNA, Bacterial/chemistry/genetics ; Drug Resistance, Bacterial ; Escherichia coli/classification/*genetics/isolation &amp; purification ; Escherichia coli Infections/microbiology ; Fimbriae Proteins/genetics ; Fluoroquinolones/pharmacology ; *Genetic Variation ; *Homologous Recombination ; Molecular Sequence Data ; Sequence Analysis, DNA ; }, abstract = {The contribution of homologous exchange (recombination) of core genes in the adaptive evolution of bacterial pathogens is not well understood. To investigate this, we analyzed fully assembled genomes of two Escherichia coli strains from sequence type 131 (ST131), a clonal group that is both the leading cause of extraintestinal E. coli infections and the main source of fluoroquinolone-resistant E. coli. Although the sequences of each of the seven multilocus sequence typing genes were identical in the two ST131 isolates, the strains diverged from one another by homologous recombination that affected at least 9% of core genes. This was on a par with the contribution to genomic diversity of horizontal gene transfer and point gene mutation. The genomic positions of recombinant and mobile genetic regions were partially linked, suggesting their concurrent occurrence. One of the genes affected by homologous recombination was fimH, which encodes mannose-specific type 1 fimbrial adhesin, resulting in functionally distinct copies of the gene in ST131 strains. One strain, a uropathogenic isolate, had a pathoadaptive variant of fimH that was acquired by homologous replacement into the commensal strain background. Close examination of FimH structure and function in additional ST131 isolates revealed that recombination led to acquisition of several functionally distinct variants that, upon homologous exchange, were targeted by a variety of pathoadaptive mutations under strong positive selection. Different recombinant fimH strains also showed a strong clonal association with ST131 isolates that had distinct fluoroquinolone resistance profiles. Thus, homologous recombination of core genes plays a significant role in adaptive diversification of bacterial pathogens, especially at the level of clonally related groups of isolates.}, }
@article {pmid23122510, year = {2013}, author = {Georgalaki, M and Papadimitriou, K and Anastasiou, R and Pot, B and Van Driessche, G and Devreese, B and Tsakalidou, E}, title = {Macedovicin, the second food-grade lantibiotic produced by Streptococcus macedonicus ACA-DC 198.}, journal = {Food microbiology}, volume = {33}, number = {1}, pages = {124-130}, doi = {10.1016/j.fm.2012.09.008}, pmid = {23122510}, issn = {1095-9998}, mesh = {Bacterial Proteins/chemistry/genetics/metabolism ; Bacteriocins/*biosynthesis/chemistry/genetics ; Molecular Sequence Data ; Molecular Weight ; Multigene Family ; Phylogeny ; Sequence Alignment ; Streptococcus/classification/genetics/*metabolism ; Streptococcus bovis/classification/genetics/metabolism ; }, abstract = {Streptococcus macedonicus ACA-DC 198 was found to produce a second lantibiotic named macedovicin in addition to macedocin. Macedovicin was purified to homogeneity and mass spectrometric analysis identified a peptide of approximately 3.4 kDa. Partial N-terminal sequence analysis and tandem mass spectrometry revealed that macedovicin was identical to bovicin HJ50 and thermophilin 1277 produced by Streptococcus bovis and Streptococcus thermophilus, respectively. Macedovicin inhibits a broad spectrum of lactic acid bacteria, several food spoilage species (e.g. Clostridium spp.) and oral streptococci. We determined the complete biosynthetic gene cluster of macedovicin. Even though the gene clusters of macedovicin, thermophilin 1277 and bovicin HJ50 were almost identical at the nucleotide level, there were important differences in their predicted genes and proteins. Bovicin HJ50-like lantibiotics were also found to be encoded by Streptococcus suis strains SC84 and D12, Enterococcus columbae PLCH2, Clostridium perfringens JGS1721 and several Bacillus strains. All these lantibiotics contained a number of conserved amino acids that may be important for their biosynthesis and activity, while phylogenetic analysis supported their dispersion by horizontal gene transfer. In conclusion, the production of multiple bacteriocins may enhance the bio-protective potential of S. macedonicus during food fermentation.}, }
@article {pmid23116195, year = {2012}, author = {Meehan, CJ and Beiko, RG}, title = {Lateral gene transfer of an ABC transporter complex between major constituents of the human gut microbiome.}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {248}, pmid = {23116195}, issn = {1471-2180}, support = {CMF-108026//Canadian Institutes of Health Research/Canada ; }, mesh = {ATP-Binding Cassette Transporters/*genetics ; Bacterial Proteins/*genetics ; Cluster Analysis ; Gastrointestinal Tract/*microbiology ; *Gene Transfer, Horizontal ; Humans ; Metagenome ; Nickel/metabolism ; Phylogeny ; Sequence Homology ; }, abstract = {BACKGROUND: Several links have been established between the human gut microbiome and conditions such as obesity and inflammatory bowel syndrome. This highlights the importance of understanding what properties of the gut microbiome can affect the health of the human host. Studies have been undertaken to determine the species composition of this microbiome and infer functional profiles associated with such host properties. However, lateral gene transfer (LGT) between community members may result in misleading taxonomic attributions for the recipient organisms, thus making species-function links difficult to establish.<br><br>RESULTS: We identified a peptides/nickel transport complex whose components differed in abundance based upon levels of host obesity, and assigned the encoded proteins to members of the microbial community. Each protein was assigned to several distinct taxonomic groups, with moderate levels of agreement observed among different proteins in the complex. Phylogenetic trees of these proteins produced clusters that differed greatly from taxonomic attributions and indicated that habitat-directed LGT of this complex is likely to have occurred, though not always between the same partners.<br><br>CONCLUSIONS: These findings demonstrate that certain membrane transport systems may be an important factor within an obese-associated gut microbiome and that such complexes may be acquired several times by different strains of the same species. Additionally, an example of individual proteins from different organisms being transferred into one operon was observed, potentially demonstrating a functional complex despite the donors of the subunits being taxonomically disparate. Our results also highlight the potential impact of habitat-directed LGT on the resident microbiota.}, }
@article {pmid23116146, year = {2013}, author = {Oravcova, V and Ghosh, A and Zurek, L and Bardon, J and Guenther, S and Cizek, A and Literak, I}, title = {Vancomycin-resistant enterococci in rooks (Corvus frugilegus) wintering throughout Europe.}, journal = {Environmental microbiology}, volume = {15}, number = {2}, pages = {548-556}, doi = {10.1111/1462-2920.12002}, pmid = {23116146}, issn = {1462-2920}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics ; Carbon-Oxygen Ligases/genetics ; Cluster Analysis ; Crows/genetics/*microbiology ; Disease Reservoirs/*microbiology ; Electrophoresis, Gel, Pulsed-Field ; Enterococcus/*drug effects/genetics/isolation &amp; purification/*physiology ; Europe ; Feces/microbiology ; Gene Transfer, Horizontal/genetics ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Vancomycin/*pharmacology ; *Vancomycin Resistance/genetics ; }, abstract = {This study's aims were to assess the prevalence of, and to characterize, vancomycin-resistant enterococci (VRE) from rooks (Corvus frugilegus) wintering in Europe during 2010/2011. Faeces samples were cultivated selectively for VRE and characterized. Pulsed-field gel electrophoresis and multilocus sequence typing (MLST) were used to examine epidemiologic relationships of vanA-containing VRE. The vanA-carrying VRE were tested in vitro for mobility of vancomycin resistance traits. VRE were found in 62 (6%) of 1073 rook samples. Enterococcal species diversity comprised Enterococcus gallinarum (48 isolates), followed by E. faecium (9) and E. faecalis (5). Eight VRE harboured the vanA and ermB genes. Seven vanA-carrying VRE originated from the Czech Republic and one from Germany. All vanA-carrying VRE were identified as E. faecium. Based on MLST analysis, six vanA-positive isolates were grouped as ST92 type, one isolate belonged to ST121, and the remaining one was described as a novel type ST671. Seven out of eight isolates were able to transfer the vancomycin resistance trait via filter mating with a transfer rate of 8.95 ± 3.25 × 10(-7) transconjugants per donor. In conclusion, wintering rooks in some European countries may disseminate clinically important enterococci and pose a risk for environmental contamination.}, }
@article {pmid23113333, year = {2012}, author = {Krylov, SV and Kropinski, AM and Pleteneva, EA and Shaburova, OV and Burkal'tseva, MV and Miroshnikov, KA and Krylov, VN}, title = {[Properties of the new D3-like Pseudomonas aeruginosa bacteriophage phiPMG1: genome structure and prospects for the use in phage therapy].}, journal = {Genetika}, volume = {48}, number = {9}, pages = {1057-1067}, pmid = {23113333}, issn = {0016-6758}, mesh = {Gene Transfer, Horizontal ; *Genes, Viral ; *Genome, Viral ; Pseudomonas Phages/*genetics/physiology ; Pseudomonas aeruginosa/*genetics/virology ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {Results of studying the novel virulent phage phiPMG1 active on Pseudomonas aeruginosa are presented. phiPMG1 was shown to exhibit detectable homology and resemblance in the total genome structure with temperate converting phage D3. Phage phiPMG1 differs from D3 in that it fails to stably lysogenize bacteria and can grow on strains carrying plasmids that cause growth inhibition of phage D3 and some other phages. This significantly diminishes the probability of horizontal gene transfer with phage phiPMG1 and suggests the possible employment of this phage in phage therapy. A comparison of genome structures in phages phiPMG1 and D3 demonstrated not only high homology of 65 genes, but also the presence in the phiPMG1 genome of 16 genes that were not recorded in the files of NCBI database. Apparently, the evolution of genomes in phages of this species is mostly associated with migrations into other species of bacteria and recombinations with phages of other species (for example, F116). Detailed structural analysis a genome region in which the essential nonhomology is exhibited between three D3-like phages (D3, phiPMG1, and PAJU2) revealed that the phiPMG1 genome supposedly is phylogenetically closer than the others to the genome of a hypothetical ancestor phage belonging to this species.}, }
@article {pmid23112186, year = {2012}, author = {Kitahara, K and Yasutake, Y and Miyazaki, K}, title = {Mutational robustness of 16S ribosomal RNA, shown by experimental horizontal gene transfer in Escherichia coli.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {47}, pages = {19220-19225}, pmid = {23112186}, issn = {1091-6490}, mesh = {Base Sequence ; Escherichia coli/*genetics ; *Gene Transfer Techniques ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/genetics ; Molecular Sequence Data ; Mutation/*genetics ; Nucleic Acid Conformation ; Nucleotides/genetics ; Phylogeny ; Protein Binding ; RNA, Bacterial/chemistry/*genetics ; RNA, Ribosomal, 16S/chemistry/*genetics ; Ribosomal Proteins/metabolism ; }, abstract = {The bacterial ribosome consists of three rRNA molecules and 57 proteins and plays a crucial role in translating mRNA-encoded information into proteins. Because of the ribosome's structural and mechanistic complexity, it is believed that each ribosomal component coevolves to maintain its function. Unlike 5S rRNA, 16S and 23S rRNAs appear to lack mutational robustness, because they form the structural core of the ribosome. However, using Escherichia coli Δ7 (null mutant of operons) as a host, we have recently shown that an active hybrid ribosome whose 16S rRNA has been specifically substituted with that from non-E. coli bacteria can be reconstituted in vivo. To investigate the mutational robustness of 16S rRNA and the structural basis for its functionality, we used a metagenomic approach to screen for 16S rRNA genes that complement the growth of E. coli Δ7. Various functional genes were obtained from the Gammaproteobacteria and Betaproteobacteria lineages. Despite the large sequence diversity (80.9-99.0% identity with E. coli 16S rRNA) of the functional 16S rRNA molecules, the doubling times (DTs) of each mutant increased only modestly with decreasing sequence identity (average increase in DT, 4.6 s per mutation). The three-dimensional structure of the 30S ribosome showed that at least 40.7% (628/1,542) of the nucleotides were variable, even at ribosomal protein-binding sites, provided that the secondary structures were properly conserved. Our results clearly demonstrate that 16S rRNA functionality largely depends on the secondary structure but not on the sequence itself.}, }
@article {pmid23111870, year = {2012}, author = {Deng, L and Gregory, A and Yilmaz, S and Poulos, BT and Hugenholtz, P and Sullivan, MB}, title = {Contrasting life strategies of viruses that infect photo- and heterotrophic bacteria, as revealed by viral tagging.}, journal = {mBio}, volume = {3}, number = {6}, pages = {}, pmid = {23111870}, issn = {2150-7511}, support = {CA 023074/CA/NCI NIH HHS/United States ; }, mesh = {Bacteriophages/growth &amp; development/isolation &amp; purification/*physiology ; Flow Cytometry ; *Heterotrophic Processes ; Microbial Interactions ; *Phototrophic Processes ; Pseudoalteromonas/growth &amp; development/metabolism/*physiology/*virology ; Staining and Labeling ; Synechococcus/growth &amp; development/metabolism/*physiology/*virology ; Water Microbiology ; }, abstract = {Ocean viruses are ubiquitous and abundant and play important roles in global biogeochemical cycles by means of their mortality, horizontal gene transfer, and manipulation of host metabolism. However, the obstacles involved in linking viruses to their hosts in a high-throughput manner bottlenecks our ability to understand virus-host interactions in complex communities. We have developed a method called viral tagging (VT), which combines mixtures of host cells and fluorescent viruses with flow cytometry. We investigated multiple viruses which infect each of two model marine bacteria that represent the slow-growing, photoautotrophic genus Synechococcus (Cyanobacteria) and the fast-growing, heterotrophic genus Pseudoalteromonas (Gammaproteobacteria). Overall, viral tagging results for viral infection were consistent with plaque and liquid infection assays for cyanobacterial myo-, podo- and siphoviruses and some (myo- and podoviruses) but not all (four siphoviruses) heterotrophic bacterial viruses. Virus-tagged Pseudoalteromonas organisms were proportional to the added viruses under varied infection conditions (virus-bacterium ratios), while no more than 50% of the Synechococcus organisms were virus tagged even at viral abundances that exceeded (5 to 10×) that of their hosts. Further, we found that host growth phase minimally impacts the fraction of virus-tagged Synechococcus organisms while greatly affecting phage adsorption to Pseudoalteromonas. Together these findings suggest that at least two contrasting viral life strategies exist in the oceans and that they likely reflect adaptation to their host microbes. Looking forward to the point at which the virus-tagging signature is well understood (e.g., for Synechococcus), application to natural communities should begin to provide population genomic data at the proper scale for predictively modeling two of the most abundant biological entities on Earth. Viral study suffers from an inability to link viruses to hosts en masse, and yet delineating "who infects whom" is fundamental to viral ecology and predictive modeling. This article describes viral tagging-a high-throughput method to investigate virus-host interactions by combining the fluorescent labeling of viruses for "tagging" host cells that can be analyzed and sorted using flow cytometry. Two cultivated hosts (the cyanobacterium Synechococcus and the gammaproteobacterium Pseudoalteromonas) and their viruses (podo-, myo-, and siphoviruses) were investigated to validate the method. These lab-based experiments indicate that for most virus-host pairings, VT (viral tagging) adsorption is equivalent to traditional infection by liquid and plaque assays, with the exceptions being confined to promiscuous adsorption by Pseudoalteromonas siphoviruses. These experiments also reveal variability in life strategies across these oceanic virus-host systems with respect to infection conditions and host growth status, which highlights the need for further model system characterization to break open this virus-host interaction "black box."}, }
@article {pmid23111319, year = {2013}, author = {Naor, A and Gophna, U}, title = {Cell fusion and hybrids in Archaea: prospects for genome shuffling and accelerated strain development for biotechnology.}, journal = {Bioengineered}, volume = {4}, number = {3}, pages = {126-129}, pmid = {23111319}, issn = {2165-5987}, mesh = {Archaea/cytology/*genetics ; Biotechnology ; Cell Fusion ; DNA Shuffling ; *Gene Transfer, Horizontal ; *Genome, Archaeal ; }, abstract = {The ability to exchange DNA between cells is a molecular process that exists in different species in the domain Archaea. Such horizontal gene transfer events were shown to take place between distant species of archaea and to result in the transfer of large genomic regions. Here we describe recent progress in this field, discuss the potential use of natural gene exchange processes to perform genome shuffling and argue its possible biotechnological applications.}, }
@article {pmid23109887, year = {2012}, author = {Martínez-Nieto, MI and Encarna Merlo, M and Mota, JF and Salmerón-Sánchez, E and Segarra-Moragues, JG}, title = {Microsatellite loci in the Gypsophyte Lepidium subulatum (Brassicaceae), and transferability to other Lepidieae.}, journal = {International journal of molecular sciences}, volume = {13}, number = {9}, pages = {11861-11869}, pmid = {23109887}, issn = {1422-0067}, mesh = {*Gene Transfer, Horizontal ; *Genetic Loci ; *Lepidium/classification/genetics ; *Microsatellite Repeats ; *Phylogeny ; *Polymorphism, Genetic ; }, abstract = {Polymorphic microsatellite markers were developed for the Ibero-North African, strict gypsophyte Lepidium subulatum to unravel the effects of habitat fragmentation in levels of genetic diversity, genetic structure and gene flow among its populations. Using 454 pyrosequencing 12 microsatellite loci including di- and tri-nucleotide repeats were characterized in L. subulatum. They amplified a total of 80 alleles (2-12 alleles per locus) in a sample of 35 individuals of L. subulatum, showing relatively high levels of genetic diversity, H(O) = 0.645, H(E) = 0.627. Cross-species transferability of all 12 loci was successful for the Iberian endemics Lepidium cardamines, Lepidium stylatum, and the widespread, Lepidium graminifolium and one species each of two related genera, Cardaria draba and Coronopus didymus. These microsatellite primers will be useful to investigate genetic diversity, population structure and to address conservation genetics in species of Lepidium.}, }
@article {pmid23106652, year = {2013}, author = {Jousselin, E and Cœur d'Acier, A and Vanlerberghe-Masutti, F and Duron, O}, title = {Evolution and diversity of Arsenophonus endosymbionts in aphids.}, journal = {Molecular ecology}, volume = {22}, number = {1}, pages = {260-270}, doi = {10.1111/mec.12092}, pmid = {23106652}, issn = {1365-294X}, mesh = {Animals ; Aphids/*microbiology ; *Biological Evolution ; DNA, Bacterial/genetics ; Enterobacteriaceae/*classification/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Molecular Sequence Data ; *Phylogeny ; Symbiosis/genetics ; }, abstract = {Endosymbiotic bacteria are important drivers of insect evolutionary ecology, acting both as partners that contribute to host adaptation and as subtle parasites that manipulate host reproduction. Among them, the genus Arsenophonus is emerging as one of the most widespread lineages. Its biology is, however, entirely unknown in most cases, and it is therefore unclear how infections spread through insect populations. Here we examine the incidence and evolutionary history of Arsenophonus in aphid populations from 86 species, characterizing the processes that shape their diversity. We identify aphids as harbouring an important diversity of Arsenophonus strains. Present in 7% of the sampled species, incidence was especially high in the Aphis genus with more than 31% of the infected species. Phylogenetic investigations revealed that these Arseno-phonus strains do not cluster within an aphid-specific clade but rather exhibit distinct evolutionary origins showing that they undergo repeated horizontal transfers (HT) between distantly related host species. Their diversity pattern strongly suggests that ecological interactions, such as plant mediation and parasitism, are major drivers for Arsenophonus dispersal, dictating global incidence across insect communities. Notably, plants hosting aphids may be important ecological arenas for global exchange of Arsenophonus, serving as reservoirs for HT.}, }
@article {pmid23106414, year = {2013}, author = {de la Cruz-Perera, CI and Ren, D and Blanchet, M and Dendooven, L and Marsch, R and Sørensen, SJ and Burmølle, M}, title = {The ability of soil bacteria to receive the conjugative IncP1 plasmid, pKJK10, is different in a mixed community compared to single strains.}, journal = {FEMS microbiology letters}, volume = {338}, number = {1}, pages = {95-100}, doi = {10.1111/1574-6968.12036}, pmid = {23106414}, issn = {1574-6968}, mesh = {*Conjugation, Genetic ; DNA, Bacterial/genetics ; Ecosystem ; Escherichia coli/genetics ; Flow Cytometry ; Gene Transfer, Horizontal ; Ochrobactrum/genetics ; Plasmids/*genetics ; Pseudomonas putida/genetics ; *Soil Microbiology ; Species Specificity ; }, abstract = {Horizontal gene transfer by conjugation is common among bacterial populations in soil. It is well known that the host range of plasmids depends on several factors, including the identity of the plasmid host cell. In the present study, however, we demonstrate that the composition of the recipient community is also determining for the dissemination of a conjugative plasmid. We isolated 15 different bacterial strains from soil and assessed the conjugation frequencies of the IncP1 plasmid, pKJK10, by flow cytometry, from two different donors, Escherichia coli and Pseudomonas putida, to either 15 different bacterial strains or to the mixed community composed of all the 15 strains. We detected transfer of pKJK10 from P. putida to Stenotrophomonas rhizophila in a diparental mating, but no transfer was observed to the mixed community. In contrast, for E. coli, transfer was observed only to the mixed community, where Ochrobactrum rhizosphaerae was identified as the dominating plasmid recipient. Our results indicate that the presence of a bacterial community impacts the plasmid permissiveness by affecting the ability of strains to receive the conjugative plasmid.}, }
@article {pmid23106190, year = {2013}, author = {Ramsay, JP and Major, AS and Komarovsky, VM and Sullivan, JT and Dy, RL and Hynes, MF and Salmond, GP and Ronson, CW}, title = {A widely conserved molecular switch controls quorum sensing and symbiosis island transfer in Mesorhizobium loti through expression of a novel antiactivator.}, journal = {Molecular microbiology}, volume = {87}, number = {1}, pages = {1-13}, doi = {10.1111/mmi.12079}, pmid = {23106190}, issn = {1365-2958}, support = {BB/F009666/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/H013261/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {4-Butyrolactone/analogs &amp; derivatives/pharmacology ; Amino Acid Sequence ; Bacterial Proteins/genetics/metabolism ; Conjugation, Genetic ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; *Genomic Islands ; Homoserine/analogs &amp; derivatives/pharmacology ; Lotus/metabolism/microbiology ; Mesorhizobium/genetics/metabolism/*physiology ; Nitrogen Fixation/genetics ; Plasmids/genetics ; Promoter Regions, Genetic ; Quorum Sensing/*genetics ; RNA, Messenger/genetics/metabolism ; Symbiosis/genetics ; Transcription Factors/*genetics/metabolism ; Transcription, Genetic/drug effects ; *Transcriptional Activation/drug effects ; }, abstract = {ICEMlSym(R7A) of Mesorhizobium loti is an integrative and conjugative element (ICE) that confers the ability to form a nitrogen-fixing symbiosis with Lotus species. Horizontal transfer is activated by TraR and N-acyl-homoserine lactone (AHL), which can stimulate ICE excision in 100% of cells. However, in wild-type cultures, the ICE is excised at low frequency. Here we show that QseM, a widely conserved ICE-encoded protein, is an antiactivator of TraR. Mutation of qseM resulted in TraR-dependent activation of AHL production and excision, but did not affect transcription of traR. QseM and TraR directly interacted in a bacterial two-hybrid assay in the presence of AHL. qseM expression was repressed by a DNA-binding protein QseC, which also activated qseC expression from a leaderless transcript. QseC differentially bound two adjacent operator sites, the lower affinity of which overlapped the -35 regions of the divergent qseC-qseM promoters. QseC homologues were identified on ICEs, TraR/TraM-regulated plasmids and restriction-modification cassettes, suggesting a conserved mode of regulation. Six QseC variants with distinct operators were identified that showed evidence of reassortment between mobile elements. We propose that QseC and QseM comprise a bimodal switch that restricts quorum sensing and ICEMlSym(R7A) transfer to a small proportion of cells in the population.}, }
@article {pmid23105923, year = {2012}, author = {Lee, JY and Kim, S}, title = {CysQ of Cryptosporidium parvum, a Protozoa, May Have Been Acquired from Bacteria by Horizontal Gene Transfer.}, journal = {Genomics &amp; informatics}, volume = {10}, number = {1}, pages = {9-15}, pmid = {23105923}, issn = {2234-0742}, abstract = {Horizontal gene transfer (HGT) is the movement of genetic material between kingdoms and is considered to play a positive role in adaptation. Cryptosporidium parvum is a parasitic protozoan that causes an infectious disease. Its genome sequencing reported 14 bacteria-like proteins in the nuclear genome. Among them, cgd2_1810, which has been annotated as CysQ, a sulfite synthesis pathway protein, is listed as one of the candidates of genes horizontally transferred from bacterial origin. In this report, we examined this issue using phylogenetic analysis. Our BLAST search showed that C. parvum CysQ protein had the highest similarity with that of proteobacteria. Analysis with NCBI's Conserved Domain Tree showed phylogenetic incongruence, in that C. parvum CysQ protein was located within a branch of proteobacteria in the cd01638 domain, a bacterial member of the inositol monophosphatase family. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, the sulfate assimilation pathway, where CysQ plays an important role, is well conserved in most eukaryotes as well as prokaryotes. However, the Apicomplexa, including C. parvum, largely lack orthologous genes of the pathway, suggesting its loss in those protozoan lineages. Therefore, we conclude that C. parvum regained cysQ from proteobacteria by HGT, although its functional role is elusive.}, }
@article {pmid23102968, year = {2012}, author = {Sarker, SA and McCallin, S and Barretto, C and Berger, B and Pittet, AC and Sultana, S and Krause, L and Huq, S and Bibiloni, R and Bruttin, A and Reuteler, G and Brüssow, H}, title = {Oral T4-like phage cocktail application to healthy adult volunteers from Bangladesh.}, journal = {Virology}, volume = {434}, number = {2}, pages = {222-232}, doi = {10.1016/j.virol.2012.09.002}, pmid = {23102968}, issn = {1096-0341}, mesh = {Administration, Oral ; Adult ; Bangladesh ; Biological Products/*administration &amp; dosage/adverse effects ; Biological Therapy/*methods ; Feces/virology ; Female ; Human Experimentation ; Humans ; Male ; Placebos/administration &amp; dosage ; *T-Phages ; Young Adult ; }, abstract = {The genomic diversity of 99 T4-like coliphages was investigated by sequencing an equimolar mixture with Illumina technology and screening them against different databases for horizontal gene transfer and undesired genes. A 9-phage cocktail was given to 15 healthy adults from Bangladesh at a dose of 3×10(9) and 3×10(7) plaque-forming units and placebo respectively. Phages were detected in 64% of the stool samples when subjects were treated with higher titer phage, compared to 30% and 28% with lower-titer phage and placebo, respectively. No Escherichia coli was present in initial stool samples, and no amplification of phage was observed. One percent of the administered oral phage was recovered from the feces. No adverse events were observed by self-report, clinical examination, or from laboratory tests for liver, kidney, and hematology function. No impact of oral phage was seen on the fecal microbiota composition with respect to bacterial 16S rRNA from stool.}, }
@article {pmid23098915, year = {2013}, author = {Segura, A and Ramos, JL}, title = {Plant-bacteria interactions in the removal of pollutants.}, journal = {Current opinion in biotechnology}, volume = {24}, number = {3}, pages = {467-473}, doi = {10.1016/j.copbio.2012.09.011}, pmid = {23098915}, issn = {1879-0429}, mesh = {Bacteria/genetics/*metabolism ; *Biodegradation, Environmental ; Gene Transfer, Horizontal ; Plant Roots/metabolism/microbiology ; Plants/*metabolism/*microbiology ; *Rhizosphere ; Soil Pollutants/*metabolism ; Symbiosis/genetics ; }, abstract = {Rhizoremediation surged in popularity among scientist as an attractive strategy because plant roots provide a rich niche for bacteria to grow at the expense of root exudates; in turn bacteria act as biocatalysts that remove pollutants. The complexity of the beneficial relationships between plants and bacteria is an exciting area of research which has shown steady progress in the last decade. Despite the advances in the field, specific aspects of the interactions between contaminant-degrading rhizobacteria and plants are still unknown; including the expression of degradation genes in the rhizosphere, the influence of horizontal gene transfer in rhizoremediation, and the possibilities of the selection of specific bacteria by plant rhizosphere. We discuss the recent advances in our understanding of the plant-bacteria interactions during rhizoremediation of organic compounds.}, }
@article {pmid23096693, year = {2012}, author = {Guo, FB and Wei, W and Wang, XL and Lin, H and Ding, H and Huang, J and Rao, N}, title = {Co-evolution of genomic islands and their bacterial hosts revealed through phylogenetic analyses of 17 groups of homologous genomic islands.}, journal = {Genetics and molecular research : GMR}, volume = {11}, number = {4}, pages = {3735-3743}, doi = {10.4238/2012.October.15.5}, pmid = {23096693}, issn = {1676-5680}, mesh = {Bacteria/*genetics ; *Evolution, Molecular ; Genomic Islands/*genetics ; Host-Pathogen Interactions/*genetics ; *Phylogeny ; Proteome/genetics ; Staphylococcus aureus/genetics ; }, abstract = {Horizontal gene transfer is an important mechanism for the evolution of microbial genomes, and many horizontal gene transfer events are facilitated by genomic islands (GIs). Until now, few reports have provided evidence for the co-evolution of horizontally transferred genes and their hosts. We obtained 17 groups of homologous GIs, all of which appear in 8 or more bacterial strains of the same species or genus. Using phylogenetic analyses, we found that the topological structure of a distance tree based on the proteins of each group of homologous GIs was consistent with that based on the complete proteomes of the hosts. This result clearly indicates that GIs and their bacterial hosts have co-evolved. In addition to presenting and providing evidence for a novel concept, i.e., the co-evolution of GIs and their bacterial hosts, we also describe a new and interesting detail for the phylogenetic analysis of horizontally transferred genes: consistent phylogenetic trees can be obtained by focusing on homologous GIs despite the commonly accepted theory that the phylogenies of horizontally transferred sequences and host organisms should be inconsistent.}, }
@article {pmid23095575, year = {2012}, author = {Ubhayasekera, W and Karlsson, M}, title = {Bacterial and fungal chitinase chiJ orthologs evolve under different selective constraints following horizontal gene transfer.}, journal = {BMC research notes}, volume = {5}, number = {}, pages = {581}, pmid = {23095575}, issn = {1756-0500}, mesh = {Chitinases/*genetics ; Evolution, Molecular ; Fungi/*enzymology ; *Gene Transfer, Horizontal ; Models, Molecular ; Phylogeny ; Streptomyces/classification/*enzymology ; }, abstract = {BACKGROUND: Certain bacteria from the genus Streptomyces are currently used as biological control agents against plant pathogenic fungi. Hydrolytic enzymes that degrade fungal cell wall components, such as chitinases, are suggested as one possible mechanism in biocontrol interactions. Adaptive evolution of chitinases are previously reported for plant chitinases involved in defence against fungal pathogens, and in fungal chitinases involved in fungal-fungal interactions. In this study we investigated the molecular evolution of chitinase chiJ in the bacterial genus Streptomyces. In addition, as chiJ orthologs are previously reported in certain fungal species as a result from horizontal gene transfer, we conducted a comparative study of differences in evolutionary patterns between bacterial and fungal taxa.<br><br>FINDINGS: ChiJ contained three sites evolving under strong positive selection and four groups of co-evolving sites. Regions of high amino acid diversity were predicted to be surface-exposed and associated with coil regions that connect certain &#x3b1;-helices and &#x3b2;-strands in the family 18 chitinase TIM barrel structure, but not associated with the catalytic cleft. The comparative study with fungal ChiJ orthologs identified three regions that display signs of type 1 functional divergence, where unique adaptations in the bacterial and fungal taxa are driven by positive selection.<br><br>CONCLUSIONS: The identified surface-exposed regions of chitinase ChiJ where sequence diversification is driven by positive selection may putatively be related to functional divergence between bacterial and fungal orthologs. These results show that ChiJ orthologs have evolved under different selective constraints following the horizontal gene transfer event.}, }
@article {pmid23093189, year = {2012}, author = {Yue, J and Hu, X and Sun, H and Yang, Y and Huang, J}, title = {Widespread impact of horizontal gene transfer on plant colonization of land.}, journal = {Nature communications}, volume = {3}, number = {}, pages = {1152}, pmid = {23093189}, issn = {2041-1723}, mesh = {Biological Evolution ; Bryopsida/genetics/physiology ; Gene Transfer, Horizontal/*genetics/physiology ; Genes, Plant/genetics/physiology ; Multigene Family/genetics/physiology ; Phylogeny ; Plant Development/genetics/physiology ; Plant Physiological Phenomena/genetics ; Plants/*genetics ; Sequence Alignment ; }, abstract = {In complex multicellular eukaryotes such as animals and plants, horizontal gene transfer is commonly considered rare with very limited evolutionary significance. Here we show that horizontal gene transfer is a dynamic process occurring frequently in the early evolution of land plants. Our genome analyses of the moss Physcomitrella patens identified 57 families of nuclear genes that were acquired from prokaryotes, fungi or viruses. Many of these gene families were transferred to the ancestors of green or land plants. Available experimental evidence shows that these anciently acquired genes are involved in some essential or plant-specific activities such as xylem formation, plant defence, nitrogen recycling as well as the biosynthesis of starch, polyamines, hormones and glutathione. These findings suggest that horizontal gene transfer had a critical role in the transition of plants from aquatic to terrestrial environments. On the basis of these findings, we propose a model of horizontal gene transfer mechanism in nonvascular and seedless vascular plants.}, }
@article {pmid23091803, year = {2012}, author = {Raoult, D and Koonin, EV}, title = {Microbial genomics challenge Darwin.}, journal = {Frontiers in cellular and infection microbiology}, volume = {2}, number = {}, pages = {127}, pmid = {23091803}, issn = {2235-2988}, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; *Genetics, Microbial ; Selection, Genetic ; }, }
@article {pmid23091700, year = {2012}, author = {Skippington, E and Ragan, MA}, title = {Phylogeny rather than ecology or lifestyle biases the construction of Escherichia coli-Shigella genetic exchange communities.}, journal = {Open biology}, volume = {2}, number = {9}, pages = {120112}, pmid = {23091700}, issn = {2046-2441}, mesh = {Computer Simulation ; Ecosystem ; Escherichia coli/*classification/*genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Models, Genetic ; Phylogeny ; Shigella/*classification/*genetics ; }, abstract = {Genetic material can be transmitted not only vertically from parent to offspring, but also laterally (horizontally) from one bacterial lineage to another. Lateral genetic transfer is non-uniform; biases in its nature or frequency construct communities of genetic exchange. These biases have been proposed to arise from phylogenetic relatedness, shared ecology and/or common lifestyle. Here, we test these hypotheses using a graph-based abstraction of inferred genetic-exchange relationships among 27 Escherichia coli and Shigella genomes. We show that although barriers to inter-phylogenetic group lateral transfer are low, E. coli and Shigella are more likely to have exchanged genetic material with close relatives. We find little evidence of bias arising from shared environment or lifestyle. More than one-third of donor-recipient pairs in our analysis show some level of fragmentary gene transfer. Thus, within the E. coli-Shigella clade, intact genes and gene fragments have been disseminated non-uniformly and at appreciable frequency, constructing communities that transgress environmental and lifestyle boundaries.}, }
@article {pmid23091042, year = {2013}, author = {Li, X and Ewis, H and Hice, RH and Malani, N and Parker, N and Zhou, L and Feschotte, C and Bushman, FD and Atkinson, PW and Craig, NL}, title = {A resurrected mammalian hAT transposable element and a closely related insect element are highly active in human cell culture.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {6}, pages = {E478-87}, pmid = {23091042}, issn = {1091-6490}, support = {R01 AI045741/AI/NIAID NIH HHS/United States ; AI45741/AI/NIAID NIH HHS/United States ; GM076425/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; AI52845/AI/NIAID NIH HHS/United States ; R01 AI052845/AI/NIAID NIH HHS/United States ; R01 GM076425/GM/NIGMS NIH HHS/United States ; GM077582/GM/NIGMS NIH HHS/United States ; R01 GM077582/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Binding Sites/genetics ; DNA Transposable Elements/*genetics ; Gene Transfer, Horizontal ; Genes, Insect ; Genetic Engineering ; HeLa Cells ; Humans ; Molecular Sequence Data ; Phylogeny ; Saccharomyces cerevisiae/genetics ; Sequence Homology, Amino Acid ; Species Specificity ; Transposases/metabolism ; Tribolium/genetics ; }, abstract = {Chromosome structure and function are influenced by transposable elements, which are mobile DNA segments that can move from place to place. hAT elements are a superfamily of DNA cut and paste elements that move by excision and integration. We have characterized two hAT elements, TcBuster and Space Invaders (SPIN), that are members of a recently described subfamily of hAT elements called Buster elements. We show that TcBuster, from the red flour beetle Tribolium castaneum, is highly active in human cells. SPIN elements are currently inactive elements that were recently highly active in multiple vertebrate genomes, and the high level of sequence similarity across widely diverged species and patchy phylogenetic distribution suggest that they may have moved between genomes by horizontal transfer. We have generated an intact version of this element, SPIN(ON), which is highly active in human cells. In vitro analysis of TcBuster and SPIN(ON) shows that no proteins other than transposase are essential for recombination, a property that may contribute to the ability of SPIN to successfully invade multiple organisms. We also analyze the target site preferences of de novo insertions in the human genome of TcBuster and SPIN(ON) and compare them with the preferences of Sleeping Beauty and piggyBac, showing that each superfamily has a distinctive pattern of insertion. The high-frequency transposition of both TcBuster and SPIN(ON) suggests that these transposon systems offer powerful tools for genome engineering. Finally, we describe a Saccharomyces cerevisiae assay for TcBuster that will provide a means for isolation of hyperactive and other interesting classes of transposase mutants.}, }
@article {pmid23091024, year = {2012}, author = {Redrejo-Rodríguez, M and Muñoz-Espín, D and Holguera, I and Mencía, M and Salas, M}, title = {Functional eukaryotic nuclear localization signals are widespread in terminal proteins of bacteriophages.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {45}, pages = {18482-18487}, pmid = {23091024}, issn = {1091-6490}, mesh = {Amino Acid Sequence ; Animals ; Bacillus Phages/metabolism ; Bacteriophages/*metabolism ; COS Cells ; Cell Nucleus/metabolism/virology ; Chlorocebus aethiops ; DNA, Viral/metabolism ; Eukaryota/*metabolism ; Gene Transfer, Horizontal ; Models, Biological ; Molecular Sequence Data ; Nuclear Localization Signals/chemistry/*metabolism ; Prokaryotic Cells/virology ; Protein Structure, Tertiary ; Viral Proteins/*chemistry/metabolism ; }, abstract = {A number of prokaryotic proteins have been shown to contain nuclear localization signals (NLSs), although its biological role remains sometimes unclear. Terminal proteins (TPs) of bacteriophages prime DNA replication and become covalently linked to the genome ends. We predicted NLSs within the TPs of bacteriophages from diverse families and hosts and, indeed, the TPs of Φ29, Nf, PRD1, Bam35, and Cp-1, out of seven TPs tested, were found to localize to the nucleus when expressed in mammalian cells. Detailed analysis of Φ29 TP led us to identify a bona fide NLS within residues 1-37. Importantly, gene delivery into the eukaryotic nucleus is enhanced by the presence of Φ29 TP attached to the 5' DNA ends. These findings show a common feature of TPs from diverse bacteriophages targeting the eukaryotic nucleus and suggest a possible common function by facilitating the horizontal transfer of genes between prokaryotes and eukaryotes.}, }
@article {pmid23088190, year = {2012}, author = {Scott, E and Dyer, DW}, title = {Divergence of the SigB regulon and pathogenesis of the Bacillus cereus sensu lato group.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {564}, pmid = {23088190}, issn = {1471-2164}, support = {P20RR016478/RR/NCRR NIH HHS/United States ; }, mesh = {Bacillus/classification/genetics/*pathogenicity ; Bacterial Proteins/*genetics ; Binding Sites ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial ; Multigene Family ; Phylogeny ; *Regulon ; Sigma Factor/*genetics ; }, abstract = {BACKGROUND: The Bacillus cereus sensu lato group currently includes seven species (B. cereus, B. anthracis, B. mycoides, B. pseudomycoides, B. thuringiensis, B. weihenstephanensis and B. cytotoxicus) that recent phylogenetic and phylogenomic analyses suggest are likely a single species, despite their varied phenotypes. Although horizontal gene transfer and insertion-deletion events are clearly important for promoting divergence among these genomes, recent studies have demonstrated that a major basis for phenotypic diversity in these organisms may be differential regulation of the highly similar gene content shared by these organisms. To explore this hypothesis, we used an in silico approach to evaluate the relationship of pathogenic potential and the divergence of the SigB-dependent general stress response within the B. cereus sensu lato group, since SigB has been demonstrated to support pathogenesis in Bacillus, Listeria and Staphylococcus species.<br><br>RESULTS: During the divergence of these organisms from a common "SigB-less" ancestor, the placement of SigB promoters at varied locations in the B. cereus sensu lato genomes predict alternative structures for the SigB regulon in different organisms. Predicted promoter changes suggesting differential transcriptional control of a common gene pool predominate over evidence of indels or horizontal gene transfer for explaining SigB regulon divergence.<br><br>CONCLUSIONS: Four lineages of the SigB regulon have arisen that encompass different gene contents and suggest different strategies for supporting pathogenesis. This is consistent with the hypothesis that divergence within the B. cereus sensu lato group rests in part on alternative strategies for regulation of a common gene pool.}, }
@article {pmid23087842, year = {2012}, author = {Challacombe, J and Kuske, C}, title = {Mobile genetic elements in the bacterial phylum Acidobacteria.}, journal = {Mobile genetic elements}, volume = {2}, number = {4}, pages = {179-183}, pmid = {23087842}, issn = {2159-2543}, abstract = {Analysis of the genome of Candidatus Solibacter usitatus Ellin6076, a member of the phylum Acidobacteria, revealed a large number of genes associated with mobile genetic elements. These genes encoded transposases, insertion sequence elements and phage integrases. When the amino acid sequences of the mobile element-associated genes were compared, many of them had high (90-100%) amino acid sequence identities, suggesting that these genes may have recently duplicated and dispersed throughout the genome. Although phage integrase encoding genes were prevalent in the Can. S. usitatus Ellin6076 genome, no intact prophage regions were found. This suggests that the Can. S. usitatus Ellin6076 large genome arose by horizontal gene transfer via ancient bacteriophage and/or plasmid-mediated transduction, followed by widespread small-scale gene duplications, resulting in an increased number of paralogs encoding traits that could provide selective metabolic, defensive and regulatory advantages in the soil environment. Here we examine the mobile element repertoire of Can. S. usitatus Ellin6076 in comparison to other genomes from the Acidobacteria phylum, reviewing published studies and contributing some new analyses. We also discuss the presence and potential roles of mobile elements in members of this phylum that inhabit a variety of environments.}, }
@article {pmid23087676, year = {2012}, author = {Boyd, ES and Barkay, T}, title = {The mercury resistance operon: from an origin in a geothermal environment to an efficient detoxification machine.}, journal = {Frontiers in microbiology}, volume = {3}, number = {}, pages = {349}, pmid = {23087676}, issn = {1664-302X}, abstract = {Mercuric mercury (Hg[II]) is a highly toxic and mobile element that is likely to have had a pronounced and adverse effect on biology since Earth's oxygenation ∼2.4 billion years ago due to its high affinity for protein sulfhydryl groups, which upon binding destabilize protein structure and decrease enzyme activity, resulting in a decreased organismal fitness. The central enzyme in the microbial mercury detoxification system is the mercuric reductase (MerA) protein, which catalyzes the reduction of Hg(II) to volatile Hg(0). In addition to MerA, mer operons encode for proteins involved in regulation, Hg binding, and organomercury degradation. Mer-mediated approaches have had broad applications in the bioremediation of mercury-contaminated environments and industrial waste streams. Here, we examine the composition of 272 individual mer operons and quantitatively map the distribution of mer-encoded functions on both taxonomic SSU rRNA gene and MerA phylogenies. The results indicate an origin and early evolution of MerA among thermophilic bacteria and an overall increase in the complexity of mer operons through evolutionary time, suggesting continual gene recruitment and evolution leading to an improved efficiency and functional potential of the Mer detoxification system. Consistent with a positive relationship between the evolutionary history and topology of MerA and SSU rRNA gene phylogenies (Mantel R = 0.81, p < 0.01), the distribution of the majority of mer functions, when mapped on these phylograms, indicates an overall tendency to inherit mer-encoded functions through vertical descent. However, individual mer functions display evidence of a variable degree of vertical inheritance, with several genes exhibiting strong evidence for acquisition via lateral gene transfer and/or gene loss. Collectively, these data suggest that (i) mer has evolved from a simple system in geothermal environments to a widely distributed and more complex and efficient detoxification system, and (ii) merA is a suitable biomarker for examining the functional diversity of Hg detoxification and for predicting the composition of mer operons in natural environments.}, }
@article {pmid23086537, year = {2013}, author = {Edrington, TS and Farrow, RL and Hume, ME and Anderson, PN and Hagevoort, GR and Caldwell, DJ and Callaway, TR and Anderson, RC and Nisbet, DJ}, title = {Evaluation of the potential antimicrobial resistance transfer from a multi-drug resistant Escherichia coli to Salmonella in dairy calves.}, journal = {Current microbiology}, volume = {66}, number = {2}, pages = {132-137}, pmid = {23086537}, issn = {1432-0991}, mesh = {Animals ; Cattle ; Disease Models, Animal ; *Drug Resistance, Bacterial ; Escherichia coli/*drug effects/*genetics ; Escherichia coli Infections/microbiology ; Gastrointestinal Tract/microbiology ; *Gene Transfer, Horizontal ; Salmonella/*drug effects/*genetics ; Salmonella Infections, Animal/microbiology ; }, abstract = {Previous research conducted in our laboratory found a significant prevalence of multi-drug resistant (MDR) Salmonella and MDR Escherichia coli (MDR EC) in dairy calves and suggests that the MDR EC population may be an important reservoir for resistance elements that could potentially transfer to Salmonella. Therefore, the objective of the current research was to determine if resistance transfers from MDR EC to susceptible strains of inoculated Salmonella. The experiment utilized Holstein calves (approximately 3 weeks old) naturally colonized with MDR EC and fecal culture negative for Salmonella. Fecal samples were collected for culture of Salmonella and MDR EC throughout the experiment following experimental inoculation with the susceptible Salmonella strains. Results initially suggested that resistance did transfer from the MDR E. coli to the inoculated strains of Salmonella, with these stains demonstrating resistance to multiple antibiotics following in vivo exposure to MDR EC. However, serogrouping and serotyping results from a portion of the Salmonella isolates recovered from the calves post-challenge, identified two new strains of Salmonella; therefore transfer of resistance was not demonstrated under these experimental conditions.}, }
@article {pmid23085995, year = {2013}, author = {Portal-Celhay, C and Nehrke, K and Blaser, MJ}, title = {Effect of Caenorhabditis elegans age and genotype on horizontal gene transfer in intestinal bacteria.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {27}, number = {2}, pages = {760-768}, pmid = {23085995}, issn = {1530-6860}, support = {P40 OD010440/OD/NIH HHS/United States ; R01 GM063270/GM/NIGMS NIH HHS/United States ; R01 GM63270/GM/NIGMS NIH HHS/United States ; }, mesh = {Age Factors ; Animals ; Base Sequence ; Caenorhabditis elegans/*genetics/metabolism/*microbiology ; Caenorhabditis elegans Proteins/genetics ; Conjugation, Genetic ; DNA, Bacterial/genetics ; Escherichia coli/*genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genes, Helminth ; Genotype ; Hydrogen-Ion Concentration ; Intestinal Mucosa/metabolism ; Intestines/*microbiology ; Mutation ; Nerve Tissue Proteins/genetics ; Phosphatidylinositol 3-Kinases/genetics ; Plasmids/genetics ; Random Amplified Polymorphic DNA Technique ; Temperature ; }, abstract = {Horizontal gene transfer (HGT) between bacteria occurs in the intestinal tract of their animal hosts and facilitates both virulence and antibiotic resistance. A model in which both the pathogen and the host are genetically tractable facilitates developing insight into mechanistic processes enabling or restricting the transfer of antibiotic resistance genes. Here we develop an in vivo experimental system to study HGT in bacteria using Caenorhabditis elegans as a model host. Using a thermosensitive conjugative system, we provide evidence that conjugation between two Escherichia coli strains can take place in the intestinal lumen of N2 wild-type worms at a rate of 10(-3) and 10(-2) per donor. We also show that C. elegans age and genotype are important determinants of the frequency of conjugation. Whereas ∼1 transconjugant for every 100 donor cells could be recovered from the intestine of N2 C. elegans, for the age-1 and tol-1 mutants, the detected rate of transconjugation (10(-3) and 10(-4) per donor cell, respectively) was significantly lower. This work demonstrates that increased recombination among lumenal microbial populations is a phenotype associated with host aging, and the model provides a framework to study the dynamics of bacterial horizontal gene transfer within the intestinal environment.}, }
@article {pmid23084774, year = {2012}, author = {Wu, H and Qu, H and Wan, N and Zhang, Z and Hu, S and Yu, J}, title = {Strand-biased gene distribution in bacteria is related to both horizontal gene transfer and strand-biased nucleotide composition.}, journal = {Genomics, proteomics &amp; bioinformatics}, volume = {10}, number = {4}, pages = {186-196}, pmid = {23084774}, issn = {2210-3244}, mesh = {Bacteria/*genetics ; Bacterial Proteins/genetics ; Base Composition ; DNA, Bacterial/chemistry/*genetics ; DNA-Directed DNA Polymerase/genetics ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Genome, Bacterial ; Nucleotides/genetics ; Purines/analysis ; }, abstract = {Although strand-biased gene distribution (SGD) was described some two decades ago, the underlying molecular mechanisms and their relationship remain elusive. Its facets include, but are not limited to, the degree of biases, the strand-preference of genes, and the influence of background nucleotide composition variations. Using a dataset composed of 364 non-redundant bacterial genomes, we sought to illustrate our current understanding of SGD. First, when we divided the collection of bacterial genomes into non-polC and polC groups according to their possession of DnaE isoforms that correlate closely with taxonomy, the SGD of the polC group stood out more significantly than that of the non-polC group. Second, when examining horizontal gene transfer, coupled with gene functional conservation (essentiality) and expressivity (level of expression), we realized that they all contributed to SGD. Third, we further demonstrated a weaker G-dominance on the leading strand of the non-polC group but strong purine dominance (both G and A) on the leading strand of the polC group. We propose that strand-biased nucleotide composition plays a decisive role for SGD since the polC-bearing genomes are not only AT-rich but also have pronounced purine-rich leading strands, and we believe that a special mutation spectrum that leads to a strong purine asymmetry and a strong strand-biased nucleotide composition coupled with functional selections for genes and their functions are both at work.}, }
@article {pmid23084421, year = {2012}, author = {Cornelissen, A and Ceyssens, PJ and Krylov, VN and Noben, JP and Volckaert, G and Lavigne, R}, title = {Identification of EPS-degrading activity within the tail spikes of the novel Pseudomonas putida phage AF.}, journal = {Virology}, volume = {434}, number = {2}, pages = {251-256}, doi = {10.1016/j.virol.2012.09.030}, pmid = {23084421}, issn = {1096-0341}, mesh = {DNA, Viral/chemistry/genetics ; Genome, Viral ; Hydrolysis ; Molecular Sequence Data ; Polysaccharides/*metabolism ; Pseudomonas Phages/*enzymology ; Pseudomonas putida/*virology ; Sequence Analysis, DNA ; Viral Tail Proteins/*metabolism ; }, abstract = {We report the study of phage AF, the first member of the canonical lambdoid phage group infecting Pseudomonas putida. Its 42.6 kb genome is related to the "epsilon15-like viruses" and the "BPP-1-like viruses", a clade of bacteriophages shaped by extensive horizontal gene transfer. The AF virions display exopolysaccharide (EPS)-degrading activity, which originates from the action of the C-terminal domain of the tail spike (Gp19). This protein shows high similarity to the tail spike of the T7-like P. putida-infecting phage φ15. These unrelated phages have an identical host spectrum and EPS degradation characteristics, designating the C-terminal part of Gp19 as sole determinant for these functions. While intact AF particles have biofilm-degrading properties, Gp19 and non-infectious AF particles do not, emphasizing the role of phage amplification in biofilm degradation.}, }
@article {pmid23082760, year = {2013}, author = {Tomasoni, S and Longaretti, L and Rota, C and Morigi, M and Conti, S and Gotti, E and Capelli, C and Introna, M and Remuzzi, G and Benigni, A}, title = {Transfer of growth factor receptor mRNA via exosomes unravels the regenerative effect of mesenchymal stem cells.}, journal = {Stem cells and development}, volume = {22}, number = {5}, pages = {772-780}, pmid = {23082760}, issn = {1557-8534}, mesh = {Acute Kidney Injury/genetics/metabolism ; Adult ; Animals ; Bone Marrow Cells/metabolism ; Cell Communication ; Cell Proliferation ; Cells, Cultured ; *Exosomes ; *Gene Transfer, Horizontal ; Humans ; Insulin-Like Growth Factor I/genetics ; Kidney Tubules, Proximal/metabolism ; Mesenchymal Stem Cells/*physiology ; Mice ; Mice, Inbred C57BL ; RNA Interference ; RNA, Messenger/*genetics ; RNA, Small Interfering ; Receptors, Growth Factor/*genetics ; }, abstract = {Bone marrow-mesenchymal stem cells (BM-MSC) ameliorate renal dysfunction and repair tubular damage of acute kidney injury by locally releasing growth factors, including the insulin-like growth factor-1 (IGF-1). The restricted homing of BM-MSC at the site of injury led us to investigate a possible gene-based communication mechanism between BM-MSC and tubular cells. Human BM-MSC (hBM-MSC) released microparticles and exosomes (Exo) enriched in mRNAs. A selected pattern of transcripts was detected in Exo versus parental cells. Exo expressed the IGF-1 receptor (IGF-1R), but not IGF-1 mRNA, while hBM-MSC contained both mRNAs. R- cells lacking IGF-1R exposed to hBM-MSC-derived Exo acquired the human IGF-1R transcript that was translated in the corresponding protein. Transfer of IGF-1R mRNA from Exo to cisplatin-damaged proximal tubular cells (proximal tubular epithelial cell [PTEC]) increased PTEC proliferation. Coincubation of damaged PTEC with Exo and soluble IGF-1 further enhanced cell proliferation. These findings suggest that horizontal transfer of the mRNA for IGF-1R to tubular cells through Exo potentiates tubular cell sensitivity to locally produced IGF-1 providing a new mechanism underlying the powerful renoprotection of few BM-MSC observed in vivo.}, }
@article {pmid23082106, year = {2012}, author = {Williams, TM and Loman, NJ and Ebruke, C and Musher, DM and Adegbola, RA and Pallen, MJ and Weinstock, GM and Antonio, M}, title = {Genome analysis of a highly virulent serotype 1 strain of Streptococcus pneumoniae from West Africa.}, journal = {PloS one}, volume = {7}, number = {10}, pages = {e26742}, pmid = {23082106}, issn = {1932-6203}, support = {MC_U190074190/MRC_/Medical Research Council/United Kingdom ; U54 HG004968/HG/NHGRI NIH HHS/United States ; U54HG003079/HG/NHGRI NIH HHS/United States ; U54HG004968/HG/NHGRI NIH HHS/United States ; MC_U190081991/MRC_/Medical Research Council/United Kingdom ; U54 HG003079/HG/NHGRI NIH HHS/United States ; }, mesh = {Africa, Western ; Animals ; Bacterial Proteins/genetics/metabolism ; Chromosomes, Bacterial/genetics ; Conserved Sequence/genetics ; Disease Models, Animal ; Female ; Genes, Bacterial/genetics ; Genome, Bacterial/*genetics ; Humans ; Mice ; Polymorphism, Single Nucleotide/genetics ; Prophages/genetics ; Serotyping ; Streptococcal Vaccines/immunology ; Streptococcus pneumoniae/classification/*genetics/isolation &amp; purification/*pathogenicity ; Survival Analysis ; Virulence/genetics ; Virulence Factors/metabolism ; }, abstract = {Streptococcus pneumoniae is a leading cause of pneumonia, meningitis, and bacteremia, estimated to cause 2 million deaths annually. The majority of pneumococcal mortality occurs in developing countries, with serotype 1 a leading cause in these areas. To begin to better understand the larger impact that serotype 1 strains have in developing countries, we characterized virulence and genetic content of PNI0373, a serotype 1 strain from a diseased patient in The Gambia. PNI0373 and another African serotype 1 strain showed high virulence in a mouse intraperitoneal challenge model, with 20% survival at a dose of 1 cfu. The PNI0373 genome sequence was similar in structure to other pneumococci, with the exception of a 100 kb inversion. PNI0373 showed only 15 lineage specific CDS when compared to the pan-genome of pneumococcus. However analysis of non-core orthologs of pneumococcal genomes, showed serotype 1 strains to be closely related. Three regions were found to be serotype 1 associated and likely products of horizontal gene transfer. A detailed inventory of known virulence factors showed that some functions associated with colonization were absent, consistent with the observation that carriage of this highly virulent serotype is unusual. The African serotype 1 strains thus appear to be closely related to each other and different from other pneumococci despite similar genetic content.}, }
@article {pmid23077201, year = {2012}, author = {Christin, PA and Wallace, MJ and Clayton, H and Edwards, EJ and Furbank, RT and Hattersley, PW and Sage, RF and Macfarlane, TD and Ludwig, M}, title = {Multiple photosynthetic transitions, polyploidy, and lateral gene transfer in the grass subtribe Neurachninae.}, journal = {Journal of experimental botany}, volume = {63}, number = {17}, pages = {6297-6308}, pmid = {23077201}, issn = {1460-2431}, mesh = {*Biological Evolution ; Carbon Isotopes/analysis ; Cell Nucleus/genetics ; *Gene Transfer, Horizontal ; Genetic Markers ; Genome Size ; Photosynthesis/*genetics ; Phylogeny ; Plant Leaves/classification/genetics/physiology ; Plastids/genetics ; Poaceae/classification/*genetics/physiology ; *Polyploidy ; }, abstract = {The Neurachninae is the only grass lineage known to contain C(3), C(4), and C(3)-C(4) intermediate species, and as such has been suggested as a model system for studies of photosynthetic pathway evolution in the Poaceae; however, a lack of a robust phylogenetic framework has hindered this possibility. In this study, plastid and nuclear markers were used to reconstruct evolutionary relationships among Neurachninae species. In addition, photosynthetic types were determined with carbon isotope ratios, and genome sizes with flow cytometry. A high frequency of autopolyploidy was found in the Neurachninae, including in Neurachne munroi F.Muell. and Paraneurachne muelleri S.T.Blake, which independently evolved C(4) photosynthesis. Phylogenetic analyses also showed that following their separate C(4) origins, these two taxa exchanged a gene encoding the C(4) form of phosphoenolpyruvate carboxylase. The C(3)-C(4) intermediate Neurachne minor S.T.Blake is phylogenetically distinct from the two C(4) lineages, indicating that intermediacy in this species evolved separately from transitional stages preceding C(4) origins. The Neurachninae shows a substantial capacity to evolve new photosynthetic pathways repeatedly. Enablers of these transitions might include anatomical pre-conditions in the C(3) ancestor, and frequent autopolyploidization. Transfer of key C(4) genetic elements between independently evolved C(4) taxa may have also facilitated a rapid adaptation of photosynthesis in these grasses that had to survive in the harsh climate appearing during the late Pliocene in Australia.}, }
@article {pmid23076327, year = {2012}, author = {Faruque, SM and Mekalanos, JJ}, title = {Phage-bacterial interactions in the evolution of toxigenic Vibrio cholerae.}, journal = {Virulence}, volume = {3}, number = {7}, pages = {556-565}, pmid = {23076327}, issn = {2150-5608}, support = {R01 AI070963/AI/NIAID NIH HHS/United States ; R01 GM068851/GM/NIGMS NIH HHS/United States ; AI070963-01A1/AI/NIAID NIH HHS/United States ; 2R01-GM068851/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteriophages/*genetics ; *Biological Evolution ; Cholera Toxin/*genetics ; Fimbriae Proteins/genetics ; Gene Transfer, Horizontal ; Genomic Islands ; *Host-Parasite Interactions ; Humans ; Prophages/*genetics ; Selection, Genetic ; Vibrio cholerae/*genetics/*virology ; Virulence Factors/genetics ; }, abstract = {Understanding the genetic and ecological factors which support the emergence of new clones of pathogenic bacteria is vital to develop preventive measures. Vibrio cholerae the causative agent of cholera epidemics represents a paradigm for this process in that this organism evolved from environmental non-pathogenic strains by acquisition of virulence genes. The major virulence factors of V. cholerae, cholera toxin (CT) and toxin coregulated pilus (TCP) are encoded by a lysogenic bacteriophage (CTXφ) and a pathogenicity island, respectively. Additional phages which cooperate with the CTXφ in horizontal transfer of genes in V. cholerae have been characterized, and the potential exists for discovering yet new phages or genetic elements which support the transfer of genes for environmental fitness and virulence leading to the emergence of new epidemic strains. Phages have also been shown to play a crucial role in modulating seasonal cholera epidemics. Thus, the complex array of natural phenomena driving the evolution of pathogenic V. cholerae includes, among other factors, phages that either participate in horizontal gene transfer or in a bactericidal selection process favoring the emergence of new clones of V. cholerae.}, }
@article {pmid23074966, year = {2012}, author = {Kozub, NO and Pylypenko, LA and Sozinov, IO and Blium, IaB and Sozinov, OO}, title = {[Genetically modified plants and the problems of plant protection: progress and estimation of potential risks].}, journal = {TSitologiia i genetika}, volume = {46}, number = {4}, pages = {73-86}, pmid = {23074966}, issn = {0564-3783}, mesh = {Agrobacterium tumefaciens/genetics ; Ecology ; Gene Transfer Techniques ; Gene Transfer, Horizontal ; Humans ; Introduced Species ; *Plant Immunity ; Plants/*genetics/immunology ; Plants, Genetically Modified ; Risk ; Transformation, Genetic ; *Transgenes ; }, abstract = {The review deals with advances and prospects in development of transgenic plants. At present virtually all commercial GM crops are those created for solving plant protection problems--they carry transgenes conferring resistance to herbicides, pests, viruses. Approaches employed for development of commercial GM crops with herbicide, pest and virus resistance, as well as strategies and prospects of development of commercial GM plants with resistance to fungal and bacterial diseases and nematodes, are considered. Ecological (including agronomical) and social risks associated with commercial growing of transgenic plants are briefly discussed.}, }
@article {pmid23074963, year = {2012}, author = {Rozhok, AI and Ievdokymenko, KS and Kozeretska, IA}, title = {On the persistence of P element in cultured lineages of Drosophila melanogaster.}, journal = {TSitologiia i genetika}, volume = {46}, number = {4}, pages = {55-58}, pmid = {23074963}, issn = {0564-3783}, mesh = {Animals ; Cell Lineage/*genetics ; Cells, Cultured ; DNA Transposable Elements/*genetics ; Drosophila melanogaster/*genetics ; Female ; Gene Transfer, Horizontal ; *Genome, Insect ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {P transposon is known to have invaded the Drosophila melanogaster genome in the 1950s as a result of horizontal transmission from D. willistoni. Part of the evidence supporting the timing of its invasion comes from analyses of cultured drosophila lineages originating from wild flies cultivated long time in laboratory before analysis. Such analyses have shown that P element was absent from the genomes of cultured lineages established from wild flies caught from the wild before the 1950s. Although the hypothesis of P element transmission has obtained multiple lines of evidence and is beyond doubt today, we decided to test whether analysis of cultured lineages can provide some temporal information on the P element population dynamics. In the present work we demonstrate that P element present the in wild-caught flies may be lost in the cultured fly lineages after some generations. This result is in accordance with the results of at least one published work and suggests that analysis of the cultured fly lineages may sometimes be unreliable in establishing historical trends in P element population dynamics, as the transposon may be occasionally lost, perhaps in the highly inbred lineages in which not all founding females carry it.}, }
@article {pmid23070174, year = {2013}, author = {Del Castillo, CS and Hikima, J and Jang, HB and Nho, SW and Jung, TS and Wongtavatchai, J and Kondo, H and Hirono, I and Takeyama, H and Aoki, T}, title = {Comparative sequence analysis of a multidrug-resistant plasmid from Aeromonas hydrophila.}, journal = {Antimicrobial agents and chemotherapy}, volume = {57}, number = {1}, pages = {120-129}, pmid = {23070174}, issn = {1098-6596}, mesh = {Acinetobacter baumannii/genetics ; Aeromonas hydrophila/drug effects/*genetics/metabolism ; Animals ; Anti-Bacterial Agents/pharmacology ; DNA Transposable Elements ; Drug Resistance, Multiple, Bacterial/drug effects/*genetics ; Fisheries ; Gene Regulatory Networks ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Integrons ; Phylogeny ; Phylogeography ; Plasmids/*chemistry/isolation &amp; purification ; Sequence Analysis, DNA ; Tilapia/microbiology ; beta-Lactamases/*genetics ; }, abstract = {Aeromonas hydrophila is a pathogenic bacterium that has been implicated in fish, animal, and human disease. Recently, a multidrug resistance (MDR) plasmid, pR148, was isolated from A. hydrophila obtained from a tilapia (Oreochromis niloticus) farm in Thailand. pR148 is a 165,906-bp circular plasmid containing 147 coding regions showing highest similarity to pNDM-1_Dok1, an MDR plasmid isolated from a human pathogen. pR148 was also very similar to other IncA/C plasmids isolated from humans, animals, food, and fish. pR148 contains a mercuric resistance operon and encodes the complete set of genes for the type 4 secretion system. pR148 encodes a Tn21 type transposon. This transposon contains the drug resistance genes qacH, bla(OXA-10), aadA1, and sul1 in a class 1 integron; tetA and tetR in transposon Tn1721; and catA2 and a duplicate sul1 in a locus showing 100% similarity to IncU plasmids isolated from fish. The bla(OXA-10) and aadA1 genes showed 100% similarity to those from the Acinetobacter baumannii AYE genome. The similarity of pR148 to a human pathogen-derived plasmid indicates that the plasmids were either transferred between different genera or that they are derived from a common origin. Previous studies have shown that IncA/C plasmids retain a conserved backbone, while the accessory region points to lateral gene transfer. These observations point out the dangers of indiscriminate use of antibiotics in humans and in animals and the necessity of understanding how drug resistance determinants are disseminated and transferred.}, }
@article {pmid23070154, year = {2013}, author = {Bryant, KA and Van Schooneveld, TC and Thapa, I and Bastola, D and Williams, LO and Safranek, TJ and Hinrichs, SH and Rupp, ME and Fey, PD}, title = {KPC-4 Is encoded within a truncated Tn4401 in an IncL/M plasmid, pNE1280, isolated from Enterobacter cloacae and Serratia marcescens.}, journal = {Antimicrobial agents and chemotherapy}, volume = {57}, number = {1}, pages = {37-41}, pmid = {23070154}, issn = {1098-6596}, support = {P20 RR16469/RR/NCRR NIH HHS/United States ; 2P20RR018788-06/RR/NCRR NIH HHS/United States ; U50 CI723775/CI/NCPDCID CDC HHS/United States ; P20 RR016469/RR/NCRR NIH HHS/United States ; P20 RR018788/RR/NCRR NIH HHS/United States ; /ImNIH/Intramural NIH HHS/United States ; 1S10RR027754-01/RR/NCRR NIH HHS/United States ; S10 RR027754/RR/NCRR NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Coinfection ; *DNA Transposable Elements ; Enterobacter cloacae/drug effects/*genetics/isolation &amp; purification ; Enterobacteriaceae Infections/drug therapy/microbiology ; Fatal Outcome ; Female ; *Gene Transfer, Horizontal ; Humans ; Middle Aged ; *Plasmids ; Sequence Analysis, DNA ; Serratia Infections/drug therapy/microbiology ; Serratia marcescens/drug effects/*genetics/isolation &amp; purification ; beta-Lactam Resistance/*genetics ; beta-Lactamases/genetics ; }, abstract = {We describe the transfer of bla(KPC-4) from Enterobacter cloacae to Serratia marcescens in a single patient. DNA sequencing revealed that KPC-4 was encoded on an IncL/M plasmid, pNE1280, closely related to pCTX-M360. Further analysis found that KPC-4 was encoded within a novel Tn4401 element (Tn4401f) containing a truncated tnpA and lacking tnpR, ISKpn7 left, and Tn4401 IRL-1, which are conserved in other Tn4401 transposons. This study highlights the continued evolution of Tn4401 transposons and movement to multiple plasmid backbones that results in acquisition by multiple species of Gram-negative bacilli.}, }
@article {pmid23068075, year = {2012}, author = {Kleiner, M and Petersen, JM and Dubilier, N}, title = {Convergent and divergent evolution of metabolism in sulfur-oxidizing symbionts and the role of horizontal gene transfer.}, journal = {Current opinion in microbiology}, volume = {15}, number = {5}, pages = {621-631}, doi = {10.1016/j.mib.2012.09.003}, pmid = {23068075}, issn = {1879-0364}, mesh = {Animals ; Aquatic Organisms/microbiology/physiology ; Bacteria/*genetics/*metabolism ; Bacterial Physiological Phenomena ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genetic Variation ; Genomics/methods ; Invertebrates/microbiology/physiology ; Metabolic Networks and Pathways/*genetics ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfur Compounds/*metabolism ; Symbiosis ; }, abstract = {Symbioses between marine invertebrates and autotrophic sulfur-oxidizing bacteria have evolved from multiple lineages within the Gammaproteobacteria in a striking example of convergent evolution. These GammaSOX symbionts all perform the same basic function: they provide their hosts with nutrition through the fixation of CO(2) into biomass using reduced sulfur compounds as an energy source. However, our review of recent -omics based studies and genome mining for this study revealed that the GammaSOX symbionts diverge in many other metabolic capabilities and functions, and we show how these divergences could reflect adaptations to different hosts and habitat conditions. Our phylogenetic analyses of key metabolic genes in GammaSOX symbionts revealed that these differed markedly from 16S rRNA phylogenies. We hypothesize that horizontal gene transfer (HGT) would explain many of these incongruencies, and conclude that HGT may have played a significant role in shaping the metabolic evolution of GammaSOX symbionts.}, }
@article {pmid23066170, year = {2012}, author = {Chan, CX and Soares, MB and Bonaldo, MF and Wisecaver, JH and Hackett, JD and Anderson, DM and Erdner, DL and Bhattacharya, D}, title = {ANALYSIS OF ALEXANDRIUM TAMARENSE (DINOPHYCEAE) GENES REVEALS THE COMPLEX EVOLUTIONARY HISTORY OF A MICROBIAL EUKARYOTE().}, journal = {Journal of phycology}, volume = {48}, number = {5}, pages = {1130-1142}, pmid = {23066170}, issn = {0022-3646}, support = {P50 ES012742/ES/NIEHS NIH HHS/United States ; R01 ES013679/ES/NIEHS NIH HHS/United States ; }, abstract = {Microbial eukaryotes may extinguish much of their nuclear phylogenetic history due to endosymbiotic/horizontal gene transfer (E/HGT). We studied E/HGT in 32,110 contigs of expressed sequence tags (ESTs) from the dinoflagellate Alexandrium tamarense (Dinophyceae) using a conservative phylogenomic approach. The vast majority of predicted proteins (86.4%) in this alga are novel or dinoflagellate-specific. We searched for putative homologs of these predicted proteins against a taxonomically broadly sampled protein database that includes all currently available data from algae and protists and reconstructed a phylogeny from each of the putative homologous protein sets. Of the 2,523 resulting phylogenies, 14-17% are potentially impacted by E/HGT involving both prokaryote and eukaryote lineages, with 2-4% showing clear evidence of reticulate evolution. The complex evolutionary histories of the remaining proteins, many of which may also have been affected by E/HGT, cannot be interpreted using our approach with currently available gene data. We present empirical evidence of reticulate genome evolution that combined with inadequate or highly complex phylogenetic signal in many proteins may impede genome-wide approaches to infer the tree of microbial eukaryotes.}, }
@article {pmid23063896, year = {2012}, author = {Igaz, P and Nagy, Z and Vásárhelyi, B and Buzás, E and Falus, A and Rácz, K}, title = {[Potential role for microRNAs in inter-individual and inter-species communication].}, journal = {Orvosi hetilap}, volume = {153}, number = {42}, pages = {1647-1650}, doi = {10.1556/OH.2012.29463}, pmid = {23063896}, issn = {0030-6002}, mesh = {Animals ; Biomarkers/*analysis ; Body Fluids/chemistry ; Gene Expression Regulation ; *Gene Transfer, Horizontal ; Humans ; *MicroRNAs/analysis/metabolism ; Milk, Human/*chemistry ; *RNA Processing, Post-Transcriptional ; }, abstract = {MicroRNAs are major regulators of gene expression at the posttranscriptional level. Besides being detected intracellularly, microRNAs have been found in body fluids, as well. Circulating microRNAs may have hormone like features, since they might affect distant cells as mediators of intercellular communication. MicroRNAs occurring in serum, urine, stool and saliva can be exploited as biomarkers of several diseases, and intensive research efforts are being performed in this field. MicroRNAs are also found in breast milk, and it cannot be excluded that these may act on the baby as a form of inter-individual transfer of epigenetic information. The presence of food-derived microRNAs is even more astonishing, thus plant microRNAs have been detected in the circulation, and these could be functionally active in the human/animal organism. Based on these observations, microRNAs could be involved in the transfer of gene expressional/epigenetic information between different individuals, but also between different species, even cross-kingdom. This microRNA-mediated communication might alter our concepts on the functioning of nature and on the development of diseases, as well.}, }
@article {pmid23063065, year = {2012}, author = {Mazel, D and Mobashery, S}, title = {Antibiotics as physiological stress inducers and bacterial response to the challenge.}, journal = {Current opinion in microbiology}, volume = {15}, number = {5}, pages = {553-554}, doi = {10.1016/j.mib.2012.09.002}, pmid = {23063065}, issn = {1879-0364}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects ; Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Mutation ; Selection, Genetic ; *Stress, Physiological ; }, }
@article {pmid23061022, year = {2012}, author = {Patrick, S and Blakely, GW}, title = {Crossing the eukaryote-prokaryote divide: A ubiquitin homolog in the human commensal bacterium Bacteroides fragilis.}, journal = {Mobile genetic elements}, volume = {2}, number = {3}, pages = {149-151}, pmid = {23061022}, issn = {2159-2543}, abstract = {The resident microbiota of the human gastrointestinal (GI) tract is comprised of ~2000 bacterial species, the majority of which are anaerobes. Colonization of the GI tract is important for normal development of the immune system and provides a reservoir of catabolic enzymes that degrade ingested plant polysaccharides. Bacteroides fragilis is an important member of the microbiota because it contributes to T helper cell development, but is also the most frequently isolated Gram-negative anaerobe from clinical infections. During the annotation of the B. fragilis genome sequence, we identified a gene predicted to encode a homolog of the eukaryotic protein modifier, ubiquitin. Previously, ubiquitin had only been found in eukaryotes, indicating the bacterial acquisition as a potential inter-kingdom horizontal gene transfer event. Here we discuss the possible roles of B. fragilis ubiquitin and the implications for health and disease.}, }
@article {pmid23059975, year = {2012}, author = {Koyanagi, T and Nakagawa, A and Sakurama, H and Yamamoto, K and Sakurai, N and Takagi, Y and Minami, H and Katayama, T and Kumagai, H}, title = {Eukaryotic-type aromatic amino acid decarboxylase from the root colonizer Pseudomonas putida is highly specific for 3,4-dihydroxyphenyl-L-alanine, an allelochemical in the rhizosphere.}, journal = {Microbiology (Reading, England)}, volume = {158}, number = {Pt 12}, pages = {2965-2974}, doi = {10.1099/mic.0.062463-0}, pmid = {23059975}, issn = {1465-2080}, mesh = {Aromatic-L-Amino-Acid Decarboxylases/genetics/isolation &amp; purification/*metabolism ; DNA, Bacterial/chemistry/genetics ; Gene Expression Profiling ; Kinetics ; Levodopa/*metabolism ; Molecular Sequence Data ; Multigene Family ; Pheromones/metabolism ; Plant Roots/microbiology ; Pseudomonas putida/*enzymology/genetics/isolation &amp; purification ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Substrate Specificity ; Transcription, Genetic ; }, abstract = {Aromatic amino acid decarboxylases (AADCs) are found in various organisms and play distinct physiological roles. AADCs from higher eukaryotes have been well studied because they are involved in the synthesis of biologically important molecules such as neurotransmitters and alkaloids. In contrast, bacterial AADCs have received less attention because of their simplicity in physiology and in target substrate (tyrosine). In the present study, we found that Pseudomonas putida KT2440 possesses an AADC homologue (PP_2552) that is more closely related to eukaryotic enzymes than to bacterial enzymes, and determined the genetic and enzymic characteristics of the homologue. The purified enzyme converted 3,4-dihydroxyphenyl-l-alanine (DOPA) to dopamine with K(m) and k(cat) values of 0.092 mM and 1.8 s(-1), respectively. The enzyme was essentially inactive towards other aromatic amino acids such as 5-hydroxy-l-tryptophan, l-phenylalanine, l-tryptophan and l-tyrosine. The observed strict substrate specificity is distinct from that of any AADC characterized so far. The proposed name of this enzyme is DOPA decarboxylase (DDC). Expression of the gene was induced by DOPA, as revealed by quantitative RT-PCR analysis. DDC is encoded in a cluster together with a LysR-type transcriptional regulator and a major facilitator superfamily transporter. This genetic organization is conserved among all sequenced P. putida strains that inhabit the rhizosphere environment, where DOPA acts as a strong allelochemical. These findings suggest the possible involvement of this enzyme in detoxification of the allelochemical in the rhizosphere, and the potential occurrence of a horizontal gene transfer event between the pseudomonad and its host organism.}, }
@article {pmid23059972, year = {2012}, author = {Touchon, M and Charpentier, S and Pognard, D and Picard, B and Arlet, G and Rocha, EP and Denamur, E and Branger, C}, title = {Antibiotic resistance plasmids spread among natural isolates of Escherichia coli in spite of CRISPR elements.}, journal = {Microbiology (Reading, England)}, volume = {158}, number = {Pt 12}, pages = {2997-3004}, doi = {10.1099/mic.0.060814-0}, pmid = {23059972}, issn = {1465-2080}, mesh = {Animals ; DNA, Bacterial/genetics ; *Drug Resistance, Bacterial ; Escherichia coli/*drug effects/*genetics/isolation &amp; purification ; Escherichia coli Infections/microbiology/veterinary ; *Gene Transfer, Horizontal ; Humans ; *Plasmids ; }, abstract = {Clustered, regularly interspaced, short palindromic repeats (CRISPRs) are implicated in defence against foreign DNA in various archaeal and bacterial species. They have also been associated with a slower spread of antibiotic resistance. However, experimental and evolutionary studies raise doubts about the role of CRISPRs as a sort of immune system in Escherichia coli. We studied a collection of 263 natural E. coli isolates from human and animal hosts, representative of the phylogenetic and lifestyle diversity of the species and exhibiting various levels of plasmid-encoded antibiotic resistance. We characterized the strains in terms of CRISPRs, performed replicon typing of the plasmids and tested for class 1 integrons to explore the possible association between CRISPRs and the absence of plasmids and mobile antibiotic resistance determinants. We found no meaningful association between the presence/absence of the cas genes, reflecting the activity of the CRISPRs, and the presence of plasmids, integrons or antibiotic resistance. No CRISPR in the collection contained a spacer that matched an antibiotic resistance gene or element involved in antibiotic resistance gene mobilization, and 79.8% (210/263) of the strains lacked spacers matching sequences in the 2282 plasmid genomes available. Hence, E. coli CRISPRs do not seem to be efficient barriers to the spread of plasmids and antibiotic resistance, consistent with what has been reported for phages, and contrary to reports concerning other species.}, }
@article {pmid23057602, year = {2012}, author = {Spang, A and Poehlein, A and Offre, P and Zumbrägel, S and Haider, S and Rychlik, N and Nowka, B and Schmeisser, C and Lebedeva, EV and Rattei, T and Böhm, C and Schmid, M and Galushko, A and Hatzenpichler, R and Weinmaier, T and Daniel, R and Schleper, C and Spieck, E and Streit, W and Wagner, M}, title = {The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations.}, journal = {Environmental microbiology}, volume = {14}, number = {12}, pages = {3122-3145}, doi = {10.1111/j.1462-2920.2012.02893.x}, pmid = {23057602}, issn = {1462-2920}, support = {I 487/FWF_/Austrian Science Fund FWF/Austria ; P 23000/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Adaptation, Biological/physiology ; Ammonia/*metabolism ; Biological Evolution ; Biological Transport ; Carbon/metabolism ; Chemotaxis/physiology ; Ecosystem ; Energy Metabolism/physiology ; Euryarchaeota/*genetics/*metabolism/ultrastructure ; *Genome, Bacterial ; Metals, Heavy/toxicity ; Oxidation-Reduction ; Phylogeny ; }, abstract = {The cohort of the ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota is a diverse, widespread and functionally important group of microorganisms in many ecosystems. However, our understanding of their biology is still very rudimentary in part because all available genome sequences of this phylum are from members of the Nitrosopumilus cluster. Here we report on the complete genome sequence of Candidatus Nitrososphaera gargensis obtained from an enrichment culture, representing a different evolutionary lineage of AOA frequently found in high numbers in many terrestrial environments. With its 2.83 Mb the genome is much larger than that of other AOA. The presence of a high number of (active) IS elements/transposases, genomic islands, gene duplications and a complete CRISPR/Cas defence system testifies to its dynamic evolution consistent with low degree of synteny with other thaumarchaeal genomes. As expected, the repertoire of conserved enzymes proposed to be required for archaeal ammonia oxidation is encoded by N. gargensis, but it can also use urea and possibly cyanate as alternative ammonia sources. Furthermore, its carbon metabolism is more flexible at the central pyruvate switch point, encompasses the ability to take up small organic compounds and might even include an oxidative pentose phosphate pathway. Furthermore, we show that thaumarchaeota produce cofactor F420 as well as polyhydroxyalkanoates. Lateral gene transfer from bacteria and euryarchaeota has contributed to the metabolic versatility of N. gargensis. This organisms is well adapted to its niche in a heavy metal-containing thermal spring by encoding a multitude of heavy metal resistance genes, chaperones and mannosylglycerate as compatible solute and has the genetic ability to respond to environmental changes by signal transduction via a large number of two-component systems, by chemotaxis and flagella-mediated motility and possibly even by gas vacuole formation. These findings extend our understanding of thaumarchaeal evolution and physiology and offer many testable hypotheses for future experimental research on these nitrifiers.}, }
@article {pmid23055526, year = {2012}, author = {Sukharnikov, LO and Alahuhta, M and Brunecky, R and Upadhyay, A and Himmel, ME and Lunin, VV and Zhulin, IB}, title = {Sequence, structure, and evolution of cellulases in glycoside hydrolase family 48.}, journal = {The Journal of biological chemistry}, volume = {287}, number = {49}, pages = {41068-41077}, pmid = {23055526}, issn = {1083-351X}, mesh = {Cellulase/*chemistry ; Cellulose/chemistry ; Circular Dichroism ; Cloning, Molecular ; Clostridium/enzymology ; Computational Biology/methods ; Conserved Sequence ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genomics ; Glycoside Hydrolases/*chemistry ; Models, Genetic ; Phylogeny ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sequence Analysis, DNA ; Software ; }, abstract = {Currently, the cost of cellulase enzymes remains a key economic impediment to commercialization of biofuels. Enzymes from glycoside hydrolase family 48 (GH48) are a critical component of numerous natural lignocellulose-degrading systems. Although computational mining of large genomic data sets is a promising new approach for identifying novel cellulolytic activities, current computational methods are unable to distinguish between cellulases and enzymes with different substrate specificities that belong to the same protein family. We show that by using a robust computational approach supported by experimental studies, cellulases and non-cellulases can be effectively identified within a given protein family. Phylogenetic analysis of GH48 showed non-monophyletic distribution, an indication of horizontal gene transfer. Enzymatic function of GH48 proteins coded by horizontally transferred genes was verified experimentally, which confirmed that these proteins are cellulases. Computational and structural studies of GH48 enzymes identified structural elements that define cellulases and can be used to computationally distinguish them from non-cellulases. We propose that the structural element that can be used for in silico discrimination between cellulases and non-cellulases belonging to GH48 is an ω-loop located on the surface of the molecule and characterized by highly conserved rare amino acids. These markers were used to screen metagenomics data for "true" cellulases.}, }
@article {pmid23055004, year = {2012}, author = {Qi, X and Pan, Y and Qin, Y and Zu, R and Tang, F and Zhou, M and Wang, H and Song, Y}, title = {Molecular characterization of avian-like H1N1 swine influenza a viruses isolated in Eastern China, 2011.}, journal = {Virologica Sinica}, volume = {27}, number = {5}, pages = {292-298}, pmid = {23055004}, issn = {1995-820X}, mesh = {Amino Acid Substitution ; Animals ; China ; Codon, Nonsense ; Gene Transfer, Horizontal ; Genome, Viral ; Glycosylation ; Hemagglutinin Glycoproteins, Influenza Virus/genetics/metabolism ; Infectious Disease Transmission, Vertical ; Influenza A Virus, H1N1 Subtype/classification/*genetics/*isolation &amp; purification ; Lung/virology ; Orthomyxoviridae Infections/*veterinary/virology ; Phylogeny ; RNA, Viral/genetics ; Sequence Analysis, DNA ; Swine ; Swine Diseases/*virology ; Viral Matrix Proteins/genetics ; Viral Nonstructural Proteins/genetics ; Viral Proteins/genetics ; }, abstract = {Currently, three predominant subtypes of influenza virus are prevalent in pig populations worldwide: H1N1, H3N2, and H1N2. European avian-like H1N1 viruses, which were initially detected in European pig populations in 1979, have been circulating in pigs in eastern China since 2007. In this study, six influenza A viruses were isolated from 60 swine lung samples collected from January to April 2011 in eastern China. Based on whole genome sequencing, molecular characteristics of two isolates were determined. Phylogenetic analysis showed the eight genes of the two isolates were closely related to those of the avian-like H1N1 viruses circulating in pig populations, especially similar to those found in China. Four potential glycosylation sites were observed at positions 13, 26, 198, 277 in the HA1 proteins of the two isolates. Due to the presence of a stop codon at codon 12, the isolates contained truncated PB1-F2 proteins. In this study, the isolates contained 591Q, 627E and 701N in the polymerase subunit PB2, which had been shown to be determinants of virulence and host adaptation. The isolates also had a D rather than E at position 92 of the NS1, a marker of mammalian adaptation. Both isolates contained the GPKV motif at the PDZ ligand domain of the 3' end of the NS1, a characteristic marker of the European avian-like swine viruses since about 1999, which is distinct from those of avian, human and classical swine viruses. The M2 proteins of the isolates have the mutation (S31N), a characteristic marker of the European avian-like swine viruses since about 1987, which may confer resistance to amantadine and rimantadine antivirals. Our findings further emphasize the importance of surveillance on the genetic diversity of influenza A viruses in pigs, and raise more concerns about the occurrence of cross-species transmission events.}, }
@article {pmid23051057, year = {2012}, author = {Park, J and Zhang, Y and Buboltz, AM and Zhang, X and Schuster, SC and Ahuja, U and Liu, M and Miller, JF and Sebaihia, M and Bentley, SD and Parkhill, J and Harvill, ET}, title = {Comparative genomics of the classical Bordetella subspecies: the evolution and exchange of virulence-associated diversity amongst closely related pathogens.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {545}, pmid = {23051057}, issn = {1471-2164}, support = {R01 AI053075/AI/NIAID NIH HHS/United States ; R01 GM083113/GM/NIGMS NIH HHS/United States ; 5R01GM083113/GM/NIGMS NIH HHS/United States ; 098051/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Biological Evolution ; Bordetella/classification/*genetics/*pathogenicity ; Chromosome Mapping ; *Gene Transfer, Horizontal ; Genetic Variation ; *Genome, Bacterial ; Genome-Wide Association Study ; Genomics ; Host Specificity ; Humans ; O Antigens/*genetics ; Pertussis Toxin/*genetics ; Phylogeny ; Polymorphism, Single Nucleotide ; Sheep ; Species Specificity ; Virulence ; Virulence Factors, Bordetella/*genetics ; }, abstract = {BACKGROUND: The classical Bordetella subspecies are phylogenetically closely related, yet differ in some of the most interesting and important characteristics of pathogens, such as host range, virulence and persistence. The compelling picture from previous comparisons of the three sequenced genomes was of genome degradation, with substantial loss of genome content (up to 24%) associated with adaptation to humans.<br><br>RESULTS: For a more comprehensive picture of lineage evolution, we employed comparative genomic and phylogenomic analyses using seven additional diverse, newly sequenced Bordetella isolates. Genome-wide single nucleotide polymorphism (SNP) analysis supports a reevaluation of the phylogenetic relationships between the classical Bordetella subspecies, and suggests a closer link between ovine and human B. parapertussis lineages than has been previously proposed. Comparative analyses of genome content revealed that only 50% of the pan-genome is conserved in all strains, reflecting substantial diversity of genome content in these closely related pathogens that may relate to their different host ranges, virulence and persistence characteristics. Strikingly, these analyses suggest possible horizontal gene transfer (HGT) events in multiple loci encoding virulence factors, including O-antigen and pertussis toxin (Ptx). Segments of the pertussis toxin locus (ptx) and its secretion system locus (ptl) appear to have been acquired by the classical Bordetella subspecies and are divergent in different lineages, suggesting functional divergence in the classical Bordetellae.<br><br>CONCLUSIONS: Together, these observations, especially in key virulence factors, reveal that multiple mechanisms, such as point mutations, gain or loss of genes, as well as HGTs, contribute to the substantial phenotypic diversity of these versatile subspecies in various hosts.}, }
@article {pmid23050224, year = {2012}, author = {Wan, Z and Goddard, NL}, title = {Competition between conjugation and M13 phage infection in Escherichia coli in the absence of selection pressure: a kinetic study.}, journal = {G3 (Bethesda, Md.)}, volume = {2}, number = {10}, pages = {1137-1144}, pmid = {23050224}, issn = {2160-1836}, support = {G12 MD007599/MD/NIMHD NIH HHS/United States ; G12 RR003037/RR/NCRR NIH HHS/United States ; G12-RR-003037/RR/NCRR NIH HHS/United States ; 8-G12-MD-007599/MD/NIMHD NIH HHS/United States ; }, mesh = {Algorithms ; Bacteriophage M13/*physiology ; Computer Simulation ; *Conjugation, Genetic ; Escherichia coli/*genetics/*virology ; Kinetics ; Models, Genetic ; }, abstract = {Inter- and intraspecies horizontal gene transfer enabled by bacterial secretion systems is a powerful mechanism for bacterial genome plasticity. The type IV secretion system of Escherichia coli, encoded by the F plasmid, enables cell-to-cell contact and subsequent DNA transfer known as conjugation. Conjugation is compromised by phage infection that specifically targets the secretion machinery. Hence, the use of phages to regulate the spread of genes, such as acquired antibiotic resistance or as general biosanitation agents, has gained interest. To predict the potential efficacy, the competition kinetics must first be understood. Using quantitative PCR to enumerate genomic loci in a resource-limited batch culture, we quantify the infection kinetics of the nonlytic phage M13 and its impact on conjugation in the absence of selection pressure (isogenic set). Modeling the resulting experimental data reveals the cellular growth rate to be reduced to 60% upon phage infection. We also find a maximum phage infection rate of 3×10(-11) mL phage(-1) min(-1) which is only 1 order of magnitude slower than the maximum conjugation rate (3×10(-10) mL cell(-1) min(-1)), suggesting phages must be in significant abundance to be effective antagonists to horizontal gene transfer. In the regime where the number of susceptible cells (F(+)) and phages are equal upon initial infection, we observe the spread of the conjugative plasmid throughout the cell population despite phage infection, but only at 10% of the uninfected rate. This has interesting evolutionary implications, as even in the absence of selection pressure, cells maintain the ability to conjugate despite phage vulnerability and the associated growth consequences.}, }
@article {pmid23049857, year = {2012}, author = {McNulty, SN and Abubucker, S and Simon, GM and Mitreva, M and McNulty, NP and Fischer, K and Curtis, KC and Brattig, NW and Weil, GJ and Fischer, PU}, title = {Transcriptomic and proteomic analyses of a Wolbachia-free filarial parasite provide evidence of trans-kingdom horizontal gene transfer.}, journal = {PloS one}, volume = {7}, number = {9}, pages = {e45777}, pmid = {23049857}, issn = {1932-6203}, support = {R01 AI081803/AI/NIAID NIH HHS/United States ; T32 AI007172/AI/NIAID NIH HHS/United States ; T32-AI007172/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Brugia malayi ; Conserved Sequence ; Gene Expression Regulation ; *Gene Transfer, Horizontal ; Genome ; Gerbillinae ; Immunohistochemistry/methods ; Mass Spectrometry/methods ; Onchocerca/*microbiology ; Parasites/genetics ; Protein Structure, Tertiary ; Proteomics/*methods ; Symbiosis/genetics ; *Transcription, Genetic ; Transcriptome ; Wolbachia/*genetics ; }, abstract = {Most filarial parasites in the subfamilies Onchocercinae and Dirofilariinae depend on Wolbachia endobacteria to successfully carry out their life cycle. Recently published data indicate that the few Wolbachia-free species in these subfamilies were infected in the distant past and have subsequently shed their endosymbionts. We used an integrated transcriptomic and proteomic analysis of Onchocerca flexuosa to explore the molecular mechanisms that allow worms of this species to survive without a bacterial partner. Roche/454 sequencing of the adult transcriptome produced 16,814 isogroup and 47,252 singleton sequences that are estimated to represent approximately 41% of the complete gene set. Sequences similar to 97 Wolbachia genes were identified from the transcriptome, some of which appear on the same transcripts as sequences similar to nematode genes. Computationally predicted peptides, including those with similarity to Wolbachia proteins, were classified at the domain and pathway levels in order to assess the metabolic capabilities of O. flexuosa and compare against the Wolbachia-dependent model filaria, Brugia malayi. Transcript data further facilitated a shotgun proteomic analysis of O. flexuosa adult worm lysate, resulting in the identification of 1,803 proteins. Three of the peptides detected by mass spectroscopy map to two ABC transport-related proteins from Wolbachia. Antibodies raised to one of the Wolbachia-like peptides labeled a single 38 kDa band on Western blots of O. flexuosa lysate and stained specific worm tissues by immunohistology. Future studies will be required to determine the exact functions of Wolbachia-like peptides and proteins in O. flexuosa and to assess their roles in worm biology.}, }
@article {pmid23049803, year = {2012}, author = {Vegge, CS and Brøndsted, L and Ligowska-Marzęta, M and Ingmer, H}, title = {Natural transformation of Campylobacter jejuni occurs beyond limits of growth.}, journal = {PloS one}, volume = {7}, number = {9}, pages = {e45467}, pmid = {23049803}, issn = {1932-6203}, mesh = {Adenosine Triphosphate/metabolism ; Bacterial Load ; Bacterial Proteins/*genetics/metabolism ; Campylobacter jejuni/*genetics/growth &amp; development/metabolism ; DNA Damage ; DNA, Bacterial/analysis/*genetics ; Electron Transport/genetics ; Endopeptidase Clp/*genetics/metabolism ; *Gene Transfer, Horizontal ; Glycosylation ; Humans ; Kinetics ; Mutation ; Protein Biosynthesis ; *Transformation, Bacterial ; }, abstract = {Campylobacter jejuni is a human bacterial pathogen. While poultry is considered to be a major source of food borne campylobacteriosis, C. jejuni is frequently found in the external environment, and water is another well-known source of human infections. Natural transformation is considered to be one of the main mechanisms for mediating transfer of genetic material and evolution of the organism. Given the diverse habitats of C. jejuni we set out to examine how environmental conditions and physiological processes affect natural transformation of C. jejuni. We show that the efficiency of transformation is correlated to the growth conditions, but more importantly that transformation occurs at growth-restrictive conditions as well as in the late stationary phase; hence revealing that growth per se is not required for C. jejuni to be competent. Yet, natural transformation of C. jejuni is an energy dependent process, that occurs in the absence of transcription but requires an active translational machinery. Moreover, we show the ATP dependent ClpP protease to be important for transformation, which possibly could be associated with reduced protein glycosylation in the ClpP mutant. In contrast, competence of C. jejuni was neither found to be involved in DNA repair following DNA damage nor to provide a growth benefit. Kinetic studies revealed that several transformation events occur per cell cycle indicating that natural transformation of C. jejuni is a highly efficient process. Thus, our findings suggest that horizontal gene transfer by natural transformation takes place in various habitats occupied by C. jejuni.}, }
@article {pmid23049536, year = {2012}, author = {Lurie-Weinberger, MN and Peeri, M and Tuller, T and Gophna, U}, title = {Extensive Inter-Domain Lateral Gene Transfer in the Evolution of the Human Commensal Methanosphaera stadtmanae.}, journal = {Frontiers in genetics}, volume = {3}, number = {}, pages = {182}, pmid = {23049536}, issn = {1664-8021}, abstract = {Methanosphaera stadtmanae is a commensal methanogenic archaeon found in the human gut. As most of its niche-neighbors are bacteria, it is expected that lateral gene transfer (LGT) from bacteria might have contributed to the evolutionary history of this organism. We performed a phylogenomic survey of putative LGT events in M. stadtmanae, using a phylogenetic pipeline. Our analysis indicates that a substantial fraction of the proteins of M. stadtmanae are inferred to have been involved in inter-domain LGT. Laterally acquired genes have had a large contribution to surface functions, by providing novel glycosyltransferase functions. In addition, several ABC transporters seem to be of bacterial origin, including the molybdate transporter. Thus, bacterial genes contributed to the adaptation of M. stadtmanae to a host-dependent lifestyle by allowing a larger variation in surface structures and increasing transport efficiency in the gut niche which is diverse and competitive.}, }
@article {pmid23046950, year = {2012}, author = {Dufour, YS and Donohue, TJ}, title = {Signal correlations in ecological niches can shape the organization and evolution of bacterial gene regulatory networks.}, journal = {Advances in microbial physiology}, volume = {61}, number = {}, pages = {1-36}, pmid = {23046950}, issn = {2162-5468}, support = {R01 GM075273/GM/NIGMS NIH HHS/United States ; GM075273/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*genetics/*metabolism ; Bacterial Proteins/genetics/*metabolism ; *Evolution, Molecular ; Gene Expression Regulation, Bacterial ; *Gene Regulatory Networks ; *Signal Transduction ; Transcription Factors/genetics/*metabolism ; }, abstract = {Transcriptional regulation plays a significant role in the biological response of bacteria to changing environmental conditions. Therefore, mapping transcriptional regulatory networks is an important step not only in understanding how bacteria sense and interpret their environment but also to identify the functions involved in biological responses to specific conditions. Recent experimental and computational developments have facilitated the characterization of regulatory networks on a genome-wide scale in model organisms. In addition, the multiplication of complete genome sequences has encouraged comparative analyses to detect conserved regulatory elements and infer regulatory networks in other less well-studied organisms. However, transcription regulation appears to evolve rapidly, thus, creating challenges for the transfer of knowledge to nonmodel organisms. Nevertheless, the mechanisms and constraints driving the evolution of regulatory networks have been the subjects of numerous analyses, and several models have been proposed. Overall, the contributions of mutations, recombination, and horizontal gene transfer are complex. Finally, the rapid evolution of regulatory networks plays a significant role in the remarkable capacity of bacteria to adapt to new or changing environments. Conversely, the characteristics of environmental niches determine the selective pressures and can shape the structure of regulatory network accordingly.}, }
@article {pmid23046409, year = {2012}, author = {Kidane, D and Ayora, S and Sweasy, JB and Graumann, PL and Alonso, JC}, title = {The cell pole: the site of cross talk between the DNA uptake and genetic recombination machinery.}, journal = {Critical reviews in biochemistry and molecular biology}, volume = {47}, number = {6}, pages = {531-555}, pmid = {23046409}, issn = {1549-7798}, support = {K01 CA154854/CA/NCI NIH HHS/United States ; K01 CA15485401A/CA/NCI NIH HHS/United States ; }, mesh = {Bacillus subtilis/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Cytosol/metabolism ; DNA/*metabolism ; DNA Repair ; DNA Replication ; *DNA Transformation Competence ; DNA, Single-Stranded/*metabolism ; DNA-Binding Proteins/genetics/metabolism ; Gene Transfer, Horizontal ; Plasmids ; Rec A Recombinases/genetics/metabolism ; *Recombination, Genetic ; }, abstract = {Natural transformation is a programmed mechanism characterized by binding of free double-stranded (ds) DNA from the environment to the cell pole in rod-shaped bacteria. In Bacillus subtilis some competence proteins, which process the dsDNA and translocate single-stranded (ss) DNA into the cytosol, recruit a set of recombination proteins mainly to one of the cell poles. A subset of single-stranded binding proteins, working as "guardians", protects ssDNA from degradation and limit the RecA recombinase loading. Then, the "mediators" overcome the inhibitory role of guardians, and recruit RecA onto ssDNA. A RecA·ssDNA filament searches for homology on the chromosome and, in a process that is controlled by "modulators", catalyzes strand invasion with the generation of a displacement loop (D-loop). A D-loop resolvase or "resolver" cleaves this intermediate, limited DNA replication restores missing information and a DNA ligase seals the DNA ends. However, if any step fails, the "rescuers" will repair the broken end to rescue chromosomal transformation. If the ssDNA does not share homology with resident DNA, but it contains information for autonomous replication, guardian and mediator proteins catalyze plasmid establishment after inhibition of RecA. DNA replication and ligation reconstitute the molecule (plasmid transformation). In this review, the interacting network that leads to a cross talk between proteins of the uptake and genetic recombination machinery will be placed into prospective.}, }
@article {pmid23046150, year = {2013}, author = {Amábile-Cuevas, CF}, title = {Antibiotic resistance: from Darwin to Lederberg to Keynes.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {19}, number = {2}, pages = {73-87}, doi = {10.1089/mdr.2012.0115}, pmid = {23046150}, issn = {1931-8448}, mesh = {Anti-Bacterial Agents/*pharmacology/therapeutic use ; Bacterial Infections/drug therapy/microbiology ; Biological Evolution ; DNA Transposable Elements ; Drug Resistance, Multiple, Bacterial/drug effects/*genetics ; Gene Transfer, Horizontal ; Gram-Negative Bacteria/drug effects/*genetics/metabolism ; Gram-Positive Bacteria/drug effects/*genetics/metabolism ; Humans ; Selection, Genetic/drug effects/genetics ; }, abstract = {The emergence and spread of antibiotic-resistant bacteria reflects both, a gradual, completely Darwinian evolution, which mostly yields slight decreases in antibiotic susceptibility, along with phenotypes that are not precisely characterized as "resistance"; and sudden changes, from full susceptibility to full resistance, which are driven by a vast array of horizontal gene transfer mechanisms. Antibiotics select for more than just antibiotic resistance (i.e., increased virulence and enhanced gene exchange abilities); and many non-antibiotic agents or conditions select for or maintain antibiotic resistance traits as a result of a complex network of underlying and often overlapping mechanisms. Thus, the development of new antibiotics and thoughtful, integrated anti-infective strategies is needed to address the immediate and long-term threat of antibiotic resistance. Since the biology of resistance is complex, these new drugs and strategies will not come from free-market forces, or from "incentives" for pharmaceutical companies.}, }
@article {pmid23043116, year = {2012}, author = {Szöllosi, GJ and Boussau, B and Abby, SS and Tannier, E and Daubin, V}, title = {Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {43}, pages = {17513-17518}, pmid = {23043116}, issn = {1091-6490}, mesh = {*Gene Transfer, Horizontal ; Likelihood Functions ; *Models, Genetic ; *Phylogeny ; *Species Specificity ; }, abstract = {The timing of the evolution of microbial life has largely remained elusive due to the scarcity of prokaryotic fossil record and the confounding effects of the exchange of genes among possibly distant species. The history of gene transfer events, however, is not a series of individual oddities; it records which lineages were concurrent and thus provides information on the timing of species diversification. Here, we use a probabilistic model of genome evolution that accounts for differences between gene phylogenies and the species tree as series of duplication, transfer, and loss events to reconstruct chronologically ordered species phylogenies. Using simulations we show that we can robustly recover accurate chronologically ordered species phylogenies in the presence of gene tree reconstruction errors and realistic rates of duplication, transfer, and loss. Using genomic data we demonstrate that we can infer rooted species phylogenies using homologous gene families from complete genomes of 10 bacterial and archaeal groups. Focusing on cyanobacteria, distinguished among prokaryotes by a relative abundance of fossils, we infer the maximum likelihood chronologically ordered species phylogeny based on 36 genomes with 8,332 homologous gene families. We find the order of speciation events to be in full agreement with the fossil record and the inferred phylogeny of cyanobacteria to be consistent with the phylogeny recovered from established phylogenomics methods. Our results demonstrate that lateral gene transfers, detected by probabilistic models of genome evolution, can be used as a source of information on the timing of evolution, providing a valuable complement to the limited prokaryotic fossil record.}, }
@article {pmid23042997, year = {2012}, author = {Tripathi, VN and Harding, WC and Willingham-Lane, JM and Hondalus, MK}, title = {Conjugal transfer of a virulence plasmid in the opportunistic intracellular actinomycete Rhodococcus equi.}, journal = {Journal of bacteriology}, volume = {194}, number = {24}, pages = {6790-6801}, pmid = {23042997}, issn = {1098-5530}, support = {R01 AI060469/AI/NIAID NIH HHS/United States ; }, mesh = {Actinomycetales Infections/microbiology/pathology/veterinary ; Animals ; Bacterial Proteins/genetics ; *Conjugation, Genetic ; DNA, Bacterial/genetics ; Deoxyribonucleases/metabolism ; Gene Transfer, Horizontal ; Horse Diseases/microbiology ; Horses ; Macrophages/microbiology ; Plasmids/*genetics ; Rhodococcus equi/*genetics/*pathogenicity ; Sequence Analysis, DNA ; }, abstract = {Rhodococcus equi is a facultative intracellular, Gram-positive, soilborne actinomycete which can cause severe pyogranulomatous pneumonia with abscessation in young horses (foals) and in immunocompromised people, such as persons with AIDS. All strains of R. equi isolated from foals and approximately a third isolated from humans contain a large, ~81-kb plasmid which is essential for the intramacrophage growth of the organism and for virulence in foals and murine in vivo model systems. We found that the entire virulence plasmid could be transferred from plasmid-containing strains of R. equi (donor) to plasmid-free R. equi strains (recipient) at a high frequency and that plasmid transmission reestablished the capacity for intracellular growth in macrophages. Plasmid transfer required living cells and cell-to-cell contact and was unaffected by the presence of DNase, factors pointing to conjugation as the major means of genetic transfer. Deletion of a putative relaxase-encoding gene, traA, located in the proposed conjugative region of the plasmid, abolished plasmid transfer. Reversion of the traA mutation restored plasmid transmissibility. Finally, plasmid transmission to other Rhodococcus species and some additional related organisms was demonstrated. This is the first study showing a virulence plasmid transfer in R. equi, and it establishes a mechanism by which the virulence plasmid can move among bacteria in the soil.}, }
@article {pmid23042564, year = {2012}, author = {Armbruster, CE and Mobley, HL}, title = {Merging mythology and morphology: the multifaceted lifestyle of Proteus mirabilis.}, journal = {Nature reviews. Microbiology}, volume = {10}, number = {11}, pages = {743-754}, pmid = {23042564}, issn = {1740-1534}, support = {AI59722/AI/NIAID NIH HHS/United States ; DK94777/DK/NIDDK NIH HHS/United States ; F32 AI102552/AI/NIAID NIH HHS/United States ; AI43363/AI/NIAID NIH HHS/United States ; R01 AI059722/AI/NIAID NIH HHS/United States ; R56 AI043363/AI/NIAID NIH HHS/United States ; R01 AI043363/AI/NIAID NIH HHS/United States ; R01 DK094777/DK/NIDDK NIH HHS/United States ; F32AI102552/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Adhesion ; Bacterial Proteins/metabolism ; Bacterial Secretion Systems/physiology ; Catheter-Related Infections/microbiology ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Humans ; Immune Evasion ; Proteus Infections/*microbiology ; Proteus mirabilis/genetics/*pathogenicity/*physiology ; Urinary Tract Infections/*microbiology ; Virulence Factors/metabolism ; }, abstract = {Proteus mirabilis, named for the Greek god who changed shape to avoid capture, has fascinated microbiologists for more than a century with its unique swarming differentiation, Dienes line formation and potent urease activity. Transcriptome profiling during both host infection and swarming motility, coupled with the availability of the complete genome sequence for P. mirabilis, has revealed the occurrence of interbacterial competition and killing through a type VI secretion system, and the reciprocal regulation of adhesion and motility, as well as the intimate connections between metabolism, swarming and virulence. This Review addresses some of the unique and recently described aspects of P. mirabilis biology and pathogenesis, and emphasizes the potential role of this bacterium in single-species and polymicrobial urinary tract infections.}, }
@article {pmid23039906, year = {2012}, author = {Merlo, MA and Cross, I and Palazón, JL and Ubeda-Manzanaro, M and Sarasquete, C and Rebordinos, L}, title = {Evidence for 5S rDNA horizontal transfer in the toadfish Halobatrachus didactylus (Schneider, 1801) based on the analysis of three multigene families.}, journal = {BMC evolutionary biology}, volume = {12}, number = {}, pages = {201}, pmid = {23039906}, issn = {1471-2148}, mesh = {Animals ; Base Sequence ; Batrachoidiformes/*genetics ; DNA, Ribosomal/chemistry/classification/*genetics ; DNA, Ribosomal Spacer/chemistry/classification/genetics ; Electrophoresis, Agar Gel ; *Gene Transfer, Horizontal ; In Situ Hybridization, Fluorescence ; Molecular Sequence Data ; *Multigene Family ; Perciformes/genetics ; Phylogeny ; RNA, Ribosomal, 5S/*genetics ; RNA, Small Nuclear/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {BACKGROUND: The Batrachoididae family is a group of marine teleosts that includes several species with more complicated physiological characteristics, such as their excretory, reproductive, cardiovascular and respiratory systems. Previous studies of the 5S rDNA gene family carried out in four species from the Western Atlantic showed two types of this gene in two species but only one in the other two, under processes of concerted evolution and birth-and-death evolution with purifying selection. Here we present results of the 5S rDNA and another two gene families in Halobatrachus didactylus, an Eastern Atlantic species, and draw evolutionary inferences regarding the gene families. In addition we have also mapped the genes on the chromosomes by two-colour fluorescence in situ hybridization (FISH).<br><br>RESULTS: Two types of 5S rDNA were observed, named type &#x3b1; and type &#x3b2;. Molecular analysis of the 5S rDNA indicates that H. didactylus does not share the non-transcribed spacer (NTS) sequences with four other species of the family; therefore, it must have evolved in isolation. Amplification with the type &#x3b2; specific primers amplified a specific band in 9 specimens of H. didactylus and two of Sparus aurata. Both types showed regulatory regions and a secondary structure which mark them as functional genes. However, the U2 snRNA gene and the ITS-1 sequence showed one electrophoretic band and with one type of sequence. The U2 snRNA sequence was the most variable of the three multigene families studied. Results from two-colour FISH showed no co-localization of the gene coding from three multigene families and provided the first map of the chromosomes of the species.<br><br>CONCLUSIONS: A highly significant finding was observed in the analysis of the 5S rDNA, since two such distant species as H. didactylus and Sparus aurata share a 5S rDNA type. This 5S rDNA type has been detected in other species belonging to the Batrachoidiformes and Perciformes orders, but not in the Pleuronectiformes and Clupeiformes orders. Two hypotheses have been outlined: one is the possible vertical permanence of the shared type in some fish lineages, and the other is the possibility of a horizontal transference event between ancient species of the Perciformes and Batrachoidiformes orders. This finding opens a new perspective in fish evolution and in the knowledge of the dynamism of the 5S rDNA. Cytogenetic analysis allowed some evolutionary trends to be roughed out, such as the progressive change in the U2 snDNA and the organization of (GATA)n repeats, from dispersed to localized in one locus. The accumulation of (GATA)n repeats in one chromosome pair could be implicated in the evolution of a pair of proto-sex chromosomes. This possibility could situate H. didactylus as the most highly evolved of the Batrachoididae family in terms of sex chromosome biology.}, }
@article {pmid23036836, year = {2013}, author = {Azad, RK and Li, J}, title = {Interpreting genomic data via entropic dissection.}, journal = {Nucleic acids research}, volume = {41}, number = {1}, pages = {e23}, pmid = {23036836}, issn = {1362-4962}, support = {R01-GM078092/GM/NIGMS NIH HHS/United States ; R01-LM008991/LM/NLM NIH HHS/United States ; }, mesh = {Bayes Theorem ; Cell Line, Tumor ; Cluster Analysis ; DNA Copy Number Variations ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Genome, Bacterial ; Genomics/*methods ; Humans ; Neoplasms/genetics ; Salmonella typhi/genetics ; }, abstract = {Since the emergence of high-throughput genome sequencing platforms and more recently the next-generation platforms, the genome databases are growing at an astronomical rate. Tremendous efforts have been invested in recent years in understanding intriguing complexities beneath the vast ocean of genomic data. This is apparent in the spurt of computational methods for interpreting these data in the past few years. Genomic data interpretation is notoriously difficult, partly owing to the inherent heterogeneities appearing at different scales. Methods developed to interpret these data often suffer from their inability to adequately measure the underlying heterogeneities and thus lead to confounding results. Here, we present an information entropy-based approach that unravels the distinctive patterns underlying genomic data efficiently and thus is applicable in addressing a variety of biological problems. We show the robustness and consistency of the proposed methodology in addressing three different biological problems of significance--identification of alien DNAs in bacterial genomes, detection of structural variants in cancer cell lines and alignment-free genome comparison.}, }
@article {pmid23036091, year = {2012}, author = {Yutin, N and Koonin, EV}, title = {Proteorhodopsin genes in giant viruses.}, journal = {Biology direct}, volume = {7}, number = {}, pages = {34}, pmid = {23036091}, issn = {1745-6150}, mesh = {Amino Acid Sequence ; Gene Transfer, Horizontal ; Haptophyta/genetics/metabolism/virology ; Molecular Sequence Data ; Phycodnaviridae/chemistry/*genetics/metabolism ; Phylogeny ; Rhodopsin/chemistry/*genetics ; Rhodopsins, Microbial ; Sequence Alignment ; Sequence Analysis, Protein ; Viral Proteins/chemistry/*genetics ; }, abstract = {Viruses with large genomes encode numerous proteins that do not directly participate in virus biogenesis but rather modify key functional systems of infected cells. We report that a distinct group of giant viruses infecting unicellular eukaryotes that includes Organic Lake Phycodnaviruses and Phaeocystis globosa virus encode predicted proteorhodopsins that have not been previously detected in viruses. Search of metagenomic sequence data shows that putative viral proteorhodopsins are extremely abundant in marine environments. Phylogenetic analysis suggests that giant viruses acquired proteorhodopsins via horizontal gene transfer from proteorhodopsin-encoding protists although the actual donor(s) could not be presently identified. The pattern of conservation of the predicted functionally important amino acid residues suggests that viral proteorhodopsin homologs function as sensory rhodopsins. We hypothesize that viral rhodopsins modulate light-dependent signaling, in particular phototaxis, in infected protists.}, }
@article {pmid23035839, year = {2012}, author = {Kurre, R and Höne, A and Clausen, M and Meel, C and Maier, B}, title = {PilT2 enhances the speed of gonococcal type IV pilus retraction and of twitching motility.}, journal = {Molecular microbiology}, volume = {86}, number = {4}, pages = {857-865}, doi = {10.1111/mmi.12022}, pmid = {23035839}, issn = {1365-2958}, mesh = {Fimbriae Proteins/genetics/*metabolism ; Fimbriae, Bacterial/*metabolism ; Gene Knockout Techniques ; *Locomotion ; Neisseria gonorrhoeae/genetics/metabolism/*physiology ; }, abstract = {Type IV pilus (T4P) dynamics is important for various bacterial functions including host cell interaction, surface motility, and horizontal gene transfer. T4P retract rapidly by depolymerization, generating large mechanical force. The gene that encodes the pilus retraction ATPase PilT has multiple paralogues, whose number varies between different bacterial species, but their role in regulating physical parameters of T4P dynamics remains unclear. Here, we address this question in the human pathogen Neisseria gonorrhoeae, which possesses two pilT paralogues, namely pilT2 and pilU. We show that the speed of twitching motility is strongly reduced in a pilT2 deletion mutant, while directional persistence time and sensitivity of speed to oxygen are unaffected. Using laser tweezers, we found that the speed of single T4P retraction was reduced by a factor of ≈ 2 in a pilT2 deletion strain, whereas pilU deletion showed a minor effect. The maximum force and the probability for switching from retraction to elongation under application of high force were not significantly affected. We conclude that the physical parameters of T4P are fine-tuned through PilT2.}, }
@article {pmid23035691, year = {2012}, author = {Broadbent, JR and Neeno-Eckwall, EC and Stahl, B and Tandee, K and Cai, H and Morovic, W and Horvath, P and Heidenreich, J and Perna, NT and Barrangou, R and Steele, JL}, title = {Analysis of the Lactobacillus casei supragenome and its influence in species evolution and lifestyle adaptation.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {533}, pmid = {23035691}, issn = {1471-2164}, mesh = {Adaptation, Physiological/*genetics ; *Biological Evolution ; Cluster Analysis ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomic Islands ; Lacticaseibacillus casei/*genetics ; Phylogeny ; }, abstract = {BACKGROUND: The broad ecological distribution of L. casei makes it an insightful subject for research on genome evolution and lifestyle adaptation. To explore evolutionary mechanisms that determine genomic diversity of L. casei, we performed comparative analysis of 17 L. casei genomes representing strains collected from dairy, plant, and human sources.<br><br>RESULTS: Differences in L. casei genome inventory revealed an open pan-genome comprised of 1,715 core and 4,220 accessory genes. Extrapolation of pan-genome data indicates L. casei has a supragenome approximately 3.2 times larger than the average genome of individual strains. Evidence suggests horizontal gene transfer from other bacterial species, particularly lactobacilli, has been important in adaptation of L. casei to new habitats and lifestyles, but evolution of dairy niche specialists also appears to involve gene decay.<br><br>CONCLUSIONS: Genome diversity in L. casei has evolved through gene acquisition and decay. Acquisition of foreign genomic islands likely confers a fitness benefit in specific habitats, notably plant-associated niches. Loss of unnecessary ancestral traits in strains collected from bacterial-ripened cheeses supports the hypothesis that gene decay contributes to enhanced fitness in that niche. This study gives the first evidence for a L. casei supragenome and provides valuable insights into mechanisms for genome evolution and lifestyle adaptation of this ecologically flexible and industrially important lactic acid bacterium. Additionally, our data confirm the Distributed Genome Hypothesis extends to non-pathogenic, ecologically flexible species like L. casei.}, }
@article {pmid23035642, year = {2012}, author = {Franzén, O and Talavera-López, C and Ochaya, S and Butler, CE and Messenger, LA and Lewis, MD and Llewellyn, MS and Marinkelle, CJ and Tyler, KM and Miles, MA and Andersson, B}, title = {Comparative genomic analysis of human infective Trypanosoma cruzi lineages with the bat-restricted subspecies T. cruzi marinkellei.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {531}, pmid = {23035642}, issn = {1471-2164}, mesh = {Acetyltransferases/genetics ; Animals ; Chagas Disease/parasitology ; Chiroptera/*parasitology ; Computational Biology ; DNA Copy Number Variations ; DNA, Protozoan/genetics ; Genetic Linkage ; Humans ; Retroelements/genetics ; Trypanosoma/classification/*genetics ; Trypanosoma cruzi/classification/*genetics ; }, abstract = {BACKGROUND: Trypanosoma cruzi marinkellei is a bat-associated parasite of the subgenus Schizotrypanum and it is regarded as a T. cruzi subspecies. Here we report a draft genome sequence of T. c. marinkellei and comparison with T. c. cruzi. Our aims were to identify unique sequences and genomic features, which may relate to their distinct niches.<br><br>RESULTS: The T. c. marinkellei genome was found to be ~11% smaller than that of the human-derived parasite T. c. cruzi Sylvio X10. The genome size difference was attributed to copy number variation of coding and non-coding sequences. The sequence divergence in coding regions was ~7.5% between T. c. marinkellei and T. c. cruzi Sylvio X10. A unique acetyltransferase gene was identified in T. c. marinkellei, representing an example of a horizontal gene transfer from eukaryote to eukaryote. Six of eight examined gene families were expanded in T. c. cruzi Sylvio X10. The DGF gene family was expanded in T. c. marinkellei. T. c. cruzi Sylvio X10 contained ~1.5 fold more sequences related to VIPER and L1Tc elements. Experimental infections of mammalian cell lines indicated that T. c. marinkellei has the capacity to invade non-bat cells and undergo intracellular replication.<br><br>CONCLUSIONS: Several unique sequences were identified in the comparison, including a potential subspecies-specific gene acquisition in T. c. marinkellei. The identified differences reflect the distinct evolutionary trajectories of these parasites and represent targets for functional investigation.}, }
@article {pmid23033934, year = {2012}, author = {Moktali, V and Park, J and Fedorova-Abrams, ND and Park, B and Choi, J and Lee, YH and Kang, S}, title = {Systematic and searchable classification of cytochrome P450 proteins encoded by fungal and oomycete genomes.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {525}, pmid = {23033934}, issn = {1471-2164}, mesh = {Cluster Analysis ; Cytochrome P-450 Enzyme System/classification/*genetics ; Databases, Protein ; Evolution, Molecular ; Fungi/*genetics/metabolism ; *Genome ; Genome, Fungal ; Models, Genetic ; Oomycetes/*genetics/metabolism ; Phylogeny ; }, abstract = {BACKGROUND: Cytochrome P450 proteins (CYPs) play diverse and pivotal roles in fungal metabolism and adaptation to specific ecological niches. Fungal genomes encode extremely variable "CYPomes" ranging from one to more than 300 CYPs. Despite the rapid growth of sequenced fungal and oomycete genomes and the resulting influx of predicted CYPs, the vast majority of CYPs remain functionally uncharacterized. To facilitate the curation and functional and evolutionary studies of CYPs, we previously developed Fungal Cytochrome P450 Database (FCPD), which included CYPs from 70 fungal and oomycete species. Here we present a new version of FCPD (1.2) with more data and an improved classification scheme.<br><br>RESULTS: The new database contains 22,940 CYPs from 213 species divided into 2,579 clusters and 115 clans. By optimizing the clustering pipeline, we were able to uncover 36 novel clans and to assign 153 orphan CYP families to specific clans. To augment their functional annotation, CYP clusters were mapped to David Nelson's P450 databases, which archive a total of 12,500 manually curated CYPs. Additionally, over 150 clusters were functionally classified based on sequence similarity to experimentally characterized CYPs. Comparative analysis of fungal and oomycete CYPomes revealed cases of both extreme expansion and contraction. The most dramatic expansions in fungi were observed in clans CYP58 and CYP68 (Pezizomycotina), clans CYP5150 and CYP63 (Agaricomycotina), and family CYP509 (Mucoromycotina). Although much of the extraordinary diversity of the pan-fungal CYPome can be attributed to gene duplication and adaptive divergence, our analysis also suggests a few potential horizontal gene transfer events. Updated families and clans can be accessed through the new version of the FCPD database.<br><br>CONCLUSIONS: FCPD version 1.2 provides a systematic and searchable catalogue of 9,550 fungal CYP sequences (292 families) encoded by 108 fungal species and 147 CYP sequences (9 families) encoded by five oomycete species. In comparison to the first version, it offers a more comprehensive clan classification, is fully compatible with Nelson's P450 databases, and has expanded functional categorization. These features will facilitate functional annotation and classification of CYPs encoded by newly sequenced fungal and oomycete genomes. Additionally, the classification system will aid in studying the roles of CYPs in the evolution of fungal adaptation to specific ecological niches.}, }
@article {pmid23033473, year = {2012}, author = {Jorth, P and Whiteley, M}, title = {An evolutionary link between natural transformation and CRISPR adaptive immunity.}, journal = {mBio}, volume = {3}, number = {5}, pages = {}, pmid = {23033473}, issn = {2150-7511}, support = {F31 DE021633/DE/NIDCR NIH HHS/United States ; R01 DE020100/DE/NIDCR NIH HHS/United States ; 5F31DE021633-02/DE/NIDCR NIH HHS/United States ; 1R01DE020100/DE/NIDCR NIH HHS/United States ; }, mesh = {*DNA Transformation Competence ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; Genome, Bacterial ; *Host Specificity ; Pasteurellaceae/*genetics/*physiology ; *Recombination, Genetic ; *Transformation, Genetic ; }, abstract = {UNLABELLED: Natural transformation by competent bacteria is a primary means of horizontal gene transfer; however, evidence that competence drives bacterial diversity and evolution has remained elusive. To test this theory, we used a retrospective comparative genomic approach to analyze the evolutionary history of Aggregatibacter actinomycetemcomitans, a bacterial species with both competent and noncompetent sister strains. Through comparative genomic analyses, we reveal that competence is evolutionarily linked to genomic diversity and speciation. Competence loss occurs frequently during evolution and is followed by the loss of clustered regularly interspaced short palindromic repeats (CRISPRs), bacterial adaptive immune systems that protect against parasitic DNA. Relative to noncompetent strains, competent bacteria have larger genomes containing multiple rearrangements. In contrast, noncompetent bacterial genomes are extremely stable but paradoxically susceptible to infective DNA elements, which contribute to noncompetent strain genetic diversity. Moreover, incomplete noncompetent strain CRISPR immune systems are enriched for self-targeting elements, which suggests that the CRISPRs have been co-opted for bacterial gene regulation, similar to eukaryotic microRNAs derived from the antiviral RNA interference pathway.<br><br>IMPORTANCE: The human microbiome is rich with thousands of diverse bacterial species. One mechanism driving this diversity is horizontal gene transfer by natural transformation, whereby naturally competent bacteria take up environmental DNA and incorporate new genes into their genomes. Competence is theorized to accelerate evolution; however, attempts to test this theory have proved difficult. Through genetic analyses of the human periodontal pathogen Aggregatibacter actinomycetemcomitans, we have discovered an evolutionary connection between competence systems promoting gene acquisition and CRISPRs (clustered regularly interspaced short palindromic repeats), adaptive immune systems that protect bacteria against genetic parasites. We show that competent A. actinomycetemcomitans strains have numerous redundant CRISPR immune systems, while noncompetent bacteria have lost their CRISPR immune systems because of inactivating mutations. Together, the evolutionary data linking the evolution of competence and CRISPRs reveals unique mechanisms promoting genetic heterogeneity and the rise of new bacterial species, providing insight into complex mechanisms underlying bacterial diversity in the human body.}, }
@article {pmid23032610, year = {2012}, author = {Sorhannus, U}, title = {Evolution of Type II Antifreeze Protein Genes in Teleost Fish: A Complex Scenario Involving Lateral Gene Transfers and Episodic Directional Selection.}, journal = {Evolutionary bioinformatics online}, volume = {8}, number = {}, pages = {535-544}, pmid = {23032610}, issn = {1176-9343}, abstract = {I examined hypotheses about lateral transfer of type II antifreeze protein (AFP) genes among "distantly" related teleost fish. The effects of episodic directional selection on amino acid evolution were also investigated. The strict consensus results showed that the type II AFP and type II antifreeze-like protein genes were transferred from Osmerus mordax to Clupea harengus, from the ancestral lineage of the Brachyopsis rostratus-Hemitripterus americanus clade to the ancestor of the Hypomesus nipponensis-Osmerus mordax group and from the ancestral lineage of Brachyopsis rostratus-Hemitripterus americanus-Siniperca chuatsi-Perca flavescens to Perca flavescens. At the present time, the available evidence is more consistent with the LGT hypothesis than with other alternative explanations. The overall results indicate that evolutionary history of the type II AFP gene is complex, and that episodic directional selection was instrumental in the evolution of this freeze-preventing protein from a C-type lectin precursor.}, }
@article {pmid23030400, year = {2012}, author = {Azmuda, N and Rahman, MZ and Sultana, M and Jenssen, EL and Khan, SI and Birkeland, NK}, title = {Evidence of interspecies O antigen gene cluster transfer between Shigella boydii 15 and Escherichia fergusonii.}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {120}, number = {12}, pages = {959-966}, doi = {10.1111/j.1600-0463.2012.02926.x}, pmid = {23030400}, issn = {1600-0463}, mesh = {Antigens, Bacterial/genetics/immunology ; Antigens, Surface/genetics/immunology ; DNA, Bacterial/genetics ; Escherichia/drug effects/*genetics/immunology ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Microbial Sensitivity Tests ; O Antigens/chemistry/*genetics/immunology ; Phylogeny ; Shigella boydii/*genetics/immunology ; }, abstract = {An environmental bacterial isolate, Iso10, previously found to show serological cross-reactivity with type-specific Shigella boydii 15 antisera was subjected to further molecular and serological analyses that revealed interspecies transfer of the O antigen gene cluster. Western blot analysis of Iso10 cell surface extracts and purified lipopolysaccharides demonstrated strong cross-reactivity with S. boydii 15-specific monovalent antisera and a lipopolysaccharide gel banding profile similar to that of S. boydii 15. Biochemical and phylogenetic analyses identified the Iso10 isolate as Escherichia fergusonii. O antigen gene cluster analyses of Iso10, carried out by restriction fragment length analysis of the amplified ~10-kb O antigen-encoding gene cluster, revealed a profile highly similar to that of S. boydii 15, confirming the presence of the S. boydii 15 somatic antigen in Iso10. To the best of our knowledge, this is the first report of interspecies transfer of O antigen-encoding genes between S. boydii and E. fergusonii, and it has implications for our understanding of the role of lateral gene transfer in the emergence of novel Shigella serotypes.}, }
@article {pmid23029591, year = {2012}, author = {Pětrošová, H and Zobaníková, M and Čejková, D and Mikalová, L and Pospíšilová, P and Strouhal, M and Chen, L and Qin, X and Muzny, DM and Weinstock, GM and Šmajs, D}, title = {Whole genome sequence of Treponema pallidum ssp. pallidum, strain Mexico A, suggests recombination between yaws and syphilis strains.}, journal = {PLoS neglected tropical diseases}, volume = {6}, number = {9}, pages = {e1832}, pmid = {23029591}, issn = {1935-2735}, support = {H75 TP000326/TP/OPHPR CDC HHS/United States ; }, mesh = {DNA, Bacterial/*chemistry/*genetics ; *Genome, Bacterial ; Humans ; Male ; Mexico ; Molecular Sequence Data ; Open Reading Frames ; Recombination, Genetic ; *Sequence Analysis, DNA ; Synteny ; Syphilis/*microbiology ; Treponema pallidum/*genetics/isolation &amp; purification ; Yaws/*microbiology ; }, abstract = {BACKGROUND: Treponema pallidum ssp. pallidum (TPA), the causative agent of syphilis, and Treponema pallidum ssp. pertenue (TPE), the causative agent of yaws, are closely related spirochetes causing diseases with distinct clinical manifestations. The TPA Mexico A strain was isolated in 1953 from male, with primary syphilis, living in Mexico. Attempts to cultivate TPA Mexico A strain under in vitro conditions have revealed lower growth potential compared to other tested TPA strains.<br><br>The complete genome sequence of the TPA Mexico A strain was determined using the Illumina sequencing technique. The genome sequence assembly was verified using the whole genome fingerprinting technique and the final sequence was annotated. The genome size of the Mexico A strain was determined to be 1,140,038 bp with 1,035 predicted ORFs. The Mexico A genome sequence was compared to the whole genome sequences of three TPA (Nichols, SS14 and Chicago) and three TPE (CDC-2, Samoa D and Gauthier) strains. No large rearrangements in the Mexico A genome were found and the identified nucleotide changes occurred most frequently in genes encoding putative virulence factors. Nevertheless, the genome of the Mexico A strain, revealed two genes (TPAMA_0326 (tp92) and TPAMA_0488 (mcp2-1)) which combine TPA- and TPE- specific nucleotide sequences. Both genes were found to be under positive selection within TPA strains and also between TPA and TPE strains.<br><br>CONCLUSIONS/SIGNIFICANCE: The observed mosaic character of the TPAMA_0326 and TPAMA_0488 loci is likely a result of inter-strain recombination between TPA and TPE strains during simultaneous infection of a single host suggesting horizontal gene transfer between treponemal subspecies.}, }
@article {pmid23029440, year = {2012}, author = {Sangwan, N and Lata, P and Dwivedi, V and Singh, A and Niharika, N and Kaur, J and Anand, S and Malhotra, J and Jindal, S and Nigam, A and Lal, D and Dua, A and Saxena, A and Garg, N and Verma, M and Kaur, J and Mukherjee, U and Gilbert, JA and Dowd, SE and Raman, R and Khurana, P and Khurana, JP and Lal, R}, title = {Comparative metagenomic analysis of soil microbial communities across three hexachlorocyclohexane contamination levels.}, journal = {PloS one}, volume = {7}, number = {9}, pages = {e46219}, pmid = {23029440}, issn = {1932-6203}, mesh = {Archaea/classification/*genetics/metabolism ; Bacteria/classification/*genetics/metabolism ; Bacterial Proteins/genetics ; Biodegradation, Environmental ; Chemotaxis/genetics ; Fusarium/*genetics/metabolism ; Gene Transfer, Horizontal ; Genes, Bacterial ; Hexachlorocyclohexane/*metabolism ; Lyases/genetics ; *Metagenomics ; Microbial Consortia/*genetics ; Plasmids/genetics ; RNA, Ribosomal, 16S/classification/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Soil Pollutants/*metabolism ; }, abstract = {This paper presents the characterization of the microbial community responsible for the in-situ bioremediation of hexachlorocyclohexane (HCH). Microbial community structure and function was analyzed using 16S rRNA amplicon and shotgun metagenomic sequencing methods for three sets of soil samples. The three samples were collected from a HCH-dumpsite (450 mg HCH/g soil) and comprised of a HCH/soil ratio of 0.45, 0.0007, and 0.00003, respectively. Certain bacterial; (Chromohalobacter, Marinimicrobium, Idiomarina, Salinosphaera, Halomonas, Sphingopyxis, Novosphingobium, Sphingomonas and Pseudomonas), archaeal; (Halobacterium, Haloarcula and Halorhabdus) and fungal (Fusarium) genera were found to be more abundant in the soil sample from the HCH-dumpsite. Consistent with the phylogenetic shift, the dumpsite also exhibited a relatively higher abundance of genes coding for chemotaxis/motility, chloroaromatic and HCH degradation (lin genes). Reassembly of a draft pangenome of Chromohalobacter salaxigenes sp. (∼8X coverage) and 3 plasmids (pISP3, pISP4 and pLB1; 13X coverage) containing lin genes/clusters also provides an evidence for the horizontal transfer of HCH catabolism genes.}, }
@article {pmid23029142, year = {2012}, author = {Rohrer, S and Holsten, L and Weiss, E and Benghezal, M and Fischer, W and Haas, R}, title = {Multiple pathways of plasmid DNA transfer in Helicobacter pylori.}, journal = {PloS one}, volume = {7}, number = {9}, pages = {e45623}, pmid = {23029142}, issn = {1932-6203}, mesh = {Chromosomes, Bacterial ; DNA/*genetics ; Electroporation ; Helicobacter pylori/*genetics ; *Plasmids ; Polymerase Chain Reaction ; Random Amplified Polymorphic DNA Technique ; Transformation, Bacterial ; }, abstract = {Many Helicobacter pylori (Hp) strains carry cryptic plasmids of different size and gene content, the function of which is not well understood. A subgroup of these plasmids (e.g. pHel4, pHel12), contain a mobilisation region, but no cognate type IV secretion system (T4SS) for conjugative transfer. Instead, certain H. pylori strains (e.g. strain P12 carrying plasmid pHel12) can harbour up to four T4SSs in their genome (cag-T4SS, comB, tfs3, tfs4). Here, we show that such indigenous plasmids can be efficiently transferred between H. pylori strains, even in the presence of extracellular DNaseI eliminating natural transformation. Knockout of a plasmid-encoded mobA relaxase gene significantly reduced plasmid DNA transfer in the presence of DNaseI, suggesting a DNA conjugation or mobilisation process. To identify the T4SS involved in this conjugative DNA transfer, each individual T4SS was consecutively deleted from the bacterial chromosome. Using a marker-free counterselectable gene deletion procedure (rpsL counterselection method), a P12 mutant strain was finally obtained with no single T4SS (P12ΔT4SS). Mating experiments using these mutants identified the comB T4SS in the recipient strain as the major mediator of plasmid DNA transfer between H. pylori strains, both in a DNaseI-sensitive (natural transformation) as well as a DNaseI-resistant manner (conjugative transfer). However, transfer of a pHel12::cat plasmid from a P12ΔT4SS donor strain into a P12ΔT4SS recipient strain provided evidence for the existence of a third, T4SS-independent mechanism of DNA transfer. This novel type of plasmid DNA transfer, designated as alternate DNaseI-Resistant (ADR) mechanism, is observed at a rather low frequency under in vitro conditions. Taken together, our study describes for the first time the existence of three distinct pathways of plasmid DNA transfer between H. pylori underscoring the importance of horizontal gene transfer for this species.}, }
@article {pmid23028586, year = {2012}, author = {Duan, C and Zhu, L and Xu, Y and Lau, GW}, title = {Saturated alanine scanning mutagenesis of the pneumococcus competence stimulating peptide identifies analogs that inhibit genetic transformation.}, journal = {PloS one}, volume = {7}, number = {9}, pages = {e44710}, pmid = {23028586}, issn = {1932-6203}, support = {C06 RR016515/RR/NCRR NIH HHS/United States ; R01 HL090699/HL/NHLBI NIH HHS/United States ; C06 RR 16515-01/RR/NCRR NIH HHS/United States ; HL090699/HL/NHLBI NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/*metabolism ; Mutagenesis/genetics/*physiology ; Streptococcus pneumoniae/*genetics/*metabolism ; Transformation, Bacterial/genetics/*physiology ; }, abstract = {Antibiotic resistance is a major challenge to modern medicine. Intraspecies and interspecies dissemination of antibiotic resistance genes among bacteria can occur through horizontal gene transfer. Competence-mediated gene transfer has been reported to contribute to the spread of antibiotic resistance genes in Streptococcus pneumoniae. Induction of the competence regulon is mediated by a 17-amino acid peptide pheromone called the competence stimulating peptide (CSP). Thus, synthetic analogs that competitively inhibit CSPs may reduce horizontal gene transfer. We performed saturated alanine scanning mutagenesis and other amino acid substitutions on CSP1 to screen for analogs that disable genetic transformation in S. pneumoniae. Substitution of the glutamate residue at the first position created analogs that could competitively inhibit CSP1-mediated competence development in a concentration-dependent manner. Additional substitutions of the negatively-charged glutamate residue with amino acids of different charge, acidity and hydrophobicity, as well as enantiomeric D-glutamate, generated analogs that efficiently outcompeted CSP1, suggesting the importance of negative charge and enantiomericity of the first glutamate residue for the function of CSP1. Collectively, these results indicate that glutamate residue at the first position is important for the ability of CSP1 to induce ComD, but is dispensable for the peptide to bind the receptor. Furthermore, these results demonstrate the potential applicability of competitive CSP analogs to control horizontal transfer of antibiotic resistance genes in S. pneumoniae.}, }
@article {pmid23028337, year = {2012}, author = {Gardiner, DM and McDonald, MC and Covarelli, L and Solomon, PS and Rusu, AG and Marshall, M and Kazan, K and Chakraborty, S and McDonald, BA and Manners, JM}, title = {Comparative pathogenomics reveals horizontally acquired novel virulence genes in fungi infecting cereal hosts.}, journal = {PLoS pathogens}, volume = {8}, number = {9}, pages = {e1002952}, pmid = {23028337}, issn = {1553-7374}, mesh = {Base Sequence ; Fungal Proteins/genetics ; Fusarium/classification/*genetics/pathogenicity ; Gene Transfer, Horizontal ; *Genome, Fungal ; Hordeum/*microbiology ; Molecular Sequence Data ; Phylogeny ; Plant Diseases/*microbiology ; Sequence Analysis, DNA ; Triticum/*microbiology ; }, abstract = {Comparative analyses of pathogen genomes provide new insights into how pathogens have evolved common and divergent virulence strategies to invade related plant species. Fusarium crown and root rots are important diseases of wheat and barley world-wide. In Australia, these diseases are primarily caused by the fungal pathogen Fusarium pseudograminearum. Comparative genomic analyses showed that the F. pseudograminearum genome encodes proteins that are present in other fungal pathogens of cereals but absent in non-cereal pathogens. In some cases, these cereal pathogen specific genes were also found in bacteria associated with plants. Phylogenetic analysis of selected F. pseudograminearum genes supported the hypothesis of horizontal gene transfer into diverse cereal pathogens. Two horizontally acquired genes with no previously known role in fungal pathogenesis were studied functionally via gene knockout methods and shown to significantly affect virulence of F. pseudograminearum on the cereal hosts wheat and barley. Our results indicate using comparative genomics to identify genes specific to pathogens of related hosts reveals novel virulence genes and illustrates the importance of horizontal gene transfer in the evolution of plant infecting fungal pathogens.}, }
@article {pmid23023974, year = {2012}, author = {Wegmann, U and Overweg, K and Jeanson, S and Gasson, M and Shearman, C}, title = {Molecular characterization and structural instability of the industrially important composite metabolic plasmid pLP712.}, journal = {Microbiology (Reading, England)}, volume = {158}, number = {Pt 12}, pages = {2936-2945}, doi = {10.1099/mic.0.062554-0}, pmid = {23023974}, issn = {1465-2080}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Conjugation, Genetic ; DNA, Bacterial/*chemistry/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genomic Instability ; Industrial Microbiology ; Lactococcus lactis/genetics/isolation &amp; purification ; Metabolic Networks and Pathways/*genetics ; Molecular Sequence Data ; *Plasmids ; Recombination, Genetic ; Sequence Analysis, DNA ; Sequence Homology ; Transformation, Genetic ; }, abstract = {The widely used plasmid-free Lactococcus lactis strain MG1363 was derived from the industrial dairy starter strain NCDO712. This strain carries a 55.39 kb plasmid encoding genes for lactose catabolism and a serine proteinase involved in casein degradation. We report the DNA sequencing and annotation of pLP712, which revealed additional metabolic genes, including peptidase F, d-lactate dehydrogenase and α-keto acid dehydrogenase (E3 complex). Comparison of pLP712 with other large lactococcal lactose and/or proteinase plasmids from L. lactis subsp. cremoris SK11 (pSK11L, pSK11P) and the plant strain L. lactis NCDO1867 (pGdh442) revealed their close relationship. The plasmid appears to have evolved through a series of genetic events as a composite of pGdh442, pSK11L and pSK11P. We describe in detail a scenario by which the metabolic genes relevant to the growth of its host in a milk environment have been unified on one replicon, reflecting the evolution of L. lactis as it changed its biological niche from plants to dairy environments. The extensive structural instability of pLP712 allows easy isolation of derivative plasmids lacking genes for casein degradation and/or lactose catabolism. Plasmid pLP712 is transferable by transduction and conjugation, and both of these processes result in significant molecular rearrangements. We report the detailed molecular analysis of insertion sequence element-mediated genetic rearrangements within pLP712 and several different mechanisms, including homologous recombination and adjacent deletion. Analysis of the integration of the lactose operon into the chromosome highlights the fluidity of the MG1363 integration hotspot and the potential for frequent movement of genes between plasmids and chromosomes in Lactococcus.}, }
@article {pmid23022563, year = {2012}, author = {Naumoff, DG and Dedysh, SN}, title = {Lateral gene transfer between the Bacteroidetes and Acidobacteria: the case of α-L-rhamnosidases.}, journal = {FEBS letters}, volume = {586}, number = {21}, pages = {3843-3851}, doi = {10.1016/j.febslet.2012.09.005}, pmid = {23022563}, issn = {1873-3468}, mesh = {Acidobacteria/classification/enzymology/*genetics ; Amino Acid Sequence ; Bacterial Proteins/classification/*genetics/metabolism ; Bacteroidetes/classification/enzymology/*genetics ; *Gene Transfer, Horizontal ; Glycoside Hydrolases/classification/*genetics/metabolism ; Hydrolysis ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Rhamnose/metabolism ; Sequence Alignment ; }, abstract = {α-L-Rhamnosidases catalyze the hydrolysis of the terminal α-L-rhamnose residues in various carbohydrates. The catalytic domains in most of these enzymes belong to the families GH78 and GH106 of glycoside hydrolases. In this study, we show that almost all genes encoding the GH78- and GH106-containing proteins from members of the poorly characterized bacterial phylum Acidobacteria originated from precursors belonging to the phylum Bacteroidetes. Members of the Acidobacteria and Bacteroidetes display similar functional capabilities and specialize on degradation of plant-derived organic matter. Several proposed lateral gene transfers between the Acidobacteria and Bacteroidetes occurred presumably during specialization of these bacteria for their environments.}, }
@article {pmid23019363, year = {2012}, author = {Beauchemin, M and Roy, S and Daoust, P and Dagenais-Bellefeuille, S and Bertomeu, T and Letourneau, L and Lang, BF and Morse, D}, title = {Dinoflagellate tandem array gene transcripts are highly conserved and not polycistronic.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {39}, pages = {15793-15798}, pmid = {23019363}, issn = {1091-6490}, mesh = {Base Sequence ; Dinoflagellida/*genetics/metabolism ; Genes, Protozoan/*physiology ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis/methods ; RNA, Protozoan/*genetics/metabolism ; Transcription, Genetic/physiology ; }, abstract = {Dinoflagellates are an important component of the marine biota, but a large genome with high-copy number (up to 5,000) tandem gene arrays has made genomic sequencing problematic. More importantly, little is known about the expression and conservation of these unusual gene arrays. We assembled de novo a gene catalog of 74,655 contigs for the dinoflagellate Lingulodinium polyedrum from RNA-Seq (Illumina) reads. The catalog contains 93% of a Lingulodinium EST dataset deposited in GenBank and 94% of the enzymes in 16 primary metabolic KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways, indicating it is a good representation of the transcriptome. Analysis of the catalog shows a marked underrepresentation of DNA-binding proteins and DNA-binding domains compared with other algae. Despite this, we found no evidence to support the proposal of polycistronic transcription, including a marked underrepresentation of sequences corresponding to the intergenic spacers of two tandem array genes. We also have used RNA-Seq to assess the degree of sequence conservation in tandem array genes and found their transcripts to be highly conserved. Interestingly, some of the sequences in the catalog have only bacterial homologs and are potential candidates for horizontal gene transfer. These presumably were transferred as single-copy genes, and because they are now all GC-rich, any derived from AT-rich contexts must have experienced extensive mutation. Our study not only has provided the most complete dinoflagellate gene catalog known to date, it has also exploited RNA-Seq to address fundamental issues in basic transcription mechanisms and sequence conservation in these algae.}, }
@article {pmid23010940, year = {2012}, author = {Friedman, R and Ely, B}, title = {Codon usage methods for horizontal gene transfer detection generate an abundance of false positive and false negative results.}, journal = {Current microbiology}, volume = {65}, number = {5}, pages = {639-642}, pmid = {23010940}, issn = {1432-0991}, mesh = {Caulobacter/classification/*genetics ; *Codon ; *Gene Transfer, Horizontal ; Genetic Techniques/*standards ; Methylobacterium/classification/*genetics ; Phylogeny ; }, abstract = {Bacteria acquire new DNA in a process known as horizontal gene transfer (HGT). To investigate the evolutionary impact of this transfer of DNA, various methods have been developed to detect past HGT events. For example, codon usage-based methods detect the presence of transferred genes by identifying atypical patterns of codon usage. However, some inherited genes exhibit atypical codon usage and some transferred genes have codon usage patterns similar to those of the inherited genes. In this study, we used a comparative phylogenetic approach with Methylobacterium and Caulobacter species to demonstrate that even well-designed codon usage methods fail to detect many HGT events and generate a high rate of false positives (60-75 %) and false negatives (23-61 %). Therefore, we recommend caution when employing codon usage methods to identify transferred genes and suggest that the rapidly increasing availability of bacterial genome sequences makes the phylogenetic approach the method of choice.}, }
@article {pmid23009612, year = {2012}, author = {Graham, LA and Li, J and Davidson, WS and Davies, PL}, title = {Smelt was the likely beneficiary of an antifreeze gene laterally transferred between fishes.}, journal = {BMC evolutionary biology}, volume = {12}, number = {}, pages = {190}, pmid = {23009612}, issn = {1471-2148}, support = {106612//Canadian Institutes of Health Research/Canada ; }, mesh = {Animals ; Antifreeze Proteins, Type II/*genetics ; Base Sequence ; Chromosomes, Artificial, Bacterial ; Evolution, Molecular ; Expressed Sequence Tags ; Fish Proteins/*genetics ; *Gene Transfer, Horizontal ; Lectins, C-Type/genetics ; Molecular Sequence Annotation ; Molecular Sequence Data ; Osmeriformes/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Type II antifreeze protein (AFP) from the rainbow smelt, Osmerus mordax, is a calcium-dependent C-type lectin homolog, similar to the AFPs from herring and sea raven. While C-type lectins are ubiquitous, type II AFPs are only found in a few species in three widely separated branches of teleost fishes. Furthermore, several other non-homologous AFPs are found in intervening species. We have previously postulated that this sporadic distribution has resulted from lateral gene transfer. The alternative hypothesis, that the AFP evolved from a lectin present in a shared ancestor and that this gene was lost in most species, is not favored because both the exon and intron sequences are highly conserved.<br><br>RESULTS: Here we have sequenced and annotated a 160 kb smelt BAC clone containing a centrally-located AFP gene along with 14 other genes. Quantitative PCR indicates that there is but a single copy of this gene within the smelt genome, which is atypical for fish AFP genes. The corresponding syntenic region has been identified and searched in a number of other species and found to be devoid of lectin or AFP sequences. Unlike the introns of the AFP gene, the intronic sequences of the flanking genes are not conserved between species. As well, the rate and pattern of mutation in the AFP gene are radically different from those seen in other smelt and herring genes.<br><br>CONCLUSIONS: These results provide stand-alone support for an example of lateral gene transfer between vertebrate species. They should further inform the debate about genetically modified organisms by showing that gene transfer between 'higher' eukaryotes can occur naturally. Analysis of the syntenic regions from several fishes strongly suggests that the smelt acquired the AFP gene from the herring.}, }
@article {pmid22998633, year = {2012}, author = {James, CE and Fothergill, JL and Kade, H and Hall, AJ and Cottell, J and Brockhurst, MA and Winstanley, C}, title = {Differential infection properties of three inducible prophages from an epidemic strain of Pseudomonas aeruginosa.}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {216}, pmid = {22998633}, issn = {1471-2180}, support = {089215/Z/09/Z//Wellcome Trust/United Kingdom ; }, mesh = {Adult ; Animals ; Anti-Bacterial Agents/metabolism ; Child ; Child, Preschool ; Cystic Fibrosis/complications ; Fimbriae, Bacterial/physiology ; Humans ; Lysogeny ; Norfloxacin/metabolism ; Prophages/*growth &amp; development/isolation &amp; purification/physiology ; Pseudomonas Infections/epidemiology/*microbiology ; Pseudomonas aeruginosa/drug effects/isolation &amp; purification/*virology ; Siphoviridae/growth &amp; development/isolation &amp; purification/physiology ; Transduction, Genetic ; Viral Plaque Assay ; Virus Activation/drug effects ; Virus Internalization ; }, abstract = {BACKGROUND: Pseudomonas aeruginosa is the most common bacterial pathogen infecting the lungs of patients with cystic fibrosis (CF). The Liverpool Epidemic Strain (LES) is transmissible, capable of superseding other P. aeruginosa populations and is associated with increased morbidity. Previously, multiple inducible prophages have been found to coexist in the LES chromosome and to constitute a major component of the accessory genome not found in other sequenced P. aerugionosa strains. LES phages confer a competitive advantage in a rat model of chronic lung infection and may, therefore underpin LES prevalence. Here the infective properties of three LES phages were characterised.<br><br>RESULTS: This study focuses on three of the five active prophages (LES&#x3c6;2, LES&#x3c6;3 and LES&#x3c6;4) that are members of the Siphoviridae. All were induced from LESB58 by norfloxacin. Lytic production of LES&#x3c6;2 was considerably higher than that of LES&#x3c6;3 and LES&#x3c6;4. Each phage was capable of both lytic and lysogenic infection of the susceptible P. aeruginosa host, PAO1, producing phage-specific plaque morphologies. In the PAO1 host background, the LES&#x3c6;2 prophage conferred immunity against LES&#x3c6;3 infection and reduced susceptibility to LES&#x3c6;4 infection. Each prophage was less stable in the PAO1 chromosome with substantially higher rates of spontaneous phage production than when residing in the native LESB58 host. We show that LES phages are capable of horizontal gene transfer by infecting P. aeruginosa strains from different sources and that type IV pili are required for infection by all three phages.<br><br>CONCLUSIONS: Multiple inducible prophages with diverse infection properties have been maintained in the LES genome. Our data suggest that LES&#x3c6;2 is more sensitive to induction into the lytic cycle or has a more efficient replicative cycle than the other LES phages.}, }
@article {pmid22998436, year = {2012}, author = {Oliver, R}, title = {Genomic tillage and the harvest of fungal phytopathogens.}, journal = {The New phytologist}, volume = {196}, number = {4}, pages = {1015-1023}, doi = {10.1111/j.1469-8137.2012.04330.x}, pmid = {22998436}, issn = {1469-8137}, mesh = {Biological Evolution ; DNA Transposable Elements ; Evolution, Molecular ; Fungi/*genetics/*pathogenicity ; Fusarium/genetics/pathogenicity ; Gene Transfer, Horizontal ; *Genome, Fungal ; Magnaporthe/genetics/pathogenicity ; Phylogeny ; Plants/*microbiology ; }, abstract = {Genome sequencing has been carried out on a small selection of major fungal ascomycete pathogens. These studies show that simple models whereby pathogens evolved from phylogenetically related saprobes by the acquisition or modification of a small number of key genes cannot be sustained.The genomes show that pathogens cannot be divided into three clearly delineated classes (biotrophs, hemibiotrophs and necrotrophs) but rather into a complex matrix of categories each with subtly different properties. It is clear that the evolution of pathogenicity is ancient, rapid and ongoing. Fungal pathogens have undergone substantial genomic rearrangements that can be appropriately described as 'genomic tillage'. Genomic tillage underpins the evolution and expression of large families of genes - known as effectors - that manipulate and exploit metabolic and defence processes of plants so as to allow the proliferation of pathogens.}, }
@article {pmid22997235, year = {2012}, author = {Lee, YC and Langley, CH}, title = {Long-term and short-term evolutionary impacts of transposable elements on Drosophila.}, journal = {Genetics}, volume = {192}, number = {4}, pages = {1411-1432}, pmid = {22997235}, issn = {1943-2631}, mesh = {Animals ; *DNA Transposable Elements ; Drosophila Proteins/genetics ; Drosophila melanogaster/*genetics/immunology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genetic Variation ; Genetics, Population ; Genome, Insect ; Host-Pathogen Interactions/genetics ; Immunity/genetics ; Methyltransferases/genetics ; Models, Genetic ; Selection, Genetic ; }, abstract = {Transposable elements (TEs) are considered to be genomic parasites and their interactions with their hosts have been likened to the coevolution between host and other nongenomic, horizontally transferred pathogens. TE families, however, are vertically inherited as integral segments of the nuclear genome. This transmission strategy has been suggested to weaken the selective benefits of host alleles repressing the transposition of specific TE variants. On the other hand, the elevated rates of TE transposition and high incidences of deleterious mutations observed during the rare cases of horizontal transfers of TE families between species could create at least a transient process analogous to the influence of horizontally transmitted pathogens. Here, we formally address this analogy, using empirical and theoretical analysis to specify the mechanism of how host-TE interactions may drive the evolution of host genes. We found that host TE-interacting genes actually have more pervasive evidence of adaptive evolution than immunity genes that interact with nongenomic pathogens in Drosophila. Yet, both our theoretical modeling and empirical observations comparing Drosophila melanogaster populations before and after the horizontal transfer of P elements, which invaded D. melanogaster early last century, demonstrated that horizontally transferred TEs have only a limited influence on host TE-interacting genes. We propose that the more prevalent and constant interaction with multiple vertically transmitted TE families may instead be the main force driving the fast evolution of TE-interacting genes, which is fundamentally different from the gene-for-gene interaction of host-pathogen coevolution.}, }
@article {pmid22997182, year = {2013}, author = {Tucker, RP}, title = {Horizontal gene transfer in choanoflagellates.}, journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution}, volume = {320}, number = {1}, pages = {1-9}, doi = {10.1002/jez.b.22480}, pmid = {22997182}, issn = {1552-5015}, mesh = {*Biological Evolution ; Choanoflagellata/*genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Protozoan/*genetics ; Nerve Tissue Proteins/genetics ; Phosphofructokinases/genetics ; *Phylogeny ; Species Specificity ; Tenascin/genetics ; }, abstract = {Horizontal gene transfer (HGT), also known as lateral gene transfer, results in the rapid acquisition of genes from another organism. HGT has long been known to be a driving force in speciation in prokaryotes, and there is evidence for HGT from symbiotic and infectious bacteria to metazoans, as well as from protists to bacteria. Recently, it has become clear that as many as a 1,000 genes in the genome of the choanoflagellate Monosiga brevicollis may have been acquired by HGT. Interestingly, these genes reportedly come from algae, bacteria, and other choanoflagellate prey. Some of these genes appear to have allowed an ancestral choanoflagellate to exploit nutrient-poor environments and were not passed on to metazoan descendents. However, some of these genes are also found in animal genomes, suggesting that HGT into a common ancestor of choanozoans and animals may have contributed to metazoan evolution.}, }
@article {pmid22993722, year = {2012}, author = {Koonin, EV and Wolf, YI}, title = {Evolution of microbes and viruses: a paradigm shift in evolutionary biology?.}, journal = {Frontiers in cellular and infection microbiology}, volume = {2}, number = {}, pages = {119}, pmid = {22993722}, issn = {2235-2988}, mesh = {Adaptation, Biological ; Archaea/*genetics ; Bacteria/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; Selection, Genetic ; Viruses/*genetics ; }, abstract = {When Charles Darwin formulated the central principles of evolutionary biology in the Origin of Species in 1859 and the architects of the Modern Synthesis integrated these principles with population genetics almost a century later, the principal if not the sole objects of evolutionary biology were multicellular eukaryotes, primarily animals and plants. Before the advent of efficient gene sequencing, all attempts to extend evolutionary studies to bacteria have been futile. Sequencing of the rRNA genes in thousands of microbes allowed the construction of the three- domain "ribosomal Tree of Life" that was widely thought to have resolved the evolutionary relationships between the cellular life forms. However, subsequent massive sequencing of numerous, complete microbial genomes revealed novel evolutionary phenomena, the most fundamental of these being: (1) pervasive horizontal gene transfer (HGT), in large part mediated by viruses and plasmids, that shapes the genomes of archaea and bacteria and call for a radical revision (if not abandonment) of the Tree of Life concept, (2) Lamarckian-type inheritance that appears to be critical for antivirus defense and other forms of adaptation in prokaryotes, and (3) evolution of evolvability, i.e., dedicated mechanisms for evolution such as vehicles for HGT and stress-induced mutagenesis systems. In the non-cellular part of the microbial world, phylogenomics and metagenomics of viruses and related selfish genetic elements revealed enormous genetic and molecular diversity and extremely high abundance of viruses that come across as the dominant biological entities on earth. Furthermore, the perennial arms race between viruses and their hosts is one of the defining factors of evolution. Thus, microbial phylogenomics adds new dimensions to the fundamental picture of evolution even as the principle of descent with modification discovered by Darwin and the laws of population genetics remain at the core of evolutionary biology.}, }
@article {pmid22993235, year = {2013}, author = {Pillet, L and Pawlowski, J}, title = {Transcriptome analysis of foraminiferan Elphidium margaritaceum questions the role of gene transfer in kleptoplastidy.}, journal = {Molecular biology and evolution}, volume = {30}, number = {1}, pages = {66-69}, doi = {10.1093/molbev/mss226}, pmid = {22993235}, issn = {1537-1719}, mesh = {Chloroplasts/genetics ; Diatoms/genetics ; Evolution, Molecular ; Expressed Sequence Tags ; Foraminifera/*genetics ; Gene Expression Profiling/*methods ; *Gene Transfer, Horizontal ; Photosynthesis ; Phylogeny ; Plastids/*genetics ; Sequence Analysis ; Symbiosis ; }, abstract = {Foraminifera from the genus Elphidium are heterotrophic protists that graze on diatoms and sequester chloroplasts from their algal preys, while digesting the rest of the diatom cell. During that process, known as kleptoplastidy, the acquired plastids remain active inside the foraminiferan cell for several months. As most of the genes required to sustain the activity of the chloroplasts are encoded in the diatom nucleus, it is unknown how the host cell can maintain the photosynthetic activity without this information. It has been proposed that maintenance of kleptoplastids could be explained by horizontal gene transfer (HGT). To test this hypothesis we obtained 17,125 EST sequences of Elphidium margaritaceum, and we screened this data set for diatom nuclear-encoded proteins having a function in photosynthetic activity or plastid maintenance. Our analyses show no evidence for the presence of such transcriptionally active genes and suggest that HGT hypothesis alone cannot explain the chloroplast's longevity in Elphidium.}, }
@article {pmid22991467, year = {2012}, author = {Ram, G and Chen, J and Kumar, K and Ross, HF and Ubeda, C and Damle, PK and Lane, KD and Penadés, JR and Christie, GE and Novick, RP}, title = {Staphylococcal pathogenicity island interference with helper phage reproduction is a paradigm of molecular parasitism.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {40}, pages = {16300-16305}, pmid = {22991467}, issn = {1091-6490}, support = {R01 AI022159/AI/NIAID NIH HHS/United States ; R21 AI067654/AI/NIAID NIH HHS/United States ; R56 AI081837/AI/NIAID NIH HHS/United States ; R01AI02215/AI/NIAID NIH HHS/United States ; }, mesh = {Antibiosis/*genetics ; Cloning, Molecular ; Escherichia coli ; Gene Transfer, Horizontal/*genetics ; Genomic Islands/*genetics ; Microscopy, Electron ; Real-Time Polymerase Chain Reaction ; Staphylococcus Phages/*physiology ; Staphylococcus aureus/*genetics/pathogenicity/virology ; Two-Hybrid System Techniques ; Viral Plaque Assay ; Virus Replication/*physiology ; }, abstract = {Staphylococcal pathogenicity islands (SaPIs) carry superantigen and resistance genes and are extremely widespread in Staphylococcus aureus and in other Gram-positive bacteria. SaPIs represent a major source of intrageneric horizontal gene transfer and a stealth conduit for intergeneric gene transfer; they are phage satellites that exploit the life cycle of their temperate helper phages with elegant precision to enable their rapid replication and promiscuous spread. SaPIs also interfere with helper phage reproduction, blocking plaque formation, sharply reducing burst size and enhancing the survival of host cells following phage infection. Here, we show that SaPIs use several different strategies for phage interference, presumably the result of convergent evolution. One strategy, not described previously in the bacteriophage microcosm, involves a SaPI-encoded protein that directly and specifically interferes with phage DNA packaging by blocking the phage terminase small subunit. Another strategy involves interference with phage reproduction by diversion of the vast majority of virion proteins to the formation of SaPI-specific small infectious particles. Several SaPIs use both of these strategies, and at least one uses neither but possesses a third. Our studies illuminate a key feature of the evolutionary strategy of these mobile genetic elements, in addition to their carriage of important genes-interference with helper phage reproduction, which could ensure their transferability and long-term persistence.}, }
@article {pmid22990210, year = {2013}, author = {Liu, HF and Li, W and Lu, MB and Yu, LJ}, title = {Pharmacokinetics and risk evaluation of DNA vaccine against Schistosoma japonicum.}, journal = {Parasitology research}, volume = {112}, number = {1}, pages = {59-67}, pmid = {22990210}, issn = {1432-1955}, mesh = {Animals ; Antibodies, Helminth/blood ; Antigens, Helminth/genetics/*immunology ; Enzyme-Linked Immunosorbent Assay ; Fluorescence ; Gastrointestinal Tract/microbiology ; Gene Transfer, Horizontal ; Genes, Reporter ; Green Fluorescent Proteins/analysis/genetics ; Helminth Proteins/genetics/*immunology ; Injections, Intramuscular ; Male ; Membrane Proteins/genetics/*immunology ; Mice ; Mice, Inbred BALB C ; Plasmids/administration &amp; dosage/adverse effects/pharmacokinetics ; Polymerase Chain Reaction ; Recombinant Fusion Proteins/genetics/immunology ; Schistosoma japonicum/genetics/*immunology ; Time Factors ; Tissue Distribution ; Vaccines, DNA/administration &amp; dosage/*adverse effects/immunology/*pharmacokinetics ; }, abstract = {DNA plasmid immunization is a novel approach of preventive and therapeutic vaccine. More than 100 DNA vaccines have been on preclinical or clinical phase trials, and four kinds of DNA vaccines for livestock have been approved by USDA, CFIA, and APVMA. Schistosomiasis is a worldwide parasitic disease, and vaccine immunization is supposed to be a promising approach to control the health crisis. On the basis of former preclinical studies, we further focused on the pharmacokinetics and risk evaluation of DNA vaccine in vivo. In the present study, enhanced green fluorescent protein (EGFP) report gene was fused with Schistosoma japonicum 23 kDa transmembrane protein antigen gene (Sj23) and constructed into DNA vaccine pVIVO2-Sj23.EGFP. After intramuscularly injecting 100 μg of purified DNA vaccine plasmid to immunizate BALB/c mice, we studied the tissue distribution of DNA plasmid and expressed Sj23.EGFP antigen, the persistence time of elicited antibodies, and the risk of DNA vaccine transferred into intestinal microorganisms. The results showed that DNA vaccine plasmid could be distributed into all tissues of the body after injection; however, only few organs including the injected muscle were detected DNA vaccine at postimmunization until the 100 days by PCR technology; the detection of green fluorescence protein displayed that DNA vaccine could be expressed in almost every tissue and organs; the ELISA assay indicated the immune antibody against Sj23 could persist over 70 days; and the DNA vaccine transferring intestinal flora results was negative. The results indicated that the DNA vaccine has systemic protection and long-lasting effectivity and is safe to intestinal flora.}, }
@article {pmid22987427, year = {2013}, author = {Nishida, H}, title = {Phylogenetic analyses of phytoplasmas based on whole-genome comparison.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {938}, number = {}, pages = {319-327}, doi = {10.1007/978-1-62703-089-2_27}, pmid = {22987427}, issn = {1940-6029}, mesh = {Bacterial Proteins/chemistry/genetics ; Computational Biology/methods ; Databases, Genetic ; *Genome, Bacterial ; *Phylogeny ; Phytoplasma/*classification/genetics ; }, abstract = {It is no longer as difficult to determine genomic DNA sequences of uncultured bacteria as it once was, due to the development of DNA sequencing technology. It is likely that the number of whole-genome sequences of phytoplasmas will increase. In this chapter, two major strategies of whole-genome comparison studies, viz. gene content and orthologous protein sequence comparisons, are described. In general, horizontal gene transfer has greater influence on gene content-based phylogenetic analysis than orthologous protein sequence-based analysis. However, horizontal gene transfer has occurred rarely during the evolution of Mollicutes. Thus, the two phylogenetic topologies of the Mollicutes based on the two different strategies are similar.}, }
@article {pmid22987250, year = {2013}, author = {Memon, D and Singh, AK and Pakrasi, HB and Wangikar, PP}, title = {A global analysis of adaptive evolution of operons in cyanobacteria.}, journal = {Antonie van Leeuwenhoek}, volume = {103}, number = {2}, pages = {331-346}, doi = {10.1007/s10482-012-9813-0}, pmid = {22987250}, issn = {1572-9699}, mesh = {*Biological Evolution ; Cyanobacteria/*genetics ; *Evolution, Molecular ; *Operon ; }, abstract = {Operons are an important feature of prokaryotic genomes. Evolution of operons is hypothesized to be adaptive and has contributed significantly towards coordinated optimization of functions. Two conflicting theories, based on (i) in situ formation to achieve co-regulation and (ii) horizontal gene transfer of functionally linked gene clusters, are generally considered to explain why and how operons have evolved. Furthermore, effects of operon evolution on genomic traits such as intergenic spacing, operon size and co-regulation are relatively less explored. Based on the conservation level in a set of diverse prokaryotes, we categorize the operonic gene pair associations and in turn the operons as ancient and recently formed. This allowed us to perform a detailed analysis of operonic structure in cyanobacteria, a morphologically and physiologically diverse group of photoautotrophs. Clustering based on operon conservation showed significant similarity with the 16S rRNA-based phylogeny, which groups the cyanobacterial strains into three clades. Clade C, dominated by strains that are believed to have undergone genome reduction, shows a larger fraction of operonic genes that are tightly packed in larger sized operons. Ancient operons are in general larger, more tightly packed, better optimized for co-regulation and part of key cellular processes. A sub-clade within Clade B, which includes Synechocystis sp. PCC 6803, shows a reverse trend in intergenic spacing. Our results suggest that while in situ formation and vertical descent may be a dominant mechanism of operon evolution in cyanobacteria, optimization of intergenic spacing and co-regulation are part of an ongoing process in the life-cycle of operons.}, }
@article {pmid22985693, year = {2012}, author = {Milani, NA and Lawrence, DP and Arnold, AE and VanEtten, HD}, title = {Origin of pisatin demethylase (PDA) in the genus Fusarium.}, journal = {Fungal genetics and biology : FG &amp; B}, volume = {49}, number = {11}, pages = {933-942}, doi = {10.1016/j.fgb.2012.08.007}, pmid = {22985693}, issn = {1096-0937}, mesh = {Cytochrome P-450 Enzyme System/*genetics/metabolism ; Evolution, Molecular ; Fungal Proteins/*genetics/metabolism ; Fusarium/classification/*enzymology/*genetics/physiology ; Gene Transfer, Horizontal ; Host Specificity ; Molecular Sequence Data ; Nectria/classification/enzymology/genetics/physiology ; Oxidoreductases, O-Demethylating/*genetics/metabolism ; Pisum sativum/microbiology ; Phylogeny ; Plant Diseases/microbiology ; Pterocarpans/metabolism ; }, abstract = {Host specificity of plant pathogens can be dictated by genes that enable pathogens to circumvent host defenses. Upon recognition of a pathogen, plants initiate defense responses that can include the production of antimicrobial compounds such as phytoalexins. The pea pathogen Nectria haematococca mating population VI (MPVI) is a filamentous ascomycete that contains a cluster of genes known as the pea pathogenicity (PEP) cluster in which the pisatin demethylase (PDA) gene resides. The PDA gene product is responsible for the detoxification of the phytoalexin pisatin, which is produced by the pea plant (Pisum sativum L.). This detoxification activity allows the pathogen to evade the phytoalexin defense mechanism. It has been proposed that the evolution of PDA and the PEP cluster reflects horizontal gene transfer (HGT). Previous observations consistent with this hypothesis include the location of the PEP cluster and PDA gene on a dispensable portion of the genome (a supernumerary chromosome), a phylogenetically discontinuous distribution of the cluster among closely related species, and a bias in G+C content and codon usage compared to other regions of the genome. In this study we compared the phylogenetic history of PDA, beta-tubulin, and translation elongation factor 1-alpha in three closely related fungi (Nectria haematococca, Fusarium oxysporum, and Neocosmospora species) to formally evaluate hypotheses regarding the origin and evolution of PDA. Our results, coupled with previous work, robustly demonstrate discordance between the gene genealogy of PDA and the organismal phylogeny of these species, and illustrate how HGT of pathogenicity genes can contribute to the expansion of host specificity in plant-pathogenic fungi.}, }
@article {pmid22983963, year = {2012}, author = {Nasuno, E and Kimura, N and Fujita, MJ and Nakatsu, CH and Kamagata, Y and Hanada, S}, title = {Phylogenetically novel LuxI/LuxR-type quorum sensing systems isolated using a metagenomic approach.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {22}, pages = {8067-8074}, pmid = {22983963}, issn = {1098-5336}, mesh = {Acyl-Butyrolactones/metabolism ; Bacteria/*genetics ; Biosensing Techniques/methods ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; Escherichia coli/genetics ; Fluorescence ; Genes, Reporter ; Green Fluorescent Proteins/genetics/metabolism ; *Metagenomics ; Molecular Sequence Data ; Phylogeny ; *Quorum Sensing ; Sequence Analysis, DNA ; Sewage/*microbiology ; *Signal Transduction ; *Soil Microbiology ; }, abstract = {A great deal of research has been done to understand bacterial cell-to-cell signaling systems, but there is still a large gap in our current knowledge because the majority of microorganisms in natural environments do not have cultivated representatives. Metagenomics is one approach to identify novel quorum sensing (QS) systems from uncultured bacteria in environmental samples. In this study, fosmid metagenomic libraries were constructed from a forest soil and an activated sludge from a coke plant, and the target genes were detected using a green fluorescent protein (GFP)-based Escherichia coli biosensor strain whose fluorescence was screened by spectrophotometry. DNA sequence analysis revealed two pairs of new LuxI family N-acyl-L-homoserine lactone (AHL) synthases and LuxR family transcriptional regulators (clones N16 and N52, designated AubI/AubR and AusI/AusR, respectively). AubI and AusI each produced an identical AHL, N-dodecanoyl-L-homoserine lactone (C(12)-HSL), as determined by nuclear magnetic resonance (NMR) and mass spectrometry. Phylogenetic analysis based on amino acid sequences suggested that AusI/AusR was from an uncultured member of the Betaproteobacteria and AubI/AubR was very deeply branched from previously described LuxI/LuxR homologues in isolates of the Proteobacteria. The phylogenetic position of AubI/AubR indicates that they represent a QS system not acquired recently from the Proteobacteria by horizontal gene transfer but share a more ancient ancestry. We demonstrated that metagenomic screening is useful to provide further insight into the phylogenetic diversity of bacterial QS systems by describing two new LuxI/LuxR-type QS systems from uncultured bacteria.}, }
@article {pmid22983002, year = {2012}, author = {Routh, A and Domitrovic, T and Johnson, JE}, title = {Packaging host RNAs in small RNA viruses: an inevitable consequence of an error-prone polymerase?.}, journal = {Cell cycle (Georgetown, Tex.)}, volume = {11}, number = {20}, pages = {3713-3714}, pmid = {22983002}, issn = {1551-4005}, support = {R01 GM054076/GM/NIGMS NIH HHS/United States ; }, mesh = {Capsid Proteins/genetics/metabolism ; Eukaryotic Cells/*metabolism/virology ; Gene Transfer, Horizontal ; Models, Molecular ; RNA/*genetics/metabolism ; RNA Viruses/*genetics/metabolism ; RNA-Dependent RNA Polymerase/genetics/*metabolism ; Virion/genetics/metabolism ; }, }
@article {pmid22978676, year = {2012}, author = {Liu, Y and Li, XY and Wan, LG and Jiang, WY and Li, FQ and Yang, JH}, title = {Molecular characterization of the bla(KPC-2) gene in clinical isolates of carbapenem-resistant Klebsiella pneumoniae from the pediatric wards of a Chinese hospital.}, journal = {Canadian journal of microbiology}, volume = {58}, number = {10}, pages = {1167-1173}, doi = {10.1139/w2012-094}, pmid = {22978676}, issn = {1480-3275}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Carbapenems/pharmacology ; Child ; Child, Preschool ; China ; Cross Infection/*microbiology ; Drug Resistance, Bacterial/genetics ; Electrophoresis, Gel, Pulsed-Field ; Female ; Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Genotype ; Hospitals, Pediatric ; Humans ; Infant ; Klebsiella Infections/*microbiology ; Klebsiella pneumoniae/classification/drug effects/*genetics/isolation &amp; purification ; Male ; Methyltransferases/genetics ; Microbial Sensitivity Tests ; Plasmids/genetics ; beta-Lactamases/genetics ; }, abstract = {The present study was conducted to confirm the presence of Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae associated with a nosocomial outbreak in a Chinese pediatric hospital. From July 2009 to January 2011, 124 nonduplicated K. pneumoniae isolates were collected from specimens from patients of pediatric units in the hospital. Twelve of the 124 isolates possessed the bla(KPC-2) gene and showed 7 different pulsed-field gel electrophoresis (PFGE) patterns. Meanwhile, 16S rRNA methylase, acc(6')-Ib-cr, and several types of β-lactamases were also produced by the majority of the KPC-producing isolates. Class 1 integron-encoded intI1 integrase gene was subsequently found in all strains, and amplification, sequencing, and comparison of DNA between 5' conserved segment and 3' conserved segment region showed the presence of several known antibiotic resistance gene cassettes of various sizes. The conjugation and plasmid-curing experiments indicated some KPC-2-encoding genes were transmissible. In addition, conjugal cotransfer of multidrug-resistant phenotypes with KPC-positive phenotypes was observed in KPC-producing strains. Restriction endonuclease analysis and DNA hybridization with a KPC-specific probe showed that the bla(KPC-2) gene was carried by plasmid DNA from K. pneumoniae of PFGE pattern B. The overall results indicate that the emergence and outbreak of KPC-producing K. pneumoniae in our pediatric wards occurred in conjunction with plasmids coharboring 16S rRNA methylase and extended-spectrum β-lactamases.}, }
@article {pmid22977066, year = {2012}, author = {Sloan, DB and Moran, NA}, title = {Endosymbiotic bacteria as a source of carotenoids in whiteflies.}, journal = {Biology letters}, volume = {8}, number = {6}, pages = {986-989}, pmid = {22977066}, issn = {1744-957X}, support = {F32 GM099334/GM/NIGMS NIH HHS/United States ; 1F32GM099334/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Arizona ; Base Sequence ; Carotenoids/*biosynthesis ; Chromosome Mapping ; Genome, Bacterial/*genetics ; Halomonadaceae/*genetics/*metabolism ; Hemiptera/metabolism/*microbiology ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Symbiosis/*genetics ; }, abstract = {Although carotenoids serve important biological functions, animals are generally unable to synthesize these pigments and instead obtain them from food. However, many animals, such as sap-feeding insects, may have limited access to carotenoids in their diet, and it was recently shown that aphids have acquired the ability to produce carotenoids by lateral transfer of fungal genes. Whiteflies also contain carotenoids but show no evidence of the fungus-derived genes found in aphids. Because many sap-feeding insects harbour intracellular bacteria, it has long been hypothesized that these endosymbionts could serve as an alternative source of carotenoid biosynthesis. We sequenced the genome of the obligate bacterial endosymbiont Portiera from the whitefly Bemisia tabaci. The genome exhibits typical signatures of obligate endosymbionts in sap-feeding insects, including extensive size reduction (358.2 kb) and enrichment for genes involved in essential amino acid biosynthesis. Unlike other sequenced insect endosymbionts, however, Portiera has bacterial homologues of the fungal carotenoid biosynthesis genes in aphids. Therefore, related lineages of sap-feeding insects appear to have convergently acquired the same functional trait by distinct evolutionary mechanisms-bacterial endosymbiosis versus fungal lateral gene transfer.}, }
@article {pmid22976450, year = {2013}, author = {Lyska, D and Meierhoff, K and Westhoff, P}, title = {How to build functional thylakoid membranes: from plastid transcription to protein complex assembly.}, journal = {Planta}, volume = {237}, number = {2}, pages = {413-428}, pmid = {22976450}, issn = {1432-2048}, mesh = {Cell Nucleus/metabolism ; Chloroplast Proteins/genetics/*metabolism ; *Gene Expression Regulation, Plant ; Photosynthetic Reaction Center Complex Proteins/genetics/*metabolism ; Plants/genetics/metabolism ; Plastids/genetics/*metabolism ; Protein Biosynthesis ; Protein Processing, Post-Translational ; Protein Transport ; RNA Editing ; RNA Splicing ; RNA, Plant/genetics/metabolism ; Thylakoids/genetics/*metabolism ; *Transcription, Genetic ; }, abstract = {Chloroplasts are the endosymbiotic descendants of cyanobacterium-like prokaryotes. Present genomes of plant and green algae chloroplasts (plastomes) contain ~100 genes mainly encoding for their transcription-/translation-machinery, subunits of the thylakoid membrane complexes (photosystems II and I, cytochrome b (6) f, ATP synthase), and the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase. Nevertheless, proteomic studies have identified several thousand proteins in chloroplasts indicating that the majority of the plastid proteome is not encoded by the plastome. Indeed, plastid and host cell genomes have been massively rearranged in the course of their co-evolution, mainly through gene loss, horizontal gene transfer from the cyanobacterium/chloroplast to the nucleus of the host cell, and the emergence of new nuclear genes. Besides structural components of thylakoid membrane complexes and other (enzymatic) complexes, the nucleus provides essential factors that are involved in a variety of processes inside the chloroplast, like gene expression (transcription, RNA-maturation and translation), complex assembly, and protein import. Here, we provide an overview on regulatory factors that have been described and characterized in the past years, putting emphasis on mechanisms regulating the expression and assembly of the photosynthetic thylakoid membrane complexes.}, }
@article {pmid22976336, year = {2012}, author = {Vedantam, G and Viswanathan, VK}, title = {Spirochaetes and their twisted ways.}, journal = {Gut microbes}, volume = {3}, number = {5}, pages = {399-400}, doi = {10.4161/gmic.22051}, pmid = {22976336}, issn = {1949-0984}, mesh = {Bacteria/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Spirochaetales/*cytology/*genetics ; }, abstract = {Biological systematists have had a long tradition of encountering organisms that are not quite what they seem to be. Among the microbes, horizontal gene transfer and evolutionary pressures result in organisms that have distinguished themselves from their closest relatives. The recent analyses of several Spirochetes reveal members that are not spiral shaped, and ones that appear to have extensively acquired genetic material from phylogenetically distant, but environmentally proximate, organisms.}, }
@article {pmid22974303, year = {2012}, author = {Brisson, D and Drecktrah, D and Eggers, CH and Samuels, DS}, title = {Genetics of Borrelia burgdorferi.}, journal = {Annual review of genetics}, volume = {46}, number = {}, pages = {515-536}, pmid = {22974303}, issn = {1545-2948}, support = {AI076342/AI/NIAID NIH HHS/United States ; R01 AI076342/AI/NIAID NIH HHS/United States ; AI088131/AI/NIAID NIH HHS/United States ; R01 AI051486/AI/NIAID NIH HHS/United States ; R21 AI088131/AI/NIAID NIH HHS/United States ; AI051486/AI/NIAID NIH HHS/United States ; }, mesh = {Alleles ; Animals ; Antigenic Variation ; Antigens, Bacterial/genetics/immunology/metabolism ; Bacterial Outer Membrane Proteins/genetics/metabolism ; Bacterial Proteins/genetics/immunology/metabolism ; Bacteriophages/genetics/metabolism/pathogenicity ; Borrelia burgdorferi/*genetics/immunology/pathogenicity/virology ; DNA, Bacterial/*genetics/metabolism ; Electroporation ; Evolution, Molecular ; *Genes, Bacterial ; Genetic Variation ; Humans ; Ixodes/microbiology ; Linkage Disequilibrium ; Lipoproteins/genetics/immunology/metabolism ; Lyme Disease/microbiology ; Plasmids/genetics/metabolism ; Prophages/genetics/*metabolism ; Recombination, Genetic ; Selection, Genetic ; Species Specificity ; Transduction, Genetic ; Transformation, Genetic ; }, abstract = {The spirochetes in the Borrelia burgdorferi sensu lato genospecies group cycle in nature between tick vectors and vertebrate hosts. The current assemblage of B. burgdorferi sensu lato, of which three species cause Lyme disease in humans, originated from a rapid species radiation that occurred near the origin of the clade. All of these species share a unique genome structure that is highly segmented and predominantly composed of linear replicons. One of the circular plasmids is a prophage that exists as several isoforms in each cell and can be transduced to other cells, likely contributing to an otherwise relatively anemic level of horizontal gene transfer, which nevertheless appears to be adequate to permit strong natural selection and adaptation in populations of B. burgdorferi. Although the molecular genetic toolbox is meager, several antibiotic-resistant mutants have been isolated, and the resistance alleles, as well as some exogenous genes, have been fashioned into markers to dissect gene function. Genetic studies have probed the role of the outer membrane lipoprotein OspC, which is maintained in nature by multiple niche polymorphisms and negative frequency-dependent selection. One of the most intriguing genetic systems in B. burgdorferi is vls recombination, which generates antigenic variation during infection of mammalian hosts.}, }
@article {pmid22974200, year = {2012}, author = {Vollan, HS and Tannaes, T and Yamaoka, Y and Bukholm, G}, title = {In silico evolutionary analysis of Helicobacter pylori outer membrane phospholipase A (OMPLA).}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {206}, pmid = {22974200}, issn = {1471-2180}, support = {R01 DK062813/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacterial Outer Membrane Proteins/*genetics ; Computational Biology ; *Evolution, Molecular ; Helicobacter pylori/*enzymology/*genetics ; Molecular Sequence Data ; Phospholipases A1/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: In the past decade, researchers have proposed that the pldA gene for outer membrane phospholipase A (OMPLA) is important for bacterial colonization of the human gastric ventricle. Several conserved Helicobacter pylori genes have distinct genotypes in different parts of the world, biogeographic patterns that can be analyzed through phylogenetic trees. The current study will shed light on the importance of the pldA gene in H. pylori. In silico sequence analysis will be used to investigate whether the bacteria are in the process of preserving, optimizing, or rejecting the pldA gene. The pldA gene will be phylogenetically compared to other housekeeping (HK) genes, and a possible origin via horizontal gene transfer (HGT) will be evaluated through both intra- and inter-species evolutionary analyses.<br><br>RESULTS: In this study, pldA gene sequences were phylogenetically analyzed and compared with a large reference set of concatenated HK gene sequences. A total of 246 pldA nucleotide sequences were used; 207 were from Norwegian isolates, 20 were from Korean isolates, and 19 were from the NCBI database. Best-fit evolutionary models were determined with MEGA5 ModelTest for the pldA (K80 + I + G) and HK (GTR + I + G) sequences, and maximum likelihood trees were constructed. Both HK and pldA genes showed biogeographic clustering. Horizontal gene transfer was inferred based on significantly different GC contents, the codon adaptation index, and a phylogenetic conflict between a tree of OMPLA protein sequences representing 171 species and a tree of the AtpA HK protein for 169 species. Although a vast majority of the residues in OMPLA were predicted to be under purifying selection, sites undergoing positive selection were also found.<br><br>CONCLUSIONS: Our findings indicate that the pldA gene could have been more recently acquired than seven of the HK genes found in H. pylori. However, the common biogeographic patterns of both the HK and pldA sequences indicated that the transfer occurred long ago. Our results indicate that the bacterium is preserving the function of OMPLA, although some sites are still being evolutionarily optimized.}, }
@article {pmid22973561, year = {2012}, author = {Segerman, B}, title = {The genetic integrity of bacterial species: the core genome and the accessory genome, two different stories.}, journal = {Frontiers in cellular and infection microbiology}, volume = {2}, number = {}, pages = {116}, pmid = {22973561}, issn = {2235-2988}, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genetic Variation ; *Genome, Bacterial ; }, abstract = {Strains within a bacterial species typically have a set of conserved core genes and a variable set of accessory genes. The accessory genes often appear to move laterally between strains, thereby forming new trait combinations. Sometimes, genetic material also moves laterally between species, thereby resulting in diffuse borders between them. The growing number of genome sequences offers new possibilities to study these processes. Ten species for which abundant genomic data exists were here selected for analysis of the species border integrity. The average core genome similarities and relative core genome sizes (RCGSs) were determined for strain pairs within the species and for strain pairs crossing the species border. The variability within the species as well as the border integrity varies for different bacterial species. Some have very distinct borders while others are more or less indefinable. From the growing amount of genomic data, it becomes even clearer that the concept of bacterial species is, in many cases, far from absolute.}, }
@article {pmid22973559, year = {2012}, author = {Merhej, V and Raoult, D}, title = {Rhizome of life, catastrophes, sequence exchanges, gene creations, and giant viruses: how microbial genomics challenges Darwin.}, journal = {Frontiers in cellular and infection microbiology}, volume = {2}, number = {}, pages = {113}, pmid = {22973559}, issn = {2235-2988}, mesh = {*Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genetic Variation ; *Genetics, Microbial ; *Selection, Genetic ; }, abstract = {Darwin's theory about the evolution of species has been the object of considerable dispute. In this review, we have described seven key principles in Darwin's book The Origin of Species and tried to present how genomics challenge each of these concepts and improve our knowledge about evolution. Darwin believed that species evolution consists on a positive directional selection ensuring the "survival of the fittest." The most developed state of the species is characterized by increasing complexity. Darwin proposed the theory of "descent with modification" according to which all species evolve from a single common ancestor through a gradual process of small modification of their vertical inheritance. Finally, the process of evolution can be depicted in the form of a tree. However, microbial genomics showed that evolution is better described as the "biological changes over time." The mode of change is not unidirectional and does not necessarily favors advantageous mutations to increase fitness it is rather subject to random selection as a result of catastrophic stochastic processes. Complexity is not necessarily the completion of development: several complex organisms have gone extinct and many microbes including bacteria with intracellular lifestyle have streamlined highly effective genomes. Genomes evolve through large events of gene deletions, duplications, insertions, and genomes rearrangements rather than a gradual adaptative process. Genomes are dynamic and chimeric entities with gene repertoires that result from vertical and horizontal acquisitions as well as de novo gene creation. The chimeric character of microbial genomes excludes the possibility of finding a single common ancestor for all the genes recorded currently. Genomes are collections of genes with different evolutionary histories that cannot be represented by a single tree of life (TOL). A forest, a network or a rhizome of life may be more accurate to represent evolutionary relationships among species.}, }
@article {pmid22969418, year = {2012}, author = {Sanguinetti, L and Toti, S and Reguzzi, V and Bagnoli, F and Donati, C}, title = {A novel computational method identifies intra- and inter-species recombination events in Staphylococcus aureus and Streptococcus pneumoniae.}, journal = {PLoS computational biology}, volume = {8}, number = {9}, pages = {e1002668}, pmid = {22969418}, issn = {1553-7358}, mesh = {Algorithms ; Base Sequence ; Chromosome Mapping/*methods ; Computer Simulation ; Conserved Sequence/genetics ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial/*genetics ; *Models, Genetic ; Molecular Sequence Data ; Sequence Analysis, DNA/*methods ; Species Specificity ; Staphylococcus aureus/*genetics ; Streptococcus pneumoniae/*genetics ; }, abstract = {Advances in high-throughput DNA sequencing technologies have determined an explosion in the number of sequenced bacterial genomes. Comparative sequence analysis frequently reveals evidences of homologous recombination occurring with different mechanisms and rates in different species, but the large-scale use of computational methods to identify recombination events is hampered by their high computational costs. Here, we propose a new method to identify recombination events in large datasets of whole genome sequences. Using a filtering procedure of the gene conservation profiles of a test genome against a panel of strains, this algorithm identifies sets of contiguous genes acquired by homologous recombination. The locations of the recombination breakpoints are determined using a statistical test that is able to account for the differences in the natural rate of evolution between different genes. The algorithm was tested on a dataset of 75 genomes of Staphylococcus aureus and 50 genomes comprising different streptococcal species, and was able to detect intra-species recombination events in S. aureus and in Streptococcus pneumoniae. Furthermore, we found evidences of an inter-species exchange of genetic material between S. pneumoniae and Streptococcus mitis, a closely related commensal species that colonizes the same ecological niche. The method has been implemented in an R package, Reco, which is freely available from supplementary material, and provides a rapid screening tool to investigate recombination on a genome-wide scale from sequence data.}, }
@article {pmid22965120, year = {2012}, author = {Saini, V and Raghuvanshi, S and Khurana, JP and Ahmed, N and Hasnain, SE and Tyagi, AK and Tyagi, AK}, title = {Massive gene acquisitions in Mycobacterium indicus pranii provide a perspective on mycobacterial evolution.}, journal = {Nucleic acids research}, volume = {40}, number = {21}, pages = {10832-10850}, pmid = {22965120}, issn = {1362-4962}, mesh = {Bacterial Proteins/classification/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Genetic Speciation ; Genome, Bacterial ; Hemerythrin/genetics ; Interspersed Repetitive Sequences ; Membrane Transport Proteins/genetics ; Multigene Family ; Mycobacterium/*genetics/immunology/metabolism ; Plasmids/genetics ; Proteome/genetics ; Selection, Genetic ; }, abstract = {Understanding the evolutionary and genomic mechanisms responsible for turning the soil-derived saprophytic mycobacteria into lethal intracellular pathogens is a critical step towards the development of strategies for the control of mycobacterial diseases. In this context, Mycobacterium indicus pranii (MIP) is of specific interest because of its unique immunological and evolutionary significance. Evolutionarily, it is the progenitor of opportunistic pathogens belonging to M. avium complex and is endowed with features that place it between saprophytic and pathogenic species. Herein, we have sequenced the complete MIP genome to understand its unique life style, basis of immunomodulation and habitat diversification in mycobacteria. As a case of massive gene acquisitions, 50.5% of MIP open reading frames (ORFs) are laterally acquired. We show, for the first time for Mycobacterium, that MIP genome has mosaic architecture. These gene acquisitions have led to the enrichment of selected gene families critical to MIP physiology. Comparative genomic analysis indicates a higher antigenic potential of MIP imparting it a unique ability for immunomodulation. Besides, it also suggests an important role of genomic fluidity in habitat diversification within mycobacteria and provides a unique view of evolutionary divergence and putative bottlenecks that might have eventually led to intracellular survival and pathogenic attributes in mycobacteria.}, }
@article {pmid22963406, year = {2012}, author = {Bonnin-Jusserand, M and Grandvalet, C and Rieu, A and Weidmann, S and Alexandre, H}, title = {Tyrosine-containing peptides are precursors of tyramine produced by Lactobacillus plantarum strain IR BL0076 isolated from wine.}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {199}, pmid = {22963406}, issn = {1471-2180}, mesh = {Bacterial Proteins/biosynthesis/genetics ; DNA, Bacterial/chemistry/genetics ; Gene Expression Profiling ; Lactobacillus plantarum/isolation &amp; purification/*metabolism ; Molecular Sequence Data ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Tyramine/*metabolism ; Wine/*microbiology ; }, abstract = {BACKGROUND: Biogenic amines are molecules with allergenic properties. They are found in fermented products and are synthesized by lactic acid bacteria through the decarboxylation of amino acids present in the food matrix. The concentration of biogenic amines in fermented foodstuffs is influenced by many environmental factors, and in particular, biogenic amine accumulation depends on the quantity of available precursors. Enological practices which lead to an enrichment in nitrogen compounds therefore favor biogenic amine production in wine. Free amino acids are the only known precursors for the synthesis of biogenic amines, and no direct link has previously been demonstrated between the use of peptides by lactic acid bacteria and biogenic amine synthesis.<br><br>RESULTS: Here we demonstrate for the first time that a Lactobacillus plantarum strain isolated from a red wine can produce the biogenic amine tyramine from peptides containing tyrosine. In our conditions, most of the tyramine was produced during the late exponential growth phase, coinciding with the expression of the tyrDC and tyrP genes. The DNA sequences of tyrDC and tyrP in this strain share 98% identity with those in Lactobacillus brevis consistent with horizontal gene transfer from L. brevis to L. plantarum.<br><br>CONCLUSION: Peptides amino acids are precursors of biogenic amines for Lactobacillus plantarum strain IR BL0076.}, }
@article {pmid22962460, year = {2012}, author = {Stolzer, M and Lai, H and Xu, M and Sathaye, D and Vernot, B and Durand, D}, title = {Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees.}, journal = {Bioinformatics (Oxford, England)}, volume = {28}, number = {18}, pages = {i409-i415}, pmid = {22962460}, issn = {1367-4811}, mesh = {*Algorithms ; *Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; Models, Genetic ; *Multigene Family ; Phylogeny ; Software ; }, abstract = {MOTIVATION: Gene duplication (D), transfer (T), loss (L) and incomplete lineage sorting (I) are crucial to the evolution of gene families and the emergence of novel functions. The history of these events can be inferred via comparison of gene and species trees, a process called reconciliation, yet current reconciliation algorithms model only a subset of these evolutionary processes.<br><br>RESULTS: We present an algorithm to reconcile a binary gene tree with a nonbinary species tree under a DTLI parsimony criterion. This is the first reconciliation algorithm to capture all four evolutionary processes driving tree incongruence and the first to reconcile non-binary species trees with a transfer model. Our algorithm infers all optimal solutions and reports complete, temporally feasible event histories, giving the gene and species lineages in which each event occurred. It is fixed-parameter tractable, with polytime complexity when the maximum species outdegree is fixed. Application of our algorithms to prokaryotic and eukaryotic data show that use of an incomplete event model has substantial impact on the events inferred and resulting biological conclusions.<br><br>AVAILABILITY: Our algorithms have been implemented in Notung, a freely available phylogenetic reconciliation software package, available at http://www.cs.cmu.edu/~durand/Notung.<br><br>CONTACT: mstolzer@andrew.cmu.edu.}, }
@article {pmid22960016, year = {2012}, author = {Wybouw, N and Balabanidou, V and Ballhorn, DJ and Dermauw, W and Grbić, M and Vontas, J and Van Leeuwen, T}, title = {A horizontally transferred cyanase gene in the spider mite Tetranychus urticae is involved in cyanate metabolism and is differentially expressed upon host plant change.}, journal = {Insect biochemistry and molecular biology}, volume = {42}, number = {12}, pages = {881-889}, doi = {10.1016/j.ibmb.2012.08.002}, pmid = {22960016}, issn = {1879-0240}, mesh = {Amino Acid Sequence ; Animals ; Arthropod Proteins/*genetics/metabolism ; Carbon-Nitrogen Lyases/*genetics/metabolism ; Escherichia coli ; Female ; Gene Expression ; *Host-Parasite Interactions ; Hydrogen Cyanide/metabolism ; Magnoliopsida/parasitology ; Molecular Sequence Data ; Phylogeny ; Recombinant Proteins/metabolism ; Sequence Analysis, DNA ; Tetranychidae/enzymology/*genetics ; }, abstract = {The genome of the phytophagous two-spotted spider mite Tetranychus urticae was recently sequenced, representing the first complete chelicerate genome, but also the first genome of a highly polyphagous agricultural pest. Genome analysis revealed the presence of an unexpected high number of cases of putative horizontal gene transfers, including a gene that encodes a cyanase or cyanate lyase. In this study we show by recombinant expression that the T. urticae cyanase remained functionally active after horizontal gene transfer and has a high affinity for cyanate. Cyanases were also detected in other plant parasitic spider mites species such as Tetranychus evansi and Panonychus citri, suggesting that an ancient gene transfer occurred before the diversification within the Tetranychidae family. To investigate the potential role of cyanase in the evolution of plant parasitic spider mites, we studied cyanase expression patterns in T. urticae in relation to host plant range and cyanogenesis, a common plant defense mechanism. Spider mites can alter cyanase expression levels after transfer to several new host plants, including the cyanogenic Phaseolus lunatus. However, the role of cyanase is probably not restricted to cyanide response, but likely to the plant nutritional quality as a whole. We finally discuss potential interactions between cyanase activity and pyrimidine and amino acid synthesis.}, }
@article {pmid22958895, year = {2012}, author = {Zhang, Y and Lin, K}, title = {A phylogenomic analysis of Escherichia coli / Shigella group: implications of genomic features associated with pathogenicity and ecological adaptation.}, journal = {BMC evolutionary biology}, volume = {12}, number = {}, pages = {174}, pmid = {22958895}, issn = {1471-2148}, mesh = {Adaptation, Biological ; Base Sequence ; *Biological Evolution ; Escherichia coli/*classification/genetics/pathogenicity ; *Genome, Bacterial ; Genomics ; Molecular Sequence Data ; *Phylogeny ; Shigella/*classification/genetics/pathogenicity ; }, abstract = {BACKGROUND: The Escherichia coli species contains a variety of commensal and pathogenic strains, and its intraspecific diversity is extraordinarily high. With the availability of an increasing number of E. coli strain genomes, a more comprehensive concept of their evolutionary history and ecological adaptation can be developed using phylogenomic analyses. In this study, we constructed two types of whole-genome phylogenies based on 34 E. coli strains using collinear genomic segments. The first phylogeny was based on the concatenated collinear regions shared by all of the studied genomes, and the second phylogeny was based on the variable collinear regions that are absent from at least one genome. Intuitively, the first phylogeny is likely to reveal the lineal evolutionary history among these strains (i.e., an evolutionary phylogeny), whereas the latter phylogeny is likely to reflect the whole-genome similarities of extant strains (i.e., a similarity phylogeny).<br><br>RESULTS: Within the evolutionary phylogeny, the strains were clustered in accordance with known phylogenetic groups and phenotypes. When comparing evolutionary and similarity phylogenies, a concept emerges that Shigella may have originated from at least three distinct ancestors and evolved into a single clade. By scrutinizing the properties that are shared amongst Shigella strains but missing in other E. coli genomes, we found that the common regions of the Shigella genomes were mainly influenced by mobile genetic elements, implying that they may have experienced convergent evolution via horizontal gene transfer. Based on an inspection of certain key branches of interest, we identified several collinear regions that may be associated with the pathogenicity of specific strains. Moreover, by examining the annotated genes within these regions, further detailed evidence associated with pathogenicity was revealed.<br><br>CONCLUSIONS: Collinear regions are reliable genomic features used for phylogenomic analysis among closely related genomes while linking the genomic diversity with phenotypic differences in a meaningful way. The pathogenicity of a strain may be associated with both the arrival of virulence factors and the modification of genomes via mutations. Such phylogenomic studies that compare collinear regions of whole genomes will help to better understand the evolution and adaptation of closely related microbes and E. coli in particular.}, }
@article {pmid22957938, year = {2012}, author = {English, G and Trunk, K and Rao, VA and Srikannathasan, V and Hunter, WN and Coulthurst, SJ}, title = {New secreted toxins and immunity proteins encoded within the Type VI secretion system gene cluster of Serratia marcescens.}, journal = {Molecular microbiology}, volume = {86}, number = {4}, pages = {921-936}, pmid = {22957938}, issn = {1365-2958}, support = {/WT_/Wellcome Trust/United Kingdom ; 083481/WT_/Wellcome Trust/United Kingdom ; 082596/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Sequence ; Anti-Bacterial Agents/metabolism ; Bacterial Proteins/chemistry/genetics/*metabolism ; Bacterial Secretion Systems/*genetics ; Bacterial Toxins/genetics/*metabolism ; Crystallography, X-Ray ; Evolution, Molecular ; Gene Transfer, Horizontal ; Models, Molecular ; Molecular Sequence Data ; *Multigene Family ; Protein Binding ; Protein Conformation ; Sequence Alignment ; Serratia marcescens/*genetics/*metabolism ; }, abstract = {Protein secretion systems are critical to bacterial virulence and interactions with other organisms. The Type VI secretion system (T6SS) is found in many bacterial species and is used to target either eukaryotic cells or competitor bacteria. However, T6SS-secreted proteins have proven surprisingly elusive. Here, we identified two secreted substrates of the antibacterial T6SS from the opportunistic human pathogen, Serratia marcescens. Ssp1 and Ssp2, both encoded within the T6SS gene cluster, were confirmed as antibacterial toxins delivered by the T6SS. Four related proteins encoded around the Ssp proteins ('Rap' proteins) included two specifically conferring self-resistance ('immunity') against T6SS-dependent Ssp1 or Ssp2 toxicity. Biochemical characterization revealed specific, tight binding between cognate Ssp-Rap pairs, forming complexes of 2:2 stoichiometry. The atomic structures of two Rap proteins were solved, revealing a novel helical fold, dependent on a structural disulphide bond, a structural feature consistent with their functional localization. Homologues of the Serratia Ssp and Rap proteins are found encoded together within other T6SS gene clusters, thus they represent founder members of new families of T6SS-secreted and cognate immunity proteins. We suggest that Ssp proteins are the original substrates of the S. marcescens T6SS, before horizontal acquisition of other T6SS-secreted toxins. Molecular insight has been provided into how pathogens utilize antibacterial T6SSs to overcome competitors and succeed in polymicrobial niches.}, }
@article {pmid22955834, year = {2012}, author = {Cordero, OX and Wildschutte, H and Kirkup, B and Proehl, S and Ngo, L and Hussain, F and Le Roux, F and Mincer, T and Polz, MF}, title = {Ecological populations of bacteria act as socially cohesive units of antibiotic production and resistance.}, journal = {Science (New York, N.Y.)}, volume = {337}, number = {6099}, pages = {1228-1231}, doi = {10.1126/science.1219385}, pmid = {22955834}, issn = {1095-9203}, mesh = {Anti-Bacterial Agents/*biosynthesis ; *Antibiosis ; DNA Transposable Elements ; *Drug Resistance, Bacterial ; *Ecosystem ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Genotype ; *Microbial Interactions ; Molecular Sequence Data ; Oceans and Seas ; Polyketide Synthases/genetics ; Seawater/*microbiology ; Vibrio/*drug effects/genetics/metabolism/*physiology ; }, abstract = {In animals and plants, social structure can reduce conflict within populations and bias aggression toward competing populations; however, for bacteria in the wild it remains unknown whether such population-level organization exists. Here, we show that environmental bacteria are organized into socially cohesive units in which antagonism occurs between rather than within ecologically defined populations. By screening approximately 35,000 possible mutual interactions among Vibrionaceae isolates from the ocean, we show that genotypic clusters known to have cohesive habitat association also act as units in terms of antibiotic production and resistance. Genetic analyses show that within populations, broad-range antibiotics are produced by few genotypes, whereas all others are resistant, suggesting cooperation between conspecifics. Natural antibiotics may thus mediate competition between populations rather than solely increase the success of individuals.}, }
@article {pmid22954750, year = {2012}, author = {Dantas, G and Sommer, MO}, title = {Context matters - the complex interplay between resistome genotypes and resistance phenotypes.}, journal = {Current opinion in microbiology}, volume = {15}, number = {5}, pages = {577-582}, doi = {10.1016/j.mib.2012.07.004}, pmid = {22954750}, issn = {1879-0364}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics ; Bacterial Infections/*microbiology ; *Environmental Microbiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genotype ; Humans ; Phenotype ; }, abstract = {Application of metagenomic functional selections to study antibiotic resistance genes is revealing a highly diverse and complex network of genetic exchange between bacterial pathogens and environmental reservoirs, which likely contributes significantly to increasing resistance levels in pathogens. In some cases, clinically relevant resistance genes have been acquired from organisms where their native function is not antibiotic resistance, and which may not even confer a resistance phenotype in their native context. In this review, we attempt to distinguish the resistance phenotype from the resistome genotype, and we highlight examples of genes and their hosts where this distinction becomes important in order to understand the relevance of environmental niches that contribute most to clinical problems associated with antibiotic resistance.}, }
@article {pmid22953741, year = {2012}, author = {Lay, KK and Koowattananukul, C and Chansong, N and Chuanchuen, R}, title = {Antimicrobial resistance, virulence, and phylogenetic characteristics of Escherichia coli isolates from clinically healthy swine.}, journal = {Foodborne pathogens and disease}, volume = {9}, number = {11}, pages = {992-1001}, doi = {10.1089/fpd.2012.1175}, pmid = {22953741}, issn = {1556-7125}, mesh = {Animals ; Anti-Infective Agents/*pharmacology ; Bacterial Proteins/*genetics ; DNA Gyrase/genetics ; DNA Topoisomerase IV/genetics ; DNA, Bacterial/chemistry/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/classification/drug effects/*genetics/pathogenicity ; Escherichia coli Infections/microbiology/*veterinary ; Gene Transfer, Horizontal ; Genotype ; Integrons/genetics ; Microbial Sensitivity Tests ; Mutation ; Phenotype ; Phylogeny ; Sequence Analysis, DNA ; Swine ; Swine Diseases/*microbiology ; Thailand ; Virulence/genetics ; Virulence Factors/genetics ; }, abstract = {A total of 344 commensal Escherichia coli isolates from clinically healthy pigs were examined for antimicrobial resistance phenotypes, class 1 integrons, resistance genes, virulence gene profile, and phylogenetic groups. The majority of E. coli isolates were resistant to tetracycline (96.2%) and ampicillin (91.6%). Up to 98% were multidrug resistant. Seventy-three percent of the isolates carried class 1 integrons. Inserted-gene cassette arrays in variable regions included incomplete sat, aadA22, aadA1, dfrA12-aadA2, and sat-psp-aadA2, of which the aadA2 gene cassette was most prevalent (42.9%). Horizontal transfer was detected in eight E. coli isolates carrying class 1 integrons with dfrA12-aadA2 gene cassette array. Sixteen resistance genes were identified among the E. coli isolates with corresponding resistance phenotype. Ten virulence genes (including elt, estA, estB, astA, faeG, fasA, fedA, eaeA, paa, and sepA) were detected, of which fasA was most commonly found (98.3%). Most of the E. coli isolates belonged to phylogenetic group B1. Significantly positive associations were observed between some virulence genes and some resistance phenotypes and genotypes (p < 0.05). The results support a finding that commensal E. coli have a role as reservoirs for antimicrobial resistance-encoding genes and virulence determinants.}, }
@article {pmid22952830, year = {2012}, author = {Song, J and Shi, L and Li, D and Sun, Y and Niu, Y and Chen, Z and Luo, H and Pang, X and Sun, Z and Liu, C and Lv, A and Deng, Y and Larson-Rabin, Z and Wilkinson, M and Chen, S}, title = {Extensive pyrosequencing reveals frequent intra-genomic variations of internal transcribed spacer regions of nuclear ribosomal DNA.}, journal = {PloS one}, volume = {7}, number = {8}, pages = {e43971}, pmid = {22952830}, issn = {1932-6203}, mesh = {Cell Nucleus/*genetics ; DNA Barcoding, Taxonomic ; DNA, Ribosomal Spacer/*genetics ; Evolution, Molecular ; Genetic Variation/*genetics ; Genome, Plant/*genetics ; Plants/classification/genetics ; Reproducibility of Results ; *Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Internal transcribed spacer of nuclear ribosomal DNA (nrDNA) is already one of the most popular phylogenetic and DNA barcoding markers. However, the existence of its multiple copies has complicated such usage and a detailed characterization of intra-genomic variations is critical to address such concerns.<br><br>In this study, we used sequence-tagged pyrosequencing and genome-wide analyses to characterize intra-genomic variations of internal transcribed spacer 2 (ITS2) regions from 178 plant species. We discovered that mutation of ITS2 is frequent, with a mean of 35 variants per species. And on average, three of the most abundant variants make up 91% of all ITS2 copies. Moreover, we found different congeneric species share identical variants in 13 genera. Interestingly, different species across different genera also share identical variants. In particular, one minor variant of ITS2 in Eleutherococcus giraldii was found identical to the ITS2 major variant of Panax ginseng, both from Araliaceae family. In addition, DNA barcoding gap analysis showed that the intra-genomic distances were markedly smaller than those of the intra-specific or inter-specific variants. When each of 5543 variants were examined for its species discrimination efficiency, a 97% success rate was obtained at the species level.<br><br>CONCLUSIONS: Identification of identical ITS2 variants across intra-generic or inter-generic species revealed complex species evolutionary history, possibly, horizontal gene transfer and ancestral hybridization. Although intra-genomic multiple variants are frequently found within each genome, the usage of the major variants alone is sufficient for phylogeny construction and species determination in most cases. Furthermore, the inclusion of minor variants further improves the resolution of species identification.}, }
@article {pmid22947466, year = {2012}, author = {Tremblay, CL and Letellier, A and Quessy, S and Daignault, D and Archambault, M}, title = {Antibiotic-resistant Enterococcus faecalis in abattoir pigs and plasmid colocalization and cotransfer of tet(M) and erm(B) genes.}, journal = {Journal of food protection}, volume = {75}, number = {9}, pages = {1595-1602}, doi = {10.4315/0362-028X.JFP-12-047}, pmid = {22947466}, issn = {1944-9097}, mesh = {Abattoirs ; Animals ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/*genetics ; Canada/epidemiology ; Drug Resistance, Multiple, Bacterial/*genetics ; *Enterococcus faecalis/drug effects/genetics/isolation &amp; purification ; Food Microbiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Microbial Sensitivity Tests ; Swine/*microbiology ; }, abstract = {This study was conducted to determine plasmid colocalization and transferability of both erm(B) and tet(M) genes in Enterococcus faecalis isolates from abattoir pigs in Canada. A total of 124 E. faecalis isolates from cecal contents of abattoir pigs were examined for antibiotic susceptibility. High percentages of resistance to macrolides and tetracyclines were found. Two predominant multiresistance patterns of E. faecalis were examined by PCR and sequencing for the presence of genes encoding antibiotic resistance. Various combinations of antibiotic resistance genes were detected; erm(B) and tet(M) were the most common genes. Plasmid profiling and hybridization revealed that both genes were colocated on a ~9-kb transferable plasmid in six strains with the two predominant multiresistant patterns. Plasmid colocalization and cotransfer of tet(M) and erm(B) genes in porcine E. faecalis isolates indicates that antibiotic coselection and transferability could occur via this single genetic element. To our knowledge, this is the first report on plasmid colocalization and transferability of erm(B) and tet(M) genes in E. faecalis on a mobile genetic element of ~9 kb. Physical linkage between important antibiotic resistance determinants in enterococci is of interest for predicting potential transfer to other bacterial genera.}, }
@article {pmid22947175, year = {2012}, author = {Mappley, LJ and Black, ML and AbuOun, M and Darby, AC and Woodward, MJ and Parkhill, J and Turner, AK and Bellgard, MI and La, T and Phillips, ND and La Ragione, RM and Hampson, DJ}, title = {Comparative genomics of Brachyspira pilosicoli strains: genome rearrangements, reductions and correlation of genetic compliment with phenotypic diversity.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {454}, pmid = {22947175}, issn = {1471-2164}, mesh = {Amino Acid Oxidoreductases/genetics ; Animals ; Bacterial Proteins/*genetics ; Bacteriophages/genetics ; Birds/microbiology ; Brachyspira/*genetics ; *Gene Rearrangement ; *Genetic Association Studies ; Genetic Variation ; Genome Size ; *Genome, Bacterial ; *Genomics ; Genotype ; Host Specificity ; Humans/microbiology ; Interspersed Repetitive Sequences ; Multienzyme Complexes/genetics ; Peptide Hydrolases/genetics ; Phenotype ; Swine/microbiology ; Transposases/genetics ; }, abstract = {BACKGROUND: The anaerobic spirochaete Brachyspira pilosicoli causes enteric disease in avian, porcine and human hosts, amongst others. To date, the only available genome sequence of B. pilosicoli is that of strain 95/1000, a porcine isolate. In the first intra-species genome comparison within the Brachyspira genus, we report the whole genome sequence of B. pilosicoli B2904, an avian isolate, the incomplete genome sequence of B. pilosicoli WesB, a human isolate, and the comparisons with B. pilosicoli 95/1000. We also draw on incomplete genome sequences from three other Brachyspira species. Finally we report the first application of the high-throughput Biolog phenotype screening tool on the B. pilosicoli strains for detailed comparisons between genotype and phenotype.<br><br>RESULTS: Feature and sequence genome comparisons revealed a high degree of similarity between the three B. pilosicoli strains, although the genomes of B2904 and WesB were larger than that of 95/1000 (~2,765, 2.890 and 2.596 Mb, respectively). Genome rearrangements were observed which correlated largely with the positions of mobile genetic elements. Through comparison of the B2904 and WesB genomes with the 95/1000 genome, features that we propose are non-essential due to their absence from 95/1000 include a peptidase, glycine reductase complex components and transposases. Novel bacteriophages were detected in the newly-sequenced genomes, which appeared to have involvement in intra- and inter-species horizontal gene transfer. Phenotypic differences predicted from genome analysis, such as the lack of genes for glucuronate catabolism in 95/1000, were confirmed by phenotyping.<br><br>CONCLUSIONS: The availability of multiple B. pilosicoli genome sequences has allowed us to demonstrate the substantial genomic variation that exists between these strains, and provides an insight into genetic events that are shaping the species. In addition, phenotype screening allowed determination of how genotypic differences translated to phenotype. Further application of such comparisons will improve understanding of the metabolic capabilities of Brachyspira species.}, }
@article {pmid22940801, year = {2013}, author = {Peng, P and Yang, H and Jia, R and Li, L}, title = {Biodegradation of dioxin by a newly isolated Rhodococcus sp. with the involvement of self-transmissible plasmids.}, journal = {Applied microbiology and biotechnology}, volume = {97}, number = {12}, pages = {5585-5595}, doi = {10.1007/s00253-012-4363-y}, pmid = {22940801}, issn = {1432-0614}, mesh = {Bacillus cereus/genetics ; Biotransformation ; Carbon/metabolism ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Dioxins/*metabolism ; Gene Transfer, Horizontal ; Metabolic Networks and Pathways/genetics ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; *Plasmids ; RNA, Ribosomal, 16S/genetics ; Rhodococcus/classification/genetics/isolation &amp; purification/*metabolism ; Sequence Analysis, DNA ; }, abstract = {A newly isolated Rhodococcus sp. strain p52 could aerobically utilize dibenzofuran as the sole source of carbon and energy, and completely remove dibenzofuran at 500 mg l(-1) within 48 h. The strain metabolizes dibenzofuran by initial angular dioxygenation to yield 2,2',3-trihydroxybiphenyl. Strain p52 could also remove 70 % of 100 mg l(-1) 2-chlorodibenzofuran within 96 h and could metabolize a variety of aromatic compounds, namely dibenzo-p-dioxin, 2,8-dichlorodibenzofuran, dibenzothiophene, biphenyl, naphthalene, fluorene, phenanthrene, anthracene, carbazole, indole, xanthene, phenoxathiin, xanthone, and 9-fluorenone. Two distinct gene clusters encoding angular dioxygenases (DbfA and DfdA) were amplified and sequenced. The dbfA and dfdA gene clusters are located on two circular plasmids, pDF01 and pDF02, respectively. Both plasmids are self-transmissible; that is, they can transfer to the Gram-positive bacterium Bacillus cereus by conjugation.}, }
@article {pmid22937899, year = {2012}, author = {Gazi, AD and Sarris, PF and Fadouloglou, VE and Charova, SN and Mathioudakis, N and Panopoulos, NJ and Kokkinidis, M}, title = {Phylogenetic analysis of a gene cluster encoding an additional, rhizobial-like type III secretion system that is narrowly distributed among Pseudomonas syringae strains.}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {188}, pmid = {22937899}, issn = {1471-2180}, mesh = {Bacterial Secretion Systems/*genetics ; Evolution, Molecular ; Gene Expression Profiling ; Gene Order ; Gene Transfer, Horizontal ; *Multigene Family ; *Phylogeny ; Plasmids ; Pseudomonas syringae/*genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Rhizobium/genetics ; Synteny ; }, abstract = {BACKGROUND: The central role of Type III secretion systems (T3SS) in bacteria-plant interactions is well established, yet unexpected findings are being uncovered through bacterial genome sequencing. Some Pseudomonas syringae strains possess an uncharacterized cluster of genes encoding putative components of a second T3SS (T3SS-2) in addition to the well characterized Hrc1 T3SS which is associated with disease lesions in host plants and with the triggering of hypersensitive response in non-host plants. The aim of this study is to perform an in silico analysis of T3SS-2, and to compare it with other known T3SSs.<br><br>RESULTS: Based on phylogenetic analysis and gene organization comparisons, the T3SS-2 cluster of the P. syringae pv. phaseolicola strain is grouped with a second T3SS found in the pNGR234b plasmid of Rhizobium sp. These additional T3SS gene clusters define a subgroup within the Rhizobium T3SS family. Although, T3SS-2 is not distributed as widely as the Hrc1 T3SS in P. syringae strains, it was found to be constitutively expressed in P. syringae pv phaseolicola through RT-PCR experiments.<br><br>CONCLUSIONS: The relatedness of the P. syringae T3SS-2 to a second T3SS from the pNGR234b plasmid of Rhizobium sp., member of subgroup II of the rhizobial T3SS family, indicates common ancestry and/or possible horizontal transfer events between these species. Functional analysis and genome sequencing of more rhizobia and P. syringae pathovars may shed light into why these bacteria maintain a second T3SS gene cluster in their genome.}, }
@article {pmid22936717, year = {2013}, author = {Sen, D and Brown, CJ and Top, EM and Sullivan, J}, title = {Inferring the evolutionary history of IncP-1 plasmids despite incongruence among backbone gene trees.}, journal = {Molecular biology and evolution}, volume = {30}, number = {1}, pages = {154-166}, pmid = {22936717}, issn = {1537-1719}, support = {P20 RR016448/RR/NCRR NIH HHS/United States ; P20RR16448/RR/NCRR NIH HHS/United States ; }, mesh = {Bayes Theorem ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genomics ; Phylogeny ; Plasmids/*genetics ; Proteobacteria/classification/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Plasmids of the incompatibility group IncP-1 can transfer and replicate in many genera of the Proteobacteria. They are composed of backbone genes that encode a variety of essential functions and accessory genes that have implications for human health and environmental remediation. Although it is well understood that the accessory genes are transferred horizontally between plasmids, recent studies have also provided examples of recombination in the backbone genes of IncP-1 plasmids. As a consequence, phylogeny estimation based on backbone genes is expected to produce conflicting gene tree topologies. The main goal of this study was therefore to infer the evolutionary history of IncP-1 plasmids in the presence of both vertical and horizontal gene transfer. This was achieved by quantifying the incongruence among gene trees and attributing it to known causes such as 1) phylogenetic uncertainty, 2) coalescent stochasticity, and 3) horizontal inheritance. Topologies of gene trees exhibited more incongruence than could be attributed to phylogenetic uncertainty alone. Species-tree estimation using a Bayesian framework that takes coalescent stochasticity into account was well supported, but it differed slightly from the maximum-likelihood tree estimated by concatenation of backbone genes. After removal of the gene that demonstrated a signal of intergroup recombination, the concatenated tree was congruent with the species-tree estimate, which itself was robust to inclusion/exclusion of the recombinant gene. Thus, in spite of horizontal gene exchange both within and among IncP-1 subgroups, the backbone genome of these IncP-1 plasmids retains a detectable vertical evolutionary history.}, }
@article {pmid22936033, year = {2012}, author = {Saccardo, F and Martini, M and Palmano, S and Ermacora, P and Scortichini, M and Loi, N and Firrao, G}, title = {Genome drafts of four phytoplasma strains of the ribosomal group 16SrIII.}, journal = {Microbiology (Reading, England)}, volume = {158}, number = {Pt 11}, pages = {2805-2814}, doi = {10.1099/mic.0.061432-0}, pmid = {22936033}, issn = {1465-2080}, mesh = {Bacterial Proteins/genetics ; Base Sequence ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Dictamnus/*microbiology ; *Genome, Bacterial ; Heracleum/*microbiology ; Molecular Sequence Data ; Phytoplasma/classification/*genetics/isolation &amp; purification ; Plant Diseases/*microbiology ; RNA, Ribosomal, 16S/*genetics ; Vaccinium/*microbiology ; }, abstract = {By applying a coverage-based read selection and filtration through a healthy plant dataset, and a post-assembly contig selection based on homology and linkage, genome sequence drafts were obtained for four phytoplasma strains belonging to the 16SrIII group (X disease clade), namely Vaccinium Witches' Broom phytoplasma (647 754 nt in 272 contigs), Italian Clover Phyllody phytoplasma strain MA (597 245 nt in 197 contigs), Poinsettia branch-inducing phytoplasma strain JR1 (631 440 nt in 185 contigs) and Milkweed Yellows phytoplasma (583 806 nt in 158 contigs). Despite assignment to different 16SrIII subgroups, the genomes of the four strains were similar, comprising a highly conserved core (92-98 % similar in their nucleotide sequence among each other over alignments about 500 kb in length) and a minor strain-specific component. As far as their protein complement was concerned, they did not differ significantly in their basic metabolism potential from the genomes of other wide-host-range phytoplasmas sequenced previously, but were distinct from strains of other species, as well as among each other, in genes encoding functions conceivably related to interactions with the host, such as membrane trafficking components, proteases, DNA methylases, effectors and several hypothetical proteins of unknown function, some of which are likely secreted through the Sec-dependent secretion system. The four genomes displayed a group of genes encoding hypothetical proteins with high similarity to a central domain of IcmE/DotG, a core component of the type IVB secretion system of Gram-negative Legionella spp. Conversely, genes encoding functional GroES/GroEL chaperones were not detected in any of the four drafts. The results also indicated the significant role of horizontal gene transfer among different 'Candidatus Phytoplasma' species in shaping phytoplasma genomes and promoting their diversity.}, }
@article {pmid22934638, year = {2012}, author = {Syvanen, M}, title = {Evolutionary implications of horizontal gene transfer.}, journal = {Annual review of genetics}, volume = {46}, number = {}, pages = {341-358}, doi = {10.1146/annurev-genet-110711-155529}, pmid = {22934638}, issn = {1545-2948}, mesh = {Animals ; Bacteria/classification/*genetics ; Computational Biology ; DNA Transposable Elements ; Eukaryota/classification/*genetics ; *Evolution, Molecular ; Gene Flow ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomic Islands ; Mutation ; Phylogeny ; Reproduction/genetics ; Selection, Genetic ; }, abstract = {The flow of genes between different species represents a form of genetic variation whose implications have not been fully appreciated. Here I examine some key findings on the extent of horizontal gene transfer (HGT) revealed by comparative genome analysis and their theoretical implications. In theoretical terms, HGT affects ideas pertaining to the tree of life, the notion of a last universal common ancestor, and the biological unities, as well as the rules of taxonomic nomenclature. This review discusses the emergence of the eukaryotic cell and the occurrence of HGT among metazoan phyla involving both transposable elements and structural genes for normal housekeeping functions. I also discuss the bacterial pangenome, which provides an important case study on the permeability of species boundaries. An interesting observation about bdelloid rotifers and their reversion to asexual reproduction as it pertains to HGT is included.}, }
@article {pmid22934248, year = {2012}, author = {Bordeleau, E and Ghinet, MG and Burrus, V}, title = {Diversity of integrating conjugative elements in actinobacteria: Coexistence of two mechanistically different DNA-translocation systems.}, journal = {Mobile genetic elements}, volume = {2}, number = {2}, pages = {119-124}, pmid = {22934248}, issn = {2159-2543}, abstract = {Conjugation is certainly the most widespread and promiscuous mechanism of horizontal gene transfer in bacteria. During conjugation, DNA translocation across membranes of two cells forming a mating pair is mediated by two types of mobile genetic elements: conjugative plasmids and integrating conjugative elements (ICEs). The vast majority of conjugative plasmids and ICEs employ a sophisticated protein secretion apparatus called type IV secretion system to transfer to a recipient cell. Yet another type of conjugative DNA translocation machinery exists and to date appears to be unique to conjugative plasmids and ICEs of the Actinomycetales order, a sub-group of high G + C Gram-positive bacteria. This conjugative system is reminiscent of the machinery that allows segregation of chromosomal DNA during bacterial cell division and sporulation, and relies on a single FtsK-homolog protein to translocate double-stranded DNA molecules to the recipient cell. Recent thorough sequence analyses reveal that while this latter strategy appears to be used by the majority of ICEs in Actinomycetales, the former is also predicted to be important in exchange of genetic material in actinobacteria.}, }
@article {pmid22934244, year = {2012}, author = {Chan, CX and Bhattacharya, D and Reyes-Prieto, A}, title = {Endosymbiotic and horizontal gene transfer in microbial eukaryotes: Impacts on cell evolution and the tree of life.}, journal = {Mobile genetic elements}, volume = {2}, number = {2}, pages = {101-105}, pmid = {22934244}, issn = {2159-2543}, abstract = {The evolution of microbial eukaryotes, in particular of photosynthetic lineages, is complicated by multiple instances of endosymbiotic and horizontal gene transfer (E/HGT) resulting from plastid origin(s). Our recent analysis of diatom membrane transporters provides evidence of red and/or green algal origins of 172 of the genes encoding these proteins (ca. 25% of the examined phylogenies), with the majority putatively derived from green algae. These data suggest that E/HGT has been an important driver of evolutionary innovation among diatoms (and likely other stramenopiles), and lend further support to the hypothesis of an ancient, cryptic green algal endosymbiosis in "chromalveolate" lineages. Here, we discuss the implications of our findings on the understanding of eukaryote evolution and inference of the tree of life.}, }
@article {pmid22934241, year = {2012}, author = {Arias, MC and Danchin, EG and Coutinho, P and Henrissat, B and Ball, S}, title = {Eukaryote to gut bacteria transfer of a glycoside hydrolase gene essential for starch breakdown in plants.}, journal = {Mobile genetic elements}, volume = {2}, number = {2}, pages = {81-87}, pmid = {22934241}, issn = {2159-2543}, abstract = {Lateral gene transfer (LGT) between bacteria constitutes a strong force in prokaryote evolution, transforming the hierarchical tree of life into a network of relationships between species. In contrast, only a few cases of LGT from eukaryotes to prokaryotes have been reported so far. The distal animal intestine is predominantly a bacterial ecosystem, supplying the host with energy from dietary polysaccharides through carbohydrate-active enzymes absent from its genome. It has been suggested that LGT is particularly important for the human microbiota evolution. Here we show evidence for the first eukaryotic gene identified in multiple gut bacterial genomes. We found in the genome sequence of several gut bacteria, a typically eukaryotic glycoside-hydrolase necessary for starch breakdown in plants. The distribution of this gene is patchy in gut bacteria with presence otherwise detected only in a few environmental bacteria. We speculate that the transfer of this gene to gut bacteria occurred by a sequence of two key LGT events; first, an original eukaryotic gene was transferred probably from Archaeplastida to environmental bacteria specialized in plant polysaccharides degradation and second, the gene was transferred from the environmental bacteria to gut microbes.}, }
@article {pmid22933562, year = {2012}, author = {Ryall, B and Eydallin, G and Ferenci, T}, title = {Culture history and population heterogeneity as determinants of bacterial adaptation: the adaptomics of a single environmental transition.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {76}, number = {3}, pages = {597-625}, pmid = {22933562}, issn = {1098-5557}, mesh = {*Adaptation, Physiological ; Bacteria/classification/genetics/*growth &amp; development/metabolism ; *Bacterial Physiological Phenomena ; Culture Media ; *Gene Expression Regulation, Bacterial ; *Genetic Variation ; Genotype ; Humans ; Phenotype ; }, abstract = {Diversity in adaptive responses is common within species and populations, especially when the heterogeneity of the frequently large populations found in environments is considered. By focusing on events in a single clonal population undergoing a single transition, we discuss how environmental cues and changes in growth rate initiate a multiplicity of adaptive pathways. Adaptation is a comprehensive process, and stochastic, regulatory, epigenetic, and mutational changes can contribute to fitness and overlap in timing and frequency. We identify culture history as a major determinant of both regulatory adaptations and microevolutionary change. Population history before a transition determines heterogeneities due to errors in translation, stochastic differences in regulation, the presence of aged, damaged, cheating, or dormant cells, and variations in intracellular metabolite or regulator concentrations. It matters whether bacteria come from dense, slow-growing, stressed, or structured states. Genotypic adaptations are history dependent due to variations in mutation supply, contingency gene changes, phase variation, lateral gene transfer, and genome amplifications. Phenotypic adaptations underpin genotypic changes in situations such as stress-induced mutagenesis or prophage induction or in biofilms to give a continuum of adaptive possibilities. Evolutionary selection additionally provides diverse adaptive outcomes in a single transition and generally does not result in single fitter types. The totality of heterogeneities in an adapting population increases the chance that at least some individuals meet immediate or future challenges. However, heterogeneity complicates the adaptomics of single transitions, and we propose that subpopulations will need to be integrated into future population biology and systems biology predictions of bacterial behavior.}, }
@article {pmid22928673, year = {2013}, author = {Seitz, P and Blokesch, M}, title = {Cues and regulatory pathways involved in natural competence and transformation in pathogenic and environmental Gram-negative bacteria.}, journal = {FEMS microbiology reviews}, volume = {37}, number = {3}, pages = {336-363}, doi = {10.1111/j.1574-6976.2012.00353.x}, pmid = {22928673}, issn = {1574-6976}, mesh = {DNA/genetics/metabolism ; *DNA Transformation Competence ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Gram-Negative Bacteria/*genetics/metabolism ; }, abstract = {Bacterial genomics is flourishing, as whole-genome sequencing has become affordable, readily available and rapid. As a result, it has become clear how frequently horizontal gene transfer (HGT) occurs in bacteria. The potential implications are highly significant because HGT contributes to several processes, including the spread of antibiotic-resistance cassettes, the distribution of toxin-encoding phages and the transfer of pathogenicity islands. Three modes of HGT are recognized in bacteria: conjugation, transduction and natural transformation. In contrast to the first two mechanisms, natural competence for transformation does not rely on mobile genetic elements but is driven solely by a developmental programme in the acceptor bacterium. Once the bacterium becomes competent, it is able to take up DNA from the environment and to incorporate the newly acquired DNA into its own chromosome. The initiation and duration of competence differ significantly among bacteria. In this review, we outline the latest data on representative naturally transformable Gram-negative bacteria and how their competence windows differ. We also summarize how environmental cues contribute to the initiation of competence in a subset of naturally transformable Gram-negative bacteria and how the complexity of the niche might dictate the fine-tuning of the competence window.}, }
@article {pmid22926720, year = {2012}, author = {Traglia, GM and Almuzara, M and Merkier, AK and Adams, C and Galanternik, L and Vay, C and Centrón, D and Ramírez, MS}, title = {Achromobacter xylosoxidans: an emerging pathogen carrying different elements involved in horizontal genetic transfer.}, journal = {Current microbiology}, volume = {65}, number = {6}, pages = {673-678}, pmid = {22926720}, issn = {1432-0991}, support = {T37 MD001368/MD/NIMHD NIH HHS/United States ; 5T37MD001368-14/MD/NIMHD NIH HHS/United States ; }, mesh = {Achromobacter denitrificans/drug effects/*genetics/isolation &amp; purification/*pathogenicity ; Anti-Bacterial Agents/pharmacology ; Argentina ; Cross Infection/microbiology ; DNA Transposable Elements/*genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal/*genetics ; Gram-Negative Bacterial Infections/microbiology ; Humans ; Microbial Sensitivity Tests ; Sequence Analysis, DNA ; }, abstract = {In the last few years, numerous cases of multidrug-resistant Achromobacter xylosoxidans infections have been documented in immunocompromised and cystic fibrosis patients. To gain insights into the molecular mechanisms and mobile elements related to multidrug resistance in this bacterium, we studied 24 non-epidemiological A. xylosoxidans clinical isolates from Argentina. Specific primers for plasmids, transposons, insertion sequences, bla(ampC), intI1, and intI2 genes were used in PCR reactions. The obtained results showed the presence of wide host range IncP plasmids in ten isolates and a high dispersion of class 1 integrons (n = 10) and class 2 integrons (n = 3). Four arrays in the variable region (vr) of class 1 integrons were identified carrying different gene cassettes as the aminoglycoside resistance aac(6')-Ib and aadA1, the trimethoprim resistance dfrA1 and dfrA16, and the β-lactamase bla(OXA-2). In only one of the class 2 integrons, a vr was amplified that includes sat2-aadA1. The bla(ampC) gene was found in all isolates, confirming its ubiquitous nature. Our results show that A. xylosoxidans clinical isolates contain a rich variety of genetic elements commonly associated with resistance genes and their dissemination. This supports the hypothesis that A. xylosoxidans is becoming a reservoir of horizontal genetic transfer elements commonly involved in spreading antibiotic resistance.}, }
@article {pmid22925495, year = {2012}, author = {Moreau, H and Verhelst, B and Couloux, A and Derelle, E and Rombauts, S and Grimsley, N and Van Bel, M and Poulain, J and Katinka, M and Hohmann-Marriott, MF and Piganeau, G and Rouzé, P and Da Silva, C and Wincker, P and Van de Peer, Y and Vandepoele, K}, title = {Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage.}, journal = {Genome biology}, volume = {13}, number = {8}, pages = {R74}, pmid = {22925495}, issn = {1474-760X}, mesh = {Base Composition ; Chlorophyta/classification/*genetics ; Chromosomes, Plant/*genetics ; Evolution, Molecular ; Gene Order ; Gene Transfer, Horizontal ; Genome, Plant/*genetics ; Genomics ; Introns ; N-Acetylneuraminic Acid/metabolism ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Bathycoccus prasinos is an extremely small cosmopolitan marine green alga whose cells are covered with intricate spider's web patterned scales that develop within the Golgi cisternae before their transport to the cell surface. The objective of this work is to sequence and analyze its genome, and to present a comparative analysis with other known genomes of the green lineage.<br><br>RESEARCH: Its small genome of 15 Mb consists of 19 chromosomes and lacks transposons. Although 70% of all B. prasinos genes share similarities with other Viridiplantae genes, up to 428 genes were probably acquired by horizontal gene transfer, mainly from other eukaryotes. Two chromosomes, one big and one small, are atypical, an unusual synapomorphic feature within the Mamiellales. Genes on these atypical outlier chromosomes show lower GC content and a significant fraction of putative horizontal gene transfer genes. Whereas the small outlier chromosome lacks colinearity with other Mamiellales and contains many unknown genes without homologs in other species, the big outlier shows a higher intron content, increased expression levels and a unique clustering pattern of housekeeping functionalities. Four gene families are highly expanded in B. prasinos, including sialyltransferases, sialidases, ankyrin repeats and zinc ion-binding genes, and we hypothesize that these genes are associated with the process of scale biogenesis.<br><br>CONCLUSION: The minimal genomes of the Mamiellophyceae provide a baseline for evolutionary and functional analyses of metabolic processes in green plants.}, }
@article {pmid22924345, year = {2012}, author = {Puerto-Galán, L and Vioque, A}, title = {Expression and processing of an unusual tRNA gene cluster in the cyanobacterium Anabaena sp. PCC 7120.}, journal = {FEMS microbiology letters}, volume = {337}, number = {1}, pages = {10-17}, doi = {10.1111/j.1574-6968.2012.02664.x}, pmid = {22924345}, issn = {1574-6968}, mesh = {Amino Acyl-tRNA Synthetases/metabolism ; Anabaena/*genetics/metabolism ; Gene Expression ; *Multigene Family ; Plasmids ; RNA Processing, Post-Transcriptional ; RNA, Transfer/*genetics/metabolism ; Ribonuclease P/metabolism ; Sequence Deletion ; }, abstract = {Anabaena sp. PCC 7120 is a filamentous cyanobacterium that bears a cluster of 26 tRNA genes and pseudogenes in the delta plasmid. The sequences of these tRNAs suggest that they have been acquired by horizontal gene transfer from another organism. The cluster is transcribed as a single transcript that is quickly processed to individual tRNAs. RNase P and RNase Z, in vitro, are able to process precursors containing some of these tRNAs. Deletion of the cluster causes no obvious phenotype or effect on growth under diverse culture conditions, indicating that the tRNAs encoded in the cluster are not required for growth under laboratory conditions, although they are aminoacylated in vivo. We have studied a possible tRNA(Ser) [tRNA(Ser) GCU(2)] present in the cluster with a sequence that deviates from consensus. This tRNA is processed in vitro by RNase P at the expected position. In addition, this tRNA(Ser) GCU is specifically aminoacylated with serine by an Anabaena sp. PCC 7120 crude extract. These data indicate that tRNA(Ser) GCU(2) is fully functional, despite its unusual structure. Similar clusters are found in other three cyanobacteria whose genomes have been sequenced.}, }
@article {pmid22923402, year = {2012}, author = {Meessen-Pinard, M and Sekulovic, O and Fortier, LC}, title = {Evidence of in vivo prophage induction during Clostridium difficile infection.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {21}, pages = {7662-7670}, pmid = {22923402}, issn = {1098-5336}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Aza Compounds/pharmacology ; Base Sequence ; Ciprofloxacin/pharmacology ; *Clostridioides difficile/drug effects/genetics/pathogenicity/virology ; Clostridium Infections/genetics/microbiology/*virology ; DNA, Viral/genetics ; Feces/microbiology/*virology ; Fluoroquinolones ; Genetic Variation ; Genome, Viral ; Humans ; Levofloxacin ; Lysogeny ; Microbial Sensitivity Tests ; Mitomycin/pharmacology ; Molecular Sequence Data ; Moxifloxacin ; Myoviridae/genetics/*isolation &amp; purification/*physiology ; Ofloxacin/pharmacology ; Prophages/genetics/isolation &amp; purification/physiology ; Quinolines/pharmacology ; Sequence Analysis, DNA ; *Virus Activation/genetics ; }, abstract = {Prophages contribute to the evolution and virulence of most bacterial pathogens, but their role in Clostridium difficile is unclear. Here we describe the isolation of four Myoviridae phages, ΦMMP01, ΦMMP02, ΦMMP03, and ΦMMP04, that were recovered as free viral particles in the filter-sterilized stool supernatants of patients suffering from C. difficile infection (CDI). Furthermore, identical prophages were found in the chromosomes of C. difficile isolated from the corresponding fecal samples. We therefore provide, for the first time, evidence of in vivo prophage induction during CDI. We completely sequenced the genomes of ΦMMP02 and ΦMMP04, and bioinformatics analyses did not reveal the presence of virulence factors but underlined the unique character of ΦMMP04. We also studied the mobility of ΦMMP02 and ΦMMP04 prophages in vitro. Both prophages were spontaneously induced, with 4 to 5 log PFU/ml detected in the culture supernatants of the corresponding lysogens. When lysogens were grown in the presence of subinhibitory concentrations of ciprofloxacin, moxifloxacin, levofloxacin, or mitomycin C, the phage titers further increased, reaching 8 to 9 log PFU/ml in the case of ΦMMP04. In summary, our study highlights the extensive genetic diversity and mobility of C. difficile prophages. Moreover, antibiotics known to represent risk factors for CDI, such as quinolones, can stimulate prophage mobility in vitro and probably in vivo as well, which underscores their potential impact on phage-mediated horizontal gene transfer events and the evolution of C. difficile.}, }
@article {pmid22923103, year = {2012}, author = {Zhong, Z and Wang, Y and Xu, J and Chen, Y and Ke, Y and Zhou, X and Yuan, X and Zhou, D and Yang, Y and Yang, R and Peng, G and Jiang, H and Yuan, J and Song, H and Cui, B and Huang, L and Chen, Z}, title = {Parallel gene loss and acquisition among strains of different Brucella species and biovars.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {50}, number = {4}, pages = {567-574}, pmid = {22923103}, issn = {1976-3794}, mesh = {Animals ; Brucella/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genetic Variation ; Genomic Islands ; Humans ; Microarray Analysis ; Multigene Family ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; *Recombination, Genetic ; }, abstract = {The genus Brucella is divided into six species; of these, B. melitensis and B. abortus are pathogenic to humans, and B. ovis and B. neotomae are nonpathogenic to humans. The definition of gene loss and acquisition is essential for understanding Brucella's ecology, evolutionary history, and host relationships. A DNA microarray containing unique genes of B. melitensis Type strain 16MT and B. abortus 9-941 was constructed and used to determine the gene contents of the representative strains of Brucella. Phylogenetic relationships were inferred from sequences of housekeeping genes. Gene loss and acquisition of different Brucella species were inferred. A total of 214 genes were found to be differentially distributed, and 173 of them were clustered into 15 genomic islands (GIs). Evidence of horizontal gene transfer was observed for 10 GIs. Phylogenetic analysis indicated that the 19 strains formed five clades, and some of the GIs had been lost or acquired independently among the different lineages. The derivation of Brucella lineages is concomitant with the parallel loss or acquisition of GIs, indicating a complex interaction between various Brucella species and hosts.}, }
@article {pmid22923046, year = {2012}, author = {Judelson, HS}, title = {Dynamics and innovations within oomycete genomes: insights into biology, pathology, and evolution.}, journal = {Eukaryotic cell}, volume = {11}, number = {11}, pages = {1304-1312}, pmid = {22923046}, issn = {1535-9786}, mesh = {Adaptation, Biological ; Epigenesis, Genetic ; *Evolution, Molecular ; Gene Fusion ; *Genome ; Genome Size ; Oomycetes/classification/*genetics/*pathogenicity ; Phylogeny ; Plants/parasitology ; *Polymorphism, Genetic ; Retroelements ; Transcription, Genetic ; }, abstract = {The eukaryotic microbes known as oomycetes are common inhabitants of terrestrial and aquatic environments and include saprophytes and pathogens. Lifestyles of the pathogens extend from biotrophy to necrotrophy, obligate to facultative pathogenesis, and narrow to broad host ranges on plants or animals. Sequencing of several pathogens has revealed striking variation in genome size and content, a plastic set of genes related to pathogenesis, and adaptations associated with obligate biotrophy. Features of genome evolution include repeat-driven expansions, deletions, gene fusions, and horizontal gene transfer in a landscape organized into gene-dense and gene-sparse sectors and influenced by transposable elements. Gene expression profiles are also highly dynamic throughout oomycete life cycles, with transcriptional polymorphisms as well as differences in protein sequence contributing to variation. The genome projects have set the foundation for functional studies and should spur the sequencing of additional species, including more diverse pathogens and nonpathogens.}, }
@article {pmid22922659, year = {2013}, author = {Harada, K and Yamashita, E and Nakagawa, A and Miyafusa, T and Tsumoto, K and Ueno, T and Toyama, Y and Takeda, S}, title = {Crystal structure of the C-terminal domain of Mu phage central spike and functions of bound calcium ion.}, journal = {Biochimica et biophysica acta}, volume = {1834}, number = {1}, pages = {284-291}, doi = {10.1016/j.bbapap.2012.08.015}, pmid = {22922659}, issn = {0006-3002}, mesh = {Bacteriophage mu/*chemistry/metabolism ; Calcium/chemistry/metabolism ; Cell Membrane/chemistry/metabolism/virology ; Crystallography, X-Ray ; Escherichia coli/chemistry/metabolism/virology ; Protein Structure, Tertiary ; Viral Envelope Proteins/*chemistry/metabolism ; Virus Internalization ; }, abstract = {Bacteriophage Mu, which has a contractile tail, is one of the most famous genus of Myoviridae. It has a wide host range and is thought to contribute to horizontal gene transfer. The Myoviridae infection process is initiated by adhesion to the host surface. The phage then penetrates the host cell membrane using its tail to inject its genetic material into the host. In this penetration process, Myoviridae phages are proposed to puncture the membrane of the host cell using a central spike located beneath its baseplate. The central spike of the Mu phage is thought to be composed of gene 45 product (gp45), which has a significant sequence homology with the central spike of P2 phage (gpV). We determined the crystal structure of shortened Mu gp45Δ1-91 (Arg92-Gln197) at 1.5Å resolution and showed that Mu gp45 is a needlelike structure that punctures the membrane. The apex of Mu gp45 and that of P2 gpV contained iron, chloride, and calcium ions. Although the C-terminal domain of Mu gp45 was sufficient for binding to the E. coli membrane, a mutant D188A, in which the Asp amino acid residue that coordinates the calcium ion was replaced by Ala, did not exhibit a propensity to bind to the membrane. Therefore, we concluded that calcium ion played an important role in interaction with the host cell membrane.}, }
@article {pmid22920867, year = {2012}, author = {Daubin, V and Abby, S}, title = {[Healing the tree of life with lateral gene transfers].}, journal = {Medecine sciences : M/S}, volume = {28}, number = {8-9}, pages = {695-698}, doi = {10.1051/medsci/2012288007}, pmid = {22920867}, issn = {0767-0974}, mesh = {Bacteria/genetics ; *Evolution, Molecular ; Extinction, Biological ; *Gene Transfer, Horizontal ; Genetic Speciation ; Microbial Viability/genetics ; *Phylogeny ; Selection, Genetic ; }, }
@article {pmid22920653, year = {2012}, author = {Nasir, A and Kim, KM and Caetano-Anolles, G}, title = {Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya.}, journal = {BMC evolutionary biology}, volume = {12}, number = {}, pages = {156}, pmid = {22920653}, issn = {1471-2148}, mesh = {Archaea/virology ; Bacteria/virology ; *Biological Evolution ; Eukaryota/virology ; Gene Transfer, Horizontal ; Mimiviridae ; Models, Molecular ; *Phylogeny ; Protein Biosynthesis ; Protein Folding ; Protein Structure, Tertiary ; Proteome/analysis ; Viral Proteins/analysis ; Viruses/*classification/*genetics ; }, abstract = {BACKGROUND: The discovery of giant viruses with genome and physical size comparable to cellular organisms, remnants of protein translation machinery and virus-specific parasites (virophages) have raised intriguing questions about their origin. Evidence advocates for their inclusion into global phylogenomic studies and their consideration as a distinct and ancient form of life.<br><br>RESULTS: Here we reconstruct phylogenies describing the evolution of proteomes and protein domain structures of cellular organisms and double-stranded DNA viruses with medium-to-very-large proteomes (giant viruses). Trees of proteomes define viruses as a 'fourth supergroup' along with superkingdoms Archaea, Bacteria, and Eukarya. Trees of domains indicate they have evolved via massive and primordial reductive evolutionary processes. The distribution of domain structures suggests giant viruses harbor a significant number of protein domains including those with no cellular representation. The genomic and structural diversity embedded in the viral proteomes is comparable to the cellular proteomes of organisms with parasitic lifestyles. Since viral domains are widespread among cellular species, we propose that viruses mediate gene transfer between cells and crucially enhance biodiversity.<br><br>CONCLUSIONS: Results call for a change in the way viruses are perceived. They likely represent a distinct form of life that either predated or coexisted with the last universal common ancestor (LUCA) and constitute a very crucial part of our planet's biosphere.}, }
@article {pmid22920560, year = {2012}, author = {Jiang, RH and Tyler, BM}, title = {Mechanisms and evolution of virulence in oomycetes.}, journal = {Annual review of phytopathology}, volume = {50}, number = {}, pages = {295-318}, doi = {10.1146/annurev-phyto-081211-172912}, pmid = {22920560}, issn = {1545-2107}, support = {HHSN27220090018C//PHS HHS/United States ; }, mesh = {Animals ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome/genetics ; Host Specificity ; Host-Pathogen Interactions ; Oomycetes/genetics/*pathogenicity/physiology ; Plant Diseases/*parasitology ; Plant Immunity ; Plants/*parasitology ; Virulence/genetics ; Virulence Factors/*genetics ; }, abstract = {Many destructive diseases of plants and animals are caused by oomycetes, a group of eukaryotic pathogens important to agricultural, ornamental, and natural ecosystems. Understanding the mechanisms underlying oomycete virulence and the genomic processes by which those mechanisms rapidly evolve is essential to developing effective long-term control measures for oomycete diseases. Several common mechanisms underlying oomycete virulence, including protein toxins and cell-entering effectors, have emerged from comparing oomycetes with different genome characteristics, parasitic lifestyles, and host ranges. Oomycete genomes display a strongly bipartite organization in which conserved housekeeping genes are concentrated in syntenic gene-rich blocks, whereas virulence genes are dispersed into highly dynamic, repeat-rich regions. There is also evidence that key virulence genes have been acquired by horizontal transfer from other eukaryotic and prokaryotic species.}, }
@article {pmid22920519, year = {2012}, author = {Siefert, JL and Souza, V and Eguiarte, L and Olmedo-Alvarez, G}, title = {Microbial stowaways: inimitable survivors or hopeless pioneers?.}, journal = {Astrobiology}, volume = {12}, number = {7}, pages = {710-715}, doi = {10.1089/ast.2012.0833}, pmid = {22920519}, issn = {1557-8070}, mesh = {Bacteria/*metabolism ; Earth, Planet ; *Exobiology ; Life ; Mars ; }, abstract = {The resiliency of prokaryotic life has provided colonization across the globe and in the recesses of Earth's most extreme environments. Horizontal gene transfer provides access to a global bank of genetic resources that creates diversity and allows real-time adaptive potential to the clonal prokaryotic world. We assess the likelihood that this Earth-based strategy could provide survival and adaptive potential, in the case of microbial stowaways off Earth.}, }
@article {pmid22920513, year = {2012}, author = {Souza, V and Eguiarte, LE and Travisano, M and Elser, JJ and Rooks, C and Siefert, JL}, title = {Travel, sex, and food: what's speciation got to do with it?.}, journal = {Astrobiology}, volume = {12}, number = {7}, pages = {634-640}, pmid = {22920513}, issn = {1557-8070}, mesh = {Bacteria/*genetics/*metabolism ; Gene Flow/*genetics ; Gene Transfer, Horizontal/*genetics ; *Genetic Speciation ; Mexico ; }, abstract = {We discuss the potential interactions among travel (dispersal and gene flow), bacterial "sex" (mainly as horizontal gene transfer), and food (metabolic plasticity and responses to nutrient availability) in shaping microbial communities. With regard to our work at a unique desert oasis, the Cuatro Ciénegas Basin in Coahuila, Mexico, we propose that diversification and low phosphorus availability, in combination with mechanisms for nutrient recycling and community cohesion, result in enhanced speciation through reproductive as well as geographic isolation. We also discuss these mechanisms in the broader sense of ecology and evolution. Of special relevance to astrobiology and central to evolutionary biology, we ask why there are so many species on Earth and provide a working hypothesis and a conceptual framework within which to consider the question. Key Words: Microbial ecology-Microbial mats-Evolution-Horizontal gene transfer-Metabolism.}, }
@article {pmid22919697, year = {2012}, author = {Bertelli, C and Greub, G}, title = {Lateral gene exchanges shape the genomes of amoeba-resisting microorganisms.}, journal = {Frontiers in cellular and infection microbiology}, volume = {2}, number = {}, pages = {110}, pmid = {22919697}, issn = {2235-2988}, mesh = {Amoeba/*microbiology ; Bacteria/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genetic Variation ; Genome, Bacterial ; Selection, Genetic ; }, abstract = {Based on Darwin's concept of the tree of life, vertical inheritance was thought to be dominant, and mutations, deletions, and duplication were streaming the genomes of living organisms. In the current genomic era, increasing data indicated that both vertical and lateral gene inheritance interact in space and time to trigger genome evolution, particularly among microorganisms sharing a given ecological niche. As a paradigm to their diversity and their survival in a variety of cell types, intracellular microorganisms, and notably intracellular bacteria, were considered as less prone to lateral genetic exchanges. Such specialized microorganisms generally have a smaller gene repertoire because they do rely on their host's factors for some basic regulatory and metabolic functions. Here we review events of lateral gene transfer (LGT) that illustrate the genetic exchanges among intra-amoebal microorganisms or between the microorganism and its amoebal host. We tentatively investigate the functions of laterally transferred genes in the light of the interaction with their host as they should confer a selective advantage and success to the amoeba-resisting microorganisms (ARMs).}, }
@article {pmid22919695, year = {2012}, author = {Forterre, P}, title = {Darwin's goldmine is still open: variation and selection run the world.}, journal = {Frontiers in cellular and infection microbiology}, volume = {2}, number = {}, pages = {106}, pmid = {22919695}, issn = {2235-2988}, mesh = {*Biological Evolution ; *Genetic Variation ; Humans ; *Selection, Genetic ; }, abstract = {The scientific contribution of Darwin, still agonized in many religious circles, has now been recognized and celebrated by scientists from various disciplines. However, in recent years, several evolutionists have criticized Darwin as outdated, arguing that "Darwinism," assimilated to the "tree of life," cannot explain microbial evolution, or else was not operating in early life evolution. These critics either confuse "Darwinism" and old versions of "neo-Darwinism" or misunderstand the role of gene transfers in evolution. The core of Darwin explanation of evolution (variation/selection) remains necessary and sufficient to decipher the history of life. The enormous diversity of mechanisms underlying variations has been successfully interpreted by evolutionists in this framework and has considerably enriched the corpus of evolutionary biology without the necessity to kill the father. However, it remains for evolutionists to acknowledge interactions between cells and viruses (unknown for Darwin) as a major driving force in life evolution.}, }
@article {pmid22919687, year = {2012}, author = {Bhandari, V and Naushad, HS and Gupta, RS}, title = {Protein based molecular markers provide reliable means to understand prokaryotic phylogeny and support Darwinian mode of evolution.}, journal = {Frontiers in cellular and infection microbiology}, volume = {2}, number = {}, pages = {98}, pmid = {22919687}, issn = {2235-2988}, mesh = {Archaea/*genetics ; Archaeal Proteins/*genetics ; Bacteria/*genetics ; Bacterial Proteins/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Phylogeny ; }, abstract = {The analyses of genome sequences have led to the proposal that lateral gene transfers (LGTs) among prokaryotes are so widespread that they disguise the interrelationships among these organisms. This has led to questioning of whether the Darwinian model of evolution is applicable to prokaryotic organisms. In this review, we discuss the usefulness of taxon-specific molecular markers such as conserved signature indels (CSIs) and conserved signature proteins (CSPs) for understanding the evolutionary relationships among prokaryotes and to assess the influence of LGTs on prokaryotic evolution. The analyses of genomic sequences have identified large numbers of CSIs and CSPs that are unique properties of different groups of prokaryotes ranging from phylum to genus levels. The species distribution patterns of these molecular signatures strongly support a tree-like vertical inheritance of the genes containing these molecular signatures that is consistent with phylogenetic trees. Recent detailed studies in this regard on the Thermotogae and Archaea, which are reviewed here, have identified large numbers of CSIs and CSPs that are specific for the species from these two taxa and a number of their major clades. The genetic changes responsible for these CSIs (and CSPs) initially likely occurred in the common ancestors of these taxa and then vertically transferred to various descendants. Although some CSIs and CSPs in unrelated groups of prokaryotes were identified, their small numbers and random occurrence has no apparent influence on the consistent tree-like branching pattern emerging from other markers. These results provide evidence that although LGT is an important evolutionary force, it does not mask the tree-like branching pattern of prokaryotes or understanding of their evolutionary relationships. The identified CSIs and CSPs also provide novel and highly specific means for identification of different groups of microbes and for taxonomical and biochemical studies.}, }
@article {pmid22919680, year = {2012}, author = {Aravind, L and Anantharaman, V and Zhang, D and de Souza, RF and Iyer, LM}, title = {Gene flow and biological conflict systems in the origin and evolution of eukaryotes.}, journal = {Frontiers in cellular and infection microbiology}, volume = {2}, number = {}, pages = {89}, pmid = {22919680}, issn = {2235-2988}, mesh = {Adaptation, Biological ; Eukaryota/*genetics ; *Evolution, Molecular ; *Gene Flow ; Gene Transfer, Horizontal ; *Symbiosis ; }, abstract = {The endosymbiotic origin of eukaryotes brought together two disparate genomes in the cell. Additionally, eukaryotic natural history has included other endosymbiotic events, phagotrophic consumption of organisms, and intimate interactions with viruses and endoparasites. These phenomena facilitated large-scale lateral gene transfer and biological conflicts. We synthesize information from nearly two decades of genomics to illustrate how the interplay between lateral gene transfer and biological conflicts has impacted the emergence of new adaptations in eukaryotes. Using apicomplexans as example, we illustrate how lateral transfer from animals has contributed to unique parasite-host interfaces comprised of adhesion- and O-linked glycosylation-related domains. Adaptations, emerging due to intense selection for diversity in the molecular participants in organismal and genomic conflicts, being dispersed by lateral transfer, were subsequently exapted for eukaryote-specific innovations. We illustrate this using examples relating to eukaryotic chromatin, RNAi and RNA-processing systems, signaling pathways, apoptosis and immunity. We highlight the major contributions from catalytic domains of bacterial toxin systems to the origin of signaling enzymes (e.g., ADP-ribosylation and small molecule messenger synthesis), mutagenic enzymes for immune receptor diversification and RNA-processing. Similarly, we discuss contributions of bacterial antibiotic/siderophore synthesis systems and intra-genomic and intra-cellular selfish elements (e.g., restriction-modification, mobile elements and lysogenic phages) in the emergence of chromatin remodeling/modifying enzymes and RNA-based regulation. We develop the concept that biological conflict systems served as evolutionary "nurseries" for innovations in the protein world, which were delivered to eukaryotes via lateral gene flow to spur key evolutionary innovations all the way from nucleogenesis to lineage-specific adaptations.}, }
@article {pmid22919651, year = {2012}, author = {Georgiades, K and Raoult, D}, title = {How microbiology helps define the rhizome of life.}, journal = {Frontiers in cellular and infection microbiology}, volume = {2}, number = {}, pages = {60}, pmid = {22919651}, issn = {2235-2988}, mesh = {*Evolution, Molecular ; *Gene Transfer, Horizontal ; *Recombination, Genetic ; *Selection, Genetic ; }, abstract = {In contrast to the tree of life (TOF) theory, species are mosaics of gene sequences with different origins. Observations of the extensive lateral sequence transfers in all organisms have demonstrated that the genomes of all life forms are collections of genes with different evolutionary histories that cannot be represented by a single TOF. Moreover, genes themselves commonly have several origins due to recombination. The human genome is not free from recombination events, so it is a mosaic like other organisms' genomes. Recent studies have demonstrated evidence for the integration of parasitic DNA into the human genome. Lateral transfer events have been accepted as major contributors of genome evolution in free-living bacteria. Furthermore, the accumulation of genomic sequence data provides evidence for extended genetic exchanges in intracellular bacteria and suggests that such events constitute an agent that promotes and maintains all bacterial species. Archaea and viruses also form chimeras containing primarily bacterial but also eukaryotic sequences. In addition to lateral transfers, orphan genes are indicative of the fact that gene creation is a permanent and unsettled phenomenon. Currently, a rhizome may more adequately represent the multiplicity and de novo creation of a genome. We wanted to confirm that the term "rhizome" in evolutionary biology applies to the entire cellular life history. This view of evolution should resemble a clump of roots representing the multiple origins of the repertoires of the genes of each species.}, }
@article {pmid22919641, year = {2012}, author = {Ramulu, HG and Raoult, D and Pontarotti, P}, title = {The rhizome of life: what about metazoa?.}, journal = {Frontiers in cellular and infection microbiology}, volume = {2}, number = {}, pages = {50}, pmid = {22919641}, issn = {2235-2988}, mesh = {Animals ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Mammals ; Nematoda ; Recombination, Genetic ; }, abstract = {The increase in huge number of genomic sequences in recent years has contributed to various genetic events such as horizontal gene transfer (HGT), gene duplication and hybridization of species. Among them HGT has played an important role in the genome evolution and was believed to occur only in Bacterial and Archaeal genomes. As a result, genomes were found to be chimeric and the evolution of life was represented in different forms such as forests, networks and species evolution was described more like a rhizome, rather than a tree. However, in the last few years, HGT has also been evidenced in other group such as metazoa (for example in root-knot nematodes, bdelloid rotifers and mammals). In addition to HGT, other genetic events such as transfer by retrotransposons and hybridization between more closely related lineages are also well established. Therefore, in the light of such genetic events, whether the evolution of metazoa exists in the form of a tree, network or rhizome is highly questionable and needs to be determined. In the current review, we will focus on the role of HGT, retrotransposons and hybridization in the metazoan evolution.}, }
@article {pmid22919640, year = {2012}, author = {Monk, IR and Foster, TJ}, title = {Genetic manipulation of Staphylococci-breaking through the barrier.}, journal = {Frontiers in cellular and infection microbiology}, volume = {2}, number = {}, pages = {49}, pmid = {22919640}, issn = {2235-2988}, mesh = {*DNA Restriction-Modification Enzymes ; Escherichia coli/genetics ; Gene Transfer Techniques ; *Gene Transfer, Horizontal ; Plasmids ; Staphylococcus aureus/*genetics ; Staphylococcus epidermidis/*genetics ; }, abstract = {Most strains of Staphylococcus aureus and Staphylococcus epidermidis possess a strong restriction barrier that hinders exchange of DNA. Recently, major advances have been made in identifying and characterizing the restriction-modification (RM) systems involved. In particular a novel type IV restriction enzyme that recognizes cytosine methylated DNA has been shown to be the major barrier to transfer of plasmid DNA from Escherichia coli into S. aureus and S. epidermidis. While the conserved type I RM system provides a further barrier. Here we review the recent advances in understanding of restriction systems in staphylococci and highlight how this has been exploited to improve our ability to manipulate genetically previously untransformable strains.}, }
@article {pmid22919619, year = {2012}, author = {Danchin, EG and Rosso, MN}, title = {Lateral gene transfers have polished animal genomes: lessons from nematodes.}, journal = {Frontiers in cellular and infection microbiology}, volume = {2}, number = {}, pages = {27}, pmid = {22919619}, issn = {2235-2988}, mesh = {Animals ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Nematoda/*genetics/physiology ; Plants/parasitology ; }, abstract = {It is now accepted that lateral gene transfers (LGT), have significantly contributed to the composition of bacterial genomes. The amplitude of the phenomenon is considered so high in prokaryotes that it challenges the traditional view of a binary hierarchical tree of life to correctly represent the evolutionary history of species. Given the plethora of transfers between prokaryotes, it is currently impossible to infer the last common ancestral gene set for any extant species. For this ensemble of reasons, it has been proposed that the Darwinian binary tree of life may be inappropriate to correctly reflect the actual relations between species, at least in prokaryotes. In contrast, the contribution of LGT to the composition of animal genomes is less documented. In the light of recent analyses that reported series of LGT events in nematodes, we discuss the importance of this phenomenon in the evolutionary history and in the current composition of an animal genome. Far from being neutral, it appears that besides having contributed to nematode genome contents, LGT have favored the emergence of important traits such as plant-parasitism.}, }
@article {pmid22919598, year = {2012}, author = {McCarthy, AJ and Witney, AA and Lindsay, JA}, title = {Staphylococcus aureus temperate bacteriophage: carriage and horizontal gene transfer is lineage associated.}, journal = {Frontiers in cellular and infection microbiology}, volume = {2}, number = {}, pages = {6}, pmid = {22919598}, issn = {2235-2988}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Gene Transfer, Horizontal ; Genotype ; Humans ; Lysogeny ; Prophages/classification/*genetics ; Staphylococcal Infections/microbiology ; Staphylococcus Phages/classification/*genetics ; Staphylococcus aureus/*virology ; Virulence Factors/genetics ; }, abstract = {Staphylococcus aureus is a major cause of human and animal infections. Bacteriophage are a class of mobile genetic element (MGE) that carry virulence genes and disseminate them horizontally, including Panton-Valentine leukocidin (PVL), the immune evasion cluster (IEC) associated with human specificity, and enterotoxin A the major toxin associated with food poisoning. S. aureus isolates group into major clonal complex (CC) lineages that largely evolve independently due to possession of different restriction-modification (RM) systems. We aimed to better understand the horizontal and vertical transmission dynamics of virulence and resistance genes by bacteriophage by using (i) bioinformatic approaches to analyze bacteriophage genomes from the first 79 sequenced S. aureus isolates and (ii) S. aureus microarrays to analyze the distribution of bacteriophage and virulence genes in S. aureus isolates from a broader range of lineages. The distribution of eight bacteriophage families was highly variable but lineage associated. Nevertheless, there was evidence of frequent acquisition and loss and not just vertical transmission. Most bacteriophage genes were dispensable, and extensive mosaicism was seen. Surprisingly, virulence genes were tightly associated with specific phage families. This data suggests S. aureus bacteriophage evolve rapidly, and the horizontal gene transfer (HGT) of virulence genes encoded by bacteriophage is restricted by bacteriophage family and the lineage of the host bacterium, delaying the evolution of fully resistant and virulent strains.}, }
@article {pmid22916001, year = {2012}, author = {Quan, DN and Bentley, WE}, title = {Gene network homology in prokaryotes using a similarity search approach: queries of quorum sensing signal transduction.}, journal = {PLoS computational biology}, volume = {8}, number = {8}, pages = {e1002637}, pmid = {22916001}, issn = {1553-7358}, mesh = {Bacterial Physiological Phenomena ; *Gene Regulatory Networks ; Operon ; Prokaryotic Cells ; *Quorum Sensing ; *Signal Transduction ; }, abstract = {Bacterial cell-cell communication is mediated by small signaling molecules known as autoinducers. Importantly, autoinducer-2 (AI-2) is synthesized via the enzyme LuxS in over 80 species, some of which mediate their pathogenicity by recognizing and transducing this signal in a cell density dependent manner. AI-2 mediated phenotypes are not well understood however, as the means for signal transduction appears varied among species, while AI-2 synthesis processes appear conserved. Approaches to reveal the recognition pathways of AI-2 will shed light on pathogenicity as we believe recognition of the signal is likely as important, if not more, than the signal synthesis. LMNAST (Local Modular Network Alignment Similarity Tool) uses a local similarity search heuristic to study gene order, generating homology hits for the genomic arrangement of a query gene sequence. We develop and apply this tool for the E. coli lac and LuxS regulated (Lsr) systems. Lsr is of great interest as it mediates AI-2 uptake and processing. Both test searches generated results that were subsequently analyzed through a number of different lenses, each with its own level of granularity, from a binary phylogenetic representation down to trackback plots that preserve genomic organizational information. Through a survey of these results, we demonstrate the identification of orthologs, paralogs, hitchhiking genes, gene loss, gene rearrangement within an operon context, and also horizontal gene transfer (HGT). We found a variety of operon structures that are consistent with our hypothesis that the signal can be perceived and transduced by homologous protein complexes, while their regulation may be key to defining subsequent phenotypic behavior.}, }
@article {pmid22915603, year = {2012}, author = {Shukla, SK and Pantrangi, M and Stahl, B and Briska, AM and Stemper, ME and Wagner, TK and Zentz, EB and Callister, SM and Lovrich, SD and Henkhaus, JK and Dykes, CW}, title = {Comparative whole-genome mapping to determine Staphylococcus aureus genome size, virulence motifs, and clonality.}, journal = {Journal of clinical microbiology}, volume = {50}, number = {11}, pages = {3526-3533}, pmid = {22915603}, issn = {1098-660X}, support = {R01 AI061385/AI/NIAID NIH HHS/United States ; AI061385/AI/NIAID NIH HHS/United States ; }, mesh = {*Chromosome Mapping ; Cluster Analysis ; DNA, Bacterial/*genetics ; Genes, Bacterial ; Genome Size ; Genotype ; Humans ; Prophages/genetics ; Staphylococcal Infections/microbiology ; Staphylococcus aureus/classification/*genetics/isolation &amp; purification/pathogenicity ; Virulence ; Virulence Factors/genetics ; }, abstract = {Despite being a clonal pathogen, Staphylococcus aureus continues to acquire virulence and antibiotic-resistant genes located on mobile genetic elements such as genomic islands, prophages, pathogenicity islands, and the staphylococcal chromosomal cassette mec (SCCmec) by horizontal gene transfer from other staphylococci. The potential virulence of a S. aureus strain is often determined by comparing its pulsed-field gel electrophoresis (PFGE) or multilocus sequence typing profiles to that of known epidemic or virulent clones and by PCR of the toxin genes. Whole-genome mapping (formerly optical mapping), which is a high-resolution ordered restriction mapping of a bacterial genome, is a relatively new genomic tool that allows comparative analysis across entire bacterial genomes to identify regions of genomic similarities and dissimilarities, including small and large insertions and deletions. We explored whether whole-genome maps (WGMs) of methicillin-resistant S. aureus (MRSA) could be used to predict the presence of methicillin resistance, SCCmec type, and Panton-Valentine leukocidin (PVL)-producing genes on an S. aureus genome. We determined the WGMs of 47 diverse clinical isolates of S. aureus, including well-characterized reference MRSA strains, and annotated the signature restriction pattern in SCCmec types, arginine catabolic mobile element (ACME), and PVL-carrying prophage, PhiSa2 or PhiSa2-like regions on the genome. WGMs of these isolates accurately characterized them as MRSA or methicillin-sensitive S. aureus based on the presence or absence of the SCCmec motif, ACME and the unique signature pattern for the prophage insertion that harbored the PVL genes. Susceptibility to methicillin resistance and the presence of mecA, SCCmec types, and PVL genes were confirmed by PCR. A WGM clustering approach was further able to discriminate isolates within the same PFGE clonal group. These results showed that WGMs could be used not only to genotype S. aureus but also to identify genetic motifs in MRSA that may predict virulence.}, }
@article {pmid22913355, year = {2012}, author = {Chancey, ST and Zähner, D and Stephens, DS}, title = {Acquired inducible antimicrobial resistance in Gram-positive bacteria.}, journal = {Future microbiology}, volume = {7}, number = {8}, pages = {959-978}, pmid = {22913355}, issn = {1746-0921}, support = {R01 AI070829/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*metabolism ; *Drug Resistance, Bacterial ; Gene Expression Regulation, Bacterial/*drug effects ; Gene Transfer, Horizontal ; Gram-Positive Bacteria/*drug effects/*genetics ; Humans ; Interspersed Repetitive Sequences ; }, abstract = {A major contributor to the emergence of antibiotic resistance in Gram-positive bacterial pathogens is the expansion of acquired, inducible genetic elements. Although acquired, inducible antibiotic resistance is not new, the interest in its molecular basis has been accelerated by the widening distribution and often 'silent' spread of the elements responsible, the diagnostic challenges of such resistance and the mounting limitations of available agents to treat Gram-positive infections. Acquired, inducible antibiotic resistance elements belong to the accessory genome of a species and are horizontally acquired by transformation/recombination or through the transfer of mobile DNA elements. The two key, but mechanistically very different, induction mechanisms are: ribosome-sensed induction, characteristic of the macrolide-lincosamide-streptogramin B antibiotics and tetracycline resistance, leading to ribosomal modifications or efflux pump activation; and resistance by cell surface-associated sensing of β-lactams (e.g., oxacillin), glycopeptides (e.g., vancomycin) and the polypeptide bacitracin, leading to drug inactivation or resistance due to cell wall alterations.}, }
@article {pmid22911826, year = {2012}, author = {Feng, J and Liu, B and Zhang, Z and Ren, Y and Li, Y and Gan, F and Huang, Y and Chen, X and Shen, P and Wang, L and Tang, B and Tang, XF}, title = {The complete genome sequence of Natrinema sp. J7-2, a haloarchaeon capable of growth on synthetic media without amino acid supplements.}, journal = {PloS one}, volume = {7}, number = {7}, pages = {e41621}, pmid = {22911826}, issn = {1932-6203}, mesh = {Amino Acids/biosynthesis/*pharmacology ; Archaeal Proteins/genetics/metabolism ; Base Sequence ; Biosynthetic Pathways/drug effects/genetics ; Carbohydrate Metabolism/drug effects/genetics ; Carbon/metabolism/pharmacology ; Culture Media/*pharmacology ; Genome, Archaeal/*genetics ; Halobacteriaceae/drug effects/*genetics/*growth &amp; development ; Molecular Sequence Data ; Nitrogen/metabolism/pharmacology ; Phylogeny ; }, abstract = {Natrinema sp. J7-2 is an extreme haloarchaeon capable of growing on synthetic media without amino acid supplements. Here we report the complete genome sequence of Natrinema sp. J7-2 which is composed of a 3,697,626-bp chromosome and a 95,989-bp plasmid pJ7-I. This is the first complete genome sequence of a member of the genus Natrinema. We demonstrate that Natrinema sp. J7-2 can use gluconate, glycerol, or acetate as the sole carbon source and that its genome encodes complete metabolic pathways for assimilating these substrates. The biosynthetic pathways for all 20 amino acids have been reconstructed, and we discuss a possible evolutionary relationship between the haloarchaeal arginine synthetic pathway and the bacterial lysine synthetic pathway. The genome harbors the genes for assimilation of ammonium and nitrite, but not nitrate, and has a denitrification pathway to reduce nitrite to N(2)O. Comparative genomic analysis suggests that most sequenced haloarchaea employ the TrkAH system, rather than the Kdp system, to actively uptake potassium. The genomic analysis also reveals that one of the three CRISPR loci in the Natrinema sp. J7-2 chromosome is located in an integrative genetic element and is probably propagated via horizontal gene transfer (HGT). Finally, our phylogenetic analysis of haloarchaeal genomes provides clues about evolutionary relationships of haloarchaea.}, }
@article {pmid22911766, year = {2012}, author = {Moreno Switt, AI and den Bakker, HC and Cummings, CA and Rodriguez-Rivera, LD and Govoni, G and Raneiri, ML and Degoricija, L and Brown, S and Hoelzer, K and Peters, JE and Bolchacova, E and Furtado, MR and Wiedmann, M}, title = {Identification and characterization of novel Salmonella mobile elements involved in the dissemination of genes linked to virulence and transmission.}, journal = {PloS one}, volume = {7}, number = {7}, pages = {e41247}, pmid = {22911766}, issn = {1932-6203}, mesh = {Animals ; Drug Resistance, Bacterial/genetics ; Gene Order ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Genome, Viral ; Genomic Islands ; *Interspersed Repetitive Sequences ; Operon ; Phylogeny ; Plasmids/genetics ; Prophages/genetics ; Salmonella/classification/*genetics/isolation &amp; purification/pathogenicity ; Salmonella Infections/microbiology ; Virulence/genetics ; }, abstract = {The genetic diversity represented by >2,500 different Salmonella serovars provides a yet largely uncharacterized reservoir of mobile elements that can contribute to the frequent emergence of new pathogenic strains of this important zoonotic pathogen. Currently, our understanding of Salmonella mobile elements is skewed by the fact that most studies have focused on highly virulent or common serovars. To gain a more global picture of mobile elements in Salmonella, we used prediction algorithms to screen for mobile elements in 16 sequenced Salmonella genomes representing serovars for which no prior genome scale mobile element data were available. From these results, selected mobile elements underwent further analyses in the form of validation studies, comparative analyses, and PCR-based population screens. Through this analysis we identified a novel plasmid that has two cointegrated replicons (IncI1-IncFIB); this plasmid type was found in four genomes representing different Salmonella serovars and contained a virulence gene array that had not been previously identified. A Salmonella Montevideo isolate contained an IncHI and an IncN2 plasmid, which both encoded antimicrobial resistance genes. We also identified two novel genomic islands (SGI2 and SGI3), and 42 prophages with mosaic architecture, seven of them harboring known virulence genes. Finally, we identified a novel integrative conjugative element (ICE) encoding a type IVb pilus operon in three non-typhoidal Salmonella serovars. Our analyses not only identified a considerable number of mobile elements that have not been previously reported in Salmonella, but also found evidence that these elements facilitate transfer of genes that were previously thought to be limited in their distribution among Salmonella serovars. The abundance of mobile elements encoding pathogenic properties may facilitate the emergence of strains with novel combinations of pathogenic traits.}, }
@article {pmid22910565, year = {2012}, author = {Makobe, CK and Sang, WK and Kikuvi, G and Kariuki, S}, title = {Molecular characterization of virulence factors in diarrhoeagenic Escherichia coli isolates from children in Nairobi, Kenya.}, journal = {Journal of infection in developing countries}, volume = {6}, number = {8}, pages = {598-604}, doi = {10.3855/jidc.2082}, pmid = {22910565}, issn = {1972-2680}, mesh = {Child, Preschool ; DNA, Bacterial/genetics ; Diarrhea/*microbiology ; Escherichia coli/*genetics/isolation &amp; purification/*pathogenicity ; Escherichia coli Infections/*microbiology ; Escherichia coli Proteins/genetics ; Female ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genotype ; Humans ; Infant ; Interspersed Repetitive Sequences ; Kenya ; Male ; Polymerase Chain Reaction ; Virulence Factors/*genetics ; }, abstract = {INTRODUCTION: Among the bacterial causes, diarrheagenic Escherichia coli (DEC) is the most important etiologic agent of childhood diarrhoea and represents a major public health problem in developing countries. New evidence suggests that major differences in virulence among groups of DEC pathotypes may be related to the presence of specific pathogenicity islands (PAIs).<br><br>METHODOLOGY: Multiplex and conventional PCR assays were used to identify the DEC pathotypes and PAIs respectively from 207 E. coli isolates.<br><br>RESULTS: The predominant DEC pathotype isolated was EPEC 19.3% (40/207), followed by ETEC 7.25% (15/207), EAEC 3.86% (8/207), STEC 0.97% (2/207) and EIEC 0.48% (1/207). The PAIs detected were enteropathogenic secreted protein C (EspC) 12.2% (8/66), locus of enterocyte effacement (LEE) 62.1% (41/66), and high pathogenicity island (HPI) 57.6% (38/66). Six percent (4/66) expressed only fyuA gene, 12.2% (8/66) irp2 only, and 39.4% (26/66) expressed both fyuA and irp2 genes. SHI-2 39.4% (26/66), she 6% (4/66) and O island 33.3% (22/66), 19.8% (13/66) expressed only efa/lifA gene, 7.6% (5/66) pagC gene only and 6.1% (4/66) expressed both efa/lifA and pagC genes. Toxigenic invasion A (TIA) PAI was not detected.<br><br>CONCLUSION: This study revealed that in addition to eaeA, stx, aat, einv, st and lt virulence genes exhibited in the different DEC pathotypes there are numerous PAIs in the DEC pathotypes. The PAIs can increase gene mobility within various motile elements, which has implications for the spread of virulence factors from DEC to commensal E. coli.}, }
@article {pmid22909268, year = {2012}, author = {Haws, DC and Huggins, P and O'Neill, EM and Weisrock, DW and Yoshida, R}, title = {A support vector machine based test for incongruence between sets of trees in tree space.}, journal = {BMC bioinformatics}, volume = {13}, number = {}, pages = {210}, pmid = {22909268}, issn = {1471-2105}, support = {5R01GM086888/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Sequence ; Gene Duplication ; Gene Transfer, Horizontal ; Genes ; *Phylogeny ; Sequence Analysis, DNA/*methods ; *Software ; *Support Vector Machine ; }, abstract = {BACKGROUND: The increased use of multi-locus data sets for phylogenetic reconstruction has increased the need to determine whether a set of gene trees significantly deviate from the phylogenetic patterns of other genes. Such unusual gene trees may have been influenced by other evolutionary processes such as selection, gene duplication, or horizontal gene transfer.<br><br>RESULTS: Motivated by this problem we propose a nonparametric goodness-of-fit test for two empirical distributions of gene trees, and we developed the software GeneOut to estimate a p-value for the test. Our approach maps trees into a multi-dimensional vector space and then applies support vector machines (SVMs) to measure the separation between two sets of pre-defined trees. We use a permutation test to assess the significance of the SVM separation. To demonstrate the performance of GeneOut, we applied it to the comparison of gene trees simulated within different species trees across a range of species tree depths. Applied directly to sets of simulated gene trees with large sample sizes, GeneOut was able to detect very small differences between two set of gene trees generated under different species trees. Our statistical test can also include tree reconstruction into its test framework through a variety of phylogenetic optimality criteria. When applied to DNA sequence data simulated from different sets of gene trees, results in the form of receiver operating characteristic (ROC) curves indicated that GeneOut performed well in the detection of differences between sets of trees with different distributions in a multi-dimensional space. Furthermore, it controlled false positive and false negative rates very well, indicating a high degree of accuracy.<br><br>CONCLUSIONS: The non-parametric nature of our statistical test provides fast and efficient analyses, and makes it an applicable test for any scenario where evolutionary or other factors can lead to trees with different multi-dimensional distributions. The software GeneOut is freely available under the GNU public license.}, }
@article {pmid22908214, year = {2014}, author = {Lapierre, P and Lasek-Nesselquist, E and Gogarten, JP}, title = {The impact of HGT on phylogenomic reconstruction methods.}, journal = {Briefings in bioinformatics}, volume = {15}, number = {1}, pages = {79-90}, doi = {10.1093/bib/bbs050}, pmid = {22908214}, issn = {1477-4054}, mesh = {Computational Biology ; Computer Simulation ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genomics/statistics &amp; numerical data ; *Models, Genetic ; *Phylogeny ; Sequence Alignment/statistics &amp; numerical data ; }, abstract = {Supermatrix and supertree analyses are frequently used to more accurately recover vertical evolutionary history but debate still exists over which method provides greater reliability. Traditional methods that resolve relationships among organisms from single genes are often unreliable because of the frequent lack of strong phylogenetic signal and the presence of systematic artifacts. Methods developed to reconstruct organismal history from multiple genes can be divided into supermatrix and supertree approaches. A supermatrix analysis consists of the concatenation of multiple genes into a single, possibly partitioned alignment, from which phylogenies are reconstructed using a variety of approaches. Supertrees build consensus trees from the topological information contained within individual gene trees. Both methods are now widely used and have been demonstrated to solve previously ambiguous or unresolved phylogenies with high statistical support. However, the amount of misleading signal needed to induce erroneous phylogenies for both strategies is still unknown. Using genome simulations, we test the accuracy of supertree and supermatrix approaches in recovering the true organismal phylogeny under increased amounts of horizontally transferred genes and changes in substitution rates. Our results show that overall, supermatrix approaches are preferable when a low amount of gene transfer is suspected to be present in the dataset, while supertrees have greater reliability in the presence of a moderate amount of misleading gene transfers. In the face of very high or very low substitution rates without horizontal gene transfers, supermatrix approaches outperform supertrees as individual gene trees remain unresolved and additional sequences contribute to a congruent phylogenetic signal.}, }
@article {pmid22908152, year = {2012}, author = {Hess, D and Wu, A and Golparian, D and Esmaili, S and Pandori, W and Sena, E and Klausner, JD and Barry, P and Unemo, M and Pandori, M}, title = {Genome sequencing of a Neisseria gonorrhoeae isolate of a successful international clone with decreased susceptibility and resistance to extended-spectrum cephalosporins.}, journal = {Antimicrobial agents and chemotherapy}, volume = {56}, number = {11}, pages = {5633-5641}, pmid = {22908152}, issn = {1098-6596}, support = {H25 PS001411/PS/NCHHSTP CDC HHS/United States ; PS001411-03/PS/NCHHSTP CDC HHS/United States ; }, mesh = {Alleles ; Anti-Bacterial Agents/pharmacology/*therapeutic use ; Bacterial Proteins/*genetics/metabolism ; Cephalosporin Resistance/drug effects/*genetics ; Cephalosporins/pharmacology/*therapeutic use ; Contig Mapping ; Europe/epidemiology ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Gonorrhea/*drug therapy/epidemiology/microbiology ; Humans ; Mosaicism ; Neisseria gonorrhoeae/classification/*drug effects/*genetics/isolation &amp; purification ; Phylogeny ; Sequence Analysis, DNA ; United States/epidemiology ; }, abstract = {The recent emergence of Neisseria gonorrhoeae strains with decreased susceptibility to extended-spectrum cephalosporins is a major concern globally. We sequenced the genome of an N. gonorrhoeae multiantigen sequence typing (NG-MAST) ST1407 isolate (SM-3) with decreased susceptibility and resistance to oral extended-spectrum cephalosporins. The isolate was cultured in 2008 in San Francisco, CA, and possessed mosaic penA allele XXXIV, which is associated with an international clone that possesses decreased susceptibility as well as resistance to oral extended-spectrum cephalosporins globally. The genome sequence of strain NCCP11945 was used as a scaffold, and our assembly resulted in 91 contigs covering 2,029,064 bp (91%; >150× coverage) of the genome. Numerous instances of suspected horizontal genetic transfer events with other Neisseria species were identified, and two genes, opa and txf, acquired from nongonococcal Neisseria species, were identified. Strains possessing mosaic penA alleles (n = 108) and nonmosaic penA alleles (n = 169) from the United States and Europe (15 countries), cultured in 2002 to 2009, were screened for the presence of these genes. The opa gene was detected in most (82%) penA mosaic-containing isolates (mainly from 2007 to 2009) but not in any penA nonmosaic isolates. The txf gene was found in all strains containing opa but also in several (18%) penA nonmosaic strains. Using opa and txf as genetic markers, we identified a strain that possesses mosaic penA allele XXXIV, but the majority of its genome is not genetically related to strain SM-3. This implies that penA mosaic allele XXXIV was transferred horizontally. Such isolates also possessed decreased susceptibility and resistance to oral extended-spectrum cephalosporins. These findings support that genetic screening for particular penA mosaic alleles can be a valuable method for tracking strains with decreased susceptibility as well as resistance to oral extended-spectrum cephalosporins worldwide and that screening using only NG-MAST may not be sufficient.}, }
@article {pmid22905268, year = {2012}, author = {McDaniel, LD and Young, EC and Ritchie, KB and Paul, JH}, title = {Environmental factors influencing gene transfer agent (GTA) mediated transduction in the subtropical ocean.}, journal = {PloS one}, volume = {7}, number = {8}, pages = {e43506}, pmid = {22905268}, issn = {1932-6203}, mesh = {Alphaproteobacteria/metabolism ; Gene Transfer Techniques ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Techniques ; Lysogeny ; Models, Genetic ; *Oceans and Seas ; Prophages/genetics ; Rhodobacter capsulatus/*genetics ; Rhodobacteraceae/genetics ; Software ; Species Specificity ; Viruses/metabolism ; Water Microbiology ; }, abstract = {Microbial genomic sequence analyses have indicated widespread horizontal gene transfer (HGT). However, an adequate mechanism accounting for the ubiquity of HGT has been lacking. Recently, high frequencies of interspecific gene transfer have been documented, catalyzed by Gene Transfer Agents (GTAs) of marine α-Proteobacteria. It has been proposed that the presence of bacterial genes in highly purified viral metagenomes may be due to GTAs. However, factors influencing GTA-mediated gene transfer in the environment have not yet been determined. Several genomically sequenced strains containing complete GTA sequences similar to Rhodobacter capsulatus (RcGTA, type strain) were screened to ascertain if they produced putative GTAs, and at what abundance. Five of nine marine strains screened to date spontaneously produced virus-like particles (VLP's) in stationary phase. Three of these strains have demonstrated gene transfer activity, two of which were documented by this lab. These two strains Roseovarius nubinhibens ISM and Nitratireductor 44B9s, were utilized to produce GTAs designated RnGTA and NrGTA and gene transfer activity was verified in culture. Cell-free preparations of purified RnGTA and NrGTA particles from marked donor strains were incubated with natural microbial assemblages to determine the level of GTA-mediated gene transfer. In conjunction, several ambient environmental parameters were measured including lysogeny indicated by prophage induction. GTA production in culture systems indicated that approximately half of the strains produced GTA-like particles and maximal GTA counts ranged from 10-30% of host abundance. Modeling of GTA-mediated gene transfer frequencies in natural samples, along with other measured environmental variables, indicated a strong relationship between GTA mediated gene transfer and the combined factors of salinity, multiplicity of infection (MOI) and ambient bacterial abundance. These results indicate that GTA-mediated HGT in the marine environment with the strains examined is favored during times of elevated bacterial and GTA abundance as well as in areas of higher salinity.}, }
@article {pmid22905214, year = {2012}, author = {Xiong, D and Xiao, F and Liu, L and Hu, K and Tan, Y and He, S and Gao, X}, title = {Towards a better detection of horizontally transferred genes by combining unusual properties effectively.}, journal = {PloS one}, volume = {7}, number = {8}, pages = {e43126}, pmid = {22905214}, issn = {1932-6203}, mesh = {Computational Biology/methods ; DNA, Bacterial/genetics ; Databases, Genetic ; False Negative Reactions ; False Positive Reactions ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Genomics/methods ; Models, Genetic ; Models, Statistical ; Phylogeny ; Reproducibility of Results ; Software ; Support Vector Machine ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT) is one of the major mechanisms contributing to microbial genome diversification. A number of computational methods for finding horizontally transferred genes have been proposed in the past decades; however none of them has provided a reliable detector yet. In existing parametric approaches, only one single compositional property can participate in the detection process, or the results obtained through each single property are just simply combined. It's known that different properties may mean different information, so the single property can't sufficiently contain the information encoded by gene sequences. In addition, the class imbalance problem in the datasets, which also results in great errors for the gene detection, hasn't been considered by the published methods. Here we developed an effective classifier system (Hgtident) that used support vector machine (SVM) by combining unusual properties effectively for HGT detection.<br><br>RESULTS: Our approach Hgtident includes the introduction of more representative datasets, optimization of SVM model, feature selection, handling of imbalance problem in the datasets and extensive performance evaluation via systematic cross-validation methods. Through feature selection, we found that JS-DN and JS-CB have higher discriminating power for HGT detection, while GC1-GC3 and k-mer (k = 1, 2, &#x2026;, 7) make the least contribution. Extensive experiments indicated the new classifier could reduce Mean error dramatically, and also improve Recall by a certain level. For the testing genomes, compared with the existing popular multiple-threshold approach, on average, our Recall and Mean error was respectively improved by 2.81% and reduced by 26.32%, which means that numerous false positives were identified correctly.<br><br>CONCLUSIONS: Hgtident introduced here is an effective approach for better detecting HGT. Combining multiple features of HGT is also essential for a wider range of HGT events detection.}, }
@article {pmid22904077, year = {2012}, author = {Aslankoohi, E and Voordeckers, K and Sun, H and Sanchez-Rodriguez, A and van der Zande, E and Marchal, K and Verstrepen, KJ}, title = {Nucleosomes affect local transformation efficiency.}, journal = {Nucleic acids research}, volume = {40}, number = {19}, pages = {9506-9512}, pmid = {22904077}, issn = {1362-4962}, support = {241426/ERC_/European Research Council/International ; }, mesh = {Base Sequence ; DNA, Fungal/chemistry ; Nucleosomes/*chemistry ; Saccharomyces cerevisiae/genetics ; *Transformation, Genetic ; }, abstract = {Genetic transformation is a natural process during which foreign DNA enters a cell and integrates into the genome. Apart from its relevance for horizontal gene transfer in nature, transformation is also the cornerstone of today's recombinant gene technology. Despite its importance, relatively little is known about the factors that determine transformation efficiency. We hypothesize that differences in DNA accessibility associated with nucleosome positioning may affect local transformation efficiency. We investigated the landscape of transformation efficiency at various positions in the Saccharomyces cerevisiae genome and correlated these measurements with nucleosome positioning. We find that transformation efficiency shows a highly significant inverse correlation with relative nucleosome density. This correlation was lost when the nucleosome pattern, but not the underlying sequence was changed. Together, our results demonstrate a novel role for nucleosomes and also allow researchers to predict transformation efficiency of a target region and select spots in the genome that are likely to yield higher transformation efficiency.}, }
@article {pmid22904051, year = {2012}, author = {Katharios-Lanwermeyer, S and Rakic-Martinez, M and Elhanafi, D and Ratani, S and Tiedje, JM and Kathariou, S}, title = {Coselection of cadmium and benzalkonium chloride resistance in conjugative transfers from nonpathogenic Listeria spp. to other Listeriae.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {21}, pages = {7549-7556}, pmid = {22904051}, issn = {1098-5336}, mesh = {Anti-Infective Agents, Local/pharmacology ; Bacterial Proteins/genetics ; Benzalkonium Compounds/*pharmacology ; Cadmium/*pharmacology ; Conjugation, Genetic ; Drug Resistance, Bacterial/*genetics ; Food Handling ; Gene Transfer, Horizontal ; Listeria/*drug effects/*genetics/pathogenicity ; Temperature ; }, abstract = {Resistance to the quaternary ammonium disinfectant benzalkonium chloride (BC) may be an important contributor to the ability of Listeria spp. to persist in the processing plant environment. Although a plasmid-borne disinfectant resistance cassette (bcrABC) has been identified in Listeria monocytogenes, horizontal transfer of these genes has not been characterized. Nonpathogenic Listeria spp. such as L. innocua and L. welshimeri are more common than L. monocytogenes in food processing environments and may contribute to the dissemination of disinfectant resistance genes in listeriae, including L. monocytogenes. In this study, we investigated conjugative transfer of resistance to BC and to cadmium from nonpathogenic Listeria spp. to other nonpathogenic listeriae, as well as to L. monocytogenes. BC-resistant L. welshimeri and L. innocua harboring bcrABC, along with the cadmium resistance determinant cadA2, were able to transfer resistance to other nonpathogenic listeriae as well as to L. monocytogenes of diverse serotypes, including strains from the 2011 cantaloupe outbreak. Transfer among nonpathogenic Listeria spp. was noticeably higher at 25°C than at 37°C, whereas acquisition of resistance by L. monocytogenes was equally efficient at 25 and 37°C. When the nonpathogenic donors were resistant to both BC and cadmium, acquisition of cadmium resistance was an effective surrogate for transfer of resistance to BC, suggesting coselection between these resistance attributes. The results suggest that nonpathogenic Listeria spp. may behave as reservoirs for disinfectant and heavy metal resistance genes for other listeriae, including the pathogenic species L. monocytogenes.}, }
@article {pmid22903157, year = {2012}, author = {Redis, RS and Calin, S and Yang, Y and You, MJ and Calin, GA}, title = {Cell-to-cell miRNA transfer: from body homeostasis to therapy.}, journal = {Pharmacology &amp; therapeutics}, volume = {136}, number = {2}, pages = {169-174}, pmid = {22903157}, issn = {1879-016X}, support = {R01 CA135444/CA/NCI NIH HHS/United States ; R01 CA164346/CA/NCI NIH HHS/United States ; CA100632/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; *Cell Communication ; *Gene Transfer, Horizontal ; *Homeostasis ; Humans ; MicroRNAs/blood/genetics/*metabolism ; Tumor Microenvironment ; }, abstract = {The role of non-protein coding RNAs (ncRNAs), microRNAs (miRNAs) in particular, as fine-tuners of both pathological and physiological processes is no longer a matter of debate. With the recent discovery of miRNAs in a wide variety of body fluids and considering them as tools employed in horizontal gene transfer between cells, a new horizon opens in the field of diagnosis and therapeutics. Circulating miRNAs not only enable the communication among cells, but also provide insight into the pathological and physiological state of the originating cells. In this review we summarize the recent advances made in this field, arguing for compelling translation of miRNAs into clinical practice. Moreover, we provide overview of their characteristics and how they impact the evolution of tumor microenvironment and cell-to-cell communication, advancing the idea that miRNAs may function as hormones.}, }
@article {pmid22902729, year = {2012}, author = {Harrington, C and Del Casale, A and Kennedy, J and Neve, H and Picton, BE and Mooij, MJ and O'Gara, F and Kulakov, LA and Larkin, MJ and Dobson, ADW}, title = {Evidence of bacteriophage-mediated horizontal transfer of bacterial 16S rRNA genes in the viral metagenome of the marine sponge Hymeniacidon perlevis.}, journal = {Microbiology (Reading, England)}, volume = {158}, number = {Pt 11}, pages = {2789-2795}, doi = {10.1099/mic.0.057943-0}, pmid = {22902729}, issn = {1465-2080}, mesh = {Animals ; Bacteria/*genetics ; Bacteriophages/classification/*genetics/isolation &amp; purification/physiology ; DNA, Bacterial/*genetics/metabolism ; DNA, Viral/genetics ; *Gene Transfer, Horizontal ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; Porifera/genetics/*virology ; RNA, Ribosomal, 16S/*genetics/metabolism ; Seawater/chemistry/microbiology/virology ; }, abstract = {Marine sponges have never been directly examined with respect to the presence of viruses or their potential involvement in horizontal gene transfer. Here we demonstrate for the first time, to our knowledge, the presence of viruses in the marine sponge Hymeniacidon perlevis. Moreover, bacterial 16S rDNA was detected in DNA isolated from these viruses, indicating that phage-derived transduction appears to occur in H. perlevis. Phylogenetic analysis revealed that bacterial 16S rDNA isolated from sponge-derived viral and total DNA differed significantly, indicating that not all species are equally involved in transduction.}, }
@article {pmid22901901, year = {2012}, author = {Aswad, A and Katzourakis, A}, title = {Paleovirology and virally derived immunity.}, journal = {Trends in ecology &amp; evolution}, volume = {27}, number = {11}, pages = {627-636}, doi = {10.1016/j.tree.2012.07.007}, pmid = {22901901}, issn = {1872-8383}, mesh = {Animals ; *Biological Evolution ; Gene Transfer, Horizontal ; Genome ; Host-Pathogen Interactions/*genetics/*immunology ; Humans ; Immunity/*genetics ; Virus Diseases/*genetics/immunology/virology ; Viruses/*genetics/immunology/pathogenicity ; }, abstract = {Paleovirology, the study of viruses on evolutionary timescales, can exploit information from endogenous viral elements (EVEs), which are the result of heritable horizontal gene transfer (HGT) from viruses to hosts. The availability of genomic data has increased opportunities to study EVEs, and bioinformatics techniques have been crucial in cataloguing EVE diversity and taxonomic coverage. Recent advances show that some EVEs have been co-opted as cellular genes, often as inhibitors of viral infection. These genes are an intriguing strategy in virus-host evolutionary battles in that genetic material is transferred from virus to host, and then used by the host against the virus. In this review, we consider the genes and processes involved in EVE-derived immunity (EDI), assess factors leading to its emergence, and outline how future work will benefit from incorporating evolutionary approaches.}, }
@article {pmid22901538, year = {2012}, author = {Bikard, D and Hatoum-Aslan, A and Mucida, D and Marraffini, LA}, title = {CRISPR interference can prevent natural transformation and virulence acquisition during in vivo bacterial infection.}, journal = {Cell host &amp; microbe}, volume = {12}, number = {2}, pages = {177-186}, doi = {10.1016/j.chom.2012.06.003}, pmid = {22901538}, issn = {1934-6069}, mesh = {Animals ; Bacterial Proteins/genetics/metabolism ; Base Sequence ; Gene Transfer, Horizontal ; Humans ; *Inverted Repeat Sequences ; Mice ; Molecular Sequence Data ; Pneumococcal Infections/*microbiology ; Streptococcus pneumoniae/*genetics/*pathogenicity/physiology ; *Transformation, Genetic ; Virulence ; }, abstract = {Pathogenic bacterial strains emerge largely due to transfer of virulence and antimicrobial resistance genes between bacteria, a process known as horizontal gene transfer (HGT). Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci of bacteria and archaea encode a sequence-specific defense mechanism against bacteriophages and constitute a programmable barrier to HGT. However, the impact of CRISPRs on the emergence of virulence is unknown. We programmed the human pathogen Streptococcus pneumoniae with CRISPR sequences that target capsule genes, an essential pneumococcal virulence factor, and show that CRISPR interference can prevent transformation of nonencapsulated, avirulent pneumococci into capsulated, virulent strains during infection in mice. Further, at low frequencies bacteria can lose CRISPR function, acquire capsule genes, and mount a successful infection. These results demonstrate that CRISPR interference can prevent the emergence of virulence in vivo and that strong selective pressure for virulence or antibiotic resistance can lead to CRISPR loss in bacterial pathogens.}, }
@article {pmid22899338, year = {2012}, author = {Salvador, R and Ferrelli, ML and Berretta, MF and Mitsuhashi, W and Biedma, ME and Romanowski, V and Sciocco-Cap, A}, title = {Analysis of EpapGV gp37 gene reveals a close relationship between granulovirus and entomopoxvirus.}, journal = {Virus genes}, volume = {45}, number = {3}, pages = {610-613}, pmid = {22899338}, issn = {1572-994X}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Entomopoxvirinae/classification/*genetics/immunology/pathogenicity ; Gene Transfer, Horizontal ; *Genes, Viral ; Glycosylation ; Granulovirus/classification/*genetics/immunology/pathogenicity ; Immune Sera/immunology ; Lepidoptera/virology ; Open Reading Frames ; Phylogeny ; Sequence Homology, Amino Acid ; Viral Envelope Proteins/*genetics/immunology ; Viral Proteins/genetics/immunology ; }, abstract = {The Epinotia aporema Granulovirus GP37 protein gene has been identified, located, and sequenced. This gene was similar to other baculovirus gp37, to entomopoxvirus fusolin gene, and to the chitin-binding protein gene of bacteria. Sequence analysis indicated that the open reading frame is 669 bp long (the smallest gp37 sequenced at present) and encodes a predicted 222-amino acid protein. This protein is glycosylated and specifically recognized by an entomopoxvirus fusolin antiserum. The pairwise comparison of EpapGV gp37 gene product with all the baculovirus sequences in GenBank yields high similarity values ranging from 45 to 63 % with Cydia pomonella Granulovirus gp37 being the most closely related. The phylogenetic analysis interestingly grouped the granuloviruses in a cluster more closely related to entomopoxviruses than to nucleopolyhedroviruses, suggesting a possible horizontal transfer event between the granulovirus group and the entomopoxvirus group.}, }
@article {pmid22893385, year = {2012}, author = {Bliska, JB and van der Velden, AW}, title = {Salmonella "sops" up a preferred electron receptor in the inflamed intestine.}, journal = {mBio}, volume = {3}, number = {4}, pages = {e00226-12}, pmid = {22893385}, issn = {2150-7511}, mesh = {Animals ; Bacterial Proteins/metabolism ; Colitis/*microbiology/pathology ; Colon/*microbiology ; Disease Models, Animal ; Host-Pathogen Interactions ; Mice ; Nitrates/metabolism ; Nitric Oxide/metabolism ; Nitric Oxide Synthase/metabolism ; Salmonella Infections, Animal/*microbiology/pathology ; Salmonella typhimurium/growth &amp; development/*metabolism/*pathogenicity ; Virulence Factors/metabolism ; }, abstract = {The microbiota of the mammalian intestinal tract represents a formidable barrier to colonization by pathogens. To overcome this resistance to colonization, bacterial pathogens use virulence factors to induce intestinal inflammation, which liberates nutrients for selective use by the infecting microbe. Studies of Salmonella enterica serovar Typhimurium (S. Typhimurium) infection in a streptomycin-treated mouse colitis model show how virulence factor-induced inflammation can produce nutrients used selectively by the pathogen. Type III secreted effectors of invading S. Typhimurium induce inflammation in the intestine (epithelial cells and lamina propria macrophages) that causes changes in the composition of the lumen. For example, neutrophils entering the intestine produce superoxide, resulting in production of tetrathionate, which S. Typhimurium in the lumen uses as an electron acceptor for anaerobic respiration. In their recent study, Lopez et al. demonstrate that S. Typhimurium strains that are lysogenized with a phage encoding type III effector SopE induce the host to produce nitric oxide synthetase (iNOS) in the intestine (C. A. Lopez et al., mBio 3:e00143-12, 2012). Nitric oxide is converted to a highly favorable electron acceptor, nitrate. As a result, growth of sopE(+) S. Typhimurium in the intestine lumen is boosted by nitrate respiration. This is a striking example of how acquisition of a virulence factor by horizontal gene transfer can increase the metabolic fitness of a pathogen. Interestingly, survival of the invading bacteria is probably decreased as a result of the SopE-induced immune response, and yet the S. Typhimurium bacteria that multiply in the lumen of the intestine can efficiently disseminate to another host, ensuring success for the pathogen.}, }
@article {pmid22891620, year = {2012}, author = {Dávalos, LM and Cirranello, AL and Geisler, JH and Simmons, NB}, title = {Understanding phylogenetic incongruence: lessons from phyllostomid bats.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {87}, number = {4}, pages = {991-1024}, pmid = {22891620}, issn = {1469-185X}, mesh = {Adaptation, Physiological/*genetics ; Animals ; Chiroptera/*genetics ; *Genetic Speciation ; *Phylogeny ; }, abstract = {All characters and trait systems in an organism share a common evolutionary history that can be estimated using phylogenetic methods. However, differential rates of change and the evolutionary mechanisms driving those rates result in pervasive phylogenetic conflict. These drivers need to be uncovered because mismatches between evolutionary processes and phylogenetic models can lead to high confidence in incorrect hypotheses. Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species. For more than a decade, evolutionary relationships among members of the New World bat family Phyllostomidae inferred from morphological and molecular data have been in conflict. Here, we develop and apply methods to minimize systematic biases, uncover the biological mechanisms underlying phylogenetic conflict, and outline data requirements for future phylogenomic and morphological data collection. We introduce new morphological data for phyllostomids and outgroups and expand previous molecular analyses to eliminate methodological sources of phylogenetic conflict such as taxonomic sampling, sparse character sampling, or use of different algorithms to estimate the phylogeny. We also evaluate the impact of biological sources of conflict: saturation in morphological changes and molecular substitutions, and other processes that result in incongruent trees, including convergent morphological and molecular evolution. Methodological sources of incongruence play some role in generating phylogenetic conflict, and are relatively easy to eliminate by matching taxa, collecting more characters, and applying the same algorithms to optimize phylogeny. The evolutionary patterns uncovered are consistent with multiple biological sources of conflict, including saturation in morphological and molecular changes, adaptive morphological convergence among nectar-feeding lineages, and incongruent gene trees. Applying methods to account for nucleotide sequence saturation reduces, but does not completely eliminate, phylogenetic conflict. We ruled out paralogy, lateral gene transfer, and poor taxon sampling and outgroup choices among the processes leading to incongruent gene trees in phyllostomid bats. Uncovering and countering the possible effects of introgression and lineage sorting of ancestral polymorphism on gene trees will require great leaps in genomic and allelic sequencing in this species-rich mammalian family. We also found evidence for adaptive molecular evolution leading to convergence in mitochondrial proteins among nectar-feeding lineages. In conclusion, the biological processes that generate phylogenetic conflict are ubiquitous, and overcoming incongruence requires better models and more data than have been collected even in well-studied organisms such as phyllostomid bats.}, }
@article {pmid22890188, year = {2012}, author = {Blázquez, J and Couce, A and Rodríguez-Beltrán, J and Rodríguez-Rojas, A}, title = {Antimicrobials as promoters of genetic variation.}, journal = {Current opinion in microbiology}, volume = {15}, number = {5}, pages = {561-569}, doi = {10.1016/j.mib.2012.07.007}, pmid = {22890188}, issn = {1879-0364}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects ; DNA Damage ; Gene Transfer, Horizontal ; Genetic Variation/*drug effects ; Mutation/*drug effects ; Oxidative Stress ; SOS Response, Genetics ; Selection, Genetic ; }, abstract = {The main causes of antibiotic resistance are the selection of naturally occurring resistant variants and horizontal gene transfer processes. In recent years, the implications of antibiotic contact or treatment in drug resistance acquisition by bacteria have been gradually more evident. The ultimate source of bacterial genetic alterations to face antibiotic toxicity is mutation. All evidence points to antibiotics, especially when present at sublethal concentrations, as responsible for increasing genetic variation and therefore participating in the emergence of antibiotic resistance. Antibiotics may cause genetic changes by means of different pathways involving an increase of free radicals inside the cell or oxidative stress, by inducing error-prone polymerases mediated by SOS response, misbalancing nucleotide metabolism or acting directly on DNA. In addition, the concerted action of certain environmental conditions with subinhibitory concentrations of antimicrobials may contribute to increasing the mutagenic effect of antibiotics even more. Here we review and discuss in detail the recent advances concerning these issues and their relevance in the field of antibiotic resistance.}, }
@article {pmid22890137, year = {2012}, author = {Ali, A and Soares, SC and Santos, AR and Guimarães, LC and Barbosa, E and Almeida, SS and Abreu, VA and Carneiro, AR and Ramos, RT and Bakhtiar, SM and Hassan, SS and Ussery, DW and On, S and Silva, A and Schneider, MP and Lage, AP and Miyoshi, A and Azevedo, V}, title = {Campylobacter fetus subspecies: comparative genomics and prediction of potential virulence targets.}, journal = {Gene}, volume = {508}, number = {2}, pages = {145-156}, doi = {10.1016/j.gene.2012.07.070}, pmid = {22890137}, issn = {1879-0038}, mesh = {Animals ; Campylobacter Infections/microbiology ; Campylobacter fetus/*classification/*genetics/pathogenicity ; Cattle ; DNA, Bacterial/genetics ; *Genes, Bacterial ; *Genome, Bacterial ; Genomic Islands/*genetics ; Humans ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Virulence/*genetics ; Virulence Factors/*genetics ; }, abstract = {The genus Campylobacter contains pathogens causing a wide range of diseases, targeting both humans and animals. Among them, the Campylobacter fetus subspecies fetus and venerealis deserve special attention, as they are the etiological agents of human bacterial gastroenteritis and bovine genital campylobacteriosis, respectively. We compare the whole genomes of both subspecies to get insights into genomic architecture, phylogenetic relationships, genome conservation and core virulence factors. Pan-genomic approach was applied to identify the core- and pan-genome for both C. fetus subspecies and members of the genus. The C. fetus subspecies conserved (76%) proteome were then analyzed for their subcellular localization and protein functions in biological processes. Furthermore, with pathogenomic strategies, unique candidate regions in the genomes and several potential core-virulence factors were identified. The potential candidate factors identified for attenuation and/or subunit vaccine development against C. fetus subspecies contain: nucleoside diphosphate kinase (Ndk), type IV secretion systems (T4SS), outer membrane proteins (OMP), substrate binding proteins CjaA and CjaC, surface array proteins, sap gene, and cytolethal distending toxin (CDT). Significantly, many of those genes were found in genomic regions with signals of horizontal gene transfer and, therefore, predicted as putative pathogenicity islands. We found CRISPR loci and dam genes in an island specific for C. fetus subsp. fetus, and T4SS and sap genes in an island specific for C. fetus subsp. venerealis. The genomic variations and potential core and unique virulence factors characterized in this study would lead to better insight into the species virulence and to more efficient use of the candidates for antibiotic, drug and vaccine development.}, }
@article {pmid22889204, year = {2012}, author = {Suzuki, S and Kimura, M and Agusa, T and Rahman, HM}, title = {Vanadium accelerates horizontal transfer of tet(M) gene from marine Photobacterium to Escherichia coli.}, journal = {FEMS microbiology letters}, volume = {336}, number = {1}, pages = {52-56}, doi = {10.1111/j.1574-6968.2012.02653.x}, pmid = {22889204}, issn = {1574-6968}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics/metabolism ; Escherichia coli/drug effects/*genetics ; Gene Transfer, Horizontal/*drug effects ; Geologic Sediments/analysis ; Photobacterium/drug effects/*genetics/isolation &amp; purification ; Seawater/microbiology ; Tetracycline/pharmacology ; Tetracycline Resistance ; Vanadium/analysis/*pharmacology ; }, abstract = {Vanadium is a contaminant from steel additive and ship fuel in coastal and port areas, and its effect on marine microbes remains largely unknown. We showed that vanadium accelerates transfer of the tetracycline resistance gene tet(M) from Photobacterium to Escherichia coli, and found a positive correlation between the concentration of vanadium in natural marine sediment and the rate of oxytetracycline resistance. These results suggest the possibility that vanadium may play a role in the preservation and horizontal transfer of antibiotic resistance genes in the marine environment.}, }
@article {pmid22889115, year = {2012}, author = {Sotto, A and Lavigne, JP}, title = {A mathematical model to guide antibiotic treatment strategies.}, journal = {BMC medicine}, volume = {10}, number = {}, pages = {90}, pmid = {22889115}, issn = {1741-7015}, mesh = {Anti-Bacterial Agents/*administration &amp; dosage ; Bacteria/*drug effects/genetics/pathogenicity ; Bacterial Infections/*drug therapy/*microbiology ; Drug Resistance, Bacterial ; Humans ; *Models, Biological ; Prescriptions ; }, abstract = {Over the past few decades, the emergence of multidrug resistance (MDR) to antibiotics in bacteria has led to major difficulties in the management of infected patients. At present, there is a serious lack of development of new antibacterial agents. Mathematical models are one approach to understand how antibiotic usage patterns may be optimized. However, the classical approach to modeling the emergence of MDR relies on the simplifying assumption that resistance is acquired at a constant rate. In their model, Obolski and Hadany introduce the notion of horizontal gene transfer and stress-induced mutation, with antibiotics constituting an environmental stressor of particular relevance. Finally, from this complex mathematical model, the authors propose predictions for minimizing MDR in bacteria depending on strategies of antibiotic treatment. Please see related article: http://www.biomedcentral.com/1741-7015/10/89.}, }
@article {pmid22889082, year = {2012}, author = {Obolski, U and Hadany, L}, title = {Implications of stress-induced genetic variation for minimizing multidrug resistance in bacteria.}, journal = {BMC medicine}, volume = {10}, number = {}, pages = {89}, pmid = {22889082}, issn = {1741-7015}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics ; *Bacterial Physiological Phenomena ; Cross Infection/microbiology ; *Drug Resistance, Multiple, Bacterial ; *Gene Transfer, Horizontal ; Genetic Variation ; Hospitals ; Humans ; Models, Biological ; *Stress, Physiological ; }, abstract = {BACKGROUND: Antibiotic resistance in bacterial infections is a growing threat to public health. Recent evidence shows that when exposed to stressful conditions, some bacteria perform higher rates of horizontal gene transfer and mutation, and thus acquire antibiotic resistance more rapidly.<br><br>METHODS: We incorporate this new notion into a mathematical model for the emergence of antibiotic multi-resistance in a hospital setting.<br><br>RESULTS: We show that when stress has a considerable effect on genetic variation, the emergence of antibiotic resistance is dramatically affected. A strategy in which patients receive a combination of antibiotics (combining) is expected to facilitate the emergence of multi-resistant bacteria when genetic variation is stress-induced. The preference between a strategy in which one of two effective drugs is assigned randomly to each patient (mixing), and a strategy where only one drug is administered for a specific period of time (cycling) is determined by the resistance acquisition mechanisms. We discuss several features of the mechanisms by which stress affects variation and predict the conditions for success of different antibiotic treatment strategies.<br><br>CONCLUSIONS: These findings should encourage research on the mechanisms of stress-induced genetic variation and establish the importance of incorporating data about these mechanisms when considering antibiotic treatment strategies.}, }
@article {pmid22887657, year = {2012}, author = {Gorlas, A and Robert, C and Gimenez, G and Drancourt, M and Raoult, D}, title = {Complete genome sequence of Methanomassiliicoccus luminyensis, the largest genome of a human-associated Archaea species.}, journal = {Journal of bacteriology}, volume = {194}, number = {17}, pages = {4745}, pmid = {22887657}, issn = {1098-5530}, mesh = {Base Sequence ; Chromosome Mapping ; Euryarchaeota/classification/*genetics/isolation &amp; purification ; Feces/microbiology ; *Genome, Archaeal ; Humans ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The present study describes the complete and annotated genome sequence of Methanomassiliicoccus luminyensis strain B10 (DSM 24529(T), CSUR P135), which was isolated from human feces. The 2.6-Mb genome represents the largest genome of a methanogenic euryarchaeon isolated from humans. The genome data of M. luminyensis reveal unique features and horizontal gene transfer events, which might have occurred during its adaptation and/or evolution in the human ecosystem.}, }
@article {pmid22887124, year = {2012}, author = {Kuraku, S and Qiu, H and Meyer, A}, title = {Horizontal transfers of Tc1 elements between teleost fishes and their vertebrate parasites, lampreys.}, journal = {Genome biology and evolution}, volume = {4}, number = {9}, pages = {929-936}, pmid = {22887124}, issn = {1759-6653}, mesh = {Animals ; *DNA Transposable Elements ; Evolution, Molecular ; Fishes/classification/genetics/*parasitology ; *Gene Transfer, Horizontal ; Genomics ; Petromyzon/*genetics ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Transposases/genetics/metabolism ; }, abstract = {Horizontal gene transfer (HGT) has been recognized to be an important mechanism that shaped the evolution and genomes of prokaryotes and unicellular eukaryotes. However, HGT is regarded to be exceedingly rare among eukaryotes. We discovered massive transfers of a DNA transposon, a Tc1 element encoding a transposase, between multiple teleost fishes and lampreys that last shared a common ancestor over 500 Ma. Members of this group of Tc1 elements were found to exhibit a mosaic phylogenetic distribution, yet their sequences were highly similar even between distantly related lineages (95%-99% identity). Our molecular phylogenetic analyses suggested that horizontal transfers of this element happened repeatedly, involving multiple teleost fishes that are phylogenetically only distantly related. Interestingly, almost all the affected teleost lineages are also known to be subject to lamprey parasitism, suggesting that the horizontal transfers between vertebrates might have occurred through parasite-host interaction. The genomes of several northern hemisphere lamprey species, including that of the sea lamprey (Petromyzon marinus), were found to contain thousands of copies of the foreign elements. Impact of this event is discussed in relation to other peculiar genomic features of lampreys.}, }
@article {pmid22876202, year = {2012}, author = {Epstein, B and Branca, A and Mudge, J and Bharti, AK and Briskine, R and Farmer, AD and Sugawara, M and Young, ND and Sadowsky, MJ and Tiffin, P}, title = {Population genomics of the facultatively mutualistic bacteria Sinorhizobium meliloti and S. medicae.}, journal = {PLoS genetics}, volume = {8}, number = {8}, pages = {e1002868}, pmid = {22876202}, issn = {1553-7404}, mesh = {Biological Evolution ; *Chromosomes, Bacterial ; Gene Transfer, Horizontal ; Medicago truncatula/*microbiology ; *Metagenomics ; Nitrogen Fixation/genetics ; Phylogeny ; Plasmids/genetics ; Polymorphism, Genetic ; RNA, Ribosomal, 16S/classification/*genetics ; Sequence Analysis, DNA ; Sinorhizobium/classification/*genetics ; Sinorhizobium meliloti/classification/*genetics ; Symbiosis/genetics ; }, abstract = {The symbiosis between rhizobial bacteria and legume plants has served as a model for investigating the genetics of nitrogen fixation and the evolution of facultative mutualism. We used deep sequence coverage (>100×) to characterize genomic diversity at the nucleotide level among 12 Sinorhizobium medicae and 32 S. meliloti strains. Although these species are closely related and share host plants, based on the ratio of shared polymorphisms to fixed differences we found that horizontal gene transfer (HGT) between these species was confined almost exclusively to plasmid genes. Three multi-genic regions that show the strongest evidence of HGT harbor genes directly involved in establishing or maintaining the mutualism with host plants. In both species, nucleotide diversity is 1.5-2.5 times greater on the plasmids than chromosomes. Interestingly, nucleotide diversity in S. meliloti but not S. medicae is highly structured along the chromosome - with mean diversity (θ(π)) on one half of the chromosome five times greater than mean diversity on the other half. Based on the ratio of plasmid to chromosome diversity, this appears to be due to severely reduced diversity on the chromosome half with less diversity, which is consistent with extensive hitchhiking along with a selective sweep. Frequency-spectrum based tests identified 82 genes with a signature of adaptive evolution in one species or another but none of the genes were identified in both species. Based upon available functional information, several genes identified as targets of selection are likely to alter the symbiosis with the host plant, making them attractive targets for further functional characterization.}, }
@article {pmid22876180, year = {2012}, author = {Domingues, S and Harms, K and Fricke, WF and Johnsen, PJ and da Silva, GJ and Nielsen, KM}, title = {Natural transformation facilitates transfer of transposons, integrons and gene cassettes between bacterial species.}, journal = {PLoS pathogens}, volume = {8}, number = {8}, pages = {e1002837}, pmid = {22876180}, issn = {1553-7374}, mesh = {DNA, Bacterial/genetics/*metabolism ; Gene Transfer, Horizontal/*physiology ; Gram-Negative Bacteria/*physiology ; Integrons/*physiology ; Transformation, Bacterial/*physiology ; }, abstract = {We have investigated to what extent natural transformation acting on free DNA substrates can facilitate transfer of mobile elements including transposons, integrons and/or gene cassettes between bacterial species. Naturally transformable cells of Acinetobacter baylyi were exposed to DNA from integron-carrying strains of the genera Acinetobacter, Citrobacter, Enterobacter, Escherichia, Pseudomonas, and Salmonella to determine the nature and frequency of transfer. Exposure to the various DNA sources resulted in acquisition of antibiotic resistance traits as well as entire integrons and transposons, over a 24 h exposure period. DNA incorporation was not solely dependent on integrase functions or the genetic relatedness between species. DNA sequence analyses revealed that several mechanisms facilitated stable integration in the recipient genome depending on the nature of the donor DNA; homologous or heterologous recombination and various types of transposition (Tn21-like and IS26-like). Both donor strains and transformed isolates were extensively characterized by antimicrobial susceptibility testing, integron- and cassette-specific PCRs, DNA sequencing, pulsed field gel electrophoreses (PFGE), Southern blot hybridizations, and by re-transformation assays. Two transformant strains were also genome-sequenced. Our data demonstrate that natural transformation facilitates interspecies transfer of genetic elements, suggesting that the transient presence of DNA in the cytoplasm may be sufficient for genomic integration to occur. Our study provides a plausible explanation for why sequence-conserved transposons, IS elements and integrons can be found disseminated among bacterial species. Moreover, natural transformation of integron harboring populations of competent bacteria revealed that interspecies exchange of gene cassettes can be highly efficient, and independent on genetic relatedness between donor and recipient. In conclusion, natural transformation provides a much broader capacity for horizontal acquisitions of genetic elements and hence, resistance traits from divergent species than previously assumed.}, }
@article {pmid22872698, year = {2012}, author = {Lee, Y and El Andaloussi, S and Wood, MJ}, title = {Exosomes and microvesicles: extracellular vesicles for genetic information transfer and gene therapy.}, journal = {Human molecular genetics}, volume = {21}, number = {R1}, pages = {R125-34}, doi = {10.1093/hmg/dds317}, pmid = {22872698}, issn = {1460-2083}, support = {G-1109/PUK_/Parkinson's UK/United Kingdom ; G0900887/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Cell Communication/genetics ; Cell-Derived Microparticles/metabolism ; Endosomes/metabolism ; Exosomes/*metabolism ; *Gene Transfer Techniques ; *Gene Transfer, Horizontal ; Genetic Therapy/*methods ; Humans ; MicroRNAs/metabolism ; RNA Interference ; Stem Cells/physiology/ultrastructure ; }, abstract = {Exosomes and microvesicles are extracellular nanovesicles released by most but not all cells. They are specifically equipped to mediate intercellular communication via the transfer of genetic information, including the transfer of both coding and non-coding RNAs, to recipient cells. As a result, both exosomes and microvesicles play a fundamental biological role in the regulation of normal physiological as well as aberrant pathological processes, via altered gene regulatory networks and/or via epigenetic programming. For example, microvesicle-mediated genetic transfer can regulate the maintenance of stem cell plasticity and induce beneficial cell phenotype modulation. Alternatively, such vesicles play a role in tumor pathogenesis and the spread of neurodegenerative diseases via the transfer of specific microRNAs and pathogenic proteins. Given this natural property for genetic information transfer, the possibility of exploiting these vesicles for therapeutic purposes is now being investigated. Stem cell-derived microvesicles appear to be naturally equipped to mediate tissue regeneration under certain conditions, while recent evidence suggests that exosomes might be harnessed for the targeted delivery of human genetic therapies via the introduction of exogenous genetic cargoes such as siRNA. Thus, extracellular vesicles are emerging as potent genetic information transfer agents underpinning a range of biological processes and with therapeutic potential.}, }
@article {pmid22872449, year = {2012}, author = {Dahmen, S and Haenni, M and Madec, JY}, title = {IncI1/ST3 plasmids contribute to the dissemination of the blaCTX-M-1 gene in Escherichia coli from several animal species in France.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {67}, number = {12}, pages = {3011-3012}, doi = {10.1093/jac/dks308}, pmid = {22872449}, issn = {1460-2091}, mesh = {Animals ; Escherichia coli/*enzymology/*genetics/isolation &amp; purification ; Escherichia coli Infections/microbiology/*veterinary ; France ; Gene Transfer, Horizontal ; Genotype ; Microbial Sensitivity Tests ; Plasmids/*analysis/classification ; beta-Lactam Resistance ; beta-Lactamases/*genetics ; }, }
@article {pmid22870994, year = {2012}, author = {Fu, XH and Wang, L and Le, YQ and Hu, JJ}, title = {Persistence and renaturation efficiency of thermally treated waste recombinant DNA in defined aquatic microcosms.}, journal = {Journal of environmental science and health. Part A, Toxic/hazardous substances &amp; environmental engineering}, volume = {47}, number = {13}, pages = {1975-1983}, doi = {10.1080/10934529.2012.695260}, pmid = {22870994}, issn = {1532-4117}, mesh = {DNA, Recombinant/*genetics ; Gene Transfer, Horizontal/genetics ; Nucleic Acid Denaturation/*genetics ; Plasmids/genetics ; Temperature ; Water Microbiology ; }, abstract = {To validate the possibility of horizontal gene transfer (HGT) from thermally denatured recombinant DNA discharged into the eco-system, a constructed plasmid was used to investigate the persistence and renaturation efficiency of thermally denatured recombinant DNA in defined aquatic microcosms. The results revealed that there was undecayed recombinant plasmid pMDLKJ material being discharged into the aquatic microcosms even after thermal treatment at either 100°C (using boiling water) or at 120°C (using an autoclave). The plasmid had a relatively long persistence time. At least 10(2) copies μL(-1) of a specific 245 bp fragment of the plasmid could be detected after 12 h and a specific 628 bp fragment could be detected up to 2 h. The thermally denatured recombinant DNA could efficiently renature and recover its functional double stranded structure in aquatic microcosms and the highest concentration of double-stranded DNA (dsDNA) occurred around 1 h after the thermally denatured DNA was added to the system. These results imply that when thermally treated recombinant DNAs are discharged into aquatic environments, they have enough time to renature and possibly transfer to other organisms. In addition, the recombinant DNA added to aquatic microcosms could be absorbed by the seston particles in water, such as mineral, organic and colloids particles with a maximum absorption value of about 5.18 ng L(-1). This absorbed DNA could persist longer in aquatic environments than free recombinant DNA, thus further favoring HGT.}, }
@article {pmid22868206, year = {2012}, author = {Li, P and Chen, B and Song, Z and Song, Y and Yang, Y and Ma, P and Wang, H and Ying, J and Ren, P and Yang, L and Gao, G and Jin, S and Bao, Q and Yang, H}, title = {Bioinformatic analysis of the Acinetobacter baumannii phage AB1 genome.}, journal = {Gene}, volume = {507}, number = {2}, pages = {125-134}, doi = {10.1016/j.gene.2012.07.029}, pmid = {22868206}, issn = {1879-0038}, mesh = {Acinetobacter baumannii/pathogenicity/*virology ; Bacteriophages/*genetics/physiology ; Base Sequence ; Capsid Proteins/genetics ; Computational Biology ; DNA Modification Methylases/genetics ; DNA Replication/genetics ; DNA, Viral/genetics ; DNA-Directed RNA Polymerases/genetics ; Evolution, Molecular ; *Genome, Viral ; Humans ; Nucleic Acid Conformation ; Open Reading Frames ; Phylogeny ; RNA, Transfer/chemistry/genetics ; RNA, Viral/chemistry/genetics ; Recombinases/genetics ; Viral Tail Proteins/genetics ; Virus Assembly/genetics ; Virus Replication/genetics ; }, abstract = {As one of the pathogens of hospital-acquired infections, Acinetobacter baumannii poses great challenges to the public health. A. baumannii phage could be an effective way to fight multi-resistant A. baumannii. Here, we completed the whole genome sequencing of the complete genome of A. baumannii phage AB1, which consists of 45,159 bp and is a double-stranded DNA molecule with an average GC content of 37.7%. The genome encodes one tRNA gene and 85 open reading frames (ORFs) and the average size of the ORF is 531 bp in length. Among 85 ORFs, only 14 have been identified to share significant sequence similarities to the genes with known functions, while 28 are similar in sequence to the genes with function-unknown genes in the database and 43 ORFs are uniquely present in the phage AB1 genome. Fourteen function-assigned genes with putative functions include five phage structure proteins, an RNA polymerase, a big sub-unit and a small sub-unit of a terminase, a methylase and a recombinase and the proteins involved in DNA replication and so on. Multiple sequence alignment was conducted among those homologous proteins and the phylogenetic trees were reconstructed to analyze the evolutionary courses of these essential genes. From comparative genomics analysis, it turned out clearly that the frame of the phage genome mainly consisted of genes from Xanthomonas phages, Burkholderia ambifaria phages and Enterobacteria phages and while it comprises genes of its host A. baumannii only sporadically. The mosaic feature of the phage genome suggested that the horizontal gene transfer occurred among the phage genomes and between the phages and the host bacterium genomes. Analyzing the genome sequences of the phages should lay sound foundation to investigate how phages adapt to the environment and infect their hosts, and even help to facilitate the development of biological agents to deal with pathogenic bacteria.}, }
@article {pmid22865076, year = {2012}, author = {Lefèvre, CT and Schmidt, ML and Viloria, N and Trubitsyn, D and Schüler, D and Bazylinski, DA}, title = {Insight into the evolution of magnetotaxis in Magnetospirillum spp., based on mam gene phylogeny.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {20}, pages = {7238-7248}, pmid = {22865076}, issn = {1098-5336}, mesh = {Bacterial Proteins/*genetics ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Gene Transfer, Horizontal ; *Locomotion ; *Magnetics ; Magnetospirillum/*genetics/isolation &amp; purification/physiology ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Southwestern United States ; Water Microbiology ; }, abstract = {Vibrioid- to helical-shaped magnetotactic bacteria phylogenetically related to the genus Magnetospirillum were isolated in axenic cultures from a number of freshwater and brackish environments located in the southwestern United States. Based on 16S rRNA gene sequences, most of the new isolates represent new Magnetospirillum species or new strains of known Magnetospirillum species, while one isolate appears to represent a new genus basal to Magnetospirillum. Partial sequences of conserved mam genes, genes reported to be involved in the magnetosome and magnetosome chain formation, and form II of the ribulose-1,5-bisphosphate carboxylase/oxygenase gene (cbbM) were determined in the new isolates and compared. The cbbM gene was chosen for comparison because it is not involved in magnetosome synthesis; it is highly conserved and is present in all but possibly one of the genomes of the magnetospirilla and the new isolates. Phylogenies based on 16S rRNA, cbbM, and mam gene sequences were reasonably congruent, indicating that the genes involved in magnetotaxis were acquired by a common ancestor of the Magnetospirillum clade. However, in one case, magnetosome genes might have been acquired through horizontal gene transfer. Our results also extend the known diversity of the Magnetospirillum group and show that they are widespread in freshwater environments.}, }
@article {pmid22860902, year = {2012}, author = {Mardanov, AV and Ravin, NV}, title = {The impact of genomics on research in diversity and evolution of archaea.}, journal = {Biochemistry. Biokhimiia}, volume = {77}, number = {8}, pages = {799-812}, doi = {10.1134/S0006297912080019}, pmid = {22860902}, issn = {1608-3040}, mesh = {Archaea/*genetics ; *Evolution, Molecular ; *Genetic Research ; *Genomics ; Phylogeny ; }, abstract = {Since the definition of archaea as a separate domain of life along with bacteria and eukaryotes, they have become one of the most interesting objects of modern microbiology, molecular biology, and biochemistry. Sequencing and analysis of archaeal genomes were especially important for studies on archaea because of a limited availability of genetic tools for the majority of these microorganisms and problems associated with their cultivation. Fifteen years since the publication of the first genome of an archaeon, more than one hundred complete genome sequences of representatives of different phylogenetic groups have been determined. Analysis of these genomes has expanded our knowledge of biology of archaea, their diversity and evolution, and allowed identification and characterization of new deep phylogenetic lineages of archaea. The development of genome technologies has allowed sequencing the genomes of uncultivated archaea directly from enrichment cultures, metagenomic samples, and even from single cells. Insights have been gained into the evolution of key biochemical processes in archaea, such as cell division and DNA replication, the role of horizontal gene transfer in the evolution of archaea, and new relationships between archaea and eukaryotes have been revealed.}, }
@article {pmid22860002, year = {2012}, author = {Chandry, PS and Gladman, S and Moore, SC and Seemann, T and Crandall, KA and Fegan, N}, title = {A Genomic Island in Salmonella enterica ssp. salamae provides new insights on the genealogy of the locus of enterocyte effacement.}, journal = {PloS one}, volume = {7}, number = {7}, pages = {e41615}, pmid = {22860002}, issn = {1932-6203}, mesh = {Bacterial Secretion Systems/genetics ; *Genes, Bacterial ; Genes, Essential ; *Genetic Loci ; Genetic Variation ; *Genomic Islands ; Humans ; Operon ; Phylogeny ; Recombination, Genetic ; Salmonella enterica/*genetics/physiology ; Sequence Analysis, DNA ; Virulence Factors/genetics ; }, abstract = {The genomic island encoding the locus of enterocyte effacement (LEE) is an important virulence factor of the human pathogenic Escherichia coli. LEE typically encodes a type III secretion system (T3SS) and secreted effectors capable of forming attaching and effacing lesions. Although prominent in the pathogenic E. coli such as serotype O157:H7, LEE has also been detected in Citrobacter rodentium, E. albertii, and although not confirmed, it is likely to also be in Shigella boydii. Previous phylogenetic analysis of LEE indicated the genomic island was evolving through stepwise acquisition of various components. This study describes a new LEE region from two strains of Salmonella enterica subspecies salamae serovar Sofia along with a phylogenetic analysis of LEE that provides new insights into the likely evolution of this genomic island. The Salmonella LEE contains 36 of the 41 genes typically observed in LEE within a genomic island of 49, 371 bp that encodes a total of 54 genes. A phylogenetic analysis was performed on the entire T3SS and four T3SS genes (escF, escJ, escN, and escV) to elucidate the genealogy of LEE. Phylogenetic analysis inferred that the previously known LEE islands are members of a single lineage distinct from the new Salmonella LEE lineage. The previously known lineage of LEE diverged between islands found in Citrobacter and those in Escherichia and Shigella. Although recombination and horizontal gene transfer are important factors in the genealogy of most genomic islands, the phylogeny of the T3SS of LEE can be interpreted with a bifurcating tree. It seems likely that the LEE island entered the Enterobacteriaceae through horizontal gene transfer as a single unit, rather than as separate subsections, which was then subjected to the forces of both mutational change and recombination.}, }
@article {pmid22857004, year = {2013}, author = {Martínez, JL}, title = {Bacterial pathogens: from natural ecosystems to human hosts.}, journal = {Environmental microbiology}, volume = {15}, number = {2}, pages = {325-333}, doi = {10.1111/j.1462-2920.2012.02837.x}, pmid = {22857004}, issn = {1462-2920}, mesh = {Bacteria/*genetics/*pathogenicity/virology ; Bacteriophages/genetics/physiology ; *Biological Evolution ; *Ecosystem ; Gene Transfer, Horizontal ; Host-Pathogen Interactions ; Humans ; Virulence/*genetics ; }, abstract = {The analysis of the genomes of bacterial pathogens indicates that they have acquired their pathogenic capability by incorporating different genetic elements through horizontal gene transfer. The ancestors of virulent bacteria, as well as the origin of virulence determinants, lay most likely in the environmental microbiota. Studying the role that these determinants may have in non-clinical ecosystems is thus of value for understanding in detail the evolution and the ecology of bacterial pathogens. In this article, I propose that classical virulence determinants might be relevant for basic metabolic processes (for instance iron-uptake systems) or in modulating prey/predator relationships (toxins) in natural, non-infective ecosystems. The different role that horizontal gene transfer and mutation may have in the evolution of bacterial pathogens either for their speciation or in short-sighted evolution processes is also discussed.}, }
@article {pmid22856147, year = {2012}, author = {Shabliĭ, VA and Lukash, LL and Lobintseva, HS}, title = {[The role of some donor-host cell interactions in conditions of the regenerative process microenvironment].}, journal = {TSitologiia i genetika}, volume = {46}, number = {3}, pages = {65-74}, pmid = {22856147}, issn = {0564-3783}, mesh = {Cell Fusion ; Cell Transdifferentiation/genetics ; Cellular Microenvironment/genetics ; Gene Transfer, Horizontal/genetics ; Heart/*physiology/physiopathology ; *Hematopoietic Stem Cell Transplantation ; Humans ; Liver Regeneration/*genetics ; *Mesenchymal Stem Cell Transplantation ; Regeneration/*genetics ; Tissue Donors ; }, abstract = {The review is devoted to the analysis of experimental data about possible mechanisms of transdifferentiation or plasticity of tissue specific stem cells. Considerable attention is focused on the mechanisms and genetic consequences of fusion of different types of donor cells with the cells of recipient tissues which investigated on the models of cellular therapy of liver and heart diseases. The role of various kinds of cell contacts and their role in stem cells integration, reparation and regeneration of injured tissue and horizontal genes transfer are considered.}, }
@article {pmid22854120, year = {2012}, author = {Sarwar, S and Ahmed, M and Hasnain, S}, title = {Phylogenomic analysis of polyketide synthase genes in actinomycetes: structural analysis of KS domains and modules of polyketide synthases.}, journal = {International journal of computational biology and drug design}, volume = {5}, number = {2}, pages = {89-110}, doi = {10.1504/IJCBDD.2012.048281}, pmid = {22854120}, issn = {1756-0756}, mesh = {Actinobacteria/enzymology/*genetics ; Amino Acid Sequence ; *Genes, Bacterial ; *Genomics ; Molecular Sequence Data ; *Phylogeny ; Polyketide Synthases/chemistry/*genetics ; Sequence Homology, Amino Acid ; }, abstract = {Polyketides are complex and diverse secondary metabolites, synthesised by large multifunctional enzymes, Polyketide Synthases (PKS). The phylogenomic analysis of β-ketosynthase (KS) domains and PKSs within actinomycetes suggests the contribution of point mutations, gene duplications, horizontal gene transfer and homologous recombination in the evolution of PKSs. PKS genealogy suggested the ancestral module structure with KS-AT-ACP domain composition. KS domains showed similar core and highly variable loop regions at the dimer interface, which seems to affect the selectivity of the primer unit. In PKS modules, the linker regions comprise a significant fraction of the module. The reducing domains (ketoreductase and dehydrogenase) protrude out from the central axis of the module and also responsible for extreme variability in the final products. Thus, phylogenomic and structural analysis of PKSs can assist in the artificial reprogramming of PKSs.}, }
@article {pmid22848782, year = {2012}, author = {Zhu, L and Kreth, J}, title = {The role of hydrogen peroxide in environmental adaptation of oral microbial communities.}, journal = {Oxidative medicine and cellular longevity}, volume = {2012}, number = {}, pages = {717843}, pmid = {22848782}, issn = {1942-0994}, support = {R00 DE018400/DE/NIDCR NIH HHS/United States ; R00DE018400/DE/NIDCR NIH HHS/United States ; }, mesh = {*Adaptation, Physiological ; Animals ; *Environment ; Host-Pathogen Interactions/physiology ; Humans ; Hydrogen Peroxide/*metabolism ; Microbial Consortia/*physiology ; Mouth/*microbiology ; }, abstract = {Oral streptococci are able to produce growth-inhibiting amounts of hydrogen peroxide (H(2)O(2)) as byproduct of aerobic metabolism. Several recent studies showed that the produced H(2)O(2) is not a simple byproduct of metabolism but functions in several aspects of oral bacterial biofilm ecology. First, the release of DNA from cells is closely associated to the production of H(2)O(2) in Streptococcus sanguinis and Streptococcus gordonii. Extracellular DNA is crucial for biofilm development and stabilization and can also serve as source for horizontal gene transfer between oral streptococci. Second, due to the growth inhibiting nature of H(2)O(2), H(2)O(2) compatible species associate with the producers. H(2)O(2) production therefore might help in structuring the initial biofilm development. On the other hand, the oral environment harbors salivary peroxidases that are potent in H(2)O(2) scavenging. Therefore, the effects of biofilm intrinsic H(2)O(2) production might be locally confined. However, taking into account that 80% of initial oral biofilm constituents are streptococci, the influence of H(2)O(2) on biofilm development and environmental adaptation might be under appreciated in current research.}, }
@article {pmid22845836, year = {2012}, author = {Sheng, R and Bereg, S}, title = {Approximating metrics with planar boundary-labeled phylogenetic networks.}, journal = {Journal of bioinformatics and computational biology}, volume = {10}, number = {6}, pages = {1250017}, doi = {10.1142/S0219720012500175}, pmid = {22845836}, issn = {1757-6334}, mesh = {Algorithms ; Animals ; Computational Biology/*methods ; Gene Transfer, Horizontal ; Humans ; *Phylogeny ; }, abstract = {Phylogenetic networks are useful for visualizing evolutionary relationships between species with reticulate events such as hybridizations and horizontal gene transfers. In this paper, we consider the problem of constructing undirected phylogenetic networks that (1) are planar graphs and (2) admit embeddings in the plane where the vertices labeling all taxa are on the boundary of the network. We develop a new algorithm for constructing phylogenetic networks satisfying these constraints. First, we show that only approximate networks can be constructed for some distance matrices with at least five taxa. Then we prove that any five-point metric can be represented approximately by a planar boundary-labeled network with guaranteed fit value of 94.79. We extend the networks constructed in the proof to design an algorithm for computing planar boundary-labeled networks for any number of taxa.}, }
@article {pmid22845467, year = {2013}, author = {Hurwitz, BL and Deng, L and Poulos, BT and Sullivan, MB}, title = {Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics.}, journal = {Environmental microbiology}, volume = {15}, number = {5}, pages = {1428-1440}, pmid = {22845467}, issn = {1462-2920}, mesh = {Biodiversity ; *Metagenomics ; Reproducibility of Results ; Seawater/virology ; Viral Proteins/analysis/genetics ; Virology/*methods ; Viruses/*genetics/*isolation &amp; purification ; *Water Microbiology ; }, abstract = {Viruses have global impact through mortality, nutrient cycling and horizontal gene transfer, yet their study is limited by complex methodologies with little validation. Here, we use triplicate metagenomes to compare common aquatic viral concentration and purification methods across four combinations as follows: (i) tangential flow filtration (TFF) and DNase + CsCl, (ii) FeCl3 precipitation and DNase, (iii) FeCl3 precipitation and DNase + CsCl and (iv) FeCl3 precipitation and DNase + sucrose. Taxonomic data (30% of reads) suggested that purification methods were statistically indistinguishable at any taxonomic level while concentration methods were significantly different at family and genus levels. Specifically, TFF-concentrated viral metagenomes had significantly fewer abundant viral types (Podoviridae and Phycodnaviridae) and more variability among Myoviridae than FeCl3 -precipitated viral metagenomes. More comprehensive analyses using protein clusters (66% of reads) and k-mers (100% of reads) showed 50-53% of these data were common to all four methods, and revealed trace bacterial DNA contamination in TFF-concentrated metagenomes and one of three replicates concentrated using FeCl3 and purified by DNase alone. Shared k-mer analyses also revealed that polymerases used in amplification impact the resulting metagenomes, with TaKaRa enriching for 'rare' reads relative to PfuTurbo. Together these results provide empirical data for making experimental design decisions in culture-independent viral ecology studies.}, }
@article {pmid22844638, year = {2012}, author = {Swithers, KS and Soucy, SM and Gogarten, JP}, title = {The role of reticulate evolution in creating innovation and complexity.}, journal = {International journal of evolutionary biology}, volume = {2012}, number = {}, pages = {418964}, pmid = {22844638}, issn = {2090-052X}, abstract = {Reticulate evolution encompasses processes that conflict with traditional Tree of Life efforts. These processes, horizontal gene transfer (HGT), gene and whole-genome duplications through allopolyploidization, are some of the main driving forces for generating innovation and complexity. HGT has a profound impact on prokaryotic and eukaryotic evolution. HGTs can lead to the invention of new metabolic pathways and the expansion and enhancement of previously existing pathways. It allows for organismal adaptation into new ecological niches and new host ranges. Although many HGTs appear to be selected for because they provide some benefit to their recipient lineage, other HGTs may be maintained by chance through random genetic drift. Moreover, some HGTs that may initially seem parasitic in nature can cause complexity to arise through pathways of neutral evolution. Another mechanism for generating innovation and complexity, occurring more frequently in eukaryotes than in prokaryotes, is gene and genome duplications, which often occur through allopolyploidizations. We discuss how these different evolutionary processes contribute to generating innovation and complexity.}, }
@article {pmid22844447, year = {2012}, author = {Burmølle, M and Norman, A and Sørensen, SJ and Hansen, LH}, title = {Sequencing of IncX-plasmids suggests ubiquity of mobile forms of a biofilm-promoting gene cassette recruited from Klebsiella pneumoniae.}, journal = {PloS one}, volume = {7}, number = {7}, pages = {e41259}, pmid = {22844447}, issn = {1932-6203}, mesh = {Biofilms/*growth &amp; development ; Escherichia coli/genetics/physiology ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/*genetics ; Klebsiella pneumoniae/*genetics/*physiology ; Plasmids/*genetics ; Replicon/genetics ; *Sequence Analysis, DNA ; Waste Disposal, Fluid ; Wastewater/microbiology ; }, abstract = {Plasmids are a highly effective means with which genetic traits that influence human health, such as virulence and antibiotic resistance, are disseminated through bacterial populations. The IncX-family is a hitherto sparsely populated group of plasmids that are able to thrive within Enterobacteriaceae. In this study, a replicon-centric screening method was used to locate strains from wastewater sludge containing plasmids belonging to the IncX-family. A transposon aided plasmid capture method was then employed to transport IncX-plasmids from their original hosts (and co-hosted plasmids) into a laboratory strain (Escherichia coli Genehogs®) for further study. The nucleotide sequences of the three newly isolated IncX-plasmids (pLN126_33, pMO17_54, pMO440_54) and the hitherto un-sequenced type-plasmid R485 revealed a remarkable occurrence of whole or partial gene cassettes that promote biofilm-formation in Klebsiella pneumonia or E. coli, in all four instances. Two of the plasmids (R485 and pLN126_33) were shown to directly induce biofilm formation in a crystal violet retention assay in E. coli. Sequence comparison revealed that all plasmid-borne forms of the type 3 fimbriae encoding gene cassette mrkABCDF were variations of a composite transposon Tn6011 first described in the E. coli IncX plasmid pOLA52. In conclusion, IncX-plasmids isolated from Enterobacteriaceae over almost 40 years and on three different continents have all been shown to carry a type 3 fimbriae gene cassette mrkABCDF stemming from pathogenic K. pneumoniae. Apart from contributing general knowledge about IncX-plasmids, this study also suggests an apparent ubiquity of a mobile form of an important virulence factor and is an illuminating example of the recruitment, evolution and dissemination of genetic traits through plasmid-mediated horizontal gene transfer.}, }
@article {pmid22843572, year = {2012}, author = {Kang, X and Ling, N and Sun, G and Zhou, Q and Zhang, L and Sheng, Q}, title = {Complete genome sequence of Streptococcus thermophilus strain MN-ZLW-002.}, journal = {Journal of bacteriology}, volume = {194}, number = {16}, pages = {4428-4429}, pmid = {22843572}, issn = {1098-5530}, mesh = {Base Composition ; Biosynthetic Pathways/genetics ; DNA, Bacterial/*chemistry/*genetics ; Food Microbiology ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Lactobacillales/genetics ; Molecular Sequence Data ; Multigene Family ; Open Reading Frames ; Polysaccharides, Bacterial/metabolism ; *Sequence Analysis, DNA ; Streptococcus thermophilus/*genetics/isolation &amp; purification/metabolism ; }, abstract = {Streptococcus thermophilus MN-ZLW-002 was originally isolated from traditionally fermented Chinese dairy products. One of the strain-dependent characteristics of this bacterium is its ability to produce exopolysaccharides (EPSs). This study determined and analyzed the genome sequence of MN-ZLW-002. Its complete genome comprised 2,046 genes and 1,848,520 nucleotides with an average GC content of 39%. The EPS cluster of MN-ZLW-002 includes 25 open reading frames (ORFs), and some results indicate a horizontal gene transfer between MN-ZLW-002 and other lactic acid bacteria (LAB).}, }
@article {pmid22841660, year = {2012}, author = {Liu, L and Chen, X and Skogerbø, G and Zhang, P and Chen, R and He, S and Huang, DW}, title = {The human microbiome: a hot spot of microbial horizontal gene transfer.}, journal = {Genomics}, volume = {100}, number = {5}, pages = {265-270}, doi = {10.1016/j.ygeno.2012.07.012}, pmid = {22841660}, issn = {1089-8646}, mesh = {*Biota ; Computational Biology ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/*genetics ; Genomics/*methods ; Humans ; Metagenome/*genetics ; Molecular Sequence Annotation ; }, abstract = {The human body harbors numerous microbes, and here exists a close relationship between microbes and human health. The Human Microbiome Project has generated whole genome sequences of several hundred human microbes. In this study, we identified horizontal gene transfer (HGT) events in human microbes and tried to elucidate the relationships between the gene-transferring microbes. A total of 13,514 high confidence HGT genes were identified in 308 human microbes. The horizontally transferred genes were enriched for Gene Ontology terms pertaining to catalytic functions and metabolic processes. Construction of an HGT event network suggested that the human microbes could be divided into specific communities which only partly overlap their distribution in human body. Our research suggests that human microbiome may facilitate frequent horizontal gene transfer among bacteria in human body. Awareness of HGT in human microbiome may aid our understanding of the relationship between the human microbiome and human health.}, }
@article {pmid22839777, year = {2012}, author = {Fernández-Gómez, B and Fernàndez-Guerra, A and Casamayor, EO and González, JM and Pedrós-Alió, C and Acinas, SG}, title = {Patterns and architecture of genomic islands in marine bacteria.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {347}, pmid = {22839777}, issn = {1471-2164}, mesh = {Aquatic Organisms/genetics ; Bacteria/*genetics ; Databases, Genetic ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genomic Islands ; Molecular Sequence Annotation ; Phylogeny ; Water Microbiology ; }, abstract = {BACKGROUND: Genomic Islands (GIs) have key roles since they modulate the structure and size of bacterial genomes displaying a diverse set of laterally transferred genes. Despite their importance, GIs in marine bacterial genomes have not been explored systematically to uncover possible trends and to analyze their putative ecological significance.<br><br>RESULTS: We carried out a comprehensive analysis of GIs in 70 selected marine bacterial genomes detected with IslandViewer to explore the distribution, patterns and functional gene content in these genomic regions. We detected 438 GIs containing a total of 8152 genes. GI number per genome was strongly and positively correlated with the total GI size. In 50% of the genomes analyzed the GIs accounted for approximately 3% of the genome length, with a maximum of 12%. Interestingly, we found transposases particularly enriched within Alphaproteobacteria GIs, and site-specific recombinases in Gammaproteobacteria GIs. We described specific Homologous Recombination GIs (HR-GIs) in several genera of marine Bacteroidetes and in Shewanella strains among others. In these HR-GIs, we recurrently found conserved genes such as the &#x3b2;-subunit of DNA-directed RNA polymerase, regulatory sigma factors, the elongation factor Tu and ribosomal protein genes typically associated with the core genome.<br><br>CONCLUSIONS: Our results indicate that horizontal gene transfer mediated by phages, plasmids and other mobile genetic elements, and HR by site-specific recombinases play important roles in the mobility of clusters of genes between taxa and within closely related genomes, modulating the flexible pool of the genome. Our findings suggest that GIs may increase bacterial fitness under environmental changing conditions by acquiring novel foreign genes and/or modifying gene transcription and/or transduction.}, }
@article {pmid22837698, year = {2012}, author = {Yang, Y and Ramelot, TA and Cort, JR and Garcia, M and Yee, A and Arrowsmith, CH and Kennedy, MA}, title = {Solution NMR structure of hypothetical protein CV_2116 encoded by a viral prophage element in Chromobacterium violaceum.}, journal = {International journal of molecular sciences}, volume = {13}, number = {6}, pages = {7354-7364}, pmid = {22837698}, issn = {1422-0067}, support = {U54 GM074958/GM/NIGMS NIH HHS/United States ; U54 GM094597/GM/NIGMS NIH HHS/United States ; U54-GM094597/GM/NIGMS NIH HHS/United States ; U54-GM074958/GM/NIGMS NIH HHS/United States ; }, mesh = {*Chromobacterium/chemistry/virology ; Databases, Protein ; Nuclear Magnetic Resonance, Biomolecular ; Prophages/*chemistry ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Viral Proteins/*chemistry ; }, abstract = {CV_2116 is a small hypothetical protein of 82 amino acids from the Gram-negative coccobacillus Chromobacterium violaceum. A PSI-BLAST search using the CV_2116 sequence as a query identified only one hit (E = 2e(-07)) corresponding to a hypothetical protein OR16_04617 from Cupriavidus basilensis OR16, which failed to provide insight into the function of CV_2116. The CV_2116 gene was cloned into the p15TvLic expression plasmid, transformed into E. coli, and (13)C- and (15)N-labeled NMR samples of CV_2116 were overexpressed in E. coli and purified for structure determination using NMR spectroscopy. The resulting high-quality solution NMR structure of CV_2116 revealed a novel α + β fold containing two anti-parallel β-sheets in the N-terminal two-thirds of the protein and one α-helix in the C-terminal third of the protein. CV_2116 does not belong to any known protein sequence family and a Dali search indicated that no similar structures exist in the protein data bank. Although no function of CV_2116 could be derived from either sequence or structural similarity searches, the neighboring genes of CV_2116 encode various proteins annotated as similar to bacteriophage tail assembly proteins. Interestingly, C. violaceum exhibits an extensive network of bacteriophage tail-like structures that likely result from lateral gene transfer by incorporation of viral DNA into its genome (prophages) due to bacteriophage infection. Indeed, C. violaceum has been shown to contain four prophage elements and CV_2116 resides in the fourth of these elements. Analysis of the putative operon in which CV_2116 resides indicates that CV_2116 might be a component of the bacteriophage tail-like assembly that occurs in C. violaceum.}, }
@article {pmid22835476, year = {2013}, author = {Doudoumis, V and Alam, U and Aksoy, E and Abd-Alla, AM and Tsiamis, G and Brelsfoard, C and Aksoy, S and Bourtzis, K}, title = {Tsetse-Wolbachia symbiosis: comes of age and has great potential for pest and disease control.}, journal = {Journal of invertebrate pathology}, volume = {112 Suppl}, number = {0}, pages = {S94-103}, pmid = {22835476}, issn = {1096-0805}, support = {AI06892/AI/NIAID NIH HHS/United States ; R03TW008413/TW/FIC NIH HHS/United States ; R03 TW008755/TW/FIC NIH HHS/United States ; D43 TW007391/TW/FIC NIH HHS/United States ; R01 AI051584/AI/NIAID NIH HHS/United States ; D43TW007391/TW/FIC NIH HHS/United States ; R01 AI068932/AI/NIAID NIH HHS/United States ; R03 TW008413/TW/FIC NIH HHS/United States ; }, mesh = {Animals ; Gene Transfer, Horizontal/genetics ; Humans ; Pest Control, Biological/*methods ; *Symbiosis/genetics ; Trypanosomiasis, African/prevention &amp; control ; Tsetse Flies/genetics/*microbiology ; *Wolbachia/genetics ; }, abstract = {Tsetse flies (Diptera: Glossinidae) are the sole vectors of African trypanosomes, the causative agent of sleeping sickness in human and nagana in animals. Like most eukaryotic organisms, Glossina species have established symbiotic associations with bacteria. Three main symbiotic bacteria have been found in tsetse flies: Wigglesworthia glossinidia, an obligate symbiotic bacterium, the secondary endosymbiont Sodalis glossinidius and the reproductive symbiont Wolbachia pipientis. In the present review, we discuss recent studies on the detection and characterization of Wolbachia infections in Glossina species, the horizontal transfer of Wolbachia genes to tsetse chromosomes, the ability of this symbiont to induce cytoplasmic incompatibility in Glossina morsitans morsitans and also how new environment-friendly tools for disease control could be developed by harnessing Wolbachia symbiosis.}, }
@article {pmid22835381, year = {2012}, author = {Lommer, M and Specht, M and Roy, AS and Kraemer, L and Andreson, R and Gutowska, MA and Wolf, J and Bergner, SV and Schilhabel, MB and Klostermeier, UC and Beiko, RG and Rosenstiel, P and Hippler, M and LaRoche, J}, title = {Genome and low-iron response of an oceanic diatom adapted to chronic iron limitation.}, journal = {Genome biology}, volume = {13}, number = {7}, pages = {R66}, pmid = {22835381}, issn = {1474-760X}, mesh = {Adaptation, Biological ; Biological Evolution ; Diatoms/genetics/*physiology ; Gene Expression Regulation ; Gene Transfer, Horizontal ; *Genome ; Genomics/methods ; *Iron Deficiencies ; Molecular Sequence Data ; Photosynthesis ; Sequence Analysis, RNA ; Species Specificity ; }, abstract = {BACKGROUND: Biogeochemical elemental cycling is driven by primary production of biomass via phototrophic phytoplankton growth, with 40% of marine productivity being assigned to diatoms. Phytoplankton growth is widely limited by the availability of iron, an essential component of the photosynthetic apparatus. The oceanic diatom Thalassiosira oceanica shows a remarkable tolerance to low-iron conditions and was chosen as a model for deciphering the cellular response upon shortage of this essential micronutrient.<br><br>RESULTS: The combined efforts in genomics, transcriptomics and proteomics reveal an unexpected metabolic flexibility in response to iron availability for T. oceanica CCMP1005. The complex response comprises cellular retrenchment as well as remodeling of bioenergetic pathways, where the abundance of iron-rich photosynthetic proteins is lowered, whereas iron-rich mitochondrial proteins are preserved. As a consequence of iron deprivation, the photosynthetic machinery undergoes a remodeling to adjust the light energy utilization with the overall decrease in photosynthetic electron transfer complexes.<br><br>CONCLUSIONS: Beneficial adaptations to low-iron environments include strategies to lower the cellular iron requirements and to enhance iron uptake. A novel contribution enhancing iron economy of phototrophic growth is observed with the iron-regulated substitution of three metal-containing fructose-bisphosphate aldolases involved in metabolic conversion of carbohydrates for enzymes that do not contain metals. Further, our data identify candidate components of a high-affinity iron-uptake system, with several of the involved genes and domains originating from duplication events. A high genomic plasticity, as seen from the fraction of genes acquired through horizontal gene transfer, provides the platform for these complex adaptations to a low-iron world.}, }
@article {pmid22834929, year = {2012}, author = {Lopez-Sanchez, MJ and Sauvage, E and Da Cunha, V and Clermont, D and Ratsima Hariniaina, E and Gonzalez-Zorn, B and Poyart, C and Rosinski-Chupin, I and Glaser, P}, title = {The highly dynamic CRISPR1 system of Streptococcus agalactiae controls the diversity of its mobilome.}, journal = {Molecular microbiology}, volume = {85}, number = {6}, pages = {1057-1071}, doi = {10.1111/j.1365-2958.2012.08172.x}, pmid = {22834929}, issn = {1365-2958}, mesh = {Conjugation, Genetic ; DNA Transposable Elements ; DNA, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genetic Variation ; *Interspersed Repetitive Sequences ; Molecular Sequence Data ; *Recombination, Genetic ; *Repetitive Sequences, Nucleic Acid ; Sequence Analysis, DNA ; Streptococcus agalactiae/*genetics ; }, abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR) confer immunity against mobile genetic elements (MGEs) in prokaryotes. Streptococcus agalactiae, a leading cause of neonatal infections contains in its genome two CRISPR/Cas systems. We show that type 1-C CRISPR2 is present in few strains but type 2-A CRISPR1 is ubiquitous. Comparative sequence analysis of the CRISPR1 spacer content of 351 S. agalactiae strains revealed that it is extremely diverse due to the acquisition of new spacers, spacer duplications and spacer deletions that witness the dynamics of this system. The spacer content profile mirrors the S. agalactiae population structure. Transfer of a conjugative transposon targeted by CRISPR1 selected for spacer rearrangements, suggesting that deletions and duplications pre-exist in the population. The comparison of protospacers located within MGE or the core genome and protospacer-associated motif-shuffling demonstrated that the GG motif is sufficient to discriminate self and non-self and for spacer selection and integration. Strikingly more than 40% of the 949 different CRISPR1 spacers identified target MGEs found in S. agalactiae genomes. We thus propose that the S. agalactiae type II-A CRISPR1/Cas system modulates the cohabitation of the species with its mobilome, as such contributing to the diversity of MGEs in the population.}, }
@article {pmid22833222, year = {2012}, author = {Stucken, K and Ilhan, J and Roettger, M and Dagan, T and Martin, WF}, title = {Transformation and conjugal transfer of foreign genes into the filamentous multicellular cyanobacteria (subsection V) Fischerella and Chlorogloeopsis.}, journal = {Current microbiology}, volume = {65}, number = {5}, pages = {552-560}, pmid = {22833222}, issn = {1432-0991}, support = {232975/ERC_/European Research Council/International ; }, mesh = {*Conjugation, Genetic ; Cyanobacteria/*genetics/*growth &amp; development/metabolism ; Electroporation ; Gene Transfer Techniques ; *Gene Transfer, Horizontal ; Genes, Reporter ; Green Fluorescent Proteins/genetics/metabolism ; *Transformation, Genetic ; }, abstract = {Cyanobacteria of subsection V grow as filaments with asymmetrical cell divisions that can generate a true-branching phenotype. Members of the genera Fischerella and Chlorogloeopsis furthermore differentiate akinetes (spore-like resting stages), heterocysts (specialized in nitrogen fixation) and hormogonia (cell aggregates with gliding motility for colonization and dispersal). Genetic approaches to studying the complex morphology and differentiations of these prokaryotes require transformation techniques. For Fischerella and Chlorogloeopsis reliable protocols for introducing foreign genes are lacking. Here, we explored conjugation, electroporation, and biolistic DNA transfer methods in Fischerella and Chlorogloeopsis, using the cyanobacterial replicon pRL25C as a marker. We successfully transformed Fischerella muscicola PCC 7414 and Chlorogloeopsis fritschii PCC 6912 and were able to express the GFP reporter protein under two different promoters: the nitrogen regulated (p) glnA and the strong E. coli hybrid (p) trc. For Fischerella all methods worked, for Chlorogloeopsis electroporation was unsuccessful. For both strains conjugation delivered the most reproducible results, whereby partial removal of the exopolysaccharide sheath by salt washing was a critical step.}, }
@article {pmid22831841, year = {2012}, author = {Ruiz, J and Pons, MJ and Gomes, C}, title = {Transferable mechanisms of quinolone resistance.}, journal = {International journal of antimicrobial agents}, volume = {40}, number = {3}, pages = {196-203}, doi = {10.1016/j.ijantimicag.2012.02.011}, pmid = {22831841}, issn = {1872-7913}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/*genetics ; Bacterial Infections/microbiology ; *Drug Resistance, Bacterial ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Phylogeny ; Plasmids ; Quinolones/*pharmacology ; }, abstract = {Quinolones were introduced into clinical practice in the late 1960s. Although quinolone resistance was described early, no transferable mechanism of quinolone resistance (TMQR) was confirmed until 1998. To date, five different TMQRs have been described in the literature, including target protection (Qnr), quinolone modification (AAC(6')-Ib-cr), plasmid-encoded efflux systems (e.g. QepA or OqxAB, amongst others), effect on bacterial growth rates and natural transformation. Although TMQRs usually only result in a slight increase in the minimum inhibitory concentrations of quinolones, they possess an additive effect and may facilitate the acquisition of full quinolone resistance. The emergence of new related genes may continue in the next years.}, }
@article {pmid22826456, year = {2012}, author = {Sormacheva, I and Smyshlyaev, G and Mayorov, V and Blinov, A and Novikov, A and Novikova, O}, title = {Vertical evolution and horizontal transfer of CR1 non-LTR retrotransposons and Tc1/mariner DNA transposons in Lepidoptera species.}, journal = {Molecular biology and evolution}, volume = {29}, number = {12}, pages = {3685-3702}, doi = {10.1093/molbev/mss181}, pmid = {22826456}, issn = {1537-1719}, mesh = {Animals ; Base Sequence ; Cloning, Molecular ; Cluster Analysis ; Computational Biology ; DNA Primers/genetics ; Electrophoresis, Agar Gel ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Immunoblotting ; Lepidoptera/*genetics ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Retroelements/*genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Horizontal transfer (HT) is a complex phenomenon usually used as an explanation of phylogenetic inconsistence, which cannot be interpreted in terms of vertical evolution. Most examples of HT of eukaryotic genes involve transposable elements. An intriguing feature of HT is that its frequency differs among transposable elements classes. Although HT is well known for DNA transposons and long terminal repeat (LTR) retrotransposons, non-LTR retrotransposons rarely undergo HT, and their phylogenies are largely congruent to those of their hosts. Previously, we described HT of CR1-like non-LTR retrotransposons between butterflies (Maculinea) and moths (Bombyx), which occurred less than 5 million years ago (Novikova O, Sliwinska E, Fet V, Settele J, Blinov A, Woyciechowski M. 2007. CR1 clade of non-LTR retrotransposons from Maculinea butterflies (Lepidoptera: Lycaenidae): evidence for recent horizontal transmission. BMC Evol Biol. 7:93). In this study, we continued to explore the diversity of CR1 non-LTR retrotransposons among lepidopterans providing additional evidences to support HT hypothesis. We also hypothesized that DNA transposons could be involved in HT of non-LTR retrotransposons. Thus, we performed analysis of one of the groups of DNA transposons, mariner-like DNA elements, as potential vectors for HT of non-LTR retrotransposons. Our results demonstrate multiple HTs between Maculinea and Bombyx genera. Although we did not find strong evidence for our hypothesis of the involvement of DNA transposons in HT of non-LTR retrotransposons, we demonstrated that recurrent and/or simultaneous flow of TEs took place between distantly related moths and butterflies.}, }
@article {pmid22825498, year = {2012}, author = {Looft, T and Allen, HK}, title = {Collateral effects of antibiotics on mammalian gut microbiomes.}, journal = {Gut microbes}, volume = {3}, number = {5}, pages = {463-467}, pmid = {22825498}, issn = {1949-0984}, mesh = {Animals ; Anti-Bacterial Agents/*administration &amp; dosage ; *Biota ; Escherichia coli/drug effects/growth &amp; development ; Gastrointestinal Tract/*microbiology ; Gene Transfer, Horizontal/drug effects ; Humans ; Mammals ; Metagenome/*drug effects ; }, abstract = {Antibiotics are an essential component of the modern lifestyle. They improve our lives by treating disease, preventing disease, and in the case of agricultural animals by improving feed efficiency. However, antibiotic usage is not without collateral effects. The development and spread of antibiotic resistance is the most notorious concern associated with antibiotic use. New technologies have enabled the study of how the microbiota responds to the antibiotic disturbance, including how the community recovers after the antibiotic is removed. One common theme in studies of antibiotic effects is a rapid increase in Escherichia coli followed by a gradual decline. Increases in E. coli are also associated with systemic host stresses, and may be an indicator of ecosystem disturbances of the intestinal microbiota. Moreover, recent studies have shown additional effects mediated by antibiotics on the gut microbiota, such as the stimulation of gene transfer among gut bacteria and the reduction of immune responses in peripheral organs. Querying the microbiota after antibiotic treatment has led to intriguing hypotheses regarding predicting or mitigating unfavorable treatment outcomes. Here we explore the varied effects of antibiotics on human and animal microbiotas.}, }
@article {pmid22824460, year = {2012}, author = {Imsoonthornruksa, S and Srirattana, K and Phewsoi, W and Tunwattana, W and Parnpai, R and Ketudat-Cairns, M}, title = {Segregation of donor cell mitochondrial DNA in gaur-bovine interspecies somatic cell nuclear transfer embryos, fetuses and an offspring.}, journal = {Mitochondrion}, volume = {12}, number = {5}, pages = {506-513}, doi = {10.1016/j.mito.2012.07.108}, pmid = {22824460}, issn = {1872-8278}, mesh = {Animals ; Cattle ; Cloning, Organism ; *DNA, Mitochondrial ; Embryonic Development ; Female ; Fetus ; *Gene Transfer, Horizontal ; Male ; *Nuclear Transfer Techniques ; Ruminants/*genetics ; }, abstract = {The fate of foreign mitochondrial DNA (mtDNA) following somatic cell nuclear transfer (SCNT) is still controversial. In this study, we examined the transmission of the heteroplasmic mtDNA of gaur donor cells and recipient bovine oocytes to an offspring and aborted and mummified fetuses at various levels during the development of gaur-bovine interspecies SCNT (iSCNT) embryos. High levels of the donor cell mtDNA were found in various tissue samples but they did not have any beneficial effect to the survival of iSCNT offspring. However, the factors on mtDNA inheritance are unique for each iSCNT experiment and depend on the recipient oocyte and donor cell used, which might play an important role in the efficiency of iSCNT.}, }
@article {pmid22824459, year = {2012}, author = {Valach, M and Pryszcz, LP and Tomaska, L and Gacser, A and Gabaldón, T and Nosek, J}, title = {Mitochondrial genome variability within the Candida parapsilosis species complex.}, journal = {Mitochondrion}, volume = {12}, number = {5}, pages = {514-519}, doi = {10.1016/j.mito.2012.07.109}, pmid = {22824459}, issn = {1872-8278}, support = {2-R03-TW005654-04A1/TW/FIC NIH HHS/United States ; 55005622//Howard Hughes Medical Institute/United States ; }, mesh = {Candida/*classification/*genetics ; DNA, Circular/genetics ; DNA, Mitochondrial/*genetics ; Gene Transfer, Horizontal ; *Genetic Variation ; *Genome, Mitochondrial ; }, abstract = {Candida parapsilosis species complex includes three closely related species, namely C. parapsilosis (sensu stricto), C. orthopsilosis, and C. metapsilosis. Unlike most other yeast lineages, members of this species complex possess a linear mitochondrial genome. Yet, its circularized mutant form was identified in strains of C. orthopsilosis and C. metapsilosis. To investigate the underlying variability, we performed comparative analyses of the complete mitochondrial DNA sequences in a collection of strains. Our results demonstrate that in contrast to C. parapsilosis and C. metapsilosis, C. orthopsilosis exhibits remarkably high nucleotide diversity whose pattern is consistent with intraspecific genetic exchange.}, }
@article {pmid22823479, year = {2012}, author = {Dias, ES and Carareto, CM}, title = {Ancestral polymorphism and recent invasion of transposable elements in Drosophila species.}, journal = {BMC evolutionary biology}, volume = {12}, number = {}, pages = {119}, pmid = {22823479}, issn = {1471-2148}, mesh = {Animals ; *DNA Transposable Elements ; Drosophila/classification/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Insect ; Hybridization, Genetic ; Likelihood Functions ; *Phylogeny ; *Polymorphism, Genetic ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: During the evolution of transposable elements, some processes, such as ancestral polymorphisms and horizontal transfer of sequences between species, can produce incongruences in phylogenies. We investigated the evolutionary history of the transposable elements Bari and 412 in the sequenced genomes of the Drosophila melanogaster group and in the sibling species D. melanogaster and D. simulans using traditional phylogenetic and network approaches.<br><br>RESULTS: Maximum likelihood (ML) phylogenetic analyses revealed incongruences and unresolved relationships for both the Bari and 412 elements. The DNA transposon Bari within the D. ananassae genome is more closely related to the element of the melanogaster complex than to the sequence in D. erecta, which is inconsistent with the species phylogeny. Divergence analysis and the comparison of the rate of synonymous substitutions per synonymous site of the Bari and host gene sequences explain the incongruence as an ancestral polymorphism that was inherited stochastically by the derived species. Unresolved relationships were observed in the ML phylogeny of both elements involving D. melanogaster, D. simulans and D. sechellia. A network approach was used to attempt to resolve these relationships. The resulting tree suggests recent transfers of both elements between D. melanogaster and D. simulans. The divergence values of the elements between these species support this conclusion.<br><br>CONCLUSIONS: We showed that ancestral polymorphism and recent invasion of genomes due to introgression or horizontal transfer between species occurred during the evolutionary history of the Bari and 412 elements in the melanogaster group. These invasions likely occurred in Africa during the Pleistocene, before the worldwide expansion of D. melanogaster and D. simulans.}, }
@article {pmid22821560, year = {2012}, author = {Furuta, Y and Kobayashi, I}, title = {Movement of DNA sequence recognition domains between non-orthologous proteins.}, journal = {Nucleic acids research}, volume = {40}, number = {18}, pages = {9218-9232}, pmid = {22821560}, issn = {1362-4962}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/classification/*genetics ; DNA Modification Methylases/chemistry/classification/*genetics ; DNA Restriction-Modification Enzymes/genetics ; DNA-Binding Proteins/chemistry/classification/*genetics ; *Evolution, Molecular ; Genes, Bacterial ; Genetic Loci ; Genetic Variation ; Genome, Bacterial ; Helicobacter/genetics ; Helicobacter pylori/*genetics ; Homologous Recombination ; Molecular Sequence Data ; Phylogeny ; Protein Interaction Domains and Motifs ; Sequence Alignment ; Treponema denticola/genetics ; }, abstract = {Comparisons of proteins show that they evolve through the movement of domains. However, in many cases, the underlying mechanisms remain unclear. Here, we observed the movements of DNA recognition domains between non-orthologous proteins within a prokaryote genome. Restriction-modification (RM) systems, consisting of a sequence-specific DNA methyltransferase and a restriction enzyme, contribute to maintenance/evolution of genomes/epigenomes. RM systems limit horizontal gene transfer but are themselves mobile. We compared Type III RM systems in Helicobacter pylori genomes and found that target recognition domain (TRD) sequences are mobile, moving between different orthologous groups that occupy unique chromosomal locations. Sequence comparisons suggested that a likely underlying mechanism is movement through homologous recombination of similar DNA sequences that encode amino acid sequence motifs that are conserved among Type III DNA methyltransferases. Consistent with this movement, incongruence was observed between the phylogenetic trees of TRD regions and other regions in proteins. Horizontal acquisition of diverse TRD sequences was suggested by detection of homologs in other Helicobacter species and distantly related bacterial species. One of these RM systems in H. pylori was inactivated by insertion of another RM system that likely transferred from an oral bacterium. TRD movement represents a novel route for diversification of DNA-interacting proteins.}, }
@article {pmid22821452, year = {2012}, author = {Wagner, A}, title = {Metabolic networks and their evolution.}, journal = {Advances in experimental medicine and biology}, volume = {751}, number = {}, pages = {29-52}, doi = {10.1007/978-1-4614-3567-9_2}, pmid = {22821452}, issn = {0065-2598}, mesh = {Animals ; Bacteria ; Eukaryotic Cells/*enzymology ; *Evolution, Molecular ; Fungi ; Gene Duplication ; Gene Transfer, Horizontal ; Kinetics ; Metabolic Networks and Pathways/*genetics ; Metabolomics ; Models, Biological ; Prokaryotic Cells/*enzymology ; Systems Biology ; }, abstract = {Since the last decade of the twentieth century, systems biology has gained the ability to study the structure and function of genome-scale metabolic networks. These are systems of hundreds to thousands of chemical reactions that sustain life. Most of these reactions are catalyzed by enzymes which are encoded by genes. A metabolic network extracts chemical elements and energy from the environment, and converts them into forms that the organism can use. The function of a whole metabolic network constrains evolutionary changes in its parts. I will discuss here three classes of such changes, and how they are constrained by the function of the whole. These are the accumulation of amino acid changes in enzyme-coding genes, duplication of enzyme-coding genes, and changes in the regulation of enzymes. Conversely, evolutionary change in network parts can alter the function of the whole network. I will discuss here two such changes, namely the elimination of reactions from a metabolic network through loss of function mutations in enzyme-coding genes, and the addition of metabolic reactions, for example through mechanisms such as horizontal gene transfer. Reaction addition also provides a window into the evolution of metabolic innovations, the ability of a metabolism to sustain life on new sources of energy and of chemical elements.}, }
@article {pmid22820331, year = {2012}, author = {Beuls, E and Modrie, P and Deserranno, C and Mahillon, J}, title = {High-salt stress conditions increase the pAW63 transfer frequency in Bacillus thuringiensis.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {19}, pages = {7128-7131}, pmid = {22820331}, issn = {1098-5336}, mesh = {Bacillus thuringiensis/*drug effects/*genetics ; Conjugation, Genetic/drug effects ; Culture Media/chemistry ; Gene Transfer, Horizontal/*drug effects ; *Osmotic Pressure ; *Plasmids ; *Salts ; Stress, Physiological ; }, abstract = {Conjugation experiments with Bacillus thuringiensis and transfer kinetics demonstrated that salt stress has a positive impact on plasmid transfer efficiency. Compared to standard osmotic conditions (0.5% NaCl), plasmid transfer occurred more rapidly, and at higher frequencies (>100-fold), when bacteria were exposed to a high-salt stress (5% NaCl) in liquid brain heart infusion (BHI). Under milder salt conditions (2.5% NaCl), only a 10-fold effect was observed in Luria-Bertani broth and no difference was detected in BHI. These observations are particularly relevant in the scope of potential gene exchanges among members of the Bacillus cereus group, which includes food-borne contaminants and pathogens.}, }
@article {pmid22816041, year = {2012}, author = {Hoshino, T and Fujiwara, T and Kawabata, S}, title = {Evolution of cariogenic character in Streptococcus mutans: horizontal transmission of glycosyl hydrolase family 70 genes.}, journal = {Scientific reports}, volume = {2}, number = {}, pages = {518}, pmid = {22816041}, issn = {2045-2322}, mesh = {Base Sequence ; Catalytic Domain/genetics ; Chromosome Mapping ; *Evolution, Molecular ; Gene Order ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Glucans/metabolism ; Glucosyltransferases/chemistry/classification/*genetics ; Models, Biological ; Molecular Sequence Data ; *Multigene Family ; Phylogeny ; Protein Binding ; Protein Interaction Domains and Motifs/genetics ; Streptococcus mutans/enzymology/*genetics ; }, abstract = {Acquisition of the ability to produce polysaccharides from sucrose, i.e. the gtf gene encoding glucosyltransferase (GTF), is the key evolutionary event enabling dental biofilm formation by streptococci. To clarify the ancestry of streptococcal GTFs, time of its occurrence, and order of specific events, we investigated the distribution of GTFs among bacteria by phylogenetic analysis of the glycosyl hydrolase family 70 enzymes. We found that streptococcal GTFs were derived from other lactic acid bacteria such as Lactobacillus and Leuconostoc, and propose the following evolutionary model: horizontal gene transfer via transposons occurred when streptococci encountered lactic acid bacteria contained in fermented food. Intra-genomic gene duplication occurred by a secondary selection pressure such as consumption of refined sugar. Our findings concerning this evolution in Streptococcus mutans provide an important background for studies of the relationship between the historical spread of dental caries and anthropological factors.}, }
@article {pmid22815936, year = {2012}, author = {Liu, Y and Han, Y and Huang, W and Duan, Y and Mou, L and Jiang, Z and Fa, P and Xie, J and Diao, R and Chen, Y and Ye, Y and Yang, R and Chen, J and Sun, X and Li, Z and Tang, A and Gui, Y and Cai, Z}, title = {Whole-genome synthesis and characterization of viable S13-like bacteriophages.}, journal = {PloS one}, volume = {7}, number = {7}, pages = {e41124}, pmid = {22815936}, issn = {1932-6203}, mesh = {Adsorption ; Bacteriophages/*genetics ; Calcium/chemistry ; Electroporation ; Escherichia coli/metabolism/virology ; Gene Transfer, Horizontal ; Genetic Engineering/methods ; Genetic Markers ; Genome, Bacterial ; Genome, Viral ; Hydrogen-Ion Concentration ; Models, Genetic ; Mutation ; Open Reading Frames ; Phylogeny ; Sequence Analysis, DNA ; Temperature ; Ultraviolet Rays ; }, abstract = {BACKGROUND: Unprecedented progresses in high-throughput DNA sequencing and de novo gene synthesis technologies have allowed us to create living organisms in the absence of natural template.<br><br>The sequence of wild-type S13 phage genome was downloaded from GenBank. Two synonymous mutations were introduced into wt-S13 genome to generate m1-S13 genome. Another mutant, m2-S13 genome, was obtained by engineering two nonsynonymous mutations in the capsid protein coding region of wt-S13 genome. A chimeric phage genome was designed by replacing the F capsid protein open reading frame (ORF) from phage S13 with the F capsid protein ORF from phage G4. The whole genomes of all four phages were assembled from a series of chemically synthesized short overlapping oligonucleotides. The linear synthesized genomes were circularized and electroporated into E.coli C, the standard laboratory host of S13 phage. All four phages were recovered and plaques were visualized. The results of sequencing showed the accuracy of these synthetic genomes. The synthetic phages were capable of lysing their bacterial host and tolerating general environmental conditions. While no phenotypic differences among the variant strains were observed when grown in LB medium with CaCl(2), the S13/G4 chimera was found to be much more sensitive to the absence of calcium and to have a lower adsorption rate under calcium free condition.<br><br>CONCLUSIONS/SIGNIFICANCE: The bacteriophage S13 and its variants can be chemically synthesized. The major capsid gene of phage G4 is functional in the phage S13 life cycle. These results support an evolutional hypothesis which has been proposed that a homologous recombination event involving gene F of quite divergent ancestral lineages should be included in the history of the microvirid family.}, }
@article {pmid22815791, year = {2012}, author = {Swanson, MM and Reavy, B and Makarova, KS and Cock, PJ and Hopkins, DW and Torrance, L and Koonin, EV and Taliansky, M}, title = {Novel bacteriophages containing a genome of another bacteriophage within their genomes.}, journal = {PloS one}, volume = {7}, number = {7}, pages = {e40683}, pmid = {22815791}, issn = {1932-6203}, support = {G0900740/MRC_/Medical Research Council/United Kingdom ; /ImNIH/Intramural NIH HHS/United States ; }, mesh = {Bacillus Phages/genetics/isolation &amp; purification ; Bacillus subtilis/virology ; Bacteriophages/*genetics/isolation &amp; purification/ultrastructure ; Genes, Viral/genetics ; Genome, Viral/*genetics ; Host Specificity/genetics ; Open Reading Frames/genetics ; Phylogeny ; Siphoviridae/genetics/isolation &amp; purification/ultrastructure ; Sporosarcina/virology ; Viral Proteins/chemistry/genetics ; Virion/ultrastructure ; }, abstract = {A novel bacteriophage infecting Staphylococus pasteuri was isolated during a screen for phages in Antarctic soils. The phage named SpaA1 is morphologically similar to phages of the family Siphoviridae. The 42,784 bp genome of SpaA1 is a linear, double-stranded DNA molecule with 3' protruding cohesive ends. The SpaA1 genome encompasses 63 predicted protein-coding genes which cluster within three regions of the genome, each of apparently different origin, in a mosaic pattern. In two of these regions, the gene sets resemble those in prophages of Bacillus thuringiensis kurstaki str. T03a001 (genes involved in DNA replication/transcription, cell entry and exit) and B. cereus AH676 (additional regulatory and recombination genes), respectively. The third region represents an almost complete genome (except for the short terminal segments) of a distinct bacteriophage, MZTP02. Nearly the same gene module was identified in prophages of B. thuringiensis serovar monterrey BGSC 4AJ1 and B. cereus Rock4-2. These findings suggest that MZTP02 can be shuttled between genomes of other bacteriophages and prophages, leading to the formation of chimeric genomes. The presence of a complete phage genome in the genome of other phages apparently has not been described previously and might represent a 'fast track' route of virus evolution and horizontal gene transfer. Another phage (BceA1) nearly identical in sequence to SpaA1, and also including the almost complete MZTP02 genome within its own genome, was isolated from a bacterium of the B. cereus/B. thuringiensis group. Remarkably, both SpaA1 and BceA1 phages can infect B. cereus and B. thuringiensis, but only one of them, SpaA1, can infect S. pasteuri. This finding is best compatible with a scenario in which MZTP02 was originally contained in BceA1 infecting Bacillus spp, the common hosts for these two phages, followed by emergence of SpaA1 infecting S. pasteuri.}, }
@article {pmid22815353, year = {2012}, author = {Haenni, M and Saras, E and Métayer, V and Doublet, B and Cloeckaert, A and Madec, JY}, title = {Spread of the blaTEM-52 gene is mainly ensured by IncI1/ST36 plasmids in Escherichia coli isolated from cattle in France.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {67}, number = {11}, pages = {2774-2776}, doi = {10.1093/jac/dks282}, pmid = {22815353}, issn = {1460-2091}, mesh = {Animals ; Cattle ; Cattle Diseases/*microbiology ; DNA Transposable Elements ; Escherichia coli/*enzymology/*genetics/isolation &amp; purification ; Escherichia coli Infections/microbiology/*veterinary ; France ; *Gene Transfer, Horizontal ; Genotype ; Microbial Sensitivity Tests ; Molecular Typing ; *Plasmids ; beta-Lactamases/*genetics ; }, }
@article {pmid22814175, year = {2012}, author = {Schuster, LN and Sommer, RJ}, title = {Expressional and functional variation of horizontally acquired cellulases in the nematode Pristionchus pacificus.}, journal = {Gene}, volume = {506}, number = {2}, pages = {274-282}, doi = {10.1016/j.gene.2012.07.013}, pmid = {22814175}, issn = {1879-0038}, mesh = {Animals ; Carbohydrates/chemistry ; Carboxymethylcellulose Sodium/chemistry ; Catalytic Domain ; Cellulase/*chemistry ; Escherichia coli/enzymology ; Gene Expression Regulation ; Gene Expression Regulation, Developmental ; *Gene Expression Regulation, Enzymologic ; Gene Transfer Techniques ; Gene Transfer, Horizontal ; Genomics ; Glycoside Hydrolases/chemistry ; Mass Spectrometry/methods ; Models, Genetic ; Nematoda ; Phylogeny ; RNA/metabolism ; }, abstract = {Various whole genome-sequencing projects in the nematode phylum have revealed the widespread occurrence of horizontal gene transfer from different sources. Pristionchus pacificus was the first non-plant parasitic nematode that was found to contain cellulase genes in its genome and to have cellulolytic activity when grown in a monoxenic culture on Escherichia coli. The P. pacificus reference strain PS312 has seven cellulase genes, all of which were acquired by horizontal gene transfer. Previous phylogenomic studies indicated that the acquisition occurred at the base of the genus Pristionchus and was followed by rapid gene duplications and gene turnover. However, little was known about the protein domain architecture, gene expression and the functionality of individual proteins. Here, we analyzed the protein domain architecture, studied the expression at various developmentally stages and tried to induce cellulase gene expression by feeding nematodes with different polysaccharides. Only two of the encoded proteins, Ppa-CEL-2 and Ppa-CEL-3, have a carbohydrate-binding module. Interestingly, these were also the ones with developmental gene expression regulation. Ppa-cel-2 shows high expression in larval and adult stages but is only low expressed in eggs, while Ppa-cel-3 is highly upregulated in adult worms but hardly detectable in any other stage. Ppa-CEL-1, has a catalytic domain similar to Ppa-CEL-2 and Ppa-CEL-3, but lacks a carbohydrate-binding module. The other four cellulases have a very low transcriptional expression correlating with putative incompleteness of their catalytic domain. While, the expression of none of the genes is inducible by polysaccharides, zymographic studies and mass spectrometry indicate that Ppa-CEL-2 and Ppa-CEL-3 are the only two cellulases contributing to cellulase activity in carboxymethylcellulose. Thus, the cellulases of P. pacificus differ in their protein domain architecture, gene expression and functionality. These results indicate that horizontal gene transfer-acquired genes undergo rapid evolutionary changes that affect all aspects of their molecular biology.}, }
@article {pmid22812485, year = {2012}, author = {Keramati, M and Roohvand, F and Eslaminejad, Z and Mirzaie, A and Nikbin, VS and Aslani, MM}, title = {PCR/RFLP-based allelic variants of streptokinase and their plasminogen activation potencies.}, journal = {FEMS microbiology letters}, volume = {335}, number = {2}, pages = {79-85}, doi = {10.1111/j.1574-6968.2012.02640.x}, pmid = {22812485}, issn = {1574-6968}, mesh = {*Alleles ; Analysis of Variance ; Base Sequence ; Colorimetry ; DNA, Bacterial/analysis/chemistry ; *Genes, Bacterial ; Humans ; Iran ; Molecular Sequence Data ; Plasminogen/metabolism ; Polymerase Chain Reaction/*methods ; Polymorphism, Restriction Fragment Length/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Streptococcal Infections/microbiology ; Streptococcus/enzymology/*genetics ; Streptokinase/*genetics/metabolism ; }, abstract = {PCR-restriction fragment length polymorphism (PCR/RFLP)-based analysis of β-domain variable region of streptokinase genes (sk) has previously identified 14 sk alleles (sk1-sk14) in group A (GAS), C (GCS) and G (GGS) streptococci isolates from a few geographically distinct regions. However, the relation of sk allelic variants to their plasminogen activation potencies remained as a matter of debate. Herein, employing the same PCR/RFLP assay, we analysed sk allelic variants of GAS and GCS/GGS isolates from Iranian patients. In total, 21 sk allelic variants including 14 new alleles (sk14-sk28) were identified. Results implied the horizontal gene transfer of sk fragments between GAS and GCS/GGS strains and did not prove the specificity of particular sk alleles to GCS/GGS or GAS groups. Measurement of streptokinase (SK) activity in streptococcal culture supernatants by colorimetric assay (S2251 substrate) ranged from 9 to 182 IU mL(-1). Although some strains with the highest SK activity were detected in definite variants, no significant correlation between sk alleles and plasminogen activation was detected (P value > 0.05). Analysis of DNA sequences and restriction site mapping of selective sk variants with similar SK activity pointed to the inadequacy of the currently available PCR/RFLP method for differentiation of critical/silent nucleotides to precisely categorize sk alleles for their functional properties.}, }
@article {pmid22808158, year = {2012}, author = {Roux, S and Krupovic, M and Poulet, A and Debroas, D and Enault, F}, title = {Evolution and diversity of the Microviridae viral family through a collection of 81 new complete genomes assembled from virome reads.}, journal = {PloS one}, volume = {7}, number = {7}, pages = {e40418}, pmid = {22808158}, issn = {1932-6203}, mesh = {Base Sequence ; Capsid Proteins/chemistry/genetics ; Conserved Sequence ; Environmental Microbiology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Viral ; *Genetic Variation ; Genome, Viral/*genetics ; Humans ; *Metagenome ; Microviridae/*genetics ; Phylogeny ; *Sequence Analysis, DNA ; }, abstract = {Recent studies suggest that members of the Microviridae (a family of ssDNA bacteriophages) might play an important role in a broad spectrum of environments, as they were found in great number among the viral fraction from seawater and human gut samples. 24 completely sequenced Microviridae have been described so far, divided into three distinct groups named Microvirus, Gokushovirinae and Alpavirinae, this last group being only composed of prophages. In this study, we present the analysis of 81 new complete Microviridae genomes, assembled from viral metagenomes originating from various ecosystems. The phylogenetic analysis of the core genes highlights the existence of four groups, confirming the three sub-families described so far and exhibiting a new group, named Pichovirinae. The genomic organizations of these viruses are strikingly coherent with their phylogeny, the Pichovirinae being the only group of this family with a different organization of the three core genes. Analysis of the structure of the major capsid protein reveals the presence of mushroom-like insertions conserved within all the groups except for the microviruses. In addition, a peptidase gene was found in 10 Microviridae and its analysis indicates a horizontal gene transfer that occurred several times between these viruses and their bacterial hosts. This is the first report of such gene transfer in Microviridae. Finally, searches against viral metagenomes revealed the presence of highly similar sequences in a variety of biomes indicating that Microviridae probably have both an important role in these ecosystems and an ancient origin.}, }
@article {pmid22807690, year = {2012}, author = {Miyazaki, R and Minoia, M and Pradervand, N and Sulser, S and Reinhard, F and van der Meer, JR}, title = {Cellular variability of RpoS expression underlies subpopulation activation of an integrative and conjugative element.}, journal = {PLoS genetics}, volume = {8}, number = {7}, pages = {e1002818}, pmid = {22807690}, issn = {1553-7404}, mesh = {Bacterial Proteins/*genetics ; Chromosomes, Bacterial ; *Conjugation, Genetic ; DNA-Binding Proteins ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Integrases/genetics/metabolism ; Interspersed Repetitive Sequences/genetics ; Mutation ; Promoter Regions, Genetic ; Pseudomonas/*genetics/growth &amp; development ; Sigma Factor/*genetics ; Transcription Factors/genetics ; }, abstract = {Conjugative transfer of the integrative and conjugative element ICEclc in the bacterium Pseudomonas knackmussii is the consequence of a bistable decision taken in some 3% of cells in a population during stationary phase. Here we study the possible control exerted by the stationary phase sigma factor RpoS on the bistability decision. The gene for RpoS in P. knackmussii B13 was characterized, and a loss-of-function mutant was produced and complemented. We found that, in absence of RpoS, ICEclc transfer rates and activation of two key ICEclc promoters (P(int) and P(inR)) decrease significantly in cells during stationary phase. Microarray and gene reporter analysis indicated that the most direct effect of RpoS is on P(inR), whereas one of the gene products from the P(inR)-controlled operon (InrR) transmits activation to P(int) and other ICEclc core genes. Addition of a second rpoS copy under control of its native promoter resulted in an increase of the proportion of cells expressing the P(int) and P(inR) promoters to 18%. Strains in which rpoS was replaced by an rpoS-mcherry fusion showed high mCherry fluorescence of individual cells that had activated P(int) and P(inR), whereas a double-copy rpoS-mcherry-containing strain displayed twice as much mCherry fluorescence. This suggested that high RpoS levels are a prerequisite for an individual cell to activate P(inR) and thus ICEclc transfer. Double promoter-reporter fusions confirmed that expression of P(inR) is dominated by extrinsic noise, such as being the result of cellular variability in RpoS. In contrast, expression from P(int) is dominated by intrinsic noise, indicating it is specific to the ICEclc transmission cascade. Our results demonstrate how stochastic noise levels of global transcription factors can be transduced to a precise signaling cascade in a subpopulation of cells leading to ICE activation.}, }
@article {pmid22807567, year = {2012}, author = {Willems, RJ and Top, J and van Schaik, W and Leavis, H and Bonten, M and Sirén, J and Hanage, WP and Corander, J}, title = {Restricted gene flow among hospital subpopulations of Enterococcus faecium.}, journal = {mBio}, volume = {3}, number = {4}, pages = {e00151-12}, pmid = {22807567}, issn = {2150-7511}, support = {/WT_/Wellcome Trust/United Kingdom ; U54 GM088558/GM/NIGMS NIH HHS/United States ; /ImNIH/Intramural NIH HHS/United States ; GM088558-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cross Infection/*microbiology ; Enterococcus faecalis/classification/genetics/isolation &amp; purification ; Enterococcus faecium/*classification/*genetics/isolation &amp; purification ; *Gene Flow ; Gram-Positive Bacterial Infections/*microbiology/*veterinary ; Humans ; Molecular Sequence Data ; Phylogeny ; Recombination, Genetic ; Swine ; Swine Diseases/*microbiology ; }, abstract = {UNLABELLED: Enterococcus faecium has recently emerged as an important multiresistant nosocomial pathogen. Defining population structure in this species is required to provide insight into the existence, distribution, and dynamics of specific multiresistant or pathogenic lineages in particular environments, like the hospital. Here, we probe the population structure of E. faecium using Bayesian-based population genetic modeling implemented in Bayesian Analysis of Population Structure (BAPS) software. The analysis involved 1,720 isolates belonging to 519 sequence types (STs) (491 for E. faecium and 28 for Enterococcus faecalis). E. faecium isolates grouped into 13 BAPS (sub)groups, but the large majority (80%) of nosocomial isolates clustered in two subgroups (2-1 and 3-3). Phylogenetic and eBURST analysis of BAPS groups 2 and 3 confirmed the existence of three separate hospital lineages (17, 18, and 78), highlighting different evolutionary trajectories for BAPS 2-1 (lineage 78) and 3-3 (lineage 17 and lineage 18) isolates. Phylogenomic analysis of 29 E. faecium isolates showed agreement between BAPS assignment of STs and their relative positions in the phylogenetic tree. Odds ratio calculation confirmed the significant association between hospital isolates with BAPS 3-3 and lineages 17, 18, and 78. Admixture analysis showed a scarce number of recombination events between the different BAPS groups. For the E. faecium hospital population, we propose an evolutionary model in which strains with a high propensity to colonize and infect hospitalized patients arise through horizontal gene transfer. Once adapted to the distinct hospital niche, this subpopulation becomes isolated, and recombination with other populations declines.<br><br>IMPORTANCE: Multiresistant Enterococcus faecium has become one of the most important nosocomial pathogens, causing increasing numbers of nosocomial infections worldwide. Here, we used Bayesian population genetic analysis to identify groups of related E. faecium strains and show a significant association of hospital and farm animal isolates to different genetic groups. We also found that hospital isolates could be divided into three lineages originating from sequence types (STs) 17, 18, and 78. We propose that, driven by the selective pressure in hospitals, the three hospital lineages have arisen through horizontal gene transfer, but once adapted to the distinct pathogenic niche, this population has become isolated and recombination with other populations declines. Elucidation of the population structure is a prerequisite for effective control of multiresistant E. faecium since it provides insight into the processes that have led to the progressive change of E. faecium from an innocent commensal to a multiresistant hospital-adapted pathogen.}, }
@article {pmid22806731, year = {2012}, author = {Chen, S and Tulloss, RE and Liu, Y and Feng, B and Zhao, Z and Yang, ZL}, title = {Lateral gene transfer occurring in haloarchaea: an interpretative imitation study.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {28}, number = {9}, pages = {2913-2918}, pmid = {22806731}, issn = {1573-0972}, mesh = {Culture Media/chemistry ; DNA, Bacterial/genetics ; Escherichia coli/genetics/metabolism ; *Evolution, Molecular ; Fresh Water/chemistry ; *Gene Transfer Techniques ; *Genome, Archaeal ; Haloferax/classification/*genetics/metabolism ; Halorubrum/classification/*genetics/metabolism ; RNA, Ribosomal, 16S/genetics/isolation &amp; purification ; Salinity ; Salts/metabolism ; Sequence Analysis, DNA ; Transformation, Bacterial ; }, abstract = {Lateral gene transfer (LGT) plays an important role in the molecular evolution of haloarchaea. Polyethylene glycol-mediated LGT in haloarchaea has been demonstrated in the laboratory, yet few explanations have been put forward for the apparently common, natural occurrence of plentiful plasmids within haloarchaeal cells. In this study, LGT was induced in two genera of haloarchaea, Haloferax and Halorubrum, by modification of salt concentration of media-a factor that may vary naturally in native haloarchaeal habitat. Minimal growth salt concentrations (MGSCs) of four strains of haloarchaea from these two genera were established, and transformations using two circular double-stranded DNAs (dsDNAs), pSY1 and pWL102, were then produced in media at strain-appropriate MGSCs. The four strains of haloarchaea were transformed successfully by both kinds of dsDNAs with an efficiency of 10(2)-10(3) transformants per microgram dsDNA. The transformation under reduced salt concentration may be an imitation of natural LGT of dsDNA into haloarchaea when salinity in normally hypersaline environments is altered by sudden introduction of fresh water--for example, by rainfall, snow-melt, or flooding--providing a reasonable interpretation for haloarchaea being naturally richer in plasmids than any other known organisms.}, }
@article {pmid22806025, year = {2012}, author = {Maravić, A and Skočibušić, M and Samanić, I and Puizina, J}, title = {Antibiotic susceptibility profiles and first report of TEM extended-spectrum β-lactamase in Pseudomonas fluorescens from coastal waters of the Kaštela Bay, Croatia.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {28}, number = {5}, pages = {2039-2045}, pmid = {22806025}, issn = {1573-0972}, mesh = {Anti-Bacterial Agents/*pharmacology ; Cluster Analysis ; Conjugation, Genetic ; Croatia ; DNA, Bacterial/chemistry/genetics ; Gene Transfer, Horizontal ; Genotype ; Microbial Sensitivity Tests ; Molecular Typing ; Polymerase Chain Reaction ; Pseudomonas fluorescens/drug effects/enzymology/genetics/*isolation &amp; purification ; Random Amplified Polymorphic DNA Technique ; Seawater/*microbiology ; Sequence Analysis, DNA ; beta-Lactamases/genetics/*metabolism ; }, abstract = {The aim of this study was to investigate the antibiotic susceptibility profiles and the presence of extended-spectrum-β-lactamases (ESBLs) in Pseudomonas fluorescens isolates from coastal waters of the Kaštela Bay, Croatia. Twenty-two water samples were collected during 2009. Isolates were tested for susceptibilities to 13 antibiotics by Etest. ESBL production was confirmed by double-disk synergy test carried out on Mueller-Hinton agar plates containing efflux pump inhibitor Phe-Arg-β-naphthylamide dihydrochloride. PCR and DNA sequencing analysis were used to identify ESBL-encoding genes. The transferability of cephalosporin resistance was tested by conjugation experiments. Genetic relatedness of ESBL-producing isolates was determined by random amplified polymorphic DNA (RAPD) analysis. Out of 185 P. fluorescens isolates recovered, 70 (37.8%) demonstrated multiresistance phenotype with highest rates of resistance to tetracycline (61.6%), aztreonam (31.9%), meropenem (17.3%), ceftazidime (15.1%) and cefotaxime (12.4%). Ten (5.4%) isolates were identified as ESBL producers. All isolates carried chromosomally located bla (TEM-116) gene. RAPD analysis identified four different genotypes. Here, we demonstrated a baseline profiles of antimicrobial resistance of P. fluorescens from coastal waters of the Kaštela Bay, Croatia. To our knowledge, this is the first report of the presence of TEM-type ESBL in P. fluorescens, indicating this bacterium as a reservoir of antibiotic resistance genes with clinical relevance.}, }
@article {pmid22805823, year = {2012}, author = {Shoeb, E and Badar, U and Akhter, J and Shams, H and Sultana, M and Ansari, MA}, title = {Horizontal gene transfer of stress resistance genes through plasmid transport.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {28}, number = {3}, pages = {1021-1025}, pmid = {22805823}, issn = {1573-0972}, mesh = {Ampicillin/toxicity ; Conjugation, Genetic ; Copper/toxicity ; Drug Tolerance ; Enterobacter cloacae/*genetics/isolation &amp; purification/physiology ; Escherichia coli/*genetics/isolation &amp; purification/physiology ; *Gene Transfer, Horizontal ; *Plasmids ; Seawater/microbiology ; Soil Microbiology ; *Stress, Physiological ; Transformation, Bacterial ; }, abstract = {The horizontal gene transfer of plasmid-determined stress tolerance was achieved under lab conditions. Bacterial isolates, Enterobacter cloacae (DGE50) and Escherichia coli (DGE57) were used throughout the study. Samples were collected from contaminated marine water and soil to isolate bacterial strains having tolerance against heavy metals and antimicrobial agents. We have demonstrated plasmid transfer, from Amp(+)Cu(+)Zn(-) strain (DGE50) to Amp(-)Cu(-)Zn(+) strain (DGE57), producing Amp(+)Cu(+)Zn(+) transconjugants (DGE(TC50→57)) and Amp(+)Cu(-)Zn(+) transformants (DGE(TF50→57)). DGE57 did not carry any plasmid, therefore, it can be speculated that zinc tolerance gene in DGE57 is located on chromosome. DGE50 was found to carry three plasmids, out of which two were transferred through conjugation into DGE57, and only one was transferred through transformation. Plasmid transferred through transformation was one out of the two transferred through conjugation. Through the results of transformation it was revealed that the genes of copper and ampicillin tolerance in DGE50 were located on separate plasmids, since only ampicillin tolerance genes were transferred through transformation as a result of one plasmid transfer. By showing transfer of plasmids under lab conditions and monitoring retention of respective phenotype via conjugation and transformation, it is very well demonstrated how multiple stress tolerant strains are generated in nature.}, }
@article {pmid22805218, year = {2012}, author = {Liu, QH and Guo, ZG and Ren, JH}, title = {[Phylogenetic application and analysis of horizontal transfer based on the prokaryote eno gene].}, journal = {Yi chuan = Hereditas}, volume = {34}, number = {7}, pages = {907-918}, doi = {10.3724/sp.j.1005.2012.00907}, pmid = {22805218}, issn = {0253-9772}, mesh = {Bacteria/*classification/*genetics ; Base Composition ; Codon ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Phosphopyruvate Hydratase/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; }, abstract = {The phenomenon of conflicting gene trees has become a remarkable and difficult problem. Application of multiple genes has been a widespread practice to reconstruct phylogenies in phylogenetic studies. Enolase is a key glycolytic enzyme, The enzymes from a large variety of organisms, including archaebacteria, eubacteria and eukaryotes, were studied. We downloaded eno sequences from the genomes of bacteria and archaea that have been completely sequenced. The comprehensive homology search and phylogenetic analysis of the eno were used, and nineteen horizontally transferred genes were identified. The results of analysis showed lots of differences between the features of horizontal transferred genes and the ones of whole genomic genes, such as nucleotide composition, gene combination, codon usage bias, and selection pressure. These results reconfirmed that the horizontally transferred genes were exogenous. The result revealed that prokaryote eno genes were highly conserved, medium-sized, is a good material in the phylogenetic. This paper can provide a reference in study of life habit and evolutionary history of donor and receptor, and enolase structure and function.}, }
@article {pmid22802648, year = {2012}, author = {Pombert, JF and Selman, M and Burki, F and Bardell, FT and Farinelli, L and Solter, LF and Whitman, DW and Weiss, LM and Corradi, N and Keeling, PJ}, title = {Gain and loss of multiple functionally related, horizontally transferred genes in the reduced genomes of two microsporidian parasites.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {31}, pages = {12638-12643}, pmid = {22802648}, issn = {1091-6490}, support = {R01 AI031788/AI/NIAID NIH HHS/United States ; AI31788/AI/NIAID NIH HHS/United States ; MOP-42517/CAPMC/CIHR/Canada ; }, mesh = {Animals ; Base Sequence ; Chromosomes, Fungal/*genetics/metabolism ; Encephalitozoon cuniculi/*physiology ; *Evolution, Molecular ; Folic Acid/genetics/metabolism ; Gene Transfer, Horizontal/*physiology ; Genome, Fungal/*physiology ; Molecular Sequence Data ; Purines/metabolism ; Telomere/genetics/metabolism ; }, abstract = {Microsporidia of the genus Encephalitozoon are widespread pathogens of animals that harbor the smallest known nuclear genomes. Complete sequences from Encephalitozoon intestinalis (2.3 Mbp) and Encephalitozoon cuniculi (2.9 Mbp) revealed massive gene losses and reduction of intergenic regions as factors leading to their drastically reduced genome size. However, microsporidian genomes also have gained genes through horizontal gene transfers (HGT), a process that could allow the parasites to exploit their hosts more fully. Here, we describe the complete sequences of two intermediate-sized genomes (2.5 Mbp), from Encephalitozoon hellem and Encephalitozoon romaleae. Overall, the E. hellem and E. romaleae genomes are strikingly similar to those of Encephalitozoon cuniculi and Encephalitozoon intestinalis in both form and content. However, in addition to the expected expansions and contractions of known gene families in subtelomeric regions, both species also were found to harbor a number of protein-coding genes that are not found in any other microsporidian. All these genes are functionally related to the metabolism of folate and purines but appear to have originated by several independent HGT events from different eukaryotic and prokaryotic donors. Surprisingly, the genes are all intact in E. hellem, but in E. romaleae those involved in de novo synthesis of folate are all pseudogenes. Overall, these data suggest that a recent common ancestor of E. hellem and E. romaleae assembled a complete metabolic pathway from multiple independent HGT events and that one descendent already is dispensing with much of this new functionality, highlighting the transient nature of transferred genes.}, }
@article {pmid22798452, year = {2012}, author = {Swithers, KS and Petrus, AK and Secinaro, MA and Nesbø, CL and Gogarten, JP and Noll, KM and Butzin, NC}, title = {Vitamin B(12) synthesis and salvage pathways were acquired by horizontal gene transfer to the Thermotogales.}, journal = {Genome biology and evolution}, volume = {4}, number = {8}, pages = {730-739}, pmid = {22798452}, issn = {1759-6653}, mesh = {Bacteria/classification/*genetics/*metabolism ; Bacterial Proteins/*genetics/metabolism ; *Biosynthetic Pathways ; Cobamides/biosynthesis ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Vitamin B 12/*biosynthesis ; }, abstract = {The availability of genome sequences of Thermotogales species from across the order allows an examination of the evolutionary origins of phenotypic characteristics in this lineage. Several studies have shown that the Thermotogales have acquired large numbers of genes from distantly related lineages, particularly Firmicutes and Archaea. Here, we report the finding that some Thermotogales acquired the ability to synthesize vitamin B(12) by acquiring the requisite genes from these distant lineages. Thermosipho species, uniquely among the Thermotogales, contain genes that encode the means to synthesize vitamin B(12) de novo from glutamate. These genes are split into two gene clusters: the corrinoid synthesis gene cluster, that is unique to the Thermosipho and the cobinamide salvage gene cluster. The corrinoid synthesis cluster was acquired from the Firmicutes lineage, whereas the salvage pathway is an amalgam of bacteria- and archaea-derived proteins. The cobinamide salvage gene cluster has a patchy distribution among Thermotogales species, and ancestral state reconstruction suggests that this pathway was present in the common Thermotogales ancestor. We show that Thermosipho africanus can grow in the absence of vitamin B(12), so its de novo pathway is functional. We detected vitamin B(12) in the extracts of T. africanus cells to verify the synthetic pathway. Genes in T. africanus with apparent B(12) riboswitches were found to be down-regulated in the presence of vitamin B(12) consistent with their roles in B(12) synthesis and cobinamide salvage.}, }
@article {pmid22798451, year = {2012}, author = {Zhaxybayeva, O and Swithers, KS and Foght, J and Green, AG and Bruce, D and Detter, C and Han, S and Teshima, H and Han, J and Woyke, T and Pitluck, S and Nolan, M and Ivanova, N and Pati, A and Land, ML and Dlutek, M and Doolittle, WF and Noll, KM and Nesbø, CL}, title = {Genome sequence of the mesophilic Thermotogales bacterium Mesotoga prima MesG1.Ag.4.2 reveals the largest Thermotogales genome to date.}, journal = {Genome biology and evolution}, volume = {4}, number = {8}, pages = {700-708}, pmid = {22798451}, issn = {1759-6653}, mesh = {Bacterial Proteins/genetics ; Base Sequence ; Gene Transfer, Horizontal ; Genome Size ; *Genome, Bacterial ; Gram-Negative Bacteria/classification/*genetics ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Here we describe the genome of Mesotoga prima MesG1.Ag4.2, the first genome of a mesophilic Thermotogales bacterium. Mesotoga prima was isolated from a polychlorinated biphenyl (PCB)-dechlorinating enrichment culture from Baltimore Harbor sediments. Its 2.97 Mb genome is considerably larger than any previously sequenced Thermotogales genomes, which range between 1.86 and 2.30 Mb. This larger size is due to both higher numbers of protein-coding genes and larger intergenic regions. In particular, the M. prima genome contains more genes for proteins involved in regulatory functions, for instance those involved in regulation of transcription. Together with its closest relative, Kosmotoga olearia, it also encodes different types of proteins involved in environmental and cell-cell interactions as compared with other Thermotogales bacteria. Amino acid composition analysis of M. prima proteins implies that this lineage has inhabited low-temperature environments for a long time. A large fraction of the M. prima genome has been acquired by lateral gene transfer (LGT): a DarkHorse analysis suggests that 766 (32%) of predicted protein-coding genes have been involved in LGT after Mesotoga diverged from the other Thermotogales lineages. A notable example of a lineage-specific LGT event is a reductive dehalogenase gene-a key enzyme in dehalorespiration, indicating M. prima may have a more active role in PCB dechlorination than was previously assumed.}, }
@article {pmid22798450, year = {2012}, author = {Baymann, F and Schoepp-Cothenet, B and Lebrun, E and van Lis, R and Nitschke, W}, title = {Phylogeny of Rieske/cytb complexes with a special focus on the Haloarchaeal enzymes.}, journal = {Genome biology and evolution}, volume = {4}, number = {8}, pages = {720-729}, pmid = {22798450}, issn = {1759-6653}, mesh = {Amino Acid Sequence ; Archaea/chemistry/classification/*enzymology/genetics ; Archaeal Proteins/chemistry/*genetics/metabolism ; Cytochromes b/chemistry/*genetics/metabolism ; Electron Transport Complex III/chemistry/*genetics/metabolism ; Molecular Sequence Data ; *Phylogeny ; Protein Binding ; Sequence Alignment ; }, abstract = {Rieske/cytochrome b (Rieske/cytb) complexes are proton pumping quinol oxidases that are present in most bacteria and Archaea. The phylogeny of their subunits follows closely the 16S-rRNA phylogeny, indicating that chemiosmotic coupling was already present in the last universal common ancestor of Archaea and bacteria. Haloarchaea are the only organisms found so far that acquired Rieske/cytb complexes via interdomain lateral gene transfer. They encode two Rieske/cytb complexes in their genomes; one of them is found in genetic context with nitrate reductase genes and has its closest relatives among Actinobacteria and the Thermus/Deinococcus group. It is likely to function in nitrate respiration. The second Rieske/cytb complex of Haloarchaea features a split cytochrome b sequence as do Cyanobacteria, chloroplasts, Heliobacteria, and Bacilli. It seems that Haloarchaea acquired this complex from an ancestor of the above-mentioned phyla. Its involvement in the bioenergetic reaction chains of Haloarchaea is unknown. We present arguments in favor of the hypothesis that the ancestor of Haloarchaea, which relied on a highly specialized bioenergetic metabolism, that is, methanogenesis, and was devoid of quinones and most enzymes of anaerobic or aerobic bioenergetic reaction chains, integrated laterally transferred genes into its genome to respond to a change in environmental conditions that made methanogenesis unfavorable.}, }
@article {pmid22798449, year = {2012}, author = {Wallau, GL and Ortiz, MF and Loreto, EL}, title = {Horizontal transposon transfer in eukarya: detection, bias, and perspectives.}, journal = {Genome biology and evolution}, volume = {4}, number = {8}, pages = {689-699}, pmid = {22798449}, issn = {1759-6653}, mesh = {Animals ; *DNA Transposable Elements ; Eukaryota/classification/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome ; Species Specificity ; }, abstract = {The genetic similarity observed among species is normally attributed to the existence of a common ancestor. However, a growing body of evidence suggests that the exchange of genetic material is not limited to the transfer from parent to offspring but can also occur through horizontal transfer (HT). Transposable elements (TEs) are DNA fragments with an innate propensity for HT; they are mobile and possess parasitic characteristics that allow them to exist and proliferate within host genomes. However, horizontal transposon transfer (HTT) is not easily detected, primarily because the complex TE life cycle can generate phylogenetic patterns similar to those expected for HTT events. The increasingly large number of new genome projects, in all branches of life, has provided an unprecedented opportunity to evaluate the TE content and HTT events in these species, although a standardized method of HTT detection is required before trends in the HTT rates can be evaluated in a wide range of eukaryotic taxa and predictions about these events can be made. Thus, we propose a straightforward hypothesis test that can be used by TE specialists and nonspecialists alike to discriminate between HTT events and natural TE life cycle patterns. We also discuss several plausible explanations and predictions for the distribution and frequency of HTT and for the inherent biases of HTT detection. Finally, we discuss some of the methodological concerns for HTT detection that may result in the underestimation and overestimation of HTT rates during eukaryotic genome evolution.}, }
@article {pmid22798391, year = {2012}, author = {Vicente, JB and Tran, V and Pinto, L and Teixeira, M and Singh, U}, title = {A detoxifying oxygen reductase in the anaerobic protozoan Entamoeba histolytica.}, journal = {Eukaryotic cell}, volume = {11}, number = {9}, pages = {1112-1118}, pmid = {22798391}, issn = {1535-9786}, support = {R01 AI053724/AI/NIAID NIH HHS/United States ; AI-053724/AI/NIAID NIH HHS/United States ; }, mesh = {Entamoeba histolytica/*enzymology/genetics ; Gene Expression Regulation, Enzymologic ; Oxidoreductases/*genetics/metabolism ; Oxygen/metabolism ; Protozoan Proteins/*genetics/metabolism ; }, abstract = {We report the characterization of a bacterial-type oxygen reductase abundant in the cytoplasm of the anaerobic protozoan parasite Entamoeba histolytica. Upon host infection, E. histolytica is confronted with various oxygen tensions in the host intestine, as well as increased reactive oxygen and nitrogen species at the site of local tissue inflammation. Resistance to oxygen-derived stress thus plays an important role in the pathogenic potential of E. histolytica. The genome of E. histolytica has four genes that encode flavodiiron proteins, which are bacterial-type oxygen or nitric oxide reductases and were likely acquired by lateral gene transfer from prokaryotes. The EhFdp1 gene has higher expression in virulent than in nonvirulent Entamoeba strains and species, hinting that the response to oxidative stress may be one correlate of virulence potential. We demonstrate that EhFdp1 is abundantly expressed in the cytoplasm of E. histolytica and that the protein levels are markedly increased (up to ~5-fold) upon oxygen exposure. Additionally, we produced fully functional recombinant EhFdp1 and demonstrated that this enzyme is a specific and robust oxygen reductase but has poor nitric oxide reductase activity. This observation represents a new mechanism of oxygen resistance in the anaerobic protozoan pathogen E. histolytica.}, }
@article {pmid22793044, year = {2012}, author = {Yaguchi, T and Dwidar, M and Byun, CK and Leung, B and Lee, S and Cho, YK and Mitchell, RJ and Takayama, S}, title = {Aqueous two-phase system-derived biofilms for bacterial interaction studies.}, journal = {Biomacromolecules}, volume = {13}, number = {9}, pages = {2655-2661}, doi = {10.1021/bm300500y}, pmid = {22793044}, issn = {1526-4602}, mesh = {Ampicillin/pharmacology ; Ampicillin Resistance ; Biofilms/drug effects/*growth &amp; development ; DNA, Bacterial/*analysis ; Dextrans/*chemistry ; Diffusion ; Escherichia coli/drug effects/enzymology/genetics ; Gene Transfer, Horizontal ; Microbial Interactions/genetics ; Plankton/drug effects/*growth &amp; development ; Polyethylene Glycols/*chemistry ; Pseudomonas aeruginosa/drug effects/enzymology/genetics ; Water/chemistry ; beta-Lactamases/genetics/metabolism ; }, abstract = {We describe patterning of bacterial biofilms using polymer-based aqueous two-phase system (ATPS) microprinting protocols. The fully aqueous but selectively bacteria-partitioning nature of the ATPS allows spatially distinct localization of suspensions of bacteria such as Pseudomonas aeruginosa and Escherichia coli with high precision. The ATPS patterned bacterial suspensions form spatially distinct biofilms over time. Due to the fully aqueous and gentle noncontact printing procedures employed, coculture biofilms composed of multiple types of bacteria could be printed not only adjacent to each other but also directly over another layer of existing biofilm. In addition, the ATPS environment also allows free diffusion of small molecules between spatially distinct and localized bacterial suspensions and biofilms. This enables biofilms to chemically affect or be affected by neighboring biofilms or planktonic cells, even if they consist of different strains or species. We show that a β-lactamase producing biofilm confers ampicillin resistance to neighboring nonresistant planktonic cells, as seen by a 3,600-fold increase in survival of the ampicillin-sensitive strain. These examples demonstrate the ability of ATPS-based biofilm patterning methods to enable unique studies on commensalistic effects between bacterial species.}, }
@article {pmid22791963, year = {2012}, author = {Van Meervenne, E and Van Coillie, E and Kerckhof, FM and Devlieghere, F and Herman, L and De Gelder, LS and Top, EM and Boon, N}, title = {Strain-specific transfer of antibiotic resistance from an environmental plasmid to foodborne pathogens.}, journal = {Journal of biomedicine &amp; biotechnology}, volume = {2012}, number = {}, pages = {834598}, pmid = {22791963}, issn = {1110-7251}, support = {R01 AI084918/AI/NIAID NIH HHS/United States ; R01AI084918/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/*genetics ; Escherichia coli Infections/microbiology ; Escherichia coli O157/drug effects/*genetics ; Flow Cytometry ; Foodborne Diseases/microbiology ; *Gene Transfer, Horizontal ; Humans ; Phenotype ; Plasmids/*genetics ; Polymerase Chain Reaction ; Salmonella/drug effects/*genetics ; Salmonella Infections/microbiology ; }, abstract = {Pathogens resistant to multiple antibiotics are rapidly emerging, entailing important consequences for human health. This study investigated if the broad-host-range multiresistance plasmid pB10, isolated from a wastewater treatment plant, harbouring amoxicillin, streptomycin, sulfonamide, and tetracycline resistance genes, was transferable to the foodborne pathogens Salmonella spp. or E. coli O157:H7 and how this transfer alters the phenotype of the recipients. The transfer ratio was determined by both plating and flow cytometry. Antibiotic resistance profiles were determined for both recipients and transconjugants using the disk diffusion method. For 14 of the 15 recipient strains, transconjugants were detected. Based on plating, transfer ratios were between 6.8 × 10[-9] and 3.0 × 10[-2] while using flow cytometry, transfer ratios were between <1.0 × 10[-5] and 1.9 × 10[-2]. With a few exceptions, the transconjugants showed phenotypically increased resistance, indicating that most of the transferred resistance genes were expressed. In summary, we showed that an environmental plasmid can be transferred into foodborne pathogenic bacteria at high transfer ratios. However, the transfer ratio seemed to be recipient strain dependent. Moreover, the newly acquired resistance genes could turn antibiotic susceptible strains into resistant ones, paving the way to compromise human health.}, }
@article {pmid22789727, year = {2012}, author = {Ciusa, ML and Furi, L and Knight, D and Decorosi, F and Fondi, M and Raggi, C and Coelho, JR and Aragones, L and Moce, L and Visa, P and Freitas, AT and Baldassarri, L and Fani, R and Viti, C and Orefici, G and Martinez, JL and Morrissey, I and Oggioni, MR and , }, title = {A novel resistance mechanism to triclosan that suggests horizontal gene transfer and demonstrates a potential selective pressure for reduced biocide susceptibility in clinical strains of Staphylococcus aureus.}, journal = {International journal of antimicrobial agents}, volume = {40}, number = {3}, pages = {210-220}, doi = {10.1016/j.ijantimicag.2012.04.021}, pmid = {22789727}, issn = {1872-7913}, mesh = {DNA, Bacterial/chemistry/genetics ; Disinfectants/*pharmacology ; *Drug Resistance, Bacterial ; *Gene Transfer, Horizontal ; Genotype ; Humans ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Mutation ; Phenotype ; Selection, Genetic ; Sequence Analysis, DNA ; Staphylococcal Infections/microbiology ; Staphylococcus aureus/*drug effects/isolation &amp; purification ; Triclosan/*pharmacology ; }, abstract = {The widely used biocide triclosan selectively targets FabI, the NADH-dependent trans-2-enoyl-acyl carrier protein reductase, which is an important target for narrow-spectrum antimicrobial drug development. In relation to the growing concern about biocide resistance, we compared in vitro mutants and clinical isolates of Staphylococcus aureus with reduced triclosan susceptibility. Clinical isolates of S. aureus as well as laboratory-generated mutants were assayed for minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) phenotypes and genotypes related to reduced triclosan susceptibility. A potential epidemiological cut-off (ECOFF) MBC of >4 mg/L was observed for triclosan in clinical isolates of S. aureus. These showed significantly lower MICs and higher MBCs than laboratory mutants. These groups of strains also had few similarities in the triclosan resistance mechanism. Molecular analysis identified novel resistance mechanisms linked to the presence of an additional sh-fabI allele derived from Staphylococcus haemolyticus. The lack of predictive value of in-vitro-selected mutations for clinical isolates indicates that laboratory tests in the present form appear to be of limited value. More importantly, detection of sh-fabI as a novel resistance mechanism with high potential for horizontal gene transfer demonstrates for the first time that a biocide could exert a selective pressure able to drive the spread of a resistance determinant in a human pathogen.}, }
@article {pmid22759432, year = {2012}, author = {Zhou, Z and Gu, J and Li, YQ and Wang, Y}, title = {Genome plasticity and systems evolution in Streptomyces.}, journal = {BMC bioinformatics}, volume = {13 Suppl 10}, number = {Suppl 10}, pages = {S8}, pmid = {22759432}, issn = {1471-2105}, support = {SC1 GM081068/GM/NIGMS NIH HHS/United States ; AI067543/AI/NIAID NIH HHS/United States ; GM081068/GM/NIGMS NIH HHS/United States ; RR013646/RR/NCRR NIH HHS/United States ; SC1 GM100806/GM/NIGMS NIH HHS/United States ; G12 MD007591/MD/NIMHD NIH HHS/United States ; G12 RR013646/RR/NCRR NIH HHS/United States ; AI080579/AI/NIAID NIH HHS/United States ; SC1 AI080579/AI/NIAID NIH HHS/United States ; }, mesh = {DNA, Bacterial/genetics ; Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Molecular Sequence Annotation ; Multigene Family ; Phylogeny ; Sequence Analysis, DNA/*methods ; Streptomyces/*genetics ; }, abstract = {BACKGROUND: Streptomycetes are filamentous soil-dwelling bacteria. They are best known as the producers of a great variety of natural products such as antibiotics, antifungals, antiparasitics, and anticancer agents and the decomposers of organic substances for carbon recycling. They are also model organisms for the studies of gene regulatory networks, morphological differentiation, and stress response. The availability of sets of genomes from closely related Streptomyces strains makes it possible to assess the mechanisms underlying genome plasticity and systems adaptation.<br><br>RESULTS: We present the results of a comprehensive analysis of the genomes of five Streptomyces species with distinct phenotypes. These streptomycetes have a pan-genome comprised of 17,362 orthologous families which includes 3,096 components in the core genome, 5,066 components in the dispensable genome, and 9,200 components that are uniquely present in only one species. The core genome makes up about 33%-45% of each genome repertoire. It contains important genes for Streptomyces biology including those involved in gene regulation, secretion, secondary metabolism and morphological differentiation. Abundant duplicate genes have been identified, with 4%-11% of the whole genomes composed of lineage-specific expansions (LSEs), suggesting that frequent gene duplication or lateral gene transfer events play a role in shaping the genome diversification within this genus. Two patterns of expansion, single gene expansion and chromosome block expansion are observed, representing different scales of duplication.<br><br>CONCLUSIONS: Our results provide a catalog of genome components and their potential functional roles in gene regulatory networks and metabolic networks. The core genome components reveal the minimum requirement for streptomycetes to sustain a successful lifecycle in the soil environment, reflecting the effects of both genome evolution and environmental stress acting upon the expressed phenotypes. A better understanding of the LSE gene families will, on the other hand, bring a wealth of new insights into the mechanisms underlying strain-specific phenotypes, such as the production of novel antibiotics, pathogenesis, and adaptive response to environmental challenges.}, }
@article {pmid22759418, year = {2012}, author = {Mozhayskiy, V and Tagkopoulos, I}, title = {Horizontal gene transfer dynamics and distribution of fitness effects during microbial in silico evolution.}, journal = {BMC bioinformatics}, volume = {13 Suppl 10}, number = {Suppl 10}, pages = {S13}, pmid = {22759418}, issn = {1471-2105}, mesh = {Adaptation, Biological ; Algorithms ; Bacteria/*genetics ; *Computer Simulation ; *Directed Molecular Evolution ; Environment ; Gene Regulatory Networks ; *Gene Transfer, Horizontal ; *Genetic Fitness ; Metabolic Networks and Pathways ; Models, Theoretical ; Phenotype ; Phylogeny ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT) is a process that facilitates the transfer of genetic material between organisms that are not directly related, and thus can affect both the rate of evolution and emergence of traits. Recent phylogenetic studies reveal HGT events are likely ubiquitous in the Tree of Life. However, our knowledge of HGT's role in evolution and biological organization is very limited, mainly due to the lack of ancestral evolutionary signatures and the difficulty to observe complex evolutionary dynamics in a laboratory setting. Here, we utilize a multi-scale microbial evolution model to comprehensively study the effect of HGT on the evolution of complex traits and organization of gene regulatory networks.<br><br>RESULTS: Large-scale simulations reveal a distinct signature of the Distribution of Fitness Effect (DFE) for HGT events: during evolution, while mutation fitness effects become more negative and neutral, HGT events result in a balanced effect distribution. In either case, lethal events are significantly decreased during evolution (33.0% to 3.2%), a clear indication of mutational robustness. Interestingly, evolution was accelerated when populations were exposed to correlated environments of increasing complexity, especially in the presence of HGT, a phenomenon that warrants further investigation. High HGT rates were found to be disruptive, while the average transferred fragment size was linked to functional module size in the underlying biological network. Network analysis reveals that HGT results in larger regulatory networks, but with the same sparsity level as those evolved in its absence. Observed phenotypic variability and co-existing solutions were traced to individual gain/loss of function events, while subsequent re-wiring after fragment integration was necessary for complex traits to emerge.}, }
@article {pmid22759415, year = {2012}, author = {Mozhayskiy, V and Tagkopoulos, I}, title = {Guided evolution of in silico microbial populations in complex environments accelerates evolutionary rates through a step-wise adaptation.}, journal = {BMC bioinformatics}, volume = {13 Suppl 10}, number = {Suppl 10}, pages = {S10}, pmid = {22759415}, issn = {1471-2105}, mesh = {Adaptation, Physiological/*genetics ; Bacteria/*genetics ; *Biological Evolution ; *Computer Simulation ; *Directed Molecular Evolution ; Environment ; *Gene Transfer, Horizontal ; Genetic Fitness ; Mutation ; Phenotype ; }, abstract = {BACKGROUND: During their lifetime, microbes are exposed to environmental variations, each with its distinct spatio-temporal dynamics. Microbial communities display a remarkable degree of phenotypic plasticity, and highly-fit individuals emerge quite rapidly during microbial adaptation to novel environments. However, there exists a high variability when it comes to adaptation potential, and while adaptation occurs rapidly in certain environmental transitions, in others organisms struggle to adapt. Here, we investigate the hypothesis that the rate of evolution can both increase or decrease, depending on the similarity and complexity of the intermediate and final environments. Elucidating such dependencies paves the way towards controlling the rate and direction of evolution, which is of interest to industrial and medical applications.<br><br>RESULTS: Our results show that the rate of evolution can be accelerated by evolving cell populations in sequential combinations of environments that are increasingly more complex. To quantify environmental complexity, we evaluate various information-theoretic metrics, and we provide evidence that multivariate mutual information between environmental signals in a given environment correlates well with the rate of evolution in that environment, as measured in our simulations. We find that strong positive and negative correlations between the intermediate and final environments lead to the increase of evolutionary rates, when the environmental complexity increases. Horizontal Gene Transfer is shown to further augment this acceleration, under certain conditions. Interestingly, our simulations show that weak environmental correlations lead to deceleration of evolution, regardless of environmental complexity. Further analysis of network evolution provides a mechanistic explanation of this phenomenon, as exposing cells to intermediate environments can trap the population to local neighborhoods of sub-optimal fitness.}, }
@article {pmid22776361, year = {2012}, author = {League, GP and Slot, JC and Rokas, A}, title = {The ASP3 locus in Saccharomyces cerevisiae originated by horizontal gene transfer from Wickerhamomyces.}, journal = {FEMS yeast research}, volume = {12}, number = {7}, pages = {859-863}, doi = {10.1111/j.1567-1364.2012.00828.x}, pmid = {22776361}, issn = {1567-1364}, mesh = {Adaptation, Biological ; Asparaginase/*genetics/metabolism ; Asparagine/metabolism ; Cluster Analysis ; Evolution, Molecular ; Gene Dosage ; *Gene Transfer, Horizontal ; Metabolic Networks and Pathways/genetics ; Multigene Family ; Phylogeny ; Saccharomycetales/*enzymology/*genetics/metabolism ; }, abstract = {The asparagine degradation pathway in the S288c laboratory strain of Saccharomyces cerevisiae is comprised of genes located at two separate loci. ASP1 is located on chromosome IV and encodes for cytosolic l-asparaginase I, whereas ASP3 contains a gene cluster located on chromosome XII comprised of four identical genes, ASP3-1, ASP3-2, ASP3-3, and ASP3-4, which encode for cell wall-associated l-asparaginase II. Interestingly, the ASP3 locus appears to be only present, in variable copy number, in S. cerevisiae strains isolated from laboratory or industrial environments and is completely absent from the genomes of 128 diverse fungal species. Investigation of the evolutionary history of ASP3 across these 128 genomes as well as across the genomes of 43 S. cerevisiae strains shows that ASP3 likely arose in a S. cerevisiae strain via horizontal gene transfer (HGT) from, or a close relative of, the wine yeast Wickerhamomyces anomalus, which co-occurs with S. cerevisiae in several biotechnological processes. Thus, because the ASP3 present in the S288c laboratory strain of S. cerevisiae is induced in response to nitrogen starvation, its acquisition may have aided yeast adaptation to artificial environments. Our finding that the ASP3 locus in S. cerevisiae originated via HGT further highlights the importance of gene sharing between yeasts in the evolution of their remarkable metabolic diversity.}, }
@article {pmid22773788, year = {2012}, author = {Lalaouna, D and Fochesato, S and Barakat, M and Ortet, P and Achouak, W}, title = {Multiple transcription-activating sequences regulate the RsmZ regulatory small RNA of Pseudomonas brassicacearum.}, journal = {Journal of bacteriology}, volume = {194}, number = {18}, pages = {4888-4893}, pmid = {22773788}, issn = {1098-5530}, mesh = {Artificial Gene Fusion ; Binding Sites ; Computational Biology/methods ; Consensus Sequence ; DNA, Bacterial/genetics ; Gene Expression Profiling ; *Gene Expression Regulation, Bacterial ; Genes, Reporter ; Promoter Regions, Genetic ; Pseudomonas/*genetics ; RNA, Bacterial/biosynthesis ; RNA, Small Interfering/*biosynthesis ; Software ; *Transcription, Genetic ; beta-Galactosidase/analysis/genetics ; }, abstract = {The mutS-rpoS region is known to be a highly polymorphic segment of the chromosome owing to horizontal gene transfer and evolutionary processes. In Pseudomonas, mutS-fdxA-rsmZ-rpoS organization is highly conserved, as well as the promoter region of the RsmZ small RNA (sRNA)-encoding gene. One exception to this conservation is in Pseudomonas brassicacearum, where a 308-nucleotide (nt) sequence, predicted to form a hairpin structure in single-stranded DNA (ssDNA), is inserted between the rpoS and rsmZ genes. Using MEME software, we identified nine consensus motifs in the rsmZ promoter region of 16 sequenced Pseudomonas genomes. We observed that an upstream activation sequence (UAS) and an M1 motif (located between the -10 promoter element and the UAS) are shared among examined Pseudomonas genomes. A third motif, the M2 motif, is localized within the coding sequence of the rpoS gene. Constructs fusing the different identified motifs to the lacZ reporter were produced. Our in vivo analysis of the rsmZ-activating elements indicates that the palindromic UAS located 180 bp upstream of the rsmZ transcriptional start in P. brassicacearum NFM 421 is essential, but not sufficient, for full rsmZ expression. Here, we demonstrate a role for the three motifs in the activation of the rsmZ gene, and we hypothesize the role of additional transcriptional factors, along with the DNA structuring role of the hairpin in the complex network controlling the expression of rsmZ.}, }
@article {pmid22773653, year = {2012}, author = {Eberhart, LJ and Deringer, JR and Brayton, KA and Sawant, AA and Besser, TE and Call, DR}, title = {Characterization of a novel microcin that kills enterohemorrhagic Escherichia coli O157:H7 and O26.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {18}, pages = {6592-6599}, pmid = {22773653}, issn = {1098-5336}, mesh = {Anti-Bacterial Agents/*isolation &amp; purification/*toxicity ; *Antibiosis ; Bacteriocins/*isolation &amp; purification/*toxicity ; DNA, Bacterial/chemistry/genetics ; Enterohemorrhagic Escherichia coli/*drug effects/*physiology ; Escherichia coli Proteins/genetics ; Gene Deletion ; Gene Expression Profiling ; Gene Transfer, Horizontal ; Genes, Bacterial ; Molecular Sequence Data ; Operon ; Plasmids ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {A novel phenotype was recently identified in which specific strains of Escherichia coli inhibit competing E. coli strains via a mechanism that was designated "proximity-dependent inhibition" (PDI). PDI-expressing (PDI(+)) E. coli is known to inhibit susceptible (PDI(-)) E. coli strains, including several enterohemorrhagic (EHEC) and enterotoxigenic (ETEC) E. coli strains. In this study, every strain from a genetically diverse panel of E. coli O157:H7 (n = 25) and additional strains of E. coli serovar O26 were susceptible to the PDI phenotype. LIVE/DEAD staining was consistent with inhibition by killing of susceptible cells. Comparative genome analysis identified the genetic component of PDI, which is composed of a plasmid-borne (Incl1) operon encoding a putative microcin and associated genes for transport, immunity, and microcin activation. Transfer of the plasmid to a PDI(-) strain resulted in transfer of the phenotype, and deletion of the genes within the operon resulted in loss of the inhibition phenotype. Deletion of chromosomally encoded tolC also resulted in loss of the inhibitory phenotype, and this confirmed that the putative microcin is most likely secreted via a type I secretion pathway. Deletion of an unrelated plasmid gene did not affect the PDI phenotype. Quantitative reverse transcription (RT)-PCR demonstrated that microcin expression is correlated with logarithmic-phase growth. The ability to inhibit a diversity of E. coli strains indicates that this microcin may influence gut community composition and could be useful for control of important enteric pathogens.}, }
@article {pmid22772895, year = {2013}, author = {Nishida, H}, title = {Genome DNA Sequence Variation, Evolution, and Function in Bacteria and Archaea.}, journal = {Current issues in molecular biology}, volume = {15}, number = {}, pages = {19-24}, pmid = {22772895}, issn = {1467-3045}, mesh = {Archaea/classification/*genetics/physiology ; Bacteria/classification/*genetics ; Bacterial Physiological Phenomena ; Base Composition ; Clustered Regularly Interspaced Short Palindromic Repeats ; Gene Transfer, Horizontal ; Mutation ; }, abstract = {Comparative genomics has revealed that variations in bacterial and archaeal genome DNA sequences cannot be explained by only neutral mutations. Virus resistance and plasmid distribution systems have resulted in changes in bacterial and archaeal genome sequences during evolution. The restriction-modification system, a virus resistance system, leads to avoidance of palindromic DNA sequences in genomes. Clustered, regularly interspaced, short palindromic repeats (CRISPRs) found in genomes represent yet another virus resistance system. Comparative genomics has shown that bacteria and archaea have failed to gain any DNA with GC content higher than the GC content of their chromosomes. Thus, horizontally transferred DNA regions have lower GC content than the host chromosomal DNA does. Some nucleoid-associated proteins bind DNA regions with low GC content and inhibit the expression of genes contained in those regions. This form of gene repression is another type of virus resistance system. On the other hand, bacteria and archaea have used plasmids to gain additional genes. Virus resistance systems influence plasmid distribution. Interestingly, the restriction-modification system and nucleoid-associated protein genes have been distributed via plasmids. Thus, GC content and genomic signatures do not reflect bacterial and archaeal evolutionary relationships.}, }
@article {pmid22768237, year = {2012}, author = {Aguado-Urda, M and Gibello, A and Blanco, MM and López-Campos, GH and Cutuli, MT and Fernández-Garayzábal, JF}, title = {Characterization of plasmids in a human clinical strain of Lactococcus garvieae.}, journal = {PloS one}, volume = {7}, number = {6}, pages = {e40119}, pmid = {22768237}, issn = {1932-6203}, mesh = {Aged ; Amino Acid Sequence ; Base Sequence ; Chromosome Mapping ; DNA Replication/genetics ; Drug Resistance, Bacterial/genetics ; Electrophoresis, Agar Gel ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/genetics ; Humans ; Lactococcus/*genetics/pathogenicity ; Male ; Molecular Sequence Data ; Phylogeny ; Plasmids/*genetics ; Sequence Analysis, DNA ; Virulence Factors/metabolism ; }, abstract = {The present work describes the molecular characterization of five circular plasmids found in the human clinical strain Lactococcus garvieae 21881. The plasmids were designated pGL1-pGL5, with molecular sizes of 4,536 bp, 4,572 bp, 12,948 bp, 14,006 bp and 68,798 bp, respectively. Based on detailed sequence analysis, some of these plasmids appear to be mosaics composed of DNA obtained by modular exchange between different species of lactic acid bacteria. Based on sequence data and the derived presence of certain genes and proteins, the plasmid pGL2 appears to replicate via a rolling-circle mechanism, while the other four plasmids appear to belong to the group of lactococcal theta-type replicons. The plasmids pGL1, pGL2 and pGL5 encode putative proteins related with bacteriocin synthesis and bacteriocin secretion and immunity. The plasmid pGL5 harbors genes (txn, orf5 and orf25) encoding proteins that could be considered putative virulence factors. The gene txn encodes a protein with an enzymatic domain corresponding to the family actin-ADP-ribosyltransferases toxins, which are known to play a key role in pathogenesis of a variety of bacterial pathogens. The genes orf5 and orf25 encode two putative surface proteins containing the cell wall-sorting motif LPXTG, with mucin-binding and collagen-binding protein domains, respectively. These proteins could be involved in the adherence of L. garvieae to mucus from the intestine, facilitating further interaction with intestinal epithelial cells and to collagenous tissues such as the collagen-rich heart valves. To our knowledge, this is the first report on the characterization of plasmids in a human clinical strain of this pathogen.}, }
@article {pmid22763649, year = {2012}, author = {Sorokin, DY and Lücker, S and Vejmelkova, D and Kostrikina, NA and Kleerebezem, R and Rijpstra, WI and Damsté, JS and Le Paslier, D and Muyzer, G and Wagner, M and van Loosdrecht, MC and Daims, H}, title = {Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi.}, journal = {The ISME journal}, volume = {6}, number = {12}, pages = {2245-2256}, pmid = {22763649}, issn = {1751-7370}, support = {P 24101/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Bioreactors/*microbiology ; Chemoautotrophic Growth ; Chloroflexi/*classification/genetics/isolation &amp; purification/physiology ; Genome, Bacterial ; Genomics ; *Nitrification ; Nitrites/*metabolism ; Phylogeny ; Sewage/microbiology ; }, abstract = {Nitrite-oxidizing bacteria (NOB) catalyze the second step of nitrification, a major process of the biogeochemical nitrogen cycle, but the recognized diversity of this guild is surprisingly low and only two bacterial phyla contain known NOB. Here, we report on the discovery of a chemolithoautotrophic nitrite oxidizer that belongs to the widespread phylum Chloroflexi not previously known to contain any nitrifying organism. This organism, named Nitrolancetus hollandicus, was isolated from a nitrifying reactor. Its tolerance to a broad temperature range (25-63 °C) and low affinity for nitrite (K(s)=1 mM), a complex layered cell envelope that stains Gram positive, and uncommon membrane lipids composed of 1,2-diols distinguish N. hollandicus from all other known nitrite oxidizers. N. hollandicus grows on nitrite and CO(2), and is able to use formate as a source of energy and carbon. Genome sequencing and analysis of N. hollandicus revealed the presence of all genes required for CO(2) fixation by the Calvin cycle and a nitrite oxidoreductase (NXR) similar to the NXR forms of the proteobacterial nitrite oxidizers, Nitrobacter and Nitrococcus. Comparative genomic analysis of the nxr loci unexpectedly indicated functionally important lateral gene transfer events between Nitrolancetus and other NOB carrying a cytoplasmic NXR, suggesting that horizontal transfer of the NXR module was a major driver for the spread of the capability to gain energy from nitrite oxidation during bacterial evolution. The surprising discovery of N. hollandicus significantly extends the known diversity of nitrifying organisms and likely will have implications for future research on nitrification in natural and engineered ecosystems.}, }
@article {pmid22761574, year = {2012}, author = {Pilar, AV and Reid-Yu, SA and Cooper, CA and Mulder, DT and Coombes, BK}, title = {GogB is an anti-inflammatory effector that limits tissue damage during Salmonella infection through interaction with human FBXO22 and Skp1.}, journal = {PLoS pathogens}, volume = {8}, number = {6}, pages = {e1002773}, pmid = {22761574}, issn = {1553-7374}, support = {MOP82704//Canadian Institutes of Health Research/Canada ; }, mesh = {Animals ; Bacterial Proteins/immunology/*metabolism ; Blotting, Western ; F-Box Proteins/immunology/*metabolism ; Female ; Gene Knockdown Techniques ; Gene Transfer, Horizontal ; Host-Parasite Interactions/*immunology ; Humans ; Immunoprecipitation ; Mice ; Mice, Inbred C57BL ; NF-kappa B/immunology/metabolism ; Real-Time Polymerase Chain Reaction ; Receptors, Cytoplasmic and Nuclear/immunology/*metabolism ; S-Phase Kinase-Associated Proteins/immunology/*metabolism ; Salmonella Infections/immunology/*metabolism ; }, abstract = {Bacterial pathogens often manipulate host immune pathways to establish acute and chronic infection. Many Gram-negative bacteria do this by secreting effector proteins through a type III secretion system that alter the host response to the pathogen. In this study, we determined that the phage-encoded GogB effector protein in Salmonella targets the host SCF E3 type ubiquitin ligase through an interaction with Skp1 and the human F-box only 22 (FBXO22) protein. Domain mapping and functional knockdown studies indicated that GogB-containing bacteria inhibited IκB degradation and NFκB activation in macrophages, which required Skp1 and a eukaryotic-like F-box motif in the C-terminal domain of GogB. GogB-deficient Salmonella were unable to limit NFκB activation, which lead to increased proinflammatory responses in infected mice accompanied by extensive tissue damage and enhanced colonization in the gut during long-term chronic infections. We conclude that GogB is an anti-inflammatory effector that helps regulate inflammation-enhanced colonization by limiting tissue damage during infection.}, }
@article {pmid22761331, year = {2012}, author = {Knight, GM and Budd, EL and Whitney, L and Thornley, A and Al-Ghusein, H and Planche, T and Lindsay, JA}, title = {Shift in dominant hospital-associated methicillin-resistant Staphylococcus aureus (HA-MRSA) clones over time.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {67}, number = {10}, pages = {2514-2522}, doi = {10.1093/jac/dks245}, pmid = {22761331}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/pharmacology ; Cross Infection/*epidemiology/microbiology ; Drug Prescriptions/statistics &amp; numerical data ; Drug Resistance, Multiple, Bacterial ; Fluoroquinolones/pharmacology ; Hospitals, Teaching ; Humans ; Incidence ; London/epidemiology ; Methicillin-Resistant Staphylococcus aureus/*classification/isolation &amp; purification ; Microbial Sensitivity Tests ; Molecular Epidemiology ; *Molecular Typing ; Staphylococcal Infections/*epidemiology/microbiology ; Time Factors ; }, abstract = {OBJECTIVES: The majority of HA-MRSA infections are caused by endogenous infection and by only a small number of clones. The reasons for the success of some clones over others are unknown.<br><br>METHODS: We investigated the evolution of an MRSA population from a large, acute-care teaching hospital in London, UK over a 10 year period. MRSA incidence and antibiotic prescribing were correlated with changes in resistance genes and prevalence of clonal groups.<br><br>RESULTS: Three clones caused the majority of infections, CC30 SCCmecII (EMRSA-16), CC22 SCCmecIV (EMRSA-15) and ST239 SCCmecIII. Clones that were multidrug resistant were selected for, and CC22 became dominant once it acquired a wide range of extra resistance genes. CC22 MRSA was also the fittest clone in an independent growth assay&#xa0;and a competition assay, and had a greater ability to survive desiccation. No individual isolate was fully drug resistant, and there was evidence of substantial horizontal gene transfer (HGT) as well as resistance gene loss within the clonal groups. The exception was fluoroquinolone resistance, which was rarely lost by any of the dominant hospital clones, suggesting that this resistance contributes to selection and survival of HA-MRSA. In support of this, a decrease in hospital-wide ciprofloxacin (a fluoroquinolone) prescribing was strongly associated with an overall decrease in MRSA infection.<br><br>CONCLUSION: Our data suggest successful HA-MRSA clones such as CC22 SCCmecIV are resistant to fluoroquinolones as well as fitter and able to acquire, but not necessarily accumulate, resistance to a wide range of additional antibiotics.}, }
@article {pmid22759228, year = {2013}, author = {Juárez, JF and Zamarro, MT and Eberlein, C and Boll, M and Carmona, M and Díaz, E}, title = {Characterization of the mbd cluster encoding the anaerobic 3-methylbenzoyl-CoA central pathway.}, journal = {Environmental microbiology}, volume = {15}, number = {1}, pages = {148-166}, doi = {10.1111/j.1462-2920.2012.02818.x}, pmid = {22759228}, issn = {1462-2920}, mesh = {Acyl Coenzyme A/*genetics/*metabolism ; Amino Acid Sequence ; Anaerobiosis ; Azoarcus/classification/*enzymology/*genetics ; Benzoates/metabolism ; Gene Expression Regulation, Bacterial ; Multigene Family/*genetics ; Operon ; Oxidoreductases Acting on CH-CH Group Donors/genetics/metabolism ; Phylogeny ; Xylenes/metabolism ; }, abstract = {The mbd cluster encoding genes of the 3-methylbenzoyl-CoA pathway involved in the anaerobic catabolism of 3-methylbenzoate and m-xylene was characterized for the first time in the denitrifying β-Proteobacterium Azoarcus sp. CIB. The mbdA gene product was identified as a 3-methylbenzoate-CoA ligase required for 3-methylbenzoate activation; its substrate spectrum was unique in activating all three methylbenzoate isomers. An inducible 3-methylbenzoyl-CoA reductase (mbdONQP gene products), displaying significant amino acid sequence similarities to known class I benzoyl-CoA reductases catalysed the ATP-dependent reduction of 3-methylbenzoyl-CoA to a methyldienoyl-CoA. The mbdW gene encodes a methyldienoyl-CoA hydratase that hydrated the methyldienoyl-CoA to a methyl-6-hydroxymonoenoyl-CoA compound. The mbd cluster also contains the genes predicted to be involved in the subsequent steps of the 3-methylbenzoyl-CoA pathway as well as the electron donor system for the reductase activity. Whereas the catabolic mbd genes are organized in two divergent inducible operons, the putative mbdR regulatory gene was transcribed separately and showed constitutive expression. The efficient expression of the mbd genes required the oxygen-dependent AcpR activator, and it was subject of carbon catabolite repression by some organic acids and amino acids. Sequence analyses suggest that the mbd gene cluster was recruited by Azoarcus sp. CIB through horizontal gene transfer.}, }
@article {pmid22754748, year = {2012}, author = {Labbate, M and Boucher, Y and Luu, I and Chowdhury, PR and Stokes, HW}, title = {Integron associated mobile genes: Just a collection of plug in apps or essential components of cell network hardware?.}, journal = {Mobile genetic elements}, volume = {2}, number = {1}, pages = {13-18}, pmid = {22754748}, issn = {2159-2543}, abstract = {Lateral gene transfer (LGT) impacts on the evolution of prokaryotes in both the short and long-term. The short-term impacts of mobilized genes are a concern to humans since LGT explains the global rise of multi drug resistant pathogens seen in the past 70 years. However, LGT has been a feature of prokaryotes from the earliest days of their existence and the concept of a bifurcating tree of life is not entirely applicable to prokaryotes since most genes in extant prokaryotic genomes have probably been acquired from other lineages. Successful transfer and maintenance of a gene in a new host is understandable if it acts independently of cell networks and confers an advantage. Antibiotic resistance provides an example of this whereby a gene can be advantageous in virtually any cell across broad species backgrounds. In a longer evolutionary context however laterally transferred genes can be assimilated into even essential cell networks. How this happens is not well understood and we discuss recent work that identifies a mobile gene, unique to a cell lineage, which is detrimental to the cell when lost. We also present some additional data and believe our emerging model will be helpful in understanding how mobile genes integrate into cell networks.}, }
@article {pmid22750647, year = {2012}, author = {Zhao, J and Xu, J and Wang, J and Zhao, Y and Zhang, L and He, J and Chu, M and Li, N}, title = {Impacts of human lysozyme transgene on the microflora of pig feces and the surrounding soil.}, journal = {Journal of biotechnology}, volume = {161}, number = {4}, pages = {437-444}, doi = {10.1016/j.jbiotec.2012.05.018}, pmid = {22750647}, issn = {1873-4863}, mesh = {Animals ; Animals, Genetically Modified ; DNA/analysis ; Humans ; Intestines/microbiology ; Manure/analysis/*microbiology ; Muramidase/*genetics ; Nitrogen/analysis ; Phosphorus/analysis ; Soil/analysis ; *Soil Microbiology ; Swine/*genetics ; *Transgenes ; }, abstract = {The rapid development of genetic engineering and extensive applications of genetically engineered (GE) animals have provided many research benefits, but concerns have been raised over the potential environmental impact of transgenic animals. We investigated the effects of human lysozyme (hLZ) transgenic pigs which can express hLZ in their mammary glands on the surrounding environment from the angle of the changes of pig feces and the surrounding soil, including the probability of horizontal gene transfer (HGT), the impact on microbial communities in pig gastrointestinal (GI) tracts and soil, and the influence on the total nitrogen (TN) and total phosphorus (TP) content of pig excrement and surrounding soil. Results showed that hLZ gene was not detected by polymerase chain reaction (PCR) or quantitative real-time PCR (Q-PCR) in gut microbial DNA extracts of manure or microbial DNA extracts of topsoil. PCR-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) analysis and 16S rDNA sequence analysis showed that hLZ gene had no impact on the microflora structure of pig guts or soil. Finally, TN and TP contents were not significantly different in pig manure or soils taken at different distances from the pig site (P>0.25).}, }
@article {pmid22748811, year = {2012}, author = {Łobocka, M and Hejnowicz, MS and Dąbrowski, K and Gozdek, A and Kosakowski, J and Witkowska, M and Ulatowska, MI and Weber-Dąbrowska, B and Kwiatek, M and Parasion, S and Gawor, J and Kosowska, H and Głowacka, A}, title = {Genomics of staphylococcal Twort-like phages--potential therapeutics of the post-antibiotic era.}, journal = {Advances in virus research}, volume = {83}, number = {}, pages = {143-216}, doi = {10.1016/B978-0-12-394438-2.00005-0}, pmid = {22748811}, issn = {1557-8399}, mesh = {Biological Products/pharmacology ; Biological Therapy/*methods ; Conserved Sequence ; Evolution, Molecular ; Gene Order ; Genes, Viral ; Genome, Viral ; Mutagenesis, Insertional ; Polymorphism, Single Nucleotide ; Sequence Deletion ; Staphylococcus Phages/*genetics/growth &amp; development ; Staphylococcus aureus/virology ; Staphylococcus epidermidis/virology ; Synteny ; }, abstract = {Polyvalent bacteriophages of the genus Twort-like that infect clinically relevant Staphylococcus strains may be among the most promising phages with potential therapeutic applications. They are obligatorily lytic, infect the majority of Staphylococcus strains in clinical strain collections, propagate efficiently and do not transfer foreign DNA by transduction. Comparative genomic analysis of 11 S. aureus/S. epidermidis Twort-like phages, as presented in this chapter, emphasizes their strikingly high similarity and clear divergence from phage Twort of the same genus, which might have evolved in hosts of a different species group. Genetically, these phages form a relatively isolated group, which minimizes the risk of acquiring potentially harmful genes. The order of genes in core parts of their 127 to 140-kb genomes is conserved and resembles that found in related representatives of the Spounavirinae subfamily of myoviruses. Functions of certain conserved genes can be predicted based on their homology to prototypical genes of model spounavirus SPO1. Deletions in the genomes of certain phages mark genes that are dispensable for phage development. Nearly half of the genes of these phages have no known homologues. Unique genes are mostly located near termini of the virion DNA molecule and are expressed early in phage development as implied by analysis of their potential transcriptional signals. Thus, many of them are likely to play a role in host takeover. Single genes encode homologues of bacterial virulence-associated proteins. They were apparently acquired by a common ancestor of these phages by horizontal gene transfer but presumably evolved towards gaining functions that increase phage infectivity for bacteria or facilitate mature phage release. Major differences between the genomes of S. aureus/S. epidermidis Twort-like phages consist of single nucleotide polymorphisms and insertions/deletions of short stretches of nucleotides, single genes, or introns of group I. Although the number and location of introns may vary between particular phages, intron shuffling is unlikely to be a major factor responsible for specificity differences.}, }
@article {pmid22748513, year = {2012}, author = {Llosa, M and Schröder, G and Dehio, C}, title = {New perspectives into bacterial DNA transfer to human cells.}, journal = {Trends in microbiology}, volume = {20}, number = {8}, pages = {355-359}, doi = {10.1016/j.tim.2012.05.008}, pmid = {22748513}, issn = {1878-4380}, mesh = {Bacterial Proteins/metabolism ; *Bacterial Secretion Systems ; Bartonella henselae/*genetics/physiology ; Biological Transport ; DNA, Bacterial/*genetics ; *Gene Transfer, Horizontal ; Humans ; }, abstract = {The type IV secretion system (T4SS) VirB/D4 of the facultative intracellular pathogen Bartonella henselae is known to translocate bacterial effector proteins into human cells. Two recent reports on DNA transfer into human cells have demonstrated the versatility of this bacterial secretion system for macromolecular substrate transfer. Moreover, these findings have opened the possibility for developing new tools for DNA delivery into specific human cell types. DNA can be introduced into these cells covalently attached to a site-specific integrase with potential target sequences in the human genome. This novel DNA delivery system is discussed in the context of existing methods for genetic modification of human cells.}, }
@article {pmid22748314, year = {2012}, author = {Naor, A and Lapierre, P and Mevarech, M and Papke, RT and Gophna, U}, title = {Low species barriers in halophilic archaea and the formation of recombinant hybrids.}, journal = {Current biology : CB}, volume = {22}, number = {15}, pages = {1444-1448}, doi = {10.1016/j.cub.2012.05.056}, pmid = {22748314}, issn = {1879-0445}, mesh = {Haloferax mediterranei/*genetics ; Haloferax volcanii/*genetics ; *Hybridization, Genetic ; *Recombination, Genetic ; }, abstract = {Speciation of sexually reproducing organisms requires reproductive barriers. Prokaryotes reproduce asexually but often exchange DNA by lateral gene transfer mechanisms and recombination [1], yet distinct lineages are still observed. Thus, barriers to gene flow such as geographic isolation, genetic incompatibility or a physiological inability to transfer DNA represent potential underlying mechanisms behind preferred exchange groups observed in prokaryotes [2-6]. In Bacteria, experimental evidence showed that sequence divergence impedes homologous recombination between bacterial species [7-11]. Here we study interspecies gene exchange in halophilic archaea that possess a parasexual mechanism of genetic exchange that is functional between species [12, 13]. In this process, cells fuse forming a diploid state containing the full genetic repertoire of both parental cells, which facilitates genetic exchange and recombination. Later, cells separate, occasionally resulting in hybrids of the parental strains [14]. We show high recombination frequencies between Haloferax volcanii and Haloferax mediterranei, two species that have an average nucleotide sequence identity of 86.6%. Whole genome sequencing of Haloferax interspecies hybrids revealed the exchange of chromosomal fragments ranging from 310Kb to 530Kb. These results show that recombination barriers may be more permissive in halophilic archaea than they are in bacteria.}, }
@article {pmid22747834, year = {2012}, author = {Otto, M}, title = {MRSA virulence and spread.}, journal = {Cellular microbiology}, volume = {14}, number = {10}, pages = {1513-1521}, pmid = {22747834}, issn = {1462-5822}, support = {ZIA AI000904/ImNIH/Intramural NIH HHS/United States ; ZIA AI000904-10/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Community-Acquired Infections/microbiology/pathology/transmission ; Cross Infection/microbiology/pathology/transmission ; Gene Transfer, Horizontal ; Humans ; Methicillin-Resistant Staphylococcus aureus/genetics/*pathogenicity ; Molecular Epidemiology ; Staphylococcal Infections/*microbiology/*pathology/transmission ; Virulence ; Virulence Factors/genetics/*metabolism ; }, abstract = {Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most frequent causes of hospital- and community-associated infections. Resistance to the entire class of β-lactam antibiotics, such as methicillin and penicillin, makes MRSA infections difficult to treat. Hospital-associated MRSA strains are often multi-drug-resistant, leaving only lower efficiency drugs such as vancomycin as treatments options. Like many other S. aureus strains, MRSA strains produce a series of virulence factors, such as toxins and adhesion proteins. Recent findings have shed some new light on the molecular events that underlie MRSA epidemic waves. Newly emerging MRSA clones appear to have acquired phenotypic traits that render them more virulent or able to colonize better, either via mobile genetic elements or via adaptation of gene expression. Acquisition of Panton-Valentine leukocidin genes and increased expression of core genome-encoded toxins are being discussed as potentially contributing to the success of the recently emerged community-associated MRSA strains. However, the molecular factors underlying the spread of hospital- and community-associated MRSA strains are still far from being completely understood, a situation calling for enhanced research efforts in that area.}, }
@article {pmid22746823, year = {2012}, author = {Crook, MB and Lindsay, DP and Biggs, MB and Bentley, JS and Price, JC and Clement, SC and Clement, MJ and Long, SR and Griffitts, JS}, title = {Rhizobial plasmids that cause impaired symbiotic nitrogen fixation and enhanced host invasion.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {25}, number = {8}, pages = {1026-1033}, pmid = {22746823}, issn = {0894-0282}, support = {R01 GM093628/GM/NIGMS NIH HHS/United States ; R01GM093628/GM/NIGMS NIH HHS/United States ; }, mesh = {Gene Transfer, Horizontal ; Medicago/*microbiology ; Molecular Sequence Data ; Nitrogen Fixation/*genetics ; Phenotype ; Plasmids ; Rhizobium/*genetics ; Root Nodules, Plant/microbiology ; Sinorhizobium/genetics ; Symbiosis/*genetics ; }, abstract = {The genetic rules that dictate legume-rhizobium compatibility have been investigated for decades, but the causes of incompatibility occurring at late stages of the nodulation process are not well understood. An evaluation of naturally diverse legume (genus Medicago) and rhizobium (genus Sinorhizobium) isolates has revealed numerous instances in which Sinorhizobium strains induce and occupy nodules that are only minimally beneficial to certain Medicago hosts. Using these ineffective strain-host pairs, we identified gain-of-compatibility (GOC) rhizobial variants. We show that GOC variants arise by loss of specific large accessory plasmids, which we call HR plasmids due to their effect on symbiotic host range. Transfer of HR plasmids to a symbiotically effective rhizobium strain can convert it to incompatibility, indicating that HR plasmids can act autonomously in diverse strain backgrounds. We provide evidence that HR plasmids may encode machinery for their horizontal transfer. On hosts in which HR plasmids impair N fixation, the plasmids also enhance competitiveness for nodule occupancy, showing that naturally occurring, transferrable accessory genes can convert beneficial rhizobia to a more exploitative lifestyle. This observation raises important questions about agricultural management, the ecological stability of mutualisms, and the genetic factors that distinguish beneficial symbionts from parasites.}, }
@article {pmid22746333, year = {2012}, author = {Capra, EJ and Laub, MT}, title = {Evolution of two-component signal transduction systems.}, journal = {Annual review of microbiology}, volume = {66}, number = {}, pages = {325-347}, pmid = {22746333}, issn = {1545-3251}, support = {R01 GM082899/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; Bacterial Physiological Phenomena ; *Biological Evolution ; Gene Expression Regulation, Bacterial ; Signal Transduction/*genetics ; Stress, Physiological ; }, abstract = {To exist in a wide range of environmental niches, bacteria must sense and respond to a variety of external signals. A primary means by which this occurs is through two-component signal transduction pathways, typically composed of a sensor histidine kinase that receives the input stimuli and then phosphorylates a response regulator that effects an appropriate change in cellular physiology. Histidine kinases and response regulators have an intrinsic modularity that separates signal input, phosphotransfer, and output response; this modularity has allowed bacteria to dramatically expand and diversify their signaling capabilities. Recent work has begun to reveal the molecular basis by which two-component proteins evolve. How and why do orthologous signaling proteins diverge? How do cells gain new pathways and recognize new signals? What changes are needed to insulate a new pathway from existing pathways? What constraints are there on gene duplication and lateral gene transfer? Here, we review progress made in answering these questions, highlighting how the integration of genome sequence data with experimental studies is providing major new insights.}, }
@article {pmid22745266, year = {2012}, author = {Akochy, PM and Lapointe, J and Roy, PH}, title = {Natural insertion of the bro-1 β-lactamase gene into the gatCAB operon affects Moraxella catarrhalis aspartyl-tRNA(Asn) amidotransferase activity.}, journal = {Microbiology (Reading, England)}, volume = {158}, number = {Pt 9}, pages = {2363-2371}, doi = {10.1099/mic.0.060095-0}, pmid = {22745266}, issn = {1465-2080}, support = {MT-13564//Canadian Institutes of Health Research/Canada ; }, mesh = {Gene Transfer, Horizontal ; Humans ; Kinetics ; Moraxella catarrhalis/*enzymology/*genetics ; *Mutagenesis, Insertional ; Nitrogenous Group Transferases/*genetics/*metabolism ; Operon ; beta-Lactam Resistance ; beta-Lactamases/*genetics ; }, abstract = {Only about half of bacterial species use an asparaginyl-tRNA synthetase (AsnRS) to attach Asn to its cognate tRNA(Asn). Other bacteria, including the human pathogen Moraxella catarrhalis, a causative agent of otitis media, lack a gene encoding AsnRS, and form Asn-tRNA(Asn) by an indirect pathway catalysed by two enzymes: first, a non-discriminating aspartyl-tRNA synthetase (ND-AspRS) catalyses the formation of aspartyl-tRNA(Asn) (Asp-tRNA(Asn)); then, a tRNA-dependent amidotransferase (GatCAB) transamidates this 'incorrect' product into Asn-tRNA(Asn). As M. catarrhalis has a Gln-tRNA synthetase, its GatCAB functions as an Asp-tRNA(Asn) amidotransferase. This pathogen rapidly evolved to about 90 % ampicillin resistance worldwide by insertion of a bro-1 β-lactamase gene within the gatCAB operon. Comparison of the GatCAB subunits from bro-1 β-lactamase-positive and bro-negative strains showed that the laterally transferred bro-1 gene, inserted into the gatCAB operon, affected the C-terminal sequence of GatA. The identity between the C-terminal sequences of GatA(wt) (residues 479-491) and of GatA(BRO-1) (residues 479-492) was about 36 %, whereas the rest of the GatA sequence was relatively conserved. The characterization of these two distinct GatCABs as well as the hybrid GatCAB containing GatA(1-478)(wt)(479-492)(BRO-1) and truncated GatCAB enzymes of M. catarrhalis showed that the substitution in GatA(wt) of residues 479-492 of GatA(BRO-1) causes increased specificity for glutamine, and decreased specificity for Asp-tRNA(Asn) in the transamidation reaction. We conclude that the bro gene insertion has altered the kinetic parameters of Asp-tRNA(Asn) amidotransferase, and we propose a model for gatA evolution after the insertion of bro-1 at the carboxyl end of gatA.}, }
@article {pmid22741028, year = {2012}, author = {Wang, Z and O'Shaughnessy, TJ and Soto, CM and Rahbar, AM and Robertson, KL and Lebedev, N and Vora, GJ}, title = {Function and regulation of Vibrio campbellii proteorhodopsin: acquired phototrophy in a classical organoheterotroph.}, journal = {PloS one}, volume = {7}, number = {6}, pages = {e38749}, pmid = {22741028}, issn = {1932-6203}, mesh = {Bacterial Proteins/genetics/metabolism ; Light ; Phototrophic Processes/genetics/*physiology ; Rhodopsin/genetics/*metabolism ; Rhodopsins, Microbial ; Vibrio/genetics/*metabolism/*radiation effects ; }, abstract = {Proteorhodopsins (PRs) are retinal-binding photoproteins that mediate light-driven proton translocation across prokaryotic cell membranes. Despite their abundance, wide distribution and contribution to the bioenergy budget of the marine photic zone, an understanding of PR function and physiological significance in situ has been hampered as the vast majority of PRs studied to date are from unculturable bacteria or culturable species that lack the tools for genetic manipulation. In this study, we describe the presence and function of a horizontally acquired PR and retinal biosynthesis gene cluster in the culturable and genetically tractable bioluminescent marine bacterium Vibrio campbellii. Pigmentation analysis, absorption spectroscopy and photoinduction assays using a heterologous over-expression system established the V. campbellii PR as a functional green light absorbing proton pump. In situ analyses comparing PR expression and function in wild type (WT) V. campbellii with an isogenic ΔpR deletion mutant revealed a marked absence of PR membrane localization, pigmentation and light-induced proton pumping in the ΔpR mutant. Comparative photoinduction assays demonstrated the distinct upregulation of pR expression in the presence of light and PR-mediated photophosphorylation in WT cells that resulted in the enhancement of cellular survival during respiratory stress. In addition, we demonstrate that the master regulator of adaptive stress response and stationary phase, RpoS1, positively regulates pR expression and PR holoprotein pigmentation. Taken together, the results demonstrate facultative phototrophy in a classical marine organoheterotrophic Vibrio species and provide a salient example of how this organism has exploited lateral gene transfer to further its adaptation to the photic zone.}, }
@article {pmid22740635, year = {2012}, author = {Retchless, AC and Lawrence, JG}, title = {Ecological adaptation in bacteria: speciation driven by codon selection.}, journal = {Molecular biology and evolution}, volume = {29}, number = {12}, pages = {3669-3683}, pmid = {22740635}, issn = {1537-1719}, support = {R01 GM078092/GM/NIGMS NIH HHS/United States ; GM078092/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Biological/*genetics ; Analysis of Variance ; Bacteria/*genetics ; Codon/*genetics ; *Environment ; Gene Transfer, Horizontal/*genetics ; Likelihood Functions ; Models, Genetic ; Operon/genetics ; *Phylogeny ; Principal Component Analysis ; Selection, Genetic/*genetics ; Species Specificity ; }, abstract = {In bacteria, physiological change may be effected by a single gene acquisition, producing ecological differentiation without genetic isolation. Natural selection acting on such differences can reduce the frequency of genotypes that arise from recombination at these loci. However, gene acquisition can only account for recombination interference in the fraction of the genome that is tightly linked to the integration site. To identify additional loci that contribute to adaptive differences, we examined orthologous genes in species of Enterobacteriaceae to identify significant differences in the degree of codon selection. Significance was assessed using the Adaptive Codon Enrichment metric, which accounts for the variation in codon usage bias that is expected to arise from mutation and drift; large differences in codon usage bias were identified in more genes than would be expected to arise from stochastic processes alone. Genes in the same operon showed parallel differences in codon usage bias, suggesting that changes in the overall levels of gene expression led to changes in the degree of adaptive codon usage. Most significant differences between orthologous operons were found among those involved with specific environmental adaptations, whereas "housekeeping" genes rarely showed significant changes. When considered together, the loci experiencing significant changes in codon selection outnumber potentially adaptive gene acquisition events. The identity of genes under strong codon selection seems to be influenced by the habitat from which the bacteria were isolated. We propose a two-stage model for how adaptation to different selective regimes can drive bacterial speciation. Initially, gene acquisitions catalyze rapid ecological differentiation, which modifies the utilization of genes, thereby changing the strength of codon selection on them. Alleles develop fitness variation by substitution, producing recombination interference at these loci in addition to those flanking acquired genes, allowing sequences to diverge across the entire genome and establishing genetic isolation (i.e., protection from frequent homologous recombination).}, }
@article {pmid22737089, year = {2012}, author = {Lo Scrudato, M and Blokesch, M}, title = {The regulatory network of natural competence and transformation of Vibrio cholerae.}, journal = {PLoS genetics}, volume = {8}, number = {6}, pages = {e1002778}, pmid = {22737089}, issn = {1553-7404}, mesh = {Animals ; Biofilms/growth &amp; development ; Catabolite Repression/genetics ; *Chitin/genetics/metabolism ; *DNA Transformation Competence/genetics ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; Quorum Sensing/genetics ; Signal Transduction ; Single-Cell Analysis ; *Vibrio cholerae/genetics/growth &amp; development ; Zooplankton/microbiology ; }, abstract = {The human pathogen Vibrio cholerae is an aquatic bacterium frequently encountered in rivers, lakes, estuaries, and coastal regions. Within these environmental reservoirs, the bacterium is often found associated with zooplankton and more specifically with their chitinous exoskeleton. Upon growth on such chitinous surfaces, V. cholerae initiates a developmental program termed "natural competence for genetic transformation." Natural competence for transformation is a mode of horizontal gene transfer in bacteria and contributes to the maintenance and evolution of bacterial genomes. In this study, we investigated competence gene expression within this organism at the single cell level. We provide evidence that under homogeneous inducing conditions the majority of the cells express competence genes. A more heterogeneous expression pattern was observable on chitin surfaces. We hypothesize that this was the case due to the heterogeneity around the chitin surface, which might vary extensively with respect to chitin degradation products and autoinducers; these molecules contribute to competence induction based on carbon catabolite repression and quorum-sensing pathways, respectively. Therefore, we investigated the contribution of these two signaling pathways to natural competence in detail using natural transformation assays, transcriptional reporter fusions, quantitative RT-PCR, and immunological detection of protein levels using Western blot analysis. The results illustrate that all tested competence genes are dependent on the transformation regulator TfoX. Furthermore, intracellular cAMP levels play a major role in natural transformation. Finally, we demonstrate that only a minority of genes involved in natural transformation are regulated in a quorum-sensing-dependent manner and that these genes determine the fate of the surrounding DNA. We conclude with a model of the regulatory circuit of chitin-induced natural competence in V. cholerae.}, }
@article {pmid22737074, year = {2012}, author = {Achtman, M and Wain, J and Weill, FX and Nair, S and Zhou, Z and Sangal, V and Krauland, MG and Hale, JL and Harbottle, H and Uesbeck, A and Dougan, G and Harrison, LH and Brisse, S and , }, title = {Multilocus sequence typing as a replacement for serotyping in Salmonella enterica.}, journal = {PLoS pathogens}, volume = {8}, number = {6}, pages = {e1002776}, pmid = {22737074}, issn = {1553-7374}, support = {//Wellcome Trust/United Kingdom ; G0600805/MRC_/Medical Research Council/United Kingdom ; UL1 TR000005/TR/NCATS NIH HHS/United States ; }, mesh = {Bacterial Typing Techniques/*methods ; Phylogeny ; Salmonella enterica/*classification/genetics ; Serotyping/*methods ; }, abstract = {Salmonella enterica subspecies enterica is traditionally subdivided into serovars by serological and nutritional characteristics. We used Multilocus Sequence Typing (MLST) to assign 4,257 isolates from 554 serovars to 1092 sequence types (STs). The majority of the isolates and many STs were grouped into 138 genetically closely related clusters called eBurstGroups (eBGs). Many eBGs correspond to a serovar, for example most Typhimurium are in eBG1 and most Enteritidis are in eBG4, but many eBGs contained more than one serovar. Furthermore, most serovars were polyphyletic and are distributed across multiple unrelated eBGs. Thus, serovar designations confounded genetically unrelated isolates and failed to recognize natural evolutionary groupings. An inability of serotyping to correctly group isolates was most apparent for Paratyphi B and its variant Java. Most Paratyphi B were included within a sub-cluster of STs belonging to eBG5, which also encompasses a separate sub-cluster of Java STs. However, diphasic Java variants were also found in two other eBGs and monophasic Java variants were in four other eBGs or STs, one of which is in subspecies salamae and a second of which includes isolates assigned to Enteritidis, Dublin and monophasic Paratyphi B. Similarly, Choleraesuis was found in eBG6 and is closely related to Paratyphi C, which is in eBG20. However, Choleraesuis var. Decatur consists of isolates from seven other, unrelated eBGs or STs. The serological assignment of these Decatur isolates to Choleraesuis likely reflects lateral gene transfer of flagellar genes between unrelated bacteria plus purifying selection. By confounding multiple evolutionary groups, serotyping can be misleading about the disease potential of S. enterica. Unlike serotyping, MLST recognizes evolutionary groupings and we recommend that Salmonella classification by serotyping should be replaced by MLST or its equivalents.}, }
@article {pmid22736983, year = {2012}, author = {Tiaden, A and Hilbi, H}, title = {α-Hydroxyketone synthesis and sensing by Legionella and Vibrio.}, journal = {Sensors (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {2899-2919}, pmid = {22736983}, issn = {1424-8220}, mesh = {Biofilms ; *Biosensing Techniques ; Cell Communication ; Host-Pathogen Interactions ; Ketones/chemistry/*metabolism ; Legionella pneumophila/pathogenicity/*physiology ; Quorum Sensing ; Signal Transduction ; Vibrio cholerae/pathogenicity/*physiology ; }, abstract = {Bacteria synthesize and sense low molecular weight signaling molecules, termed autoinducers, to measure their population density and community complexity. One class of autoinducers, the α-hydroxyketones (AHKs), is produced and detected by the water-borne opportunistic pathogens Legionella pneumophila and Vibrio cholerae, which cause Legionnaires' disease and cholera, respectively. The "Legionella quorum sensing" (lqs) or "cholera quorum sensing" (cqs) genes encode enzymes that produce and sense the AHK molecules "Legionella autoinducer-1" (LAI-1; 3-hydroxypentadecane-4-one) or cholera autoinducer-1 (CAI-1; 3-hydroxytridecane-4-one). AHK signaling regulates the virulence of L. pneumophila and V. cholerae, pathogen-host cell interactions, formation of biofilms or extracellular filaments, expression of a genomic "fitness island" and competence. Here, we outline the processes, wherein AHK signaling plays a role, and review recent insights into the function of proteins encoded by the lqs and cqs gene clusters. To this end, we will focus on the autoinducer synthases catalysing the biosynthesis of AHKs, on the cognate trans-membrane sensor kinases detecting the signals, and on components of the down-stream phosphorelay cascade that promote the transmission and integration of signaling events regulating gene expression.}, }
@article {pmid22730123, year = {2012}, author = {Mashburn-Warren, L and Morrison, DA and Federle, MJ}, title = {The cryptic competence pathway in Streptococcus pyogenes is controlled by a peptide pheromone.}, journal = {Journal of bacteriology}, volume = {194}, number = {17}, pages = {4589-4600}, pmid = {22730123}, issn = {1098-5530}, support = {R01 AI091779/AI/NIAID NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; AI091779/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/metabolism ; *DNA Transformation Competence ; Endopeptidase Clp ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Peptides/genetics/*metabolism ; Pheromones/genetics/*metabolism ; *Quorum Sensing ; Serine Endopeptidases/genetics/metabolism ; Sigma Factor/*genetics/metabolism ; Streptococcus pyogenes/*genetics/metabolism ; Trans-Activators/genetics/metabolism ; Transformation, Bacterial ; }, abstract = {Horizontal gene transfer is an important means of bacterial evolution that is facilitated by transduction, conjugation, and natural genetic transformation. Transformation occurs after bacterial cells enter a state of competence, where naked DNA is acquired from the extracellular environment. Induction of the competent state relies on signals that activate master regulators, causing the expression of genes involved in DNA uptake, processing, and recombination. All streptococcal species contain the master regulator SigX and SigX-dependent effector genes required for natural genetic transformation; however, not all streptococcal species have been shown to be naturally competent. We recently demonstrated that competence development in Streptococcus mutans requires the type II ComRS quorum-sensing circuit, comprising an Rgg transcriptional activator and a novel peptide pheromone (L. Mashburn-Warren, D. A. Morrison, and M. J. Federle, Mol. Microbiol. 78:589-606, 2010). The type II ComRS system is shared by the pyogenic, mutans, and bovis streptococci, including the clinically relevant pathogen Streptococcus pyogenes. Here, we describe the activation of sigX by a small-peptide pheromone and an Rgg regulator of the type II ComRS class. We confirm previous reports that SigX is functional and able to activate sigX-dependent gene expression within the competence regulon, and that SigX stability is influenced by the cytoplasmic protease ClpP. Genomic analyses of available S. pyogenes genomes revealed the presence of intact genes within the competence regulon. While this is the first report to show natural induction of sigX, S. pyogenes remained nontransformable under laboratory conditions. Using radiolabeled DNA, we demonstrate that transformation is blocked at the stage of DNA uptake.}, }
@article {pmid22723256, year = {2012}, author = {Arduino, SM and Quiroga, MP and Ramírez, MS and Merkier, AK and Errecalde, L and Di Martino, A and Smayevsky, J and Kaufman, S and Centrón, D}, title = {Transposons and integrons in colistin-resistant clones of Klebsiella pneumoniae and Acinetobacter baumannii with epidemic or sporadic behaviour.}, journal = {Journal of medical microbiology}, volume = {61}, number = {Pt 10}, pages = {1417-1420}, doi = {10.1099/jmm.0.038968-0}, pmid = {22723256}, issn = {1473-5644}, mesh = {Acinetobacter Infections/epidemiology/*microbiology ; Acinetobacter baumannii/*drug effects/genetics/metabolism ; Anti-Bacterial Agents/pharmacology ; Argentina/epidemiology ; Colistin/pharmacology ; Cross Infection/epidemiology/*microbiology ; DNA Transposable Elements ; Drug Resistance, Bacterial ; Epidemics ; Gene Expression Regulation, Bacterial ; Hospitals ; Humans ; Integrons ; Klebsiella Infections/epidemiology/*microbiology ; Klebsiella pneumoniae/*drug effects/genetics/metabolism ; South America ; }, abstract = {Multiple transposons, integrons and carbapenemases were found in Klebsiella pneumoniae colistin-resistant isolates as well as a genomic resistance island of the AbaR type in Acinetobacter baumannii colistin-resistant isolates from different hospitals from Buenos Aires City. PFGE analysis showed a polyclonal dissemination of antimicrobial resistance mechanisms among K. pneumoniae isolates, while in A. baumannii isolates the epidemic clone 1 from South America was found. Resistance determinants associated with horizontal gene transfer are contributing to the evolution to pandrug resistance in both epidemic and sporadic clones.}, }
@article {pmid22722235, year = {2012}, author = {Mee, MT and Wang, HH}, title = {Engineering ecosystems and synthetic ecologies.}, journal = {Molecular bioSystems}, volume = {8}, number = {10}, pages = {2470-2483}, pmid = {22722235}, issn = {1742-2051}, support = {DP5 OD009172/OD/NIH HHS/United States ; 1DP5OD009172-01/OD/NIH HHS/United States ; }, mesh = {Bioengineering/*methods ; *Biofilms ; Computer Simulation ; Ecology ; *Ecosystem ; Gene Flow ; Gene Transfer, Horizontal ; Metabolic Networks and Pathways ; Microbial Consortia/*physiology ; Models, Biological ; Mutation ; Synthetic Biology/*methods ; }, abstract = {Microbial ecosystems play an important role in nature. Engineering these systems for industrial, medical, or biotechnological purposes are important pursuits for synthetic biologists and biological engineers moving forward. Here we provide a review of recent progress in engineering natural and synthetic microbial ecosystems. We highlight important forward engineering design principles, theoretical and quantitative models, new experimental and manipulation tools, and possible applications of microbial ecosystem engineering. We argue that simply engineering individual microbes will lead to fragile homogenous populations that are difficult to sustain, especially in highly heterogeneous and unpredictable environments. Instead, engineered microbial ecosystems are likely to be more robust and able to achieve complex tasks at the spatial and temporal resolution needed for truly programmable biology.}, }
@article {pmid22722012, year = {2012}, author = {Doi, Y and Adams-Haduch, JM and Peleg, AY and D'Agata, EM}, title = {The role of horizontal gene transfer in the dissemination of extended-spectrum beta-lactamase-producing Escherichia coli and Klebsiella pneumoniae isolates in an endemic setting.}, journal = {Diagnostic microbiology and infectious disease}, volume = {74}, number = {1}, pages = {34-38}, pmid = {22722012}, issn = {1879-0070}, support = {K22 AI080584/AI/NIAID NIH HHS/United States ; UL1 RR024153/RR/NCRR NIH HHS/United States ; UL1 TR000005/TR/NCATS NIH HHS/United States ; K22AI080584/AI/NIAID NIH HHS/United States ; }, mesh = {Aged, 80 and over ; Carrier State/microbiology ; Cluster Analysis ; Cohort Studies ; Electrophoresis, Gel, Pulsed-Field ; *Endemic Diseases ; Escherichia coli/*enzymology/genetics ; Escherichia coli Infections/*epidemiology/microbiology ; Feces/microbiology ; Female ; *Gene Transfer, Horizontal ; Genotype ; Health Facilities ; Humans ; Klebsiella Infections/*epidemiology/microbiology ; Klebsiella pneumoniae/*enzymology/genetics ; Long-Term Care ; Male ; Molecular Epidemiology ; Molecular Typing ; Plasmids ; beta-Lactamases/genetics/*metabolism ; }, abstract = {The contribution of horizontal gene transmission (HGT) in the emergence and spread of extended-spectrum beta-lactamase (ESBL)-producing Gram-negative bacteria during periods of endemicity is unclear. Over a 12-month period, rectal colonization with SHV-5- and SHV-12-producing Escherichia coli and Klebsiella pneumoniae was quantified among a cohort of residents in a long-term care facility. Demographic and clinical data were collected on colonized residents. Transferability of SHV-encoding plasmids and pulsed-field gel electrophoresis were performed to quantify the contribution of HGT and cross-transmission, respectively. A total of 25 (12%) of 214 enrolled patients were colonized with 11 SHV-5- and 17 SVH-12-producing E. coli and K. pneumoniae. Clonally related isolates were detected among multiple residents residing on the same and different wards. Among 12 clonally distinct isolates, HGT of SHV-5- and SHV-12-encoding plasmids was identified among 6 (50%) isolates. HGT among clonally distinct strains contributes to the transmission dynamics of these ESBL-producing Gram-negative bacteria and should be considered when evaluating the spread of these pathogens.}, }
@article {pmid22720044, year = {2012}, author = {De Ingeniis, J and Kazanov, MD and Shatalin, K and Gelfand, MS and Osterman, AL and Sorci, L}, title = {Glutamine versus ammonia utilization in the NAD synthetase family.}, journal = {PloS one}, volume = {7}, number = {6}, pages = {e39115}, pmid = {22720044}, issn = {1932-6203}, support = {R01 AI066244/AI/NIAID NIH HHS/United States ; AI066244/AI/NIAID NIH HHS/United States ; }, mesh = {Amide Synthases/*metabolism ; Ammonia/*metabolism ; Glutamine/*metabolism ; Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction ; Thermus thermophilus/genetics ; }, abstract = {NAD is a ubiquitous and essential metabolic redox cofactor which also functions as a substrate in certain regulatory pathways. The last step of NAD synthesis is the ATP-dependent amidation of deamido-NAD by NAD synthetase (NADS). Members of the NADS family are present in nearly all species across the three kingdoms of Life. In eukaryotic NADS, the core synthetase domain is fused with a nitrilase-like glutaminase domain supplying ammonia for the reaction. This two-domain NADS arrangement enabling the utilization of glutamine as nitrogen donor is also present in various bacterial lineages. However, many other bacterial members of NADS family do not contain a glutaminase domain, and they can utilize only ammonia (but not glutamine) in vitro. A single-domain NADS is also characteristic for nearly all Archaea, and its dependence on ammonia was demonstrated here for the representative enzyme from Methanocaldococcus jannaschi. However, a question about the actual in vivo nitrogen donor for single-domain members of the NADS family remained open: Is it glutamine hydrolyzed by a committed (but yet unknown) glutaminase subunit, as in most ATP-dependent amidotransferases, or free ammonia as in glutamine synthetase? Here we addressed this dilemma by combining evolutionary analysis of the NADS family with experimental characterization of two representative bacterial systems: a two-subunit NADS from Thermus thermophilus and a single-domain NADS from Salmonella typhimurium providing evidence that ammonia (and not glutamine) is the physiological substrate of a typical single-domain NADS. The latter represents the most likely ancestral form of NADS. The ability to utilize glutamine appears to have evolved via recruitment of a glutaminase subunit followed by domain fusion in an early branch of Bacteria. Further evolution of the NADS family included lineage-specific loss of one of the two alternative forms and horizontal gene transfer events. Lastly, we identified NADS structural elements associated with glutamine-utilizing capabilities.}, }
@article {pmid22717884, year = {2012}, author = {Thole, S and Kalhoefer, D and Voget, S and Berger, M and Engelhardt, T and Liesegang, H and Wollherr, A and Kjelleberg, S and Daniel, R and Simon, M and Thomas, T and Brinkhoff, T}, title = {Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life.}, journal = {The ISME journal}, volume = {6}, number = {12}, pages = {2229-2244}, pmid = {22717884}, issn = {1751-7370}, mesh = {Adaptation, Physiological ; Australia ; Bacterial Adhesion ; DNA, Bacterial/genetics ; *Genome, Bacterial ; Genomics ; Molecular Sequence Annotation ; Rhodobacteraceae/classification/*genetics/physiology ; Sequence Alignment ; Spain ; Synteny ; Tropolone/analogs &amp; derivatives/metabolism ; }, abstract = {Phaeobacter gallaeciensis, a member of the abundant marine Roseobacter clade, is known to be an effective colonizer of biotic and abiotic marine surfaces. Production of the antibiotic tropodithietic acid (TDA) makes P. gallaeciensis a strong antagonist of many bacteria, including fish and mollusc pathogens. In addition to TDA, several other secondary metabolites are produced, allowing the mutualistic bacterium to also act as an opportunistic pathogen. Here we provide the manually annotated genome sequences of the P. gallaeciensis strains DSM 17395 and 2.10, isolated at the Atlantic coast of north western Spain and near Sydney, Australia, respectively. Despite their isolation sites from the two different hemispheres, the genome comparison demonstrated a surprisingly high level of synteny (only 3% nucleotide dissimilarity and 88% and 93% shared genes). Minor differences in the genomes result from horizontal gene transfer and phage infection. Comparison of the P. gallaeciensis genomes with those of other roseobacters revealed unique genomic traits, including the production of iron-scavenging siderophores. Experiments supported the predicted capacity of both strains to grow on various algal osmolytes. Transposon mutagenesis was used to expand the current knowledge on the TDA biosynthesis pathway in strain DSM 17395. This first comparative genomic analysis of finished genomes of two closely related strains belonging to one species of the Roseobacter clade revealed features that provide competitive advantages and facilitate surface attachment and interaction with eukaryotic hosts.}, }
@article {pmid22716092, year = {2012}, author = {Liu, H and Fu, Y and Xie, J and Cheng, J and Ghabrial, SA and Li, G and Peng, Y and Yi, X and Jiang, D}, title = {Evolutionary genomics of mycovirus-related dsRNA viruses reveals cross-family horizontal gene transfer and evolution of diverse viral lineages.}, journal = {BMC evolutionary biology}, volume = {12}, number = {}, pages = {91}, pmid = {22716092}, issn = {1471-2148}, mesh = {Amino Acid Sequence ; Ascomycota/*virology ; Cloning, Molecular ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Viral ; Molecular Sequence Data ; *Phylogeny ; RNA Viruses/*classification/genetics/isolation &amp; purification ; RNA, Double-Stranded/genetics ; Sequence Analysis, RNA ; }, abstract = {BACKGROUND: Double-stranded (ds) RNA fungal viruses are typically isometric single-shelled particles that are classified into three families, Totiviridae, Partitiviridae and Chrysoviridae, the members of which possess monopartite, bipartite and quadripartite genomes, respectively. Recent findings revealed that mycovirus-related dsRNA viruses are more diverse than previously recognized. Although an increasing number of viral complete genomic sequences have become available, the evolution of these diverse dsRNA viruses remains to be clarified. This is particularly so since there is little evidence for horizontal gene transfer (HGT) among dsRNA viruses.<br><br>RESULTS: In this study, we report the molecular properties of two novel dsRNA mycoviruses that were isolated from a field strain of Sclerotinia sclerotiorum, Sunf-M: one is a large monopartite virus representing a distinct evolutionary lineage of dsRNA viruses; the other is a new member of the family Partitiviridae. Comprehensive phylogenetic analysis and genome comparison revealed that there are at least ten monopartite, three bipartite, one tripartite and three quadripartite lineages in the known dsRNA mycoviruses and that the multipartite lineages have possibly evolved from different monopartite dsRNA viruses. Moreover, we found that homologs of the S7 Domain, characteristic of members of the genus phytoreovirus in family Reoviridae are widely distributed in diverse dsRNA viral lineages, including chrysoviruses, endornaviruses and some unclassified dsRNA mycoviruses. We further provided evidence that multiple HGT events may have occurred among these dsRNA viruses from different families.<br><br>CONCLUSIONS: Our study provides an insight into the phylogeny and evolution of mycovirus-related dsRNA viruses and reveals that the occurrence of HGT between different virus species and the development of multipartite genomes during evolution are important macroevolutionary mechanisms in dsRNA viruses.}, }
@article {pmid22715894, year = {2012}, author = {Koonin, EV and Dolja, VV}, title = {Expanding networks of RNA virus evolution.}, journal = {BMC biology}, volume = {10}, number = {}, pages = {54}, pmid = {22715894}, issn = {1741-7007}, mesh = {*Evolution, Molecular ; Genome, Viral ; RNA Viruses/*genetics ; RNA, Viral/*genetics ; }, abstract = {In a recent BMC Evolutionary Biology article, Huiquan Liu and colleagues report two new genomes of double-stranded RNA (dsRNA) viruses from fungi and use these as a springboard to perform an extensive phylogenomic analysis of dsRNA viruses. The results support the old scenario of polyphyletic origin of dsRNA viruses from different groups of positive-strand RNA viruses and additionally reveal extensive horizontal gene transfer between diverse viruses consistent with the network-like rather than tree-like mode of viral evolution. Together with the unexpected discoveries of the first putative archaeal RNA virus and a RNA-DNA virus hybrid, this work shows that RNA viral genomics has major surprises to deliver.}, }
@article {pmid22713571, year = {2012}, author = {Kurre, R and Maier, B}, title = {Oxygen depletion triggers switching between discrete speed modes of gonococcal type IV pili.}, journal = {Biophysical journal}, volume = {102}, number = {11}, pages = {2556-2563}, pmid = {22713571}, issn = {1542-0086}, mesh = {Anaerobiosis/drug effects ; Fimbriae, Bacterial/*drug effects/*physiology ; Humans ; Models, Biological ; Movement/drug effects ; Neisseria gonorrhoeae/*drug effects/*physiology ; Oxygen/*pharmacology ; Oxygen Consumption/drug effects ; }, abstract = {Type IV pili are polymeric bacterial appendages that affect host cell interaction, motility, biofilm formation, and horizontal gene transfer. These force-generating motors work in at least three distinct velocity modes-elongation, and retraction at two distinct speeds, high and low. Yet it is unclear which regulatory inputs control their speeds. Here, we addressed this question for the human pathogen Neisseria gonorrhoeae. Using a combination of image analysis and surface analytics, we simultaneously monitored the speed of twitching motility and the concentration of oxygen. While oxygen was detectable, bacteria moved in the high-speed mode (1.5 μm/s). Upon full depletion of oxygen, gonococci simultaneously switched into the low-speed mode (0.5 μm/s). Speed switching was complete within seconds, independent of transcription, and reversible upon oxygen restoration. Using laser tweezers, we found that oxygen depletion triggered speed switching of the pilus motor at the single-molecule level. In the transition regime, single pili switched between both modes, indicating bistability. Switching is well described by a two-state model whereby the oxygen level controls the occupancy of the states.}, }
@article {pmid22712530, year = {2012}, author = {Sinha, A and Sommer, RJ and Dieterich, C}, title = {Divergent gene expression in the conserved dauer stage of the nematodes Pristionchus pacificus and Caenorhabditis elegans.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {254}, pmid = {22712530}, issn = {1471-2164}, mesh = {Animals ; Biological Evolution ; Caenorhabditis elegans/*genetics/growth &amp; development ; Cluster Analysis ; *Gene Expression Regulation ; Gene Transfer, Horizontal ; *Genes, Helminth ; Larva/genetics/metabolism ; Nematoda/*genetics/growth &amp; development ; Species Specificity ; Transcriptome/*genetics ; }, abstract = {BACKGROUND: An organism can respond to changing environmental conditions by adjusting gene regulation and by forming alternative phenotypes. In nematodes, these mechanisms are coupled because many species will form dauer larvae, a stress-resistant and non-aging developmental stage, when exposed to unfavorable environmental conditions, and execute gene expression programs that have been selected for the survival of the animal in the wild. These dauer larvae represent an environmentally induced, homologous developmental stage across many nematode species, sharing conserved morphological and physiological properties. Hence it can be expected that some core components of the associated transcriptional program would be conserved across species, while others might diverge over the course of evolution. However, transcriptional and metabolic analysis of dauer development has been largely restricted to Caenorhabditis elegans. Here, we use a transcriptomic approach to compare the dauer stage in the evolutionary model system Pristionchus pacificus with the dauer stage in C. elegans.<br><br>RESULTS: We have employed Agilent microarrays, which represent 20,446 P. pacificus and 20,143 C. elegans genes to show an unexpected divergence in the expression profiles of these two nematodes in dauer and dauer exit samples. P. pacificus and C. elegans differ in the dynamics and function of genes that are differentially expressed. We find that only a small number of orthologous gene pairs show similar expression pattern in the dauers of the two species, while the non-orthologous fraction of genes is a major contributor to the active transcriptome in dauers. Interestingly, many of the genes acquired by horizontal gene transfer and orphan genes in P. pacificus, are differentially expressed suggesting that these genes are of evolutionary and functional importance.<br><br>CONCLUSION: Our data set provides a catalog for future functional investigations and indicates novel insight into evolutionary mechanisms. We discuss the limited conservation of core developmental and transcriptional programs as a common aspect of animal evolution.}, }
@article {pmid22711282, year = {2012}, author = {Mulangi, V and Chibucos, MC and Phuntumart, V and Morris, PF}, title = {Kinetic and phylogenetic analysis of plant polyamine uptake transporters.}, journal = {Planta}, volume = {236}, number = {4}, pages = {1261-1273}, pmid = {22711282}, issn = {1432-2048}, mesh = {Arabidopsis/*genetics/metabolism ; Biological Transport ; Cation Transport Proteins/genetics/metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Complementation Test ; Kinetics ; Leishmania major/genetics/metabolism ; Membrane Transport Proteins/*genetics/metabolism ; Organ Specificity ; Oryza/*genetics/metabolism ; *Phylogeny ; Plant Proteins/genetics/metabolism ; Polyamines/*metabolism ; Protozoan Proteins/genetics/metabolism ; Putrescine/metabolism ; Saccharomyces cerevisiae/genetics/growth &amp; development/metabolism ; Spermidine/metabolism ; Substrate Specificity ; Time Factors ; Trypanosoma cruzi/genetics/metabolism ; }, abstract = {The rice gene Polyamine Uptake Transporter1 (PUT1) was originally identified based on its homology to the polyamine uptake transporters LmPOT1 and TcPAT12 in Leishmania major and Trypanosoma cruzi, respectively. Here we show that five additional transporters from rice and Arabidopsis that cluster in the same clade as PUT1 all function as high affinity spermidine uptake transporters. Yeast expression assays of these genes confirmed that uptake of spermidine was minimally affected by 166 fold or greater concentrations of amino acids. Characterized polyamine transporters from both Arabidopsis thaliana and Oryza sativa along with the two polyamine transporters from L. major and T. cruzi were aligned and used to generate a hidden Markov model. This model was used to identify significant matches to proteins in other angiosperms, bryophytes, chlorophyta, discicristates, excavates, stramenopiles and amoebozoa. No significant matches were identified in fungal or metazoan genomes. Phylogenic analysis showed that some sequences from the haptophyte, Emiliania huxleyi, as well as sequences from oomycetes and diatoms clustered closer to sequences from plant genomes than from a homologous sequence in the red algal genome Galdieria sulphuraria, consistent with the hypothesis that these polyamine transporters were acquired by horizontal transfer from green algae. Leishmania and Trypansosoma formed a separate cluster with genes from other Discicristates and two Entamoeba species. We surmise that the genes in Entamoeba species were acquired by phagotrophy of Discicristates. In summary, phylogenetic and functional analysis has identified two clades of genes that are predictive of polyamine transport activity.}, }
@article {pmid22710162, year = {2012}, author = {Wohlleben, W and Mast, Y and Muth, G and Röttgen, M and Stegmann, E and Weber, T}, title = {Synthetic biology of secondary metabolite biosynthesis in actinomycetes: Engineering precursor supply as a way to optimize antibiotic production.}, journal = {FEBS letters}, volume = {586}, number = {15}, pages = {2171-2176}, doi = {10.1016/j.febslet.2012.04.025}, pmid = {22710162}, issn = {1873-3468}, mesh = {Actinobacteria/genetics/*metabolism ; Anti-Bacterial Agents/*biosynthesis/chemistry ; Evolution, Molecular ; Gene Transfer, Horizontal ; Multigene Family/genetics ; Synthetic Biology/*methods ; }, abstract = {Actinomycetes are a rich source for the synthesis of medically and technically useful natural products. The genes encoding the enzymes for their biosynthesis are normally organized in gene clusters, which include also the information for resistance (in the case of antibacterial compounds), regulation, and transport. This facilitates the manipulation of such pathways by molecular genetic techniques. Recent advances in DNA sequencing and analytical chemistry revealed that not only new strains isolated from yet unexplored habitats, but also already known strains possess a large potential for the synthesis of novel compounds. Synthetic Biology now offers a new perspective to exploit this potential further by generating novel pathways, and thereby novel products, by combining different biosynthetic steps originating from different bacteria. The supply of precursors, which are subsequently incorporated into the final product, is often already organized in a modular manner in nature and may directly be exploited for Synthetic Biology. Here we report examples for the synthesis of building blocks and possibilities to modify and optimize antibiotic biosynthesis, exemplary for the synthesis of the manipulation of the synthesis of the glycopeptide antibiotic balhimycin.}, }
@article {pmid22710115, year = {2012}, author = {Palmieri, C and Magi, G and Mingoia, M and Bagnarelli, P and Ripa, S and Varaldo, PE and Facinelli, B}, title = {Characterization of a Streptococcus suis tet(O/W/32/O)-carrying element transferable to major streptococcal pathogens.}, journal = {Antimicrobial agents and chemotherapy}, volume = {56}, number = {9}, pages = {4697-4702}, pmid = {22710115}, issn = {1098-6596}, mesh = {Animals ; Bacterial Proteins/genetics ; Carrier Proteins/genetics ; *DNA, Bacterial ; *DNA, Circular ; Drug Resistance, Multiple, Bacterial/genetics ; Gene Transfer, Horizontal ; Genetic Loci ; Humans ; *Interspersed Repetitive Sequences ; Multigene Family ; Open Reading Frames ; Protein Isoforms/genetics ; Streptococcal Infections/microbiology/*veterinary ; Streptococcus/*genetics ; Streptococcus suis/*genetics/isolation &amp; purification ; Swine ; Swine Diseases/*microbiology ; }, abstract = {Mosaic tetracycline resistance determinants are a recently discovered class of hybrids of ribosomal protection tet genes. They may show different patterns of mosaicism, but their final size has remained unaltered. Initially thought to be confined to a small group of anaerobic bacteria, mosaic tet genes were then found to be widespread. In the genus Streptococcus, a mosaic tet gene [tet(O/W/32/O)] was first discovered in Streptococcus suis, an emerging drug-resistant pig and human pathogen. In this study, we report the molecular characterization of a tet(O/W/32/O) gene-carrying mobile element from an S. suis isolate. tet(O/W/32/O) was detected, in tandem with tet(40), in a circular 14,741-bp genetic element (39.1% G+C; 17 open reading frames [ORFs] identified). The novel element, which we designated 15K, also carried the macrolide resistance determinant erm(B) and an aminoglycoside resistance four-gene cluster including aadE (streptomycin) and aphA (kanamycin). 15K appeared to be an unstable genetic element that, in the absence of recombinases, is capable of undergoing spontaneous excision under standard growth conditions. In the integrated form, 15K was found inside a 54,879-bp integrative and conjugative element (ICE) (50.5% G+C; 55 ORFs), which we designated ICESsu32457. An ∼1.3-kb segment that apparently served as the att site for excision of the unstable 15K element was identified. The novel ICE was transferable at high frequency to recipients from pathogenic Streptococcus species (S. suis, Streptococcus pyogenes, Streptococcus pneumoniae, and Streptococcus agalactiae), suggesting that the multiresistance 15K element can successfully spread within streptococcal populations.}, }
@article {pmid22710114, year = {2012}, author = {Rieber, H and Frontzek, A and Pfeifer, Y}, title = {Emergence of metallo-β-lactamase GIM-1 in a clinical isolate of Serratia marcescens.}, journal = {Antimicrobial agents and chemotherapy}, volume = {56}, number = {9}, pages = {4945-4947}, pmid = {22710114}, issn = {1098-6596}, mesh = {Anti-Bacterial Agents/therapeutic use ; Bacteremia/complications/drug therapy/microbiology ; Cross Infection/complications/drug therapy/microbiology ; Gene Transfer, Horizontal ; Germany ; Humans ; Integrons/genetics ; Microbial Sensitivity Tests ; Middle Aged ; Pseudomonas aeruginosa/drug effects/*genetics ; Serratia Infections/complications/drug therapy/microbiology ; Serratia marcescens/drug effects/*genetics/isolation &amp; purification ; beta-Lactam Resistance/drug effects/*genetics ; beta-Lactamases/*genetics ; }, abstract = {The metallo-β-lactamase GIM-1 (German imipenemase) has been found so far only in clinical isolates of Pseudomonas aeruginosa from Germany. Here we report the detection of bla(GIM-1) in a clinical strain of Serratia marcescens that was isolated from urine, blood, and wound samples over a period of 20 months. The strain was repeatedly isolated from one patient in two German hospitals and an outpatient department located in the region in which all previously described GIM-1-producing P. aeruginosa strains were identified.}, }
@article {pmid22706053, year = {2012}, author = {Wei, H and Håvarstein, LS}, title = {Fratricide is essential for efficient gene transfer between pneumococci in biofilms.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {16}, pages = {5897-5905}, pmid = {22706053}, issn = {1098-5336}, mesh = {Amidohydrolases/*metabolism ; Bacterial Proteins/*metabolism ; Bacteriolysis ; Biofilms/*growth &amp; development ; *DNA Transformation Competence ; *Gene Transfer, Horizontal ; N-Acetylmuramoyl-L-alanine Amidase/metabolism ; Streptococcus pneumoniae/genetics/*physiology ; }, abstract = {Streptococcus pneumoniae and a number of commensal streptococcal species are competent for natural genetic transformation. The natural habitat of these bacteria is multispecies biofilms in the human oral cavity and nasopharynx. Studies investigating lateral transfer of virulence and antibiotic resistance determinants among streptococci have shown that interspecies as well as intraspecies gene exchange takes place in these environments. We have previously shown that the action of a competence-specific murein hydrolase termed CbpD strongly increases the rate of gene transfer between pneumococci grown in liquid cultures. CbpD is the key component of a bacteriolytic mechanism termed the fratricide mechanism. It is secreted by competent pneumococci and mediates the release of donor DNA from sensitive streptococci present in the same environment. However, in nature, gene exchange between streptococci takes place in biofilms and not in liquid cultures. In the present study, we therefore investigated whether CbpD affects the rate of gene transfer in laboratory-grown biofilms. Our results show that the fratricide mechanism has a strong positive impact on intrabiofilm gene exchange, indicating that it is important for active acquisition of homologous donor DNA under natural conditions. Furthermore, we found that competent biofilm cells of S. pneumoniae acquire a Nov(r) marker much more efficiently from neighboring cells than from the growth medium. Efficient lysis of target cells requires that CbpD act in conjunction with the murein hydrolase LytC. In contrast, the major autolysin LytA does not seem to be important for fratricide-mediated gene exchange in a biofilm environment.}, }
@article {pmid22705922, year = {2012}, author = {Hao, L and Liu, X and Wang, H and Lin, J and Pang, X and Lin, J}, title = {Detection and validation of a small broad-host-range plasmid pBBR1MCS-2 for use in genetic manipulation of the extremely acidophilic Acidithiobacillus sp.}, journal = {Journal of microbiological methods}, volume = {90}, number = {3}, pages = {309-314}, doi = {10.1016/j.mimet.2012.06.003}, pmid = {22705922}, issn = {1872-8359}, mesh = {Acidithiobacillus thiooxidans/drug effects/*genetics ; Anti-Bacterial Agents/pharmacology ; Cloning, Molecular ; Conjugation, Genetic ; Drug Resistance, Bacterial/genetics ; Escherichia coli/drug effects ; Gene Transfer, Horizontal ; Genes, Reporter ; Genetic Engineering ; Plasmids/*genetics ; Species Specificity ; Streptomycin/pharmacology ; }, abstract = {An efficient genetic system for introducing genes into biomining microorganisms is essential not only to experimentally determine the functions of genes predicted based on bioinformatic analysis, but also for their genetic breeding. In this study, a small broad-host-range vector named pBBR1MCS-2, which does not belong to the IncQ, IncW, or IncP groups, was studied for the feasibility of its use in conjugative gene transfer into extremely acidophilic strains of Acidithiobacillus. To do this, a recombinant plasmid pBBR-tac-Sm, a derivative of pBBR1MCS-2, was constructed and the streptomycin resistant gene (Sm(r)) was used as the reporter gene. Using conjugation, pBBR-tac-Sm was successfully transferred into three tested strains of Acidithiobacillus. Then we measured its transfer frequency, its stability in Acidithiobacillus cells, and the level of resistance to streptomycin of the transconjugants and compared this with the IncQ plasmid pJRD215 control. Our results indicate that pBBR1MCS-2 provides a new and useful tool in the genetic manipulation of Acidithiobacillus strains.}, }
@article {pmid22705839, year = {2012}, author = {Ikuma, K and Gunsch, CK}, title = {Genetic bioaugmentation as an effective method for in situ bioremediation: functionality of catabolic plasmids following conjugal transfers.}, journal = {Bioengineered}, volume = {3}, number = {4}, pages = {236-241}, pmid = {22705839}, issn = {2165-5987}, mesh = {Base Composition ; Biodegradation, Environmental ; Biotransformation ; Carbon/metabolism ; Conjugation, Genetic ; Escherichia coli/*genetics/metabolism ; *Gene Transfer, Horizontal ; Genetic Engineering ; Metagenome ; Microbial Consortia/genetics ; Phylogeny ; Plasmids/*genetics/metabolism ; Pseudomonas putida/*genetics/metabolism ; Serratia marcescens/*genetics/metabolism ; Soil Pollutants/*metabolism ; Toluene/*metabolism ; }, abstract = {Genetic bioaugmentation is an in situ bioremediation method that stimulates horizontal transfer of catabolic plasmids between exogenous donor cells and indigenous bacteria to increase the biodegradation potential of contaminants. A critical outcome of genetic bioaugmentation is the expression of an active catabolic phenotype upon plasmid conjugation. Using a pWW0-derivative TOL plasmid, we showed that certain genetic characteristics of the recipient bacteria, including genomic guanine-cytosine (G + C) content and phylogeny, may limit the expression of the transferred catabolic pathway. However, such genetic limitations observed in transconjugants could be overcome by the presence of an additional carbon source. Glucose and Luria-Bertani broth were shown to enhance the toluene degradation rates of transconjugants; these enhancement effects were dependent on transconjugant genomic G + C contents. Based on these observations, thorough genetic characterization of the indigenous microbial community in the contaminated environment of interest may provide a predictive tool for assessing the success of genetic bioaugmentation.}, }
@article {pmid22702893, year = {2012}, author = {Elhai, J and Liu, H and Taton, A}, title = {Detection of horizontal transfer of individual genes by anomalous oligomer frequencies.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {245}, pmid = {22702893}, issn = {1471-2164}, mesh = {Base Composition ; Bayes Theorem ; Cyanobacteria/classification/*genetics ; Gene Frequency ; Gene Transfer, Horizontal/*genetics ; *Genome, Bacterial ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Understanding the history of life requires that we understand the transfer of genetic material across phylogenetic boundaries. Detecting genes that were acquired by means other than vertical descent is a basic step in that process. Detection by discordant phylogenies is computationally expensive and not always definitive. Many have used easily computed compositional features as an alternative procedure. However, different compositional methods produce different predictions, and the effectiveness of any method is not well established.<br><br>RESULTS: The ability of octamer frequency comparisons to detect genes artificially seeded in cyanobacterial genomes was markedly increased by using as a training set those genes that are highly conserved over all bacteria. Using a subset of octamer frequencies in such tests also increased effectiveness, but this depended on the specific target genome and the source of the contaminating genes. The presence of high frequency octamers and the GC content of the contaminating genes were important considerations. A method comprising best practices from these tests was devised, the Core Gene Similarity (CGS) method, and it performed better than simple octamer frequency analysis, codon bias, or GC contrasts in detecting seeded genes or naturally occurring transposons. From a comparison of predictions with phylogenetic trees, it appears that the effectiveness of the method is confined to horizontal transfer events that have occurred recently in evolutionary time.<br><br>CONCLUSIONS: The CGS method may be an improvement over existing surrogate methods to detect genes of foreign origin.}, }
@article {pmid22701585, year = {2012}, author = {Ghosh, N and McKillop, TJ and Jowitt, TA and Howard, M and Davies, H and Holmes, DF and Roberts, IS and Bella, J}, title = {Collagen-like proteins in pathogenic E. coli strains.}, journal = {PloS one}, volume = {7}, number = {6}, pages = {e37872}, pmid = {22701585}, issn = {1932-6203}, support = {BB/E527355/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Base Sequence ; Cloning, Molecular ; Collagen/genetics/*metabolism ; Escherichia coli O157/genetics/*metabolism/pathogenicity ; Microscopy, Electron, Scanning ; Molecular Sequence Data ; Open Reading Frames/genetics ; Prophages/*genetics ; *Protein Conformation ; Protein Structure, Tertiary ; Recombinant Proteins/*chemistry/ultrastructure ; Sequence Analysis, DNA ; Shiga Toxins/genetics ; Species Specificity ; Ultracentrifugation ; Virulence ; }, abstract = {The genome sequences of enterohaemorrhagic E. coli O157:H7 strains show multiple open-reading frames with collagen-like sequences that are absent from the common laboratory strain K-12. These putative collagens are included in prophages embedded in O157:H7 genomes. These prophages carry numerous genes related to strain virulence and have been shown to be inducible and capable of disseminating virulence factors by horizontal gene transfer. We have cloned two collagen-like proteins from E. coli O157:H7 into a laboratory strain and analysed the structure and conformation of the recombinant proteins and several of their constituting domains by a variety of spectroscopic, biophysical, and electron microscopy techniques. We show that these molecules exhibit many of the characteristics of vertebrate collagens, including trimer formation and the presence of a collagen triple helical domain. They also contain a C-terminal trimerization domain, and a trimeric α-helical coiled-coil domain with an unusual amino acid sequence almost completely lacking leucine, valine or isoleucine residues. Intriguingly, these molecules show high thermal stability, with the collagen domain being more stable than those of vertebrate fibrillar collagens, which are much longer and post-translationally modified. Under the electron microscope, collagen-like proteins from E. coli O157:H7 show a dumbbell shape, with two globular domains joined by a hinged stalk. This morphology is consistent with their likely role as trimeric phage side-tail proteins that participate in the attachment of phage particles to E. coli target cells, either directly or through assembly with other phage tail proteins. Thus, collagen-like proteins in enterohaemorrhagic E. coli genomes may have a direct role in the dissemination of virulence-related genes through infection of harmless strains by induced bacteriophages.}, }
@article {pmid22699508, year = {2012}, author = {Fan, L and Reynolds, D and Liu, M and Stark, M and Kjelleberg, S and Webster, NS and Thomas, T}, title = {Functional equivalence and evolutionary convergence in complex communities of microbial sponge symbionts.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {27}, pages = {E1878-87}, pmid = {22699508}, issn = {1091-6490}, mesh = {Animals ; Archaea/classification/*genetics ; Bacteria/*classification/genetics ; Bacteriophages/classification/genetics ; *Biological Evolution ; Cyanobacteria/classification/genetics ; *Ecosystem ; Genetic Variation ; Metagenome/physiology ; Metagenomics/*methods ; Nitrogen/metabolism ; Phylogeny ; Porifera/metabolism/*microbiology ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Symbiosis/physiology ; }, abstract = {Microorganisms often form symbiotic relationships with eukaryotes, and the complexity of these relationships can range from those with one single dominant symbiont to associations with hundreds of symbiont species. Microbial symbionts occupying equivalent niches in different eukaryotic hosts may share functional aspects, and convergent genome evolution has been reported for simple symbiont systems in insects. However, for complex symbiont communities, it is largely unknown how prevalent functional equivalence is and whether equivalent functions are conducted by evolutionarily convergent mechanisms. Sponges represent an evolutionarily divergent group of species with common physiological and ecological traits. They also host complex communities of microbial symbionts and thus are the ideal model to test whether functional equivalence and evolutionary convergence exist in complex symbiont communities across phylogenetically divergent hosts. Here we use a sampling design to determine the phylogenetic and functional profiles of microbial communities associated with six sponge species. We identify common functions in the six microbiomes, demonstrating the existence of functional equivalence. These core functions are consistent with our current understanding of the biological and ecological roles of sponge-associated microorganisms and also provide insight into symbiont functions. Importantly, core functions also are provided in each sponge species by analogous enzymes and biosynthetic pathways. Moreover, the abundance of elements involved in horizontal gene transfer suggests their key roles in the genomic evolution of symbionts. Our data thus demonstrate evolutionary convergence in complex symbiont communities and reveal the details and mechanisms that underpin the process.}, }
@article {pmid22697236, year = {2012}, author = {Bayzid, MS and Warnow, T}, title = {Estimating optimal species trees from incomplete gene trees under deep coalescence.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {19}, number = {6}, pages = {591-605}, doi = {10.1089/cmb.2012.0037}, pmid = {22697236}, issn = {1557-8666}, mesh = {*Algorithms ; Computer Simulation ; Gene Duplication ; Gene Transfer, Horizontal ; Genetic Speciation ; *Models, Genetic ; *Phylogeny ; Sequence Alignment ; }, abstract = {The estimation of species trees typically involves the estimation of trees and alignments on many different genes, so that the species tree can be based on many different parts of the genome. This kind of phylogenomic approach to species tree estimation has the potential to produce more accurate species tree estimates, especially when gene trees can differ from the species tree due to processes such as incomplete lineage sorting (ILS), gene duplication and loss, and horizontal gene transfer. Because ILS (also called "deep coalescence") is a frequent problem in systematics, many methods have been developed to estimate species trees from gene trees or alignments that specifically take ILS into consideration. In this paper we consider the problem of estimating species trees from gene trees and alignments for the general case where the gene trees and alignments can be incomplete, which means that not all the genes contain sequences for all the species. We formalize optimization problems for this context and prove theoretical results for these problems. We also present the results of a simulation study evaluating existing methods for estimating species trees from incomplete gene trees. Our simulation study shows that *BEAST, a statistical method for estimating species trees from gene sequence alignments, produces by far the most accurate species trees. However, *BEAST can only be run on small datasets. The second most accurate method, MRP (a standard supertree method), can analyze very large datasets and produces very good trees, making MRP a potentially acceptable alternative to *BEAST for large datasets.}, }
@article {pmid22694720, year = {2012}, author = {Andam, CP and Harlow, TJ and Papke, RT and Gogarten, JP}, title = {Ancient origin of the divergent forms of leucyl-tRNA synthetases in the Halobacteriales.}, journal = {BMC evolutionary biology}, volume = {12}, number = {}, pages = {85}, pmid = {22694720}, issn = {1471-2148}, mesh = {Archaeal Proteins/genetics ; DNA, Archaeal/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Archaeal ; Halobacteriales/*classification/enzymology/genetics ; Leucine-tRNA Ligase/*genetics ; Likelihood Functions ; Multilocus Sequence Typing ; *Phylogeny ; RNA, Transfer, Leu/genetics ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT) has greatly impacted the genealogical history of many lineages, particularly for prokaryotes, with genes frequently moving in and out of a line of descent. Many genes that were acquired by a lineage in the past likely originated from ancestral relatives that have since gone extinct. During the course of evolution, HGT has played an essential role in the origin and dissemination of genetic and metabolic novelty.<br><br>RESULTS: Three divergent forms of leucyl-tRNA synthetase (LeuRS) exist in the archaeal order Halobacteriales, commonly known as haloarchaea. Few haloarchaeal genomes have the typical archaeal form of this enzyme and phylogenetic analysis indicates it clusters within the Euryarchaeota as expected. The majority of sequenced halobacterial genomes possess a bacterial form of LeuRS. Phylogenetic reconstruction puts this larger group of haloarchaea at the base of the bacterial domain. The most parsimonious explanation is that an ancient transfer of LeuRS took place from an organism related to the ancestor of the bacterial domain to the haloarchaea. The bacterial form of LeuRS further underwent gene duplications and/or gene transfers within the haloarchaea, with some genomes possessing two distinct types of bacterial LeuRS. The cognate tRNALeu also reveals two distinct clusters for the haloarchaea; however, these tRNALeu clusters do not coincide with the groupings found in the LeuRS tree, revealing that LeuRS evolved independently of its cognate tRNA.<br><br>CONCLUSIONS: The study of leucyl-tRNA synthetase in haloarchaea illustrates the importance of gene transfer originating in lineages that went extinct since the transfer occurred. The haloarchaeal LeuRS and tRNALeu did not co-evolve.}, }
@article {pmid22693604, year = {2012}, author = {Qi, J and Guo, A and Cui, P and Chen, Y and Mustafa, R and Ba, X and Hu, C and Bai, Z and Chen, X and Shi, L and Chen, H}, title = {Comparative geno-plasticity analysis of Mycoplasma bovis HB0801 (Chinese isolate).}, journal = {PloS one}, volume = {7}, number = {5}, pages = {e38239}, pmid = {22693604}, issn = {1932-6203}, mesh = {Animals ; Antigens, Bacterial/genetics ; Bacterial Outer Membrane Proteins/genetics ; Base Sequence ; Cattle ; China ; Chromosome Inversion/genetics ; Gene Transfer, Horizontal/genetics ; Genome Components/genetics ; Genome, Bacterial/*genetics ; Genomics ; Multigene Family/genetics ; Mycoplasma bovis/*genetics/isolation &amp; purification/pathogenicity ; Species Specificity ; }, abstract = {Mycoplasma bovis pneumonia in cattle has been epidemic in China since 2008. To investigate M. bovis pathogenesis, we completed genome sequencing of strain HB0801 isolated from a lesioned bovine lung from Hubei, China. The genomic plasticity was determined by comparing HB0801 with M. bovis strain ATCC® 25523™/PG45 from cow mastitis milk, Chinese strain Hubei-1 from lesioned lung tissue, and 16 other Mycoplasmas species. Compared to PG45, the genome size of HB0801 was reduced by 11.7 kb. Furthermore, a large chromosome inversion (580 kb) was confirmed in all Chinese isolates including HB0801, HB1007, a strain from cow mastitis milk, and Hubei-1. In addition, the variable surface lipoproteins (vsp) gene cluster existed in HB0801, but contained less than half of the genes, and had poor identity to that in PG45, but they had conserved structures. Further inter-strain comparisons revealed other mechanisms of gene acquisition and loss in HB0801 that primarily involved insertion sequence (IS) elements, integrative conjugative element, restriction and modification systems, and some lipoproteins and transmembrane proteins. Subsequently, PG45 and HB0801 virulence in cattle was compared. Results indicated that both strains were pathogenic to cattle. The scores of gross pathological assessment for the control group, and the PG45- and HB0801-infected groups were 3, 13 and 9, respectively. Meanwhile the scores of lung lesion for these three groups were 36, 70, and 69, respectively. In addition, immunohistochemistry detection demonstrated that both strains were similarly distributed in lungs and lymph nodes. Although PG45 showed slightly higher virulence in calves than HB0801, there was no statistical difference between the strains (P>0.05). Compared to Hubei-1, a total of 122 SNP loci were disclosed in HB0801. In conclusion, although genomic plasticity was thought to be an evolutionary advantage, it did not apparently affect virulence of M. bovis strains in cattle.}, }
@article {pmid22691391, year = {2012}, author = {Lopez, CA and Winter, SE and Rivera-Chávez, F and Xavier, MN and Poon, V and Nuccio, SP and Tsolis, RM and Bäumler, AJ}, title = {Phage-mediated acquisition of a type III secreted effector protein boosts growth of salmonella by nitrate respiration.}, journal = {mBio}, volume = {3}, number = {3}, pages = {}, pmid = {22691391}, issn = {2150-7511}, support = {T32 AI060555/AI/NIAID NIH HHS/United States ; R21 AI088122/AI/NIAID NIH HHS/United States ; AI096528/AI/NIAID NIH HHS/United States ; AI060555/AI/NIAID NIH HHS/United States ; AI088122/AI/NIAID NIH HHS/United States ; R01 AI096528/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacterial Proteins/genetics/*metabolism ; Cattle ; Colitis/microbiology/pathology ; Disease Models, Animal ; Feces/microbiology ; Gastrointestinal Tract/microbiology/pathology ; *Gene Transfer, Horizontal ; Mice ; Mice, Inbred C57BL ; Mice, Inbred CBA ; Nitrates/*metabolism ; Oxidation-Reduction ; Salmonella Infections, Animal/microbiology/pathology ; Salmonella Phages/*genetics ; Salmonella typhimurium/growth &amp; development/metabolism/*pathogenicity/*virology ; Transduction, Genetic ; Virulence Factors/genetics/*metabolism ; }, abstract = {Information on how emerging pathogens can invade and persist and spread within host populations remains sparse. In the 1980s, a multidrug-resistant Salmonella enterica serotype Typhimurium clone lysogenized by a bacteriophage carrying the sopE virulence gene caused an epidemic among cattle and humans in Europe. Here we show that phage-mediated horizontal transfer of the sopE gene enhances the production of host-derived nitrate, an energetically highly valuable electron acceptor, in a mouse colitis model. In turn, nitrate fuels a bloom of S. Typhimurium in the gut lumen through anaerobic nitrate respiration while suppressing genes for the utilization of energetically inferior electron acceptors such as tetrathionate. Through this mechanism, horizontal transfer of sopE can enhance the fitness of S. Typhimurium, resulting in its significantly increased abundance in the feces. IMPORTANCE During gastroenteritis, Salmonella enterica serotype Typhimurium can use tetrathionate respiration to edge out competing microbes in the gut lumen. However, the concept that tetrathionate respiration confers a growth benefit in the inflamed gut is not broadly applicable to other host-pathogen combinations because tetrathionate respiration is a signature trait used to differentiate Salmonella serotypes from most other members of the family Enterobacteriaceae. Here we show that by acquiring the phage-carried sopE gene, S. Typhimurium can drive the host to generate an additional respiratory electron acceptor, nitrate. Nitrate suppresses genes for the utilization of energetically inferior electron acceptors such as tetrathionate while enhancing the luminal growth of S. Typhimurium through anaerobic nitrate respiration. Pathways for anaerobic nitrate respiration are widely conserved among members of the family Enterobacteriaceae, thereby making our observations relevant to other enteric pathogens whose relative abundance in the intestinal lumen increases during infection.}, }
@article {pmid22691167, year = {2012}, author = {McCarthy, AJ and Lindsay, JA}, title = {The distribution of plasmids that carry virulence and resistance genes in Staphylococcus aureus is lineage associated.}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {104}, pmid = {22691167}, issn = {1471-2180}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Cluster Analysis ; Computational Biology ; DNA Restriction-Modification Enzymes ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Microarray Analysis ; Plasmids/*analysis/classification ; Staphylococcal Infections/microbiology/veterinary ; Staphylococcus aureus/classification/*drug effects/genetics/*pathogenicity ; Virulence Factors/*genetics ; }, abstract = {BACKGROUND: Staphylococcus aureus is major human and animal pathogen. Plasmids often carry resistance genes and virulence genes that can disseminate through S. aureus populations by horizontal gene transfer (HGT) mechanisms. Sequences of S. aureus plasmids in the public domain and data from multi-strain microarrays were analysed to investigate (i) the distribution of resistance genes and virulence genes on S. aureus plasmids, and (ii) the distribution of plasmids between S. aureus lineages.<br><br>RESULTS: A total of 21 plasmid rep gene families, of which 13 were novel to this study, were characterised using a previously proposed classification system. 243 sequenced plasmids were assigned to 39 plasmid groups that each possessed a unique combination of rep genes. We show some resistance genes (including ermC and cat) and virulence genes (including entA, entG, entJ, entP) were associated with specific plasmid groups suggesting there are genetic pressures preventing recombination of these genes into novel plasmid groups. Whole genome microarray analysis revealed that plasmid rep, resistance and virulence genes were associated with S. aureus lineages, suggesting restriction-modification (RM) barriers to HGT of plasmids between strains exist. Conjugation transfer (tra) complex genes were rare.<br><br>CONCLUSION: This study argues that genetic pressures are restraining the spread of resistance and virulence genes amongst S. aureus plasmids, and amongst S. aureus populations, delaying the emergence of fully virulent and resistant strains.}, }
@article {pmid22690978, year = {2012}, author = {Ni, T and Yue, J and Sun, G and Zou, Y and Wen, J and Huang, J}, title = {Ancient gene transfer from algae to animals: mechanisms and evolutionary significance.}, journal = {BMC evolutionary biology}, volume = {12}, number = {}, pages = {83}, pmid = {22690978}, issn = {1471-2148}, mesh = {Animals ; Choanoflagellata/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Multigene Family ; Phylogeny ; Plants/*genetics ; Plastids/genetics ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT) is traditionally considered to be rare in multicellular eukaryotes such as animals. Recently, many genes of miscellaneous algal origins were discovered in choanoflagellates. Considering that choanoflagellates are the existing closest relatives of animals, we speculated that ancient HGT might have occurred in the unicellular ancestor of animals and affected the long-term evolution of animals.<br><br>RESULTS: Through genome screening, phylogenetic and domain analyses, we identified 14 gene families, including 92 genes, in the tunicate Ciona intestinalis that are likely derived from miscellaneous photosynthetic eukaryotes. Almost all of these gene families are distributed in diverse animals, suggesting that they were mostly acquired by the common ancestor of animals. Their miscellaneous origins also suggest that these genes are not derived from a particular algal endosymbiont. In addition, most genes identified in our analyses are functionally related to molecule transport, cellular regulation and methylation signaling, suggesting that the acquisition of these genes might have facilitated the intercellular communication in the ancestral animal.<br><br>CONCLUSIONS: Our findings provide additional evidence that algal genes in aplastidic eukaryotes are not exclusively derived from historical plastids and thus important for interpreting the evolution of eukaryotic photosynthesis. Most importantly, our data represent the first evidence that more anciently acquired genes might exist in animals and that ancient HGT events have played an important role in animal evolution.}, }
@article {pmid22689773, year = {2012}, author = {Bansal, MS and Alm, EJ and Kellis, M}, title = {Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss.}, journal = {Bioinformatics (Oxford, England)}, volume = {28}, number = {12}, pages = {i283-91}, pmid = {22689773}, issn = {1367-4811}, support = {R01 HG004037/HG/NHGRI NIH HHS/United States ; RC2 HG005639/HG/NHGRI NIH HHS/United States ; }, mesh = {*Algorithms ; *Evolution, Molecular ; Gene Deletion ; *Gene Duplication ; *Gene Transfer, Horizontal ; Genomics ; Multigene Family ; Phylogeny ; Software ; }, abstract = {MOTIVATION: Gene family evolution is driven by evolutionary events such as speciation, gene duplication, horizontal gene transfer and gene loss, and inferring these events in the evolutionary history of a given gene family is a fundamental problem in comparative and evolutionary genomics with numerous important applications. Solving this problem requires the use of a reconciliation framework, where the input consists of a gene family phylogeny and the corresponding species phylogeny, and the goal is to reconcile the two by postulating speciation, gene duplication, horizontal gene transfer and gene loss events. This reconciliation problem is referred to as duplication-transfer-loss (DTL) reconciliation and has been extensively studied in the literature. Yet, even the fastest existing algorithms for DTL reconciliation are too slow for reconciling large gene families and for use in more sophisticated applications such as gene tree or species tree reconstruction.<br><br>RESULTS: We present two new algorithms for the DTL reconciliation problem that are dramatically faster than existing algorithms, both asymptotically and in practice. We also extend the standard DTL reconciliation model by considering distance-dependent transfer costs, which allow for more accurate reconciliation and give an efficient algorithm for DTL reconciliation under this extended model. We implemented our new algorithms and demonstrated up to 100 000-fold speed-up over existing methods, using both simulated and biological datasets. This dramatic improvement makes it possible to use DTL reconciliation for performing rigorous evolutionary analyses of large gene families and enables its use in advanced reconciliation-based gene and species tree reconstruction methods.<br><br>AVAILABILITY: Our programs can be freely downloaded from http://compbio.mit.edu/ranger-dtl/.}, }
@article {pmid22689374, year = {2012}, author = {Kovacevic, G}, title = {Value of the Hydra model system for studying symbiosis.}, journal = {The International journal of developmental biology}, volume = {56}, number = {6-8}, pages = {627-635}, doi = {10.1387/ijdb.123510gk}, pmid = {22689374}, issn = {1696-3547}, mesh = {Animals ; Chlorella/*physiology ; Chlorophyta/physiology ; Hydra/anatomy &amp; histology/*physiology ; *Symbiosis ; }, abstract = {Green Hydra is used as a classical example for explaining symbiosis in schools as well as an excellent research model. Indeed the cosmopolitan green Hydra (Hydra viridissima) provides a potent experimental framework to investigate the symbiotic relationships between a complex eumetazoan organism and a unicellular photoautotrophic green algae named Chlorella. Chlorella populates a single somatic cell type, the gastrodermal myoepithelial cells (also named digestive cells) and the oocyte at the time of sexual reproduction. This symbiotic relationship is stable, well-determined and provides biological advantages to the algal symbionts, but also to green Hydra over the related non-symbiotic Hydra i.e. brown hydra. These advantages likely result from the bidirectional flow of metabolites between the host and the symbiont. Moreover genetic flow through horizontal gene transfer might also participate in the establishment of these selective advantages. However, these relationships between the host and the symbionts may be more complex. Thus, Jolley and Smith showed that the reproductive rate of the algae increases dramatically outside of Hydra cells, although this endosymbiont isolation is debated. Recently it became possible to keep different species of endosymbionts isolated from green Hydra in stable and permanent cultures and compare them to free-living Chlorella species. Future studies testing metabolic relationships and genetic flow should help elucidate the mechanisms that support the maintenance of symbiosis in a eumetazoan species.}, }
@article {pmid22685606, year = {2012}, author = {Béven, L and Charenton, C and Dautant, A and Bouyssou, G and Labroussaa, F and Sköllermo, A and Persson, A and Blanchard, A and Sirand-Pugnet, P}, title = {Specific evolution of F1-like ATPases in mycoplasmas.}, journal = {PloS one}, volume = {7}, number = {6}, pages = {e38793}, pmid = {22685606}, issn = {1932-6203}, mesh = {Adenosine Triphosphatases/chemistry/*genetics/metabolism ; Adenosine Triphosphate/metabolism ; Animals ; Bacterial Proteins/chemistry/*genetics/metabolism ; Biocatalysis ; *Evolution, Molecular ; Gene Dosage ; Gene Transfer, Horizontal ; Genome, Bacterial/genetics ; Humans ; Immunoblotting ; Models, Molecular ; Multigene Family/genetics ; Mycoplasma/classification/enzymology/*genetics ; Mycoplasma Infections/microbiology ; Mycoplasma mycoides/enzymology/genetics ; Phylogeny ; Protein Structure, Secondary ; Protein Subunits/chemistry/genetics/metabolism ; Substrate Specificity ; }, abstract = {F(1)F(0) ATPases have been identified in most bacteria, including mycoplasmas which have very small genomes associated with a host-dependent lifestyle. In addition to the typical operon of eight genes encoding genuine F(1)F(0) ATPase (Type 1), we identified related clusters of seven genes in many mycoplasma species. Four of the encoded proteins have predicted structures similar to the α, β, γ and ε subunits of F(1) ATPases and could form an F(1)-like ATPase. The other three proteins display no similarity to any other known proteins. Two of these proteins are probably located in the membrane, as they have three and twelve predicted transmembrane helices. Phylogenomic studies identified two types of F(1)-like ATPase clusters, Type 2 and Type 3, characterized by a rapid evolution of sequences with the conservation of structural features. Clusters encoding Type 2 and Type 3 ATPases were assumed to originate from the Hominis group of mycoplasmas. We suggest that Type 3 ATPase clusters may spread to other phylogenetic groups by horizontal gene transfer between mycoplasmas in the same host, based on phylogeny and genomic context. Functional analyses in the ruminant pathogen Mycoplasma mycoides subsp. mycoides showed that the Type 3 cluster genes were organized into an operon. Proteomic analyses demonstrated that the seven encoded proteins were produced during growth in axenic media. Mutagenesis and complementation studies demonstrated an association of the Type 3 cluster with a major ATPase activity of membrane fractions. Thus, despite their tendency toward genome reduction, mycoplasmas have evolved and exchanged specific F(1)-like ATPases with no known equivalent in other bacteria. We propose a model, in which the F(1)-like structure is associated with a hypothetical X(0) sector located in the membrane of mycoplasma cells.}, }
@article {pmid22685400, year = {2012}, author = {Kisiela, DI and Chattopadhyay, S and Libby, SJ and Karlinsey, JE and Fang, FC and Tchesnokova, V and Kramer, JJ and Beskhlebnaya, V and Samadpour, M and Grzymajlo, K and Ugorski, M and Lankau, EW and Mackie, RI and Clegg, S and Sokurenko, EV}, title = {Evolution of Salmonella enterica virulence via point mutations in the fimbrial adhesin.}, journal = {PLoS pathogens}, volume = {8}, number = {6}, pages = {e1002733}, pmid = {22685400}, issn = {1553-7374}, support = {R01 GM084318/GM/NIGMS NIH HHS/United States ; R21 AI091966/AI/NIAID NIH HHS/United States ; R21 AI91966-02/AI/NIAID NIH HHS/United States ; }, mesh = {Adhesins, Bacterial/*genetics ; Amino Acid Sequence ; Animals ; Base Sequence ; Biological Evolution ; Gene Knockout Techniques ; Humans ; Macrophages/microbiology ; Mice ; Mice, Inbred BALB C ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; *Phylogeny ; *Point Mutation ; Salmonella Infections/*genetics ; Salmonella enterica/*genetics/*pathogenicity ; Virulence/genetics ; }, abstract = {Whereas the majority of pathogenic Salmonella serovars are capable of infecting many different animal species, typically producing a self-limited gastroenteritis, serovars with narrow host-specificity exhibit increased virulence and their infections frequently result in fatal systemic diseases. In our study, a genetic and functional analysis of the mannose-specific type 1 fimbrial adhesin FimH from a variety of serovars of Salmonella enterica revealed that specific mutant variants of FimH are common in host-adapted (systemically invasive) serovars. We have found that while the low-binding shear-dependent phenotype of the adhesin is preserved in broad host-range (usually systemically non-invasive) Salmonella, the majority of host-adapted serovars express FimH variants with one of two alternative phenotypes: a significantly increased binding to mannose (as in S. Typhi, S. Paratyphi C, S. Dublin and some isolates of S. Choleraesuis), or complete loss of the mannose-binding activity (as in S. Paratyphi B, S. Choleraesuis and S. Gallinarum). The functional diversification of FimH in host-adapted Salmonella results from recently acquired structural mutations. Many of the mutations are of a convergent nature indicative of strong positive selection. The high-binding phenotype of FimH that leads to increased bacterial adhesiveness to and invasiveness of epithelial cells and macrophages usually precedes acquisition of the non-binding phenotype. Collectively these observations suggest that activation or inactivation of mannose-specific adhesive properties in different systemically invasive serovars of Salmonella reflects their dynamic trajectories of adaptation to a life style in specific hosts. In conclusion, our study demonstrates that point mutations are the target of positive selection and, in addition to horizontal gene transfer and genome degradation events, can contribute to the differential pathoadaptive evolution of Salmonella.}, }
@article {pmid22685277, year = {2012}, author = {Ohtsubo, Y and Ishibashi, Y and Naganawa, H and Hirokawa, S and Atobe, S and Nagata, Y and Tsuda, M}, title = {Conjugal transfer of polychlorinated biphenyl/biphenyl degradation genes in Acidovorax sp. strain KKS102, which are located on an integrative and conjugative element.}, journal = {Journal of bacteriology}, volume = {194}, number = {16}, pages = {4237-4248}, pmid = {22685277}, issn = {1098-5530}, mesh = {Biotransformation ; Comamonadaceae/*genetics/*metabolism ; *Conjugation, Genetic ; *Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences ; Metabolic Networks and Pathways/*genetics ; Multigene Family ; Polychlorinated Biphenyls/*metabolism ; Real-Time Polymerase Chain Reaction ; Sequence Homology ; }, abstract = {A polychlorinated biphenyl (PCB)/biphenyl degradation gene cluster in Acidovorax sp. strain KKS102, which is very similar to that in Tn4371 from Cupriavidus oxalaticus A5, was transferred to several proteobacterial strains by conjugation. The mobilized DNA fragment consisted of 61,807 bp and carried genes for mating-pair formation (mpf), DNA transfer (dtr), integrase (int), and replication-partition proteins (rep-parAB). In the transconjugants, transferred DNA was integrated at ATTGCATCAG or similar sequences. The circular-form integrative and conjugative element (ICE) was detected by PCR, and quantitative PCR analyses revealed that, in KKS102 cells, the ratio of the circular form to the integrated form was very low (approximately 10(-5)). The circular form was not detected in a mutant of the int gene, which was located at the extreme left and transcribed in the inward direction, and the level of int transcriptional activity was much higher in the circular form than in the integrated form. These findings clearly demonstrated that the genes for PCB/biphenyl degradation in KKS102 cells are located on an ICE, which was named ICE(KKS102)4677. Comparisons of similar ICE-like elements collected from the public database suggested that those of beta- and gammaproteobacteria were distinguishable from other ICE-like elements, including those in alphaproteobacteria, with respect to the gene composition and gene organization.}, }
@article {pmid22683880, year = {2012}, author = {Lang, AS and Zhaxybayeva, O and Beatty, JT}, title = {Gene transfer agents: phage-like elements of genetic exchange.}, journal = {Nature reviews. Microbiology}, volume = {10}, number = {7}, pages = {472-482}, pmid = {22683880}, issn = {1740-1534}, support = {93779-1//Canadian Institutes of Health Research/Canada ; }, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Bacteriophages/genetics ; Biological Evolution ; *Gene Transfer, Horizontal ; }, abstract = {Horizontal gene transfer is important in the evolution of bacterial and archaeal genomes. An interesting genetic exchange process is carried out by diverse phage-like gene transfer agents (GTAs) that are found in a wide range of prokaryotes. Although GTAs resemble phages, they lack the hallmark capabilities that define typical phages, and they package random pieces of the producing cell's genome. In this Review, we discuss the defining characteristics of the GTAs that have been identified to date, along with potential functions for these agents and the possible evolutionary forces that act on the genes involved in their production.}, }
@article {pmid22683366, year = {2012}, author = {Das, D and Das, D and Prasad, A}, title = {Giant number fluctuations in microbial ecologies.}, journal = {Journal of theoretical biology}, volume = {308}, number = {}, pages = {96-104}, doi = {10.1016/j.jtbi.2012.05.030}, pmid = {22683366}, issn = {1095-8541}, mesh = {Bacteria/genetics/*growth &amp; development ; Bacteriolysis ; Colony Count, Microbial ; *Ecosystem ; Gene Transfer, Horizontal ; Linear Models ; Lysogeny ; *Models, Biological ; Mutation/genetics ; }, abstract = {Statistical fluctuations in population sizes of microbes may be quite large depending on the nature of their underlying stochastic dynamics. For example, the variance of the population size of a microbe undergoing a pure birth process with unlimited resources is proportional to the square of its mean. We refer to such large fluctuations, with the variance growing as square of the mean, as giant number fluctuations (GNF). Luria and Delbrück showed that spontaneous mutation processes in microbial populations exhibit GNF. We explore whether GNF can arise in other microbial ecologies. We study certain simple ecological models evolving via stochastic processes: (i) bi-directional mutation, (ii) lysis-lysogeny of bacteria by bacteriophage, and (iii) horizontal gene transfer (HGT). For the case of bi-directional mutation process, we show analytically exactly that the GNF relationship holds at large times. For the ecological model of bacteria undergoing lysis or lysogeny under viral infection, we show that if the viral population can be experimentally manipulated to stay quasi-stationary, the process of lysogeny maps essentially to one-way mutation process and hence the GNF property of the lysogens follows. Finally, we show that even the process of HGT may map to the mutation process at large times, and thereby exhibits GNF.}, }
@article {pmid22682566, year = {2012}, author = {Vázquez-Limón, C and Hoogewijs, D and Vinogradov, SN and Arredondo-Peter, R}, title = {The evolution of land plant hemoglobins.}, journal = {Plant science : an international journal of experimental plant biology}, volume = {191-192}, number = {}, pages = {71-81}, doi = {10.1016/j.plantsci.2012.04.013}, pmid = {22682566}, issn = {1873-2259}, mesh = {Embryophyta/*metabolism ; *Evolution, Molecular ; Hemoglobins/chemistry/*metabolism ; Phylogeny ; Symbiosis ; Time Factors ; }, abstract = {This review discusses the evolution of land plant hemoglobins within the broader context of eukaryote hemoglobins and the three families of bacterial globins. Most eukaryote hemoglobins, including metazoan globins and the symbiotic and non-symbiotic plant hemoglobins, are homologous to the bacterial 3/3-fold flavohemoglobins. The remaining plant hemoglobins are homologous to the bacterial 2/2-fold group 2 hemoglobins. We have proposed that all eukaryote globins were acquired via horizontal gene transfer concomitant with the endosymbiotic events responsible for the origin of mitochondria and chloroplasts. Although the 3/3 hemoglobins originated in the ancestor of green algae and plants prior to the emergence of embryophytes at about 450 mya, the 2/2 hemoglobins appear to have originated via horizontal gene transfer from a bacterium ancestral to present day Chloroflexi. Unlike the 2/2 hemoglobins, the evolution of the 3/3 hemoglobins was accompanied by duplication, diversification, and functional adaptations. Duplication of the ancestral plant nshb gene into the nshb-1 and nshb-2 lineages occurred prior to the monocot-dicot divergence at ca. 140 mya. It was followed by the emergence of symbiotic hemoglobins from a non-symbiotic hemoglobin precursor and further specialization, leading to leghemoglobins in N2-fixing legume nodules concomitant with the origin of nodulation at ca. 60 mya. The transition of non-symbiotic to symbiotic hemoglobins (including to leghemoglobins) was accompanied by the alteration of heme-Fe coordination from hexa- to penta-coordination. Additional genomic information about Charophyte algae, the sister group to land plants, is required for the further clarification of plant globin phylogeny.}, }
@article {pmid22681756, year = {2012}, author = {Xi, Z and Bradley, RK and Wurdack, KJ and Wong, K and Sugumaran, M and Bomblies, K and Rest, JS and Davis, CC}, title = {Horizontal transfer of expressed genes in a parasitic flowering plant.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {227}, pmid = {22681756}, issn = {1471-2164}, mesh = {Codon/genetics ; DNA, Plant/genetics ; Gene Transfer, Horizontal/*genetics ; Host-Parasite Interactions/genetics ; Magnoliopsida/classification/*genetics/parasitology ; Phylogeny ; Transcriptome/genetics ; }, abstract = {BACKGROUND: Recent studies have shown that plant genomes have potentially undergone rampant horizontal gene transfer (HGT). In plant parasitic systems HGT appears to be facilitated by the intimate physical association between the parasite and its host. HGT in these systems has been invoked when a DNA sequence obtained from a parasite is placed phylogenetically very near to its host rather than with its closest relatives. Studies of HGT in parasitic plants have relied largely on the fortuitous discovery of gene phylogenies that indicate HGT, and no broad systematic search for HGT has been undertaken in parasitic systems where it is most expected to occur.<br><br>RESULTS: We analyzed the transcriptomes of the holoparasite Rafflesia cantleyi Solms-Laubach and its obligate host Tetrastigma rafflesiae Miq. using phylogenomic approaches. Our analyses show that several dozen actively transcribed genes, most of which appear to be encoded in the nuclear genome, are likely of host origin. We also find that hundreds of vertically inherited genes (VGT) in this parasitic plant exhibit codon usage properties that are more similar to its host than to its closest relatives.<br><br>CONCLUSIONS: Our results establish for the first time a substantive number of HGTs in a plant host-parasite system. The elevated rate of unidirectional host-to- parasite gene transfer raises the possibility that HGTs may provide a fitness benefit to Rafflesia for maintaining these genes. Finally, a similar convergence in codon usage of VGTs has been shown in microbes with high HGT rates, which may help to explain the increase of HGTs in these parasitic plants.}, }
@article {pmid22675653, year = {2012}, author = {Pylro, VS and Vespoli, Lde S and Duarte, GF and Yotoko, KS}, title = {Detection of horizontal gene transfers from phylogenetic comparisons.}, journal = {International journal of evolutionary biology}, volume = {2012}, number = {}, pages = {813015}, pmid = {22675653}, issn = {2090-052X}, abstract = {Bacterial phylogenies have become one of the most important challenges for microbial ecology. This field started in the mid-1970s with the aim of using the sequence of the small subunit ribosomal RNA (16S) tool to infer bacterial phylogenies. Phylogenetic hypotheses based on other sequences usually give conflicting topologies that reveal different evolutionary histories, which in some cases may be the result of horizontal gene transfer events. Currently, one of the major goals of molecular biology is to understand the role that horizontal gene transfer plays in species adaptation and evolution. In this work, we compared the phylogenetic tree based on 16S with the tree based on dszC, a gene involved in the cleavage of carbon-sulfur bonds. Bacteria of several genera perform this survival task when living in environments lacking free mineral sulfur. The biochemical pathway of the desulphurization process was extensively studied due to its economic importance, since this step is expensive and indispensable in fuel production. Our results clearly show that horizontal gene transfer events could be detected using common phylogenetic methods with gene sequences obtained from public sequence databases.}, }
@article {pmid22675651, year = {2012}, author = {Sudheesh, PS and Al-Ghabshi, A and Al-Mazrooei, N and Al-Habsi, S}, title = {Comparative pathogenomics of bacteria causing infectious diseases in fish.}, journal = {International journal of evolutionary biology}, volume = {2012}, number = {}, pages = {457264}, pmid = {22675651}, issn = {2090-052X}, abstract = {Fish living in the wild as well as reared in the aquaculture facilities are susceptible to infectious diseases caused by a phylogenetically diverse collection of bacterial pathogens. Control and treatment options using vaccines and drugs are either inadequate, inefficient, or impracticable. The classical approach in studying fish bacterial pathogens has been looking at individual or few virulence factors. Recently, genome sequencing of a number of bacterial fish pathogens has tremendously increased our understanding of the biology, host adaptation, and virulence factors of these important pathogens. This paper attempts to compile the scattered literature on genome sequence information of fish pathogenic bacteria published and available to date. The genome sequencing has uncovered several complex adaptive evolutionary strategies mediated by horizontal gene transfer, insertion sequence elements, mutations and prophage sequences operating in fish pathogens, and how their genomes evolved from generalist environmental strains to highly virulent obligatory pathogens. In addition, the comparative genomics has allowed the identification of unique pathogen-specific gene clusters. The paper focuses on the comparative analysis of the virulogenomes of important fish bacterial pathogens, and the genes involved in their evolutionary adaptation to different ecological niches. The paper also proposes some new directions on finding novel vaccine and chemotherapeutic targets in the genomes of bacterial pathogens of fish.}, }
@article {pmid22675075, year = {2012}, author = {Boc, A and Diallo, AB and Makarenkov, V}, title = {T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks.}, journal = {Nucleic acids research}, volume = {40}, number = {Web Server issue}, pages = {W573-9}, pmid = {22675075}, issn = {1362-4962}, mesh = {Computer Graphics ; *Gene Transfer, Horizontal ; Internet ; *Phylogeny ; *Software ; }, abstract = {T-REX (Tree and reticulogram REConstruction) is a web server dedicated to the reconstruction of phylogenetic trees, reticulation networks and to the inference of horizontal gene transfer (HGT) events. T-REX includes several popular bioinformatics applications such as MUSCLE, MAFFT, Neighbor Joining, NINJA, BioNJ, PhyML, RAxML, random phylogenetic tree generator and some well-known sequence-to-distance transformation models. It also comprises fast and effective methods for inferring phylogenetic trees from complete and incomplete distance matrices as well as for reconstructing reticulograms and HGT networks, including the detection and validation of complete and partial gene transfers, inference of consensus HGT scenarios and interactive HGT identification, developed by the authors. The included methods allows for validating and visualizing phylogenetic trees and networks which can be built from distance or sequence data. The web server is available at: www.trex.uqam.ca.}, }
@article {pmid22672006, year = {2012}, author = {Ishitani, Y and Kamikawa, R and Yabuki, A and Tsuchiya, M and Inagaki, Y and Takishita, K}, title = {Evolution of elongation factor-like (EFL) protein in Rhizaria is revised by radiolarian EFL gene sequences.}, journal = {The Journal of eukaryotic microbiology}, volume = {59}, number = {4}, pages = {367-373}, doi = {10.1111/j.1550-7408.2012.00626.x}, pmid = {22672006}, issn = {1550-7408}, mesh = {Cluster Analysis ; DNA, Protozoan/chemistry/genetics ; *Evolution, Molecular ; Molecular Sequence Data ; Peptide Elongation Factors/*genetics ; Phylogeny ; Protozoan Proteins/*genetics ; Rhizaria/*classification/*genetics ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; }, abstract = {Elongation factor 1α (EF-1α) and elongation factor-like (EFL) proteins are considered to carry out equivalent functions in translation in eukaryotic cells. Elongation factor 1α and EFL genes are patchily distributed in the global eukaryotic tree, suggesting that the evolution of these elongation factors cannot be reconciled without multiple lateral gene transfer and/or ancestral co-occurrence followed by differential loss of either of the two factors. Our current understanding of the EF-1α/EFL evolution in the eukaryotic group Rhizaria, composed of Foraminifera, Radiolaria, Filosa, and Endomyxa, remains insufficient, as no information on EF-1α/EFL gene is available for any members of Radiolaria. In this study, EFL genes were experimentally isolated from four polycystine radiolarians (i.e. Dictyocoryne, Eucyrtidium, Collozoum, and Sphaerozoum), as well as retrieved from publicly accessible expressed sequence tag data of two acantharean radiolarians (i.e. Astrolonche and Phyllostaurus) and the endomyxan Gromia. The EFL homologs from radiolarians, foraminiferans, and Gromia formed a robust clade in both maximum-likelihood and Bayesian phylogenetic analyses, suggesting that EFL genes were vertically inherited from their common ancestor. We propose an updated model for EF-1α/EFL evolution in Rhizaria by incorporating new EFL data obtained in this study.}, }
@article {pmid22671555, year = {2012}, author = {Xiao, JH and Wang, NX and Murphy, RW and Cook, J and Jia, LY and Huang, DW}, title = {Wolbachia infection and dramatic intraspecific mitochondrial DNA divergence in a fig wasp.}, journal = {Evolution; international journal of organic evolution}, volume = {66}, number = {6}, pages = {1907-1916}, doi = {10.1111/j.1558-5646.2011.01561.x}, pmid = {22671555}, issn = {1558-5646}, mesh = {Animals ; Base Sequence ; DNA Primers ; DNA, Mitochondrial/genetics ; Gene Transfer, Horizontal ; Gram-Negative Bacterial Infections/*genetics/microbiology ; Haplotypes ; Polymerase Chain Reaction ; Wasps/*genetics ; Wolbachia/*isolation &amp; purification ; }, abstract = {Mitochondria and Wolbachia are maternally inherited genomes that exhibit strong linkage disequilibrium in many organisms. We surveyed Wolbachia infections in 187 specimens of the fig wasp species, Ceratosolen solmsi, and found an infection prevalence of 89.3%. DNA sequencing of 20 individuals each from Wolbachia-infected and -uninfected subpopulations revealed extreme mtDNA divergence (up to 9.2% and 15.3% in CO1 and cytochrome b, respectively) between infected and uninfected wasps. Further, mtDNA diversity was significantly reduced within the infected group. Our sequencing of a large part of the mitochondrial genome from both Wolbachia-infected and -uninfected individuals revealed that high sequence divergence is common throughout the mitochondrial genome. These patterns suggest a partial selective sweep of mitochondria subsequent to the introduction of Wolbachia into C. solsmi, by hybrid introgression from a related species.}, }
@article {pmid22669901, year = {2012}, author = {O'Hanlon, KA and Margison, GP and Hatch, A and Fitzpatrick, DA and Owens, RA and Doyle, S and Jones, GW}, title = {Molecular characterization of an adaptive response to alkylating agents in the opportunistic pathogen Aspergillus fumigatus.}, journal = {Nucleic acids research}, volume = {40}, number = {16}, pages = {7806-7820}, pmid = {22669901}, issn = {1362-4962}, support = {//Cancer Research UK/United Kingdom ; }, mesh = {Adaptation, Physiological ; Alkylating Agents/*toxicity ; Aspergillus fumigatus/drug effects/enzymology/*genetics ; DNA Damage ; *DNA Repair ; Gene Deletion ; Methylnitronitrosoguanidine/toxicity ; Methyltransferases/*genetics/metabolism/physiology ; O(6)-Methylguanine-DNA Methyltransferase/biosynthesis/*genetics/metabolism ; Phylogeny ; }, abstract = {An adaptive response to alkylating agents based upon the conformational change of a methylphosphotriester (MPT) DNA repair protein to a transcriptional activator has been demonstrated in a number of bacterial species, but this mechanism appears largely absent from eukaryotes. Here, we demonstrate that the human pathogen Aspergillus fumigatus elicits an adaptive response to sub-lethal doses of the mono-functional alkylating agent N-methyl-N'-nitro-N-nitrosoguanidine (MNNG). We have identified genes that encode MPT and O(6)-alkylguanine DNA alkyltransferase (AGT) DNA repair proteins; deletions of either of these genes abolish the adaptive response and sensitize the organism to MNNG. In vitro DNA repair assays confirm the ability of MPT and AGT to repair methylphosphotriester and O(6)-methylguanine lesions respectively. In eukaryotes, the MPT protein is confined to a select group of fungal species, some of which are major mammalian and plant pathogens. The evolutionary origin of the adaptive response is bacterial and rooted within the Firmicutes phylum. Inter-kingdom horizontal gene transfer between Firmicutes and Ascomycete ancestors introduced the adaptive response into the Fungal kingdom. Our data constitute the first detailed characterization of the molecular mechanism of the adaptive response in a lower eukaryote and has applications for development of novel fungal therapeutics targeting this DNA repair system.}, }
@article {pmid22669634, year = {2013}, author = {Ma, H and Bryers, JD}, title = {Non-invasive determination of conjugative transfer of plasmids bearing antibiotic-resistance genes in biofilm-bound bacteria: effects of substrate loading and antibiotic selection.}, journal = {Applied microbiology and biotechnology}, volume = {97}, number = {1}, pages = {317-328}, pmid = {22669634}, issn = {1432-0614}, support = {R01 EB007575/EB/NIBIB NIH HHS/United States ; R03 AI079461/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Biofilms/*drug effects ; Colony Count, Microbial ; *Conjugation, Genetic ; *Drug Resistance, Bacterial ; Flow Cytometry ; *Gene Transfer, Horizontal ; Humans ; Image Processing, Computer-Assisted ; Microscopy, Confocal ; Plasmids ; Pseudomonas putida/genetics/*physiology ; Selection, Genetic ; }, abstract = {Biofilms cause much of all human microbial infections. Attempts to eradicate biofilm-based infections rely on disinfectants and antibiotics. Unfortunately, biofilm bacteria are significantly less responsive to antibiotic stressors than their planktonic counterparts. Sublethal doses of antibiotics can actually enhance biofilm formation. Here, we have developed a non-invasive microscopic image analyses to quantify plasmid conjugation within a developing biofilm. Corroborating destructive samples were analyzed by a cultivation-independent flow cytometry analysis and a selective plate count method to cultivate transconjugants. Increases in substrate loading altered biofilm 3-D architecture and subsequently affected the frequency of plasmid conjugation (decreases at least two times) in the absence of any antibiotic selective pressure. More importantly, donor populations in biofilms exposed to a sublethal dose of kanamycin exhibited enhanced transfer efficiency of plasmids containing the kanamycin resistance gene, up to tenfold. However, when stressed with a different antibiotic, imipenem, transfer of plasmids containing the kan(R+) gene was not enhanced. These preliminary results suggest biofilm bacteria "sense" antibiotics to which they are resistant, which enhances the spread of that resistance. Confocal scanning microscopy coupled with our non-invasive image analysis was able to estimate plasmid conjugative transfer efficiency either averaged over the entire biofilm landscape or locally with individual biofilm clusters.}, }
@article {pmid22664438, year = {2012}, author = {Lim, KT and Hanifah, YA and Yusof, M and Thong, KL}, title = {ermA, ermC , tetM and tetK are essential for erythromycin and tetracycline resistance among methicillin-resistant Staphylococcus aureus strains isolated from a tertiary hospital in Malaysia.}, journal = {Indian journal of medical microbiology}, volume = {30}, number = {2}, pages = {203-207}, doi = {10.4103/0255-0857.96693}, pmid = {22664438}, issn = {1998-3646}, mesh = {Anti-Bacterial Agents/*pharmacology ; *Drug Resistance, Multiple, Bacterial ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Hospitals ; Humans ; Interspersed Repetitive Sequences ; Malaysia ; Methicillin-Resistant Staphylococcus aureus/*drug effects/*genetics/isolation &amp; purification ; Microbial Sensitivity Tests ; Staphylococcal Infections/*microbiology ; }, abstract = {The objective of this study was to determine the expression and transferability of tetracycline and erythromycin resistance among 188 MRSA strains from a Malaysian tertiary hospital. The minimum inhibitory concentrations (MICs) for oxacillin, erythromycin, tetracycline and ciprofloxacin ranged from 4 to 512 μg/ml, 0.25 to 256 μg/ml, 0.5 to 256 μg/ml and 0.5 to 512 μg/ml, respectively. Tetracycline-resistant strains showed co-resistance towards ciprofloxacin and erythromycin. There was a significant increase (P<0.05) of high-level tetracycline (≥MIC 256 μg/ml) and erythromycin (≥MIC 128 μg/ml) resistant strains in between the years 2003 and 2008. All erythromycin-resistant strains harboured ermA or ermC gene and all tetracycline-resistant strains harboured tetM or tetK gene. The blaZ was detected in all MRSA strains, whereas ermA, tetM, ermC, tetK and msrA genes were detected in 157 (84%), 92 (49%), 40 (21%), 39 (21%) and 4 (2%) MRSA strains, respectively. The blaZ, tetM, ermC and tetK genes were plasmid-encoded, with ermC gene being easily transmissible. Tn5801-like transposon was present in 78 tetM-positive strains. ermA and tetM genes were the most prevalent erythromycin and tetracycline resistance determinants, respectively, in MRSA strains. The association of resistance genes with mobile genetic elements possibly enhances the spread of resistant traits in MRSA.}, }
@article {pmid22664427, year = {2012}, author = {Agarwal, J and Srivastava, S and Singh, M}, title = {Pathogenomics of uropathogenic Escherichia coli.}, journal = {Indian journal of medical microbiology}, volume = {30}, number = {2}, pages = {141-149}, doi = {10.4103/0255-0857.96657}, pmid = {22664427}, issn = {1998-3646}, mesh = {Escherichia coli Infections/*microbiology/pathology ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genomic Islands ; Humans ; Urinary Tract Infections/*microbiology/pathology ; Uropathogenic Escherichia coli/*genetics/*pathogenicity ; Virulence ; Virulence Factors/*genetics/metabolism ; }, abstract = {Subset of faecal E. coli that can enter, colonize urinary tract and cause infection are known as uropathogenic E. coli (UPEC). UPEC strains act as opportunistic intracellular pathogens taking advantage of host susceptibility using a diverse array of virulence factors. Presence of specific virulence associated genes on genomic/pathogenicity islands and involvement of horizontal gene transfer appears to account for evolution and diversity of UPEC. Recent success in large-scale genome sequencing and comparative genomics has helped in unravelling UPEC pathogenomics. Here we review recent findings regarding virulence characteristics of UPEC and mechanisms involved in pathogenesis of urinary tract infection.}, }
@article {pmid22660700, year = {2012}, author = {Yoshii, A and Moriyama, H and Fukuhara, T}, title = {The novel kasugamycin 2'-N-acetyltransferase gene aac(2')-IIa, carried by the IncP island, confers kasugamycin resistance to rice-pathogenic bacteria.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {16}, pages = {5555-5564}, pmid = {22660700}, issn = {1098-5336}, mesh = {Acetyltransferases/*genetics/metabolism ; Aminoglycosides/*metabolism/pharmacology ; Anti-Bacterial Agents/*metabolism/pharmacology ; Burkholderia/*drug effects/enzymology/genetics/isolation &amp; purification ; Comamonadaceae/*drug effects/enzymology/genetics/isolation &amp; purification ; Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Oryza/*microbiology ; Plant Diseases/microbiology ; Plasmids ; Sequence Analysis, DNA ; }, abstract = {Kasugamycin (KSM), a unique aminoglycoside antibiotic, has been used in agriculture for many years to control not only rice blast caused by the fungus Magnaporthe grisea but also rice bacterial grain and seedling rot or rice bacterial brown stripe caused by Burkholderia glumae or Acidovorax avenae subsp. avenae, respectively. Since both bacterial pathogens are seed-borne and cause serious injury to rice seedlings, the emergence of KSM-resistant B. glumae and A. avenae isolates highlights the urgent need to understand the mechanism of resistance to KSM. Here, we identified a novel gene, aac(2')-IIa, encoding a KSM 2'-N-acetyltransferase from both KSM-resistant pathogens but not from KSM-sensitive bacteria. AAC(2')-IIa inactivates KSM, although it reveals no cross-resistance to other aminoglycosides. The aac(2')-IIa gene from B. glumae strain 5091 was identified within the IncP genomic island inserted into the bacterial chromosome, indicating the acquisition of this gene by horizontal gene transfer. Although excision activity of the IncP island and conjugational gene transfer was not detected under the conditions tested, circular intermediates containing the aac(2')-IIa gene were detected. These results indicate that the aac(2')-IIa gene had been integrated into the IncP island of a donor bacterial species. Molecular detection of the aac(2')-IIa gene could distinguish whether isolates are resistant or susceptible to KSM. This may contribute to the production of uninfected rice seeds and lead to the effective control of these pathogens by KSM.}, }
@article {pmid22646228, year = {2012}, author = {Paralanov, V and Lu, J and Duffy, LB and Crabb, DM and Shrivastava, S and Methé, BA and Inman, J and Yooseph, S and Xiao, L and Cassell, GH and Waites, KB and Glass, JI}, title = {Comparative genome analysis of 19 Ureaplasma urealyticum and Ureaplasma parvum strains.}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {88}, pmid = {22646228}, issn = {1471-2180}, mesh = {Animals ; DNA, Bacterial/*chemistry/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; Molecular Sequence Data ; *Sequence Analysis, DNA ; Ureaplasma/*genetics/isolation &amp; purification ; Ureaplasma urealyticum/*genetics/isolation &amp; purification ; Virulence Factors/genetics ; }, abstract = {BACKGROUND: Ureaplasma urealyticum (UUR) and Ureaplasma parvum (UPA) are sexually transmitted bacteria among humans implicated in a variety of disease states including but not limited to: nongonococcal urethritis, infertility, adverse pregnancy outcomes, chorioamnionitis, and bronchopulmonary dysplasia in neonates. There are 10 distinct serotypes of UUR and 4 of UPA. Efforts to determine whether difference in pathogenic potential exists at the ureaplasma serovar level have been hampered by limitations of antibody-based typing methods, multiple cross-reactions and poor discriminating capacity in clinical samples containing two or more serovars.<br><br>RESULTS: We determined the genome sequences of the American Type Culture Collection (ATCC) type strains of all UUR and UPA serovars as well as four clinical isolates of UUR for which we were not able to determine serovar designation. UPA serovars had 0.75-0.78 Mbp genomes and UUR serovars were 0.84-0.95 Mbp. The original classification of ureaplasma isolates into distinct serovars was largely based on differences in the major ureaplasma surface antigen called the multiple banded antigen (MBA) and reactions of human and animal sera to the organisms. Whole genome analysis of the 14 serovars and the 4 clinical isolates showed the mba gene was part of a large superfamily, which is a phase variable gene system, and that some serovars have identical sets of mba genes. Most of the differences among serovars are hypothetical genes, and in general the two species and 14 serovars are extremely similar at the genome level.<br><br>CONCLUSIONS: Comparative genome analysis suggests UUR is more capable of acquiring genes horizontally, which may contribute to its greater virulence for some conditions. The overwhelming evidence of extensive horizontal gene transfer among these organisms from our previous studies combined with our comparative analysis indicates that ureaplasmas exist as quasi-species rather than as stable serovars in their native environment. Therefore, differential pathogenicity and clinical outcome of a ureaplasmal infection is most likely not on the serovar level, but rather may be due to the presence or absence of potential pathogenicity factors in an individual ureaplasma clinical isolate and/or patient to patient differences in terms of autoimmunity and microbiome.}, }
@article {pmid22645259, year = {2012}, author = {Zwick, ME and Joseph, SJ and Didelot, X and Chen, PE and Bishop-Lilly, KA and Stewart, AC and Willner, K and Nolan, N and Lentz, S and Thomason, MK and Sozhamannan, S and Mateczun, AJ and Du, L and Read, TD}, title = {Genomic characterization of the Bacillus cereus sensu lato species: backdrop to the evolution of Bacillus anthracis.}, journal = {Genome research}, volume = {22}, number = {8}, pages = {1512-1524}, pmid = {22645259}, issn = {1549-5469}, support = {G0600719/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Bacillus anthracis/classification/*genetics ; Bacillus cereus/classification/*genetics ; Base Sequence ; Chromosomes, Bacterial/genetics ; DNA, Bacterial/analysis/genetics ; *Evolution, Molecular ; Genetic Variation ; Genome Size ; *Genome, Bacterial ; Homologous Recombination ; Multilocus Sequence Typing ; Phylogeny ; Selection, Genetic ; Sequence Alignment ; Soil Microbiology ; }, abstract = {The key genes required for Bacillus anthracis to cause anthrax have been acquired recently by horizontal gene transfer. To understand the genetic background for the evolution of B. anthracis virulence, we obtained high-redundancy genome sequences of 45 strains of the Bacillus cereus sensu lato (s.l.) species that were chosen for their genetic diversity within the species based on the existing multilocus sequence typing scheme. From the resulting data, we called more than 324,000 new genes representing more than 12,333 new gene families for this group. The core genome size for the B. cereus s.l. group was ∼1750 genes, with another 2150 genes found in almost every genome constituting the extended core. There was a paucity of genes specific and conserved in any clade. We found no evidence of recent large-scale gene loss in B. anthracis or for unusual accumulation of nonsynonymous DNA substitutions in the chromosome; however, several B. cereus genomes isolated from soil and not previously associated with human disease were degraded to various degrees. Although B. anthracis has undergone an ecological shift within the species, its chromosome does not appear to be exceptional on a macroscopic scale compared with close relatives.}, }
@article {pmid22644383, year = {2012}, author = {Zucko, J and Long, PF and Hranueli, D and Cullum, J}, title = {Horizontal gene transfer and gene conversion drive evolution of modular polyketide synthases.}, journal = {Journal of industrial microbiology &amp; biotechnology}, volume = {39}, number = {10}, pages = {1541-1547}, pmid = {22644383}, issn = {1476-5535}, mesh = {Bacteria/genetics/metabolism ; *Evolution, Molecular ; *Gene Conversion/genetics ; *Gene Transfer, Horizontal/genetics ; Models, Genetic ; Phylogeny ; Polyketide Synthases/*chemistry/*genetics/metabolism ; }, abstract = {Soil bacteria live in a very competitive environment and produce many secondary metabolites; there appears to be strong selective pressure for evolution of new compounds. Secondary metabolites are the most important source of chemical structures for the pharmaceutical industry and an understanding of the evolutionary process should help in finding novel chemical entities. Modular polyketide synthases are a particularly interesting case for evolutionary studies, because much of the chemical structure can be predicted from DNA sequence. Previous evolutionary studies have concentrated on individual modules or domains and were not able to study the evolution of orthologues. This study overcame this problem by considering complete clusters as "organisms", so that orthologous modules and domains could be identified and used to characterise evolutionary pathways. Seventeen modular polyketide synthase clusters were identified that fell into six classes. Gene conversion within clusters was very common (affecting about 15 % of domains) and was detected by discordance in phylogenetic trees. An evolutionary model is proposed in which a single cross over between two different clusters (i.e. horizontal gene transfer) would generate a cluster of very different architecture with radically different chemical products; subsequent gene conversion and deletions would explore chemical variants. Two probable examples of such recombination were found. This model suggests strategies for detecting horizontal gene transfer in cluster evolution.}, }
@article {pmid22642116, year = {2012}, author = {Gorbunov, KIu and Liubetskiĭ, VA}, title = {[A fast algorithm to build a supertree with a set of gene trees].}, journal = {Molekuliarnaia biologiia}, volume = {46}, number = {1}, pages = {176-183}, pmid = {22642116}, issn = {0026-8984}, mesh = {*Algorithms ; Computer Simulation ; *Gene Transfer, Horizontal ; Humans ; *Phylogeny ; Software ; }, abstract = {Important desired properties of an algorithm to construct a supertree (species tree) by reconciling input trees are its low complexity and applicability to large biological data. In its common statement the problem is proved to be NP-hard, i.e. to have an exponential complexity in practice. We propose a reformulation of the supertree building problem that allows a computationally effective solution. We introduce a biologically natural requirement that the supertree is sought for such that it does not contain clades incompatible with those existing in the input trees. The algorithm was tested with simulated and biological trees and was shown to possess an almost square complexity even if horizontal transfers are allowed. If HGTs are not assumed, the algorithm is mathematically correct and possesses the longest running time of n3 x[V0]3, where n is the number of input trees and [V0] is the total number of species. The authors are unaware of analogous solutions in published evidence. The corresponding inferring program, its usage examples and manual are freely available at http://lab6.iitp.ru/en/super3gl. The available program does not implement HGTs. The generalized case is described in the publication "A tree nearest in average to a set of trees" (Information Transmission Problems, 2011).}, }
@article {pmid22641711, year = {2012}, author = {Chen, ZZ and Deng, F and Wang, L}, title = {Simultaneous identification of duplications, losses, and lateral gene transfers.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {9}, number = {5}, pages = {1515-1528}, doi = {10.1109/TCBB.2012.79}, pmid = {22641711}, issn = {1557-9964}, mesh = {*Algorithms ; Evolution, Molecular ; *Gene Duplication ; Gene Transfer, Horizontal/*genetics ; Models, Genetic ; }, abstract = {We give a fixed-parameter algorithm for the problem of enumerating all minimum-cost LCA-reconciliations involving gene duplications, gene losses, and lateral gene transfers (LGTs) for a given species tree S and a given gene tree G. Our algorithm can work for the weighted version of the problem, where the costs of a gene duplication, a gene loss, and an LGT are left to the user's discretion. The algorithm runs in O(m + 3(k/c)n) time, where m is the number of vertices in S, n is the number of vertices in G, c is the smaller between a gene duplication cost and an LGT cost, and k is the minimum cost of an LCA-reconciliation between S and G. The time complexity is indeed better if the cost of a gene loss is greater than 0. In particular, when the cost of a gene loss is at least 0.614c, the running time of the algorithm is O(m + 2.78(k/c)n).}, }
@article {pmid22640804, year = {2012}, author = {Hynes, AP and Mercer, RG and Watton, DE and Buckley, CB and Lang, AS}, title = {DNA packaging bias and differential expression of gene transfer agent genes within a population during production and release of the Rhodobacter capsulatus gene transfer agent, RcGTA.}, journal = {Molecular microbiology}, volume = {85}, number = {2}, pages = {314-325}, doi = {10.1111/j.1365-2958.2012.08113.x}, pmid = {22640804}, issn = {1365-2958}, mesh = {Amino Acid Sequence ; Bacterial Proteins/*biosynthesis/genetics ; *DNA Packaging ; DNA, Bacterial/genetics/*metabolism ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Genes, Reporter ; Molecular Sequence Data ; Rhodobacter capsulatus/*genetics/*metabolism ; }, abstract = {Rhodobacter capsulatus produces a gene transfer agent (GTA) called RcGTA. RcGTA is a phage-like particle that packages R. capsulatus DNA and transfers it to other R. capsulatus cells. We quantified the relative frequency of packaging for each gene in the genome by hybridization of DNA from RcGTA particles to an R. capsulatus microarray. All genes were found within the RcGTA particles. However, the genes encoding the RcGTA particle were under-packaged compared with other regions. Gene transfer bioassays confirmed that the transfer of genes within the RcGTA structural cluster is reduced relative to those of other genes. Single-cell expression analysis, by flow cytometry analysis of cells containing RcGTA-reporter gene fusion constructs, demonstrated that RcGTA gene expression is not uniform within a culture. This phenomenon was accentuated when the constructs were placed in a strain lacking a putative lysis gene involved in RcGTA release; a small subpopulation was found to be responsible for ∼ 95% of RcGTA activity. We propose a mechanism whereby high levels of RcGTA gene transcription in the most active RcGTA-producing cells cause a reduction in their packaging frequency. This subpopulation's role in producing and releasing the RcGTA particles explains the lack of observed cell lysis in cultures.}, }
@article {pmid22638584, year = {2012}, author = {Steczkiewicz, K and Muszewska, A and Knizewski, L and Rychlewski, L and Ginalski, K}, title = {Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily.}, journal = {Nucleic acids research}, volume = {40}, number = {15}, pages = {7016-7045}, pmid = {22638584}, issn = {1362-4962}, mesh = {Amino Acid Sequence ; Catalytic Domain ; DNA Restriction Enzymes/chemistry ; Gene Transfer, Horizontal ; Models, Molecular ; Molecular Sequence Data ; Phosphoric Diester Hydrolases/*chemistry/*classification/genetics ; Protein Structure, Tertiary ; Sequence Alignment ; Sequence Analysis, Protein ; }, abstract = {Proteins belonging to PD-(D/E)XK phosphodiesterases constitute a functionally diverse superfamily with representatives involved in replication, restriction, DNA repair and tRNA-intron splicing. Their malfunction in humans triggers severe diseases, such as Fanconi anemia and Xeroderma pigmentosum. To date there have been several attempts to identify and classify new PD-(D/E)KK phosphodiesterases using remote homology detection methods. Such efforts are complicated, because the superfamily exhibits extreme sequence and structural divergence. Using advanced homology detection methods supported with superfamily-wide domain architecture and horizontal gene transfer analyses, we provide a comprehensive reclassification of proteins containing a PD-(D/E)XK domain. The PD-(D/E)XK phosphodiesterases span over 21,900 proteins, which can be classified into 121 groups of various families. Eleven of them, including DUF4420, DUF3883, DUF4263, COG5482, COG1395, Tsp45I, HaeII, Eco47II, ScaI, HpaII and Replic_Relax, are newly assigned to the PD-(D/E)XK superfamily. Some groups of PD-(D/E)XK proteins are present in all domains of life, whereas others occur within small numbers of organisms. We observed multiple horizontal gene transfers even between human pathogenic bacteria or from Prokaryota to Eukaryota. Uncommon domain arrangements greatly elaborate the PD-(D/E)XK world. These include domain architectures suggesting regulatory roles in Eukaryotes, like stress sensing and cell-cycle regulation. Our results may inspire further experimental studies aimed at identification of exact biological functions, specific substrates and molecular mechanisms of reactions performed by these highly diverse proteins.}, }
@article {pmid22636769, year = {2012}, author = {Li, F and Alvarez-Martinez, C and Chen, Y and Choi, KJ and Yeo, HJ and Christie, PJ}, title = {Enterococcus faecalis PrgJ, a VirB4-like ATPase, mediates pCF10 conjugative transfer through substrate binding.}, journal = {Journal of bacteriology}, volume = {194}, number = {15}, pages = {4041-4051}, pmid = {22636769}, issn = {1098-5530}, support = {R01 GM048746/GM/NIGMS NIH HHS/United States ; GM48476/GM/NIGMS NIH HHS/United States ; }, mesh = {Adenosine Triphosphatases/genetics/*metabolism ; Adenosine Triphosphate/metabolism ; Amino Acid Substitution ; Bacterial Secretion Systems/genetics ; *Conjugation, Genetic ; DNA/metabolism ; Enterococcus faecalis/*enzymology/*genetics ; *Gene Transfer, Horizontal ; Hydrolysis ; Models, Biological ; Mutant Proteins/genetics/metabolism ; Mutation, Missense ; *Plasmids ; Protein Binding ; Protein Interaction Mapping ; Protein Multimerization ; }, abstract = {The Enterococcus faecalis prg and pcf genes of plasmid pCF10 encode a type IV secretion system (T4SS) required for conjugative transfer. PrgJ is a member of the VirB4 family of ATPases that are universally associated with T4SSs. Here, we report that purified PrgJ dimers displayed ATP binding and hydrolysis activities. A PrgJ nucleoside triphosphate (NTP) binding site mutation (K471E) slightly diminished ATP binding but abolished ATP hydrolysis in vitro and blocked pCF10 transfer in vivo. As shown with affinity pulldown assays, PrgJ and the K471E mutant protein interacted with the substrate receptor PcfC and with relaxase PcfG and accessory factor PcfF, which together form the relaxosome at the oriT sequence to initiate plasmid processing. The purified PrgJ and K471E proteins also bound single- and double-stranded DNA substrates without sequence specificity in vitro, and both PrgJ derivatives bound pCF10 in vivo by a mechanism dependent on an intact oriT sequence and cosynthesis of PcfC, PcfF, and PcfG, as shown by a formaldehyde-cross-linking assay. Our findings support a model in which the PcfC receptor coordinates with the PrgJ ATPase to drive early steps of pCF10 processing/transfer: (i) PcfC first binds the pCF10 relaxosome through contacts with PcfF, PcfG, and DNA; (ii) PcfC delivers the plasmid substrate to PrgJ; and (iii) PrgJ catalyzes substrate transfer to the membrane translocase. Substrate engagement with a VirB4-like subunit has not been previously described; consequently, our studies point to a novel function for these signature T4SS ATPases in mediating early steps of type IV secretion.}, }
@article {pmid22617954, year = {2012}, author = {Choi, SC and Rasmussen, MD and Hubisz, MJ and Gronau, I and Stanhope, MJ and Siepel, A}, title = {Replacing and additive horizontal gene transfer in Streptococcus.}, journal = {Molecular biology and evolution}, volume = {29}, number = {11}, pages = {3309-3320}, pmid = {22617954}, issn = {1537-1719}, support = {R01 AI073368/AI/NIAID NIH HHS/United States ; AI073368-01A2/AI/NIAID NIH HHS/United States ; }, mesh = {Gene Duplication/genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/genetics ; Genes, Essential/genetics ; Humans ; Models, Genetic ; *Phylogeny ; Selection, Genetic ; Streptococcus/*genetics ; }, abstract = {The prominent role of Horizontal Gene Transfer (HGT) in the evolution of bacteria is now well documented, but few studies have differentiated between evolutionary events that predominantly cause genes in one lineage to be replaced by homologs from another lineage ("replacing HGT") and events that result in the addition of substantial new genomic material ("additive HGT"). Here in, we make use of the distinct phylogenetic signatures of replacing and additive HGTs in a genome-wide study of the important human pathogen Streptococcus pyogenes (SPY) and its close relatives S. dysgalactiae subspecies equisimilis (SDE) and S. dysgalactiae subspecies dysgalactiae (SDD). Using recently developed statistical models and computational methods, we find evidence for abundant gene flow of both kinds within each of the SPY and SDE clades and of reduced levels of exchange between SPY and SDD. In addition, our analysis strongly supports a pronounced asymmetry in SPY-SDE gene flow, favoring the SPY-to-SDE direction. This finding is of particular interest in light of the recent increase in virulence of pathogenic SDE. We find much stronger evidence for SPY-SDE gene flow among replacing than among additive transfers, suggesting a primary influence from homologous recombination between co-occurring SPY and SDE cells in human hosts. Putative virulence genes are correlated with transfer events, but this correlation is found to be driven by additive, not replacing, HGTs. The genes affected by additive HGTs are enriched for functions having to do with transposition, recombination, and DNA integration, consistent with previous findings, whereas replacing HGTs seen to influence a more diverse set of genes. Additive transfers are also found to be associated with evidence of positive selection. These findings shed new light on the manner in which HGT has shaped pathogenic bacterial genomes.}, }
@article {pmid22613788, year = {2012}, author = {Kemen, E and Jones, JD}, title = {Obligate biotroph parasitism: can we link genomes to lifestyles?.}, journal = {Trends in plant science}, volume = {17}, number = {8}, pages = {448-457}, doi = {10.1016/j.tplants.2012.04.005}, pmid = {22613788}, issn = {1878-4372}, support = {233376/ERC_/European Research Council/International ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Adaptation, Physiological ; Biological Evolution ; Fungi/*genetics/pathogenicity/physiology ; Gene Transfer, Horizontal ; *Genome, Fungal ; Host-Pathogen Interactions ; Oomycetes/*genetics/pathogenicity/physiology ; Phenotype ; Plant Diseases/microbiology ; Plants/microbiology ; Reproduction, Asexual ; Species Specificity ; Spores, Fungal/genetics/physiology ; }, abstract = {Although the oomycetes and fungi are evolutionarily very distantly related, both taxa evolved biotrophy on plant hosts several times independently, giving rise to rust- and mildew-like phenotypes. Differences in host colonization and adaptation may be reflected in genome size and by gain and loss of genes. In this opinion article we combine classical knowledge with recently sequenced pathogen genomes and present new hypotheses about the convergent evolution that led to these two distinct phenotypes in obligate biotrophs.}, }
@article {pmid22606358, year = {2012}, author = {Nishimura, Y and Kamikawa, R and Hashimoto, T and Inagaki, Y}, title = {Separate origins of group I introns in two mitochondrial genes of the katablepharid Leucocryptos marina.}, journal = {PloS one}, volume = {7}, number = {5}, pages = {e37307}, pmid = {22606358}, issn = {1932-6203}, mesh = {Base Sequence ; Cytochromes b/genetics ; Electron Transport Complex IV/genetics ; Eukaryota/classification/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, Mitochondrial ; Genome, Mitochondrial ; Introns ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; RNA/chemistry/genetics ; }, abstract = {Mitochondria are descendants of the endosymbiotic α-proteobacterium most likely engulfed by the ancestral eukaryotic cells, and the proto-mitochondrial genome should have been severely streamlined in terms of both genome size and gene repertoire. In addition, mitochondrial (mt) sequence data indicated that frequent intron gain/loss events contributed to shaping the modern mt genome organizations, resulting in the homologous introns being shared between two distantly related mt genomes. Unfortunately, the bulk of mt sequence data currently available are of phylogenetically restricted lineages, i.e., metazoans, fungi, and land plants, and are insufficient to elucidate the entire picture of intron evolution in mt genomes. In this work, we sequenced a 12 kbp-fragment of the mt genome of the katablepharid Leucocryptos marina. Among nine protein-coding genes included in the mt genome fragment, the genes encoding cytochrome b and cytochrome c oxidase subunit I (cob and cox1) were interrupted by group I introns. We further identified that the cob and cox1 introns host open reading frames for homing endonucleases (HEs) belonging to distantly related superfamilies. Phylogenetic analyses recovered an affinity between the HE in the Leucocryptos cob intron and two green algal HEs, and that between the HE in the Leucocryptos cox1 intron and a fungal HE, suggesting that the Leucocryptos cob and cox1 introns possess distinct evolutionary origins. Although the current intron (and intronic HE) data are insufficient to infer how the homologous introns were distributed to distantly related mt genomes, the results presented here successfully expanded the evolutionary dynamism of group I introns in mt genomes.}, }
@article {pmid22596260, year = {2012}, author = {Risitano, A and Beaulieu, LM and Vitseva, O and Freedman, JE}, title = {Platelets and platelet-like particles mediate intercellular RNA transfer.}, journal = {Blood}, volume = {119}, number = {26}, pages = {6288-6295}, pmid = {22596260}, issn = {1528-0020}, support = {P01 AI078894/AI/NIAID NIH HHS/United States ; T32 HL007224/HL/NHLBI NIH HHS/United States ; P01 A1078894//PHS HHS/United States ; }, mesh = {Animals ; Blood Platelets/cytology/metabolism/*physiology ; Cell Communication/genetics/*physiology ; Cell-Derived Microparticles/metabolism/*physiology ; Cells, Cultured ; Coculture Techniques ; Gene Transfer, Horizontal/*physiology ; Human Umbilical Vein Endothelial Cells/cytology/physiology ; Humans ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Paracrine Communication/physiology ; RNA/*metabolism ; }, abstract = {The role of platelets in hemostasis and thrombosis is clearly established; however, the mechanisms by which platelets mediate inflammatory and immune pathways are less well understood. Platelets interact and modulate the function of blood and vascular cells by releasing bioactive molecules. Although the platelet is anucleate, it contains transcripts that may mirror disease. Platelet mRNA is only associated with low-level protein translation; however, platelets have a unique membrane structure allowing for the passage of small molecules, leading to the possibility that its cytoplasmic RNA may be passed to nucleated cells. To examine this question, platelet-like particles with labeled RNA were cocultured with vascular cells. Coculture of platelet-like particles with activated THP-1, monocytic, and endothelial cells led to visual and functional RNA transfer. Posttransfer microarray gene expression analysis of THP-1 cells showed an increase in HBG1/HBG2 and HBA1/HBA2 expression that was directly related to the transfer. Infusion of wild-type platelets into a TLR2-deficient mouse model established in vivo confirmation of select platelet RNA transfer to leukocytes. By specifically transferring green fluorescent protein, we also observed external RNA was functional in the recipient cells. The observation that platelets possess the capacity to transfer cytosolic RNA suggests a new function for platelets in the regulation of vascular homeostasis.}, }
@article {pmid22593553, year = {2012}, author = {Burki, F and Flegontov, P and Oborník, M and Cihlár, J and Pain, A and Lukes, J and Keeling, PJ}, title = {Re-evaluating the green versus red signal in eukaryotes with secondary plastid of red algal origin.}, journal = {Genome biology and evolution}, volume = {4}, number = {6}, pages = {626-635}, pmid = {22593553}, issn = {1759-6653}, mesh = {Alveolata/*genetics/physiology ; Chlorophyta/classification/cytology/*genetics/physiology ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Phylogeny ; Plastids/*genetics ; Rhodophyta/classification/cytology/*genetics/physiology ; Symbiosis ; }, abstract = {The transition from endosymbiont to organelle in eukaryotic cells involves the transfer of significant numbers of genes to the host genomes, a process known as endosymbiotic gene transfer (EGT). In the case of plastid organelles, EGTs have been shown to leave a footprint in the nuclear genome that can be indicative of ancient photosynthetic activity in present-day plastid-lacking organisms, or even hint at the existence of cryptic plastids. Here, we evaluated the impact of EGT on eukaryote genomes by reanalyzing the recently published EST dataset for Chromera velia, an interesting test case of a photosynthetic alga closely related to apicomplexan parasites. Previously, 513 genes were reported to originate from red and green algae in a 1:1 ratio. In contrast, by manually inspecting newly generated trees indicating putative algal ancestry, we recovered only 51 genes congruent with EGT, of which 23 and 9 were of red and green algal origin, respectively, whereas 19 were ambiguous regarding the algal provenance. Our approach also uncovered 109 genes that branched within a monocot angiosperm clade, most likely representing a contamination. We emphasize the lack of congruence and the subjectivity resulting from independent phylogenomic screens for EGT, which appear to call for extreme caution when drawing conclusions for major evolutionary events.}, }
@article {pmid22593225, year = {2012}, author = {Hepburn, NJ and Schmidt, DW and Mower, JP}, title = {Loss of two introns from the Magnolia tripetala mitochondrial cox2 gene implicates horizontal gene transfer and gene conversion as a novel mechanism of intron loss.}, journal = {Molecular biology and evolution}, volume = {29}, number = {10}, pages = {3111-3120}, doi = {10.1093/molbev/mss130}, pmid = {22593225}, issn = {1537-1719}, mesh = {Base Sequence ; Cyclooxygenase 2/*genetics ; Gene Conversion/*genetics ; Gene Expression Regulation, Plant ; Gene Transfer, Horizontal/*genetics ; Genes, Mitochondrial/*genetics ; Genes, Plant/genetics ; Introns/*genetics ; Magnolia/*enzymology/*genetics ; Models, Genetic ; Molecular Sequence Data ; RNA Editing/genetics ; RNA Processing, Post-Transcriptional ; }, abstract = {Intron loss is often thought to occur through retroprocessing, which is the reverse transcription and genomic integration of a spliced transcript. In plant mitochondria, several unambiguous examples of retroprocessing are supported by the parallel loss of an intron and numerous adjacent RNA edit sites, but in most cases, the evidence for intron loss via retroprocessing is weak or lacking entirely. To evaluate mechanisms of intron loss, we designed a polymerase chain reaction (PCR)-based assay to detect recent intron losses from the mitochondrial cox2 gene within genus Magnolia, which was previously suggested to have variability in cox2 intron content. Our assay showed that all 22 examined species have a cox2 gene with two introns. However, one species, Magnolia tripetala, contains an additional cox2 gene that lacks both introns. Quantitative PCR showed that both M. tripetala cox2 genes are present in the mitochondrial genome. Although the intronless gene has lost several ancestral RNA edit sites, their distribution is inconsistent with retroprocessing models. Instead, phylogenetic and gene conversion analyses indicate that the intronless gene was horizontally acquired from a eudicot and then underwent gene conversion with the native intron-containing gene. The models are presented to summarize the roles of horizontal gene transfer and gene conversion as a novel mechanism of intron loss.}, }
@article {pmid22589287, year = {2012}, author = {Caro-Quintero, A and Ritalahti, KM and Cusick, KD and Löffler, FE and Konstantinidis, KT}, title = {The chimeric genome of Sphaerochaeta: nonspiral spirochetes that break with the prevalent dogma in spirochete biology.}, journal = {mBio}, volume = {3}, number = {3}, pages = {}, pmid = {22589287}, issn = {2150-7511}, mesh = {Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; Lyme Disease/microbiology ; Molecular Sequence Data ; Phylogeny ; Spirochaeta/classification/*cytology/*genetics/isolation &amp; purification ; Spirochaetales/classification/*genetics/isolation &amp; purification ; Spirochaetales Infections/microbiology ; }, abstract = {UNLABELLED: Spirochaetes is one of a few bacterial phyla that are characterized by a unifying diagnostic feature, namely, the helical morphology and motility conferred by axial periplasmic flagella. Their unique morphology and mode of propulsion also represent major pathogenicity factors of clinical spirochetes. Here we describe the genome sequences of two coccoid isolates of the recently described genus Sphaerochaeta which are members of the phylum Spirochaetes based on 16S rRNA gene and whole-genome phylogenies. Interestingly, the Sphaerochaeta genomes completely lack the motility and associated signal transduction genes present in all sequenced spirochete genomes. Additional analyses revealed that the lack of flagella is associated with a unique, nonrigid cell wall structure hallmarked by a lack of transpeptidase and transglycosylase genes, which is also unprecedented in spirochetes. The Sphaerochaeta genomes are highly enriched in fermentation and carbohydrate metabolism genes relative to other spirochetes, indicating a fermentative lifestyle. Remarkably, most of the enriched genes appear to have been acquired from nonspirochetes, particularly clostridia, in several massive horizontal gene transfer events (>40% of the total number of genes in each genome). Such a high level of direct interphylum genetic exchange is extremely rare among mesophilic organisms and has important implications for the assembly of the prokaryotic tree of life.<br><br>IMPORTANCE: Spiral shape and motility historically have been the unifying hallmarks of the phylum Spirochaetes. These features also represent important virulence factors of highly invasive pathogenic spirochetes such as the causative agents of syphilis and Lyme disease. Through the integration of genome sequencing, microscopy, and physiological studies, we conclusively show that the spiral morphology and motility of spirochetes are not universal morphological properties. In particular, we found that the genomes of the members of the recently described genus Sphaerochaeta lack the genes encoding the characteristic flagellar apparatus and, in contrast to most other spirochetes, have acquired many metabolic and fermentation genes from clostridia. These findings have major implications for the isolation and study of spirochetes, the diagnosis of spirochete-caused diseases, and the reconstruction of the evolutionary history of this important bacterial phylum. The Sphaerochaeta sp. genomes offer new avenues to link ecophysiology with the functionality and evolution of the spirochete flagellar apparatus.}, }
@article {pmid22588203, year = {2012}, author = {Everroad, RC and Wood, AM}, title = {Phycoerythrin evolution and diversification of spectral phenotype in marine Synechococcus and related picocyanobacteria.}, journal = {Molecular phylogenetics and evolution}, volume = {64}, number = {3}, pages = {381-392}, doi = {10.1016/j.ympev.2012.04.013}, pmid = {22588203}, issn = {1095-9513}, mesh = {*Biological Evolution ; DNA, Bacterial/genetics ; *Gene Transfer, Horizontal ; Gulf of Mexico ; Phenotype ; Phycobilins/analysis ; Phycoerythrin/analysis/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Selection, Genetic ; Sequence Analysis, DNA ; Synechococcus/classification/*genetics ; Urobilin/analogs &amp; derivatives/analysis ; }, abstract = {In marine Synechococcus there is evidence for the adaptive evolution of spectrally distinct forms of the major light harvesting pigment phycoerythrin (PE). Recent research has suggested that these spectral forms of PE have a different evolutionary history than the core genome. However, a lack of explicit statistical testing of alternative hypotheses or for selection on these genes has made it difficult to evaluate the evolutionary relationships between spectral forms of PE or the role horizontal gene transfer (HGT) may have had in the adaptive phenotypic evolution of the pigment system in marine Synechococcus. In this work, PE phylogenies of picocyanobacteria with known spectral phenotypes, including newly co-isolated strains of marine Synechococcus from the Gulf of Mexico, were constructed to explore the diversification of spectral phenotype and PE evolution in this group more completely. For the first time, statistical evaluation of competing evolutionary hypotheses and tests for positive selection on the PE locus in picocyanobacteria were performed. Genes for PEs associated with specific PE spectral phenotypes formed strongly supported monophyletic clades within the PE tree with positive directional selection driving evolution towards higher phycourobilin (PUB) content. The presence of the PUB-lacking phenotype in PE-containing marine picocyanobacteria from cyanobacterial lineages identified as Cyanobium is best explained by HGT into this group from marine Synechococcus. Taken together, these data provide strong examples of adaptive evolution of a single phenotypic trait in bacteria via mutation, positive directional selection and horizontal gene transfer.}, }
@article {pmid22587825, year = {2012}, author = {Zhou, Y and Call, DR and Broschat, SL}, title = {Genetic relationships among 527 Gram-negative bacterial plasmids.}, journal = {Plasmid}, volume = {68}, number = {2}, pages = {133-141}, doi = {10.1016/j.plasmid.2012.05.002}, pmid = {22587825}, issn = {1095-9890}, support = {N01-A1-30055//PHS HHS/United States ; }, mesh = {Gram-Negative Bacteria/*classification/*genetics ; Phylogeny ; Plasmids/*genetics ; }, abstract = {Plasmids are mosaic in composition with a maintenance "backbone" as well as "accessory" genes obtained via horizontal gene transfer. This horizontal gene transfer complicates the study of their genetic relationships. We describe a method for relating a large number of Gram-negative (GN) bacterial plasmids based on their genetic sequences. Complete coding gene sequences of 527 GN bacterial plasmids were obtained from NCBI. Initial classification of their genetic relationships was accomplished using a computational approach analogous to hybridization of "mixed-genome microarrays." Because of this similarity, the phrase "virtual hybridization" is used to describe this approach. Protein sequences generated from the gene sequences were randomly chosen to serve as "probes" for the virtual arrays, and virtual hybridization for each GN plasmid was achieved using BLASTp. Each resulting intensity matrix was used to generate a distance matrix from which an initial tree was constructed. Relationships were refined for several clusters by identifying conserved proteins within a cluster. Multiple-sequence alignment was applied to the concatenated conserved proteins, and maximum likelihood was used to generate relationships from the results of the alignment. While it is not possible to prove that the genetic relationships among the 527 GN bacterial plasmids obtained in this study are correct, replication of identical results produced in a separate study for a small group of IncA/C plasmids provides evidence that the approach used can correctly predict genetic relationships. In addition, results obtained for clusters of Borrelia plasmids are consistent with the expected exclusivity for plasmids from this genus. Finally, the 527-plasmid tree was used to study the distribution of four common antibiotic resistance genes.}, }
@article {pmid22586130, year = {2012}, author = {Tian, CF and Zhou, YJ and Zhang, YM and Li, QQ and Zhang, YZ and Li, DF and Wang, S and Wang, J and Gilbert, LB and Li, YR and Chen, WX}, title = {Comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {22}, pages = {8629-8634}, pmid = {22586130}, issn = {1091-6490}, mesh = {Adaptation, Physiological/*genetics ; Bacterial Proteins/genetics ; Bradyrhizobium/classification/genetics/physiology ; China ; Cluster Analysis ; Evolution, Molecular ; Genes, Bacterial/*genetics ; Genome, Bacterial/genetics ; Genomics/*methods ; Geography ; Host-Pathogen Interactions ; Phylogeny ; Plant Root Nodulation ; Rhizobium/classification/*genetics/physiology ; Root Nodules, Plant/microbiology ; Sinorhizobium/classification/genetics/physiology ; Glycine max/microbiology ; Species Specificity ; Symbiosis ; }, abstract = {The rhizobium-legume symbiosis has been widely studied as the model of mutualistic evolution and the essential component of sustainable agriculture. Extensive genetic and recent genomic studies have led to the hypothesis that many distinct strategies, regardless of rhizobial phylogeny, contributed to the varied rhizobium-legume symbiosis. We sequenced 26 genomes of Sinorhizobium and Bradyrhizobium nodulating soybean to test this hypothesis. The Bradyrhizobium core genome is disproportionally enriched in lipid and secondary metabolism, whereas several gene clusters known to be involved in osmoprotection and adaptation to alkaline pH are specific to the Sinorhizobium core genome. These features are consistent with biogeographic patterns of these bacteria. Surprisingly, no genes are specifically shared by these soybean microsymbionts compared with other legume microsymbionts. On the other hand, phyletic patterns of 561 known symbiosis genes of rhizobia reflected the species phylogeny of these soybean microsymbionts and other rhizobia. Similar analyses with 887 known functional genes or the whole pan genome of rhizobia revealed that only the phyletic distribution of functional genes was consistent with the species tree of rhizobia. Further evolutionary genetics revealed that recombination dominated the evolution of core genome. Taken together, our results suggested that faithfully vertical genes were rare compared with those with history of recombination including lateral gene transfer, although rhizobial adaptations to symbiotic interactions and other environmental conditions extensively recruited lineage-specific shell genes under direct or indirect control through the speciation process.}, }
@article {pmid22583543, year = {2012}, author = {Kumar, N and Creasy, T and Sun, Y and Flowers, M and Tallon, LJ and Dunning Hotopp, JC}, title = {Efficient subtraction of insect rRNA prior to transcriptome analysis of Wolbachia-Drosophila lateral gene transfer.}, journal = {BMC research notes}, volume = {5}, number = {}, pages = {230}, pmid = {22583543}, issn = {1756-0500}, mesh = {Actins/genetics ; Animals ; Drosophila/*genetics/*microbiology ; Gene Expression Profiling/*methods ; Gene Transfer, Horizontal/*genetics ; Genes, Insect/genetics ; RNA, Messenger/genetics/metabolism ; RNA, Ribosomal, 18S/genetics/*isolation &amp; purification ; Wolbachia/*genetics ; }, abstract = {BACKGROUND: Numerous methods exist for enriching bacterial or mammalian mRNA prior to transcriptome experiments. Yet there persists a need for methods to enrich for mRNA in non-mammalian animal systems. For example, insects contain many important and interesting obligate intracellular bacteria, including endosymbionts and vector-borne pathogens. Such obligate intracellular bacteria are difficult to study by traditional methods. Therefore, genomics has greatly increased our understanding of these bacteria. Efficient subtraction methods are needed for removing both bacteria and insect rRNA in these systems to enable transcriptome-based studies.<br><br>FINDINGS: A method is described that efficiently removes >95% of insect rRNA from total RNA samples, as determined by microfluidics and transcriptome sequencing. This subtraction yielded a 6.2-fold increase in mRNA abundance. Such a host rRNA-depletion strategy, in combination with bacterial rRNA depletion, is necessary to analyze transcription of obligate intracellular bacteria. Here, transcripts were identified that arise from a lateral gene transfer of an entire Wolbachia bacterial genome into a Drosophila ananassae chromosome. In this case, an rRNA depletion strategy is preferred over polyA-based enrichment since transcripts arising from bacteria-to-animal lateral gene transfer may not be poly-adenylated.<br><br>CONCLUSIONS: This enrichment method yields a significant increase in mRNA abundance when poly-A selection is not suitable. It can be used in combination with bacterial rRNA subtraction to enable experiments to simultaneously measure bacteria and insect mRNA in vector and endosymbiont biology experiments.}, }
@article {pmid22577862, year = {2012}, author = {Guy, L and Nystedt, B and Sun, Y and Näslund, K and Berglund, EC and Andersson, SG}, title = {A genome-wide study of recombination rate variation in Bartonella henselae.}, journal = {BMC evolutionary biology}, volume = {12}, number = {}, pages = {65}, pmid = {22577862}, issn = {1471-2148}, mesh = {Bacterial Secretion Systems/genetics ; Bartonella henselae/*genetics ; *Comparative Genomic Hybridization ; DNA, Bacterial/genetics ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Multigene Family ; Phylogeny ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Rates of recombination vary by three orders of magnitude in bacteria but the reasons for this variation is unclear. We performed a genome-wide study of recombination rate variation among genes in the intracellular bacterium Bartonella henselae, which has among the lowest estimated ratio of recombination relative to mutation in prokaryotes.<br><br>RESULTS: The 1.9&#x2009;Mb genomes of B. henselae strains IC11, UGA10 and Houston-1 genomes showed only minor gene content variation. Nucleotide sequence divergence levels were less than 1% and the relative rate of recombination to mutation was estimated to 1.1 for the genome overall. Four to eight segments per genome presented significantly enhanced divergences, the most pronounced of which were the virB and trw gene clusters for type IV secretion systems that play essential roles in the infection process. Consistently, multiple recombination events were identified inside these gene clusters. High recombination frequencies were also observed for a gene putatively involved in iron metabolism. A phylogenetic study of this gene in 80 strains of Bartonella quintana, B. henselae and B. grahamii indicated different population structures for each species and revealed horizontal gene transfers across Bartonella species with different host preferences.<br><br>CONCLUSIONS: Our analysis has shown little novel gene acquisition in B. henselae, indicative of a closed pan-genome, but higher recombination frequencies within the population than previously estimated. We propose that the dramatically increased fixation rate for recombination events at gene clusters for type IV secretion systems is driven by selection for sequence variability.}, }
@article {pmid22577106, year = {2012}, author = {Hennequin, C and Aumeran, C and Robin, F and Traore, O and Forestier, C}, title = {Antibiotic resistance and plasmid transfer capacity in biofilm formed with a CTX-M-15-producing Klebsiella pneumoniae isolate.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {67}, number = {9}, pages = {2123-2130}, doi = {10.1093/jac/dks169}, pmid = {22577106}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/pharmacology ; Biofilms/*growth &amp; development ; Cross Infection/epidemiology/microbiology ; Disease Outbreaks ; France/epidemiology ; *Gene Transfer, Horizontal ; Humans ; Klebsiella Infections/epidemiology/microbiology ; Klebsiella pneumoniae/*drug effects/genetics/*physiology ; Microbial Sensitivity Tests ; *Plasmids ; *beta-Lactam Resistance ; beta-Lactamases/*genetics ; beta-Lactams/pharmacology ; }, abstract = {OBJECTIVES: To characterize a CTX-M-15-producing Klebsiella pneumoniae isolate that was identified during an outbreak involving 16 patients who had undergone endoscopic retrograde cholangiopancreatography between December 2008 and August 2009. The strain was also detected in one endoscope used for these examinations.<br><br>METHODS: Disc diffusion assays, MICs and isoelectric focusing were used to characterize the plasmidic CTX-M-15 &#x3b2;-lactamase. PCRs were used to check for the presence of genes associated with virulence or antibiotic resistance. Antibiotic tolerance tests and plasmid transfer were carried out in both planktonic and biofilm conditions.<br><br>RESULTS: The strain belonged to sequence type 14 and to the virulent capsular serotype K2, but produced little glucuronic acid. It contained a 62.5 kb conjugative plasmid carrying the bla(CTX-M-15), bla(OXA-1) and aac(6')-Ib-cr genes and harboured few virulence genes (uge, wabG, kfu and mrkD). The strain was highly resistant to cefotaxime (MIC 516 mg/L) and the presence of this antibiotic at sub-MIC concentrations enhanced biofilm formation. The isolate was susceptible to ofloxacin (MIC 2 mg/L), but the bactericidal effect of this antibiotic was greater in planktonic cultures and 6 h old biofilm than in 24 or 48 h old biofilms. The K. pneumoniae strain was notable for its ability to transfer its plasmid, especially in biofilm conditions, in which the rate of plasmid transfer was about 0.5/donor.<br><br>CONCLUSIONS: These findings demonstrate the ability of this strain to survive in a hospital environment and to transfer its extended-spectrum &#x3b2;-lactamase-encoding plasmid.}, }
@article {pmid22574681, year = {2012}, author = {Kahlke, T and Goesmann, A and Hjerde, E and Willassen, NP and Haugen, P}, title = {Unique core genomes of the bacterial family vibrionaceae: insights into niche adaptation and speciation.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {179}, pmid = {22574681}, issn = {1471-2164}, mesh = {Adaptation, Biological/*genetics ; Cluster Analysis ; Databases, Genetic ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Multigene Family ; Phylogeny ; Software ; Species Specificity ; Vibrionaceae/classification/*genetics ; }, abstract = {BACKGROUND: The criteria for defining bacterial species and even the concept of bacterial species itself are under debate, and the discussion is apparently intensifying as more genome sequence data is becoming available. However, it is still unclear how the new advances in genomics should be used most efficiently to address this question. In this study we identify genes that are common to any group of genomes in our dataset, to determine whether genes specific to a particular taxon exist and to investigate their potential role in adaptation of bacteria to their specific niche. These genes were named unique core genes. Additionally, we investigate the existence and importance of unique core genes that are found in isolates of phylogenetically non-coherent groups. These groups of isolates, that share a genetic feature without sharing a closest common ancestor, are termed genophyletic groups.<br><br>RESULTS: The bacterial family Vibrionaceae was used as the model, and we compiled and compared genome sequences of 64 different isolates. Using the software orthoMCL we determined clusters of homologous genes among the investigated genome sequences. We used multilocus sequence analysis to build a host phylogeny and mapped the numbers of unique core genes of all distinct groups of isolates onto the tree. The results show that unique core genes are more likely to be found in monophyletic groups of isolates. Genophyletic groups of isolates, in contrast, are less common especially for large groups of isolate. The subsequent annotation of unique core genes that are present in genophyletic groups indicate a high degree of horizontally transferred genes. Finally, the annotation of the unique core genes of Vibrio cholerae revealed genes involved in aerotaxis and biosynthesis of the iron-chelator vibriobactin.<br><br>CONCLUSION: The presented work indicates that genes specific for any taxon inside the bacterial family Vibrionaceae exist. These unique core genes encode conserved metabolic functions that can shed light on the adaptation of a species to its ecological niche. Additionally, our study suggests that unique core genes can be used to aid classification of bacteria and contribute to a bacterial species definition on a genomic level. Furthermore, these genes may be of importance in clinical diagnostics and drug development.}, }
@article {pmid22574114, year = {2012}, author = {Sánchez, MB and Martínez, JL}, title = {Differential epigenetic compatibility of qnr antibiotic resistance determinants with the chromosome of Escherichia coli.}, journal = {PloS one}, volume = {7}, number = {5}, pages = {e35149}, pmid = {22574114}, issn = {1932-6203}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics ; Chromosomes, Bacterial/drug effects/*genetics ; Drug Resistance, Bacterial/*genetics ; Epigenesis, Genetic/drug effects/*genetics ; Escherichia coli/drug effects/*genetics ; Gene Transfer, Horizontal/drug effects/*genetics ; Genome, Bacterial/genetics ; Mutation ; Plasmids/genetics ; Quinolones/*pharmacology ; Shewanella/drug effects/genetics ; }, abstract = {Environmental bacteria harbor a plethora of genes that, upon their horizontal transfer to new hosts, may confer resistance to antibiotics, although the number of such determinants actually acquired by pathogenic bacteria is very low. The founder effect, fitness costs and ecological connectivity all influence the chances of resistance transfer being successful. We examined the importance of these bottlenecks using the family of quinolone resistance determinants Qnr. The results indicate the epigenetic compatibility of a determinant with the host genome to be of great importance in the acquisition and spread of resistance. A plasmid carrying the widely distributed QnrA determinant was stable in Escherichia coli, whereas the SmQnr determinant was unstable despite both proteins having very similar tertiary structures. This indicates that the fitness costs associated with the acquisition of antibiotic resistance may not derive from a non-specific metabolic burden, but from the acquired gene causing specific changes in bacterial metabolic and regulatory networks. The observed stabilization of the plasmid encoding SmQnr by chromosomal mutations, including a mutant lacking the global regulator H-NS, reinforces this idea. Since quinolones are synthetic antibiotics, and since the origin of QnrA is the environmental bacterium Shewanella algae, the role of QnrA in this organism is unlikely to be that of conferring resistance. Its evolution toward this may have occurred through mutations or because of an environmental change (exaptation). The present results indicate that the chromosomally encoded Qnr determinants of S. algae can confer quinolone resistance upon their transfer to E. coli without the need of any further mutation. These results suggest that exaptation is important in the evolution of antibiotic resistance.}, }
@article {pmid22573173, year = {2012}, author = {Seshasayee, AS and Singh, P and Krishna, S}, title = {Context-dependent conservation of DNA methyltransferases in bacteria.}, journal = {Nucleic acids research}, volume = {40}, number = {15}, pages = {7066-7073}, pmid = {22573173}, issn = {1362-4962}, mesh = {Bacteria/*enzymology ; Base Sequence ; Conserved Sequence ; DNA Modification Methylases/chemistry/*genetics/metabolism ; DNA Restriction Enzymes/metabolism ; Gene Transfer, Horizontal ; Genome, Bacterial ; }, abstract = {DNA methytransferases (MTs) in bacteria are best understood in the context of restriction-modification (R-M) systems, which act as bacterial immune systems against incoming DNA including phages, but have also been described as selfish elements. But several orphan MTs, which are not associated with any restriction enzyme, have also been characterized and may protect against parasitism by R-M systems. The occurrence of MTs in these two contexts, namely as part of R-M systems or as orphans, is poorly understood. Here we report the results of a comparative genomic survey of DNA MTs across ∼1000 bacterial genomes. We show that orphan MTs overwhelm R-M systems in their occurrence. In general, R-M MTs are poorly conserved, whereas orphans are nearly as conserved within a genus as any average gene. However, oligonucleotide usage and conservation patterns across genera suggest that both forms of MTs might have been horizontally acquired. We suggest that many orphan MTs might be 'degradation' products of R-M systems, based on the properties of orphan MTs encoded adjacent to highly diverged REs. In addition, several fully degraded R-M systems exist in which both the MT and the RE are highly divergent from their corresponding reference R-M pair. Despite their sporadic occurrence, conserved R-M systems are present in strength in two highly transformable genera, in which they may contribute to selection against integration of foreign DNA.}, }
@article {pmid22572858, year = {2012}, author = {Dodd, MC}, title = {Potential impacts of disinfection processes on elimination and deactivation of antibiotic resistance genes during water and wastewater treatment.}, journal = {Journal of environmental monitoring : JEM}, volume = {14}, number = {7}, pages = {1754-1771}, doi = {10.1039/c2em00006g}, pmid = {22572858}, issn = {1464-0333}, mesh = {Bacteria/drug effects/*genetics ; *Disinfection ; Drug Resistance, Microbial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Waste Disposal, Fluid ; *Water Microbiology ; }, abstract = {Antibiotic resistance genes (ARGs), in association with antibiotic resistant bacteria (ARB), have been identified as widespread contaminants of treated drinking waters and wastewaters. As a consequence, concerns have been raised that ARB or ARG transport between aquatic compartments may enhance the spread of antibiotic resistance amongst non-resistant bacterial communities by means of horizontal gene transfer processes. Most often, discussion of horizontal gene transfer focuses on the probable role of conjugative plasmid or transposon exchange, which requires live ARB donor cells. Conventional water and wastewater disinfection processes generally provide highly effective means for mitigating the transport of live ARB; thereby minimizing risks of conjugative gene transfer. However, even if ARB present in a treated water are fully inactivated during a disinfection process, the possibility remains that intact remnants of DNA contained within the resulting cell debris could still confer resistance genotypes to downstream bacterial populations by means of natural transformation and/or transduction, which do not require live donor cells. Thus, a systematic evaluation of the capability of common disinfection technologies to ensure the destruction of bacterial DNA, in addition to pathogen inactivation, seems warranted. With that objective in mind, this review seeks to provide a concise introduction to the significance of ARB and ARG occurrence in environmental systems, coupled with a review of the role that commonly used water and wastewater disinfection processes may play in minimizing ARG transport and dissemination.}, }
@article {pmid22569756, year = {2011}, author = {César, CE and Álvarez, L and Bricio, C and van Heerden, E and Littauer, D and Berenguer, J}, title = {Unconventional lateral gene transfer in extreme thermophilic bacteria.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {14}, number = {4}, pages = {187-199}, doi = {10.2436/20.1501.01.148}, pmid = {22569756}, issn = {1618-1905}, mesh = {Bacterial Proteins/genetics/metabolism ; Conjugation, Genetic ; Conserved Sequence ; DNA Transformation Competence ; *Gene Transfer, Horizontal ; Thermus/*genetics ; }, abstract = {Conjugation and natural competence are two major mechanisms that explain the acquisition of foreign genes throughout bacterial evolution. In recent decades, several studies in model organisms have revealed in great detail the steps involved in such processes. The findings support the idea that the major basis of these mechanisms is essentially similar in all bacteria. However, recent work has pinpointed the existence of new, evolutionarily different processes underlying lateral gene transfer. In Thermus thermophilus HB27, at least 16 proteins are required for the activity of one of the most efficient natural competence systems known so far. Many of those proteins have no similarities to proteins involved in natural competence in other well-known models. This unusual competence system is conserved, in association with the chromosome, in all other Thermus spp. genomes so far available, it being functional even in strains from isolated environments, such as deep mines. Conjugation is also possible among Thermus spp. Homologues to proteins implicated in conjugation in model bacteria are encoded in the genome of a recently sequenced strain of Thermus thermophilus and shared by other members of the genus. Nevertheless, processive DNA transfer in the absence of a functional natural competence system in strains in which no conjugation homologous genes can be found hints at the existence of an additional and unconventional conjugation mechanism in these bacteria.}, }
@article {pmid22569516, year = {2012}, author = {Gardner, SP and Olson, JW}, title = {Barriers to Horizontal Gene Transfer in Campylobacter jejuni.}, journal = {Advances in applied microbiology}, volume = {79}, number = {}, pages = {19-42}, doi = {10.1016/B978-0-12-394318-7.00002-4}, pmid = {22569516}, issn = {0065-2164}, mesh = {Campylobacter ; *Campylobacter jejuni ; Escherichia coli/genetics ; *Gene Transfer, Horizontal ; Plasmids ; }, abstract = {Campylobacter jejuni is among the most frequent agent of foodborne gastroenteritis in the world, but its physiology and pathogenesis is less well understood than other bacterial enteric pathogens. This is due in part to the incompatibility of the molecular tools that have enabled advances in the characterization of other bacterial species. Most notably, the dearth of plasmid-based complementation, reporter assays, and plasmid-based unmarked mutagenesis procedures in many of the type strains has hindered research progress. The techniques themselves are not inadequate in Campylobacter species, but rather the barrier to genetic transfer of these genetic constructs from non-Campylobacter cloning stains such as Escherichia coli. Here, we review the modes of genetic transfer in C. jejuni and review the current state of research into the mechanism of each. Also reviewed are two systems (CRISPR-Cas and restriction modification) that are common to many strains of C. jejuni and are at least partly responsible for these barriers.}, }
@article {pmid23814665, year = {2012}, author = {Martins, LD and Posada, D}, title = {Proving universal common ancestry with similar sequences.}, journal = {Trends in evolutionary biology}, volume = {4}, number = {1}, pages = {}, pmid = {23814665}, issn = {2036-2641}, support = {203161/ERC_/European Research Council/International ; }, abstract = {Douglas Theobald recently developed an interesting test putatively capable of quantifying the evidence for a Universal Common Ancestry uniting the three domains of life (Eukarya, Archaea and Bacteria) against hypotheses of Independent Origins for some of these domains. We review here his model, in particular in relation to the treatment of Horizontal Gene Transfer (HGT) and to the quality of sequence alignment.}, }
@article {pmid22567121, year = {2012}, author = {Raymond, JA and Kim, HJ}, title = {Possible role of horizontal gene transfer in the colonization of sea ice by algae.}, journal = {PloS one}, volume = {7}, number = {5}, pages = {e35968}, pmid = {22567121}, issn = {1932-6203}, mesh = {Algal Proteins/genetics/physiology ; Diatoms/genetics/physiology ; Gene Transfer, Horizontal/genetics/*physiology ; Haptophyta/genetics/physiology ; *Ice Cover ; Phylogeny ; }, abstract = {Diatoms and other algae not only survive, but thrive in sea ice. Among sea ice diatoms, all species examined so far produce ice-binding proteins (IBPs), whereas no such proteins are found in non-ice-associated diatoms, which strongly suggests that IBPs are essential for survival in ice. The restricted occurrence also raises the question of how the IBP genes were acquired. Proteins with similar sequences and ice-binding activities are produced by ice-associated bacteria, and so it has previously been speculated that the genes were acquired by horizontal transfer (HGT) from bacteria. Here we report several new IBP sequences from three types of ice algae, which together with previously determined sequences reveal a phylogeny that is completely incongruent with algal phylogeny, and that can be most easily explained by HGT. HGT is also supported by the finding that the closest matches to the algal IBP genes are all bacterial genes and that the algal IBP genes lack introns. We also describe a highly freeze-tolerant bacterium from the bottom layer of Antarctic sea ice that produces an IBP with 47% amino acid identity to a diatom IBP from the same layer, demonstrating at least an opportunity for gene transfer. Together, these results suggest that the success of diatoms and other algae in sea ice can be at least partly attributed to their acquisition of prokaryotic IBP genes.}, }
@article {pmid22564249, year = {2012}, author = {Harrison, E and Brockhurst, MA}, title = {Plasmid-mediated horizontal gene transfer is a coevolutionary process.}, journal = {Trends in microbiology}, volume = {20}, number = {6}, pages = {262-267}, doi = {10.1016/j.tim.2012.04.003}, pmid = {22564249}, issn = {1878-4380}, mesh = {Adaptation, Biological ; Bacteria/*genetics/metabolism ; *Conjugation, Genetic ; Energy Metabolism ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Plasmids ; }, abstract = {Conjugative plasmids are key agents of horizontal gene transfer (HGT) that accelerate bacterial adaptation by vectoring ecologically important traits between strains and species. However, although many conjugative plasmids carry beneficial traits, all plasmids exert physiological costs-of-carriage on bacteria. The existence of conjugative plasmids, therefore, presents a paradox because non-beneficial plasmids should be lost to purifying selection, whereas beneficial genes carried on plasmids should be integrated into the bacterial chromosome. Several ecological solutions to the paradox have been proposed, but none account for co-adaptation of bacteria and conjugative plasmids. Drawing upon evidence from experimental evolution, we argue that HGT via conjugation can only be fully understood in a coevolutionary framework.}, }
@article {pmid22563400, year = {2012}, author = {Math, RK and Jin, HM and Kim, JM and Hahn, Y and Park, W and Madsen, EL and Jeon, CO}, title = {Comparative genomics reveals adaptation by Alteromonas sp. SN2 to marine tidal-flat conditions: cold tolerance and aromatic hydrocarbon metabolism.}, journal = {PloS one}, volume = {7}, number = {4}, pages = {e35784}, pmid = {22563400}, issn = {1932-6203}, mesh = {Alteromonas/*genetics/isolation &amp; purification ; Cold Temperature ; Databases, Genetic ; Genome, Bacterial ; *Genomics ; Geologic Sediments/microbiology ; Hydrocarbons, Aromatic/*metabolism ; Molecular Chaperones/genetics/metabolism ; Molecular Sequence Data ; Multigene Family ; RNA, Transfer/genetics/metabolism ; RNA, Untranslated/genetics/metabolism ; Signal Transduction/genetics ; }, abstract = {Alteromonas species are globally distributed copiotrophic bacteria in marine habitats. Among these, sea-tidal flats are distinctive: undergoing seasonal temperature and oxygen-tension changes, plus periodic exposure to petroleum hydrocarbons. Strain SN2 of the genus Alteromonas was isolated from hydrocarbon-contaminated sea-tidal flat sediment and has been shown to metabolize aromatic hydrocarbons there. Strain SN2's genomic features were analyzed bioinformatically and compared to those of Alteromonas macleodii ecotypes: AltDE and ATCC 27126. Strain SN2's genome differs from that of the other two strains in: size, average nucleotide identity value, tRNA genes, noncoding RNAs, dioxygenase gene content, signal transduction genes, and the degree to which genes collected during the Global Ocean Sampling project are represented. Patterns in genetic characteristics (e.g., GC content, GC skew, Karlin signature, CRISPR gene homology) indicate that strain SN2's genome architecture has been altered via horizontal gene transfer (HGT). Experiments proved that strain SN2 was far more cold tolerant, especially at 5°C, than the other two strains. Consistent with the HGT hypothesis, a total of 15 genomic islands in strain SN2 likely confer ecological fitness traits (especially membrane transport, aromatic hydrocarbon metabolism, and fatty acid biosynthesis) specific to the adaptation of strain SN2 to its seasonally cold sea-tidal flat habitat.}, }
@article {pmid22563396, year = {2012}, author = {Riccombeni, A and Vidanes, G and Proux-Wéra, E and Wolfe, KH and Butler, G}, title = {Sequence and analysis of the genome of the pathogenic yeast Candida orthopsilosis.}, journal = {PloS one}, volume = {7}, number = {4}, pages = {e35750}, pmid = {22563396}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Candida/classification/*genetics/pathogenicity ; Cluster Analysis ; *Genome, Fungal ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Candida orthopsilosis is closely related to the fungal pathogen Candida parapsilosis. However, whereas C. parapsilosis is a major cause of disease in immunosuppressed individuals and in premature neonates, C. orthopsilosis is more rarely associated with infection. We sequenced the C. orthopsilosis genome to facilitate the identification of genes associated with virulence. Here, we report the de novo assembly and annotation of the genome of a Type 2 isolate of C. orthopsilosis. The sequence was obtained by combining data from next generation sequencing (454 Life Sciences and Illumina) with paired-end Sanger reads from a fosmid library. The final assembly contains 12.6 Mb on 8 chromosomes. The genome was annotated using an automated pipeline based on comparative analysis of genomes of Candida species, together with manual identification of introns. We identified 5700 protein-coding genes in C. orthopsilosis, of which 5570 have an ortholog in C. parapsilosis. The time of divergence between C. orthopsilosis and C. parapsilosis is estimated to be twice as great as that between Candida albicans and Candida dubliniensis. There has been an expansion of the Hyr/Iff family of cell wall genes and the JEN family of monocarboxylic transporters in C. parapsilosis relative to C. orthopsilosis. We identified one gene from a Maltose/Galactoside O-acetyltransferase family that originated by horizontal gene transfer from a bacterium to the common ancestor of C. orthopsilosis and C. parapsilosis. We report that TFB3, a component of the general transcription factor TFIIH, undergoes alternative splicing by intron retention in multiple Candida species. We also show that an intein in the vacuolar ATPase gene VMA1 is present in C. orthopsilosis but not C. parapsilosis, and has a patchy distribution in Candida species. Our results suggest that the difference in virulence between C. parapsilosis and C. orthopsilosis may be associated with expansion of gene families.}, }
@article {pmid22561821, year = {2012}, author = {Kriegeskorte, A and Peters, G}, title = {Horizontal gene transfer boosts MRSA spreading.}, journal = {Nature medicine}, volume = {18}, number = {5}, pages = {662-663}, pmid = {22561821}, issn = {1546-170X}, mesh = {Animals ; Female ; Humans ; Methicillin-Resistant Staphylococcus aureus/*pathogenicity ; }, abstract = {Mechanisms triggering methicillin-resistant Staphylococcus aureus (MRSA) epidemics are poorly understood. A recent study provides new evidence that horizontal gene transfer may be the culprit for the emergence of new resistant and virulent MRSA clones.}, }
@article {pmid22559316, year = {2012}, author = {Hu, J and Chen, C and Peever, T and Dang, H and Lawrence, C and Mitchell, T}, title = {Genomic characterization of the conditionally dispensable chromosome in Alternaria arborescens provides evidence for horizontal gene transfer.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {171}, pmid = {22559316}, issn = {1471-2164}, mesh = {Alternaria/classification/*genetics ; Blotting, Southern ; *Chromosomes, Fungal ; Codon ; Contig Mapping ; Databases, Genetic ; *Gene Transfer, Horizontal ; Genome, Fungal/*genetics ; Solanum lycopersicum/microbiology ; Multigene Family ; Mycotoxins/biosynthesis/genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Fungal plant pathogens cause serious agricultural losses worldwide. Alternaria arborescens is a major pathogen of tomato, with its virulence determined by the presence of a conditionally dispensable chromosome (CDC) carrying host-specific toxin genes. Genes encoding these toxins are well-studied, however the genomic content and organization of the CDC is not known.<br><br>RESULTS: To gain a richer understanding of the molecular determinants of virulence and the evolution of pathogenicity, we performed whole genome sequencing of A. arborescens. Here we present the de-novo assembly of the CDC and its predicted gene content. Also presented is hybridization data validating the CDC assembly. Predicted genes were functionally annotated through BLAST. Gene ontology terms were assigned, and conserved domains were identified. Differences in nucleotide usage were found between CDC genes and those on the essential chromosome (EC), including GC3-content, codon usage bias, and repeat region load. Genes carrying PKS and NRPS domains were identified in clusters on the CDC and evidence supporting the origin of the CDC through horizontal transfer from an unrelated fungus was found.<br><br>CONCLUSIONS: We provide evidence supporting the hypothesis that the CDC in A. arborescens was acquired through horizontal transfer, likely from an unrelated fungus. We also identified several predicted CDC genes under positive selection that may serve as candidate virulence factors.}, }
@article {pmid22559054, year = {2012}, author = {Peters, DL and Pretorius, PJ}, title = {Continuous adaptation through genetic communication - a putative role for cell-free DNA.}, journal = {Expert opinion on biological therapy}, volume = {12 Suppl 1}, number = {}, pages = {S127-32}, doi = {10.1517/14712598.2012.668518}, pmid = {22559054}, issn = {1744-7682}, mesh = {*Adaptation, Physiological ; Cell-Free System ; DNA/genetics/*physiology ; Genome ; Humans ; }, abstract = {INTRODUCTION: The virtosome fraction of cell-free DNA, being newly synthesised, capable of horizontal gene transfer (HGT) and subsequent genomic incorporation and expression, may play crucial roles in the biological functions of higher organisms. In order to unlock the full potential of cell-free DNA as a biomarker, we need to fully understand its biological roles.<br><br>AREAS COVERED: Metabolic DNA is possibly the precursor to the bulk of cell-free DNA, which is actively released as lipoprotein complexes. These released lipoprotein complexes are referred to as virtosomes. Research suggests that acquired characteristics, including physical and behavioural traits can be inherited in contrast to the neo-Darwinian dogma. We consider the virtosome fraction of cell-free DNA to be involved in this process. We suggest that at least one process of endoreplication is responsible for the synthesis of metabolic DNA and that this DNA follows apoptotic-like breakdown prior to release.<br><br>EXPERT OPINION: If individual cellular genomes are capable of acquiring and donating the active parts of their genomes, selection of viable genetic information occurs not only through natural selection of whole organisms, but occurs continuously at a subgenomic level. The process of homeostatic adaptation in higher organisms is influenced by the characteristics of HGT.}, }
@article {pmid22558224, year = {2012}, author = {Zheng, Q and Zhang, R and Fogg, PC and Beatty, JT and Wang, Y and Jiao, N}, title = {Gain and loss of phototrophic genes revealed by comparison of two Citromicrobium bacterial genomes.}, journal = {PloS one}, volume = {7}, number = {4}, pages = {e35790}, pmid = {22558224}, issn = {1932-6203}, support = {93779-1//Canadian Institutes of Health Research/Canada ; }, mesh = {Base Sequence ; Biological Evolution ; Gene Transfer, Horizontal/*genetics ; *Genes, Bacterial ; *Genome, Bacterial ; Molecular Sequence Data ; Multigene Family ; Operon ; Photosynthesis/*genetics ; Phylogeny ; Proteobacteria/classification/*genetics ; RNA, Ribosomal, 16S/analysis/*biosynthesis ; }, abstract = {Proteobacteria are thought to have diverged from a phototrophic ancestor, according to the scattered distribution of phototrophy throughout the proteobacterial clade, and so the occurrence of numerous closely related phototrophic and chemotrophic microorganisms may be the result of the loss of genes for phototrophy. A widespread form of bacterial phototrophy is based on the photochemical reaction center, encoded by puf and puh operons that typically are in a 'photosynthesis gene cluster' (abbreviated as the PGC) with pigment biosynthesis genes. Comparison of two closely related Citromicrobial genomes (98.1% sequence identity of complete 16S rRNA genes), Citromicrobium sp. JL354, which contains two copies of reaction center genes, and Citromicrobium strain JLT1363, which is chemotrophic, revealed evidence for the loss of phototrophic genes. However, evidence of horizontal gene transfer was found in these two bacterial genomes. An incomplete PGC (pufLMC-puhCBA) in strain JL354 was located within an integrating conjugative element, which indicates a potential mechanism for the horizontal transfer of genes for phototrophy.}, }
@article {pmid22558202, year = {2012}, author = {Krauland, MG and Dunning Hotopp, JC and Riley, DR and Daugherty, SC and Marsh, JW and Messonnier, NE and Mayer, LW and Tettelin, H and Harrison, LH}, title = {Whole genome sequencing to investigate the emergence of clonal complex 23 Neisseria meningitidis serogroup Y disease in the United States.}, journal = {PloS one}, volume = {7}, number = {4}, pages = {e35699}, pmid = {22558202}, issn = {1932-6203}, mesh = {Alleles ; Antigens, Bacterial/*genetics ; Chromosome Mapping ; Fimbriae Proteins/genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genotype ; High-Throughput Nucleotide Sequencing ; Humans ; Incidence ; Iron/metabolism ; Meningococcal Infections/*epidemiology/microbiology ; Neisseria meningitidis, Serogroup Y/classification/*genetics/isolation &amp; purification ; Phylogeny ; Serotyping ; United States ; }, abstract = {In the United States, serogroup Y, ST-23 clonal complex Neisseria meningitidis was responsible for an increase in meningococcal disease incidence during the 1990s. This increase was accompanied by antigenic shift of three outer membrane proteins, with a decrease in the population that predominated in the early 1990s as a different population emerged later in that decade. To understand factors that may have been responsible for the emergence of serogroup Y disease, we used whole genome pyrosequencing to investigate genetic differences between isolates from early and late N. meningitidis populations, obtained from meningococcal disease cases in Maryland in the 1990s. The genomes of isolates from the early and late populations were highly similar, with 1231 of 1776 shared genes exhibiting 100% amino acid identity and an average π(N) = 0.0033 and average π(S) = 0.0216. However, differences were found in predicted proteins that affect pilin structure and antigen profile and in predicted proteins involved in iron acquisition and uptake. The observed changes are consistent with acquisition of new alleles through horizontal gene transfer. Changes in antigen profile due to the genetic differences found in this study likely allowed the late population to emerge due to escape from population immunity. These findings may predict which antigenic factors are important in the cyclic epidemiology of meningococcal disease.}, }
@article {pmid22553940, year = {2012}, author = {Varga, M and Kuntová, L and Pantůček, R and Mašlaňová, I and Růžičková, V and Doškař, J}, title = {Efficient transfer of antibiotic resistance plasmids by transduction within methicillin-resistant Staphylococcus aureus USA300 clone.}, journal = {FEMS microbiology letters}, volume = {332}, number = {2}, pages = {146-152}, doi = {10.1111/j.1574-6968.2012.02589.x}, pmid = {22553940}, issn = {1574-6968}, mesh = {Bacteriophages/*genetics ; *Drug Resistance, Bacterial ; *Gene Transfer, Horizontal ; Humans ; Methicillin-Resistant Staphylococcus aureus/*genetics/isolation &amp; purification/*virology ; *Plasmids ; Prophages/genetics ; Staphylococcal Infections/microbiology ; *Transduction, Genetic ; }, abstract = {The epidemic community-associated methicillin-resistant clone Staphylococcus aureus USA300 is a major source of skin and soft tissue infections and involves strains with a diverse set of resistance genes. In this study, we report efficient transduction of penicillinase and tetracycline resistance plasmids by bacteriophages φ80α and φJB between clinical isolates belonging to the USA300 clone. High transduction frequencies (10(-5) - 10(-6) CFU/PFU) were observed using phages propagated on donor strains as well as prophages induced from donors by ultraviolet light. Quantitative real-time PCR was employed to detect penicillinase plasmids in transducing phage particles and determine the ratio of transducing particles in phage lysates to infectious phage particles (determined as approximately 1 : 1700). Successful transfer of plasmids between strains in USA300 clone proves transduction is an effective mechanism for spreading plasmids within the clone. Such events contribute to its evolution and to emergence of new multiple drug-resistant strains of this successful clone.}, }
@article {pmid22553140, year = {2012}, author = {Karczmarczyk, M and Stephan, R and Hächler, H and Fanning, S}, title = {Complete nucleotide sequence of pVQS1 containing a quinolone resistance determinant from Salmonella enterica serovar Virchow associated with foreign travel.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {67}, number = {8}, pages = {1861-1864}, doi = {10.1093/jac/dks158}, pmid = {22553140}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/*pharmacology ; Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Humans ; Molecular Sequence Data ; Plasmids/*analysis ; Polymerase Chain Reaction ; Quinolones/*pharmacology ; Salmonella Infections/*microbiology ; Salmonella enterica/*drug effects/*genetics/isolation &amp; purification ; Sequence Analysis, DNA ; Switzerland ; Travel ; }, abstract = {OBJECTIVES: Nalidixic acid-resistant Salmonella enterica serovars Kentucky (n = 5) and Virchow (n = 6) cultured from individuals were investigated for the presence of plasmid-mediated quinolone resistance (PMQR) determinants.<br><br>METHODS: PMQR markers and mutations within the quinolone resistance-determining regions of the target genes were investigated by PCR followed by DNA sequencing. Conjugation, plasmid profiling and targeted PCR were performed to demonstrate the transferability of the qnrS1 gene. Subsequently, a plasmid was identified that carried a quinolone resistance marker and this was completely sequenced.<br><br>RESULTS: A Salmonella Virchow isolate carried a qnrS1 gene associated with an IncN incompatibility group conjugative plasmid of 40&#x200a;995 bp, which was designated pVQS1. The latter conferred resistance to ampicillin and nalidixic acid and showed sequence similarity in its core region to plasmid R46, whilst the resistance-encoding region was similar to pAH0376 from Shigella flexneri and pINF5 from Salmonella Infantis and contained an IS26 remnant, a complete Tn3 structure, a truncated IS2 element and a qnrS1 marker, followed by IS26. In contrast to pINF5, IS26 was identified immediately downstream of the qnrS1 gene.<br><br>CONCLUSIONS: This is the first known report of a qnrS1 gene in Salmonella spp. in Switzerland. Analysis of the complete nucleotide sequence of the qnrS1-containing plasmid showed a novel arrangement of this antibiotic resistance-encoding region.}, }
@article {pmid22549164, year = {2012}, author = {Morton, ER and Fuqua, C}, title = {Phenotypic analyses of Agrobacterium.}, journal = {Current protocols in microbiology}, volume = {Chapter 3}, number = {}, pages = {Unit 3D.3.}, pmid = {22549164}, issn = {1934-8533}, support = {R01 GM080546/GM/NIGMS NIH HHS/United States ; R01 GM092660/GM/NIGMS NIH HHS/United States ; GM092660/GM/NIGMS NIH HHS/United States ; GM080546/GM/NIGMS NIH HHS/United States ; }, mesh = {Agrobacterium tumefaciens/enzymology/genetics/pathogenicity/*physiology ; *Bacterial Adhesion ; Biofilms/*growth &amp; development ; Flagella/physiology ; Genes, Reporter ; *Locomotion ; Plant Tumors/*microbiology ; Plants/*microbiology ; beta-Galactosidase/genetics/metabolism ; }, abstract = {Agrobacterium species are plant-associated relatives of the rhizobia. Several species cause plant diseases such as crown gall and hairy root, although there are also avirulent species. A. tumefaciens is the most intensively studied species and causes crown gall, a neoplastic disease that occurs on a variety of plants. Virulence is specified by large plasmids, and in the case of A. tumefaciens this is called the Ti (tumor-inducing) plasmid. During pathogenesis virulent agrobacteria copy a segment of the Ti plasmid and transfer it to the plant, where it subsequently integrates into the plant genome, and expresses genes that result in the disease symptoms. A. tumefaciens has been used extensively as a plant genetic engineering tool and is also a model microorganism that has been well studied for host-microbe associations, horizontal gene transfer, cell-cell communication, and biofilm formation. This unit describes standard protocols for simple phenotypic characterizations of A. tumefaciens.}, }
@article {pmid22549163, year = {2012}, author = {Morton, ER and Fuqua, C}, title = {Genetic manipulation of Agrobacterium.}, journal = {Current protocols in microbiology}, volume = {Chapter 3}, number = {}, pages = {Unit 3D.2.}, pmid = {22549163}, issn = {1934-8533}, support = {R01 GM080546/GM/NIGMS NIH HHS/United States ; R01 GM092660/GM/NIGMS NIH HHS/United States ; }, mesh = {Agrobacterium tumefaciens/*genetics/pathogenicity ; Gene Transfer Techniques ; Genetic Engineering/*methods ; Genetic Vectors ; Genetics, Microbial/*methods ; Host-Pathogen Interactions ; Plant Diseases/microbiology ; Plant Tumor-Inducing Plasmids ; Plants/genetics/microbiology ; Plants, Genetically Modified/microbiology ; Virulence ; }, abstract = {Agrobacterium species are plant-associated relatives of the rhizobia. Several species cause plant diseases such as crown gall and hairy root, although there are also avirulent species. A. tumefaciens is the most intensively studied species and causes crown gall, a neoplastic disease that occurs on a variety of plants. Virulence is specified by large plasmids, and in the case of A. tumefaciens, this is called the Ti (tumor-inducing) plasmid. During pathogenesis virulent agrobacteria copy a segment of the Ti plasmid and transfer it to the plant, where it subsequently integrates into the plant genome, and expresses genes that result in the disease symptoms. A. tumefaciens has been used extensively as a plant genetic engineering tool and is also a model microorganism that has been well studied for host-microbe associations, horizontal gene transfer, cell-cell communication, and biofilm formation. This unit describes standard protocols for genetic manipulation of A. tumefaciens.}, }
@article {pmid22549024, year = {2012}, author = {Flegontova, O and Lukeš, J and Flegontov, P}, title = {Lack of evidence for integration of Trypanosoma cruzi minicircle DNA in South American human genomes.}, journal = {International journal for parasitology}, volume = {42}, number = {5}, pages = {437-441}, doi = {10.1016/j.ijpara.2012.04.001}, pmid = {22549024}, issn = {1879-0135}, mesh = {Colombia ; DNA, Kinetoplast/*genetics ; *Genome, Human ; Humans ; Peru ; *Recombination, Genetic ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Trypanosoma cruzi/*genetics ; }, abstract = {Horizontal gene transfer involving kinetoplast DNA minicircles between Trypanosoma cruzi and its mammalian hosts has recently been proposed as a usual consequence of infection (Hecht et al., 2010). However, we have found no sequences longer than 29 bp perfectly matching minicircles of T. cruzi in the unassembled reads from Colombian and Peruvian human populations provided by the 1,000 Genome project (129 individuals in total, coverage from 1.4× to 36.3×, read length from 42 to 101 bp). The weak sequence matches that were identified are shared with a Finnish population used as a control from a non-endemic area.}, }
@article {pmid22548759, year = {2012}, author = {Iorizzo, M and Senalik, D and Szklarczyk, M and Grzebelus, D and Spooner, D and Simon, P}, title = {De novo assembly of the carrot mitochondrial genome using next generation sequencing of whole genomic DNA provides first evidence of DNA transfer into an angiosperm plastid genome.}, journal = {BMC plant biology}, volume = {12}, number = {}, pages = {61}, pmid = {22548759}, issn = {1471-2229}, mesh = {DNA, Plant/*genetics ; Daucus carota/*genetics ; *Gene Transfer, Horizontal ; *Genome, Mitochondrial ; *Genome, Plant ; High-Throughput Nucleotide Sequencing/*methods ; Magnoliopsida/genetics ; Molecular Sequence Annotation ; Molecular Sequence Data ; }, abstract = {BACKGROUND: Sequence analysis of organelle genomes has revealed important aspects of plant cell evolution. The scope of this study was to develop an approach for de novo assembly of the carrot mitochondrial genome using next generation sequence data from total genomic DNA.<br><br>RESULTS: Sequencing data from a carrot 454 whole genome library were used to develop a de novo assembly of the mitochondrial genome. Development of a new bioinformatic tool allowed visualizing contig connections and elucidation of the de novo assembly. Southern hybridization demonstrated recombination across two large repeats. Genome annotation allowed identification of 44 protein coding genes, three rRNA and 17 tRNA. Identification of the plastid genome sequence allowed organelle genome comparison. Mitochondrial intergenic sequence analysis allowed detection of a fragment of DNA specific to the carrot plastid genome. PCR amplification and sequence analysis across different Apiaceae species revealed consistent conservation of this fragment in the mitochondrial genomes and an insertion in Daucus plastid genomes, giving evidence of a mitochondrial to plastid transfer of DNA. Sequence similarity with a retrotransposon element suggests a possibility that a transposon-like event transferred this sequence into the plastid genome.<br><br>CONCLUSIONS: This study confirmed that whole genome sequencing is a practical approach for de novo assembly of higher plant mitochondrial genomes. In addition, a new aspect of intercompartmental genome interaction was reported providing the first evidence for DNA transfer into an angiosperm plastid genome. The approach used here could be used more broadly to sequence and assemble mitochondrial genomes of diverse species. This information will allow us to better understand intercompartmental interactions and cell evolution.}, }
@article {pmid22547565, year = {2012}, author = {Dorrell, RG and Howe, CJ}, title = {What makes a chloroplast? Reconstructing the establishment of photosynthetic symbioses.}, journal = {Journal of cell science}, volume = {125}, number = {Pt 8}, pages = {1865-1875}, doi = {10.1242/jcs.102285}, pmid = {22547565}, issn = {1477-9137}, support = {BB/F017464/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Chloroplasts/genetics/*metabolism ; Eukaryota/genetics/*physiology ; Gene Transfer, Horizontal ; *Photosynthesis ; *Symbiosis ; }, abstract = {Earth is populated by an extraordinary diversity of photosynthetic eukaryotes. Many eukaryotic lineages contain chloroplasts, obtained through the endosymbiosis of a wide range of photosynthetic prokaryotes or eukaryotes, and a wide variety of otherwise non-photosynthetic species form transient associations with photosynthetic symbionts. Chloroplast lineages are likely to be derived from pre-existing transient symbioses, but it is as yet poorly understood what steps are required for the establishment of permanent chloroplasts from photosynthetic symbionts. In the past decade, several species that contain relatively recently acquired chloroplasts, such as the rhizarian Paulinella chromatophora, and non-photosynthetic taxa that maintain photosynthetic symbionts, such as the sacoglossan sea slug Elysia, the ciliate Myrionecta rubra and the dinoflagellate Dinophysis, have emerged as potential model organisms in the study of chloroplast establishment. In this Commentary, we compare recent molecular insights into the maintenance of chloroplasts and photosynthetic symbionts from these lineages, and others that might represent the early stages of chloroplast establishment. We emphasise the importance in the establishment of chloroplasts of gene transfer events that minimise oxidative stress acting on the symbiont. We conclude by assessing whether chloroplast establishment is facilitated in some lineages by a mosaic of genes, derived from multiple symbiotic associations, encoded in the host nucleus.}, }
@article {pmid22545240, year = {2011}, author = {Guglielmini, J and Van Melderen, L}, title = {Bacterial toxin-antitoxin systems: Translation inhibitors everywhere.}, journal = {Mobile genetic elements}, volume = {1}, number = {4}, pages = {283-290}, pmid = {22545240}, issn = {2159-2543}, abstract = {Toxin-antitoxin (TA) systems are composed of two elements: a toxic protein and an antitoxin which is either an RNA (type I and III) or a protein (type II). Type II systems are abundant in bacterial genomes in which they move via horizontal gene transfer. They are generally composed of two genes organized in an operon, encoding a toxin and a labile antitoxin. When carried by mobile genetic elements, these small modules contribute to their stability by a phenomenon denoted as addiction. Recently, we developed a bioinformatics procedure that, along with experimental validation, allowed the identification of nine novel toxin super-families. Here, considering that some toxin super-families exhibit dramatic sequence diversity but similar structure, bioinformatics tools were used to predict tertiary structures of novel toxins. Seven of the nine novel super-families did not show any structural homology with known toxins, indicating that combination of sequence similarity and three-dimensional structure prediction allows a consistent classification. Interestingly, the novel super-families are translation inhibitors similar to the majority of known toxins indicating that this activity might have been selected rather than more detrimental traits such as DNA-gyrase inhibitors, which are very toxic for cells.}, }
@article {pmid22545237, year = {2011}, author = {Danchin, EG}, title = {What Nematode genomes tell us about the importance of horizontal gene transfers in the evolutionary history of animals.}, journal = {Mobile genetic elements}, volume = {1}, number = {4}, pages = {269-273}, pmid = {22545237}, issn = {2159-2543}, abstract = {Horizontal gene transfer (HGT), the transmission of a gene from one species to another by means other than direct vertical descent from a common ancestor, has been recognized as an important phenomenon in the evolutionary biology of prokaryotes. In eukaryotes, in contrast, the importance of HGT has long been overlooked and its evolutionary significance has been considered to be mostly negligible. However, a series of genome analyses has now shown that HGT not only do probably occur at a higher frequency than originally thought in eukaryotes but recent examples have also shown that they have been subject to natural selection, thus suggesting a significant role in the evolutionary history of the receiver species. Surprisingly, these examples are not from protists in which integration and fixation of foreign genes intuitively appear relatively straightforward, because there is no clear distinction between the germline and the somatic genome. Instead, these examples are from nematodes, multicellular animals that do have distinct cells and tissues and do possess a separate germline. Hence, the mechanisms of gene transfer appears in this case much more complicated. In this commentary, I will further discuss two recent publications that describe HGT in nematodes, one that highlights the importance of HGT in the emergence of plant parasitism and another one that probably represents the most convincing example of a potential transfer between two different metazoan animals, an insect and a nematode.}, }
@article {pmid22545235, year = {2011}, author = {Hao, W and Palmer, JD}, title = {HGT turbulence: Confounding phylogenetic influence of duplicative horizontal transfer and differential gene conversion.}, journal = {Mobile genetic elements}, volume = {1}, number = {4}, pages = {256-261}, pmid = {22545235}, issn = {2159-2543}, support = {R01 GM070612/GM/NIGMS NIH HHS/United States ; }, abstract = {Horizontal gene transfer (HGT) often leads to phylogenetic incongruence. When "duplicative HGT" introduces a second copy of a pre-existing gene, the two copies may then engage in gene conversion, leading to phylogenetically mosiac genes. When duplicative HGT is followed by differential gene conversion among descendant lineages, as under the DH-DC model, phylogenetic analysis is further complicated. To explore the effects of DH-DC on phylogeny reconstruction, we analyzed two sets of sequences: (1) an augmented set of plant mitochondrial atp1 sequences for which we recently published evidence of DH-DC; and (2) a set of simulated sequences for which we varied the extent of chimerism, the number of chimeric genes and nucleotide substitution rates. We show that the phylogenetic behavior of evolutionarily chimeric genes is highly volatile and depends on both the degree of chimerism and the number of differentially chimeric genes present in the analysis. Furthermore, we show that the presence of chimeric genes in gene trees can spuriously affect the phylogenetic position of purely native sequences, especially by attracting these sequences toward basal positions in trees. We propose the term "HGT turbulence" to describe these complex effects of evolutionarily chimeric genes on phylogenetic results.}, }
@article {pmid22545234, year = {2011}, author = {Selman, M and Corradi, N}, title = {Microsporidia: Horizontal gene transfers in vicious parasites.}, journal = {Mobile genetic elements}, volume = {1}, number = {4}, pages = {251-255}, pmid = {22545234}, issn = {2159-2543}, abstract = {Microsporidia are obligate intracellular parasites whose genomes have been shaped by an extreme lifestyle. Specifically, their obligate intracellular parasitism has resulted in the loss of many genes and biochemical pathways, but these reductive processes have been often offset by the acquisition of several genes by means of horizontal gene transfer (HGT). Until recently, these HGTs were all found to have derived from prokaryotic donors, but a recent study suggests that some species took advantage of this mechanism to acquire one gene from an animal, which they maintained in their genome for metabolic purposes. The gene encodes for a purine nucleoside phosphorylase, and shows a strong phylogenetic signal of arthropod origin. Here, we briefly review our current knowledge of HGTs discovered across microsporidian genomes and discuss the implications of the most recent findings in this research area for understanding the origin and evolution of this highly adapted group of intracellular parasites. A novel gene potentially transferred by means of HGT to one microsporidia is also reported.}, }
@article {pmid22542236, year = {2012}, author = {Lu, N and Mylon, SE and Kong, R and Bhargava, R and Zilles, JL and Nguyen, TH}, title = {Interactions between dissolved natural organic matter and adsorbed DNA and their effect on natural transformation of Azotobacter vinelandii.}, journal = {The Science of the total environment}, volume = {426}, number = {}, pages = {430-435}, doi = {10.1016/j.scitotenv.2012.03.063}, pmid = {22542236}, issn = {1879-1026}, mesh = {Adaptation, Physiological ; Adsorption ; Azotobacter vinelandii ; Calcium/chemistry/metabolism ; Cations, Divalent ; DNA/*chemistry/metabolism ; Environmental Pollutants/chemistry/metabolism ; Gene Transfer, Horizontal ; *Humic Substances ; Kinetics ; Magnesium/chemistry/metabolism ; Phosphates/chemistry/metabolism ; Plasmids/metabolism ; Silicon Dioxide/chemistry/metabolism ; }, abstract = {To better understand gene transfer in the soil environment, the interactions between dissolved natural organic matter (NOM) and chromosomal or plasmid DNA adsorbed to silica surfaces were investigated. The rates of NOM adsorption onto silica surfaces coated with DNA were measured by quartz crystal microbalance (QCM) and showed a positive correlation with carboxylate group density for both soil and aquatic NOM in solutions containing either 1mM Ca(2+) or Mg(2+). Increasing total dissolved organic carbon (DOC) concentrations of the NOM solution also resulted in an increase in the adsorption rates, likely due to divalent cation complexation with NOM carboxylate groups and the phosphate backbones of the DNA. The results from Fourier transform infrared spectroscopy (FTIR) for dissolved DNA and DNA adsorbed on silica beads also suggest that adsorption may result from divalent cation complexation with the DNA's phosphate backbone. The interactions, between DNA and NOM, however, did not influence natural transformation of Azotobacter vinelandii by DNA. These results suggest that DNA adsorbed to NOM-coated silica or otherwise complexed with NOM remains available for natural transformation in the environment.}, }
@article {pmid22539163, year = {2012}, author = {Koppell, JH and Parker, MA}, title = {Phylogenetic clustering of Bradyrhizobium symbionts on legumes indigenous to North America.}, journal = {Microbiology (Reading, England)}, volume = {158}, number = {Pt 8}, pages = {2050-2059}, doi = {10.1099/mic.0.059238-0}, pmid = {22539163}, issn = {1465-2080}, mesh = {Bacterial Proteins/genetics ; Bradyrhizobium/*classification/genetics/isolation &amp; purification/physiology ; Fabaceae/*microbiology/physiology ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Nitrogenase/genetics ; North America ; *Phylogeny ; *Symbiosis ; }, abstract = {To analyse determinants of biogeographic structure in members of the genus Bradyrhizobium, isolates were obtained from 41 legume genera, originating from North American sites spanning 48.5 ° of latitude (Alaska to Panama). Sequencing of portions of six gene loci (3674 bp) in 203 isolates showed that there was only a weak trend towards higher nucleotide diversity in tropical regions. Phylogenetic relationships for nifD, in the symbiosis island region of the Bradyrhizobium chromosome, conflicted substantially with a tree inferred for five housekeeping gene loci. For both nifD and housekeeping gene trees, bacteria from each region were significantly more similar, on average, than would be expected if the source location was permuted at random on the tree. Within-region permutation tests also showed that bacteria clustered significantly on particular host plant clades at all levels in the phylogeny of legumes (from genus up to subfamily). Nevertheless, some bacterial groups were dispersed across multiple regions and were associated with diverse legume host lineages. These results indicate that migration, horizontal gene transfer and host interactions have all influenced the geographical divergence of Bradyrhizobium populations on a continental scale.}, }
@article {pmid22537274, year = {2012}, author = {Lee, CC and Lo, WC and Lai, SM and Chen, YP and Tang, CY and Lyu, PC}, title = {Metabolic classification of microbial genomes using functional probes.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {157}, pmid = {22537274}, issn = {1471-2164}, mesh = {Bacteria/*genetics/*metabolism ; Gene Transfer, Horizontal/genetics ; Genomics/*methods ; Phylogeny ; Proteomics ; }, abstract = {BACKGROUND: Microorganisms able to grow under artificial culture conditions comprise only a small proportion of the biosphere's total microbial community. Until recently, scientists have been unable to perform thorough analyses of difficult-to-culture microorganisms due to limitations in sequencing technology. As modern techniques have dramatically increased sequencing rates and rapidly expanded the number of sequenced genomes, in addition to traditional taxonomic classifications which focus on the evolutionary relationships of organisms, classifications of the genomes based on alternative points of view may help advance our understanding of the delicate relationships of organisms.<br><br>RESULTS: We have developed a proteome-based method for classifying microbial species. This classification method uses a set of probes comprising short, highly conserved amino acid sequences. For each genome, in silico translation is performed to obtained its proteome, based on which a probe-set frequency pattern is generated. Then, the probe-set frequency patterns are used to cluster the proteomes/genomes.<br><br>CONCLUSIONS: Features of the proposed method include a high running speed in challenge of a large number of genomes, and high applicability for classifying organisms with incomplete genome sequences. Moreover, the probe-set clustering method is sensitive to the metabolic phenotypic similarities/differences among species and is thus supposed potential for the classification or differentiation of closely-related organisms.}, }
@article {pmid22536150, year = {2012}, author = {Braakman, R and Smith, E}, title = {The emergence and early evolution of biological carbon-fixation.}, journal = {PLoS computational biology}, volume = {8}, number = {4}, pages = {e1002455}, pmid = {22536150}, issn = {1553-7358}, mesh = {Animals ; Carbon Cycle/*genetics ; Computer Simulation ; *Evolution, Molecular ; Humans ; *Models, Genetic ; Proteome/*genetics ; Signal Transduction/*genetics ; }, abstract = {The fixation of CO2 into living matter sustains all life on Earth, and embeds the biosphere within geochemistry. The six known chemical pathways used by extant organisms for this function are recognized to have overlaps, but their evolution is incompletely understood. Here we reconstruct the complete early evolutionary history of biological carbon-fixation, relating all modern pathways to a single ancestral form. We find that innovations in carbon-fixation were the foundation for most major early divergences in the tree of life. These findings are based on a novel method that fully integrates metabolic and phylogenetic constraints. Comparing gene-profiles across the metabolic cores of deep-branching organisms and requiring that they are capable of synthesizing all their biomass components leads to the surprising conclusion that the most common form for deep-branching autotrophic carbon-fixation combines two disconnected sub-networks, each supplying carbon to distinct biomass components. One of these is a linear folate-based pathway of CO2 reduction previously only recognized as a fixation route in the complete Wood-Ljungdahl pathway, but which more generally may exclude the final step of synthesizing acetyl-CoA. Using metabolic constraints we then reconstruct a "phylometabolic" tree with a high degree of parsimony that traces the evolution of complete carbon-fixation pathways, and has a clear structure down to the root. This tree requires few instances of lateral gene transfer or convergence, and instead suggests a simple evolutionary dynamic in which all divergences have primary environmental causes. Energy optimization and oxygen toxicity are the two strongest forces of selection. The root of this tree combines the reductive citric acid cycle and the Wood-Ljungdahl pathway into a single connected network. This linked network lacks the selective optimization of modern fixation pathways but its redundancy leads to a more robust topology, making it more plausible than any modern pathway as a primitive universal ancestral form.}, }
@article {pmid22534306, year = {2012}, author = {Kim, SE and Moon, JS and Choi, WS and Lee, SH and Kim, SU}, title = {Monitoring of horizontal gene transfer from agricultural microorganisms to soil bacteria and analysis of microbial community in soils.}, journal = {Journal of microbiology and biotechnology}, volume = {22}, number = {4}, pages = {563-566}, doi = {10.4014/jmb.1110.10066}, pmid = {22534306}, issn = {1738-8872}, mesh = {Bacillus subtilis/*genetics ; Bacteria/classification/*genetics/isolation &amp; purification ; Cucumis sativus/*microbiology ; *Gene Transfer, Horizontal ; Solanum lycopersicum/*microbiology ; Pseudomonas fluorescens/*genetics ; Soil Microbiology ; }, abstract = {To investigate the possibility of horizontal gene transfer between agricultural microorganisms and soil microorganisms in the environment, Bacillus subtilis KB producing iturin and the PGPR recombinant strain Pseudomonas fluorescens MX1 were used as model microorganisms. The soil samples of cucumber or tomato plants cultivated in pots and the greenhouse for a six month period were investigated by PCR, real-time PCR, Southern hybridization, and terminal restriction fragment length polymorphism (T-RFLP) fingerprinting. Our data from Southern blotting and TRFLP patterns suggest that the model bacteria do not give significant impacts on the other bacteria in the pots and greenhouse during cultivation.}, }
@article {pmid22534164, year = {2012}, author = {Yahara, K and Kawai, M and Furuta, Y and Takahashi, N and Handa, N and Tsuru, T and Oshima, K and Yoshida, M and Azuma, T and Hattori, M and Uchiyama, I and Kobayashi, I}, title = {Genome-wide survey of mutual homologous recombination in a highly sexual bacterial species.}, journal = {Genome biology and evolution}, volume = {4}, number = {5}, pages = {628-640}, pmid = {22534164}, issn = {1759-6653}, mesh = {Computational Biology/methods ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial ; Genetic Variation ; *Genome, Bacterial ; Helicobacter pylori/*genetics ; Homologous Recombination/*genetics ; Phylogeny ; Sequence Alignment ; }, abstract = {The nature of a species remains a fundamental and controversial question. The era of genome/metagenome sequencing has intensified the debate in prokaryotes because of extensive horizontal gene transfer. In this study, we conducted a genome-wide survey of outcrossing homologous recombination in the highly sexual bacterial species Helicobacter pylori. We conducted multiple genome alignment and analyzed the entire data set of one-to-one orthologous genes for its global strains. We detected mosaic structures due to repeated recombination events and discordant phylogenies throughout the genomes of this species. Most of these genes including the "core" set of genes and horizontally transferred genes showed at least one recombination event. Taking into account the relationship between the nucleotide diversity and the minimum number of recombination events per nucleotide, we evaluated the recombination rate in every gene. The rate appears constant across the genome, but genes with a particularly high or low recombination rate were detected. Interestingly, genes with high recombination included those for DNA transformation and for basic cellular functions, such as biosynthesis and metabolism. Several highly divergent genes with a high recombination rate included those for host interaction, such as outer membrane proteins and lipopolysaccharide synthesis. These results provide a global picture of genome-wide distribution of outcrossing homologous recombination in a bacterial species for the first time, to our knowledge, and illustrate how a species can be shaped by mutual homologous recombination.}, }
@article {pmid22533374, year = {2012}, author = {Siu, LK and Lin, JC and Gomez, E and Eng, R and Chiang, T}, title = {Virulence and plasmid transferability of KPC Klebsiella pneumoniae at the Veterans Affairs Healthcare System of New Jersey.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {18}, number = {4}, pages = {380-384}, doi = {10.1089/mdr.2011.0241}, pmid = {22533374}, issn = {1931-8448}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Antigens, Bacterial/genetics ; Antigens, Surface/genetics ; Bacterial Proteins/*genetics ; Carbapenems/pharmacology ; Escherichia coli/*genetics ; Gene Transfer, Horizontal ; Humans ; Klebsiella pneumoniae/*genetics/isolation &amp; purification/*pathogenicity ; Mice ; Microbial Sensitivity Tests ; Neutrophils/physiology ; New Jersey ; Phagocytosis ; Plasmids ; Polymerase Chain Reaction ; Species Specificity ; Veterans ; Virulence/genetics ; Virulence Factors/genetics ; beta-Lactamases/*genetics ; }, abstract = {Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella pneumoniae infections are associated with high mortality; however, little is known about the virulence determinants of KPC-producing K. pneumoniae. At the Veterans Affairs New Jersey Healthcare System (VA NJHCS), we investigated the virulence and plasmid transferability of 60 clinically unique KPC-containing K. pneumoniae isolates. All 60 isolates were negative for known virulence factors K1, K2, and K5 capsular antigens; rmpA; and the aerobactin gene by polymerase chain reaction. Isolates varied in their susceptibility to neutrophil phagocytosis, but were less resistant than the virulent serotype K1 isolate. Additionally, no deaths were seen on murine lethality studies. Conjugation results of this study showed that the bla(KPC) gene can be transferred into an Escherichia coli J-53 strain but not to E. coli JP-995. However, the stability is very limited as E. coli J-53 does not retain bla(KPC)-containing plasmids for any period of time. The lack of virulence factors in the set of KPC-producing K. pneumoniae studied suggests that morbidity and mortality may be due to detection issues or lack of effective antibiotics.}, }
@article {pmid22532467, year = {2012}, author = {Dimou, V and Dhanji, H and Pike, R and Livermore, DM and Woodford, N}, title = {Characterization of Enterobacteriaceae producing OXA-48-like carbapenemases in the UK.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {67}, number = {7}, pages = {1660-1665}, doi = {10.1093/jac/dks124}, pmid = {22532467}, issn = {1460-2091}, mesh = {Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; Enterobacteriaceae/classification/*enzymology/genetics/isolation &amp; purification ; Enterobacteriaceae Infections/microbiology ; Gene Transfer, Horizontal ; Genotype ; Hospitals ; Humans ; Molecular Typing ; Plasmids/analysis ; Restriction Mapping ; Sequence Analysis, DNA ; United Kingdom ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: To characterize UK clinical isolates of Enterobacteriaceae producing OXA-48-like carbapenemases and to compare their resistance plasmids.<br><br>METHODS: Twenty-six enterobacteria producing OXA-48-like enzymes were studied. These were from 22 diverse hospitals in the UK. Isolates of Escherichia coli and Klebsiella pneumoniae were assigned to clonal lineages by multilocus sequence typing. Carbapenemase genes and their genetic environments were characterized by PCR and sequencing. Resistance plasmids were transferred by transformation or conjugation and compared by restriction analysis and PCR for genes encoding critical plasmid functions.<br><br>RESULTS: Thirteen isolates of K. pneumoniae, 10 E. coli and 2 Enterobacter cloacae harboured a classical bla(OXA-48) gene; the K. pneumoniae isolates belonged to 11 sequence types (STs) and the E. coli to 7 STs, including ST131 and ST38. The bla(OXA-48) genes were located within either Tn1999 or Tn1999.2 transposons on related &#x2248; 50 kb or &#x2248; 62 kb plasmids, which lacked other resistance genes or, in one isolate, on an &#x2248; 140 kb plasmid that also encoded OXA-9 and CTX-M group-9 &#x3b2;-lactamases. One India-linked K. pneumoniae isolate had a bla(OXA-181) gene in association with an ISEcp1 insertion sequence on a 7 kb plasmid.<br><br>CONCLUSIONS: Horizontal transfer of related plasmids has facilitated the spread of OXA-48 carbapenemase into multiple strains of several Enterobacteriaceae species. The clonal diversity of the producers suggests repeated introduction into the UK. Low carbapenem MICs for some producers complicates detection and creates a risk for unrecognized spread.}, }
@article {pmid22530965, year = {2012}, author = {Hain, T and Ghai, R and Billion, A and Kuenne, CT and Steinweg, C and Izar, B and Mohamed, W and Mraheil, MA and Domann, E and Schaffrath, S and Kärst, U and Goesmann, A and Oehm, S and Pühler, A and Merkl, R and Vorwerk, S and Glaser, P and Garrido, P and Rusniok, C and Buchrieser, C and Goebel, W and Chakraborty, T}, title = {Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {144}, pmid = {22530965}, issn = {1471-2164}, mesh = {Animals ; Bacteriophages/genetics ; Disease Models, Animal ; Flagellin/metabolism ; Gene Duplication/genetics ; Gene Expression Profiling/*methods ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal/genetics ; Genes, Viral/genetics ; Genetic Loci/genetics ; Genome, Bacterial ; Genomics/*methods ; Humans ; Listeria monocytogenes/*genetics/metabolism/pathogenicity/virology ; Listeriosis/microbiology ; Membrane Proteins/metabolism ; Mice ; Molecular Sequence Data ; Multigene Family/genetics ; Mutation/genetics ; Nucleotide Motifs/genetics ; Nucleotides/genetics ; *Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Repetitive Sequences, Nucleic Acid/genetics ; Virulence/genetics ; }, abstract = {BACKGROUND: Listeria monocytogenes is a food-borne pathogen that causes infections with a high-mortality rate and has served as an invaluable model for intracellular parasitism. Here, we report complete genome sequences for two L. monocytogenes strains belonging to serotype 4a (L99) and 4b (CLIP80459), and transcriptomes of representative strains from lineages I, II, and III, thereby permitting in-depth comparison of genome- and transcriptome -based data from three lineages of L. monocytogenes. Lineage III, represented by the 4a L99 genome is known to contain strains less virulent for humans.<br><br>RESULTS: The genome analysis of the weakly pathogenic L99 serotype 4a provides extensive evidence of virulence gene decay, including loss of several important surface proteins. The 4b CLIP80459 genome, unlike the previously sequenced 4b F2365 genome harbours an intact inlB invasion gene. These lineage I strains are characterized by the lack of prophage genes, as they share only a single prophage locus with other L. monocytogenes genomes 1/2a EGD-e and 4a L99. Comparative transcriptome analysis during intracellular growth uncovered adaptive expression level differences in lineages I, II and III of Listeria, notable amongst which was a strong intracellular induction of flagellar genes in strain 4a L99 compared to the other lineages. Furthermore, extensive differences between strains are manifest at levels of metabolic flux control and phosphorylated sugar uptake. Intriguingly, prophage gene expression was found to be a hallmark of intracellular gene expression. Deletion mutants in the single shared prophage locus of lineage II strain EGD-e 1/2a, the lma operon, revealed severe attenuation of virulence in a murine infection model.<br><br>CONCLUSION: Comparative genomics and transcriptome analysis of L. monocytogenes strains from three lineages implicate prophage genes in intracellular adaptation and indicate that gene loss and decay may have led to the emergence of attenuated lineages.}, }
@article {pmid22529932, year = {2012}, author = {Geng, J and Chiu, CH and Tang, P and Chen, Y and Shieh, HR and Hu, S and Chen, YY}, title = {Complete genome and transcriptomes of Streptococcus parasanguinis FW213: phylogenic relations and potential virulence mechanisms.}, journal = {PloS one}, volume = {7}, number = {4}, pages = {e34769}, pmid = {22529932}, issn = {1932-6203}, mesh = {Alcohols/metabolism ; Chromosome Mapping ; Chromosomes, Bacterial ; Comparative Genomic Hybridization ; Endocarditis, Bacterial/etiology ; Extracellular Matrix/metabolism ; Gene Expression Profiling ; Gene Order ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomic Islands ; Molecular Sequence Data ; Open Reading Frames ; Operon ; Oxidative Stress/genetics ; Peptides/metabolism ; Phylogeny ; Protein Binding ; Streptococcus/classification/*genetics/pathogenicity ; Transcription Initiation Site ; *Transcriptome ; Virulence/genetics ; Virulence Factors/genetics ; }, abstract = {Streptococcus parasanguinis, a primary colonizer of the tooth surface, is also an opportunistic pathogen for subacute endocarditis. The complete genome of strain FW213 was determined using the traditional shotgun sequencing approach and further refined by the transcriptomes of cells in early exponential and early stationary growth phases in this study. The transcriptomes also discovered 10 transcripts encoding known hypothetical proteins, one pseudogene, five transcripts matched to the Rfam and additional 87 putative small RNAs within the intergenic regions defined by the GLIMMER analysis. The genome contains five acquired genomic islands (GIs) encoding proteins which potentially contribute to the overall pathogenic capacity and fitness of this microbe. The differential expression of the GIs and various open reading frames outside the GIs at the two growth phases suggested that FW213 possess a range of mechanisms to avoid host immune clearance, to colonize host tissues, to survive within oral biofilms and to overcome various environmental insults. Furthermore, the comparative genome analysis of five S. parasanguinis strains indicates that albeit S. parasanguinis strains are highly conserved, variations in the genome content exist. These variations may reflect differences in pathogenic potential between the strains.}, }
@article {pmid22529840, year = {2012}, author = {Techtmann, SM and Lebedinsky, AV and Colman, AS and Sokolova, TG and Woyke, T and Goodwin, L and Robb, FT}, title = {Evidence for horizontal gene transfer of anaerobic carbon monoxide dehydrogenases.}, journal = {Frontiers in microbiology}, volume = {3}, number = {}, pages = {132}, pmid = {22529840}, issn = {1664-302X}, abstract = {Carbon monoxide (CO) is commonly known as a toxic gas, yet both cultivation studies and emerging genome sequences of bacteria and archaea establish that CO is a widely utilized microbial growth substrate. In this study, we determined the prevalence of anaerobic carbon monoxide dehydrogenases ([Ni,Fe]-CODHs) in currently available genomic sequence databases. Currently, 185 out of 2887, or 6% of sequenced bacterial and archaeal genomes possess at least one gene encoding [Ni,Fe]-CODH, the key enzyme for anaerobic CO utilization. Many genomes encode multiple copies of [Ni,Fe]-CODH genes whose functions and regulation are correlated with their associated gene clusters. The phylogenetic analysis of this extended protein family revealed six distinct clades; many clades consisted of [Ni,Fe]-CODHs that were encoded by microbes from disparate phylogenetic lineages, based on 16S rRNA sequences, and widely ranging physiology. To more clearly define if the branching patterns observed in the [Ni,Fe]-CODH trees are due to functional conservation vs. evolutionary lineage, the genomic context of the [Ni,Fe]-CODH gene clusters was examined, and superimposed on the phylogenetic trees. On the whole, there was a correlation between genomic contexts and the tree topology, but several functionally similar [Ni,Fe]-CODHs were found in different clades. In addition, some distantly related organisms have similar [Ni,Fe]-CODH genes. Thermosinus carboxydivorans was used to observe horizontal gene transfer (HGT) of [Ni,Fe]-CODH gene clusters by applying Kullback-Leibler divergence analysis methods. Divergent tetranucleotide frequency and codon usage showed that the gene cluster of T. carboxydivorans that encodes a [Ni,Fe]-CODH and an energy-converting hydrogenase is dissimilar to its whole genome but is similar to the genome of the phylogenetically distant Firmicute, Carboxydothermus hydrogenoformans. These results imply that T carboxydivorans acquired this gene cluster via HGT from a relative of C. hydrogenoformans.}, }
@article {pmid22527689, year = {2011}, author = {Wallau, GL and Kaminski, VL and Loreto, EL}, title = {The role of vertical and horizontal transfer in the evolution of Paris-like elements in drosophilid species.}, journal = {Genetica}, volume = {139}, number = {11-12}, pages = {1487-1497}, pmid = {22527689}, issn = {1573-6857}, mesh = {Animals ; Base Sequence ; *DNA Transposable Elements ; Drosophila/classification/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Insect ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Terminal Repeat Sequences ; }, abstract = {The transposable element (TE) Paris was described in a Drosophila virilis strain (virilis species group) as causing a hybrid dysgenesis with other mobile genetic elements. Since then, the element Paris has only been found in D. buzzatii, a species from the repleta group. In this study, we performed a search for Paris-like elements in 56 species of drosophilids to improve the knowledge about the distribution and evolution of this element. Paris-like elements were found in 30 species from the Drosophila genus, 15 species from the Drosophila subgenus and 15 species from the Sophophora subgenus. Analysis of the complete sequences obtained from the complete available Drosophila genomes has shown that there are putative active elements in five species (D. elegans, D. kikkawai, D. ananassae, D. pseudoobscura and D. mojavensis). The Paris-like elements showed an approximately 242-bp-long terminal inverted repeats in the 5' and 3' boundaries (called LIR: long inverted repeat), with two 28-bp-long direct repeats in each LIR. All potentially active elements presented degeneration in the internal region of terminal inverted repeat. Despite the degeneration of the LIR, the distance of 185 bp between the direct repeats was always maintained. This conservation suggests that the spacing between direct repeats is important for transposase binding. The distribution analysis showed that these elements are widely distributed in other Drosophila groups beyond the virilis and repleta groups. The evolutionary analysis of Paris-like elements suggests that they were present as two subfamilies with the common ancestor of the Drosophila genus. Since then, these TEs have been primarily maintained by vertical transmission with some events of stochastic loss and horizontal transfer.}, }
@article {pmid22526316, year = {2012}, author = {Grosso, F and Quinteira, S and Poirel, L and Novais, &#xc2; and Peixe, L}, title = {Role of common blaOXA-24/OXA-40-carrying platforms and plasmids in the spread of OXA-24/OXA-40 among Acinetobacter species clinical isolates.}, journal = {Antimicrobial agents and chemotherapy}, volume = {56}, number = {7}, pages = {3969-3972}, pmid = {22526316}, issn = {1098-6596}, mesh = {Acinetobacter/*enzymology/*genetics ; Acinetobacter baumannii/enzymology/genetics ; Gene Transfer, Horizontal/genetics ; Molecular Sequence Data ; Plasmids/*genetics ; Polymerase Chain Reaction ; beta-Lactamases/genetics ; }, abstract = {The spread of OXA-24/OXA-40 (OXA-24/40)-producing Acinetobacter spp. in the Iberian Peninsula has been strongly influenced by clonal expansion, but the role of horizontal gene transfer has scarcely been explored. bla(OXA-24/40)-carrying plasmids and genetic environments were characterized in representative (n = 15) Acinetobacter species clinical isolates (obtained between 2001 and 2007) by Acinetobacter baumannii PCR-based replicon typing, sequencing, hybridization, and restriction fragment length polymorphism. Besides the identification of bla(OXA-24/40) within the chromosomes of some isolates, the circulation of common bla(OXA-24/40)-carrying plasmids (30-kb repA_AB; 10-kb aci2) and genetic backbones among Acinetobacter spp. was demonstrated.}, }
@article {pmid22523317, year = {2012}, author = {Hammerum, AM and Jakobsen, L and Olsen, SS and Agersø, Y}, title = {Characterization of CTX-M-14- and CTX-M-15-producing Escherichia coli of porcine origin.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {67}, number = {8}, pages = {2047-2049}, doi = {10.1093/jac/dks148}, pmid = {22523317}, issn = {1460-2091}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Cluster Analysis ; Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/*classification/enzymology/genetics/*isolation &amp; purification ; Escherichia coli Infections/microbiology/*veterinary ; Gene Transfer, Horizontal ; Genotype ; Multilocus Sequence Typing ; Swine ; Swine Diseases/*microbiology ; beta-Lactam Resistance ; beta-Lactamases/*metabolism ; }, }
@article {pmid22522561, year = {2012}, author = {Li, M and Du, X and Villaruz, AE and Diep, BA and Wang, D and Song, Y and Tian, Y and Hu, J and Yu, F and Lu, Y and Otto, M}, title = {MRSA epidemic linked to a quickly spreading colonization and virulence determinant.}, journal = {Nature medicine}, volume = {18}, number = {5}, pages = {816-819}, pmid = {22522561}, issn = {1546-170X}, support = {ZIA AI000904-10/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Animals ; China ; Female ; Humans ; Methicillin-Resistant Staphylococcus aureus/genetics/isolation &amp; purification/*pathogenicity ; Mice ; Mice, Hairless ; Mice, Inbred ICR ; Virulence ; }, abstract = {The molecular processes underlying epidemic waves of methicillin-resistant Staphylococcus aureus (MRSA) infection are poorly understood(1). Although a major role has been attributed to the acquisition of virulence determinants by horizontal gene transfer(2), there are insufficient epidemiological and functional data supporting that concept. We here report the spread of clones containing a previously extremely rare(3,4) mobile genetic element–encoded gene, sasX. We demonstrate that sasX has a key role in MRSA colonization and pathogenesis, substantially enhancing nasal colonization, lung disease and abscess formation and promoting mechanisms of immune evasion. Moreover, we observed the recent spread of sasX from sequence type 239 (ST239) to invasive clones belonging to other sequence types. Our study identifies sasX as a quickly spreading crucial determinant of MRSA pathogenic success and a promising target for therapeutic interference. Our results provide proof of principle that horizontal gene transfer of key virulence determinants drives MRSA epidemic waves.}, }
@article {pmid22520826, year = {2012}, author = {Francis, AR and Tanaka, MM}, title = {Evolution of variation in presence and absence of genes in bacterial pathways.}, journal = {BMC evolutionary biology}, volume = {12}, number = {}, pages = {55}, pmid = {22520826}, issn = {1471-2148}, mesh = {Bacteria/*genetics/*metabolism ; *Biological Evolution ; Gastrointestinal Tract/microbiology ; Gene Transfer, Horizontal ; Humans ; *Metabolic Networks and Pathways ; *Models, Genetic ; }, abstract = {BACKGROUND: Bacterial genomes exhibit a remarkable degree of variation in the presence and absence of genes, which probably extends to the level of individual pathways. This variation may be a consequence of the significant evolutionary role played by horizontal gene transfer, but might also be explained by the loss of genes through mutation. A challenge is to understand why there would be variation in gene presence within pathways if they confer a benefit only when complete.<br><br>RESULTS: Here, we develop a mathematical model to study how variation in pathway content is produced by horizontal transfer, gene loss and partial exposure of a population to a novel environment.<br><br>CONCLUSIONS: We discuss the possibility that variation in gene presence acts as cryptic genetic variation on which selection acts when the appropriate environment occurs. We find that a high level of variation in gene presence can be readily explained by decay of the pathway through mutation when there is no longer exposure to the selective environment, or when selection becomes too weak to maintain the genes. In the context of pathway variation the role of horizontal gene transfer is probably the initial introduction of a complete novel pathway rather than in building up the variation in a genome without the pathway.}, }
@article {pmid22519798, year = {2012}, author = {Mc Ginty, S&#xc9; and Rankin, DJ}, title = {The evolution of conflict resolution between plasmids and their bacterial hosts.}, journal = {Evolution; international journal of organic evolution}, volume = {66}, number = {5}, pages = {1662-1670}, doi = {10.1111/j.1558-5646.2011.01549.x}, pmid = {22519798}, issn = {1558-5646}, mesh = {Bacteria/*genetics ; *Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Models, Genetic ; Plasmids/*genetics ; }, abstract = {It has recently been proposed that mobile elements may be a significant driver of cooperation in microorganisms. This may drive a potential conflict, where cooperative genes are transmitted independently of the rest of the genome, resulting in scenarios where horizontally spread cooperative genes are favored, whereas a chromosomal equivalent would not be. This can lead to the whole genome being exploited by surrounding noncooperative individuals. Given that there are costs associated with mobile elements themselves, infection with a plasmid carrying a cooperative trait may lead to a significant conflict within the host genome. Here, we model the mechanisms that allow the host to resolve this conflict, either by exhibiting complete resistance to the mobile element or by controlling its gene expression via a chromosomally based suppressor. We find that the gene suppression mechanism will be more stable than full resistance, implying that suppressing the expression of costly genes within a cell is preferable to preventing the acquisition of the mobile element, for the resolution of conflict within a genome.}, }
@article {pmid22514550, year = {2012}, author = {Thames, CH and Pruden, A and James, RE and Ray, PP and Knowlton, KF}, title = {Excretion of antibiotic resistance genes by dairy calves fed milk replacers with varying doses of antibiotics.}, journal = {Frontiers in microbiology}, volume = {3}, number = {}, pages = {139}, pmid = {22514550}, issn = {1664-302X}, abstract = {Elevated levels of antibiotic resistance genes (ARGs) in soil and water have been linked to livestock farms and in some cases feed antibiotics may select for antibiotic resistant gut microbiota. The purpose of this study was to examine the establishment of ARGs in the feces of calves receiving milk replacer containing no antibiotics versus subtherapeutic or therapeutic doses of tetracycline and neomycin. The effect of antibiotics on calf health was also of interest. Twenty-eight male and female dairy calves were assigned to one of the three antibiotic treatment groups at birth and fecal samples were collected at weeks 6, 7 (prior to weaning), and 12 (5 weeks after weaning). ARGs corresponding to the tetracycline (tetC, tetG, tetO, tetW, and tetX), macrolide (ermB, ermF), and sulfonamide (sul1, sul2) classes of antibiotics along with the class I integron gene, intI1, were monitored by quantitative polymerase chain reaction as potential indicators of direct selection, co-selection, or horizontal gene transfer of ARGs. Surprisingly, there was no significant effect of antibiotic treatment on the absolute abundance (gene copies per gram wet manure) of any of the ARGs except ermF, which was lower in the antibiotic-treated calf manure, presumably because a significant portion of host bacterial cells carrying ermF were not resistant to tetracycline or neomycin. However, relative abundance (gene copies normalized to 16S rRNA genes) of tetO was higher in calves fed the highest dose of antibiotic than in the other treatments. All genes, except tetC and intI1, were detectable in feces from 6 weeks onward, and tetW and tetG significantly increased (P < 0.10), even in control calves. Overall, the results provide new insight into the colonization of calf gut flora with ARGs in the early weeks. Although feed antibiotics exerted little effect on the ARGs monitored in this study, the fact that they also provided no health benefit suggests that the greater than conventional nutritional intake applied in this study overrides previously reported health benefits of antibiotics. The results suggest potential benefit of broader management strategies, and that cost and risk may be avoided by minimizing incorporation of antibiotics in milk replacer.}, }
@article {pmid22514263, year = {2012}, author = {Garza-Ramos, U and Barrios, H and Hernandez-Vargas, MJ and Rojas-Moreno, T and Reyna-Flores, F and Tinoco, P and Othon, V and Poirel, L and Nordmann, P and Cattoir, V and Ruiz-Palacios, G and Fernandez, JL and Santamaria, RI and Bustos, P and Castro, N and Silva-Sanchez, J}, title = {Transfer of quinolone resistance gene qnrA1 to Escherichia coli through a 50 kb conjugative plasmid resulting from the splitting of a 300 kb plasmid.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {67}, number = {7}, pages = {1627-1634}, doi = {10.1093/jac/dks123}, pmid = {22514263}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/*pharmacology ; Blotting, Southern ; Conjugation, Genetic ; DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; *Drug Resistance, Bacterial ; Escherichia coli/*drug effects/enzymology/*genetics/isolation &amp; purification ; Escherichia coli Infections/microbiology ; *Gene Transfer, Horizontal ; Humans ; Molecular Sequence Data ; *Plasmids ; Polymorphism, Restriction Fragment Length ; Quinolones/*pharmacology ; Recombination, Genetic ; Sequence Analysis, DNA ; beta-Lactamases/genetics ; }, abstract = {OBJECTIVES: To analyse the in vitro transfer of the qnrA1 gene by a 50 kb (pSZ50) self-transferable plasmid that derives from a 300 kb plasmid (pSZ300) and to determine the complete nucleotide sequence of plasmid pSZ50.<br><br>METHODS: Extended-spectrum &#x3b2;-lactamase (ESBL) and plasmid-mediated quinolone resistance (PMQR) genes of an Escherichia coli clinical isolate were analysed. Plasmid analysis included conjugation and selection on seven antibiotics examined by antimicrobial susceptibility testing, RFLP comparison, Southern hybridization, incompatibility group identification and shotgun sequencing.<br><br>RESULTS: The E. coli 5509 isolate carries the genes encoding the ESBL CTX-M-15 and the quinolone resistance determinants qnrA1, qnrB2 and aac(6')-Ib-cr on a 300 kb plasmid. Seven transfer resistances were analysed by conjugation under two conditions (30 and 37&#xb0;C), leading to two distinct transconjugant phenotypes with different resistances. Transconjugants of phenotype A harboured a 300 kb plasmid named pSZ300 that conferred resistance to eight antibiotics and harboured the qnrA1, aac(6')-Ib-cr and bla(CTX-M-15) genes. Transconjugants of phenotype B were resistant to three antibiotics and they harboured the qnrA1 gene on an &#x2248; 50 kb plasmid named pSZ50. Both plasmids were self-transferable at a frequency of 1 &#xd7; 10(-3). Plasmid pSZ300 was typed to be both an IncF and IncN plasmid, whereas pSZ50 corresponded only to type IncN. Fingerprinting and Southern hybridization showed that plasmid pSZ50 derived from pSZ300. The complete nucleotide sequence of plasmid pSZ50 was determined (51556 bp) and 55 open reading frames were predicted. The qnrA1 gene was identified in a tandem duplicate inside a sul1-type integron structure.<br><br>CONCLUSIONS: The plasmid pSZ300 represented a fusion of two replicons (IncF and IncN), and our observations suggest that the plasmid pSZ50 (IncN) may split and transfer antibiotic resistance determinants. This mechanism could be advantageous in the dissemination of antibiotic resistance genes.}, }
@article {pmid22511965, year = {2012}, author = {Lamrabet, O and Merhej, V and Pontarotti, P and Raoult, D and Drancourt, M}, title = {The genealogic tree of mycobacteria reveals a long-standing sympatric life into free-living protozoa.}, journal = {PloS one}, volume = {7}, number = {4}, pages = {e34754}, pmid = {22511965}, issn = {1932-6203}, mesh = {Acanthamoeba/microbiology ; Coculture Techniques ; Dictyostelium/microbiology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Legionella pneumophila/genetics ; Mycobacteriaceae/*genetics ; Mycobacterium avium/genetics ; Phylogeny ; *Sympatry ; }, abstract = {Free-living protozoa allow horizontal gene transfer with and between the microorganisms that they host. They host mycobacteria for which the sources of transferred genes remain unknown. Using BLASTp, we searched within the genomes of 15 mycobacteria for homologous genes with 34 amoeba-resistant bacteria and the free-living protozoa Dictyostelium discoideum. Subsequent phylogenetic analysis of these sequences revealed that eight mycobacterial open-reading frames (ORFs) were probably acquired via horizontal transfer from beta- and gamma-Proteobacteria and from Firmicutes, but the transfer histories could not be reliably established in details. One further ORF encoding a pyridine nucleotide disulfide oxidoreductase (pyr-redox) placed non-tuberculous mycobacteria in a clade with Legionella spp., Francisella spp., Coxiella burnetii, the ciliate Tetrahymena thermophila and D. discoideum with a high reliability. Co-culturing Mycobacterium avium and Legionella pneumophila with the amoeba Acanthamoeba polyphaga demonstrated that these two bacteria could live together in amoebae for five days, indicating the biological relevance of intra-amoebal transfer of the pyr-redox gene. In conclusion, the results of this study support the hypothesis that protists can serve as a source and a place for gene transfer in mycobacteria.}, }
@article {pmid22510370, year = {2012}, author = {Guzmán, D and Balderrama-Subieta, A and Cardona-Ortuño, C and Guevara-Martínez, M and Callisaya-Quispe, N and Quillaguamán, J}, title = {Evolutionary patterns of carbohydrate transport and metabolism in Halomonas boliviensis as derived from its genome sequence: influences on polyester production.}, journal = {Aquatic biosystems}, volume = {8}, number = {1}, pages = {9}, pmid = {22510370}, issn = {2046-9063}, abstract = {BACKGROUND: Halomonas boliviensis is a halophilic bacterium that is included in the γ-Proteobacteria sub-group, and is able to assimilate different types of carbohydrates. H. boliviensis is also able to produce poly(3-hydroxybutyrate) (PHB) in high yields using glucose as the carbon precursor. Accumulation of PHB by microorganisms is induced by excess of intracellular NADH.The genome sequences and organization in microorganisms should be the result of evolution and adaptation influenced by mutation, gene duplication, horizontal gen transfer (HGT) and recombination. Furthermore, the nearly neutral theory of evolution sustains that genetic modification of DNA could be neutral or selected, albeit most mutations should be at the border between neutrality and selection, i.e. slightly deleterious base substitutions in DNA are followed by a slightly advantageous substitutions.<br><br>RESULTS: This article reports the genome sequence of H. boliviensis. The chromosome size of H. boliviensis was 4 119 979 bp, and contained 3 863 genes. A total of 160 genes of H. boliviensis were related to carbohydrate transport and metabolism, and were organized as: 70 genes for metabolism of carbohydrates; 47 genes for ABC transport systems and 43 genes for TRAP-type C4-dicarboxylate transport systems. Protein sequences of H. boliviensis related to carbohydrate transport and metabolism were selected from clusters of orthologous proteins (COGs). Similar proteins derived from the genome sequences of other 41 archaea and 59 bacteria were used as reference. We found that most of the 160 genes in H. boliviensis, c.a. 44%, were obtained from other bacteria by horizontal gene transfer, while 13% of the genes were acquired from haloarchaea and thermophilic archaea, only 34% of the genes evolved among Proteobacteria and the remaining genes encoded proteins that did not cluster with any of the proteins obtained from the reference strains. Furthermore, the diversity of the enzymes derived from these genes led to polymorphism in glycolysis and gluconeogenesis. We found further that an optimum ratio of glucose and sucrose in the culture medium of H. boliviensis favored cell growth and PHB production.<br><br>CONCLUSIONS: Results obtained in this article depict that most genetic modifications and enzyme polymorphism in the genome of H. boliviensis were mainly influenced by HGT rather than nearly neutral mutations. Molecular adaptation and evolution experienced by H. boliviensis were also a response to environmental conditions such as the type and amount of carbohydrates in its ecological niche. Consequently, the genome evolution of H. boliviensis showed to be strongly influenced by the type of microorganisms, genetic interaction among microbial species and its environment. Such trend should also be experienced by other prokaryotes. A system for PHB production by H. boliviensis that takes into account the evolutionary adaptation of this bacterium to the assimilation of combinations of carbohydrates suggests the feasibility of a bioprocess economically viable and environmentally friendly.}, }
@article {pmid22507952, year = {2012}, author = {Harvey, A and Salter, B}, title = {Governing the moral economy: animal engineering, ethics and the liberal government of science.}, journal = {Social science &amp; medicine (1982)}, volume = {75}, number = {1}, pages = {193-199}, pmid = {22507952}, issn = {1873-5347}, support = {086034//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Bioengineering/*ethics/instrumentation/methods ; Culture ; Disease Models, Animal ; *Ethics, Medical ; *Ethics, Research ; Gene Transfer, Horizontal ; Health Policy/economics/*legislation &amp; jurisprudence/trends ; Humans ; *Morals ; Public Policy ; Science/economics/ethics/*legislation &amp; jurisprudence ; United Kingdom ; }, abstract = {The preferred Western model for science governance has come to involve attending to the perspectives of the public. In practice, however, this model has been criticised for failing to promote democracy along participatory lines. We argue that contemporary approaches to science policy making demonstrate less the failure of democracy and more the success of liberal modes of government in adapting to meet new governance challenges. Using a case study of recent UK policy debates on scientific work mixing human and animal biological material, we show first how a 'moral economy' is brought into being as a regulatory domain and second how this domain is governed to align cultural with scientific values. We suggest that it is through these practices that the state assures its aspirations for enhancing individual and collective prosperity through technological advance are met.}, }
@article {pmid22507450, year = {2012}, author = {Singh, SP and Häder, DP and Sinha, RP}, title = {Bioinformatics evidence for the transfer of mycosporine-like amino acid core (4-deoxygadusol) synthesizing gene from cyanobacteria to dinoflagellates and an attempt to mutate the same gene (YP_324358) in Anabaena variabilis PCC 7937.}, journal = {Gene}, volume = {500}, number = {2}, pages = {155-163}, doi = {10.1016/j.gene.2012.03.063}, pmid = {22507450}, issn = {1879-0038}, mesh = {Amino Acid Sequence ; Amino Acids/biosynthesis/*genetics ; Anabaena variabilis/classification/*genetics ; Cluster Analysis ; Computational Biology ; Conjugation, Genetic ; Cyclohexanols/metabolism ; DNA, Bacterial/genetics ; Dinoflagellida/classification/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Genetic Vectors ; Homologous Recombination ; Molecular Sequence Data ; Mutation ; Phosphorus-Oxygen Lyases/biosynthesis/genetics ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Synechococcus/classification/*genetics ; }, abstract = {We have identified a homologue of 4-deoxygadusol (core of mycosporine-like amino acids) synthesizing gene (ZP_05036788) from Synechococcus sp. PCC 7335 that was found to have additional functionally unknown N-terminal domain similar to homologues from dinoflagellates based on the ClustalW analysis. Phylogenetic analysis revealed that Synechococcus sp. (ZP_05036788) makes a clade together with dinoflagellates and was closest to the Oxyrrhis marina. This study shows for the first time that N-terminal additional sequences that possess upstream plastid targeting sequence in Heterocapsa triquetra and Karlodinium micrum were already evolved in cyanobacteria, and plastid targeting sequence were evolved later in dinoflagellates after divergence from chloroplast lacking Oxyrrhis marina. Thus, MAAs synthesizing genes were transferred from cyanobacteria to dinoflagellates and possibly Synechococcus sp. PCC 7335 acted as a donor during lateral gene transfer event. In addition, we also tried to mutate 4-deoxygadusol synthesizing gene (YP_324358) of Anabaena variabilis PCC 7937 by homologous recombination, however, all approaches to get complete segregation of the mutants from the wild-type were unsuccessful, showing the essentiality of YP_324358 for A. variabilis PCC 7937.}, }
@article {pmid22505998, year = {2012}, author = {Marron, AO and Akam, M and Walker, G}, title = {Nitrile hydratase genes are present in multiple eukaryotic supergroups.}, journal = {PloS one}, volume = {7}, number = {4}, pages = {e32867}, pmid = {22505998}, issn = {1932-6203}, support = {BB/E527604/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; CCC-1-10//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {DNA Barcoding, Taxonomic/methods ; Eukaryota/*enzymology/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Hydro-Lyases/*genetics ; Introns ; Phylogeny ; Protein Structure, Tertiary ; }, abstract = {BACKGROUND: Nitrile hydratases are enzymes involved in the conversion of nitrile-containing compounds into ammonia and organic acids. Although they are widespread in prokaryotes, nitrile hydratases have only been reported in two eukaryotes: the choanoflagellate Monosiga brevicollis and the stramenopile Aureococcus anophagefferens. The nitrile hydratase gene in M. brevicollis was believed to have arisen by lateral gene transfer from a prokaryote, and is a fusion of beta and alpha nitrile hydratase subunits. Only the alpha subunit has been reported in A. anophagefferens.<br><br>Here we report the detection of nitrile hydratase genes in five eukaryotic supergroups: opisthokonts, amoebozoa, archaeplastids, CCTH and SAR. Beta-alpha subunit fusion genes are found in the choanoflagellates, ichthyosporeans, apusozoans, haptophytes, rhizarians and stramenopiles, and potentially also in the amoebozoans. An individual alpha subunit is found in a dinoflagellate and an individual beta subunit is found in a haptophyte. Phylogenetic analyses recover a clade of eukaryotic-type nitrile hydratases in the Opisthokonta, Amoebozoa, SAR and CCTH; this is supported by analyses of introns and gene architecture. Two nitrile hydratase sequences from an animal and a plant resolve in the prokaryotic nitrile hydratase clade.<br><br>CONCLUSIONS/SIGNIFICANCE: The evidence presented here demonstrates that nitrile hydratase genes are present in multiple eukaryotic supergroups, suggesting that a subunit fusion gene was present in the last common ancestor of all eukaryotes. The absence of nitrile hydratase from several sequenced species indicates that subunits were lost in multiple eukaryotic taxa. The presence of nitrile hydratases in many other eukaryotic groups is unresolved due to insufficient data and taxon sampling. The retention and expression of the gene in distantly related eukaryotic species suggests that it plays an important metabolic role. The novel family of eukaryotic nitrile hydratases presented in this paper represents a promising candidate for research into their molecular biology and possible biotechnological applications.}, }
@article {pmid22505685, year = {2012}, author = {Lee, CA and Thomas, J and Grossman, AD}, title = {The Bacillus subtilis conjugative transposon ICEBs1 mobilizes plasmids lacking dedicated mobilization functions.}, journal = {Journal of bacteriology}, volume = {194}, number = {12}, pages = {3165-3172}, pmid = {22505685}, issn = {1098-5530}, support = {R01 GM050895/GM/NIGMS NIH HHS/United States ; GM50895/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacillus subtilis/*genetics ; Bacterial Proteins/*genetics ; *Conjugation, Genetic ; *DNA Transposable Elements ; *Gene Transfer, Horizontal ; *Plasmids ; }, abstract = {Integrative and conjugative elements (ICEs, also known as conjugative transposons) are mobile elements that are found integrated in a host genome and can excise and transfer to recipient cells via conjugation. ICEs and conjugative plasmids are found in many bacteria and are important agents of horizontal gene transfer and microbial evolution. Conjugative elements are capable of self-transfer and also capable of mobilizing other DNA elements that are not able to self-transfer. Plasmids that can be mobilized by conjugative elements are generally thought to contain an origin of transfer (oriT), from which mobilization initiates, and to encode a mobilization protein (Mob, a relaxase) that nicks a site in oriT and covalently attaches to the DNA to be transferred. Plasmids that do not have both an oriT and a cognate mob are thought to be nonmobilizable. We found that Bacillus subtilis carrying the integrative and conjugative element ICEBs1 can transfer three different plasmids to recipient bacteria at high frequencies. Strikingly, these plasmids do not have dedicated mobilization-oriT functions. Plasmid mobilization required conjugation proteins of ICEBs1, including the putative coupling protein. In contrast, plasmid mobilization did not require the ICEBs1 conjugative relaxase or cotransfer of ICEBs1, indicating that the putative coupling protein likely interacts with the plasmid replicative relaxase and directly targets the plasmid DNA to the ICEBs1 conjugation apparatus. These results blur the current categorization of mobilizable and nonmobilizable plasmids and indicate that conjugative elements play a role in horizontal gene transfer even more significant than previously recognized.}, }
@article {pmid22505676, year = {2012}, author = {Trost, E and Blom, J and Soares, Sde C and Huang, IH and Al-Dilaimi, A and Schröder, J and Jaenicke, S and Dorella, FA and Rocha, FS and Miyoshi, A and Azevedo, V and Schneider, MP and Silva, A and Camello, TC and Sabbadini, PS and Santos, CS and Santos, LS and Hirata, R and Mattos-Guaraldi, AL and Efstratiou, A and Schmitt, MP and Ton-That, H and Tauch, A}, title = {Pangenomic study of Corynebacterium diphtheriae that provides insights into the genomic diversity of pathogenic isolates from cases of classical diphtheria, endocarditis, and pneumonia.}, journal = {Journal of bacteriology}, volume = {194}, number = {12}, pages = {3199-3215}, pmid = {22505676}, issn = {1098-5530}, mesh = {Corynebacterium diphtheriae/*genetics/*isolation &amp; purification ; DNA, Bacterial/chemistry/genetics ; Diphtheria/*microbiology ; Endocarditis, Bacterial/*microbiology ; Gene Deletion ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genetic Variation ; *Genome, Bacterial ; Genomic Islands ; Glycolipids/genetics ; Humans ; Molecular Sequence Data ; Mutagenesis, Insertional ; Pneumonia, Bacterial/*microbiology ; Prophages/genetics ; Regulon ; Sequence Analysis, DNA ; }, abstract = {Corynebacterium diphtheriae is one of the most prominent human pathogens and the causative agent of the communicable disease diphtheria. The genomes of 12 strains isolated from patients with classical diphtheria, endocarditis, and pneumonia were completely sequenced and annotated. Including the genome of C. diphtheriae NCTC 13129, we herewith present a comprehensive comparative analysis of 13 strains and the first characterization of the pangenome of the species C. diphtheriae. Comparative genomics showed extensive synteny and revealed a core genome consisting of 1,632 conserved genes. The pangenome currently comprises 4,786 protein-coding regions and increases at an average of 65 unique genes per newly sequenced strain. Analysis of prophages carrying the diphtheria toxin gene tox revealed that the toxoid vaccine producer C. diphtheriae Park-Williams no. 8 has been lysogenized by two copies of the ω(tox)(+) phage, whereas C. diphtheriae 31A harbors a hitherto-unknown tox(+) corynephage. DNA binding sites of the tox-controlling regulator DtxR were detected by genome-wide motif searches. Comparative content analysis showed that the DtxR regulons exhibit marked differences due to gene gain, gene loss, partial gene deletion, and DtxR binding site depletion. Most predicted pathogenicity islands of C. diphtheriae revealed characteristics of horizontal gene transfer. The majority of these islands encode subunits of adhesive pili, which can play important roles in adhesion of C. diphtheriae to different host tissues. All sequenced isolates contain at least two pilus gene clusters. It appears that variation in the distributed genome is a common strategy of C. diphtheriae to establish differences in host-pathogen interactions.}, }
@article {pmid22502997, year = {2012}, author = {Van Houdt, R and Leplae, R and Lima-Mendez, G and Mergeay, M and Toussaint, A}, title = {Towards a more accurate annotation of tyrosine-based site-specific recombinases in bacterial genomes.}, journal = {Mobile DNA}, volume = {3}, number = {1}, pages = {6}, pmid = {22502997}, issn = {1759-8753}, abstract = {BACKGROUND: Tyrosine-based site-specific recombinases (TBSSRs) are DNA breaking-rejoining enzymes. In bacterial genomes, they play a major role in the comings and goings of mobile genetic elements (MGEs), such as temperate phage genomes, integrated conjugative elements (ICEs) or integron cassettes. TBSSRs are also involved in the segregation of plasmids and chromosomes, the resolution of plasmid dimers and of co-integrates resulting from the replicative transposition of transposons. With the aim of improving the annotation of TBSSR genes in genomic sequences and databases, which so far is far from robust, we built a set of over 1,300 TBSSR protein sequences tagged with their genome of origin. We organized them in families to investigate: i) whether TBSSRs tend to be more conserved within than between classes of MGE types and ii) whether the (sub)families may help in understanding more about the function of TBSSRs associated in tandem or trios on plasmids and chromosomes.<br><br>RESULTS: A total of 67% of the TBSSRs in our set are MGE type specific. We define a new class of actinobacterial transposons, related to Tn554, containing one abnormally long TBSSR and one of typical size, and we further characterize numerous TBSSRs trios present in plasmids and chromosomes of &#x3b1;- and &#x3b2;-proteobacteria.<br><br>CONCLUSIONS: The simple in silico procedure described here, which uses a set of reference TBSSRs from defined MGE types, could contribute to greatly improve the annotation of tyrosine-based site-specific recombinases in plasmid, (pro)phage and other integrated MGE genomes. It also reveals TBSSRs families whose distribution among bacterial taxa suggests they mediate lateral gene transfer.}, }
@article {pmid22500732, year = {2012}, author = {Goldenberg, DM}, title = {Horizontal transmission of malignancy by cell-cell fusion.}, journal = {Expert opinion on biological therapy}, volume = {12 Suppl 1}, number = {}, pages = {S133-9}, doi = {10.1517/14712598.2012.671807}, pmid = {22500732}, issn = {1744-7682}, mesh = {Animals ; *Cell Fusion ; Cricetinae ; *Gene Transfer, Horizontal ; Humans ; Hybrid Cells ; Neoplasms/genetics/*pathology ; }, abstract = {INTRODUCTION: The crosstalk between tumor and stromal cells has become an increasing important subject of the biology of oncogenesis, also involving new therapy paradigms for treating tumor-reactive host cells and vasculature.<br><br>AREAS COVERED: This article describes the long-term propagation in hamsters of a human glioblastoma which was derived from the in-vivo fusion of the human tumor cells with hamster stromal cells. The hybrid tumor cells retained at least seven human genes, of which three were able to translate their protein products during serial passages in vitro and in vivo, as well as features of the original tumor's histological appearance. This heterospecific fusion of cancer and normal host stromal cells is discussed as a mechanism for the horizontal transmission of malignancy, which may be a more common phenomenon in human cancer than appreciated previously.<br><br>EXPERT OPINION: Cell-cell fusion in vivo is one of several mechanisms by which genetic information can be transmitted from tumor to host cells, resulting in new and different (more aggressive) tumor cell populations.}, }
@article {pmid22500246, year = {2012}, author = {Nishida, H and Abe, R and Nagayama, T and Yano, K}, title = {Genome Signature Difference between Deinococcus radiodurans and Thermus thermophilus.}, journal = {International journal of evolutionary biology}, volume = {2012}, number = {}, pages = {205274}, pmid = {22500246}, issn = {2090-052X}, abstract = {The extremely radioresistant bacteria of the genus Deinococcus and the extremely thermophilic bacteria of the genus Thermus belong to a common taxonomic group. Considering the distinct living environments of Deinococcus and Thermus, different genes would have been acquired through horizontal gene transfer after their divergence from a common ancestor. Their guanine-cytosine (GC) contents are similar; however, we hypothesized that their genomic signatures would be different. Our findings indicated that the genomes of Deinococcus radiodurans and Thermus thermophilus have different tetranucleotide frequencies. This analysis showed that the genome signature of D. radiodurans is most similar to that of Pseudomonas aeruginosa, whereas the genome signature of T. thermophilus is most similar to that of Thermanaerovibrio acidaminovorans. This difference in genome signatures may be related to the different evolutionary backgrounds of the 2 genera after their divergence from a common ancestor.}, }
@article {pmid22499996, year = {2012}, author = {Poirel, L and Potron, A and Nordmann, P}, title = {OXA-48-like carbapenemases: the phantom menace.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {67}, number = {7}, pages = {1597-1606}, doi = {10.1093/jac/dks121}, pmid = {22499996}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/metabolism ; Bacterial Proteins/genetics/*metabolism ; Carbapenems/metabolism ; Enterobacteriaceae/*enzymology/genetics ; Enterobacteriaceae Infections/*epidemiology/*microbiology ; Gene Transfer, Horizontal ; Global Health ; Humans ; Hydrolysis ; Penicillins/metabolism ; Plasmids ; Prevalence ; *beta-Lactam Resistance ; beta-Lactamases/genetics/*metabolism ; }, abstract = {OXA-48-type carbapenem-hydrolysing class D β-lactamases are increasingly reported in enterobacterial species. To date, six OXA-48-like variants have been identified, with OXA-48 being the most widespread. They differ by a few amino acid substitutions or deletions (one to five amino acids). The enzymes hydrolyse penicillins at a high level and carbapenems at a low level, sparing broad-spectrum cephalosporins, and are not susceptible to β-lactamase inhibitors. When combining permeability defects, OXA-48-like producers may exhibit a high level of resistance to carbapenems. OXA-163 is an exception, hydrolysing broad-spectrum cephalosporins but carbapenems at a very low level, and being susceptible to β-lactamase inhibitors. The bla(OXA-48)-type genes are always plasmid-borne and have been identified in association with insertion sequences involved in their acquisition and expression. The current spread of the bla(OXA-48) gene is mostly linked to the dissemination of a single IncL/M-type self-transferable plasmid of 62 kb that does not carry any additional resistance gene. OXA-48-type carbapenemases have been identified mainly from North African countries, the Middle East, Turkey and India, those areas constituting the most important reservoirs; however, occurrence of OXA-48 producers in European countries is now well documented, with some reported hospital outbreaks. Since many OXA-48-like producers do not exhibit resistance to broad-spectrum cephalosporins, or only decreased susceptibility to carbapenems, their recognition and detection can be challenging. Adequate screening and detection methods are therefore required to prevent and control their dissemination.}, }
@article {pmid22497891, year = {2012}, author = {Kurono, N and Matsuda, A and Etchuya, R and Sobue, R and Sasaki, Y and Ito, M and Ando, T and Maeda, S}, title = {Genome-wide screening of Escherichia coli genes involved in execution and promotion of cell-to-cell transfer of non-conjugative plasmids: rodZ (yfgA) is essential for plasmid acceptance in recipient cells.}, journal = {Biochemical and biophysical research communications}, volume = {421}, number = {1}, pages = {119-123}, doi = {10.1016/j.bbrc.2012.03.127}, pmid = {22497891}, issn = {1090-2104}, mesh = {Conjugation, Genetic/genetics ; Cytoskeletal Proteins/genetics/*physiology ; DNA/genetics ; Escherichia coli/*genetics ; Escherichia coli Proteins/genetics/*physiology ; Gene Transfer, Horizontal/*genetics ; *Genome-Wide Association Study ; Plasmids/*genetics ; Transformation, Bacterial/*genetics ; }, abstract = {Acquisition of new genetic traits by horizontal gene transfer is a bacterial strategy for adaptation to the environment. We previously showed that Escherichia coli can transmit non-conjugative plasmids laterally in a co-culture containing strains with and without the plasmid. In this study, using the Keio collection, a comprehensive library of E. coli knock-out mutants for non-essential genes, we screened for genes responsible for the execution and promotion of cell-to-cell plasmid transfer in recipient cells. By stepwise screening of 'transfer-down' mutants, two essential genes and six promoting genes were obtained. One of the essential genes was priA, which is involved in DNA replication. This priA mutant was also unable to be transformed by artificial transformation methods, probably due to the deficiency of the plasmid maintenance function. The other essential gene was rodZ (yfgA), a gene involved in the regulation of rod-shaped structure of E. coli cells. This rodZ mutant was transformable by all three methods of artificial transformation tested, suggesting that this gene is essential for cell-to-cell plasmid transfer but not for artificial transformation. These are the first data that suggest that rodZ plays an essential role in DNA acquisition.}, }
@article {pmid22496839, year = {2012}, author = {Kuykendall, LD and Shao, JY and Hartung, JS}, title = {Conservation of gene order and content in the circular chromosomes of 'Candidatus Liberibacter asiaticus' and other Rhizobiales.}, journal = {PloS one}, volume = {7}, number = {4}, pages = {e34673}, pmid = {22496839}, issn = {1932-6203}, mesh = {Chromosomes, Bacterial/*genetics ; Gene Order/*genetics ; Genome, Bacterial/genetics ; Molecular Sequence Data ; Rhizobiaceae/*genetics ; *Ring Chromosomes ; Sequence Analysis, DNA ; }, abstract = {'Ca. Liberibacter asiaticus,' an insect-vectored, obligate intracellular bacterium associated with citrus-greening disease, also called "HLB," is a member of the Rhizobiales along with nitrogen-fixing microsymbionts Sinorhizobium meliloti and Bradyrhizobium japonicum, plant pathogen Agrobacterium tumefaciens and facultative intracellular mammalian pathogen Bartonella henselae. Comparative analyses of their circular chromosomes identified 514 orthologous genes shared among all five species. Shared among all five species are 50 identical blocks of microsyntenous orthologous genes (MOGs), containing a total of 283 genes. While retaining highly conserved genomic blocks of microsynteny, divergent evolution, horizontal gene transfer and niche specialization have disrupted macrosynteny among the five circular chromosomes compared. Highly conserved microsyntenous gene clusters help define the Rhizobiales, an order previously defined by 16S RNA gene similarity and herein represented by the three families: Bartonellaceae, Bradyrhizobiaceae and Rhizobiaceae. Genes without orthologs in the other four species help define individual species. The circular chromosomes of each of the five Rhizobiales species examined had genes lacking orthologs in the other four species. For example, 63 proteins are encoded by genes of 'Ca. Liberibacter asiaticus' not shared with other members of the Rhizobiales. Of these 63 proteins, 17 have predicted functions related to DNA replication or RNA transcription, and some of these may have roles related to low genomic GC content. An additional 17 proteins have predicted functions relevant to cellular processes, particularly modifications of the cell surface. Seventeen unshared proteins have specific metabolic functions including a pathway to synthesize cholesterol encoded by a seven-gene operon. The remaining 12 proteins encoded by 'Ca. Liberibacter asiaticus' genes not shared with other Rhizobiales are of bacteriophage origin. 'Ca. Liberibacter asiaticus' shares 11 genes with only Sinorhizobium meliloti and 12 genes are shared with only Bartonella henselae.}, }
@article {pmid22496439, year = {2012}, author = {Attenborough, RM and Hayward, DC and Kitahara, MV and Miller, DJ and Ball, EE}, title = {A "neural" enzyme in nonbilaterian animals and algae: preneural origins for peptidylglycine α-amidating monooxygenase.}, journal = {Molecular biology and evolution}, volume = {29}, number = {10}, pages = {3095-3109}, doi = {10.1093/molbev/mss114}, pmid = {22496439}, issn = {1537-1719}, mesh = {Alternative Splicing/genetics ; Amidine-Lyases/chemistry/metabolism ; Amino Acid Sequence ; Animals ; Anthozoa/*enzymology/genetics ; Biocatalysis ; Chlorophyta/*enzymology ; Evolution, Molecular ; Gene Expression Regulation, Enzymologic ; Mixed Function Oxygenases/chemistry/*genetics/metabolism ; Molecular Sequence Data ; Multienzyme Complexes/chemistry/*genetics/metabolism ; Neurons/*enzymology ; Phylogeny ; Protein Structure, Tertiary ; Sequence Homology, Amino Acid ; Time Factors ; }, abstract = {Secreted peptides, produced by enzymatic processing of larger precursor molecules, are found throughout the animal kingdom and play important regulatory roles as neurotransmitters and hormones. Many require a carboxy-terminal modification, involving the conversion of a glycine residue into an α-amide, for their biological activity. Two sequential enzymatic activities catalyze this conversion: a monooxygenase (peptidylglycine α-hydroxylating monooxygenase or PHM) and an amidating lyase (peptidyl-α-hydroxyglycine α-amidating lyase or PAL). In vertebrates, these activities reside in a single polypeptide known as peptidylglycine α-amidating monooxygenase (PAM), which has been extensively studied in the context of neuropeptide modification. Bifunctional PAMs have been reported from some invertebrates, but the phylogenetic distribution of PAMs and their evolutionary relationship to PALs and PHMs is unclear. Here, we report sequence and expression data for two PAMs from the coral Acropora millepora (Anthozoa, Cnidaria), as well as providing a comprehensive survey of the available sequence data from other organisms. These analyses indicate that bifunctional PAMs predate the origins of the nervous and endocrine systems, consistent with the idea that within the Metazoa their ancestral function may have been to amidate epitheliopeptides. More surprisingly, the phylogenomic survey also revealed the presence of PAMs in green algae (but not in higher plants or fungi), implying that the bifunctional enzyme either predates the plant/animal divergence and has subsequently been lost in a number of lineages or perhaps that convergent evolution or lateral gene transfer has occurred. This finding is consistent with recent discoveries that other molecules once thought of as "neural" predate nervous systems.}, }
@article {pmid22494803, year = {2012}, author = {Al-Quadan, T and Price, CT and Abu Kwaik, Y}, title = {Exploitation of evolutionarily conserved amoeba and mammalian processes by Legionella.}, journal = {Trends in microbiology}, volume = {20}, number = {6}, pages = {299-306}, pmid = {22494803}, issn = {1878-4380}, support = {R01 AI069321-05/AI/NIAID NIH HHS/United States ; R01AI43965/AI/NIAID NIH HHS/United States ; R01 AI120244/AI/NIAID NIH HHS/United States ; R01 AI069321/AI/NIAID NIH HHS/United States ; R01AI069321/AI/NIAID NIH HHS/United States ; R01 AI043965/AI/NIAID NIH HHS/United States ; }, mesh = {Amoeba/*microbiology ; Animals ; Humans ; Legionella pneumophila/growth &amp; development/*physiology ; Mammals/*microbiology ; Models, Biological ; }, abstract = {Legionella pneumophila proliferates within various protists and metazoan cells, where a cadre of ∼300 effectors is injected into the host cell by the defect in organelle trafficking/intracellular multiplication (Dot/Icm) type IVB translocation system. Interkingdom horizontal gene transfer of genes of protists and their subsequent convergent evolution to become translocated effectors has probably enabled L. pneumophila to adapt to the intracellular life within various protists and metazoan cells through exploitation of evolutionarily eukaryotic processes, such as endoplasmic reticulum-to-Golgi vesicle traffic, phosphoinositol metabolism, AMPylation, deAMPylation, prenylation, polyubiquitination, proteasomal degradation and cytosolic amino- and oligo-peptidases. This is highlighted by the ankyrin B (AnkB) F-box effector that exploits multiple conserved eukaryotic machineries to generate high levels of free amino acids as sources of carbon and energy essential for intracellular proliferation in protists and metazoan cells and for manifestation of pulmonary disease in mammals.}, }
@article {pmid22493757, year = {2012}, author = {Bhattacharya, D and Price, DC and Yoon, HS and Yang, EC and Poulton, NJ and Andersen, RA and Das, SP}, title = {Single cell genome analysis supports a link between phagotrophy and primary plastid endosymbiosis.}, journal = {Scientific reports}, volume = {2}, number = {}, pages = {356}, pmid = {22493757}, issn = {2045-2322}, abstract = {Two cases of primary plastid endosymbiosis are known. The first occurred ca. 1.6 billion years ago and putatively gave rise to the canonical plastid in algae and plants. The second is restricted to a genus of rhizarian amoebae that includes Paulinella chromatophora. Photosynthetic Paulinella species gained their plastid from an α-cyanobacterial source and are sister to plastid-lacking phagotrophs such as Paulinella ovalis that ingest cyanobacteria. To study the role of feeding behavior in plastid origin, we analyzed single-cell genome assemblies from six P. ovalis-like cells isolated from Chesapeake Bay, USA. Dozens of contigs in these cell assemblies were derived from prey DNA of α-cyanobacterial origin and associated cyanophages. We found two examples of horizontal gene transfer (HGT) in P. ovalis-like nuclear DNA from cyanobacterial sources. This work suggests the first evidence of a link between feeding behavior in wild-caught cells, HGT, and plastid primary endosymbiosis in the monophyletic Paulinella lineage.}, }
@article {pmid22493593, year = {2012}, author = {Hickey, WJ and Chen, S and Zhao, J}, title = {The phn Island: A New Genomic Island Encoding Catabolism of Polynuclear Aromatic Hydrocarbons.}, journal = {Frontiers in microbiology}, volume = {3}, number = {}, pages = {125}, pmid = {22493593}, issn = {1664-302X}, abstract = {Bacteria are key in the biodegradation of polycyclic aromatic hydrocarbons (PAH), which are widespread environmental pollutants. At least six genotypes of PAH degraders are distinguishable via phylogenies of the ring-hydroxylating dioxygenase (RHD) that initiates bacterial PAH metabolism. A given RHD genotype can be possessed by a variety of bacterial genera, suggesting horizontal gene transfer (HGT) is an important process for dissemination of PAH-degrading genes. But, mechanisms of HGT for most RHD genotypes are unknown. Here, we report in silico and functional analyses of the phenanthrene-degrading bacterium Delftia sp. Cs1-4, a representative of the phn(AFK2) RHD group. The phn(AFK2) genotype predominates PAH degrader communities in some soils and sediments, but, until now, their genomic biology has not been explored. In the present study, genes for the entire phenanthrene catabolic pathway were discovered on a novel ca. 232 kb genomic island (GEI), now termed the phn island. This GEI had characteristics of an integrative and conjugative element with a mobilization/stabilization system similar to that of SXT/R391-type GEI. But, it could not be grouped with any known GEI, and was the first member of a new GEI class. The island also carried genes predicted to encode: synthesis of quorum sensing signal molecules, fatty acid/polyhydroxyalkanoate biosynthesis, a type IV secretory system, a PRTRC system, DNA mobilization functions and >50 hypothetical proteins. The 50% G + C content of the phn gene cluster differed significantly from the 66.7% G + C level of the island as a whole and the strain Cs1-4 chromosome, indicating a divergent phylogenetic origin for the phn genes. Collectively, these studies added new insights into the genetic elements affecting the PAH biodegradation capacity of microbial communities specifically, and the potential vehicles of HGT in general.}, }
@article {pmid22493534, year = {2012}, author = {Woodrow, P and Ciarmiello, LF and Fantaccione, S and Annunziata, MG and Pontecorvo, G and Carillo, P}, title = {Ty1-copia group retrotransposons and the evolution of retroelements in several angiosperm plants: evidence of horizontal transmission.}, journal = {Bioinformation}, volume = {8}, number = {6}, pages = {267-271}, pmid = {22493534}, issn = {0973-2063}, abstract = {The phylogenetic relationships among thirty-seven new Ty1-copia group retrotransposons in seven angiosperm plants were examined by reverse transcriptase and ribonuclease H sequence analysis. Distribution pattern of the retrotransposons of closely related plant species generally reflects a close phylogenetic relationship. In contrast, we found that several retrotransposon sequences from the same genome exhibited a high degree of divergence and had a relatively high degree of identity versus retrotransposon sequences from widely divergent species, including an ancestral phytopathogen fungus. This finding supports the hypothesis that the horizontal transmission from phytopatogen organism to the host flowering plants could have played a role in the evolutionary dynamics of Ty1-copia group retrotransposons.}, }
@article {pmid22492445, year = {2012}, author = {Hung, YL and Chen, HJ and Liu, JC and Chen, YC}, title = {Catalytic efficiency diversification of duplicate β-1,3-1,4-glucanases from Neocallimastix patriciarum J11.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {12}, pages = {4294-4300}, pmid = {22492445}, issn = {1098-5336}, mesh = {Cloning, Molecular ; DNA, Bacterial/chemistry/genetics ; DNA, Fungal/chemistry/genetics ; Endo-1,3(4)-beta-Glucanase/chemistry/genetics/*metabolism ; Enzyme Stability ; Escherichia coli/enzymology/genetics ; Hydrogen-Ion Concentration ; Kinetics ; Molecular Sequence Data ; Neocallimastix/*enzymology/genetics ; Recombinant Proteins/chemistry/genetics/metabolism ; Ruminococcus/enzymology/genetics ; Sequence Analysis, DNA ; Streptococcus/enzymology/genetics ; Substrate Specificity ; Temperature ; }, abstract = {Four types of β-1,3-1,4 glucanase (β-glucanase, EC 3.2.1.73) genes, designated bglA13, bglA16, bglA51, and bglM2, were found in the cDNA library of Neocallimastix patriciarum J11. All were highly homologous with each other and demonstrated a close phylogenetic relationship with and a similar codon bias to Streptococcus equinus. The presence of expansion and several predicted secondary structures in the 3' untranslated regions (3'UTRs) of bglA16 and bglM2 suggest that these two genes were duplicated recently, whereas bglA13 and bglA16, which contain very short 3'UTRs, were replicated earlier. These findings indicate that the β-glucanase genes from N. patriciarum J11 may have arisen by horizontal transfer from the bacterium and subsequent duplication in the rumen fungus. β-Glucanase genes of Streptococcus equinus, Ruminococcus albus 7, and N. patriciarum J11 were cloned and expressed by Escherichia coli. The recombinant β-glucanases cloned from S. equinus, R. albus 7, and N. patriciarum J11 were endo-acting and had similar substrate specificity, but they demonstrated different properties in other tests. The specific activities and catalytic efficiency of the bacterial β-glucanases were also significantly lower than those of the fungal β-glucanases. Our results also revealed that the activities and some characteristics of enzymes were changed during the horizontal gene transfer event. The specific activities of the fungal β-glucanases ranged from 26,529 to 41,209 U/mg of protein when barley-derived β-glucan was used as the substrate. They also demonstrated similar pH and temperature optima, substrate specificity, substrate affinity, and hydrolysis patterns. Nevertheless, BglA16 and BglM2, two recently duplicated β-glucanases, showed much higher k(cat) values than others. These results support the notion that duplicated β-glucanase genes, namely, bglA16 and bglM2, increase the reaction efficiency of β-glucanases and suggest that the catalytic efficiency of β-glucanase is likely to be a criterion determining the evolutionary fate of duplicate forms in N. patriciarum J11.}, }
@article {pmid22491847, year = {2012}, author = {Shapiro, BJ and Friedman, J and Cordero, OX and Preheim, SP and Timberlake, SC and Szabó, G and Polz, MF and Alm, EJ}, title = {Population genomics of early events in the ecological differentiation of bacteria.}, journal = {Science (New York, N.Y.)}, volume = {336}, number = {6077}, pages = {48-51}, pmid = {22491847}, issn = {1095-9203}, support = {U54 GM088558/GM/NIGMS NIH HHS/United States ; U54 GM088558-02/GM/NIGMS NIH HHS/United States ; }, mesh = {Chromosomes, Bacterial/genetics ; *Ecosystem ; *Evolution, Molecular ; Gene Flow ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Variation ; *Genome, Bacterial ; Models, Genetic ; Molecular Sequence Data ; Mutation ; Oceans and Seas ; Phylogeny ; Polymorphism, Single Nucleotide ; *Recombination, Genetic ; Seawater/*microbiology ; *Selection, Genetic ; Vibrio/classification/*genetics ; }, abstract = {Genetic exchange is common among bacteria, but its effect on population diversity during ecological differentiation remains controversial. A fundamental question is whether advantageous mutations lead to selection of clonal genomes or, as in sexual eukaryotes, sweep through populations on their own. Here, we show that in two recently diverged populations of ocean bacteria, ecological differentiation has occurred akin to a sexual mechanism: A few genome regions have swept through subpopulations in a habitat-specific manner, accompanied by gradual separation of gene pools as evidenced by increased habitat specificity of the most recent recombinations. These findings reconcile previous, seemingly contradictory empirical observations of the genetic structure of bacterial populations and point to a more unified process of differentiation in bacteria and sexual eukaryotes than previously thought.}, }
@article {pmid22491069, year = {2012}, author = {Layeghifard, M and Peres-Neto, PR and Makarenkov, V}, title = {Using directed phylogenetic networks to retrace species dispersal history.}, journal = {Molecular phylogenetics and evolution}, volume = {64}, number = {1}, pages = {190-197}, doi = {10.1016/j.ympev.2012.03.016}, pmid = {22491069}, issn = {1095-9513}, mesh = {Animals ; Cluster Analysis ; Computational Biology ; *Demography ; Electron Transport Complex IV/genetics ; Fishes/*genetics ; Fresh Water ; Gene Transfer, Horizontal/*genetics ; *Models, Genetic ; *Phylogeny ; Phylogeography ; Quebec ; Species Specificity ; }, abstract = {Methods designed for inferring phylogenetic trees have been widely applied to reconstruct biogeographic history. Because traditional phylogenetic methods used in biogeographic reconstruction are based on trees rather than networks, they follow the strict assumption in which dispersal among geographical units have occurred on the basis of single dispersal routes across regions and are, therefore, incapable of modelling multiple alternative dispersal scenarios. The goal of this study is to describe a new method that allows for retracing species dispersal by means of directed phylogenetic networks obtained using a horizontal gene transfer (HGT) detection method as well as to draw parallels between the processes of HGT and biogeographic reconstruction. In our case study, we reconstructed the biogeographic history of the postglacial dispersal of freshwater fishes in the Ontario province of Canada. This case study demonstrated the utility and robustness of the new method, indicating that the most important events were south-to-north dispersal patterns, as one would expect, with secondary faunal interchange among regions. Finally, we showed how our method can be used to explore additional questions regarding the commonalities in dispersal history patterns and phylogenetic similarities among species.}, }
@article {pmid22490821, year = {2012}, author = {Miyagishima, SY and Suzuki, K and Okazaki, K and Kabeya, Y}, title = {Expression of the nucleus-encoded chloroplast division genes and proteins regulated by the algal cell cycle.}, journal = {Molecular biology and evolution}, volume = {29}, number = {10}, pages = {2957-2970}, doi = {10.1093/molbev/mss102}, pmid = {22490821}, issn = {1537-1719}, mesh = {Algal Proteins/*genetics/metabolism ; Cell Cycle/*genetics ; Cell Nucleus/*genetics ; Chlamydomonas reinhardtii/cytology/genetics ; Chloroplasts/*genetics ; Cyanobacteria/genetics ; Eukaryota/cytology/*genetics ; *Gene Expression Regulation ; Gene Transfer, Horizontal/genetics ; Genes, Chloroplast/*genetics ; Glaucophyta/cytology/genetics ; Rhodophyta/cytology/genetics ; Symbiosis/genetics ; Time Factors ; }, abstract = {Chloroplasts have evolved from a cyanobacterial endosymbiont and their continuity has been maintained by chloroplast division, which is performed by the constriction of a ring-like division complex at the division site. It is believed that the synchronization of the endosymbiotic and host cell division events was a critical step in establishing a permanent endosymbiotic relationship, such as is commonly seen in existing algae. In the majority of algal species, chloroplasts divide once per specific period of the host cell division cycle. In order to understand both the regulation of the timing of chloroplast division in algal cells and how the system evolved, we examined the expression of chloroplast division genes and proteins in the cell cycle of algae containing chloroplasts of cyanobacterial primary endosymbiotic origin (glaucophyte, red, green, and streptophyte algae). The results show that the nucleus-encoded chloroplast division genes and proteins of both cyanobacterial and eukaryotic host origin are expressed specifically during the S phase, except for FtsZ in one graucophyte alga. In this glaucophyte alga, FtsZ is persistently expressed throughout the cell cycle, whereas the expression of the nucleus-encoded MinD and MinE as well as FtsZ ring formation are regulated by the phases of the cell cycle. In contrast to the nucleus-encoded division genes, it has been shown that the expression of chloroplast-encoded division genes is not regulated by the host cell cycle. The endosymbiotic gene transfer of minE and minD from the chloroplast to the nuclear genome occurred independently on multiple occasions in distinct lineages, whereas the expression of nucleus-encoded MIND and MINE is regulated by the cell cycle in all lineages examined in this study. These results suggest that the timing of chloroplast division in algal cell cycle is restricted by the cell cycle-regulated expression of some but not all of the chloroplast division genes. In addition, it is suggested that the regulation of each division-related gene was established shortly after the endosymbiotic gene transfer, and this event occurred multiple times independently in distinct genes and in distinct lineages.}, }
@article {pmid22489505, year = {2012}, author = {Liu, J and Mao, DQ and Ren, J and Luo, Y and Cao, WQ}, title = {[Analysis of conserved flanking elements associated with antibiotic resistance genes dissemination].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {23}, number = {1}, pages = {240-246}, pmid = {22489505}, issn = {1001-9332}, mesh = {Bacteria/classification/drug effects/isolation &amp; purification ; Base Sequence ; DNA Transposable Elements/*genetics ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Geologic Sediments/microbiology ; Molecular Sequence Data ; Repressor Proteins/genetics ; Rivers/microbiology ; Tetracycline Resistance/*genetics ; *Water Microbiology ; }, abstract = {The overuse of antibiotics in medicine, animal husbandry, and aquiculture industry increases the emergence of antibiotic resistant bacteria and antibiotic resistance genes (ARGs), and also, accelerates the dissemination of ARGs within environmental bacteria. In this study, the total DNA was directly extracted from environmental samples, and the upstream and downstream of antibiotic resistance genes were directly amplified by thermal asymmetric interlaced PCR (Tail-PCR) technique. By optimizing the Tail-PCR program, the multiple flanking sequences of tetW, including 6 upstream sequences and 9 downstream sequences, were simultaneously acquired. Through the bioinformatics analysis, the upstream of tetW presented a perfect inverted repeat (IR), a known tetW regulator peptide, and an insertional sequence (IS), whereas the downstream of tetW presented a most conservative fragment and a common open reading frame (ORF) coding methyltransferase. This study not only revealed several conserved flanking tetW gene modules, but also supplied a highly-efficient and convenient methodology for the research of tetW's dissemination within bacteria, i. e., several flanking sequences could be concisely obtained from one sample by using Tail-PCR program.}, }
@article {pmid22489455, year = {2012}, author = {Cai, H}, title = {[Gene transfer agent--a novel and widespread occurrence mechanism of gene exchange in ocean-a review].}, journal = {Wei sheng wu xue bao = Acta microbiologica Sinica}, volume = {52}, number = {1}, pages = {12-21}, pmid = {22489455}, issn = {0001-6209}, mesh = {Bacteria/*genetics ; *Gene Transfer, Horizontal ; Oceans and Seas ; *Water Microbiology ; }, abstract = {Gene Transfer Agent (GTA) particles are released by bacteria and resemble small, tailed bacteriophages. GTA particles contain small, random pieces of host DNA rather than GTA structural genes or a phage genome. Gene transfer mediated by GTA is efficient and species specific based on knowledge of currently best studied GTAs produced by 4 anaerobes. Genome sequencing projects have revealed a remarkable distribution of GTA gene clusters in the genomes of marine bacterioplankton, implying GTA may be an important mechanism for horizontal gene transfer in ocean. On basis of characterization of the 4 best studied GTAs, this review described GTAs released by numerically dominant marine bacteria, discussed their properties that were important for horizontal gene transfer in ocean, and gave future perspectives to advance GTA research.}, }
@article {pmid22489145, year = {2012}, author = {Guo, FB and Wei, W}, title = {Prediction of genomic islands in three bacterial pathogens of pneumonia.}, journal = {International journal of molecular sciences}, volume = {13}, number = {3}, pages = {3134-3144}, pmid = {22489145}, issn = {1422-0067}, mesh = {Base Composition ; Chlamydial Pneumonia/microbiology ; Chlamydophila pneumoniae/genetics/pathogenicity ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genomic Islands ; Humans ; Mycoplasma pneumoniae/genetics/pathogenicity ; Pneumonia, Bacterial/*microbiology ; Pneumonia, Mycoplasma/microbiology ; Pneumonia, Pneumococcal/microbiology ; Streptococcus pneumoniae/genetics/pathogenicity ; }, abstract = {Pneumonia is one kind of common infectious disease, which is usually caused by bacteria, viruses, or fungi. In this paper, we predicted genomic islands in three bacterial pathogens of pneumonia. They are Chlamydophila pneumoniae, Mycoplasma pneumoniae and Streptococcus pneumoniae, respectively. For each pathogen, one clinical strain is involved. After implementing the cumulative GC profile combined with h and BCN index, eight genomic islands are found in three pathogens. Among them, six genomic islands are found to have mobility elements, which constitute a kind of conserved character of genomic islands, and this introduces the possibility that they are genuine genomic islands. The present results show that the cumulative GC profile when combined with h and BCN indexes is a good method for predicting genomic islands in bacteria and it has lower false positive rate than the SIGI method. Specially, three genomic islands are found to contain clusters of genes coding for production of virulence factors and this is useful for research into the pathogenicity of these pathogens and helpful for the treatment of diseases caused by them.}, }
@article {pmid22487988, year = {2012}, author = {Willson, SJ}, title = {CSD homomorphisms between phylogenetic networks.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {9}, number = {4}, pages = {1128-1138}, doi = {10.1109/TCBB.2012.52}, pmid = {22487988}, issn = {1557-9964}, mesh = {Computational Biology/*methods ; Gene Transfer, Horizontal ; Hybridization, Genetic ; *Models, Genetic ; *Phylogeny ; }, abstract = {Since Darwin, species trees have been used as a simplified description of the relationships which summarize the complicated network N of reality. Recent evidence of hybridization and lateral gene transfer, however, suggest that there are situations where trees are inadequate. Consequently it is important to determine properties that characterize networks closely related to N and possibly more complicated than trees but lacking the full complexity of N. A connected surjective digraph map (CSD) is a map f from one network N to another network M such that every arc is either collapsed to a single vertex or is taken to an arc, such that f is surjective, and such that the inverse image of a vertex is always connected. CSD maps are shown to behave well under composition. It is proved that if there is a CSD map from N to M, then there is a way to lift an undirected version of M into N, often with added resolution. A CSD map from N to M puts strong constraints on N. In general, it may be useful to study classes of networks such that, for any N, there exists a CSD map from N to some standard member of that class.}, }
@article {pmid22486703, year = {2012}, author = {Smith, J}, title = {Tragedy of the commons among antibiotic resistance plasmids.}, journal = {Evolution; international journal of organic evolution}, volume = {66}, number = {4}, pages = {1269-1274}, doi = {10.1111/j.1558-5646.2011.01531.x}, pmid = {22486703}, issn = {1558-5646}, support = {GM33782-17/GM/NIGMS NIH HHS/United States ; }, mesh = {*Biological Evolution ; *Drug Resistance, Microbial ; Escherichia coli/*genetics/pathogenicity ; Gene Transfer, Horizontal ; Genetic Fitness ; Microbial Interactions ; Models, Biological ; Plasmids/*genetics ; Virulence ; }, abstract = {As social interactions are increasingly recognized as important determinants of microbial fitness, sociobiology is being enlisted to better understand the evolution of clinically relevant microbes and, potentially, to influence their evolution to aid human health. Of special interest are situations in which there exists a "tragedy of the commons," where natural selection leads to a net reduction in fitness for all members of a population. Here, I demonstrate the existence of a tragedy of the commons among antibiotic resistance plasmids of bacteria. In serial transfer culture, plasmids evolved a greater ability to superinfect already-infected bacteria, increasing plasmid fitness when evolved genotypes were rare. Evolved plasmids, however, fell victim to their own success, reducing the density of their bacterial hosts when they became common and suffering reduced fitness through vertical transmission. Social interactions can thus be an important determinant of evolution for the molecular endosymbionts of bacteria. These results also identify an avenue of evolution that reduces proliferation of both antibiotic resistance genes and their bacterial hosts.}, }
@article {pmid22484699, year = {2012}, author = {Cuenca, A and Petersen, G and Seberg, O and Jahren, AH}, title = {Genes and processed paralogs co-exist in plant mitochondria.}, journal = {Journal of molecular evolution}, volume = {74}, number = {3-4}, pages = {158-169}, pmid = {22484699}, issn = {1432-1432}, mesh = {Alismatales/genetics ; Evolution, Molecular ; *Gene Duplication ; Gene Transfer, Horizontal ; *Genes, Mitochondrial ; *Genes, Plant ; Genome, Plant ; Mitochondria/genetics ; Phylogeny ; *RNA Editing ; }, abstract = {RNA-mediated gene duplication has been proposed to create processed paralogs in the plant mitochondrial genome. A processed paralog may retain signatures left by the maturation process of its RNA precursor, such as intron removal and no need of RNA editing. Whereas it is well documented that an RNA intermediary is involved in the transfer of mitochondrial genes to the nucleus, no direct evidence exists for insertion of processed paralogs in the mitochondria (i.e., processed and un-processed genes have never been found simultaneously in the mitochondrial genome). In this study, we sequenced a region of the mitochondrial gene nad1, and identified a number of taxa were two different copies of the region co-occur in the mitochondria. The two nad1 paralogs differed in their (a) presence or absence of a group II intron, and (b) number of edited sites. Thus, this work provides the first evidence of co-existence of processed paralogs and their precursors within the plant mitochondrial genome. In addition, mapping the presence/absence of the paralogs provides indirect evidence of RNA-mediated gene duplication as an essential process shaping the mitochondrial genome in plants.}, }
@article {pmid22482837, year = {2012}, author = {Francis, I and De Keyser, A and De Backer, P and Simón-Mateo, C and Kalkus, J and Pertry, I and Ardiles-Diaz, W and De Rycke, R and Vandeputte, OM and El Jaziri, M and Holsters, M and Vereecke, D}, title = {pFiD188, the linear virulence plasmid of Rhodococcus fascians D188.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {25}, number = {5}, pages = {637-647}, doi = {10.1094/MPMI-08-11-0215}, pmid = {22482837}, issn = {0894-0282}, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics ; Base Sequence ; Biofilms/growth &amp; development ; Conjugation, Genetic ; DNA Mutational Analysis ; DNA, Bacterial/chemistry/genetics ; Gene Expression Regulation/genetics ; Genes, Bacterial/genetics ; Molecular Sequence Data ; Operon/genetics ; Plant Diseases/*microbiology ; Plant Leaves/microbiology ; Plasmids/*genetics ; Replicon/genetics ; Rhodococcus/enzymology/*genetics/pathogenicity/ultrastructure ; Sequence Alignment ; Sequence Analysis, DNA ; Telomere ; Nicotiana/*microbiology ; Virulence/genetics ; }, abstract = {Rhodococcus fascians is currently the only phytopathogen of which the virulence genes occur on a linear plasmid. To get insight into the origin of this replicon and into the virulence strategy of this broad-spectrum phytopathogen, the sequence of the linear plasmid of strain D188, pFiD188, was determined. Analysis of the 198,917 bp revealed four syntenic regions with linear plasmids of R. erythropolis, R. jostii, and R. opacus, suggesting a common origin of these replicons. Mutational analysis of pFi_086 and pFi_102, similar to cutinases and type IV peptidases, respectively, showed that conserved region R2 was involved in plasmid dispersal and pointed toward a novel function for actinobacterial cutinases in conjugation. Additionally, pFiD188 had three regions that were unique for R. fascians. Functional analysis of the stk and nrp loci of regions U2 and U3, respectively, indicated that their role in symptom development was limited compared with that of the previously identified fas, att, and hyp virulence loci situated in region U1. Thus, pFiD188 is a typical rhodococcal linear plasmid with a composite structure that encodes core functions involved in plasmid maintenance and accessory functions, some possibly acquired through horizontal gene transfer, implicated in virulence and the interaction with the host.}, }
@article {pmid22482720, year = {2012}, author = {Hlouchova, K and Rudolph, J and Pietari, JM and Behlen, LS and Copley, SD}, title = {Pentachlorophenol hydroxylase, a poorly functioning enzyme required for degradation of pentachlorophenol by Sphingobium chlorophenolicum.}, journal = {Biochemistry}, volume = {51}, number = {18}, pages = {3848-3860}, pmid = {22482720}, issn = {1520-4995}, support = {R01 GM078554/GM/NIGMS NIH HHS/United States ; GM078554/GM/NIGMS NIH HHS/United States ; }, mesh = {Biodegradation, Environmental ; Catalysis ; Hydrogen Peroxide/metabolism ; Metabolic Networks and Pathways ; Mixed Function Oxygenases/*metabolism ; Pentachlorophenol/*metabolism ; Pesticides/metabolism ; Sphingomonadaceae/enzymology ; Structure-Activity Relationship ; Substrate Specificity ; }, abstract = {Several strains of Sphingobium chlorophenolicum have been isolated from soil that was heavily contaminated with pentachlorophenol (PCP), a toxic pesticide introduced in the 1930s. S. chlorophenolicum appears to have assembled a poorly functioning pathway for degradation of PCP by patching enzymes recruited via two independent horizontal gene transfer events into an existing metabolic pathway. Flux through the pathway is limited by PCP hydroxylase. PCP hydroxylase is a dimeric protein that belongs to the family of flavin-dependent phenol hydroxylases. In the presence of NADPH, PCP hydroxylase converts PCP to tetrachlorobenzoquinone (TCBQ). The k(cat) for PCP (0.024 s(-1)) is very low, suggesting that the enzyme is not well evolved for turnover of this substrate. Structure-activity studies reveal that substrate binding and activity are enhanced by a low pK(a) for the phenolic proton, increased hydrophobicity, and the presence of a substituent ortho to the hydroxyl group of the phenol. PCP hydroxylase exhibits substantial uncoupling; the C4a-hydroxyflavin intermediate, instead of hydroxylating the substrate, can decompose to produce H(2)O(2) in a futile cycle that consumes NADPH. The extent of uncoupling varies from 0 to 100% with different substrates. The extent of uncoupling is increased by the presence of bulky substituents at position 3, 4, or 5 and decreased by the presence of a chlorine in the ortho position. The effectiveness of PCP hydroxylase is additionally hindered by its promiscuous activity with tetrachlorohydroquinone (TCHQ), a downstream metabolite in the degradation pathway. The conversion of TCHQ to TCBQ reverses flux through the pathway. Substantial uncoupling also occurs during the reaction with TCHQ.}, }
@article {pmid22481309, year = {2012}, author = {Acosta-Cruz, E and Wisniewski-Dyé, F and Rouy, Z and Barbe, V and Valdés, M and Mavingui, P}, title = {Insights into the 1.59-Mbp largest plasmid of Azospirillum brasilense CBG497.}, journal = {Archives of microbiology}, volume = {194}, number = {9}, pages = {725-736}, doi = {10.1007/s00203-012-0805-2}, pmid = {22481309}, issn = {1432-072X}, mesh = {Amino Acid Sequence ; Azospirillum/genetics ; Azospirillum brasilense/classification/*genetics/growth &amp; development ; Base Sequence ; Gene Transfer, Horizontal ; Hydrogen-Ion Concentration ; Mexico ; Molecular Sequence Data ; Phylogeny ; Plasmids/*genetics ; Sequence Analysis ; }, abstract = {The plant growth-promoting proteobacterium Azospirillum brasilense enhances growth of many economically important crops, such as wheat, maize, and rice. The sequencing and annotation of the 1.59-Mbp replicon of A. brasilense CBG497, a strain isolated from a maize rhizosphere grown on an alkaline soil in the northeast of Mexico, revealed a GC content of 68.7 % and the presence of 1,430 potential protein-encoding genes, 1,147 of them classified into clusters of orthologous groups categories, and 16 tRNA genes representing 11 tRNA species. The presence of sixty-two genes representatives of the minimal gene set and chromid core genes suggests its importance in bacterial survival. The phaAB → G operon, reported as involved in the bacterial adaptation to alkaline pH in the presence of K(+), was also found on this replicon and detected in several Azospirillum strains. Phylogenetic analysis suggests that it was laterally acquired. We were not able to show its inference on the adaptation to basic pH, giving a hint about the presence of an alternative system for adaptation to alkaline pH.}, }
@article {pmid22479693, year = {2011}, author = {Jackson, DJ}, title = {The evolution of an ancient metazoan biomineralization strategy was supported by a horizontal gene transfer.}, journal = {Mobile genetic elements}, volume = {1}, number = {3}, pages = {242-246}, pmid = {22479693}, issn = {2159-2543}, abstract = {The molecular mechanisms that generate morphological novelty are of great interest to evolutionary biologists because these are the processes that can explain how the diversity of life on earth arose. With advances in sequencing technologies, the high-throughput analysis and comparison of entire genomes is now possible. Bioinformatic mining of such genome-wide data sets often includes a search for horizontal gene transfers (HGTs) as these events can provide exciting insight into how morphological, or physiological novelties may have arisen. A recent paper by Jackson et al.1 demonstrates that a HGT into the genome of the sponge Astrosclera willeyana likely supported the evolution of this animal's biomineralization strategy. This HGT, which occurred deep in time, was perhaps a key event in the evolution of this animal's body form and would not have been detected by certain in silico methods commonly used to screen large data sets.}, }
@article {pmid22479689, year = {2011}, author = {Skarin, H and Segerman, B}, title = {Horizontal gene transfer of toxin genes in Clostridium botulinum: Involvement of mobile elements and plasmids.}, journal = {Mobile genetic elements}, volume = {1}, number = {3}, pages = {213-215}, pmid = {22479689}, issn = {2159-2543}, abstract = {Intoxication with the potent botulinum neurotoxin (BoNT) gives rise to the serious paralytic illness botulism. BoNT is part of a complex that consists of the neurotoxin and several associated components, all encoded by the bont gene cluster. This gene cluster has likely been subjected to horizontal gene transfer between different groups of clostridia, which has given rise to the genetically diverse species Clostridium botulinum. C. botulinum is divided into four physiological groups (I-IV), where group I and II cause disease in humans and group III in animals. Analysis of the genomes of group I, II and III has revealed that toxin genes, including the bont cluster, often are plasmid-borne. The genomes analyzed from group III contain an unusually high number of plasmids carrying different toxin genes. Some of these genes are also found in other Clostridium species and some have moved between different plasmids within the same physiological group. This indicates that horizontal transfer of toxin genes is taking place within and between species of Clostridium. The abundance of mobile elements, especially in genomes of group III, is likely connected to accelerated genome plasticity and gene transfer events.}, }
@article {pmid22479525, year = {2012}, author = {Balasubramanian, D and Schneper, L and Merighi, M and Smith, R and Narasimhan, G and Lory, S and Mathee, K}, title = {The regulatory repertoire of Pseudomonas aeruginosa AmpC ß-lactamase regulator AmpR includes virulence genes.}, journal = {PloS one}, volume = {7}, number = {3}, pages = {e34067}, pmid = {22479525}, issn = {1932-6203}, support = {S06 GM008205/GM/NIGMS NIH HHS/United States ; SC1 AI081376/AI/NIAID NIH HHS/United States ; S06 GM08205/GM/NIGMS NIH HHS/United States ; 5SC1AI081376/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics/physiology ; Biofilms ; Caenorhabditis elegans ; Drug Resistance, Bacterial ; Gene Deletion ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Mutation ; Oligonucleotide Array Sequence Analysis ; Phenotype ; Polymerase Chain Reaction/methods ; Pseudomonas aeruginosa/*genetics/*pathogenicity ; Transcriptome ; Virulence ; Virulence Factors/metabolism ; beta-Lactamases/*genetics/physiology ; }, abstract = {In Enterobacteriaceae, the transcriptional regulator AmpR, a member of the LysR family, regulates the expression of a chromosomal β-lactamase AmpC. The regulatory repertoire of AmpR is broader in Pseudomonas aeruginosa, an opportunistic pathogen responsible for numerous acute and chronic infections including cystic fibrosis. In addition to regulating ampC, P. aeruginosa AmpR regulates the sigma factor AlgT/U and production of some quorum sensing (QS)-regulated virulence factors. In order to better understand the ampR regulon, we compared the transcriptional profile generated using DNA microarrays of the prototypic P. aeruginosa PAO1 strain with its isogenic ampR deletion mutant, PAOΔampR. Transcriptome analysis demonstrates that the AmpR regulon is much more extensive than previously thought, with the deletion of ampR influencing the differential expression of over 500 genes. In addition to regulating resistance to β-lactam antibiotics via AmpC, AmpR also regulates non-β-lactam antibiotic resistance by modulating the MexEF-OprN efflux pump. Other virulence mechanisms including biofilm formation and QS-regulated acute virulence factors are AmpR-regulated. Real-time PCR and phenotypic assays confirmed the microarray data. Further, using a Caenorhabditis elegans model, we demonstrate that a functional AmpR is required for P. aeruginosa pathogenicity. AmpR, a member of the core genome, also regulates genes in the regions of genome plasticity that are acquired by horizontal gene transfer. Further, we show differential regulation of other transcriptional regulators and sigma factors by AmpR, accounting for the extensive AmpR regulon. The data demonstrates that AmpR functions as a global regulator in P. aeruginosa and is a positive regulator of acute virulence while negatively regulating biofilm formation, a chronic infection phenotype. Unraveling this complex regulatory circuit will provide a better understanding of the bacterial response to antibiotics and how the organism coordinately regulates a myriad of virulence factors in response to antibiotic exposure.}, }
@article {pmid22476322, year = {2012}, author = {Vieira de Souza, F and Roque, R and Silva Moreira, JL and Resende de Souza, M and Nicoli, JR and Neumann, E and Cantini Nunes, &#xc1;}, title = {Transfer of antibiotic resistance determinants between lactobacilli isolates from the gastrointestinal tract of chicken.}, journal = {Beneficial microbes}, volume = {3}, number = {2}, pages = {137-144}, doi = {10.3920/BM2011.0058}, pmid = {22476322}, issn = {1876-2891}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Chickens ; Conjugation, Genetic ; *Drug Resistance, Bacterial ; Female ; Gastrointestinal Tract/*microbiology ; *Gene Transfer, Horizontal ; Germ-Free Life ; Lactobacillus/*drug effects/genetics/*isolation &amp; purification ; Male ; Mice ; Microbial Sensitivity Tests ; }, abstract = {The aim of this study was to assess the potential horizontal transfer of genetic traits for antibiotic resistance between lactobacilli isolated from the chicken gut, both in vitro and in vivo. Thirty-seven Lactobacillus spp. strains isolated from the gizzard, small and large intestines and caeca of free-range broiler chickens showed multi-drug resistance as assessed by disc diffusion assays. The minimum inhibitory concentration (MIC) for vancomycin, tetracycline, erythromycin and chloramphenicol was determined in De Man, Rogosa and Sharpe broth in a microplate assay. Almost all the lactobacilli isolates were resistant to vancomycin (except strains belonging to the Lactobacillus acidophilus group) and to tetracycline (MIC≥128 μg/ml). Only five strains were resistant to erythromycin, and six to chloramphenicol. The transfer rate in filter mating experiments performed using L. acidophilus strain 4M14E (EmR), Lactobacillus vaginalis strain 5M14E (CmR), Lactobacillus salivarius strain 5C14C (EmR), and the 4G14L and 3C14C strains of Lactobacillus reuteri (CmR) showed a frequency of approximately 1×104 cfu/ml of double-resistant transconjugants for the different combinations. The exception was the L. salivarius 5C14C (EmR) and L. vaginalis 5M14E (CmR) mating combination, which produced no transconjugants. In vivo experiments performed in gnotobiotic mice by mating L. acidophilus 4M14E (EmR) with L. reuteri 3C14C (CmR), L. reuteri 4G14L (CmR) or L. vaginalis 5M14E (CmR) resulted in transconjugants at 3.95±0.29, 3.16±0.33, and 4.55±1.52 log10 cfu/g of faeces, respectively. Taken together, these data suggest that genetic exchange may occur between native bacterial strains within the gastrointestinal tract of chickens, which might maintain a dynamic gene pool conferring antibiotic resistance upon indigenous microbiota components, even in the absence of the pathogens. This possibility must be taken into account as a complementary criterion when lactobacilli are screened for probiotic use.}, }
@article {pmid22475940, year = {2012}, author = {Jans, C and Gerber, A and Bugnard, J and Njage, PM and Lacroix, C and Meile, L}, title = {Novel Streptococcus infantarius subsp. infantarius variants harboring lactose metabolism genes homologous to Streptococcus thermophilus.}, journal = {Food microbiology}, volume = {31}, number = {1}, pages = {33-42}, doi = {10.1016/j.fm.2012.02.001}, pmid = {22475940}, issn = {1095-9998}, mesh = {Animals ; Camelus ; Cultured Milk Products/*microbiology ; DNA, Bacterial/genetics/*isolation &amp; purification ; Galactose/metabolism ; Genotype ; Kenya ; Lac Operon ; Lactose/*metabolism ; Phenotype ; Sequence Analysis, DNA ; Somalia ; Streptococcus/*genetics/isolation &amp; purification/metabolism ; Streptococcus thermophilus/*genetics/metabolism ; beta-Galactosidase/genetics/metabolism ; }, abstract = {Streptococcus infantarius subsp. infantarius belongs to the Streptococcus bovis/Streptococcus equinus complex (SBSEC) commonly associated with human and animal infections. We elucidated the lactose metabolism of S. infantarius subsp. infantarius predominant in African fermented milk products. S. infantarius subsp. infantarius isolates (n = 192) were identified in 88% of spontaneously fermented camel milk suusac samples (n = 24) from Kenya and Somalia at log10 8.2-8.5 CFU mL[-1]. African S. infantarius isolates excreted stoichiometric amounts of galactose when grown on lactose, exhibiting a metabolism similar to Streptococcus thermophilus and distinct from their type strain. African S. infantarius subsp. infantarius CJ18 harbors a regular gal operon with 99.7-100% sequence identity to S. infantarius subsp. infantarius ATCC BAA-102(T) and a gal-lac operon with 91.7-97.6% sequence identity to S. thermophilus, absent in all sequenced SBSEC strains analyzed. The expression and functionality of lacZ was demonstrated in a β-galactosidase assay. The gal-lac operon was identified in 100% of investigated S. infantarius isolates (n = 46) from suusac samples and confirmed in Malian fermented cow milk isolates. The African S. infantarius variant potentially evolved through horizontal gene transfer of an S. thermophilus-homologous lactose pathway. Safety assessments are needed to identify any putative health risks of this novel S. infantarius variant.}, }
@article {pmid22465020, year = {2012}, author = {Fernie, AR and Obata, T and Allen, AE and Araújo, WL and Bowler, C}, title = {Leveraging metabolomics for functional investigations in sequenced marine diatoms.}, journal = {Trends in plant science}, volume = {17}, number = {7}, pages = {395-403}, doi = {10.1016/j.tplants.2012.02.005}, pmid = {22465020}, issn = {1878-4372}, mesh = {Adaptation, Biological ; Biological Evolution ; Diatoms/*genetics/metabolism ; Gene Transfer, Horizontal ; Genome ; Iron/metabolism ; Metabolic Networks and Pathways ; *Metabolomics ; Ornithine/metabolism ; Symbiosis ; Urea/metabolism ; }, abstract = {Recent years have witnessed the genomic decoding of a wide range of photosynthetic organisms from the model plant Arabidopsis thaliana and the complex genomes of important crop species to single-celled marine phytoplankton. The comparative sequencing of green, red and brown algae has provided considerable insight into a number of important questions concerning their evolution, physiology and metabolism. The combinatorial application of metabolomics has further deepened our understanding both of the function of individual genes and of metabolic processes. Here we discuss the power of utilising metabolomics in conjunction with sequencing data to gain greater insight into the metabolic hierarchies underpinning the function of individual organisms, using unicellular marine diatoms as a case study to exemplify the advantages of this approach.}, }
@article {pmid22463741, year = {2012}, author = {Nordgård, L and Brusetti, L and Raddadi, N and Traavik, T and Averhoff, B and Nielsen, KM}, title = {An investigation of horizontal transfer of feed introduced DNA to the aerobic microbiota of the gastrointestinal tract of rats.}, journal = {BMC research notes}, volume = {5}, number = {}, pages = {170}, pmid = {22463741}, issn = {1756-0500}, mesh = {Acinetobacter/drug effects/genetics/growth &amp; development ; Aerobiosis ; Animal Feed/*analysis ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics/growth &amp; development ; Bacterial Load ; DNA/*analysis/genetics ; DNA, Bacterial/analysis/genetics ; Drug Resistance, Bacterial/genetics ; Female ; Gastrointestinal Tract/*microbiology ; *Gene Transfer, Horizontal ; Male ; Metagenome/*genetics ; Plasmids/genetics ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Rats ; Rats, Wistar ; }, abstract = {BACKGROUND: Horizontal gene transfer through natural transformation of members of the microbiota of the lower gastrointestinal tract (GIT) of mammals has not yet been described. Insufficient DNA sequence similarity for homologous recombination to occur has been identified as the major barrier to interspecies transfer of chromosomal DNA in bacteria. In this study we determined if regions of high DNA similarity between the genomes of the indigenous bacteria in the GIT of rats and feed introduced DNA could lead to homologous recombination and acquisition of antibiotic resistance genes.<br><br>RESULTS: Plasmid DNA with two resistance genes (nptI and aadA) and regions of high DNA similarity to 16S rRNA and 23S rRNA genes present in a broad range of bacterial species present in the GIT, were constructed and added to standard rat feed. Six rats, with a normal microbiota, were fed DNA containing pellets daily over four days before sampling of the microbiota from the different GI compartments (stomach, small intestine, cecum and colon). In addition, two rats were included as negative controls. Antibiotic resistant colonies growing on selective media were screened for recombination with feed introduced DNA by PCR targeting unique sites in the putatively recombined regions. No transformants were identified among 441 tested isolates.<br><br>CONCLUSIONS: The analyses showed that extensive ingestion of DNA (100 &#x3bc;g plasmid) per day did not lead to increased proportions of kanamycin resistant bacteria, nor did it produce detectable transformants among the aerobic microbiota examined for 6 rats (detection limit < 1 transformant per 1,1 &#xd7; 10(8) cultured bacteria). The key methodological challenges to HGT detection in animal feedings trials are identified and discussed. This study is consistent with other studies suggesting natural transformation is not detectable in the GIT of mammals.}, }
@article {pmid22462721, year = {2012}, author = {Kraus, RH and Kerstens, HH and van Hooft, P and Megens, HJ and Elmberg, J and Tsvey, A and Sartakov, D and Soloviev, SA and Crooijmans, RP and Groenen, MA and Ydenberg, RC and Prins, HH}, title = {Widespread horizontal genomic exchange does not erode species barriers among sympatric ducks.}, journal = {BMC evolutionary biology}, volume = {12}, number = {}, pages = {45}, pmid = {22462721}, issn = {1471-2148}, mesh = {Animals ; Ducks/*genetics ; Female ; Gene Frequency ; Gene Transfer, Horizontal ; *Genetic Speciation ; Genotyping Techniques ; Linkage Disequilibrium ; Male ; Polymorphism, Single Nucleotide ; Principal Component Analysis ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The study of speciation and maintenance of species barriers is at the core of evolutionary biology. During speciation the genome of one population becomes separated from other populations of the same species, which may lead to genomic incompatibility with time. This separation is complete when no fertile offspring is produced from inter-population matings, which is the basis of the biological species concept. Birds, in particular ducks, are recognised as a challenging and illustrative group of higher vertebrates for speciation studies. There are many sympatric and ecologically similar duck species, among which fertile hybrids occur relatively frequently in nature, yet these species remain distinct.<br><br>RESULTS: We show that the degree of shared single nucleotide polymorphisms (SNPs) between five species of dabbling ducks (genus Anas) is an order of magnitude higher than that previously reported between any pair of eukaryotic species with comparable evolutionary distances. We demonstrate that hybridisation has led to sustained exchange of genetic material between duck species on an evolutionary time scale without disintegrating species boundaries. Even though behavioural, genetic and ecological factors uphold species boundaries in ducks, we detect opposing forces allowing for viable interspecific hybrids, with long-term evolutionary implications. Based on the superspecies concept we here introduce the novel term "supra-population" to explain the persistence of SNPs identical by descent within the studied ducks despite their history as distinct species dating back millions of years.<br><br>CONCLUSIONS: By reviewing evidence from speciation theory, palaeogeography and palaeontology we propose a fundamentally new model of speciation to accommodate our genetic findings in dabbling ducks. This model, we argue, may also shed light on longstanding unresolved general speciation and hybridisation patterns in higher organisms, e.g. in other bird groups with unusually high hybridisation rates. Observed parallels to horizontal gene transfer in bacteria facilitate the understanding of why ducks have been such an evolutionarily successful group of animals. There is large evolutionary potential in the ability to exchange genes among species and the resulting dramatic increase of effective population size to counter selective constraints.}, }
@article {pmid22461309, year = {2012}, author = {Pasteran, F and Albornoz, E and Faccone, D and Gomez, S and Valenzuela, C and Morales, M and Estrada, P and Valenzuela, L and Matheu, J and Guerriero, L and Arbizú, E and Calderón, Y and Ramon-Pardo, P and Corso, A}, title = {Emergence of NDM-1-producing Klebsiella pneumoniae in Guatemala.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {67}, number = {7}, pages = {1795-1797}, doi = {10.1093/jac/dks101}, pmid = {22461309}, issn = {1460-2091}, mesh = {Adult ; Anti-Bacterial Agents ; Conjugation, Genetic ; *Disease Outbreaks ; Gene Transfer, Horizontal ; Guatemala/epidemiology ; Humans ; Infant ; Klebsiella Infections/*epidemiology/*microbiology ; Klebsiella pneumoniae/*enzymology/genetics/*isolation &amp; purification ; Microbial Sensitivity Tests ; beta-Lactamases/genetics/*metabolism ; }, }
@article {pmid22460782, year = {2012}, author = {Dalhoff, A}, title = {Resistance surveillance studies: a multifaceted problem--the fluoroquinolone example.}, journal = {Infection}, volume = {40}, number = {3}, pages = {239-262}, pmid = {22460782}, issn = {1439-0973}, mesh = {Anti-Bacterial Agents/*pharmacology/therapeutic use ; Bacteria/*drug effects ; Bacterial Infections/drug therapy/epidemiology/*microbiology ; Drug Prescriptions/standards ; *Drug Resistance, Bacterial ; Fluoroquinolones/*pharmacology/therapeutic use ; Humans ; Incidence ; Microbial Sensitivity Tests/methods/standards ; Population Surveillance/methods ; Prevalence ; Public Health ; Research Design/standards ; }, abstract = {INTRODUCTION: This review summarizes data on the fluoroquinolone resistance epidemiology published in the previous 5 years.<br><br>MATERIALS AND METHODS: The data reviewed are stratified according to the different prescription patterns by either primary- or tertiary-care givers and by indication. Global surveillance studies demonstrate that fluoroquinolone- resistance rates increased in the past several years in almost all bacterial species except Staphylococcus pneumoniae and Haemophilus influenzae causing community-acquired respiratory tract infections (CARTIs), as well as Enterobacteriaceae causing community-acquired urinary tract infections. Geographically and quantitatively varying fluoroquinolone resistance rates were recorded among Gram-positive and Gram-negative pathogens causing healthcare-associated respiratory tract infections. One- to two-thirds of Enterobacteriaceae producing extended-spectrum &#x3b2;-lactamases (ESBLs) were fluoroquinolone resistant too, thus, limiting the fluoroquinolone use in the treatment of community- as well as healthcare-acquired urinary tract and intra-abdominal infections. The remaining ESBL-producing or plasmid-mediated quinolone resistance mechanisms harboring Enterobacteriaceae were low-level quinolone resistant. Furthermore, 10-30 % of H. influenzae and S. pneumoniae causing CARTIs harbored first-step quinolone resistance determining region (QRDR) mutations. These mutants pass susceptibility testing unnoticed and are primed to acquire high-level fluoroquinolone resistance rapidly, thus, putting the patient at risk. The continued increase in fluoroquinolone resistance affects patient management and necessitates changes in some current guidelines for the treatment of intra-abdominal infections or even precludes the use of fluoroquinolones in certain indications like gonorrhea and pelvic inflammatory diseases in those geographic areas in which fluoroquinolone resistance rates and/or ESBL production is high. Fluoroquinolone resistance has been selected among the commensal flora colonizing the gut, nose, oropharynx, and skin, so that horizontal gene transfer between the commensal flora and the offending pathogen as well as inter- and intraspecies recombinations contribute to the emergence and spread of fluoroquinolone resistance among pathogenic streptococci. Although interspecies recombinations are not yet the major cause for the emergence of fluoroquinolone resistance, its existence indicates that a large reservoir of fluoroquinolone resistance exists. Thus, a scenario resembling that of a worldwide spread of &#x3b2;-lactam resistance in pneumococci is conceivable. However, many resistance surveillance studies suffer from inaccuracies like the sampling of a selected patient population, restricted geographical sampling, and undefined requirements of the user, so that the results are biased. The number of national centers is most often limited with one to two participating laboratories, so that such studies are point prevalence but not surveillance studies. Selected samples are analyzed predominantly as either hospitalized patients or patients at risk or those in whom therapy failed are sampled; however, fluoroquinolones are most frequently prescribed by the general practitioner. Selected sampling results in a significant over-estimation of fluoroquinolone resistance in outpatients. Furthermore, the requirements of the users are often not met; the prescribing physician, the microbiologist, the infection control specialist, public health and regulatory authorities, and the pharmaceutical industry have diverse interests, which, however, are not addressed by different designs of a surveillance study. Tools should be developed to provide customer-specific datasets.<br><br>CONCLUSION: Consequently, most surveillance studies suffer from well recognized but uncorrected biases or inaccuracies. Nevertheless, they provide important information that allows the identification of trends in pathogen incidence and antimicrobial resistance.}, }
@article {pmid22459247, year = {2012}, author = {Gillings, MR and Stokes, HW}, title = {Are humans increasing bacterial evolvability?.}, journal = {Trends in ecology &amp; evolution}, volume = {27}, number = {6}, pages = {346-352}, doi = {10.1016/j.tree.2012.02.006}, pmid = {22459247}, issn = {1872-8383}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/*genetics/*pathogenicity ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/*genetics ; Environmental Pollution ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; Genome ; Humans ; Mutation ; Phenotype ; Selection, Genetic ; }, abstract = {Attempts to control bacterial pathogens have led to an increase in antibiotic-resistant cells and the genetic elements that confer resistance phenotypes. These cells and genes are disseminated simultaneously with the original selective agents via human waste streams. This might lead to a second, unintended consequence of antimicrobial therapy; an increase in the evolvability of all bacterial cells. The genetic variation upon which natural selection acts is a consequence of mutation, recombination and lateral gene transfer (LGT). These processes are under selection, balancing genomic integrity against the advantages accrued by genetic innovation. Saturation of the environment with selective agents might cause directional selection for higher rates of mutation, recombination and LGT, producing unpredictable consequences for humans and the biosphere.}, }
@article {pmid22457982, year = {2012}, author = {Breitbart, M}, title = {Marine viruses: truth or dare.}, journal = {Annual review of marine science}, volume = {4}, number = {}, pages = {425-448}, doi = {10.1146/annurev-marine-120709-142805}, pmid = {22457982}, issn = {1941-1405}, mesh = {Bacteria/*virology ; Bacteriophages/*physiology ; Environmental Monitoring ; Oceans and Seas ; Seawater/*virology ; *Water Microbiology ; }, abstract = {Over the past two decades, marine virology has progressed from a curiosity to an intensely studied topic of critical importance to oceanography. At concentrations of approximately 10 million viruses per milliliter of surface seawater, viruses are the most abundant biological entities in the oceans. The majority of these viruses are phages (viruses that infect bacteria). Through lysing their bacterial hosts, marine phages control bacterial abundance, affect community composition, and impact global biogeochemical cycles. In addition, phages influence their hosts through selection for resistance, horizontal gene transfer, and manipulation of bacterial metabolism. Recent work has also demonstrated that marine phages are extremely diverse and can carry a variety of auxiliary metabolic genes encoding critical ecological functions. This review is structured as a scientific "truth or dare," revealing several well-established "truths" about marine viruses and presenting a few "dares" for the research community to undertake in future studies.}, }
@article {pmid22457715, year = {2012}, author = {Gawthorne, JA and Beatson, SA and Srikhanta, YN and Fox, KL and Jennings, MP}, title = {Origin of the diversity in DNA recognition domains in phasevarion associated modA genes of pathogenic Neisseria and Haemophilus influenzae.}, journal = {PloS one}, volume = {7}, number = {3}, pages = {e32337}, pmid = {22457715}, issn = {1932-6203}, mesh = {Alleles ; Amino Acid Sequence ; DNA, Bacterial/*genetics ; *Genes, Bacterial ; Haemophilus influenzae/*genetics ; Molecular Sequence Data ; Neisseria/*genetics ; Phylogeny ; Recombination, Genetic ; Sequence Homology, Amino Acid ; Species Specificity ; }, abstract = {Phase variable restriction-modification (R-M) systems have been identified in a range of pathogenic bacteria. In some it has been demonstrated that the random switching of the mod (DNA methyltransferase) gene mediates the coordinated expression of multiple genes and constitutes a phasevarion (phase variable regulon). ModA of Neisseria and Haemophilus influenzae contain a highly variable, DNA recognition domain (DRD) that defines the target sequence that is modified by methylation and is used to define modA alleles. 18 distinct modA alleles have been identified in H. influenzae and the pathogenic Neisseria. To determine the origin of DRD variability, the 18 modA DRDs were used to search the available databases for similar sequences. Significant matches were identified between several modA alleles and mod gene from distinct bacterial species, indicating one source of the DRD variability was via horizontal gene transfer. Comparison of DRD sequences revealed significant mosaicism, indicating exchange between the Neisseria and H. influenzae modA alleles. Regions of high inter- and intra-allele similarity indicate that some modA alleles had undergone recombination more frequently than others, generating further diversity. Furthermore, the DRD from some modA alleles, such as modA12, have been transferred en bloc to replace the DRD from different modA alleles.}, }
@article {pmid22457309, year = {2012}, author = {Stokes, HW and Martinez, E and Roy Chowdhury, P and Djordjevic, S}, title = {Class 1 integron-associated spread of resistance regions in Pseudomonas aeruginosa: plasmid or chromosomal platforms?.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {67}, number = {7}, pages = {1799-1800}, doi = {10.1093/jac/dks116}, pmid = {22457309}, issn = {1460-2091}, mesh = {*Chromosomes, Bacterial ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Humans ; *Integrons ; *Plasmids ; Pseudomonas aeruginosa/*drug effects/*genetics ; }, }
@article {pmid22456736, year = {2012}, author = {Joseph, SJ and Read, TD}, title = {Genome-wide recombination in Chlamydia trachomatis.}, journal = {Nature genetics}, volume = {44}, number = {4}, pages = {364-366}, pmid = {22456736}, issn = {1546-1718}, mesh = {Chlamydia Infections/*genetics ; Chlamydia trachomatis/*classification/*genetics ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; *Recombination, Genetic ; }, abstract = {A new study reports comparative genomic analysis of 52 geographically diverse strains of Chlamydia trachomatis. The authors reconstruct a genome-wide phylogeny of the species and report extensive genome-wide recombination across multiple lineages of this intracellular bacterial pathogen.}, }
@article {pmid22453942, year = {2012}, author = {Mackrill, JJ}, title = {Ryanodine receptor calcium release channels: an evolutionary perspective.}, journal = {Advances in experimental medicine and biology}, volume = {740}, number = {}, pages = {159-182}, doi = {10.1007/978-94-007-2888-2_7}, pmid = {22453942}, issn = {0065-2598}, mesh = {Animals ; Calcium/metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Humans ; Protein Structure, Tertiary ; Ryanodine Receptor Calcium Release Channel/chemistry/genetics/*physiology ; }, abstract = {Ryanodine receptors (RyRs), along with the related inositol 1,4,5-trisphosphate receptors (IP(3)Rs), mediate the release of Ca(2+) from intracellular organelles of eukaryotes. As discussed in other chapters, such increases in intracellular Ca(2+) levels act a fundamental second messenger, regulating a diverse array of cellular processes. For over two decades, it has been reported that vertebrates express multiple RYR genes, whereas non-vertebrate multicellular organisms possess a single homologue within their genomes. Recently, the existence of RyR-like channels in unicellular organisms has also been reported. This chapter exploits recent expansions in available genome data to generate an overview of the expression of RyR-like genes in organisms representing a broad range of viral, archaeal, bacterial and eukaryotic taxa. Analyses of the multidomain structures and phylogenetic relationships of these proteins has lead to a model in which, early during eukaryotic evolution, IP(3)R-like ancestral Ca(2+) release channels were converted to RyR proteins via the addition of promiscuous protein domains, possibly via horizontal gene transfer mechanisms.}, }
@article {pmid22452844, year = {2012}, author = {Okubo, T and Tsukui, T and Maita, H and Okamoto, S and Oshima, K and Fujisawa, T and Saito, A and Futamata, H and Hattori, R and Shimomura, Y and Haruta, S and Morimoto, S and Wang, Y and Sakai, Y and Hattori, M and Aizawa, S and Nagashima, KV and Masuda, S and Hattori, T and Yamashita, A and Bao, Z and Hayatsu, M and Kajiya-Kanegae, H and Yoshinaga, I and Sakamoto, K and Toyota, K and Nakao, M and Kohara, M and Anda, M and Niwa, R and Jung-Hwan, P and Sameshima-Saito, R and Tokuda, S and Yamamoto, S and Yamamoto, S and Yokoyama, T and Akutsu, T and Nakamura, Y and Nakahira-Yanaka, Y and Takada Hoshino, Y and Hirakawa, H and Mitsui, H and Terasawa, K and Itakura, M and Sato, S and Ikeda-Ohtsubo, W and Sakakura, N and Kaminuma, E and Minamisawa, K}, title = {Complete genome sequence of Bradyrhizobium sp. S23321: insights into symbiosis evolution in soil oligotrophs.}, journal = {Microbes and environments}, volume = {27}, number = {3}, pages = {306-315}, pmid = {22452844}, issn = {1347-4405}, mesh = {Bacterial Proteins/genetics ; Base Composition ; Bradyrhizobium/*genetics/isolation &amp; purification/physiology ; DNA, Bacterial/*chemistry/*genetics ; *Genome, Bacterial ; Metabolic Networks and Pathways/genetics ; Molecular Sequence Data ; Open Reading Frames ; RNA, Untranslated/genetics ; *Sequence Analysis, DNA ; Soil Microbiology ; Symbiosis ; Synteny ; }, abstract = {Bradyrhizobium sp. S23321 is an oligotrophic bacterium isolated from paddy field soil. Although S23321 is phylogenetically close to Bradyrhizobium japonicum USDA110, a legume symbiont, it is unable to induce root nodules in siratro, a legume often used for testing Nod factor-dependent nodulation. The genome of S23321 is a single circular chromosome, 7,231,841 bp in length, with an average GC content of 64.3%. The genome contains 6,898 potential protein-encoding genes, one set of rRNA genes, and 45 tRNA genes. Comparison of the genome structure between S23321 and USDA110 showed strong colinearity; however, the symbiosis islands present in USDA110 were absent in S23321, whose genome lacked a chaperonin gene cluster (groELS3) for symbiosis regulation found in USDA110. A comparison of sequences around the tRNA-Val gene strongly suggested that S23321 contains an ancestral-type genome that precedes the acquisition of a symbiosis island by horizontal gene transfer. Although S23321 contains a nif (nitrogen fixation) gene cluster, the organization, homology, and phylogeny of the genes in this cluster were more similar to those of photosynthetic bradyrhizobia ORS278 and BTAi1 than to those on the symbiosis island of USDA110. In addition, we found genes encoding a complete photosynthetic system, many ABC transporters for amino acids and oligopeptides, two types (polar and lateral) of flagella, multiple respiratory chains, and a system for lignin monomer catabolism in the S23321 genome. These features suggest that S23321 is able to adapt to a wide range of environments, probably including low-nutrient conditions, with multiple survival strategies in soil and rhizosphere.}, }
@article {pmid22450512, year = {2012}, author = {Watanabe, M and Tagami, Y and Miura, K and Kageyama, D and Stouthamer, R}, title = {Distribution patterns of Wolbachia endosymbionts in the closely related flower bugs of the genus Orius: implications for coevolution and horizontal transfer.}, journal = {Microbial ecology}, volume = {64}, number = {2}, pages = {537-545}, pmid = {22450512}, issn = {1432-184X}, mesh = {Animals ; *Biological Evolution ; Cloning, Molecular ; Flowers/*parasitology ; *Gene Transfer, Horizontal ; Heteroptera/classification/*microbiology ; Japan ; Molecular Sequence Data ; Multilocus Sequence Typing ; Phylogeny ; Recombination, Genetic ; Sequence Analysis, DNA ; Species Specificity ; *Symbiosis ; Wolbachia/classification/*genetics/physiology ; }, abstract = {Vertical transmission is the primary route of the endosymbiont Wolbachia for its own spread among invertebrate hosts, but horizontal transmission between different hosts is believed to have occurred multiple times. However, it is not well known how Wolbachia commonly spread among closely related hosts. We focused on the closely related species of the minute pirate bugs belonging to the genus Orius, which are important biological control agents in agricultural crops because they are the most useful natural enemy of various tiny pests, such as thrips. Here, we examined five Orius species (Orius sauteri, Orius nagaii, Orius minutus, Orius strigicollis, and Orius tantillus) from eight geographic localities in Japan for Wolbachia infection. Two distinct strains, wOus1 and wOus2, were detected based on Wolbachia surface protein (wsp) gene sequencing. Furthermore, multilocus sequence typing revealed that each of the strains comprised two variants that differed in a single nucleotide. The overall distribution patterns of the two Wolbachia strains were found to differ among host species: prevalent double infection with wOus1 and wOus2 in O. strigicollis; fixation of single infection with wOus2 in O. nagaii; occurrence of single infection with wOus1 in O. sauteri; prevalence of single infection with wOus1 in O. minutus with an exception in a single population; and lack of Wolbachia infection in O. tantillus. Such differences in the distribution patterns of Wolbachia may reflect the evolutionary history of Wolbachia infection among Orius species and/or ecological and physiological differences among the Orius species that determine the invasiveness and maintenance of the two Wolbachia strains.}, }
@article {pmid22449772, year = {2012}, author = {Feng, Y and Liu, J and Li, YG and Cao, FL and Johnston, RN and Zhou, J and Liu, GR and Liu, SL}, title = {Inheritance of the Salmonella virulence plasmids: mostly vertical and rarely horizontal.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {12}, number = {5}, pages = {1058-1063}, doi = {10.1016/j.meegid.2012.03.004}, pmid = {22449772}, issn = {1567-7257}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Cluster Analysis ; Evolution, Molecular ; Gene Transfer, Horizontal ; Phylogeny ; Plasmids/*classification/genetics ; Salmonella/*classification/genetics/pathogenicity ; Salmonella enteritidis/classification/genetics/pathogenicity ; Virulence/genetics ; }, abstract = {Salmonella virulence plasmids (VPs) contribute to pathogenesis during the systemic phase of infection. Only eight serovars have been found to contain VP, and the size of VP is unique to the host serovar, suggesting VPs are mainly transmitted vertically. According to this hypothesis, VPs should have the same phylogenetic relationships as the chromosomes among the bacteria that carry the VPs. To test this hypothesis, we sequenced VPs from the serovar Enteritidis and Pullorum, named pSENV and pSPUV, respectively, and compared them with VPs from other Salmonella serovars. The overall results supported our hypothesis with the exception of pSENV, which was more similar to VPs from the more distantly related serovars Typhimuirum, Choleraesuis and Paratyphi C than to those from the very closely related serovars Dublin and Gallinarum/Pullorum with regard to either gene content or nucleotide similarity. These findings demonstrate that Enteritidis acquired pSENV by horizontal transfer.}, }
@article {pmid22449397, year = {2012}, author = {Cui, P and Lin, Q and Ding, F and Hu, S and Yu, J}, title = {The transcript-centric mutations in human genomes.}, journal = {Genomics, proteomics &amp; bioinformatics}, volume = {10}, number = {1}, pages = {11-22}, pmid = {22449397}, issn = {2210-3244}, mesh = {Gene Duplication ; Genes, Essential ; *Genome, Human ; High-Throughput Nucleotide Sequencing ; Humans ; *Mutation ; *Polymorphism, Single Nucleotide ; Selection, Genetic ; Sequence Analysis, RNA ; *Transcription, Genetic ; }, abstract = {Since the human genome is mostly transcribed, genetic variations must exhibit sequence signatures reflecting the relationship between transcription processes and chromosomal structures as we have observed in unicellular organisms. In this study, a set of 646 ubiquitous expression-invariable genes (EIGs) which are present in germline cells were defined and examined based on RNA-sequencing data from multiple high-throughput transcriptomic data. We demonstrated a relationship between gene expression level and transcript-centric mutations in the human genome based on single nucleotide polymorphism (SNP) data. A significant positive correlation was shown between gene expression and mutation, where highly-expressed genes accumulate more mutations than lowly-expressed genes. Furthermore, we found four major types of transcript-centric mutations: C→T, A→G, C→G, and G→T in human genomes and identified a negative gradient of the sequence variations aligning from the 5' end to the 3' end of the transcription units (TUs). The periodical occurrence of these genetic variations across TUs is associated with nucleosome phasing. We propose that transcript-centric mutations are one of the major driving forces for gene and genome evolution along with creation of new genes, gene/genome duplication, and horizontal gene transfer.}, }
@article {pmid22446310, year = {2012}, author = {Nonaka, L and Maruyama, F and Miyamoto, M and Miyakoshi, M and Kurokawa, K and Masuda, M}, title = {Novel conjugative transferable multiple drug resistance plasmid pAQU1 from Photobacterium damselae subsp. damselae isolated from marine aquaculture environment.}, journal = {Microbes and environments}, volume = {27}, number = {3}, pages = {263-272}, pmid = {22446310}, issn = {1347-4405}, mesh = {Anti-Bacterial Agents/*pharmacology ; Aquaculture ; Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; *Drug Resistance, Multiple, Bacterial ; Enterobacteriaceae/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Japan ; Molecular Sequence Data ; Photobacterium/*drug effects/*genetics/isolation &amp; purification ; Phylogeny ; *Plasmids ; Seawater/*microbiology ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Vibrionaceae/genetics ; }, abstract = {The emergence of drug-resistant bacteria is a severe problem in aquaculture. The ability of drug resistance genes to transfer from a bacterial cell to another is thought to be responsible for the wide dissemination of these genes in the aquaculture environment; however, little is known about the gene transfer mechanisms in marine bacteria. In this study, we show that a tetracycline-resistant strain of Photobacterium damselae subsp. damselae, isolated from seawater at a coastal aquaculture site in Japan, harbors a novel multiple drug resistance plasmid. This plasmid named pAQU1 can be transferred to Escherichia coli by conjugation. Nucleotide sequencing showed that the plasmid was 204,052 base pairs and contained 235 predicted coding sequences. Annotation showed that pAQU1 did not have known repA, suggesting a new replicon, and contained seven drug resistance genes: bla(CARB-9)-like, floR, mph(A)-like, mef(A)-like, sul2, tet(M) and tet(B). The plasmid has a complete set of genes encoding the apparatus for the type IV secretion system with a unique duplication of traA. Phylogenetic analysis of the deduced amino acid sequence of relaxase encoded by traI in pAQU1 demonstrated that the conjugative transfer system of the plasmid belongs to MOB(H12), a sub-group of the MOB(H) plasmid family, closely related to the IncA/C type of plasmids and SXT/R391 widely distributed among species of Enterobacteriaceae and Vibrionaceae. Our data suggest that conjugative transfer is involved in horizontal gene transfer among marine bacteria and provide useful insights into the molecular basis for the dissemination of drug resistance genes among bacteria in the aquaculture environment.}, }
@article {pmid22444301, year = {2012}, author = {Madsen, JS and Burmølle, M and Hansen, LH and Sørensen, SJ}, title = {The interconnection between biofilm formation and horizontal gene transfer.}, journal = {FEMS immunology and medical microbiology}, volume = {65}, number = {2}, pages = {183-195}, doi = {10.1111/j.1574-695X.2012.00960.x}, pmid = {22444301}, issn = {1574-695X}, mesh = {Bacteria/*genetics ; *Bacterial Physiological Phenomena ; Biofilms/*growth &amp; development ; *Gene Transfer, Horizontal ; Interspersed Repetitive Sequences ; Plasmids ; }, abstract = {Recent research has revealed that horizontal gene transfer and biofilm formation are connected processes. Although published research investigating this interconnectedness is still limited, we will review this subject in order to highlight the potential of these observations because of their believed importance in the understanding of the adaptation and subsequent evolution of social traits in bacteria. Here, we discuss current evidence for such interconnectedness centred on plasmids. Horizontal transfer rates are typically higher in biofilm communities compared with those in planktonic states. Biofilms, furthermore, promote plasmid stability and may enhance the host range of mobile genetic elements that are transferred horizontally. Plasmids, on the other hand, are very well suited to promote the evolution of social traits such as biofilm formation. This, essentially, transpires because plasmids are independent replicons that enhance their own success by promoting inter-bacterial interactions. They typically also carry genes that heighten their hosts' direct fitness. Furthermore, current research shows that the so-called mafia traits encoded on mobile genetic elements can enforce bacteria to maintain stable social interactions. It also indicates that horizontal gene transfer ultimately enhances the relatedness of bacteria carrying the mobile genetic elements of the same origin. The perspective of this review extends to an overall interconnectedness between horizontal gene transfer, mobile genetic elements and social evolution of bacteria.}, }
@article {pmid22443515, year = {2012}, author = {Van Houdt, R and Monsieurs, P and Mijnendonckx, K and Provoost, A and Janssen, A and Mergeay, M and Leys, N}, title = {Variation in genomic islands contribute to genome plasticity in Cupriavidus metallidurans.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {111}, pmid = {22443515}, issn = {1471-2164}, mesh = {Bacterial Proteins/genetics ; Cerebrospinal Fluid/microbiology ; Cupriavidus/drug effects/*genetics/physiology ; Drug Resistance, Bacterial/genetics ; Environment ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/*genetics ; Genomic Islands/*genetics ; Metals/pharmacology ; Oligonucleotide Array Sequence Analysis ; Sigma Factor/genetics ; Stress, Physiological/genetics ; }, abstract = {BACKGROUND: Different Cupriavidus metallidurans strains isolated from metal-contaminated and other anthropogenic environments were genotypically and phenotypically compared with C. metallidurans type strain CH34. The latter is well-studied for its resistance to a wide range of metals, which is carried for a substantial part by its two megaplasmids pMOL28 and pMOL30.<br><br>RESULTS: Comparative genomic hybridization (CGH) indicated that the extensive arsenal of determinants involved in metal resistance was well conserved among the different C. metallidurans strains. Contrary, the mobile genetic elements identified in type strain CH34 were not present in all strains but clearly showed a pattern, although, not directly related to a particular biotope nor location (geographical). One group of strains carried almost all mobile genetic elements, while these were much less abundant in the second group. This occurrence was also reflected in their ability to degrade toluene and grow autotrophically on hydrogen gas and carbon dioxide, which are two traits linked to separate genomic islands of the Tn4371-family. In addition, the clear pattern of genomic islands distribution allowed to identify new putative genomic islands on chromosome 1 and 2 of C. metallidurans CH34.<br><br>CONCLUSIONS: Metal resistance determinants are shared by all C. metallidurans strains and their occurrence is apparently irrespective of the strain's isolation type and place. Cupriavidus metallidurans strains do display substantial differences in the diversity and size of their mobile gene pool, which may be extensive in some (including the type strain) while marginal in others.}, }
@article {pmid22443140, year = {2012}, author = {Mercer, RG and Quinlan, M and Rose, AR and Noll, S and Beatty, JT and Lang, AS}, title = {Regulatory systems controlling motility and gene transfer agent production and release in Rhodobacter capsulatus.}, journal = {FEMS microbiology letters}, volume = {331}, number = {1}, pages = {53-62}, doi = {10.1111/j.1574-6968.2012.02553.x}, pmid = {22443140}, issn = {1574-6968}, support = {93779-1//Canadian Institutes of Health Research/Canada ; }, mesh = {Bacterial Proteins ; Caulobacter crescentus/genetics ; DNA-Binding Proteins ; Flagella/*physiology ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Locomotion ; Rhodobacter capsulatus/*genetics/physiology ; Transcription Factors ; United States ; }, abstract = {Production of the gene transfer agent of Rhodobacter capsulatus, RcGTA, is dependent upon several cellular regulatory systems, including a putative phosphorelay involving the CtrA and CckA proteins. These proteins are also involved in flagellar motility in R. capsulatus. The interactions of proteins in this system are best understood in Caulobacter crescentus where CtrA is activated by phosphorylation by the CckA-ChpT phosphorelay. CtrA~P activity is further controlled by SciP, which represses ctrA transcription and CtrA activation of transcription. We show that R. capsulatus chpT and cckA mutants both have greatly reduced motility and RcGTA activity. Unlike the ctrA mutant where RcGTA gene transcription is absent, the decrease in RcGTA activity is because of reduced release of RcGTA from the cells. The sciP mutant is not affected for RcGTA production but our results support the C. crescentus model of SciP repression of flagellar motility genes. We show that both unphosphorylated and phosphorylated CtrA can activate RcGTA gene expression, while CtrA~P seems to be required for release of the particle and expression of motility genes. This has led us to a new model of how this regulatory system controls motility and production of RcGTA in R. capsulatus.}, }
@article {pmid22443110, year = {2012}, author = {Rodriguez-R, LM and Grajales, A and Arrieta-Ortiz, ML and Salazar, C and Restrepo, S and Bernal, A}, title = {Genomes-based phylogeny of the genus Xanthomonas.}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {43}, pmid = {22443110}, issn = {1471-2180}, mesh = {Computational Biology ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Multigene Family ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Xanthomonas/*classification/genetics ; }, abstract = {BACKGROUND: The genus Xanthomonas comprises several plant pathogenic bacteria affecting a wide range of hosts. Despite the economic, industrial and biological importance of Xanthomonas, the classification and phylogenetic relationships within the genus are still under active debate. Some of the relationships between pathovars and species have not been thoroughly clarified, with old pathovars becoming new species. A change in the genus name has been recently suggested for Xanthomonas albilineans, an early branching species currently located in this genus, but a thorough phylogenomic reconstruction would aid in solving these and other discrepancies in this genus.<br><br>RESULTS: Here we report the results of the genome-wide analysis of DNA sequences from 989 orthologous groups from 17 Xanthomonas spp. genomes available to date, representing all major lineages within the genus. The phylogenetic and computational analyses used in this study have been automated in a Perl package designated Unus, which provides a framework for phylogenomic analyses which can be applied to other datasets at the genomic level. Unus can also be easily incorporated into other phylogenomic pipelines.<br><br>CONCLUSIONS: Our phylogeny agrees with previous phylogenetic topologies on the genus, but revealed that the genomes of Xanthomonas citri and Xanthomonas fuscans belong to the same species, and that of Xanthomonas albilineans is basal to the joint clade of Xanthomonas and Xylella fastidiosa. Genome reduction was identified in the species Xanthomonas vasicola in addition to the previously identified reduction in Xanthomonas albilineans. Lateral gene transfer was also observed in two gene clusters.}, }
@article {pmid22441985, year = {2012}, author = {Jiang, XY and Du, XD and Tian, YM and Shen, RJ and Sun, CF and Zou, SM}, title = {Goldfish transposase Tgf2 presumably from recent horizontal transfer is active.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {26}, number = {7}, pages = {2743-2752}, doi = {10.1096/fj.11-199273}, pmid = {22441985}, issn = {1530-6860}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; DNA Transposable Elements/genetics ; Evolution, Molecular ; Female ; Fish Proteins/*genetics ; Gene Expression Regulation, Developmental ; *Gene Transfer, Horizontal ; Goldfish/embryology/*genetics/metabolism ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Genetic ; RNA, Messenger/genetics/metabolism ; Sequence Homology, Amino Acid ; Transposases/*genetics ; }, abstract = {Hobo/Activator/Tam3 (hAT) superfamily transposons occur in plants and animals and play a role in genomic evolution. Certain hAT transposons are active and have been developed as incisive genetic tools. Active vertebrate elements are rarely discovered; however, Tgf2 transposon was recently discovered in goldfish (Carassius auratus). Here, we found that the endogenous Tgf2 element can transpose in goldfish genome. Seven different goldfish mRNA transcripts, encoding three lengths of Tgf2 transposase, were identified. Tgf2 transposase mRNA was detected in goldfish embryos, mainly in epithelial cells; levels were high in ovaries and mature eggs and in all adult tissues tested. Endogenous Tgf2 transposase mRNA is active in mature eggs and can mediate high rates of transposition (>30%) when injected with donor plasmids harboring a Tgf2 cis-element. When donor plasmid was coinjected with capped Tgf2 transposase mRNA, the insertion rate reached >90% at 1 yr. Nonautonomous copies of the Tgf2 transposon with large-fragment deletions and low levels of point mutations were also detected in common goldfish. Phylogenetic analysis indicates the taxonomic distribution of Tgf2 in goldfish is not due to vertical inheritance. We propose that the goldfish Tgf2 transposon originated by recent horizontal transfer and maintains a highly native activity.}, }
@article {pmid22436996, year = {2012}, author = {Park, C and Zhang, J}, title = {High expression hampers horizontal gene transfer.}, journal = {Genome biology and evolution}, volume = {4}, number = {4}, pages = {523-532}, pmid = {22436996}, issn = {1759-6653}, support = {R01 GM067030/GM/NIGMS NIH HHS/United States ; R01GM067030/GM/NIGMS NIH HHS/United States ; }, mesh = {Escherichia coli/classification/*genetics ; Escherichia coli Proteins/*genetics ; Evolution, Molecular ; *Gene Expression ; *Gene Transfer, Horizontal ; Models, Genetic ; Phylogeny ; }, abstract = {Horizontal gene transfer (HGT), the movement of genetic material from one species to another, is a common phenomenon in prokaryotic evolution. Although the rate of HGT is known to vary among genes, our understanding of the cause of this variation, currently summarized by two rules, is far from complete. The first rule states that informational genes, which are involved in DNA replication, transcription, and translation, have lower transferabilities than operational genes. The second rule asserts that protein interactivity negatively impacts gene transferability. Here, we hypothesize that high expression hampers HGT, because the fitness cost of an HGT to the recipient, arising from the 1) energy expenditure in transcription and translation, 2) cytotoxic protein misfolding, 3) reduction in cellular translational efficiency, 4) detrimental protein misinteraction, and 5) disturbance of the optimal protein concentration or cell physiology, increases with the expression level of the transferred gene. To test this hypothesis, we examined laboratory and natural HGTs to Escherichia coli. We observed lower transferabilities of more highly expressed genes, even after controlling the confounding factors from the two established rules and the genic GC content. Furthermore, expression level predicts gene transferability better than all other factors examined. We also confirmed the significant negative impact of gene expression on the rate of HGTs to 127 of 133 genomes of eubacteria and archaebacteria. Together, these findings establish the gene expression level as a major determinant of horizontal gene transferability. They also suggest that most successful HGTs are initially slightly deleterious, fixed because of their negligibly low costs rather than high benefits to the recipient.}, }
@article {pmid22431592, year = {2012}, author = {Brown Kav, A and Sasson, G and Jami, E and Doron-Faigenboim, A and Benhar, I and Mizrahi, I}, title = {Insights into the bovine rumen plasmidome.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {14}, pages = {5452-5457}, pmid = {22431592}, issn = {1091-6490}, mesh = {Animals ; Cattle ; Phylogeny ; *Plastids ; Rumen/*microbiology ; }, abstract = {Plasmids are self-replicating genetic elements capable of mobilization between different hosts. Plasmids often serve as mediators of lateral gene transfer, a process considered to be a strong and sculpting evolutionary force in microbial environments. Our aim was to characterize the overall plasmid population in the environment of the bovine rumen, which houses a complex and dense microbiota that holds enormous significance for humans. We developed a procedure for the isolation of total rumen plasmid DNA, termed rumen plasmidome, and subjected it to deep sequencing using the Illumina paired-end protocol and analysis using public and custom-made bioinformatics tools. A large number of plasmidome contigs aligned with plasmids of rumen bacteria isolated from different locations and at various time points, suggesting that not only the bacterial taxa, but also their plasmids, are defined by the ecological niche. The bacterial phylum distribution of the plasmidome was different from that of the rumen bacterial taxa. Nevertheless, both shared a dominance of the phyla Firmicutes, Bacteroidetes, and Proteobacteria. Evidently, the rumen plasmidome is of a highly mosaic nature that can cross phyla. Interestingly, when we compared the functional profile of the rumen plasmidome to two plasmid databases and two recently published rumen metagenomes, it became apparent that the rumen plasmidome codes for functions, which are enriched in the rumen ecological niche and could confer advantages to their hosts, suggesting that the functional profiles of mobile genetic elements are associated with their environment, as has been previously implied for viruses.}, }
@article {pmid22429905, year = {2012}, author = {Cantas, L and Midtlyng, PJ and Sørum, H}, title = {Impact of antibiotic treatments on the expression of the R plasmid tra genes and on the host innate immune activity during pRAS1 bearing Aeromonas hydrophila infection in zebrafish (Danio rerio).}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {37}, pmid = {22429905}, issn = {1471-2180}, mesh = {Aeromonas hydrophila/*drug effects/genetics ; Animals ; Anti-Bacterial Agents/*pharmacology ; Conjugation, Genetic ; Drug Resistance, Multiple, Bacterial/genetics ; Female ; Fish Diseases/immunology/microbiology ; Fluoroquinolones/pharmacology ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Gram-Negative Bacterial Infections/immunology/microbiology/veterinary ; *Immunity, Innate ; Intestines/immunology/microbiology ; Male ; Metagenome ; *R Factors ; RNA, Ribosomal, 16S/genetics ; Tetracycline/pharmacology ; Trimethoprim/pharmacology ; Zebrafish/*immunology/microbiology ; }, abstract = {BACKGROUND: The transfer of R plasmids between bacteria has been well studied under laboratory conditions and the transfer frequency has been found to vary between plasmids and under various physical conditions. For the first time, we here study the expression of the selected plasmid mobility genes traD, virB11 and virD4 in the 45 kb IncU plasmid, pRAS1, conferring resistance to tetracycline, trimethoprim and sulphonamide, using an in vivo zebrafish infection- treatment model.<br><br>RESULTS: Three days after oral infection of adult zebrafish with Aeromonas hydrophila harboring pRAS1, elevated expression of pro-inflammatory cytokine (TNF &#x3b1;, IL-1&#x3b2; and IL-8) and complement C3 genes in the intestine coincided with disease symptoms. Tetracycline, trimethoprim and an ineffective concentration of flumequine given 48 h prior to sampling, strongly increased expression of plasmid mobility genes, whereas an effective dosage of flumequine resulted in lower levels of mRNA copies of these genes relative to placebo treatment. Following effective treatment with flumequine, and ineffective treatments with a low concentration of flumequine, with trimethoprim or with sulphonamide, the intestinal expression of immune genes was strongly induced compared to placebo treated control fish.<br><br>CONCLUSIONS: Treatment of zebrafish infected with an antibiotic resistant (TcR, TmR, SuR) A. hydrophila with ineffective concentrations of flumequine or the ineffective antimicrobials tetracycline and trimethoprim strongly induced expression of genes mediating conjugative transfer of the R-plasmid pRAS1. Simultaneously, there was a strong induction of selected inflammatory and immune response genes, which was again evident in fish subjected to ineffective treatment protocols. Our findings point to the essential role of therapeutic practices in escalation or control of antibiotic resistance transfer, and suggest that antibiotic substances, even in sub-inhibitory concentrations, may stimulate innate defenses against bacterial infections.}, }
@article {pmid22426345, year = {2012}, author = {Ménigaud, S and Mallet, L and Picord, G and Churlaud, C and Borrel, A and Deschavanne, P}, title = {GOHTAM: a website for 'Genomic Origin of Horizontal Transfers, Alignment and Metagenomics'.}, journal = {Bioinformatics (Oxford, England)}, volume = {28}, number = {9}, pages = {1270-1271}, pmid = {22426345}, issn = {1367-4811}, mesh = {Bacteria/classification/genetics ; *Gene Transfer, Horizontal ; Genome ; Genome, Bacterial ; Metagenomics/*methods ; *Phylogeny ; Sequence Alignment/methods ; Sequence Analysis, DNA/methods ; }, abstract = {MOTIVATION: This website allows the detection of horizontal transfers based on a combination of parametric methods and proposes an origin by researching neighbors in a bank of genomic signatures. This bank is also used to research an origin to DNA fragments from metagenomics studies.<br><br>RESULTS: Different services are provided like the possibility of inferring a phylogenetic tree with sequence signatures or comparing two genomes and displaying the rearrangements that happened since their separation.<br><br>http://gohtam.rpbs.univ-paris-diderot.fr/}, }
@article {pmid22425644, year = {2012}, author = {Sun, Y and Zeng, F and Zhang, W and Qiao, J}, title = {Structure-based phylogeny of polyene macrolide antibiotic glycosyltransferases.}, journal = {Gene}, volume = {499}, number = {2}, pages = {288-296}, doi = {10.1016/j.gene.2012.02.050}, pmid = {22425644}, issn = {1879-0038}, mesh = {Eukaryota/enzymology/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Glucosyltransferases/*chemistry/*genetics ; Macrolides ; Models, Chemical ; Phylogeny ; Protein Structure, Tertiary ; Streptomyces/*enzymology/genetics ; }, abstract = {Antibiotic glycosyltransferases (AGts) attach unusual deoxy-sugars to aglycons so antibiotics can exert function. It has been reported that polyene macrolide (PEM) AGts have different evolutionary origin when compared with other polyketide AGts, and our previous analysis have suggested that they could be results of horizontal gene transfer (HGT) from eukaryotes. In this paper, we compared the structures of PEM AGts with structures of eukaryotes and other AGts, and then built models of the representative PEM AGts and GT-1 glycosyltransferases. We also constructed the Neighbor-Joining (NJ) trees based on the normalized Root Mean Square (RMS) distance, the Bayesian tree guided by structural alignments, and carried out analysis on several key conserved residues in PEM AGts. The NJ tree showed a close relationship between PEM AGts and eukaryotic glycosyltransferases, and Bayesian tree further supported their affinity with UDP-glucuronosyltransferases (UGTs). Analysis on key conserved residues showed that PEM AGts may have similar interaction mechanism such as in the formation of hydrogen bonds as eukaryotic glycosyltransferases. Using structure-based phylogenetic approaches, this study further supported that PEM AGts were the result of HGT between prokaryotes and eukaryotes.}, }
@article {pmid22420856, year = {2012}, author = {Szczepankowska, A}, title = {Role of CRISPR/cas system in the development of bacteriophage resistance.}, journal = {Advances in virus research}, volume = {82}, number = {}, pages = {289-338}, doi = {10.1016/B978-0-12-394621-8.00011-X}, pmid = {22420856}, issn = {1557-8399}, mesh = {Bacteriophages/*genetics/growth &amp; development/pathogenicity ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Gram-Negative Bacteria/genetics/*immunology/virology ; Gram-Positive Bacteria/genetics/*immunology/virology ; Host-Pathogen Interactions ; Inverted Repeat Sequences/*genetics ; Lysogeny ; Phylogeny ; }, abstract = {Acquisition of foreign DNA can be of advantage or disadvantage to the host cell. New DNAs can increase the fitness of an organism to certain environmental conditions; however, replication and maintenance of incorporated nucleotide sequences can be a burden for the host cell. These circumstances have resulted in the development of certain cellular mechanisms limiting horizontal gene transfer, including the immune system of vertebrates or RNA interference mechanisms in eukaryotes. Also, in prokaryotes, specific systems have been characterized, which are aimed especially at limiting the invasion of bacteriophage DNA, for example, adsorption inhibition, injection blocking, restriction/modification, or abortive infection. Quite recently, another distinct mechanism limiting horizontal transfer of genetic elements has been identified in procaryotes and shown to protect microbial cells against exogenous nucleic acids of phage or plasmid origin. This system has been termed CRISPR/cas and consists of two main components: (i) the CRISPR (clustered, regularly interspaced short palindromic regions) locus and (ii) cas genes, encoding CRISPR-associated (Cas) proteins. In simplest words, the mechanism of CRISPR/cas activity is based on the active integration of small fragments (proto-spacers) of the invading DNAs (phage or plasmids) into microbial genomes, which are subsequently transcribed into short RNAs that direct the degradation of foreign invading DNA elements. In this way, the host organism acquires immunity toward mobile elements carrying matching sequences. The CRISPR/cas system is regarded as one of the earliest defense system that has evolved in prokaryotic organisms. It is inheritable, but at the same time is unstable when regarding the evolutionary scale. Comparative sequence analyses indicate that CRISPR/cas systems play an important role in the evolution of microbial genomes and their predators, bacteriophages.}, }
@article {pmid22419842, year = {2012}, author = {Hasan, MS and Liu, Q and Wang, H and Fazekas, J and Chen, B and Che, D}, title = {GIST: Genomic island suite of tools for predicting genomic islands in genomic sequences.}, journal = {Bioinformation}, volume = {8}, number = {4}, pages = {203-205}, pmid = {22419842}, issn = {0973-2063}, abstract = {UNLABELLED: Genomic Islands (GIs) are genomic regions that are originally from other organisms, through a process known as Horizontal Gene Transfer (HGT). Detection of GIs plays a significant role in biomedical research since such align genomic regions usually contain important features, such as pathogenic genes. We have developed a use friendly graphic user interface, Genomic Island Suite of Tools (GIST), which is a platform for scientific users to predict GIs. This software package includes five commonly used tools, AlienHunter, IslandPath, Colombo SIGI-HMM, INDeGenIUS and Pai-Ida. It also includes an optimization program EGID that ensembles the result of existing tools for more accurate prediction. The tools in GIST can be used either separately or sequentially. GIST also includes a downloadable feature that facilitates collecting the input genomes automatically from the FTP server of the National Center for Biotechnology Information (NCBI). GIST was implemented in Java, and was compiled and executed on Linux/Unix operating systems.<br><br>AVAILABILITY: The database is available for free at http://www5.esu.edu/cpsc/bioinfo/software/GIST.}, }
@article {pmid22419839, year = {2012}, author = {Singh, S and Singh, G and Sagar, N and Yadav, PK and Jain, PA and Gautam, B and Wadhwa, G}, title = {Insight into trichomonas vaginalis genome evolution through metabolic pathways comparison.}, journal = {Bioinformation}, volume = {8}, number = {4}, pages = {189-195}, pmid = {22419839}, issn = {0973-2063}, abstract = {Trichomonas vaginalis causes the trichomoniasis, in women and urethritis and prostate cancer in men. Its genome draft published by TIGR in 2007 presents many unusual genomic and biochemical features like, exceptionally large genome size, the presence of hydrogenosome, gene duplication, lateral gene transfer mechanism and the presence of miRNA. To understand some of genomic features we have performed a comparative analysis of metabolic pathways of the T. vaginalis with other 22 significant common organisms. Enzymes from the biochemical pathways of T. vaginalis and other selected organisms were retrieved from the KEGG metabolic pathway database. The metabolic pathways of T. vaginalis common in other selected organisms were identified. Total 101 enzymes present in different metabolic pathways of T. vaginalis were found to be orthologous by using BLASTP program against the selected organisms. Except two enzymes all identified orthologous enzymes were also identified as paralogous enzymes. Seventy-five of identified enzymes were also identified as essential for the survival of T. vaginalis, while 26 as non-essential. The identified essential enzymes also represent as good candidate for novel drug targets. Interestingly, some of the identified orthologous and paralogous enzymes were found playing significant role in the key metabolic activities while others were found playing active role in the process of pathogenesis. The N-acetylneuraminate lyase was analyzed as the candidate of lateral genes transfer. These findings clearly suggest the active participation of lateral gene transfer and gene duplication during evolution of T. vaginalis from the enteric to the pathogenic urogenital environment.}, }
@article {pmid22416906, year = {2012}, author = {Tiendrébéogo, F and Lefeuvre, P and Hoareau, M and Harimalala, MA and De Bruyn, A and Villemot, J and Traoré, VS and Konaté, G and Traoré, AS and Barro, N and Reynaud, B and Traoré, O and Lett, JM}, title = {Evolution of African cassava mosaic virus by recombination between bipartite and monopartite begomoviruses.}, journal = {Virology journal}, volume = {9}, number = {}, pages = {67}, pmid = {22416906}, issn = {1743-422X}, mesh = {Begomovirus/classification/*genetics ; DNA, Viral ; Evolution, Molecular ; Gene Order ; *Gene Transfer, Horizontal ; Manihot ; Phylogeny ; }, abstract = {BACKGROUND: Cassava mosaic disease (CMD) is a major constraint on cassava cultivation in Africa. The disease is endemic and is caused by seven distinct cassava mosaic geminiviruses (CMGs), some of them including several variants.<br><br>FINDINGS: From cassava leaf samples presenting CMD symptoms collected in Burkina Faso, four DNA-A begomovirus components were cloned and sequenced, showing 99.9% nucleotide identity among them. These isolates are most closely related to African cassava mosaic virus (ACMV) but share less than 89% nucleotide identity (taxonomic threshold) with any previously described begomovirus. A DNA-B genomic component, sharing 93% nucleotide identity with DNA-B of ACMV, was also characterized. Since all genomic components have a typical genome organization of Old World bipartite begomoviruses, this new species was provisionally named African cassava mosaic Burkina Faso virus (ACMBFV). Recombination analysis of the new virus demonstrated an interspecies recombinant origin, with major parents related to West African isolates of ACMV, and minor parents related to Tomato leaf curl Cameroon virus and Cotton leaf curl Gezira virus.<br><br>CONCLUSION: This is the first report of an ACMV-like recombinant begomovirus arisen by interspecific recombination between bipartite and monopartite African begomoviruses.}, }
@article {pmid22416123, year = {2012}, author = {Abby, SS and Tannier, E and Gouy, M and Daubin, V}, title = {Lateral gene transfer as a support for the tree of life.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {13}, pages = {4962-4967}, pmid = {22416123}, issn = {1091-6490}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Models, Genetic ; *Phylogeny ; Species Specificity ; }, abstract = {Lateral gene transfer (LGT), the acquisition of genes from other species, is a major evolutionary force. However, its success as an adaptive process makes the reconstruction of the history of life an intricate puzzle: If no gene has remained unaffected during the course of life's evolution, how can one rely on molecular markers to reconstruct the relationships among species? Here, we take a completely different look at LGT and its impact for the reconstruction of the history of life. Rather than trying to remove the effect of LGT in phylogenies, and ignoring as a result most of the information of gene histories, we use an explicit phylogenetic model of gene transfer to reconcile gene histories with the tree of species. We studied 16 bacterial and archaeal phyla, representing a dataset of 12,000 gene families distributed in 336 genomes. Our results show that, in most phyla, LGT provides an abundant phylogenetic signal on the pattern of species diversification and that this signal is robust to the choice of gene families under study. We also find that LGT brings an abundant signal on the location of the root of species trees, which has been previously overlooked. Our results quantify the great variety of gene transfer rates among lineages of the tree of life and provide strong support for the "complexity hypothesis," which states that genes whose products participate to macromolecular protein complexes are relatively resistant to transfer.}, }
@article {pmid22416119, year = {2012}, author = {de Jonge, R and van Esse, HP and Maruthachalam, K and Bolton, MD and Santhanam, P and Saber, MK and Zhang, Z and Usami, T and Lievens, B and Subbarao, KV and Thomma, BP}, title = {Tomato immune receptor Ve1 recognizes effector of multiple fungal pathogens uncovered by genome and RNA sequencing.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {13}, pages = {5110-5115}, pmid = {22416119}, issn = {1091-6490}, mesh = {Alleles ; Base Sequence ; Disease Resistance/genetics ; Evolution, Molecular ; Fungal Proteins/metabolism ; Fusarium/genetics ; Gene Transfer, Horizontal ; Genes, Fungal/genetics ; Genetic Variation ; Genome, Fungal/*genetics ; Genomics ; Solanum lycopersicum/*immunology/*microbiology ; Molecular Sequence Data ; Plant Diseases/genetics/immunology/microbiology ; Plant Proteins/*metabolism ; Receptors, Cell Surface/*metabolism ; Sequence Analysis, RNA/*methods ; Sequence Homology, Amino Acid ; Nicotiana/genetics/microbiology ; Transcriptome/genetics ; Verticillium/*genetics/pathogenicity ; Virulence/genetics ; }, abstract = {Fungal plant pathogens secrete effector molecules to establish disease on their hosts, and plants in turn use immune receptors to try to intercept these effectors. The tomato immune receptor Ve1 governs resistance to race 1 strains of the soil-borne vascular wilt fungi Verticillium dahliae and Verticillium albo-atrum, but the corresponding Verticillium effector remained unknown thus far. By high-throughput population genome sequencing, a single 50-Kb sequence stretch was identified that only occurs in race 1 strains, and subsequent transcriptome sequencing of Verticillium-infected Nicotiana benthamiana plants revealed only a single highly expressed ORF in this region, designated Ave1 (for Avirulence on Ve1 tomato). Functional analyses confirmed that Ave1 activates Ve1-mediated resistance and demonstrated that Ave1 markedly contributes to fungal virulence, not only on tomato but also on Arabidopsis. Interestingly, Ave1 is homologous to a widespread family of plant natriuretic peptides. Besides plants, homologous proteins were only found in the bacterial plant pathogen Xanthomonas axonopodis and the plant pathogenic fungi Colletotrichum higginsianum, Cercospora beticola, and Fusarium oxysporum f. sp. lycopersici. The distribution of Ave1 homologs, coincident with the presence of Ave1 within a flexible genomic region, strongly suggests that Verticillium acquired Ave1 from plants through horizontal gene transfer. Remarkably, by transient expression we show that also the Ave1 homologs from F. oxysporum and C. beticola can activate Ve1-mediated resistance. In line with this observation, Ve1 was found to mediate resistance toward F. oxysporum in tomato, showing that this immune receptor is involved in resistance against multiple fungal pathogens.}, }
@article {pmid22415963, year = {2012}, author = {Wei, KF and Wu, LJ and Chen, J and Chen, YF and Xie, DX}, title = {Structural evolution and functional diversification analyses of argonaute protein.}, journal = {Journal of cellular biochemistry}, volume = {113}, number = {8}, pages = {2576-2585}, doi = {10.1002/jcb.24133}, pmid = {22415963}, issn = {1097-4644}, mesh = {Amino Acid Sequence ; Animals ; Argonaute Proteins/*chemistry/genetics/*metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics/physiology ; Humans ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA Interference ; }, abstract = {Argonaute (AGO) proteins are highly specialized small-RNA-binding modules and small RNAs are anchored to their specific binding pockets guiding AGO proteins to target mRNA molecules for silencing or destruction. The 135 full-length AGO protein sequences derived from 36 species covering prokaryote, archaea, and eukaryote are chosen for structural and functional analyses. The results show that bacteria and archaeal AGO proteins are clustered in the same clade and there exist multiple AGO proteins in most eukaryotic species, demonstrating that the increase of AGO gene copy number and horizontal gene transfer (HGT) have been the main evolutionary driving forces for adaptability and biodiversity. And the emergence of PAZ domain in AGO proteins is the unique evolutionary event. The analysis of middle domain (MID)-nucleotide contaction shows that either the position of sulfate I bond in Nc_QDE2 or the site of phosphate I bond in Hs_AGO2 represents the 5'-nucleotide binding site of miRNA. Also, H334, T335, and Y336 of Hs_AGO1 can form hydrogen bonds with 3'-overhanging ends of miRNAs and the same situation exists in Hs_AGO2, Hs_AGO3, Hs_AGO4, Dm_AGO1, and Ce_Alg1. Some PIWI domains containing conserved DDH motif have no slicer activity, and post-translational modifications may be associated with the endonucleolytic activities of AGOs. With the numbers of AGO genes increasing and fewer crystal structures available, the evolutionary and functional analyses of AGO proteins can help clarify the molecular mechanism of function diversification in response to environmental changes, and solve major issues including host defense mechanism against virus infection and molecular basis of disease.}, }
@article {pmid22414918, year = {2012}, author = {Boggs, JM and South, AH and Hughes, AL}, title = {Phylogenetic analysis supports horizontal gene transfer of L-amino acid oxidase gene in Streptococcus oligofermentans.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {12}, number = {5}, pages = {1005-1009}, pmid = {22414918}, issn = {1567-7257}, support = {R01 GM043940/GM/NIGMS NIH HHS/United States ; R01 GM043940-21/GM/NIGMS NIH HHS/United States ; GM43940/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacterial Proteins/*genetics ; Cluster Analysis ; *Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; L-Amino Acid Oxidase/*genetics ; Linear Models ; Phylogeny ; Sequence Alignment ; Streptococcus/classification/enzymology/*genetics ; }, abstract = {Phylogenetic analysis of 10 amino acid sequences from 19 Streptococcus species showed that S. oligofermentans clustered within the mitis group. However, the l-amino acid oxidase (LAAO) of S. oligofermentans showed a different clustering pattern from the other proteins analyzed implicating horizontal gene transfer (HGT) in the origin of the S. oligofermentans LAAO gene. LAAO of S. oligofermentans is known to confer ability to compete with other oral cavity bacteria, most notably S. mutans; therefore, the HGT event may have been important in extending the ecological niche occupied by this species, consistent with those of other studies suggesting that HGT can play a key role in enabling bacterial species to occupy new ecological niches.}, }
@article {pmid22412380, year = {2012}, author = {Lesic, B and Zouine, M and Ducos-Galand, M and Huon, C and Rosso, ML and Prévost, MC and Mazel, D and Carniel, E}, title = {A natural system of chromosome transfer in Yersinia pseudotuberculosis.}, journal = {PLoS genetics}, volume = {8}, number = {3}, pages = {e1002529}, pmid = {22412380}, issn = {1553-7404}, mesh = {Adaptation, Physiological ; Biological Evolution ; *Chromosomes, Bacterial ; *DNA Transposable Elements/genetics ; Escherichia coli/genetics ; *Gene Transfer, Horizontal ; Plasmids/genetics ; Yersinia pseudotuberculosis/*genetics/pathogenicity ; }, abstract = {The High Pathogenicity Island of Yersinia pseudotuberculosis IP32637 was previously shown to be horizontally transferable as part of a large chromosomal segment. We demonstrate here that at low temperature other chromosomal loci, as well as a non-mobilizable plasmid (pUC4K), are also transferable. This transfer, designated GDT4 (Generalized DNA Transfer at 4°C), required the presence of an IP32637 endogenous plasmid (pGDT4) that carries several mobile genetic elements and a conjugation machinery. We established that cure of this plasmid or inactivation of its sex pilus fully abrogates this process. Analysis of the mobilized pUC4K recovered from transconjugants revealed the insertion of one of the pGDT4-borne ISs, designated ISYps1, at different sites on the transferred plasmid molecules. This IS belongs to the IS6 family, which moves by replicative transposition, and thus could drive the formation of cointegrates between pGDT4 and the host chromosome and could mediate the transfer of chromosomal regions in an Hfr-like manner. In support of this model, we show that a suicide plasmid carrying ISYps1 is able to integrate itself, flanked by ISYps1 copies, at multiple locations into the Escherichia coli chromosome. Furthermore, we demonstrate the formation of RecA-independent cointegrates between the ISYps1-harboring plasmid and an ISYps1-free replicon, leading to the passive transfer of the non-conjugative plasmid. We thus demonstrate here a natural mechanism of horizontal gene exchange, which is less constrained and more powerful than the classical Hfr mechanism, as it only requires the presence of an IS6-type element on a conjugative replicon to drive the horizontal transfer of any large block of plasmid or chromosomal DNA. This natural mechanism of chromosome transfer, which occurs under conditions mimicking those found in the environment, may thus play a significant role in bacterial evolution, pathogenesis, and adaptation to new ecological niches.}, }
@article {pmid22411854, year = {2012}, author = {Moran, Y and Fredman, D and Szczesny, P and Grynberg, M and Technau, U}, title = {Recurrent horizontal transfer of bacterial toxin genes to eukaryotes.}, journal = {Molecular biology and evolution}, volume = {29}, number = {9}, pages = {2223-2230}, pmid = {22411854}, issn = {1537-1719}, support = {P 24858/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Amino Acid Sequence ; Animals ; Bacterial Toxins/chemistry/*genetics/metabolism ; Cnidaria/genetics/metabolism ; Eukaryota/*genetics/metabolism ; Evolution, Molecular ; Gene Expression ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; Pore Forming Cytotoxic Proteins/chemistry/genetics/metabolism ; Sequence Alignment ; }, abstract = {In this work, we report likely recurrent horizontal (lateral) gene transfer events of genes encoding pore-forming toxins of the aerolysin family between species belonging to different kingdoms of life. Clustering based on pairwise similarity and phylogenetic analysis revealed several distinct aerolysin sequence groups, each containing proteins from multiple kingdoms of life. These results strongly support at least six independent transfer events between distantly related phyla in the evolutionary history of one protein family and discount selective retention of ancestral genes as a plausible explanation for this patchy phylogenetic distribution. We discuss the possible roles of these proteins and show evidence for a convergent new function in two extant species. We hypothesize that certain gene families are more likely to be maintained following horizontal gene transfer from commensal or pathogenic organism to its host if they 1) can function alone; and 2) are immediately beneficial for the ecology of the organism, as in the case of pore-forming toxins which can be utilized in multicellular organisms for defense and predation.}, }
@article {pmid22411796, year = {2012}, author = {Qiu, Z and Yu, Y and Chen, Z and Jin, M and Yang, D and Zhao, Z and Wang, J and Shen, Z and Wang, X and Qian, D and Huang, A and Zhang, B and Li, JW}, title = {Nanoalumina promotes the horizontal transfer of multiresistance genes mediated by plasmids across genera.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {13}, pages = {4944-4949}, pmid = {22411796}, issn = {1091-6490}, mesh = {Aluminum Oxide/*pharmacology ; Antioxidants/metabolism ; Cell Membrane/drug effects/metabolism ; Conjugation, Genetic/drug effects ; Drug Resistance, Multiple, Bacterial/*drug effects/*genetics ; Escherichia coli/cytology/drug effects/*genetics/ultrastructure ; Gene Expression Regulation, Bacterial/drug effects ; Gene Transfer, Horizontal/*drug effects/genetics ; Genes, Bacterial/genetics ; Nanostructures/ultrastructure ; Oxidative Stress/drug effects/genetics ; Plasmids/*genetics ; RNA, Messenger/genetics/metabolism ; Salmonella/cytology/drug effects/*genetics ; }, abstract = {Antibiotic resistance is a worldwide public health concern. Conjugative transfer between closely related strains or species of bacteria is an important method for the horizontal transfer of multidrug-resistance genes. The extent to which nanomaterials are able to cause an increase in antibiotic resistance by the regulation of the conjugative transfer of antibiotic-resistance genes in bacteria, especially across genera, is still unknown. Here we show that nanomaterials in water can significantly promote the horizontal conjugative transfer of multidrug-resistance genes mediated by the RP4, RK2, and pCF10 plasmids. Nanoalumina can promote the conjugative transfer of the RP4 plasmid from Escherichia coli to Salmonella spp. by up to 200-fold compared with untreated cells. We also explored the mechanisms behind this phenomenon and demonstrate that nanoalumina is able to induce oxidative stress, damage bacterial cell membranes, enhance the expression of mating pair formation genes and DNA transfer and replication genes, and depress the expression of global regulatory genes that regulate the conjugative transfer of RP4. These findings are important in assessing the risk of nanomaterials to the environment, particularly from water and wastewater treatment systems, and in the estimation of the effect of manufacture and use of nanomaterials on the environment.}, }
@article {pmid22409355, year = {2012}, author = {Moura, A and Oliveira, C and Henriques, I and Smalla, K and Correia, A}, title = {Broad diversity of conjugative plasmids in integron-carrying bacteria from wastewater environments.}, journal = {FEMS microbiology letters}, volume = {330}, number = {2}, pages = {157-164}, doi = {10.1111/j.1574-6968.2012.02544.x}, pmid = {22409355}, issn = {1574-6968}, mesh = {Aeromonas/*genetics/isolation &amp; purification ; Anti-Bacterial Agents/pharmacology ; *Conjugation, Genetic ; DNA, Bacterial/genetics/isolation &amp; purification ; Drug Resistance, Bacterial ; Enterobacteriaceae/*genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; *Integrons ; Plasmids/*analysis/classification ; Restriction Mapping ; Sewage/*microbiology ; *Water Microbiology ; }, abstract = {In this study we assessed the occurrence, diversity and conjugative potential of plasmids in integron-carrying Aeromonas and Enterobacteriaceae from wastewaters. Sixty-six strains were included as donors in mating assays using rifampicin-resistant Escherichia coli and Pseudomonas putida recipient strains. The diversity of plasmids from donors and transconjugants (resistant to tetracycline or streptomycin) was evaluated by restriction analysis and replicon typing targeting 19 incompatibility groups. Restriction patterns revealed a diverse plasmid pool present in these strains. Plasmids were assigned to FrepB (Aeromonas salmonicida, Aeromonas veronii, Aeromonas sp., E. coli, Enterobacter sp.), FIC (A. salmonicida, Aeromonas sp.), FIA (Shigella sp.), I1 (A. veronii, Aeromonas sp., E. coli), HI1 (E. coli) and U (Aeromonas media) replicons. Nevertheless, 50% of the plasmids could not be assigned to any replicon type. Among integron-positive transconjugants, FrepB, I1 and HI1 replicons were detected. Results showed that wastewaters enclose a rich plasmid pool associated with integron-carrying bacteria, capable of conjugating to different bacterial hosts. Moreover, replicons detected in this study in Aeromonas strains expand our current knowledge of plasmid diversity in this genus.}, }
@article {pmid22408157, year = {2012}, author = {Plagens, A and Tjaden, B and Hagemann, A and Randau, L and Hensel, R}, title = {Characterization of the CRISPR/Cas subtype I-A system of the hyperthermophilic crenarchaeon Thermoproteus tenax.}, journal = {Journal of bacteriology}, volume = {194}, number = {10}, pages = {2491-2500}, pmid = {22408157}, issn = {1098-5530}, mesh = {Adaptation, Physiological ; Archaeal Proteins/genetics/*metabolism ; Bacteriophages ; Cloning, Molecular ; Culture Media ; Gene Expression Regulation, Archaeal/*physiology ; Gene Transfer, Horizontal ; Inverted Repeat Sequences/*genetics ; Osmolar Concentration ; Thermoproteus/*physiology ; Ultraviolet Rays ; }, abstract = {CRISPR (clustered regularly interspaced short palindromic repeats) elements and cas (CRISPR-associated) genes are widespread in Bacteria and Archaea. The CRISPR/Cas system operates as a defense mechanism against mobile genetic elements (i.e., viruses or plasmids). Here, we investigate seven CRISPR loci in the genome of the crenarchaeon Thermoproteus tenax that include spacers with significant similarity not only to archaeal viruses but also to T. tenax genes. The analysis of CRISPR RNA (crRNA) transcription reveals transcripts of a length between 50 and 130 nucleotides, demonstrating the processing of larger crRNA precursors. The organization of identified cas genes resembles CRISPR/Cas subtype I-A, and the core cas genes are shown to be arranged on two polycistronic transcripts: cascis (cas4, cas1/2, and csa1) and cascade (csa5, cas7, cas5a, cas3, cas3', and cas8a2). Changes in the environmental parameters such as UV-light exposure or high ionic strength modulate cas gene transcription. Two reconstitution protocols were established for the production of two discrete multipartite Cas protein complexes that correspond to their operonic gene arrangement. These data provide insights into the specialized mechanisms of an archaeal CRISPR/Cas system and allow selective functional analyses of Cas protein complexes in the future.}, }
@article {pmid22407713, year = {2012}, author = {Azad, RK and Lawrence, JG}, title = {Detecting laterally transferred genes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {855}, number = {}, pages = {281-308}, doi = {10.1007/978-1-61779-582-4_10}, pmid = {22407713}, issn = {1940-6029}, support = {GM078092/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Gene Transfer, Horizontal/*genetics ; Genome/genetics ; Genomics/*methods ; Humans ; Phylogeny ; }, abstract = {Methods for identifying alien genes in genomes fall into two general classes. Phylogenetic methods examine the distribution of a gene's homologues among genomes to find those with relationships not consistent with vertical inheritance. These approaches include identifying orphan genes which lack homologues in closely related genomes and genes with unduly high levels of similarity to genes in otherwise unrelated genomes. Rigorous statistical tests are available to place confidence intervals for predicted alien genes. Parametric methods examine the compositional properties of genes within a genome to find those with atypical properties, likely indicating the directional mutational pressures of a donor genome. These methods may compare the properties of genes to genomic averages, properties of genes to each other, or properties of large, multigene regions of the chromosome. Here, we discuss the strengths and weaknesses of each approach.}, }
@article {pmid22406642, year = {2012}, author = {Harris, SR and Clarke, IN and Seth-Smith, HM and Solomon, AW and Cutcliffe, LT and Marsh, P and Skilton, RJ and Holland, MJ and Mabey, D and Peeling, RW and Lewis, DA and Spratt, BG and Unemo, M and Persson, K and Bjartling, C and Brunham, R and de Vries, HJ and Morré, SA and Speksnijder, A and Bébéar, CM and Clerc, M and de Barbeyrac, B and Parkhill, J and Thomson, NR}, title = {Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing.}, journal = {Nature genetics}, volume = {44}, number = {4}, pages = {413-9, S1}, pmid = {22406642}, issn = {1546-1718}, support = {089472/WT_/Wellcome Trust/United Kingdom ; 937/DH_/Department of Health/United Kingdom ; 098051/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 080348/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacterial Outer Membrane Proteins/genetics ; Base Sequence ; Chlamydia Infections/*genetics ; Chlamydia trachomatis/*classification/*genetics ; DNA, Bacterial/genetics ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; Lymphogranuloma Venereum/genetics/microbiology ; Molecular Sequence Data ; Phylogeny ; Plasmids ; Polymorphism, Single Nucleotide ; RNA, Ribosomal, 16S/genetics ; *Recombination, Genetic ; Sequence Analysis, DNA ; Trachoma/microbiology ; }, abstract = {Chlamydia trachomatis is responsible for both trachoma and sexually transmitted infections, causing substantial morbidity and economic cost globally. Despite this, our knowledge of its population and evolutionary genetics is limited. Here we present a detailed phylogeny based on whole-genome sequencing of representative strains of C. trachomatis from both trachoma and lymphogranuloma venereum (LGV) biovars from temporally and geographically diverse sources. Our analysis shows that predicting phylogenetic structure using ompA, which is traditionally used to classify Chlamydia, is misleading because extensive recombination in this region masks any true relationships present. We show that in many instances, ompA is a chimera that can be exchanged in part or as a whole both within and between biovars. We also provide evidence for exchange of, and recombination within, the cryptic plasmid, which is another key diagnostic target. We used our phylogenetic framework to show how genetic exchange has manifested itself in ocular, urogenital and LGV C. trachomatis strains, including the epidemic LGV serotype L2b.}, }
@article {pmid22404882, year = {2012}, author = {Pade, N and Compaoré, J and Klähn, S and Stal, LJ and Hagemann, M}, title = {The marine cyanobacterium Crocosphaera watsonii WH8501 synthesizes the compatible solute trehalose by a laterally acquired OtsAB fusion protein.}, journal = {Environmental microbiology}, volume = {14}, number = {5}, pages = {1261-1271}, doi = {10.1111/j.1462-2920.2012.02709.x}, pmid = {22404882}, issn = {1462-2920}, mesh = {Animals ; Cyanobacteria/classification/genetics/metabolism/*physiology ; Gene Expression Regulation, Bacterial ; Genome, Bacterial/genetics ; Glucosyltransferases/genetics/metabolism ; Phylogeny ; Recombinant Proteins/*genetics/*metabolism ; Salt Tolerance ; Trehalose/*biosynthesis ; }, abstract = {Compatible solutes are small organic molecules that are involved in the acclimation to various stresses such as temperature and salinity. Marine or moderate halotolerant cyanobacteria accumulate glucosylglycerol, while cyanobacteria with low salt tolerance (freshwater strains) usually accumulate sucrose or trehalose as the main compatible solutes. The screening of the genome of the marine, unicellular N(2) -fixing cyanobacterium Crocosphaera watsonii WH8501 revealed that instead of genes for glucosylglycerol biosynthesis, a fusion protein for the synthesis of trehalose was found that displayed similarities to trehalose-phosphate-synthase and -phosphatase (OtsAB pathway) from enterobacteria. Accordingly, cells of Crocosphaera showed salt-stimulated expression of the otsAB gene as well as a salt-dependent trehalose accumulation. The biochemical characterization of recombinant full-length OtsAB and truncated OtsB versions revealed that the otsAB gene in Crocosphaera encodes for an active trehalose-phosphate-synthase/phosphatase fusion protein. Genes coding for such proteins were not found in the genomes of other cyanobacteria but were present in many other, non-related marine bacteria, suggesting that otsAB might have been acquired by lateral gene transfer into the Crocosphaera genome.}, }
@article {pmid22401897, year = {2012}, author = {Roalson, EH}, title = {C(4) photosynthesis: need a gene? Borrow one!.}, journal = {Current biology : CB}, volume = {22}, number = {5}, pages = {R161-3}, doi = {10.1016/j.cub.2012.01.043}, pmid = {22401897}, issn = {1879-0445}, mesh = {Gene Transfer, Horizontal/*genetics ; Photosynthesis/*genetics ; Poaceae/*genetics ; }, abstract = {Horizontal gene transfer has been increasingly documented between eukaryotes, but a new study suggests a much larger role for horizontal gene transfer in physiological adaption through the transfer of photosynthetic pathway genes.}, }
@article {pmid22399455, year = {2012}, author = {Puigbò, P and Wolf, YI and Koonin, EV}, title = {Genome-wide comparative analysis of phylogenetic trees: the prokaryotic forest of life.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {856}, number = {}, pages = {53-79}, pmid = {22399455}, issn = {1940-6029}, support = {Z99 CL999999/ImNIH/Intramural NIH HHS/United States ; Z99 HL999999/ImNIH/Intramural NIH HHS/United States ; Z99 LM999999/ImNIH/Intramural NIH HHS/United States ; Z99 MH999999/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Algorithms ; Archaea/*genetics ; Bacteria/*genetics ; Gene Transfer, Horizontal/genetics ; Genomics/*methods ; *Phylogeny ; }, abstract = {Genome-wide comparison of phylogenetic trees is becoming an increasingly common approach in evolutionary genomics, and a variety of approaches for such comparison have been developed. In this article, we present several methods for comparative analysis of large numbers of phylogenetic trees. To compare phylogenetic trees taking into account the bootstrap support for each internal branch, the Boot-Split Distance (BSD) method is introduced as an extension of the previously developed Split Distance method for tree comparison. The BSD method implements the straightforward idea that comparison of phylogenetic trees can be made more robust by treating tree splits differentially depending on the bootstrap support. Approaches are also introduced for detecting tree-like and net-like evolutionary trends in the phylogenetic Forest of Life (FOL), i.e., the entirety of the phylogenetic trees for conserved genes of prokaryotes. The principal method employed for this purpose includes mapping quartets of species onto trees to calculate the support of each quartet topology and so to quantify the tree and net contributions to the distances between species. We describe the application of these methods to analyze the FOL and the results obtained with these methods. These results support the concept of the Tree of Life (TOL) as a central evolutionary trend in the FOL as opposed to the traditional view of the TOL as a "species tree."}, }
@article {pmid22399453, year = {2012}, author = {Anderson, CN and Liu, L and Pearl, D and Edwards, SV}, title = {Tangled trees: the challenge of inferring species trees from coalescent and noncoalescent genes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {856}, number = {}, pages = {3-28}, doi = {10.1007/978-1-61779-585-5_1}, pmid = {22399453}, issn = {1940-6029}, mesh = {Animals ; Computational Biology/*methods ; Gene Duplication/genetics ; Gene Flow/genetics ; Gene Transfer, Horizontal/genetics ; Humans ; Models, Genetic ; *Phylogeny ; Selection, Genetic/genetics ; }, abstract = {Phylogenies based on different genes can produce conflicting phylogenies; methods that resolve such ambiguities are becoming more popular, and offer a number of advantages for phylogenetic analysis. We review so-called species tree methods and the biological forces that can undermine them by violating important aspects of the underlying models. Such forces include horizontal gene transfer, gene duplication, and natural selection. We review ways of detecting loci influenced by such forces and offer suggestions for identifying or accommodating them. The way forward involves identifying outlier loci, as is done in population genetic analysis of neutral and selected loci, and removing them from further analysis, or developing more complex species tree models that can accommodate such loci.}, }
@article {pmid22392282, year = {2012}, author = {Lasek, R and Dziewit, L and Bartosik, D}, title = {Plasmid pP62BP1 isolated from an Arctic Psychrobacter sp. strain carries two highly homologous type II restriction-modification systems and a putative organic sulfate metabolism operon.}, journal = {Extremophiles : life under extreme conditions}, volume = {16}, number = {3}, pages = {363-376}, pmid = {22392282}, issn = {1433-4909}, mesh = {DNA Restriction-Modification Enzymes/*genetics/metabolism ; Gene Transfer, Horizontal/*physiology ; Genes, Bacterial/*physiology ; Plasmids ; Psychrobacter/*genetics/metabolism ; Sequence Analysis, DNA/methods ; Sulfuric Acid Esters/*metabolism ; }, abstract = {The complete nucleotide sequence of plasmid pP62BP1 (34,467 bp), isolated from Arctic Psychrobacter sp. DAB_AL62B, was determined and annotated. The conserved plasmid backbone is composed of several genetic modules, including a replication system (REP) with similarities to the REP region of the iteron-containing plasmid pPS10 of Pseudomonas syringae. The additional genetic load of pP62BP1 includes two highly related type II restriction-modification systems and a set of genes (slfRCHSL) encoding enzymes engaged in the metabolism of organic sulfates, plus a putative transcriptional regulator (SlfR) of the AraC family. The pP62BP1 slf locus has a compact and unique structure. It is predicted that the enzymes SlfC, SlfH, SlfS and SlfL carry out a chain of reactions leading to the transformation of alkyl sulfates into acyl-CoA, with dodecyl sulfate (SDS) as a possible starting substrate. Comparative analysis of the nucleotide sequences of pP62BP1 and other Psychrobacter spp. plasmids revealed their structural diversity. However, the presence of a few highly conserved DNA segments in pP62BP1, plasmid 1 of P. cryohalolentis K5 and pRWF-101 of Psychrobacter sp. PRwf-1 is indicative of recombinational shuffling of genetic information, and is evidence of lateral gene transfer in the Arctic environment.}, }
@article {pmid22385639, year = {2012}, author = {Beceiro, A and Tomás, M and Bou, G}, title = {[Antimicrobial resistance and virulence: a beneficial relationship for the microbial world?].}, journal = {Enfermedades infecciosas y microbiologia clinica}, volume = {30}, number = {8}, pages = {492-499}, doi = {10.1016/j.eimc.2012.01.011}, pmid = {22385639}, issn = {1578-1852}, mesh = {Bacteria/genetics ; Bacterial Infections/drug therapy/microbiology ; *Bacterial Physiological Phenomena ; Bacterial Proteins/genetics/physiology ; Biofilms ; Biological Transport/genetics/physiology ; Cell Wall/genetics ; Conjugation, Genetic ; DNA Transposable Elements/genetics ; Drug Resistance, Microbial/*physiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Fitness ; Host-Pathogen Interactions ; Humans ; Mutation ; Plasmids/genetics ; Selection, Genetic ; Transformation, Bacterial ; Virulence/*physiology ; Virulence Factors/genetics/*physiology ; }, abstract = {While bacterial virulence has experienced a long host/pathogen-dependent evolutionary process, antimicrobial resistance has had a very different, shorting and changing evolution due to the biological pressure caused by the introduction of the antimicrobials in human medicine. This strong pressure has forced the microorganisms to adapt to these changing conditions, continuously acquiring or developing new resistance mechanisms, causing major changes in cellular functions and finally influencing the virulence and bacterial fitness. Multiple factors may mediate in the relationship between virulence and resistance. The genes often involved in both phenomena have the same transport and dispersion mediums. Islands, integrons, transposons and other genetic elements could also facilitate the combined selection of virulence and resistance genes. The increase in resistance can affect virulence in different ways, mainly depending on the bacterial species, the environment, and the mechanism of resistance. This review presents the different phenomena in which the genetic mechanism that provides an advantage over the antimicrobials directly affects the virulence and fitness, such as changes in the structure of the cellular wall, efflux pumps, porins or two-component regulatory systems. The co-selection of virulence and antimicrobial resistance factors and the relative ease of bacteria to develop compensatory mutations can favour, particularly in environments with high antibiotic pressure, the emergence of prevalent clones. These can be virulent and with few treatment options, and could be a major health problem in the near future.}, }
@article {pmid22385320, year = {2012}, author = {Glenn, LM and Englen, MD and Lindsey, RL and Frank, JF and Turpin, JE and Berrang, ME and Meinersmann, RJ and Fedorka-Cray, PJ and Frye, JG}, title = {Analysis of antimicrobial resistance genes detected in multiple-drug-resistant Escherichia coli isolates from broiler chicken carcasses.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {18}, number = {4}, pages = {453-463}, doi = {10.1089/mdr.2011.0224}, pmid = {22385320}, issn = {1931-8448}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Chickens ; Drug Resistance, Multiple, Bacterial/drug effects/*genetics ; Escherichia coli/drug effects/*genetics/isolation &amp; purification ; Escherichia coli Infections/microbiology/*veterinary ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Integrons ; Microarray Analysis ; Microbial Sensitivity Tests ; Phylogeny ; Plasmids ; Polymerase Chain Reaction ; Poultry Diseases/*microbiology ; }, abstract = {Multi-drug-resistant (MDR) bacteria in food animals are a potential problem in both animal and human health. In this study, MDR commensal Escherichia coli isolates from poultry were examined. Thirty-two E. coli isolates from broiler carcass rinses were selected based on their resistance to aminoglycosides, β-lactams, chloramphenicols, tetracyclines, and sulfonamide antimicrobials. Microarray analysis for the presence of antimicrobial resistance and plasmid genes identified aminoglycoside [aac(6), aac(3), aadA, aph, strA, and strB], β-lactam (bla(AmpC), bla(TEM), bla(CMY), and bla(PSE-1)), chloramphenicol (cat, flo, and cmlA), sulfamethoxazole (sulI and sulII), tetracycline [tet(A), tet(C), tet(D), and tetR], and trimethoprim (dfrA) resistance genes. IncA/C plasmid core genes were detected in 27 isolates, while IncHI1 plasmid genes were detected in one isolate, indicating the likely presence of these plasmids. PCR assays for 18 plasmid replicon types often associated with MDR in Enterobacteriaceae also detected one or more replicon types in all 32 isolates. Class I integrons were investigated by PCR amplification of the integrase I gene, intI1, and the cassette region flanked by conserved sequences. Twenty-five isolates were positive for the intI1 gene, and class I integrons ranging in size from ~1,000 to 3,300 bp were identified in 19 of them. The presence of class I integrons, IncA/C plasmid genes, and MDR-associated plasmid replicons in the isolates indicates the importance of these genetic elements in the accumulation and potential spread of antimicrobial resistance genes in the microbial community associated with poultry.}, }
@article {pmid22384938, year = {2012}, author = {Dal Grande, F and Widmer, I and Wagner, HH and Scheidegger, C}, title = {Vertical and horizontal photobiont transmission within populations of a lichen symbiosis.}, journal = {Molecular ecology}, volume = {21}, number = {13}, pages = {3159-3172}, doi = {10.1111/j.1365-294X.2012.05482.x}, pmid = {22384938}, issn = {1365-294X}, mesh = {Chlorophyta/genetics/*physiology ; DNA, Algal/genetics ; DNA, Fungal/genetics ; Fungi/genetics/*physiology ; Gene Transfer, Horizontal ; Genetic Variation ; Genotype ; Lichens/genetics/*microbiology ; Microsatellite Repeats ; Models, Genetic ; Mutation ; *Symbiosis ; }, abstract = {Lichens are widespread symbioses and play important roles in many terrestrial ecosystems. The genetic structure of lichens is the result of the association between fungal and algal populations constituting the lichen thallus. Using eight fungus- and seven alga-specific highly variable microsatellite markers on within-population spatial genetic data from 62 replicate populations across Europe, North America, Asia and Africa, we investigated the contributions of vertical and horizontal transmission of the photobiont to the genetic structure of the epiphytic lichen Lobaria pulmonaria. Based on pairwise comparisons of multilocus genotypes defined separately for the mycobiont and for the photobiont, we inferred the transmission mode of the photobiont and the relative contribution of somatic mutation and recombination. After constraining the analysis of one symbiont to pairs of individuals with genetically identical symbiotic partners, we found that 77% of fungal and 70% of algal pairs were represented by clones. Thus, the predominant dispersal mode was by means of symbiotic vegetative propagules (vertical transmission), which dispersed fungal and algal clones co-dependently over a short distance, thus shaping the spatial genetic structure up to distances of 20m. Evidence for somatic mutation generating genetic diversity was found in both symbionts, accounting for 30% of pairwise comparisons in the alga and 15% in the fungus. While the alga did not show statistically significant evidence of recombination, recombination accounted for 7.7% of fungal pairs with identical algae. This implies that, even in a mostly vegetatively reproducing species, horizontal transmission plays a role in shaping the symbiotic association, as shown in many coral and other symbioses in nature.}, }
@article {pmid22369715, year = {2011}, author = {Kinjo, AR and Kumagai, Y and Dinh, H and Takeuchi, O and Standley, DM}, title = {Functional characterization of protein domains common to animal viruses and mouse.}, journal = {BMC genomics}, volume = {12 Suppl 3}, number = {Suppl 3}, pages = {S21}, pmid = {22369715}, issn = {1471-2164}, mesh = {Animals ; Cytokines/chemistry/metabolism ; Databases, Protein ; Dendritic Cells/immunology/metabolism ; Internet ; Mice ; Phosphotransferases/chemistry/metabolism ; Protein Structure, Tertiary ; Proteins/*chemistry/immunology/metabolism ; Receptors, Cytokine/chemistry/metabolism ; Search Engine ; T-Lymphocytes/immunology/metabolism ; User-Computer Interface ; Viral Proteins/*chemistry/immunology/*metabolism ; Viruses/genetics/immunology/*metabolism ; }, abstract = {BACKGROUND: Many viruses contain genes that originate from their hosts. Some of these acquired genes give viruses the ability to interfere with host immune responses by various mechanisms. Genes of host origin that appear commonly in viruses code for proteins that span a wide range of functions, from kinases and phosphotases, to cytokines and their receptors, to ubiquitin ligases and proteases. While many important cases of such lateral gene transfer in viruses have been documented, there has yet to be a genome-wide survey of viral-encoded genes acquired from animal hosts.<br><br>RESULTS: Here we carry out such a survey in order to gain insight into the host immune system. We made the results available in the form of a web-based tool that allows viral-centered or host-centered queries to be performed (http://imm.ifrec.osaka-u.ac.jp/musvirus/). We examine the relationship between acquired genes and immune function, and compare host-virus homology with gene expression data in stimulated dendritic cells and T-cells. We found that genes whose expression changes significantly during the innate antiviral immune response had more homologs in animal virus than genes whose expression did not change or genes involved in the adaptive immune response.<br><br>CONCLUSIONS: Statistics gathered from the MusVirus database support earlier reports of gene transfer from host to virus and indicate that viruses are more likely to acquire genes involved in innate antiviral immune responses than those involved in acquired immune responses.}, }
@article {pmid22384369, year = {2011}, author = {Shearer, JE and Wireman, J and Hostetler, J and Forberger, H and Borman, J and Gill, J and Sanchez, S and Mankin, A and Lamarre, J and Lindsay, JA and Bayles, K and Nicholson, A and O'Brien, F and Jensen, SO and Firth, N and Skurray, RA and Summers, AO}, title = {Major families of multiresistant plasmids from geographically and epidemiologically diverse staphylococci.}, journal = {G3 (Bethesda, Md.)}, volume = {1}, number = {7}, pages = {581-591}, pmid = {22384369}, issn = {2160-1836}, support = {R01 AI072445/AI/NIAID NIH HHS/United States ; U24 AI050139/AI/NIAID NIH HHS/United States ; }, abstract = {Staphylococci are increasingly aggressive human pathogens suggesting that active evolution is spreading novel virulence and resistance phenotypes. Large staphylococcal plasmids commonly carry antibiotic resistances and virulence loci, but relatively few have been completely sequenced. We determined the plasmid content of 280 staphylococci isolated in diverse geographical regions from the 1940s to the 2000s and found that 79% of strains carried at least one large plasmid >20 kb and that 75% of these large plasmids were 20-30 kb. Using restriction fragment length polymorphism (RFLP) analysis, we grouped 43% of all large plasmids into three major families, showing remarkably conserved intercontinental spread of multiresistant staphylococcal plasmids over seven decades. In total, we sequenced 93 complete and 57 partial staphylococcal plasmids ranging in size from 1.3 kb to 64.9 kb, tripling the number of complete sequences for staphylococcal plasmids >20 kb in the NCBI RefSeq database. These plasmids typically carried multiple antimicrobial and metal resistances and virulence genes, transposases and recombinases. Remarkably, plasmids within each of the three main families were >98% identical, apart from insertions and deletions, despite being isolated from strains decades apart and on different continents. This suggests enormous selective pressure has optimized the content of certain plasmids despite their large size and complex organization.}, }
@article {pmid22384087, year = {2012}, author = {Hoogewijs, D and Dewilde, S and Vierstraete, A and Moens, L and Vinogradov, SN}, title = {A phylogenetic analysis of the globins in fungi.}, journal = {PloS one}, volume = {7}, number = {2}, pages = {e31856}, pmid = {22384087}, issn = {1932-6203}, mesh = {Bacteria/genetics ; Bayes Theorem ; Candida/genetics ; Computational Biology/methods ; Evolution, Molecular ; Fungi/genetics/*metabolism ; *Gene Expression Regulation, Fungal ; Genome ; Genome, Fungal ; Globins/*chemistry ; Neurospora/genetics ; Phylogeny ; Protein Structure, Tertiary ; Saccharomyces cerevisiae/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {BACKGROUND: All globins belong to one of three families: the F (flavohemoglobin) and S (sensor) families that exhibit the canonical 3/3 α-helical fold, and the T (truncated 3/3 fold) globins characterized by a shortened 2/2 α-helical fold. All eukaryote 3/3 hemoglobins are related to the bacterial single domain F globins. It is known that Fungi contain flavohemoglobins and single domain S globins. Our aims are to provide a census of fungal globins and to examine their relationships to bacterial globins.<br><br>RESULTS: Examination of 165 genomes revealed that globins are present in >90% of Ascomycota and ~60% of Basidiomycota genomes. The S globins occur in Blastocladiomycota and Chytridiomycota in addition to the phyla that have FHbs. Unexpectedly, group 1 T globins were found in one Blastocladiomycota and one Chytridiomycota genome. Phylogenetic analyses were carried out on the fungal globins, alone and aligned with representative bacterial globins. The Saccharomycetes and Sordariomycetes with two FHbs form two widely divergent clusters separated by the remaining fungal sequences. One of the Saccharomycete groups represents a new subfamily of FHbs, comprising a previously unknown N-terminal and a FHb missing the C-terminal moiety of its reductase domain. The two Saccharomycete groups also form two clusters in the presence of bacterial FHbs; the surrounding bacterial sequences are dominated by Proteobacteria and Bacilli (Firmicutes). The remaining fungal FHbs cluster with Proteobacteria and Actinobacteria. The Sgbs cluster separately from their bacterial counterparts, except for the intercalation of two Planctomycetes and a Proteobacterium between the Fungi incertae sedis and the Blastocladiomycota and Chytridiomycota.<br><br>CONCLUSION: Our results are compatible with a model of globin evolution put forward earlier, which proposed that eukaryote F, S and T globins originated via horizontal gene transfer of their bacterial counterparts to the eukaryote ancestor, resulting from the endosymbiotic events responsible for the origin of mitochondria and chloroplasts.}, }
@article {pmid22383560, year = {2012}, author = {Papenfort, K and Podkaminski, D and Hinton, JC and Vogel, J}, title = {The ancestral SgrS RNA discriminates horizontally acquired Salmonella mRNAs through a single G-U wobble pair.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {13}, pages = {E757-64}, pmid = {22383560}, issn = {1091-6490}, mesh = {Bacterial Proteins/biosynthesis/genetics ; Base Pairing/*genetics ; Base Sequence ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/genetics ; Molecular Sequence Data ; Open Reading Frames/genetics ; Phosphoenolpyruvate Sugar Phosphotransferase System/genetics/metabolism ; *Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Protein Binding ; Protein Biosynthesis ; RNA, Bacterial/*genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Repressor Proteins/metabolism ; Salmonella/*genetics ; Virulence Factors/biosynthesis/genetics ; }, abstract = {SgrS RNA is a model for the large class of Hfq-associated small RNAs that act to posttranscriptionally regulate bacterial mRNAs. The function of SgrS is well-characterized in nonpathogenic Escherichia coli, where it was originally shown to counteract glucose-phosphate stress by acting as a repressor of the ptsG mRNA, which encodes the major glucose transporter. We have discovered additional SgrS targets in Salmonella Typhimurium, a pathogen related to E. coli that recently acquired one-quarter of all genes by horizontal gene transfer. We show that the conserved short seed region of SgrS that recognizes ptsG was recruited to target the Salmonella-specific sopD mRNA of a secreted virulence protein. The SgrS-sopD interaction is exceptionally selective; we find that sopD2 mRNA, whose gene arose from sopD duplication during Salmonella evolution, is deaf to SgrS because of a nonproductive G-U pair in the potential SgrS-sopD2 RNA duplex vs. G-C in SgrS-sopD. In other words, SgrS discriminates the two virulence factor mRNAs at the level of a single hydrogen bond. Our study suggests that bacterial pathogens use their large suites of conserved Hfq-associated regulators to integrate horizontally acquired genes into existing posttranscriptional networks, just as conserved transcription factors are recruited to tame foreign genes at the DNA level. The results graphically illustrate the importance of the seed regions of bacterial small RNAs to select new targets with high fidelity and suggest that target predictions must consider all or none decisions by individual seed nucleotides.}, }
@article {pmid22382962, year = {2012}, author = {Dana, GV and Kuiken, T and Rejeski, D and Snow, AA}, title = {Synthetic biology: Four steps to avoid a synthetic-biology disaster.}, journal = {Nature}, volume = {483}, number = {7387}, pages = {29}, doi = {10.1038/483029a}, pmid = {22382962}, issn = {1476-4687}, mesh = {Adaptation, Physiological ; Biohazard Release/*prevention &amp; control ; Disasters/*prevention &amp; control ; *Ecosystem ; Gene Transfer, Horizontal ; Humans ; *Laboratories ; Risk Assessment ; Synthetic Biology/economics/*standards ; }, }
@article {pmid22380427, year = {2012}, author = {Gillings, MR}, title = {How evolution generates complexity without design: language as an instructional metaphor.}, journal = {Evolution; international journal of organic evolution}, volume = {66}, number = {3}, pages = {617-622}, doi = {10.1111/j.1558-5646.2011.01511.x}, pmid = {22380427}, issn = {1558-5646}, mesh = {*Biological Evolution ; Biology/*education ; Gene Transfer, Horizontal ; Genetic Variation ; *Language ; Mutation ; Recombination, Genetic ; Religious Philosophies ; Selection, Genetic ; }, abstract = {One of the major stumbling blocks to understanding evolution is the difficulty in reconciling the emergence of complexity with the apparently undirected forces that drive evolutionary processes. This difficulty was originally framed as the "Watch and Watchmaker" argument and more recently revived by proponents of "intelligent design." Undergraduates in particular often attribute purpose and forethought as the driving force behind biological phenomena, and have difficulty understanding evolutionary processes. To demonstrate that complexity can arise solely through mutations that fix in populations via natural selection or drift, we can use analogies where processes can be observed across short time frames and where the key data are accessible to those without specialized biological knowledge. The evolution of language provides such an example. Processes of natural selection, mutation, genetic drift, acquisition of new functions, punctuated equilibria, and lateral gene transfer can be illustrated using examples of changing spellings, neologism, and acquisition of words from other languages. The examples presented in this article are readily accessible, and demonstrate to students that languages have dynamically increased in complexity, simply driven by the usage patterns of their speakers.}, }
@article {pmid22377718, year = {2012}, author = {Namouchi, A and Didelot, X and Schöck, U and Gicquel, B and Rocha, EP}, title = {After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection.}, journal = {Genome research}, volume = {22}, number = {4}, pages = {721-734}, pmid = {22377718}, issn = {1549-5469}, support = {G0600719/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Cluster Analysis ; Gene Transfer, Horizontal ; *Genetic Variation ; Genome, Bacterial/*genetics ; Humans ; *Mutation ; Mycobacterium tuberculosis/classification/*genetics/metabolism ; Phylogeny ; Polymorphism, Single Nucleotide ; *Recombination, Genetic ; *Selection, Genetic ; Species Specificity ; Tuberculosis/microbiology ; }, abstract = {Many of the most virulent bacterial pathogens show low genetic diversity and sexual isolation. Accordingly, Mycobacterium tuberculosis, the deadliest human pathogen, is thought to be clonal and evolve by genetic drift. Yet, its genome shows few of the concomitant signs of genome degradation. We analyzed 24 genomes and found an excess of genetic diversity in regions encoding key adaptive functions including the type VII secretion system and the ancient horizontally transferred virulence-related regions. Four different approaches showed evident signs of recombination in M. tuberculosis. Recombination tracts add a high density of polymorphisms, and many are thus predicted to arise from outside the clade. Some of these tracts match Mycobacterium canettii sequences. Recombination introduced an excess of non-synonymous diversity in general and even more in genes expected to be under positive or diversifying selection, e.g., cell wall component genes. Mutations leading to non-synonymous SNPs are effectively purged in MTBC, which shows dominance of purifying selection. MTBC mutation bias toward AT nucleotides is not compensated by biased gene conversion, suggesting the action of natural selection also on synonymous changes. Together, all of these observations point to a strong imprint of recombination and selection in the genome affecting both non-synonymous and synonymous positions. Hence, contrary to some other pathogens and previous proposals concerning M. tuberculosis, this lineage may have come out of its ancestral bottleneck as a very successful pathogen that is rapidly diversifying by the action of mutation, recombination, and natural selection.}, }
@article {pmid22377146, year = {2012}, author = {Gao, P and Mao, D and Luo, Y and Wang, L and Xu, B and Xu, L}, title = {Occurrence of sulfonamide and tetracycline-resistant bacteria and resistance genes in aquaculture environment.}, journal = {Water research}, volume = {46}, number = {7}, pages = {2355-2364}, doi = {10.1016/j.watres.2012.02.004}, pmid = {22377146}, issn = {1879-2448}, mesh = {*Aquaculture ; Bacillus/*genetics ; Base Sequence ; China ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Genes, MDR/genetics ; Molecular Sequence Data ; *Phylogeny ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {The occurrence of sulfonamide and tetracycline resistance and their pollution profile in the aquaculture environment of Tianjin, northern China, were investigated. The presence of antibiotic-resistant bacteria was identified and the corresponding antibiotic resistance genes (ARGs) were quantified at 6 aquaculture farms in Tianjin. Sulfonamide-resistance genes were prevalent and their concentrations were the highest detected (3.0 × 10(-5) to 3.3 × 10(-4) for sul1/16S rDNA, 2.0 × 10(-4) to 1.8 × 10(-3) for sul2/16S rDNA) among the various ARGs, most likely because the use of sulfonamides is more prevalent than tetracyclines in this area. Bacillus was the most dominant bacterial genus in both sulfamethoxazole resistant bacteria (63.27% of the total resistant bacteria) and tetracycline-resistant bacteria (57.14% of the total resistant bacteria). At least two of those genes (tetM, tetO, tetT, tetW, sul1 and sul2) were detected in the isolates of Bacillus cereus, Bacillus subtilis, Bacillus megaterium and Acinetobacter lwofii, and all of the above genes were detected in B. cereus, suggesting the occurrence of multi-resistance in the studied area. The genetic transfer of sul1 between intestinal bacteria (e.g., Enterococcus spp.) and indigenous bacteria (e.g., Bacillus spp.) was implied by phylogenetic analysis. Several strains of resistant opportunistic pathogens (e.g., Acinetobacter spp.) were found in indigenous bacteria, which increase the risk of ARGs to public health. Overall, this is the first study to comprehensively investigate the antibiotic resistance profile by analyzing the species of antibiotic-resistant bacteria and adopting qualitative and quantitative methods to investigate ARGs at a typical aquaculture area in northern China.}, }
@article {pmid22376198, year = {2012}, author = {Machtelinckx, T and Van Leeuwen, T and Van De Wiele, T and Boon, N and De Vos, WH and Sanchez, JA and Nannini, M and Gheysen, G and De Clercq, P}, title = {Microbial community of predatory bugs of the genus Macrolophus (Hemiptera: Miridae).}, journal = {BMC microbiology}, volume = {12 Suppl 1}, number = {Suppl 1}, pages = {S9}, pmid = {22376198}, issn = {1471-2180}, mesh = {Animals ; Female ; Gene Transfer, Horizontal ; Hemiptera/*microbiology ; In Situ Hybridization, Fluorescence ; Male ; Microbiota ; Ovary/microbiology ; Phylogeny ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis/genetics ; Rickettsia/*classification/genetics/*isolation &amp; purification ; Sequence Analysis, RNA/methods ; Wolbachia/*isolation &amp; purification ; }, abstract = {BACKGROUND: The predatory mirids of the genus Macrolophus are key natural enemies of various economically important agricultural pests. Both M. caliginosus and M. pygmaeus are commercially available for the augmentative biological control of arthropod pests in European greenhouses. The latter species is known to be infected with Wolbachia -inducing cytoplasmic incompatibility in its host- but the presence of other endosymbionts has not been demonstrated. In the present study, the microbial diversity was examined in various populations of M. caliginosus and M. pygmaeus by 16S rRNA sequencing and denaturing gradient gel electrophoresis.<br><br>RESULTS: Besides Wolbachia, a co-infection of 2 Rickettsia species was detected in all M. pygmaeus populations. Based on a concatenated alignment of the 16S rRNA gene, the gltA gene and the coxA gene, the first is phylogenetically related to Rickettsia bellii, whereas the other is closely related to Rickettsia limoniae. All M. caliginosus populations were infected with the same Wolbachia and limoniae-like Rickettsia strain as M. pygmaeus, but did not harbour the bellii-like Rickettsia strain. Interestingly, individuals with a single infection were not found. A PCR assay on the ovaries of M. pygmaeus and M. caliginosus indicated that all endosymbionts are vertically transmitted. The presence of Wolbachia and Rickettsia in oocytes was confirmed by a fluorescence in situ hybridisation. A bio-assay comparing an infected and an uninfected M. pygmaeus population suggested that the endosymbionts had minor effects on nymphal development of their insect host and did not influence its fecundity.<br><br>CONCLUSION: Two species of the palaearctic mirid genus Macrolophus are infected with multiple endosymbionts, including Wolbachia and Rickettsia. Independent of the origin, all tested populations of both M. pygmaeus and M. caliginosus were infected with three and two endosymbionts, respectively. There was no indication that infection with endosymbiotic bacteria had a fitness cost in terms of development and fecundity of the predators.}, }
@article {pmid22376025, year = {2012}, author = {Doudoumis, V and Tsiamis, G and Wamwiri, F and Brelsfoard, C and Alam, U and Aksoy, E and Dalaperas, S and Abd-Alla, A and Ouma, J and Takac, P and Aksoy, S and Bourtzis, K}, title = {Detection and characterization of Wolbachia infections in laboratory and natural populations of different species of tsetse flies (genus Glossina).}, journal = {BMC microbiology}, volume = {12 Suppl 1}, number = {Suppl 1}, pages = {S3}, pmid = {22376025}, issn = {1471-2180}, support = {AI06892/AI/NIAID NIH HHS/United States ; R03TW008413/TW/FIC NIH HHS/United States ; D43 TW007391/TW/FIC NIH HHS/United States ; R01 AI051584/AI/NIAID NIH HHS/United States ; R03 TW008413/TW/FIC NIH HHS/United States ; D43TW007391/TW/FIC NIH HHS/United States ; }, mesh = {Africa ; Animals ; Bacterial Typing Techniques ; Cell Nucleus/genetics ; Gene Transfer, Horizontal ; Genome, Insect ; Molecular Sequence Data ; Multilocus Sequence Typing ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Tsetse Flies/classification/genetics/*microbiology ; Wolbachia/classification/*isolation &amp; purification ; }, abstract = {BACKGROUND: Wolbachia is a genus of endosymbiotic α-Proteobacteria infecting a wide range of arthropods and filarial nematodes. Wolbachia is able to induce reproductive abnormalities such as cytoplasmic incompatibility (CI), thelytokous parthenogenesis, feminization and male killing, thus affecting biology, ecology and evolution of its hosts. The bacterial group has prompted research regarding its potential for the control of agricultural and medical disease vectors, including Glossina spp., which transmits African trypanosomes, the causative agents of sleeping sickness in humans and nagana in animals.<br><br>RESULTS: In the present study, we employed a Wolbachia specific 16S rRNA PCR assay to investigate the presence of Wolbachia in six different laboratory stocks as well as in natural populations of nine different Glossina species originating from 10 African countries. Wolbachia was prevalent in Glossina morsitans morsitans, G. morsitans centralis and G. austeni populations. It was also detected in G. brevipalpis, and, for the first time, in G. pallidipes and G. palpalis gambiensis. On the other hand, Wolbachia was not found in G. p. palpalis, G. fuscipes fuscipes and G. tachinoides. Wolbachia infections of different laboratory and natural populations of Glossina species were characterized using 16S rRNA, the wsp (Wolbachia Surface Protein) gene and MLST (Multi Locus Sequence Typing) gene markers. This analysis led to the detection of horizontal gene transfer events, in which Wobachia genes were inserted into the tsetse flies fly nuclear genome.<br><br>CONCLUSIONS: Wolbachia infections were detected in both laboratory and natural populations of several different Glossina species. The characterization of these Wolbachia strains promises to lead to a deeper insight in tsetse flies-Wolbachia interactions, which is essential for the development and use of Wolbachia-based biological control methods.}, }
@article {pmid22375811, year = {2012}, author = {Mouton, L and Thierry, M and Henri, H and Baudin, R and Gnankine, O and Reynaud, B and Zchori-Fein, E and Becker, N and Fleury, F and Delatte, H}, title = {Evidence of diversity and recombination in Arsenophonus symbionts of the Bemisia tabaci species complex.}, journal = {BMC microbiology}, volume = {12 Suppl 1}, number = {Suppl 1}, pages = {S10}, pmid = {22375811}, issn = {1471-2180}, mesh = {Animals ; Codon, Terminator ; DNA, Bacterial/analysis ; Enterobacteriaceae/*classification/genetics/*isolation &amp; purification/physiology ; Gene Transfer, Horizontal ; Genetic Variation ; Hemiptera/classification/*microbiology/physiology ; Phylogeny ; Symbiosis ; }, abstract = {BACKGROUND: Maternally inherited bacterial symbionts infecting arthropods have major implications on host ecology and evolution. Among them, the genus Arsenophonus is particularly characterized by a large host spectrum and a wide range of symbiotic relationships (from mutualism to parasitism), making it a good model to study the evolution of host-symbiont associations. However, few data are available on the diversity and distribution of Arsenophonus within host lineages. Here, we propose a survey on Arsenophonus diversity in whitefly species (Hemiptera), in particular the Bemisia tabaci species complex. This polyphagous insect pest is composed of genetic groups that differ in many ecological aspects. They harbor specific bacterial communities, among them several lineages of Arsenophonus, enabling a study of the evolutionary history of these bacteria at a fine host taxonomic level, in association to host geographical range and ecology.<br><br>RESULTS: Among 152 individuals, our analysis identified 19 allelic profiles and 6 phylogenetic groups, demonstrating this bacterium's high diversity. These groups, based on Arsenophonus phylogeny, correlated with B. tabaci genetic groups with two exceptions reflecting horizontal transfers. None of three genes analyzed provided evidence of intragenic recombination, but intergenic recombination events were detected. A mutation inducing a STOP codon on one gene in a strain infecting one B. tabaci genetic group was also found. Phylogenetic analyses of the three concatenated loci revealed the existence of two clades of Arsenophonus. One, composed of strains found in other Hemiptera, could be the ancestral clade in whiteflies. The other, which regroups strains found in Hymenoptera and Diptera, may have been acquired more recently by whiteflies through lateral transfers.<br><br>CONCLUSIONS: This analysis of the genus Arsenophonus revealed a diversity within the B. tabaci species complex which resembles that reported on the larger scale of insect taxonomy. We also provide evidence for recombination events within the Arsenophonus genome and horizontal transmission of strains among insect taxa. This work provides further insight into the evolution of the Arsenophonus genome, the infection dynamics of this bacterium and its influence on its insect host's ecology.}, }
@article {pmid22375546, year = {2012}, author = {Choudhary, S and Islam, E and Kazy, SK and Sar, P}, title = {Uranium and other heavy metal resistance and accumulation in bacteria isolated from uranium mine wastes.}, journal = {Journal of environmental science and health. Part A, Toxic/hazardous substances &amp; environmental engineering}, volume = {47}, number = {4}, pages = {622-637}, doi = {10.1080/10934529.2012.650584}, pmid = {22375546}, issn = {1532-4117}, mesh = {Bacteria/genetics/*metabolism ; Base Sequence ; DNA Primers ; *Drug Resistance, Microbial ; Metals, Heavy/*metabolism ; Microbial Sensitivity Tests ; *Mining ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Uranium/*metabolism ; }, abstract = {Ten bacterial strains isolated from uranium mine wastes were characterized in terms of their uranium and other metal resistance and accumulation. 16S rRNA gene sequence analysis identified the strains as members of genera Bacillus, Serratia, and Arthrobacter. Strains were able to utilize various carbon sources, particularly aromatic hydrocarbons, grow at broad pH and temperature ranges and produce non specific acid phosphatase relevant for metal phosphate precipitation in contaminated environment. The isolates exhibited high uranium and other heavy metals (Ni, Co, Cu and Cd) resistance and accumulation capacities. Particularly, Arthrobacter sp. J001 and Bacillus sp. J003 were superior in terms of U resistance at low pH (pH 4.0) along with metals and actinides (U and Th) removal with maximum cell loading of 1088 μmol U, 1293 μmol Th, 425 μmol Cu, 305 μmol Cd, 377 μmol Zn, 250 μmol Ni g(-1) cell dry wt. Genes encoding P(1B)-type ATPases (Cu-CPx and Zn-CPx) and ABC transporters (nik) as catalytic tools for maintaining cellular metal homeostasis were detected within several Bacillus spp., with possible incidence of horizontal gene transfer for the later gene showing phylogenetic lineage to α Proteobacteria members. The study provides evidence on intrinsic abilities of indigenous bacteria from U-mine suitable for survival and cleaning up of contaminated mine sites.}, }
@article {pmid22374962, year = {2012}, author = {Huang, Y and Li, H and Rensing, C and Zhao, K and Johnstone, L and Wang, G}, title = {Genome sequence of the facultative anaerobic arsenite-oxidizing and nitrate-reducing bacterium Acidovorax sp. strain NO1.}, journal = {Journal of bacteriology}, volume = {194}, number = {6}, pages = {1635-1636}, pmid = {22374962}, issn = {1098-5530}, mesh = {Anaerobiosis ; Arsenites/metabolism/toxicity ; Comamonadaceae/*genetics/isolation &amp; purification/metabolism ; DNA, Bacterial/*chemistry/*genetics ; Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; Metabolic Networks and Pathways/genetics ; Metals/toxicity ; Molecular Sequence Data ; Nitrates/metabolism ; Oxidation-Reduction ; Phosphates/metabolism ; Sequence Analysis, DNA ; Soil Microbiology ; }, abstract = {Acidovorax sp. strain NO1, isolated from gold mine soil, was shown to be a facultative anaerobic arsenite-oxidizing and nitrate-reducing bacterium. The reported draft genome predicts the presence of genes involved in arsenic metabolism, nitrate reduction, phosphate transport, and multiple metal resistances and indicates putative horizontal gene transfer events.}, }
@article {pmid22372525, year = {2012}, author = {Widhalm, JR and Ducluzeau, AL and Buller, NE and Elowsky, CG and Olsen, LJ and Basset, GJ}, title = {Phylloquinone (vitamin K(1)) biosynthesis in plants: two peroxisomal thioesterases of Lactobacillales origin hydrolyze 1,4-dihydroxy-2-naphthoyl-CoA.}, journal = {The Plant journal : for cell and molecular biology}, volume = {71}, number = {2}, pages = {205-215}, doi = {10.1111/j.1365-313X.2012.04972.x}, pmid = {22372525}, issn = {1365-313X}, mesh = {Acyl Coenzyme A/*metabolism ; Arabidopsis/cytology/*enzymology/genetics ; Arabidopsis Proteins/genetics/isolation &amp; purification/metabolism ; Bacterial Proteins/genetics ; Gene Knockout Techniques ; Gene Transfer, Horizontal ; Genetic Complementation Test ; Genomics ; Genotype ; Hydrolysis ; Lactobacillales/*enzymology/genetics ; Mutagenesis, Insertional ; Peroxisomes/*enzymology/metabolism ; Phylogeny ; Plant Leaves/enzymology/metabolism ; Recombinant Fusion Proteins ; Substrate Specificity ; Synechocystis/enzymology/genetics ; Thiolester Hydrolases/*genetics/isolation &amp; purification/metabolism ; Vitamin K 1/*analogs &amp; derivatives/chemistry/*metabolism ; Vitamins/chemistry/*metabolism ; }, abstract = {It is not known how plants cleave the thioester bond of 1,4-dihydroxy-2-naphthoyl-CoA (DHNA-CoA), a necessary step to form the naphthoquinone ring of phylloquinone (vitamin K(1)). In fact, only recently has the hydrolysis of DHNA-CoA been demonstrated to be enzyme driven in vivo, and the cognate thioesterase characterized in the cyanobacterium Synechocystis. With a few exceptions in certain prokaryotic (Sorangium and Opitutus) and eukaryotic (Cyanidium, Cyanidioschyzon and Paulinella) organisms, orthologs of DHNA-CoA thioesterase are missing outside of the cyanobacterial lineage. In this study, genomic approaches and functional complementation experiments identified two Arabidopsis genes encoding functional DHNA-CoA thioesterases. The deduced plant proteins display low percentages of identity with cyanobacterial DHNA-CoA thioesterases, and do not even share the same catalytic motif. GFP-fusion experiments demonstrated that the Arabidopsis proteins are targeted to peroxisomes, and subcellular fractionations of Arabidopsis leaves confirmed that DHNA-CoA thioesterase activity occurs in this organelle. In vitro assays with various aromatic and aliphatic acyl-CoA thioester substrates showed that the recombinant Arabidopsis enzymes preferentially hydrolyze DHNA-CoA. Cognate T-DNA knock-down lines display reduced DHNA-CoA thioesterase activity and phylloquinone content, establishing in vivo evidence that the Arabidopsis enzymes are involved in phylloquinone biosynthesis. Extraordinarily, structure-based phylogenies coupled to comparative genomics demonstrate that plant DHNA-CoA thioesterases originate from a horizontal gene transfer with a bacterial species of the Lactobacillales order.}, }
@article {pmid22371593, year = {2012}, author = {Acuña, R and Padilla, BE and Flórez-Ramos, CP and Rubio, JD and Herrera, JC and Benavides, P and Lee, SJ and Yeats, TH and Egan, AN and Doyle, JJ and Rose, JK}, title = {Adaptive horizontal transfer of a bacterial gene to an invasive insect pest of coffee.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {11}, pages = {4197-4202}, pmid = {22371593}, issn = {1091-6490}, mesh = {Adaptation, Biological/*genetics ; Animals ; Coffea/*parasitology ; Coleoptera/*genetics ; DNA/genetics ; Eukaryotic Cells/metabolism ; Fruit/parasitology ; Galactose/analogs &amp; derivatives ; Gastrointestinal Tract/enzymology ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/*genetics ; Genes, Insect/genetics ; Geography ; Hydrolysis ; Insect Proteins/genetics/metabolism ; *Introduced Species ; Mannans/metabolism ; Mannosidases/metabolism ; Molecular Sequence Data ; Mutagenesis, Insertional ; Phylogeny ; Recombinant Proteins/metabolism ; }, abstract = {Horizontal gene transfer (HGT) involves the nonsexual transmission of genetic material across species boundaries. Although often detected in prokaryotes, examples of HGT involving animals are relatively rare, and any evolutionary advantage conferred to the recipient is typically obscure. We identified a gene (HhMAN1) from the coffee berry borer beetle, Hypothenemus hampei, a devastating pest of coffee, which shows clear evidence of HGT from bacteria. HhMAN1 encodes a mannanase, representing a class of glycosyl hydrolases that has not previously been reported in insects. Recombinant HhMAN1 protein hydrolyzes coffee berry galactomannan, the major storage polysaccharide in this species and the presumed food of H. hampei. HhMAN1 was found to be widespread in a broad biogeographic survey of H. hampei accessions, indicating that the HGT event occurred before radiation of the insect from West Africa to Asia and South America. However, the gene was not detected in the closely related species H. obscurus (the tropical nut borer or "false berry borer"), which does not colonize coffee beans. Thus, HGT of HhMAN1 from bacteria represents a likely adaptation to a specific ecological niche and may have been promoted by intensive agricultural practices.}, }
@article {pmid22369247, year = {2012}, author = {Parker, MA}, title = {Legumes select symbiosis island sequence variants in Bradyrhizobium.}, journal = {Molecular ecology}, volume = {21}, number = {7}, pages = {1769-1778}, doi = {10.1111/j.1365-294X.2012.05497.x}, pmid = {22369247}, issn = {1365-294X}, mesh = {Bradyrhizobium/*genetics ; DNA, Bacterial/genetics ; Fabaceae/*microbiology ; Gene Transfer, Horizontal ; *Genomic Islands ; Linkage Disequilibrium ; Phylogeny ; *Selection, Genetic ; Sequence Analysis, DNA ; Symbiosis/*genetics ; }, abstract = {Bradyrhizobium strains sampled from 14 legume genera native to eastern North America showed substantial host-related phylogenetic clustering at three loci in the symbiotic island (SI) region (nodC, nifD, nifH), indicating selection of distinct suites of SI lineages by different legumes. Bacteria assorted consistently with particular legumes across two regions separated by 800 km, implying recurrent assembly of the same symbiotic combinations. High genetic polymorphism of all three SI loci relative to four nonsymbiotic loci supported the inference that a form of multiple-niche balancing selection has acted on the SI region, arising from differential symbiont utilization by different legume taxa. Extensive discordance between the tree for SI variants and a phylogenetic tree inferred for four housekeeping loci implied that lateral transfer of the symbiosis island region has been common (at least 26 transfer events among 85 Bradyrhizobium strains analysed). Patterns of linkage disequilibrium also supported the conclusion that recombination has impacted symbiotic and nonsymbiotic regions unequally. The high prevalence of lateral transfer suggests that acquisition of a novel SI variant may often confer a strong selective advantage for recipient cells.}, }
@article {pmid22367953, year = {2012}, author = {Han, SH and Kim, YA and Wang, M and Lee, Y and Chung, HS and Yum, JH and Yong, D and Lee, K and Kim, JM}, title = {Comparison of the genetic structures surrounding qnrA1 in Korean Enterobacter cloacae and Chinese Escherichia coli strains isolated in the early 2000s: evidence for qnrA mobilization via Inc HI2 type plasmid.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {50}, number = {1}, pages = {166-169}, pmid = {22367953}, issn = {1976-3794}, mesh = {Blotting, Southern ; China ; Enterobacter cloacae/*genetics/*isolation &amp; purification ; Enterobacteriaceae Infections/*microbiology ; Escherichia coli/*genetics/*isolation &amp; purification ; Gene Order ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Plasmids ; Republic of Korea ; Restriction Mapping ; Sequence Homology ; Synteny ; }, abstract = {The flanking genetic structure of qnrA1 in Korean Enterobacter loacae was identical to that of the Chinese Escherichia coli strain, the first qnrA1-carrying strain reported in Asia. Analysis of restriction enzyme sites and Southern blot hybridization results showed that qnrA1 was transferred between E. cloacae and E. coli via Inc HI2 type plasmid.}, }
@article {pmid22367613, year = {2013}, author = {Ikuma, K and Gunsch, CK}, title = {Functionality of the TOL plasmid under varying environmental conditions following conjugal transfer.}, journal = {Applied microbiology and biotechnology}, volume = {97}, number = {1}, pages = {395-408}, doi = {10.1007/s00253-012-3949-8}, pmid = {22367613}, issn = {1432-0614}, mesh = {Base Composition ; Catechol 2,3-Dioxygenase/metabolism ; *Conjugation, Genetic ; *Environmental Microbiology ; Gene Expression ; *Gene Transfer, Horizontal ; Genomic Instability ; Glucose/metabolism ; Gram-Negative Bacteria/*genetics/metabolism ; Metabolic Networks and Pathways ; Phylogeny ; *Plasmids ; Soil Pollutants/*metabolism ; Toluene/*metabolism ; }, abstract = {Conjugation of catabolic plasmids in contaminated environments is a naturally occurring horizontal gene transfer phenomenon, which could be utilized in genetic bioaugmentation. The potentially important parameters for genetic bioaugmentation include gene regulation of transferred catabolic plasmids that may be controlled by the genetic characteristics of transconjugants as well as environmental conditions that may alter the expression of the contaminant-degrading phenotype. This study showed that both genomic guanine-cytosine contents and phylogenetic characteristics of transconjugants were important in controlling the phenotype functionality of the TOL plasmid. These genetic characteristics had no apparent impact on the stability of the TOL plasmid, which was observed to be highly variable among strains. Within the environmental conditions tested, the addition of glucose resulted in the largest enhancement of the activities of enzymes encoded by the TOL plasmid in all transconjugant strains. Glucose (1 g/L) enhanced the phenotype functionality by up to 16.4 (±2.22), 30.8 (±7.03), and 90.8 (±4.56)-fold in toluene degradation rates, catechol 2,3-dioxygenase enzymatic activities, and xylE gene expression, respectively. These results suggest that genetic limitations of the expression of horizontally acquired genes may be overcome by the presence of alternate carbon substrates. Such observations may be utilized in improving the effectiveness of genetic bioaugmentation.}, }
@article {pmid22365347, year = {2012}, author = {Gazzola, S and Fontana, C and Bassi, D and Cocconcelli, PS}, title = {Assessment of tetracycline and erythromycin resistance transfer during sausage fermentation by culture-dependent and -independent methods.}, journal = {Food microbiology}, volume = {30}, number = {2}, pages = {348-354}, doi = {10.1016/j.fm.2011.12.005}, pmid = {22365347}, issn = {1095-9998}, mesh = {Conjugation, Genetic ; Culture Media ; Denaturing Gradient Gel Electrophoresis ; Drug Resistance, Microbial/*genetics ; Enterococcus faecalis/drug effects/genetics/growth &amp; development ; Erythromycin/*pharmacology ; *Fermentation ; *Gene Transfer, Horizontal ; Meat/*microbiology ; Polymerase Chain Reaction ; Tetracycline Resistance/*genetics ; }, abstract = {The food chain is considered one of the main routes of antibiotic resistance diffusion between animal and human population. The resistance to antimicrobial agents among enterococci could be related to the efficient exchange of transferable genetic elements. In this study a sausage model was used to evaluate the persistence of antibiotic resistant enterococci during meat fermentation and to assess horizontal gene transfer among bacteria involved in meat fermentation. Enterococcus faecalis OG1rf harbouring either pCF10 or pAMβ1 plasmid was used as donor strain. The analysis of population dynamics during fermentation confirmed that the human isolate E. faecalis OG1rf was able to colonize the meat ecosystem with similar growth kinetics to that of food origin enterococci and to transfer the mobile genetic elements coding for tetracycline and erythromycin resistances. Transconjugant strains were detected after only two days of fermentation and increased their numbers during ripening even in the absence of selective antibiotic pressure. By means of culture-dependent and -independent molecular techniques, transconjugant strains carrying both tetracycline and erythromycin resistance genes were identified in enterococci, pediococci, lactobacilli and staphylococci groups. Our results suggest that the sausage model provides a suitable environment for horizontal transfer of conjugative plasmids and antibiotic resistance genes among food microbiota.}, }
@article {pmid22365240, year = {2012}, author = {Briales, A and Rodríguez-Martínez, JM and Velasco, C and de Alba, PD and Rodríguez-Baño, J and Martínez-Martínez, L and Pascual, A}, title = {Prevalence of plasmid-mediated quinolone resistance determinants qnr and aac(6')-Ib-cr in Escherichia coli and Klebsiella pneumoniae producing extended-spectrum β-lactamases in Spain.}, journal = {International journal of antimicrobial agents}, volume = {39}, number = {5}, pages = {431-434}, doi = {10.1016/j.ijantimicag.2011.12.009}, pmid = {22365240}, issn = {1872-7913}, mesh = {Adult ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Child, Preschool ; Conjugation, Genetic ; DNA Gyrase/genetics ; DNA Topoisomerase IV/genetics ; *Drug Resistance, Bacterial ; Escherichia coli/drug effects/*genetics/isolation &amp; purification ; Escherichia coli Infections/*epidemiology/microbiology ; Escherichia coli Proteins/genetics ; Female ; Gene Transfer, Horizontal ; Humans ; Klebsiella Infections/*epidemiology/microbiology ; Klebsiella pneumoniae/drug effects/*genetics/isolation &amp; purification ; Microbial Sensitivity Tests ; *Plasmids ; Prevalence ; Quinolones/pharmacology ; Spain/epidemiology ; beta-Lactamases/genetics ; beta-Lactams/pharmacology ; }, abstract = {The presence of the plasmid-mediated quinolone resistance determinants qnrA, qnrB, qnrS and aac(6')-Ib-cr was evaluated in a collection of 382 isolates of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli and Klebsiella pneumoniae collected between February and March 2006 for the nationwide Spanish GEIH-ESBL 2006 project. In total, 14 isolates (3.7%) were positive for qnr genes (3 qnrA1, 5 qnrB-like and 6 qnrS1) and 62 isolates (16.2%) were positive for the mutant variant of aac(6')-Ib-cr. The Aac(6')-Ib-cr enzyme was the most prevalent plasmid-mediated mechanism of quinolone resistance in Spain. Most of the Aac(6')-Ib-cr-producing E. coli isolates (94.2%) carried two mutations in gyrA and two in parC, whilst only 57.2% of K. pneumoniae harbouring this enzyme were gyrA and/or parC mutants. Most qnr plasmids were transferable, but only four were conjugative. Plasmid incompatibility groups were identified for only four plasmids, belonging to FIA, HI2 and I1γ. The most prevalent ESBLs associated with qnr plasmids belonged to the SHV and CTX-M families. The present study highlights the broad geographical spread of qnr-like determinants in Spain and their association with the SHV-12 and CTX-M-9 ESBLs in human clinical isolates.}, }
@article {pmid22363744, year = {2012}, author = {Pehl, MJ and Jamieson, WD and Kong, K and Forbester, JL and Fredendall, RJ and Gregory, GA and McFarland, JE and Healy, JM and Orwin, PM}, title = {Genes that influence swarming motility and biofilm formation in Variovorax paradoxus EPS.}, journal = {PloS one}, volume = {7}, number = {2}, pages = {e31832}, pmid = {22363744}, issn = {1932-6203}, support = {R15 GM090242/GM/NIGMS NIH HHS/United States ; S06 GM073842/GM/NIGMS NIH HHS/United States ; R15 GM090242-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics/metabolism ; Biofilms/*growth &amp; development ; Biological Assay ; Biopolymers/*metabolism ; Catalytic Domain ; Cell Membrane/metabolism ; Colony Count, Microbial ; Comamonadaceae/*genetics/growth &amp; development/*physiology ; Conserved Sequence/genetics ; Extracellular Space/*metabolism ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/*genetics ; Genetic Complementation Test ; Genetic Testing ; Molecular Sequence Data ; Movement ; Mutation/genetics ; Nucleotides/genetics ; Phylogeny ; Polymerase Chain Reaction ; }, abstract = {BACKGROUND: Variovorax paradoxus is an aerobic soil bacterium associated with important biodegradative processes in nature. We use V. paradoxus EPS to study multicellular behaviors on surfaces.<br><br>METHODOLOGY: We recovered flanking sequence from 123 clones in a Tn5 mutant library, with insertions in 29 different genes, selected based on observed surface behavior phenotypes. We identified three genes, Varpa_4665, Varpa_4680, and Varpa_5900, for further examination. These genes were cloned into pBBR1MCS2 and used to complement the insertion mutants. We also analyzed expression of Varpa_4680 and Varpa_5900 under different growth conditions by qPCR.<br><br>RESULTS: The 29 genes we identified had diverse predicted functions, many in exopolysaccharide synthesis. Varpa_4680, the most commonly recovered insertion site, encodes a putative N-acetyl-L-fucosamine transferase similar to WbuB. Expression of this gene in trans complemented the mutant fully. Several unique insertions were identified in Varpa_5900, which is one of three predicted pilY1 homologs in the EPS genome. No insertions in the two other putative pilY1 homologs present in the genome were identified. Expression of Varpa_5900 altered the structure of the wild type swarm, as did disruption of the chromosomal gene. The swarming phenotype was complemented by expression of Varpa_5900 from a plasmid, but biofilm formation was not restored. Both Varpa_4680 and Varpa_5900 transcripts were downregulated in biofilms and upregulated during swarming when compared to log phase culture. We identified a putative two component system (Varpa_4664-4665) encoding a response regulator (shkR) and a sensor histidine kinase (shkS), respectively. Biofilm formation increased and swarming was strongly delayed in the Varpa_4665 (shkS) mutant. Complementation of shkS restored the biofilm phenotype but swarming was still delayed. Expression of shkR in trans suppressed biofilm formation in either genetic background, and partially restored swarming in the mutant.<br><br>CONCLUSIONS: The data presented here point to complex regulation of these surface behaviors.}, }
@article {pmid22363326, year = {2012}, author = {Altermann, E}, title = {Tracing lifestyle adaptation in prokaryotic genomes.}, journal = {Frontiers in microbiology}, volume = {3}, number = {}, pages = {48}, pmid = {22363326}, issn = {1664-302X}, abstract = {Lifestyle adaptation of microbes due to changes in their ecological niches or acquisition of new environments is a major driving force for genetic changes in their respective genomes. Moving into more specialized niches often results in the acquisition of new gene sets via horizontal gene transfer to utilize previously unavailable metabolites, while genetic ballast is shed by gene loss and/or gene inactivation. In some cases, larger genome rearrangements can be observed, such as the incorporation of whole genetic islands, providing a range of new phenotypic capabilities. Until recently these changes could not be comprehensively followed and identified due to the lack of complete microbial genome sequences. The advent of high-throughput DNA sequencing has dramatically changed the scientific landscape and today microbial genomes have become increasingly abundant. Currently, more than 2,900 genomes are published and more than 11,000 genome projects are listed in the Genomes Online Database. Although this wealth of information provides many new opportunities to assess microbial functionality, it also creates a new array of challenges when a comparison between multiple microbial genomes is required. Here, functional genome distribution (FGD) is introduced, analyzing the diversity between microbes based on their predicted ORFeome. FGD is therefore a comparative genomics approach, emphasizing the assessments of gene complements. To further facilitate the comparison between two or more genomes, degrees of amino-acid similarities between ORFeomes can be visualized in the Artemis comparison tool, graphically depicting small and large scale genome rearrangements, insertion and deletion events, and levels of similarity between individual open reading frames. FGD provides a new tool for comparative microbial genomics and the interpretation of differences in the genetic makeup of bacteria.}, }
@article {pmid22363321, year = {2012}, author = {Townsend, JP and Bøhn, T and Nielsen, KM}, title = {Assessing the probability of detection of horizontal gene transfer events in bacterial populations.}, journal = {Frontiers in microbiology}, volume = {3}, number = {}, pages = {27}, pmid = {22363321}, issn = {1664-302X}, abstract = {Experimental approaches to identify horizontal gene transfer (HGT) events of non-mobile DNA in bacteria have typically relied on detection of the initial transformants or their immediate offspring. However, rare HGT events occurring in large and structured populations are unlikely to be detected in a short time frame. Population genetic modeling of the growth dynamics of bacterial genotypes is therefore necessary to account for natural selection and genetic drift during the time lag and to predict realistic time frames for detection with a given sampling design. Here we draw on statistical approaches to population genetic theory to construct a cohesive probabilistic framework for investigation of HGT of exogenous DNA into bacteria. In particular, the stochastic timing of rare HGT events is accounted for. Integrating over all possible event timings, we provide an equation for the probability of detection, given that HGT actually occurred. Furthermore, we identify the key variables determining the probability of detecting HGT events in four different case scenarios that are representative of bacterial populations in various environments. Our theoretical analysis provides insight into the temporal aspects of dissemination of genetic material, such as antibiotic resistance genes or transgenes present in genetically modified organisms. Due to the long time scales involved and the exponential growth of bacteria with differing fitness, quantitative analyses incorporating bacterial generation time, and levels of selection, such as the one presented here, will be a necessary component of any future experimental design and analysis of HGT as it occurs in natural settings.}, }
@article {pmid22360528, year = {2012}, author = {Martínez-Rosales, C and Fullana, N and Musto, H and Castro-Sowinski, S}, title = {Antarctic DNA moving forward: genomic plasticity and biotechnological potential.}, journal = {FEMS microbiology letters}, volume = {331}, number = {1}, pages = {1-9}, doi = {10.1111/j.1574-6968.2012.02531.x}, pmid = {22360528}, issn = {1574-6968}, mesh = {Antarctic Regions ; Biotechnology/*methods ; Computational Biology ; DNA, Bacterial/*genetics ; *Environmental Microbiology ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genomics ; Interspersed Repetitive Sequences ; *Metagenome ; Recombination, Genetic ; }, abstract = {Antarctica is the coldest, driest, and windiest continent, where only cold-adapted organisms survive. It has been frequently cited as a pristine place, but it has a highly diverse microbial community that is continually seeded by nonindigenous microorganisms. In addition to the intromission of 'alien' microorganisms, global warming strongly affects microbial Antarctic communities, changing the genes (qualitatively and quantitatively) potentially available for horizontal gene transfer. Several mobile genetic elements have been described in Antarctic bacteria (including plasmids, transposons, integrons, and genomic islands), and the data support that they are actively involved in bacterial evolution in the Antarctic environment. In addition, this environment is a genomic source for the identification of novel molecules, and many investigators have used culture-dependent and culture-independent approaches to identify cold-adapted proteins. Some of them are described in this review. We also describe studies for the design of new recombinant technologies for the production of 'difficult' proteins.}, }
@article {pmid22360305, year = {2012}, author = {Ceotto, H and Dias, RC and Nascimento, Jdos S and Brito, MA and Giambiagi-Demarval, M and Bastos, Mdo C}, title = {Aureocin A70 production is disseminated amongst genetically unrelated Staphylococcus aureus involved in bovine mastitis.}, journal = {Letters in applied microbiology}, volume = {54}, number = {5}, pages = {455-461}, doi = {10.1111/j.1472-765X.2012.03226.x}, pmid = {22360305}, issn = {1472-765X}, mesh = {Animals ; Anti-Infective Agents/metabolism ; Argentina ; Bacteriocins/*metabolism ; Brazil ; Cattle ; Electrophoresis, Gel, Pulsed-Field ; Female ; Mastitis, Bovine/*microbiology ; Staphylococcal Infections/microbiology/*veterinary ; Staphylococcus aureus/classification/genetics/isolation &amp; purification/*metabolism ; }, abstract = {AIMS: The main aim of this study was to analyse the genetic relationship amongst 46 Staphylococcus aureus Bac(+) strains isolated in Brazil from 12 geographically distant dairy herds, including 34 isolates that produce the antimicrobial peptide aureocin A70.<br><br>METHODS AND RESULTS: &#x2002; The comparison of 46 Staph. aureus Bac(+) strains was performed by pulsed-field gel electrophoresis (PFGE). Thirteen different pulsotypes were identified, and the subtype A(1) was the most prevalent one. Nine strains belong to pulsotype F, the second most prevalent and mostly confined to a single herd. The PFGE patterns of the 34 Staph. aureus aureocin A70-producers, isolated in Brazil, were also compared with those of strains isolated from bovine mastitis cases in Argentina and revealed that these strains are not genetically related.<br><br>CONCLUSIONS: Although a previous study has suggested that a prevalent pulsotype of aureocin A70-producer Staph. aureus involved in bovine mastitis is disseminated in Argentina, this does not occur in Brazil. Additionally, it was possible to demonstrate that closely related staphylococcal strains can produce distinct staphylococcins.<br><br>This study corroborates the hypothesis of horizontal gene transfer of aureocin A70 genes amongst distinct staphylococcal strains involved in bovine mastitis, giving them a selective advantage when colonizing the mammary glands.}, }
@article {pmid22359677, year = {2012}, author = {Dziewit, L and Baj, J and Szuplewska, M and Maj, A and Tabin, M and Czyzkowska, A and Skrzypczyk, G and Adamczuk, M and Sitarek, T and Stawinski, P and Tudek, A and Wanasz, K and Wardal, E and Piechucka, E and Bartosik, D}, title = {Insights into the transposable mobilome of Paracoccus spp. (Alphaproteobacteria).}, journal = {PloS one}, volume = {7}, number = {2}, pages = {e32277}, pmid = {22359677}, issn = {1932-6203}, mesh = {Alphaproteobacteria/*genetics ; Biological Evolution ; DNA Transposable Elements/*physiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Paracoccus/*genetics ; Plasmids/genetics ; Promoter Regions, Genetic ; }, abstract = {Several trap plasmids (enabling positive selection of transposition events) were used to identify a pool of functional transposable elements (TEs) residing in bacteria of the genus Paracoccus (Alphaproteobacteria). Complex analysis of 25 strains representing 20 species of this genus led to the capture and characterization of (i) 37 insertion sequences (ISs) representing 9 IS families (IS3, IS5, IS6, IS21, IS66, IS256, IS1182, IS1380 and IS1634), (ii) a composite transposon Tn6097 generated by two copies of the ISPfe2 (IS1634 family) containing two predicted genetic modules, involved in the arginine deiminase pathway and daunorubicin/doxorubicin resistance, (iii) 3 non-composite transposons of the Tn3 family, including Tn5393 carrying streptomycin resistance and (iv) a transposable genomic island TnPpa1 (45 kb). Some of the elements (e.g. Tn5393, Tn6097 and ISs of the IS903 group of the IS5 family) were shown to contain strong promoters able to drive transcription of genes placed downstream of the target site of transposition. Through the application of trap plasmid pCM132TC, containing a promoterless tetracycline resistance reporter gene, we identified five ways in which transposition can supply promoters to transcriptionally silent genes. Besides highlighting the diversity and specific features of several TEs, the analyses performed in this study have provided novel and interesting information on (i) the dynamics of the process of transposition (e.g. the unusually high frequency of transposition of TnPpa1) and (ii) structural changes in DNA mediated by transposition (e.g. the generation of large deletions in the recipient molecule upon transposition of ISPve1 of the IS21 family). We also demonstrated the great potential of TEs and transposition in the generation of diverse phenotypes as well as in the natural amplification and dissemination of genetic information (of adaptative value) by horizontal gene transfer, which is considered the driving force of bacterial evolution.}, }
@article {pmid22358420, year = {2011}, author = {Gardella, N and Fernandez, S and Di Gregorio, S and Cuirolo, A and Gutkind, G and Mollerach, M}, title = {[Comparative study of clones from isolates methicillin-resistant Staphylococcus aureus prevalent in Argentina].}, journal = {Revista panamericana de salud publica = Pan American journal of public health}, volume = {30}, number = {6}, pages = {665-666}, doi = {10.1590/s1020-49892011001200028}, pmid = {22358420}, issn = {1680-5348}, mesh = {Argentina/epidemiology ; Biofilms ; Clone Cells ; Cross Infection/epidemiology/microbiology ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Methicillin-Resistant Staphylococcus aureus/drug effects/genetics/*isolation &amp; purification/pathogenicity ; Prevalence ; Staphylococcal Infections/epidemiology/*microbiology ; Virulence/genetics ; }, }
@article {pmid22357598, year = {2012}, author = {Baumdicker, F and Hess, WR and Pfaffelhuber, P}, title = {The infinitely many genes model for the distributed genome of bacteria.}, journal = {Genome biology and evolution}, volume = {4}, number = {4}, pages = {443-456}, pmid = {22357598}, issn = {1759-6653}, mesh = {Bacterial Proteins/genetics ; Evolution, Molecular ; *Genome, Bacterial ; *Models, Genetic ; Phylogeny ; Prochlorococcus/classification/*genetics ; Synechococcus/classification/*genetics ; }, abstract = {The distributed genome hypothesis states that the gene pool of a bacterial taxon is much more complex than that found in a single individual genome. However, the possible fitness advantage, why such genomic diversity is maintained, whether this variation is largely adaptive or neutral, and why these distinct individuals can coexist, remains poorly understood. Here, we present the infinitely many genes (IMG) model, which is a quantitative, evolutionary model for the distributed genome. It is based on a genealogy of individual genomes and the possibility of gene gain (from an unbounded reservoir of novel genes, e.g., by horizontal gene transfer from distant taxa) and gene loss, for example, by pseudogenization and deletion of genes, during reproduction. By implementing these mechanisms, the IMG model differs from existing concepts for the distributed genome, which cannot differentiate between neutral evolution and adaptation as drivers of the observed genomic diversity. Using the IMG model, we tested whether the distributed genome of 22 full genomes of picocyanobacteria (Prochlorococcus and Synechococcus) shows signs of adaptation or neutrality. We calculated the effective population size of Prochlorococcus at 1.01 × 10(11) and predicted 18 distinct clades for this population, only six of which have been isolated and cultured thus far. We predicted that the Prochlorococcus pangenome contains 57,792 genes and found that the evolution of the distributed genome of Prochlorococcus was possibly neutral, whereas that of Synechococcus and the combined sample shows a clear deviation from neutrality.}, }
@article {pmid22355329, year = {2012}, author = {Soares, SC and Abreu, VA and Ramos, RT and Cerdeira, L and Silva, A and Baumbach, J and Trost, E and Tauch, A and Hirata, R and Mattos-Guaraldi, AL and Miyoshi, A and Azevedo, V}, title = {PIPS: pathogenicity island prediction software.}, journal = {PloS one}, volume = {7}, number = {2}, pages = {e30848}, pmid = {22355329}, issn = {1932-6203}, mesh = {Bacteria/*genetics/*pathogenicity ; Bacterial Infections/genetics/microbiology/*pathology ; Computational Biology ; Genome, Bacterial ; Genomic Islands/*genetics ; *Software ; Virulence/*genetics ; }, abstract = {The adaptability of pathogenic bacteria to hosts is influenced by the genomic plasticity of the bacteria, which can be increased by such mechanisms as horizontal gene transfer. Pathogenicity islands play a major role in this type of gene transfer because they are large, horizontally acquired regions that harbor clusters of virulence genes that mediate the adhesion, colonization, invasion, immune system evasion, and toxigenic properties of the acceptor organism. Currently, pathogenicity islands are mainly identified in silico based on various characteristic features: (1) deviations in codon usage, G+C content or dinucleotide frequency and (2) insertion sequences and/or tRNA genetic flanking regions together with transposase coding genes. Several computational techniques for identifying pathogenicity islands exist. However, most of these techniques are only directed at the detection of horizontally transferred genes and/or the absence of certain genomic regions of the pathogenic bacterium in closely related non-pathogenic species. Here, we present a novel software suite designed for the prediction of pathogenicity islands (pathogenicity island prediction software, or PIPS). In contrast to other existing tools, our approach is capable of utilizing multiple features for pathogenicity island detection in an integrative manner. We show that PIPS provides better accuracy than other available software packages. As an example, we used PIPS to study the veterinary pathogen Corynebacterium pseudotuberculosis, in which we identified seven putative pathogenicity islands.}, }
@article {pmid22355227, year = {2011}, author = {Jain, R and Ramineni, S and Parekh, N}, title = {IGIPT - Integrated genomic island prediction tool.}, journal = {Bioinformation}, volume = {7}, number = {6}, pages = {307-310}, pmid = {22355227}, issn = {0973-2063}, abstract = {UNLABELLED: IGIPT is a web-based integrated platform for the identification of genomic islands (GIs). It incorporates thirteen parametric measures based on anomalous nucleotide composition on a single platform, thus improving the predictive power of a horizontally acquired region, since it is known that no single measure can absolutely predict a horizontally transferred region. The tool filters putative GIs based on standard deviation from genomic average and also provides raw output in MS excel format for further analysis. To facilitate the identification of various structural features, viz., tRNA integration sites, repeats, etc. in the vicinity of GIs, the tool provides option to extract the predicted regions and its flanking regions.<br><br>AVAILABILITY: The database is available for free at http://bioinf.iiit.ac.in/IGIPT/}, }
@article {pmid22354297, year = {2012}, author = {Tamang, MD and Nam, HM and Jang, GC and Kim, SR and Chae, MH and Jung, SC and Byun, JW and Park, YH and Lim, SK}, title = {Molecular characterization of extended-spectrum-β-lactamase-producing and plasmid-mediated AmpC β-lactamase-producing Escherichia coli isolated from stray dogs in South Korea.}, journal = {Antimicrobial agents and chemotherapy}, volume = {56}, number = {5}, pages = {2705-2712}, pmid = {22354297}, issn = {1098-6596}, mesh = {Animals ; Animals, Wild ; Anti-Bacterial Agents/*pharmacology ; Cephalosporin Resistance/drug effects/*genetics ; Cephalosporins/*pharmacology ; Dog Diseases/*microbiology ; Dogs ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/classification/drug effects/*genetics/isolation &amp; purification ; Escherichia coli Infections/drug therapy/microbiology/*veterinary ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Phylogeny ; Plasmids/*genetics ; Republic of Korea ; beta-Lactamases/*genetics ; }, abstract = {A total of 47 extended-spectrum-cephalosporin-resistant Escherichia coli strains isolated from stray dogs in 2006 and 2007 in the Republic of Korea were investigated using molecular methods. Extended-spectrum β-lactamase (ESBL) and AmpC β-lactamase phenotypes were identified in 12 and 23 E. coli isolates, respectively. All 12 ESBL-producing isolates carried bla(CTX-M) genes. The most common CTX-M types were CTX-M-14 (n = 5) and CTX-M-24 (n = 3). Isolates producing CTX-M-3, CTX-M-55, CTX-M-27, and CTX-M-65 were also identified. Twenty-one of 23 AmpC β-lactamase-producing isolates were found to carry bla(CMY-2) genes. TEM-1 was associated with CTX-M and CMY-2 β-lactamases in 4 and 15 isolates, respectively. In addition to bla(TEM-1), two isolates carried bla(DHA-1), and one of them cocarried bla(CMY-2). Both CTX-M and CMY-2 genes were located on large (40 to 170 kb) conjugative plasmids that contained the insertion sequence ISEcp1 upstream of the bla genes. Only in the case of CTX-M genes was there an IS903 sequence downstream of the gene. The spread of ESBLs and AmpC β-lactamases occurred via both horizontal gene transfer, accounting for much of the CTX-M gene dissemination, and clonal spread, accounting for CMY-2 gene dissemination. The horizontal dissemination of bla(CTX-M) and bla(CMY-2) genes was mediated by IncF and IncI1-Iγ plasmids, respectively. The clonal spread of bla(CMY-2) was driven mainly by E. coli strains of virulent phylogroup D lineage ST648. To our knowledge, this is the first report of bla(DHA-1) in E. coli strains isolated from companion animals. This study also represents the first report of CMY-2 β-lactamase-producing E. coli isolates from dogs in the Republic of Korea.}, }
@article {pmid22354295, year = {2012}, author = {Giske, CG and Fröding, I and Hasan, CM and Turlej-Rogacka, A and Toleman, M and Livermore, D and Woodford, N and Walsh, TR}, title = {Diverse sequence types of Klebsiella pneumoniae contribute to the dissemination of blaNDM-1 in India, Sweden, and the United Kingdom.}, journal = {Antimicrobial agents and chemotherapy}, volume = {56}, number = {5}, pages = {2735-2738}, pmid = {22354295}, issn = {1098-6596}, support = {G1100135/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Electrophoresis, Gel, Pulsed-Field ; Gene Transfer, Horizontal ; Humans ; India ; Klebsiella pneumoniae/*genetics/isolation &amp; purification/pathogenicity ; Multilocus Sequence Typing ; Phylogeography ; Plasmids/genetics ; Polymerase Chain Reaction ; Replicon/genetics ; Serotyping ; Sweden ; United Kingdom ; beta-Lactam Resistance/*genetics ; beta-Lactamases/*genetics ; }, abstract = {Clinical isolates of Klebsiella pneumoniae producing NDM-1 carbapenemase from India (n = 22), the United Kingdom (n = 13), and Sweden (n = 4) were subjected to multilocus sequence typing (MLST), automated repetitive sequence-based PCR (rep-PCR), serotyping, virulence gene screening, and plasmid replicon typing. The most frequently detected MLST sequence types (STs) were ST14 (n = 13; all serotype K2), ST11, ST149, ST231, and ST147. The correlation between MLST and automated rep-PCR was excellent. IncA/C was the most frequently detected plasmid replicon type (n = 14). ST14, ST11, and other successful clones may be important for the dissemination of bla(NDM-1).}, }
@article {pmid22351985, year = {2011}, author = {Isaza, LA and Opelt, K and Wagner, T and Mattes, E and Bieber, E and Hatley, EO and Roth, G and Sanjuán, J and Fischer, HM and Sandermann, H and Hartmann, A and Ernst, D}, title = {Lack of glyphosate resistance gene transfer from Roundup Ready soybean to Bradyrhizobium japonicum under field and laboratory conditions.}, journal = {Zeitschrift fur Naturforschung. C, Journal of biosciences}, volume = {66}, number = {11-12}, pages = {595-604}, doi = {10.1515/znc-2011-11-1209}, pmid = {22351985}, issn = {0939-5075}, mesh = {Base Sequence ; Bradyrhizobium/*genetics ; DNA Primers ; *Gene Transfer Techniques ; Glycine/*analogs &amp; derivatives/pharmacology ; Insecticide Resistance/*genetics ; Plants, Genetically Modified ; Polymerase Chain Reaction ; Glycine max/*genetics ; Glyphosate ; }, abstract = {A field study was conducted at the Russell E. Larson Agricultural Research Center to determine the effect of transgenic glyphosate-resistant soybean in combination with herbicide (Roundup) application on its endosymbiont Bradyrhizobium japonicum. DNA of bacteroids from isolated nodules was analysed for the presence of the transgenic 5-enolpyruvylshikimate-3-phosphate synthase (CP4-EPSPS) DNA sequence using polymerase chain reaction (PCR). To further assess the likelihood that the EPSPS gene may be transferred from the Roundup Ready (RR) soybean to B. japonicum, we have examined the natural transformation efficiency of B. japonicum strain 110spc4. Analyses of nodules showed the presence of the transgenic EPSPS DNA sequence. In bacteroids that were isolated from nodules of transgenic soybean plants and then cultivated in the presence of glyphosate this sequence could not be detected. This indicates that no stable horizontal gene transfer (HGT) of the EPSPS gene had occurred under field conditions. Under laboratory conditions, no natural transformation was detected in B. japonicum strain 110spc4 in the presence of various amounts of recombinant plasmid DNA. Our results indicate that no natural competence state exists in B. japonicum 110spc4. Results from field and laboratory studies indicate the lack of functional transfer of the CP4-EPSPS gene from glyphosate-tolerant soybean treated with glyphosate to root-associated B. japonicum.}, }
@article {pmid22348436, year = {2012}, author = {Ignacio-Espinoza, JC and Sullivan, MB}, title = {Phylogenomics of T4 cyanophages: lateral gene transfer in the 'core' and origins of host genes.}, journal = {Environmental microbiology}, volume = {14}, number = {8}, pages = {2113-2126}, doi = {10.1111/j.1462-2920.2012.02704.x}, pmid = {22348436}, issn = {1462-2920}, mesh = {Bacteriophage T4/*classification/*genetics ; Biological Evolution ; Cyanobacteria/virology ; *Gene Transfer, Horizontal ; *Genome, Viral ; Oceans and Seas ; *Phylogeny ; Prochlorococcus/genetics/virology ; Recombination, Genetic ; }, abstract = {The last two decades have revealed that phages (viruses that infect bacteria) are abundant and play fundamental roles in the Earth System, with the T4-like myoviruses (herein T4-like phages) emerging as a dominant 'signal' in wild populations. Here we examine 27 T4-like phage genomes, with a focus on 17 that infect ocean picocyanobacteria (cyanophages), to evaluate lateral gene transfer (LGT) in this group. First, we establish a reference tree by evaluating concatenated core gene supertrees and whole genome gene content trees. Next, we evaluate what fraction of these 'core genes' shared by all 17 cyanophages appear prone to LGT. Most (47 out of 57 core genes) were vertically transferred as inferred from tree tests and genomic synteny. Of those 10 core genes that failed the tree tests, the bulk (8 of 10) remain syntenic in the genomes with only a few (3 of the 10) having identifiable signatures of mobile elements. Notably, only one of these 10 is shared not only by the 17 cyanophages, but also by all 27 T4-like phages (thymidylate synthase); its evolutionary history suggests cyanophages may be the origin of these genes to Prochlorococcus. Next, we examined intragenic recombination among the core genes and found that it did occur, even among these core genes, but that the rate was significantly higher between closely related phages, perhaps reducing any detectable LGT signal and leading to taxon cohesion. Finally, among 18 auxiliary metabolic genes (AMGs, a.k.a. 'host' genes), we found that half originated from their immediate hosts, in some cases multiple times (e.g. psbA, psbD, pstS), while the remaining have less clear evolutionary origins ranging from cyanobacteria (4 genes) or microbes (5 genes), with particular diversity among viral TalC and Hsp20 sequences. Together, these findings highlight the patterns and limits of vertical evolution, as well as the ecological and evolutionary roles of LGT in shaping T4-like phage genomes.}, }
@article {pmid22347461, year = {2012}, author = {Yue, WF and Du, M and Zhu, MJ}, title = {High temperature in combination with UV irradiation enhances horizontal transfer of stx2 gene from E. coli O157:H7 to non-pathogenic E. coli.}, journal = {PloS one}, volume = {7}, number = {2}, pages = {e31308}, pmid = {22347461}, issn = {1932-6203}, support = {P20 RR016474/RR/NCRR NIH HHS/United States ; P20RR016474/RR/NCRR NIH HHS/United States ; }, mesh = {Escherichia coli/*genetics ; Escherichia coli O157/*genetics ; *Gene Transfer, Horizontal/radiation effects ; *Hot Temperature ; Shiga Toxin/genetics ; *Ultraviolet Rays ; }, abstract = {BACKGROUND: Shiga toxin (stx) genes have been transferred to numerous bacteria, one of which is E. coli O157:H7. It is a common belief that stx gene is transferred by bacteriophages, because stx genes are located on lambdoid prophages in the E. coli O157:H7 genome. Both E. coli O157:H7 and non-pathogenic E. coli are highly enriched in cattle feedlots. We hypothesized that strong UV radiation in combination with high temperature accelerates stx gene transfer into non-pathogenic E. coli in feedlots.<br><br>E. coli O157:H7 EDL933 strain were subjected to different UV irradiation (0 or 0.5 kJ/m(2)) combination with different temperature (22, 28, 30, 32, and 37 &#xb0;C) treatments, and the activation of lambdoid prophages was analyzed by plaque forming unit while induction of Stx2 prophages was quantified by quantitative real-time PCR. Data showed that lambdoid prophages in E. coli O157:H7, including phages carrying stx2, were activated under UV radiation, a process enhanced by elevated temperature. Consistently, western blotting analysis indicated that the production of Shiga toxin 2 was also dramatically increased by UV irradiation and high temperature. In situ colony hybridization screening indicated that these activated Stx2 prophages were capable of converting laboratory strain of E. coli K12 into new Shiga toxigenic E. coli, which were further confirmed by PCR and ELISA analysis.<br><br>CONCLUSIONS/SIGNIFICANCE: These data implicate that high environmental temperature in combination with UV irradiation accelerates the spread of stx genes through enhancing Stx prophage induction and Stx phage mediated gene transfer. Cattle feedlot sludge are teemed with E. coli O157:H7 and non-pathogenic E. coli, and is frequently exposed to UV radiation via sunlight, which may contribute to the rapid spread of stx gene to non-pathogenic E. coli and diversity of shiga toxin producing E. coli.}, }
@article {pmid22346340, year = {2012}, author = {Zhu, B and Zhou, Q and Xie, G and Zhang, G and Zhang, X and Wang, Y and Sun, G and Li, B and Jin, G}, title = {Interkingdom gene transfer may contribute to the evolution of phytopathogenicity in botrytis cinerea.}, journal = {Evolutionary bioinformatics online}, volume = {8}, number = {}, pages = {105-117}, pmid = {22346340}, issn = {1176-9343}, abstract = {The ascomycete Botrytis cinerea is a phytopathogenic fungus infecting and causing significant yield losses in a number of crops. The genome of B. cinerea has been fully sequenced while the importance of horizontal gene transfer (HGT) to extend the host range in plant pathogenic fungi has been recently appreciated. However, recent data confirm that the B. cinerea fungus shares conserved virulence factors with other fungal plant pathogens with narrow host range. Therefore, interkingdom HGT may contribute to the evolution of phytopathogenicity in B. cinerea. In this study, a stringent genome comparison pipeline was used to identify potential genes that have been obtained by B. cinerea but not by other fungi through interkingdom HGT. This search led to the identification of four genes: a UDP-glucosyltransferase (UGT), a lipoprotein and two alpha/beta hydrolase fold proteins. Phylogenetic analysis of the four genes suggests that B. cinerea acquired UGT from plants and the other 3 genes from bacteria. Based on the known gene functions and literature searching, a correlation between gene acquision and the evolution of pathogenicity in B. cinerea can be postulated.}, }
@article {pmid22345387, year = {2012}, author = {Bogaerts, P and Rezende de Castro, R and Roisin, S and Deplano, A and Huang, TD and Hallin, M and Denis, O and Glupczynski, Y}, title = {Emergence of NDM-1-producing Acinetobacter baumannii in Belgium.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {67}, number = {6}, pages = {1552-1553}, doi = {10.1093/jac/dks041}, pmid = {22345387}, issn = {1460-2091}, mesh = {Acinetobacter Infections/*epidemiology/*microbiology ; Acinetobacter baumannii/*enzymology/isolation &amp; purification ; Anti-Bacterial Agents/pharmacology ; Belgium/epidemiology ; Gene Transfer, Horizontal ; Humans ; Male ; Microbial Sensitivity Tests ; Plasmids ; beta-Lactamases/*metabolism ; beta-Lactams/pharmacology ; }, }
@article {pmid22344442, year = {2012}, author = {Price, DC and Chan, CX and Yoon, HS and Yang, EC and Qiu, H and Weber, AP and Schwacke, R and Gross, J and Blouin, NA and Lane, C and Reyes-Prieto, A and Durnford, DG and Neilson, JA and Lang, BF and Burger, G and Steiner, JM and Löffelhardt, W and Meuser, JE and Posewitz, MC and Ball, S and Arias, MC and Henrissat, B and Coutinho, PM and Rensing, SA and Symeonidi, A and Doddapaneni, H and Green, BR and Rajah, VD and Boore, J and Bhattacharya, D}, title = {Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants.}, journal = {Science (New York, N.Y.)}, volume = {335}, number = {6070}, pages = {843-847}, doi = {10.1126/science.1213561}, pmid = {22344442}, issn = {1095-9203}, support = {MSP-14226//Canadian Institutes of Health Research/Canada ; }, mesh = {Biological Evolution ; Cyanobacteria/genetics ; Cyanophora/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Plant ; Molecular Sequence Data ; Photosynthesis/*genetics ; Phylogeny ; Symbiosis ; }, abstract = {The primary endosymbiotic origin of the plastid in eukaryotes more than 1 billion years ago led to the evolution of algae and plants. We analyzed draft genome and transcriptome data from the basally diverging alga Cyanophora paradoxa and provide evidence for a single origin of the primary plastid in the eukaryote supergroup Plantae. C. paradoxa retains ancestral features of starch biosynthesis, fermentation, and plastid protein translocation common to plants and algae but lacks typical eukaryotic light-harvesting complex proteins. Traces of an ancient link to parasites such as Chlamydiae were found in the genomes of C. paradoxa and other Plantae. Apparently, Chlamydia-like bacteria donated genes that allow export of photosynthate from the plastid and its polymerization into storage polysaccharide in the cytosol.}, }
@article {pmid22342748, year = {2012}, author = {Christin, PA and Edwards, EJ and Besnard, G and Boxall, SF and Gregory, R and Kellogg, EA and Hartwell, J and Osborne, CP}, title = {Adaptive evolution of C(4) photosynthesis through recurrent lateral gene transfer.}, journal = {Current biology : CB}, volume = {22}, number = {5}, pages = {445-449}, doi = {10.1016/j.cub.2012.01.054}, pmid = {22342748}, issn = {1879-0445}, support = {BB/F009313/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Biological Evolution ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Molecular Sequence Data ; Photosynthesis/*genetics ; Phylogeny ; Plant Leaves/genetics ; Plant Proteins/genetics/metabolism ; Poaceae/classification/cytology/*genetics ; Sequence Alignment ; Sequence Analysis, Protein ; Transcriptome ; }, abstract = {C(4) photosynthesis is a complex trait that confers higher productivity under warm and arid conditions. It has evolved more than 60 times via the co-option of genes present in C(3) ancestors followed by alteration of the patterns and levels of expression and adaptive changes in the coding sequences, but the evolutionary path to C(4) photosynthesis is still poorly understood. The grass lineage Alloteropsis offers unparalleled opportunities for studying C(4) evolution, because it includes a C(3) taxon and five C(4) species that vary significantly in C(4) anatomy and biochemistry. Using phylogenetic analyses of nuclear genes and leaf transcriptomes, we show that fundamental elements of the C(4) pathway in the grass lineage Alloteropsis were acquired via a minimum of four independent lateral gene transfers from C(4) taxa that diverged from this group more than 20 million years ago. The transfer of genes that were already fully adapted for C(4) function has occurred periodically over at least the last 10 million years and has been a recurrent source for the optimization of the C(4) pathway. This report shows that plant-plant lateral nuclear gene transfers can be a potent source of genetic novelty and adaptation in flowering plants.}, }
@article {pmid22337920, year = {2012}, author = {Chan, CX and Zäuner, S and Wheeler, G and Grossman, AR and Prochnik, SE and Blouin, NA and Zhuang, Y and Benning, C and Berg, GM and Yarish, C and Eriksen, RL and Klein, AS and Lin, S and Levine, I and Brawley, SH and Bhattacharya, D}, title = {Analysis of Porphyra membrane transporters demonstrates gene transfer among photosynthetic eukaryotes and numerous sodium-coupled transport systems.}, journal = {Plant physiology}, volume = {158}, number = {4}, pages = {2001-2012}, pmid = {22337920}, issn = {1532-2548}, mesh = {Aquaporins/metabolism ; Biological Transport/genetics ; Calcium Signaling/genetics ; Eukaryota/*genetics ; Evolution, Molecular ; Expressed Sequence Tags ; Fresh Water ; Gene Transfer, Horizontal/*genetics ; Genes ; Ion Transport/genetics ; Lipid Metabolism/genetics ; Membrane Transport Proteins/*genetics/metabolism ; Molecular Sequence Data ; Nitrates/metabolism ; Photosynthesis/*genetics ; Phylogeny ; Porphyra/*genetics ; Quaternary Ammonium Compounds/metabolism ; Seawater ; Sodium/*metabolism ; Transcriptome/genetics ; }, abstract = {Membrane transporters play a central role in many cellular processes that rely on the movement of ions and organic molecules between the environment and the cell, and between cellular compartments. Transporters have been well characterized in plants and green algae, but little is known about transporters or their evolutionary histories in the red algae. Here we examined 482 expressed sequence tag contigs that encode putative membrane transporters in the economically important red seaweed Porphyra (Bangiophyceae, Rhodophyta). These contigs are part of a comprehensive transcriptome dataset from Porphyra umbilicalis and Porphyra purpurea. Using phylogenomics, we identified 30 trees that support the expected monophyly of red and green algae/plants (i.e. the Plantae hypothesis) and 19 expressed sequence tag contigs that show evidence of endosymbiotic/horizontal gene transfer involving stramenopiles. The majority (77%) of analyzed contigs encode transporters with unresolved phylogenies, demonstrating the difficulty in resolving the evolutionary history of genes. We observed molecular features of many sodium-coupled transport systems in marine algae, and the potential for coregulation of Porphyra transporter genes that are associated with fatty acid biosynthesis and intracellular lipid trafficking. Although both the tissue-specific and subcellular locations of the encoded proteins require further investigation, our study provides red algal gene candidates associated with transport functions and novel insights into the biology and evolution of these transporters.}, }
@article {pmid22334601, year = {2012}, author = {Schink, AK and Kadlec, K and Schwarz, S}, title = {Detection of qnr genes among Escherichia coli isolates of animal origin and complete sequence of the conjugative qnrB19-carrying plasmid pQNR2078.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {67}, number = {5}, pages = {1099-1102}, doi = {10.1093/jac/dks024}, pmid = {22334601}, issn = {1460-2091}, mesh = {Animals ; Cluster Analysis ; Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; Escherichia coli/classification/*genetics/*isolation &amp; purification ; Escherichia coli Infections/microbiology/*veterinary ; Escherichia coli Proteins/*genetics ; Gene Transfer, Horizontal ; Genotype ; Horse Diseases/*microbiology ; Horses ; Molecular Sequence Data ; Multilocus Sequence Typing ; *Plasmids ; Sequence Analysis, DNA ; }, abstract = {OBJECTIVES: The aims of this study were to identify qnr genes among quinolone-resistant Escherichia coli isolates from defined disease conditions of companion and farm animals obtained in the BfT-GermVet study, and to gain insight into their localization and the organization of the qnr gene regions.<br><br>METHODS: The qnr genes were detected by PCR and confirmed by sequencing. qnr-positive isolates were checked for mutations in DNA gyrase and topoisomerase IV genes by PCR and sequencing of the quinolone resistance-determining regions. Multilocus sequence typing (MLST) was performed for the qnr-positive E. coli isolates. Plasmids harbouring qnr genes were transferred by conjugation into E. coli recipients, subjected to PCR-based replicon typing and plasmid-MLST, and one qnrB19-carrying plasmid was sequenced completely.<br><br>RESULTS: Only 2 of 417 E. coli isolates investigated carried qnr genes. Both isolates originated from horses and showed MLST type ST86. They harboured conjugative qnrB19-carrying plasmids, which proved to be indistinguishable by restriction analysis, belonged to incompatibility group IncN, showed plasmid-MLST type ST8 and did not carry other resistance genes. The qnrB19 gene was flanked by copies of the insertion sequence IS26. One of these plasmids, pQNR2078, was sequenced completely and had a size of 42&#x200a;379 bp. Except for the resistance gene region, plasmid pQNR2078 closely resembled the bla(CTX-M-65)-carrying plasmid pKC396 from E. coli.<br><br>CONCLUSIONS: qnr genes were rarely detected among E. coli from animals in the BfT-GermVet study. The qnrB19 gene was detected on conjugative plasmids, with IS26 being likely involved in the mobility of qnrB19.}, }
@article {pmid22331590, year = {2012}, author = {Wang, Y and He, T and Schwarz, S and Zhou, D and Shen, Z and Wu, C and Wang, Y and Ma, L and Zhang, Q and Shen, J}, title = {Detection of the staphylococcal multiresistance gene cfr in Escherichia coli of domestic-animal origin.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {67}, number = {5}, pages = {1094-1098}, doi = {10.1093/jac/dks020}, pmid = {22331590}, issn = {1460-2091}, mesh = {Animals ; Animals, Domestic ; Bacterial Proteins/*genetics ; Blotting, Southern ; Chickens ; Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; Ducks ; Escherichia coli/*genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Plasmids ; Polymerase Chain Reaction ; Promoter Regions, Genetic ; Sequence Analysis, DNA ; Swine ; Transcription Initiation Site ; }, abstract = {OBJECTIVES: To investigate the presence and the genetic environment of the multiresistance gene cfr in Escherichia coli found in domestic animals.<br><br>METHODS: A total of 1230 E. coli isolates, collected from pigs, chickens and ducks, were screened by PCR for the cfr gene. The location of the cfr gene was determined by Southern blotting, the transferability of cfr gene was tested by conjugation and transformation, and the regions flanking the cfr gene were sequenced by a modified random primer walking strategy. The location of the cfr promoter sequence was analysed by mapping the cfr transcription start site using rapid amplification of 5' cDNA ends (5' RACE).<br><br>RESULTS: Only a single strain from the nasal swab of a pig harboured the cfr gene. Southern blotting indicated that the cfr gene was located on a ~110 kb plasmid, designated pEC-01. A cfr-carrying segment of 1545 bp with a sequence identical to that of the cfr-harbouring plasmid pSCFS1 was flanked by two IS26 elements in the same orientation. The IS26 transposition created a new hybrid promoter in which the -35 region was part of the left inverted repeat of IS26 while the -10-like sequence was part of the original cfr upstream region.<br><br>CONCLUSIONS: To the best of our knowledge, this is the first report of the cfr gene in a naturally occurring E. coli strain. Continued surveillance of the presence of the cfr gene in Gram-negative bacteria of domestic-animal origin is warranted.}, }
@article {pmid22330911, year = {2012}, author = {Novais, &#xc2; and Viana, D and Baquero, F and Martínez-Botas, J and Cantón, R and Coque, TM}, title = {Contribution of IncFII and broad-host IncA/C and IncN plasmids to the local expansion and diversification of phylogroup B2 Escherichia coli ST131 clones carrying blaCTX-M-15 and qnrS1 genes.}, journal = {Antimicrobial agents and chemotherapy}, volume = {56}, number = {5}, pages = {2763-2766}, pmid = {22330911}, issn = {1098-6596}, mesh = {Anti-Bacterial Agents/pharmacology ; Clone Cells ; Drug Resistance, Multiple, Bacterial/genetics ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/drug effects/*genetics/isolation &amp; purification/pathogenicity ; Escherichia coli Infections/microbiology ; Escherichia coli Proteins/*genetics ; Gene Transfer, Horizontal ; Host Specificity ; Humans ; Phylogeny ; Plasmids/*genetics ; Recombination, Genetic ; Spain ; beta-Lactamases/*genetics ; }, abstract = {The recent increase of CTX-M-15-producing Escherichia coli isolates in our institution was caused by diverse clonal backgrounds, including mainly B2 sequence type 131 (ST131) clones presenting variable virulence profiles but also A(1) (ST617, ST410), B1, and D(1) (ST405) clones. Besides IncFII-pC15-1a, we detected multidrug-resistant IncA/C(2) and IncN plasmids carrying bla(CTX-M-15) and/or qnrS1. Our study highlights the diversification of highly transmissible resistant and virulent clones and the recombinogenic potential of broad-host plasmids contributing to the expansion of genetic regions coding for multidrug resistance to other bacterial lineages.}, }
@article {pmid22330759, year = {2012}, author = {Zámocký, M and Gasselhuber, B and Furtmüller, PG and Obinger, C}, title = {Molecular evolution of hydrogen peroxide degrading enzymes.}, journal = {Archives of biochemistry and biophysics}, volume = {525}, number = {2}, pages = {131-144}, pmid = {22330759}, issn = {1096-0384}, support = {W 1224/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Bacterial Proteins/metabolism ; Catalase/chemistry/metabolism ; Catalytic Domain ; Escherichia coli Proteins/metabolism ; Evolution, Molecular ; Gene Transfer Techniques ; Heme/chemistry ; Hydrogen Peroxide/*chemistry ; Manganese/chemistry ; Models, Chemical ; Peroxidase/chemistry ; Phylogeny ; Proteins/chemistry ; Sequence Analysis, DNA ; }, abstract = {For efficient removal of intra- and/or extracellular hydrogen peroxide by dismutation to harmless dioxygen and water (2H(2)O(2) → O(2) + 2H(2)O), nature designed three metalloenzyme families that differ in oligomeric organization, monomer architecture as well as active site geometry and catalytic residues. Here we report on the updated reconstruction of the molecular phylogeny of these three gene families. Ubiquitous typical (monofunctional) heme catalases are found in all domains of life showing a high structural conservation. Their evolution was directed from large subunit towards small subunit proteins and further to fused proteins where the catalase fold was retained but lost its original functionality. Bifunctional catalase-peroxidases were at the origin of one of the two main heme peroxidase superfamilies (i.e. peroxidase-catalase superfamily) and constitute a protein family predominantly present among eubacteria and archaea, but two evolutionary branches are also found in the eukaryotic world. Non-heme manganese catalases are a relatively small protein family with very old roots only present among bacteria and archaea. Phylogenetic analyses of the three protein families reveal features typical (i) for the evolution of whole genomes as well as (ii) for specific evolutionary events including horizontal gene transfer, paralog formation and gene fusion. As catalases have reached a striking diversity among prokaryotic and eukaryotic pathogens, understanding their phylogenetic and molecular relationship and function will contribute to drug design for prevention of diseases of humans, animals and plants.}, }
@article {pmid22328943, year = {2012}, author = {Dana, CE and Glauber, KM and Chan, TA and Bridge, DM and Steele, RE}, title = {Incorporation of a horizontally transferred gene into an operon during cnidarian evolution.}, journal = {PloS one}, volume = {7}, number = {2}, pages = {e31643}, pmid = {22328943}, issn = {1932-6203}, support = {R01 AG037965/AG/NIA NIH HHS/United States ; R24 GM080537/GM/NIGMS NIH HHS/United States ; 1R01AG037965-01/AG/NIA NIH HHS/United States ; 1R24GM080537-01A1/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; Cnidaria/classification/*genetics ; Gene Transfer, Horizontal/*genetics ; Genome/genetics ; Phylogeny ; }, abstract = {Genome sequencing has revealed examples of horizontally transferred genes, but we still know little about how such genes are incorporated into their host genomes. We have previously reported the identification of a gene (flp) that appears to have entered the Hydra genome through horizontal transfer. Here we provide additional evidence in support of our original hypothesis that the transfer was from a unicellular organism, and we show that the transfer occurred in an ancestor of two medusozoan cnidarian species. In addition we show that the gene is part of a bicistronic operon in the Hydra genome. These findings identify a new animal phylum in which trans-spliced leader addition has led to the formation of operons, and define the requirements for evolution of an operon in Hydra. The identification of operons in Hydra also provides a tool that can be exploited in the construction of transgenic Hydra strains.}, }
@article {pmid22328640, year = {2012}, author = {Smet, A and Boyen, F and Flahou, B and Doublet, B and Praud, K and Martens, A and Butaye, P and Cloeckaert, A and Haesebrouck, F}, title = {Emergence of CTX-M-2-producing Escherichia coli in diseased horses: evidence of genetic exchanges of bla(CTX-M-2) linked to ISCR1.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {67}, number = {5}, pages = {1289-1291}, doi = {10.1093/jac/dks016}, pmid = {22328640}, issn = {1460-2091}, mesh = {Animals ; Escherichia coli/*enzymology/*isolation &amp; purification ; Escherichia coli Infections/microbiology/*veterinary ; Gene Transfer, Horizontal ; Horse Diseases/*microbiology ; Horses ; Plasmids ; beta-Lactamases/*metabolism ; }, }
@article {pmid22327591, year = {2012}, author = {Lee, S and Ward, TJ and Siletzky, RM and Kathariou, S}, title = {Two novel type II restriction-modification systems occupying genomically equivalent locations on the chromosomes of Listeria monocytogenes strains.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {8}, pages = {2623-2630}, pmid = {22327591}, issn = {1098-5336}, mesh = {Bacteriophages/growth &amp; development ; *Chromosomes, Bacterial ; Cluster Analysis ; DNA Restriction-Modification Enzymes/*genetics ; DNA, Bacterial/chemistry/genetics/metabolism ; Electrophoresis, Gel, Pulsed-Field ; Listeria monocytogenes/classification/*enzymology/*genetics/virology ; Molecular Sequence Data ; Molecular Typing ; Sequence Analysis, DNA ; *Synteny ; }, abstract = {Listeria monocytogenes is responsible for the potentially life-threatening food-borne disease listeriosis. One epidemic-associated clonal group of L. monocytogenes, epidemic clone I (ECI), harbors a Sau3AI-like restriction-modification (RM) system also present in the same genomic region in certain strains of other lineages. In this study, we identified and characterized two other, novel type II RM systems, LmoJ2 and LmoJ3, at this same locus. LmoJ2 and LmoJ3 appeared to recognize GCWGC (W = A or T) and GCNGC, respectively. Both RM systems consisted of genes with GC content below the genome average and were in the same genomic region in strains of different serotypes and lineages, suggesting site-specific horizontal gene transfer. Genomic DNA from the LmoJ2 and LmoJ3 strains grown at various temperatures (4 to 42°C) was resistant to digestion with restriction enzymes recognizing GCWGC or GCNGC, indicating that the methyltransferases were expressed under these conditions. Phages propagated in an LmoJ2-harboring strain exhibited moderately increased infectivity for this strain at 4 and 8°C but not at higher temperatures, while phages propagated in an LmoJ3 strain had dramatically increased infectivity for this strain at all temperatures. Among the sequenced Listeria phages, lytic phages possessed significantly fewer recognition sites for these RM systems than lysogenic phages, suggesting that in lytic phages sequence content evolved toward reduced susceptibility to such RM systems. The ability of LmoJ2 and LmoJ3 to protect against phages may affect the efficiency of phages as biocontrol agents for L. monocytogenes strains harboring these RM systems.}, }
@article {pmid22326849, year = {2012}, author = {Eikmeyer, F and Hadiati, A and Szczepanowski, R and Wibberg, D and Schneiker-Bekel, S and Rogers, LM and Brown, CJ and Top, EM and Pühler, A and Schlüter, A}, title = {The complete genome sequences of four new IncN plasmids from wastewater treatment plant effluent provide new insights into IncN plasmid diversity and evolution.}, journal = {Plasmid}, volume = {68}, number = {1}, pages = {13-24}, doi = {10.1016/j.plasmid.2012.01.011}, pmid = {22326849}, issn = {1095-9890}, mesh = {Base Sequence ; Conserved Sequence ; DNA Replication ; DNA Transposable Elements ; Drug Resistance, Microbial/*genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Integrons ; Molecular Sequence Data ; Phylogeny ; Plasmids/*genetics ; Replication Origin ; Waste Disposal, Fluid/*methods ; }, abstract = {The dissemination of antibiotic resistance genes among bacteria often occurs by means of plasmids. Wastewater treatment plants (WWTP) were previously recognized as hot spots for the horizontal transfer of genetic material. One of the plasmid groups that is often associated with drug resistance is the incompatibility group IncN. The aim of this study was to gain insights into the diversity and evolutionary history of IncN plasmids by determining and comparing the complete genome sequences of the four novel multi-drug resistance plasmids pRSB201, pRSB203, pRSB205 and pRSB206 that were exogenously isolated from the final effluent of a municipal WWTP. Their sizes range between 42,875 bp and 56,488 bp and they share a common set of backbone modules that encode plasmid replication initiation, conjugative transfer, and plasmid maintenance and control. All plasmids are transferable at high rates between Escherichia coli strains, but did not show a broad host range. Different genes conferring resistances to ampicillin, streptomycin, spectinomycin, sulfonamides, tetracycline and trimethoprim were identified in accessory modules inserted in these plasmids. Comparative analysis of the four WWTP IncN plasmids and IncN plasmids deposited in the NCBI database enabled the definition of a core set of backbone genes for this group. Moreover, this approach revealed a close phylogenetic relationship between the IncN plasmids isolated from environmental and clinical samples. Phylogenetic analysis also suggests the existence of host-specific IncN plasmid subgroups. In conclusion, IncN plasmids likely contribute to the dissemination of resistance determinants between environmental bacteria and clinical strains. This is of particular importance since multi-drug resistance IncN plasmids have been previously identified in members of the Enterobacteriaceae that cause severe infections in humans.}, }
@article {pmid22325062, year = {2012}, author = {Bohlin, J and van Passel, MW and Snipen, L and Kristoffersen, AB and Ussery, D and Hardy, SP}, title = {Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {66}, pmid = {22325062}, issn = {1471-2164}, mesh = {Bacteriophages/*genetics ; Chromosomes, Bacterial/*genetics ; DNA, Bacterial/chemistry ; Entropy ; Gene Transfer, Horizontal ; *Genomic Islands ; Mycobacterium leprae/genetics ; Mycobacterium tuberculosis/genetics ; Plasmids/*genetics ; }, abstract = {BACKGROUND: We sought to assess whether the concept of relative entropy (information capacity), could aid our understanding of the process of horizontal gene transfer in microbes. We analyzed the differences in information capacity between prokaryotic chromosomes, genomic islands (GI), phages, and plasmids. Relative entropy was estimated using the Kullback-Leibler measure.<br><br>RESULTS: Relative entropy was highest in bacterial chromosomes and had the sequence chromosomes > GI > phage > plasmid. There was an association between relative entropy and AT content in chromosomes, phages, plasmids and GIs with the strongest association being in phages. Relative entropy was also found to be lower in the obligate intracellular Mycobacterium leprae than in the related M. tuberculosis when measured on a shared set of highly conserved genes.<br><br>CONCLUSIONS: We argue that relative entropy differences reflect how plasmids, phages and GIs interact with microbial host chromosomes and that all these biological entities are, or have been, subjected to different selective pressures. The rate at which amelioration of horizontally acquired DNA occurs within the chromosome is likely to account for the small differences between chromosomes and stably incorporated GIs compared to the transient or independent replicons such as phages and plasmids.}, }
@article {pmid22319625, year = {2012}, author = {Wang, J and Wang, A and Han, Z and Zhang, Z and Li, F and Li, X}, title = {Characterization of three novel SINE families with unusual features in Helicoverpa armigera.}, journal = {PloS one}, volume = {7}, number = {2}, pages = {e31355}, pmid = {22319625}, issn = {1932-6203}, mesh = {Animals ; Gene Transfer, Horizontal ; Genes, Insect/*genetics ; Insecta ; RNA, Ribosomal, 5S ; RNA, Transfer ; *Short Interspersed Nucleotide Elements ; }, abstract = {Although more than 120 families of short interspersed nuclear elements (SINEs) have been isolated from the eukaryotic genomes, little is known about SINEs in insects. Here, we characterize three novel SINEs from the cotton bollworm, Helicoverpa armigera. Two of them, HaSE1 and HaSE2, share similar 5' -structure including a tRNA-related region immediately followed by conserved central domain. The 3' -tail of HaSE1 is significantly similar to that of one LINE retrotransposon element, HaRTE1.1, in H. armigera genome. The 3' -region of HaSE2 showed high identity with one mariner-like element in H. armigera. The third family, termed HaSE3, is a 5S rRNA-derived SINE and shares both body part and 3'-tail with HaSE1, thus may represent the first example of a chimera generated by recombination between 5S rRNA and tRNA-derived SINE in insect species. Further database searches revealed the presence of these SINEs in several other related insect species, but not in the silkworm, Bombyx mori, indicating a relatively narrow distribution of these SINEs in Lepidopterans. Apart from above, we found a copy of HaSE2 in the GenBank EST entry for the cotton aphid, Aphis gossypii, suggesting the occurrence of horizontal transfer.}, }
@article {pmid22319613, year = {2012}, author = {Ishikawa, FH and Souza, EA and Shoji, JY and Connolly, L and Freitag, M and Read, ND and Roca, MG}, title = {Heterokaryon incompatibility is suppressed following conidial anastomosis tube fusion in a fungal plant pathogen.}, journal = {PloS one}, volume = {7}, number = {2}, pages = {e31175}, pmid = {22319613}, issn = {1932-6203}, support = {R01 GM097637/GM/NIGMS NIH HHS/United States ; BB/E010741/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Cell Nucleus ; Fungi/*genetics ; Gene Transfer, Horizontal ; *Genetic Variation ; Hyphae ; Plants/*microbiology ; Spores, Fungal ; }, abstract = {It has been hypothesized that horizontal gene/chromosome transfer and parasexual recombination following hyphal fusion between different strains may contribute to the emergence of wide genetic variability in plant pathogenic and other fungi. However, the significance of vegetative (heterokaryon) incompatibility responses, which commonly result in cell death, in preventing these processes is not known. In this study, we have assessed this issue following different types of hyphal fusion during colony initiation and in the mature colony. We used vegetatively compatible and incompatible strains of the common bean pathogen Colletotrichum lindemuthianum in which nuclei were labelled with either a green or red fluorescent protein in order to microscopically monitor the fates of nuclei and heterokaryotic cells following hyphal fusion. As opposed to fusion of hyphae in mature colonies that resulted in cell death within 3 h, fusions by conidial anastomosis tubes (CAT) between two incompatible strains during colony initiation did not induce the vegetative incompatibility response. Instead, fused conidia and germlings survived and formed heterokaryotic colonies that in turn produced uninucleate conidia that germinated to form colonies with phenotypic features different to those of either parental strain. Our results demonstrate that the vegetative incompatibility response is suppressed during colony initiation in C. lindemuthianum. Thus, CAT fusion may allow asexual fungi to increase their genetic diversity, and to acquire new pathogenic traits.}, }
@article {pmid22319513, year = {2011}, author = {Martínez, JL}, title = {Bottlenecks in the transferability of antibiotic resistance from natural ecosystems to human bacterial pathogens.}, journal = {Frontiers in microbiology}, volume = {2}, number = {}, pages = {265}, pmid = {22319513}, issn = {1664-302X}, abstract = {It is generally accepted that resistance genes acquired by human pathogens through horizontal gene transfer originated in environmental, non-pathogenic bacteria. As a consequence, there is increasing concern on the roles that natural, non-clinical ecosystems, may play in the evolution of resistance. Recent studies have shown that the variability of determinants that can provide antibiotic resistance on their expression in a heterologous host is much larger than what is actually found in human pathogens, which implies the existence of bottlenecks modulating the transfer, spread, and stability of antibiotic resistance genes. In this review, the role that different factors such as founder effects, ecological connectivity, fitness costs, or second-order selection may have on the establishment of a specific resistance determinant in a population of bacterial pathogens is analyzed.}, }
@article {pmid22319444, year = {2012}, author = {Gama, JA and Abby, SS and Vieira-Silva, S and Dionisio, F and Rocha, EP}, title = {Immune subversion and quorum-sensing shape the variation in infectious dose among bacterial pathogens.}, journal = {PLoS pathogens}, volume = {8}, number = {2}, pages = {e1002503}, pmid = {22319444}, issn = {1553-7374}, mesh = {Bacteria/genetics/*immunology/*pathogenicity ; Bacterial Infections/immunology/*pathology ; Gene Expression Regulation, Bacterial ; Host-Pathogen Interactions ; Humans ; Immune Evasion ; Phagocytes/microbiology ; Quorum Sensing/*genetics ; Virulence/genetics ; Virulence Factors/*genetics ; }, abstract = {Many studies have been devoted to understand the mechanisms used by pathogenic bacteria to exploit human hosts. These mechanisms are very diverse in the detail, but share commonalities whose quantification should enlighten the evolution of virulence from both a molecular and an ecological perspective. We mined the literature for experimental data on infectious dose of bacterial pathogens in humans (ID50) and also for traits with which ID50 might be associated. These compilations were checked and complemented with genome analyses. We observed that ID50 varies in a continuous way by over 10 orders of magnitude. Low ID50 values are very strongly associated with the capacity of the bacteria to kill professional phagocytes or to survive in the intracellular milieu of these cells. Inversely, high ID50 values are associated with motile and fast-growing bacteria that use quorum-sensing based regulation of virulence factors expression. Infectious dose is not associated with genome size and shows insignificant phylogenetic inertia, in line with frequent virulence shifts associated with the horizontal gene transfer of a small number of virulence factors. Contrary to previous proposals, infectious dose shows little dependence on contact-dependent secretion systems and on the natural route of exposure. When all variables are combined, immune subversion and quorum-sensing are sufficient to explain two thirds of the variance in infectious dose. Our results show the key role of immune subversion in effective human infection by small bacterial populations. They also suggest that cooperative processes might be important for successful infection by bacteria with high ID50. Our results suggest that trade-offs between selection for population growth-related traits and selection for the ability to subvert the immune system shape bacterial infectiousness. Understanding these trade-offs provides guidelines to study the evolution of virulence and in particular the micro-evolutionary paths of emerging pathogens.}, }
@article {pmid22319434, year = {2012}, author = {Rappoport, N and Linial, M}, title = {Viral proteins acquired from a host converge to simplified domain architectures.}, journal = {PLoS computational biology}, volume = {8}, number = {2}, pages = {e1002364}, pmid = {22319434}, issn = {1553-7358}, mesh = {Amino Acid Sequence ; Animals ; Cluster Analysis ; Conserved Sequence ; DNA, Viral/chemistry ; *Gene Transfer, Horizontal ; *Host-Pathogen Interactions ; Humans ; Mammals/genetics ; *Models, Genetic ; Molecular Sequence Data ; Mutagenesis, Insertional ; Protein Structure, Tertiary ; RNA, Viral/chemistry ; Sequence Alignment ; Viral Proteins/*chemistry/genetics ; Viruses/chemistry/genetics ; }, abstract = {The infection cycle of viruses creates many opportunities for the exchange of genetic material with the host. Many viruses integrate their sequences into the genome of their host for replication. These processes may lead to the virus acquisition of host sequences. Such sequences are prone to accumulation of mutations and deletions. However, in rare instances, sequences acquired from a host become beneficial for the virus. We searched for unexpected sequence similarity among the 900,000 viral proteins and all proteins from cellular organisms. Here, we focus on viruses that infect metazoa. The high-conservation analysis yielded 187 instances of highly similar viral-host sequences. Only a small number of them represent viruses that hijacked host sequences. The low-conservation sequence analysis utilizes the Pfam family collection. About 5% of the 12,000 statistical models archived in Pfam are composed of viral-metazoan proteins. In about half of Pfam families, we provide indirect support for the directionality from the host to the virus. The other families are either wrongly annotated or reflect an extensive sequence exchange between the viruses and their hosts. In about 75% of cross-taxa Pfam families, the viral proteins are significantly shorter than their metazoan counterparts. The tendency for shorter viral proteins relative to their related host proteins accounts for the acquisition of only a fragment of the host gene, the elimination of an internal domain and shortening of the linkers between domains. We conclude that, along viral evolution, the host-originated sequences accommodate simplified domain compositions. We postulate that the trimmed proteins act by interfering with the fundamental function of the host including intracellular signaling, post-translational modification, protein-protein interaction networks and cellular trafficking. We compiled a collection of hijacked protein sequences. These sequences are attractive targets for manipulation of viral infection.}, }
@article {pmid22319135, year = {2012}, author = {Pierce, SK and Fang, X and Schwartz, JA and Jiang, X and Zhao, W and Curtis, NE and Kocot, KM and Yang, B and Wang, J}, title = {Transcriptomic evidence for the expression of horizontally transferred algal nuclear genes in the photosynthetic sea slug, Elysia chlorotica.}, journal = {Molecular biology and evolution}, volume = {29}, number = {6}, pages = {1545-1556}, doi = {10.1093/molbev/msr316}, pmid = {22319135}, issn = {1537-1719}, mesh = {Animals ; Base Sequence ; Chlorophyta/*genetics ; Gastropoda/*genetics ; *Gene Expression ; Gene Expression Profiling ; *Gene Transfer, Horizontal ; *Genes, Chloroplast ; Genome ; Molecular Sequence Annotation ; Molecular Sequence Data ; Photosynthesis/*genetics ; RNA, Messenger/genetics/metabolism ; Sequence Analysis, DNA ; }, abstract = {Analysis of the transcriptome of the kleptoplastic sea slug, Elysia chlorotica, has revealed the presence of at least 101 chloroplast-encoded gene sequences and 111 transcripts matching 52 nuclear-encoded genes from the chloroplast donor, Vaucheria litorea. These data clearly show that the symbiotic chloroplasts are translationally active and, of even more interest, that a variety of functional algal genes have been transferred into the slug genome, as has been suggested by earlier indirect experiments. Both the chloroplast- and nuclear-encoded sequences were rare within the E. chlorotica transcriptome, suggesting that their copy numbers and synthesis rates are low, and required both a large amount of sequence data and native algal sequences to find. These results show that the symbiotic chloroplasts residing inside the host molluscan cell are maintained by an interaction of both organellar and host biochemistry directed by the presence of transferred genes.}, }
@article {pmid22314808, year = {2012}, author = {Chen, X and Liang, H and Zhang, J and Zen, K and Zhang, CY}, title = {Horizontal transfer of microRNAs: molecular mechanisms and clinical applications.}, journal = {Protein &amp; cell}, volume = {3}, number = {1}, pages = {28-37}, pmid = {22314808}, issn = {1674-8018}, mesh = {Animals ; Diagnosis ; Extracellular Space/genetics ; *Gene Transfer, Horizontal ; Humans ; MicroRNAs/*genetics/metabolism ; Therapeutics ; }, abstract = {A new class of RNA regulatory genes known as microRNAs (miRNAs) has been found to introduce a whole new layer of gene regulation in eukaryotes. The intensive studies of the past several years have demonstrated that miRNAs are not only found intracellularly, but are also detectable outside cells, including in various body fluids (e.g. serum, plasma, saliva, urine and milk). This phenomenon raises questions about the biological function of such extracellular miRNAs. Substantial amounts of extracellular miRNAs are enclosed in small membranous vesicles (e.g. exosomes, shedding vesicles and apoptotic bodies) or packaged with RNA-binding proteins (e.g. high-density lipoprotein, Argonaute 2 and nucleophosmin 1). These miRNAs may function as secreted signaling molecules to influence the recipient cell phenotypes. Furthermore, secreted extracellular miRNAs may reflect molecular changes in the cells from which they are derived and can therefore potentially serve as diagnostic indicators of disease. Several studies also point to the potential application of siRNA/miRNA delivery as a new therapeutic strategy for treating diseases. In this review, we summarize what is known about the mechanism of miRNA secretion. In addition, we describe the pathophysiological roles of secreted miRNAs and their clinical potential as diagnostic biomarkers and therapeutic drugs. We believe that miRNA transfer between cells will have a significant impact on biological research in the coming years.}, }
@article {pmid22312895, year = {2011}, author = {Baĭmiev, AKh and Ivanova, ES and Ptitsyn, KG and Chubukova, OV and Baĭmiev, AKh}, title = {[Phylogenetic analysis of symbiotic genes of nodule bacteria in the plants of the genus Lathyrus (L.) (Fabaceae)].}, journal = {Molekuliarnaia genetika, mikrobiologiia i virusologiia}, volume = {}, number = {4}, pages = {14-17}, pmid = {22312895}, issn = {0208-0613}, mesh = {Acyltransferases/genetics ; Agrobacterium/*genetics ; Bacterial Proteins/genetics ; Gene Transfer, Horizontal/genetics ; *Genes, Bacterial ; Genome, Plant ; Lathyrus/*microbiology ; Oxidoreductases/genetics ; Phyllobacteriaceae/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/*classification/genetics ; Rhizobium leguminosarum/*genetics ; Rhizobium tropici/*genetics ; Root Nodules, Plant/microbiology ; Symbiosis/*genetics ; }, abstract = {The comparative analysis of the symbiotic genes nifD, nifH, nodA of wild-growing Lathyrus L. species (Fabaceae) connected by genes sequences of 16S aRNA to Rhizobium leguminosarum bv. viceae, Rhizobium tropici, Agrobacterium sp., and Phyllobacterium sp. was carried out. It was demonstrated that all tested genes of strains taken for analysis had high degree of homology with analogous genes of Rhizobium leguminosarum bv. viceae. It was suggested that symbiotic genes were introduced into Rhizobium tropici, Agrobacterium sp., and Phyllobacterium sp. strains by means of horizontal gene transfer over from Rhizobium leguminosarum bv. viceae strain. The recombinant strains were formed, capable to nodulate Lathyrus L. species that earlier was not considered characteristic for these plants.}, }
@article {pmid22312594, year = {2011}, author = {van Passel, MW}, title = {Tracing common origins of Genomic Islands in prokaryotes based on genome signature analyses.}, journal = {Mobile genetic elements}, volume = {1}, number = {3}, pages = {247-249}, pmid = {22312594}, issn = {2159-2543}, abstract = {Horizontal gene transfer constitutes a powerful and innovative force in evolution, but often little is known about the actual origins of transferred genes. Sequence alignments are generally of limited use in tracking the original donor, since still only a small fraction of the total genetic diversity is thought to be uncovered. Alternatively, approaches based on similarities in the genome specific relative oligonucleotide frequencies do not require alignments. Even though the exact origins of horizontally transferred genes may still not be established using these compositional analyses, it does suggest that compositionally very similar regions are likely to have had a common origin. These analyses have shown that up to a third of large acquired gene clusters that reside in the same genome are compositionally very similar, indicative of a shared origin. This brings us closer to uncovering the original donors of horizontally transferred genes, and could help in elucidating possible regulatory interactions between previously unlinked sequences.}, }
@article {pmid22312592, year = {2011}, author = {Domazet-Lošo, M and Haubold, B}, title = {Alignment-free detection of horizontal gene transfer between closely related bacterial genomes.}, journal = {Mobile genetic elements}, volume = {1}, number = {3}, pages = {230-235}, pmid = {22312592}, issn = {2159-2543}, abstract = {Bacterial epidemics are often caused by strains that have acquired their increased virulence through horizontal gene transfer. Due to this association with disease, the detection of horizontal gene transfer continues to receive attention from microbiologists and bioinformaticians alike. Most software for detecting transfer events is based on alignments of sets of genes or of entire genomes. But despite great advances in the design of algorithms and computer programs, genome alignment remains computationally challenging. We have therefore developed an alignment-free algorithm for rapidly detecting horizontal gene transfer between closely related bacterial genomes. Our implementation of this algorithm is called alfy for "ALignment Free local homologY" and is freely available from http://guanine.evolbio.mpg.de/alfy/. In this comment we demonstrate the application of alfy to the genomes of Staphylococcus aureus. We also argue that-contrary to popular belief and in spite of increasing computer speed-algorithmic optimization is becoming more, not less, important if genome data continues to accumulate at the present rate.}, }
@article {pmid22309969, year = {2012}, author = {Nicol, P and Gill, R and Fosu-Nyarko, J and Jones, MG}, title = {de novo analysis and functional classification of the transcriptome of the root lesion nematode, Pratylenchus thornei, after 454 GS FLX sequencing.}, journal = {International journal for parasitology}, volume = {42}, number = {3}, pages = {225-237}, doi = {10.1016/j.ijpara.2011.11.010}, pmid = {22309969}, issn = {1879-0135}, mesh = {Animals ; Expressed Sequence Tags ; Gene Expression Profiling ; Helminth Proteins/*genetics ; Hordeum/parasitology ; Molecular Sequence Annotation ; Plant Diseases/*parasitology ; Plant Roots/parasitology ; Sequence Analysis, DNA ; *Transcriptome ; Triticum/parasitology ; Tylenchoidea/classification/*genetics ; }, abstract = {The migratory endoparasitic root lesion nematode Pratylenchus thornei is a major pest of the cereals wheat and barley. In what we believe to be the first global transcriptome analysis for P. thornei, using Roche GS FLX sequencing, 787,275 reads were assembled into 34,312 contigs using two assembly programs, to yield 6,989 contigs common to both. These contigs were annotated, resulting in functional assignments for 3,048. Specific transcripts studied in more detail included carbohydrate active enzymes potentially involved in cell wall degradation, neuropeptides, putative plant nematode parasitism genes, and transcripts that could be secreted by the nematode. Transcripts for cell wall degrading enzymes were similar to bacterial genes, suggesting that they were acquired by horizontal gene transfer. Contigs matching 14 parasitism genes found in sedentary endoparasitic nematodes were identified. These genes are thought to function in suppression of host defenses and in feeding site development, but their function in P. thornei may differ. Comparison of the common contigs from P. thornei with other nematodes showed that 2,039 were common to sequences of the Heteroderidae, 1,947 to the Meloidogynidae, 1,218 to Radopholus similis, 1,209 matched expressed sequence tags (ESTs) of Pratylenchus penetrans and Pratylenchus vulnus, and 2,940 to contigs of Pratylenchus coffeae. There were 2,014 contigs common to Caenarhabditis elegans, with 15.9% being common to all three groups. Twelve percent of contigs with matches to the Heteroderidae and the Meloidogynidae had no homology to any C. elegans protein. Fifty-seven percent of the contigs did not match known sequences and some could be unique to P. thornei. These data provide substantial new information on the transcriptome of P. thornei, those genes common to migratory and sedentary endoparasitic nematodes, and provide additional understanding of genes required for different forms of parasitism. The data can also be used to identify potential genes to study host interactions and for crop protection.}, }
@article {pmid22308402, year = {2012}, author = {Routh, A and Domitrovic, T and Johnson, JE}, title = {Host RNAs, including transposons, are encapsidated by a eukaryotic single-stranded RNA virus.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {6}, pages = {1907-1912}, pmid = {22308402}, issn = {1091-6490}, support = {R37 GM034220/GM/NIGMS NIH HHS/United States ; R37-GM034220/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Capsid/*metabolism/ultrastructure ; Cell Line ; DNA Transposable Elements/*genetics ; Eukaryota/*genetics ; Gene Expression Regulation, Viral ; Genome, Viral/genetics ; Host-Pathogen Interactions/*genetics ; Mutation Rate ; RNA Viruses/*genetics ; RNA, Messenger/genetics/metabolism ; RNA, Viral/*genetics/isolation &amp; purification ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis, RNA ; Virion/ultrastructure ; Virus Assembly/genetics ; }, abstract = {Next-generation sequencing is a valuable tool in our growing understanding of the genetic diversity of viral populations. Using this technology, we have investigated the RNA content of a purified nonenveloped single-stranded RNA virus, flock house virus (FHV). We have also investigated the RNA content of virus-like particles (VLPs) of FHV and the related Nudaurelia capensis omega virus. VLPs predominantly package ribosomal RNA and transcripts of their baculoviral expression vectors. In addition, we find that 5.3% of the packaged RNAs are transposable elements derived from the Sf21 genome. This observation may be important when considering the therapeutic use of VLPs. We find that authentic FHV virions also package a variety of host RNAs, accounting for 1% of the packaged nucleic acid. Significant quantities of host messenger RNAs, ribosomal RNA, noncoding RNAs, and transposable elements are readily detected. The packaging of these host RNAs elicits the possibility of horizontal gene transfer between eukaryotic hosts that share a viral pathogen. We conclude that the genetic content of nonenveloped RNA viruses is variable, not just by genome mutation, but also in the diversity of RNA transcripts that are packaged.}, }
@article {pmid22308367, year = {2012}, author = {Stegemann, S and Keuthe, M and Greiner, S and Bock, R}, title = {Horizontal transfer of chloroplast genomes between plant species.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {7}, pages = {2434-2438}, pmid = {22308367}, issn = {1091-6490}, mesh = {Base Sequence ; Chloroplasts/*genetics ; DNA Primers ; DNA, Mitochondrial/genetics ; DNA, Plant/genetics ; *Gene Transfer, Horizontal ; *Genome, Plant ; Plastids ; Polymerase Chain Reaction ; Recombination, Genetic ; Nicotiana/genetics ; }, abstract = {The genomes of DNA-containing cell organelles (mitochondria, chloroplasts) can be laterally transmitted between organisms, a process known as organelle capture. Organelle capture often occurs in the absence of detectable nuclear introgression, and the capture mechanism is unknown. Here, we have considered horizontal genome transfer across natural grafts as a mechanism underlying chloroplast capture in plants. By grafting sexually incompatible species, we show that complete chloroplast genomes can travel across the graft junction from one species into another. We demonstrate that, consistent with reported phylogenetic evidence, replacement of the resident plastid genome by the alien genome occurs in the absence of intergenomic recombination. Our results provide a plausible mechanism for organelle capture in plants and suggest natural grafting as a path for horizontal gene and genome transfer between sexually incompatible species.}, }
@article {pmid22307549, year = {2012}, author = {Morton, ER and Fuqua, C}, title = {Laboratory maintenance of Agrobacterium.}, journal = {Current protocols in microbiology}, volume = {Chapter 1}, number = {}, pages = {Unit3D.1}, pmid = {22307549}, issn = {1934-8533}, support = {GM092660/GM/NIGMS NIH HHS/United States ; GM080546/GM/NIGMS NIH HHS/United States ; R01 GM092660/GM/NIGMS NIH HHS/United States ; R01 GM080546-05/GM/NIGMS NIH HHS/United States ; R01 GM080546/GM/NIGMS NIH HHS/United States ; }, mesh = {Agrobacterium tumefaciens/genetics/*growth &amp; development ; Bacteriological Techniques/*methods ; Maintenance ; Plant Diseases/microbiology ; Plant Tumor-Inducing Plasmids ; Plants/microbiology ; Virulence Factors/genetics ; }, abstract = {Agrobacterium species are plant-associated relatives of the rhizobia. Several species cause plant diseases such as crown gall and hairy root, although there are also avirulent species. A. tumefaciens is the most intensively studied species and causes crown gall, a neoplastic disease that occurs on a variety of plants. Virulence is specified by large plasmids, and in the case of A. tumefaciens this is called the Ti (tumor-inducing) plasmid. During pathogenesis, virulent agrobacteria copy a segment of the Ti plasmid and transfer it to the plant, where it subsequently integrates into the plant genome and expresses genes that result in the disease symptoms. A. tumefaciens has been used extensively as a plant genetic engineering tool, and is also a model microorganism that has been well studied for host-microbe associations, horizontal gene transfer, cell-cell communication, and biofilm formation. This unit describes standard protocols for laboratory cultivation of A. tumefaciens.}, }
@article {pmid22300955, year = {2012}, author = {Naseer, U and Eriksen, BO and Sundsfjord, A and Samuelsen, &#xd8;}, title = {Fecal colonization of VIM-1-producing Klebsiella pneumoniae and in vivo transfer of multidrug-resistant IncN plasmid in a renal transplant patient.}, journal = {Diagnostic microbiology and infectious disease}, volume = {72}, number = {4}, pages = {363-366}, doi = {10.1016/j.diagmicrobio.2011.12.010}, pmid = {22300955}, issn = {1879-0070}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; DNA, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/drug effects/genetics ; Feces/*microbiology ; *Gene Transfer, Horizontal ; Humans ; Kidney Transplantation/*adverse effects ; Klebsiella Infections/microbiology ; Klebsiella pneumoniae/drug effects/enzymology/*growth &amp; development/isolation &amp; purification ; Plasmids/*genetics ; Polymerase Chain Reaction ; beta-Lactamases/biosynthesis/genetics ; }, abstract = {We report a case of long-term colonization of a carbapenemase (VIM)-producing Klebsiella pneumoniae clone in a renal transplant patient and demonstrate the in vivo transmission of a broad-host-range multidrug-resistant IncN plasmid containing bla(VIM), bla(SHV-12), and qnrS to Escherichia coli.}, }
@article {pmid22297216, year = {2012}, author = {Doughari, HJ and Ndakidemi, PA and Human, IS and Benade, S}, title = {Virulence, resistance genes, and transformation amongst environmental isolates of Escherichia coli and Acinetobacter spp.}, journal = {Journal of microbiology and biotechnology}, volume = {22}, number = {1}, pages = {25-33}, doi = {10.4014/jmb.1107.07029}, pmid = {22297216}, issn = {1738-8872}, mesh = {Acinetobacter/genetics/*isolation &amp; purification ; Bacterial Toxins/genetics/metabolism ; Blood Bactericidal Activity ; Cell Wall/chemistry ; *Drug Resistance, Bacterial ; *Environmental Microbiology ; Escherichia coli/genetics/*isolation &amp; purification ; Gene Transfer, Horizontal ; Hydrophobic and Hydrophilic Interactions ; Plasmids ; *Transformation, Bacterial ; Virulence Factors/*genetics ; beta-Lactamases/metabolism ; }, abstract = {The association of verotoxic E. coli and Acinetobacter spp. with various antibiotic-resistant, diarrhogenic, and nosocomial infections has been a cause for concern worldwide. E. coli and A. haemolyticus isolated on a number of selective media were screened for virulence factors, antibiotic resistance, and transformation of resistance genes. Out of 69 E. coli isolates obtained, 25 (35.23%), 14 (20.30%), and 28 (40.58%) were positive for Vtx1&amp;2, Vtx1, and Vtx2, respectively, 49 (71.015%) for extendedspectrum beta-lactamases (ESBLs), 34 (49.28%) for serum resistance, 57 (82.61%) for cell surface hydrophobicity, 48 (69.57%) for gelatinase production, and 37 (53.62%) for hemolysin production. For the 14 A. haemolyticus isolates, only 2 (14.29%) in each case from all the samples investigated were positive for Vtx1, Vtx2 and Vtx1&amp;2 respectively, 8 (57.14%) for ESBLs, 7 (50.00%) for serum resistance, 11 (78.57%) for cell surface hydrophobicity, 4 (28.57%) for gelatinase production, and 8 (57.14%) for hemolysin production. Although transformation occurred among the E. coli and Acinetobacter isolates (transformation frequency: 13.3 × 10(-7) -53.4(-7)), there was poor curing of the plasmid genes, a confirmation of the presence of stable antibiotic-resistant genes (DNA concentration between 42.7 and 123.8 microgram) and intragenetic transfer of multidrugresistant genes among the isolates. The isolates were potentially virulent and contained potentially transferable antibiotic resistance genes. Detection of virulence factors, antibiotic resistance genes, and transformation among these isolates is a very significant outcome that will influence approaches to proactive preventive and control measures and future investigations. However, continued surveillance for drug resistance among these bacteria and further investigation of the mechanism of action of their virulence factors are a necessity.}, }
@article {pmid22296756, year = {2012}, author = {Takishita, K and Chikaraishi, Y and Leger, MM and Kim, E and Yabuki, A and Ohkouchi, N and Roger, AJ}, title = {Lateral transfer of tetrahymanol-synthesizing genes has allowed multiple diverse eukaryote lineages to independently adapt to environments without oxygen.}, journal = {Biology direct}, volume = {7}, number = {}, pages = {5}, pmid = {22296756}, issn = {1745-6150}, support = {MOP-62809//Canadian Institutes of Health Research/Canada ; }, mesh = {*Adaptation, Biological ; Amino Acid Sequence ; Anaerobiosis ; Cell Membrane/chemistry ; Eukaryota/chemistry/classification/*genetics ; Gas Chromatography-Mass Spectrometry ; *Gene Transfer, Horizontal ; Lipids/analysis/chemistry/genetics ; Lyases/genetics ; Oxygen/chemistry ; Phagocytosis ; Phylogeny ; Sequence Alignment ; Species Specificity ; Triterpenes/*chemistry ; }, abstract = {Sterols are key components of eukaryotic cellular membranes that are synthesized by multi-enzyme pathways that require molecular oxygen. Because prokaryotes fundamentally lack sterols, it is unclear how the vast diversity of bacterivorous eukaryotes that inhabit hypoxic environments obtain, or synthesize, sterols. Here we show that tetrahymanol, a triterpenoid that does not require molecular oxygen for its biosynthesis, likely functions as a surrogate of sterol in eukaryotes inhabiting oxygen-poor environments. Genes encoding the tetrahymanol synthesizing enzyme squalene-tetrahymanol cyclase were found from several phylogenetically diverged eukaryotes that live in oxygen-poor environments and appear to have been laterally transferred among such eukaryotes.}, }
@article {pmid22294679, year = {2012}, author = {Tribble, GD and Rigney, TW and Dao, DH and Wong, CT and Kerr, JE and Taylor, BE and Pacha, S and Kaplan, HB}, title = {Natural competence is a major mechanism for horizontal DNA transfer in the oral pathogen Porphyromonas gingivalis.}, journal = {mBio}, volume = {3}, number = {1}, pages = {}, pmid = {22294679}, issn = {2150-7511}, support = {R01 DE019634/DE/NIDCR NIH HHS/United States ; DE-019634/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacterial Proteins/*metabolism ; Bacteroidaceae Infections/microbiology ; Biofilms/growth &amp; development ; Conjugation, Genetic ; *DNA Transformation Competence ; DNA, Bacterial/*genetics/*metabolism ; *Gene Transfer, Horizontal ; Humans ; Mouth/microbiology ; Porphyromonas gingivalis/*genetics/pathogenicity ; Transformation, Bacterial ; }, abstract = {UNLABELLED: Porphyromonas gingivalis is a Gram-negative anaerobe that resides exclusively in the human oral cavity. Long-term colonization by P. gingivalis requires the bacteria to evade host immune responses while adapting to the changing host physiology and alterations in the composition of the oral microflora. The genetic diversity of P. gingivalis appears to reflect the variability of its habitat; however, little is known about the molecular mechanisms generating this diversity. Previously, our research group established that chromosomal DNA transfer occurs between P. gingivalis strains. In this study, we examine the role of putative DNA transfer genes in conjugation and transformation and demonstrate that natural competence mediated by comF is the dominant form of chromosomal DNA transfer, with transfer by a conjugation-like mechanism playing a minor role. Our results reveal that natural competence mechanisms are present in multiple strains of P. gingivalis, and DNA uptake is not sensitive to DNA source or modification status. Furthermore, extracellular DNA was observed for the first time in P. gingivalis biofilms and is predicted to be the major DNA source for horizontal transfer and allelic exchange between strains. We propose that exchange of DNA in plaque biofilms by a transformation-like process is of major ecological importance in the survival and persistence of P. gingivalis in the challenging oral environment.<br><br>IMPORTANCE: P. gingivalis colonizes the oral cavities of humans worldwide. The long-term persistence of these bacteria can lead to the development of chronic periodontitis and host morbidity associated with tooth loss. P. gingivalis is a genetically diverse species, and this variability is believed to contribute to its successful colonization and survival in diverse human hosts, as well as evasion of host immune defenses and immunization strategies. We establish here that natural competence is the major driving force behind P. gingivalis DNA exchange and that conjugative DNA transfer plays a minor role. Furthermore, we reveal for the first time the presence of extracellular DNA in P. gingivalis biofilms, which is most likely the source of DNA exchanged between strains within dental plaque. These studies expand our understanding of the mechanisms used by this important member of the human oral flora to transition its relationship with the host from a commensal to a pathogenic relationship.}, }
@article {pmid22294497, year = {2012}, author = {Campbell, MA and Rokas, A and Slot, JC}, title = {Horizontal transfer and death of a fungal secondary metabolic gene cluster.}, journal = {Genome biology and evolution}, volume = {4}, number = {3}, pages = {289-293}, pmid = {22294497}, issn = {1759-6653}, mesh = {Botrytis/genetics ; Fungal Proteins/*genetics ; Fusarium/genetics ; Gene Transfer, Horizontal/*genetics ; Multigene Family/*genetics ; Pseudogenes/genetics ; Xanthones ; }, abstract = {A cluster composed of four structural and two regulatory genes found in several species of the fungal genus Fusarium (class Sordariomycetes) is responsible for the production of the red pigment bikaverin. We discovered that the unrelated fungus Botrytis cinerea (class Leotiomycetes) contains a cluster of five genes that is highly similar in sequence and gene order to the Fusarium bikaverin cluster. Synteny conservation, nucleotide composition, and phylogenetic analyses of the cluster genes indicate that the B. cinerea cluster was acquired via horizontal transfer from a Fusarium donor. Upon or subsequent to the transfer, the B. cinerea gene cluster became inactivated; one of the four structural genes is missing, two others are pseudogenes, and the fourth structural gene shows an accelerated rate of nonsynonymous substitutions along the B. cinerea lineage, consistent with relaxation of selective constraints. Interestingly, the bik4 regulatory gene is still intact and presumably functional, whereas bik5, which is a pathway-specific regulator, also shows a mild but significant acceleration of evolutionary rate along the B. cinerea lineage. This selective preservation of the bik4 regulator suggests that its conservation is due to its likely involvement in other non-bikaverin-related biological processes in B. cinerea. Thus, in addition to novel metabolism, horizontal transfer of wholesale metabolic gene clusters might also be contributing novel regulation.}, }
@article {pmid22293462, year = {2012}, author = {Ienne, S and Pappas, G and Benabdellah, K and González, A and Zingales, B}, title = {Horizontal gene transfer confers fermentative metabolism in the respiratory-deficient plant trypanosomatid Phytomonas serpens.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {12}, number = {3}, pages = {539-548}, doi = {10.1016/j.meegid.2012.01.016}, pmid = {22293462}, issn = {1567-7257}, mesh = {Adaptation, Biological ; Amino Acid Sequence ; Base Sequence ; Carbohydrate Metabolism ; Carboxy-Lyases/genetics/metabolism ; Cloning, Molecular ; Conserved Sequence ; DNA, Protozoan/genetics/metabolism ; Enzyme Activation ; Ethanol/metabolism ; *Fermentation ; *Gene Transfer, Horizontal ; *Genes, Protozoan ; Magnoliopsida/parasitology ; Phylogeny ; Pyruvic Acid/metabolism ; Trypanosomatina/classification/*enzymology/*genetics/isolation &amp; purification ; }, abstract = {Among trypanosomatids, the genus Phytomonas is the only one specifically adapted to infect plants. These hosts provide a particular habitat with a plentiful supply of carbohydrates. Phytomonas sp. lacks a cytochrome-mediated respiratory chain and Krebs cycle, and ATP production relies predominantly on glycolysis. We have characterised the complete gene encoding a putative pyruvate/indolepyruvate decarboxylase (PDC/IPDC) (548 amino acids) of P. serpens, that displays high amino acid sequence similarity with phytobacteria and Leishmania enzymes. No orthologous PDC/IPDC genes were found in Trypanosoma cruzi or T. brucei. Conservation of the PDC/IPDC gene sequence was verified in 14 Phytomonas isolates. A phylogenetic analysis shows that Phytomonas protein is robustly monophyletic with Leishmania spp. and C. fasciculata enzymes. In the trees this clade appears as a sister group of indolepyruvate decarboxylases of γ-proteobacteria. This supports the proposition that a horizontal gene transfer event from a donor phytobacteria to a recipient ancestral trypanosome has occurred prior to the separation between Phytomonas, Leishmania and Crithidia. We have measured the PDC activity in P. serpens cell extracts. The enzyme has a Km value for pyruvate of 1.4mM. The acquisition of a PDC, a key enzyme in alcoholic fermentation, explains earlier observations that ethanol is one of the major end-products of glucose catabolism under aerobic and anaerobic conditions. This represents an alternative and necessary route to reoxidise part of the NADH produced in the highly demanding glycolytic pathway and highlights the importance of this type of event in metabolic adaptation.}, }
@article {pmid22292021, year = {2012}, author = {Plantard, O and Bouju-Albert, A and Malard, MA and Hermouet, A and Capron, G and Verheyden, H}, title = {Detection of Wolbachia in the tick Ixodes ricinus is due to the presence of the hymenoptera endoparasitoid Ixodiphagus hookeri.}, journal = {PloS one}, volume = {7}, number = {1}, pages = {e30692}, pmid = {22292021}, issn = {1932-6203}, mesh = {Animals ; Bacterial Outer Membrane Proteins/analysis/genetics ; Female ; Food Chain ; Host-Parasite Interactions/genetics/*physiology ; Host-Pathogen Interactions/genetics/physiology ; Hymenoptera/*microbiology/physiology ; Ixodes/*microbiology/*parasitology/physiology ; Phylogeny ; Symbiosis/physiology ; Tick Infestations/microbiology ; Wolbachia/classification/genetics/*isolation &amp; purification/physiology ; }, abstract = {The identification of micro-organisms carried by ticks is an important issue for human and animal health. In addition to their role as pathogen vectors, ticks are also the hosts for symbiotic bacteria whose impact on tick biology is poorly known. Among these, the bacterium Wolbachia pipientis has already been reported associated with Ixodes ricinus and other tick species. However, the origins of Wolbachia in ticks and their consequences on tick biology (known to be very diverse in invertebrates, ranging from nutritional symbionts in nematodes to reproductive manipulators in insects) are unknown. Here we report that the endoparasitoid wasp Ixodiphagus hookeri (Hymenoptera, Chalcidoidea, Encyrtidae)--strictly associated with ticks for their development--infested at almost 100% prevalence by a W. pipientis strain belonging to a Wolbachia supergroup that has already been reported as associated with other hymenopteran parasitoids. In a natural population of I. ricinus that suffers high parasitism rates due to I. hookeri, we used specific PCR primers for both hymenopteran and W. pipientis gene fragments to show that all unfed tick nymphs parasitized by I. hookeri also harbored Wolbachia, while unparasitized ticks were Wolbachia-free. We demonstrated experimentally that unfed nymphs obtained from larvae exposed to I. hookeri while gorging on their vertebrate host also harbor Wolbachia. We hypothesize that previous studies that have reported W. pipientis in ticks are due to the cryptic presence of the endoparasitoid wasp I. hookeri. This association has remained hidden until now because parasitoids within ticks cannot be detected until engorgement of the nymphs brings the wasp eggs out of diapause. Finally, we discuss the consequences of this finding for our understanding of the tick microbiome, and their possible role in horizontal gene transfer among pathogenic and symbiotic bacteria.}, }
@article {pmid22291979, year = {2012}, author = {Zhang, T and Fang, Y and Wang, X and Deng, X and Zhang, X and Hu, S and Yu, J}, title = {The complete chloroplast and mitochondrial genome sequences of Boea hygrometrica: insights into the evolution of plant organellar genomes.}, journal = {PloS one}, volume = {7}, number = {1}, pages = {e30531}, pmid = {22291979}, issn = {1932-6203}, mesh = {Base Sequence ; Chloroplasts/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Plant ; *Genome, Chloroplast ; *Genome, Mitochondrial ; Genome, Plant/genetics ; Magnoliopsida/*genetics ; Models, Genetic ; Molecular Sequence Data ; Organelles/genetics ; Plastids/genetics ; RNA, Transfer/genetics ; *Sequence Analysis, DNA/methods ; }, abstract = {The complete nucleotide sequences of the chloroplast (cp) and mitochondrial (mt) genomes of resurrection plant Boea hygrometrica (Bh, Gesneriaceae) have been determined with the lengths of 153,493 bp and 510,519 bp, respectively. The smaller chloroplast genome contains more genes (147) with a 72% coding sequence, and the larger mitochondrial genome have less genes (65) with a coding faction of 12%. Similar to other seed plants, the Bh cp genome has a typical quadripartite organization with a conserved gene in each region. The Bh mt genome has three recombinant sequence repeats of 222 bp, 843 bp, and 1474 bp in length, which divide the genome into a single master circle (MC) and four isomeric molecules. Compared to other angiosperms, one remarkable feature of the Bh mt genome is the frequent transfer of genetic material from the cp genome during recent Bh evolution. We also analyzed organellar genome evolution in general regarding genome features as well as compositional dynamics of sequence and gene structure/organization, providing clues for the understanding of the evolution of organellar genomes in plants. The cp-derived sequences including tRNAs found in angiosperm mt genomes support the conclusion that frequent gene transfer events may have begun early in the land plant lineage.}, }
@article {pmid22291881, year = {2012}, author = {Qu, Z and Li, L and Luo, J and Wang, P and Yu, S and Mou, T and Zheng, X and Hu, Z}, title = {QTL mapping of combining ability and heterosis of agronomic traits in rice backcross recombinant inbred lines and hybrid crosses.}, journal = {PloS one}, volume = {7}, number = {1}, pages = {e28463}, pmid = {22291881}, issn = {1932-6203}, mesh = {Agriculture ; Analysis of Variance ; Chimera/*genetics ; *Chromosome Mapping/methods ; Chromosomes, Plant/genetics ; *Crosses, Genetic ; Gene Transfer, Horizontal/genetics ; Genome, Plant ; Genotype ; Hybrid Vigor/*genetics ; Inbreeding/methods ; Mosaicism ; Oryza/*genetics ; Plants, Genetically Modified ; Quantitative Trait Loci/*genetics ; }, abstract = {BACKGROUND: Combining ability effects are very effective genetic parameters in deciding the next phase of breeding programs. Although some breeding strategies on the basis of evaluating combining ability have been utilized extensively in hybrid breeding, little is known about the genetic basis of combining ability. Combining ability is a complex trait that is controlled by polygenes. With the advent and development of molecular markers, it is feasible to evaluate the genetic bases of combining ability and heterosis of elite rice hybrids through QTL analysis.<br><br>In the present study, we first developed a QTL-mapping method for dissecting combining ability and heterosis of agronomic traits. With three testcross populations and a BCRIL population in rice, biometric and QTL analyses were conducted for ten agronomic traits. The significance of general combining ability and special combining ability for most of the traits indicated the importance of both additive and non-additive effects on expression levels. A large number of additive effect QTLs associated with performance per se of BCRIL and general combining ability, and dominant effect QTLs associated with special combining ability and heterosis were identified for the ten traits.<br><br>CONCLUSIONS/SIGNIFICANCE: The combining ability of agronomic traits could be analyzed by the QTL mapping method. The characteristics revealed by the QTLs for combining ability of agronomic traits were similar with those by multitudinous QTLs for agronomic traits with performance per se of BCRIL. Several QTLs (1-6 in this study) were identified for each trait for combining ability. It demonstrated that some of the QTLs were pleiotropic or linked tightly with each other. The identification of QTLs responsible for combining ability and heterosis in the present study provides valuable information for dissecting genetic basis of combining ability.}, }
@article {pmid22289895, year = {2012}, author = {del Campo, I and Ruiz, R and Cuevas, A and Revilla, C and Vielva, L and de la Cruz, F}, title = {Determination of conjugation rates on solid surfaces.}, journal = {Plasmid}, volume = {67}, number = {2}, pages = {174-182}, doi = {10.1016/j.plasmid.2012.01.008}, pmid = {22289895}, issn = {1095-9890}, mesh = {*Conjugation, Genetic ; Escherichia coli/*genetics/metabolism ; Flow Cytometry ; Gene Transfer, Horizontal ; Plasmids/genetics/metabolism ; }, abstract = {A cytometric method for the estimation of end-point conjugation rates is developed and adapted to surface conjugation. This method improves the through-put of conjugation assays based on replica-plating and results in less noisy experimental data. Although conjugation on solid surfaces deviates from ideal conditions in which cells are continuously mixed, results show that, within the limits of high initial population densities and short mating times, end-point estimates of the conjugation rates are robust measurements. They are independent of the donor/recipient ratios and, to some extent, of the sampling time. Remixing the mating population in the course of a conjugation experiment results in a boost in the frequency of transconjugants.}, }
@article {pmid22287520, year = {2012}, author = {Baharoglu, Z and Krin, E and Mazel, D}, title = {Connecting environment and genome plasticity in the characterization of transformation-induced SOS regulation and carbon catabolite control of the Vibrio cholerae integron integrase.}, journal = {Journal of bacteriology}, volume = {194}, number = {7}, pages = {1659-1667}, pmid = {22287520}, issn = {1098-5530}, mesh = {Bacterial Proteins/*genetics/metabolism ; Base Sequence ; Carbon/*metabolism ; Cyclic AMP Receptor Protein/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Gene Expression Regulation, Enzymologic ; *Genome, Bacterial ; Integrases/*genetics/metabolism ; Integrons ; Molecular Sequence Data ; *SOS Response, Genetics ; *Transformation, Bacterial ; Vibrio cholerae/*enzymology/*genetics/metabolism ; }, abstract = {The human pathogen Vibrio cholerae carries a chromosomal superintegron (SI). The SI contains an array of hundreds of gene cassettes organized in tandem which are stable under conditions when no particular stress is applied to bacteria (such as during laboratory growth). Rearrangements of these cassettes are catalyzed by the activity of the associated integron integrase. Understanding the regulation of integrase expression is pivotal to fully comprehending the role played by this genetic reservoir for bacterial adaptation and its connection with the development of antibiotic resistance. Our previous work established that the integrase is regulated by the bacterial SOS response and that it is induced during bacterial conjugation. Here, we show that transformation, another horizontal gene transfer (HGT) mechanism, also triggers integrase expression through SOS induction, underlining the importance of HGT in genome plasticity. Moreover, we report a new cyclic AMP (cAMP)-cAMP receptor protein (CRP)-dependent regulation mechanism of the integrase, highlighting the influence of the extracellular environment on chromosomal gene content. Altogether, our data suggest an interplay between different stress responses and regulatory pathways for the modulation of the recombinase expression, thus showing how the SI remodeling mechanism is merged into bacterial physiology.}, }
@article {pmid22287011, year = {2012}, author = {Jiang, Y and Xiao, P and Yu, G and Sano, T and Pan, Q and Li, R}, title = {Molecular basis and phylogenetic implications of deoxycylindrospermopsin biosynthesis in the cyanobacterium Raphidiopsis curvata.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {7}, pages = {2256-2263}, pmid = {22287011}, issn = {1098-5336}, mesh = {Alkaloids/*biosynthesis ; Amino Acid Sequence ; Bacterial Proteins/*genetics/metabolism ; Base Sequence ; China ; Cyanobacteria/*genetics/isolation &amp; purification/metabolism ; Cyanobacteria Toxins ; DNA, Bacterial/analysis/isolation &amp; purification ; Molecular Sequence Data ; Multigene Family ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {New insights into the distribution and biochemistry of the cyanotoxin cylindrospermopsin (CYN) have been provided by the recent determination of its biosynthesis gene cluster (cyr) in several cyanobacterial species. Raphidiopsis curvata CHAB1150 isolated from China was analyzed for CYN analogues. Only 7-deoxy-CYN was detected in the cell extracts. The cyr gene cluster of R. curvata CHAB1150 was sequenced, and the cyr genes of this strain were found to have extremely high similarities (96% to 100%) to those from other nostocalean species. These species include Cylindrospermopsis raciborskii AWT205, Aphanizomenon sp. strain 10E6, and Aphanizomenon ovalisporum ILC-146. Insertion mutation was identified within the cyrI gene, and transcripts of cyrI and another functional gene cyrJ were detected in R. curvata CHAB1150. General congruence between the phylogenetic trees based on both cyr and 16S rrn was displayed. Neutral evolution was found on the whole sequences of the cyr genes, and 0 to 89 negative selected codons were detected in each gene. Therefore, the function of CyrI is to catalyze the oxygenation of 7-deoxy-CYN in CYN biosynthesis. The transcripts of the mutated cyrI gene may result from polycistronic transcription. The high conservation of the cyr genes may be ascribed to purifying selection and horizontal gene transfer.}, }
@article {pmid22286044, year = {2011}, author = {Coutinho, BG and Coelho, ML and Ceotto, H and Bastos, Mdo C}, title = {Revealing the latent mobilization capability of the staphylococcal bacteriocinogenic plasmid pRJ9.}, journal = {Journal of molecular microbiology and biotechnology}, volume = {21}, number = {3-4}, pages = {173-183}, doi = {10.1159/000335356}, pmid = {22286044}, issn = {1660-2412}, mesh = {Amino Acid Sequence ; Bacterial Proteins/*metabolism ; Bacteriocins/metabolism ; Base Sequence ; *Conjugation, Genetic ; DNA, Bacterial/genetics ; Gene Order ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Complementation Test ; Molecular Sequence Data ; *Plasmids ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Staphylococcus aureus/*genetics ; }, abstract = {Plasmid pRJ9 is a non-self-mobilizable bacteriocinogenic plasmid from Staphylococcus aureus. Despite this feature, DNA sequencing and RT-PCR experiments showed that it presents a Mob region with three genes (mobCAB), transcribed as an operon. In silico analysis of the Mob proteins encoded by pRJ9 showed that they present all the conserved functional features reported until present as being essential for plasmid mobilization. Moreover, they showed a high identity to Mob proteins encoded by mobilizable plasmids from Staphylococcus spp., especially to those encoded by plasmid pRJ6, which presents four mob genes (mobCDAB). A putative oriT region was also found upstream of the pRJ9 mob operon. pRJ9 could only be successfully mobilized by pGO1 when pRJ6 was present in the same strain. Further experiments showed that the pRJ9 oriT can be recognized by the pRJ6 Mob proteins, confirming its functionality. As pRJ9 does not possess a mobD gene while pRJ6 does, the absence of this gene was believed to be responsible for its lack of mobilization. However, conjugation experiments with a donor strain carrying also mobD cloned into an S. aureus vector showed that pRJ9 does not become mobilized even in the presence of the protein MobD encoded by pRJ6. Therefore, the reasons for pRJ9 failure to be mobilized are presently unknown.}, }
@article {pmid23653804, year = {2012}, author = {Klein, JR and Gulsvig, T}, title = {Using Bioinformatics to Develop and Test Hypotheses: E. coli-Specific Virulence Determinants.}, journal = {Journal of microbiology &amp; biology education}, volume = {13}, number = {2}, pages = {161-169}, pmid = {23653804}, issn = {1935-7877}, abstract = {Bioinformatics, the use of computer resources to understand biological information, is an important tool in research, and can be easily integrated into the curriculum of undergraduate courses. Such an example is provided in this series of four activities that introduces students to the field of bioinformatics as they design PCR based tests for pathogenic E. coli strains. A variety of computer tools are used including BLAST searches at NCBI, bacterial genome searches at the Integrated Microbial Genomes (IMG) database, protein analysis at Pfam and literature research at PubMed. In the process, students also learn about virulence factors, enzyme function and horizontal gene transfer. Some or all of the four activities can be incorporated into microbiology or general biology courses taken by students at a variety of levels, ranging from high school through college. The activities build on one another as they teach and reinforce knowledge and skills, promote critical thinking, and provide for student collaboration and presentation. The computer-based activities can be done either in class or outside of class, thus are appropriate for inclusion in online or blended learning formats. Assessment data showed that students learned general microbiology concepts related to pathogenesis and enzyme function, gained skills in using tools of bioinformatics and molecular biology, and successfully developed and tested a scientific hypothesis.}, }
@article {pmid23461166, year = {2012}, author = {Onishchenko, GG and Sheveleva, SA and Khotimchenko, SA}, title = {[New aspects of safety assessment and food contamination with antibiotics of tetracycline group in the light of harmonization of hygienic standards in Russia and Customs Union with the international standards].}, journal = {Voprosy pitaniia}, volume = {81}, number = {5}, pages = {4-12}, pmid = {23461166}, issn = {0042-8833}, mesh = {Anti-Bacterial Agents/*analysis/pharmacology ; Drug Resistance, Bacterial/genetics ; European Union ; Food Contamination/legislation &amp; jurisprudence/*prevention &amp; control ; Food Microbiology ; Food Quality ; *Food Safety ; Gene Transfer, Horizontal ; Hygiene/legislation &amp; jurisprudence/*standards ; International Cooperation ; *Legislation, Food ; Russia ; Tetracyclines/*analysis/pharmacology ; World Health Organization ; }, abstract = {To address the issue of harmonization of Russian MRLs for tetracycline in food and on the basis of the tasks of preserving the value of hygienic standard for the more restrictive level than similar standards of the Codex Alimentarius Commission in this survey we analyzed the evidences of the negative effects of subingibitory amounts of these antibiotics (lying below the MIC for clinically relevant microorganisms). The inadequacy of the microbiological JECFA ADI and the necessity of using of methodology of analyzing the effects of biological active substances in small doses for assessing the risk of food contamination of tetracycline subingibitory concentrations were demonstrated. Current scientific information on the functions of antibiotics as signaling molecules in the microbial world and the role of tetracycline as a leading factor in the regulation of transcription in microorganisms and activation of the horizontal transfer of resistance genes transferred to the family of conjugative transposons Tn916-Tn1545 also was reviewed in paper. Evidence-based data regarding the basic contribution of subingibitory concentrations of tetracycline in the spread of worst transmissible type of antibiotic resistance and the formation of new pathogens, associated with it, are represented. To reduce the risk of direct adverse effects on microbial ecosystem in the human body and its habitat, and to minimize the indirect risk of new infections, the necessity of saving the current Russian level residues of tetracycline (< or = 0.01 mg/kg of product), which is low by contrast to the Codex MRLs (< or = 0.1-1.2 mg/kg), was proved. Tetracycline concentrations in food, regulated in Russian Federation, below 0.1 MIC for clinically significant microorganisms which aren't capable to initiation of the above described negative changes.}, }
@article {pmid22881207, year = {2010}, author = {De Leenheer, P and Dockery, J and Gedeon, T and Pilyugin, SS}, title = {The chemostat with lateral gene transfer.}, journal = {Journal of biological dynamics}, volume = {4}, number = {6}, pages = {607-620}, doi = {10.1080/17513750903540858}, pmid = {22881207}, issn = {1751-3766}, mesh = {Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal/*genetics ; *Models, Biological ; }, abstract = {We investigate the standard chemostat model when lateral gene transfer is taken into account. We will show that when the different genotypes have growth rate functions that are sufficiently close to a common growth rate function, and when the yields of the genotypes are sufficiently close to a common value, then the population evolves to a globally stable steady state, at which all genotypes coexist. These results can explain why the antibiotic-resistant strains persist in the pathogen population.}, }
@article {pmid22823257, year = {2010}, author = {Kurosawa, K and Maceachran, DP and Sinskey, AJ}, title = {Antibiotic biosynthesis following horizontal gene transfer: new milestone for novel natural product discovery?.}, journal = {Expert opinion on drug discovery}, volume = {5}, number = {9}, pages = {819-825}, doi = {10.1517/17460441.2010.505599}, pmid = {22823257}, issn = {1746-045X}, abstract = {Bacteria obtain a significant proportion of their genetic diversity via acquisition of DNA from distantly related organisms, a phenomenon known as horizontal gene transfer. The focus of horizontal gene transfer investigations has been primarily on the impact of this phenomenon on the ecological and/or pathogenic characteristics of bacterial species, with very little effort devoted to investigating horizontal gene transfer as a means of drug discovery. Here, we describe a novel approach to harness the power of horizontal gene transfer to produce novel chemotherapeutic molecules, a process that is easily scalable. We describe the state of the art in this field and discuss the current limiting factors associated with this phenomenon. Utilising a horizontal gene transfer method, we have identified and characterised a novel antimicrobial compound. Production of this antibiotic, termed rhodostreptomycin, is associated with the transfer of DNA from a species of Streptomyces to Rhodococcus by an as yet identified mechanism. We believe that horizontal gene transfer may represent the future of natural product discovery and engineering.}, }
@article {pmid22736827, year = {2009}, author = {Craig, JP and Bekal, S and Niblack, T and Domier, L and Lambert, KN}, title = {Evidence for horizontally transferred genes involved in the biosynthesis of vitamin B(1), B(5), and B(7) in Heterodera glycines.}, journal = {Journal of nematology}, volume = {41}, number = {4}, pages = {281-290}, pmid = {22736827}, issn = {0022-300X}, abstract = {Heterodera glycines is a nematode that is highly adapted to manipulate and parasitize plant hosts. The molecular players involved in these interactions have only recently begun to be identified. Here, the sequencing of the second stage juvenile transcriptome, followed by a bioinformatic screen for novel genes, identified seven new genes involved in biosynthesis and salvage of vitamins B1, B5, and B7. With no confirmed reports in the literature, each of these biosynthesis pathways is believed to have been lost in multicellular animals. However, eukaryotic-like introns in the genomic sequences of the genes confirmed eukaryotic origin and nematode-specific splice leaders found on five of the cDNAs confirmed their nematode origin. Two of the genes were found to be flanked by known nematode sequences and quantitative polymerase chain reactions on individual nematodes showed similar and consistent amplification between the vitamin B biosynthesis genes and other known H. glycines genes. This further confirmed their presence in the nematode genome. Similarity to bacterial sequences at the amino acid level suggested a prokaryotic ancestry and phylogenetic analysis of the genes supported a likely horizontal gene transfer event, suggesting H. glycines re-appropriated the genes from the prokaryotic kingdom. This finding complements the previous discovery of a vitamin B6 biosynthesis pathway within the nematode. However, unlike the complete vitamin B6 pathway, many of these vitamin B pathways appear to be missing the initial enzymes required for full de novo biosynthesis, suggesting that initial substrates in the pathways are obtained exogenously. These partial vitamin B biosynthesis enzymes have recently been identified in other single-celled eukaryotic parasites and on rhizobia symbiosis plasmids, indicating that they may play an important role in host-parasite interactions and survival within the plant environment.}, }
@article {pmid23765855, year = {2009}, author = {Cornelis, P and Bodilis, J}, title = {A survey of TonB-dependent receptors in fluorescent pseudomonads.}, journal = {Environmental microbiology reports}, volume = {1}, number = {4}, pages = {256-262}, doi = {10.1111/j.1758-2229.2009.00041.x}, pmid = {23765855}, issn = {1758-2229}, abstract = {For bacteria with an aerobic lifestyle, iron is in the oxidized Fe(3+) form, hence poorly soluble. The solution is the synthesis and excretion of siderophores with a high affinity for iron. These ferrisiderophores are recognized by TonB-dependent outer membrane receptors in Gram-negative bacteria. Haem is also a source of iron and is captured via TonB-dependent receptors as well. In many cases bacterial genomes encode genes for receptors for siderophores produced by other microorganisms (xenosiderophores). Pseudomonads are known for their high adaptive capacity and it is therefore not surprising to find a relatively large number of genes encoding these receptors. In this study we analysed the genomes of three fluorescent pseudomonads available in the Pseudomonas genome database (http://www.pseudomonas.com; P. aeruginosa, P. putida, P. syringae) in order to extract the genes coding for TonB-dependent receptors. As expected we observed differences between species for the number of receptors. We also report differences within species, suggesting the acquisition of some genes via horizontal gene transfer, including those coding for the ferripyoverdine receptors. We also report cases where duplications of receptor genes are observed and the presence of 'receptor islands'. Our study strongly supports the notion of 'core' and 'accessory' TonB-dependent receptors within each species, with the ferripyoverdine receptors belonging to the last category.}, }
@article {pmid23100716, year = {2008}, author = {Lal, S and Cheema, S and Kalia, VC}, title = {Phylogeny vs genome reshuffling: horizontal gene transfer.}, journal = {Indian journal of microbiology}, volume = {48}, number = {2}, pages = {228-242}, pmid = {23100716}, issn = {0046-8991}, abstract = {The evolutionary events in organisms can be tracked to the transfer of genetic material. The inheritance of genetic material among closely related organisms is a slow evolutionary process. On the other hand, the movement of genes among distantly related species can account for rapid evolution. The later process has been quite evident in the appearance of antibiotic resistance genes among human and animal pathogens. Phylogenetic trees based on such genes and those involved in metabolic activities reflect the incongruencies in comparison to the 16S rDNA gene, generally used for taxonomic relationships. Such discrepancies in gene inheritance have been termed as horizontal gene transfer (HGT) events. In the post-genomic era, the explosion of known sequences through large-scale sequencing projects has unraveled the weakness of traditional 16S rDNA gene tree based evolutionary model. Various methods to scrutinize HGT events include atypical composition, abnormal sequence similarity, anomalous phylogenetic distribution, unusual phyletic patterns, etc. Since HGT generates greater genetic diversity, it is likely to increase resource use and ecosystem resilience.}, }
@article {pmid23345874, year = {2004}, author = {Qi, Z and Cui, Y and Fang, W and Ling, L and Chen, R}, title = {Autosomal similarity revealed by eukaryotic genomic comparison.}, journal = {Journal of biological physics}, volume = {30}, number = {4}, pages = {305-312}, pmid = {23345874}, issn = {0092-0606}, abstract = {To describe eukaryotic autosomes quantitatively and determine differences between them in terms of amino acid sequences of genes, functional classification of proteins, and complete DNA sequences, we applied two theoretical methods, the Proteome-vector method and the function of degree of disagreement (FDOD) method, that are based on function and sequence similarity respectively, to autosomes from nine eukaryotes. No matter what aspect of the autosome is considered, the autosomal differences within each organism were less than that between species. Our results show that eukaryotic autosomes resemble each other within a species while those from different organisms differ. We propose a hypothesis (named intra-species autosomal random shuffling) as an explanation for our results and suggest that lateral gene transfer (LGT) did not occur frequently during the evolution of eukarya.}, }
@article {pmid22281184, year = {2012}, author = {Tyson, T and O'Mahony Zamora, G and Wong, S and Skelton, M and Daly, B and Jones, JT and Mulvihill, ED and Elsworth, B and Phillips, M and Blaxter, M and Burnell, AM}, title = {A molecular analysis of desiccation tolerance mechanisms in the anhydrobiotic nematode Panagrolaimus superbus using expressed sequenced tags.}, journal = {BMC research notes}, volume = {5}, number = {}, pages = {68}, pmid = {22281184}, issn = {1756-0500}, support = {G0900740/MRC_/Medical Research Council/United Kingdom ; }, abstract = {BACKGROUND: Some organisms can survive extreme desiccation by entering into a state of suspended animation known as anhydrobiosis. Panagrolaimus superbus is a free-living anhydrobiotic nematode that can survive rapid environmental desiccation. The mechanisms that P. superbus uses to combat the potentially lethal effects of cellular dehydration may include the constitutive and inducible expression of protective molecules, along with behavioural and/or morphological adaptations that slow the rate of cellular water loss. In addition, inducible repair and revival programmes may also be required for successful rehydration and recovery from anhydrobiosis.<br><br>RESULTS: To identify constitutively expressed candidate anhydrobiotic genes we obtained 9,216 ESTs from an unstressed mixed stage population of P. superbus. We derived 4,009 unigenes from these ESTs. These unigene annotations and sequences can be accessed at http://www.nematodes.org/nembase4/species_info.php?species=PSC. We manually annotated a set of 187 constitutively expressed candidate anhydrobiotic genes from P. superbus. Notable among those is a putative lineage expansion of the lea (late embryogenesis abundant) gene family. The most abundantly expressed sequence was a member of the nematode specific sxp/ral-2 family that is highly expressed in parasitic nematodes and secreted onto the surface of the nematodes' cuticles. There were 2,059 novel unigenes (51.7% of the total), 149 of which are predicted to encode intrinsically disordered proteins lacking a fixed tertiary structure. One unigene may encode an exo-&#x3b2;-1,3-glucanase (GHF5 family), most similar to a sequence from Phytophthora infestans. GHF5 enzymes have been reported from several species of plant parasitic nematodes, with horizontal gene transfer (HGT) from bacteria proposed to explain their evolutionary origin. This P. superbus sequence represents another possible HGT event within the Nematoda. The expression of five of the 19 putative stress response genes tested was upregulated in response to desiccation. These were the antioxidants glutathione peroxidase, dj-1 and 1-Cys peroxiredoxin, an shsp sequence and an lea gene.<br><br>CONCLUSIONS: P. superbus appears to utilise a strategy of combined constitutive and inducible gene expression in preparation for entry into anhydrobiosis. The apparent lineage expansion of lea genes, together with their constitutive and inducible expression, suggests that LEA3 proteins are important components of the anhydrobiotic protection repertoire of P. superbus.}, }
@article {pmid22279609, year = {2011}, author = {Dubreuil, R and Segev, N}, title = {Bringing host-cell takeover by pathogenic bacteria to center stage.}, journal = {Cellular logistics}, volume = {1}, number = {4}, pages = {120-124}, pmid = {22279609}, issn = {2159-2780}, abstract = {Intracellular pathogenic bacteria contrive processes in their host cell to create a niche for their own reproduction. One way that has emerged by which bacteria do that is delivery of secreted virulence factors, SVFs, to the cytoplasm of the host cells using the bacterial type IV secretion system, T4SS. These SVFs modulate the activity of their target host proteins, which in turn control key cellular processes. A major mechanism for the evolution of SVFs that modulate targets that do not exist in the bacterial kingdom is horizontal gene transfer. Recently, a number of bacterial SVFs were shown to act on two types of targets in host cells. First, a group of several SVFs modulate the activity and localization of one protein: Rab1 GTPase, a key regulator of intracellular trafficking. Second, ankyrin repeats-containing SVFs, referred to by microbiologists as Anks, interact with various binding proteins, which in turn regulate a myriad of cellular processes, including apoptosis. Modulation of trafficking and apoptosis are two examples of how invading bacteria takeover their host phagocyte, which instead of destroying the bacteria becomes a factory for its reproduction.}, }
@article {pmid22274828, year = {2011}, author = {Pavan, ME and Pettinari, MJ and Cairó, F and Pavan, EE and Cataldi, AA}, title = {[Bacillus anthracis: a molecular look at a famous pathogen].}, journal = {Revista Argentina de microbiologia}, volume = {43}, number = {4}, pages = {294-310}, doi = {10.1590/S0325-75412011000400010}, pmid = {22274828}, issn = {0325-7541}, mesh = {Animals ; Anthrax/epidemiology/*microbiology/veterinary ; Antigens, Bacterial/immunology/physiology ; Bacillus/classification ; Bacillus anthracis/classification/genetics/pathogenicity/*physiology ; Bacterial Capsules/physiology ; Bacterial Toxins ; Bacterial Typing Techniques ; Base Sequence ; DNA, Bacterial/genetics ; Genomic Islands/physiology ; Humans ; Membrane Proteins/genetics/physiology ; Microfilament Proteins ; Minisatellite Repeats ; Molecular Sequence Data ; Neoplasm Proteins/genetics/physiology ; Plasmids ; Polymorphism, Single Nucleotide ; Receptors, Cell Surface/genetics/physiology ; Receptors, Peptide ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Virulence/genetics/physiology ; Zoonoses ; }, abstract = {Bacillus anthracis, a gram-positive rod belonging to the Bacillus cereus group, has an extremely monomorphic genome, and presents high structural and physiological similarity with B. cereus and Bacillus thuringiensis. In this work, the new molecular methods for the identification and typing of B. anthracis developed in the last years, based on variable number tandem repeats or on genetic differences detected through sequencing, are described. The molecular aspects of traditional virulence factors: capsule, protective antigen, lethal factor and edema factor are described in depth, together with virulence factors recently proposed, such as the siderophores petrobactin and bacillibactin, the S-layer adhesin and the MntA lipoprotein. It is detailed the molecular organization of megaplasmids pXO1 and pXO2, including the pathogenicity island of pXO1. The genetic skeleton of these plasmids has been observed in related species, and this could be attributed to lateral gene transfer. Finally, the two anthrax toxin protective antigen receptors, ANTXR1/TEM8 and ANTXR2/CMG2, essential for the interaction of the pathogen with the host, are presented. The molecular studies performed in recent years have greatly increased knowledge in different aspects of this microorganism and its relationship with the host, but at the same time they have raised new questions about this noted pathogen.}, }
@article {pmid22271862, year = {2012}, author = {Martinez, E and Marquez, C and Ingold, A and Merlino, J and Djordjevic, SP and Stokes, HW and Chowdhury, PR}, title = {Diverse mobilized class 1 integrons are common in the chromosomes of pathogenic Pseudomonas aeruginosa clinical isolates.}, journal = {Antimicrobial agents and chemotherapy}, volume = {56}, number = {4}, pages = {2169-2172}, pmid = {22271862}, issn = {1098-6596}, mesh = {Australia ; Chromosomes, Bacterial/*genetics ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/drug effects ; Electrophoresis, Gel, Pulsed-Field ; Genes, Bacterial/genetics ; Genomic Islands/genetics ; Integrons/*genetics ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Polymerase Chain Reaction ; Pseudomonas Infections/genetics/*microbiology ; Pseudomonas aeruginosa/*genetics ; Uruguay ; }, abstract = {Eleven clinical class 1 integron-containing Pseudomonas aeruginosa isolates from Australia and Uruguay were investigated for the genomic locations of these elements. Several novel class 1 integrons/transposons were found in at least four distinct locations in the chromosome, including genomic islands. These elements seem to be undergoing successful dispersal by lateral gene transfer since integrons were identified across several lineages and more than one clonal line.}, }
@article {pmid22271778, year = {2012}, author = {Rasmussen, MD and Kellis, M}, title = {Unified modeling of gene duplication, loss, and coalescence using a locus tree.}, journal = {Genome research}, volume = {22}, number = {4}, pages = {755-765}, pmid = {22271778}, issn = {1549-5469}, support = {R01 HG004037/HG/NHGRI NIH HHS/United States ; }, mesh = {*Algorithms ; Animals ; *Evolution, Molecular ; Gene Deletion ; Gene Duplication ; Gene Transfer, Horizontal ; Genetic Loci/genetics ; Genome/genetics ; Humans ; *Models, Genetic ; Models, Statistical ; Mutation ; *Phylogeny ; Species Specificity ; Yeasts/classification/genetics ; }, abstract = {Gene phylogenies provide a rich source of information about the way evolution shapes genomes, populations, and phenotypes. In addition to substitutions, evolutionary events such as gene duplication and loss (as well as horizontal transfer) play a major role in gene evolution, and many phylogenetic models have been developed in order to reconstruct and study these events. However, these models typically make the simplifying assumption that population-related effects such as incomplete lineage sorting (ILS) are negligible. While this assumption may have been reasonable in some settings, it has become increasingly problematic as increased genome sequencing has led to denser phylogenies, where effects such as ILS are more prominent. To address this challenge, we present a new probabilistic model, DLCoal, that defines gene duplication and loss in a population setting, such that coalescence and ILS can be directly addressed. Interestingly, this model implies that in addition to the usual gene tree and species tree, there exists a third tree, the locus tree, which will likely have many applications. Using this model, we develop the first general reconciliation method that accurately infers gene duplications and losses in the presence of ILS, and we show its improved inference of orthologs, paralogs, duplications, and losses for a variety of clades, including flies, fungi, and primates. Also, our simulations show that gene duplications increase the frequency of ILS, further illustrating the importance of a joint model. Going forward, we believe that this unified model can offer insights to questions in both phylogenetics and population genetics.}, }
@article {pmid22265597, year = {2012}, author = {Aserse, AA and Räsänen, LA and Assefa, F and Hailemariam, A and Lindström, K}, title = {Phylogeny and genetic diversity of native rhizobia nodulating common bean (Phaseolus vulgaris L.) in Ethiopia.}, journal = {Systematic and applied microbiology}, volume = {35}, number = {2}, pages = {120-131}, doi = {10.1016/j.syapm.2011.11.005}, pmid = {22265597}, issn = {1618-0984}, mesh = {Amplified Fragment Length Polymorphism Analysis ; Bacterial Proteins/genetics ; Base Sequence ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Ethiopia ; Genetic Variation ; Molecular Sequence Data ; N-Acetylglucosaminyltransferases/genetics ; Oxidoreductases/genetics ; Phaseolus/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/analysis/genetics ; Rec A Recombinases/genetics ; Rhizobiaceae/*classification/*genetics/isolation &amp; purification ; Rhizosphere ; Sequence Analysis, DNA ; Soil Microbiology ; }, abstract = {The diversity and phylogeny of 32 rhizobial strains isolated from nodules of common bean plants grown on 30 sites in Ethiopia were examined using AFLP fingerprinting and MLSA. Based on cluster analysis of AFLP fingerprints, test strains were grouped into six genomic clusters and six single positions. In a tree built from concatenated sequences of recA, glnII, rpoB and partial 16S rRNA genes, the strains were distributed into seven monophyletic groups. The strains in the groups B, D, E, G1 and G2 could be classified as Rhizobium phaseoli, R. etli, R. giardinii, Agrobacterium tumefaciens complex and A. radiobacter, respectively, whereas the strains in group C appeared to represent a novel species. R. phaseoli, R. etli, and the novel group were the major bean nodulating rhizobia in Ethiopia. The strains in group A were linked to R. leguminosarum species lineages but not resolved. Based on recA, rpoB and 16S rRNA genes sequences analysis, a single test strain was assigned as R. leucaenae. In the nodC tree the strains belonging to the major nodulating groups were clustered into two closely linked clades. They also had almost identical nifH gene sequences. The phylogenies of nodC and nifH genes of the strains belonging to R. leguminosarum, R. phaseoli, R. etli and the putative new species (collectively called R. leguminosarum species complex) were not consistent with the housekeeping genes, suggesting symbiotic genes have a common origin which is different from the core genome of the species and indicative of horizontal gene transfer among these rhizobia.}, }
@article {pmid22265293, year = {2012}, author = {Ladero, V and Fernández, M and Calles-Enríquez, M and Sánchez-Llana, E and Cañedo, E and Martín, MC and Alvarez, MA}, title = {Is the production of the biogenic amines tyramine and putrescine a species-level trait in enterococci?.}, journal = {Food microbiology}, volume = {30}, number = {1}, pages = {132-138}, doi = {10.1016/j.fm.2011.12.016}, pmid = {22265293}, issn = {1095-9998}, mesh = {DNA Primers ; DNA, Bacterial/genetics ; Enterococcus faecalis/genetics/*metabolism ; Enterococcus faecium/genetics/*metabolism ; Food Microbiology ; Polymerase Chain Reaction/methods ; Putrescine/*biosynthesis ; Tyramine/*biosynthesis ; }, abstract = {Biogenic amines (BA) are toxic nitrogenous compounds that can be accumulated in foods via the microbial decarboxylation of certain amino acids. Lactic acid bacteria (LAB) strains belonging to different species and genera have been described as BA producers and are mainly responsible for their synthesis in fermented foods. It is generally accepted that the capacity to produced BAs is strain-dependent. However, the large number of enterococci identified as BA producers suggests that the aminogenic trait may be a species-level characteristic. Enterococcus faecalis, Enterococcus faecium and Enterococcus durans strains of different origin were analysed to determine their capacity to produce tyramine and putrescine. The presence of the genes responsible for this and the identity of their flanking regions were checked by PCR. The results suggest that tyramine biosynthesis is a species-level characteristic in E. faecalis, E. faecium and E. durans. Putrescine synthesis was found to be a species-level trait of E. faecalis, with production occurring via the agmatine deamination pathway. Some E. faecium strains of human origin also produced putrescine; this trait was probably acquired via horizontal gene transfer.}, }
@article {pmid22265250, year = {2012}, author = {Ali, SS and Xia, B and Liu, J and Navarre, WW}, title = {Silencing of foreign DNA in bacteria.}, journal = {Current opinion in microbiology}, volume = {15}, number = {2}, pages = {175-181}, doi = {10.1016/j.mib.2011.12.014}, pmid = {22265250}, issn = {1879-0364}, support = {MOP-15107//Canadian Institutes of Health Research/Canada ; MOP-86683//Canadian Institutes of Health Research/Canada ; MSH-87729//Canadian Institutes of Health Research/Canada ; }, mesh = {AT Rich Sequence ; Bacteria/*genetics ; Bacterial Proteins/chemistry/genetics/*metabolism ; DNA, Bacterial/*genetics ; DNA-Binding Proteins/chemistry/genetics/*metabolism ; Gene Expression Regulation, Bacterial ; *Gene Silencing ; Models, Molecular ; }, abstract = {Xenogeneic silencing proteins facilitate horizontal gene transfer by silencing expression of AT-rich sequences. By virtue of their activity these proteins serve as master regulators of a variety of important functions including motility, drug resistance, and virulence. Three families of silencers have been identified to date: the H-NS like proteins of Gram-negative bacteria, the MvaT like proteins of Pseudomonacae, and the Lsr2 proteins of Actinobacteria. Structural and biochemical characterization of these proteins have revealed that they share surprising commonalities in mechanism and function despite extensive divergence in both sequence and structure. Here we discuss the mechanisms that underlie the ability of these proteins to selectively target AT-rich DNA and the contradictory data regarding the mode by which H-NS forms nucleoprotein complexes.}, }
@article {pmid22265093, year = {2012}, author = {Hirschi, KD}, title = {New foods for thought.}, journal = {Trends in plant science}, volume = {17}, number = {3}, pages = {123-125}, doi = {10.1016/j.tplants.2012.01.004}, pmid = {22265093}, issn = {1878-4372}, mesh = {Animals ; *Food ; Gene Transfer, Horizontal ; Humans ; MicroRNAs/genetics ; Phytotherapy ; Plants/genetics/metabolism ; }, abstract = {Recent findings show that genetic material in plant foods may survive digestion, circulate through our bodies and modulate our gene expression. These findings could alter our understanding of nutrition, genetic regulation and open up new vistas for engineering foods.}, }
@article {pmid22253924, year = {2012}, author = {Valente, C and Hinds, J and Pinto, F and Brugger, SD and Gould, K and Mühlemann, K and de Lencastre, H and Sá-Leão, R}, title = {Decrease in pneumococcal co-colonization following vaccination with the seven-valent pneumococcal conjugate vaccine.}, journal = {PloS one}, volume = {7}, number = {1}, pages = {e30235}, pmid = {22253924}, issn = {1932-6203}, support = {//Wellcome Trust/United Kingdom ; 086547//Wellcome Trust/United Kingdom ; }, mesh = {Child ; Child, Preschool ; Colony Count, Microbial ; Heptavalent Pneumococcal Conjugate Vaccine ; Humans ; Infant ; Multivariate Analysis ; Oligonucleotide Array Sequence Analysis ; Pneumococcal Vaccines/*immunology ; Polymorphism, Restriction Fragment Length ; Reproducibility of Results ; Risk Factors ; Serotyping ; Streptococcus pneumoniae/classification/*growth &amp; development/*immunology/isolation &amp; purification ; *Vaccination ; }, abstract = {Understanding the epidemiology of pneumococcal co-colonization is important for monitoring vaccine effectiveness and the occurrence of horizontal gene transfer between pneumococcal strains. In this study we aimed to evaluate the impact of the seven-valent pneumococcal conjugate vaccine (PCV7) on pneumococcal co-colonization among Portuguese children. Nasopharyngeal samples from children up to 6 years old yielding a pneumococcal culture were clustered into three groups: pre-vaccine era (n = 173), unvaccinated children of the vaccine era (n = 169), and fully vaccinated children (4 doses; n = 150). Co-colonization, serotype identification, and relative serotype abundance were detected by analysis of DNA of the total bacterial growth of the primary culture plate using the plyNCR-RFLP method and a molecular serotyping microarray-based strategy. The plyNCR-RFLP method detected an overall co-colonization rate of 20.1%. Microarray analysis confirmed the plyNCR-RFLP results. Vaccination status was the only factor found to be significantly associated with co-colonization: co-colonization rates were significantly lower (p = 0.004; Fisher's exact test) among fully vaccinated children (8.0%) than among children from the pre-PCV7 era (17.3%) or unvaccinated children of the PCV7 era (18.3%). In the PCV7 era there were significantly less non-vaccine type (NVT) co-colonization events than would be expected based on the NVT distribution observed in the pre-PCV7 era (p = 0.024). In conclusion, vaccination with PCV7 resulted in a lower co-colonization rate due to an asymmetric distribution between NVTs found in single and co-colonized samples. We propose that some NVTs prevalent in the PCV7 era are more competitive than others, hampering their co-existence in the same niche. This result may have important implications since a decrease in co-colonization events is expected to translate in decreased opportunities for horizontal gene transfer, hindering pneumococcal evolution events such as acquisition of antibiotic resistance determinants or capsular switch. This might represent a novel potential benefit of conjugate vaccines.}, }
@article {pmid22253534, year = {2011}, author = {Sorhannus, U}, title = {Evolution of antifreeze protein genes in the diatom genus fragilariopsis: evidence for horizontal gene transfer, gene duplication and episodic diversifying selection.}, journal = {Evolutionary bioinformatics online}, volume = {7}, number = {}, pages = {279-289}, pmid = {22253534}, issn = {1176-9343}, abstract = {Hypotheses about horizontal transfer of antifreeze protein genes to ice-living diatoms were addressed using two different statistical methods available in the program Prunier. The role of diversifying selection in driving the differentiation of a set of antifreeze protein genes in the diatom genus Fragilariopsis was also investigated. Four horizontal gene transfer events were identified. Two of these took place between two major eukaryote lineages, that is from the diatom Chaetoceros neogracile to the copepod Stephos longipes and from a basidiomycete clade to a monophyletic group, consisting of the diatom species Fragilariopsis curta and Fragilariopsis cylindrus. The remaining two events included transfers from an ascomycete lineage to the proteobacterium Stigmatella aurantiaca and from the proteobacterium Polaribacter irgensii to a group composed of 4 proteobacterium species. After the Fragilariopsis lineage acquired the antifreeze protein gene from the basidiomycetes, it duplicated and went through episodic evolution, characterized by strong positive selection acting on short segments of the branches in the tree. This selection pattern suggests that the paralogs differentiated functionally over relatively short time periods. Taken together, the results obtained here indicate that the group of antifreeze protein genes considered here have a complex evolutionary history.}, }
@article {pmid22252871, year = {2012}, author = {Shima, A and Hinenoya, A and Asakura, M and Sugimoto, N and Tsukamoto, T and Ito, H and Nagita, A and Faruque, SM and Yamasaki, S}, title = {Molecular characterizations of cytolethal distending toxin produced by Providencia alcalifaciens strains isolated from patients with diarrhea.}, journal = {Infection and immunity}, volume = {80}, number = {4}, pages = {1323-1332}, pmid = {22252871}, issn = {1098-5522}, mesh = {Animals ; Bacterial Toxins/chemistry/*genetics/immunology/toxicity ; Base Sequence ; CHO Cells ; Caco-2 Cells ; Cell Cycle Checkpoints ; Cell Line ; Child ; Child, Preschool ; Chlorocebus aethiops ; Cricetinae ; DNA, Bacterial/analysis/*genetics ; Diarrhea/epidemiology/*microbiology ; Enterobacteriaceae Infections/microbiology ; Escherichia coli/genetics ; Escherichia coli Infections/epidemiology/microbiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; HeLa Cells ; Histones/metabolism ; Humans ; Mice ; Molecular Sequence Data ; NIH 3T3 Cells ; Phosphorylation ; Providencia/*genetics/*isolation &amp; purification ; Rabbits ; Recombinant Proteins/immunology ; Sequence Analysis, DNA ; Shigella boydii/enzymology/genetics ; Vero Cells ; }, abstract = {Cytolethal distending toxins (CDTs), which block eukaryotic cell proliferation by acting as inhibitory cyclomodulins, are produced by diverse groups of Gram-negative bacteria. Active CDT is composed of three polypeptides--CdtA, CdtB, and CdtC--encoded by the genes cdtA, cdtB, and cdtC, respectively. We developed a PCR-restriction fragment length polymorphism assay for the detection and differentiation of five alleles of cdtB (Cdt-I through Cdt-V) in Escherichia coli and used the assay to investigate the prevalence and characteristic of CDT-producing E. coli in children with diarrhea (A. Hinenoya et al., Microbiol. Immunol. 53:206-215, 2009). In these assays, two untypable cdtB genes were detected and the organisms harboring the cdtB gene were identified as Providencia alcalifaciens (strains AH-31 and AS-1). Nucleotide sequence analysis of the cdt gene cluster revealed that the cdtA, cdtB, and cdtC genes of P. alcalifaciens are of 750, 810, and 549 bp, respectively. To understand the possible horizontal transfer of the cdt genes among closely related species, the presence of cdt genes was screened in various Providencia spp. by colony hybridization assay, and the cdt gene cluster was found in only limited strains of P. alcalifaciens. Genome walking revealed that the cdt gene cluster of P. alcalifaciens is located adjacent to a putative transposase gene, suggesting the locus might be horizontally transferable. Interestingly, the CDT of P. alcalifaciens (PaCDT) showed some homology with the CDT of Shigella boydii. Whereas filter-sterilized lysates of strains AH-31 and AS-1 showed distention of CHO but not of HeLa cells, E. coli CDT-I exhibited distention of both cells. This activity of PaCDT was confirmed by generating recombinant PaCDT protein, which could also be neutralized by rabbit anti-PaCdtB antibody. Furthermore, recombinant PaCDT was found to induce G(2)/M cell cycle arrest and phosphorylation of host histone H2AX, a sensitive marker of DNA double-strand breaks. To our knowledge, this is the first report showing that certain clinical P. alcalifaciens strains could produce variants of the CDTs compared.}, }
@article {pmid22252506, year = {2013}, author = {Bichsel, M and Barbour, AD and Wagner, A}, title = {Estimating the fitness effect of an insertion sequence.}, journal = {Journal of mathematical biology}, volume = {66}, number = {1-2}, pages = {95-114}, pmid = {22252506}, issn = {1432-1416}, mesh = {*DNA Transposable Elements ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; *Genetic Fitness ; Genome, Bacterial ; Interspersed Repetitive Sequences ; Likelihood Functions ; Mathematical Concepts ; *Models, Genetic ; Proteobacteria/genetics ; }, abstract = {Since its discovery, mobile DNA has fascinated researchers. In particular, many researchers have debated why insertion sequences persist in prokaryote genomes and populations. While some authors think that insertion sequences persist only because of occasional beneficial effects they have on their hosts, others argue that horizontal gene transfer is strong enough to overcome their generally detrimental effects. In this study, we model the long-term fate of a prokaryote cell population, of which a small proportion of cells has been infected with one insertion sequence per cell. Based on our model and the distribution of IS5, an insertion sequence for which sufficient data is available in 525 fully sequenced proteobacterial genomes, we show that the fitness cost of insertion sequences is so small that they are effectively neutral or only slightly detrimental. We also show that an insertion sequence infection can persist and reach the empirically observed distribution if the rate of horizontal gene transfer is at least as large as the fitness cost, and that this rate is well within the rates of horizontal gene transfer observed in nature. In addition, we show that the time needed to reach the observed prevalence of IS5 is unrealistically long for the fitness cost and horizontal gene transfer rate that we computed. Occasional beneficial effects may thus have played an important role in the fast spreading of insertion sequences like IS5.}, }
@article {pmid22248925, year = {2012}, author = {Reisner, A and Wolinski, H and Zechner, EL}, title = {In situ monitoring of IncF plasmid transfer on semi-solid agar surfaces reveals a limited invasion of plasmids in recipient colonies.}, journal = {Plasmid}, volume = {67}, number = {2}, pages = {155-161}, pmid = {22248925}, issn = {1095-9890}, support = {P 21434/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Conjugation, Genetic ; Escherichia coli/*genetics/*growth &amp; development ; *Gene Transfer, Horizontal ; Phenotype ; Plasmids/*genetics/metabolism ; }, abstract = {Most natural conjugative IncF plasmids encode a fertility inhibition system that represses transfer gene expression in the majority of plasmid-carrying cells. The successful spread of these plasmids in clinically relevant bacteria has been suggested to be supported by a transitory derepression of transfer gene expression in newly formed transconjugants. In this study, we aimed to monitor the extent of transitory derepression during agar surface matings in situ by comparing plasmid spread of the IncF plasmid R1 and its derepressed mutant R1drd19 at low initial cell densities. A zygotic induction strategy was used to visualize the spatial distribution of fluorescent transconjugants within the heterogeneous environment. Epifluorescence and confocal microscopy revealed different transfer patterns for both plasmids, however, spread beyond the first five recipient cell layers adjacent to the donor cells was not observed. Similar results were observed for other prototypical conjugative plasmids. These results cannot rule out that transitory derepression contributes to the limited R1 plasmid invasion, but other factors like nutrient availability or spatial structure seem to limit plasmid spread.}, }
@article {pmid22248540, year = {2011}, author = {Gordo, I and Perfeito, L and Sousa, A}, title = {Fitness effects of mutations in bacteria.}, journal = {Journal of molecular microbiology and biotechnology}, volume = {21}, number = {1-2}, pages = {20-35}, doi = {10.1159/000332747}, pmid = {22248540}, issn = {1660-2412}, mesh = {*Adaptation, Biological ; Bacteria/*genetics/*growth &amp; development/metabolism ; Bacterial Infections/drug therapy/microbiology ; Gene Transfer, Horizontal ; Humans ; *Mutation ; Selection, Genetic ; *Stress, Physiological ; }, abstract = {Mutation is the primary source of variation in any organism. Without it, natural selection cannot operate and organisms cannot adapt to novel environments. Mutation is also generally a source of defect: many mutations are not neutral but cause fitness decreases in the organisms where they arise. In bacteria, another important source of variation is horizontal gene transfer. This source of variation can also cause beneficial or deleterious effects. Determining the distribution of fitness effects of mutations in different environments and genetic backgrounds is an active research field. In bacteria, knowledge of these distributions is key for understanding important traits. For example, for determining the dynamics of microorganisms with a high genomic mutation rate (mutators), and for understanding the evolution of antibiotic resistance, and the emergence of pathogenic traits. All of these characteristics are extremely relevant for human health both at the individual and population levels. Experimental evolution has been a valuable tool to address these questions. Here, we review some of the important findings of mutation effects in bacteria revealed through laboratory experiments.}, }
@article {pmid22247511, year = {2012}, author = {Seth-Smith, HM and Fookes, MC and Okoro, CK and Baker, S and Harris, SR and Scott, P and Pickard, D and Quail, MA and Churcher, C and Sanders, M and Harmse, J and Dougan, G and Parkhill, J and Thomson, NR}, title = {Structure, diversity, and mobility of the Salmonella pathogenicity island 7 family of integrative and conjugative elements within Enterobacteriaceae.}, journal = {Journal of bacteriology}, volume = {194}, number = {6}, pages = {1494-1504}, pmid = {22247511}, issn = {1098-5530}, support = {098051//Wellcome Trust/United Kingdom ; }, mesh = {Bacterial Proteins/*genetics ; Cluster Analysis ; DNA Mutational Analysis ; DNA, Bacterial/chemistry/genetics ; Enterobacteriaceae/*genetics/*pathogenicity ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genomic Islands ; *Interspersed Repetitive Sequences ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Virulence Factors/*genetics ; }, abstract = {Integrative and conjugative elements (ICEs) are self-mobile genetic elements found in the genomes of some bacteria. These elements may confer a fitness advantage upon their host bacteria through the cargo genes that they carry. Salmonella pathogenicity island 7 (SPI-7), found within some pathogenic strains of Salmonella enterica, possesses features indicative of an ICE and carries genes implicated in virulence. We aimed to identify and fully analyze ICEs related to SPI-7 within the genus Salmonella and other Enterobacteriaceae. We report the sequence of two novel SPI-7-like elements, found within strains of Salmonella bongori, which share 97% nucleotide identity over conserved regions with SPI-7 and with each other. Although SPI-7 within Salmonella enterica serovar Typhi appears to be fixed within the chromosome, we present evidence that these novel elements are capable of excision and self-mobility. Phylogenetic analyses show that these Salmonella mobile elements share an ancestor which existed approximately 3.6 to 15.8 million years ago. Additionally, we identified more distantly related ICEs, with distinct cargo regions, within other strains of Salmonella as well as within Citrobacter, Erwinia, Escherichia, Photorhabdus, and Yersinia species. In total, we report on a collection of 17 SPI-7 related ICEs within enterobacterial species, of which six are novel. Using comparative and mutational studies, we have defined a core of 27 genes essential for conjugation. We present a growing family of SPI-7-related ICEs whose mobility, abundance, and cargo variability indicate that these elements may have had a large impact on the evolution of the Enterobacteriaceae.}, }
@article {pmid22247173, year = {2012}, author = {Hanna, LF and Matthews, TD and Dinsdale, EA and Hasty, D and Edwards, RA}, title = {Characterization of the ELPhiS prophage from Salmonella enterica serovar Enteritidis strain LK5.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {6}, pages = {1785-1793}, pmid = {22247173}, issn = {1098-5336}, mesh = {DNA, Viral/chemistry/genetics ; Gene Order ; Gene Transfer, Horizontal ; Genes, Viral ; Host Specificity ; Lysogeny ; Molecular Sequence Data ; Prophages/*genetics/growth &amp; development/*isolation &amp; purification ; Salmonella enteritidis/*virology ; Sequence Analysis, DNA ; Virulence ; Virus Activation ; }, abstract = {Phages are a primary driving force behind the evolution of bacterial pathogens by transferring a variety of virulence genes into their hosts. Similar to other bacterial genomes, the Salmonella enterica serovar Enteritidis LK5 genome contains several regions that are homologous to phages. Although genomic analysis demonstrated the presence of prophages, it was unable to confirm which phage elements within the genome were viable. Genetic markers were used to tag one of the prophages in the genome to allow monitoring of phage induction. Commonly used laboratory strains of Salmonella were resistant to phage infection, and therefore a rapid screen was developed to identify susceptible hosts. This approach showed that a genetically tagged prophage, ELPhiS (Enteritidis lysogenic phage S), was capable of infecting Salmonella serovars that are diverse in host range and virulence and has the potential to laterally transfer genes between these serovars via lysogenic conversion. The rapid screen approach is adaptable to any system with a large collection of isolates and may be used to test the viability of prophages found by sequencing the genomes of various bacterial pathogens.}, }
@article {pmid22241047, year = {2012}, author = {Bisgaard, M and Nørskov-Lauritsen, N and de Wit, SJ and Hess, C and Christensen, H}, title = {Multilocus sequence phylogenetic analysis of Avibacterium.}, journal = {Microbiology (Reading, England)}, volume = {158}, number = {Pt 4}, pages = {993-1004}, doi = {10.1099/mic.0.054429-0}, pmid = {22241047}, issn = {1465-2080}, mesh = {Bacterial Typing Techniques ; Consensus Sequence ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Multilocus Sequence Typing ; Pasteurellaceae/*classification/genetics/isolation &amp; purification ; Phenotype ; *Phylogeny ; }, abstract = {This study examined 49 field isolates of the genus Avibacterium, with the 49 being allocated to 36 epidemiologically unrelated groups and one isolate from each group being examined in detail. In addition, six type and reference strains were investigated. Phylogenetic analysis of partially sequenced recN, rpoB, infB, pgi and sodA genes confirmed the existence of the species Avibacterium paragallinarum, while a species complex encompassing Avibacterium volantium, Avibacterium avium, Avibacterium gallinarum, Avibacterium endocarditis and Avibacterium sp. A could not be resolved. All isolates shared at least one identical sequence in one gene, indicating low diversity or horizontal gene transfer (HGT) between isolates. Such HGT between isolates of defined species and unclassified isolates combined with high sequence similarity can be explained as the result of an ongoing speciation process. The alternative explanation is that Av. volantium, Av. avium and Avibacterium sp. A were misclassified originally. Except for Av. paragallinarum, identification of species of Avibacterium seems problematic, even by DNA sequencing, as shown in the present investigation. The results indicate that Avibacterium probably contains only two or three species. Until the taxonomic revision is completed we recommend that isolates that do not fit with named species by genotype and phenotype be designated Avibacterium sp.}, }
@article {pmid22240474, year = {2012}, author = {Langille, MG and Meehan, CJ and Beiko, RG}, title = {Human microbiome: a genetic bazaar for microbes?.}, journal = {Current biology : CB}, volume = {22}, number = {1}, pages = {R20-2}, doi = {10.1016/j.cub.2011.11.023}, pmid = {22240474}, issn = {1879-0445}, mesh = {DNA Transposable Elements ; *Gene Transfer, Horizontal ; Humans ; *Metagenome ; }, abstract = {A recent study suggests that lateral gene transfer has been particularly intense among human-associated microbes. What can this tell us about our relationship with our internal microbial world?}, }
@article {pmid22238262, year = {2012}, author = {Latysheva, N and Junker, VL and Palmer, WJ and Codd, GA and Barker, D}, title = {The evolution of nitrogen fixation in cyanobacteria.}, journal = {Bioinformatics (Oxford, England)}, volume = {28}, number = {5}, pages = {603-606}, doi = {10.1093/bioinformatics/bts008}, pmid = {22238262}, issn = {1367-4811}, mesh = {Bacterial Proteins/metabolism ; Biological Evolution ; Cyanobacteria/classification/*genetics/*metabolism ; Gene Transfer, Horizontal ; Nitrogen Fixation ; Nitrogenase/genetics ; Phylogeny ; }, abstract = {MOTIVATION: Fixed nitrogen is an essential requirement for the biosynthesis of cellular nitrogenous compounds. Some cyanobacteria can fix nitrogen, contributing significantly to the nitrogen cycle, agriculture and biogeochemical history of Earth. The rate and position on the species phylogeny of gains and losses of this ability, as well as of the underlying nif genes, are controversial.<br><br>RESULTS: We use probabilistic models of trait evolution to investigate the presence and absence of cyanobacterial nitrogen-fixing ability. We estimate rates of change on the species phylogeny, pinpoint probable changes and reconstruct the state and nif gene complement of the ancestor. Our results are consistent with a nitrogen-fixing cyanobacterial ancestor, repeated loss of nitrogen fixation and vertical descent, with little horizontal transfer of the genes involved.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid22237545, year = {2012}, author = {Pfreundt, U and Stal, LJ and Voß, B and Hess, WR}, title = {Dinitrogen fixation in a unicellular chlorophyll d-containing cyanobacterium.}, journal = {The ISME journal}, volume = {6}, number = {7}, pages = {1367-1377}, pmid = {22237545}, issn = {1751-7370}, mesh = {Australia ; Chlorophyll/*metabolism ; Cyanobacteria/classification/enzymology/*genetics/*metabolism ; Light ; *Nitrogen Fixation ; Nitrogenase/genetics ; *Photosynthesis ; Phylogeny ; Seawater/*microbiology ; }, abstract = {Marine cyanobacteria of the genus Acaryochloris are the only known organisms that use chlorophyll d as a photosynthetic pigment. However, based on chemical sediment analyses, chlorophyll d has been recognized to be widespread in oceanic and lacustrine environments. Therefore it is highly relevant to understand the genetic basis for different physiologies and possible niche adaptation in this genus. Here we show that unlike all other known isolates of Acaryochloris, the strain HICR111A, isolated from waters around Heron Island, Great Barrier Reef, possesses a unique genomic region containing all the genes for the structural and enzymatically active proteins of nitrogen fixation and cofactor biosynthesis. Their phylogenetic analysis suggests a close relation to nitrogen fixation genes from certain other marine cyanobacteria. We show that nitrogen fixation in Acaryochloris sp. HICR111A is regulated in a light-dark-dependent fashion. We conclude that nitrogen fixation, one of the most complex physiological traits known in bacteria, might be transferred among oceanic microbes by horizontal gene transfer more often than anticipated so far. Our data show that the two powerful processes of oxygenic photosynthesis and nitrogen fixation co-occur in one and the same cell also in this branch of marine microbes and characterize Acaryochloris as a physiologically versatile inhabitant of an ecological niche, which is primarily driven by the absorption of far-red light.}, }
@article {pmid22235347, year = {2012}, author = {Rabello, MC and Matsumoto, CK and Almeida, LG and Menendez, MC and Oliveira, RS and Silva, RM and Garcia, MJ and Leão, SC}, title = {First description of natural and experimental conjugation between Mycobacteria mediated by a linear plasmid.}, journal = {PloS one}, volume = {7}, number = {1}, pages = {e29884}, pmid = {22235347}, issn = {1932-6203}, mesh = {*Gene Transfer Techniques ; *Gene Transfer, Horizontal ; Mycobacterium avium/*genetics ; Mycobacterium bovis/genetics ; Mycobacterium kansasii/*genetics ; Plasmids/*genetics ; Sequence Analysis ; }, abstract = {BACKGROUND: In a previous study, we detected the presence of a Mycobacterium avium species-specific insertion sequence, IS1245, in Mycobacterium kansasii. Both species were isolated from a mixed M. avium-M. kansasii bone marrow culture from an HIV-positive patient. The transfer mechanism of this insertion sequence to M. kansasii was investigated here.<br><br>A linear plasmid (pMA100) was identified in all colonies isolated from the M. avium-M. kansasii mixed culture carrying the IS1245 element. The linearity of pMA100 was confirmed. Other analyses suggested that pMA100 contained a covalently bound protein in the terminal regions, a characteristic of invertron linear replicons. Partial sequencing of pMA100 showed that it bears one intact copy of IS1245 inserted in a region rich in transposase-related sequences. These types of sequences have been described in other linear mycobacterial plasmids. Mating experiments were performed to confirm that pMA100 could be transferred in vitro from M. avium to M. kansasii. pMA100 was transferred by in vitro conjugation not only to the M. kansasii strain from the mixed culture, but also to two other unrelated M. kansasii clinical isolates, as well as to Mycobacterium bovis BCG Moreau.<br><br>CONCLUSIONS/SIGNIFICANCE: Horizontal gene transfer (HGT) is one of most important mechanisms leading to the evolution and diversity of bacteria. This work provides evidence for the first time on the natural occurrence of HGT between different species of mycobacteria. Gene transfer, mediated by a novel conjugative plasmid, was detected and experimentally reproduced.}, }
@article {pmid22233824, year = {2011}, author = {Drago, L and Rodighiero, V and Mattina, R and Toscano, M and DE Vecchi, E}, title = {In vitro selection and transferability of antibiotic resistance in the probiotic strain Lactobacillus reuteri DSM 17938.}, journal = {Journal of chemotherapy (Florence, Italy)}, volume = {23}, number = {6}, pages = {371-373}, doi = {10.1179/joc.2011.23.6.371}, pmid = {22233824}, issn = {1973-9478}, mesh = {Animals ; Drug Resistance, Microbial ; Gastrointestinal Tract/*drug effects/metabolism ; *Gene Transfer, Horizontal ; Humans ; Limosilactobacillus reuteri/*drug effects/*genetics ; Mutation ; *Probiotics ; }, }
@article {pmid22233546, year = {2012}, author = {Giusti, Mde L and Pistorio, M and Lozano, MJ and Tejerizo, GA and Salas, ME and Martini, MC and López, JL and Draghi, WO and Del Papa, MF and Pérez-Mendoza, D and Sanjuán, J and Lagares, A}, title = {Genetic and functional characterization of a yet-unclassified rhizobial Dtr (DNA-transfer-and-replication) region from a ubiquitous plasmid conjugal system present in Sinorhizobium meliloti, in Sinorhizobium medicae, and in other nonrhizobial Gram-negative bacteria.}, journal = {Plasmid}, volume = {67}, number = {3}, pages = {199-210}, doi = {10.1016/j.plasmid.2011.12.010}, pmid = {22233546}, issn = {1095-9890}, mesh = {Base Sequence ; Conjugation, Genetic ; DNA, Bacterial/genetics/*isolation &amp; purification ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Gram-Negative Bacteria/classification/*genetics ; Medicago/microbiology ; Molecular Sequence Data ; Nitrogen Fixation ; Phylogeny ; Plant Roots/microbiology ; Plasmids ; Sinorhizobium/classification/*genetics ; Sinorhizobium meliloti/classification/*genetics ; *Soil Microbiology ; Symbiosis/genetics ; Sympatry ; }, abstract = {Rhizobia are Gram-negative bacteria that live in soils and associate with leguminous plants to establish nitrogen-fixing symbioses. The ability of these bacteria to undergo horizontal gene transfer (HGT) is thought to be one of the main features to explain both the origin of their symbiotic life-style and the plasticity and dynamics of their genomes. In our laboratory we have previously characterized at the species level the non-pSym plasmid mobilome in Sinorhizobium meliloti, the symbiont of Medicago spp., and have found a high incidence of conjugal activity in many plasmids (Pistorio et al., 2008). In this work we characterized the Dtr (DNA-transfer-and-replication) region of one of those plasmids, pSmeLPU88b. This mobilization region was found to represent a previously unclassified Dtr type in rhizobia (hereafter type-IV), highly ubiquitous in S. meliloti and found in other genera of Gram-negative bacteria as well; including Agrobacterium, Ochrobactrum, and Chelativorans. The oriT of the type-IV Dtr described here could be located by function within a DNA fragment of 278 bp, between the divergent genes parA and mobC. The phylogenetic analysis of the cognate relaxase MobZ indicated that this protein groups close to the previously defined MOB(P3) and MOB(P4) type of enzymes, but is located in a separate and novel cluster that we have designated MOB(P0). Noteworthy, MOB(P0) and MOB(P4) relaxases were frequently associated with plasmids present in rhizospheric soil bacteria. A comparison of the nod-gene locations with the phylogenetic topology of the rhizobial relaxases revealed that the symbiotic genes are found on diverse plasmids bearing any of the four Dtr types, thus indicating that pSym plasmids are not specifically associated with any particular mobilization system. Finally, we demonstrated that the type-IV Dtr promoted the mobilization of plasmids from S. meliloti to Sinorhizobium medicae as well as from these rhizobia to other bacteria by means of their own helper functions. The results present an as-yet-unclassified and seemingly ubiquitous conjugal system that provides a mechanistic support for the HGT between sympatric rhizobia of Medicago roots, and between other soil and rhizospheric bacteria.}, }
@article {pmid22232693, year = {2012}, author = {Stecher, B and Denzler, R and Maier, L and Bernet, F and Sanders, MJ and Pickard, DJ and Barthel, M and Westendorf, AM and Krogfelt, KA and Walker, AW and Ackermann, M and Dobrindt, U and Thomson, NR and Hardt, WD}, title = {Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {4}, pages = {1269-1274}, pmid = {22232693}, issn = {1091-6490}, support = {/WT_/Wellcome Trust/United Kingdom ; 076964/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Bacteriocin Plasmids/genetics ; Base Sequence ; *Biological Evolution ; Colitis/*microbiology ; Computational Biology ; DNA Primers/genetics ; Enterobacteriaceae/*genetics/growth &amp; development ; Escherichia coli/genetics ; Gene Transfer, Horizontal/*genetics ; Mice ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salmonella typhimurium/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {The mammalian gut harbors a dense microbial community interacting in multiple ways, including horizontal gene transfer (HGT). Pangenome analyses established particularly high levels of genetic flux between Gram-negative Enterobacteriaceae. However, the mechanisms fostering intraenterobacterial HGT are incompletely understood. Using a mouse colitis model, we found that Salmonella-inflicted enteropathy elicits parallel blooms of the pathogen and of resident commensal Escherichia coli. These blooms boosted conjugative HGT of the colicin-plasmid p2 from Salmonella enterica serovar Typhimurium to E. coli. Transconjugation efficiencies of ~100% in vivo were attributable to high intrinsic p2-transfer rates. Plasmid-encoded fitness benefits contributed little. Under normal conditions, HGT was blocked by the commensal microbiota inhibiting contact-dependent conjugation between Enterobacteriaceae. Our data show that pathogen-driven inflammatory responses in the gut can generate transient enterobacterial blooms in which conjugative transfer occurs at unprecedented rates. These blooms may favor reassortment of plasmid-encoded genes between pathogens and commensals fostering the spread of fitness-, virulence-, and antibiotic-resistance determinants.}, }
@article {pmid22228423, year = {2012}, author = {Bello-López, JM and Vázquez-Ocampo, NJ and Fernández-Rendón, E and Curiel-Quesada, E}, title = {Inability of some Aeromonas hydrophila strains to act as recipients of plasmid pRAS1 in conjugal transfer experiments.}, journal = {Current microbiology}, volume = {64}, number = {4}, pages = {332-337}, pmid = {22228423}, issn = {1432-0991}, mesh = {Aeromonas hydrophila/*genetics ; *Conjugation, Genetic ; *Gene Transfer, Horizontal ; *Plasmids ; *Transformation, Bacterial ; }, abstract = {Plasmids belonging to the IncU incompatibility group are mobile genetic elements isolated frequently from Aeromonas spp. These plasmids share structural and functional characteristics and often carry Class-1 integrons bearing antibiotic resistance genes. In this work the ability of two IncU plasmids, pAr-32 and pRAS1 to establish in different A. hydrophila strains after conjugal transfer was studied. In vitro transfer frequencies on solid surface ranged from 10(-1) to 10(-6) for pAr-32 and from 10(-3) to 10(-5) for pRAS1. While carrying out these experiments we detected four strains unable to acquire plasmid pRAS1, indicating that the genetic background of recipients affects the establishment of the plasmid. We explored the possible reasons why these strains failed to yield transconjugants after mating experiments using A. salmonicida 718 as a donor. Factors included donor cell recognition, incompatibility, surface exclusion and restriction of incoming DNA. We found that none of these factors could explain the refractivity of non-receptive A. hydrophila strains to yield transconjugants. Although we do not know the reasons of this refractivity, we may speculate that these isolates lack a product necessary to replicate or stabilize plasmid pRAS1. Alternatively, these strains could contain a product that impedes plasmid establishment.}, }
@article {pmid22226958, year = {2012}, author = {Allemand, JF and Maier, B and Smith, DE}, title = {Molecular motors for DNA translocation in prokaryotes.}, journal = {Current opinion in biotechnology}, volume = {23}, number = {4}, pages = {503-509}, pmid = {22226958}, issn = {1879-0429}, support = {R01 GM088186/GM/NIGMS NIH HHS/United States ; R01 GM088186-01A2/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Proteins/*metabolism ; Bacteriophages/genetics/metabolism ; *Biological Transport ; Capsid/metabolism ; DNA/*metabolism ; Molecular Motor Proteins/*metabolism ; Prokaryotic Cells/*metabolism ; }, abstract = {DNA transport is an essential life process. From chromosome separation during cell division or sporulation, to DNA virus ejection or encapsidation, to horizontal gene transfer, it is ubiquitous in all living organisms. Directed DNA translocation is often energetically unfavorable and requires an active process that uses energy, namely the action of molecular motors. In this review we present recent advances in the understanding of three molecular motors involved in DNA transport in prokaryotes, paying special attention to recent studies using single-molecule techniques. We first discuss DNA transport during cell division, then packaging of DNA in phage capsids, and then DNA import during bacterial transformation.}, }
@article {pmid22225844, year = {2012}, author = {Gerth, ML and Ferla, MP and Rainey, PB}, title = {The origin and ecological significance of multiple branches for histidine utilization in Pseudomonas aeruginosa PAO1.}, journal = {Environmental microbiology}, volume = {14}, number = {8}, pages = {1929-1940}, doi = {10.1111/j.1462-2920.2011.02691.x}, pmid = {22225844}, issn = {1462-2920}, mesh = {*Environment ; Formiminoglutamic Acid/metabolism ; Gene Expression Regulation, Bacterial ; Genome, Bacterial/genetics ; Glutamic Acid/biosynthesis ; Histidine/*metabolism ; Mutation ; Operon/genetics ; Phylogeny ; Pseudomonas aeruginosa/classification/genetics/*metabolism ; }, abstract = {Pseudomonas proliferate in a wide spectrum of harsh and variable environments. In many of these environments, amino acids, such as histidine, are a valuable source of carbon, nitrogen and energy. Here, we demonstrate that the histidine uptake and utilization (hut) pathway of Pseudomonas aeruginosa PAO1 contains two branches from the intermediate formiminoglutamate to the product glutamate. Genetic analysis revealed that the four-step route is dispensable as long as the five-step route is present (and vice versa). Mutants with deletions of either the four-step (HutE) or five-step (HutFG) branches were competed against each other and the wild-type strain to test the hypothesis of ecological redundancy; that is, that the presence of two pathways confers no benefit beyond that delivered by the individual pathways. Fitness assays performed under several environmental conditions led us to reject this hypothesis; the four-step pathway can provide an advantage when histidine is the sole carbon source. An IclR-type regulator (HutR) was identified that regulates the four-step pathway. Comparison of sequenced genomes revealed that P.aeruginosa strains and P.fluorescens Pf-5 have branched hut pathways. Phylogenetic analyses suggests that the gene encoding formiminoglutamase (hutE) was acquired by horizontal gene transfer from a Ralstonia-like ancestor. Potential barriers to inter-species transfer of the hutRE module were explored by transferring it from P.aeruginosa PAO1 to P.fluorescens SBW25. Transfer of the operon conferred the ability to utilize histidine via the four-step pathway in a single step, but the fitness cost of acquiring this new operon was found to be environment dependent.}, }
@article {pmid22223756, year = {2012}, author = {Skippington, E and Ragan, MA}, title = {Evolutionary dynamics of small RNAs in 27 Escherichia coli and Shigella genomes.}, journal = {Genome biology and evolution}, volume = {4}, number = {3}, pages = {330-345}, pmid = {22223756}, issn = {1759-6653}, mesh = {Escherichia coli/*genetics ; *Evolution, Molecular ; Gene Expression Regulation, Bacterial/genetics ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/*genetics ; Phylogeny ; RNA, Bacterial/*genetics ; Shigella/*genetics ; }, abstract = {Small RNAs (sRNAs) are widespread in bacteria and play critical roles in regulating physiological processes. They are best characterized in Escherichia coli K-12 MG1655, where 83 sRNAs constitute nearly 2% of the gene complement. Most sRNAs act by base pairing with a target mRNA, modulating its translation and/or stability; many of these RNAs share only limited complementarity to their mRNA target, and require the chaperone Hfq to facilitate base pairing. Little is known about the evolutionary dynamics of bacterial sRNAs. Here, we apply phylogenetic and network analyses to investigate the evolutionary processes and principles that govern sRNA gene distribution in 27 E. coli and Shigella genomes. We identify core (encoded in all 27 genomes) and variable sRNAs; more than two-thirds of the E. coli K-12 MG1655 sRNAs are core, whereas the others show patterns of presence and absence that are principally due to genetic loss, not duplication or lateral genetic transfer. We present evidence that variable sRNAs are less tightly integrated into cellular genetic regulatory networks than are the core sRNAs, and that Hfq facilitates posttranscriptional cross talk between the E. coli-Shigella core and variable genomes. Finally, we present evidence that more than 80% of genes targeted by Hfq-associated core sRNAs have been transferred within the E. coli-Shigella clade, and that most of these genes have been transferred intact. These results suggest that Hfq and sRNAs help integrate laterally acquired genes into established regulatory networks.}, }
@article {pmid22223227, year = {2012}, author = {Crémet, L and Bourigault, C and Lepelletier, D and Guillouzouic, A and Juvin, ME and Reynaud, A and Corvec, S and Caroff, N}, title = {Nosocomial outbreak of carbapenem-resistant Enterobacter cloacae highlighting the interspecies transferability of the blaOXA-48 gene in the gut flora.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {67}, number = {4}, pages = {1041-1043}, doi = {10.1093/jac/dkr547}, pmid = {22223227}, issn = {1460-2091}, mesh = {Aged ; Anti-Bacterial Agents/pharmacology ; Carbapenems/*pharmacology ; Cross Infection/*epidemiology/microbiology ; *Disease Outbreaks ; Enterobacter cloacae/drug effects/*isolation &amp; purification ; Enterobacteriaceae Infections/*epidemiology/microbiology ; Gastrointestinal Tract/microbiology ; Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; *beta-Lactam Resistance ; beta-Lactamases/*genetics ; beta-Lactams/pharmacology ; }, }
@article {pmid22221749, year = {2012}, author = {Haque, SF and Ali, SZ and Tp, M and Khan, AU}, title = {Prevalence of plasmid mediated bla(TEM-1) and bla(CTX-M-15) type extended spectrum beta-lactamases in patients with sepsis.}, journal = {Asian Pacific journal of tropical medicine}, volume = {5}, number = {2}, pages = {98-102}, doi = {10.1016/S1995-7645(12)60003-0}, pmid = {22221749}, issn = {2352-4146}, mesh = {Anti-Infective Agents/*pharmacology/therapeutic use ; Bacteremia/*drug therapy/epidemiology/*microbiology ; Drug Resistance, Bacterial ; Escherichia coli/drug effects ; Escherichia coli Infections/drug therapy ; Female ; Gram-Negative Bacterial Infections/*drug therapy/epidemiology/*microbiology ; Humans ; India/epidemiology ; Klebsiella/drug effects ; Klebsiella Infections/drug therapy ; Male ; Middle Aged ; Molecular Epidemiology ; Plasmids ; Polymerase Chain Reaction ; Prevalence ; Prospective Studies ; Pseudomonas/drug effects ; beta-Lactamases/drug effects/*metabolism ; }, abstract = {OBJECTIVE: To characterize the bacterial pathogens in patients having gram negative septicaemia. Further, to evaluate the antimicrobial resistance and underlying molecular mechanisms in these strains.<br><br>METHODS: A total number of 70 cases of gram negative sepsis were included in this prospective, open labeled, observational study. Standard methods for isolation and identification of bacteria were used. Antimicrobial susceptibility and ESBL testing was performed by the standard disc diffusion method. PCR amplification was performed to identify bla(CTX-M), bla(SHV) and bla(TEM) type ESBLs. Conjugation experiments were performed to show resistant marker transfer.<br><br>RESULTS: The most prevalent isolates Escherichia coli (E. coli) 58.6%, Klebsiella Spp. 32.9% and Pseudomonas 8.6%, were resistant to most of the antimicrobials including cefazolin, ceftriaxone, cefuroxime, ampicillin and co-trimoxazole but sensitive to imipenem and meropenem. ESBL and MBL production was seen 7.3% and 12.2% of E. coli isolates respectively. Three isoaltes were found to have bla(CTX-M-15) and two of them also showed bla(TEM-1) type enxyme. Whereas, none of them showed bla(SHV). Conjugation experiments using J-53 cells confirmed these resistant markers as plasmid mediated.<br><br>CONCLUSIONS: This work highlights the molecular epidemiology of escalating antimicrobial resistance and likely switch over of bla(CTX-M-15) type extended spectrum beta-lactamases by bla(TEM) type ESBLs in India. Further, the antimicrobial resistance by horizontal gene transfer was predominant among Enterobacteraceae in the community setting.}, }
@article {pmid22218456, year = {2012}, author = {Grassi, L and Caselle, M and Lercher, MJ and Lagomarsino, MC}, title = {Horizontal gene transfers as metagenomic gene duplications.}, journal = {Molecular bioSystems}, volume = {8}, number = {3}, pages = {790-795}, doi = {10.1039/c2mb05330f}, pmid = {22218456}, issn = {1742-2051}, mesh = {Evolution, Molecular ; *Gene Duplication ; *Gene Transfer, Horizontal ; Genome, Bacterial ; *Metagenome ; Metagenomics/*methods ; Proteobacteria/*genetics ; }, abstract = {While it is well accepted that horizontal gene transfer plays an important role in the evolution and the diversification of prokaryotic genomes, many questions remain open regarding its functional mechanisms of action and its interplay with the extant genome. This study addresses the relationship between proteome innovation by horizontal gene transfer and genome content in Proteobacteria. We characterize the transferred genes, focusing on the protein domain compositions and their relationships with the existing protein domain superfamilies in the genome. In agreement with previous observations, we find that the protein domain architectures of horizontally transferred genes are significantly shorter than the genomic average. Furthermore, protein domains that are more common in the total pool of genomes appear to have a proportionally higher chance to be transferred. This suggests that transfer events behave as if they were drawn randomly from a cross-genomic community gene pool, much like gene duplicates are drawn from a genomic gene pool. Finally, horizontally transferred genes carry domains of exogenous families less frequently for larger genomes, although they might do it more than expected by chance.}, }
@article {pmid22216014, year = {2011}, author = {Wisniewski-Dyé, F and Borziak, K and Khalsa-Moyers, G and Alexandre, G and Sukharnikov, LO and Wuichet, K and Hurst, GB and McDonald, WH and Robertson, JS and Barbe, V and Calteau, A and Rouy, Z and Mangenot, S and Prigent-Combaret, C and Normand, P and Boyer, M and Siguier, P and Dessaux, Y and Elmerich, C and Condemine, G and Krishnen, G and Kennedy, I and Paterson, AH and González, V and Mavingui, P and Zhulin, IB}, title = {Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments.}, journal = {PLoS genetics}, volume = {7}, number = {12}, pages = {e1002430}, pmid = {22216014}, issn = {1553-7404}, mesh = {Aquatic Organisms/*genetics ; Azospirillum/*genetics ; Base Sequence ; *Biological Evolution ; *Ecosystem ; Gene Transfer, Horizontal/*genetics ; Genes, Essential/genetics ; Genome, Bacterial/*genetics ; Glycoside Hydrolases/genetics/metabolism ; Phylogeny ; Plant Roots/microbiology ; RNA, Ribosomal, 16S/genetics ; Rhodospirillaceae/*genetics ; }, abstract = {Fossil records indicate that life appeared in marine environments ∼3.5 billion years ago (Gyr) and transitioned to terrestrial ecosystems nearly 2.5 Gyr. Sequence analysis suggests that "hydrobacteria" and "terrabacteria" might have diverged as early as 3 Gyr. Bacteria of the genus Azospirillum are associated with roots of terrestrial plants; however, virtually all their close relatives are aquatic. We obtained genome sequences of two Azospirillum species and analyzed their gene origins. While most Azospirillum house-keeping genes have orthologs in its close aquatic relatives, this lineage has obtained nearly half of its genome from terrestrial organisms. The majority of genes encoding functions critical for association with plants are among horizontally transferred genes. Our results show that transition of some aquatic bacteria to terrestrial habitats occurred much later than the suggested initial divergence of hydro- and terrabacterial clades. The birth of the genus Azospirillum approximately coincided with the emergence of vascular plants on land.}, }
@article {pmid22215814, year = {2012}, author = {Kennaway, CK and Taylor, JEN and Song, CF and Potrzebowski, W and Nicholson, W and White, JH and Swiderska, A and Obarska-Kosinska, A and Callow, P and Cooper, LP and Roberts, GA and Artero, JB and Bujnicki, JM and Trinick, J and Kneale, GG and Dryden, DT}, title = {Structure and operation of the DNA-translocating type I DNA restriction enzymes.}, journal = {Genes &amp; development}, volume = {26}, number = {1}, pages = {92-104}, pmid = {22215814}, issn = {1549-5477}, support = {080304/WT_/Wellcome Trust/United Kingdom ; 080304/Z/06/Z/WT_/Wellcome Trust/United Kingdom ; BB/D522589/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; BB/D001870/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {DNA Restriction Enzymes/*chemistry/*ultrastructure ; Deoxyribonucleases, Type I Site-Specific/chemistry/ultrastructure ; Microscopy, Electron ; *Models, Molecular ; Negative Staining ; Protein Structure, Tertiary ; }, abstract = {Type I DNA restriction/modification (RM) enzymes are molecular machines found in the majority of bacterial species. Their early discovery paved the way for the development of genetic engineering. They control (restrict) the influx of foreign DNA via horizontal gene transfer into the bacterium while maintaining sequence-specific methylation (modification) of host DNA. The endonuclease reaction of these enzymes on unmethylated DNA is preceded by bidirectional translocation of thousands of base pairs of DNA toward the enzyme. We present the structures of two type I RM enzymes, EcoKI and EcoR124I, derived using electron microscopy (EM), small-angle scattering (neutron and X-ray), and detailed molecular modeling. DNA binding triggers a large contraction of the open form of the enzyme to a compact form. The path followed by DNA through the complexes is revealed by using a DNA mimic anti-restriction protein. The structures reveal an evolutionary link between type I RM enzymes and type II RM enzymes.}, }
@article {pmid22210753, year = {2012}, author = {Doumith, M and Dhanji, H and Ellington, MJ and Hawkey, P and Woodford, N}, title = {Characterization of plasmids encoding extended-spectrum β-lactamases and their addiction systems circulating among Escherichia coli clinical isolates in the UK.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {67}, number = {4}, pages = {878-885}, doi = {10.1093/jac/dkr553}, pmid = {22210753}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/pharmacology ; DNA, Bacterial/chemistry/genetics ; Electroporation ; Escherichia coli/enzymology/*genetics/*isolation &amp; purification ; Escherichia coli Infections/*microbiology ; Gene Transfer Techniques ; Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; Plasmids/*analysis ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Transformation, Bacterial ; United Kingdom ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: To characterize plasmids encoding extended-spectrum β-lactamases (ESBLs) from a recent UK collection of clinical Escherichia coli isolates.<br><br>METHODS: The isolates comprised 118 ESBL producers referred from 54 laboratories. Plasmids were transferred by electroporation, and their incompatibility groups, associated addiction systems and resistance genes with the flanking genetic environments were identified by PCR or sequencing.<br><br>RESULTS: Seventy isolates had plasmids encoding CTX-M-15 (n = 53), CTX-M-14 (n =9), CTX-M-27 (n = 1), CTX-M-3 (n = 2) and SHV-12 (n = 5) ESBLs that were transformable; non-transformable ESBLs were mainly CTX-M enzymes (42/48). Most transformable bla(CTX-M-15) genes (43/53) were harboured on single replicon or multireplicon IncF plasmids, with IncFIA4-FIB1-FII31 (n = 11) and IncFIA1-FII2 (n = 15) being most frequent; the latter included eight pEK499 plasmids, typical of UK epidemic strain A. Plasmids harbouring bla(CTX-M-14) belonged variously to IncF, IncI1 and IncHI2 types, and 16 encoding CTX-M or SHV enzymes were non-typeable. Only IncF plasmid types carried the addiction systems sought and those with bla(CTX-M-15) frequently harboured bla(OXA-1) and aac(6')-Ib-cr, and often transferred trimethoprim and tetracycline resistance; those with bla(CTX-M-14) encoded trimethoprim, sulphonamide, streptomycin and tetracycline resistance. Most ESBL genes were associated with the well-known mobile elements ISEcp1 and IS26, but nearly half (23/55) of the ISEcp1 sequences upstream of bla(CTX-M-15) were interrupted by an IS26 at various positions.<br><br>CONCLUSIONS: Most ESBLs (70/118) were encoded by transformable plasmids, although a sizable minority could not be transformed. The majority of transformable plasmids (51/70; 72.9%) were diverse multiresistant IncF types possessing multiple addiction systems. The spread of bla(CTX-M-15) can be attributed not just to clonal expansion, but also to the horizontal dissemination of related plasmids.}, }
@article {pmid22209721, year = {2012}, author = {Chen, C and Ai, L and Zhou, F and Ren, J and Sun, K and Zhang, H and Chen, W and Guo, B}, title = {Complete nucleotide sequence of plasmid pST-III from Lactobacillus plantarum ST-III.}, journal = {Plasmid}, volume = {67}, number = {3}, pages = {236-244}, doi = {10.1016/j.plasmid.2011.12.005}, pmid = {22209721}, issn = {1095-9890}, mesh = {Bacterial Proteins/*genetics/metabolism ; Base Sequence ; DNA Repair ; DNA Replication ; DNA, Bacterial/*genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; Genes, Bacterial ; Lactobacillus plantarum/classification/*genetics/growth &amp; development ; Molecular Sequence Data ; Phylogeny ; Plasmids/*genetics ; Replicon ; Sequence Analysis, DNA ; }, abstract = {The complete nucleotide sequence of the 53,560-bp plasmid pST-III from Lactobacillus plantarum ST-III has been determined. The plasmid contains 42 predicted protein-coding sequences, and the functions of 34 coding sequences could be assigned. Homology analysis for the replication protein and the typical features of the origin of replication suggested that pST-III replicates via the theta-type mechanism. Among the predicted genes, we identified a kdp gene cluster (a high-affinity K(+)-transport system) for the first time in the Lactobacillus genus and a system for osmolyte transport. Analysis of the plasmid-encoded functions and the plasmid-cured experiment showed that the genes of pST-III could serve for the niche adaptations of L. plantarum ST-III and make significant contributions to its viability under hyperosmotic conditions. Furthermore, the relative copy number of pST-III was determined to be 6.79±1.55 copies per cell.}, }
@article {pmid22209425, year = {2012}, author = {Shadwick, JD and Ruiz-Trillo, I}, title = {A genomic survey shows that the haloarchaeal type tyrosyl tRNA synthetase is not a synapomorphy of opisthokonts.}, journal = {European journal of protistology}, volume = {48}, number = {1}, pages = {89-93}, pmid = {22209425}, issn = {1618-0429}, support = {206883/ERC_/European Research Council/International ; }, mesh = {Archaea/classification/*genetics ; Eukaryota/classification/*genetics ; *Genomics ; Tyrosine-tRNA Ligase/*genetics ; }, abstract = {The haloarchaeal-type tyrosyl tRNA synthetase (tyrRS) have previously been proposed to be a molecular synapomorphy of the opisthokonts. To re-evaluate this we have performed a taxon-wide genomic survey of tyrRS in eukaryotes and prokaryotes. Our phylogenetic trees group eukaryotes with archaea, with all opisthokonts sharing the haloarchaeal-type tyrRS. However, this type of tyrRS is not exclusive to opisthokonts, since it also encoded by two amoebozoans. Whether this is a consequence of lateral gene transfer or lineage sorting remains unsolved, but in any case haloarchaeal-type tyrRS is not a synapomorphy of opisthokonts. This demonstrates that molecular markers should be re-evaluated once a better taxon sampling becomes available.}, }
@article {pmid22207293, year = {2011}, author = {Asadollahi, K and Taherikalani, M and Maleki, A and Alizadeh, E and Valadbaigi, H and Soroush, S and Maleki, H and Asadollahi, P and Emaneini, M}, title = {Diversity of aminoglycoside modifying enzyme genes among multidrug resistant Acinetobacter baumannii genotypes isolated from nosocomial infections in Tehran hospitals and their association with class 1 integrons.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {58}, number = {4}, pages = {359-370}, doi = {10.1556/AMicr.58.2011.4.11}, pmid = {22207293}, issn = {1217-8950}, mesh = {Acinetobacter baumannii/drug effects/*genetics ; Aminoglycosides/*metabolism ; Anti-Bacterial Agents/*metabolism ; Cross Infection/*microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Genetic Variation ; Genotype ; Humans ; *Integrons ; Random Amplified Polymorphic DNA Technique ; }, abstract = {The aim of the present study was to investigate, for the first time, the diversity of the genes encoding aminoglycoside-modifying enzymes (AME) and their association with class 1 integrons in Iranian Acinetobacter baumannii strains. A total of 100 multidrug resistant A. baumannii, isolated from eight distinct hospitals in Tehran, were enrolled in this study. Susceptibility of these isolates to antimicrobial agents including gentamicin and amikacin was determined by E-test. Aminoglycoside resistant isolates were then tested by PCR for AME genes, including aphA6, aacC1, aacC2, aacA4, aadB, aadA1, classes 1 integron, 5'-CS-3' and typed by RAPD PCR. The rate of resistance to imipenem, meropenem, gentamicin and amikacin were 39%, 39%, 38% and 32%, respectively. Intermediate resistance phenotype to gentamicin and amikacin was observed in 2% and 5% of all the isolates, respectively. After aph6 with 90% (n = 36/40), aadA1, aacC1 and aadB with 82.5% (n = 33/40), 65% (n = 26/40) and 20% (n = 8/40) were the most prevalent AME genes among aminoglycosides resistant A. baumannii isolates. A combination of two to four different resistance genes was observed in 39 of 40 strains (97.5%), with a total of 7 different combinations. PCR of integrase genes revealed that AME gene was associated with 67% of class 1 integrons. RAPD analysis showed three predominant genotypes A (n = 20), B (n = 10) and 10 unrelated genotypes. The occurrence of identical resistance genes, gene combinations and class 1 integrons associated with these genes in clonally distinct strains indicates that horizontal gene transfer plays a major role in the dissemination of aminoglycoside resistance in A. baumannii.}, }
@article {pmid22202887, year = {2012}, author = {Oberbeckmann, S and Fuchs, BM and Meiners, M and Wichels, A and Wiltshire, KH and Gerdts, G}, title = {Seasonal dynamics and modeling of a Vibrio community in coastal waters of the North Sea.}, journal = {Microbial ecology}, volume = {63}, number = {3}, pages = {543-551}, pmid = {22202887}, issn = {1432-184X}, mesh = {Models, Biological ; North Sea ; Seasons ; Seawater/chemistry/*microbiology ; Vibrio/classification/genetics/*isolation &amp; purification ; }, abstract = {Vibrio species are ubiquitously distributed in marine waters all over the world. High genome plasticity due to frequent mutation, recombination, and lateral gene transfer enables Vibrio to adapt rapidly to environmental changes. The genus Vibrio comprises several human pathogens, which commonly cause outbreaks of severe diarrhea in tropical regions. In recent years, pathogenic Vibrio emerged also in coastal European waters. Little is known about factors driving the proliferation of Vibrio spp. in temperate waters such as the North Sea. In this study a quantification of Vibrio in the North Sea and their response to biotic and abiotic parameters were assessed. Between January and December 2009, Vibrio at Helgoland Roads (North Sea, Germany) were quantified using fluorescence in situ hybridization. Vibrio numbers up to 3.4 × 10(4) cells × mL(-1) (2.2% of total microbial counts) were determined in summer, but their abundance was significantly lower in winter (5 × 10(2) cells × mL(-1)). Correlations between Vibrio and nutrients (SiO(2), PO(4) (3-), DIN), Secchi depth, temperature, salinity, and chlorophyll a were calculated using Spearman rank analysis. Multiple stepwise regression analysis was carried out to analyze the additive influence of multiple factors on Vibrio. Based on these calculations, we found that high water temperature and low salinity best explained the increase of Vibrio cell numbers. Other environmental parameters, especially nutrients and chlorophyll a, also had an influence. All variables were shown to be subject to the overall seasonal dynamics at Helgoland Roads. Multiple regression models could represent an efficient and reliable tool to predict Vibrio abundances in response to the climate change in European waters.}, }
@article {pmid22202098, year = {2012}, author = {Espedido, BA and Gosbell, IB}, title = {Chromosomal mutations involved in antibiotic resistance in Staphylococcus aureus.}, journal = {Frontiers in bioscience (Scholar edition)}, volume = {4}, number = {3}, pages = {900-915}, doi = {10.2741/s307}, pmid = {22202098}, issn = {1945-0524}, mesh = {Anti-Bacterial Agents/pharmacology ; Chromosomes, Bacterial/*genetics ; Drug Resistance, Microbial ; Gene Transfer, Horizontal ; Humans ; Methicillin-Resistant Staphylococcus aureus/drug effects/genetics ; *Mutation ; Staphylococcal Infections/drug therapy/*microbiology ; Staphylococcus aureus/*drug effects/*genetics ; }, abstract = {Staphylococcus aureus is an important pathogen involved in infections in both the community and hospital setting. Strains that are resistant to multiple classes of antibiotics, particularly methicillin-resistant strains (MRSA), are prevalent in nosocomial infections and are associated with high morbidity and mortality rates. Such antibiotic-resistant strains limit the therapeutic options and place a burden on the health care system. In the hospital setting, horizontal gene transfer plays an important role in disseminating antibiotic resistant determinants among S. aureus. However, resistance to all known classes of antibiotics have been attributed to genes found within the S. aureus chromosome or to due to mutation as a result of selection pressure. Spontaneous mutations, in particular, are pivotal in the emergence of novel resistances. Consequently, newer drugs with better activity and/or antibacterial agents with novel targets need to be developed to combat and control the further spread of antibiotic resistance.}, }
@article {pmid22202093, year = {2012}, author = {Bu, Y and Cao, D}, title = {The origin of cancer stem cells.}, journal = {Frontiers in bioscience (Scholar edition)}, volume = {4}, number = {3}, pages = {819-830}, doi = {10.2741/s302}, pmid = {22202093}, issn = {1945-0524}, mesh = {Animals ; Cell Differentiation/physiology ; Cell Fusion ; Disease Progression ; Humans ; Neoplasms/*pathology/therapy ; Neoplastic Stem Cells/*pathology ; Stem Cells/pathology ; }, abstract = {Cancer stem cells (CSCs), also known as tumor-initiating cells (TICs), are cancer cells that possess capability of proliferation, differentiation, and self-renewal. It is widely believed that CSCs play critical role in the initiation, metastasis, and relapse of cancers, but the origin of CSCs remains unclear. Up to date, several hypotheses have been described, and cell fusion and horizontal gene transfer, which may occur during development and tissue repair process, are considered as important origins of CSCs. In addition, critical gene mutations in stem cells, progenitor cells or even differentiated cells may also contribute to the formation of CSCs, and cell microenvironment is critical to CSC self-renewal and differentiation. The ongoing efforts to identify the CSCs origins may shed more light on understanding of cancer initiation and progression, as well as the development of novel cancer therapies.}, }
@article {pmid22200905, year = {2011}, author = {Fournier, GP and Andam, CP and Alm, EJ and Gogarten, JP}, title = {Molecular evolution of aminoacyl tRNA synthetase proteins in the early history of life.}, journal = {Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life}, volume = {41}, number = {6}, pages = {621-632}, pmid = {22200905}, issn = {1573-0875}, mesh = {Amino Acids/chemistry/genetics/metabolism ; Amino Acyl-tRNA Synthetases/*chemistry/*genetics/metabolism ; Biological Evolution ; *Evolution, Molecular ; Evolution, Planetary ; *Gene Transfer, Horizontal ; Genetic Code ; *Phylogeny ; Protein Biosynthesis ; }, abstract = {Aminoacyl-tRNA synthetases (aaRS) consist of several families of functionally conserved proteins essential for translation and protein synthesis. Like nearly all components of the translation machinery, most aaRS families are universally distributed across cellular life, being inherited from the time of the Last Universal Common Ancestor (LUCA). However, unlike the rest of the translation machinery, aaRS have undergone numerous ancient horizontal gene transfers, with several independent events detected between domains, and some possibly involving lineages diverging before the time of LUCA. These transfers reveal the complexity of molecular evolution at this early time, and the chimeric nature of genomes within cells that gave rise to the major domains. Additionally, given the role of these protein families in defining the amino acids used for protein synthesis, sequence reconstruction of their pre-LUCA ancestors can reveal the evolutionary processes at work in the origin of the genetic code. In particular, sequence reconstructions of the paralog ancestors of isoleucyl- and valyl- RS provide strong empirical evidence that at least for this divergence, the genetic code did not co-evolve with the aaRSs; rather, both amino acids were already part of the genetic code before their cognate aaRSs diverged from their common ancestor. The implications of this observation for the early evolution of RNA-directed protein biosynthesis are discussed.}, }
@article {pmid22195008, year = {2011}, author = {Chan, CX and Reyes-Prieto, A and Bhattacharya, D}, title = {Red and green algal origin of diatom membrane transporters: insights into environmental adaptation and cell evolution.}, journal = {PloS one}, volume = {6}, number = {12}, pages = {e29138}, pmid = {22195008}, issn = {1932-6203}, support = {R01 ES013679/ES/NIEHS NIH HHS/United States ; R01-ES013679-01A2/ES/NIEHS NIH HHS/United States ; }, mesh = {Adaptation, Physiological/*genetics ; Chlorophyta/*genetics ; Cluster Analysis ; Diatoms/*cytology/*genetics ; *Environment ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes ; Membrane Transport Proteins/*genetics ; Phylogeny ; Rhodophyta/genetics ; Symbiosis/genetics ; }, abstract = {Membrane transporters (MTs) facilitate the movement of molecules between cellular compartments. The evolutionary history of these key components of eukaryote genomes remains unclear. Many photosynthetic microbial eukaryotes (e.g., diatoms, haptophytes, and dinoflagellates) appear to have undergone serial endosymbiosis and thereby recruited foreign genes through endosymbiotic/horizontal gene transfer (E/HGT). Here we used the diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum as models to examine the evolutionary origin of MTs in this important group of marine primary producers. Using phylogenomics, we used 1,014 diatom MTs as query against a broadly sampled protein sequence database that includes novel genome data from the mesophilic red algae Porphyridium cruentum and Calliarthron tuberculosum, and the stramenopile Ectocarpus siliculosus. Our conservative approach resulted in 879 maximum likelihood trees of which 399 genes show a non-lineal history between diatoms and other eukaryotes and prokaryotes (at the bootstrap value ≥70%). Of the eukaryote-derived MTs, 172 (ca. 25% of 697 examined phylogenies) have members of both red/green algae as sister groups, with 103 putatively arising from green algae, 19 from red algae, and 50 have an unresolved affiliation to red and/or green algae. We used topology tests to analyze the most convincing cases of non-lineal gene history in which red and/or green algae were nested within stramenopiles. This analysis showed that ca. 6% of all trees (our most conservative estimate) support an algal origin of MTs in stramenopiles with the majority derived from green algae. Our findings demonstrate the complex evolutionary history of photosynthetic eukaryotes and indicate a reticulate origin of MT genes in diatoms. We postulate that the algal-derived MTs acquired via E/HGT provided diatoms and other related microbial eukaryotes the ability to persist under conditions of fluctuating ocean chemistry, likely contributing to their great success in marine environments.}, }
@article {pmid22192777, year = {2012}, author = {Shlykov, MA and Zheng, WH and Chen, JS and Saier, MH}, title = {Bioinformatic characterization of the 4-Toluene Sulfonate Uptake Permease (TSUP) family of transmembrane proteins.}, journal = {Biochimica et biophysica acta}, volume = {1818}, number = {3}, pages = {703-717}, pmid = {22192777}, issn = {0006-3002}, support = {R01 GM077402/GM/NIGMS NIH HHS/United States ; 2 R01 GM077402-05A1/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Motifs ; Archaeal Proteins ; Computational Biology/methods ; Eukaryota/*genetics ; *Evolution, Molecular ; Membrane Transport Proteins/*genetics ; *Phylogeny ; *Prokaryotic Cells ; *Sequence Analysis, Protein ; }, abstract = {The ubiquitous sequence diverse 4-Toluene Sulfonate Uptake Permease (TSUP) family contains few characterized members and is believed to catalyze the transport of several sulfur-based compounds. Prokaryotic members of the TSUP family outnumber the eukaryotic members substantially, and in prokaryotes, but not eukaryotes, extensive lateral gene transfer occurred during family evolution. Despite unequal representation, homologues from the three taxonomic domains of life share well-conserved motifs. We show that the prototypical eight TMS topology arose from an intragenic duplication of a four transmembrane segment (TMS) unit. Possibly, a two TMS α-helical hairpin structure was the precursor of the 4 TMS repeat unit. Genome context analyses confirmed the proposal of a sulfur-based compound transport role for many TSUP homologues, but functional outliers appear to be prevalent as well. Preliminary results suggest that the TSUP family is a member of a large novel superfamily that includes rhodopsins, integral membrane chaperone proteins, transmembrane electron flow carriers and several transporter families. All of these proteins probably arose via the same pathway: 2→4→8 TMSs followed by loss of a TMS either at the N- or C-terminus, depending on the family, to give the more frequent 7 TMS topology.}, }
@article {pmid22188759, year = {2011}, author = {Brodt, A and Lurie-Weinberger, MN and Gophna, U}, title = {CRISPR loci reveal networks of gene exchange in archaea.}, journal = {Biology direct}, volume = {6}, number = {1}, pages = {65}, pmid = {22188759}, issn = {1745-6150}, mesh = {Archaea/*genetics ; Base Sequence ; *Gene Transfer, Horizontal ; *Genetic Loci ; *Genome, Archaeal ; Inverted Repeat Sequences ; }, abstract = {BACKGROUND: CRISPR (Clustered, Regularly, Interspaced, Short, Palindromic Repeats) loci provide prokaryotes with an adaptive immunity against viruses and other mobile genetic elements. CRISPR arrays can be transcribed and processed into small crRNA molecules, which are then used by the cell to target the foreign nucleic acid. Since spacers are accumulated by active CRISPR/Cas systems, the sequences of these spacers provide a record of the past "infection history" of the organism.<br><br>RESULTS: Here we analyzed all currently known spacers present in archaeal genomes and identified their source by DNA similarity. While nearly 50% of archaeal spacers matched mobile genetic elements, such as plasmids or viruses, several others matched chromosomal genes of other organisms, primarily other archaea. Thus, networks of gene exchange between archaeal species were revealed by the spacer analysis, including many cases of inter-genus and inter-species gene transfer events. Spacers that recognize viral sequences tend to be located further away from the leader sequence, implying that there exists a selective pressure for their retention.<br><br>CONCLUSIONS: CRISPR spacers provide direct evidence for extensive gene exchange in archaea, especially within genera, and support the current dogma where the primary role of the CRISPR/Cas system is anti-viral and anti-plasmid defense.<br><br>OPEN PEER REVIEW: This article was reviewed by: Profs. W. Ford Doolittle, John van der Oost, Christa Schleper (nominated by board member Prof. J Peter Gogarten).}, }
@article {pmid22188618, year = {2012}, author = {Huang, S and Wang, K and Jiao, N and Chen, F}, title = {Genome sequences of siphoviruses infecting marine Synechococcus unveil a diverse cyanophage group and extensive phage-host genetic exchanges.}, journal = {Environmental microbiology}, volume = {14}, number = {2}, pages = {540-558}, doi = {10.1111/j.1462-2920.2011.02667.x}, pmid = {22188618}, issn = {1462-2920}, mesh = {Bacteriophages/classification/*genetics ; Base Sequence ; Biological Evolution ; Cyanobacteria/virology ; *Gene Transfer, Horizontal ; Genetic Variation ; Genome, Viral ; Metagenome ; Molecular Sequence Data ; Oceans and Seas ; Phylogeny ; Prochlorococcus/virology ; Seawater/microbiology/*virology ; Siphoviridae/*classification/genetics/physiology ; Synechococcus/physiology/*virology ; }, abstract = {Investigating the interactions between marine cyanobacteria and their viruses (phages) is important towards understanding the dynamic of ocean's primary productivity. Genome sequencing of marine cyanophages has greatly advanced our understanding about their ecology and evolution. Among 24 reported genomes of cyanophages that infect marine picocyanobacteria, 17 are from cyanomyoviruses and six from cyanopodoviruses, and only one from cyanosiphovirus (Prochlorococcus phage P-SS2). Here we present four complete genome sequences of siphoviruses (S-CBS1, S-CBS2, S-CBS3 and S-CBS4) that infect four different marine Synechococcus strains. Three distinct subtypes were recognized among the five known marine siphoviruses (including P-SS2) in terms of morphology, genome architecture, gene content and sequence similarity. Our study revealed that cyanosiphoviruses are genetically diverse with polyphyletic origin. No core genes were found across these five cyanosiphovirus genomes, and this is in contrast to the fact that many core genes have been found in cyanomyovirus or cyanopodovirus genomes. Interestingly, genes encoding three structural proteins and a lysozyme of S-CBS1 and S-CBS3 showed homology to a prophage-like genetic element in two freshwater Synechococcus elongatus genomes. Re-annotation of the prophage-like genomic region suggests that S. elongatus may contain an intact prophage. Cyanosiphovirus genes involved in DNA metabolism and replication share high sequence homology with those in cyanobacteria, and further phylogenetic analysis based on these genes suggests that ancient and selective genetic exchanges occurred, possibly due to past prophage integration. Metagenomic analysis based on the Global Ocean Sampling database showed that cyanosiphoviruses are present in relatively low abundance in the ocean surface water compared to cyanomyoviruses and cyanopodoviruses.}, }
@article {pmid22188370, year = {2012}, author = {Zhang, C and Anderson, AJ}, title = {Polycyclic aromatic hydrocarbon degrading gene islands in five pyrene-degrading Mycobacterium isolates from different geographic locations.}, journal = {Canadian journal of microbiology}, volume = {58}, number = {1}, pages = {102-111}, doi = {10.1139/w11-093}, pmid = {22188370}, issn = {1480-3275}, mesh = {Biodegradation, Environmental ; Chromosomes, Bacterial/genetics ; Gene Duplication ; Gene Expression Regulation, Bacterial/drug effects ; Genes, Bacterial/*genetics ; Genomic Islands/*genetics ; Multigene Family/genetics ; Mycobacterium/*genetics/isolation &amp; purification/*metabolism ; Plasmids/genetics ; Polycyclic Aromatic Hydrocarbons/*metabolism ; Pyrenes/*metabolism/pharmacology ; Sequence Homology, Nucleic Acid ; Synteny ; United States ; Water Pollutants, Chemical/pharmacology ; }, abstract = {Mycobacterium sp. strain KMS utilizes pyrene, a high-molecular weight polycyclic aromatic hydrocarbon (PAH), as a sole carbon source. Bioinformatic analysis of the genome of isolate KMS predicted 25 genes with the potential to encode 17 pyrene-induced proteins identified by proteomics; these genes were clustered on both the chromosome and a circular plasmid. RT-PCR analysis of total RNA isolated from KMS cells grown with or without pyrene showed that the presence of pyrene increased the transcript accumulation of 20 of the predicted chromosome- and plasmid-located genes encoding pyrene-induced proteins. The transcribed genes from both the chromosome and a circular plasmid were within larger regions containing genes required for PAH degradation constituting PAH-degrading gene islands. Genes encoding integrases and transposases were found within and outside the PAH-degrading gene islands. The lower GC content of the genes within the gene island (61%-64%) compared with the average genome content (68%) suggested that these mycobacteria initially acquired these genes by horizontal gene transfer. Synteny was detected for the PAH-degrading islands in the genomes of two additional Mycobacterium isolates from the same PAH-polluted site and of two other pyrene-degrading Mycobacterium from different sites in the United States of America. Consequently, the gene islands have been conserved from a common ancestral strain.}, }
@article {pmid22152123, year = {2011}, author = {Yang, J and Warnow, T}, title = {Fast and accurate methods for phylogenomic analyses.}, journal = {BMC bioinformatics}, volume = {12 Suppl 9}, number = {Suppl 9}, pages = {S4}, pmid = {22152123}, issn = {1471-2105}, mesh = {Algorithms ; Genes ; Genomics/*methods ; *Phylogeny ; }, abstract = {BACKGROUND: Species phylogenies are not estimated directly, but rather through phylogenetic analyses of different gene datasets. However, true gene trees can differ from the true species tree (and hence from one another) due to biological processes such as horizontal gene transfer, incomplete lineage sorting, and gene duplication and loss, so that no single gene tree is a reliable estimate of the species tree. Several methods have been developed to estimate species trees from estimated gene trees, differing according to the specific algorithmic technique used and the biological model used to explain differences between species and gene trees. Relatively little is known about the relative performance of these methods.<br><br>RESULTS: We report on a study evaluating several different methods for estimating species trees from sequence datasets, simulating sequence evolution under a complex model including indels (insertions and deletions), substitutions, and incomplete lineage sorting. The most important finding of our study is that some fast and simple methods are nearly as accurate as the most accurate methods, which employ sophisticated statistical methods and are computationally quite intensive. We also observe that methods that explicitly consider errors in the estimated gene trees produce more accurate trees than methods that assume the estimated gene trees are correct.<br><br>CONCLUSIONS: Our study shows that highly accurate estimations of species trees are achievable, even when gene trees differ from each other and from the species tree, and that these estimations can be obtained using fairly simple and computationally tractable methods.}, }
@article {pmid22151831, year = {2011}, author = {Collins, RE and Merz, H and Higgs, PG}, title = {Origin and evolution of gene families in Bacteria and Archaea.}, journal = {BMC bioinformatics}, volume = {12 Suppl 9}, number = {Suppl 9}, pages = {S14}, pmid = {22151831}, issn = {1471-2105}, mesh = {Cluster Analysis ; *Evolution, Molecular ; Gene Duplication ; *Genes, Archaeal ; *Genes, Bacterial ; Genome Size ; Genome, Archaeal ; Genome, Bacterial ; Genomics/methods ; *Multigene Family ; }, abstract = {BACKGROUND: Comparison of complete genomes of Bacteria and Archaea shows that gene content varies considerably and that genomes evolve quite rapidly via gene duplication and deletion and horizontal gene transfer. We analyze a diverse set of 92 Bacteria and 79 Archaea in order to investigate the processes governing the origin and evolution of families of related genes within genomes.<br><br>RESULTS: Genes were clustered into related groups using similarity criteria derived from BLAST. Most clusters contained genes from only one or a small number of genomes, and relatively few core clusters were found that spanned all genomes. Gene clusters found in larger numbers of genomes tended to have larger numbers of genes per genome; however, clusters with unusually large numbers of genes per genome were found among both narrowly and widely distributed clusters. Larger genomes were found to have larger mean gene family sizes and a greater proportion of families of very large size. We used a model of birth, death, and innovation to predict the distribution of gene family sizes. The key parameter is r, the ratio of duplications to deletions. It was found that the model can give a good fit to the observed distribution only if there are several classes of genes with different values of r. The preferred model in most cases had three classes of genes.<br><br>CONCLUSIONS: There appears to be a rapid rate of origination of new gene families within individual genomes. Most of these gene families are deleted before they spread to large numbers of genomes, which suggests that they may not be generally beneficial to the organisms. The family size distribution is best described by a large fraction of families that tend to have only one or two genes and a small fraction of families of multi-copy genes that are highly prone to duplication. Larger families occur more frequently in larger genomes, indicating higher r in these genomes, possibly due to a greater tolerance for non-beneficial gene duplicates. The smallest genomes contain very few multi-copy families, suggesting a high rate of deletion of all but the most beneficial genes in these genomes.}, }
@article {pmid22183669, year = {2012}, author = {van der Does, HC and Rep, M}, title = {Horizontal transfer of supernumerary chromosomes in fungi.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {835}, number = {}, pages = {427-437}, doi = {10.1007/978-1-61779-501-5_26}, pmid = {22183669}, issn = {1940-6029}, mesh = {Chromosomes, Fungal/*genetics ; Fungi/*genetics ; *Gene Transfer, Horizontal ; Genetic Techniques ; Genome, Fungal ; Plant Diseases/microbiology ; Plants/microbiology ; }, abstract = {Several species of filamentous fungi contain so-called dispensable or supernumerary chromosomes. These chromosomes are dispensable for the fungus to survive, but may carry genes required for specialized functions, such as infection of a host plant. It has been shown that at least some dispensable chromosomes are able to transfer horizontally (i.e., in the absence of a sexual cycle) from one fungal strain to another. In this paper, we describe a method by which this can be shown. Horizontal chromosome transfer (HCT) occurs during co-incubation of two strains. To document the actual occurrence of HCT, it is necessary to select for HCT progeny. This is accomplished by transforming two different drug-resistance genes into the two parent strains before their co-incubation. In one of the strains (the "donor"), a drug-resistance gene should be integrated in a chromosome of which the propensity for HCT is under investigation. In the "tester" or "recipient" strain, another drug-resistance gene should be integrated somewhere in the core genome. In this way, after co-incubation, HCT progeny can be selected on plates containing both drugs. HCT can be initiated with equal amounts of asexual spores of both strains, plated on regular growth medium for the particular fungus, followed by incubation until new asexual spores are formed. The new asexual spores are then harvested and plated on plates containing both drugs. Double drug-resistant colonies that appear should carry at least one chromosome from each parental strain. Finally, double drug-resistant strains need to be analysed to assess whether HCT has actually occurred. This can be done by various genome mapping methods, like CHEF-gels, AFLP, RFLP, PCR markers, optical maps, or even complete genome sequencing.}, }
@article {pmid22179583, year = {2012}, author = {Copley, SD and Rokicki, J and Turner, P and Daligault, H and Nolan, M and Land, M}, title = {The whole genome sequence of Sphingobium chlorophenolicum L-1: insights into the evolution of the pentachlorophenol degradation pathway.}, journal = {Genome biology and evolution}, volume = {4}, number = {2}, pages = {184-198}, pmid = {22179583}, issn = {1759-6653}, support = {R01 GM078554/GM/NIGMS NIH HHS/United States ; GM078554/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/metabolism ; Base Sequence ; Biodegradation, Environmental ; Chromosome Mapping ; Chromosomes, Bacterial/genetics ; Conserved Sequence/genetics ; *Evolution, Molecular ; Genes, Bacterial/genetics ; Genome, Bacterial/*genetics ; Hydroxylation ; Metabolic Networks and Pathways/*genetics ; Pentachlorophenol/chemistry/*metabolism ; Quinone Reductases/genetics ; Replicon/genetics ; *Sequence Analysis, DNA ; Sphingomonadaceae/*genetics ; }, abstract = {Sphingobium chlorophenolicum Strain L-1 can mineralize the toxic pesticide pentachlorophenol (PCP). We have sequenced the genome of S. chlorophenolicum Strain L-1. The genome consists of a primary chromosome that encodes most of the genes for core processes, a secondary chromosome that encodes primarily genes that appear to be involved in environmental adaptation, and a small plasmid. The genes responsible for degradation of PCP are found on chromosome 2. We have compared the genomes of S. chlorophenolicum Strain L-1 and Sphingobium japonicum, a closely related Sphingomonad that degrades lindane. Our analysis suggests that the genes encoding the first three enzymes in the PCP degradation pathway were acquired via two different horizontal gene transfer events, and the genes encoding the final two enzymes in the pathway were acquired from the most recent common ancestor of these two bacteria.}, }
@article {pmid22178648, year = {2012}, author = {Al-Reedy, RM and Malireddy, R and Dillman, CB and Kennell, JC}, title = {Comparative analysis of Fusarium mitochondrial genomes reveals a highly variable region that encodes an exceptionally large open reading frame.}, journal = {Fungal genetics and biology : FG &amp; B}, volume = {49}, number = {1}, pages = {2-14}, doi = {10.1016/j.fgb.2011.11.008}, pmid = {22178648}, issn = {1096-0937}, mesh = {DNA, Fungal/chemistry/*genetics ; DNA, Mitochondrial/chemistry/*genetics ; Evolution, Molecular ; Fusarium/*genetics ; Gene Transfer, Horizontal ; *Genome, Mitochondrial ; Introns ; Molecular Sequence Data ; *Open Reading Frames ; *Polymorphism, Genetic ; Recombination, Genetic ; Sequence Analysis, DNA ; }, abstract = {The mitochondrial (mt) genomes of Fusarium verticillioides, Fusarium solani and Fusarium graminearum were annotated and found to be 53.7, 63.0 and 95.7 kb in length, respectively. The genomes encode all genes typically associated with mtDNAs of filamentous fungi yet are considerably larger than the mt genome of F. oxysporum. Size differences are largely due to the number of group I introns. Surprisingly, the genomes contain a highly variable region of 7-9 kb that encodes an exceptionally large, unidentified open reading frame (uORF). The region has the hallmarks of a horizontally transmitted DNA and was likely acquired prior to the divergence of Fusarium species. Two additional uORFs were detected that are also under positive selection. DNA repeats associated with the uORFs suggest that 3' gene duplication may be an adaptive mechanism to modify coding regions or generate new ORFs. The acquisition of these new genes contrasts to the wide-scale size reduction experienced by fungal mt genomes.}, }
@article {pmid22173187, year = {2011}, author = {Quesada-Gómez, C}, title = {Bacteroides mobilizable and conjugative genetic elements: antibiotic resistance among clinical isolates.}, journal = {Revista espanola de quimioterapia : publicacion oficial de la Sociedad Espanola de Quimioterapia}, volume = {24}, number = {4}, pages = {184-190}, pmid = {22173187}, issn = {1988-9518}, mesh = {Anti-Bacterial Agents/*pharmacology ; Antiporters/genetics ; Bacterial Proteins/genetics ; Bacteroides/*drug effects/*genetics ; Bacteroides Infections/*microbiology ; Conjugation, Genetic ; DNA Transposable Elements ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Humans ; Methyltransferases/genetics ; Microbial Sensitivity Tests ; Operon ; Plasmids/genetics ; }, abstract = {The conjugation is one of the most important mechanisms of horizontal gene transfer in prokaryotes, leading to genetic variation within a species and the acquisition of new traits, such as antibiotic resistance. Bacteroides is an obligate anaerobe of the colon and a significant opportunistic pathogen. Antibiotic resistance among Bacteroides spp. is rapidly increasing, largely due to the dissemination of DNA transfer factors (plasmids and transposons) harbored by members of this genus. Transfer factors can be divided into two classes, conjugative and mobilizable. Species of the intestinal Bacteroides have yielded different resistance plasmids, all of which have been intensely studied, the plasmids encode high-level MLS resistance conferred by a conserved erm gene. It has been reported an interesting observation associated with the transfer of several of these types of elements, all of which conferred Tcr and displayed greatly increased transfer efficiency following exposure to tetracycline. Many of the conjugative transposons (CTns) in Bacteroides are related to various genetic elements (such as CTnDOT, CTnERL, NBU and others). CTnDOT carries a tetracycline resistance gene, tetQ, and an erythromycin resistance gene, ermF. Resistance to drugs used to treat Bacteroides infections, such as clindamycin, has also been increasing. These conjugal elements have been found in Bacteroides clinical isolates. Thus, horizontal gene transfer could conceivably have played a role in the rising incidence of resistance in this bacterial group.}, }
@article {pmid22169783, year = {2011}, author = {Bourjilat, F and Bouchrif, B and Dersi, N and Claude, JD and Amarouch, H and Timinouni, M}, title = {Emergence of extended-spectrum beta-lactamases-producing Escherichia coli in community-acquired urinary infections in Casablanca, Morocco.}, journal = {Journal of infection in developing countries}, volume = {5}, number = {12}, pages = {850-855}, doi = {10.3855/jidc.1490}, pmid = {22169783}, issn = {1972-2680}, mesh = {Cluster Analysis ; Community-Acquired Infections/*epidemiology/*microbiology ; Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/*enzymology/*isolation &amp; purification ; Escherichia coli Infections/*epidemiology/*microbiology ; Escherichia coli Proteins/genetics ; Gene Transfer, Horizontal ; Genotype ; Humans ; Molecular Epidemiology ; Molecular Typing ; Morocco/epidemiology ; Plasmids/analysis ; Polymerase Chain Reaction ; Prevalence ; Sequence Analysis, DNA ; beta-Lactamases/*metabolism ; }, abstract = {INTRODUCTION: Extended-spectrum beta-lactamase- (ESBL)-producing Escherichia coli are an increasingly significant cause of community-acquired infection worldwide. The aim of this study was to assess the prevalence of ESBL-producing E. coli in a community, to analyze the relationship between strains studied, and to characterize the ESBL genes involved in this resistance.<br><br>METHODOLOGY: ESBL production was detected by the double disk synergy test. Genes encoding ESBLs (blaTEM, blaCTM, blaSHV) were identified by PCR and DNA sequencing. Conjugation experiments were performed to check the transferability of antibiotic resistance genes. Strain inter-relationships were studied by pulsed field gel electrophoresis.<br><br>RESULTS: Seven ESBL-producing E. coli were identified among the 535 E. coli isolates. Most of them expressed a CTX-M enzyme (6/7) with a predominance of CTX-M-15 (6/6). Two strains possessed TEM in combination with CTX-M-15 or SHV-5.&#xa0; Plasmid content and gene transfer analysis showed that resistance genes were carried by high molecular weight conjugative plasmids. PFGE analysis showed that the strains were not clonal.<br><br>CONCLUSIONS: ESBL-producing E. coli from urinary tract infections in Casablanca belong to different clones and carry mobile beta-lactamase genes.&#xa0; It is therefore essential to monitor the epidemiology of ESBLs in E. coli and related organisms locally to effectively combat resistance.}, }
@article {pmid22169356, year = {2012}, author = {Mizuta, M and Satoh, E and Katoh, C and Tanaka, K and Moriguchi, K and Suzuki, K}, title = {Screening for yeast mutants defective in recipient ability for transkingdom conjugation with Escherichia coli revealed importance of vacuolar ATPase activity in the horizontal DNA transfer phenomenon.}, journal = {Microbiological research}, volume = {167}, number = {5}, pages = {311-316}, doi = {10.1016/j.micres.2011.10.001}, pmid = {22169356}, issn = {1618-0623}, mesh = {*Conjugation, Genetic ; Escherichia coli/*genetics/metabolism ; *Gene Transfer, Horizontal ; Plasmids/genetics/metabolism ; Saccharomyces cerevisiae/*enzymology/*genetics ; Saccharomyces cerevisiae Proteins/genetics/*metabolism ; Vacuolar Proton-Translocating ATPases/genetics/*metabolism ; }, abstract = {Proteobacterium Escherichia coli strains harboring wide-transfer-range conjugative plasmids are able to transfer these plasmids to several yeast species. Whole plasmid DNA is mobilizable in the transkingdom conjugation phenomenon. Owing to the availability of various conjugative plasmids in bacteria, the horizontal DNA transfer has potential to occur between various bacteria and eukaryotes. In order to know host factor genes involved in such conjugation, we systematically tested the conjugability of strains among a yeast library comprising single-gene-knockout mutants in this study. This genome-wide screen identified 26 host chromosomal genes whose absence reduced the efficiency of the transkingdom conjugation. Among the 26 genes, 20 are responsible for vacuolar ATPase activity, while 5 genes (SHP1, CSG2, CCR4, NOT5, and HOF1) seem to play a role in maintaining the cell surface. Lack of either ZUO1 gene or SSZ1 gene, each of which encodes a component of the ribosome-associated cytoplasmic molecular chaperone, also strongly affected transkingdom conjugation.}, }
@article {pmid22168471, year = {2011}, author = {Brown, AM and Hoopes, SL and White, RH and Sarisky, CA}, title = {Purine biosynthesis in archaea: variations on a theme.}, journal = {Biology direct}, volume = {6}, number = {}, pages = {63}, pmid = {22168471}, issn = {1745-6150}, mesh = {Archaea/chemistry/enzymology/*genetics ; Carbon-Nitrogen Ligases/chemistry/genetics ; Carbon-Nitrogen Ligases with Glutamine as Amide-N-Donor/chemistry/genetics ; Carboxy-Lyases/chemistry/genetics ; Catalytic Domain ; Enzyme Activation ; Gene Duplication ; Gene Transfer, Horizontal ; *Genes, Archaeal ; Peptide Synthases/chemistry/genetics ; Phosphoribosylglycinamide Formyltransferase/chemistry/genetics ; Purines/*biosynthesis/chemistry ; }, abstract = {BACKGROUND: The ability to perform de novo biosynthesis of purines is present in organisms in all three domains of life, reflecting the essentiality of these molecules to life. Although the pathway is quite similar in eukaryotes and bacteria, the archaeal pathway is more variable. A careful manual curation of genes in this pathway demonstrates the value of manual curation in archaea, even in pathways that have been well-studied in other domains.<br><br>RESULTS: We searched the Integrated Microbial Genome system (IMG) for the 17 distinct genes involved in the 11 steps of de novo purine biosynthesis in 65 sequenced archaea, finding 738 predicted proteins with sequence similarity to known purine biosynthesis enzymes. Each sequence was manually inspected for the presence of active site residues and other residues known or suspected to be required for function.Many apparently purine-biosynthesizing archaea lack evidence for a single enzyme, either glycinamide ribonucleotide formyltransferase or inosine monophosphate cyclohydrolase, suggesting that there are at least two more gene variants in the purine biosynthetic pathway to discover. Variations in domain arrangement of formylglycinamidine ribonucleotide synthetase and substantial problems in aminoimidazole carboxamide ribonucleotide formyltransferase and inosine monophosphate cyclohydrolase assignments were also identified.Manual curation revealed some overly specific annotations in the IMG gene product name, with predicted proteins without essential active site residues assigned product names implying enzymatic activity (21 proteins, 2.8% of proteins inspected) or Enzyme Commission (E. C.) numbers (57 proteins, 7.7%). There were also 57 proteins (7.7%) assigned overly generic names and 78 proteins (10.6%) without E.C. numbers as part of the assigned name when a specific enzyme name and E. C. number were well-justified.<br><br>CONCLUSIONS: The patchy distribution of purine biosynthetic genes in archaea is consistent with a pathway that has been shaped by horizontal gene transfer, duplication, and gene loss. Our results indicate that manual curation can improve upon automated annotation for a small number of automatically-annotated proteins and can reveal a need to identify further pathway components even in well-studied pathways.}, }
@article {pmid22160766, year = {2012}, author = {Dalquen, DA and Anisimova, M and Gonnet, GH and Dessimoz, C}, title = {ALF--a simulation framework for genome evolution.}, journal = {Molecular biology and evolution}, volume = {29}, number = {4}, pages = {1115-1123}, pmid = {22160766}, issn = {1537-1719}, mesh = {Algorithms ; Base Composition ; Computational Biology/*methods ; Computer Simulation ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Speciation ; *Genome ; *Models, Genetic ; Mutagenesis ; *Software ; }, abstract = {In computational evolutionary biology, verification and benchmarking is a challenging task because the evolutionary history of studied biological entities is usually not known. Computer programs for simulating sequence evolution in silico have shown to be viable test beds for the verification of newly developed methods and to compare different algorithms. However, current simulation packages tend to focus either on gene-level aspects of genome evolution such as character substitutions and insertions and deletions (indels) or on genome-level aspects such as genome rearrangement and speciation events. Here, we introduce Artificial Life Framework (ALF), which aims at simulating the entire range of evolutionary forces that act on genomes: nucleotide, codon, or amino acid substitution (under simple or mixture models), indels, GC-content amelioration, gene duplication, gene loss, gene fusion, gene fission, genome rearrangement, lateral gene transfer (LGT), or speciation. The other distinctive feature of ALF is its user-friendly yet powerful web interface. We illustrate the utility of ALF with two possible applications: 1) we reanalyze data from a study of selection after globin gene duplication and test the statistical significance of the original conclusions and 2) we demonstrate that LGT can dramatically decrease the accuracy of two well-established orthology inference methods. ALF is available as a stand-alone application or via a web interface at http://www.cbrg.ethz.ch/alf.}, }
@article {pmid22159605, year = {2012}, author = {Hara, Y and Kadotani, N and Izui, H and Katashkina, JI and Kuvaeva, TM and Andreeva, IG and Golubeva, LI and Malko, DB and Makeev, VJ and Mashko, SV and Kozlov, YI}, title = {The complete genome sequence of Pantoea ananatis AJ13355, an organism with great biotechnological potential.}, journal = {Applied microbiology and biotechnology}, volume = {93}, number = {1}, pages = {331-341}, pmid = {22159605}, issn = {1432-0614}, mesh = {Chromosomes, Bacterial ; Conjugation, Genetic ; DNA, Bacterial/*chemistry/*genetics ; DNA, Circular/chemistry/genetics ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Molecular Sequence Data ; Pantoea/*genetics ; Plasmids ; Recombination, Genetic ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {Pantoea ananatis AJ13355 is a newly identified member of the Enterobacteriaceae family with promising biotechnological applications. This bacterium is able to grow at an acidic pH and is resistant to saturating concentrations of L-glutamic acid, making this organism a suitable host for the production of L-glutamate. In the current study, the complete genomic sequence of P. ananatis AJ13355 was determined. The genome was found to consist of a single circular chromosome consisting of 4,555,536 bp [DDBJ: AP012032] and a circular plasmid, pEA320, of 321,744 bp [DDBJ: AP012033]. After automated annotation, 4,071 protein-coding sequences were identified in the P. ananatis AJ13355 genome. For 4,025 of these genes, functions were assigned based on homologies to known proteins. A high level of nucleotide sequence identity (99%) was revealed between the genome of P. ananatis AJ13355 and the previously published genome of P. ananatis LMG 20103. Short colinear regions, which are identical to DNA sequences in the Escherichia coli MG1655 chromosome, were found to be widely dispersed along the P. ananatis AJ13355 genome. Conjugal gene transfer from E. coli to P. ananatis, mediated by homologous recombination between short identical sequences, was also experimentally demonstrated. The determination of the genome sequence has paved the way for the directed metabolic engineering of P. ananatis to produce biotechnologically relevant compounds.}, }
@article {pmid22157758, year = {2012}, author = {Piacente, F and Marin, M and Molinaro, A and De Castro, C and Seltzer, V and Salis, A and Damonte, G and Bernardi, C and Claverie, JM and Abergel, C and Tonetti, M}, title = {Giant DNA virus mimivirus encodes pathway for biosynthesis of unusual sugar 4-amino-4,6-dideoxy-D-glucose (Viosamine).}, journal = {The Journal of biological chemistry}, volume = {287}, number = {5}, pages = {3009-3018}, pmid = {22157758}, issn = {1083-351X}, mesh = {Acanthamoeba/virology ; DNA, Viral/genetics/metabolism ; *Evolution, Molecular ; Genes, Viral/physiology ; Glucosamine/*analogs &amp; derivatives/genetics/metabolism ; Glycosylation ; Mimiviridae/*enzymology/*genetics ; Transaminases/*genetics/*metabolism ; Uridine Diphosphate Sugars/genetics/metabolism ; }, abstract = {Mimivirus is one the largest DNA virus identified so far, infecting several Acanthamoeba species. Analysis of its genome revealed the presence of a nine-gene cluster containing genes potentially involved in glycan formation. All of these genes are co-expressed at late stages of infection, suggesting their role in the formation of the long fibers covering the viral surface. Among them, we identified the L136 gene as a pyridoxal phosphate-dependent sugar aminotransferase. This enzyme was shown to catalyze the formation of UDP-4-amino-4,6-dideoxy-D-glucose (UDP-viosamine) from UDP-4-keto-6-deoxy-D-glucose, a key compound involved also in the biosynthesis of L-rhamnose. This finding further supports the hypothesis that Mimivirus encodes a glycosylation system that is completely independent of the amoebal host. Viosamine, together with rhamnose, (N-acetyl)glucosamine, and glucose, was found as a major component of the viral glycans. Most of the sugars were associated with the fibers, confirming a capsular-like nature of the viral surface. Phylogenetic analysis clearly indicated that L136 was not a recent acquisition from bacteria through horizontal gene transfer, but it was acquired very early during evolution. Implications for the origin of the glycosylation machinery in giant DNA virus are also discussed.}, }
@article {pmid22155825, year = {2012}, author = {Arpin, C and Thabet, L and Yassine, H and Messadi, AA and Boukadida, J and Dubois, V and Coulange-Mayonnove, L and Andre, C and Quentin, C}, title = {Evolution of an incompatibility group IncA/C plasmid harboring blaCMY-16 and qnrA6 genes and its transfer through three clones of Providencia stuartii during a two-year outbreak in a Tunisian burn unit.}, journal = {Antimicrobial agents and chemotherapy}, volume = {56}, number = {3}, pages = {1342-1349}, pmid = {22155825}, issn = {1098-6596}, mesh = {Adolescent ; Adult ; Aged ; Anti-Bacterial Agents/*administration &amp; dosage ; Bacterial Typing Techniques ; Burn Units ; Cephalosporins/administration &amp; dosage ; Child ; DNA Restriction Enzymes/metabolism ; *Disease Outbreaks ; Drug Resistance, Multiple, Bacterial/*genetics ; Enterobacteriaceae Infections/drug therapy/*epidemiology/microbiology ; Female ; Gene Transfer, Horizontal ; Gentamicins/administration &amp; dosage ; Humans ; Integrons/genetics ; Male ; Middle Aged ; Mutagenesis, Insertional ; Plasmids ; Providencia/drug effects/*genetics/isolation &amp; purification ; Sequence Deletion ; Tunisia/epidemiology ; beta-Lactamases/*genetics ; }, abstract = {During a 2-year period in 2005 and 2006, 64 multidrug-resistant Providencia stuartii isolates, including 58 strains from 58 patients and 6 strains obtained from the same tracheal aspirator, were collected in a burn unit of a Tunisian hospital. They divided into four antibiotypes (ATB1 to ATB4) and three SmaI pulsotypes (PsA to PsC), including 49 strains belonging to clone PsA (48 of ATB1 and 1 of ATB4), 11 strains to clone PsB (7 of ATB2 and 4 of ATB3), and 4 strains to clone PsC (ATB3). All strains, except for the PsA/ATB4 isolate, were highly resistant to broad-spectrum cephalosporins due to the production of the plasmid-mediated CMY-16 β-lactamase. In addition, the 15 strains of ATB2 and ATB3 exhibited decreased quinolone susceptibility associated with QnrA6. Most strains (ATB1 and ATB3) were gentamicin resistant, related to an AAC(6')-Ib' enzyme. All these genes were located on a conjugative plasmid belonging to the incompatibility group IncA/C(2) of 195, 175, or 100 kb. Despite differences in size and in number of resistance determinants, they derived from the same plasmid, as demonstrated by similar profiles in plasmid restriction analysis and strictly homologous sequences of repAIncA/C(2), unusual antibiotic resistance genes (e.g., aphA-6), and their genetic environments. Further investigation suggested that deletions, acquisition of the ISCR1 insertion sequence, and integron cassette mobility accounted for these variations. Thus, this outbreak was due to both the spread of three clonal strains and the dissemination of a single IncA/C(2) plasmid which underwent a remarkable evolution during the epidemic period.}, }
@article {pmid22151572, year = {2012}, author = {Caro-Quintero, A and Konstantinidis, KT}, title = {Bacterial species may exist, metagenomics reveal.}, journal = {Environmental microbiology}, volume = {14}, number = {2}, pages = {347-355}, doi = {10.1111/j.1462-2920.2011.02668.x}, pmid = {22151572}, issn = {1462-2920}, mesh = {Bacteria/classification/*genetics ; Biodiversity ; Classification ; Gene Transfer, Horizontal ; *Metagenomics ; Phylogeny ; Transformation, Bacterial ; }, abstract = {Whether or not bacterial species exist remains an unresolved issue of paramount theoretical as well as practical consequences. Here we review and synthesize the findings emerging from metagenomic surveys of natural microbial populations and argue that microbial communities are predominantly organized in genetically and ecologically discernible populations, which possess the attributes expected for species. These sequence-discrete populations represent a major foundation for beginning high-resolution investigations on how populations are organized, interact, and evolve within communities. We also attempt to reconcile these findings with those of previous studies that reported indiscrete species and a genetic continuum within bacterial taxa and discuss the implications for the current bacterial species definition.}, }
@article {pmid22151541, year = {2011}, author = {Li, ZW and Shen, YH and Xiang, ZH and Zhang, Z}, title = {Pathogen-origin horizontally transferred genes contribute to the evolution of Lepidopteran insects.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {356}, pmid = {22151541}, issn = {1471-2148}, mesh = {Amino Acid Sequence ; Animals ; Bacteria/classification/*genetics ; Bombyx/*genetics/*microbiology ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Sequence Alignment ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT), a source of genetic variation, is generally considered to facilitate hosts' adaptability to environments. However, convincing evidence supporting the significant contribution of the transferred genes to the evolution of metazoan recipients is rare.<br><br>RESULTS: In this study, based on sequence data accumulated to date, we used a unified method consisting of similarity search and phylogenetic analysis to detect horizontally transferred genes (HTGs) between prokaryotes and five insect species including Drosophila melanogaster, Anopheles gambiae, Bombyx mori, Tribolium castaneum and Apis mellifera. Unexpectedly, the candidate HTGs were not detected in D. melanogaster, An. gambiae and T. castaneum, and 79 genes in Ap. mellifera sieved by the same method were considered as contamination based on other information. Consequently, 14 types of 22 HTGs were detected only in the silkworm. Additionally, 13 types of the detected silkworm HTGs share homologous sequences in species of other Lepidopteran superfamilies, suggesting that the majority of these HTGs were derived from ancient transfer events before the radiation of Ditrysia clade. On the basis of phylogenetic topologies and BLAST search results, donor bacteria of these genes were inferred, respectively. At least half of the predicted donor organisms may be entomopathogenic bacteria. The predicted biochemical functions of these genes include four categories: glycosyl hydrolase family, oxidoreductase family, amino acid metabolism, and others.<br><br>CONCLUSIONS: The products of HTGs detected in this study may take part in comprehensive physiological metabolism. These genes potentially contributed to functional innovation and adaptability of Lepidopteran hosts in their ancient lineages associated with the diversification of angiosperms. Importantly, our results imply that pathogens may be advantageous to the subsistence and prosperity of hosts through effective HGT events at a large evolutionary scale.}, }
@article {pmid22146877, year = {2012}, author = {Kumarasamy, K and Krishnan, P}, title = {Report of a Salmonella enterica serovar Typhi isolate from India producing CMY-2 AmpC β-lactamase.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {67}, number = {3}, pages = {775-776}, doi = {10.1093/jac/dkr514}, pmid = {22146877}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/pharmacology ; Child ; Conjugation, Genetic ; Gene Transfer, Horizontal ; Humans ; India ; Microbial Sensitivity Tests ; Plasmids ; Salmonella typhi/*drug effects/*enzymology/genetics/isolation &amp; purification ; Typhoid Fever/*microbiology ; *beta-Lactam Resistance ; beta-Lactamases/genetics/*metabolism ; beta-Lactams/pharmacology ; }, }
@article {pmid22144149, year = {2012}, author = {Lima-Mendez, G}, title = {Reticulate classification of mosaic microbial genomes using NeAT website.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {804}, number = {}, pages = {81-91}, doi = {10.1007/978-1-61779-361-5_5}, pmid = {22144149}, issn = {1940-6029}, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Bacteriophages/genetics ; Classification/*methods ; Cluster Analysis ; Gene Transfer, Horizontal/*genetics ; Genomics/methods ; Models, Genetic ; *Phylogeny ; *Software ; }, abstract = {The tree of life is the classical representation of the evolutionary relationships between existent species. A tree is appropriate to display the divergence of species through mutation, i.e., by vertical descent. However, lateral gene transfer (LGT) is excluded from such representations. When LGT contribution to genome evolution cannot be neglected (e.g., for prokaryotes and mobile genetic elements), the tree becomes misleading. Networks appear as an intuitive way to represent both vertical and horizontal relationships, while overlapping groups within such graphs are more suitable for their classification. Here, we describe a method to represent both vertical and horizontal relationships. We start with a set of genomes whose coded proteins have been grouped into families based on sequence similarity. Next, all pairs of genomes are compared, counting the number of proteins classified into the same family. From this comparison, we derive a weighted graph where genomes with a significant number of similar proteins are linked. Finally, we apply a two-step clustering of this graph to produce a classification where nodes can be assigned to multiple clusters. The procedure can be performed using the Network Analysis Tools (NeAT) website.}, }
@article {pmid22144148, year = {2012}, author = {Toussaint, A and Chandler, M}, title = {Prokaryote genome fluidity: toward a system approach of the mobilome.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {804}, number = {}, pages = {57-80}, doi = {10.1007/978-1-61779-361-5_4}, pmid = {22144148}, issn = {1940-6029}, mesh = {Bacteriophages/classification/genetics ; Conjugation, Genetic/physiology ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome, Archaeal/*genetics ; Genome, Bacterial/*genetics ; Homologous Recombination/physiology ; Interspersed Repetitive Sequences/*genetics ; Molecular Sequence Annotation/methods ; Systems Biology/*methods ; Transformation, Bacterial/physiology ; }, abstract = {The importance of horizontal/lateral gene transfer (LGT) in shaping the genomes of prokaryotic organisms has been recognized in recent years as a result of analysis of the increasing number of available genome sequences. LGT is largely due to the transfer and recombination activities of mobile genetic elements (MGEs). Bacterial and archaeal genomes are mosaics of vertically and horizontally transmitted DNA segments. This generates reticulate relationships between members of the prokaryotic world that are better represented by networks than by "classical" phylogenetic trees. In this review we summarize the nature and activities of MGEs, and the problems that presently limit their analysis on a large scale. We propose routes to improve their annotation in the flow of genomic and metagenomic sequences that currently exist and those that become available. We describe network analysis of evolutionary relationships among some MGE categories and sketch out possible developments of this type of approach to get more insight into the role of the mobilome in bacterial adaptation and evolution.}, }
@article {pmid22143526, year = {2012}, author = {Poirel, L and Bonnin, RA and Boulanger, A and Schrenzel, J and Kaase, M and Nordmann, P}, title = {Tn125-related acquisition of blaNDM-like genes in Acinetobacter baumannii.}, journal = {Antimicrobial agents and chemotherapy}, volume = {56}, number = {2}, pages = {1087-1089}, pmid = {22143526}, issn = {1098-6596}, mesh = {Acinetobacter Infections/*epidemiology/microbiology ; Acinetobacter baumannii/*drug effects/enzymology/*genetics ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics ; Carbapenems/pharmacology ; DNA Transposable Elements/*genetics ; Drug Resistance, Multiple, Bacterial ; Gene Transfer, Horizontal/*genetics ; Humans ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Sequence Analysis, DNA ; Switzerland/epidemiology ; beta-Lactam Resistance ; beta-Lactamases/*genetics ; beta-Lactams/pharmacology ; }, abstract = {A multidrug-resistant Acinetobacter baumannii isolate recovered from a patient hospitalized in Switzerland after a transfer from Serbia produced the NDM-1 carbapenemase. The bla(NDM-1) gene was part of a chromosomally located Tn125 composite transposon bracketed by two copies of the same insertion sequence, ISAba125. This transposon was also associated with the acquisition and expression of the bla(NDM-2) gene in an A. baumannii isolate in Germany. Tn125 appears to be the main vehicle for dissemination of bla(NDM) genes in that species.}, }
@article {pmid22142724, year = {2011}, author = {Nagata, Y and Natsui, S and Endo, R and Ohtsubo, Y and Ichikawa, N and Ankai, A and Oguchi, A and Fukui, S and Fujita, N and Tsuda, M}, title = {Genomic organization and genomic structural rearrangements of Sphingobium japonicum UT26, an archetypal γ-hexachlorocyclohexane-degrading bacterium.}, journal = {Enzyme and microbial technology}, volume = {49}, number = {6-7}, pages = {499-508}, doi = {10.1016/j.enzmictec.2011.10.005}, pmid = {22142724}, issn = {1879-0909}, mesh = {ATP-Binding Cassette Transporters/genetics/metabolism ; Adipates/metabolism ; Bacterial Proteins/genetics/metabolism ; Biodegradation, Environmental ; Gene Deletion ; Gene Rearrangement ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Hexachlorocyclohexane/*metabolism ; Metabolic Networks and Pathways ; Models, Genetic ; Phylogeny ; Replication Origin ; Replicon ; Species Specificity ; Sphingomonadaceae/*genetics/*metabolism ; }, abstract = {The complete genome sequencing of a γ-hexachlorocyclohexane-degrading strain, Sphingobium japonicum UT26, revealed that the genome consists of two circular chromosomes [with sizes of 3.5 Mb (Chr1) and 682kb (Chr2)], a 191-kb large plasmid (pCHQ1), and two small plasmids with sizes of 32 and 5kb. The lin genes are dispersed on Chr1, Chr2, and pCHQ1. Comparison of the UT26 genome with those of other sphingomonad strains demonstrated that the "specific"lin genes for conversion of γ-HCH to β-ketoadipate (linA, linB, linC, linRED, and linF) are located on the DNA regions unique to the UT26 genome, suggesting the acquisition of these lin genes by horizontal transfer events. On the other hand, linGHIJ and linKLMN are located on the regions conserved in the genomes of sphingomonads, suggesting that the linGHIJ-encoded β-ketoadipate pathway and the LinKLMN-type ABC transporter system are involved in core functions of sphingomonads. Based on these results, we propose a hypothesis that UT26 was created by recruiting the specific lin genes into a strain having core functions of sphingomonads. Most of the specific lin genes in UT26 are associated with IS6100. Our analysis of spontaneous linA-, linC-, and linRED-deletion mutants of UT26 revealed the involvement of IS6100 in their deduced genome rearrangements. These facts strongly suggest that IS6100 plays important roles both in the dissemination of the specific lin genes and in the genome rearrangements.}, }
@article {pmid22140558, year = {2011}, author = {Lawrence, DP and Kroken, S and Pryor, BM and Arnold, AE}, title = {Interkingdom gene transfer of a hybrid NPS/PKS from bacteria to filamentous Ascomycota.}, journal = {PloS one}, volume = {6}, number = {11}, pages = {e28231}, pmid = {22140558}, issn = {1932-6203}, mesh = {Ascomycota/*enzymology/*genetics ; Bacteria/*enzymology/*genetics ; Gene Transfer, Horizontal/*genetics ; Molecular Sequence Data ; Peptide Synthases/chemistry/*genetics ; Phylogeny ; Polyketide Synthases/chemistry/*genetics ; Protein Structure, Tertiary ; }, abstract = {Nonribosomal peptides (NRPs) and polyketides (PKs) are ecologically important secondary metabolites produced by bacteria and fungi using multidomain enzymes called nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), respectively. Previous phylogenetic analyses of fungal NRPSs and PKSs have suggested that a few of these genes were acquired by fungi via horizontal gene transfer (HGT) from bacteria, including a hybrid NPS/PKS found in Cochliobolus heterostrophus (Dothideomycetes, Ascomycota). Here, we identify this hybrid gene in fungi representing two additional classes of Ascomycota (Aspergillus spp., Microsporum canis, Arthroderma spp., and Trichophyton spp., Eurotiomycetes; Chaetomium spp. and Metarhizium spp., Sordariomycetes) and use phylogenetic analyses of the most highly conserved domains from NRPSs (adenylation (A) domain) and PKSs (ketoacyl synthase (KS) domain) to examine the hypothesis that the hybrid NPS7/PKS24 was acquired by fungi from bacteria via HGT relatively early in the evolution of the Pezizomycotina. Our results reveal a unique ancestry of the A domain and KS domain in the hybrid gene relative to known fungal NRPSs and PKSs, provide strong evidence for HGT of the hybrid gene from a putative bacterial donor in the Burkholderiales, and suggest the HGT event occurred early in the evolution of the filamentous Ascomycota.}, }
@article {pmid22140533, year = {2011}, author = {Voss, M and Nimtz, M and Leimkühler, S}, title = {Elucidation of the dual role of Mycobacterial MoeZR in molybdenum cofactor biosynthesis and cysteine biosynthesis.}, journal = {PloS one}, volume = {6}, number = {11}, pages = {e28170}, pmid = {22140533}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/isolation &amp; purification/*metabolism ; Circular Dichroism ; Coenzymes/*biosynthesis ; Cysteine/*biosynthesis ; Escherichia coli/enzymology ; Genes, Bacterial/genetics ; Genetic Complementation Test ; Kinetics ; Metalloproteins/*biosynthesis ; Models, Biological ; Molecular Sequence Data ; Molybdenum Cofactors ; Mycobacterium/genetics/*metabolism ; Nitrate Reductase/metabolism ; Pteridines ; Sequence Homology, Amino Acid ; Spectrometry, Mass, Electrospray Ionization ; Sulfurtransferases/metabolism ; }, abstract = {The pathway of molybdenum cofactor biosynthesis has been studied in detail by using proteins from Mycobacterium species, which contain several homologs associated with the first steps of Moco biosynthesis. While all Mycobacteria species contain a MoeZR, only some strains have acquired an additional homolog, MoeBR, by horizontal gene transfer. The role of MoeBR and MoeZR was studied in detail for the interaction with the two MoaD-homologs involved in Moco biosynthesis, MoaD1 and MoaD2, in addition to the CysO protein involved in cysteine biosynthesis. We show that both proteins have a role in Moco biosynthesis, while only MoeZR, but not MoeBR, has an additional role in cysteine biosynthesis. MoeZR and MoeBR were able to complement an E. coli moeB mutant strain, but only in conjunction with the Mycobacterial MoaD1 or MoaD2 proteins. Both proteins were able to sulfurate MoaD1 and MoaD2 in vivo, while only MoeZR additionally transferred the sulfur to CysO. Our in vivo studies show that Mycobacteria have acquired several homologs to maintain Moco biosynthesis. MoeZR has a dual role in Moco- and cysteine biosynthesis and is involved in the sulfuration of MoaD and CysO, whereas MoeBR only has a role in Moco biosynthesis, which is not an essential function for Mycobacteria.}, }
@article {pmid22138999, year = {2012}, author = {Lee, S and Ward, TJ and Graves, LM and Wolf, LA and Sperry, K and Siletzky, RM and Kathariou, S}, title = {Atypical Listeria monocytogenes serotype 4b strains harboring a lineage II-specific gene cassette.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {3}, pages = {660-667}, pmid = {22138999}, issn = {1098-5336}, mesh = {DNA, Bacterial/chemistry/*genetics ; Food Microbiology ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Haplotypes ; Listeria monocytogenes/classification/*genetics/isolation &amp; purification ; Listeriosis/microbiology ; Molecular Epidemiology ; Molecular Sequence Data ; Molecular Typing ; Multiplex Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Serotyping ; United States/epidemiology ; }, abstract = {Listeria monocytogenes is the etiological agent of listeriosis, a severe food-borne illness. The population of L. monocytogenes is divided into four lineages (I to IV), and serotype 4b in lineage I has been involved in numerous outbreaks. Several serotype 4b epidemic-associated clonal groups (ECI, -II, and -Ia) have been identified. In this study, we characterized a panel of strains of serotype 4b that produced atypical results with a serotype-specific multiplex PCR and possessed the lmo0734 to lmo0739 gene cassette that had been thought to be specific to lineage II. The cassette was harbored in a genomically syntenic locus in these isolates and in lineage II strains. Three distinct clonal groups (groups 1 to 3) were identified among these isolates based on single-nucleotide polymorphism-based multilocus genotyping (MLGT) and DNA hybridization data. Groups 1 and 2 had MLGT haplotypes previously encountered among clinical isolates and were composed of clinical isolates from multiple states in the United States. In contrast, group 3 consisted of clinical and environmental isolates solely from North Carolina and exhibited a novel haplotype. In addition, all group 3 isolates had DNA that was resistant to MboI, suggesting methylation of adenines at GATC sites. Sequence analysis of the lmo0734 to lmo0739 gene cassette from two strains (group 1 and group 3) revealed that the genes were highly conserved (>99% identity). The data suggest relatively recent horizontal gene transfer from lineage II L. monocytogenes into L. monocytogenes serotype 4b and subsequent dissemination among at least three distinct clonal groups of L. monocytogenes serotype 4b, one of which exhibits restrictions in regional distribution.}, }
@article {pmid22138997, year = {2012}, author = {Arends, K and Schiwon, K and Sakinc, T and Hübner, J and Grohmann, E}, title = {Green fluorescent protein-labeled monitoring tool to quantify conjugative plasmid transfer between Gram-positive and Gram-negative bacteria.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {3}, pages = {895-899}, pmid = {22138997}, issn = {1098-5336}, mesh = {*Conjugation, Genetic ; Enterococcus faecalis/*genetics ; Escherichia coli/*genetics ; *Gene Transfer, Horizontal ; Genes, Reporter ; Green Fluorescent Proteins/genetics/metabolism ; Plasmids ; Staining and Labeling ; }, abstract = {On the basis of pIP501, a green fluorescent protein (GFP)-tagged monitoring tool was constructed for quantifying plasmid mobilization among Gram-positive bacteria and between Gram-positive Enterococcus faecalis and Gram-negative Escherichia coli. Furthermore, retromobilization of the GFP-tagged monitoring tool was shown from E. faecalis OG1X into the clinical isolate E. faecalis T9.}, }
@article {pmid22133219, year = {2011}, author = {Engelmoer, DJ and Rozen, DE}, title = {Competence increases survival during stress in Streptococcus pneumoniae.}, journal = {Evolution; international journal of organic evolution}, volume = {65}, number = {12}, pages = {3475-3485}, doi = {10.1111/j.1558-5646.2011.01402.x}, pmid = {22133219}, issn = {1558-5646}, support = {BB/F002068/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Biological Evolution ; DNA Damage ; Recombination, Genetic ; Streptococcus pneumoniae/drug effects/genetics/*physiology ; *Stress, Physiological ; }, abstract = {Horizontal gene transfer mediated by transformation is of central importance in bacterial evolution. However, numerous questions remain about the maintenance of processes that underlie transformation. Most hypotheses for the benefits of transformation focus on what bacteria might do with DNA, but ignore the important fact that transformation is subsumed within the broader process of competence. Accordingly, the apparent benefits of transformation might rely less on recombination than on other potential benefits associated with the broader suite of traits regulated by competence. We examined the importance of this distinction in the naturally competent species Streptococcus pneumoniae, focusing specifically on predictions of the DNA-for-repair hypothesis. We confirm earlier results in other naturally competent species that transformation protects against DNA-damaging stress. In addition, we show that the stress-protection extends to non-DNA-damaging stress. More important, we find that for some forms of stress transformation is not required for cells to benefit from the induction of competence. This rejects the narrowly defined DNA-for-repair hypotheses and provides the first support for Claverys' hypothesis that competence, but not necessarily transformation, may act as a general process to relieve stress. Our results highlight the need to distinguish benefits of transformation from broader benefits of competence that do not rely on DNA uptake and recombination.}, }
@article {pmid22131950, year = {2011}, author = {Mansson, M and Gram, L and Larsen, TO}, title = {Production of bioactive secondary metabolites by marine vibrionaceae.}, journal = {Marine drugs}, volume = {9}, number = {9}, pages = {1440-1468}, pmid = {22131950}, issn = {1660-3397}, mesh = {Anti-Bacterial Agents/biosynthesis ; Ecology ; Genetic Variation ; Phylogeny ; Quorum Sensing ; Siderophores/biosynthesis ; Vibrionaceae/classification/genetics/*metabolism ; }, abstract = {Bacteria belonging to the Vibrionaceae family are widespread in the marine environment. Today, 128 species of vibrios are known. Several of them are infamous for their pathogenicity or symbiotic relationships. Despite their ability to interact with eukaryotes, the vibrios are greatly underexplored for their ability to produce bioactive secondary metabolites and studies have been limited to only a few species. Most of the compounds isolated from vibrios so far are non-ribosomal peptides or hybrids thereof, with examples of N-containing compounds produced independent of nonribosomal peptide synthetases (NRPS). Though covering a limited chemical space, vibrios produce compounds with attractive biological activities, including antibacterial, anticancer, and antivirulence activities. This review highlights some of the most interesting structures from this group of bacteria. Many compounds found in vibrios have also been isolated from other distantly related bacteria. This cosmopolitan occurrence of metabolites indicates a high incidence of horizontal gene transfer, which raises interesting questions concerning the ecological function of some of these molecules. This account underlines the pending potential for exploring new bacterial sources of bioactive compounds and the challenges related to their investigation.}, }
@article {pmid22130968, year = {2012}, author = {Tamminen, M and Virta, M and Fani, R and Fondi, M}, title = {Large-scale analysis of plasmid relationships through gene-sharing networks.}, journal = {Molecular biology and evolution}, volume = {29}, number = {4}, pages = {1225-1240}, doi = {10.1093/molbev/msr292}, pmid = {22130968}, issn = {1537-1719}, mesh = {Cluster Analysis ; Databases, Genetic ; Drug Resistance, Bacterial ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; *Models, Genetic ; Phylogeny ; Plasmids/*genetics ; }, abstract = {Plasmids are vessels of genetic exchange in microbial communities. They are known to transfer between different host organisms and acquire diverse genetic elements from chromosomes and/or other plasmids. Therefore, they constitute an important element in microbial evolution by rapidly disseminating various genetic properties among different communities. A paradigmatic example of this is the dissemination of antibiotic resistance (AR) genes that has resulted in the emergence of multiresistant pathogenic bacterial strains. To globally analyze the evolutionary dynamics of plasmids, we built a large graph in which 2,343 plasmids (nodes) are connected according to the proteins shared by each other. The analysis of this gene-sharing network revealed an overall coherence between network clustering and the phylogenetic classes of the corresponding microorganisms, likely resulting from genetic barriers to horizontal gene transfer between distant phylogenetic groups. Habitat was not a crucial factor in clustering as plasmids from organisms inhabiting different environments were often found embedded in the same cluster. Analyses of network metrics revealed a statistically significant correlation between plasmid mobility and their centrality within the network, providing support to the observation that mobile plasmids are particularly important in spreading genes in microbial communities. Finally, our study reveals an extensive (and previously undescribed) sharing of AR genes between Actinobacteria and Gammaproteobacteria, suggesting that the former might represent an important reservoir of AR genes for the latter.}, }
@article {pmid22128857, year = {2012}, author = {Lynch, MJ and Fox, EM and O'Connor, L and Jordan, K and Murphy, M}, title = {Surveillance of verocytotoxigenic Escherichia coli in Irish bovine dairy herds.}, journal = {Zoonoses and public health}, volume = {59}, number = {4}, pages = {264-271}, doi = {10.1111/j.1863-2378.2011.01443.x}, pmid = {22128857}, issn = {1863-2378}, mesh = {Animals ; Cattle ; Cattle Diseases/epidemiology/microbiology ; Dairying ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli Infections/epidemiology/microbiology/*veterinary ; Feces/*microbiology ; Humans ; Immunomagnetic Separation ; Ireland/epidemiology ; Milk/*microbiology ; Prevalence ; Real-Time Polymerase Chain Reaction ; Sentinel Surveillance ; Serotyping ; Shiga Toxins/*genetics ; Shiga-Toxigenic Escherichia coli/classification/*genetics/isolation &amp; purification/*pathogenicity ; Surveys and Questionnaires ; Virulence/genetics ; Virulence Factors ; }, abstract = {Verocytotoxigenic Escherichia coli (VTEC) are highly significant zoonotic threats to public health, and have been the causative agent implicated in numerous high-profile outbreaks affecting large numbers of people. Serovar O157 is most frequently linked with human illness; however, other serovars, such as O26, O103, O111 and O145, have also been implicated. This study aimed to characterize the prevalence and virulence determinants of these five serovars in Irish dairy farm herds, and their milk. Using real-time PCR (RTi-PCR), bovine rectal faecal swabs and raw milk samples, along with milk filters, were screened for the presence of vt genes. Positive samples were then screened for the five serovars using sero-specific PCR. Serovar-positive samples were subjected to immunomagnetic separation, to isolate viable VTEC strains. These isolates were subsequently screened for four virulence factors: vt1, vt2, eaeA and hlyA. Three hundred and eighty six of the 600 rectal faecal swabs, 85 of the 117 milk-filters and 43 of the 120 bulk-tank milk samples, were positive for vt genes. From these 514 total vt-positive samples, 58 O26, 162 O103, 1 O111, 324 O145 and 26 O157 positives were detected by sero-specific RTi-PCR. Immunomagnetic separation yielded 12 O26, 26 O103, 0 O111, 19 O145 and 10 O157 isolates. Ten of these isolates contained at least one of the four virulence determinants screened for (i.e. vt1, vt2, eaeA and hlyA). Of these 10 isolates, pulsed-field gel electrophoresis showed that two of the O26 isolates from different farms were indistinguishable. Two O157 isolates were also indistinguishable. This study found serovars O103 and O145 to be the most prevalent in samples tested. Apart from the occurrence of VTEC in dairy herds, this study shows a high occurrence of vt genes in the environment, creating the possibility of horizontal gene transfer and emergence of new VTEC strains.}, }
@article {pmid22128332, year = {2011}, author = {Karberg, KA and Olsen, GJ and Davis, JJ}, title = {Similarity of genes horizontally acquired by Escherichia coli and Salmonella enterica is evidence of a supraspecies pangenome.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {50}, pages = {20154-20159}, pmid = {22128332}, issn = {1091-6490}, mesh = {Codon/genetics ; Escherichia coli/*genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/*genetics ; Phylogeny ; Salmonella enterica/*genetics ; *Sequence Homology, Nucleic Acid ; Species Specificity ; }, abstract = {Most bacterial and archaeal genomes contain many genes with little or no similarity to other genes, a property that impedes identification of gene origins. By comparing the codon usage of genes shared among strains (primarily vertically inherited genes) and genes unique to one strain (primarily recently horizontally acquired genes), we found that the plurality of unique genes in Escherichia coli and Salmonella enterica are much more similar to each other than are their vertically inherited genes. We conclude that E. coli and S. enterica derive these unique genes from a common source, a supraspecies phylogenetic group that includes the organisms themselves. The phylogenetic range of the sharing appears to include other (but not all) members of the Enterobacteriaceae. We found evidence of similar gene sharing in other bacterial and archaeal taxa. Thus, we conclude that frequent gene exchange, particularly that of genetic novelties, extends well beyond accepted species boundaries.}, }
@article {pmid22126996, year = {2011}, author = {Krupovic, M and Prangishvili, D and Hendrix, RW and Bamford, DH}, title = {Genomics of bacterial and archaeal viruses: dynamics within the prokaryotic virosphere.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {75}, number = {4}, pages = {610-635}, pmid = {22126996}, issn = {1098-5557}, support = {R01 GM051975/GM/NIGMS NIH HHS/United States ; }, mesh = {Archaeal Viruses/classification/*genetics ; Bacteriophages/classification/*genetics ; *Genome, Viral ; *Genomics ; Interspersed Repetitive Sequences/genetics ; Transduction, Genetic ; }, abstract = {Prokaryotes, bacteria and archaea, are the most abundant cellular organisms among those sharing the planet Earth with human beings (among others). However, numerous ecological studies have revealed that it is actually prokaryotic viruses that predominate on our planet and outnumber their hosts by at least an order of magnitude. An understanding of how this viral domain is organized and what are the mechanisms governing its evolution is therefore of great interest and importance. The vast majority of characterized prokaryotic viruses belong to the order Caudovirales, double-stranded DNA (dsDNA) bacteriophages with tails. Consequently, these viruses have been studied (and reviewed) extensively from both genomic and functional perspectives. However, albeit numerous, tailed phages represent only a minor fraction of the prokaryotic virus diversity. Therefore, the knowledge which has been generated for this viral system does not offer a comprehensive view of the prokaryotic virosphere. In this review, we discuss all families of bacterial and archaeal viruses that contain more than one characterized member and for which evolutionary conclusions can be attempted by use of comparative genomic analysis. We focus on the molecular mechanisms of their genome evolution as well as on the relationships between different viral groups and plasmids. It becomes clear that evolutionary mechanisms shaping the genomes of prokaryotic viruses vary between different families and depend on the type of the nucleic acid, characteristics of the virion structure, as well as the mode of the life cycle. We also point out that horizontal gene transfer is not equally prevalent in different virus families and is not uniformly unrestricted for diverse viral functions.}, }
@article {pmid22125388, year = {2011}, author = {Horiike, T and Miyata, D and Tateno, Y and Minai, R}, title = {HGT-Gen: a tool for generating a phylogenetic tree with horizontal gene transfer.}, journal = {Bioinformation}, volume = {7}, number = {5}, pages = {211-213}, pmid = {22125388}, issn = {0973-2063}, abstract = {UNLABELLED: Horizontal gene transfer (HGT) is a common event in prokaryotic evolution. Therefore, it is very important to consider HGT in the study of molecular evolution of prokaryotes. This is true also for conducting computer simulations of their molecular phylogeny because HGT is known to be a serious disturbing factor for estimating their correct phylogeny. To the best of our knowledge, no existing computer program has generated a phylogenetic tree with HGT from an original phylogenetic tree. We developed a program called HGT-Gen that generates a phylogenetic tree with HGT on the basis of an original phylogenetic tree of a protein or gene. HGT-Gen converts an operational taxonomic unit or a clade from one place to another in a given phylogenetic tree. We have also devised an algorithm to compute the average length between any pair of branches in the tree. It defines and computes the relative evolutionary time to normalize evolutionary time for each lineage. The algorithm can generate an HGT between a pair of donor and acceptor lineages at the same evolutionary time. HGT-Gen is used with a sequence-generating program to evaluate the influence of HGT on the molecular phylogeny of prokaryotes in a computer simulation study.<br><br>AVAILABILITY: The database is available for free at http://www.grl.shizuoka.ac.jp/&#x2dc;thoriike/HGT-Gen.html.}, }
@article {pmid22123249, year = {2012}, author = {Srinivasan, T and Bruno, WJ and Wan, R and Yen, A and Duong, J and Dean, D}, title = {In vitro recombinants of antibiotic-resistant Chlamydia trachomatis strains have statistically more breakpoints than clinical recombinants for the same sequenced loci and exhibit selection at unexpected loci.}, journal = {Journal of bacteriology}, volume = {194}, number = {3}, pages = {617-626}, pmid = {22123249}, issn = {1098-5530}, support = {R01 AI059647/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Base Sequence ; Chlamydia Infections/*microbiology ; Chlamydia trachomatis/classification/drug effects/*genetics/metabolism ; *Drug Resistance, Bacterial ; Genetic Engineering ; Humans ; Molecular Sequence Data ; Phylogeny ; *Recombination, Genetic ; }, abstract = {Lateral gene transfer (LGT) is essential for generating between-strain genomic recombinants of Chlamydia trachomatis to facilitate the organism's evolution. Because there is no reliable laboratory-based gene transfer system for C. trachomatis, in vitro generation of recombinants from antibiotic-resistant strains is being used to study LGT. However, selection pressures imposed on in vitro recombinants likely affect statistical properties of recombination relative to naturally occurring clinical recombinants, including prevalence at particular loci. We examined multiple loci for 16 in vitro-derived recombinants of ofloxacin- and rifampin-resistant L(1) and D strains, respectively, grown with both antibiotics, and compared these with the same sequenced loci among 11 clinical recombinants. Breakpoints and recombination frequency were examined using phylogenetics, bioinformatics, and statistics. In vitro and clinical isolates clustered perfectly into two groups, without misclassification, using Ward's minimum variance based on breakpoint data. As expected, gyrA (confers ofloxacin resistance) and rpoB (confers rifampin resistance) had significantly more breakpoints among in vitro recombinants than among clinical recombinants (P < 0.0001 and P = 0.02, respectively, using the Wilcoxon rank sum test). Unexpectedly, trpA also had significantly more breakpoints for in vitro recombinants (P < 0.0001). There was also significant selection at other loci. The strongest bias was for ompA in strain D (P = 3.3 × 10(-8)). Our results indicate that the in vitro model differs statistically from natural recombination events. Additional genomic studies are needed to determine the factors responsible for the observed selection biases at unexpected loci and whether these are important for LGT to inform approaches for genetically manipulating C. trachomatis.}, }
@article {pmid22122442, year = {2011}, author = {Casas, V and Maloy, S}, title = {Role of bacteriophage-encoded exotoxins in the evolution of bacterial pathogens.}, journal = {Future microbiology}, volume = {6}, number = {12}, pages = {1461-1473}, doi = {10.2217/fmb.11.124}, pmid = {22122442}, issn = {1746-0921}, mesh = {Animals ; Bacteria/*pathogenicity/*virology ; Bacterial Toxins/*biosynthesis/genetics ; Bacteriophages/genetics/*physiology ; *Biological Evolution ; Environmental Microbiology ; Exotoxins/*biosynthesis/genetics ; Gene Transfer, Horizontal ; Humans ; *Lysogeny ; }, abstract = {Recent advances in metagenomics research have generated a bounty of information that provides insight into the dynamic genetic exchange occurring between bacteriophage (phage) and their bacterial hosts. Metagenomic studies of the microbiomes from a variety of environments have shown that many of the genes sequenced are of phage origin. Among these genes are phage-encoded exotoxin genes. When phage that carry these genes infect an appropriate bacterial host, the bacterium undergoes lysogenic conversion, converting the bacterium from an avirulent strain to a pathogen that can cause human disease. Transfer of the exotoxin genes between bacteria has been shown to occur in marine environments, animal and human intestines and sewage treatment plants. Surprisingly, phage that encode exotoxin genes are commonly found in environments that lack the cognate bacteria commonly associated with the specific toxin-mediated disease and have been found to be associated with alternative environmental bacterial hosts. These findings suggest that the exotoxin genes may play a beneficial role for the bacterial host in nature, and that this environmental reservoir of exotoxin genes may play a role in the evolution of new bacterial pathogens.}, }
@article {pmid22119898, year = {2012}, author = {Ramírez, MS and Merkier, AK and Quiroga, MP and Centrón, D}, title = {Acinetobacter baumannii is able to gain and maintain a plasmid harbouring In35 found in Enterobacteriaceae isolates from Argentina.}, journal = {Current microbiology}, volume = {64}, number = {3}, pages = {211-213}, pmid = {22119898}, issn = {1432-0991}, mesh = {Acinetobacter baumannii/enzymology/*genetics/isolation &amp; purification ; Anti-Bacterial Agents/pharmacology ; Argentina ; Cephalosporins/pharmacology ; *Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; *Plasmids ; Proteus mirabilis/*genetics/isolation &amp; purification ; Transformation, Bacterial ; beta-Lactamases/*genetics ; }, abstract = {The aim of this study was to determine the presence of bla (CTX-M-2) in our A. baumannii population and their putative role as an alternative mechanism of resistance to third-generation cephalosporins in this species. The bla (CTX-M-2) gene is widespread among the Enterobacteriaceae isolates from our country; however, it was not found in 76 isolates A. baumannii non-epidemiologically related clinical isolates resistant to third-generation cephalosporins isolated since 1982 in hospitals from Buenos Aires City. A plasmid isolated from Proteus mirabilis that possesses the complex class 1 integron In35::ISCR1::bla (CTX-M-2) was used to transform the natural competent A. baumannii clinical strain A118. PCR, plasmid extraction, DNA restriction, and susceptibility test confirmed that A118 could gain and maintain the plasmid possessing In35::ISCR1::bla (CTX-M-2), the genetic platform where the bla (CTX-M-2) gene is dispersing in Argentina.}, }
@article {pmid22117008, year = {2012}, author = {Hare, JM and Bradley, JA and Lin, CL and Elam, TJ}, title = {Diverse responses to UV light exposure in Acinetobacter include the capacity for DNA damage-induced mutagenesis in the opportunistic pathogens Acinetobacter baumannii and Acinetobacter ursingii.}, journal = {Microbiology (Reading, England)}, volume = {158}, number = {Pt 3}, pages = {601-611}, pmid = {22117008}, issn = {1465-2080}, support = {P20 RR016481/RR/NCRR NIH HHS/United States ; R15 GM085722/GM/NIGMS NIH HHS/United States ; 2P20RR016481-09/RR/NCRR NIH HHS/United States ; 1R15GM085722-01A1/GM/NIGMS NIH HHS/United States ; }, mesh = {Acinetobacter/*genetics/*radiation effects ; *DNA Damage ; *DNA Repair ; DNA Repair Enzymes/metabolism ; DNA-Directed DNA Polymerase/metabolism ; Genetic Variation ; Microbial Viability/radiation effects ; Molecular Sequence Data ; *Mutagenesis ; SOS Response, Genetics ; Sequence Analysis, DNA ; *Ultraviolet Rays ; }, abstract = {Error-prone and error-free DNA damage repair responses that are induced in most bacteria after exposure to various chemicals, antibiotics or radiation sources were surveyed across the genus Acinetobacter. The error-prone SOS mutagenesis response occurs when DNA damage induces a cell's umuDC- or dinP-encoded error-prone polymerases. The model strain Acinetobacter baylyi ADP1 possesses an unusual, regulatory umuD allele (umuDAb) with an extended 5' region and only incomplete fragments of umuC. Diverse Acinetobacter species were investigated for the presence of umuDC and their ability to conduct UV-induced mutagenesis. Unlike ADP1, most Acinetobacter strains possessed multiple umuDC loci containing either umuDAb or a umuD allele resembling that of Escherichia coli. The nearly omnipresent umuDAb allele was the ancestral umuD in Acinetobacter, with horizontal gene transfer accounting for over half of the umuDC operons. Despite multiple umuD(Ab)C operons in many strains, only three species conducted UV-induced mutagenesis: Acinetobacter baumannii, Acinetobacter ursingii and Acinetobacter beijerinckii. The type of umuDC locus or mutagenesis phenotype a strain possessed was not correlated with its error-free response of survival after UV exposure, but similar diversity was apparent. The survival of 30 Acinetobacter strains after UV treatment ranged over five orders of magnitude, with the Acinetobacter calcoaceticus-A. baumannii (Acb) complex and haemolytic strains having lower survival than non-Acb or non-haemolytic strains. These observations demonstrate that a genus can possess a range of DNA damage response mechanisms, and suggest that DNA damage-induced mutation could be an important part of the evolution of the emerging pathogens A. baumannii and A. ursingii.}, }
@article {pmid22115438, year = {2011}, author = {Gounder, K and Brzuszkiewicz, E and Liesegang, H and Wollherr, A and Daniel, R and Gottschalk, G and Reva, O and Kumwenda, B and Srivastava, M and Bricio, C and Berenguer, J and van Heerden, E and Litthauer, D}, title = {Sequence of the hyperplastic genome of the naturally competent Thermus scotoductus SA-01.}, journal = {BMC genomics}, volume = {12}, number = {}, pages = {577}, pmid = {22115438}, issn = {1471-2164}, mesh = {Adaptation, Biological/genetics ; Chromosomes, Bacterial ; Comparative Genomic Hybridization ; DNA, Bacterial/genetics ; Gene Rearrangement ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Molecular Sequence Annotation ; Sequence Analysis, DNA ; Synteny ; Thermus/*genetics/metabolism ; Thermus thermophilus/genetics ; }, abstract = {BACKGROUND: Many strains of Thermus have been isolated from hot environments around the world. Thermus scotoductus SA-01 was isolated from fissure water collected 3.2 km below surface in a South African gold mine. The isolate is capable of dissimilatory iron reduction, growth with oxygen and nitrate as terminal electron acceptors and the ability to reduce a variety of metal ions, including gold, chromate and uranium, was demonstrated. The genomes from two different Thermus thermophilus strains have been completed. This paper represents the completed genome from a second Thermus species - T. scotoductus.<br><br>RESULTS: The genome of Thermus scotoductus SA-01 consists of a chromosome of 2,346,803 bp and a small plasmid which, together are about 11% larger than the Thermus thermophilus genomes. The T. thermophilus megaplasmid genes are part of the T. scotoductus chromosome and extensive rearrangement, deletion of nonessential genes and acquisition of gene islands have occurred, leading to a loss of synteny between the chromosomes of T. scotoductus and T. thermophilus. At least nine large inserts of which seven were identified as alien, were found, the most remarkable being a denitrification cluster and two operons relating to the metabolism of phenolics which appear to have been acquired from Meiothermus ruber. The majority of acquired genes are from closely related species of the Deinococcus-Thermus group, and many of the remaining genes are from microorganisms with a thermophilic or hyperthermophilic lifestyle. The natural competence of Thermus scotoductus was confirmed experimentally as expected as most of the proteins of the natural transformation system of Thermus thermophilus are present. Analysis of the metabolic capabilities revealed an extensive energy metabolism with many aerobic and anaerobic respiratory options. An abundance of sensor histidine kinases, response regulators and transporters for a wide variety of compounds are indicative of an oligotrophic lifestyle.<br><br>CONCLUSIONS: The genome of Thermus scotoductus SA-01 shows remarkable plasticity with the loss, acquisition and rearrangement of large portions of its genome compared to Thermus thermophilus. Its ability to naturally take up foreign DNA has helped it adapt rapidly to a subsurface lifestyle in the presence of a dense and diverse population which acted as source of nutrients. The genome of Thermus scotoductus illustrates how rapid adaptation can be achieved by a highly dynamic and plastic genome.}, }
@article {pmid22114709, year = {2011}, author = {Ghinet, MG and Bordeleau, E and Beaudin, J and Brzezinski, R and Roy, S and Burrus, V}, title = {Uncovering the prevalence and diversity of integrating conjugative elements in actinobacteria.}, journal = {PloS one}, volume = {6}, number = {11}, pages = {e27846}, pmid = {22114709}, issn = {1932-6203}, mesh = {Actinobacteria/*genetics ; Chromosomes, Bacterial/*genetics ; Conjugation, Genetic/*genetics ; DNA Replication ; DNA Transposable Elements/*genetics ; DNA, Bacterial/genetics ; Genes, Bacterial ; Genome, Bacterial ; Phylogeny ; Plasmids/genetics ; Recombination, Genetic ; }, abstract = {Horizontal gene transfer greatly facilitates rapid genetic adaptation of bacteria to shifts in environmental conditions and colonization of new niches by allowing one-step acquisition of novel functions. Conjugation is a major mechanism of horizontal gene transfer mediated by conjugative plasmids and integrating conjugative elements (ICEs). While in most bacterial conjugative systems DNA translocation requires the assembly of a complex type IV secretion system (T4SS), in Actinobacteria a single DNA FtsK/SpoIIIE-like translocation protein is required. To date, the role and diversity of ICEs in Actinobacteria have received little attention. Putative ICEs were searched for in 275 genomes of Actinobacteria using HMM-profiles of proteins involved in ICE maintenance and transfer. These exhaustive analyses revealed 144 putative FtsK/SpoIIIE-type ICEs and 17 putative T4SS-type ICEs. Grouping of the ICEs based on the phylogenetic analyses of maintenance and transfer proteins revealed extensive exchanges between different sub-families of ICEs. 17 ICEs were found in Actinobacteria from the genus Frankia, globally important nitrogen-fixing microorganisms that establish root nodule symbioses with actinorhizal plants. Structural analysis of ICEs from Frankia revealed their unexpected diversity and a vast array of predicted adaptive functions. Frankia ICEs were found to excise by site-specific recombination from their host's chromosome in vitro and in planta suggesting that they are functional mobile elements whether Frankiae live as soil saprophytes or plant endosymbionts. Phylogenetic analyses of proteins involved in ICEs maintenance and transfer suggests that active exchange between ICEs cargo-borne and chromosomal genes took place within the Actinomycetales order. Functionality of Frankia ICEs in vitro as well as in planta lets us anticipate that conjugation and ICEs could allow the development of genetic manipulation tools for this challenging microorganism and for many other Actinobacteria.}, }
@article {pmid22114557, year = {2011}, author = {Cordeiro, TN and Schmidt, H and Madrid, C and Juárez, A and Bernadó, P and Griesinger, C and García, J and Pons, M}, title = {Indirect DNA readout by an H-NS related protein: structure of the DNA complex of the C-terminal domain of Ler.}, journal = {PLoS pathogens}, volume = {7}, number = {11}, pages = {e1002380}, pmid = {22114557}, issn = {1553-7374}, mesh = {Arginine/metabolism ; DNA, B-Form/*metabolism ; DNA-Binding Proteins/chemistry ; Escherichia coli/*pathogenicity ; Escherichia coli Proteins/chemistry/*metabolism/*physiology ; Fimbriae Proteins/chemistry/*physiology ; Gene Transfer, Horizontal ; Genomic Islands ; Protein Structure, Tertiary ; Trans-Activators/chemistry/*metabolism ; }, abstract = {Ler, a member of the H-NS protein family, is the master regulator of the LEE pathogenicity island in virulent Escherichia coli strains. Here, we determined the structure of a complex between the DNA-binding domain of Ler (CT-Ler) and a 15-mer DNA duplex. CT-Ler recognizes a preexisting structural pattern in the DNA minor groove formed by two consecutive regions which are narrower and wider, respectively, compared with standard B-DNA. The compressed region, associated with an AT-tract, is sensed by the side chain of Arg90, whose mutation abolishes the capacity of Ler to bind DNA. The expanded groove allows the approach of the loop in which Arg90 is located. This is the first report of an experimental structure of a DNA complex that includes a protein belonging to the H-NS family. The indirect readout mechanism not only explains the capacity of H-NS and other H-NS family members to modulate the expression of a large number of genes but also the origin of the specificity displayed by Ler. Our results point to a general mechanism by which horizontally acquired genes may be specifically recognized by members of the H-NS family.}, }
@article {pmid22113826, year = {2012}, author = {Kolman, MA and Torres, LL and Martin, ML and Salerno, GL}, title = {Sucrose synthase in unicellular cyanobacteria and its relationship with salt and hypoxic stress.}, journal = {Planta}, volume = {235}, number = {5}, pages = {955-964}, pmid = {22113826}, issn = {1432-2048}, mesh = {Adaptation, Physiological/genetics ; Cell Hypoxia/physiology ; Cyanobacteria/*enzymology/*genetics ; Gene Expression Regulation, Bacterial ; Gene Expression Regulation, Enzymologic ; Gene Transfer, Horizontal ; Genes, Bacterial ; Glucosyltransferases/genetics/*metabolism ; Microcystis/enzymology/genetics ; Salinity ; Salt-Tolerant Plants/enzymology/genetics ; Sodium Chloride/*metabolism ; Species Specificity ; Stress, Physiological/*physiology ; Sucrose/*metabolism ; }, abstract = {Higher plants and cyanobacteria metabolize sucrose (Suc) by a similar set of enzymes. Suc synthase (SuS, A/UDP-glucose: D: -fructose 2-α-D: -glucosyl transferase) catalyzes a reversible reaction. However, it is in the cleavage of Suc that this enzyme plays an important role in vivo, providing sugar nucleotides for polysaccharide biosynthesis. In cyanobacteria, SuS occurrence has been reported in heterocyst-forming strains, where it was shown to be involved also in nitrogen fixation. We investigated the presence of sequences homologous to SuS-encoding genes (sus) in recently sequenced cyanobacterial genomes. In this work, we show for the first time the presence of SuS in unicellular cyanobacterium strains (Microcystis aeruginosa PCC 7806, Gloebacter violaceus PCC 7421, and Thermosynechococcus elongatus BP-1). After functional characterization of SuS encoding genes, we demonstrated an increase in their transcript levels after a salt treatment or hypoxic stress in M. aeruginosa and G. violaceus cells. Based on phylogenetic analysis and on the presence of sus homologs in the most recently radiated cyanobacterium strains, we propose that sus genes in unicellular cyanobacteria may have been acquired through horizontal gene transfer. Taken together, our data indicate that SuS acquisition by cyanobacteria might be related to open up new ecological niches.}, }
@article {pmid22113690, year = {2011}, author = {Grbić, M and Van Leeuwen, T and Clark, RM and Rombauts, S and Rouzé, P and Grbić, V and Osborne, EJ and Dermauw, W and Ngoc, PC and Ortego, F and Hernández-Crespo, P and Diaz, I and Martinez, M and Navajas, M and Sucena, &#xc9; and Magalhães, S and Nagy, L and Pace, RM and Djuranović, S and Smagghe, G and Iga, M and Christiaens, O and Veenstra, JA and Ewer, J and Villalobos, RM and Hutter, JL and Hudson, SD and Velez, M and Yi, SV and Zeng, J and Pires-daSilva, A and Roch, F and Cazaux, M and Navarro, M and Zhurov, V and Acevedo, G and Bjelica, A and Fawcett, JA and Bonnet, E and Martens, C and Baele, G and Wissler, L and Sanchez-Rodriguez, A and Tirry, L and Blais, C and Demeestere, K and Henz, SR and Gregory, TR and Mathieu, J and Verdon, L and Farinelli, L and Schmutz, J and Lindquist, E and Feyereisen, R and Van de Peer, Y}, title = {The genome of Tetranychus urticae reveals herbivorous pest adaptations.}, journal = {Nature}, volume = {479}, number = {7374}, pages = {487-492}, pmid = {22113690}, issn = {1476-4687}, support = {T32 GM007464/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Physiological/*genetics/physiology ; Animals ; Ecdysterone/analogs &amp; derivatives/genetics ; Evolution, Molecular ; Fibroins/genetics ; Gene Expression Regulation ; Gene Transfer, Horizontal/genetics ; Genes, Homeobox/genetics ; Genome/*genetics ; Genomics ; Herbivory/*genetics/physiology ; Molecular Sequence Data ; Molting/genetics ; Multigene Family/genetics ; Nanostructures/chemistry ; Plants/parasitology ; Silk/biosynthesis/chemistry ; Tetranychidae/*genetics/*physiology ; Transcriptome/genetics ; }, abstract = {The spider mite Tetranychus urticae is a cosmopolitan agricultural pest with an extensive host plant range and an extreme record of pesticide resistance. Here we present the completely sequenced and annotated spider mite genome, representing the first complete chelicerate genome. At 90 megabases T. urticae has the smallest sequenced arthropod genome. Compared with other arthropods, the spider mite genome shows unique changes in the hormonal environment and organization of the Hox complex, and also reveals evolutionary innovation of silk production. We find strong signatures of polyphagy and detoxification in gene families associated with feeding on different hosts and in new gene families acquired by lateral gene transfer. Deep transcriptome analysis of mites feeding on different plants shows how this pest responds to a changing host environment. The T. urticae genome thus offers new insights into arthropod evolution and plant-herbivore interactions, and provides unique opportunities for developing novel plant protection strategies.}, }
@article {pmid22113193, year = {2012}, author = {Kempf, M and Rolain, JM}, title = {Emergence of resistance to carbapenems in Acinetobacter baumannii in Europe: clinical impact and therapeutic options.}, journal = {International journal of antimicrobial agents}, volume = {39}, number = {2}, pages = {105-114}, doi = {10.1016/j.ijantimicag.2011.10.004}, pmid = {22113193}, issn = {1872-7913}, mesh = {Acinetobacter Infections/drug therapy/*epidemiology/*microbiology ; Acinetobacter baumannii/*drug effects ; Anti-Bacterial Agents/*pharmacology/therapeutic use ; Carbapenems/*pharmacology/therapeutic use ; Carrier State/epidemiology/microbiology ; Colistin/pharmacology/therapeutic use ; Community-Acquired Infections/epidemiology/microbiology ; Cross Infection/epidemiology/microbiology ; *Drug Resistance, Multiple, Bacterial ; Europe/epidemiology ; Gene Transfer, Horizontal ; Humans ; }, abstract = {Despite having a reputation of low virulence, Acinetobacter baumannii is an emerging multidrug-resistant (MDR) pathogen responsible for community- and hospital-acquired infections that are difficult to control and treat. Interest in this pathogen emerged about one decade ago because of its natural MDR phenotype, its capability of acquiring new mechanisms of resistance and the existence of nosocomial outbreaks. Recent advances in molecular biology, including full genome sequencing of several A. baumannii isolates, has led to the discovery of the extraordinary plasticity of their genomes, which is linked to their great propensity to adapt to any environment, including hospitals. In this context, as well as the increasing antimicrobial resistance amongst A. baumannii isolates to the last-line antibiotics carbapenems and colistin, therapeutic options are very limited or absent in some cases of infections with pandrug-resistant bacteria. However, a large proportion of patients may be colonised by such MDR bacteria without any sign of infection, leading to a recurrent question for clinicians as to whether antibiotic treatment should be given and will be effective in the presence of resistance mechanisms. The worldwide emergence of A. baumannii strains resistant to colistin is worrying and the increasing use of colistin to treat infections caused by MDR bacteria will inevitably increase the recovery rate of colistin-resistant isolates in the future. Current knowledge about A. baumannii, including biological and epidemiological aspects as well as resistance to antibiotics and antibiotic therapy, are reviewed in this article, in addition to therapeutic recommendations.}, }
@article {pmid22113192, year = {2012}, author = {Jamal, W and Rotimi, VO and Albert, MJ and Khodakhast, F and Udo, EE and Poirel, L}, title = {Emergence of nosocomial New Delhi metallo-β-lactamase-1 (NDM-1)-producing Klebsiella pneumoniae in patients admitted to a tertiary care hospital in Kuwait.}, journal = {International journal of antimicrobial agents}, volume = {39}, number = {2}, pages = {183-184}, doi = {10.1016/j.ijantimicag.2011.10.002}, pmid = {22113192}, issn = {1872-7913}, mesh = {Aged, 80 and over ; Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; Cross Infection/*microbiology ; Escherichia coli/drug effects/genetics ; Gene Transfer, Horizontal ; Hospitals ; Humans ; Klebsiella Infections/*microbiology ; Klebsiella pneumoniae/drug effects/*enzymology/genetics/isolation &amp; purification ; Kuwait ; Male ; Microbial Sensitivity Tests ; Middle Aged ; beta-Lactamases/genetics/*metabolism ; }, }
@article {pmid22113034, year = {2012}, author = {Caspi-Fluger, A and Inbar, M and Mozes-Daube, N and Katzir, N and Portnoy, V and Belausov, E and Hunter, MS and Zchori-Fein, E}, title = {Horizontal transmission of the insect symbiont Rickettsia is plant-mediated.}, journal = {Proceedings. Biological sciences}, volume = {279}, number = {1734}, pages = {1791-1796}, pmid = {22113034}, issn = {1471-2954}, mesh = {Animals ; DNA, Bacterial/analysis ; *Gene Transfer, Horizontal ; Gossypium/*microbiology ; Hemiptera/*microbiology ; In Situ Hybridization, Fluorescence ; Phloem/microbiology ; Plant Leaves/*microbiology ; Plants/microbiology ; Polymerase Chain Reaction ; Rickettsia/genetics/*physiology ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {Bacteria in the genus Rickettsia, best known as vertebrate pathogens vectored by blood-feeding arthropods, can also be found in phytophagous insects. The presence of closely related bacterial symbionts in evolutionarily distant arthropod hosts presupposes a means of horizontal transmission, but no mechanism for this transmission has been described. Using a combination of experiments with live insects, molecular analyses and microscopy, we found that Rickettsia were transferred from an insect host (the whitefly Bemisia tabaci) to a plant, moved inside the phloem, and could be acquired by other whiteflies. In one experiment, Rickettsia was transferred from the whitefly host to leaves of cotton, basil and black nightshade, where the bacteria were restricted to the phloem cells of the plant. In another experiment, Rickettsia-free adult whiteflies, physically segregated but sharing a cotton leaf with Rickettsia-plus individuals, acquired the Rickettsia at a high rate. Plants can serve as a reservoir for horizontal transmission of Rickettsia, a mechanism which may explain the occurrence of phylogenetically similar symbionts among unrelated phytophagous insect species. This plant-mediated transmission route may also exist in other insect-symbiont systems and, since symbionts may play a critical role in the ecology and evolution of their hosts, serve as an immediate and powerful tool for accelerated evolution.}, }
@article {pmid22112233, year = {2012}, author = {Fitzpatrick, DA}, title = {Horizontal gene transfer in fungi.}, journal = {FEMS microbiology letters}, volume = {329}, number = {1}, pages = {1-8}, doi = {10.1111/j.1574-6968.2011.02465.x}, pmid = {22112233}, issn = {1574-6968}, mesh = {Adaptation, Biological ; Computational Biology/methods ; Evolution, Molecular ; Fungi/*genetics ; *Gene Transfer, Horizontal ; *Genes, Fungal ; Recombination, Genetic ; }, abstract = {Horizontal gene transfer (HGT) is frequently observed in prokaryotes and until recently was assumed to be of limited importance to eukaryotes. However, there is an increasing body of evidence to suggest that HGT is an important mechanism in eukaryotic genome evolution, particularly in unicellular organisms. The transfer of individual genes, gene clusters or entire chromosomes can have significant impacts on niche specification, disease emergence or shift in metabolic capabilities. In terms of genomic sequencing, the fungal kingdom is one of the most densely sampled eukaryotic lineages and is at the forefront of eukaryote comparative genomics and enables us to use fungi to study eukaryotic evolutionary mechanisms including HGT. This review describes the bioinformatics-based methodologies commonly used to locate HGT in fungal genomes and investigates the possible mechanisms involved in transferring genetic material laterally into fungal species. I will highlight a number of fungal HGT events and discuss the impact they have played on fungal evolution and discuss the implications HGT may have on the fungal tree of life.}, }
@article {pmid22111657, year = {2011}, author = {Siddaramappa, S and Challacombe, JF and Duncan, AJ and Gillaspy, AF and Carson, M and Gipson, J and Orvis, J and Zaitshik, J and Barnes, G and Bruce, D and Chertkov, O and Detter, JC and Han, CS and Tapia, R and Thompson, LS and Dyer, DW and Inzana, TJ}, title = {Horizontal gene transfer in Histophilus somni and its role in the evolution of pathogenic strain 2336, as determined by comparative genomic analyses.}, journal = {BMC genomics}, volume = {12}, number = {}, pages = {570}, pmid = {22111657}, issn = {1471-2164}, mesh = {Chromosomes, Bacterial ; *Comparative Genomic Hybridization ; DNA, Bacterial/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Pasteurellaceae/*genetics ; }, abstract = {BACKGROUND: Pneumonia and myocarditis are the most commonly reported diseases due to Histophilus somni, an opportunistic pathogen of the reproductive and respiratory tracts of cattle. Thus far only a few genes involved in metabolic and virulence functions have been identified and characterized in H. somni using traditional methods. Analyses of the genome sequences of several Pasteurellaceae species have provided insights into their biology and evolution. In view of the economic and ecological importance of H. somni, the genome sequence of pneumonia strain 2336 has been determined and compared to that of commensal strain 129Pt and other members of the Pasteurellaceae.<br><br>RESULTS: The chromosome of strain 2336 (2,263,857 bp) contained 1,980 protein coding genes, whereas the chromosome of strain 129Pt (2,007,700 bp) contained only 1,792 protein coding genes. Although the chromosomes of the two strains differ in size, their average GC content, gene density (total number of genes predicted on the chromosome), and percentage of sequence (number of genes) that encodes proteins were similar. The chromosomes of these strains also contained a number of discrete prophage regions and genomic islands. One of the genomic islands in strain 2336 contained genes putatively involved in copper, zinc, and tetracycline resistance. Using the genome sequence data and comparative analyses with other members of the Pasteurellaceae, several H. somni genes that may encode proteins involved in virulence (e.g., filamentous haemaggutinins, adhesins, and polysaccharide biosynthesis/modification enzymes) were identified. The two strains contained a total of 17 ORFs that encode putative glycosyltransferases and some of these ORFs had characteristic simple sequence repeats within them. Most of the genes/loci common to both the strains were located in different regions of the two chromosomes and occurred in opposite orientations, indicating genome rearrangement since their divergence from a common ancestor.<br><br>CONCLUSIONS: Since the genome of strain 129Pt was ~256,000 bp smaller than that of strain 2336, these genomes provide yet another paradigm for studying evolutionary gene loss and/or gain in regard to virulence repertoire and pathogenic ability. Analyses of the complete genome sequences revealed that bacteriophage- and transposon-mediated horizontal gene transfer had occurred at several loci in the chromosomes of strains 2336 and 129Pt. It appears that these mobile genetic elements have played a major role in creating genomic diversity and phenotypic variability among the two H. somni strains.}, }
@article {pmid22110385, year = {2011}, author = {Hurwitz, I and Fieck, A and Read, A and Hillesland, H and Klein, N and Kang, A and Durvasula, R}, title = {Paratransgenic control of vector borne diseases.}, journal = {International journal of biological sciences}, volume = {7}, number = {9}, pages = {1334-1344}, pmid = {22110385}, issn = {1449-2288}, support = {R01 AI066045/AI/NIAID NIH HHS/United States ; R01AI66045-4/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Chagas Disease/prevention &amp; control/transmission ; Insect Vectors/genetics/*metabolism/*parasitology ; Leishmania donovani/pathogenicity ; Psychodidae/parasitology ; Rhodnius/parasitology ; Risk Assessment ; Trypanosoma cruzi/pathogenicity ; }, abstract = {Conventional methodologies to control vector borne diseases with chemical pesticides are often associated with environmental toxicity, adverse effects on human health and the emergence of insect resistance. In the paratransgenic strategy, symbiotic or commensal microbes of host insects are transformed to express gene products that interfere with pathogen transmission. These genetically altered microbes are re-introduced back to the insect where expression of the engineered molecules decreases the host's ability to transmit the pathogen. We have successfully utilized this strategy to reduce carriage rates of Trypanosoma cruzi, the causative agent of Chagas disease, in the triatomine bug, Rhodnius prolixus, and are currently developing this methodology to control the transmission of Leishmania donovani by the sand fly Phlebotomus argentipes. Several effector molecules, including antimicrobial peptides and highly specific single chain antibodies, are currently being explored for their anti-parasite activities in these two systems. In preparation for eventual field use, we are actively engaged in risk assessment studies addressing the issue of horizontal gene transfer from the modified bacteria to environmental microbes.}, }
@article {pmid22107596, year = {2011}, author = {Cefalo, AD and Broadbent, JR and Welker, DL}, title = {Intraspecific and interspecific interactions among proteins regulating exopolysaccharide synthesis in Streptococcus thermophilus, Streptococcus iniae, and Lactococcus lactis subsp. cremoris and the assessment of potential lateral gene transfer.}, journal = {Canadian journal of microbiology}, volume = {57}, number = {12}, pages = {1002-1015}, doi = {10.1139/w11-090}, pmid = {22107596}, issn = {1480-3275}, mesh = {Amino Acid Sequence ; Bacterial Capsules/biosynthesis/genetics/metabolism ; Bacterial Proteins/chemistry/genetics/*metabolism ; Enzymes/chemistry/metabolism ; *Gene Transfer, Horizontal ; *Lactococcus lactis/genetics/metabolism ; Molecular Sequence Data ; Sequence Alignment ; Sequence Homology, Amino Acid ; Species Specificity ; *Streptococcus/genetics/metabolism ; *Streptococcus thermophilus/genetics/metabolism ; Two-Hybrid System Techniques ; }, abstract = {Using the yeast two-hybrid system, intraspecific protein interactions were detected in Streptococcus iniae and Lactococcus lactis subsp. cremoris between the transmembrane activation protein (CpsC and EpsA, respectively) and the protein tyrosine kinase (CpsD and EpsB, respectively), between two protein tyrosine kinases, and between the protein tyrosine kinase and the phosphotyrosine phosphatase (CpsB and EpsC, respectively). For each of these intraspecific interactions, interspecific interactions were also detected when one protein was from S. iniae and the other was from Streptococcus thermophilus . Interactions were also observed between two protein tyrosine kinases when one protein was from either of the Streptococcus species and the other from L. lactis subsp. cremoris. The results and sequence comparisons performed in this study support the conclusion that interactions among the components of the tyrosine kinase - phosphatase regulatory system are conserved in the order Lactobacillales and that interspecific genetic exchanges of the genes that encode these proteins have the potential to form functional recombinants. A better understanding of intraspecific and interspecific protein interactions involved in regulating exopolysaccharide biosynthesis may facilitate construction of improved strains for industrial uses as well as identification of factors needed to form functional regulatory complexes in naturally occurring recombinants.}, }
@article {pmid22103353, year = {2012}, author = {Mayr, UB and Kudela, P and Atrasheuskaya, A and Bukin, E and Ignatyev, G and Lubitz, W}, title = {Rectal single dose immunization of mice with Escherichia coli O157:H7 bacterial ghosts induces efficient humoral and cellular immune responses and protects against the lethal heterologous challenge.}, journal = {Microbial biotechnology}, volume = {5}, number = {2}, pages = {283-294}, pmid = {22103353}, issn = {1751-7915}, mesh = {Administration, Rectal ; Animals ; Antibodies, Bacterial/*immunology ; Disease Models, Animal ; Escherichia coli Infections/immunology/microbiology/*prevention &amp; control ; Escherichia coli O157/*immunology ; Escherichia coli Vaccines/*administration &amp; dosage/*immunology ; Mice ; Survival Analysis ; T-Lymphocytes/*immunology ; Vaccination/*methods ; }, abstract = {Bacterial ghosts (BGs) have been applied through oral, aerogenic, intraocular or intranasal routes for mucosal immunization using a wide range of experimental animals. All these applications required a booster after primary immunization to achieve protective immunity against the lethal challenge. Here we report for the first time that a single rectal dose of BGs produced from enterohaemorrhagic Escherichia coli (EHEC) O157:H7 fully protects mice against a 50% lethal challenge with a heterologous EHEC strain given at day 55. BGs from EHEC O157:H7 were prepared by a combination of protein E-mediated cell lysis and expression of staphylococcal nuclease A guaranteeing the complete degradation of pathogen residual DNA. The lack of genetic material in the EHEC BGs vaccine abolished any potential hazard for horizontal gene transfer of plasmid encoded antibiotic resistance genes or pathogenic islands to the recipient's gut flora. Single rectal immunization using EHEC O157:H7 BGs without any addition of adjuvant significantly stimulated efficient humoral and cellular immune responses, and was equally protective as two immunizations, which indicates the possibility to develop a novel efficacious single dose mucosal EHEC O157:H7 BGs vaccine using a simplified immunization regimen.}, }
@article {pmid22102881, year = {2011}, author = {Barbagallo, M and Di Martino, ML and Marcocci, L and Pietrangeli, P and De Carolis, E and Casalino, M and Colonna, B and Prosseda, G}, title = {A new piece of the Shigella Pathogenicity puzzle: spermidine accumulation by silencing of the speG gene [corrected].}, journal = {PloS one}, volume = {6}, number = {11}, pages = {e27226}, pmid = {22102881}, issn = {1932-6203}, mesh = {Animals ; Bacterial Proteins/*antagonists &amp; inhibitors/genetics/metabolism ; Cell Survival ; Cells, Cultured ; Dysentery, Bacillary/*genetics/microbiology ; Escherichia coli/genetics/pathogenicity ; *Gene Silencing ; Macrophages, Peritoneal/metabolism ; Male ; Mice ; Mice, Inbred BALB C ; Oxidative Stress ; Plasmids/genetics ; RNA, Messenger/genetics ; Real-Time Polymerase Chain Reaction ; Regulon ; Shigella flexneri/genetics/*pathogenicity ; Spermidine/*metabolism ; Transcriptome ; Virulence Factors/genetics ; }, abstract = {The genome of Shigella, a gram negative bacterium which is the causative agent of bacillary dysentery, shares strong homologies with that of its commensal ancestor, Escherichia coli. The acquisition, by lateral gene transfer, of a large plasmid carrying virulence determinants has been a crucial event in the evolution towards the pathogenic lifestyle and has been paralleled by the occurrence of mutations affecting genes, which negatively interfere with the expression of virulence factors. In this context, we have analysed to what extent the presence of the plasmid-encoded virF gene, the major activator of the Shigella regulon for invasive phenotype, has modified the transcriptional profile of E. coli. Combining results from transcriptome assays and comparative genome analyses we show that in E. coli VirF, besides being able to up-regulate several chromosomal genes, which potentially influence bacterial fitness within the host, also activates genes which have been lost by Shigella. We have focused our attention on the speG gene, which encodes spermidine acetyltransferase, an enzyme catalysing the conversion of spermidine into the physiologically inert acetylspermidine, since recent evidence stresses the involvement of polyamines in microbial pathogenesis. Through identification of diverse mutations, which prevent expression of a functional SpeG protein, we show that the speG gene has been silenced by convergent evolution and that its inactivation causes the marked increase of intracellular spermidine in all Shigella spp. This enhances the survival of Shigella under oxidative stress and allows it to better face the adverse conditions it encounters inside macrophage. This is supported by the outcome of infection assays performed in mouse peritoneal macrophages and of a competitive-infection assay on J774 macrophage cell culture. Our observations fully support the pathoadaptive nature of speG inactivation in Shigella and reveal that the accumulation of spermidine is a key determinant in the pathogenicity strategy adopted by this microrganism.}, }
@article {pmid22098378, year = {2012}, author = {Sparo, M and Urbizu, L and Solana, MV and Pourcel, G and Delpech, G and Confalonieri, A and Ceci, M and Sánchez Bruni, SF}, title = {High-level resistance to gentamicin: genetic transfer between Enterococcus faecalis isolated from food of animal origin and human microbiota.}, journal = {Letters in applied microbiology}, volume = {54}, number = {2}, pages = {119-125}, doi = {10.1111/j.1472-765X.2011.03182.x}, pmid = {22098378}, issn = {1472-765X}, mesh = {Animal Feed/*microbiology ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacterial Load ; Conjugation, Genetic ; Drug Resistance, Bacterial/*genetics ; Enterococcus faecalis/drug effects/*genetics/isolation &amp; purification ; Feces/microbiology ; Gastrointestinal Tract/microbiology ; *Gene Transfer, Horizontal ; Gentamicins/pharmacology ; Humans ; Metagenome/*genetics ; Mice ; Mice, Inbred BALB C ; Microbial Sensitivity Tests ; Plasmids ; Random Amplified Polymorphic DNA Technique ; }, abstract = {AIMS: To investigate the in vivo gene transfer of high-level gentamicin resistance (HLRG) from Enterococcus faecalis isolated from the food of animal origin to a human isolate, using a mouse model of intestinally colonized human microbiota.<br><br>METHODS AND RESULTS: &#x2002; In vitro study: The presence of plasmids involved in HLRG coding was investigated. After the conjugation experiment, the recipient strain, Ent. faecalis JH2-SS, acquired a plasmid responsible for HLRG [minimal inhibitory concentration (MIC) >800 &#x3bc;g ml(-1) ], in a similar position to the donor cells. In vivo study: Seven BALB/c mice were dosed with ceftriaxone (400 mg kg(-1)) and then inoculated with a dilution of 1/100 of human faeces (HFc). After 72 h, Ent. faecalis JH2-SS (recipient) was inoculated and then, after a further 72 h, the animals were given Ent. faecalis CS19, isolated from the food of animal origin, involved in HLRG (donor). The presence of transconjugant strains in HFc was subsequently recorded on a daily basis until the end of the experiment. The clonal relationship between Ent. faecalis and Escherichia coli in faeces was assessed by RAPD-PCR. Both the in vitro and in vivo studies showed that the receptor strain acquired a plasmid responsible for HLRG (MICs >800 &#x3bc;g ml(-1)), which migrated with a similar relative mobility value. Transconjugant strains were detected from 24 h after the donor strain inoculation and persisted until the end of the experiment.<br><br>CONCLUSIONS: &#x2002; The in vivo gene transfer of HLRG from Ent. faecalis strains, isolated from the food of animal origin, to human microbiota has been demonstrated in a mouse model.<br><br>&#x2002; The complexity found on the therapeutic responses of invasive infectious diseases caused by Ent. faecalis facilitates the assessment of food of animal origin as a resistant pathogen reservoir. In addition, this study may contribute to the understanding of antimicrobials' resistance gene transfer between Ent. faecalis strains from food and human GI tract.}, }
@article {pmid22096554, year = {2011}, author = {Gendoo, DM and Harrison, PM}, title = {Origins and evolution of the HET-s prion-forming protein: searching for other amyloid-forming solenoids.}, journal = {PloS one}, volume = {6}, number = {11}, pages = {e27342}, pmid = {22096554}, issn = {1932-6203}, mesh = {Amyloid ; *Evolution, Molecular ; Fungal Proteins/classification/*genetics ; Gene Transfer, Horizontal ; Phylogeny ; Podospora/genetics/*metabolism ; Prions ; Protein Structure, Tertiary ; }, abstract = {The HET-s prion-forming domain from the filamentous fungus Podospora anserina is gaining considerable interest since it yielded the first well-defined atomic structure of a functional amyloid fibril. This structure has been identified as a left-handed beta solenoid with a triangular hydrophobic core. To delineate the origins of the HET-s prion-forming protein and to discover other amyloid-forming proteins, we searched for all homologs of the HET-s protein in a database of protein domains and fungal genomes, using a combined application of HMM, psi-blast and pGenThreader techniques, and performed a comparative evolutionary analysis of the N-terminal alpha-helical domain and the C-terminal prion-forming domain of HET-s. By assessing the tandem evolution of both domains, we observed that the prion-forming domain is restricted to Sordariomycetes, with a marginal additional sequence homolog in Arthroderma otae as a likely case of horizontal transfer. This suggests innovation and rapid evolution of the solenoid fold in the Sordariomycetes clade. In contrast, the N-terminal domain evolves at a slower rate (in Sordariomycetes) and spans many diverse clades of fungi. We performed a full three-dimensional protein threading analysis on all identified HET-s homologs against the HET-s solenoid fold, and present detailed structural annotations for identified structural homologs to the prion-forming domain. An analysis of the physicochemical characteristics in our set of structural models indicates that the HET-s solenoid shape can be readily adopted in these homologs, but that they are all less optimized for fibril formation than the P. anserina HET-s sequence itself, due chiefly to the presence of fewer asparagine ladders and salt bridges. Our combined structural and evolutionary analysis suggests that the HET-s shape has "limited scope" for amyloidosis across the wider protein universe, compared to the 'generic' left-handed beta helix. We discuss the implications of our findings on future identification of amyloid-forming proteins sharing the solenoid fold.}, }
@article {pmid22094562, year = {2011}, author = {Montanaro, L and Poggi, A and Visai, L and Ravaioli, S and Campoccia, D and Speziale, P and Arciola, CR}, title = {Extracellular DNA in biofilms.}, journal = {The International journal of artificial organs}, volume = {34}, number = {9}, pages = {824-831}, doi = {10.5301/ijao.5000051}, pmid = {22094562}, issn = {1724-6040}, mesh = {Animals ; Apoptosis ; Bacterial Infections/genetics/immunology/*microbiology ; *Bacteriolysis ; Biofilms/*growth &amp; development ; DNA, Bacterial/immunology/*metabolism ; *Gene Transfer, Horizontal ; Humans ; Immunity, Innate ; Inflammation/immunology/microbiology ; Phagocytosis ; Quorum Sensing ; }, abstract = {Extracellular DNA (eDNA) is an important biofilm component that was recently discovered. Its presence has been initially observed in biofilms of Pseudomonas aeruginosa, Streptococcus intermedius, Streptococcus mutans, then Enterococcus faecalis and staphylococci. Autolysis is the common mechanism by which eDNA is released. In P. aeruginosa eDNA is generated by lysis of a bacterial subpopulation, under control of quorum sensing system. In E. faecalis autolysis proceeds in a fratricide mode, resulting from a process similar to necrosis of eukaryotic cells. In Staphylococcus aureus autolysis originates by an altruistic suicide, i.e., a programmed cell death similar to apoptosis of eukaryotic cells. In S. aureus autolysis is mediated by murein hydrolase, while in S. epidermidis by the autolysin protein AtlE. In P. aeruginosa eDNA is located primarily in the stalks of mushroom-shaped multicellular structures. In S. aureus the crucial role of eDNA in stabilizing biofilm is highlighted by the disgregating effect of DNase I. eDNA represents an important mechanism for horizontal gene transfer in bacteria. eDNA and other microbial structural motifs are recognized by the innate immune system via the TLR family of pattern recognition receptors (PRRs).}, }
@article {pmid22093957, year = {2011}, author = {Labbate, M and Boucher, Y and Chowdhury, PR and Stokes, HW}, title = {Integration of a laterally acquired gene into a cell network important for growth in a strain of Vibrio rotiferianus.}, journal = {BMC microbiology}, volume = {11}, number = {}, pages = {253}, pmid = {22093957}, issn = {1471-2180}, mesh = {Adaptation, Biological/*genetics ; Animals ; Evolution, Molecular ; Gene Expression ; Gene Transfer, Horizontal/*physiology ; Integrons/*genetics ; Porins/*genetics/metabolism ; Vibrio/*genetics/growth &amp; development ; }, abstract = {BACKGROUND: Lateral Gene Transfer (LGT) is a major contributor to bacterial evolution and up to 25% of a bacterium's genome may have been acquired by this process over evolutionary periods of time. Successful LGT requires both the physical transfer of DNA and its successful incorporation into the host cell. One system that contributes to this latter step by site-specific recombination is the integron. Integrons are found in many diverse bacterial Genera and is a genetic system ubiquitous in vibrios that captures mobile DNA at a dedicated site. The presence of integron-associated genes, contained within units of mobile DNA called gene cassettes makes up a substantial component of the vibrio genome (1-3%). Little is known about the role of this system since the vast majority of genes in vibrio arrays are highly novel and functions cannot be ascribed. It is generally regarded that strain-specific mobile genes cannot be readily integrated into the cellular machinery since any perturbation of core metabolism is likely to result in a loss of fitness.<br><br>RESULTS: In this study, at least one mobile gene contained within the Vibrio rotiferianus strain DAT722, but lacking close relatives elsewhere, is shown to greatly reduce host fitness when deleted and tested in growth assays. The precise role of the mobile gene product is unknown but impacts on the regulation of outermembrane porins. This demonstrates that strain specific laterally acquired mobile DNA can be integrated rapidly into bacterial networks such that it becomes advantageous for survival and adaptation in changing environments.<br><br>CONCLUSIONS: Mobile genes that are highly strain specific are generally believed to act in isolation. This is because perturbation of existing cell machinery by the acquisition of a new gene by LGT is highly likely to lower fitness. In contrast, we show here that at least one mobile gene, apparently unique to a strain, encodes a product that has integrated into central cellular metabolic processes such that it greatly lowers fitness when lost under those conditions likely to be commonly encountered for the free living cell. This has ramifications for our understanding of the role mobile gene encoded products play in the cell from a systems biology perspective.}, }
@article {pmid22093578, year = {2011}, author = {Puri, V and Goyal, A and Sankaranarayanan, R and Enright, AJ and Vaidya, T}, title = {Evolutionary and functional insights into Leishmania META1: evidence for lateral gene transfer and a role for META1 in secretion.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {334}, pmid = {22093578}, issn = {1471-2148}, support = {079643/Z/06/Z//Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics ; Base Composition ; DNA, Protozoan/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Leishmania/*genetics/metabolism/pathogenicity ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Phylogeny ; Protein Structure, Tertiary ; Protozoan Proteins/*genetics/metabolism ; Selection, Genetic ; Sequence Alignment ; Sequence Analysis, DNA ; Virulence/genetics ; }, abstract = {BACKGROUND: Leishmania META1 has for long been a candidate molecule for involvement in virulence: META1 transcript and protein are up-regulated in metacyclic Leishmania. Yet, how META1 contributes to virulence remains unclear. We sought insights into the possible functions of META1 by studying its evolutionary origins.<br><br>RESULTS: Using multiple criteria including sequence similarity, nucleotide composition, phylogenetic analysis and selection pressure on gene sequence, we present evidence that META1 originated in trypanosomatids as a result of a lateral gene transfer of a bacterial heat-inducible protein, HslJ. Furthermore, within the Leishmania genome, META1 sequence is under negative selection pressure against change/substitution. Using homology modeling of Leishmania META1 based on solved NMR structure of HslJ, we show that META1 and HslJ share a similar structural fold. The best hit for other proteins with similar fold is MxiM, a protein involved in the type III secretion system in Shigella. The striking structural similarity shared by META1, HslJ and MxiM suggests a possibility of shared functions. Upon structural superposition with MxiM, we have observed a putative hydrophobic cavity in META1. Mutagenesis of select hydrophobic residues in this cavity affects the secretion of the secreted acid phosphatase (SAP), indicating META1's involvement in secretory processes in Leishmania.<br><br>CONCLUSIONS: Overall, this work uses an evolutionary biology approach, 3D-modeling and site-directed mutagenesis to arrive at new insights into functions of Leishmania META1.}, }
@article {pmid22093079, year = {2012}, author = {Domenzain, C and Camarena, L and Osorio, A and Dreyfus, G and Poggio, S}, title = {Evolutionary origin of the Rhodobacter sphaeroides specialized RpoN sigma factors.}, journal = {FEMS microbiology letters}, volume = {327}, number = {2}, pages = {93-102}, doi = {10.1111/j.1574-6968.2011.02459.x}, pmid = {22093079}, issn = {1574-6968}, mesh = {Bacterial Proteins/*genetics/metabolism ; *Evolution, Molecular ; Gene Dosage ; Gene Expression Regulation, Bacterial ; Molecular Sequence Data ; Phylogeny ; Rhodobacter sphaeroides/classification/*genetics/metabolism ; Sigma Factor/*genetics/metabolism ; }, abstract = {Gene duplication and horizontal gene transfer (HGT) are two events that enable the generation of new genes. Rhodobacter sphaeroides (WS8 and 2.4.1 strains) has four copies of the rpoN gene that are not functionally interchangeable. Until now, this is the only example of specialization of this sigma factor. In this work, we aimed to determine whether the multiple copies of this gene originated from HGT or through gene duplication. Our results suggest a multiplication origin of the different rpoN copies that occurred after the Rhodobacter clade separated. Functional tests indicate that the specialization of the rpoN genes is not restricted to R. sphaeroides. We propose that the rpoN copy involved in nitrogen fixation is the ancestral gene and that the other rpoN genes have acquired new specificities.}, }
@article {pmid22092861, year = {2011}, author = {Maehara, T and Itaya, M and Ogura, M and Tanaka, T}, title = {Effect of Bacillus subtilis BsuM restriction-modification on plasmid transfer by polyethylene glycol-induced protoplast fusion.}, journal = {FEMS microbiology letters}, volume = {325}, number = {1}, pages = {49-55}, doi = {10.1111/j.1574-6968.2011.02410.x}, pmid = {22092861}, issn = {1574-6968}, mesh = {Bacillus subtilis/*enzymology/*genetics/metabolism ; Cell Fusion ; *DNA Restriction-Modification Enzymes ; DNA, Bacterial/metabolism ; Gene Transfer, Horizontal ; *Plasmids ; Polyethylene Glycols/metabolism ; *Protoplasts ; *Transformation, Bacterial ; }, abstract = {Polyethylene glycol (PEG)-induced cell fusion is a promising method to transfer larger DNA from one cell to another than conventional genetic DNA transfer systems. The laboratory strain Bacillus subtilis 168 contains a restriction (R) and modification (M) system, BsuM, which recognizes the sequence 5'-CTCGAG-3'. To study whether the BsuM system affects DNA transfer by the PEG-induced cell fusion between R(+)M(+) and R(-)M(-) strains, we examined transfer of plasmids pHV33 and pLS32neo carrying no and eight BsuM sites, respectively. It was shown that although the transfer of pLS32neo but not pHV33 from the R(-)M(-) to R(+)M(+) cells was severely restricted, significant levels of transfer of both plasmids from the R(+)M(+) to R(-)M(-) cells were observed. The latter result shows that the chromosomal DNA in the R(-)M(-) cell used as the recipient partially survived restriction from the donor R(+)M(+) cell, indicating that the BsuM R(-)M(-) strain is useful as a host for accepting DNA from cells carrying a restriction system(s). Two such examples were manifested for plasmid transfer from Bacillus circulans and Bacillus stearothermophilus strains to a BsuM-deficient mutant, B. subtilis RM125.}, }
@article {pmid22092811, year = {2011}, author = {Potron, A and Poirel, L and Nordmann, P}, title = {Plasmid-mediated transfer of the bla(NDM-1) gene in Gram-negative rods.}, journal = {FEMS microbiology letters}, volume = {324}, number = {2}, pages = {111-116}, doi = {10.1111/j.1574-6968.2011.02392.x}, pmid = {22092811}, issn = {1574-6968}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics/metabolism ; Conjugation, Genetic ; Drug Resistance, Bacterial ; Enterobacteriaceae/drug effects/*enzymology/*genetics/isolation &amp; purification ; Enterobacteriaceae Infections/microbiology ; *Gene Transfer, Horizontal ; Gram-Positive Rods/drug effects/*genetics/metabolism ; Humans ; Microbial Sensitivity Tests ; Plasmids/*genetics/metabolism ; beta-Lactamases/*genetics/metabolism ; }, abstract = {The latest threat of multidrug-resistant Gram-negative bacteria corresponds to the emergence of carbapenemase NDM-1 (New Delhi metallo-β-lactamase) producers, mostly in Enterobacteriacae. Five bla(NDM) (-1) -positive plasmids of different incompatibility groups (IncL/M, FII, A/C and two untypeable plasmids) from clinical Enterobacteriaceae were evaluated for conjugation properties and host specificity. Successful conjugative transfers were obtained using all tested enterobacterial species as recipients (Escherichia coli, Klebsiella pneumoniae, Salmonella typhimurium and Proteus mirabilis) and all plasmid types. Conjugation frequencies varied from 1 × 10(-4) to 6 × 10(-8) transconjugants per donor. Higher conjugation rates were obtained for two plasmids at 30 °C compared with that observed at 25 and 37 °C. Carbapenems used as selector did not lead to higher conjugation frequencies. None of the five plasmids was transferable to Acinetobacter baumannii or Pseudomonas aeruginosa by conjugation. This work underlines how efficient the spread of the carbapenemase bla(NDM) (-1) gene could be among Enterobacteriaceae.}, }
@article {pmid22092764, year = {2011}, author = {Dziewit, L and Kuczkowska, K and Adamczuk, M and Radlinska, M and Bartosik, D}, title = {Functional characterization of the type II PamI restriction-modification system derived from plasmid pAMI7 of Paracoccus aminophilus JCM 7686.}, journal = {FEMS microbiology letters}, volume = {324}, number = {1}, pages = {56-63}, doi = {10.1111/j.1574-6968.2011.02388.x}, pmid = {22092764}, issn = {1574-6968}, mesh = {Amino Acid Sequence ; DNA/metabolism ; DNA Restriction-Modification Enzymes/*genetics/*metabolism ; Deoxyribonucleases, Type II Site-Specific/*genetics/*metabolism ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Paracoccus/*enzymology/*genetics ; *Plasmids ; Sequence Homology ; Substrate Specificity ; }, abstract = {Plasmid pAMI7 of the methylotrophic bacterium Paracoccus aminophilus JCM 7686 (Alphaproteobacteria) encodes a functional type II restriction-modification (R-M) system designated PamI. Homologous systems were identified in the genomes of distinct taxonomic groups of Bacteria and Archaea, which provides evidence that horizontal gene transfer has contributed to the wide dissemination of R-M modules - even between domains. Analysis of the cleavage specificity of the R.PamI endonuclease revealed that this protein is an isoschizomer of restriction enzyme NcoI. Interestingly, bioinformatic analyses suggest that R.PamI and NcoI are accompanied by methyltransferases of different methylation specificities (C5-methylcytosine and N4-methylcytosine methyltransferases, respectively), which possibly exemplifies recombinational shuffling of genes coding for individual components of R-M systems. The PamI system can stabilize plasmid pAMI7 in a bacterial population, most probably at the postsegregational level. Therefore, it functions in an analogous manner to plasmid-encoded toxin-antitoxin (TA) systems. Since the TA system of pAMI7 is nonfunctional, it is highly probable that this lack is compensated by the stabilizing activity of PamI. This indicates the crucial role of the analyzed R-M system in the stable maintenance of pAMI7, which is, to our knowledge, the first report of 'symbiosis' between a R-M system and a plasmid in the Alphaproteobacteria.}, }
@article {pmid22092700, year = {2012}, author = {Smorawinska, M and Szuplewska, M and Zaleski, P and Wawrzyniak, P and Maj, A and Plucienniczak, A and Bartosik, D}, title = {Mobilizable narrow host range plasmids as natural suicide vectors enabling horizontal gene transfer among distantly related bacterial species.}, journal = {FEMS microbiology letters}, volume = {326}, number = {1}, pages = {76-82}, doi = {10.1111/j.1574-6968.2011.02432.x}, pmid = {22092700}, issn = {1574-6968}, mesh = {Alphaproteobacteria/genetics ; Base Sequence ; Conjugation, Genetic ; DNA Helicases/genetics ; Escherichia coli/*genetics ; Gammaproteobacteria/genetics ; *Gene Transfer, Horizontal ; *Genetic Vectors ; Host Specificity ; Klebsiella pneumoniae/genetics ; Molecular Sequence Data ; Plasmids/*genetics ; Sequence Analysis, DNA ; Trans-Activators/genetics ; }, abstract = {Klebsiella pneumoniae 287-w carries three small narrow host range (NHR) plasmids (pIGMS31, pIGMS32, and pIGRK), which could be maintained in several closely related species of Gammaproteobacteria, but not in Alphaproteobacteria. The plasmids contain different mobilization systems (MOB), whose activity in Escherichia coli was demonstrated in the presence of the helper transfer system originating from plasmid RK2. The MOBs of pIGMS31 and pIGMS32 are highly conserved in many bacterial plasmids (members of the MOB family), while the predicted MOB of pIGRK has a unique structure, encoding a protein similar to phage-related integrases. The MOBs of pIGMS31 and pIGMS32 enabled the transfer of heterologous replicons from E. coli into both gammaproteobacterial and alphaproteobacterial hosts, which suggests that these NHR plasmids contain broad host range MOB systems. Such plasmids therefore represent efficient carrier molecules, which may act as natural suicide vectors promoting the spread of diverse genetic information (including other types of mobile elements, e.g. resistance transposons) among evolutionarily distinct bacterial species. Thus, mobilizable NHR plasmids may play a much more important role in horizontal gene transfer than previously thought.}, }
@article {pmid22088149, year = {2011}, author = {Mattos, IB and Alves, DA and Hollanda, LM and Ceragiogli, HJ and Baranauskas, V and Lancellotti, M}, title = {Effects of multi-walled carbon nanotubes (MWCNT) under Neisseria meningitidis transformation process.}, journal = {Journal of nanobiotechnology}, volume = {9}, number = {}, pages = {53}, pmid = {22088149}, issn = {1477-3155}, mesh = {Bacterial Capsules/*genetics ; Gene Transfer Techniques ; Gene Transfer, Horizontal/*drug effects/physiology ; Humans ; Nanotubes, Carbon/adverse effects/*chemistry ; Neisseria meningitidis/*genetics ; Spectrum Analysis, Raman ; *Transformation, Bacterial ; }, abstract = {BACKGROUND: This study aimed at verifying the action of multi-walled carbon nanotubes (MWCNT) under the naturally transformable Neisseria meningitidis against two different DNA obtained from isogenic mutants of this microorganism, an important pathogen implicated in the genetic horizontal transfer of DNA, causing the escape of the principal vaccination measured worldwide by the capsular switching process.<br><br>MATERIALS AND METHODS: The bacterium receptor strain C2135 was cultivated and had its mutant DNA donor M2 and M6, which received a receptor strain and MWCNT at three different concentrations. The inhibition effect of DNAse on the DNA in contact with nanoparticles was evaluated.<br><br>RESULTS: The results indicated an in increase in the transformation capacity of N. meninigtidis in different concentrations of MWCNT when compared with negative control without nanotubes. A final analysis of the interaction between DNA and MWCNT was carried out using Raman Spectroscopy.<br><br>CONCLUSION: These increases in the transformation capacity mediated by MWCNT, in meningococci, indicate the interaction of these particles with the virulence acquisition of these bacteria, as well as with the increase in the vaccination escape process.}, }
@article {pmid22087229, year = {2011}, author = {Pieper, R and Zhang, Q and Clark, DJ and Huang, ST and Suh, MJ and Braisted, JC and Payne, SH and Fleischmann, RD and Peterson, SN and Tzipori, S}, title = {Characterizing the Escherichia coli O157:H7 proteome including protein associations with higher order assemblies.}, journal = {PloS one}, volume = {6}, number = {11}, pages = {e26554}, pmid = {22087229}, issn = {1932-6203}, support = {N01AI15447/AI/NIAID NIH HHS/United States ; N01AI30050/AI/NIAID NIH HHS/United States ; N01-AI-30050/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Escherichia coli O157/*chemistry ; Escherichia coli Proteins/*analysis ; Intestines/microbiology ; Membrane Proteins ; Multiprotein Complexes/analysis ; Proteome/*analysis ; Proteomics/*methods ; Swine ; }, abstract = {BACKGROUND: The recent outbreak of severe infections with Shiga toxin (Stx) producing Escherichia coli (STEC) serotype O104:H4 highlights the need to understand horizontal gene transfer among E. coli strains, identify novel virulence factors and elucidate their pathogenesis. Quantitative shotgun proteomics can contribute to such objectives, allowing insights into the part of the genome translated into proteins and the connectivity of biochemical pathways and higher order assemblies of proteins at the subcellular level.<br><br>We examined protein profiles in cell lysate fractions of STEC strain 86-24 (serotype O157:H7), following growth in cell culture or bacterial isolation from intestines of infected piglets, in the context of functionally and structurally characterized biochemical pathways of E. coli. Protein solubilization in the presence of Triton X-100, EDTA and high salt was followed by size exclusion chromatography into the approximate M(r) ranges greater than 280 kDa, 280-80 kDa and 80-10 kDa. Peptide mixtures resulting from these and the insoluble fraction were analyzed by quantitative 2D-LC-nESI-MS/MS. Of the 2521 proteins identified at a 1% false discovery rate, representing 47% of all predicted E. coli O157:H7 gene products, the majority of integral membrane proteins were enriched in the high M(r) fraction. Hundreds of proteins were enriched in a M(r) range higher than that predicted for a monomer supporting their participation in protein complexes. The insoluble STEC fraction revealed enrichment of aggregation-prone proteins, including many that are part of large structure/function entities such as the ribosome, cytoskeleton and O-antigen biosynthesis cluster.<br><br>SIGNIFICANCE: Nearly all E. coli O157:H7 proteins encoded by prophage regions were expressed at low abundance levels or not detected. Comparative quantitative analyses of proteins from distinct cell lysate fractions allowed us to associate uncharacterized proteins with membrane attachment, potential participation in stable protein complexes, and susceptibility to aggregation as part of larger structural assemblies.}, }
@article {pmid22085859, year = {2011}, author = {Zarowiecki, M}, title = {Animals learn new tricks from microorganisms.}, journal = {Nature reviews. Microbiology}, volume = {9}, number = {12}, pages = {836}, pmid = {22085859}, issn = {1740-1534}, mesh = {Animals ; Bacteria/*genetics ; Fungi/*genetics ; Gene Transfer, Horizontal/*genetics ; Genomics ; Nematoda/*genetics ; }, }
@article {pmid22084639, year = {2011}, author = {Anderson, RE and Brazelton, WJ and Baross, JA}, title = {Is the genetic landscape of the deep subsurface biosphere affected by viruses?.}, journal = {Frontiers in microbiology}, volume = {2}, number = {}, pages = {219}, pmid = {22084639}, issn = {1664-302X}, abstract = {Viruses are powerful manipulators of microbial diversity, biogeochemistry, and evolution in the marine environment. Viruses can directly influence the genetic capabilities and the fitness of their hosts through the use of fitness factors and through horizontal gene transfer. However, the impact of viruses on microbial ecology and evolution is often overlooked in studies of the deep subsurface biosphere. Subsurface habitats connected to hydrothermal vent systems are characterized by constant fluid flux, dynamic environmental variability, and high microbial diversity. In such conditions, high adaptability would be an evolutionary asset, and the potential for frequent host-virus interactions would be high, increasing the likelihood that cellular hosts could acquire novel functions. Here, we review evidence supporting this hypothesis, including data indicating that microbial communities in subsurface hydrothermal fluids are exposed to a high rate of viral infection, as well as viral metagenomic data suggesting that the vent viral assemblage is particularly enriched in genes that facilitate horizontal gene transfer and host adaptability. Therefore, viruses are likely to play a crucial role in facilitating adaptability to the extreme conditions of these regions of the deep subsurface biosphere. We also discuss how these results might apply to other regions of the deep subsurface, where the nature of virus-host interactions would be altered, but possibly no less important, compared to more energetic hydrothermal systems.}, }
@article {pmid22084562, year = {2011}, author = {Zhu, B and Zhou, S and Lou, M and Zhu, J and Li, B and Xie, G and Jin, G and De Mot, R}, title = {Characterization and inference of gene gain/loss along burkholderia evolutionary history.}, journal = {Evolutionary bioinformatics online}, volume = {7}, number = {}, pages = {191-200}, pmid = {22084562}, issn = {1176-9343}, abstract = {A comparative analysis of 60 complete Burkholderia genomes was conducted to obtain insight in the evolutionary history behind the diversity and pathogenicity at species level. A concatenated multiprotein phyletic pattern and a dataset with Burkholderia clusters of orthologous genes (BuCOGs) were constructed. The extent of horizontal gene transfer (HGT) was assessed using a Markov based probabilistic method. A reconstruction of the gene gains and losses history shows that more than half of the Burkholderia genes families are inferred to have experienced HGT at least once during their evolution. Further analysis revealed that the number of gene gain and loss was correlated with the branch length. Genomic islands (GEIs) analysis based on evolutionary history reconstruction not only revealed that most genes in ancient GEIs were gained but also suggested that the fraction of the genome located in GEIs in the small chromosomes is higher than in the large chromosomes in Burkholderia. The mapping of coexpressed genes onto biological pathway schemes revealed that pathogenicity of Burkholderia strains is probably mainly determined by the gained genes in its ancestor. Taken together, our results strongly support that gene gain and loss especially in ancient evolutionary history play an important role in strain divergence, pathogenicity determinants of Burkholderia and GEIs formation.}, }
@article {pmid22079532, year = {2012}, author = {Shu, JC and Chia, JH and Siu, LK and Kuo, AJ and Huang, SH and Su, LH and Wu, TL}, title = {Interplay between mutational and horizontally acquired resistance mechanisms and its association with carbapenem resistance amongst extensively drug-resistant Pseudomonas aeruginosa (XDR-PA).}, journal = {International journal of antimicrobial agents}, volume = {39}, number = {3}, pages = {217-222}, pmid = {22079532}, issn = {1872-7913}, mesh = {Bacterial Outer Membrane Proteins/genetics/metabolism ; Carbapenems/*pharmacology ; Disease Transmission, Infectious ; *Drug Resistance, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genotype ; Membrane Transport Proteins/genetics/metabolism ; Microbial Sensitivity Tests ; *Mutation ; Porins/genetics/metabolism ; Pseudomonas Infections/microbiology ; Pseudomonas aeruginosa/*drug effects/genetics/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; beta-Lactamases/genetics/metabolism ; }, abstract = {Between 2003 and 2009, the prevalence of extensively drug-resistant Pseudomonas aeruginosa (XDR-PA) increased significantly in northern Taiwan from 1.0% to 2.1%. Molecular methods were used to investigate the genetic relatedness and carbapenem resistance mechanisms of a collection of 203 non-repetitive XDR-PA isolates available for study. Using pulsed-field gel electrophoresis (PFGE), 52 genotypes were observed; one predominant genotype (pulsotype 1) was found in 57.6% of the isolates. Polymerase chain reaction (PCR), sequencing and quantitative reverse-transcriptase PCR analyses demonstrated that one horizontally acquired mechanism [metallo-β-lactamase (MBL) genes] and two mutational mechanisms (efflux and porins) accounted for the carbapenem resistance. The most predominant horizontally acquired mechanism was carriage of bla(VIM-3), which was found in 61.1% of isolates. Decreased expression of oprD was the most prevalent mutational mechanism and was found in 70.0% of the XDR-PA isolates, whereas overexpression of mexA was found in 27.6% of the isolates. The highlight of this study was the discovery of statistically significant relationships between certain horizontally acquired and mutational resistance mechanisms and their contribution to carbapenem susceptibility. MBL-producers expressed significantly lower MexAB and higher OprD than non-MBL-producers. Amongst isolates without an acquired β-lactamase gene, oprD expression was significantly reduced, whilst expression of efflux pumps was increased. Reduced OprD expression alone or the production of VIM-type MBLs showed similar contributions to a low to intermediate MIC(50) (minimum inhibitory concentration for 50% of the organisms) for carbapenems. Isolates with reduced OprD expression that simultaneously harboured bla(VIM) exhibited high levels of resistance to carbapenems, which implied that these two mechanisms had a synergistic effect on the MICs.}, }
@article {pmid22078906, year = {2012}, author = {Shigemoto, N and Kuwahara, R and Kayama, S and Shimizu, W and Onodera, M and Yokozaki, M and Hisatsune, J and Kato, F and Ohge, H and Sugai, M}, title = {Emergence in Japan of an imipenem-susceptible, meropenem-resistant Klebsiella pneumoniae carrying blaIMP-6.}, journal = {Diagnostic microbiology and infectious disease}, volume = {72}, number = {1}, pages = {109-112}, doi = {10.1016/j.diagmicrobio.2011.09.019}, pmid = {22078906}, issn = {1879-0070}, mesh = {Aged, 80 and over ; Anti-Bacterial Agents/*pharmacology ; Conjugation, Genetic ; Female ; Gene Transfer, Horizontal ; Humans ; Imipenem/*pharmacology ; Japan ; Klebsiella Infections/*microbiology ; Klebsiella pneumoniae/drug effects/*enzymology/genetics/isolation &amp; purification ; Male ; Meropenem ; Plasmids/analysis ; Thienamycins/*pharmacology ; *beta-Lactam Resistance ; beta-Lactamases/*metabolism ; }, abstract = {We identified 5 Klebsiella pneumoniae isolates showing high resistance to β-lactams except imipenem and designated them ISMRK (imipenem-susceptible but meropenem-resistant Klebsiella). They carried the bla(IMP-6) and bla(CTX-M-2) on a self-transmissible plasmid. ISMRK may be falsely categorized as susceptible to carbapenems if imipenem is used to screen carbapenem resistance.}, }
@article {pmid22078325, year = {2011}, author = {Nordmann, P and Poirel, L and Walsh, TR and Livermore, DM}, title = {The emerging NDM carbapenemases.}, journal = {Trends in microbiology}, volume = {19}, number = {12}, pages = {588-595}, doi = {10.1016/j.tim.2011.09.005}, pmid = {22078325}, issn = {1878-4380}, mesh = {Bacterial Proteins/*genetics/*metabolism ; Carbapenems/*pharmacology ; Disease Outbreaks ; Enterobacteriaceae/*drug effects/*enzymology/isolation &amp; purification ; Gene Transfer, Horizontal ; Gram-Negative Bacterial Infections/*microbiology ; Humans ; Plasmids ; Pseudomonas/drug effects/enzymology/isolation &amp; purification ; Vibrionaceae/drug effects/enzymology/isolation &amp; purification ; *beta-Lactam Resistance ; beta-Lactamases/*genetics/*metabolism ; }, abstract = {Carbapenems were the last β-lactams retaining near-universal anti-Gram-negative activity, but carbapenemases are spreading, conferring resistance. New Delhi metallo-β-lactamase (NDM) enzymes are the latest carbapenemases to be recognized and since 2008 have been reported worldwide, mostly in bacteria from patients epidemiologically linked to the Indian subcontinent, where they occur widely in hospital and community infections, and also in contaminated urban water. The main type is NDM-1, but minor variants occur. NDM enzymes are present largely in Enterobacteriaceae, but also in non-fermenters and Vibrionaceae. Dissemination predominantly involves transfer of the blaNDM-1 gene among promiscuous plasmids and clonal outbreaks. Bacteria with NDM-1 are typically resistant to nearly all antibiotics, and reliable detection and surveillance are crucial.}, }
@article {pmid22075114, year = {2012}, author = {Moszczynski, K and Mackiewicz, P and Bodyl, A}, title = {Evidence for horizontal gene transfer from bacteroidetes bacteria to dinoflagellate minicircles.}, journal = {Molecular biology and evolution}, volume = {29}, number = {3}, pages = {887-892}, doi = {10.1093/molbev/msr276}, pmid = {22075114}, issn = {1537-1719}, mesh = {Bacteroidetes/*genetics ; Bayes Theorem ; DNA, Kinetoplast/*genetics ; Dinoflagellida/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Models, Genetic ; Open Reading Frames/genetics ; *Phylogeny ; }, abstract = {Dinoflagellate protists harbor a characteristic peridinin-containing plastid that evolved from a red or haptophyte alga. In contrast to typical plastids that have ∼100-200 kb circular genomes, the dinoflagellate plastid genome is composed of minicircles that each encode 0-5 genes. It is commonly assumed that dinoflagellate minicircles are derived from a standard plastid genome through drastic reduction and fragmentation. However, we demonstrate that the ycf16 and ycf24 genes (encoded on the Ceratium AF490364 minicircle), as well as rpl28 and rpl33 (encoded on the Pyrocystis AF490367 minicircle), are related to sequences from Algoriphagus and/or Cytophaga bacteria belonging to the Bacteroidetes clade. Moreover, we identified a new open reading frame on the Pyrocystis minicircle encoding a SRP54 N domain, which is typical of FtsY proteins. Because neither of these minicircles share sequence similarity with any other dinoflagellate minicircles, and their genes resemble bacterial operons, we propose that these Ceratium and Pyrocystis minicircles resulted from a horizontal gene transfer (HGT) from a Bacteroidetes donor. Our findings are the first indication of HGT to dinoflagellate minicircles, highlighting yet another peculiar aspect of this plastid genome.}, }
@article {pmid22074255, year = {2011}, author = {Case, RJ and Boucher, Y}, title = {Molecular musings in microbial ecology and evolution.}, journal = {Biology direct}, volume = {6}, number = {}, pages = {58}, pmid = {22074255}, issn = {1745-6150}, mesh = {Archaea/classification/genetics ; Bacteria/classification/*genetics ; Biota ; *Ecology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, Archaeal ; *Genes, Bacterial ; Genes, rRNA ; Genetic Markers ; Genetic Variation ; Microbiological Phenomena ; Phylogeny ; Ribosomes/genetics ; }, abstract = {A few major discoveries have influenced how ecologists and evolutionists study microbes. Here, in the format of an interview, we answer questions that directly relate to how these discoveries are perceived in these two branches of microbiology, and how they have impacted on both scientific thinking and methodology.The first question is "What has been the influence of the 'Universal Tree of Life' based on molecular markers?" For evolutionists, the tree was a tool to understand the past of known (cultured) organisms, mapping the invention of various physiologies on the evolutionary history of microbes. For ecologists the tree was a guide to discover the current diversity of unknown (uncultured) organisms, without much knowledge of their physiology.The second question we ask is "What was the impact of discovering frequent lateral gene transfer among microbes?" In evolutionary microbiology, frequent lateral gene transfer (LGT) made a simple description of relationships between organisms impossible, and for microbial ecologists, functions could not be easily linked to specific genotypes. Both fields initially resisted LGT, but methods or topics of inquiry were eventually changed in one to incorporate LGT in its theoretical models (evolution) and in the other to achieve its goals despite that phenomenon (ecology).The third and last question we ask is "What are the implications of the unexpected extent of diversity?" The variation in the extent of diversity between organisms invalidated the universality of species definitions based on molecular criteria, a major obstacle to the adaptation of models developed for the study of macroscopic eukaryotes to evolutionary microbiology. This issue has not overtly affected microbial ecology, as it had already abandoned species in favor of the more flexible operational taxonomic units. This field is nonetheless moving away from traditional methods to measure diversity, as they do not provide enough resolution to uncover what lies below the species level.The answers of the evolutionary microbiologist and microbial ecologist to these three questions illustrate differences in their theoretical frameworks. These differences mean that both fields can react quite distinctly to the same discovery, incorporating it with more or less difficulty in their scientific practice.}, }
@article {pmid22074055, year = {2012}, author = {Kazmi, RH and Khan, N and Willems, LA and VAN Heusden, AW and Ligterink, W and Hilhorst, HW}, title = {Complex genetics controls natural variation among seed quality phenotypes in a recombinant inbred population of an interspecific cross between Solanum lycopersicum × Solanum pimpinellifolium.}, journal = {Plant, cell &amp; environment}, volume = {35}, number = {5}, pages = {929-951}, doi = {10.1111/j.1365-3040.2011.02463.x}, pmid = {22074055}, issn = {1365-3040}, mesh = {Breeding ; Chromosome Mapping ; Chromosomes, Plant ; Cold Temperature ; Epistasis, Genetic ; Gene Transfer, Horizontal ; Genetic Variation/*genetics ; Genotype ; Germination/physiology ; Hot Temperature ; Solanum lycopersicum/drug effects/*genetics/physiology ; Osmotic Pressure ; Oxidative Stress ; Phenotype ; Quantitative Trait Loci/*genetics ; Seeds/drug effects/genetics/*physiology ; Sodium Chloride/pharmacology ; Stress, Physiological/*genetics ; }, abstract = {Seed quality in tomato is associated with many complex physiological and genetic traits. While plant processes are frequently controlled by the action of small- to large-effect genes that follow classic Mendelian inheritance, our study suggests that seed quality is primarily quantitative and genetically complex. Using a recombinant inbred line population of Solanum lycopersicum × Solanum pimpinellifolium, we identified quantitative trait loci (QTLs) influencing seed quality phenotypes under non-stress, as well as salt, osmotic, cold, high-temperature and oxidative stress conditions. In total, 42 seed quality traits were analysed and 120 QTLs were identified for germination traits under different conditions. Significant phenotypic correlations were observed between germination traits under optimal conditions, as well as under different stress conditions. In conclusion, one or more QTLs were identified for each trait with some of these QTLs co-locating. Co-location of QTLs for different traits can be an indication that a locus has pleiotropic effects on multiple traits due to a common mechanistic basis. However, several QTLs also dissected seed quality in its separate components, suggesting different physiological mechanisms and signalling pathways for different seed quality attributes.}, }
@article {pmid22073942, year = {2011}, author = {Fan, G and Li, J}, title = {Regions identity between the genome of vertebrates and non-retroviral families of insect viruses.}, journal = {Virology journal}, volume = {8}, number = {}, pages = {511}, pmid = {22073942}, issn = {1743-422X}, mesh = {Animals ; Evolution, Molecular ; Gene Transfer, Horizontal ; Insect Viruses/*genetics ; Interspersed Repetitive Sequences ; *Sequence Homology ; Vertebrates/*genetics ; }, abstract = {BACKGROUND: The scope of our understanding of the evolutionary history between viruses and animals is limited. The fact that the recent availability of many complete insect virus genomes and vertebrate genomes as well as the ability to screen these sequences makes it possible to gain a new perspective insight into the evolutionary interaction between insect viruses and vertebrates. This study is to determine the possibility of existence of sequence identity between the genomes of insect viruses and vertebrates, attempt to explain this phenomenon in term of genetic mobile element, and try to investigate the evolutionary relationship between these short regions of identity among these species.<br><br>RESULTS: Some of studied insect viruses contain variable numbers of short regions of sequence identity to the genomes of vertebrate with nucleotide sequence length from 28 bp to 124 bp. They are found to locate in multiple sites of the vertebrate genomes. The ontology of animal genes with identical regions involves in several processes including chromatin remodeling, regulation of apoptosis, signaling pathway, nerve system development and some enzyme-like catalysis. Phylogenetic analysis reveals that at least some short regions of sequence identity in the genomes of vertebrate are derived the ancestral of insect viruses.<br><br>CONCLUSION: Short regions of sequence identity were found in the vertebrates and insect viruses. These sequences played an important role not only in the long-term evolution of vertebrates, but also in promotion of insect virus. This typical win-win strategy may come from natural selection.}, }
@article {pmid22073223, year = {2011}, author = {Szczepankowska, AK and Prestel, E and Mariadassou, M and Bardowski, JK and Bidnenko, E}, title = {Phylogenetic and complementation analysis of a single-stranded DNA binding protein family from lactococcal phages indicates a non-bacterial origin.}, journal = {PloS one}, volume = {6}, number = {11}, pages = {e26942}, pmid = {22073223}, issn = {1932-6203}, mesh = {Bacteriophages/*metabolism ; Cluster Analysis ; DNA, Single-Stranded/*analysis/genetics ; Escherichia coli/genetics ; *Genetic Complementation Test ; Lactococcus/*virology ; *Phylogeny ; }, abstract = {BACKGROUND: The single-stranded-nucleic acid binding (SSB) protein superfamily includes proteins encoded by different organisms from Bacteria and their phages to Eukaryotes. SSB proteins share common structural characteristics and have been suggested to descend from an ancestor polypeptide. However, as other proteins involved in DNA replication, bacterial SSB proteins are clearly different from those found in Archaea and Eukaryotes. It was proposed that the corresponding genes in the phage genomes were transferred from the bacterial hosts. Recently new SSB proteins encoded by the virulent lactococcal bacteriophages (Orf14(bIL67)-like proteins) have been identified and characterized structurally and biochemically.<br><br>This study focused on the determination of phylogenetic relationships between Orf14(bIL67)-like proteins and other SSBs. We have performed a large scale phylogenetic analysis and pairwise sequence comparisons of SSB proteins from different phyla. The results show that, in remarkable contrast to other phage SSBs, the Orf14(bIL67)-like proteins form a distinct, self-contained and well supported phylogenetic group connected to the archaeal SSBs. Functional studies demonstrated that, despite the structural and amino acid sequence differences from bacterial SSBs, Orf14(bIL67) protein complements the conditional lethal ssb-1 mutation of Escherichia coli.<br><br>CONCLUSIONS/SIGNIFICANCE: Here we identified for the first time a group of phages encoded SSBs which are clearly distinct from their bacterial counterparts. All methods supported the recognition of these phage proteins as a new family within the SSB superfamily. Our findings suggest that unlike other phages, the virulent lactococcal phages carry ssb genes that were not acquired from their hosts, but transferred from an archaeal genome. This represents a unique example of a horizontal gene transfer between Archaea and bacterial phages.}, }
@article {pmid22072497, year = {2012}, author = {Ranellou, K and Kadlec, K and Poulou, A and Voulgari, E and Vrioni, G and Schwarz, S and Tsakris, A}, title = {Detection of Pseudomonas aeruginosa isolates of the international clonal complex 11 carrying the blaPER-1 extended-spectrum β-lactamase gene in Greece.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {67}, number = {2}, pages = {357-361}, doi = {10.1093/jac/dkr471}, pmid = {22072497}, issn = {1460-2091}, mesh = {Aged ; Anti-Bacterial Agents/pharmacology ; Ceftazidime/pharmacology ; Cluster Analysis ; DNA Fingerprinting ; DNA Transposable Elements ; DNA, Bacterial/genetics ; Electrophoresis, Gel, Pulsed-Field ; Female ; Gene Transfer, Horizontal ; Genotype ; Greece ; Humans ; Male ; Microbial Sensitivity Tests/methods ; Middle Aged ; Multilocus Sequence Typing ; Polymerase Chain Reaction ; Pseudomonas aeruginosa/classification/*enzymology/genetics/*isolation &amp; purification ; Sequence Analysis, DNA ; beta-Lactam Resistance ; beta-Lactamases/*metabolism ; }, abstract = {OBJECTIVES: The extended-spectrum β-lactamase (ESBL) PER-1 initially disseminated among Pseudomonas aeruginosa strains in Turkey. Despite reports from other European countries, such strains have not been detected in Greece until now. We describe the first bla(PER-1)-positive P. aeruginosa isolates from Greece and their genetic environment.<br><br>METHODS: From January 2008 to December 2009, 287 consecutive non-duplicate P. aeruginosa isolates with reduced susceptibility or resistance to ceftazidime (MIC >8 mg/L) were screened for ESBL production with a modified boronic acid-based double-disc synergy test. Phenotypically ESBL-positive isolates were subjected to agar dilution, PFGE and multilocus sequence typing (MLST). Broad-spectrum bla genes were identified by PCR and sequencing. Plasmid analysis and conjugation experiments were performed. The location of the bla(PER-1) gene was detected by Southern blotting and its genetic environment was characterized using inverse PCR.<br><br>RESULTS: Five isolates were phenotypically positive for ESBL production, exhibited resistance to cefepime, ceftazidime, aztreonam and meropenem, and carried the bla(PER-1) gene. MLST showed that they belonged to sequence type (ST) 235, which belongs to the international clonal complex 11. Four isolates had the same PFGE pattern. Southern blotting revealed the chromosomal location of the bla(PER-1) gene. Analysis of the bla(PER-1) flanking regions showed identity to transposon Tn1213 downstream and 1406 bp upstream of bla(PER-1). Further upstream, an orfA gene and ISPa12 were identified; both were truncated by the insertion of IS6100.<br><br>CONCLUSIONS: This study confirmed the presence of PER-1-producing P. aeruginosa strains in Greece. The chromosomal location of bla(PER-1), as part of a truncated transposon, suggests clonal expansion rather than horizontal gene transfer.}, }
@article {pmid22071790, year = {2011}, author = {Doroghazi, JR and Buckley, DH}, title = {A model for the effect of homologous recombination on microbial diversification.}, journal = {Genome biology and evolution}, volume = {3}, number = {}, pages = {1349-1356}, pmid = {22071790}, issn = {1759-6653}, mesh = {Bacteria/*genetics ; Computer Simulation ; *Gene Transfer, Horizontal ; Genetic Speciation ; *Homologous Recombination ; Models, Biological ; Multilocus Sequence Typing ; Mutation ; }, abstract = {The effect of homologous recombination (HR) on the evolution of microbial genomes remains contentious as competing hypotheses seek to explain the evolutionary dynamics of microbial species. Evidence for HR between microbial genomes is widespread, and this process has been proposed to act as a cohesive force that can constrain the diversification of microbial lineages. We seek to characterize the evolutionary dynamics of sympatric populations to explore the impact of HR on microbial speciation. We describe a simple equation for quantifying the cohesive effect of HR on microbial populations as a function of their nucleotide divergence, μ/ρ=πg10(-20 πg). The model was verified using a forward-time microbial population simulator that can explore the evolutionary dynamics of sympatric populations in nonoverlapping niche space. The model was also evaluated using multilocus sequence data from a range of microbial species, providing criteria for dividing them into either cohesively recombining or clonally diverging lineages. We conclude that models of microbial diversification that appear contradictory can be explained in a unified manner as the natural and predictable consequence of variation in a small number of population parameters.}, }
@article {pmid22069523, year = {2011}, author = {Villarreal, LP}, title = {Viral ancestors of antiviral systems.}, journal = {Viruses}, volume = {3}, number = {10}, pages = {1933-1958}, pmid = {22069523}, issn = {1999-4915}, mesh = {Adaptive Immunity/*genetics/immunology ; Animals ; Archaea/*virology ; Bacteria/*virology ; Biological Evolution ; Eukaryota/*virology ; Gene Transfer, Horizontal ; Humans ; Viruses/*genetics/*immunology ; }, abstract = {All life must survive their corresponding viruses. Thus antiviral systems are essential in all living organisms. Remnants of virus derived information are also found in all life forms but have historically been considered mostly as junk DNA. However, such virus derived information can strongly affect host susceptibility to viruses. In this review, I evaluate the role viruses have had in the origin and evolution of host antiviral systems. From Archaea through bacteria and from simple to complex eukaryotes I trace the viral components that became essential elements of antiviral immunity. I conclude with a reexamination of the 'Big Bang' theory for the emergence of the adaptive immune system in vertebrates by horizontal transfer and note how viruses could have and did provide crucial and coordinated features.}, }
@article {pmid22066957, year = {2011}, author = {Lang, S and Kirchberger, PC and Gruber, CJ and Redzej, A and Raffl, S and Zellnig, G and Zangger, K and Zechner, EL}, title = {An activation domain of plasmid R1 TraI protein delineates stages of gene transfer initiation.}, journal = {Molecular microbiology}, volume = {82}, number = {5}, pages = {1071-1085}, pmid = {22066957}, issn = {1365-2958}, mesh = {Bacteriolysis ; Conjugation, Genetic ; DNA Helicases/*metabolism ; Escherichia coli/genetics/*metabolism/*virology ; Escherichia coli Proteins/*metabolism ; Fimbriae, Bacterial/metabolism ; *Gene Transfer, Horizontal ; Levivirus/genetics/*physiology ; Membrane Proteins/metabolism ; Models, Biological ; Plasmids/genetics/*metabolism ; Protein Binding ; Protein Interaction Mapping ; Protein Multimerization ; Replication Origin ; *Virus Internalization ; }, abstract = {Bacterial conjugation is a form of type IV secretion that transports protein and DNA to recipient cells. Specific bacteriophage exploit the conjugative pili and cell envelope spanning protein machinery of these systems to invade bacterial cells. Infection by phage R17 requires F-like pili and coupling protein TraD, which gates the cytoplasmic entrance of the secretion channel. Here we investigate the role of TraD in R17 nucleoprotein uptake and find parallels to secretion mechanisms. The relaxosome of IncFII plasmid R1 is required. A ternary complex of plasmid oriT, TraD and a novel activation domain within the N-terminal 992 residues of TraI contributes a key mechanism involving relaxase-associated properties of TraI, protein interaction and the TraD ATPase. Helicase-associated activities of TraI are dispensable. These findings distinguish for the first time specific protein domains and complexes that process extracellular signals into distinct activation stages in the type IV initiation pathway. The study also provided insights into the evolutionary interplay of phage and the plasmids they exploit. Related plasmid F adapted to R17 independently of TraI. It follows that selection for phage resistance drives not only variation in TraA pilins but diversifies TraD and its binding partners in a plasmid-specific manner.}, }
@article {pmid22066900, year = {2011}, author = {Coleman, JJ and Wasmann, CC and Usami, T and White, GJ and Temporini, ED and McCluskey, K and VanEtten, HD}, title = {Characterization of the gene encoding pisatin demethylase (FoPDA1) in Fusarium oxysporum.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {24}, number = {12}, pages = {1482-1491}, doi = {10.1094/MPMI-05-11-0119}, pmid = {22066900}, issn = {0894-0282}, mesh = {Base Sequence ; Chromosome Mapping ; Cloning, Molecular ; Cluster Analysis ; Cytochrome P-450 Enzyme System/genetics/*metabolism ; DNA, Plant/chemistry/genetics ; Fusarium/*enzymology/genetics/metabolism/*pathogenicity ; Gene Transfer, Horizontal ; Host-Pathogen Interactions ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Oxidoreductases, O-Demethylating/genetics/*metabolism ; Pisum sativum/*microbiology ; Phylogeny ; Plant Diseases/*microbiology ; Pterocarpans/*metabolism ; RNA, Fungal/genetics ; RNA, Messenger/genetics ; Sequence Analysis, DNA ; Time Factors ; Virulence ; }, abstract = {The pea pathogen Fusarium oxysporum f. sp. pisi is able to detoxify pisatin produced as a defense response by pea, and the gene encoding this detoxification mechanism, FoPDA1, was 82% identical to the cytochrome P450 pisatin demethylase PDA1 gene in Nectria haematococca. A survey of F. oxysporum f. sp. pisi isolates demonstrated that, as in N. haematococca, the PDA gene of F. oxysporum f. sp. pisi is generally located on a small chromosome. In N. haematococca, PDA1 is in a cluster of pea pathogenicity (PEP) genes. Homologs of these PEP genes also were found in the F. oxysporum f. sp. pisi isolates, and PEP1 and PEP5 were sometimes located on the same small chromosomes as the FoPDA1 homologs. Transforming FoPDA1 into a pda(?) F. oxysporum f. sp. lini isolate conferred pda activity and promoted pathogenicity on pea to some transformants. Different hybridization patterns of FoPDA1 were found in F. oxysporum f. sp. pisi but these did not correlate with the races of the fungus, suggesting that races within this forma specialis arose independently of FoPDA1. FoPDA1 also was present in the formae speciales lini, glycines, and dianthi of F. oxysporum but they had mutations resulting in nonfunctional proteins. However, an active FoPDA1 was present in F. oxysporum f. sp. phaseoli and it was virulent on pea. Despite their evolutionary distance, the amino acid sequences of FoPDA1 of F. oxysporum f. sp. pisi and F. oxysporum f. sp. phaseoli revealed only six amino acid differences, consistent with a horizontal gene transfer event accounting for the origin of these genes.}, }
@article {pmid22062000, year = {2012}, author = {Haegeman, A and Mantelin, S and Jones, JT and Gheysen, G}, title = {Functional roles of effectors of plant-parasitic nematodes.}, journal = {Gene}, volume = {492}, number = {1}, pages = {19-31}, doi = {10.1016/j.gene.2011.10.040}, pmid = {22062000}, issn = {1879-0038}, support = {BB/H000801/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Helminth Proteins/metabolism/*physiology ; *Host-Parasite Interactions/genetics ; Nematoda/*physiology ; Plant Growth Regulators/physiology ; *Plant Immunity ; Plants/parasitology ; Signal Transduction ; Ubiquitination ; }, abstract = {Plant pathogens have evolved a variety of different strategies that allow them to successfully infect their hosts. Plant-parasitic nematodes secrete numerous proteins into their hosts. These proteins, called effectors, have various functions in the plant cell. The most studied effectors to date are the plant cell wall degrading enzymes, which have an interesting evolutionary history since they are believed to have been acquired from bacteria or fungi by horizontal gene transfer. Extensive genome, transcriptome and proteome studies have shown that plant-parasitic nematodes secrete many additional effectors. The function of many of these is less clear although during the last decade, several research groups have determined the function of some of these effectors. Even though many effectors remain to be investigated, it has already become clear that they can have very diverse functions. Some are involved in suppression of plant defences, while others can specifically interact with plant signalling or hormone pathways to promote the formation of nematode feeding sites. In this review, the most recent progress in the understanding of the function of plant-parasitic nematode effectors is discussed.}, }
@article {pmid22060770, year = {2011}, author = {Lamikanra, A and Crowe, JL and Lijek, RS and Odetoyin, BW and Wain, J and Aboderin, AO and Okeke, IN}, title = {Rapid evolution of fluoroquinolone-resistant Escherichia coli in Nigeria is temporally associated with fluoroquinolone use.}, journal = {BMC infectious diseases}, volume = {11}, number = {}, pages = {312}, pmid = {22060770}, issn = {1471-2334}, support = {//Howard Hughes Medical Institute/United States ; //Wellcome Trust/United Kingdom ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; DNA Gyrase/genetics ; DNA Topoisomerase IV/genetics ; DNA, Bacterial/chemistry/genetics ; *Drug Resistance, Bacterial ; *Drug Utilization ; Escherichia coli/*drug effects/isolation &amp; purification ; Feces/*microbiology ; Fluoroquinolones/*pharmacology ; Gene Transfer, Horizontal ; Human Experimentation ; Humans ; Nigeria ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Antibiotic resistance has necessitated fluoroquinolone use but little is known about the selective forces and resistance trajectory in malaria-endemic settings, where selection from the antimalarial chloroquine for fluoroquinolone-resistant bacteria has been proposed.<br><br>METHODS: Antimicrobial resistance was studied in fecal Escherichia coli isolates in a Nigerian community. Quinolone-resistance determining regions of gyrA and parC were sequenced in nalidixic acid resistant strains and horizontally-transmitted quinolone-resistance genes were sought by PCR. Antimicrobial prescription practices were compared with antimicrobial resistance rates over a period spanning three decades.<br><br>RESULTS: Before 2005, quinolone resistance was limited to low-level nalixidic acid resistance in fewer than 4% of E. coli isolates. In 2005, the proportion of isolates demonstrating low-level quinolone resistance due to elevated efflux increased and high-level quinolone resistance and resistance to the fluoroquinolones appeared. Fluoroquinolone resistance was attributable to single nucleotide polymorphisms in quinolone target genes gyrA and/or parC. By 2009, 35 (34.5%) of isolates were quinolone non-susceptible with nine carrying gyrA and parC SNPs and six bearing identical qnrS1 alleles. The antimalarial chloroquine was heavily used throughout the entire period but E. coli with quinolone-specific resistance mechanisms were only detected in the final half decade, immediately following the introduction of the fluoroquinolone antibacterial ciprofloxacin.<br><br>CONCLUSIONS: Fluoroquinolones, and not chloroquine, appear to be the selective force for fluoroquinolone-resistant fecal E. coli in this setting. Rapid evolution to resistance following fluoroquinolone introduction points the need to implement resistant containment strategies when new antibacterials are introduced into resource-poor settings with high infectious disease burdens.}, }
@article {pmid22059960, year = {2012}, author = {Rizzi, A and Raddadi, N and Sorlini, C and Nordgrd, L and Nielsen, KM and Daffonchio, D}, title = {The stability and degradation of dietary DNA in the gastrointestinal tract of mammals: implications for horizontal gene transfer and the biosafety of GMOs.}, journal = {Critical reviews in food science and nutrition}, volume = {52}, number = {2}, pages = {142-161}, doi = {10.1080/10408398.2010.499480}, pmid = {22059960}, issn = {1549-7852}, mesh = {Animal Feed ; Animals ; Bacteria/genetics ; DNA/*genetics ; DNA, Bacterial/genetics ; Digestion/physiology ; Gastrointestinal Tract/*physiology ; Gene Transfer, Horizontal/*genetics/physiology ; Humans ; Plants, Genetically Modified/*genetics/*metabolism ; Risk Assessment ; Transduction, Genetic/methods ; }, abstract = {The fate of dietary DNA in the gastrointestinal tract (GIT) of animals has gained renewed interest after the commercial introduction of genetically modified organisms (GMO). Among the concerns regarding GM food, are the possible consequences of horizontal gene transfer (HGT) of recombinant dietary DNA to bacteria or animal cells. The exposure of the GIT to dietary DNA is related to the extent of food processing, food composition, and to the level of intake. Animal feeding studies have demonstrated that a minor amount of fragmented dietary DNA may resist the digestive process. Mammals have been shown to take up dietary DNA from the GIT, but stable integration and expression of internalized DNA has not been demonstrated. Despite the ability of several bacterial species to acquire external DNA by natural transformation, in vivo transfer of dietary DNA to bacteria in the intestine has not been detected in the few experimental studies conducted so far. However, major methodological limitations and knowledge gaps of the mechanistic aspects of HGT calls for methodological improvements and further studies to understand the fate of various types of dietary DNA in the GIT.}, }
@article {pmid22057012, year = {2012}, author = {Konrad, A and Yarunova, E and Tinta, T and Piškur, J and Liberles, DA}, title = {The global distribution and evolution of deoxyribonucleoside kinases in bacteria.}, journal = {Gene}, volume = {492}, number = {1}, pages = {117-120}, doi = {10.1016/j.gene.2011.10.039}, pmid = {22057012}, issn = {1879-0038}, mesh = {*Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Gram-Negative Bacteria/genetics ; Phosphotransferases (Alcohol Group Acceptor)/*genetics ; Phylogeny ; }, abstract = {Deoxyribonucleoside kinases (dNKs) are important to DNA metabolism, especially in environments where nucleosides are freely available to be absorbed and used for the salvage pathway. Little has previously been known about the complement of dNKs in different bacterial genomes. However, it was believed that Gram-negative bacteria had a single dNK, while Gram-positive bacteria possessed several. An analysis of 992 fully sequenced bacterial genomes, including both Gram-positive and Gram-negative organisms, was conducted to investigate the phylogenetic relationship of all TK1-like and non-TK1-like dNKs. It was illustrated that both gene families evolved through a number of duplications and horizontal gene transfers, leading to the presence of multiple dNKs in different types of bacteria. The findings of this study provide a backbone for further studies into the evolution of the interplay between the de novo and salvage pathways in DNA synthesis with respect to environmental availability of deoxyribonucleosides and metabolic processes generating the provisions of different dNTPs.}, }
@article {pmid22056789, year = {2012}, author = {Lurie-Weinberger, MN and Peeri, M and Gophna, U}, title = {Contribution of lateral gene transfer to the gene repertoire of a gut-adapted methanogen.}, journal = {Genomics}, volume = {99}, number = {1}, pages = {52-58}, doi = {10.1016/j.ygeno.2011.10.005}, pmid = {22056789}, issn = {1089-8646}, mesh = {ATP-Binding Cassette Transporters/genetics ; Adaptation, Physiological ; Adhesins, Bacterial/genetics ; Biological Evolution ; DNA Transposable Elements ; Gastrointestinal Tract/microbiology ; *Gene Transfer, Horizontal ; Genes, Archaeal ; Glycosyltransferases/genetics ; Humans ; Methanobrevibacter/*genetics ; Phylogeny ; }, abstract = {Methanobrevibacter smithii is the most abundant archaeon in the human colon. As most of its neighbors are bacterial species, it is expected that lateral gene acquisition from bacteria might have contributed to the evolution and adaptation of this archaeon. We performed a tree-based genome-wide survey of putative lateral gene transfer products in M. smithii, using a phylogenetic pipeline. Over 15% of the coding genes of M. smithii are inferred to be bacterial in origin, based on this analysis. Laterally acquired genes have had the largest contribution to surface functions, and encode glycosyl-transferases and adhesin-like proteins. In addition, several important ABC transporters, especially metal transporters are of bacterial origin. Thus, bacterial genes contributed to the host-adaptation by allowing a larger variety of surface structures and increasing the efficiency of metal ion uptake in the competitive gut niche.}, }
@article {pmid22050575, year = {2012}, author = {Bonnefoy, V and Holmes, DS}, title = {Genomic insights into microbial iron oxidation and iron uptake strategies in extremely acidic environments.}, journal = {Environmental microbiology}, volume = {14}, number = {7}, pages = {1597-1611}, doi = {10.1111/j.1462-2920.2011.02626.x}, pmid = {22050575}, issn = {1462-2920}, mesh = {Acidithiobacillus/genetics/*metabolism ; Acids/*chemistry ; Archaea/classification/genetics/metabolism ; Ferric Compounds/*metabolism ; Homeostasis ; Hydrogen-Ion Concentration ; Iron/*metabolism ; Metabolic Networks and Pathways ; Oxidation-Reduction ; Phylogeny ; Siderophores/*metabolism ; }, abstract = {This minireview presents recent advances in our understanding of iron oxidation and homeostasis in acidophilic Bacteria and Archaea. These processes influence the flux of metals and nutrients in pristine and man-made acidic environments such as acid mine drainage and industrial bioleaching operations. Acidophiles are also being studied to understand life in extreme conditions and their role in the generation of biomarkers used in the search for evidence of existing or past extra-terrestrial life. Iron oxidation in acidophiles is best understood in the model organism Acidithiobacillus ferrooxidans. However, recent functional genomic analysis of acidophiles is leading to a deeper appreciation of the diversity of acidophilic iron-oxidizing pathways. Although it is too early to paint a detailed picture of the role played by lateral gene transfer in the evolution of iron oxidation, emerging evidence tends to support the view that iron oxidation arose independently more than once in evolution. Acidic environments are generally rich in soluble iron and extreme acidophiles (e.g. the Leptospirillum genus) have considerably fewer iron uptake systems compared with neutrophiles. However, some acidophiles have been shown to grow as high as pH 6 and, in the case of the Acidithiobacillus genus, to have multiple iron uptake systems. This could be an adaption allowing them to respond to different iron concentrations via the use of a multiplicity of different siderophores. Both Leptospirillum spp. and Acidithiobacillus spp. are predicted to synthesize the acid stable citrate siderophore for Fe(III) uptake. In addition, both groups have predicted receptors for siderophores produced by other microorganisms, suggesting that competition for iron occurs influencing the ecophysiology of acidic environments. Little is known about the genetic regulation of iron oxidation and iron uptake in acidophiles, especially how the use of iron as an energy source is balanced with its need to take up iron for metabolism. It is anticipated that integrated and complex regulatory networks sensing different environmental signals, such as the energy source and/or the redox state of the cell as well as the oxygen availability, are involved.}, }
@article {pmid22048956, year = {2012}, author = {Perron, GG and Lee, AE and Wang, Y and Huang, WE and Barraclough, TG}, title = {Bacterial recombination promotes the evolution of multi-drug-resistance in functionally diverse populations.}, journal = {Proceedings. Biological sciences}, volume = {279}, number = {1733}, pages = {1477-1484}, pmid = {22048956}, issn = {1471-2954}, mesh = {Acinetobacter/drug effects/*genetics ; Anti-Bacterial Agents/*pharmacology ; DNA Mutational Analysis ; DNA, Bacterial/chemistry ; Drug Resistance, Multiple, Bacterial/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; *Recombination, Genetic ; }, abstract = {Bacterial recombination is believed to be a major factor explaining the prevalence of multi-drug-resistance (MDR) among pathogenic bacteria. Despite extensive evidence for exchange of resistance genes from retrospective sequence analyses, experimental evidence for the evolutionary benefits of bacterial recombination is scarce. We compared the evolution of MDR between populations of Acinetobacter baylyi in which we manipulated both the recombination rate and the initial diversity of strains with resistance to single drugs. In populations lacking recombination, the initial presence of multiple strains resistant to different antibiotics inhibits the evolution of MDR. However, in populations with recombination, the inhibitory effect of standing diversity is alleviated and MDR evolves rapidly. Moreover, only the presence of DNA harbouring resistance genes promotes the evolution of resistance, ruling out other proposed benefits for recombination. Together, these results provide direct evidence for the fitness benefits of bacterial recombination and show that this occurs by mitigation of functional interference between genotypes resistant to single antibiotics. Although analogous to previously described mechanisms of clonal interference among alternative beneficial mutations, our results actually highlight a different mechanism by which interactions among co-occurring strains determine the benefits of recombination for bacterial evolution.}, }
@article {pmid22048742, year = {2012}, author = {Gao, B and Gupta, RS}, title = {Microbial systematics in the post-genomics era.}, journal = {Antonie van Leeuwenhoek}, volume = {101}, number = {1}, pages = {45-54}, doi = {10.1007/s10482-011-9663-1}, pmid = {22048742}, issn = {1572-9699}, mesh = {Bacteria/*classification/*genetics ; Classification/*methods ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genomics/methods ; *Phylogeny ; Recombination, Genetic ; }, abstract = {Microbial systematics and phylogeny should form the foundation and guiding light for a comprehensive understanding of different aspects of microbiology. However, there are many critical issues in microbial systematics that are currently not resolved. Some of these include: how to define and delimit a prokaryotic species; development of rationale criteria for the assignment of higher taxonomic ranks; understanding what unique properties distinguish species from different groups; and understanding the branching order and interrelationship among higher prokaryotic clades. The sequencing of genomes from large numbers of cultured as well as uncultured microbes covering prokaryotic diversity provides unique means to achieve these important objectives. Prokaryotic genomes are found to be very diverse and dynamic and horizontal gene transfers (HGTs) are indicated to have played important role in species/genome evolution. Although HGT adds a layer of complexity in terms of understanding the genomes and species evolution, it is contended that vast majority of genes and genetic characteristics that are distinctive characteristics of higher prokaryotic taxa are vertically inherited and based on them a solid foundation for microbial systematics can be developed. We describe two kinds of molecular markers consisting of conserved indels in protein sequences and whole proteins that are specific for different groups that are proving particularly valuable in defining different prokaryotic groups in clear molecular terms and in understanding their interrelationships. The genetic and biochemical studies on these taxa-specific molecular markers also open the way to discover novel biochemical and physiological characteristics that are unique properties of these groups.}, }
@article {pmid22047552, year = {2011}, author = {Gimenez, G and Bertelli, C and Moliner, C and Robert, C and Raoult, D and Fournier, PE and Greub, G}, title = {Insight into cross-talk between intra-amoebal pathogens.}, journal = {BMC genomics}, volume = {12}, number = {}, pages = {542}, pmid = {22047552}, issn = {1471-2164}, mesh = {Amoeba/*microbiology ; Chlamydiales/*genetics ; Cluster Analysis ; DNA, Bacterial/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Legionella/*genetics ; Operon ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Amoebae are phagocytic protists where genetic exchanges might take place between amoeba-resistant bacteria. These amoebal pathogens are able to escape the phagocytic behaviour of their host. They belong to different bacterial phyla and often show a larger genome size than human-infecting pathogens. This characteristic is proposed to be the result of frequent gene exchanges with other bacteria that share a sympatric lifestyle and contrasts with the genome reduction observed among strict human pathogens.<br><br>RESULTS: We sequenced the genome of a new amoebal pathogen, Legionella drancourtii, and compared its gene content to that of a Chlamydia-related bacterium, Parachlamydia acanthamoebae. Phylogenetic reconstructions identified seven potential horizontal gene transfers (HGTs) between the two amoeba-resistant bacteria, including a complete operon of four genes that encodes an ABC-type transporter. These comparisons pinpointed potential cases of gene exchange between P. acanthamoebae and Legionella pneumophila, as well as gene exchanges between other members of the Legionellales and Chlamydiales orders. Moreover, nine cases represent possible HGTs between representatives from the Legionellales or Chlamydiales and members of the Rickettsiales order.<br><br>CONCLUSIONS: This study identifies numerous gene exchanges between intracellular Legionellales and Chlamydiales bacteria, which could preferentially occur within common inclusions in their amoebal hosts. Therefore it contributes to improve our knowledge on the intra-amoebal gene properties associated to their specific lifestyle.}, }
@article {pmid22045996, year = {2012}, author = {Tucker, RP and Beckmann, J and Leachman, NT and Schöler, J and Chiquet-Ehrismann, R}, title = {Phylogenetic analysis of the teneurins: conserved features and premetazoan ancestry.}, journal = {Molecular biology and evolution}, volume = {29}, number = {3}, pages = {1019-1029}, pmid = {22045996}, issn = {1537-1719}, mesh = {Alternative Splicing ; Animals ; Base Sequence ; Chickens ; Ciona intestinalis ; Cluster Analysis ; Computational Biology ; Conserved Sequence/genetics ; DNA Primers/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Humans ; Mice ; Molecular Sequence Data ; Multigene Family/*genetics ; Nerve Tissue Proteins/*genetics ; *Phylogeny ; Protein Structure, Tertiary ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; Tenascin/*genetics ; Zebrafish ; }, abstract = {Teneurins are type II transmembrane proteins expressed during pattern formation and neurogenesis with an intracellular domain that can be transported to the nucleus and an extracellular domain that can be shed into the extracellular milieu. In Drosophila melanogaster, Caenorhabditis elegans, and mouse the knockdown or knockout of teneurin expression can lead to abnormal patterning, defasciculation, and abnormal pathfinding of neurites, and the disruption of basement membranes. Here, we have identified and analyzed teneurins from a broad range of metazoan genomes for nuclear localization sequences, protein interaction domains, and furin cleavage sites and have cloned and sequenced the intracellular domains of human and avian teneurins to analyze alternative splicing. The basic organization of teneurins is highly conserved in Bilateria: all teneurins have epidermal growth factor (EGF) repeats, a cysteine-rich domain, and a large region identical in organization to the carboxy-half of prokaryotic YD-repeat proteins. Teneurins were not found in the genomes of sponges, cnidarians, or placozoa, but the choanoflagellate Monosiga brevicollis has a gene encoding a predicted teneurin with a transmembrane domain, EGF repeats, a cysteine-rich domain, and a region homologous to YD-repeat proteins. Further examination revealed that most of the extracellular domain of the M. brevicollis teneurin is encoded on a single huge 6,829-bp exon and that the cysteine-rich domain is similar to sequences found in an enzyme expressed by the diatom Phaeodactylum tricornutum. This leads us to suggest that teneurins are complex hybrid fusion proteins that evolved in a choanoflagellate via horizontal gene transfer from both a prokaryotic gene and a diatom or algal gene, perhaps to improve the capacity of the choanoflagellate to bind to its prokaryotic prey. As choanoflagellates are considered to be the closest living relatives of animals, the expression of a primitive teneurin by an ancestral choanoflagellate may have facilitated the evolution of multicellularity and complex histogenesis in metazoa.}, }
@article {pmid22045989, year = {2011}, author = {Mathers, AJ and Cox, HL and Kitchel, B and Bonatti, H and Brassinga, AK and Carroll, J and Scheld, WM and Hazen, KC and Sifri, CD}, title = {Molecular dissection of an outbreak of carbapenem-resistant enterobacteriaceae reveals Intergenus KPC carbapenemase transmission through a promiscuous plasmid.}, journal = {mBio}, volume = {2}, number = {6}, pages = {e00204-11}, pmid = {22045989}, issn = {2150-7511}, support = {T32 AI007046/AI/NIAID NIH HHS/United States ; T32 AI055432/AI/NIAID NIH HHS/United States ; T32AI055432/AI/NIAID NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacterial Proteins/*genetics/metabolism ; Carbapenems/*pharmacology ; DNA Transposable Elements ; Disease Outbreaks ; *Drug Resistance, Bacterial ; Enterobacteriaceae/classification/drug effects/enzymology/*genetics ; Enterobacteriaceae Infections/epidemiology/*microbiology ; Female ; Gene Transfer, Horizontal ; Humans ; Klebsiella pneumoniae/*enzymology/genetics ; Male ; Middle Aged ; Phylogeny ; Plasmids/*genetics/metabolism ; Young Adult ; beta-Lactamases/*genetics/metabolism ; }, abstract = {Carbapenem-resistant Enterobacteriaceae (CRE) have emerged as major causes of health care-associated infections worldwide. This diverse collection of organisms with various resistance mechanisms is associated with increased lengths of hospitalization, costs of care, morbidity, and mortality. The global spread of CRE has largely been attributed to dissemination of a dominant strain of Klebsiella pneumoniae producing a serine β-lactamase, termed K. pneumoniae carbapenemase (KPC). Here we report an outbreak of KPC-producing CRE infections in which the degree of horizontal transmission between strains and species of a promiscuous plasmid is unprecedented. Sixteen isolates, comprising 11 unique strains, 6 species, and 4 genera of bacteria, were obtained from 14 patients over the first 8 months of the outbreak. Of the 11 unique strains, 9 harbored the same highly promiscuous plasmid carrying the KPC gene bla(KPC). The remaining strains harbored distinct bla(KPC) plasmids, one of which was carried in a strain of Klebsiella oxytoca coisolated from the index patient and the other generated from transposition of the bla(KPC) element Tn4401. All isolates could be genetically traced to the index patient. Molecular epidemiological investigation of the outbreak was aided by the adaptation of nested arbitrary PCR (ARB-PCR) for rapid plasmid identification. This detailed molecular genetic analysis, combined with traditional epidemiological investigation, provides insights into the highly fluid dynamics of drug resistance transmission during the outbreak. IMPORTANCE The ease of horizontal transmission of carbapenemase resistance plasmids across strains, species, and genera of bacteria observed in this study has several important public health and epidemiological implications. First, it has the potential to promote dissemination of carbapenem resistance to new populations of Enterobacteriaceae, including organisms of low virulence, leading to the establishment of reservoirs of carbapenem resistance genes in patients and/or the environment and of high virulence, raising the specter of untreatable community-associated infections. Second, recognition of plasmid-mediated outbreaks, such as those described here, is problematic because analysis of resistance plasmids from clinical isolates is laborious and technically challenging. Adaptation of nested arbitrary PCR (ARB-PCR) to investigate the plasmid outbreak facilitated our investigation, and the method may be broadly applicable to other outbreaks due to other conserved mobile genetic elements. Whether infection control measures that focus on preventing transmission of drug-resistant clones are effective in controlling dissemination of these elements is unknown.}, }
@article {pmid22044686, year = {2011}, author = {Gomez-Valero, L and Rusniok, C and Jarraud, S and Vacherie, B and Rouy, Z and Barbe, V and Medigue, C and Etienne, J and Buchrieser, C}, title = {Extensive recombination events and horizontal gene transfer shaped the Legionella pneumophila genomes.}, journal = {BMC genomics}, volume = {12}, number = {}, pages = {536}, pmid = {22044686}, issn = {1471-2164}, mesh = {Biological Evolution ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Legionella pneumophila/classification/*genetics ; Phylogeny ; Polymorphism, Genetic ; *Recombination, Genetic ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Legionella pneumophila is an intracellular pathogen of environmental protozoa. When humans inhale contaminated aerosols this bacterium may cause a severe pneumonia called Legionnaires' disease. Despite the abundance of dozens of Legionella species in aquatic reservoirs, the vast majority of human disease is caused by a single serogroup (Sg) of a single species, namely L. pneumophila Sg1. To get further insights into genome dynamics and evolution of Sg1 strains, we sequenced strains Lorraine and HL 0604 1035 (Sg1) and compared them to the available sequences of Sg1 strains Paris, Lens, Corby and Philadelphia, resulting in a comprehensive multigenome analysis.<br><br>RESULTS: We show that L. pneumophila Sg1 has a highly conserved and syntenic core genome that comprises the many eukaryotic like proteins and a conserved repertoire of over 200 Dot/Icm type IV secreted substrates. However, recombination events and horizontal gene transfer are frequent. In particular the analyses of the distribution of nucleotide polymorphisms suggests that large chromosomal fragments of over 200 kbs are exchanged between L. pneumophila strains and contribute to the genome dynamics in the natural population. The many secretion systems present might be implicated in exchange of these fragments by conjugal transfer. Plasmids also play a role in genome diversification and are exchanged among strains and circulate between different Legionella species.<br><br>CONCLUSION: Horizontal gene transfer among bacteria and from eukaryotes to L. pneumophila as well as recombination between strains allows different clones to evolve into predominant disease clones and others to replace them subsequently within relatively short periods of time.}, }
@article {pmid22040376, year = {2011}, author = {Cai, L and Tan, D and Aibaidula, G and Dong, XR and Chen, JC and Tian, WD and Chen, GQ}, title = {Comparative genomics study of polyhydroxyalkanoates (PHA) and ectoine relevant genes from Halomonas sp. TD01 revealed extensive horizontal gene transfer events and co-evolutionary relationships.}, journal = {Microbial cell factories}, volume = {10}, number = {}, pages = {88}, pmid = {22040376}, issn = {1475-2859}, mesh = {Amino Acid Sequence ; Amino Acids, Diamino/*metabolism ; Bacterial Proteins/chemistry/*genetics/metabolism ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genomics ; Halomonas/chemistry/classification/*genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; Polyhydroxyalkanoates/*metabolism ; Sequence Alignment ; }, abstract = {BACKGROUND: Halophilic bacteria have shown their significance in industrial production of polyhydroxyalkanoates (PHA) and are gaining more attention for genetic engineering modification. Yet, little information on the genomics and PHA related genes from halophilic bacteria have been disclosed so far.<br><br>RESULTS: The draft genome of moderately halophilic bacterium, Halomonas sp. TD01, a strain of great potential for industrial production of short-chain-length polyhydroxyalkanoates (PHA), was analyzed through computational methods to reveal the osmoregulation mechanism and the evolutionary relationship of the enzymes relevant to PHA and ectoine syntheses. Genes involved in the metabolism of PHA and osmolytes were annotated and studied in silico. Although PHA synthase, depolymerase, regulator/repressor and phasin were all involved in PHA metabolic pathways, they demonstrated different horizontal gene transfer (HGT) events between the genomes of different strains. In contrast, co-occurrence of ectoine genes in the same genome was more frequently observed, and ectoine genes were more likely under coincidental horizontal gene transfer than PHA related genes. In addition, the adjacent organization of the homologues of PHA synthase phaC1 and PHA granule binding protein phaP was conserved in the strain TD01, which was also observed in some halophiles and non-halophiles exclusively from &#x3b3;-proteobacteria. In contrast to haloarchaea, the proteome of Halomonas sp. TD01 did not show obvious inclination towards acidity relative to non-halophilic Escherichia coli MG1655, which signified that Halomonas sp. TD01 preferred the accumulation of organic osmolytes to ions in order to balance the intracellular osmotic pressure with the environment.<br><br>CONCLUSIONS: The accessibility of genome information would facilitate research on the genetic engineering of halophilic bacteria including Halomonas sp. TD01.}, }
@article {pmid22038968, year = {2011}, author = {Lin, Y and Hao, X and Johnstone, L and Miller, SJ and Baltrus, DA and Rensing, C and Wei, G}, title = {Draft genome of Streptomyces zinciresistens K42, a novel metal-resistant species isolated from copper-zinc mine tailings.}, journal = {Journal of bacteriology}, volume = {193}, number = {22}, pages = {6408-6409}, pmid = {22038968}, issn = {1098-5530}, mesh = {Base Sequence ; Copper/*metabolism ; *Genome, Bacterial ; Mining ; Molecular Sequence Data ; Streptomyces/*genetics/isolation &amp; purification/*metabolism ; Zinc/*metabolism ; }, abstract = {A draft genome sequence of Streptomyces zinciresistens K42, a novel Streptomyces species displaying a high level of resistance to zinc and cadmium, is presented here. The genome contains a large number of genes encoding proteins predicted to be involved in conferring metal resistance. Many of these genes appear to have been acquired through horizontal gene transfer.}, }
@article {pmid22037611, year = {2012}, author = {Wu, B and Gong, J and Liu, L and Li, T and Wei, T and Bai, Z}, title = {Evolution of prokaryotic homologues of the eukaryotic SEFIR protein domain.}, journal = {Gene}, volume = {492}, number = {1}, pages = {160-166}, doi = {10.1016/j.gene.2011.10.033}, pmid = {22037611}, issn = {1879-0038}, mesh = {Amino Acid Sequence ; Animals ; Cluster Analysis ; Eukaryota/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Phylogeny ; *Prokaryotic Cells ; Protein Structure, Tertiary/genetics ; Receptors, Interleukin-17/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {SEF/IL17 receptor (SEFIR) domains are mainly found in IL17 receptors (IL17Rs) and their adaptor proteins CIKS (connection to IKK and SAPK/JNK), which exert a host defense role in numbers of infectious diseases and promote inflammatory pathology in autoimmunity. Exploring the evolutionary pathway of SEFIR domains will provide further insight into their functions. Here, we have identified 84 SEFIR domain-containing proteins from more than 1400 prokaryotic genomes. As most SEFIR domain-containing bacterial genomes possess a single SEFIR encoding gene and the SEFIR protein domain forms homodimeric complexes like the Toll/IL1 receptor (TIR) domain, the single bacterial SEFIR proteins may receive binding partners from other organisms. Through comparative and phylogenetic sequence analyses, we show that bacterial SEFIR domain is more similar to that of vertebrate CIKS than IL17R, and it possibly emerges via a lateral gene transfer (LGT) from animals. In addition, our secondary and three-dimensional structural predictions of SEFIR domains reveal that human and pathogenic bacterial SEFIR domains share similar structural and electrostatic features. Our findings provide important clues for further experimental researches on determining the functions of SEFIR proteins in pathogenic prokaryotes.}, }
@article {pmid22037308, year = {2011}, author = {Smillie, CS and Smith, MB and Friedman, J and Cordero, OX and David, LA and Alm, EJ}, title = {Ecology drives a global network of gene exchange connecting the human microbiome.}, journal = {Nature}, volume = {480}, number = {7376}, pages = {241-244}, pmid = {22037308}, issn = {1476-4687}, support = {T32 GM087237/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*genetics/isolation &amp; purification/metabolism/pathogenicity ; *Biological Evolution ; Drug Resistance, Microbial/genetics ; *Ecosystem ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/genetics ; Genome, Bacterial/genetics ; Humans ; Metagenome/*genetics ; Organ Specificity ; Phylogeny ; Phylogeography ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Horizontal gene transfer (HGT), the acquisition of genetic material from non-parental lineages, is known to be important in bacterial evolution. In particular, HGT provides rapid access to genetic innovations, allowing traits such as virulence, antibiotic resistance and xenobiotic metabolism to spread through the human microbiome. Recent anecdotal studies providing snapshots of active gene flow on the human body have highlighted the need to determine the frequency of such recent transfers and the forces that govern these events. Here we report the discovery and characterization of a vast, human-associated network of gene exchange, large enough to directly compare the principal forces shaping HGT. We show that this network of 10,770 unique, recently transferred (more than 99% nucleotide identity) genes found in 2,235 full bacterial genomes, is shaped principally by ecology rather than geography or phylogeny, with most gene exchange occurring between isolates from ecologically similar, but geographically separated, environments. For example, we observe 25-fold more HGT between human-associated bacteria than among ecologically diverse non-human isolates (P = 3.0 × 10(-270)). We show that within the human microbiome this ecological architecture continues across multiple spatial scales, functional classes and ecological niches with transfer further enriched among bacteria that inhabit the same body site, have the same oxygen tolerance or have the same ability to cause disease. This structure offers a window into the molecular traits that define ecological niches, insight that we use to uncover sources of antibiotic resistance and identify genes associated with the pathology of meningitis and other diseases.}, }
@article {pmid22035052, year = {2011}, author = {Skippington, E and Ragan, MA}, title = {Within-species lateral genetic transfer and the evolution of transcriptional regulation in Escherichia coli and Shigella.}, journal = {BMC genomics}, volume = {12}, number = {}, pages = {532}, pmid = {22035052}, issn = {1471-2164}, mesh = {*Biological Evolution ; Escherichia coli/classification/*genetics ; Gene Regulatory Networks ; *Gene Transfer, Horizontal ; Phylogeny ; Shigella/classification/*genetics ; Transcription Factors/genetics ; }, abstract = {BACKGROUND: Changes in transcriptional regulation underlie many of the phenotypic differences observed within and between species of bacteria. Lateral genetic transfer (LGT) can significantly impact the transcription factor (TF) genes which drive these transcriptional changes. Although much emphasis has been placed on LGT of intact genes, the units of transfer and recombination do not necessarily correspond to regions delineated by exact gene boundaries. Here we apply phylogenetic and network-based methods to investigate the relationship between units of lateral transfer and recombination within the Escherichia coli - Shigella clade and the topological properties of genes in the E. coli transcriptional regulatory network (TRN).<br><br>RESULTS: We carried out a systematic phylogenetic study of genetic transfer among 5282 sets of putatively orthologous genes from 27 strains belonging to the E. coli - Shigella clade. We then used these results to examine the evolutionary histories of TF genes, as well as the transcriptional regulation of lateral genes. We found evidence of LGT in 2655 (50.3%) gene sets: 678 (12.8%) show evidence of recombination breakpoints within the gene boundaries. Thus, within- and whole- gene lateral transfer is widespread among strains of E. coli and Shigella. We found that unlike global regulators, which have mostly evolved vertically, neighbour regulators (genes which regulate adjacent genes on the chromosome) have frequently been subject to transfer within the E. coli - Shigella clade. At least 56 (62%) of the 90 neighbour regulator gene sets examined show evidence of LGT, 19 (34%) of which have internal recombination breakpoints. Neighbour regulators show no evidence of co-transfer with their nearby target genes. Rather, the frequency of recombination breakpoints, and conflicting evolutionary histories among neighbour regulators and their target genes, suggest that the genomic regions encoding these genes have been constructed through successive layering of LGT events within the clade. We find no difference in the relative complexity of regulation (i.e. the number of regulators) of lateral versus vertical genes.<br><br>CONCLUSIONS: Neighbour regulators show higher frequencies of transfer than other types of regulatory genes. This implicates the topological properties of regulatory genes in the TRN, and their physical proximity to targets on the chromosome, as contributing to successful LGT. The prevalence of recombination breakpoints within regulatory and target gene sets indicates that within-gene transfer has had a significant cumulative effect on the evolution of regulatory interactions in E. coli and Shigella.}, }
@article {pmid22034222, year = {2011}, author = {Elliott, KT and Neidle, EL}, title = {Acinetobacter baylyi ADP1: transforming the choice of model organism.}, journal = {IUBMB life}, volume = {63}, number = {12}, pages = {1075-1080}, doi = {10.1002/iub.530}, pmid = {22034222}, issn = {1521-6551}, mesh = {Acinetobacter/*genetics ; Conjugation, Genetic/genetics ; Gene Amplification/*genetics ; Gene Duplication/*genetics ; Gene Transfer, Horizontal/genetics ; Genetic Engineering/*methods ; Metabolic Engineering/*methods ; *Models, Genetic ; Mutation/genetics ; Transformation, Bacterial/genetics ; Transformation, Genetic/*genetics ; }, abstract = {For more than 25 years, Acinetobacter baylyi ADP1 has been used in molecular biology studies that address a broad range of questions. Recently, the rapid accumulation of data from DNA sequencing, gene expression, protein structure, and other high-throughput methodology has increased the ability to tackle complex topics using sophisticated approaches to metabolic and genetic engineering. While the genetic malleability of ADP1 makes it an ideal organism for such investigations, A. baylyi ADP1 has yet to become a common choice for bacterial studies. This review describes examples of ADP1-based studies that exploit its highly efficient system for natural transformation and chromosomal incorporation of exogenous DNA. These studies focus on a wide array of problems, including gene duplication and amplification, horizontal gene transfer, bioreporters, and metabolic reconstruction. Interesting results in these diverse areas highlight the utility of using A. baylyi in laboratory and industrial settings.}, }
@article {pmid22034163, year = {2012}, author = {Singh, R and Rajpara, N and Tak, J and Patel, A and Mohanty, P and Vinothkumar, K and Chowdhury, G and Ramamurthy, T and Ghosh, A and Bhardwaj, AK}, title = {Clinical isolates of Vibrio fluvialis from Kolkata, India, obtained during 2006: plasmids, the qnr gene and a mutation in gyrase A as mechanisms of multidrug resistance.}, journal = {Journal of medical microbiology}, volume = {61}, number = {Pt 3}, pages = {369-374}, doi = {10.1099/jmm.0.037226-0}, pmid = {22034163}, issn = {1473-5644}, mesh = {Anti-Bacterial Agents/pharmacology ; Cholera/microbiology ; Conjugation, Genetic ; DNA Gyrase/*genetics ; DNA, Bacterial/chemistry/genetics ; *Drug Resistance, Multiple, Bacterial ; Gene Transfer, Horizontal ; Humans ; India ; Microbial Sensitivity Tests ; Molecular Sequence Data ; *Mutation, Missense ; Plasmids/*analysis ; Quinolones/pharmacology ; Sequence Analysis, DNA ; Vibrio/*genetics/*isolation &amp; purification ; }, abstract = {Resistance profiles and their correlation with genetic factors were investigated in 12 isolates of Vibrio fluvialis obtained from hospitalized patients in Kolkata, India, in 2006. All the strains displayed drug resistance with varying antibiograms. However, resistance to ampicillin and neomycin was common to all of them. Three isolates harboured plasmids carrying drug-resistance genes that could be transferred to recipient strains by conjugation and transformation. PCR results indicated the absence of class 1 integrons and SXT elements in these isolates. A mutation in gyrase A (serine 83→isoleucine) and the presence of the qnrVC-like [corrected] gene were found to contribute towards quinolone resistance. In the 12 isolates, the qnrVC-like [corrected] gene was associated only with two plasmid-bearing isolates, L10734 and L9978, which displayed resistance to quinolones. The gene was transferable during transformation and conjugation, indicating that it was plasmid-borne. Taken together, these data indicate that plasmids, the qnrVC-like [corrected] gene and a mutation in gyrase A were responsible for the observed drug resistance in these strains. To the best of our knowledge, this is the first report of the presence of the qnrVC-like [corrected] allele in V. fluvialis isolates from India.}, }
@article {pmid22027104, year = {2012}, author = {Zhan, Y and Yan, Y and Zhang, W and Chen, M and Lu, W and Ping, S and Lin, M}, title = {Comparative analysis of the complete genome of an Acinetobacter calcoaceticus strain adapted to a phenol-polluted environment.}, journal = {Research in microbiology}, volume = {163}, number = {1}, pages = {36-43}, doi = {10.1016/j.resmic.2011.10.006}, pmid = {22027104}, issn = {1769-7123}, mesh = {Acinetobacter/classification/*genetics ; Acinetobacter baumannii/classification/*genetics/isolation &amp; purification ; Acinetobacter calcoaceticus/classification/*genetics/isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics/metabolism ; *Genome, Bacterial ; Molecular Sequence Data ; Phenol/*metabolism ; Phylogeny ; Sewage/microbiology ; Water Pollutants, Chemical/*metabolism ; }, abstract = {The complete genome sequence of Acinetobacter calcoaceticus PHEA-2, a non-pathogenic phenol-degrading bacterium previously isolated from industrial wastewater of an oil refinery in China, has been established. This is the first sequence of an A. calcoaceticus strain. We report here a comparative genomic analysis of PHEA-2 with two other Acinetobacter species having different lifestyles, Acinetobacter baumannii AYE, a pathogenic human-adapted strain, and Acinetobacter baylyi ADP1, a soil-living strain. For a long time, A. calcoaceticus could not be easily distinguished from A. baumannii strains. Indeed, whole-genome comparison revealed high synteny between A. calcoaceticus and A. baumannii genomes, but most genes for multiple drug resistance as well as those presumably involved in pathogenicity were not present in the PHEA-2 genome and phylogenetic analysis showed that A. calcoaceticus differed from A. baumannii antibiotic-susceptible strains. It also revealed that many genes associated with environmental adaptation were acquired by horizontal gene transfer, including an 8-kb phenol degradation gene cluster. A relatively higher proportion of transport-related proteins were found in PHEA-2 than in ADP1 and AYE. Overall, these findings highlight the remarkable capacity of A. calcoaceticus PHEA-2 to effectively adapt to a phenol-polluted wastewater environment.}, }
@article {pmid22026421, year = {2012}, author = {Gonçalves, LG and Borges, N and Serra, F and Fernandes, PL and Dopazo, H and Santos, H}, title = {Evolution of the biosynthesis of di-myo-inositol phosphate, a marker of adaptation to hot marine environments.}, journal = {Environmental microbiology}, volume = {14}, number = {3}, pages = {691-701}, doi = {10.1111/j.1462-2920.2011.02621.x}, pmid = {22026421}, issn = {1462-2920}, mesh = {Acclimatization/*physiology ; Archaea/genetics/*metabolism/physiology ; Bacteria/genetics/metabolism ; Biomarkers/metabolism ; Environment ; Gene Transfer, Horizontal ; Genome ; *Hot Temperature ; Inositol Phosphates/*biosynthesis ; Nucleotidyltransferases/biosynthesis/metabolism ; Phylogeny ; Seawater/chemistry/microbiology ; }, abstract = {The synthesis of di-myo-inositol phosphate (DIP), a common compatible solute in hyperthermophiles, involves the consecutive actions of inositol-1-phosphate cytidylyltransferase (IPCT) and di-myo-inositol phosphate phosphate synthase (DIPPS). In most cases, both activities are present in a single gene product, but separate genes are also found in a few organisms. Genes for IPCT and DIPPS were found in the genomes of 33 organisms, all with thermophilic/hyperthermophilic lifestyles. Phylogeny of IPCT/DIPPS revealed an incongruent topology with 16S RNA phylogeny, thus suggesting horizontal gene transfer. The phylogenetic tree of the DIPPS domain was rooted by using phosphatidylinositol phosphate synthase sequences as out-group. The root locates at the separation of genomes with fused and split genes. We propose that the gene encoding DIPPS was recruited from the biosynthesis of phosphatidylinositol. The last DIP-synthesizing ancestor harboured separated genes for IPCT and DIPPS and this architecture was maintained in a crenarchaeal lineage, and transferred by horizontal gene transfer to hyperthermophilic marine Thermotoga species. It is plausible that the driving force for the assembly of those two genes in the early ancestor is related to the acquired advantage of DIP producers to cope with high temperature. This work corroborates the view that Archaea were the first hyperthermophilic organisms.}, }
@article {pmid22025737, year = {2011}, author = {Rüdinger, M and Fritz-Laylin, L and Polsakiewicz, M and Knoop, V}, title = {Plant-type mitochondrial RNA editing in the protist Naegleria gruberi.}, journal = {RNA (New York, N.Y.)}, volume = {17}, number = {12}, pages = {2058-2062}, pmid = {22025737}, issn = {1469-9001}, mesh = {Biological Evolution ; Genome, Mitochondrial ; Naegleria/*genetics/metabolism ; Protozoan Proteins/genetics ; RNA/*metabolism ; *RNA Editing ; RNA, Mitochondrial ; }, abstract = {RNA editing converts hundreds of cytidines into uridines in plant mitochondrial and chloroplast transcripts. Recognition of the RNA editing sites in the organelle transcriptomes requires numerous specific, nuclear-encoded RNA-binding pentatricopeptide repeat (PPR) proteins with characteristic carboxy-terminal protein domain extensions (E/DYW) previously thought to be unique to plants. However, a small gene family of such plant-like PPR proteins of the DYW-type was recently discovered in the genome of the protist Naegleria gruberi. This raised the possibility that plant-like RNA editing may occur in this amoeboflagellate. Accordingly, we have investigated the mitochondrial transcriptome of Naegleria gruberi and here report on identification of two sites of C-to-U RNA editing in the cox1 gene and in the cox3 gene, both of which reconstitute amino acid codon identities highly conserved in evolution. An estimated 1.5 billion years of evolution separate the heterolobosean protist Naegleria from the plant lineage. The new findings either suggest horizontal gene transfer of RNA editing factors or that plant-type RNA editing is evolutionarily much more ancestral than previously thought and yet to be discovered in many other ancient eukaryotic lineages.}, }
@article {pmid22024628, year = {2011}, author = {Merhej, V and Notredame, C and Royer-Carenzi, M and Pontarotti, P and Raoult, D}, title = {The rhizome of life: the sympatric Rickettsia felis paradigm demonstrates the random transfer of DNA sequences.}, journal = {Molecular biology and evolution}, volume = {28}, number = {11}, pages = {3213-3223}, doi = {10.1093/molbev/msr239}, pmid = {22024628}, issn = {1537-1719}, mesh = {Cluster Analysis ; Computational Biology ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genomics/methods ; Models, Genetic ; Open Reading Frames/genetics ; *Phylogeny ; Recombination, Genetic/genetics ; Rickettsia felis/*genetics ; }, abstract = {The intracellular flea symbiont, Rickettsia felis, may meet other organisms intracellularly such as R. typhi. We used a single-gene phylogenetic approach of the 1375 R. felis genes to look for horizontal transfers that occurred as a result of the bacterial promiscuity with other organisms. Our results showed that besides genes that are linked to the Spotted Fever Group, 165 genes have a different history and are linked to other Rickettsia such as R. bellii (107 genes), R. typhi (15 genes), or to other bacteria such as Legionella sp. and Francisella sp. or to eukaryotes. Among these genes, we identified 73 individual genes and 34 spatial clusters containing 2-4 adjacent genes, a total of 79 genes, with evidence of en bloc transfer. We described 13 chimeric genes resulting from gene recombination with sympatric R. typhi. The transferred DNA sequences present different sizes and functions, suggesting that the horizontal transfer in R. felis is random and neutral within its specific host. Our study shows that the strict intracellular bacteria R. felis exhibits a mosaic genome. We therefore developed a new representation for the evolutionary history of R. felis showing its different putative ancestors in the form of a rhizome.}, }
@article {pmid22023596, year = {2011}, author = {Leclercq, S and Cordaux, R}, title = {Do phages efficiently shuttle transposable elements among prokaryotes?.}, journal = {Evolution; international journal of organic evolution}, volume = {65}, number = {11}, pages = {3327-3331}, doi = {10.1111/j.1558-5646.2011.01395.x}, pmid = {22023596}, issn = {1558-5646}, mesh = {Bacteriophages/*genetics ; DNA Transposable Elements/*genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Essential/genetics ; Plasmids/*genetics ; Statistics, Nonparametric ; Transposases/genetics ; }, abstract = {The distribution, dynamics, and evolution of insertion sequences (IS), the most frequent class of prokaryotic transposable elements, are conditioned by their ability to horizontally transfer between cells. IS horizontal transfer (HT) requires shuttling by other mobile genetic elements. It is widely assumed in the literature that these vectors are phages and plasmids. By examining the relative abundance of IS in 454 plasmid and 446 phage genomes, we found that IS are very frequent in plasmids but, surprisingly, very rare in phages. Our results indicate that IS rarity in phages reflects very strong and efficient postinsertional purifying selection, mainly caused by a higher density of deleterious insertion sites in phages compared to plasmids. As they do not tolerate IS insertions, we conclude that phages may be rather poor vectors of IS HT in prokaryotes, in sharp contrast with the conventional view.}, }
@article {pmid22023392, year = {2011}, author = {Berry, TM and Christie, PJ}, title = {Caught in the act: the dialogue between bacteriophage R17 and the type IV secretion machine of plasmid R1.}, journal = {Molecular microbiology}, volume = {82}, number = {5}, pages = {1039-1043}, pmid = {22023392}, issn = {1365-2958}, support = {R01 GM048746/GM/NIGMS NIH HHS/United States ; R01 GM048746-19/GM/NIGMS NIH HHS/United States ; GM48746/GM/NIGMS NIH HHS/United States ; }, mesh = {DNA Helicases/*metabolism ; Escherichia coli/*metabolism/*virology ; Escherichia coli Proteins/*metabolism ; *Gene Transfer, Horizontal ; Levivirus/*physiology ; Plasmids/*metabolism ; *Virus Internalization ; }, abstract = {Bacteria communicate with each other through contact-independent and -dependent signalling mechanisms. Sensory perception of both types of signals is needed for conjugative transfer of mobile DNA elements via type IV secretion systems (T4SSs) to bacterial or eukaryotic target cells. While the regulatory circuitries coupling extracellular quorum and environmental signals to transcription of T4SS genes are increasingly understood, it remains fundamentally unknown how a potential recipient cell stimulates donor conjugative DNA transfer upon contact. In this issue, Lang et al. (2011) report use of the male-specific bacteriophage R17, a phage that binds conjugative pili elaborated by IncF plasmid R1, to define requirements for phage-contact-mediated T4SS activation and phage penetration. They report that R17 penetrates only through T4SS channels engaged for delivery of their plasmid cargo to recipient cells. Engagement requires docking of catalytically active relaxase TraI bound at oriT with the TraD substrate receptor (also termed the T4CP). The data, together with recent ultrastructural and biochemical findings, support an intriguing new model that the T4CP cumulatively senses an intracellular signal (substrate docking) and an extracellular signal (pilus bound by phage or a recipient cell) to co-ordinate a late stage morphogenetic or gating reaction that enables bidirectional transmission of nucleoprotein substrates through the T4SS.}, }
@article {pmid22022440, year = {2011}, author = {Ausec, L and Zakrzewski, M and Goesmann, A and Schlüter, A and Mandic-Mulec, I}, title = {Bioinformatic analysis reveals high diversity of bacterial genes for laccase-like enzymes.}, journal = {PloS one}, volume = {6}, number = {10}, pages = {e25724}, pmid = {22022440}, issn = {1932-6203}, mesh = {Bacteria/*enzymology/*genetics ; Base Sequence ; Computational Biology/*methods ; Data Collection ; Databases, Genetic ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/*genetics ; *Genetic Variation ; Laccase/chemistry/classification/*genetics ; Markov Chains ; Metagenomics ; Oceans and Seas ; Protein Structure, Tertiary ; }, abstract = {Fungal laccases have been used in various fields ranging from processes in wood and paper industries to environmental applications. Although a few bacterial laccases have been characterized in recent years, prokaryotes have largely been neglected as a source of novel enzymes, in part due to the lack of knowledge about the diversity and distribution of laccases within Bacteria. In this work genes for laccase-like enzymes were searched for in over 2,200 complete and draft bacterial genomes and four metagenomic datasets, using the custom profile Hidden Markov Models for two- and three-domain laccases. More than 1,200 putative genes for laccase-like enzymes were retrieved from chromosomes and plasmids of diverse bacteria. In 76% of the genes, signal peptides were predicted, indicating that these bacterial laccases may be exported from the cytoplasm, which contrasts with the current belief. Moreover, several examples of putatively horizontally transferred bacterial laccase genes were described. Many metagenomic sequences encoding fragments of laccase-like enzymes could not be phylogenetically assigned, indicating considerable novelty. Laccase-like genes were also found in anaerobic bacteria, autotrophs and alkaliphiles, thus opening new hypotheses regarding their ecological functions. Bacteria identified as carrying laccase genes represent potential sources for future biotechnological applications.}, }
@article {pmid22022434, year = {2011}, author = {Bezuidt, O and Pierneef, R and Mncube, K and Lima-Mendez, G and Reva, ON}, title = {Mainstreams of horizontal gene exchange in enterobacteria: consideration of the outbreak of enterohemorrhagic E. coli O104:H4 in Germany in 2011.}, journal = {PloS one}, volume = {6}, number = {10}, pages = {e25702}, pmid = {22022434}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; Cattle ; Cluster Analysis ; CpG Islands/genetics ; *Disease Outbreaks ; Enterohemorrhagic Escherichia coli/*genetics ; Escherichia coli Infections/*epidemiology/genetics/*microbiology ; Gene Transfer, Horizontal/*genetics ; Germany/epidemiology ; Humans ; Molecular Sequence Annotation ; Plasmids/genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {BACKGROUND: Escherichia coli O104:H4 caused a severe outbreak in Europe in 2011. The strain TY-2482 sequenced from this outbreak allowed the discovery of its closest relatives but failed to resolve ways in which it originated and evolved. On account of the previous statement, may we expect similar upcoming outbreaks to occur recurrently or spontaneously in the future? The inability to answer these questions shows limitations of the current comparative and evolutionary genomics methods.<br><br>PRINCIPAL FINDINGS: The study revealed oscillations of gene exchange in enterobacteria, which originated from marine &#x3b3;-Proteobacteria. These mobile genetic elements have become recombination hotspots and effective 'vehicles' ensuring a wide distribution of successful combinations of fitness and virulence genes among enterobacteria. Two remarkable peculiarities of the strain TY-2482 and its relatives were observed: i) retaining the genetic primitiveness by these strains as they somehow avoided the main fluxes of horizontal gene transfer which effectively penetrated other enetrobacteria; ii) acquisition of antibiotic resistance genes in a plasmid genomic island of &#x3b2;-Proteobacteria origin which ontologically is unrelated to the predominant genomic islands of enterobacteria.<br><br>CONCLUSIONS: Oscillations of horizontal gene exchange activity were reported which result from a counterbalance between the acquired resistance of bacteria towards existing mobile vectors and the generation of new vectors in the environmental microflora. We hypothesized that TY-2482 may originate from a genetically primitive lineage of E. coli that has evolved in confined geographical areas and brought by human migration or cattle trade onto an intersection of several independent streams of horizontal gene exchange. Development of a system for monitoring the new and most active gene exchange events was proposed.}, }
@article {pmid22020507, year = {2012}, author = {Xue, H and Xu, Y and Boucher, Y and Polz, MF}, title = {High frequency of a novel filamentous phage, VCY φ, within an environmental Vibrio cholerae population.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {1}, pages = {28-33}, pmid = {22020507}, issn = {1098-5336}, mesh = {Base Sequence ; DNA, Bacterial/isolation &amp; purification ; DNA, Viral/isolation &amp; purification ; Genome, Viral ; Inovirus/genetics/*isolation &amp; purification/physiology ; Molecular Sequence Data ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; Ponds/*microbiology ; Vibrio cholerae/*virology ; *Water Microbiology ; }, abstract = {Environmental Vibrio cholerae strains isolated from a coastal brackish pond (Oyster Pond, Woods Hole, MA) carried a novel filamentous phage, VCY, which can exist as a host genome integrative form (IF) and a plasmid-like replicative form (RF). Outside the cell, the phage displays a morphology typical of Inovirus, with filamentous particles ∼1.8 μm in length and 7 nm in width. Four independent RF isolates had identical genomes, except for 8 single nucleotide polymorphisms clustered in two regions. The overall genome size is 7,103 bp with 11 putative open reading frames organized into three functional modules (replication, structure and assembly, and regulation). VCY shares sequence similarity with other filamentous phages (including cholera disease-associated CTX) in a highly mosaic manner, indicating evolution by horizontal gene transfer and recombination. VCY integrates in the vicinity of the putative translation initiation factor Sui1 in chromosome II of V. cholerae. A screen of 531 closely related host isolates showed that ∼40% harbored phages, with 27% and 13% carrying the IF and RF, respectively. The relative frequencies of the RF and IF differed among strains isolated from the pond or lagoon of Oyster Pond, suggesting that the host habitat influences intracellular phage biology. The overall high prevalence within the host population shows that filamentous phages can be an important component of the environmental biology of V. cholerae.}, }
@article {pmid22017974, year = {2011}, author = {Leister, D and Kleine, T}, title = {Role of intercompartmental DNA transfer in producing genetic diversity.}, journal = {International review of cell and molecular biology}, volume = {291}, number = {}, pages = {73-114}, doi = {10.1016/B978-0-12-386035-4.00003-3}, pmid = {22017974}, issn = {1937-6448}, mesh = {Animals ; Base Sequence ; Biological Evolution ; Cell Nucleus/*genetics/metabolism ; DNA/genetics/*metabolism ; *Gene Transfer, Horizontal ; *Genetic Variation ; Genome ; Humans ; Mitochondria/*genetics/metabolism ; Plastids/*genetics/metabolism ; RNA, Transfer/genetics/metabolism ; Symbiosis/genetics ; Nicotiana/genetics ; }, abstract = {In eukaryotic cells, genes are found in three compartments-the nucleus, mitochondria, and plastids-and extensive gene transfer has occurred between them. Most organellar genes in the nucleus migrated there long ago, but transfer is ongoing and ubiquitous. It now generates mostly noncoding nuclear DNA, can also disrupt gene functions, and reshape genes by adding novel exons. Plastid or nuclear sequences have also contributed to the formation of mitochondrial tRNA genes. It is now clear that organelle-to-nucleus DNA transfer involves the escape of DNA molecules from the organelles at times of stress or at certain developmental stages, and their subsequent incorporation at sites of double-stranded breaks in nuclear DNA by nonhomologous recombination. Intercompartmental DNA transfer thus appears to be an inescapable phenomenon that has had a broad impact on eukaryotic evolution, affecting DNA repair, gene and genome evolution, and redirecting proteins to different target compartments.}, }
@article {pmid22017109, year = {2011}, author = {Eugenia Marquina, M and Enrique González, N and Castro, Y}, title = {[Phenotypic and genotypic characterization of twelve rhizobial isolates from different regions of Venezuela].}, journal = {Revista de biologia tropical}, volume = {59}, number = {3}, pages = {1017-1036}, pmid = {22017109}, issn = {0034-7744}, mesh = {Genotype ; Phenotype ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; Rhizobium/classification/*genetics/isolation &amp; purification ; Sensitivity and Specificity ; *Soil Microbiology ; Venezuela ; }, abstract = {Rhizobial taxonomy and systematics have progressed substantially, nevertheless, few studies have been developed on venezuelan species. This study evaluated the phenotypic and genetic variation between 12 venezuelan indigenous rhizobial isolates and 10 international referential strains, by phenotypical traits and DNA molecular markers. In this regard, a PCR-RFLP of the 16S rDNA gene, the presence of large plasmids, metabolic assays in solid media, salinity resistance, pH and temperature growth conditions, and intrinsic antibiotic resistance were assayed. In reference to the phenotypic attributes, we recognized three main groups: A group I, which comprised all the strains metabolizing between 67.5%-90% of the C and N sources. They were also acid-tolerant, as well as acid producers, capable of growing at 40 degrees C and in high salinity conditions (2-2.5% NaCl). With regard to the antibiotic sensitivity, this group was susceptible to a 30% of the antibiotic assayed. Strains belonging to Group II exhibited a lower salt tolerance (0.1-1.5%NaCl), as well as a lower acid tolerance, since they grew well at pH values equal or higher than 5.0. This group appeared to be resistant to all of the antibiotics assayed and only metabolized between 52.5%-82.5% of the C and N sources. Group III was represented by a single bacterial strain: it has a extremely low salt tolerance (0.1% NaCl). This strain grew at a pH equal or higher than 5.6, was susceptible to 50% of the antibiotics assayed and metabolized 72% of the C and N sources. On the basis of a PCR- RFLP of the 16S rDNA, three groups were also obtained. Members of the group A showed a close resemblance to Rhizobium tropici CIAT 899 and Sinorhizobium americanum CFN-EI 156, while Group B was closely related to Bradyrhizobium spp. Group C, was also represented by only one isolate. The Trebol isolate, was the only one strain able to form nodules and does not appear to be related to any of the referential rhizobial strains, suggesting a possible symbiotic horizontal gene transfer. Finally, in this work, there are evidences of a genetic diversity in the venezuelan rhizobial strains. A different geographical origin is perhaps an important factor affecting the diversity of the indigenous rhizobia in this study.}, }
@article {pmid22016852, year = {2011}, author = {Anderson, MT and Seifert, HS}, title = {Neisseria gonorrhoeae and humans perform an evolutionary LINE dance.}, journal = {Mobile genetic elements}, volume = {1}, number = {1}, pages = {85-87}, pmid = {22016852}, issn = {2159-2543}, support = {F32 AI080083/AI/NIAID NIH HHS/United States ; R01 AI044239/AI/NIAID NIH HHS/United States ; R37 AI033493/AI/NIAID NIH HHS/United States ; }, abstract = {Horizontal gene transfer is an important mechanism for generating genetic diversity. As the number of sequenced genomes continues to increase, so do the examples of horizontal genetic exchange between both related and divergent organisms. Here we discuss the recent finding that certain strains of the human pathogen Neisseria gonorrhoeae have incorporated a small fragment of human DNA sequence into their genomes. The horizontally acquired sequence exhibits 98-100% nucleotide identity to a 685 bp portion of the highly repetitive retrotransposable element L1 and its presence in the gonococcal genome has been confirmed by multiple molecular techniques. The possibility of similar L1 horizontal gene transfer events having occurred in other bacteria based on genomic sequence evidence is explored. Potential mechanisms of how N. gonorrhoeae was able to acquire and maintain this human sequence are also discussed in addition to the evolutionary implications of such an event.}, }
@article {pmid22016851, year = {2011}, author = {Miyazaki, R and van der Meer, JR}, title = {How can a dual oriT system contribute to efficient transfer of an integrative and conjugative element?.}, journal = {Mobile genetic elements}, volume = {1}, number = {1}, pages = {82-84}, pmid = {22016851}, issn = {2159-2543}, abstract = {Integrative and conjugative elements (ICEs) are particularly interesting model systems for horizontal gene transfer, because they normally reside in an integrated state in the host chromosome but can excise and self-transfer under particular conditions, typically requiring exquisite regulatory cascades. Despite important advances in our understanding of the transfer mechanisms of a number of ICE, many essential details are lacking. Recently we reported that ICEclc, a 103 kb ICE of Pseudomonas knackmussii B13, has two active origins of transfer (oriTs), which is very much unlike conjugative plasmids that usually employ a single oriT. We discuss here how this dual oriT system could function and how it actually could have presented an evolutionary advantage for ICEclc distribution.}, }
@article {pmid22016850, year = {2011}, author = {Velimirov, B and Hagemann, S}, title = {Mobilizable bacterial DNA packaged into membrane vesicles induces serial transduction.}, journal = {Mobile genetic elements}, volume = {1}, number = {1}, pages = {80-81}, pmid = {22016850}, issn = {2159-2543}, abstract = {Experiments where the amino acid deficient strain E. coli AB1157 was exposed to a particle fraction harvested from a marine oligotrophic environment, ranging in diameter size between 100-130 nm indicated evidence for horizontal gene transfer resulting in revertant cells with restoration of all genetic deficiencies with frequencies up to 1.94 × 10(-5). None of the markers was preferentially transferred indicating that the DNA-transfer is performed by generalized transduction. The highest transfer frequency obtained for single markers was 1.04 × 10(-2). All revertant strains were able to produce particles of comparable size that were again infectious, appearing at the beginning of the stationary phase. Ultra structural investigation showed a structural resemblance with membrane vesicles, however, Field Gel Electrophoresis indicated that the DNA content of some of the particles was 370 kbp; much higher than that of the so far known previously described membrane vesicles providing evidence of a new mechanism for horizontal gene transfer.}, }
@article {pmid22016848, year = {2011}, author = {Tuller, T}, title = {Codon bias, tRNA pools and horizontal gene transfer.}, journal = {Mobile genetic elements}, volume = {1}, number = {1}, pages = {75-77}, pmid = {22016848}, issn = {2159-2543}, abstract = {Horizontal Gene Transfer (HGT) is a major force in bacterial evolution. Bacteria are under a strong selection to optimize their growth rate by improving features related to their codon usage. In a recent study we have shown that these two forces are coupled: (1) the codon bias of transferred genes has a strong influence on the probability that they will become fixed in the new genome and (2) frequent HGTs may increase the similarity in the tRNA pools of organisms within the same community. Thus, methods for inferring HGTs probably underestimate their number.We believe that that the principles that affect microorganisms may also apply to mobile genetic elements (including plasmids, viruses and transposons).}, }
@article {pmid22016806, year = {2011}, author = {Zhang, T and Zhang, XX and Ye, L}, title = {Plasmid metagenome reveals high levels of antibiotic resistance genes and mobile genetic elements in activated sludge.}, journal = {PloS one}, volume = {6}, number = {10}, pages = {e26041}, pmid = {22016806}, issn = {1932-6203}, mesh = {Anti-Bacterial Agents/*pharmacology ; Databases, Genetic ; Drug Resistance, Bacterial/*genetics ; Genetic Variation/genetics ; High-Throughput Nucleotide Sequencing ; Integrons/genetics ; Interspersed Repetitive Sequences/*genetics ; Metagenome/drug effects/*genetics ; Plasmids/drug effects/*genetics ; Sewage/*microbiology ; Virulence Factors/genetics ; Waste Disposal, Fluid ; }, abstract = {The overuse or misuse of antibiotics has accelerated antibiotic resistance, creating a major challenge for the public health in the world. Sewage treatment plants (STPs) are considered as important reservoirs for antibiotic resistance genes (ARGs) and activated sludge characterized with high microbial density and diversity facilitates ARG horizontal gene transfer (HGT) via mobile genetic elements (MGEs). However, little is known regarding the pool of ARGs and MGEs in sludge microbiome. In this study, the transposon aided capture (TRACA) system was employed to isolate novel plasmids from activated sludge of one STP in Hong Kong, China. We also used Illumina Hiseq 2000 high-throughput sequencing and metagenomics analysis to investigate the plasmid metagenome. Two novel plasmids were acquired from the sludge microbiome by using TRACA system and one novel plasmid was identified through metagenomics analysis. Our results revealed high levels of various ARGs as well as MGEs for HGT, including integrons, transposons and plasmids. The application of the TRACA system to isolate novel plasmids from the environmental metagenome, coupled with subsequent high-throughput sequencing and metagenomic analysis, highlighted the prevalence of ARGs and MGEs in microbial community of STPs.}, }
@article {pmid22014084, year = {2011}, author = {Georgiades, K and Raoult, D}, title = {The rhizome of Reclinomonas americana, Homo sapiens, Pediculus humanus and Saccharomyces cerevisiae mitochondria.}, journal = {Biology direct}, volume = {6}, number = {}, pages = {55}, pmid = {22014084}, issn = {1745-6150}, mesh = {Alphaproteobacteria/genetics/metabolism ; Animals ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genes, Fungal ; *Genes, Mitochondrial ; Genome, Human ; Humans ; Mitochondria/*genetics/metabolism ; Pediculus/*genetics/metabolism ; Phylogeny ; Ribosomal Proteins/genetics/metabolism ; Ribosomes/genetics/metabolism ; Saccharomyces cerevisiae/*genetics/metabolism ; }, abstract = {BACKGROUND: Mitochondria are thought to have evolved from eubacteria-like endosymbionts; however, the origin of the mitochondrion remains a subject of debate. In this study, we investigated the phenomenon of chimerism in mitochondria to shed light on the origin of these organelles by determining which species played a role in their formation. We used the mitochondria of four distinct organisms, Reclinomonas americana, Homo sapiens, Saccharomyces cerevisiae and multichromosome Pediculus humanus, and attempted to identify the origin of each mitochondrial gene.<br><br>RESULTS: Our results suggest that the origin of mitochondrial genes is not limited to the Rickettsiales and that the creation of these genes did not occur in a single event, but through multiple successive events. Some of these events are very old and were followed by events that are more recent and occurred through the addition of elements originating from current species. The points in time that the elements were added and the parental species of each gene in the mitochondrial genome are different to the individual species. These data constitute strong evidence that mitochondria do not have a single common ancestor but likely have numerous ancestors, including proto-Rickettsiales, proto-Rhizobiales and proto-Alphaproteobacteria, as well as current alphaproteobacterial species. The analysis of the multichromosome P. humanus mitochondrion supports this mechanism.<br><br>CONCLUSIONS: The most plausible scenario of the origin of the mitochondrion is that ancestors of Rickettsiales and Rhizobiales merged in a proto-eukaryotic cell approximately one billion years ago. The fusion of the Rickettsiales and Rhizobiales cells was followed by gene loss, genomic rearrangements and the addition of alphaproteobacterial elements through ancient and more recent recombination events. Each gene of each of the four studied mitochondria has a different origin, while in some cases, multichromosomes may allow for enhanced gene exchange. Therefore, the tree of life is not sufficient to explain the chimeric structure of current genomes, and the theory of a single common ancestor and a top-down tree does not reflect our current state of knowledge. Mitochondrial evolution constitutes a rhizome, and it should be represented as such.}, }
@article {pmid22012657, year = {2012}, author = {Pires, R and Rolo, D and Morais, A and Brito-Avô, A and Johansson, C and Henriques-Normark, B and Gonçalo-Marques, J and Santos-Sanches, I}, title = {Description of macrolide-resistant and potential virulent clones of Streptococcus pyogenes causing asymptomatic colonization during 2000-2006 in the Lisbon area.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {31}, number = {5}, pages = {849-857}, pmid = {22012657}, issn = {1435-4373}, mesh = {Adolescent ; Adult ; Anti-Bacterial Agents/*pharmacology ; Antigens, Bacterial/genetics ; Bacterial Outer Membrane Proteins/genetics ; Carrier Proteins/genetics ; Carrier State/*epidemiology/microbiology ; Child ; Child, Preschool ; Cluster Analysis ; *Drug Resistance, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Genotype ; Humans ; Infant ; Macrolides/*pharmacology ; Molecular Epidemiology ; Multilocus Sequence Typing ; Oropharynx/microbiology ; Portugal/epidemiology ; Prevalence ; Streptococcal Infections/*epidemiology/microbiology ; Streptococcus pyogenes/classification/drug effects/*isolation &amp; purification/pathogenicity ; Virulence ; Virulence Factors/genetics ; }, abstract = {The asymptomatic oropharyngeal colonization rate by Streptococcus pyogenes was 10.7% in children (901 among 8,405 children 0-16 years old) and 3.3% in adults (37 among 1,126 households of children) in the Lisbon area during 2000-2006. Macrolide-resistant S. pyogenes from children (n = 149) was variable with time: 9.8-10.7% in 2000-2002, 28.1% in 2003, 19.6-2.7% in 2004-2005 and 14.6% in 2006. Eight lineages (97.3% of isolates) were identified based on at least 80% similarity of PFGE patterns, T types, emm types and multilocus sequence types (ST). The elevated frequency of macrolide resistance was associated with M phenotype lineages I (emm12/ST36) and V (emm4, emm75/ST39 and a novel emmstMrp6 type) and with one cMLS(B) lineage IV (emm28/ST52) known to be associated with upper respiratory tract and invasive infections. Significant associations (p < 0.05) between emm type/virulence genotype were found, such as emm1/speA (+) ssa (-), emm4/ssa (+) prtF1 (+), emm12/speA (-) ssa (-). The high prevalence (>20%) of speC, prtF1 or ssa was probably caused either by clonal dissemination (speC), or to horizontal gene transfer events (prtF1 and ssa). This report contributes to a better understanding of the molecular epidemiology and evolution of macrolide-resistant S. pyogenes causing symptom-free oropharyngeal colonization. These colonizing strains carry macrolide resistance and virulence genes capable of being transferred to other bacterial species sharing the same niche.}, }
@article {pmid22012399, year = {2011}, author = {Smeulders, MJ and Barends, TR and Pol, A and Scherer, A and Zandvoort, MH and Udvarhelyi, A and Khadem, AF and Menzel, A and Hermans, J and Shoeman, RL and Wessels, HJ and van den Heuvel, LP and Russ, L and Schlichting, I and Jetten, MS and Op den Camp, HJ}, title = {Evolution of a new enzyme for carbon disulphide conversion by an acidothermophilic archaeon.}, journal = {Nature}, volume = {478}, number = {7369}, pages = {412-416}, pmid = {22012399}, issn = {1476-4687}, mesh = {Acidianus/classification/*enzymology/genetics ; Carbon Disulfide/*metabolism ; Catalytic Domain ; Crystallography, X-Ray ; *Evolution, Molecular ; Hydrolases/chemistry/*genetics ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Phylogeny ; Protein Structure, Tertiary ; }, abstract = {Extremophilic organisms require specialized enzymes for their exotic metabolisms. Acid-loving thermophilic Archaea that live in the mudpots of volcanic solfataras obtain their energy from reduced sulphur compounds such as hydrogen sulphide (H(2)S) and carbon disulphide (CS(2)). The oxidation of these compounds into sulphuric acid creates the extremely acidic environment that characterizes solfataras. The hyperthermophilic Acidianus strain A1-3, which was isolated from the fumarolic, ancient sauna building at the Solfatara volcano (Naples, Italy), was shown to rapidly convert CS(2) into H(2)S and carbon dioxide (CO(2)), but nothing has been known about the modes of action and the evolution of the enzyme(s) involved. Here we describe the structure, the proposed mechanism and evolution of a CS(2) hydrolase from Acidianus A1-3. The enzyme monomer displays a typical β-carbonic anhydrase fold and active site, yet CO(2) is not one of its substrates. Owing to large carboxy- and amino-terminal arms, an unusual hexadecameric catenane oligomer has evolved. This structure results in the blocking of the entrance to the active site that is found in canonical β-carbonic anhydrases and the formation of a single 15-Å-long, highly hydrophobic tunnel that functions as a specificity filter. The tunnel determines the enzyme's substrate specificity for CS(2), which is hydrophobic. The transposon sequences that surround the gene encoding this CS(2) hydrolase point to horizontal gene transfer as a mechanism for its acquisition during evolution. Our results show how the ancient β-carbonic anhydrase, which is central to global carbon metabolism, was transformed by divergent evolution into a crucial enzyme in CS(2) metabolism.}, }
@article {pmid22006845, year = {2012}, author = {Tsai, HH and Shu, HW and Yang, CC and Chen, CW}, title = {Translesion-synthesis DNA polymerases participate in replication of the telomeres in Streptomyces.}, journal = {Nucleic acids research}, volume = {40}, number = {3}, pages = {1118-1130}, pmid = {22006845}, issn = {1362-4962}, mesh = {Actinobacteria/genetics ; Alkylation ; Chromosomes, Bacterial/chemistry ; Conjugation, Genetic ; DNA/metabolism ; DNA Damage ; DNA Polymerase III/classification/genetics/*physiology ; DNA Polymerase beta/classification/genetics/*physiology ; DNA Repair ; *DNA Replication ; Gene Deletion ; Gene Duplication ; Gene Transfer, Horizontal ; Phylogeny ; Plasmids/biosynthesis ; Streptomyces/*enzymology/*genetics ; Synteny ; Telomere/*metabolism ; Ultraviolet Rays ; }, abstract = {Linear chromosomes and linear plasmids of Streptomyces are capped by terminal proteins that are covalently bound to the 5'-ends of DNA. Replication is initiated from an internal origin, which leaves single-stranded gaps at the 3'-ends. These gaps are patched by terminal protein-primed DNA synthesis. Streptomyces contain five DNA polymerases: one DNA polymerase I (Pol I), two DNA polymerases III (Pol III) and two DNA polymerases IV (Pol IV). Of these, one Pol III, DnaE1, is essential for replication, and Pol I is not required for end patching. In this study, we found the two Pol IVs (DinB1 and DinB2) to be involved in end patching. dinB1 and dinB2 could not be co-deleted from wild-type strains containing a linear chromosome, but could be co-deleted from mutant strains containing a circular chromosome. The resulting ΔdinB1 ΔdinB2 mutants supported replication of circular but not linear plasmids, and exhibited increased ultraviolet sensitivity and ultraviolet-induced mutagenesis. In contrast, the second Pol III, DnaE2, was not required for replication, end patching, or ultraviolet resistance and mutagenesis. All five polymerase genes are relatively syntenous in the Streptomyces chromosomes, including a 4-bp overlap between dnaE2 and dinB2. Phylogenetic analysis showed that the dinB1-dinB2 duplication occurred in a common actinobacterial ancestor.}, }
@article {pmid22006824, year = {2011}, author = {White, JA}, title = {Caught in the act: rapid, symbiont-driven evolution: endosymbiont infection is a mechanism generating rapid evolution in some arthropods--but how widespread is the phenomenon?.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {33}, number = {11}, pages = {823-829}, doi = {10.1002/bies.201100095}, pmid = {22006824}, issn = {1521-1878}, mesh = {Animals ; Arthropods/genetics/*microbiology/physiology ; Bacteria/*growth &amp; development/pathogenicity ; *Biological Evolution ; Female ; Gene Transfer, Horizontal ; Male ; Phenotype ; Reproduction ; Selection, Genetic ; *Symbiosis ; }, abstract = {Facultative bacterial endosymbionts can transfer horizontally among lineages of their arthropod hosts, providing the recipient with a suite of traits that can lead to rapid evolutionary response, as has been recently demonstrated. But how common is symbiont-driven evolution? Evidence suggests that successful symbiont transfers are most likely within a species or among closely related species, although more distant transfers have occurred over evolutionary history. Symbiont-driven evolution need not be a function of a recent horizontal transfer, however. Many endosymbionts infect only a small proportion of a host population, but could quickly increase in frequency under favorable selection regimes. Some host species appear to accumulate a diversity of facultative endosymbionts, and it is among these species that symbiont-driven evolution should be most prevalent. It remains to be determined how frequently symbionts enable rapid evolutionary response by their hosts, but substantial ecological effects are a likely consequence whenever it does occur.}, }
@article {pmid22004549, year = {2012}, author = {Berg Miller, ME and Yeoman, CJ and Chia, N and Tringe, SG and Angly, FE and Edwards, RA and Flint, HJ and Lamed, R and Bayer, EA and White, BA}, title = {Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome.}, journal = {Environmental microbiology}, volume = {14}, number = {1}, pages = {207-227}, doi = {10.1111/j.1462-2920.2011.02593.x}, pmid = {22004549}, issn = {1462-2920}, mesh = {Animals ; Bacteria/genetics/isolation &amp; purification/*virology ; Bacteriophages/*genetics/isolation &amp; purification/metabolism ; Biodiversity ; Cattle ; Computational Biology ; DNA, Bacterial/genetics ; DNA, Viral/genetics ; Genotype ; Interspersed Repetitive Sequences ; Inverted Repeat Sequences ; Metabolome ; *Metagenome ; Rumen/*microbiology/*virology ; Sequence Analysis, DNA ; }, abstract = {Viruses are the most abundant biological entities on the planet and play an important role in balancing microbes within an ecosystem and facilitating horizontal gene transfer. Although bacteriophages are abundant in rumen environments, little is known about the types of viruses present or their interaction with the rumen microbiome. We undertook random pyrosequencing of virus-enriched metagenomes (viromes) isolated from bovine rumen fluid and analysed the resulting data using comparative metagenomics. A high level of diversity was observed with up to 28,000 different viral genotypes obtained from each environment. The majority (~78%) of sequences did not match any previously described virus. Prophages outnumbered lytic phages approximately 2:1 with the most abundant bacteriophage and prophage types being associated with members of the dominant rumen phyla (Firmicutes and Proteobacteria). Metabolic profiling based on SEED subsystems revealed an enrichment of sequences with putative functional roles in DNA and protein metabolism, but a surprisingly low proportion of sequences assigned to carbohydrate and amino acid metabolism. We expanded our analysis to include previously described metagenomic data and 14 reference genomes. Clustered regularly interspaced short palindromic repeats (CRISPR) were detected in most of the microbial genomes, suggesting previous interactions between viral and microbial communities.}, }
@article {pmid22004448, year = {2011}, author = {Acosta, JL and Eguiarte, LE and Santamaría, RI and Bustos, P and Vinuesa, P and Martínez-Romero, E and Dávila, G and González, V}, title = {Genomic lineages of Rhizobium etli revealed by the extent of nucleotide polymorphisms and low recombination.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {305}, pmid = {22004448}, issn = {1471-2148}, mesh = {DNA, Bacterial/*genetics ; Genetic Variation ; Genome, Bacterial ; Phylogeny ; *Polymorphism, Single Nucleotide ; *Recombination, Genetic ; Rhizobium etli/*genetics ; }, abstract = {BACKGROUND: Most of the DNA variations found in bacterial species are in the form of single nucleotide polymorphisms (SNPs), but there is some debate regarding how much of this variation comes from mutation versus recombination. The nitrogen-fixing symbiotic bacteria Rhizobium etli is highly variable in both genomic structure and gene content. However, no previous report has provided a detailed genomic analysis of this variation at nucleotide level or the role of recombination in generating diversity in this bacterium. Here, we compared draft genomic sequences versus complete genomic sequences to obtain reliable measures of genetic diversity and then estimated the role of recombination in the generation of genomic diversity among Rhizobium etli.<br><br>RESULTS: We identified high levels of DNA polymorphism in R. etli, and found that there was an average divergence of 4% to 6% among the tested strain pairs. DNA recombination events were estimated to affect 3% to 10% of the genomic sample analyzed. In most instances, the nucleotide diversity (&#x3c0;) was greater in DNA segments with recombinant events than in non-recombinant segments. However, this degree of recombination was not sufficiently large to disrupt the congruence of the phylogenetic trees, and further evaluation of recombination in strains quartets indicated that the recombination levels in this species are proportionally low.<br><br>CONCLUSION: Our data suggest that R. etli is a species composed of separated lineages with low homologous recombination among the strains. Horizontal gene transfer, particularly via the symbiotic plasmid characteristic of this species, seems to play an important role in diversity but the lineages maintain their evolutionary cohesiveness.}, }
@article {pmid22003042, year = {2012}, author = {Zhang, YM and Li, Y and Chen, WF and Wang, ET and Sui, XH and Li, QQ and Zhang, YZ and Zhou, YG and Chen, WX}, title = {Bradyrhizobium huanghuaihaiense sp. nov., an effective symbiotic bacterium isolated from soybean (Glycine max L.) nodules.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {62}, number = {Pt 8}, pages = {1951-1957}, doi = {10.1099/ijs.0.034546-0}, pmid = {22003042}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; Bradyrhizobium/*classification/genetics/isolation &amp; purification ; China ; DNA, Bacterial/genetics ; Fatty Acids/analysis ; Genes, Bacterial ; Molecular Sequence Data ; Phospholipids/analysis ; *Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Root Nodules, Plant/*microbiology ; Sequence Analysis, DNA ; Glycine max/*microbiology ; *Symbiosis ; }, abstract = {In a survey of the biodiversity and biogeography of rhizobia associated with soybean (Glycine max L.) in different sites of the Northern (Huang-Huai-Hai) Plain of China, ten strains were defined as representing a novel genomic species in the genus of Bradyrhizobium. They were distinguished from defined species in restriction fragment length polymorphism (RFLP) analysis of the 16S rRNA gene and the 16S-23S rRNA gene intergenic spacer (IGS). In BOX-PCR, these strains presented two patterns that shared 94% similarity, demonstrating that they were a homogenous group with limited diversity. In phylogenetic analyses of the 16S rRNA gene, IGS and housekeeping gene sequences, four representative strains formed a distant lineage within the genus Bradyrhizobium, which was consistent with the results of DNA-DNA hybridization. The strains of this novel group formed effective nodules with G. max, Glycine soja and Vigna unguiculata in cross-nodulation tests and harboured symbiotic genes (nodC and nifH) identical to those of reference strains of Bradyrhizobium japonicum, Bradyrhizobium liaoningense and 'Bradyrhizobium daqingense' originating from soybean, implying that the novel group may have obtained these symbiotic genes by lateral gene transfer. In analyses of cellular fatty acids and phenotypic features, some differences were found between the novel group and related Bradyrhizobium species, demonstrating that the novel group is distinct phenotypically from other Bradyrhizobium species. Based upon the data obtained, these strains are proposed to represent a novel species, Bradyrhizobium huanghuaihaiense sp. nov., with CCBAU 23303(T) (= LMG 26136(T) = CGMCC 1.10948(T) = HAMBI 3180(T)) as the type strain. The DNA G+C content of strain CCBAU 23303(T) is 61.5 mol% (T(m)).}, }
@article {pmid22003022, year = {2011}, author = {Creuzburg, K and Heeren, S and Lis, CM and Kranz, M and Hensel, M and Schmidt, H}, title = {Genetic background and mobility of variants of the gene nleA in attaching and effacing Escherichia coli.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {24}, pages = {8705-8713}, pmid = {22003022}, issn = {1098-5336}, mesh = {Adhesins, Bacterial/*metabolism ; DNA, Bacterial/chemistry/genetics ; Enteropathogenic Escherichia coli/*genetics/pathogenicity ; Escherichia coli Proteins/*genetics/*metabolism ; Gene Order ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Prophages/genetics ; Sequence Analysis, DNA ; Shiga-Toxigenic Escherichia coli/*genetics/pathogenicity ; Synteny ; Virulence Factors/*genetics ; }, abstract = {In this study, we characterized the genetic background of various nleA variants in 106 Shiga toxin-producing Escherichia coli (STEC) and enteropathogenic Escherichia coli (EPEC) strains. The flanking regions of eight nleA variants were analyzed by DNA sequencing and compared with the corresponding regions of five previously described NleA-encoding prophages. The analyzed nleA variants were all located downstream of the DNA region responsible for phage morphogenesis. In particular, the type III effector genes avrA, ospB, nleH, and nleG and IS elements were detected in the neighborhood of nleA. The structure of the eight analyzed regions flanking nleA primarily resembled the corresponding region of the NleA4795-encoding prophage BP-4795. Using PCR, the gene order flanking 13 nleA variants in strains of different serogroups was compared to the respective regions in reference strains. The analyses showed that strains which harbor prophages with conserved flanking regions of a particular nleA variant predominantly occurred, and IS elements were additionally detected in these regions. We were able to mobilize nleA by transduction in 20% of strains determined, which comprised in particular EPEC strains harboring an nleA variant, the gene encoding the protein known as "EspI-like." Plaque hybridization was used to identify phages that harbor the genes stx and nleA. However, only two strains harbored variant nleA4795 in the genome of an Stx1 prophage.}, }
@article {pmid22001176, year = {2012}, author = {Michael, GB and Kadlec, K and Sweeney, MT and Brzuszkiewicz, E and Liesegang, H and Daniel, R and Murray, RW and Watts, JL and Schwarz, S}, title = {ICEPmu1, an integrative conjugative element (ICE) of Pasteurella multocida: structure and transfer.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {67}, number = {1}, pages = {91-100}, doi = {10.1093/jac/dkr411}, pmid = {22001176}, issn = {1460-2091}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/*genetics ; Cattle ; Cattle Diseases/microbiology ; DNA, Bacterial/chemistry/genetics ; *Drug Resistance, Multiple, Bacterial ; Escherichia coli/genetics ; *Gene Transfer, Horizontal ; Mannheimia haemolytica/genetics ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Pasteurella Infections/microbiology/veterinary ; Pasteurella multocida/drug effects/*genetics/isolation &amp; purification ; Respiratory Tract Diseases/microbiology/veterinary ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Integrative and conjugative elements (ICEs) have not been detected in Pasteurella multocida. In this study the multiresistance ICEPmu1 from bovine P. multocida was analysed for its core genes and its ability to conjugatively transfer into strains of the same and different genera.<br><br>METHODS: ICEPmu1 was identified during whole genome sequencing. Coding sequences were predicted by bioinformatic tools and manually curated using the annotation software ERGO. Conjugation into P. multocida, Mannheimia haemolytica and Escherichia coli recipients was performed by mating assays. The presence of ICEPmu1 and its circular intermediate in the recipient strains was confirmed by PCR and sequence analysis. Integration sites were sequenced. Susceptibility testing of the ICEPmu1-carrying recipients was conducted by broth microdilution.<br><br>RESULTS: The 82&#x200a;214 bp ICEPmu1 harbours 88 genes. The core genes of ICEPmu1, which are involved in excision/integration and conjugative transfer, resemble those found in a 66&#x200a;641 bp ICE from Histophilus somni. ICEPmu1 integrates into a tRNA(Leu) and is flanked by 13 bp direct repeats. It is able to conjugatively transfer to P. multocida, M. haemolytica and E. coli, where it also uses a tRNA(Leu) for integration and produces closely related 13 bp direct repeats. PCR assays and susceptibility testing confirmed the presence and the functional activity of the ICEPmu1-associated resistance genes in the recipient strains.<br><br>CONCLUSIONS: The observation that the multiresistance ICEPmu1 is present in a bovine P. multocida and can easily spread across strain and genus boundaries underlines the risk of a rapid dissemination of multiple resistance genes, which will distinctly decrease the therapeutic options.}, }
@article {pmid22001175, year = {2012}, author = {Michael, GB and Kadlec, K and Sweeney, MT and Brzuszkiewicz, E and Liesegang, H and Daniel, R and Murray, RW and Watts, JL and Schwarz, S}, title = {ICEPmu1, an integrative conjugative element (ICE) of Pasteurella multocida: analysis of the regions that comprise 12 antimicrobial resistance genes.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {67}, number = {1}, pages = {84-90}, doi = {10.1093/jac/dkr406}, pmid = {22001175}, issn = {1460-2091}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/*genetics ; Cattle ; Cattle Diseases/microbiology ; DNA, Bacterial/chemistry/genetics ; *Drug Resistance, Multiple, Bacterial ; Gene Order ; Genome, Bacterial ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Pasteurella Infections/microbiology/veterinary ; Pasteurella multocida/drug effects/*genetics/isolation &amp; purification ; Respiratory Tract Diseases/microbiology/veterinary ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: In recent years, multiresistant Pasteurella multocida isolates from bovine respiratory tract infections have been identified. These isolates have exhibited resistance to most classes of antimicrobial agents commonly used in veterinary medicine, the genetic basis of which, however, is largely unknown.<br><br>METHODS: Genomic DNA of a representative P. multocida isolate was subjected to whole genome sequencing. Genes have been predicted by the YACOP program, compared with the SWISSProt/EMBL databases and manually curated using the annotation software ERGO. Susceptibility testing was performed by broth microdilution according to CLSI recommendations.<br><br>RESULTS: The analysis of one representative P. multocida isolate identified an 82 kb integrative and conjugative element (ICE) integrated into the chromosomal DNA. This ICE, designated ICEPmu1, harboured 11 resistance genes, which confer resistance to streptomycin/spectinomycin (aadA25), streptomycin (strA and strB), gentamicin (aadB), kanamycin/neomycin (aphA1), tetracycline [tetR-tet(H)], chloramphenicol/florfenicol (floR), sulphonamides (sul2), tilmicosin/clindamycin [erm(42)] or tilmicosin/tulathromycin [msr(E)-mph(E)]. In addition, a complete bla(OXA-2) gene was detected, which, however, appeared to be functionally inactive in P. multocida. These resistance genes were organized in two regions of approximately 15.7 and 9.8 kb. Based on the sequences obtained, it is likely that plasmids, gene cassettes and insertion sequences have played a role in the development of the two resistance gene regions within this ICE.<br><br>CONCLUSIONS: The observation that 12 resistance genes, organized in two resistance gene regions, represent part of an ICE in P. multocida underlines the risk of simultaneous acquisition of multiple resistance genes via a single horizontal gene transfer event.}, }
@article {pmid22000739, year = {2011}, author = {Muzzi, A and Donati, C}, title = {Population genetics and evolution of the pan-genome of Streptococcus pneumoniae.}, journal = {International journal of medical microbiology : IJMM}, volume = {301}, number = {8}, pages = {619-622}, doi = {10.1016/j.ijmm.2011.09.008}, pmid = {22000739}, issn = {1618-0607}, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Variation ; *Genome, Bacterial ; Genotype ; Humans ; Phylogeny ; Pneumococcal Infections/microbiology ; Streptococcus pneumoniae/*classification/*genetics/isolation &amp; purification ; }, abstract = {The genetic variability in bacterial species is much larger than in other kingdoms of life. The gene content between pairs of isolates can diverge by as much as 30% in species like Escherichia coli or Streptococcus pneumoniae. This unexpected finding led to the introduction of the concept of the pan-genome, the set of genes that can be found in a given bacterial species. The genome of any isolate is thus composed by a "core genome" shared by all strains and characteristic of the species, and a "dispensable genome" that accounts for many of the phenotypic differences between strains. The pan-genome is usually much larger than the genome of any single isolate and, given the ability of many bacteria to exchange genetic material with the environment, constitutes a reservoir that could enhance their ability to survive in a mutating environment. To understand the evolution of the pan-genome of an important pathogen and its interactions with the commensal microbial flora, we have analyzed the genomes of 44 strains of Streptococcus pneumoniae, one of the most important causes of microbial diseases in humans. Despite evidence of extensive homologous recombination, the S. pneumoniae phylogenetic tree reconstructed from polymorphisms in the core genome identified major groups of genetically related strains. With the exception of serotype 1, the tree correlated poorly with capsular serotype, geographical site of isolation and disease outcome. The distribution of dispensable genes was consistent with phylogeny, although horizontal gene transfer events attenuated this correlation in the case of ancient lineages. Homologous recombination, involving short stretches of DNA, was the dominant evolutionary process of the core genome of S. pneumoniae. Genetic exchange with related species sharing the same ecological niche was the main mechanism of evolution of S. pneumonia; and S. mitis was the main reservoir of genetic diversity of S. pneumoniae. The pan-genome of S. pneumoniae increased logarithmically with the number of strains and linearly with the variability of the sample, suggesting that acquired genes accumulate proportionately to the age of clones.}, }
@article {pmid21999488, year = {2011}, author = {Ajon, M and Fröls, S and van Wolferen, M and Stoecker, K and Teichmann, D and Driessen, AJ and Grogan, DW and Albers, SV and Schleper, C}, title = {UV-inducible DNA exchange in hyperthermophilic archaea mediated by type IV pili.}, journal = {Molecular microbiology}, volume = {82}, number = {4}, pages = {807-817}, doi = {10.1111/j.1365-2958.2011.07861.x}, pmid = {21999488}, issn = {1365-2958}, mesh = {Biological Transport ; DNA, Archaeal/*metabolism ; Gene Transfer, Horizontal/*radiation effects ; In Situ Hybridization, Fluorescence ; Recombination, Genetic ; Sulfolobus/*genetics/*radiation effects ; }, abstract = {Archaea, like bacteria and eukaryotes, contain proteins involved in various mechanisms of DNA repair, highlighting the importance of these processes for all forms of life. Species of the order Sulfolobales of hyperthermophilic crenarchaeota are equipped with a strongly UV-inducible type IV pilus system that promotes cellular aggregation. Here we demonstrate by fluorescence in situ hybridization that cellular aggregates are formed based on a species-specific recognition process and that UV-induced cellular aggregation mediates chromosomal marker exchange with high frequency. Recombination rates exceeded those of uninduced cultures by up to three orders of magnitude. Knockout strains of Sulfolobus acidocaldarius incapable of pilus production could not self-aggregate, but were partners in mating experiments with wild-type strains indicating that one cellular partner can mediate the DNA transfer. Since pilus knockout strains showed decreased survival upon UV treatment, we conclude that the UV-inducible DNA transfer process and subsequent homologous recombination represents an important mechanism to maintain chromosome integrity in Sulfolobus. It might also contribute substantially to the frequent chromosomal DNA exchange and horizontal gene transfer in these archaea in their natural habitat.}, }
@article {pmid21994936, year = {2011}, author = {Reiss, K and Kirchner, E and Gijzen, M and Zocher, G and Löffelhardt, B and Nürnberger, T and Stehle, T and Brunner, F}, title = {Structural and phylogenetic analyses of the GP42 transglutaminase from Phytophthora sojae reveal an evolutionary relationship between oomycetes and marine Vibrio bacteria.}, journal = {The Journal of biological chemistry}, volume = {286}, number = {49}, pages = {42585-42593}, pmid = {21994936}, issn = {1083-351X}, mesh = {Amino Acid Sequence ; Catalytic Domain ; Crystallography, X-Ray/methods ; DNA Mutational Analysis ; Evolution, Molecular ; Immunity, Innate ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Oomycetes/*metabolism ; Petroselinum/microbiology ; Phylogeny ; Phytophthora/*genetics ; Recombinant Proteins/metabolism ; Sequence Homology, Amino Acid ; Solanum tuberosum/microbiology ; Transglutaminases/metabolism ; Vibrio/*metabolism ; Water Microbiology ; }, abstract = {Transglutaminases (TGases) are ubiquitous enzymes that catalyze selective cross-linking between protein-bound glutamine and lysine residues; the resulting isopeptide bond confers high resistance to proteolysis. Phytophthora sojae, a pathogen of soybean, secretes a Ca(2+)-dependent TGase (GP42) that is activating defense responses in both host and non-host plants. A GP42 fragment of 13 amino acids, termed Pep-13, was shown to be absolutely indispensable for both TGase and elicitor activity. GP42 does not share significant primary sequence similarity with known TGases from mammals or bacteria. This suggests that GP42 has evolved novel structural and catalytic features to support enzymatic activity. We have solved the crystal structure of the catalytically inactive point mutant GP42 (C290S) at 2.95 Å resolution and identified residues involved in catalysis by mutational analysis. The protein comprises three domains that assemble into an elongated structure. Although GP42 has no structural homolog, its core region displays significant similarity to the catalytic core of the Mac-1 cysteine protease from Group A Streptococcus, a member of the papain-like superfamily of cysteine proteases. Proteins that are taxonomically related to GP42 are only present in plant pathogenic oomycetes belonging to the order of the Peronosporales (e.g. Phytophthora, Hyaloperonospora, and Pythium spp.) and in marine Vibrio bacteria. This suggests that a lateral gene transfer event may have occurred between bacteria and oomycetes. Our results offer a basis to design and use highly specific inhibitors of the GP42-like TGase family that may impair the growth of important oomycete and bacterial pathogens.}, }
@article {pmid21992746, year = {2011}, author = {Carattoli, A}, title = {Plasmids in Gram negatives: molecular typing of resistance plasmids.}, journal = {International journal of medical microbiology : IJMM}, volume = {301}, number = {8}, pages = {654-658}, doi = {10.1016/j.ijmm.2011.09.003}, pmid = {21992746}, issn = {1618-0607}, mesh = {Animals ; Drug Resistance, Bacterial ; Enterobacteriaceae/drug effects/*genetics ; Gene Transfer, Horizontal ; Genotype ; Humans ; *Molecular Typing ; Plasmids/*analysis ; Selection, Genetic ; }, abstract = {A plasmid is defined as a double stranded, circular DNA molecule capable of autonomous replication. By definition, plasmids do not carry genes essential for the growth of host cells under non-stressed conditions but they have systems which guarantee their autonomous replication also controlling the copy number and ensuring stable inheritance during cell division. Most of the plasmids confer positively selectable phenotypes by the presence of antimicrobial resistance genes. Plasmids evolve as an integral part of the bacterial genome, providing resistance genes that can be easily exchanged among bacteria of different origin and source by conjugation. A multidisciplinary approach is currently applied to study the acquisition and spread of antimicrobial resistance in clinically relevant bacterial pathogens and the established surveillance can be implemented by replicon typing of plasmids. Particular plasmid families are more frequently detected among Enterobacteriaceae and play a major role in the diffusion of specific resistance genes. For instance, IncFII, IncA/C, IncL/M, IncN and IncI1 plasmids carrying extended-spectrum beta-lactamase genes and acquired AmpC genes are currently considered to be "epidemic resistance plasmids", being worldwide detected in Enterobacteriaceae of different origin and sources. The recognition of successful plasmids is an essential first step to design intervention strategies preventing their spread.}, }
@article {pmid21992544, year = {2011}, author = {Allers, T}, title = {Swapping genes to survive - a new role for archaeal type IV pili.}, journal = {Molecular microbiology}, volume = {82}, number = {4}, pages = {789-791}, doi = {10.1111/j.1365-2958.2011.07860.x}, pmid = {21992544}, issn = {1365-2958}, mesh = {DNA, Archaeal/*metabolism ; Gene Transfer, Horizontal/*radiation effects ; Sulfolobus/*genetics/*radiation effects ; }, abstract = {Type IV pili are filamentous structures that are found on the surface of many bacterial and archaeal cells, they are involved in cell motility and surface adhesion. In the crenarchaeon Sulfolobus solfataricus, type IV pili formation is strongly induced by UV irradiation and leads to cellular aggregation. The study by Ajon et al. (2011) published in this issue of Molecular Microbiology shows that UV-induced cellular aggregation greatly stimulates the exchange of chromosomal markers among irradiated cells, and that this strategy helps with cell survival. Sulfolobus knockout strains that are incapable of forming pili proved to be deficient in aggregation, and also showed decreased cellular survival after UV irradiation. The UV-induced pili of three different Sulfolobus species had distinct morphologies, and correspondingly these three species were able to aggregate only with their own kind. This work has defined a new role for type IV pili in both the transfer of genes within species and the recovery from UV-induced DNA damage.}, }
@article {pmid21990049, year = {2012}, author = {Sandegren, L and Linkevicius, M and Lytsy, B and Melhus, &#xc5; and Andersson, DI}, title = {Transfer of an Escherichia coli ST131 multiresistance cassette has created a Klebsiella pneumoniae-specific plasmid associated with a major nosocomial outbreak.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {67}, number = {1}, pages = {74-83}, doi = {10.1093/jac/dkr405}, pmid = {21990049}, issn = {1460-2091}, mesh = {Conjugation, Genetic ; Cross Infection/*epidemiology/microbiology ; DNA, Bacterial/chemistry/genetics ; *Disease Outbreaks ; Drug Resistance, Multiple, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/genetics ; *Gene Transfer, Horizontal ; Host Specificity ; Humans ; Klebsiella Infections/*epidemiology/microbiology ; Klebsiella pneumoniae/drug effects/genetics/*isolation &amp; purification ; Molecular Sequence Data ; Molecular Typing ; Multiplex Polymerase Chain Reaction ; *Plasmids ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; beta-Lactamases/genetics ; }, abstract = {OBJECTIVES: To characterize the complete sequence, horizontal spread and stability of the CTX-M-15-encoding multiresistance plasmid of a Klebsiella pneumoniae strain involved in a large nosocomial outbreak.<br><br>METHODS: The 220 kbp plasmid pUUH239.2 was completely sequenced using 454 technology. The conjugational host range, conjugation frequencies, plasmid stability and fitness cost of plasmid carriage were studied in vitro. Conjugational spread during the outbreak was assessed retrospectively by multiplex PCR screening, restriction fragment length polymorphism and PFGE.<br><br>RESULTS: Plasmid pUUH239.2 encodes resistance to &#x3b2;-lactams (bla(CTX-M-15), bla(TEM-1) and bla(OXA-1)), aminoglycosides [aac-(6')-1b-cr and aadA2], tetracyclines [tet(A) and tetR], trimethoprim (dhfrXII), sulphonamides (sul1), quaternary ammonium compounds (qacE&#x394;1), macrolides [mph(A)-mxr-mphR(A)] and heavy metal ions (silver, copper and arsenic). The plasmid consists of a backbone, highly similar to the K. pneumoniae plasmid pKPN3, and a 41 kbp resistance region, highly similar to the resistance regions of plasmids pEK499 and pC15-1a previously isolated from Escherichia coli strains belonging to the outbreak lineage ST131 (where ST stands for sequence type). The pUUH239.2 plasmid is stable in K. pneumoniae but unstable in E. coli and confers a fitness cost when introduced into a naive host cell. Transfer of pUUH239.2 from the outbreak K. pneumoniae clone to the E. coli of the patients' intestinal floras has occurred on multiple occasions during the outbreak.<br><br>CONCLUSIONS: The plasmid pUUH239.2 is a composite of the pKPN3 K. pneumoniae plasmid backbone and the bla(CTX-M-15)-encoding multiresistance cassette associated with the internationally recognized outbreak strain E. coli ST131. The resulting plasmid differs in stability between K. pneumoniae and E. coli, and this has probably limited the spread of this plasmid during the outbreak.}, }
@article {pmid21987179, year = {2011}, author = {Lai, LB and Bernal-Bayard, P and Mohannath, G and Lai, SM and Gopalan, V and Vioque, A}, title = {A functional RNase P protein subunit of bacterial origin in some eukaryotes.}, journal = {Molecular genetics and genomics : MGG}, volume = {286}, number = {5-6}, pages = {359-369}, pmid = {21987179}, issn = {1617-4623}, mesh = {*Bacterial Proteins ; *Biological Evolution ; Eukaryota/*enzymology/genetics ; Gene Transfer, Horizontal ; Protein Subunits ; Ribonuclease P/*physiology ; Sequence Homology, Amino Acid ; }, abstract = {RNase P catalyzes 5'-maturation of tRNAs. While bacterial RNase P comprises an RNA catalyst and a protein cofactor, the eukaryotic (nuclear) variant contains an RNA and up to ten proteins, all unrelated to the bacterial protein. Unexpectedly, a nuclear-encoded bacterial RNase P protein (RPP) homolog is found in several prasinophyte algae including Ostreococcus tauri. We demonstrate that recombinant O. tauri RPP can functionally reconstitute with bacterial RNase P RNAs (RPRs) but not with O. tauri organellar RPRs, despite the latter's presumed bacterial origins. We also show that O. tauri PRORP, a homolog of Arabidopsis PRORP-1, displays tRNA 5'-processing activity in vitro. We discuss the implications of the striking diversity of RNase P in O. tauri, the smallest known free-living eukaryote.}, }
@article {pmid21986830, year = {2012}, author = {Dheilly, A and Le Devendec, L and Mourand, G and Bouder, A and Jouy, E and Kempf, I}, title = {Resistance gene transfer during treatments for experimental avian colibacillosis.}, journal = {Antimicrobial agents and chemotherapy}, volume = {56}, number = {1}, pages = {189-196}, pmid = {21986830}, issn = {1098-6596}, mesh = {Amoxicillin/administration &amp; dosage ; Animals ; Anti-Bacterial Agents/*administration &amp; dosage ; Bacterial Typing Techniques ; *Bird Diseases/drug therapy/microbiology ; Chickens ; Drug Resistance, Bacterial/drug effects ; Electrophoresis, Gel, Pulsed-Field ; Enrofloxacin ; Escherichia coli/drug effects/*genetics ; *Escherichia coli Infections/drug therapy/microbiology/veterinary ; Escherichia coli Proteins/*genetics ; Feces/microbiology ; Fluoroquinolones/administration &amp; dosage ; *Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Oxytetracycline/administration &amp; dosage ; Plasmids/genetics ; Sulfadimethoxine/administration &amp; dosage ; Trimethoprim/administration &amp; dosage ; }, abstract = {An experiment was conducted in animal facilities to compare the impacts of four avian colibacillosis treatments-oxytetracycline (OTC), trimethoprim-sulfadimethoxine (SXT), amoxicillin (AMX), or enrofloxacin (ENR)-on the susceptibility of Escherichia coli in broiler intestinal tracts. Birds were first orally inoculated with rifampin-resistant E. coli strains bearing plasmid genes conferring resistance to fluoroquinolones (qnr), cephalosporins (bla(CTX-M) or bla(FOX)), trimethoprim-sulfonamides, aminoglycosides, or tetracyclines. Feces samples were collected before, during, and after antimicrobial treatments. The susceptibilities of E. coli strains were studied, and resistance gene transfer was analyzed. An increase in the tetracycline-resistant E. coli population was observed only in OTC-treated birds, whereas multiresistant E. coli was detected in the dominant E. coli populations of SXT-, AMX-, or ENR-treated birds. Most multiresistant E. coli strains were susceptible to rifampin and exhibited various pulsed-field gel electrophoresis profiles, suggesting the transfer of one of the multiresistance plasmids from the inoculated strains to other E. coli strains in the intestinal tract. In conclusion, this study clearly illustrates how, in E. coli, "old" antimicrobials may coselect antimicrobial resistance to recent and critical molecules.}, }
@article {pmid21985229, year = {2011}, author = {Ugalde, JA and Podell, S and Narasingarao, P and Allen, EE}, title = {Xenorhodopsins, an enigmatic new class of microbial rhodopsins horizontally transferred between archaea and bacteria.}, journal = {Biology direct}, volume = {6}, number = {}, pages = {52}, pmid = {21985229}, issn = {1745-6150}, support = {R21HG005107-02/HG/NHGRI NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Archaea/*chemistry/classification/genetics ; Bacteria/*chemistry/classification/genetics ; *Gene Transfer, Horizontal ; *Genes, Archaeal ; *Genes, Bacterial ; Molecular Sequence Data ; Phylogeny ; Rhodopsins, Microbial/*chemistry/genetics ; Sequence Alignment ; }, abstract = {Based on unique, coherent properties of phylogenetic analysis, key amino acid substitutions and structural modeling, we have identified a new class of unusual microbial rhodopsins related to the Anabaena sensory rhodopsin (ASR) protein, including multiple homologs not previously recognized. We propose the name xenorhodopsin for this class, reflecting a taxonomically diverse membership spanning five different Bacterial phyla as well as the Euryarchaeotal class Nanohaloarchaea. The patchy phylogenetic distribution of xenorhodopsin homologs is consistent with historical dissemination through horizontal gene transfer. Shared characteristics of xenorhodopsin-containing microbes include the absence of flagellar motility and isolation from high light habitats.}, }
@article {pmid21984796, year = {2011}, author = {Itzek, A and Zheng, L and Chen, Z and Merritt, J and Kreth, J}, title = {Hydrogen peroxide-dependent DNA release and transfer of antibiotic resistance genes in Streptococcus gordonii.}, journal = {Journal of bacteriology}, volume = {193}, number = {24}, pages = {6912-6922}, pmid = {21984796}, issn = {1098-5530}, support = {R01 DE018893-03/DE/NIDCR NIH HHS/United States ; DE018400/DE/NIDCR NIH HHS/United States ; K99 DE018400/DE/NIDCR NIH HHS/United States ; R01 DE018893/DE/NIDCR NIH HHS/United States ; DE018725/DE/NIDCR NIH HHS/United States ; R00 DE018400/DE/NIDCR NIH HHS/United States ; R03 DE018725/DE/NIDCR NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics/metabolism ; DNA, Bacterial/genetics/*metabolism ; *Drug Resistance, Microbial ; *Gene Transfer, Horizontal ; Hydrogen Peroxide/*metabolism ; Streptococcus gordonii/drug effects/*genetics/*metabolism ; }, abstract = {Certain oral streptococci produce H(2)O(2) under aerobic growth conditions to inhibit competing species like Streptococcus mutans. Additionally, H(2)O(2) production causes the release of extracellular DNA (eDNA). eDNA can participate in several important functions: biofilm formation and cell-cell aggregation are supported by eDNA, while eDNA can serve as a nutrient and as an antimicrobial agent by chelating essential cations. eDNA contains DNA fragments of a size that has the potential to transfer genomic information. By using Streptococcus gordonii as a model organism for streptococcal H(2)O(2) production, H(2)O(2)-dependent eDNA release was further investigated. Under defined growth conditions, the eDNA release process was shown to be entirely dependent on H(2)O(2). Chromosomal DNA damage seems to be the intrinsic signal for the release, although only actively growing cells were proficient eDNA donors. Interestingly, the process of eDNA production was found to be coupled with the induction of the S. gordonii natural competence system. Consequently, the production of H(2)O(2) triggered the transfer of antibiotic resistance genes. These results suggest that H(2)O(2) is potentially much more than a simple toxic metabolic by-product; rather, its production could serve as an important environmental signal that facilitates species evolution by transfer of genetic information and an increase in the mutation rate.}, }
@article {pmid21980581, year = {2011}, author = {Chan, CX and Bhattacharya, D}, title = {Non-random sharing of Plantae genes.}, journal = {Communicative &amp; integrative biology}, volume = {4}, number = {3}, pages = {361-363}, pmid = {21980581}, issn = {1942-0889}, abstract = {The power of eukaryote genomics relies strongly on taxon sampling. This point was underlined in a recent analysis of red algal genome evolution in which we tested the Plantae hypothesis that posits the monophyly of red, green (including plants) and glaucophyte algae. The inclusion of novel genome data from two mesophilic red algae enabled us to robustly demonstrate the sisterhood of red and green algae in the tree of life. Perhaps more exciting was the finding that >1,800 putative genes in the unicellular red alga Porphyridium cruentum showed evidence of gene-sharing with diverse lineages of eukaryotes and prokaryotes. Here we assessed the correlation between the putative functions of these shared genes and their susceptibility to transfer. It turns out that genes involved in complex interactive networks such as biological regulation and transcription/translation are less susceptible to endosymbiotic or horizontal gene transfer, when compared to genes with metabolic and transporter functions.}, }
@article {pmid21980067, year = {2012}, author = {Mata, C and Miró, E and Alvarado, A and Garcillán-Barcia, MP and Toleman, M and Walsh, TR and de la Cruz, F and Navarro, F}, title = {Plasmid typing and genetic context of AmpC β-lactamases in Enterobacteriaceae lacking inducible chromosomal ampC genes: findings from a Spanish hospital 1999-2007.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {67}, number = {1}, pages = {115-122}, doi = {10.1093/jac/dkr412}, pmid = {21980067}, issn = {1460-2091}, mesh = {Bacterial Proteins/*genetics ; Blotting, Southern ; Cluster Analysis ; Electrophoresis, Gel, Pulsed-Field ; Enterobacteriaceae/*enzymology/*genetics/isolation &amp; purification ; Enterobacteriaceae Infections/*microbiology ; *Gene Transfer, Horizontal ; Genotype ; Hospitals ; Interspersed Repetitive Sequences ; Molecular Typing ; Plasmids/*analysis ; Polymerase Chain Reaction ; Spain ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: To gain insights into ampC transmission between bacterial strains.<br><br>METHODS: We examined the genetic context of 117 acquired ampC genes from 27119 Enterobacteriaceae collected between 1999 and 2007. Plasmid analysis was carried out by PCR-based replicon or relaxase typing, S1-PFGE and Southern hybridization. I-CeuI/PFGE was used for isolates not characterized by plasmid analysis. PCR reactions were used to map the genetic organization of the ampC genes.<br><br>RESULTS: Among the isolates studied, 81.2% of ampC genes were located on plasmids of known Inc/MOB groups, 7.7% were chromosomally located and 11.1% were not determined. A/C, I1 and K were the most commonly found replicons in plasmids carrying bla(CMY-2), while L/M replicons were associated with bla(DHA-1). bla(ACC-1) was linked to I1 and MOB(F11) plasmids; bla(CMY-27) was associated with IncF and MOB(P12) plasmids; the plasmid carrying bla(CMY-25) could not be typed, and bla(CMY-40) was chromosomally located. All 87 isolates carrying bla(CMY-2), bla(CMY-4), bla(CMY-25), bla(CMY-27), bla(CMY-40) or bla(ACC-1) displayed the transposon-like structures ISEcp1/&#x394;ISEcp1-bla(CMY)-blc-sugE or &#x394;ISEcp1-bla(ACC-1)-gdha. The most prevalent structure in bla(DHA-1) (93.3% of cases) was identical to that described in the Klebsiella pneumoniae pTN60013 plasmid. Remarkably, in three isolates containing chromosomal bla(CMY-2), this gene was mobilized by conjugation.<br><br>CONCLUSIONS: Although plasmids are the main cause of the rapid dissemination of ampC genes among bacteria, we need to be aware that other mobile genetic elements such as integrative and conjugative elements (ICEs) can be involved in the mobilization of these genes.}, }
@article {pmid21979160, year = {2011}, author = {Arber, W}, title = {Molecular Darwinism: the contingency of spontaneous genetic variation.}, journal = {Genome biology and evolution}, volume = {3}, number = {}, pages = {1090-1092}, pmid = {21979160}, issn = {1759-6653}, mesh = {Biological Evolution ; Computational Biology ; DNA/genetics ; *Evolution, Molecular ; Gene Rearrangement ; Gene Transfer, Horizontal ; *Genetic Variation ; Reproducibility of Results ; Sequence Analysis, DNA ; }, abstract = {The availability of spontaneously occurring genetic variants is an important driving force of biological evolution. Largely thanks to experimental investigations by microbial geneticists, we know today that several different molecular mechanisms contribute to the overall genetic variations. These mechanisms can be assigned to three natural strategies to generate genetic variants: 1) local sequence changes, 2) intragenomic reshuffling of DNA segments, and 3) acquisition of a segment of foreign DNA. In these processes, specific gene products are involved in cooperation with different nongenetic elements. Some genetic variations occur fully at random along the DNA filaments, others rather with a statistical reproducibility, although at many possible sites. We have to be aware that evolution in natural ecosystems is of higher complexity than under most laboratory conditions, not at least in view of symbiotic associations and the occurrence of horizontal gene transfer. The encountered contingency of genetic variation can possibly best ensure a long-term persistence of life under steadily changing living conditions.}, }
@article {pmid21978154, year = {2011}, author = {Fu, M and Deng, R and Wang, J and Wang, X}, title = {Horizontal gene transfer in herpesviruses identified by using support vector machine.}, journal = {Acta virologica}, volume = {55}, number = {3}, pages = {203-217}, doi = {10.4149/av_2011_03_203}, pmid = {21978154}, issn = {0001-723X}, mesh = {DNA, Viral/genetics ; Databases, Genetic ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Viral ; Herpesviridae/*genetics ; Sequence Analysis, DNA ; *Support Vector Machine ; }, abstract = {Horizontal gene transfer (HGT) is the probable origin of new genes. Identification of HGT-introduced genes would be helpful to the understanding of the genome evolution and the function prediction of new genes. In this study, a method using support vector machine (SVM) was used to distinguish horizontally transferred genes and non-horizontally transferred genes of mammalian herpesviruses based on the atypical composition identification, with accuracy higher than 95% within a reasonable length of time by using just a common PC. This identified 302 putative horizontally transferred genes, 171 genes being identified for the first time. Although most putative transferred genes are of unknown function, many genes have been discovered or predicted to encode glycoproteins or membrane proteins.}, }
@article {pmid21975191, year = {2011}, author = {Akiyama, Y and Goel, S and Conner, JA and Hanna, WW and Yamada-Akiyama, H and Ozias-Akins, P}, title = {Evolution of the apomixis transmitting chromosome in Pennisetum.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {289}, pmid = {21975191}, issn = {1471-2148}, mesh = {Apomixis/*genetics ; Base Sequence ; Bayes Theorem ; Chromosomes, Plant/*genetics ; DNA Primers/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Models, Genetic ; Molecular Sequence Data ; Pennisetum/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Apomixis is an intriguing trait in plants that results in maternal clones through seed reproduction. Apomixis is an elusive, but potentially revolutionary, trait for plant breeding and hybrid seed production. Recent studies arguing that apomicts are not evolutionary dead ends have generated further interest in the evolution of asexual flowering plants.<br><br>RESULTS: In the present study, we investigate karyotypic variation in a single chromosome responsible for transmitting apomixis, the Apospory-Specific Genomic Region carrier chromosome, in relation to species phylogeny in the genera Pennisetum and Cenchrus. A 1 kb region from the 3' end of the ndhF gene and a 900 bp region from trnL-F were sequenced from 12 apomictic and eight sexual species in the genus Pennisetum and allied genus Cenchrus. An 800 bp region from the Apospory-Specific Genomic Region also was sequenced from the 12 apomicts. Molecular cytological analysis was conducted in sixteen Pennisetum and two Cenchrus species. Our results indicate that the Apospory-Specific Genomic Region is shared by all apomictic species while it is absent from all sexual species or cytotypes. Contrary to our previous observations in Pennisetum squamulatum and Cenchrus ciliaris, retrotransposon sequences of the Opie-2-like family were not closely associated with the Apospory-Specific Genomic Region in all apomictic species, suggesting that they may have been accumulated after the Apospory-Specific Genomic Region originated.<br><br>CONCLUSIONS: Given that phylogenetic analysis merged Cenchrus and newly investigated Pennisetum species into a single clade containing a terminal cluster of Cenchrus apomicts, the presumed monophyletic origin of Cenchrus is supported. The Apospory-Specific Genomic Region likely preceded speciation in Cenchrus and its lateral transfer through hybridization and subsequent chromosome repatterning may have contributed to further speciation in the two genera.}, }
@article {pmid21967404, year = {2012}, author = {Liang, B and Jiang, J and Zhang, J and Zhao, Y and Li, S}, title = {Horizontal transfer of dehalogenase genes involved in the catalysis of chlorinated compounds: evidence and ecological role.}, journal = {Critical reviews in microbiology}, volume = {38}, number = {2}, pages = {95-110}, doi = {10.3109/1040841X.2011.618114}, pmid = {21967404}, issn = {1549-7828}, mesh = {Biotransformation ; Ecosystem ; *Environmental Microbiology ; Environmental Pollutants/metabolism ; *Gene Transfer, Horizontal ; Hydrocarbons, Chlorinated/*metabolism ; Hydrolases/*genetics/*metabolism ; }, abstract = {Horizontal gene transfer (HGT) of dehalogenase genes is considered an important mechanism of genomic evolution, the metabolic resilience of biotopes, and microbial community adaptation in chlorinated compound-contaminated ecosystems. In this review, we summarize the current evidence for the HGT of dehalogenase genes involved in the catalysis of various chlorinated compounds, such as chlorinated alkanes and alkanoic acids, chlorinated ethenes, chlorinated herbicide, and chlorinated aromatics. We also highlight the ecological role of HGT as it relates to the contribution to the diversification of dehalogenating microorganisms and the resulting facilitation of rapid microbial community adaptation to ecosystem contaminated with chlorinated compounds.}, }
@article {pmid21967050, year = {2011}, author = {Dassa, E}, title = {Natural history of ABC systems: not only transporters.}, journal = {Essays in biochemistry}, volume = {50}, number = {1}, pages = {19-42}, doi = {10.1042/bse0500019}, pmid = {21967050}, issn = {1744-1358}, mesh = {ATP-Binding Cassette Transporters/genetics/*physiology ; Biological Evolution ; Phylogeny ; }, abstract = {In recent years, our understanding of the functioning of ABC (ATP-binding cassette) systems has been boosted by the combination of biochemical and structural approaches. However, the origin and the distribution of ABC proteins among living organisms are difficult to understand in a phylogenetic perspective, because it is hard to discriminate orthology and paralogy, due to the existence of horizontal gene transfer. In this chapter, I present an update of the classification of ABC systems and discuss a hypothetical scenario of their evolution. The hypothetical presence of ABC ATPases in the last common ancestor of modern organisms is discussed, as well as the additional possibility that ABC systems might have been transmitted to eukaryotes, after the two endosymbiosis events that led to the constitution of eukaryotic organelles. I update the functional information of selected ABC systems and introduce new families of ABC proteins that have been included recently into this vast superfamily, thanks to the availability of high-resolution three-dimensional structures.}, }
@article {pmid21966566, year = {2011}, author = {Vinogradov, SN and Hoogewijs, D and Arredondo-Peter, R}, title = {What are the origins and phylogeny of plant hemoglobins?.}, journal = {Communicative &amp; integrative biology}, volume = {4}, number = {4}, pages = {443-445}, pmid = {21966566}, issn = {1942-0889}, abstract = {Land plants and algae are now represented by about 40 genomes. Although most are incomplete, putative globins appear to be present in all the ca. 30 land plant genomes and in all except one algal genomes. The globins have either the canonical 3/3 α-helical fold characteristic of vertebrate myoglobin (Mb) or 2/2 α-helical folds, characteristic of bacterial globins with a truncated Mb-fold. In view of the fairly complete picture of the globin superfamily that is now available from analyses of over 1,000 bacterial genomes and >200 other eukaryote genomes, it is now possible to seek answers to the following twin questions: what is the phylogenetic relationship of plant and algal globins to those of other eukaryotes and what is their likely bacterial origin? We summarize below the available results. Molecular phylogenetic analyses indicate that plant and algal 3/3 globins are related to bacterial flavohemoglobins and vertebrate neuroglobins. Furthermore, they also suggest that plant and algal 3/3 and group 1 2/2 Hbs originated from the horizontal gene transfers that accompanied the two generally accepted endosymbioses of a proteobacterium and a cyanobacterium with a eukaryote ancestor. In contrast, the origin of the group 2 2/2 Hbs unexpectedly appears to involve horizontal gene transfer from a bacterium ancestral to Chloroflexi, Deinococcales, Bacillli and Actinomycetes. We present additional results which indicate that the shared ancestry is likely to be with the Chloroflexi alone.}, }
@article {pmid21966487, year = {2011}, author = {Skapski, A and Hygonenq, MC and Sagné, E and Guiral, S and Citti, C and Baranowski, E}, title = {Genome-scale analysis of Mycoplasma agalactiae loci involved in interaction with host cells.}, journal = {PloS one}, volume = {6}, number = {9}, pages = {e25291}, pmid = {21966487}, issn = {1932-6203}, mesh = {Animals ; Bacterial Proteins/genetics/metabolism ; Blotting, Western ; Cell Line ; Genome, Bacterial ; Goats ; HeLa Cells ; Host-Pathogen Interactions ; Humans ; Mutation ; Mycoplasma agalactiae/*genetics/*metabolism ; Promoter Regions, Genetic/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {Mycoplasma agalactiae is an important pathogen of small ruminants, in which it causes contagious agalactia. It belongs to a large group of "minimal bacteria" with a small genome and reduced metabolic capacities that are dependent on their host for nutrients. Mycoplasma survival thus relies on intimate contact with host cells, but little is known about the factors involved in these interactions or in the more general infectious process. To address this issue, an assay based on goat epithelial and fibroblastic cells was used to screen a M. agalactiae knockout mutant library. Mutants with reduced growth capacities in cell culture were selected and 62 genomic loci were identified as contributing to this phenotype. As expected for minimal bacteria, "transport and metabolism" was the functional category most commonly implicated in this phenotype, but 50% of the selected mutants were disrupted in coding sequences (CDSs) with unknown functions, with surface lipoproteins being most commonly represented in this category. Since mycoplasmas lack a cell wall, lipoproteins are likely to be important in interactions with the host. A few intergenic regions were also identified that may act as regulatory sequences under co-culture conditions. Interestingly, some mutants mapped to gene clusters that are highly conserved across mycoplasma species but located in different positions. One of these clusters was found in a transcriptionally active region of the M. agalactiae chromosome, downstream of a cryptic promoter. A possible scenario for the evolution of these loci is discussed. Finally, several CDSs identified here are conserved in other important pathogenic mycoplasmas, and some were involved in horizontal gene transfer with phylogenetically distant species. These results provide a basis for further deciphering functions mediating mycoplasma-host interactions.}, }
@article {pmid21966432, year = {2011}, author = {Zähner, D and Gandhi, AR and Yi, H and Stephens, DS}, title = {Mitis group streptococci express variable pilus islet 2 pili.}, journal = {PloS one}, volume = {6}, number = {9}, pages = {e25124}, pmid = {21966432}, issn = {1932-6203}, support = {R01 AI070829/AI/NIAID NIH HHS/United States ; R01AI070829/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/*metabolism ; Fimbriae, Bacterial/genetics/*metabolism ; Molecular Sequence Data ; Polymerase Chain Reaction ; Streptococcus mitis/genetics/*metabolism ; Streptococcus oralis/genetics/*metabolism ; Streptococcus sanguis/genetics/*metabolism ; }, abstract = {BACKGROUND: Streptococcus oralis, Streptococcus mitis, and Streptococcus sanguinis are members of the Mitis group of streptococci and agents of oral biofilm, dental plaque and infective endocarditis, disease processes that involve bacteria-bacteria and bacteria-host interactions. Their close relative, the human pathogen S. pneumoniae uses pilus-islet 2 (PI-2)-encoded pili to facilitate adhesion to eukaryotic cells.<br><br>PI-2 pilus-encoding genetic islets were identified in S. oralis, S. mitis, and S. sanguinis, but were absent from other isolates of these species. The PI-2 islets resembled the genetic organization of the PI-2 islet of S. pneumoniae, but differed in the genes encoding the structural pilus proteins PitA and PitB. Two and three variants of pitA (a pseudogene in S. pneumoniae) and pitB, respectively, were identified that showed &#x2248;20% difference in nucleotide as well as corresponding protein sequence. Species-independent combinations of pitA and pitB variants indicated prior intra- and interspecies horizontal gene transfer events. Polyclonal antisera developed against PitA and PitB of S. oralis type strain ATCC35037 revealed that PI-2 pili in oral streptococci were composed of PitA and PitB. Electronmicrographs showed pilus structures radiating >700 nm from the bacterial surface in the wild type strain, but not in an isogenic PI-2 deletion mutant. Anti-PitB-antiserum only reacted with pili containing the same PitB variant, whereas anti-PitA antiserum was cross-reactive with the other PitA variant. Electronic multilocus sequence analysis revealed that all PI-2-encoding oral streptococci were closely-related and cluster with non-PI-2-encoding S. oralis strains.<br><br>CONCLUSIONS/SIGNIFICANCE: This is the first identification of PI-2 pili in Mitis group oral streptococci. The findings provide a striking example of intra- and interspecies horizontal gene transfer. The PI-2 pilus diversity provides a possible key to link strain-specific bacterial interactions and/or tissue tropisms with pathogenic traits in the Mitis group streptococci.}, }
@article {pmid21966396, year = {2011}, author = {Hu, P and Yang, M and Zhang, A and Wu, J and Chen, B and Hua, Y and Yu, J and Chen, H and Xiao, J and Jin, M}, title = {Comparative genomics study of multi-drug-resistance mechanisms in the antibiotic-resistant Streptococcus suis R61 strain.}, journal = {PloS one}, volume = {6}, number = {9}, pages = {e24988}, pmid = {21966396}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Animals ; Anti-Bacterial Agents/pharmacology ; China ; *Drug Resistance, Bacterial ; Drug Resistance, Multiple/*genetics ; Genetic Variation ; Genome, Bacterial ; Genomics ; Humans ; Microbial Sensitivity Tests ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Phylogeny ; Sequence Homology, Amino Acid ; Streptococcus suis/genetics/*metabolism ; Swine ; }, abstract = {BACKGROUND: Streptococcus suis infections are a serious problem for both humans and pigs worldwide. The emergence and increasing prevalence of antibiotic-resistant S. suis strains pose significant clinical and societal challenges.<br><br>RESULTS: In our study, we sequenced one multi-drug-resistant S. suis strain, R61, and one S. suis strain, A7, which is fully sensitive to all tested antibiotics. Comparative genomic analysis revealed that the R61 strain is phylogenetically distinct from other S. suis strains, and the genome of R61 exhibits extreme levels of evolutionary plasticity with high levels of gene gain and loss. Our results indicate that the multi-drug-resistant strain R61 has evolved three main categories of resistance.<br><br>CONCLUSIONS: Comparative genomic analysis of S. suis strains with diverse drug-resistant phenotypes provided evidence that horizontal gene transfer is an important evolutionary force in shaping the genome of multi-drug-resistant strain R61. In this study, we discovered novel and previously unexamined mutations that are strong candidates for conferring drug resistance. We believe that these mutations will provide crucial clues for designing new drugs against this pathogen. In addition, our work provides a clear demonstration that the use of drugs has driven the emergence of the multi-drug-resistant strain R61.}, }
@article {pmid21966247, year = {2011}, author = {Pöggeler, S}, title = {Evolution of multicopper oxidase genes in coprophilous and non-coprophilous members of the order sordariales.}, journal = {Current genomics}, volume = {12}, number = {2}, pages = {95-103}, pmid = {21966247}, issn = {1875-5488}, abstract = {Multicopper oxidases (MCO) catalyze the biological oxidation of various aromatic substrates and have been identified in plants, insects, bacteria, and wood rotting fungi. In nature, they are involved in biodegradation of biopolymers such as lignin and humic compounds, but have also been tested for various industrial applications. In fungi, MCOs have been shown to play important roles during their life cycles, such as in fruiting body formation, pigment formation and pathogenicity. Coprophilous fungi, which grow on the dung of herbivores, appear to encode an unexpectedly high number of enzymes capable of at least partly degrading lignin. This study compared the MCO-coding capacity of the coprophilous filamentous ascomycetes Podospora anserina and Sordaria macrospora with closely related non-coprophilous members of the order Sordariales. An increase of MCO genes in coprophilic members of the Sordariales most probably occurred by gene duplication and horizontal gene transfer events.}, }
@article {pmid21965566, year = {2011}, author = {Chattoraj, P and Mohapatra, SS and Rao, JL and Biswas, I}, title = {Regulation of transcription by SMU.1349, a TetR family regulator, in Streptococcus mutans.}, journal = {Journal of bacteriology}, volume = {193}, number = {23}, pages = {6605-6613}, pmid = {21965566}, issn = {1098-5530}, support = {R01 DE016686/DE/NIDCR NIH HHS/United States ; DE016686/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/*metabolism ; *Gene Expression Regulation, Bacterial ; Operon ; Promoter Regions, Genetic ; Protein Binding ; Repressor Proteins/genetics/metabolism ; Streptococcus mutans/genetics/*metabolism ; Trans-Activators/genetics/metabolism ; *Transcription, Genetic ; }, abstract = {The TetR family of transcriptional regulators is ubiquitous in bacteria, where it plays an important role in bacterial gene expression. Streptococcus mutans, a gram-positive pathogen considered to be the primary etiological agent in the formation of dental caries, encodes at least 18 TetR regulators. Here we characterized one such TetR regulator, SMU.1349, encoded by the TnSmu2 operon, which appeared to be acquired by the organism via horizontal gene transfer. SMU.1349 is transcribed divergently from the rest of the genes encoded by the operon. By the use of a transcriptional reporter system and semiquantitative reverse transcription-PCR (RT-PCR), we demonstrated that SMU.1349 activates the transcription of several genes that are encoded within the TnSmu2 operon. Gel mobility shift and DNase I footprinting assays with purified SMU.1349 protein demonstrated binding to the intergenic region between SMU.1349 and the TnSmu2 operon; therefore, SMU.1349 is directly involved in gene transcription. Using purified S. mutans RpoD and Escherichia coli RNA polymerase, we also demonstrated in an in vitro transcription assay that SMU.1349 could activate transcription from the TnSmu2 operon promoter. Furthermore, we showed that SMU.1349 could also repress transcription from its own promoter by binding to the intergenic region, suggesting that SMU.1349 acts as both an activator and a repressor. Thus, unlike most of the TetR family proteins, which generally function as transcriptional repressors, SMU.1349 is unique in that it can function as both.}, }
@article {pmid21965536, year = {2011}, author = {Li, G and Ma, Q and Mao, X and Yin, Y and Zhu, X and Xu, Y}, title = {Integration of sequence-similarity and functional association information can overcome intrinsic problems in orthology mapping across bacterial genomes.}, journal = {Nucleic acids research}, volume = {39}, number = {22}, pages = {e150}, pmid = {21965536}, issn = {1362-4962}, mesh = {*Algorithms ; Chromosome Mapping/*methods ; DNA, Bacterial/chemistry ; Enzymes/genetics ; Escherichia coli/genetics ; Gene Fusion ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Sequence Homology, Nucleic Acid ; Software ; }, abstract = {Existing methods for orthologous gene mapping suffer from two general problems: (i) they are computationally too slow and their results are difficult to interpret for automated large-scale applications when based on phylogenetic analyses; or (ii) they are too prone to making mistakes in dealing with complex situations involving horizontal gene transfers and gene fusion due to the lack of a sound basis when based on sequence similarity information. We present a novel algorithm, Global Optimization Strategy (GOST), for orthologous gene mapping through combining sequence similarity and contextual (working partners) information, using a combinatorial optimization framework. Genome-scale applications of GOST show substantial improvements over the predictions by three popular sequence similarity-based orthology mapping programs. Our analysis indicates that our algorithm overcomes the intrinsic issues faced by sequence similarity-based methods, when orthology mapping involves gene fusions and horizontal gene transfers. Our program runs as efficiently as the most efficient sequence similarity-based algorithm in the public domain. GOST is freely downloadable at http://csbl.bmb.uga.edu/~maqin/GOST.}, }
@article {pmid21959051, year = {2011}, author = {Changey, F and Devers-Lamrani, M and Rouard, N and Martin-Laurent, F}, title = {In vitro evolution of an atrazine-degrading population under cyanuric acid selection pressure: evidence for the selective loss of a 47 kb region on the plasmid ADP1 containing the atzA, B and C genes.}, journal = {Gene}, volume = {490}, number = {1-2}, pages = {18-25}, doi = {10.1016/j.gene.2011.09.005}, pmid = {21959051}, issn = {1879-0038}, mesh = {Adaptation, Biological ; Atrazine/*metabolism ; *Biological Evolution ; Gene Deletion ; Genes, Bacterial ; Herbicides/metabolism ; Homologous Recombination ; Pseudomonas/*genetics ; *Selection, Genetic ; Triazines/*pharmacology ; }, abstract = {The adaptation of microorganisms to pesticide biodegradation relies on the recruitment of catabolic genes by horizontal gene transfer and homologous recombination mediated by insertion sequences (IS). This environment-friendly function is maintained in the degrading population but it has a cost which could diminish its fitness. The loss of genes in the course of evolution being a major mechanism of ecological specialization, we mimicked evolution in vitro by sub-culturing the atrazine-degrading Pseudomonas sp. ADP in a liquid medium containing cyanuric acid as the sole source of nitrogen. After 120 generations, a new population evolved, which replaced the original one. This new population grew faster on cyanuric acid but showed a similar cyanuric acid degrading ability. Plasmid profiles and Southern blot analyses revealed the deletion of a 47 kb region from pADP1 containing the atzABC genes coding for the enzymes that turn atrazine into cyanuric acid. Long PCR and sequencing analyses revealed that this deletion resulted from a homologous recombination between two direct repeats of a 110-bp, identical to ISPps1 of Pseudomonas huttiensis, flanking the deleted 47 kb region. The loss of a region containing three functional genes constitutively expressed thereby constituting a genetic burden under cyanuric acid selection pressure was responsible for the gain in fitness of the new population. It highlights the IS-mediated plasticity of the pesticide-degrading potential and shows that IS not only favours the expansion of the degrading genetic potential thanks to dispersion and duplication events but also contribute to its reduction thanks to deletion events.}, }
@article {pmid21954306, year = {2011}, author = {Bannam, TL and Yan, XX and Harrison, PF and Seemann, T and Keyburn, AL and Stubenrauch, C and Weeramantri, LH and Cheung, JK and McClane, BA and Boyce, JD and Moore, RJ and Rood, JI}, title = {Necrotic enteritis-derived Clostridium perfringens strain with three closely related independently conjugative toxin and antibiotic resistance plasmids.}, journal = {mBio}, volume = {2}, number = {5}, pages = {}, pmid = {21954306}, issn = {2150-7511}, support = {R01 AI056177/AI/NIAID NIH HHS/United States ; 5R01AI056177-08/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Toxins/*genetics ; Clostridium perfringens/drug effects/*genetics/*isolation &amp; purification/pathogenicity ; Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; *Drug Resistance, Bacterial ; Enterocolitis, Necrotizing/*microbiology ; Enterotoxins/*genetics ; Gene Knockout Techniques ; Gene Transfer, Horizontal ; Humans ; Molecular Sequence Data ; Mutagenesis, Insertional ; *Plasmids ; Sequence Analysis, DNA ; }, abstract = {UNLABELLED: The pathogenesis of avian necrotic enteritis involves NetB, a pore-forming toxin produced by virulent avian isolates of Clostridium perfringens type A. To determine the location and mobility of the netB structural gene, we examined a derivative of the tetracycline-resistant necrotic enteritis strain EHE-NE18, in which netB was insertionally inactivated by the chloramphenicol and thiamphenicol resistance gene catP. Both tetracycline and thiamphenicol resistance could be transferred either together or separately to a recipient strain in plate matings. The separate transconjugants could act as donors in subsequent matings, which demonstrated that the tetracycline resistance determinant and the netB gene were present on different conjugative elements. Large plasmids were isolated from the transconjugants and analyzed by high-throughput sequencing. Analysis of the resultant data indicated that there were actually three large conjugative plasmids present in the original strain, each with its own toxin or antibiotic resistance locus. Each plasmid contained a highly conserved 40-kb region that included plasmid replication and transfer regions that were closely related to the 47-kb conjugative tetracycline resistance plasmid pCW3 from C. perfringens. The plasmids were as follows: (i) a conjugative 49-kb tetracycline resistance plasmid that was very similar to pCW3, (ii) a conjugative 82-kb plasmid that contained the netB gene and other potential virulence genes, and (iii) a 70-kb plasmid that carried the cpb2 gene, which encodes a different pore-forming toxin, beta2 toxin.<br><br>IMPORTANCE: The anaerobic bacterium Clostridium perfringens can cause an avian gastrointestinal disease known as necrotic enteritis. Disease pathogenesis is not well understood, although the plasmid-encoded pore-forming toxin NetB, is an important virulence factor. In this work, we have shown that the plasmid that carries the netB gene is conjugative and has a 40-kb region that is very similar to replication and transfer regions found within each of the sequenced conjugative plasmids from C. perfringens. We also showed that this strain contained two additional large plasmids that were also conjugative and carried a similar 40-kb region. One of these plasmids encoded beta2 toxin, and the other encoded tetracycline resistance. To our knowledge, this is the first report of a bacterial strain that carries three closely related but different independently conjugative plasmids. These results have significant implications for our understanding of the transmission of virulence and antibiotic resistance genes in pathogenic bacteria.}, }
@article {pmid21949820, year = {2011}, author = {Kent, BN and Funkhouser, LJ and Setia, S and Bordenstein, SR}, title = {Evolutionary genomics of a temperate bacteriophage in an obligate intracellular bacteria (Wolbachia).}, journal = {PloS one}, volume = {6}, number = {9}, pages = {e24984}, pmid = {21949820}, issn = {1932-6203}, support = {R01 GM085163/GM/NIGMS NIH HHS/United States ; R01 GM085163-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteriophages/*genetics ; *Evolution, Molecular ; Genes, Bacterial ; Genome, Bacterial ; *Genomics ; Lysogeny ; Phylogeny ; Recombination, Genetic ; Selection, Genetic ; Wolbachia/*genetics ; }, abstract = {Genome evolution of bacteria is usually influenced by ecology, such that bacteria with a free-living stage have large genomes and high rates of horizontal gene transfer, while obligate intracellular bacteria have small genomes with typically low amounts of gene exchange. However, recent studies indicate that obligate intracellular species that host-switch frequently harbor agents of horizontal transfer such as mobile elements. For example, the temperate double-stranded DNA bacteriophage WO in Wolbachia persistently transfers between bacterial coinfections in the same host. Here we show that despite the phage's rampant mobility between coinfections, the prophage's genome displays features of constraint related to its intracellular niche. First, there is always at least one intact prophage WO and usually several degenerate, independently-acquired WO prophages in each Wolbachia genome. Second, while the prophage genomes are modular in composition with genes of similar function grouping together, the modules are generally not interchangeable with other unrelated phages and thus do not evolve by the Modular Theory. Third, there is an unusual core genome that strictly consists of head and baseplate genes; other gene modules are frequently deleted. Fourth, the prophage recombinases are diverse and there is no conserved integration sequence. Finally, the molecular evolutionary forces acting on prophage WO are point mutation, intragenic recombination, deletion, and purifying selection. Taken together, these analyses indicate that while lateral transfer of phage WO is pervasive between Wolbachia with occasional new gene uptake, constraints of the intracellular niche obstruct extensive mixture between WO and the global phage population. Although the Modular Theory has long been considered the paradigm of temperate bacteriophage evolution in free-living bacteria, it appears irrelevant in phages of obligate intracellular bacteria.}, }
@article {pmid21949776, year = {2011}, author = {Challacombe, JF and Eichorst, SA and Hauser, L and Land, M and Xie, G and Kuske, CR}, title = {Biological consequences of ancient gene acquisition and duplication in the large genome of Candidatus Solibacter usitatus Ellin6076.}, journal = {PloS one}, volume = {6}, number = {9}, pages = {e24882}, pmid = {21949776}, issn = {1932-6203}, mesh = {Acidobacteria/*genetics ; Codon/genetics ; Gene Duplication/*genetics ; Genes, Bacterial/genetics ; Genome Size/genetics ; Genome, Bacterial/*genetics ; Likelihood Functions ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Selection, Genetic ; Sequence Homology, Nucleic Acid ; }, abstract = {Members of the bacterial phylum Acidobacteria are widespread in soils and sediments worldwide, and are abundant in many soils. Acidobacteria are challenging to culture in vitro, and many basic features of their biology and functional roles in the soil have not been determined. Candidatus Solibacter usitatus strain Ellin6076 has a 9.9 Mb genome that is approximately 2-5 times as large as the other sequenced Acidobacteria genomes. Bacterial genome sizes typically range from 0.5 to 10 Mb and are influenced by gene duplication, horizontal gene transfer, gene loss and other evolutionary processes. Our comparative genome analyses indicate that the Ellin6076 large genome has arisen by horizontal gene transfer via ancient bacteriophage and/or plasmid-mediated transduction, and widespread small-scale gene duplications, resulting in an increased number of paralogs. Low amino acid sequence identities among functional group members, and lack of conserved gene order and orientation in regions containing similar groups of paralogs, suggest that most of the paralogs are not the result of recent duplication events. The genome sizes of additional cultured Acidobacteria strains were estimated using pulsed-field gel electrophoresis to determine the prevalence of the large genome trait within the phylum. Members of subdivision 3 had larger genomes than those of subdivision 1, but none were as large as the Ellin6076 genome. The large genome of Ellin6076 may not be typical of the phylum, and encodes traits that could provide a selective metabolic, defensive and regulatory advantage in the soil environment.}, }
@article {pmid21949266, year = {2011}, author = {Doyon, JP and Ranwez, V and Daubin, V and Berry, V}, title = {Models, algorithms and programs for phylogeny reconciliation.}, journal = {Briefings in bioinformatics}, volume = {12}, number = {5}, pages = {392-400}, doi = {10.1093/bib/bbr045}, pmid = {21949266}, issn = {1477-4054}, mesh = {*Algorithms ; Animals ; Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; Genome ; Genomics/*methods ; Humans ; Models, Genetic ; *Phylogeny ; Species Specificity ; }, abstract = {Gene sequences contain a gold mine of phylogenetic information. But unfortunately for taxonomists this information does not only tell the story of the species from which it was collected. Genes have their own complex histories which record speciation events, of course, but also many other events. Among them, gene duplications, transfers and losses are especially important to identify. These events are crucial to account for when reconstructing the history of species, and they play a fundamental role in the evolution of genomes, the diversification of organisms and the emergence of new cellular functions. We review reconciliations between gene and species trees, which are rigorous approaches for identifying duplications, transfers and losses that mark the evolution of a gene family. Existing reconciliation models and algorithms are reviewed and difficulties in modeling gene transfers are discussed. We also compare different reconciliation programs along with their advantages and disadvantages.}, }
@article {pmid21948832, year = {2011}, author = {Eloe, EA and Malfatti, F and Gutierrez, J and Hardy, K and Schmidt, WE and Pogliano, K and Pogliano, J and Azam, F and Bartlett, DH}, title = {Isolation and characterization of a psychropiezophilic alphaproteobacterium.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {22}, pages = {8145-8153}, pmid = {21948832}, issn = {1098-5336}, support = {R01 GM057045/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics ; Cluster Analysis ; Cold Temperature ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Hydrostatic Pressure ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Roseobacter/*classification/genetics/growth &amp; development/*isolation &amp; purification ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Cultivated psychropiezophilic (low-temperature- and high-pressure-adapted) bacteria are currently restricted to phylogenetically narrow groupings capable of growth under nutrient-replete conditions, limiting current knowledge of the extant functional attributes and evolutionary constraints of diverse microorganisms inhabiting the cold, deep ocean. This study documents the isolation of a deep-sea bacterium following dilution-to-extinction cultivation using a natural seawater medium at high hydrostatic pressure and low temperature. To our knowledge, this isolate, designated PRT1, is the slowest-growing (minimal doubling time, 36 h) and lowest cell density-producing (maximal densities of 5.0 × 10[6] cells ml[-1]) piezophile yet obtained. Optimal growth was at 80 MPa, correlating with the depth of capture (8,350 m), and 10°C, with average cell sizes of 1.46 μm in length and 0.59 μm in width. Through detailed growth studies, we provide further evidence for the temperature-pressure dependence of the growth rate for deep-ocean bacteria. PRT1 was phylogenetically placed within the Roseobacter clade, a bacterial lineage known for widespread geographic distribution and assorted lifestyle strategies in the marine environment. Additionally, the gene transfer agent (GTA) g5 capsid protein gene was amplified from PRT1, indicating a potential mechanism for increased genetic diversification through horizontal gene transfer within the hadopelagic environment. This study provides a phylogenetically novel isolate for future investigations of high-pressure adaptation, expands the known physiological traits of cultivated members of the Roseobacter lineage, and demonstrates the feasibility of cultivating novel microbial members from the deep ocean using natural seawater.}, }
@article {pmid21948416, year = {2011}, author = {Costello, C and Kreft, JU and Thomas, CM and Mendes, PM}, title = {Protein nanoarrays for high-resolution patterning of bacteria on gold surfaces.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {790}, number = {}, pages = {191-200}, doi = {10.1007/978-1-61779-319-6_15}, pmid = {21948416}, issn = {1940-6029}, mesh = {Bacterial Proteins/chemistry/metabolism ; Cell Communication ; Cells, Immobilized/cytology ; Culture Techniques/*instrumentation ; Dimethylpolysiloxanes/chemistry ; Escherichia coli/*cytology ; Gold/*chemistry ; Mannose-Binding Lectin/chemistry/metabolism ; Mannosides/chemistry/metabolism ; Nanotechnology/*instrumentation ; Printing ; Protein Array Analysis/*instrumentation ; Surface Properties ; }, abstract = {In recent years, the majority of research on surface patterning, as a means of precisely controlling cell -positioning and adhesion on surfaces, has focused on eukaryotic cells. Such research has led to new insights into cell biology, advances in tissue engineering, and cell motility. In contrast, considerably less work has been reported on tightly controlled patterning of bacteria, despite its potential in a wide variety of applications, including fabrication of in vitro model systems for studies of bacterial processes, such as quorum sensing and horizontal gene transfer. This is partly due to their small size - often 1-3 μm or less. To study these processes, microscale and nanoscale engineered material surfaces must be developed to create in vitro bacteria arrays, which can allow valuable insights into natural systems such as the soil or the human gut, and are often complex and spatially structured habitats. Here, we outline a protocol to create defined patterns of bacteria to study such systems at the single cell level that is based on the formation of protein nanoarrays on mannoside-terminated self-assembled monolayers via nanocontact printing and the subsequent deposition of bacteria from solution on the unpatterned regions of the mannoside-terminated substrate.}, }
@article {pmid21945051, year = {2012}, author = {Müller, MJ and von Mühlen, C and Valiati, VH and da Silva Valente, VL}, title = {Wolbachia pipientis is associated with different mitochondrial haplotypes in natural populations of Drosophila willistoni.}, journal = {Journal of invertebrate pathology}, volume = {109}, number = {1}, pages = {152-155}, doi = {10.1016/j.jip.2011.08.011}, pmid = {21945051}, issn = {1096-0805}, mesh = {Animals ; Brazil ; DNA, Mitochondrial/genetics ; Drosophila/genetics/*microbiology ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; Gram-Negative Bacterial Infections/microbiology/*veterinary ; Haplotypes ; Host-Pathogen Interactions ; Mitochondria/*genetics/microbiology ; Pest Control, Biological ; Symbiosis ; Wolbachia/*pathogenicity/physiology ; }, abstract = {The prevalence of the endosymbiont Wolbachia pipientis and its effects on mitochondrial genetic diversity were analyzed in natural populations of Drosophila willistoni, a neotropical species recently infected. Total infection rate was 55% and no evidence was found that the Wolbachia infection decreased the diversity of mtDNA. Wolbachia was seen to be associated with different mitochondria, suggesting multiple horizontal transmission events and/or transmission paternal leakage of mitochondrial and/or Wolbachia. These hypotheses are evaluated in the context of the present study and other research.}, }
@article {pmid21943226, year = {2011}, author = {Sanchez-Puerta, MV and Abbona, CC and Zhuo, S and Tepe, EJ and Bohs, L and Olmstead, RG and Palmer, JD}, title = {Multiple recent horizontal transfers of the cox1 intron in Solanaceae and extended co-conversion of flanking exons.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {277}, pmid = {21943226}, issn = {1471-2148}, support = {BB R03 TW008353-01/BB/FDA HHS/United States ; R01-GM-70612/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Sequence ; Computational Biology ; Cyclooxygenase 1/*genetics ; DNA Primers/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Introns/*genetics ; Likelihood Functions ; Models, Genetic ; *Phylogeny ; Sequence Alignment ; Solanaceae/*enzymology/genetics ; }, abstract = {BACKGROUND: The most frequent case of horizontal transfer in plants involves a group I intron in the mitochondrial gene cox1, which has been acquired via some 80 separate plant-to-plant transfer events among 833 diverse angiosperms examined. This homing intron encodes an endonuclease thought to promote the intron's promiscuous behavior. A promising experimental approach to study endonuclease activity and intron transmission involves somatic cell hybridization, which in plants leads to mitochondrial fusion and genome recombination. However, the cox1 intron has not yet been found in the ideal group for plant somatic genetics - the Solanaceae. We therefore undertook an extensive survey of this family to find members with the intron and to learn more about the evolutionary history of this exceptionally mobile genetic element.<br><br>RESULTS: Although 409 of the 426 species of Solanaceae examined lack the cox1 intron, it is uniformly present in three phylogenetically disjunct clades. Despite strong overall incongruence of cox1 intron phylogeny with angiosperm phylogeny, two of these clades possess nearly identical intron sequences and are monophyletic in intron phylogeny. These two clades, and possibly the third also, contain a co-conversion tract (CCT) downstream of the intron that is extended relative to all previously recognized CCTs in angiosperm cox1. Re-examination of all published cox1 genes uncovered additional cases of extended co-conversion and identified a rare case of putative intron loss, accompanied by full retention of the CCT.<br><br>CONCLUSIONS: We infer that the cox1 intron was separately and recently acquired by at least three different lineages of Solanaceae. The striking identity of the intron and CCT from two of these lineages suggests that one of these three intron captures may have occurred by a within-family transfer event. This is consistent with previous evidence that horizontal transfer in plants is biased towards phylogenetically local events. The discovery of extended co-conversion suggests that other cox1 conversions may be longer than realized but obscured by the exceptional conservation of plant mitochondrial sequences. Our findings provide further support for the rampant-transfer model of cox1 intron evolution and recommend the Solanaceae as a model system for the experimental analysis of cox1 intron transfer in plants.}, }
@article {pmid21943216, year = {2011}, author = {Liu, H and Fu, Y and Li, B and Yu, X and Xie, J and Cheng, J and Ghabrial, SA and Li, G and Yi, X and Jiang, D}, title = {Widespread horizontal gene transfer from circular single-stranded DNA viruses to eukaryotic genomes.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {276}, pmid = {21943216}, issn = {1471-2148}, mesh = {Base Sequence ; Cluster Analysis ; Computational Biology ; DNA Viruses/*genetics ; DNA, Single-Stranded/*genetics ; DNA, Viral/*genetics ; Databases, Genetic ; Eukaryota/*genetics/virology ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: In addition to vertical transmission, organisms can also acquire genes from other distantly related species or from their extra-chromosomal elements (plasmids and viruses) via horizontal gene transfer (HGT). It has been suggested that phages represent substantial forces in prokaryotic evolution. In eukaryotes, retroviruses, which can integrate into host genome as an obligate step in their replication strategy, comprise approximately 8% of the human genome. Unlike retroviruses, few members of other virus families are known to transfer genes to host genomes.<br><br>RESULTS: Here we performed a systematic search for sequences related to circular single-stranded DNA (ssDNA) viruses in publicly available eukaryotic genome databases followed by comprehensive phylogenetic analysis. We conclude that the replication initiation protein (Rep)-related sequences of geminiviruses, nanoviruses and circoviruses have been frequently transferred to a broad range of eukaryotic species, including plants, fungi, animals and protists. Some of the transferred viral genes were conserved and expressed, suggesting that these genes have been coopted to assume cellular functions in the host genomes. We also identified geminivirus-like and parvovirus-like transposable elements in genomes of fungi and lower animals, respectively, and thereby provide direct evidence that eukaryotic transposons could derive from ssDNA viruses.<br><br>CONCLUSIONS: Our discovery extends the host range of circular ssDNA viruses and sheds light on the origin and evolution of these viruses. It also suggests that ssDNA viruses act as an unforeseen source of genetic innovation in their hosts.}, }
@article {pmid21943130, year = {2011}, author = {Fernandez, FJ and Garces, F and López-Estepa, M and Aguilar, J and Baldomà, L and Coll, M and Badia, J and Vega, MC}, title = {The UlaG protein family defines novel structural and functional motifs grafted on an ancient RNase fold.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {273}, pmid = {21943130}, issn = {1471-2148}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Archaea/chemistry/enzymology/genetics ; Bacteria/chemistry/*enzymology/*genetics ; Carboxylic Ester Hydrolases/*chemistry/genetics ; *Evolution, Molecular ; Genome, Bacterial ; Models, Molecular ; Molecular Sequence Data ; *Phylogeny ; Protein Conformation ; Protein Folding ; Ribonucleases/*chemistry/genetics ; Sequence Alignment ; Structural Homology, Protein ; }, abstract = {BACKGROUND: Bacterial populations are highly successful at colonizing new habitats and adapting to changing environmental conditions, partly due to their capacity to evolve novel virulence and metabolic pathways in response to stress conditions and to shuffle them by horizontal gene transfer (HGT). A common theme in the evolution of new functions consists of gene duplication followed by functional divergence. UlaG, a unique manganese-dependent metallo-β-lactamase (MBL) enzyme involved in L-ascorbate metabolism by commensal and symbiotic enterobacteria, provides a model for the study of the emergence of new catalytic activities from the modification of an ancient fold. Furthermore, UlaG is the founding member of the so-called UlaG-like (UlaGL) protein family, a recently established and poorly characterized family comprising divalent (and perhaps trivalent) metal-binding MBLs that catalyze transformations on phosphorylated sugars and nucleotides.<br><br>RESULTS: Here we combined protein structure-guided and sequence-only molecular phylogenetic analyses to dissect the molecular evolution of UlaG and to study its phylogenomic distribution, its relatedness with present-day UlaGL protein sequences and functional conservation. Phylogenetic analyses indicate that UlaGL sequences are present in Bacteria and Archaea, with bona fide orthologs found mainly in mammalian and plant-associated Gram-negative and Gram-positive bacteria. The incongruence between the UlaGL tree and known species trees indicates exchange by HGT and suggests that the UlaGL-encoding genes provided a growth advantage under changing conditions. Our search for more distantly related protein sequences aided by structural homology has uncovered that UlaGL sequences have a common evolutionary origin with present-day RNA processing and metabolizing MBL enzymes widespread in Bacteria, Archaea, and Eukarya. This observation suggests an ancient origin for the UlaGL family within the broader trunk of the MBL superfamily by duplication, neofunctionalization and fixation.<br><br>CONCLUSIONS: Our results suggest that the forerunner of UlaG was present as an RNA metabolizing enzyme in the last common ancestor, and that the modern descendants of that ancestral gene have a wide phylogenetic distribution and functional roles. We propose that the UlaGL family evolved new metabolic roles among bacterial and possibly archeal phyla in the setting of a close association with metazoans, such as in the mammalian gastrointestinal tract or in animal and plant pathogens, as well as in environmental settings. Accordingly, the major evolutionary forces shaping the UlaGL family include vertical inheritance and lineage-specific duplication and acquisition of novel metabolic functions, followed by HGT and numerous lineage-specific gene loss events.}, }
@article {pmid21943043, year = {2011}, author = {Schneider, G and Dobrindt, U and Middendorf, B and Hochhut, B and Szijártó, V and Emody, L and Hacker, J}, title = {Mobilisation and remobilisation of a large archetypal pathogenicity island of uropathogenic Escherichia coli in vitro support the role of conjugation for horizontal transfer of genomic islands.}, journal = {BMC microbiology}, volume = {11}, number = {}, pages = {210}, pmid = {21943043}, issn = {1471-2180}, mesh = {*Conjugation, Genetic ; *Gene Transfer, Horizontal ; *Genomic Islands ; Uropathogenic Escherichia coli/*genetics ; }, abstract = {BACKGROUND: A substantial amount of data has been accumulated supporting the important role of genomic islands (GEIs)--including pathogenicity islands (PAIs)--in bacterial genome plasticity and the evolution of bacterial pathogens. Their instability and the high level sequence similarity of different (partial) islands suggest an exchange of PAIs between strains of the same or even different bacterial species by horizontal gene transfer (HGT). Transfer events of archetypal large genomic islands of enterobacteria which often lack genes required for mobilisation or transfer have been rarely investigated so far.<br><br>RESULTS: To study mobilisation of such large genomic regions in prototypic uropathogenic E. coli (UPEC) strain 536, PAI II536 was supplemented with the mobRP4 region, an origin of replication (oriVR6K), an origin of transfer (oriTRP4) and a chloramphenicol resistance selection marker. In the presence of helper plasmid RP4, conjugative transfer of the 107-kb PAI II536 construct occured from strain 536 into an E. coli K-12 recipient. In transconjugants, PAI II536 existed either as a cytoplasmic circular intermediate (CI) or integrated site-specifically into the recipient's chromosome at the leuX tRNA gene. This locus is the chromosomal integration site of PAI II536 in UPEC strain 536. From the E. coli K-12 recipient, the chromosomal PAI II536 construct as well as the CIs could be successfully remobilised and inserted into leuX in a PAI II536 deletion mutant of E. coli 536.<br><br>CONCLUSIONS: Our results corroborate that mobilisation and conjugal transfer may contribute to evolution of bacterial pathogens through horizontal transfer of large chromosomal regions such as PAIs. Stabilisation of these mobile genetic elements in the bacterial chromosome result from selective loss of mobilisation and transfer functions of genomic islands.}, }
@article {pmid21943000, year = {2011}, author = {Andam, CP and Gogarten, JP}, title = {Biased gene transfer and its implications for the concept of lineage.}, journal = {Biology direct}, volume = {6}, number = {}, pages = {47}, pmid = {21943000}, issn = {1745-6150}, mesh = {Alleles ; Archaea/classification/*genetics/metabolism ; Bacteria/classification/*genetics/metabolism ; Biological Evolution ; Databases, Protein ; *Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; Genes, rRNA ; Phenylalanine-tRNA Ligase/genetics/metabolism ; Phylogeny ; RNA, Transfer/genetics/metabolism ; Sequence Alignment ; Serine-tRNA Ligase/*genetics/metabolism ; Threonine-tRNA Ligase/*genetics/metabolism ; }, abstract = {BACKGROUND: In the presence of horizontal gene transfer (HGT), the concepts of lineage and genealogy in the microbial world become more ambiguous because chimeric genomes trace their ancestry from a myriad of sources, both living and extinct.<br><br>RESULTS: We present the evolutionary histories of three aminoacyl-tRNA synthetases (aaRS) to illustrate that the concept of organismal lineage in the prokaryotic world is defined by both vertical inheritance and reticulations due to HGT. The acquisition of a novel gene from a distantly related taxon can be considered as a shared derived character that demarcates a group of organisms, as in the case of the spirochaete Phenylalanyl-tRNA synthetase (PheRS). On the other hand, when organisms transfer genetic material with their close kin, the similarity and therefore relatedness observed among them is essentially shaped by gene transfer. Studying the distribution patterns of divergent genes with identical functions, referred to as homeoalleles, can reveal preferences for transfer partners. We describe the very ancient origin and the distribution of the archaeal homeoalleles for Threonyl-tRNA synthetases (ThrRS) and Seryl-tRNA synthetases (SerRS).<br><br>CONCLUSIONS: Patterns created through biased HGT can be undistinguishable from those created through shared organismal ancestry. A re-evaluation of the definition of lineage is necessary to reflect genetic relatedness due to both HGT and vertical inheritance. In most instances, HGT bias will maintain and strengthen similarity within groups. Only in cases where HGT bias is due to other factors, such as shared ecological niche, do patterns emerge from gene phylogenies that are in conflict with those reflecting shared organismal ancestry.}, }
@article {pmid21941462, year = {2011}, author = {Angelov, A and Voss, J and Liebl, W}, title = {Characterization of plasmid pPO1 from the hyperacidophile Picrophilus oshimae.}, journal = {Archaea (Vancouver, B.C.)}, volume = {2011}, number = {}, pages = {723604}, pmid = {21941462}, issn = {1472-3654}, mesh = {DNA Replication ; DNA Transposable Elements ; DNA, Archaeal/chemistry/genetics ; Escherichia coli ; Euryarchaeota ; Gene Transfer, Horizontal ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Open Reading Frames ; *Plasmids ; Recombination, Genetic ; Sequence Analysis, DNA ; Sulfuric Acids/metabolism ; Thermoplasmales/*genetics ; Transcription Initiation Site ; }, abstract = {Picrophilus oshimae and Picrophilus torridus are free-living, moderately thermophilic and acidophilic organisms from the lineage of Euryarchaeota. With a pH optimum of growth at pH 0.7 and the ability to even withstand molar concentrations of sulphuric acid, these organisms represent the most extreme acidophiles known. So far, nothing is known about plasmid biology in these hyperacidophiles. Also, there are no genetic tools available for this genus. We have mobilized the 7.6 Kbp plasmid from P. oshimae in E. coli by introducing origin-containing transposons and described the plasmid in terms of its nucleotide sequence, copy number in the native host, mode of replication, and transcriptional start sites of the encoded ORFs. Plasmid pPO1 may encode a restriction/modification system in addition to its replication functions. The information gained from the pPO1 plasmid may prove useful in developing a cloning system for this group of extreme acidophiles.}, }
@article {pmid21941461, year = {2011}, author = {Ehlers, C and Jäger, D and Schmitz, RA}, title = {Establishing a markerless genetic exchange system for Methanosarcina mazei strain Gö1 for constructing chromosomal mutants of small RNA genes.}, journal = {Archaea (Vancouver, B.C.)}, volume = {2011}, number = {}, pages = {439608}, pmid = {21941461}, issn = {1472-3654}, mesh = {Chromosomes, Archaeal ; Gene Deletion ; Gene Transfer, Horizontal ; Genetics, Microbial/*methods ; Hypoxanthine Phosphoribosyltransferase/genetics ; Methanosarcina/*genetics ; Plasmids ; RNA, Archaeal/*genetics ; RNA, Untranslated/*genetics ; *Recombination, Genetic ; Selection, Genetic ; }, abstract = {A markerless genetic exchange system was successfully established in Methanosarcina mazei strain Gö1 using the hpt gene coding for hypoxanthine phosphoribosyltransferase. First, a chromosomal deletion mutant of the hpt gene was generated conferring resistance to the purine analog 8-aza-2,6-diaminopurine (8-ADP). The nonreplicating allelic exchange vector (pRS345) carrying the pac-resistance cassette for direct selection of chromosomal integration, and the hpt gene for counterselection was introduced into this strain. By a pop-in and ultimately pop-out event of the plasmid from the chromosome, allelic exchange is enabled. Using this system, we successfully generated a M. mazei deletion mutant of the gene encoding the regulatory non-coding RNA sRNA(154). Characterizing M. mazei ΔsRNA(154) under nitrogen limiting conditions demonstrated differential expression of at least three cytoplasmic proteins and reduced growth strongly arguing for a prominent role of sRNA(154) in regulation of nitrogen fixation by posttranscriptional regulation.}, }
@article {pmid21941121, year = {2011}, author = {Chen, XL and Tang, DJ and Jiang, RP and He, YQ and Jiang, BL and Lu, GT and Tang, JL}, title = {sRNA-Xcc1, an integron-encoded transposon- and plasmid-transferred trans-acting sRNA, is under the positive control of the key virulence regulators HrpG and HrpX of Xanthomonas campestris pathovar campestris.}, journal = {RNA biology}, volume = {8}, number = {6}, pages = {947-953}, pmid = {21941121}, issn = {1555-8584}, mesh = {Bacterial Proteins/*genetics ; Base Sequence ; Blotting, Northern ; DNA Transposable Elements/genetics ; Gene Expression Regulation, Bacterial ; Integrons/genetics ; Molecular Sequence Data ; Mutation ; Nucleic Acid Conformation ; Phylogeny ; Plasmids/genetics ; Promoter Regions, Genetic/genetics ; RNA, Bacterial/chemistry/classification/*genetics ; RNA, Small Untranslated/chemistry/classification/*genetics ; Sequence Homology, Nucleic Acid ; Trans-Activators/*genetics ; Transcription Factors/*genetics ; Virulence/genetics ; Xanthomonas campestris/*genetics/pathogenicity ; }, abstract = {sRNA-Xcc1 is a trans-acting sRNA recently identified from the plant pathogenic bacterium Xanthomonas campestris pathovar campestris (Xcc). Here, the phylogenetic distribution, predicted secondary structure and regulation of expression of sRNA-Xcc1 were analyzed. The analysis showed (1) a total 81 sRNA-Xcc1 homologs that are found in some bacterial strains that are taxonomically unrelated, belonging to the α-, β-, γ- and δ-proteobacteria (2) that some sRNA-Xcc1 homologs are located in a plasmid-borne transposon or near a transposase coding gene, (3) that sRNA-Xcc1 is encoded by a integron gene cassette in Xcc and sRNA-Xcc1 homologs occur in integron gene cassettes of some uncultured bacteria and (4) that sRNA-Xcc1 homologs have a highly conserved sequence motif and a stable consensus secondary structure. These findings strongly support the idea that sRNA-Xcc1 represents a novel family of sRNAs which may be originally captured by integrons from natural environments and then spread among different bacterial species via horizontal gene transfer, possibly by means of transposons and plasmids. The expression analysis results demonstrated that the transcription of sRNA-Xcc1 is under the positive control of the key virulence regulators HrpG and HrpX, indicating that sRNA-Xcc1 may be involved in the virulence regulation of Xcc.}, }
@article {pmid21940655, year = {2012}, author = {Zhao, WH and Chen, G and Ito, R and Kimura, S and Hu, ZQ}, title = {Identification of a plasmid-borne blaIMP-11 gene in clinical isolates of Escherichia coli and Klebsiella pneumoniae.}, journal = {Journal of medical microbiology}, volume = {61}, number = {Pt 2}, pages = {246-251}, doi = {10.1099/jmm.0.035626-0}, pmid = {21940655}, issn = {1473-5644}, mesh = {Anti-Bacterial Agents/pharmacology ; Carbapenems/pharmacology ; Cluster Analysis ; Escherichia coli/*enzymology/genetics/isolation &amp; purification ; Escherichia coli Infections/*microbiology ; Gene Transfer, Horizontal ; Humans ; Infant ; Infant, Newborn ; Integrons ; Klebsiella Infections/*microbiology ; Klebsiella pneumoniae/*enzymology/genetics/isolation &amp; purification ; Microbial Sensitivity Tests ; Phylogeny ; *Plasmids ; Sequence Analysis, DNA ; Sequence Homology ; beta-Lactam Resistance ; beta-Lactamases/*genetics ; }, abstract = {The acquired metallo-β-lactamases represent a significant clinical threat due to their unrivalled hydrolysis spectrum and their resistance to therapeutic inhibitors of β-lactamase. In this study, we identified plasmid- and integron-borne bla(IMP-11) in clinical isolates of Escherichia coli and Klebsiella pneumoniae. The bla(IMP-11) gene cassette was carried by a typical class 1 integron together with aacA1 and orfG gene cassettes. The integron, intI1-bla(IMP-11)-aacA1-orfG-qacEΔ1-sul1, was easily transferred by intraspecies and intergenus conjugation of bacteria, indicating that the integron is located on a transferable plasmid. The integrated genes were preceded by TGGACA-N(17)-TAAACT, a hybrid P(c) promoter. Similar to the wild-type donors, the transconjugants also showed reduced susceptibility or resistance to carbapenems, amikacin and kanamycin. The identical integron was detected in four bacterial strains which were genetically different but were isolated from infant inpatients in the same paediatric department. These results demonstrate the colonization of the plasmid- and integron-borne bla(IMP-11) and aacA1 in the hospital environment, highlighting the importance of surveying and controlling the spread of such resistance determinants in nosocomial pathogens.}, }
@article {pmid21938538, year = {2012}, author = {Chouchani, C and El Salabi, A and Marrakchi, R and Ferchichi, L and Walsh, TR}, title = {Characterization of IncA/C conjugative plasmid harboring bla TEM-52 and bla CTX-M-15 extended-spectrum β-lactamases in clinical isolates of Escherichia coli in Tunisia.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {31}, number = {6}, pages = {1081-1087}, pmid = {21938538}, issn = {1435-4373}, mesh = {Aged ; Conjugation, Genetic ; Escherichia coli/*enzymology/genetics/*isolation &amp; purification ; Escherichia coli Infections/*microbiology ; Female ; Gene Transfer, Horizontal ; Humans ; Male ; Middle Aged ; Molecular Typing ; Plasmids/*classification ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; Tunisia ; Urinary Tract Infections/microbiology ; beta-Lactamases/*genetics ; }, abstract = {To characterize the extended-spectrum β-lactamases (ESBLs) as well as their genetic environment in different isolates of Escherichia coli from patients with repeated urinary tract infections, large multidrug resistance (MDR) plasmids have been found. Definitive evidence for the presence of an A/C incompatibility complex (IncA/C) plasmid in the MDR isolates was provided by the probing of plasmids extracted from the clinical isolates. Conjugation experiments showed that bla genes were transferred by conjugation from the ten E. coli clinical isolates to E. coli XL1-Blue recipient. A comparative restriction fragment length polymorphism (RFLP) analysis of these plasmids showed that they are genetically similar, while the overall similarity of these plasmids supports the likelihood of recent movements among these E. coli isolates. Polymerase chain reaction (PCR) amplification and sequencing of the amplicons showed that the IncA/C plasmids harbor two ESBLs, identified as TEM-52 and CTX-M-15. Analysis of the plasmid DNA surrounding the bla (CTX-M-15) gene in the clinical isolates under study revealed a partially truncated fragment of ISEcp1 tnpA transposase. This result indicates the variety of genetic events that have enabled associations between ISEcp1 sequences and bla (CTX-M-15) genes in these clinical isolates.}, }
@article {pmid21936906, year = {2011}, author = {Williams, D and Fournier, GP and Lapierre, P and Swithers, KS and Green, AG and Andam, CP and Gogarten, JP}, title = {A rooted net of life.}, journal = {Biology direct}, volume = {6}, number = {}, pages = {45}, pmid = {21936906}, issn = {1745-6150}, mesh = {Archaea/genetics ; Bacteria/genetics ; Biological Evolution ; Gene Transfer, Horizontal ; Genes, rRNA ; *Genome, Archaeal ; *Genome, Bacterial ; *Models, Genetic ; Multigene Family ; *Phylogeny ; Ribosomal Proteins/genetics ; Ribosomes/*genetics ; }, abstract = {Phylogenetic reconstruction using DNA and protein sequences has allowed the reconstruction of evolutionary histories encompassing all life. We present and discuss a means to incorporate much of this rich narrative into a single model that acknowledges the discrete evolutionary units that constitute the organism. Briefly, this Rooted Net of Life genome phylogeny is constructed around an initial, well resolved and rooted tree scaffold inferred from a supermatrix of combined ribosomal genes. Extant sampled ribosomes form the leaves of the tree scaffold. These leaves, but not necessarily the deeper parts of the scaffold, can be considered to represent a genome or pan-genome, and to be associated with members of other gene families within that sequenced (pan)genome. Unrooted phylogenies of gene families containing four or more members are reconstructed and superimposed over the scaffold. Initially, reticulations are formed where incongruities between topologies exist. Given sufficient evidence, edges may then be differentiated as those representing vertical lines of inheritance within lineages and those representing horizontal genetic transfers or endosymbioses between lineages.}, }
@article {pmid21931687, year = {2011}, author = {Remenant, B and de Cambiaire, JC and Cellier, G and Jacobs, JM and Mangenot, S and Barbe, V and Lajus, A and Vallenet, D and Medigue, C and Fegan, M and Allen, C and Prior, P}, title = {Ralstonia syzygii, the Blood Disease Bacterium and some Asian R. solanacearum strains form a single genomic species despite divergent lifestyles.}, journal = {PloS one}, volume = {6}, number = {9}, pages = {e24356}, pmid = {21931687}, issn = {1932-6203}, mesh = {Asia ; Base Sequence ; Genes, Bacterial ; Genome, Bacterial/*genetics ; Molecular Sequence Data ; Phylogeny ; Ralstonia/classification/*genetics ; Ralstonia solanacearum/classification/*genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {The Ralstonia solanacearum species complex includes R. solanacearum, R. syzygii, and the Blood Disease Bacterium (BDB). All colonize plant xylem vessels and cause wilt diseases, but with significant biological differences. R. solanacearum is a soilborne bacterium that infects the roots of a broad range of plants. R. syzygii causes Sumatra disease of clove trees and is actively transmitted by cercopoid insects. BDB is also pathogenic to a single host, banana, and is transmitted by pollinating insects. Sequencing and DNA-DNA hybridization studies indicated that despite their phenotypic differences, these three plant pathogens are actually very closely related, falling into the Phylotype IV subgroup of the R. solanacearum species complex. To better understand the relationships among these bacteria, we sequenced and annotated the genomes of R. syzygii strain R24 and BDB strain R229. These genomes were compared to strain PSI07, a closely related Phylotype IV tomato isolate of R. solanacearum, and to five additional R. solanacearum genomes. Whole-genome comparisons confirmed previous phylogenetic results: the three phylotype IV strains share more and larger syntenic regions with each other than with other R. solanacearum strains. Furthermore, the genetic distances between strains, assessed by an in-silico equivalent of DNA-DNA hybridization, unambiguously showed that phylotype IV strains of BDB, R. syzygii and R. solanacearum form one genomic species. Based on these comprehensive data we propose a revision of the taxonomy of the R. solanacearum species complex. The BDB and R. syzygii genomes encoded no obvious unique metabolic capacities and contained no evidence of horizontal gene transfer from bacteria occupying similar niches. Genes specific to R. syzygii and BDB were almost all of unknown function or extrachromosomal origin. Thus, the pathogenic life-styles of these organisms are more probably due to ecological adaptation and genomic convergence during vertical evolution than to the acquisition of DNA by horizontal transfer.}, }
@article {pmid21930924, year = {2011}, author = {Bonocora, RP and Zeng, Q and Abel, EV and Shub, DA}, title = {A homing endonuclease and the 50-nt ribosomal bypass sequence of phage T4 constitute a mobile DNA cassette.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {39}, pages = {16351-16356}, pmid = {21930924}, issn = {1091-6490}, support = {U54 AI057158/AI/NIAID NIH HHS/United States ; U54-AI057158/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacteriophage T4/enzymology/*genetics ; Base Sequence ; DNA Topoisomerases, Type I/genetics/metabolism ; DNA, Viral/*genetics ; Endonucleases/chemistry/*metabolism ; Gene Transfer, Horizontal ; Genes, Viral ; Hydrolysis ; Introns ; Molecular Sequence Data ; Sequence Homology, Amino Acid ; }, abstract = {Since its initial description more than two decades ago, the ribosome bypass (or "hop") sequence of phage T4 stands out as a uniquely extreme example of programmed translational frameshifting. The gene for a DNA topoisomerase subunit of T4 has been split by a 1-kb insertion into two genes that retain topoisomerase function. A second 50-nt insertion, beginning with an in-phase stop codon, is inserted near the start of the newly created downstream gene 60. Instead of terminating at this stop codon, approximately half of the ribosomes skip 50 nucleotides and continue translation in a new reading frame. However, no functions, regulatory or otherwise, have been imputed for the truncated peptide that results from termination at codon 46 or for the bypass sequence itself. Moreover, how this unusual mRNA organization arose and why it is maintained have never been explained. We show here that a homing endonuclease (MobA) is encoded in the insertion that created gene 60, and the mobA gene together with the bypass sequence constitute a mobile DNA cassette. The bypass sequence provides protection against self-cleavage by the nuclease, whereas the nuclease promotes horizontal spread of the entire cassette to related bacteriophages. Group I introns frequently provide protection against self-cleavage by associated homing endonucleases. We present a scenario by which the bypass sequence, which is otherwise a unique genetic element, might have been derived from a degenerate group I intron.}, }
@article {pmid21930755, year = {2011}, author = {Warren, AE and Boulianne-Larsen, CM and Chandler, CB and Chiotti, K and Kroll, E and Miller, SR and Taddei, F and Sermet-Gaudelus, I and Ferroni, A and McInnerney, K and Franklin, MJ and Rosenzweig, F}, title = {Genotypic and phenotypic variation in Pseudomonas aeruginosa reveals signatures of secondary infection and mutator activity in certain cystic fibrosis patients with chronic lung infections.}, journal = {Infection and immunity}, volume = {79}, number = {12}, pages = {4802-4818}, pmid = {21930755}, issn = {1098-5522}, support = {P20 RR016455/RR/NCRR NIH HHS/United States ; R15 AI079708/AI/NIAID NIH HHS/United States ; R15-AI079708/AI/NIAID NIH HHS/United States ; }, mesh = {Adolescent ; Bacterial Proteins/genetics/metabolism ; Child ; Child, Preschool ; Chronic Disease ; Cystic Fibrosis/*complications/microbiology ; Drug Resistance, Bacterial ; Gene Expression Regulation, Bacterial/physiology ; *Genetic Variation ; Genotype ; Humans ; Infant ; Lung Diseases/complications/*microbiology ; Molecular Sequence Data ; Mutation ; Phenotype ; Phylogeny ; Pseudomonas Infections/*microbiology ; Pseudomonas aeruginosa/classification/*genetics/pathogenicity ; Virulence Factors/genetics ; Young Adult ; }, abstract = {Evolutionary adaptation of Pseudomonas aeruginosa to the cystic fibrosis lung is limited by genetic variation, which depends on rates of horizontal gene transfer and mutation supply. Because each may increase following secondary infection or mutator emergence, we sought to ascertain the incidence of secondary infection and genetic variability in populations containing or lacking mutators. Forty-nine strains collected over 3 years from 16 patients were phenotyped for antibiotic resistance and mutator status and were genotyped by repetitive-sequence PCR (rep-PCR), pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST). Though phenotypic and genetic polymorphisms were widespread and clustered more strongly within than between longitudinal series, their distribution revealed instances of secondary infection. Sequence data, however, indicated that interlineage recombination predated initial strain isolation. Mutator series were more likely to be multiply antibiotic resistant, but not necessarily more variable in their nucleotide sequences, than nonmutators. One mutator and one nonmutator series were sequenced at mismatch repair loci and analyzed for gene content using DNA microarrays. Both were wild type with respect to mutL, but mutators carried an 8-bp mutS deletion causing a frameshift mutation. Both series lacked 126 genes encoding pilins, siderophores, and virulence factors whose inactivation has been linked to adaptation during chronic infection. Mutators exhibited loss of severalfold more genes having functions related to mobile elements, motility, and attachment. A 105-kb, 86-gene deletion was observed in one nonmutator that resulted in loss of virulence factors related to pyoverdine synthesis and elements of the multidrug efflux regulon. Diminished DNA repair activity may facilitate but not be absolutely required for rapid evolutionary change.}, }
@article {pmid21930573, year = {2011}, author = {Roy, S and Singh, AK and Viswanathan, R and Nandy, RK and Basu, S}, title = {Transmission of imipenem resistance determinants during the course of an outbreak of NDM-1 Escherichia coli in a sick newborn care unit.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {66}, number = {12}, pages = {2773-2780}, doi = {10.1093/jac/dkr376}, pmid = {21930573}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/*pharmacology ; DNA, Bacterial/chemistry/genetics ; *Disease Outbreaks ; Escherichia coli/drug effects/*enzymology/isolation &amp; purification ; Escherichia coli Infections/epidemiology/microbiology ; Gene Transfer, Horizontal ; Humans ; Imipenem/*pharmacology ; Infant, Newborn ; Male ; Molecular Sequence Data ; Sepsis/epidemiology/microbiology ; Sequence Analysis, DNA ; *beta-Lactam Resistance ; beta-Lactamases/*metabolism ; }, abstract = {OBJECTIVES: This study reports a cluster of septicaemic newborns with imipenem-resistant Escherichia coli in the blood and delineates the possible mechanisms of transmission of imipenem resistance with respect to the New Delhi metallo-β-lactamase (NDM-1) gene.<br><br>METHODS: During a point prevalence survey, attempts were made to isolate Gram-negative bacilli (GNB) from the environment of a sick newborn care unit (SNCU) and body sites of neonates. Subsequently, four fresh neonates admitted to the SNCU developed sepsis with E. coli. E. coli isolates from body sites and blood of the newborns were analysed in terms of clonality, carbapenemases, integrons, virulence factors, porins and transmissibility.<br><br>RESULTS: During the survey, both imipenem-resistant and imipenem-susceptible E. coli were isolated from the body sites of neonates, but none from the environment. None of these neonates developed sepsis. The freshly admitted septicaemic neonates had imipenem-resistant E. coli in their blood, which were similar to the imipenem-susceptible E. coli obtained from the body sites (during the survey) in terms of clonality, phylogroup, virulence and other resistance genes, except possession of bla(NDM-1). Imipenem-resistant E. coli from blood and body sites were not clonal, though both had bla(NDM-1). Besides E. coli, other GNB isolated from the environment and body sites also harboured bla(NDM-1). Imipenem-resistant and imipenem-susceptible E. coli from the blood and body sites respectively, possessed a novel AmpC &#x3b2;-lactamase, bla(CMY-59). The plasmid carrying bla(NDM-1) was transferable.<br><br>CONCLUSIONS: The time frame of isolation and clonal identity indicated a possible transfer of bla(NDM-1) from imipenem-resistant GNB to the imipenem-susceptible E. coli, which subsequently caused septicaemia. This establishes the promiscuous nature of bla(NDM-1) and emphasizes the need for the early recognition of similar isolates.}, }
@article {pmid21926215, year = {2011}, author = {Touchon, M and Barbier, P and Bernardet, JF and Loux, V and Vacherie, B and Barbe, V and Rocha, EP and Duchaud, E}, title = {Complete genome sequence of the fish pathogen Flavobacterium branchiophilum.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {21}, pages = {7656-7662}, pmid = {21926215}, issn = {1098-5336}, mesh = {Adhesins, Bacterial/genetics ; Animals ; Bacterial Toxins/genetics ; Catfishes/microbiology ; DNA, Bacterial/*chemistry/*genetics ; Fish Diseases/microbiology ; Flavobacterium/*genetics/isolation &amp; purification ; Gene Order ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Hungary ; Molecular Sequence Data ; RNA, Bacterial/genetics ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; Virulence Factors/genetics ; }, abstract = {Members of the genus Flavobacterium occur in a variety of ecological niches and represent an interesting diversity of lifestyles. Flavobacterium branchiophilum is the main causative agent of bacterial gill disease, a severe condition affecting various cultured freshwater fish species worldwide, in particular salmonids in Canada and Japan. We report here the complete genome sequence of strain FL-15 isolated from a diseased sheatfish (Silurus glanis) in Hungary. The analysis of the F. branchiophilum genome revealed putative mechanisms of pathogenicity strikingly different from those of the other, closely related fish pathogen Flavobacterium psychrophilum, including the first cholera-like toxin in a non-Proteobacteria and a wealth of adhesins. The comparison with available genomes of other Flavobacterium species revealed a small genome size, large differences in chromosome organization, and fewer rRNA and tRNA genes, in line with its more fastidious growth. In addition, horizontal gene transfer shaped the evolution of F. branchiophilum, as evidenced by its virulence factors, genomic islands, and CRISPR (clustered regularly interspaced short palindromic repeats) systems. Further functional analysis should help in the understanding of host-pathogen interactions and in the development of rational diagnostic tools and control strategies in fish farms.}, }
@article {pmid21923904, year = {2011}, author = {Stiller, JW}, title = {Experimental design and statistical rigor in phylogenomics of horizontal and endosymbiotic gene transfer.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {259}, pmid = {21923904}, issn = {1471-2148}, mesh = {Computational Biology/*methods ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome/*genetics ; Genomics/methods ; *Models, Genetic ; *Phylogeny ; Symbiosis/*genetics ; }, abstract = {A growing number of phylogenomic investigations from diverse eukaryotes are examining conflicts among gene trees as evidence of horizontal gene transfer. If multiple foreign genes from the same eukaryotic lineage are found in a given genome, it is increasingly interpreted as concerted gene transfers during a cryptic endosymbiosis in the organism's evolutionary past, also known as "endosymbiotic gene transfer" or EGT. A number of provocative hypotheses of lost or serially replaced endosymbionts have been advanced; to date, however, these inferences largely have been post-hoc interpretations of genomic-wide conflicts among gene trees. With data sets as large and complex as eukaryotic genome sequences, it is critical to examine alternative explanations for intra-genome phylogenetic conflicts, particularly how much conflicting signal is expected from directional biases and statistical noise. The availability of genome-level data both permits and necessitates phylogenomics that test explicit, a priori predictions of horizontal gene transfer, using rigorous statistical methods and clearly defined experimental controls.}, }
@article {pmid21920958, year = {2012}, author = {Altincicek, B and Kovacs, JL and Gerardo, NM}, title = {Horizontally transferred fungal carotenoid genes in the two-spotted spider mite Tetranychus urticae.}, journal = {Biology letters}, volume = {8}, number = {2}, pages = {253-257}, pmid = {21920958}, issn = {1744-957X}, mesh = {Animals ; Carotenoids/analysis/*biosynthesis/genetics ; Female ; *Gene Transfer, Horizontal ; *Genes, Fungal ; *Genes, Insect ; Male ; Phylogeny ; Pigmentation/genetics ; Pigments, Biological/chemistry ; Sequence Analysis, DNA ; Tetranychidae/*genetics/growth &amp; development/*metabolism/microbiology ; }, abstract = {Carotenoids are organic pigments commonly synthesized by plants, algae and some micro-organisms. Through absorption of light energy, carotenoids facilitate photosynthesis and provide protection against photo-oxidation. While it was presumed that all carotenoids in animals were sequestered from their diets, aphids were recently shown to harbour genomic copies of functional carotenoid biosynthesis genes that were acquired via horizontal gene transfer from fungi. Our search of available animal transcripts revealed the presence of two related genes in the two-spotted spider mite Tetranychus urticae. Phylogenetic analyses suggest that the T. urticae genes were transferred from fungi into the spider mite genome, probably in a similar manner as recently suggested for aphids. The genes are expressed in both green and red morphs, with red morphs exhibiting higher levels of gene expression. Additionally, there appear to be changes in the expression of these genes during diapause. As carotenoids are associated with diapause induction in these animals, our results add to recent findings highlighting the importance of eukaryotic horizontal gene transfer in the ecology and evolution of higher animals.}, }
@article {pmid21917854, year = {2011}, author = {Boc, A and Makarenkov, V}, title = {Towards an accurate identification of mosaic genes and partial horizontal gene transfers.}, journal = {Nucleic acids research}, volume = {39}, number = {21}, pages = {e144}, pmid = {21917854}, issn = {1362-4962}, mesh = {Escherichia coli Proteins/genetics ; *Gene Transfer, Horizontal ; Monte Carlo Method ; *Mosaicism ; Phylogeny ; Recombination, Genetic ; Ribulose-Bisphosphate Carboxylase/genetics ; Sequence Alignment ; }, abstract = {Many bacteria and viruses adapt to varying environmental conditions through the acquisition of mosaic genes. A mosaic gene is composed of alternating sequence polymorphisms either belonging to the host original allele or derived from the integrated donor DNA. Often, the integrated sequence contains a selectable genetic marker (e.g. marker allowing for antibiotic resistance). An effective identification of mosaic genes and detection of corresponding partial horizontal gene transfers (HGTs) are among the most important challenges posed by evolutionary biology. We developed a method for detecting partial HGT events and related intragenic recombination giving rise to the formation of mosaic genes. A bootstrap procedure incorporated in our method is used to assess the support of each predicted partial gene transfer. The proposed method can be also applied to confirm or discard complete (i.e. traditional) horizontal gene transfers detected by any HGT inferring method. While working on a full-genome scale, the new method can be used to assess the level of mosaicism in the considered genomes as well as the rates of complete and partial HGT underlying their evolution.}, }
@article {pmid21917725, year = {2012}, author = {Fort, P and Albertini, A and Van-Hua, A and Berthomieu, A and Roche, S and Delsuc, F and Pasteur, N and Capy, P and Gaudin, Y and Weill, M}, title = {Fossil rhabdoviral sequences integrated into arthropod genomes: ontogeny, evolution, and potential functionality.}, journal = {Molecular biology and evolution}, volume = {29}, number = {1}, pages = {381-390}, doi = {10.1093/molbev/msr226}, pmid = {21917725}, issn = {1537-1719}, mesh = {Animals ; Arthropods/*genetics ; Bayes Theorem ; Databases, Genetic ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Insect ; Phylogeny ; Rhabdoviridae/*genetics ; }, abstract = {Retroelements represent a considerable fraction of many eukaryotic genomes and are considered major drives for adaptive genetic innovations. Recent discoveries showed that despite not normally using DNA intermediates like retroviruses do, Mononegaviruses (i.e., viruses with nonsegmented, negative-sense RNA genomes) can integrate gene fragments into the genomes of their hosts. This was shown for Bornaviridae and Filoviridae, the sequences of which have been found integrated into the germ line cells of many vertebrate hosts. Here, we show that Rhabdoviridae sequences, the major Mononegavirales family, have integrated only into the genomes of arthropod species. We identified 185 integrated rhabdoviral elements (IREs) coding for nucleoproteins, glycoproteins, or RNA-dependent RNA polymerases; they were mostly found in the genomes of the mosquito Aedes aegypti and the blacklegged tick Ixodes scapularis. Phylogenetic analyses showed that most IREs in A. aegypti derived from multiple independent integration events. Since RNA viruses are submitted to much higher substitution rates as compared with their hosts, IREs thus represent fossil traces of the diversity of extinct Rhabdoviruses. Furthermore, analyses of orthologous IREs in A. aegypti field mosquitoes sampled worldwide identified an integrated polymerase IRE fragment that appeared under purifying selection within several million years, which supports a functional role in the host's biology. These results show that A. aegypti was subjected to repeated Rhabdovirus infectious episodes during its evolution history, which led to the accumulation of many integrated sequences. They also suggest that like retroviruses, integrated rhabdoviral sequences may participate actively in the evolution of their hosts.}, }
@article {pmid21910623, year = {2012}, author = {Pflughoeft, KJ and Versalovic, J}, title = {Human microbiome in health and disease.}, journal = {Annual review of pathology}, volume = {7}, number = {}, pages = {99-122}, doi = {10.1146/annurev-pathol-011811-132421}, pmid = {21910623}, issn = {1553-4014}, mesh = {Animals ; Disease/*etiology ; Disease Susceptibility ; Gene Transfer, Horizontal ; Humans ; *Metagenome ; Metagenomics ; Microbial Interactions ; Sequence Analysis, DNA/methods ; Systems Biology ; }, abstract = {Mammals are complex assemblages of mammalian and bacterial cells organized into functional organs, tissues, and cellular communities. Human biology can no longer concern itself only with human cells: Microbiomes at different body sites and functional metagenomics must be considered part of systems biology. The emergence of metagenomics has resulted in the generation of vast data sets of microbial genes and pathways present in different body habitats. The profound differences between microbiomes in various body sites reveal how metagenomes contribute to tissue and organ function. As next-generation DNA-sequencing methods provide whole-metagenome data in addition to gene-expression profiling, metaproteomics, and metabonomics, differences in microbial composition and function are being linked to health and disease states in different organs and tissues. Global parameters of microbial communities may provide valuable information regarding human health status and disease predisposition. More detailed knowledge of the human microbiome will yield next-generation diagnostics and therapeutics for various acute, chronic, localized, and systemic human diseases.}, }
@article {pmid21909280, year = {2011}, author = {Zhu, L and Lau, GW}, title = {Inhibition of competence development, horizontal gene transfer and virulence in Streptococcus pneumoniae by a modified competence stimulating peptide.}, journal = {PLoS pathogens}, volume = {7}, number = {9}, pages = {e1002241}, pmid = {21909280}, issn = {1553-7374}, support = {C06 RR016515/RR/NCRR NIH HHS/United States ; R01 HL090699/HL/NHLBI NIH HHS/United States ; C06 RR 16515-01/RR/NCRR NIH HHS/United States ; HL090699/HL/NHLBI NIH HHS/United States ; }, mesh = {Amidohydrolases/antagonists &amp; inhibitors ; Amino Acid Substitution ; Animals ; Bacterial Proteins/antagonists &amp; inhibitors/genetics/*physiology ; DNA Transformation Competence/*drug effects ; Drug Resistance, Bacterial/drug effects ; Gene Transfer, Horizontal/*drug effects ; Mice ; Pneumococcal Infections/prevention &amp; control ; Regulon/drug effects ; Streptococcus pneumoniae/*genetics/physiology ; Virulence/*drug effects ; }, abstract = {Competence stimulating peptide (CSP) is a 17-amino acid peptide pheromone secreted by Streptococcus pneumoniae. Upon binding of CSP to its membrane-associated receptor kinase ComD, a cascade of signaling events is initiated, leading to activation of the competence regulon by the response regulator ComE. Genes encoding proteins that are involved in DNA uptake and transformation, as well as virulence, are upregulated. Previous studies have shown that disruption of key components in the competence regulon inhibits DNA transformation and attenuates virulence. Thus, synthetic analogues that competitively inhibit CSPs may serve as attractive drugs to control pneumococcal infection and to reduce horizontal gene transfer during infection. We performed amino acid substitutions on conserved amino acid residues of CSP1 in an effort to disable DNA transformation and to attenuate the virulence of S. pneumoniae. One of the mutated peptides, CSP1-E1A, inhibited development of competence in DNA transformation by outcompeting CSP1 in time and concentration-dependent manners. CSP1-E1A reduced the expression of pneumococcal virulence factors choline binding protein D (CbpD) and autolysin A (LytA) in vitro, and significantly reduced mouse mortality after lung infection. Furthermore, CSP1-E1A attenuated the acquisition of an antibiotic resistance gene and a capsule gene in vivo. Finally, we demonstrated that the strategy of using a peptide inhibitor is applicable to other CSP subtype, including CSP2. CSP1-E1A and CSP2-E1A were able to cross inhibit the induction of competence and DNA transformation in pneumococcal strains with incompatible ComD subtypes. These results demonstrate the applicability of generating competitive analogues of CSPs as drugs to control horizontal transfer of antibiotic resistance and virulence genes, and to attenuate virulence during infection by S. pneumoniae.}, }
@article {pmid21909270, year = {2011}, author = {Kikuchi, T and Cotton, JA and Dalzell, JJ and Hasegawa, K and Kanzaki, N and McVeigh, P and Takanashi, T and Tsai, IJ and Assefa, SA and Cock, PJ and Otto, TD and Hunt, M and Reid, AJ and Sanchez-Flores, A and Tsuchihara, K and Yokoi, T and Larsson, MC and Miwa, J and Maule, AG and Sahashi, N and Jones, JT and Berriman, M}, title = {Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus.}, journal = {PLoS pathogens}, volume = {7}, number = {9}, pages = {e1002219}, pmid = {21909270}, issn = {1553-7374}, support = {//Wellcome Trust/United Kingdom ; WT 085775/Z/08/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Sequence ; Animals ; Cell Wall/metabolism ; Cellulases/genetics/metabolism ; Evolution, Molecular ; Lysosomes/genetics/metabolism ; Molecular Sequence Data ; Neuropeptides/biosynthesis ; Peptide Hydrolases/genetics ; Plants/*parasitology ; Tylenchida/*genetics/growth &amp; development ; }, abstract = {Bursaphelenchus xylophilus is the nematode responsible for a devastating epidemic of pine wilt disease in Asia and Europe, and represents a recent, independent origin of plant parasitism in nematodes, ecologically and taxonomically distinct from other nematodes for which genomic data is available. As well as being an important pathogen, the B. xylophilus genome thus provides a unique opportunity to study the evolution and mechanism of plant parasitism. Here, we present a high-quality draft genome sequence from an inbred line of B. xylophilus, and use this to investigate the biological basis of its complex ecology which combines fungal feeding, plant parasitic and insect-associated stages. We focus particularly on putative parasitism genes as well as those linked to other key biological processes and demonstrate that B. xylophilus is well endowed with RNA interference effectors, peptidergic neurotransmitters (including the first description of ins genes in a parasite) stress response and developmental genes and has a contracted set of chemosensory receptors. B. xylophilus has the largest number of digestive proteases known for any nematode and displays expanded families of lysosome pathway genes, ABC transporters and cytochrome P450 pathway genes. This expansion in digestive and detoxification proteins may reflect the unusual diversity in foods it exploits and environments it encounters during its life cycle. In addition, B. xylophilus possesses a unique complement of plant cell wall modifying proteins acquired by horizontal gene transfer, underscoring the impact of this process on the evolution of plant parasitism by nematodes. Together with the lack of proteins homologous to effectors from other plant parasitic nematodes, this confirms the distinctive molecular basis of plant parasitism in the Bursaphelenchus lineage. The genome sequence of B. xylophilus adds to the diversity of genomic data for nematodes, and will be an important resource in understanding the biology of this unusual parasite.}, }
@article {pmid21908672, year = {2011}, author = {Makarova, KS and Wolf, YI and Snir, S and Koonin, EV}, title = {Defense islands in bacterial and archaeal genomes and prediction of novel defense systems.}, journal = {Journal of bacteriology}, volume = {193}, number = {21}, pages = {6039-6056}, pmid = {21908672}, issn = {1098-5530}, support = {Z01 LM000073-12//Intramural NIH HHS/United States ; }, mesh = {Archaeal Viruses/*growth &amp; development ; Bacterial Toxins/genetics ; Bacteriophages/*growth &amp; development ; Computational Biology/methods ; DNA Restriction-Modification Enzymes/genetics ; *Genome, Archaeal ; *Genome, Bacterial ; *Genomic Islands ; Interspersed Repetitive Sequences ; Multigene Family ; Operon ; }, abstract = {The arms race between cellular life forms and viruses is a major driving force of evolution. A substantial fraction of bacterial and archaeal genomes is dedicated to antivirus defense. We analyzed the distribution of defense genes and typical mobilome components (such as viral and transposon genes) in bacterial and archaeal genomes and demonstrated statistically significant clustering of antivirus defense systems and mobile genes and elements in genomic islands. The defense islands are enriched in putative operons and contain numerous overrepresented gene families. A detailed sequence analysis of the proteins encoded by genes in these families shows that many of them are diverged variants of known defense system components, whereas others show features, such as characteristic operonic organization, that are suggestive of novel defense systems. Thus, genomic islands provide abundant material for the experimental study of bacterial and archaeal antivirus defense. Except for the CRISPR-Cas systems, different classes of defense systems, in particular toxin-antitoxin and restriction-modification systems, show nonrandom clustering in defense islands. It remains unclear to what extent these associations reflect functional cooperation between different defense systems and to what extent the islands are genomic "sinks" that accumulate diverse nonessential genes, particularly those acquired via horizontal gene transfer. The characteristics of defense islands resemble those of mobilome islands. Defense and mobilome genes are nonrandomly associated in islands, suggesting nonadaptive evolution of the islands via a preferential attachment-like mechanism underpinned by the addictive properties of defense systems such as toxins-antitoxins and an important role of horizontal mobility in the evolution of these islands.}, }
@article {pmid21906669, year = {2011}, author = {Wu, DD and Zhang, YP}, title = {Eukaryotic origin of a metabolic pathway in virus by horizontal gene transfer.}, journal = {Genomics}, volume = {98}, number = {5}, pages = {367-369}, doi = {10.1016/j.ygeno.2011.08.006}, pmid = {21906669}, issn = {1089-8646}, mesh = {Animals ; Bombyx/*genetics/virology ; *DNA Replication ; *Gene Transfer, Horizontal ; Genes, Viral ; *Genome, Insect ; Glycine Hydroxymethyltransferase/genetics/metabolism ; Insect Viruses/classification/*enzymology/genetics/physiology ; *Metabolic Networks and Pathways ; Phylogeny ; Sequence Analysis, Protein ; Tetrahydrofolate Dehydrogenase/genetics/metabolism ; Thymidylate Synthase/genetics/metabolism ; Virus Replication ; }, abstract = {Horizontal gene transfer, the movement of genetic materials across the normal mating barriers between organisms occurs frequently and contributes significantly to the evolution of both eukaryotic and prokaryotic genomes. However, few concurrent transfers of functionally related genes implemented in a pathway from eukaryotes to prokaryotes are observed. Here, we did phylogenetic analyses to support that the genes, i.e. dihydrofolate reductase, glycine hydroxymethyltransferase, and thymidylate synthase involved in thymidylate metabolism, in Hz-1 virus were obtained from insect genome recently by independent horizontal gene transfers. In addition, five other related genes in nucleotide metabolism show evidences of horizontal gene transfers. These genes demonstrate similar expression pattern, and they may have formatted a functionally related pathway (e.g. thymidylate synthesis, and DNA replication) in Hz-1 virus. In conclusion, we provide an example of horizontal gene transfer of functionally related genes in a pathway to prokaryote from eukaryote.}, }
@article {pmid21906413, year = {2012}, author = {Wozniak, A and Rojas, P and Rodríguez, C and Undabarrena, A and Garate, C and Riedel, I and Román, JC and Kalergis, AM and García, P}, title = {M-protein gene-type distribution and hyaluronic acid capsule in group A Streptococcus clinical isolates in Chile: association of emm gene markers with csrR alleles.}, journal = {Epidemiology and infection}, volume = {140}, number = {7}, pages = {1286-1295}, doi = {10.1017/S0950268811001889}, pmid = {21906413}, issn = {1469-4409}, mesh = {Alleles ; Antigens, Bacterial/*genetics ; Bacterial Capsules/*metabolism ; Bacterial Outer Membrane Proteins/*genetics ; Bacterial Proteins/*genetics ; Carrier Proteins/*genetics ; Chile ; Genotype ; Humans ; Hyaluronic Acid/*metabolism ; Phenotype ; Repressor Proteins/*genetics ; Statistics as Topic ; Streptococcal Infections/*microbiology ; Streptococcus pyogenes/*classification/genetics/*isolation &amp; purification/metabolism ; Virulence Factors/genetics ; }, abstract = {Streptococcus pyogenes causes a variety of infections because of virulence factors such as capsular hyaluronic acid and M protein. The aim of this study was to determine emm types and capsule phenotype in 110 isolates of S. pyogenes from patients with invasive (sterile sites) and non-invasive (mainly pharyngitis) infections in Chile, and the relationship between both virulence factors. The most abundant types found were emm12, emm1, emm4 and emm28 and their distribution was similar to that seen in Latin America and developed countries, but very different from that in Asia and Pacific Island countries. Ten of 16 emm types identified in pharyngeal isolates were found in sterile-site isolates, and three of nine emm types of sterile-site isolates occurred in pharyngeal isolates; three emm subtypes were novel. The amount of hyaluronic acid was significantly higher in sterile-site isolates but did not differ substantially among emm types. Only three isolates were markedly capsulate and two of them had mutations in the csrR gene that codes for a repressor of capsule synthesis genes. We found a non-random association between emm types and csrR gene alleles suggesting that horizontal gene transfer is not freely occurring in the population.}, }
@article {pmid21906350, year = {2011}, author = {Bordi, C and de Bentzmann, S}, title = {Hacking into bacterial biofilms: a new therapeutic challenge.}, journal = {Annals of intensive care}, volume = {1}, number = {1}, pages = {19}, pmid = {21906350}, issn = {2110-5820}, abstract = {Microbiologists have extensively worked during the past decade on a particular phase of the bacterial cell cycle known as biofilm, in which single-celled individuals gather together to form a sedentary but dynamic community within a complex structure, displaying spatial and functional heterogeneity. In response to the perception of environmental signals by sensing systems, appropriate responses are triggered, leading to biofilm formation. This process involves various molecular systems that enable bacteria to identify appropriate surfaces on which to anchor themselves, to stick to those surfaces and to each other, to construct multicellular communities several hundreds of micrometers thick, and to detach from the community. The biofilm microbial community is a unique, highly competitive, and crowded environment facilitating microevolutionary processes and horizontal gene transfer between distantly related microorganisms. It is governed by social rules, based on the production and use of "public" goods, with actors and recipients. Biofilms constitute a unique shield against external aggressions, including drug treatment and immune reactions. Biofilm-associated infections in humans have therefore generated major problems for the diagnosis and treatment of diseases. Improvements in our understanding of biofilms have led to innovative research designed to interfere with this process.}, }
@article {pmid21899749, year = {2011}, author = {Yang, Y and Maruyama, S and Sekimoto, H and Sakayama, H and Nozaki, H}, title = {An extended phylogenetic analysis reveals ancient origin of "non-green" phosphoribulokinase genes from two lineages of "green" secondary photosynthetic eukaryotes: Euglenophyta and Chlorarachniophyta.}, journal = {BMC research notes}, volume = {4}, number = {}, pages = {330}, pmid = {21899749}, issn = {1756-0500}, abstract = {BACKGROUND: Euglenophyta and Chlorarachniophyta are groups of photosynthetic eukaryotes harboring secondary plastids of distinct green algal origins. Although previous phylogenetic analyses of genes encoding Calvin cycle enzymes demonstrated the presence of genes apparently not derived from green algal endosymbionts in the nuclear genomes of Euglena gracilis (Euglenophyta) and Bigelowiella natans (Chlorarachniophyta), the origins of these "non-green" genes in "green" secondary phototrophs were unclear due to the limited taxon sampling.<br><br>RESULTS: Here, we sequenced five new phosphoribulokinase (PRK) genes (from one euglenophyte, two chlorarachniophytes, and two glaucophytes) and performed an extended phylogenetic analysis of the genes based on a phylum-wide taxon sampling from various photosynthetic eukaryotes. Our phylogenetic analyses demonstrated that the PRK sequences form two genera of Euglenophyta formed a robust monophyletic group within a large clade including stramenopiles, haptophytes and a cryptophyte, and three genera of Chlorarachniophyta were placed within the red algal clade. These "non-green" affiliations were supported by the taxon-specific insertion/deletion sequences in the PRK alignment, especially between euglenophytes and stramenopiles. In addition, phylogenetic analysis of another Calvin cycle enzyme, plastid-targeted sedoheptulose-bisphosphatase (SBP), showed that the SBP sequences from two genera of Chlorarachniophyta were positioned within a red algal clade.<br><br>CONCLUSIONS: Our results suggest that PRK genes may have been transferred from a "stramenopile" ancestor to Euglenophyta and from a "red algal" ancestor to Chlorarachniophyta before radiation of extant taxa of these two "green" secondary phototrophs. The presence of two of key Calvin cycle enzymes, PRK and SBP, of red algal origins in Chlorarachniophyta indicate that the contribution of "non-green" algae to the plastid proteome in the "green" secondary phototrophs is more significant than ever thought. These "non-green" putative plastid-targeted enzymes from Chlorarachniophyta are likely to have originated from an ancestral red alga via horizontal gene transfer, or from a cryptic red algal endosymbiosis in the common ancestor of the extant chlorarachniophytes.}, }
@article {pmid21899737, year = {2011}, author = {Yoshida, T and Claverie, JM and Ogata, H}, title = {Mimivirus reveals Mre11/Rad50 fusion proteins with a sporadic distribution in eukaryotes, bacteria, viruses and plasmids.}, journal = {Virology journal}, volume = {8}, number = {}, pages = {427}, pmid = {21899737}, issn = {1743-422X}, mesh = {Acid Anhydride Hydrolases ; Animals ; Aquatic Organisms/*genetics ; Archaeal Proteins/genetics ; Bacteria/genetics ; Bacterial Proteins/genetics ; Computational Biology ; DNA Breaks, Double-Stranded ; DNA Repair ; DNA Repair Enzymes/chemistry/*genetics ; DNA-Binding Proteins/chemistry/*genetics ; Databases, Genetic ; Deoxyribonucleases/genetics ; Endodeoxyribonucleases/chemistry/*genetics ; Escherichia coli Proteins/genetics ; Exodeoxyribonucleases/chemistry/*genetics ; Exonucleases/genetics ; Gene Transfer, Horizontal ; *Genome, Viral ; Humans ; *Metagenome ; Metagenomics ; Mimiviridae/chemistry/*genetics ; Phylogeny ; Plasmids/chemistry/genetics ; Saccharomyces cerevisiae Proteins/chemistry/*genetics ; Viral Fusion Proteins/chemistry/*genetics ; Viral Proteins/chemistry/*genetics ; }, abstract = {BACKGROUND: The Mre11/Rad50 complex and the homologous SbcD/SbcC complex in bacteria play crucial roles in the metabolism of DNA double-strand breaks, including DNA repair, genome replication, homologous recombination and non-homologous end-joining in cellular life forms and viruses. Here we investigated the amino acid sequence of the Mimivirus R555 gene product, originally annotated as a Rad50 homolog, and later shown to have close homologs in marine microbial metagenomes.<br><br>RESULTS: Our bioinformatics analysis revealed that R555 protein sequence is constituted from the fusion of an N-terminal Mre11-like domain with a C-terminal Rad50-like domain. A systematic database search revealed twelve additional cases of Mre11/Rad50 (or SbcD/SbcC) fusions in a wide variety of unrelated organisms including unicellular and multicellular eukaryotes, the megaplasmid of a bacterium associated to deep-sea hydrothermal vents (Deferribacter desulfuricans) and the plasmid of Clostridium kluyveri. We also showed that R555 homologs are abundant in the metagenomes from different aquatic environments and that they most likely belong to aquatic viruses. The observed phyletic distribution of these fusion proteins suggests their recurrent creation and lateral gene transfers across organisms.<br><br>CONCLUSIONS: The existence of the fused version of protein sequences is consistent with known functional interactions between Mre11 and Rad50, and the gene fusion probably enhanced the opportunity for lateral transfer. The abundance of the Mre11/Rad50 fusion genes in viral metagenomes and their sporadic phyletic distribution in cellular organisms suggest that viruses, plasmids and transposons played a crucial role in the formation of the fusion proteins and their propagation into cellular genomes.}, }
@article {pmid21899418, year = {2011}, author = {Bansal, MS and Banay, G and Gogarten, JP and Shamir, R}, title = {Detecting highways of horizontal gene transfer.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {18}, number = {9}, pages = {1087-1114}, doi = {10.1089/cmb.2011.0066}, pmid = {21899418}, issn = {1557-8666}, mesh = {Algorithms ; *Computer Simulation ; Cyanobacteria/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Models, Genetic ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In a horizontal gene transfer (HGT) event, a gene is transferred between two species that do not have an ancestor-descendant relationship. Typically, no more than a few genes are horizontally transferred between any two species. However, several studies identified pairs of species between which many different genes were horizontally transferred. Such a pair is said to be linked by a highway of gene sharing. We present a method for inferring such highways. Our method is based on the fact that the evolutionary histories of horizontally transferred genes disagree with the corresponding species phylogeny. Specifically, given a set of gene trees and a trusted rooted species tree, each gene tree is first decomposed into its constituent quartet trees and the quartets that are inconsistent with the species tree are identified. Our method finds a pair of species such that a highway between them explains the largest (normalized) fraction of inconsistent quartets. For a problem on n species and m input quartet trees, we give an efficient O(m + n(2))-time algorithm for detecting highways, which is optimal with respect to the quartets input size. An application of our method to a dataset of 1128 genes from 11 cyanobacterial species, as well as to simulated datasets, illustrates the efficacy of our method.}, }
@article {pmid21899303, year = {2012}, author = {DeBruyn, JM and Mead, TJ and Sayler, GS}, title = {Horizontal transfer of PAH catabolism genes in Mycobacterium: evidence from comparative genomics and isolated pyrene-degrading bacteria.}, journal = {Environmental science &amp; technology}, volume = {46}, number = {1}, pages = {99-106}, doi = {10.1021/es201607y}, pmid = {21899303}, issn = {1520-5851}, mesh = {Biodegradation, Environmental ; Chromosomes, Bacterial/genetics ; Conserved Sequence/genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/*genetics ; Genomics/*methods ; Mycobacterium/*genetics/*isolation &amp; purification ; Phylogeny ; Polycyclic Aromatic Hydrocarbons/*metabolism ; Pyrenes/*metabolism ; Sequence Homology, Nucleic Acid ; }, abstract = {Biodegradation of high molecular weight polycyclic aromatic hydrocarbons (PAHs), such as pyrene and benzo[a]pyrene, has only been observed in a few genera, namely fast-growing Mycobacterium and Rhodococcus. In M. vanbaalenii PYR-1, multiple aromatic ring hydroxylating dioxygenase (ARHDOs) genes including pyrene dioxygenases nidAB and nidA3B3 are localized in one genomic region. Here we examine the homologous genomic regions in four other PAH-degrading Mycobacterium (strains JLS, KMS, and MCS, and M. gilvum PYR-GCK), presenting evidence for past horizontal gene transfer events. Seven distinct types of ARHDO genes are present in all five genomes, and display conserved syntenic architecture with respect to gene order, orientation, and association with other genes. Duplications and putative integrase and transposase genes suggest past gene shuffling. To corroborate these observations, pyrene-degrading strains were isolated from two PAH-contaminated sediments: Chattanooga Creek (Tennessee) and Lake Erie (western basin). Some were related to fast-growing Mycobacterium spp. and carried both nidA and nidA3 genes. Other isolates belonged to Microbacteriaceae and Intrasporangiaceae presenting the first evidence of pyrene degradation in these families. These isolates had nidA (and some, nidA3) genes that were homologous to Mycobacterial ARHDO genes, suggesting that horizontal gene transfer events have occurred.}, }
@article {pmid21893116, year = {2012}, author = {Zhang, J and Dong, J and Xu, Y and Wu, J}, title = {V2 protein encoded by Tomato yellow leaf curl China virus is an RNA silencing suppressor.}, journal = {Virus research}, volume = {163}, number = {1}, pages = {51-58}, doi = {10.1016/j.virusres.2011.08.009}, pmid = {21893116}, issn = {1872-7492}, mesh = {Agrobacterium/genetics ; Bacterial Proteins ; Begomovirus/immunology/*pathogenicity ; China ; Cytoplasm/chemistry ; Gene Expression ; Gene Transfer, Horizontal ; Genes, Reporter ; Green Fluorescent Proteins/genetics/metabolism ; Solanum lycopersicum ; Photoreceptors, Microbial ; Plant Diseases/*virology ; Protein Binding ; *RNA Interference ; RNA, Plant/metabolism ; RNA, Small Interfering/metabolism ; Nicotiana/virology ; Transformation, Genetic ; Viral Proteins/*metabolism ; Virulence Factors/*metabolism ; }, abstract = {The V2 protein of Tomato yellow leaf curl China virus (TYLCCNV) was identified as an RNA silencing suppressor by Agrobacterium-mediated co-infiltration. The V2 protein could inhibit local RNA silencing, systemic RNA silencing of the green fluorescent protein (GFP) gene and the spread of a systemic GFP RNA silencing signal. However, the V2 could not interfere with the cell-to-cell spread of RNA silencing. Subcellular localization assay indicated that the V2 protein was distributed in the cytoplasm of Nicotiana benthamiana cells, and accumulated in irregular cytoplasmic bodies. The V2 bound 21nt and 24nt small interfering RNA (siRNA) duplexes and 24nt single-stranded (ss)-siRNA but not 21nt ss-siRNA in electrophoresis mobility shift assays. Expression of the V2 protein via the Potato virus X (PVX) vectors heterogenous system induced severe symptoms in N. benthamiana. In a yeast two-hybrid system, TYLCCNV V2 could interact with itself, but not with SlSGS3, which is known to been involved in RNA silencing pathway and to interact with a closely related Tomato yellow leaf curl virus (TYLCV) V2. These results indicate that TYLCCNV V2 is an RNA silencing suppressor, possibly through sequestering siRNA molecules.}, }
@article {pmid21890771, year = {2011}, author = {Woerther, PL and Angebault, C and Jacquier, H and Hugede, HC and Janssens, AC and Sayadi, S and El Mniai, A and Armand-Lefèvre, L and Ruppé, E and Barbier, F and Raskine, L and Page, AL and de Rekeneire, N and Andremont, A}, title = {Massive increase, spread, and exchange of extended spectrum β-lactamase-encoding genes among intestinal Enterobacteriaceae in hospitalized children with severe acute malnutrition in Niger.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {53}, number = {7}, pages = {677-685}, doi = {10.1093/cid/cir522}, pmid = {21890771}, issn = {1537-6591}, mesh = {Carrier State/epidemiology/microbiology ; Child, Hospitalized ; Child, Preschool ; Electrophoresis, Gel, Pulsed-Field ; Enterobacteriaceae Infections/*epidemiology/*microbiology ; Escherichia coli/classification/*enzymology/genetics/isolation &amp; purification ; Female ; *Gene Transfer, Horizontal ; Humans ; Infant ; Klebsiella pneumoniae/classification/*enzymology/genetics/isolation &amp; purification ; Male ; Malnutrition/*complications ; Molecular Typing ; Niger/epidemiology ; Polymerase Chain Reaction ; beta-Lactamases/*genetics/metabolism ; }, abstract = {BACKGROUND: From the time of CTX-M emergence, extended-spectrum β-lactamase-producing enterobacteria (ESBL-E) have spread worldwide in community settings as well as in hospitals, particularly in developing countries. Although their dissemination appears linked to Escherichia coli intestinal carriage, precise paths of this dynamic are largely unknown.<br><br>METHODS: Children from a pediatric renutrition center were prospectively enrolled in a fecal carriage study. Antibiotic exposure was recorded. ESBL-E strains were isolated using selective media from fecal samples obtained at admission and, when negative, also at discharge. ESBL-encoding genes were identified, their environments and plasmids were characterized, and clonality was assessed with polymerase chain reaction-based methods and pulsed-field gel electrophoresis for E. coli and Klebsiella pneumoniae. E. coli strains were subjected to multilocus sequence typing.<br><br>RESULTS: The ESBL-E carriage rate was 31% at admission in the 55 children enrolled. All children enrolled received antibiotics during hospitalization. Among the ESBL-E-negative children, 16 were resampled at discharge, and the acquisition rate was 94%. The bla(CTX-M-15) gene was found in >90% of the carriers. Genetic environments and plasmid characterization evidenced the roles of a worldwide, previously described, multidrug-resistant region and of IncF plasmids in CTX-M-15 E. coli dissemination. Diversity of CTX-M-15-carrying genetic structures and clonality of acquired ESBL E. coli suggested horizontal genetic transfer and underlined the potential of some ST types for nosocomial cross-transmission.<br><br>CONCLUSIONS: Cross-transmission and high selective pressure lead to very high acquisition of ESBL-E carriage, contributing to dissemination in the community. Strict hygiene measures as well as careful balancing of benefit-risk ratio of current antibiotic policies need to be reevaluated.}, }
@article {pmid21887050, year = {2011}, author = {Idowu, OJ and Onipede, AO and Orimolade, AE and Akinyoola, LA and Babalola, GO}, title = {Extended-spectrum Beta-lactamase Orthopedic Wound Infections in Nigeria.}, journal = {Journal of global infectious diseases}, volume = {3}, number = {3}, pages = {211-215}, pmid = {21887050}, issn = {0974-8245}, abstract = {BACKGROUND: Extended-spectrum beta-lactamase (ESBL)-producing Gram-negative bacteria are emerging and impacting significantly on the management of patients and hospital costs. Besides, they are not being routinely sought after in diagnostic laboratories thus contributing to treatment failure.<br><br>MATERIALS AND METHODS: Bacterial isolates from wounds of 45 patients were identified using commercial identification kits and antibiotic susceptibility was evaluated by the Bauer-Kirby method. Screening and phenotypic confirmation of ESBL production were done as prescribed by the Clinical and Laboratory Standards Institute. The conjugation experiment was performed by the mating assay in broth between the ESBL producers and E. coli ATCC 25922 as the recipient.<br><br>RESULTS: Out of 102 Gram-negative bacteria isolated, 36 were positive for ESBL mainly of the Enterobacteriaceae family (33) and the rest were oxidase-positive bacilli (3). The predominant bacteria were Klebsiella spp. and E. coli. Others were Serratia rubidae, Citrobacter freundii, Morganella morgannii, Proteus spp., Providencia stuartii, and Enterobacter spp. There was a significant association between treatment with third-generation cephalosporins (3GCs) and isolation of ESBLs (P=0.0020). The ESBL producers were multiply resistant and moderately sensitive to colistin. The conjugation experiment showed that the ESBL gene was transferred horizontally and tetracycline, cotrimoxazole, nitrofurantoin, gentamicin, and aztreonam resistance genes were co-transferred. No mortality was recorded but the mean length of stay in the hospital was 82 days.<br><br>CONCLUSION: The development and spread of ESBL among Gram-negative bacteria and possible horizontal transfer calls for concern, especially in view of treatment failure, high treatment cost, and consequent discomfort to patients.}, }
@article {pmid21885481, year = {2011}, author = {Patrick, S and Jobling, KL and O'Connor, D and Thacker, Z and Dryden, DTF and Blakely, GW}, title = {A unique homologue of the eukaryotic protein-modifier ubiquitin present in the bacterium Bacteroides fragilis, a predominant resident of the human gastrointestinal tract.}, journal = {Microbiology (Reading, England)}, volume = {157}, number = {Pt 11}, pages = {3071-3078}, pmid = {21885481}, issn = {1465-2080}, support = {/WT_/Wellcome Trust/United Kingdom ; 090288/WT_/Wellcome Trust/United Kingdom ; WT090288MA/WT_/Wellcome Trust/United Kingdom ; BB-C505875-1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics/*metabolism ; Bacteroides fragilis/*enzymology/genetics ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; Humans ; Molecular Sequence Data ; Protein Sorting Signals ; Ubiquitin/genetics/*metabolism ; Ubiquitination ; }, abstract = {In the complete genome sequences of Bacteroides fragilis NCTC9343 and 638R, we have discovered a gene, ubb, the product of which has 63 % identity to human ubiquitin and cross-reacts with antibodies raised against bovine ubiquitin. The sequence of ubb is closest in identity (76 %) to the ubiquitin gene from a migratory grasshopper entomopoxvirus, suggesting acquisition by inter-kingdom horizontal gene transfer. We have screened clinical isolates of B. fragilis from diverse geographical regions and found that ubb is present in some, but not all, strains. The gene is transcribed and the mRNA is translated in B. fragilis, but deletion of ubb did not have a detrimental effect on growth. BfUbb has a predicted signal sequence; both full-length and processed forms were detected in whole-cell extracts, while the processed form was found in concentrated culture supernatants. Purified recombinant BfUbb inhibited in vitro ubiquitination and was able to covalently bind the human E1 activating enzyme, suggesting it could act as a suicide substrate in vivo. B. fragilis is one of the predominant members of the normal human gastrointestinal microbiota with estimates of up to >10[11] cells per g faeces by culture. These data indicate that the gastro-intestinal tract of some individuals could contain a significant amount of aberrant ubiquitin with the potential to inappropriately activate the host immune system and/or interfere with eukaryotic ubiquitin activity. This discovery could have profound implications in relation to our understanding of human diseases such as inflammatory bowel and autoimmune diseases.}, }
@article {pmid21883006, year = {2011}, author = {Yu, Y and Hu, W and Wu, B and Zhang, P and Chen, J and Wang, S and Fang, W}, title = {Vibrio parahaemolyticus isolates from southeastern Chinese coast are genetically diverse with circulation of clonal complex 3 strains since 2002.}, journal = {Foodborne pathogens and disease}, volume = {8}, number = {11}, pages = {1169-1176}, doi = {10.1089/fpd.2011.0865}, pmid = {21883006}, issn = {1556-7125}, mesh = {Alleles ; Bacterial Typing Techniques ; China ; DNA, Bacterial/chemistry/genetics ; *Environmental Microbiology ; *Food Microbiology ; Genetic Variation/*genetics ; Genetics, Population ; Genotype ; Humans ; Molecular Epidemiology ; Molecular Sequence Data ; Multilocus Sequence Typing ; Phylogeny ; Seafood/microbiology ; Sequence Analysis, DNA ; Species Specificity ; Vibrio Infections/microbiology ; Vibrio parahaemolyticus/*classification/*genetics/isolation &amp; purification ; }, abstract = {Multilocus sequence typing (MLST) was used to examine the clonal relationship and genetic diversity of 71 Vibrio parahaemolyticus isolates from clinical and seafood-related sources in southeastern Chinese coast between 2002 and 2009. The tested isolates fell into 61 sequence types (STs). Of 17 clinical isolates, 7 belonged to ST3 of the pandemic clonal complex 3, with 3 strains isolated in 2002. Although there was no apparent clonal relationship found between clinical strains and those from seafood-related sources positive with pathogenic markers, there were clonal relationships between clinical strains from this study and those from environmental sources in other parts of China. Phylogenetic analysis showed that strains of 112 STs (61 STs from this study and 51 retrieved from PUBMLST database covering different continents) could be divided into four branches. The vast majority of our isolates and those from other countries were genetically diverse and clustered into two major branches of mixed distribution (of geographic origins and sample sources), whereas five STs representing six isolates split as two minor branches because of divergence of their recA genes, which had 80%-82% nucleotide identity to typical V. parahaemolyticus strains and 73.3%-76.9% identity to the CDS24 of a Vibrio sp. plasmid p23023, indicating that the recA gene might have recombined by lateral gene transfer. This was further supported by a high ratio of recombination to mutation (3.038) for recA. In conclusion, MLST with fully extractable database is a powerful system for analysis of clonal relationship for strains of a particular region in a national or global scale as well as between clinical and environmental or food-related strains.}, }
@article {pmid21883005, year = {2011}, author = {Folster, JP and Pecic, G and McCullough, A and Rickert, R and Whichard, JM}, title = {Characterization of bla(CMY)-encoding plasmids among Salmonella isolated in the United States in 2007.}, journal = {Foodborne pathogens and disease}, volume = {8}, number = {12}, pages = {1289-1294}, doi = {10.1089/fpd.2011.0944}, pmid = {21883005}, issn = {1556-7125}, mesh = {Alleles ; Anti-Infective Agents/*pharmacology ; Conjugation, Genetic ; Gene Transfer, Horizontal ; Genotype ; Humans ; Microbial Sensitivity Tests ; Plasmids/*genetics ; Replicon/genetics ; Salmonella Infections/*microbiology ; Salmonella enterica/drug effects/enzymology/*genetics ; Sequence Analysis, DNA ; United States ; beta-Lactam Resistance/genetics ; beta-Lactamases/*genetics ; }, abstract = {Salmonella enterica is one of the most common bacterial causes of foodborne illness, and nontyphoidal Salmonella is estimated to cause ∼1.2 million illnesses in the United States each year. Plasmids are mobile genetic elements that play a critical role in the dissemination of antimicrobial resistance determinants. AmpC-type CMY β-lactamases (bla(CMY)) confer resistance to extended-spectrum cephalosporins and β-lactam/β-lactamase inhibitor combinations and are commonly plasmid-encoded. A variety of plasmids have been shown to encode CMY β-lactamases and certain plasmids may be associated with particular Salmonella serotypes or environmental sources. In this study, we characterized bla(CMY) β-lactamase-encoding plasmids among Salmonella isolates. Isolates of Salmonella from specimens collected from humans in 2007 were submitted to the Centers for Disease Control and Prevention National Antimicrobial Resistance Monitoring System laboratory for susceptibility testing. Three percent (65/2161) of Salmonella isolates displayed resistance to ceftriaxone (minimum inhibitory concentration [MIC] ≥4 mg/L) and amoxicillin/clavulanic acid (MIC ≥32 mg/L), a combination associated with the presence of a bla(CMY) mechanism of resistance. Sixty-four (98.5%) isolates were polymerase chain reaction-positive for bla(CMY) genes. Transformation and conjugation studies showed that 95% (61/64) of the bla(CMY) genes were plasmid-encoded. Most of the bla(CMY)-positive isolates were serotype Typhimurium, Newport, Heidelberg, and Agona. Forty-three plasmids were replicon type IncA/C, 15 IncI1, 2 contained multiple replicon loci, and 1 was untypeable. IncI1 plasmids conferred only the bla(CMY)-associated resistance phenotype, whereas IncA/C plasmids conferred additional multi-drug resistance (MDR) phenotypes to drugs such as chloramphenicol, sulfisoxazole, and tetracycline. Most of the IncI1 plasmids (12/15) were sequence type 12 by plasmid multi-locus sequence typing. CMY β-lactamase-encoding plasmids among human isolates of Salmonella in the United States tended to be large MDR IncA/C plasmids or single resistance determinant IncI1 plasmids. In general, IncI1 plasmids were identified among serotypes commonly associated with poultry, whereas IncA/C plasmids were more likely to be identified among cattle/beef-associated serotypes.}, }
@article {pmid21880661, year = {2011}, author = {Williams, WM and Verry, IM and Ansari, HA and Hussain, SW and Ullah, I and Williamson, ML and Ellison, NW}, title = {Eco-geographically divergent diploids, Caucasian clover (Trifolium ambiguum) and western clover (T. occidentale), retain most requirements for hybridization.}, journal = {Annals of botany}, volume = {108}, number = {7}, pages = {1269-1277}, pmid = {21880661}, issn = {1095-8290}, mesh = {Chimera/*genetics ; Chromosome Pairing ; *Diploidy ; Europe ; Gene Flow ; Gene Transfer, Horizontal ; Genetic Speciation ; Genome, Plant ; Hybridization, Genetic ; Trifolium/*genetics ; Triploidy ; }, abstract = {BACKGROUND AND AIMS: DNA sequence similarities and hybridization patterns in Trifolium (clovers) section Trifoliastrum suggest that rapid radiation from a common ancestral source led to this complex of diverse species distributed across Europe, western Asia and North Africa. Two of the most geographically and ecologically divergent of these species are the rhizomatous T. ambiguum from high altitudes in eastern Europe and western Asia and the stoloniferous T. occidentale from sea level in western Europe. Attempts were made to hybridize these species to ascertain whether, despite this separation, gene flow could be achieved, indicating the retention of the genetic factors necessary for hybridization.<br><br>METHODS: Three F(1) hybrids formed after embryo rescue were described, characterized by conventional and molecular cytogenetics, subjected to fertility tests and progeny generations were developed.<br><br>RESULTS AND CONCLUSIONS: Partially fertile hybrids between Trifolium ambiguum and T. occidentale were obtained for the first time. The F(1) hybrids produced seeds after open-pollination, and also produced triploid progeny in backcrosses to T. occidentale from the functioning of unreduced gametes in the hybrids. These plants were fertile and produced progeny with T. occidentale and with T. repens. Meiotic chromosome pairing in the F(1) showed six to eight bivalents per pollen mother cell, indicating pairing between the parental genomes. A chromosome-doubled form of one hybrid, produced using colchicine, showed some multivalents, indicative of interspecific chromosome pairing. The hybrid plants were robust and combined phenotypic characteristics of both species, having stolons, thick roots and a few rhizomes. Results show that despite separation by the entire breadth of Europe, the speciation process is incomplete, and these taxa have partially retained most of the genetic compatibilities needed for hybridization (possibly except for endosperm development, which was not tested). The fertile progeny populations could lead to new clover breeding strategies based on new hybrid forms.}, }
@article {pmid21878901, year = {2011}, author = {Vandermeulen, G and Marie, C and Scherman, D and Préat, V}, title = {New generation of plasmid backbones devoid of antibiotic resistance marker for gene therapy trials.}, journal = {Molecular therapy : the journal of the American Society of Gene Therapy}, volume = {19}, number = {11}, pages = {1942-1949}, pmid = {21878901}, issn = {1525-0024}, mesh = {Animals ; Drug Resistance, Bacterial/*genetics ; *Genetic Therapy ; Genetic Vectors/*genetics ; Humans ; Plasmids/*genetics ; }, abstract = {Since it has been established that the injection of plasmid DNA can lead to an efficient expression of a specific protein in vivo, nonviral gene therapy approaches have been considerably improved, allowing clinical trials. However, the use of antibiotic resistance genes as selection markers for plasmid production raises safety concerns which are often pointed out by the regulatory authorities. Indeed, a horizontal gene transfer to patient's bacteria cannot be excluded, and residual antibiotic in the final product could provoke allergic reactions in sensitive individuals. A new generation of plasmid backbones devoid of antibiotic resistance marker has emerged to increase the safety profile of nonviral gene therapy trials. This article reviews the existing strategies for plasmid maintenance and, in particular, those that do not require the use of antibiotic resistance genes. They are based either on the complementation of auxotrophic strain, toxin-antitoxin systems, operator-repressor titration, RNA markers, or on the overexpression of a growth essential gene. Minicircles that allow removing of the antibiotic resistance gene from the initial vector will also be discussed. Furthermore, reported use of antibiotic-free plasmids in preclinical or clinical studies will be listed to provide a comprehensive view of these innovative technologies.}, }
@article {pmid21878683, year = {2012}, author = {Nováková, E and Moran, NA}, title = {Diversification of genes for carotenoid biosynthesis in aphids following an ancient transfer from a fungus.}, journal = {Molecular biology and evolution}, volume = {29}, number = {1}, pages = {313-323}, doi = {10.1093/molbev/msr206}, pmid = {21878683}, issn = {1537-1719}, mesh = {Animals ; Aphids/*genetics/*metabolism/microbiology ; Carotenoids/*biosynthesis/genetics ; *Gene Transfer, Horizontal ; *Genes, Fungal ; *Genome, Insect ; Genomics ; Oxidoreductases/*genetics ; Phylogeny ; }, abstract = {The pea aphid genome was recently found to harbor genes for carotenoid biosynthesis, reflecting an ancestral transfer from a fungus. To explore the evolution of the carotene desaturase gene family within aphids, sequences were retrieved from a set of 34 aphid species representing numerous deeply diverging lineages of aphids and analyzed together with fungal sequences retrieved from databases. All aphids have at least one copy of this gene and some aphid species have up to seven, whereas fungal genomes consistently have a single copy. The closest relatives of aphids, adelgids, also have carotene desaturase; these sequences are most closely related to those from aphids, supporting a shared origin from a fungal to insect transfer predating the divergence of adelgids and aphids. Likewise, all aphids, and adelgids, have carotenoid profiles that are consistent with their biosynthesis using the acquired genes of fungal origin rather than derivation from food plants. The carotene desaturase was acquired from a fungal species outside of Ascomycota or Basidiomycota and closest to Mucoromycotina among sequences available in databases. In aphids, an ongoing pattern of gene duplication is indicated by the presence of both anciently and recently diverged paralogs within genomes and by the presence of a high frequency of pseudogenes that appear to be recently inactivated. Recombination among paralogs is evident, making analyses of patterns of selection difficult, but tests of selection for a nonrecombining region indicates that duplications tend to be followed by bouts of positive selection. Species of Macrosiphini, which often show color polymorphisms, typically have a larger number of desaturase copies relative to other species sampled in the study. These results indicate that aphid evolution has been accompanied by ongoing evolution of carotenogenic genes, which have undergone duplication, recombination, and occasional positive selection to yield a wide variety of carotenoid profiles in different aphid species.}, }
@article {pmid21878562, year = {2011}, author = {Richards, TA and Soanes, DM and Jones, MD and Vasieva, O and Leonard, G and Paszkiewicz, K and Foster, PG and Hall, N and Talbot, NJ}, title = {Horizontal gene transfer facilitated the evolution of plant parasitic mechanisms in the oomycetes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {37}, pages = {15258-15263}, pmid = {21878562}, issn = {1091-6490}, support = {BB/G00885X/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Biological Evolution ; Fungi/genetics ; Gene Transfer, Horizontal/*genetics ; Host-Parasite Interactions/*genetics ; Phylogeny ; Phytophthora/*genetics ; Plants/*parasitology ; Proteome/metabolism ; }, abstract = {Horizontal gene transfer (HGT) can radically alter the genomes of microorganisms, providing the capacity to adapt to new lifestyles, environments, and hosts. However, the extent of HGT between eukaryotes is unclear. Using whole-genome, gene-by-gene phylogenetic analysis we demonstrate an extensive pattern of cross-kingdom HGT between fungi and oomycetes. Comparative genomics, including the de novo genome sequence of Hyphochytrium catenoides, a free-living sister of the oomycetes, shows that these transfers largely converge within the radiation of oomycetes that colonize plant tissues. The repertoire of HGTs includes a large number of putatively secreted proteins; for example, 7.6% of the secreted proteome of the sudden oak death parasite Phytophthora ramorum has been acquired from fungi by HGT. Transfers include gene products with the capacity to break down plant cell walls and acquire sugars, nucleic acids, nitrogen, and phosphate sources from the environment. Predicted HGTs also include proteins implicated in resisting plant defense mechanisms and effector proteins for attacking plant cells. These data are consistent with the hypothesis that some oomycetes became successful plant parasites by multiple acquisitions of genes from fungi.}, }
@article {pmid21876769, year = {2011}, author = {Swithers, KS and Fournier, GP and Green, AG and Gogarten, JP and Lapierre, P}, title = {Reassessment of the lineage fusion hypothesis for the origin of double membrane bacteria.}, journal = {PloS one}, volume = {6}, number = {8}, pages = {e23774}, pmid = {21876769}, issn = {1932-6203}, mesh = {Bacteria/*genetics ; Bacterial Proteins/metabolism ; Cell Membrane/*metabolism ; *Membrane Fusion ; *Models, Biological ; *Phylogeny ; }, abstract = {In 2009, James Lake introduced a new hypothesis in which reticulate phylogeny reconstruction is used to elucidate the origin of gram-negative bacteria (Nature 460: 967-971). The presented data supported the gram-negative bacteria originating from an ancient endosymbiosis between the Actinobacteria and Clostridia. His conclusion was based on a presence-absence analysis of protein families that divided all prokaryotes into five groups: Actinobacteria, Double Membrane bacteria (DM), Clostridia, Archaea and Bacilli. Of these five groups, the DM are by far the largest and most diverse group compared to the other groupings. While the fusion hypothesis for the origin of double membrane bacteria is enticing, we show that the signal supporting an ancient symbiosis is lost when the DM group is broken down into smaller subgroups. We conclude that the signal detected in James Lake's analysis in part results from a systematic artifact due to group size and diversity combined with low levels of horizontal gene transfer.}, }
@article {pmid21876740, year = {2011}, author = {Iguchi, A and Shirai, H and Seto, K and Ooka, T and Ogura, Y and Hayashi, T and Osawa, K and Osawa, R}, title = {Wide distribution of O157-antigen biosynthesis gene clusters in Escherichia coli.}, journal = {PloS one}, volume = {6}, number = {8}, pages = {e23250}, pmid = {21876740}, issn = {1932-6203}, mesh = {Antigens, Bacterial/*biosynthesis/*genetics ; Base Sequence ; Escherichia coli O157/*genetics/*immunology ; Genes, Bacterial/genetics ; Genotype ; Humans ; Molecular Sequence Data ; Multigene Family/*genetics ; Phenotype ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {Most Escherichia coli O157-serogroup strains are classified as enterohemorrhagic E. coli (EHEC), which is known as an important food-borne pathogen for humans. They usually produce Shiga toxin (Stx) 1 and/or Stx2, and express H7-flagella antigen (or nonmotile). However, O157 strains that do not produce Stxs and express H antigens different from H7 are sometimes isolated from clinical and other sources. Multilocus sequence analysis revealed that these 21 O157:non-H7 strains tested in this study belong to multiple evolutionary lineages different from that of EHEC O157:H7 strains, suggesting a wide distribution of the gene set encoding the O157-antigen biosynthesis in multiple lineages. To gain insight into the gene organization and the sequence similarity of the O157-antigen biosynthesis gene clusters, we conducted genomic comparisons of the chromosomal regions (about 59 kb in each strain) covering the O-antigen gene cluster and its flanking regions between six O157:H7/non-H7 strains. Gene organization of the O157-antigen gene cluster was identical among O157:H7/non-H7 strains, but was divided into two distinct types at the nucleotide sequence level. Interestingly, distribution of the two types did not clearly follow the evolutionary lineages of the strains, suggesting that horizontal gene transfer of both types of O157-antigen gene clusters has occurred independently among E. coli strains. Additionally, detailed sequence comparison revealed that some positions of the repetitive extragenic palindromic (REP) sequences in the regions flanking the O-antigen gene clusters were coincident with possible recombination points. From these results, we conclude that the horizontal transfer of the O157-antigen gene clusters induced the emergence of multiple O157 lineages within E. coli and speculate that REP sequences may involve one of the driving forces for exchange and evolution of O-antigen loci.}, }
@article {pmid21876735, year = {2011}, author = {Brouwer, MS and Warburton, PJ and Roberts, AP and Mullany, P and Allan, E}, title = {Genetic organisation, mobility and predicted functions of genes on integrated, mobile genetic elements in sequenced strains of Clostridium difficile.}, journal = {PloS one}, volume = {6}, number = {8}, pages = {e23014}, pmid = {21876735}, issn = {1932-6203}, support = {/WT_/Wellcome Trust/United Kingdom ; G0601176/MRC_/Medical Research Council/United Kingdom ; WT078131AIA/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacterial Proteins/metabolism ; Base Sequence ; Clostridioides difficile/*genetics ; Conjugation, Genetic ; DNA Transposable Elements/*genetics ; DNA, Bacterial/genetics ; DNA, Circular/genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/*genetics ; Humans ; Molecular Sequence Data ; *Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Clostridium difficile is the leading cause of hospital-associated diarrhoea in the US and Europe. Recently the incidence of C. difficile-associated disease has risen dramatically and concomitantly with the emergence of 'hypervirulent' strains associated with more severe disease and increased mortality. C. difficile contains numerous mobile genetic elements, resulting in the potential for a highly plastic genome. In the first sequenced strain, 630, there is one proven conjugative transposon (CTn), Tn5397, and six putative CTns (CTn1, CTn2 and CTn4-7), of which, CTn4 and CTn5 were capable of excision. In the second sequenced strain, R20291, two further CTns were described.<br><br>RESULTS: CTn1, CTn2 CTn4, CTn5 and CTn7 were shown to excise from the genome of strain 630 and transfer to strain CD37. A putative CTn from R20291, misleadingly termed a phage island previously, was shown to excise and to contain three putative mobilisable transposons, one of which was capable of excision. In silico probing of C. difficile genome sequences with recombinase gene fragments identified new putative conjugative and mobilisable transposons related to the elements in strains 630 and R20291. CTn5-like elements were described occupying different insertion sites in different strains, CTn1-like elements that have lost the ability to excise in some ribotype 027 strains were described and one strain was shown to contain CTn5-like and CTn7-like elements arranged in tandem. Additionally, using bioinformatics, we updated previous gene annotations and predicted novel functions for the accessory gene products on these new elements.<br><br>CONCLUSIONS: The genomes of the C. difficile strains examined contain highly related CTns suggesting recent horizontal gene transfer. Several elements were capable of excision and conjugative transfer. The presence of antibiotic resistance genes and genes predicted to promote adaptation to the intestinal environment suggests that CTns play a role in the interaction of C. difficile with its human host.}, }
@article {pmid21876676, year = {2011}, author = {Guglielmini, J and Quintais, L and Garcillán-Barcia, MP and de la Cruz, F and Rocha, EP}, title = {The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation.}, journal = {PLoS genetics}, volume = {7}, number = {8}, pages = {e1002222}, pmid = {21876676}, issn = {1553-7404}, mesh = {Chromosomes/genetics ; *Conjugation, Genetic ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Variation ; *Genome ; Genomics ; Phylogeny ; Plasmids/genetics ; Prokaryotic Cells/*metabolism ; Proteins/*genetics/metabolism ; }, abstract = {Horizontal gene transfer shapes the genomes of prokaryotes by allowing rapid acquisition of novel adaptive functions. Conjugation allows the broadest range and the highest gene transfer input per transfer event. While conjugative plasmids have been studied for decades, the number and diversity of integrative conjugative elements (ICE) in prokaryotes remained unknown. We defined a large set of protein profiles of the conjugation machinery to scan over 1,000 genomes of prokaryotes. We found 682 putative conjugative systems among all major phylogenetic clades and showed that ICEs are the most abundant conjugative elements in prokaryotes. Nearly half of the genomes contain a type IV secretion system (T4SS), with larger genomes encoding more conjugative systems. Surprisingly, almost half of the chromosomal T4SS lack co-localized relaxases and, consequently, might be devoted to protein transport instead of conjugation. This class of elements is preponderant among small genomes, is less commonly associated with integrases, and is rarer in plasmids. ICEs and conjugative plasmids in proteobacteria have different preferences for each type of T4SS, but all types exist in both chromosomes and plasmids. Mobilizable elements outnumber self-conjugative elements in both ICEs and plasmids, which suggests an extensive use of T4SS in trans. Our evolutionary analysis indicates that switch of plasmids to and from ICEs were frequent and that extant elements began to differentiate only relatively recently. According to the present results, ICEs are the most abundant conjugative elements in practically all prokaryotic clades and might be far more frequently domesticated into non-conjugative protein transport systems than previously thought. While conjugative plasmids and ICEs have different means of genomic stabilization, their mechanisms of mobility by conjugation show strikingly conserved patterns, arguing for a unitary view of conjugation in shaping the genomes of prokaryotes by horizontal gene transfer.}, }
@article {pmid21876149, year = {2011}, author = {Field, B and Fiston-Lavier, AS and Kemen, A and Geisler, K and Quesneville, H and Osbourn, AE}, title = {Formation of plant metabolic gene clusters within dynamic chromosomal regions.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {38}, pages = {16116-16121}, pmid = {21876149}, issn = {1091-6490}, support = {BBS/E/J/00000614/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Acyltransferases/genetics/metabolism ; Arabidopsis/*genetics/*metabolism ; Arabidopsis Proteins/classification/genetics/metabolism ; Chromosome Mapping ; Chromosomes, Plant/*genetics ; Cytochrome P-450 Enzyme System/genetics/metabolism ; Gas Chromatography-Mass Spectrometry ; Gene Duplication ; Gene Expression Regulation, Plant ; Genome, Plant/genetics ; Intramolecular Transferases/genetics/metabolism ; Models, Genetic ; Molecular Structure ; *Multigene Family ; Mutation ; Phylogeny ; Plant Leaves/genetics/metabolism ; Plant Roots/genetics/metabolism ; Plants, Genetically Modified ; Triterpenes/analysis/chemistry/metabolism ; }, abstract = {In bacteria, genes with related functions often are grouped together in operons and are cotranscribed as a single polycistronic mRNA. In eukaryotes, functionally related genes generally are scattered across the genome. Notable exceptions include gene clusters for catabolic pathways in yeast, synthesis of secondary metabolites in filamentous fungi, and the major histocompatibility complex in animals. Until quite recently it was thought that gene clusters in plants were restricted to tandem duplicates (for example, arrays of leucine-rich repeat disease-resistance genes). However, operon-like clusters of coregulated nonhomologous genes are an emerging theme in plant biology, where they may be involved in the synthesis of certain defense compounds. These clusters are unlikely to have arisen by horizontal gene transfer, and the mechanisms behind their formation are poorly understood. Previously in thale cress (Arabidopsis thaliana) we identified an operon-like gene cluster that is required for the synthesis and modification of the triterpene thalianol. Here we characterize a second operon-like triterpene cluster (the marneral cluster) from A. thaliana, compare the features of these two clusters, and investigate the evolutionary events that have led to cluster formation. We conclude that common mechanisms are likely to underlie the assembly and control of operon-like gene clusters in plants.}, }
@article {pmid21874606, year = {2012}, author = {Shi, DS and Wang, WP and Kuai, SG and Shao, HF and Huang, M}, title = {Identification of bla KPC-2 on different plasmids of three Morganella morganii isolates.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {31}, number = {5}, pages = {797-803}, pmid = {21874606}, issn = {1435-4373}, mesh = {Anti-Bacterial Agents/pharmacology ; Carbapenems/pharmacology ; Cluster Analysis ; Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; Electrophoresis, Gel, Pulsed-Field ; Enterobacteriaceae Infections/microbiology ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Genotype ; Humans ; Intensive Care Units ; Molecular Typing ; Morganella morganii/*enzymology/genetics/isolation &amp; purification ; *Plasmids ; Sequence Analysis, DNA ; beta-Lactam Resistance ; beta-Lactamases/*genetics ; }, abstract = {Three Morganella morganii strains resistant to carbapenems were recovered from the surgical intensive care unit (SICU) in our hospital. Carbapenemases and extended-spectrum β-lactamases (ESBLs) were respectively detected by the modified Hodge test and the modified Clinical and Laboratory Standards Institute (CLSI) ESBL confirmatory test in all isolates. Amplification of whole-cell and plasmid DNAs extracted from isolates with primers specific for the bla (KPC) produced an amplicon confirmed to be bla (KPC-2) by sequence analysis. Pulsed-field gel electrophoresis (PFGE) typing revealed that three isolates belonged to two closely related types. Plasmids electrophoresis and restriction analysis revealed that the bla (KPC-2) was located on different plasmids. The transfer of carbapenem resistance from the three original isolates to Escherichia coli EC600 was successful by conjugation. An examination of the outer membrane proteins showed a lack of a 38-kDa outer membrane protein (OMP) compared with M. morganii susceptible to carbapenems. The production of KPC-2 and ESBLs, combined with OMP deficiency, resulted in high-level carbapenem resistance in the M. morganii strains. The genetic environment around bla (KPC-2) analysis revealed that this β-lactamase was located on the same mobile genetic elements which could transfer between different plasmids.}, }
@article {pmid21873630, year = {2012}, author = {Böhne, A and Zhou, Q and Darras, A and Schmidt, C and Schartl, M and Galiana-Arnoux, D and Volff, JN}, title = {Zisupton--a novel superfamily of DNA transposable elements recently active in fish.}, journal = {Molecular biology and evolution}, volume = {29}, number = {2}, pages = {631-645}, doi = {10.1093/molbev/msr208}, pmid = {21873630}, issn = {1537-1719}, mesh = {Amino Acid Sequence ; Animals ; Cloning, Molecular ; Cyprinodontiformes/*genetics ; Cysteine Endopeptidases/genetics ; DNA Transposable Elements/*genetics ; Evolution, Molecular ; Genetic Variation ; Genome ; Male ; Molecular Sequence Data ; Mutagenesis, Insertional ; Phylogeny ; Polymorphism, Genetic ; SUMO-1 Protein/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Testis/cytology ; Transposases/*genetics ; Y Chromosome/genetics ; }, abstract = {Transposable elements are widespread mobile DNA sequences able to integrate into new locations within genomes. Through transposition and recombination, they significantly contribute to genome plasticity and evolution. They can also regulate gene expression and provide regulatory and coding sequences (CDSs) for the evolution of novel gene functions. We have identified a new superfamily of DNA transposon on the Y chromosome of the platyfish Xiphophorus maculatus. This element is 11 kb in length and carries a single CDS of 24 exons. The N-terminal part of the putative protein, which is expressed in all adult tissues tested, contains several nucleic acid- and protein-binding domains and might correspond to a novel type of transposase/integrase not described so far in any transposon. In addition, a testis-specific splice isoform encodes a C-terminal Ulp1 SUMO protease domain, suggesting a function in posttranslational protein modification mediated by SUMO and/or ubiquitin small peptides. Accordingly, this element was called Zisupton, for Zinc finger SUMO protease transposon. Beside the Y-chromosomal sequence, five other very similar copies were identified in the platyfish genome. All copies are delimited by 99-bp conserved subterminal inverted repeats and flanked by copy-specific 8-nt target site duplications reflecting their integration at different positions in the genome. Zisupton elements are inserted at different genomic locations in different poeciliid species but also in different populations of X. maculatus. Such insertion polymorphisms between related species and populations indicate relatively recent transposition activity, with a high degree of nucleotide identity between species suggesting possible implication of horizontal gene transfer. Zisupton sequences were detected in other fish species, in urochordates, cephalochordates, and hemichordates as well as in more distant organisms, such as basidiomycete fungi, filamentous brown algae, and green algae. Possible examples of nuclear genes derived from Zisupton have been identified. To conclude, our analysis has uncovered a new superfamily of DNA transposons with potential roles in genome diversity and evolutionary innovation in fish and other organisms.}, }
@article {pmid21873290, year = {2011}, author = {Sóki, J and Gonzalez, SM and Urbán, E and Nagy, E and Ayala, JA}, title = {Molecular analysis of the effector mechanisms of cefoxitin resistance among Bacteroides strains.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {66}, number = {11}, pages = {2492-2500}, doi = {10.1093/jac/dkr339}, pmid = {21873290}, issn = {1460-2091}, mesh = {Bacterial Proteins/genetics/metabolism ; Bacteroides/*drug effects/*genetics/isolation &amp; purification ; Base Sequence ; Cefoxitin/metabolism/*pharmacology ; *DNA Transposable Elements ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Membrane Proteins/genetics/metabolism ; Microbial Sensitivity Tests ; Mutation ; Penicillin-Binding Proteins/genetics/metabolism ; Sequence Analysis, DNA ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: The characterization of Bacteroides strains with regard to the cfxA gene, the MTn4555 mobilizable transposon, the role of penicillin-binding proteins (PBPs) and heterogeneous cefoxitin resistance.<br><br>METHODS: Eighty-four randomly selected and 11 heterogeneously or highly cefoxitin-resistant Bacteroides isolates were included. Agar dilution and Etest methods were used for the determination of cefoxitin MICs. PCR experiments and nucleotide sequencing were used to detect the cfxA gene and the molecular features of MTn4555. Cefoxitin-binding experiments to determine its affinity (IC(50)) for PBPs and cefoxitinase assays were also applied. Southern blotting was used to determine the copy number of the cfxA genes.<br><br>RESULTS: Sixteen strains from the random collection proved to be positive for cfxA, and the MIC distribution for the cfxA-negative and -positive strains did not display a clear separation. The majority of the cfxA-positive strains in this collection harboured a 1.2 kb common region at the 3' end of MTn4555. This region encoded an open reading frame that exhibited homology to abortive phage infection proteins (AbiD). The cfxA genes were transferable only at low frequencies in conjugation experiments. In PBP affinity studies, the PBP-A and PBP3 species were largely insensitive to cefoxitin, whereas the other PBP species were affected at very low concentrations. Seven of the heterogeneously resistant strains were positive for cfxA and most of them had mutations in the regulatory regions of cfxA.<br><br>CONCLUSIONS: Major and minor roles for Bacteroides fragilis PBPs and the CfxA cefoxitinase, respectively, were inferred. The role of the newly recognized abiD may be to control the copy number of cfxA.}, }
@article {pmid21864345, year = {2011}, author = {Roos, TE and van Passel, MW}, title = {A quantitative account of genomic island acquisitions in prokaryotes.}, journal = {BMC genomics}, volume = {12}, number = {}, pages = {427}, pmid = {21864345}, issn = {1471-2164}, mesh = {DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Archaeal ; *Genome, Bacterial ; *Genomic Islands ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Microbial genomes do not merely evolve through the slow accumulation of mutations, but also, and often more dramatically, by taking up new DNA in a process called horizontal gene transfer. These innovation leaps in the acquisition of new traits can take place via the introgression of single genes, but also through the acquisition of large gene clusters, which are termed Genomic Islands. Since only a small proportion of all the DNA diversity has been sequenced, it can be hard to find the appropriate donors for acquired genes via sequence alignments from databases. In contrast, relative oligonucleotide frequencies represent a remarkably stable genomic signature in prokaryotes, which facilitates compositional comparisons as an alignment-free alternative for phylogenetic relatedness. In this project, we test whether Genomic Islands identified in individual bacterial genomes have a similar genomic signature, in terms of relative dinucleotide frequencies, and can therefore be expected to originate from a common donor species.<br><br>RESULTS: When multiple Genomic Islands are present within a single genome, we find that up to 28% of these are compositionally very similar to each other, indicative of frequent recurring acquisitions from the same donor to the same acceptor.<br><br>CONCLUSIONS: This represents the first quantitative assessment of common directional transfer events in prokaryotic evolutionary history. We suggest that many of the resident Genomic Islands per prokaryotic genome originated from the same source, which may have implications with respect to their regulatory interactions, and for the elucidation of the common origins of these acquired gene clusters.}, }
@article {pmid21861918, year = {2011}, author = {McInerney, JO and Pisani, D and Bapteste, E and O'Connell, MJ}, title = {The Public Goods Hypothesis for the evolution of life on Earth.}, journal = {Biology direct}, volume = {6}, number = {}, pages = {41}, pmid = {21861918}, issn = {1745-6150}, mesh = {Base Sequence ; *Biological Evolution ; Earth, Planet ; *Gene Transfer, Horizontal ; Genes, rRNA ; Interspersed Repetitive Sequences ; *Models, Genetic ; Phylogeny ; Prokaryotic Cells/*cytology ; Selection, Genetic ; }, abstract = {It is becoming increasingly difficult to reconcile the observed extent of horizontal gene transfers with the central metaphor of a great tree uniting all evolving entities on the planet. In this manuscript we describe the Public Goods Hypothesis and show that it is appropriate in order to describe biological evolution on the planet. According to this hypothesis, nucleotide sequences (genes, promoters, exons, etc.) are simply seen as goods, passed from organism to organism through both vertical and horizontal transfer. Public goods sequences are defined by having the properties of being largely non-excludable (no organism can be effectively prevented from accessing these sequences) and non-rival (while such a sequence is being used by one organism it is also available for use by another organism). The universal nature of genetic systems ensures that such non-excludable sequences exist and non-excludability explains why we see a myriad of genes in different combinations in sequenced genomes. There are three features of the public goods hypothesis. Firstly, segments of DNA are seen as public goods, available for all organisms to integrate into their genomes. Secondly, we expect the evolution of mechanisms for DNA sharing and of defense mechanisms against DNA intrusion in genomes. Thirdly, we expect that we do not see a global tree-like pattern. Instead, we expect local tree-like patterns to emerge from the combination of a commonage of genes and vertical inheritance of genomes by cell division. Indeed, while genes are theoretically public goods, in reality, some genes are excludable, particularly, though not only, when they have variant genetic codes or behave as coalition or club goods, available for all organisms of a coalition to integrate into their genomes, and non-rival within the club. We view the Tree of Life hypothesis as a regionalized instance of the Public Goods hypothesis, just like classical mechanics and euclidean geometry are seen as regionalized instances of quantum mechanics and Riemannian geometry respectively. We argue for this change using an axiomatic approach that shows that the Public Goods hypothesis is a better accommodation of the observed data than the Tree of Life hypothesis.}, }
@article {pmid21861622, year = {2011}, author = {Witte, W and Cuny, C}, title = {Emergence and spread of cfr-mediated multiresistance in staphylococci: an interdisciplinary challenge.}, journal = {Future microbiology}, volume = {6}, number = {8}, pages = {925-931}, doi = {10.2217/fmb.11.69}, pmid = {21861622}, issn = {1746-0921}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology/therapeutic use ; Bacterial Proteins/genetics/*metabolism ; Cross Infection/drug therapy/microbiology ; Drug Resistance, Microbial/genetics ; *Drug Resistance, Multiple, Bacterial ; Europe ; Gene Transfer, Horizontal ; Humans ; Plasmids ; Staphylococcal Infections/*microbiology/*veterinary ; Staphylococcus/*drug effects/genetics ; Swine ; Swine Diseases/drug therapy/microbiology ; United States ; }, abstract = {In staphylococci, methylation of A2503 of 23S rRNA leads to resistance against several classes of antibiotics (oxazolidinones, phenicols, streptogramin compounds, lincosamidins and pleuromutilins). The corresponding resistance gene cfr is located on plasmid(s) and is transferable within and between staphylococcal species including Staphylococcus aureus. It first emerged in coagulase-negative staphylococci, later in Central Europe also in S. aureus ST9 and in methicillin-resistant S. aureus ST398, which have their main reservoir in pigs, and meanwhile also in nosocomial coagulase-negative staphylococci from Southern Europe and the USA, and furthermore in nosocomial methicillin-resistant S. aureus in Spain. Timely detection and targeted prevention of further dissemination in both human and veterinary medicine is warranted for preserving the activity linezolid as an important antibiotic for treatment of staphylococcal infections.}, }
@article {pmid21860116, year = {2011}, author = {Roy, S and Mukherjee, S and Singh, AK and Basu, S}, title = {CTX-M-9 group extended-spectrum β-lactamases in neonatal stool isolates: emergence in India.}, journal = {Indian journal of medical microbiology}, volume = {29}, number = {3}, pages = {305-308}, doi = {10.4103/0255-0857.83919}, pmid = {21860116}, issn = {1998-3646}, mesh = {Anti-Bacterial Agents/pharmacology ; Escherichia coli/drug effects/*enzymology/*isolation &amp; purification ; Escherichia coli Proteins/*metabolism ; Feces/*microbiology ; Gene Transfer, Horizontal ; Humans ; India ; Infant, Newborn ; Klebsiella pneumoniae/drug effects/*enzymology/*isolation &amp; purification ; Microbial Sensitivity Tests ; beta-Lactamases/*metabolism ; }, abstract = {The study reports for the first time the identification of CTX-M-14-like and CTX-M-27-like extended-spectrum β-lactamases (ESBLs) belonging to the CTX-M-9 group in Klebsiella pneumoniae and Escherichia coli isolated from the neonatal stool in India. The plasmid carrying the blaCTX-M-9 group in both the isolates was transferable. Till date, no other CTX-M group, except the CTX-M-1 group, has been reported from India. A total of 77% of the neonates had ESBL-producing K. pneumoniae or E. coli in their stool, and blaCTX-M-15 was the predominant ESBL gene. Although the CTX-M-9 group was found in the stool and did not cause infection, the detection of the CTX-M-9 group might be a prelude to future infections.}, }
@article {pmid21860106, year = {2011}, author = {Lahlaoui, H and Dahmen, S and Moussa, MB and Omrane, B}, title = {First detection of TEM-116 extended-spectrum β-lactamase in a Providencia stuartii isolate from a Tunisian hospital.}, journal = {Indian journal of medical microbiology}, volume = {29}, number = {3}, pages = {258-261}, doi = {10.4103/0255-0857.83909}, pmid = {21860106}, issn = {1998-3646}, mesh = {Anti-Bacterial Agents/pharmacology ; Cephalosporins/pharmacology ; Conjugation, Genetic ; Enterobacteriaceae Infections/*microbiology ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Hospitals ; Humans ; Plasmids ; Polymerase Chain Reaction ; Providencia/drug effects/*enzymology/genetics/*isolation &amp; purification ; Sequence Analysis, DNA ; Tunisia ; beta-Lactam Resistance ; beta-Lactamases/*genetics ; }, abstract = {PURPOSE: To study the resistance to third-generation cephalosporins in Providencia stuartii strain isolated from hospitalized patient in Tunisia and to identify the responsible genes<br><br>MATERIALS AND METHODS: This strain was analysed by PCR and sequencing to identify the genes responsible for the &#x3b2;-lactamase resistance phenotypes. The transferability of the phenotypes was tested by conjugation to Escherichia coli J53. The isoelectric point was determinate by isoelectrofocalisation.<br><br>RESULTS: This resistance was carried by a 60 kb plasmid that encoded a &#x3b2;-lactamase with a pI of 5.4. This &#x3b2;-lactamase revealed identity with the blaTEM-1 gene encoding the TEM-1 &#x3b2;-lactamase, except for a replacement of the Val residue at position 84 by Ile, and the Ala residue at position 184 by Val. These two mutations were encountered in TEM-116 &#x3b2;-lactamase.<br><br>CONCLUSION: This study demonstrates the &#xfb01;rst description of TEM-116 in the P. stuartii species in the world and the &#xfb01;rst one in a Tunisian hospital.}, }
@article {pmid21859815, year = {2011}, author = {Zhang, W and Luo, Y and Li, J and Lin, L and Ma, Y and Hu, C and Jin, S and Ran, L and Cui, S}, title = {Wide dissemination of multidrug-resistant Shigella isolates in China.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {66}, number = {11}, pages = {2527-2535}, doi = {10.1093/jac/dkr341}, pmid = {21859815}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Typing Techniques ; Base Sequence ; Cephalosporins/pharmacology ; China ; Ciprofloxacin/pharmacology ; Clavulanic Acids/pharmacology ; DNA Gyrase/genetics ; DNA Topoisomerase IV/genetics ; DNA, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Dysentery, Bacillary/microbiology ; Enterobacteriaceae Infections/microbiology ; Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; Mutation ; Quinolones/pharmacology ; Sequence Analysis, DNA ; Serotyping ; Shigella flexneri/classification/*drug effects/*genetics/isolation &amp; purification ; beta-Lactamases/genetics/isolation &amp; purification ; }, abstract = {OBJECTIVES: To evaluate the prevalence of antimicrobial resistance and selected antimicrobial resistance mechanisms in Shigella isolates recovered in outpatients from 1997 to 2009 in China.<br><br>METHODS: The isolates were subjected to serotyping and antimicrobial susceptibility testing. Shigella isolates producing extended-spectrum &#x3b2;-lactamases (ESBLs) or resistance to ciprofloxacin were further characterized by PFGE to determine the genetic relatedness. These isolates were also screened for &#x3b2;-lactamase genes and mutations in the quinolone resistance-determining regions (QRDRs) by PCR. DNA sequence analysis was also performed.<br><br>RESULTS: After serotyping, 301 Shigella isolates were grouped into three subgroups and 13 distinct serotypes. The antimicrobial resistance profiles differed among subgroups and serotypes. Ciprofloxacin-resistant isolates were mainly Shigella flexneri serotypes f2a and f4a, which were resistant to at least four additional non-quinolone antimicrobials. Three point mutations in the QRDRs of gyrA and parC were identified in all 30 ciprofloxacin-resistant S. flexneri isolates. Plasmid-mediated bla(CMY-2), bla(CTX-M-14), bla(CTX-M-15) and bla(CTX-M-55)-like genes were found in 29 ESBL-producing isolates and three clavulanic-acid-resistant isolates, and six isolates also exhibited resistance to ciprofloxacin. Distinct genetic differences in both serotypes and PFGE profiles were observed for these ciprofloxacin- or extended-spectrum-cephalosporin-resistant isolates.<br><br>CONCLUSIONS: ESBL-producing or fluoroquinolone-resistant Shigella is no longer an unusual phenomenon in the local community. The monitoring programme in China should stay vigilant to the dissemination of these isolates and the health agencies must take appropriate measures to restrict the abuse of antimicrobials, especially in the community.}, }
@article {pmid21858844, year = {2011}, author = {McInerney, JO and Martin, WF and Koonin, EV and Allen, JF and Galperin, MY and Lane, N and Archibald, JM and Embley, TM}, title = {Planctomycetes and eukaryotes: a case of analogy not homology.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {33}, number = {11}, pages = {810-817}, pmid = {21858844}, issn = {1521-1878}, support = {Z99 MH999999/ImNIH/Intramural NIH HHS/United States ; Z99 LM999999/ImNIH/Intramural NIH HHS/United States ; Z01 LM000073-13/ImNIH/Intramural NIH HHS/United States ; Z99 CL999999/ImNIH/Intramural NIH HHS/United States ; Z99 HL999999/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/physiology ; Biological Evolution ; Cell Nucleus/physiology ; Chlamydia/classification/*cytology/genetics/physiology ; Endoplasmic Reticulum/physiology ; Eukaryota/classification/*cytology/genetics/physiology ; Gene Transfer, Horizontal ; Mitochondria/genetics/physiology ; Nuclear Envelope/physiology ; Phylogeny ; Planctomycetales/classification/*cytology/genetics/physiology ; Verrucomicrobia/classification/*cytology/genetics/physiology ; }, abstract = {Planctomycetes, Verrucomicrobia and Chlamydia are prokaryotic phyla, sometimes grouped together as the PVC superphylum of eubacteria. Some PVC species possess interesting attributes, in particular, internal membranes that superficially resemble eukaryotic endomembranes. Some biologists now claim that PVC bacteria are nucleus-bearing prokaryotes and are considered evolutionary intermediates in the transition from prokaryote to eukaryote. PVC prokaryotes do not possess a nucleus and are not intermediates in the prokaryote-to-eukaryote transition. Here we summarise the evidence that shows why all of the PVC traits that are currently cited as evidence for aspiring eukaryoticity are either analogous (the result of convergent evolution), not homologous, to eukaryotic traits; or else they are the result of horizontal gene transfers.}, }
@article {pmid21858108, year = {2011}, author = {Fernández-Alarcón, C and Singer, RS and Johnson, TJ}, title = {Comparative genomics of multidrug resistance-encoding IncA/C plasmids from commensal and pathogenic Escherichia coli from multiple animal sources.}, journal = {PloS one}, volume = {6}, number = {8}, pages = {e23415}, pmid = {21858108}, issn = {1932-6203}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Antiporters/genetics ; Bacterial Proteins/genetics ; Cattle ; Chile ; Cluster Analysis ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/*genetics ; Escherichia coli Infections/microbiology ; Escherichia coli Proteins/genetics ; Gene Order ; Gene Transfer, Horizontal ; Genomics/*methods ; Humans ; Molecular Sequence Data ; Phylogeny ; Plasmids/classification/*genetics ; Sequence Analysis, DNA ; Swine ; Tetracycline Resistance/genetics ; Thiamphenicol/analogs &amp; derivatives/pharmacology ; Turkeys ; United States ; beta-Lactamases/genetics ; }, abstract = {Incompatibility group A/C (IncA/C) plasmids have received recent attention for their broad host range and ability to confer resistance to multiple antimicrobial agents. Due to the potential spread of multidrug resistance (MDR) phenotypes from foodborne pathogens to human pathogens, the dissemination of these plasmids represents a public health risk. In this study, four animal-source IncA/C plasmids isolated from Escherichia coli were sequenced and analyzed, including isolates from commercial dairy cows, pigs and turkeys in the U.S. and Chile. These plasmids were initially selected because they either contained the floR and tetA genes encoding for florfenicol and tetracycline resistance, respectively, and/or the bla(CMY-2) gene encoding for extended spectrum β-lactamase resistance. Overall, sequence analysis revealed that each of the four plasmids retained a remarkably stable and conserved backbone sequence, with differences observed primarily within their accessory regions, which presumably have evolved via horizontal gene transfer events involving multiple modules. Comparison of these plasmids with other available IncA/C plasmid sequences further defined the core and accessory elements of these plasmids in E. coli and Salmonella. Our results suggest that the bla(CMY-2) plasmid lineage appears to have derived from an ancestral IncA/C plasmid type harboring floR-tetAR-strAB and Tn21-like accessory modules. Evidence is mounting that IncA/C plasmids are widespread among enteric bacteria of production animals and these emergent plasmids have flexibility in their acquisition of MDR-encoding modules, necessitating further study to understand the evolutionary mechanisms involved in their dissemination and stability in bacterial populations.}, }
@article {pmid21857904, year = {2011}, author = {Lazcano, A}, title = {Natural history, microbes and sequences: shouldn't we look back again to organisms?.}, journal = {PloS one}, volume = {6}, number = {8}, pages = {e21334}, pmid = {21857904}, issn = {1932-6203}, mesh = {Bacteria/*classification/*genetics/growth &amp; development ; Biodiversity ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; Recombination, Genetic ; Species Specificity ; }, abstract = {The discussion on the existence of prokaryotic species is reviewed. The demonstration that several different mechanisms of genetic exchange and recombination exist has led some to a radical rejection of the possibility of bacterial species and, in general, the applicability of traditional classification categories to the prokaryotic domains. However, in spite of intense gene traffic, prokaryotic groups are not continuously variable but form discrete clusters of phenotypically coherent, well-defined, diagnosable groups of individual organisms. Molecularization of life sciences has led to biased approaches to the issue of the origins of biodiversity, which has resulted in the increasingly extended tendency to emphasize genes and sequences and not give proper attention to organismal biology. As argued here, molecular and organismal approaches that should be seen as complementary and not opposed views of biology.}, }
@article {pmid21856840, year = {2011}, author = {Karczmarczyk, M and Walsh, C and Slowey, R and Leonard, N and Fanning, S}, title = {Molecular characterization of multidrug-resistant Escherichia coli isolates from Irish cattle farms.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {20}, pages = {7121-7127}, pmid = {21856840}, issn = {1098-5336}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Cattle ; Conjugation, Genetic ; Disease Reservoirs ; *Drug Resistance, Multiple, Bacterial ; Escherichia coli/classification/*drug effects/genetics/*isolation &amp; purification ; Escherichia coli Infections/microbiology/*veterinary ; Escherichia coli Proteins/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Variation ; Integrons ; Ireland ; Plasmids ; Polymerase Chain Reaction ; Virulence Factors/genetics ; }, abstract = {This study describes the genotypic characteristics of a collection of 100 multidrug-resistant (MDR) Escherichia coli strains recovered from cattle and the farm environment in Ireland in 2007. The most prevalent antimicrobial resistance identified was to streptomycin (100%), followed by tetracycline (99%), sulfonamides (98%), ampicillin (82%), and neomycin (62%). Resistance was mediated predominantly by strA-strB (92%), tetA (67%), sul2 (90%), bla(TEM) (79%), and aphA1 (63%) gene markers, respectively. Twenty-seven isolates harbored a class 1 integrase (intI1), while qacEΔ1 and sul1 markers were identified in 25 and 26 isolates, respectively. The variable regions of these integrons contained aminoglycoside, trimethoprim, and β-lactam resistance determinants (aadA12, aadB-aadA1, bla(OXA-30)-aadA1, dfrA1-aadA1, dfrA7). Class 2 integrons were identified less frequently (4%) and contained the gene cassette array dfrA1-sat1-aadA1. Resistance to ampicillin, neomycin, streptomycin, sulfonamide, and tetracycline was associated with transferable high-molecular-weight plasmids, as demonstrated by conjugation assays. A panel of virulence markers was screened for by PCR, and genes identified included vt1, K5 in 2 isolates, papC in 10 isolates, and PAI IV(536) in 37 isolates. MDR commensal E. coli isolates from Irish cattle displayed considerable diversity with respect to the genes identified. Our findings highlight the importance of the commensal microflora of food-producing animals as a reservoir of transferable MDR.}, }
@article {pmid21856835, year = {2011}, author = {Karczmarczyk, M and Abbott, Y and Walsh, C and Leonard, N and Fanning, S}, title = {Characterization of multidrug-resistant Escherichia coli isolates from animals presenting at a university veterinary hospital.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {20}, pages = {7104-7112}, pmid = {21856835}, issn = {1098-5336}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; *Drug Resistance, Multiple, Bacterial ; Escherichia coli/*drug effects/genetics/*isolation &amp; purification ; Escherichia coli Infections/microbiology/*veterinary ; Gene Transfer, Horizontal ; Genes, Bacterial ; Hospitals, Animal ; Integrons ; Ireland ; Microbial Sensitivity Tests ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Universities ; }, abstract = {In this study, we examined molecular mechanisms associated with multidrug resistance (MDR) in a collection of Escherichia coli isolates recovered from hospitalized animals in Ireland. PCR and DNA sequencing were used to identify genes associated with resistance. Class 1 integrons were prevalent (94.6%) and contained gene cassettes recognized previously and implicated mainly in resistance to aminoglycosides, β-lactams, and trimethoprim (aadA1, dfrA1-aadA1, dfrA17-aadA5, dfrA12-orfF-aadA2, bla(OXA-30)-aadA1, aacC1-orf1-orf2-aadA1, dfr7). Class 2 integrons (13.5%) contained the dfrA1-sat1-aadA1 gene array. The most frequently occurring phenotypes included resistance to ampicillin (97.3%), chloramphenicol (75.4%), florfenicol (40.5%), gentamicin (54%), neomycin (43.2%), streptomycin (97.3%), sulfonamide (98.6%), and tetracycline (100%). The associated resistance determinants detected included bla(TEM), cat, floR, aadB, aphA1, strA-strB, sul2, and tet(B), respectively. The bla(CTX-M-2) gene, encoding an extended-spectrum β-lactamase (ESβL), and bla(CMY-2), encoding an AmpC-like enzyme, were identified in 8 and 18 isolates, respectively. The mobility of the resistance genes was demonstrated using conjugation assays with a representative selection of isolates. High-molecular-weight plasmids were found to be responsible for resistance to multiple antimicrobial compounds. The study demonstrated that animal-associated commensal E. coli isolates possess a diverse repertoire of transferable genetic determinants. Emergence of ESβLs and AmpC-like enzymes is particularly significant. To our knowledge, the bla(CTX-M-2) gene has not previously been reported in Ireland.}, }
@article {pmid21856213, year = {2011}, author = {Popa, O and Dagan, T}, title = {Trends and barriers to lateral gene transfer in prokaryotes.}, journal = {Current opinion in microbiology}, volume = {14}, number = {5}, pages = {615-623}, doi = {10.1016/j.mib.2011.07.027}, pmid = {21856213}, issn = {1879-0364}, mesh = {Evolution, Molecular ; *Gene Transfer, Horizontal ; Prokaryotic Cells/*physiology ; }, abstract = {Gene acquisition by lateral gene transfer (LGT) is an important mechanism for natural variation among prokaryotes. Laboratory experiments show that protein-coding genes can be laterally transferred extremely fast among microbial cells, inherited to most of their descendants, and adapt to a new regulatory regime within a short time. Recent advance in the phylogenetic analysis of microbial genomes using networks approach reveals a substantial impact of LGT during microbial genome evolution. Phylogenomic networks of LGT among prokaryotes reconstructed from completely sequenced genomes uncover barriers to LGT in multiple levels. Here we discuss the kinds of barriers to gene acquisition in nature including physical barriers for gene transfer between cells, genomic barriers for the integration of acquired DNA, and functional barriers for the acquisition of new genes.}, }
@article {pmid21854875, year = {2011}, author = {Tsai, YH and Maron, SB and McGann, P and Nightingale, KK and Wiedmann, M and Orsi, RH}, title = {Recombination and positive selection contributed to the evolution of Listeria monocytogenes lineages III and IV, two distinct and well supported uncommon L. monocytogenes lineages.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {11}, number = {8}, pages = {1881-1890}, pmid = {21854875}, issn = {1567-7257}, support = {R01 GM063259/GM/NIGMS NIH HHS/United States ; R01 GM063259-04/GM/NIGMS NIH HHS/United States ; T32 CA009566/CA/NCI NIH HHS/United States ; R01GM63259-04/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; Gene Transfer, Horizontal ; Humans ; Listeria monocytogenes/*classification/*genetics/pathogenicity ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; *Recombination, Genetic ; *Selection, Genetic ; }, abstract = {Listeriamonocytogenes lineages III and IV represent two uncommon lineages of the human and animal pathogen L. monocytogenes, characterized by occurrence of unusual phenotypic and genetic characteristics that differentiate them from the common lineages I and II. To gain further insights into the evolution of lineages III and IV, we amplified and sequenced housekeeping genes (i.e., gap, prs, purM, ribC, and sigB), internalin genes (i.e., inlA, inlB, inlC, inlG, inlC2, inlD, inlE, inlF, and inlH) and the virulence gene cluster containing prfA, plcA, hly, mpl, actA, and plcB for lineages III (n = 7) and IV (n = 4) isolates. Phylogenetic analyses of the sequences obtained along with previously reported sequence data for 40 isolates representing lineages I (n = 18), II (n = 21), and III (n = 1), showed that lineages III and IV represent divergent and monophyletic lineages. The virulence gene cluster as well as the inlAB operon were present in all isolates, with inlF absent from all lineages III and IV isolates. While all lineage IV isolates contained only inlC (in addition to inlAB), lineage III isolates showed considerable diversity with regard to internalin gene presence, including presence of (i) only inlC (n = 2), (ii) inlC and inlGC2DE (n = 3), (iii) only inlGC2DE (n = 2), and (iv) inlC and inlC2DE (n = 1). In addition to evidence for horizontal gene transfer events, among lineages III and IV isolates, in prs, actA, plcB, mpl, inlA, inlB, inlG, inlD, and inlE, we also found significant evidence for positive selection in the hly promoter region and, along the lineages III and IV branches, for actA (including in sites recognized for interactions with proteins involved in actin tail polymerization). In conclusion, lineages III and IV represent two distinct monophyletic groups with contributions of intragenic recombination to the evolution of their internalin genes as well as contributions of positive selection to evolution of the virulence genes island.}, }
@article {pmid21854517, year = {2012}, author = {Luo, H and Löytynoja, A and Moran, MA}, title = {Genome content of uncultivated marine Roseobacters in the surface ocean.}, journal = {Environmental microbiology}, volume = {14}, number = {1}, pages = {41-51}, doi = {10.1111/j.1462-2920.2011.02528.x}, pmid = {21854517}, issn = {1462-2920}, support = {GR078968//Wellcome Trust/United Kingdom ; }, mesh = {Computational Biology ; DNA, Bacterial/genetics ; *Genome, Bacterial ; *Metagenome ; Metagenomics ; Multigene Family ; Oceans and Seas ; Phylogeny ; Roseobacter/classification/*genetics/metabolism ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Understanding of the ecological roles and evolutionary histories of marine bacterial taxa can be complicated by mismatches in genome content between wild populations and their better-studied cultured relatives. We used computed patterns of non-synonymous (amino acid-altering) nucleotide diversity in marine metagenomic data to provide high-confidence identification of DNA fragments from uncultivated members of the Roseobacter clade, an abundant taxon of heterotrophic marine bacterioplankton in the world's oceans. Differences in gene stoichiometry in the Global Ocean Survey metagenomic data set compared with 39 sequenced isolates indicated that natural Roseobacter populations differ systematically in several genomic attributes from their cultured representatives, including fewer genes for signal transduction and cell surface modifications but more genes for Sec-like protein secretion systems, anaplerotic CO(2) incorporation, and phosphorus and sulfate uptake. Several of these trends match well with characteristics previously identified as distinguishing r- versus K-selected ecological strategies in bacteria, suggesting that the r-strategist model assigned to cultured roseobacters may be less applicable to their free-living oceanic counterparts. The metagenomic Roseobacter DNA fragments revealed several traits with evolutionary histories suggestive of horizontal gene transfer from other marine bacterioplankton taxa or viruses, including pyrophosphatases and glycosylation proteins.}, }
@article {pmid21854262, year = {2011}, author = {Xia, LN and Tao, XQ and Shen, JZ and Dai, L and Wang, Y and Chen, X and Wu, CM}, title = {A survey of β-lactamase and 16S rRNA methylase genes among fluoroquinolone-resistant Escherichia coli isolates and their horizontal transmission in Shandong, China.}, journal = {Foodborne pathogens and disease}, volume = {8}, number = {12}, pages = {1241-1248}, doi = {10.1089/fpd.2011.0868}, pmid = {21854262}, issn = {1556-7125}, mesh = {Animals ; Anti-Infective Agents/pharmacology ; Chickens ; China/epidemiology ; Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; Drug Resistance, Bacterial/genetics ; Escherichia coli/drug effects/enzymology/*genetics/isolation &amp; purification ; Escherichia coli Infections/epidemiology/*microbiology/transmission ; Escherichia coli Proteins/genetics ; Fluoroquinolones/pharmacology ; Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; Nucleic Acid Hybridization ; Plasmids ; Poultry Diseases/epidemiology/*microbiology/transmission ; RNA, Ribosomal, 16S/genetics/metabolism ; Swine ; Swine Diseases/epidemiology/*microbiology/transmission ; beta-Lactamases/*genetics ; tRNA Methyltransferases/*genetics ; }, abstract = {The prevalence of β-lactamase, 16S rRNA methylase genes, and plasmid-mediated fluoroquinolone-resistance (PMQR) determinants (qnrC and qnrD) was determined by polymerase chain reaction in fluoroquinolone-resistant Escherichia coli isolated from a chicken farm, a pig farm, and a hospital in Shandong, China in 2007. The bla(TEM) and bla(CTX-M) were the most prevalent β-lactamase genes in isolates from chickens (88.4%, 175/198 and 81.3%, 161/198) and hospitalized patients (87.8%, 122/139 and 69.1%, 96/139). The bla(TEM) was the most prevalent β-lactamase gene observed in isolates from pigs (98.5%, 135/137). The gene bla(CMY-2) was also predominant among isolates from chickens (20.2%, 40/198). The bla(LAP-1) gene was first detected in one strain from chickens and humans (pig farm workers) in China. Only one strain from hospitalized patients was found to possess bla(SHV). The rmtB was the most prevalent 16S rRNA methylase gene detected in isolates from chickens (19.7%, 39/198) and hospitalized patients (15.8%, 22/139). To our knowledge, this is the first report of the detection of the qnrD gene in E. coli from chickens and pigs in China. The qnrC and bla(KPC) genes were not detected in any of the isolates. Results of southern hybridization revealed that PMQR determinants, β-lactamases, and 16S rRNA methylase genes were located on the same plasmid in E. coli strains derived from patients. Also, PMQR determinants and β-lactamase genes were localized on the same plasmid in an E. coli strain of animal origin. Results of conjugation experiments revealed that all of these plasmid-based resistance genes can be transferred by conjugation through horizontal transmission.}, }
@article {pmid21853145, year = {2011}, author = {Alves, JM and Voegtly, L and Matveyev, AV and Lara, AM and da Silva, FM and Serrano, MG and Buck, GA and Teixeira, MM and Camargo, EP}, title = {Identification and phylogenetic analysis of heme synthesis genes in trypanosomatids and their bacterial endosymbionts.}, journal = {PloS one}, volume = {6}, number = {8}, pages = {e23518}, pmid = {21853145}, issn = {1932-6203}, mesh = {Animals ; Bacteria/*genetics ; Biosynthetic Pathways/genetics ; DNA, Kinetoplast/genetics ; Genes, Bacterial/*genetics ; Genes, Protozoan/*genetics ; Heme/*biosynthesis ; Likelihood Functions ; *Phylogeny ; Symbiosis/*genetics ; Trypanosomatina/*genetics/microbiology ; }, abstract = {It has been known for decades that some insect-infecting trypanosomatids can survive in culture without heme supplementation while others cannot, and that this capability is associated with the presence of a betaproteobacterial endosymbiont in the flagellate's cytoplasm. However, the specific mechanisms involved in this process remained obscure. In this work, we sequence and phylogenetically analyze the heme pathway genes from the symbionts and from their hosts, as well as from a number of heme synthesis-deficient Kinetoplastida. Our results show that the enzymes responsible for synthesis of heme are encoded on the symbiont genomes and produced in close cooperation with the flagellate host. Our evidence suggests that this synergistic relationship is the end result of a history of extensive gene loss and multiple lateral gene transfer events in different branches of the phylogeny of the Trypanosomatidae.}, }
@article {pmid21852287, year = {2011}, author = {Yao, Q and Zeng, Z and Hou, J and Deng, Y and He, L and Tian, W and Zheng, H and Chen, Z and Liu, JH}, title = {Dissemination of the rmtB gene carried on IncF and IncN plasmids among Enterobacteriaceae in a pig farm and its environment.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {66}, number = {11}, pages = {2475-2479}, doi = {10.1093/jac/dkr328}, pmid = {21852287}, issn = {1460-2091}, mesh = {Aminoglycosides/pharmacology ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Drug Resistance, Bacterial/*genetics ; Enterobacteriaceae/drug effects/*genetics/isolation &amp; purification ; Escherichia coli Proteins/*genetics ; Gene Transfer, Horizontal ; Methyltransferases/*genetics ; Microbial Sensitivity Tests ; Plasmids/*genetics ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Sus scrofa ; }, abstract = {OBJECTIVES: To investigate the prevalence and characterization of 16S rRNA methylase-producing bacteria in a pig farm and its environment in East China.<br><br>METHODS: Enterobacteriaceae isolates and metagenomic DNA from 102 pig faecal samples from a pig farm and 97 soil samples taken in or around the farm were screened for the presence of 16S rRNA methylase genes. The clonal relationships of 16S rRNA methylase-positive isolates, plasmid content and other associated resistance genes were also characterized.<br><br>RESULTS: Fifty-six rmtB-positive Enterobacteriaceae isolates, including 54 Escherichia coli, 1 Morganella morganii and 1 Proteus mirabilis, were recovered from 55 pig faecal samples. Nineteen rmtB-positive bacteria, including 13 E. coli, 2 M. morganii, 2 Leclercia adecarboxylata, 1 Enterobacter aerogenes and 1 Enterobacter cloacae, were recovered from 16 soil samples. Among the 75 rmtB-positive isolates, 31 and 25 also carried the qepA and bla(CTX-M) genes, respectively. The qepA gene co-localized with rmtB on the F2:A-:B1 plasmids and the bla(CTX-M-65) gene co-localized with rmtB on the F33:A-:B- plasmids. The rmtB gene was also found to be associated with the IncN plasmids. Clonal transmission of rmtB-positive E. coli isolates was observed between different pig groups and soil samples.<br><br>CONCLUSIONS: Both horizontal gene transfer and clonal spread could be responsible for the dissemination of the rmtB gene in the pig farm and its environment. To our knowledge, this study is the first report of rmtB-positive bacteria from farmland soils and indicates that these antibiotic-resistant bacteria and/or resistance genes could be acquired by humans through the food chain.}, }
@article {pmid21851326, year = {2012}, author = {Carter, CJ}, title = {Vaccinia and other viruses with available vaccines show marked homology with the HIV-1 envelope glycoprotein: the prospect of using existing vaccines to stem the AIDS pandemic.}, journal = {Immunopharmacology and immunotoxicology}, volume = {34}, number = {2}, pages = {222-231}, pmid = {21851326}, issn = {1532-2513}, mesh = {Amino Acid Sequence ; Arthritis-Encephalitis Virus, Caprine/genetics/immunology ; Cross Reactions/genetics/immunology ; Dengue Virus/genetics/immunology ; Epitopes, B-Lymphocyte/genetics/immunology ; GB virus C/genetics/immunology ; Gene Products, env/genetics/immunology ; Gene Products, gag/genetics/immunology ; Genome, Viral/genetics/*immunology ; HIV Infections/*prevention &amp; control ; HIV-1/genetics/immunology ; Human T-lymphotropic virus 2/genetics/immunology ; Human T-lymphotropic virus 3/genetics/immunology ; Humans ; Immunodeficiency Virus, Feline/genetics/immunology ; Infectious Anemia Virus, Equine/genetics/immunology ; Lentivirus/genetics/immunology ; Measles virus/genetics/immunology ; Molecular Sequence Data ; *Sequence Homology, Amino Acid ; Vaccinia virus/*genetics/immunology ; Viral Vaccines/*genetics/immunology/therapeutic use ; Viruses/*genetics/immunology ; Visna-maedi virus/genetics/immunology ; env Gene Products, Human Immunodeficiency Virus/*genetics/immunology ; gag Gene Products, Human Immunodeficiency Virus/genetics/immunology ; nef Gene Products, Human Immunodeficiency Virus/genetics/immunology ; tat Gene Products, Human Immunodeficiency Virus/genetics/immunology ; }, abstract = {Cross-reactive immunity occurs when infection with or vaccination against one virus protects against another related family member. A search for homologues of the HIV-1 envelope glycoprotein revealed that it is composed of thousands of intercalating and overlapping viral matches of pentapeptide or longer gapped consensi, belonging to over 70% of the currently sequenced virome, infecting all kingdoms from bacteria to man. It was also highly homologous to proteins from the Visna/Maedi and other ovine viruses, while other proteins (nef/tat/gag/pol) were homologous to proteins from the equine infectious anaemia virus and HTLV-2/HTLV-3 viruses. This phenomenon suggests that horizontal gene transfer from coinfecting RNA and DNA viruses to retroviruses is extensive, providing a route for the subsequent insertion of non-retroviral genes into human and other genomes via retroviral integration. This homology includes all viruses for which vaccines already exist. Cross-reactive immunity may be operative in AIDS, as Vaccinia vaccination decreases viral replication in HIV-1 infected patients' cells, for the CCR5 tropic form. Measles, Dengue virus, or GB virus C infections also decrease the HIV-1 viral load. A resumption of Vaccinia/smallpox vaccination might be expected to have a significant effect on the AIDS pandemic, and a careful study of the potential uses of other existing viral and bacterial vaccines merits close attention. This phenomenon may also be relevant to other recalcitrant viruses, bacteria, and parasites for which no vaccine exists and the armory of existing vaccines may have a role to play in diseases other than those for which they were designed.}, }
@article {pmid21850220, year = {2011}, author = {Creevey, CJ and Doerks, T and Fitzpatrick, DA and Raes, J and Bork, P}, title = {Universally distributed single-copy genes indicate a constant rate of horizontal transfer.}, journal = {PloS one}, volume = {6}, number = {8}, pages = {e22099}, pmid = {21850220}, issn = {1932-6203}, mesh = {Acidobacteria/genetics ; Archaea/genetics ; Bacillus/genetics ; Bacteria/genetics ; Bacteroides/genetics ; Base Composition/genetics ; Ecosystem ; Euryarchaeota/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Proteobacteria/genetics ; Tenericutes/genetics ; }, abstract = {Single copy genes, universally distributed across the three domains of life and encoding mostly ancient parts of the translation machinery, are thought to be only rarely subjected to horizontal gene transfer (HGT). Indeed it has been proposed to have occurred in only a few genes and implies a rare, probably not advantageous event in which an ortholog displaces the original gene and has to function in a foreign context (orthologous gene displacement, OGD). Here, we have utilised an automatic method to identify HGT based on a conservative statistical approach capable of robustly assigning both donors and acceptors. Applied to 40 universally single copy genes we found that as many as 68 HGTs (implying OGDs) have occurred in these genes with a rate of 1.7 per family since the last universal common ancestor (LUCA). We examined a number of factors that have been claimed to be fundamental to HGT in general and tested their validity in the subset of universally distributed single copy genes. We found that differing functional constraints impact rates of OGD and the more evolutionarily distant the donor and acceptor, the less likely an OGD is to occur. Furthermore, species with larger genomes are more likely to be subjected to OGD. Most importantly, regardless of the trends above, the number of OGDs increases linearly with time, indicating a neutral, constant rate. This suggests that levels of HGT above this rate may be indicative of positively selected transfers that may allow niche adaptation or bestow other benefits to the recipient organism.}, }
@article {pmid21845185, year = {2011}, author = {Aminov, RI}, title = {Horizontal gene exchange in environmental microbiota.}, journal = {Frontiers in microbiology}, volume = {2}, number = {}, pages = {158}, pmid = {21845185}, issn = {1664-302X}, abstract = {Horizontal gene transfer (HGT) plays an important role in the evolution of life on the Earth. This view is supported by numerous occasions of HGT that are recorded in the genomes of all three domains of living organisms. HGT-mediated rapid evolution is especially noticeable among the Bacteria, which demonstrate formidable adaptability in the face of recent environmental changes imposed by human activities, such as the use of antibiotics, industrial contamination, and intensive agriculture. At the heart of the HGT-driven bacterial evolution and adaptation are highly sophisticated natural genetic engineering tools in the form of a variety of mobile genetic elements (MGEs). The main aim of this review is to give a brief account of the occurrence and diversity of MGEs in natural ecosystems and of the environmental factors that may affect MGE-mediated HGT.}, }
@article {pmid21844337, year = {2011}, author = {Schröder, G and Schuelein, R and Quebatte, M and Dehio, C}, title = {Conjugative DNA transfer into human cells by the VirB/VirD4 type IV secretion system of the bacterial pathogen Bartonella henselae.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {35}, pages = {14643-14648}, pmid = {21844337}, issn = {1091-6490}, mesh = {Bacterial Proteins/*physiology ; Bartonella henselae/*genetics ; Base Sequence ; Cell Division ; *Conjugation, Genetic ; *Gene Transfer, Horizontal ; Green Fluorescent Proteins/genetics ; Humans ; Molecular Sequence Data ; Plasmids ; }, abstract = {Bacterial type IV secretion systems (T4SS) mediate interbacterial conjugative DNA transfer and transkingdom protein transfer into eukaryotic host cells in bacterial pathogenesis. The sole bacterium known to naturally transfer DNA into eukaryotic host cells via a T4SS is the plant pathogen Agrobacterium tumefaciens. Here we demonstrate T4SS-mediated DNA transfer from a human bacterial pathogen into human cells. We show that the zoonotic pathogen Bartonella henselae can transfer a cryptic plasmid occurring in the bartonellae into the human endothelial cell line EA.hy926 via its T4SS VirB/VirD4. DNA transfer into EA.hy926 cells was demonstrated by using a reporter derivative of this Bartonella-specific mobilizable plasmid generated by insertion of a eukaryotic egfp-expression cassette. Fusion of the C-terminal secretion signal of the endogenous VirB/VirD4 protein substrate BepD with the plasmid-encoded DNA-transport protein Mob resulted in a 100-fold increased DNA transfer rate. Expression of the delivered egfp gene in EA.hy926 cells required cell division, suggesting that nuclear envelope breakdown may facilitate passive entry of the transferred ssDNA into the nucleus as prerequisite for complementary strand synthesis and transcription of the egfp gene. Addition of an eukaryotic neomycin phosphotransferase expression cassette to the reporter plasmid facilitated selection of stable transgenic EA.hy926 cell lines that display chromosomal integration of the transferred plasmid DNA. Our data suggest that T4SS-dependent DNA transfer into host cells may occur naturally during human infection with Bartonella and that these chronically infecting pathogens have potential for the engineering of in vivo gene-delivery vectors with applications in DNA vaccination and therapeutic gene therapy.}, }
@article {pmid21843549, year = {2011}, author = {Johnson, TJ and Shepard, SM and Rivet, B and Danzeisen, JL and Carattoli, A}, title = {Comparative genomics and phylogeny of the IncI1 plasmids: a common plasmid type among porcine enterotoxigenic Escherichia coli.}, journal = {Plasmid}, volume = {66}, number = {3}, pages = {144-151}, doi = {10.1016/j.plasmid.2011.07.003}, pmid = {21843549}, issn = {1095-9890}, mesh = {Animals ; Drug Resistance, Bacterial/genetics ; Enterotoxigenic Escherichia coli/*genetics ; Gene Order ; *Genomics ; *Phylogeny ; Plasmids/classification/*genetics ; Swine ; }, abstract = {Increasing reports of multidrug resistance conferred by conjugative plasmids of Enterobacteriaceae necessitate a better understanding of their evolution. One such group is the narrow-host-range IncI1 plasmid type, known for their ability to carry genes encoding resistance to extended-spectrum beta lactamases. The focus of this study was to perform comparative sequencing of IncI1 plasmids from porcine enterotoxigenic Escherichia coli (ETEC), isolated irrespective of antimicrobial susceptibility phenotype. Five IncI1 plasmids of porcine ETEC origin and one IncI1 plasmid from a Salmonella enterica serovar Kentucky isolate from a healthy broiler chicken were sequenced and compared to existing IncI1 plasmid sequences in an effort to better understand the overall genetic composition of the IncI1 plasmid lineages. Overall, the sequenced porcine ETEC IncI1 plasmids were divergent from other sequenced IncI1 plasmids based upon multiple means of inferred phylogeny. High occurrences of IncI1 and IncA/C plasmid-associated genes and the blaTEM and blaCMY-2 beta lactamase genes were observed among porcine ETEC. However, the presence of blaTEM and blaCMY-2 did not strongly correlate with IncI1 plasmid possession, suggesting that these plasmids in porcine ETEC are not primarily associated with the carriage of such resistance genes. Overall, this work suggests a conservation of the IncI1 plasmid backbone among sequenced plasmids with a single locus for the acquisition of accessory genes, such as those associated with antimicrobial resistance. Furthermore, the high occurrence of IncI1 and IncA/C plasmids among clinical E. coli from commercial swine facilities is indicative of extensive horizontal gene transfer among porcine ETEC.}, }
@article {pmid21843315, year = {2011}, author = {Rödelsperger, C and Sommer, RJ}, title = {Computational archaeology of the Pristionchus pacificus genome reveals evidence of horizontal gene transfers from insects.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {239}, pmid = {21843315}, issn = {1471-2148}, mesh = {Animals ; Base Composition/genetics ; Cellulase/genetics ; Codon/genetics ; Coleoptera/*genetics ; Gene Transfer, Horizontal/*genetics ; Genome/*genetics ; Nematoda/*genetics ; Neuropeptides/genetics ; *Phylogeny ; Species Specificity ; }, abstract = {BACKGROUND: The recent sequencing of nematode genomes has laid the basis for comparative genomics approaches to study the impact of horizontal gene transfer (HGT) on the adaptation to new environments and the evolution of parasitism. In the beetle associated nematode Pristionchus pacificus HGT events were found to involve cellulase genes of microbial origin and Diapausin genes that are known from beetles, but not from other nematodes. The insect-to-nematode horizontal transfer is of special interest given that P. pacificus shows a tight association with insects.<br><br>RESULTS: In this study we utilized the observation that horizontally transferred genes often exhibit codon usage patterns more similar to that of the donor than that of the acceptor genome. We introduced GC-normalized relative codon frequencies as a measure to detect characteristic features of P. pacificus orphan genes that show no homology to other nematode genes. We found that atypical codon usage is particularly prevalent in P. pacificus orphans. By comparing codon usage profiles of 71 species, we detected the most significant enrichment in insect-like codon usage profiles. In cross-species comparisons, we identified 509 HGT candidates that show a significantly higher similarity to insect-like profiles than genes with nematode homologs. The most abundant gene family among these genes are non-LTR retrotransposons. Speculating that retrotransposons might have served as carriers of foreign genetic material, we found a significant local clustering tendency of orphan genes in the vicinity of retrotransposons.<br><br>CONCLUSIONS: Our study combined codon usage bias, phylogenetic analysis, and genomic colocalization into a general picture of the computational archaeology of the P. pacificus genome and suggests that a substantial fraction of the gene repertoire is of insect origin. We propose that the Pristionchus-beetle association has facilitated HGT and discuss potential vectors of these events.}, }
@article {pmid21843206, year = {2011}, author = {Cook, L and Chatterjee, A and Barnes, A and Yarwood, J and Hu, WS and Dunny, G}, title = {Biofilm growth alters regulation of conjugation by a bacterial pheromone.}, journal = {Molecular microbiology}, volume = {81}, number = {6}, pages = {1499-1510}, pmid = {21843206}, issn = {1365-2958}, support = {R01 AI058134-06A1/AI/NIAID NIH HHS/United States ; T32 GM008347/GM/NIGMS NIH HHS/United States ; R56 AI058134/AI/NIAID NIH HHS/United States ; R01 GM081388/GM/NIGMS NIH HHS/United States ; AI058134/AI/NIAID NIH HHS/United States ; R01 GM049530/GM/NIGMS NIH HHS/United States ; GM081888/GM/NIGMS NIH HHS/United States ; R01 GM081388-04/GM/NIGMS NIH HHS/United States ; 2T32GM0082445/GM/NIGMS NIH HHS/United States ; R01 AI058134/AI/NIAID NIH HHS/United States ; GM049530/GM/NIGMS NIH HHS/United States ; R01 GM049530-26A1/GM/NIGMS NIH HHS/United States ; T32GM008347/GM/NIGMS NIH HHS/United States ; }, mesh = {Biofilms/*growth &amp; development ; Conjugation, Genetic/*drug effects ; Enterococcus faecalis/growth &amp; development/metabolism/*physiology ; Gene Dosage ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Models, Theoretical ; Pheromones/*metabolism ; Plasmids ; }, abstract = {Conjugation is an important mode of horizontal gene transfer in bacteria, enhancing the spread of antibiotic resistance. In clinical settings, biofilms are likely locations for antibiotic resistance transfer events involving nosocomial pathogens such as Enterococcus faecalis. Here we demonstrate that growth in biofilms alters the induction of conjugation by a sex pheromone in E. faecalis. Mathematical modelling suggested that a higher plasmid copy number in biofilm cells would enhance a switch-like behaviour in the pheromone response of donor cells with a delayed, but increased response to the mating signal. Alterations in plasmid copy number, and a bimodal response to induction of conjugation in populations of plasmid-containing donor cells were both observed in biofilms, consistent with the predictions of the model. The pheromone system may have evolved such that donor cells in biofilms are only induced to transfer when they are in extremely close proximity to potential recipients in the biofilm community. These results may have important implications for development of chemotherapeutic agents to block resistance transfer and treat biofilm-related clinical infections.}, }
@article {pmid21838889, year = {2011}, author = {Jackson, DJ and Macis, L and Reitner, J and Wörheide, G}, title = {A horizontal gene transfer supported the evolution of an early metazoan biomineralization strategy.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {238}, pmid = {21838889}, issn = {1471-2148}, mesh = {Amino Acid Sequence ; Animals ; Bacteria/*genetics/metabolism ; Base Sequence ; *Biological Evolution ; Calcification, Physiologic ; *Gene Transfer, Horizontal ; Minerals/metabolism ; Molecular Sequence Data ; Phylogeny ; Porifera/genetics/*physiology ; Proteins/genetics/metabolism ; }, abstract = {BACKGROUND: The synchronous and widespread adoption of the ability to biomineralize was a defining event for metazoan evolution during the late Precambrian/early Cambrian 545 million years ago. However our understanding on the molecular level of how animals first evolved this capacity is poor. Because sponges are the earliest branching phylum of biomineralizing metazoans, we have been studying how biocalcification occurs in the coralline demosponge Astrosclera willeyana.<br><br>RESULTS: We have isolated and characterized a novel protein directly from the calcified spherulites of A. willeyana. Using three independent lines of evidence (genomic architecture of the gene in A. willeyana, spatial expression of the gene product in A. willeyana and genomic architecture of the gene in the related demosponge Amphimedon queenslandica), we show that the gene that encodes this protein was horizontally acquired from a bacterium, and is now highly and exclusively expressed in spherulite forming cells.<br><br>CONCLUSIONS: Our findings highlight the ancient and close association that exists between sponges and bacteria, and provide support for the notion that horizontal gene transfer may have been an important mechanism that supported the evolution of this early metazoan biomineralisation strategy.}, }
@article {pmid21835815, year = {2011}, author = {Jeridi, M and Bakry, F and Escoute, J and Fondi, E and Carreel, F and Ferchichi, A and D'Hont, A and Rodier-Goud, M}, title = {Homoeologous chromosome pairing between the A and B genomes of Musa spp. revealed by genomic in situ hybridization.}, journal = {Annals of botany}, volume = {108}, number = {5}, pages = {975-981}, pmid = {21835815}, issn = {1095-8290}, mesh = {*Chromosome Pairing ; *Chromosomes, Plant ; DNA, Plant/genetics ; Gene Transfer, Horizontal ; Hybridization, Genetic ; In Situ Hybridization ; Musa/cytology/*genetics ; Polyploidy ; }, abstract = {BACKGROUND AND AIMS: Most cooking banana and several desert bananas are interspecific triploid hybrids between Musa acuminata (A genome) and Musa balbisiana (B genome). In addition, M. balbisiana has agronomical characteristics such as resistance to biotic and abiotic stresses that could be useful to improve monospecific acuminata cultivars. To develop efficient breeding strategies for improving Musa cultivars, it is therefore important to understand the possibility of chromosome exchange between these two species.<br><br>METHODS: A protocol was developed to prepare chromosome at meiosis metaphase I suitable for genomic in situ hybridization. A series of technical challenges were encountered, the main ones being the hardness of the cell wall and the density of the microsporocyte's cytoplasm, which hampers accessibility of the probes to the chromosomes. Key parameters in solving these problems were addition of macerozyme in the enzyme mix, the duration of digestion and temperature during the spreading phase.<br><br>RESULTS AND CONCLUSIONS: This method was applied to analyse chromosome pairing in metaphase from triploid interspecific cultivars, and it was clearly demonstrated that interspecific recombinations between M. acuminata and M. balbisiana chromosomes do occur and may be frequent in triploid hybrids. These results provide new insight into Musa cultivar evolution and have important implications for breeding.}, }
@article {pmid21835695, year = {2011}, author = {Martínez, JL and Baquero, F and Andersson, DI}, title = {Beyond serial passages: new methods for predicting the emergence of resistance to novel antibiotics.}, journal = {Current opinion in pharmacology}, volume = {11}, number = {5}, pages = {439-445}, doi = {10.1016/j.coph.2011.07.005}, pmid = {21835695}, issn = {1471-4973}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics ; Clone Cells ; *Drug Resistance, Bacterial/genetics ; Forecasting ; Gene Transfer, Horizontal ; Genetic Fitness ; Humans ; Interspersed Repetitive Sequences ; Microbial Sensitivity Tests ; Serial Passage ; }, abstract = {Market launching of a new antibiotic requires knowing in advance its benefits and possible risks, and among them how rapidly resistance will emerge and spread among bacterial pathogens. This information is not only useful from a public health point of view, but also for pharmaceutical industry, in order to reduce potential waste of resources in the development of a compound that might be discontinued at the short term because of resistance development. Most assays currently used for predicting the emergence of resistance are based on culturing the target bacteria by serial passages in the presence of increasing concentrations of antibiotics. Whereas these assays may be valuable for identifying mutations that might cause resistance, they are not useful to establish how fast resistance might appear, neither to address the risk of spread of resistance genes by horizontal gene transfer. In this article, we review recent information pertinent for a more accurate prediction on the emergence and dispersal of antibiotic resistance.}, }
@article {pmid21833341, year = {2011}, author = {Gregersen, LH and Bryant, DA and Frigaard, NU}, title = {Mechanisms and evolution of oxidative sulfur metabolism in green sulfur bacteria.}, journal = {Frontiers in microbiology}, volume = {2}, number = {}, pages = {116}, pmid = {21833341}, issn = {1664-302X}, abstract = {Green sulfur bacteria (GSB) constitute a closely related group of photoautotrophic and thiotrophic bacteria with limited phenotypic variation. They typically oxidize sulfide and thiosulfate to sulfate with sulfur globules as an intermediate. Based on genome sequence information from 15 strains, the distribution and phylogeny of enzymes involved in their oxidative sulfur metabolism was investigated. At least one homolog of sulfide:quinone oxidoreductase (SQR) is present in all strains. In all sulfur-oxidizing GSB strains except the earliest diverging Chloroherpeton thalassium, the sulfide oxidation product is further oxidized to sulfite by the dissimilatory sulfite reductase (DSR) system. This system consists of components horizontally acquired partly from sulfide-oxidizing and partly from sulfate-reducing bacteria. Depending on the strain, the sulfite is probably oxidized to sulfate by one of two different mechanisms that have different evolutionary origins: adenosine-5'-phosphosulfate reductase or polysulfide reductase-like complex 3. Thiosulfate utilization by the SOX system in GSB has apparently been acquired horizontally from Proteobacteria. SoxCD does not occur in GSB, and its function in sulfate formation in other bacteria has been replaced by the DSR system in GSB. Sequence analyses suggested that the conserved soxJXYZAKBW gene cluster was horizontally acquired by Chlorobium phaeovibrioides DSM 265 from the Chlorobaculum lineage and that this acquisition was mediated by a mobile genetic element. Thus, the last common ancestor of currently known GSB was probably photoautotrophic, hydrogenotrophic, and contained SQR but not DSR or SOX. In addition, the predominance of the Chlorobium-Chlorobaculum-Prosthecochloris lineage among cultured GSB could be due to the horizontally acquired DSR and SOX systems. Finally, based upon structural, biochemical, and phylogenetic analyses, a uniform nomenclature is suggested for sqr genes in prokaryotes.}, }
@article {pmid21833302, year = {2011}, author = {Roberts, MC}, title = {Environmental macrolide-lincosamide-streptogramin and tetracycline resistant bacteria.}, journal = {Frontiers in microbiology}, volume = {2}, number = {}, pages = {40}, pmid = {21833302}, issn = {1664-302X}, abstract = {Bacteria can become resistant to antibiotics by mutation, transformation, and/or acquisition of new genes which are normally associated with mobile elements (plasmids, transposons, and integrons). Mobile elements are the main driving force in horizontal gene transfer between strains, species, and genera and are responsible for the rapid spread of particular elements throughout a bacterial community and between ecosystems. Today, antibiotic resistant bacteria are widely distributed throughout the world and have even been isolated from environments that are relatively untouched by human civilization. In this review macrolides, lincosamides, streptogramins, and tetracycline resistance genes and bacteria will be discussed with an emphasis on the resistance genes which are unique to environmental bacteria which are defined for this review as species and genera that are primarily found outside of humans and animals.}, }
@article {pmid21831988, year = {2011}, author = {Bielak, E and Bergenholtz, RD and Jørgensen, MS and Sørensen, SJ and Hansen, LH and Hasman, H}, title = {Investigation of diversity of plasmids carrying the blaTEM-52 gene.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {66}, number = {11}, pages = {2465-2474}, doi = {10.1093/jac/dkr331}, pmid = {21831988}, issn = {1460-2091}, mesh = {Animals ; DNA Transposable Elements/genetics ; DNA, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; *Escherichia coli/drug effects/genetics/isolation &amp; purification ; Europe ; Gene Transfer, Horizontal ; Genetic Variation ; Humans ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; *Plasmids/isolation &amp; purification ; Polymorphism, Restriction Fragment Length ; *Salmonella enterica/drug effects/genetics/isolation &amp; purification ; Transposases/genetics ; beta-Lactam Resistance/genetics ; beta-Lactamases/*genetics ; beta-Lactams/pharmacology ; }, abstract = {OBJECTIVES: To investigate the diversity of plasmids that carry bla(TEM-52) genes among Escherichia coli and Salmonella enterica originating from animals, meat products and humans.<br><br>METHODS: A collection of 22 bla(TEM-52)-encoding plasmids was characterized by restriction fragment length polymorphism (RFLP), replicon typing (by PCR or replicon sequencing), susceptibility testing, assessment of plasmid ability to self-transfer by conjugation and typing of the genetic environment of the bla(TEM-52) gene. Detected IncI1 plasmids underwent further plasmid multilocus sequence typing.<br><br>RESULTS: RFLP profiles demonstrated dissemination of bla(TEM-52) in Denmark (imported meat from Germany), France, Belgium and the Netherlands from 2000 to 2006 by mainly two different plasmids, one encoding bla(TEM-52b) (IncX1A, 45 kb) and the other bla(TEM-52c) (IncI1, 80 kb). In addition, bla(TEM-52b) was also found to be located on various other plasmids belonging to IncA/C and IncL/M, while bla(TEM-52c) was found on IncN-like as well as on IncR plasmids. In the majority of cases (n&#x200a;=&#x200a;21) the bla(TEM-52) gene was located on a Tn3 transposon. Seven out of 10 bla(TEM-52) plasmids tested in conjugation experiments were shown to be capable of self-transfer to a plasmid-free E. coli recipient.<br><br>CONCLUSIONS: The bla(TEM-52) gene found in humans could have been transmitted on transferable plasmids originating from animal sources. Some of the bla(TEM-52) plasmids carry replicons that differ from the classical ones. Two novel replicons were detected, IncX1A and IncN-like. Unlike its predecessor bla(TEM-1), the bla(TEM-52) gene was not detected on F-type replicons suggesting that this gene evolved on other types of plasmid scaffolds.}, }
@article {pmid21829651, year = {2011}, author = {Margus, T and Remm, M and Tenson, T}, title = {A computational study of elongation factor G (EFG) duplicated genes: diverged nature underlying the innovation on the same structural template.}, journal = {PloS one}, volume = {6}, number = {8}, pages = {e22789}, pmid = {21829651}, issn = {1932-6203}, mesh = {*Gene Duplication ; Genome ; Peptide Elongation Factor G/*genetics ; Phylogeny ; }, abstract = {BACKGROUND: Elongation factor G (EFG) is a core translational protein that catalyzes the elongation and recycling phases of translation. A more complex picture of EFG's evolution and function than previously accepted is emerging from analyzes of heterogeneous EFG family members. Whereas the gene duplication is postulated to be a prominent factor creating functional novelty, the striking divergence between EFG paralogs can be interpreted in terms of innovation in gene function.<br><br>We present a computational study of the EFG protein family to cover the role of gene duplication in the evolution of protein function. Using phylogenetic methods, genome context conservation and insertion/deletion (indel) analysis we demonstrate that the EFG gene copies form four subfamilies: EFG I, spdEFG1, spdEFG2, and EFG II. These ancient gene families differ by their indispensability, degree of divergence and number of indels. We show the distribution of EFG subfamilies and describe evidences for lateral gene transfer and recent duplications. Extended studies of the EFG II subfamily concern its diverged nature. Remarkably, EFG II appears to be a widely distributed and a much-diversified subfamily whose subdivisions correlate with phylum or class borders. The EFG II subfamily specific characteristics are low conservation of the GTPase domain, domains II and III; absence of the trGTPase specific G2 consensus motif "RGITI"; and twelve conserved positions common to the whole subfamily. The EFG II specific functional changes could be related to changes in the properties of nucleotide binding and hydrolysis and strengthened ionic interactions between EFG II and the ribosome, particularly between parts of the decoding site and loop I of domain IV.<br><br>CONCLUSIONS/SIGNIFICANCE: Our work, for the first time, comprehensively identifies and describes EFG subfamilies and improves our understanding of the function and evolution of EFG duplicated genes.}, }
@article {pmid21826786, year = {2012}, author = {Hall, BK and Kerney, R}, title = {Levels of biological organization and the origin of novelty.}, journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution}, volume = {318}, number = {6}, pages = {428-437}, doi = {10.1002/jez.b.21425}, pmid = {21826786}, issn = {1552-5015}, mesh = {Adaptation, Physiological/*genetics ; Animals ; *Biological Evolution ; Classification ; Genotype ; Phenotype ; }, abstract = {The concept of novelty in evolutionary biology pertains to multiple tiers of biological organization from behavioral and morphological changes to changes at the molecular level. Identifying novel features requires assessments of similarity (homology and homoplasy) of relationships (phylogenetic history) and of shared developmental and genetic pathways or networks. After a brief discussion of how novelty is used in recent literature, we discuss whether the evolutionary approach to homology and homoplasy initially formulated by Lankester in the 19th century informs our understanding of novelty today. We then discuss six examples of morphological features described in the recent literature as novelties, and assess the basis upon which they are regarded as novel. The six are: origin of the turtle shell, transition from fish fins to tetrapod limbs, origination of the neural crest and neural crest cells, cement glands in frogs and casquettes in fish, whale bone-eating tubeworms, and the digestion of plant proteins by nematodes. The article concludes with a discussion of means of acquiring novel genetic information that can account for novelty recognized at higher levels. These are co-options of existing genetic circuitry, gene duplication followed by neofunctionalization, gene rearrangements through mobile genetic elements, and lateral gene transfer. We conclude that on the molecular level only the latter category provides novel genetic information, in that there is no homologous precursor. However, novel phenotypes can be generated through both neofunctionalization and gene rearrangements. Therefore, assigning phenotypic or genotypic "novelty" is contingent on the level of biological organization addressed.}, }
@article {pmid21825119, year = {2011}, author = {Snitkin, ES and Zelazny, AM and Montero, CI and Stock, F and Mijares, L and ,  and Murray, PR and Segre, JA}, title = {Genome-wide recombination drives diversification of epidemic strains of Acinetobacter baumannii.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {33}, pages = {13758-13763}, pmid = {21825119}, issn = {1091-6490}, support = {//Intramural NIH HHS/United States ; }, mesh = {Acinetobacter Infections/epidemiology ; Acinetobacter baumannii/classification/*genetics ; Cross Infection/genetics ; Epidemics ; Genetic Speciation ; Genome, Bacterial/*genetics ; Hospitals ; Humans ; Molecular Sequence Data ; *Recombination, Genetic ; }, abstract = {Acinetobacter baumannii is an emerging human pathogen and a significant cause of nosocomial infections among hospital patients worldwide. The enormous increase in multidrug resistance among hospital isolates and the recent emergence of pan-drug-resistant strains underscores the urgency to understand how A. baumannii evolves in hospital environments. To this end, we undertook a genomic study of a polyclonal outbreak of multidrug-resistant A. baumannii at the research-based National Institutes of Health Clinical Center. Comparing the complete genome sequences of the three dominant outbreak strain types enabled us to conclude that, despite all belonging to the same epidemic lineage, the three strains diverged before their arrival at the National Institutes of Health. The simultaneous presence of three divergent strains from this lineage supports its increasing prevalence in international hospitals and suggests an ongoing adaptation to the hospital environment. Further genomic comparisons uncovered that much of the diversification that occurred since the divergence of the three outbreak strains was mediated by homologous recombination across 20% of their genomes. Inspection of recombinant regions revealed that several regions were associated with either the loss or swapping out of genes encoding proteins that are exposed to the cell surface or that synthesize cell-surface molecules. Extending our analysis to a larger set of international clinical isolates revealed a previously unappreciated ability of A. baumannii to vary surface molecules through horizontal gene transfer, with subsequent intraspecies dissemination by homologous recombination. These findings have immediate implications in surveillance, prevention, and treatment of A. baumannii infections.}, }
@article {pmid21824433, year = {2011}, author = {Bosi, E and Fani, R and Fondi, M}, title = {The mosaicism of plasmids revealed by atypical genes detection and analysis.}, journal = {BMC genomics}, volume = {12}, number = {}, pages = {403}, pmid = {21824433}, issn = {1471-2164}, mesh = {Archaea/genetics ; Bacteria/genetics ; Base Composition ; Genes, Archaeal/genetics ; Genes, Bacterial/genetics ; *Genomics ; Multigene Family/genetics ; Plasmids/chemistry/*genetics ; }, abstract = {BACKGROUND: From an evolutionary viewpoint, prokaryotic genomes are extremely plastic and dynamic, since large amounts of genetic material are continuously added and/or lost through promiscuous gene exchange. In this picture, plasmids play a key role, since they can be transferred between different cells and, through genetic rearrangement(s), undergo gene(s) load, leading, in turn, to the appearance of important metabolic innovations that might be relevant for cell life. Despite their central position in bacterial evolution, a massive analysis of newly acquired functional blocks [likely the result of horizontal gene transfer (HGT) events] residing on plasmids is still missing.<br><br>RESULTS: We have developed a computational, composition-based, pipeline to scan almost 2000 plasmids for genes that differ significantly from their hosting molecule. Plasmids atypical genes (PAGs) were about 6% of the total plasmids ORFs and, on average, each plasmid possessed 4.4 atypical genes. Nevertheless, conjugative plasmids were shown to possess an amount of atypical genes than that found in not mobilizable plasmids, providing strong support for the central role suggested for conjugative plasmids in the context of HGT. Part of the retrieved PAGs are organized into (mainly short) clusters and are involved in important biological processes (detoxification, antibiotic resistance, virulence), revealing the importance of HGT in the spreading of metabolic pathways within the whole microbial community. Lastly, our analysis revealed that PAGs mainly derive from other plasmid (rather than coming from phages and/or chromosomes), suggesting that plasmid-plasmid DNA exchange might be the primary source of metabolic innovations in this class of mobile genetic elements.<br><br>CONCLUSIONS: In this work we have performed the first large scale analysis of atypical genes that reside on plasmid molecules to date. Our findings on PAGs function, organization, distribution and spreading reveal the importance of plasmids-mediated HGT within the complex bacterial evolutionary network and in the dissemination of important biological traits.}, }
@article {pmid21824414, year = {2011}, author = {Hinse, D and Vollmer, T and Rückert, C and Blom, J and Kalinowski, J and Knabbe, C and Dreier, J}, title = {Complete genome and comparative analysis of Streptococcus gallolyticus subsp. gallolyticus, an emerging pathogen of infective endocarditis.}, journal = {BMC genomics}, volume = {12}, number = {}, pages = {400}, pmid = {21824414}, issn = {1471-2164}, mesh = {Bacterial Proteins/genetics ; Chromosomes, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; Endocarditis, Bacterial/*microbiology ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/genetics ; *Genomics ; Humans ; Plasmids/genetics ; Streptococcus/drug effects/*genetics/pathogenicity ; Tetracycline/pharmacology ; Virulence Factors/genetics ; }, abstract = {BACKGROUND: Streptococcus gallolyticus subsp. gallolyticus is an important causative agent of infectious endocarditis, while the pathogenicity of this species is widely unclear. To gain insight into the pathomechanisms and the underlying genetic elements for lateral gene transfer, we sequenced the entire genome of this pathogen.<br><br>RESULTS: We sequenced the whole genome of S. gallolyticus subsp. gallolyticus strain ATCC BAA-2069, consisting of a 2,356,444 bp circular DNA molecule with a G+C-content of 37.65% and a novel 20,765 bp plasmid designated as pSGG1. Bioinformatic analysis predicted 2,309 ORFs and the presence of 80 tRNAs and 21 rRNAs in the chromosome. Furthermore, 21 ORFs were detected on the plasmid pSGG1, including tetracycline resistance genes telL and tet(O/W/32/O). Screening of 41 S. gallolyticus subsp. gallolyticus isolates revealed one plasmid (pSGG2) homologous to pSGG1. We further predicted 21 surface proteins containing the cell wall-sorting motif LPxTG, which were shown to play a functional role in the adhesion of bacteria to host cells. In addition, we performed a whole genome comparison to the recently sequenced S. gallolyticus subsp. gallolyticus strain UCN34, revealing significant differences.<br><br>CONCLUSIONS: The analysis of the whole genome sequence of S. gallolyticus subsp. gallolyticus promotes understanding of genetic factors concerning the pathogenesis and adhesion to ECM of this pathogen. For the first time we detected the presence of the mobilizable pSGG1 plasmid, which may play a functional role in lateral gene transfer and promote a selective advantage due to a tetracycline resistance.}, }
@article {pmid21823094, year = {2011}, author = {Ghanem, S}, title = {Cloning of the nptII gene of Escherichia coli and construction of a recombinant strain harboring functional recA and nptII antibiotic resistance.}, journal = {Genetics and molecular research : GMR}, volume = {10}, number = {3}, pages = {1445-1454}, doi = {10.4238/vol10-3gmr1334}, pmid = {21823094}, issn = {1676-5680}, mesh = {Aminoglycosides/pharmacology ; Drug Resistance, Microbial/genetics/*physiology ; Escherichia coli/drug effects/*genetics ; Escherichia coli Proteins/genetics ; Kanamycin Kinase/*genetics ; Plasmids ; Polymerase Chain Reaction ; Rec A Recombinases/genetics ; }, abstract = {In an attempt to clone the ORF of the nptII gene of Escherichia coli K12 (ATCC 10798), two degenerate primers were designed based on the nptII sequence of its Tn5 transposon. The nptII ORF was placed under the control of the E. coli hybrid trc promoter, in the pKK388-1 vector, transformed into E. coli DH5α ΔrecA (recombinant, deficient strain). Transferred cells were tested for ampicillin, tetracycline, kanamycin, neomycin, geneticin, paromomycin, penicillin, and UV resistance. The neomycin phosphotransferase gene of E. coli was cloned successfully and conferred kanamycin, neomycin, geneticin, and paromomycin resistance to recombinant DH5α; this did not inhibit insertion of additional antibiotic resistance against ampicillin and tetracycline, meaning the trc promoter can express two different genes carried by two different plasmids harbored in the same cell. This resistance conferral process could be considered as an emulation of horizontal gene transfer occurring in nature and would be a useful tool for understanding mechanisms of evolution of multidrug-resistant strains.}, }
@article {pmid21821767, year = {2011}, author = {Lee, CN and Tseng, TT and Lin, JW and Fu, YC and Weng, SF and Tseng, YH}, title = {Lytic myophage Abp53 encodes several proteins similar to those encoded by host Acinetobacter baumannii and phage phiKO2.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {19}, pages = {6755-6762}, pmid = {21821767}, issn = {1098-5336}, mesh = {Acinetobacter baumannii/genetics/*virology ; Bacteriolysis ; Bacteriophages/*genetics/growth &amp; development/isolation &amp; purification/ultrastructure ; DNA, Viral/chemistry/genetics ; Electrophoresis, Polyacrylamide Gel ; Humans ; Klebsiella/virology ; Magnesium/metabolism ; Molecular Sequence Data ; Molecular Weight ; Myoviridae/*genetics/growth &amp; development/isolation &amp; purification/ultrastructure ; Open Reading Frames ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Sputum/virology ; Viral Proteins/chemistry/*genetics/isolation &amp; purification ; Virion/ultrastructure ; Virus Attachment/drug effects ; }, abstract = {Acinetobacter baumannii is an important Gram-negative opportunistic pathogen causing nosocomial infections. The emergence of multiple-drug-resistant A. baumannii isolates has increased in recent years. Directed toward phage therapy, a lytic phage of A. baumannii, designated Abp53, was isolated from a sputum sample in this study. Abp53 has an isometric head and a contractile tail with tail fibers (belonging to Myoviridae), a latent period of about 10 min, and a burst size of approximately 150 PFU per infected cell. Abp53 could completely lyse 27% of the A. baumannii isolates tested, which were all multiple drug resistant, but not other bacteria. Mg(2+) enhanced the adsorption and productivity of, and host lysis by, Abp53. Twenty Abp53 virion proteins were visualized in SDS-polyacrylamide gel electrophoresis, with a 47-kDa protein being the predicted major capsid protein. Abp53 has a double-stranded DNA genome of 95 kb. Sequence analyses of a 10-kb region revealed 8 open reading frames. Five of the encoded proteins, including 3 tail components and 2 hypothetical proteins, were similar to proteins encoded by A. baumannii strain ACICU. ORF1176 (one of the tail components, 1,176 amino acids [aa]), which is also similar to tail protein gp21 of Klebsiella phage phiKO2, contained repeated domains similar to those within the ACICU_02717 protein of A. baumannii ACICU and gp21. These findings suggest a common ancestry and horizontal gene transfer during evolution. As phages can expand the host range by domain duplication in tail fiber proteins, repeated domains in ORF1176 might have a similar significance in Abp53.}, }
@article {pmid21820956, year = {2012}, author = {Dittami, SM and Riisberg, I and John, U and Orr, RJ and Jakobsen, KS and Edvardsen, B}, title = {Analysis of expressed sequence tags from the marine microalga Pseudochattonella farcimen (Dictyochophyceae).}, journal = {Protist}, volume = {163}, number = {1}, pages = {143-161}, doi = {10.1016/j.protis.2011.07.004}, pmid = {21820956}, issn = {1618-0941}, mesh = {Eukaryota/classification/*genetics/metabolism ; Eutrophication ; *Expressed Sequence Tags ; Microalgae/classification/*genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; Proteins/genetics/metabolism ; Seawater ; }, abstract = {Pseudochattonella farcimen (Eikrem, Edvardsen, et Throndsen) is a unicellular alga belonging to the Dictyochophyceae (Heterokonta). It forms recurring blooms in Scandinavian coastal waters, and has been associated to fish mortality. Here we report the sequencing and analysis of 10,368 expressed sequence tags (ESTs) corresponding to 8,149 unique gene models from this species. Compared to EST libraries from other heterokonts, P. farcimen contains a high number of genes with functions related to cell communication and signaling. We found several genes encoding proteins related to fatty acid metabolism, including eight fatty acid desaturases and two phospholipase A2 genes. Three desaturases are highly similar to Δ4-desaturases from haptophytes. P. farcimen also possesses three putative polyketide synthases (PKSs), belonging to two different families. Some of these genes may have been acquired via horizontal gene transfer by a common ancestor of brown algae and dictyochophytes, together with genes involved in mannitol metabolism, which are also present in P. farcimen. Our findings may explain the unusual fatty acid profile previously observed in P. farcimen, and are discussed from an evolutionary perspective and in relation to the ichthyotoxicity of this alga.}, }
@article {pmid21820617, year = {2011}, author = {Selman, M and Pombert, JF and Solter, L and Farinelli, L and Weiss, LM and Keeling, P and Corradi, N}, title = {Acquisition of an animal gene by microsporidian intracellular parasites.}, journal = {Current biology : CB}, volume = {21}, number = {15}, pages = {R576-7}, pmid = {21820617}, issn = {1879-0445}, support = {R01 AI031788/AI/NIAID NIH HHS/United States ; 5R01AI031788-19/AI/NIAID NIH HHS/United States ; MOP-42517/CAPMC/CIHR/Canada ; }, mesh = {Animals ; *Gene Transfer Techniques ; *Host-Parasite Interactions ; Microsporidia/*genetics ; }, abstract = {Parasites have adapted to their specialised way of life by a number of means, including the acquisition of genes by horizontal gene transfer. These newly acquired genes seem to come from a variety of sources, but seldom from the host, even in the most intimate associations between obligate intracellular parasite and host [1]. Microsporidian intracellular parasites have acquired a handful of genes, mostly from bacteria, that help them take energy from their hosts or protect them from the environment [2,3]. To date, however, no animal genes have been documented in any microsporidian genome. Here, we have surveyed the genome of the microsporidian Encephalitozoon romaleae, which parasitises arthropods for evidence of animal genes. We found one protein-encoding gene that is absent from publicly available sequence data from other microsporidia. The gene encodes a component of the purine salvage pathway, and has been independently acquired by other parasites through horizontal gene transfer from other donors. In this case, however, the gene shows a very strong phylogenetic signal for arthropod origin.}, }
@article {pmid21820313, year = {2011}, author = {Dagan, T}, title = {Phylogenomic networks.}, journal = {Trends in microbiology}, volume = {19}, number = {10}, pages = {483-491}, doi = {10.1016/j.tim.2011.07.001}, pmid = {21820313}, issn = {1878-4380}, mesh = {Bacteria/classification/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; *Genome, Bacterial ; Models, Genetic ; *Phylogeny ; Recombination, Genetic ; }, abstract = {Phylogenomics is aimed at studying functional and evolutionary aspects of genome biology using phylogenetic analysis of whole genomes. Current approaches to genome phylogenies are commonly founded in terms of phylogenetic trees. However, several evolutionary processes are non tree-like in nature, including recombination and lateral gene transfer (LGT). Phylogenomic networks are a special type of phylogenetic network reconstructed from fully sequenced genomes. The network model, comprising genomes connected by pairwise evolutionary relations, enables the reconstruction of both vertical and LGT events. Modeling genome evolution in the form of a network enables the use of an extensive toolbox developed for network research. The structural properties of phylogenomic networks open up fundamentally new insights into genome evolution.}, }
@article {pmid21819231, year = {2011}, author = {Hayes, F and Van Melderen, L}, title = {Toxins-antitoxins: diversity, evolution and function.}, journal = {Critical reviews in biochemistry and molecular biology}, volume = {46}, number = {5}, pages = {386-408}, doi = {10.3109/10409238.2011.600437}, pmid = {21819231}, issn = {1549-7798}, support = {BB/G003114/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteria/*genetics/*metabolism ; Bacterial Toxins/chemistry/*classification/*genetics ; Endoribonucleases/chemistry/metabolism ; Escherichia coli/genetics/metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial ; Molecular Sequence Data ; Plasmids/*genetics ; Protein Biosynthesis ; Transcription, Genetic ; }, abstract = {Genes for toxin-antitoxin (TA) complexes are widespread in prokaryote genomes, and species frequently possess tens of plasmid and chromosomal TA loci. The complexes are categorized into three types based on genetic organization and mode of action. The toxins universally are proteins directed against specific intracellular targets, whereas the antitoxins are either proteins or small RNAs that neutralize the toxin or inhibit toxin synthesis. Within the three types of complex, there has been extensive evolutionary shuffling of toxin and antitoxin genes leading to considerable diversity in TA combinations. The intracellular targets of the protein toxins similarly are varied. Numerous toxins, many of which are sequence-specific endoribonucleases, dampen protein synthesis levels in response to a range of stress and nutritional stimuli. Key resources are conserved as a result ensuring the survival of individual cells and therefore the bacterial population. The toxin effects generally are transient and reversible permitting a set of dynamic, tunable responses that reflect environmental conditions. Moreover, by harboring multiple toxins that intercede in protein synthesis in response to different physiological cues, bacteria potentially sense an assortment of metabolic perturbations that are channeled through different TA complexes. Other toxins interfere with the action of topoisomersases, cell wall assembly, or cytoskeletal structures. TAs also play important roles in bacterial persistence, biofilm formation and multidrug tolerance, and have considerable potential both as new components of the genetic toolbox and as targets for novel antibacterial drugs.}, }
@article {pmid21818306, year = {2011}, author = {Tarrío, R and Ayala, FJ and Rodríguez-Trelles, F}, title = {The Vein Patterning 1 (VEP1) gene family laterally spread through an ecological network.}, journal = {PloS one}, volume = {6}, number = {7}, pages = {e22279}, pmid = {21818306}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Catalytic Domain ; *Ecosystem ; Eukaryota/*genetics ; Gene Transfer, Horizontal/*genetics ; Likelihood Functions ; Molecular Sequence Data ; Multigene Family/*genetics ; Phylogeny ; Prokaryotic Cells/*metabolism ; Proteins/chemistry/genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {Lateral gene transfer (LGT) is a major evolutionary mechanism in prokaryotes. Knowledge about LGT--particularly, multicellular--eukaryotes has only recently started to accumulate. A widespread assumption sees the gene as the unit of LGT, largely because little is yet known about how LGT chances are affected by structural/functional features at the subgenic level. Here we trace the evolutionary trajectory of VEin Patterning 1, a novel gene family known to be essential for plant development and defense. At the subgenic level VEP1 encodes a dinucleotide-binding Rossmann-fold domain, in common with members of the short-chain dehydrogenase/reductase (SDR) protein family. We found: i) VEP1 likely originated in an aerobic, mesophilic and chemoorganotrophic α-proteobacterium, and was laterally propagated through nets of ecological interactions, including multiple LGTs between phylogenetically distant green plant/fungi-associated bacteria, and five independent LGTs to eukaryotes. Of these latest five transfers, three are ancient LGTs, implicating an ancestral fungus, the last common ancestor of land plants and an ancestral trebouxiophyte green alga, and two are recent LGTs to modern embryophytes. ii) VEP1's rampant LGT behavior was enabled by the robustness and broad utility of the dinucleotide-binding Rossmann-fold, which provided a platform for the evolution of two unprecedented departures from the canonical SDR catalytic triad. iii) The fate of VEP1 in eukaryotes has been different in different lineages, being ubiquitous and highly conserved in land plants, whereas fungi underwent multiple losses. And iv) VEP1-harboring bacteria include non-phytopathogenic and phytopathogenic symbionts which are non-randomly distributed with respect to the type of harbored VEP1 gene. Our findings suggest that VEP1 may have been instrumental for the evolutionary transition of green plants to land, and point to a LGT-mediated 'Trojan Horse' mechanism for the evolution of bacterial pathogenesis against plants. VEP1 may serve as tool for revealing microbial interactions in plant/fungi-associated environments.}, }
@article {pmid21816767, year = {2011}, author = {Fancello, L and Desnues, C and Raoult, D and Rolain, JM}, title = {Bacteriophages and diffusion of genes encoding antimicrobial resistance in cystic fibrosis sputum microbiota.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {66}, number = {11}, pages = {2448-2454}, doi = {10.1093/jac/dkr315}, pmid = {21816767}, issn = {1460-2091}, support = {242729/ERC_/European Research Council/International ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteriophages/*genetics ; Bacteroidetes/drug effects/genetics ; Cyanobacteria/drug effects/genetics ; Cystic Fibrosis/*microbiology/*virology ; DNA, Ribosomal/isolation &amp; purification ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia/drug effects/genetics ; Fluoroquinolones/pharmacology ; Gene Transfer, Horizontal ; Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/isolation &amp; purification ; Sputum/microbiology/virology ; beta-Lactamases/pharmacology ; }, abstract = {OBJECTIVES: The cystic fibrosis (CF) airway is now considered the site of a complex microbiota, where cross-talking between microbes and lateral gene transfer are believed to contribute to the adaptation of bacteria to this specific environment and to the emergence of multidrug-resistant bacteria. The objective of this study was to retrieve and analyse specific sequences associated with antimicrobial resistance from the CF viromes database.<br><br>METHODS: Specific sequences from CF metagenomic studies related to the 'antibiotic and toxic compound resistance' dataset were retrieved from the MG-RAST web site, assembled and functionally annotated for identification of the genes. Phylogenetic trees were constructed using a minimum parsimony starting tree topology search strategy.<br><br>RESULTS: Overall, we found 1031 short sequences in the CF virome putatively encoding resistance to antimicrobials versus only 3 reads in the non-CF virome dataset (P&#x200a;=&#x200a;0.001). Among them, we could confidently identify 66 efflux pump genes, 15 fluoroquinolone resistance genes and 9 &#x3b2;-lactamase genes. Evolutionary relatedness determined using phylogenetic information demonstrates the different origins of these genes among the CF microbiota. Interestingly, among annotated sequences within CF viromes, we also found matching 16S rDNA sequences from Escherichia, Cyanobacteria and Bacteroidetes.<br><br>CONCLUSIONS: Our results suggest that phages in the CF sputum microbiota represent a reservoir of mobilizable genes associated with antimicrobial resistance that may spread in this specific niche. This phenomenon could explain the fantastic adaptation of CF strains to their niche and may represent a new potential therapeutic target to prevent the emergence of multidrug-resistant bacteria, which are responsible for most of the deaths in CF.}, }
@article {pmid21816764, year = {2011}, author = {Ciric, L and Mullany, P and Roberts, AP}, title = {Antibiotic and antiseptic resistance genes are linked on a novel mobile genetic element: Tn6087.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {66}, number = {10}, pages = {2235-2239}, pmid = {21816764}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/*pharmacology ; Anti-Infective Agents, Local/*pharmacology ; Bacterial Proteins/genetics ; Base Sequence ; Cetrimonium ; Cetrimonium Compounds/pharmacology ; Conjugation, Genetic ; DNA, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal ; Humans ; *Interspersed Repetitive Sequences ; Microbial Sensitivity Tests ; Minocycline/pharmacology ; Mutation ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; Streptococcus oralis/*drug effects/*genetics ; Tetracycline Resistance/genetics ; }, abstract = {OBJECTIVES: Tn916-like elements are one of the most common types of integrative and conjugative element (ICE). In this study we aimed to determine whether novel accessory genes, i.e. genes whose products are not involved in mobility or regulation, were present on a Tn916-like element (Tn6087) isolated from Streptococcus oralis from the human oral cavity.<br><br>METHODS: A minocycline-resistant isolate was analysed using restriction fragment length polymorphism (RFLP) analysis on amplicons derived from Tn916 and DNA sequencing to determine whether there were genetic differences in Tn6087 compared with Tn916. Mutational analysis was used to determine whether the novel accessory gene found was responsible for an observed extra phenotype.<br><br>RESULTS: A novel Tn916-like element, Tn6087, is described that encodes both antibiotic and antiseptic resistance. The antiseptic resistance protein is encoded by a novel small multidrug resistance gene, designated qrg, that was shown to encode resistance to cetyltrimethylammonium bromide (CTAB), also known as cetrimide bromide.<br><br>CONCLUSIONS: This is the first Tn916-like element described that confers both antibiotic and antiseptic resistance, suggesting that selection of either antibiotic or antiseptic resistance will also select for the other and further highlights the need for prudent use of both types of compound.}, }
@article {pmid21816665, year = {2011}, author = {Bidle, KD and Vardi, A}, title = {A chemical arms race at sea mediates algal host-virus interactions.}, journal = {Current opinion in microbiology}, volume = {14}, number = {4}, pages = {449-457}, doi = {10.1016/j.mib.2011.07.013}, pmid = {21816665}, issn = {1879-0364}, mesh = {Biomarkers ; Caspases/metabolism ; Cell Death ; Enzyme Activation ; Eutrophication ; Gene Transfer, Horizontal ; *Genes, Viral ; Glycosphingolipids/chemistry ; Haptophyta/chemistry/genetics/virology ; *Host-Pathogen Interactions ; Oceans and Seas ; Phycodnaviridae/*chemistry/genetics/pathogenicity/physiology ; Phytoplankton/chemistry/genetics/*virology ; Virus Replication ; Water Microbiology ; }, abstract = {Despite the critical importance of viruses in shaping marine microbial ecosystems and lubricating upper ocean biogeochemical cycles, relatively little is known about the molecular mechanisms mediating phytoplankton host-virus interactions. Recent work in algal host-virus systems has begun to shed novel insight into the elegant strategies of viral infection and subcellular regulation of cell fate, which not only reveal tantalizing aspects of viral replication and host resistance strategies but also provide new diagnostic tools toward elucidating the impact of virus-mediated processes in the ocean. Widespread lateral gene transfer between viruses and their hosts plays a prominent role in host-virus diversification and in the regulation of host-virus infection mechanisms by allowing viruses to manipulate and 'rewire' host metabolic pathways to facilitate infection.}, }
@article {pmid21816042, year = {2011}, author = {Håfström, T and Jansson, DS and Segerman, B}, title = {Complete genome sequence of Brachyspira intermedia reveals unique genomic features in Brachyspira species and phage-mediated horizontal gene transfer.}, journal = {BMC genomics}, volume = {12}, number = {}, pages = {395}, pmid = {21816042}, issn = {1471-2164}, mesh = {Bacteriophages/*genetics ; Brachyspira/*genetics/*virology ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial/genetics ; *Genomics ; Multigene Family/genetics ; Plasmids/genetics ; Species Specificity ; }, abstract = {BACKGROUND: Brachyspira spp. colonize the intestines of some mammalian and avian species and show different degrees of enteropathogenicity. Brachyspira intermedia can cause production losses in chickens and strain PWS/AT now becomes the fourth genome to be completed in the genus Brachyspira.<br><br>RESULTS: 15 classes of unique and shared genes were analyzed in B. intermedia, B. murdochii, B. hyodysenteriae and B. pilosicoli. The largest number of unique genes was found in B. intermedia and B. murdochii. This indicates the presence of larger pan-genomes. In general, hypothetical protein annotations are overrepresented among the unique genes. A 3.2 kb plasmid was found in B. intermedia strain PWS/AT. The plasmid was also present in the B. murdochii strain but not in nine other Brachyspira isolates. Within the Brachyspira genomes, genes had been translocated and also frequently switched between leading and lagging strands, a process that can be followed by different AT-skews in the third positions of synonymous codons. We also found evidence that bacteriophages were being remodeled and genes incorporated into them.<br><br>CONCLUSIONS: The accessory gene pool shapes species-specific traits. It is also influenced by reductive genome evolution and horizontal gene transfer. Gene-transfer events can cross both species and genus boundaries and bacteriophages appear to play an important role in this process. A mechanism for horizontal gene transfer appears to be gene translocations leading to remodeling of bacteriophages in combination with broad tropism.}, }
@article {pmid21815987, year = {2011}, author = {Gutierrez, A and Cantamutto, M and Poverene, M}, title = {Persistence of sunflower crop traits and fitness in Helianthus petiolaris populations.}, journal = {Plant biology (Stuttgart, Germany)}, volume = {13}, number = {5}, pages = {821-830}, doi = {10.1111/j.1438-8677.2010.00433.x}, pmid = {21815987}, issn = {1438-8677}, mesh = {Argentina ; Crops, Agricultural/*genetics ; Fertility ; Gene Transfer, Horizontal ; Helianthus/*genetics ; Hybridization, Genetic/ethics ; Introduced Species ; Plants, Genetically Modified/*genetics ; Risk Assessment ; }, abstract = {Transgenic plants have increased interest in the study of crop gene introgression in wild populations. Genes (or transgenes) conferring adaptive advantages persist in introgressed populations, enhancing competitiveness of wild or weedy plants. This represents an ecological risk that could increase problems of weed control. Introgression of cultivar alleles into wild plant populations via crop-wild hybridisations is primarily governed by their fitness effect. To evaluate this, we studied the second generation of seven wild-crop interspecific hybrids between weedy Helianthus petiolaris and cultivated sunflower, H. annuus var. macrocarpus. The second generation comprised open-pollinated progeny and backcrosses to the wild parent, mimicking crosses that occur in natural situations. We compared a number of morphological, life history and fitness traits. Multivariate analysis showed that the parental species H. annuus and H. petiolaris differed in a number of morphological traits, while the second hybrid generation between them was intermediate. Sunflower crop introgression lowered fitness of interspecific hybrids, but fitness parameters tended to recover in the following generation. Relative frequency of wild/weedy and introgressed plants was estimated through four generations, based on male and female parent fitness. In spite of several negative selection coefficients observed in the second generation, introgressed plants could be detected in stands of <100 weedy H. petiolaris populations. The rapid recovery of fecundity parameters leads to prediction that any trait conferring an ecological advantage will diffuse into the wild or weedy population, even if F1 hybrids have low fitness.}, }
@article {pmid21815642, year = {2011}, author = {Ma, Y and Wilson, CA and Novak, JT and Riffat, R and Aynur, S and Murthy, S and Pruden, A}, title = {Effect of various sludge digestion conditions on sulfonamide, macrolide, and tetracycline resistance genes and class I integrons.}, journal = {Environmental science &amp; technology}, volume = {45}, number = {18}, pages = {7855-7861}, doi = {10.1021/es200827t}, pmid = {21815642}, issn = {1520-5851}, mesh = {Bacteria/classification/genetics/isolation &amp; purification ; Denaturing Gradient Gel Electrophoresis ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Hot Temperature ; Integrons/genetics ; Macrolides ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; Sulfonamides ; Tetracyclines ; }, abstract = {Wastewater treatment processes are of growing interest as a potential means to limit the dissemination of antibiotic resistance. This study examines the response of nine representative antibiotic resistance genes (ARGs) encoding resistance to sulfonamide (sulI, sulII), erythromycin (erm(B), erm(F)), and tetracycline (tet(O), tet(W), tet(C), tet(G), tet(X)) to various laboratory-scale sludge digestion processes. The class I integron gene (intI1) was also monitored as an indicator of horizontal gene transfer potential and multiple antibiotic resistance. Mesophilic anaerobic digestion at both 10 and 20 day solids retention times (SRTs) significantly reduced sulI, suII, tet(C), tet(G), and tet(X) with longer SRT exhibiting a greater extent of removal; however, tet(W), erm(B) and erm(F) genes increased relative to the feed. Thermophilic anaerobic digesters operating at 47 °C, 52 °C, and 59 °C performed similarly to each other and provided more effective reduction of erm(B), erm(F), tet(O), and tet(W) compared to mesophilic digestion. However, thermophilic digestion resulted in similar or poorer removal of all other ARGs and intI1. Thermal hydrolysis pretreatment drastically reduced all ARGs, but they generally rebounded during subsequent anaerobic and aerobic digestion treatments. To gain insight into potential mechanisms driving ARG behavior in the digesters, the dominant bacterial communities were compared by denaturing gradient gel electrophoresis. The overall results suggest that bacterial community composition of the sludge digestion process, as controlled by the physical operating characteristics, drives the distribution of ARGs present in the produced biosolids, more so than the influent ARG composition.}, }
@article {pmid21811613, year = {2011}, author = {Ghosh, A and Dowd, SE and Zurek, L}, title = {Dogs leaving the ICU carry a very large multi-drug resistant enterococcal population with capacity for biofilm formation and horizontal gene transfer.}, journal = {PloS one}, volume = {6}, number = {7}, pages = {e22451}, pmid = {21811613}, issn = {1932-6203}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Biodiversity ; Biofilms/drug effects/*growth &amp; development ; Clone Cells ; Cluster Analysis ; Conjugation, Genetic/drug effects ; Dog Diseases/microbiology ; Dogs ; *Drug Resistance, Multiple, Bacterial/drug effects ; Electrophoresis, Gel, Pulsed-Field ; Enterococcus/drug effects/*genetics/pathogenicity/*physiology ; Feces/microbiology ; Gene Transfer, Horizontal/drug effects/*genetics ; Gram-Positive Bacterial Infections/microbiology/*veterinary ; Humans ; *Intensive Care Units ; Microbial Sensitivity Tests ; Sequence Analysis, DNA ; Species Specificity ; Virulence Factors/metabolism ; }, abstract = {The enterococcal community from feces of seven dogs treated with antibiotics for 2-9 days in the veterinary intensive care unit (ICU) was characterized. Both, culture-based approach and culture-independent 16S rDNA amplicon 454 pyrosequencing, revealed an abnormally large enterococcal community: 1.4±0.8×10(8) CFU gram(-1) of feces and 48.9±11.5% of the total 16,228 sequences, respectively. The diversity of the overall microbial community was very low which likely reflects a high selective antibiotic pressure. The enterococcal diversity based on 210 isolates was also low as represented by Enterococcus faecium (54.6%) and Enterococcus faecalis (45.4%). E. faecium was frequently resistant to enrofloxacin (97.3%), ampicillin (96.5%), tetracycline (84.1%), doxycycline (60.2%), erythromycin (53.1%), gentamicin (48.7%), streptomycin (42.5%), and nitrofurantoin (26.5%). In E. faecalis, resistance was common to tetracycline (59.6%), erythromycin (56.4%), doxycycline (53.2%), and enrofloxacin (31.9%). No resistance was detected to vancomycin, tigecycline, linezolid, and quinupristin/dalfopristin in either species. Many isolates carried virulence traits including gelatinase, aggregation substance, cytolysin, and enterococcal surface protein. All E. faecalis strains were biofilm formers in vitro and this phenotype correlated with the presence of gelE and/or esp. In vitro intra-species conjugation assays demonstrated that E. faecium were capable of transferring tetracycline, doxycycline, streptomycin, gentamicin, and erythromycin resistance traits to human clinical strains. Multi-locus variable number tandem repeat analysis (MLVA) and pulsed-field gel electrophoresis (PFGE) of E. faecium strains showed very low genotypic diversity. Interestingly, three E. faecium clones were shared among four dogs suggesting their nosocomial origin. Furthermore, multi-locus sequence typing (MLST) of nine representative MLVA types revealed that six sequence types (STs) originating from five dogs were identical or closely related to STs of human clinical isolates and isolates from hospital outbreaks. It is recommended to restrict close physical contact between pets released from the ICU and their owners to avoid potential health risks.}, }
@article {pmid21811415, year = {2011}, author = {Chen, HD and Jewett, MW and Groisman, EA}, title = {Ancestral genes can control the ability of horizontally acquired loci to confer new traits.}, journal = {PLoS genetics}, volume = {7}, number = {7}, pages = {e1002184}, pmid = {21811415}, issn = {1553-7404}, support = {42336//PHS HHS/United States ; //Howard Hughes Medical Institute/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics/metabolism ; DNA, Bacterial/chemistry/genetics ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/drug effects/genetics/metabolism ; Escherichia coli Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Kinetics ; Magnesium/pharmacology ; Molecular Sequence Data ; Phosphorylation ; Polymyxin B/*pharmacology ; Reverse Transcriptase Polymerase Chain Reaction ; Salmonella typhimurium/drug effects/genetics/metabolism ; Sequence Analysis, DNA ; Transcription Factors/genetics/metabolism ; Transformation, Bacterial ; }, abstract = {Horizontally acquired genes typically function as autonomous units conferring new abilities when introduced into different species. However, we reasoned that proteins preexisting in an organism might constrain the functionality of a horizontally acquired gene product if it operates on an ancestral pathway. Here, we determine how the horizontally acquired pmrD gene product activates the ancestral PmrA/PmrB two-component system in Salmonella enterica but not in the closely related bacterium Escherichia coli. The Salmonella PmrD protein binds to the phosphorylated PmrA protein (PmrA-P), protecting it from dephosphorylation by the PmrB protein. This results in transcription of PmrA-dependent genes, including those conferring polymyxin B resistance. We now report that the E. coli PmrD protein can activate the PmrA/PmrB system in Salmonella even though it cannot do it in E. coli, suggesting that these two species differ in an additional component controlling PmrA-P levels. We establish that the E. coli PmrB displays higher phosphatase activity towards PmrA-P than the Salmonella PmrB, and we identified a PmrB subdomain responsible for this property. Replacement of the E. coli pmrB gene with the Salmonella homolog was sufficient to render E. coli resistant to polymyxin B under PmrD-inducing conditions. Our findings provide a singular example whereby quantitative differences in the biochemical activities of orthologous ancestral proteins dictate the ability of a horizontally acquired gene product to confer species-specific traits. And they suggest that horizontally acquired genes can potentiate selection at ancestral loci.}, }
@article {pmid21808635, year = {2011}, author = {Klockgether, J and Cramer, N and Wiehlmann, L and Davenport, CF and Tümmler, B}, title = {Pseudomonas aeruginosa Genomic Structure and Diversity.}, journal = {Frontiers in microbiology}, volume = {2}, number = {}, pages = {150}, pmid = {21808635}, issn = {1664-302X}, abstract = {The Pseudomonas aeruginosa genome (G + C content 65-67%, size 5.5-7 Mbp) is made up of a single circular chromosome and a variable number of plasmids. Sequencing of complete genomes or blocks of the accessory genome has revealed that the genome encodes a large repertoire of transporters, transcriptional regulators, and two-component regulatory systems which reflects its metabolic diversity to utilize a broad range of nutrients. The conserved core component of the genome is largely collinear among P. aeruginosa strains and exhibits an interclonal sequence diversity of 0.5-0.7%. Only a few loci of the core genome are subject to diversifying selection. Genome diversity is mainly caused by accessory DNA elements located in 79 regions of genome plasticity that are scattered around the genome and show an anomalous usage of mono- to tetradecanucleotides. Genomic islands of the pKLC102/PAGI-2 family that integrate into tRNA(Lys) or tRNA(Gly) genes represent hotspots of inter- and intraclonal genomic diversity. The individual islands differ in their repertoire of metabolic genes that make a large contribution to the pangenome. In order to unravel intraclonal diversity of P. aeruginosa, the genomes of two members of the PA14 clonal complex from diverse habitats and geographic origin were compared. The genome sequences differed by less than 0.01% from each other. One hundred ninety-eight of the 231 single nucleotide substitutions (SNPs) were non-randomly distributed in the genome. Non-synonymous SNPs were mainly found in an integrated Pf1-like phage and in genes involved in transcriptional regulation, membrane and extracellular constituents, transport, and secretion. In summary, P. aeruginosa is endowed with a highly conserved core genome of low sequence diversity and a highly variable accessory genome that communicates with other pseudomonads and genera via horizontal gene transfer.}, }
@article {pmid21803914, year = {2011}, author = {Fallico, V and McAuliffe, O and Fitzgerald, GF and Ross, RP}, title = {Plasmids of raw milk cheese isolate Lactococcus lactis subsp. lactis biovar diacetylactis DPC3901 suggest a plant-based origin for the strain.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {18}, pages = {6451-6462}, pmid = {21803914}, issn = {1098-5336}, mesh = {Amino Acid Sequence ; Cheese/*microbiology ; DNA, Bacterial/chemistry/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; Lactococcus lactis/genetics/*isolation &amp; purification ; Molecular Sequence Data ; Open Reading Frames ; Plasmids/*analysis ; Recombination, Genetic ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {The four-plasmid complement of the raw milk cheese isolate Lactococcus lactis subsp. lactis biovar diacetylactis DPC3901 was sequenced, and some genetic features were functionally analyzed. The complete sequences of pVF18 (18,977 bp), pVF21 (21,739 bp), pVF22 (22,166 bp), and pVF50 (53,876 bp) were obtained. Each plasmid contained genes not previously described for Lactococcus, in addition to genes associated with plant-derived lactococcal strains. Most of the novel genes were found on pVF18 and encoded functions typical of bacteria associated with plants, such as activities of plant cell wall modification (orf11 and orf25). In addition, a predicted high-affinity regulated system for the uptake of cobalt was identified (orf19 to orf21 [orf19-21]), which has a single database homolog on a plant-derived Leuconostoc plasmid and whose functionality was demonstrated following curing of pVF18. pVF21 and pVF22 encode additional metal transporters, which, along with orf19-21 of pVF18, could enhance host ability to uptake growth-limiting amounts of biologically essential ions within the soil. In addition, vast regions from pVF50 and pVF21 share significant homology with the plant-derived lactococcal plasmid pGdh442, which is indicative of extensive horizontal gene transfer and recombination between these plasmids and suggests a common plant niche for their hosts. Phenotypes associated with these regions include glutamate dehydrogenase activity and Na(+) and K(+) transport. The presence of numerous plant-associated markers in L. lactis DPC3901 suggests a plant origin for the raw milk cheese isolate and provides for the first time the genetic basis to support the concept of the plant-milk transition for Lactococcus strains.}, }
@article {pmid21802160, year = {2011}, author = {Meng, H and Zhang, Z and Chen, M and Su, Y and Li, L and Miyoshi, S and Yan, H and Shi, L}, title = {Characterization and horizontal transfer of class 1 integrons in Salmonella strains isolated from food products of animal origin.}, journal = {International journal of food microbiology}, volume = {149}, number = {3}, pages = {274-277}, doi = {10.1016/j.ijfoodmicro.2011.07.006}, pmid = {21802160}, issn = {1879-3460}, mesh = {Animals ; Chickens ; Conjugation, Genetic ; *Drug Resistance, Bacterial ; *Gene Transfer, Horizontal ; Humans ; *Integrons ; Meat/*microbiology ; Plasmids ; Salmonella/*classification/*genetics/isolation &amp; purification ; Salmonella Infections/microbiology ; Seafood/*microbiology ; Swine ; Transformation, Genetic ; }, abstract = {A total of 81 Salmonella isolates from retail meats and seafood in Hebei province, China, were assayed for the presence of and horizontal transfer of class 1 integrons. By the PCR screening for the integrons, class 1 integron was detected from strains in serotypes of Derby, Indiana, London and Choleraesuis, which were isolated from pork, chicken or seafood; however, two isolates contained the empty integron that lacked the resistance cassette, a potential hotspot for development of the multidrug resistance. In contrast, two other isolates had the antibiotic resistance gene cassettes within the class 1 integron, which were dfrA1-aadA1 and aadB-cmlA, respectively. The conjugation experiments demonstrated the plasmid-mediated transfer of the class 1 integrons. Furthermore, each of the integrons was transmitted to Streptococcus mutans via natural gene transformation. These findings suggest the possible transfer of class 1 integrons from foodborne pathogens to human residential bacteria via horizontal gene transfer.}, }
@article {pmid21801381, year = {2011}, author = {Bilewitch, JP and Degnan, SM}, title = {A unique horizontal gene transfer event has provided the octocoral mitochondrial genome with an active mismatch repair gene that has potential for an unusual self-contained function.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {228}, pmid = {21801381}, issn = {1471-2148}, mesh = {Amino Acid Sequence ; Animals ; Anthozoa/*genetics ; Computational Biology ; DNA Repair/genetics/*physiology ; *Evolution, Molecular ; Gene Expression Profiling ; Gene Transfer, Horizontal/*genetics ; Genome, Mitochondrial/*genetics ; *Models, Molecular ; Molecular Sequence Data ; MutS DNA Mismatch-Binding Protein/chemistry/*genetics ; Mutation/genetics ; Sequence Alignment ; Species Specificity ; }, abstract = {BACKGROUND: The mitochondrial genome of the Octocorallia has several characteristics atypical for metazoans, including a novel gene suggested to function in DNA repair. This mtMutS gene is favored for octocoral molecular systematics, due to its high information content. Several hypotheses concerning the origins of mtMutS have been proposed, and remain equivocal, although current weight of support is for a horizontal gene transfer from either an epsilonproteobacterium or a large DNA virus. Here we present new and compelling evidence on the evolutionary origin of mtMutS, and provide the very first data on its activity, functional capacity and stability within the octocoral mitochondrial genome.<br><br>RESULTS: The mtMutS gene has the expected conserved amino acids, protein domains and predicted tertiary protein structure. Phylogenetic analysis indicates that mtMutS is not a member of the MSH family and therefore not of eukaryotic origin. MtMutS clusters closely with representatives of the MutS7 lineage; further support for this relationship derives from the sharing of a C-terminal endonuclease domain that confers a self-contained mismatch repair function. Gene expression analyses confirm that mtMutS is actively transcribed in octocorals. Rates of mitochondrial gene evolution in mtMutS-containing octocorals are lower than in their hexacoral sister-group, which lacks the gene, although paradoxically the mtMutS gene itself has higher rates of mutation than other octocoral mitochondrial genes.<br><br>CONCLUSIONS: The octocoral mtMutS gene is active and codes for a protein with all the necessary components for DNA mismatch repair. A lower rate of mitochondrial evolution, and the presence of a nicking endonuclease domain, both indirectly support a theory of self-sufficient DNA mismatch repair within the octocoral mitochondrion. The ancestral affinity of mtMutS to non-eukaryotic MutS7 provides compelling support for an origin by horizontal gene transfer. The immediate vector of transmission into octocorals can be attributed to either an epsilonproteobacterium in an endosymbiotic association or to a viral infection, although DNA viruses are not currently known to infect both bacteria and eukaryotes, nor mitochondria in particular. In consolidating the first known case of HGT into an animal mitochondrial genome, these findings suggest the need for reconsideration of the means by which metazoan mitochondrial genomes evolve.}, }
@article {pmid21795732, year = {2011}, author = {Talianova, M and Janousek, B}, title = {What can we learn from tobacco and other Solanaceae about horizontal DNA transfer?.}, journal = {American journal of botany}, volume = {98}, number = {8}, pages = {1231-1242}, doi = {10.3732/ajb.1000370}, pmid = {21795732}, issn = {1537-2197}, mesh = {Agrobacterium/genetics ; Cell Nucleus/genetics ; Chloroplasts/genetics ; DNA, Bacterial/*genetics ; DNA, Chloroplast/genetics ; DNA, Fungal/*genetics ; DNA, Plant/*genetics ; DNA, Viral/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Mycorrhizae/genetics ; Plant Viruses/genetics ; Solanaceae/*genetics/microbiology/virology ; Nicotiana/*genetics/microbiology/virology ; Transformation, Genetic ; }, abstract = {In eukaryotic organisms, horizontal gene transfer (HGT) is regarded as an important though infrequent source of reticulate evolution. Many confirmed instances of natural HGT involving multicellular eukaryotes come from flowering plants. This review intends to provide a synthesis of present knowledge regarding HGT in higher plants, with an emphasis on tobacco and other species in the Solanaceae family because there are numerous detailed reports concerning natural HGT events, involving various donors, in this family. Moreover, in-depth experimental studies using transgenic tobacco are of great importance for understanding this process. Valuable insights are offered concerning the mechanisms of HGT, the adaptive role and regulation of natural transgenes, and new routes for gene trafficking. With an increasing amount of data on HGT, a synthetic view is beginning to emerge.}, }
@article {pmid21793656, year = {2011}, author = {Garcia-Migura, L and Sanchez-Valenzuela, AJ and Jensen, LB}, title = {Presence of glycopeptide-encoding plasmids in enterococcal isolates from food and humans in Denmark.}, journal = {Foodborne pathogens and disease}, volume = {8}, number = {11}, pages = {1191-1197}, doi = {10.1089/fpd.2011.0897}, pmid = {21793656}, issn = {1556-7125}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/*genetics ; Carbon-Oxygen Ligases/*genetics ; DNA Transposable Elements ; Denmark ; Enterococcus faecalis/drug effects/*genetics/isolation &amp; purification ; Enterococcus faecium/drug effects/*genetics/isolation &amp; purification ; Food Microbiology ; Gene Transfer, Horizontal ; Glycopeptides/genetics/*pharmacology ; Gram-Positive Bacterial Infections/microbiology ; Humans ; Meat/microbiology ; Phenotype ; Pheromones/genetics ; Plasmids ; Replicon/genetics ; Vancomycin/pharmacology ; Vancomycin Resistance/*genetics ; }, abstract = {Enterococci and especially glycopeptides-resistant enterococci (GRE) are a growing concern due to their ability to cause infections in hospitals. Transmission of antimicrobial resistance between reservoirs such as animals, meat, and humans are in most cases linked to transmission of mobile genetic elements (MGE) such as plasmids and transposons. Presence of MGE was tested in all GRE isolated from food in Denmark in 2005-2007 including the first vanA mediated Enterococcus faecalis isolated from food. The ability of these plasmids to transfer and persist among enterococci was investigated using newly developed techniques for classification of plasmids. Replicons associated with sex pheromone-inducible plasmids were detected in all GR E. faecalis, whereas GR Enterococcus faecium contained plasmids known to be widely distributed among enterococci. vanA resistance is common in E. faecium isolates from meat and animals in Europe and is rarely found in E. faecalis. This article describes the first characterization of MGE from vanA mediated E. faecalis, thus linking this resistance genotype to pheromone responding plasmids.}, }
@article {pmid21792223, year = {2011}, author = {Giraud, T and Shykoff, JA}, title = {Bacterial cooperation controlled by mobile elements: kin selection versus infectivity.}, journal = {Heredity}, volume = {107}, number = {3}, pages = {277-8; author reply 279-81}, pmid = {21792223}, issn = {1365-2540}, mesh = {Bacteria/*genetics ; *Gene Transfer, Horizontal ; Interspersed Repetitive Sequences/*genetics ; Plasmids/*genetics ; }, }
@article {pmid21791580, year = {2011}, author = {Brazelton, WJ and Mehta, MP and Kelley, DS and Baross, JA}, title = {Physiological differentiation within a single-species biofilm fueled by serpentinization.}, journal = {mBio}, volume = {2}, number = {4}, pages = {}, pmid = {21791580}, issn = {2150-7511}, mesh = {Biofilms/*growth &amp; development ; DNA, Archaeal/chemistry/genetics ; Genes, Archaeal ; Hot Springs/*microbiology ; Hot Temperature ; Hydrogen/metabolism ; Hydrogen-Ion Concentration ; Intracellular Membranes/ultrastructure ; Metabolic Networks and Pathways/genetics ; Metagenome ; Methane/metabolism ; Methanosarcinales/*cytology/growth &amp; development/metabolism/*physiology ; Microscopy, Electron, Transmission ; Molecular Sequence Data ; Oxidation-Reduction ; Sequence Analysis, DNA ; }, abstract = {UNLABELLED: Carbonate chimneys at the Lost City hydrothermal field are coated in biofilms dominated by a single phylotype of archaea known as Lost City Methanosarcinales. In this study, we have detected surprising physiological complexity in single-species biofilms, which is typically indicative of multispecies biofilm communities. Multiple cell morphologies were visible within the biofilms by transmission electron microscopy, and some cells contained intracellular membranes that may facilitate methane oxidation. Both methane production and oxidation were detected at 70 to 80°C and pH 9 to 10 in samples containing the single-species biofilms. Both processes were stimulated by the presence of hydrogen (H(2)), indicating that methane production and oxidation are part of a syntrophic interaction. Metagenomic data included a sequence encoding AMP-forming acetyl coenzyme A synthetase, indicating that acetate may play a role in the methane-cycling syntrophy. A wide range of nitrogen fixation genes were also identified, many of which were likely acquired via lateral gene transfer (LGT). Our results indicate that cells within these single-species biofilms may have differentiated into multiple physiological roles to form multicellular communities linked by metabolic interactions and LGT. Communities similar to these Lost City biofilms are likely to have existed early in the evolution of life, and we discuss how the multicellular characteristics of ancient hydrogen-fueled biofilm communities could have stimulated ecological diversification, as well as unity of biochemistry, during the earliest stages of cellular evolution.<br><br>IMPORTANCE: Our previous work at the Lost City hydrothermal field has shown that its carbonate chimneys host microbial biofilms dominated by a single uncultivated "species" of archaea. In this paper, we integrate evidence from these previous studies with new data on the metabolic activity and cellular morphology of these archaeal biofilms. We conclude that the archaeal biofilm must contain cells that are physiologically and possibly genetically differentiated with respect to each other. These results are especially interesting considering the possibility that the first cells originated and evolved in hydrothermal systems similar to Lost City.}, }
@article {pmid21791114, year = {2011}, author = {Lacher, MD and Shiina, M and Chang, P and Keller, D and Tiirikainen, MI and Korn, WM}, title = {ZEB1 limits adenoviral infectability by transcriptionally repressing the coxsackie virus and adenovirus receptor.}, journal = {Molecular cancer}, volume = {10}, number = {}, pages = {91}, pmid = {21791114}, issn = {1476-4598}, support = {P30 CA82103/CA/NCI NIH HHS/United States ; R01 CA095701/CA/NCI NIH HHS/United States ; R01 CA118545/CA/NCI NIH HHS/United States ; }, mesh = {Adenoviridae/*genetics ; Adenoviridae Infections/genetics/prevention &amp; control ; Base Sequence ; Cell Line, Tumor ; Coxsackie and Adenovirus Receptor-Like Membrane Protein ; Down-Regulation/genetics ; Epithelial-Mesenchymal Transition/genetics ; Female ; Gene Expression Regulation ; Gene Transfer, Horizontal/genetics/physiology ; Genetic Vectors ; Homeodomain Proteins/genetics/metabolism/*physiology ; Humans ; Molecular Sequence Data ; Receptors, Virus/*genetics/metabolism ; Sequence Homology, Nucleic Acid ; Transcription Factors/genetics/metabolism/*physiology ; Zinc Finger E-box-Binding Homeobox 1 ; }, abstract = {BACKGROUND: We have previously reported that RAS-MEK (Cancer Res. 2003 May 1;63(9):2088-95) and TGF-β (Cancer Res. 2006 Feb 1;66(3):1648-57) signaling negatively regulate coxsackie virus and adenovirus receptor (CAR) cell-surface expression and adenovirus uptake. In the case of TGF-β, down-regulation of CAR occurred in context of epithelial-to-mesenchymal transition (EMT), a process associated with transcriptional repression of E-cadherin by, for instance, the E2 box-binding factors Snail, Slug, SIP1 or ZEB1. While EMT is crucial in embryonic development, it has been proposed to contribute to the formation of invasive and metastatic carcinomas by reducing cell-cell contacts and increasing cell migration.<br><br>RESULTS: Here, we show that ZEB1 represses CAR expression in both PANC-1 (pancreatic) and MDA-MB-231 (breast) human cancer cells. We demonstrate that ZEB1 physically associates with at least one of two closely spaced and conserved E2 boxes within the minimal CAR promoter here defined as genomic region -291 to -1 relative to the translational start ATG. In agreement with ZEB1's established role as a negative regulator of the epithelial phenotype, silencing its expression in MDA-MB-231 cells induced a partial Mesenchymal-to-Epithelial Transition (MET) characterized by increased levels of E-cadherin and CAR, and decreased expression of fibronectin. Conversely, knockdown of ZEB1 in PANC-1 cells antagonized both the TGF-&#x3b2;-induced down-regulation of E-cadherin and CAR and the reduction of adenovirus uptake. Interestingly, even though ZEB1 clearly contributes to the TGF-&#x3b2;-induced mesenchymal phenotype of PANC-1 cells, TGF-&#x3b2; did not seem to affect ZEB1's protein levels or subcellular localization. These findings suggest that TGF-&#x3b2; may inhibit CAR expression by regulating factor(s) that cooperate with ZEB1 to repress the CAR promoter, rather than by regulating ZEB1 expression levels. In addition to the negative E2 box-mediated regulation the minimal CAR promoter is positively regulated through conserved ETS and CRE elements.<br><br>CONCLUSIONS: This report provides evidence that inhibition of ZEB1 may improve adenovirus uptake of cancer cells that have undergone EMT and for which ZEB1 is necessary to maintain the mesenchymal phenotype. Targeting of ZEB1 may reverse some aspects of EMT including the down-regulation of CAR.}, }
@article {pmid21788459, year = {2011}, author = {Deng, Y and He, L and Chen, S and Zheng, H and Zeng, Z and Liu, Y and Sun, Y and Ma, J and Chen, Z and Liu, JH}, title = {F33:A-:B- and F2:A-:B- plasmids mediate dissemination of rmtB-blaCTX-M-9 group genes and rmtB-qepA in Enterobacteriaceae isolates from pets in China.}, journal = {Antimicrobial agents and chemotherapy}, volume = {55}, number = {10}, pages = {4926-4929}, pmid = {21788459}, issn = {1098-6596}, mesh = {Aminoglycosides/pharmacology ; Animals ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics ; Cats ; China ; Dogs ; Drug Resistance, Multiple, Bacterial ; Enterobacteriaceae/drug effects/*genetics/isolation &amp; purification ; Escherichia coli Proteins/*genetics ; Gene Transfer, Horizontal ; Methyltransferases/*genetics ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Pets/*microbiology ; Plasmids/*genetics ; RNA, Ribosomal, 16S/genetics ; beta-Lactamases/*genetics ; }, abstract = {This study investigated the prevalence of 16S rRNA methylase genes in 267 Enterobacteriaceae isolates collected from pets. The rmtB gene was detected in 69 isolates, most of which were clonally unrelated. The coexistence of the rmtB gene with the bla(CTX-M-9) group genes and/or qepA within the same IncFII replicons was commonly detected. The two dominant types of IncF plasmids, F2:A-:B-, carrying rmtB-qepA, and F33:A-:B-, carrying the rmtB-bla(CTX-M-9) group genes (and especially bla(CTX-M-65)), shared restriction patterns within each incompatibility group.}, }
@article {pmid21784912, year = {2011}, author = {Zhang, YM and Li, Y and Chen, WF and Wang, ET and Tian, CF and Li, QQ and Zhang, YZ and Sui, XH and Chen, WX}, title = {Biodiversity and biogeography of rhizobia associated with soybean plants grown in the North China Plain.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {18}, pages = {6331-6342}, pmid = {21784912}, issn = {1098-5336}, mesh = {Bacterial Proteins/genetics ; *Biodiversity ; China ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Molecular Sequence Data ; N-Acetylglucosaminyltransferases/genetics ; Oxidoreductases/genetics ; *Phylogeography ; Rhizobiaceae/*classification/genetics/*isolation &amp; purification ; Sequence Analysis, DNA ; Glycine max/*microbiology ; }, abstract = {As the putative center of origin for soybean and the second largest region of soybean production in China, the North China Plain covers temperate and subtropical regions with diverse soil characteristics. However, the soybean rhizobia in this plain have not been sufficiently studied. To investigate the biodiversity and biogeography of soybean rhizobia in this plain, a total of 309 isolates of symbiotic bacteria from the soybean nodules collected from 16 sampling sites were studied by molecular characterization. These isolates were classified into 10 genospecies belonging to the genera Sinorhizobium and Bradyrhizobium, including four novel groups, with S. fredii (68.28%) as the dominant group. The phylogeny of symbiotic genes nodC and nifH defined four lineages among the isolates associated with Sinorhizobium fredii, Bradyrhizobium elkanii, B. japonicum, and B. yuanmingense, demonstrating the different origins of symbiotic genes and their coevolution with the chromosome. The possible lateral transfer of symbiotic genes was detected in several cases. The association between soil factors (available N, P, and K and pH) and the distribution of genospecies suggest clear biogeographic patterns: Sinorhizobium spp. were superdominant in sampling sites with alkaline-saline soils, while Bradyrhizobium spp. were more abundant in neutral soils. This study clarified the biodiversity and biogeography of soybean rhizobia in the North China Plain.}, }
@article {pmid21784909, year = {2011}, author = {Li, X and Alvarez, V and Harper, WJ and Wang, HH}, title = {Persistent, toxin-antitoxin system-independent, tetracycline resistance-encoding plasmid from a dairy Enterococcus faecium isolate.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {20}, pages = {7096-7103}, pmid = {21784909}, issn = {1098-5336}, mesh = {Anti-Bacterial Agents/*pharmacology ; DNA, Bacterial/chemistry/genetics ; Dairy Products/*microbiology ; Enterococcus faecalis/drug effects/genetics ; Enterococcus faecium/*drug effects/genetics/*isolation &amp; purification ; Gene Expression Profiling ; Gene Order ; Gene Transfer, Horizontal ; Genes, Bacterial ; Molecular Sequence Data ; Multigene Family ; Open Reading Frames ; *Plasmids ; Real-Time Polymerase Chain Reaction ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Streptococcus mutans/drug effects/genetics ; Tetracycline/*pharmacology ; *Tetracycline Resistance ; }, abstract = {A tetracycline-resistant (Tet(r)) dairy Enterococcus faecium isolate designated M7M2 was found to carry both tet(M) and tet(L) genes on a 19.6-kb plasmid. After consecutive transfer in the absence of tetracycline, the resistance-encoding plasmid persisted in 99% of the progenies. DNA sequence analysis revealed that the 19.6-kb plasmid contained 28 open reading frames (ORFs), including a tet(M)-tet(L)-mob gene cluster, as well as a 10.6-kb backbone highly homologous (99.9%) to the reported plasmid pRE25, but without an identified toxin-antitoxin (TA) plasmid stabilization system. The derived backbone plasmid without the Tet(r) determinants exhibited a 100% retention rate in the presence of acridine orange, suggesting the presence of a TA-independent plasmid stabilization mechanism, with its impact on the persistence of a broad spectrum of resistance-encoding traits still to be elucidated. The tet(M)-tet(L) gene cluster from M7M2 was functional and transmissible and led to acquired resistance in Enterococcus faecalis OG1RF by electroporation and in Streptococcus mutans UA159 by natural transformation. Southern hybridization showed that both the tet(M) and tet(L) genes were integrated into the chromosome of S. mutans UA159, while the whole plasmid was transferred to and retained in E. faecalis OG1RF. Quantitative real-time reverse transcription-PCR (RT-PCR) indicated tetracycline-induced transcription of both the tet(M) and tet(L) genes of pM7M2. The results indicated that multiple mechanisms might have contributed to the persistence of antibiotic resistance-encoding genes and that the plasmids pM7M2, pIP816, and pRE25 are likely correlated evolutionarily.}, }
@article {pmid21777852, year = {2011}, author = {Wang, L and Wang, FF and Qian, W}, title = {Evolutionary rewiring and reprogramming of bacterial transcription regulation.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {38}, number = {7}, pages = {279-288}, doi = {10.1016/j.jgg.2011.06.001}, pmid = {21777852}, issn = {1673-8527}, mesh = {Adaptation, Biological/genetics ; Bacteria/*genetics ; DNA Transposable Elements ; *Evolution, Molecular ; Gene Duplication ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; *Genetic Speciation ; Genome, Bacterial ; Recombination, Genetic ; Transcription, Genetic ; }, abstract = {Rewiring and reprogramming of transcriptional regulation took place during bacterial speciation. The mechanistic alterations among transcription factors, cis-regulatory elements and target genes confer bacteria novel ability to adapt to stochastic environmental changes. This process is critical to their survival, especially for bacterial pathogens subjected to accelerated evolution. In the past two decades, the investigators not only completed the sequences of numerous bacterial genomes, but also made great progress in understanding the molecular basis of evolution. Here we briefly reviewed the current knowledge on the mechanistic changes among orthologous, paralogous and xenogenic regulatory circuits, which were caused by genetic recombinations such as gene duplication, horizontal gene transfer, transposable elements and different genetic contexts. We also discussed the potential impact of this area on theoretical and applied studies of microbes.}, }
@article {pmid21776603, year = {2011}, author = {Thuillard, M and Moulton, V}, title = {Identifying and reconstructing lateral transfers from distance matrices by combining the minimum contradiction method and neighbor-net.}, journal = {Journal of bioinformatics and computational biology}, volume = {9}, number = {4}, pages = {453-470}, doi = {10.1142/s0219720011005409}, pmid = {21776603}, issn = {1757-6334}, mesh = {Algorithms ; Bacteria/classification/genetics ; Biological Evolution ; Computational Biology/*methods/statistics &amp; numerical data ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Models, Genetic ; Models, Statistical ; Phylogeny ; }, abstract = {Identifying lateral gene transfers is an important problem in evolutionary biology. Under a simple model of evolution, the expected values of an evolutionary distance matrix describing a phylogenetic tree fulfill the so-called Kalmanson inequalities. The Minimum Contradiction method for identifying lateral gene transfers exploits the fact that lateral transfers may generate large deviations from the Kalmanson inequalities. Here a new approach is presented to deal with such cases that combines the Neighbor-Net algorithm for computing phylogenetic networks with the Minimum Contradiction method. A subset of taxa, prescribed using Neighbor-Net, is obtained by measuring how closely the Kalmanson inequalities are fulfilled by each taxon. A criterion is then used to identify the taxa, possibly involved in a lateral transfer between nonconsecutive taxa. We illustrate the utility of the new approach by applying it to a distance matrix for Archaea, Bacteria, and Eukaryota.}, }
@article {pmid21776602, year = {2011}, author = {Wong, L}, title = {Brief introduction to some new papers on lateral transfer reconstruction, drug candidate screening, disease gene identification, and other results.}, journal = {Journal of bioinformatics and computational biology}, volume = {9}, number = {4}, pages = {v-vii}, doi = {10.1142/s0219720011005653}, pmid = {21776602}, issn = {1757-6334}, mesh = {Biological Evolution ; *Computational Biology ; Disease/genetics ; Drug Evaluation, Preclinical/statistics &amp; numerical data ; Gene Expression Profiling/statistics &amp; numerical data ; Gene Transfer, Horizontal ; Humans ; Systems Biology ; }, }
@article {pmid21774799, year = {2011}, author = {Beauregard-Racine, J and Bicep, C and Schliep, K and Lopez, P and Lapointe, FJ and Bapteste, E}, title = {Of woods and webs: possible alternatives to the tree of life for studying genomic fluidity in E. coli.}, journal = {Biology direct}, volume = {6}, number = {}, pages = {39; discussion 39}, pmid = {21774799}, issn = {1745-6150}, mesh = {DNA, Bacterial/genetics ; Escherichia coli/*genetics ; *Evolution, Molecular ; Gene Regulatory Networks ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Variation ; *Genome, Bacterial ; Interspersed Repetitive Sequences ; Multigene Family ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: We introduce several forest-based and network-based methods for exploring microbial evolution, and apply them to the study of thousands of genes from 30 strains of E. coli. This case study illustrates how additional analyses could offer fast heuristic alternatives to standard tree of life (TOL) approaches.<br><br>RESULTS: We use gene networks to identify genes with atypical modes of evolution, and genome networks to characterize the evolution of genetic partnerships between E. coli and mobile genetic elements. We develop a novel polychromatic quartet method to capture patterns of recombination within E. coli, to update the clanistic toolkit, and to search for the impact of lateral gene transfer and of pathogenicity on gene evolution in two large forests of trees bearing E. coli. We unravel high rates of lateral gene transfer involving E. coli (about 40% of the trees under study), and show that both core genes and shell genes of E. coli are affected by non-tree-like evolutionary processes. We show that pathogenic lifestyle impacted the structure of 30% of the gene trees, and that pathogenic strains are more likely to transfer genes with one another than with non-pathogenic strains. In addition, we propose five groups of genes as candidate mobile modules of pathogenicity. We also present strong evidence for recent lateral gene transfer between E. coli and mobile genetic elements.<br><br>CONCLUSIONS: Depending on which evolutionary questions biologists want to address (i.e. the identification of modules, genetic partnerships, recombination, lateral gene transfer, or genes with atypical evolutionary modes, etc.), forest-based and network-based methods are preferable to the reconstruction of a single tree, because they provide insights and produce hypotheses about the dynamics of genome evolution, rather than the relative branching order of species and lineages. Such a methodological pluralism - the use of woods and webs - is to be encouraged to analyse the evolutionary processes at play in microbial evolution.This manuscript was reviewed by: Ford Doolittle, Tal Pupko, Richard Burian, James McInerney, Didier Raoult, and Yan Boucher.}, }
@article {pmid21771716, year = {2012}, author = {Gilbert, C and Hernandez, SS and Flores-Benabib, J and Smith, EN and Feschotte, C}, title = {Rampant horizontal transfer of SPIN transposons in squamate reptiles.}, journal = {Molecular biology and evolution}, volume = {29}, number = {2}, pages = {503-515}, pmid = {21771716}, issn = {1537-1719}, support = {R01 GM077582/GM/NIGMS NIH HHS/United States ; R01GM77582/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA Transposable Elements/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, RAG-1/genetics ; Genes, mos/genetics ; Molecular Sequence Data ; Phylogeny ; Reptiles/classification/*genetics ; Sequence Analysis, DNA ; }, abstract = {Transposable elements (TEs) are highly abundant in the genome and capable of mobility, two properties that make them particularly prone to transfer horizontally between organisms. Although the impact of horizontal transfer (HT) of TEs is well recognized in prokaryotes, the frequency of this phenomenon and its contribution to genome evolution in eukaryotes remain poorly appreciated. Here, we provide evidence that a DNA transposon called SPIN has colonized the genome of 17 species of reptiles representing nearly every major lineage of squamates, including 14 families of lizards, snakes, and amphisbaenians. Slot blot analyses indicate that SPIN has amplified to high copy numbers in most of these species, ranging from 2,000-28,000 copies per haploid genome. In contrast, we could not detect the presence of SPIN in any of the turtles (seven species from seven families) and crocodiles (four species) examined. Genetic distances between SPIN sequences from species belonging to different squamate families are consistently very low (average = 0.1), considering the deep evolutionary divergence of the families investigated (most are >100 My diverged). Furthermore, these distances fall below interfamilial distances calculated for two genes known to have evolved under strong functional constraint in vertebrates (RAG1, average = 0.24 and C-mos, average = 0.27). These data, combined with phylogenetic analyses, indicate that the widespread distribution of SPIN among squamates is the result of at least 13 independent events of HTs. Molecular dating and paleobiogeographical data suggest that these transfers took place during the last 50 My on at least three different continents (North America, South America and, Africa). Together, these results triple the number of known SPIN transfer events among tetrapods, provide evidence for a previously hypothesized transoceanic movement of SPIN transposons during the Cenozoic, and further underscore the role of HT in the evolution of vertebrate genomes.}, }
@article {pmid21769188, year = {2011}, author = {Bokhari, H and Anwar, M and Mirza, HB and Gillevet, PM}, title = {Evidences of lateral gene transfer between archaea and pathogenic bacteria.}, journal = {Bioinformation}, volume = {6}, number = {8}, pages = {293-296}, pmid = {21769188}, issn = {0973-2063}, abstract = {Acquisition of new genetic material through horizontal gene transfer has been shown to be an important feature in the evolution of many pathogenic bacteria. Changes in the genetic repertoire, occurring through gene acquisition and deletion, are the major events underlying the emergence and evolution of bacterial pathogens. However, horizontal gene transfer across the domains i.e. archaea and bacteria is not so common. In this context, we explore events of horizontal gene transfer between archaea and bacteria. In order to determine whether the acquisition of archaeal genes by lateral gene transfer is an important feature in the evolutionary history of the pathogenic bacteria, we have developed a scheme of stepwise eliminations that identifies archaeal-like genes in various bacterial genomes. We report the presence of 9 genes of archaeal origin in the genomes of various bacteria, a subset of which is also unique to the pathogenic members and are not found in respective non-pathogenic counterparts. We believe that these genes, having been retained in the respective genomes through selective advantage, have key functions in the organism's biology and may play a role in pathogenesis.}, }
@article {pmid21764928, year = {2011}, author = {Mussi, MA and Limansky, AS and Relling, V and Ravasi, P and Arakaki, A and Actis, LA and Viale, AM}, title = {Horizontal gene transfer and assortative recombination within the Acinetobacter baumannii clinical population provide genetic diversity at the single carO gene, encoding a major outer membrane protein channel.}, journal = {Journal of bacteriology}, volume = {193}, number = {18}, pages = {4736-4748}, pmid = {21764928}, issn = {1098-5530}, support = {R01 AI070174/AI/NIAID NIH HHS/United States ; AI070174/AI/NIAID NIH HHS/United States ; }, mesh = {Acinetobacter Infections/microbiology ; Acinetobacter baumannii/*genetics/isolation &amp; purification ; Amino Acid Sequence ; Antigens, Bacterial/chemistry/genetics/immunology/metabolism ; Argentina ; Bacterial Outer Membrane Proteins/chemistry/*genetics/immunology/metabolism ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; *Gene Transfer, Horizontal ; *Genetic Variation ; Hospitals ; Humans ; Molecular Sequence Data ; Ornithine/metabolism ; Phylogeny ; Protein Multimerization ; *Recombination, Genetic ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; }, abstract = {We described previously the presence in Acinetobacter baumannii of a novel outer membrane (OM) protein, CarO, which functions as an L-ornithine OM channel and whose loss was concomitant with increased carbapenem resistance among clonally related nosocomial isolates of this opportunistic pathogen. Here, we describe the existence of extensive genetic diversity at the carO gene within the A. baumannii clinical population. The systematic analysis of carO sequences from A. baumannii isolates obtained from public hospitals in Argentina revealed the existence of four highly polymorphic carO variants among them. Sequence polymorphism between the different A. baumannii CarO variants was concentrated in three well-defined protein regions that superimposed mostly to predicted surface-exposed loops. Polymorphism among A. baumannii CarO variants was manifested in differential electrophoretic mobilities, antigenic properties, abilities to form stable oligomeric structures, and l-ornithine influx abilities through the A. baumannii OM under in vivo conditions. Incongruence between the phylogenies of the clinical A. baumannii isolates analyzed and those of the carO variants they harbor suggests the existence of assortative (entire-gene) carO recombinational exchange within the A. baumannii population. Exchange of carO variants possessing differential characteristics mediated by horizontal gene transfer may constitute an A. baumannii population strategy to survive radically changing environmental conditions, such as the leap from inanimate sources to human hosts and vice versa, persistence in a compromised host, and/or survival in health care facilities.}, }
@article {pmid21764378, year = {2011}, author = {Kissinger, JC and DeBarry, J}, title = {Genome cartography: charting the apicomplexan genome.}, journal = {Trends in parasitology}, volume = {27}, number = {8}, pages = {345-354}, pmid = {21764378}, issn = {1471-5007}, support = {R01 AI068908/AI/NIAID NIH HHS/United States ; R01 AI068908-04/AI/NIAID NIH HHS/United States ; }, mesh = {Apicomplexa/*genetics ; Centromere/genetics ; Chromatin/*genetics ; Chromosome Mapping ; Evolution, Molecular ; Gene Expression Regulation ; Gene Transfer, Horizontal ; *Genes, Protozoan ; *Genome ; Mitochondria/genetics ; Synteny ; Telomere ; }, abstract = {Genes reside in particular genomic contexts that can be mapped at many levels. Historically, 'genetic maps' were used primarily to locate genes. Recent technological advances in the determination of genome sequences have made the analysis and comparison of whole genomes possible and increasingly tractable. What do we see if we shift our focus from gene content (the 'inventory' of genes contained within a genome) to the composition and organization of a genome? This review examines what has been learned about the evolution of the apicomplexan genome as well as the significance and impact of genomic location on our understanding of the eukaryotic genome and parasite biology.}, }
@article {pmid21763465, year = {2011}, author = {Vestrheim, DF and Gaustad, P and Aaberge, IS and Caugant, DA}, title = {Pherotypes of pneumococcal strains co-existing in healthy children.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {11}, number = {7}, pages = {1703-1708}, doi = {10.1016/j.meegid.2011.07.003}, pmid = {21763465}, issn = {1567-7257}, mesh = {Bacterial Proteins/genetics ; Base Sequence ; Child ; Cross-Sectional Studies ; DNA Transformation Competence/genetics ; DNA, Bacterial/genetics ; Genes, Bacterial ; Genetic Variation ; Humans ; Multilocus Sequence Typing ; Nasopharynx/microbiology ; Norway ; Serotyping ; Streptococcus pneumoniae/*classification/*genetics/isolation &amp; purification ; }, abstract = {Genetic diversity in the species Streptococcus pneumoniae is mainly driven by horizontal gene transfer. S. pneumoniae is naturally competent for transformation. Competence is induced by a pheromone termed competence stimulating peptide (CSP) by a quorum-sensing mechanism. Two CSP pherotypes predominate amongst clinical isolates of S. pneumoniae, CSP-1 and CSP-2, with ability to trigger competence in bacteria of the homologue pherotype. Opposing theories on the effect of pherotypes on speciation have been proposed, either as a barrier for intra-pherotype gene transfer, or as a mechanism for fratricide resulting in lysis of non-competent bacterial cells. The aim of the present study was to determine pherotype distribution in strains of S. pneumococci isolated from the nasopharynges of healthy children. We sequenced the locus encoding CSP, comC, in sets of strains obtained from children colonised by multiple pneumococcal strains simultaneously. The impact of pherotype on co-colonisation was determined by comparing the observed distribution of pherotypes in co-colonising strains with the estimated pair-wise probability based on the overall pherotype distribution in the sample set. Five distinct comC alleles were identified, encoding CSP belonging to the two dominating pherotypes, CSP-1 (62.7%) and CSP-2 (37.3%). The observed distribution of pherotypes in sets of co-colonising pneumococcal strains did not differ from the probability estimate. Thus, co-colonisation of S. pneumoniae in healthy children is not restricted by pherotype.}, }
@article {pmid21750254, year = {2011}, author = {Brandvain, Y and Goodnight, C and Wade, MJ}, title = {Horizontal transmission rapidly erodes disequilibria between organelle and symbiont genomes.}, journal = {Genetics}, volume = {189}, number = {1}, pages = {397-404}, pmid = {21750254}, issn = {1943-2631}, support = {R01 GM084238/GM/NIGMS NIH HHS/United States ; R01-GM084238/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Computer Simulation ; Female ; *Gene Transfer, Horizontal ; *Genome ; Host-Parasite Interactions ; Models, Genetic ; Organelles/*genetics ; Symbiosis/*genetics ; }, abstract = {We investigate the generation and decay of interspecific disequilibrium (ID) between organelle and symbiont genomes as a function of the rate of horizontal transmission. We show that rare horizontal transmission greatly diminishes the covariance between organelle and symbiont genomes. This result has two important implications. First, a low level of ID does not indicate low levels of vertical transmission. Second, even with low levels of horizontal transmission, the additive effects of host and symbiont loci will determine the response to selection, while epistatic effects will not be selectable.}, }
@article {pmid21747788, year = {2011}, author = {Poole, K}, title = {Pseudomonas aeruginosa: resistance to the max.}, journal = {Frontiers in microbiology}, volume = {2}, number = {}, pages = {65}, pmid = {21747788}, issn = {1664-302X}, abstract = {Pseudomonas aeruginosa is intrinsically resistant to a variety of antimicrobials and can develop resistance during anti-pseudomonal chemotherapy both of which compromise treatment of infections caused by this organism. Resistance to multiple classes of antimicrobials (multidrug resistance) in particular is increasingly common in P. aeruginosa, with a number of reports of pan-resistant isolates treatable with a single agent, colistin. Acquired resistance in this organism is multifactorial and attributable to chromosomal mutations and the acquisition of resistance genes via horizontal gene transfer. Mutational changes impacting resistance include upregulation of multidrug efflux systems to promote antimicrobial expulsion, derepression of ampC, AmpC alterations that expand the enzyme's substrate specificity (i.e., extended-spectrum AmpC), alterations to outer membrane permeability to limit antimicrobial entry and alterations to antimicrobial targets. Acquired mechanisms contributing to resistance in P. aeruginosa include β-lactamases, notably the extended-spectrum β-lactamases and the carbapenemases that hydrolyze most β-lactams, aminoglycoside-modifying enzymes, and 16S rRNA methylases that provide high-level pan-aminoglycoside resistance. The organism's propensity to grow in vivo as antimicrobial-tolerant biofilms and the occurrence of hypermutator strains that yield antimicrobial resistant mutants at higher frequency also compromise anti-pseudomonal chemotherapy. With limited therapeutic options and increasing resistance will the untreatable P. aeruginosa infection soon be upon us?}, }
@article {pmid21746949, year = {2011}, author = {Kumar, V and Sun, P and Vamathevan, J and Li, Y and Ingraham, K and Palmer, L and Huang, J and Brown, JR}, title = {Comparative genomics of Klebsiella pneumoniae strains with different antibiotic resistance profiles.}, journal = {Antimicrobial agents and chemotherapy}, volume = {55}, number = {9}, pages = {4267-4276}, pmid = {21746949}, issn = {1098-6596}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Aminoglycosides/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Fluoroquinolones/pharmacology ; Genome, Bacterial/*genetics ; Genomics/*methods ; Klebsiella pneumoniae/drug effects/*genetics ; Sulfamethoxazole/pharmacology ; Trimethoprim/pharmacology ; beta-Lactams/pharmacology ; }, abstract = {There is a global emergence of multidrug-resistant (MDR) strains of Klebsiella pneumoniae, a Gram-negative enteric bacterium that causes nosocomial and urinary tract infections. While the epidemiology of K. pneumoniae strains and occurrences of specific antibiotic resistance genes, such as plasmid-borne extended-spectrum β-lactamases (ESBLs), have been extensively studied, only four complete genomes of K. pneumoniae are available. To better understand the multidrug resistance factors in K. pneumoniae, we determined by pyrosequencing the nearly complete genome DNA sequences of two strains with disparate antibiotic resistance profiles, broadly drug-susceptible strain JH1 and strain 1162281, which is resistant to multiple clinically used antibiotics, including extended-spectrum β-lactams, fluoroquinolones, aminoglycosides, trimethoprim, and sulfamethoxazoles. Comparative genomic analysis of JH1, 1162281, and other published K. pneumoniae genomes revealed a core set of 3,631 conserved orthologous proteins, which were used for reconstruction of whole-genome phylogenetic trees. The close evolutionary relationship between JH1 and 1162281 relative to other K. pneumoniae strains suggests that a large component of the genetic and phenotypic diversity of clinical isolates is due to horizontal gene transfer. Using curated lists of over 400 antibiotic resistance genes, we identified all of the elements that differentiated the antibiotic profile of MDR strain 1162281 from that of susceptible strain JH1, such as the presence of additional efflux pumps, ESBLs, and multiple mechanisms of fluoroquinolone resistance. Our study adds new and significant DNA sequence data on K. pneumoniae strains and demonstrates the value of whole-genome sequencing in characterizing multidrug resistance in clinical isolates.}, }
@article {pmid21745695, year = {2012}, author = {Bogicevic, B and Irmler, S and Portmann, R and Meile, L and Berthoud, H}, title = {Characterization of the cysK2-ctl1-cysE2 gene cluster involved in sulfur metabolism in Lactobacillus casei.}, journal = {International journal of food microbiology}, volume = {152}, number = {3}, pages = {211-219}, doi = {10.1016/j.ijfoodmicro.2011.06.015}, pmid = {21745695}, issn = {1879-3460}, mesh = {Carbon-Sulfur Lyases/genetics ; Cysteine/biosynthesis ; Lacticaseibacillus casei/enzymology/*genetics/metabolism ; Methionine/metabolism ; Molecular Sequence Data ; Multigene Family ; *Mutagenesis, Insertional ; Open Reading Frames ; Sulfur/*metabolism ; }, abstract = {The up- and downstream regions of ctl1 and ctl2 that encode a cystathionine lyase were analyzed in various Lactobacillus casei strains. ctl1 and ctl2 were found to be part of a gene cluster encoding two other open reading frames. One of the two open reading frames precedes ctl1 and encodes a putative cysteine synthase. The other open reading frame lies downstream of ctl1 and encodes a putative serine acetyltransferase. The gene cluster is not present in the publicly available genome sequences of L. casei ATCC 334, BL23 and Zhang. Apparently, the gene cluster was acquired by a horizontal gene transfer event and can also be found in other lactic acid bacteria such as Lactobacillus helveticus, Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus. RT-PCR was used to analyze the expression of the gene cluster. Additionally, an mass spectrometry-based selected reaction monitoring method was developed for quantifying Ctl1 in a cell-free extract of lactic acid bacteria. The gene cluster cysK2-ctl1-cysE2 was expressed as single transcript, and expression was down-regulated by cysteine. In addition, cystathionine lyase activity present in cell-free extracts disappeared when L. casei was grown in the presence of cysteine. Whereas the transcript and the gene product of ctl1 protein were found in all studied ctl1(+)L. casei strains, only the transcript but not the protein or cystathionine lyase activity was detected in L. helveticus FAM2888, L. delbrueckii subsp. bulgaricus ATCC 11842 and S. thermophilus FAM17014, which actually possess a homolog of the cysK2-ctl1-cysE2 gene cluster.}, }
@article {pmid21745255, year = {2012}, author = {Findlay, J and Hamouda, A and Dancer, SJ and Amyes, SG}, title = {Rapid acquisition of decreased carbapenem susceptibility in a strain of Klebsiella pneumoniae arising during meropenem therapy.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {18}, number = {2}, pages = {140-146}, doi = {10.1111/j.1469-0691.2011.03515.x}, pmid = {21745255}, issn = {1469-0691}, mesh = {Anti-Bacterial Agents/*administration &amp; dosage/pharmacology ; Bacterial Outer Membrane Proteins/analysis/chemistry ; Catheter-Related Infections/drug therapy/microbiology ; Conjugation, Genetic ; DNA, Bacterial/genetics ; Electrophoresis, Gel, Pulsed-Field ; Ertapenem ; Gene Expression Profiling ; Gene Transfer, Horizontal ; Genotype ; Humans ; Klebsiella Infections/*drug therapy/*microbiology ; Klebsiella pneumoniae/classification/*drug effects/genetics/isolation &amp; purification ; Meropenem ; Microbial Sensitivity Tests ; Molecular Typing ; Molecular Weight ; Mutation ; Plasmids ; Reverse Transcriptase Polymerase Chain Reaction ; Selection, Genetic ; Thienamycins/*administration &amp; dosage/pharmacology ; Urinary Tract Infections/drug therapy/microbiology ; Urine/microbiology ; *beta-Lactam Resistance ; beta-Lactams/pharmacology ; }, abstract = {A strain of Klebsiella pneumoniae (K1) was isolated from a catheterized patient with a urinary tract infection. The patient was subsequently treated with meropenem, after which K. pneumoniae (K2) was once again isolated from the patient's urine. Susceptibility testing showed that strain K1 was fully susceptible to carbapenem antibiotics with the exception of ertapenem, to which it exhibited intermediate resistance, whilst K2 was resistant to ertapenem and meropenem. From pulsed-field gel electrophoresis profiling both strains exhibited identical banding patterns. Both contained CTX-M-15, OXA-1, SHV-1 and TEM-1 β-lactamase genes following PCR analyses. Outer membrane protein analysis demonstrated that K1 and K2 lacked an OMP of c. 40 kDa, with an additional OMP of c. 36 kDa missing from K2. Mutation studies showed that the K2 OMP phenotype could be selected by single-step carbapenem-resistant mutants of K1. Expression of transcriptional activator ramA and efflux pump component gene acrA were up-regulated in both strains by RT-PCR. Neither strain expressed ompK35, but ompK36 was found in both. Sequence analysis revealed gene sequences of ompK35, ompK36 and ramR in both strains; notably, ramR contained a mutation resulting in a premature stop codon. Transconjugation studies demonstrated transfer of a plasmid into E. coli encoding the CTX-M-15, TEM-1 and OXA-1 β-lactamases. We concluded that the carbapenem-resistant phenotype observed from this patient was attributable to a combination of CTX-M-15 β-lactamase, up-regulated efflux and altered outer membrane permeability, and that K2 arose from K1 as a direct result of meropenem therapy.}, }
@article {pmid21742987, year = {2011}, author = {Alverson, AJ and Rice, DW and Dickinson, S and Barry, K and Palmer, JD}, title = {Origins and recombination of the bacterial-sized multichromosomal mitochondrial genome of cucumber.}, journal = {The Plant cell}, volume = {23}, number = {7}, pages = {2499-2513}, pmid = {21742987}, issn = {1532-298X}, support = {F32 GM080079/GM/NIGMS NIH HHS/United States ; R01 GM070612/GM/NIGMS NIH HHS/United States ; 1F32GM080079-01A1/GM/NIGMS NIH HHS/United States ; R01-GM-70612/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Sequence ; Chromosome Mapping ; Chromosomes, Plant/*genetics/*ultrastructure ; Cucumis sativus/*genetics ; DNA, Mitochondrial/analysis/genetics ; DNA, Plant/analysis/genetics ; Gene Transfer, Horizontal ; Genes, Plant ; *Genome, Mitochondrial ; *Genome, Plant ; Introns/genetics ; Molecular Sequence Data ; *Recombination, Genetic ; Repetitive Sequences, Nucleic Acid ; }, abstract = {Members of the flowering plant family Cucurbitaceae harbor the largest known mitochondrial genomes. Here, we report the 1685-kb mitochondrial genome of cucumber (Cucumis sativus). We help solve a 30-year mystery about the origins of its large size by showing that it mainly reflects the proliferation of dispersed repeats, expansions of existing introns, and the acquisition of sequences from diverse sources, including the cucumber nuclear and chloroplast genomes, viruses, and bacteria. The cucumber genome has a novel structure for plant mitochondria, mapping as three entirely or largely autonomous circular chromosomes (lengths 1556, 84, and 45 kb) that vary in relative abundance over a twofold range. These properties suggest that the three chromosomes replicate independently of one another. The two smaller chromosomes are devoid of known functional genes but nonetheless contain diagnostic mitochondrial features. Paired-end sequencing conflicts reveal differences in recombination dynamics among chromosomes, for which an explanatory model is developed, as well as a large pool of low-frequency genome conformations, many of which may result from asymmetric recombination across intermediate-sized and sometimes highly divergent repeats. These findings highlight the promise of genome sequencing for elucidating the recombinational dynamics of plant mitochondrial genomes.}, }
@article {pmid21741306, year = {2012}, author = {Danne, JC and Gornik, SG and Waller, RF}, title = {An assessment of vertical inheritance versus endosymbiont transfer of nucleus-encoded genes for mitochondrial proteins following tertiary endosymbiosis in Karlodinium micrum.}, journal = {Protist}, volume = {163}, number = {1}, pages = {76-90}, doi = {10.1016/j.protis.2011.03.002}, pmid = {21741306}, issn = {1618-0941}, mesh = {Cell Nucleus/*genetics ; Dinoflagellida/classification/*genetics/physiology ; Gene Transfer, Horizontal ; Mitochondrial Proteins/*genetics ; Molecular Sequence Data ; Phylogeny ; Plastids/genetics ; Protozoan Proteins/*genetics ; Rhodophyta/*genetics/physiology ; *Symbiosis ; }, abstract = {Most photosynthetic dinoflagellates harbour a red alga-derived secondary plastid. In the dinoflagellate Karlodinium micrum, this plastid was replaced by a subsequent endosymbiosis, resulting in a tertiary plastid derived from a haptophyte. Evolution of endosymbionts entails substantial relocation of endosymbiont genes to the host nucleus: a process called endosymbiotic gene transfer (EGT). In K. micrum, numerous plastid genes from the haptophyte nucleus are found in the host nucleus, providing evidence for EGT in this system. In other cases of endosymbiosis, notably ancient primary endosymbiotic events, EGT has been inferred to contribute to remodeling of other cell functions by expression of proteins in compartments other than the endosymbiont from which they derived. K. micrum provides a more recently derived endosymbiotic system to test for evidence of EGT and gain of function in non-plastid compartments. In this study, we test for gain of haptophyte-derived proteins for mitochondrial function in K. micrum. Using molecular phylogenies we have analysed whether nucleus-encoded mitochondrial proteins were inherited by EGT from the haptophyte endosymbiont, or vertically inherited from the dinoflagellate host lineage. From this dataset we found no evidence of haptophyte-derived mitochondrial genes, and the only cases of non-vertical inheritance were genes derived from lateral gene transfer events.}, }
@article {pmid21740576, year = {2011}, author = {Rhodes, ME and Spear, JR and Oren, A and House, CH}, title = {Differences in lateral gene transfer in hypersaline versus thermal environments.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {199}, pmid = {21740576}, issn = {1471-2148}, mesh = {Archaea/classification/*genetics/metabolism ; *Ecosystem ; *Gene Transfer, Horizontal ; Hot Temperature ; Molecular Sequence Data ; Phylogeny ; Sodium Chloride/metabolism ; Transformation, Genetic ; Water/analysis ; Water Microbiology ; }, abstract = {BACKGROUND: The role of lateral gene transfer (LGT) in the evolution of microorganisms is only beginning to be understood. While most LGT events occur between closely related individuals, inter-phylum and inter-domain LGT events are not uncommon. These distant transfer events offer potentially greater fitness advantages and it is for this reason that these "long distance" LGT events may have significantly impacted the evolution of microbes. One mechanism driving distant LGT events is microbial transformation. Theoretically, transformative events can occur between any two species provided that the DNA of one enters the habitat of the other. Two categories of microorganisms that are well-known for LGT are the thermophiles and halophiles.<br><br>RESULTS: We identified potential inter-class LGT events into both a thermophilic class of Archaea (Thermoprotei) and a halophilic class of Archaea (Halobacteria). We then categorized these LGT genes as originating in thermophiles and halophiles respectively. While more than 68% of transfer events into Thermoprotei taxa originated in other thermophiles, less than 11% of transfer events into Halobacteria taxa originated in other halophiles.<br><br>CONCLUSIONS: Our results suggest that there is a fundamental difference between LGT in thermophiles and halophiles. We theorize that the difference lies in the different natures of the environments. While DNA degrades rapidly in thermal environments due to temperature-driven denaturization, hypersaline environments are adept at preserving DNA. Furthermore, most hypersaline environments, as topographical minima, are natural collectors of cellular debris. Thus halophiles would in theory be exposed to a greater diversity and quantity of extracellular DNA than thermophiles.}, }
@article {pmid21740557, year = {2011}, author = {Sun, G and Yang, Z and Kosch, T and Summers, K and Huang, J}, title = {Evidence for acquisition of virulence effectors in pathogenic chytrids.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {195}, pmid = {21740557}, issn = {1471-2148}, mesh = {Amphibians/*microbiology ; Animals ; Chytridiomycota/chemistry/classification/*genetics/pathogenicity ; Fungal Proteins/*genetics/metabolism ; *Gene Transfer, Horizontal ; Mycoses/microbiology/*veterinary ; Oomycetes/genetics ; Phylogeny ; Serine Proteases/genetics/metabolism ; Virulence Factors/*genetics/metabolism ; }, abstract = {BACKGROUND: The decline in amphibian populations across the world is frequently linked to the infection of the chytrid fungus Batrachochytrium dendrobatidis (Bd). This is particularly perplexing because Bd was only recently discovered in 1999 and no chytrid fungus had previously been identified as a vertebrate pathogen.<br><br>RESULTS: In this study, we show that two large families of known virulence effector genes, crinkler (CRN) proteins and serine peptidases, were acquired by Bd from oomycete pathogens and bacteria, respectively. These two families have been duplicated after their acquisition by Bd. Additional selection analyses indicate that both families evolved under strong positive selection, suggesting that they are involved in the adaptation of Bd to its hosts.<br><br>CONCLUSIONS: We propose that the acquisition of virulence effectors, in combination with habitat disruption and climate change, may have driven the Bd epidemics and the decline in amphibian populations. This finding provides a starting point for biochemical investigations of chytridiomycosis.}, }
@article {pmid21737495, year = {2011}, author = {Lee, HJ and Kim, JM and Lee, SH and Park, M and Lee, K and Madsen, EL and Jeon, CO}, title = {Gentisate 1,2-dioxygenase, in the third naphthalene catabolic gene cluster of Polaromonas naphthalenivorans CJ2, has a role in naphthalene degradation.}, journal = {Microbiology (Reading, England)}, volume = {157}, number = {Pt 10}, pages = {2891-2903}, doi = {10.1099/mic.0.049387-0}, pmid = {21737495}, issn = {1465-2080}, mesh = {Bacterial Proteins/chemistry/genetics/*metabolism ; Biodegradation, Environmental ; Comamonadaceae/chemistry/enzymology/genetics/*metabolism ; Dioxygenases/chemistry/genetics/*metabolism ; Gentisates/metabolism ; Kinetics ; *Multigene Family ; Naphthalenes/*metabolism ; }, abstract = {Polaromonas naphthalenivorans strain CJ2 metabolizes naphthalene via the gentisate pathway and has recently been shown to carry a third copy of gentisate 1,2-dioxygenase (GDO), encoded by nagI3, within a previously uncharacterized naphthalene catabolic gene cluster. The role of this cluster (especially nagI3) in naphthalene metabolism of strain CJ2 was investigated by documenting patterns in regulation, transcription and enzyme activity. Transcriptional analysis of wild-type cells showed the third cluster to be polycistronic and that nagI3 was expressed at a relatively high level. Individual knockout mutants of all three nagI genes were constructed and their influence on both GDO activity and cell growth was evaluated. Of the three knockout strains, CJ2ΔnagI3 showed severely diminished GDO activity and grew slowest on aromatic substrates. These observations are consistent with the hypothesis that nagI3 may prevent toxic intracellular levels of gentisate from accumulating in CJ2 cells. All three nagI genes from strain CJ2 were cloned into Escherichia coli: the nagI2 and nagI3 genes were successfully overexpressed. The subunit mass of the GDOs were ~36-39 kDa, and their structures were deduced to be dimeric. The K(m) values of NagI2 and NagI3 were 31 and 10 µM, respectively, indicating that the higher affinity of NagI3 for gentisate may protect the wild-type cells from gentisate toxicity. These results provide clues for explaining why the third gene cluster, particularly the nagI3 gene, is important in strain CJ2. The organization of genes in the third gene cluster matched that of clusters in Polaromonas sp. JS666 and Leptothrix cholodnii SP-6. While horizontal gene transfer (HGT) is one hypothesis for explaining this genetic motif, gene duplication within the ancestral lineage is equally valid. The HGT hypothesis was discounted by noting that the nagI3 allele of strain CJ2 did not share high sequence identity with its homologues in Polaromonas sp. JS666 and L. cholodnii SP-6.}, }
@article {pmid21733190, year = {2011}, author = {Casas, V and Sobrepeña, G and Rodriguez-Mueller, B and Ahtye, J and Maloy, SR}, title = {Bacteriophage-encoded shiga toxin gene in atypical bacterial host.}, journal = {Gut pathogens}, volume = {3}, number = {1}, pages = {10}, pmid = {21733190}, issn = {1757-4749}, abstract = {BACKGROUND: Contamination from fecal bacteria in recreational waters is a major health concern since bacteria capable of causing human disease can be found in animal feces. The Dog Beach area of Ocean Beach in San Diego, California is a beach prone to closures due to high levels of fecal indicator bacteria (FIB). A potential source of these FIB could be the canine feces left behind by owners who do not clean up after their pets. We tested this hypothesis by screening the DNA isolated from canine feces for the bacteriophage-encoded stx gene normally found in the virulent strains of the fecal bacterium Escherichia coli.<br><br>RESULTS: Twenty canine fecal samples were collected, processed for total and bacterial fraction DNA, and screened by PCR for the stx gene. The stx gene was detected in the total and bacterial fraction DNA of one fecal sample. Bacterial isolates were then cultivated from the stx-positive fecal sample. Eighty nine of these canine fecal bacterial isolates were screened by PCR for the stx gene. The stx gene was detected in five of these isolates. Sequencing and phylogenetic analyses of 16S rRNA gene PCR products from the canine fecal bacterial isolates indicated that they were Enterococcus and not E. coli.<br><br>CONCLUSIONS: The bacteriophage-encoded stx gene was found in multiple species of bacteria cultivated from canine fecal samples gathered at the shoreline of the Dog Beach area of Ocean Beach in San Diego, California. The canine fecal bacteria carrying the stx gene were not the typical E. coli host and were instead identified through phylogenetic analyses as Enterococcus. This suggests a large degree of horizontal gene transfer of exotoxin genes in recreational waters.}, }
@article {pmid21732292, year = {2011}, author = {Soares, SC and Dorella, FA and Pacheco, LG and Hirata, R and Mattos-Guaraldi, AL and Azevedo, V and Miyoshi, A}, title = {Plasticity of Corynebacterium diphtheriae pathogenicity islands revealed by PCR.}, journal = {Genetics and molecular research : GMR}, volume = {10}, number = {2}, pages = {1290-1294}, doi = {10.4238/vol10-2gmr1211}, pmid = {21732292}, issn = {1676-5680}, mesh = {Base Sequence ; Corynebacterium diphtheriae/genetics/*pathogenicity ; DNA Primers ; Genes, Bacterial ; Polymerase Chain Reaction/*methods ; Virulence/*genetics ; }, abstract = {Despite the existence of a vaccine against diphtheria, this disease remains endemic and is reemerging in several regions due to many factors, including variations in genes coding for virulence factors. One common feature of virulence factors is their high concentration in pathogenicity islands (PAIs), very unstable regions acquired via horizontal gene transfer, which has lead to the emergence of various bacterial pathogens. The 13 putative PAIs in Corynebacterium diphtheriae NCTC 13129 and the reemergence of this disease point to the great variability in the PAIs of this species, which may reflect on bacterial life style and physiological versatility. We investigated the relationships between the large number of PAIs in C. diphtheriae and the possible implications of their plasticity in virulence. The GenoFrag software was used to design primers to analyze the genome plasticity of two pathogenicity islands of the reference strain (PiCds 3 and 8) in 11 different strains. We found that PiCd 3 was absent in only two strains, showing genes playing putative important roles in virulence and that only one strain harbored PiCd 8, due to its location in a putative "hotspot" for horizontal gene transfer events.}, }
@article {pmid21732034, year = {2011}, author = {Deng, MR and Guo, J and Li, X and Zhu, CH and Zhu, HH}, title = {Granaticins and their biosynthetic gene cluster from Streptomyces vietnamensis: evidence of horizontal gene transfer.}, journal = {Antonie van Leeuwenhoek}, volume = {100}, number = {4}, pages = {607-617}, doi = {10.1007/s10482-011-9615-9}, pmid = {21732034}, issn = {1572-9699}, mesh = {Anti-Bacterial Agents/*biosynthesis/chemistry ; Bacterial Proteins/*genetics/metabolism ; Base Sequence ; Biosynthetic Pathways ; Cloning, Molecular ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; *Multigene Family ; Naphthoquinones/chemistry/metabolism ; Open Reading Frames ; Phylogeny ; Streptomyces/chemistry/classification/*genetics/*metabolism ; }, abstract = {Streptomyces vietnamensis, a recently designated species isolated from tropical forest soil, was found to be a new granaticin producer. The granaticin biosynthetic gene cluster (gra) and flanking genes from S. vietnamensis were cloned and sequenced by a sequential cloning strategy. All biosynthetic genes were found as expected. The high overall homology of the gra cluster from S. vietnamensis to that of Streptomyces violaceoruber Tü22 indicated a recent common ancestor of the two clusters. However, a flanking gene orf35 was missing from the gra cluster of S. vietnamensis, and high frequency of insertions and deletions of short fragment (shorter than 63 bp) were observed throughout the sequenced region compared to that of S. violaceoruber Tü22. These revealed a rapid evolution of the gra cluster and suggested that small insertions and deletions might be one of the basic evolution mechanisms for streptomycete genomes. The phylogenetic incongruence between 16S rDNA and the gra cluster and the scattered distribution of the granaticin producers within Streptomyces implicated horizontal gene transfer (HGT) being involved in the gra cluster dispersion. The remnants of orf35 found in S. vietnamensis present a scenario on how the antibiotic gene clusters evolved after HGT. The contemporary gra cluster residing in S. vietnamensis could be interpreted as a combination of HGT and highly variable vertical transmission.}, }
@article {pmid21731720, year = {2011}, author = {Higashi, DL and Biais, N and Weyand, NJ and Agellon, A and Sisko, JL and Brown, LM and So, M}, title = {N. elongata produces type IV pili that mediate interspecies gene transfer with N. gonorrhoeae.}, journal = {PloS one}, volume = {6}, number = {6}, pages = {e21373}, pmid = {21731720}, issn = {1932-6203}, support = {R01 AI068033/AI/NIAID NIH HHS/United States ; S10 RR024728/RR/NCRR NIH HHS/United States ; S10 RR024728-01A1/RR/NCRR NIH HHS/United States ; AI068033/AI/NIAID NIH HHS/United States ; }, mesh = {Base Sequence ; DNA, Bacterial/metabolism ; Drug Resistance, Bacterial/drug effects ; Epithelial Cells/drug effects/microbiology/ultrastructure ; Fimbriae, Bacterial/drug effects/genetics/*metabolism/ultrastructure ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/*genetics ; Humans ; Mutation/genetics ; Neisseria elongata/drug effects/genetics/*metabolism/ultrastructure ; Neisseria gonorrhoeae/drug effects/*genetics/ultrastructure ; Rifampin/pharmacology ; Species Specificity ; Surface Properties/drug effects ; Transcription, Genetic/drug effects ; Transformation, Bacterial/drug effects/genetics ; }, abstract = {The genus Neisseria contains at least eight commensal and two pathogenic species. According to the Neisseria phylogenetic tree, commensals are basal to the pathogens. N. elongata, which is at the opposite end of the tree from N. gonorrhoeae, has been observed to be fimbriated, and these fimbriae are correlated with genetic competence in this organism. We tested the hypothesis that the fimbriae of N. elongata are Type IV pili (Tfp), and that Tfp functions in genetic competence. We provide evidence that the N. elongata fimbriae are indeed Tfp. Tfp, as well as the DNA Uptake Sequence (DUS), greatly enhance N. elongata DNA transformation. Tfp allows N. elongata to make intimate contact with N. gonorrhoeae and to mediate the transfer of antibiotic resistance markers between these two species. We conclude that Tfp functional for genetic competence is a trait of a commensal member of the Neisseria genus. Our findings provide a mechanism for the horizontal gene transfer that has been observed among Neisseria species.}, }
@article {pmid21731695, year = {2011}, author = {Wang, D and Wang, H and Zhou, Y and Zhang, Q and Zhang, F and Du, P and Wang, S and Chen, C and Kan, B}, title = {Genome sequencing reveals unique mutations in characteristic metabolic pathways and the transfer of virulence genes between V. mimicus and V. cholerae.}, journal = {PloS one}, volume = {6}, number = {6}, pages = {e21299}, pmid = {21731695}, issn = {1932-6203}, mesh = {Alleles ; Base Sequence ; DNA, Circular/genetics ; Evolution, Molecular ; Fermentation/genetics ; Gene Deletion ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/genetics ; Genomic Islands/genetics ; Metabolic Networks and Pathways/*genetics ; Molecular Sequence Data ; Mutation/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; Species Specificity ; Sucrose/metabolism ; Vibrio cholerae/*genetics/metabolism/*pathogenicity ; Vibrio mimicus/*genetics/metabolism/pathogenicity ; Virulence/genetics ; }, abstract = {Vibrio mimicus, the species most similar to V. cholerae, is a microbe present in the natural environmental and sometimes causes diarrhea and internal infections in humans. It shows similar phenotypes to V. cholerae but differs in some biochemical characteristics. The molecular mechanisms underlying the differences in biochemical metabolism between V. mimicus and V. cholerae are currently unclear. Several V. mimicus isolates have been found that carry cholera toxin genes (ctxAB) and cause cholera-like diarrhea in humans. Here, the genome of the V. mimicus isolate SX-4, which carries an intact CTX element, was sequenced and annotated. Analysis of its genome, together with those of other Vibrio species, revealed extensive differences within the Vibrionaceae. Common mutations in gene clusters involved in three biochemical metabolism pathways that are used for discrimination between V. mimicus and V. cholerae were found in V. mimicus strains. We also constructed detailed genomic structures and evolution maps for the general types of genomic drift associated with pathogenic characters in polysaccharides, CTX elements and toxin co-regulated pilus (TCP) gene clusters. Overall, the whole-genome sequencing of the V. mimicus strain carrying the cholera toxin gene provides detailed information for understanding genomic differences among Vibrio spp. V. mimicus has a large number of diverse gene and nucleotide differences from its nearest neighbor, V. cholerae. The observed mutations in the characteristic metabolism pathways may indicate different adaptations to different niches for these species and may be caused by ancient events in evolution before the divergence of V. cholerae and V. mimicus. Horizontal transfers of virulence-related genes from an uncommon clone of V. cholerae, rather than the seventh pandemic strains, have generated the pathogenic V. mimicus strain carrying cholera toxin genes.}, }
@article {pmid21731639, year = {2011}, author = {Li, Y and Zheng, H and Liu, Y and Jiang, Y and Xin, J and Chen, W and Song, Z}, title = {The complete genome sequence of Mycoplasma bovis strain Hubei-1.}, journal = {PloS one}, volume = {6}, number = {6}, pages = {e20999}, pmid = {21731639}, issn = {1932-6203}, mesh = {Base Sequence ; Chromosomes, Bacterial/genetics ; DNA Repair/genetics ; DNA Replication/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/*genetics ; Molecular Sequence Data ; Mutagenesis, Insertional/genetics ; Mycoplasma bovis/*genetics/metabolism/pathogenicity ; Phylogeny ; Protein Biosynthesis/genetics ; Pseudogenes/genetics ; Replication Origin/genetics ; Sequence Homology, Nucleic Acid ; Tandem Repeat Sequences/genetics ; Transcription, Genetic ; Virulence/genetics ; }, abstract = {Infection by Mycoplasma bovis (M. bovis) can induce diseases, such as pneumonia and otitis media in young calves and mastitis and arthritis in older animals. Here, we report the finished and annotated genome sequence of M. bovis strain Hubei-1, a strain isolated in 2008 that caused calf pneumonia on a Chinese farm. The genome of M. bovis strain Hubei-1 contains a single circular chromosome of 953,114 bp with a 29.37% GC content. We identified 803 open reading frames (ORFs) that occupy 89.5% of the genome. While 34 ORFs were Hubei-1 specific, 662 ORFs had orthologs in the M. bovis type strain PG45 genome. Genome analysis validated lateral gene transfer between M. bovis and the Mycoplasma mycoides subspecies mycoides, while phylogenetic analysis found that the closest M. bovis neighbor is Mycoplasma agalactiae. Glycerol may be the main carbon and energy source of M. bovis, and most of the biosynthesis pathways were incomplete. We report that 47 lipoproteins, 12 extracellular proteins and 18 transmembrane proteins are phase-variable and may help M. bovis escape the immune response. Besides lipoproteins and phase-variable proteins, genomic analysis found two possible pathogenicity islands, which consist of four genes and 11 genes each, and several other virulence factors including hemolysin, lipoate protein ligase, dihydrolipoamide dehydrogenase, extracellular cysteine protease and 5'-nucleotidase.}, }
@article {pmid21728847, year = {2011}, author = {Lubbers, BV and Peterson, GJ and Narayanan, SK and Havel, JA and Coetzee, JF and Apley, MD}, title = {Effects of two simulated oxytetracycline dosing regimens on horizontal transfer of antimicrobial resistance plasmids in an in vitro pharmacodynamic model.}, journal = {American journal of veterinary research}, volume = {72}, number = {7}, pages = {877-883}, doi = {10.2460/ajvr.72.7.877}, pmid = {21728847}, issn = {1943-5681}, mesh = {Anti-Bacterial Agents/administration &amp; dosage/*pharmacokinetics/pharmacology ; Bacterial Proteins/genetics/metabolism ; Conjugation, Genetic ; Escherichia coli/drug effects/*genetics ; *Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Oxytetracycline/administration &amp; dosage/*pharmacokinetics/pharmacology ; *Plasmids ; Salmonella typhimurium/drug effects/*genetics ; Selection, Genetic ; *Tetracycline Resistance ; }, abstract = {OBJECTIVE: To evaluate the impact of oxytetracycline exposure on horizontal transfer of an antimicrobial resistance plasmid.<br><br>SAMPLE: Populations of Salmonella enterica subsp enterica serovar Typhimurium and Escherichia coli.<br><br>PROCEDURES: Mixed populations of plasmid donor (Salmonella Typhimurium) and recipient (E coli) bacteria were assigned to 1 of 2 simulated oxytetracycline dosing regimens (high peak concentration-short elimination half-life [HC-SHL] or low peak concentration-long elimination half-life [LC-LHL]) or served as untreated control replicates. Donor, recipient, and transconjugant (E coli that acquired the plasmid) bacteria populations were quantified at 12, 24, and 36 hours after oxytetracycline administration by use of culture on selective bacterial growth media.<br><br>RESULTS: The ratio of transconjugant to donor bacteria was significantly reduced in the oxytetracycline-exposed replicates, compared with the ratio for the control replicates, at 12 hours. At 24 and 36 hours, results for the HC-SHL regimens were not significantly different from results for the respective control replicates, and results for the LC-LHL regimens also were not significantly different from results for the respective control replicates. The oxytetracycline concentration at these time points (12 hours in the HC-SHL regimen and all 3 time points in the LC-LHL regimen) were in excess of the minimum inhibitory concentration of the recipient bacteria.<br><br>Transfer of antimicrobial resistance plasmids may be suppressed in vitro by oxytetracycline exposure at concentrations greater than the minimum inhibitory concentration of the recipient bacteria.}, }
@article {pmid21727640, year = {2011}, author = {Chattaway, MA and Dallman, T and Okeke, IN and Wain, J}, title = {Enteroaggregative E. coli O104 from an outbreak of HUS in Germany 2011, could it happen again?.}, journal = {Journal of infection in developing countries}, volume = {5}, number = {6}, pages = {425-436}, doi = {10.3855/jidc.2166}, pmid = {21727640}, issn = {1972-2680}, mesh = {Bacteriological Techniques/methods ; *Disease Outbreaks ; Escherichia coli/*isolation &amp; purification ; Escherichia coli Infections/*epidemiology/*microbiology ; Gene Transfer, Horizontal ; Germany/epidemiology ; Hemolytic-Uremic Syndrome/*epidemiology/*microbiology ; Humans ; Sentinel Surveillance ; Virulence Factors/genetics ; }, abstract = {Enterohaemorrhagic E. coli (EHEC) particularly O157:H7 (Sequence type 11 complex), is the best documented and most well-known of E. coli that cause diarrhoea. The importance of EHEC lies in the severity of disease. Outbreaks can infect thousands of people causing bloody diarrhoea and haemolytic uremic syndrome (HUS) that in turn can result in protracted illness or even death. The ability of EHEC to colonise the human gut is normally associated with the presence of genes from another group of diarrhoeagenic E. coli, the enteropathogenic E. coli (EPEC), via the locus of enterocyte effacement. However, the massive outbreak in Germany was caused by an EHEC which had acquired virulence genes from yet another group of diarrhoeagenic E. coli, the enteroaggregative E. coli (EAEC). In reality EAEC is probably the most common bacterial cause of diarrhoea but is not identified in most diagnostic laboratories. This outbreak emphasises the importance of being able to detect all diarrhoeagenic E. coli and not to focus on E. coli O157:H7 alone. Routine surveillance systems for EAEC, a once ignored global pathogen, would go a long way to reaching this goal. This review describes methods for identifying non-O157 EHEC and describes the key genetic features of EHEC and EAEC. Our aim is to provide information for laboratories and policy makers which enables them to make informed decisions about the best methods available for detecting newly emergent strains of diarrhoeagenic E. coli.}, }
@article {pmid21722725, year = {2011}, author = {Pan, A and Chanda, I and Chakrabarti, J}, title = {Analysis of the genome and proteome composition of Bdellovibrio bacteriovorus: indication for recent prey-derived horizontal gene transfer.}, journal = {Genomics}, volume = {98}, number = {3}, pages = {213-222}, doi = {10.1016/j.ygeno.2011.06.007}, pmid = {21722725}, issn = {1089-8646}, mesh = {Bacterial Proteins/*genetics/metabolism ; Bdellovibrio/*genetics/metabolism ; Codon ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Multivariate Analysis ; Phylogeny ; Protein Biosynthesis ; Protein Structure, Secondary ; Proteome/*genetics ; }, abstract = {The genome/proteome composition of Bdellovibrio bacteriovorus, the predatory microorganism that preys on other Gram-negative bacteria, has been analyzed. The study elucidates that translational selection plays a major role in genome compositional variation with higher intensity compared to other deltaproteobacteria. Other sources of variations having relatively minor contributions are local GC-bias, horizontal gene transfer and strand-specific mutational bias. The study identifies a group of AT-rich genes with distinct codon composition that is presumably acquired by Bdellovibrio recently from Gram-negative prey-bacteria other than deltaproteobacteria. The proteome composition of this species is influenced by various physico-chemical factors, viz, alcoholicity, residue-charge, aromaticity and hydropathy. Cell-wall-surface-anchor-family (CSAPs) and transporter proteins with distinct amino acid composition and specific secondary-structure also contribute notably to proteome compositional variation. CSAPs, which are low molecular-weight, outer-membrane proteins with highly disordered secondary-structure, have preference toward polar-uncharged residues and cysteine that presumably help in prey-predator interaction by providing particular bonds of attachment.}, }
@article {pmid21722203, year = {2011}, author = {Bellanger, X and Morel, C and Gonot, F and Puymege, A and Decaris, B and Guédon, G}, title = {Site-specific accretion of an integrative conjugative element together with a related genomic island leads to cis mobilization and gene capture.}, journal = {Molecular microbiology}, volume = {81}, number = {4}, pages = {912-925}, doi = {10.1111/j.1365-2958.2011.07737.x}, pmid = {21722203}, issn = {1365-2958}, mesh = {*Conjugation, Genetic ; Gene Transfer, Horizontal ; *Genomic Islands ; *Recombination, Genetic ; Streptococcus thermophilus/*genetics ; }, abstract = {Genomic islands, flanked by attachment sites, devoid of conjugation and recombination modules and related to the integrative and conjugative element (ICE) ICESt3, were previously found in Streptococcus thermophilus. Here, we show that ICESt3 transfers to a recipient harbouring a similar engineered genomic island, CIMEL3catR3, and integrates by site-specific recombination into its attachment sites, leading to their accretion. The resulting composite island can excise, showing that ICESt3 mobilizes CIMEL3catR3, in cis. ICESt3, CIMEL3catR3, and the whole composite element can transfer from the strain harbouring the composite structure. The ICESt3 transfer to a recipient bearing CIMEL3catR3, can also lead to retromobilization, i.e. its capture by the donor. This is the first demonstration of specific conjugative mobilization of a genomic island in cis and the first report of ICE-mediated retromobilization. CIMEL3catR3, would be the prototype of a novel class of non-autonomous mobile elements (CIMEs: CIs mobilizable elements), which hijack the recombination and conjugation machinery of related ICEs to excise, transfer and integrate. Few genome analyses have shown that CIMEs could be widespread and have revealed internal repeats that could result from accretions in numerous genomic islands, suggesting that accretion and cis mobilization have a key role in evolution of genomic islands.}, }
@article {pmid21722146, year = {2011}, author = {Cantón, R and Morosini, MI}, title = {Emergence and spread of antibiotic resistance following exposure to antibiotics.}, journal = {FEMS microbiology reviews}, volume = {35}, number = {5}, pages = {977-991}, doi = {10.1111/j.1574-6976.2011.00295.x}, pmid = {21722146}, issn = {1574-6976}, mesh = {Anti-Bacterial Agents/pharmacokinetics/pharmacology/*therapeutic use ; Bacteria/*drug effects/genetics ; Bacterial Infections/*drug therapy/microbiology ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Humans ; *Mutation ; *Selection, Genetic ; Time Factors ; }, abstract = {Within a susceptible wild-type population, a small fraction of cells, even <10(-9) , is not affected when challenged by an antimicrobial agent. This subpopulation has mutations that impede antimicrobial action, allowing their selection during clinical treatment. Emergence of resistance occurs in the frame of a selective compartment termed a mutant selection window (MSW). The lower margin corresponds to the minimum inhibitory concentration of the susceptible cells, whereas the upper boundary, named the mutant prevention concentration (MPC), restricts the growth of the entire population, including that of the resistant mutants. By combining pharmacokinetic/pharmacodynamic concepts and an MPC strategy, the selection of resistant mutants can be limited. Early treatment avoiding an increase of the inoculum size as well as a regimen restricting the time within the MSW can reduce the probability of emergence of the resistant mutants. Physiological and, possibly, genetic adaptation in biofilms and a high proportion of mutator clones that may arise during chronic infections influence the emergence of resistant mutants. Moreover, a resistant population can emerge in a specific selective compartment after acquiring a resistance trait by horizontal gene transfer, but this may also be avoided to some extent when the MPC is reached. Known linkage between antimicrobial use and resistance should encourage actions for the design of antimicrobial treatment regimens that minimize the emergence of resistance. Emergence of a resistant bacterial subpopulation within a susceptible wild-type population can be restricted with a regimen using an antibiotic dose that is sufficiently high to inhibit both susceptible and resistant bacteria.}, }
@article {pmid21721943, year = {2011}, author = {Sommer, RJ and Streit, A}, title = {Comparative genetics and genomics of nematodes: genome structure, development, and lifestyle.}, journal = {Annual review of genetics}, volume = {45}, number = {}, pages = {1-20}, doi = {10.1146/annurev-genet-110410-132417}, pmid = {21721943}, issn = {1545-2948}, mesh = {Animals ; Biological Evolution ; Female ; Gene Expression Regulation, Developmental ; Gene Transfer, Horizontal ; Genetic Variation ; *Genome, Helminth ; *Life Cycle Stages ; Male ; Nematoda/classification/*genetics/growth &amp; development/pathogenicity ; Phylogeny ; Species Specificity ; }, abstract = {Nematodes are found in virtually all habitats on earth. Many of them are parasites of plants and animals, including humans. The free-living nematode, Caenorhabditis elegans, is one of the genetically best-studied model organisms and was the first metazoan whose genome was fully sequenced. In recent years, the draft genome sequences of another six nematodes representing four of the five major clades of nematodes were published. Compared to mammalian genomes, all these genomes are very small. Nevertheless, they contain almost the same number of genes as the human genome. Nematodes are therefore a very attractive system for comparative genetic and genomic studies, with C. elegans as an excellent baseline. Here, we review the efforts that were made to extend genetic analysis to nematodes other than C. elegans, and we compare the seven available nematode genomes. One of the most striking findings is the unexpectedly high incidence of gene acquisition through horizontal gene transfer (HGT).}, }
@article {pmid21720356, year = {2011}, author = {Partensky, F and Garczarek, L}, title = {Microbiology: Arms race in a drop of sea water.}, journal = {Nature}, volume = {474}, number = {7353}, pages = {582-583}, pmid = {21720356}, issn = {1476-4687}, mesh = {Aquatic Organisms ; Bacteriophages/genetics/*physiology/ultrastructure ; Biological Evolution ; Cyanobacteria/genetics/*virology ; Gene Transfer, Horizontal/genetics ; *Water Microbiology ; }, }
@article {pmid21720212, year = {2011}, author = {Dittami, SM and Aas, HT and Paulsen, BS and Boyen, C and Edvardsen, B and Tonon, T}, title = {Mannitol in six autotrophic stramenopiles and Micromonas.}, journal = {Plant signaling &amp; behavior}, volume = {6}, number = {8}, pages = {1237-1239}, pmid = {21720212}, issn = {1559-2324}, mesh = {Chlorophyta/genetics/*metabolism ; Diatoms/genetics/metabolism ; Mannitol/*metabolism ; Phylogeny ; Stramenopiles/genetics/*metabolism ; }, abstract = {Mannitol plays a central role in brown algal physiology since it represents an important pathway used to store photoassimilate. Several specific enzymes are directly involved in the synthesis and recycling of mannitol, altogether forming the mannitol cycle. The recent analysis of algal genomes has allowed tracing back the origin of this cycle in brown seaweeds to a horizontal gene transfer from bacteria, and furthermore suggested a subsequent transfer to the green microalga Micromonas. Interestingly, genes of the mannitol cycle were not found in any of the currently sequenced diatoms, but were recently discovered in pelagophytes and dictyochophytes. In this study, we quantified the mannitol content in a number of ochrophytes (autotrophic stramenopiles) from different classes, as well as in Micromonas. Our results show that, in accordance with recent observations from EST libraries and genome analyses, this polyol is produced by most ochrophytes, as well as the green alga tested, although it was found at a wide range of concentrations. Thus, the mannitol cycle was probably acquired by a common ancestor of most ochrophytes, possibly after the separation from diatoms, and may play different physiological roles in different classes.}, }
@article {pmid21719670, year = {2011}, author = {Tadmor, AD and Ottesen, EA and Leadbetter, JR and Phillips, R}, title = {Probing individual environmental bacteria for viruses by using microfluidic digital PCR.}, journal = {Science (New York, N.Y.)}, volume = {333}, number = {6038}, pages = {58-62}, pmid = {21719670}, issn = {1095-9203}, support = {DP1 OD000217-05/OD/NIH HHS/United States ; R01 GM085286/GM/NIGMS NIH HHS/United States ; DP1 OD000217/OD/NIH HHS/United States ; R01 GM098465/GM/NIGMS NIH HHS/United States ; R01 GM085286-01S/GM/NIGMS NIH HHS/United States ; }, mesh = {Alleles ; Amino Acid Sequence ; Animals ; Bacteriophages/classification/genetics/*physiology ; Ecosystem ; Endodeoxyribonucleases/genetics ; Genes, Viral ; Genes, rRNA ; Genetic Variation ; Intestines/microbiology ; Isoptera/*microbiology ; *Microbial Interactions ; *Microfluidic Analytical Techniques ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/*methods ; Prophages/genetics ; Sequence Alignment ; Treponema/classification/genetics/*virology ; }, abstract = {Viruses may very well be the most abundant biological entities on the planet. Yet neither metagenomic studies nor classical phage isolation techniques have shed much light on the identity of the hosts of most viruses. We used a microfluidic digital polymerase chain reaction (PCR) approach to physically link single bacterial cells harvested from a natural environment with a viral marker gene. When we implemented this technique on the microbial community residing in the termite hindgut, we found genus-wide infection patterns displaying remarkable intragenus selectivity. Viral marker allelic diversity revealed restricted mixing of alleles between hosts, indicating limited lateral gene transfer of these alleles despite host proximity. Our approach does not require culturing hosts or viruses and provides a method for examining virus-bacterium interactions in many environments.}, }
@article {pmid21716306, year = {2012}, author = {Martinez-Garcia, M and Swan, BK and Poulton, NJ and Gomez, ML and Masland, D and Sieracki, ME and Stepanauskas, R}, title = {High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton.}, journal = {The ISME journal}, volume = {6}, number = {1}, pages = {113-123}, pmid = {21716306}, issn = {1751-7370}, mesh = {Actinobacteria/genetics/*isolation &amp; purification/physiology ; Bacteroidetes/genetics/*isolation &amp; purification/physiology ; Chemoautotrophic Growth ; Flow Cytometry ; Fresh Water/*microbiology ; Metagenomics/methods ; Molecular Sequence Data ; Phototrophic Processes ; Phylogeny ; Proteobacteria/genetics/*isolation &amp; purification/physiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; Single-Cell Analysis/methods ; Verrucomicrobia/*isolation &amp; purification/physiology ; }, abstract = {Recent discoveries suggest that photoheterotrophs (rhodopsin-containing bacteria (RBs) and aerobic anoxygenic phototrophs (AAPs)) and chemoautotrophs may be significant for marine and freshwater ecosystem productivity. However, their abundance and taxonomic identities remain largely unknown. We used a combination of single-cell and metagenomic DNA sequencing to study the predominant photoheterotrophs and chemoautotrophs inhabiting the euphotic zone of temperate, physicochemically diverse freshwater lakes. Multi-locus sequencing of 712 single amplified genomes, generated by fluorescence-activated cell sorting and whole genome multiple displacement amplification, showed that most of the cosmopolitan freshwater clusters contain photoheterotrophs. These comprised at least 10-23% of bacterioplankton, and RBs were the dominant fraction. Our data demonstrate that Actinobacteria, including clusters acI, Luna and acSTL, are the predominant freshwater RBs. We significantly broaden the known taxonomic range of freshwater RBs, to include Alpha-, Beta-, Gamma- and Deltaproteobacteria, Verrucomicrobia and Sphingobacteria. By sequencing single cells, we found evidence for inter-phyla horizontal gene transfer and recombination of rhodopsin genes and identified specific taxonomic groups involved in these evolutionary processes. Our data suggest that members of the ubiquitous betaproteobacteria Polynucleobacter spp. are the dominant AAPs in temperate freshwater lakes. Furthermore, the RuBisCO (ribulose 1,5-bisphosphate carboxylase/oxygenase) gene was found in several single cells of Betaproteobacteria, Bacteroidetes and Gammaproteobacteria, suggesting that chemoautotrophs may be more prevalent among aerobic bacterioplankton than previously thought. This study demonstrates the power of single-cell DNA sequencing addressing previously unresolved questions about the metabolic potential and evolutionary histories of uncultured microorganisms, which dominate most natural environments.}, }
@article {pmid21714942, year = {2011}, author = {Martin, WF}, title = {Early evolution without a tree of life.}, journal = {Biology direct}, volume = {6}, number = {}, pages = {36}, pmid = {21714942}, issn = {1745-6150}, mesh = {Adenosine Triphosphate/metabolism ; *Biological Evolution ; *Energy Metabolism ; Environment ; Eukaryotic Cells/chemistry/cytology ; Genes ; Hydrogen/chemistry ; Mitochondria/chemistry/genetics ; Origin of Life ; Oxygen/chemistry ; Phagocytosis ; Phylogeny ; Prokaryotic Cells/chemistry/cytology ; Symbiosis ; }, abstract = {Life is a chemical reaction. Three major transitions in early evolution are considered without recourse to a tree of life. The origin of prokaryotes required a steady supply of energy and electrons, probably in the form of molecular hydrogen stemming from serpentinization. Microbial genome evolution is not a treelike process because of lateral gene transfer and the endosymbiotic origins of organelles. The lack of true intermediates in the prokaryote-to-eukaryote transition has a bioenergetic cause.}, }
@article {pmid21714941, year = {2011}, author = {Lane, N}, title = {Energetics and genetics across the prokaryote-eukaryote divide.}, journal = {Biology direct}, volume = {6}, number = {}, pages = {35}, pmid = {21714941}, issn = {1745-6150}, mesh = {Adenosine Triphosphate/metabolism ; *Biological Evolution ; Cell Cycle ; Cell Membrane/physiology ; Cell Nucleus/genetics ; Cytoplasm/genetics/physiology ; *Energy Metabolism ; Eukaryotic Cells/*cytology/physiology ; Gene Transfer, Horizontal ; Genes, Mitochondrial ; Introns ; Mitochondria/genetics/physiology ; Mutation ; Oxidative Phosphorylation ; Phylogeny ; Prokaryotic Cells/*cytology/physiology ; Selection, Genetic ; *Symbiosis ; }, abstract = {BACKGROUND: All complex life on Earth is eukaryotic. All eukaryotic cells share a common ancestor that arose just once in four billion years of evolution. Prokaryotes show no tendency to evolve greater morphological complexity, despite their metabolic virtuosity. Here I argue that the eukaryotic cell originated in a unique prokaryotic endosymbiosis, a singular event that transformed the selection pressures acting on both host and endosymbiont.<br><br>RESULTS: The reductive evolution and specialisation of endosymbionts to mitochondria resulted in an extreme genomic asymmetry, in which the residual mitochondrial genomes enabled the expansion of bioenergetic membranes over several orders of magnitude, overcoming the energetic constraints on prokaryotic genome size, and permitting the host cell genome to expand (in principle) over 200,000-fold. This energetic transformation was permissive, not prescriptive; I suggest that the actual increase in early eukaryotic genome size was driven by a heavy early bombardment of genes and introns from the endosymbiont to the host cell, producing a high mutation rate. Unlike prokaryotes, with lower mutation rates and heavy selection pressure to lose genes, early eukaryotes without genome-size limitations could mask mutations by cell fusion and genome duplication, as in allopolyploidy, giving rise to a proto-sexual cell cycle. The side effect was that a large number of shared eukaryotic basal traits accumulated in the same population, a sexual eukaryotic common ancestor, radically different to any known prokaryote.<br><br>CONCLUSIONS: The combination of massive bioenergetic expansion, release from genome-size constraints, and high mutation rate favoured a protosexual cell cycle and the accumulation of eukaryotic traits. These factors explain the unique origin of eukaryotes, the absence of true evolutionary intermediates, and the evolution of sex in eukaryotes but not prokaryotes.<br><br>REVIEWERS: This article was reviewed by: Eugene Koonin, William Martin, Ford Doolittle and Mark van der Giezen. For complete reports see the Reviewers' Comments section.}, }
@article {pmid21714939, year = {2011}, author = {Beiko, RG}, title = {Telling the whole story in a 10,000-genome world.}, journal = {Biology direct}, volume = {6}, number = {}, pages = {34}, pmid = {21714939}, issn = {1745-6150}, mesh = {Algorithms ; Archaea/classification/genetics ; Bacteria/classification/*genetics ; Bacterial Proteins/chemistry/genetics ; *Biological Evolution ; Computer Graphics ; Databases, Protein ; Gene Transfer, Horizontal ; Genomics/methods ; Metagenome ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {BACKGROUND: Genome sequencing has revolutionized our view of the relationships among genomes, particularly in revealing the confounding effects of lateral genetic transfer (LGT). Phylogenomic techniques have been used to construct purported trees of microbial life. Although such trees are easily interpreted and allow the use of a subset of genomes as "proxies" for the full set, LGT and other phenomena impact the positioning of different groups in genome trees, confounding and potentially invalidating attempts to construct a phylogeny-based taxonomy of microorganisms. Network and graph approaches can reveal complex sets of relationships, but applying these techniques to large data sets is a significant challenge. Notwithstanding the question of what exactly it might represent, generating and interpreting a Tree or Network of All Genomes will only be feasible if current algorithms can be improved upon.<br><br>RESULTS: Complex relationships among even the most-similar genomes demonstrate that proxy-based approaches to simplifying large sets of genomes are not alone sufficient to solve the analysis problem. A phylogenomic analysis of 1173 sequenced bacterial and archaeal genomes generated phylogenetic trees for 159,905 distinct homologous gene sets. The relationships inferred from this set can be heavily dependent on the inclusion of other taxa: for example, phyla such as Spirochaetes, Proteobacteria and Firmicutes are recovered as cohesive groups or split depending on the presence of other specific lineages. Furthermore, named groups such as Acidithiobacillus, Coprothermobacter and Brachyspira show a multitude of affiliations that are more consistent with their ecology than with small subunit ribosomal DNA-based taxonomy. Network and graph representations can illustrate the multitude of conflicting affinities, but all methods impose constraints on the input data and create challenges of construction and interpretation.<br><br>CONCLUSIONS: These complex relationships highlight the need for an inclusive approach to genomic data, and current methods with minor alterations will likely scale to allow the analysis of data sets with 10,000 or more genomes. The main challenges lie in the visualization and interpretation of genomic relationships, and the redefinition of microbial taxonomy when subsets of genomic data are so evidently in conflict with one another, and with the "canonical" molecular taxonomy.}, }
@article {pmid21714793, year = {2011}, author = {Baquero, F and Coque, TM}, title = {Multilevel population genetics in antibiotic resistance.}, journal = {FEMS microbiology reviews}, volume = {35}, number = {5}, pages = {705-706}, doi = {10.1111/j.1574-6976.2011.00293.x}, pmid = {21714793}, issn = {1574-6976}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects ; Bacterial Infections/microbiology ; *Drug Resistance, Bacterial ; *Gene Transfer, Horizontal ; Humans ; *Mutation ; *Selection, Genetic ; }, }
@article {pmid21712432, year = {2011}, author = {Leigh, JW and Lapointe, FJ and Lopez, P and Bapteste, E}, title = {Evaluating phylogenetic congruence in the post-genomic era.}, journal = {Genome biology and evolution}, volume = {3}, number = {}, pages = {571-587}, pmid = {21712432}, issn = {1759-6653}, mesh = {Algorithms ; Computational Biology ; Eukaryota/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome ; *Genomics ; Likelihood Functions ; *Models, Genetic ; *Phylogeny ; Prokaryotic Cells ; Viruses/genetics ; }, abstract = {Congruence is a broadly applied notion in evolutionary biology used to justify multigene phylogeny or phylogenomics, as well as in studies of coevolution, lateral gene transfer, and as evidence for common descent. Existing methods for identifying incongruence or heterogeneity using character data were designed for data sets that are both small and expected to be rarely incongruent. At the same time, methods that assess incongruence using comparison of trees test a null hypothesis of uncorrelated tree structures, which may be inappropriate for phylogenomic studies. As such, they are ill-suited for the growing number of available genome sequences, most of which are from prokaryotes and viruses, either for phylogenomic analysis or for studies of the evolutionary forces and events that have shaped these genomes. Specifically, many existing methods scale poorly with large numbers of genes, cannot accommodate high levels of incongruence, and do not adequately model patterns of missing taxa for different markers. We propose the development of novel incongruence assessment methods suitable for the analysis of the molecular evolution of the vast majority of life and support the investigation of homogeneity of evolutionary process in cases where markers do not share identical tree structures.}, }
@article {pmid21711564, year = {2011}, author = {Saccardo, F and Cettul, E and Palmano, S and Noris, E and Firrao, G}, title = {On the alleged origin of geminiviruses from extrachromosomal DNAs of phytoplasmas.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {185}, pmid = {21711564}, issn = {1471-2148}, mesh = {Amino Acid Sequence ; *Biological Evolution ; Capsid Proteins/genetics ; DNA Replication ; DNA, Bacterial/*genetics ; *Extrachromosomal Inheritance ; Geminiviridae/*genetics ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; Phytoplasma/classification/*genetics ; Viral Proteins/genetics ; }, abstract = {BACKGROUND: Several phytoplasmas, wall-less phloem limited plant pathogenic bacteria, have been shown to contain extrachromosomal DNA (EcDNA) molecules encoding a replication associated protein (Rep) similar to that of geminiviruses, a major group of single stranded (ss) DNA plant viruses. On the basis of that observation and of structural similarities between the capsid proteins of geminiviruses and the Satellite tobacco necrosis virus, it has been recently proposed that geminiviruses evolved from phytoplasmal EcDNAs by acquiring a capsid protein coding gene from a co-invading plant RNA virus.<br><br>RESULTS: Here we show that this hypothesis has to be rejected because (i) the EcDNA encoded Rep is not of phytoplasmal origin but has been acquired by phytoplasmas through horizontal transfer from a geminivirus or its ancestor; and (ii) the evolution of geminivirus capsid protein in land plants implies missing links, while the analysis of metagenomic data suggests an alternative scenario implying a more ancient evolution in marine environments.<br><br>CONCLUSION: The hypothesis of geminiviruses evolving in plants from DNA molecules of phytoplasma origin contrasts with other findings. An alternative scenario concerning the origin and spread of Rep coding phytoplasmal EcDNA is presented and its implications on the epidemiology of phytoplasmas are discussed.}, }
@article {pmid21711510, year = {2011}, author = {Nagler, C and Hardt, C and Zänker, KS and Dittmar, T}, title = {Co-cultivation of murine BMDCs with 67NR mouse mammary carcinoma cells give rise to highly drug resistant cells.}, journal = {Cancer cell international}, volume = {11}, number = {1}, pages = {21}, pmid = {21711510}, issn = {1475-2867}, abstract = {BACKGROUND: Tumor tissue resembles chronically inflamed tissue. Since chronic inflammatory conditions are a strong stimulus for bone marrow-derived cells (BMDCs) it can be assumed that recruitment of BMDCs into cancer tissue should be a common phenomenon. Several data have outlined that BMDC can influence tumor growth and metastasis, e.g., by inducing a paracrine acting feedback loop in tumor cells. Likewise, cell fusion and horizontal gene transfer are further mechanisms how BMDCs can trigger tumor progression.<br><br>RESULTS: Hygromycin resistant murine 67NR-Hyg mammary carcinoma cells were co-cultivated with puromycin resistant murine BMDCs from Tg(GFPU)5Nagy/J mice. Isolation of hygromycin/puromycin resistant mBMDC/67NR-Hyg cell clones was performed by a dual drug selection procedure. PCR analysis revealed an overlap of parental markers in mBMDC/67NR-Hyg cell clones, suggesting that dual resistant cells originated by cell fusion. By contrast, both STR and SNP data analysis indicated that only parental 67NR-Hyg alleles were found in mBMDC/67NR-Hyg cell clones favoring horizontal gene transfer as the mode of origin. RealTime-PCR-array analysis showed a marked up-regulation of Abcb1a and Abcb1b ABC multidrug transporters in mBMDC/67NR-Hyg clones, which was verified by Western Blot analysis. Moreover, the markedly increased Abcb1a/Abcb1b expression was correlated to an efficient Rhodamine 123 efflux, which was completely inhibited by verapamil, a well-known Abcb1a/Abcb1b inhibitor. Likewise, mBMDCs/67NR-Hyg clones revealed a marked resistance towards chemotherapeutic drugs including 17-DMAG, doxorubicin, etoposide and paclitaxel. In accordance to Rhodamine 123 efflux data, chemotherapeutic drug resistance of mBMDC/67NR-Hyg cells was impaired by verapamil mediated blockage of Abc1a/Abcb1b multidrug transporter function.<br><br>CONCLUSION: Co-cultivation of mBMDCs and mouse 67NR-Hyg mammary carcinoma cells gave rise to highly drug resistant cells. Even though it remains unknown whether mBMDC/67NR-Hyg clones originated by cell fusion or horizontal gene transfer, our data indicate that the exchange of genetic information between two cellular entities is crucial for the origin of highly drug resistant cancer (hybrid) cells, which might be capable to survive chemotherapy.}, }
@article {pmid21711367, year = {2011}, author = {Wiedenbeck, J and Cohan, FM}, title = {Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches.}, journal = {FEMS microbiology reviews}, volume = {35}, number = {5}, pages = {957-976}, doi = {10.1111/j.1574-6976.2011.00292.x}, pmid = {21711367}, issn = {1574-6976}, mesh = {*Adaptation, Biological ; Bacteria/*genetics ; *Biological Evolution ; *Gene Transfer, Horizontal ; Genetic Variation ; Plasmids ; Recombination, Genetic ; Selection, Genetic ; }, abstract = {Horizontal genetic transfer (HGT) has played an important role in bacterial evolution at least since the origins of the bacterial divisions, and HGT still facilitates the origins of bacterial diversity, including diversity based on antibiotic resistance. Adaptive HGT is aided by unique features of genetic exchange in bacteria such as the promiscuity of genetic exchange and the shortness of segments transferred. Genetic exchange rates are limited by the genetic and ecological similarity of organisms. Adaptive transfer of genes is limited to those that can be transferred as a functional unit, provide a niche-transcending adaptation, and are compatible with the architecture and physiology of other organisms. Horizontally transferred adaptations may bring about fitness costs, and natural selection may ameliorate these costs. The origins of ecological diversity can be analyzed by comparing the genomes of recently divergent, ecologically distinct populations, which can be discovered as sequence clusters. Such genome comparisons demonstrate the importance of HGT in ecological diversification. Newly divergent populations cannot be discovered as sequence clusters when their ecological differences are coded by plasmids, as is often the case for antibiotic resistance; the discovery of such populations requires a screen for plasmid-coded functions. This paper reviews the features of bacterial genetics that allow HGT, the similarities between organisms that foster HGT between them, the limits to the kinds of adaptations that can be transferred, and amelioration of fitness costs associated with HGT; the paper also reviews approaches to discover the origins of new, ecologically distinct bacterial populations and the role that HGT plays in their founding.}, }
@article {pmid21711366, year = {2011}, author = {Garcillán-Barcia, MP and Alvarado, A and de la Cruz, F}, title = {Identification of bacterial plasmids based on mobility and plasmid population biology.}, journal = {FEMS microbiology reviews}, volume = {35}, number = {5}, pages = {936-956}, doi = {10.1111/j.1574-6976.2011.00291.x}, pmid = {21711366}, issn = {1574-6976}, mesh = {Bacterial Infections/microbiology/veterinary ; Bacterial Proteins/*genetics ; DNA, Bacterial/*genetics ; Drug Resistance, Bacterial ; Environmental Microbiology ; Gammaproteobacteria/*genetics/isolation &amp; purification ; *Gene Transfer, Horizontal ; Humans ; *Interspersed Repetitive Sequences ; *Plasmids ; Virulence Factors/genetics ; }, abstract = {Plasmids contain a backbone of core genes that remains relatively stable for long evolutionary periods, making sense to speak about plasmid species. The identification and characterization of the core genes of a plasmid species has a special relevance in the study of its epidemiology and modes of transmission. Besides, this knowledge will help to unveil the main routes that genes, for example antibiotic resistance (AbR) genes, use to travel from environmental reservoirs to human pathogens. Global dissemination of multiple antibiotic resistances and virulence traits by plasmids is an increasing threat for the treatment of many bacterial infectious diseases. To follow the dissemination of virulence and AbR genes, we need to identify the causative plasmids and follow their path from reservoirs to pathogens. In this review, we discuss how the existing diversity in plasmid genetic structures gives rise to a large diversity in propagation strategies. We would like to propose that, using an identification methodology based on plasmid mobility types, we can follow the propagation routes of most plasmids in Gammaproteobacteria, as well as their cargo genes, in complex ecosystems. Once the dissemination routes are known, designing antidissemination drugs and testing their efficacy will become feasible. We discuss in this review how the existing diversity in plasmid genetic structures gives rise to a large diversity in propagation strategies. We would like to propose that, by using an identification methodology based on plasmid mobility types, we can follow the propagation routes of most plasmids in ?-proteobacteria, as well as their cargo genes, in complex ecosystems.}, }
@article {pmid21707669, year = {2011}, author = {Andersson, DI and Hughes, D}, title = {Persistence of antibiotic resistance in bacterial populations.}, journal = {FEMS microbiology reviews}, volume = {35}, number = {5}, pages = {901-911}, doi = {10.1111/j.1574-6976.2011.00289.x}, pmid = {21707669}, issn = {1574-6976}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects ; Bacterial Infections/microbiology/transmission ; *Drug Resistance, Bacterial ; Evolution, Molecular ; Gene Transfer, Horizontal ; Humans ; Models, Theoretical ; Selection, Genetic ; }, abstract = {Unfortunately for mankind, it is very likely that the antibiotic resistance problem we have generated during the last 60 years due to the extensive use and misuse of antibiotics is here to stay for the foreseeable future. This view is based on theoretical arguments, mathematical modeling, experiments and clinical interventions, suggesting that even if we could reduce antibiotic use, resistant clones would remain persistent and only slowly (if at all) be outcompeted by their susceptible relatives. In this review, we discuss the multitude of mechanisms and processes that are involved in causing the persistence of chromosomal and plasmid-borne resistance determinants and how we might use them to our advantage to increase the likelihood of reversing the problem. Of particular interest is the recent demonstration that a very low antibiotic concentration can be enriching for resistant bacteria and the implication that antibiotic release into the environment could contribute to the selection for resistance. Several mechanisms are contributing to the stability of antibiotic resistance in bacterial populations and even if antibiotic use is reduced it is likely that most resistance mechanisms will persist for considerable times.}, }
@article {pmid21707466, year = {2011}, author = {Zhao, WH and Hu, ZQ}, title = {IMP-type metallo-β-lactamases in Gram-negative bacilli: distribution, phylogeny, and association with integrons.}, journal = {Critical reviews in microbiology}, volume = {37}, number = {3}, pages = {214-226}, doi = {10.3109/1040841X.2011.559944}, pmid = {21707466}, issn = {1549-7828}, mesh = {Anti-Bacterial Agents/pharmacology ; DNA Transposable Elements ; Gene Transfer, Horizontal ; Gram-Negative Bacteria/drug effects/*enzymology/*genetics ; Humans ; *Integrons ; *Phylogeny ; Plasmids ; beta-Lactam Resistance ; beta-Lactamases/*biosynthesis/*genetics ; beta-Lactams/pharmacology ; }, abstract = {Twenty-nine IMP-type β-lactamases (IMPs) have been identified in at least 26 species of clinically important Gram-negative bacilli from more than 24 countries/regions. Most of bla(IMP) genes are harbored by class 1 integrons that are usually embedded in transposons and/or plasmids, footnoting their horizontal transfer and worldwide distribution. bla(IMP) genes usually co-exist with other resistance genes, such as aacA, catB, and bla(OXA), resulting in multi-drug resistance. Compared to other gene cassettes, 76.3% of the bla(IMP) gene cassettes are located adjacent to Pc promoter of the class 1 integrons, indicating that the bla(IMP) genes are readily expressed in most of bacterial hosts.}, }
@article {pmid21705590, year = {2011}, author = {Abriouel, H and Benomar, N and Pulido, RP and Cañamero, MM and Gálvez, A}, title = {Annotated genome sequence of Lactobacillus pentosus MP-10, which has probiotic potential, from naturally fermented Aloreña green table olives.}, journal = {Journal of bacteriology}, volume = {193}, number = {17}, pages = {4559-4560}, pmid = {21705590}, issn = {1098-5530}, mesh = {*Fermentation ; Food Handling/*methods ; *Food Microbiology ; Gene Transfer, Horizontal ; Genes, rRNA ; *Genome, Bacterial ; Hydrogen-Ion Concentration ; Lactobacillus/*genetics/*isolation &amp; purification ; Molecular Sequence Data ; Olea/microbiology ; RNA, Transfer/genetics ; Sequence Analysis, RNA ; }, abstract = {Lactobacillus pentosus MP-10 was isolated from brines of naturally fermented Aloreña green table olives. MP-10 has potential probiotic traits, including inhibition of human pathogenic bacteria, survival at low pH (1.5), and bile salt tolerance (3%). Here, we report for the first time the annotated genome sequence of L. pentosus.}, }
@article {pmid21704702, year = {2011}, author = {Xiong, J and Li, D and Li, H and He, M and Miller, SJ and Yu, L and Rensing, C and Wang, G}, title = {Genome analysis and characterization of zinc efflux systems of a highly zinc-resistant bacterium, Comamonas testosteroni S44.}, journal = {Research in microbiology}, volume = {162}, number = {7}, pages = {671-679}, doi = {10.1016/j.resmic.2011.06.002}, pmid = {21704702}, issn = {1769-7123}, mesh = {Bacterial Proteins/genetics/metabolism ; Biological Transport ; Comamonas testosteroni/classification/*genetics/isolation &amp; purification/metabolism ; Gene Expression Regulation, Bacterial ; *Genome, Bacterial ; Molecular Sequence Data ; Soil Microbiology ; Zinc/*metabolism ; }, abstract = {A novel and multiple metal(loid)-resistant strain Comamonas testosteroni S44 with a high Zn(2+) resistance level (10 mM) was isolated. To understand the molecular basis for the high zinc resistance, whole genome sequencing was performed and revealed a large number of genes encoding putative metal(loid) resistance proteins, mobile genetic elements (MGEs) and horizontal gene transfer (HGT) events that may have occurred to adapt to a metal(loid)-contaminated environment. In particular, 9 putative Zn(2+) transporters [4 znt operons encoding putative Zn(2+)-translocating P-type ATPases and 5 czc operons encoding putative RND-driven (resistance, nodulation, cell division protein family)] tripartite protein complexes were identified. Real-time RT-PCR analysis revealed that the four zntA-like genes were all induced by Zn(2+), while czcA genes were either Zn(2+)-induced or downregulated by Zn(2+). Furthermore, a zntR1A1 operon encoding a ZntR-type regulator and a P-type ATPase was studied in detail. The zntR1 deletion strain (S44ΔzntR1) displayed intermediate resistance to Zn(2+) (6 mM) and accumulated more intracellular Zn(2+). Reporter gene expression assays indicated that ZntR1 responded to Zn(2+), Cd(2+) and Pb(2+), with Zn(2+) being the best inducer. Gene transcription analysis indicated that ZntR1 was a regulator for transcription of zntA1, while other putative ZntR-type regulators may also regulate the transcription expression of zntA1.}, }
@article {pmid21704701, year = {2011}, author = {Halter, D and Cordi, A and Gribaldo, S and Gallien, S and Goulhen-Chollet, F and Heinrich-Salmeron, A and Carapito, C and Pagnout, C and Montaut, D and Seby, F and Van Dorsselaer, A and Schaeffer, C and Bertin, PN and Bauda, P and Arsène-Ploetze, F}, title = {Taxonomic and functional prokaryote diversity in mildly arsenic-contaminated sediments.}, journal = {Research in microbiology}, volume = {162}, number = {9}, pages = {877-887}, doi = {10.1016/j.resmic.2011.06.001}, pmid = {21704701}, issn = {1769-7123}, mesh = {Adaptation, Physiological ; Archaea/classification/*genetics/isolation &amp; purification/metabolism ; Arsenic/*metabolism ; Bacteria/classification/*genetics/isolation &amp; purification/metabolism ; Biodiversity ; DNA, Archaeal/analysis/genetics ; DNA, Bacterial/analysis/genetics ; Ecosystem ; Environmental Pollutants/metabolism ; France ; Gene Transfer, Horizontal ; Geologic Sediments/*microbiology ; Microbial Consortia/*physiology ; Phylogeny ; Polymerase Chain Reaction ; *Proteomics ; RNA, Ribosomal, 16S/analysis/genetics ; Rivers/*microbiology ; }, abstract = {Arsenic-resistant prokaryote diversity is far from being exhaustively explored. In this study, the arsenic-adapted prokaryotic community present in a moderately arsenic-contaminated site near Sainte-Marie-aux-Mines (France) was characterized, using metaproteomic and 16S rRNA-encoding gene amplification. High prokaryotic diversity was observed, with a majority of Proteobacteria, Acidobacteria and Bacteroidetes, and a large archaeal community comprising Euryarchaeaota and Thaumarchaeota. Metaproteomic analysis revealed that Proteobacteria, Planctomycetes and Cyanobacteria are among the active bacteria in this ecosystem. Taken together, these results highlight the unsuspected high diversity of the arsenic-adapted prokaryotic community, with some phyla never having been described in highly arsenic-exposed sites.}, }
@article {pmid21702991, year = {2011}, author = {Cervantes, L and Bustos, P and Girard, L and Santamaría, RI and Dávila, G and Vinuesa, P and Romero, D and Brom, S}, title = {The conjugative plasmid of a bean-nodulating Sinorhizobium fredii strain is assembled from sequences of two Rhizobium plasmids and the chromosome of a Sinorhizobium strain.}, journal = {BMC microbiology}, volume = {11}, number = {}, pages = {149}, pmid = {21702991}, issn = {1471-2180}, mesh = {Conjugation, Genetic ; DNA, Bacterial/chemistry/*genetics ; *Evolution, Molecular ; Fabaceae/microbiology ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Open Reading Frames ; *Plasmids ; *Recombination, Genetic ; Sequence Analysis, DNA ; Sinorhizobium fredii/*genetics/isolation &amp; purification ; Spain ; }, abstract = {BACKGROUND: Bean-nodulating Rhizobium etli originated in Mesoamerica, while soybean-nodulating Sinorhizobium fredii evolved in East Asia. S. fredii strains, such as GR64, have been isolated from bean nodules in Spain, suggesting the occurrence of conjugative transfer events between introduced and native strains. In R. etli CFN42, transfer of the symbiotic plasmid (pRet42d) requires cointegration with the endogenous self-transmissible plasmid pRet42a. Aiming at further understanding the generation of diversity among bean nodulating strains, we analyzed the plasmids of S. fredii GR64: pSfr64a and pSfr64b (symbiotic plasmid).<br><br>RESULTS: The conjugative transfer of the plasmids of strain GR64 was analyzed. Plasmid pSfr64a was self-transmissible, and required for transfer of the symbiotic plasmid. We sequenced pSfr64a, finding 166 ORFs. pSfr64a showed three large segments of different evolutionary origins; the first one presented 38 ORFs that were highly similar to genes located on the chromosome of Sinorhizobium strain NGR234; the second one harbored 51 ORFs with highest similarity to genes from pRet42d, including the replication, but not the symbiosis genes. Accordingly, pSfr64a was incompatible with the R. etli CFN42 symbiotic plasmid, but did not contribute to symbiosis. The third segment contained 36 ORFs with highest similarity to genes localized on pRet42a, 20 of them involved in conjugative transfer. Plasmid pRet42a was unable to substitute pSfr64a for induction of pSym transfer, and its own transfer was significantly diminished in GR64 background. The symbiotic plasmid pSfr64b was found to differ from typical R. etli symbiotic plasmids.<br><br>CONCLUSIONS: S. fredii GR64 contains a chimeric transmissible plasmid, with segments from two R. etli plasmids and a S. fredii chromosome, and a symbiotic plasmid different from the one usually found in R. etli bv phaseoli. We infer that these plasmids originated through the transfer of a symbiotic-conjugative-plasmid cointegrate from R. etli to a S. fredii strain, and at least two recombination events among the R. etli plasmids and the S. fredii genome. As in R. etli CFN42, the S. fredii GR64 transmissible plasmid is required for the conjugative transfer of the symbiotic plasmid. In spite of the similarity in the conjugation related genes, the transfer process of these plasmids shows a host-specific behaviour.}, }
@article {pmid21702931, year = {2011}, author = {Escobar, JS and Scornavacca, C and Cenci, A and Guilhaumon, C and Santoni, S and Douzery, EJ and Ranwez, V and Glémin, S and David, J}, title = {Multigenic phylogeny and analysis of tree incongruences in Triticeae (Poaceae).}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {181}, pmid = {21702931}, issn = {1471-2148}, mesh = {Bayes Theorem ; Chloroplasts/genetics ; Genes, Plant ; *Phylogeny ; Poaceae/*genetics ; Recombination, Genetic ; }, abstract = {BACKGROUND: Introgressive events (e.g., hybridization, gene flow, horizontal gene transfer) and incomplete lineage sorting of ancestral polymorphisms are a challenge for phylogenetic analyses since different genes may exhibit conflicting genealogical histories. Grasses of the Triticeae tribe provide a particularly striking example of incongruence among gene trees. Previous phylogenies, mostly inferred with one gene, are in conflict for several taxon positions. Therefore, obtaining a resolved picture of relationships among genera and species of this tribe has been a challenging task. Here, we obtain the most comprehensive molecular dataset to date in Triticeae, including one chloroplastic and 26 nuclear genes. We aim to test whether it is possible to infer phylogenetic relationships in the face of (potentially) large-scale introgressive events and/or incomplete lineage sorting; to identify parts of the evolutionary history that have not evolved in a tree-like manner; and to decipher the biological causes of gene-tree conflicts in this tribe.<br><br>RESULTS: We obtain resolved phylogenetic hypotheses using the supermatrix and Bayesian Concordance Factors (BCF) approaches despite numerous incongruences among gene trees. These phylogenies suggest the existence of 4-5 major clades within Triticeae, with Psathyrostachys and Hordeum being the deepest genera. In addition, we construct a multigenic network that highlights parts of the Triticeae history that have not evolved in a tree-like manner. Dasypyrum, Heteranthelium and genera of clade V, grouping Secale, Taeniatherum, Triticum and Aegilops, have evolved in a reticulated manner. Their relationships are thus better represented by the multigenic network than by the supermatrix or BCF trees. Noteworthy, we demonstrate that gene-tree incongruences increase with genetic distance and are greater in telomeric than centromeric genes. Together, our results suggest that recombination is the main factor decoupling gene trees from multigenic trees.<br><br>CONCLUSIONS: Our study is the first to propose a comprehensive, multigenic phylogeny of Triticeae. It clarifies several aspects of the relationships among genera and species of this tribe, and pinpoints biological groups with likely reticulate evolution. Importantly, this study extends previous results obtained in Drosophila by demonstrating that recombination can exacerbate gene-tree conflicts in phylogenetic reconstructions.}, }
@article {pmid21699590, year = {2011}, author = {Kitazaki, K and Kubo, T and Kagami, H and Matsumoto, T and Fujita, A and Matsuhira, H and Matsunaga, M and Mikami, T}, title = {A horizontally transferred tRNA(Cys) gene in the sugar beet mitochondrial genome: evidence that the gene is present in diverse angiosperms and its transcript is aminoacylated.}, journal = {The Plant journal : for cell and molecular biology}, volume = {68}, number = {2}, pages = {262-272}, doi = {10.1111/j.1365-313X.2011.04684.x}, pmid = {21699590}, issn = {1365-313X}, mesh = {Amino Acyl-tRNA Synthetases/*genetics/metabolism ; Aminoacylation/*genetics ; Beta vulgaris/enzymology/*genetics/metabolism ; Biological Evolution ; DNA, Complementary/genetics ; DNA, Mitochondrial/genetics ; DNA, Plant/genetics ; Databases, Nucleic Acid ; Gene Dosage ; Gene Transfer, Horizontal ; Genome, Mitochondrial/*genetics ; Magnoliopsida/enzymology/*genetics/metabolism ; Mitochondria/genetics/metabolism ; Nucleic Acid Conformation ; Plant Proteins/genetics/metabolism ; RNA, Plant/genetics ; RNA, Transfer, Cys/genetics/*metabolism ; Sequence Analysis, DNA ; }, abstract = {Of the two tRNA(Cys) (GCA) genes, trnC1-GCA and trnC2-GCA, previously identified in mitochondrial genome of sugar beet, the former is a native gene and probably a pseudo-copy, whereas the latter, of unknown origin, is transcribed into a tRNA [tRNA(Cys2) (GCA)]. In this study, the trnC2-GCA sequence was mined from various public databases. To evaluate whether or not the trnC2-GCA sequence is located in the mitochondrial genome, the relative copy number of its sequence to nuclear gene was assessed in a number of angiosperm species, using a quantitative real-time PCR assay. The trnC2-GCA sequence was found to exist sporadically in the mitochondrial genomes of a wide range of angiosperms. The mitochondrial tRNA(Cys2) (GCA) species from sugar beet (Beta vulgaris), spinach (Spinacea oleracea) and cucumber (Cucumis sativus) were found to be aminoacylated, indicating that they may participate in translation. We also identified a sugar beet nuclear gene that encodes cysteinyl-tRNA synthetase, which is dual-targeted to mitochondria and plastids, and may aminoacylate tRNA(Cys2) (GCA). What is of particular interest is that trnC1-GCA and trnC2-GCA co-exist in the mitochondrial genomes of eight diverse angiosperms, including spinach, and that the spinach tRNA(Cys1) (GCA) is also aminoacylated. Taken together, our observations lead us to surmise that trnC2-GCA may have been horizontally transferred to a common ancestor of eudicots, followed by co-existence and dual expression of trnC1-GCA and trnC2-GCA in mitochondria with occasional loss or inactivation of either trnC-GCA gene during evolution.}, }
@article {pmid21698163, year = {2011}, author = {Williams, TA and Embley, TM and Heinz, E}, title = {Informational gene phylogenies do not support a fourth domain of life for nucleocytoplasmic large DNA viruses.}, journal = {PloS one}, volume = {6}, number = {6}, pages = {e21080}, pmid = {21698163}, issn = {1932-6203}, mesh = {Cell Nucleus/*virology ; Cytoplasm/*virology ; DNA Viruses/classification/*genetics ; Gene Transfer, Horizontal ; *Phylogeny ; }, abstract = {Mimivirus is a nucleocytoplasmic large DNA virus (NCLDV) with a genome size (1.2 Mb) and coding capacity (1000 genes) comparable to that of some cellular organisms. Unlike other viruses, Mimivirus and its NCLDV relatives encode homologs of broadly conserved informational genes found in Bacteria, Archaea, and Eukaryotes, raising the possibility that they could be placed on the tree of life. A recent phylogenetic analysis of these genes showed the NCLDVs emerging as a monophyletic group branching between Eukaryotes and Archaea. These trees were interpreted as evidence for an independent "fourth domain" of life that may have contributed DNA processing genes to the ancestral eukaryote. However, the analysis of ancient evolutionary events is challenging, and tree reconstruction is susceptible to bias resulting from non-phylogenetic signals in the data. These include compositional heterogeneity and homoplasy, which can lead to the spurious grouping of compositionally-similar or fast-evolving sequences. Here, we show that these informational gene alignments contain both significant compositional heterogeneity and homoplasy, which were not adequately modelled in the original analysis. When we use more realistic evolutionary models that better fit the data, the resulting trees are unable to reject a simple null hypothesis in which these informational genes, like many other NCLDV genes, were acquired by horizontal transfer from eukaryotic hosts. Our results suggest that a fourth domain is not required to explain the available sequence data.}, }
@article {pmid21697961, year = {2011}, author = {Klatt, CG and Wood, JM and Rusch, DB and Bateson, MM and Hamamura, N and Heidelberg, JF and Grossman, AR and Bhaya, D and Cohan, FM and Kühl, M and Bryant, DA and Ward, DM}, title = {Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential.}, journal = {The ISME journal}, volume = {5}, number = {8}, pages = {1262-1278}, pmid = {21697961}, issn = {1751-7370}, mesh = {Chlorobi/genetics/isolation &amp; purification ; Chloroflexi/genetics/isolation &amp; purification ; Cyanobacteria/*classification/genetics/*isolation &amp; purification/physiology ; Gene Transfer, Horizontal ; Hot Springs/*microbiology ; *Metagenome ; Phylogeny ; Synechococcus/genetics/isolation &amp; purification ; United States ; }, abstract = {Phototrophic microbial mat communities from 60°C and 65°C regions in the effluent channels of Mushroom and Octopus Springs (Yellowstone National Park, WY, USA) were investigated by shotgun metagenomic sequencing. Analyses of assembled metagenomic sequences resolved six dominant chlorophototrophic populations and permitted the discovery and characterization of undescribed but predominant community members and their physiological potential. Linkage of phylogenetic marker genes and functional genes showed novel chlorophototrophic bacteria belonging to uncharacterized lineages within the order Chlorobiales and within the Kingdom Chloroflexi. The latter is the first chlorophototrophic member of Kingdom Chloroflexi that lies outside the monophyletic group of chlorophototrophs of the Order Chloroflexales. Direct comparison of unassembled metagenomic sequences to genomes of representative isolates showed extensive genetic diversity, genomic rearrangements and novel physiological potential in native populations as compared with genomic references. Synechococcus spp. metagenomic sequences showed a high degree of synteny with the reference genomes of Synechococcus spp. strains A and B', but synteny declined with decreasing sequence relatedness to these references. There was evidence of horizontal gene transfer among native populations, but the frequency of these events was inversely proportional to phylogenetic relatedness.}, }
@article {pmid21697330, year = {2011}, author = {Xiao, L and Paralanov, V and Glass, JI and Duffy, LB and Robertson, JA and Cassell, GH and Chen, Y and Waites, KB}, title = {Extensive horizontal gene transfer in ureaplasmas from humans questions the utility of serotyping for diagnostic purposes.}, journal = {Journal of clinical microbiology}, volume = {49}, number = {8}, pages = {2818-2826}, pmid = {21697330}, issn = {1098-660X}, support = {N01AI30071/AI/NIAID NIH HHS/United States ; AI 28279/AI/NIAID NIH HHS/United States ; }, mesh = {Adult ; Child ; Child, Preschool ; Female ; *Gene Transfer, Horizontal ; Genetic Variation ; Humans ; Infant ; Male ; Pregnancy ; Real-Time Polymerase Chain Reaction/methods ; *Recombination, Genetic ; Serotyping ; Sexually Transmitted Diseases, Bacterial/*microbiology ; Ureaplasma/*classification/genetics/isolation &amp; purification ; Ureaplasma Infections/*microbiology ; Ureaplasma urealyticum/*classification/genetics/isolation &amp; purification ; }, abstract = {Ureaplasma parvum and Ureaplasma urealyticum are sexually transmitted, opportunistic pathogens of the human urogenital tract. There are 14 known serovars distributed between the two species. For decades, it has been postulated based upon limited data that virulence is related to serotype specificity. The results were often inconclusive due to the small sample size and extensive cross-reactivity between certain serovars. We developed real-time quantitative PCRs that allow reliable differentiation of the two species and type strains of each of the 14 serovars. To investigate species and serovar distributions, we typed 1,061 clinical isolates of human ureaplasmas from diverse patient populations. There was only a tenuous association between individual Ureaplasma serovars and certain patient populations. This may in part be explained by the fact that almost 40% of the isolates were genetic mosaics, apparently arising from the recombination of multiple serovars. This explains the extensive cross-reactivity based upon serotyping and the lack of consistent association of given serotypes with disease.}, }
@article {pmid21695201, year = {2011}, author = {Murata, M and Fujimoto, H and Nishimura, K and Charoensuk, K and Nagamitsu, H and Raina, S and Kosaka, T and Oshima, T and Ogasawara, N and Yamada, M}, title = {Molecular strategy for survival at a critical high temperature in Eschierichia coli.}, journal = {PloS one}, volume = {6}, number = {6}, pages = {e20063}, pmid = {21695201}, issn = {1932-6203}, mesh = {Adaptation, Physiological/genetics ; Computational Biology ; Down-Regulation/genetics ; Escherichia coli K12/*genetics/*growth &amp; development ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/genetics ; Heat-Shock Response/genetics ; *Hot Temperature ; Microbial Viability/*genetics ; Oxidative Stress/genetics ; Up-Regulation/genetics ; }, abstract = {The molecular mechanism supporting survival at a critical high temperature (CHT) in Escherichia coli was investigated. Genome-wide screening with a single-gene knockout library provided a list of genes indispensable for growth at 47°C, called thermotolerant genes. Genes for which expression was affected by exposure to CHT were identified by DNA chip analysis. Unexpectedly, the former contents did not overlap with the latter except for dnaJ and dnaK, indicating that a specific set of non-heat shock genes is required for the organism to survive under such a severe condition. More than half of the mutants of the thermotolerant genes were found to be sensitive to H(2)O(2) at 30°C, suggesting that the mechanism of thermotolerance partially overlaps with that of oxidative stress resistance. Their encoded enzymes or proteins are related to outer membrane organization, DNA double-strand break repair, tRNA modification, protein quality control, translation control or cell division. DNA chip analyses of essential genes suggest that many of the genes encoding ribosomal proteins are down-regulated at CHT. Bioinformatics analysis and comparison with the genomic information of other microbes suggest that E. coli possesses several systems for survival at CHT. This analysis allows us to speculate that a lipopolysaccharide biosynthesis system for outer membrane organization and a sulfur-relay system for tRNA modification have been acquired by horizontal gene transfer.}, }
@article {pmid21693016, year = {2011}, author = {Kalhoefer, D and Thole, S and Voget, S and Lehmann, R and Liesegang, H and Wollher, A and Daniel, R and Simon, M and Brinkhoff, T}, title = {Comparative genome analysis and genome-guided physiological analysis of Roseobacter litoralis.}, journal = {BMC genomics}, volume = {12}, number = {}, pages = {324}, pmid = {21693016}, issn = {1471-2164}, mesh = {Genome, Bacterial ; Genomic Islands ; Glycogen/metabolism ; Metals, Heavy/metabolism ; Molecular Sequence Data ; Photosynthesis/genetics ; Plasmids/chemistry/genetics ; Roseobacter/*genetics/physiology ; Species Specificity ; }, abstract = {BACKGROUND: Roseobacter litoralis OCh149, the type species of the genus, and Roseobacter denitrificans OCh114 were the first described organisms of the Roseobacter clade, an ecologically important group of marine bacteria. Both species were isolated from seaweed and are able to perform aerobic anoxygenic photosynthesis.<br><br>RESULTS: The genome of R. litoralis OCh149 contains one circular chromosome of 4,505,211 bp and three plasmids of 93,578 bp (pRLO149_94), 83,129 bp (pRLO149_83) and 63,532 bp (pRLO149_63). Of the 4537 genes predicted for R. litoralis, 1122 (24.7%) are not present in the genome of R. denitrificans. Many of the unique genes of R. litoralis are located in genomic islands and on plasmids. On pRLO149_83 several potential heavy metal resistance genes are encoded which are not present in the genome of R. denitrificans. The comparison of the heavy metal tolerance of the two organisms showed an increased zinc tolerance of R. litoralis. In contrast to R. denitrificans, the photosynthesis genes of R. litoralis are plasmid encoded. The activity of the photosynthetic apparatus was confirmed by respiration rate measurements, indicating a growth-phase dependent response to light. Comparative genomics with other members of the Roseobacter clade revealed several genomic regions that were only conserved in the two Roseobacter species. One of those regions encodes a variety of genes that might play a role in host association of the organisms. The catabolism of different carbon and nitrogen sources was predicted from the genome and combined with experimental data. In several cases, e.g. the degradation of some algal osmolytes and sugars, the genome-derived predictions of the metabolic pathways in R. litoralis differed from the phenotype.<br><br>CONCLUSIONS: The genomic differences between the two Roseobacter species are mainly due to lateral gene transfer and genomic rearrangements. Plasmid pRLO149_83 contains predominantly recently acquired genetic material whereas pRLO149_94 was probably translocated from the chromosome. Plasmid pRLO149_63 and one plasmid of R. denitrifcans (pTB2) seem to have a common ancestor and are important for cell envelope biosynthesis. Several new mechanisms of substrate degradation were indicated from the combination of experimental and genomic data. The photosynthetic activity of R. litoralis is probably regulated by nutrient availability.}, }
@article {pmid21690563, year = {2011}, author = {Collingro, A and Tischler, P and Weinmaier, T and Penz, T and Heinz, E and Brunham, RC and Read, TD and Bavoil, PM and Sachse, K and Kahane, S and Friedman, MG and Rattei, T and Myers, GS and Horn, M}, title = {Unity in variety--the pan-genome of the Chlamydiae.}, journal = {Molecular biology and evolution}, volume = {28}, number = {12}, pages = {3253-3270}, pmid = {21690563}, issn = {1537-1719}, support = {R01 AI051472/AI/NIAID NIH HHS/United States ; 1R01AI051472/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Outer Membrane Proteins/chemistry/genetics ; Bacterial Proteins/chemistry/genetics ; Bacterial Secretion Systems/genetics ; Base Sequence ; Cell Membrane ; Chlamydia/classification/*genetics/pathogenicity ; Chlamydiales/classification/*genetics/pathogenicity ; DNA, Bacterial/analysis/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; *Genome, Bacterial ; Host-Pathogen Interactions ; Molecular Sequence Data ; Phylogeny ; Plasmids ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {Chlamydiae are evolutionarily well-separated bacteria that live exclusively within eukaryotic host cells. They include important human pathogens such as Chlamydia trachomatis as well as symbionts of protozoa. As these bacteria are experimentally challenging and genetically intractable, our knowledge about them is still limited. In this study, we obtained the genome sequences of Simkania negevensis Z, Waddlia chondrophila 2032/99, and Parachlamydia acanthamoebae UV-7. This enabled us to perform the first comprehensive comparative and phylogenomic analysis of representative members of four major families of the Chlamydiae, including the Chlamydiaceae. We identified a surprisingly large core gene set present in all genomes and a high number of diverse accessory genes in those Chlamydiae that do not primarily infect humans or animals, including a chemosensory system in P. acanthamoebae and a type IV secretion system. In S. negevensis, the type IV secretion system is encoded on a large conjugative plasmid (pSn, 132 kb). Phylogenetic analyses suggested that a plasmid similar to the S. negevensis plasmid was originally acquired by the last common ancestor of all four families and that it was subsequently reduced, integrated into the chromosome, or lost during diversification, ultimately giving rise to the extant virulence-associated plasmid of pathogenic chlamydiae. Other virulence factors, including a type III secretion system, are conserved among the Chlamydiae to variable degrees and together with differences in the composition of the cell wall reflect adaptation to different host cells including convergent evolution among the four chlamydial families. Phylogenomic analysis focusing on chlamydial proteins with homology to plant proteins provided evidence for the acquisition of 53 chlamydial genes by a plant progenitor, lending further support for the hypothesis of an early interaction between a chlamydial ancestor and the primary photosynthetic eukaryote.}, }
@article {pmid21687533, year = {2011}, author = {Clokie, MR and Millard, AD and Letarov, AV and Heaphy, S}, title = {Phages in nature.}, journal = {Bacteriophage}, volume = {1}, number = {1}, pages = {31-45}, pmid = {21687533}, issn = {2159-7073}, abstract = {Bacteriophages or phages are the most abundant organisms in the biosphere and they are a ubiquitous feature of prokaryotic existence. A bacteriophage is a virus which infects a bacterium. Archaea are also infected by viruses, whether these should be referred to as 'phages' is debatable, but they are included as such in the scope this article. Phages have been of interest to scientists as tools to understand fundamental molecular biology, as vectors of horizontal gene transfer and drivers of bacterial evolution, as sources of diagnostic and genetic tools and as novel therapeutic agents. Unraveling the biology of phages and their relationship with their hosts is key to understanding microbial systems and their exploitation. In this article we describe the roles of phages in different host systems and show how modeling, microscopy, isolation, genomic and metagenomic based approaches have come together to provide unparalleled insights into these small but vital constituents of the microbial world.}, }
@article {pmid21687415, year = {2011}, author = {Al-Quadan, T and Kwaik, YA}, title = {Molecular Characterization of Exploitation of the Polyubiquitination and Farnesylation Machineries of Dictyostelium Discoideum by the AnkB F-Box Effector of Legionella Pneumophila.}, journal = {Frontiers in microbiology}, volume = {2}, number = {}, pages = {23}, pmid = {21687415}, issn = {1664-302X}, support = {R01 AI043965/AI/NIAID NIH HHS/United States ; R01 AI069321/AI/NIAID NIH HHS/United States ; }, abstract = {The Dot/Icm-translocated Ankyrin B (AnkB) F-box effector of Legionella pneumophila is essential for intra-vacuolar proliferation and functions as a platform for the docking of polyubiquitinated proteins to the Legionella-containing vacuole (LCV) within macrophages and ameba. Here we show that ectopically expressed AnkB in Dictyostelium discoideum is targeted to the plasma membrane where it recruits polyubiquitinated proteins and it trans-rescues the intracellular growth defect of the ankB null mutant, which has never been demonstrated for any effector in ameba. Using co-immunoprecipitation and bimolecular fluorescence complementation we show specific interaction of Skp1 of D. discoideum with the F-box domain of AnkB, which has never been demonstrated in ameba. We show that anchoring of AnkB to the cytosolic face of the LCV membrane in D. discoideum is mediated by the host farnesylation of the C-terminal eukaryotic CaaX motif of AnkB and is independent of the F-box and the two ANK domains, which has never been demonstrated in ameba. Importantly, the three host farnesylation enzymes farnesyl transferase, RCE-1, and isoprenyl cysteine carboxyl methyl transferase of D. discoideum are recruited to the LCV in a Dot/Icm-dependent manner, which has never been demonstrated in ameba. We conclude that the polyubiquitination and farnesylation enzymatic machineries of D. discoideum are recruited to the LCV in a Dot/Icm-dependent manner and the AnkB effector exploits the two evolutionarily conserved eukaryotic machineries to proliferate within ameba, similar to mammalian cells. We propose that L. pneumophila has acquired ankB through inter-kingdom horizontal gene transfer from primitive eukaryotes, which facilitated proliferation of L. pneumophila within human cells and the emergence of Legionnaires' disease.}, }
@article {pmid21685715, year = {2011}, author = {Carvalho, G and Almeida, B and Fradinho, J and Oehmen, A and Reis, MA and Crespo, MT}, title = {Microbial characterization of mercury-reducing mixed cultures enriched with different carbon sources.}, journal = {Microbes and environments}, volume = {26}, number = {4}, pages = {293-300}, doi = {10.1264/jsme2.me11112}, pmid = {21685715}, issn = {1347-4405}, mesh = {Acetates/metabolism ; Bacteria/*classification/genetics/*metabolism ; *Biota ; Carbon/*metabolism ; Cluster Analysis ; DNA Fingerprinting ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; Drug Resistance, Bacterial ; *Environmental Microbiology ; Ethanol/metabolism ; Gammaproteobacteria ; Glucose/metabolism ; Mercury/*metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics ; Phylogeny ; RNA/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Verbenaceae ; }, abstract = {The use of mixed microbial cultures enriched for biological mercury removal is explored in this paper, focusing on the ecological shifts occurring throughout acclimatization to mercury and on the long-term stability of four microbial enrichments. The 16S rRNA genetic profiles obtained by denaturing gradient gel electrophoresis (DGGE) revealed that the glucose and ethanol cultures had similar profiles, whereas the acetate cultures diverged into a totally dissimilar cluster. Quantification of the merA gene copies in each enrichment showed higher values for the glucose culture, followed by the ethanol and then the acetate cultures, which was consistent with the mercury removal performance throughout the study. Isolates were obtained from the four cultures and analyzed with respect to their genetic (16S rRNA) and functional (merA) phylogenies in order to identify mercury-resistant species enriched with different carbon sources. All mercury-resistant isolates obtained from the glucose and ethanol cultures belonged to the Gammaproteobacteria, whereas acetate cultures also contained members of other phyla, with differences in merA sequences. Higher phylogenetic than functional diversity of the isolates, together with increasing merA copies even after culture stabilisation, highlight the role of horizontal gene transfer in the acclimatization process.}, }
@article {pmid21685201, year = {2011}, author = {García-Fulgueiras, V and Bado, I and Mota, MI and Robino, L and Cordeiro, NF and Varela, A and Algorta, G and Gutkind, G and Ayala, JA and Vignoli, R}, title = {Extended-spectrum β-lactamases and plasmid-mediated quinolone resistance in enterobacterial clinical isolates in the paediatric hospital of Uruguay.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {66}, number = {8}, pages = {1725-1729}, doi = {10.1093/jac/dkr222}, pmid = {21685201}, issn = {1460-2091}, mesh = {Adolescent ; Anti-Bacterial Agents/*pharmacology ; Child ; Child, Preschool ; Conjugation, Genetic ; DNA, Bacterial/genetics ; *Drug Resistance, Bacterial ; Enterobacteriaceae/*drug effects/enzymology/isolation &amp; purification ; Enterobacteriaceae Infections/epidemiology/microbiology ; Gene Transfer, Horizontal ; Hospitals, Pediatric ; Humans ; Infant ; Infant, Newborn ; *Plasmids ; Polymerase Chain Reaction ; Prevalence ; Quinolones/*pharmacology ; Uruguay/epidemiology ; beta-Lactamases/*biosynthesis/genetics ; beta-Lactams/*pharmacology ; }, abstract = {OBJECTIVES: To analyse the prevalence of resistance to β-lactams and plasmid-mediated quinolone resistance in Enterobacteriaceae in the paediatric hospital of Uruguay.<br><br>METHODS: A total of 368 enterobacterial isolates collected between 1 May and 30 November 2009 were studied for the presence of extended-spectrum &#x3b2;-lactamases (ESBLs), qnr alleles and aac(6')Ib by phenotypic and molecular methods. The genomic context and transferability of &#x3b2;-lactamase and qnr genes were examined by PCR and conjugation, respectively.<br><br>RESULTS: The proportion of inpatients having an infection caused by ESBL-producing enterobacteria was 0.23% (16/7073) in paediatrics wards, 0.64&#x2030; (3/4696) in the neonatology department and 0.03&#x2030; (1/32&#x200a;557) in the emergency department. ESBL-carrying enterobacteria constituted a total of 21.6% (16/74), 13% (3/23) and 0.37% (1/271) when samples were obtained from paediatrics wards, the neonatology department and the emergency department, respectively. Overall, CTX-M-2 (n&#x200a;=&#x200a;7), CTX-M-9 (n&#x200a;=&#x200a;3), CTX-M-8 (n&#x200a;=&#x200a;2), CTX-M-15 (n&#x200a;=&#x200a;1), SHV-5 (n&#x200a;=&#x200a;5) and SHV-2 (n&#x200a;=&#x200a;2) &#x3b2;-lactamases were detected. Thirteen out of 20 ESBL-producing isolates also carried the aac(6')Ib gene, and the cr variant was detected in one of them. qnr alleles were detected in four isolates comprising two qnrA1 genes, a qnrB8-like variant and a new qnrB gene showing 26 amino acid differences from QnrB1.<br><br>CONCLUSIONS: The proportion of ESBL-producing enterobacteria in Uruguay's paediatric hospital during the study period was 2.3 per 1000 hospitalized patients. The number of different microorganisms detected, as well as the various EBSLs, suggests the occurrence of sporadic episodes instead of nosocomial outbreaks. Nevertheless, the presence of new resistance genes reinforces the necessity for permanent surveillance programmes.}, }
@article {pmid21685078, year = {2011}, author = {Scornavacca, C and Zickmann, F and Huson, DH}, title = {Tanglegrams for rooted phylogenetic trees and networks.}, journal = {Bioinformatics (Oxford, England)}, volume = {27}, number = {13}, pages = {i248-56}, pmid = {21685078}, issn = {1367-4811}, mesh = {Algorithms ; Animals ; *Biological Evolution ; Biology/methods ; Computational Biology/*methods ; Computer Simulation ; Ficus/genetics ; Gene Transfer, Horizontal ; Hybridization, Genetic ; *Phylogeny ; Wasps/genetics ; }, abstract = {MOTIVATION: In systematic biology, one is often faced with the task of comparing different phylogenetic trees, in particular in multi-gene analysis or cospeciation studies. One approach is to use a tanglegram in which two rooted phylogenetic trees are drawn opposite each other, using auxiliary lines to connect matching taxa. There is an increasing interest in using rooted phylogenetic networks to represent evolutionary history, so as to explicitly represent reticulate events, such as horizontal gene transfer, hybridization or reassortment. Thus, the question arises how to define and compute a tanglegram for such networks.<br><br>RESULTS: In this article, we present the first formal definition of a tanglegram for rooted phylogenetic networks and present a heuristic approach for computing one, called the NN-tanglegram method. We compare the performance of our method with existing tree tanglegram algorithms and also show a typical application to real biological datasets. For maximum usability, the algorithm does not require that the trees or networks are bifurcating or bicombining, or that they are on identical taxon sets.<br><br>AVAILABILITY: The algorithm is implemented in our program Dendroscope 3, which is freely available from www.dendroscope.org.<br><br>CONTACT: scornava@informatik.uni-tuebingen.de; huson@informatik.uni-tuebingen.de.}, }
@article {pmid21684870, year = {2011}, author = {Duan, HR and Qiu, DB and Gong, CL and Huang, ML}, title = {[Analysis of horizontal transfer gene of Bombyx mori NPV].}, journal = {Yi chuan = Hereditas}, volume = {33}, number = {6}, pages = {636-647}, doi = {10.3724/sp.j.1005.2011.00636}, pmid = {21684870}, issn = {0253-9772}, mesh = {Animals ; Bombyx/*virology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Viral/genetics ; Genomics/*methods ; Nucleopolyhedroviruses/*genetics ; Phylogeny ; Selection, Genetic ; Software ; }, abstract = {For research on genetic characters and evolutionary origin of the genome of baculoviruses, a comprehensive homology search and phylogenetic analysis of the complete genomes of Bombyx mori NPV and Bombyx mori were used. Three horizontally transferred genes (inhibitor of apoptosis, chitinase, and UDP-glucosyltransferase) were identified, and there was evidence that all of these genes were derived from the insect host. The results of analysis showed lots of differences between the features of horizontal transferred genes and the ones of whole genomic genes, such as nucleotide composition, codon usagebias and selection pressure. These results reconfirmed that the horizontally transferred genes are exogenous. The analysis of gene function suggested that horizontally transferred genes acquired from an ancestral host insect can increase the efficiency of baculoviruses transmission.}, }
@article {pmid21684863, year = {2011}, author = {Wang, Y and Xie, H and Chen, LP}, title = {[Progress in research on plant graft-induced genetic variation].}, journal = {Yi chuan = Hereditas}, volume = {33}, number = {6}, pages = {585-590}, doi = {10.3724/sp.j.1005.2011.00585}, pmid = {21684863}, issn = {0253-9772}, mesh = {Epigenesis, Genetic ; Gene Transfer, Horizontal ; *Genetic Variation ; Plants/*genetics ; Transplantation ; }, abstract = {Inheritable variation induced by plant grafting is a universal phenomenon; however, its mechanism has always been a controversial subject. In recent years, research on horizontal transfer of genetic materials between stock and scion has made great progress. The latest studies have found that genetic information in grafted plants is transported through plasmodesma and phloem to modulate the growth and development of the scion plants. Furthermore, non-coding RNAs could induce epigenetic modification, which facilitates plants to adapt to the grafting-caused stress. This article focuses on the review of recent advances in the induction and maintenance of the graft-induced genetic variation and could be helpful in thoroughly understanding the mechanism.}, }
@article {pmid21684094, year = {2011}, author = {Browning, GF and Marenda, MS and Noormohammadi, AH and Markham, PF}, title = {The central role of lipoproteins in the pathogenesis of mycoplasmoses.}, journal = {Veterinary microbiology}, volume = {153}, number = {1-2}, pages = {44-50}, doi = {10.1016/j.vetmic.2011.05.031}, pmid = {21684094}, issn = {1873-2542}, mesh = {Animals ; Gene Transfer, Horizontal ; Humans ; Lipoproteins/*metabolism ; Mycoplasma/genetics/*pathogenicity/physiology ; Mycoplasma Infections/genetics/immunology/*veterinary ; Virulence ; }, abstract = {Mycoplasmas are a diverse group of pathogens responsible for disease in a wide range of animal species. In recent years there have been considerable advances in knowledge of the proteins and structures involved in adherence in some mycoplasmas, but understanding of the biochemical functions and roles in virulence of another central feature of mycoplasmas, their lipoproteins, continues to develop. The aim of this review is to examine current knowledge of the roles of lipoproteins in the pathogenicity and the evolution of virulence in those mycoplasmas causing disease in domestic animals. Those lipoproteins that have been characterised have roles in adherence, in transport of nutrients into the mycoplasma cell, and in enzymatic interactions with the host. Furthermore they appear to play a prominent role in both inducing the host immune response to infection and in facilitating evasion of this response, particularly through the generation of dramatic levels of antigenic variation on the cell surface. Recent genomic comparisons of several pathogenic mycoplasmas have identified a further level of interaction between lipoproteins and pathogenicity. In several pathogens large scale horizontal gene transfer between distantly related mycoplasma species has resulted in the acquisition of a large number of genes, including those encoding lipoproteins thought to play a role in virulence, by one mycoplasma from another inhabiting the same host species. The interactions between these horizontally transferred genes, their new mycoplasma host and the animal that it infects may be an important contributing factor in the pathogenesis of some mycoplasmoses.}, }
@article {pmid21683552, year = {2011}, author = {Chowdhury, G and Pazhani, GP and Nair, GB and Ghosh, A and Ramamurthy, T}, title = {Transferable plasmid-mediated quinolone resistance in association with extended-spectrum β-lactamases and fluoroquinolone-acetylating aminoglycoside-6'-N-acetyltransferase in clinical isolates of Vibrio fluvialis.}, journal = {International journal of antimicrobial agents}, volume = {38}, number = {2}, pages = {169-173}, doi = {10.1016/j.ijantimicag.2011.04.013}, pmid = {21683552}, issn = {1872-7913}, mesh = {Acetyltransferases/*genetics ; Anti-Bacterial Agents/*pharmacology ; Conjugation, Genetic ; DNA Gyrase/genetics ; DNA Topoisomerase IV/genetics ; *Drug Resistance, Bacterial ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Humans ; India ; Microbial Sensitivity Tests ; Mutation, Missense ; *Plasmids ; Quinolones/*pharmacology ; Vibrio/drug effects/genetics/*isolation &amp; purification ; Vibrio Infections/microbiology ; beta-Lactamases/*genetics ; }, abstract = {Vibrio fluvialis, which causes cholera-like diarrhoea in humans, is one of the aetiological agents of acute diarrhoea in Kolkata, India, and is resistant to many antimicrobial agents. Two V. fluvialis isolates resistant to fluoroquinolones and β-lactam antimicrobials were found to have mutations in the quinolone resistance-determining regions (QRDRs) of GyrA at position 83 and of ParC at position 85 as well as carrying a 150 kb plasmid harbouring the quinolone resistance gene qnrA1, the ciprofloxacin-modifying enzyme-encoding gene aac(6')-Ib-cr and genes encoding for extended-spectrum β-lactamases such as bla(SHV) and bla(CTX-M-3). When this large plasmid was transferred to Escherichia coli by conjugation, the transconjugants showed a 10-75-fold increase in the minimum inhibitory concentrations of ciprofloxacin and norfloxacin. The qnrA1 gene was identified in a complex sul1-type integron in a plasmid of the transconjugants. Southern hybridisation and sequence analysis of qnrA1 and its flanking regions confirmed the presence of aac(6')-Ib-cr and bla(CTX-M-3) but these were not associated with the sul1-type integron. Pulsed-field gel electrophoresis (PFGE) revealed that the two V. fluvialis isolates belonged to different clones. Although the presence of many qnr alleles has been reported amongst enteric bacteria in Asian countries, this is the first report on the emergence of qnrA1 in India. qnrA1 along with aac(6')-Ib-cr and bla(CTX-M-3) genes on a mobile plasmid may spread to other bacterial species that are under the selective pressure of fluoroquinolones and β-lactam antimicrobials in this region.}, }
@article {pmid21683165, year = {2012}, author = {Reyes, JF and Chan, CH and Tanaka, MM}, title = {Impact of homoplasy on variable numbers of tandem repeats and spoligotypes in Mycobacterium tuberculosis.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {12}, number = {4}, pages = {811-818}, doi = {10.1016/j.meegid.2011.05.018}, pmid = {21683165}, issn = {1567-7257}, mesh = {Algorithms ; Computer Simulation ; DNA, Bacterial/*chemistry ; Evolution, Molecular ; *Genotype ; Humans ; *Minisatellite Repeats ; Models, Genetic ; Models, Statistical ; Mutation Rate ; Mycobacterium tuberculosis/classification/*genetics ; Tuberculosis/epidemiology/transmission ; }, abstract = {Homoplasy is the occurrence of genotypes that are identical by state but not by descent. It arises through a number of means including convergent and reverse evolution, and horizontal gene transfer. When using molecular markers that are based on sequences possessing a finite number of character states, such as VNTR or spoligotypes, this is an unavoidable phenomenon. Here we discuss the extent of homoplasy and its impact on inferences drawn from spoligotypes and VNTR in epidemiological studies of tuberculosis. To further explore this problem, we developed a computer simulation model combining the processes of mutation and transmission. Our results show that while the extent of homoplasy is not negligible, its effect on the proportion of isolates clustered ("n-1 method") is likely to be relatively low for spoligotyping. For VNTR-typing, homoplasy occurs at a low rate provided the number of loci used is high and the mutation rate is relatively high. However, deep phylogenetic inferences using spoligotypes or VNTRs with a small number of loci are likely to be unreliable.}, }
@article {pmid21682644, year = {2011}, author = {Wisecaver, JH and Hackett, JD}, title = {Dinoflagellate genome evolution.}, journal = {Annual review of microbiology}, volume = {65}, number = {}, pages = {369-387}, doi = {10.1146/annurev-micro-090110-102841}, pmid = {21682644}, issn = {1545-3251}, mesh = {Bacteria/genetics ; Cell Nucleus/genetics ; Dinoflagellida/classification/*genetics/microbiology ; *Evolution, Molecular ; Gene Expression Regulation ; Gene Transfer, Horizontal ; Genome, Mitochondrial ; *Genome, Protozoan ; Phylogeny ; Plastids/genetics ; }, abstract = {The dinoflagellates are an ecologically important group of microbial eukaryotes that have evolved many novel genomic characteristics. They possess some of the largest nuclear genomes among eukaryotes arranged on permanently condensed liquid-crystalline chromosomes. Recent advances have revealed the presence of genes arranged in tandem arrays, trans-splicing of messenger RNAs, and a reduced role for transcriptional regulation compared to other eukaryotes. In contrast, the mitochondrial and plastid genomes have the smallest gene content among functional eukaryotic organelles. Dinoflagellate biology and genome evolution have been dramatically influenced by lateral transfer of individual genes and large-scale transfer of genes through endosymbiosis. Next-generation sequencing technologies have only recently made genome-scale analyses of these organisms possible, and these new methods are helping researchers better understand the biology and evolution of this enigmatic group of eukaryotes.}, }
@article {pmid21681998, year = {2010}, author = {Sun, Y and Zeng, Z and Chen, S and Ma, J and He, L and Liu, Y and Deng, Y and Lei, T and Zhao, J and Liu, JH}, title = {High prevalence of bla(CTX-M) extended-spectrum β-lactamase genes in Escherichia coli isolates from pets and emergence of CTX-M-64 in China.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {16}, number = {9}, pages = {1475-1481}, doi = {10.1111/j.1469-0691.2010.03127.x}, pmid = {21681998}, issn = {1469-0691}, mesh = {Animals ; Bacterial Typing Techniques ; Cats ; China ; Cluster Analysis ; Dogs ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/classification/*enzymology/genetics/*isolation &amp; purification ; Escherichia coli Infections/*veterinary ; Gene Transfer, Horizontal ; Genotype ; Molecular Typing ; Pets/*microbiology ; beta-Lactamases/*genetics ; }, abstract = {As a cause of community-acquired infections, extended-spectrum β-lactamase (ESBL)-producing Escherichia coli constitute an emerging public-health concern. Few data on the molecular epidemiology of ESBL-producing E. coli isolates from pets are available in China. Detection and characterization of ESBL genes (bla(CTX-M), bla(SHV) and bla(TEM)) was conducted among 240 E. coli isolates recovered from healthy and sick pets in South China from 2007 to 2008. The clonal relatedness of ESBL-producing E. coli isolates was assessed by pulsed field gel electrophoresis. ESBL-encoding genes were identified in 97 (40.4%) of the 240 isolates and 96 (40.0%) of them harbored CTX-M. The most common CTX-M types were CTX-M-14 (n = 45) and CTX-M-55 (n = 24). The recently reported CTX-M-64 was identified in three isolates. Isolates producing CTX-M-27, -15, -65, -24, -3 and -9 were also identified. Ten isolates carried two or three CTX-M types, with the combination of CTX-M-14 and CTX-M-55 being the most frequent (n = 6). ISEcp1 was identified in the upstream region of 93 out of the 107 bla(CTX-M) genes (86.9%). The sequence of the spacer region (45 bp) between ISEcp1 and the start codon of all bla(CTX-M-55) genes (except four) was identical to that of bla(CTX-M-64). No major clonal relatedness was observed among these CTX-M producers. It is suggested that the horizontal transfer of bla(CTX-M) genes, mediated by mobile elements, contributes to their dissemination among E. coli isolates from pets. Our finding of high prevalence of ESBL in E. coli of companion animal origin illustrates the importance of molecular surveillance in tracking CTX-M-producing E. coli strains in pets.}, }
@article {pmid21680869, year = {2012}, author = {McDonald, TR and Dietrich, FS and Lutzoni, F}, title = {Multiple horizontal gene transfers of ammonium transporters/ammonia permeases from prokaryotes to eukaryotes: toward a new functional and evolutionary classification.}, journal = {Molecular biology and evolution}, volume = {29}, number = {1}, pages = {51-60}, pmid = {21680869}, issn = {1537-1719}, mesh = {Ammonia/*metabolism ; Animals ; Archaea/genetics ; Bacteria/genetics ; Cation Transport Proteins/*genetics/metabolism ; Chlorophyta/genetics ; Eukaryota/genetics ; *Evolution, Molecular ; Fungi/genetics ; *Gene Transfer, Horizontal ; Phylogeny ; Quaternary Ammonium Compounds/*metabolism ; Rhodophyta/genetics ; }, abstract = {The proteins of the ammonium transporter/methylammonium permease/Rhesus factor family (AMT/MEP/Rh family) are responsible for the movement of ammonia or ammonium ions across the cell membrane. Although it has been established that the Rh proteins are distantly related to the other members of the family, the evolutionary history of the AMT/MEP/Rh family remains unclear. Here, we use phylogenetic analysis to infer the evolutionary history of this family of proteins across 191 genomes representing all main lineages of life and to provide a new classification of the proteins in this family. Our phylogenetic analysis suggests that what has heretofore been conceived of as a protein family with two clades (AMT/MEP and Rh) is instead a protein family with three clades (AMT, MEP, and Rh). We show that the AMT/MEP/Rh family illustrates two contrasting modes of gene transmission: The AMT family as defined here exhibits vertical gene transfer (i.e., standard parent-to-offspring inheritance), whereas the MEP family as defined here is characterized by several ancient independent horizontal gene transfers (HGTs). These ancient HGT events include a gene replacement during the early evolution of the fungi, which could be a defining trait for the kingdom Fungi, a gene gain from hyperthermophilic chemoautolithotrophic prokaryotes during the early evolution of land plants (Embryophyta), and an independent gain of this same gene in the filamentous ascomycetes (Pezizomycotina) that was subsequently lost in most lineages but retained in even distantly related lichenized fungi. This recircumscription of the ammonium transporters/ammonia permeases family into MEP and AMT families informs the debate on the mechanism of transport in these proteins and on the nature of the transported molecule because published crystal structures of proteins from the MEP and Rh clades may not be representative of the AMT clade. The clades as depicted in this phylogenetic study appear to correspond to functionally different groups, with AMTs and ammonia permeases forming two distinct and possibly monophyletic groups.}, }
@article {pmid21675128, year = {2011}, author = {Hryniewicz, W}, title = {[Antibiotic resistance--what we have to do now?].}, journal = {Polski merkuriusz lekarski : organ Polskiego Towarzystwa Lekarskiego}, volume = {30}, number = {179}, pages = {305-309}, pmid = {21675128}, issn = {1426-9686}, mesh = {Animals ; Anti-Bacterial Agents/*therapeutic use ; Communicable Diseases/*drug therapy ; *Drug Resistance, Microbial ; Drug Utilization/trends ; Drug and Narcotic Control/methods ; Forecasting ; Humans ; Policy Making ; }, abstract = {Antibiotics introduced about 60 years ago as miracle drugs are getting less effications. This is a result of the emergence and dynamic dissemination of resistance due to the clonal spread of resistant strains and horizontal gene transfer. This has decreased therapeutic options and has reached an alarming level, a threat to public health and patient care. The WHO and ECDC call for immediate action aimed at the introduction of rationale therapy, and the enhancement of microbiological diagnostics and infection control programs. Lack of action in this field may lead to a post antibiotic era.}, }
@article {pmid21672261, year = {2011}, author = {Du, P and Yang, Y and Wang, H and Liu, D and Gao, GF and Chen, C}, title = {A large scale comparative genomic analysis reveals insertion sites for newly acquired genomic islands in bacterial genomes.}, journal = {BMC microbiology}, volume = {11}, number = {}, pages = {135}, pmid = {21672261}, issn = {1471-2180}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; *Genome, Archaeal ; *Genome, Bacterial ; *Genomic Islands ; Recombination, Genetic ; }, abstract = {BACKGROUND: Bacterial virulence enhancement and drug resistance are major threats to public health worldwide. Interestingly, newly acquired genomic islands (GIs) from horizontal transfer between different bacteria strains were found in Vibrio cholerae, Streptococcus suis, and Mycobacterium tuberculosis, which caused outbreak of epidemic diseases in recently years.<br><br>RESULTS: Using a large-scale comparative genomic analysis of 1088 complete genomes from all available bacteria (1009) and Archaea (79), we found that newly acquired GIs are often anchored around switch sites of GC-skew (sGCS). After calculating correlations between relative genomic distances of genomic islands to sGCSs and the evolutionary distances of the genomic islands themselves, we found that newly acquired genomic islands are closer to sGCSs than the old ones, indicating that regions around sGCSs are hotspots for genomic island insertion.<br><br>CONCLUSIONS: Based on our results, we believe that genomic regions near sGCSs are hotspots for horizontal transfer of genomic islands, which may significantly affect key properties of epidemic disease-causing pathogens, such as virulence and adaption to new environments.}, }
@article {pmid21669325, year = {2011}, author = {Hoa, PT and Managaki, S and Nakada, N and Takada, H and Shimizu, A and Anh, DH and Viet, PH and Suzuki, S}, title = {Antibiotic contamination and occurrence of antibiotic-resistant bacteria in aquatic environments of northern Vietnam.}, journal = {The Science of the total environment}, volume = {409}, number = {15}, pages = {2894-2901}, doi = {10.1016/j.scitotenv.2011.04.030}, pmid = {21669325}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents/*analysis ; Bacteria/*genetics/growth &amp; development/isolation &amp; purification ; Drug Resistance, Bacterial/*genetics ; Environmental Monitoring ; Erythromycin/analysis ; Sulfamethazine/analysis ; Sulfamethoxazole/analysis ; Vietnam ; Water Microbiology ; Water Pollutants, Chemical/*analysis ; Water Pollution, Chemical/statistics &amp; numerical data ; }, abstract = {The ubiquitous application and release of antibiotics to the environment can result in bacterial antibiotic resistance, which in turn can be a serious risk to humans and other animals. Southeast Asian countries commonly apply an integrated recycling farm system called VAC (Vegetable, Aquaculture and Caged animal). In the VAC environment, antibiotics are released from animal and human origins, which would cause antibiotic-resistant bacteria (ARB). This study evaluated occurrence of ARB in the VAC environment in northern Vietnam, with quantitative analysis of antibiotic pollution. We found that sulfonamides were commonly detected at all sites. In dry season, while sulfamethazine was a major contaminant in pig farm pond (475-6662 ng/l) and less common in city canal and aquaculture sites, sulfamethoxazole was a major one in city canal (612-4330 ng/l). Erythromycin (154-2246 ng/l) and clarithromycin (2.8-778 ng/ml) were the common macrolides in city canal, but very low concentrations in pig farm pond and aquaculture sites. High frequencies of sulfamethoxazole-resistant bacteria (2.14-94.44%) were found whereas the occurrence rates of erythromycin-resistant bacteria were lower (<0.01-38.8%). A positive correlation was found between sulfamethoxazole concentration and occurrence of sulfamethoxazole-resistant bacteria in dry season. The sulfamethoxazole-resistant isolates were found to belong to 25 genera. Acinetobacter and Aeromonas were the major genera. Twenty three of 25 genera contained sul genes. This study showed specific contamination patterns in city and VAC environments and concluded that ARB occurred not only within contaminated sites but also those less contaminated. Various species can obtain resistance in VAC environment, which would be reservoir of drug resistance genes. Occurrence of ARB is suggested to relate with rainfall condition and horizontal gene transfer in diverse microbial community.}, }
@article {pmid21666709, year = {2011}, author = {Andam, CP and Gogarten, JP}, title = {Biased gene transfer in microbial evolution.}, journal = {Nature reviews. Microbiology}, volume = {9}, number = {7}, pages = {543-555}, pmid = {21666709}, issn = {1740-1534}, mesh = {Amino Acyl-tRNA Synthetases/genetics ; Archaea/*genetics ; Bacteria/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Phylogeny ; }, abstract = {Horizontal gene transfer (HGT) is an important evolutionary process that allows the spread of innovations between distantly related organisms. We present evidence that prokaryotes (bacteria and archaea) are more likely to transfer genetic material with their close relatives than with distantly related lineages. This bias in transfer partners can create phylogenetic signals that are difficult to distinguish from the signal created through shared ancestry. Preferences for transfer partners can be revealed by studying the distribution patterns of divergent genes with identical functions. In many respects, these genes are similar to alleles in a population, except that they coexist only in higher taxonomic groupings and are acquired by a species through HGT. We also discuss the role of biased gene transfer in the formation of taxonomically recognizable natural groups in the tree or net of life.}, }
@article {pmid21666019, year = {2011}, author = {Nelson, WC and Wollerman, L and Bhaya, D and Heidelberg, JF}, title = {Analysis of insertion sequences in thermophilic cyanobacteria: exploring the mechanisms of establishing, maintaining, and withstanding high insertion sequence abundance.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {15}, pages = {5458-5466}, pmid = {21666019}, issn = {1098-5336}, mesh = {Base Sequence ; DNA Transposable Elements/*genetics ; Gene Transfer, Horizontal/*genetics ; Genetic Variation ; Genome ; Genome, Bacterial ; Hot Springs/microbiology ; Metagenomics ; Phylogeny ; Sequence Analysis, DNA ; Synechococcus/*genetics/isolation &amp; purification/metabolism ; }, abstract = {Insertion sequences (ISs) are simple mobile genetic elements capable of relocating within a genome. Through this transposition activity, they are known to create mutations which are mostly deleterious to the cell, although occasionally they are beneficial. Two closely related isolates of thermophilic Synechococcus species from hot spring microbial mats are known to harbor a large number of diverse ISs. To explore the mechanism of IS acquisition within natural populations and survival in the face of high IS abundance, we examined IS content and location in natural populations of Synechococcus by comparing metagenomic data to the genomes of fully sequenced cultured isolates. The observed IS distribution in the metagenome was equivalent to the distribution in the isolates, indicating that the cultured isolates are appropriate models for the environmental population. High sequence conservation between IS families shared between the two isolates suggests that ISs are able to move between individuals within populations and between species via lateral gene transfer, consistent with models for IS family accumulation. Most IS families show evidence of recent activity, and interruption of critical genes in some individuals was observed, demonstrating that transposition is an ongoing mutational force in the populations.}, }
@article {pmid21664819, year = {2011}, author = {Breidenstein, EB and de la Fuente-Núñez, C and Hancock, RE}, title = {Pseudomonas aeruginosa: all roads lead to resistance.}, journal = {Trends in microbiology}, volume = {19}, number = {8}, pages = {419-426}, doi = {10.1016/j.tim.2011.04.005}, pmid = {21664819}, issn = {1878-4380}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Biofilms ; Cystic Fibrosis/microbiology ; *Drug Resistance, Multiple, Bacterial ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genomic Library ; Humans ; Membranes/drug effects/metabolism ; Mutation ; Pseudomonas Infections/microbiology ; Pseudomonas aeruginosa/*drug effects/genetics/pathogenicity ; Virulence ; }, abstract = {Pseudomonas aeruginosa is often resistant to multiple antibiotics and consequently has joined the ranks of 'superbugs' due to its enormous capacity to engender resistance. It demonstrates decreased susceptibility to most antibiotics due to low outer membrane permeability coupled to adaptive mechanisms and can readily achieve clinical resistance. Newer research, using mutant library screens, microarray technologies and mutation frequency analysis, has identified very large collections of genes (the resistome) that when mutated lead to resistance as well as new forms of adaptive resistance that can be triggered by antibiotics themselves, in in vivo growth conditions or complex adaptations such as biofilm growth or swarming motility.}, }
@article {pmid21658103, year = {2011}, author = {Antonova, ES and Hammer, BK}, title = {Quorum-sensing autoinducer molecules produced by members of a multispecies biofilm promote horizontal gene transfer to Vibrio cholerae.}, journal = {FEMS microbiology letters}, volume = {322}, number = {1}, pages = {68-76}, doi = {10.1111/j.1574-6968.2011.02328.x}, pmid = {21658103}, issn = {1574-6968}, mesh = {4-Butyrolactone/*analogs &amp; derivatives/metabolism ; Bacterial Proteins/genetics/metabolism ; *Biofilms ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Homoserine/*analogs &amp; derivatives/metabolism ; Lactones/*metabolism ; *Quorum Sensing ; Vibrio/genetics/physiology ; Vibrio cholerae/*genetics/physiology ; }, abstract = {Vibrio cholerae, the causative agent of cholera and a natural inhabitant of aquatic environments, regulates numerous behaviors using a quorum-sensing (QS) system conserved among many members of the marine genus Vibrio. The Vibrio QS response is mediated by two extracellular autoinducer (AI) molecules: CAI-I, which is produced only by Vibrios, and AI-2, which is produced by many bacteria. In marine biofilms on chitinous surfaces, QS-proficient V. cholerae become naturally competent to take up extracellular DNA. Because the direct role of AIs in this environmental behavior had not been determined, we sought to define the contribution of CAI-1 and AI-2 in controlling transcription of the competence gene, comEA, and in DNA uptake. In this study we demonstrated that comEA transcription and the horizontal acquisition of DNA by V. cholerae are induced in response to purified CAI-1 and AI-2, and also by autoinducers derived from other Vibrios co-cultured with V. cholerae within a mixed-species biofilm. These results suggest that autoinducer communication within a consortium may promote DNA exchange among Vibrios, perhaps contributing to the evolution of these bacterial pathogens.}, }
@article {pmid21658089, year = {2011}, author = {Haug, MC and Tanner, SA and Lacroix, C and Stevens, MJ and Meile, L}, title = {Monitoring horizontal antibiotic resistance gene transfer in a colonic fermentation model.}, journal = {FEMS microbiology ecology}, volume = {78}, number = {2}, pages = {210-219}, doi = {10.1111/j.1574-6941.2011.01149.x}, pmid = {21658089}, issn = {1574-6941}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/drug effects/*genetics ; Enterococcus faecalis/drug effects/*genetics ; Feces/microbiology ; Fermentation ; Gastrointestinal Tract/microbiology ; Gene Transfer, Horizontal/*physiology ; Genes, Bacterial ; Humans ; Infant ; Listeria monocytogenes/drug effects/*genetics ; Models, Biological ; Plasmids/genetics ; Tetracycline Resistance/drug effects/genetics ; }, abstract = {The human microbiota is suggested to be a reservoir of antibiotic resistance (ABR) genes, which are exchangeable between transient colonizers and residing bacteria. In this study, the transfer of ABR genes from Enterococcus faecalis to Listeria monocytogenes and to commensal bacteria of the human gut microbiota was demonstrated in a colonic fermentation model. In the first fermentation, an E. faecalis donor harboring the marked 50-kb conjugative plasmid pRE25(*) and a chromosomal marker was co-immobilized with L. monocytogenes and infant feces. In this complex environment, the transfer of pRE25(*) to L. monocytogenes was observed. In a second fermentation, only the E. faecalis donor and feces were co-immobilized. Enumeration of pRE25(*) and the donor strain by quantitative PCR revealed an increasing ratio of pRE25(*) to the donor throughout the 16-day fermentation, indicating the transfer of pRE25(*) . An Enterococcus avium transconjugant was isolated, demonstrating that ABR gene transfer to gut commensals occurred. Moreover, pRE25(*) was still functional in both the E. avium and the L. monocytogenes transconjugant and transmittable to other genera in filter mating experiments. Our study reveals that the transfer of a multiresistance plasmid to commensal bacteria in the presence of competing fecal microbiota occurs in a colonic model, suggesting that commensal bacteria contribute to the increasing prevalence of antibiotic-resistant bacteria.}, }
@article {pmid21658083, year = {2011}, author = {Willems, RJ and Hanage, WP and Bessen, DE and Feil, EJ}, title = {Population biology of Gram-positive pathogens: high-risk clones for dissemination of antibiotic resistance.}, journal = {FEMS microbiology reviews}, volume = {35}, number = {5}, pages = {872-900}, pmid = {21658083}, issn = {1574-6976}, support = {GM088558-01/GM/NIGMS NIH HHS/United States ; AI-061454/AI/NIAID NIH HHS/United States ; R21 AI061454-01/AI/NIAID NIH HHS/United States ; R01 GM060793-01/GM/NIGMS NIH HHS/United States ; R01 GM060793/GM/NIGMS NIH HHS/United States ; U54 GM088558/GM/NIGMS NIH HHS/United States ; R21 AI061454/AI/NIAID NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; GM-60793/GM/NIGMS NIH HHS/United States ; U54 GM088558-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; *Bacterial Typing Techniques ; *Drug Resistance, Multiple, Bacterial ; Gene Transfer, Horizontal ; Genetic Variation ; Genotype ; Gram-Positive Bacteria/*classification/drug effects/*genetics ; Gram-Positive Bacterial Infections/*epidemiology/microbiology/*transmission ; Humans ; Recombination, Genetic ; }, abstract = {Infections caused by multiresistant Gram-positive bacteria represent a major health burden in the community as well as in hospitalized patients. Staphylococcus aureus, Enterococcus faecalis and Enterococcus faecium are well-known pathogens of hospitalized patients, frequently linked with resistance against multiple antibiotics, compromising effective therapy. Streptococcus pneumoniae and Streptococcus pyogenes are important pathogens in the community and S. aureus has recently emerged as an important community-acquired pathogen. Population genetic studies reveal that recombination prevails as a driving force of genetic diversity in E. faecium, E. faecalis, S. pneumoniae and S. pyogenes, and thus, these species are weakly clonal. Although recombination has a relatively modest role driving the genetic variation of the core genome of S. aureus, the horizontal acquisition of resistance and virulence genes plays a key role in the emergence of new clinically relevant clones in this species. In this review, we discuss the population genetics of E. faecium, E. faecalis, S. pneumoniae, S. pyogenes and S. aureus. Knowledge of the population structure of these pathogens is not only highly relevant for (molecular) epidemiological research but also for identifying the genetic variation that underlies changes in clinical behaviour, to improve our understanding of the pathogenic behaviour of particular clones and to identify novel targets for vaccines or immunotherapy.}, }
@article {pmid21658082, year = {2011}, author = {Roberts, AP and Mullany, P}, title = {Tn916-like genetic elements: a diverse group of modular mobile elements conferring antibiotic resistance.}, journal = {FEMS microbiology reviews}, volume = {35}, number = {5}, pages = {856-871}, doi = {10.1111/j.1574-6976.2011.00283.x}, pmid = {21658082}, issn = {1574-6976}, support = {G0601176//Medical Research Council/United Kingdom ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Conjugation, Genetic ; *DNA Transposable Elements ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Gram-Positive Bacteria/*drug effects/*genetics ; Gram-Positive Bacterial Infections/microbiology ; Humans ; Recombination, Genetic ; }, abstract = {Antibiotic-resistant Gram-positive bacteria are responsible for morbidity and mortality in healthcare environments. Enterococcus faecium, Enterococcus faecalis, Staphylococcus aureus and Streptococcus pneumoniae can all exhibit clinically relevant multidrug resistance phenotypes due to acquired resistance genes on mobile genetic elements. It is possible that clinically relevant multidrug-resistant Clostridium difficile strains will appear in the future, as the organism is adept at acquiring mobile genetic elements (plasmids and transposons). Conjugative transposons of the Tn916/Tn1545 family, which carry major antibiotic resistance determinants, are transmissible between these different bacteria by a conjugative mechanism during which the elements are excised by a staggered cut from donor cells, converted to a circular form, transferred by cell-cell contact and inserted into recipient cells by a site-specific recombinase. The ability of these conjugative transposons to acquire additional, clinically relevant antibiotic resistance genes importantly contributes to the emergence of multidrug resistance.}, }
@article {pmid21655311, year = {2011}, author = {Howe, CJ and Windram, HF}, title = {Phylomemetics--evolutionary analysis beyond the gene.}, journal = {PLoS biology}, volume = {9}, number = {5}, pages = {e1001069}, pmid = {21655311}, issn = {1545-7885}, mesh = {Animals ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genomics/*methods ; Humans ; Models, Genetic ; *Phylogeny ; }, abstract = {Genes are propagated by error-prone copying, and the resulting variation provides the basis for phylogenetic reconstruction of evolutionary relationships. Horizontal gene transfer may be superimposed on a tree-like evolutionary pattern, with some relationships better depicted as networks. The copying of manuscripts by scribes is very similar to the replication of genes, and phylogenetic inference programs can be used directly for reconstructing the copying history of different versions of a manuscript text. Phylogenetic methods have also been used for some time to analyse the evolution of languages and the development of physical cultural artefacts. These studies can help to answer a range of anthropological questions. We propose the adoption of the term "phylomemetics" for phylogenetic analysis of reproducing non-genetic elements.}, }
@article {pmid21654106, year = {2011}, author = {Al Sweih, N and Salama, MF and Jamal, W and Al Hashem, G and Rotimi, VO}, title = {An outbreak of CTX-M-15-producing Klebsiella pneumoniae isolates in an intensive care unit of a teaching hospital in Kuwait.}, journal = {Indian journal of medical microbiology}, volume = {29}, number = {2}, pages = {130-135}, doi = {10.4103/0255-0857.81791}, pmid = {21654106}, issn = {1998-3646}, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacterial Typing Techniques ; Bacteriological Techniques ; Blood/microbiology ; Conjugation, Genetic ; *Disease Outbreaks ; Electrophoresis, Gel, Pulsed-Field ; Female ; Gene Transfer, Horizontal ; Genotype ; Hospitals, Teaching ; Humans ; Intensive Care Units ; Klebsiella Infections/*epidemiology/*microbiology ; Klebsiella pneumoniae/classification/*enzymology/genetics/isolation &amp; purification ; Kuwait/epidemiology ; Male ; Middle Aged ; Molecular Typing ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sputum/microbiology ; Urine/microbiology ; beta-Lactamases/*biosynthesis/genetics ; }, abstract = {OBJECTIVE: This study reports an outbreak of Klebsiella pneumoniae infections in 14 patients during a 2-month period (August-September, 2008) in the intensive care unit (ICU) of a teaching hospital in Kuwait.<br><br>MATERIALS AND METHODS: The clinical sources were blood (9), urine (3) and respiratory secretions (2) identified by the automated VITEK-2 ID System. Susceptibility testing was performed by the E-test method. Extended-spectrum &#x3b2;-lactamase (ESBL) production was assessed using the ESBL E-test and confirmed by PCR. Carriage of bla genes was determined by PCR and sequence analysis. The transferability of resistance phenotypes was demonstrated by conjugation experiments and clonal relatedness was determined by PFGE.<br><br>RESULTS: The isolates were susceptible to imipenem, meropenem, and tigecycline and produced ESBL. All isolates yielded an amplicon of 499 bp with universal consensus primers (MA primers). DNA sequence analysis showed that they all harboured bla CTX-M-15 and bla TEM-1 genes. The environmental isolate obtained from a suction machine was also CTX-M-15/TEM-1 producer. The resistance phenotypes were transferrable to the Escherichia coli J53 r strain. PFGE, revealed two clones, A and B, related with a Dice coefficient of >94.1%. A mortality rate of 21.4% was recorded.<br><br>CONCLUSION: The outbreak was contained by robust and aggressive infection control measures. This study highlights the first outbreak of CTX-M-15-producing K. pneumoniae associated with high mortality in an adult medical ICU in Kuwait.}, }
@article {pmid21652779, year = {2011}, author = {Matthews, TD and Rabsch, W and Maloy, S}, title = {Chromosomal rearrangements in Salmonella enterica serovar Typhi strains isolated from asymptomatic human carriers.}, journal = {mBio}, volume = {2}, number = {3}, pages = {e00060-11}, pmid = {21652779}, issn = {2150-7511}, support = {U54 CA132379/CA/NCI NIH HHS/United States ; U54 CA132384/CA/NCI NIH HHS/United States ; 1U54CA132379/CA/NCI NIH HHS/United States ; 1U54CA132384/CA/NCI NIH HHS/United States ; }, mesh = {Bacteriophage Typing ; Carrier State/*microbiology ; Chromosomes, Bacterial/*genetics ; Female ; *Gene Rearrangement ; Genomic Instability ; Humans ; Longitudinal Studies ; Recombination, Genetic ; Salmonella typhi/classification/*genetics/*isolation &amp; purification ; Typhoid Fever/*microbiology ; rRNA Operon ; }, abstract = {Host-specific serovars of Salmonella enterica often have large-scale chromosomal rearrangements that occur by recombination between rrn operons. Two hypotheses have been proposed to explain these rearrangements: (i) replichore imbalance from horizontal gene transfer drives the rearrangements to restore balance, or (ii) the rearrangements are a consequence of the host-specific lifestyle. Although recent evidence has refuted the replichore balance hypothesis, there has been no direct evidence for the lifestyle hypothesis. To test this hypothesis, we determined the rrn arrangement type for 20 Salmonella enterica serovar Typhi strains obtained from human carriers at periodic intervals over multiple years. These strains were also phage typed and analyzed for rearrangements that occurred over long-term storage versus routine culturing. Strains isolated from the same carrier at different time points often exhibited different arrangement types. Furthermore, colonies isolated directly from the Dorset egg slants used to store the strains also had different arrangement types. In contrast, colonies that were repeatedly cultured always had the same arrangement type. Estimated replichore balance of isolated strains did not improve over time, and some of the rearrangements resulted in decreased replicore balance. Our results support the hypothesis that the restricted lifestyle of host-specific Salmonella is responsible for the frequent chromosomal rearrangements in these serovars.}, }
@article {pmid21651684, year = {2012}, author = {Mazard, S and Ostrowski, M and Partensky, F and Scanlan, DJ}, title = {Multi-locus sequence analysis, taxonomic resolution and biogeography of marine Synechococcus.}, journal = {Environmental microbiology}, volume = {14}, number = {2}, pages = {372-386}, doi = {10.1111/j.1462-2920.2011.02514.x}, pmid = {21651684}, issn = {1462-2920}, support = {G0900740/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Aquatic Organisms ; Base Sequence ; Biological Evolution ; Cyanobacteria/classification/genetics ; Ecotype ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sequence Analysis, DNA ; Synechococcus/classification/*genetics ; Water Microbiology ; }, abstract = {Conserved markers such as the 16S rRNA gene do not provide sufficient molecular resolution to identify spatially structured populations of marine Synechococcus, or 'ecotypes' adapted to distinct ecological niches. Multi-locus sequence analysis targeting seven 'core' genes was employed to taxonomically resolve Synechococcus isolates and correlate previous phylogenetic analyses encompassing a range of markers. Despite the recognized importance of lateral gene transfer in shaping the genomes of marine cyanobacteria, multi-locus sequence analysis of more than 120 isolates reflects a clonal population structure of major lineages and subgroups. A single core genome locus, petB, encoding the cytochrome b(6) subunit of the cytochrome b(6) f complex, was selected to expand our understanding of the diversity and ecology of marine Synechococcus populations. Environmental petB sequences cloned from contrasting sites highlight numerous genetically and ecologically distinct clusters, some of which represent novel, environmentally abundant clades without cultured representatives. With a view to scaling ecological analyses, the short sequence, taxonomic resolution and accurate automated alignment of petB is ideally suited to high-throughput and high-resolution sequencing projects to explore links between the ecology, evolution and biology of marine Synechococcus.}, }
@article {pmid21642400, year = {2011}, author = {Król, JE and Nguyen, HD and Rogers, LM and Beyenal, H and Krone, SM and Top, EM}, title = {Increased transfer of a multidrug resistance plasmid in Escherichia coli biofilms at the air-liquid interface.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {15}, pages = {5079-5088}, pmid = {21642400}, issn = {1098-5336}, support = {R01 GM073821/GM/NIGMS NIH HHS/United States ; 1R01 GM73821/GM/NIGMS NIH HHS/United States ; 1S10RR02260601/RR/NCRR NIH HHS/United States ; }, mesh = {*Biofilms ; Cell Count ; Conjugation, Genetic/genetics ; Culture Media ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/*genetics/physiology ; Gene Transfer, Horizontal/*genetics ; Microscopy, Confocal ; Mutation ; Oxygen/metabolism ; Plasmids/*genetics/*metabolism ; }, abstract = {Although biofilms represent a common bacterial lifestyle in clinically and environmentally important habitats, there is scant information on the extent of gene transfer in these spatially structured populations. The objective of this study was to gain insight into factors that affect transfer of the promiscuous multidrug resistance plasmid pB10 in Escherichia coli biofilms. Biofilms were grown in different experimental settings, and plasmid transfer was monitored using laser scanning confocal microscopy and plate counting. In closed flow cells, plasmid transfer in surface-attached submerged biofilms was negligible. In contrast, a high plasmid transfer efficiency was observed in a biofilm floating at the air-liquid interface in an open flow cell with low flow rates. A vertical flow cell and a batch culture biofilm reactor were then used to detect plasmid transfer at different depths away from the air-liquid interface. Extensive plasmid transfer occurred only in a narrow zone near that interface. The much lower transfer frequencies in the lower zones coincided with rapidly decreasing oxygen concentrations. However, when an E. coli csrA mutant was used as the recipient, a thick biofilm was obtained at all depths, and plasmid transfer occurred at similar frequencies throughout. These results and data from separate aerobic and anaerobic matings suggest that oxygen can affect IncP-1 plasmid transfer efficiency, not only directly but also indirectly, through influencing population densities and therefore colocalization of donors and recipients. In conclusion, the air-liquid interface can be a hot spot for plasmid-mediated gene transfer due to high densities of juxtaposed donor and recipient cells.}, }
@article {pmid21640142, year = {2011}, author = {Demanèche, S and Brard, C and Lima, O and Binet, F and Simonet, P}, title = {Development of a new tool to improve gene transfer frequency calculations.}, journal = {Journal of microbiological methods}, volume = {86}, number = {2}, pages = {255-257}, doi = {10.1016/j.mimet.2011.05.014}, pmid = {21640142}, issn = {1872-8359}, mesh = {Acinetobacter/*genetics ; *Gene Transfer Techniques ; *Gene Transfer, Horizontal ; Genetics, Microbial/*methods ; }, abstract = {Gene transfer frequency can be determined experimentally on plates, but the methods currently in use do not discriminate between independent transfers and clonal multiplication of initial transformants. In order to overcome this bias, we engineered an Acinetobacter baylyi population in which cells differed by a specific molecular signature and used it as recipient in transformation experiments. Our results suggest that a corrective factor of 0.52 should be applied in order to accurately report natural transformation when using the plate counting method.}, }
@article {pmid21639932, year = {2011}, author = {de la Chaux, N and Wagner, A}, title = {BEL/Pao retrotransposons in metazoan genomes.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {154}, pmid = {21639932}, issn = {1471-2148}, mesh = {Animals ; Databases, Genetic ; *Evolution, Molecular ; *Genome ; *Retroelements ; *Terminal Repeat Sequences ; }, abstract = {BACKGROUND: Long terminal repeat (LTR) retrotransposons are a widespread kind of transposable element present in eukaryotic genomes. They are a major factor in genome evolution due to their ability to create large scale mutations and genome rearrangements. Compared to other transposable elements, little attention has been paid to elements belonging to the metazoan BEL/Pao subclass of LTR retrotransposons. No comprehensive characterization of these elements is available so far. The aim of this study was to describe all BEL/Pao elements in a set of 62 sequenced metazoan genomes, and to analyze their phylogenetic relationship.<br><br>RESULTS: We identified a total of 7,861 BEL/Pao elements in 53 of our 62 study genomes. We identified BEL/Pao elements in 20 genomes where such elements had not been found so far. Our analysis shows that BEL/Pao elements are the second-most abundant class of LTR retrotransposons in the genomes we study, more abundant than Ty1/Copia elements, and second only to Ty3/Gypsy elements. They occur in multiple phyla, including basal metazoan phyla, suggesting that BEL/Pao elements arose early in animal evolution. We confirm findings from previous studies that BEL/Pao elements do not occur in mammals. The elements we found can be grouped into more than 1725 families, 1623 of which are new, previously unknown families. These families fall into seven superfamilies, only five of which have been characterized so far. One new superfamily is a major subdivision of the Pao superfamily which we propose to call Dan, because it is restricted to the genome of the zebrafish Danio rerio. The other new superfamily comprises 83 elements and is restricted to lower aquatic eumetazoans. We propose to call this superfamily Flow. BEL/Pao elements do not show any signs of recent horizontal gene transfer between distantly related species.<br><br>CONCLUSIONS: In sum, our analysis identifies thousands of new BEL/Pao elements and provides new insights into their distribution, abundance, and evolution.}, }
@article {pmid21638804, year = {2011}, author = {Paziewska, A}, title = {[Diversity of blood parasites of genus Bartonella in wild rodents in Mazury Lakes District].}, journal = {Wiadomosci parazytologiczne}, volume = {57}, number = {1}, pages = {53-54}, pmid = {21638804}, issn = {0043-5163}, mesh = {Animals ; Bartonella/classification/genetics/*isolation &amp; purification/pathogenicity ; Bartonella Infections/*epidemiology/*veterinary ; Coinfection ; Genotype ; Lakes/parasitology ; Poland/epidemiology ; Prevalence ; Rodent Diseases/*epidemiology/*microbiology ; Rodentia/*microbiology ; Species Specificity ; Trees/parasitology ; }, abstract = {This long-term study of genetic diversity and epidemiology of the alpha-proteobacterium Bartonella in wild rodents from forest (Myodes glareolus and Apodemus flavicollis) and abandoned farmland (Microtus arvalis and Mi. oeconomus) was carried out in the years 2007-2009 in the Mazury Lakes District. In total, 1193 rodents were marked and recaptured, and 2226 blood samples were collected. The highest Bartonella prevalence was found in A. flavicollis (43.5%), the lowest in Mi. oeconomus (9.4%), while prevalence in My. glareolus and Mi. arvalis was, respectively, 13.2% and 11.8% (PCR of citrate synthase gltA gene fragment). Prevalence varied according to year and season, as well as sex of rodents. For woodland animals, a rapid decrease of prevalence was observed in late 2008, due to the dilution effect. Multiple (different species/genotypes of Bartonella in successive months) and mixed infections (more than one bacteria genotype in the same blood sample) were also diagnosed. Between 2835 and 4800000 colony forming units (CFU) per ml blood were recorded, with, for B. taylorii, significant differences between isolates from hosts belonging to different host families. Sequence analysis of 147 isolates revealed 37 gltA variants. In all four rodents, B. taylorii was the most prevalent, and could be divided into three main clades. One clade of B. grahamii was present in My. glareolus, A. flavicollis and Mi. arvalis, and both Microtus species were infected with a single clade of B. doshiae. A single isolate of B. birtlesii from A. flavicollis was collected, while two isolates could not be assigned to any known species. Nested clade analysis showed host specificity of 1st step clades (connected with rodent species) and 2nd step clades (connected with rodent family). Analysis was then extended to other housekeeping genes (cell division proteinftsZ, heat shock protein groEl, riboflavin synthase ribC, beta subunit RNA polymerase rpoB) and gene encoding 16S rRNA. Comparison of alleles of these genes in 27 isolates revealed numerous recombinant events, primarily involving groEl and 16S rRNA genes. Moreover, genetic recombination within housekeeping genes was also identified, and one of the unidentified Bartonella isolates was found to involve recombination within gltA between B. grahamii and B. taylorii. Examination of two T4SS pathogenicity genes (virB5 and bepA), revealed a similar pattern of extensive recombination. BepA from 17 isolates showed little diversity, concomitant with its role as an intra-cellular messenger. The virB5 gene (encoding a putative extra-cellular adhesin) from 22 isolates from voles (Arvicolidae) and A. flavicollis was distinctively different in sequence and putative structure, and showed a clear signature of horizontal gene transfer. Moreover, these recombinant events were often identified in the same isolates in which recombination of groEl or 16S rRNA was observed, suggesting that selection for this pathogenicity gene is important in the microevolution of Bartonella within rodents. In particular, Microtus spp. was central in the appearance of novel Bartonella isolates.}, }
@article {pmid21637841, year = {2011}, author = {Lin, A and Jimenez, J and Derr, J and Vera, P and Manapat, ML and Esvelt, KM and Villanueva, L and Liu, DR and Chen, IA}, title = {Inhibition of bacterial conjugation by phage M13 and its protein g3p: quantitative analysis and model.}, journal = {PloS one}, volume = {6}, number = {5}, pages = {e19991}, pmid = {21637841}, issn = {1932-6203}, support = {P50 GM068763/GM/NIGMS NIH HHS/United States ; R01GM065400/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; GM068763/GM/NIGMS NIH HHS/United States ; R01 GM065400/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteriophage M13/genetics/*metabolism/physiology ; *Conjugation, Genetic ; Escherichia coli/growth &amp; development/virology ; F Factor/metabolism ; Genes, Viral/genetics ; *Models, Biological ; Pili, Sex/metabolism ; Time Factors ; Viral Proteins/*metabolism ; Virus Replication ; }, abstract = {Conjugation is the main mode of horizontal gene transfer that spreads antibiotic resistance among bacteria. Strategies for inhibiting conjugation may be useful for preserving the effectiveness of antibiotics and preventing the emergence of bacterial strains with multiple resistances. Filamentous bacteriophages were first observed to inhibit conjugation several decades ago. Here we investigate the mechanism of inhibition and find that the primary effect on conjugation is occlusion of the conjugative pilus by phage particles. This interaction is mediated primarily by phage coat protein g3p, and exogenous addition of the soluble fragment of g3p inhibited conjugation at low nanomolar concentrations. Our data are quantitatively consistent with a simple model in which association between the pili and phage particles or g3p prevents transmission of an F plasmid encoding tetracycline resistance. We also observe a decrease in the donor ability of infected cells, which is quantitatively consistent with a reduction in pili elaboration. Since many antibiotic-resistance factors confer susceptibility to phage infection through expression of conjugative pili (the receptor for filamentous phage), these results suggest that phage may be a source of soluble proteins that slow the spread of antibiotic resistance genes.}, }
@article {pmid21633962, year = {2011}, author = {Abroi, A and Gough, J}, title = {Are viruses a source of new protein folds for organisms? - Virosphere structure space and evolution.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {33}, number = {8}, pages = {626-635}, doi = {10.1002/bies.201000126}, pmid = {21633962}, issn = {1521-1878}, support = {BB/G022771/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Databases, Factual ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; Genome, Viral ; Phylogeny ; *Protein Folding ; Protein Structure, Tertiary ; Viral Proteins/*chemistry ; Viruses/*chemistry/classification/genetics ; }, abstract = {A crucially important part of the biosphere - the virosphere - is too often overlooked. Inclusion of the virosphere into the global picture of protein structure space reveals that 63 protein domain superfamilies in viruses do not have any structural and evolutionary relatives in modern cellular organisms. More than half of these have functions which are not virus-specific and thus might be a source of new folds and functions for cellular life. The number of viruses on the planet exceeds that of cells by an order of magnitude and viruses evolve up to six orders of magnitude faster. As a result, cellular species are subject to a constitutive 'flow-through' of new viral genetic material. Due to this and the relaxed evolutionary constraints in viruses, the transfer of domains between host-to-virus could be a mechanism for accelerated protein evolution. The virosphere could be an engine for the genesis of protein structures, and may even have been so before the last universal common ancestor of cellular life.}, }
@article {pmid21629834, year = {2011}, author = {Shulse, CN and Allen, EE}, title = {Widespread occurrence of secondary lipid biosynthesis potential in microbial lineages.}, journal = {PloS one}, volume = {6}, number = {5}, pages = {e20146}, pmid = {21629834}, issn = {1932-6203}, mesh = {Bacterial Proteins/*genetics/metabolism ; Docosahexaenoic Acids/metabolism ; Eicosapentaenoic Acid/metabolism ; Fatty Acid Synthases/classification/*genetics/metabolism ; Likelihood Functions ; Multigene Family/genetics/physiology ; *Phylogeny ; Polyketide Synthases/classification/*genetics/metabolism ; Vibrio/genetics/metabolism ; }, abstract = {Bacterial production of long-chain omega-3 polyunsaturated fatty acids (PUFAs), such as eicosapentaenoic acid (EPA, 20:5n-3) and docosahexaenoic acid (DHA, 22:6n-3), is constrained to a narrow subset of marine γ-proteobacteria. The genes responsible for de novo bacterial PUFA biosynthesis, designated pfaEABCD, encode large, multi-domain protein complexes akin to type I iterative fatty acid and polyketide synthases, herein referred to as "Pfa synthases". In addition to the archetypal Pfa synthase gene products from marine bacteria, we have identified homologous type I FAS/PKS gene clusters in diverse microbial lineages spanning 45 genera representing 10 phyla, presumed to be involved in long-chain fatty acid biosynthesis. In total, 20 distinct types of gene clusters were identified. Collectively, we propose the designation of "secondary lipids" to describe these biosynthetic pathways and products, a proposition consistent with the "secondary metabolite" vernacular. Phylogenomic analysis reveals a high degree of functional conservation within distinct biosynthetic pathways. Incongruence between secondary lipid synthase functional clades and taxonomic group membership combined with the lack of orthologous gene clusters in closely related strains suggests horizontal gene transfer has contributed to the dissemination of specialized lipid biosynthetic activities across disparate microbial lineages.}, }
@article {pmid21628303, year = {2011}, author = {Poirel, L and Schrenzel, J and Cherkaoui, A and Bernabeu, S and Renzi, G and Nordmann, P}, title = {Molecular analysis of NDM-1-producing enterobacterial isolates from Geneva, Switzerland.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {66}, number = {8}, pages = {1730-1733}, doi = {10.1093/jac/dkr174}, pmid = {21628303}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/pharmacology ; Carbapenems/pharmacology ; Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; Enterobacteriaceae/classification/drug effects/*enzymology/*genetics ; Enterobacteriaceae Infections/*epidemiology/*microbiology ; Gene Transfer, Horizontal ; Hospitals, University ; Humans ; Multilocus Sequence Typing ; Plasmids/analysis ; Polymerase Chain Reaction ; Quinolones/pharmacology ; Sequence Analysis, DNA ; Switzerland/epidemiology ; *beta-Lactam Resistance ; beta-Lactamases/*genetics ; tRNA Methyltransferases/genetics ; }, abstract = {OBJECTIVES: To analyse the mechanisms responsible for decreased susceptibility or resistance to carbapenems in several enterobacterial isolates recovered in 2009-10 in Geneva University Hospitals, Switzerland.<br><br>METHODS: PCR and sequencing were used to identify &#x3b2;-lactamases, 16S RNA methylases and plasmid-mediated quinolone resistance genes. The transferable properties of the plasmids were analysed, as well as their plasmid type. The strains were typed by multilocus sequence typing.<br><br>RESULTS: Three patients were found to be positive for NDM-1-producing enterobacterial isolates (one with Escherichia coli and Klebsiella pneumoniae, one with K. pneumoniae only and one with Proteus mirabilis), where NDM-1 stands for New Delhi metallo-&#x3b2;-lactamase-1. The bla(NDM-1) carbapenemase gene was detected in all isolates in addition to genes encoding narrow-spectrum &#x3b2;-lactamases (TEM-1, SHV-11, OXA-1, OXA-9 and OXA-10), extended-spectrum &#x3b2;-lactamases (CTX-M-15, CMY-16 and CMY-30), ArmA and quinolone resistance determinants (Qnr). The bla(NDM-1) gene was located on conjugative IncA/C- or IncF-type plasmids. Upstream of the bla(NDM-1) gene, part of ISAba125, previously identified in NDM-1-negative Acinetobacter baumannii, was found. Downstream of the bla(NDM-1) gene, variable sequences were found.<br><br>CONCLUSIONS: This work constitutes the first identification of NDM-1 producers in Switzerland. Interestingly, patients from whom these NDM-1-producing isolates were recovered had a link with the Indian subcontinent or the Balkans.}, }
@article {pmid21625519, year = {2011}, author = {Gal-Mor, O and Elhadad, D and Deng, W and Rahav, G and Finlay, BB}, title = {The Salmonella enterica PhoP directly activates the horizontally acquired SPI-2 gene sseL and is functionally different from a S. bongori ortholog.}, journal = {PloS one}, volume = {6}, number = {5}, pages = {e20024}, pmid = {21625519}, issn = {1932-6203}, support = {//Canadian Institutes of Health Research/Canada ; //Howard Hughes Medical Institute/United States ; }, mesh = {Bacterial Proteins/*metabolism ; Base Sequence ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Molecular Sequence Data ; Promoter Regions, Genetic ; Salmonella enterica/genetics/*metabolism ; Sequence Homology, Nucleic Acid ; Transcription, Genetic ; }, abstract = {To establish a successful infection within the host, a pathogen must closely regulate multiple virulence traits to ensure their accurate temporal and spatial expression. As a highly adapted intracellular pathogen, Salmonella enterica has acquired during its evolution various virulence genes via numerous lateral transfer events, including the acquisition of the Salmonella Pathogenicity Island 2 (SPI-2) and its associated effectors. Beneficial use of horizontally acquired genes requires that their expression is effectively coordinated with the already existing virulence programs and the regulatory set-up in the bacterium. As an example for such a mechanism, we show here that the ancestral PhoPQ system of Salmonella enterica is able to regulate directly the SPI-2 effector gene sseL (encoding a secreted deubiquitinase) in an SsrB-independent manner and that PhoP plays a part in a feed-forward regulatory loop, which fine-tunes the cellular level of SseL. Additionally, we demonstrate the presence of conserved cis regulatory elements in the promoter region of sseL and show direct binding of purified PhoP to this region. Interestingly, in contrast to the S. enterica PhoP, an ortholog regulator from a S. bongori SARC 12 strain was found to be impaired in promoting transcription of sseL and other genes from the PhoP regulon. These findings have led to the identification of a previously uncharacterized residue in the DNA-binding domain of PhoP, which is required for the transcriptional activation of PhoP regulated genes in Salmonella spp. Collectively our data demonstrate an interesting interface between the acquired SsrB regulon and the ancestral PhoPQ regulatory circuit, provide novel insights into the function of PhoP, and highlight a mechanism of regulatory integration of horizontally acquired genes into the virulence network of Salmonella enterica.}, }
@article {pmid21625460, year = {2011}, author = {Xue, H and Lu, H and Zhao, X}, title = {Sequence diversities of serine-aspartate repeat genes among Staphylococcus aureus isolates from different hosts presumably by horizontal gene transfer.}, journal = {PloS one}, volume = {6}, number = {5}, pages = {e20332}, pmid = {21625460}, issn = {1932-6203}, mesh = {Animals ; Aspartic Acid/*genetics ; Base Sequence ; Cattle ; DNA, Bacterial ; Female ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Mastitis, Bovine/microbiology ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Nucleic Acid ; Serine/*genetics ; Staphylococcus aureus/classification/*genetics/isolation &amp; purification ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT) is recognized as one of the major forces for bacterial genome evolution. Many clinically important bacteria may acquire virulence factors and antibiotic resistance through HGT. The comparative genomic analysis has become an important tool for identifying HGT in emerging pathogens. In this study, the Serine-Aspartate Repeat (Sdr) family has been compared among different sources of Staphylococcus aureus (S. aureus) to discover sequence diversities within their genomes.<br><br>Four sdr genes were analyzed for 21 different S. aureus strains and 218 mastitis-associated S. aureus isolates from Canada. Comparative genomic analyses revealed that S. aureus strains from bovine mastitis (RF122 and mastitis isolates in this study), ovine mastitis (ED133), pig (ST398), chicken (ED98), and human methicillin-resistant S. aureus (MRSA) (TCH130, MRSA252, Mu3, Mu50, N315, 04-02981, JH1 and JH9) were highly associated with one another, presumably due to HGT. In addition, several types of insertion and deletion were found in sdr genes of many isolates. A new insertion sequence was found in mastitis isolates, which was presumably responsible for the HGT of sdrC gene among different strains. Moreover, the sdr genes could be used to type S. aureus. Regional difference of sdr genes distribution was also indicated among the tested S. aureus isolates. Finally, certain associations were found between sdr genes and subclinical or clinical mastitis isolates.<br><br>CONCLUSIONS: Certain sdr gene sequences were shared in S. aureus strains and isolates from different species presumably due to HGT. Our results also suggest that the distributional assay of virulence factors should detect the full sequences or full functional regions of these factors. The traditional assay using short conserved regions may not be accurate or credible. These findings have important implications with regard to animal husbandry practices that may inadvertently enhance the contact of human and animal bacterial pathogens.}, }
@article {pmid21624495, year = {2011}, author = {Canepa, GE and Carrillo, C and Miranda, MR and Sayé, M and Pereira, CA}, title = {Arginine kinase in Phytomonas, a trypanosomatid parasite of plants.}, journal = {Comparative biochemistry and physiology. Part B, Biochemistry &amp; molecular biology}, volume = {160}, number = {1}, pages = {40-43}, doi = {10.1016/j.cbpb.2011.05.006}, pmid = {21624495}, issn = {1879-1107}, mesh = {Amino Acid Sequence ; Animals ; Arginine Kinase/classification/genetics/*metabolism ; Biological Evolution ; Humans ; Isoenzymes/genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; Plants/*parasitology ; Sequence Alignment ; Trypanosomatina/classification/*enzymology/genetics/*pathogenicity ; }, abstract = {Phytomonas are trypanosomatid plant parasites closely related to parasites that cause several human diseases. Little is known about the biology of these organisms including aspects of their metabolism. Arginine kinase (E.C. 2.7.3.3) is a phosphotransferase which catalyzes the interconversion between the phosphagen phosphoarginine and ATP. This enzyme is present in some invertebrates and is a homolog of another widely distributed phosphosphagen kinase, creatine kinase. In this work, a single canonical arginine kinase isoform was detected in Phytomonas Jma by enzymatic activity assays, PCR, and Western Blot. This arginine kinase is very similar to the canonical isoforms found in T. cruzi and T. brucei, presenting about 70% of amino acid sequence identity and a very similar molecular weight (40kDa). The Phytomonas phosphagen system seems to be very similar to T. cruzi, which has only one isoform, or T. brucei (three isoforms); establishing a difference with other trypanosomatids, such as Leishmania, which completely lacks phosphagen kinases, probably by the presence of the arginine-consuming enzyme, arginase. Finally, phylogenetic analysis suggests that Kinetoplastids' arginine kinase was acquired, during evolution, from the arthropod vectors by horizontal gene transfer.}, }
@article {pmid21622749, year = {2011}, author = {Chan, CX and Beiko, RG and Ragan, MA}, title = {Lateral transfer of genes and gene fragments in Staphylococcus extends beyond mobile elements.}, journal = {Journal of bacteriology}, volume = {193}, number = {15}, pages = {3964-3977}, pmid = {21622749}, issn = {1098-5530}, mesh = {*Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; *Interspersed Repetitive Sequences ; Phylogeny ; Staphylococcal Infections/microbiology ; Staphylococcus/classification/*genetics ; }, abstract = {The widespread presence of antibiotic resistance and virulence among Staphylococcus isolates has been attributed in part to lateral genetic transfer (LGT), but little is known about the broader extent of LGT within this genus. Here we report the first systematic study of the modularity of genetic transfer among 13 Staphylococcus genomes covering four distinct named species. Using a topology-based phylogenetic approach, we found, among 1,354 sets of homologous genes examined, strong evidence of LGT in 368 (27.1%) gene sets, and weaker evidence in another 259 (19.1%). Within-gene and whole-gene transfer contribute almost equally to the topological discordance of these gene sets against a reference phylogeny. Comparing genetic transfer in single-copy and in multicopy gene sets, we observed a higher frequency of LGT in the latter, and a substantial functional bias in cases of whole-gene transfer (little such bias was observed in cases of fragmentary genetic transfer). We found evidence that lateral transfer, particularly of entire genes, impacts not only functions related to antibiotic, drug, and heavy-metal resistance, as well as membrane transport, but also core informational and metabolic functions not associated with mobile elements. Although patterns of sequence similarity support the cohesion of recognized species, LGT within S. aureus appears frequently to disrupt clonal complexes. Our results demonstrate that LGT and gene duplication play important parts in functional innovation in staphylococcal genomes.}, }
@article {pmid21620885, year = {2011}, author = {Mazur, A and Majewska, B and Stasiak, G and Wielbo, J and Skorupska, A}, title = {repABC-based replication systems of Rhizobium leguminosarum bv. trifolii TA1 plasmids: incompatibility and evolutionary analyses.}, journal = {Plasmid}, volume = {66}, number = {2}, pages = {53-66}, doi = {10.1016/j.plasmid.2011.04.002}, pmid = {21620885}, issn = {1095-9890}, mesh = {Bacterial Proteins/genetics/metabolism ; Base Sequence ; Biological Evolution ; DNA Replication ; Gene Transfer, Horizontal ; Genes, Bacterial ; Molecular Sequence Data ; Phylogeny ; Plasmids ; Replicon ; Rhizobium leguminosarum/*genetics ; Sequence Analysis, DNA ; Symbiosis/genetics ; Trifolium/microbiology ; }, abstract = {Soil bacteria of the genus Rhizobium possess complex genomes consisting of a chromosome and in addition, often, multiple extrachromosomal replicons, which are usually equipped with repABC genes that control their replication and partition. The replication regions of four plasmids of Rhizobium leguminosarum bv. trifolii TA1 (RtTA1) were identified and characterized. They all contained a complete set of repABC genes. The structural diversity of the rep regions of RtTA1 plasmids was demonstrated for parS and incα elements, and this was especially apparent in the case of symbiotic plasmid (pSym). Incompatibility assays with recombinant constructs containing parS or incα demonstrated that RtTA1 plasmids belong to different incompatibility groups. Horizontal acquisition was plausibly the main contributor to the origin of RtTA1 plasmids and pSym is probably the newest plasmid of this strain. Phylogenetic and incompatibility analyses of repABC regions of three closely related strains: RtTA1, R. leguminosarum bv. viciae 3841 and Rhizobium etli CFN42, provided data on coexistence of their replicons in a common genomic framework.}, }
@article {pmid21616910, year = {2011}, author = {de Mendoza, A and Ruiz-Trillo, I}, title = {The mysterious evolutionary origin for the GNE gene and the root of bilateria.}, journal = {Molecular biology and evolution}, volume = {28}, number = {11}, pages = {2987-2991}, pmid = {21616910}, issn = {1537-1719}, support = {206883/ERC_/European Research Council/International ; }, mesh = {Animals ; Carbohydrate Epimerases/biosynthesis/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Invertebrates/*genetics ; Likelihood Functions ; Models, Genetic ; *Phylogeny ; }, abstract = {Phylogenomic analyses have revealed several important metazoan clades, such as the Ecdysozoa and the Lophotrochozoa. However, the phylogenetic positions of a few taxa, such as ctenophores, chaetognaths, acoelomorphs, and Xenoturbella, remain contentious. Thus, the findings of qualitative markers or "rare genomic changes" seem ideal to independently test previous phylogenetic hypotheses. We here describe a rare genomic change, the presence of the gene UDP-GlcNAc 2-epimerase/N-acetylmannosamine kinase (GNE). We show that GNE is encoded in the genomes of deuterostomes, acoelomorphs and Xenoturbella, whereas it is absent in protostomes and nonbilaterians. Moreover, the GNE has a complex evolutionary origin involving unique lateral gene transfer events and/or extensive hidden paralogy for each protein domain. However, rather than using GNE as a phylogenetic character, we argue that rare genomic changes such as the one presented here should be used with caution.}, }
@article {pmid21615910, year = {2011}, author = {Joseph, SJ and Didelot, X and Gandhi, K and Dean, D and Read, TD}, title = {Interplay of recombination and selection in the genomes of Chlamydia trachomatis.}, journal = {Biology direct}, volume = {6}, number = {}, pages = {28}, pmid = {21615910}, issn = {1745-6150}, support = {R01 AI059647/AI/NIAID NIH HHS/United States ; }, mesh = {Base Sequence ; Chlamydia trachomatis/classification/*genetics ; DNA, Bacterial/genetics ; Evolution, Molecular ; *Genome, Bacterial ; Linkage Disequilibrium ; Phylogeny ; *Recombination, Genetic ; *Selection, Genetic ; Sequence Alignment ; }, abstract = {BACKGROUND: Chlamydia trachomatis is an obligate intracellular bacterial parasite, which causes several severe and debilitating diseases in humans. This study uses comparative genomic analyses of 12 complete published C. trachomatis genomes to assess the contribution of recombination and selection in this pathogen and to understand the major evolutionary forces acting on the genome of this bacterium.<br><br>RESULTS: The conserved core genes of C. trachomatis are a large proportion of the pan-genome: we identified 836 core genes in C. trachomatis out of a range of 874-927 total genes in each genome. The ratio of recombination events compared to mutation (&#x3c1;/&#x3b8;) was 0.07 based on ancestral reconstructions using the ClonalFrame tool, but recombination had a significant effect on genetic diversification (r/m=0.71). The distance-dependent decay of linkage disequilibrium also indicated that C. trachomatis populations behaved intermediately between sexual and clonal extremes. Fifty-five genes were identified as having a history of recombination and 92 were under positive selection based on statistical tests. Twenty-three genes showed evidence of being under both positive selection and recombination, which included genes with a known role in virulence and pathogencity (e.g., ompA, pmps, tarp). Analysis of inter-clade recombination flux indicated non-uniform currents of recombination between clades, which suggests the possibility of spatial population structure in C. trachomatis infections.<br><br>CONCLUSIONS: C. trachomatis is the archetype of a bacterial species where recombination is relatively frequent yet gene gains by horizontal gene transfer (HGT) and losses (by deletion) are rare. Gene conversion occurs at sites across the whole C. trachomatis genome but may be more often fixed in genes that are under diversifying selection. Furthermore, genome sequencing will reveal patterns of serotype specific gene exchange and selection that will generate important research questions for understanding C. trachomatis pathogenesis.<br><br>REVIEWERS: This article was reviewed by Dr. Jeremy Selengut, Dr. Lee S. Katz (nominated by Dr. I. King Jordan) and Dr. Arcady Mushegian.}, }
@article {pmid21608271, year = {2011}, author = {Li, H and Zhou, LS and Wang, YF and Top, EM and Zhang, Y and Xu, H}, title = {[Degradative mobile genetic elements (MGEs) and their potential use in MGE-mediated biodegradation].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {22}, number = {2}, pages = {526-536}, pmid = {21608271}, issn = {1001-9332}, mesh = {Adaptation, Physiological/genetics ; Bacteria/genetics/*metabolism ; Biodegradation, Environmental ; Biotransformation ; Environmental Pollutants/*metabolism ; Gene Transfer, Horizontal/*genetics ; *Interspersed Repetitive Sequences ; Xenobiotics/*metabolism ; }, abstract = {The horizontal transfer of mobile genetic elements (MGEs) in environmental microbial communities plays an important role in the evolution of bacterial genomes and the adaption of microbial populations to specific environmental stress. Inoculation of the bacterial strains with MGEs with pollutant-degrading gene and the subsequent horizontal transfer of the MGEs to one or various well-established and competitive indigenous bacterial populations in an ecosystem will allow the catabolic gene to be transferred and expressed in indigenous microbial populations, and hence, the survival of the introduced donor strains is no longer needed to be considered. The MGE-mediated bioremediation provides the feasibility for developing new bioremediation strategies. This paper summarized the diversity of MGEs with pollutant-degrading gene in the environment and the important roles of these MGEs in promoting pollutant degradation, introduced the methodological approaches for the isolation of the MGEs from environmental samples, and listed several studies that monitored the horizontal transfer of the MGEs in polluted soil, activated sludge, and other bioreactors.}, }
@article {pmid21602382, year = {2011}, author = {Subbiah, M and Top, EM and Shah, DH and Call, DR}, title = {Selection pressure required for long-term persistence of blaCMY-2-positive IncA/C plasmids.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {13}, pages = {4486-4493}, pmid = {21602382}, issn = {1098-5336}, support = {N01AI30055/AI/NIAID NIH HHS/United States ; R01 AI084918/AI/NIAID NIH HHS/United States ; R01AI084918/AI/NIAID NIH HHS/United States ; }, mesh = {Conjugation, Genetic ; Escherichia coli/enzymology/*genetics ; Gene Transfer, Horizontal ; *Genomic Instability ; *Plasmids ; Salmonella enterica/enzymology/*genetics ; *Selection, Genetic ; beta-Lactamases/*biosynthesis/genetics ; }, abstract = {Multidrug resistance blaCMY-2 plasmids that confer resistance to expanded-spectrum cephalosporins have been found in multiple bacterial species collected from different hosts worldwide. The widespread distribution of blaCMY-2 plasmids may be driven by antibiotic use that selects for the dissemination and persistence of these plasmids. Alternatively, these plasmids may persist and spread in bacterial populations in the absence of selection pressure if a balance exists among conjugative transfer, segregation loss during cell division, and fitness cost to the host. We conducted a series of experiments (both in vivo and in vitro) to study these mechanisms for three blaCMY-2 plasmids, peH4H, pAR060302, and pAM04528. Results of filter mating experiments showed that the conjugation efficiency of blaCMY-2 plasmids is variable, from <10(-7) for pAM04528 and peH4H to ∼10(-3) for pAR060302. Neither peH4H nor pAM04528 was transferred from Escherichia coli strain DH10B, but peH4H was apparently mobilized by the coresident trimethoprim resistance-encoding plasmid pTmpR. Competition studies showed that carriage of blaCMY-2 plasmids imposed a measurable fitness cost on the host bacteria both in vitro (0.095 to 0.25) and in vivo (dairy calf model). Long-term passage experiments in the absence of antibiotics demonstrated that plasmids with limited antibiotic resistance phenotypes arose, but eventually drug-sensitive, plasmid-free clones dominated the populations. Given that plasmid decay or loss is inevitable, we infer that some level of selection is required for the long-term persistence of blaCMY-2 plasmids in bacterial populations.}, }
@article {pmid21602291, year = {2011}, author = {Ng, DW and Zhang, C and Miller, M and Palmer, G and Whiteley, M and Tholl, D and Chen, ZJ}, title = {cis- and trans-Regulation of miR163 and target genes confers natural variation of secondary metabolites in two Arabidopsis species and their allopolyploids.}, journal = {The Plant cell}, volume = {23}, number = {5}, pages = {1729-1740}, pmid = {21602291}, issn = {1532-298X}, support = {R01 AI075068/AI/NIAID NIH HHS/United States ; R01 AI075068-04/AI/NIAID NIH HHS/United States ; }, mesh = {Alamethicin/pharmacology ; Arabidopsis/*genetics/growth &amp; development/metabolism ; Arabidopsis Proteins/*genetics/metabolism ; DNA, Complementary/genetics ; Epigenesis, Genetic ; Fatty Acids, Unsaturated/metabolism ; Gene Expression Regulation, Plant/*genetics ; Gene Transfer, Horizontal ; Genes, Plant/genetics ; Genome, Plant/genetics ; Methyltransferases/drug effects/genetics/*metabolism ; MicroRNAs/*genetics ; Mutagenesis, Insertional ; Plant Leaves/genetics/metabolism ; Polyploidy ; Promoter Regions, Genetic/*genetics ; RNA, Plant/genetics ; Sequence Analysis, DNA ; Species Specificity ; Stress, Physiological ; }, abstract = {MicroRNAs (miRNAs) play essential roles in plant and animal development, but the cause and effect of miRNA expression divergence between closely related species and in interspecific hybrids or allopolyploids are unknown. Here, we show differential regulation of a miR163-mediated pathway in allotetraploids and their progenitors, Arabidopsis thaliana and Arabidopsis arenosa. miR163 is a recently evolved miRNA in A. thaliana and highly expressed in A. thaliana, but its expression was undetectable in A. arenosa and repressed in resynthesized allotetraploids. Repression of A. arenosa MIR163 (Aa MIR163) is caused by a weak cis-acting promoter and putative trans-acting repressor(s) present in A. arenosa and allotetraploids. Moreover, ectopic Aa MIR163 precursors were processed more efficiently in A. thaliana than in resynthesized allotetraploids, suggesting a role of posttranscriptional regulation in mature miR163 abundance. Target genes of miR163 encode a family of small molecule methyltransferases involved in secondary metabolite biosynthetic pathways that are inducible by a fungal elicitor, alamethicin. Loss of miR163 or overexpression of miR163 in mir163 mutant plants alters target transcript and secondary metabolite profiles. We suggest that cis- and trans-regulation of miRNA and other genes provides a molecular basis for natural variation of biochemical and metabolic pathways that are important to growth vigor and stress responses in Arabidopsis-related species and allopolyploids.}, }
@article {pmid21601510, year = {2011}, author = {Monier, JM and Demanèche, S and Delmont, TO and Mathieu, A and Vogel, TM and Simonet, P}, title = {Metagenomic exploration of antibiotic resistance in soil.}, journal = {Current opinion in microbiology}, volume = {14}, number = {3}, pages = {229-235}, doi = {10.1016/j.mib.2011.04.010}, pmid = {21601510}, issn = {1879-0364}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/*genetics ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Humans ; *Metagenome ; *Soil Microbiology ; }, abstract = {The ongoing development of metagenomic approaches is providing the means to explore antibiotic resistance in nature and address questions that could not be answered previously with conventional culture-based strategies. The number of available environmental metagenomic sequence datasets is rapidly expanding and henceforth offer the ability to gain a more comprehensive understanding of antibiotic resistance at the global scale. Although there is now evidence that the environment constitutes a vast reservoir of antibiotic resistance gene determinants (ARGDs) and that the majority of ARGDs acquired by human pathogens may have an environmental origin, a better understanding of their diversity, prevalence and ecological significance may help predict the emergence and spreading of newly acquired resistances. Recent applications of metagenomic approaches to the study of ARGDs in natural environments such as soil should help overcome challenges concerning expanding antibiotic resistances.}, }
@article {pmid21600774, year = {2011}, author = {Rohmer, L and Hocquet, D and Miller, SI}, title = {Are pathogenic bacteria just looking for food? Metabolism and microbial pathogenesis.}, journal = {Trends in microbiology}, volume = {19}, number = {7}, pages = {341-348}, pmid = {21600774}, issn = {1878-4380}, support = {U54 AI057141/AI/NIAID NIH HHS/United States ; U54 AI057141-07/AI/NIAID NIH HHS/United States ; U54 AI057141-08/AI/NIAID NIH HHS/United States ; U54AI057141/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics/*metabolism/pathogenicity ; Biological Evolution ; Gene Transfer, Horizontal ; *Host-Pathogen Interactions ; Humans ; Intestines/*microbiology ; *Metabolomics ; Multigene Family ; Mutation ; N-Acetylneuraminic Acid/metabolism ; Urease/metabolism ; Virulence Factors/genetics/metabolism ; }, abstract = {It is interesting to speculate that the evolutionary drive for microbes to develop pathogenic characteristics was to access the nutrient resources that animals provided. Animal environments that pathogens colonize have likely driven the evolution of new bacterial characteristics to maximize these new nutritional opportunities. This review focuses on genomic and functional aspects of pathogen metabolism that allow efficient utilization of nutrient resources provided by animals. Similar to genes encoding specific virulence traits, genes encoding metabolic functions have been horizontally acquired by pathogens to provide a selective advantage in host tissues. Selective advantage in host tissues can also be gained by loss of function mutations that alter metabolic capabilities. Greater understanding of bacterial metabolism within host tissues should be important for increased understanding of host-pathogen interactions and the development of future therapeutic strategies.}, }
@article {pmid21599729, year = {2011}, author = {Dutta, A and Kundu, JK and Chatterjee, R and Chaudhuri, K}, title = {In silico comparative study of the genomic islands of Vibrio cholerae MJ1236 with those of Classical and El Tor N16961 strains of Vibrio cholerae.}, journal = {FEMS microbiology letters}, volume = {321}, number = {1}, pages = {75-81}, doi = {10.1111/j.1574-6968.2011.02316.x}, pmid = {21599729}, issn = {1574-6968}, mesh = {Biological Evolution ; *Computational Biology ; Gene Transfer, Horizontal/genetics ; Genetic Variation ; Genome, Bacterial/*genetics ; Genomic Islands/*genetics ; Open Reading Frames/genetics ; Vibrio cholerae/*genetics ; }, abstract = {The evolution of microbial genomes is greatly influenced by horizontal gene transfer (HGT), where large blocks of horizontally acquired foreign sequences, often encoding virulence determinants, occur in chromosomes of pathogenic bacteria. A program design-island developed in our laboratory was used on three completely sequenced Vibrio cholerae genomes, V. cholerae Classical O395, El Tor N16961 and MJ1236, in order to identify the putative horizontally acquired regions. The putative genomic islands (GIs) were graphically represented and analyzed. The study identified distinct regions in the GIs of V. cholerae MJ1236 which were shared either with the Classical or the El Tor strain of V. cholerae. A cluster comprising of 38 ORFs was common to V. cholerae strains of MJ1236 and Classical O395 but absent in El Tor N16961. About 5% of the predicted GIs of V. cholerae MJ1236 were unique to itself. Among these unique ORFs, a region of mostly hypothetical genes was identified, where the ORFs were present in a large cluster. The results show that the HGT had played a significant role in the evolution and the differentiation of V. cholerae MJ1236.}, }
@article {pmid21596752, year = {2011}, author = {Nguyen, GK and Zhang, S and Nguyen, NT and Nguyen, PQ and Chiu, MS and Hardjojo, A and Tam, JP}, title = {Discovery and characterization of novel cyclotides originated from chimeric precursors consisting of albumin-1 chain a and cyclotide domains in the Fabaceae family.}, journal = {The Journal of biological chemistry}, volume = {286}, number = {27}, pages = {24275-24287}, pmid = {21596752}, issn = {1083-351X}, mesh = {Amino Acid Sequence ; Anti-Infective Agents/metabolism/pharmacology ; *Clitoria/genetics/metabolism ; *Cyclotides/genetics/metabolism/pharmacology ; Cytotoxins/genetics/metabolism/pharmacology ; Escherichia coli/growth &amp; development ; *Evolution, Molecular ; Gene Transfer, Horizontal/physiology ; Genome, Plant/physiology ; HeLa Cells ; Humans ; Molecular Sequence Data ; *Plant Proteins/genetics/metabolism/pharmacology ; *Protein Precursors/genetics/metabolism ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sequence Homology, Amino Acid ; }, abstract = {The tropical plant Clitoria ternatea is a member of the Fabaceae family well known for its medicinal values. Heat extraction of C. ternatea revealed that the bioactive fractions contained heat-stable cysteine-rich peptides (CRPs). The CRP family of A1b (Albumin-1 chain b/leginsulins), which is a linear cystine knot CRP, has been shown to present abundantly in the Fabaceae. In contrast, the cyclotide family, which also belongs to the cystine knot CRPs but with a cyclic structure, is commonly found in the Rubiaceae, Violaceae, and Cucurbitaceae families. In this study, we report the discovery of a panel of 15 heat-stable CRPs, of which 12 sequences (cliotide T1-T12) are novel. We show unambiguously that the cliotides are cyclotides and not A1bs, as determined by their sequence homology, disulfide connectivity, and membrane active properties indicated by their antimicrobial activities against Escherichia coli and cytotoxicities to HeLa cells. We also show that cliotides are prevalent in C. ternatea and are found in every plant tissue examined, including flowers, seeds, and nodules. In addition, we demonstrate that their precursors are chimeras, half from cyclotide and the other half from Albumin-1, with the cyclotide domain displacing the A1b domain in the precursor. Their chimeric structures likely originate from either horizontal gene transfer or convergent evolution in plant nuclear genomes, which are exceedingly rare events. Such atypical genetic arrangement also implies a different mechanism of biosynthetic processing of cyclotides in the Fabaceae and provides new understanding of their evolution in plants.}, }
@article {pmid21595916, year = {2011}, author = {Zhu, B and Lou, MM and Xie, GL and Zhang, GQ and Zhou, XP and Li, B and Jin, GL}, title = {Horizontal gene transfer in silkworm, Bombyx mori.}, journal = {BMC genomics}, volume = {12}, number = {}, pages = {248}, pmid = {21595916}, issn = {1471-2164}, mesh = {Animals ; Biodiversity ; Bombyx/*genetics/immunology/metabolism ; Energy Metabolism/genetics ; Gene Transfer, Horizontal/*genetics ; Immunity, Innate/genetics ; Proteome/genetics/metabolism ; Toxins, Biological/metabolism ; }, abstract = {BACKGROUND: The domesticated silkworm, Bombyx mori, is the model insect for the order Lepidoptera, has economically important values, and has gained some representative behavioral characteristics compared to its wild ancestor. The genome of B. mori has been fully sequenced while function analysis of BmChi-h and BmSuc1 genes revealed that horizontal gene transfer (HGT) maybe bestow a clear selective advantage to B. mori. However, the role of HGT in the evolutionary history of B. mori is largely unexplored. In this study, we compare the whole genome of B. mori with those of 382 prokaryotic and eukaryotic species to investigate the potential HGTs.<br><br>RESULTS: Ten candidate HGT events were defined in B. mori by comprehensive sequence analysis using Maximum Likelihood and Bayesian method combining with EST checking. Phylogenetic analysis of the candidate HGT genes suggested that one HGT was plant-to- B. mori transfer while nine were bacteria-to- B. mori transfer. Furthermore, functional analysis based on expression, coexpression and related literature searching revealed that several HGT candidate genes have added important characters, such as resistance to pathogen, to B. mori.<br><br>CONCLUSIONS: Results from this study clearly demonstrated that HGTs play an important role in the evolution of B. mori although the number of HGT events in B. mori is in general smaller than those of microbes and other insects. In particular, interdomain HGTs in B. mori may give rise to functional, persistent, and possibly evolutionarily significant new genes.}, }
@article {pmid21595768, year = {2011}, author = {Dyer, KA and Burke, C and Jaenike, J}, title = {Wolbachia-mediated persistence of mtDNA from a potentially extinct species.}, journal = {Molecular ecology}, volume = {20}, number = {13}, pages = {2805-2817}, doi = {10.1111/j.1365-294X.2011.05128.x}, pmid = {21595768}, issn = {1365-294X}, mesh = {Animals ; Base Sequence ; Biological Evolution ; DNA, Mitochondrial/*genetics ; Drosophila/*genetics/microbiology ; Female ; Gene Transfer, Horizontal ; Haplotypes ; Maine ; Models, Genetic ; Molecular Sequence Data ; Multilocus Sequence Typing ; New York ; Pennsylvania ; Phylogeny ; Polymorphism, Genetic ; Sequence Analysis, DNA ; Symbiosis ; Time Factors ; Wolbachia/*genetics ; }, abstract = {Drosophila quinaria is polymorphic for infection with Wolbachia, a maternally transmitted endosymbiont. Wolbachia-infected individuals carry mtDNA that is only distantly related to the mtDNA of uninfected individuals, and the clade encompassing all mtDNA haplotypes within D. quinaria also includes the mtDNA of several other species of Drosophila. Nuclear gene variation reveals no difference between the Wolbachia-infected and uninfected individuals of D. quinaria, indicating that they all belong to the same interbreeding biological species. We suggest that the Wolbachia and the mtDNA with which it is associated were derived via interspecific hybridization and introgression. The sequences in the Wolbachia and the associated mtDNA are ≥6% divergent from those of any known Drosophila species. Thus, in spite of nearly complete species sampling, the sequences from which these mitochondria were derived remain unknown, raising the possibility that the donor species is extinct. The association between Wolbachia infection and mtDNA type within D. quinaria suggests that Wolbachia may be required for the continued persistence of the mtDNA from an otherwise extinct Drosophila species. We hypothesize that pathogen-protective effects conferred by Wolbachia operate in a negative frequency-dependent manner, thus bringing about a stable polymorphism for Wolbachia infection.}, }
@article {pmid21592744, year = {2011}, author = {Flemming, HC}, title = {The perfect slime.}, journal = {Colloids and surfaces. B, Biointerfaces}, volume = {86}, number = {2}, pages = {251-259}, doi = {10.1016/j.colsurfb.2011.04.025}, pmid = {21592744}, issn = {1873-4367}, mesh = {Adsorption ; *Biofilms/drug effects ; Biofouling/prevention &amp; control ; Disinfectants/pharmacology ; Extracellular Matrix/*physiology/ultrastructure ; Models, Molecular ; Polymers/chemistry ; Pseudomonas aeruginosa/drug effects/*physiology/ultrastructure ; Streptococcus/drug effects/*physiology/ultrastructure ; Surface Properties ; Water ; }, abstract = {The biofilm mode of life is only possible because biofilm organisms are transiently immobilized in a matrix of extracellular polymeric substances (EPS), also known as "slime". The matrix can be considered an emerging property of microorganisms, allowing them to form stable synergistic consortia, supporting interaction by signaling molecules and horizontal gene transfer and, eventually being activated by extracellular enzymes which turn the matrix into an external digestion system. As unsightly it is, this matrix is--although seemingly stochastic--a highly differentiated and functional immediate environment for biofilm cells.}, }
@article {pmid21586577, year = {2011}, author = {Durand, E and Alphonse, S and Brochier-Armanet, C and Ball, G and Douzi, B and Filloux, A and Bernard, C and Voulhoux, R}, title = {The assembly mode of the pseudopilus: a hallmark to distinguish a novel secretion system subtype.}, journal = {The Journal of biological chemistry}, volume = {286}, number = {27}, pages = {24407-24416}, pmid = {21586577}, issn = {1083-351X}, mesh = {*Bacterial Proteins/genetics/metabolism ; Bacterial Secretion Systems/*physiology ; *Evolution, Molecular ; Fimbriae, Bacterial/genetics/metabolism ; Gene Transfer, Horizontal/*physiology ; *Pseudomonas aeruginosa/genetics/metabolism ; }, abstract = {In gram-negative bacteria, type II secretion systems assemble a piston-like structure, called pseudopilus, which expels exoproteins out of the cell. The pseudopilus is constituted by a major pseudopilin that when overproduced multimerizes into a long cell surface structure named hyper-pseudopilus. Pseudomonas aeruginosa possesses two type II secretion systems, Xcp and Hxc. Although major pseudopilins are exchangeable among type II secretion systems, we show that XcpT and HxcT are not. We demonstrate that HxcT does not form a hyper-pseudopilus and is different in amino acid sequence and multimerization properties. Using structure-based mutagenesis, we observe that five mutations are sufficient to revert HxcT into a functional XcpT-like protein, which also becomes capable of forming a hyper-pseudopilus. Phylogenetic and experimental analysis showed that the whole Hxc system was acquired by P. aeruginosa PAO1 and other Pseudomonas species through horizontal gene transfer. We thus identified a new type II secretion subfamily, of which the P. aeruginosa Hxc system is the archetype. This finding demonstrates how similar bacterial machineries evolve toward distinct mechanisms that may contribute specific functions.}, }
@article {pmid21576759, year = {2011}, author = {Zhang, L}, title = {From gene trees to species trees II: species tree inference by minimizing deep coalescence events.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {8}, number = {6}, pages = {1685-1691}, doi = {10.1109/TCBB.2011.83}, pmid = {21576759}, issn = {1557-9964}, mesh = {Algorithms ; *Gene Duplication ; *Gene Transfer, Horizontal ; Genes ; Genetic Speciation ; Phylogeny ; }, abstract = {When gene copies are sampled from various species, the resulting gene tree might disagree with the containing species tree. The primary causes of gene tree and species tree discord include incomplete lineage sorting, horizontal gene transfer, and gene duplication and loss. Each of these events yields a different parsimony criterion for inferring the (containing) species tree from gene trees. With incomplete lineage sorting, species tree inference is to find the tree minimizing extra gene lineages that had to coexist along species lineages; with gene duplication, it becomes to find the tree minimizing gene duplications and/or losses. In this paper, we present the following results: 1) The deep coalescence cost is equal to the number of gene losses minus two times the gene duplication cost in the reconciliation of a uniquely leaf labeled gene tree and a species tree. The deep coalescence cost can be computed in linear time for any arbitrary gene tree and species tree. 2) The deep coalescence cost is always not less than the gene duplication cost in the reconciliation of an arbitrary gene tree and a species tree. 3) Species tree inference by minimizing deep coalescence events is NP-hard.}, }
@article {pmid21576078, year = {2011}, author = {Lee, YI and Chang, FC and Chung, MC}, title = {Chromosome pairing affinities in interspecific hybrids reflect phylogenetic distances among lady's slipper orchids (Paphiopedilum).}, journal = {Annals of botany}, volume = {108}, number = {1}, pages = {113-121}, pmid = {21576078}, issn = {1095-8290}, mesh = {Breeding ; Chromosome Pairing/*genetics ; DNA, Ribosomal/genetics ; Gene Transfer, Horizontal/*genetics ; Genetic Loci ; Genome, Plant/*genetics ; In Situ Hybridization/*methods ; In Situ Hybridization, Fluorescence ; Karyotyping ; Meiosis/genetics ; Orchidaceae/*genetics/ultrastructure ; Phylogeny ; Pollen/genetics ; Species Specificity ; }, abstract = {BACKGROUND AND AIMS: Lady's slipper orchids (Paphiopedilum) are of high value in floriculture, and interspecific hybridization has long been used for breeding improved cultivars; however, information regarding the genome affinities of species and chromosome pairing behaviour of the hybrids remains almost unknown. The present work analyses the meiotic behaviour of interspecific hybrids by genomic in situ hybridization and cytologically evaluates the genomic relationships among parental species.<br><br>METHODS: Eight interspecific F(1) hybrids of Paphiopedilum species in various subgenera or sections were investigated in this study. The chromosome behaviour in meiosis of these interspecific hybrids was analysed and subjected to genomic in situ hybridization and fluorescent in situ hybridization.<br><br>KEY RESULTS: Genomic in situ hybridization was demonstrated as an efficient method to differentiate between Paphiopedilum genomes and to visualize the chromosome pairing affinities in interspecific F(1) hybrids, clarifying the phylogenetic distances among these species. Comparatively regular chromosome pairing observed in the hybrids of P. delenatii &#xd7; P. bellatulum, P. delenatii &#xd7; P. rothschildianum and P. rothschildianum &#xd7; P. bellatulum suggested high genomic affinities and close relationships between parents of each hybrid. In contrast, irregular chromosome associations, such as univalents, trivalents and quadrivalents occurred frequently in the hybrids derived from distant parents with divergent karyotypes, such as P. delenatii &#xd7; P. callosum, P. delenatii &#xd7; P. glaucophyllum, P. rothschildianum &#xd7; P. micranthum and P. rothschildianum &#xd7; P. moquetteanum. The existence of multivalents and autosyndesis demonstrated by genomic in situ hybridization in this study indicates that some micro-rearrangements and other structural alterations may also play a part in differentiating Paphiopedilum species at chromosomal level, demonstrated as different chromosome pairing affinities in interspecific hybrids.<br><br>CONCLUSIONS: The results indicate that genome homology and the interaction of genetic factors, but not chromosome number nor karyotype similarity, determine the chromosome pairing behaviour in Paphiopedilum hybrids.}, }
@article {pmid21573110, year = {2011}, author = {Nozawa, T and Furukawa, N and Aikawa, C and Watanabe, T and Haobam, B and Kurokawa, K and Maruyama, F and Nakagawa, I}, title = {CRISPR inhibition of prophage acquisition in Streptococcus pyogenes.}, journal = {PloS one}, volume = {6}, number = {5}, pages = {e19543}, pmid = {21573110}, issn = {1932-6203}, mesh = {DNA, Intergenic/genetics ; Genetic Loci/genetics ; Genome, Bacterial/genetics ; Humans ; Inverted Repeat Sequences/*genetics ; Phylogeny ; Prophages/*physiology ; Recombination, Genetic/genetics ; Sequence Deletion/genetics ; Streptococcus pyogenes/*genetics/*virology ; Virus Integration/physiology ; }, abstract = {Streptococcus pyogenes, one of the major human pathogens, is a unique species since it has acquired diverse strain-specific virulence properties mainly through the acquisition of streptococcal prophages. In addition, S. pyogenes possesses clustered regularly interspaced short palindromic repeats (CRISPR)/Cas systems that can restrict horizontal gene transfer (HGT) including phage insertion. Therefore, it was of interest to examine the relationship between CRISPR and acquisition of prophages in S. pyogenes. Although two distinct CRISPR loci were found in S. pyogenes, some strains lacked CRISPR and these strains possess significantly more prophages than CRISPR harboring strains. We also found that the number of spacers of S. pyogenes CRISPR was less than for other streptococci. The demonstrated spacer contents, however, suggested that the CRISPR appear to limit phage insertions. In addition, we found a significant inverse correlation between the number of spacers and prophages in S. pyogenes. It was therefore suggested that S. pyogenes CRISPR have permitted phage insertion by lacking its own spacers. Interestingly, in two closely related S. pyogenes strains (SSI-1 and MGAS315), CRISPR activity appeared to be impaired following the insertion of phage genomes into the repeat sequences. Detailed analysis of this prophage insertion site suggested that MGAS315 is the ancestral strain of SSI-1. As a result of analysis of 35 additional streptococcal genomes, it was suggested that the influences of the CRISPR on the phage insertion vary among species even within the same genus. Our results suggested that limitations in CRISPR content could explain the characteristic acquisition of prophages and might contribute to strain-specific pathogenesis in S. pyogenes.}, }
@article {pmid21572525, year = {2011}, author = {John, SG and Mendez, CB and Deng, L and Poulos, B and Kauffman, AK and Kern, S and Brum, J and Polz, MF and Boyle, EA and Sullivan, MB}, title = {A simple and efficient method for concentration of ocean viruses by chemical flocculation.}, journal = {Environmental microbiology reports}, volume = {3}, number = {2}, pages = {195-202}, pmid = {21572525}, issn = {1758-2229}, abstract = {Ocean viruses alter ecosystems through host mortality, horizontal gene transfer and by facilitating remineralization of limiting nutrients. However, the study of wild viral populations is limited by inefficient and unreliable concentration techniques. Here, we develop a new technique to recover viruses from natural waters using iron-based flocculation and large-pore-size filtration, followed by resuspension of virus-containing precipitates in a pH 6 buffer. Recovered viruses are amenable to gene sequencing, and a variable proportion of phages, depending upon the phage, retain their infectivity when recovered. This Fe-based virus flocculation, filtration and resuspension method (FFR) is efficient (> 90% recovery), reliable, inexpensive and adaptable to many aspects of marine viral ecology and genomics research.}, }
@article {pmid21572095, year = {2011}, author = {Castoe, TA and Hall, KT and Guibotsy Mboulas, ML and Gu, W and de Koning, AP and Fox, SE and Poole, AW and Vemulapalli, V and Daza, JM and Mockler, T and Smith, EN and Feschotte, C and Pollock, DD}, title = {Discovery of highly divergent repeat landscapes in snake genomes using high-throughput sequencing.}, journal = {Genome biology and evolution}, volume = {3}, number = {}, pages = {641-653}, pmid = {21572095}, issn = {1759-6653}, support = {GM77582/GM/NIGMS NIH HHS/United States ; R01 GM083127/GM/NIGMS NIH HHS/United States ; R01 GM077582/GM/NIGMS NIH HHS/United States ; LM009451/LM/NLM NIH HHS/United States ; T15 LM009451/LM/NLM NIH HHS/United States ; GM083127/GM/NIGMS NIH HHS/United States ; }, mesh = {Agkistrodon/*genetics ; Animals ; Biological Evolution ; Boidae/*genetics ; DNA Transposable Elements/genetics ; Gene Duplication/genetics ; Gene Transfer, Horizontal/genetics ; *Genome ; High-Throughput Nucleotide Sequencing/methods ; Microsatellite Repeats/genetics ; Repetitive Sequences, Nucleic Acid/*genetics ; }, abstract = {We conducted a comprehensive assessment of genomic repeat content in two snake genomes, the venomous copperhead (Agkistrodon contortrix) and the Burmese python (Python molurus bivittatus). These two genomes are both relatively small (∼1.4 Gb) but have surprisingly extensive differences in the abundance and expansion histories of their repeat elements. In the python, the readily identifiable repeat element content is low (21%), similar to bird genomes, whereas that of the copperhead is higher (45%), similar to mammalian genomes. The copperhead's greater repeat content arises from the recent expansion of many different microsatellites and transposable element (TE) families, and the copperhead had 23-fold greater levels of TE-related transcripts than the python. This suggests the possibility that greater TE activity in the copperhead is ongoing. Expansion of CR1 LINEs in the copperhead genome has resulted in TE-mediated microsatellite expansion ("microsatellite seeding") at a scale several orders of magnitude greater than previously observed in vertebrates. Snakes also appear to be prone to horizontal transfer of TEs, particularly in the copperhead lineage. The reason that the copperhead has such a small genome in the face of so much recent expansion of repeat elements remains an open question, although selective pressure related to extreme metabolic performance is an obvious candidate. TE activity can affect gene regulation as well as rates of recombination and gene duplication, and it is therefore possible that TE activity played a role in the evolution of major adaptations in snakes; some evidence suggests this may include the evolution of venom repertoires.}, }
@article {pmid21571879, year = {2011}, author = {Heinrich-Salmeron, A and Cordi, A and Brochier-Armanet, C and Halter, D and Pagnout, C and Abbaszadeh-fard, E and Montaut, D and Seby, F and Bertin, PN and Bauda, P and Arsène-Ploetze, F}, title = {Unsuspected diversity of arsenite-oxidizing bacteria as revealed by widespread distribution of the aoxB gene in prokaryotes.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {13}, pages = {4685-4692}, pmid = {21571879}, issn = {1098-5336}, mesh = {Archaea/*enzymology/genetics/isolation &amp; purification/*metabolism ; Arsenites/*metabolism ; Bacteria/*enzymology/genetics/isolation &amp; purification/*metabolism ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; *Environmental Microbiology ; France ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {In this study, new strains were isolated from an environment with elevated arsenic levels, Sainte-Marie-aux-Mines (France), and the diversity of aoxB genes encoding the arsenite oxidase large subunit was investigated. The distribution of bacterial aoxB genes is wider than what was previously thought. AoxB subfamilies characterized by specific signatures were identified. An exhaustive analysis of AoxB sequences from this study and from public databases shows that horizontal gene transfer has likely played a role in the spreading of aoxB in prokaryotic communities.}, }
@article {pmid21571751, year = {2011}, author = {Soge, OO and Roberts, MC}, title = {tet(M)-carrying Haemophilus influenzae as a potential reservoir for mobile antibiotic resistance genes.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {66}, number = {7}, pages = {1642-1643}, doi = {10.1093/jac/dkr189}, pmid = {21571751}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/*genetics ; Cystic Fibrosis/complications ; DNA Transposable Elements ; *Drug Resistance, Bacterial ; *Gene Transfer, Horizontal ; Haemophilus Infections/microbiology ; Haemophilus influenzae/*drug effects/*genetics/isolation &amp; purification ; Humans ; *Interspersed Repetitive Sequences ; Macrolides/pharmacology ; Tetracyclines/pharmacology ; }, }
@article {pmid21570257, year = {2011}, author = {Drieux, L and Bourgeois-Nicolaos, N and Cremniter, J and Lawrence, C and Jarlier, V and Doucet-Populaire, F and Sougakoff, W}, title = {Accumulation of carbapenemase-producing Gram-negative bacteria in a single patient linked to the acquisition of multiple carbapenemase producers and to the in vivo transfer of a plasmid encoding VIM-1.}, journal = {International journal of antimicrobial agents}, volume = {38}, number = {2}, pages = {179-180}, doi = {10.1016/j.ijantimicag.2011.03.017}, pmid = {21570257}, issn = {1872-7913}, mesh = {Bacterial Proteins/*biosynthesis/genetics ; DNA, Bacterial/chemistry/genetics ; *Gene Transfer, Horizontal ; Gram-Negative Bacteria/drug effects/*enzymology/genetics/isolation &amp; purification ; Gram-Negative Bacterial Infections/*microbiology ; Humans ; Male ; Middle Aged ; Molecular Sequence Data ; *Plasmids ; Sequence Analysis, DNA ; beta-Lactamases/*biosynthesis/genetics ; }, }
@article {pmid21569540, year = {2011}, author = {Matthews, S and Rao, VS and Durvasula, RV}, title = {Modeling horizontal gene transfer (HGT) in the gut of the Chagas disease vector Rhodnius prolixus.}, journal = {Parasites &amp; vectors}, volume = {4}, number = {}, pages = {77}, pmid = {21569540}, issn = {1756-3305}, support = {R01 AI06604501/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Antimicrobial Cationic Peptides/*genetics/metabolism ; Antiprotozoal Agents/metabolism ; Chagas Disease/prevention &amp; control ; *Disease Vectors ; Gastrointestinal Tract/*microbiology ; *Gene Transfer, Horizontal ; Gordonia Bacterium/genetics ; Pest Control, Biological/methods ; Rhodnius/*microbiology ; Rhodococcus/*genetics/growth &amp; development ; Trypanosoma cruzi/drug effects/growth &amp; development ; }, abstract = {BACKGROUND: Paratransgenesis is an approach to reducing arthropod vector competence using genetically modified symbionts. When applied to control of Chagas disease, the symbiont bacterium Rhodococcus rhodnii, resident in the gut lumen of the triatomine vector Rhodnius prolixus (Hemiptera: Reduviidae), is transformed to export cecropin A, an insect immune peptide. Cecropin A is active against Trypanosoma cruzi, the causative agent of Chagas disease. While proof of concept has been achieved in laboratory studies, a rigorous and comprehensive risk assessment is required prior to consideration of field release. An important part of this assessment involves estimating probability of transgene horizontal transfer to environmental organisms (HGT). This article presents a two-part risk assessment methodology: a theoretical model predicting HGT in the gut of R. prolixus from the genetically transformed symbiont R. rhodnii to a closely related non-target bacterium, Gordona rubropertinctus, in the absence of selection pressure, and a series of laboratory trials designed to test the model.<br><br>RESULTS: The model predicted an HGT frequency of less than 1.14 &#xd7; 10(-16) per 100,000 generations at the 99% certainty level. The model was iterated twenty times, with the mean of the ten highest outputs evaluated at the 99% certainty level. Laboratory trials indicated no horizontal gene transfer, supporting the conclusions of the model.<br><br>CONCLUSIONS: The model treats HGT as a composite event, the probability of which is determined by the joint probability of three independent events: gene transfer through the modalities of transformation, transduction, and conjugation. Genes are represented in matrices and Monte Carlo method and Markov chain analysis are used to simulate and evaluate environmental conditions. The model is intended as a risk assessment instrument and predicts HGT frequency of less than 1.14 &#xd7; 10(-16) per 100,000 generations. With laboratory studies that support the predictions of this model, it may be possible to argue that HGT is a negligible consideration in risk assessment of genetically modified R. rhodnii released for control of Chagas disease.}, }
@article {pmid21565807, year = {2011}, author = {Ktari, S and Mnif, B and Louati, F and Rekik, S and Mezghani, S and Mahjoubi, F and Hammami, A}, title = {Spread of Klebsiella pneumoniae isolates producing OXA-48 β-lactamase in a Tunisian university hospital.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {66}, number = {7}, pages = {1644-1646}, doi = {10.1093/jac/dkr181}, pmid = {21565807}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/*pharmacology ; Conjugation, Genetic ; Cross Infection/*epidemiology/microbiology ; Gene Transfer, Horizontal ; Hospitals, University ; Humans ; Klebsiella Infections/*epidemiology/microbiology ; Klebsiella pneumoniae/*enzymology/genetics/isolation &amp; purification ; Microbial Sensitivity Tests ; Tunisia/epidemiology ; *beta-Lactam Resistance ; beta-Lactamases/*biosynthesis ; beta-Lactams/*pharmacology ; }, }
@article {pmid21564143, year = {2011}, author = {Demanèche, S and Monier, JM and Dugat-Bony, E and Simonet, P}, title = {Exploration of horizontal gene transfer between transplastomic tobacco and plant-associated bacteria.}, journal = {FEMS microbiology ecology}, volume = {78}, number = {1}, pages = {129-136}, doi = {10.1111/j.1574-6941.2011.01126.x}, pmid = {21564143}, issn = {1574-6941}, mesh = {Bacteria/genetics/growth &amp; development ; Base Sequence ; DNA, Plant/genetics ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal/*physiology ; Genome, Chloroplast/physiology ; Molecular Sequence Data ; Plants, Genetically Modified/*genetics/microbiology ; Soil Microbiology ; Spectinomycin/toxicity ; Nicotiana/*genetics/microbiology ; Transgenes ; }, abstract = {The likelihood of gene transfer from transgenic plants to bacteria is dependent on the transgene copy number and on the presence of homologous sequences for recombination. The large number of chloroplast genomes in a plant cell as well as the prokaryotic origin of the transgene may thus significantly increase the likelihood of gene transfer from transplastomic plants to bacteria. In order to assess the probability of such a transfer, bacterial isolates, screened for their ability to colonize decaying tobacco plant tissue and possessing DNA sequence similarity to the chloroplastic genes accD and rbcL flanking the transgene (aadA), were tested for their ability to take up extracellular DNA (broad host-range pBBR1MCS-3-derived plasmid, transplastomic plant DNA and PCR products containing the genes accD-aadA-rbcL) by natural or electrotransformation. The results showed that among the 16 bacterial isolates tested, six were able to accept foreign DNA and acquire the spectinomycin resistance conferred by the aadA gene on plasmid, but none of them managed to integrate transgenic DNA in their chromosome. Our results provide no indication that the theoretical gene transfer-enhancing properties of transplastomic plants cause horizontal gene transfer at rates above those found in other studies with nuclear transgenes.}, }
@article {pmid21564142, year = {2011}, author = {Partridge, SR}, title = {Analysis of antibiotic resistance regions in Gram-negative bacteria.}, journal = {FEMS microbiology reviews}, volume = {35}, number = {5}, pages = {820-855}, doi = {10.1111/j.1574-6976.2011.00277.x}, pmid = {21564142}, issn = {1574-6976}, mesh = {Anti-Bacterial Agents/*pharmacology ; *Drug Resistance, Multiple, Bacterial ; *Gene Order ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Gram-Negative Bacteria/*drug effects/*genetics ; *Interspersed Repetitive Sequences ; Recombination, Genetic ; }, abstract = {Antibiotic resistance in Gram-negative bacteria is often due to the acquisition of resistance genes from a shared pool. In multiresistant isolates these genes, together with associated mobile elements, may be found in complex conglomerations on plasmids or on the chromosome. Analysis of available sequences reveals that these multiresistance regions (MRR) are modular, mosaic structures composed of different combinations of components from a limited set arranged in a limited number of ways. Components common to different MRR provide targets for homologous recombination, allowing these regions to evolve by combinatorial evolution, but our understanding of this process is far from complete. Advances in technology are leading to increasing amounts of sequence data, but currently available automated annotation methods usually focus on identifying ORFs and predicting protein function by homology. In MRR, where the genes are often well characterized, the challenge is to identify precisely which genes are present and to define the boundaries of complete and fragmented mobile elements. This review aims to summarize the types of mobile elements involved in multiresistance in Gram-negative bacteria and their associations with particular resistance genes, to describe common components of MRR and to illustrate methods for detailed analysis of these regions.}, }
@article {pmid21562599, year = {2011}, author = {Thompson, AW and Huang, K and Saito, MA and Chisholm, SW}, title = {Transcriptome response of high- and low-light-adapted Prochlorococcus strains to changing iron availability.}, journal = {The ISME journal}, volume = {5}, number = {10}, pages = {1580-1594}, pmid = {21562599}, issn = {1751-7370}, mesh = {Bacterial Proteins/genetics/metabolism ; *Gene Expression Profiling ; *Gene Expression Regulation, Bacterial ; Iron/*metabolism ; Light ; Light-Harvesting Protein Complexes/genetics/metabolism ; Oceans and Seas ; Prochlorococcus/*genetics/*physiology ; }, abstract = {Prochlorococcus contributes significantly to ocean primary productivity. The link between primary productivity and iron in specific ocean regions is well established and iron limitation of Prochlorococcus cell division rates in these regions has been shown. However, the extent of ecotypic variation in iron metabolism among Prochlorococcus and the molecular basis for differences is not understood. Here, we examine the growth and transcriptional response of Prochlorococcus strains, MED4 and MIT9313, to changing iron concentrations. During steady state, MIT9313 sustains growth at an order-of-magnitude lower iron concentration than MED4. To explore this difference, we measured the whole-genome transcriptional response of each strain to abrupt iron starvation and rescue. Only four of the 1159 orthologs of MED4 and MIT9313 were differentially expressed in response to iron in both strains. However, in each strain, the expression of over a hundred additional genes changed, many of which are in labile genomic regions, suggesting a role for lateral gene transfer in establishing diversity of iron metabolism among Prochlorococcus. Furthermore, we found that MED4 lacks three genes near the iron-deficiency-induced gene (idiA) that are present and induced by iron stress in MIT9313. These genes are interesting targets for studying the adaptation of natural Prochlorococcus assemblages to local iron conditions as they show more diversity than other genomic regions in environmental metagenomic databases.}, }
@article {pmid21562596, year = {2011}, author = {Gorfer, M and Blumhoff, M and Klaubauf, S and Urban, A and Inselsbacher, E and Bandian, D and Mitter, B and Sessitsch, A and Wanek, W and Strauss, J}, title = {Community profiling and gene expression of fungal assimilatory nitrate reductases in agricultural soil.}, journal = {The ISME journal}, volume = {5}, number = {11}, pages = {1771-1783}, pmid = {21562596}, issn = {1751-7370}, mesh = {Biomass ; Ecosystem ; Fungi/*enzymology/*genetics/metabolism ; Genes, Fungal ; Nitrate Reductases/*genetics/metabolism ; Nitrates/metabolism ; Nitrogen/metabolism ; Nitrogen Fixation ; Phylogeny ; Quaternary Ammonium Compounds/metabolism ; *Soil Microbiology ; }, abstract = {Although fungi contribute significantly to the microbial biomass in terrestrial ecosystems, little is known about their contribution to biogeochemical nitrogen cycles. Agricultural soils usually contain comparably high amounts of inorganic nitrogen, mainly in the form of nitrate. Many studies focused on bacterial and archaeal turnover of nitrate by nitrification, denitrification and assimilation, whereas the fungal role remained largely neglected. To enable research on the fungal contribution to the biogeochemical nitrogen cycle tools for monitoring the presence and expression of fungal assimilatory nitrate reductase genes were developed. To the ~100 currently available fungal full-length gene sequences, another 109 partial sequences were added by amplification from individual culture isolates, representing all major orders occurring in agricultural soils. The extended database led to the discovery of new horizontal gene transfer events within the fungal kingdom. The newly developed PCR primers were used to study gene pools and gene expression of fungal nitrate reductases in agricultural soils. The availability of the extended database allowed affiliation of many sequences to known species, genera or families. Energy supply by a carbon source seems to be the major regulator of nitrate reductase gene expression for fungi in agricultural soils, which is in good agreement with the high energy demand of complete reduction of nitrate to ammonium.}, }
@article {pmid21559082, year = {2011}, author = {Laverde Gomez, JA and Hendrickx, AP and Willems, RJ and Top, J and Sava, I and Huebner, J and Witte, W and Werner, G}, title = {Intra- and interspecies genomic transfer of the Enterococcus faecalis pathogenicity island.}, journal = {PloS one}, volume = {6}, number = {4}, pages = {e16720}, pmid = {21559082}, issn = {1932-6203}, mesh = {Animals ; Bacterial Infections/*microbiology ; Bacterial Proteins/metabolism ; Biofilms ; Conjugation, Genetic ; Enterococcus faecalis/*genetics ; Female ; Flow Cytometry ; Gene Transfer Techniques ; *Genomic Islands ; Membrane Proteins/metabolism ; Mice ; Mice, Inbred BALB C ; Models, Genetic ; Phenotype ; Species Specificity ; Virulence ; Virulence Factors/genetics ; }, abstract = {Enterococci are the third leading cause of hospital associated infections and have gained increased importance due to their fast adaptation to the clinical environment by acquisition of antibiotic resistance and pathogenicity traits. Enterococcus faecalis harbours a pathogenicity island (PAI) of 153 kb containing several virulence factors including the enterococcal surface protein (esp). Until now only internal fragments of the PAI or larger chromosomal regions containing it have been transferred. Here we demonstrate precise excision, circularization and horizontal transfer of the entire PAI element from the chromosome of E. faecalis strain UW3114. This PAI (ca. 200 kb) contained some deletions and insertions as compared to the PAI of the reference strain MMH594, transferred precisely and integrated site-specifically into the chromosome of E. faecalis (intergenic region) and Enterococcus faecium (tRNAlys). The internal PAI structure was maintained after transfer. We assessed phenotypic changes accompanying acquisition of the PAI and expression of some of its determinants. The esp gene is expressed on the surface of donor and both transconjugants. Biofilm formation and cytolytic activity were enhanced in E. faecalis transconjugants after acquisition of the PAI. No differences in pathogenicity of E. faecalis were detected using a mouse bacteraemia and a mouse peritonitis models (tail vein and intraperitoneal injection). A 66 kb conjugative pheromone-responsive plasmid encoding erm(B) (pLG2) that was transferred in parallel with the PAI was sequenced. pLG2 is a pheromone responsive plasmid that probably promotes the PAI horizontal transfer, encodes antibiotic resistance features and contains complete replication and conjugation modules of enterococcal origin in a mosaic-like composition. The E. faecalis PAI can undergo precise intra- and interspecies transfer probably with the help of conjugative elements like conjugative resistance plasmids, supporting the role of horizontal gene transfer and antibiotic selective pressure in the successful establishment of certain enterococci as nosocomial pathogens.}, }
@article {pmid21555917, year = {2011}, author = {Guinane, CM and Penadés, JR and Fitzgerald, JR}, title = {The role of horizontal gene transfer in Staphylococcus aureus host adaptation.}, journal = {Virulence}, volume = {2}, number = {3}, pages = {241-243}, doi = {10.4161/viru.2.3.16193}, pmid = {21555917}, issn = {2150-5608}, support = {BB/I013873/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/D521222/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Adaptation, Biological ; Animals ; *Gene Transfer, Horizontal ; Genomic Islands ; Humans ; Ruminants ; Staphylococcus aureus/*genetics/*pathogenicity ; Virulence Factors/genetics/metabolism ; }, abstract = {Staphylococcus aureus is an important human pathogen that also causes economically important infections of livestock. In a recent paper, we employed a population genomic approach to investigate the molecular basis of ruminant host adaptation by S. aureus. The data suggest that the common pathogenic clone associated with small ruminants originated in humans but has since adapted to its adopted host through a combination of allelic diversification, gene loss and acquisition of mobile genetic elements. In particular, a new subfamily of staphylococcal pathogenicity islands (SaPI) was identified encoding a novel von Willebrand factor-binding protein (vWBP) with ruminant-specific coagulase activity. The wide distribution of vWBP-encoding SaPIs among ruminant strains implies an important role in host-adaptation. In the current article we summarize the findings of the paper and comment on the implications of the study for our understanding of the molecular basis of bacterial host adaptation.}, }
@article {pmid21552483, year = {2011}, author = {Lin, H and Lou, B and Glynn, JM and Doddapaneni, H and Civerolo, EL and Chen, C and Duan, Y and Zhou, L and Vahling, CM}, title = {The complete genome sequence of 'Candidatus Liberibacter solanacearum', the bacterium associated with potato zebra chip disease.}, journal = {PloS one}, volume = {6}, number = {4}, pages = {e19135}, pmid = {21552483}, issn = {1932-6203}, mesh = {Amino Acids/metabolism ; Biological Transport/genetics ; Carbohydrate Metabolism/genetics ; Cell Division/genetics ; Cell Proliferation ; Citrus/microbiology ; DNA Replication/genetics ; DNA, Bacterial/biosynthesis/metabolism ; Energy Metabolism/genetics ; Genome, Bacterial/*genetics ; Genomics ; Nitrogen/metabolism ; Nucleotides/metabolism ; Plant Diseases/*microbiology ; Prophages/genetics ; Proteobacteria/cytology/*genetics/metabolism/physiology ; Solanum tuberosum/*microbiology ; Sulfur/metabolism ; Vitamins/biosynthesis/metabolism ; }, abstract = {Zebra Chip (ZC) is an emerging plant disease that causes aboveground decline of potato shoots and generally results in unusable tubers. This disease has led to multi-million dollar losses for growers in the central and western United States over the past decade and impacts the livelihood of potato farmers in Mexico and New Zealand. ZC is associated with 'Candidatus Liberibacter solanacearum', a fastidious alpha-proteobacterium that is transmitted by a phloem-feeding psyllid vector, Bactericera cockerelli Sulc. Research on this disease has been hampered by a lack of robust culture methods and paucity of genome sequence information for 'Ca. L. solanacearum'. Here we present the sequence of the 1.26 Mbp metagenome of 'Ca. L. solanacearum', based on DNA isolated from potato psyllids. The coding inventory of the 'Ca. L. solanacearum' genome was analyzed and compared to related Rhizobiaceae to better understand 'Ca. L. solanacearum' physiology and identify potential targets to develop improved treatment strategies. This analysis revealed a number of unique transporters and pathways, all potentially contributing to ZC pathogenesis. Some of these factors may have been acquired through horizontal gene transfer. Taxonomically, 'Ca. L. solanacearum' is related to 'Ca. L. asiaticus', a suspected causative agent of citrus huanglongbing, yet many genome rearrangements and several gene gains/losses are evident when comparing these two Liberibacter. species. Relative to 'Ca. L. asiaticus', 'Ca. L. solanacearum' probably has reduced capacity for nucleic acid modification, increased amino acid and vitamin biosynthesis functionalities, and gained a high-affinity iron transport system characteristic of several pathogenic microbes.}, }
@article {pmid21548908, year = {2011}, author = {Vela, D and Guerreiro, MP and Fontdevila, A}, title = {Adaptation of the AFLP technique as a new tool to detect genetic instability and transposition in interspecific hybrids.}, journal = {BioTechniques}, volume = {50}, number = {4}, pages = {247-250}, doi = {10.2144/000113655}, pmid = {21548908}, issn = {1940-9818}, mesh = {Amplified Fragment Length Polymorphism Analysis/*methods ; Animals ; *DNA Transposable Elements ; Drosophila/genetics ; Female ; *Gene Transfer, Horizontal ; Genetic Markers/genetics ; *Genomic Instability ; In Situ Hybridization, Fluorescence ; Male ; Polymerase Chain Reaction ; }, abstract = {An adapted amplified fragment length polymorphism (AFLP) protocol is presented for detection of hybrid instability in the genome of interspecific hybrids between Drosophila buzzatii and D. koepferae species. Analyses of 15 AFLP instability markers (new bands detected in hybrids) show that up to 81% are the result of transposable element (TE) activity. Twenty TEs associated with AFLP instability markers have been detected by this method in backcross hybrids and segmental hybrids, demonstrating its validity in detecting transposition events occurring during the hybridization process. New insertions of Helena TE have been observed in the hybrid genome after hybridization of the TGTCG22 instability marker by FISH. The AFLP marker technique proved to be an efficient method that improves upon traditional and bioinformatic tools previously used to detect TE mobilization. This newly adapted AFLP protocol may also be applied to a large number of organisms outside the Drosophila genus, making it of interest to evolutionary and population genetic researchers working with species where the knowledge of the genome is scarce.}, }
@article {pmid21546307, year = {2011}, author = {Heuer, H and Schmitt, H and Smalla, K}, title = {Antibiotic resistance gene spread due to manure application on agricultural fields.}, journal = {Current opinion in microbiology}, volume = {14}, number = {3}, pages = {236-243}, doi = {10.1016/j.mib.2011.04.009}, pmid = {21546307}, issn = {1879-0364}, mesh = {Agriculture/*methods ; Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/*genetics ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Humans ; Interspersed Repetitive Sequences ; Manure/*microbiology ; Selection, Genetic ; }, abstract = {The usage of antibiotics in animal husbandry has promoted the development and abundance of antibiotic resistance in farm environments. Manure has become a reservoir of resistant bacteria and antibiotic compounds, and its application to agricultural soils is assumed to significantly increase antibiotic resistance genes and selection of resistant bacterial populations in soil. The genome location of resistance genes is likely to shift towards mobile genetic elements such as broad-host-range plasmids, integrons, and transposable elements. Horizontal transfer of these elements to bacteria adapted to soil or other habitats supports their environmental transmission independent of the original host. The human exposure to soil-borne resistance has yet to be determined, but is likely to be severely underestimated.}, }
@article {pmid21543515, year = {2011}, author = {Andersen, MR and Salazar, MP and Schaap, PJ and van de Vondervoort, PJ and Culley, D and Thykaer, J and Frisvad, JC and Nielsen, KF and Albang, R and Albermann, K and Berka, RM and Braus, GH and Braus-Stromeyer, SA and Corrochano, LM and Dai, Z and van Dijck, PW and Hofmann, G and Lasure, LL and Magnuson, JK and Menke, H and Meijer, M and Meijer, SL and Nielsen, JB and Nielsen, ML and van Ooyen, AJ and Pel, HJ and Poulsen, L and Samson, RA and Stam, H and Tsang, A and van den Brink, JM and Atkins, A and Aerts, A and Shapiro, H and Pangilinan, J and Salamov, A and Lou, Y and Lindquist, E and Lucas, S and Grimwood, J and Grigoriev, IV and Kubicek, CP and Martinez, D and van Peij, NN and Roubos, JA and Nielsen, J and Baker, SE}, title = {Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88.}, journal = {Genome research}, volume = {21}, number = {6}, pages = {885-897}, pmid = {21543515}, issn = {1549-5469}, mesh = {Aspergillus niger/*genetics ; Base Sequence ; Computational Biology/*methods ; *Evolution, Molecular ; Gene Expression Profiling ; Gene Rearrangement/genetics ; Gene Transfer, Horizontal/genetics ; *Genetic Variation ; Genome, Fungal/*genetics ; Genomics/methods ; Molecular Sequence Data ; *Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Sequence Analysis, DNA ; Species Specificity ; Synteny/genetics ; }, abstract = {The filamentous fungus Aspergillus niger exhibits great diversity in its phenotype. It is found globally, both as marine and terrestrial strains, produces both organic acids and hydrolytic enzymes in high amounts, and some isolates exhibit pathogenicity. Although the genome of an industrial enzyme-producing A. niger strain (CBS 513.88) has already been sequenced, the versatility and diversity of this species compel additional exploration. We therefore undertook whole-genome sequencing of the acidogenic A. niger wild-type strain (ATCC 1015) and produced a genome sequence of very high quality. Only 15 gaps are present in the sequence, and half the telomeric regions have been elucidated. Moreover, sequence information from ATCC 1015 was used to improve the genome sequence of CBS 513.88. Chromosome-level comparisons uncovered several genome rearrangements, deletions, a clear case of strain-specific horizontal gene transfer, and identification of 0.8 Mb of novel sequence. Single nucleotide polymorphisms per kilobase (SNPs/kb) between the two strains were found to be exceptionally high (average: 7.8, maximum: 160 SNPs/kb). High variation within the species was confirmed with exo-metabolite profiling and phylogenetics. Detailed lists of alleles were generated, and genotypic differences were observed to accumulate in metabolic pathways essential to acid production and protein synthesis. A transcriptome analysis supported up-regulation of genes associated with biosynthesis of amino acids that are abundant in glucoamylase A, tRNA-synthases, and protein transporters in the protein producing CBS 513.88 strain. Our results and data sets from this integrative systems biology analysis resulted in a snapshot of fungal evolution and will support further optimization of cell factories based on filamentous fungi.}, }
@article {pmid21543359, year = {2011}, author = {Giakkoupi, P and Papagiannitsis, CC and Miriagou, V and Pappa, O and Polemis, M and Tryfinopoulou, K and Tzouvelekis, LS and Vatopoulos, AC}, title = {An update of the evolving epidemic of blaKPC-2-carrying Klebsiella pneumoniae in Greece (2009-10).}, journal = {The Journal of antimicrobial chemotherapy}, volume = {66}, number = {7}, pages = {1510-1513}, doi = {10.1093/jac/dkr166}, pmid = {21543359}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/pharmacology ; Cluster Analysis ; DNA, Bacterial/genetics ; Electrophoresis, Gel, Pulsed-Field ; Gene Transfer, Horizontal ; Genotype ; Greece/epidemiology ; Humans ; Klebsiella Infections/*epidemiology/microbiology ; Klebsiella pneumoniae/classification/*enzymology/genetics/isolation &amp; purification ; Microbial Sensitivity Tests ; Molecular Epidemiology ; Molecular Typing ; Plasmids ; beta-Lactamases/*biosynthesis/genetics ; }, abstract = {OBJECTIVES: To follow the epidemic of KPC-2-producing Klebsiella pneumoniae in Greece.<br><br>METHODS: KPC-2-producing isolates (n&#x200a;=&#x200a;378) were collected during January 2009-April 2010 in 40 Greek hospitals. bla(KPC) and bla(VIM) were detected by PCR. Carbapenemase production was confirmed by spectrophotometry. Sequences flanking bla(KPC-2) and their plasmid carriers were studied. Isolates were typed by PFGE and multilocus sequence typing (MLST).<br><br>RESULTS: All 378 isolates were bla(KPC-2) positive; 18 also carried bla(VIM-1/VIM-4). Higher isolation frequencies were observed in Athens and Crete. Isolates were classified into 13 PFGE types and 11 sequence types (STs). ST258 was predominant (n = 322), followed by ST147 (n = 20), ST383 (n = 9), ST133 (n = 6), ST274 (n = 4) and ST323 (n = 3). Of the remaining isolates, seven were distributed into five STs (11, 17, 340 and the novel 494 and 495) and seven were not typed. bla(KPC-2) could not be transferred from ST258 isolates, in contrast to isolates of ST17, ST133, ST147, ST274, ST494 and ST495. All bla(KPC-2)-encoding plasmids were of similar size (&#x223c;100 kb) and showed indistinguishable restriction fragment length polymorphism (RFLP) patterns except those from the ST340 isolates. Sequences flanking bla(KPC-2) revealed that the Tn4401a isoform was present in plasmids from all STs except ST340 containing Tn4401b. Co-production of VIM enzymes was observed in isolates of ST147, ST323 and ST383.<br><br>CONCLUSIONS: Apart from the epidemic of KPC-2-producing K. pneumoniae belonging to ST258 in Greece, diffusion of bla(KPC-2) to at least 10 additional STs has taken place. Notably, strains from three of the latter STs (147, 323 and 383) were found to carry both bla(KPC-2) and bla(VIM).}, }
@article {pmid21542933, year = {2011}, author = {Arvizu-Gómez, JL and Hernández-Morales, A and Pastor-Palacios, G and Brieba, LG and Álvarez-Morales, A}, title = {Integration Host Factor (IHF) binds to the promoter region of the phtD operon involved in phaseolotoxin synthesis in P. syringae pv. phaseolicola NPS3121.}, journal = {BMC microbiology}, volume = {11}, number = {}, pages = {90}, pmid = {21542933}, issn = {1471-2180}, mesh = {DNA, Bacterial/*metabolism ; Down-Regulation ; Gene Expression Regulation, Bacterial ; Integration Host Factors/*metabolism ; *Operon ; Ornithine/*analogs &amp; derivatives/biosynthesis/genetics ; *Promoter Regions, Genetic ; Protein Binding ; Pseudomonas syringae/*genetics/*metabolism ; }, abstract = {BACKGROUND: Pseudomonas syringae pv. phaseolicola, the causal agent of halo blight disease in beans, produces a toxin known as phaseolotoxin, in whose synthesis participate a group of genes organized within the genome in a region known as the "Pht cluster". This region, which is thought to have been acquired by horizontal gene transfer, includes 5 transcriptional units, two monocistronic (argK, phtL) and three polycistronic (phtA, phtD, phtM), whose expression is temperature dependent. So far, the regulatory mechanisms involved in phaseolotoxin synthesis have not been elucidated and the only well-established fact is the requirement of low temperatures for its synthesis. In this work, we searched for regulatory proteins that could be involved in phaseolotoxin synthesis, focusing on the regulation of the phtD operon.<br><br>RESULTS: In this study we identified the global regulator IHF (Integration Host Factor), which binds to the promoter region of the phtD operon, exerting a negative effect on the expression of this operon. This is the first regulatory protein identified as part of the phaseolotoxin synthesis system. Our findings suggest that the Pht cluster was similarly regulated in the ancestral cluster by IHF or similar protein, and integrated into the global regulatory mechanism of P. syringae pv. phaseolicola, after the horizontal gene transfer event by using the host IHF protein.<br><br>CONCLUSION: This study identifies the IHF protein as one element involved in the regulation of phaseolotoxin synthesis in P. syringae pv. phaseolicola NPS3121 and provides new insights into the regulatory mechanisms involved in phaseolotoxin production.}, }
@article {pmid21541312, year = {2011}, author = {Joseph, B and Schwarz, RF and Linke, B and Blom, J and Becker, A and Claus, H and Goesmann, A and Frosch, M and Müller, T and Vogel, U and Schoen, C}, title = {Virulence evolution of the human pathogen Neisseria meningitidis by recombination in the core and accessory genome.}, journal = {PloS one}, volume = {6}, number = {4}, pages = {e18441}, pmid = {21541312}, issn = {1932-6203}, mesh = {Cluster Analysis ; Comparative Genomic Hybridization ; *Evolution, Molecular ; Gene Pool ; Genome, Bacterial/*genetics ; Humans ; Multilocus Sequence Typing ; Neisseria meningitidis/classification/*genetics/*pathogenicity ; Phylogeny ; Recombination, Genetic/*genetics ; Serotyping ; Virulence/*genetics ; }, abstract = {BACKGROUND: Neisseria meningitidis is a naturally transformable, facultative pathogen colonizing the human nasopharynx. Here, we analyze on a genome-wide level the impact of recombination on gene-complement diversity and virulence evolution in N. meningitidis. We combined comparative genome hybridization using microarrays (mCGH) and multilocus sequence typing (MLST) of 29 meningococcal isolates with computational comparison of a subset of seven meningococcal genome sequences.<br><br>PRINCIPAL FINDINGS: We found that lateral gene transfer of minimal mobile elements as well as prophages are major forces shaping meningococcal population structure. Extensive gene content comparison revealed novel associations of virulence with genetic elements besides the recently discovered meningococcal disease associated (MDA) island. In particular, we identified an association of virulence with a recently described canonical genomic island termed IHT-E and a differential distribution of genes encoding RTX toxin- and two-partner secretion systems among hyperinvasive and non-hyperinvasive lineages. By computationally screening also the core genome for signs of recombination, we provided evidence that about 40% of the meningococcal core genes are affected by recombination primarily within metabolic genes as well as genes involved in DNA replication and repair. By comparison with the results of previous mCGH studies, our data indicated that genetic structuring as revealed by mCGH is stable over time and highly similar for isolates from different geographic origins.<br><br>CONCLUSIONS: Recombination comprising lateral transfer of entire genes as well as homologous intragenic recombination has a profound impact on meningococcal population structure and genome composition. Our data support the hypothesis that meningococcal virulence is polygenic in nature and that differences in metabolism might contribute to virulence.}, }
@article {pmid21539752, year = {2011}, author = {Lackner, G and Moebius, N and Partida-Martinez, LP and Boland, S and Hertweck, C}, title = {Evolution of an endofungal lifestyle: Deductions from the Burkholderia rhizoxinica genome.}, journal = {BMC genomics}, volume = {12}, number = {}, pages = {210}, pmid = {21539752}, issn = {1471-2164}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics/metabolism ; Biological Transport ; Burkholderia/drug effects/*genetics/metabolism/*physiology ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Multiple/genetics ; *Evolution, Molecular ; Fimbriae, Bacterial/genetics/metabolism ; Genome, Bacterial/genetics ; Genomics/*methods ; Lipopolysaccharides/metabolism ; Pseudogenes/genetics ; *Rhizopus/metabolism ; Symbiosis/*genetics ; }, abstract = {BACKGROUND: Burkholderia rhizoxinica is an intracellular symbiont of the phytopathogenic zygomycete Rhizopus microsporus, the causative agent of rice seedling blight. The endosymbiont produces the antimitotic macrolide rhizoxin for its host. It is vertically transmitted within vegetative spores and is essential for spore formation of the fungus. To shed light on the evolution and genetic potential of this model organism, we analysed the whole genome of B. rhizoxinica HKI 0454 - a type strain of endofungal Burkholderia species.<br><br>RESULTS: The genome consists of a structurally conserved chromosome and two plasmids. Compared to free-living Burkholderia species, the genome is smaller in size and harbors less transcriptional regulator genes. Instead, we observed accumulation of transposons over the genome. Prediction of primary metabolic pathways and transporters suggests that endosymbionts consume host metabolites like citrate, but might deliver some amino acids and cofactors to the host. The rhizoxin biosynthesis gene cluster shows evolutionary traces of horizontal gene transfer. Furthermore, we analysed gene clusters coding for nonribosomal peptide synthetases (NRPS). Notably, B. rhizoxinica lacks common genes which are dedicated to quorum sensing systems, but is equipped with a large number of virulence-related factors and putative type III effectors.<br><br>CONCLUSIONS: B. rhizoxinica is the first endofungal bacterium, whose genome has been sequenced. Here, we present models of evolution, metabolism and tools for host-symbiont interaction of the endofungal bacterium deduced from whole genome analyses. Genome size and structure suggest that B. rhizoxinica is in an early phase of adaptation to the intracellular lifestyle (genome in transition). By analysis of tranporters and metabolic pathways we predict how metabolites might be exchanged between the symbiont and its host. Gene clusters for biosynthesis of secondary metabolites represent novel targets for genomic mining of cryptic natural products. In silico analyses of virulence-associated genes, secreted proteins and effectors might inspire future studies on molecular mechanisms underlying bacterial-fungal interaction.}, }
@article {pmid21539433, year = {2011}, author = {Haegeman, A and Jones, JT and Danchin, EG}, title = {Horizontal gene transfer in nematodes: a catalyst for plant parasitism?.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {24}, number = {8}, pages = {879-887}, doi = {10.1094/MPMI-03-11-0055}, pmid = {21539433}, issn = {0894-0282}, mesh = {Animals ; *Gene Transfer, Horizontal ; Host-Parasite Interactions ; Nematoda/*genetics/metabolism ; Phylogeny ; Plants/*parasitology ; }, abstract = {The origin of plant parasitism within the phylum Nematoda is intriguing. The ability to parasitize plants has originated independently at least three times during nematode evolution and, as more molecular data has emerged, it has become clear that multiple instances of horizontal gene transfer (HGT) from bacteria and fungi have played a crucial role in the nematode's adaptation to this new lifestyle. The first reported HGT cases in plant-parasitic nematodes were genes encoding plant cell wall-degrading enzymes. Other putative examples of HGT were subsequently described, including genes that may be involved in the modulation of the plant's defense system, the establishment of a nematode feeding site, and the synthesis or processing of nutrients. Although, in many cases, it is difficult to pinpoint the donor organism, candidate donors are usually soil dwelling and are either plant-pathogenic or plant-associated microorganisms, hence occupying the same ecological niche as the nematodes. The exact mechanisms of transfer are unknown, although close contacts with donor microorganisms, such as symbiotic or trophic interactions, are a possibility. The widespread occurrence of horizontally transferred genes in evolutionarily independent plant-parasitic nematode lineages suggests that HGT may be a prerequisite for successful plant parasitism in nematodes.}, }
@article {pmid21536150, year = {2011}, author = {Richards, VP and Lang, P and Bitar, PD and Lefébure, T and Schukken, YH and Zadoks, RN and Stanhope, MJ}, title = {Comparative genomics and the role of lateral gene transfer in the evolution of bovine adapted Streptococcus agalactiae.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {11}, number = {6}, pages = {1263-1275}, pmid = {21536150}, issn = {1567-7257}, support = {R01 AI073368/AI/NIAID NIH HHS/United States ; R01 AI073368-04/AI/NIAID NIH HHS/United States ; AI073368-01A2/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacterial Proteins/genetics ; Cattle ; DNA Transposable Elements ; Drug Resistance, Bacterial/genetics ; *Evolution, Molecular ; Female ; Fructose/metabolism ; Gene Order ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; Mastitis, Bovine/*microbiology ; Metabolic Networks and Pathways/genetics ; Multigene Family ; Mutagenesis, Insertional ; Prophages/genetics ; Recombinases/genetics ; Repetitive Sequences, Nucleic Acid ; Sequence Analysis, DNA ; Streptococcus agalactiae/*genetics/pathogenicity ; Virulence Factors ; }, abstract = {In addition to causing severe invasive infections in humans, Streptococcus agalactiae, or group B Streptococcus (GBS), is also a major cause of bovine mastitis. Here we provide the first genome sequence for S. agalactiae isolated from a cow diagnosed with clinical mastitis (strain FSL S3-026). Comparison to eight S. agalactiae genomes obtained from human disease isolates revealed 183 genes specific to the bovine strain. Subsequent polymerase chain reaction (PCR) screening for the presence/absence of a subset of these loci in additional bovine and human strains revealed strong differentiation between the two groups (Fisher exact test: p<0.0001). The majority of the bovine strain-specific genes (∼ 85%) clustered tightly into eight genomic islands, suggesting these genes were acquired through lateral gene transfer (LGT). This bovine GBS also contained an unusually high proportion of insertion sequences (4.3% of the total genome), suggesting frequent genomic rearrangement. Comparison to other mastitis-causing species of bacteria provided strong evidence for two cases of interspecies LGT within the shared bovine environment: bovine S. agalactiae with Streptococcus uberis (nisin U operon) and Streptococcus dysgalactiae subsp. dysgalactiae (lactose operon). We also found evidence for LGT, involving the salivaricin operon, between the bovine S. agalactiae strain and either Streptococcus pyogenes or Streptococcus salivarius. Our findings provide insight into mechanisms facilitating environmental adaptation and acquisition of potential virulence factors, while highlighting both the key role LGT has played in the recent evolution of the bovine S. agalactiae strain, and the importance of LGT among pathogens within a shared environment.}, }
@article {pmid21535427, year = {2011}, author = {Muniesa, M and Imamovic, L and Jofre, J}, title = {Bacteriophages and genetic mobilization in sewage and faecally polluted environments.}, journal = {Microbial biotechnology}, volume = {4}, number = {6}, pages = {725-734}, pmid = {21535427}, issn = {1751-7915}, mesh = {Bacteria/*genetics/*virology ; Bacteriophages/*genetics ; *Environmental Microbiology ; *Gene Transfer, Horizontal ; Sewage/*microbiology ; *Transduction, Genetic ; }, abstract = {Bacteriophages are one of the most abundant entities on the planet and are present in high concentrations within humans and animals, mostly in the gut. Phages that infect intestinal bacteria are released by defecation and remain free in extra-intestinal environments, where they usually persist for longer than their bacterial hosts. Recent studies indicate that a large amount of the genetic information in bacterial genomes and in natural environments is of phage origin. In addition, metagenomic analysis reveals that a substantial number of bacterial genes are present in viral DNA in different environments. These facts support the belief that phages can play a significant role in horizontal gene transfer between bacteria. Bacteriophages are known to transfer genes by generalized and specialized transduction and indeed there are some examples of phages found in the environment carrying and transducing genes of bacterial origin. A successful transduction in the environment requires certain conditions, e.g. phage and bacterial numbers need to exceed certain threshold concentrations, the bacteria need to exist in an infection-competent physiological state, and lastly, the physical conditions in the environment (pH, temperature, etc. of the supporting matrix) have to be suitable for phage infection. All three factors are reviewed here, and the available information suggests: (i) that the number of intestinal bacteria and phages in faecally contaminated environments guarantees bacteria-phage encounters, (ii) that transduction to intestinal bacteria in the environment is probable, and (iii) that transduction is more frequent than previously thought. Therefore, we suggest that phage-mediated horizontal transfer between intestinal bacteria, or between intestinal and autochthonous bacteria in extra-intestinal environments, might take place and that its relevance for the emergence of new bacterial strains and potential pathogens should not be ignored.}, }
@article {pmid21533100, year = {2011}, author = {Guinane, CM and Kent, RM and Norberg, S and Hill, C and Fitzgerald, GF and Stanton, C and Ross, RP}, title = {Host specific diversity in Lactobacillus johnsonii as evidenced by a major chromosomal inversion and phage resistance mechanisms.}, journal = {PloS one}, volume = {6}, number = {4}, pages = {e18740}, pmid = {21533100}, issn = {1932-6203}, mesh = {Bacteriophages/*physiology ; *Chromosome Inversion ; DNA Transposable Elements ; Lactobacillus/classification/genetics/*physiology ; Phylogeny ; }, abstract = {Genetic diversity and genomic rearrangements are a driving force in bacterial evolution and niche adaptation. We sequenced and annotated the genome of Lactobacillus johnsonii DPC6026, a strain isolated from the porcine intestinal tract. Although the genome of DPC6026 is similar in size (1.97 mbp) and GC content (34.8%) to the sequenced human isolate L. johnsonii NCC 533, a large symmetrical inversion of approximately 750 kb differentiated the two strains. Comparative analysis among 12 other strains of L. johnsonii including 8 porcine, 3 human and 1 poultry isolate indicated that the genome architecture found in DPC6026 is more common within the species than that of NCC 533. Furthermore a number of unique features were annotated in DPC6026, some of which are likely to have been acquired by horizontal gene transfer (HGT) and contribute to protection against phage infection. A putative type III restriction-modification system was identified, as were novel Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) elements. Interestingly, these particular elements are not widely distributed among L. johnsonii strains. Taken together these data suggest intra-species genomic rearrangements and significant genetic diversity within the L. johnsonii species and indicate towards a host-specific divergence of L. johnsonii strains with respect to genome inversion and phage exposure.}, }
@article {pmid21533033, year = {2011}, author = {Schneider, KL and Marrero, G and Alvarez, AM and Presting, GG}, title = {Classification of plant associated bacteria using RIF, a computationally derived DNA marker.}, journal = {PloS one}, volume = {6}, number = {4}, pages = {e18496}, pmid = {21533033}, issn = {1932-6203}, mesh = {Base Sequence ; DNA, Bacterial/*genetics ; Gene Transfer, Horizontal ; *Genetic Markers ; Genome, Bacterial ; Molecular Sequence Data ; Plants/*microbiology ; Sequence Homology, Nucleic Acid ; Xanthomonas/*classification/genetics ; }, abstract = {A DNA marker that distinguishes plant associated bacteria at the species level and below was derived by comparing six sequenced genomes of Xanthomonas, a genus that contains many important phytopathogens. This DNA marker comprises a portion of the dnaA replication initiation factor (RIF). Unlike the rRNA genes, dnaA is a single copy gene in the vast majority of sequenced bacterial genomes, and amplification of RIF requires genus-specific primers. In silico analysis revealed that RIF has equal or greater ability to differentiate closely related species of Xanthomonas than the widely used ribosomal intergenic spacer region (ITS). Furthermore, in a set of 263 Xanthomonas, Ralstonia and Clavibacter strains, the RIF marker was directly sequenced in both directions with a success rate approximately 16% higher than that for ITS. RIF frameworks for Xanthomonas, Ralstonia and Clavibacter were constructed using 682 reference strains representing different species, subspecies, pathovars, races, hosts and geographic regions, and contain a total of 109 different RIF sequences. RIF sequences showed subspecific groupings but did not place strains of X. campestris or X. axonopodis into currently named pathovars nor R. solanacearum strains into their respective races, confirming previous conclusions that pathovar and race designations do not necessarily reflect genetic relationships. The RIF marker also was sequenced for 24 reference strains from three genera in the Enterobacteriaceae: Pectobacterium, Pantoea and Dickeya. RIF sequences of 70 previously uncharacterized strains of Ralstonia, Clavibacter, Pectobacterium and Dickeya matched, or were similar to, those of known reference strains, illustrating the utility of the frameworks to classify bacteria below the species level and rapidly match unknown isolates to reference strains. The RIF sequence frameworks are available at the online RIF database, RIFdb, and can be queried for diagnostic purposes with RIF sequences obtained from unknown strains in both chromatogram and FASTA format.}, }
@article {pmid21532315, year = {2011}, author = {Lee, YE and Yang, SH and Bae, TW and Kang, HG and Lim, PO and Lee, HY}, title = {Effects of field-grown genetically modified Zoysia grass on bacterial community structure.}, journal = {Journal of microbiology and biotechnology}, volume = {21}, number = {4}, pages = {333-340}, pmid = {21532315}, issn = {1738-8872}, mesh = {Bacteria/classification/drug effects/genetics/*isolation &amp; purification ; Biodiversity ; Gene Transfer, Horizontal ; Herbicides/pharmacology ; Molecular Sequence Data ; Phylogeny ; Plants, Genetically Modified/drug effects/genetics/growth &amp; development/*microbiology ; Poaceae/drug effects/*genetics/growth &amp; development/*microbiology ; Rhizosphere ; *Soil Microbiology ; }, abstract = {Herbicide-tolerant Zoysia grass has been previously developed through Agrobacterium-mediated transformation. We investigated the effects of genetically modified (GM) Zoysia grass and the associated herbicide application on bacterial community structure by using culture-independent approaches. To assess the possible horizontal gene transfer (HGT) of transgenic DNA to soil microorganisms, total soil DNAs were amplified by PCR with two primer sets for the bar and hpt genes, which were introduced into the GM Zoysia grass by a callus-type transformation. The transgenic genes were not detected from the total genomic DNAs extracted from 1.5 g of each rhizosphere soils of GM and non-GM Zoysia grasses. The structures and diversities of the bacterial communities in rhizosphere soils of GM and non-GM Zoysia grasses were investigated by constructing 16S rDNA clone libraries. Classifier, provided in the RDP II, assigned 100 clones in the 16S rRNA gene sequences library into 11 bacterial phyla. The most abundant phyla in both clone libraries were Acidobacteria and Proteobacteria. The bacterial diversity of the GM clone library was lower than that of the non- GM library. The former contained four phyla, whereas the latter had seven phyla. Phylogenetic trees were constructed to confirm these results. Phylogenetic analyses of the two clone libraries revealed considerable difference from each other. The significance of difference between clone libraries was examined with LIBSHUFF statistics. LIBSHUFF analysis revealed that the two clone libraries differed significantly (P〈0.025), suggesting alterations in the composition of the microbial community associated with GM Zoysia grass.}, }
@article {pmid21531921, year = {2011}, author = {Luo, H and Friedman, R and Tang, J and Hughes, AL}, title = {Genome reduction by deletion of paralogs in the marine cyanobacterium Prochlorococcus.}, journal = {Molecular biology and evolution}, volume = {28}, number = {10}, pages = {2751-2760}, pmid = {21531921}, issn = {1537-1719}, support = {/WT_/Wellcome Trust/United Kingdom ; R01 GM043940/GM/NIGMS NIH HHS/United States ; GM078991003S1/GM/NIGMS NIH HHS/United States ; GM43940/GM/NIGMS NIH HHS/United States ; }, mesh = {Cluster Analysis ; *Evolution, Molecular ; Genes, Bacterial ; Genome Size/*genetics ; *Genome, Bacterial ; Genomics ; Phylogeny ; Prochlorococcus/classification/*genetics ; Sequence Deletion/*genetics ; Synechococcus/classification/genetics ; }, abstract = {Several isolates of the marine cyanobacterial genus Prochlorococcus have smaller genome sizes than those of the closely related genus Synechococcus. In order to test whether loss of protein-coding genes has contributed to genome size reduction in Prochlorococcus, we reconstructed events of gene family evolution over a strongly supported phylogeny of 12 Prochlorococcus genomes and 9 Synechococcus genomes. Significantly, more events both of loss of paralogs within gene families and of loss of entire gene families occurred in Prochlorococcus than in Synechococcus. The number of nonancestral gene families in genomes of both genera was positively correlated with the extent of genomic islands (GIs), consistent with the hypothesis that horizontal gene transfer (HGT) is associated with GIs. However, even when only isolates with comparable extents of GIs were compared, significantly more events of gene family loss and of paralog loss were seen in Prochlorococcus than in Synechococcus, implying that HGT is not the primary reason for the genome size difference between the two genera.}, }
@article {pmid21531520, year = {2011}, author = {Perrineau, MM and Le Roux, C and de Faria, SM and de Carvalho Balieiro, F and Galiana, A and Prin, Y and Béna, G}, title = {Genetic diversity of symbiotic Bradyrhizobium elkanii populations recovered from inoculated and non-inoculated Acacia mangium field trials in Brazil.}, journal = {Systematic and applied microbiology}, volume = {34}, number = {5}, pages = {376-384}, doi = {10.1016/j.syapm.2011.03.003}, pmid = {21531520}, issn = {1618-0984}, mesh = {Acacia/*microbiology ; Acyltransferases/genetics ; Bacterial Proteins/genetics ; Bradyrhizobium/classification/*genetics/isolation &amp; purification ; Brazil ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Loci ; *Genetic Variation ; Phylogeny ; Plant Root Nodulation ; Root Nodules, Plant/*microbiology ; Sequence Alignment ; Sequence Analysis, DNA ; *Soil Microbiology ; Symbiosis ; }, abstract = {Acacia mangium is a legume tree native to Australasia. Since the eighties, it has been introduced into many tropical countries, especially in a context of industrial plantations. Many field trials have been set up to test the effects of controlled inoculation with selected symbiotic bacteria versus natural colonization with indigenous strains. In the introduction areas, A. mangium trees spontaneously nodulate with local and often ineffective bacteria. When inoculated, the persistence of inoculants and possible genetic recombination with local strains remain to be explored. The aim of this study was to describe the genetic diversity of bacteria spontaneously nodulating A. mangium in Brazil and to evaluate the persistence of selected strains used as inoculants. Three different sites, several hundred kilometers apart, were studied, with inoculated and non-inoculated plots in two of them. Seventy-nine strains were isolated from nodules and sequenced on three housekeeping genes (glnII, dnaK and recA) and one symbiotic gene (nodA). All but one of the strains belonged to the Bradyrhizobium elkanii species. A single case of housekeeping gene transfer was detected among the 79 strains, suggesting an extremely low rate of recombination within B. elkanii, whereas the nodulation gene nodA was found to be frequently transferred. The fate of the inoculant strains varied depending on the site, with a complete disappearance in one case, and persistence in another. We compared our results with the sister species Bradyrhizobium japonicum, both in terms of population genetics and inoculant strain destiny.}, }
@article {pmid21530923, year = {2011}, author = {Rank, C and Nielsen, KF and Larsen, TO and Varga, J and Samson, RA and Frisvad, JC}, title = {Distribution of sterigmatocystin in filamentous fungi.}, journal = {Fungal biology}, volume = {115}, number = {4-5}, pages = {406-420}, doi = {10.1016/j.funbio.2011.02.013}, pmid = {21530923}, issn = {1878-6146}, mesh = {Aflatoxins/analysis/biosynthesis/*metabolism ; Aspergillus/chemistry/genetics/*metabolism ; DNA, Fungal ; Fungi/metabolism ; Penicillium/chemistry/genetics/*metabolism ; Phylogeny ; Sterigmatocystin/*biosynthesis/metabolism ; Talaromyces/chemistry ; }, abstract = {During the last 50y, the carcinogenic mycotoxin sterigmatocystin (ST) has been reported in several phylogenetically and phenotypically different genera: Aschersonia, Aspergillus, Bipolaris, Botryotrichum, Chaetomium, Emericella, Eurotium, Farrowia, Fusarium, Humicola, Moelleriella, Monocillium and Podospora. We have reexamined all available strains of the original producers, in addition to ex type and further strains of each species reported to produce ST and the biosynthetically derived aflatoxins. We also screened strains of all available species in Penicillium and Aspergillus for ST and aflatoxin. Six new ST producing fungi were discovered: Aspergillus asperescens, Aspergillus aureolatus, Aspergillus eburneocremeus, Aspergillus protuberus, Aspergillus tardus, and Penicillium inflatum and one new aflatoxin producer: Aspergillus togoensis (=Stilbothamnium togoense). ST was confirmed in 23 Emericella, four Aspergillus, five Chaetomium, one Botryotrichum and one Humicola species grown on a selection of secondary metabolite inducing media, and using multiple detection methods: HPLC-UV/Vis DAD, - HRMS and - MS/MS. The immediate precursor for aflatoxin, O-methylsterigmatocystin was found in Chaetomium cellulolyticum, Chaetomium longicolleum, Chaetomium malaysiense and Chaetomium virescens, but aflatoxin was not detected from any Chaetomium species. In all 55 species, representing more than 11 clades throughout the Pezizomycotina, can be reliably claimed to be ST producers and 13 of these can also produce aflatoxins. It is not known yet whether the ST/aflatoxin pathway has been developed independently 11 times, or is the result of partial horizontal gene transfer.}, }
@article {pmid21527470, year = {2011}, author = {Naito, M and Sato, K and Shoji, M and Yukitake, H and Ogura, Y and Hayashi, T and Nakayama, K}, title = {Characterization of the Porphyromonas gingivalis conjugative transposon CTnPg1: determination of the integration site and the genes essential for conjugal transfer.}, journal = {Microbiology (Reading, England)}, volume = {157}, number = {Pt 7}, pages = {2022-2032}, doi = {10.1099/mic.0.047803-0}, pmid = {21527470}, issn = {1465-2080}, mesh = {Attachment Sites, Microbiological/genetics ; Bacterial Proteins/genetics ; *Conjugation, Genetic ; DNA Topoisomerases, Type I/metabolism ; *DNA Transposable Elements ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Integrases/genetics/metabolism ; Periodontal Diseases/microbiology ; Polymerase Chain Reaction ; Porphyromonas gingivalis/enzymology/*genetics ; Rec A Recombinases/genetics/metabolism ; }, abstract = {In our previous study, extensive genomic rearrangements were found in two strains of the Gram-negative anaerobic bacterium Porphyromonas (Por.) gingivalis, and most of these rearrangements were associated with mobile genetic elements such as insertion sequences and conjugative transposons (CTns). CTnPg1, identified in Por. gingivalis strain ATCC 33277, was the first complete CTn reported for the genus Porphyromonas. In the present study, we found that CTnPg1 can be transferred from strain ATCC 33277 to another Por. gingivalis strain, W83, at a frequency of 10(-7) to 10(-6). The excision of CTnPg1 from the chromosome in a donor cell depends on an integrase (Int; PGN_0094) encoded in CTnPg1, whereas CTnPg1 excision is independent of PGN_0084 (a DNA topoisomerase I homologue; Exc) encoded within CTnPg1 and recA (PGN_1057) on the donor chromosome. Intriguingly, however, the transfer of CTnPg1 between Por. gingivalis strains requires RecA function in the recipient. Sequencing analysis of CTnPg1-integrated sites on the chromosomes of transconjugants revealed that the consensus attachment (att) sequence is a 13 bp sequence, TTTTCNNNNAAAA. We further report that CTnPg1 is able to transfer to two other bacterial species, Bacteroides thetaiotaomicron and Prevotella oralis. In addition, CTnPg1-like CTns are located in the genomes of other oral anaerobic bacteria, Porphyromonas endodontalis, Prevotella buccae and Prevotella intermedia, with the same consensus att sequence. These results suggest that CTns in the CTnPg1 family are widely distributed among oral anaerobic Gram-negative bacteria found in humans and play important roles in horizontal gene transfer among these bacteria.}, }
@article {pmid21527469, year = {2011}, author = {Zeigler, DR}, title = {The genome sequence of Bacillus subtilis subsp. spizizenii W23: insights into speciation within the B. subtilis complex and into the history of B. subtilis genetics.}, journal = {Microbiology (Reading, England)}, volume = {157}, number = {Pt 7}, pages = {2033-2041}, doi = {10.1099/mic.0.048520-0}, pmid = {21527469}, issn = {1465-2080}, mesh = {Bacillus subtilis/*classification/*genetics ; Base Sequence ; *Chromosome Mapping ; DNA, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Speciation ; Genetic Variation ; *Genome, Bacterial ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {The genome sequence of Bacillus subtilis subsp. spizizenii W23 has been determined. The sequence strongly suggests that W23 is a direct descendant of B. subtilis ATCC 6633. W23 shares a 3.6 Mb core genome with the intensively studied model organism B. subtilis subsp. subtilis 168, and gene order within this core has been strongly conserved. Additionally, the W23 genome has 157 accessory (that is, non-core) genome segments that are not found in 168, while the 168 genome has 141 segments not found in W23. The distribution of sequences similar to these accessory segments among other genomes of the B. subtilis species complex shows that those sequences having entered into the phylogeny of the complex more recently tend to be larger and more AT-rich than those having entered earlier. A simple model can account for these observations, in which parasitic or symbiotic DNAs are transferred into the genome and then are reduced in size and modified in base composition during speciation.}, }
@article {pmid21526515, year = {2011}, author = {Sanchez, C}, title = {Horizontal gene transfer: eukaryotes under a new light.}, journal = {Nature reviews. Microbiology}, volume = {9}, number = {4}, pages = {228}, pmid = {21526515}, issn = {1740-1534}, }
@article {pmid21526325, year = {2011}, author = {Millanao B, A and Barrientos H, M and Gómez C, C and Tomova, A and Buschmann, A and Dölz, H and Cabello, FC}, title = {[Injudicious and excessive use of antibiotics: public health and salmon aquaculture in Chile].}, journal = {Revista medica de Chile}, volume = {139}, number = {1}, pages = {107-118}, pmid = {21526325}, issn = {0717-6163}, mesh = {Animals ; Anti-Bacterial Agents/*adverse effects ; Antibiotic Prophylaxis/adverse effects ; Chile ; *Drug Resistance, Bacterial ; Fisheries/*standards ; Humans ; *Public Health ; *Salmon ; }, abstract = {Salmon aquaculture was one of the major growing and exporting industries in Chile. Its development was accompanied by an increasing and excessive use of large amounts of antimicrobials, such as quinolones, tetracyclines and florfenicol. The examination of the sanitary conditions in the industry as part of a more general investigation into the uncontrolled and extensive dissemination of the ISA virus epizootic in 2008, found numerous and wide-ranging shortcomings and limitations in management of preventive fish health. There was a growing industrial use of large amounts of antimicrobials as an attempt at prophylaxis of bacterial infections resulting from widespread unsanitary and unhealthy fish rearing conditions. As might be expected, these attempts were unsuccessful and this heavy antimicrobial use failed to prevent viral and parasitic epizootics. Comparative analysis of the amounts of antimicrobials, especially quinolones, consumed in salmon aquaculture and in human medicine in Chile robustly suggests that the most important selective pressure for antibiotic resistant bacteria in the country will be excessive antibiotic use in this industry. This excessive use will facilitate selection of resistant bacteria and resistance genes in water environments. The commonality of antibiotic resistance genes and the mobilome between environmental aquatic bacteria, fish pathogens and pathogens of terrestrial animals and humans suggests that horizontal gene transfer occurs between the resistome of these apparently independent and isolated bacterial populations. Thus, excessive antibiotic use in the marine environment in aquaculture is not innocuous and can potentially negatively affect therapy of bacterial infections of humans and terrestrial animals.}, }
@article {pmid21521723, year = {2011}, author = {Shafer, WM and Ohneck, EA}, title = {Taking the gonococcus-human relationship to a whole new level: implications for the coevolution of microbes and humans.}, journal = {mBio}, volume = {2}, number = {3}, pages = {e00067-11}, pmid = {21521723}, issn = {2150-7511}, support = {T32 AI007470/AI/NIAID NIH HHS/United States ; 2T32 AI 007470-16/AI/NIAID NIH HHS/United States ; R37 AI201150-26/AI/NIAID NIH HHS/United States ; AI-0311496-20/AI/NIAID NIH HHS/United States ; }, mesh = {*Gene Transfer, Horizontal ; Gonorrhea/*genetics ; *Host-Pathogen Interactions ; Humans ; *Long Interspersed Nucleotide Elements ; Neisseria gonorrhoeae/*genetics ; }, abstract = {While horizontal gene transfer occurs frequently among bacterial species, evidence for the transfer of DNA from host to microbe is exceptionally rare. However, the recent report by Anderson and Seifert [mBio 2(1):e00005-11, 2011] provides evidence for such an event with the finding that 11% of Neisseria gonorrhoeae strains harbor a 685-bp sequence that is 98 to 100% identical to the human long interspersed nuclear element L1. While the function of this element in gonococci remains unclear, this finding significantly impacts our consideration of the coevolution of hosts and microbes, particularly that of humans and pathogens.}, }
@article {pmid21521245, year = {2011}, author = {Andam, CP and Fournier, GP and Gogarten, JP}, title = {Multilevel populations and the evolution of antibiotic resistance through horizontal gene transfer.}, journal = {FEMS microbiology reviews}, volume = {35}, number = {5}, pages = {756-767}, doi = {10.1111/j.1574-6976.2011.00274.x}, pmid = {21521245}, issn = {1574-6976}, mesh = {Alleles ; Amino Acyl-tRNA Synthetases/genetics ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/*genetics ; *Drug Resistance, Bacterial ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Phylogeny ; *Recombination, Genetic ; *Selection, Genetic ; }, abstract = {Horizontal gene transfer (HGT) can create diversity in the genetic repertoire of a lineage. Successful gene transfer likely occurs more frequently between more closely related organisms, leading to the formation of higher-level exchange groups that in some respects are comparable to single-species populations. Genes that appear fixed in a single species can be replaced through distant homologs or iso-functional analogs acquired through HGT. These genes may originate from other species or they may be acquired by an individual strain from the species pan-genome. Because of their similarity to alleles in a population, we label these gene variants that are exchanged between related species as homeoalleles. In a case study, we show that biased gene transfer plays an important role in the evolution of aminoacyl-tRNA synthetases (aaRS). Many microorganisms make use of these genes against naturally occurring antibiotics. We suggest that the resistance against naturally occurring antibiotics is the likely driving force behind the frequent switching between divergent aaRS types and the reason for the maintenance of these homeoalleles in higher-level exchange groups. Resistance to naturally occurring antibiotics may lead to the maintenance of different types of aminoacyl-tRNA synthetases in Bacteria through gene transfer.}, }
@article {pmid21519913, year = {2011}, author = {Zhou, K and Zhang, X and Zhang, F and Li, Z}, title = {Phylogenetically diverse cultivable fungal community and polyketide synthase (PKS), non-ribosomal peptide synthase (NRPS) genes associated with the South China Sea sponges.}, journal = {Microbial ecology}, volume = {62}, number = {3}, pages = {644-654}, pmid = {21519913}, issn = {1432-184X}, mesh = {Animals ; China ; DNA, Fungal/genetics ; Fungi/enzymology/*genetics/isolation &amp; purification ; Oceans and Seas ; Peptide Synthases/*genetics ; *Phylogeny ; Polyketide Synthases/*genetics ; Polymorphism, Restriction Fragment Length ; Porifera/*microbiology ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; }, abstract = {Compared with sponge-associated bacteria, the phylogenetic diversity of fungi in sponge and the association of sponge fungi remain largely unknown. Meanwhile, no detection of polyketide synthase (PKS) or non-ribosomal peptide synthase (NRPS) genes in sponge-associated fungi has been attempted. In this study, diverse and novel cultivable fungi including 10 genera (Aspergillus, Ascomycete, Fusarium, Isaria, Penicillium, Plectosphaerella, Pseudonectria, Simplicillium, Trichoderma, and Volutella) in four orders (Eurotiales, Hypocreales, Microascales, and Phyllachorales) of phylum Ascomycota were isolated from 10 species marine sponges in the South China Sea. Eurotiales and Hypocreales fungi were suggested as sponge generalists. The predominant isolates were Penicillium and Aspergillus in Eurotiales followed by Volutella in Hypocreales. Based on the conserved Beta-ketosynthase of PKS and A domain of NRPS, 15 polyketide synthases, and four non-ribosomal peptides synthesis genes, including non-reducing and reducing PKSs and hybrid PKS-NRPS, were detected in these fungal isolates. A lateral gene transfer event was indicated in the comparison between the phylogenetic diversity of 18S rRNA genes and β-ketoacyl synthase domain sequences. Some fungi, especially those with PKS or NRPS genes, showed antimicrobial activity against P. fluorescens, S. aureus and B. subtilis. It was the first time to investigate PKS and NRPS genes in sponge-associated fungi. Based on the detected antibiotics biosynthesis-related PKS and NRPS genes and antimicrobial activity, the potential ecological role of sponge-associated fungi in the chemical defense for sponge host was suggested. This study extended our knowledge of sponge-associated fungal phylogenetic diversity and their potential roles in the chemical defense.}, }
@article {pmid21519847, year = {2011}, author = {Silverio, AL and Saier, MH}, title = {Bioinformatic characterization of the trimeric intracellular cation-specific channel protein family.}, journal = {The Journal of membrane biology}, volume = {241}, number = {2}, pages = {77-101}, pmid = {21519847}, issn = {1432-1424}, support = {R01 GM077402/GM/NIGMS NIH HHS/United States ; GM077402/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Archaea/genetics ; Bacteria/genetics ; Computational Biology ; Data Mining ; Evolution, Molecular ; Humans ; Hydrophobic and Hydrophilic Interactions ; Ion Channels/*genetics ; Mice ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {Trimeric intracellular cation-specific (TRIC) channels are integral to muscle excitation-contraction coupling. TRIC channels provide counter-ionic flux when calcium is rapidly transported from intracellular stores to the cell cytoplasm. Until recently, knowledge of the presence of these proteins was limited to animals. We analyzed the TRIC family and identified a profusion of prokaryotic family members with topologies and motifs similar to those of their eukaryotic counterparts. Prokaryotic members far outnumber eukaryotic members, and although none has been functionally characterized, the evidence suggests that they function as secondary carriers. The presence of fused N- or C-terminal domains of known biochemical functions as well as genomic context analyses provide clues about the functions of these prokaryotic homologs. They are proposed to function in metabolite (e.g., amino acid/nucleotide) efflux. Phylogenetic analysis revealed that TRIC channel homologs diverged relatively early during evolutionary history and that horizontal gene transfer was frequent in prokaryotes but not in eukaryotes. Topological analyses of TRIC channels revealed that these proteins possess seven putative transmembrane segments (TMSs), which arose by intragenic duplication of a three-TMS polypeptide-encoding genetic element followed by addition of a seventh TMS at the C terminus to give the precursor of all current TRIC family homologs. We propose that this family arose in prokaryotes.}, }
@article {pmid21518847, year = {2011}, author = {Rumbo, C and Fernández-Moreira, E and Merino, M and Poza, M and Mendez, JA and Soares, NC and Mosquera, A and Chaves, F and Bou, G}, title = {Horizontal transfer of the OXA-24 carbapenemase gene via outer membrane vesicles: a new mechanism of dissemination of carbapenem resistance genes in Acinetobacter baumannii.}, journal = {Antimicrobial agents and chemotherapy}, volume = {55}, number = {7}, pages = {3084-3090}, pmid = {21518847}, issn = {1098-6596}, mesh = {Acinetobacter baumannii/*drug effects/*genetics/metabolism/ultrastructure ; Bacterial Proteins/*genetics/metabolism ; Carbapenems/*pharmacology ; Cell Membrane/*metabolism/ultrastructure ; Gene Transfer, Horizontal/genetics/*physiology ; Microscopy, Electron, Transmission ; Polymerase Chain Reaction ; Transport Vesicles/*metabolism ; beta-Lactamases/*genetics/metabolism ; }, abstract = {The resistance of Acinetobacter baumannii strains to carbapenems is a worrying problem in hospital settings. The main mechanism of carbapenem resistance is the expression of β-lactamases (metalloenzymes or class D enzymes). The mechanisms of the dissemination of these genes among A. baumannii strains are not fully understood. In this study we used two carbapenem-resistant clinical strains of A. baumannii (AbH12O-A2 and AbH12O-CU3) expressing the plasmid-borne bla(OXA-24) gene (plasmids pMMA2 and pMMCU3, respectively) to demonstrate that A. baumannii releases outer membrane vesicles (OMVs) during in vitro growth. The use of hybridization studies enabled us to show that these OMVs harbored the bla(OXA-24) gene. The incubation of these OMVs with the carbapenem-susceptible A. baumannii ATCC 17978 host strain yielded full resistance to carbapenems. The presence of the original plasmids harboring the bla(OXA-24) gene was detected in strain ATCC 17978 after the transformation of OMVs. New OMVs harboring bla(OXA-24) were released by A. baumannii ATCC 17978 after it was transformed with the original OMV-mediated plasmids, indicating the universality of the process. We present the first experimental evidence that clinical isolates of A. baumannii may release OMVs as a mechanism of horizontal gene transfer whereby carbapenem resistance genes are delivered to surrounding A. baumannii bacterial isolates.}, }
@article {pmid21517914, year = {2011}, author = {Stokes, HW and Gillings, MR}, title = {Gene flow, mobile genetic elements and the recruitment of antibiotic resistance genes into Gram-negative pathogens.}, journal = {FEMS microbiology reviews}, volume = {35}, number = {5}, pages = {790-819}, doi = {10.1111/j.1574-6976.2011.00273.x}, pmid = {21517914}, issn = {1574-6976}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; *Drug Resistance, Bacterial ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Gram-Negative Bacteria/*drug effects/*genetics ; Humans ; *Interspersed Repetitive Sequences ; Recombination, Genetic ; Selection, Genetic ; }, abstract = {Antibiotics were one of the great discoveries of the 20th century. However, resistance appeared even in the earliest years of the antibiotic era. Antibiotic resistance continues to become worse, despite the ever-increasing resources devoted to combat the problem. One of the most important factors in the development of resistance to antibiotics is the remarkable ability of bacteria to share genetic resources via Lateral Gene Transfer (LGT). LGT occurs on a global scale, such that in theory, any gene in any organism anywhere in the microbial biosphere might be mobilized and spread. With sufficiently strong selection, any gene may spread to a point where it establishes a global presence. From an antibiotic resistance perspective, this means that a resistance phenotype can appear in a diverse range of infections around the globe nearly simultaneously. We discuss the forces and agents that make this LGT possible and argue that the problem of resistance can ultimately only be managed by understanding the problem from a broad ecological and evolutionary perspective. We also argue that human activities are exacerbating the problem by increasing the tempo of LGT and bacterial evolution for many traits that are important to humans.}, }
@article {pmid21517871, year = {2011}, author = {Szadkowski, E and Eber, F and Huteau, V and Lodé, M and Coriton, O and Jenczewski, E and Chèvre, AM}, title = {Polyploid formation pathways have an impact on genetic rearrangements in resynthesized Brassica napus.}, journal = {The New phytologist}, volume = {191}, number = {3}, pages = {884-894}, doi = {10.1111/j.1469-8137.2011.03729.x}, pmid = {21517871}, issn = {1469-8137}, mesh = {Alleles ; Brassica napus/*genetics ; Chromosomes, Plant/genetics ; Crosses, Genetic ; Fertility ; Gene Dosage ; Gene Transfer, Horizontal/*genetics ; Genome, Plant/*genetics ; Germ Cells, Plant ; Hybridization, Genetic ; Meiosis/genetics ; *Polyploidy ; Translocation, Genetic ; }, abstract = {• Polyploids can be produced by the union of unreduced gametes or through somatic doubling of F(1) interspecific hybrids. The first route is suspected to produce allopolyploid species under natural conditions, whereas experimental data have only been thoroughly gathered for the latter. • We analyzed the meiotic behavior of an F(1) interspecific hybrid (by crossing Brassica oleracea and B.rapa, progenitors of B.napus) and the extent to which recombined homoeologous chromosomes were transmitted to its progeny. These results were then compared with results obtained for a plant generated by somatic doubling of this F1 hybrid (CD.S0) and an amphidiploid (UG.S0) formed via a pathway involving unreduced gametes; we studied the impact of this method of polyploid formation on subsequent generations. • This study revealed that meiosis of the F1 interspecific hybrid generated more gametes with recombined chromosomes than did meiosis of the plant produced by somatic doubling, although the size of these translocations was smaller. In the progeny of the UG.S0 plant, there was an unexpected increase in the frequency at which the C1 chromosome was replaced by the A1 chromosome. • We conclude that polyploid formation pathways differ in their genetic outcome. Our study opens up perspectives for the understanding of polyploid origins.}, }
@article {pmid21516790, year = {2011}, author = {Krylov, SV and Pletneva, EA and Burkal'tseva, MV and Shaburova, OV and Miroshnikov, KA and Lavigne, R and Cornelissen, A and Krylov, VN}, title = {[Genome instability of Pseudomonas aeruginosa phages of the EL species: examination of virulent mutants].}, journal = {Genetika}, volume = {47}, number = {2}, pages = {183-189}, pmid = {21516790}, issn = {0016-6758}, mesh = {Bacteriophages/*pathogenicity/*physiology ; Genome, Viral/*physiology ; Lysogeny/*physiology ; *Mutation ; Phylogeny ; Pseudomonas aeruginosa/*virology ; }, abstract = {The article continues a study of pseudolysogeny in Pseudominas aeruginosa infected with phiKZ-like phages of the EL species. Analysis was performed for several newly isolated virulent mutants of EL phages (EL and RU) that were virulent (capable of causing lysis of bacteria infected with the wild-type phage) and a lower extent of opalescence of negative colonies (NCs). Wile-type recombinants were detected in crosses of virulent mutants of phages EL and RU to confirm the polygenic control of virulence. Since a deletion mutation was found in one of the virulent EL mutants and high genetic instability was characteristic of another mutant, a mobile genetic element was assumed to play a role in mutagenesis. Pseudolysogeny of bacteria provides for horizontal gene transfer between different bacterial strains. Hence, sequencing of the phage genome and demonstration of the lack of toxic gene products are insufficient for the phage to be included into a therapeutic mixture. To use live phages, it is essential to study in detail the possible consequences of their interaction with host bacteria.}, }
@article {pmid21515778, year = {2011}, author = {Zhang, G and Deng, A and Xu, Q and Liang, Y and Chen, N and Wen, T}, title = {Complete genome sequence of Bacillus amyloliquefaciens TA208, a strain for industrial production of guanosine and ribavirin.}, journal = {Journal of bacteriology}, volume = {193}, number = {12}, pages = {3142-3143}, pmid = {21515778}, issn = {1098-5530}, mesh = {Bacillus/*classification/*genetics ; *Genome, Bacterial ; Guanosine/*metabolism ; Molecular Sequence Data ; Ribavirin/*metabolism ; }, abstract = {Here, we report the complete genome sequence of Bacillus amyloliquefaciens TA208, a strain for industrial production of guanosine and synthesis of ribavirin by assimilation of formamide. Comparison of its genome sequence with those of strains DSM7 and FZB42 revealed horizontal gene transfer represented by unique prophages and restriction-modification systems and indicated significant accumulation of guanosine.}, }
@article {pmid21513796, year = {2011}, author = {Lâm, TT and Claus, H and Frosch, M and Vogel, U}, title = {Sequence analysis of serotype-specific synthesis regions II of Haemophilus influenzae serotypes c and d: evidence for common ancestry of capsule synthesis in Pasteurellaceae and Neisseria meningitidis.}, journal = {Research in microbiology}, volume = {162}, number = {5}, pages = {483-487}, doi = {10.1016/j.resmic.2011.04.002}, pmid = {21513796}, issn = {1769-7123}, mesh = {Bacterial Capsules/*biosynthesis/chemistry ; Bacterial Proteins/genetics/metabolism ; *Evolution, Molecular ; Haemophilus influenzae/chemistry/classification/*genetics/metabolism ; Molecular Sequence Data ; Neisseria meningitidis/*genetics/metabolism ; Operon ; Pasteurellaceae/*genetics/metabolism ; Sequence Analysis, DNA ; }, abstract = {Sequencing of yet unknown Haemophilus influenzae serotype c (Hic) and d (Hid) capsule synthesis regions II revealed four (ccs1-4) and five (dcs1-5) open reading frames, respectively. The inferred gene functions were in line with capsular polysaccharide structures. One or more proteins encoded by the Hic capsule synthesis region II showed similarity to Actinobacillus pleuropneumoniae serotype 1 and Actinobacillus suis K1 enzymes. Orthologues to the complete operon were observed in Actinobacillus minor strain 202, where even the gene order was conserved. Furthermore, Ccs4 was related to the capsule O-acetyltransferase of Neisseria meningitidis serogroup W-135. For the Hid locus, similarities to Hie, Mannheimia haemolytica A1 and N. meningitidis serogroup A were identified and the succession of genes was similar in the different species. The resemblance of genes and gene organization found for Hic and Hid with other species suggested horizontal gene transfer during capsule evolution across the bacterial classes.}, }
@article {pmid21511548, year = {2011}, author = {Dunlop, RL and Eadie, P}, title = {Idiopathic neonatal necrotising fasciitis caused by community-acquired MSSA encoding Panton Valentine Leukocidin genes.}, journal = {Journal of plastic, reconstructive &amp; aesthetic surgery : JPRAS}, volume = {64}, number = {11}, pages = {1522-1524}, doi = {10.1016/j.bjps.2011.03.041}, pmid = {21511548}, issn = {1878-0539}, mesh = {Bacterial Toxins/genetics ; Bacterial Typing Techniques ; Buttocks ; Combined Modality Therapy ; Community-Acquired Infections/*microbiology/therapy ; Exotoxins/genetics ; Fasciitis, Necrotizing/*microbiology/therapy ; Gene Transfer, Horizontal/genetics ; Humans ; Infant, Newborn ; Leukocidins/genetics ; Male ; Methicillin Resistance/genetics ; Microbial Sensitivity Tests ; Staphylococcal Infections/*microbiology/therapy ; Staphylococcus aureus/genetics ; }, abstract = {Neonatal necrotising fasciitis is very rare in comparison to the adult presentation of the disease and a Plastic Surgeon may only encounter one such case during his or her career. Often this is initially misdiagnosed and managed as simple cellulitis. It generally affects previously healthy babies, the site is often the lower back area and a history of minor skin trauma may be elicited. The causative organism is usually Streptococcus or polymicrobial, as is the case in the adult population. We present the case of a previously healthy 11-day-old infant with idiopathic, rapidly progressive necrotising fasciitis of the back, cause by Methicillin sensitive Staphylococcus aureus (MSSA) infection. The strain was isolated and found to encode the Panton-Valentine Leukocidin genes, which have been associated with particularly severe necrotising infections in other sites, with high mortality. These strains are the subject of specific treatment and eradication guidance in the UK but awareness of this and the importance of obtaining detailed culture typing is likely to be low amongst Plastic Surgeons.}, }
@article {pmid21506007, year = {2011}, author = {Sinkovics, JG}, title = {Horizontal gene transfers with or without cell fusions in all categories of the living matter.}, journal = {Advances in experimental medicine and biology}, volume = {714}, number = {}, pages = {5-89}, pmid = {21506007}, issn = {0065-2598}, mesh = {Animals ; Archaea/genetics ; Cell Fusion ; Cell Survival ; Epithelial-Mesenchymal Transition ; *Gene Transfer, Horizontal ; Herpesviridae/genetics ; Humans ; Mimiviridae/genetics ; Neoplasms/pathology/therapy ; Proto-Oncogenes ; Retroelements ; Vibrio cholerae/genetics ; Virulence/genetics ; }, abstract = {This article reviews the history of widespread exchanges of genetic segments initiated over 3 billion years ago, to be part of their life style, by sphero-protoplastic cells, the ancestors of archaea, prokaryota, and eukaryota. These primordial cells shared a hostile anaerobic and overheated environment and competed for survival. "Coexist with, or subdue and conquer, expropriate its most useful possessions, or symbiose with it, your competitor" remain cellular life's basic rules. This author emphasizes the role of viruses, both in mediating cell fusions, such as the formation of the first eukaryotic cell(s) from a united crenarchaeon and prokaryota, and the transfer of host cell genes integrated into viral (phages) genomes. After rising above the Darwinian threshold, rigid rules of speciation and vertical inheritance in the three domains of life were established, but horizontal gene transfers with or without cell fusions were never abolished. The author proves with extensive, yet highly selective documentation, that not only unicellular microorganisms, but the most complex multicellular entities of the highest ranks resort to, and practice, cell fusions, and donate and accept horizontally (laterally) transferred genes. Cell fusions and horizontally exchanged genetic materials remain the fundamental attributes and inherent characteristics of the living matter, whether occurring accidentally or sought after intentionally. These events occur to cells stagnating for some 3 milliard years at a lower yet amazingly sophisticated level of evolution, and to cells achieving the highest degree of differentiation, and thus functioning in dependence on the support of a most advanced multicellular host, like those of the human brain. No living cell is completely exempt from gene drains or gene insertions.}, }
@article {pmid21506006, year = {2011}, author = {Dittmar, T and Zänker, KS}, title = {Cell fusion in health and disease. Volume II: cell fusion in disease. Introduction.}, journal = {Advances in experimental medicine and biology}, volume = {714}, number = {}, pages = {1-3}, doi = {10.1007/978-94-007-0782-5_1}, pmid = {21506006}, issn = {0065-2598}, mesh = {Animals ; *Cell Fusion ; Humans ; *Periodicals as Topic ; }, abstract = {Although cell fusion is an omnipresent process in life, to date considerably less is still known about the mechanisms and the molecules being involved in this biological phenomenon in higher organisms. Cell Fusion in Health and Disease Volume 2 is covering the dark side of cell fusion: namely its role in pathophysiological processes. International leading experts will present up-to-date overviews about cell fusion mediated horizontal gene transfer in bacteria and viruses, class III viral membrane fusion proteins, trophoblast fusion in trisomy 21, and the role of microvesicles in malignancies. Particular attention is paid on cell fusion in cancer and how this biological phenomenon may initiate the origin of (recurrence) cancer stem cells as well as drive the progression of multiple myeloma, colon cancer, breast cancer, and malignant melanoma. Thus, Cell Fusion in Health and Disease Volume 2 represents a state-of-the-art work for researchers, physicians or professionals being interested in reflecting the dark side of cell fusion.}, }
@article {pmid21505418, year = {2011}, author = {Vogelmann, J and Ammelburg, M and Finger, C and Guezguez, J and Linke, D and Flötenmeyer, M and Stierhof, YD and Wohlleben, W and Muth, G}, title = {Conjugal plasmid transfer in Streptomyces resembles bacterial chromosome segregation by FtsK/SpoIIIE.}, journal = {The EMBO journal}, volume = {30}, number = {11}, pages = {2246-2254}, pmid = {21505418}, issn = {1460-2075}, mesh = {Bacterial Proteins/*metabolism ; Binding Sites ; Chromosome Segregation ; Chromosomes, Bacterial/genetics ; *Conjugation, Genetic ; DNA/metabolism ; DNA, Bacterial/metabolism ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Phylogeny ; *Plasmids ; Protein Binding ; Protein Multimerization ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Streptomyces coelicolor/*genetics ; }, abstract = {Conjugation is a major route of horizontal gene transfer, the driving force in the evolution of bacterial genomes. Antibiotic producing soil bacteria of the genus Streptomyces transfer DNA in a unique process involving a single plasmid-encoded protein TraB and a double-stranded DNA molecule. However, the molecular function of TraB in directing DNA transfer from a donor into a recipient cell is unknown. Here, we show that TraB constitutes a novel conjugation system that is clearly distinguished from DNA transfer by a type IV secretion system. We demonstrate that TraB specifically recognizes and binds to repeated 8 bp motifs on the conjugative plasmid. The specific DNA recognition is mediated by helix α3 of the C-terminal winged-helix-turn-helix domain of TraB. We show that TraB assembles to a hexameric ring structure with a central ∼3.1 nm channel and forms pores in lipid bilayers. Structure, sequence similarity and DNA binding characteristics of TraB indicate that TraB is derived from an FtsK-like ancestor protein, suggesting that Streptomyces adapted the FtsK/SpoIIIE chromosome segregation system to transfer DNA between two distinct Streptomyces cells.}, }
@article {pmid21504537, year = {2011}, author = {Boyd, ES and Anbar, AD and Miller, S and Hamilton, TL and Lavin, M and Peters, JW}, title = {A late methanogen origin for molybdenum-dependent nitrogenase.}, journal = {Geobiology}, volume = {9}, number = {3}, pages = {221-232}, doi = {10.1111/j.1472-4669.2011.00278.x}, pmid = {21504537}, issn = {1472-4669}, mesh = {Bacterial Proteins/genetics ; Euryarchaeota/*enzymology/genetics ; *Evolution, Molecular ; Gene Duplication ; Gene Fusion ; Molybdenum/*metabolism ; *Nitrogen Cycle ; Nitrogenase/*metabolism ; Photosynthesis ; Phylogeny ; }, abstract = {Mounting evidence indicates the presence of a near complete biological nitrogen cycle in redox-stratified oceans during the late Archean to early Proterozoic (c. 2.5-2.0 Ga). It has been suggested that the iron (Fe)- or vanadium (V)-dependent nitrogenase rather than molybdenum (Mo)-dependent form was responsible for dinitrogen fixation during this time because oceans were depleted in Mo and rich in Fe. We evaluated this hypothesis by examining the phylogenetic relationships of proteins that are required for the biosynthesis of the active site cofactor of Mo-nitrogenase in relation to structural proteins required for Fe-, V- and Mo-nitrogenase. The results are highly suggestive that among extant nitrogen-fixing organisms for which genomic information exists, Mo-nitrogenase is unlikely to have been associated with the Last Universal Common Ancestor. Rather, the origin of Mo-nitrogenase can be traced to an ancestor of the anaerobic and hydrogenotrophic methanogens with acquisition in the bacterial domain via lateral gene transfer involving an anaerobic member of the Firmicutes. A comparison of substitution rates estimated for proteins required for the biosynthesis of the nitrogenase active site cofactor and for a set of paralogous proteins required for the biosynthesis of bacteriochlorophyll suggests that Nif emerged from a nitrogenase-like ancestor approximately 1.5-2.2 Ga. An origin and ensuing proliferation of Mo-nitrogenase under anoxic conditions would likely have occurred in an environment where anaerobic methanogens and Firmicutes coexisted and where Mo was at least episodically available, such as in a redox-stratified Proterozoic ocean basin.}, }
@article {pmid21501489, year = {2011}, author = {Maruyama, S and Suzaki, T and Weber, AP and Archibald, JM and Nozaki, H}, title = {Eukaryote-to-eukaryote gene transfer gives rise to genome mosaicism in euglenids.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {105}, pmid = {21501489}, issn = {1471-2148}, mesh = {Chlorophyta/*genetics/physiology ; Euglenida/classification/*genetics/physiology ; *Gene Transfer, Horizontal ; *Genome ; Molecular Sequence Data ; *Mosaicism ; Phylogeny ; Plastids/genetics ; Rhodophyta/*genetics/physiology ; Symbiosis ; }, abstract = {BACKGROUND: Euglenophytes are a group of photosynthetic flagellates possessing a plastid derived from a green algal endosymbiont, which was incorporated into an ancestral host cell via secondary endosymbiosis. However, the impact of endosymbiosis on the euglenophyte nuclear genome is not fully understood due to its complex nature as a 'hybrid' of a non-photosynthetic host cell and a secondary endosymbiont.<br><br>RESULTS: We analyzed an EST dataset of the model euglenophyte Euglena gracilis using a gene mining program designed to detect laterally transferred genes. We found E. gracilis genes showing affinity not only with green algae, from which the secondary plastid in euglenophytes evolved, but also red algae and/or secondary algae containing red algal-derived plastids. Phylogenetic analyses of these 'red lineage' genes suggest that E. gracilis acquired at least 14 genes via eukaryote-to-eukaryote lateral gene transfer from algal sources other than the green algal endosymbiont that gave rise to its current plastid. We constructed an EST library of the aplastidic euglenid Peranema trichophorum, which is a eukaryovorous relative of euglenophytes, and also identified 'red lineage' genes in its genome.<br><br>CONCLUSIONS: Our data show genome mosaicism in E. gracilis and P. trichophorum. One possible explanation for the presence of these genes in these organisms is that some or all of them were independently acquired by lateral gene transfer and contributed to the successful integration and functioning of the green algal endosymbiont as a secondary plastid. Alternative hypotheses include the presence of a phagocytosed alga as the single source of those genes, or a cryptic tertiary endosymbiont harboring secondary plastid of red algal origin, which the eukaryovorous ancestor of euglenophytes had acquired prior to the secondary endosymbiosis of a green alga.}, }
@article {pmid21499969, year = {2011}, author = {Soto, SM and Zúñiga, S and Ulleryd, P and Vila, J}, title = {Acquisition of a pathogenicity island in an Escherichia coli clinical isolate causing febrile urinary tract infection.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {30}, number = {12}, pages = {1543-1550}, pmid = {21499969}, issn = {1435-4373}, mesh = {Cluster Analysis ; DNA, Bacterial/genetics ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/*genetics/isolation &amp; purification ; Escherichia coli Infections/*microbiology ; Gene Transfer, Horizontal ; *Genomic Islands ; Genotype ; Humans ; Male ; Molecular Typing ; Recurrence ; Urinary Tract Infections/*microbiology ; Virulence Factors/genetics ; }, abstract = {Urinary tract infections (UTI) are less common in men than in women, and uropathogenic Escherichia coli (UPEC) is the most frequent etiological agent. Recurrent UTI in men have often been reported as a relapse with the same strain as the index infection. The persistence of the same E. coli strain within the urinary tract has often been explained by a prostatic focus. The aim of this study was to determine whether recurrence was associated with relapse or reinfection and the possible effect of treatment on the content of virulence factors of the isolates causing these infections. Thirty E. coli isolates were collected from 15 patients with a febrile UTI having a bacteriological recurrence during long-term follow-up. These isolates were analyzed by pulsed-field gel electrophoresis (PFGE) and virulence profiling in order to determine whether they constituted relapse or reinfection. Five recurrences were categorized as relapse and nine as reinfections. The results obtained showed that the horizontal transfer of virulence factors contained in a pathogenicity island had occurred in one isolate. This event is possible in vivo and allows bacteria to become more virulent and, perhaps, cause greater damage. The acquisition of virulence genes by horizontal gene transfer is an ongoing process of evolution that continuously leads to new bacterial pathotypes.}, }
@article {pmid21498744, year = {2011}, author = {Liang, B and Wang, G and Zhao, Y and Chen, K and Li, S and Jiang, J}, title = {Facilitation of bacterial adaptation to chlorothalonil-contaminated sites by horizontal transfer of the chlorothalonil hydrolytic dehalogenase gene.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {12}, pages = {4268-4272}, pmid = {21498744}, issn = {1098-5336}, mesh = {*Adaptation, Biological ; Bacteria/*enzymology/genetics/*metabolism ; Biotransformation ; DNA, Bacterial/chemistry/genetics ; *Gene Transfer, Horizontal ; Hydrolases/*genetics/*metabolism ; Molecular Sequence Data ; Nitriles/*metabolism ; Sequence Analysis, DNA ; }, abstract = {Horizontal transfer of the chlorothalonil hydrolytic dehalogenase gene (chd) is proposed based on the high conservation of the chd gene and its close association with a novel insertion sequence, ISOcsp1, in 16 isolated chlorothalonil-dechlorinating strains belonging to eight different genera. The ecological role of horizontal gene transfer is assumed to facilitate bacterial adaptation to chlorothalonil-contaminated sites, through detoxification of chlorothalonil to less toxic 2,4,5-trichloro-6-hydroxybenzene-1,3-dicarbonitrile.}, }
@article {pmid21497473, year = {2011}, author = {Ampomah, OY and Huss-Danell, K}, title = {Genetic diversity of root nodule bacteria nodulating Lotus corniculatus and Anthyllis vulneraria in Sweden.}, journal = {Systematic and applied microbiology}, volume = {34}, number = {4}, pages = {267-275}, doi = {10.1016/j.syapm.2011.01.006}, pmid = {21497473}, issn = {1618-0984}, mesh = {Acyltransferases/genetics ; Bacteria/*classification/*genetics/isolation &amp; purification ; Bacterial Proteins/genetics ; Bacterial Typing Techniques ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/genetics ; Fabaceae/*microbiology ; *Genetic Variation ; Molecular Sequence Data ; Molecular Typing ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Root Nodules, Plant/*microbiology ; Sequence Analysis, DNA ; Sweden ; }, abstract = {Very little is known about the genetic diversity and phylogeny of rhizobia nodulating Lotus species in northern temperate regions. We have therefore studied the genetic diversity among a total of 61 root nodule bacteria isolated from Lotus corniculatus and Anthyllis vulneraria from different geographic sites and habitats in Sweden by restriction fragment length polymorphism (RFLP) of the internal transcribed spacer between their 16S rRNA and 23S rRNA (IGS) region. A high diversity consisting of 26 IGS types from 54 L. corniculatus isolates and five IGS types from seven A. vulneraria isolates was found. The 16S rRNA sequences and phylogeny of representatives of the different IGS types showed four interesting exceptions from the majority of the isolates belonging to the genus Mesorhizobium: Two isolates were both found to be closely related to Rhodococcus spp., and two other isolates showed close relationship with Geobacillus spp. and Paenibacillus spp., respectively. The nodA sequences and phylogeny showed that all the isolates, including those not belonging to the traditional rhizobia genera, harbored nodA sequences which were typical of Mesorhizobium loti. Generally, the 16S rRNA and nodA phylogenetic trees were not congruent in that isolates with similar 16S rRNA sequences were associated with isolates harboring different nodA sequences. All the isolates were confirmed to nodulate L. corniculatus in an inoculation test. This is the first report of members of these non-rhizobia genera being able to nodulate legumes, and we suggest that they may have acquired their nodulating properties through lateral gene transfer.}, }
@article {pmid21496063, year = {2011}, author = {Guo, X and Xia, R and Han, N and Xu, H}, title = {Genetic diversity analyses of class 1 integrons and their associated antimicrobial resistance genes in Enterobacteriaceae strains recovered from aquatic habitats in China.}, journal = {Letters in applied microbiology}, volume = {52}, number = {6}, pages = {667-675}, doi = {10.1111/j.1472-765X.2011.03059.x}, pmid = {21496063}, issn = {1472-765X}, mesh = {China ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial ; Enterobacteriaceae/drug effects/*genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; *Genetic Variation ; Hospitals ; *Integrons ; Polymorphism, Restriction Fragment Length ; Sewage/microbiology ; }, abstract = {AIMS: To characterize the molecular diversity of class 1 integrons and antibiotic resistance (AR) genes of Enterobacteriaceae strains recovered from aquatic habitats in Jinan, Shandong Province, China.<br><br>METHODS AND RESULTS: Six hundred and thirty-eight antimicrobial-resistant Enterobacteriaceae isolated from wastewater were examined for class 1 integron. Of these, 293 were positive for the class 1 integrase gene intI1; among these, 34 gene cassettes and 29 AR genes were detected. Twenty-nine distinct gene cassette arrays were identified by restriction fragment length polymorphism (RFLP). Seven strains harboring novel gene cassette arrays were subjected to further study, in which antimicrobial susceptibility profiles were determined, and the presence of other AR genes outside of the integrons was assayed. Several of the resistance determinants were found to be transferable by conjugation or transformation.<br><br>CONCLUSIONS: This study established the assessment of class 1 integron and antimicrobial resistance gene patterns among environmental Enterobacteriaceae. Also, a restriction enzyme EcoRII was employed to develop a rapid and simple method for characterizing gene cassette arrays by RFLP analysis, which facilitated further study of novel gene cassette arrays.<br><br>These data not only illustrated the diversity of class 1 integron gene cassettes but also provided direct evidence that integrons mobilized gene cassettes, generating new linkages of resistance genes, and they could be integrated in gene transfer units such as conjugative plasmids to contribute to the dissemination of AR genes by horizontal gene transfer (HGT) in aquatic environments.}, }
@article {pmid21495477, year = {2011}, author = {Arnold, C}, title = {To share and share alike.}, journal = {Scientific American}, volume = {304}, number = {4}, pages = {30-31}, doi = {10.1038/scientificamerican0411-30}, pmid = {21495477}, issn = {0036-8733}, mesh = {Archaea/genetics ; Bacteria/*genetics ; Gene Transfer, Horizontal/*genetics ; }, }
@article {pmid21491175, year = {2011}, author = {Sorlí, L and Miró, E and Segura, C and Navarro, F and Grau, S and Salvado, M and Horcajada, JP}, title = {Intra- and inter-species spread of carbapenemase genes in a non-hospitalized patient.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {30}, number = {12}, pages = {1551-1555}, pmid = {21491175}, issn = {1435-4373}, mesh = {Aged ; Anti-Bacterial Agents/pharmacology ; Bacteremia/microbiology ; Bacterial Proteins/*genetics ; Catheters/microbiology ; Cluster Analysis ; DNA, Bacterial/genetics ; Electrophoresis, Gel, Pulsed-Field ; *Gene Transfer, Horizontal ; Genotype ; Gram-Negative Bacteria/classification/*enzymology/*genetics/isolation &amp; purification ; Gram-Negative Bacterial Infections/*microbiology ; Humans ; Male ; Microbial Sensitivity Tests ; Molecular Typing ; Plasmids/analysis ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; beta-Lactamases/*genetics ; }, abstract = {The purpose of this study was to report intra- and inter-species spread of carbapenemase genes between gram negative rods isolated from a non-hospitalized patient with bacteremia. The approach included chart review, antibiotic susceptibility testing and phenotypic screening for metallo-β-lactamase (MBL) detection, PCR and sequencing of bla, aac(6')-Ib and qnr genes, and plasmid analysis by PCR-based replicon typing. The clonal relationships between the isolates were analysed by comparing PFGE profiles. A non-hospitalized patient presented bacteraemia due to wild type Enterobacter cloacae (4.08), a VIM-1-producing E. cloacae (5.08), a VIM-1- and CTX-M-9-producing E. cloacae (7.08), a VIM-2-producing Pseudomonas aeruginosa, and catheter colonization by VIM-1-producing Klebsiella oxytoca. The patient had no previous hospitalization but had recently undergone an ambulatory colonoscopy. In E. cloacae 7.08 and K. oxytoca isolates, the bla(VIM-1) gene was located on a transferable plasmid of 48.5 kb, while in E. cloacae 5.08 the bla(VIM-1) gene was encoded on a 194 kb non-transferable plasmid. The bla(CTX-M-9) gene detected in E. cloacae was encoded on an HI2 plasmid of 290 kb. To date the prevalence of VIM-1 enzymes in the community is low. This molecular finding suggests an intra-species and/or inter-species horizontal spread of the MBL gene in the same non-hospitalized patient.}, }
@article {pmid21487201, year = {2011}, author = {Djedidi, S and Yokoyama, T and Ohkama-Ohtsu, N and Risal, CP and Abdelly, C and Sekimoto, H}, title = {Stress tolerance and symbiotic and phylogenic features of root nodule bacteria associated with Medicago species in different bioclimatic regions of Tunisia.}, journal = {Microbes and environments}, volume = {26}, number = {1}, pages = {36-45}, doi = {10.1264/jsme2.me10138}, pmid = {21487201}, issn = {1347-4405}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; Climate ; Gene Transfer, Horizontal ; Genetic Variation ; Medicago/*microbiology/physiology ; Molecular Sequence Data ; *Phylogeny ; Root Nodules, Plant/*microbiology/physiology ; Sodium Chloride/metabolism ; Soil Microbiology ; Stress, Physiological ; *Symbiosis ; Tunisia ; }, abstract = {Thirty two rhizobial isolates were obtained from different bioclimatic regions of Tunisia using as trap plants, Medicago sativa, Medicago ciliaris, Medicago polymorpha and Medicago minima. To study their diversity and characterize them in relation to Mediterranean conditions, abiotic stress resistance, symbiotic properties and genetic diversity in terms of 16S rRNA and nodA sequences were assessed. Five isolates from M. sativa, three from M. ciliaris and three from M. minima could grow at 45°C. Only two isolates from M. sativa grew at 4% NaCl. The most stress tolerant isolates were obtained from arid soils. A phylogenetic analysis of 16S rRNA genes revealed 29 isolates to be closely related to Ensifer including one (Pl.3-9) that showed a 16S rRNA sequence similar to that of Ensifer meliloti and nodA sequence similar to that of Ensifer medicae. However, three isolates were categorized into Agrobacterium containing the nodA of Ensifer. Furthermore, these isolates developed nodules on original hosts. The results for the four isolates suggest horizontal gene transfer between the species.}, }
@article {pmid21483493, year = {2011}, author = {Adékambi, T and Butler, RW and Hanrahan, F and Delcher, AL and Drancourt, M and Shinnick, TM}, title = {Core gene set as the basis of multilocus sequence analysis of the subclass Actinobacteridae.}, journal = {PloS one}, volume = {6}, number = {3}, pages = {e14792}, pmid = {21483493}, issn = {1932-6203}, mesh = {Actinobacteria/classification/*genetics ; Bacterial Proteins/classification/*genetics ; Multilocus Sequence Typing/*methods ; Phylogeny ; }, abstract = {Comparative genomic sequencing is shedding new light on bacterial identification, taxonomy and phylogeny. An in silico assessment of a core gene set necessary for cellular functioning was made to determine a consensus set of genes that would be useful for the identification, taxonomy and phylogeny of the species belonging to the subclass Actinobacteridae which contained two orders Actinomycetales and Bifidobacteriales. The subclass Actinobacteridae comprised about 85% of the actinobacteria families. The following recommended criteria were used to establish a comprehensive gene set; the gene should (i) be long enough to contain phylogenetically useful information, (ii) not be subject to horizontal gene transfer, (iii) be a single copy (iv) have at least two regions sufficiently conserved that allow the design of amplification and sequencing primers and (v) predict whole-genome relationships. We applied these constraints to 50 different Actinobacteridae genomes and made 1,224 pairwise comparisons of the genome conserved regions and gene fragments obtained by using Sequence VARiability Analysis Program (SVARAP), which allow designing the primers. Following a comparative statistical modeling phase, 3 gene fragments were selected, ychF, rpoB, and secY with R2>0.85. Selected sets of broad range primers were tested from the 3 gene fragments and were demonstrated to be useful for amplification and sequencing of 25 species belonging to 9 genera of Actinobacteridae. The intraspecies similarities were 96.3-100% for ychF, 97.8-100% for rpoB and 96.9-100% for secY among 73 strains belonging to 15 species of the subclass Actinobacteridae compare to 99.4-100% for 16S rRNA. The phylogenetic topology obtained from the combined datasets ychF+rpoB+secY was globally similar to that inferred from the 16S rRNA but with higher confidence. It was concluded that multi-locus sequence analysis using core gene set might represent the first consensus and valid approach for investigating the bacterial identification, phylogeny and taxonomy.}, }
@article {pmid21481756, year = {2011}, author = {Zhaxybayeva, O and Doolittle, WF}, title = {Lateral gene transfer.}, journal = {Current biology : CB}, volume = {21}, number = {7}, pages = {R242-6}, doi = {10.1016/j.cub.2011.01.045}, pmid = {21481756}, issn = {1879-0445}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Bacteria/*genetics ; Bacterial Physiological Phenomena/genetics ; *Gene Transfer, Horizontal ; Phylogeny ; }, }
@article {pmid21479820, year = {2011}, author = {Mullineux, ST and Willows, K and Hausner, G}, title = {Evolutionary dynamics of the mS952 intron: a novel mitochondrial group II intron encoding a LAGLIDADG homing endonuclease gene.}, journal = {Journal of molecular evolution}, volume = {72}, number = {5-6}, pages = {433-449}, pmid = {21479820}, issn = {1432-1432}, mesh = {Ascomycota/classification/*genetics ; Biological Evolution ; Endonucleases/*genetics ; *Genes, Fungal ; Introns/*genetics ; Mitochondria/*genetics ; Models, Genetic ; Phylogeny ; }, abstract = {Examination of the mitochondrial small subunit ribosomal RNA (rns) gene of five species of the fungal genus Leptographium revealed that the gene has been invaded at least once at position 952 by a group II intron encoding a LAGLIDADG homing endonuclease gene. Phylogenetic analyses of the intron and homing endonuclease sequences indicated that each element in Leptographium species forms a single clade and is closely related to the group II intron/homing endonuclease gene composite element previously reported at position 952 of the mitochondrial rns gene of Cordyceps species and of Cryphonectria parasitica. The results of an intron survey of the mt rns gene of Leptographium species superimposed onto the phylogenetic analysis of the host organisms suggest that the composite element was transmitted vertically in Leptographium lundbergii. However, its stochastic distribution among strains of L. wingfieldii, L. terebrantis, and L. truncatum suggests that it has been horizontally transmitted by lateral gene transfer among these species, although the random presence of the intron may reflect multiple random loss events. A model is proposed describing the initial invasion of the group II intron in the rns gene of L. lundbergii by a LAGLIDADG homing endonuclease gene and subsequent evolution of this gene to recognize a novel DNA target site, which may now promote the mobility of the intron and homing endonuclease gene as a composite element.}, }
@article {pmid21478390, year = {2012}, author = {de la Haba, RR and Márquez, MC and Papke, RT and Ventosa, A}, title = {Multilocus sequence analysis of the family Halomonadaceae.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {62}, number = {Pt 3}, pages = {520-538}, doi = {10.1099/ijs.0.032938-0}, pmid = {21478390}, issn = {1466-5034}, mesh = {Bacterial Proteins/genetics ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Halomonadaceae/*classification/*genetics ; Molecular Sequence Data ; *Multilocus Sequence Typing ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Sequence Analysis, DNA ; }, abstract = {Multilocus sequence analysis (MLSA) protocols have been developed for species circumscription for many taxa. However, at present, no studies based on MLSA have been performed within any moderately halophilic bacterial group. To test the usefulness of MLSA with these kinds of micro-organisms, the family Halomonadaceae, which includes mainly halophilic bacteria, was chosen as a model. This family comprises ten genera with validly published names and 85 species of environmental, biotechnological and clinical interest. In some cases, the phylogenetic relationships between members of this family, based on 16S rRNA gene sequence comparisons, are not clear and a deep phylogenetic analysis using several housekeeping genes seemed appropriate. Here, MLSA was applied using the 16S rRNA, 23S rRNA, atpA, gyrB, rpoD and secA genes for species of the family Halomonadaceae. Phylogenetic trees based on the individual and concatenated gene sequences revealed that the family Halomonadaceae formed a monophyletic group of micro-organisms within the order Oceanospirillales. With the exception of the genera Halomonas and Modicisalibacter, all other genera within this family were phylogenetically coherent. Five of the six studied genes (16S rRNA, 23S rRNA, gyrB, rpoD and secA) showed a consistent evolutionary history. However, the results obtained with the atpA gene were different; thus, this gene may not be considered useful as an individual gene phylogenetic marker within this family. The phylogenetic methods produced variable results, with those generated from the maximum-likelihood and neighbour-joining algorithms being more similar than those obtained by maximum-parsimony methods. Horizontal gene transfer (HGT) plays an important evolutionary role in the family Halomonadaceae; however, the impact of recombination events in the phylogenetic analysis was minimized by concatenating the six loci, which agreed with the current taxonomic scheme for this family. Finally, the findings of this study also indicated that the 16S rRNA, gyrB and rpoD genes were the most suitable genes for future taxonomic studies using MLSA within the family Halomonadaceae.}, }
@article {pmid21478055, year = {2011}, author = {Shahid, M}, title = {Environmental dissemination of NDM-1: time to act sensibly.}, journal = {The Lancet. Infectious diseases}, volume = {11}, number = {5}, pages = {334-335}, doi = {10.1016/S1473-3099(11)70074-3}, pmid = {21478055}, issn = {1474-4457}, mesh = {Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Bacterial/genetics ; Gene Expression Regulation, Bacterial/physiology ; Gene Expression Regulation, Enzymologic/physiology ; Gene Transfer, Horizontal ; Gram-Negative Bacteria/drug effects/*enzymology/*genetics ; Humans ; Water Microbiology ; beta-Lactamases/*genetics/*physiology ; }, }
@article {pmid21477200, year = {2011}, author = {Biernat, MA and Ros, VI and Vlak, JM and van Oers, MM}, title = {Baculovirus cyclobutane pyrimidine dimer photolyases show a close relationship with lepidopteran host homologues.}, journal = {Insect molecular biology}, volume = {20}, number = {4}, pages = {457-464}, doi = {10.1111/j.1365-2583.2011.01076.x}, pmid = {21477200}, issn = {1365-2583}, mesh = {Animals ; Baculoviridae/*enzymology/genetics ; Deoxyribodipyrimidine Photo-Lyase/genetics/*metabolism ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Insect ; Genes, Viral ; Host-Pathogen Interactions ; Lepidoptera/*enzymology/genetics/virology ; Phylogeny ; }, abstract = {Cyclobutane pyrimidine dimer (CPD) photolyases repair ultraviolet (UV)-induced DNA damage using blue light. To get insight in the origin of baculovirus CPD photolyase (phr) genes, homologues in the lepidopteran insects Chrysodeixis chalcites, Spodoptera exigua and Trichoplusia ni were identified and characterized. Lepidopteran and baculovirus phr genes each form a monophyletic group, and together form a well-supported clade within the insect photolyases. This suggests that baculoviruses obtained their phr genes from an ancestral lepidopteran insect host. A likely evolutionary scenario is that a granulovirus, Spodoptera litura GV or a direct ancestor, obtained a phr gene. Subsequently, it was horizontally transferred from this granulovirus to several group II nucleopolyhedroviruses (NPVs), including those that infect noctuids of the Plusiinae subfamily.}, }
@article {pmid21475726, year = {2011}, author = {Theerachat, M and Virunanon, C and Chulalaksananukul, S and Sinbuathong, N and Chulalaksananukul, W}, title = {NirK and nirS Nitrite reductase genes from non-agricultural forest soil bacteria in Thailand.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {27}, number = {4}, pages = {999-1003}, pmid = {21475726}, issn = {1573-0972}, abstract = {The genetic heterogeneity of the nitrite reductase gene (nirK and nirS) fragments from denitrifying prokaryotes in a non-agricultural forest soil in Thailand was investigated using soil samples from the Plant Germplasm-Royal Initiation Project area in Kanchanaburi Province, Thailand. Soil bacteria were screened for denitrification activity and 13 (from 211) positive isolates were obtained and further evaluated for their ability to reduce nitrate and to accumulate or reduce nitrite. Three species with potentially previously unreported denitrifying activities were recorded. Analysis of the partial nirK and nirS sequences of these 13 strains revealed a diverse sequence heterogeneity in these two genes within the same environment and even potentially within the same host species, the potential existence of lateral gene transfer and the first record of both nirK and nirS homologues in one bacterial species. Finally, isolates of two species of bacteria (Corynebacterium propinquum and Micrococcus lylae) are recorded as denitrifiers for the first time.}, }
@article {pmid21474478, year = {2011}, author = {Kiiru, J and Kariuki, S and Goddeeris, BM and Revathi, G and Maina, TW and Ndegwa, DW and Muyodi, J and Butaye, P}, title = {Escherichia coli strains from Kenyan patients carrying conjugatively transferable broad-spectrum β-lactamase, qnr, aac(6')-Ib-cr and 16S rRNA methyltransferase genes.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {66}, number = {7}, pages = {1639-1642}, doi = {10.1093/jac/dkr149}, pmid = {21474478}, issn = {1460-2091}, mesh = {Acetyltransferases/genetics ; Anti-Bacterial Agents/pharmacology ; *Conjugation, Genetic ; DNA Transposable Elements ; *Drug Resistance, Multiple, Bacterial ; Escherichia coli/*drug effects/*genetics/isolation &amp; purification ; Escherichia coli Infections/*microbiology ; Escherichia coli Proteins/*genetics ; *Gene Transfer, Horizontal ; Humans ; Integrons ; Kenya ; Microbial Sensitivity Tests ; Plasmids ; beta-Lactamases/genetics ; tRNA Methyltransferases/genetics ; }, }
@article {pmid21471011, year = {2011}, author = {Domazet-Lošo, M and Haubold, B}, title = {Alignment-free detection of local similarity among viral and bacterial genomes.}, journal = {Bioinformatics (Oxford, England)}, volume = {27}, number = {11}, pages = {1466-1472}, doi = {10.1093/bioinformatics/btr176}, pmid = {21471011}, issn = {1367-4811}, mesh = {Escherichia coli/genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genome, Viral ; Genomics/methods ; HIV-1/genetics ; Humans ; *Sequence Analysis, DNA ; *Sequence Homology, Nucleic Acid ; Software ; }, abstract = {MOTIVATION: Bacterial and viral genomes are often affected by horizontal gene transfer observable as abrupt switching in local homology. In addition to the resulting mosaic genome structure, they frequently contain regions not found in close relatives, which may play a role in virulence mechanisms. Due to this connection to medical microbiology, there are numerous methods available to detect horizontal gene transfer. However, these are usually aimed at individual genes and viral genomes rather than the much larger bacterial genomes. Here, we propose an efficient alignment-free approach to describe the mosaic structure of viral and bacterial genomes, including their unique regions.<br><br>RESULTS: Our method is based on the lengths of exact matches between pairs of sequences. Long matches indicate close homology, short matches more distant homology or none at all. These exact match lengths can be looked up efficiently using an enhanced suffix array. Our program implementing this approach, alfy (ALignment-Free local homologY), efficiently and accurately detects the recombination break points in simulated DNA sequences and among recombinant HIV-1 strains. We also apply alfy to Escherichia coli genomes where we detect new evidence for the hypothesis that strains pathogenic in poultry can infect humans.<br><br>AVAILABILITY: alfy is written in standard C and its source code is available under the GNU General Public License from http://guanine.evolbio.mpg.de/alfy/. The software package also includes documentation and example data.}, }
@article {pmid21470960, year = {2011}, author = {Letunic, I and Bork, P}, title = {Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy.}, journal = {Nucleic acids research}, volume = {39}, number = {Web Server issue}, pages = {W475-8}, pmid = {21470960}, issn = {1362-4962}, mesh = {Gene Transfer, Horizontal ; Internet ; Molecular Sequence Annotation ; *Phylogeny ; *Software ; User-Computer Interface ; }, abstract = {Interactive Tree Of Life (http://itol.embl.de) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. It is freely available and open to everyone. In addition to classical tree viewer functions, iTOL offers many novel ways of annotating trees with various additional data. Current version introduces numerous new features and greatly expands the number of supported data set types. Trees can be interactively manipulated and edited. A free personal account system is available, providing management and sharing of trees in user defined workspaces and projects. Export to various bitmap and vector graphics formats is supported. Batch access interface is available for programmatic access or inclusion of interactive trees into other web services.}, }
@article {pmid21468227, year = {2010}, author = {Jones, BV}, title = {The human gut mobile metagenome: a metazoan perspective.}, journal = {Gut microbes}, volume = {1}, number = {6}, pages = {415-431}, pmid = {21468227}, issn = {1949-0984}, support = {//Medical Research Council/United Kingdom ; }, mesh = {Bacteria/*genetics ; Gastrointestinal Tract/*microbiology ; Humans ; *Metagenome ; Plasmids/*analysis ; }, abstract = {Using the culture independent TRACA system in conjunction with a comparative metagenomic approach, we have recently explored the pool of plasmids associated with the human gut mobile metagenome. This revealed that some plasmids or plasmid families are present in the gut microbiomes of geographically isolated human hosts with a broad global distribution (America, Japan and Europe), and are potentially unique to the human gut microbiome. Functions encoded by the most widely distributed plasmid (pTRACA22) were found to be enriched in the human gut microbiome when compared to microbial communities from other environments, and of particular interest was the increased prevalence of a putative RelBE toxin-antitoxin (TA) addiction module. Subsequent analysis revealed that this was most closely related to putative TA modules from gut associated bacteria belonging to the Firmicutes, but homologues of the RelE toxin were associated with all major bacterial divisions comprising the human gut microbiota. In this addendum, functions of the gut mobile metagenome are considered from the perspective of the human host, and within the context of the hologenome theory of human evolution. In doing so, our original analysis is also extended to include the gut metagenomes of a further 124 individuals comprising the METAHIT dataset. Differences in the incidence and relative abundance of pTRACA22 and associated TA modules between healthy individuals and those with inflammatory bowel diseases are explored, and potential functions of pTRACA22 type RelBE modules in the human gut microbiome are discussed.}, }
@article {pmid21468020, year = {2011}, author = {Norberg, P and Bergström, M and Jethava, V and Dubhashi, D and Hermansson, M}, title = {The IncP-1 plasmid backbone adapts to different host bacterial species and evolves through homologous recombination.}, journal = {Nature communications}, volume = {2}, number = {}, pages = {268}, pmid = {21468020}, issn = {2041-1723}, mesh = {Bacteria/classification/*genetics ; DNA Transposable Elements ; *Evolution, Molecular ; Molecular Sequence Data ; Phylogeny ; Plasmids/*genetics ; *Recombination, Genetic ; }, abstract = {Plasmids are important members of the bacterial mobile gene pool, and are among the most important contributors to horizontal gene transfer between bacteria. They typically harbour a wide spectrum of host beneficial traits, such as antibiotic resistance, inserted into their backbones. Although these inserted elements have drawn considerable interest, evolutionary information about the plasmid backbones, which encode plasmid related traits, is sparse. Here we analyse 25 complete backbone genomes from the broad-host-range IncP-1 plasmid family. Phylogenetic analysis reveals seven clades, in which two plasmids that we isolated from a marine biofilm represent a novel clade. We also found that homologous recombination is a prominent feature of the plasmid backbone evolution. Analysis of genomic signatures indicates that the plasmids have adapted to different host bacterial species. Globally circulating IncP-1 plasmids hence contain mosaic structures of segments derived from several parental plasmids that have evolved in, and adapted to, different, phylogenetically very distant host bacterial species.}, }
@article {pmid21467045, year = {2011}, author = {Martin-Galiano, AJ and Oliva, MA and Sanz, L and Bhattacharyya, A and Serna, M and Yebenes, H and Valpuesta, JM and Andreu, JM}, title = {Bacterial tubulin distinct loop sequences and primitive assembly properties support its origin from a eukaryotic tubulin ancestor.}, journal = {The Journal of biological chemistry}, volume = {286}, number = {22}, pages = {19789-19803}, pmid = {21467045}, issn = {1083-351X}, mesh = {Amino Acid Substitution ; Bacterial Proteins/*genetics/metabolism ; Eukaryotic Cells/*physiology ; *Evolution, Molecular ; Gene Transfer, Horizontal/*physiology ; Gram-Negative Bacteria/*physiology ; Guanosine Diphosphate/genetics/metabolism ; Guanosine Triphosphate/genetics/metabolism ; Mutation, Missense ; *Protein Folding ; Protein Structure, Secondary ; Tubulin/*genetics/metabolism ; }, abstract = {The structure of the unique bacterial tubulin BtubA/B from Prosthecobacter is very similar to eukaryotic αβ-tubulin but, strikingly, BtubA/B fold without eukaryotic chaperones. Our sequence comparisons indicate that BtubA and BtubB do not really correspond to either α- or β-tubulin but have mosaic sequences with intertwining features from both. Their nucleotide-binding loops are more conserved, and their more divergent sequences correspond to discrete surface zones of tubulin involved in microtubule assembly and binding to eukaryotic cytosolic chaperonin, which is absent from the Prosthecobacter dejongeii draft genome. BtubA/B cooperatively assembles over a wider range of conditions than αβ-tubulin, forming pairs of protofilaments that coalesce into bundles instead of microtubules, and it lacks the ability to differentially interact with divalent cations and bind typical tubulin drugs. Assembled BtubA/B contain close to one bound GTP and GDP. Both BtubA and BtubB subunits hydrolyze GTP, leading to disassembly. The mutant BtubA/B-S144G in the tubulin signature motif GGG(T/S)G(S/T)G has strongly inhibited GTPase, but BtubA-T147G/B does not, suggesting that BtubB is a more active GTPase, like β-tubulin. BtubA/B chimera bearing the β-tubulin loops M, H1-S2, and S9-S10 in BtubB fold, assemble, and have reduced GTPase activity. However, introduction of the α-tubulin loop S9-S10 with its unique eight-residue insertion impaired folding. From the sequence analyses, its primitive assembly features, and the properties of the chimeras, we propose that BtubA/B were acquired shortly after duplication of a spontaneously folding α- and β-tubulin ancestor, possibly by horizontal gene transfer from a primitive eukaryotic cell, followed by divergent evolution.}, }
@article {pmid21463532, year = {2011}, author = {Villaseñor, T and Brom, S and Dávalos, A and Lozano, L and Romero, D and Los Santos, AG}, title = {Housekeeping genes essential for pantothenate biosynthesis are plasmid-encoded in Rhizobium etli and Rhizobium leguminosarum.}, journal = {BMC microbiology}, volume = {11}, number = {}, pages = {66}, pmid = {21463532}, issn = {1471-2180}, mesh = {Biosynthetic Pathways/*genetics ; Cluster Analysis ; Evolution, Molecular ; Gene Deletion ; *Genes, Bacterial ; Multigene Family ; Pantothenic Acid/*biosynthesis ; Phylogeny ; *Plasmids ; Rhizobium etli/*genetics/metabolism ; Rhizobium leguminosarum/*genetics/metabolism ; Sequence Homology ; }, abstract = {BACKGROUND: A traditional concept in bacterial genetics states that housekeeping genes, those involved in basic metabolic functions needed for maintenance of the cell, are encoded in the chromosome, whereas genes required for dealing with challenging environmental conditions are located in plasmids. Exceptions to this rule have emerged from genomic sequence data of bacteria with multipartite genomes. The genome sequence of R. etli CFN42 predicts the presence of panC and panB genes clustered together on the 642 kb plasmid p42f and a second copy of panB on plasmid p42e. They encode putative pantothenate biosynthesis enzymes (pantoate-β-alanine ligase and 3-methyl-2-oxobutanoate hydroxymethyltransferase, respectively). Due to their ubiquitous distribution and relevance in the central metabolism of the cell, these genes are considered part of the core genome; thus, their occurrence in a plasmid is noteworthy. In this study we investigate the contribution of these genes to pantothenate biosynthesis, examine whether their presence in plasmids is a prevalent characteristic of the Rhizobiales with multipartite genomes, and assess the possibility that the panCB genes may have reached plasmids by horizontal gene transfer.<br><br>RESULTS: Analysis of mutants confirmed that the panC and panB genes located on plasmid p42f are indispensable for the synthesis of pantothenate. A screening of the location of panCB genes among members of the Rhizobiales showed that only R. etli and R. leguminosarum strains carry panCB genes in plasmids. The panCB phylogeny attested a common origin for chromosomal and plasmid-borne panCB sequences, suggesting that the R. etli and R. leguminosarum panCB genes are orthologs rather than xenologs. The panCB genes could not totally restore the ability of a strain cured of plasmid p42f to grow in minimal medium.<br><br>CONCLUSIONS: This study shows experimental evidence that core panCB genes located in plasmids of R. etli and R. leguminosarum are indispensable for the synthesis of pantothenate. The unusual presence of panCB genes in plasmids of Rhizobiales may be due to an intragenomic transfer from chromosome to plasmid. Plasmid p42f encodes other functions required for growth in minimal medium. Our results support the hypothesis of cooperation among different replicons for basic cellular functions in multipartite rhizobia genomes.}, }
@article {pmid21461370, year = {2011}, author = {Moreno-Letelier, A and Olmedo, G and Eguiarte, LE and Martinez-Castilla, L and Souza, V}, title = {Parallel Evolution and Horizontal Gene Transfer of the pst Operon in Firmicutes from Oligotrophic Environments.}, journal = {International journal of evolutionary biology}, volume = {2011}, number = {}, pages = {781642}, pmid = {21461370}, issn = {2090-052X}, abstract = {The high affinity phosphate transport system (pst) is crucial for phosphate uptake in oligotrophic environments. Cuatro Cienegas Basin (CCB) has extremely low P levels and its endemic Bacillus are closely related to oligotrophic marine Firmicutes. Thus, we expected the pst operon of CCB to share the same evolutionary history and protein similarity to marine Firmicutes. Orthologs of the pst operon were searched in 55 genomes of Firmicutes and 13 outgroups. Phylogenetic reconstructions were performed for the pst operon and 14 concatenated housekeeping genes using maximum likelihood methods. Conserved domains and 3D structures of the phosphate-binding protein (PstS) were also analyzed. The pst operon of Firmicutes shows two highly divergent clades with no correlation to the type of habitat nor a phylogenetic congruence, suggesting horizontal gene transfer. Despite sequence divergence, the PstS protein had a similar 3D structure, which could be due to parallel evolution after horizontal gene transfer events.}, }
@article {pmid21460108, year = {2011}, author = {Rezzonico, F and Smits, TH and Duffy, B}, title = {Diversity, evolution, and functionality of clustered regularly interspaced short palindromic repeat (CRISPR) regions in the fire blight pathogen Erwinia amylovora.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {11}, pages = {3819-3829}, pmid = {21460108}, issn = {1098-5336}, mesh = {Bacterial Typing Techniques ; Cluster Analysis ; Erwinia amylovora/*genetics/isolation &amp; purification ; Europe ; *Evolution, Molecular ; Genotype ; India ; *Inverted Repeat Sequences ; Middle East ; Molecular Typing ; New Zealand ; Plasmids/analysis ; *Polymorphism, Genetic ; Rosaceae/microbiology ; United States ; }, abstract = {The clustered regularly interspaced short palindromic repeat (CRISPR)/Cas system confers acquired heritable immunity against mobile nucleic acid elements in prokaryotes, limiting phage infection and horizontal gene transfer of plasmids. In CRISPR arrays, characteristic repeats are interspersed with similarly sized nonrepetitive spacers derived from transmissible genetic elements and acquired when the cell is challenged with foreign DNA. New spacers are added sequentially and the number and type of CRISPR units can differ among strains, providing a record of phage/plasmid exposure within a species and giving a valuable typing tool. The aim of this work was to investigate CRISPR diversity in the highly homogeneous species Erwinia amylovora, the causal agent of fire blight. A total of 18 CRISPR genotypes were defined within a collection of 37 cosmopolitan strains. Strains from Spiraeoideae plants clustered in three major groups: groups II and III were composed exclusively of bacteria originating from the United States, whereas group I generally contained strains of more recent dissemination obtained in Europe, New Zealand, and the Middle East. Strains from Rosoideae and Indian hawthorn (Rhaphiolepis indica) clustered separately and displayed a higher intrinsic diversity than that of isolates from Spiraeoideae plants. Reciprocal exclusion was generally observed between plasmid content and cognate spacer sequences, supporting the role of the CRISPR/Cas system in protecting against foreign DNA elements. However, in several group III strains, retention of plasmid pEU30 is inconsistent with a functional CRISPR/Cas system.}, }
@article {pmid21458879, year = {2011}, author = {Taylor, NG and Verner-Jeffreys, DW and Baker-Austin, C}, title = {Aquatic systems: maintaining, mixing and mobilising antimicrobial resistance?.}, journal = {Trends in ecology &amp; evolution}, volume = {26}, number = {6}, pages = {278-284}, doi = {10.1016/j.tree.2011.03.004}, pmid = {21458879}, issn = {1872-8383}, mesh = {Bacteria/*metabolism ; *Biological Evolution ; Drug Resistance, Microbial/genetics/*physiology ; *Ecosystem ; Gene Transfer, Horizontal/*genetics ; Genes, MDR/*genetics ; Hydrobiology/*methods ; *Water Microbiology ; Water Pollutants, Chemical/metabolism ; }, abstract = {Bacteria showing antimicrobial resistance (AMR) pose a significant global healthcare problem. Although many mechanisms conferring AMR are understood, the ecological processes facilitating its persistence and spread are less well characterised. Aquatic systems represent an important milieu for the environmental release, mixing, persistence and spread of AMR bacteria and resistance genes associated with horizontally transferable genetic elements. Additionally, owing to the use and discharge of antimicrobials and biocides, and the accumulation and abundance of other pollutants, mechanisms that confer AMR might evolve in aquatic systems. In this review, we hypothesise that aquatic systems have an important ecological and evolutionary role in driving the persistence, emergence and spread of AMR, which could have consequences when attempting to reduce its occurrence in clinical settings.}, }
@article {pmid21458359, year = {2011}, author = {Schmidt, SM and Panstruga, R}, title = {Pathogenomics of fungal plant parasites: what have we learnt about pathogenesis?.}, journal = {Current opinion in plant biology}, volume = {14}, number = {4}, pages = {392-399}, doi = {10.1016/j.pbi.2011.03.006}, pmid = {21458359}, issn = {1879-0356}, mesh = {Evolution, Molecular ; Fungal Proteins/genetics/*metabolism ; Fungi/*genetics/metabolism/*pathogenicity ; Gene Expression Regulation, Fungal ; Gene Transfer, Horizontal ; Genes, Fungal ; Host Specificity ; *Host-Pathogen Interactions ; Plant Diseases/microbiology ; Plants/*microbiology ; Virulence ; }, abstract = {Members of the kingdom fungi comprise numerous plant pathogens, including the causal agents of many agriculturally relevant plant diseases such as rust, powdery mildew, rice blast and cereal head blight. Data from recent sequencing projects provide deep insight into the genomes of a range of fungi that infect different organs of monocotyledonous or dicotyledonous hosts and that have diverse pathogenic lifestyles. These studies have revealed that, similar to sequenced phytopathogenic oomycetes, these plant parasites possess very plastic and dynamic genomes, which typically encode several hundred candidate secreted effector proteins that can be highly divergent even among related species. A new insight is the presence of lineage-specific genes on mobile and partly dispensable chromosomes that are transferred intraspecifically and possibly interspecifically, thereby constituting pathogenicity and host range determinants. Convergent lifestyle-specific adaptations have shaped the parasite genomes to maximize pathogenic success according to the different infection strategies employed.}, }
@article {pmid21457552, year = {2011}, author = {Sitkiewicz, I and Green, NM and Guo, N and Mereghetti, L and Musser, JM}, title = {Lateral gene transfer of streptococcal ICE element RD2 (region of difference 2) encoding secreted proteins.}, journal = {BMC microbiology}, volume = {11}, number = {}, pages = {65}, pmid = {21457552}, issn = {1471-2180}, mesh = {Bacterial Proteins/*genetics/metabolism ; Female ; *Gene Transfer, Horizontal ; Humans ; Interspersed Repetitive Sequences ; Sequence Homology ; Streptococcal Infections/microbiology ; Streptococcus agalactiae/genetics/isolation &amp; purification ; Streptococcus pyogenes/*genetics/isolation &amp; purification ; Streptococcus thermophilus/genetics ; Synteny ; }, abstract = {BACKGROUND: The genome of serotype M28 group A Streptococcus (GAS) strain MGAS6180 contains a novel genetic element named Region of Difference 2 (RD2) that encodes seven putative secreted extracellular proteins. RD2 is present in all serotype M28 strains and strains of several other GAS serotypes associated with female urogenital infections. We show here that the GAS RD2 element is present in strain MGAS6180 both as an integrative chromosomal form and a circular extrachromosomal element. RD2-like regions were identified in publicly available genome sequences of strains representing three of the five major group B streptococcal serotypes causing human disease. Ten RD2-encoded proteins have significant similarity to proteins involved in conjugative transfer of Streptococcus thermophilus integrative chromosomal elements (ICEs).<br><br>RESULTS: We transferred RD2 from GAS strain MGAS6180 (serotype M28) to serotype M1 and M4 GAS strains by filter mating. The copy number of the RD2 element was rapidly and significantly increased following treatment of strain MGAS6180 with mitomycin C, a DNA damaging agent. Using a PCR-based method, we also identified RD2-like regions in multiple group C and G strains of Streptococcus dysgalactiae subsp.equisimilis cultured from invasive human infections.<br><br>CONCLUSIONS: Taken together, the data indicate that the RD2 element has disseminated by lateral gene transfer to genetically diverse strains of human-pathogenic streptococci.}, }
@article {pmid21457008, year = {2011}, author = {Koonin, EV and Puigbò, P and Wolf, YI}, title = {Comparison of phylogenetic trees and search for a central trend in the "forest of life".}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {18}, number = {7}, pages = {917-924}, pmid = {21457008}, issn = {1557-8666}, support = {//Intramural NIH HHS/United States ; }, mesh = {*Biological Evolution ; Computational Biology/*methods ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Models, Genetic ; *Phylogeny ; Prokaryotic Cells/physiology ; }, abstract = {The widespread exchange of genes among prokaryotes, known as horizontal gene transfer (HGT), is often considered to "uproot" the Tree of Life (TOL). Indeed, it is by now fully clear that genes in general possess different evolutionary histories. However, the possibility remains that the TOL concept can be reformulated and remain valid as a statistical central trend in the phylogenetic "Forest of Life" (FOL). This article describes a computational pipeline developed to chart the FOL by comparative analysis of thousands of phylogenetic trees. This analysis reveals a distinct, consistent phylogenetic signal that is particularly strong among the Nearly Universal Trees (NUTs), which correspond to genes represented in all or most of the analyzed organisms. Despite the substantial amount of apparent HGT seen even among the NUTs, these gene transfers appear to be distributed randomly and do not obscure the central tree-like trend.}, }
@article {pmid21453780, year = {2011}, author = {Martin, SH and Wingfield, BD and Wingfield, MJ and Steenkamp, ET}, title = {Structure and evolution of the Fusarium mating type locus: new insights from the Gibberellafujikuroi complex.}, journal = {Fungal genetics and biology : FG &amp; B}, volume = {48}, number = {7}, pages = {731-740}, doi = {10.1016/j.fgb.2011.03.005}, pmid = {21453780}, issn = {1096-0937}, mesh = {DNA, Fungal/chemistry/genetics ; *Evolution, Molecular ; *Gene Order ; *Genes, Mating Type, Fungal ; Gibberella/*genetics ; Molecular Sequence Data ; Sequence Analysis, DNA ; }, abstract = {Mating type genes are central to sexual reproduction and compatibility in Ascomycete fungi. However the "MAT" loci experience unique evolutionary pressures that can result in rapid divergence and enhanced inter-specific gene-flow (lateral gene transfer). In this study, molecular evolution of MAT loci was considered using the genus Fusarium (Teleomorph: Gibberella) as a model. Both MAT1-1 and MAT1-2 "idiomorphs" from eleven species of the Gibberellafujikuroi species complex were sequenced. Molecular evolution of the MAT loci from these heterothallic (self-sterile) species was compared with that of the MAT loci from nine homothallic (self-fertile) species in the Fusariumgraminearum species complex. Although Fusarium has previously been thought to have the same complement of four MAT genes that are found in Neurospora, we found evidence of a novel gene, MAT1-2-3, that may be specific to the Hypocreales. All MAT genes share a similar set of cis-regulatory motifs, although homothallic species might have recruited novel regulatory elements, which could potentially facilitate alternate expression of MAT1-1-1 and MAT1-2-1. FusariumMAT loci displayed evidence consistent with historical lateral gene-flow. Most notably, the MAT1-1 idiomorph of Fusariumsacchari appears to be unrelated to those of other species in the G.fujikuroi complex. In general, FusariumMAT genes are highly divergent. Both positive selection and relaxed selective constraint could account for this phenomenon. However, the extent of both recombination and inter-specific gene-flow in the MAT locus also appears to affect the rate of divergence.}, }
@article {pmid21451967, year = {2011}, author = {Dupuy, C and Periquet, G and Serbielle, C and Bézier, A and Louis, F and Drezen, JM}, title = {Transfer of a chromosomal Maverick to endogenous bracovirus in a parasitoid wasp.}, journal = {Genetica}, volume = {139}, number = {4}, pages = {489-496}, pmid = {21451967}, issn = {1573-6857}, mesh = {Animals ; Base Sequence ; Chromosomes, Insect/*genetics ; Gene Order ; Gene Transfer, Horizontal/*genetics ; Genome, Insect ; Molecular Sequence Data ; Phylogeny ; Polydnaviridae/*genetics ; Sequence Alignment ; Viral Proteins/genetics ; Virus Integration/genetics ; Wasps/*genetics ; }, abstract = {Bracoviruses are used by parasitoid wasps to allow development of their progeny within the body of lepidopteran hosts. In parasitoid wasps, the bracovirus exists as a provirus, integrated in a wasp chromosome. Viral replication occurs in wasp ovaries and leads to formation of particles containing dsDNA circles (segments) that are injected into the host body during wasp oviposition. We identified a large DNA transposon Maverick in a parasitoid wasp bracovirus. Closely related elements are present in parasitoid wasp genomes indicating that the element in CcBV corresponds to the insertion of an endogenous wasp Maverick in CcBV provirus. The presence of the Maverick in a bracovirus genome suggests the possibility of transposon transfers from parasitoids to lepidoptera via bracoviruses.}, }
@article {pmid21450808, year = {2011}, author = {Ferrer, MD and Quiles-Puchalt, N and Harwich, MD and Tormo-Más, M&#xc1; and Campoy, S and Barbé, J and Lasa, I and Novick, RP and Christie, GE and Penadés, JR}, title = {RinA controls phage-mediated packaging and transfer of virulence genes in Gram-positive bacteria.}, journal = {Nucleic acids research}, volume = {39}, number = {14}, pages = {5866-5878}, pmid = {21450808}, issn = {1362-4962}, support = {R21 AI067654/AI/NIAID NIH HHS/United States ; R56 AI081837/AI/NIAID NIH HHS/United States ; R01AI022159-23A2/AI/NIAID NIH HHS/United States ; }, mesh = {*Gene Expression Regulation, Viral ; *Gene Transfer, Horizontal ; Genomic Islands ; Gram-Positive Bacteria/pathogenicity/virology ; Lysogeny/genetics ; Operon ; Promoter Regions, Genetic ; Sequence Deletion ; Staphylococcus Phages/*genetics ; Trans-Activators/genetics/*metabolism ; Transcription Factors/genetics/*metabolism ; Transcriptional Activation ; Viral Proteins/genetics/*metabolism ; Virion/metabolism ; Virulence Factors/*genetics ; Virus Assembly/*genetics ; }, abstract = {Phage-mediated transfer of microbial genetic elements plays a crucial role in bacterial life style and evolution. In this study, we identify the RinA family of phage-encoded proteins as activators required for transcription of the late operon in a large group of temperate staphylococcal phages. RinA binds to a tightly regulated promoter region, situated upstream of the terS gene, that controls expression of the morphogenetic and lysis modules of the phage, activating their transcription. As expected, rinA deletion eliminated formation of functional phage particles and significantly decreased the transfer of phage and pathogenicity island encoded virulence factors. A genetic analysis of the late promoter region showed that a fragment of 272 bp contains both the promoter and the region necessary for activation by RinA. In addition, we demonstrated that RinA is the only phage-encoded protein required for the activation of this promoter region. This region was shown to be divergent among different phages. Consequently, phages with divergent promoter regions carried allelic variants of the RinA protein, which specifically recognize its own promoter sequence. Finally, most Gram-postive bacteria carry bacteriophages encoding RinA homologue proteins. Characterization of several of these proteins demonstrated that control by RinA of the phage-mediated packaging and transfer of virulence factor is a conserved mechanism regulating horizontal gene transfer.}, }
@article {pmid21447149, year = {2011}, author = {Strope, PK and Nickerson, KW and Harris, SD and Moriyama, EN}, title = {Molecular evolution of urea amidolyase and urea carboxylase in fungi.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {80}, pmid = {21447149}, issn = {1471-2148}, support = {R01LM009219/LM/NLM NIH HHS/United States ; }, mesh = {Bacteria/enzymology/genetics ; Carbon-Nitrogen Ligases/chemistry/*genetics ; *Evolution, Molecular ; Fungi/*enzymology/*genetics/metabolism ; Gene Transfer, Horizontal ; Phylogeny ; Protein Structure, Tertiary ; Sequence Homology, Amino Acid ; }, abstract = {BACKGROUND: Urea amidolyase breaks down urea into ammonia and carbon dioxide in a two-step process, while another enzyme, urease, does this in a one step-process. Urea amidolyase has been found only in some fungal species among eukaryotes. It contains two major domains: the amidase and urea carboxylase domains. A shorter form of urea amidolyase is known as urea carboxylase and has no amidase domain. Eukaryotic urea carboxylase has been found only in several fungal species and green algae. In order to elucidate the evolutionary origin of urea amidolyase and urea carboxylase, we studied the distribution of urea amidolyase, urea carboxylase, as well as other proteins including urease, across kingdoms.<br><br>RESULTS: Among the 64 fungal species we examined, only those in two Ascomycota classes (Sordariomycetes and Saccharomycetes) had the urea amidolyase sequences. Urea carboxylase was found in many but not all of the species in the phylum Basidiomycota and in the subphylum Pezizomycotina (phylum Ascomycota). It was completely absent from the class Saccharomycetes (phylum Ascomycota; subphylum Saccharomycotina). Four Sordariomycetes species we examined had both the urea carboxylase and the urea amidolyase sequences. Phylogenetic analysis showed that these two enzymes appeared to have gone through independent evolution since their bacterial origin. The amidase domain and the urea carboxylase domain sequences from fungal urea amidolyases clustered strongly together with the amidase and urea carboxylase sequences, respectively, from a small number of beta- and gammaproteobacteria. On the other hand, fungal urea carboxylase proteins clustered together with another copy of urea carboxylases distributed broadly among bacteria. The urease proteins were found in all the fungal species examined except for those of the subphylum Saccharomycotina.<br><br>CONCLUSIONS: We conclude that the urea amidolyase genes currently found only in fungi are the results of a horizontal gene transfer event from beta-, gamma-, or related species of proteobacteria. The event took place before the divergence of the subphyla Pezizomycotina and Saccharomycotina but after the divergence of the subphylum Taphrinomycotina. Urea carboxylase genes currently found in fungi and other limited organisms were also likely derived from another ancestral gene in bacteria. Our study presented another important example showing plastic and opportunistic genome evolution in bacteria and fungi and their evolutionary interplay.}, }
@article {pmid21445262, year = {2011}, author = {Brown, NF and Coombes, BK and Bishop, JL and Wickham, ME and Lowden, MJ and Gal-Mor, O and Goode, DL and Boyle, EC and Sanderson, KL and Finlay, BB}, title = {Salmonella phage ST64B encodes a member of the SseK/NleB effector family.}, journal = {PloS one}, volume = {6}, number = {3}, pages = {e17824}, pmid = {21445262}, issn = {1932-6203}, support = {//Canadian Institutes of Health Research/Canada ; //Howard Hughes Medical Institute/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins/chemistry/*genetics/metabolism ; Base Sequence ; Cell Line ; DNA Primers ; Flow Cytometry ; Genes, Viral ; Genome, Viral ; Mice ; Molecular Sequence Data ; Protein Transport ; Salmonella/pathogenicity ; Salmonella Phages/*genetics ; Sequence Homology, Amino Acid ; Virulence ; }, abstract = {Salmonella enterica is a species of bacteria that is a major cause of enteritis across the globe, while certain serovars cause typhoid, a more serious disease associated with a significant mortality rate. Type III secreted effectors are major contributors to the pathogenesis of Salmonella infections. Genes encoding effectors are acquired via horizontal gene transfer, and a subset are encoded within active phage lysogens. Because the acquisition of effectors is in flux, the complement of effectors possessed by various Salmonella strains frequently differs. By comparing the genome sequences of S. enterica serovar Typhimurium strain SL1344 with LT2, we identified a gene with significant similarity to SseK/NleB type III secreted effector proteins within a phage ST64B lysogen that is absent from LT2. We have named this gene sseK3. SseK3 was co-regulated with the SPI-2 type III secretion system in vitro and inside host cells, and was also injected into infected host cells. While no role for SseK3 in virulence could be identified, a role for the other family members in murine typhoid was found. SseK3 and other phage-encoded effectors were found to have a significant but sparse distribution in the available Salmonella genome sequences, indicating the potential for more uncharacterised effectors to be present in less studied serovars. These phage-encoded effectors may be principle subjects of contemporary selective processes shaping Salmonella-host interactions.}, }
@article {pmid21443624, year = {2011}, author = {Chu, HY and Wegel, E and Osbourn, A}, title = {From hormones to secondary metabolism: the emergence of metabolic gene clusters in plants.}, journal = {The Plant journal : for cell and molecular biology}, volume = {66}, number = {1}, pages = {66-79}, doi = {10.1111/j.1365-313X.2011.04503.x}, pmid = {21443624}, issn = {1365-313X}, support = {BBS/E/J/00000614/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/C504435/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteria/genetics ; Evolution, Molecular ; Gene Expression Regulation, Plant ; Gene Transfer, Horizontal ; Genes, Plant ; Inheritance Patterns ; Metabolic Networks and Pathways/*genetics ; *Multigene Family ; Operon ; Plant Growth Regulators/*genetics ; Plants/*genetics ; }, abstract = {Gene clusters for the synthesis of secondary metabolites are a common feature of microbial genomes. Well-known examples include clusters for the synthesis of antibiotics in actinomycetes, and also for the synthesis of antibiotics and toxins in filamentous fungi. Until recently it was thought that genes for plant metabolic pathways were not clustered, and this is certainly true in many cases; however, five plant secondary metabolic gene clusters have now been discovered, all of them implicated in synthesis of defence compounds. An obvious assumption might be that these eukaryotic gene clusters have arisen by horizontal gene transfer from microbes, but there is compelling evidence to indicate that this is not the case. This raises intriguing questions about how widespread such clusters are, what the significance of clustering is, why genes for some metabolic pathways are clustered and those for others are not, and how these clusters form. In answering these questions we may hope to learn more about mechanisms of genome plasticity and adaptive evolution in plants. It is noteworthy that for the five plant secondary metabolic gene clusters reported so far, the enzymes for the first committed steps all appear to have been recruited directly or indirectly from primary metabolic pathways involved in hormone synthesis. This may or may not turn out to be a common feature of plant secondary metabolic gene clusters as new clusters emerge.}, }
@article {pmid21440553, year = {2011}, author = {McGeehan, JE and Streeter, SD and Thresh, SJ and Taylor, JEN and Shevtsov, MB and Kneale, GG}, title = {Structural analysis of a novel class of R-M controller proteins: C.Csp231I from Citrobacter sp. RFL231.}, journal = {Journal of molecular biology}, volume = {409}, number = {2}, pages = {177-188}, pmid = {21440553}, issn = {1089-8638}, support = {BB/E000878/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/H00680X/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Bacterial Proteins/*chemistry/*metabolism ; Citrobacter/*metabolism ; Crystallography, X-Ray ; DNA, Bacterial/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Promoter Regions, Genetic ; Protein Conformation ; Protein Multimerization ; Sequence Homology, Amino Acid ; }, abstract = {Controller proteins play a key role in the temporal regulation of gene expression in bacterial restriction-modification (R-M) systems and are important mediators of horizontal gene transfer. They form the basis of a highly cooperative, concentration-dependent genetic switch involved in both activation and repression of R-M genes. Here we present biophysical, biochemical, and high-resolution structural analysis of a novel class of controller proteins, exemplified by C.Csp231I. In contrast to all previously solved C-protein structures, each protein subunit has two extra helices at the C-terminus, which play a large part in maintaining the dimer interface. The DNA binding site of the protein is also novel, having largely AAAA tracts between the palindromic recognition half-sites, suggesting tight bending of the DNA. The protein structure shows an unusual positively charged surface that could form the basis for wrapping the DNA completely around the C-protein dimer.}, }
@article {pmid21439036, year = {2011}, author = {Denoeud, F and Roussel, M and Noel, B and Wawrzyniak, I and Da Silva, C and Diogon, M and Viscogliosi, E and Brochier-Armanet, C and Couloux, A and Poulain, J and Segurens, B and Anthouard, V and Texier, C and Blot, N and Poirier, P and Ng, GC and Tan, KS and Artiguenave, F and Jaillon, O and Aury, JM and Delbac, F and Wincker, P and Vivarès, CP and El Alaoui, H}, title = {Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite.}, journal = {Genome biology}, volume = {12}, number = {3}, pages = {R29}, pmid = {21439036}, issn = {1474-760X}, mesh = {Animals ; Antioxidants/metabolism ; Base Sequence ; Blastocystis/*genetics/metabolism ; Drug Resistance, Multiple/genetics ; Gene Transfer, Horizontal ; *Genome, Protozoan ; Host-Pathogen Interactions ; Humans ; Metabolic Networks and Pathways ; Mitochondria/genetics/metabolism ; Proteome ; Stramenopiles/*genetics/metabolism ; Symbiosis/genetics ; Virulence Factors ; }, abstract = {BACKGROUND: Blastocystis is a highly prevalent anaerobic eukaryotic parasite of humans and animals that is associated with various gastrointestinal and extraintestinal disorders. Epidemiological studies have identified different subtypes but no one subtype has been definitively correlated with disease.<br><br>RESULTS: Here we report the 18.8 Mb genome sequence of a Blastocystis subtype 7 isolate, which is the smallest stramenopile genome sequenced to date. The genome is highly compact and contains intriguing rearrangements. Comparisons with other available stramenopile genomes (plant pathogenic oomycete and diatom genomes) revealed effector proteins potentially involved in the adaptation to the intestinal environment, which were likely acquired via horizontal gene transfer. Moreover, Blastocystis living in anaerobic conditions harbors mitochondria-like organelles. An incomplete oxidative phosphorylation chain, a partial Krebs cycle, amino acid and fatty acid metabolisms and an iron-sulfur cluster assembly are all predicted to occur in these organelles. Predicted secretory proteins possess putative activities that may alter host physiology, such as proteases, protease-inhibitors, immunophilins and glycosyltransferases. This parasite also possesses the enzymatic machinery to tolerate oxidative bursts resulting from its own metabolism or induced by the host immune system.<br><br>CONCLUSIONS: This study provides insights into the genome architecture of this unusual stramenopile. It also proposes candidate genes with which to study the physiopathology of this parasite and thus may lead to further investigations into Blastocystis-host interactions.}, }
@article {pmid21438681, year = {2011}, author = {Hohmann-Marriott, MF and Blankenship, RE}, title = {Evolution of photosynthesis.}, journal = {Annual review of plant biology}, volume = {62}, number = {}, pages = {515-548}, doi = {10.1146/annurev-arplant-042110-103811}, pmid = {21438681}, issn = {1545-2123}, mesh = {Bacteria/metabolism ; *Biological Evolution ; Carbon/metabolism ; Chlorophyll/metabolism/physiology ; Electron Transport ; Iron-Sulfur Proteins/physiology ; Photosynthesis/*physiology ; Photosynthetic Reaction Center Complex Proteins/physiology ; Plant Proteins/physiology ; Plants/*metabolism/microbiology ; Quinones/metabolism ; Sensory Rhodopsins/physiology ; Sunlight ; Symbiosis ; }, abstract = {Energy conversion of sunlight by photosynthetic organisms has changed Earth and life on it. Photosynthesis arose early in Earth's history, and the earliest forms of photosynthetic life were almost certainly anoxygenic (non-oxygen evolving). The invention of oxygenic photosynthesis and the subsequent rise of atmospheric oxygen approximately 2.4 billion years ago revolutionized the energetic and enzymatic fundamentals of life. The repercussions of this revolution are manifested in novel biosynthetic pathways of photosynthetic cofactors and the modification of electron carriers, pigments, and existing and alternative modes of photosynthetic carbon fixation. The evolutionary history of photosynthetic organisms is further complicated by lateral gene transfer that involved photosynthetic components as well as by endosymbiotic events. An expanding wealth of genetic information, together with biochemical, biophysical, and physiological data, reveals a mosaic of photosynthetic features. In combination, these data provide an increasingly robust framework to formulate and evaluate hypotheses concerning the origin and evolution of photosynthesis.}, }
@article {pmid21431727, year = {2011}, author = {Blazso, P and Sinko, I and Katona, RL}, title = {Engineered chromosomes in transgenics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {738}, number = {}, pages = {161-181}, doi = {10.1007/978-1-61779-099-7_12}, pmid = {21431727}, issn = {1940-6029}, mesh = {Animals ; Blastocyst/cytology/metabolism ; Breeding ; Chimera/*genetics ; Chromosomes, Artificial, Mammalian/*genetics ; Embryo Transfer ; Embryonic Stem Cells/cytology/metabolism ; Female ; Gene Transfer Techniques ; *Genetic Engineering ; Injections ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic/*genetics ; Morula/cytology/metabolism ; Needles ; Transformation, Genetic ; Zona Pellucida/metabolism ; }, abstract = {Horizontal gene transfer or simply transgenic technology has evolved much since 1980. Gene delivery strategies, systems, and equipments have become more and more precise and efficient. It has also been shown that even chromosomes can be used besides traditional plasmid and viral vectors for zygote or embryonic stem cell transformation. Artificial chromosomes and their loadable variants have brought their advantages over traditional genetic information carriers into the field of transgenesis. Engineered chromosomes are appealing vectors for gene transfer since they have large transgene carrying capacity, they are non-integrating, and stably expressing in eukaryotic cells. Embryonic stem cell lines can be established that carry engineered chromosomes and ultimately used in transgenic mouse chimera creation. The demonstrated protocol describes all the steps necessary for the successful production of transgenic mouse chimeras with engineered chromosome bearer embryonic stem cells.}, }
@article {pmid21430389, year = {2011}, author = {Andersson, JO}, title = {Evolution of patchily distributed proteins shared between eukaryotes and prokaryotes: Dictyostelium as a case study.}, journal = {Journal of molecular microbiology and biotechnology}, volume = {20}, number = {2}, pages = {83-95}, doi = {10.1159/000324505}, pmid = {21430389}, issn = {1660-2412}, mesh = {Bacteria/genetics ; Dictyostelium/*genetics ; Entamoeba/genetics ; *Evolution, Molecular ; Fungi/genetics ; *Gene Transfer, Horizontal ; Naegleria/genetics ; *Phylogeny ; Protozoan Proteins/*genetics ; Sequence Homology, Amino Acid ; }, abstract = {Protein families are often patchily distributed in the tree of life; they are present in distantly related organisms, but absent in more closely related lineages. This could either be the result of lateral gene transfer between ancestors of organisms that encode them, or losses in the lineages that lack them. Here a novel approach is developed to study the evolution of patchily distributed proteins shared between prokaryotes and eukaryotes. Proteins encoded in the genome of cellular slime mold Dictyostelium discoideum and a restricted number of other lineages, including at least one prokaryote, were identified. Analyses of the phylogenetic distribution of 49 such patchily distributed protein families showed conflicts with organismal phylogenies; 25 are shared with the distantly related amoeboflagellate Naegleria (Excavata), whereas only two are present in the more closely related Entamoeba. Most protein families show unexpected topologies in phylogenetic analyses; eukaryotes are polyphyletic in 85% of the trees. These observations suggest that gene transfers have been an important mechanism for the distribution of patchily distributed proteins across all domains of life. Further studies of this exchangeable gene fraction are needed for a better understanding of the origin and evolution of eukaryotic genes and the diversification process of eukaryotes.}, }
@article {pmid21429206, year = {2011}, author = {Ceyssens, PJ and Glonti, T and Kropinski, NM and Lavigne, R and Chanishvili, N and Kulakov, L and Lashkhi, N and Tediashvili, M and Merabishvili, M}, title = {Phenotypic and genotypic variations within a single bacteriophage species.}, journal = {Virology journal}, volume = {8}, number = {}, pages = {134}, pmid = {21429206}, issn = {1743-422X}, mesh = {Bacteriophages/genetics/isolation &amp; purification/*physiology ; *Biodiversity ; *Genome, Viral ; Genotype ; Host Specificity ; Molecular Sequence Data ; Phenotype ; Pseudomonas aeruginosa/*virology ; }, abstract = {BACKGROUND: Although horizontal gene transfer plays a pivotal role in bacteriophage evolution, many lytic phage genomes are clearly shaped by vertical evolution. We investigated the influence of minor genomic deletions and insertions on various phage-related phenotypic and serological properties.<br><br>FINDINGS: We collected ten different isolates of Pseudomonas aeruginosa bacteriophage &#x3d5;KMV. All sequenced genomes (42-43 kb, long direct terminal repeats) are nearly identical, which intuitively implied strongly similar infections cycles. However, their latent periods vary between 21 and 28 minutes and they are able to lyse between 5 and 58% of a collection of 107 clinical P. aeruginosa strains. We also noted that phages with identical tail structures displayed profound differences in host spectra. Moreover, point mutations in tail and spike proteins were sufficient to evade neutralization by two phage-specific antisera, isolated from rabbits.<br><br>CONCLUSION: Although all analyzed phages are 83-97% identical at the genome level, they display a surprisingly large variation in various phenotypic properties. The small overlap in host spectrum and their ability to readily escape immune defences against a nearly identical phage are promising elements for the application of these phages in phage therapy.}, }
@article {pmid21423766, year = {2011}, author = {Galeote, V and Bigey, F and Beyne, E and Novo, M and Legras, JL and Casaregola, S and Dequin, S}, title = {Amplification of a Zygosaccharomyces bailii DNA segment in wine yeast genomes by extrachromosomal circular DNA formation.}, journal = {PloS one}, volume = {6}, number = {3}, pages = {e17872}, pmid = {21423766}, issn = {1932-6203}, mesh = {Base Sequence ; Blotting, Southern ; Chromosome Breakpoints ; Chromosomes, Fungal/genetics ; DNA, Circular/*genetics ; DNA, Fungal/*genetics ; Diploidy ; Electrophoresis, Gel, Pulsed-Field ; Evolution, Molecular ; Extrachromosomal Inheritance/genetics ; Gene Amplification/*genetics ; Gene Dosage/genetics ; Genetic Variation ; Genome, Fungal/*genetics ; Models, Genetic ; Molecular Sequence Data ; Mutagenesis, Insertional/genetics ; Saccharomyces cerevisiae/*genetics ; Wine/*microbiology ; Zygosaccharomyces/*genetics ; }, abstract = {We recently described the presence of large chromosomal segments resulting from independent horizontal gene transfer (HGT) events in the genome of Saccharomyces cerevisiae strains, mostly of wine origin. We report here evidence for the amplification of one of these segments, a 17 kb DNA segment from Zygosaccharomyces bailii, in the genome of S. cerevisiae strains. The copy number, organization and location of this region differ considerably between strains, indicating that the insertions are independent and that they are post-HGT events. We identified eight different forms in 28 S. cerevisiae strains, mostly of wine origin, with up to four different copies in a single strain. The organization of these forms and the identification of an autonomously replicating sequence functional in S. cerevisiae, strongly suggest that an extrachromosomal circular DNA (eccDNA) molecule serves as an intermediate in the amplification of the Z. bailii region in yeast genomes. We found little or no sequence similarity at the breakpoint regions, suggesting that the insertions may be mediated by nonhomologous recombination. The diversity between these regions in S. cerevisiae represents roughly one third the divergence among the genomes of wine strains, which confirms the recent origin of this event, posterior to the start of wine strain expansion. This is the first report of a circle-based mechanism for the expansion of a DNA segment, mediated by nonhomologous recombination, in natural yeast populations.}, }
@article {pmid21422074, year = {2011}, author = {Leplae, R and Geeraerts, D and Hallez, R and Guglielmini, J and Drèze, P and Van Melderen, L}, title = {Diversity of bacterial type II toxin-antitoxin systems: a comprehensive search and functional analysis of novel families.}, journal = {Nucleic acids research}, volume = {39}, number = {13}, pages = {5513-5525}, pmid = {21422074}, issn = {1362-4962}, mesh = {Bacterial Proteins/classification/genetics/metabolism ; Bacterial Toxins/*classification/genetics/metabolism ; Escherichia coli/genetics ; Evolution, Molecular ; Genetic Variation ; Genome, Bacterial ; Genomics ; }, abstract = {Type II toxin-antitoxin (TA) systems are generally composed of two genes organized in an operon, encoding a labile antitoxin and a stable toxin. They were first discovered on plasmids where they contribute to plasmid stability by a phenomenon denoted as 'addiction', and subsequently in bacterial chromosomes. To discover novel families of antitoxins and toxins, we developed a bioinformatics approach based on the 'guilt by association' principle. Extensive experimental validation in Escherichia coli of predicted antitoxins and toxins increased significantly the number of validated systems and defined novel toxin and antitoxin families. Our data suggest that toxin families as well as antitoxin families originate from distinct ancestors that were assembled multiple times during evolution. Toxin and antitoxin families found on plasmids tend to be promiscuous and widespread, indicating that TA systems move through horizontal gene transfer. We propose that due to their addictive properties, TA systems are likely to be maintained in chromosomes even though they do not necessarily confer an advantage to their bacterial hosts. Therefore, addiction might play a major role in the evolutionary success of TA systems both on mobile genetic elements and in bacterial chromosomes.}, }
@article {pmid21421783, year = {2011}, author = {Asteri, IA and Boutou, E and Anastasiou, R and Pot, B and Vorgias, CE and Tsakalidou, E and Papadimitriou, K}, title = {In silico evidence for the horizontal transfer of gsiB, a σ(B)-regulated gene in gram-positive bacteria, to lactic acid bacteria.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {10}, pages = {3526-3531}, pmid = {21421783}, issn = {1098-5336}, mesh = {Bacterial Proteins/*genetics/metabolism ; Computational Biology/methods ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Gram-Positive Bacteria/*genetics ; Sigma Factor/metabolism ; }, abstract = {gsiB, coding for glucose starvation-inducible protein B, is a characteristic member of the σ(Β) stress regulon of Bacillus subtilis and several other Gram-positive bacteria. Here we provide in silico evidence for the horizontal transfer of gsiB in lactic acid bacteria that are devoid of the σ(Β) factor.}, }
@article {pmid21419838, year = {2011}, author = {Peterson, G and Kumar, A and Gart, E and Narayanan, S}, title = {Catecholamines increase conjugative gene transfer between enteric bacteria.}, journal = {Microbial pathogenesis}, volume = {51}, number = {1-2}, pages = {1-8}, doi = {10.1016/j.micpath.2011.03.002}, pmid = {21419838}, issn = {1096-1208}, mesh = {Bacterial Proteins/genetics/metabolism ; Catecholamines/*pharmacology ; Conjugation, Genetic/*drug effects/genetics ; Enterobacteriaceae/drug effects/*genetics ; Escherichia coli/drug effects/genetics ; Gene Transfer, Horizontal/*drug effects ; Humans ; Norepinephrine/*pharmacology ; Plasmids/genetics ; Salmonella typhimurium/drug effects/genetics ; Virulence ; }, abstract = {The ability of pathogenic bacteria to sense and respond to periods of host stress is critical to their lifestyle. Adrenaline and norepinephrine are catecholamines that mediate acute host stress in vertebrates and invertebrates. Catecholamines are also used as environmental cues to enhance growth, motility and virulence of bacterial pathogens via specific binding receptors. Incidence of multidrug resistant and highly virulent bacterial pathogens is on the rise, and majority of the genes for antimicrobial resistance (AMR) and virulence are carried on horizontally transferable genetic elements. Conjugation machinery offers an efficient method for acquisition of AMR and virulence genes, which may be responsible for propelling the evolution of pathogenic bacteria. Here we show that norepinephrine (NE) at physiological concentrations enhances horizontal gene transfer (HGT) efficiencies of a conjugative plasmid from a clinical strain of Salmonella Typhimurium to an Escherichia coli recipient in vitro. Expressions of plasmid encoded transfer (tra) genes necessary for conjugation were also significantly upregulated in the presence of NE. Phentolamine, an α-adrenergic receptor antagonist, negated the effects of NE on conjugation more strongly than propranolol, a β-adrenergic receptor antagonist. This study for the first time provides evidence that innate mediators of acute host stress may influence evolution and adaptation of bacterial pathogens.}, }
@article {pmid21415114, year = {2011}, author = {Coton, M and Fernández, M and Trip, H and Ladero, V and Mulder, NL and Lolkema, JS and Alvarez, MA and Coton, E}, title = {Characterization of the tyramine-producing pathway in Sporolactobacillus sp. P3J.}, journal = {Microbiology (Reading, England)}, volume = {157}, number = {Pt 6}, pages = {1841-1849}, doi = {10.1099/mic.0.046367-0}, pmid = {21415114}, issn = {1465-2080}, mesh = {Bacillales/*enzymology/genetics/isolation &amp; purification ; Bacterial Proteins/genetics/*metabolism ; Beverages/microbiology ; Culture Media ; France ; *Gene Expression Regulation, Bacterial ; Malus ; Molecular Sequence Data ; *Multigene Family ; Sequence Analysis, DNA ; Species Specificity ; Tyramine/*biosynthesis ; Tyrosine/metabolism ; Tyrosine Decarboxylase/chemistry/genetics/*metabolism ; }, abstract = {A sporulated lactic acid bacterium (LAB) isolated from cider must was shown to harbour the tdc gene encoding tyrosine decarboxylase. The isolate belonged to the Sporolactobacillus genus and may correspond to a novel species. The ability of the tdc-positive strain, Sporolactobacillus sp. strain P3J, to produce tyramine in vitro was demonstrated by using HPLC. A 7535 bp nucleotide sequence harbouring the putative tdc gene was determined. Analysis of the obtained sequence showed that four tyramine production-associated genes [tyrosyl-tRNA synthetase (tyrS), tyrosine decarboxylase (tdc), tyrosine permease (tyrP) and Na(+)/H(+) antiporter (nhaC)] were present and were organized as already described in other tyramine-producing LAB. This operon was surrounded by genes showing the highest identities with mobile elements: a putative phage terminase and a putative transposase (downstream and upstream, respectively), suggesting that the tyramine-forming trait was acquired through horizontal gene transfer. Transcription analyses of the tdc gene cluster suggested that tyrS and nhaC are expressed as monocistronic genes while tdc would be part of a polycistronic mRNA together with tyrP. The presence of tyrosine in the culture medium induced the expression of all genes except for tyrS. A clear correlation was observed between initial tyrosine concentration and tyramine production combined with an increase in the final pH reached by the culture. Finally, cloning and expression of the tyrP gene in Lactococcus lactis demonstrated that its product catalyses the exchange of tyrosine and tyramine.}, }
@article {pmid21415040, year = {2011}, author = {Kim, J and Bae, IK and Jeong, SH and Chang, CL and Lee, CH and Lee, K}, title = {Characterization of IncF plasmids carrying the blaCTX-M-14 gene in clinical isolates of Escherichia coli from Korea.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {66}, number = {6}, pages = {1263-1268}, doi = {10.1093/jac/dkr106}, pmid = {21415040}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Typing Techniques ; Cefotaxime/pharmacology ; Ceftazidime/pharmacology ; DNA, Bacterial/chemistry/genetics/metabolism ; Deoxyribonucleases, Type II Site-Specific/metabolism ; Escherichia coli/classification/*enzymology/genetics/*isolation &amp; purification ; Escherichia coli Infections/*epidemiology/*microbiology ; Gene Transfer, Horizontal ; Korea/epidemiology ; Molecular Epidemiology ; Molecular Sequence Data ; Molecular Typing ; *Plasmids ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; beta-Lactam Resistance ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: The purpose of this study was to investigate the molecular epidemiology of CTX-M-14-producing Escherichia coli clinical isolates from Korea.<br><br>METHODS: A total of 138 non-duplicate E. coli clinical isolates showing reduced susceptibility or resistance to ceftazidime and/or cefotaxime were included in the study. Resistance genes, genetic environment, R plasmid size and replicon type, sequence type (ST) and XbaI-macrorestriction patterns were determined.<br><br>RESULTS: Among 138 isolates, 35 were found to carry the bla(CTX-M-14) gene. The ISEcp1 element was identified in the upstream region of the bla(CTX-M-14) gene in 32 isolates. The bla(CTX-M-14) gene was located on an IncF plasmid in 21 isolates, on an IncA/C plasmid in 1 isolate, on the chromosome in 8 isolates and on both the chromosome and an IncF plasmid in 5 isolates. The most prevalent ST was ST405 (n&#x200a;=&#x200a;8), followed by ST354 (n&#x200a;=&#x200a;4), ST38 (n&#x200a;=&#x200a;3), ST69 (n&#x200a;=&#x200a;3) and the intercontinental ST, ST131 (n&#x200a;=&#x200a;3). PFGE and multilocus sequence typing experiments demonstrated no major clonal relationship among the CTX-M-14-producing isolates.<br><br>CONCLUSIONS: The bla(CTX-M-14) gene was probably mobilized by IncF plasmids, which can readily spread in E. coli, causing horizontal dissemination of the resistance gene in Korea.}, }
@article {pmid21414219, year = {2011}, author = {Huang, S and Zhang, Y and Chen, F and Jiao, N}, title = {Complete genome sequence of a marine roseophage provides evidence into the evolution of gene transfer agents in alphaproteobacteria.}, journal = {Virology journal}, volume = {8}, number = {}, pages = {124}, pmid = {21414219}, issn = {1743-422X}, mesh = {Alphaproteobacteria/*genetics/*virology ; Bacteriophages/classification/*genetics/isolation &amp; purification ; *Biological Evolution ; *Gene Transfer, Horizontal ; *Genome, Viral ; Molecular Sequence Data ; Phylogeny ; Prophages/classification/genetics/isolation &amp; purification ; Seawater/*virology ; }, abstract = {Roseophage RDJLΦ1 is a siphovirus isolated from South China Sea on Roseobacter denitrificans OCh114. Its virion encapsulates 62.7 kb genome that encodes 87 gene products. RDJLΦ1 shares similar genome organization and gene content with the marine bacteriophage ΦJL001 and Pseudomonas phages YuA and M6, which are different from those of typical λ- or Mu-like phages. Four hallmark genes (ORFs 81 to 84) of RDJLΦ1 were highly homologous to RcGTA-like genes 12 to 15. The largest gene (ORF 84) was predicted to encode a tail fibre protein that could be involved in host recognition. Extended phylogenetic and comparative genomic analyses based on 77 RcGTA-like element-containing bacterial genomes revealed that RcGTA-like genes 12 to 15 together appear to be a conserved modular element that could also be found in some phage or prophage genomes. Our study suggests that RcGTA-like genes-containing phages and prophages and complete RcGTAs possibly descended from a same prophage ancestor that had diverged and then evolved vertically. The complete genome of RDJLΦ1 provides evidence into the hypothesis that extant RcGTA may be a prophage remnant.}, }
@article {pmid21411573, year = {2011}, author = {Richter, SN and Frasson, I and Bergo, C and Parisi, S and Cavallaro, A and Palù, G}, title = {Transfer of KPC-2 Carbapenemase from Klebsiella pneumoniae to Escherichia coli in a patient: first case in Europe.}, journal = {Journal of clinical microbiology}, volume = {49}, number = {5}, pages = {2040-2042}, pmid = {21411573}, issn = {1098-660X}, mesh = {Anti-Bacterial Agents/therapeutic use ; Escherichia coli/*enzymology/*genetics ; Europe ; *Gene Transfer, Horizontal ; Humans ; Klebsiella pneumoniae/enzymology/genetics ; Male ; Meropenem ; Middle Aged ; Plasmids/analysis ; Selection, Genetic ; Thienamycins/therapeutic use ; beta-Lactamases/*biosynthesis/*genetics ; }, abstract = {The first case in Europe of Klebsiella pneumoniae carbapenemase (KPC) 2 transfer from K. pneumoniae to Escherichia coli in the same patient is described. KPC-positive plasmids from the two species were identical, indicating horizontal plasmid transfer. Selection of the KPC-producing E. coli strain was triggered by therapy with meropenem.}, }
@article {pmid21406598, year = {2011}, author = {Babic, A and Berkmen, MB and Lee, CA and Grossman, AD}, title = {Efficient gene transfer in bacterial cell chains.}, journal = {mBio}, volume = {2}, number = {2}, pages = {}, pmid = {21406598}, issn = {2150-7511}, support = {R01 GM050895/GM/NIGMS NIH HHS/United States ; GM50895/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacillus subtilis/*genetics ; Conjugation, Genetic ; DNA, Bacterial/*genetics/*metabolism ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Microscopy, Fluorescence ; }, abstract = {Horizontal gene transfer contributes to evolution and the acquisition of new traits. In bacteria, horizontal gene transfer is often mediated by conjugative genetic elements that transfer directly from cell to cell. Integrative and conjugative elements (ICEs; also known as conjugative transposons) are mobile genetic elements that reside within a host genome but can excise to form a circle and transfer by conjugation to recipient cells. ICEs contribute to the spread of genes involved in pathogenesis, symbiosis, metabolism, and antibiotic resistance. Despite its importance, little is known about the mechanisms of conjugation in Gram-positive bacteria or how quickly or frequently transconjugants become donors. We visualized the transfer of the integrative and conjugative element ICEBs1 from a Bacillus subtilis donor to recipient cells in real time using fluorescence microscopy. We found that transfer of DNA from a donor to a recipient appeared to occur at a cell pole or along the lateral cell surface of either cell. Most importantly, we found that when acquired by 1 cell in a chain, ICEBs1 spread rapidly from cell to cell within the chain by additional sequential conjugation events. This intrachain conjugation is inherently more efficient than conjugation that is due to chance encounters between individual cells. Many bacterial species, including pathogenic, commensal, symbiotic, and nitrogen-fixing organisms, harbor ICEs and grow in chains, often as parts of microbial communities. It is likely that efficient intrachain spreading is a general feature of conjugative DNA transfer and serves to amplify the number of cells that acquire conjugative mobile genetic elements. IMPORTANCE Conjugative elements contribute to horizontal gene transfer and the acquisition of new traits. They are largely responsible for spreading antibiotic resistance in bacterial communities. To study the cell biology of conjugation, we visualized conjugative DNA transfer between Bacillus subtilis cells in real time using fluorescence microscopy. In contrast to previous predictions that transfer would occur preferentially from the donor cell pole, we found that transfer of DNA from a donor to a recipient appeared to occur at a cell pole or along the lateral cell surface of either cell. Most importantly, we found that when acquired by 1 cell in a chain, the conjugative DNA spread rapidly from cell to cell within the chain through sequential conjugation events. Since many bacterial species grow naturally in chains, this intrachain transfer is likely a common mechanism for accelerating the spread of conjugative elements within microbial communities.}, }
@article {pmid21406433, year = {2011}, author = {Mataseje, LF and Boyd, DA and Willey, BM and Prayitno, N and Kreiswirth, N and Gelosia, A and Poutanen, SM and Low, DE and Jenkins, SG and Katz, K and Mulvey, MR}, title = {Plasmid comparison and molecular analysis of Klebsiella pneumoniae harbouring bla(KPC) from New York City and Toronto.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {66}, number = {6}, pages = {1273-1277}, doi = {10.1093/jac/dkr092}, pmid = {21406433}, issn = {1460-2091}, mesh = {Aged ; Aged, 80 and over ; Anti-Bacterial Agents/pharmacology ; Bacterial Outer Membrane Proteins/genetics ; Bacterial Typing Techniques ; Canada ; Carbapenems/pharmacology ; Electrophoresis, Gel, Pulsed-Field ; Female ; Gene Transfer, Horizontal ; Humans ; Klebsiella Infections/*microbiology ; Klebsiella pneumoniae/classification/*enzymology/*genetics/isolation &amp; purification ; Male ; Microbial Sensitivity Tests ; Middle Aged ; Molecular Epidemiology ; Molecular Typing ; Multilocus Sequence Typing ; New York City ; *Plasmids ; Transformation, Bacterial ; *beta-Lactam Resistance ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: This study examined Klebsiella pneumoniae clinical isolates and their bla(KPC) plasmids to determine potential relatedness of the isolates and their plasmids harbouring carbapenem resistance mechanisms.<br><br>METHODS: K. pneumoniae carbapenemase (KPC)-producing K. pneumoniae from New York City (NYC) (n&#x200a;=&#x200a;19) and Toronto (n&#x200a;=&#x200a;2) were typed by PFGE and multilocus sequence typing (MLST). bla(KPC)-harbouring plasmids were transformed into Escherichia coli DH10B(TM), restricted using EcoRI and analysed for bla content and replicon (rep) type. Susceptibility profiles for clinical and transformed strains were determined by automated microbroth dilution using CLSI breakpoints. Outer membrane protein (OMP) genes were analysed by sequencing of ompk35 and ompk36.<br><br>RESULTS: PFGE analysis identified 17 related strains (&#x2265; 80% similarity; 11 KPC-2, 6 KPC-3) where ST258 was the dominant clonal type. All clinical isolates contained both bla(SHV) and bla(TEM-1) and, with the exception of one isolate, were multidrug resistant (MDR). Transformed KPC plasmids (n&#x200a;=&#x200a;21) carried TEM-1 (n&#x200a;=&#x200a;18) and were MDR (n&#x200a;=&#x200a;5). Three plasmid clusters, repFIIA (n&#x200a;=&#x200a;10), repR (n&#x200a;=&#x200a;3) and an unknown type (n&#x200a;=&#x200a;3), were observed. repFllA plasmids were observed from both NYC and Toronto strains. OMP gene analysis revealed premature stop codons in ompk35 and numerous deletions and insertions in ompk36.<br><br>CONCLUSIONS: The dissemination of bla(KPC) is due both to carriage of similar KPC-harbouring plasmids within genetically distinct K. pneumoniae and to clonal spread of K. pneumoniae with unrelated KPC plasmids.}, }
@article {pmid21404212, year = {2010}, author = {Arias, CR and Olivares-Fuster, O and Goris, J}, title = {High intragenomic heterogeneity of 16S rRNA genes in a subset of Vibrio vulnificus strains from the western Mediterranean coast.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {13}, number = {4}, pages = {179-188}, doi = {10.2436/20.1501.01.124}, pmid = {21404212}, issn = {1618-1905}, mesh = {Animals ; Bacterial Typing Techniques ; Base Sequence ; Bivalvia/microbiology ; Consensus Sequence ; *Genetic Variation ; Genotype ; Mediterranean Sea ; Molecular Sequence Data ; Nucleic Acid Conformation ; Polymorphism, Restriction Fragment Length ; Polymorphism, Single-Stranded Conformational ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; Seawater/microbiology ; Sequence Analysis, DNA ; Spain ; Vibrio vulnificus/*genetics ; }, abstract = {Heterogeneity among ribosomal operons in Vibrio vulnificus is purported as a probabilistic indicator of strain virulence and classifies V. vulnificus strains as 16S rRNA genes type A and B. In this study, 16S rRNA genes typing of V. vulnificus strains isolated from the Valencia city coast, in the western Mediterranean, showed that 24 out of 30 isolates were type A, one was type B and five could not be typed. Single strand conformation polymorphism (SSCP) analysis of this gene region revealed complex patterns indicative of intragenomic ribosomal operon sequence heterogeneity. The 16S rRNA genes of three untypeable isolates C27, C30, and C34, along with type A (ATCC 27562) and B (C7184) reference strains, were amplified, cloned and sequenced. The number of unique 16S rRNA gene sequences was 4, 3, and 4 for the environmental isolates. The type strain of the species (ATCC 27562) presented only two 16S rRNA gene types, while the reference isolate C7184 of clinical origin had only one 16S rRNA gene type. Sequences differed from five to 35 bp (99.6% to 97.6% sequence similarity). Areas of variability concentrated in helices 10, 18, and 37 and included variants with short intervening sequences in helix 10. Most of the substitutions showed compensatory mutations suggesting ancient sequence divergence generated by lateral gene transfer.}, }
@article {pmid21395947, year = {2011}, author = {Jung, CM and Crocker, FH and Eberly, JO and Indest, KJ}, title = {Horizontal gene transfer (HGT) as a mechanism of disseminating RDX-degrading activity among Actinomycete bacteria.}, journal = {Journal of applied microbiology}, volume = {110}, number = {6}, pages = {1449-1459}, doi = {10.1111/j.1365-2672.2011.04995.x}, pmid = {21395947}, issn = {1365-2672}, mesh = {Biodegradation, Environmental ; Conjugation, Genetic ; *Gene Transfer, Horizontal ; Gordonia Bacterium/*genetics/growth &amp; development/metabolism ; Nitrogen/metabolism ; Nocardia/genetics/growth &amp; development/*metabolism ; Plasmids/genetics ; Rhodococcus/genetics/growth &amp; development/*metabolism ; Triazines/*metabolism ; }, abstract = {AIMS: Hexahydro-1,3,5-trinitro-1,3,5,-triazine (RDX) is a cyclic nitramine explosive that is a major component in many high-explosive formulations and has been found as a contaminant of soil and groundwater. The RDX-degrading gene locus xplAB, located on pGKT2 in Gordonia sp. KTR9, is highly conserved among isolates from disparate geographical locations suggesting a horizontal gene transfer (HGT) event. It was our goal to determine whether Gordonia sp. KTR9 is capable of transferring pGKT2 and the associated RDX degradation ability to other bacteria.<br><br>METHODS AND RESULTS: We demonstrate the successful conjugal transfer of pGKT2 from Gordonia sp. KTR9 to Gordonia polyisoprenivorans, Rhodococcus jostii RHA1 and Nocardia sp. TW2. Through growth and RDX degradation studies, it was demonstrated that pGKT2 conferred to transconjugants the ability to degrade and utilize RDX as a nitrogen source. The inhibitory effect of exogenous inorganic nitrogen sources on RDX degradation in transconjugant strains was found to be strain specific.<br><br>CONCLUSIONS: Plasmid pGKT2 can be transferred by conjugation, along with the ability to degrade RDX, to related bacteria, providing evidence of at least one mechanism for the dissemination and persistence of xplAB in the environment.<br><br>These results provide evidence of one mechanism for the environmental dissemination of xplAB and provide a framework for future field relevant bioremediation practices.}, }
@article {pmid21393204, year = {2011}, author = {Dolejska, M and Duskova, E and Rybarikova, J and Janoszowska, D and Roubalova, E and Dibdakova, K and Maceckova, G and Kohoutova, L and Literak, I and Smola, J and Cizek, A}, title = {Plasmids carrying blaCTX-M-1 and qnr genes in Escherichia coli isolates from an equine clinic and a horseback riding centre.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {66}, number = {4}, pages = {757-764}, doi = {10.1093/jac/dkq500}, pmid = {21393204}, issn = {1460-2091}, mesh = {Animals ; Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; Diptera/microbiology ; Environmental Microbiology ; Escherichia coli/*genetics/*isolation &amp; purification ; Escherichia coli Proteins/*genetics ; Feces/microbiology ; Horses/*microbiology ; Molecular Sequence Data ; *Plasmids ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: The aim of this study was to determine the occurrence of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli at an equine clinic and a horseback riding centre, and to discuss the impact of antimicrobial treatment on resistance selection.<br><br>METHODS: Faeces from horses, environmental smears and flies were sampled at both the clinic and riding centre. Staff at the equine clinic were also examined. The samples were cultivated on MacConkey agar with cefotaxime (2 mg/L) to isolate ESBL-producing E. coli. The presence of bla and qnr genes was tested by PCR, and transferability was determined by conjugation. Replicon typing and restriction analysis of plasmids harbouring ESBL and qnr genes were performed.<br><br>RESULTS: E. coli with the blaCTX-M-1 gene were isolated from horses, staff, environmental smears and flies at the two sites. E. coli isolates from the equine clinic harboured an IncHI1 conjugative 235-285 kb plasmid containing blaCTX-M-1, catA1, strA, sul2 and tet(B) genes. Some of these were positive for qnrS1 and/or qnrB19, and were located on 40 or 45 kb IncN or IncX1 conjugative plasmids. The gene blaCTX-M-1 in isolates from the riding centre was carried by IncN (30 kb) and IncI1 (85 kb) conjugative plasmids. Horizontal gene transfer seems to be involved in disseminating E. coli with ESBL and qnr genes at the clinic and riding centre.<br><br>CONCLUSIONS: The study illustrates that ESBL-producing E. coli, as well as plasmids carrying ESBL genes of clinical interest, can be easily transferred among horses, humans and flies living in close contact.}, }
@article {pmid21390549, year = {2011}, author = {Shigenobu, S and Wilson, AC}, title = {Genomic revelations of a mutualism: the pea aphid and its obligate bacterial symbiont.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {68}, number = {8}, pages = {1297-1309}, pmid = {21390549}, issn = {1420-9071}, mesh = {Animals ; Aphids/*genetics/*microbiology ; Buchnera/genetics/*physiology ; *Gene Transfer, Horizontal ; *Symbiosis ; }, abstract = {The symbiosis of the pea aphid Acyrthosphion pisum with the bacterium Buchnera aphidicola APS represents the best-studied insect obligate symbiosis. Here we present a refined picture of this symbiosis by linking pre-genomic observations to new genomic data that includes the complete genomes of the eukaryotic and prokaryotic symbiotic partners. In doing so, we address four issues central to understanding the patterns and processes operating at the A. pisum/Buchnera APS interface. These four issues include: (1) lateral gene transfer, (2) host immunity, (3) symbiotic metabolism, and (4) regulation.}, }
@article {pmid21390267, year = {2011}, author = {Deshpande, CN and Harrop, SJ and Boucher, Y and Hassan, KA and Di Leo, R and Xu, X and Cui, H and Savchenko, A and Chang, C and Labbate, M and Paulsen, IT and Stokes, HW and Curmi, PM and Mabbutt, BC}, title = {Crystal structure of an integron gene cassette-associated protein from Vibrio cholerae identifies a cationic drug-binding module.}, journal = {PloS one}, volume = {6}, number = {3}, pages = {e16934}, pmid = {21390267}, issn = {1932-6203}, support = {P50 GM062414/GM/NIGMS NIH HHS/United States ; U54 GM094585/GM/NIGMS NIH HHS/United States ; GM62414-0/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacterial Proteins/*chemistry/genetics ; Cations ; Conserved Sequence/genetics ; Crystallography, X-Ray ; Genes, Bacterial/*genetics ; Integrons/*genetics ; Ligands ; Molecular Sequence Data ; Pharmaceutical Preparations/*metabolism ; Phylogeny ; Protein Binding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sequence Alignment ; Structural Homology, Protein ; Vibrio cholerae/*genetics ; }, abstract = {BACKGROUND: The direct isolation of integron gene cassettes from cultivated and environmental microbial sources allows an assessment of the impact of the integron/gene cassette system on the emergence of new phenotypes, such as drug resistance or virulence. A structural approach is being exploited to investigate the modularity and function of novel integron gene cassettes.<br><br>We report the 1.8 &#xc5; crystal structure of Cass2, an integron-associated protein derived from an environmental V. cholerae. The structure defines a monomeric beta-barrel protein with a fold related to the effector-binding portion of AraC/XylS transcription activators. The closest homologs of Cass2 are multi-drug binding proteins, such as BmrR. Consistent with this, a binding pocket made up of hydrophobic residues and a single glutamate side chain is evident in Cass2, occupied in the crystal form by polyethylene glycol. Fluorescence assays demonstrate that Cass2 is capable of binding cationic drug compounds with submicromolar affinity. The Cass2 module possesses a protein interaction surface proximal to its drug-binding cavity with features homologous to those seen in multi-domain transcriptional regulators.<br><br>CONCLUSIONS/SIGNIFICANCE: Genetic analysis identifies Cass2 to be representative of a larger family of independent effector-binding proteins associated with lateral gene transfer within Vibrio and closely-related species. We propose that the Cass2 family not only has capacity to form functional transcription regulator complexes, but represents possible evolutionary precursors to multi-domain regulators associated with cationic drug compounds.}, }
@article {pmid21388698, year = {2011}, author = {Kwit, C and Moon, HS and Warwick, SI and Stewart, CN}, title = {Transgene introgression in crop relatives: molecular evidence and mitigation strategies.}, journal = {Trends in biotechnology}, volume = {29}, number = {6}, pages = {284-293}, doi = {10.1016/j.tibtech.2011.02.003}, pmid = {21388698}, issn = {1879-3096}, mesh = {Crosses, Genetic ; *Gene Transfer, Horizontal ; Plant Weeds/*genetics ; *Plants, Genetically Modified ; }, abstract = {Incorporation of crop genes into wild and weedy relative populations (i.e. introgression) has long been of interest to ecologists and weed scientists. Potential negative outcomes that result from crop transgene introgression (e.g. extinction of native wild relative populations; invasive spread by wild or weedy hosts) have not been documented, and few examples of transgene introgression exist. However, molecular evidence of introgression from non-transgenic crops to their relatives continues to emerge, even for crops deemed low-risk candidates for transgene introgression. We posit that transgene introgression monitoring and mitigation strategies are warranted in cases in which transgenes are predicted to confer selective advantages and disadvantages to recipient hosts. The utility and consequences of such strategies are examined, and future directions provided.}, }
@article {pmid21387023, year = {2011}, author = {Kumar, M and Balaji, PV}, title = {Comparative genomics analysis of completely sequenced microbial genomes reveals the ubiquity of N-linked glycosylation in prokaryotes.}, journal = {Molecular bioSystems}, volume = {7}, number = {5}, pages = {1629-1645}, doi = {10.1039/c0mb00259c}, pmid = {21387023}, issn = {1742-2051}, mesh = {Archaea/classification/*genetics ; Archaeal Proteins/genetics ; Bacteria/classification/*genetics ; Bacterial Proteins/genetics ; Enzymes/genetics ; Genetic Variation ; Genome, Archaeal/*genetics ; Genome, Bacterial/*genetics ; Genomics/*methods ; Glycosylation ; *Phylogeny ; Signal Transduction/genetics ; Software ; Species Specificity ; }, abstract = {Glycosylation of proteins in prokaryotes has been known for the last few decades. Glycan structures and/or the glycosylation pathways have been experimentally characterized in only a small number of prokaryotes. Even this has become possible only during the last decade or so, primarily due to technological and methodological developments. Glycosylated proteins are diverse in their function and localization. Glycosylation has been shown to be associated with a wide range of biological phenomena. Characterization of the various types of glycans and the glycosylation machinery is critical to understand such processes. Such studies can help in the identification of novel targets for designing drugs, diagnostics, and engineering of therapeutic proteins. In view of this, the experimentally characterized pgl system of Campylobacter jejuni, responsible for N-linked glycosylation, has been used in this study to identify glycosylation loci in 865 prokaryotes whose genomes have been completely sequenced. Results from the present study show that only a small number of organisms have homologs for all the pgl enzymes and a few others have homologs for none of the pgl enzymes. Most of the organisms have homologs for only a subset of the pgl enzymes. There is no specific pattern for the presence or absence of pgl homologs vis-à-vis the 16S rRNA sequence-based phylogenetic tree. This may be due to differences in the glycan structures, high sequence divergence, horizontal gene transfer or non-orthologous gene displacement. Overall, the presence of homologs for pgl enzymes in a large number of organisms irrespective of their habitat, pathogenicity, energy generation mechanism, etc., hints towards the ubiquity of N-linked glycosylation in prokaryotes.}, }
@article {pmid21385829, year = {2011}, author = {Szabová, J and Ruzicka, P and Verner, Z and Hampl, V and Lukes, J}, title = {Experimental examination of EFL and MATX eukaryotic horizontal gene transfers: coexistence of mutually exclusive transcripts predates functional rescue.}, journal = {Molecular biology and evolution}, volume = {28}, number = {8}, pages = {2371-2378}, doi = {10.1093/molbev/msr060}, pmid = {21385829}, issn = {1537-1719}, mesh = {Biological Evolution ; Cell Proliferation ; Gene Expression Regulation ; *Gene Transfer, Horizontal ; Methionine Adenosyltransferase/*genetics/metabolism ; Peptide Elongation Factor 1/*genetics/metabolism ; RNA Interference ; RNA, Messenger/genetics ; *Transcription, Genetic ; Trypanosoma brucei brucei/genetics/metabolism ; }, abstract = {Many eukaryotic genes do not follow simple vertical inheritance. Elongation factor 1α (EF-1α) and methionine adenosyl transferase (MAT) are enzymes with complicated evolutionary histories and, interestingly, the two cases have several features in common. These essential enzymes occur as two relatively divergent paralogs (EF-1α/EFL, MAT/MATX) that have patchy distributions in eukaryotic lineages that are nearly mutually exclusive. To explain such distributions, we must invoke either multiple eukaryote-to-eukaryote horizontal gene transfers (HGTs) followed by functional replacement or presence of both paralogs in the common ancestor followed by long-term coexistence and differential losses in various eukaryotic lineages. To understand the evolution of these paralogs, we have performed in vivo experiments in Trypanosoma brucei addressing the consequences of long-term coexpression and functional replacement. In the first experiment of its kind, we have demonstrated that EF-1α and MAT can be simultaneously expressed with EFL and MATX, respectively, without affecting the growth of the flagellates. After the endogenous MAT or EF-1α was downregulated by RNA interference, MATX immediately substituted for its paralog, whereas EFL was not able to substitute for EF-1α, leading to mortality. We conclude that MATX is naturally capable of evolving patchy paralog distribution via HGTs and/or long- term coexpression and differential losses. The capability of EFL to spread by HGT is lower and so the patchy distribution of EF-1α/EFL paralogs was probably shaped mainly by deep paralogy followed by long-term coexistence and differential losses.}, }
@article {pmid21385089, year = {2011}, author = {Frye, JG and Lindsey, RL and Meinersmann, RJ and Berrang, ME and Jackson, CR and Englen, MD and Turpin, JB and Fedorka-Cray, PJ}, title = {Related antimicrobial resistance genes detected in different bacterial species co-isolated from swine fecal samples.}, journal = {Foodborne pathogens and disease}, volume = {8}, number = {6}, pages = {663-679}, doi = {10.1089/fpd.2010.0695}, pmid = {21385089}, issn = {1556-7125}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacterial Typing Techniques ; Campylobacter/classification/drug effects/*genetics/isolation &amp; purification ; Cluster Analysis ; Drug Resistance, Bacterial/genetics ; Enterobacteriaceae/classification/drug effects/*genetics/isolation &amp; purification ; Enterococcus/classification/drug effects/*genetics/isolation &amp; purification ; Escherichia coli/classification/drug effects/genetics/isolation &amp; purification ; Feces/microbiology ; *Gene Transfer, Horizontal ; Genes, Bacterial ; *Genes, MDR ; Microbial Sensitivity Tests ; Oligonucleotide Array Sequence Analysis ; R Factors/*genetics ; Salmonella enterica/classification/drug effects/genetics/isolation &amp; purification ; Sus scrofa ; United States ; }, abstract = {A potential factor leading to the spread of antimicrobial resistance (AR) in bacteria is the horizontal transfer of resistance genes between bacteria in animals or their environment. To investigate this, swine fecal samples were collected on-farm and cultured for Escherichia coli, Salmonella enterica, Campylobacter spp., and Enterococcus spp. which are all commonly found in swine. Forty-nine of the samples from which all four bacteria were recovered were selected yielding a total of 196 isolates for analysis. Isolates were tested for antimicrobial susceptibility followed by hybridization to a DNA microarray designed to detect 775 AR-related genes. E. coli and Salmonella isolated from the same fecal sample had the most AR genes in common among the four bacteria. Genes detected encoded resistance to aminoglycosides (aac(3), aadA1, aadB, and strAB), β-lactams (ampC, ampR, and bla(TEM)), chloramphenicols (cat and floR), sulfanillic acid (sul1/sulI), tetracyclines (tet(A), tet(D), tet(C), tet(G), and tet(R)), and trimethoprim (dfrA1 and dfh). Campylobacter coli and Enterococcus isolated from the same sample frequently had tet(O) and aphA-3 genes detected in common. Almost half (47%) of E. coli and Salmonella isolated from the same fecal sample shared resistance genes at a significant level (χ[2], p < 0.0000001). These data suggest that there may have been horizontal exchange of AR genes between these bacteria or there may be a common source of AR genes in the swine environment for E. coli and Salmonella.}, }
@article {pmid21384330, year = {2010}, author = {Pirondini, A and Marmiroli, N}, title = {Environmental risk assessment in GMO analysis.}, journal = {Rivista di biologia}, volume = {103}, number = {2-3}, pages = {371-402}, pmid = {21384330}, issn = {0035-6050}, mesh = {Animals ; *Environment ; Gene Transfer, Horizontal ; Humans ; *Organisms, Genetically Modified ; Risk Assessment ; }, abstract = {Genetically modified or engineered organisms (GMOs, GEOs) are utilised in agriculture, expressing traits of interest, such as insect or herbicide resistance. Soybean, maize, cotton and oilseed rape are the GM crops with the largest acreage in the world. The distribution of GM acreage in the different countries is related with the different positions concerning labelling of GMO products: based on the principle of substantial equivalence, or rather based on the precautionary principle. The paper provides an overview on how the risks associated with release of GMO in the environments can be analysed and predicted, in view of a possible coexistence of GM and non-GM organisms in agriculture.Risk assessment procedures, both qualitative and quantitative, are compared in the context of application to GMOs considering also legislation requirements (Directive 2001/18/EC). Criteria and measurable properties to assess harm for human health and environmental safety are listed, and the possible consequences are evaluated in terms of significance.Finally, a mapping of the possible risks deriving from GMO release is reported, focusing on gene transfer to related species, horizontal gene transfer, direct and indirect effects on non target organisms, development of resistance in target organisms, and effects on biodiversity.}, }
@article {pmid21384181, year = {2011}, author = {Rae, BD and Förster, B and Badger, MR and Price, GD}, title = {The CO2-concentrating mechanism of Synechococcus WH5701 is composed of native and horizontally-acquired components.}, journal = {Photosynthesis research}, volume = {109}, number = {1-3}, pages = {59-72}, pmid = {21384181}, issn = {1573-5079}, mesh = {Bacterial Proteins/*genetics/metabolism ; Biological Evolution ; Biological Transport ; Carbon/*metabolism ; Carbon Dioxide/*metabolism/pharmacology ; Computational Biology ; Cyanobacteria/classification/genetics ; Fresh Water/microbiology ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal/*genetics ; Genomic Islands ; Photosynthesis ; Phylogeny ; RNA, Bacterial/genetics ; Ribulose-Bisphosphate Carboxylase/genetics/metabolism ; Ribulosephosphates/metabolism ; Seawater/microbiology ; Sequence Alignment ; Synechococcus/classification/genetics/metabolism/*physiology ; }, abstract = {The cyanobacterial CO(2)-concentrating mechanism (CCM) is an effective adaptation that increases the carbon dioxide (CO(2)) concentration around the primary photosynthetic enzyme Ribulose-1,5-bisphosphate Carboxylase/Oxygenase (RuBisCO). α-Cyanobacteria (those containing Form1-A RuBisCO within cso-type α-carboxysomes) have a limited CCM composed of a small number of Ci-transporters whereas β-cyanobacteria (those species containing Form-1B RuBisCO within ccm-type β-carboxysomes) exhibit a more diverse CCM with a greater variety in Ci-transporter complement and regulation. In the coastal species Synechococcus sp. WH5701 (α-cyanobacteria), the minimal α-cyanobacterial CCM has been supplemented with β-cyanobacterial Ci transporters through the process of horizontal gene transfer (HGT). These transporters are transcriptionally regulated in response to external Ci-depletion however this change in transcript abundance is not correlated with a physiological induction. WH5701 exhibits identical physiological responses grown at 4% CO(2) (K (1/2) ≈ 31 μM Ci) and after induction with 0.04% CO(2) (K (1/2) ≈ 29 μM Ci). Insensitivity to external Ci concentration is an unusual characteristic of the WH5701 CCM which is a result of evolution by HGT. Our bioinformatic and physiological data support the hypothesis that WH5701 represents a clade of α-cyanobacterial species in transition from the marine/oligotrophic environment to a coastal/freshwater environment.}, }
@article {pmid21380435, year = {2011}, author = {Zhou, Z and Zhang, W and Chen, M and Pan, J and Lu, W and Ping, S and Yan, Y and Hou, X and Yuan, M and Zhan, Y and Lin, M}, title = {Genome-wide transcriptome and proteome analysis of Escherichia coli expressing IrrE, a global regulator of Deinococcus radiodurans.}, journal = {Molecular bioSystems}, volume = {7}, number = {5}, pages = {1613-1620}, doi = {10.1039/c0mb00336k}, pmid = {21380435}, issn = {1742-2051}, mesh = {Bacterial Proteins/genetics/metabolism ; Deinococcus/genetics/metabolism ; Electrophoresis, Gel, Two-Dimensional ; Escherichia coli/genetics/metabolism ; Escherichia coli Proteins/*analysis/genetics/metabolism ; Gene Expression Profiling/*methods ; Gene Expression Regulation, Bacterial ; Genes, Regulator/genetics ; Genome, Bacterial/genetics ; Metabolic Networks and Pathways/genetics ; Oligonucleotide Array Sequence Analysis ; Proteome/*analysis/genetics/metabolism ; Proteomics/*methods ; Salt Tolerance/genetics ; Transformation, Genetic ; }, abstract = {Gram-negative bacterium Escherichia coli and the Gram-positive Deinococcus radiodurans fundamentally differ in their cell structures and gene regulations. We have previously reported that IrrE, a Deinococcus genus-specific global regulator, confers significantly enhanced tolerance to various abiotic stresses. To better understand the global effects of IrrE on the regulatory networks, we carried out combined transcriptome and proteome analysis of E. coli expressing the IrrE protein. Our analysis showed that 216 (4.8%) of all E. coli genes were induced and 149 (3.3%) genes were repressed, including those for trehalose biosynthesis, nucleotides biosynthesis, carbon source utilization, amino acid utilization, acid resistance, a hydrogenase and an oxidase. Also regulated were the EvgSA two-component system, the GadE, GadX and PurR master regulators, and 10 transcription factors (AppY, GadW, YhiF, AsnC, BetI, CynR, MhpR, PrpR, TdcA and KdgR). These results demonstrated that IrrE acts as global regulator and consequently improves abiotic stress tolerances in the heterologous host E. coli. The implication of our findings is discussed in relation to the evolutionary role of horizontal gene transfer in bacterial regulatory networks and environmental adaptation.}, }
@article {pmid21379317, year = {2011}, author = {Diao, Y and Qi, Y and Ma, Y and Xia, A and Sharakhov, I and Chen, X and Biedler, J and Ling, E and Tu, ZJ}, title = {Next-generation sequencing reveals recent horizontal transfer of a DNA transposon between divergent mosquitoes.}, journal = {PloS one}, volume = {6}, number = {2}, pages = {e16743}, pmid = {21379317}, issn = {1932-6203}, support = {AI042121/AI/NIAID NIH HHS/United States ; R21AI081023/AI/NIAID NIH HHS/United States ; R01 AI042121/AI/NIAID NIH HHS/United States ; R29 AI042121/AI/NIAID NIH HHS/United States ; R21 AI081023/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; Culicidae/*classification/*genetics ; DNA Transposable Elements/*genetics ; Gene Transfer, Horizontal/*physiology ; *Genetic Speciation ; High-Throughput Nucleotide Sequencing/methods ; In Situ Hybridization, Fluorescence ; Molecular Sequence Data ; Phylogeny ; Species Specificity ; Time Factors ; }, abstract = {Horizontal transfer of genetic material between complex organisms often involves transposable elements (TEs). For example, a DNA transposon mariner has been shown to undergo horizontal transfer between different orders of insects and between different phyla of animals. Here we report the discovery and characterization of an ITmD37D transposon, MJ1, in Anopheles sinensis. We show that some MJ1 elements in Aedes aegypti and An. sinensis contain intact open reading frames and share nearly 99% nucleotide identity over the entire transposon, which is unexpectedly high given that these two genera had diverged 145-200 million years ago. Chromosomal hybridization and TE-display showed that MJ1 copy number is low in An. sinensis. Among 24 mosquito species surveyed, MJ1 is only found in Ae. aegypti and the hyrcanus group of anopheline mosquitoes to which An. sinensis belongs. Phylogenetic analysis is consistent with horizontal transfer and provides the basis for inference of its timing and direction. Although report of horizontal transfer of DNA transposons between higher eukaryotes is accumulating, our analysis is one of a small number of cases in which horizontal transfer of nearly identical TEs among highly divergent species has been thoroughly investigated and strongly supported. Horizontal transfer involving mosquitoes is of particular interest because there are ongoing investigations of the possibility of spreading pathogen-resistant genes into mosquito populations to control malaria and other infectious diseases. The initial indication of horizontal transfer of MJ1 came from comparisons between a 0.4x coverage An. sinensis 454 sequence database and available TEs in mosquito genomes. Therefore we have shown that it is feasible to use low coverage sequencing to systematically uncover horizontal transfer events. Expanding such efforts across a wide range of species will generate novel insights into the relative frequency of horizontal transfer of different TEs and provide the evolutionary context of these lateral transfer events.}, }
@article {pmid21378184, year = {2011}, author = {Wang, J and Hu, W and Lux, R and He, X and Li, Y and Shi, W}, title = {Natural transformation of Myxococcus xanthus.}, journal = {Journal of bacteriology}, volume = {193}, number = {9}, pages = {2122-2132}, pmid = {21378184}, issn = {1098-5530}, support = {R01 GM054666/GM/NIGMS NIH HHS/United States ; GM54666/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/metabolism ; DNA, Bacterial/genetics ; Gene Expression Regulation, Bacterial/physiology ; Mutation ; Myxococcus xanthus/classification/*genetics ; Plasmids ; Polysaccharides, Bacterial/metabolism ; Transformation, Genetic/*genetics ; }, abstract = {Myxococcus xanthus belongs to the delta class of the proteobacteria and is notable for its complex life-style with social behaviors and relatively large genome. Although previous observations have suggested the existence of horizontal gene transfer in M. xanthus, its ability to take up exogenous DNA via natural transformation has not been experimentally demonstrated. In this study, we achieved natural transformation in M. xanthus using the autonomously replicating myxobacterial plasmid pZJY41 as donor DNA. M. xanthus exopolysaccharide (EPS) was shown to be an extracellular barrier for transformation. Cells deficient in EPS production, e.g., mutant strains carrying ΔdifA or ΔepsA, became naturally transformable. Among the inner barriers to transformation were restriction-modification systems in M. xanthus, which could be partially overcome by methylating DNA in vitro using cell extracts of M. xanthus prior to transformation. In addition, the incubation time of DNA with cells and the presence of divalent magnesium ion affected transformation frequency of M. xanthus. Furthermore, we also observed a potential involvement of the type IV pilus system in the DNA uptake machinery of M. xanthus. The natural transformation was totally eliminated in the ΔpilQ/epsA and Δtgl/epsA mutants, and null mutation of pilB or pilC in an ΔepsA background diminished the transformation rate. Our study, to the best of our knowledge, provides the first example of a naturally transformable species among deltaproteobacteria.}, }
@article {pmid21378103, year = {2011}, author = {de Graaf, RM and Ricard, G and van Alen, TA and Duarte, I and Dutilh, BE and Burgtorf, C and Kuiper, JW and van der Staay, GW and Tielens, AG and Huynen, MA and Hackstein, JH}, title = {The organellar genome and metabolic potential of the hydrogen-producing mitochondrion of Nyctotherus ovalis.}, journal = {Molecular biology and evolution}, volume = {28}, number = {8}, pages = {2379-2391}, pmid = {21378103}, issn = {1537-1719}, mesh = {Biological Evolution ; Cell Nucleus/genetics/metabolism ; Ciliophora/classification/*genetics/*metabolism ; Gene Transfer, Horizontal ; Genes, Protozoan/genetics ; Genome, Mitochondrial/*genetics ; Hydrogen/*metabolism ; Mitochondria/*genetics/*metabolism ; Organelles/genetics/metabolism ; Phylogeny ; Protozoan Proteins/genetics/metabolism ; }, abstract = {It is generally accepted that hydrogenosomes (hydrogen-producing organelles) evolved from a mitochondrial ancestor. However, until recently, only indirect evidence for this hypothesis was available. Here, we present the almost complete genome of the hydrogen-producing mitochondrion of the anaerobic ciliate Nyctotherus ovalis and show that, except for the notable absence of genes encoding electron transport chain components of Complexes III, IV, and V, it has a gene content similar to the mitochondrial genomes of aerobic ciliates. Analysis of the genome of the hydrogen-producing mitochondrion, in combination with that of more than 9,000 genomic DNA and cDNA sequences, allows a preliminary reconstruction of the organellar metabolism. The sequence data indicate that N. ovalis possesses hydrogen-producing mitochondria that have a truncated, two step (Complex I and II) electron transport chain that uses fumarate as electron acceptor. In addition, components of an extensive protein network for the metabolism of amino acids, defense against oxidative stress, mitochondrial protein synthesis, mitochondrial protein import and processing, and transport of metabolites across the mitochondrial membrane were identified. Genes for MPV17 and ACN9, two hypothetical proteins linked to mitochondrial disease in humans, were also found. The inferred metabolism is remarkably similar to the organellar metabolism of the phylogenetically distant anaerobic Stramenopile Blastocystis. Notably, the Blastocystis organelle and that of the related flagellate Proteromonas lacertae also lack genes encoding components of Complexes III, IV, and V. Thus, our data show that the hydrogenosomes of N. ovalis are highly specialized hydrogen-producing mitochondria.}, }
@article {pmid21371654, year = {2011}, author = {Livermore, DM and Walsh, TR and Toleman, M and Woodford, N}, title = {Balkan NDM-1: escape or transplant?.}, journal = {The Lancet. Infectious diseases}, volume = {11}, number = {3}, pages = {164}, doi = {10.1016/S1473-3099(11)70048-2}, pmid = {21371654}, issn = {1474-4457}, mesh = {Bacteria/*drug effects/*enzymology/genetics ; Drug Resistance, Microbial/genetics/*physiology ; Europe/epidemiology ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Humans ; India/epidemiology ; beta-Lactamases/*genetics/metabolism ; }, }
@article {pmid21369977, year = {2011}, author = {Zo, YG}, title = {Reductive divergence of enterobacterial repetitive intergenic consensus sequences among Gammaproteobacteria genomes.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {49}, number = {1}, pages = {35-45}, pmid = {21369977}, issn = {1976-3794}, mesh = {*DNA Transposable Elements ; DNA, Bacterial/*genetics ; Evolution, Molecular ; Gammaproteobacteria/*genetics ; Gene Dosage ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Polymorphism, Genetic ; *Repetitive Sequences, Nucleic Acid ; }, abstract = {Enterobacterial repetitive intergenic consensus (ERIC) sequence is a transcription-modulating, nonautonomous, miniature inverted-repeat transposable element. Its origin and the mechanism of highly varying incidences, limited to Enterobacteriaceae and Vibrionaceae, have not been identified. In this study, distribution and divergence of ERICs along bacterial taxonomie units were analyzed. ERICs were found among five families of gammaproteobacteria, with the copy numbers varying with exponential increments. The variability was explained by genus (45%) and species (36%) affiliations, indicating that copy numbers are specific to sub-family taxa. ERICs were interspersed in genomes with considerable divergences. Locations of ERICs in a genome appeared to be strongly conserved in a strain, moderately in a species or a genus, and weakly in a family. ERICs in different species of a genus were from the identical population of sequences while ERICs in different genera of a family were nearly identical. However, ERICs in different families formed distinct monophylectic groups, implying vertical transmission of diverging population of sequences. In spite of large difference in copy numbers, overall intra-genome evolutionary distances among ERICs were similar among different species, except for a few genomes. The exceptions substantiated hypotheses of genetic drifts and horizontal gene transfers of mobility capacity. Therefore, the confined, variable distribution of ERIC could be explained as a two-step evolution: introduction and proliferation of ERIC in one of the progenitors of gammaproteobacteria, followed by vertical transmission under negative selection. Deterioration of sequences and reduction in copy number were concluded to be the predominant patterns in the evolution of ERIC loci.}, }
@article {pmid21369871, year = {2011}, author = {Nyquist, OL and McLeod, A and Brede, DA and Snipen, L and Aakra, &#xc5; and Nes, IF}, title = {Comparative genomics of Lactobacillus sakei with emphasis on strains from meat.}, journal = {Molecular genetics and genomics : MGG}, volume = {285}, number = {4}, pages = {297-311}, pmid = {21369871}, issn = {1617-4623}, mesh = {Adaptation, Physiological/genetics ; Bacteriocins/genetics ; Cluster Analysis ; Comparative Genomic Hybridization ; Food Handling ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/genetics ; Genetic Variation ; Genomics/*methods ; Lactobacillus/*genetics/metabolism ; Meat/*microbiology ; Microbial Viability/genetics ; }, abstract = {Lactobacillus sakei is a lactic acid bacterium important in food microbiology mainly due to its ability to ferment and preserve meat. The genome sequence of L. sakei strain 23K has revealed specialized metabolic capacities that reflect the bacterium's adaption to meat products, and that differentiate it from other LAB. An extensive genomic diversity analysis was conducted to elucidate the core features of the species, and to provide a better comprehension of niche adaptation of the organism. Here, we describe the genomic comparison of 18 strains of L. sakei originating mainly from processed meat against the 23K strain by comparative genome hybridization. Pulsed field gel electrophoresis was used to estimate the genome sizes of the strains, which varied from 1.880 to 2.175 Mb, and the 23K genome was among the smallest. Consequently, a large part of the genome of this strain belongs to a common gene pool invariant in this species. The majority of genes important in adaption to meat products, the ability to flexibly use meat components, and robustness during meat processing and storage were conserved, such as genes involved in nucleoside scavenging, catabolism of arginine, and the ability to cope with changing redox and oxygen levels, which is indicative of the role these genes play in niche specialization within the L. sakei species. Moreover, an additional set of sequenced L. sakei genes beyond the 23K genome was present on the microarray used, and it was demonstrated that all the strains carry remnants of or complete bacteriocin operons. The genomic divergence corresponded mainly to five regions in the 23K genome, which showed features consistent with horizontal gene transfer. Carbohydrate-fermentation profiles of the strains were evaluated in light of the CGH data, and for most substrates, the genotypes were consistent with the phenotypes. We have demonstrated a highly conserved organization of the L. sakei genomes investigated, and the 23K strain is a suitable model organism to study core features of the L. sakei species.}, }
@article {pmid21369358, year = {2011}, author = {Yew, JY and Dreisewerd, K and de Oliveira, CC and Etges, WJ}, title = {Male-specific transfer and fine scale spatial differences of newly identified cuticular hydrocarbons and triacylglycerides in a Drosophila species pair.}, journal = {PloS one}, volume = {6}, number = {2}, pages = {e16898}, pmid = {21369358}, issn = {1932-6203}, mesh = {Animals ; Carbohydrate Metabolism/genetics/physiology ; Cell Wall/metabolism ; Drosophila/genetics/*metabolism ; Evolution, Molecular ; Female ; Gene Transfer, Horizontal ; Genetic Speciation ; Hydrocarbons/*metabolism ; Male ; Sex Characteristics ; Sexual Behavior, Animal/physiology ; Species Specificity ; Tissue Distribution/genetics ; Triglycerides/genetics/*metabolism ; }, abstract = {We analyzed epicuticular hydrocarbon variation in geographically isolated populations of D. mojavensis cultured on different rearing substrates and a sibling species, D. arizonae, with ultraviolet laser desorption/ionization mass spectrometry (UV-LDI MS). Different body parts, i.e. legs, proboscis, and abdomens, of both species showed qualitatively similar hydrocarbon profiles consisting mainly of long-chain monoenes, dienes, trienes, and tetraenes. However, D. arizonae had higher amounts of most hydrocarbons than D. mojavensis and females of both species exhibited greater hydrocarbon amounts than males. Hydrocarbon profiles of D. mojavensis populations were significantly influenced by sex and rearing substrates, and differed between body parts. Lab food-reared flies had lower amounts of most hydrocarbons than flies reared on fermenting cactus substrates. We discovered 48 male- and species-specific hydrocarbons ranging in size from C(22) to C(50) in the male anogenital region of both species, most not described before. These included several oxygen-containing hydrocarbons in addition to high intensity signals corresponding to putative triacylglycerides, amounts of which were influenced by larval rearing substrates. Some of these compounds were transferred to female cuticles in high amounts during copulation. This is the first study showing that triacylglycerides may be a separate class of courtship-related signaling molecules in drosophilids. This study also extends the kind and number of epicuticular hydrocarbons in these species and emphasizes the role of larval ecology in influencing amounts of these compounds, many of which mediate courtship success within and between species.}, }
@article {pmid21368324, year = {2011}, author = {Chung, Y and Ané, C}, title = {Comparing two Bayesian methods for gene tree/species tree reconstruction: simulations with incomplete lineage sorting and horizontal gene transfer.}, journal = {Systematic biology}, volume = {60}, number = {3}, pages = {261-275}, doi = {10.1093/sysbio/syr003}, pmid = {21368324}, issn = {1076-836X}, mesh = {*Bayes Theorem ; Computational Biology/*methods ; Computer Simulation ; *Gene Transfer, Horizontal ; Genetic Speciation ; *Phylogeny ; *Software ; }, abstract = {With the increasing interest in recognizing the discordance between gene genealogies, various gene tree/species tree reconciliation methods have been developed. We present here the first attempt to assess and compare two such Bayesian methods, Bayesian estimation of species trees (BEST) and BUCKy (Bayesian untangling of concordance knots), in the presence of several known processes of gene tree discordance. DNA alignments were simulated under the influence of incomplete lineage sorting (ILS) and of horizontal gene transfer (HGT). BEST and BUCKy both account for uncertainty in gene tree estimation but differ substantially in their assumptions of what caused gene tree discordance. BEST estimates a species tree using the coalescent model, assuming that all gene tree discordance is due to ILS. BUCKy does not assume any specific biological process of gene tree discordance through the use of a nonparametric clustering of concordant genes. BUCKy estimates the concordance factor (CF) of a clade, which is defined as the proportion of genes that truly have the clade in their trees. The estimated concordance tree is then built from clades with the highest estimated CFs. Because of their different assumptions, it was expected that BEST would perform better in the presence of ILS and that BUCKy would perform better in the presence of HGT. As expected, the species tree was more accurately reconstructed by BUCKy in the presence of HGT, when the HGT events were unevenly placed across the species tree. BUCKy and BEST performed similarly in most other cases, including in the presence of strong ILS and of HGT events that were evenly placed across the tree. However, BUCKy was shown to underestimate the uncertainty in CF estimation, with short credibility intervals. Despite this, the discordance pattern estimated by BUCKy could be compared with the signature of ILS. The resulting test for the adequacy of the coalescent model proved to have low Type I error. It was powerful when HGT was the major source of discordance and when HGT events were unevenly placed across the species tree.}, }
@article {pmid21368196, year = {2011}, author = {Budroni, S and Siena, E and Dunning Hotopp, JC and Seib, KL and Serruto, D and Nofroni, C and Comanducci, M and Riley, DR and Daugherty, SC and Angiuoli, SV and Covacci, A and Pizza, M and Rappuoli, R and Moxon, ER and Tettelin, H and Medini, D}, title = {Neisseria meningitidis is structured in clades associated with restriction modification systems that modulate homologous recombination.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {11}, pages = {4494-4499}, pmid = {21368196}, issn = {1091-6490}, mesh = {Base Sequence ; Chromosome Inversion/genetics ; Chromosome Segregation/genetics ; Conserved Sequence/genetics ; DNA Restriction-Modification Enzymes/*genetics ; DNA, Bacterial/genetics ; Gene Conversion/genetics ; Genes, Bacterial/genetics ; Host-Pathogen Interactions/genetics ; Humans ; Mutagenesis, Insertional/genetics ; Neisseria meningitidis/*classification/*genetics/growth &amp; development/pathogenicity ; Operon/genetics ; *Phylogeny ; *Recombination, Genetic ; Species Specificity ; }, abstract = {Molecular data on a limited number of chromosomal loci have shown that the population of Neisseria meningitidis (Nm), a deadly human pathogen, is structured in distinct lineages. Given that the Nm population undergoes substantial recombination, the mechanisms resulting in the evolution of these lineages, their persistence in time, and the implications for the pathogenicity of the bacterium are not yet completely understood. Based on whole-genome sequencing, we show that Nm is structured in phylogenetic clades. Through acquisition of specific genes and through insertions and rearrangements, each clade has acquired and remodeled specific genomic tracts, with the potential to impact on the commensal and virulence behavior of Nm. Despite this clear evidence of a structured population, we confirm high rates of detectable recombination throughout the whole Nm chromosome. However, gene conversion events were found to be longer within clades than between clades, suggesting a DNA cleavage mechanism associated with the phylogeny of the species. We identify 22 restriction modification systems, probably acquired by horizontal gene transfer from outside of the species/genus, whose distribution in the different strains coincides with the phylogenetic clade structure. We provide evidence that these clade-associated restriction modification systems generate a differential barrier to DNA exchange consistent with the observed population structure. These findings have general implications for the emergence of lineage structure and virulence in recombining bacterial populations, and they could provide an evolutionary framework for the population biology of a number of other bacterial species that show contradictory population structure and dynamics.}, }
@article {pmid21366819, year = {2011}, author = {Le Fourn, C and Brasseur, G and Brochier-Armanet, C and Pieulle, L and Brioukhanov, A and Ollivier, B and Dolla, A}, title = {An oxygen reduction chain in the hyperthermophilic anaerobe Thermotoga maritima highlights horizontal gene transfer between Thermococcales and Thermotogales.}, journal = {Environmental microbiology}, volume = {13}, number = {8}, pages = {2132-2145}, doi = {10.1111/j.1462-2920.2011.02439.x}, pmid = {21366819}, issn = {1462-2920}, mesh = {Bacteria, Anaerobic/genetics/metabolism ; *Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Oxygen/*metabolism ; Phylogeny ; Thermococcales/classification/*genetics ; Thermotoga maritima/classification/enzymology/*genetics/*metabolism ; }, abstract = {The hyperthermophile Thermotoga maritima, although strictly anaerobic, is able to grow in the presence of low amounts of O(2). Here, we show that this bacterium consumes O(2) via a three-partner chain involving an NADH oxidoreductase (NRO), a rubredoxin (Rd) and a flavo-diiron protein (FprA) (locus tags: TM_0754, TM_0659 and TM_0755, respectively). In vitro experiments showed that the NADH-dependent O(2) consumption rate was 881.9 (± 106.7) mol O(2) consumed min(-1) per mol of FprA at 37°C and that water was the main end-product of the reaction. We propose that this O(2) reduction chain plays a central role in the O(2) tolerance of T. maritima. Phylogenetic analyses suggest that the genes coding for these three components were acquired by an ancestor of Thermotogales from an ancestor of Thermococcales via a single gene transfer. This event likely also involved two ROS scavenging enzymes (neelaredoxin and rubrerythrin) that are encoded by genes clustered with those coding for FprA, NRO and Rd in the ancestor of Thermococcales. Such genomic organization would have provided the ancestor of Thermotogales with a complete set of enzymes dedicated to O(2)-toxicity defence. Beside Thermotogales and Thermococcales, horizontal gene transfers have played a major role in disseminating these enzymes within the hyperthermophilic anaerobic prokaryotic communities, allowing them to cope with fluctuating oxidative conditions that exist in situ.}, }
@article {pmid21362638, year = {2011}, author = {Ané, C}, title = {Detecting phylogenetic breakpoints and discordance from genome-wide alignments for species tree reconstruction.}, journal = {Genome biology and evolution}, volume = {3}, number = {}, pages = {246-258}, pmid = {21362638}, issn = {1759-6653}, mesh = {Animals ; Bayes Theorem ; *Chromosome Breakpoints ; Computational Biology/*methods ; Computer Simulation ; Databases, Genetic ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Association Studies/*methods ; Humans ; Models, Genetic ; *Phylogeny ; Recombination, Genetic ; Sequence Alignment/*methods ; Sequence Analysis, DNA ; }, abstract = {With the easy acquisition of sequence data, it is now possible to obtain and align whole genomes across multiple related species or populations. In this work, I assess the performance of a statistical method to reconstruct the whole distribution of phylogenetic trees along the genome, estimate the proportion of the genome for which a given clade is true, and infer a concordance tree that summarizes the dominant vertical inheritance pattern. There are two main issues when dealing with whole-genome alignments, as opposed to multiple genes: the size of the data and the detection of recombination breakpoints. These breakpoints partition the genomic alignment into phylogenetically homogeneous loci, where sites within a given locus all share the same phylogenetic tree topology. To delimitate these loci, I describe here a method based on the minimum description length (MDL) principle, implemented with dynamic programming for computational efficiency. Simulations show that combining MDL partitioning with Bayesian concordance analysis provides an efficient and robust way to estimate both the vertical inheritance signal and the horizontal phylogenetic signal. The method performed well both in the presence of incomplete lineage sorting and in the presence of horizontal gene transfer. A high level of systematic bias was found here, highlighting the need for good individual tree building methods, which form the basis for more elaborate gene tree/species tree reconciliation methods.}, }
@article {pmid21361998, year = {2011}, author = {Chiura, HX and Kogure, K and Hagemann, S and Ellinger, A and Velimirov, B}, title = {Evidence for particle-induced horizontal gene transfer and serial transduction between bacteria.}, journal = {FEMS microbiology ecology}, volume = {76}, number = {3}, pages = {576-591}, doi = {10.1111/j.1574-6941.2011.01077.x}, pmid = {21361998}, issn = {1574-6941}, mesh = {Bacteriophages/physiology ; DNA, Bacterial/analysis/genetics ; Escherichia coli/*genetics ; *Gene Transfer, Horizontal ; Microbial Viability ; Microscopy, Electron, Transmission ; Particle Size ; Seawater/analysis ; *Transduction, Genetic ; }, abstract = {Incubation of the amino acid-deficient strain Escherichia coli AB1157 with particles harvested from an oligotrophic environment revealed evidence of horizontal gene transfer (HGT) with restoration of all deficiencies in revertant cells with frequencies up to 1.94 × 10(-5). None of the markers were preferentially transferred, indicating that the DNA transfer is performed by generalized transduction. The highest gene transfer frequencies were obtained for single markers, with values up to 1.04 × 10(-2). All revertants were able to produce particles of comparable size, appearing at the beginning of the stationary phase. Examination of the revertants using electron microscopy showed bud-like structures with electron-dense bodies. The particles that display the structural features of membrane vesicles were again infectious to E. coli AB1157, producing new infectious particles able to transduce genetic information, a phenomenon termed serial transduction. Thus, the <0.2-μm particle fraction from seawater contains a particle size fraction with high potential for gene transfer. Biased sinusoidal field gel electrophoresis indicated a DNA content for the particles of 370 kbp, which was higher than that of known membrane vesicles. These findings provide evidence of a new method of HGT, in which mobilizable DNA is trafficked from donor to recipient cells via particles.}, }
@article {pmid21361996, year = {2011}, author = {Silby, MW and Winstanley, C and Godfrey, SA and Levy, SB and Jackson, RW}, title = {Pseudomonas genomes: diverse and adaptable.}, journal = {FEMS microbiology reviews}, volume = {35}, number = {4}, pages = {652-680}, doi = {10.1111/j.1574-6976.2011.00269.x}, pmid = {21361996}, issn = {1574-6976}, mesh = {Adaptation, Physiological/*genetics ; Animals ; Base Sequence ; Biodegradation, Environmental ; DNA, Bacterial/genetics ; Evolution, Molecular ; Genetic Variation/*genetics ; Genome, Bacterial/*genetics ; Genomics/*methods ; Humans ; Insecta/microbiology ; Nitrogen Fixation ; Pest Control, Biological ; Phylogeny ; Plant Development ; Plants/microbiology ; Pseudomonas/classification/*genetics/metabolism/pathogenicity ; Virulence ; }, abstract = {Members of the genus Pseudomonas inhabit a wide variety of environments, which is reflected in their versatile metabolic capacity and broad potential for adaptation to fluctuating environmental conditions. Here, we examine and compare the genomes of a range of Pseudomonas spp. encompassing plant, insect and human pathogens, and environmental saprophytes. In addition to a large number of allelic differences of common genes that confer regulatory and metabolic flexibility, genome analysis suggests that many other factors contribute to the diversity and adaptability of Pseudomonas spp. Horizontal gene transfer has impacted the capability of pathogenic Pseudomonas spp. in terms of disease severity (Pseudomonas aeruginosa) and specificity (Pseudomonas syringae). Genome rearrangements likely contribute to adaptation, and a considerable complement of unique genes undoubtedly contributes to strain- and species-specific activities by as yet unknown mechanisms. Because of the lack of conserved phenotypic differences, the classification of the genus has long been contentious. DNA hybridization and genome-based analyses show close relationships among members of P. aeruginosa, but that isolates within the Pseudomonas fluorescens and P. syringae species are less closely related and may constitute different species. Collectively, genome sequences of Pseudomonas spp. have provided insights into pathogenesis and the genetic basis for diversity and adaptation.}, }
@article {pmid21359229, year = {2011}, author = {Kristiansson, E and Fick, J and Janzon, A and Grabic, R and Rutgersson, C and Weijdegård, B and Söderström, H and Larsson, DG}, title = {Pyrosequencing of antibiotic-contaminated river sediments reveals high levels of resistance and gene transfer elements.}, journal = {PloS one}, volume = {6}, number = {2}, pages = {e17038}, pmid = {21359229}, issn = {1932-6203}, mesh = {Anti-Bacterial Agents/*adverse effects ; Bacteria/drug effects/genetics ; *Biota ; DNA Transposable Elements/physiology ; *Drug Resistance, Bacterial/drug effects/genetics ; Gene Transfer, Horizontal/*drug effects/physiology ; Geologic Sediments/chemistry/*microbiology ; Humans ; Rivers/chemistry ; Sequence Analysis, DNA/*methods ; Water Microbiology ; Water Pollutants, Chemical/*adverse effects ; }, abstract = {The high and sometimes inappropriate use of antibiotics has accelerated the development of antibiotic resistance, creating a major challenge for the sustainable treatment of infections world-wide. Bacterial communities often respond to antibiotic selection pressure by acquiring resistance genes, i.e. mobile genetic elements that can be shared horizontally between species. Environmental microbial communities maintain diverse collections of resistance genes, which can be mobilized into pathogenic bacteria. Recently, exceptional environmental releases of antibiotics have been documented, but the effects on the promotion of resistance genes and the potential for horizontal gene transfer have yet received limited attention. In this study, we have used culture-independent shotgun metagenomics to investigate microbial communities in river sediments exposed to waste water from the production of antibiotics in India. Our analysis identified very high levels of several classes of resistance genes as well as elements for horizontal gene transfer, including integrons, transposons and plasmids. In addition, two abundant previously uncharacterized resistance plasmids were identified. The results suggest that antibiotic contamination plays a role in the promotion of resistance genes and their mobilization from environmental microbes to other species and eventually to human pathogens. The entire life-cycle of antibiotic substances, both before, under and after usage, should therefore be considered to fully evaluate their role in the promotion of resistance.}, }
@article {pmid21359176, year = {2011}, author = {Silver, AC and Williams, D and Faucher, J and Horneman, AJ and Gogarten, JP and Graf, J}, title = {Complex evolutionary history of the Aeromonas veronii group revealed by host interaction and DNA sequence data.}, journal = {PloS one}, volume = {6}, number = {2}, pages = {e16751}, pmid = {21359176}, issn = {1932-6203}, mesh = {Aeromonas/*genetics/growth &amp; development/pathogenicity/*physiology ; Animals ; Base Sequence ; DNA, Bacterial/genetics ; *Evolution, Molecular ; Genotype ; Gram-Negative Bacterial Infections/*genetics ; Host-Pathogen Interactions/*genetics ; Molecular Sequence Data ; Phenotype ; Phylogeny ; *Sequence Analysis, DNA ; Symbiosis/genetics/physiology ; }, abstract = {Aeromonas veronii biovar sobria, Aeromonas veronii biovar veronii, and Aeromonas allosaccharophila are a closely related group of organisms, the Aeromonas veronii Group, that inhabit a wide range of host animals as a symbiont or pathogen. In this study, the ability of various strains to colonize the medicinal leech as a model for beneficial symbiosis and to kill wax worm larvae as a model for virulence was determined. Isolates cultured from the leech out-competed other strains in the leech model, while most strains were virulent in the wax worms. Three housekeeping genes, recA, dnaJ and gyrB, the gene encoding chitinase, chiA, and four loci associated with the type three secretion system, ascV, ascFG, aexT, and aexU were sequenced. The phylogenetic reconstruction failed to produce one consensus tree that was compatible with most of the individual genes. The Approximately Unbiased test and the Genetic Algorithm for Recombination Detection both provided further support for differing evolutionary histories among this group of genes. Two contrasting tests detected recombination within aexU, ascFG, ascV, dnaJ, and gyrB but not in aexT or chiA. Quartet decomposition analysis indicated a complex recent evolutionary history for these strains with a high frequency of horizontal gene transfer between several but not among all strains. In this study we demonstrate that at least for some strains, horizontal gene transfer occurs at a sufficient frequency to blur the signal from vertically inherited genes, despite strains being adapted to distinct niches. Simply increasing the number of genes included in the analysis is unlikely to overcome this challenge in organisms that occupy multiple niches and can exchange DNA between strains specialized to different niches. Instead, the detection of genes critical in the adaptation to specific niches may help to reveal the physiological specialization of these strains.}, }
@article {pmid21357454, year = {2011}, author = {Menna, P and Hungria, M}, title = {Phylogeny of nodulation and nitrogen-fixation genes in Bradyrhizobium: supporting evidence for the theory of monophyletic origin, and spread and maintenance by both horizontal and vertical transfer.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {61}, number = {Pt 12}, pages = {3052-3067}, doi = {10.1099/ijs.0.028803-0}, pmid = {21357454}, issn = {1466-5034}, mesh = {Bacterial Proteins/*genetics/metabolism ; *Biological Evolution ; Bradyrhizobium/*classification/*genetics/isolation &amp; purification/physiology ; Fabaceae/microbiology/physiology ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Nitrogen Fixation ; Nitrogenase/*genetics/metabolism ; *Phylogeny ; Plant Root Nodulation ; Root Nodules, Plant/microbiology ; Symbiosis ; }, abstract = {Bacteria belonging to the genus Bradyrhizobium are capable of establishing symbiotic relationships with a broad range of plants belonging to the three subfamilies of the family Leguminosae (=Fabaceae), with the formation of specialized structures on the roots called nodules, where fixation of atmospheric nitrogen takes place. Symbiosis is under the control of finely tuned expression of common and host-specific nodulation genes and also of genes related to the assembly and activity of the nitrogenase, which, in Bradyrhizobium strains investigated so far, are clustered in a symbiotic island. Information about the diversity of these genes is essential to improve our current poor understanding of their origin, spread and maintenance and, in this study, we provide information on 40 Bradyrhizobium strains, mostly of tropical origin. For the nodulation trait, common (nodA), Bradyrhizobium-specific (nodY/K) and host-specific (nodZ) nodulation genes were studied, whereas for fixation ability, the diversity of nifH was investigated. In general, clustering of strains in all nod and nifH trees was similar and the Bradyrhizobium group could be clearly separated from other rhizobial genera. However, the congruence of nod and nif genes with ribosomal and housekeeping genes was low. nodA and nodY/K were not detected in three strains by amplification or hybridization with probes using Bradyrhizobium japonicum and Bradyrhizobium elkanii type strains, indicating the high diversity of these genes or that strains other than photosynthetic Bradyrhizobium must have alternative mechanisms to initiate the process of nodulation. For a large group of strains, the high diversity of nod genes (with an emphasis on nodZ), the low relationship between nod genes and the host legume, and some evidence of horizontal gene transfer might indicate strategies to increase host range. On the other hand, in a group of five symbionts of Acacia mearnsii, the high congruence between nod and ribosomal/housekeeping genes, in addition to shorter nodY/K sequences and the absence of nodZ, highlights a co-evolution process. Additionally, in a group of B. japonicum strains that were symbionts of soybean, vertical transfer seemed to represent the main genetic event. In conclusion, clustering of nodA and nifH gives additional support to the theory of monophyletic origin of the symbiotic genes in Bradyrhizobium and, in addition to the analysis of nodY/K and nodZ, indicates spread and maintenance of nod and nif genes through both vertical and horizontal transmission, apparently with the dominance of one or other of these events in some groups of strains.}, }
@article {pmid21356102, year = {2011}, author = {Sucgang, R and Kuo, A and Tian, X and Salerno, W and Parikh, A and Feasley, CL and Dalin, E and Tu, H and Huang, E and Barry, K and Lindquist, E and Shapiro, H and Bruce, D and Schmutz, J and Salamov, A and Fey, P and Gaudet, P and Anjard, C and Babu, MM and Basu, S and Bushmanova, Y and van der Wel, H and Katoh-Kurasawa, M and Dinh, C and Coutinho, PM and Saito, T and Elias, M and Schaap, P and Kay, RR and Henrissat, B and Eichinger, L and Rivero, F and Putnam, NH and West, CM and Loomis, WF and Chisholm, RL and Shaulsky, G and Strassmann, JE and Queller, DC and Kuspa, A and Grigoriev, IV}, title = {Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum.}, journal = {Genome biology}, volume = {12}, number = {2}, pages = {R20}, pmid = {21356102}, issn = {1474-760X}, support = {HG0022/HG/NHGRI NIH HHS/United States ; MC_U105115237/MRC_/Medical Research Council/United Kingdom ; HD39691/HD/NICHD NIH HHS/United States ; R01 GM087371/GM/NIGMS NIH HHS/United States ; MC_U105185859/MRC_/Medical Research Council/United Kingdom ; 1 T90 DA022885/DA/NIDA NIH HHS/United States ; BB/D013453/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 1 R90 DA023418/DA/NIDA NIH HHS/United States ; R01 GM064426-10/GM/NIGMS NIH HHS/United States ; R01 GM087371-04/GM/NIGMS NIH HHS/United States ; R01 GM064426/GM/NIGMS NIH HHS/United States ; BB/E016308/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; P01 HD039691/HD/NICHD NIH HHS/United States ; GM84383/GM/NIGMS NIH HHS/United States ; GM64426/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; *Biological Evolution ; Conserved Sequence/genetics ; Dictyostelium/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Speciation ; *Genome ; Genome Size ; Genomics/*methods ; Histidine Kinase ; Humans ; Microsatellite Repeats ; Molecular Sequence Data ; Phylogeny ; Polyketide Synthases/genetics ; Protein Kinases/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {BACKGROUND: The social amoebae (Dictyostelia) are a diverse group of Amoebozoa that achieve multicellularity by aggregation and undergo morphogenesis into fruiting bodies with terminally differentiated spores and stalk cells. There are four groups of dictyostelids, with the most derived being a group that contains the model species Dictyostelium discoideum.<br><br>RESULTS: We have produced a draft genome sequence of another group dictyostelid, Dictyostelium purpureum, and compare it to the D. discoideum genome. The assembly (8.41 &#xd7; coverage) comprises 799 scaffolds totaling 33.0 Mb, comparable to the D. discoideum genome size. Sequence comparisons suggest that these two dictyostelids shared a common ancestor approximately 400 million years ago. In spite of this divergence, most orthologs reside in small clusters of conserved synteny. Comparative analyses revealed a core set of orthologous genes that illuminate dictyostelid physiology, as well as differences in gene family content. Interesting patterns of gene conservation and divergence are also evident, suggesting function differences; some protein families, such as the histidine kinases, have undergone little functional change, whereas others, such as the polyketide synthases, have undergone extensive diversification. The abundant amino acid homopolymers encoded in both genomes are generally not found in homologous positions within proteins, so they are unlikely to derive from ancestral DNA triplet repeats. Genes involved in the social stage evolved more rapidly than others, consistent with either relaxed selection or accelerated evolution due to social conflict.<br><br>CONCLUSIONS: The findings from this new genome sequence and comparative analysis shed light on the biology and evolution of the Dictyostelia.}, }
@article {pmid21354209, year = {2011}, author = {Huang, F and Cao, S and Cui, X and Xiong, C and Wang, M and Lu, Y and Wang, W and Ye, J and Liu, X}, title = {Efficient gene delivery into fish cells by an improved recombinant baculovirus.}, journal = {Journal of virological methods}, volume = {173}, number = {2}, pages = {294-299}, doi = {10.1016/j.jviromet.2011.02.022}, pmid = {21354209}, issn = {1879-0984}, mesh = {Animals ; Baculoviridae/*genetics ; Cell Line ; Culture Media/chemistry ; Cytomegalovirus/genetics ; Fishes ; Flow Cytometry ; *Gene Transfer, Horizontal ; Genes, Reporter ; *Genetic Vectors ; Green Fluorescent Proteins/genetics/metabolism ; Promoter Regions, Genetic ; Transduction, Genetic/*methods ; }, abstract = {Studies on transduction of mammalian cells have shown that baculovirus can be used as an effective vector for gene delivery. However, previous studies have found the gene delivery efficiency to be very low in differentiated fish cells. In this study, an improved recombinant baculovirus, containing cytomegalovirus immediate-early (CMV-IE) promoter and an enhanced green fluorescent protein (EGFP) gene as the reporter gene, was constructed. The transduction efficiency of recombinant baculovirus in several fish cell lines was measured by flow cytometry (FCM) and the persistence of EGFP was monitored by fluorescence microscopy. The results demonstrated that baculovirus can mediate the high efficiency of gene delivery into differentiated fish cells. Furthermore, it was found that growth medium is superior to PBS as the surrounding solution to enhance the transduction efficiency in some fish cells. In addition, transgene expression can persist for a lengthy period in fish cells, and attained highest level several days later after transduction. This study suggest that the improved recombinant baculovirus can be an excellent gene delivery vector for fish cells and also providing new insights into the transduction of vertebrate cells with baculovirus.}, }
@article {pmid21354204, year = {2011}, author = {Pandeeti, EV and Chakka, D and Pandey, JP and Siddavattam, D}, title = {Indigenous organophosphate-degrading (opd) plasmid pCMS1 of Brevundimonasdiminuta is self-transmissible and plays a key role in horizontal mobility of the opd gene.}, journal = {Plasmid}, volume = {65}, number = {3}, pages = {226-231}, doi = {10.1016/j.plasmid.2011.02.003}, pmid = {21354204}, issn = {1095-9890}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Caulobacteraceae/*genetics ; Conjugation, Genetic/genetics ; Gene Order ; Gene Transfer, Horizontal ; Genes, Bacterial ; Plasmids/*genetics ; Pseudomonas putida/genetics ; }, abstract = {A fosmid library of the 66kb indigenous organophosphate-degrading (opd) plasmid pCMS1 of Brevundimonas diminuta was tagged with mini-transposon EZTn5 <R6Kγori/KAN-2>, to determine its sequence using transposon-specific primers. The sequence revealed the presence of a number of tra genes suggesting their role in conjugal transfer of pCMS1. Consistent with the presence of the tra genes, the B. diminuta plasmid, pCMS1::tet, generated by replacing the opd gene with opd::tet, served as a donor for transferring pCMS1::tet into recipient strain Pseudomonas putida. The self-transmissibility of the opd-containing plasmid pCMS1 and the existence of identical opd genes on otherwise dissimilar plasmids suggests a probable role of indigenous opd plasmids like pCMS1 in transferring the opd gene among soil bacteria.}, }
@article {pmid21353627, year = {2011}, author = {Dunny, GM and Johnson, CM}, title = {Regulatory circuits controlling enterococcal conjugation: lessons for functional genomics.}, journal = {Current opinion in microbiology}, volume = {14}, number = {2}, pages = {174-180}, pmid = {21353627}, issn = {1879-0364}, support = {R56 AI058134/AI/NIAID NIH HHS/United States ; AI58134/AI/NIAID NIH HHS/United States ; GM49530/GM/NIGMS NIH HHS/United States ; R01 GM049530/GM/NIGMS NIH HHS/United States ; R01 AI058134/AI/NIAID NIH HHS/United States ; R01 GM049530-26A1/GM/NIGMS NIH HHS/United States ; }, mesh = {*Conjugation, Genetic ; Enterococcus faecalis/genetics/*physiology ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Pheromones/metabolism ; Plasmids/metabolism ; Signal Transduction ; }, abstract = {The regulatory system controlling pheromone-induced plasmid transfer in Enterococcus faecalis is the most thoroughly studied genetic system of this species. Transcription initiation from the target promoter is controlled by a pheromone receptor/repressor protein whose activity is determined by its interaction with two peptide signaling molecules that compete for the same binding site, but have opposing effects on the activity of the receptor protein. For the system to function as a sensitive and robust biological switch, several additional levels of post-transcriptional regulation are also required. Expression of important functions encoded within the enterococcal core genome may also be controlled by multilayered regulatory circuitry. The pheromone system may serve as a useful paradigm to guide comprehensive functional genomic analysis of E. faecalis.}, }
@article {pmid21350630, year = {2010}, author = {Oshima, K and Ueda, K and Beppu, T and Nishida, H}, title = {Unique Evolution of Symbiobacterium thermophilum Suggested from Gene Content and Orthologous Protein Sequence Comparisons.}, journal = {International journal of evolutionary biology}, volume = {2011}, number = {}, pages = {376831}, pmid = {21350630}, issn = {2090-052X}, abstract = {Comparisons of gene content and orthologous protein sequence constitute a major strategy in whole-genome comparison studies. It is expected that horizontal gene transfer between phylogenetically distant organisms and lineage-specific gene loss have greater influence on gene content-based phylogenetic analysis than orthologous protein sequence-based phylogenetic analysis. To determine the evolution of the syntrophic bacterium Symbiobacterium thermophilum, we analyzed phylogenetic relationships among Clostridia on the basis of gene content and orthologous protein sequence comparisons. These comparisons revealed that these 2 phylogenetic relationships are topologically different. Our results suggest that each Clostridia has a species-specific gene content because frequent genetic exchanges or gene losses have occurred during evolution. Specifically, the phylogenetic positions of syntrophic Clostridia were different between these 2 phylogenetic analyses, suggesting that large diversity in the living environments may cause the observed species-specific gene content. S. thermophilum occupied the most distant position from the other syntrophic Clostridia in the gene content-based phylogenetic tree. We identified 32 genes (14 under relaxed selection and 18 under functional constraint) evolving under Symbiobacterium-specific selection on the basis of synonymous-to-nonsynonymous substitution ratios. Five of the 14 genes under relaxed selection are related to transcription. In contrast, none of the 18 genes under functional constraint is related to transcription.}, }
@article {pmid21347612, year = {2011}, author = {Gomolplitinant, KM and Saier, MH}, title = {Evolution of the oligopeptide transporter family.}, journal = {The Journal of membrane biology}, volume = {240}, number = {2}, pages = {89-110}, pmid = {21347612}, issn = {1432-1424}, support = {R01 GM077402/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Archaea/genetics ; Archaeal Proteins/genetics ; Bacteria/genetics ; Bacterial Proteins/genetics ; Computational Biology/*methods ; Conserved Sequence/genetics ; Dictyosteliida/genetics ; *Evolution, Molecular ; Fungal Proteins/genetics ; Fungi/genetics ; Membrane Transport Proteins/chemistry/*genetics ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/genetics ; Plants/genetics ; Protozoan Proteins/genetics ; Sequence Alignment ; Software ; }, abstract = {The oligopeptide transporter (OPT) family of peptide and iron-siderophore transporters includes members from both prokaryotes and eukaryotes but with restricted distribution in the latter domain. Eukaryotic members were found only in fungi and plants with a single slime mold homologue clustering with the fungal proteins. All functionally characterized eukaryotic peptide transporters segregate from the known iron-siderophore transporters on a phylogenetic tree. Prokaryotic members are widespread, deriving from many different phyla. Although they belong only to the iron-siderophore subdivision, genome context analyses suggest that many of them are peptide transporters. OPT family proteins have 16 or occasionally 17 transmembrane-spanning α-helical segments (TMSs). We provide statistical evidence that the 16-TMS topology arose via three sequential duplication events followed by a gene-fusion event for proteins with a seventeenth TMS. The proposed pathway is as follows: 2 TMSs → 4 TMSs → 8 TMSs → 16 TMSs → 17 TMSs. The seventeenth C-terminal TMS, which probably arose just once, is found in just one phylogenetic group of these homologues. Analyses for orthology revealed that a few phylogenetic clusters consist exclusively of orthologues but most have undergone intermixing, suggestive of horizontal transfer. It appears that in this family horizontal gene transfer was frequent among prokaryotes, rare among eukaryotes and largely absent between prokaryotes and eukaryotes as well as between plants and fungi. These observations provide guides for future structural and functional analyses of OPT family members.}, }
@article {pmid21346789, year = {2011}, author = {Brochier-Armanet, C and Deschamps, P and López-García, P and Zivanovic, Y and Rodríguez-Valera, F and Moreira, D}, title = {Complete-fosmid and fosmid-end sequences reveal frequent horizontal gene transfers in marine uncultured planktonic archaea.}, journal = {The ISME journal}, volume = {5}, number = {8}, pages = {1291-1302}, pmid = {21346789}, issn = {1751-7370}, mesh = {Archaea/classification/*genetics/physiology ; Crenarchaeota/classification/genetics ; Euryarchaeota/classification/genetics ; Gene Library ; *Gene Transfer, Horizontal ; Genes, Archaeal ; Metagenomics ; Oceans and Seas ; Phylogeny ; Plankton/classification/genetics ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The extent of horizontal gene transfer (HGT) among marine pelagic prokaryotes and the role that HGT may have played in their adaptation to this particular environment remain open questions. This is partly due to the paucity of cultured species and genomic information for many widespread groups of marine bacteria and archaea. Molecular studies have revealed a large diversity and relative abundance of marine planktonic archaea, in particular of Thaumarchaeota (also known as group I Crenarchaeota) and Euryarchaeota of groups II and III, but only one species (the thaumarchaeote Candidatus Nitrosopumilus maritimus) has been isolated in pure culture so far. Therefore, metagenomics remains the most powerful approach to study these environmental groups. To investigate the impact of HGT in marine archaea, we carried out detailed phylogenetic analyses of all open reading frames of 21 archaeal 16S rRNA gene-containing fosmids and, to extend our analysis to other genomic regions, also of fosmid-end sequences of 12 774 fosmids from three different deep-sea locations (South Atlantic and Adriatic Sea at 1000 m depth, and Ionian Sea at 3000 m depth). We found high HGT rates in both marine planktonic Thaumarchaeota and Euryarchaeota, with remarkable converging values estimated from complete-fosmid and fosmid-end sequence analysis (25 and 21% of the genes, respectively). Most HGTs came from bacterial donors (mainly from Proteobacteria, Firmicutes and Chloroflexi) but also from other archaea and eukaryotes. Phylogenetic analyses showed that in most cases HGTs are shared by several representatives of the studied groups, implying that they are ancient and have been conserved over relatively long evolutionary periods. This, together with the functions carried out by these acquired genes (mostly related to energy metabolism and transport of metabolites across membranes), suggests that HGT has played an important role in the adaptation of these archaea to the cold and nutrient-depleted deep marine environment.}, }
@article {pmid21343180, year = {2011}, author = {Tuller, T and Girshovich, Y and Sella, Y and Kreimer, A and Freilich, S and Kupiec, M and Gophna, U and Ruppin, E}, title = {Association between translation efficiency and horizontal gene transfer within microbial communities.}, journal = {Nucleic acids research}, volume = {39}, number = {11}, pages = {4743-4755}, pmid = {21343180}, issn = {1362-4962}, support = {AI056034/AI/NIAID NIH HHS/United States ; GM07104/GM/NIGMS NIH HHS/United States ; }, mesh = {Codon ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; *Protein Biosynthesis ; RNA, Transfer/genetics ; }, abstract = {Horizontal gene transfer (HGT) is a major force in microbial evolution. Previous studies have suggested that a variety of factors, including restricted recombination and toxicity of foreign gene products, may act as barriers to the successful integration of horizontally transferred genes. This study identifies an additional central barrier to HGT-the lack of co-adaptation between the codon usage of the transferred gene and the tRNA pool of the recipient organism. Analyzing the genomic sequences of more than 190 microorganisms and the HGT events that have occurred between them, we show that the number of genes that were horizontally transferred between organisms is positively correlated with the similarity between their tRNA pools. Those genes that are better adapted to the tRNA pools of the target genomes tend to undergo more frequent HGT. At the community (or environment) level, organisms that share a common ecological niche tend to have similar tRNA pools. These results remain significant after controlling for diverse ecological and evolutionary parameters. Our analysis demonstrates that there are bi-directional associations between the similarity in the tRNA pools of organisms and the number of HGT events occurring between them. Similar tRNA pools between a donor and a host tend to increase the probability that a horizontally acquired gene will become fixed in its new genome. Our results also suggest that frequent HGT may be a homogenizing force that increases the similarity in the tRNA pools of organisms within the same community.}, }
@article {pmid21342537, year = {2011}, author = {Scholl, EH and Bird, DM}, title = {Computational and phylogenetic validation of nematode horizontal gene transfer.}, journal = {BMC biology}, volume = {9}, number = {}, pages = {9}, pmid = {21342537}, issn = {1741-7007}, mesh = {Animals ; Cellulase/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Helminth ; Molecular Sequence Data ; Nematoda/classification/*genetics ; Phylogeny ; }, abstract = {Sequencing of expressed genes has shown that nematodes, particularly the plant-parasitic nematodes, have genes purportedly acquired from other kingdoms by horizontal gene transfer. The prevailing orthodoxy is that such transfer has been a driving force in the evolution of niche specificity, and a recent paper in BMC Evolutionary Biology that presents a detailed phylogenetic analysis of cellulase genes in the free-living nematode Pristionchus pacificus at the species, genus and family levels substantiates this hypothesis.}, }
@article {pmid21337329, year = {2011}, author = {Chang, CH and Cheng, WJ and Chen, SY and Kao, MC and Chiang, CJ and Chao, YP}, title = {Engineering of Escherichia coli for targeted delivery of transgenes to HER2/neu-positive tumor cells.}, journal = {Biotechnology and bioengineering}, volume = {108}, number = {7}, pages = {1662-1672}, doi = {10.1002/bit.23095}, pmid = {21337329}, issn = {1097-0290}, mesh = {Antibodies/immunology/metabolism ; Cell Adhesion ; Cell Line, Tumor ; Escherichia coli/*genetics/*physiology ; *Gene Transfer Techniques ; *Gene Transfer, Horizontal ; Humans ; Protein Binding ; Receptor, ErbB-2/immunology/metabolism ; *Transgenes ; }, abstract = {Targeting of non-phagocytic tumor cells and prompt release of gene cargos upon entry into tumors are two limiting steps in the bacterial gene delivery path. To tackle these problems, the non-pathogenic Escherichia coli strain BL21(DE3) was engineered to display the anti-HER2/neu affibody on the surface. After co-incubation with tumor cells for 3 h, the anti-HER2/neu affibody-presenting E. coli strain was selectively internalized into HER2/neu-positive SKBR-3 cells. The invasion efficiency reached as high as 30%. Furthermore, the bacteria were equipped with the phage ϕX174 lysin gene E-mediated autolysis system. Carrying the transgene (e.g., eukaryotic green fluorescent protein, GFP), the tumor-targeting bacteria were subjected to the thermal shock to trigger the autolysis system upon entry into HER2/neu-positive cells. Flow cytometric analysis revealed that 3% of infected cells expressed GFP 24 h post thermal induction. Overall, the results show a promise of the proposed approach for developing bacteria as a delivery carrier.}, }
@article {pmid21336962, year = {2011}, author = {Wallau, GL and Hua-Van, A and Capy, P and Loreto, EL}, title = {The evolutionary history of mariner-like elements in Neotropical drosophilids.}, journal = {Genetica}, volume = {139}, number = {3}, pages = {327-338}, pmid = {21336962}, issn = {1573-6857}, mesh = {Animals ; DNA Transposable Elements/*genetics ; Drosophilidae/classification/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Phylogeny ; Time Factors ; }, abstract = {The evolutionary history of mariner-like elements (MLEs) in 49 mainly Neotropical drosophilid species is described. So far, the investigations about the distribution of MLEs were performed mainly using hybridization assays with the Mos1 element (the first mariner active element described) in a widely range of drosophilid species and these sequences were found principally in species that arose in Afrotropical and Sino-Indian regions. Our analysis in mainly Neotropical drosophilid species shows that twenty-three species presented MLEs from three different subfamilies in their genomes: eighteen species had MLEs from subfamily mellifera, fifteen from subfamily mauritiana and three from subfamily irritans. Eleven of these species exhibited elements from more than one subfamily in their genome. In two subfamilies, the analyzed coding region was uninterrupted and contained conserved catalytic motifs. This suggests that these sequences were probably derived from active elements. The species with these putative active elements are Drosophila mediopunctata and D. busckii for the mauritiana subfamily, and D. paramediostriata for the mellifera subfamily. The phylogenetic analysis of MLE, shows a complex evolutionary pattern, exhibiting vertical transfer, stochastic loss and putative events of horizontal transmission occurring between different Drosophilidae species, and even those belonging to more distantly related taxa such as Bactrocera tryoni (Tephritidae family), Sphyracephala europaea (Diopsoidea superfamily) and Buenoa sp. (Hemiptera order). Moreover, our data show that the distribution of MLEs is not restricted to Afrotropical and Sino-Indian species. Conversely, these TEs are also widely distributed in drosophilid species arisen in the Neotropical region.}, }
@article {pmid21335390, year = {2011}, author = {Singer, E and Webb, EA and Nelson, WC and Heidelberg, JF and Ivanova, N and Pati, A and Edwards, KJ}, title = {Genomic potential of Marinobacter aquaeolei, a biogeochemical "opportunitroph".}, journal = {Applied and environmental microbiology}, volume = {77}, number = {8}, pages = {2763-2771}, pmid = {21335390}, issn = {1098-5336}, mesh = {DNA, Bacterial/chemistry/genetics ; *Genome, Bacterial ; Iron/metabolism ; Marinobacter/chemistry/*genetics/metabolism ; Nitrogen/metabolism ; Organophosphonates/metabolism ; Oxygen Consumption ; Phylogeny ; Sequence Analysis, DNA ; Signal Transduction ; Urea/metabolism ; }, abstract = {The genus of Marinobacter is one of the most ubiquitous in the global oceans and assumed to significantly impact various biogeochemical cycles. The genome structure and content of Marinobacter aquaeolei VT8 was analyzed and compared with those from other organisms with diverse adaptive strategies. Here, we report the many "opportunitrophic" genetic characteristics and strategies that M. aquaeolei has adopted to promote survival under various environmental conditions. Genome analysis revealed its metabolic potential to utilize oxygen and nitrate as terminal electron acceptors, iron as an electron donor, and urea, phosphonate, and various hydrocarbons as alternative N, P, and C sources, respectively. Miscellaneous sensory and defense mechanisms, apparently acquired via horizontal gene transfer, are involved in the perception of environmental fluctuations and antibiotic, phage, toxin, and heavy metal resistance, enabling survival under adverse conditions, such as oil-polluted water. Multiple putative integrases, transposases, and plasmids appear to have introduced additional metabolic potential, such as phosphonate degradation. The genomic potential of M. aquaeolei and its similarity to other opportunitrophs are consistent with its cosmopolitan occurrence in diverse environments and highly variable lifestyles.}, }
@article {pmid21334300, year = {2011}, author = {Richards, TA}, title = {Genome evolution: horizontal movements in the fungi.}, journal = {Current biology : CB}, volume = {21}, number = {4}, pages = {R166-8}, doi = {10.1016/j.cub.2011.01.028}, pmid = {21334300}, issn = {1879-0445}, mesh = {*Biological Evolution ; Energy Metabolism ; Gene Transfer, Horizontal/*physiology ; *Genome, Fungal ; Multigene Family ; Phylogeny ; }, abstract = {Fungi possess robust cell walls and do not engulf prey cells by phagotrophy. As a consequence they are thought to be relatively immune from the invasion of foreign genes. Nonetheless, a growing body of evidence suggests gene transfer has amended the metabolic networks of many fungal species.}, }
@article {pmid21334091, year = {2011}, author = {Dunning Hotopp, JC}, title = {Horizontal gene transfer between bacteria and animals.}, journal = {Trends in genetics : TIG}, volume = {27}, number = {4}, pages = {157-163}, pmid = {21334091}, issn = {0168-9525}, support = {DP2 OD007372/OD/NIH HHS/United States ; DP2 OD007372-01/OD/NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*genetics ; Biological Evolution ; *Gene Transfer, Horizontal ; Genome ; Humans ; }, abstract = {Horizontal gene transfer is increasingly described between bacteria and animals. Such transfers that are vertically inherited have the potential to influence the evolution of animals. One classic example is the transfer of DNA from mitochondria and chloroplasts to the nucleus after the acquisition of these organelles by eukaryotes. Even today, many of the described instances of bacteria-to-animal transfer occur as part of intimate relationships such as those of endosymbionts and their invertebrate hosts, particularly insects and nematodes, while numerous transfers are also found in asexual animals. Both of these observations are consistent with modern evolutionary theory, in particular the serial endosymbiotic theory and Muller's ratchet. Although it is tempting to suggest that these particular lifestyles promote horizontal gene transfer, it is difficult to ascertain given the nonrandom sampling of animal genome sequencing projects and the lack of a systematic analysis of animal genomes for such transfers.}, }
@article {pmid21330111, year = {2011}, author = {López-Cerero, L and Egea, P and Serrano, L and Navarro, D and Mora, A and Blanco, J and Doi, Y and Paterson, DL and Rodríguez-Baño, J and Pascual, A}, title = {Characterisation of clinical and food animal Escherichia coli isolates producing CTX-M-15 extended-spectrum β-lactamase belonging to ST410 phylogroup A.}, journal = {International journal of antimicrobial agents}, volume = {37}, number = {4}, pages = {365-367}, doi = {10.1016/j.ijantimicag.2011.01.001}, pmid = {21330111}, issn = {1872-7913}, mesh = {Base Sequence ; DNA Primers ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/classification/enzymology/*isolation &amp; purification ; *Food Microbiology ; Nucleic Acid Hybridization ; Polymerase Chain Reaction ; beta-Lactamases/*biosynthesis ; }, abstract = {Seven phylogroup A CTX-M-15-producing Escherichia coli isolates recovered from clinical and meat samples were further characterised. All of them belonged to sequence type ST410. Only 2 of the 22 virulence genes investigated were detected. All isolates carried the fimH gene encoding type 1 fimbriae, and five isolates harboured the iucD gene encoding aerobactin siderophore. A group of five isolates showed 81.2% similarity by pulsed-field gel electrophoresis (PFGE), comprising three clinical isolates belonging to ONT:H9 and two food isolates belonging to O55:H9. Different HpaI digestion patterns were observed for plasmids, but all of them belonged to IncFIB group and harboured bla(CTX-M-15) associated with bla(OXA-1), bla(TEM), tetA, catB3 and aac(6')-Ib surrounded by an identical genetic environment. These findings showed the possibility of lateral gene transfer of bla(CTX-M-15) as well as other antibiotic resistance determinants between low-virulence food and clinical isolates.}, }
@article {pmid21328413, year = {2011}, author = {Gill, EE and Brinkman, FS}, title = {The proportional lack of archaeal pathogens: Do viruses/phages hold the key?.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {33}, number = {4}, pages = {248-254}, pmid = {21328413}, issn = {1521-1878}, mesh = {Archaea/genetics/*pathogenicity/virology ; Archaeal Viruses/genetics/metabolism ; Bacteria/genetics/virology ; Bacteriophages/genetics/metabolism ; Biological Evolution ; Communicable Diseases/*microbiology ; Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; Humans ; Phylogeny ; Receptors, Virus/metabolism ; Virulence ; Virulence Factors/genetics ; }, abstract = {Although Archaea inhabit the human body and possess some characteristics of pathogens, there is a notable lack of pathogenic archaeal species identified to date. We hypothesize that the scarcity of disease-causing Archaea is due, in part, to mutually-exclusive phage and virus populations infecting Bacteria and Archaea, coupled with an association of bacterial virulence factors with phages or mobile elements. The ability of bacterial phages to infect Bacteria and then use them as a vehicle to infect eukaryotes may be difficult for archaeal viruses to evolve independently. Differences in extracellular structures between Bacteria and Archaea would make adsorption of bacterial phage particles onto Archaea (i.e. horizontal transfer of virulence) exceedingly hard. If phage and virus populations are indeed exclusive to their respective host Domains, this has important implications for both the evolution of pathogens and approaches to infectious disease control.}, }
@article {pmid21326607, year = {2011}, author = {Erauso, G and Lakhal, F and Bidault-Toffin, A and Le Chevalier, P and Bouloc, P and Paillard, C and Jacq, A}, title = {Evidence for the role of horizontal transfer in generating pVT1, a large mosaic conjugative plasmid from the clam pathogen, Vibrio tapetis.}, journal = {PloS one}, volume = {6}, number = {2}, pages = {e16759}, pmid = {21326607}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; Bivalvia/*microbiology ; Cloning, Molecular ; Conjugation, Genetic/*genetics ; Gene Dosage ; Gene Transfer, Horizontal/*physiology ; Models, Genetic ; Mosaicism ; Phylogeny ; Plasmids/*genetics ; Sequence Analysis, DNA ; Vibrio/*genetics/pathogenicity ; Vibrio Infections/genetics/microbiology/veterinary ; }, abstract = {The marine bacterium Vibrio tapetis is the causative agent of the brown ring disease, which affects the clam Ruditapes philippinarum and causes heavy economic losses in North of Europe and in Eastern Asia. Further characterization of V. tapetis isolates showed that all the investigated strains harbored at least one large plasmid. We determined the sequence of the 82,266 bp plasmid pVT1 from the CECT4600(T) reference strain and analyzed its genetic content. pVT1 is a mosaic plasmid closely related to several conjugative plasmids isolated from Vibrio vulnificus strains and was shown to be itself conjugative in Vibrios. In addition, it contains DNA regions that have similarity with several other plasmids from marine bacteria (Vibrio sp., Shewanella sp., Listonella anguillarum and Photobacterium profundum). pVT1 contains a number of mobile elements, including twelve Insertion Sequences or inactivated IS genes and an RS1 phage element related to the CTXphi phage of V. cholerae. The genetic organization of pVT1 underscores an important role of horizontal gene transfer through conjugative plasmid shuffling and transposition events in the acquisition of new genetic resources and in generating the pVT1 modular organization. In addition, pVT1 presents a copy number of 9, relatively high for a conjugative plasmid, and appears to belong to a new type of replicon, which may be specific to Vibrionaceae and Shewanelleacae.}, }
@article {pmid21325040, year = {2011}, author = {Anderson, MT and Seifert, HS}, title = {Opportunity and means: horizontal gene transfer from the human host to a bacterial pathogen.}, journal = {mBio}, volume = {2}, number = {1}, pages = {e00005-11}, pmid = {21325040}, issn = {2150-7511}, support = {F32 AI080083/AI/NIAID NIH HHS/United States ; R01 AI044239/AI/NIAID NIH HHS/United States ; R37 AI033493/AI/NIAID NIH HHS/United States ; F32AI080083./AI/NIAID NIH HHS/United States ; }, mesh = {Base Sequence ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Gonorrhea/*genetics/microbiology ; *Host-Pathogen Interactions ; Humans ; *Long Interspersed Nucleotide Elements ; Molecular Sequence Data ; Neisseria gonorrhoeae/*genetics ; }, abstract = {The acquisition and incorporation of genetic material between nonmating species, or horizontal gene transfer (HGT), has been frequently described for phylogenetically related organisms, but far less evidence exists for HGT between highly divergent organisms. Here we report the identification and characterization of a horizontally transferred fragment of the human long interspersed nuclear element L1 to the genome of the strictly human pathogen Neisseria gonorrhoeae. A 685-bp sequence exhibiting 98 to 100% identity to copies of the human L1 element was identified adjacent to the irg4 gene in some N. gonorrhoeae genomes. The L1 fragment was observed in ~11% of the N. gonorrhoeae population sampled but was not detected in Neisseria meningitidis or commensal Neisseria isolates. In addition, N. gonorrhoeae transcripts containing the L1 sequence were detected by reverse transcription-PCR, indicating that an L1-derived gene product may be produced. The high degree of identity between human and gonococcal L1 sequences, together with the absence of L1 sequences from related Neisseria species, indicates that this HGT event occurred relatively recently in evolutionary history. The identification of L1 sequences in N. gonorrhoeae demonstrates that HGT can occur between a mammalian host and a resident bacterium, which has important implications for the coevolution of both humans and their associated microorganisms.}, }
@article {pmid21318865, year = {2011}, author = {Michael, AJ}, title = {Exploring polyamine biosynthetic diversity through comparative and functional genomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {720}, number = {}, pages = {39-50}, doi = {10.1007/978-1-61779-034-8_2}, pmid = {21318865}, issn = {1940-6029}, mesh = {Acyltransferases/metabolism ; Alanine Racemase/metabolism ; Animals ; Biosynthetic Pathways/*genetics ; Genomics/*methods ; Humans ; Polyamines/*metabolism ; Spermidine Synthase/metabolism ; }, abstract = {The existence of multiple, alternative pathways for polyamine biosynthesis, and the presence of alternative polyamine structural analogs, is an indication of the physiological importance of polyamines and their long evolutionary history. Polyamine biosynthesis is modular: diamines are synthesized directly or indirectly from amino acids, and triamines are synthesized from diamines by transfer of aminopropyl, carboxyaminopropyl, or aminobutyl groups to the diamine. Diversification of polyamine biosynthesis has depended on gene duplication and functional divergence, on gene fusion, and on horizontal gene transfer. Four examples of polyamine biosynthetic diversification are presented here with a discussion of methodological and conceptual approaches for identification of new pathways.}, }
@article {pmid21318188, year = {2011}, author = {Schjørring, S and Krogfelt, KA}, title = {Assessment of bacterial antibiotic resistance transfer in the gut.}, journal = {International journal of microbiology}, volume = {2011}, number = {}, pages = {312956}, pmid = {21318188}, issn = {1687-9198}, abstract = {We assessed horizontal gene transfer between bacteria in the gastrointestinal (GI) tract. During the last decades, the emergence of antibiotic resistant strains and treatment failures of bacterial infections have increased the public awareness of antibiotic usage. The use of broad spectrum antibiotics creates a selective pressure on the bacterial flora, thus increasing the emergence of multiresistant bacteria, which results in a vicious circle of treatments and emergence of new antibiotic resistant bacteria. The human gastrointestinal tract is a massive reservoir of bacteria with a potential for both receiving and transferring antibiotic resistance genes. The increased use of fermented food products and probiotics, as food supplements and health promoting products containing massive amounts of bacteria acting as either donors and/or recipients of antibiotic resistance genes in the human GI tract, also contributes to the emergence of antibiotic resistant strains. This paper deals with the assessment of antibiotic resistance gene transfer occurring in the gut.}, }
@article {pmid21317332, year = {2011}, author = {Zheng, Q and Zhang, R and Jiao, N}, title = {Genome sequence of Citromicrobium strain JLT1363, isolated from the South China Sea.}, journal = {Journal of bacteriology}, volume = {193}, number = {8}, pages = {2074-2075}, pmid = {21317332}, issn = {1098-5530}, mesh = {China ; DNA, Bacterial/*chemistry/*genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Molecular Sequence Data ; Recombination, Genetic ; Seawater/microbiology ; Sequence Analysis, DNA ; Sphingomonadaceae/*genetics/isolation &amp; purification ; }, abstract = {Citromicrobium is a member of the alpha-4 subcluster in the Alphaproteobacteria and is identified as a typical aerobic anoxygenic phototrophic bacterium (AAPB). Here we report the draft genome sequence of a non-AAPB strain, Citromicrobium sp. JLT1363. The genome sequence reveals a multimechanism of horizontal gene transfer, as well.}, }
@article {pmid21310089, year = {2011}, author = {Haiko, J and Laakkonen, L and Westerlund-Wikström, B and Korhonen, TK}, title = {Molecular adaptation of a plant-bacterium outer membrane protease towards plague virulence factor Pla.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {43}, pmid = {21310089}, issn = {1471-2148}, mesh = {Adhesins, Bacterial/genetics ; Amino Acid Sequence ; Bacterial Outer Membrane Proteins/*genetics ; Cell Line ; DNA, Bacterial/genetics ; Escherichia coli/genetics ; Evolution, Molecular ; Humans ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Plasminogen/metabolism ; Plasminogen Activators/genetics ; Protein Structure, Tertiary ; Sequence Alignment ; Serine Endopeptidases/*genetics ; Virulence ; Virulence Factors/*genetics ; Yersinia pestis/*genetics/pathogenicity ; alpha-2-Antiplasmin/metabolism ; }, abstract = {BACKGROUND: Omptins are a family of outer membrane proteases that have spread by horizontal gene transfer in Gram-negative bacteria that infect vertebrates or plants. Despite structural similarity, the molecular functions of omptins differ in a manner that reflects the life style of their host bacteria. To simulate the molecular adaptation of omptins, we applied site-specific mutagenesis to make Epo of the plant pathogenic Erwinia pyrifoliae exhibit virulence-associated functions of its close homolog, the plasminogen activator Pla of Yersinia pestis. We addressed three virulence-associated functions exhibited by Pla, i.e., proteolytic activation of plasminogen, proteolytic degradation of serine protease inhibitors, and invasion into human cells.<br><br>RESULTS: Pla and Epo expressed in Escherichia coli are both functional endopeptidases and cleave human serine protease inhibitors, but Epo failed to activate plasminogen and to mediate invasion into a human endothelial-like cell line. Swapping of ten amino acid residues at two surface loops of Pla and Epo introduced plasminogen activation capacity in Epo and inactivated the function in Pla. We also compared the structure of Pla and the modeled structure of Epo to analyze the structural variations that could rationalize the different proteolytic activities. Epo-expressing bacteria managed to invade human cells only after all extramembranous residues that differ between Pla and Epo and the first transmembrane &#x3b2;-strand had been changed.<br><br>CONCLUSIONS: We describe molecular adaptation of a protease from an environmental setting towards a virulence factor detrimental for humans. Our results stress the evolvability of bacterial &#x3b2;-barrel surface structures and the environment as a source of progenitor virulence molecules of human pathogens.}, }
@article {pmid21304512, year = {2011}, author = {Slamovits, CH and Okamoto, N and Burri, L and James, ER and Keeling, PJ}, title = {A bacterial proteorhodopsin proton pump in marine eukaryotes.}, journal = {Nature communications}, volume = {2}, number = {}, pages = {183}, pmid = {21304512}, issn = {2041-1723}, support = {MOP 84265//Canadian Institutes of Health Research/Canada ; }, mesh = {Amino Acid Sequence ; Base Sequence ; *Biological Evolution ; Blotting, Western ; Dinoflagellida/*genetics/metabolism ; Expressed Sequence Tags ; Fluorescent Antibody Technique ; Gene Transfer, Horizontal/*genetics ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Protein Structure, Secondary ; Proton Pumps/genetics/*metabolism ; Rhodopsin/genetics/*metabolism ; Rhodopsins, Microbial ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Proteorhodopsins are light-driven proton pumps involved in widespread phototrophy. Discovered in marine proteobacteria just 10 years ago, proteorhodopsins are now known to have been spread by lateral gene transfer across diverse prokaryotes, but are curiously absent from eukaryotes. In this study, we show that proteorhodopsins have been acquired by horizontal gene transfer from bacteria at least twice independently in dinoflagellate protists. We find that in the marine predator Oxyrrhis marina, proteorhodopsin is indeed the most abundantly expressed nuclear gene and its product localizes to discrete cytoplasmic structures suggestive of the endomembrane system. To date, photosystems I and II have been the only known mechanism for transducing solar energy in eukaryotes; however, it now appears that some abundant zooplankton use this alternative pathway to harness light to power biological functions.}, }
@article {pmid21303508, year = {2011}, author = {Georgiades, K and Merhej, V and El Karkouri, K and Raoult, D and Pontarotti, P}, title = {Gene gain and loss events in Rickettsia and Orientia species.}, journal = {Biology direct}, volume = {6}, number = {}, pages = {6}, pmid = {21303508}, issn = {1745-6150}, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Genome, Bacterial/genetics ; Orientia tsutsugamushi/*genetics ; Phylogeny ; Rickettsia/*genetics ; Species Specificity ; }, abstract = {BACKGROUND: Genome degradation is an ongoing process in all members of the Rickettsiales order, which makes these bacterial species an excellent model for studying reductive evolution through interspecies variation in genome size and gene content. In this study, we evaluated the degree to which gene loss shaped the content of some Rickettsiales genomes. We shed light on the role played by horizontal gene transfers in the genome evolution of Rickettsiales.<br><br>RESULTS: Our phylogenomic tree, based on whole-genome content, presented a topology distinct from that of the whole core gene concatenated phylogenetic tree, suggesting that the gene repertoires involved have different evolutionary histories. Indeed, we present evidence for 3 possible horizontal gene transfer events from various organisms to Orientia and 6 to Rickettsia spp., while we also identified 3 possible horizontal gene transfer events from Rickettsia and Orientia to other bacteria. We found 17 putative genes in Rickettsia spp. that are probably the result of de novo gene creation; 2 of these genes appear to be functional. On the basis of these results, we were able to reconstruct the gene repertoires of "proto-Rickettsiales" and "proto-Rickettsiaceae", which correspond to the ancestors of Rickettsiales and Rickettsiaceae, respectively. Finally, we found that 2,135 genes were lost during the evolution of the Rickettsiaceae to an intracellular lifestyle.<br><br>CONCLUSIONS: Our phylogenetic analysis allowed us to track the gene gain and loss events occurring in bacterial genomes during their evolution from a free-living to an intracellular lifestyle. We have shown that the primary mechanism of evolution and specialization in strictly intracellular bacteria is gene loss. Despite the intracellular habitat, we found several horizontal gene transfers between Rickettsiales species and various prokaryotic, viral and eukaryotic species.<br><br>OPEN PEER REVIEW: Reviewed by Arcady Mushegian, Eugene V. Koonin and Patrick Forterre. For the full reviews please go to the Reviewers' comments section.}, }
@article {pmid21303394, year = {2011}, author = {Woodford, N and Turton, JF and Livermore, DM}, title = {Multiresistant Gram-negative bacteria: the role of high-risk clones in the dissemination of antibiotic resistance.}, journal = {FEMS microbiology reviews}, volume = {35}, number = {5}, pages = {736-755}, doi = {10.1111/j.1574-6976.2011.00268.x}, pmid = {21303394}, issn = {1574-6976}, mesh = {Anti-Bacterial Agents/*pharmacology/therapeutic use ; Cluster Analysis ; *Drug Resistance, Multiple, Bacterial ; Gene Transfer, Horizontal ; Genotype ; Gram-Negative Bacteria/*classification/*drug effects/genetics ; Gram-Negative Bacterial Infections/*epidemiology/microbiology/*transmission ; Humans ; Molecular Epidemiology ; *Molecular Typing ; Phylogeny ; }, abstract = {Multilocus sequence typing reveals that many bacterial species have a clonal structure and that some clones are widespread. This underlying phylogeny was not revealed by pulsed-field gel electrophoresis, a method better suited to short-term outbreak investigation. Some global clones are multiresistant and it is easy to assume that these have disseminated from single foci. Such conclusions need caution, however, unless there is a clear epidemiological trail, as with KPC carbapenemase-positive Klebsiella pneumoniae ST258 from Greece to northwest Europe. Elsewhere, established clones may have repeatedly and independently acquired resistance. Thus, the global ST131 Escherichia coli clone most often has CTX-M-15 extended-spectrum β-lactamase (ESBL), but also occurs without ESBLs and as a host of many other ESBL types. We explore this interaction of clone and resistance for E. coli, K. pneumoniae, Acinetobacter baumannii- a species where three global lineages dominate--and Pseudomonas aeruginosa, which shows clonal diversity, but includes the relatively 'tight' serotype O12/Burst Group 4 cluster that has proved adept at acquiring resistances--from PSE-1 to VIM-1 β-lactamases--for over 20 years. In summary, 'high-risk clones' play a major role in the spread of resistance, with the risk lying in their tenacity--deriving from poorly understood survival traits--and a flexible ability to accumulate and switch resistance, rather than to constant resistance batteries.}, }
@article {pmid21300273, year = {2011}, author = {Richards, TA and Archibald, JM}, title = {Cell evolution: gene transfer agents and the origin of mitochondria.}, journal = {Current biology : CB}, volume = {21}, number = {3}, pages = {R112-4}, doi = {10.1016/j.cub.2010.12.036}, pmid = {21300273}, issn = {1879-0445}, mesh = {Alphaproteobacteria/*genetics ; Biological Evolution ; DNA Transposable Elements ; *Gene Transfer, Horizontal ; Mitochondria/*genetics ; *Models, Genetic ; Oceans and Seas ; Phylogeny ; Seawater/microbiology ; }, abstract = {Recently, α-proteobacteria have been shown to possess virus-like gene transfer agents that facilitate high frequency gene transfer in natural environments between distantly related lineages. This system could have driven the genomic integration of the mitochondrial progenitor and its proto-eukaryote host and contributed to the evolutionary mosaic of genes seen in modern-day prokaryotic and eukaryotic genomes.}, }
@article {pmid21298028, year = {2011}, author = {Treangen, TJ and Rocha, EP}, title = {Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes.}, journal = {PLoS genetics}, volume = {7}, number = {1}, pages = {e1001284}, pmid = {21298028}, issn = {1553-7404}, mesh = {Bacillus/genetics ; Bacteria/*genetics ; Bradyrhizobiaceae/genetics ; Computational Biology ; Enterobacteriaceae/genetics ; *Evolution, Molecular ; Gene Duplication/*genetics ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Helicobacter/genetics ; Multigene Family/genetics ; Neisseria/genetics ; Phylogeny ; Pseudomonas/genetics ; Streptococcus/genetics ; Sulfolobus/genetics ; }, abstract = {Gene duplication followed by neo- or sub-functionalization deeply impacts the evolution of protein families and is regarded as the main source of adaptive functional novelty in eukaryotes. While there is ample evidence of adaptive gene duplication in prokaryotes, it is not clear whether duplication outweighs the contribution of horizontal gene transfer in the expansion of protein families. We analyzed closely related prokaryote strains or species with small genomes (Helicobacter, Neisseria, Streptococcus, Sulfolobus), average-sized genomes (Bacillus, Enterobacteriaceae), and large genomes (Pseudomonas, Bradyrhizobiaceae) to untangle the effects of duplication and horizontal transfer. After removing the effects of transposable elements and phages, we show that the vast majority of expansions of protein families are due to transfer, even among large genomes. Transferred genes--xenologs--persist longer in prokaryotic lineages possibly due to a higher/longer adaptive role. On the other hand, duplicated genes--paralogs--are expressed more, and, when persistent, they evolve slower. This suggests that gene transfer and gene duplication have very different roles in shaping the evolution of biological systems: transfer allows the acquisition of new functions and duplication leads to higher gene dosage. Accordingly, we show that paralogs share most protein-protein interactions and genetic regulators, whereas xenologs share very few of them. Prokaryotes invented most of life's biochemical diversity. Therefore, the study of the evolution of biology systems should explicitly account for the predominant role of horizontal gene transfer in the diversification of protein families.}, }
@article {pmid21297116, year = {2011}, author = {Azad, RK and Lawrence, JG}, title = {Towards more robust methods of alien gene detection.}, journal = {Nucleic acids research}, volume = {39}, number = {9}, pages = {e56}, pmid = {21297116}, issn = {1362-4962}, support = {GM078092/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Cluster Analysis ; Gene Transfer, Horizontal ; Genes, Archaeal ; *Genes, Bacterial ; Genome, Bacterial ; Genomics/*methods ; }, abstract = {Because the properties of horizontally-transferred genes will reflect the mutational proclivities of their donor genomes, they often show atypical compositional properties relative to native genes. Parametric methods use these discrepancies to identify bacterial genes recently acquired by horizontal transfer. However, compositional patterns of native genes vary stochastically, leaving no clear boundary between typical and atypical genes. As a result, while strongly atypical genes are readily identified as alien, genes of ambiguous character are poorly classified when a single threshold separates typical and atypical genes. This limitation affects all parametric methods that examine genes independently, and escaping it requires the use of additional genomic information. We propose that the performance of all parametric methods can be improved by using a multiple-threshold approach. First, strongly atypical alien genes and strongly typical native genes would be identified using conservative thresholds. Genes with ambiguous compositional features would then be classified by examining gene context, including the class (native or alien) of flanking genes. By including additional genomic information in a multiple-threshold framework, we observed a remarkable improvement in the performance of several popular, but algorithmically distinct, methods for alien gene detection.}, }
@article {pmid21296924, year = {2011}, author = {Papke, RT and White, E and Reddy, P and Weigel, G and Kamekura, M and Minegishi, H and Usami, R and Ventosa, A}, title = {A multilocus sequence analysis approach to the phylogeny and taxonomy of the Halobacteriales.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {61}, number = {Pt 12}, pages = {2984-2995}, doi = {10.1099/ijs.0.029298-0}, pmid = {21296924}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques/*methods ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Halobacteriales/*classification/genetics/*isolation &amp; purification/metabolism ; Molecular Sequence Data ; Multilocus Sequence Typing/*methods ; *Phylogeny ; }, abstract = {Members of the order Halobacteriales are obligate extreme halophiles that belong to the domain Archaea. The classification of the Halobacteriales currently relies on a polyphasic approach, which integrates phenotypic, genotypic and chemotaxonomic characterization. However, the most utilized genetic marker for phylogeny, the 16S rRNA gene, has multiple drawbacks for use with the Halobacteriales: the species of many genera exhibit large intragenic differences between multiple ribosomal RNA operons, the gene is too conserved to discriminate reliably at the species level and it appears to be the most frequently recombined gene between closely related species. Moreover, the Halobacteriales is a rapidly expanding group due to recent successes at cultivating novel strains from a diverse set of hypersaline environments; a fast, reliable, inexpensive, portable molecular method for discriminating species is required for their investigation. Recently, multilocus sequence analysis (MLSA) has been shown to be an effective tool for strain identification and taxonomic designation, even for those taxa that experience frequent lateral gene transfer and homologous recombination. In this study, MLSA was utilized for evolutionary and taxonomic investigation of the Halobacteriales. Efficacy of the MLSA approach was tested across a hierarchical gradient using 52 halobacterial strains, representing 33 species (including names without standing in nomenclature) and 14 genera. A subset of 21 strains from the genus Haloarcula was analysed separately to test the sensitivity and relevance of the MLSA approach among closely related strains and species. The results demonstrated that MLSA differentiated individual strains, reliably grouped strains into species and species into genera and identified potential novel species and also family-like relationships. This study demonstrates that MLSA is a rapid and informative molecular method that will probably accommodate strain analysis at any taxonomic level within the Halobacteriales.}, }
@article {pmid21293046, year = {2011}, author = {Stairs, CW and Roger, AJ and Hampl, V}, title = {Eukaryotic pyruvate formate lyase and its activating enzyme were acquired laterally from a Firmicute.}, journal = {Molecular biology and evolution}, volume = {28}, number = {7}, pages = {2087-2099}, doi = {10.1093/molbev/msr032}, pmid = {21293046}, issn = {1537-1719}, support = {MOP 62809//Canadian Institutes of Health Research/Canada ; }, mesh = {Acetyltransferases/*genetics ; Archamoebae/enzymology/genetics ; Bacterial Proteins/genetics ; Bayes Theorem ; Computer Simulation ; Enzymes/*genetics ; Eukaryota/enzymology/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Gram-Positive Bacteria/enzymology/*genetics ; Phylogeny ; }, abstract = {Most of the major groups of eukaryotes have microbial representatives that thrive in low oxygen conditions. Those that have been studied in detail generate ATP via pathways involving anaerobically functioning enzymes of pyruvate catabolism that are typically absent in aerobic eukaryotes and whose origins remain controversial. These enzymes include pyruvate:ferredoxin oxidoreductase, pyruvate:NADP(+) oxidoreductase, and pyruvate formate lyase (Pfl). Pfl catalyzes the nonoxidative generation of formate and acetyl-Coenzyme A (CoA) from pyruvate and CoA and is activated by Pfl activating enzyme (Pfla). Within eukaryotes, this extremely oxygen-sensitive pathway was first described in the hydrogenosomes of anaerobic chytrid fungi and has more recently been characterized in the mitochondria and chloroplasts of the chlorophyte alga Chlamydomonas reinhardtii. To clarify the origins of this pathway, we have comprehensively searched for homologs of Pfl and Pfla in publicly available large-scale eukaryotic genomic and cDNA sequencing data, including our own from the anaerobic amoebozoan Mastigamoeba balamuthi. Surprisingly, we find that these enzymes are widely distributed and are present in diverse facultative or obligate anaerobic eukaryotic representatives of the archaeplastidan, metazoan, amoebozoan, and haptophyte lineages. Using maximum likelihood and Bayesian phylogenetic methods, we show that the eukaryotic Pfl and Pfla sequences each form monophyletic groups that are most closely related to homologs in firmicute gram-positive bacteria. Topology tests exclude both α-proteobacterial and cyanobacterial affinities for these genes suggesting that neither originated from the endosymbiotic ancestors of mitochondria or chloroplasts. Furthermore, the topologies of the eukaryote portion of the Pfl and Pfla trees significantly differ from well-accepted eukaryote relationships. Collectively, these results indicate that the Pfl pathway was first acquired by lateral gene transfer into a eukaryotic lineage most probably from a firmicute bacterial lineage and that it has since been spread across diverse eukaryotic groups by more recent eukaryote-to-eukaryote transfer events.}, }
@article {pmid21292630, year = {2011}, author = {Kent, BN and Salichos, L and Gibbons, JG and Rokas, A and Newton, IL and Clark, ME and Bordenstein, SR}, title = {Complete bacteriophage transfer in a bacterial endosymbiont (Wolbachia) determined by targeted genome capture.}, journal = {Genome biology and evolution}, volume = {3}, number = {}, pages = {209-218}, pmid = {21292630}, issn = {1759-6653}, support = {F31 AI091343/AI/NIAID NIH HHS/United States ; R01 GM085163/GM/NIGMS NIH HHS/United States ; R24 GM084917/GM/NIGMS NIH HHS/United States ; R01 GM085163-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteriophages/*genetics/physiology ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Symbiosis ; Wolbachia/*genetics/physiology/*virology ; }, abstract = {Bacteriophage flux can cause the majority of genetic diversity in free-living bacteria. This tenet of bacterial genome evolution generally does not extend to obligate intracellular bacteria owing to their reduced contact with other microbes and a predominance of gene deletion over gene transfer. However, recent studies suggest intracellular coinfections in the same host can facilitate exchange of mobile elements between obligate intracellular bacteria-a means by which these bacteria can partially mitigate the reductive forces of the intracellular lifestyle. To test whether bacteriophages transfer as single genes or larger regions between coinfections, we sequenced the genome of the obligate intracellular Wolbachia strain wVitB from the parasitic wasp Nasonia vitripennis and compared it against the prophage sequences of the divergent wVitA coinfection. We applied, for the first time, a targeted sequence capture array to specifically trap the symbiont's DNA from a heterogeneous mixture of eukaryotic, bacterial, and viral DNA. The tiled array successfully captured the genome with 98.3% efficiency. Examination of the genome sequence revealed the largest transfer of bacteriophage and flanking genes (52.2 kb) to date between two obligate intracellular coinfections. The mobile element transfer occurred in the recent evolutionary past based on the 99.9% average nucleotide identity of the phage sequences between the two strains. In addition to discovering an evolutionary recent and large-scale horizontal phage transfer between coinfecting obligate intracellular bacteria, we demonstrate that "targeted genome capture" can enrich target DNA to alleviate the problem of isolating symbiotic microbes that are difficult to culture or purify from the conglomerate of organisms inside eukaryotes.}, }
@article {pmid21290260, year = {2011}, author = {Tanaka, T and Fukuda, Y and Yoshino, T and Maeda, Y and Muto, M and Matsumoto, M and Mayama, S and Matsunaga, T}, title = {High-throughput pyrosequencing of the chloroplast genome of a highly neutral-lipid-producing marine pennate diatom, Fistulifera sp. strain JPCC DA0580.}, journal = {Photosynthesis research}, volume = {109}, number = {1-3}, pages = {223-229}, pmid = {21290260}, issn = {1573-5079}, mesh = {Aquatic Organisms/genetics ; Base Sequence ; Biological Evolution ; Chloroplasts/*genetics ; DNA/chemistry/genetics ; Diatoms/*genetics ; Gene Transfer, Horizontal ; Genome, Chloroplast/*genetics ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Molecular Sequence Data ; Open Reading Frames/*genetics ; Photosystem II Protein Complex/genetics ; Sequence Analysis, DNA ; }, abstract = {The chloroplast genome of the highly neutral-lipid-producing marine pennate diatom Fistulifera sp. strain JPCC DA0580 was fully sequenced using high-throughput pyrosequencing. The general features and gene content were compared with three other complete diatom chloroplast genomes. The chloroplast genome is 134,918 bp with an inverted repeat of 13,330 bp and is slightly larger than the other diatom chloroplast genomes due to several low gene-density regions lacking similarity to the other diatom chloroplast genomes. Protein-coding genes were nearly identical to those from Phaeodactylum tricornutum. On the other hand, we found unique sequence variations in genes of photosystem II which differ from the consensus in other diatom chloroplasts. Furthermore, five functional unknown ORFs and a putative serine recombinase gene, serC2, are located in the low gene-density regions. SerC2 was also identified in the plasmids of another pennate diatom, Cylindrotheca fusiformis, and in the plastid genome of the diatom endosymbiont of Kryptoperidinium foliaceum. Exogenous plasmids might have been incorporated into the chloroplast genome of Fistulifera sp. by lateral gene transfer. Chloroplast genome sequencing analysis of this novel diatom provides many important insights into diatom evolution.}, }
@article {pmid21288483, year = {2011}, author = {Muller, EE and Bringel, F and Vuilleumier, S}, title = {Dichloromethane-degrading bacteria in the genomic age.}, journal = {Research in microbiology}, volume = {162}, number = {9}, pages = {869-876}, doi = {10.1016/j.resmic.2011.01.008}, pmid = {21288483}, issn = {1769-7123}, mesh = {Adaptation, Physiological ; Aerobiosis ; Bacteria/classification/*genetics/isolation &amp; purification/metabolism ; Biodegradation, Environmental ; Environmental Pollutants/*metabolism ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genomics ; Methylene Chloride/*metabolism ; Microbial Consortia/*physiology ; Phylogeny ; }, abstract = {Dichloromethane (DCM) is a volatile toxic halogenated solvent mainly produced and used industrially. DCM-degrading bacteria have long been models of choice for studying bacterial dehalogenation metabolism at the physiological, biochemical and genetic levels, and have also been used in bioremediation processes. DCM-degrading strains isolated in recent years will be discussed in the context of enzymes known to catalyze dehalogenation of DCM. Insights into the modes of adaptation of bacteria to DCM gained by comparative genomic analysis, highlight the importance of horizontal gene transfer in the dissemination of genes for DCM metabolism in the environment.}, }
@article {pmid21286720, year = {2011}, author = {Vignaroli, C and Zandri, G and Aquilanti, L and Pasquaroli, S and Biavasco, F}, title = {Multidrug-resistant enterococci in animal meat and faeces and co-transfer of resistance from an Enterococcus durans to a human Enterococcus faecium.}, journal = {Current microbiology}, volume = {62}, number = {5}, pages = {1438-1447}, pmid = {21286720}, issn = {1432-0991}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics/metabolism ; Chickens/*microbiology ; Conjugation, Genetic ; Disease Reservoirs/microbiology ; *Drug Resistance, Multiple, Bacterial ; Enterococcus/classification/drug effects/genetics/*isolation &amp; purification ; Enterococcus faecium/classification/drug effects/genetics/isolation &amp; purification ; Feces/*microbiology ; *Gene Transfer, Horizontal ; Gram-Positive Bacterial Infections/microbiology ; Humans ; Meat/*microbiology ; Molecular Sequence Data ; Phylogeny ; Swine/*microbiology ; }, abstract = {Forty-eight isolates resistant to at least two antibiotics were selected from 53 antibiotic-resistant enterococci from chicken and pig meat and faeces and analysed for specific resistance determinants. Of the 48 multidrug-resistant (MDR) strains, 31 were resistant to two antibiotics (29 to erythromycin and tetracycline, 1 to erythromycin and vancomycin, 1 to vancomycin and tetracycline), 14 to three (erythromycin, tetracycline and vancomycin or ampicillin) and 3 to four (erythromycin, vancomycin, ampicillin and gentamicin). erm(B), tet(M), vanA and aac (6')-Ie aph (2'')-Ia were the antibiotic resistance genes most frequently detected. All 48 MDR enterococci were susceptible to linezolid and daptomycin. Enterococcus faecalis (16), Enterococcus faecium (8), Enterococcus mundtii (2) and Enterococcus gallinarum (1) were identified in meat, and E. faecium (13) and Enterococcus durans (13) in faeces. Clonal spread was not detected, suggesting a large role of gene transfer in the dissemination of antibiotic resistance. Conjugative transfer of resistance genes was more successful when donors were enterococcal strains isolated from faeces; co-transfer of vanA and erm(B) to a human E. faecium occurred from both E. faecium and E. durans pig faecal strains. These data show that multidrug resistance can be found in food and animal species other than E. faecium and E. faecalis, and that these species can efficiently transfer antibiotic resistance to human strains in inter-specific matings. In particular, the occurrence of MDR E. durans in the animal reservoir could have a role in the emergence of human enterococcal infections difficult to eradicate with antibiotics.}, }
@article {pmid21285958, year = {2011}, author = {Balaj, L and Lessard, R and Dai, L and Cho, YJ and Pomeroy, SL and Breakefield, XO and Skog, J}, title = {Tumour microvesicles contain retrotransposon elements and amplified oncogene sequences.}, journal = {Nature communications}, volume = {2}, number = {}, pages = {180}, pmid = {21285958}, issn = {2041-1723}, support = {R21 CA141226/CA/NCI NIH HHS/United States ; P50 CA086355/CA/NCI NIH HHS/United States ; CA86355/CA/NCI NIH HHS/United States ; CA141150/CA/NCI NIH HHS/United States ; R01 CA141150/CA/NCI NIH HHS/United States ; R01 CA109467/CA/NCI NIH HHS/United States ; CA69246/CA/NCI NIH HHS/United States ; CA109467/CA/NCI NIH HHS/United States ; CA141226/CA/NCI NIH HHS/United States ; P01 CA069246/CA/NCI NIH HHS/United States ; R21 CA141226-02/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Cell Line, Tumor ; DNA, Complementary/genetics ; Electrophoresis, Agar Gel ; Endothelial Cells/metabolism ; Gene Dosage ; Humans ; Mice ; Neoplasms/*metabolism ; Polymorphism, Single Nucleotide/genetics ; Proto-Oncogene Proteins c-myc/*metabolism ; RNA Precursors/genetics/*metabolism ; Retroelements/*genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Secretory Vesicles/*metabolism ; Umbilical Veins/cytology ; }, abstract = {Tumour cells release an abundance of microvesicles containing a selected set of proteins and RNAs. Here, we show that tumour microvesicles also carry DNA, which reflects the genetic status of the tumour, including amplification of the oncogene c-Myc. We also find amplified c-Myc in serum microvesicles from tumour-bearing mice. Further, we find remarkably high levels of retrotransposon RNA transcripts, especially for some human endogenous retroviruses, such as LINE-1 and Alu retrotransposon elements, in tumour microvesicles and these transposable elements could be transferred to normal cells. These findings expand the nucleic acid content of tumour microvesicles to include: elevated levels of specific coding and non-coding RNA and DNA, mutated and amplified oncogene sequences and transposable elements. Thus, tumour microvesicles contain a repertoire of genetic information available for horizontal gene transfer and potential use as blood biomarkers for cancer.}, }
@article {pmid21285367, year = {2011}, author = {Wang, L and Chen, S and Vergin, KL and Giovannoni, SJ and Chan, SW and DeMott, MS and Taghizadeh, K and Cordero, OX and Cutler, M and Timberlake, S and Alm, EJ and Polz, MF and Pinhassi, J and Deng, Z and Dedon, PC}, title = {DNA phosphorothioation is widespread and quantized in bacterial genomes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {7}, pages = {2963-2968}, pmid = {21285367}, issn = {1091-6490}, support = {P30 ES002109/ES/NIEHS NIH HHS/United States ; }, mesh = {Base Sequence ; Chromatography, Liquid ; Cloning, Molecular ; Cluster Analysis ; Computational Biology ; DNA Primers/genetics ; DNA, Bacterial/*metabolism ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/*genetics ; Genome, Bacterial/*genetics ; Genomics ; Molecular Sequence Data ; Phosphorothioate Oligonucleotides/*metabolism ; *Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sulfur/metabolism ; Tandem Mass Spectrometry ; Vibrionaceae/*genetics ; }, abstract = {Phosphorothioate (PT) modification of DNA, with sulfur replacing a nonbridging phosphate oxygen, was recently discovered as a product of the dnd genes found in bacteria and archaea. Given our limited understanding of the biological function of PT modifications, including sequence context, genomic frequencies, and relationships to the diversity of dnd gene clusters, we undertook a quantitative study of PT modifications in prokaryotic genomes using a liquid chromatography-coupled tandem quadrupole mass spectrometry approach. The results revealed a diversity of unique PT sequence contexts and three discrete genomic frequencies in a wide range of bacteria. Metagenomic analyses of PT modifications revealed unique ecological distributions, and a phylogenetic comparison of dnd genes and PT sequence contexts strongly supports the horizontal transfer of dnd genes. These results are consistent with the involvement of PT modifications in a type of restriction-modification system with wide distribution in prokaryotes.}, }
@article {pmid21284853, year = {2011}, author = {Camilli, R and Bonnal, RJ and Del Grosso, M and Iacono, M and Corti, G and Rizzi, E and Marchetti, M and Mulas, L and Iannelli, F and Superti, F and Oggioni, MR and De Bellis, G and Pantosti, A}, title = {Complete genome sequence of a serotype 11A, ST62 Streptococcus pneumoniae invasive isolate.}, journal = {BMC microbiology}, volume = {11}, number = {}, pages = {25}, pmid = {21284853}, issn = {1471-2180}, mesh = {Chromosomes, Bacterial/genetics ; DNA Transposable Elements ; DNA, Bacterial/genetics ; *Genome, Bacterial ; Molecular Sequence Annotation ; Molecular Sequence Data ; Prophages/genetics ; Sequence Analysis, DNA ; Streptococcus pneumoniae/classification/*genetics/isolation &amp; purification ; }, abstract = {BACKGROUND: Streptococcus pneumoniae is an important human pathogen representing a major cause of morbidity and mortality worldwide. We sequenced the genome of a serotype 11A, ST62 S. pneumoniae invasive isolate (AP200), that was erythromycin-resistant due to the presence of the erm(TR) determinant, and carried out analysis of the genome organization and comparison with other pneumococcal genomes.<br><br>RESULTS: The genome sequence of S. pneumoniae AP200 is 2,130,580 base pair in length. The genome carries 2216 coding sequences (CDS), 56 tRNA, and 12 rRNA genes. Of the CDSs, 72.9% have a predicted biological known function. AP200 contains the pilus islet 2 and, although its phenotype corresponds to serotype 11A, it contains an 11D capsular locus. Chromosomal rearrangements resulting from a large inversion across the replication axis, and horizontal gene transfer events were observed. The chromosomal inversion is likely implicated in the rebalance of the chromosomal architecture affected by the insertions of two large exogenous elements, the erm(TR)-carrying Tn1806 and a functional prophage designated &#x3c6;Spn_200. Tn1806 is 52,457 bp in size and comprises 49 ORFs. Comparative analysis of Tn1806 revealed the presence of a similar genetic element or part of it in related species such as Streptococcus pyogenes and also in the anaerobic species Finegoldia magna, Anaerococcus prevotii and Clostridium difficile. The genome of &#x3c6;Spn_200 is 35,989 bp in size and is organized in 47 ORFs grouped into five functional modules. Prophages similar to &#x3c6;Spn_200 were found in pneumococci and in other streptococcal species, showing a high degree of exchange of functional modules. &#x3c6;Spn_200 viral particles have morphologic characteristics typical of the Siphoviridae family and are capable of infecting a pneumococcal recipient strain.<br><br>CONCLUSIONS: The sequence of S. pneumoniae AP200 chromosome revealed a dynamic genome, characterized by chromosomal rearrangements and horizontal gene transfers. The overall diversity of AP200 is driven mainly by the presence of the exogenous elements Tn1806 and &#x3c6;Spn_200 that show large gene exchanges with other genetic elements of different bacterial species. These genetic elements likely provide AP200 with additional genes, such as those conferring antibiotic-resistance, promoting its adaptation to the environment.}, }
@article {pmid21284206, year = {2010}, author = {Sun, M and Zheng, B and Gao, GF and Zhu, B}, title = {[Arms racing between human beings and pathogens: NDM-1 and superbugs].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {26}, number = {11}, pages = {1461-1472}, pmid = {21284206}, issn = {1000-3061}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/*genetics ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; *Mutation ; Plasmids/genetics ; beta-Lactamases/*genetics ; }, abstract = {Throughout human history, pandemic bacterial diseases such as the plague and tuberculosis have posed an enormous threat to human beings. The discovery of antibiotics has provided us with powerful arsenal for the defense against bacterial infections. However, bacteria are acquiring more and more resistance genes to shield off antibiotics through mutation and horizontal gene transfer. Therefore, novel antibiotics must be produced and the arms race between bacterial pathogens and antibiotics is becoming increasingly intense. Recently, researchers have found that plasmids carrying a new metallo-beta-lactamase gene, blaNDM-1, and many other antibiotics resistance genes can easily spread through bacterial populations and confer recipient stains resistance to nearly all of the current antibiotics. It is a threat to the human health and a great challenge for our medical science, which we are facing. We need to find new ways to fight and win this arms racing.}, }
@article {pmid21278269, year = {2011}, author = {Hoang, KV and Stern, NJ and Saxton, AM and Xu, F and Zeng, X and Lin, J}, title = {Prevalence, development, and molecular mechanisms of bacteriocin resistance in Campylobacter.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {7}, pages = {2309-2316}, pmid = {21278269}, issn = {1098-5336}, support = {R21 AI069133/AI/NIAID NIH HHS/United States ; 1 R21 AI069133-01A2/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteriocins/*pharmacology ; Biological Transport, Active ; Campylobacter coli/*drug effects/isolation &amp; purification ; Campylobacter jejuni/*drug effects/isolation &amp; purification ; Chickens/microbiology ; DNA Transposable Elements ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Membrane Transport Proteins/genetics/metabolism ; Microarray Analysis ; Microbial Sensitivity Tests ; Mutagenesis, Insertional ; Oligonucleotide Array Sequence Analysis ; Prevalence ; Transformation, Bacterial ; }, abstract = {Bacteriocins (BCNs) are antimicrobial peptides produced by bacteria with narrow or broad spectra of antimicrobial activity. Recently, several unique anti-Campylobacter BCNs have been identified from commensal bacteria isolated from chicken intestines. These BCNs dramatically reduced C. jejuni colonization in poultry and are being directed toward on-farm control of Campylobacter. However, no information concerning prevalence, development, and mechanisms of BCN resistance in Campylobacter exists. In this study, susceptibilities of 137 C. jejuni isolates and 20 C. coli isolates to the anti-Campylobacter BCNs OR-7 and E-760 were examined. Only one C. coli strain displayed resistance to the BCNs (MIC, 64 μg/ml), while others were susceptible, with MICs ranging from 0.25 to 4 μg/ml. The C. coli mutants resistant to BCN OR-7 also were obtained by in vitro selection, but all displayed only low-level resistance to OR-7 (MIC, 8 to 16 μg/ml). The acquired BCN resistance in C. coli could be transferred at intra- and interspecies levels among Campylobacter strains by biphasic natural transformation. Genomic examination of the OR-7-resistant mutants by using DNA microarray and random transposon mutagenesis revealed that the multidrug efflux pump CmeABC contributes to both intrinsic resistance and acquired resistance to the BCNs. Altogether, this study represents the first report of and a major step forward in understanding BCN resistance in Campylobacter, which will facilitate the development of effective BCN-based strategies to reduce the Campylobacter loads in poultry.}, }
@article {pmid21277778, year = {2011}, author = {Veyrier, FJ and Dufort, A and Behr, MA}, title = {The rise and fall of the Mycobacterium tuberculosis genome.}, journal = {Trends in microbiology}, volume = {19}, number = {4}, pages = {156-161}, doi = {10.1016/j.tim.2010.12.008}, pmid = {21277778}, issn = {1878-4380}, mesh = {*Evolution, Molecular ; *Genome, Bacterial ; Humans ; Mycobacterium tuberculosis/*genetics/pathogenicity ; Recombination, Genetic ; }, abstract = {When studied from the perspective of non-tuberculous mycobacteria (NTM) it is apparent that Mycobacterium tuberculosis has undergone a biphasic evolutionary process involving genome expansion (gene acquisition and duplication) and reductive evolution (deletions). This scheme can instruct descriptive and experimental studies that determine the importance of ancestral events (including horizontal gene transfer) in shaping the present-day pathogen. For example, heterologous complementation in an NTM can test the functional importance of M. tuberculosis-specific genetic insertions. An appreciation of both phases of M. tuberculosis evolution is expected to improve our fundamental understanding of its pathogenicity and facilitate the evaluation of novel diagnostics and vaccines.}, }
@article {pmid21277292, year = {2011}, author = {Peters, DL and Pretorius, PJ}, title = {Origin, translocation and destination of extracellular occurring DNA--a new paradigm in genetic behaviour.}, journal = {Clinica chimica acta; international journal of clinical chemistry}, volume = {412}, number = {11-12}, pages = {806-811}, doi = {10.1016/j.cca.2011.01.026}, pmid = {21277292}, issn = {1873-3492}, mesh = {Biological Transport ; DNA/chemistry/*genetics/*metabolism ; Exosomes/metabolism ; Extracellular Space/*metabolism ; Humans ; Nucleosomes/chemistry/metabolism ; Terminology as Topic ; }, abstract = {The diagnostic value of extracellular occurring DNA (eoDNA) is limited by our lack of understanding its biological function. eoDNA exists in a number of forms, namely vesicle bound DNA (apoptotic bodies, micro particles, micro vesicles and exosomes), histone/DNA complexes or nucleosomes and virtosomes. These forms of DNA can also be categorized under the terms circulating DNA, cell free DNA, free DNA and extracellular DNA. The DNA can be released by means of form-specific mechanisms and seem to be governed by cell cycle phases and apoptosis. Active release is supported by evidence of energy dependent release mechanisms and various immunological- and messenger functions. Sequencing has shown that eoDNA sequences present in the nucleosome reflects traits and distribution of genome sequences and are regulated by ways of release and/or clearance. eoDNA enables the horizontal transfer of gene sequences from one cell to another, over various distances. The ability of eoDNA to partake in horizontal gene transfer makes it an important facet in the field of epigenetic variation. Clinical implementation of eoDNA diagnostics requires that all of the subgroups of eoDNA be properly investigated.}, }
@article {pmid21276666, year = {2011}, author = {Dolejska, M and Jurcickova, Z and Literak, I and Pokludova, L and Bures, J and Hera, A and Kohoutova, L and Smola, J and Cizek, A}, title = {IncN plasmids carrying bla CTX-M-1 in Escherichia coli isolates on a dairy farm.}, journal = {Veterinary microbiology}, volume = {149}, number = {3-4}, pages = {513-516}, doi = {10.1016/j.vetmic.2010.11.032}, pmid = {21276666}, issn = {1873-2542}, mesh = {Animals ; Cattle/microbiology ; Cattle Diseases/*microbiology ; Cephalosporin Resistance ; Cephalosporins/pharmacology ; Czech Republic ; DNA, Bacterial/genetics ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/classification/genetics/*isolation &amp; purification ; Escherichia coli Infections/microbiology/*veterinary ; Escherichia coli Proteins/genetics ; Female ; Gene Transfer, Horizontal ; Plasmids/genetics ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; beta-Lactamases/*genetics ; }, abstract = {The aim of the study was to compare the prevalence of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli bovine isolates on a conventional dairy cattle farm with high consumption of parenteral and intramammary cephalosporins (farm A) and on an organic dairy farm with no cephalosporin use (farm B). ESBL-producing E. coli were isolated from rectal swabs and milk filters by selective cultivation on MacConkey agar with cefotaxime (2mg/l). ESBL genes were identified by polymerase chain reaction (PCR) and sequencing, and the genetic diversity of the isolates was determined by XbaI pulsed field gel electrophoresis (PFGE). Conjugative transfer, incompatibility group, and restriction fragment length polymorphism (RFLP) profiles of the ESBL-carrying plasmids were studied. Higher prevalence (39%, n(rectal samples in cows)=309) of CTX-M-1-producing E. coli isolates was found on farm A compared to farm B (<1%, n(rectal samples in cows)=154; 0%, n(rectal samples in calves)=46). Using PFGE, the isolates from farm A were divided into nine pulsotypes. In all ESBL-positive isolates, the bla(CTX-M-1) gene was carried on 40 kb IncN conjugative plasmids of three related HincII restriction profiles. Horizontal gene transfer through transmission of IncN plasmids harboring bla(CTX-M-1) as well as clonal dissemination of a particular clone seems to be involved in dissemination of CTX-M-1-producing E. coli isolates in cows on the farm using cephalosporins in treating bacterial infections. The study demonstrates a possible role of cephalosporin use in the widespread occurrence of CTX-M-1-producing E. coli on the conventional dairy cattle farm compared to the organic farm.}, }
@article {pmid21276171, year = {2011}, author = {Kudryashev, M and Cyrklaff, M and Alex, B and Lemgruber, L and Baumeister, W and Wallich, R and Frischknecht, F}, title = {Evidence of direct cell-cell fusion in Borrelia by cryogenic electron tomography.}, journal = {Cellular microbiology}, volume = {13}, number = {5}, pages = {731-741}, doi = {10.1111/j.1462-5822.2011.01571.x}, pmid = {21276171}, issn = {1462-5822}, mesh = {Antigenic Variation/genetics/immunology ; Borrelia/genetics/metabolism/*ultrastructure ; Cell Fusion ; Cell Membrane/metabolism/*ultrastructure ; Electron Microscope Tomography ; Gene Transfer, Horizontal ; }, abstract = {Some Borrelia species are the causative agents of tick-borne Lyme disease responsible for different disabilities depending on species and hosts. Borrelia are highly motile bacterial cells, and light microscopy shows that these spirochetes can associate with each other during movement. Using cryo-electron tomography, we observed closely associated Borrelia cells. Some of these showed a single outer membrane surrounding two longitudinally arranged cytoplasmic cylinders. We also observed fusion of two cytoplasmic cylinders and differences in the surface layer density of fused spirochetes. These processes could play a role in the interaction of Borrelia species with the host's immune system.}, }
@article {pmid21270172, year = {2011}, author = {Popa, O and Hazkani-Covo, E and Landan, G and Martin, W and Dagan, T}, title = {Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes.}, journal = {Genome research}, volume = {21}, number = {4}, pages = {599-609}, pmid = {21270172}, issn = {1549-5469}, support = {R01 LM010009/LM/NLM NIH HHS/United States ; LM010009-01/LM/NLM NIH HHS/United States ; }, mesh = {Base Composition/genetics ; Computational Biology ; DNA Repair/*genetics ; DNA, Bacterial/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome/*genetics ; Prokaryotic Cells/*metabolism ; Sequence Homology, Nucleic Acid ; }, abstract = {Lateral gene transfer (LGT) plays a major role in prokaryote evolution with only a few genes that are resistant to it; yet the nature and magnitude of barriers to lateral transfer are still debated. Here, we implement directed networks to investigate donor-recipient events of recent lateral gene transfer among 657 sequenced prokaryote genomes. For 2,129,548 genes investigated, we detected 446,854 recent lateral gene transfer events through nucleotide pattern analysis. Among these, donor-recipient relationships could be specified through phylogenetic reconstruction for 7% of the pairs, yielding 32,028 polarized recent gene acquisition events, which constitute the edges of our directed networks. We find that the frequency of recent LGT is linearly correlated both with genome sequence similarity and with proteome similarity of donor-recipient pairs. Genome sequence similarity accounts for 25% of the variation in gene-transfer frequency, with proteome similarity adding only 1% to the variability explained. The range of donor-recipient GC content similarity within the network is extremely narrow, with 86% of the LGTs occurring between donor-recipient pairs having ≤5% difference in GC content. Hence, genome sequence similarity and GC content similarity are strong barriers to LGT in prokaryotes. But they are not insurmountable, as we detected 1530 recent transfers between distantly related genomes. The directed network revealed that recipient genomes of distant transfers encode proteins of nonhomologous end-joining (NHEJ; a DNA repair mechanism) far more frequently than the recipient lacking that mechanism. This implicates NHEJ in genes spread across distantly related prokaryotes through bypassing the donor-recipient sequence similarity barrier.}, }
@article {pmid21258064, year = {2011}, author = {Tsafnat, G and Schaeffer, J and Clayphan, A and Iredell, JR and Partridge, SR and Coiera, E}, title = {Computational inference of grammars for larger-than-gene structures from annotated gene sequences.}, journal = {Bioinformatics (Oxford, England)}, volume = {27}, number = {6}, pages = {791-796}, doi = {10.1093/bioinformatics/btr036}, pmid = {21258064}, issn = {1367-4811}, mesh = {*Algorithms ; Bayes Theorem ; DNA/genetics ; Databases, Genetic ; Electronic Data Processing/*methods ; Markov Chains ; Molecular Sequence Annotation ; Sequence Analysis, DNA/*methods ; }, abstract = {MOTIVATION: Larger than gene structures (LGS) are DNA segments that include at least one gene and often other segments such as inverted repeats and gene promoters. Mobile genetic elements (MGE) such as integrons are LGS that play an important role in horizontal gene transfer, primarily in Gram-negative organisms. Known LGS have a profound effect on organism virulence, antibiotic resistance and other properties of the organism due to the number of genes involved. Expert-compiled grammars have been shown to be an effective computational representation of LGS, well suited to automating annotation, and supporting de novo gene discovery. However, development of LGS grammars by experts is labour intensive and restricted to known LGS.<br><br>OBJECTIVES: This study uses computational grammar inference methods to automate LGS discovery. We compare the ability of six algorithms to infer LGS grammars from DNA sequences annotated with genes and other short sequences. We compared the predictive power of learned grammars against an expert-developed grammar for gene cassette arrays found in Class 1, 2 and 3 integrons, which are modular LGS containing up to 9 of about 240 cassette types.<br><br>RESULTS: Using a Bayesian generalization algorithm our inferred grammar was able to predict > 95% of MGE structures in a corpus of 1760 sequences obtained from Genbank (F-score 75%). Even with 100% noise added to the training and test sets, we obtained an F-score of 68%, indicating that the method is robust and has the potential to predict de novo LGS structures when the underlying gene features are known.<br><br>AVAILABILITY: http://www2.chi.unsw.edu.au/attacca.}, }
@article {pmid21257793, year = {2011}, author = {Tomazic, ML and Najle, SR and Nusblat, AD and Uttaro, AD and Nudel, CB}, title = {A novel sterol desaturase-like protein promoting dealkylation of phytosterols in Tetrahymena thermophila.}, journal = {Eukaryotic cell}, volume = {10}, number = {3}, pages = {423-434}, pmid = {21257793}, issn = {1535-9786}, mesh = {Amino Acid Sequence ; Dealkylation ; Fatty Acid Desaturases/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Phylogeny ; Phytosterols/*metabolism ; Sequence Alignment ; Sterols/*metabolism ; Tetrahymena thermophila/chemistry/classification/*enzymology/genetics ; }, abstract = {The gene TTHERM_00438800 (DES24) from the ciliate Tetrahymena thermophila encodes a protein with three conserved histidine clusters, typical of the fatty acid hydroxylase superfamily. Despite its high similarity to sterol desaturase-like enzymes, the phylogenetic analysis groups Des24p in a separate cluster more related to bacterial than to eukaryotic proteins, suggesting a possible horizontal gene transfer event. A somatic knockout of DES24 revealed that the gene encodes a protein, Des24p, which is involved in the dealkylation of phytosterols. Knocked-out mutants were unable to eliminate the C-24 ethyl group from C(29) sterols, whereas the ability to introduce other modifications, such as desaturations at positions C-5(6), C-7(8), and C-22(23), were not altered. Although C-24 dealkylations have been described in other organisms, such as insects, neither the enzymes nor the corresponding genes have been identified to date. Therefore, this is the first identification of a gene involved in sterol dealkylation. Moreover, the knockout mutant and wild-type strain differed significantly in growth and morphology only when cultivated with C(29) sterols; under this culture condition, a change from the typical pear-like shape to a round shape and an alteration in the regulation of tetrahymanol biosynthesis were observed. Sterol analysis upon culture with various substrates and inhibitors indicate that the removal of the C-24 ethyl group in Tetrahymena may proceed by a mechanism different from the one currently known.}, }
@article {pmid21256980, year = {2011}, author = {Fourie, G and Steenkamp, ET and Ploetz, RC and Gordon, TR and Viljoen, A}, title = {Current status of the taxonomic position of Fusarium oxysporum formae specialis cubense within the Fusarium oxysporum complex.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {11}, number = {3}, pages = {533-542}, doi = {10.1016/j.meegid.2011.01.012}, pmid = {21256980}, issn = {1567-7257}, mesh = {Amplified Fragment Length Polymorphism Analysis ; Biological Evolution ; Fusarium/*classification/pathogenicity/physiology ; Magnoliopsida/*microbiology ; Plant Diseases/*microbiology ; Polymorphism, Restriction Fragment Length ; Random Amplified Polymorphic DNA Technique ; Repetitive Sequences, Nucleic Acid ; }, abstract = {Fusarium oxysporum is an asexual fungal species that includes human and animal pathogens and a diverse range of nonpathogens. Pathogenic and nonpathogenic strains of this species can be distinguished from each other with pathogenicity tests, but not with morphological analysis or sexual compatibility studies. Substantial genetic diversity among isolates has led to the realization that F. oxysporum represents a complex of cryptic species. F. oxysporum f. sp cubense (Foc), causal agent of Fusarium wilt of banana, is one of the more than 150 plant pathogenic forms of F. oxysporum. Multi-gene phylogenetic studies of Foc revealed at least eight phylogenetic lineages, a finding that was supported by random amplified polymorphic DNAs, restriction fragment length polymorphisms and amplified fragment length polymorphisms. Most of these lineages consist of isolates in closely related vegetative compatibility groups, some of which possess opposite mating type alleles, MAT-1 and MAT-2; thus, the evolutionary history of this fungus may have included recent sexual reproduction. The ability to cause disease on all or some of the current race differential cultivars has evolved convergently in the taxon, as members of some races appear in different phylogenetic lineages. Therefore, various factors including co-evolution the plant host and horizontal gene transfer are thought to have shaped the evolutionary history of Foc. This review discusses the evolution of Foc as a model formae specialis in F. oxysporum in relation to recent research findings involving DNA-based studies.}, }
@article {pmid21255425, year = {2011}, author = {Atkinson, GC and Hauryliuk, V and Tenson, T}, title = {An ancient family of SelB elongation factor-like proteins with a broad but disjunct distribution across archaea.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {22}, pmid = {21255425}, issn = {1471-2148}, mesh = {Amino Acid Sequence ; Archaea/chemistry/classification/*genetics/metabolism ; Archaeal Proteins/chemistry/*genetics/metabolism ; Binding Sites ; Molecular Sequence Data ; *Multigene Family ; Peptide Elongation Factors/chemistry/*genetics/metabolism ; Phylogeny ; Protein Conformation ; Sequence Alignment ; }, abstract = {BACKGROUND: SelB is the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome. In archaea, only a subset of methanogens utilizes selenocysteine and encodes archaeal SelB (aSelB). A SelB-like (aSelBL) homolog has previously been identified in an archaeon that does not encode selenosysteine, and has been proposed to be a pyrrolysyl-tRNA-specific elongation factor (EF-Pyl). However, elongation factor EF-Tu is capable of binding archaeal Pyl-tRNA in bacteria, suggesting the archaeal ortholog EF1A may also be capable of delivering Pyl-tRNA to the ribosome without the need of a specialized factor.<br><br>RESULTS: We have phylogenetically characterized the aSelB and aSelBL families in archaea. We find the distribution of aSelBL to be wider than both selenocysteine and pyrrolysine usage. The aSelBLs also lack the carboxy terminal domain usually involved in recognition of the selenocysteine insertion sequence in the target mRNA. While most aSelBL-encoding archaea are methanogenic Euryarchaea, we also find aSelBL representatives in Sulfolobales and Thermoproteales of Crenarchaea, and in the recently identified phylum Thaumarchaea, suggesting that aSelBL evolution has involved horizontal gene transfer and/or parallel loss. Severe disruption of the GTPase domain suggests that some family members may employ a hitherto unknown mechanism of nucleotide hydrolysis, or have lost their GTPase ability altogether. However, patterns of sequence conservation indicate that aSelBL is still capable of binding the ribosome and aminoacyl-tRNA.<br><br>CONCLUSIONS: Although it is closely related to SelB, aSelBL appears unlikely to either bind selenocysteinyl-tRNA or function as a classical GTP hydrolyzing elongation factor. We propose that following duplication of aSelB, the resultant aSelBL was recruited for binding another aminoacyl-tRNA. In bacteria, aminoacylation with selenocysteine is essential for efficient thermodynamic coupling of SelB binding to tRNA and GTP. Therefore, change in tRNA specificity of aSelBL could have disrupted its GTPase cycle, leading to relaxation of selective pressure on the GTPase domain and explaining its apparent degradation. While the specific role of aSelBL is yet to be experimentally tested, its broad phylogenetic distribution, surpassing that of aSelB, indicates its importance.}, }
@article {pmid21255116, year = {2011}, author = {Miyazaki, R and van der Meer, JR}, title = {A dual functional origin of transfer in the ICEclc genomic island of Pseudomonas knackmussii B13.}, journal = {Molecular microbiology}, volume = {79}, number = {3}, pages = {743-758}, doi = {10.1111/j.1365-2958.2010.07484.x}, pmid = {21255116}, issn = {1365-2958}, mesh = {*Conjugation, Genetic ; DNA Replication/genetics ; Genes, Bacterial/genetics ; Genetic Complementation Test ; Genetic Loci/genetics ; Genomic Islands/*genetics ; Green Fluorescent Proteins/metabolism ; Mutation/genetics ; Plasmids/genetics ; Pseudomonas/*genetics ; Repetitive Sequences, Nucleic Acid/genetics ; Time Factors ; }, abstract = {Genomic islands (GEIs) are large DNA segments, present in most bacterial genomes, that are most likely acquired via horizontal gene transfer. Here, we study the self-transfer system of the integrative and conjugative element ICEclc of Pseudomonas knackmussii B13, which stands model for a larger group of ICE/GEI with syntenic core gene organization. Functional screening revealed that unlike conjugative plasmids and other ICEs ICEclc carries two separate origins of transfer, with different sequence context but containing a similar repeat motif. Conjugation experiments with GFP-labelled ICEclc variants showed that both oriTs are used for transfer and with indistinguishable efficiencies, but that having two oriTs results in an estimated fourfold increase of ICEclc transfer rates in a population compared with having a single oriT. A gene for a relaxase essential for ICEclc transfer was also identified, but in vivo strand exchange assays suggested that the relaxase processes both oriTs in a different manner. This unique dual origin of transfer system might have provided an evolutionary advantage for distribution of ICE, a hypothesis that is supported by the fact that both oriT regions are conserved in several GEIs related to ICEclc.}, }
@article {pmid21252347, year = {2011}, author = {Khomyakova, M and Bükmez, &#xd6; and Thomas, LK and Erb, TJ and Berg, IA}, title = {A methylaspartate cycle in haloarchaea.}, journal = {Science (New York, N.Y.)}, volume = {331}, number = {6015}, pages = {334-337}, doi = {10.1126/science.1196544}, pmid = {21252347}, issn = {1095-9203}, mesh = {Acetates/*metabolism ; Acetyl Coenzyme A/metabolism ; Archaeal Proteins/metabolism ; Fumarates/metabolism ; Gene Transfer, Horizontal ; Genes, Archaeal ; Glutamic Acid/metabolism ; Glyoxylates/metabolism ; Haloarcula marismortui/enzymology/genetics/*metabolism ; Malates/metabolism ; Maleates/metabolism ; *Metabolic Networks and Pathways ; N-Methylaspartate/*metabolism ; Oxidation-Reduction ; Proteome ; Succinic Acid/metabolism ; }, abstract = {Access to novel ecological niches often requires adaptation of metabolic pathways to cope with new environments. For conversion to cellular building blocks, many substrates enter central carbon metabolism via acetyl-coenzyme A (acetyl-CoA). Until now, only two such pathways have been identified: the glyoxylate cycle and the ethylmalonyl-CoA pathway. Prokaryotes in the haloarchaea use a third pathway by which acetyl-CoA is oxidized to glyoxylate via the key intermediate methylaspartate. Glyoxylate condensation with another acetyl-CoA molecule yields malate, the final assimilation product. This cycle combines reactions that originally belonged to different metabolic processes in different groups of prokaryotes, which suggests lateral gene transfer and evolutionary tinkering of acetate assimilation. Moreover, it requires elevated intracellular glutamate concentrations, as well as coupling carbon assimilation with nitrogen metabolism.}, }
@article {pmid21252340, year = {2011}, author = {Rebbeck, CA and Leroi, AM and Burt, A}, title = {Mitochondrial capture by a transmissible cancer.}, journal = {Science (New York, N.Y.)}, volume = {331}, number = {6015}, pages = {303}, doi = {10.1126/science.1197696}, pmid = {21252340}, issn = {1095-9203}, mesh = {Animals ; Coyotes/genetics ; Dog Diseases/*genetics/metabolism/pathology ; Dogs/genetics ; Gene Transfer, Horizontal ; *Genome, Mitochondrial ; *Mitochondria/genetics/metabolism ; Phylogeny ; Polymorphism, Genetic ; Selection, Genetic ; Sequence Analysis, DNA ; Venereal Tumors, Veterinary/*genetics/*metabolism/pathology ; Wolves/genetics ; }, abstract = {Canine transmissible venereal tumor (CTVT) is an infectious cell line circulating in many feral dog populations. It originated once, about 10,000 years ago. Phylogenetic analyses of mitochondrial sequences from dogs, wolves, and a geographically diverse collection of CTVT samples indicate that the cancer has periodically acquired mitochondria from its host. We suggest that this may be because the cancer's own mitochondria have a tendency to degenerate, due to high mutation rates and relaxed selection, resulting in host mitochondria being more fit.}, }
@article {pmid21252338, year = {2011}, author = {Ensign, SA}, title = {Microbiology. Another microbial pathway for acetate assimilation.}, journal = {Science (New York, N.Y.)}, volume = {331}, number = {6015}, pages = {294-295}, doi = {10.1126/science.1201252}, pmid = {21252338}, issn = {1095-9203}, mesh = {Acetates/*metabolism ; Gene Transfer, Horizontal ; Glutamic Acid/metabolism ; Glyoxylates/metabolism ; Haloarcula marismortui/enzymology/genetics/*metabolism ; Isocitrates/metabolism ; *Metabolic Networks and Pathways ; N-Methylaspartate/*metabolism ; Succinic Acid/metabolism ; }, }
@article {pmid21252274, year = {2011}, author = {Zacharczuk, K and Piekarska, K and Szych, J and Jagielski, M and Hidalgo, L and San Millán, &#xc1; and Gutiérrez, B and Rastawicki, W and González-Zorn, B and Gierczyński, R}, title = {Plasmid-borne 16S rRNA methylase ArmA in aminoglycoside-resistant Klebsiella pneumoniae in Poland.}, journal = {Journal of medical microbiology}, volume = {60}, number = {Pt 9}, pages = {1306-1311}, doi = {10.1099/jmm.0.024026-0}, pmid = {21252274}, issn = {1473-5644}, mesh = {Aminoglycosides/*pharmacology ; Anti-Bacterial Agents/*pharmacology ; DNA Transposable Elements ; DNA, Bacterial/genetics ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Humans ; Klebsiella Infections/*microbiology ; Klebsiella pneumoniae/*enzymology/*genetics/isolation &amp; purification ; Methylation ; Methyltransferases/*biosynthesis/genetics ; Microbial Sensitivity Tests ; Plasmids ; Poland ; RNA, Bacterial/metabolism ; RNA, Ribosomal, 16S/metabolism ; beta-Lactamases/genetics ; }, abstract = {We characterized 17 clinical isolates of Klebsiella pneumoniae producing 16S rRNA methylase ArmA. The isolates originated in Poland from 2002 to May 2010 and encompassed four XbaI-PFGE clusters. All the isolates were resistant to amikacin, gentamicin and kanamycin (MIC range: 256-1024 mg l(-1)) and carried the armA gene on a large plasmid of approximately 90 or 130 kb in 15 and 2 isolates, respectively. The armA gene was found in a ~10 kb ClaI restriction fragment of the large plasmid and was flanked by the same elements as in Tn1548. All the isolates carried the bla(CTX-M) gene for a CTX-M-type extended-spectrum β-lactamase. Our results show that ArmA has disseminated horizontally among K. pneumoniae isolates in Poland on the ~90 kb plasmid of the pCTX-M3 family.}, }
@article {pmid21251250, year = {2011}, author = {Bernhardsson, S and Gerlee, P and Lizana, L}, title = {Structural correlations in bacterial metabolic networks.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {20}, pmid = {21251250}, issn = {1471-2148}, mesh = {Bacteria/genetics/*metabolism ; *Biological Evolution ; *Metabolic Networks and Pathways ; Models, Biological ; }, abstract = {BACKGROUND: Evolution of metabolism occurs through the acquisition and loss of genes whose products acts as enzymes in metabolic reactions, and from a presumably simple primordial metabolism the organisms living today have evolved complex and highly variable metabolisms. We have studied this phenomenon by comparing the metabolic networks of 134 bacterial species with known phylogenetic relationships, and by studying a neutral model of metabolic network evolution.<br><br>RESULTS: We consider the 'union-network' of 134 bacterial metabolisms, and also the union of two smaller subsets of closely related species. Each reaction-node is tagged with the number of organisms it belongs to, which we denote organism degree (OD), a key concept in our study. Network analysis shows that common reactions are found at the centre of the network and that the average OD decreases as we move to the periphery. Nodes of the same OD are also more likely to be connected to each other compared to a random OD relabelling based on their occurrence in the real data. This trend persists up to a distance of around five reactions. A simple growth model of metabolic networks is used to investigate the biochemical constraints put on metabolic-network evolution. Despite this seemingly drastic simplification, a 'union-network' of a collection of unrelated model networks, free of any selective pressure, still exhibit similar structural features as their bacterial counterpart.<br><br>CONCLUSIONS: The OD distribution quantifies topological properties of the evolutionary history of bacterial metabolic networks, and lends additional support to the importance of horizontal gene transfer during bacterial metabolic evolution where new reactions are attached at the periphery of the network. The neutral model of metabolic network growth can reproduce the main features of real networks, but we observe that the real networks contain a smaller common core, while they are more similar at the periphery of the network. This suggests that natural selection and biochemical correlations can act both to diversify and to narrow down metabolic evolution.}, }
@article {pmid21249334, year = {2011}, author = {Sleator, RD}, title = {Phylogenetics.}, journal = {Archives of microbiology}, volume = {193}, number = {4}, pages = {235-239}, doi = {10.1007/s00203-011-0677-x}, pmid = {21249334}, issn = {1432-072X}, mesh = {Algorithms ; Bayes Theorem ; *Biological Evolution ; Genomics/*methods ; Likelihood Functions ; *Phylogeny ; }, abstract = {The recent rapid expansion in the DNA and protein databases, arising from large-scale genomic and metagenomic sequence projects, has forced significant development in the field of phylogenetics: the study of the evolutionary relatedness of the planet's inhabitants. Advances in phylogenetic analysis have greatly transformed our view of the landscape of evolutionary biology, transcending the view of the tree of life that has shaped evolutionary theory since Darwinian times. Indeed, modern phylogenetic analysis no longer focuses on the restricted Darwinian-Mendelian model of vertical gene transfer, but must also consider the significant degree of lateral gene transfer, which connects and shapes almost all living things. Herein, I review the major tree-building methods, their strengths, weaknesses and future prospects.}, }
@article {pmid21248858, year = {2011}, author = {Sims, IM and Frese, SA and Walter, J and Loach, D and Wilson, M and Appleyard, K and Eason, J and Livingston, M and Baird, M and Cook, G and Tannock, GW}, title = {Structure and functions of exopolysaccharide produced by gut commensal Lactobacillus reuteri 100-23.}, journal = {The ISME journal}, volume = {5}, number = {7}, pages = {1115-1124}, pmid = {21248858}, issn = {1751-7370}, mesh = {Animals ; Culture Media ; Fructans/biosynthesis/*chemistry ; Gastrointestinal Contents/microbiology ; Genes, Bacterial ; Hexosyltransferases/genetics ; Limosilactobacillus reuteri/genetics/growth &amp; development/*metabolism ; Mice ; Mice, Inbred BALB C ; Mutagenesis, Insertional ; Polysaccharides, Bacterial/biosynthesis/*chemistry ; Spleen/cytology/immunology ; Stomach/*microbiology ; Sucrose/metabolism ; T-Lymphocytes, Regulatory/microbiology ; }, abstract = {Lactobacillus reuteri strain 100-23 together with a Lactobacillus-free mouse model, provides a system with which the molecular traits underpinning bacterial commensalism in vertebrates can be studied. A polysaccharide was extracted from sucrose-containing liquid cultures of strain 100-23. Chemical analysis showed that this exopolysaccharide was a levan (β-2, 6-linked fructan). Mutation of the fructosyl transferase (ftf) gene resulted in loss of exopolysaccharide production. The ftf mutant was able to colonise the murine gastrointestinal tract in the absence of competition, but colonisation was impaired in competition with the wild type. Biofilm formation by the mutant on the forestomach epithelial surface was not impaired and the matrix between cells was indistinguishable from that of the wild type in electron micrographs. Colonisation of the mouse gut by the wild-type strain led to increased proportions of regulatory T cells (Foxp3+) in the spleen, whereas colonisation by the ftf mutant did not. Survival of the mutant in sucrose-containing medium was markedly reduced relative to the wild type. Comparison of the genomic ftf loci of strain 100-23 with other L. reuteri strains suggested that the ftf gene was acquired by lateral gene transfer early in the evolution of the species and subsequently diversified at accelerated rates. Levan production by L. reuteri 100-23 may represent a function acquired by the bacterial species for life in moderate to high-sucrose extra-gastrointestinal environments that has subsequently been diverted to novel uses, including immunomodulation, that aid in colonisation of the murine gut.}, }
@article {pmid21244532, year = {2011}, author = {Li, M and Shen, X and Yan, J and Han, H and Zheng, B and Liu, D and Cheng, H and Zhao, Y and Rao, X and Wang, C and Tang, J and Hu, F and Gao, GF}, title = {GI-type T4SS-mediated horizontal transfer of the 89K pathogenicity island in epidemic Streptococcus suis serotype 2.}, journal = {Molecular microbiology}, volume = {79}, number = {6}, pages = {1670-1683}, pmid = {21244532}, issn = {1365-2958}, mesh = {Bacterial Proteins/*genetics/metabolism ; Base Sequence ; Conjugation, Genetic ; Epidemics ; *Gene Transfer, Horizontal ; *Genomic Islands ; Humans ; Molecular Sequence Data ; Streptococcal Infections/epidemiology/*microbiology ; Streptococcus suis/*genetics/metabolism ; }, abstract = {Pathogenicity islands (PAIs), a distinct type of genomic island (GI), play important roles in the rapid adaptation and increased virulence of pathogens. 89K is a newly identified PAI in epidemic Streptococcus suis isolates that are related to the two recent large-scale outbreaks of human infection in China. However, its mechanism of evolution and contribution to the epidemic spread of S. suis 2 remain unknown. In this study, the potential for mobilization of 89K was evaluated, and its putative transfer mechanism was investigated. We report that 89K can spontaneously excise to form an extrachromosomal circular product. The precise excision is mediated by an 89K-borne integrase through site-specific recombination, with help from an excisionase. The 89K excision intermediate acts as a substrate for lateral transfer to non-89K S. suis 2 recipients, where it reintegrates site-specifically into the target site. The conjugal transfer of 89K occurred via a GI type IV secretion system (T4SS) encoded in 89K, at a frequency of 10(-6) transconjugants per donor. This is the first demonstration of horizontal transfer of a Gram-positive PAI mediated by a GI-type T4SS. We propose that these genetic events are important in the emergence, pathogenesis and persistence of epidemic S. suis 2 strains.}, }
@article {pmid21239560, year = {2011}, author = {Tamamura, Y and Uchida, I and Tanaka, K and Okazaki, H and Tezuka, S and Hanyu, H and Kataoka, N and Makino, S and Kishima, M and Kubota, T and Kanno, T and Hatama, S and Ishihara, R and Hata, E and Yamada, H and Nakaoka, Y and Akiba, M}, title = {Molecular epidemiology of Salmonella enterica serovar typhimurium isolates from cattle in hokkaido, Japan: evidence of clonal replacement and characterization of the disseminated clone.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {5}, pages = {1739-1750}, pmid = {21239560}, issn = {1098-5336}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Bacterial Typing Techniques ; Cattle ; Cattle Diseases/*epidemiology/*microbiology ; Cluster Analysis ; Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; Drug Resistance, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Japan/epidemiology ; Molecular Epidemiology ; Molecular Sequence Data ; Molecular Typing ; Plasmids ; Salmonella Infections, Animal/*epidemiology/*microbiology ; Salmonella typhimurium/*classification/genetics/*isolation &amp; purification ; Sequence Analysis, DNA ; Virulence Factors/genetics ; }, abstract = {The molecular epidemiology of 545 Salmonella enterica serovar Typhimurium isolates collected between 1977 and 2009 from cattle in Hokkaido, Japan, was investigated using pulsed-field gel electrophoresis (PFGE). Nine main clusters were identified from 116 PFGE patterns. Cluster I comprised 248 isolates, 243 of which possessed a sequence specific to definitive phage type 104 (DT104) or U302. The cluster I isolates were dominant in 1993 to 2003, but their numbers declined beginning in 2004. Beginning in 2002, an increase was observed in the number of cluster VII isolates, consisting of 21 PFGE patterns comprising 165 isolates. A total of 116 isolates representative of the 116 PFGE profiles were analyzed by multilocus variable-number tandem-repeat analysis (MLVA). Other than two drug-sensitive isolates, 19 isolates within cluster VII were classified in the same cluster by MLVA. Among the cluster VII isolates, an antibiotic resistance type showing resistance to ampicillin, chloramphenicol, streptomycin, sulfonamides, tetracycline, kanamycin, cefazolin, and sulfamethoxazole-trimethoprim and a resistance type showing resistance to ampicillin, streptomycin, sulfonamides, tetracycline, and kanamycin were found in 23 and 125 isolates, respectively. In the 19 isolates representative of cluster VII, the bla(TEM-1) gene was found on a Salmonella serotype Typhimurium virulence plasmid, which was transferred to Escherichia coli by electroporation along with resistance to two to four other antimicrobials. Genomic analysis by subtractive hybridization and plasmid analysis suggested that the bla(TEM-1)-carrying virulence plasmid has a mosaic structure composed of elements of different origin. These results indicate an emerging multidrug-resistant S. Typhimurium clone carrying a virulence-resistance plasmid among cattle in Hokkaido, Japan.}, }
@article {pmid21239150, year = {2011}, author = {Chen, D and Lin, J and Che, Y and Liu, X and Lin, J}, title = {Construction of recombinant mercury resistant Acidithiobacillus caldus.}, journal = {Microbiological research}, volume = {166}, number = {7}, pages = {515-520}, doi = {10.1016/j.micres.2010.10.003}, pmid = {21239150}, issn = {1618-0623}, mesh = {Acidithiobacillus/*drug effects/*genetics ; Anti-Bacterial Agents/*toxicity ; Conjugation, Genetic ; *Drug Resistance, Bacterial ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Genetic Vectors ; Mercury/*toxicity ; Microbial Sensitivity Tests ; Plasmids ; }, abstract = {A mercury-resistant plasmid of pTMJ212 which was able to shuttle between Acidithiobacillus caldus and Escherichia coli was constructed by inserting the mercury resistant determinants, the mer operon of Acidithiobacillus ferrooxidans, into the IncQ plasmid of pJRD215. pTMJ212 was transferred from Escherichia coli into Acidithiobacillus caldus through conjugation. Furthermore, pTMJ212 was transferred back from Acidithiobacillus caldus into Escherichia coli, thereby confirming the initial transfer of pTMJ212 from Escherichia coli to Acidithiobacillus caldus. Compared to the control, the cell growth of the recombinant Acidithiobacillus caldus increased markedly under mercury (Hg(2+)) stress especially at Hg(2+) concentrations ranging from 2.0 to 4.5 μg/ml.}, }
@article {pmid21234755, year = {2011}, author = {de Niederhäusern, S and Bondi, M and Messi, P and Iseppi, R and Sabia, C and Manicardi, G and Anacarso, I}, title = {Vancomycin-resistance transferability from VanA enterococci to Staphylococcus aureus.}, journal = {Current microbiology}, volume = {62}, number = {5}, pages = {1363-1367}, pmid = {21234755}, issn = {1432-0991}, mesh = {Bacterial Proteins/*genetics/metabolism ; Carbon-Oxygen Ligases/*genetics/metabolism ; Conjugation, Genetic ; Enterococcus/drug effects/enzymology/*genetics ; *Gene Transfer, Horizontal ; Gram-Positive Bacterial Infections/microbiology ; Humans ; Microbial Sensitivity Tests ; Staphylococcal Infections/microbiology ; Staphylococcus aureus/drug effects/*genetics ; Vancomycin/pharmacology ; Vancomycin Resistance ; }, abstract = {In last decade methicillin-resistant Staphylococcus aureus with high level of vancomycin-resistance (VRSA) have been reported and generally the patients with VRSA infection were also infected with a vancomycin-resistant Enterococcus (VRE). Considering that the high level of vancomycin-resistance in VRSA isolates seems to involve the horizontal transfer of Tn1546 transposon containing vanA gene from coinfecting VRE strains, the authors have studied the "in vitro" conjugative transfer of this resistance from VanA enterococci to S. aureus. Out of 25 matings performed combining five vancomycin-resistant enterococci as donors (three Enterococcus faecalis and two Enterococcus faecium), and five S. aureus as recipients, all clinical isolates, two have been successful using E. faecalis as donor. The transfer of vancomycin-resistance was confirmed by vanA gene amplification in both transconjugants and the resistance was expressed at lower levels (MIC 32 μg/ml) in comparison with the respective VRE donors (MIC > 128 μg/ml). The vancomycin-resistance of trasconjugants was maintained even after subsequent overnight passages on MSA plates containing subinhibitory levels of vancomycin. This study shows that the vanA gene transfer can be achieved through techniques "in vitro" without the use of laboratory animals employed, in the only similar experiment previously carried out by other authors, as substrate for the trasconjugant growth. Moreover, in that previous experiment, contrary to this study, the vancomycin resistant S. aureus trasconjugants were selected on erythromycin agar and not by direct vancomycin agar selection.}, }
@article {pmid21234750, year = {2011}, author = {Eng, C and Thibessard, A and Danielsen, M and Rasmussen, TB and Mari, JF and Leblond, P}, title = {In silico prediction of horizontal gene transfer in Streptococcus thermophilus.}, journal = {Archives of microbiology}, volume = {193}, number = {4}, pages = {287-297}, doi = {10.1007/s00203-010-0671-8}, pmid = {21234750}, issn = {1432-072X}, mesh = {Algorithms ; Data Mining ; Databases, Genetic ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; Genomic Islands ; Markov Chains ; Molecular Sequence Annotation ; Phylogeny ; Stochastic Processes ; Streptococcus thermophilus/*genetics ; }, abstract = {A combination of gene loss and acquisition through horizontal gene transfer (HGT) is thought to drive Streptococcus thermophilus adaptation to its niche, i.e. milk. In this study, we describe an in silico analysis combining a stochastic data mining method, analysis of homologous gene distribution and the identification of features frequently associated with horizontally transferred genes to assess the proportion of the S. thermophilus genome that could originate from HGT. Our mining approach pointed out that about 17.7% of S. thermophilus genes (362 CDSs of 1,915) showed a composition bias; these genes were called 'atypical'. For 22% of them, their functional annotation strongly support their acquisition through HGT and consisted mainly in genes encoding mobile genetic recombinases, exopolysaccharide (EPS) biosynthesis enzymes or resistance mechanisms to bacteriophages. The distribution of the atypical genes in the Firmicutes phylum as well as in S. thermophilus species was sporadic and supported the HGT prediction for more than a half (52%, 189). Among them, 46 were found specific to S. thermophilus. Finally, by combining our method, gene annotation and sequence specific features, new genome islands were suggested in the S. thermophilus genome.}, }
@article {pmid21233529, year = {2011}, author = {Tofigh, A and Hallett, M and Lagergren, J}, title = {Simultaneous identification of duplications and lateral gene transfers.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {8}, number = {2}, pages = {517-535}, doi = {10.1109/TCBB.2010.14}, pmid = {21233529}, issn = {1557-9964}, mesh = {*Algorithms ; Evolution, Molecular ; *Gene Duplication ; Gene Transfer, Horizontal/*genetics ; Models, Genetic ; }, abstract = {The incongruency between a gene tree and a corresponding species tree can be attributed to evolutionary events such as gene duplication and gene loss. This paper describes a combinatorial model where so-called DTL-scenarios are used to explain the differences between a gene tree and a corresponding species tree taking into account gene duplications, gene losses, and lateral gene transfers (also known as horizontal gene transfers). The reasonable biological constraint that a lateral gene transfer may only occur between contemporary species leads to the notion of acyclic DTL-scenarios. Parsimony methods are introduced by defining appropriate optimization problems. We show that finding most parsimonious acyclic DTL-scenarios is NP-hard. However, by dropping the condition of acyclicity, the problem becomes tractable, and we provide a dynamic programming algorithm as well as a fixed-parameter tractable algorithm for finding most parsimonious DTL-scenarios.}, }
@article {pmid21233422, year = {2011}, author = {Goulas, T and Arolas, JL and Gomis-Rüth, FX}, title = {Structure, function and latency regulation of a bacterial enterotoxin potentially derived from a mammalian adamalysin/ADAM xenolog.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {5}, pages = {1856-1861}, pmid = {21233422}, issn = {1091-6490}, mesh = {Animals ; Bacteroides fragilis/*metabolism ; Enterotoxins/chemistry/*toxicity ; Hydrolysis ; Metalloendopeptidases/*metabolism ; Models, Molecular ; Protein Conformation ; Structure-Activity Relationship ; }, abstract = {Enterotoxigenic Bacteroides fragilis is the most frequent disease-causing anaerobe in the intestinal tract of humans and livestock and its specific virulence factor is fragilysin, also known as B. fragilis toxin. This is a 21-kDa zinc-dependent metallopeptidase existing in three closely related isoforms that hydrolyze E-cadherin and contribute to secretory diarrhea, and possibly to inflammatory bowel disease and colorectal cancer. Here we studied the function and zymogenic structure of fragilysin-3 and found that its activity is repressed by a ∼170-residue prodomain, which is the largest hitherto structurally characterized for a metallopeptidase. This prodomain plays a role in both the latency and folding stability of the catalytic domain and it has no significant sequence similarity to any known protein. The prodomain adopts a novel fold and inhibits the protease domain via an aspartate-switch mechanism. The catalytic fragilysin-3 moiety is active against several protein substrates and its structure reveals a new family prototype within the metzincin clan of metallopeptidases. It shows high structural similarity despite negligible sequence identity to adamalysins/ADAMs, which have only been described in eukaryotes. Because no similar protein has been found outside enterotoxigenic B. fragilis, our findings support that fragilysins derived from a mammalian adamalysin/ADAM xenolog that was co-opted by B. fragilis through a rare case of horizontal gene transfer from a eukaryotic cell to a bacterial cell. Subsequently, this co-opted peptidase was provided with a unique chaperone and latency maintainer in the time course of evolution to render a robust and dedicated toxin to compromise the intestinal epithelium of mammalian hosts.}, }
@article {pmid21233162, year = {2011}, author = {Holkenbrink, C and Barbas, SO and Mellerup, A and Otaki, H and Frigaard, NU}, title = {Sulfur globule oxidation in green sulfur bacteria is dependent on the dissimilatory sulfite reductase system.}, journal = {Microbiology (Reading, England)}, volume = {157}, number = {Pt 4}, pages = {1229-1239}, doi = {10.1099/mic.0.044669-0}, pmid = {21233162}, issn = {1465-2080}, mesh = {Chlorobi/genetics/growth &amp; development/*metabolism ; Gene Deletion ; Genes, Bacterial/genetics ; Hydrogensulfite Reductase/genetics/*metabolism ; Metabolic Networks and Pathways/genetics ; Models, Biological ; Multigene Family ; Oxidation-Reduction ; Sulfates/metabolism ; Sulfides/metabolism ; Sulfur/*metabolism ; Thiosulfates/metabolism ; }, abstract = {Green sulfur bacteria (GSB) oxidize sulfide and thiosulfate to sulfate, with extracellular globules of elemental sulfur as an intermediate. Here we investigated which genes are involved in the formation and consumption of these sulfur globules in the green sulfur bacterium Chlorobaculum tepidum. We show that sulfur globule oxidation is strictly dependent on the dissimilatory sulfite reductase (DSR) system. Deletion of dsrM/CT2244 or dsrT/CT2245, or the two dsrCABL clusters (CT0851-CT0854, CT2247-2250), abolished sulfur globule oxidation and prevented formation of sulfate from sulfide, whereas deletion of dsrU/CT2246 had no effect. The DSR system also seems to be involved in the formation of thiosulfate, because thiosulfate was released from wild-type cells during sulfide oxidation, but not from the dsr mutants. The dsr mutants incapable of complete substrate oxidation oxidized sulfide and thiosulfate about twice as fast as the wild-type, while having only slightly lower growth rates (70-80 % of wild-type). The increased oxidation rates seem to compensate for the incomplete substrate oxidation to satisfy the requirement for reducing equivalents during growth. A mutant in which two sulfide : quinone oxidoreductases (sqrD/CT0117 and sqrF/CT1087) were deleted exhibited a decreased sulfide oxidation rate (~50 % of wild-type), yet formation and consumption of sulfur globules were not affected. The observation that mutants lacking the DSR system maintain efficient growth suggests that the DSR system is dispensable in environments with sufficiently high sulfide concentrations. Thus, the DSR system in GSB may have been acquired by horizontal gene transfer as a response to a need for enhanced substrate utilization in sulfide-limiting habitats.}, }
@article {pmid21232122, year = {2011}, author = {Mayer, WE and Schuster, LN and Bartelmes, G and Dieterich, C and Sommer, RJ}, title = {Horizontal gene transfer of microbial cellulases into nematode genomes is associated with functional assimilation and gene turnover.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {13}, pmid = {21232122}, issn = {1471-2148}, mesh = {Amino Acid Sequence ; Animals ; Cellulase/chemistry/*genetics/*metabolism ; *Gene Transfer, Horizontal ; *Genome, Helminth ; Helminth Proteins/chemistry/*genetics/*metabolism ; Molecular Sequence Data ; Nematoda/classification/*enzymology/genetics ; Sequence Alignment ; }, abstract = {BACKGROUND: Natural acquisition of novel genes from other organisms by horizontal or lateral gene transfer is well established for microorganisms. There is now growing evidence that horizontal gene transfer also plays important roles in the evolution of eukaryotes. Genome-sequencing and EST projects of plant and animal associated nematodes such as Brugia, Meloidogyne, Bursaphelenchus and Pristionchus indicate horizontal gene transfer as a key adaptation towards parasitism and pathogenicity. However, little is known about the functional activity and evolutionary longevity of genes acquired by horizontal gene transfer and the mechanisms favoring such processes.<br><br>RESULTS: We examine the transfer of cellulase genes to the free-living and beetle-associated nematode Pristionchus pacificus, for which detailed phylogenetic knowledge is available, to address predictions by evolutionary theory for successful gene transfer. We used transcriptomics in seven Pristionchus species and three other related diplogastrid nematodes with a well-defined phylogenetic framework to study the evolution of ancestral cellulase genes acquired by horizontal gene transfer. We performed intra-species, inter-species and inter-genic analysis by comparing the transcriptomes of these ten species and tested for cellulase activity in each species. Species with cellulase genes in their transcriptome always exhibited cellulase activity indicating functional integration into the host's genome and biology. The phylogenetic profile of cellulase genes was congruent with the species phylogeny demonstrating gene longevity. Cellulase genes show notable turnover with elevated birth and death rates. Comparison by sequencing of three selected cellulase genes in 24 natural isolates of Pristionchus pacificus suggests these high evolutionary dynamics to be associated with copy number variations and positive selection.<br><br>CONCLUSION: We could demonstrate functional integration of acquired cellulase genes into the nematode's biology as predicted by theory. Thus, functional assimilation, remarkable gene turnover and selection might represent key features of horizontal gene transfer events in nematodes.}, }
@article {pmid21227922, year = {2011}, author = {Dam, P and Kataeva, I and Yang, SJ and Zhou, F and Yin, Y and Chou, W and Poole, FL and Westpheling, J and Hettich, R and Giannone, R and Lewis, DL and Kelly, R and Gilbert, HJ and Henrissat, B and Xu, Y and Adams, MW}, title = {Insights into plant biomass conversion from the genome of the anaerobic thermophilic bacterium Caldicellulosiruptor bescii DSM 6725.}, journal = {Nucleic acids research}, volume = {39}, number = {8}, pages = {3240-3254}, pmid = {21227922}, issn = {1362-4962}, mesh = {Bacterial Adhesion ; Bacterial Proteins/genetics ; Biomass ; Carbohydrate Metabolism/*genetics ; Gene Expression Profiling ; Genes, Bacterial ; *Genome, Bacterial ; Genomics ; Gram-Positive Bacteria/*genetics/metabolism/ultrastructure ; Plants/metabolism ; Proteomics ; }, abstract = {Caldicellulosiruptor bescii DSM 6725 utilizes various polysaccharides and grows efficiently on untreated high-lignin grasses and hardwood at an optimum temperature of ∼ 80 °C. It is a promising anaerobic bacterium for studying high-temperature biomass conversion. Its genome contains 2666 protein-coding sequences organized into 1209 operons. Expression of 2196 genes (83%) was confirmed experimentally. At least 322 genes appear to have been obtained by lateral gene transfer (LGT). Putative functions were assigned to 364 conserved/hypothetical protein (C/HP) genes. The genome contains 171 and 88 genes related to carbohydrate transport and utilization, respectively. Growth on cellulose led to the up-regulation of 32 carbohydrate-active (CAZy), 61 sugar transport, 25 transcription factor and 234 C/HP genes. Some C/HPs were overproduced on cellulose or xylan, suggesting their involvement in polysaccharide conversion. A unique feature of the genome is enrichment with genes encoding multi-modular, multi-functional CAZy proteins organized into one large cluster, the products of which are proposed to act synergistically on different components of plant cell walls and to aid the ability of C. bescii to convert plant biomass. The high duplication of CAZy domains coupled with the ability to acquire foreign genes by LGT may have allowed the bacterium to rapidly adapt to changing plant biomass-rich environments.}, }
@article {pmid21226929, year = {2011}, author = {Delaye, L and González-Domenech, CM and Garcillán-Barcia, MP and Peretó, J and de la Cruz, F and Moya, A}, title = {Blueprint for a minimal photoautotrophic cell: conserved and variable genes in Synechococcus elongatus PCC 7942.}, journal = {BMC genomics}, volume = {12}, number = {}, pages = {25}, pmid = {21226929}, issn = {1471-2164}, mesh = {Bacterial Proteins/blood/*genetics ; Base Composition/genetics ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/genetics ; Genomic Islands/genetics ; Open Reading Frames/genetics ; Phylogeny ; Synechococcus/*genetics ; }, abstract = {BACKGROUND: Simpler biological systems should be easier to understand and to engineer towards pre-defined goals. One way to achieve biological simplicity is through genome minimization. Here we looked for genomic islands in the fresh water cyanobacteria Synechococcus elongatus PCC 7942 (genome size 2.7 Mb) that could be used as targets for deletion. We also looked for conserved genes that might be essential for cell survival.<br><br>RESULTS: By using a combination of methods we identified 170 xenologs, 136 ORFans and 1401 core genes in the genome of S. elongatus PCC 7942. These represent 6.5%, 5.2% and 53.6% of the annotated genes respectively. We considered that genes in genomic islands could be found if they showed a combination of: a) unusual G+C content; b) unusual phylogenetic similarity; and/or c) a small number of the highly iterated palindrome 1 (HIP1) motif plus an unusual codon usage. The origin of the largest genomic island by horizontal gene transfer (HGT) could be corroborated by lack of coverage among metagenomic sequences from a fresh water microbialite. Evidence is also presented that xenologous genes tend to cluster in operons. Interestingly, most genes coding for proteins with a diguanylate cyclase domain are predicted to be xenologs, suggesting a role for horizontal gene transfer in the evolution of Synechococcus sensory systems.<br><br>CONCLUSIONS: Our estimates of genomic islands in PCC 7942 are larger than those predicted by other published methods like SIGI-HMM. Our results set a guide to non-essential genes in S. elongatus PCC 7942 indicating a path towards the engineering of a model photoautotrophic bacterial cell.}, }
@article {pmid21223537, year = {2011}, author = {Shimomura, Y and Okumura, K and Murayama, SY and Yagi, J and Ubukata, K and Kirikae, T and Miyoshi-Akiyama, T}, title = {Complete genome sequencing and analysis of a Lancefield group G Streptococcus dysgalactiae subsp. equisimilis strain causing streptococcal toxic shock syndrome (STSS).}, journal = {BMC genomics}, volume = {12}, number = {}, pages = {17}, pmid = {21223537}, issn = {1471-2164}, mesh = {Animals ; Bacterial Toxins/genetics ; Female ; *Genome, Bacterial ; Humans ; Mice ; Prophages/genetics ; Shock, Septic/*microbiology ; Streptococcus/*genetics/pathogenicity/virology ; Virulence Factors/genetics ; }, abstract = {BACKGROUND: Streptococcus dysgalactiae subsp. equisimilis (SDSE) causes invasive streptococcal infections, including streptococcal toxic shock syndrome (STSS), as does Lancefield group A Streptococcus pyogenes (GAS). We sequenced the entire genome of SDSE strain GGS_124 isolated from a patient with STSS.<br><br>RESULTS: We found that GGS_124 consisted of a circular genome of 2,106,340 bp. Comparative analyses among bacterial genomes indicated that GGS_124 was most closely related to GAS. GGS_124 and GAS, but not other streptococci, shared a number of virulence factor genes, including genes encoding streptolysin O, NADase, and streptokinase A, distantly related to SIC (DRS), suggesting the importance of these factors in the development of invasive disease. GGS_124 contained 3 prophages, with one containing a virulence factor gene for streptodornase. All 3 prophages were significantly similar to GAS prophages that carry virulence factor genes, indicating that these prophages had transferred these genes between pathogens. SDSE was found to contain a gene encoding a superantigen, streptococcal exotoxin type G, but lacked several genes present in GAS that encode virulence factors, such as other superantigens, cysteine protease speB, and hyaluronan synthase operon hasABC. Similar to GGS_124, the SDSE strains contained larger numbers of clustered, regularly interspaced, short palindromic repeats (CRISPR) spacers than did GAS, suggesting that horizontal gene transfer via streptococcal phages between SDSE and GAS is somewhat restricted, although they share phage species.<br><br>CONCLUSION: Genome wide comparisons of SDSE with GAS indicate that SDSE is closely and quantitatively related to GAS. SDSE, however, lacks several virulence factors of GAS, including superantigens, SPE-B and the hasABC operon. CRISPR spacers may limit the horizontal transfer of phage encoded GAS virulence genes into SDSE. These findings may provide clues for dissecting the pathological roles of the virulence factors in SDSE and GAS that cause STSS.}, }
@article {pmid21223328, year = {2011}, author = {Del Casale, A and Flanagan, PV and Larkin, MJ and Allen, CC and Kulakov, LA}, title = {Analysis of transduction in wastewater bacterial populations by targeting the phage-derived 16S rRNA gene sequences.}, journal = {FEMS microbiology ecology}, volume = {76}, number = {1}, pages = {100-108}, doi = {10.1111/j.1574-6941.2010.01034.x}, pmid = {21223328}, issn = {1574-6941}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; Bacteriophages/*genetics ; DNA, Bacterial/genetics ; DNA, Viral/genetics ; Denaturing Gradient Gel Electrophoresis ; Gene Library ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Metagenome ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; *Transduction, Genetic ; Waste Disposal, Fluid ; Water Microbiology ; }, abstract = {Bacterial 16S rRNA genes transduced by bacteriophages were identified and analyzed in order to estimate the extent of the bacteriophage-mediated horizontal gene transfer in the wastewater environment. For this purpose, phage and bacterial DNA was isolated from the oxidation tank of a municipal wastewater treatment plant. Phylogenetic analysis of the 16S rRNA gene sequences cloned from a phage metagenome revealed that bacteriophages transduce genetic material in several major groups of bacteria. The groups identified were as follows: Betaproteobacteria, Gammaproteobacteria, Alphaproteobacteria, Actinomycetales and Firmicutes. Analysis of the 16S rRNA gene sequences in the total bacterial DNA from the same sample revealed that several bacterial groups found in the oxidation tank were not present in the phage metagenome (e.g. Deltaproteobacteria, Nitrospira, Planctomycetes and many Actinobacteria genera). These results suggest that transduction in a wastewater environment occurs in several bacterial groups; however, not all species are equally involved into this process. The data also showed that a number of distinctive bacterial strains participate in transduction-mediated gene transfer within identified bacterial groupings. Denaturing gradient gel electrophoresis analysis confirmed that profiles of the transduced 16S rRNA gene sequences and those present in the whole microbial community show significant differences.}, }
@article {pmid21223323, year = {2011}, author = {Mehrabi, R and Bahkali, AH and Abd-Elsalam, KA and Moslem, M and Ben M'barek, S and Gohari, AM and Jashni, MK and Stergiopoulos, I and Kema, GH and de Wit, PJ}, title = {Horizontal gene and chromosome transfer in plant pathogenic fungi affecting host range.}, journal = {FEMS microbiology reviews}, volume = {35}, number = {3}, pages = {542-554}, doi = {10.1111/j.1574-6976.2010.00263.x}, pmid = {21223323}, issn = {1574-6976}, mesh = {Ascomycota/*genetics/pathogenicity/physiology ; Chromosomes, Fungal/*genetics ; *Gene Transfer, Horizontal ; *Host Specificity ; Plant Diseases/*microbiology ; Plants/*microbiology ; }, abstract = {Plant pathogenic fungi adapt quickly to changing environments including overcoming plant disease resistance genes. This is usually achieved by mutations in single effector genes of the pathogens, enabling them to avoid recognition by the host plant. In addition, horizontal gene transfer (HGT) and horizontal chromosome transfer (HCT) provide a means for pathogens to broaden their host range. Recently, several reports have appeared in the literature on HGT, HCT and hybridization between plant pathogenic fungi that affect their host range, including species of Stagonospora/Pyrenophora, Fusarium and Alternaria. Evidence is given that HGT of the ToxA gene from Stagonospora nodorum to Pyrenophora tritici-repentis enabled the latter fungus to cause a serious disease in wheat. A nonpathogenic Fusarium species can become pathogenic on tomato by HCT of a pathogenicity chromosome from Fusarium oxysporum f.sp lycopersici, a well-known pathogen of tomato. Similarly, Alternaria species can broaden their host range by HCT of a single chromosome carrying a cluster of genes encoding host-specific toxins that enabled them to become pathogenic on new hosts such as apple, Japanese pear, strawberry and tomato, respectively. The mechanisms HGT and HCT and their impact on potential emergence of fungal plant pathogens adapted to new host plants will be discussed.}, }
@article {pmid21223321, year = {2011}, author = {Skippington, E and Ragan, MA}, title = {Lateral genetic transfer and the construction of genetic exchange communities.}, journal = {FEMS microbiology reviews}, volume = {35}, number = {5}, pages = {707-735}, doi = {10.1111/j.1574-6976.2010.00261.x}, pmid = {21223321}, issn = {1574-6976}, mesh = {*Adaptation, Biological ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/*genetics ; Bacterial Infections/microbiology ; Drug Resistance, Bacterial ; *Gene Transfer, Horizontal ; Humans ; Recombination, Genetic ; *Selection, Genetic ; }, abstract = {Lateral genetic transfer (LGT) is a major source of phenotypic innovation among bacteria. Determinants for antibiotic resistance and other adaptive traits can spread rapidly, particularly by conjugative plasmids, but also phages and natural transformation. Each successive step from the uptake of foreign DNA, its genetic recombination and regulatory integration, to its establishment in the host population presents differential barriers and opportunities. The emergence of successive multidrug-resistant strains of Staphylococcus aureus illustrates the ongoing role of LGT in the combinatorial assembly of pathogens. The dynamic interplay among hosts, vectors, DNA elements, combinations of genetic determinants and environments constructs communities of genetic exchange. These relations can be abstracted as a graph, within which an exchange community might correspond to a path, transitively closed set, clique or near-clique. We provide a set-based definition, and review the features of actual genetic exchange communities (GECs), adopting first a knowledge-driven approach based on literature, and then a synoptic data-centric bioinformatic approach. GECs are diverse, but share some common features. Differential opportunity and barriers to lateral genetic transfer create bacterial communities of exchange.}, }
@article {pmid21221780, year = {2011}, author = {Xu, J and Zhao, J and Wang, J and Zhao, Y and Zhang, L and Chu, M and Li, N}, title = {Molecular-based environmental risk assessment of three varieties of genetically engineered cows.}, journal = {Transgenic research}, volume = {20}, number = {5}, pages = {1043-1054}, pmid = {21221780}, issn = {1573-9368}, mesh = {Animals ; Animals, Genetically Modified/genetics/microbiology/*physiology ; Base Sequence ; Cattle/genetics/microbiology/*physiology ; Ecological and Environmental Phenomena ; Gene Transfer, Horizontal ; Humans ; Lactalbumin/genetics/metabolism ; Lactoferrin/genetics/metabolism ; Manure/microbiology ; Molecular Sequence Data ; Muramidase/genetics/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Risk Assessment ; *Soil Microbiology ; Transgenes/genetics ; }, abstract = {The development of animal biotechnology has led to an increase in attention to biosafety issues. Here we evaluated the impact of genetically engineered cows on the environment. The probability of horizontal gene transfer and the impact on the microbial communities in cow gut and soil were tested using three varieties of genetically engineered cows that were previously transformed with a human gene encoding lysozyme, lactoferrin, or human alpha lactalbumin. The results showed that the transgenes were not detectable by polymerase chain reaction (PCR) or quantitative real-time PCR in gut microbial DNA extracts of manure or microbial DNA extracts of topsoil. In addition, the transgenes had no impact on the microbial communities in cow gut or soil as assessed by PCR-denaturing gradient gel electrophoresis or 16S rDNA sequencing. Furthermore, phylogenetic analyses showed that the manure bacteria sampled during each of the four seasons belonged primarily to two groups, Firmicutes and Bacteroidetes, and the soil bacteria belonged to four groups, Firmicutes, Bacteroidetes, Actinobacteria, and α-proteobacteria. Other groups, such as β-proteobacteria, γ-proteobacteria, δ-proteobacteria, ε-proteobacteria, Spirochaetes, Acidobacteria, Chloroflexi, and Nitrospira, were not dominant in the manure or soil.}, }
@article {pmid21212956, year = {2011}, author = {Nawaz, M and Wang, J and Zhou, A and Ma, C and Wu, X and Moore, JE and Millar, BC and Xu, J}, title = {Characterization and transfer of antibiotic resistance in lactic acid bacteria from fermented food products.}, journal = {Current microbiology}, volume = {62}, number = {3}, pages = {1081-1089}, pmid = {21212956}, issn = {1432-0991}, mesh = {Anti-Bacterial Agents/pharmacology ; China ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Drug Resistance, Bacterial ; Enterococcus faecalis/classification/drug effects/*genetics/isolation &amp; purification ; *Food Microbiology ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Lactobacillus/classification/drug effects/*genetics/isolation &amp; purification ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Streptococcus thermophilus/classification/drug effects/*genetics/isolation &amp; purification ; }, abstract = {The study provides phenotypic and molecular analyses of the antibiotic resistance in lactic acid bacteria (LAB) from fermented foods in Xi'an, China. LAB strains (n = 84) belonging to 16 species of Lactobacillus (n = 73), and Streptococcus thermophilus (n = 11) were isolated and identified by sequencing their 16S rRNA gene. All strains were susceptible to ampicillin, bacitracin, and cefsulodin, and intrinsically resistant to nalidixic acid, kanamycin, and vancomycin (except L. bulgaricus, L. acidophilus, and S. thermophilus, which were susceptible to vancomycin). Some strains had acquired resistance for penicillin (n = 2), erythromycin (n = 9), clindamycin (n = 5), and tetracycline (n = 14), while resistance to gentamycin, ciprofloxacin, streptomycin, and chloramphenicol was species dependent. Minimum inhibitory concentrations presented in this study will help to review microbiological breakpoints for some of the species of Lactobacillus. The erm(B) gene was detected from two strains of each of L. fermentum and L. vaginalis, and one strain of each of L. plantarum, L. salivarius, L. acidophilus, L. animalis, and S. thermophilus. The tet genes were identified from 12 strains of lactobacilli from traditional foods. This is the first time, the authors identified tet(S) gene from L. brevis and L. kefiri. The erm(B) gene from L. fermentum NWL24 and L. salivarius NWL33, and tet(M) gene from L. plantarum NWL22 and L. brevis NWL59 were successfully transferred to Enterococcus faecalis 181 by filter mating. It was concluded that acquired antibiotic resistance is well dispersed in fermented food products in Xi'an, China and its transferability to other genera should be monitored closely.}, }
@article {pmid21212120, year = {2011}, author = {Sheppard, SK and McCarthy, ND and Jolley, KA and Maiden, MCJ}, title = {Introgression in the genus Campylobacter: generation and spread of mosaic alleles.}, journal = {Microbiology (Reading, England)}, volume = {157}, number = {Pt 4}, pages = {1066-1074}, pmid = {21212120}, issn = {1465-2080}, support = {//Wellcome Trust/United Kingdom ; 087622//Wellcome Trust/United Kingdom ; }, mesh = {Alleles ; Bacterial Proteins/*genetics ; Campylobacter coli/classification/*genetics ; Campylobacter jejuni/classification/*genetics ; *Polymorphism, Genetic ; *Recombination, Genetic ; Sequence Homology ; }, abstract = {Horizontal genetic exchange strongly influences the evolution of many bacteria, substantially contributing to difficulties in defining their position in taxonomic groups. In particular, how clusters of related bacterial genotypes - currently classified as microbiological species - evolve and are maintained remains controversial. The nature and magnitude of gene exchange between two closely related (approx. 15 % nucleotide divergence) microbiologically defined species, Campylobacter jejuni and Campylobacter coli, was investigated by the examination of mosaic alleles, those with some ancestry from each population. A total of 1738 alleles from 2953 seven-locus housekeeping gene sequence types (STs) were probabilistically assigned to each species group with the model-based clustering algorithm structure. Alleles with less than 75 % assignment probability to one of the populations were confirmed as mosaics using the structure linkage model. For each of these, the putative source of the recombinant region was determined and the allele was mapped onto a clonalframe genealogy derived from concatenated ST sequences. This enabled the direction and frequency of introgression between the two populations to be established, with 8.3 % of C. coli clade 1 alleles having acquired C. jejuni sequence, compared to 0.5 % for the reciprocal process. Once generated, mosaic genes spread within C. coli clade 1 by a combination of clonal expansion and lateral gene transfer, with some evidence of erosion of the mosaics by reacquisition of C. coli sequence. These observations confirm previous analyses of the exchange of complete housekeeping alleles and extend this work by describing the processes of horizontal gene transfer and subsequent spread within recipient species.}, }
@article {pmid21210735, year = {2011}, author = {Collins, J and Linz, S and Semple, C}, title = {Quantifying hybridization in realistic time.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {18}, number = {10}, pages = {1305-1318}, doi = {10.1089/cmb.2009.0166}, pmid = {21210735}, issn = {1557-8666}, mesh = {*Algorithms ; *Biological Evolution ; Computational Biology/*methods ; Computer Simulation ; Evolution, Molecular ; Hybridization, Genetic/*genetics ; *Models, Genetic ; Time Factors ; }, abstract = {Recently, numerous practical and theoretical studies in evolutionary biology aim at calculating the extent to which reticulation-for example, horizontal gene transfer, hybridization, or recombination-has influenced the evolution for a set of present-day species. It has been shown that inferring the minimum number of hybridization events that is needed to simultaneously explain the evolutionary history for a set of trees is an NP-hard and also fixed-parameter tractable problem. In this article, we give a new fixed-parameter algorithm for computing the minimum number of hybridization events for when two rooted binary phylogenetic trees are given. This newly developed algorithm is based on interleaving-a technique using repeated kernelization steps that are applied throughout the exhaustive search part of a fixed-parameter algorithm. To show that our algorithm runs efficiently to be applicable to a wide range of practical problem instances, we apply it to a grass data set and highlight the significant improvements in terms of running times in comparison to an algorithm that has previously been implemented.}, }
@article {pmid21210187, year = {2011}, author = {Wu, M and Sun, Z and Luo, G and Hu, C and Zhang, W and Han, Z}, title = {Cloning and characterization of piggyBac-like elements in lepidopteran insects.}, journal = {Genetica}, volume = {139}, number = {1}, pages = {149-154}, pmid = {21210187}, issn = {1573-6857}, mesh = {Amino Acid Sequence ; Animals ; China ; *Cloning, Molecular ; DNA Transposable Elements/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Lepidoptera/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Terminal Repeat Sequences ; Transposases/genetics ; }, abstract = {PiggyBac-like elements (PLE) are widespread in variety of organisms, however, few of them are active or have an intact transposon structure. To further define the distribution PLEs in Lepidoptera, where the original active piggyBac IFP2 was discovered, and potentially isolate new functional elements, a survey for PLEs by PCR amplification and Southern dot blots was performed. Two new PLEs, AyPLE and AaPLE, were successfully isolated from the noctuid species, Agrotis ypsilon and Argyrogramma agnate, respectively. These elements were found to be closely related to each other by sequence similarity, and by sharing the same 16 bp inverted terminal repeat sequences. The AyPLE1.1 and AaPLE1.1 elements are structurally intact having characteristic TTAA target site duplications, inverted terminal repeats and intact open reading frames encoding putative transposases with the presumed piggyBac DDD domains, which are features consistent with autonomous functional transposons. Phylogenetic analysis revealed that AyPLE1.1 and AaPLE1.1 cluster with another noctuid species element, HaPLE1.1, suggesting a common ancestor for the three types of PLEs. This contributes to our understanding of the distribution and evolution of piggyBac in Lepidoptera.}, }
@article {pmid21210168, year = {2011}, author = {Rose, I and Biuković, G and Aderhold, P and Müller, V and Grüber, G and Averhoff, B}, title = {Identification and characterization of a unique, zinc-containing transport ATPase essential for natural transformation in Thermus thermophilus HB27.}, journal = {Extremophiles : life under extreme conditions}, volume = {15}, number = {2}, pages = {191-202}, pmid = {21210168}, issn = {1433-4909}, mesh = {Adenosine Triphosphatases/*chemistry/*genetics ; Adenosine Triphosphate/chemistry ; Amino Acid Sequence ; Chromatography, Gel ; DNA, Bacterial/genetics ; Fimbriae Proteins/genetics ; Gene Expression Regulation, Bacterial ; Gene Expression Regulation, Enzymologic ; Molecular Motor Proteins/genetics ; Molecular Sequence Data ; Mutation ; Protein Structure, Tertiary ; Sequence Homology, Amino Acid ; Spectrophotometry, Atomic/methods ; Thermus thermophilus/*genetics ; Zinc/chemistry ; }, abstract = {Thermus thermophilus is a model strain to unravel the molecular basis of horizontal gene transfer in hot environments. Previous genetic studies led to the identification of a macromolecular transport machinery mediating DNA uptake in an energy-dependent manner. Here, we have addressed how the transporter is energized. Inspection of the genome sequence revealed four putative transport (AAA) ATPases but only the deletion of one, PilF, led to a transformation defect. PilF is similar to transport ATPases of type IV and type II secretions systems but has a unique N-terminal sequence that carries a triplicated GSPII domain. To characterize PilF biochemically it was produced in Escherichia coli and purified. The recombinant protein displayed NTPase activity with a preference for ATP. Gel filtration analyses combined with dynamic light scattering demonstrated that PilF is monodispersed in solution and forms a complex of 590 ± 30 kDa, indicating a homooligomer of six subunits. It contains a tetracysteine motif, previously shown to bind Zn(2+) in related NTPases. Using atomic absorption spectroscopy, indeed Zn(2+) was detected in the enzyme, but in contrast to all known zinc-binding traffic NTPases only one zinc atom was bound to the hexamer. Deletion of the four cysteine residues led to a loss of Zn(2+). Nevertheless, the mutant protein retained ATPase activity and hexameric complex formation.}, }
@article {pmid21203520, year = {2010}, author = {Johnson, TJ and Thorsness, JL and Anderson, CP and Lynne, AM and Foley, SL and Han, J and Fricke, WF and McDermott, PF and White, DG and Khatri, M and Stell, AL and Flores, C and Singer, RS}, title = {Horizontal gene transfer of a ColV plasmid has resulted in a dominant avian clonal type of Salmonella enterica serovar Kentucky.}, journal = {PloS one}, volume = {5}, number = {12}, pages = {e15524}, pmid = {21203520}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; Chickens ; Electrophoresis, Gel, Pulsed-Field ; Gene Deletion ; *Gene Transfer Techniques ; Genes, Bacterial ; Geography ; Models, Genetic ; Molecular Sequence Data ; Plasmids/metabolism ; Polymerase Chain Reaction/methods ; Salmonella enterica/*genetics ; Virulence ; }, abstract = {Salmonella enterica continues to be a significant cause of foodborne gastrointestinal illness in humans. A wide variety of Salmonella serovars have been isolated from production birds and from retail poultry meat. Recently, though, S. enterica subsp. enterica serovar Kentucky has emerged as one of the prominent Salmonella serovars isolated from broiler chickens. Recent work suggests that its emergence apparently coincides with its acquisition of a ColV virulence plasmid. In the present study, we examined 902 Salmonella isolates belonging to 59 different serovars for the presence of this plasmid. Of the serovars examined, the ColV plasmid was found only among isolates belonging to the serovars Kentucky (72.9%), Typhimurium (15.0%) and Heidelberg (1.7%). We demonstrated that a single PFGE clonal type of S. Kentucky harbors this plasmid, and acquisition of this plasmid by S. Kentucky significantly increased its ability to colonize the chicken cecum and cause extraintestinal disease. Comparison of the completed sequences of three ColV plasmids from S. Kentucky isolated from different geographical locales, timepoints and sources revealed a nearly identical genetic structure with few single nucleotide changes or insertions/deletions. Overall, it appears that the ColV plasmid was recently acquired by a single clonal type S. Kentucky and confers to its host enhanced colonization and fitness capabilities. Thus, the potential for horizontal gene transfer of virulence and fitness factors to Salmonella from other enteric bacteria exists in poultry, representing a potential human health hazard.}, }
@article {pmid21199581, year = {2011}, author = {Vogan, AA and Higgs, PG}, title = {The advantages and disadvantages of horizontal gene transfer and the emergence of the first species.}, journal = {Biology direct}, volume = {6}, number = {}, pages = {1}, pmid = {21199581}, issn = {1745-6150}, mesh = {Algorithms ; Cluster Analysis ; Computer Simulation ; Evolution, Molecular ; Gene Deletion ; Gene Transfer, Horizontal/*physiology ; Genetic Fitness/physiology ; *Genetic Speciation ; Genome/physiology ; *Models, Genetic ; Phylogeny ; }, abstract = {BACKGROUND: Horizontal Gene Transfer (HGT) is beneficial to a cell if the acquired gene confers a useful function, but is detrimental if the gene has no function, if it is incompatible with existing genes, or if it is a selfishly replicating mobile element. If the balance of these effects is beneficial on average, we would expect cells to evolve high rates of acceptance of horizontally transferred genes, whereas if it is detrimental, cells should reduce the rate of HGT as far as possible. It has been proposed that the rate of HGT was very high in the early stages of prokaryotic evolution, and hence there were no separate lineages of organisms. Only when the HGT rate began to fall, would lineages begin to emerge with their own distinct sets of genes. Evolution would then become more tree-like. This phenomenon has been called the Darwinian Threshold.<br><br>RESULTS: We study a model for genome evolution that incorporates both beneficial and detrimental effects of HGT. We show that if rate of gene loss during genome replication is high, as was probably the case in the earliest genomes before the time of the last universal common ancestor, then a high rate of HGT is favourable. HGT leads to the rapid spread of new genes and allows the build-up of larger, fitter genomes than could be achieved by purely vertical inheritance. In contrast, if the gene loss rate is lower, as in modern prokaryotes, then HGT is, on average, unfavourable.<br><br>CONCLUSIONS: Modern cells should therefore evolve to reduce HGT if they can, although the prevalence of independently replicating mobile elements and viruses may mean that cells cannot avoid HGT in practice. In the model, natural selection leads to gradual improvement of the replication accuracy and gradual decrease in the optimal rate of HGT. By clustering genomes based on gene content, we show that there are no separate lineages of organisms when the rate of HGT is high; however, as the rate of HGT decreases, a tree-like structure emerges with well-defined lineages. The model therefore passes through a Darwinian Threshold.}, }
@article {pmid21199254, year = {2011}, author = {Davey, HM and Hexley, P}, title = {Red but not dead? Membranes of stressed Saccharomyces cerevisiae are permeable to propidium iodide.}, journal = {Environmental microbiology}, volume = {13}, number = {1}, pages = {163-171}, doi = {10.1111/j.1462-2920.2010.02317.x}, pmid = {21199254}, issn = {1462-2920}, mesh = {Cell Membrane/*metabolism ; *Cell Membrane Permeability ; Flow Cytometry ; Microbial Viability ; Microscopy, Fluorescence ; Propidium/*metabolism ; Saccharomyces cerevisiae/*cytology/metabolism ; Staining and Labeling ; Stress, Physiological ; }, abstract = {Flow cytometric monitoring of propidium iodide (PI) uptake is a well-established and rapid method for monitoring cell death and is used on the basis that the intact membrane of viable cells excludes the propidium ion and that loss of this permeability barrier represents irreparable damage and thus cell death. These assumptions are typically based on analysis of live and killed cells. Here we have identified stress levels that lead to a loss of viability of a proportion of Saccharomyces cerevisiae cells and under these conditions we show that there is a subpopulation of cells that can take up PI during and immediately following exposure to stress but that a short incubation allows repair of the membrane damage such that subsequent exposure to PI does not result in staining. Irrespective of the stress applied, approximately 7% of cells exhibited the ability to repair. These results indicate that the level of damage that the yeast cell membrane can sustain and yet retain the ability to repair is greater than previously recognized and care must therefore be taken in using the terms 'PI-positive' and 'dead' synonymously. We discuss these findings in the context of the potential for such environmental stress-induced, transient membrane permeability to have evolutionary implications via the facilitation of horizontal gene transfer.}, }
@article {pmid21194949, year = {2011}, author = {Slot, JC and Rokas, A}, title = {Horizontal transfer of a large and highly toxic secondary metabolic gene cluster between fungi.}, journal = {Current biology : CB}, volume = {21}, number = {2}, pages = {134-139}, doi = {10.1016/j.cub.2010.12.020}, pmid = {21194949}, issn = {1879-0445}, mesh = {Aspergillus nidulans/*genetics/metabolism ; DNA, Fungal/*genetics/metabolism ; Expressed Sequence Tags ; Gene Transfer, Horizontal/*physiology ; Multigene Family ; Phylogeny ; Podospora/*genetics/metabolism ; Sterigmatocystin/*metabolism ; }, abstract = {Genes involved in intermediary and secondary metabolism in fungi are frequently physically linked or clustered. For example, in Aspergillus nidulans the entire pathway for the production of sterigmatocystin (ST), a highly toxic secondary metabolite and a precursor to the aflatoxins (AF), is located in a ∼54 kb, 23 gene cluster. We discovered that a complete ST gene cluster in Podospora anserina was horizontally transferred from Aspergillus. Phylogenetic analysis shows that most Podospora cluster genes are adjacent to or nested within Aspergillus cluster genes, although the two genera belong to different taxonomic classes. Furthermore, the Podospora cluster is highly conserved in content, sequence, and microsynteny with the Aspergillus ST/AF clusters and its intergenic regions contain 14 putative binding sites for AflR, the transcription factor required for activation of the ST/AF biosynthetic genes. Examination of ∼52,000 Podospora expressed sequence tags identified transcripts for 14 genes in the cluster, with several expressed at multiple life cycle stages. The presence of putative AflR-binding sites and the expression evidence for several cluster genes, coupled with the recent independent discovery of ST production in Podospora [1], suggest that this HGT event probably resulted in a functional cluster. Given the abundance of metabolic gene clusters in fungi, our finding that one of the largest known metabolic gene clusters moved intact between species suggests that such transfers might have significantly contributed to fungal metabolic diversity. PAPERFLICK:}, }
@article {pmid21193902, year = {2011}, author = {van Reenen, CA and Dicks, LM}, title = {Horizontal gene transfer amongst probiotic lactic acid bacteria and other intestinal microbiota: what are the possibilities? A review.}, journal = {Archives of microbiology}, volume = {193}, number = {3}, pages = {157-168}, doi = {10.1007/s00203-010-0668-3}, pmid = {21193902}, issn = {1432-072X}, mesh = {DNA, Bacterial/genetics ; *Gene Transfer, Horizontal ; Intestines/*microbiology ; Lactobacillaceae/*genetics/pathogenicity ; *Metagenome ; *Probiotics ; Virulence ; }, abstract = {Probiotics are live cultures, usually lactic acid bacteria, which are ingested to promote a healthy gastrointestinal tract. These organisms require certain traits to survive and compete in this niche, but these traits may be transferred to other microbiota in the gastrointestinal tract (GIT). Similarly, virulence factors from pathogens may be acquired by probiotic strains. Bacteria have developed a plethora of methods to transfer genetic material between strains, species and genera. In this review, the possible factors that may be exchanged and the methods of exchange are discussed.}, }
@article {pmid21193609, year = {2011}, author = {Rego, RO and Bestor, A and Rosa, PA}, title = {Defining the plasmid-borne restriction-modification systems of the Lyme disease spirochete Borrelia burgdorferi.}, journal = {Journal of bacteriology}, volume = {193}, number = {5}, pages = {1161-1171}, pmid = {21193609}, issn = {1098-5530}, support = {//Intramural NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; Borrelia burgdorferi/*metabolism ; DNA Methylation ; DNA Restriction-Modification Enzymes/genetics/*metabolism ; DNA, Bacterial ; Gene Expression Regulation, Bacterial/physiology ; Gene Transfer, Horizontal ; Humans ; Lyme Disease/*microbiology ; Mice ; Mice, Inbred C3H ; Molecular Sequence Data ; Mutation ; Plasmids/genetics/*metabolism ; }, abstract = {The restriction-modification (R-M) systems of many bacteria present a barrier to the stable introduction of foreign DNA. The Lyme disease spirochete Borrelia burgdorferi has two plasmid-borne putative R-M genes, bbe02 and bbq67, whose presence limits transformation by shuttle vector DNA from Escherichia coli. We show that both the bbe02 and bbq67 loci in recipient B. burgdorferi limit transformation with shuttle vector DNA from E. coli, irrespective of its dam, dcm, or hsd methylation status. However, plasmid DNA purified from B. burgdorferi transformed naïve B. burgdorferi much more efficiently than plasmid DNA from E. coli, particularly when the bbe02 and bbq67 genotypes of the B. burgdorferi DNA source matched those of the recipient. We detected adenine methylation of plasmid DNA prepared from B. burgdorferi that carried bbe02 and bbq67. These results indicate that the bbe02 and bbq67 loci of B. burgdorferi encode distinct R-M enzymes that methylate endogenous DNA and cleave foreign DNA lacking the same sequence-specific modification. Our findings have basic implications for horizontal gene transfer among B. burgdorferi strains with distinct plasmid contents. Further characterization and identification of the nucleotide sequences recognized by BBE02 and BBQ67 will facilitate efficient genetic manipulation of this pathogenic spirochete.}, }
@article {pmid21193022, year = {2011}, author = {Thomas, J and Sorourian, M and Ray, D and Baker, RJ and Pritham, EJ}, title = {The limited distribution of Helitrons to vesper bats supports horizontal transfer.}, journal = {Gene}, volume = {474}, number = {1-2}, pages = {52-58}, doi = {10.1016/j.gene.2010.12.007}, pmid = {21193022}, issn = {1879-0038}, mesh = {Animals ; Base Sequence ; Chiroptera/*genetics ; DNA Transposable Elements/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genetic Variation ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Transposable elements (TEs) have the unique ability to move and replicate within the genome and therefore engender dramatic changes to genome architecture. Among different types of TEs, rolling-circle transposons (Helitrons) are well known for their ability to capture and amplify host gene fragments. Bioinformatic analysis revealed that Helitrons constitute ~3% of the Myotis lucifugus, (little brown bat) genome, while no Helitrons were found in any of the other 44+ sequenced mammalian genomes. Recently horizontal transfer has been implicated for some of the M. lucifugus Helitrons, in part explaining this disparate distribution among mammals. The purpose of this work is to determine both the distribution of Helitrons among bats and to estimate the number of independent invasions. We employed a combination of in silico, PCR and hybridization based techniques to identify Helitrons from diverse bat species belonging to ten different families. This work reveals that Helitrons invaded the vesper bat lineage, at least once. Indeed, Helitrons were not identified in the sister taxa 'Miniopterus', which suggests that the amplification of Helibat occurred (30-36 mya) only in the vesper bat lineage. The estimated age of amplification of the Helibats and the rapid radiation of vesper bats are roughly coincidental and suggest that the invasion and amplification of these elements might have influenced their evolutionary trajectory potentially contributing to phenotypic and genotypic diversity.}, }
@article {pmid21191098, year = {2011}, author = {Jogler, C and Wanner, G and Kolinko, S and Niebler, M and Amann, R and Petersen, N and Kube, M and Reinhardt, R and Schüler, D}, title = {Conservation of proteobacterial magnetosome genes and structures in an uncultivated member of the deep-branching Nitrospira phylum.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {3}, pages = {1134-1139}, pmid = {21191098}, issn = {1091-6490}, mesh = {Bacteria/*genetics/ultrastructure ; Base Sequence ; Conserved Sequence/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Magnetosomes/*genetics/ultrastructure ; Metagenomics/methods ; Micromanipulation ; Microscopy, Electron ; Molecular Sequence Data ; Multigene Family/*genetics ; Nucleic Acid Amplification Techniques ; *Phylogeny ; Sequence Analysis, DNA ; Sequence Homology ; Species Specificity ; }, abstract = {Magnetotactic bacteria (MTB) are a phylogenetically diverse group which uses intracellular membrane-enclosed magnetite crystals called magnetosomes for navigation in their aquatic habitats. Although synthesis of these prokaryotic organelles is of broad interdisciplinary interest, its genetic analysis has been restricted to a few closely related members of the Proteobacteria, in which essential functions required for magnetosome formation are encoded within a large genomic magnetosome island. However, because of the lack of cultivated representatives from other phyla, it is unknown whether the evolutionary origin of magnetotaxis is monophyletic, and it has been questioned whether homologous mechanisms and structures are present in unrelated MTB. Here, we present the analysis of the uncultivated "Candidatus Magnetobacterium bavaricum" from the deep branching Nitrospira phylum by combining micromanipulation and whole genome amplification (WGA) with metagenomics. Target-specific sequences obtained by WGA of cells, which were magnetically collected and individually sorted from sediment samples, were used for PCR screening of metagenomic libraries. This led to the identification of a genomic cluster containing several putative magnetosome genes with homology to those in Proteobacteria. A variety of advanced electron microscopic imaging tools revealed a complex cell envelope and an intricate magnetosome architecture. The presence of magnetosome membranes as well as cytoskeletal magnetosome filaments suggests a similar mechanism of magnetosome formation in "Cand. M. bavaricum" as in Proteobacteria. Altogether, our findings suggest a monophyletic origin of magnetotaxis, and relevant genes were likely transferred horizontally between Proteobacteria and representatives of the Nitrospira phylum.}, }
@article {pmid21191018, year = {2011}, author = {Lee, MH and Padmashali, R and Andreadis, ST}, title = {JNK1 is required for lentivirus entry and gene transfer.}, journal = {Journal of virology}, volume = {85}, number = {6}, pages = {2657-2665}, pmid = {21191018}, issn = {1098-5514}, support = {R01 EB000876/EB/NIBIB NIH HHS/United States ; }, mesh = {Cells, Cultured ; Gene Knockdown Techniques ; *Gene Transfer, Horizontal ; Humans ; Keratinocytes/virology ; Lentivirus/*physiology ; Mitogen-Activated Protein Kinase 8/antagonists &amp; inhibitors/genetics/*metabolism ; Phosphorylation ; *Transduction, Genetic ; *Virus Internalization ; }, abstract = {Although a lot of progress has been made in development of lentiviral vectors for gene therapy, the interactions of these vectors with cellular factors have not been explored adequately. Here we show that lentivirus infection phosphorylates JNK and that blocking the kinase activity of JNK decreases gene transfer in a dose-dependent manner, regardless of the viral envelope glycoprotein. Knockdown by small interfering RNA (siRNA) revealed that JNK1 but not JNK2 was required for productive gene transfer. The effect of JNK on gene transfer was not due to changes in the cell cycle, as JNK knockdown did not affect the cell cycle profile of target cells and even increased cell proliferation. In addition, confluent cell monolayers also exhibited JNK phosphorylation upon lentivirus infection and a dose-dependent decrease in gene transfer efficiency upon JNK inhibition. On the other hand, JNK activation was necessary for lentivirus internalization into the cell cytoplasm, while inhibition of JNK activity decreased virus entry without affecting binding to the cell surface. These experiments suggest that JNK is required for lentivirus entry into target cells and may have implications for gene transfer or for development of antiviral agents.}, }
@article {pmid21190441, year = {2011}, author = {Coupat-Goutaland, B and Bernillon, D and Guidot, A and Prior, P and Nesme, X and Bertolla, F}, title = {Ralstonia solanacearum virulence increased following large interstrain gene transfers by natural transformation.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {24}, number = {4}, pages = {497-505}, doi = {10.1094/MPMI-09-10-0197}, pmid = {21190441}, issn = {0894-0282}, mesh = {Comparative Genomic Hybridization ; DNA, Bacterial/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Genetic Variation ; Genome, Bacterial ; Solanum lycopersicum/*microbiology ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; Plasmids/genetics ; Polymerase Chain Reaction ; Ralstonia solanacearum/classification/*genetics/*pathogenicity ; Sequence Analysis, DNA ; *Transformation, Genetic ; Virulence/genetics ; }, abstract = {Horizontal gene transfer (HGT) is a major driving force of evolution and is also likely to play an important role in the threatening emergence of novel pathogens, especially if it involves distantly related strains with substantially different pathogenicity. In this study, the impact of natural transformation on pathogenicity in six strains belonging to the four phylotypes of the plant-pathogenic bacterium Ralstonia solanacearum was investigated. The study focused on genomic regions that vary between donor and recipient strains and that carry genes involved in pathogenicity such as type III effectors. First, strains from R. solanacearum species complex were naturally transformed with heterologous genomic DNA. Transferred DNA regions were then determined by comparative genomic hybridization and polymerase chain reaction sequencing. We identified three transformant strains that acquired large DNA regions of up to 80 kb. In one case, strain Psi07 (phylotype IV tomato isolate) acquired 39.4 kb from GMI1000 (phylotype I tomato isolate). Investigations revealed that i) 24.4 kb of the acquired region contained 20 new genes, ii) an allelic exchange of 12 genes occurred, and iii) 27 genes (33.4 kb) formerly present in Psi07 were lost. Virulence tests with the three transformants revealed a significant increase in the aggressiveness of BCG20 over its Psi07 parent on tomato. These findings demonstrate the potential importance of HGT in the pathogenic evolution of R. solanacearum strains and open new avenues for studying pathogen emergence.}, }
@article {pmid21187861, year = {2010}, author = {Foster, JM and Davis, PJ and Raverdy, S and Sibley, MH and Raleigh, EA and Kumar, S and Carlow, CK}, title = {Evolution of bacterial phosphoglycerate mutases: non-homologous isofunctional enzymes undergoing gene losses, gains and lateral transfers.}, journal = {PloS one}, volume = {5}, number = {10}, pages = {e13576}, pmid = {21187861}, issn = {1932-6203}, support = {2R44 A1061865-02//PHS HHS/United States ; }, mesh = {Bacteria/*enzymology/genetics/growth &amp; development ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genetic Complementation Test ; Genome, Archaeal ; Genome, Bacterial ; Phosphoglycerate Kinase/*genetics ; Species Specificity ; }, abstract = {BACKGROUND: The glycolytic phosphoglycerate mutases exist as non-homologous isofunctional enzymes (NISE) having independent evolutionary origins and no similarity in primary sequence, 3D structure, or catalytic mechanism. Cofactor-dependent PGM (dPGM) requires 2,3-bisphosphoglycerate for activity; cofactor-independent PGM (iPGM) does not. The PGM profile of any given bacterium is unpredictable and some organisms such as Escherichia coli encode both forms.<br><br>METHODS/PRINCIPAL FINDINGS: To examine the distribution of PGM NISE throughout the Bacteria, and gain insight into the evolutionary processes that shape their phyletic profiles, we searched bacterial genome sequences for the presence of dPGM and iPGM. Both forms exhibited patchy distributions throughout the bacterial domain. Species within the same genus, or even strains of the same species, frequently differ in their PGM repertoire. The distribution is further complicated by the common occurrence of dPGM paralogs, while iPGM paralogs are rare. Larger genomes are more likely to accommodate PGM paralogs or both NISE forms. Lateral gene transfers have shaped the PGM profiles with intradomain and interdomain transfers apparent. Archaeal-type iPGM was identified in many bacteria, often as the sole PGM. To address the function of PGM NISE in an organism encoding both forms, we analyzed recombinant enzymes from E. coli. Both NISE were active mutases, but the specific activity of dPGM greatly exceeded that of iPGM, which showed highest activity in the presence of manganese. We created PGM null mutants in E. coli and discovered the &#x394;dPGM mutant grew slowly due to a delay in exiting stationary phase. Overexpression of dPGM or iPGM overcame this defect.<br><br>CONCLUSIONS/SIGNIFICANCE: Our biochemical and genetic analyses in E. coli firmly establish dPGM and iPGM as NISE. Metabolic redundancy is indicated since only larger genomes encode both forms. Non-orthologous gene displacement can fully account for the non-uniform PGM distribution we report across the bacterial domain.}, }
@article {pmid21187143, year = {2011}, author = {Murillo, J and Bardaji, L and Navarro de la Fuente, L and Führer, ME and Aguilera, S and Alvarez-Morales, A}, title = {Variation in conservation of the cluster for biosynthesis of the phytotoxin phaseolotoxin in Pseudomonas syringae suggests at least two events of horizontal acquisition.}, journal = {Research in microbiology}, volume = {162}, number = {3}, pages = {253-261}, doi = {10.1016/j.resmic.2010.10.011}, pmid = {21187143}, issn = {1769-7123}, mesh = {Biosynthetic Pathways/*genetics ; Cluster Analysis ; *Conserved Sequence ; DNA, Bacterial/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genomic Islands ; *Multigene Family ; Nucleic Acid Hybridization ; Ornithine/*analogs &amp; derivatives/biosynthesis ; Phylogeny ; Polymerase Chain Reaction ; Pseudomonas syringae/*genetics/*metabolism ; Sequence Analysis, DNA ; }, abstract = {Certain strains of Pseudomonas syringae pathovars phaseolicola and actinidiae and P. syringae pv. syringae strain CFBP3388 produce the chlorosis-inducing phytotoxin phaseolotoxin, which inhibits biosynthesis of arginine and polyamines. The 25 kb Pht cluster, responsible for phaseolotoxin biosynthesis, is included in a putative pathogenicity island that is nearly identical in selected strains of the pathovars phaseolicola and actinidiae, suggesting that it has been recently acquired by horizontal transfer. The history of pathogenicity islands is pivotal for our understanding of the evolution of virulence in plant pathogenic bacteria; nevertheless, our knowledge of the origins, biology and genetics of this island is currently rather limited. The aim of this work was to explore the conservation of phaseolotoxin biosynthesis genes in a broader collection of isolates and in strain CFBP3388, in order to better understand its evolution and gene dynamics. PCR, hybridization and sequence analysis showed that the island is highly conserved among a diversity of strains of pathovars phaseolicola and actinidiae, suggesting that it was acquired only once by each pathovar. Strain CFBP3388 contained DNA homologous to the Pht cluster, and an insertional mutant in the regulatory gene phtL did not synthesize the toxin. A 6.5 kb fragment from strain CFBP3388 was syntenic to the Pht cluster, but showed nucleotide identity of only 85.3%. This contrasts with an identity higher than 99.8% among clusters of pathovars phaseolicola and actinidiae, in spite of the fact that pv. syringae is phylogenetically closer to pv. phaseolicola. In addition, strain CFBP3388 lacked the four integrases that are putatively responsible for the mobility of the pathogenicity island. These results indicate that genes for the biosynthesis of phaseolotoxin have a complex evolutionary history and were acquired by pathovars of P. syringae at least twice during evolution.}, }
@article {pmid21187035, year = {2010}, author = {Gilbert, C and Schaack, S and Feschotte, C}, title = {[Mobile elements jump between parasites and vertebrate hosts].}, journal = {Medecine sciences : M/S}, volume = {26}, number = {12}, pages = {1025-1027}, doi = {10.1051/medsci/201026121025}, pmid = {21187035}, issn = {0767-0974}, mesh = {Animals ; DNA Transposable Elements/genetics/*physiology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome ; Host-Parasite Interactions/*genetics ; Humans ; Opossums/genetics ; Rhodnius/genetics ; Rodentia/genetics ; Saimiri/genetics ; Species Specificity ; Trypanosoma cruzi/genetics ; }, }
@article {pmid21182879, year = {2011}, author = {Zhang, J and van Aartsen, JJ and Jiang, X and Shao, Y and Tai, C and He, X and Tan, Z and Deng, Z and Jia, S and Rajakumar, K and Ou, HY}, title = {Expansion of the known Klebsiella pneumoniae species gene pool by characterization of novel alien DNA islands integrated into tmRNA gene sites.}, journal = {Journal of microbiological methods}, volume = {84}, number = {2}, pages = {283-289}, doi = {10.1016/j.mimet.2010.12.016}, pmid = {21182879}, issn = {1872-8359}, mesh = {Animals ; Chromosomes, Bacterial ; DNA, Bacterial/chemistry/genetics ; Environmental Microbiology ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genomic Islands ; Humans ; Klebsiella Infections/microbiology ; Klebsiella pneumoniae/*genetics/isolation &amp; purification ; Molecular Sequence Data ; *Mutagenesis, Insertional ; Plasmids ; Polymerase Chain Reaction ; RNA, Bacterial/*genetics ; Sequence Analysis, DNA ; }, abstract = {Klebsiella pneumoniae is an important bacterial pathogen of man that is commonly associated with opportunistic and hospital-associated infections. Increasing levels of multiple-antibiotic resistance associated with this species pose a major emerging clinical problem. This organism also occurs naturally in other diverse environments, including the soil. Consistent with its varied lifestyle and membership of the Enterobacteriaceae family, K. pneumoniae genomes exhibit highly plastic architecture comprising a core genome backbone interspersed with numerous and varied alien genomic islands. In this study the size of the presently known K. pneumoniae pan-genome gene pool was estimated through analysis of complete sequences of three chromosomes and 31 plasmids belonging to K. pneumoniae strains. In addition, using a PCR-based strategy the genomic content of eight tRNA/tmRNA gene sites that serve as DNA insertion hotspots were investigated in 28 diverse environmental and clinical strains of K. pneumoniae. Sequencing and characterization of five newly identified horizontally-acquired tmRNA-associated islands further expanded the archived K. pneumoniae gene pool to a total of 7648 unique gene members. Large-scale investigation of the content of tRNA/tmRNA hotspots will be useful to identify and/or survey accessory sequences dispersed amongst hundreds to thousands of members of many key bacterial species.}, }
@article {pmid21182545, year = {2011}, author = {do Carmo Ferreira, N and Schuenck, RP and dos Santos, KR and de Freire Bastos, Mdo C and Giambiagi-deMarval, M}, title = {Diversity of plasmids and transmission of high-level mupirocin mupA resistance gene in Staphylococcus haemolyticus.}, journal = {FEMS immunology and medical microbiology}, volume = {61}, number = {2}, pages = {147-152}, doi = {10.1111/j.1574-695X.2010.00756.x}, pmid = {21182545}, issn = {1574-695X}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/*genetics ; Bacterial Typing Techniques ; Brazil ; *Drug Resistance, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; *Gene Transfer, Horizontal ; Genotype ; Hospitals ; Humans ; Molecular Typing ; Mupirocin/*pharmacology ; Nuclear Proteins/*genetics ; *Plasmids ; Polymorphism, Genetic ; Staphylococcal Infections/microbiology ; Staphylococcus haemolyticus/classification/*drug effects/genetics/isolation &amp; purification ; }, abstract = {The coagulase-negative staphylococci are known for their ability to acquire resistance genes, which limits the choice of therapeutic options for the treatment of infections caused by these microorganisms. In this study, the diversity of high-level mupirocin resistance plasmids (Mup(R)) was investigated in four strains of Staphylococcus haemolyticus belonging to different pulsed-field gel electrophoresis (PFGE) types or subtypes, isolated in a Brazilian hospital. These strains harbor the mupA gene in large plasmids. In addition, the presence of IS257 sequences flanking the mupA gene was also shown. Two isolates belonging to two different PFGE types exhibited a similar polymorphism for a fragment of the mupA gene and the closest proximal flanking copies of the IS257, suggesting horizontal transmission of S. haemolyticus mupirocin resistance plasmids in the environment and a role of this species as a reservoir of the mupA gene.}, }
@article {pmid21178459, year = {2010}, author = {Sommer, MO and Church, GM and Dantas, G}, title = {The human microbiome harbors a diverse reservoir of antibiotic resistance genes.}, journal = {Virulence}, volume = {1}, number = {4}, pages = {299-303}, doi = {10.4161/viru.1.4.12010}, pmid = {21178459}, issn = {2150-5608}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics ; DNA, Bacterial/analysis/genetics/isolation &amp; purification ; Drug Resistance, Microbial/*genetics ; Feces/microbiology ; *Genes, Bacterial ; Humans ; Metagenome/*genetics ; Metagenomics ; Polymerase Chain Reaction ; Saliva/microbiology ; }, abstract = {The increasing levels of multi-drug resistance in human pathogenic bacteria are compromising our ability to treat infectious disease. Since antibiotic resistance determinants are readily exchanged between bacteria through lateral gene transfer, there is an increasing interest in investigating reservoirs of antibiotic resistance accessible to pathogens. Due to the high likelihood of contact and genetic exchange with pathogens during disease progression, the human microflora warrants special attention as perhaps the most accessible reservoir of resistance genes. Indeed, numerous previous studies have demonstrated substantial antibiotic resistance in cultured isolates from the human microflora. By applying metagenomic functional selections, we recently demonstrated that the functional repertoire of resistance genes in the human microbiome is much more diverse than suggested using previous culture-dependent methods. We showed that many resistance genes from cultured proteobacteria from human fecal samples are identical to resistance genes harbored by human pathogens, providing strong support for recent genetic exchange of this resistance machinery. In contrast, most of the resistance genes we identified with culture independent metagenomic sampling from the same samples were novel when compared to all known genes in public databases. While this clearly demonstrates that the antibiotic resistance reservoir of the large fraction of the human microbiome recalcitrant to culturing is severely under sampled, it may also suggest that barriers exist to lateral gene transfer between these bacteria and readily cultured human pathogens. If we hope to turn the tide against multidrug resistant infections, we must urgently commit to quantitatively characterizing the resistance reservoirs encoded by our diverse human microbiomes, with a particular focus on routes of exchange of these reservoirs with other microbial communities.}, }
@article {pmid21177950, year = {2011}, author = {Rumpho, ME and Pelletreau, KN and Moustafa, A and Bhattacharya, D}, title = {The making of a photosynthetic animal.}, journal = {The Journal of experimental biology}, volume = {214}, number = {Pt 2}, pages = {303-311}, pmid = {21177950}, issn = {1477-9145}, support = {R01 ES013679/ES/NIEHS NIH HHS/United States ; T32 GM008629/GM/NIGMS NIH HHS/United States ; R01ES013679/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Chlorophyta/*genetics/metabolism ; Gene Expression Profiling ; *Gene Transfer, Horizontal ; Mollusca/*genetics/metabolism ; *Photosynthesis ; Plastids/genetics/metabolism ; *Symbiosis ; }, abstract = {Symbiotic animals containing green photobionts challenge the common perception that only plants are capable of capturing the sun's rays and converting them into biological energy through photoautotrophic CO(2) fixation (photosynthesis). 'Solar-powered' sacoglossan molluscs, or sea slugs, have taken this type of symbiotic association one step further by solely harboring the photosynthetic organelle, the plastid (=chloroplast). One such sea slug, Elysia chlorotica, lives as a 'plant' when provided with only light and air as a result of acquiring plastids during feeding on its algal prey Vaucheria litorea. The captured plastids (kleptoplasts) are retained intracellularly in cells lining the digestive diverticula of the sea slug, a phenomenon sometimes referred to as kleptoplasty. Photosynthesis by the plastids provides E. chlorotica with energy and fixed carbon for its entire lifespan of ~10 months. The plastids are not transmitted vertically (i.e. are absent in eggs) and do not undergo division in the sea slug. However, de novo protein synthesis continues, including plastid- and nuclear-encoded plastid-targeted proteins, despite the apparent absence of algal nuclei. Here we discuss current data and provide hypotheses to explain how long-term photosynthetic activity is maintained by the kleptoplasts. This fascinating 'green animal' provides a unique model to study the evolution of photosynthesis in a multicellular heterotrophic organism.}, }
@article {pmid21177671, year = {2011}, author = {Oguri, S and Matsuo, J and Hayashi, Y and Nakamura, S and Hanawa, T and Fukumoto, T and Mizutani, Y and Yao, T and Akizawa, K and Suzuki, H and Shimizu, C and Matsuno, K and Kamiya, S and Yamaguchi, H}, title = {Ciliates promote the transfer of the gene encoding the extended-spectrum β-lactamase CTX-M-27 between Escherichia coli strains.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {66}, number = {3}, pages = {527-530}, doi = {10.1093/jac/dkq487}, pmid = {21177671}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/pharmacology ; Cefotaxime/pharmacology ; Ciliophora/*physiology ; Culture Media/chemistry ; Drug Resistance, Bacterial ; Escherichia coli/genetics/*physiology ; Escherichia coli Proteins/*genetics ; *Gene Transfer, Horizontal ; Humans ; *Microbial Interactions ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: The mechanism by which Escherichia coli acquires multidrug resistance genes from other bacteria in the natural environment or livestock is still unclear. The ability of ciliates to promote the transfer of genes encoding extended-spectrum β-lactamases (ESBLs) between the CTX-M-27 donor and clinically isolated recipient E. coli strains was investigated.<br><br>METHODS: Equal amounts (&#x223c;10(9) cfu) of donor cefotaxime-resistant E. coli and recipient ciprofloxacin-resistant E. coli strains were mixed together in the presence or absence of 10(5) ciliates in Page's amoeba saline for 24 h, in the presence or absence of certain drugs (cytochalasin D, cycloheximide and latrunculin B).<br><br>RESULTS: Gene transfer frequency in the presence of ciliates was estimated at &#x223c;10(-6); in the absence of ciliates it was &#x223c;10(-10). Protein synthesis (cycloheximide) or phagocytosis (cytochalasin D or latrunculin B) inhibitors significantly reduced the frequency of gene transfer.<br><br>CONCLUSIONS: Ciliates promote the transfer of genes encoding ESBLs between E. coli strains, implying that the presence of ciliates may provide a significant impact on emerging multidrug-resistant bacteria.}, }
@article {pmid21176856, year = {2011}, author = {Yan, Y and Cui, Y and Han, H and Xiao, X and Wong, HC and Tan, Y and Guo, Z and Liu, X and Yang, R and Zhou, D}, title = {Extended MLST-based population genetics and phylogeny of Vibrio parahaemolyticus with high levels of recombination.}, journal = {International journal of food microbiology}, volume = {145}, number = {1}, pages = {106-112}, doi = {10.1016/j.ijfoodmicro.2010.11.038}, pmid = {21176856}, issn = {1879-3460}, mesh = {Alleles ; Bacterial Typing Techniques ; DNA, Bacterial/genetics ; Genetic Variation ; *Genetics, Population ; Multilocus Sequence Typing/*methods ; Mutation ; *Phylogeny ; Polymerase Chain Reaction ; Recombination, Genetic ; Selection, Genetic ; Sequence Analysis, DNA ; Vibrio parahaemolyticus/classification/*genetics/isolation &amp; purification ; }, abstract = {A collection of 174 global isolates of Vibrio parahaemolyticus were analyzed by multilocus sequence typing (MLST) on the basis of ten conserved genes. The results showed a high level of nucleotide and allelic diversity with the evidence of purifying selection and of frequent recombination. Recombination played a much greater role than mutation in generating genetic heterogeneity. The 174 strains could be assigned into 89 different sequence types, which could be further separated into six clonal complexes (CCs; CC1 to CC6) plus 71 singletons. The three major CCs, namely CC1 to CC3, corresponded to the groups of pre-1996 clinical old-O3:K6 strains (trh(+), T3SS2β(+), tdh(-), T3SS2α(-), and GS-PCR(-)), post-1996 pandemic strains (trh(-), T3SS2β(-), tdh(+), T3SS2α(+), and GS-PCR(+)) and non-clinical isolates (trh(-), T3SS2β(-), tdh(-), T3SS2α(-), and GS-PCR(-)), respectively. The MLST data enable the construction of a phylogenetic structure from the allelic profiles rather the nucleotide sequences, so as to reduce the affect of frequent recombination. The six CCs arose on a background of mutation and recombination, and according to the previously reported data, this bacterium could be evolved fast due to lateral acquisition of foreign genes especially including those encoding virulence determinants. V. parahaemolyticus had a typical epidemic population structure that is driven by mutation, recombination and lateral gene transfer.}, }
@article {pmid21176244, year = {2010}, author = {Archibald, JM and Richards, TA}, title = {Gene transfer: anything goes in plant mitochondria.}, journal = {BMC biology}, volume = {8}, number = {}, pages = {147}, pmid = {21176244}, issn = {1741-7007}, mesh = {DNA, Mitochondrial/genetics ; Gene Conversion ; *Gene Transfer, Horizontal ; *Genes, Mitochondrial ; *Genes, Plant ; Mosaicism ; Plant Physiological Phenomena ; Plants/*genetics ; }, abstract = {Parasitic plants and their hosts have proven remarkably adept at exchanging fragments of mitochondrial DNA. Two recent studies provide important mechanistic insights into the pattern, process and consequences of horizontal gene transfer, demonstrating that genes can be transferred in large chunks and that gene conversion between foreign and native genes leads to intragenic mosaicism. A model involving duplicative horizontal gene transfer and differential gene conversion is proposed as a hitherto unrecognized source of genetic diversity.}, }
@article {pmid21176201, year = {2010}, author = {Mower, JP and Stefanović, S and Hao, W and Gummow, JS and Jain, K and Ahmed, D and Palmer, JD}, title = {Horizontal acquisition of multiple mitochondrial genes from a parasitic plant followed by gene conversion with host mitochondrial genes.}, journal = {BMC biology}, volume = {8}, number = {}, pages = {150}, pmid = {21176201}, issn = {1741-7007}, support = {R01-GM-70612/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Sequence ; Cuscuta/genetics/physiology ; Gene Conversion/*physiology ; Gene Transfer, Horizontal/*physiology ; Genes, Mitochondrial/*genetics ; Genes, Plant/physiology ; Genetic Variation/physiology ; Host-Parasite Interactions/*genetics ; Molecular Sequence Data ; Phylogeny ; Plant Development ; Plantago/genetics/parasitology ; Plants/*genetics ; Pseudogenes ; Sequence Homology, Nucleic Acid ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT) is relatively common in plant mitochondrial genomes but the mechanisms, extent and consequences of transfer remain largely unknown. Previous results indicate that parasitic plants are often involved as either transfer donors or recipients, suggesting that direct contact between parasite and host facilitates genetic transfer among plants.<br><br>RESULTS: In order to uncover the mechanistic details of plant-to-plant HGT, the extent and evolutionary fate of transfer was investigated between two groups: the parasitic genus Cuscuta and a small clade of Plantago species. A broad polymerase chain reaction (PCR) survey of mitochondrial genes revealed that at least three genes (atp1, atp6 and matR) were recently transferred from Cuscuta to Plantago. Quantitative PCR assays show that these three genes have a mitochondrial location in the one species line of Plantago examined. Patterns of sequence evolution suggest that these foreign genes degraded into pseudogenes shortly after transfer and reverse transcription (RT)-PCR analyses demonstrate that none are detectably transcribed. Three cases of gene conversion were detected between native and foreign copies of the atp1 gene. The identical phylogenetic distribution of the three foreign genes within Plantago and the retention of cytidines at ancestral positions of RNA editing indicate that these genes were probably acquired via a single, DNA-mediated transfer event. However, samplings of multiple individuals from two of the three species in the recipient Plantago clade revealed complex and perplexing phylogenetic discrepancies and patterns of sequence divergence for all three of the foreign genes.<br><br>CONCLUSIONS: This study reports the best evidence to date that multiple mitochondrial genes can be transferred via a single HGT event and that transfer occurred via a strictly DNA-level intermediate. The discovery of gene conversion between co-resident foreign and native mitochondrial copies suggests that transferred genes may be evolutionarily important in generating mitochondrial genetic diversity. Finally, the complex relationships within each lineage of transferred genes imply a surprisingly complicated history of these genes in Plantago subsequent to their acquisition via HGT and this history probably involves some combination of additional transfers (including intracellular transfer), gene duplication, differential loss and mutation-rate variation. Unravelling this history will probably require sequencing multiple mitochondrial and nuclear genomes from Plantago. See Commentary: http://www.biomedcentral.com/1741-7007/8/147.}, }
@article {pmid21172835, year = {2011}, author = {Schliep, K and Lopez, P and Lapointe, FJ and Bapteste, E}, title = {Harvesting evolutionary signals in a forest of prokaryotic gene trees.}, journal = {Molecular biology and evolution}, volume = {28}, number = {4}, pages = {1393-1405}, doi = {10.1093/molbev/msq323}, pmid = {21172835}, issn = {1537-1719}, mesh = {Archaea/*classification/*genetics ; Bacteria/*classification/*genetics ; *Biological Evolution ; Databases, Genetic ; Phylogeny ; Prokaryotic Cells/classification ; }, abstract = {Phylogenomic studies produce increasingly large phylogenetic forests of trees with patchy taxonomical sampling. Typically, prokaryotic data generate thousands of gene trees of all sizes that are difficult, if not impossible, to root. Their topologies do not match the genealogy of lineages, as they are influenced not only by duplication, losses, and vertical descent but also by lateral gene transfer (LGT) and recombination. Because this complexity in part reflects the diversity of evolutionary processes, the study of phylogenetic forests is thus a great opportunity to improve our understanding of prokaryotic evolution. Here, we show how the rich evolutionary content of such novel phylogenetic objects can be exploited through the development of new approaches designed specifically for extracting the multiple evolutionary signals present in the forest of life, that is, by slicing up trees into remarkable bits and pieces: clans, slices, and clips. We harvested a forest of 6,901 unrooted gene trees comprising up to 100 prokaryotic genomes (41 archaea and 59 bacteria) to search for evolutionary events that a species tree would not account for. We identified 1) trees and partitions of trees that reflected the lifestyle of organisms rather than their taxonomy, 2) candidate lifestyle-specific genetic modules, used by distinct unrelated organisms to adapt to the same environment, 3) gene families, nonrandomly distributed in the functional space, that were frequently exchanged between archaea and bacteria, sometimes without major changes in their sequences. Finally, 4) we reconstructed polarized networks of genetic partnerships between archaea and bacteria to describe some of the rules affecting LGT between these two Domains.}, }
@article {pmid21172458, year = {2011}, author = {Smyth, DS and Wong, A and Robinson, DA}, title = {Cross-species spread of SCCmec IV subtypes in staphylococci.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {11}, number = {2}, pages = {446-453}, pmid = {21172458}, issn = {1567-7257}, support = {R01 GM080602/GM/NIGMS NIH HHS/United States ; R01 GM080602-06/GM/NIGMS NIH HHS/United States ; GM080602/GM/NIGMS NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics ; Base Sequence ; DNA, Bacterial ; *Gene Transfer, Horizontal ; Genetic Linkage ; Host Specificity ; Humans ; Interspersed Repetitive Sequences/genetics ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Oxacillin/pharmacology ; Penicillin-Binding Proteins ; Polymerase Chain Reaction ; Staphylococcal Infections/epidemiology/*microbiology ; Staphylococcus aureus/classification/drug effects/*genetics ; Staphylococcus epidermidis/classification/drug effects/*genetics ; beta-Lactam Resistance/*genetics ; }, abstract = {Staphylococcal chromosomal cassette mec (SCCmec) is a mobile genetic element that carries resistance genes for beta-lactam antibiotics. Coagulase-negative staphylococci, such as S. epidermidis, are thought to be a reservoir of diverse SCCmec elements that can spread to the most virulent staphylococcal species, S. aureus, but very little is known about the extent of cross-species spread of these elements in natural populations or their dynamics in different species. We addressed these questions using a sample of 86 S. aureus and S. epidermidis isolates with SCCmec type IV that were collected from a single hospital over a period of 6 months. To subtype SCCmec IV, we used multiplex PCR to detect structural variations and we used sequences from a fragment of the ccrB gene and from the dru repeats to detect additional variations. Multiplex PCR had significantly lower typeability than ccrB:dru sequencing, due to more nontypeable isolates among S. epidermidis. No statistically significant differences in diversity were detected by subtyping method or species. Interestingly, while only 4 of 24 subtypes (17%) were shared between species, these so-called shared subtypes represented 58 of 86 isolates (67%). The shared subtypes differed significantly between species in their frequencies. The shared subtypes were also significantly more concordant with genetic backgrounds in S. aureus than in S. epidermidis. Moreover, the shared subtypes had significantly higher minimum inhibitory concentrations to oxacillin in S. aureus than in S. epidermidis. This study has identified particular SCCmec IV subtypes with an important role in spreading beta-lactam resistance between species, and has further revealed some species differences in their abundance, linkage to genetic background, and antibiotic resistance level.}, }
@article {pmid21170026, year = {2011}, author = {David, LA and Alm, EJ}, title = {Rapid evolutionary innovation during an Archaean genetic expansion.}, journal = {Nature}, volume = {469}, number = {7328}, pages = {93-96}, pmid = {21170026}, issn = {1476-4687}, mesh = {Algorithms ; Archaea/*genetics/metabolism ; Biodiversity ; Cell Respiration/genetics ; Electron Transport/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Archaeal/genetics ; Genome, Archaeal/*genetics ; History, Ancient ; Oxygen/metabolism ; *Phylogeny ; Time Factors ; Uncertainty ; }, abstract = {The natural history of Precambrian life is still unknown because of the rarity of microbial fossils and biomarkers. However, the composition of modern-day genomes may bear imprints of ancient biogeochemical events. Here we use an explicit model of macroevolution including gene birth, transfer, duplication and loss events to map the evolutionary history of 3,983 gene families across the three domains of life onto a geological timeline. Surprisingly, we find that a brief period of genetic innovation during the Archaean eon, which coincides with a rapid diversification of bacterial lineages, gave rise to 27% of major modern gene families. A functional analysis of genes born during this Archaean expansion reveals that they are likely to be involved in electron-transport and respiratory pathways. Genes arising after this expansion show increasing use of molecular oxygen (P = 3.4 × 10(-8)) and redox-sensitive transition metals and compounds, which is consistent with an increasingly oxygenating biosphere.}, }
@article {pmid21169481, year = {2011}, author = {Charpentier, X and Kay, E and Schneider, D and Shuman, HA}, title = {Antibiotics and UV radiation induce competence for natural transformation in Legionella pneumophila.}, journal = {Journal of bacteriology}, volume = {193}, number = {5}, pages = {1114-1121}, pmid = {21169481}, issn = {1098-5530}, support = {R01 AI023549/AI/NIAID NIH HHS/United States ; R01 AI064481/AI/NIAID NIH HHS/United States ; AI23549/AI/NIAID NIH HHS/United States ; AI064481/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics/metabolism ; DNA Damage ; DNA Repair ; DNA, Bacterial ; Gene Expression Regulation, Bacterial/physiology ; Gene Transfer, Horizontal ; Humans ; Legionella pneumophila/*drug effects/*radiation effects ; *Ultraviolet Rays ; }, abstract = {Natural transformation by competence is a major mechanism of horizontal gene transfer in bacteria. Competence is defined as the genetically programmed physiological state that enables bacteria to actively take up DNA from the environment. The conditions that signal competence development are multiple and elusive, complicating the understanding of its evolutionary significance. We used expression of the competence gene comEA as a reporter of competence development and screened several hundred molecules for their ability to induce competence in the freshwater living pathogen Legionella pneumophila. We found that comEA expression is induced by chronic exposure to genotoxic molecules such as mitomycin C and antibiotics of the fluoroquinolone family. These results indicated that, in L. pneumophila, competence may be a response to genotoxic stress. Sunlight-emitted UV light represents a major source of genotoxic stress in the environment and we found that exposure to UV radiation effectively induces competence development. For the first time, we show that genetic exchanges by natural transformation occur within an UV-stressed population. Genotoxic stress induces the RecA-dependent SOS response in many bacteria. However, genetic and phenotypic evidence suggest that L. pneumophila lacks a prototypic SOS response and competence development in response to genotoxic stress is RecA independent. Our results strengthen the hypothesis that competence may have evolved as a DNA damage response in SOS-deficient bacteria. This parasexual response to DNA damage may have enabled L. pneumophila to acquire and propagate foreign genes, contributing to the emergence of this human pathogen.}, }
@article {pmid21169443, year = {2011}, author = {Alvarez, L and Bricio, C and Gómez, MJ and Berenguer, J}, title = {Lateral transfer of the denitrification pathway genes among Thermus thermophilus strains.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {4}, pages = {1352-1358}, pmid = {21169443}, issn = {1098-5336}, mesh = {Base Sequence ; Denitrification/genetics ; Gene Expression ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Genetic Linkage ; Multigene Family ; Nitrate Reductase/chemistry/metabolism ; Nitrates/metabolism ; Nitric Oxide/metabolism ; Nitrites/metabolism ; *Plasmids ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Thermus thermophilus/enzymology/*genetics/*metabolism ; }, abstract = {Nitrate respiration is a common and strain-specific property in Thermus thermophilus encoded by the nitrate respiration conjugative element (NCE) that can be laterally transferred by conjugation. In contrast, nitrite respiration and further denitrification steps are restricted to a few isolates of this species. These later steps of the denitrification pathway are under the regulatory control of an NCE-encoded transcription factor, but nothing is known about their coding sequences or its putative genetic linkage to the NCE. In this study we examine the genetic linkage between nitrate and nitrite respiration through lateral gene transfer (LGT) assays and describe a cluster of genes encoding the nitrite-nitric oxide respiration in T. thermophilus PRQ25. We show that the whole denitrification pathway can be transferred from the denitrificant strain PRQ25 to an aerobic strain, HB27, and that the genes coding for nitrite and nitric oxide respiration are encoded near the NCE. Sequence data from the draft genome of PRQ25 confirmed these results and allowed us to describe the most compact nor-nir cluster known thus far and to demonstrate the expression and activities of the encoded enzymes in the HB27 denitrificant derivatives obtained by LGT. We conclude that this NCE nor-nir supercluster constitutes a whole denitrification island that can be spread by lateral transfer among Thermus thermophilus strains.}, }
@article {pmid21166898, year = {2011}, author = {Cerdà-Costa, N and Guevara, T and Karim, AY and Ksiazek, M and Nguyen, KA and Arolas, JL and Potempa, J and Gomis-Rüth, FX}, title = {The structure of the catalytic domain of Tannerella forsythia karilysin reveals it is a bacterial xenologue of animal matrix metalloproteinases.}, journal = {Molecular microbiology}, volume = {79}, number = {1}, pages = {119-132}, pmid = {21166898}, issn = {1365-2958}, support = {R01 DE009761/DE/NIDCR NIH HHS/United States ; R01 DE009761-19/DE/NIDCR NIH HHS/United States ; DE 09761/DE/NIDCR NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Bacteroidetes/*enzymology ; Calcium/metabolism ; *Catalytic Domain ; Cations, Divalent/metabolism ; Coenzymes/metabolism ; Crystallography, X-Ray ; Evolution, Molecular ; Insecta/enzymology ; Magnesium/metabolism ; Mammals ; Matrix Metalloproteinases/*chemistry/genetics ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Protein Binding ; Protein Structure, Tertiary ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {Metallopeptidases (MPs) are among virulence factors secreted by pathogenic bacteria at the site of infection. One such pathogen is Tannerella forsythia, a member of the microbial consortium that causes peridontitis, arguably the most prevalent infective chronic inflammatory disease known to mankind. The only reported MP secreted by T. forsythia is karilysin, a 52 kDa multidomain protein comprising a central 18 kDa catalytic domain (CD), termed Kly18, flanked by domains unrelated to any known protein. We analysed the 3D structure of Kly18 in the absence and presence of Mg(2+) or Ca(2+) , which are required for function and stability, and found that it evidences most of the structural features characteristic of the CDs of mammalian matrix metalloproteinases (MMPs). Unexpectedly, a peptide was bound to the active-site cleft of Kly18 mimicking a left-behind cleavage product, which revealed that the specificity pocket accommodates bulky hydrophobic side-chains of substrates as in mammalian MMPs. In addition, Kly18 displayed a unique Mg(2+) or Ca(2+) binding site and two flexible segments that could play a role in substrate binding. Phylogenetic and sequence similarity studies revealed that Kly18 is evolutionarily much closer to winged-insect and mammalian MMPs than to potential bacterial counterparts found by genomic sequencing projects. Therefore, we conclude that this first structurally characterized non-mammalian MMP is a xenologue co-opted through horizontal gene transfer during the intimate coexistence between T. forsythia and humans or other animals, in a very rare case of gene shuffling from eukaryotes to prokaryotes. Subsequently, this protein would have evolved in a bacterial environment to give rise to full-length karilysin that is furnished with unique flanking domains that do not conform to the general multidomain architecture of animal MMPs.}, }
@article {pmid21166560, year = {2011}, author = {Kannan, L and Li, H and Mushegian, A}, title = {A polynomial-time algorithm computing lower and upper bounds of the rooted subtree prune and regraft distance.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {18}, number = {5}, pages = {743-757}, doi = {10.1089/cmb.2010.0045}, pmid = {21166560}, issn = {1557-8666}, mesh = {*Algorithms ; Biological Evolution ; Computational Biology/*methods ; Computer Simulation ; *Phylogeny ; Software ; }, abstract = {Rooted, leaf-labeled trees are used in biology to represent hierarchical relationships of various entities, most notably the evolutionary history of molecules and organisms. Rooted Subtree Prune and Regraft (rSPR) operation is a tree rearrangement operation that is used to transform a tree into another tree that has the same set of leaf labels. The minimum number of rSPR operations that transform one tree into another is denoted by d(rSPR) and gives a measure of dissimilarity between the trees, which can be used to compare trees obtained by different approaches, or, in the context of phylogenetic analysis, to detect horizontal gene transfer events by finding incongruences between trees of different evolving characters. The problem of computing the exact d(rSPR) measure is NP-hard, and most algorithms resort to finding sequences of rSPR operations that are sufficient for transforming one tree into another, thereby giving upper bound heuristics for the distance. In this article, we present an O(n[4]) recursive algorithm D-Clust that gives both lower bound and upper bound heuristics for the distance between trees with n shared leaves and also gives a sequence of operations that transforms one tree into another. Our experiments on simulated pairs of trees containing up to 100 leaves showed that the two bounds are almost equal for small distances, thereby giving the nearly-precise actual value, and that the upper bound tends to be close to the upper bounds given by other approaches for all pairs of trees.}, }
@article {pmid21159175, year = {2010}, author = {Kato, O and Youn, JW and Stansen, KC and Matsui, D and Oikawa, T and Wendisch, VF}, title = {Quinone-dependent D-lactate dehydrogenase Dld (Cg1027) is essential for growth of Corynebacterium glutamicum on D-lactate.}, journal = {BMC microbiology}, volume = {10}, number = {}, pages = {321}, pmid = {21159175}, issn = {1471-2180}, mesh = {Bacterial Proteins/genetics/*metabolism ; Benzoquinones/*metabolism ; Corynebacterium glutamicum/*enzymology/genetics/*growth &amp; development/metabolism ; Gene Expression Regulation, Bacterial ; Lactate Dehydrogenases/genetics/*metabolism ; Lactic Acid/*metabolism ; }, abstract = {BACKGROUND: Corynebacterium glutamicum is able to grow with lactate as sole or combined carbon and energy source. Quinone-dependent L-lactate dehydrogenase LldD is known to be essential for utilization of L-lactate by C. glutamicum. D-lactate also serves as sole carbon source for C. glutamicum ATCC 13032.<br><br>RESULTS: Here, the gene cg1027 was shown to encode the quinone-dependent D-lactate dehydrogenase (Dld) by enzymatic analysis of the protein purified from recombinant E. coli. The absorption spectrum of purified Dld indicated the presence of FAD as bound cofactor. Inactivation of dld resulted in the loss of the ability to grow with D-lactate, which could be restored by plasmid-borne expression of dld. Heterologous expression of dld from C. glutamicum ATCC 13032 in C. efficiens enabled this species to grow with D-lactate as sole carbon source. Homologs of dld of C. glutamicum ATCC 13032 are not encoded in the sequenced genomes of other corynebacteria and mycobacteria. However, the dld locus of C. glutamicum ATCC 13032 shares 2367 bp of 2372 bp identical nucleotides with the dld locus of Propionibacterium freudenreichii subsp. shermanii, a bacterium used in Swiss-type cheese making. Both loci are flanked by insertion sequences of the same family suggesting a possible event of horizontal gene transfer.<br><br>CONCLUSIONS: Cg1067 encodes quinone-dependent D-lactate dehydrogenase Dld of Corynebacterium glutamicum. Dld is essential for growth with D-lactate as sole carbon source. The genomic region of dld likely has been acquired by horizontal gene transfer.}, }
@article {pmid21159005, year = {2011}, author = {Sun, G and Huang, J}, title = {Horizontally acquired DAP pathway as a unit of self-regulation.}, journal = {Journal of evolutionary biology}, volume = {24}, number = {3}, pages = {587-595}, doi = {10.1111/j.1420-9101.2010.02192.x}, pmid = {21159005}, issn = {1420-9101}, mesh = {Aspartate Kinase/metabolism ; Aspartic Acid/*metabolism ; Choanoflagellata/*genetics/*metabolism ; Diaminopimelic Acid/*metabolism ; Gene Expression Regulation/physiology ; Gene Transfer, Horizontal/*genetics ; Phylogeny ; }, abstract = {In this study, we report the acquisition of the diaminopimelic acid (DAP) pathway of lysine biosynthesis in choanoflagellate Monosiga brevicollis and investigate how this pathway is incorporated and regulated in the established metabolic network. Our data show that all major genes related to the DAP pathway in Monosiga were acquired from bacteria and algae. Although an endogenous lysC exists in Monosiga, the newly acquired lysC is fused to lysA and used specifically for lysine biosynthesis. In addition, these acquired genes encode two key rate-limiting enzymes, thus conferring Monosiga a self-regulated unit with ability to generate lysine. Our data suggest that a newly acquired metabolic capability can be added to the recipient organism without disturbing the previously established metabolic network. This finding also implies that the biochemical system of the recipient organism may determine the type and function of genes to be acquired.}, }
@article {pmid21149709, year = {2011}, author = {Gophna, U and Ofran, Y}, title = {Lateral acquisition of genes is affected by the friendliness of their products.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {1}, pages = {343-348}, pmid = {21149709}, issn = {1091-6490}, mesh = {Adaptation, Biological/*genetics ; Amino Acid Sequence ; Computational Biology ; Databases, Protein ; Escherichia coli K12 ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genomics/methods ; Protein Interaction Domains and Motifs/*genetics ; Sequence Alignment ; Statistics, Nonparametric ; Systems Biology/methods ; }, abstract = {A major factor in the evolution of microbial genomes is the lateral acquisition of genes that evolved under the functional constraints of other species. Integration of foreign genes into a genome that has different components and circuits poses an evolutionary challenge. Moreover, genes belonging to complex modules in the pretransfer species are unlikely to maintain their functionality when transferred alone to new species. Thus, it is widely accepted that lateral gene transfer favors proteins with only a few protein-protein interactions. The propensity of proteins to participate in protein-protein interactions can be assessed using computational methods that identify putative interaction sites on the protein. Here we report that laterally acquired proteins contain significantly more putative interaction sites than native proteins. Thus, genes encoding proteins with multiple protein-protein interactions may in fact be more prone to transfer than genes with fewer interactions. We suggest that these proteins have a greater chance of forming new interactions in new species, thus integrating into existing modules. These results reveal basic principles for the incorporation of novel genes into existing systems.}, }
@article {pmid21149642, year = {2011}, author = {Cohen, O and Gophna, U and Pupko, T}, title = {The complexity hypothesis revisited: connectivity rather than function constitutes a barrier to horizontal gene transfer.}, journal = {Molecular biology and evolution}, volume = {28}, number = {4}, pages = {1481-1489}, doi = {10.1093/molbev/msq333}, pmid = {21149642}, issn = {1537-1719}, mesh = {*Biological Evolution ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Models, Genetic ; Phylogeny ; Stochastic Processes ; }, abstract = {Horizontal gene transfer (HGT) is a prevalent and a highly important phenomenon in microbial species evolution. One of the important challenges in HGT research is to better understand the factors that determine the tendency of genes to be successfully transferred and retained in evolution (i.e., transferability). It was previously observed that transferability of genes depends on the cellular process in which they are involved where genes involved in transcription or translation are less likely to be transferred than metabolic genes. It was further shown that gene connectivity in the protein-protein interaction network affects HGT. These two factors were shown to be correlated, and their influence on HGT is collectively termed the "Complexity Hypothesis". In this study, we used a stochastic mapping method utilizing advanced likelihood-based evolutionary models to quantify gene family acquisition events by HGT. We applied our methodology to an extensive across-species genome-wide dataset that enabled us to estimate the overall extent of transfer events in evolution and to study the trends and barriers to gene transferability. Focusing on the biological function and the connectivity of genes, we obtained novel insights regarding the "complexity hypothesis." Specifically, we aimed to disentangle the relationships between protein connectivity, cellular function, and transferability and to quantify the relative contribution of each of these factors in determining transferability. We show that the biological function of a gene family is an insignificant factor in the determination of transferability when proteins with similar levels of connectivity are compared. In contrast, we found that connectivity is an important and a statistically significant factor in determining transferability when proteins with a similar function are compared.}, }
@article {pmid21147969, year = {2011}, author = {Boschetti, C and Pouchkina-Stantcheva, N and Hoffmann, P and Tunnacliffe, A}, title = {Foreign genes and novel hydrophilic protein genes participate in the desiccation response of the bdelloid rotifer Adineta ricciae.}, journal = {The Journal of experimental biology}, volume = {214}, number = {Pt 1}, pages = {59-68}, doi = {10.1242/jeb.050328}, pmid = {21147969}, issn = {1477-9145}, support = {233232/ERC_/European Research Council/International ; 8/S19912/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/F020856/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cluster Analysis ; Computational Biology ; Dehydration/*genetics ; *Expressed Sequence Tags ; Gene Expression Regulation/*genetics/physiology ; Gene Library ; Gene Transfer, Horizontal/*genetics ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; Rotifera/*genetics/physiology ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Bdelloid rotifers are aquatic micro-invertebrates with the ability to survive extreme desiccation, or anhydrobiosis, at any life stage. To gain insight into the molecular mechanisms used by bdelloids during anhydrobiosis, we constructed a cDNA library enriched for genes that are upregulated in Adineta ricciae 24 h after onset of dehydration. Resulting expressed sequence tags (ESTs) were analysed and sequences grouped into categories according to their probable identity. Of 75 unique sequences, approximately half (36) were similar to known genes from other species. These included genes encoding an unusual group 3 late embryogenesis abundant protein, and a number of other stress-related and DNA repair proteins. Open reading frames from a further 39 novel sequences, without counterparts in the database, were screened for the characteristics of intrinsically disordered proteins, i.e. hydrophilicity and lack of stable secondary structure. Such proteins have been implicated in desiccation tolerance and at least five were found. The majority of the genes identified was confirmed by real-time quantitative PCR to be capable of upregulation in response to evaporative water loss. Remarkably, further database and phylogenetic analysis highlighted four ESTs that are present in the A. ricciae genome but which represent genes probably arising from fungi or bacteria by horizontal gene transfer. Therefore, not only can bdelloid rotifers accumulate foreign genes and render them transcriptionally competent, but their expression pattern can be modified for participation in the desiccation stress response, and is presumably adaptive in this context.}, }
@article {pmid21147268, year = {2011}, author = {Napolitano, MG and Almagro-Moreno, S and Boyd, EF}, title = {Dichotomy in the evolution of pathogenicity island and bacteriophage encoded integrases from pathogenic Escherichia coli strains.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {11}, number = {2}, pages = {423-436}, doi = {10.1016/j.meegid.2010.12.003}, pmid = {21147268}, issn = {1567-7257}, mesh = {Base Composition ; Base Sequence ; Coliphages/enzymology/*genetics ; Conserved Sequence/genetics ; DNA, Bacterial/genetics ; Escherichia coli/classification/genetics/*pathogenicity ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genomic Islands/*genetics ; Integrases/*genetics ; *Interspersed Repetitive Sequences ; Phylogeny ; RNA, Transfer/genetics ; Recombination, Genetic ; Sequence Alignment ; Virulence Factors/genetics ; }, abstract = {The evolutionary histories of mobile and integrative genetic elements (MIGEs), key factors in the emergence of pathogenic bacteria, remain obscure due to their widespread distribution and diversity in gene content. Pathogenicity islands (PAIs) are large chromosomal regions that encode bacterial virulence factors present in pathogenic isolates and absent from non-pathogenic isolates. We examined the utility of PAI-encoded integrases as a marker to determine PAI phylogeny and evolutionary relationships to other MIGEs particularly bacteriophages. We examined 68 tyrosine recombinase (TR) integrases from 27 PAIs and 39 phages from five fully sequenced pathogenic Escherichia coli strains in the database. In general, all PAI regions identified were integrated adjacent to tRNA loci and had a percent GC content that differed from the host chromosome, which was not the case for most phages examined. Our phylogenetic analysis demonstrated that PAI-encoded integrases clustered within a distinct lineage, separate from phage-encoded integrases, which suggested a discrete evolutionary history. The tree branch lengths among PAI integrases were shorter than those among phage integrases suggesting that PAIs may be a more recent addition to E. coli. Further phylogenetic comparisons of these 68 integrases with 53 TR integrases from other characterized MIGEs also demonstrated that PAI-encode integrases form a distinct lineage, suggesting that these PAIs in E. coli are not remnants of other MIGEs. We identified recombination directionality factors/excisionases in the proximity of many of the E. coli PAI integrases, factors that were previously not shown to be present in E. coli PAIs. Overall this work is the first to demonstrate a dichotomy in the evolution of integrases encoded on PAIs and phages from pathogenic E. coli suggesting that PAIs are an evolutionary distinct genetic element.}, }
@article {pmid21146720, year = {2011}, author = {Gomez, S and Rapoport, M and Togneri, A and Viegas-Caetano, J and Faccone, D and Corso, A and Petroni, A and Pasteran, F}, title = {Emergence of metallo-β-lactamases in Enterobacteriaceae from Argentina.}, journal = {Diagnostic microbiology and infectious disease}, volume = {69}, number = {1}, pages = {94-97}, doi = {10.1016/j.diagmicrobio.2010.08.025}, pmid = {21146720}, issn = {1879-0070}, mesh = {Aged, 80 and over ; Anti-Bacterial Agents/pharmacology ; Argentina ; Carbapenems/pharmacology ; Conjugation, Genetic ; Drug Resistance, Multiple, Bacterial ; Enterobacteriaceae/drug effects/*enzymology/isolation &amp; purification ; Enterobacteriaceae Infections/*microbiology ; Female ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Microbial Sensitivity Tests ; Multigene Family ; beta-Lactamases/*biosynthesis/genetics ; }, abstract = {Carbapenem susceptibility in Enterobacteriaceae (M9921, M9959) revealed the presence of MBLs bla(VIM-2) (M9959) and bla(IMP-8) (M9921), both as first cassettes of class-1-integrons. ESBL bla(PER-2) was detected in both strains and M9921 also harboured qnrB10, aac(6')-Ib and aac(6')-Ib-cr. This is the first report of MBLs in Enterobacteriaceae from Argentina.}, }
@article {pmid21145349, year = {2011}, author = {García-Quintanilla, M and Casadesús, J}, title = {Virulence plasmid interchange between strains ATCC 14028, LT2, and SL1344 of Salmonella enterica serovar Typhimurium.}, journal = {Plasmid}, volume = {65}, number = {2}, pages = {169-175}, doi = {10.1016/j.plasmid.2010.12.001}, pmid = {21145349}, issn = {1095-9890}, mesh = {Amino Acid Substitution ; Animals ; Bacterial Proteins/genetics/metabolism ; Conjugation, Genetic ; Female ; *Gene Transfer, Horizontal ; Mice ; Mice, Inbred BALB C ; Mutation ; Plasmids/*genetics/*metabolism ; Salmonella Infections, Animal/virology ; Salmonella typhimurium/*genetics/*pathogenicity ; Virulence/*genetics ; }, abstract = {Strains ATCC 14028 and SL1344 of Salmonella enterica serovar Typhimurium are more virulent than LT2 in the BALB/c mouse model. Virulence plasmid swapping between strains ATCC 14208, LT2, and SL1344 does not alter their competitive indexes during mouse infection, indicating that the three plasmids are functionally equivalent, and that their contribution to virulence is independent from the host background. Strains ATCC 14028 and LT2 are more efficient than SL1344 as conjugal donors of the virulence plasmid. Virulence plasmid swapping indicates that reduced ability of conjugal transfer is a property of the SL1344 plasmid, not of the host strain. An A→V amino acid substitution in the TraG protein appears to be the major cause that reduces conjugal transfer in the virulence plasmid of SL1344. Additional sequence differences in the tra operon are found between the SL1344 plasmid and the ATCC 14028 and LT2 plasmids. Divergence in the tra operon may reflect the occurrence of genetic drift either after laboratory domestication or in the environment. The latter might provide evidence that possession of conjugal transfer functions is a neutral trait in Salmonella populations, a view consistent with the abundance of Salmonella isolates whose virulence plasmids are non-conjugative.}, }
@article {pmid21143941, year = {2010}, author = {Lundin, D and Gribaldo, S and Torrents, E and Sjöberg, BM and Poole, AM}, title = {Ribonucleotide reduction - horizontal transfer of a required function spans all three domains.}, journal = {BMC evolutionary biology}, volume = {10}, number = {}, pages = {383}, pmid = {21143941}, issn = {1471-2148}, mesh = {Archaea/enzymology/genetics ; Bacteria/enzymology/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Phylogeny ; Ribonucleotide Reductases/*genetics ; Ribonucleotides/*metabolism ; Sequence Analysis, Protein ; Viruses/enzymology/genetics ; }, abstract = {BACKGROUND: Ribonucleotide reduction is the only de novo pathway for synthesis of deoxyribonucleotides, the building blocks of DNA. The reaction is catalysed by ribonucleotide reductases (RNRs), an ancient enzyme family comprised of three classes. Each class has distinct operational constraints, and are broadly distributed across organisms from all three domains, though few class I RNRs have been identified in archaeal genomes, and classes II and III likewise appear rare across eukaryotes. In this study, we examine whether this distribution is best explained by presence of all three classes in the Last Universal Common Ancestor (LUCA), or by horizontal gene transfer (HGT) of RNR genes. We also examine to what extent environmental factors may have impacted the distribution of RNR classes.<br><br>RESULTS: Our phylogenies show that the Last Eukaryotic Common Ancestor (LECA) possessed a class I RNR, but that the eukaryotic class I enzymes are not directly descended from class I RNRs in Archaea. Instead, our results indicate that archaeal class I RNR genes have been independently transferred from bacteria on two occasions. While LECA possessed a class I RNR, our trees indicate that this is ultimately bacterial in origin. We also find convincing evidence that eukaryotic class I RNR has been transferred to the Bacteroidetes, providing a stunning example of HGT from eukaryotes back to Bacteria. Based on our phylogenies and available genetic and genomic evidence, class II and III RNRs in eukaryotes also appear to have been transferred from Bacteria, with subsequent within-domain transfer between distantly-related eukaryotes. Under the three-domains hypothesis the RNR present in the last common ancestor of Archaea and eukaryotes appears, through a process of elimination, to have been a dimeric class II RNR, though limited sampling of eukaryotes precludes a firm conclusion as the data may be equally well accounted for by HGT.<br><br>CONCLUSIONS: Horizontal gene transfer has clearly played an important role in the evolution of the RNR repertoire of organisms from all three domains of life. Our results clearly show that class I RNRs have spread to Archaea and eukaryotes via transfers from the bacterial domain, indicating that class I likely evolved in the Bacteria. However, against the backdrop of ongoing transfers, it is harder to establish whether class II or III RNRs were present in the LUCA, despite the fact that ribonucleotide reduction is an essential cellular reaction and was pivotal to the transition from RNA to DNA genomes. Instead, a general pattern of ongoing horizontal transmission emerges wherein environmental and enzyme operational constraints, especially the presence or absence of oxygen, are likely to be major determinants of the RNR repertoire of genomes.}, }
@article {pmid21143712, year = {2011}, author = {Smet, A and Rasschaert, G and Martel, A and Persoons, D and Dewulf, J and Butaye, P and Catry, B and Haesebrouck, F and Herman, L and Heyndrickx, M}, title = {In situ ESBL conjugation from avian to human Escherichia coli during cefotaxime administration.}, journal = {Journal of applied microbiology}, volume = {110}, number = {2}, pages = {541-549}, doi = {10.1111/j.1365-2672.2010.04907.x}, pmid = {21143712}, issn = {1365-2672}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Cecum/microbiology ; Cefotaxime/pharmacology ; Colon/microbiology ; *Conjugation, Genetic ; Denaturing Gradient Gel Electrophoresis ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/*genetics/growth &amp; development/isolation &amp; purification ; *Gene Transfer, Horizontal ; Humans ; Plasmids/genetics ; Polymerase Chain Reaction ; Poultry/*microbiology ; beta-Lactamases/*genetics ; }, abstract = {AIMS: The behaviour of an Escherichia coli isolate of broiler origin harbouring a bla(TEM-52) -carrying plasmid (lactose-negative mutant of B1-54, IncII group) was studied in an in situ continuous flow culture system, simulating the human caecum and the ascending colon during cefotaxime administration.<br><br>METHODS AND RESULTS: Fresh faeces from a healthy volunteer, negative for cephalosporin-resistant E. coli, were selected to prepare inocula. The microbiota was monitored by plating on diverse selective media, and a shift in the populations of bacteria was examined by 16S rDNA PCR denaturing gradient gel electrophoresis. Escherichia coli transconjugants were verified by plasmid and pulsed-field gel electrophoresis profiles (PFGE). The avian extended-spectrum &#x3b2;-lactamase-positive E. coli was able to proliferate without selective pressure of cefotaxime, and E. coli transconjugants of human origin were detected 24 h after inoculation of the donor strain. Upon administration of cefotaxime to the fresh medium, an increase in the population size of E. coli B1-54 and the transconjugants was observed. PFGE and plasmid analysis revealed a limited number of human E. coli clones receptive for the bla(TEM-52) -carrying plasmid.<br><br>CONCLUSIONS: These observations provide evidence of the maintenance of an E. coli strain of poultry origin and the horizontal gene transfer in the human commensal bowel microbiota even without antimicrobial treatment.<br><br>The fact that an E. coli strain of poultry origin might establish itself and transfer its bla gene to commensal human E. coli raises public health concerns.}, }
@article {pmid21141884, year = {2011}, author = {Cummings, DE and Archer, KF and Arriola, DJ and Baker, PA and Faucett, KG and Laroya, JB and Pfeil, KL and Ryan, CR and Ryan, KR and Zuill, DE}, title = {Broad dissemination of plasmid-mediated quinolone resistance genes in sediments of two urban coastal wetlands.}, journal = {Environmental science &amp; technology}, volume = {45}, number = {2}, pages = {447-454}, doi = {10.1021/es1029206}, pmid = {21141884}, issn = {1520-5851}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {Anti-Infective Agents/*analysis/metabolism ; Bacteria/classification/genetics/metabolism ; Bacterial Proteins/analysis/genetics/metabolism ; Base Sequence ; Cities ; Drug Resistance, Bacterial/*genetics ; Environmental Monitoring/methods ; *Genes, Bacterial ; Geologic Sediments/*chemistry/microbiology ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Plasmids/genetics ; Quinolones/*analysis/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Seasons ; Water Microbiology ; Water Pollutants, Chemical/analysis/metabolism ; Wetlands ; }, abstract = {Contamination of soil and water with antibiotic-resistant bacteria may create reservoirs of antibiotic resistance genes that have the potential to negatively impact future public health through horizontal gene transfer. The plasmid-mediated quinolone resistance genes qnrA, qnrB, qnrS, qepA, and aac(6')-Ib-cr were detected by PCR amplification of metagenomic DNA from surface sediments of the Tijuana River Estuary, a sewage-impacted coastal wetland along the U.S.-Mexico border; sediments of Famosa Slough, a nearby urban wetland that is largely unaffected by sewage, contained only qnrB, qnrS, and qepA. The number of PCR-positive sites and replicates increased in both wetlands after rainfall. Real-time quantitative PCR revealed a significant increase (p < 0.0005) in qnrA abundance (copies per gram sediment or per 16S rDNA copy) in Tijuana River Estuary sediments immediately following rainfall, but no significant change was measured at Famosa Slough (p > 0.1). Nucleotide sequences of cloned qnrA amplicons were all affiliated with qnrA genes found on plasmids of clinical isolates with one exception that was most similar to the chromosomal qnrA gene found in Shewanella algae. Our results suggest that urban wetlands may become reservoirs of antibiotic resistance genes, particularly where wastewater is improperly managed.}, }
@article {pmid21141668, year = {2010}, author = {Bowler, C and Vardi, A and Allen, AE}, title = {Oceanographic and biogeochemical insights from diatom genomes.}, journal = {Annual review of marine science}, volume = {2}, number = {}, pages = {333-365}, doi = {10.1146/annurev-marine-120308-081051}, pmid = {21141668}, issn = {1941-1405}, mesh = {Climate Change ; Diatoms/*genetics ; *Genome ; Geological Phenomena ; Oceanography ; Oceans and Seas ; }, abstract = {Diatoms are the most successful group of eukaryotic phytoplankton in the modern ocean and have risen to dominance relatively quickly over the last 100 million years. Recently completed whole genome sequences from two species of diatom, Thalassiosira pseudonana and Phaeodactylum tricornutum, have revealed a wealth of information about the evolutionary origins and metabolic adaptations that have led to their ecological success. A major finding is that they have incorporated genes both from their endosymbiotic ancestors and by horizontal gene transfer from marine bacteria. This unique melting pot of genes encodes novel capacities for metabolic management, for example, allowing the integration of a urea cycle into a photosynthetic cell. In this review we show how genome-enabled approaches are being leveraged to explore major phenomena of oceanographic and biogeochemical relevance, such as nutrient assimilation and life histories in diatoms. We also discuss how diatoms may be affected by climate change-induced alterations in ocean processes.}, }
@article {pmid21141462, year = {2010}, author = {Wang, H and Liu, N and Huang, Y}, title = {[Phylogenomic analysis of modular polyketide synthases in actinomycetes and its application in product screening].}, journal = {Wei sheng wu xue bao = Acta microbiologica Sinica}, volume = {50}, number = {10}, pages = {1293-1304}, pmid = {21141462}, issn = {0001-6209}, mesh = {Actinobacteria/classification/enzymology/*genetics ; Acyltransferases/metabolism ; Amino Acid Sequence ; DNA Primers ; Genome, Plant/*genetics ; Molecular Sequence Data ; Multienzyme Complexes/*metabolism ; Phylogeny ; Polyketide Synthases/classification/*genetics ; }, abstract = {OBJECTIVE: To elucidate phylogenetic relationships of modular polyketide synthases (PKS) in actinomycetes, and to provide a guide for screening and discovery of polyketides.<br><br>METHODS: We retrieved amino acid sequences of 190 ketosynthases (KS) and 195 acyltransferase (AT) of 20 modular polyketide synthases from database PKSDB, and constructed Neighbor-Joining trees based on amino acid sequences of KS, AT and KS + AT respectively using MEGA 4.0. We computed the mean distances within and between groups of KSs. We designed a pair of degenerate primers based on two conserved regions of KS, and screened 20 bioactive isolates by PCR. After sequencing the KS genes of positive strains, we constructed a Neighbor-joining tree of the 89 KSs identified in this study with the 160 known ones. We also fermented 13 KS-positive isolates and carried out chemical analysis of the fermentation extracts.<br><br>RESULTS: KSs from the same PKSs of actinomycetes tended to group respectively into clades, and KSs responsible for synthesis of products with similar structures tended to cluster together. The mean distances within groups of KSs from each PKS pathway were less than 0.300, and the mean distances between groups of KSs from different PKS pathways were generally more than 0.300. All the ATs grouped into two big clades according to the substrate specificity. Some ATs from the same pathway were grouped within the two big clades respectively, and the rest were scattered. The tree of KS + AT integrated the topological structures of both KS tree and AT tree. The majority KSs from individual isolates tended to group into clades. Most KSs from four of the isolates grouped into four distinct clades, and most KSs from another five isolates respectively fell into four clades of known pathways. We isolated and identified three predicted compounds as expected.<br><br>CONCLUSION: Vertical evolution is likely to be the dominant evolutionary mode of KS genes in actinomycetes, while AT genes may have evolved mainly through horizontal gene transfer. Considering that KSs cluster according to the corresponding product structures, and that the mean distances 0.300 between groups of KSs could sever as an evaluation criteria for different PKS pathways, the phylogenomic analysis of KS is more suitable than that of AT or KS + AT for guiding the screening of polyketide compounds from actinomycetes.}, }
@article {pmid21139625, year = {2011}, author = {Kinashi, H}, title = {Giant linear plasmids in Streptomyces: a treasure trove of antibiotic biosynthetic clusters.}, journal = {The Journal of antibiotics}, volume = {64}, number = {1}, pages = {19-25}, doi = {10.1038/ja.2010.146}, pmid = {21139625}, issn = {1881-1469}, mesh = {Anti-Bacterial Agents/*biosynthesis ; Gene Transfer, Horizontal ; Multigene Family ; Plasmids/*genetics/metabolism ; Recombination, Genetic ; Streptomyces/*genetics/metabolism ; }, abstract = {Many giant linear plasmids have been isolated from Streptomyces by using pulsed-field gel electrophoresis and some of them were found to carry an antibiotic biosynthetic cluster(s); SCP1 carries biosynthetic genes for methylenomycin, pSLA2-L for lankacidin and lankamycin, and pKSL for lasalocid and echinomycin. Accumulated data suggest that giant linear plasmids have played critical roles in genome evolution and horizontal transfer of secondary metabolism. In this review, I summarize typical examples of giant linear plasmids whose involvement in antibiotic production has been studied in some detail, emphasizing their finding processes and interaction with the host chromosomes. A hypothesis on horizontal transfer of secondary metabolism involving giant linear plasmids is proposed at the end.}, }
@article {pmid21138562, year = {2010}, author = {Trombert, AN and Berrocal, L and Fuentes, JA and Mora, GC}, title = {S. Typhimurium sseJ gene decreases the S. Typhi cytotoxicity toward cultured epithelial cells.}, journal = {BMC microbiology}, volume = {10}, number = {}, pages = {312}, pmid = {21138562}, issn = {1471-2180}, mesh = {Bacterial Proteins/genetics/*metabolism ; Cell Line ; Cell Proliferation ; Epithelial Cells/*microbiology ; Genetic Complementation Test ; Humans ; Mutation ; Pseudogenes ; Salmonella Infections/microbiology ; Salmonella typhi/genetics/pathogenicity/*physiology ; Salmonella typhimurium/genetics/*metabolism/pathogenicity ; Virulence ; }, abstract = {BACKGROUND: Salmonella enterica serovar Typhi and Typhimurium are closely related serovars as indicated by >96% DNA sequence identity between shared genes. Nevertheless, S. Typhi is a strictly human-specific pathogen causing a systemic disease, typhoid fever. In contrast, S. Typhimurium is a broad host range pathogen causing only a self-limited gastroenteritis in immunocompetent humans. We hypothesize that these differences have arisen because some genes are unique to each serovar either gained by horizontal gene transfer or by the loss of gene activity due to mutation, such as pseudogenes. S. Typhi has 5% of genes as pseudogenes, much more than S. Typhimurium which contains 1%. As a consequence, S. Typhi lacks several protein effectors implicated in invasion, proliferation and/or translocation by the type III secretion system that are fully functional proteins in S. Typhimurium. SseJ, one of these effectors, corresponds to an acyltransferase/lipase that participates in SCV biogenesis in human epithelial cell lines and is needed for full virulence of S. Typhimurium. In S. Typhi, sseJ is a pseudogene. Therefore, we suggest that sseJ inactivation in S. Typhi has an important role in the development of the systemic infection.<br><br>RESULTS: We investigated whether the S. Typhi trans-complemented with the functional sseJ gene from S. Typhimurium (STM) affects the cytotoxicity toward cultured cell lines. It was found that S. Typhi harbouring sseJSTM presents a similar cytotoxicity level and intracellular retention/proliferation of cultured epithelial cells (HT-29 or HEp-2) as wild type S. Typhimurium. These phenotypes are significantly different from wild type S. Typhi<br><br>CONCLUSIONS: Based on our results we conclude that the mutation that inactivate the sseJ gene in S. Typhi resulted in evident changes in the behaviour of bacteria in contact with eukaryotic cells, plausibly contributing to the S. Typhi adaptation to the systemic infection in humans.}, }
@article {pmid21133668, year = {2010}, author = {Roberts, AP and Mullany, P}, title = {Oral biofilms: a reservoir of transferable, bacterial, antimicrobial resistance.}, journal = {Expert review of anti-infective therapy}, volume = {8}, number = {12}, pages = {1441-1450}, doi = {10.1586/eri.10.106}, pmid = {21133668}, issn = {1744-8336}, mesh = {Anti-Bacterial Agents/metabolism/pharmacology/*therapeutic use ; Bacteria/drug effects/*genetics/*growth &amp; development ; Bacterial Adhesion/genetics ; Biofilms/*growth &amp; development ; Dental Caries/microbiology ; Dental Plaque/*microbiology ; Drug Resistance, Bacterial/*genetics ; *Gene Transfer, Horizontal ; Humans ; Mouth/*microbiology ; Periodontal Diseases/microbiology ; }, abstract = {Oral microbes are responsible for dental caries and periodontal diseases and have also been implicated in a range of other diseases beyond the oral cavity. These bacteria live primarily as complex, polymicrobial biofilms commonly called dental plaque. Cells growing within a biofilm often exhibit altered phenotypes, such as increased antibiotic resistance. The stable structural properties and close proximity of the bacterial cells within the biofilm appears to be an excellent environment for horizontal gene transfer, which can lead to the spread of antibiotic resistance genes amongst the biofilm inhabitants. This article will present an overview of the different types and amount of resistance to antibiotics that have been found in the human oral microbiota and will discuss the oral inhabitants' role as a reservoir of antimicrobial resistance genes. In addition, data on the genetic support for these resistance genes will be detailed and the evidence for horizontal gene transfer reviewed, demonstrating that the bacteria inhabiting the oral cavity are a reservoir of transferable antibiotic resistance.}, }
@article {pmid21131517, year = {2011}, author = {La Gioia, F and Rizzotti, L and Rossi, F and Gardini, F and Tabanelli, G and Torriani, S}, title = {Identification of a tyrosine decarboxylase gene (tdcA) in Streptococcus thermophilus 1TT45 and analysis of its expression and tyramine production in milk.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {3}, pages = {1140-1144}, pmid = {21131517}, issn = {1098-5336}, mesh = {Animals ; Bacterial Proteins/genetics/metabolism ; Cheese/microbiology ; Dairying ; Milk/*chemistry/metabolism ; Molecular Sequence Data ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Streptococcus thermophilus/*enzymology/genetics/metabolism ; Tyramine/*biosynthesis ; Tyrosine Decarboxylase/*genetics/*metabolism ; }, abstract = {In this study, a tyrosine decarboxylase gene (tdcA) was identified in 1 among 83 Streptococcus thermophilus strains tested. Its sequence, nearly identical to that of a tdcA of Lactobacillus curvatus, indicated a horizontal gene transfer event. Transcription in milk and the formation of critical levels of tyramine were observed in the presence of tyrosine.}, }
@article {pmid21131318, year = {2011}, author = {Werner, G and Freitas, AR and Coque, TM and Sollid, JE and Lester, C and Hammerum, AM and Garcia-Migura, L and Jensen, LB and Francia, MV and Witte, W and Willems, RJ and Sundsfjord, A}, title = {Host range of enterococcal vanA plasmids among Gram-positive intestinal bacteria.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {66}, number = {2}, pages = {273-282}, doi = {10.1093/jac/dkq455}, pmid = {21131318}, issn = {1460-2091}, mesh = {Conjugation, Genetic ; DNA Transposable Elements/*genetics ; Enterococcus faecalis/*genetics ; Enterococcus faecium/*genetics ; Gene Transfer, Horizontal ; Host Specificity/*genetics ; Microbial Sensitivity Tests ; *Plasmids ; Polymerase Chain Reaction ; Vancomycin Resistance ; }, abstract = {OBJECTIVES: The most prevalent type of acquired glycopeptide resistance is encoded by the vanA transposon Tn1546 located mainly on transferable plasmids in Enterococcus faecium. The limited occurrence in other species could be due to the lack of inter-species transferability and/or stability of Tn1546-containing plasmids in other species. We investigated the in vitro transferability of 14 pre-characterized vanA-containing plasmids hosted by E. faecium (n = 9), Enterococcus faecalis (n = 4) and Enterococcus raffinosus (n = 1) into several enterococcal, lactobacterial, lactococcal and bifidobacterial recipients.<br><br>METHODS: A filter-mating protocol was harmonized using procedures of seven partner laboratories. Donor strains were mated with three E. faecium recipients, three E. faecalis recipients, a Lactobacillus acidophilus recipient, a Lactococcus lactis recipient and two Bifidobacterium recipients. Transfer rates were calculated per donor and recipient. Transconjugants were confirmed by determining their phenotypic and genotypic properties. Stability of plasmids in the new host was assessed in long-term growth experiments.<br><br>RESULTS: In total, 282 enterococcal matings and 73 inter-genus matings were performed and evaluated. In summary, intra-species transfer was far more frequent than inter-species transfer, if that was detectable at all. All recipients of the same species behaved similarly. Inter-genus transfer was shown for broad host range control plasmids (pIP501/pAM&#x3b2;1) only. Acquired resistance plasmids remained stable in the new host.<br><br>CONCLUSIONS: Intra-species transfer of enterococcal vanA plasmids was far more frequent than transfer across species or genus barriers and may thus explain the preferred prevalence of vanA-containing plasmids among E. faecium. A reservoir of vanA plasmids in non-enterococcal intestinal colonizers does not seem to be reasonable.}, }
@article {pmid21127873, year = {2011}, author = {Ren, X and Li, H and Chen, S}, title = {Cloning of the chlorothalonil-degrading gene cluster and evidence of its horizontal transfer.}, journal = {Current microbiology}, volume = {62}, number = {3}, pages = {1068-1073}, pmid = {21127873}, issn = {1432-0991}, mesh = {*Cloning, Molecular ; DNA, Bacterial/chemistry/genetics ; Escherichia coli/*genetics/metabolism ; *Gene Transfer, Horizontal ; Metabolic Networks and Pathways/*genetics ; Molecular Sequence Data ; *Multigene Family ; Nitriles/*metabolism ; Ochrobactrum/*genetics/metabolism ; Sequence Analysis, DNA ; }, abstract = {Strain Ochrobactrum lupine TP-D1 was found to degrade chlorothalonil (TPN) to 4-hydroxy-chlorothalonil (TPN-OH). To clone the related degrading gene, genomic library of TP-D1 was constructed using Escherichia coli DH10B and two positive clones 889 and 838 were gained. However, no plasmid was detected in clone 889. And in clone 838, a 3494 bp fragment was cloned which contains a 984 bp hydrolytic dehalogenase (chd) gene and a 1926 bp insertion element IS-Olup. The insertion element contains a transposase coding region (1026 bp), an ATP-binding protein coding region (657 bp) and flanked by 20 bp inverted repeat sequences. Further isolation provided another seven TPN-degrading strains, they belonged to the genera of Pseudomonas sp., Achromobacter sp., Ochrobactrum sp., Ralstonia sp., and Lysobacter sp. PCR strategy showed that they all contain the same structure of chd gene and the upstream IS-Olup. Our evidences collectively suggest that chd gene may be disseminated through horizontal gene transfer based on phylogenetic analysis of the cluster and their host bacterial strains. At the same time, the chd gene was amplified from genome of the positive clone 889, which also provides some potential evidence to the gene horizontal transfer.}, }
@article {pmid21124976, year = {2010}, author = {Férandon, C and Moukha, S and Callac, P and Benedetto, JP and Castroviejo, M and Barroso, G}, title = {The Agaricus bisporus cox1 gene: the longest mitochondrial gene and the largest reservoir of mitochondrial group i introns.}, journal = {PloS one}, volume = {5}, number = {11}, pages = {e14048}, pmid = {21124976}, issn = {1932-6203}, mesh = {Agaricus/enzymology/*genetics ; Amino Acid Sequence ; Base Sequence ; DNA, Mitochondrial/chemistry/genetics ; Electron Transport Complex IV/*genetics ; Fungal Proteins/*genetics ; Fungi/classification/genetics ; Gene Transfer, Horizontal ; Genome, Mitochondrial/*genetics ; Introns/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Species Specificity ; }, abstract = {In eukaryotes, introns are located in nuclear and organelle genes from several kingdoms. Large introns (up to 5 kbp) are frequent in mitochondrial genomes of plant and fungi but scarce in Metazoa, even if these organisms are grouped with fungi among the Opisthokonts. Mitochondrial introns are classified in two groups (I and II) according to their RNA secondary structure involved in the intron self-splicing mechanism. Most of these mitochondrial group I introns carry a "Homing Endonuclease Gene" (heg) encoding a DNA endonuclease acting in transfer and site-specific integration ("homing") and allowing intron spreading and gain after lateral transfer even between species from different kingdoms. Opposed to this gain mechanism, is another which implies that introns, which would have been abundant in the ancestral genes, would mainly evolve by loss. The importance of both mechanisms (loss and gain) is matter of debate. Here we report the sequence of the cox1 gene of the button mushroom Agaricus bisporus, the most widely cultivated mushroom in the world. This gene is both the longest mitochondrial gene (29,902 nt) and the largest group I intron reservoir reported to date with 18 group I and 1 group II. An exhaustive analysis of the group I introns available in cox1 genes shows that they are mobile genetic elements whose numerous events of loss and gain by lateral transfer combine to explain their wide and patchy distribution extending over several kingdoms. An overview of intron distribution, together with the high frequency of eroded heg, suggests that they are evolving towards loss. In this landscape of eroded and lost intron sequences, the A. bisporus cox1 gene exhibits a peculiar dynamics of intron keeping and catching, leading to the largest collection of mitochondrial group I introns reported to date in a Eukaryote.}, }
@article {pmid21124445, year = {2010}, author = {Whiteman, NK and Gloss, AD}, title = {Parasitology: Nematode debt to bacteria.}, journal = {Nature}, volume = {468}, number = {7324}, pages = {641-642}, pmid = {21124445}, issn = {1476-4687}, mesh = {Animals ; Cell Wall/parasitology ; Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/*genetics ; Genes, Helminth/genetics ; Helminth Proteins/genetics/metabolism ; Nematoda/*genetics/*pathogenicity ; Parasites/genetics/pathogenicity ; Plant Roots/parasitology ; Plants/*parasitology ; }, }
@article {pmid21121023, year = {2010}, author = {Zheng, H and Wu, H}, title = {Short prokaryotic DNA fragment binning using a hierarchical classifier based on linear discriminant analysis and principal component analysis.}, journal = {Journal of bioinformatics and computational biology}, volume = {8}, number = {6}, pages = {995-1011}, doi = {10.1142/s0219720010005051}, pmid = {21121023}, issn = {1757-6334}, mesh = {Algorithms ; Computational Biology ; Computer Simulation ; DNA/*classification/*genetics ; Databases, Nucleic Acid/statistics &amp; numerical data ; *Discriminant Analysis ; Gene Library ; Gene Transfer, Horizontal ; Genetics, Microbial ; *Metagenome ; Metagenomics/*statistics &amp; numerical data ; *Principal Component Analysis ; Sequence Analysis, DNA ; }, abstract = {Metagenomics is an emerging field in which the power of genomic analysis is applied to an entire microbial community, bypassing the need to isolate and culture individual microbial species. Assembling of metagenomic DNA fragments is very much like the overlap-layout-consensus procedure for assembling isolated genomes, but is augmented by an additional binning step to differentiate scaffolds, contigs and unassembled reads into various taxonomic groups. In this paper, we employed n-mer oligonucleotide frequencies as the features and developed a hierarchical classifier (PCAHIER) for binning short (≤ 1,000 bps) metagenomic fragments. The principal component analysis was used to reduce the high dimensionality of the feature space. The hierarchical classifier consists of four layers of local classifiers that are implemented based on the linear discriminant analysis. These local classifiers are responsible for binning prokaryotic DNA fragments into superkingdoms, of the same superkingdom into phyla, of the same phylum into genera, and of the same genus into species, respectively. We evaluated the performance of the PCAHIER by using our own simulated data sets as well as the widely used simHC synthetic metagenome data set from the IMG/M system. The effectiveness of the PCAHIER was demonstrated through comparisons against a non-hierarchical classifier, and two existing binning algorithms (TETRA and Phylopythia).}, }
@article {pmid21119020, year = {2010}, author = {Kung, VL and Ozer, EA and Hauser, AR}, title = {The accessory genome of Pseudomonas aeruginosa.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {74}, number = {4}, pages = {621-641}, pmid = {21119020}, issn = {1098-5557}, support = {5K02 AI065615/AI/NIAID NIH HHS/United States ; 1R01 AI075191/AI/NIAID NIH HHS/United States ; F30 ES016487/ES/NIEHS NIH HHS/United States ; F32 AI089068/AI/NIAID NIH HHS/United States ; 5T32 AI007476-13/AI/NIAID NIH HHS/United States ; T32 AI007476/AI/NIAID NIH HHS/United States ; K02 AI065615/AI/NIAID NIH HHS/United States ; 5F30 ES016487-03/ES/NIEHS NIH HHS/United States ; R01 AI053674/AI/NIAID NIH HHS/United States ; R21 AI088286/AI/NIAID NIH HHS/United States ; 2R01 AI053674/AI/NIAID NIH HHS/United States ; R01 AI075191/AI/NIAID NIH HHS/United States ; 1R21 AI088286/AI/NIAID NIH HHS/United States ; }, mesh = {DNA Transposable Elements/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomic Islands/genetics ; Prophages/genetics ; Pseudomonas Infections/virology ; Pseudomonas aeruginosa/*genetics ; }, abstract = {Pseudomonas aeruginosa strains exhibit significant variability in pathogenicity and ecological flexibility. Such interstrain differences reflect the dynamic nature of the P. aeruginosa genome, which is composed of a relatively invariable "core genome" and a highly variable "accessory genome." Here we review the major classes of genetic elements comprising the P. aeruginosa accessory genome and highlight emerging themes in the acquisition and functional importance of these elements. Although the precise phenotypes endowed by the majority of the P. aeruginosa accessory genome have yet to be determined, rapid progress is being made, and a clearer understanding of the role of the P. aeruginosa accessory genome in ecology and infection is emerging.}, }
@article {pmid21116630, year = {2011}, author = {Brown, DW}, title = {The KP4 killer protein gene family.}, journal = {Current genetics}, volume = {57}, number = {1}, pages = {51-62}, pmid = {21116630}, issn = {1432-0983}, mesh = {Amino Acid Sequence ; Animals ; Ascomycota/chemistry/*genetics ; Chromosomes, Fungal ; Conserved Sequence ; Fungal Proteins/chemistry/*genetics ; Genome, Fungal ; Introns ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; }, abstract = {Killer protein 4 (KP4) is a well studied viral toxin secreted by the maize smut fungus Ustilago maydis that kills sensitive Ustilago strains as well as inhibits Fusarium and plant root growth by inhibiting calcium uptake. Numerous small, cysteine-rich proteins have been shown to play a critical role in fungal-plant-bacterial associations. The discovery of six KP4-like genes in F. verticillioides precipitated efforts to understand their function and evolutionary origin. Analysis of publicly available genomic sequence identified 31 additional KP4-like genes from a range of Ascomycota, a Basidiomycota, and the moss Physcomitrella patens. Sequence comparison and phylogenetic analysis indicate that the viral KP4 and the moss and fungal KP4-like genes evolved from a common ancestor providing evidence for lateral gene transfer between kingdoms. Six genes of the 37 total genes are predicted to encode a protein with two, non-identical KP4-like domains in tandem separated by 29-56 amino acids. The results suggest that two independent events led to the dual-domain KP4 genes present in different lineages of the Ascomycota. Understanding the nature and function of KP4-like proteins in mycotoxin-producing species like Fusarium may help to limit plant diseases and increase food safety and food production.}, }
@article {pmid21115831, year = {2010}, author = {Hao, W and Richardson, AO and Zheng, Y and Palmer, JD}, title = {Gorgeous mosaic of mitochondrial genes created by horizontal transfer and gene conversion.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {50}, pages = {21576-21581}, pmid = {21115831}, issn = {1091-6490}, support = {R01 GM070612/GM/NIGMS NIH HHS/United States ; R01-GM-70612/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Base Sequence ; *Biological Evolution ; *Gene Conversion ; *Gene Transfer, Horizontal ; *Genes, Mitochondrial ; Genes, Plant ; Genetic Speciation ; Genome, Bacterial ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; }, abstract = {The best known outcome of horizontal gene transfer (HGT) is the introduction of novel genes, but other outcomes have been described. When a transferred gene has a homolog in the recipient genome, the native gene may be functionally replaced (and subsequently lost) or partially overwritten by gene conversion with transiently present foreign DNA. Here we report the discovery, in two lineages of plant mitochondrial genes, of novel gene combinations that arose by conversion between coresident native and foreign homologs. These lineages have undergone intricate conversion between native and foreign copies, with conversion occurring repeatedly and differentially over the course of speciation, leading to radiations of mosaic genes involved in respiration and intron splicing. Based on these findings, we develop a model--the duplicative HGT and differential gene conversion model--that integrates HGT and ongoing gene conversion in the context of speciation. Finally, we show that one of these HGT-driven gene-conversional radiations followed two additional types of conversional chimerism, namely, intramitochondrial retroprocessing and interorganellar gene conversion across the 2 billion year divide between mitochondria and chloroplasts. These findings expand our appreciation of HGT and gene conversion as creative evolutionary forces, establish plant mitochondria as a premiere system for studying the evolutionary dynamics of HGT and its genetic reverberations, and recommend careful examination of bacterial and other genomes for similar, likely overlooked phenomena.}, }
@article {pmid21115709, year = {2011}, author = {Machielsen, R and Siezen, RJ and van Hijum, SA and van Hylckama Vlieg, JE}, title = {Molecular description and industrial potential of Tn6098 conjugative transfer conferring alpha-galactoside metabolism in Lactococcus lactis.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {2}, pages = {555-563}, pmid = {21115709}, issn = {1098-5336}, mesh = {*Conjugation, Genetic ; *DNA Transposable Elements ; DNA, Bacterial/genetics ; Food Industry ; Galactosides/*metabolism ; *Gene Transfer, Horizontal ; *Industrial Microbiology ; Lactococcus lactis/*genetics/*metabolism/physiology ; Polymerase Chain Reaction ; Recombination, Genetic ; Sequence Analysis, DNA ; Soy Milk/metabolism ; }, abstract = {A novel 51-kb conjugative transposon of Lactococcus lactis, designated Tn6098, encoding the capacity to utilize α-galactosides such as raffinose and stachyose, was identified and characterized. Alpha-galactosides are a dominant carbon source in many plant-derived foods. Most dairy lactococcus strains are unable to use α-galactosides as a growth substrate, yet many of these strains are known to have beneficial industrial traits. Conjugal transfer of Tn6098 was demonstrated from the plant-derived donor strain L. lactis KF147 to the recipient L. lactis NZ4501, a derivative of the dairy model strain L. lactis MG1363. The integration of Tn6098 into the genome of the recipient strain was confirmed by Illumina sequencing of the transconjugant L. lactis NIZO3921. The molecular structure of the integration site was confirmed by a PCR product spanning the insertion site. A 15-bp direct repeat sequence (TTATACCATAATTAC) is present on either side of Tn6098 in the chromosome of L. lactis KF147. One copy of this sequence is also present in the L. lactis MG1363 chromosome and represents the sole integration site. Phenotypic characterization of all strains showed that the transconjugant has not only acquired the ability to grow well in soy milk, a substrate rich in α-galactosides, but also has retained the flavor-forming capabilities of the recipient strain L. lactis MG1363. This study demonstrates how (induced) conjugation can be used to exploit the beneficial industrial traits of industrial dairy lactic acid bacteria in fermentation of plant-derived substrates.}, }
@article {pmid21115109, year = {2011}, author = {Obembe, OO and Popoola, JO and Leelavathi, S and Reddy, SV}, title = {Advances in plant molecular farming.}, journal = {Biotechnology advances}, volume = {29}, number = {2}, pages = {210-222}, doi = {10.1016/j.biotechadv.2010.11.004}, pmid = {21115109}, issn = {1873-1899}, mesh = {Biological Products/*biosynthesis ; Biotechnology/*methods ; Gene Transfer, Horizontal ; *Molecular Farming ; Plant Proteins/*metabolism ; Plants, Genetically Modified/chemistry ; Recombinant Proteins/*biosynthesis ; Technology, Pharmaceutical/methods ; }, abstract = {Plant molecular farming (PMF) is a new branch of plant biotechnology, where plants are engineered to produce recombinant pharmaceutical and industrial proteins in large quantities. As an emerging subdivision of the biopharmaceutical industry, PMF is still trying to gain comparable social acceptance as the already established production systems that produce these high valued proteins in microbial, yeast, or mammalian expression systems. This article reviews the various cost-effective technologies and strategies, which are being developed to improve yield and quality of the plant-derived pharmaceuticals, thereby making plant-based production system suitable alternatives to the existing systems. It also attempts to overview the different novel plant-derived pharmaceuticals and non-pharmaceutical protein products that are at various stages of clinical development or commercialization. It then discusses the biosafety and regulatory issues, which are crucial (if strictly adhered to) to eliminating potential health and environmental risks, which in turn is necessary to earning favorable public perception, thus ensuring the success of the industry.}, }
@article {pmid21115076, year = {2011}, author = {Szczepanowski, R and Eikmeyer, F and Harfmann, J and Blom, J and Rogers, LM and Top, EM and Schlüter, A}, title = {Sequencing and comparative analysis of IncP-1α antibiotic resistance plasmids reveal a highly conserved backbone and differences within accessory regions.}, journal = {Journal of biotechnology}, volume = {155}, number = {1}, pages = {95-103}, doi = {10.1016/j.jbiotec.2010.11.018}, pmid = {21115076}, issn = {1873-4863}, mesh = {Base Sequence ; Chromosome Mapping ; Conserved Sequence ; DNA Transposable Elements/*genetics ; DNA, Bacterial/*chemistry/genetics ; Drug Resistance, Bacterial/*genetics ; Molecular Sequence Data ; Phylogeny ; Plasmids/*genetics ; Sequence Analysis, DNA ; Sewage/microbiology ; }, abstract = {Although IncP-1 plasmids are important for horizontal gene transfer among bacteria, in particular antibiotic resistance spread, so far only three plasmids from the subgroup IncP-1α have been completely sequenced. In this study we doubled this number. The three IncP-1α plasmids pB5, pB11 and pSP21 were isolated from bacteria of two different sewage treatment plants and sequenced by a combination of next-generation and capillary sequencing technologies. A comparative analysis including the previously analysed IncP-1α plasmids RK2, pTB11 and pBS228 revealed a highly conserved plasmid backbone (at least 99.9% DNA sequence identity) comprising 54 core genes. The accessory elements of the plasmid pB5 constitute a class 1 integron interrupting the parC gene and an IS6100 copy inserted into the integron. In addition, the tetracycline resistance genes tetAR and the ISTB11-like element are located between the klc operon and the trfA-ssb operon. Plasmid pB11 is loaded with a Tn5053-like mercury resistance transposon between the parCBA and parDE operons and contains tetAR that are identical to those identified in plasmid pB5 and the insertion sequence ISSP21. Plasmid pSP21 harbours an ISPa7 element in a Tn402 transposon including a class 1 integron between the partitioning genes parCBA and parDE. The IS-element ISSP21 (99.89% DNA sequence identity to ISSP21 from pB11), inserted downstream of the tetR gene and a copy of ISTB11 (identical to ISTB11 on pTB11) inserted between the genes pncA and pinR. On all three plasmids the accessory genes are almost always located between the backbone modules confirming the importance of the backbone functions for plasmid maintenance. The striking backbone conservation among the six completely sequenced IncP-1α plasmids is in contrast to the much higher diversity within the IncP-1β subgroup.}, }
@article {pmid21110998, year = {2011}, author = {Zhang, Q and Zmasek, CM and Cai, X and Godzik, A}, title = {TIR domain-containing adaptor SARM is a late addition to the ongoing microbe-host dialog.}, journal = {Developmental and comparative immunology}, volume = {35}, number = {4}, pages = {461-468}, pmid = {21110998}, issn = {1879-0089}, support = {P20 GM076221-01/GM/NIGMS NIH HHS/United States ; P20 GM076221/GM/NIGMS NIH HHS/United States ; GM076221/GM/NIGMS NIH HHS/United States ; R01 GM087218/GM/NIGMS NIH HHS/United States ; R01 GM087218-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cytoskeletal Proteins/chemistry/*genetics/*immunology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Host-Pathogen Interactions ; Humans ; Metagenomics ; Models, Molecular ; Phylogeny ; Protein Structure, Tertiary ; Receptors, Interleukin-1/chemistry/genetics/immunology ; Signal Transduction ; }, abstract = {Toll/interleukin-1 receptor (TIR) domain-containing proteins play important roles in defense against pathogens in both animals and plants, connecting the immunity signaling pathways via a chain of specific protein-protein interactions. Among them is SARM, the only TIR domain-containing adaptor that can negatively regulate TLR signaling. By extensive phylogenetic analysis, we show here that SARM is closely related to bacterial proteins with TIR domains, suggesting that this family has a different evolutionary history from other animal TIR-containing adaptors, possibly emerging via a lateral gene transfer from bacteria to animals. We also show evidence of several similar, independent transfer events, none of which, however, survived in vertebrates. An evolutionary relationship between the animal SARM adaptor and bacterial proteins with TIR domains illustrates the possible role that bacterial TIR-containing proteins play in regulating eukaryotic immune responses and how this mechanism was possibly adapted by the eukaryotes themselves.}, }
@article {pmid21110068, year = {2011}, author = {Hussain, S and Devers-Lamrani, M and El Azhari, N and Martin-Laurent, F}, title = {Isolation and characterization of an isoproturon mineralizing Sphingomonas sp. strain SH from a French agricultural soil.}, journal = {Biodegradation}, volume = {22}, number = {3}, pages = {637-650}, doi = {10.1007/s10532-010-9437-x}, pmid = {21110068}, issn = {1572-9729}, mesh = {Bacterial Proteins/genetics/metabolism ; France ; Molecular Sequence Data ; Phenylurea Compounds/*metabolism ; Phylogeny ; *Soil Microbiology ; Sphingomonas/classification/genetics/isolation &amp; purification/*metabolism ; }, abstract = {The phenylurea herbicide isoproturon, 3-(4-isopropylphenyl)-1,1-dimethylurea (IPU), was found to be rapidly mineralized in an agricultural soil in France that had been periodically exposed to IPU. Enrichment cultures from samples of this soil isolated a bacterial strain able to mineralize IPU. 16S rRNA sequence analysis showed that this strain belonged to the phylogeny of the genus Sphingomonas (96% similarity with Sphingomonas sp. JEM-14, AB219361) and was designated Sphingomonas sp. strain SH. From this strain, a partial sequence of a 1,2-dioxygenase (catA) gene coding for an enzyme degrading catechol putatively formed during IPU mineralization was amplified. Phylogenetic analysis revealed that the catA sequence was related to Sphingomonas spp. and showed a lack of congruence between the catA and 16S rRNA based phylogenies, implying horizontal gene transfer of the catA gene cluster between soil microbiota. The IPU degrading ability of strain SH was strongly influenced by pH with maximum degradation taking place at pH 7.5. SH was only able to mineralize IPU and its known metabolites including 4-isopropylaniline and it could not degrade other structurally related phenylurea herbicides such as diuron, linuron, monolinuron and chlorotoluron or their aniline derivatives. These observations suggest that the catabolic abilities of the strain SH are highly specific to the metabolism of IPU.}, }
@article {pmid21106583, year = {2011}, author = {Nelson-Sathi, S and List, JM and Geisler, H and Fangerau, H and Gray, RD and Martin, W and Dagan, T}, title = {Networks uncover hidden lexical borrowing in Indo-European language evolution.}, journal = {Proceedings. Biological sciences}, volume = {278}, number = {1713}, pages = {1794-1803}, pmid = {21106583}, issn = {1471-2954}, mesh = {*Cultural Evolution ; Humans ; *Language ; Linguistics ; *Models, Theoretical ; }, abstract = {Language evolution is traditionally described in terms of family trees with ancestral languages splitting into descendent languages. However, it has long been recognized that language evolution also entails horizontal components, most commonly through lexical borrowing. For example, the English language was heavily influenced by Old Norse and Old French; eight per cent of its basic vocabulary is borrowed. Borrowing is a distinctly non-tree-like process--akin to horizontal gene transfer in genome evolution--that cannot be recovered by phylogenetic trees. Here, we infer the frequency of hidden borrowing among 2346 cognates (etymologically related words) of basic vocabulary distributed across 84 Indo-European languages. The dataset includes 124 (5%) known borrowings. Applying the uniformitarian principle to inventory dynamics in past and present basic vocabularies, we find that 1373 (61%) of the cognates have been affected by borrowing during their history. Our approach correctly identified 117 (94%) known borrowings. Reconstructed phylogenetic networks that capture both vertical and horizontal components of evolutionary history reveal that, on average, eight per cent of the words of basic vocabulary in each Indo-European language were involved in borrowing during evolution. Basic vocabulary is often assumed to be relatively resistant to borrowing. Our results indicate that the impact of borrowing is far more widespread than previously thought.}, }
@article {pmid21103966, year = {2010}, author = {Zhang, X}, title = {Human in check: new threat from superbugs equipped with NDM-1.}, journal = {Protein &amp; cell}, volume = {1}, number = {12}, pages = {1051-1052}, pmid = {21103966}, issn = {1674-8018}, mesh = {Anti-Bacterial Agents/metabolism/pharmacology ; Bacterial Proteins/*genetics/*metabolism ; Biological Evolution ; Enterobacteriaceae/*enzymology/pathogenicity ; Gene Transfer, Horizontal ; Host-Parasite Interactions ; Humans ; beta-Lactam Resistance/drug effects/genetics ; beta-Lactamases/*genetics/*metabolism ; }, }
@article {pmid21103900, year = {2011}, author = {Kittang, BR and Skrede, S and Langeland, N and Haanshuus, CG and Mylvaganam, H}, title = {emm gene diversity, superantigen gene profiles and presence of SlaA among clinical isolates of group A, C and G streptococci from western Norway.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {30}, number = {3}, pages = {423-433}, pmid = {21103900}, issn = {1435-4373}, mesh = {Amino Acid Sequence ; Antigens, Bacterial/chemistry/*genetics ; Bacterial Outer Membrane Proteins/chemistry/*genetics/immunology ; Carrier Proteins/chemistry/*genetics ; Frameshift Mutation ; Gene Transfer, Horizontal ; Genetic Variation ; Humans ; Molecular Sequence Data ; Norway ; Phospholipases A2/*genetics ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Recombination, Genetic ; Sequence Analysis, Protein ; Streptococcal Infections/microbiology ; Streptococcus/*genetics/immunology/pathogenicity ; Streptococcus pyogenes/*genetics/immunology/isolation &amp; purification/pathogenicity ; Superantigens/*genetics/immunology ; }, abstract = {In order to investigate molecular characteristics of beta-hemolytic streptococcal isolates from western Norway, we analysed the entire emm gene sequences, obtained superantigen gene profiles and determined the prevalence of the gene encoding streptococcal phospholipase A2 (SlaA) of 165 non-invasive and 34 contemporary invasive group A, C and G streptococci (GAS, GCS and GGS). Among the 25 GAS and 26 GCS/GGS emm subtypes identified, only emm3.1 was significantly associated with invasive disease. M protein size variation within GAS and GCS/GGS emm types was frequently identified. Two non-invasive and one invasive GGS possessed emm genes that translated to truncated M proteins as a result of frameshift mutations. Results suggestive of recombinations between emm or emm-like gene segments were found in isolates of emm4 and stG485 types. One non-invasive GGS possessed speC, speG, speH, speI and smeZ, and another non-invasive GGS harboured SlaA. speA and SlaA were over-represented among invasive GAS, probably because they were associated with emm3. speG(dys) was identified in 83% of invasive and 63% of non-invasive GCS/GGS and correlated with certain emm subtypes. Our results indicate the invasive potential of isolates belonging to emm3, and show substantial emm gene diversity and possible lateral gene transfers in our streptococcal population.}, }
@article {pmid21098248, year = {2011}, author = {Izumiya, H and Sekizuka, T and Nakaya, H and Taguchi, M and Oguchi, A and Ichikawa, N and Nishiko, R and Yamazaki, S and Fujita, N and Watanabe, H and Ohnishi, M and Kuroda, M}, title = {Whole-genome analysis of Salmonella enterica serovar Typhimurium T000240 reveals the acquisition of a genomic island involved in multidrug resistance via IS1 derivatives on the chromosome.}, journal = {Antimicrobial agents and chemotherapy}, volume = {55}, number = {2}, pages = {623-630}, pmid = {21098248}, issn = {1098-6596}, mesh = {Anti-Bacterial Agents/*pharmacology ; Base Sequence ; Chromosomes, Bacterial/*genetics ; DNA Transposable Elements/*genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Genome, Bacterial/genetics ; Genomic Islands/*genetics ; Genomics/*methods ; Humans ; Integrons/genetics ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Recombination, Genetic ; Salmonella typhimurium/*drug effects/genetics ; Sequence Analysis, DNA ; }, abstract = {Salmonella enterica serovar Typhimurium is frequently associated with life-threatening systemic infections, and the recent global emergence of multidrug resistance in S. enterica isolates from agricultural and clinical settings has raised concerns. In this study, we determined the whole-genome sequence of fluoroquinolone-resistant S. enterica serovar Typhimurium T000240 strain (DT12) isolated from human gastroenteritis in 2000. Comparative genome analysis revealed that T000240 displays high sequence similarity to strain LT2, which was originally isolated in 1940, indicating that progeny of LT2 might be reemerging. T000240 possesses a unique 82-kb genomic island, designated as GI-DT12, which is composed of multidrug resistance determinants, including a Tn2670-like composite transposon (class 1 integron [intI1, bla(oxa-30), aadA1, qacEΔ1, and sul1], mercury resistance proteins, and chloramphenicol acetyltransferase), a Tn10-like tetracycline resistance protein (tetA), the aerobactin iron-acquisition siderophore system (lutA and lucABC), and an iron transporter (sitABCD). Since GI-DT12 is flanked by IS1 derivatives, IS1-mediated recombination likely played a role in the acquisition of this genomic island through horizontal gene transfer. The aminoglycoside-(3)-N-acetyltransferase (aac(3)) gene and a class 1 integron harboring the dfrA1 gene cassette responsible for gentamicin and trimethoprim resistance, respectively, were identified on plasmid pSTMDT12_L and appeared to have been acquired through homologous recombination with IS26. This study represents the first characterization of the unique genomic island GI-DT12 that appears to be associated with possible IS1-mediated recombination in S. enterica serovar Typhimurium. It is expected that future whole-genome studies will aid in the characterization of the horizontal gene transfer events for the emerging S. enterica serovar Typhimurium strains.}, }
@article {pmid21092314, year = {2010}, author = {Chaudhary, R and Bansal, MS and Wehe, A and Fernández-Baca, D and Eulenstein, O}, title = {iGTP: a software package for large-scale gene tree parsimony analysis.}, journal = {BMC bioinformatics}, volume = {11}, number = {}, pages = {574}, pmid = {21092314}, issn = {1471-2105}, mesh = {Algorithms ; Databases, Genetic ; Evolution, Molecular ; Gene Duplication ; Genome ; Genomics/*methods ; *Phylogeny ; *Software ; }, abstract = {BACKGROUND: The ever-increasing wealth of genomic sequence information provides an unprecedented opportunity for large-scale phylogenetic analysis. However, species phylogeny inference is obfuscated by incongruence among gene trees due to evolutionary events such as gene duplication and loss, incomplete lineage sorting (deep coalescence), and horizontal gene transfer. Gene tree parsimony (GTP) addresses this issue by seeking a species tree that requires the minimum number of evolutionary events to reconcile a given set of incongruent gene trees. Despite its promise, the use of gene tree parsimony has been limited by the fact that existing software is either not fast enough to tackle large data sets or is restricted in the range of evolutionary events it can handle.<br><br>RESULTS: We introduce iGTP, a platform-independent software program that implements state-of-the-art algorithms that greatly speed up species tree inference under the duplication, duplication-loss, and deep coalescence reconciliation costs. iGTP significantly extends and improves the functionality and performance of existing gene tree parsimony software and offers advanced features such as building effective initial trees using stepwise leaf addition and the ability to have unrooted gene trees in the input. Moreover, iGTP provides a user-friendly graphical interface with integrated tree visualization software to facilitate analysis of the results.<br><br>CONCLUSIONS: iGTP enables, for the first time, gene tree parsimony analyses of thousands of genes from hundreds of taxa using the duplication, duplication-loss, and deep coalescence reconciliation costs, all from within a convenient graphical user interface.}, }
@article {pmid21085634, year = {2010}, author = {Smits, WK and Grossman, AD}, title = {The transcriptional regulator Rok binds A+T-rich DNA and is involved in repression of a mobile genetic element in Bacillus subtilis.}, journal = {PLoS genetics}, volume = {6}, number = {11}, pages = {e1001207}, pmid = {21085634}, issn = {1553-7404}, support = {GM50895/GM/NIGMS NIH HHS/United States ; R37 GM041934/GM/NIGMS NIH HHS/United States ; R01 GM050895/GM/NIGMS NIH HHS/United States ; R01 GM041934/GM/NIGMS NIH HHS/United States ; GM41934/GM/NIGMS NIH HHS/United States ; }, mesh = {AT Rich Sequence/*genetics ; Bacillus subtilis/*genetics ; Bacterial Proteins/chemistry/*metabolism ; Chromosomes, Bacterial/metabolism ; DNA, Bacterial/*metabolism ; Escherichia coli ; Fluorescence ; Genes, Bacterial/genetics ; Interspersed Repetitive Sequences/*genetics ; Protein Binding ; Protein Structure, Tertiary ; Protein Transport ; Recombinant Fusion Proteins/metabolism ; Repressor Proteins/chemistry/*metabolism ; *Transcription, Genetic ; }, abstract = {The rok gene of Bacillus subtilis was identified as a negative regulator of competence development. It also controls expression of several genes not related to competence. We found that Rok binds to extended regions of the B. subtilis genome. These regions are characterized by a high A+T content and are known or believed to have been acquired by horizontal gene transfer. Some of the Rok binding regions are in known mobile genetic elements. A deletion of rok resulted in higher excision of one such element, ICEBs1, a conjugative transposon found integrated in the B. subtilis genome. When expressed in the Gram negative E. coli, Rok also associated with A+T-rich DNA and a conserved C-terminal region of Rok contributed to this association. Together with previous work, our findings indicate that Rok is a nucleoid associated protein that serves to help repress expression of A+T-rich genes, many of which appear to have been acquired by horizontal gene transfer. In these ways, Rok appears to be functionally analogous to H-NS, a nucleoid associated protein found in Gram negative bacteria and Lsr2 of high G+C Mycobacteria.}, }
@article {pmid21082171, year = {2011}, author = {Caetano-Anollés, D and Kim, KM and Mittenthal, JE and Caetano-Anollés, G}, title = {Proteome evolution and the metabolic origins of translation and cellular life.}, journal = {Journal of molecular evolution}, volume = {72}, number = {1}, pages = {14-33}, pmid = {21082171}, issn = {1432-1432}, mesh = {Base Sequence ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Hydrolases/chemistry ; Origin of Life ; Phylogeny ; Protein Biosynthesis/*genetics ; Protein Folding ; *Protein Structure, Tertiary ; Proteins/*chemistry/genetics ; *Proteome/genetics ; RNA ; RNA Processing, Post-Transcriptional ; Sequence Alignment ; }, abstract = {The origin of life has puzzled molecular scientists for over half a century. Yet fundamental questions remain unanswered, including which came first, the metabolic machinery or the encoding nucleic acids. In this study we take a protein-centric view and explore the ancestral origins of proteins. Protein domain structures in proteomes are highly conserved and embody molecular functions and interactions that are needed for cellular and organismal processes. Here we use domain structure to study the evolution of molecular function in the protein world. Timelines describing the age and function of protein domains at fold, fold superfamily, and fold family levels of structural complexity were derived from a structural phylogenomic census in hundreds of fully sequenced genomes. These timelines unfold congruent hourglass patterns in rates of appearance of domain structures and functions, functional diversity, and hierarchical complexity, and revealed a gradual build up of protein repertoires associated with metabolism, translation and DNA, in that order. The most ancient domain architectures were hydrolase enzymes and the first translation domains had catalytic functions for the aminoacylation and the molecular switch-driven transport of RNA. Remarkably, the most ancient domains had metabolic roles, did not interact with RNA, and preceded the gradual build-up of translation. In fact, the first translation domains had also a metabolic origin and were only later followed by specialized translation machinery. Our results explain how the generation of structure in the protein world and the concurrent crystallization of translation and diversified cellular life created further opportunities for proteomic diversification.}, }
@article {pmid21081560, year = {2011}, author = {Palmeira, L and Penel, S and Lotteau, V and Rabourdin-Combe, C and Gautier, C}, title = {PhEVER: a database for the global exploration of virus-host evolutionary relationships.}, journal = {Nucleic acids research}, volume = {39}, number = {Database issue}, pages = {D569-75}, pmid = {21081560}, issn = {1362-4962}, mesh = {Cluster Analysis ; *Databases, Genetic ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Viral ; Genome, Viral ; Genomics ; Host-Pathogen Interactions/*genetics ; Phylogeny ; Sequence Homology ; User-Computer Interface ; Viral Proteins/chemistry/classification/genetics ; Viruses/classification/*genetics ; }, abstract = {Fast viral adaptation and the implication of this rapid evolution in the emergence of several new infectious diseases have turned this issue into a major challenge for various research domains. Indeed, viruses are involved in the development of a wide range of pathologies and understanding how viruses and host cells interact in the context of adaptation remains an open question. In order to provide insights into the complex interactions between viruses and their host organisms and namely in the acquisition of novel functions through exchanges of genetic material, we developed the PhEVER database. This database aims at providing accurate evolutionary and phylogenetic information to analyse the nature of virus-virus and virus-host lateral gene transfers. PhEVER (http://pbil.univ-lyon1.fr/databases/phever) is a unique database of homologous families both (i) between sequences from different viruses and (ii) between viral sequences and sequences from cellular organisms. PhEVER integrates extensive data from up-to-date completely sequenced genomes (2426 non-redundant viral genomes, 1007 non-redundant prokaryotic genomes, 43 eukaryotic genomes ranging from plants to vertebrates) and offers a clustering of proteins into homologous families containing at least one viral sequences, as well as alignments and phylogenies for each of these families. Public access to PhEVER is available through its webpage and through all dedicated ACNUC retrieval systems.}, }
@article {pmid21081549, year = {2011}, author = {Roberts, MC and Soge, OO and No, DB}, title = {Characterization of macrolide resistance genes in Haemophilus influenzae isolated from children with cystic fibrosis.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {66}, number = {1}, pages = {100-104}, doi = {10.1093/jac/dkq425}, pmid = {21081549}, issn = {1460-2091}, mesh = {Adolescent ; Anti-Bacterial Agents/*pharmacology/therapeutic use ; Azithromycin/pharmacology/therapeutic use ; Child ; Conjugation, Genetic ; Cystic Fibrosis/*complications ; DNA, Bacterial/genetics ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Haemophilus Infections/drug therapy/*microbiology ; Haemophilus influenzae/*drug effects/isolation &amp; purification ; Humans ; Macrolides/*pharmacology/therapeutic use ; Microbial Sensitivity Tests ; Nucleic Acid Hybridization ; Polymerase Chain Reaction ; Prevalence ; Randomized Controlled Trials as Topic ; Sequence Analysis, DNA ; }, abstract = {OBJECTIVES: to determine the mechanism(s) of macrolide resistance in Haemophilus influenzae isolated from cystic fibrosis (CF) patients participating in a randomized placebo-controlled trial of azithromycin.<br><br>METHODS: macrolide susceptibility, mutations and carriage of the macrolide resistance genes erm(A), erm(B), erm(C), erm(F) and mef(A) were determined using PCR assays and sequencing or hybridization of the PCR products. H. influenzae isolates were used as donors in conjugation studies with H. influenzae and Enterococcus faecalis recipients. Transconjugant susceptibility and the macrolide resistance genes carried were determined.<br><br>RESULTS: of the 106 H. influenzae isolates, 27 were resistant and 78 intermediate resistant to azithromycin and/or erythromycin. All isolates carried one or more macrolide resistance gene(s), with the mef(A), erm(B) and erm(F) genes found in 74%, 31% and 29% of the isolates, respectively. None of the selected isolates had L4 or L22 mutations. Twenty-five donors, with various macrolide MICs, transferred macrolide resistance genes to H. influenzae Rd (3.5 &#xd7; 10(-7)-1 &#xd7; 10(-10)) and/or E. faecalis (1 &#xd7; 10(-7)-1 &#xd7; 10(-8)) recipients. The H. influenzae transconjugants were phenotypically resistant or intermediate to both macrolides while E. faecalis transconjugants were erythromycin resistant.<br><br>CONCLUSIONS: this is the first identification of erm(A), erm(C) and erm(F) genes in H. influenzae or bacteria from CF patients and the first characterization of macrolide gene transfer from H. influenzae donors. The high level of H. influenzae macrolide gene carriage suggests that the use of azithromycin in the CF population may ultimately reduce the effectiveness of continued or repeated macrolide therapy.}, }
@article {pmid21081480, year = {2011}, author = {Tong, J and Dolezal, P and Selkrig, J and Crawford, S and Simpson, AG and Noinaj, N and Buchanan, SK and Gabriel, K and Lithgow, T}, title = {Ancestral and derived protein import pathways in the mitochondrion of Reclinomonas americana.}, journal = {Molecular biology and evolution}, volume = {28}, number = {5}, pages = {1581-1591}, pmid = {21081480}, issn = {1537-1719}, mesh = {Active Transport, Cell Nucleus ; Amino Acid Sequence ; Cell Nucleus/metabolism ; Cyclooxygenase 2/genetics/metabolism ; Eukaryota/*genetics/ultrastructure ; Evolution, Molecular ; Gene Transfer, Horizontal ; Hydrophobic and Hydrophilic Interactions ; Mitochondria/ultrastructure ; Mitochondrial Membrane Transport Proteins/*genetics/metabolism ; Models, Genetic ; Molecular Sequence Data ; Protein Sorting Signals/genetics ; Protein Transport/*genetics ; Recombinant Proteins/genetics/metabolism ; Saccharomyces cerevisiae/genetics/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {The evolution of mitochondria from ancestral bacteria required that new protein transport machinery be established. Recent controversy over the evolution of these new molecular machines hinges on the degree to which ancestral bacterial transporters contributed during the establishment of the new protein import pathway. Reclinomonas americana is a unicellular eukaryote with the most gene-rich mitochondrial genome known, and the large collection of membrane proteins encoded on the mitochondrial genome of R. americana includes a bacterial-type SecY protein transporter. Analysis of expressed sequence tags shows R. americana also has components of a mitochondrial protein translocase or "translocase in the inner mitochondrial membrane complex." Along with several other membrane proteins encoded on the mitochondrial genome Cox11, an assembly factor for cytochrome c oxidase retains sequence features suggesting that it is assembled by the SecY complex in R. americana. Despite this, protein import studies show that the RaCox11 protein is suited for import into mitochondria and functional complementation if the gene is transferred into the nucleus of yeast. Reclinomonas americana provides direct evidence that bacterial protein transport pathways were retained, alongside the evolving mitochondrial protein import machinery, shedding new light on the process of mitochondrial evolution.}, }
@article {pmid21081312, year = {2011}, author = {Huson, DH and Scornavacca, C}, title = {A survey of combinatorial methods for phylogenetic networks.}, journal = {Genome biology and evolution}, volume = {3}, number = {}, pages = {23-35}, pmid = {21081312}, issn = {1759-6653}, mesh = {Animals ; *Evolution, Molecular ; Humans ; Models, Genetic ; *Phylogeny ; }, abstract = {The evolutionary history of a set of species is usually described by a rooted phylogenetic tree. Although it is generally undisputed that bifurcating speciation events and descent with modifications are major forces of evolution, there is a growing belief that reticulate events also have a role to play. Phylogenetic networks provide an alternative to phylogenetic trees and may be more suitable for data sets where evolution involves significant amounts of reticulate events, such as hybridization, horizontal gene transfer, or recombination. In this article, we give an introduction to the topic of phylogenetic networks, very briefly describing the fundamental concepts and summarizing some of the most important combinatorial methods that are available for their computation.}, }
@article {pmid21080671, year = {2011}, author = {Wozniak, CA and Martinez, JC}, title = {U.S. EPA regulation of plant-incorporated protectants: assessment of impacts of gene flow from pest-resistant plants.}, journal = {Journal of agricultural and food chemistry}, volume = {59}, number = {11}, pages = {5859-5864}, doi = {10.1021/jf1030168}, pmid = {21080671}, issn = {1520-5118}, mesh = {Animals ; *Ecosystem ; Environment ; *Gene Flow ; *Gene Transfer, Horizontal ; Humans ; Insecta/physiology ; Plants, Genetically Modified/*adverse effects/*genetics/physiology ; Risk Assessment ; United States ; *United States Environmental Protection Agency ; }, abstract = {The U.S. Environmental Protection Agency licenses pesticide-expressing plants under the authority of the Federal Insecticide, Fungicide and Rodenticide Act (FIFRA). Transgenes and their pesticidal products represent pesticides under FIFRA and are referred to as plant-incorporated protectants (PIPs). When sexually compatible wild relatives (SCWR) are sympatric with PIP crops, there is a need to assess the potential for adverse effects to man and the environment resulting from transgene introgression in accord with FIFRA requirements. Genetic compatibility, introgression, weediness of SCWR × PIP hybrids, seed dispersal, and dormancy, among other parameters, as well as effects on other species (herbivores and beneficial insects), all need to be considered as part of the risk assessment for experimental use under Section 5 or registration under Section 3 of FIFRA. EPA is currently developing data requirements and guidance toward addressing potential gene flow impacts from PIPs.}, }
@article {pmid21080492, year = {2010}, author = {Szklarczyk, R and Huynen, MA}, title = {Mosaic origin of the mitochondrial proteome.}, journal = {Proteomics}, volume = {10}, number = {22}, pages = {4012-4024}, doi = {10.1002/pmic.201000329}, pmid = {21080492}, issn = {1615-9861}, mesh = {Animals ; Biological Evolution ; Humans ; Mice ; Mitochondria/*genetics/metabolism ; *Proteome ; Symbiosis ; }, abstract = {Although the origin of mitochondria from the endosymbiosis of an α-proteobacterium is well established, the nature of the host cell, the metabolic complexity of the endosymbiont and the subsequent evolution of the proto-mitochondrion into all its current appearances are still the subject of discovery and sometimes debate. Here we review what has been inferred about the original composition and subsequent evolution of the mitochondrial proteome and essential mitochondrial systems. The evolutionary mosaic that currently constitutes mitochondrial proteomes contains (i) endosymbiotic proteins (15-45%), (ii) proteins without detectable orthologs outside the eukaryotic lineage (40%), and (iii) proteins that are derived from non-proteobacterial Bacteria, Bacteriophages and Archaea (15%, specifically multiple tRNA-modification proteins). Protein complexes are of endosymbiotic origin, but have greatly expanded with novel eukaryotic proteins; in contrast to mitochondrial enzymes that are both of proteobacterial and non-proteobacterial origin. This disparity is consistent with the complexity hypothesis, which argues that proteins that are a part of large, multi-subunit complexes are unlikely to undergo horizontal gene transfer. We observe that they neither change their subcellular compartments in the course of evolution, even when their genes do.}, }
@article {pmid21076133, year = {2011}, author = {Murray, SA and Mihali, TK and Neilan, BA}, title = {Extraordinary conservation, gene loss, and positive selection in the evolution of an ancient neurotoxin.}, journal = {Molecular biology and evolution}, volume = {28}, number = {3}, pages = {1173-1182}, doi = {10.1093/molbev/msq295}, pmid = {21076133}, issn = {1537-1719}, mesh = {Animals ; Conserved Sequence/*genetics ; Cyanobacteria/classification/genetics ; Evolution, Molecular ; Gene Deletion ; Gene Duplication ; Genes, Bacterial/physiology ; Humans ; Multigene Family ; Neurotoxins/biosynthesis/classification/*genetics/poisoning ; Phylogeny ; Potassium Channel Blockers/metabolism/poisoning ; Potassium Channels/metabolism ; Recombination, Genetic ; Saxitoxin/biosynthesis/classification/*genetics/poisoning ; Selection, Genetic ; Sequence Alignment ; Sequence Analysis, DNA ; Synteny/genetics ; }, abstract = {The recent determination of the genetic basis for the biosynthesis of the neurotoxin, saxitoxin, produced by cyanobacteria, has revealed a highly complex sequence of reactions, involving over 30 biosynthetic steps encoded by up to 26 genes clustered at one genomic locus, sxt. Insights into evolutionary-ecological processes have been found through the study of such secondary metabolites because they consist of a measurable phenotype with clear ecological consequences, synthesized by known genes in a small number of species. However, the processes involved in and timing of the divergence of prokaryotic secondary metabolites have been difficult to determine due to their antiquity and the possible frequency of horizontal gene transfer and homologous recombination. Through analyses of gene synteny, phylogenies of individual genes, and analyses of recombination and selection, we identified the evolutionary processes of this cluster in five species of cyanobacteria. Here, we provide evidence that the sxt cluster appears to have been largely vertically inherited and was therefore likely present early in the divergence of the Nostocales, at least 2,100 Ma, the earliest reliably dated appearance of a secondary metabolite. The sxt cluster has been extraordinarily conserved through stabilizing selection. Genes have been lost and rearranged, have undergone intra- and interspecific recombination, and have been subject to duplication followed by positive selection along the duplicated lineage, with likely consequences for the toxin analogues produced. Several hypotheses exist as to the ecophysiological role of saxitoxin: as a method of chemical defense, cellular nitrogen storage, DNA metabolism, or chemical signaling. The antiquity of this gene cluster indicates that potassium channels, not sodium channels, may have been the original targets of this compound. The extraordinary conservation of the machinery for saxitoxin synthesis, under radically changing environmental conditions, shows that it has continued to play an important adaptive role in some cyanobacteria.}, }
@article {pmid21075892, year = {2011}, author = {Roig, FJ and González-Candelas, F and Amaro, C}, title = {Domain organization and evolution of multifunctional autoprocessing repeats-in-toxin (MARTX) toxin in Vibrio vulnificus.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {2}, pages = {657-668}, pmid = {21075892}, issn = {1098-5336}, mesh = {Bacterial Toxins/*genetics ; Bacterial Typing Techniques ; DNA, Bacterial/chemistry/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Geography ; Molecular Sequence Data ; Protein Structure, Tertiary ; Sequence Analysis, DNA ; Vibrio vulnificus/classification/*enzymology/*genetics/isolation &amp; purification ; }, abstract = {The objective of this study was to analyze multifunctional autoprocessing repeats-in-toxin (MARTX) toxin domain organization within the aquatic species Vibrio vulnificus as well as to study the evolution of the rtxA1 gene. The species is subdivided into three biotypes that differ in host range and geographical distribution. We have found three different types (I, II, and III) of V. vulnificus MARTX (MARTX(Vv)) toxins with common domains (an autocatalytic cysteine protease domain [CPD], an α/β-hydrolase domain, and a domain resembling that of the LifA protein of Escherichia coli O127:H6 E2348/69 [Efa/LifA]) and specific domains (a Rho-GTPase inactivation domain [RID], a domain of unknown function [DUF], a domain resembling that of the rtxA protein of Photorhabdus asymbiotica [rtxA(PA)], and an actin cross-linking domain [ACD]). Biotype 1 isolates harbor MARTX(Vv) toxin types I and II, biotype 2 isolates carry MARTX(Vv) toxin type III, and biotype 3 isolates have MARTX(Vv) toxin type II. The analyzed biotype 2 isolates harbor two identical copies of rtxA1, one chromosomal and the other plasmidic. The evolutionary history of the gene demonstrates that MARTX(Vv) toxins are mosaics, comprising pieces with different evolutionary histories, some of which have been acquired by intra- or interspecific horizontal gene transfer. Finally, we have found evidence that the evolutionary history of the rtxA1 gene for biotype 2 differs totally from the gene history of biotypes 1 and 3.}, }
@article {pmid21073312, year = {2010}, author = {Hall, RM}, title = {Salmonella genomic islands and antibiotic resistance in Salmonella enterica.}, journal = {Future microbiology}, volume = {5}, number = {10}, pages = {1525-1538}, doi = {10.2217/fmb.10.122}, pmid = {21073312}, issn = {1746-0921}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; *Drug Resistance, Bacterial ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genomic Islands ; Humans ; Proteus mirabilis/genetics ; Salmonella enterica/*drug effects/genetics/isolation &amp; purification/*pathogenicity ; }, abstract = {Antibiotic resistance in several Salmonella enterica serovars that cause gastrointestinal disease in humans is due to a set of related genomic islands carrying a class 1 integron, which carries the resistance genes. Salmonella genomic island 1 (SGI1), the first island of this type, was found in S. enterica serovar Typhimurium DT104 isolates, which are resistant to ampicillin, chloramphenicol, florfenicol, streptomycin, spectinomycin, sulfonamides and tetracycline. Several Salmonella serovars and Proteus mirablis have since been shown to harbor SGI1 or related islands carrying various sets of resistance genes and some distinct groups have emerged. SGI1 is an integrative mobilizable element and can be transferred experimentally into Escherichia coli. However, within serovars, isolates recovered from different parts of the world appear to be clonal, indicating that SGI1 movement may be rare. Potential reservoirs in food-producing animals or in ornamental fish have been identified for some serovars.}, }
@article {pmid21071191, year = {2011}, author = {Kamikawa, R and Yabuki, A and Nakayama, T and Ishida, K and Hashimoto, T and Inagaki, Y}, title = {Cercozoa comprises both EF-1α-containing and EFL-containing members.}, journal = {European journal of protistology}, volume = {47}, number = {1}, pages = {24-28}, doi = {10.1016/j.ejop.2010.08.002}, pmid = {21071191}, issn = {1618-0429}, mesh = {Cercozoa/*genetics ; Evolution, Molecular ; Gene Deletion ; Gene Transfer, Horizontal ; Peptide Elongation Factors/*genetics ; *Phylogeny ; Protozoan Proteins/*genetics ; Sequence Homology, Amino Acid ; }, abstract = {Elongation factor 1α (EF-1α) and elongation factor-like protein (EFL) are considered to be functionally equivalent proteins involved in peptide synthesis. Eukaryotes can be fundamentally divided into 'EF-1α-containing' and 'EFL-containing' types. Recently, EF-1α and EFL genes have been surveyed across the diversity of eukaryotes to explore the origin and evolution of EFL genes. Although the phylum Cercozoa is a diverse group, gene data for either EFL or EF-1α are absent from all cercozoans except chlorarachniophytes which were previously defined as EFL-containing members. Our survey revealed that two members of the cercozoan subphylum Filosa (Thaumatomastix sp. and strain YPF610) are EFL-containing members. Importantly, we identified EF-1α genes from two members of Filosa (Paracercomonas marina and Paulinella chromatophora) and a member of the other subphylum Endomyxa (Filoreta japonica). All cercozoan EFL homologues could not be recovered as a monophyletic group in maximum-likelihood and Bayesian analyses, suggesting that lateral gene transfer was involved in the EFL evolution in this protist assemblage. In contrast, EF-1α analysis successfully recovered a monophyly of three homologues sampled from the two cercozoan subphyla. Based on the results, we postulate that cercozoan EF-1α genes have been vertically inherited, and the current EFL-containing species may have secondarily lost their EF-1α genes.}, }
@article {pmid21067672, year = {2010}, author = {Li, X and Wang, HH}, title = {Tetracycline resistance associated with commensal bacteria from representative ready-to-consume deli and restaurant foods.}, journal = {Journal of food protection}, volume = {73}, number = {10}, pages = {1841-1848}, doi = {10.4315/0362-028x-73.10.1841}, pmid = {21067672}, issn = {0362-028X}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/drug effects/*genetics ; Drug Resistance, Bacterial/genetics ; *Food Microbiology ; Gene Transfer, Horizontal ; Humans ; Meat Products/*microbiology ; Microbial Sensitivity Tests ; Restaurants ; Tetracycline Resistance/*genetics ; }, abstract = {Proper knowledge of antibiotic resistance (AR) dissemination is essential for effective mitigation. This study examined the profiles of tetracycline-resistant (Tetr) commensal bacteria from representative ready-to-consume food samples from salad bars at local grocery stores and restaurants. Out of 900 Tetr isolates examined, 158 (17.6%) carried one or more of tetM, tetL, tetS, and tetK genes by conventional PCR, 28 harbored more than one Tetr determinants. The most prevalent genotype was tetM, which was detected in 70.9% of the AR gene carriers, followed by tetL (31.6%), tetS (13.9%), and tetK (2.5%). Identified AR gene carriers included Enterococcus, Lactococcus, Staphylococcus, Brochothrix, Carnobacterium, Stenotrophomonas, Pseudomonas, and Sphingobacterium, by 16S rRNA gene sequence analysis. AR determinants were successfully transmitted, and led to resistance in Streptococcus mutans via natural gene transformation and Enterococcus faecalis via electroporation, suggesting the functionality and mobility of the AR genes from the food commensal bacteria. In addition, the AR traits in many isolates are quite stable, even in the absence of the selective pressure. The identification of new commensal carriers for representative AR genes revealed the involvement of a broad spectrum of bacteria in the horizontal transmission of AR genes. Meanwhile, the spectrum of the antibiotic-resistant bacteria differed from the spectrum of the total bacteria (by denaturing gradient gel electrophoresis) associated with the food items. Our data revealed a common avenue in AR exposure and will assist in proper risk assessment and the development of comprehensive mitigation strategies to effectively combat AR.}, }
@article {pmid21062328, year = {2011}, author = {Jasser, I and Królicka, A and Karnkowska-Ishikawa, A}, title = {A novel phylogenetic clade of picocyanobacteria from the Mazurian lakes (Poland) reflects the early ontogeny of glacial lakes.}, journal = {FEMS microbiology ecology}, volume = {75}, number = {1}, pages = {89-98}, doi = {10.1111/j.1574-6941.2010.00990.x}, pmid = {21062328}, issn = {1574-6941}, mesh = {Cyanobacteria/classification/*genetics ; Fresh Water/microbiology ; Gene Transfer, Horizontal ; *Genetic Variation ; Operon ; Phycocyanin/genetics ; Phycoerythrin/genetics ; *Phylogeny ; Poland ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {The community of picocyanobacteria inhabiting the Great Mazurian Lakes system (comprising lakes ranging from mesotrophic to hypertrophic) is dominated by phycoerythrin-rich cells, which outnumber phycocyanin-rich cells, even in hypertrophic lakes. The genetic diversity and phylogeny of 43 strains of picocyanobacteria isolated from four Mazurian lakes were studied by analyzing the nucleotide sequences of the 16S rRNA gene and cpcBA-IGS operon. Phylogenetic analyses assigned some of the strains to several previously described clusters (Groups A, B, C, E and I) and revealed the existence of a novel clade, Group M (Mazurian), which exhibited a low level of similarity to the other clusters. Both phycocyanin and phycoerythrin picocyanobacteria were assigned to this clade based on an analysis of the 16S rRNA gene. The cpcBA sequence analysis assigned only phycocyanin strains to Group M, whereas the phycoerythrin strains from the M ribogroup were assigned to Groups B and E. We hypothesize that Group M originally contained only phycocyanin picocyanobacteria. The phycoerythrin found in strains belonging to ribogroup M seems to have been acquired through horizontal gene transfer as an adaptation to the changing environment early in the ontogeny of these glacial lakes.}, }
@article {pmid21059789, year = {2011}, author = {Kloesges, T and Popa, O and Martin, W and Dagan, T}, title = {Networks of gene sharing among 329 proteobacterial genomes reveal differences in lateral gene transfer frequency at different phylogenetic depths.}, journal = {Molecular biology and evolution}, volume = {28}, number = {2}, pages = {1057-1074}, pmid = {21059789}, issn = {1537-1719}, mesh = {Conjugation, Genetic ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Phylogeny ; Proteobacteria/*classification/*genetics ; }, abstract = {Lateral gene transfer (LGT) is an important mechanism of natural variation among prokaryotes. Over the full course of evolution, most or all of the genes resident in a given prokaryotic genome have been affected by LGT, yet the frequency of LGT can vary greatly across genes and across prokaryotic groups. The proteobacteria are among the most diverse of prokaryotic taxa. The prevalence of LGT in their genome evolution calls for the application of network-based methods instead of tree-based methods to investigate the relationships among these species. Here, we report networks that capture both vertical and horizontal components of evolutionary history among 1,207,272 proteins distributed across 329 sequenced proteobacterial genomes. The network of shared proteins reveals modularity structure that does not correspond to current classification schemes. On the basis of shared protein-coding genes, the five classes of proteobacteria fall into two main modules, one including the alpha-, delta-, and epsilonproteobacteria and the other including beta- and gammaproteobacteria. The first module is stable over different protein identity thresholds. The second shows more plasticity with regard to the sequence conservation of proteins sampled, with the gammaproteobacteria showing the most chameleon-like evolutionary characteristics within the present sample. Using a minimal lateral network approach, we compared LGT rates at different phylogenetic depths. In general, gene evolution by LGT within proteobacteria is very common. At least one LGT event was inferred to have occurred in at least 75% of the protein families. The average LGT rate at the species and class depth is about one LGT event per protein family, the rate doubling at the phylum level to an average of two LGT events per protein family. Hence, our results indicate that the rate of gene acquisition per protein family is similar at the level of species (by recombination) and at the level of classes (by LGT). The frequency of LGT per genome strongly depends on the species lifestyle, with endosymbionts showing far lower LGT frequencies than free-living species. Moreover, the nature of the transferred genes suggests that gene transfer in proteobacteria is frequently mediated by conjugation.}, }
@article {pmid21058506, year = {2010}, author = {Lal, D and Lal, R}, title = {Evolution of mercuric reductase (merA) gene: a case of horizontal gene transfer.}, journal = {Mikrobiologiia}, volume = {79}, number = {4}, pages = {524-531}, pmid = {21058506}, issn = {0026-3656}, mesh = {Bacteria/enzymology/*genetics ; Base Composition ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Mercury/metabolism ; Operon ; Oxidoreductases/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In the present study the role of horizontal gene transfer events in providing the mercury resistance is depicted. merA is key gene in mer operon and has been used for this study. Phylogenetic analysis of aligned merA sequences shows broad similarities to the established 16S rRNA phylogeny. But there is no separation of bacterial merA from archael merA which suggests that merA gene in both these groups share considerable sequence homology. However, inconsistencies between merA and 16S rRNA gene phylogenetic trees are apparent for some taxa. These discrepancies in the phylogenetic trees for merA gene and 16S rRNA gene have lead to the suggestion that horizontal gene transfer (HGT) is a major contributor for its evolution. The close association among members of different groups in merA gene tree, as supported by high bootstrap values, deviations in GC content and codon usage pattern indicate the possibility that horizontal gene transfer events might have taken place during the evolution of this gene.}, }
@article {pmid21057109, year = {2010}, author = {Techtmann, SM and Robb, FT}, title = {Archaeal-like chaperonins in bacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {47}, pages = {20269-20274}, pmid = {21057109}, issn = {1091-6490}, mesh = {Adenosine Triphosphate/metabolism ; Archaea/genetics ; Base Sequence ; Chaperonins/*classification/*genetics/metabolism ; Cluster Analysis ; DNA Primers/genetics ; Electrophoresis, Polyacrylamide Gel ; Gene Components ; Gram-Positive Bacteria/*genetics ; Microscopy, Electron ; Models, Genetic ; *Models, Molecular ; Molecular Sequence Data ; *Phylogeny ; *Protein Folding ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Chaperonins (CPN) are ubiquitous oligomeric protein machines that mediate the ATP-dependent folding of polypeptide chains. These chaperones have not only been assigned stress response and normal housekeeping functions but also have a role in certain human disease states. A longstanding convention divides CPNs into two groups that share many conserved sequence motifs but differ in both structure and distribution. Group I complexes are the well known GroEL/ES heat-shock proteins in bacteria, that also occur in some species of mesophilic archaea and in the endosymbiotic organelles of eukaryotes. Group II CPNs are found only in the cytosol of archaea and eukaryotes. Here we report a third, divergent group of CPNs found in several species of bacteria. We propose to name these Group III CPNs because of their distant relatedness to both Group I and II CPNs as well as their unique genomic context, within the hsp70 operon. The prototype Group III CPN, Carboxydothermus hydrogenoformans chaperonin (Ch-CPN), is able to refold denatured proteins in an ATP-dependent manner and is structurally similar to the Group II CPNs, forming a 16-mer with each subunit contributing to a flexible lid domain. The Group III CPN represent a divergent group of bacterial CPNs distinct from the GroEL/ES CPN found in all bacteria. The Group III lineage may represent an ancient horizontal gene transfer from an archaeon into an early Firmicute lineage. An analysis of their functional and structural characteristics may provide important insights into the early history of this ubiquitous family of proteins.}, }
@article {pmid21054359, year = {2011}, author = {Smith, J}, title = {Superinfection drives virulence evolution in experimental populations of bacteria and plasmids.}, journal = {Evolution; international journal of organic evolution}, volume = {65}, number = {3}, pages = {831-841}, pmid = {21054359}, issn = {1558-5646}, support = {R01 GM033782/GM/NIGMS NIH HHS/United States ; R01 GM091875/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R01 GM033782-17/GM/NIGMS NIH HHS/United States ; GM33782-17/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*genetics/*pathogenicity ; *Biological Evolution ; Gene Transfer, Horizontal ; Genetic Fitness ; *Host-Pathogen Interactions ; Humans ; Plasmids/*genetics ; Superinfection/microbiology ; Virulence ; }, abstract = {A prominent hypothesis proposes that pathogen virulence evolves in large part due to a trade-off between infectiousness and damage to hosts. Other explanations emphasize how virulence evolves in response to competition among pathogens within hosts. Given the proliferation of theoretical possibilities, what best predicts how virulence evolves in real biological systems? Here, I show that virulence evolution in experimental populations of bacteria and self-transmissible plasmids is best explained by within-host competition. Plasmids evolved to severely reduce the fitness of their hosts even in the absence of uninfected cells. This result is inconsistent with the trade-off hypothesis, which predicts that under these conditions vertically transmitted pathogens would evolve to be less virulent. Plasmid virulence was strongly correlated with the ability to superinfect cells containing competing plasmid genotypes, suggesting a key role for within-host competition. When virulent genotypes became common, hosts evolved resistance to plasmid infection. These results show that the trade-off hypothesis can incorrectly predict virulence evolution when within-host interactions are neglected. They also show that symbioses between bacteria and plasmids can evolve to be surprisingly antagonistic.}, }
@article {pmid21047698, year = {2011}, author = {Steele, RE and David, CN and Technau, U}, title = {A genomic view of 500 million years of cnidarian evolution.}, journal = {Trends in genetics : TIG}, volume = {27}, number = {1}, pages = {7-13}, pmid = {21047698}, issn = {0168-9525}, support = {P 21108/FWF_/Austrian Science Fund FWF/Austria ; R24 GM080537/GM/NIGMS NIH HHS/United States ; R24 GM080537-01A1/GM/NIGMS NIH HHS/United States ; 1R24GM080537-01A/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; Cnidaria/classification/*genetics ; Evolution, Molecular ; Gene Expression Regulation ; Gene Transfer, Horizontal ; Genome ; Phylogeny ; }, abstract = {Cnidarians (corals, anemones, jellyfish and hydras) are a diverse group of animals of interest to evolutionary biologists, ecologists and developmental biologists. With the publication of the genome sequences of Hydra and Nematostella, whose last common ancestor was the stem cnidarian, researchers are beginning to see the genomic underpinnings of cnidarian biology. Cnidarians are known for the remarkable plasticity of their morphology and life cycles. This plasticity is reflected in the Hydra and Nematostella genomes, which differ to an exceptional degree in size, base composition, transposable element content and gene conservation. It is now known what cnidarian genomes, given 500 million years, are capable of; as we discuss here, the next challenge is to understand how this genomic history has led to the striking diversity seen in this group.}, }
@article {pmid21041110, year = {2010}, author = {Van Melderen, L}, title = {Toxin-antitoxin systems: why so many, what for?.}, journal = {Current opinion in microbiology}, volume = {13}, number = {6}, pages = {781-785}, doi = {10.1016/j.mib.2010.10.006}, pmid = {21041110}, issn = {1879-0364}, mesh = {Bacteria/*genetics ; Bacterial Proteins/*metabolism ; Bacterial Toxins/*metabolism ; Cell Death ; DNA, Bacterial/metabolism ; *Genomic Instability ; *Plasmids ; }, abstract = {Toxin-antitoxin (TA) systems are small genetic modules that are abundant in bacterial genomes. Three types have been described so far, depending on the nature and mode of action of the antitoxin component. While type II systems are surprisingly highly represented because of their capacity to move by horizontal gene transfer, type I systems appear to have evolved by gene duplication and are more constrained. Type III is represented by a unique example located on a plasmid. Type II systems promote stability of mobile genetic elements and might act at the selfish level. Conflicting hypotheses about chromosomally encoded systems, from programmed cell death and starvation-induced stasis to protection against invading DNA and stabilization of large genomic fragments have been proposed.}, }
@article {pmid21040749, year = {2011}, author = {Smits, TH and Rezzonico, F and Duffy, B}, title = {Evolutionary insights from Erwinia amylovora genomics.}, journal = {Journal of biotechnology}, volume = {155}, number = {1}, pages = {34-39}, doi = {10.1016/j.jbiotec.2010.10.075}, pmid = {21040749}, issn = {1873-4863}, mesh = {Bacterial Secretion Systems/genetics ; Erwinia amylovora/*genetics/metabolism/pathogenicity ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; Genomics ; Phylogeny ; Plant Diseases/genetics/microbiology ; Polysaccharides, Bacterial/genetics ; Virulence ; Virulence Factors/genetics ; }, abstract = {Evolutionary genomics is coming into focus with the recent availability of complete sequences for many bacterial species. A hypothesis on the evolution of virulence factors in the plant pathogen Erwinia amylovora, the causative agent of fire blight, was generated using comparative genomics with the genomes E. amylovora, Erwinia pyrifoliae and Erwinia tasmaniensis. Putative virulence factors were mapped to the proposed genealogy of the genus Erwinia that is based on phylogenetic and genomic data. Ancestral origin of several virulence factors was identified, including levan biosynthesis, sorbitol metabolism, three T3SS and two T6SS. Other factors appeared to have been acquired after divergence of pathogenic species, including a second flagellar gene and two glycosyltransferases involved in amylovoran biosynthesis. E. amylovora singletons include 3 unique T3SS effectors that may explain differential virulence/host ranges. E. amylovora also has a unique T1SS export system, and a unique third T6SS gene cluster. Genetic analysis revealed signatures of foreign DNA suggesting that horizontal gene transfer is responsible for some of these differential features between the three species.}, }
@article {pmid21036995, year = {2011}, author = {Bose, B and Grossman, AD}, title = {Regulation of horizontal gene transfer in Bacillus subtilis by activation of a conserved site-specific protease.}, journal = {Journal of bacteriology}, volume = {193}, number = {1}, pages = {22-29}, pmid = {21036995}, issn = {1098-5530}, support = {R01 GM050895/GM/NIGMS NIH HHS/United States ; GM50895/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacillus subtilis/*enzymology/*genetics ; Bacterial Proteins/genetics/metabolism ; Conserved Sequence ; Gene Expression Regulation, Bacterial/*physiology ; Gene Transfer, Horizontal/*genetics ; Molecular Sequence Data ; Mutation ; Peptide Hydrolases/genetics/*metabolism ; Time Factors ; }, abstract = {The mobile genetic element ICEBs1 is an integrative and conjugative element (a conjugative transposon) found in Bacillus subtilis. The RecA-dependent SOS response and the RapI-PhrI cell sensory system activate ICEBs1 gene expression by stimulating cleavage of ImmR, the ICEBs1 immunity repressor, by the protease ImmA. We found that increasing the amount of wild-type ImmA in vivo caused partial derepression of ICEBs1 gene expression. However, during RapI-mediated derepression of ICEBs1 gene expression, ImmA levels did not detectably increase, indicating that RapI likely activates the protease ImmA by increasing its specific activity. We also isolated and characterized mutations in immA (immA(h)) that cause partial derepression of ICEBs1 gene expression in the absence of inducing signals. We obtained two types of immA(h) mutations: one type caused increased amounts of the mutant proteins in vivo but no detectable effect on specific activity in vitro; the other type had no detectable effect on the amount of the mutant protein in vivo but caused increased specific activity of the protein (as measured in vitro). Together, these findings indicate that derepression of ICEBs1 gene expression is likely caused by an increase in the specific activity of ImmA. Homologs of ImmA and ImmR are found in many mobile genetic elements, so the mechanisms that regulate ImmA-mediated cleavage of ImmR may be widely conserved.}, }
@article {pmid21034474, year = {2010}, author = {Donati, C and Hiller, NL and Tettelin, H and Muzzi, A and Croucher, NJ and Angiuoli, SV and Oggioni, M and Dunning Hotopp, JC and Hu, FZ and Riley, DR and Covacci, A and Mitchell, TJ and Bentley, SD and Kilian, M and Ehrlich, GD and Rappuoli, R and Moxon, ER and Masignani, V}, title = {Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species.}, journal = {Genome biology}, volume = {11}, number = {10}, pages = {R107}, pmid = {21034474}, issn = {1474-760X}, support = {R01 DC002148/DC/NIDCD NIH HHS/United States ; N01-AI-30071/AI/NIAID NIH HHS/United States ; DC05659/DC/NIDCD NIH HHS/United States ; R01 AI080935/AI/NIAID NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; AI080935/AI/NIAID NIH HHS/United States ; DC04173/DC/NIDCD NIH HHS/United States ; DC02148/DC/NIDCD NIH HHS/United States ; }, mesh = {DNA, Bacterial/genetics ; Evolution, Molecular ; Gene Conversion ; Genes, Bacterial ; *Genetic Variation ; *Genome, Bacterial ; Linkage Disequilibrium ; Multigene Family ; Phylogeny ; Polymorphism, Single Nucleotide ; Sequence Alignment ; Sequence Analysis, DNA ; Streptococcus mitis/*genetics/pathogenicity ; Streptococcus pneumoniae/*genetics/pathogenicity ; Virulence ; }, abstract = {BACKGROUND: Streptococcus pneumoniae is one of the most important causes of microbial diseases in humans. The genomes of 44 diverse strains of S. pneumoniae were analyzed and compared with strains of non-pathogenic streptococci of the Mitis group.<br><br>RESULTS: Despite evidence of extensive recombination, the S. pneumoniae phylogenetic tree revealed six major lineages. With the exception of serotype 1, the tree correlated poorly with capsular serotype, geographical site of isolation and disease outcome. The distribution of dispensable genes--genes present in more than one strain but not in all strains--was consistent with phylogeny, although horizontal gene transfer events attenuated this correlation in the case of ancient lineages. Homologous recombination, involving short stretches of DNA, was the dominant evolutionary process of the core genome of S. pneumoniae. Genetic exchange occurred both within and across the borders of the species, and S. mitis was the main reservoir of genetic diversity of S. pneumoniae. The pan-genome size of S. pneumoniae increased logarithmically with the number of strains and linearly with the number of polymorphic sites of the sampled genomes, suggesting that acquired genes accumulate proportionately to the age of clones. Most genes associated with pathogenicity were shared by all S. pneumoniae strains, but were also present in S. mitis, S. oralis and S. infantis, indicating that these genes are not sufficient to determine virulence.<br><br>CONCLUSIONS: Genetic exchange with related species sharing the same ecological niche is the main mechanism of evolution of S. pneumoniae. The open pan-genome guarantees the species a quick and economical response to diverse environments.}, }
@article {pmid21034464, year = {2010}, author = {Linz, S}, title = {On Hill et al's conjecture for calculating the subtree prune and regraft distance between phylogenies.}, journal = {BMC evolutionary biology}, volume = {10}, number = {}, pages = {334}, pmid = {21034464}, issn = {1471-2148}, mesh = {Algorithms ; Computational Biology ; Gene Transfer, Horizontal ; Models, Genetic ; *Phylogeny ; *Software ; }, abstract = {BACKGROUND: Recently, Hill et al. 1 implemented a new software package--called SPRIT--which aims at calculating the minimum number of horizontal gene transfer events that is needed to simultaneously explain the evolution of two rooted binary phylogenetic trees on the same set of taxa. To this end, SPRIT computes the closely related so-called rooted subtree prune and regraft distance between two phylogenies. However, calculating this distance is an NP-hard problem and exact algorithms are often only applicable to small- or medium-sized problem instances. Trying to overcome this problem, Hill et al. propose a divide-and-conquer approach to speed up their algorithm and conjecture that this approach can be used to compute the rooted subtree prune and regraft distance exactly.<br><br>RESULTS: In this note, we present a counterexample to Hill et al's conjecture and subsequently show that a modified version of their conjecture holds.<br><br>CONCLUSION: While Hill et al's conjecture may result in an overestimate of the rooted subtree prune and regraft distance, a slightly more restricted version of their approach gives the desired outcome and can be applied to speed up the exact calculation of this distance between two phylogenies.}, }
@article {pmid21029434, year = {2010}, author = {Edgell, DR and Gibb, EA and Belfort, M}, title = {Mobile DNA elements in T4 and related phages.}, journal = {Virology journal}, volume = {7}, number = {}, pages = {290}, pmid = {21029434}, issn = {1743-422X}, support = {GM39422/GM/NIGMS NIH HHS/United States ; GM448844/GM/NIGMS NIH HHS/United States ; MOP77779//Canadian Institutes of Health Research/Canada ; }, mesh = {Bacteriophage T4/*genetics ; DNA, Viral/*genetics ; Endonucleases/genetics/metabolism ; Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences ; Recombination, Genetic ; Viral Proteins/genetics/metabolism ; }, abstract = {Mobile genetic elements are common inhabitants of virtually every genome where they can exert profound influences on genome structure and function in addition to promoting their own spread within and between genomes. Phage T4 and related phage have long served as a model system for understanding the molecular mechanisms by which a certain class of mobile DNA, homing endonucleases, promote their spread. Homing endonucleases are site-specific DNA endonucleases that initiate mobility by introducing double-strand breaks at defined positions in genomes lacking the endonuclease gene, stimulating repair and recombination pathways that mobilize the endonuclease coding region. In phage T4, homing endonucleases were first discovered as encoded within the self-splicing td, nrdB and nrdD introns of T4. Genomic data has revealed that homing endonucleases are extremely widespread in T-even-like phage, as evidenced by the astounding fact that ~11% of the T4 genome encodes homing endonuclease genes, with most of them located outside of self-splicing introns. Detailed studies of the mobile td intron and its encoded endonuclease, I-TevI, have laid the foundation for genetic, biochemical and structural aspects that regulate the mobility process, and more recently have provided insights into regulation of homing endonuclease function. Here, we summarize the current state of knowledge regarding T4-encoded homing endonucleases, with particular emphasis on the td/I-TevI model system. We also discuss recent progress in the biology of free-standing endonucleases, and present areas of future research for this fascinating class of mobile genetic elements.}, }
@article {pmid21029153, year = {2010}, author = {Haug, MC and Tanner, SA and Lacroix, C and Meile, L and Stevens, MJ}, title = {Construction and characterization of Enterococcus faecalis CG110/gfp/pRE25*, a tool for monitoring horizontal gene transfer in complex microbial ecosystems.}, journal = {FEMS microbiology letters}, volume = {313}, number = {2}, pages = {111-119}, doi = {10.1111/j.1574-6968.2010.02131.x}, pmid = {21029153}, issn = {1574-6968}, mesh = {Conjugation, Genetic ; DNA, Bacterial/genetics ; *Ecosystem ; Enterococcus faecalis/*genetics ; *Gene Transfer, Horizontal ; Genetic Markers ; Genetics, Microbial/methods ; Genomic Instability ; Listeria/genetics ; Plasmids ; Staining and Labeling/methods ; }, abstract = {Enterococci are among the most notorious bacteria involved in the spread of antibiotic resistance (ABR) determinants via horizontal gene transfer, a process that leads to increased prevalence of antibiotic-resistant bacteria. In complex microbial communities with a high background of ABR genes, detection of gene transfer is possible only when the ABR determinant is marked. Therefore, the conjugative multiresistance plasmid pRE25, originating from a sausage-associated Enterococcus faecalis, was tagged with a 34-bp random sequence marker spliced by tet(M). The plasmid constructed, designated pRE25(*) , was introduced into E. faecalis CG110/gfp, a strain containing a gfp gene as chromosomal marker. The plasmid pRE25(*) is fully functional compared with its parental pRE25, occurs at one to two copies per chromosome, and can be transferred to Listeria monocytogenes and Listeria innocua at frequencies of 6 × 10(-6) to 8 × 10(-8) transconjugants per donor. The markers on the chromosome and the plasmid enable independent quantification of donor and plasmid, even if ABR genes occur at high numbers in the background ecosystem. Both markers were stable for at least 200 generations, permitting application of the strain in long-running experiments. Enterococcus faecalis CG110/gfp/pRE25(*) is a potent tool for the investigation of horizontal ABR gene transfer in complex environments such as food matrices, biofilms or colonic models.}, }
@article {pmid20980981, year = {2010}, author = {Grunau, C and Boissier, J}, title = {No evidence for lateral gene transfer between salmonids and schistosomes.}, journal = {Nature genetics}, volume = {42}, number = {11}, pages = {918-919}, pmid = {20980981}, issn = {1546-1718}, mesh = {Animals ; Base Sequence ; DNA/genetics ; DNA Transposable Elements/genetics ; Female ; *Gene Transfer, Horizontal ; Male ; Polymerase Chain Reaction ; Reproducibility of Results ; Salmonidae/*genetics ; Schistosoma/*genetics ; Schistosoma japonicum/genetics ; Schistosoma mansoni/genetics ; }, }
@article {pmid20979102, year = {2011}, author = {Stern, A and Sorek, R}, title = {The phage-host arms race: shaping the evolution of microbes.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {33}, number = {1}, pages = {43-51}, pmid = {20979102}, issn = {1521-1878}, support = {R01 AI082376/AI/NIAID NIH HHS/United States ; R01 AI082376-01/AI/NIAID NIH HHS/United States ; R01 AI082376-04/AI/NIAID NIH HHS/United States ; R01AI082376-01/AI/NIAID NIH HHS/United States ; }, mesh = {*Bacteria/genetics/virology ; *Bacteriophages/genetics/pathogenicity ; Biological Evolution ; DNA Restriction Enzymes/physiology ; Gene Transfer, Horizontal/physiology ; Genomic Islands/physiology ; *Host-Pathogen Interactions/genetics ; Microbial Viability ; }, abstract = {Bacteria, the most abundant organisms on the planet, are outnumbered by a factor of 10 to 1 by phages that infect them. Faced with the rapid evolution and turnover of phage particles, bacteria have evolved various mechanisms to evade phage infection and killing, leading to an evolutionary arms race. The extensive co-evolution of both phage and host has resulted in considerable diversity on the part of both bacterial and phage defensive and offensive strategies. Here, we discuss the unique and common features of phage resistance mechanisms and their role in global biodiversity. The commonalities between defense mechanisms suggest avenues for the discovery of novel forms of these mechanisms based on their evolutionary traits.}, }
@article {pmid20976007, year = {2010}, author = {Vallenback, P and Ghatnekar, L and Bengtsson, BO}, title = {Structure of the natural transgene PgiC2 in the common grass Festuca ovina.}, journal = {PloS one}, volume = {5}, number = {10}, pages = {e13529}, pmid = {20976007}, issn = {1932-6203}, mesh = {*Genes, Plant ; *Plants, Genetically Modified ; Poaceae/*genetics ; }, abstract = {BACKGROUND: A horizontal gene transfer has brought an active nuclear gene, PgiC2, from a polyploid Poa species (P. palustris or a close relative) into the common grass sheep's fescue (Festuca ovina). The donor and the receptor species are strictly reproductively separated, and PgiC2 occurs in a polymorphic state within F. ovina. The active gene copy is normally closely linked to a very similar pseudogene.<br><br>By genome walking we have obtained the up- and downstream sequences of PgiC2 and of corresponding genes in the donor and recipient species. Comparisons of these sequences show that the complete upstream region necessary for the gene's expression is included in the transferred segment. About 1 kb upstream of PgiC2 a fragment with transposition associated properties has been found (TAF). It is present in P. palustris and its polyploid relatives, though not at the homologous position, and is absent from many other grasses, including non-transgenic F. ovina plants. It is possible that it is a part of a transposing element involved in getting the gene into a transferring agent and/or into the recipient chromosome.<br><br>CONCLUSIONS/SIGNIFICANCE: The close similarity of the up- and downstream regions with the corresponding regions in P. palustris excludes all suggestions that PgiC2 is not a HGT but the result of a duplication within the F. ovina lineage. The small size of the genetic material transferred, the complex nature of the PgiC2 locus, and the associated fragment with transposition associated properties suggest that the horizontal transfer occurred via a vector and not via illegitimate pollination.}, }
@article {pmid20975940, year = {2010}, author = {Baharoglu, Z and Bikard, D and Mazel, D}, title = {Conjugative DNA transfer induces the bacterial SOS response and promotes antibiotic resistance development through integron activation.}, journal = {PLoS genetics}, volume = {6}, number = {10}, pages = {e1001165}, pmid = {20975940}, issn = {1553-7404}, mesh = {Adaptation, Physiological/genetics ; Bacteria/*genetics/metabolism ; Conjugation, Genetic ; DNA, Single-Stranded/*genetics ; Drug Resistance, Microbial/genetics ; Escherichia coli/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Green Fluorescent Proteins/genetics/metabolism ; Integrases/genetics/metabolism ; Integrons/*genetics ; Lac Operon/genetics ; Plasmids/genetics ; Recombinant Fusion Proteins/genetics/metabolism ; SOS Response, Genetics/*genetics ; Time Factors ; Vibrio cholerae/genetics/metabolism ; }, abstract = {Conjugation is one mechanism for intra- and inter-species horizontal gene transfer among bacteria. Conjugative elements have been instrumental in many bacterial species to face the threat of antibiotics, by allowing them to evolve and adapt to these hostile conditions. Conjugative plasmids are transferred to plasmidless recipient cells as single-stranded DNA. We used lacZ and gfp fusions to address whether conjugation induces the SOS response and the integron integrase. The SOS response controls a series of genes responsible for DNA damage repair, which can lead to recombination and mutagenesis. In this manuscript, we show that conjugative transfer of ssDNA induces the bacterial SOS stress response, unless an anti-SOS factor is present to alleviate this response. We also show that integron integrases are up-regulated during this process, resulting in increased cassette rearrangements. Moreover, the data we obtained using broad and narrow host range plasmids strongly suggests that plasmid transfer, even abortive, can trigger chromosomal gene rearrangements and transcriptional switches in the recipient cell. Our results highlight the importance of environments concentrating disparate bacterial communities as reactors for extensive genetic adaptation of bacteria.}, }
@article {pmid20973741, year = {2010}, author = {Snir, S and Trifonov, E}, title = {A novel technique for detecting putative horizontal gene transfer in the sequence space.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {17}, number = {11}, pages = {1535-1548}, doi = {10.1089/cmb.2010.0095}, pmid = {20973741}, issn = {1557-8666}, mesh = {Animals ; *Base Sequence ; Computational Biology/*methods ; Computer Simulation ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Molecular Sequence Data ; Mutation ; *Phylogeny ; }, abstract = {Horizontal transfer (HT) is the event of a DNA sequence being transferred between species not by inheritance. This phenomenon violates the tree-like evolution of the species under study turning the trees into networks. At the sequence level, HT offers basic characteristics that enable not only clear identification and distinguishing from other sequence similarity cases but also the possibility of dating the events. We developed a novel, self-contained technique to identify relatively recent horizontal transfer elements (HTEs) in the sequences. Appropriate formalism allows one to obtain confidence values for the events detected. The technique does not rely on such problematic prerequisites as reliable phylogeny and/or statistically justified pairwise sequence alignment. In conjunction with the unique properties of HT, it gives rise to a two-level sequence similarity algorithm that, to the best of our knowledge, has not been explored. From evolutionary perspective, the novelty of the work is in the combination of small scale and large scale mutational events. The technique is employed on both simulated and real biological data. The simulation results show high capability of discriminating between HT and conserved regions. On the biological data, the method detected documented HTEs along with their exact locations in the recipient genomes. Supplementary Material is available online at www.libertonline.com/cmb.}, }
@article {pmid20972560, year = {2010}, author = {Xiang, H and Pan, G and Vossbrinck, CR and Zhang, R and Xu, J and Li, T and Zhou, Z and Lu, C and Xiang, Z}, title = {A tandem duplication of manganese superoxide dismutase in Nosema bombycis and its evolutionary origins.}, journal = {Journal of molecular evolution}, volume = {71}, number = {5-6}, pages = {401-414}, pmid = {20972560}, issn = {1432-1432}, mesh = {Amino Acid Sequence ; Amino Acid Substitution/genetics ; Cluster Analysis ; *Evolution, Molecular ; Gene Duplication/*genetics ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Fungal ; Genome, Fungal/genetics ; Hydrophobic and Hydrophilic Interactions ; Molecular Sequence Data ; Nosema/*enzymology/*genetics ; Phylogeny ; Protein Transport ; Selection, Genetic ; Sequence Alignment ; Sequence Homology, Amino Acid ; Subcellular Fractions/enzymology ; Superoxide Dismutase/chemistry/*genetics/metabolism ; Transcription, Genetic ; }, abstract = {Microsporidia are a group of obligate intracellular eukaryotic parasites with small genomes. They infect animals from a wide variety of phyla, including humans. Two manganese superoxide dismutase (MnSOD) genes, designated NbMnSOD1 and NbMnSOD2, were found to be organized in a tandem array within the Nosema bombycis genome. The genes, both 678 bp in length, were found to be more similar to each other than they are to homologous genes of other Microsporidia, suggesting that the tandem duplication occurred subsequent to the development of this lineage. Reverse transcript PCR shows that mRNA for both genes is present in the spores. Analysis of the primary structure, hydrophobic cluster analysis, target signal analysis, and phylogenetic analysis all indicate that NbMnSOD1 is dimeric and targeted to the cytosol. NbMnSOD2 seems to have changed more rapidly and is under less evolutionary constraint than NbMnSOD1 suggesting that NbMnSOD2 may function under different conditions or in different tissues of its host rather than simply resulting in an increase in expression. A phylogenetic analysis of MnSOD sequences from eukaryotes, Archaea, and bacteria shows the microsporidial MnSODs to be grouped with the bacteria suggesting a possible horizontal gene transfer.}, }
@article {pmid20965055, year = {2010}, author = {Ishikawa, FH and Souza, EA and Read, ND and Roca, MG}, title = {Live-cell imaging of conidial fusion in the bean pathogen, Colletotrichum lindemuthianum.}, journal = {Fungal biology}, volume = {114}, number = {1}, pages = {2-9}, doi = {10.1016/j.funbio.2009.11.006}, pmid = {20965055}, issn = {1878-6146}, support = {BB/E010741/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Cell Nucleus/metabolism ; Colletotrichum/*cytology/genetics/*physiology ; Fabaceae/*microbiology ; Green Fluorescent Proteins/metabolism ; Microscopy, Confocal ; Plant Diseases/*microbiology ; Spores, Fungal/*physiology ; Time-Lapse Imaging/*methods ; }, abstract = {Fusion of conidia and conidial germlings by means of conidial anastomosis tubes (CATs) is a common phenomenon in filamentous fungi, including many plant pathogens. It has a number of different roles, and has been speculated to facilitate parasexual recombination and horizontal gene transfer between species. The bean pathogen Colletotrichum lindemuthianum naturally undergoes CAT fusion on the host surface and within asexual fruiting bodies in anthracnose lesions on its host. It has not been previously possible to analyze the whole process of CAT fusion in this or any other pathogen using live-cell imaging techniques. Here we report the development of a robust protocol for doing this with C. lindemuthianum in vitro. The percentage of conidial germination and CAT fusion was found to be dependent on culture age, media and the fungal strain used. Increased CAT fusion was correlated with reduced germ tube formation. We show time-lapse imaging of the whole process of CAT fusion in C. lindemuthianum for the first time and monitored nuclear migration through fused CATs using nuclei labelled with GFP. CAT fusion in this pathogen was found to exhibit significant differences to that in the model system Neurospora crassa. In contrast to N. crassa, CAT fusion in C. lindemuthianum is inhibited by nutrients (it only occurs in water) and the process takes considerably longer.}, }
@article {pmid20964857, year = {2010}, author = {Friedrich, T and Rahmann, S and Weigel, W and Rabsch, W and Fruth, A and Ron, E and Gunzer, F and Dandekar, T and Hacker, J and Müller, T and Dobrindt, U}, title = {High-throughput microarray technology in diagnostics of enterobacteria based on genome-wide probe selection and regression analysis.}, journal = {BMC genomics}, volume = {11}, number = {}, pages = {591}, pmid = {20964857}, issn = {1471-2164}, mesh = {Anti-Infective Agents/pharmacology ; Bacterial Typing Techniques ; DNA Probes/*metabolism ; DNA, Bacterial/genetics ; Decision Trees ; Drug Resistance, Bacterial/drug effects/genetics ; Enterobacteriaceae/classification/drug effects/*genetics/isolation &amp; purification ; Genome, Bacterial/*genetics ; High-Throughput Screening Assays/*methods ; Molecular Diagnostic Techniques/*methods ; Nucleic Acid Hybridization/drug effects ; Oligonucleotide Array Sequence Analysis/*methods ; Regression Analysis ; }, abstract = {BACKGROUND: The Enterobacteriaceae comprise a large number of clinically relevant species with several individual subspecies. Overlapping virulence-associated gene pools and the high overall genome plasticity often interferes with correct enterobacterial strain typing and risk assessment. Array technology offers a fast, reproducible and standardisable means for bacterial typing and thus provides many advantages for bacterial diagnostics, risk assessment and surveillance. The development of highly discriminative broad-range microbial diagnostic microarrays remains a challenge, because of marked genome plasticity of many bacterial pathogens.<br><br>RESULTS: We developed a DNA microarray for strain typing and detection of major antimicrobial resistance genes of clinically relevant enterobacteria. For this purpose, we applied a global genome-wide probe selection strategy on 32 available complete enterobacterial genomes combined with a regression model for pathogen classification. The discriminative power of the probe set was further tested in silico on 15 additional complete enterobacterial genome sequences. DNA microarrays based on the selected probes were used to type 92 clinical enterobacterial isolates. Phenotypic tests confirmed the array-based typing results and corroborate that the selected probes allowed correct typing and prediction of major antibiotic resistances of clinically relevant Enterobacteriaceae, including the subspecies level, e.g. the reliable distinction of different E. coli pathotypes.<br><br>CONCLUSIONS: Our results demonstrate that the global probe selection approach based on longest common factor statistics as well as the design of a DNA microarray with a restricted set of discriminative probes enables robust discrimination of different enterobacterial variants and represents a proof of concept that can be adopted for diagnostics of a wide range of microbial pathogens. Our approach circumvents misclassifications arising from the application of virulence markers, which are highly affected by horizontal gene transfer. Moreover, a broad range of pathogens have been covered by an efficient probe set size enabling the design of high-throughput diagnostics.}, }
@article {pmid20963475, year = {2011}, author = {Kim, SH and Oh, S and Oh, TK and Park, JS and Kim, SC and Kim, SH and Kim, YS and Hong, JK and Sim, SY and Park, KS and Lee, HG and Kim, KJ and Choi, CW}, title = {Genetic diversity of tomato-infecting Tomato yellow leaf curl virus (TYLCV) isolates in Korea.}, journal = {Virus genes}, volume = {42}, number = {1}, pages = {117-127}, pmid = {20963475}, issn = {1572-994X}, mesh = {Animals ; Begomovirus/*genetics ; DNA, Viral/*genetics ; Gene Transfer, Horizontal ; *Genetic Variation ; *Genome, Viral ; Hemiptera/virology ; Insect Vectors/virology ; Solanum lycopersicum/virology ; Phylogeny ; Plant Diseases/virology ; Plant Leaves/virology ; Republic of Korea ; Sequence Analysis, DNA ; }, abstract = {Epidemic outbreaks of Tomato yellow leaf curl virus (TYLCV) diseases occurred in greenhouse grown tomato (Solanum lycopersicum) plants of Busan (TYLCV-Bus), Boseong (TYLCV-Bos), Hwaseong (TYLCV-Hwas), Jeju Island (TYLCV-Jeju), and Nonsan (TYLCV-Nons) in Korea during 2008-2009. Tomato disease by TYLCV has never occurred in Korea before. We synthesized the full-length genomes of each TYLCV isolate from the tomato plants collected at each area and determined their nucleotides (nt) sequences and deduced the amino acids of six open reading frames in the genomes. TYLCV-Bus and -Bos genomes shared higher nt identities with four Japanese isolates -Ng, -Omu, -Mis, and -Miy. On the other hand, TYLCV-Hwas, -Jeju, and -Nons genomes shared higher nt identities with five Chinese isolates TYLCV-AH1, -ZJ3, -ZJHZ12, -SH2, -Sh10, and two Japanese isolates -Han and -Tosa. On the basis of a neighbor-joining tree, five Korean TYLCV isolates were separated into three clades. TYLCV-Bus and -Bos formed the first clade, clustering with four Japanese isolates TYLCV-Mis, -Omu, -Ng, and -Miy. TYLCV-Jeju and -Nons formed the second clade, clustering with two Chinese isolates -ZJHZ212 and -Sh10. TYLCV-Hwas was clustered with two Japanese isolates -Han and -Tosa and three Chinese isolates -AH1, -ZJ3, and -SH2. Two fragments that had a potentially recombinant origin were identified using the RDP, GENECONV, BootScan, MaxChi, Chimaera, SiScan, and 3Seq methods implemented in RDP3.41. On the basis of RDP analysis, all TYLCV isolates could originated from the interspecies recombination between TYLCV-Mld[PT] isolated from Portugal as a major parent and TYLCTHV-MM isolated from Myanmar as a minor parent.}, }
@article {pmid20962892, year = {2010}, author = {Xu, J}, title = {Molecular, developmental, and evolutionary genetic studies highlight rapid evolution of genes and genetic systems.}, journal = {Genome}, volume = {53}, number = {10}, pages = {848-852}, doi = {10.1139/g10-072}, pmid = {20962892}, issn = {1480-3321}, mesh = {Animals ; Awards and Prizes ; *Evolution, Molecular ; *Genes/physiology ; Genes, Developmental/*physiology ; Genetic Techniques/*trends ; Humans ; Models, Animal ; Models, Genetic ; Molecular Biology/methods/*trends ; Reproduction/genetics ; Sex ; }, abstract = {The 53rd annual conference of the Genetics Society of Canada was held at McMaster University in Hamilton, Ontario, from 17 to 20 June 2010. About 100 geneticists from across Canada and the US attended the meeting, with a total of 27 posters and 55 oral presentations. The presentations highlighted the power of genetics for understanding a variety of biological issues from sex and recombination to alcoholism and cancer, from DNA replication to antimicrobial resistance, horizontal gene transfer, foraging, and courtship. Large-scale genomic and transcriptomic comparisons were included in many presentations to demonstrate the impact of genomics in biomedical research. The combined molecular, developmental, and evolutionary genetic investigations presented at the meeting, especially those on model organisms, highlighted that genes and genetic systems can evolve very rapidly.}, }
@article {pmid20962537, year = {2010}, author = {Chan, H and Babayan, V and Blyumin, E and Gandhi, C and Hak, K and Harake, D and Kumar, K and Lee, P and Li, TT and Liu, HY and Lo, TC and Meyer, CJ and Stanford, S and Zamora, KS and Saier, MH}, title = {The p-type ATPase superfamily.}, journal = {Journal of molecular microbiology and biotechnology}, volume = {19}, number = {1-2}, pages = {5-104}, doi = {10.1159/000319588}, pmid = {20962537}, issn = {1660-2412}, mesh = {Adenosine Triphosphatases/*classification/genetics ; *Amino Acid Motifs ; Archaea/*enzymology/genetics ; Bacteria/*enzymology/genetics ; Base Sequence ; Conserved Sequence ; Eukaryota/*enzymology/genetics ; Gene Transfer, Horizontal ; Genome, Bacterial ; Ion Pumps/metabolism ; Ion Transport ; Molecular Sequence Data ; Phylogeny ; Pseudogenes ; }, abstract = {P-type ATPases function to provide homeostasis in higher eukaryotes, but they are essentially ubiquitous, being found in all domains of life. Thever and Saier [J Memb Biol 2009;229:115-130] recently reported analyses of eukaryotic P-type ATPases, dividing them into nine functionally characterized and 13 functionally uncharacterized (FUPA) families. In this report, we analyze P-type ATPases in all major prokaryotic phyla for which complete genome sequence data are available, and we compare the results with those for eukaryotic P-type ATPases. Topological type I (heavy metal) P-type ATPases predominate in prokaryotes (approx. tenfold) while type II ATPases (specific for Na(+),K(+), H(+) Ca(2+), Mg(2+) and phospholipids) predominate in eukaryotes (approx. twofold). Many P-type ATPase families are found exclusively in prokaryotes (e.g. Kdp-type K(+) uptake ATPases (type III) and all ten prokaryotic FUPA familes), while others are restricted to eukaryotes (e.g. phospholipid flippases and all 13 eukaryotic FUPA families). Horizontal gene transfer has occurred frequently among bacteria and archaea, which have similar distributions of these enzymes, but rarely between most eukaryotic kingdoms, and even more rarely between eukaryotes and prokaryotes. In some bacterial phyla (e.g. Bacteroidetes, Flavobacteria and Fusobacteria), ATPase gene gain and loss as well as horizontal transfer occurred seldom in contrast to most other bacterial phyla. Some families (i.e. Kdp-type ATPases) underwent far less horizontal gene transfer than other prokaryotic families, possibly due to their multisubunit characteristics. Functional motifs are better conserved across family lines than across organismal lines, and these motifs can be family specific, facilitating functional predictions. In some cases, gene fusion events created P-type ATPases covalently linked to regulatory catalytic enzymes. In one family (FUPA Family 24), a type I ATPase gene (N-terminal) is fused to a type II ATPase gene (C-terminal) with retention of function only for the latter. Several pseudogene-encoded nonfunctional ATPases were identified. Genome minimalization led to preferential loss of P-type ATPase genes. We suggest that in prokaryotes and some unicellular eukaryotes, the primary function of P-type ATPases is protection from extreme environmental stress conditions. The classification of P-type ATPases of unknown function into phylogenetic families provides guides for future molecular biological studies.}, }
@article {pmid20961964, year = {2011}, author = {Kristoffersen, SM and Tourasse, NJ and Kolstø, AB and Økstad, OA}, title = {Interspersed DNA repeats bcr1-bcr18 of Bacillus cereus group bacteria form three distinct groups with different evolutionary and functional patterns.}, journal = {Molecular biology and evolution}, volume = {28}, number = {2}, pages = {963-983}, doi = {10.1093/molbev/msq269}, pmid = {20961964}, issn = {1537-1719}, mesh = {Bacillus cereus/*classification/*genetics/physiology ; DNA, Bacterial/*genetics ; Phylogeny ; Repetitive Sequences, Nucleic Acid ; }, abstract = {Many short (<400 bp) interspersed sequence repeats exist in bacteria, yet little is known about their origins, mode of generation, or possible function. Here, we present a comprehensive analysis of 18 different previously identified repeated DNA elements, bcr1-bcr18 (Økstad OA, Hegna I, Lindback T, Rishovd AL, Kolstø AB. 1999. Genome organization is not conserved between Bacillus cereus and Bacillus subtilis. Microbiology. 145:621-631.; Tourasse NJ, Helgason E, Økstad OA, Hegna IK, Kolstø AB. 2006. The Bacillus cereus group: novel aspects of population structure and genome dynamics. J Appl Microbiol. 101:579-593.), in 36 sequenced genomes from the Bacillus cereus group of bacteria. This group consists of genetically closely related species with variable pathogenic specificity toward different hosts and includes among others B. anthracis, B. cereus, and B. thuringiensis. The B. cereus group repeat elements could be classified into three categories with different properties: Group A elements (bcr1-bcr3) exhibited highly variable copy numbers ranging from 4 to 116 copies per strain, showed a nonconserved chromosomal distribution pattern between strains, and displayed several features characteristic of mobile elements. Group B repeats (bcr4-bcr6) were present in 0-10 copies per strain and were associated with strain-specific genes and disruptions of genome synteny, implying a possible contribution to genome rearrangements and/or horizontal gene transfer events. bcr5, in particular, was associated with large gene clusters showing resemblance to integrons. In agreement with their potentially mobile nature or involvement in horizontal transfers, the sequences of the repeats from Groups A and B (bcr1-bcr6) followed a phylogeny different from that of the host strains. Conversely, repeats from Group C (bcr7-bcr18) had a conserved chromosomal location and orthologous gene neighbors in the investigated B. cereus group genomes, and their phylogeny matched that of the host chromosome. Several of the group C repeats exhibited a conserved secondary structure or had parts of the structure conserved, possibly indicating functional RNAs. Accordingly, five of the repeats in group C overlapped regions encoding previously characterized riboswitches. Similarly, other group C repeats could represent novel riboswitches, encode small RNAs, and/or constitute other types of regulatory elements with specific biological functions. The current analysis suggests that the multitude of repeat elements identified in the B. cereus group promote genome dynamics and plasticity and could contribute to the flexible and adaptive life style of these bacteria.}, }
@article {pmid20961962, year = {2011}, author = {Coscollá, M and Comas, I and González-Candelas, F}, title = {Quantifying nonvertical inheritance in the evolution of Legionella pneumophila.}, journal = {Molecular biology and evolution}, volume = {28}, number = {2}, pages = {985-1001}, doi = {10.1093/molbev/msq278}, pmid = {20961962}, issn = {1537-1719}, support = {MRC_U117588500//Medical Research Council/United Kingdom ; }, mesh = {Biological Evolution ; *Gene Transfer, Horizontal ; Legionella pneumophila/classification/*genetics ; Multilocus Sequence Typing ; Phylogeny ; }, abstract = {The exchange of genetic material among bacterial strains and species is recognized as an important factor determining their evolutionary, population genetic, and epidemiological features. We present a detailed analysis of nonvertical inheritance in Legionella pneumophila, a human pathogen and facultative intracellular parasite of amoebas. We have analyzed the exchange of L. pneumophila genetic material with other bacteria at three different levels: population genetics, population genomics, and phylogenomics. At the population genetics level, we have analyzed 89 clinical and environmental isolates after sequencing six coding loci and three intergenic regions for a total of 3,923 bp. In the population genomics analysis, we have studied the roles of recombination and mutation in the common portion of the genome sequence of four L. pneumophila strains. In the phylogenomic analysis, we have studied the phylogenetic origin of 1,700 genes in the L. pneumophila pangenome. For this, we have considered 12 possible phylogenetic alternatives, derived from a reference tree obtained from 104 genes from 41 species, which have been tested under a rigorous statistical framework. The results obtained agree in assigning an important role to nonvertical inheritance in shaping the composition of the L. pneumophila genome and of the genetic variation in its populations. We have found a negative correlation between phylogenetic distance and likelihood of horizontal gene transfer. Phylogenetic proximity and increased chances resulting from sharing the ecological niche provided by the amoeba host have likely had a major influence on the rate of gene exchange in Legionella.}, }
@article {pmid20957119, year = {2010}, author = {Parnell, JJ and Rompato, G and Latta, LC and Pfrender, ME and Van Nostrand, JD and He, Z and Zhou, J and Andersen, G and Champine, P and Ganesan, B and Weimer, BC}, title = {Functional biogeography as evidence of gene transfer in hypersaline microbial communities.}, journal = {PloS one}, volume = {5}, number = {9}, pages = {e12919}, pmid = {20957119}, issn = {1932-6203}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification/metabolism ; DNA, Bacterial/genetics ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sodium Chloride/*metabolism ; Utah ; Water Microbiology ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT) plays a major role in speciation and evolution of bacteria and archaea by controlling gene distribution within an environment. However, information that links HGT to a natural community using relevant population-genetics parameters and spatial considerations is scarce. The Great Salt Lake (Utah, USA) provides an excellent model for studying HGT in the context of biogeography because it is a contiguous system with dispersal limitations due to a strong selective salinity gradient. We hypothesize that in spite of the barrier to phylogenetic dispersal, functional characteristics--in the form of HGT--expand beyond phylogenetic limitations due to selective pressure.<br><br>METHODOLOGY AND RESULTS: To assay the functional genes and microorganisms throughout the GSL, we used a 16S rRNA oligonucleotide microarray (Phylochip) and a functional gene array (GeoChip) to measure biogeographic patterns of nine microbial communities. We found a significant difference in biogeography based on microarray analyses when comparing S&#xf8;rensen similarity values for presence/absence of function and phylogeny (Student's t-test; p&#x200a;=&#x200a;0.005).<br><br>CONCLUSION AND SIGNIFICANCE: Biogeographic patterns exhibit behavior associated with horizontal gene transfer in that informational genes (16S rRNA) have a lower similarity than functional genes, and functional similarity is positively correlated with lake-wide selective pressure. Specifically, high concentrations of chromium throughout GSL correspond to an average similarity of chromium resistance genes that is 22% higher than taxonomic similarity. This suggests active HGT may be measured at the population level in microbial communities and these biogeographic patterns may serve as a model to study bacteria adaptation and speciation.}, }
@article {pmid20952646, year = {2010}, author = {Haenni, M and Saras, E and Bertin, S and Leblond, P and Madec, JY and Payot, S}, title = {Diversity and mobility of integrative and conjugative elements in bovine isolates of Streptococcus agalactiae, S. dysgalactiae subsp. dysgalactiae, and S. uberis.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {24}, pages = {7957-7965}, pmid = {20952646}, issn = {1098-5336}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Cattle ; DNA Fingerprinting ; Drug Resistance, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Genes, Bacterial ; *Genetic Variation ; Genotype ; *Interspersed Repetitive Sequences ; Lincosamides/pharmacology ; Macrolides/pharmacology ; Multilocus Sequence Typing ; RNA, Bacterial/genetics ; RNA, Transfer, Lys/genetics ; Streptococcal Infections/microbiology/*veterinary ; Streptococcus/drug effects/*genetics/*isolation &amp; purification ; Tetracycline/pharmacology ; }, abstract = {Bovine isolates of Streptococcus agalactiae (n = 76), Streptococcus dysgalactiae subsp. dysgalactiae (n = 32), and Streptococcus uberis (n = 101) were analyzed for the presence of different integrative and conjugative elements (ICEs) and their association with macrolide, lincosamide, and tetracycline resistance. The diversity of the isolates included in this study was demonstrated by multilocus sequence typing for S. agalactiae and pulsed-field gel electrophoresis for S. dysgalactiae and S. uberis. Most of the erythromycin-resistant strains carry an ermB gene. Five strains of S. uberis that are resistant to lincomycin but susceptible to erythromycin carry the lin(B) gene, and one has both linB and lnuD genes. In contrast to S. uberis, most of the S. agalactiae and S. dysgalactiae tetracycline-resistant isolates carry a tet(M) gene. A tet(S) gene was also detected in the three species. A Tn916-related element was detected in 30 to 50% of the tetracycline-resistant strains in the three species. Tetracycline resistance was successfully transferred by conjugation to an S. agalactiae strain. Most of the isolates carry an ICE integrated in the rplL gene. In addition, half of the S. agalactiae isolates have an ICE integrated in a tRNA lysine (tRNA(Lys)) gene. Such an element is also present in 20% of the isolates of S. dysgalactiae and S. uberis. A circular form of these ICEs was detected in all of the isolates tested, indicating that these genetic elements are mobile. These ICEs could thus also be a vehicle for horizontal gene transfer between streptococci of animal and/or human origin.}, }
@article {pmid20951641, year = {2011}, author = {Laverde Gomez, JA and van Schaik, W and Freitas, AR and Coque, TM and Weaver, KE and Francia, MV and Witte, W and Werner, G}, title = {A multiresistance megaplasmid pLG1 bearing a hylEfm genomic island in hospital Enterococcus faecium isolates.}, journal = {International journal of medical microbiology : IJMM}, volume = {301}, number = {2}, pages = {165-175}, doi = {10.1016/j.ijmm.2010.08.015}, pmid = {20951641}, issn = {1618-0607}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Conjugation, Genetic ; Conserved Sequence ; Cross Infection/*microbiology ; DNA, Bacterial/chemistry/genetics ; Drug Resistance, Multiple, Bacterial ; Enterococcus faecalis/genetics ; Enterococcus faecium/drug effects/genetics/isolation &amp; purification/*pathogenicity ; Gene Transfer, Horizontal ; *Genomic Islands ; Gram-Positive Bacterial Infections/*microbiology ; Humans ; Molecular Sequence Data ; Plasmids/*analysis ; Sequence Analysis, DNA ; Virulence Factors/*genetics ; }, abstract = {Enterococcus faecium is considered to be a nosocomial pathogen with increasing medical importance. The putative virulence factor, hyl(Efm), encoding a putative hyaluronidase, is enriched among the hospital-associated polyclonal subpopulation of E. faecium.. The hyl(Efm) gene is described to be part of a genomic island and was recently identified to be plasmid-located. Here, we present a description of the structure, localization, and distribution of the putative pathogenicity factor hyl(Efm) and its putative island among 39 clinical isolates and elucidate the composition and host range of pLG1, a hyl(Efm) multiresistance plasmid of approximately 281.02kb. The hyl(Efm) gene was located within a 17,824-bp element highly similar to the putative genomic island (GI) structure that had been previously described. This genomic region was conserved among 39 hyl(Efm)-positive strains with variation in a specific region downstream of hyl(Efm) in 18 strains. The putative hyl(Efm) was located on large plasmids (150-350kb) in 37 strains. pLG1 could be horizontally transferred into four different E. faecium recipient strains (n=4) but not into E. faecalis (n=3). Sequencing of pLG1 resolved putative plasmid replication, conjugation, and maintenance determinants as well as a pilin gene cluster, carbon uptake and utilization genes, heavy metal and antibiotic resistance clusters. The hyl(Efm) transferable plasmid pLG1 bears additional putative pathogenicity factors and antibiotic resistance genes. These findings suggest horizontal gene transfer of virulence factors and antibiotic resistance gene clusters by a single genetic event (conjugative transfer) which might be triggered by heavy antibiotic use common in health care units where E. faecium is increasingly prevalent.}, }
@article {pmid20944225, year = {2010}, author = {Xu, Q and Abdubek, P and Astakhova, T and Axelrod, HL and Bakolitsa, C and Cai, X and Carlton, D and Chen, C and Chiu, HJ and Clayton, T and Das, D and Deller, MC and Duan, L and Ellrott, K and Farr, CL and Feuerhelm, J and Grant, JC and Grzechnik, A and Han, GW and Jaroszewski, L and Jin, KK and Klock, HE and Knuth, MW and Kozbial, P and Krishna, SS and Kumar, A and Lam, WW and Marciano, D and Miller, MD and Morse, AT and Nigoghossian, E and Nopakun, A and Okach, L and Puckett, C and Reyes, R and Tien, HJ and Trame, CB and van den Bedem, H and Weekes, D and Wooten, T and Yeh, A and Zhou, J and Hodgson, KO and Wooley, J and Elsliger, MA and Deacon, AM and Godzik, A and Lesley, SA and Wilson, IA}, title = {Structure of a membrane-attack complex/perforin (MACPF) family protein from the human gut symbiont Bacteroides thetaiotaomicron.}, journal = {Acta crystallographica. Section F, Structural biology and crystallization communications}, volume = {66}, number = {Pt 10}, pages = {1297-1305}, pmid = {20944225}, issn = {1744-3091}, support = {U54 GM074898/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacterial Proteins/*chemistry ; Bacteroides/*chemistry ; Crystallography, X-Ray ; Models, Molecular ; Molecular Sequence Data ; Perforin/*chemistry ; Protein Structure, Tertiary ; Sequence Alignment ; Structural Homology, Protein ; }, abstract = {Membrane-attack complex/perforin (MACPF) proteins are transmembrane pore-forming proteins that are important in both human immunity and the virulence of pathogens. Bacterial MACPFs are found in diverse bacterial species, including most human gut-associated Bacteroides species. The crystal structure of a bacterial MACPF-domain-containing protein BT_3439 (Bth-MACPF) from B. thetaiotaomicron, a predominant member of the mammalian intestinal microbiota, has been determined. Bth-MACPF contains a membrane-attack complex/perforin (MACPF) domain and two novel C-terminal domains that resemble ribonuclease H and interleukin 8, respectively. The entire protein adopts a flat crescent shape, characteristic of other MACPF proteins, that may be important for oligomerization. This Bth-MACPF structure provides new features and insights not observed in two previous MACPF structures. Genomic context analysis infers that Bth-MACPF may be involved in a novel protein-transport or nutrient-uptake system, suggesting an important role for these MACPF proteins, which were likely to have been inherited from eukaryotes via horizontal gene transfer, in the adaptation of commensal bacteria to the host environment.}, }
@article {pmid20942950, year = {2010}, author = {Trost, B and Haakensen, M and Pittet, V and Ziola, B and Kusalik, A}, title = {Analysis and comparison of the pan-genomic properties of sixteen well-characterized bacterial genera.}, journal = {BMC microbiology}, volume = {10}, number = {}, pages = {258}, pmid = {20942950}, issn = {1471-2180}, mesh = {Bacteria/chemistry/*classification/*genetics ; Bacterial Proteins/analysis/*genetics ; Phylogeny ; Proteome/analysis ; RNA, Bacterial/analysis/genetics ; RNA, Ribosomal, 16S/analysis/genetics ; }, abstract = {BACKGROUND: The increasing availability of whole genome sequences allows the gene or protein content of different organisms to be compared, leading to burgeoning interest in the relatively new subfield of pan-genomics. However, while several studies have analyzed protein content relationships in specific groups of bacteria, there has yet to be a study that provides a general characterization of protein content relationships in a broad range of bacteria.<br><br>RESULTS: A variation on reciprocal BLAST hits was used to infer relationships among proteins in several groups of bacteria, and data regarding protein conservation and uniqueness in different bacterial genera are reported in terms of "core proteomes", "unique proteomes", and "singlets". We also analyzed the relationship between protein content similarity and the percent identity of the 16S rRNA gene in pairs of bacterial isolates from the same genus, and found that the strength of this relationship varied substantially depending on the genus, perhaps reflecting different rates of genome evolution and/or horizontal gene transfer. Finally, core proteomes and unique proteomes were used to study the proteomic cohesiveness of several bacterial species, revealing that some bacterial species had little cohesiveness in their protein content, with some having fewer proteins unique to that species than randomly-chosen sets of isolates from the same genus.<br><br>CONCLUSIONS: The results described in this study aid our understanding of protein content relationships in different bacterial groups, allowing us to make further inferences regarding genome-environment relationships, genome evolution, and the soundness of existing taxonomic classifications.}, }
@article {pmid20941743, year = {2010}, author = {Gahan, PB and Stroun, M}, title = {The virtosome-a novel cytosolic informative entity and intercellular messenger.}, journal = {Cell biochemistry and function}, volume = {28}, number = {7}, pages = {529-538}, doi = {10.1002/cbf.1690}, pmid = {20941743}, issn = {1099-0844}, mesh = {Animals ; Biomarkers, Tumor/blood ; Carrier Proteins/blood/*physiology ; *Cell Communication ; Cytoplasmic Structures/*physiology ; DNA/blood/*metabolism ; DNA-Binding Proteins/blood/physiology ; Gene Transfer, Horizontal ; Genetic Structures/physiology ; Host-Pathogen Interactions/physiology ; Humans ; Immunity ; Lipoproteins/blood/*metabolism ; Neoplasm Metastasis/physiopathology ; RNA/blood/*metabolism ; Ribonucleoproteins/blood/physiology ; }, abstract = {Studies on a range of prokaryote and eukaryote cells and tissues have shown that a newly synthesized DNA/RNA-lipoprotein complex is released in a regulated manner. This complex, termed a virtosome, is a novel cytosolic component of eukaryote cells. The released virtosomes can readily enter other cells where they can modify the biology of the recipient cells. Such modifications include immunological changes and transformation from normal to cancer cells. The virtosomes form a normal component of the circulating nucleic acids in plasma and serum currently used for clinical diagnostic purposes. Given the transformative powers of virtosomes released from tumour cells, the presence of such a complex in human plasma could readily offer the basis of an alternative mechanism for the initiation of metastases.}, }
@article {pmid20941392, year = {2010}, author = {Letek, M and González, P and Macarthur, I and Rodríguez, H and Freeman, TC and Valero-Rello, A and Blanco, M and Buckley, T and Cherevach, I and Fahey, R and Hapeshi, A and Holdstock, J and Leadon, D and Navas, J and Ocampo, A and Quail, MA and Sanders, M and Scortti, MM and Prescott, JF and Fogarty, U and Meijer, WG and Parkhill, J and Bentley, SD and Vázquez-Boland, JA}, title = {The genome of a pathogenic rhodococcus: cooptive virulence underpinned by key gene acquisitions.}, journal = {PLoS genetics}, volume = {6}, number = {9}, pages = {e1001145}, pmid = {20941392}, issn = {1553-7404}, support = {BB/F003722/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/I001107/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Adaptation, Physiological/genetics ; Animals ; Chromosomes, Bacterial/genetics ; *Evolution, Molecular ; Gene Duplication/genetics ; Gene Regulatory Networks/genetics ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/*genetics ; Genetic Loci/genetics ; Genomics ; Intracellular Space/microbiology ; Kinetics ; Macrophages/cytology/microbiology ; Mice ; Mutation/genetics ; Phylogeny ; Plasmids/genetics ; Rhodococcus equi/genetics/growth &amp; development/*pathogenicity/ultrastructure ; Virulence/genetics ; }, abstract = {We report the genome of the facultative intracellular parasite Rhodococcus equi, the only animal pathogen within the biotechnologically important actinobacterial genus Rhodococcus. The 5.0-Mb R. equi 103S genome is significantly smaller than those of environmental rhodococci. This is due to genome expansion in nonpathogenic species, via a linear gain of paralogous genes and an accelerated genetic flux, rather than reductive evolution in R. equi. The 103S genome lacks the extensive catabolic and secondary metabolic complement of environmental rhodococci, and it displays unique adaptations for host colonization and competition in the short-chain fatty acid-rich intestine and manure of herbivores--two main R. equi reservoirs. Except for a few horizontally acquired (HGT) pathogenicity loci, including a cytoadhesive pilus determinant (rpl) and the virulence plasmid vap pathogenicity island (PAI) required for intramacrophage survival, most of the potential virulence-associated genes identified in R. equi are conserved in environmental rhodococci or have homologs in nonpathogenic Actinobacteria. This suggests a mechanism of virulence evolution based on the cooption of existing core actinobacterial traits, triggered by key host niche-adaptive HGT events. We tested this hypothesis by investigating R. equi virulence plasmid-chromosome crosstalk, by global transcription profiling and expression network analysis. Two chromosomal genes conserved in environmental rhodococci, encoding putative chorismate mutase and anthranilate synthase enzymes involved in aromatic amino acid biosynthesis, were strongly coregulated with vap PAI virulence genes and required for optimal proliferation in macrophages. The regulatory integration of chromosomal metabolic genes under the control of the HGT-acquired plasmid PAI is thus an important element in the cooptive virulence of R. equi.}, }
@article {pmid20939741, year = {2010}, author = {Kaneene, JB and Miller, R and May, K and Hattey, JA}, title = {An outbreak of multidrug-resistant Salmonella enterica serotype Oranienburg in Michigan dairy calves.}, journal = {Foodborne pathogens and disease}, volume = {7}, number = {10}, pages = {1193-1201}, doi = {10.1089/fpd.2010.0551}, pmid = {20939741}, issn = {1556-7125}, mesh = {Animal Feed/adverse effects ; Animals ; Cattle/*microbiology ; Dairying ; Disease Outbreaks/*veterinary ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Multiple/genetics ; Electrophoresis, Gel, Pulsed-Field ; Feces/microbiology ; Female ; Food Microbiology ; Gene Transfer, Horizontal ; Michigan ; Microbial Sensitivity Tests ; Salmonella enterica/classification/genetics/*isolation &amp; purification ; Serotyping ; Weaning ; }, abstract = {The objectives of this study were to report an outbreak of highly drug-resistant Salmonella enterica serotype Oranienburg in dairy calves, and conduct an epidemiological investigation of Oranienburg identified on a dairy herd during a study to determine whether discontinuing feeding medicated milk replacer to preweaned dairy calves resulted in increased antimicrobial susceptibility in enteric bacteria. Calf fecal samples and swabs of calf and maternity pens were collected monthly over 18 months. Samples were streaked onto XLT-4 agar and characteristic colonies were subjected to biochemical tests to confirm Salmonella. Strain relatedness was examined by Xbal and BlnI pulsed-field gel electrophoresis analysis on 62 randomly selected isolates. Antimicrobial susceptibility testing, using automated microbroth dilution, was conducted using a panel containing tetracycline, amikacin, amoxicillin-clavulanic acid, ampicillin, ceftiofur, ceftriaxone, cephalothin, chloramphenicol, ciprofloxacin, cefoxitin, gentamicin, kanamycin, nalidixic acid, streptomycin, sulfamethoxazole, and trimethoprim-sulfamethoxazole. A total of 190 Salmonella spp. were isolated from 604 calf and 36 pen samples, of which 86% were Oranienburg and 97% were resistant to at least 9 agents. Environmental isolates had lower levels of resistance than fecal isolates. Pulsed-field gel electrophoresis analysis identified three strains: the most common strain was consistently present before the outbreak and at its peak. One strain was exclusively an environmental isolate, with little antimicrobial resistance. Multiresistant isolates with resistance to ciprofloxacin appeared early in the outbreak, and were replaced by multiresistant isolates with resistance to cephalothin. The differences in strains and resistance patterns suggest that the strains of Oranienburg found in fecal isolates may have different origins from environmental isolates.}, }
@article {pmid20937096, year = {2010}, author = {Liu, L and Yu, L and Edwards, SV}, title = {A maximum pseudo-likelihood approach for estimating species trees under the coalescent model.}, journal = {BMC evolutionary biology}, volume = {10}, number = {}, pages = {302}, pmid = {20937096}, issn = {1471-2148}, mesh = {Gene Transfer, Horizontal ; *Likelihood Functions ; *Models, Theoretical ; Phylogeny ; }, abstract = {BACKGROUND: Several phylogenetic approaches have been developed to estimate species trees from collections of gene trees. However, maximum likelihood approaches for estimating species trees under the coalescent model are limited. Although the likelihood of a species tree under the multispecies coalescent model has already been derived by Rannala and Yang, it can be shown that the maximum likelihood estimate (MLE) of the species tree (topology, branch lengths, and population sizes) from gene trees under this formula does not exist. In this paper, we develop a pseudo-likelihood function of the species tree to obtain maximum pseudo-likelihood estimates (MPE) of species trees, with branch lengths of the species tree in coalescent units.<br><br>RESULTS: We show that the MPE of the species tree is statistically consistent as the number M of genes goes to infinity. In addition, the probability that the MPE of the species tree matches the true species tree converges to 1 at rate O(M -1). The simulation results confirm that the maximum pseudo-likelihood approach is statistically consistent even when the species tree is in the anomaly zone. We applied our method, Maximum Pseudo-likelihood for Estimating Species Trees (MP-EST) to a mammal dataset. The four major clades found in the MP-EST tree are consistent with those in the Bayesian concatenation tree. The bootstrap supports for the species tree estimated by the MP-EST method are more reasonable than the posterior probability supports given by the Bayesian concatenation method in reflecting the level of uncertainty in gene trees and controversies over the relationship of four major groups of placental mammals.<br><br>CONCLUSIONS: MP-EST can consistently estimate the topology and branch lengths (in coalescent units) of the species tree. Although the pseudo-likelihood is derived from coalescent theory, and assumes no gene flow or horizontal gene transfer (HGT), the MP-EST method is robust to a small amount of HGT in the dataset. In addition, increasing the number of genes does not increase the computational time substantially. The MP-EST method is fast for analyzing datasets that involve a large number of genes but a moderate number of species.}, }
@article {pmid20935065, year = {2011}, author = {Jansen, RK and Saski, C and Lee, SB and Hansen, AK and Daniell, H}, title = {Complete plastid genome sequences of three Rosids (Castanea, Prunus, Theobroma): evidence for at least two independent transfers of rpl22 to the nucleus.}, journal = {Molecular biology and evolution}, volume = {28}, number = {1}, pages = {835-847}, pmid = {20935065}, issn = {1537-1719}, support = {R01 GM063879/GM/NIGMS NIH HHS/United States ; GM 63879/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Base Sequence ; Cell Nucleus/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Plant ; *Genome, Plastid ; Magnoliopsida/classification/cytology/*genetics ; Molecular Sequence Data ; Phylogeny ; Plastids/*genetics ; Prunus/*genetics ; RNA-Binding Proteins/*genetics/metabolism ; Ribosomal Proteins/*genetics/metabolism ; Sequence Alignment ; }, abstract = {Functional gene transfer from the plastid to the nucleus is rare among land plants despite evidence that DNA transfer to the nucleus is relatively frequent. During the course of sequencing plastid genomes from representative species from three rosid genera (Castanea, Prunus, Theobroma) and ongoing projects focusing on the Fagaceae and Passifloraceae, we identified putative losses of rpl22 in these two angiosperm families. We further characterized rpl22 from three species of Passiflora and one species of Quercus and identified sequences that likely represent pseudogenes. In Castanea and Quercus, both members of the Fagaceae, we identified a nuclear copy of rpl22, which consisted of two exons separated by an intron. Exon 1 encodes a transit peptide that likely targets the protein product back to the plastid and exon 2 encodes rpl22. We performed phylogenetic analyses of 97 taxa, including 93 angiosperms and four gymnosperm outgroups using alignments of 81 plastid genes to examine the phylogenetic distribution of rpl22 loss and transfer to the nucleus. Our results indicate that within rosids there have been independent transfers of rpl22 to the nucleus in Fabaceae and Fagaceae and a putative third transfer in Passiflora. The high level of sequence divergence between the transit peptides in Fabaceae and Fagaceae strongly suggest that these represent independent transfers. Furthermore, Blast searches did not identify the "donor" genes of the transit peptides, suggesting a de novo origin. We also performed phylogenetic analyses of rpl22 for 87 angiosperms and four gymnosperms, including nuclear-encoded copies for five species of Fabaceae and Fagaceae. The resulting trees indicated that the transfer of rpl22 to the nucleus does not predate the origin of angiosperms as suggested in an earlier study. Using previously published angiosperm divergence time estimates, we suggest that these transfers occurred approximately 56-58, 34-37, and 26-27 Ma for the Fabaceae, Fagaceae, and Passifloraceae, respectively.}, }
@article {pmid20929956, year = {2011}, author = {Bratcher, PE and Park, IH and Oliver, MB and Hortal, M and Camilli, R and Hollingshead, SK and Camou, T and Nahm, MH}, title = {Evolution of the capsular gene locus of Streptococcus pneumoniae serogroup 6.}, journal = {Microbiology (Reading, England)}, volume = {157}, number = {Pt 1}, pages = {189-198}, pmid = {20929956}, issn = {1465-2080}, support = {R01 AI031473/AI/NIAID NIH HHS/United States ; R56 AI031473/AI/NIAID NIH HHS/United States ; AI-31473/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Capsules/*genetics ; Bacterial Typing Techniques ; Base Sequence ; Biosynthetic Pathways/*genetics ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; Evolution, Molecular ; Gene Order ; Gene Transfer, Horizontal ; Genetic Loci ; Genotype ; Humans ; Molecular Sequence Data ; Multilocus Sequence Typing ; Phylogeny ; Recombination, Genetic ; Sequence Alignment ; Sequence Analysis, DNA ; Serotyping ; Streptococcus pneumoniae/classification/*genetics ; }, abstract = {Streptococcus pneumoniae expressing serogroup 6 capsules frequently causes pneumococcal infections and the evolutionary origins of the serogroup 6 strains have been extensively studied. However, these studies were performed when serogroup 6 had only two known members (serotypes 6A and 6B) and before the two new members (serotypes 6C and 6D) expressing wciN(β) were found. We have therefore reinvestigated the evolutionary origins of serogroup 6 by examining the profiles of the capsule gene loci and the multilocus sequence types (MLSTs) of many serogroup 6 isolates from several continents. We confirmed that there are two classes of cps locus sequences for serogroup 6 isolates. In our study, class 2 cps sequences were limited to a few serotype 6B isolates. Neighbour-joining analysis of cps sequence profiles showed a distinct clade for 6C and moderately distinct clades for class 1 6A and 6B sequences. The serotype 6D cps profile was found within the class 1 6B clade, suggesting that it was created by recombination between 6C and 6B cps loci. Interestingly, all 6C isolates also had a unique wzy allele with a 6 bp deletion. This suggests that serotype switching to 6C involves the transfer of a large (>4 kb) gene segment that includes both the wciN(β) allele and the 'short' wzy allele. The MLST studies of serotype 6C isolates suggest that the 6C cps locus is incorporated into many different pneumococcal genomic backgrounds but that, interestingly, 6C cps may have preferentially entered strains of the same genomic backgrounds as those of serotype 6A.}, }
@article {pmid20929803, year = {2010}, author = {McDaniel, LD and Young, E and Delaney, J and Ruhnau, F and Ritchie, KB and Paul, JH}, title = {High frequency of horizontal gene transfer in the oceans.}, journal = {Science (New York, N.Y.)}, volume = {330}, number = {6000}, pages = {50}, doi = {10.1126/science.1192243}, pmid = {20929803}, issn = {1095-9203}, mesh = {Adaptation, Physiological ; DNA Transposable Elements ; Drug Resistance, Bacterial/genetics ; *Ecosystem ; Flavobacterium/drug effects/genetics ; Flexibacter/drug effects/genetics ; *Gene Transfer, Horizontal ; Kanamycin Resistance/genetics ; Oceans and Seas ; Prophages/genetics ; Rhodobacteraceae/drug effects/*genetics/virology ; Seawater/*microbiology ; Streptomycin/metabolism/pharmacology ; }, abstract = {Oceanic bacteria perform many environmental functions, including biogeochemical cycling of many elements, metabolizing of greenhouse gases, functioning in oceanic food webs (microbial loop), and producing valuable natural products and viruses. We demonstrate that the widespread capability of marine bacteria to participate in horizontal gene transfer (HGT) in coastal and oceanic environments may be the result of gene transfer agents (GTAs), viral-like particles produced by α-Proteobacteria. We documented GTA-mediated gene transfer frequencies a thousand to a hundred million times higher than prior estimates of HGT in the oceans, with as high as 47% of the culturable natural microbial community confirmed as gene recipients. These findings suggest a plausible mechanism by which marine bacteria acquire novel traits, thus ensuring resilience in the face of environmental change.}, }
@article {pmid20927138, year = {2011}, author = {Xie, W and Wang, F and Guo, L and Chen, Z and Sievert, SM and Meng, J and Huang, G and Li, Y and Yan, Q and Wu, S and Wang, X and Chen, S and He, G and Xiao, X and Xu, A}, title = {Comparative metagenomics of microbial communities inhabiting deep-sea hydrothermal vent chimneys with contrasting chemistries.}, journal = {The ISME journal}, volume = {5}, number = {3}, pages = {414-426}, pmid = {20927138}, issn = {1751-7370}, mesh = {Autotrophic Processes/genetics ; Bacteria/classification/*genetics/metabolism ; Biodiversity ; Biofilms ; Carbon/metabolism ; Carbon Cycle/genetics ; Environment ; Gene Library ; Hydrothermal Vents/*chemistry/*microbiology ; Metagenome/*genetics ; *Metagenomics ; Molecular Sequence Data ; Nitrogen/metabolism ; Oceans and Seas ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfur/metabolism ; }, abstract = {Deep-sea hydrothermal vent chimneys harbor a high diversity of largely unknown microorganisms. Although the phylogenetic diversity of these microorganisms has been described previously, the adaptation and metabolic potential of the microbial communities is only beginning to be revealed. A pyrosequencing approach was used to directly obtain sequences from a fosmid library constructed from a black smoker chimney 4143-1 in the Mothra hydrothermal vent field at the Juan de Fuca Ridge. A total of 308,034 reads with an average sequence length of 227 bp were generated. Comparative genomic analyses of metagenomes from a variety of environments by two-way clustering of samples and functional gene categories demonstrated that the 4143-1 metagenome clustered most closely with that from a carbonate chimney from Lost City. Both are highly enriched in genes for mismatch repair and homologous recombination, suggesting that the microbial communities have evolved extensive DNA repair systems to cope with the extreme conditions that have potential deleterious effects on the genomes. As previously reported for the Lost City microbiome, the metagenome of chimney 4143-1 exhibited a high proportion of transposases, implying that horizontal gene transfer may be a common occurrence in the deep-sea vent chimney biosphere. In addition, genes for chemotaxis and flagellar assembly were highly enriched in the chimney metagenomes, reflecting the adaptation of the organisms to the highly dynamic conditions present within the chimney walls. Reconstruction of the metabolic pathways revealed that the microbial community in the wall of chimney 4143-1 was mainly fueled by sulfur oxidation, putatively coupled to nitrate reduction to perform inorganic carbon fixation through the Calvin-Benson-Bassham cycle. On the basis of the genomic organization of the key genes of the carbon fixation and sulfur oxidation pathways contained in the large genomic fragments, both obligate and facultative autotrophs appear to be present and contribute to biomass production.}, }
@article {pmid20924417, year = {2010}, author = {Bavishi, A and Abhishek, A and Lin, L and Choudhary, M}, title = {Complex prokaryotic genome structure: rapid evolution of chromosome II.}, journal = {Genome}, volume = {53}, number = {9}, pages = {675-687}, doi = {10.1139/g10-046}, pmid = {20924417}, issn = {1480-3321}, mesh = {Amino Acid Substitution ; Bacteria/*genetics ; Base Sequence ; Biological Evolution ; Brucella/genetics ; Burkholderia/genetics ; Chromosomes, Bacterial/*genetics ; Conserved Sequence/genetics ; Contig Mapping ; DNA, Bacterial/chemistry ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; Ochrobactrum/genetics ; Paracoccus/genetics ; *Phylogeny ; Ralstonia/genetics ; Rhizobium/genetics ; Rhodobacter/genetics ; Sequence Alignment ; Sequence Analysis ; Vibrio/genetics ; }, abstract = {Although many bacteria with two chromosomes have been sequenced, the roles of such complex genome structuring are still unclear. To uncover levels of chromosome I (CI) and chromosome II (CII) sequence divergence, Mauve 2.2.0 was used to align the CI- and CII-specific sequences of bacteria with complex genome structuring in two sets of comparisons: the first set was conducted among the CI and CII of bacterial strains of the same species, while the second set was conducted among the CI and CII of species in Alphaproteobacteria that possess two chromosomes. The analyses revealed a rapid evolution of CII-specific DNA sequences compared with CI-specific sequences in a majority of organisms. In addition, levels of protein divergence between CI-specific and CII-specific genes were determined using phylogenetic analyses and confirmed the DNA alignment findings. Analysis of synonymous and nonsynonymous substitutions revealed that the structural and functional constraints on CI and CII genes are not significantly different. Also, horizontal gene transfer estimates in selected organisms demonstrated that CII in many species has acquired higher levels of horizontally transferred segments than CI. In summary, rapid evolution of CII may perform particular roles for organisms such as aiding in adapting to specialized niches.}, }
@article {pmid20921143, year = {2010}, author = {Nakhamchik, A and Wilde, C and Chong, H and Rowe-Magnus, DA}, title = {Evidence for the horizontal transfer of an unusual capsular polysaccharide biosynthesis locus in marine bacteria.}, journal = {Infection and immunity}, volume = {78}, number = {12}, pages = {5214-5222}, pmid = {20921143}, issn = {1098-5522}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Bacterial Capsules/genetics/metabolism ; Conserved Sequence/genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/genetics ; Genome, Bacterial/genetics ; Molecular Sequence Data ; Muramic Acids/metabolism ; Open Reading Frames/genetics ; Polysaccharides, Bacterial/biosynthesis/*genetics/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Shewanella putrefaciens/genetics ; Vibrio vulnificus/*genetics/metabolism ; Virulence Factors/biosynthesis/genetics ; }, abstract = {The most intensely studied of the Vibrio vulnificus virulence factors is the capsular polysaccharide (CPS). All virulent strains produce copious amounts of CPS. Acapsular strains are avirulent. The structure of the CPS from the clinical isolate ATCC 27562 is unusual. It is serine modified and contains, surprisingly, N-acetylmuramic acid. We identified the complete 25-kb CPS biosynthesis locus from ATCC 27562. It contained 21 open reading frames and was allelic to O-antigen biosynthesis loci. Two of the genes, murA(CPS) and murB(CPS), were paralogs of the murA(PG) and murB(PG) genes of the peptidoglycan biosynthesis pathway; only a single copy of these genes is present in the strain CMCP6 and YJ016 genomes. Although MurA(CPS) and MurB(CPS) were functional when expressed in Escherichia coli, lesions in either gene had no effect on CPS production, virulence, or growth in V. vulnificus; disruption of 8 other genes within the locus resulted in an acapsular phenotype and attenuated virulence. Thus, murA(CPS) and murB(CPS) were functional but redundant. Comparative genomic analysis revealed that while completely different CPS biosynthesis loci were found in the same chromosomal region in other V. vulnificus strains, most of the CPS locus of ATCC 27562 was conserved in another marine bacterium, Shewanella putrefaciens strain 200. However, the average GC content of the CPS locus was significantly lower than the average GC content of either genome. Furthermore, several of the encoded proteins appeared to be of Gram-positive and archaebacterial origin. These data indicate that the horizontal transfer of intact and partial CPS loci drives CPS diversity in marine bacteria.}, }
@article {pmid20890133, year = {2010}, author = {Zaltsman, A and Krichevsky, A and Kozlovsky, SV and Yasmin, F and Citovsky, V}, title = {Plant defense pathways subverted by Agrobacterium for genetic transformation.}, journal = {Plant signaling &amp; behavior}, volume = {5}, number = {10}, pages = {1245-1248}, pmid = {20890133}, issn = {1559-2324}, mesh = {Cell Nucleus/metabolism ; Mitogen-Activated Protein Kinases/metabolism ; Models, Biological ; Plant Proteins/metabolism ; Plants/enzymology/*immunology/*microbiology ; Proteasome Endopeptidase Complex/metabolism ; Protein Processing, Post-Translational ; Protein Transport ; Rhizobium/*genetics/pathogenicity ; *Signal Transduction ; Nicotiana/cytology/microbiology ; *Transformation, Genetic ; Virulence ; }, abstract = {The soil phytopathogen Agrobacterium has the unique ability to introduce single-stranded transferred DNA (T-DNA) from its tumor-inducing (Ti) plasmid into the host cell in a process known as horizontal gene transfer. Following its entry into the host cell cytoplasm, the T-DNA associates with the bacterial virulence (Vir) E2 protein, also exported from Agrobacterium, creating the T-DNA nucleoprotein complex (T-complex), which is then translocated into the nucleus where the DNA is integrated into the host chromatin. VirE2 protects the T-DNA from the host DNase activities, packages it into a helical filament, and interacts with the host proteins, one of which, VIP1, facilitates nuclear import of the T-complex and its subsequent targeting to the host chromatin. Although the VirE2 and VIP1 protein components of the T-complex are vital for its intracellular transport, they must be removed to expose the T-DNA for integration. Our recent work demonstrated that this task is aided by an host defense-related F-box protein VBF that is induced by Agrobacterium infection and that recognizes and binds VIP1. VBF destabilizes VirE2 and VIP1 in yeast and plant cells, presumably via SCF-mediated proteasomal degradation. VBF expression in and export from the Agrobacterium cell lead to increased tumorigenesis. Here, we discuss these findings in the context of the "arms race" between Agrobacterium infectivity and plant defense.}, }
@article {pmid20890096, year = {2010}, author = {Wasko, A and Polak-Berecka, M and Targonski, Z}, title = {A new protein of alpha-amylase activity from Lactococcus lactis.}, journal = {Journal of microbiology and biotechnology}, volume = {20}, number = {9}, pages = {1307-1313}, doi = {10.4014/jmb.1002.02005}, pmid = {20890096}, issn = {1017-7825}, mesh = {Bacterial Proteins/chemistry/genetics/*metabolism ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Lactococcus lactis/*enzymology/genetics ; Molecular Weight ; Phylogeny ; Plasmids ; Sequence Homology, Amino Acid ; alpha-Amylases/chemistry/genetics/*metabolism ; }, abstract = {An extracellular alpha-amylase from Lactococcus lactis IBB500 was purified and characterized. The optimum conditions for the enzyme activity were pH 4.5, temperature of 35 degrees C, enzyme molecular mass of 121 kDa. The genome analysis and a plasmid curing experiment indicated that amy+ genes were located in a plasmid of 30 kb. An analysis of phylogenetic relationships strongly supported a hypothesis of horizontal gene transfer. A strong homology was found for the peptides with the sequence of alpha-amylases from Ralstonia pikettii and Ralstonia solanacearum. The protein of alpha-amylase activity purified in this study is the first one described for the Lactococcus lactis species, and this paper is the first report on Lactococcus lactis strain as a microorganism belonging to amylolytic lactic acid bacteria (ALAB).}, }
@article {pmid20889746, year = {2010}, author = {Blanca-Ordóñez, H and Oliva-García, JJ and Pérez-Mendoza, D and Soto, MJ and Olivares, J and Sanjuán, J and Nogales, J}, title = {pSymA-dependent mobilization of the Sinorhizobium meliloti pSymB megaplasmid.}, journal = {Journal of bacteriology}, volume = {192}, number = {23}, pages = {6309-6312}, pmid = {20889746}, issn = {1098-5530}, mesh = {Bacterial Proteins/genetics/*metabolism ; *Conjugation, Genetic ; DNA Nucleotidyltransferases/genetics/metabolism ; DNA, Bacterial/genetics ; *Gene Transfer, Horizontal ; Plasmids/*metabolism ; Replication Origin ; Sinorhizobium meliloti/*genetics ; }, abstract = {Sinorhizobium meliloti 1021 carries two megaplasmids, pSymA of 1,354 kb and pSymB of 1,683 kb, which are essential in establishing symbiosis with its legume hosts and important for bacterial fitness in the rhizosphere. We have previously shown that pSymA is self-transmissible and that its conjugal functions are regulated by the transcriptional repressor RctA. Here, we show conjugal transfer of pSymB as an in trans mobilization event that requires the type IV secretion system encoded by pSymA. pSymB carries a functional oriT and an adjacent relaxase gene, traA2, that is also transcriptionally repressed by rctA. Both symbiotic megaplasmids would require the relaxase genes in cis with their respective oriTs to achieve the highest transfer efficiencies.}, }
@article {pmid20889655, year = {2010}, author = {Puigbò, P and Wolf, YI and Koonin, EV}, title = {The tree and net components of prokaryote evolution.}, journal = {Genome biology and evolution}, volume = {2}, number = {}, pages = {745-756}, pmid = {20889655}, issn = {1759-6653}, support = {//Intramural NIH HHS/United States ; }, mesh = {*Biological Evolution ; Computer Simulation ; Evolution, Molecular ; Phylogeny ; *Prokaryotic Cells ; }, abstract = {Phylogenetic trees of individual genes of prokaryotes (archaea and bacteria) generally have different topologies, largely owing to extensive horizontal gene transfer (HGT), suggesting that the Tree of Life (TOL) should be replaced by a "net of life" as the paradigm of prokaryote evolution. However, trees remain the natural representation of the histories of individual genes given the fundamentally bifurcating process of gene replication. Therefore, although no single tree can fully represent the evolution of prokaryote genomes, the complete picture of evolution will necessarily combine trees and nets. A quantitative measure of the signals of tree and net evolution is derived from an analysis of all quartets of species in all trees of the "Forest of Life" (FOL), which consists of approximately 7,000 phylogenetic trees for prokaryote genes including approximately 100 nearly universal trees (NUTs). Although diverse routes of net-like evolution collectively dominate the FOL, the pattern of tree-like evolution that reflects the consistent topologies of the NUTs is the most prominent coherent trend. We show that the contributions of tree-like and net-like evolutionary processes substantially differ across bacterial and archaeal lineages and between functional classes of genes. Evolutionary simulations indicate that the central tree-like signal cannot be realistically explained by a self-reinforcing pattern of biased HGT.}, }
@article {pmid20888816, year = {2010}, author = {Knoop, V and Rüdinger, M}, title = {DYW-type PPR proteins in a heterolobosean protist: plant RNA editing factors involved in an ancient horizontal gene transfer?.}, journal = {FEBS letters}, volume = {584}, number = {20}, pages = {4287-4291}, doi = {10.1016/j.febslet.2010.09.041}, pmid = {20888816}, issn = {1873-3468}, mesh = {*Amino Acid Motifs ; Amino Acid Sequence ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Naegleria/*genetics ; Organelles/genetics ; Phylogeny ; Protozoan Proteins/classification/*genetics ; RNA Editing ; RNA, Plant/genetics ; *Repetitive Sequences, Amino Acid ; }, abstract = {A particular type of pentatricopeptide repeat (PPR) proteins with variable length of the 35 aa PPR motifs and conserved carboxyterminal extensions, named the PLS proteins, was so far exclusively identified in land plants. Several PLS proteins with such domain extensions (E, E+, DYW) were shown to be involved in plant organellar RNA editing but their evolutionary origin had remained enigmatic. We here report the first case of DYW-type PLS proteins outside of the plant kingdom in the protist Naegleria gruberi and hypothesize on horizontal gene transfer in very early land plant evolution.}, }
@article {pmid20884693, year = {2011}, author = {Lee, I and Davies, RL}, title = {Evidence for a common gene pool and frequent recombinational exchange of the tbpBA operon in Mannheimia haemolytica, Mannheimia glucosida and Bibersteinia trehalosi.}, journal = {Microbiology (Reading, England)}, volume = {157}, number = {Pt 1}, pages = {123-135}, pmid = {20884693}, issn = {1465-2080}, support = {/WT_/Wellcome Trust/United Kingdom ; 053669/WT_/Wellcome Trust/United Kingdom ; 053669/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Alleles ; Animals ; Bacterial Proteins ; Base Sequence ; Cattle ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Genotype ; Molecular Sequence Data ; Operon ; Pasteurellaceae/*genetics/isolation &amp; purification ; Polymorphism, Genetic ; *Recombination, Genetic ; Sequence Analysis, DNA ; Sequence Homology ; Sheep ; Transferrin-Binding Protein A/genetics ; Transferrin-Binding Protein B/genetics ; }, abstract = {The tbpBA operon was sequenced in 42 representative isolates of Mannheimia haemolytica (32), Mannheimia glucosida (6) and Bibersteinia trehalosi (4). A total of 27 tbpB and 20 tbpA alleles were identified whilst the tbpBA operon was represented by 28 unique alleles that could be assigned to seven classes. There were 1566 (34.8% variation) polymorphic nucleotide sites and 482 (32.1% variation) variable inferred amino acid positions among the 42 tbpBA sequences. The tbpBA operons of serotype A2 M. haemolytica isolates are, with one exception, substantially more diverse than those of the other M. haemolytica serotypes and most likely have a different ancestral origin. The tbpBA phylogeny has been severely disrupted by numerous small- and large-scale intragenic recombination events. In addition, assortative (entire gene) recombination events, involving either the entire tbpBA operon or the individual tbpB and tbpA genes, have played a major role in shaping tbpBA structure and it's distribution in the three species. Our findings indicate that a common gene pool exists for tbpBA in M. haemolytica, M. glucosida and B. trehalosi. In particular, B. trehalosi, M. glucosida and ovine M. haemolytica isolates share a large portion of the tbpA gene, and this probably reflects selection for a conserved TbpA protein that provides effective iron uptake in sheep. Bovine and ovine serotype A2 lineages have very different tbpBA alleles. Bovine-like tbpBA alleles have been partially, or completely, replaced by ovine-like tbpBA alleles in ovine serotype A2 isolates, suggesting that different transferrin receptors are required by serotype A2 isolates for optimum iron uptake in cattle and sheep. Conversely, the tbpBA alleles of bovine-pathogenic serotype A1 and A6 isolates are very similar to those of closely related ovine isolates, suggesting a recent and common evolutionary origin.}, }
@article {pmid20880410, year = {2010}, author = {Bittar, F and Rolain, JM}, title = {Detection and accurate identification of new or emerging bacteria in cystic fibrosis patients.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {16}, number = {7}, pages = {809-820}, doi = {10.1111/j.1469-0691.2010.03236.x}, pmid = {20880410}, issn = {1469-0691}, mesh = {Bacteria/*classification/growth &amp; development/*isolation &amp; purification ; Base Sequence ; Biodiversity ; Cystic Fibrosis/*microbiology ; Cystic Fibrosis Transmembrane Conductance Regulator/genetics ; Gene Transfer, Horizontal ; Humans ; Lung/microbiology ; Microbial Consortia ; Molecular Diagnostic Techniques ; Respiratory Tract Infections/*microbiology ; Spectrometry, Mass, Fast Atom Bombardment/methods ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/*methods ; Spectroscopy, Fourier Transform Infrared/methods ; }, abstract = {Respiratory infections remain a major threat to cystic fibrosis (CF) patients. The detection and correct identification of the bacteria implicated in these infections is critical for the therapeutic management of patients. The traditional methods of culture and phenotypic identification of bacteria lack both sensitivity and specificity because many bacteria can be missed and/or misidentified. Molecular analyses have recently emerged as useful means to resolve these problems, including molecular methods for accurate identification or detection of bacteria and molecular methods for evaluation of microbial diversity. These recent molecular technologies have increased the list of new and/or emerging pathogens and epidemic strains associated with CF patients. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of intact cells has also emerged recently as a powerful and rapid method for the routine identification of bacteria in clinical microbiology laboratories and will certainly represent the method of choice also for the routine identification of bacteria in the context of CF. Finally, recent data derived from molecular culture-independent analyses indicate the presence of a previously underestimated, complex microbial community in sputa from CF patients. Interestingly, full genome sequencing of some bacteria frequently recovered from CF patients has highlighted the fact that the lungs of CF patients are hotspots for lateral gene transfer and the adaptation of these ecosystems to a specific chronic condition.}, }
@article {pmid20877579, year = {2010}, author = {Barbour, AG and Travinsky, B}, title = {Evolution and distribution of the ospC Gene, a transferable serotype determinant of Borrelia burgdorferi.}, journal = {mBio}, volume = {1}, number = {4}, pages = {}, pmid = {20877579}, issn = {2150-7511}, support = {AI-065359/AI/NIAID NIH HHS/United States ; CI 00171-01/CI/NCPDCID CDC HHS/United States ; }, mesh = {Animals ; Antigens, Bacterial/*genetics/metabolism ; Bacterial Outer Membrane Proteins/*genetics/metabolism ; Borrelia burgdorferi/classification/*genetics/isolation &amp; purification/metabolism ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Humans ; Lyme Disease/microbiology ; Molecular Sequence Data ; Phylogeny ; Recombination, Genetic ; Ticks/microbiology ; United States ; }, abstract = {Borrelia burgdorferi, an emerging bacterial pathogen, is maintained in nature by transmission from one vertebrate host to another by ticks. One of the few antigens against which mammals develop protective immunity is the highly polymorphic OspC protein, encoded by the ospC gene on the cp26 plasmid. Intragenic recombination among ospC genes is known, but the extent to which recombination extended beyond the ospC locus itself is undefined. We accessed and supplemented collections of DNA sequences of ospC and other loci from ticks in three U.S. regions (the Northeast, the Midwest, and northern California); a total of 839 ospC sequences were analyzed. Three overlapping but distinct populations of B. burgdorferi corresponded to the geographic regions. In addition, we sequenced 99 ospC flanking sequences from different lineages and compared the complete cp26 sequences of 11 strains as well as the cp26 bbb02 loci of 56 samples. Besides recombinations with traces limited to the ospC gene itself, there was evidence of lateral gene transfers that involved (i) part of the ospC gene and one of the two flanks or (ii) the entire ospC gene and different lengths of both flanks. Lateral gene transfers resulted in different linkages between the ospC gene and loci of the chromosome or other plasmids. By acquisition of the complete part or a large part of a novel ospC gene, an otherwise adapted strain would assume a new serotypic identity, thereby being comparatively fitter in an area with a high prevalence of immunity to existing OspC types.}, }
@article {pmid20876293, year = {2010}, author = {Jurik, A and Hausser, E and Kutter, S and Pattis, I and Prassl, S and Weiss, E and Fischer, W}, title = {The coupling protein Cagbeta and its interaction partner CagZ are required for type IV secretion of the Helicobacter pylori CagA protein.}, journal = {Infection and immunity}, volume = {78}, number = {12}, pages = {5244-5251}, pmid = {20876293}, issn = {1098-5522}, mesh = {Antigens, Bacterial/metabolism/*physiology ; Bacterial Proteins/metabolism/*physiology ; Bacterial Secretion Systems/*physiology ; Bacterial Translocation/physiology ; Helicobacter Infections/microbiology/physiopathology ; Helicobacter pylori/metabolism/*physiology ; Immunoblotting ; Interleukin-8/physiology ; Protein Interaction Domains and Motifs/physiology ; Two-Hybrid System Techniques ; }, abstract = {Bacterial type IV secretion systems are macromolecule transporters with essential functions for horizontal gene transfer and for symbiotic and pathogenic interactions with eukaryotic host cells. Helicobacter pylori, the causative agent of type B gastritis, peptic ulcers, gastric adenocarcinoma, and mucosa-associated lymphoid tissue (MALT) lymphoma, uses the Cag type IV secretion system to inject its effector protein CagA into gastric cells. This protein translocation results in altered host cell gene expression profiles and cytoskeletal rearrangements, and it has been linked to cancer development. Interactions of CagA with host cell proteins have been studied in great detail, but little is known about the molecular details of CagA recognition as a type IV secretion substrate or of the translocation process. Apart from components of the secretion apparatus, we previously identified several CagA translocation factors that are either required for or support CagA translocation. To identify protein-protein interactions between these translocation factors, we used a yeast two-hybrid approach comprising all cag pathogenicity island genes. Among several other interactions involving translocation factors, we found a strong interaction between the coupling protein homologue Cagβ (HP0524) and the Cag-specific translocation factor CagZ (HP0526). We show that CagZ has a stabilizing effect on Cagβ, and we demonstrate protein-protein interactions between the cytoplasmic part of Cagβ and CagA and between CagZ and Cagβ, using immunoprecipitation and pull-down assays. Together, our data suggest that these interactions represent a substrate-translocation factor complex at the bacterial cytoplasmic membrane.}, }
@article {pmid20876108, year = {2010}, author = {Danchin, EG and Rosso, MN and Vieira, P and de Almeida-Engler, J and Coutinho, PM and Henrissat, B and Abad, P}, title = {Multiple lateral gene transfers and duplications have promoted plant parasitism ability in nematodes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {41}, pages = {17651-17656}, pmid = {20876108}, issn = {1091-6490}, mesh = {Animals ; Base Composition ; Bayes Theorem ; *Biological Evolution ; Codon/genetics ; Computational Biology ; *Gene Duplication ; Gene Transfer, Horizontal/*genetics ; Glycoside Hydrolases/genetics ; Models, Genetic ; Nematoda/*genetics/physiology ; *Phylogeny ; Plants/*parasitology ; Polygalacturonase/genetics ; Polysaccharide-Lyases/genetics ; Ralstonia solanacearum/*enzymology/genetics ; }, abstract = {Lateral gene transfer from prokaryotes to animals is poorly understood, and the scarce documented examples generally concern genes of uncharacterized role in the receiver organism. In contrast, in plant-parasitic nematodes, several genes, usually not found in animals and similar to bacterial homologs, play essential roles for successful parasitism. Many of these encode plant cell wall-degrading enzymes that constitute an unprecedented arsenal in animals in terms of both abundance and diversity. Here we report that independent lateral gene transfers from different bacteria, followed by gene duplications and early gain of introns, have shaped this repertoire. We also show protein immunolocalization data that suggest additional roles for some of these cell wall-degrading enzymes in the late stages of these parasites' life cycle. Multiple functional acquisitions of exogenous genes that provide selective advantage were probably crucial for the emergence and proficiency of plant parasitism in nematodes.}, }
@article {pmid20874413, year = {2010}, author = {Belcaid, M and Bergeron, A and Poisson, G}, title = {Mosaic graphs and comparative genomics in phage communities.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {17}, number = {9}, pages = {1315-1326}, pmid = {20874413}, issn = {1557-8666}, support = {P20 RR-16467/RR/NCRR NIH HHS/United States ; }, mesh = {Bacteria/virology ; Bacteriophages/*genetics ; Base Sequence ; Evolution, Molecular ; *Genome, Viral ; Genomics/*methods ; Molecular Sequence Data ; Multigene Family ; Recombination, Genetic ; Sequence Alignment ; }, abstract = {Comparing the genomes of two closely related viruses often produces mosaics where nearly identical sequences alternate with sequences that are unique to each genome. When several closely related genomes are compared, the unique sequences are likely to be shared with third genomes, leading to virus mosaic communities. Here we present comparative analysis of sets of Staphylococcus aureus phages that share large identical sequences with up to three other genomes, and with different partners along their genomes. We introduce mosaic graphs to represent these complex recombination events, and use them to illustrate the breath and depth of sequence sharing: some genomes are almost completely made up of shared sequences, while genomes that share very large identical sequences can adopt alternate functional modules. Mosaic graphs also allow us to identify breakpoints that could eventually be used for the construction of recombination networks. These findings have several implications on phage metagenomics assembly, on the horizontal gene transfer paradigm, and more generally on the understanding of the composition and evolutionary dynamics of virus communities.}, }
@article {pmid20870714, year = {2010}, author = {Brew, K and Tumbale, P and Acharya, KR}, title = {Family 6 glycosyltransferases in vertebrates and bacteria: inactivation and horizontal gene transfer may enhance mutualism between vertebrates and bacteria.}, journal = {The Journal of biological chemistry}, volume = {285}, number = {48}, pages = {37121-37127}, pmid = {20870714}, issn = {1083-351X}, mesh = {Animals ; Bacteria/chemistry/classification/*enzymology/genetics ; *Bacterial Physiological Phenomena ; Bacterial Proteins/chemistry/genetics/*metabolism ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Glycosyltransferases/chemistry/genetics/*metabolism ; Humans ; Molecular Sequence Data ; Phylogeny ; Vertebrates/classification/genetics/*physiology ; }, abstract = {Glycosyltransferases (GTs) control the synthesis and structures of glycans. Inactivation and intense allelic variation in members of the GT6 family generate species-specific and individual variations in carbohydrate structures, including histo-blood group oligosaccharides, resulting in anti-glycan antibodies that target glycan-decorated pathogens. GT6 genes are ubiquitous in vertebrates but are otherwise rare, existing in a few bacteria, one protozoan, and cyanophages, suggesting lateral gene transfer. Prokaryotic GT6 genes correspond to one exon of vertebrate genes, yet their translated protein sequences are strikingly similar. Bacterial and phage GT6 genes influence the surface chemistry of bacteria, affecting their interactions, including those with vertebrate hosts.}, }
@article {pmid20865041, year = {2010}, author = {Yeoman, CJ and Yildirim, S and Thomas, SM and Durkin, AS and Torralba, M and Sutton, G and Buhay, CJ and Ding, Y and Dugan-Rocha, SP and Muzny, DM and Qin, X and Gibbs, RA and Leigh, SR and Stumpf, R and White, BA and Highlander, SK and Nelson, KE and Wilson, BA}, title = {Comparative genomics of Gardnerella vaginalis strains reveals substantial differences in metabolic and virulence potential.}, journal = {PloS one}, volume = {5}, number = {8}, pages = {e12411}, pmid = {20865041}, issn = {1932-6203}, support = {U54 AI084844/AI/NIAID NIH HHS/United States ; U54 HG003273/HG/NHGRI NIH HHS/United States ; N01 AI 30071/AI/NIAID NIH HHS/United States ; U54-HG004973/HG/NHGRI NIH HHS/United States ; N01 AI030071/AI/NIAID NIH HHS/United States ; U54-HG003273/HG/NHGRI NIH HHS/United States ; U54 HG004973/HG/NHGRI NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/metabolism ; Female ; Gardnerella vaginalis/classification/*genetics/*metabolism/pathogenicity ; *Genomics ; Humans ; Male ; Molecular Sequence Data ; Phylogeny ; Vagina/microbiology ; Vaginosis, Bacterial/*microbiology ; Virulence ; }, abstract = {BACKGROUND: Gardnerella vaginalis is described as a common vaginal bacterial species whose presence correlates strongly with bacterial vaginosis (BV). Here we report the genome sequencing and comparative analyses of three strains of G. vaginalis. Strains 317 (ATCC 14019) and 594 (ATCC 14018) were isolated from the vaginal tracts of women with symptomatic BV, while Strain 409-05 was isolated from a healthy, asymptomatic individual with a Nugent score of 9.<br><br>PRINCIPAL FINDINGS: Substantial genomic rearrangement and heterogeneity were observed that appeared to have resulted from both mobile elements and substantial lateral gene transfer. These genomic differences translated to differences in metabolic potential. All strains are equipped with significant virulence potential, including genes encoding the previously described vaginolysin, pili for cytoadhesion, EPS biosynthetic genes for biofilm formation, and antimicrobial resistance systems, We also observed systems promoting multi-drug and lantibiotic extrusion. All G. vaginalis strains possess a large number of genes that may enhance their ability to compete with and exclude other vaginal colonists. These include up to six toxin-antitoxin systems and up to nine additional antitoxins lacking cognate toxins, several of which are clustered within each genome. All strains encode bacteriocidal toxins, including two lysozyme-like toxins produced uniquely by strain 409-05. Interestingly, the BV isolates encode numerous proteins not found in strain 409-05 that likely increase their pathogenic potential. These include enzymes enabling mucin degradation, a trait previously described to strongly correlate with BV, although commonly attributed to non-G. vaginalis species.<br><br>CONCLUSIONS: Collectively, our results indicate that all three strains are able to thrive in vaginal environments, and therein the BV isolates are capable of occupying a niche that is unique from 409-05. Each strain has significant virulence potential, although genomic and metabolic differences, such as the ability to degrade mucin, indicate that the detection of G. vaginalis in the vaginal tract provides only partial information on the physiological potential of the organism.}, }
@article {pmid20862314, year = {2010}, author = {Hiller, NL and Ahmed, A and Powell, E and Martin, DP and Eutsey, R and Earl, J and Janto, B and Boissy, RJ and Hogg, J and Barbadora, K and Sampath, R and Lonergan, S and Post, JC and Hu, FZ and Ehrlich, GD}, title = {Generation of genic diversity among Streptococcus pneumoniae strains via horizontal gene transfer during a chronic polyclonal pediatric infection.}, journal = {PLoS pathogens}, volume = {6}, number = {9}, pages = {e1001108}, pmid = {20862314}, issn = {1553-7374}, support = {R01 DC002148/DC/NIDCD NIH HHS/United States ; R01 DC005659/DC/NIDCD NIH HHS/United States ; DC05659/DC/NIDCD NIH HHS/United States ; P41 RR006009/RR/NCRR NIH HHS/United States ; R01 DC004173/DC/NIDCD NIH HHS/United States ; AI080935/AI/NIAID NIH HHS/United States ; DC04173/DC/NIDCD NIH HHS/United States ; DC02148/DC/NIDCD NIH HHS/United States ; //Wellcome Trust/United Kingdom ; R01 AI080935/AI/NIAID NIH HHS/United States ; }, mesh = {Alleles ; Chronic Disease ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal/*physiology ; *Genetic Variation ; *Genome, Bacterial ; Humans ; Infant ; Mucous Membrane/*microbiology ; Phylogeny ; Pneumococcal Infections/*genetics/*microbiology ; Polymorphism, Single Nucleotide/genetics ; Recombination, Genetic ; Respiratory Tract Infections/genetics/microbiology ; Streptococcus pneumoniae/classification/*genetics ; }, abstract = {Although there is tremendous interest in understanding the evolutionary roles of horizontal gene transfer (HGT) processes that occur during chronic polyclonal infections, to date there have been few studies that directly address this topic. We have characterized multiple HGT events that most likely occurred during polyclonal infection among nasopharyngeal strains of Streptococcus pneumoniae recovered from a child suffering from chronic upper respiratory and middle-ear infections. Whole genome sequencing and comparative genomics were performed on six isolates collected during symptomatic episodes over a period of seven months. From these comparisons we determined that five of the isolates were genetically highly similar and likely represented a dominant lineage. We analyzed all genic and allelic differences among all six isolates and found that all differences tended to occur within contiguous genomic blocks, suggestive of strain evolution by homologous recombination. From these analyses we identified three strains (two of which were recovered on two different occasions) that appear to have been derived sequentially, one from the next, each by multiple recombination events. We also identified a fourth strain that contains many of the genomic segments that differentiate the three highly related strains from one another, and have hypothesized that this fourth strain may have served as a donor multiple times in the evolution of the dominant strain line. The variations among the parent, daughter, and grand-daughter recombinant strains collectively cover greater than seven percent of the genome and are grouped into 23 chromosomal clusters. While capturing in vivo HGT, these data support the distributed genome hypothesis and suggest that a single competence event in pneumococci can result in the replacement of DNA at multiple non-adjacent loci.}, }
@article {pmid20861243, year = {2010}, author = {Moreau, H and Piganeau, G and Desdevises, Y and Cooke, R and Derelle, E and Grimsley, N}, title = {Marine prasinovirus genomes show low evolutionary divergence and acquisition of protein metabolism genes by horizontal gene transfer.}, journal = {Journal of virology}, volume = {84}, number = {24}, pages = {12555-12563}, pmid = {20861243}, issn = {1098-5514}, mesh = {*Biological Evolution ; DNA Virus Infections/*genetics/virology ; DNA Viruses/*genetics/*pathogenicity ; DNA, Viral/physiology ; *Gene Transfer, Horizontal ; Genes, Viral/physiology ; Genetic Variation ; *Genome, Viral ; *Marine Biology ; Microalgae/*virology ; Phylogeny ; }, abstract = {Although marine picophytoplankton are at the base of the global food chain, accounting for half of the planetary primary production, they are outnumbered 10 to 1 and are largely controlled by hugely diverse populations of viruses. Eukaryotic microalgae form a ubiquitous and particularly dynamic fraction of such plankton, with environmental clone libraries from coastal regions sometimes being dominated by one or more of the three genera Bathycoccus, Micromonas, and Ostreococcus (class Prasinophyceae). The complete sequences of two double-stranded (dsDNA) Bathycoccus, one dsDNA Micromonas, and one new dsDNA Ostreococcus virus genomes are described. Genome comparison of these giant viruses revealed a high degree of conservation, both for orthologous genes and for synteny, except for one 36-kb inversion in the Ostreococcus lucimarinus virus and two very large predicted proteins in Bathycoccus prasinos viruses. These viruses encode a gene repertoire of certain amino acid biosynthesis pathways never previously observed in viruses that are likely to have been acquired from lateral gene transfer from their host or from bacteria. Pairwise comparisons of whole genomes using all coding sequences with homologous counterparts, either between viruses or between their corresponding hosts, revealed that the evolutionary divergences between viruses are lower than those between their hosts, suggesting either multiple recent host transfers or lower viral evolution rates.}, }
@article {pmid20860700, year = {2010}, author = {Rankin, DJ and Bichsel, M and Wagner, A}, title = {Mobile DNA can drive lineage extinction in prokaryotic populations.}, journal = {Journal of evolutionary biology}, volume = {23}, number = {11}, pages = {2422-2431}, doi = {10.1111/j.1420-9101.2010.02106.x}, pmid = {20860700}, issn = {1420-9101}, mesh = {Bacteria/*genetics ; Computer Simulation ; *Extinction, Biological ; *Genetics, Population ; *Models, Genetic ; Population Dynamics ; Retroelements/*genetics ; Selection, Genetic ; }, abstract = {Natural selection ultimately acts on genes and other DNA sequences. Adaptations that are good for the gene can have adverse effects at higher levels of organization, including the individual or the population. Mobile genetic elements illustrate this principle well, because they can self-replicate within a genome at a cost to their host. As they are costly and can be transmitted horizontally, mobile elements can be seen as genomic parasites. It has been suggested that mobile elements may cause the extinction of their host populations. In organisms with very large populations, such as most bacteria, individual selection is highly effective in purging genomes of deleterious elements, suggesting that extinction is unlikely. Here we investigate the conditions under which mobile DNA can drive bacterial lineages to extinction. We use a range of epidemiological and ecological models to show that harmful mobile DNA can invade, and drive populations to extinction, provided their transmission rate is high and that mobile element-induced mortality is not too high. Population extinction becomes more likely when there are more elements in the population. Even if elements are costly, extinction can still occur because of the combined effect of horizontal gene transfer, a mortality induced by mobile elements. Our study highlights the potential of mobile DNA to be selected at the population level, as well as at the individual level.}, }
@article {pmid20856925, year = {2010}, author = {Saisongkorh, W and Robert, C and La Scola, B and Raoult, D and Rolain, JM}, title = {Evidence of transfer by conjugation of type IV secretion system genes between Bartonella species and Rhizobium radiobacter in amoeba.}, journal = {PloS one}, volume = {5}, number = {9}, pages = {e12666}, pmid = {20856925}, issn = {1932-6203}, mesh = {Agrobacterium tumefaciens/classification/*genetics ; Bacterial Proteins/*genetics ; Bartonella/classification/*genetics ; *Conjugation, Genetic ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; Plasmids/genetics ; }, abstract = {BACKGROUND: Bartonella species cospeciate with mammals and live within erythrocytes. Even in these specific niches, it has been recently suggested by bioinformatic analysis of full genome sequences that Lateral Gene Transfer (LGT) may occur but this has never been demonstrated biologically. Here we describe the sequence of the B. rattaustraliani (AUST/NH4(T)) circular plasmid (pNH4) that encodes the tra cluster of the Type IV secretion system (T4SS) and we eventually provide evidence that Bartonella species may conjugate and exchange this plasmid inside amoeba.<br><br>PRINCIPAL FINDINGS: The T4SS of pNH4 is critical for intracellular viability of bacterial pathogens, exhibits bioinformatic evidence of LGT among bacteria living in phagocytic protists. For instance, 3 out of 4 T4SS encoding genes from pNH4 appear to be closely related to Rhizobiales, suggesting that gene exchange occurs between intracellular bacteria from mammals (bartonellae) and plants (Rhizobiales). We show that B. rattaustraliani and Rhizobium radiobacter both survived within the amoeba Acanthamoeba polyphaga and can conjugate together. Our findings further support the hypothesis that tra genes might also move into and out of bacterial communities by conjugation, which might be the primary means of genomic evolution for intracellular adaptation by cross-talk of interchangeable genes between Bartonella species and plant pathogens.<br><br>CONCLUSIONS: Based on this, we speculate that amoeba favor the transfer of genes as phagocytic protists, which allows for intraphagocytic survival and, as a consequence, promotes the creation of potential pathogenic organisms.}, }
@article {pmid20852019, year = {2010}, author = {Blanc, G and Duncan, G and Agarkova, I and Borodovsky, M and Gurnon, J and Kuo, A and Lindquist, E and Lucas, S and Pangilinan, J and Polle, J and Salamov, A and Terry, A and Yamada, T and Dunigan, DD and Grigoriev, IV and Claverie, JM and Van Etten, JL}, title = {The Chlorella variabilis NC64A genome reveals adaptation to photosymbiosis, coevolution with viruses, and cryptic sex.}, journal = {The Plant cell}, volume = {22}, number = {9}, pages = {2943-2955}, pmid = {20852019}, issn = {1532-298X}, support = {P20 RR016469/RR/NCRR NIH HHS/United States ; R01 GM032441/GM/NIGMS NIH HHS/United States ; GM32441/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Composition ; Cell Wall/metabolism ; Chlorella/*genetics/virology ; DNA, Plant/genetics ; *Evolution, Molecular ; Expressed Sequence Tags ; Flagella/genetics ; *Genome, Plant ; Molecular Sequence Data ; Multigene Family ; Plant Growth Regulators/genetics ; Repetitive Sequences, Nucleic Acid ; Reproduction ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {Chlorella variabilis NC64A, a unicellular photosynthetic green alga (Trebouxiophyceae), is an intracellular photobiont of Paramecium bursaria and a model system for studying virus/algal interactions. We sequenced its 46-Mb nuclear genome, revealing an expansion of protein families that could have participated in adaptation to symbiosis. NC64A exhibits variations in GC content across its genome that correlate with global expression level, average intron size, and codon usage bias. Although Chlorella species have been assumed to be asexual and nonmotile, the NC64A genome encodes all the known meiosis-specific proteins and a subset of proteins found in flagella. We hypothesize that Chlorella might have retained a flagella-derived structure that could be involved in sexual reproduction. Furthermore, a survey of phytohormone pathways in chlorophyte algae identified algal orthologs of Arabidopsis thaliana genes involved in hormone biosynthesis and signaling, suggesting that these functions were established prior to the evolution of land plants. We show that the ability of Chlorella to produce chitinous cell walls likely resulted from the capture of metabolic genes by horizontal gene transfer from algal viruses, prokaryotes, or fungi. Analysis of the NC64A genome substantially advances our understanding of the green lineage evolution, including the genomic interplay with viruses and symbiosis between eukaryotes.}, }
@article {pmid20851899, year = {2010}, author = {Suzuki, H and Yano, H and Brown, CJ and Top, EM}, title = {Predicting plasmid promiscuity based on genomic signature.}, journal = {Journal of bacteriology}, volume = {192}, number = {22}, pages = {6045-6055}, pmid = {20851899}, issn = {1098-5530}, support = {P20 RR016448/RR/NCRR NIH HHS/United States ; P20 RR016454/RR/NCRR NIH HHS/United States ; P20RR016454/RR/NCRR NIH HHS/United States ; P20RR16448/RR/NCRR NIH HHS/United States ; }, mesh = {Cluster Analysis ; *Codon ; DNA, Bacterial/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Plasmids ; }, abstract = {Despite the important contribution of self-transmissible plasmids to bacterial evolution, little is understood about the range of hosts in which these plasmids have evolved. Our goal was to infer this so-called evolutionary host range. The nucleotide composition, or genomic signature, of plasmids is often similar to that of the chromosome of their current host, suggesting that plasmids acquire their hosts' signature over time. Therefore, we examined whether the evolutionary host range of plasmids could be inferred by comparing their trinucleotide composition to that of all completely sequenced bacterial chromosomes. The diversity of candidate hosts was determined using taxonomic classification and genetic distance. The method was first tested using plasmids from six incompatibility (Inc) groups whose host ranges are generally thought to be narrow (IncF, IncH, and IncI) or broad (IncN, IncP, and IncW) and then applied to other plasmid groups. The evolutionary host range was found to be broad for IncP plasmids, narrow for IncF and IncI plasmids, and intermediate for IncH and IncN plasmids, which corresponds with their known host range. The IncW plasmids as well as several plasmids from the IncA/C, IncP, IncQ, IncU, and PromA groups have signatures that were not similar to any of the chromosomal signatures, raising the hypothesis that these plasmids have not been ameliorated in any host due to their promiscuous nature. The inferred evolutionary host range of IncA/C, IncP-9, and IncL/M plasmids requires further investigation. In this era of high-throughput sequencing, this genomic signature method is a useful tool for predicting the host range of novel mobile elements.}, }
@article {pmid20851547, year = {2010}, author = {Risal, CP and Yokoyama, T and Ohkama-Ohtsu, N and Djedidi, S and Sekimoto, H}, title = {Genetic diversity of native soybean bradyrhizobia from different topographical regions along the southern slopes of the Himalayan Mountains in Nepal.}, journal = {Systematic and applied microbiology}, volume = {33}, number = {7}, pages = {416-425}, doi = {10.1016/j.syapm.2010.06.008}, pmid = {20851547}, issn = {1618-0984}, mesh = {Bacterial Typing Techniques ; Base Sequence ; Bradyrhizobium/classification/*genetics/isolation &amp; purification/metabolism ; Climate ; Gene Transfer, Horizontal ; Genetic Variation ; Genotype ; Molecular Sequence Data ; Nepal ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/classification/*genetics ; Root Nodules, Plant/*microbiology ; Sequence Analysis, DNA ; Sequence Analysis, RNA ; Soil Microbiology ; Glycine max/*microbiology ; Symbiosis ; }, abstract = {Soybean-nodulating bradyrhizobia are genetically diverse and are classified into different species. In this study, the genetic diversity of native soybean bradyrhizobia isolated from different topographical regions along the southern slopes of the Himalayan Mountains in Nepal was explored. Soil samples were collected from three different topographical regions with contrasting climates. A local soybean cultivar, Cobb, was used as a trap plant to isolate bradyrhizobia. A total of 24 isolates selected on the basis of their colony morphology were genetically characterized. For each isolate, the full nucleotide sequence of the 16S rRNA gene and ITS region, and partial sequences of the nifD and nodD1 genes were determined. Two lineages were evident in the conserved gene phylogeny; one representing Bradyrhizobium elkanii (71% of isolates), and the other representing Bradyrhizobium japonicum (21%) and Bradyrhizobium yuanmingense (8%). Phylogenetic analyses revealed three novel lineages in the Bradyrhizobium elkanii clade, indicating high levels of genetic diversity among Bradyrhizobium isolates in Nepal. B. japonicum and B. yuanmingense strains were distributed in areas from 2420 to 2660 m above sea level (asl), which were mountain regions with a temperate climate. The B. elkanii clade was distributed in two regions; hill regions ranging from 1512 to 1935 m asl, and mountain regions ranging from 2420 to 2660 m asl. Ten multi-locus genotypes were detected; seven among B. elkanii, two among B. japonicum, and one among B. yuanmingense-related isolates. The results indicated that there was higher species-level diversity of Bradyrhizobium in the temperate region than in the sub-tropical region along the southern slopes of the Himalayan Mountains in Nepal.}, }
@article {pmid20851546, year = {2010}, author = {Aoki, S and Kondo, T and Prévost, D and Nakata, S and Kajita, T and Ito, M}, title = {Genotypic and phenotypic diversity of rhizobia isolated from Lathyrus japonicus indigenous to Japan.}, journal = {Systematic and applied microbiology}, volume = {33}, number = {7}, pages = {383-397}, doi = {10.1016/j.syapm.2010.07.001}, pmid = {20851546}, issn = {1618-0984}, mesh = {Amidohydrolases/*genetics ; Bacterial Proteins/*genetics ; Bacterial Typing Techniques ; Base Sequence ; Canada ; DNA Fingerprinting ; DNA, Bacterial/genetics ; DNA, Intergenic ; Gene Transfer, Horizontal ; Genotype ; Host Specificity ; Japan ; Lathyrus/*microbiology ; Molecular Sequence Data ; N-Acetylglucosaminyltransferases/*genetics ; Phenotype ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Rec A Recombinases/genetics ; Rhizobium/*classification/*genetics/isolation &amp; purification ; Salt Tolerance ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {Sixty-one rhizobial strains from Lathyrus japonicus nodules growing on the seashore in Japan were characterized and compared to two strains from Canada. The PCR-based method was used to identify test strains with novel taxonomic markers that were designed to discriminate between all known Lathyrus rhizobia. Three genomic groups (I, II, and III) were finally identified using RAPD, RFLP, and phylogenetic analyses. Strains in genomic group I (related to Rhizobium leguminosarum) were divided into two subgroups (Ia and Ib) and subgroup Ia was related to biovar viciae. Strains in subgroup Ib, which were all isolated from Japanese sea pea, belonged to a distinct group from other rhizobial groups in the recA phylogeny and PCR-based grouping, and were more tolerant to salt than the isolate from an inland legume. Test strains in genomic groups II and III belonged to a single clade with the reference strains of R. pisi, R. etli, and R. phaseoli in the 16S rRNA phylogeny. The PCR-based method and phylogenetic analysis of recA revealed that genomic group II was related to R. pisi. The analyses also showed that genomic group III harbored a mixed chromosomal sequence of different genomic groups, suggesting a recent horizontal gene transfer between diverse rhizobia. Although two Canadian strains belonged to subgroup Ia, molecular and physiological analyses showed the divergence between Canadian and Japanese strains. Phylogenetic analysis of nod genes divided the rhizobial strains into several groups that reflected the host range of rhizobia. Symbiosis between dispersing legumes and rhizobia at seashore is discussed.}, }
@article {pmid20851041, year = {2010}, author = {Cho, YJ and Yi, H and Lee, JH and Kim, DW and Chun, J}, title = {Genomic evolution of Vibrio cholerae.}, journal = {Current opinion in microbiology}, volume = {13}, number = {5}, pages = {646-651}, doi = {10.1016/j.mib.2010.08.007}, pmid = {20851041}, issn = {1879-0364}, mesh = {Africa ; Asia ; Bacterial Typing Techniques ; Cholera/epidemiology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomic Islands ; Genotype ; Humans ; Pandemics ; Vibrio cholerae/*classification/*genetics ; }, abstract = {Vibrio cholera, the causal agent of cholera, also occupies an autochthonous aquatic inhabitant. The current, seventh cholera pandemic is linked to O1 El Tor biotype and O139 serogroups. In the last decades, we have witnessed a shift involving genetically and phenotypically varied pandemic clones in Asia and Africa. Recent comparative genomic studies have identified a large 'mobilome', or composed of mobile genomic islands in V. cholerae. All seventh pandemic isolates have highly related genome sequences, but they can be differentiated by set of these genomic islands. A consequence of the extensive lateral gene transfer is that classically important diagnostic markers, such as serotype and biotype, are not reliable and new methods based on genomic sequences are required.}, }
@article {pmid20850375, year = {2010}, author = {Wright, GD}, title = {Antibiotic resistance in the environment: a link to the clinic?.}, journal = {Current opinion in microbiology}, volume = {13}, number = {5}, pages = {589-594}, doi = {10.1016/j.mib.2010.08.005}, pmid = {20850375}, issn = {1879-0364}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Animals ; Anti-Bacterial Agents/metabolism/*pharmacology ; Bacteria/classification/drug effects/genetics/pathogenicity ; Drug Resistance, Multiple, Bacterial/*genetics ; *Environment ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genes, MDR ; }, abstract = {The emergence of resistance to all classes of antibiotics in previously susceptible bacterial pathogens is a major challenge to infectious disease medicine. The origin of the genes associated with resistance has long been a mystery. There is a growing body of evidence that is demonstrating that environmental microbes are highly drug resistant. The genes that make up this environmental resistome have the potential to be transferred to pathogens and indeed there is some evidence that at least some clinically relevant resistance genes have originated in environmental microbes. Understanding the extent of the environmental resistome and its mobilization into pathogenic bacteria is essential for the management and discovery of antibiotics.}, }
@article {pmid20849667, year = {2010}, author = {Szitenberg, A and Rot, C and Ilan, M and Huchon, D}, title = {Diversity of sponge mitochondrial introns revealed by cox 1 sequences of Tetillidae.}, journal = {BMC evolutionary biology}, volume = {10}, number = {}, pages = {288}, pmid = {20849667}, issn = {1471-2148}, mesh = {Animals ; Anthozoa/classification/enzymology/genetics ; Cyclooxygenase 1/*genetics ; Introns/*genetics ; Mitochondrial Proteins/genetics ; Open Reading Frames/genetics ; *Phylogeny ; Porifera/*classification/*enzymology/genetics ; }, abstract = {BACKGROUND: Animal mitochondrial introns are rare. In sponges and cnidarians they have been found in the cox 1 gene of some spirophorid and homosclerophorid sponges, as well as in the cox 1 and nad 5 genes of some Hexacorallia. Their sporadic distribution has raised a debate as to whether these mobile elements have been vertically or horizontally transmitted among their hosts. The first sponge found to possess a mitochondrial intron was a spirophorid sponge from the Tetillidae family. To better understand the mode of transmission of mitochondrial introns in sponges, we studied cox 1 intron distribution among representatives of this family.<br><br>RESULTS: Seventeen tetillid cox 1 sequences were examined. Among these sequences only six were found to possess group I introns. Remarkably, three different forms of introns were found, named introns 714, 723 and 870 based on their different positions in the cox 1 alignment. These introns had distinct secondary structures and encoded LAGLIDADG ORFs belonging to three different lineages. Interestingly, sponges harboring the same intron form did not always form monophyletic groups, suggesting that their introns might have been transferred horizontally. To evaluate whether the introns were vertically or horizontally transmitted in sponges and cnidarians we used a host parasite approach. We tested for co-speciation between introns 723 (the introns with the highest number of sponge representatives) and their nesting cox 1 sequences. Reciprocal AU tests indicated that the intron and cox 1 tree are significantly different, while a likelihood ratio test was not significant. A global test of co-phylogeny had significant results; however, when cnidarian sequences were analyzed separately the results were not significant.<br><br>CONCLUSIONS: The co-speciation analyses thus suggest that a vertical transmission of introns in the ancestor of sponges and cnidarians, followed by numerous independent losses, cannot solely explain the current distribution of metazoan group I introns. An alternative scenario that includes horizontal gene transfer events appears to be more suitable to explain the incongruence between the intron 723 and the cox 1 topologies. In addition, our results suggest that three different intron forms independently colonized the cox 1 gene of tetillids. Among sponges, the Tetillidae family seems to be experiencing an unusual number of intron insertions.}, }
@article {pmid20849393, year = {2010}, author = {Meinersmann, RJ and Ladely, SR and Lindsey, RL}, title = {Ribosomal operon intergenic sequence region (ISR) heterogeneity in Campylobacter coli and Campylobacter jejuni.}, journal = {Letters in applied microbiology}, volume = {51}, number = {5}, pages = {539-545}, doi = {10.1111/j.1472-765X.2010.02930.x}, pmid = {20849393}, issn = {1472-765X}, mesh = {Base Sequence ; Campylobacter coli/chemistry/classification/*genetics ; Campylobacter jejuni/chemistry/classification/*genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/*genetics ; *Genetic Variation ; Molecular Sequence Data ; *Operon ; RNA, Ribosomal, 16S/chemistry/genetics ; RNA, Ribosomal, 23S/chemistry/genetics ; Sequence Alignment ; }, abstract = {AIMS: The intergenic sequence regions (ISR) between the 16S and 23S genes of Campylobacter jejuni and Campylobacter coli are markedly different for each species. However, in the genomic sequence for Camp. coli RM2228, two rRNA operons have an ISR that is characteristic of Camp. coli, and the third operon is characteristic of Camp. jejuni. The aim of this study was to determine the prevalence of ISR heterogeneity in these organisms.<br><br>METHODS AND RESULTS: PCR primers were designed to yield a 327-base pair (bp) product for Camp. coli and 166-bp product for Camp. jejuni. A strain like Camp. coli RM2228 should yield products of both sizes. DNA from a panel of Camp. coli (n=133) and Camp. jejuni (n=134) isolates were tested. All of the isolates yielded products of the predicted size for the species. To verify the data for Camp. coli RM2228, each ribosomal operon from the isolate was individually amplified by PCR and tested with the ISR primer pair. Products of both sizes were produced as predicted.<br><br>CONCLUSIONS: The cross-species heterogeneity of the ISR seen in Camp. coli RM2228 is uncommon.<br><br>The heterogeneity must have been caused by horizontal gene transfer at a frequency lower than predicted from housekeeping gene data. Thus, it can be expected that species identification based on the ISR can be confused in rare isolates.}, }
@article {pmid20844938, year = {2011}, author = {Schetelig, MF and Götschel, F and Viktorinová, I and Handler, AM and Wimmer, EA}, title = {Recombination technologies for enhanced transgene stability in bioengineered insects.}, journal = {Genetica}, volume = {139}, number = {1}, pages = {71-78}, pmid = {20844938}, issn = {1573-6857}, mesh = {Animals ; Animals, Genetically Modified/*genetics ; DNA Transposable Elements/*genetics ; Genetic Vectors/genetics ; Genomic Instability ; Germ Cells ; Insecta/*genetics ; Transfection ; *Transgenes ; Transposases/genetics ; }, abstract = {Transposon-based vectors currently provide the most suitable gene transfer systems for insect germ-line transformation and are used for molecular improvement of the Sterile Insect Technique. However, the long time stability of genome-integrated transposon constructs depends on the absence of transposase activity that could remobilize the transposon-embedded transgenes. To achieve transgene stability transposon vectors are usually non-autonomous, lacking a functional transposase gene, and chosen so that endogenous or related transposon activities are not present in the host. Nevertheless, the non-autonomous transposon-embedded transgenes could become unstable by the unintended presence of a mobilizing transposase that may have been undetected or subsequently entered the host species by horizontal gene transfer. Since the field release of transgenic insects will present environmental concerns relating to large populations and high mobility, it will be important to ensure that transgene constructs are stably integrated for maintaining strain integrity and eliminating the possibility for unintentional transfer into the genome of another organism. Here we review efficient methods to delete or rearrange terminal repeat sequences of transposons necessary for their mobility, subsequent to their initial genomic integration. These procedures should prevent transposase-mediated remobilization of the transgenes, ensuring their genomic stability.}, }
@article {pmid20843562, year = {2010}, author = {Högberg, LD and Heddini, A and Cars, O}, title = {The global need for effective antibiotics: challenges and recent advances.}, journal = {Trends in pharmacological sciences}, volume = {31}, number = {11}, pages = {509-515}, doi = {10.1016/j.tips.2010.08.002}, pmid = {20843562}, issn = {1873-3735}, mesh = {*Anti-Bacterial Agents/metabolism/pharmacology/therapeutic use ; Bacteria/*drug effects/genetics ; Bacterial Infections/*drug therapy/microbiology ; Biomedical Research ; Drug Discovery ; *Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Humans ; Internationality ; Policy ; Time Factors ; Treatment Outcome ; }, abstract = {The emerging problem of antibiotic resistance is a serious threat to global public health. The situation is aggravated by a substantial decline in the research and development of antibacterial agents. Hence, very few new antibacterial classes are brought to market when older classes lose their efficacy. There has been renewed and growing attention within policy groups to: (i) address the problem; (ii) discuss incentives for the development of urgently needed new treatments; (iii) preserve the efficacy of existing therapeutic options. We briefly review the basic principles of antibiotic resistance, and contrast the increasing resistance to the dwindling antibacterial 'pipeline'. We also highlight some recent policy initiatives aiming to secure the future need of effective antibiotics.}, }
@article {pmid20843356, year = {2010}, author = {Laing, C and Buchanan, C and Taboada, EN and Zhang, Y and Kropinski, A and Villegas, A and Thomas, JE and Gannon, VP}, title = {Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions.}, journal = {BMC bioinformatics}, volume = {11}, number = {}, pages = {461}, pmid = {20843356}, issn = {1471-2105}, mesh = {DNA, Bacterial/metabolism ; Escherichia coli/*genetics ; Escherichia coli O157/*genetics ; *Genome, Bacterial ; Phylogeny ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {BACKGROUND: The pan-genome of a bacterial species consists of a core and an accessory gene pool. The accessory genome is thought to be an important source of genetic variability in bacterial populations and is gained through lateral gene transfer, allowing subpopulations of bacteria to better adapt to specific niches. Low-cost and high-throughput sequencing platforms have created an exponential increase in genome sequence data and an opportunity to study the pan-genomes of many bacterial species. In this study, we describe a new online pan-genome sequence analysis program, Panseq.<br><br>RESULTS: Panseq was used to identify Escherichia coli O157:H7 and E. coli K-12 genomic islands. Within a population of 60 E. coli O157:H7 strains, the existence of 65 accessory genomic regions identified by Panseq analysis was confirmed by PCR. The accessory genome and binary presence/absence data, and core genome and single nucleotide polymorphisms (SNPs) of six L. monocytogenes strains were extracted with Panseq and hierarchically clustered and visualized. The nucleotide core and binary accessory data were also used to construct maximum parsimony (MP) trees, which were compared to the MP tree generated by multi-locus sequence typing (MLST). The topology of the accessory and core trees was identical but differed from the tree produced using seven MLST loci. The Loci Selector module found the most variable and discriminatory combinations of four loci within a 100 loci set among 10 strains in 1 s, compared to the 449 s required to exhaustively search for all possible combinations; it also found the most discriminatory 20 loci from a 96 loci E. coli O157:H7 SNP dataset.<br><br>CONCLUSION: Panseq determines the core and accessory regions among a collection of genomic sequences based on user-defined parameters. It readily extracts regions unique to a genome or group of genomes, identifies SNPs within shared core genomic regions, constructs files for use in phylogeny programs based on both the presence/absence of accessory regions and SNPs within core regions and produces a graphical overview of the output. Panseq also includes a loci selector that calculates the most variable and discriminatory loci among sets of accessory loci or core gene SNPs.<br><br>AVAILABILITY: Panseq is freely available online at http://76.70.11.198/panseq. Panseq is written in Perl.}, }
@article {pmid20841432, year = {2010}, author = {Tasse, L and Bercovici, J and Pizzut-Serin, S and Robe, P and Tap, J and Klopp, C and Cantarel, BL and Coutinho, PM and Henrissat, B and Leclerc, M and Doré, J and Monsan, P and Remaud-Simeon, M and Potocki-Veronese, G}, title = {Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes.}, journal = {Genome research}, volume = {20}, number = {11}, pages = {1605-1612}, pmid = {20841432}, issn = {1549-5469}, mesh = {Adult ; Algorithms ; Bacterial Proteins/analysis/genetics/isolation &amp; purification/metabolism ; Cluster Analysis ; Computational Biology/methods ; Data Mining/*methods ; Dietary Fiber/*metabolism ; Enzymes/analysis/*genetics/isolation &amp; purification/metabolism ; Humans ; Intestines/*microbiology ; Male ; Metabolism/genetics ; Metagenome/*genetics/physiology ; Metagenomics/*methods ; Molecular Sequence Data ; Sequence Analysis, DNA ; }, abstract = {The human gut microbiome is a complex ecosystem composed mainly of uncultured bacteria. It plays an essential role in the catabolism of dietary fibers, the part of plant material in our diet that is not metabolized in the upper digestive tract, because the human genome does not encode adequate carbohydrate active enzymes (CAZymes). We describe a multi-step functionally based approach to guide the in-depth pyrosequencing of specific regions of the human gut metagenome encoding the CAZymes involved in dietary fiber breakdown. High-throughput functional screens were first applied to a library covering 5.4 × 10(9) bp of metagenomic DNA, allowing the isolation of 310 clones showing beta-glucanase, hemicellulase, galactanase, amylase, or pectinase activities. Based on the results of refined secondary screens, sequencing efforts were reduced to 0.84 Mb of nonredundant metagenomic DNA, corresponding to 26 clones that were particularly efficient for the degradation of raw plant polysaccharides. Seventy-three CAZymes from 35 different families were discovered. This corresponds to a fivefold target-gene enrichment compared to random sequencing of the human gut metagenome. Thirty-three of these CAZy encoding genes are highly homologous to prevalent genes found in the gut microbiome of at least 20 individuals for whose metagenomic data are available. Moreover, 18 multigenic clusters encoding complementary enzyme activities for plant cell wall degradation were also identified. Gene taxonomic assignment is consistent with horizontal gene transfer events in dominant gut species and provides new insights into the human gut functional trophic chain.}, }
@article {pmid20837397, year = {2010}, author = {Palmer, KL and Kos, VN and Gilmore, MS}, title = {Horizontal gene transfer and the genomics of enterococcal antibiotic resistance.}, journal = {Current opinion in microbiology}, volume = {13}, number = {5}, pages = {632-639}, pmid = {20837397}, issn = {1879-0364}, support = {P01 AI083214/AI/NIAID NIH HHS/United States ; R01 AI072360/AI/NIAID NIH HHS/United States ; P01AI083214/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Multiple, Bacterial ; Enterococcus faecalis/*genetics/pathogenicity ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Microbial Sensitivity Tests ; Pheromones/pharmacology ; Plasmids/*genetics ; Vancomycin Resistance/*genetics ; }, abstract = {Enterococci are Gram-positive bacteria that normally colonize gastrointestinal tracts of humans and animals. They are of growing concern because of their ability to cause antibiotic resistant hospital infections. Antibiotic resistance has been acquired, and has disseminated throughout enterococci, via horizontal transfer of mobile genetic elements. This transmission has been mediated mainly by conjugative plasmids of the pheromone-responsive and broad host range incompatibility group 18 type. Genome sequencing is revealing the extent of diversity of these and other mobile elements in enterococci, as well as the extent of recombination and rearrangement resulting in new phenotypes. Pheromone-responsive plasmids were recently shown to promote genome plasticity in antibiotic resistant Enterococcus faecalis, and their involvement has been implicated in E. faecium as well. Further, incompatibility group 18 plasmids have recently played an important role in mediating transfer of vancomycin resistance from enterococci to methicillin-resistant strains of S. aureus.}, }
@article {pmid20837151, year = {2011}, author = {Waterhouse, M and Themeli, M and Bertz, H and Zoumbos, N and Finke, J and Spyridonidis, A}, title = {Horizontal DNA transfer from donor to host cells as an alternative mechanism of epithelial chimerism after allogeneic hematopoietic cell transplantation.}, journal = {Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation}, volume = {17}, number = {3}, pages = {319-329}, doi = {10.1016/j.bbmt.2010.09.001}, pmid = {20837151}, issn = {1523-6536}, mesh = {Apoptosis ; Bone Marrow Cells/cytology/metabolism ; Cell Line ; Cells, Cultured ; *Chimerism ; Chromosomes, Human, Y/genetics ; Coculture Techniques ; Enzyme Inhibitors/pharmacology ; Epithelial Cells/cytology/*physiology ; Female ; *Gene Transfer, Horizontal ; *Hematopoietic Stem Cell Transplantation ; Humans ; In Situ Hybridization, Fluorescence ; Lymphocytes/cytology/*metabolism ; Lysosomes/drug effects/physiology ; Male ; Microsatellite Repeats/genetics ; Mouth Mucosa/metabolism ; Phagocytosis ; *Recombination, Genetic ; Stromal Cells/cytology/metabolism ; }, abstract = {Animal and human studies have shown that after allogeneic hematopoietic cell transplantation, epithelial cells containing donor-derived genome emerge. The mechanisms underlying this phenomenon are still unclear. We hypothesized that horizontal transfer of the hematopoietic donor-DNA to the host epithelium confers a possible operating mechanism. In an in vitro model mimicking the lymphocyte-epithelial interaction, we cocultivated keratinocyte HaCaT cells (Y-chromosome negative) with nonapoptotic or apoptotic, CMFDA, or BrdU-labeled hematopoietic Jurkat cells (Y+) and looked for the emergence of HaCaT cells bearing Jurkat genome. We found that DNA can be horizontally transferred from hematopoietic to epithelial cell lines through phagocytosis of apoptotic bodies. The ingested genomic material was also found within the nuclear compartment and in isolated chromosomes obtained from HaCaT metaphases. Both lysosomal inhibition in HaCaT cells and repetitive load of HaCaT cells with apoptotic bodies increased the intercellular and intranuclear DNA delivery. Although recipient cells remained viable and showed to express the foreign DNA, this expression was transient. Taking into consideration these findings of horizontal DNA transfer between hematopoietic and epithelial cells, we evaluated by quantitative microsatellite analysis the amount of donor DNA in 176 buccal swabs obtained from 71 patients after allogeneic transplantation. We found a high amount of donor-DNA (mean 26.6%) in the majority (89.7%) of them, although no donor hematopoietic cells were evident in the samples by immunofluorescence. We propose that the incessant charge of the transplant recipient with donor-DNA and its "inappropriate" intranuclear delivery in host epithelium may explain the emergence of epithelial cells with donor-derived genome.}, }
@article {pmid20836863, year = {2010}, author = {Chen, F and Liu, WQ and Eisenstark, A and Johnston, RN and Liu, GR and Liu, SL}, title = {Multiple genetic switches spontaneously modulating bacterial mutability.}, journal = {BMC evolutionary biology}, volume = {10}, number = {}, pages = {277}, pmid = {20836863}, issn = {1471-2148}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Alleles ; Bacteria/*genetics ; Bacterial Proteins/genetics ; Biological Evolution ; DNA Mismatch Repair/*genetics/physiology ; Mutation/*genetics ; Tandem Repeat Sequences/genetics ; }, abstract = {BACKGROUND: All life forms need both high genetic stability to survive as species and a degree of mutability to evolve for adaptation, but little is known about how the organisms balance the two seemingly conflicting aspects of life: genetic stability and mutability. The DNA mismatch repair (MMR) system is essential for maintaining genetic stability and defects in MMR lead to high mutability. Evolution is driven by genetic novelty, such as point mutation and lateral gene transfer, both of which require genetic mutability. However, normally a functional MMR system would strongly inhibit such genomic changes. Our previous work indicated that MMR gene allele conversion between functional and non-functional states through copy number changes of small tandem repeats could occur spontaneously via slipped-strand mis-pairing during DNA replication and therefore may play a role of genetic switches to modulate the bacterial mutability at the population level. The open question was: when the conversion from functional to defective MMR is prohibited, will bacteria still be able to evolve by accepting laterally transferred DNA or accumulating mutations?<br><br>RESULTS: To prohibit allele conversion, we "locked" the MMR genes through nucleotide replacements. We then scored changes in bacterial mutability and found that Salmonella strains with MMR locked at the functional state had significantly decreased mutability. To determine the generalizability of this kind of mutability 'switching' among a wider range of bacteria, we examined the distribution of tandem repeats within MMR genes in over 100 bacterial species and found that multiple genetic switches might exist in these bacteria and may spontaneously modulate bacterial mutability during evolution.<br><br>CONCLUSIONS: MMR allele conversion through repeats-mediated slipped-strand mis-pairing may function as a spontaneous mechanism to switch between high genetic stability and mutability during bacterial evolution.}, }
@article {pmid20832353, year = {2010}, author = {Worden, AZ and Allen, AE}, title = {The voyage of the microbial eukaryote.}, journal = {Current opinion in microbiology}, volume = {13}, number = {5}, pages = {652-660}, doi = {10.1016/j.mib.2010.08.001}, pmid = {20832353}, issn = {1879-0364}, mesh = {Biodiversity ; Epigenomics ; Eukaryota/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetics, Microbial ; }, abstract = {Although genome data from unicellular marine eukaryotes is sparse, sequences from several supergroups have initiated an era of genome-enabled research aimed at understanding gene function, evolution, and adaptation in non-traditional model protists. Trends in genomic content within and between different lineages are emerging, including phylogenetically anomalous patterns, sometimes resulting from horizontal gene transfer. Some such genes have nutrient uptake and metabolism roles suggesting that bacterial and eukaryotic microbes have similar cellular-mineral-environmental constraints. Many 'accessory genome' components are of unknown function, but low gene copy numbers combined with small genomes make protists ideal for systems biology. Cultured and uncultured protists are providing insights to ecology, ancestral features and the role of cooption in development of complex traits. Various protists harbor features important in sexuality and multicellularity once believed to have originated in metazoans or other multicellular taxa.}, }
@article {pmid20829345, year = {2011}, author = {Wägele, H and Deusch, O and Händeler, K and Martin, R and Schmitt, V and Christa, G and Pinzger, B and Gould, SB and Dagan, T and Klussmann-Kolb, A and Martin, W}, title = {Transcriptomic evidence that longevity of acquired plastids in the photosynthetic slugs Elysia timida and Plakobranchus ocellatus does not entail lateral transfer of algal nuclear genes.}, journal = {Molecular biology and evolution}, volume = {28}, number = {1}, pages = {699-706}, pmid = {20829345}, issn = {1537-1719}, mesh = {Animals ; Base Sequence ; Cell Nucleus/*genetics ; Chlorophyta/cytology/*genetics ; Expressed Sequence Tags ; Gastropoda/classification/*genetics/*physiology/ultrastructure ; Gene Expression Profiling ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Photosynthesis/*genetics ; Phylogeny ; Plastids/*genetics/ultrastructure ; }, abstract = {Sacoglossan sea slugs are unique in the animal kingdom in that they sequester and maintain active plastids that they acquire from the siphonaceous algae upon which they feed, making the animals photosynthetic. Although most sacoglossan species digest their freshly ingested plastids within hours, four species from the family Plakobranchidae retain their stolen plastids (kleptoplasts) in a photosynthetically active state on timescales of weeks to months. The molecular basis of plastid maintenance within the cytosol of digestive gland cells in these photosynthetic metazoans is yet unknown but is widely thought to involve gene transfer from the algal food source to the slugs based upon previous investigations of single genes. Indeed, normal plastid development requires hundreds of nuclear-encoded proteins, with protein turnover in photosystem II in particular known to be rapid under various conditions. Moreover, only algal plastids, not the algal nuclei, are sequestered by the animals during feeding. If algal nuclear genes are transferred to the animal either during feeding or in the germ line, and if they are expressed, then they should be readily detectable with deep-sequencing methods. We have sequenced expressed mRNAs from actively photosynthesizing, starved individuals of two photosynthetic sea slug species, Plakobranchus ocellatus Van Hasselt, 1824 and Elysia timida Risso, 1818. We find that nuclear-encoded, algal-derived genes specific to photosynthetic function are expressed neither in P. ocellatus nor in E. timida. Despite their dramatic plastid longevity, these photosynthetic sacoglossan slugs do not express genes acquired from algal nuclei in order to maintain plastid function.}, }
@article {pmid20829291, year = {2010}, author = {Patrick, S and Blakely, GW and Houston, S and Moore, J and Abratt, VR and Bertalan, M and Cerdeño-Tárraga, AM and Quail, MA and Corton, N and Corton, C and Bignell, A and Barron, A and Clark, L and Bentley, SD and Parkhill, J}, title = {Twenty-eight divergent polysaccharide loci specifying within- and amongst-strain capsule diversity in three strains of Bacteroides fragilis.}, journal = {Microbiology (Reading, England)}, volume = {156}, number = {Pt 11}, pages = {3255-3269}, pmid = {20829291}, issn = {1465-2080}, support = {/WT_/Wellcome Trust/United Kingdom ; 061696/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacterial Capsules/biosynthesis/*genetics ; Bacteroides fragilis/*genetics/isolation &amp; purification ; Comparative Genomic Hybridization ; DNA, Bacterial/genetics ; *Genetic Variation ; *Genome, Bacterial ; Humans ; Molecular Sequence Data ; Sequence Analysis, DNA ; }, abstract = {Comparison of the complete genome sequence of Bacteroides fragilis 638R, originally isolated in the USA, was made with two previously sequenced strains isolated in the UK (NCTC 9343) and Japan (YCH46). The presence of 10 loci containing genes associated with polysaccharide (PS) biosynthesis, each including a putative Wzx flippase and Wzy polymerase, was confirmed in all three strains, despite a lack of cross-reactivity between NCTC 9343 and 638R surface PS-specific antibodies by immunolabelling and microscopy. Genomic comparisons revealed an exceptional level of PS biosynthesis locus diversity. Of the 10 divergent PS-associated loci apparent in each strain, none is similar between NCTC 9343 and 638R. YCH46 shares one locus with NCTC 9343, confirmed by mAb labelling, and a second different locus with 638R, making a total of 28 divergent PS biosynthesis loci amongst the three strains. The lack of expression of the phase-variable large capsule (LC) in strain 638R, observed in NCTC 9343, is likely to be due to a point mutation that generates a stop codon within a putative initiating glycosyltransferase, necessary for the expression of the LC in NCTC 9343. Other major sequence differences were observed to arise from different numbers and variety of inserted extra-chromosomal elements, in particular prophages. Extensive horizontal gene transfer has occurred within these strains, despite the presence of a significant number of divergent DNA restriction and modification systems that act to prevent acquisition of foreign DNA. The level of amongst-strain diversity in PS biosynthesis loci is unprecedented.}, }
@article {pmid20828376, year = {2010}, author = {Dai, J and Wang, S and Guerlebeck, D and Laturnus, C and Guenther, S and Shi, Z and Lu, C and Ewers, C}, title = {Suppression subtractive hybridization identifies an autotransporter adhesin gene of E. coli IMT5155 specifically associated with avian pathogenic Escherichia coli (APEC).}, journal = {BMC microbiology}, volume = {10}, number = {}, pages = {236}, pmid = {20828376}, issn = {1471-2180}, mesh = {Adhesins, Bacterial/chemistry/*genetics/metabolism ; Amino Acid Sequence ; Animals ; Bacterial Adhesion ; Bacterial Outer Membrane Proteins/chemistry/*genetics/metabolism ; Chickens ; Escherichia coli/classification/*genetics/pathogenicity/physiology ; Escherichia coli Infections/*microbiology/*veterinary ; Escherichia coli Proteins/chemistry/*genetics/metabolism ; Humans ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Phylogeny ; Poultry Diseases/*microbiology ; Sequence Alignment ; }, abstract = {BACKGROUND: Extraintestinal pathogenic E. coli (ExPEC) represent a phylogenetically diverse group of bacteria which are implicated in a large range of infections in humans and animals. Although subgroups of different ExPEC pathotypes, including uropathogenic, newborn meningitis causing, and avian pathogenic E. coli (APEC) share a number of virulence features, there still might be factors specifically contributing to the pathogenesis of a certain subset of strains or a distinct pathotype. Thus, we made use of suppression subtractive hybridization and compared APEC strain IMT5155 (O2:K1:H5; sequence type complex 95) with human uropathogenic E. coli strain CFT073 (O6:K2:H5; sequence type complex 73) to identify factors which may complete the currently existing model of APEC pathogenicity and further elucidate the position of this avian pathotype within the whole ExPEC group.<br><br>RESULTS: Twenty-eight different genomic loci were identified, which are present in IMT5155 but not in CFT073. One of these loci contained a gene encoding a putative autotransporter adhesin. The open reading frame of the gene spans a 3,498 bp region leading to a putative 124-kDa adhesive protein. A specific antibody was raised against this protein and expression of the adhesin was shown under laboratory conditions. Adherence and adherence inhibition assays demonstrated a role for the corresponding protein in adhesion to DF-1 chicken fibroblasts. Sequence analyses revealed that the flanking regions of the chromosomally located gene contained sequences of mobile genetic elements, indicating a probable spread among different strains by horizontal gene transfer. In accordance with this hypothesis, the adhesin was found to be present not only in different phylogenetic groups of extraintestinal pathogenic but also of commensal E. coli strains, yielding a significant association with strains of avian origin.<br><br>CONCLUSIONS: We identified a chromosomally located autotransporter gene in a highly virulent APEC strain which confers increased adherence of a non-fimbriated E. coli K-12 strain to a chicken fibroblast cell line. Even though flanked by mobile genetic elements and three different genetic regions upstream of the gene, most probably indicating horizontal gene transfer events, the adhesin gene was significantly linked with strains of avian origin. Due to the nucleotide sequence similarity of 98% to a recently published adhesin-related gene, located on plasmid pAPEC-O1-ColBM, the name aatA (APEC autotransporter adhesin A) was adopted from that study.Our data substantiate that AatA might not only be of relevance in APEC pathogenicity but also in facilitating their reservoir life style in the chicken intestine, which might pave the way for future intestinal preventive strategies.}, }
@article {pmid20826944, year = {2010}, author = {Shrivastava, S and Reddy, ChV and Mande, SS}, title = {INDeGenIUS, a new method for high-throughput identification of specialized functional islands in completely sequenced organisms.}, journal = {Journal of biosciences}, volume = {35}, number = {3}, pages = {351-364}, pmid = {20826944}, issn = {0973-7138}, mesh = {Algorithms ; Drug Resistance, Bacterial/genetics ; *Genomic Islands ; Genomics/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Metabolic Networks and Pathways/genetics ; Proteobacteria/*genetics/metabolism/pathogenicity ; Sequence Analysis, DNA ; Symbiosis/genetics ; }, abstract = {Genomic islands (GIs) are regions in the genome which are believed to have been acquired via horizontal gene transfer events and are thus likely to be compositionally distinct from the rest of the genome. Majority of the genes located in a GI encode a particular function. Depending on the genes they encode, GIs can be classified into various categories, such as 'metabolic islands', 'symbiotic islands', 'resistance islands', 'pathogenicity islands', etc. The computational process for GI detection is known and many algorithms for the same are available. We present a new method termed as Improved N-mer based Detection of Genomic Islands Using Sequence-clustering (INDeGenIUS) for the identification of GIs. This method was applied to 400 completely sequenced species belonging to proteobacteria. Based on the genes encoded in the identified GIs, the GIs were grouped into 6 categories: metabolic islands, symbiotic islands, resistance islands, secretion islands, pathogenicity islands and motility islands. Several new islands of interest which had previously been missed out by earlier algorithms were picked up as GIs by INDeGenIUS. The present algorithm has potential application in the identification of functionally relevant GIs in the large number of genomes that are being sequenced. Investigation of the predicted GIs in pathogens may lead to identification of potential drug/vaccine candidates.}, }
@article {pmid20825481, year = {2011}, author = {Mc Ginty, SE and Rankin, DJ and Brown, SP}, title = {Horizontal gene transfer and the evolution of bacterial cooperation.}, journal = {Evolution; international journal of organic evolution}, volume = {65}, number = {1}, pages = {21-32}, pmid = {20825481}, issn = {1558-5646}, support = {/WT_/Wellcome Trust/United Kingdom ; 082273/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacteria/*genetics ; *Biological Evolution ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Interspersed Repetitive Sequences ; *Models, Biological ; Mutation ; Plasmids ; Population Dynamics ; }, abstract = {Bacteria frequently exhibit cooperative behaviors but cooperative strains are vulnerable to invasion by cheater strains that reap the benefits of cooperation but do not perform the cooperative behavior themselves. Bacterial genomes often contain mobile genetic elements such as plasmids. When a gene for cooperative behavior exists on a plasmid, cheaters can be forced to cooperate by infection with this plasmid, rescuing cooperation in a population in which mutation or migration has allowed cheaters to arise. Here we introduce a second plasmid that does not code for cooperation and show that the social dilemma repeats itself at the plasmid level in both within-patch and metapopulation scenarios, and under various scenarios of plasmid incompatibility. Our results suggest that although plasmid carriage of cooperative genes can provide a transient defense against defection in structured environments, plasmid and chromosomal defection remain the only stable strategies in an unstructured environment. We discuss our results in the light of recent bioinformatic evidence that cooperative genes are overrepresented on mobile elements.}, }
@article {pmid20825353, year = {2010}, author = {Kerfeld, CA and Heinhorst, S and Cannon, GC}, title = {Bacterial microcompartments.}, journal = {Annual review of microbiology}, volume = {64}, number = {}, pages = {391-408}, doi = {10.1146/annurev.micro.112408.134211}, pmid = {20825353}, issn = {1545-3251}, mesh = {Bacteria/genetics/*metabolism/*ultrastructure ; Bacterial Proteins/genetics/metabolism ; Enzymes/genetics/metabolism ; Gene Transfer, Horizontal ; Genes, Bacterial ; Multigene Family ; Organelles/genetics/*metabolism/*ultrastructure ; }, abstract = {Bacterial microcompartments (BMCs) are organelles composed entirely of protein. They promote specific metabolic processes by encapsulating and colocalizing enzymes with their substrates and cofactors, by protecting vulnerable enzymes in a defined microenvironment, and by sequestering toxic or volatile intermediates. Prototypes of the BMCs are the carboxysomes of autotrophic bacteria. However, structures of similar polyhedral shape are being discovered in an ever-increasing number of heterotrophic bacteria, where they participate in the utilization of specialty carbon and energy sources. Comparative genomics reveals that the potential for this type of compartmentalization is widespread across bacterial phyla and suggests that genetic modules encoding BMCs are frequently laterally transferred among bacteria. The diverse functions of these BMCs suggest that they contribute to metabolic innovation in bacteria in a broad range of environments.}, }
@article {pmid20824276, year = {2011}, author = {Roschanski, N and Strauch, E}, title = {Assessment of the mobilizable vector plasmids pSUP202 and pSUP404.2 as genetic tools for the predatory bacterium Bdellovibrio bacteriovorus.}, journal = {Current microbiology}, volume = {62}, number = {2}, pages = {589-596}, pmid = {20824276}, issn = {1432-0991}, mesh = {Anti-Bacterial Agents/pharmacology ; Bdellovibrio/*genetics ; Cloning, Molecular/methods ; Conjugation, Genetic ; Escherichia coli K12/genetics ; Gene Transfer, Horizontal ; *Genetic Vectors ; Genomic Instability ; Molecular Sequence Data ; *Plasmids ; Selection, Genetic ; Sequence Analysis, DNA ; }, abstract = {Bdellovibrio and like organisms (BALOs) form the group of predatory bacteria which require Gram-negative bacteria as prey. Genetic studies with Bdellovibrio bacteriovorus can be performed with vectors which are introduced into the predator via conjugation. The usefulness of the two vectors pSUP202 and pSUP404.2 as genetic tools were assessed. Both vectors were transferable into B. bacteriovorus by conjugative matings with an Escherichia coli K12 strain as donor. The transfer frequency was higher for vector pSUP404.2 (approx. 10[-1]-10[-4]) as for pSUP202 (approx. 10[-5]-10[-6]). Vector pSUP202 with a pMB1 origin is unstable in the predatory bacterium, whereas pSUP404.2 is stably maintained in the absence of selective antibiotics. pSUP404.2 harbors two plasmid replicons, the p15A ori and the RSF1010 replication region The copy number of pSUP404.2 was determined by quantitative PCR in B. bacteriovorus and averages seven copies per genome. pSUP404.2 harbors two resistance genes (chloramphenicol and kanamycin) which can be used for cloning either by selection for transconjugants or by insertional inactivation.}, }
@article {pmid20819906, year = {2011}, author = {Leclercq, S and Giraud, I and Cordaux, R}, title = {Remarkable abundance and evolution of mobile group II introns in Wolbachia bacterial endosymbionts.}, journal = {Molecular biology and evolution}, volume = {28}, number = {1}, pages = {685-697}, doi = {10.1093/molbev/msq238}, pmid = {20819906}, issn = {1537-1719}, mesh = {Animals ; Base Sequence ; DNA Transposable Elements/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial ; *Introns ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Symbiosis/*genetics ; Wolbachia/classification/*genetics ; }, abstract = {The streamlined genomes of ancient obligate endosymbionts generally lack transposable elements, as a consequence of their intracellular confinement. Yet, the genomes of Wolbachia, one of the most abundant bacterial endosymbionts on Earth, are littered with transposable elements, in particular insertion sequences (ISs). This paradox raises the question of whether or not such a mobile DNA proliferation reflects a special feature of ISs. In this study, we focused on another class of transposable elements, group II introns, and conducted an in-depth analysis of their content and the microevolutionary processes responsible for their dynamics within Wolbachia genomes. We report an exceptionally high intron abundance and striking differences in copy numbers between Wolbachia strains as well as between intron families. Our bioinformatics and experimental results provide strong evidence that intron diversity is mainly caused by recent (and perhaps ongoing) mobility and horizontal transfers. Our data also support several temporally independent intron invasions during Wolbachia evolution. Furthermore, group II intron spread in some Wolbachia strains may be regulated through gene conversion-mediated inactivation of intron copies. Finally, we found introns to be involved in numerous genomic rearrangements. This underscores the high recombinogenic potential of group II introns, contrary to general expectations. Overall, our study represents the first comprehensive analysis of group II intron evolutionary dynamics in obligate intracellular bacteria. Our results show that bacterial endosymbionts with reduced genomes can sustain high loads of mobile group II introns, as hypothesized for the endosymbiont ancestor of mitochondria during early eukaryote evolution.}, }
@article {pmid20817647, year = {2010}, author = {Yero, D and Vipond, C and Climent, Y and Sardiñas, G and Feavers, IM and Pajón, R}, title = {Variation in the Neisseria meningitidis FadL-like protein: an evolutionary model for a relatively low-abundance surface antigen.}, journal = {Microbiology (Reading, England)}, volume = {156}, number = {Pt 12}, pages = {3596-3608}, doi = {10.1099/mic.0.043182-0}, pmid = {20817647}, issn = {1465-2080}, mesh = {Antigens, Bacterial/*genetics/immunology ; Antigens, Surface/*genetics/immunology ; Bacterial Proteins/*genetics/immunology ; *Evolution, Molecular ; *Genetic Variation ; Humans ; Meningitis, Meningococcal/microbiology ; Molecular Sequence Data ; Neisseria meningitidis/classification/*genetics/immunology/isolation &amp; purification ; Phylogeny ; Recombination, Genetic ; }, abstract = {The molecular diversity of a novel Neisseria meningitidis antigen, encoded by the ORF NMB0088 of MC58 (FadL-like protein), was assessed in a panel of 64 diverse meningococcal strains. The panel consisted of strains belonging to different serogroups, serotypes, serosubtypes and MLST sequence types, of different clinical sources, years and countries of isolation. Based on the sequence variability of the protein, the FadL-like protein has been divided into four variant groups in this species. Antigen variants were associated with specific serogroups and MLST clonal complexes. Maximum-likelihood analyses were used to determine the relationships among sequences and to compare the selection pressures acting on the encoded protein. Furthermore, a model of population genetics and molecular evolution was used to detect natural selection in DNA sequences using the non-synonymous : synonymous substitution (d(N) : d(S)) ratio. The meningococcal sequences were also compared with those of the related surface protein in non-pathogenic commensal Neisseria species to investigate potential horizontal gene transfer. The N. meningitidis fadL gene was subject to only weak positive selection pressure and was less diverse than meningococcal major outer-membrane proteins. The majority of the variability in fadL was due to recombination among existing alleles from the same or related species that resulted in a discrete mosaic structure in the meningococcal population. In general, the population structuring observed based on the FadL-like membrane protein indicates that it is under intermediate immune selection. However, the emergence of a new subvariant within the hyperinvasive lineages demonstrates the phenotypic adaptability of N. meningitidis, probably in response to selective pressure.}, }
@article {pmid20816882, year = {2010}, author = {Bichsel, M and Barbour, AD and Wagner, A}, title = {The early phase of a bacterial insertion sequence infection.}, journal = {Theoretical population biology}, volume = {78}, number = {4}, pages = {278-288}, doi = {10.1016/j.tpb.2010.08.003}, pmid = {20816882}, issn = {1096-0325}, mesh = {DNA Transposable Elements/*genetics ; Genes, Bacterial/*genetics ; Microbial Viability ; Models, Biological ; *Models, Genetic ; }, abstract = {Bacterial insertion sequences are the simplest form of autonomous mobile DNA. It is unknown whether they need to have beneficial effects to infect and persist in bacterial populations, or whether horizontal gene transfer suffices for their persistence. We address this question by using branching process models to investigate the critical, early phase of an insertion sequence infection. We find that the probability of a successful infection is low and depends linearly on the difference between the rate of horizontal gene transfer and the fitness cost of the insertion sequences. Our models show that the median time to extinction of an insertion sequence that dies out is very short, while the median time for a successful infection to reach a modest population size is very long. We conclude that horizontal gene transfer is strong enough to allow the persistence of insertion sequences, although infection is an erratic and slow process.}, }
@article {pmid20810725, year = {2010}, author = {Liu, H and Fu, Y and Jiang, D and Li, G and Xie, J and Cheng, J and Peng, Y and Ghabrial, SA and Yi, X}, title = {Widespread horizontal gene transfer from double-stranded RNA viruses to eukaryotic nuclear genomes.}, journal = {Journal of virology}, volume = {84}, number = {22}, pages = {11876-11887}, pmid = {20810725}, issn = {1098-5514}, mesh = {Amino Acid Sequence ; Animals ; Cell Nucleus/genetics/*virology ; Eukaryota/*genetics/*virology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome ; Molecular Sequence Data ; Phylogeny ; Plants/genetics/virology ; RNA Viruses/classification/*genetics/physiology ; RNA, Double-Stranded/genetics ; RNA, Viral/genetics ; Sequence Alignment ; }, abstract = {Horizontal gene transfer commonly occurs from cells to viruses but rarely occurs from viruses to their host cells, with the exception of retroviruses and some DNA viruses. However, extensive sequence similarity searches in public genome databases for various organisms showed that the capsid protein and RNA-dependent RNA polymerase genes from totiviruses and partitiviruses have widespread homologs in the nuclear genomes of eukaryotic organisms, including plants, arthropods, fungi, nematodes, and protozoa. PCR amplification and sequencing as well as comparative evidence of junction coverage between virus and host sequences support the conclusion that these viral homologs are real and occur in eukaryotic genomes. Sequence comparison and phylogenetic analysis suggest that these genes were likely transferred horizontally from viruses to eukaryotic genomes. Furthermore, we present evidence showing that some of the transferred genes are conserved and expressed in eukaryotic organisms and suggesting that these viral genes are also functional in the recipient genomes. Our findings imply that horizontal transfer of double-stranded RNA viral genes is widespread among eukaryotes and may give rise to functionally important new genes, thus entailing that RNA viruses may play significant roles in the evolution of eukaryotes.}, }
@article {pmid20809290, year = {2010}, author = {May, T and Ito, A and Okabe, S}, title = {Characterization and global gene expression of F- phenocopies during Escherichia coli biofilm formation.}, journal = {Molecular genetics and genomics : MGG}, volume = {284}, number = {5}, pages = {333-342}, pmid = {20809290}, issn = {1617-4623}, mesh = {*Biofilms ; Chromosomes, Bacterial ; Escherichia coli/cytology/*genetics/physiology ; Fimbriae, Bacterial/physiology ; Gene Expression Profiling ; *Gene Expression Regulation, Bacterial ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; RNA, Messenger/genetics ; }, abstract = {The ecological role of horizontal gene transfer within biofilms has been recently investigated, and it has been reported that conjugation directly induces bacteria to form biofilms via expression of conjugative pili. In this report, we described the contribution of bacterial conjugation during biofilm formation by Escherichia coli harboring a natural IncF conjugative F plasmid (F(+)). We showed that cell-to-cell pili interactions through the homosexual mating-pair formation among F(+) × F(+) cells (namely, F(-) phenocopy phenomenon) promote E. coli biofilm formation at the early development stage. The presence of F(+) × F(+) population is the result from heterogeneity within biofilms leading to sessile bacteria that grow at different rates, in which the late-stationary phase cells acted as F(-) phenocopy cells. According to global transcriptional analysis, the biofilm lifestyle shared similar gene expression pattern with F(-) phenocopies. F(-) phenocopy cells expressed specific sets of chromosomal genes (e.g., genes for general stress response and two-component systems) that control the regulation regions of F transfer operon by blocking surface exclusion proteins and DNA transfer machineries. However, mating-pair proteins were stabilized and consequently promoted F(+) × F(+) pili assembly. Thus, F(-) phenocopy phenomenon is an effective adaptive behavior of bacterial cells during biofilm formation.}, }
@article {pmid20808848, year = {2010}, author = {Winter, SE and Winter, MG and Godinez, I and Yang, HJ and Rüssmann, H and Andrews-Polymenis, HL and Bäumler, AJ}, title = {A rapid change in virulence gene expression during the transition from the intestinal lumen into tissue promotes systemic dissemination of Salmonella.}, journal = {PLoS pathogens}, volume = {6}, number = {8}, pages = {e1001060}, pmid = {20808848}, issn = {1553-7374}, support = {AI040124/AI/NIAID NIH HHS/United States ; R01 AI044170/AI/NIAID NIH HHS/United States ; R01 AI040124/AI/NIAID NIH HHS/United States ; AI088122/AI/NIAID NIH HHS/United States ; AI076246/AI/NIAID NIH HHS/United States ; AI044170/AI/NIAID NIH HHS/United States ; R21 AI079173/AI/NIAID NIH HHS/United States ; R21 AI088122/AI/NIAID NIH HHS/United States ; R01 AI076246/AI/NIAID NIH HHS/United States ; AI073120/AI/NIAID NIH HHS/United States ; R29 AI040124/AI/NIAID NIH HHS/United States ; R21 AI073120/AI/NIAID NIH HHS/United States ; AI079173/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacterial Proteins/*genetics ; Blotting, Western ; Cell Line ; Chickens ; Electrophoresis, Polyacrylamide Gel ; Flagellin/biosynthesis ; Flow Cytometry ; Gene Expression ; *Gene Expression Regulation, Bacterial ; Humans ; Immune Evasion ; Intestinal Mucosa/immunology/metabolism/*microbiology ; Mice ; Mice, Inbred C57BL ; Oligonucleotide Array Sequence Analysis ; Reverse Transcriptase Polymerase Chain Reaction ; Salmonella/genetics/immunology/*pathogenicity ; Salmonella Infections, Animal/*genetics/immunology ; Transcription Factors/*genetics ; Typhoid Fever/genetics/immunology ; Virulence/genetics ; }, abstract = {Bacterial pathogens causing systemic disease commonly evolve from organisms associated with localized infections but differ from their close relatives in their ability to overcome mucosal barriers by mechanisms that remain incompletely understood. Here we investigated whether acquisition of a regulatory gene, tviA, contributed to the ability of Salmonella enterica serotype Typhi to disseminate from the intestine to systemic sites of infection during typhoid fever. To study the consequences of acquiring a new regulator by horizontal gene transfer, tviA was introduced into the chromosome of S. enterica serotype Typhimurium, a closely related pathogen causing a localized gastrointestinal infection in immunocompetent individuals. TviA repressed expression of flagellin, a pathogen associated molecular pattern (PAMP), when bacteria were grown at osmotic conditions encountered in tissue, but not at higher osmolarity present in the intestinal lumen. TviA-mediated flagellin repression enabled bacteria to evade sentinel functions of human model epithelia and resulted in increased bacterial dissemination to the spleen in a chicken model. Collectively, our data point to PAMP repression as a novel pathogenic mechanism to overcome the mucosal barrier through innate immune evasion.}, }
@article {pmid20807206, year = {2010}, author = {Pérez Audero, ME and Podoroska, BM and Ibáñez, MM and Cauerhff, A and Checa, SK and Soncini, FC}, title = {Target transcription binding sites differentiate two groups of MerR-monovalent metal ion sensors.}, journal = {Molecular microbiology}, volume = {78}, number = {4}, pages = {853-865}, doi = {10.1111/j.1365-2958.2010.07370.x}, pmid = {20807206}, issn = {1365-2958}, mesh = {Bacterial Proteins/*metabolism ; Base Sequence ; Binding Sites ; DNA, Bacterial/genetics ; DNA-Binding Proteins/*metabolism ; *Gene Expression Regulation, Bacterial ; Ions/metabolism ; Metals/metabolism ; Molecular Sequence Data ; Operator Regions, Genetic ; Protein Binding ; Salmonella typhimurium/*genetics/metabolism ; Transcription Factors/*metabolism ; *Transcription, Genetic ; }, abstract = {The evolution of bacterial regulatory circuits often involves duplication of genes encoding transcription factors that may suffer both modifications in their detected signals, as well as, rewiring of their target operators. This, and subsequent horizontal gene transfer events contribute to generate a diverse array of regulatory pathways. In Salmonella, two homologous transcription factors CueR and GolS are responsible for Cu and Au sensing and resistance respectively. They share similarities not only in their sequence but also in their target binding sites, although they cluster separately among MerR-monovalent metal sensors. Here, we demonstrate that CueR and GolS can selectively distinguish their target binding sites by recognizing bases at positions 3' and 3 of their cognate operators. Swap of these bases results in switching regulator dependency. The differences in promoter architecture plus the environmentally controlled regulator's cytoplasmic availability warrant intra-regulon regulator-operator selectivity, and the proper response to metal injury. Furthermore, the presence of the distinctive operators' bases is widely extended among the two groups of MerR-monovalent metal sensors, providing evidence of the co-evolution of these factors and their target operators. This approach allows the prediction of regulator's dependency and the identification of transcription modules among groups of homologous transcription factors.}, }
@article {pmid20807202, year = {2010}, author = {Daccord, A and Ceccarelli, D and Burrus, V}, title = {Integrating conjugative elements of the SXT/R391 family trigger the excision and drive the mobilization of a new class of Vibrio genomic islands.}, journal = {Molecular microbiology}, volume = {78}, number = {3}, pages = {576-588}, doi = {10.1111/j.1365-2958.2010.07364.x}, pmid = {20807202}, issn = {1365-2958}, mesh = {Bacterial Proteins/*genetics ; Base Sequence ; *Conjugation, Genetic ; *DNA Transposable Elements ; *Genomic Islands ; Molecular Sequence Data ; Multigene Family ; Recombinases/genetics ; Recombination, Genetic ; Vibrio/enzymology/*genetics ; }, abstract = {In vibrios and enterobacteria lateral gene transfer is often facilitated by integrating conjugative elements (ICEs) of the SXT/R391 family. SXT/R391 ICEs integrate by site-specific recombination into prfC and transfer by conjugation, a process that is initiated at a specific locus called the origin of transfer (oriT(SXT)). We identified genomic islands (GIs) harbouring a sequence that shares >63% identity with oriT(SXT) in three species of Vibrio. Unlike SXT/R391 ICEs, these GIs are integrated into a gene coding for a putative stress-induced protein and do not appear to carry any gene coding for a conjugative machinery or for mobilization proteins. Our results show that SXT/R391 ICEs trigger the excision and mediate the conjugative transfer in trans of the three Vibrio GIs at high frequency. GIs' excision is independent of the ICE-encoded recombinase and is controlled by the ICE-encoded transcriptional activator SetCD, which is expressed during the host SOS response. Both mobI and traI, two ICE-borne genes involved in oriT recognition, are essential for GIs' transfer. We also found that SXT/R391 ICEs mobilize in trans over 1 Mb of chromosomal DNA located 5' of the GIs' integration site. Together these results support a novel mechanism of mobilization of GIs by ICEs of the SXT/R391 family.}, }
@article {pmid20805406, year = {2010}, author = {Smillie, C and Garcillán-Barcia, MP and Francia, MV and Rocha, EP and de la Cruz, F}, title = {Mobility of plasmids.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {74}, number = {3}, pages = {434-452}, pmid = {20805406}, issn = {1098-5557}, mesh = {DNA, Bacterial/genetics ; Genomics/methods ; Phylogeny ; Plasmids/*genetics ; }, abstract = {Plasmids are key vectors of horizontal gene transfer and essential genetic engineering tools. They code for genes involved in many aspects of microbial biology, including detoxication, virulence, ecological interactions, and antibiotic resistance. While many studies have decorticated the mechanisms of mobility in model plasmids, the identification and characterization of plasmid mobility from genome data are unexplored. By reviewing the available data and literature, we established a computational protocol to identify and classify conjugation and mobilization genetic modules in 1,730 plasmids. This allowed the accurate classification of proteobacterial conjugative or mobilizable systems in a combination of four mating pair formation and six relaxase families. The available evidence suggests that half of the plasmids are nonmobilizable and that half of the remaining plasmids are conjugative. Some conjugative systems are much more abundant than others and preferably associated with some clades or plasmid sizes. Most very large plasmids are nonmobilizable, with evidence of ongoing domestication into secondary chromosomes. The evolution of conjugation elements shows ancient divergence between mobility systems, with relaxases and type IV coupling proteins (T4CPs) often following separate paths from type IV secretion systems. Phylogenetic patterns of mobility proteins are consistent with the phylogeny of the host prokaryotes, suggesting that plasmid mobility is in general circumscribed within large clades. Our survey suggests the existence of unsuspected new relaxases in archaea and new conjugation systems in cyanobacteria and actinobacteria. Few genes, e.g., T4CPs, relaxases, and VirB4, are at the core of plasmid conjugation, and together with accessory genes, they have evolved into specific systems adapted to specific physiological and ecological contexts.}, }
@article {pmid20802801, year = {2010}, author = {Arnaoudova, E and Haws, DC and Huggins, P and Jaromczyk, JW and Moore, N and Schardl, CL and Yoshida, R}, title = {Statistical phylogenetic tree analysis using differences of means.}, journal = {Frontiers in neuroscience}, volume = {4}, number = {}, pages = {}, pmid = {20802801}, issn = {1662-453X}, support = {R01 GM086888/GM/NIGMS NIH HHS/United States ; }, abstract = {We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by two input alignments, instead of comparing point estimations of trees. This statistical approach can be applied to gene tree analysis for example, detecting unusual events in genome evolution such as horizontal gene transfer and reshuffling. Our method uses difference of means to compare two distributions of trees, after mapping trees into a vector space. Bootstrapping alignment columns can then be applied to obtain p-values. To compute distances between means, we employ a "kernel method" which speeds up distance calculations when trees are mapped in a high-dimensional feature space, e.g., splits or quartets feature space. In this pilot study, first we test our statistical method on data sets simulated under a coalescence model, to test whether two alignments are generated by congruent gene trees. We follow our simulation results with applications to data sets of gophers and lice, grasses and their endophytes, and different fungal genes from the same genome. A companion toolkit, Phylotree, is provided to facilitate computational experiments.}, }
@article {pmid20802057, year = {2011}, author = {Chi Fru, E}, title = {Microbial evolution of sulphate reduction when lateral gene transfer is geographically restricted.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {61}, number = {Pt 7}, pages = {1725-1735}, doi = {10.1099/ijs.0.026914-0}, pmid = {20802057}, issn = {1466-5034}, mesh = {*Biological Evolution ; DNA, Bacterial/genetics ; Gene Flow ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Variation ; Hot Springs/microbiology ; Hydrogensulfite Reductase/*genetics ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sulfates/metabolism ; Sulfur-Reducing Bacteria/*classification/genetics ; }, abstract = {Lateral gene transfer (LGT) is an important mechanism by which micro-organisms acquire new functions. This process has been suggested to be central to prokaryotic evolution in various environments. However, the influence of geographical constraints on the evolution of laterally acquired genes in microbial metabolic evolution is not yet well understood. In this study, the influence of geographical isolation on the evolution of laterally acquired dissimilatory sulphite reductase (dsr) gene sequences in the sulphate-reducing micro-organisms (SRM) was investigated. Sequences on four continental blocks related to SRM known to have received dsr by LGT were analysed using standard phylogenetic and multidimensional statistical methods. Sequences related to lineages with large genetic diversity correlated positively with habitat divergence. Those affiliated to Thermodesulfobacterium indicated strong biogeographical delineation; hydrothermal-vent sequences clustered independently from hot-spring sequences. Some of the hydrothermal-vent and hot-spring sequences suggested to have been acquired from a common ancestral source may have diverged upon isolation within distinct habitats. In contrast, analysis of some Desulfotomaculum sequences indicated they could have been transferred from different ancestral sources but converged upon isolation within the same niche. These results hint that, after lateral acquisition of dsr genes, barriers to gene flow probably play a strong role in their subsequent evolution.}, }
@article {pmid20798577, year = {2010}, author = {Pan, L and Leung, PC and Gu, JD}, title = {A new ColE1-like plasmid group revealed by comparative analysis of the replication proficient fragments of Vibrionaceae plasmids.}, journal = {Journal of microbiology and biotechnology}, volume = {20}, number = {8}, pages = {1163-1178}, doi = {10.4014/jmb.1003.03007}, pmid = {20798577}, issn = {1017-7825}, mesh = {Base Sequence ; *DNA Replication ; Molecular Sequence Data ; Nucleic Acid Conformation ; Plasmids/chemistry/*genetics ; *Replication Origin ; Sequence Alignment ; Vibrionaceae/chemistry/*genetics ; }, abstract = {Plasmids play important roles in horizontal gene transfer among Vibrionaceae, but surprisingly little is known about their replication and incompatibility systems. In this study, we successfully developed a bioinformatics-assisted strategy of experimental identification of 7 Vibrio plasmid replicons. Comparative sequences analysis of the 7 Vibrio plasmid replicons obtained in this study together with 8 published Vibrionaceae plasmid sequences revealed replication participating elements involved in the ColE1-mode of replication initiation and regulation. Like plasmid ColE1, these Vibrionaceae plasmids encode two RNA species (the primer RNA and the antisense RNA) for replication initiation and regulation and, as a result the 15 Vibrionaceae plasmids were designated as ColE1-like Vibrionaceae (CLV) plasmids. Two subgroups were obtained for the 15 CLV plasmids based on comparison of replicon organization and phylogenetic analysis of replication regions. Coexistence of CLV plasmids has been demonstrated by direct sequencing analysis and southern hybridization, strongly suggesting that the incompatibility of CLV plasmids is determined mainly by the RNAI species like the ColE1-like plasmids. Sequences resembling the conserved Xer recombination sites were also identified on the CLV plasmids, indicating that the CLV plasmids probably use the host site-specific recombination system for multimer resolution like that used by ColE1-like plasmids. All the results indicated that the 15 plasmids form a new ColE1-like group, providing basis for rapid characterization and classification of Vibrionaceae plasmids.}, }
@article {pmid20796030, year = {2011}, author = {Wu, X and Monchy, S and Taghavi, S and Zhu, W and Ramos, J and van der Lelie, D}, title = {Comparative genomics and functional analysis of niche-specific adaptation in Pseudomonas putida.}, journal = {FEMS microbiology reviews}, volume = {35}, number = {2}, pages = {299-323}, pmid = {20796030}, issn = {1574-6976}, mesh = {Adaptation, Physiological ; Bacterial Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Genome, Bacterial ; *Genomics ; Pseudomonas putida/genetics/*physiology ; }, abstract = {Pseudomonas putida is a gram-negative rod-shaped gammaproteobacterium that is found throughout various environments. Members of the species P. putida show a diverse spectrum of metabolic activities, which is indicative of their adaptation to various niches, which includes the ability to live in soils and sediments contaminated with high concentrations of heavy metals and organic contaminants. Pseudomonas putida strains are also found as plant growth-promoting rhizospheric and endophytic bacteria. The genome sequences of several P. putida species have become available and provide a unique tool to study the specific niche adaptation of the various P. putida strains. In this review, we compare the genomes of four P. putida strains: the rhizospheric strain KT2440, the endophytic strain W619, the aromatic hydrocarbon-degrading strain F1 and the manganese-oxidizing strain GB-1. Comparative genomics provided a powerful tool to gain new insights into the adaptation of P. putida to specific lifestyles and environmental niches, and clearly demonstrated that horizontal gene transfer played a key role in this adaptation process, as many of the niche-specific functions were found to be encoded on clearly defined genomic islands.}, }
@article {pmid20738845, year = {2010}, author = {Cacciotto, C and Addis, MF and Pagnozzi, D and Chessa, B and Coradduzza, E and Carcangiu, L and Uzzau, S and Alberti, A and Pittau, M}, title = {The liposoluble proteome of Mycoplasma agalactiae: an insight into the minimal protein complement of a bacterial membrane.}, journal = {BMC microbiology}, volume = {10}, number = {}, pages = {225}, pmid = {20738845}, issn = {1471-2180}, mesh = {Bacterial Proteins/chemistry/genetics/*metabolism ; Cell Membrane/chemistry/genetics/*metabolism ; Mycoplasma agalactiae/chemistry/genetics/*metabolism ; Octoxynol/chemistry ; Proteome/chemistry/genetics/*metabolism ; }, abstract = {BACKGROUND: Mycoplasmas are the simplest bacteria capable of autonomous replication. Their evolution proceeded from gram-positive bacteria, with the loss of many biosynthetic pathways and of the cell wall. In this work, the liposoluble protein complement of Mycoplasma agalactiae, a minimal bacterial pathogen causing mastitis, polyarthritis, keratoconjunctivitis, and abortion in small ruminants, was subjected to systematic characterization in order to gain insights into its membrane proteome composition.<br><br>RESULTS: The selective enrichment for M. agalactiae PG2T liposoluble proteins was accomplished by means of Triton X-114 fractionation. Liposoluble proteins were subjected to 2-D PAGE-MS, leading to the identification of 40 unique proteins and to the generation of a reference 2D map of the M. agalactiae liposoluble proteome. Liposoluble proteins from the type strain PG2 and two field isolates were then compared by means of 2D DIGE, revealing reproducible differences in protein expression among isolates. An in-depth analysis was then performed by GeLC-MS/MS in order to achieve a higher coverage of the liposoluble proteome. Using this approach, a total of 194 unique proteins were identified, corresponding to 26% of all M. agalactiae PG2T genes. A gene ontology analysis and classification for localization and function was also carried out on all protein identifications. Interestingly, the 11.5% of expressed membrane proteins derived from putative horizontal gene transfer events.<br><br>CONCLUSIONS: This study led to the in-depth systematic characterization of the M. agalactiae liposoluble protein component, providing useful insights into its membrane organization.}, }
@article {pmid20733238, year = {2011}, author = {Allman, ES and Petrović, S and Rhodes, JA and Sullivant, S}, title = {Identifiability of two-tree mixtures for group-based models.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {8}, number = {3}, pages = {710-722}, doi = {10.1109/TCBB.2010.79}, pmid = {20733238}, issn = {1557-9964}, mesh = {*Algorithms ; Computational Biology/*methods ; DNA/genetics ; Databases, Nucleic Acid ; Markov Chains ; *Models, Genetic ; *Models, Statistical ; *Phylogeny ; }, abstract = {Phylogenetic data arising on two possibly different tree topologies might be mixed through several biological mechanisms, including incomplete lineage sorting or horizontal gene transfer in the case of different topologies, or simply different substitution processes on characters in the case of the same topology. Recent work on a 2-state symmetric model of character change showed that for 4 taxa, such a mixture model has nonidentifiable parameters, and thus, it is theoretically impossible to determine the two tree topologies from any amount of data under such circumstances. Here, the question of identifiability is investigated for two-tree mixtures of the 4-state group-based models, which are more relevant to DNA sequence data. Using algebraic techniques, we show that the tree parameters are identifiable for the JC and K2P models. We also prove that generic substitution parameters for the JC mixture models are identifiable, and for the K2P and K3P models obtain generic identifiability results for mixtures on the same tree. This indicates that the full phylogenetic signal remains in such mixtures, and the 2-state symmetric result is thus a misleading guide to the behavior of other models.}, }
@article {pmid20732433, year = {2010}, author = {Peat, SM and Ffrench-Constant, RH and Waterfield, NR and Marokházi, J and Fodor, A and Adams, BJ}, title = {A robust phylogenetic framework for the bacterial genus Photorhabdus and its use in studying the evolution and maintenance of bioluminescence: a case for 16S, gyrB, and glnA.}, journal = {Molecular phylogenetics and evolution}, volume = {57}, number = {2}, pages = {728-740}, doi = {10.1016/j.ympev.2010.08.012}, pmid = {20732433}, issn = {1095-9513}, mesh = {DNA Gyrase/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Glutamate-Ammonia Ligase/*genetics ; Photorhabdus/*classification/*genetics/metabolism ; *Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {Photorhabdus spp., the only known bioluminescent terrestrial bacteria are well known for their symbiotic association with heterorhabditid nematodes. This association, along with their ability to kill insects, has aroused interest in the evolutionary relationships within this bacterial group. Currently, three species are recognized within the genus Photorhabdus; P. temperata and P. luminescens, which are endosymbionts of Heterorhabditis spp., and P. asymbiotica, which has been isolated from human wounds and has recently been shown to also have a heterorhabditid nematode vector. To examine phylogenetic relationships among these taxa, we utilize total evidence Bayesian, likelihood, and parsimony based analyses of three genetic loci (16S rRNA gene, gyrB, and glnA) to construct a robust evolutionary hypothesis for the genus Photorhabdus. Here we use this phylogeny to evaluate existing specific and sub-specific taxonomic statements within the genus, identify previously undescribed Photorhabdus strains, test the utility of 16S rRNA gene, gyrB, and glnA in resolving various levels of relationships within the genus, and, finally, to investigate the evolution of bioluminescence. The genes examined produced the most robust phylogenetic hypothesis to date for the genus Photorhabdus, as indicated by strong bootstrap and posterior probability values at previously unresolved or poorly resolved nodes. We show that glnA is particularly useful in resolving specific and intra-specific relationships poorly resolved in other studies. We conclude that P. asymbiotica is the sister group to P. luminescens and that the new strains HIT and JUN should be given a new group designation within P. asymbiotica. Furthermore, we reveal a pattern of decline in bioluminescent intensity through the evolution of Photorhabdus, suggesting that this may be a trait acquired and maintained under previous ecological (aquatic) selection pressures that is now gradually being lost in its terrestrial environment.}, }
@article {pmid20723231, year = {2010}, author = {He, M and Li, X and Guo, L and Miller, SJ and Rensing, C and Wang, G}, title = {Characterization and genomic analysis of chromate resistant and reducing Bacillus cereus strain SJ1.}, journal = {BMC microbiology}, volume = {10}, number = {}, pages = {221}, pmid = {20723231}, issn = {1471-2180}, mesh = {Bacillus cereus/drug effects/*genetics/isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biotransformation ; Chromates/*metabolism/pharmacology ; *Drug Resistance, Bacterial ; Gene Expression Regulation, Bacterial/drug effects ; *Genomics ; Molecular Sequence Data ; Oxidation-Reduction ; Sewage/microbiology ; }, abstract = {BACKGROUND: Chromium is a toxic heavy metal, which primarily exists in two inorganic forms, Cr(VI) and Cr(III). Chromate [Cr(VI)] is carcinogenic, mutational, and teratogenic due to its strong oxidizing nature. Biotransformation of Cr(VI) to less-toxic Cr(III) by chromate-resistant and reducing bacteria has offered an ecological and economical option for chromate detoxification and bioremediation. However, knowledge of the genetic determinants for chromate resistance and reduction has been limited so far. Our main aim was to investigate chromate resistance and reduction by Bacillus cereus SJ1, and to further study the underlying mechanisms at the molecular level using the obtained genome sequence.<br><br>RESULTS: Bacillus cereus SJ1 isolated from chromium-contaminated wastewater of a metal electroplating factory displayed high Cr(VI) resistance with a minimal inhibitory concentration (MIC) of 30 mM when induced with Cr(VI). A complete bacterial reduction of 1 mM Cr(VI) was achieved within 57 h. By genome sequence analysis, a putative chromate transport operon, chrIA1, and two additional chrA genes encoding putative chromate transporters that likely confer chromate resistance were identified. Furthermore, we also found an azoreductase gene azoR and four nitroreductase genes nitR possibly involved in chromate reduction. Using reverse transcription PCR (RT-PCR) technology, it was shown that expression of adjacent genes chrA1 and chrI was induced in response to Cr(VI) but expression of the other two chromate transporter genes chrA2 and chrA3 was constitutive. In contrast, chromate reduction was constitutive in both phenotypic and gene expression analyses. The presence of a resolvase gene upstream of chrIA1, an arsenic resistance operon and a gene encoding Tn7-like transposition proteins ABBCCCD downstream of chrIA1 in B. cereus SJ1 implied the possibility of recent horizontal gene transfer.<br><br>CONCLUSION: Our results indicate that expression of the chromate transporter gene chrA1 was inducible by Cr(VI) and most likely regulated by the putative transcriptional regulator ChrI. The bacterial Cr(VI)-resistant level was also inducible. The presence of an adjacent arsenic resistance gene cluster nearby the chrIA1 suggested that strong selective pressure by chromium and arsenic could cause bacterial horizontal gene transfer. Such events may favor the survival and increase the resistance level of B. cereus SJ1.}, }
@article {pmid20716256, year = {2011}, author = {Merhej, V and Raoult, D}, title = {Rickettsial evolution in the light of comparative genomics.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {86}, number = {2}, pages = {379-405}, doi = {10.1111/j.1469-185X.2010.00151.x}, pmid = {20716256}, issn = {1469-185X}, mesh = {Animals ; *Biological Evolution ; *Genome, Bacterial ; *Genomics ; Host-Pathogen Interactions ; Humans ; Rickettsia/*genetics ; }, abstract = {Rickettsia are best known as strictly intracellular vector-borne bacteria that cause mild to severe diseases in humans and other animals. Recent advances in molecular tools and biological experiments have unveiled a wide diversity of Rickettsia spp. that include species with a broad host range and some species that act as endosymbiotic associates. Molecular phylogenies of Rickettsia spp. contain some ambiguities, such as the position of R. canadensis and relationships within the spotted fever group. In the modern era of genomics, with an ever-increasing number of sequenced genomes, there is enhanced interest in the use of whole-genome sequences to understand pathogenesis and assess evolutionary relationships among rickettsial species. Rickettsia have small genomes (1.1-1.5 Mb) as a result of reductive evolution. These genomes contain split genes, gene remnants and pseudogenes that, owing to the colinearity of some rickettsial genomes, may represent different steps of the genome degradation process. Genomics reveal extreme genome reduction and massive gene loss in highly vertebrate-pathogenic Rickettsia compared to less virulent or endosymbiotic species. Information gleaned from rickettsial genomics challenges traditional concepts of pathogenesis that focused primarily on the acquisition of virulence factors. Another intriguing phenomenon about the reduced rickettsial genomes concerns the large fraction of non-coding DNA and possible functionality of these "non-coding" sequences, because of the high conservation of these regions. Despite genome streamlining, Rickettsia spp. contain gene families, selfish DNA, repeat palindromic elements and genes encoding eukaryotic-like motifs. These features participate in sequence and functional diversity and may play a crucial role in adaptation to the host cell and pathogenesis. Genome analyses have identified a large fraction of mobile genetic elements, including plasmids, suggesting the possibility of lateral gene transfer in these intracellular bacteria. Phylogenetic analyses have identified several candidates for horizontal gene acquisition among Rickettsia spp. including tra, pat2, and genes encoding for the type IV secretion system and ATP/ADP translocase that may have been acquired from bacteria living in amoebae. Gene loss, gene duplication, DNA repeats and lateral gene transfer all have shaped rickettsial genome evolution. A comprehensive analysis of the entire genome, including genes and non-coding DNA, will help to unlock the mysteries of rickettsial evolution and pathogenesis.}, }
@article {pmid20716205, year = {2010}, author = {Schmidt, MA}, title = {LEEways: tales of EPEC, ATEC and EHEC.}, journal = {Cellular microbiology}, volume = {12}, number = {11}, pages = {1544-1552}, doi = {10.1111/j.1462-5822.2010.01518.x}, pmid = {20716205}, issn = {1462-5822}, mesh = {DNA Transposable Elements ; Enterohemorrhagic Escherichia coli/genetics/pathogenicity ; Enteropathogenic Escherichia coli/genetics/pathogenicity ; Escherichia coli/*genetics/metabolism/*pathogenicity ; Escherichia coli Infections/*microbiology ; Escherichia coli Proteins/*genetics/metabolism ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Variation ; *Genomic Islands ; Humans ; Interspersed Repetitive Sequences ; Intestinal Diseases/*microbiology ; Phosphoproteins/*genetics ; Trans-Activators/genetics ; Virulence ; Virulence Factors/genetics ; }, abstract = {Intestinal pathogenic Escherichia coli are a major cause of worldwide morbidity and mortality. Currently seven intestinal pathovars are recognized causing a wide range of intestinal disorders that are sometimes associated with severe and even lethal complications. The arsenal of virulence factors is used to subvert cellular functions of the host thereby enhancing adaptation, virulence and pathogenicity. Virulence factor profiles are largely the result of the acquisition of mobile genetic elements such as prophages and pathogenicity islands. A group of highly adapted intestinal pathogenic E. coli that are characterized by the induction of 'attaching-and-effacing (A/E) lesions' have acquired a decisive pathogenicity island, the 'locus of enterocyte effacement - LEE' by horizontal gene transfer. This review focuses on recent advances in our understanding of A/E E. coli. It highlights novel functions of effector proteins, addresses the LEE flanking regions where additional genetic elements such as the LifA/Efa1 region have been identified, and points to implications for diagnostics and therapy due to the putative interconversion of A/E E. coli during infection.}, }
@article {pmid20713671, year = {2010}, author = {Jasni, AS and Mullany, P and Hussain, H and Roberts, AP}, title = {Demonstration of conjugative transposon (Tn5397)-mediated horizontal gene transfer between Clostridium difficile and Enterococcus faecalis.}, journal = {Antimicrobial agents and chemotherapy}, volume = {54}, number = {11}, pages = {4924-4926}, pmid = {20713671}, issn = {1098-6596}, support = {G0601176//Medical Research Council/United Kingdom ; }, mesh = {Clostridioides difficile/*genetics ; DNA Transposable Elements/*genetics ; Enterococcus faecalis/*genetics ; Gene Transfer, Horizontal/*genetics ; }, abstract = {Antibiotic-resistant Enterococcus faecalis and Clostridium difficile are responsible for nosocomial infections in humans, in which they inhabit the same niche. Here, we demonstrate transfer of the conjugative transposon Tn5397 from C. difficile 630 to E. faecalis JH2-2, the first reported gene transfer between these two bacteria. Furthermore, transfer from the E. faecalis EF20A transconjugant to the epidemic ribotype 027 C. difficile strain R20291 was also demonstrated. Tn5397 was shown to use a single specific target site in E. faecalis; it also has specific target sites in C. difficile. These experiments highlight the importance of continual monitoring for emerging resistances in these bacteria.}, }
@article {pmid20713629, year = {2010}, author = {Paillot, R and Darby, AC and Robinson, C and Wright, NL and Steward, KF and Anderson, E and Webb, K and Holden, MT and Efstratiou, A and Broughton, K and Jolley, KA and Priestnall, SL and Marotti Campi, MC and Hughes, MA and Radford, A and Erles, K and Waller, AS}, title = {Identification of three novel superantigen-encoding genes in Streptococcus equi subsp. zooepidemicus, szeF, szeN, and szeP.}, journal = {Infection and immunity}, volume = {78}, number = {11}, pages = {4817-4827}, pmid = {20713629}, issn = {1098-5522}, mesh = {Amino Acid Sequence ; Animals ; Cells, Cultured ; DNA, Bacterial/analysis/genetics ; Dog Diseases/microbiology ; Dogs ; Gene Transfer, Horizontal ; Genome, Bacterial ; Horse Diseases/immunology/microbiology ; Horses ; Humans ; Leukocytes, Mononuclear/immunology ; Lymphocyte Activation ; Molecular Sequence Data ; Sequence Analysis, DNA ; Streptococcal Infections/immunology/*microbiology/veterinary ; Streptococcus equi/*genetics/immunology/isolation &amp; purification/pathogenicity ; Superantigens/*genetics/immunology ; }, abstract = {The acquisition of superantigen-encoding genes by Streptococcus pyogenes has been associated with increased morbidity and mortality in humans, and the gain of four superantigens by Streptococcus equi is linked to the evolution of this host-restricted pathogen from an ancestral strain of the opportunistic pathogen Streptococcus equi subsp. zooepidemicus. A recent study determined that the culture supernatants of several S. equi subsp. zooepidemicus strains possessed mitogenic activity but lacked known superantigen-encoding genes. Here, we report the identification and activities of three novel superantigen-encoding genes. The products of szeF, szeN, and szeP share 59%, 49%, and 34% amino acid sequence identity with SPEH, SPEM, and SPEL, respectively. Recombinant SzeF, SzeN, and SzeP stimulated the proliferation of equine peripheral blood mononuclear cells, and tumor necrosis factor alpha (TNF-α) and gamma interferon (IFN-γ) production, in vitro. Although none of these superantigen genes were encoded within functional prophage elements, szeN and szeP were located next to a prophage remnant, suggesting that they were acquired by horizontal transfer. Eighty-one of 165 diverse S. equi subsp. zooepidemicus strains screened, including 7 out of 15 isolates from cases of disease in humans, contained at least one of these new superantigen-encoding genes. The presence of szeN or szeP, but not szeF, was significantly associated with mitogenic activity in the S. equi subsp. zooepidemicus population (P < 0.000001, P < 0.000001, and P = 0.104, respectively). We conclude that horizontal transfer of these novel superantigens from and within the diverse S. equi subsp. zooepidemicus population is likely to have implications for veterinary and human disease.}, }
@article {pmid20713450, year = {2010}, author = {Beraud, M and Kolb, A and Monteil, V and D'Alayer, J and Norel, F}, title = {A proteomic analysis reveals differential regulation of the σ(S)-dependent yciGFE(katN) locus by YncC and H-NS in Salmonella and Escherichia coli K-12.}, journal = {Molecular &amp; cellular proteomics : MCP}, volume = {9}, number = {12}, pages = {2601-2616}, pmid = {20713450}, issn = {1535-9484}, mesh = {Bacterial Proteins/*genetics ; Base Sequence ; Blotting, Western ; DNA Footprinting ; DNA Primers ; Escherichia coli/*genetics ; Escherichia coli Proteins/*physiology ; Fimbriae Proteins/*physiology ; Gene Expression Regulation, Developmental ; *Genes, Bacterial ; Operon ; Promoter Regions, Genetic ; *Proteomics ; Salmonella/*genetics ; Sigma Factor/*genetics ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Transcription Factors/*physiology ; Transcription, Genetic ; }, abstract = {The stationary phase sigma factor σ(S) (RpoS) controls a regulon required for general stress resistance of the closely related enterobacteria Salmonella and Escherichia coli. The σ(S)-dependent yncC gene encodes a putative DNA binding regulatory protein. Application of the surface-enhanced laser desorption/ionization-time of flight (SELDI-TOF) ProteinChip technology for proteome profiling of wild-type and mutant strains of Salmonella enterica serovar Typhimurium revealed potential protein targets for YncC regulation, which were identified by mass spectrometry, and subsequently validated. These proteins are encoded by the σ(S)-dependent operon yciGFEkatN and regulation of their expression by YncC operates at the transcriptional level, as demonstrated by gene fusion analyses and by in vitro transcription and DNase I footprinting experiments with purified YncC. The yciGFE genes are present (without katN) in E. coli K-12 but are poorly expressed, compared with the situation in Salmonella. We report that the yciGFE(katN) locus is silenced by the histone-like protein H-NS in both species, but that σ(S) efficiently relieves silencing in Salmonella but not in E. coli K-12. In Salmonella, YncC acts in concert with σ(S) to activate transcription at the yciG promoter (pyciG). When overproduced, YncC also activated σ(S)-dependent transcription at pyciG in E. coli K-12, but solely by countering the negative effect of H-NS. Our results indicate that differences between Salmonella and E. coli K-12, in the architecture of cis-acting regulatory sequences upstream of pyciG, contribute to the differential regulation of the yciGFE(katN) genes by H-NS and YncC in these two enterobacteria. In E. coli, this locus is subject to gene rearrangements and also likely to horizontal gene transfer, consistent with its repression by the xenogeneic silencer H-NS.}, }
@article {pmid20708964, year = {2011}, author = {Orsi, RH and den Bakker, HC and Wiedmann, M}, title = {Listeria monocytogenes lineages: Genomics, evolution, ecology, and phenotypic characteristics.}, journal = {International journal of medical microbiology : IJMM}, volume = {301}, number = {2}, pages = {79-96}, doi = {10.1016/j.ijmm.2010.05.002}, pmid = {20708964}, issn = {1618-0607}, mesh = {Animals ; Ecosystem ; Evolution, Molecular ; Food Microbiology ; *Genetic Variation ; Genomics ; Genotype ; Humans ; Listeria monocytogenes/*classification/genetics/physiology ; Listeriosis/microbiology/veterinary ; Phenotype ; Virulence ; Virulence Factors/biosynthesis/genetics ; }, abstract = {Listeria monocytogenes consists of at least 4 evolutionary lineages (I, II, III, and IV) with different but overlapping ecological niches. Most L. monocytogenes isolates seem to belong to lineages I and II, which harbor the serotypes more commonly associated with human clinical cases, including serotype 1/2a (lineage II) and serotypes 1/2b and 4b (lineage I). Lineage II strains are common in foods, seem to be widespread in the natural and farm environments, and are also commonly isolated from animal listeriosis cases and sporadic human clinical cases. Most human listeriosis outbreaks are associated with lineage I isolates though. In addition, a number of studies indicate that, in many countries, lineage I strains are overrepresented among human isolates, as compared to lineage II strains. Lineage III and IV strains on the other hand are rare and predominantly isolated from animal sources. The apparent differences in the distribution of strains representing the L. monocytogenes lineages has lead to a number of studies aimed at identifying phenotypic differences among the different lineages. Interestingly, lineage II isolates seem to carry more plasmids than lineage I isolates and these plasmids often confer resistance to toxic metals and possibly other compounds that may be found in the environment. Moreover, lineage II isolates seem to be more resistant to bacteriocins than lineage I isolates, which probably confers an advantage in environments where bacteriocin-producing organisms are abundant. A large number of lineage II isolates and strains have been shown to be virulence-attenuated due to premature stop codon mutations in inlA and mutations in prfA. A subset of lineage I isolates carry a listeriolysin S hemolysin, which is not present in isolates belonging to lineages II, III, or IV. While lineage II isolates also show higher recombination rates than lineage I isolates, possibly facilitating adaptation of lineage II strains to diverse environments, lineage I isolates are clonal and show a low prevalence of plasmids and IS elements, suggesting that lineage I isolates may have mechanisms that limit the acquisition of foreign DNA by horizontal gene transfer. Diversifying selection has also been shown to have played an important role during evolution of the L. monocytogenes lineages and during divergence of L. monocytogenes from the non-pathogenic species L. innocua. Overall evidence thus suggests that the 4 L. monocytogenes lineages identified so far represent distinct ecologic, genetic, and phenotypic characteristics, which appear to affect their ability to be transmitted through foods and to cause human disease. Further insights into the ecology, evolution, and characteristics of these lineages will thus not only provide an improved understanding of the evolution of this foodborne pathogen, but may also facilitate improved control of foodborne listeriosis.}, }
@article {pmid20706870, year = {2011}, author = {Kunisawa, T}, title = {Inference of the phylogenetic position of the phylum Deferribacteres from gene order comparison.}, journal = {Antonie van Leeuwenhoek}, volume = {99}, number = {2}, pages = {417-422}, doi = {10.1007/s10482-010-9492-7}, pmid = {20706870}, issn = {1572-9699}, mesh = {Bacteria/*classification/*genetics ; Evolution, Molecular ; *Gene Order ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Phylogeny ; Synteny ; }, abstract = {The phylogenetic placement of the phylum Deferribacteres was investigated on the basis of gene order comparisons of completely sequenced bacterial genomes. Two completely sequenced Deferribacteres species share five sets of gene arrangements with a group of phyla, Proteobacteria, Aquificae, Planctomycetes, Spirochaetes, Bacteroidetes, Chlorobi, Acidobacteria, Verrucomicrobia, Elusimicrobia and Nitrospirae, while the other group of phyla, Synergistetes, Firmicutes, Actinobacteria, Thermotogae, Chloroflexi and Deinococcus-Thermus, Fusobacteria, shares alternative sets of gene arrangements, suggesting that the Deferribacteres is classified in the former group of phyla. Gene transfers that are thought to have occurred in a common ancestor of the Deferribacteres, Deltaproteobacteria and Nitrospirae exclusive of virtually all other phyla were identified, which suggests that the Deferribacteres is phylogenetically proximal to the Proteobacteria and Nitrospirae.}, }
@article {pmid20705668, year = {2010}, author = {Lee, Y and Yeom, J and Kim, J and Jung, J and Jeon, CO and Park, W}, title = {Phenotypic and physiological alterations by heterologous acylhomoserine lactone synthase expression in Pseudomonas putida.}, journal = {Microbiology (Reading, England)}, volume = {156}, number = {Pt 12}, pages = {3762-3772}, doi = {10.1099/mic.0.041095-0}, pmid = {20705668}, issn = {1465-2080}, mesh = {4-Butyrolactone/analogs &amp; derivatives/metabolism ; Amino Acid Sequence ; Bacterial Proteins/chemistry/*genetics/metabolism ; Biofilms ; Chromobacterium/*enzymology ; *Gene Expression ; Gene Expression Regulation, Bacterial ; Ligases/chemistry/*genetics/metabolism ; Molecular Sequence Data ; Phenotype ; Pseudomonas putida/chemistry/genetics/*physiology ; Repressor Proteins/chemistry/genetics/metabolism ; Sequence Alignment ; Trans-Activators/chemistry/genetics/metabolism ; }, abstract = {Many bacteria harbour an incomplete quorum-sensing (QS) system, whereby they possess LuxR homologues without the QS acylhomoserine lactone (AHL) synthase, which is encoded by a luxI homologue. An artificial AHL-producing plasmid was constructed using a cviI gene encoding the C6-AHL [N-hexanoyl homoserine lactone (HHL)] synthase from Chromobacterium violaceum, and was introduced successfully into both the wild-type and a ppoR (luxR homologue) mutant of Pseudomonas putida. Our data provide evidence to suggest that the PpoR-HHL complex, but neither PpoR nor HHL alone, could attenuate growth, antibiotic resistance and biofilm formation ability. In contrast, swimming motility, siderophore production and indole degradation were enhanced by PpoR-HHL. The addition of exogenous indole increased biofilm formation and reduced swimming motility. Interestingly, indole proved ineffective in the presence of PpoR-HHL, thereby suggesting that the PpoR-HHL complex masks the effects of indole. Our data were supported by transcriptome analyses, which showed that the presence of the plasmid-encoded AHL synthase altered the expression of many genes on the chromosome in strain KT2440. Our results showed that heterologous luxI expression that occurs via horizontal gene transfer can regulate a broad range of specific target genes, resulting in alterations of the phenotype and physiology of host cells.}, }
@article {pmid20705659, year = {2010}, author = {Galeote, V and Novo, M and Salema-Oom, M and Brion, C and Valério, E and Gonçalves, P and Dequin, S}, title = {FSY1, a horizontally transferred gene in the Saccharomyces cerevisiae EC1118 wine yeast strain, encodes a high-affinity fructose/H+ symporter.}, journal = {Microbiology (Reading, England)}, volume = {156}, number = {Pt 12}, pages = {3754-3761}, doi = {10.1099/mic.0.041673-0}, pmid = {20705659}, issn = {1465-2080}, mesh = {Fermentation ; Fructose/metabolism ; Fungal Proteins/*genetics/metabolism ; Gene Expression Regulation, Fungal ; Gene Transfer, Horizontal ; Glucose/metabolism ; Membrane Transport Proteins/*genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; Saccharomyces cerevisiae/classification/genetics/*metabolism ; Wine/analysis/*microbiology ; }, abstract = {Transport of glucose and fructose in the yeast Saccharomyces cerevisiae plays a crucial role in controlling the rate of wine fermentation. In S. cerevisiae, hexoses are transported by facilitated diffusion via hexose carriers (Hxt), which prefer glucose to fructose. However, utilization of fructose by wine yeast is critically important at the end of fermentation. Here, we report the characterization of a fructose transporter recently identified by sequencing the genome of the commercial wine yeast strain EC1118 and found in many other wine yeasts. This transporter is designated Fsy1p because of its homology with the Saccharomyces pastorianus fructose/H(+) symporter Fsy1p. A strain obtained by transformation of the V5 hxt1-7Δ mutant with FSY1 grew well on fructose, but to a much lesser extent on glucose as the sole carbon source. Sugar uptake and symport experiments showed that FSY1 encodes a proton-coupled symporter with high affinity for fructose (K(m) 0.24±0.04mM). Using real-time RT-PCR, we also investigated the expression pattern of FSY1 in EC1118 growing on various carbon sources. FSY1 was repressed by high concentrations of glucose or fructose and was highly expressed on ethanol as the sole carbon source. The characteristics of this transporter indicate that its acquisition could confer a significant advantage to S. cerevisiae during the wine fermentation process. This transporter is a good example of acquisition of a new function in yeast by horizontal gene transfer.}, }
@article {pmid20702568, year = {2011}, author = {Nowack, EC and Vogel, H and Groth, M and Grossman, AR and Melkonian, M and Glöckner, G}, title = {Endosymbiotic gene transfer and transcriptional regulation of transferred genes in Paulinella chromatophora.}, journal = {Molecular biology and evolution}, volume = {28}, number = {1}, pages = {407-422}, doi = {10.1093/molbev/msq209}, pmid = {20702568}, issn = {1537-1719}, mesh = {Amino Acid Sequence ; Amino Acid Substitution ; Amoeba/*genetics ; Animals ; Base Sequence ; Biological Evolution ; Chromatophores/*physiology ; Cyanobacteria/genetics ; Exons ; *Gene Expression Regulation ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Introns ; Molecular Sequence Data ; Symbiosis/*genetics ; *Transcription, Genetic ; }, abstract = {Paulinella chromatophora is a cercozoan amoeba that contains "chromatophores," which are photosynthetic inclusions of cyanobacterial origin. The recent discovery that chromatophores evolved independently of plastids, underwent major genome reduction, and transferred at least two genes to the host nucleus has highlighted P. chromatophora as a model to infer early steps in the evolution of photosynthetic organelles. However, owing to the paucity of nuclear genome sequence data, the extent of endosymbiotic gene transfer (EGT) and host symbiont regulation are currently unknown. A combination of 454 and Illumina next generation sequencing enabled us to generate a comprehensive reference transcriptome data set for P. chromatophora on which we mapped short Illumina cDNA reads generated from cultures from the dark and light phases of a diel cycle. Combined with extensive phylogenetic analyses of the deduced protein sequences, these data revealed that 1) about 0.3-0.8% of the nuclear genes were obtained by EGT compared with 11-14% in the Plantae, 2) transferred genes show a distinct bias in that many encode small proteins involved in photosynthesis and photoacclimation, 3) host cells established control over expression of transferred genes, and 4) not only EGT, but to a minor extent also horizontal gene transfer from organisms that presumably served as food sources, helped to shape the nuclear genome of P. chromatophora. The identification of a significant number of transferred genes involved in photosynthesis and photoacclimation of thylakoid membranes as well as the observed transcriptional regulation of these genes strongly implies import of the encoded gene products into chromatophores, a feature previously thought to be restricted to canonical organelles. Thus, a possible mechanism by which P. chromatophora exerts control over the performance of its newly acquired photosynthetic organelle may involve controlling the expression of nuclear-encoded chromatophore-targeted regulatory components of the thylakoid membranes.}, }
@article {pmid20700492, year = {2010}, author = {Tsuda, ME and Kawata, M}, title = {Evolution of gene regulatory networks by fluctuating selection and intrinsic constraints.}, journal = {PLoS computational biology}, volume = {6}, number = {8}, pages = {}, pmid = {20700492}, issn = {1553-7358}, mesh = {Adaptation, Physiological/genetics ; *Biological Evolution ; Computer Simulation ; Environment ; Gene Expression ; *Gene Regulatory Networks ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genes, Duplicate ; Humans ; *Models, Genetic ; Mutation ; *Selection, Genetic ; }, abstract = {Various characteristics of complex gene regulatory networks (GRNs) have been discovered during the last decade, e.g., redundancy, exponential indegree distributions, scale-free outdegree distributions, mutational robustness, and evolvability. Although progress has been made in this field, it is not well understood whether these characteristics are the direct products of selection or those of other evolutionary forces such as mutational biases and biophysical constraints. To elucidate the causal factors that promoted the evolution of complex GRNs, we examined the effect of fluctuating environmental selection and some intrinsic constraining factors on GRN evolution by using an individual-based model. We found that the evolution of complex GRNs is remarkably promoted by fixation of beneficial gene duplications under unpredictably fluctuating environmental conditions and that some internal factors inherent in organisms, such as mutational bias, gene expression costs, and constraints on expression dynamics, are also important for the evolution of GRNs. The results indicate that various biological properties observed in GRNs could evolve as a result of not only adaptation to unpredictable environmental changes but also non-adaptive processes owing to the properties of the organisms themselves. Our study emphasizes that evolutionary models considering such intrinsic constraining factors should be used as null models to analyze the effect of selection on GRN evolution.}, }
@article {pmid20700376, year = {2010}, author = {Bohlin, L and Göransson, U and Alsmark, C and Wedén, C and Backlund, A}, title = {Natural products in modern life science.}, journal = {Phytochemistry reviews : proceedings of the Phytochemical Society of Europe}, volume = {9}, number = {2}, pages = {279-301}, pmid = {20700376}, issn = {1568-7767}, abstract = {With a realistic threat against biodiversity in rain forests and in the sea, a sustainable use of natural products is becoming more and more important. Basic research directed against different organisms in Nature could reveal unexpected insights into fundamental biological mechanisms but also new pharmaceutical or biotechnological possibilities of more immediate use. Many different strategies have been used prospecting the biodiversity of Earth in the search for novel structure-activity relationships, which has resulted in important discoveries in drug development. However, we believe that the development of multidisciplinary incentives will be necessary for a future successful exploration of Nature. With this aim, one way would be a modernization and renewal of a venerable proven interdisciplinary science, Pharmacognosy, which represents an integrated way of studying biological systems. This has been demonstrated based on an explanatory model where the different parts of the model are explained by our ongoing research. Anti-inflammatory natural products have been discovered based on ethnopharmacological observations, marine sponges in cold water have resulted in substances with ecological impact, combinatory strategy of ecology and chemistry has revealed new insights into the biodiversity of fungi, in depth studies of cyclic peptides (cyclotides) has created new possibilities for engineering of bioactive peptides, development of new strategies using phylogeny and chemography has resulted in new possibilities for navigating chemical and biological space, and using bioinformatic tools for understanding of lateral gene transfer could provide potential drug targets. A multidisciplinary subject like Pharmacognosy, one of several scientific disciplines bridging biology and chemistry with medicine, has a strategic position for studies of complex scientific questions based on observations in Nature. Furthermore, natural product research based on intriguing scientific questions in Nature can be of value to increase the attraction for young students in modern life science.}, }
@article {pmid20695894, year = {2010}, author = {Studholme, DJ and Kemen, E and MacLean, D and Schornack, S and Aritua, V and Thwaites, R and Grant, M and Smith, J and Jones, JD}, title = {Genome-wide sequencing data reveals virulence factors implicated in banana Xanthomonas wilt.}, journal = {FEMS microbiology letters}, volume = {310}, number = {2}, pages = {182-192}, doi = {10.1111/j.1574-6968.2010.02065.x}, pmid = {20695894}, issn = {1574-6968}, support = {BB/E010334/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacterial Proteins/genetics ; Gene Transfer, Horizontal ; Genome, Bacterial/*genetics ; Host Specificity ; Lipopolysaccharides/biosynthesis ; Musa/*microbiology ; Phylogeny ; Recombination, Genetic ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Virulence Factors/*genetics ; Xanthomonas/classification/*genetics/*pathogenicity ; Xanthomonas campestris/classification/*genetics/*pathogenicity ; }, abstract = {Banana Xanthomonas wilt is a newly emerging disease that is currently threatening the livelihoods of millions of farmers in East Africa. The causative agent is Xanthomonas campestris pathovar musacearum (Xcm), but previous work suggests that this pathogen is much more closely related to species Xanthomonas vasicola than to X. campestris. We have generated draft genome sequences for a banana-pathogenic strain of Xcm isolated in Uganda and for a very closely related strain of X. vasicola pathovar vasculorum, originally isolated from sugarcane, that is nonpathogenic on banana. The draft sequences revealed overlapping but distinct repertoires of candidate virulence effectors in the two strains. Both strains encode homologues of the Pseudomonas syringae effectors HopW, HopAF1 and RipT from Ralstonia solanacearum. The banana-pathogenic and non-banana-pathogenic strains also differed with respect to lipopolysaccharide synthesis and type-IV pili, and in at least several thousand single-nucleotide polymorphisms in the core conserved genome. We found evidence of horizontal transfer between X. vasicola and very distantly related bacteria, including members of other divisions of the Proteobacteria. The availability of these draft genomes will be an invaluable tool for further studies aimed at understanding and combating this important disease.}, }
@article {pmid20693155, year = {2010}, author = {Thomas, J and Schaack, S and Pritham, EJ}, title = {Pervasive horizontal transfer of rolling-circle transposons among animals.}, journal = {Genome biology and evolution}, volume = {2}, number = {}, pages = {656-664}, pmid = {20693155}, issn = {1759-6653}, mesh = {Animals ; Base Sequence ; *DNA Transposable Elements ; Evolution, Molecular ; Fishes/genetics ; Gene Dosage ; *Gene Transfer, Horizontal ; Insect Viruses/genetics ; Insecta/virology ; Mammals/genetics ; Reptiles/genetics ; *Retroelements ; Sequence Alignment ; Species Specificity ; }, abstract = {Horizontal transfer (HT) of genes is known to be an important mechanism of genetic innovation, especially in prokaryotes. The impact of HT of transposable elements (TEs), however, has only recently begun to receive widespread attention and may be significant due to their mutagenic potential, inherent mobility, and abundance. Helitrons, also known as rolling-circle transposons, are a distinctive subclass of TE with a unique transposition mechanism. Here, we describe the first evidence for the repeated HT of four different families of Helitrons in an unprecedented array of organisms, including mammals, reptiles, fish, invertebrates, and insect viruses. The Helitrons present in these species have a patchy distribution and are closely related (80-98% sequence identity), despite the deep divergence times among hosts. Multiple lines of evidence indicate the extreme conservation of sequence identity is not due to selection, including the highly fragmented nature of the Helitrons identified and the lack of any signatures of selection at the nucleotide level. The presence of horizontally transferred Helitrons in insect viruses, in particular, suggests that this may represent a potential mechanism of transfer in some taxa. Unlike genes, Helitrons that have horizontally transferred into new host genomes can amplify, in some cases reaching up to several hundred copies and representing a substantial fraction of the genome. Because Helitrons are known to frequently capture and amplify gene fragments, HT of this unique group of DNA transposons could lead to horizontal gene transfer and incur dramatic shifts in the trajectory of genome evolution.}, }
@article {pmid20691395, year = {2010}, author = {Arenas, AF and Osorio-Méndez, JF and Gutierrez, AJ and Gomez-Marin, JE}, title = {Genome-wide survey and evolutionary analysis of trypsin proteases in apicomplexan parasites.}, journal = {Genomics, proteomics &amp; bioinformatics}, volume = {8}, number = {2}, pages = {103-112}, pmid = {20691395}, issn = {2210-3244}, mesh = {Amino Acid Sequence ; Apicomplexa/*enzymology/*genetics ; DNA, Protozoan ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Protozoan ; *Genome, Protozoan ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Trypsin/*genetics ; }, abstract = {Apicomplexa are an extremely diverse group of unicellular organisms that infect humans and other animals. Despite the great advances in combating infectious diseases over the past century, these parasites still have a tremendous social and economic burden on human societies, particularly in tropical and subtropical regions of the world. Proteases from apicomplexa have been characterized at the molecular and cellular levels, and central roles have been proposed for proteases in diverse processes. In this work, 16 new genes encoding for trypsin proteases are identified in 8 apicomplexan genomes by a genome-wide survey. Phylogenetic analysis suggests that these genes were gained through both intracellular gene transfer and vertical gene transfer. Identification, characterization and understanding of the evolutionary origin of protease-mediated processes are crucial to increase the knowledge and improve the strategies for the development of novel chemotherapeutic agents and vaccines.}, }
@article {pmid20691258, year = {2010}, author = {Matsuo, J and Oguri, S and Nakamura, S and Hanawa, T and Fukumoto, T and Hayashi, Y and Kawaguchi, K and Mizutani, Y and Yao, T and Akizawa, K and Suzuki, H and Simizu, C and Matsuno, K and Kamiya, S and Yamaguchi, H}, title = {Ciliates rapidly enhance the frequency of conjugation between Escherichia coli strains through bacterial accumulation in vesicles.}, journal = {Research in microbiology}, volume = {161}, number = {8}, pages = {711-719}, doi = {10.1016/j.resmic.2010.07.004}, pmid = {20691258}, issn = {1769-7123}, mesh = {Acanthamoeba/drug effects/microbiology/*physiology ; Bridged Bicyclo Compounds, Heterocyclic/pharmacology ; *Conjugation, Genetic ; Cycloheximide/pharmacology ; Cytochalasin D/pharmacology ; Cytoplasmic Vesicles/*microbiology ; Dictyostelium/drug effects/microbiology/*physiology ; Drug Resistance, Bacterial ; Escherichia coli/drug effects/*genetics ; *Gene Transfer, Horizontal/drug effects ; Phagocytosis/drug effects ; Polymerase Chain Reaction ; Tetrahymena/drug effects/microbiology/*physiology ; Thiazolidines/pharmacology ; }, abstract = {The mechanism underlying bacterial conjugation through protozoa was investigated. Kanamycin-resistant Escherichia coli SM10λ+ carrying pRT733 with TnphoA was used as donor bacteria and introduced by conjugation into ciprofloxacin-resistant E. coli clinical isolate recipient bacteria. Equal amounts of donor and recipient bacteria were mixed together in the presence or absence of protozoa (ciliates, free-living amoebae, myxamoebae) in Page's amoeba saline for 24 h. Transconjugants were selected with Luria broth agar containing kanamycin and ciprofloxacin. The frequency of conjugation was estimated as the number of transconjugants for each recipient. Conjugation frequency in the presence of ciliates was estimated to be approximately 10[-6], but in the absence of ciliates, or in the presence of other protozoa, it was approximately 10[-8]. Conjugation also occurred in culture of ciliates at least 2 h after incubation. Successful conjugation was confirmed by the polymerase chain reaction. Addition of cycloheximide or latrunculin B resulted in suppression of conjugation. Heat killing the ciliates or bacteria had no effect on conjugation frequency. Co-localization of green fluorescent protein-expressing E. coli and PKH-67-vital-stained E. coli was observed in the same ciliate vesicles, suggesting that both donor and recipient bacteria had accumulated in the same vesicle. In this study, the conjugation frequency of bacteria was found to be significantly higher in vesicles purified from ciliates than those in culture suspension. We conclude that ciliates rapidly enhance the conjugation of E. coli strains through bacterial accumulation in vesicles.}, }
@article {pmid20688752, year = {2010}, author = {Lefébure, T and Bitar, PD and Suzuki, H and Stanhope, MJ}, title = {Evolutionary dynamics of complete Campylobacter pan-genomes and the bacterial species concept.}, journal = {Genome biology and evolution}, volume = {2}, number = {}, pages = {646-655}, pmid = {20688752}, issn = {1759-6653}, support = {N01AI30054/AI/NIAID NIH HHS/United States ; }, mesh = {Campylobacter coli/*genetics ; Campylobacter jejuni/*genetics ; Chromosome Mapping ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; }, abstract = {Defining bacterial species and understanding the relative cohesiveness of different components of their genomes remains a fundamental problem in microbiology. Bacterial species tend to be comprised of both a set of core and dispensable genes, with the sum of these two components forming the species pan-genome. The role of the core and dispensable genes in defining bacterial species and the question of whether pan-genomes are finite or infinite remain unclear. Here we demonstrate, through the analysis of 96 genome sequences derived from two closely related sympatric sister species of pathogenic bacteria (Campylobacter coli and C. jejuni), that their pan-genome is indeed finite and that there are unique and cohesive features to each of their genomes defining their genomic identity. The two species have a similar pan-genome size; however, C. coli has acquired a larger core genome and each species has evolved a number of species-specific core genes, possibly reflecting different adaptive strategies. Genome-wide assessment of the level of lateral gene transfer within and between the two sister species, as well as within the core and non-core genes, demonstrates a resistance to interspecies recombination in the core genome of the two species and therefore provides persuasive support for the core genome hypothesis for bacterial species.}, }
@article {pmid20686601, year = {2010}, author = {Bloemendaal, AL and Brouwer, EC and Fluit, AC}, title = {Methicillin resistance transfer from Staphylocccus epidermidis to methicillin-susceptible Staphylococcus aureus in a patient during antibiotic therapy.}, journal = {PloS one}, volume = {5}, number = {7}, pages = {e11841}, pmid = {20686601}, issn = {1932-6203}, mesh = {Anti-Bacterial Agents/therapeutic use ; Gene Transfer, Horizontal/genetics ; Humans ; Methicillin Resistance/*genetics ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Staphylococcal Infections/drug therapy/*microbiology ; Staphylococcus aureus/classification/*genetics/pathogenicity ; Staphylococcus epidermidis/classification/drug effects/*genetics/pathogenicity ; }, abstract = {BACKGROUND: The mecA gene, encoding methicillin resistance in staphylococci, is located on a mobile genetic element called Staphylococcal Cassette Chromosome mec (SCCmec). Horizontal, interspecies transfer of this element could be an important factor in the dissemination of methicillin-resistant S. aureus (MRSA). Previously, we reported the isolation of a closely related methicillin-susceptible Staphylococcus aureus (MSSA), MRSA and potential SCCmec donor Staphylococcus epidermidis isolate from the same patient. Based on fingerprint techniques we hypothesized that the S. epidermidis had transferred SCCmec to the MSSA to become MRSA. The aim of this study was to show that these isolates form an isogenic pair and that interspecies horizontal SCCmec transfer occurred.<br><br>METHODOLOGY/RESULTS: Whole genome sequencing of both isolates was performed and for the MSSA gaps were closed by conventional sequencing. The SCCmec of the S. epidermidis was also sequenced by conventional methods. The results show no difference in nucleotide sequence between the two isolates except for the presence of SCCmec in the MRSA. The SCCmec of the S. epidermidis and the MRSA are identical except for a single nucleotide in the ccrB gene, which results in a valine to alanine substitution. The main difference with the closely related EMRSA-16 is the presence of SaPI2 encoding toxic shock syndrome toxin and exfoliative toxin A in the MSSA-MRSA pair. No transfer of SCCmec from the S. epidermidis to the MSSA could be demonstrated in vitro.<br><br>CONCLUSION: The MSSA and MRSA form an isogenic pair except for SCCmec. This strongly supports our hypothesis that the MRSA was derived from the MSSA by interspecies horizontal transfer of SCCmec from S. epidermidis O7.1.}, }
@article {pmid20680561, year = {2010}, author = {Fecskeová, L and Piknová, M and Javorský, P and Pristas, P}, title = {Lactate dehydrogenase gene variability among predominant lactate utilizing ruminal bacteria.}, journal = {Folia microbiologica}, volume = {55}, number = {4}, pages = {315-318}, pmid = {20680561}, issn = {1874-9356}, mesh = {Animals ; Bacterial Proteins/*genetics ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; *Genetic Variation ; L-Lactate Dehydrogenase/*genetics ; Lactic Acid/*metabolism ; Megasphaera/*enzymology/genetics/isolation &amp; purification/metabolism ; Molecular Sequence Data ; Phylogeny ; Point Mutation ; Rumen/*microbiology ; Selenomonas/*enzymology/genetics/isolation &amp; purification/metabolism ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {The inter- and intraspecies variability of lactate dehydrogenase (ldh) gene was determined among the predominant ruminal lactate utilizing bacteria. Nearly complete nucleotide sequences of ldh gene, encoding NAD-dependent lactate dehydrogenase of three Megasphaera elsdenii and six Selenomonas ruminantium strains, were obtained and compared. Phylogenetic analyses revealed a limited variability between the ldh sequences studied. The majority of differences observed were silent mutations at the 3rd position of codons. Surprisingly, the intraspecies diversity of the ldh gene among S. ruminantium isolates was higher than the interspecies level between S. ruminantium and M. elsdenii, which strongly suggests the possibility of acquisition of this gene by horizontal gene transfer.}, }
@article {pmid20679508, year = {2010}, author = {Soledad Ramírez, M and Merkier, AK and Almuzara, M and Vay, C and Centrón, D}, title = {Reservoir of antimicrobial resistance determinants associated with horizontal gene transfer in clinical isolates of the genus Shewanella.}, journal = {Antimicrobial agents and chemotherapy}, volume = {54}, number = {10}, pages = {4516-4517}, pmid = {20679508}, issn = {1098-6596}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal/*genetics ; Molecular Sequence Data ; Shewanella/drug effects/*genetics ; }, }
@article {pmid20679093, year = {2011}, author = {Davis, JJ and Olsen, GJ}, title = {Characterizing the native codon usages of a genome: an axis projection approach.}, journal = {Molecular biology and evolution}, volume = {28}, number = {1}, pages = {211-221}, pmid = {20679093}, issn = {1537-1719}, mesh = {Algorithms ; Bacillus anthracis/genetics ; Base Composition/genetics ; *Codon ; Escherichia coli/genetics ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genes, Archaeal ; *Genes, Bacterial ; *Genome, Bacterial ; Pseudomonas aeruginosa/genetics ; }, abstract = {Codon usage can provide insights into the nature of the genes in a genome. Genes that are "native" to a genome (have not been recently acquired by horizontal transfer) range in codon usage from a low-bias "typical" usage to a more biased "high-expression" usage characteristic of genes encoding abundant proteins. Genes that differ from these native codon usages are candidates for foreign genes that have been recently acquired by horizontal gene transfer. In this study, we present a method for characterizing the codon usages of native genes--both typical and highly expressed--within a genome. Each gene is evaluated relative to a half line (or axis) in a 59D space of codon usage. The axis begins at the modal codon usage, the usage that matches the largest number of genes in the genome, and it passes through a point representing the codon usage of a set of genes with expression-related bias. A gene whose codon usage matches (does not significantly differ from) a point on this axis is a candidate native gene, and the location of its projection onto the axis provides a general estimate of its expression level. A gene that differs significantly from all points on the axis is a candidate foreign gene. This automated approach offers significant improvements over existing methods. We illustrate this by analyzing the genomes of Pseudomonas aeruginosa PAO1 and Bacillus anthracis A0248, which can be difficult to analyze with commonly used methods due to their biased base compositions. Finally, we use this approach to measure the proportion of candidate foreign genes in 923 bacterial and archaeal genomes. The organisms with the most homogeneous genomes (containing the fewest candidate foreign genes) are mostly endosymbionts and parasites, though with exceptions that include Pelagibacter ubique and Beutenbergia cavernae. The organisms with the most heterogeneous genomes (containing the most candidate foreign genes) include members of the genera Bacteroides, Corynebacterium, Desulfotalea, Neisseria, Xylella, and Thermobaculum.}, }
@article {pmid20678596, year = {2010}, author = {Raven, PH}, title = {Does the use of transgenic plants diminish or promote biodiversity?.}, journal = {New biotechnology}, volume = {27}, number = {5}, pages = {528-533}, doi = {10.1016/j.nbt.2010.07.018}, pmid = {20678596}, issn = {1876-4347}, mesh = {Animals ; *Biodiversity ; Crops, Agricultural/*genetics ; *Ecosystem ; Environment ; Gene Flow ; Gene Transfer, Horizontal ; Humans ; Plant Weeds/genetics ; Plants, Genetically Modified/*genetics ; }, abstract = {The protection of biodiversity and of ecosystem services ought to be a top priority, taken into consideration in the course of all human activities, because we depend on it fully now and for the future. In this context, we note that the ecological problems related to the cultivation of GE crops fail to differ in any fundamental way from the ecological problems associated with agriculture in general, except that they usually involve the application of much lower quantities of chemicals and thus tend to leave the environments in and adjacent to where they are grown in better condition than do the conventional ones. Higher productivity on cultivated lands, which is one outcome of growing GE crops, protects biodiversity by sparing lands not intensively cultivated, whereas relatively non-productive agriculture practised is highly destructive to biodiversity, since it consumes more land in an often destructive way, even though more biodiversity may be preserved among the crops themselves than in industrialized, large fields, especially if hedgerows and woodlands are not encouraged in near proximity. The major preservation of biodiversity, however, does not take place among crops! If weeds are present that are closely related to the crops, they may acquire immunity to the effects from which the crops were protected and be more difficult to control among them. The production of superweeds as a result of hybridization between cultivated crops and their wild relatives is essentially a myth. The definition of 'organic' production in the U.S. and elsewhere unjustifiably rules out GE crops, often in such a way as to damage the environment more than would be the case otherwise. Unless the definition of 'organic' is a problem, or close relatives to the crops are weedy among them, there seems to be essentially no ecological risk involved in growing GE crops.}, }
@article {pmid20678216, year = {2010}, author = {Dlugosch, KM and Barker, MS and Rieseberg, LH}, title = {NU-IN: Nucleotide evolution and input module for the EvolSimulator genome simulation platform.}, journal = {BMC research notes}, volume = {3}, number = {}, pages = {217}, pmid = {20678216}, issn = {1756-0500}, abstract = {BACKGROUND: There is increasing demand to test hypotheses that contrast the evolution of genes and gene families among genomes, using simulations that work across these levels of organization. The EvolSimulator program was developed recently to provide a highly flexible platform for forward simulations of amino acid evolution in multiple related lineages of haploid genomes, permitting copy number variation and lateral gene transfer. Synonymous nucleotide evolution is not currently supported, however, and would be highly advantageous for comparisons to full genome, transcriptome, and single nucleotide polymorphism (SNP) datasets. In addition, EvolSimulator creates new genomes for each simulation, and does not allow the input of user-specified sequences and gene family information, limiting the incorporation of further biological realism and/or user manipulations of the data.<br><br>FINDINGS: We present modified C++ source code for the EvolSimulator platform, which we provide as the extension module NU-IN. With NU-IN, synonymous and non-synonymous nucleotide evolution is fully implemented, and the user has the ability to use real or previously-simulated sequence data to initiate a simulation of one or more lineages. Gene family membership can be optionally specified, as well as gene retention probabilities that model biased gene retention. We provide PERL scripts to assist the user in deriving this information from previous simulations. We demonstrate the features of NU-IN by simulating genome duplication (polyploidy) in the presence of ongoing copy number variation in an evolving lineage. This example is initiated with real genomic data, and produces output that we analyse directly with existing bioinformatic pipelines.<br><br>CONCLUSIONS: The NU-IN extension module is a publicly available open source software (GNU GPLv3 license) extension to EvolSimulator. With the NU-IN module, users are now able to simulate both drift and selection at the nucleotide, amino acid, copy number, and gene family levels across sets of related genomes, for user-specified starting sequences and associated parameters. These features can be used to generate simulated genomic datasets under an extremely broad array of conditions, and with a high degree of biological realism.}, }
@article {pmid20676885, year = {2010}, author = {Martins, M and Dairou, J and Rodrigues-Lima, F and Dupret, JM and Silar, P}, title = {Insights into the phylogeny or arylamine N-acetyltransferases in fungi.}, journal = {Journal of molecular evolution}, volume = {71}, number = {2}, pages = {141-152}, pmid = {20676885}, issn = {1432-1432}, mesh = {Animals ; Arylamine N-Acetyltransferase/*genetics ; Ascomycota/enzymology/genetics ; Computational Biology ; Fungal Proteins/genetics ; Fungi/*enzymology/*genetics ; Gene Transfer, Horizontal/physiology ; Genome, Fungal ; Likelihood Functions ; *Phylogeny ; }, abstract = {Previous studies have shown that Eumycetes fungi can acylate arylamine thanks to arylamine N-acetyltransferases, xenobiotic-metabolizing enzymes also found in animals and bacteria. In this article, we present the results of mining 96 available fungal genome sequences for arylamine N-acetyltransferase genes and propose their phylogeny. The filamentous Pezizomycotina are shown to possess many putative N-acetyltransferases, whilst these are often lacking in other fungal groups. The evolution of the N-acetyltransferases is best explained by the presence of at least one gene in the opisthokont ancestor of the fungi and animal kingdoms, followed by recurrent gene losses and gene duplications. A possible horizontal gene transfer event may have occurred from bacteria to the basidiomycetous yeast Malassezia globosa.}, }
@article {pmid20676772, year = {2011}, author = {Green, BR}, title = {After the primary endosymbiosis: an update on the chromalveolate hypothesis and the origins of algae with Chl c.}, journal = {Photosynthesis research}, volume = {107}, number = {1}, pages = {103-115}, pmid = {20676772}, issn = {1573-5079}, mesh = {Chlorophyll/*genetics/metabolism ; Chloroplasts/genetics ; Eukaryota/*classification/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Plastid/physiology ; Genomics ; Photosynthesis/genetics ; Phylogeny ; Plastids/*genetics ; Rhodophyta/genetics ; Symbiosis/*genetics ; Time Factors ; }, abstract = {The chromalveolate hypothesis proposed by Cavalier-Smith (J Euk Microbiol 46:347-366, 1999) suggested that all the algae with chlorophyll c (heterokonts, haptophytes, cryptophytes, and dinoflagellates), as well as the ciliates, apicomplexans, oomycetes, and other non-photosynthetic relatives, shared a common ancestor that acquired a chloroplast by secondary endosymbiosis of a red alga. Much of the evidence from plastid and nuclear genomes supports a red algal origin for plastids of the photosynthetic lineages, but the number of secondary endosymbioses and the number of plastid losses have not been resolved. The issue is complicated by the fact that nuclear genomes are mosaics of genes acquired over a very long time period, not only by vertical descent but also by endosymbiotic and horizontal gene transfer. Phylogenomic analysis of the available whole-genome data has suggested major alterations to our view of eukaryotic evolution, and given rise to alternative models. The next few years may see even more changes once a more representative collection of sequenced genomes becomes available.}, }
@article {pmid20676376, year = {2010}, author = {Marri, PR and Paniscus, M and Weyand, NJ and Rendón, MA and Calton, CM and Hernández, DR and Higashi, DL and Sodergren, E and Weinstock, GM and Rounsley, SD and So, M}, title = {Genome sequencing reveals widespread virulence gene exchange among human Neisseria species.}, journal = {PloS one}, volume = {5}, number = {7}, pages = {e11835}, pmid = {20676376}, issn = {1932-6203}, support = {R01 AI068033/AI/NIAID NIH HHS/United States ; U54 HG004968/HG/NHGRI NIH HHS/United States ; R01 AI068033-01/AI/NIAID NIH HHS/United States ; U54HG004968/HG/NHGRI NIH HHS/United States ; }, mesh = {Gene Transfer, Horizontal/*genetics ; Genome, Bacterial/*genetics ; Humans ; Neisseria/*genetics/pathogenicity ; Neisseria gonorrhoeae/genetics/pathogenicity ; Neisseria lactamica/genetics/pathogenicity ; Neisseria meningitidis/genetics/pathogenicity ; Virulence/*genetics ; }, abstract = {Commensal bacteria comprise a large part of the microbial world, playing important roles in human development, health and disease. However, little is known about the genomic content of commensals or how related they are to their pathogenic counterparts. The genus Neisseria, containing both commensal and pathogenic species, provides an excellent opportunity to study these issues. We undertook a comprehensive sequencing and analysis of human commensal and pathogenic Neisseria genomes. Commensals have an extensive repertoire of virulence alleles, a large fraction of which has been exchanged among Neisseria species. Commensals also have the genetic capacity to donate DNA to, and take up DNA from, other Neisseria. Our findings strongly suggest that commensal Neisseria serve as reservoirs of virulence alleles, and that they engage extensively in genetic exchange.}, }
@article {pmid20675473, year = {2010}, author = {Nguyen, KT and Piastro, K and Gray, TA and Derbyshire, KM}, title = {Mycobacterial biofilms facilitate horizontal DNA transfer between strains of Mycobacterium smegmatis.}, journal = {Journal of bacteriology}, volume = {192}, number = {19}, pages = {5134-5142}, pmid = {20675473}, issn = {1098-5530}, support = {1T32AI055429/AI/NIAID NIH HHS/United States ; R56 AI080694/AI/NIAID NIH HHS/United States ; AI042308/AI/NIAID NIH HHS/United States ; R56AI080694/AI/NIAID NIH HHS/United States ; AI042308-08S1/AI/NIAID NIH HHS/United States ; T32 AI055429/AI/NIAID NIH HHS/United States ; R01 AI042308/AI/NIAID NIH HHS/United States ; }, mesh = {Biofilms/*growth &amp; development ; Conjugation, Genetic/genetics/physiology ; DNA, Bacterial/*genetics ; Gene Transfer, Horizontal/*genetics ; Genetic Complementation Test ; Mutagenesis ; Mutagenesis, Site-Directed ; Mycobacterium smegmatis/*genetics/*growth &amp; development ; }, abstract = {Conjugal transfer of chromosomal DNA between strains of Mycobacterium smegmatis occurs by a novel mechanism. In a transposon mutagenesis screen, three transfer-defective insertions were mapped to the lsr2 gene of the donor strain mc(2)155. Because lsr2 encodes a nonspecific DNA-binding protein, mutations of lsr2 give rise to a variety of phenotypes, including an inability to form biofilms. In this study, we show that efficient DNA transfer between strains of M. smegmatis occurs in a mixed biofilm and that the process requires expression of lsr2 in the donor but not in the recipient strain. Testing cells from different strata of standing cultures showed that transfer occurred predominantly at the biofilm air-liquid interface, as other strata containing higher cell densities produced very few transconjugants. These data suggest that the biofilm plays a role beyond mere facilitation of cell-cell contact. Surprisingly, we found that under standard assay conditions the recipient strain does not form a biofilm. Taking these results together, we conclude that for transfer to occur, the recipient strain is actively recruited into the biofilm. In support of this idea, we show that donor and recipient cells are present in almost equal numbers in biofilms that produce transconjugants. Our demonstration of genetic exchange between mycobacteria in a mixed biofilm suggests that conjugation occurs in the environment. Since biofilms are considered to be the predominant natural microhabitat for bacteria, our finding emphasizes the importance of studying biological and physical processes that occur between cells in mixed biofilms.}, }
@article {pmid20674423, year = {2010}, author = {Boyd, CA and Shennan, DB}, title = {Breast milk and gene delivery: is lysinuric protein intolerance an exemplar?.}, journal = {Molecular genetics and metabolism}, volume = {101}, number = {2-3}, pages = {296}, doi = {10.1016/j.ymgme.2010.07.002}, pmid = {20674423}, issn = {1096-7206}, mesh = {Amino Acid Metabolism, Inborn Errors/*genetics ; Exosomes/*physiology ; Female ; *Gene Transfer, Horizontal ; Humans ; Lysine/*urine ; Milk, Human/*metabolism ; }, }
@article {pmid20668530, year = {2010}, author = {McMillan, DJ and Bessen, DE and Pinho, M and Ford, C and Hall, GS and Melo-Cristino, J and Ramirez, M}, title = {Population genetics of Streptococcus dysgalactiae subspecies equisimilis reveals widely dispersed clones and extensive recombination.}, journal = {PloS one}, volume = {5}, number = {7}, pages = {e11741}, pmid = {20668530}, issn = {1932-6203}, support = {R01 AI065572/AI/NIAID NIH HHS/United States ; R01 GM060793/GM/NIGMS NIH HHS/United States ; GM-060793/GM/NIGMS NIH HHS/United States ; AI-065572/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Phylogeny ; Recombination, Genetic/*genetics ; Streptococcus/classification/*genetics ; }, abstract = {BACKGROUND: Streptococcus dysgalactiae subspecies equisimilis (SDSE) is an emerging global pathogen that can colonize and infect humans. Although most SDSE isolates possess the Lancefield group G carbohydrate, a significant minority have the group C carbohydrate. Isolates are further sub-typed on the basis of differences within the emm gene. To gain a better understanding of their molecular epidemiology and evolutionary relationships, multilocus sequence typing (MLST) analysis was performed on SDSE isolates collected from Australia, Europe and North America.<br><br>The 178 SDSE isolates, representing 37 emm types, segregate into 80 distinct sequence types (STs) that form 17 clonal complexes (CCs). Eight STs recovered from all three continents account for >50% of the isolates. Thus, a small number of STs are highly prevalent and have a wide geographic distribution. Both ST and CC strongly correlate with group carbohydrate. In contrast, eleven STs were associated with >1 emm type, suggestive of recombinational replacements involving the emm gene; furthermore, 35% of the emm types are associated with genetically distant STs. Data also reveal a history of extensive inter- and intra-species recombination involving the housekeeping genes used for MLST. Sequence analysis of single locus variants identified through goeBURST indicates that genetic change mediated by recombination occurred approximately 4.4 times more frequently than by point mutation.<br><br>CONCLUSIONS/SIGNIFICANCE: A few genetic lineages with an intercontinental distribution dominate among SDSE causing infections in humans. The distinction between group C and G isolates reflects recent evolution, and no long-term genetic isolation between them was found. Lateral gene transfer and recombination involving housekeeping genes and the emm gene are important mechanisms driving genetic variability in the SDSE population.}, }
@article {pmid20663122, year = {2010}, author = {Filipowicz, N and Renner, SS}, title = {The worldwide holoparasitic Apodanthaceae confidently placed in the Cucurbitales by nuclear and mitochondrial gene trees.}, journal = {BMC evolutionary biology}, volume = {10}, number = {}, pages = {219}, pmid = {20663122}, issn = {1471-2148}, mesh = {Australia ; Cell Nucleus/genetics ; Chile ; Cucurbitaceae/*classification/*genetics ; DNA, Mitochondrial/genetics ; DNA, Plant/genetics ; *Evolution, Molecular ; Genes, Mitochondrial ; Iran ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; United States ; }, abstract = {BACKGROUND: Of the c. 450 families of flowering plants, only two are left "unplaced" in the most recent APG classification of angiosperms. One of these is the Apodanthaceae, a clade of c. 19 holoparasitic species in two or three genera occurring in North and South America, Africa, the Near East, and Australia. Because of lateral gene transfer between Apodanthaceae and their hosts it has been difficult to infer the family's true closest relatives.<br><br>RESULTS: Here we report a phylogenetic analysis of 16 accessions representing six species of Apodanthaceae from the United States, Chile, Iran, and Australia, using the mitochondrial matR gene and the nuclear 18S gene. Data matrices include 190 matR sequences from up to 95 families in 39 orders of flowering plants and 197 18S sequences from 101 families representing the 16 orders of rosids. Analyses were performed at the nucleotide and at the amino acid level. Both gene trees agree with angiosperm phylogenies found in other studies using more genes. Apodanthaceae and the seven families of the order Cucurbitales form a clade with 100% bootstrap support from matR and 56% from 18 S. In addition, the Apodanthaceae and Cucurbitales matR gene sequences uniquely share two non-synonymous codon changes and one synonymous change, as well as a codon insertion, already found by Barkman et al. (2007).<br><br>CONCLUSIONS: Apodanthaceae belong in the Cucurbitales with which they share inferior ovaries, parietal placentation and a dioecious mating system, traits that are ancestral in Cucurbitales and which can now be interpreted as possible synapomorphies of an enlarged order Cucurbitales. The occurrence of Apodanthaceae in the Americas, Africa, the Near East, and Australia, and their adaptation to distantly related host species in the Fabaceae and Salicaceae suggest a long evolutionary history.}, }
@article {pmid20662928, year = {2010}, author = {Hazen, TH and Pan, L and Gu, JD and Sobecky, PA}, title = {The contribution of mobile genetic elements to the evolution and ecology of Vibrios.}, journal = {FEMS microbiology ecology}, volume = {74}, number = {3}, pages = {485-499}, doi = {10.1111/j.1574-6941.2010.00937.x}, pmid = {20662928}, issn = {1574-6941}, mesh = {Bacteriophages/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genomic Islands ; *Interspersed Repetitive Sequences ; Metagenomics ; Phylogeny ; Plasmids ; Vibrio/*genetics/virology ; }, abstract = {An increase in the frequency of seafood-borne gastroenteritis in humans and Vibrio-related disease of fish and invertebrates has generated interest in the ecology of disease-causing Vibrios and the mechanisms driving their evolution. Genome sequencing studies have indicated a substantial contribution of horizontal gene transfer (HGT) to the evolution of Vibrios. Of particular interest is the contribution of HGT to the evolution of Vibrios pathogens and the adaptation of disease-causing Vibrios for survival in diverse environments. In this review, we discuss the diversity and distribution of mobile genetic elements (MGEs) isolated from Vibrios and the contribution of these elements to the expansion of the ecological and pathogenic niches of the host strain. Much of the research on Vibrio MGEs has focused on understanding phages and plasmids and we will primarily discuss the evolution of these elements and also briefly highlight the other diverse elements characterized from Vibrios, which includes genomic islands and conjugative elements.}, }
@article {pmid20661289, year = {2010}, author = {Brugger, SD and Frey, P and Aebi, S and Hinds, J and Mühlemann, K}, title = {Multiple colonization with S. pneumoniae before and after introduction of the seven-valent conjugated pneumococcal polysaccharide vaccine.}, journal = {PloS one}, volume = {5}, number = {7}, pages = {e11638}, pmid = {20661289}, issn = {1932-6203}, support = {/WT_/Wellcome Trust/United Kingdom ; 086547/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Adolescent ; Adult ; Child ; Child, Preschool ; Female ; Humans ; Male ; Middle Aged ; Nasopharynx/microbiology ; Pneumococcal Infections/*immunology/*microbiology ; Pneumococcal Vaccines/administration &amp; dosage/*immunology ; Serotyping ; Streptococcus pneumoniae/*immunology ; Vaccines, Conjugate/administration &amp; dosage/*immunology ; Young Adult ; }, abstract = {BACKGROUND: Simultaneous carriage of more than one strain of Streptococcus pneumoniae promotes horizontal gene transfer events and may lead to capsule switch and acquisition of antibiotic resistance. We studied the epidemiology of cocolonization with S. pneumoniae before and after introduction of the seven-valent conjugated pneumococcal vaccine (PCV7).<br><br>METHODOLOGY: Nasopharyngeal swabs (n 1120) were collected from outpatients between 2004 and 2009 within an ongoing nationwide surveillance program. Cocolonization was detected directly from swabs by restriction fragment length polymorphism (RFLP) analysis. Serotypes were identified by agglutination, multiplex PCR and microarray.<br><br>PRINCIPAL FINDINGS: Rate of multiple colonization remained stable up to three years after PCV7 introduction. Cocolonization was associated with serotypes of low carriage prevalence in the prevaccine era. Pneumococcal colonization density was higher in cocolonized samples and cocolonizing strains were present in a balanced ratio (median 1.38). Other characteristics of cocolonization were a higher frequency at young age, but no association with recurrent acute otitis media, recent antibiotic exposure, day care usage and PCV7 vaccination status.<br><br>CONCLUSIONS: Pneumococcal cocolonization is dominated by serotypes of low carriage prevalence in the prevaccine era, which coexist in the nasopharynx. Emergence of such previously rare serotypes under vaccine selection pressure may promote cocolonization in the future.}, }
@article {pmid20660776, year = {2010}, author = {Sangari, FJ and Pérez-Gil, J and Carretero-Paulet, L and García-Lobo, JM and Rodríguez-Concepción, M}, title = {A new family of enzymes catalyzing the first committed step of the methylerythritol 4-phosphate (MEP) pathway for isoprenoid biosynthesis in bacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {32}, pages = {14081-14086}, pmid = {20660776}, issn = {1091-6490}, mesh = {Aldose-Ketose Isomerases/*metabolism ; Bacteria/*metabolism ; Enzymes ; Erythritol/*analogs &amp; derivatives/metabolism ; *Metabolic Networks and Pathways ; Multienzyme Complexes/*metabolism ; Oxidoreductases/*metabolism ; Pentosephosphates/metabolism ; Sugar Phosphates/*metabolism ; Terpenes/*metabolism ; }, abstract = {Isoprenoids are a large family of compounds with essential functions in all domains of life. Most eubacteria synthesize their isoprenoids using the methylerythritol 4-phosphate (MEP) pathway, whereas a minority uses the unrelated mevalonate pathway and only a few have both. Interestingly, Brucella abortus and some other bacteria that only use the MEP pathway lack deoxyxylulose 5-phosphate (DXP) reductoisomerase (DXR), the enzyme catalyzing the NADPH-dependent production of MEP from DXP in the first committed step of the pathway. Fosmidomycin, a specific competitive inhibitor of DXR, inhibited growth of B. abortus cells expressing the Escherichia coli GlpT transporter (required for fosmidomycin uptake), confirming that a DXR-like (DRL) activity exists in these bacteria. The B. abortus DRL protein was found to belong to a family of uncharacterized proteins similar to homoserine dehydrogenase. Subsequent experiments confirmed that DRL and DXR catalyze the same biochemical reaction. DRL homologues shown to complement a DXR-deficient E. coli strain grouped within the same phylogenetic clade. The scattered taxonomic distribution of sequences from the DRL clade and the occurrence of several paralogues in some bacterial strains might be the result of lateral gene transfer and lineage-specific gene duplications and/or losses, similar to that described for typical mevalonate and MEP pathway genes. These results reveal the existence of a novel class of oxidoreductases catalyzing the conversion of DXP into MEP in prokaryotic cells, underscoring the biochemical and genetic plasticity achieved by bacteria to synthesize essential compounds such as isoprenoids.}, }
@article {pmid20657649, year = {2010}, author = {Larson, EM and Idnurm, A}, title = {Two origins for the gene encoding alpha-isopropylmalate synthase in fungi.}, journal = {PloS one}, volume = {5}, number = {7}, pages = {e11605}, pmid = {20657649}, issn = {1932-6203}, mesh = {2-Isopropylmalate Synthase/classification/*genetics ; Genes, Fungal/*genetics/physiology ; Genetic Complementation Test ; Phycomyces/*enzymology/genetics ; Phylogeny ; }, abstract = {BACKGROUND: The biosynthesis of leucine is a biochemical pathway common to prokaryotes, plants and fungi, but absent from humans and animals. The pathway is a proposed target for antimicrobial therapy.<br><br>Here we identified the leuA gene encoding alpha-isopropylmalate synthase in the zygomycete fungus Phycomyces blakesleeanus using a genetic mapping approach with crosses between wild type and leucine auxotrophic strains. To confirm the function of the gene, Phycomyces leuA was used to complement the auxotrophic phenotype exhibited by mutation of the leu3+ gene of the ascomycete fungus Schizosaccharomyces pombe. Phylogenetic analysis revealed that the leuA gene in Phycomyces, other zygomycetes, and the chytrids is more closely related to homologs in plants and photosynthetic bacteria than ascomycetes or basidiomycetes, and suggests that the Dikarya have acquired the gene more recently.<br><br>CONCLUSIONS/SIGNIFICANCE: The identification of leuA in Phycomyces adds to the growing body of evidence that some primary metabolic pathways or parts of them have arisen multiple times during the evolution of fungi, probably through horizontal gene transfer events.}, }
@article {pmid20657646, year = {2010}, author = {Tang, K and Huang, H and Jiao, N and Wu, CH}, title = {Phylogenomic analysis of marine Roseobacters.}, journal = {PloS one}, volume = {5}, number = {7}, pages = {e11604}, pmid = {20657646}, issn = {1932-6203}, support = {U01 HG002712/HG/NHGRI NIH HHS/United States ; U01-HG02712/HG/NHGRI NIH HHS/United States ; }, mesh = {Genome, Bacterial/genetics/physiology ; Genomics/*methods ; *Phylogeny ; Roseobacter/*genetics/*metabolism ; Sulfonium Compounds/metabolism ; Vitamin B 12/metabolism ; }, abstract = {BACKGROUND: Members of the Roseobacter clade which play a key role in the biogeochemical cycles of the ocean are diverse and abundant, comprising 10-25% of the bacterioplankton in most marine surface waters. The rapid accumulation of whole-genome sequence data for the Roseobacter clade allows us to obtain a clearer picture of its evolution.<br><br>In this study about 1,200 likely orthologous protein families were identified from 17 Roseobacter bacteria genomes. Functional annotations for these genes are provided by iProClass. Phylogenetic trees were constructed for each gene using maximum likelihood (ML) and neighbor joining (NJ). Putative organismal phylogenetic trees were built with phylogenomic methods. These trees were compared and analyzed using principal coordinates analysis (PCoA), approximately unbiased (AU) and Shimodaira-Hasegawa (SH) tests. A core set of 694 genes with vertical descent signal that are resistant to horizontal gene transfer (HGT) is used to reconstruct a robust organismal phylogeny. In addition, we also discovered the most likely 109 HGT genes. The core set contains genes that encode ribosomal apparatus, ABC transporters and chaperones often found in the environmental metagenomic and metatranscriptomic data. These genes in the core set are spread out uniformly among the various functional classes and biological processes.<br><br>CONCLUSIONS/SIGNIFICANCE: Here we report a new multigene-derived phylogenetic tree of the Roseobacter clade. Of particular interest is the HGT of eleven genes involved in vitamin B12 synthesis as well as key enzynmes for dimethylsulfoniopropionate (DMSP) degradation. These aquired genes are essential for the growth of Roseobacters and their eukaryotic partners.}, }
@article {pmid20656064, year = {2010}, author = {Litrup, E and Torpdahl, M and Malorny, B and Huehn, S and Christensen, H and Nielsen, EM}, title = {Association between phylogeny, virulence potential and serovars of Salmonella enterica.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {10}, number = {7}, pages = {1132-1139}, doi = {10.1016/j.meegid.2010.07.015}, pmid = {20656064}, issn = {1567-7257}, mesh = {Animals ; Bacterial Typing Techniques ; DNA, Bacterial/genetics ; Denmark/epidemiology ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; Multilocus Sequence Typing ; Oligonucleotide Array Sequence Analysis/methods ; *Phylogeny ; Salmonella Infections/microbiology ; Salmonella Infections, Animal/epidemiology/microbiology ; Salmonella enterica/classification/*genetics/*pathogenicity ; Serotyping ; Virulence ; }, abstract = {Salmonella enterica subsp. enterica is one of the leading causes of zoonotic food-borne disease worldwide. The consequence of these infections is a serious impact on economics of the society in the form of lost productivity and expenses for medical care. The objective of this study was to analyze the difference in genomic content between selected serovars, especially the content of pathogenicity genes and this was done with a DNA microarray. Furthermore, we investigated the phylogenetic relationship between serovars using multilocus sequence typing (MLST). We chose serovars Typhimurium and Enteritidis as they are responsible for 75% of human infections in Europe. Additionally, we included serovars Derby, Dublin, Saintpaul, 4,5,12:i:-, Java and 4,5,12:b:- which are suspected to have different degrees of virulence to humans. MLST analysis clustered strains according to serovar with the exception of Java and Derby. DNA microarray clustered strains according to serovar and serogroup except for serovar 4,5,12:b:-. Differences in content of pathogenicity related genes between serovars with various host preferences and virulence towards humans were not observed. However, our strains from the supposedly less virulent serovar Derby lacked a combination of genes important for virulence. It might be speculated that other serovars can sustain their pathogenicity lacking one or two of these genes, whereas lack of many virulence genes will result in reduced virulence. A partial lack of concordance between MLST and microarray was found and this can be explained by the underlying data. On one hand, microarray data include highly variable regions which are known to be involved in horizontal gene transfer. On the other hand, MLST data is restricted to seven sequences and disregards contribution of horizontally acquired genes when evaluating evolution. The DNA microarray and MLST analysis complement each other giving a clearer image of evolution of these serovars and, furthermore, a visualization of the horizontally acquired genes.}, }
@article {pmid20651855, year = {2010}, author = {Sorger, GJ and Quinn, JS}, title = {Tetracycline-resistant coliforms in the effluent of the main sewage treatment plant in Hamilton, Ontario - do they have a common ancestral strain?.}, journal = {Canadian journal of microbiology}, volume = {56}, number = {7}, pages = {558-568}, doi = {10.1139/w10-041}, pmid = {20651855}, issn = {1480-3275}, mesh = {Amino Acid Sequence ; Anti-Bacterial Agents/pharmacology ; Bacteria/*drug effects/*genetics/isolation &amp; purification/metabolism ; Bacterial Proteins/chemistry/genetics/metabolism ; Biodiversity ; Canada ; *Drug Resistance, Bacterial ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Ontario ; Sequence Alignment ; Sewage/*microbiology ; Tetracycline/*pharmacology ; Water Microbiology ; Water Purification ; }, abstract = {Sewage, a major source of bacterial contamination of the environment, can be an important health hazard. The presence of antibiotic-resistant bacteria in sewage can exacerbate this problem. The sources of antibiotic-resistant bacteria in sewage are, for this reason, worth identifying and addressing. The bacterial flora in the effluent of the Woodward Avenue Wastewater Treatment Plant (WAWTP) in Hamilton, Ontario, Canada, contains many antibiotic-resistant coliforms. Here we ask, are the antibiotic resistance genes in the coliforms in the effluent of WAWTP descended from a recent common ancestor strain? If so, the source could be identified and eliminated. If, on the other hand, the antibiotic resistance genes in the bacterial flora of the WAWTP have more than one origin, identification and elimination of the source(s) could be difficult. There was considerable diversity of antibiotic resistance patterns and antibiotic resistance genes among the effluent and influent coliform isolates of the WAWTP, suggesting multiple genetic ancestry. The patterns of horizontal transmissibility and sequence differences in the genes tetA and tetE among these coliform isolates also suggest that they have no one predominant ancestral strain. Using the same logic, the evidence presented here is not compatible with a single ancestral origin of the antibiotic resistance genes in the isolates described herein.}, }
@article {pmid20651049, year = {2011}, author = {Lombard, J and Moreira, D}, title = {Origins and early evolution of the mevalonate pathway of isoprenoid biosynthesis in the three domains of life.}, journal = {Molecular biology and evolution}, volume = {28}, number = {1}, pages = {87-99}, doi = {10.1093/molbev/msq177}, pmid = {20651049}, issn = {1537-1719}, mesh = {Archaea/*enzymology/genetics ; Bacteria/*enzymology/genetics ; Bacterial Proteins/classification/genetics/metabolism ; *Biological Evolution ; Eukaryota/*enzymology/genetics ; Fungal Proteins/classification/genetics/metabolism ; Metabolic Networks and Pathways/genetics ; Mevalonic Acid/*metabolism ; Phylogeny ; Sequence Alignment ; Terpenes/*metabolism ; }, abstract = {Isoprenoids are a very diverse family of organic compounds widespread in the three domains of life. Although they are produced from the condensation of the same precursors in all organisms (isopentenyl pyrophosphate and dimethylallyl diphosphate), the evolutionary origin of their biosynthesis remains controversial. Two independent nonhomologous metabolic pathways are known: the mevalonate (MVA) pathway in eukaryotes and archaea and the methylerythritol phosphate (MEP) pathway in bacteria and several photosynthetic eukaryotes. The MVA pathway is also found in a few bacteria, what has been explained in previous works by recent acquisition by horizontal gene transfer (HGT) from eukaryotic or archaeal donors. To reconsider the question of the evolutionary origin of the MVA pathway, we have studied the origin and the evolution of the enzymes of this pathway using phylogenomic analyses upon a taxon-rich sequence database. On the one hand, our results confirm the conservation in archaea of an MVA pathway partially different from eukaryotes. This implies that each domain of life possesses a characteristic major isoprenoid biosynthesis pathway: the classical MVA pathway in eukaryotes, a modified MVA pathway in archaea, and the MEP pathway in bacteria. On the other hand, despite the identification of several HGT events, our analyses support that the MVA pathway was ancestral not only in archaea and eukaryotes but also in bacteria, in contradiction with previous claims that the presence of this pathway in bacteria was due to HGT from other domains. Therefore, the MVA pathway is likely an ancestral metabolic route in all the three domains of life, and hence, it was probably present in the last common ancestor of all organisms (the cenancestor). These findings open the possibility that the cenancestor had membranes containing isoprenoids.}, }
@article {pmid20646305, year = {2010}, author = {Harajly, M and Khairallah, MT and Corkill, JE and Araj, GF and Matar, GM}, title = {Frequency of conjugative transfer of plasmid-encoded ISEcp1 - blaCTX-M-15 and aac(6')-lb-cr genes in Enterobacteriaceae at a tertiary care center in Lebanon - role of transferases.}, journal = {Annals of clinical microbiology and antimicrobials}, volume = {9}, number = {}, pages = {19}, pmid = {20646305}, issn = {1476-0711}, mesh = {Acetyltransferases/*genetics ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics ; Bacterial Typing Techniques ; Cluster Analysis ; Community Health Centers ; *Conjugation, Genetic ; DNA Fingerprinting ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial ; Enterobacteriaceae/drug effects/*genetics/isolation &amp; purification ; Enterobacteriaceae Infections/microbiology ; Fluoroquinolones/pharmacology ; *Gene Transfer, Horizontal ; Genotype ; Humans ; Lebanon ; Microbial Sensitivity Tests ; Molecular Epidemiology ; *Plasmids ; Polymerase Chain Reaction ; Random Amplified Polymorphic DNA Technique ; Transferases/genetics ; beta-Lactamases/*genetics ; beta-Lactams/pharmacology ; }, abstract = {BACKGROUND: The frequency of transfer of genes encoding resistance to antimicrobial agents was determined by conjugation in ESBL-producing and/or fluoroquinolone or aminoglycoside resistant Enterobacteriaceae clinical isolates at a tertiary care center in Lebanon. In addition, the role of tra genes encoding transferases in mediating conjugation was assessed.<br><br>METHODS: Conjugation experiments were done on 53 ESBL-producing and/or fluoroquinolone resistant E. coli and K. pneumoniae and ESBL-producing S. sonnei isolates. Antimicrobial susceptibility testing on parent and transconjugant isolates, and PCR amplifications on plasmid extracts of the resistance-encoding genes: blaCTX-M-15 with the ISEcp1 insertion sequence, the aac(6')-lb-cr and qnrS genes, as well as tra encoding transferases genes were done. Random amplified polymorphic DNA (RAPD) analysis was performed to demonstrate whether conjugative isolates are clonal and whether they are linked epidemiologically to a particular source.<br><br>RESULTS: Antimicrobial susceptibility testing on transconjugants revealed that 26 out of 53 (49%) ESBL-producing Enterobacteriaceae were able to transfer antimicrobial resistance to the recipients. Transfer of high-level resistance to the transconjugants encoded by the blaCTX-M-15 gene downstream the ISEcp1 insertion sequence against 3rd generation cephalosporins, and of low-level resistance against ciprofloxacin, and variable levels of resistance against aminoglycosides encoded by aac(6')-lb-cr gene, were observed in transconjugants. tra encoding transferase genes were detected exclusively in conjugative isolates.<br><br>CONCLUSION: In conclusion, the frequency of transfer of antimicrobial resistance in non clonal Enterobacteriaceae at the tertiary care center by conjugation was 49%. Conjugation occurred in isolates expressing the tra encoding transferase genes. Multiple conjugative strains harboring the plasmid encoded antimicrobial resistant genes were circulating in the medical center. Molecular epidemiology analysis showed that conjugative isolates are neither clonal nor linked to a particular site and transfer of antimicrobial resistance is by horizontal transfer of plasmids.}, }
@article {pmid20642798, year = {2010}, author = {Wallden, K and Rivera-Calzada, A and Waksman, G}, title = {Type IV secretion systems: versatility and diversity in function.}, journal = {Cellular microbiology}, volume = {12}, number = {9}, pages = {1203-1212}, pmid = {20642798}, issn = {1462-5822}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Bacterial Proteins/genetics/*metabolism ; *Bacterial Secretion Systems ; Biological Transport ; Conjugation, Genetic ; DNA, Bacterial/metabolism ; Gram-Negative Bacteria/genetics/*metabolism/pathogenicity ; Gram-Positive Bacteria/genetics/*metabolism/pathogenicity ; Humans ; Virulence Factors/genetics/*metabolism ; }, abstract = {Type IV secretion systems (T4SSs) are large protein complexes which traverse the cell envelope of many bacteria. They contain a channel through which proteins or protein-DNA complexes can be translocated. This translocation is driven by a number of cytoplasmic ATPases which might energize large conformational changes in the translocation complex. The family of T4SSs is very versatile, shown by the great variety of functions among family members. Some T4SSs are used by pathogenic Gram-negative bacteria to translocate a wide variety of virulence factors into the host cell. Other T4SSs are utilized to mediate horizontal gene transfer, an event that greatly facilitates the adaptation to environmental changes and is the basis for the spread of antibiotic resistance among bacteria. Here we review the recent advances in the characterization of the architecture and mechanism of substrate transfer in a few representative T4SSs with a particular focus on their diversity of structure and function.}, }
@article {pmid20638608, year = {2010}, author = {Ríos, E and Rodríguez-Avial, I and Rodríguez-Avial, C and Hernandez, E and Picazo, JJ}, title = {High percentage of resistance to ciprofloxacin and qnrB19 gene identified in urinary isolates of extended-spectrum beta-lactamase-producing Escherichia coli in Madrid, Spain.}, journal = {Diagnostic microbiology and infectious disease}, volume = {67}, number = {4}, pages = {380-383}, doi = {10.1016/j.diagmicrobio.2010.03.007}, pmid = {20638608}, issn = {1879-0070}, mesh = {Anti-Bacterial Agents/*pharmacology ; Ciprofloxacin/*pharmacology ; Conjugation, Genetic ; DNA Topoisomerase IV/genetics ; *Drug Resistance, Bacterial ; Escherichia coli/*drug effects/enzymology/isolation &amp; purification ; Escherichia coli Infections/*microbiology ; Escherichia coli Proteins/biosynthesis ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genotype ; Humans ; Microbial Sensitivity Tests ; Spain ; Urinary Tract Infections/*microbiology ; beta-Lactamases/biosynthesis ; }, abstract = {The presence of qnr genes in 191 extended-spectrum beta-lactamase-producing Escherichia coli from 2005, with 75% of resistance to ciprofloxacin, was evaluated. An SHV-12-producing E. coli carried qnrB19; both genes were transferred by conjugation. No qnrA- or qnrS-positive strains were detected. In addition, we identified 3 new parC mutations (S80W, E84R, and E84A).}, }
@article {pmid20638607, year = {2010}, author = {Paniagua, R and Valverde, A and Coque, TM and Baquero, F and Cantón, R}, title = {Assessment of prevalence and changing epidemiology of extended-spectrum beta-lactamase-producing Enterobacteriaceae fecal carriers using a chromogenic medium.}, journal = {Diagnostic microbiology and infectious disease}, volume = {67}, number = {4}, pages = {376-379}, doi = {10.1016/j.diagmicrobio.2010.03.012}, pmid = {20638607}, issn = {1879-0070}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*biosynthesis/genetics ; Bacteriological Techniques/methods ; Carrier State/*epidemiology/microbiology ; Culture Media/chemistry ; Enterobacteriaceae/*enzymology/isolation &amp; purification ; Enterobacteriaceae Infections/*epidemiology/microbiology ; Feces/*microbiology ; Gene Transfer, Horizontal ; Humans ; Mass Screening/*methods ; Prevalence ; Quinolones/pharmacology ; Sensitivity and Specificity ; Spain/epidemiology ; beta-Lactamases/*biosynthesis ; tRNA Methyltransferases/genetics ; }, abstract = {Five hundred fecal samples from 462 patients (68.4% ambulatory) (February-April, 2007) from Madrid (Spain) were screened for extended-spectrum beta-lactamase (ESBL) producers using ceftazidime and cefotaxime (1 mg/L) MacConkey (MAC) agar plates and a chromogenic media (chromID ESBL; bioMérieux, Marcy-l'Etoile, France). bla(ESBL), qnr, aac(6')Ib-cr, and 16S rRNA methylase genes were assessed. A prevalence of 8.2% of ESBL fecal carriers was observed (8.9% hospitalized, 7.9% nonhospitalized patients), higher than that previously observed (1991, 0.6%; 2003, 7.0%). Sensitivity, specificity, and positive and negative predicted values were 100%, 94.8%, 63%, and 100% for chromID ESBL and 87.8%, 89.8%, 43.4%, and 98.9% for MAC, respectively. ESBL distribution was as follows: CTX-M-9-group, 40% (mainly CTX-M-14); CTX-M-1-group, 26.6% (mainly CTX-M-15); SHV-type, 29% (mainly SHV-12); and TEM-type, 4.4%. These enzymes were found in pulsed-field gel electrophoresis nonclonally related Escherichia coli and Klebsiella pneumoniae isolates. Transferable quinolone resistance was confirmed in CTX-M-9 (qnrS1), CTX-M-15 [aac(6')Ib-cr, qnrS1], and SHV-12 (qnrB7, qnrS1) producers but not 16S rRNA methylase genes. The chromID ESBL medium was reliable to screen ESBL fecal carriers with a general decrease in the laboratory workload. Time-to-time monitoring of ESBL fecal carriers is useful to ascertain current trend of ESBL epidemiology.}, }
@article {pmid20637130, year = {2010}, author = {Burgos, Y and Beutin, L}, title = {Common origin of plasmid encoded alpha-hemolysin genes in Escherichia coli.}, journal = {BMC microbiology}, volume = {10}, number = {}, pages = {193}, pmid = {20637130}, issn = {1471-2180}, mesh = {Amino Acid Sequence ; Animals ; Cattle ; Dogs ; Escherichia coli/classification/*genetics/isolation &amp; purification/metabolism ; Escherichia coli Infections/*microbiology/*veterinary ; Escherichia coli Proteins/*genetics/metabolism ; Hemolysin Proteins/*genetics/metabolism ; Humans ; Molecular Sequence Data ; Operon ; Phylogeny ; Plasmids/*genetics/metabolism ; Swine ; }, abstract = {BACKGROUND: Alpha (alpha)-hemolysin is a pore forming cytolysin and serves as a virulence factor in intestinal and extraintestinal pathogenic strains of E. coli. It was suggested that the genes encoding alpha-hemolysin (hlyCABD) which can be found on the chromosome and plasmid, were acquired through horizontal gene transfer. Plasmid-encoded alpha-hly is associated with certain enterotoxigenic (ETEC), shigatoxigenic (STEC) and enteropathogenic E. coli (EPEC) strains. In uropathogenic E. coli (UPEC), the alpha-hly genes are located on chromosomal pathogenicity islands. Previous work suggested that plasmid and chromosomally encoded alpha-hly may have evolved independently. This was explored in our study.<br><br>RESULTS: We have investigated 11 alpha-hly plasmids from animal and human ETEC, STEC and EPEC strains. The size of alpha-hly plasmids ranges from 48-157 kb and eight plasmids are conjugative. The regulatory gene (hlyR) located upstream of the hlyCABD gene operon and an IS911 element located downstream of hlyD are conserved. Chromosomally-encoded alpha-hly operons lack the hlyR and IS911 elements. The DNA sequence of hlyC and hlyA divided the plasmid- and chromosomally-encoded alpha-hemolysins into two clusters. The plasmid-encoded alpha-hly genes could be further divided into three groups based on the insertion of IS1 and IS2 in the regulatory region upstream of the alpha-hly operon. Transcription of the hlyA gene was higher than the housekeeping icdA gene in all strains (rq 4.8 to 143.2). Nucleotide sequence analysis of a chromosomally located alpha-hly determinant in Enterobacter cloacae strain indicates that it originates from an E. coli alpha-hly plasmid.<br><br>CONCLUSION: Our data indicate that plasmids encoding alpha-hly in E. coli descended from a common ancestor independent of the plasmid size and the origin of the strains. Conjugative plasmids could contribute to the spread of the alpha-hly determinant to Enterobacter cloacae. The presence of IS-elements flanking the plasmid-encoded alpha-hly indicate that they might be mobile genetic elements.}, }
@article {pmid20636373, year = {2010}, author = {Fondi, M and Fani, R}, title = {The horizontal flow of the plasmid resistome: clues from inter-generic similarity networks.}, journal = {Environmental microbiology}, volume = {12}, number = {12}, pages = {3228-3242}, doi = {10.1111/j.1462-2920.2010.02295.x}, pmid = {20636373}, issn = {1462-2920}, mesh = {Bacteria/classification/*genetics ; Drug Resistance, Bacterial/*genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Plasmids/*genetics ; }, abstract = {By integrating sequence similarity data of plasmid-encoded antibiotic resistance determinants with those coming from a less transferred molecular marker, we constructed a network in which all the sequences that most likely underwent horizontal gene transfer (HGT) were linked together. The analysis of this network revealed that either geographical barriers or taxonomical distance can often be overcome since phylogenetically unrelated bacteria, and/or those inhabiting distinct environments, were found to share common antibiotic resistance determinants, probably as a result of (one or multiple) HGT event(s). Data obtained also revealed that bacteria viable through multiple environments (ubiquitous) are likely to give a crucial contribution to the spreading of bacterial resistance towards antimicrobial compounds. These analyses represent a first attempt to give an almost global picture of the horizontal flow of antibiotic resistance determinants at the whole bacterial community level, also underlining the power of HGT among bacteria and how this 'horizontal flow' is poorly affected by both taxonomy and physical distance. Finally, data presented may be useful in the infections control procedures, suggesting which bacterial species are more likely acting as vectors of antibiotic resistance determinants.}, }
@article {pmid20635600, year = {2009}, author = {Thapa, B and Tribuddharat, C and Rugdeekha, S and Techachaiwiwat, W and Srifuengfung, S and Dhiraputra, C}, title = {Rifampin resistance in carbapenem-resistant Acinetobacter baumannii in Siriraj Hospital, Thailand.}, journal = {Nepal Medical College journal : NMCJ}, volume = {11}, number = {4}, pages = {232-237}, pmid = {20635600}, issn = {2676-1319}, mesh = {Acinetobacter Infections/*drug therapy ; Acinetobacter baumannii/*genetics/isolation &amp; purification ; Anti-Bacterial Agents/therapeutic use ; Bacterial Proteins/genetics ; Carbapenems/therapeutic use ; *Drug Resistance, Multiple, Bacterial ; Humans ; Rifampin/therapeutic use ; Thailand ; }, abstract = {There is a growing evidence on emergence of carbapenem-resistant Acinetobacter baumannii (CRAB) in Thailand and recent treatment guidelines recommend a combination therapy using carbapenem and/or polymyxin with rifampin. Rifampin would be added in a combination therapy. The susceptibility of this pathogen to rifampin is not known, so we studied the rifampin susceptibility and possible mechanisms of resistance used by CRAB. The disk diffusion test was performed on 111 clinical isolates using 5 microg rifampin disk following CLSI guidelines. The inhibition zone was interpreted based upon the recommendation for Staphylococcus aureus (inhibition zone < 20 mm = resistant). Polymerase chain reaction (PCR) using the primers specific for arr-2 encoding rifampin ADP-ribosyltransferase was performed in all isolates. The rpoB DNA sequences from two isolates, with or without arr-2, were compared. All isolates under study were rifampin resistant. Inhibition zone was < 14 mm for all isolates. The arr-2 was positive for 35 isolates (31.5%) and these isolates correlated with high level of resistance (inhibition zone < 10mm). The DNA sequences of rpoB genes in arr-2 negative isolate showed mutations L904S, P906R, K909N and M1262K that might have roles in rifampin resistance. Mutations of rpoB genes in some isolates and possession of arr-2 in class 1 integron element were mechanisms for rifampin resistance and these resistant determinants can disseminate through both vertical and horizontal gene transfer. Under this circumstance, it is not recommended to use rifampin in the treatment of carbapenem-resistant A. baumannii in Thailand.}, }
@article {pmid20633232, year = {2010}, author = {Thompson, FL and Thompson, CC and Vicente, AC and Klose, KE and , }, title = {Vibrio2009: the third international conference on the biology of Vibrios.}, journal = {Molecular microbiology}, volume = {77}, number = {5}, pages = {1065-1071}, doi = {10.1111/j.1365-2958.2010.07286.x}, pmid = {20633232}, issn = {1365-2958}, mesh = {Brazil ; Cholera/microbiology ; Environmental Microbiology ; Evolution, Molecular ; Gene Transfer, Horizontal ; Humans ; Symbiosis ; Vibrio/genetics/pathogenicity/*physiology ; }, abstract = {Vibrio2009, the third international conference on the biology of Vibrios, was held in Rio de Janeiro, Brazil, in November 2009. This conference united researchers studying various aspects of pathogenesis, symbiosis and environmental persistence of this diverse group of marine bacteria. Through many of the presentations, it became apparent how horizontal gene transfer and genetic flexibility has driven the incredible diversity of these microbes. Interestingly, unifying themes of behaviour could be seen in the interaction(s) of Vibrios with other organisms, such as with other bacteria, corals, invertebrates and humans. Presentations illuminated the idea that the path towards symbiosis is not that different from the path towards disease, and that alterations in environmental conditions, such as climate change, can tip the balance and change the Vibrio interactions from benign to pathogenic.}, }
@article {pmid20632805, year = {2010}, author = {Frost, LS and Koraimann, G}, title = {Regulation of bacterial conjugation: balancing opportunity with adversity.}, journal = {Future microbiology}, volume = {5}, number = {7}, pages = {1057-1071}, doi = {10.2217/fmb.10.70}, pmid = {20632805}, issn = {1746-0921}, support = {MT 11249//Canadian Institutes of Health Research/Canada ; }, mesh = {*Adaptation, Biological ; *Bacteriophages ; Conjugation, Genetic/genetics/*physiology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; *Plasmids ; *Recombination, Genetic ; }, abstract = {Conjugative plasmids are involved in the dissemination of important traits such as antibiotic resistance, virulence determinants and metabolic pathways involved in adapting to environmental niches, a process termed horizontal or lateral gene transfer. Conjugation is the process of transferring DNA from a donor to a recipient cell with the establishment of the incoming DNA and its cargo of genetic traits within the transconjugant. Conjugation is mediated by self-transmissible plasmids as well as phage-like sequences that have been integrated into the bacterial chromosome, such as integrative and conjugative elements (ICEs) that now include conjugative transposons. Both conjugative plasmids and ICEs can mediate the transfer of mobilizable elements by sharing their conjugative machinery. Conjugation can either be induced, usually by small molecules or peptides or by excision of the ICE from the host chromosome, or it can be tightly regulated by plasmid- and host-encoded factors. The transfer potential of these transfer regions depends on the integration of many signals in response to environmental and physiological cues. This review will focus on the mechanisms that influence transfer potential in these systems, particularly those of the IncF incompatibility group.}, }
@article {pmid20629799, year = {2010}, author = {Ramsden, SJ and Ghosh, S and Bohl, LJ and Lapara, TM}, title = {Phenotypic and genotypic analysis of bacteria isolated from three municipal wastewater treatment plants on tetracycline-amended and ciprofloxacin-amended growth media.}, journal = {Journal of applied microbiology}, volume = {109}, number = {5}, pages = {1609-1618}, doi = {10.1111/j.1365-2672.2010.04787.x}, pmid = {20629799}, issn = {1365-2672}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/*genetics/growth &amp; development/isolation &amp; purification ; Ciprofloxacin/*pharmacology ; Conjugation, Genetic ; Culture Media ; Drug Resistance, Bacterial ; Genotype ; Integrons/genetics ; Microbial Sensitivity Tests ; Phenotype ; Tetracycline/*pharmacology ; Tetracycline Resistance/genetics ; }, abstract = {AIMS: The goal of this study was to determine the antimicrobial susceptibility of bacteria isolated from three municipal wastewater treatment plants.<br><br>METHODS AND RESULTS: Numerous bacterial strains were isolated from three municipal wastewater treatment facilities on tetracycline- (n=164) and ciprofloxacin-amended (n=65) growth media. These bacteria were then characterized with respect to their resistance to as many as 10 different antimicrobials, the presence of 14 common genes that encode resistance to tetracycline, the presence of integrons and/or the ability to transfer resistance via conjugation. All of the characterized strains exhibited some degree of multiple antimicrobial resistance, with nearly 50% demonstrating resistance to every antimicrobial that was tested. Genes encoding resistance to tetracycline were commonly detected among these strains, although intriguingly the frequency of detection was slightly higher for the bacteria isolated on ciprofloxacin-amended growth media (62%) compared to the bacteria isolated on tetracycline-amended growth media (53%). Class 1 integrons were also detected in 100% of the queried tetracycline-resistant bacteria and almost half of the ciprofloxacin-resistant strains. Conjugation experiments demonstrated that at least one of the tetracycline-resistant bacteria was capable of lateral gene transfer.<br><br>CONCLUSIONS: Our results demonstrate that multiple antimicrobial resistance is a common trait among tetracycline-resistant and ciprofloxacin-resistant bacteria in municipal wastewater.<br><br>These organisms are potentially important in the proliferation of antimicrobial resistance because they appear to have acquired multiple genetic determinants that confer resistance and because they have the potential to laterally transfer these genetic determinants to strains of clinical importance.}, }
@article {pmid20629700, year = {2010}, author = {Wildschutte, H and Preheim, SP and Hernandez, Y and Polz, MF}, title = {O-antigen diversity and lateral transfer of the wbe region among Vibrio splendidus isolates.}, journal = {Environmental microbiology}, volume = {12}, number = {11}, pages = {2977-2987}, doi = {10.1111/j.1462-2920.2010.02274.x}, pmid = {20629700}, issn = {1462-2920}, support = {F32GM084640/GM/NIGMS NIH HHS/United States ; }, mesh = {Antigenic Variation ; Base Sequence ; *Gene Transfer, Horizontal ; Genetic Loci ; *Genetic Variation ; Genome, Bacterial ; Massachusetts ; Molecular Sequence Data ; Multilocus Sequence Typing ; *O Antigens/analysis/classification/genetics ; Open Reading Frames ; Phylogeny ; Sequence Analysis, DNA ; Serotyping ; Vibrio/*genetics/*immunology ; Water Microbiology ; }, abstract = {The O-antigen is a highly diverse structure expressed on the outer surface of Gram-negative bacteria. The products responsible for O-antigen synthesis are encoded in the wbe region, which exhibits extensive genetic diversity. While heterogeneous O-antigens are observed within Vibrio species, characterization of these structures has been devoted almost exclusively to pathogens. Here, we investigate O-antigen diversity among coastal marine Vibrio splendidus-like isolates. The wbe region was first identified and characterized using the sequenced genomes of strains LGP32, 12B01 and Med222. These regions were genetically diverse, reflective of their expressed O-antigen. Additional isolates from physically distinct habitats in Plum Island Estuary (MA, USA), including within animal hosts and on suspended particles, were further characterized based on multilocus sequence analysis (MLSA) and O-antigen profiles. Results showed serotype diversity within an ecological setting. Among 48 isolates which were identical in three MLSA genes, 41 showed gpm genetic diversity, a gene closely linked to the wbe locus, and at least 12 expressed different O-antigen profiles further suggesting wbe genetic diversity. Our results demonstrate O-antigen hyper-variability among these environmental strains and suggest that frequent lateral gene transfer generates wbe extensive diversity among V. splendidus and its close relatives.}, }
@article {pmid20627874, year = {2010}, author = {Sun, G and Yang, Z and Ishwar, A and Huang, J}, title = {Algal genes in the closest relatives of animals.}, journal = {Molecular biology and evolution}, volume = {27}, number = {12}, pages = {2879-2889}, doi = {10.1093/molbev/msq175}, pmid = {20627874}, issn = {1537-1719}, mesh = {Animals ; Cell Nucleus/genetics ; Choanoflagellata/genetics ; Diatoms/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Haptophyta/*genetics ; Photosynthesis/genetics ; Phylogeny ; Plastids/*genetics ; Symbiosis ; Viridiplantae/*genetics ; }, abstract = {The spread of photosynthesis is one of the most important but controversial topics in eukaryotic evolution. Because of massive gene transfer from plastids to the nucleus and because of the possibility that plastids have been lost in evolution, algal genes in aplastidic organisms often are interpreted as footprints of photosynthetic ancestors. These putative plastid losses, in turn, have been cited as support for scenarios involving the spread of plastids in broadscale eukaryotic evolution. Phylogenomic analyses identified more than 100 genes of possible algal origin in Monosiga, a unicellular species from choanoflagellates, a group considered to be the closest protozoan relatives of animals and to be primitively heterotrophic. The vast majority of these algal genes appear to be derived from haptophytes, diatoms, or green plants. Furthermore, more than 25% of these algal genes are ultimately of prokaryotic origin and were spread secondarily to Monosiga. Our results show that the presence of algal genes may be expected in many phagotrophs or taxa of phagotrophic ancestry and therefore does not necessarily represent evidence of plastid losses. The ultimate prokaryotic origin of some algal genes and their simultaneous presence in both primary and secondary photosynthetic eukaryotes either suggest recurrent gene transfer events under specific environments or support a more ancient origin of primary plastids.}, }
@article {pmid20626840, year = {2010}, author = {Röske, K and Foecking, MF and Yooseph, S and Glass, JI and Calcutt, MJ and Wise, KS}, title = {A versatile palindromic amphipathic repeat coding sequence horizontally distributed among diverse bacterial and eucaryotic microbes.}, journal = {BMC genomics}, volume = {11}, number = {}, pages = {430}, pmid = {20626840}, issn = {1471-2164}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Bacteria/*genetics ; Bacterial Proteins/chemistry/*genetics ; Base Sequence ; Eukaryota/*genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial/genetics ; Inverted Repeat Sequences/*genetics ; Membrane Proteins/chemistry/genetics ; Metagenome/genetics ; Molecular Sequence Data ; Open Reading Frames/*genetics ; Parasites/genetics ; Phenotype ; Phylogeny ; Protein Structure, Tertiary ; Tandem Repeat Sequences/genetics ; }, abstract = {BACKGROUND: Intragenic tandem repeats occur throughout all domains of life and impart functional and structural variability to diverse translation products. Repeat proteins confer distinctive surface phenotypes to many unicellular organisms, including those with minimal genomes such as the wall-less bacterial monoderms, Mollicutes. One such repeat pattern in this clade is distributed in a manner suggesting its exchange by horizontal gene transfer (HGT). Expanding genome sequence databases reveal the pattern in a widening range of bacteria, and recently among eucaryotic microbes. We examined the genomic flux and consequences of the motif by determining its distribution, predicted structural features and association with membrane-targeted proteins.<br><br>RESULTS: Using a refined hidden Markov model, we document a 25-residue protein sequence motif tandemly arrayed in variable-number repeats in ORFs lacking assigned functions. It appears sporadically in unicellular microbes from disparate bacterial and eucaryotic clades, representing diverse lifestyles and ecological niches that include host parasitic, marine and extreme environments. Tracts of the repeats predict a malleable configuration of recurring domains, with conserved hydrophobic residues forming an amphipathic secondary structure in which hydrophilic residues endow extensive sequence variation. Many ORFs with these domains also have membrane-targeting sequences that predict assorted topologies; others may comprise reservoirs of sequence variants. We demonstrate expressed variants among surface lipoproteins that distinguish closely related animal pathogens belonging to a subgroup of the Mollicutes. DNA sequences encoding the tandem domains display dyad symmetry. Moreover, in some taxa the domains occur in ORFs selectively associated with mobile elements. These features, a punctate phylogenetic distribution, and different patterns of dispersal in genomes of related taxa, suggest that the repeat may be disseminated by HGT and intra-genomic shuffling.<br><br>CONCLUSIONS: We describe novel features of PARCELs (Palindromic Amphipathic Repeat Coding ELements), a set of widely distributed repeat protein domains and coding sequences that were likely acquired through HGT by diverse unicellular microbes, further mobilized and diversified within genomes, and co-opted for expression in the membrane proteome of some taxa. Disseminated by multiple gene-centric vehicles, ORFs harboring these elements enhance accessory gene pools as part of the "mobilome" connecting genomes of various clades, in taxa sharing common niches.}, }
@article {pmid20624973, year = {2010}, author = {Lücker, S and Wagner, M and Maixner, F and Pelletier, E and Koch, H and Vacherie, B and Rattei, T and Damsté, JS and Spieck, E and Le Paslier, D and Daims, H}, title = {A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {30}, pages = {13479-13484}, pmid = {20624973}, issn = {1091-6490}, mesh = {Amino Acid Sequence ; Bacteria/classification/*genetics/*metabolism ; Bacterial Physiological Phenomena ; Bacterial Proteins/classification/genetics/metabolism ; Carbon Dioxide/metabolism ; Chromosomes, Bacterial/genetics ; Citric Acid Cycle/physiology ; *Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Genome, Bacterial/*genetics ; Metagenome/genetics ; Metagenomics ; Molecular Sequence Data ; Nitrite Reductases/genetics/metabolism ; Nitrites/*metabolism ; Oxidation-Reduction ; Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Homology, Amino Acid ; Sewage/microbiology ; }, abstract = {Nitrospira are barely studied and mostly uncultured nitrite-oxidizing bacteria, which are, according to molecular data, among the most diverse and widespread nitrifiers in natural ecosystems and biological wastewater treatment. Here, environmental genomics was used to reconstruct the complete genome of "Candidatus Nitrospira defluvii" from an activated sludge enrichment culture. On the basis of this first-deciphered Nitrospira genome and of experimental data, we show that Ca. N. defluvii differs dramatically from other known nitrite oxidizers in the key enzyme nitrite oxidoreductase (NXR), in the composition of the respiratory chain, and in the pathway used for autotrophic carbon fixation, suggesting multiple independent evolution of chemolithoautotrophic nitrite oxidation. Adaptations of Ca. N. defluvii to substrate-limited conditions include an unusual periplasmic NXR, which is constitutively expressed, and pathways for the transport, oxidation, and assimilation of simple organic compounds that allow a mixotrophic lifestyle. The reverse tricarboxylic acid cycle as the pathway for CO2 fixation and the lack of most classical defense mechanisms against oxidative stress suggest that Nitrospira evolved from microaerophilic or even anaerobic ancestors. Unexpectedly, comparative genomic analyses indicate functionally significant lateral gene-transfer events between the genus Nitrospira and anaerobic ammonium-oxidizing planctomycetes, which share highly similar forms of NXR and other proteins reflecting that two key processes of the nitrogen cycle are evolutionarily connected.}, }
@article {pmid20624849, year = {2011}, author = {Brandão, MM and Silva-Filho, MC}, title = {Evolutionary history of Arabidopsis thaliana aminoacyl-tRNA synthetase dual-targeted proteins.}, journal = {Molecular biology and evolution}, volume = {28}, number = {1}, pages = {79-85}, doi = {10.1093/molbev/msq176}, pmid = {20624849}, issn = {1537-1719}, mesh = {Amino Acyl-tRNA Synthetases/*genetics ; Arabidopsis/*enzymology/*genetics ; Arabidopsis Proteins/classification/*genetics ; Bacterial Proteins/classification/genetics ; *Biological Evolution ; Databases, Protein ; Gene Expression ; Gene Transfer, Horizontal ; Microarray Analysis ; Molecular Sequence Data ; Phylogeny ; Protein Interaction Mapping ; }, abstract = {Aminoacyl-transfer RNA (tRNA) synthetases (aaRS) are key players in translation and act early in protein synthesis by mediating the attachment of amino acids to their cognate tRNA molecules. In plants, protein synthesis may occur in three subcellular compartments (cytosol, mitochondria, and chloroplasts), which requires multiple versions of the protein to be correctly delivered to its proper destination. The organellar aaRS are nuclear encoded and equipped with targeting information at the N-terminal sequence, which enables them to be specifically translocated to their final location. Most of the aaRS families present organellar proteins that are dual targeted to mitochondria and chloroplasts. Here, we examine the dual targeting behavior of aaRS from an evolutionary perspective. Our results show that Arabidopsis thaliana aaRS sequences are a result of a horizontal gene transfer event from bacteria. However, there is no evident bias indicating one single ancestor (Cyanobacteria or Proteobacteria). The dual-targeted aaRS phylogenetic relationship was characterized into two different categories (paralogs and homologs) depending on the state recovered for both dual-targeted and cytosolic proteins. Taken together, our results suggest that the dual-targeted condition is a gain-of-function derived from gene duplication. Selection may have maintained the original function in at least one of the copies as the additional copies diverged.}, }
@article {pmid20624743, year = {2010}, author = {Cai, JJ and Petrov, DA}, title = {Relaxed purifying selection and possibly high rate of adaptation in primate lineage-specific genes.}, journal = {Genome biology and evolution}, volume = {2}, number = {}, pages = {393-409}, pmid = {20624743}, issn = {1759-6653}, mesh = {Adaptation, Biological/genetics ; Amino Acid Substitution ; Animals ; Evolution, Molecular ; Genome, Human ; Humans ; Models, Genetic ; Mutation ; Pan troglodytes/genetics ; Phylogeny ; Polymorphism, Single Nucleotide ; Primates/classification/*genetics ; Proteins/genetics ; *Selection, Genetic ; Time Factors ; }, abstract = {Genes in the same organism vary in the time since their evolutionary origin. Without horizontal gene transfer, young genes are necessarily restricted to a few closely related species, whereas old genes can be broadly distributed across the phylogeny. It has been shown that young genes evolve faster than old genes; however, the evolutionary forces responsible for this pattern remain obscure. Here, we classify human-chimp protein-coding genes into different age classes, according to the breath of their phylogenetic distribution. We estimate the strength of purifying selection and the rate of adaptive selection for genes in different age classes. We find that older genes carry fewer and less frequent nonsynonymous single-nucleotide polymorphisms than younger genes suggesting that older genes experience a stronger purifying selection at the protein-coding level. We infer the distribution of fitness effects of new deleterious mutations and find that older genes have proportionally more slightly deleterious mutations and fewer nearly neutral mutations than younger genes. To investigate the role of adaptive selection of genes in different age classes, we determine the selection coefficient (gamma = 2N(e)s) of genes using the MKPRF approach and estimate the ratio of the rate of adaptive nonsynonymous substitution to synonymous substitution (omega(A)) using the DoFE method. Although the proportion of positively selected genes (gamma > 0) is significantly higher in younger genes, we find no correlation between omega(A) and gene age. Collectively, these results provide strong evidence that younger genes are subject to weaker purifying selection and more tenuous evidence that they also undergo adaptive evolution more frequently.}, }
@article {pmid20624742, year = {2010}, author = {Dagan, T and Roettger, M and Bryant, D and Martin, W}, title = {Genome networks root the tree of life between prokaryotic domains.}, journal = {Genome biology and evolution}, volume = {2}, number = {}, pages = {379-392}, pmid = {20624742}, issn = {1759-6653}, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; *Evolution, Molecular ; *Gene Regulatory Networks ; Genome ; INDEL Mutation ; Models, Genetic ; Multigene Family ; *Phylogeny ; Prokaryotic Cells ; }, abstract = {Eukaryotes arose from prokaryotes, hence the root in the tree of life resides among the prokaryotic domains. The position of the root is still debated, although pinpointing it would aid our understanding of the early evolution of life. Because prokaryote evolution was long viewed as a tree-like process of lineage bifurcations, efforts to identify the most ancient microbial lineage split have traditionally focused on positioning a root on a phylogenetic tree constructed from one or several genes. Such studies have delivered widely conflicting results on the position of the root, this being mainly due to methodological problems inherent to deep gene phylogeny and the workings of lateral gene transfer among prokaryotes over evolutionary time. Here, we report the position of the root determined with whole genome data using network-based procedures that take into account both gene presence or absence and the level of sequence similarity among all individual gene families that are shared across genomes. On the basis of 562,321 protein-coding gene families distributed across 191 genomes, we find that the deepest divide in the prokaryotic world is interdomain, that is, separating the archaebacteria from the eubacteria. This result resonates with some older views but conflicts with the results of most studies over the last decade that have addressed the issue. In particular, several studies have suggested that the molecular distinctness of archaebacteria is not evidence for their antiquity relative to eubacteria but instead stems from some kind of inherently elevated rate of archaebacterial sequence change. Here, we specifically test for such a rate elevation across all prokaryotic lineages through the analysis of all possible quartets among eight genes duplicated in all prokaryotes, hence the last common ancestor thereof. The results show that neither the archaebacteria as a group nor the eubacteria as a group harbor evidence for elevated evolutionary rates in the sampled genes, either in the recent evolutionary past or in their common ancestor. The interdomain prokaryotic position of the root is thus not attributable to lineage-specific rate variation.}, }
@article {pmid20624734, year = {2010}, author = {Pagan, HJ and Smith, JD and Hubley, RM and Ray, DA}, title = {PiggyBac-ing on a primate genome: novel elements, recent activity and horizontal transfer.}, journal = {Genome biology and evolution}, volume = {2}, number = {}, pages = {293-303}, pmid = {20624734}, issn = {1759-6653}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cheirogaleidae/*genetics ; DNA Primers/genetics ; DNA Transposable Elements/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Primates/classification/genetics ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Time Factors ; }, abstract = {To better understand the extent of Class II transposable element activity in mammals, we investigated the mouse lemur, Microcebus murinus, whole genome shotgun (2X) draft assembly. Analysis of this strepsirrhine primate extended previous research that targeted anthropoid primates and found no activity within the last 37 Myr. We tested the hypothesis that members of the piggyBac Class II superfamily have been inactive in the strepsirrhine lineage of primates during the same period. Evidence against this hypothesis was discovered in the form of three nonautonomous piggyBac elements with activity periods within the past 40 Myr and possibly into the very recent past. In addition, a novel family of piggyBac transposons was identified, suggesting introduction via horizontal transfer. A second autonomous element was also found with high similarity to an element recently described from the little brown bat, Myotis lucifugus, further implicating horizontal transfer in the evolution of this genome. These findings indicate a more complex history of transposon activity in mammals rather than a uniform shutdown of Class II transposition, which had been suggested by analyses of more common model organisms.}, }
@article {pmid20622504, year = {2010}, author = {Kim, SE and Moon, JS and Kim, JK and Yoo, RH and Choi, WS and Lee, EN and Lee, SH and Kim, SU}, title = {Monitoring of possible horizontal gene transfer from transgenic potatoes to soil microorganisms in the potato fields and the emergence of variants in Phytophthora infestans.}, journal = {Journal of microbiology and biotechnology}, volume = {20}, number = {6}, pages = {1027-1031}, doi = {10.4014/jmb.1002.02028}, pmid = {20622504}, issn = {1017-7825}, mesh = {*Gene Transfer, Horizontal ; Genetic Variation ; Nucleoside-Diphosphate Kinase/genetics ; Phytophthora infestans/*genetics ; Plant Proteins/genetics ; Plants, Genetically Modified/*genetics/parasitology ; Soil/parasitology ; Solanum tuberosum/enzymology/*genetics/parasitology ; }, abstract = {To examine the possibility of horizontal gene transfer between transgenic potatoes and microorganisms in potato fields, the gene flow from transgenic potatoes containing nucleoside diphosphate kinase 2 (NDPK2) gene to microorganisms in soils was investigated. The soil samples collected from the potato fields from March to October in 2007 were examined by PCR, Southern hybridization, and AFLP fingerprinting. The NDPK2 gene from soil genomic DNAs was not detected by both PCR and Southern hybridization, indicating that gene-transfer did not occur in the potato fields. In addition, no discrepancy was found in pathogenicity and noticeable changes for the appearance of variants of Phytophthora infestans in each generation when serial inoculations and the analysis of genomic DNAs by AFLP was conducted. Thus, these data suggest that transgenic potatoes do not give significant impacts on the communities of soil microorganisms and the emergence of variants although continued research efforts may be necessary to make a decisive conclusion.}, }
@article {pmid20618908, year = {2010}, author = {Michel, G and Tonon, T and Scornet, D and Cock, JM and Kloareg, B}, title = {Central and storage carbon metabolism of the brown alga Ectocarpus siliculosus: insights into the origin and evolution of storage carbohydrates in Eukaryotes.}, journal = {The New phytologist}, volume = {188}, number = {1}, pages = {67-81}, doi = {10.1111/j.1469-8137.2010.03345.x}, pmid = {20618908}, issn = {1469-8137}, mesh = {Carbohydrate Metabolism/*genetics ; Carbon/*metabolism ; Carbon Cycle/genetics ; *Evolution, Molecular ; Genome/genetics ; Phaeophyceae/enzymology/*metabolism ; Phylogeny ; Starch/metabolism ; Symbiosis ; }, abstract = {• Brown algae exhibit a unique carbon (C) storage metabolism. The photoassimilate D-fructose 6-phosphate is not used to produce sucrose but is converted into D-mannitol. These seaweeds also store C as β-1,3-glucan (laminarin), thus markedly departing from most living organisms, which use α-1,4-glucans (glycogen or starch). • Using a combination of bioinformatic and phylogenetic approaches, we identified the candidate genes for the enzymes involved in C storage in the genome of the brown alga Ectocarpus siliculosus and traced their evolutionary origins. • Ectocarpus possesses a complete set of enzymes for synthesis of mannitol, laminarin and trehalose. By contrast, the pathways for sucrose, starch and glycogen are completely absent. • The synthesis of β-1,3-glucans appears to be a very ancient eukaryotic pathway. Brown algae inherited the trehalose pathway from the red algal progenitor of phaeoplasts, while the mannitol pathway was acquired by lateral gene transfer from Actinobacteria. The starch metabolism of the red algal endosymbiont was entirely lost in the ancestor of Stramenopiles. In light of these novel findings we question the validity of the 'Chromalveolate hypothesis'.}, }
@article {pmid20618907, year = {2010}, author = {Michel, G and Tonon, T and Scornet, D and Cock, JM and Kloareg, B}, title = {The cell wall polysaccharide metabolism of the brown alga Ectocarpus siliculosus. Insights into the evolution of extracellular matrix polysaccharides in Eukaryotes.}, journal = {The New phytologist}, volume = {188}, number = {1}, pages = {82-97}, doi = {10.1111/j.1469-8137.2010.03374.x}, pmid = {20618907}, issn = {1469-8137}, mesh = {Alginates/metabolism ; Biosynthetic Pathways ; Cell Wall/*metabolism ; Cellulose/biosynthesis ; *Evolution, Molecular ; Extracellular Matrix/*metabolism ; Phaeophyceae/enzymology/*genetics/*metabolism ; Phylogeny ; Polysaccharides/biosynthesis/*metabolism ; }, abstract = {• Brown algal cell walls share some components with plants (cellulose) and animals (sulfated fucans), but they also contain some unique polysaccharides (alginates). Analysis of the Ectocarpus genome provides a unique opportunity to decipher the molecular bases of these crucial metabolisms. • An extensive bioinformatic census of the enzymes potentially involved in the biogenesis and remodeling of cellulose, alginate and fucans was performed, and completed by phylogenetic analyses of key enzymes. • The routes for the biosynthesis of cellulose, alginates and sulfated fucans were reconstructed. Surprisingly, known families of cellulases, expansins and alginate lyases are absent in Ectocarpus, suggesting the existence of novel mechanisms and/or proteins for cell wall expansion in brown algae. • Altogether, our data depict a complex evolutionary history for the main components of brown algal cell walls. Cellulose synthesis was inherited from the ancestral red algal endosymbiont, whereas the terminal steps for alginate biosynthesis were acquired by horizontal gene transfer from an Actinobacterium. This horizontal gene transfer event also contributed genes for hemicellulose biosynthesis. By contrast, the biosynthetic route for sulfated fucans is an ancestral pathway, conserved with animals. These findings shine a new light on the origin and evolution of cell wall polysaccharides in other Eukaryotes.}, }
@article {pmid20618865, year = {2010}, author = {Park, AK and Kim, H and Jin, HJ}, title = {Phylogenetic analysis of rRNA methyltransferases, Erm and KsgA, as related to antibiotic resistance.}, journal = {FEMS microbiology letters}, volume = {309}, number = {2}, pages = {151-162}, doi = {10.1111/j.1574-6968.2010.02031.x}, pmid = {20618865}, issn = {1574-6968}, mesh = {Bacteria/classification/*drug effects/*enzymology/genetics ; Bacterial Proteins/*genetics ; *Drug Resistance, Bacterial ; Methyltransferases/*genetics ; Molecular Sequence Data ; *Phylogeny ; }, abstract = {It has long been speculated that erm and ksgA are related evolutionarily due to their sequence similarity and analogous catalytic reactions. We performed a comprehensive phylogenetic analysis with extensive Erm and KsgA/Dim1 sequences (Dim1 is the eukaryotic ortholog of KsgA). The tree provides insights into the evolutionary history of erm genes, showing early bifurcation of the Firmicutes and the Actinobacteria, and suggesting that the origin of the current erm genes in pathogenic bacteria cannot be explained by recent horizontal gene transfer from antibiotic producers. On the other hand, the phylogenetic analysis cannot support the commonly assumed phylogenetic relationships between erm and ksgA genes, the common ancestry of erm and ksgA or erm descended from preexisting ksgA, because the tree cannot be unequivocally rooted due to insufficient signal and long-branch attraction. The phylogenetic tree indicates that the erm gene underwent frequent horizontal gene transfer and duplication, resulting in phylogenetic anomalies and atypical phenotypes. Several electronically annotated Erm sequences were recognized as candidates for new classes of macrolide-lincosamide-streptogramin B-resistance determinants, sharing less than an 80% amino acid sequence identity with other Erm classes.}, }
@article {pmid20618852, year = {2010}, author = {Rao, T and Lund, PA}, title = {Differential expression of the multiple chaperonins of Mycobacterium smegmatis.}, journal = {FEMS microbiology letters}, volume = {310}, number = {1}, pages = {24-31}, doi = {10.1111/j.1574-6968.2010.02039.x}, pmid = {20618852}, issn = {1574-6968}, mesh = {Bacterial Proteins/*biosynthesis/genetics ; Chaperonins/*biosynthesis/genetics ; Cluster Analysis ; Escherichia coli/genetics ; Evolution, Molecular ; Gene Duplication ; Gene Expression Profiling ; *Gene Expression Regulation ; Gene Transfer, Horizontal ; Hot Temperature ; Mycobacterium smegmatis/*physiology ; Phylogeny ; RNA Processing, Post-Transcriptional ; RNA, Bacterial/metabolism ; RNA, Messenger/metabolism ; Sequence Homology, Amino Acid ; Stress, Physiological ; }, abstract = {Mycobacterium smegmatis contains three chaperonin (cpn60) genes homologous to the Escherichia coli groEL gene. One of these (cpn60.1) is required for biofilm formation, but is nonessential, whereas a second (cpn60.2) is essential. Mycobacterium smegmatis is unique among Mycobacteria in having a third chaperonin gene, cpn60.3. The cpn60.1 gene has a gene upstream (cpn10) that is homologous to the gene for the E. coli co-chaperonin GroES. Phylogenetic analysis of the mycobacterial homologues suggests that early gene duplication and sequence divergence gave rise to the cpn60.1 and cpn60.2 genes found in all Mycobacteria species, while cpn60.3 appears to have been acquired by horizontal gene transfer. Here, we show that cpn60.2 and cpn10 are expressed more strongly than cpn60.1, while cpn60.3 shows very low levels of expression. The expression of all the genes, except cpn60.3, is significantly induced by heat shock, but much less so by other stresses. We mapped mRNA 5'-ends for the cpn10 and cpn60.1 genes, and measured the promoter activity of the upstream regions of both genes. The results show that the mRNA for this operon is cleaved between the cpn10 and cpn60.1 genes. These results are consistent with the evolution of a distinct function for the cpn60.1 gene.}, }
@article {pmid20618850, year = {2010}, author = {Ehrlich, GD and Ahmed, A and Earl, J and Hiller, NL and Costerton, JW and Stoodley, P and Post, JC and DeMeo, P and Hu, FZ}, title = {The distributed genome hypothesis as a rubric for understanding evolution in situ during chronic bacterial biofilm infectious processes.}, journal = {FEMS immunology and medical microbiology}, volume = {59}, number = {3}, pages = {269-279}, pmid = {20618850}, issn = {1574-695X}, support = {R01 DC002148/DC/NIDCD NIH HHS/United States ; DC02118-16S1/DC/NIDCD NIH HHS/United States ; R01 AI080935/AI/NIAID NIH HHS/United States ; P41 RR006009/RR/NCRR NIH HHS/United States ; R01 DC004173/DC/NIDCD NIH HHS/United States ; AI080935/AI/NIAID NIH HHS/United States ; DC04173/DC/NIDCD NIH HHS/United States ; DC02148/DC/NIDCD NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; *Bacterial Adhesion ; Bacterial Infections/microbiology ; *Bacterial Physiological Phenomena ; Biofilms/*growth &amp; development ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; }, abstract = {Most chronic infectious disease processes associated with bacteria are characterized by the formation of a biofilm that provides for bacterial attachment to the host tissue or the implanted medical device. The biofilm protects the bacteria from the host's adaptive immune response as well as predation by phagocytic cells. However, the most insidious aspect of biofilm biology from the host's point of view is that the biofilm provides an ideal setting for bacterial horizontal gene transfer (HGT). HGT provides for large-scale genome content changes in situ during the chronic infectious process. Obviously, for HGT processes to result in the reassortment of alleles and genes among bacterial strains, the infection must be polyclonal (polymicrobial) in nature. In this review, we marshal the evidence that all of the factors are present in biofilm infections to support HGT that results in the ongoing production of novel strains with unique combinations of genic characteristics and that the continual production of large numbers of novel, but related bacterial strains leads to persistence. This concept of an infecting population of bacteria undergoing mutagenesis to produce a 'cloud' of similar strains to confuse and overwhelm the host's immune system parallels genetic diversity strategies used by viral and parasitic pathogens.}, }
@article {pmid20615482, year = {2011}, author = {Bailly, JL and Mirand, A and Henquell, C and Archimbaud, C and Chambon, M and Regagnon, C and Charbonné, F and Peigue-Lafeuille, H}, title = {Repeated genomic transfers from echovirus 30 to echovirus 6 lineages indicate co-divergence between co-circulating populations of the two human enterovirus serotypes.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {11}, number = {2}, pages = {276-289}, doi = {10.1016/j.meegid.2010.06.019}, pmid = {20615482}, issn = {1567-7257}, mesh = {Base Sequence ; Bayes Theorem ; Capsid Proteins/genetics ; Echovirus 6, Human/*genetics ; Echovirus Infections/epidemiology/transmission/*virology ; Enterovirus B, Human/classification/*genetics ; *Evolution, Molecular ; France ; *Gene Transfer, Horizontal ; Genome, Viral ; Genotype ; Humans ; Molecular Epidemiology ; Molecular Sequence Data ; Peptide Hydrolases/genetics ; Phylogeny ; Polymerase Chain Reaction ; *Recombination, Genetic ; Sequence Analysis, DNA ; Serotyping ; }, abstract = {Human echovirus types 6 (E-6) and 30 (E-30) cause seasonal epidemics of aseptic meningitis. These two enteroviruses are frequently observed in co-circulation, an epidemiological pattern that is prerequisite for the occurrence of dual infections, which can lead to recombination between co-infecting virus strains. Viral sequences were determined at loci 1D (VP1 capsid protein) and 3CD (non structural proteins) in 49 E-6 strains recovered in a single geographical region in France from 1999 to 2007, during the epidemiological survey of enterovirus infections. They were compared with previously recorded sequences of E-30 strains to investigate their evolutionary histories and possible recombination patterns. Phylogenetic analyses identified two distinct E-6 populations and different subpopulations. Assuming a relaxed molecular clock model and a Bayesian skyline demographic model in coalescent analyses with the BEAST program, the substitution rate in E-6 was estimated at 8.597×10(-3) and 6.252×10(-3) substitution/site/year for loci 1D and 3CD respectively. Consistent estimates of divergence times (t(MRCA)) were obtained for loci 1D and 3CD indicating that two distinct E-6 populations originated in 1997 and 1999. Incongruent phylogenetic patterns inferred for the two loci were indicative of recombination events between the two populations. Phylogenies including the E-30 3CD sequences showed close genetic relationships between E-6 and discrete E-30 subpopulations. Recombination breakpoints were located with statistical significance in E-6 and E-30 genomes. Estimates of t(MRCA) of phylogenetic recombinant clades indicated directional genetic transfers from E-30 to E-6 populations and their co-divergence over the time period studied.}, }
@article {pmid20614151, year = {2010}, author = {Zhou, Y and Yu, H and Guo, Q and Xu, X and Ye, X and Wu, S and Guo, Y and Wang, M}, title = {Distribution of 16S rRNA methylases among different species of Gram-negative bacilli with high-level resistance to aminoglycosides.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {29}, number = {11}, pages = {1349-1353}, pmid = {20614151}, issn = {1435-4373}, mesh = {Acinetobacter baumannii/drug effects/enzymology/genetics ; Aminoglycosides/*pharmacology ; Anti-Bacterial Agents/pharmacology ; China ; Drug Resistance, Bacterial/*genetics ; Enterobacteriaceae/drug effects/enzymology/genetics ; Gene Transfer, Horizontal ; Gram-Negative Bacteria/*drug effects/enzymology/*genetics ; Methyltransferases/*genetics/*metabolism ; Microbial Sensitivity Tests ; Polymerase Chain Reaction ; Pseudomonas aeruginosa/drug effects/enzymology/genetics ; *RNA, Ribosomal, 16S/metabolism ; }, abstract = {16S rRNA methylases confer high-level resistance to most aminoglycosides in Gram-negative bacteria. Seven 16S rRNA methylase genes, armA, rmtA, rmtB, rmtC, rmtD, rmtE and npmA, have been identified since 2003. We studied the distribution of methylase genes in more than 200 aminoglycoside-resistant Gram-negative clinical isolates collected in 2007 at our hospital in Shanghai, China. 16S rRNA methylase genes were amplified by polymerase chain reaction (PCR) among 217 consecutive clinical isolates of Gram-negative bacilli resistant to gentamicin and amikacin by a disk diffusion method. 16S rRNA methylase genes were present in 97.5% (193/198) of clinical isolates highly resistant to amikacin (≥512 μg/ml), with armA and rmtB detected in 67.2 and 30.3% of strains, respectively, while no 16S rRNA methylase genes were detected in 19 strains with amikacin minimum inhibitory concentration (MIC) ≤256 μg/ml. armA or rmtB genes were detected in 100% of 104 strains of Enterobacteriaceae, and these two genes were equally represented (49 vs. 55 strains). Genes for armA or rmtB were detected in 94.7% (89/94) of Acinetobacter baumannii and Pseudomonas aeruginosa strains, and armA was predominant (84 vs. 5 strains with rmtB). No rmtA, rmtC, rmtD or npmA genes were found. Enterobacterial repetitive intergenic consensus sequence (ERIC-PCR) indicated that armA and rmtB genes were spread by both horizontal transfer and clonal dissemination.}, }
@article {pmid20601965, year = {2010}, author = {Wozniak, RA and Waldor, MK}, title = {Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow.}, journal = {Nature reviews. Microbiology}, volume = {8}, number = {8}, pages = {552-563}, pmid = {20601965}, issn = {1740-1534}, support = {R37 AI042347/AI/NIAID NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R37 AI-42347/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; Chromosomes, Bacterial/genetics ; Conjugation, Genetic ; Evolution, Molecular ; *Gene Flow ; *Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences ; Recombination, Genetic ; }, abstract = {Integrative and conjugative elements (ICEs) are a diverse group of mobile genetic elements found in both Gram-positive and Gram-negative bacteria. These elements primarily reside in a host chromosome but retain the ability to excise and to transfer by conjugation. Although ICEs use a range of mechanisms to promote their core functions of integration, excision, transfer and regulation, there are common features that unify the group. This Review compares and contrasts the core functions for some of the well-studied ICEs and discusses them in the broader context of mobile-element and genome evolution.}, }
@article {pmid20597008, year = {2010}, author = {Stabler, R and Dawson, L and Wren, B}, title = {Clostridium difficile using DNA microarrays.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {646}, number = {}, pages = {149-162}, doi = {10.1007/978-1-60327-365-7_10}, pmid = {20597008}, issn = {1940-6029}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; //Wellcome Trust/United Kingdom ; }, mesh = {Bayes Theorem ; Clostridioides difficile/*genetics ; Genome, Bacterial/*genetics ; *Oligonucleotide Array Sequence Analysis ; }, abstract = {Clostridium difficile is a pathogen on the move, as evidenced by the rapid transcontinental spread of the so-called hypervirulent 027 strains, followed by the emergence of further PCR ribotypes such as 017, 078 and 106. This provides a rare opportunity to study the evolution of virulence in action. However, to fully exploit this opportunity, robust phylogenetic methods on a diverse set of characterised strains are required to provide a reference evolutionary framework to study C. difficile epidemiology, ecology and virulence. Traditional phylogenetic classification of bacteria to study evolutionary relatedness is based on the characterisation of a limited number of genes, rRNA or signature sequences. However, due to the acquisition of DNA through lateral gene transfer, the differences between closely related bacterial strains can be vast. By contrast, whole genome sequencing comparisons allow all genes to be compared. Nevertheless, whole-scale genome sequencing remains an expensive endeavour and such comparisons are limited to only a handful of strains. DNA microarrays represent an alternative technology for whole genome comparisons enabling a "birds eye view" of all the genes absent or present in a given genome as compared to the reference genome on the microarray.}, }
@article {pmid20596068, year = {2011}, author = {Caro-Quintero, A and Deng, J and Auchtung, J and Brettar, I and Höfle, MG and Klappenbach, J and Konstantinidis, KT}, title = {Unprecedented levels of horizontal gene transfer among spatially co-occurring Shewanella bacteria from the Baltic Sea.}, journal = {The ISME journal}, volume = {5}, number = {1}, pages = {131-140}, pmid = {20596068}, issn = {1751-7370}, mesh = {Adaptation, Biological/genetics ; Biological Evolution ; Gene Transfer, Horizontal/*genetics ; Genetic Speciation ; Genome, Bacterial/genetics ; Humans ; Oceans and Seas ; Oligonucleotide Array Sequence Analysis ; Shewanella/classification/*genetics ; }, abstract = {High-throughput sequencing studies during the last decade have uncovered that bacterial genomes are very diverse and dynamic, resulting primarily from the frequent and promiscuous horizontal gene exchange that characterizes the bacterial domain of life. However, a robust understanding of the rates of genetic exchange for most bacterial species under natural conditions and the influence of the ecological settings on the rates remain elusive, severely limiting our view of the microbial world. Here, we analyzed the complete genomic sequences and expressed transcriptomes of several Shewanella baltica isolates recovered from different depths in the Baltic Sea and found that isolates from more similar depths had exchanged a larger fraction of their core and auxiliary genome, up to 20% of the total, compared with isolates from more different depths. The exchanged genes seem to be ecologically important and contribute to the successful adaptation of the isolates to the unique physicochemical conditions of the depth. Importantly, the latter genes were exchanged in very recent past, presumably as an effect of isolate's seasonal migration across the water column, and reflected sexual speciation within the same depth. Therefore, our findings reveal that genetic exchange in response to environmental settings may be surprisingly rapid, which has important broader impacts for understanding bacterial speciation and evolution and for modeling bacterial responses to human-induced environmental impacts.}, }
@article {pmid20594287, year = {2010}, author = {Kim, E and Archibald, JM}, title = {Plastid evolution: gene transfer and the maintenance of 'stolen' organelles.}, journal = {BMC biology}, volume = {8}, number = {}, pages = {73}, pmid = {20594287}, issn = {1741-7007}, mesh = {*Biological Evolution ; Dinoflagellida/*genetics ; Gene Transfer, Horizontal/*genetics ; Photosynthesis/*genetics ; Plastids/*genetics ; *Symbiosis ; }, abstract = {Many heterotrophic organisms sequester plastids from prey algae and temporarily utilize their photosynthetic capacity. A recent article in BMC Genomics reveals that the dinoflagellate Dinophysis acuminata has acquired photosynthesis-related genes by horizontal gene transfer, which might explain its ability to retain 'stolen' plastids for extended periods of time. See research article http://www.biomedcentral.com/1471-2164/11/366.}, }
@article {pmid20593265, year = {2010}, author = {Wang, L and Wang, Q and Reeves, PR}, title = {The variation of O antigens in gram-negative bacteria.}, journal = {Sub-cellular biochemistry}, volume = {53}, number = {}, pages = {123-152}, doi = {10.1007/978-90-481-9078-2_6}, pmid = {20593265}, issn = {0306-0225}, mesh = {Bacteriophages/genetics/metabolism ; Carbohydrate Conformation ; Carbohydrate Sequence ; Gene Transfer, Horizontal ; Gram-Negative Bacteria/*chemistry/genetics/metabolism/pathogenicity ; Humans ; Molecular Sequence Data ; Molecular Structure ; Multigene Family ; O Antigens/*chemistry/genetics/metabolism ; Oligonucleotide Array Sequence Analysis ; Serotyping/methods ; }, abstract = {The O antigen, consisting of many repeats of an oligosaccharide unit, is part of the lipopolysaccharide (LPS) in the outer membrane of Gram-negative bacteria. It is on the cell surface and appears to be a major target for both immune system and bacteriophages, and therefore becomes one of the most variable cell constituents. The variability of the O antigen provides the major basis for serotyping schemes of Gram-negative bacteria. The genes responsible for the synthesis of O antigen are usually in a single cluster known as O antigen gene cluster, and their location on the chromosome within a species is generally conserved. Three O antigen biosynthesis pathways including Wzx/Wzy, ABC-transporter and Synthase have been discovered. In this chapter, the traditional and molecular O serotyping schemes are compared, O antigen structures and gene clusters of well-studied species are described, processes for formation and distribution of the variety of O antigens are discussed, and finally, the role of O antigen in bacterial virulence.}, }
@article {pmid20591532, year = {2010}, author = {Schaack, S and Gilbert, C and Feschotte, C}, title = {Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution.}, journal = {Trends in ecology &amp; evolution}, volume = {25}, number = {9}, pages = {537-546}, pmid = {20591532}, issn = {0169-5347}, support = {R01 GM077582/GM/NIGMS NIH HHS/United States ; R01 GM077582-04/GM/NIGMS NIH HHS/United States ; R01GM77582/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Physiological/*genetics ; Animals ; Bacteria/*genetics ; DNA/*genetics ; DNA Transposable Elements/*genetics/physiology ; *Evolution, Molecular ; Plants/*genetics ; }, abstract = {Horizontal transfer is the passage of genetic material between genomes by means other than parent-to-offspring inheritance. Although the transfer of genes is thought to be crucial in prokaryotic evolution, few instances of horizontal gene transfer have been reported in multicellular eukaryotes; instead, most cases involve transposable elements. With over 200 cases now documented, it is possible to assess the importance of horizontal transfer for the evolution of transposable elements and their host genomes. We review criteria for detecting horizontal transfers and examine recent examples of the phenomenon, shedding light on its mechanistic underpinnings, including the role of host-parasite interactions. We argue that the introduction of transposable elements by horizontal transfer in eukaryotic genomes has been a major force propelling genomic variation and biological innovation.}, }
@article {pmid20584746, year = {2010}, author = {Sadowy, E and Matynia, B and Hryniewicz, W}, title = {Population structure, virulence factors and resistance determinants of invasive, non-invasive and colonizing Streptococcus agalactiae in Poland.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {65}, number = {9}, pages = {1907-1914}, doi = {10.1093/jac/dkq230}, pmid = {20584746}, issn = {1460-2091}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Anti-Bacterial Agents/pharmacology ; *Bacterial Typing Techniques ; Carrier State/*microbiology ; DNA Fingerprinting ; DNA Transposable Elements ; DNA, Bacterial/chemistry/genetics ; *Drug Resistance, Bacterial ; Female ; Genes, Bacterial ; Genotype ; Humans ; Infant ; Infant, Newborn ; Male ; Middle Aged ; Molecular Sequence Data ; Phenotype ; Poland ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Serotyping ; Streptococcal Infections/*microbiology ; Streptococcus agalactiae/*classification/drug effects/*genetics/pathogenicity ; Virulence Factors/*genetics ; }, abstract = {OBJECTIVES: To analyse Streptococcus agalactiae (group B Streptococcus; GBS) isolates collected in Poland from various human infections and carriage in respect of their clonality, distribution of virulence factors and antimicrobial resistance determinants, including the detection of transposons involved in the dissemination of antimicrobial resistance.<br><br>METHODS: One hundred and fourteen GBS isolates were analysed by multilocus sequence typing (MLST), serotyping and detection of alp genes of the alpha-like-protein (Alp) family. Determinants of resistance to macrolides and tetracycline, and associated transposons, were detected by PCR and analysed by sequencing.<br><br>RESULTS: GBS isolates represented 30 different sequence types (STs), grouped in four clonal complexes (CCs), and belonged to seven serotypes. Serotype III was predominant (36.0%), followed by Ia, V, Ib, II, IV and VI. The most common alp genes were rib (26.3%) and alp1/alp5 (23.7%). The bac gene encoding the beta-compound of the surface C-protein was present in 17.5% of isolates. Erythromycin resistance (18.4% of isolates) was found in all CCs, but was associated with serotype V and ST1. The most prevalent determinant of resistance was erm(B), usually located on the Tn3872-like transposon. Several changes were observed in the regulatory region of erm(B), some of them resulting in elevated ketolide MICs. Resistance to tetracycline was ubiquitous (91.2%) and its most common determinant was tet(M), occurring in several variants that were typically carried on Tn916-family transposons.<br><br>CONCLUSIONS: Analysis of bacterial serotypes, alp genes and antimicrobial resistance determinants in the background of MLST-based population structure strengthened evidence of the importance of horizontal gene transfer in GBS evolution.}, }
@article {pmid20583590, year = {2010}, author = {Pertseva, MN and Shpakov, AO}, title = {[Hypothesis of evolutionary origin of several human and animal diseases].}, journal = {Zhurnal evoliutsionnoi biokhimii i fiziologii}, volume = {46}, number = {3}, pages = {261-267}, pmid = {20583590}, issn = {0044-4529}, mesh = {Animals ; *Biological Evolution ; Disease/*etiology/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Humans ; *Models, Theoretical ; }, abstract = {Studies of our Laboratory in the field of molecular and evolutionary endocrinology have allowed us to put forward a hypothesis about evolutionary origin of endocrine and other diseases of human and animals. This hypothesis is considered using a model of hormonal signal systems. It is based on the concept formulated by the authors about molecular defects in hormonal signal systems as the key causes of endocrine diseases; on evolutionary conservatism of hormonal signal systems, which stems logically from the authors' concept of the prokaryotic origin and endosymbiotic appearance in the course of evolution of chemosignal systems in the higher eukaryotes; from the fact that the process of formation of hormonal signal systems with participation of endosymbiosis including the horizontal transfer of genes is accompanied by transfer not only of normal, but also of the defected genetic material. There are considered examples of the principal possibility of transfer of defected genes between bacteria and eukaryotic organisms. Analysis of the current literature allows suggesting inheritance of pathogenic factors from evolutionary ancestors in the lineage prokaryotes--lower eukaryotes--higher eukaryotes.}, }
@article {pmid20582313, year = {2010}, author = {Klassen, JL}, title = {Phylogenetic and evolutionary patterns in microbial carotenoid biosynthesis are revealed by comparative genomics.}, journal = {PloS one}, volume = {5}, number = {6}, pages = {e11257}, pmid = {20582313}, issn = {1932-6203}, mesh = {Bacteria/metabolism ; Carotenoids/*biosynthesis ; Fungi/metabolism ; Gene Transfer, Horizontal ; *Genomics ; Oxidoreductases/metabolism ; *Phylogeny ; }, abstract = {BACKGROUND: Carotenoids are multifunctional, taxonomically widespread and biotechnologically important pigments. Their biosynthesis serves as a model system for understanding the evolution of secondary metabolism. Microbial carotenoid diversity and evolution has hitherto been analyzed primarily from structural and biosynthetic perspectives, with the few phylogenetic analyses of microbial carotenoid biosynthetic proteins using either used limited datasets or lacking methodological rigor. Given the recent accumulation of microbial genome sequences, a reappraisal of microbial carotenoid biosynthetic diversity and evolution from the perspective of comparative genomics is warranted to validate and complement models of microbial carotenoid diversity and evolution based upon structural and biosynthetic data.<br><br>Comparative genomics were used to identify and analyze in silico microbial carotenoid biosynthetic pathways. Four major phylogenetic lineages of carotenoid biosynthesis are suggested composed of: (i) Proteobacteria; (ii) Firmicutes; (iii) Chlorobi, Cyanobacteria and photosynthetic eukaryotes; and (iv) Archaea, Bacteroidetes and two separate sub-lineages of Actinobacteria. Using this phylogenetic framework, specific evolutionary mechanisms are proposed for carotenoid desaturase CrtI-family enzymes and carotenoid cyclases. Several phylogenetic lineage-specific evolutionary mechanisms are also suggested, including: (i) horizontal gene transfer; (ii) gene acquisition followed by differential gene loss; (iii) co-evolution with other biochemical structures such as proteorhodopsins; and (iv) positive selection.<br><br>CONCLUSIONS/SIGNIFICANCE: Comparative genomics analyses of microbial carotenoid biosynthetic proteins indicate a much greater taxonomic diversity then that identified based on structural and biosynthetic data, and divides microbial carotenoid biosynthesis into several, well-supported phylogenetic lineages not evident previously. This phylogenetic framework is applicable to understanding the evolution of specific carotenoid biosynthetic proteins or the unique characteristics of carotenoid biosynthetic evolution in a specific phylogenetic lineage. Together, these analyses suggest a "bramble" model for microbial carotenoid biosynthesis whereby later biosynthetic steps exhibit greater evolutionary plasticity and reticulation compared to those closer to the biosynthetic "root". Structural diversification may be constrained ("trimmed") where selection is strong, but less so where selection is weaker. These analyses also highlight likely productive avenues for future research and bioprospecting by identifying both gaps in current knowledge and taxa which may particularly facilitate carotenoid diversification.}, }
@article {pmid20581187, year = {2010}, author = {Coton, E and Mulder, N and Coton, M and Pochet, S and Trip, H and Lolkema, JS}, title = {Origin of the putrescine-producing ability of the coagulase-negative bacterium Staphylococcus epidermidis 2015B.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {16}, pages = {5570-5576}, pmid = {20581187}, issn = {1098-5336}, mesh = {Antiporters/genetics ; Bacterial Proteins/genetics ; Chromatography, High Pressure Liquid ; Cloning, Molecular ; DNA, Bacterial/chemistry/genetics ; Escherichia coli Proteins/genetics ; Lactococcus lactis/genetics/metabolism ; Molecular Sequence Data ; Ornithine/metabolism ; Ornithine Decarboxylase/genetics ; Plasmids ; Polymerase Chain Reaction ; Putrescine/*metabolism ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Staphylococcus epidermidis/genetics/*metabolism ; }, abstract = {A multiplex PCR method, aimed at the detection of genes associated with biogenic amine production, identified the odc gene encoding ornithine decarboxylase in 1 of 15 strains of Staphylococcus epidermidis. The ability of the positive strain, S. epidermidis 2015B, to produce putrescine in vitro was demonstrated by high-performance liquid chromatography (HPLC). In this strain, the odc gene was detected on plasmid DNA, suggesting that the ability to form putrescine is carried by a mobile element, which explains the fact that the trait is strain dependent within the S. epidermidis species. A 6,292-bp nucleotide sequence harboring the putative odc gene was determined. S. epidermidis ornithine decarboxylase (ODC) showed 60 to 65% sequence identity with known ODCs of Gram-positive as well as Gram-negative bacteria. Downstream of the odc gene, a gene encoding a putative amino acid transporter was found that shared 59% sequence identity with the ornithine/putrescine exchanger (PotE) of Escherichia coli. Cloning and expression of the potE gene of S. epidermis 2015B in Lactococcus lactis demonstrated that the gene product transported ornithine and putrescine into the cells and efficiently exchanged putrescine for ornithine. Analysis of the flanking regions showed high identity levels with different S. epidermidis plasmid sequences, which would confirm the plasmidic location of the odc operon. It follows that the odc and potE gene pair encodes a putrescine-producing pathway in S. epidermis 2015B that was acquired through horizontal gene transfer.}, }
@article {pmid20581182, year = {2010}, author = {Dodsworth, JA and Li, L and Wei, S and Hedlund, BP and Leigh, JA and de Figueiredo, P}, title = {Interdomain conjugal transfer of DNA from bacteria to archaea.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {16}, pages = {5644-5647}, pmid = {20581182}, issn = {1098-5336}, support = {R24 GM074783/GM/NIGMS NIH HHS/United States ; }, mesh = {*Conjugation, Genetic ; DNA, Bacterial/chemistry/*genetics ; Escherichia coli/*genetics ; Gene Transfer Techniques ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Vectors ; Methanococcus/*genetics ; Molecular Sequence Data ; Plasmids ; Sequence Analysis, DNA ; }, abstract = {Escherichia coli transforms the methanogenic archaeon Methanococcus maripaludis at frequencies ranging from 0.2 x 10(-6) to 2 x 10(-6) per recipient cell. Transformation requires cell-to-cell contact, oriT, and tra functions, is insensitive to DNase I, and otherwise displays hallmarks of conjugation.}, }
@article {pmid20580935, year = {2010}, author = {Chakraborty, S and Snijders, AP and Chakravorty, R and Ahmed, M and Tarek, AM and Hossain, MA}, title = {Comparative network clustering of direct repeats (DRs) and cas genes confirms the possibility of the horizontal transfer of CRISPR locus among bacteria.}, journal = {Molecular phylogenetics and evolution}, volume = {56}, number = {3}, pages = {878-887}, doi = {10.1016/j.ympev.2010.05.020}, pmid = {20580935}, issn = {1095-9513}, mesh = {Bacteria/classification/*genetics ; Cluster Analysis ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; *Repetitive Sequences, Nucleic Acid ; Sequence Alignment ; Sequence Analysis, RNA ; }, abstract = {CRISPRs are a diverse family of DNA repeat sequences that are widely distributed among archaea and bacteria. The CRISPR locus is usually composed of three key elements; direct repeats (DRs), spacer sequences and the cas genes. Although recent studies have suggested that spacers may be of extrachromosomal origin, the evolutionary origin of the other two elements of the CRISPR locus has remained unresolved. With the aim to elucidate the evolutionary origin and association of DRs and cas genes of the CRISPR locus, a comparative analysis of the evolutionary network clusters of DRs, cas1 and 16S rRNA genes sequences from 100 different bacteria was conducted. Significant matches of DR and cas1 gene clades imply that these CRISPR components are evolutionary closely linked and potentially evolving simultaneously as a whole locus. On the contrary, the prominent discordance between the CASS (DR and cas1) clades and the 16S rRNA clusters indicates that CRISPR locus has been transferred horizontally as a complete package. Sequence analysis also revealed that DR and cas1 genes are coevolving under analogous evolutionary pressure. This atypical evolutionary pattern also signifies the possibility of horizontal transfer event of CRISPR locus.}, }
@article {pmid20580457, year = {2010}, author = {Zago, M and Huys, G and Giraffa, G}, title = {Molecular basis and transferability of tetracycline resistance in Enterococcus italicus LMG 22195 from fermented milk.}, journal = {International journal of food microbiology}, volume = {142}, number = {1-2}, pages = {234-236}, doi = {10.1016/j.ijfoodmicro.2010.05.022}, pmid = {20580457}, issn = {1879-3460}, mesh = {Animals ; Cattle ; Enterococcus/drug effects/*genetics/isolation &amp; purification/metabolism ; *Fermentation ; *Gene Transfer, Horizontal ; Milk/*microbiology ; Plasmids/genetics ; Tetracycline/pharmacology ; *Tetracycline Resistance ; }, abstract = {A tetracycline-resistant Enterococcus italicus strain from fermented milk, LMG 22195, was found to contain a tet(S) gene located on a plasmid of approximately 20kb. Filter mating demonstrated that the tet(S) gene was transferable from LMG 22195 to the recipient Enterococcus faecalis JH2-2. PCR-based detection and Southern blot experiments revealed that the confirmed transconjugants acquired the tet(S)-carrying plasmid. Similar to the donor strain, transconjugants displayed a tetracycline MIC of 64 microg/ml. Results of this study suggest that E. italicus, like other enterococcal species, is able to disseminate antibiotic-resistance genes, although a more definitive proof on this statement will be provided when a higher number of strains will be tested. Because of the recent isolation of E. italicus from human clinical specimens and its concomitant presence in various dairy products, the ability of this organism to horizontally transfer tet(S) or other resistance genes may potentially pose safety concerns, especially for its possible use in food fermentations.}, }
@article {pmid20579371, year = {2010}, author = {Ghoshroy, S and Binder, M and Tartar, A and Robertson, DL}, title = {Molecular evolution of glutamine synthetase II: Phylogenetic evidence of a non-endosymbiotic gene transfer event early in plant evolution.}, journal = {BMC evolutionary biology}, volume = {10}, number = {}, pages = {198}, pmid = {20579371}, issn = {1471-2148}, mesh = {Bayes Theorem ; Chlorophyta/enzymology/genetics ; DNA, Algal/genetics ; *Evolution, Molecular ; Gammaproteobacteria/enzymology/genetics ; *Gene Transfer, Horizontal ; Glutamate-Ammonia Ligase/*genetics ; Likelihood Functions ; Multigene Family ; *Phylogeny ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {BACKGROUND: Glutamine synthetase (GS) is essential for ammonium assimilation and the biosynthesis of glutamine. The three GS gene families (GSI, GSII, and GSIII) are represented in both prokaryotic and eukaryotic organisms. In this study, we examined the evolutionary relationship of GSII from eubacterial and eukaryotic lineages and present robust phylogenetic evidence that GSII was transferred from gamma-Proteobacteria (Eubacteria) to the Chloroplastida.<br><br>RESULTS: GSII sequences were isolated from four species of green algae (Trebouxiophyceae), and additional green algal (Chlorophyceae and Prasinophytae) and streptophyte (Charales, Desmidiales, Bryophyta, Marchantiophyta, Lycopodiophyta and Tracheophyta) sequences were obtained from public databases. In Bayesian and maximum likelihood analyses, eubacterial (GSIIB) and eukaryotic (GSIIE) GSII sequences formed distinct clades. Both GSIIB and GSIIE were found in chlorophytes and early-diverging streptophytes. The GSIIB enzymes from these groups formed a well-supported sister clade with the gamma-Proteobacteria, providing evidence that GSIIB in the Chloroplastida arose by horizontal gene transfer (HGT). Bayesian relaxed molecular clock analyses suggest that GSIIB and GSIIE coexisted for an extended period of time but it is unclear whether the proposed HGT happened prior to or after the divergence of the primary endosymbiotic lineages (the Archaeplastida). However, GSIIB genes have not been identified in glaucophytes or red algae, favoring the hypothesis that GSIIB was gained after the divergence of the primary endosymbiotic lineages. Duplicate copies of the GSIIB gene were present in Chlamydomonas reinhardtii, Volvox carteri f. nagariensis, and Physcomitrella patens. Both GSIIB proteins in C. reinhardtii and V. carteri f. nagariensis had N-terminal transit sequences, indicating they are targeted to the chloroplast or mitochondrion. In contrast, GSIIB proteins of P. patens lacked transit sequences, suggesting a cytosolic function. GSIIB sequences were absent in vascular plants where the duplication of GSIIE replaced the function of GSIIB.<br><br>CONCLUSIONS: Phylogenetic evidence suggests GSIIB in Chloroplastida evolved by HGT, possibly after the divergence of the primary endosymbiotic lineages. Thus while multiple GS isoenzymes are common among members of the Chloroplastida, the isoenzymes may have evolved via different evolutionary processes. The acquisition of essential enzymes by HGT may provide rapid changes in biochemical capacity and therefore be favored by natural selection.}, }
@article {pmid20578915, year = {2010}, author = {Hammerum, AM and Lester, CH and Heuer, OE}, title = {Antimicrobial-resistant enterococci in animals and meat: a human health hazard?.}, journal = {Foodborne pathogens and disease}, volume = {7}, number = {10}, pages = {1137-1146}, doi = {10.1089/fpd.2010.0552}, pmid = {20578915}, issn = {1556-7125}, mesh = {Animals ; Anti-Infective Agents/administration &amp; dosage ; DNA Transposable Elements/genetics ; Drug Resistance, Bacterial/*genetics ; Enterococcus faecalis/drug effects/*genetics/growth &amp; development ; Enterococcus faecium/drug effects/*genetics/growth &amp; development ; Gene Transfer, Horizontal/genetics ; Gentamicins/administration &amp; dosage ; Gram-Positive Bacterial Infections/drug therapy ; Humans ; Intestines/microbiology ; Meat/*microbiology ; Models, Animal ; Vancomycin Resistance/genetics ; Veterinary Drugs/administration &amp; dosage ; }, abstract = {Enterococcus faecium and Enterococcus faecalis belong to the gastrointestinal flora of humans and animals. Although normally regarded harmless commensals, enterococci may cause a range of different infections in humans, including urinary tract infections, sepsis, and endocarditis. The use of avoparcin, gentamicin, and virginiamycin for growth promotion and therapy in food animals has lead to the emergence of vancomycin- and gentamicin-resistant enterococci and quinupristin/dalfopristin-resistant E. faecium in animals and meat. This implies a potential risk for transfer of resistance genes or resistant bacteria from food animals to humans. The genes encoding resistance to vancomycin, gentamicin, and quinupristin/dalfopristin have been found in E. faecium of human and animal origin; meanwhile, certain clones of E. faecium are found more frequently in samples from human patients, while other clones predominate in certain animal species. This may suggest that antimicrobial-resistant E. faecium from animals could be regarded less hazardous to humans; however, due to their excellent ability to acquire and transfer resistance genes, E. faecium of animal origin may act as donors of antimicrobial resistance genes for other more virulent enterococci. For E. faecalis, the situation appears different, as similar clones of, for example, vancomycin- and gentamicin-resistant E. faecalis have been obtained from animals and from human patients. Continuous surveillance of antimicrobial resistance in enterococci from humans and animals is essential to follow trends and detect emerging resistance.}, }
@article {pmid20576143, year = {2010}, author = {Ong, CL and Beatson, SA and Totsika, M and Forestier, C and McEwan, AG and Schembri, MA}, title = {Molecular analysis of type 3 fimbrial genes from Escherichia coli, Klebsiella and Citrobacter species.}, journal = {BMC microbiology}, volume = {10}, number = {}, pages = {183}, pmid = {20576143}, issn = {1471-2180}, mesh = {Citrobacter freundii/genetics/*metabolism ; Citrobacter koseri/genetics/*metabolism ; Escherichia coli/genetics/*metabolism ; Fimbriae Proteins/classification/genetics/*metabolism ; Gene Expression Regulation, Bacterial/physiology ; Klebsiella oxytoca/genetics/*metabolism ; Klebsiella pneumoniae/genetics/*metabolism ; Phylogeny ; }, abstract = {BACKGROUND: Catheter-associated urinary tract infection (CAUTI) is the most common nosocomial infection in the United States and is caused by a range of uropathogens. Biofilm formation by uropathogens that cause CAUTI is often mediated by cell surface structures such as fimbriae. In this study, we characterised the genes encoding type 3 fimbriae from CAUTI strains of Escherichia coli, Klebsiella pneumoniae, Klebsiella oxytoca, Citrobacter koseri and Citrobacter freundii.<br><br>RESULTS: Phylogenetic analysis of the type 3 fimbrial genes (mrkABCD) from 39 strains revealed they clustered into five distinct clades (A-E) ranging from one to twenty-three members. The majority of sequences grouped in clade A, which was represented by the mrk gene cluster from the genome sequenced K. pneumoniae MGH78578. The E. coli and K. pneumoniae mrkABCD gene sequences clustered together in two distinct clades, supporting previous evidence for the occurrence of inter-genera lateral gene transfer. All of the strains examined caused type 3 fimbriae mediated agglutination of tannic acid treated human erythrocytes despite sequence variation in the mrkD-encoding adhesin gene. Type 3 fimbriae deletion mutants were constructed in 13 representative strains and were used to demonstrate a direct role for type 3 fimbriae in biofilm formation.<br><br>CONCLUSIONS: The expression of functional type 3 fimbriae is common to many Gram-negative pathogens that cause CAUTI and is strongly associated with biofilm growth. Our data provides additional evidence for the spread of type 3 fimbrial genes by lateral gene transfer. Further work is now required to substantiate the clade structure reported here by examining more strains as well as other bacterial genera that make type 3 fimbriae and cause CAUTI.}, }
@article {pmid20573216, year = {2010}, author = {Yu, FY and Yao, D and Pan, JY and Chen, C and Qin, ZQ and Parsons, C and Yang, LH and Li, QQ and Zhang, XQ and Qu, D and Wang, LX}, title = {High prevalence of plasmid-mediated 16S rRNA methylase gene rmtB among Escherichia coli clinical isolates from a Chinese teaching hospital.}, journal = {BMC infectious diseases}, volume = {10}, number = {}, pages = {184}, pmid = {20573216}, issn = {1471-2334}, mesh = {Aminoglycosides/*pharmacology ; Anti-Bacterial Agents/pharmacology ; Bacterial Typing Techniques ; China ; Cluster Analysis ; Conjugation, Genetic ; DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; *Drug Resistance, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/*enzymology/*genetics/isolation &amp; purification ; Escherichia coli Infections/*microbiology ; Escherichia coli Proteins/*genetics ; Gene Transfer, Horizontal ; Hospitals, Teaching ; Humans ; In Situ Hybridization ; Methyltransferases/*genetics ; *Plasmids ; Polymerase Chain Reaction ; Prevalence ; Sequence Analysis, DNA ; beta-Lactamases/genetics ; }, abstract = {BACKGROUND: Recently, production of 16S rRNA methylases by Gram-negative bacilli has emerged as a novel mechanism for high-level resistance to aminoglycosides by these organisms in a variety of geographic locations. Therefore, the spread of high-level aminoglycoside resistance determinants has become a great concern.<br><br>METHODS: Between January 2006 and July 2008, 680 distinct Escherichia coli clinical isolates were collected from a teaching hospital in Wenzhou, China. PCR and DNA sequencing were used to identify 16S rRNA methylase and extended-spectrum beta-lactamase (ESBL) genes, including armA and rmtB, and in situ hybridization was performed to determine the location of 16S rRNA methylase genes. Conjugation experiments were subsequently performed to determine whether aminoglycoside resistance was transferable from the E. coli isolates via 16S rRNA methylase-bearing plasmids. Homology of the isolates harboring 16S rRNA methylase genes was determined using pulse-field gel electrophoresis (PFGE).<br><br>RESULTS: Among the 680 E. coli isolates, 357 (52.5%), 346 (50.9%) and 44 (6.5%) isolates were resistant to gentamicin, tobramycin and amikacin, respectively. Thirty-seven of 44 amikacin-resistant isolates harbored 16S rRNA methylase genes, with 36 of 37 harboring the rmtB gene and only one harboring armA. The positive rates of 16S rRNA methylase genes among all isolates and amikacin-resistant isolates were 5.4% (37/680) and 84.1% (37/44), respectively. Thirty-one isolates harboring 16S rRNA methylase genes also produced ESBLs. In addition, high-level aminoglycoside resistance could be transferred by conjugation from four rmtB-positive donors. The plasmids of incompatibility groups IncF, IncK and IncN were detected in 34, 3 and 3 isolates, respectively. Upstream regions of the armA gene contained ISCR1 and tnpU, the latter a putative transposase gene,. Another putative transposase gene, tnpD, was located within a region downstream of armA. Moreover, a transposon, Tn3, was located upstream of the rmtB. Nineteen clonal patterns were obtained by PFGE, with type H representing the prevailing pattern.<br><br>CONCLUSION: A high prevalence of plasmid-mediated rmtB gene was found among clinical E. coli isolates from a Chinese teaching hospital. Both horizontal gene transfer and clonal spread were responsible for the dissemination of the rmtB gene.}, }
@article {pmid20571942, year = {2010}, author = {Bal, EB and Bayar, S and Bal, MA}, title = {Antimicrobial susceptibilities of coagulase-negative staphylococci (CNS) and streptococci from bovine subclinical mastitis cases.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {48}, number = {3}, pages = {267-274}, pmid = {20571942}, issn = {1976-3794}, mesh = {Animals ; Base Sequence ; Cattle ; Coagulase/metabolism ; DNA Primers/genetics ; Drug Resistance, Bacterial/genetics ; Female ; Genes, Bacterial ; Humans ; Mastitis, Bovine/*drug therapy/*microbiology ; Methicillin Resistance/genetics ; Microbial Sensitivity Tests ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Staphylococcal Infections/drug therapy/microbiology/*veterinary ; Staphylococcus/*drug effects/enzymology/genetics/isolation &amp; purification ; Staphylococcus haemolyticus/drug effects/genetics/isolation &amp; purification ; Streptococcal Infections/drug therapy/microbiology/*veterinary ; Streptococcus/*drug effects/genetics/isolation &amp; purification ; }, abstract = {The prevalence and antimicrobial susceptibilities of Staphylococci and Streptococci were assessed from subclinical mastitis cases. One hundred Coagulase-Negative Staphylococci (CNS) and 34 Streptococci were identified. The most frequently isolated species were Staphylococcus haemolyticus (27%) and Staphylococcus simulans (24%). Susceptible CNS species revealed the highest resistance to penicillin G (58%), ampicillin (48%), neomycin (20%), and oleandomycin (14%). CNS methicillin resistance rates within 82 isolates were 21.95% and 1.22% by disk diffusion and PCR methods, respectively. These results suggested the disk diffusion method was more prone to yield false positives. Partial sequencing of the 16S rRNA region from the mecA carrying isolate (S. haemolyticus) was homologous with S. haemolyticus sequences/accessions obtained from GenBank. However, the mecA gene sequence from this isolate was more closely allied with the S. aureus mecA gene of human origins. Identical sequence data was acquired from the National Center for Biotechnology Information (NCBI) database, suggesting horizontal gene transfer between the two species. CNS beta-lactamase activity within 81 isolates was 29.63%. The most frequently isolated Streptococcus species were S. uberis (52%) and S. agalactiae (15%). Oleandomycin was the least effective antimicrobial agent on these isolates with 59% susceptibility. Results indicated that CNS and Streptococci exhibited various antimicrobial resistance responses. Consequently, isolation and identification of udder pathogens in herds suffering from subclinical agents is essential to select the most effective antimicrobial agent. Moreover, multiple resistance features of methicillin resistant (MR) isolates should be considered during antimicrobial susceptibility tests.}, }
@article {pmid20569494, year = {2010}, author = {Tijsse-Klasen, E and Fonville, M and van Overbeek, L and Reimerink, JH and Sprong, H}, title = {Exotic Rickettsiae in Ixodes ricinus: fact or artifact?.}, journal = {Parasites &amp; vectors}, volume = {3}, number = {}, pages = {54}, pmid = {20569494}, issn = {1756-3305}, abstract = {Several pathogenic Rickettsia species can be transmitted via Ixodes ricinus ticks to humans and animals. Surveys of I. ricinus for the presence of Rickettsiae using part of its 16S rRNA gene yield a plethora of new and different Rickettsia sequences. Interpreting these data is sometimes difficult and presenting these findings as new or potentially pathogenic Rickettsiae should be done with caution: a recent report suggested presence of a known human pathogen, R. australis, in questing I. ricinus ticks in Europe. A refined analysis of these results revealed that R. helvetica was most likely to be misinterpreted as R. australis. Evidence in the literature is accumulating that rickettsial DNA sequences found in tick lysates can also be derived from other sources than viable, pathogenic Rickettsiae. For example, from endosymbionts, environmental contamination or even horizontal gene transfer.}, }
@article {pmid20569265, year = {2010}, author = {Hegstad, K and Mikalsen, T and Coque, TM and Werner, G and Sundsfjord, A}, title = {Mobile genetic elements and their contribution to the emergence of antimicrobial resistant Enterococcus faecalis and Enterococcus faecium.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {16}, number = {6}, pages = {541-554}, doi = {10.1111/j.1469-0691.2010.03226.x}, pmid = {20569265}, issn = {1469-0691}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Typing Techniques/methods ; *Drug Resistance, Multiple, Bacterial ; Enterococcus faecalis/*drug effects/*genetics ; Enterococcus faecium/*drug effects/*genetics ; Gene Transfer, Horizontal ; Humans ; *Interspersed Repetitive Sequences ; Molecular Epidemiology/methods ; }, abstract = {Mobile genetic elements (MGEs) including plasmids and transposons are pivotal in the dissemination and persistence of antimicrobial resistance in Enterococcus faecalis and Enterococcus faecium. Enterococcal MGEs have also been shown to be able to transfer resistance determinants to more pathogenic bacteria such as Staphylococcus aureus. Despite their importance, we have a limited knowledge about the prevalence, distribution and genetic content of specific MGEs in enterococcal populations. Molecular epidemiological studies of enterococcal MGEs have been hampered by the lack of standardized molecular typing methods and relevant genome information. This review focuses on recent developments in the detection of MGEs and their contribution to the spread of antimicrobial resistance in clinically relevant enterococci.}, }
@article {pmid20566881, year = {2010}, author = {Manson, JM and Hancock, LE and Gilmore, MS}, title = {Mechanism of chromosomal transfer of Enterococcus faecalis pathogenicity island, capsule, antimicrobial resistance, and other traits.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {27}, pages = {12269-12274}, pmid = {20566881}, issn = {1091-6490}, support = {R01AI072360/AI/NIAID NIH HHS/United States ; R01 AI072360/AI/NIAID NIH HHS/United States ; P01 AI083214/AI/NIAID NIH HHS/United States ; R01 AI077782/AI/NIAID NIH HHS/United States ; P01AI083214/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Capsules/metabolism ; Bacterial Infections/microbiology ; Bacteriophages/genetics ; Chromosomes, Bacterial/*genetics ; *Conjugation, Genetic ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; Enterococcus faecalis/*genetics/metabolism/pathogenicity ; Gene Transfer, Horizontal ; Genomic Islands/*genetics ; Humans ; Mutation ; Plasmids/genetics ; Transduction, Genetic ; Vancomycin Resistance/genetics ; Virulence/genetics ; }, abstract = {The Enterococcus faecalis pathogenicity island (PAI) encodes known virulence traits and >100 additional genes with unknown roles in enterococcal biology. Phage-related integration and excision genes, and direct repeats flanking the island, suggest it moves as an integrative conjugative element (ICE). However, transfer was observed not to require these genes. Transfer only occurred from donors possessing a pheromone responsive-type of conjugative plasmid, and was invariably accompanied by transfer of flanking donor chromosome sequences. Deletion of plasmid transfer functions, including the cis-acting origin of transfer (oriT), abolished movement. In addition to demonstrating PAI movement by a mechanism involving plasmid integration, we observed transfer of a selectable marker placed virtually anywhere on the chromosome. Transfer of this selectable marker was observed to be accompanied by chromosome-chromosome transfer of vancomycin resistance, MLST markers, and capsule genes as well. Plasmid mobilization therefore appears to be a major mechanism for horizontal gene transfer in the evolution of antibiotic resistant E. faecalis strains capable of causing human infection.}, }
@article {pmid20565933, year = {2010}, author = {Minge, MA and Shalchian-Tabrizi, K and Tørresen, OK and Takishita, K and Probert, I and Inagaki, Y and Klaveness, D and Jakobsen, KS}, title = {A phylogenetic mosaic plastid proteome and unusual plastid-targeting signals in the green-colored dinoflagellate Lepidodinium chlorophorum.}, journal = {BMC evolutionary biology}, volume = {10}, number = {}, pages = {191}, pmid = {20565933}, issn = {1471-2148}, mesh = {Amino Acid Sequence ; Dinoflagellida/classification/*genetics ; Evolution, Molecular ; Gene Library ; Gene Transfer, Horizontal ; Molecular Sequence Data ; *Phylogeny ; Plastids/*genetics/metabolism ; Proteome/*genetics ; RNA, Protozoan/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Symbiosis/genetics ; }, abstract = {BACKGROUND: Plastid replacements through secondary endosymbioses include massive transfer of genes from the endosymbiont to the host nucleus and require a new targeting system to enable transport of the plastid-targeted proteins across 3-4 plastid membranes. The dinoflagellates are the only eukaryotic lineage that has been shown to have undergone several plastid replacement events, and this group is thus highly relevant for studying the processes involved in plastid evolution. In this study, we analyzed the phylogenetic origin and N-terminal extensions of plastid-targeted proteins from Lepidodinium chlorophorum, a member of the only dinoflagellate genus that harbors a green secondary plastid rather than the red algal-derived, peridinin-containing plastid usually found in photosynthetic dinoflagellates.<br><br>RESULTS: We sequenced 4,746 randomly picked clones from a L. chlorophorum cDNA library. 22 of the assembled genes were identified as genes encoding proteins functioning in plastids. Some of these were of green algal origin. This confirms that genes have been transferred from the plastid to the host nucleus of L. chlorophorum and indicates that the plastid is fully integrated as an organelle in the host. Other nuclear-encoded plastid-targeted protein genes, however, are clearly not of green algal origin, but have been derived from a number of different algal groups, including dinoflagellates, streptophytes, heterokonts, and red algae. The characteristics of N-terminal plastid-targeting peptides of all of these genes are substantially different from those found in peridinin-containing dinoflagellates and green algae.<br><br>CONCLUSIONS: L. chlorophorum expresses plastid-targeted proteins with a range of different origins, which probably arose through endosymbiotic gene transfer (EGT) and horizontal gene transfer (HGT). The N-terminal extension of the genes is different from the extensions found in green alga and other dinoflagellates (peridinin- and haptophyte plastids). These modifications have likely enabled the mosaic proteome of L. chlorophorum.}, }
@article {pmid20562341, year = {2010}, author = {Tria, F and Caglioti, E and Loreto, V and Pagnani, A}, title = {A stochastic local search algorithm for distance-based phylogeny reconstruction.}, journal = {Molecular biology and evolution}, volume = {27}, number = {11}, pages = {2587-2595}, doi = {10.1093/molbev/msq154}, pmid = {20562341}, issn = {1537-1719}, mesh = {*Algorithms ; Animals ; Computational Biology/*methods ; Gene Transfer, Horizontal/genetics ; Mutation/genetics ; *Phylogeny ; Stochastic Processes ; }, abstract = {In many interesting cases, the reconstruction of a correct phylogeny is blurred by high mutation rates and/or horizontal transfer events. As a consequence, a divergence arises between the true evolutionary distances and the differences between pairs of taxa as inferred from available data, making the phylogenetic reconstruction a challenging problem. Mathematically, this divergence translates in a loss of additivity of the actual distances between taxa. In distance-based reconstruction methods, two properties of additive distances have been extensively exploited as antagonist criteria to drive phylogeny reconstruction: On the one hand, a local property of quartets, that is, sets of four taxa in a tree, the four-points condition; on the other hand, a recently proposed formula that allows to write the tree length as a function of the distances between taxa, Pauplin's formula. Here, we introduce a new reconstruction scheme that exploits in a unified framework both the four-points condition and the Pauplin's formula. We propose, in particular, a new general class of distance-based Stochastic Local Search algorithms, which reduces in a limit case to the minimization of Pauplin's length. When tested on artificially generated phylogenies, our Stochastic Big-Quartet Swapping algorithmic scheme significantly outperforms state-of-art distance-based algorithms in cases of deviation from additivity due to high rate of back mutations. A significant improvement is also observed with respect to the state-of-art algorithms in the case of high rate of horizontal transfer.}, }
@article {pmid20558546, year = {2010}, author = {Widmann, J and Harris, JK and Lozupone, C and Wolfson, A and Knight, R}, title = {Stable tRNA-based phylogenies using only 76 nucleotides.}, journal = {RNA (New York, N.Y.)}, volume = {16}, number = {8}, pages = {1469-1477}, pmid = {20558546}, issn = {1469-9001}, support = {T32 GM008759/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; T32 GM08759/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Pairing ; Cluster Analysis ; Conserved Sequence/genetics ; Gene Transfer, Horizontal ; Genome ; Nucleotides/genetics ; *Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; }, abstract = {tRNAs are among the most ancient, highly conserved sequences on earth, but are often thought to be poor phylogenetic markers because they are short, often subject to horizontal gene transfer, and easily change specificity. Here we use an algorithm now commonly used in microbial ecology, UniFrac, to cluster 175 genomes spanning all three domains of life based on the phylogenetic relationships among their complete tRNA pools. We find that the overall pattern of similarities and differences in the tRNA pools recaptures universal phylogeny to a remarkable extent, and that the resulting tree is similar to the distribution of bootstrapped rRNA trees from the same genomes. In contrast, the trees derived from tRNAs of identical specificity or of individual isoacceptors generally produced trees of lower quality. However, some tRNA isoacceptors were very good predictors of the overall pattern of organismal evolution. These results show that UniFrac can extract meaningful biological patterns from even phylogenies with high level of statistical inaccuracy and horizontal gene transfer, and that, overall, the pattern of tRNA evolution tracks universal phylogeny and provides a background against which we can test hypotheses about the evolution of individual isoacceptors.}, }
@article {pmid20558469, year = {2010}, author = {Sletvold, H and Johnsen, PJ and Wikmark, OG and Simonsen, GS and Sundsfjord, A and Nielsen, KM}, title = {Tn1546 is part of a larger plasmid-encoded genetic unit horizontally disseminated among clonal Enterococcus faecium lineages.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {65}, number = {9}, pages = {1894-1906}, pmid = {20558469}, issn = {1460-2091}, mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins/*genetics ; Carbon-Oxygen Ligases/*genetics ; Chromosome Walking ; Cluster Analysis ; DNA Primers/genetics ; *DNA Transposable Elements ; DNA, Bacterial/chemistry/genetics ; Enterococcus faecium/*genetics/isolation &amp; purification ; France ; Gene Order ; *Gene Transfer, Horizontal ; Gram-Positive Bacterial Infections/microbiology/veterinary ; Humans ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; *Plasmids ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {OBJECTIVES: To determine the genetic composition of the first VanA-type plasmid (pIP816) reported, which was isolated from a clinical Enterococcus faecium (BM4147) strain in France in 1986, and to reveal the genetic units responsible for the dissemination of the vanA gene cluster by comparisons with current, published and additionally generated vanA-spanning plasmid sequences obtained from a heterogeneous E. faecium strain collection (n = 28).<br><br>METHODS: Plasmid sequences were produced by shotgun sequencing using ABI dye chemistry and primer walking, and were subsequently annotated. Comparative sequence analysis of the vanA region was done with published plasmids, with a partial vanA plasmid (pVEF4) reported here and to >140 kb of sequence obtained from a collection of vanA-harbouring plasmid fragments.<br><br>RESULTS: Bioinformatic analyses revealed that pIP816 from 1986 and contemporary vanA plasmids shared a conserved genetic fragment of 25 kb, spanning the 10.85 kb vanA cluster encoded by Tn1546, and that the larger unit is present in both clinical and animal complexes of E. faecium. A new group II intron in pVEF4 was characterized.<br><br>CONCLUSIONS: Comparative DNA analyses suggest that Tn1546 disseminates in and between clonal complexes of E. faecium as part of a larger genetic unit, possibly as a composite transposon flanked by IS1216 elements.}, }
@article {pmid20554693, year = {2010}, author = {Omer, S and Kovacs, A and Mazor, Y and Gophna, U}, title = {Integration of a foreign gene into a native complex does not impair fitness in an experimental model of lateral gene transfer.}, journal = {Molecular biology and evolution}, volume = {27}, number = {11}, pages = {2441-2445}, doi = {10.1093/molbev/msq145}, pmid = {20554693}, issn = {1537-1719}, mesh = {Electrophoresis, Polyacrylamide Gel ; Escherichia coli/enzymology/growth &amp; development ; *Gene Transfer Techniques ; *Genetic Fitness ; *Models, Genetic ; Mutagenesis, Insertional/*genetics ; Peptides/metabolism ; Plasmids/genetics ; Protein Binding ; Protein Subunits/metabolism ; }, abstract = {Lateral gene transfer (LGT) is a central force in microbial evolution. The observation that genes encoding subunits of complexes exhibit relatively compatible phylogenies, suggesting vertical descent, can be explained by different evolutionary scenarios. On the one hand, the failure of a new gene product to correctly interact with preexisting protein subunits can make its acquisition neutral-a theory termed the "complexity hypothesis." On the other hand, foreign subunit-encoding genes may reduce the fitness of the new host by disrupting the stoichiometric balance between complex subunits, resulting in purifying selection against gene retention. We previously showed in a model LGT system that overexpression of an orthologous subunit was neutral due to lack of interaction with host subunits. Here, we examine a case where the foreign protein is more similar to its native orthologs, by expressing the RNA polymerase β subunit (RpoB) of Bacillus subtilis in Escherichia coli. The foreign subunit is shown by coimmunoprecipitation to interact with the host subunits, and to form novel, nonspecific interactions. Nevertheless, the host did not incur any fitness disadvantage, as measured by its growth. We conclude that LGT of complex subunits may be neutral even when the transferred subunit can integrate into the host complex and that this neutrality can be a fertile ground for selective forces once the environment changes.}, }
@article {pmid20551688, year = {2010}, author = {Forterre, P}, title = {Giant viruses: conflicts in revisiting the virus concept.}, journal = {Intervirology}, volume = {53}, number = {5}, pages = {362-378}, doi = {10.1159/000312921}, pmid = {20551688}, issn = {1423-0100}, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal ; Mimiviridae/*genetics ; Recombination, Genetic ; }, abstract = {The current paradigm on the nature of viruses is based on early work of the 'phage group' (the pro-phage concept) and molecular biologists working on tumour viruses (the proto-oncogene concept). It posits that viruses evolved from either prokaryotic or eukaryotic cellular genes that became infectious via their association with capsid genes. In this view, after their emergence viruses continued to evolve by stealing cellular genes (the escape model). This paradigm has been challenged recently by scientists who propose that viruses pre-dated modern cells. In particular, the discovery of Mimivirus has stimulated a lot of discussions on the nature of viruses. There are two major schools of thought, those who defend the escape model, suggesting that giant viruses are giant pickpockets (chimera), and those who emphasize their uniqueness and ancient origin. Comparative genomics of Mimivirus and related viruses (nucleo-cytoplasmic large DNA viruses) have produced a lot of data that have been interpreted according to the prejudices of the authors and thus failed until now to generate a consensus. I briefly review here the history of these debates and how they lead to new proposals, such as the definition of viruses as capsid-encoding organisms or else the recognition of their fundamentally cellular nature, the virocell concept.}, }
@article {pmid20551687, year = {2010}, author = {Filée, J and Chandler, M}, title = {Gene exchange and the origin of giant viruses.}, journal = {Intervirology}, volume = {53}, number = {5}, pages = {354-361}, doi = {10.1159/000312920}, pmid = {20551687}, issn = {1423-0100}, mesh = {Amoeba/virology ; DNA, Viral/*genetics ; Eukaryota/virology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Interspersed Repetitive Sequences ; *Recombination, Genetic ; Viruses/*genetics ; }, abstract = {Giant viruses or nucleocytoplasmic large DNA viruses (NCLDVs) infect a wide range of eukaryotic hosts (including, algae, amoebae and metazoans) and show a very large range in genome size (between 100 kb and 1.2 Mb). Here we review some recent results concerning the extensive lateral gene transfer which appears to have occurred during NCLDV evolution. Current data suggest that giant viruses probably originated from a simple and ancient viral ancestor with a small subset of 30-35 genes encoding replication and structural proteins. A large array of lateral gene transfers from diverse cellular sources, including several families of mobile genetic elements, is probably responsible for the huge diversity of genome size and composition found in extant giant viruses.}, }
@article {pmid20551685, year = {2010}, author = {Colson, P and Raoult, D}, title = {Gene repertoire of amoeba-associated giant viruses.}, journal = {Intervirology}, volume = {53}, number = {5}, pages = {330-343}, doi = {10.1159/000312918}, pmid = {20551685}, issn = {1423-0100}, mesh = {Amoeba/*virology ; Archaea/genetics ; Bacteria/genetics ; DNA Viruses/*genetics ; Eukaryota/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, Viral ; *Genome, Viral ; Open Reading Frames ; Recombination, Genetic ; Sequence Homology ; Viral Proteins/*genetics ; }, abstract = {Acanthamoeba polyphaga mimivirus, Marseillevirus, and Sputnik, a virophage, are intra-amoebal viruses that have been isolated from water collected in cooling towers. They have provided fascinating data and have raised exciting questions about viruses definition and evolution. Mimivirus and Marseillevirus have been classified in the nucleo-cytoplasmic large DNA viruses (NCLDVs) class. Their genomes are the largest and fifth largest viral genomes sequenced so far. The gene repertoire of these amoeba-associated viruses can be divided into four groups: the core genome, genes acquired by lateral gene transfer, duplicated genes, and ORFans. Open reading frames (ORFs) that have homologs in the NCLDVs core gene set represent 2.9 and 6.1% of the Mimivirus and Marseillevirus gene contents, respectively. A substantial proportion of the Mimivirus, Marseillevirus and Sputnik ORFs exhibit sequence similarities to homologs found in bacteria, archaea, eukaryotes or viruses. The large amount of chimeric genes in these viral genomes might have resulted from acquisitions by lateral gene transfers, implicating sympatric bacteria and viruses with an intra-amoebal lifestyle. In addition, lineage-specific gene expansion may have played a major role in the genome shaping. Altogether, the data so far accumulated on amoeba-associated giant viruses are a powerful incentive to isolate and study additional strains to gain better understanding of their pangenome.}, }
@article {pmid20551684, year = {2010}, author = {Raoult, D and Boyer, M}, title = {Amoebae as genitors and reservoirs of giant viruses.}, journal = {Intervirology}, volume = {53}, number = {5}, pages = {321-329}, doi = {10.1159/000312917}, pmid = {20551684}, issn = {1423-0100}, mesh = {Amoeba/microbiology/*virology ; Bacteria/genetics/isolation &amp; purification ; DNA Viruses/genetics/*isolation &amp; purification ; Evolution, Molecular ; Fungi/genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; Recombination, Genetic ; }, abstract = {Amoebae are unicellular phagocytes that feed on microorganisms in their environment. Some amoebae have the largest genome size currently known on earth. They phagocytose any inert particle larger than 0.5 microm. Phagocytic amoebae can harbor different bacteria, fungi and giant viruses within the same cell. There is evidence of lateral gene transfer between the amoeba and its microbiological hosts. There is also evidence of gene exchange between viruses and bacteria hosted in amoebae. Moreover, there is evidence of gene transfer between viruses, such as Mimivirus and the virophage. As a consequence, viruses and intracellular bacteria living in amoebae have a sympatric lifestyle and large chimeric genome repertoires. We conclude that phagocytic protists continuously generate new species with chimeric repertoires that may succeed later if adapted to the environmental conditions and selected in a specific niche.}, }
@article {pmid20551680, year = {2010}, author = {Koonin, EV and Yutin, N}, title = {Origin and evolution of eukaryotic large nucleo-cytoplasmic DNA viruses.}, journal = {Intervirology}, volume = {53}, number = {5}, pages = {284-292}, pmid = {20551680}, issn = {1423-0100}, support = {//Intramural NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Bacteriophages/genetics ; Cluster Analysis ; Computational Biology ; DNA Viruses/*genetics ; Eukaryota/*virology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Viral ; Interspersed Repetitive Sequences ; Phylogeny ; Recombination, Genetic ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND/AIMS: The nucleo-cytoplasmic large DNA viruses (NCLDV) constitute an apparently monophyletic group that consists of 6 families of viruses infecting a broad variety of eukaryotes. A comprehensive genome comparison and maximum-likelihood reconstruction of NCLDV evolution reveal a set of approximately 50 conserved genes that can be tentatively mapped to the genome of the common ancestor of this class of eukaryotic viruses. We address the origins and evolution of NCLDV.<br><br>RESULTS: Phylogenetic analysis indicates that some of the major clades of NCLDV infect diverse animals and protists, suggestive of early radiation of the NCLDV, possibly concomitant with eukaryogenesis. The core NCLDV genes seem to have originated from different sources including homologous genes of bacteriophages, bacteria and eukaryotes. These observations are compatible with a scenario of the origin of the NCLDV at an early stage of the evolution of eukaryotes through extensive mixing of genes from widely different genomes.<br><br>CONCLUSIONS: The common ancestor of the NCLDV probably evolved from a bacteriophage as a result of recruitment of numerous eukaryotic and some bacterial genes, and concomitant loss of the majority of phage genes except for a small core of genes coding for proteins essential for virus genome replication and virion formation.}, }
@article {pmid20551677, year = {2010}, author = {Thomas, V and Greub, G}, title = {Amoeba/amoebal symbiont genetic transfers: lessons from giant virus neighbours.}, journal = {Intervirology}, volume = {53}, number = {5}, pages = {254-267}, doi = {10.1159/000312910}, pmid = {20551677}, issn = {1423-0100}, mesh = {Amoeba/*virology ; Bacteria/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Recombination, Genetic ; Viruses/*genetics ; }, abstract = {Free-living amoebae serve as hosts for a variety of amoebae-resisting microorganisms, including giant viruses and certain bacteria. The latter include symbiotic bacteria as well as bacteria exhibiting a pathogenic phenotype towards amoebae. Amoebae-resisting bacteria have been shown to be widespread in water and to use the amoebae as a reservoir, a replication niche, a protective armour as well as a training ground to select virulence traits allowing survival in the face of microbicidal effects of macrophages, the first line of defense against invading pathogens. More importantly, amoebae play a significant role as a melting pot for genetic exchanges. These ecological and evolutionary roles of amoebae might also be at play for giant viruses and knowledge derived from the study of amoebae-resisting bacteria is useful for the study and understanding of interactions between amoebae and giant viruses. This is especially important since some genes have spread in all domains of life and the exponential availability of eukaryotic genomes and metagenomic sequences will allow researchers to explore these genetic exchanges in a more comprehensive way, thus completely changing our perception of the evolutionary history of organisms. Thus, a large part of this review is dedicated to report current known gene exchanges between the different amoebae-resisting organisms and between amoebae and the internalized bacteria.}, }
@article {pmid20551435, year = {2010}, author = {Hao, W and Golding, GB}, title = {Inferring bacterial genome flux while considering truncated genes.}, journal = {Genetics}, volume = {186}, number = {1}, pages = {411-426}, pmid = {20551435}, issn = {1943-2631}, mesh = {Evolution, Molecular ; *Gene Deletion ; Genes, Bacterial/*genetics ; INDEL Mutation ; Likelihood Functions ; *Models, Genetic ; Phylogeny ; }, abstract = {Bacterial gene content variation during the course of evolution has been widely acknowledged and its pattern has been actively modeled in recent years. Gene truncation or gene pseudogenization also plays an important role in shaping bacterial genome content. Truncated genes could also arise from small-scale lateral gene transfer events. Unfortunately, the information of truncated genes has not been considered in any existing mathematical models on gene content variation. In this study, we developed a model to incorporate truncated genes. Maximum-likelihood estimates (MLEs) of the new model reveal fast rates of gene insertions/deletions on recent branches, suggesting a fast turnover of many recently transferred genes. The estimates also suggest that many truncated genes are in the process of being eliminated from the genome. Furthermore, we demonstrate that the ignorance of truncated genes in the estimation does not lead to a systematic bias but rather has a more complicated effect. Analysis using the new model not only provides more accurate estimates on gene gains/losses (or insertions/deletions), but also reduces any concern of a systematic bias from applying simplified models to bacterial genome evolution. Although not a primary purpose, the model incorporating truncated genes could be potentially used for phylogeny reconstruction using gene family content.}, }
@article {pmid20550700, year = {2010}, author = {Abby, SS and Tannier, E and Gouy, M and Daubin, V}, title = {Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests.}, journal = {BMC bioinformatics}, volume = {11}, number = {}, pages = {324}, pmid = {20550700}, issn = {1471-2105}, mesh = {*Algorithms ; Archaea/genetics ; Bacteria/genetics ; *Gene Transfer, Horizontal ; *Phylogeny ; Software ; }, abstract = {BACKGROUND: To understand the evolutionary role of Lateral Gene Transfer (LGT), accurate methods are needed to identify transferred genes and infer their timing of acquisition. Phylogenetic methods are particularly promising for this purpose, but the reconciliation of a gene tree with a reference (species) tree is computationally hard. In addition, the application of these methods to real data raises the problem of sorting out real and artifactual phylogenetic conflict.<br><br>RESULTS: We present Prunier, a new method for phylogenetic detection of LGT based on the search for a maximum statistical agreement forest (MSAF) between a gene tree and a reference tree. The program is flexible as it can use any definition of "agreement" among trees. We evaluate the performance of Prunier and two other programs (EEEP and RIATA-HGT) for their ability to detect transferred genes in realistic simulations where gene trees are reconstructed from sequences. Prunier proposes a single scenario that compares to the other methods in terms of sensitivity, but shows higher specificity. We show that LGT scenarios carry a strong signal about the position of the root of the species tree and could be used to identify the direction of evolutionary time on the species tree. We use Prunier on a biological dataset of 23 universal proteins and discuss their suitability for inferring the tree of life.<br><br>CONCLUSIONS: The ability of Prunier to take into account branch support in the process of reconciliation allows a gain in complexity, in comparison to EEEP, and in accuracy in comparison to RIATA-HGT. Prunier's greedy algorithm proposes a single scenario of LGT for a gene family, but its quality always compares to the best solutions provided by the other algorithms. When the root position is uncertain in the species tree, Prunier is able to infer a scenario per root at a limited additional computational cost and can easily run on large datasets.Prunier is implemented in C++, using the Bio++ library and the phylogeny program Treefinder. It is available at: http://pbil.univ-lyon1.fr/software/prunier.}, }
@article {pmid20549382, year = {2010}, author = {Carrapiço, F}, title = {How symbiogenic is evolution?.}, journal = {Theory in biosciences = Theorie in den Biowissenschaften}, volume = {129}, number = {2-3}, pages = {135-139}, pmid = {20549382}, issn = {1611-7530}, mesh = {Animals ; Bacterial Physiological Phenomena/genetics ; *Biological Evolution ; Chloroplasts/physiology ; Gene Transfer, Horizontal/physiology ; Humans ; Lichens/physiology ; Plant Physiological Phenomena/genetics ; Stramenopiles/physiology ; Symbiosis/*physiology ; Virus Physiological Phenomena/genetics ; }, abstract = {When new entities are formed by the integration of individual organisms, these new entities possess characteristics which go beyond the sum of the individual properties of each element of the association, resulting in the development of new attributes and capacities as an integrated whole. In this process, these new entities also agglutinate and dynamize synergies not present in the individual organisms. In this sense, evolution is a dynamic process that evolves not in the way of perfection or progress, but in the way of adaptation to new conditions. Symbiogenesis, as an evolutionary mechanism, allows a coherent conceptual rupture with some evolutionary ideas of the past and, at the same time, shows and builds a new approach to life, based on solid evolutionary ideas, expanding evolution to an adequate level of integration with the more recent data in biology. These ideas and concepts should be integrated in a post-neodarwinian approach to evolution that needs further attention from the scientific community. The development of a Symbiogenic Theory of Evolution could contribute toward a new epistemological approach of the symbiotic phenomenon in the evolutionary context. This, in our point of view, could be the beginning of a new paradigm in science that rests almost unexplored.}, }
@article {pmid20547849, year = {2010}, author = {Corvaglia, AR and François, P and Hernandez, D and Perron, K and Linder, P and Schrenzel, J}, title = {A type III-like restriction endonuclease functions as a major barrier to horizontal gene transfer in clinical Staphylococcus aureus strains.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {26}, pages = {11954-11958}, pmid = {20547849}, issn = {1091-6490}, mesh = {Amino Acid Sequence ; Base Sequence ; DNA, Bacterial/genetics ; Deoxyribonucleases, Type I Site-Specific/antagonists &amp; inhibitors/genetics/metabolism ; Deoxyribonucleases, Type III Site-Specific/genetics/*metabolism ; Enterococcus faecalis/enzymology/genetics ; Escherichia coli/genetics ; Gene Targeting ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Methicillin Resistance/genetics ; Methicillin-Resistant Staphylococcus aureus/enzymology/genetics/isolation &amp; purification ; Molecular Sequence Data ; Plasmids/genetics ; Sequence Homology, Amino Acid ; Species Specificity ; Staphylococcus aureus/*enzymology/*genetics/isolation &amp; purification ; }, abstract = {Staphylococcus aureus is an versatile pathogen that can cause life-threatening infections. Depending on the clinical setting, up to 50% of S. aureus infections are caused by methicillin-resistant strains (MRSA) that in most cases are resistant to many other antibiotics, making treatment difficult. The emergence of community-acquired MRSA drastically changed the picture by increasing the risk of MRSA infections. Horizontal transfer of genes encoding for antibiotic resistance or virulence factors is a major concern of multidrug-resistant S. aureus infections and epidemiology. We identified and characterized a type III-like restriction system present in clinical S. aureus strains that prevents transformation with DNA from other bacterial species. Interestingly, our analysis revealed that some clinical MRSA strains are deficient in this restriction system, and thus are hypersusceptible to the horizontal transfer of DNA from other species, such as Escherichia coli, and could easily acquire a vancomycin-resistance gene from enterococci. Inactivation of this restriction system dramatically increases the transformation efficiency of clinical S. aureus strains, opening the field of molecular genetic manipulation of these strains using DNA of exogenous origin.}, }
@article {pmid20547102, year = {2010}, author = {Schubert, S and Nörenberg, D and Clermont, O and Magistro, G and Wieser, A and Romann, E and Hoffmann, C and Weinert, K and Denamur, E}, title = {Prevalence and phylogenetic history of the TcpC virulence determinant in Escherichia coli.}, journal = {International journal of medical microbiology : IJMM}, volume = {300}, number = {7}, pages = {429-434}, doi = {10.1016/j.ijmm.2010.02.006}, pmid = {20547102}, issn = {1618-0607}, mesh = {Adult ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; Escherichia coli/*classification/genetics/*pathogenicity ; Escherichia coli Proteins/*genetics ; Gene Order ; Gene Transfer, Horizontal ; Genomic Islands ; Humans ; Infant, Newborn ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Recombination, Genetic ; Sequence Analysis, DNA ; Sequence Homology ; Virulence Factors/*genetics ; }, abstract = {Extraintestinal pathogenic Escherichia coli (ExPECs) possess an armament of virulence factors to colonize and infect the host, such as adhesins, toxins, capsules and iron-uptake systems. Recently, we could identify a novel virulence factor of ExPECs that interferes with the innate immune response of the host by interrupting the NF-κB signaling pathway. This protein named TcpC shows considerable homology to motifs of the Tir domain of Toll-like receptors. Here we demonstrate that the tcpC gene is widely distributed among clinical ExPEC isolates with almost half of the E. coli strains from patients suffering pyelonephritis shown to be tcpC positive as compared to only 8% in commensal isolates. However, this gene is only present in phylogenetic group B2 strains. Interestingly, the tcpC gene is strongly associated with presence of the high-pathogenicity island (HPI). The phylogenetic history of the tcpC gene, in the E. coli reference collection (ECOR) and other well-defined E. coli strains, compared to the phylogenetic histories of the HPI and the strains, showed that the tcpC gene (i) is scattered among various B2 subgroups with specific O-types, (ii) has a phylogeny incongruent with the strain phylogeny, but (iii) congruent with the HPI phylogenetic history. This, together with the strong conservation of the tcpC gene, indicates a very recent introduction of this virulence factor into E. coli by horizontal gene transfer which occurred "en bloc" with the HPI at one major hot spot of recombination in the E. coli genome. The present data provide evidence for a strong impact of homologous recombination events in the spread of the TcpC virulence trait among E. coli.}, }
@article {pmid20546576, year = {2010}, author = {Schijffelen, MJ and Boel, CH and van Strijp, JA and Fluit, AC}, title = {Whole genome analysis of a livestock-associated methicillin-resistant Staphylococcus aureus ST398 isolate from a case of human endocarditis.}, journal = {BMC genomics}, volume = {11}, number = {}, pages = {376}, pmid = {20546576}, issn = {1471-2164}, mesh = {Animals ; Animals, Domestic/*microbiology ; Endocarditis, Bacterial/*microbiology ; Female ; Genome, Bacterial/genetics ; *Genomics ; Humans ; Methicillin-Resistant Staphylococcus aureus/*genetics/*isolation &amp; purification ; Middle Aged ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Recently, a new livestock-associated methicillin-resistant Staphylococcus aureus (MRSA) Sequence Type 398 (ST398) isolate has emerged worldwide. Although there have been reports of invasive disease in humans, MRSA ST398 colonization is much more common in livestock and demonstrates especially high prevalence rates in pigs and calves. The aim of this study was to compare the genome sequence of an ST398 MRSA isolate with other S. aureus genomes in order to identify genetic traits that may explain the success of this particular lineage. Therefore, we determined the whole genome sequence of S0385, an MRSA ST398 isolate from a human case of endocarditis.<br><br>RESULTS: The entire genome sequence of S0385 demonstrated considerable accessory genome content differences relative to other S. aureus genomes. Several mobile genetic elements that confer antibiotic resistance were identified, including a novel composite of an type V (5C2&amp;5) Staphylococcal Chromosome Cassette mec (SCCmec) with distinct joining (J) regions. The presence of multiple integrative conjugative elements combined with the absence of a type I restriction and modification system on one of the two nuSa islands, could enhance horizontal gene transfer in this strain. The ST398 MRSA isolate carries a unique pathogenicity island which encodes homologues of two excreted virulence factors; staphylococcal complement inhibitor (SCIN) and von Willebrand factor-binding protein (vWbp). However, several virulence factors such as enterotoxins and phage encoded toxins, including Panton-Valentine leukocidin (PVL), were not identified in this isolate.<br><br>CONCLUSIONS: Until now MRSA ST398 isolates did not cause frequent invasive disease in humans, which may be due to the absence of several common virulence factors. However, the proposed enhanced ability of these isolates to acquire mobile elements may lead to the rapid acquisition of determinants which contribute to virulence in human infections.}, }
@article {pmid20545753, year = {2010}, author = {Barkay, T and Kritee, K and Boyd, E and Geesey, G}, title = {A thermophilic bacterial origin and subsequent constraints by redox, light and salinity on the evolution of the microbial mercuric reductase.}, journal = {Environmental microbiology}, volume = {12}, number = {11}, pages = {2904-2917}, doi = {10.1111/j.1462-2920.2010.02260.x}, pmid = {20545753}, issn = {1462-2920}, mesh = {Archaea/*enzymology/genetics ; Bacteria/classification/*enzymology/genetics ; Base Sequence ; *Databases, Nucleic Acid ; Databases, Protein ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; Hot Temperature ; Hydrogen-Ion Concentration ; Light ; Mercury/metabolism ; Operon ; Oxidation-Reduction ; Oxidoreductases/*genetics ; Phylogeny ; Salinity ; Sulfhydryl Compounds ; Water Microbiology ; }, abstract = {Mercuric reductase (MerA) is central to the mercury (Hg) resistance (mer) system, catalyzing the reduction of ionic Hg to volatile Hg(0). A total of 213 merA homologues were identified in sequence databases, the majority of which belonged to microbial lineages that occupy oxic environments. merA was absent among phototrophs and in lineages that inhabit anoxic environments. Phylogenetic reconstructions of MerA indicate that (i) merA originated in a thermophilic bacterium following the divergence of the Archaea and Bacteria with a subsequent acquisition in Archaea via horizontal gene transfer (HGT), (ii) HGT of merA was rare across phylum boundaries and (iii) MerA from marine bacteria formed distinct and strongly supported lineages. Collectively, these observations suggest that a combination of redox, light and salinity conditions constrain MerA to microbial lineages that occupy environments where the most oxidized and toxic form of Hg, Hg(II), predominates. Further, the taxon-specific distribution of MerA with and without a 70 amino acid N-terminal extension may reflect intracellular levels of thiols. In conclusion, MerA likely evolved following the widespread oxygenation of the biosphere in a thermal environment and its subsequent evolution has been modulated by the interactions of Hg with the intra- and extracellular environment of the organism.}, }
@article {pmid20543958, year = {2010}, author = {McNulty, SN and Foster, JM and Mitreva, M and Dunning Hotopp, JC and Martin, J and Fischer, K and Wu, B and Davis, PJ and Kumar, S and Brattig, NW and Slatko, BE and Weil, GJ and Fischer, PU}, title = {Endosymbiont DNA in endobacteria-free filarial nematodes indicates ancient horizontal genetic transfer.}, journal = {PloS one}, volume = {5}, number = {6}, pages = {e11029}, pmid = {20543958}, issn = {1932-6203}, support = {T32 AI007172/AI/NIAID NIH HHS/United States ; T32-AI007172/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; DNA, Bacterial/*genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Nematoda/*microbiology ; RNA, Messenger/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; *Symbiosis ; Wolbachia/*genetics/isolation &amp; purification ; }, abstract = {BACKGROUND: Wolbachia are among the most abundant symbiotic microbes on earth; they are present in about 66% of all insect species, some spiders, mites and crustaceans, and most filarial nematode species. Infected filarial nematodes, including many pathogens of medical and veterinary importance, depend on Wolbachia for proper development and survival. The mechanisms behind this interdependence are not understood. Interestingly, a minority of filarial species examined to date are naturally Wolbachia-free.<br><br>We used 454 pyrosequencing to survey the genomes of two distantly related Wolbachia-free filarial species, Acanthocheilonema viteae and Onchocerca flexuosa. This screen identified 49 Wolbachia-like DNA sequences in A. viteae and 114 in O. flexuosa. qRT-PCR reactions detected expression of 30 Wolbachia-like sequences in A. viteae and 56 in O. flexuosa. Approximately half of these appear to be transcribed from pseudogenes. In situ hybridization showed that two of these pseudogene transcripts were specifically expressed in developing embryos and testes of both species.<br><br>CONCLUSIONS/SIGNIFICANCE: These results strongly suggest that the last common ancestor of extant filarial nematodes was infected with Wolbachia and that this former endosymbiont contributed to their genome evolution. Horizontally transferred Wolbachia DNA may explain the ability of some filarial species to live and reproduce without the endosymbiont while other species cannot.}, }
@article {pmid20542651, year = {2010}, author = {Shiraishi, A and Matsushita, N and Hougetsu, T}, title = {Nodulation in black locust by the Gammaproteobacteria Pseudomonas sp. and the Betaproteobacteria Burkholderia sp.}, journal = {Systematic and applied microbiology}, volume = {33}, number = {5}, pages = {269-274}, doi = {10.1016/j.syapm.2010.04.005}, pmid = {20542651}, issn = {1618-0984}, mesh = {Bacterial Proteins/genetics ; *Betaproteobacteria/genetics/isolation &amp; purification ; Cluster Analysis ; DNA, Bacterial/genetics ; *Gammaproteobacteria/genetics/isolation &amp; purification ; Genes, Bacterial/genetics ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Robinia/*microbiology ; Root Nodules, Plant/*microbiology ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {Nodulation abilities of bacteria in the subclasses Gammaproteobacteria and Betaproteobacteria on black locust (Robinia pseudoacacia) were tested. Pseudomonas sp., Burkholderia sp., Klebsiella sp., and Paenibacillus sp. were isolated from surface-sterilized black locust nodules, but their nodulation ability is unknown. The aims of this study were to determine if these bacteria are symbiotic. The species and genera of the strains were determined by RFLP analysis and DNA sequencing of 16S rRNA gene. Inoculation tests and histological studies revealed that Pseudomonas sp. and Burkholderia sp. formed nodules on black locust and also developed differentiated nodule tissue. Furthermore, a phylogenetic analysis of nodA and a BLASTN analysis of the nodC, nifH, and nifHD genes revealed that these symbiotic genes of Pseudomonas sp. and Burkholderia sp. have high similarities with those of rhizobial species, indicating that the strains acquired the symbiotic genes from rhizobial species in the soil. Therefore, in an actual rhizosphere, bacterial diversity of nodulating legumes may be broader than expected in the Alpha-, Beta-, and Gammaproteobacteria subclasses. The results indicate the importance of horizontal gene transfer for establishing symbiotic interactions in the rhizosphere.}, }
@article {pmid20541961, year = {2010}, author = {Tenaillon, MI and Hollister, JD and Gaut, BS}, title = {A triptych of the evolution of plant transposable elements.}, journal = {Trends in plant science}, volume = {15}, number = {8}, pages = {471-478}, doi = {10.1016/j.tplants.2010.05.003}, pmid = {20541961}, issn = {1878-4372}, mesh = {*DNA Transposable Elements ; DNA, Plant/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Magnoliopsida ; Plants/*genetics ; }, abstract = {Transposable elements (TEs) constitute the majority of angiosperm DNA, but the processes that govern their accumulation remain mysterious. Here we discuss the three major forces that govern the accumulation of TEs, corresponding to the three panels of a triptych. The first force, transposition, creates new copies of TEs, but is regulated by both host- and TE-specific mechanisms. The second force, deletion of TE DNA, is capable of removing vast swaths of genomic regions via recombinational processes, but we still have very little insight into how deletion varies across species and even among TE types. Finally, we focus on the often-ignored third panel of our triptych - the population processes that determine the ultimate evolutionary fate of TE insertions.}, }
@article {pmid20540605, year = {2010}, author = {Bodył, A and Mackiewicz, P and Milanowski, R}, title = {Did trypanosomatid parasites contain a eukaryotic alga-derived plastid in their evolutionary past?.}, journal = {The Journal of parasitology}, volume = {96}, number = {2}, pages = {465-475}, doi = {10.1645/GE-1810.1}, pmid = {20540605}, issn = {1937-2345}, mesh = {*Biological Evolution ; Chlorophyta/genetics/physiology/*ultrastructure ; *Plastids/genetics ; Symbiosis/*physiology ; Trypanosomatina/*classification/genetics/physiology/ultrastructure ; }, abstract = {The Trypanosomatidae is closely related to euglenids that harbor plastids acquired from a green alga via secondary endosymbiosis. This discovery led to the idea that trypanosomatid parasites contained a green alga-derived plastid in their evolutionary past, an evolutionary scenario that was criticized based on the rarity of plant/plastid/cyanobacterium-like genes in the completely sequenced genomes of Trypanosoma and Leishmania species. Because it is difficult to identify such genes, however, their apparent rarity does not preclude a previous plastid endosymbiosis in the Trypanosomatidae. The genome of the plastid-less apicomplexan Cryptosporidium parvum preserves only a handful of plant/plastid/cyanobacterium-like genes, suggesting massive loss of plastid genes after elimination of its plastid. Additional support for such wholesale gene loss comes from fucoxanthin-containing dinoflagellates. Trypanosomatid nuclear genomes contain cyanobacterium-, green plant-, and haptophyte alga-derived genes, suggesting that they could have possessed a plastid in their evolutionary past; however, these genes also could represent examples of more typical horizontal gene transfer that did not accompany a plastid endosymbiosis. Thus, the presence of host cell genes that were adapted for use in the plastid would be much stronger evidence for a past plastid endosymbiosis in the Trypanosomatidae. Good examples of such genes are those encoding superoxide dismutases (SODs). Trypanosomatid parasites possess 4 iron-containing SODs, with 2 of them, SODA and SODC, targeted to the mitochondrion. In contrast with SODAs with classical single-domain mitochondrial targeting signals, SODCs carry bipartite pre-sequences composed of a signal peptide, followed by a transit peptide. Interestingly, these N-terminal extensions show striking similarities in length, hydropathy profiles, amino acid composition, and targeting properties to pre-sequences of proteins targeted to eukaryotic alga-derived plastids of euglenids and dinoflagellates. In turn, phylogenetic analyses indicate that SODCs originated from a mitochondrion-targeted SOD via gene duplication and were inherited vertically in the trypanosomatid lineage. These data represent a new kind of evidence for a past plastid endosymbiosis in the Trypanosomatidae, but the nature of this plastid remains unclear. It is usually assumed that the trypanosomatid plastid shared a common origin with that of euglenids, but Delta 4 desaturase phylogenies suggest that it could have originated via an independent, tertiary endosymbiosis involving a haptophyte alga. It is also possible that ancestors of the Trypanosomatidae initially possessed a primary plastid that later was replaced by a secondary or tertiary plastid.}, }
@article {pmid20538863, year = {2010}, author = {Parakkottil Chothi, M and Duncan, GA and Armirotti, A and Abergel, C and Gurnon, JR and Van Etten, JL and Bernardi, C and Damonte, G and Tonetti, M}, title = {Identification of an L-rhamnose synthetic pathway in two nucleocytoplasmic large DNA viruses.}, journal = {Journal of virology}, volume = {84}, number = {17}, pages = {8829-8838}, pmid = {20538863}, issn = {1098-5514}, support = {GM32441/GM/NIGMS NIH HHS/United States ; R01 GM032441/GM/NIGMS NIH HHS/United States ; P21RR15635/RR/NCRR NIH HHS/United States ; P20 RR015635/RR/NCRR NIH HHS/United States ; P20 RR106469/RR/NCRR NIH HHS/United States ; }, mesh = {Acanthamoeba castellanii/virology ; Biosynthetic Pathways ; Chlorella/virology ; Gene Transfer, Horizontal ; Mimiviridae/classification/enzymology/genetics/*metabolism ; Molecular Sequence Data ; Phycodnaviridae/classification/enzymology/genetics/*metabolism ; Phylogeny ; Rhamnose/*biosynthesis ; Viral Proteins/genetics/*metabolism ; }, abstract = {Nucleocytoplasmic large DNA viruses (NCLDVs) are characterized by large genomes that often encode proteins not commonly found in viruses. Two species in this group are Acanthocystis turfacea chlorella virus 1 (ATCV-1) (family Phycodnaviridae, genus Chlorovirus) and Acanthamoeba polyphaga mimivirus (family Mimiviridae), commonly known as mimivirus. ATCV-1 and other chlorovirus members encode enzymes involved in the synthesis and glycosylation of their structural proteins. In this study, we identified and characterized three enzymes responsible for the synthesis of the sugar L-rhamnose: two UDP-D-glucose 4,6-dehydratases (UGDs) encoded by ATCV-1 and mimivirus and a bifunctional UDP-4-keto-6-deoxy-D-glucose epimerase/reductase (UGER) from mimivirus. Phylogenetic analysis indicated that ATCV-1 probably acquired its UGD gene via a recent horizontal gene transfer (HGT) from a green algal host, while an earlier HGT event involving the complete pathway (UGD and UGER) probably occurred between a protozoan ancestor and mimivirus. While ATCV-1 lacks an epimerase/reductase gene, its Chlorella host may encode this enzyme. Both UGDs and UGER are expressed as late genes, which is consistent with their role in posttranslational modification of capsid proteins. The data in this study provide additional support for the hypothesis that chloroviruses, and maybe mimivirus, encode most, if not all, of the glycosylation machinery involved in the synthesis of specific glycan structures essential for virus replication and infection.}, }
@article {pmid20537944, year = {2010}, author = {Lurie-Weinberger, MN and Gomez-Valero, L and Merault, N and Glöckner, G and Buchrieser, C and Gophna, U}, title = {The origins of eukaryotic-like proteins in Legionella pneumophila.}, journal = {International journal of medical microbiology : IJMM}, volume = {300}, number = {7}, pages = {470-481}, doi = {10.1016/j.ijmm.2010.04.016}, pmid = {20537944}, issn = {1618-0607}, mesh = {Adaptation, Biological ; Bacterial Proteins/*genetics ; Cluster Analysis ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Legionella pneumophila/*genetics ; Mimiviridae/genetics ; Phylogeny ; Sequence Homology, Amino Acid ; Viral Proteins/genetics ; }, abstract = {Legionella pneumophila, the causative agent of Legionnaires' disease, is known to be an intracellular pathogen of multiple species of protozoa and is assumed to have co-evolved with these organisms for millions of years. Genome sequencing of L. pneumophila strains has revealed an abundance of eukaryotic-like proteins (ELPs). Here, we study the evolution of these ELPs, in order to investigate their origin. Thirty-four new ELPs were identified, based on a higher similarity to eukaryotic proteins than to bacterial ones. Phylogenetic analyses demonstrated that both lateral gene transfer from eukaryotic hosts and bacterial genes that became eukaryotic-like by gradual adaptation to the intracellular milieu or gene fragment acquisition, contributed to the existing repertoire of ELPs, which comprise over 3% of the putative proteome of L. pneumophila strains. A PCR survey of 72 L. pneumophila strains showed that most ELPs were conserved in nearly all of these strains, indicating that they are likely to play important roles in this species. Genes of different evolutionary origin have distinct patterns of selection, as reflected by their ratio of a synonymous vs. synonymous mutations. One ELP is common to several strains of Legionella, but outside this genus has homologs only in Acanthamoeba polyphaga mimivirus, indicating that gene exchange involving eukaryotic viruses and intracellular bacterial pathogens may also contribute to the evolution of virulence in either or both of these groups of organisms. Information on selection patterns and eukaryotic-like status was combined as a novel approach to predict type IV secretion system effectors of Legionella, which represent promising targets for future study.}, }
@article {pmid20537123, year = {2010}, author = {Wisecaver, JH and Hackett, JD}, title = {Transcriptome analysis reveals nuclear-encoded proteins for the maintenance of temporary plastids in the dinoflagellate Dinophysis acuminata.}, journal = {BMC genomics}, volume = {11}, number = {}, pages = {366}, pmid = {20537123}, issn = {1471-2164}, mesh = {Alveolata/*cytology/*genetics/metabolism ; Cell Nucleus/*genetics ; Ciliophora/cytology/genetics/metabolism ; Cryptophyta/cytology/genetics/metabolism ; Evolution, Molecular ; *Gene Expression Profiling ; Peptides/genetics/metabolism ; Phylogeny ; Plastids/*metabolism ; Protozoan Proteins/*genetics/*metabolism ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Dinophysis is exceptional among dinoflagellates, possessing plastids derived from cryptophyte algae. Although Dinophysis can be maintained in pure culture for several months, the genus is mixotrophic and needs to feed either to acquire plastids (a process known as kleptoplastidy) or obtain growth factors necessary for plastid maintenance. Dinophysis does not feed directly on cryptophyte algae, but rather on a ciliate (Myrionecta rubra) that has consumed the cryptophytes and retained their plastids. Despite the apparent absence of cryptophyte nuclear genes required for plastid function, Dinophysis can retain cryptophyte plastids for months without feeding.<br><br>RESULTS: To determine if this dinoflagellate has nuclear-encoded genes for plastid function, we sequenced cDNA from Dinophysis acuminata, its ciliate prey M. rubra, and the cryptophyte source of the plastid Geminigera cryophila. We identified five proteins complete with plastid-targeting peptides encoded in the nuclear genome of D. acuminata that function in photosystem stabilization and metabolite transport. Phylogenetic analyses show that the genes are derived from multiple algal sources indicating some were acquired through horizontal gene transfer.<br><br>CONCLUSIONS: These findings suggest that D. acuminata has some functional control of its plastid, and may be able to extend the useful life of the plastid by replacing damaged transporters and protecting components of the photosystem from stress. However, the dearth of plastid-related genes compared to other fully phototrophic algae suggests that D. acuminata does not have the nuclear repertoire necessary to maintain the plastid permanently.}, }
@article {pmid20536729, year = {2010}, author = {Zhang, Q and Ma, Q and Su, D and Li, Q and Yao, W and Wang, C}, title = {Identification of horizontal gene transfer and recombination of PsaA gene in streptococcus mitis group.}, journal = {Microbiology and immunology}, volume = {54}, number = {6}, pages = {313-319}, doi = {10.1111/j.1348-0421.2010.00216.x}, pmid = {20536729}, issn = {0385-5600}, mesh = {Adhesins, Bacterial/chemistry/*genetics ; Amino Acid Sequence ; *Gene Transfer, Horizontal ; Lipoproteins/chemistry/*genetics ; Phylogeny ; *Recombination, Genetic ; Sequence Analysis, DNA ; Streptococcus mitis/classification/*genetics ; Terminology as Topic ; }, abstract = {Pneumococcal surface adhesin A (psaA) gene is universally confirmed as one of the Streptococcus pneumoniae adhesion genes, but it is disputed whether the psaA gene is a Streptococcus pneumoniae species-specific gene. In the present study, the presence of the psaA gene in 34 streptococcus mitis group isolates was identified by the PCR approach and a comparison of sequencing PCR products (Streptococcus pneumoniae R6 as the control strain). Also, the evolutionary scenarios of these psaA genes in these streptococcus mitis group isolates were analyzed by a phylogenetic tree based on the housekeeping genes (sodA and rnpB) and psaA genes. As a result, a high degree of conservation of open reading frame sequences in all six Streptococcus pneumoniae strains (100% similarity) and in the other species of the streptococcus mitis group (92.6-100% similarity) was revealed. Further genetics research based on housekeeping genes and psaA gene phylogenies showed that the psaA gene was of vertical inheritance only in Streptococcus pneumoniae; however, high-frequency horizontal psaA gene transfer and recombination occurred in the other species of the streptococcus mitis group. These findings confirmed that the psaA gene was not a Streptococcus pneumoniae species-specific gene, and high-frequency HGT and recombination events may explain the presence of the psaA gene in the other species of the streptococcus mitis group.}, }
@article {pmid20535601, year = {2010}, author = {Sapp, J}, title = {Saltational symbiosis.}, journal = {Theory in biosciences = Theorie in den Biowissenschaften}, volume = {129}, number = {2-3}, pages = {125-133}, pmid = {20535601}, issn = {1611-7530}, mesh = {Animals ; Archaea/physiology ; Bacterial Physiological Phenomena/genetics ; Bacteriophages/physiology ; *Biological Evolution ; Chloroplasts/physiology ; Fungi/physiology ; Gene Transfer, Horizontal ; Humans ; Mitochondria/pathology ; Organelles/physiology ; Phylogeny ; Plant Physiological Phenomena/genetics ; Selection, Genetic/physiology ; Symbiosis/*physiology ; Virus Physiological Phenomena/genetics ; }, abstract = {Symbiosis has long been associated with saltational evolutionary change in contradistinction to gradual Darwinian evolution based on gene mutations and recombination between individuals of a species, as well as with super-organismal views of the individual in contrast to the classical one-genome: one organism conception. Though they have often been dismissed, and overshadowed by Darwinian theory, suggestions that symbiosis and lateral gene transfer are fundamental mechanisms of evolutionary innovation are borne out today by molecular phylogenetic research. It is time to treat these processes as central principles of evolution.}, }
@article {pmid20534806, year = {2010}, author = {Steinsland, H and Lacher, DW and Sommerfelt, H and Whittam, TS}, title = {Ancestral lineages of human enterotoxigenic Escherichia coli.}, journal = {Journal of clinical microbiology}, volume = {48}, number = {8}, pages = {2916-2924}, pmid = {20534806}, issn = {1098-660X}, support = {N01AI30058/AI/NIAID NIH HHS/United States ; N01-AI-30058/AI/NIAID NIH HHS/United States ; }, mesh = {Adult ; Animals ; Bacterial Typing Techniques ; Child ; Child, Preschool ; *Cluster Analysis ; DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; Enterotoxigenic Escherichia coli/*classification/*genetics/isolation &amp; purification ; Escherichia coli Infections/*microbiology/*veterinary ; Escherichia coli Proteins/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Humans ; Sequence Analysis, DNA ; Swine ; Virulence Factors/genetics ; }, abstract = {Enterotoxigenic Escherichia coli (ETEC) is a common cause of diarrhea among children living in and among travelers visiting developing countries. Human ETEC strains represent an epidemiologically and phenotypically diverse group of pathogens, and there is a need to identify natural groupings of these organisms that may help to explain this diversity. Here, we sought to identify most of the important human ETEC lineages that exist in the E. coli population, because strains that originate from the same lineage may also have inherited many of the same epidemiological and phenotypic traits. We performed multilocus sequence typing (MLST) on 1,019 ETEC isolates obtained from humans in different countries and analyzed the data against a backdrop of MLST data from 1,250 non-ETEC E. coli and eight ETEC isolates from pigs. A total of 42 different lineages were identified, 15 of which, representing 792 (78%) of the strains, were estimated to have emerged >900 years ago. Twenty of the lineages were represented in more than one country. There was evidence of extensive exchange of enterotoxin and colonization factor genes between different lineages. Human and porcine ETEC have probably emerged from the same ancestral ETEC lineage on at least three occasions. Our findings suggest that most ETEC strains circulating in the human population today originate from well-established, globally widespread ETEC lineages. Some of the more important lineages identified here may represent a smaller and more manageable target for the ongoing efforts to develop effective ETEC vaccines.}, }
@article {pmid20534454, year = {2010}, author = {Janouskovec, J and Horák, A and Oborník, M and Lukes, J and Keeling, PJ}, title = {A common red algal origin of the apicomplexan, dinoflagellate, and heterokont plastids.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {24}, pages = {10949-10954}, pmid = {20534454}, issn = {1091-6490}, support = {MOP 84265//Canadian Institutes of Health Research/Canada ; }, mesh = {Apicomplexa/classification/*genetics/ultrastructure ; Base Sequence ; Dinoflagellida/classification/*genetics/ultrastructure ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Plastid ; Microscopy, Electron, Transmission ; Models, Genetic ; Molecular Sequence Data ; Photosynthesis/genetics ; Phylogeny ; Plastids/*genetics/ultrastructure ; Poly U/genetics ; RNA, Messenger/genetics ; Rhodophyta/classification/*genetics/ultrastructure ; Ribulose-Bisphosphate Carboxylase/genetics ; Symbiosis/genetics ; }, abstract = {The discovery of a nonphotosynthetic plastid in malaria and other apicomplexan parasites has sparked a contentious debate about its evolutionary origin. Molecular data have led to conflicting conclusions supporting either its green algal origin or red algal origin, perhaps in common with the plastid of related dinoflagellates. This distinction is critical to our understanding of apicomplexan evolution and the evolutionary history of endosymbiosis and photosynthesis; however, the two plastids are nearly impossible to compare due to their nonoverlapping information content. Here we describe the complete plastid genome sequences and plastid-associated data from two independent photosynthetic lineages represented by Chromera velia and an undescribed alga CCMP3155 that we show are closely related to apicomplexans. These plastids contain a suite of features retained in either apicomplexan (four plastid membranes, the ribosomal superoperon, conserved gene order) or dinoflagellate plastids (form II Rubisco acquired by horizontal transfer, transcript polyuridylylation, thylakoids stacked in triplets) and encode a full collective complement of their reduced gene sets. Together with whole plastid genome phylogenies, these characteristics provide multiple lines of evidence that the extant plastids of apicomplexans and dinoflagellates were inherited by linear descent from a common red algal endosymbiont. Our phylogenetic analyses also support their close relationship to plastids of heterokont algae, indicating they all derive from the same endosymbiosis. Altogether, these findings support a relatively simple path of linear descent for the evolution of photosynthesis in a large proportion of algae and emphasize plastid loss in several lineages (e.g., ciliates, Cryptosporidium, and Phytophthora).}, }
@article {pmid20534164, year = {2010}, author = {Thomas, PD}, title = {GIGA: a simple, efficient algorithm for gene tree inference in the genomic age.}, journal = {BMC bioinformatics}, volume = {11}, number = {}, pages = {312}, pmid = {20534164}, issn = {1471-2105}, support = {R01GM081084/GM/NIGMS NIH HHS/United States ; }, mesh = {*Algorithms ; Animals ; Base Sequence ; *Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; Genome ; Humans ; Mice ; *Phylogeny ; }, abstract = {BACKGROUND: Phylogenetic relationships between genes are not only of theoretical interest: they enable us to learn about human genes through the experimental work on their relatives in numerous model organisms from bacteria to fruit flies and mice. Yet the most commonly used computational algorithms for reconstructing gene trees can be inaccurate for numerous reasons, both algorithmic and biological. Additional information beyond gene sequence data has been shown to improve the accuracy of reconstructions, though at great computational cost.<br><br>RESULTS: We describe a simple, fast algorithm for inferring gene phylogenies, which makes use of information that was not available prior to the genomic age: namely, a reliable species tree spanning much of the tree of life, and knowledge of the complete complement of genes in a species' genome. The algorithm, called GIGA, constructs trees agglomeratively from a distance matrix representation of sequences, using simple rules to incorporate this genomic age information. GIGA makes use of a novel conceptualization of gene trees as being composed of orthologous subtrees (containing only speciation events), which are joined by other evolutionary events such as gene duplication or horizontal gene transfer. An important innovation in GIGA is that, at every step in the agglomeration process, the tree is interpreted/reinterpreted in terms of the evolutionary events that created it. Remarkably, GIGA performs well even when using a very simple distance metric (pairwise sequence differences) and no distance averaging over clades during the tree construction process.<br><br>CONCLUSIONS: GIGA is efficient, allowing phylogenetic reconstruction of very large gene families and determination of orthologs on a large scale. It is exceptionally robust to adding more gene sequences, opening up the possibility of creating stable identifiers for referring to not only extant genes, but also their common ancestors. We compared trees produced by GIGA to those in the TreeFam database, and they were very similar in general, with most differences likely due to poor alignment quality. However, some remaining differences are algorithmic, and can be explained by the fact that GIGA tends to put a larger emphasis on minimizing gene duplication and deletion events.}, }
@article {pmid20533948, year = {2010}, author = {Tian, CF and Young, JP and Wang, ET and Tamimi, SM and Chen, WX}, title = {Population mixing of Rhizobium leguminosarum bv. viciae nodulating Vicia faba: the role of recombination and lateral gene transfer.}, journal = {FEMS microbiology ecology}, volume = {73}, number = {3}, pages = {563-576}, doi = {10.1111/j.1574-6941.2010.00909.x}, pmid = {20533948}, issn = {1574-6941}, mesh = {China ; DNA, Bacterial/genetics ; Europe ; *Gene Transfer, Horizontal ; Genes, Bacterial ; *Genetic Variation ; Genetics, Population ; Genotype ; Geography ; *Phylogeny ; Rhizobium leguminosarum/*genetics ; Sequence Analysis, DNA ; Symbiosis ; Vicia faba/*microbiology ; }, abstract = {The level and mechanisms of population mixing among faba bean (Vicia faba) rhizobia of different geographic origins (three ecoregions of China and several Western countries) were analysed by sequencing three chromosomal housekeeping loci (atpD, recA and glnII) and one nodulation gene (nodD). Eight distinct sublineages of Rhizobium leguminosarum bv. viciae (Rlv) were identified by concatenated sequences of chromosomal loci. structure analysis revealed admixture patterns of Rlv populations of different geographic origins. Recombination, particularly among these chromosomal loci, was revealed to be an important microevolutionary force in shaping the observed genetic diversity and the phylogeny of Rlv. The phylogeny of nodD is largely independent of that of the chromosomal loci, reflecting multiple gene transfers between sublineages and possibly selection imposed by different faba bean gene pools. The dominant nodulation genotype of faba bean rhizobia in the spring growing region of China is identical to the prevalent type of Europe, while the winter growing region of China has another related, but distinct, dominant nodulation genotype. Although several geographically specific sublineages of Rlv were observed, recombination and lateral gene transfer have driven the process of population mixing among different ecoregions of China or between China and countries to the west.}, }
@article {pmid20532745, year = {2010}, author = {Leung, MM and Florizone, SM and Taylor, TA and Lang, AS and Beatty, JT}, title = {The gene transfer agent of Rhodobacter capsulatus.}, journal = {Advances in experimental medicine and biology}, volume = {675}, number = {}, pages = {253-264}, doi = {10.1007/978-1-4419-1528-3_14}, pmid = {20532745}, issn = {0065-2598}, mesh = {*Gene Transfer, Horizontal ; Genes, Bacterial/*physiology ; Phylogeny ; Rhodobacter capsulatus/*physiology ; }, abstract = {When Rhodobacter capsulatus cultures enter the stationary phase of growth, particles of the gene transfer agent (RcGTA) are released from cells. The morphology of RcGTA resembles that of a small, tailed bacteriophage, with a protein capsid surrounding a ~4 kb linear, double-stranded fragment of DNA. However, the DNA present consists of random segments of the R. capsulatus genome, which may be transferred to another strain of R. capsulatus. The recipient in RcGTA-mediated gene transduction may acquire new alleles and thus express a new phenotype. The genes encoding the structural proteins of the RcGTA are clustered on the R. capsulatus chromosome, whereas genes that encode proteins that regulate the production of RcGTA are scattered around the chromosome. These regulatory proteins include a homoserine lactone synthase (GtaI) that produces a quorum-sensing signal, a two-component sensor-kinase protein (CckA), and a two-component response regulator protein (CtrA). We review the proposed evolutionary origin of RcGTA, as well as environmental and cellular factors involved in the induction of this unusual process of genetic exchange.}, }
@article {pmid20525631, year = {2010}, author = {Stern, A and Mayrose, I and Penn, O and Shaul, S and Gophna, U and Pupko, T}, title = {An evolutionary analysis of lateral gene transfer in thymidylate synthase enzymes.}, journal = {Systematic biology}, volume = {59}, number = {2}, pages = {212-225}, pmid = {20525631}, issn = {1076-836X}, mesh = {Base Composition ; Base Sequence ; Classification/methods ; Computational Biology ; Computer Simulation ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Likelihood Functions ; *Models, Genetic ; *Phylogeny ; Thymidylate Synthase/*genetics ; }, abstract = {Thymidylate synthases (Thy) are key enzymes in the synthesis of deoxythymidylate, 1 of the 4 building blocks of DNA. As such, they are essential for all DNA-based forms of life and therefore implicated in the hypothesized transition from RNA genomes to DNA genomes. Two evolutionally unrelated Thy enzymes, ThyA and ThyX, are known to catalyze the same biochemical reaction. Both enzymes are sporadically distributed within each of the 3 domains of life in a pattern that suggests multiple nonhomologous lateral gene transfer (LGT) events. We present a phylogenetic analysis of the evolution of the 2 enzymes, aimed at unraveling their entangled evolutionary history and tracing their origin back to early life. A novel probabilistic evolutionary model was developed, which allowed us to compute the posterior probabilities and the posterior expectation of the number of LGT events. Simulation studies were performed to validate the model's ability to accurately detect LGT events, which have occurred throughout a large phylogeny. Applying the model to the Thy data revealed widespread nonhomologous LGT between and within all 3 domains of life. By reconstructing the ThyA and ThyX gene trees, the most likely donor of each LGT event was inferred. The role of viruses in LGT of Thy is finally discussed.}, }
@article {pmid20525630, year = {2010}, author = {Boc, A and Philippe, H and Makarenkov, V}, title = {Inferring and validating horizontal gene transfer events using bipartition dissimilarity.}, journal = {Systematic biology}, volume = {59}, number = {2}, pages = {195-211}, doi = {10.1093/sysbio/syp103}, pmid = {20525630}, issn = {1076-836X}, mesh = {*Algorithms ; Classification/*methods ; *Data Interpretation, Statistical ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; *Models, Genetic ; *Phylogeny ; }, abstract = {Horizontal gene transfer (HGT) is one of the main mechanisms driving the evolution of microorganisms. Its accurate identification is one of the major challenges posed by reticulate evolution. In this article, we describe a new polynomial-time algorithm for inferring HGT events and compare 3 existing and 1 new tree comparison indices in the context of HGT identification. The proposed algorithm can rely on different optimization criteria, including least squares (LS), Robinson and Foulds (RF) distance, quartet distance (QD), and bipartition dissimilarity (BD), when searching for an optimal scenario of subtree prune and regraft (SPR) moves needed to transform the given species tree into the given gene tree. As the simulation results suggest, the algorithmic strategy based on BD, introduced in this article, generally provides better results than those based on LS, RF, and QD. The BD-based algorithm also proved to be more accurate and faster than a well-known polynomial time heuristic RIATA-HGT. Moreover, the HGT recovery results yielded by BD were generally equivalent to those provided by the exponential-time algorithm LatTrans, but a clear gain in running time was obtained using the new algorithm. Finally, a statistical framework for assessing the reliability of obtained HGTs by bootstrap analysis is also presented.}, }
@article {pmid20525618, year = {2010}, author = {Bloomquist, EW and Suchard, MA}, title = {Unifying vertical and nonvertical evolution: a stochastic ARG-based framework.}, journal = {Systematic biology}, volume = {59}, number = {1}, pages = {27-41}, pmid = {20525618}, issn = {1076-836X}, support = {AI07370/AI/NIAID NIH HHS/United States ; GM086887/GM/NIGMS NIH HHS/United States ; }, mesh = {*Algorithms ; Bayes Theorem ; Classification/*methods ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Leptospiraceae/genetics ; Likelihood Functions ; Markov Chains ; *Models, Genetic ; Monte Carlo Method ; *Phylogeny ; Saccharomyces/genetics ; }, abstract = {Evolutionary biologists have introduced numerous statistical approaches to explore nonvertical evolution, such as horizontal gene transfer, recombination, and genomic reassortment, through collections of Markov-dependent gene trees. These tree collections allow for inference of nonvertical evolution, but only indirectly, making findings difficult to interpret and models difficult to generalize. An alternative approach to explore nonvertical evolution relies on phylogenetic networks. These networks provide a framework to model nonvertical evolution but leave unanswered questions such as the statistical significance of specific nonvertical events. In this paper, we begin to correct the shortcomings of both approaches by introducing the "stochastic model for reassortment and transfer events" (SMARTIE) drawing upon ancestral recombination graphs (ARGs). ARGs are directed graphs that allow for formal probabilistic inference on vertical speciation events and nonvertical evolutionary events. We apply SMARTIE to phylogenetic data. Because of this, we can typically infer a single most probable ARG, avoiding coarse population dynamic summary statistics. In addition, a focus on phylogenetic data suggests novel probability distributions on ARGs. To make inference with our model, we develop a reversible jump Markov chain Monte Carlo sampler to approximate the posterior distribution of SMARTIE. Using the BEAST phylogenetic software as a foundation, the sampler employs a parallel computing approach that allows for inference on large-scale data sets. To demonstrate SMARTIE, we explore 2 separate phylogenetic applications, one involving pathogenic Leptospirochete and the other Saccharomyces.}, }
@article {pmid20520734, year = {2010}, author = {Nelson, DM and Cann, IK and Altermann, E and Mackie, RI}, title = {Phylogenetic evidence for lateral gene transfer in the intestine of marine iguanas.}, journal = {PloS one}, volume = {5}, number = {5}, pages = {e10785}, pmid = {20520734}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; Gene Transfer, Horizontal/*genetics ; Iguanas/*genetics ; Intestinal Mucosa/*metabolism ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Seawater ; }, abstract = {BACKGROUND: Lateral gene transfer (LGT) appears to promote genotypic and phenotypic variation in microbial communities in a range of environments, including the mammalian intestine. However, the extent and mechanisms of LGT in intestinal microbial communities of non-mammalian hosts remains poorly understood.<br><br>We sequenced two fosmid inserts obtained from a genomic DNA library derived from an agar-degrading enrichment culture of marine iguana fecal material. The inserts harbored 16S rRNA genes that place the organism from which they originated within Clostridium cluster IV, a well documented group that habitats the mammalian intestinal tract. However, sequence analysis indicates that 52% of the protein-coding genes on the fosmids have top BLASTX hits to bacterial species that are not members of Clostridium cluster IV, and phylogenetic analysis suggests that at least 10 of 44 coding genes on the fosmids may have been transferred from Clostridium cluster XIVa to cluster IV. The fosmids encoded four transposase-encoding genes and an integrase-encoding gene, suggesting their involvement in LGT. In addition, several coding genes likely involved in sugar transport were probably acquired through LGT.<br><br>CONCLUSION: Our phylogenetic evidence suggests that LGT may be common among phylogenetically distinct members of the phylum Firmicutes inhabiting the intestinal tract of marine iguanas.}, }
@article {pmid20517341, year = {2010}, author = {Toft, C and Andersson, SG}, title = {Evolutionary microbial genomics: insights into bacterial host adaptation.}, journal = {Nature reviews. Genetics}, volume = {11}, number = {7}, pages = {465-475}, pmid = {20517341}, issn = {1471-0064}, mesh = {Adaptation, Biological ; Animals ; Bacteria/*genetics ; *Biological Evolution ; Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; Symbiosis ; }, abstract = {Host-adapted bacteria include mutualists and pathogens of animals, plants and insects. Their study is therefore important for biotechnology, biodiversity and human health. The recent rapid expansion in bacterial genome data has provided insights into the adaptive, diversifying and reductive evolutionary processes that occur during host adaptation. The results have challenged many pre-existing concepts built from studies of laboratory bacterial strains. Furthermore, recent studies have revealed genetic changes associated with transitions from parasitism to mutualism and opened new research avenues to understand the functional reshaping of bacteria as they adapt to growth in the cytoplasm of a eukaryotic host.}, }
@article {pmid20511430, year = {2010}, author = {Musovic, S and Dechesne, A and Sørensen, J and Smets, BF}, title = {Novel assay to assess permissiveness of a soil microbial community toward receipt of mobile genetic elements.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {14}, pages = {4813-4818}, pmid = {20511430}, issn = {1098-5336}, mesh = {Bacteria/*genetics ; Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; *Gene Transfer, Horizontal ; Genes, Reporter ; Green Fluorescent Proteins/genetics/metabolism ; Image Processing, Computer-Assisted ; *Interspersed Repetitive Sequences ; Microscopy ; Molecular Sequence Data ; Plasmids ; Sequence Analysis, DNA ; *Soil Microbiology ; Staining and Labeling/methods ; }, abstract = {There is a wealth of evidence indicating that mobile genetic elements can spread in natural microbial communities. However, little is known regarding the fraction of the community that actually engages in this behavior. Here we report on a new approach to quantify the fraction of a bacterial community that is able to receive and maintain an exogenous conjugal plasmid termed community permissiveness. Conjugal transfer of a broad-host-range plasmid labeled with a zygotically inducible green fluorescent protein (RP4::gfp) from a donor strain (Pseudomonas putida) to a soil bacterial suspension was examined. The mixture of cells was incubated on membrane filters supported by different solid media. Plasmid transfer was scored by in situ visualization of green fluorescent transconjugant microcolonies, and host range was determined by traditional plating or microcolony isolation by using a micromanipulator. Among the conditions tested, the highest plasmid transfer incidence (approximately 1 transfer per 10(4) soil bacteria) was measured after 48 h of incubation on either a 10% soil extract or a 10-fold diluted R2A medium. Stereomicroscopy combined with image analysis allowed easy examination and enumeration of green fluorescent microcolonies. In all experiments, however, stereomicroscopy consistently underestimated the number of conjugation events (approximately 10-fold) in comparison to confocal laser scanning microscopy. The plasmid host range was broad and included bacteria belonging to the Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria classes of proteobacteria. The isolation of transconjugant microcolonies by micromanipulation greatly extended the estimated plasmid host range among soil bacteria. The new approach can be applied to examine the permissiveness of various communities toward receipt of different mobile elements.}, }
@article {pmid20508124, year = {2010}, author = {Yoshida, S and Maruyama, S and Nozaki, H and Shirasu, K}, title = {Horizontal gene transfer by the parasitic plant Striga hermonthica.}, journal = {Science (New York, N.Y.)}, volume = {328}, number = {5982}, pages = {1128}, doi = {10.1126/science.1187145}, pmid = {20508124}, issn = {1095-9203}, mesh = {Base Sequence ; Blotting, Southern ; Cell Nucleus/genetics ; Conserved Sequence ; Crops, Agricultural/genetics ; Expressed Sequence Tags ; *Gene Transfer, Horizontal ; Genome, Plant ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/genetics ; Poaceae/*genetics ; Sorghum/*genetics ; Striga/*genetics ; }, abstract = {Horizontal gene transfer has been postulated to occur between crops to co-occurring parasitic plants, but empirical evidence has been lacking. We present evidence that an HGT event moved a nuclear monocot gene into the genome of the eudicot parasite witchweed (Striga hermonthica), which infects many grass species in Africa. Analysis of expressed sequence tags revealed that the genome of S. hermonthica contains a nuclear gene that is widely conserved among grass species but is not found in other eudicots. Phylogenetically, this gene clusters with sorghum genes, the monocot host of the parasitic weed, suggesting that nuclear genes can be captured by parasitic weeds in nature.}, }
@article {pmid20508062, year = {2009}, author = {Charlesworth, B}, title = {Summary.}, journal = {Cold Spring Harbor symposia on quantitative biology}, volume = {74}, number = {}, pages = {469-474}, doi = {10.1101/sqb.2009.74.049}, pmid = {20508062}, issn = {1943-4456}, mesh = {Animals ; *Evolution, Molecular ; Humans ; }, abstract = {Advances in molecular biology have revolutionized the study of evolution. Detailed comparative studies of genomes are facilitating the analysis of phylogenies and raising new questions such as the extent of lateral gene transfer. Evolutionary analyses of development show that innovations frequently involve the reuse of existing gene products and gene networks in new ways and that changes in gene expression are important in morphological evolution. Population genetic studies are shedding increasing light on the genetic basis of traits subject to both artificial and natural selection. Laboratory models of evolution are being applied to both molecular and whole-organism systems, yielding insights into the evolution of adaptations, which complement those arising from reconstructions of evolutionary paths using molecular sequence or paleontological data. Overall, the Symposium portrayed evolution as a field that, while retaining its Darwinian roots, is exploring ever-wider areas of biology as new techniques and ideas emerge.}, }
@article {pmid20507619, year = {2010}, author = {Farnbacher, M and Jahns, T and Willrodt, D and Daniel, R and Haas, R and Goesmann, A and Kurtz, S and Rieder, G}, title = {Sequencing, annotation, and comparative genome analysis of the gerbil-adapted Helicobacter pylori strain B8.}, journal = {BMC genomics}, volume = {11}, number = {}, pages = {335}, pmid = {20507619}, issn = {1471-2164}, mesh = {*Adaptation, Physiological ; Animals ; Antigens, Bacterial/genetics ; Bacterial Proteins/genetics ; Codon/genetics ; Genetic Variation ; Genome, Bacterial/genetics ; Genomics/*methods ; Gerbillinae/*microbiology ; Helicobacter pylori/*genetics/*physiology ; Humans ; Plasmids/genetics ; Proteome/genetics ; Sequence Analysis, DNA/*methods ; Species Specificity ; Stomach/microbiology ; }, abstract = {BACKGROUND: The Mongolian gerbils are a good model to mimic the Helicobacter pylori-associated pathogenesis of the human stomach. In the current study the gerbil-adapted strain B8 was completely sequenced, annotated and compared to previous genomes, including the 73 supercontigs of the parental strain B128.<br><br>RESULTS: The complete genome of H. pylori B8 was manually curated gene by gene, to assign as much function as possible. It consists of a circular chromosome of 1,673,997 bp and of a small plasmid of 6,032 bp carrying nine putative genes. The chromosome contains 1,711 coding sequences, 293 of which are strain-specific, coding mainly for hypothetical proteins, and a large plasticity zone containing a putative type-IV-secretion system and coding sequences with unknown function. The cag-pathogenicity island is rearranged such that the cagA-gene is located 13,730 bp downstream of the inverted gene cluster cagB-cag1. Directly adjacent to the cagA-gene, there are four hypothetical genes and one variable gene with a different codon usage compared to the rest of the H. pylori B8-genome. This indicates that these coding sequences might be acquired via horizontal gene transfer.The genome comparison of strain B8 to its parental strain B128 delivers 425 unique B8-proteins. Due to the fact that strain B128 was not fully sequenced and only automatically annotated, only 12 of these proteins are definitive singletons that might have been acquired during the gerbil-adaptation process of strain B128.<br><br>CONCLUSION: Our sequence data and its analysis provide new insight into the high genetic diversity of H. pylori-strains. We have shown that the gerbil-adapted strain B8 has the potential to build, possibly by a high rate of mutation and recombination, a dynamic pool of genetic variants (e.g. fragmented genes and repetitive regions) required for the adaptation-processes. We hypothesize that these variants are essential for the colonization and persistence of strain B8 in the gerbil stomach during in ammation.}, }
@article {pmid20507608, year = {2010}, author = {Haley, BJ and Grim, CJ and Hasan, NA and Choi, SY and Chun, J and Brettin, TS and Bruce, DC and Challacombe, JF and Detter, JC and Han, CS and Huq, A and Colwell, RR}, title = {Comparative genomic analysis reveals evidence of two novel Vibrio species closely related to V. cholerae.}, journal = {BMC microbiology}, volume = {10}, number = {}, pages = {154}, pmid = {20507608}, issn = {1471-2180}, support = {1R01A139129-01//PHS HHS/United States ; N01-AI-40001/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics ; Cluster Analysis ; DNA-Directed RNA Polymerases/genetics ; Environmental Microbiology ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomic Islands ; *Genomics ; Humans ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Synteny ; Vibrio/*classification/*genetics/isolation &amp; purification ; Virulence Factors/genetics ; }, abstract = {BACKGROUND: In recent years genome sequencing has been used to characterize new bacterial species, a method of analysis available as a result of improved methodology and reduced cost. Included in a constantly expanding list of Vibrio species are several that have been reclassified as novel members of the Vibrionaceae. The description of two putative new Vibrio species, Vibrio sp. RC341 and Vibrio sp. RC586 for which we propose the names V. metecus and V. parilis, respectively, previously characterized as non-toxigenic environmental variants of V. cholerae is presented in this study.<br><br>RESULTS: Based on results of whole-genome average nucleotide identity (ANI), average amino acid identity (AAI), rpoB similarity, MLSA, and phylogenetic analysis, the new species are concluded to be phylogenetically closely related to V. cholerae and V. mimicus. Vibrio sp. RC341 and Vibrio sp. RC586 demonstrate features characteristic of V. cholerae and V. mimicus, respectively, on differential and selective media, but their genomes show a 12 to 15% divergence (88 to 85% ANI and 92 to 91% AAI) compared to the sequences of V. cholerae and V. mimicus genomes (ANI <95% and AAI <96% indicative of separate species). Vibrio sp. RC341 and Vibrio sp. RC586 share 2104 ORFs (59%) and 2058 ORFs (56%) with the published core genome of V. cholerae and 2956 (82%) and 3048 ORFs (84%) with V. mimicus MB-451, respectively. The novel species share 2926 ORFs with each other (81% Vibrio sp. RC341 and 81% Vibrio sp. RC586). Virulence-associated factors and genomic islands of V. cholerae and V. mimicus, including VSP-I and II, were found in these environmental Vibrio spp.<br><br>CONCLUSIONS: Results of this analysis demonstrate these two environmental vibrios, previously characterized as variant V. cholerae strains, are new species which have evolved from ancestral lineages of the V. cholerae and V. mimicus clade. The presence of conserved integration loci for genomic islands as well as evidence of horizontal gene transfer between these two new species, V. cholerae, and V. mimicus suggests genomic islands and virulence factors are transferred between these species.}, }
@article {pmid20506384, year = {2010}, author = {Ikuma, K and Gunsch, C}, title = {Effect of carbon source addition on toluene biodegradation by an Escherichia coli DH5alpha transconjugant harboring the TOL plasmid.}, journal = {Biotechnology and bioengineering}, volume = {107}, number = {2}, pages = {269-277}, doi = {10.1002/bit.22808}, pmid = {20506384}, issn = {1097-0290}, mesh = {Biotransformation ; Carbon/*metabolism ; Conjugation, Genetic ; Culture Media/chemistry ; Escherichia coli/genetics/*metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; Glucose/metabolism ; Metabolic Networks and Pathways ; Models, Biological ; *Plasmids ; Toluene/*metabolism ; }, abstract = {Horizontal gene transfer (HGT) of plasmids is a naturally occurring phenomenon which could be manipulated for bioremediation applications. Specifically, HGT may prove useful to enhance bioremediation through genetic bioaugmentation. However, because the transfer of a plasmid between donor and recipient cells does not always result in useful functional phenotypes, the conditions under which HGT events result in enhanced degradative capabilities must first be elucidated. The objective of this study was to determine if the addition of alternate carbon substrates could improve toluene degradation in Escherichia coli DH5alpha transconjugants. The addition of glucose (0.5-5 g/L) and Luria-Bertani (LB) broth (10-100%) resulted in enhanced toluene degradation. On average, the toluene degradation rate increased 14.1 (+/-2.1)-fold in the presence of glucose while the maximum increase was 18.4 (+/-1.7)-fold in the presence of 25% LB broth. Gene expression of xyl genes was upregulated in the presence of glucose but not LB broth, which implies different inducing mechanisms by the two types of alternate carbon source. The increased toluene degradation by the addition of glucose or LB broth was persistent over the short-term, suggesting the pulse amendment of an alternative carbon source may be helpful in bioremediation. While the effects of recipient genome GC content and other conditions must still be examined, our results suggest that changes in environmental conditions such as alternate substrate availability may significantly improve the functionality of the transferred phenotypes in HGT and therefore may be an important parameter for genetic bioaugmentation optimization.}, }
@article {pmid20502965, year = {2010}, author = {Coffey, L and Owens, E and Tambling, K and O'Neill, D and O'Connor, L and O'Reilly, C}, title = {Real-time PCR detection of Fe-type nitrile hydratase genes from environmental isolates suggests horizontal gene transfer between multiple genera.}, journal = {Antonie van Leeuwenhoek}, volume = {98}, number = {4}, pages = {455-463}, doi = {10.1007/s10482-010-9459-8}, pmid = {20502965}, issn = {1572-9699}, mesh = {Amidohydrolases/genetics/metabolism ; Australia ; Bacteria/*genetics/isolation &amp; purification/metabolism ; Base Sequence ; Biofilms ; *Gene Transfer, Horizontal ; Hydro-Lyases/chemistry/*genetics/metabolism ; Molecular Sequence Data ; Nitriles/*metabolism ; Poland ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Rhodococcus/enzymology/*genetics/isolation &amp; purification ; Seaweed/*microbiology ; Sequence Alignment ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Nitriles are widespread in the environment as a result of biological and industrial activity. Nitrile hydratases catalyse the hydration of nitriles to the corresponding amide and are often associated with amidases, which catalyze the conversion of amides to the corresponding acids. Nitrile hydratases have potential as biocatalysts in bioremediation and biotransformation applications, and several successful examples demonstrate the advantages. In this work a real-time PCR assay was designed for the detection of Fe-type nitrile hydratase genes from environmental isolates purified from nitrile-enriched soils and seaweeds. Specific PCR primers were also designed for amplification and sequencing of the genes. Identical or highly homologous nitrile hydratase genes were detected from isolates of numerous genera from geographically diverse sites, as were numerous novel genes. The genes were also detected from isolates of genera not previously reported to harbour nitrile hydratases. The results provide further evidence that many bacteria have acquired the genes via horizontal gene transfer. The real-time PCR assay should prove useful in searching for nitrile hydratases that could have novel substrate specificities and therefore potential in industrial applications.}, }
@article {pmid20495090, year = {2010}, author = {Andam, CP and Williams, D and Gogarten, JP}, title = {Biased gene transfer mimics patterns created through shared ancestry.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {23}, pages = {10679-10684}, pmid = {20495090}, issn = {1091-6490}, mesh = {Bacteria/classification/*genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial ; *Molecular Mimicry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Tyrosine-tRNA Ligase/*genetics ; }, abstract = {In phylogenetic reconstruction, two types of bacterial tyrosyl-tRNA synthetases (TyrRS) form distinct clades with many bacterial phyla represented in both clades. Very few taxa possess both forms, and maximum likelihood analysis of the distribution of TyrRS types suggests horizontal gene transfer (HGT), rather than an ancient duplication followed by differential gene loss, as the contributor to the evolutionary history of TyrRS in bacteria. However, for each TyrRS type, phylogenetic reconstruction yields phylogenies similar to the ribosomal phylogeny, revealing that frequent gene transfer has not destroyed the expected phylogeny; rather, the expected phylogenetic signal was reinforced or even created by HGT. We show that biased HGT can mimic patterns created through shared ancestry by in silico simulation. Furthermore, in cases where genomic synteny is sufficient to allow comparisons of relative gene positions, both tyrRS types occupy equivalent positions in closely related genomes, rejecting the loss hypothesis. Although the two types of bacterial TyrRS are only distantly related and only rarely coexist in a single genome, they have many features in common with alleles that are swapped between related lineages. We propose to label these functionally similar homologs as homeoalleles. We conclude that the observed phylogenetic pattern reflects both vertical inheritance and biased HGT and that the signal caused by common organismal descent is difficult to distinguish from the signal due to biased gene transfer.}, }
@article {pmid20494129, year = {2010}, author = {Holmgren, L}, title = {Horizontal gene transfer: you are what you eat.}, journal = {Biochemical and biophysical research communications}, volume = {396}, number = {1}, pages = {147-151}, doi = {10.1016/j.bbrc.2010.04.026}, pmid = {20494129}, issn = {1090-2104}, mesh = {Aneuploidy ; Animals ; *Apoptosis ; Endodeoxyribonucleases/genetics/metabolism ; Endothelial Cells/metabolism/pathology ; *Gene Transfer, Horizontal ; *Genomic Instability ; Humans ; Mice ; Neoplasms/*genetics/pathology ; Tumor Suppressor Protein p53/metabolism ; Viruses/genetics ; }, abstract = {Horizontal or lateral gene transfer is an effective mechanism for the exchange of genetic information in bacteria allowing bacterial diversification and facilitating adaptation to new environments. Recent data demonstrate that DNA may also be transferred between somatic cells via the uptake of apoptotic bodies. This process allows transfer of viral genes that have been incorporated into the genome in a receptor-independent fashion. Transferred DNA is replicated and propagated in daughter cells in cell that have an inactivated DNA response which may impact tumor progression.}, }
@article {pmid20493252, year = {2010}, author = {Pontiroli, A and Ceccherini, MT and Poté, J and Wildi, W and Kay, E and Nannipieri, P and Vogel, TM and Simonet, P and Monier, JM}, title = {Long-term persistence and bacterial transformation potential of transplastomic plant DNA in soil.}, journal = {Research in microbiology}, volume = {161}, number = {5}, pages = {326-334}, doi = {10.1016/j.resmic.2010.04.009}, pmid = {20493252}, issn = {1769-7123}, mesh = {Acinetobacter/genetics/metabolism ; Bacteria/genetics ; Base Sequence ; Chloroplasts/genetics ; DNA ; DNA, Bacterial ; DNA, Chloroplast/*genetics ; *Gene Transfer, Horizontal ; Genome, Chloroplast ; Plant Leaves/genetics ; Plants, Genetically Modified/genetics ; Plasmids/*genetics ; Polymerase Chain Reaction ; Soil/analysis ; *Soil Microbiology ; Nicotiana/genetics ; *Transformation, Bacterial ; *Transgenes ; }, abstract = {The long-term physical persistence and biological activity of transplastomic plant DNA (transgenes contained in the chloroplast genome) either purified and added to soil or naturally released by decaying tobacco leaves in soil was determined. Soil microcosms were amended with transplastomic tobacco leaves or purified plant DNA and incubated for up to 4 years. Total DNA was extracted from soil and the number of transgenes (aadA, which confers resistance to both spectinomycin and streptomycin) was quantified by quantitative PCR. The biological activity of these transgenes was assessed by transformation in the bacterial strain Acinetobacter sp. BD413(pBAB2) in vitro. While the proportion of transgenes recovered increased with the increasing amount of transplastomic DNA added, plant DNA was rapidly degraded over time. The number of transgenes recovered decreased about 10,000 fold within 2 weeks. Data reveal, however, that a small fraction of the plant DNA escaped degradation. Transgene sequences were still detected after 4 years and transformation assays showed that extracted DNA remained biologically active and could still transform competent cells of Acinetobacter sp. BD413(pBAB2). The approach presented here quantified the number of transgenes (based on quantitative PCR of 50% of the gene) released and persisting in the environment over time and provided new insights into the fate of transgenic plant DNA in soil.}, }
@article {pmid20488981, year = {2010}, author = {Lester, CH and Hammerum, AM}, title = {Transfer of vanA from an Enterococcus faecium isolate of chicken origin to a CC17 E. faecium isolate in the intestine of cephalosporin-treated mice.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {65}, number = {7}, pages = {1534-1536}, doi = {10.1093/jac/dkq170}, pmid = {20488981}, issn = {1460-2091}, mesh = {Animals ; Anti-Bacterial Agents/*administration &amp; dosage ; Bacterial Proteins/*genetics ; Carbon-Oxygen Ligases/*genetics ; Cephalosporins/*administration &amp; dosage ; Chickens/*microbiology ; Colony Count, Microbial ; Conjugation, Genetic ; Enterococcus faecium/*genetics ; Feces/microbiology ; Female ; *Gene Transfer, Horizontal ; Intestines/*microbiology ; Mice ; }, }
@article {pmid20487278, year = {2010}, author = {Joshi, MV and Mann, SG and Antelmann, H and Widdick, DA and Fyans, JK and Chandra, G and Hutchings, MI and Toth, I and Hecker, M and Loria, R and Palmer, T}, title = {The twin arginine protein transport pathway exports multiple virulence proteins in the plant pathogen Streptomyces scabies.}, journal = {Molecular microbiology}, volume = {77}, number = {1}, pages = {252-271}, doi = {10.1111/j.1365-2958.2010.07206.x}, pmid = {20487278}, issn = {1365-2958}, support = {BB/F009224/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/F009429/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Arabidopsis/microbiology ; Bacterial Proteins/genetics/*pharmacology ; Cell Membrane Permeability ; Electrophoresis, Gel, Two-Dimensional ; Gene Knockout Techniques ; Membrane Transport Proteins/genetics/*metabolism ; Plant Diseases/*microbiology ; Protein Transport ; Proteome/analysis ; Solanum tuberosum/microbiology ; Streptomyces/chemistry/*enzymology/growth &amp; development/*pathogenicity ; Virulence Factors/genetics/*metabolism ; }, abstract = {Summary Streptomyces scabies is one of a group of organisms that causes the economically important disease potato scab. Analysis of the S. scabies genome sequence indicates that it is likely to secrete many proteins via the twin arginine protein transport (Tat) pathway, including several proteins whose coding sequences may have been acquired through horizontal gene transfer and share a common ancestor with proteins in other plant pathogens. Inactivation of the S. scabies Tat pathway resulted in pleiotropic phenotypes including slower growth rate and increased permeability of the cell envelope. Comparison of the extracellular proteome of the wild type and DeltatatC strains identified 73 predicted secretory proteins that were present in reduced amounts in the tatC mutant strain, and 47 Tat substrates were verified using a Tat reporter assay. The DeltatatC strain was almost completely avirulent on Arabidopsis seedlings and was delayed in attaching to the root tip relative to the wild-type strain. Genes encoding 14 candidate Tat substrates were individually inactivated, and seven of these mutants were reduced in virulence compared with the wild-type strain. We conclude that the Tat pathway secretes multiple proteins that are required for full virulence.}, }
@article {pmid20487017, year = {2010}, author = {Mata, C and Miró, E and Mirelis, B and Garcillán-Barcia, MP and de la Cruz, F and Coll, P and Navarro, F}, title = {In vivo transmission of a plasmid coharbouring bla and qnrB genes between Escherichia coli and Serratia marcescens.}, journal = {FEMS microbiology letters}, volume = {308}, number = {1}, pages = {24-28}, doi = {10.1111/j.1574-6968.2010.01980.x}, pmid = {20487017}, issn = {1574-6968}, mesh = {Aged ; Blotting, Southern ; *Conjugation, Genetic ; DNA, Bacterial/genetics ; *Drug Resistance, Bacterial ; Escherichia coli/*genetics/isolation &amp; purification ; Escherichia coli Infections/microbiology ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Genotype ; Humans ; *Plasmids ; Polymerase Chain Reaction ; Quinolones/pharmacology ; Serratia Infections/microbiology ; Serratia marcescens/*genetics/isolation &amp; purification ; beta-Lactamases/genetics ; beta-Lactams/pharmacology ; }, abstract = {We report a Serratia marcescens and an Escherichia coli isolate simultaneously detected in the same patient. Both isolates showed susceptibility patterns suggestive of harbouring a plasmid-mediated AmpC beta-lactamase (pACBL) and a plasmid-encoded quinolone resistance (PMQR). PCR-based replicon, MOB typing, plasmid profile and Southern hybridization analyses revealed that both isolates coharboured bla(DHA-1) and qnrB genes on the same IncL/M-MOB(P13) plasmid approximately 70 kb in size. Together with the fact that both plasmids were conjugative in the laboratory, these results strongly suggest that a horizontal transfer event could take place in vivo. This is the first report of an isolate of S. marcescens harbouring a pACBL. The only phenotypic method that suggests the presence of a pACBL in an isolate harbouring an inducible chromosomal AmpC enzyme is the observation of scattered colonies near the edge of the inhibition zones of some beta-lactams. The presence of both resistance genes on the same plasmid and the reported increase in PMQR could perhaps explain the widespread distribution of bla(DHA-1) genes.}, }
@article {pmid20482588, year = {2010}, author = {Rhodes, ME and Fitz-Gibbon, ST and Oren, A and House, CH}, title = {Amino acid signatures of salinity on an environmental scale with a focus on the Dead Sea.}, journal = {Environmental microbiology}, volume = {12}, number = {9}, pages = {2613-2623}, doi = {10.1111/j.1462-2920.2010.02232.x}, pmid = {20482588}, issn = {1462-2920}, mesh = {*Amino Acid Sequence ; Archaea/classification/*genetics/metabolism ; Cluster Analysis ; DNA, Archaeal/genetics ; *Metagenome ; Metagenomics ; Oceans and Seas ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Salinity ; Seawater/microbiology ; Sequence Analysis, Protein ; *Water Microbiology ; }, abstract = {The increase of the acidic nature of proteins as an adaptation to hypersalinity has been well documented within halophile isolates. Here we explore the effect of salinity on amino acid preference on an environmental scale. Via pyrosequencing, we have obtained two distinct metagenomic data sets from the Dead Sea, one from a 1992 archaeal bloom and one from the modern Dead Sea. Our data, along with metagenomes from environments representing a range of salinities, show a strong linear correlation (R(2) = 0.97) between the salinity of an environment and the ratio of acidic to basic amino acids encoded by its inhabitants. Using the amino acid composition of putative protein-encoding reads and the results of 16S rRNA amplicon sequencing, we differentiate recovered sequences representing microorganisms indigenous to the Dead Sea from lateral gene transfer events and foreign DNA. Our methods demonstrate lateral gene transfer events between a halophilic archaeon and relatives of the thermophilic bacterial genus Thermotoga and suggest the presence of indigenous Dead Sea representatives from 10 traditionally non-hyperhalophilic bacterial lineages. The work suggests the possibility that amino acid bias of hypersaline environments might be preservable in fossil DNA or fossil amino acids, serving as a proxy for the salinity of an ancient environment. Finally, both the amino acid profile of the 2007 Dead Sea metagenome and the V9 amplicon library support the conclusion that the dominant microorganism inhabiting the Dead Sea is most closely related to a thus far uncultured relative of an alkaliphilic haloarchaeon.}, }
@article {pmid20480157, year = {2010}, author = {Udaya Prakash, NA and Jayanthi, M and Sabarinathan, R and Kangueane, P and Mathew, L and Sekar, K}, title = {Evolution, homology conservation, and identification of unique sequence signatures in GH19 family chitinases.}, journal = {Journal of molecular evolution}, volume = {70}, number = {5}, pages = {466-478}, pmid = {20480157}, issn = {1432-1432}, mesh = {Actinobacteria/genetics ; Amino Acid Motifs ; Bacterial Proteins/*genetics ; Chitinases/*genetics ; Databases, Genetic ; *Evolution, Molecular ; Models, Molecular ; Phylogeny ; Plant Proteins/*genetics ; Plants/genetics ; Proteobacteria/genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {The discovery of GH (Glycoside Hydrolase) 19 chitinases in Streptomyces sp. raises the possibility of the presence of these proteins in other bacterial species, since they were initially thought to be confined to higher plants. The present study mainly concentrates on the phylogenetic distribution and homology conservation in GH19 family chitinases. Extensive database searches are performed to identify the presence of GH19 family chitinases in the three major super kingdoms of life. Multiple sequence alignment of all the identified GH19 chitinase family members resulted in the identification of globally conserved residues. We further identified conserved sequence motifs across the major sub groups within the family. Estimation of evolutionary distance between the various bacterial and plant chitinases are carried out to better understand the pattern of evolution. Our study also supports the horizontal gene transfer theory, which states that GH19 chitinase genes are transferred from higher plants to bacteria. Further, the present study sheds light on the phylogenetic distribution and identifies unique sequence signatures that define GH19 chitinase family of proteins. The identified motifs could be used as markers to delineate uncharacterized GH19 family chitinases. The estimation of evolutionary distance between chitinase identified in plants and bacteria shows that the flowering plants are more related to chitinase in actinobacteria than that of identified in purple bacteria. We propose a model to elucidate the natural history of GH19 family chitinases.}, }
@article {pmid20479238, year = {2010}, author = {Slot, JC and Rokas, A}, title = {Multiple GAL pathway gene clusters evolved independently and by different mechanisms in fungi.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {22}, pages = {10136-10141}, pmid = {20479238}, issn = {1091-6490}, mesh = {Ascomycota/genetics/metabolism ; Base Sequence ; *Biological Evolution ; Candida/genetics/metabolism ; Cryptococcus/genetics/metabolism ; DNA, Fungal/genetics ; Evolution, Molecular ; Fungi/classification/*genetics/*metabolism ; Galactose/*metabolism ; Gene Transfer, Horizontal ; *Genes, Fungal ; Models, Genetic ; *Multigene Family ; Phylogeny ; Saccharomyces/genetics/metabolism ; Schizosaccharomyces/genetics/metabolism ; }, abstract = {A notable characteristic of fungal genomes is that genes involved in successive steps of a metabolic pathway are often physically linked or clustered. To investigate how such clusters of functionally related genes are assembled and maintained, we examined the evolution of gene sequences and order in the galactose utilization (GAL) pathway in whole-genome data from 80 diverse fungi. We found that GAL gene clusters originated independently and by different mechanisms in three unrelated yeast lineages. Specifically, the GAL cluster found in Saccharomyces and Candida yeasts originated through the relocation of native unclustered genes, whereas the GAL cluster of Schizosaccharomyces yeasts was acquired through horizontal gene transfer from a Candida yeast. In contrast, the GAL cluster of Cryptococcus yeasts was assembled independently from the Saccharomyces/Candida and Schizosaccharomyces GAL clusters and coexists in the Cryptococcus genome with unclustered GAL paralogs. These independently evolved GAL clusters represent a striking example of analogy at the genomic level. We also found that species with GAL clusters exhibited significantly higher rates of GAL pathway loss than species with unclustered GAL genes. These results suggest that clustering of metabolic genes might facilitate fungal adaptation to changing environments both through the acquisition and loss of metabolic capacities.}, }
@article {pmid20479219, year = {2010}, author = {Sebé-Pedrós, A and Roger, AJ and Lang, FB and King, N and Ruiz-Trillo, I}, title = {Ancient origin of the integrin-mediated adhesion and signaling machinery.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {22}, pages = {10142-10147}, pmid = {20479219}, issn = {1091-6490}, support = {206883/ERC_/European Research Council/International ; R01 GM089977/GM/NIGMS NIH HHS/United States ; MOP62809/CAPMC/CIHR/Canada ; }, mesh = {Amino Acid Sequence ; Animals ; CSK Tyrosine-Protein Kinase ; Cell Adhesion/*genetics/*physiology ; Cell Communication/genetics/physiology ; Choanoflagellata/genetics/physiology ; Cyanobacteria/genetics/physiology ; *Evolution, Molecular ; Focal Adhesion Protein-Tyrosine Kinases/genetics ; Fungi/genetics/physiology ; Gene Transfer, Horizontal ; Integrins/chemistry/*genetics/*physiology ; Molecular Sequence Data ; Phylogeny ; Protein-Tyrosine Kinases/genetics ; Sequence Homology, Amino Acid ; Signal Transduction/genetics/physiology ; src-Family Kinases ; }, abstract = {The evolution of animals (metazoans) from their unicellular ancestors required the emergence of novel mechanisms for cell adhesion and cell-cell communication. One of the most important cell adhesion mechanisms for metazoan development is integrin-mediated adhesion and signaling. The integrin adhesion complex mediates critical interactions between cells and the extracellular matrix, modulating several aspects of cell physiology. To date this machinery has been considered strictly metazoan specific. Here we report the results of a comparative genomic analysis of the integrin adhesion machinery, using genomic data from several unicellular relatives of Metazoa and Fungi. Unexpectedly, we found that core components of the integrin adhesion complex are encoded in the genome of the apusozoan protist Amastigomonas sp., and therefore their origins predate the divergence of Opisthokonta, the clade that includes metazoans and fungi. Furthermore, our analyses suggest that key components of this apparatus have been lost independently in fungi and choanoflagellates. Our data highlight the fact that many of the key genes that had formerly been cited as crucial for metazoan origins have a much earlier origin. This underscores the importance of gene cooption in the unicellular-to-multicellular transition that led to the emergence of the Metazoa.}, }
@article {pmid20478826, year = {2010}, author = {Fischer, W and Windhager, L and Rohrer, S and Zeiller, M and Karnholz, A and Hoffmann, R and Zimmer, R and Haas, R}, title = {Strain-specific genes of Helicobacter pylori: genome evolution driven by a novel type IV secretion system and genomic island transfer.}, journal = {Nucleic acids research}, volume = {38}, number = {18}, pages = {6089-6101}, pmid = {20478826}, issn = {1362-4962}, mesh = {Bacterial Proteins/genetics ; Base Sequence ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; *Genomic Islands ; Helicobacter pylori/enzymology/*genetics ; Molecular Sequence Data ; Recombinases/genetics/metabolism ; Species Specificity ; }, abstract = {The availability of multiple bacterial genome sequences has revealed a surprising extent of variability among strains of the same species. The human gastric pathogen Helicobacter pylori is known as one of the most genetically diverse species. We have compared the genome sequence of the duodenal ulcer strain P12 and six other H. pylori genomes to elucidate the genetic repertoire and genome evolution mechanisms of this species. In agreement with previous findings, we estimate that the core genome comprises about 1200 genes and that H. pylori possesses an open pan-genome. Strain-specific genes are preferentially located at potential genome rearrangement sites or in distinct plasticity zones, suggesting two different mechanisms of genome evolution. The P12 genome contains three plasticity zones, two of which encode type IV secretion systems and have typical features of genomic islands. We demonstrate for the first time that one of these islands is capable of self-excision and horizontal transfer by a conjugative process. We also show that excision is mediated by a protein of the XerD family of tyrosine recombinases. Thus, in addition to its natural transformation competence, conjugative transfer of genomic islands has to be considered as an important source of genetic diversity in H. pylori.}, }
@article {pmid20473409, year = {2010}, author = {Silverman, PM and Clarke, MB}, title = {New insights into F-pilus structure, dynamics, and function.}, journal = {Integrative biology : quantitative biosciences from nano to macro}, volume = {2}, number = {1}, pages = {25-31}, doi = {10.1039/b917761b}, pmid = {20473409}, issn = {1757-9708}, mesh = {Cell Surface Extensions/*physiology/*ultrastructure ; Escherichia coli/*physiology/*ultrastructure ; *Models, Anatomic ; *Models, Biological ; Structure-Activity Relationship ; }, abstract = {F-pili are thin, flexible filaments elaborated by F(+) cells of Escherichia coli. They belong to the class of Gram-negative pili that function in horizontal gene transfer. F-pili are initially required to establish contacts between DNA donor and recipient cells. Beyond that, F-pilus function, and that of other conjugative pili, has remained obscure and controversial. The idea that F-pili are dynamic structures was proposed 40 years ago. Initially, F-pili were thought to remain extended until another cell bound to the filament tip, whereupon the filament retracted to bring the contacted cell to the donor cell surface. Thereafter, secure surface-surface contacts would allow efficient DNA transfer. A later variant of this hypothesis was that F-pili are inherently dynamic, elongating and retracting even in the absence of exogenous signals. A very different hypothesis, also proposed first about 40 years ago, was that F-pili are conduits, presumably passive, for the transfer of DNA from donor to recipient. In this hypothesis, DNA transfer is not obligatorily coupled to F-pilus retraction. Here, we review recent data obtained by integrating long-established facts about the biology of F-pili with modern tools of fluorescence and electron microscopy. These data suggest that one function for F-pili is to search a large volume around donor cells in liquid culture for the presence of other cells. However, this may not be the only function. We show that F-pilin is also required at a second, largely undefined step occurring after cells have been brought into direct contact by F-pilus retraction.}, }
@article {pmid20472106, year = {2010}, author = {Arber, W}, title = {Genetic engineering compared to natural genetic variations.}, journal = {New biotechnology}, volume = {27}, number = {5}, pages = {517-521}, doi = {10.1016/j.nbt.2010.05.007}, pmid = {20472106}, issn = {1876-4347}, mesh = {Base Sequence ; *Biological Evolution ; Breeding ; Crops, Agricultural/genetics ; DNA/genetics ; Food Supply ; Gene Rearrangement ; Gene Transfer, Horizontal ; *Genetic Engineering ; *Genetic Variation ; Humans ; Mutation ; }, abstract = {By comparing strategies of genetic alterations introduced in genetic engineering with spontaneously occurring genetic variation, we have come to conclude that both processes depend on several distinct and specific molecular mechanisms. These mechanisms can be attributed, with regard to their evolutionary impact, to three different strategies of genetic variation. These are local nucleotide sequence changes, intragenomic rearrangement of DNA segments and the acquisition of a foreign DNA segment by horizontal gene transfer. Both the strategies followed in genetic engineering and the amounts of DNA sequences thereby involved are identical to, or at least very comparable with, those involved in natural genetic variation. Therefore, conjectural risks of genetic engineering must be of the same order as those for natural biological evolution and for conventional breeding methods. These risks are known to be quite low. There is no scientific reason to assume special long-term risks for GM crops. For future agricultural developments, a road map is designed that can be expected to lead, by a combination of genetic engineering and conventional plant breeding, to crops that can insure food security and eliminate malnutrition and hunger for the entire human population on our planet. Public-private partnerships should be formed with the mission to reach the set goals in the coming decades.}, }
@article {pmid20471307, year = {2010}, author = {Rep, M and Kistler, HC}, title = {The genomic organization of plant pathogenicity in Fusarium species.}, journal = {Current opinion in plant biology}, volume = {13}, number = {4}, pages = {420-426}, doi = {10.1016/j.pbi.2010.04.004}, pmid = {20471307}, issn = {1879-0356}, mesh = {Chromosomes, Fungal ; DNA Transposable Elements ; Evolution, Molecular ; Fusarium/*genetics ; Gene Transfer, Horizontal ; *Genome, Fungal ; Humans ; }, abstract = {Comparative genomics is a powerful tool to infer the molecular basis of fungal pathogenicity and its evolution by identifying differences in gene content and genomic organization between fungi with different hosts or modes of infection. Through comparative analysis, pathogenicity-related chromosomes have been identified in Fusarium oxysporum and Fusarium solani that contain genes for host-specific virulence. Lateral transfer of pathogenicity chromosomes, inferred from genomic data, now has been experimentally confirmed. Likewise, comparative genomics reveals the evolutionary relationships among toxin gene clusters whereby the loss and gain of genes from the cluster may be understood in an evolutionary context of toxin diversification. The genomic milieu of effector genes, encoding small secreted proteins, also suggests mechanisms that promote genetic diversification for the benefit of the pathogen.}, }
@article {pmid20470834, year = {2010}, author = {Týc, J and Long, S and Jirků, M and Lukes, J}, title = {YCF45 protein, usually associated with plastids, is targeted into the mitochondrion of Trypanosoma brucei.}, journal = {Molecular and biochemical parasitology}, volume = {173}, number = {1}, pages = {43-47}, doi = {10.1016/j.molbiopara.2010.05.002}, pmid = {20470834}, issn = {1872-9428}, mesh = {Cell Line ; Gene Transfer, Horizontal ; Humans ; Mitochondria/genetics/*metabolism ; Phylogeny ; Plastids/genetics/*metabolism ; Protein Transport ; Protozoan Proteins/genetics/*metabolism ; Trypanosoma brucei brucei/classification/genetics/*metabolism ; }, abstract = {YCF45 belongs to a family of proteins of unknown function usually located in the chloroplast of plants. Its highly conserved homologues were found in the genomes of several Trypanosoma and Leishmania species. HA(3)-tagging of the YCF45 protein with the start codon as annotated in the Gene(DB) revealed its cytosolic localization in the cultured procyclic stage of Trypanosoma brucei. However, when a more upstream located start codon was used in another HA(3)-tagged construct, the resulting protein was targeted to the mitochondrion. We propose that YCF45 was acquired by an ancestral trypanosomatid by horizontal gene transfer and in the absence of a plastid was re-targeted to the mitochondrion.}, }
@article {pmid20463738, year = {2010}, author = {Theobald, DL}, title = {A formal test of the theory of universal common ancestry.}, journal = {Nature}, volume = {465}, number = {7295}, pages = {219-222}, pmid = {20463738}, issn = {1476-4687}, mesh = {Animals ; Bayes Theorem ; Conserved Sequence ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Humans ; *Models, Biological ; Models, Genetic ; *Origin of Life ; *Phylogeny ; Reproducibility of Results ; Symbiosis/genetics ; }, abstract = {Universal common ancestry (UCA) is a central pillar of modern evolutionary theory. As first suggested by Darwin, the theory of UCA posits that all extant terrestrial organisms share a common genetic heritage, each being the genealogical descendant of a single species from the distant past. The classic evidence for UCA, although massive, is largely restricted to 'local' common ancestry-for example, of specific phyla rather than the entirety of life-and has yet to fully integrate the recent advances from modern phylogenetics and probability theory. Although UCA is widely assumed, it has rarely been subjected to formal quantitative testing, and this has led to critical commentary emphasizing the intrinsic technical difficulties in empirically evaluating a theory of such broad scope. Furthermore, several researchers have proposed that early life was characterized by rampant horizontal gene transfer, leading some to question the monophyly of life. Here I provide the first, to my knowledge, formal, fundamental test of UCA, without assuming that sequence similarity implies genetic kinship. I test UCA by applying model selection theory to molecular phylogenies, focusing on a set of ubiquitously conserved proteins that are proposed to be orthologous. Among a wide range of biological models involving the independent ancestry of major taxonomic groups, the model selection tests are found to overwhelmingly support UCA irrespective of the presence of horizontal gene transfer and symbiotic fusion events. These results provide powerful statistical evidence corroborating the monophyly of all known life.}, }
@article {pmid20463725, year = {2010}, author = {Steel, M and Penny, D}, title = {Origins of life: Common ancestry put to the test.}, journal = {Nature}, volume = {465}, number = {7295}, pages = {168-169}, pmid = {20463725}, issn = {1476-4687}, mesh = {Archaea ; Bacteria ; Bayes Theorem ; Conserved Sequence ; Eukaryota ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; *Models, Biological ; *Origin of Life ; *Phylogeny ; Reproducibility of Results ; }, }
@article {pmid20460399, year = {2010}, author = {Kassis-Chikhani, N and Decré, D and Ichai, P and Sengelin, C and Geneste, D and Mihaila, L and Dussaix, E and Arlet, G}, title = {Outbreak of Klebsiella pneumoniae producing KPC-2 and SHV-12 in a French hospital.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {65}, number = {7}, pages = {1539-1540}, doi = {10.1093/jac/dkq132}, pmid = {20460399}, issn = {1460-2091}, mesh = {Bacterial Proteins/*biosynthesis ; Cross Infection/epidemiology/microbiology ; *Disease Outbreaks ; France ; Gene Transfer, Horizontal ; Hospitals ; Humans ; Klebsiella Infections/*epidemiology/*microbiology ; Klebsiella pneumoniae/*enzymology/isolation &amp; purification ; Plasmids/analysis ; beta-Lactamases/*biosynthesis ; }, }
@article {pmid20459749, year = {2010}, author = {Kirkup, BC and Chang, L and Chang, S and Gevers, D and Polz, MF}, title = {Vibrio chromosomes share common history.}, journal = {BMC microbiology}, volume = {10}, number = {}, pages = {137}, pmid = {20459749}, issn = {1471-2180}, mesh = {*Chromosomes ; Cluster Analysis ; Computational Biology ; *Evolution, Molecular ; Gene Order ; Genes, Bacterial ; *Phylogeny ; Sequence Homology ; Synteny ; Vibrionaceae/*genetics ; }, abstract = {BACKGROUND: While most gamma proteobacteria have a single circular chromosome, Vibrionales have two circular chromosomes. Horizontal gene transfer is common among Vibrios, and in light of this genetic mobility, it is an open question to what extent the two chromosomes themselves share a common history since their formation.<br><br>RESULTS: Single copy genes from each chromosome (142 genes from chromosome I and 42 genes from chromosome II) were identified from 19 sequenced Vibrionales genomes and their phylogenetic comparison suggests consistent phylogenies for each chromosome. Additionally, study of the gene organization and phylogeny of the respective origins of replication confirmed the shared history.<br><br>CONCLUSIONS: Thus, while elements within the chromosomes may have experienced significant genetic mobility, the backbones share a common history. This allows conclusions based on multilocus sequence analysis (MLSA) for one chromosome to be applied equally to both chromosomes.}, }
@article {pmid20457878, year = {2010}, author = {Marquez, CP and Pritham, EJ}, title = {Phantom, a new subclass of Mutator DNA transposons found in insect viruses and widely distributed in animals.}, journal = {Genetics}, volume = {185}, number = {4}, pages = {1507-1517}, pmid = {20457878}, issn = {1943-2631}, mesh = {Amino Acid Motifs/genetics ; Amino Acid Sequence ; Animals ; Base Sequence ; DNA Transposable Elements/*genetics ; Entamoeba/genetics/virology ; Gene Transfer, Horizontal ; Insect Viruses/*genetics ; Insecta/*genetics/virology ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Transposases/classification/*genetics ; }, abstract = {Transposons of the Mutator (Mu) superfamily have been shown to play a critical role in the evolution of plant genomes. However, the identification of Mutator transposons in other eukaryotes has been quite limited. Here we describe a previously uncharacterized group of DNA transposons designated Phantom identified in the genomes of a wide range of eukaryotic taxa, including many animals, and provide evidence for its inclusion within the Mutator superfamily. Interestingly three Phantom proteins were also identified in two insect viruses and phylogenetic analysis suggests horizontal movement from insect to virus, providing a new line of evidence for the role of viruses in the horizontal transfer of DNA transposons in animals. Many of the Phantom transposases are predicted to harbor a FLYWCH domain in the amino terminus, which displays a WRKY-GCM1 fold characteristic of the DNA binding domain (DBD) of Mutator transposases and of several transcription factors. While some Phantom elements have terminal inverted repeats similar in length and structure to Mutator elements, some display subterminal inverted repeats (sub-TIRs) and others have more complex termini reminiscent of so-called Foldback (FB) transposons. The structural plasticity of Phantom and the distant relationship of its encoded protein to known transposases may have impeded the discovery of this group of transposons and it suggests that structure in itself is not a reliable character for transposon classification.}, }
@article {pmid20456068, year = {2010}, author = {Verret, F and Wheeler, G and Taylor, AR and Farnham, G and Brownlee, C}, title = {Calcium channels in photosynthetic eukaryotes: implications for evolution of calcium-based signalling.}, journal = {The New phytologist}, volume = {187}, number = {1}, pages = {23-43}, doi = {10.1111/j.1469-8137.2010.03271.x}, pmid = {20456068}, issn = {1469-8137}, support = {BB/H013814/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; REI20579/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Calcium Channels/*metabolism ; *Calcium Signaling ; Eukaryota/*metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Photosynthesis ; }, abstract = {Much of our current knowledge on the mechanisms by which Ca(2+) signals are generated in photosynthetic eukaryotes comes from studies of a relatively small number of model species, particularly green plants and algae, revealing some common features and notable differences between 'plant' and 'animal' systems. Physiological studies from a broad range of algal cell types have revealed the occurrence of animal-like signalling properties, including fast action potentials and fast propagating cytosolic Ca(2+) waves. Genomic studies are beginning to reveal the widespread occurrence of conserved channel types likely to be involved in Ca(2+) signalling. However, certain widespread 'ancient' channel types appear to have been lost by certain groups, such as the embryophytes. More recent channel gene loss is also evident from comparisons of more closely related algal species. The underlying processes that have given rise to the current distributions of Ca(2+) channel types include widespread retention of ancient Ca(2+) channel genes, horizontal gene transfer (including symbiotic gene transfer and acquisition of bacterial genes), gene loss and gene expansion within taxa. The assessment of the roles of Ca(2+) channel genes in diverse physiological, developmental and life history processes represents a major challenge for future studies.}, }
@article {pmid20455433, year = {2009}, author = {Ianeva, OD}, title = {[Mechanisms of bacteria resistance to heavy metals].}, journal = {Mikrobiolohichnyi zhurnal (Kiev, Ukraine : 1993)}, volume = {71}, number = {6}, pages = {54-65}, pmid = {20455433}, issn = {1028-0987}, mesh = {Adaptation, Biological ; Biological Evolution ; Drug Resistance, Bacterial/drug effects/genetics/*physiology ; Metals, Heavy/chemistry/*pharmacology ; }, abstract = {Bacteria have adapted to the presence of heavy metal ions in their habitats. There are five main mechanisms of heavy metal resistance in bacteria extracellular barrier, active transport of metal ions (efflux), extracellular sequestration, intracellular sequestration, reduction of metal ions. Genetic determinants of heavy metal resistance can be localized both on bacterial chromosomes and on extrachromosomal genetic elements. Horizontal gene transfer plays an important role in the spread of heavy metal resistance in nature. Interactions between bacteria and heavy metal ions are of great interest both as a fundamental process and potential bioremedial technology.}, }
@article {pmid20453921, year = {2010}, author = {Clark, GW and Tillier, ER}, title = {Loss and gain of GroEL in the Mollicutes.}, journal = {Biochemistry and cell biology = Biochimie et biologie cellulaire}, volume = {88}, number = {2}, pages = {185-194}, doi = {10.1139/o09-157}, pmid = {20453921}, issn = {1208-6002}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Chaperonin 60/chemistry/*genetics/*metabolism ; Phylogeny ; Tenericutes/chemistry/*genetics/*metabolism ; }, abstract = {GroEL is a chaperone thought of as essential for bacterial life. However, some species of Mollicutes are missing GroEL. We use phylogenetic analysis to show that the presence of GroEL is polyphyletic among the Mollicutes, and that there is evidence for lateral gene transfer of GroEL to Mycoplasma penetrans from the Proteobacteria. Furthermore, we propose that the presence of GroEL in Mycoplasma may be required for invasion of host tissue, suggesting that GroEL may act as an adhesin-invasin.}, }
@article {pmid20450979, year = {2010}, author = {Kamikawa, R and Sakaguchi, M and Matsumoto, T and Hashimoto, T and Inagaki, Y}, title = {Rooting for the root of elongation factor-like protein phylogeny.}, journal = {Molecular phylogenetics and evolution}, volume = {56}, number = {3}, pages = {1082-1088}, doi = {10.1016/j.ympev.2010.04.040}, pmid = {20450979}, issn = {1095-9513}, mesh = {Bayes Theorem ; Eukaryota/classification/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Likelihood Functions ; Peptide Elongation Factors/classification/*genetics ; *Phylogeny ; }, abstract = {Lateral gene transfer (LGT) may play a pivotal role in the evolution of elongation factor-like (EFL) genes in eukaryotes. To date, numbers of putative cases for lateral transfer of EFL genes have been postulated based on unrooted EFL phylogenies. Nevertheless, the root position in EFL phylogeny is important to validate lateral EFL gene transfer: for instance, a clade of two EFL homologs from distantly related organisms in an unrooted EFL tree does not necessarily confirm the LGT, since the possibility that the root may locate in this clade cannot be excluded. Cocquyt et al. (2009, p. 39) recently demonstrated that a putative case of lateral EFL gene transfer, which was originally proposed based on an unrooted phylogeny, could not be endorsed by the corresponding rooted analysis. Although rooting EFL phylogeny is indispensable to elucidate various aspects in EFL gene evolution, we suspected that the outgroup clade comprised of EF-1alpha and eukaryote-specific EF-1alpha paralogs erroneously attached to long EFL branches in Cocquyt et al. (2009) - a typical long branch attraction (LBA) artifact. Here, we systematically assessed the putative LBA artifact between the branch leading to the outgroup clade and long ingroup branches by analyzing the original dataset used in Cocquyt et al. (2009) with and without modifying ingroup-sequence sampling. A series of the rooted EFL analyses indicated that the root inference was highly susceptible to presence and absence of long-branched ingroup-sequences, suggesting that the rooted EFL phylogenies cannot be free from severe LBA artifact. We also discussed a new aspect in EFL gene evolution in stramenopiles identified in the course of the EFL analyses described above. Finally, the relative timing of the first emergence of EFL gene in eukaryotes was contemplated based on the current EF-1alpha/EFL distribution.}, }
@article {pmid20446871, year = {2010}, author = {Cleaves, HJ and Jonsson, CM and Jonsson, CL and Sverjensky, DA and Hazen, RM}, title = {Adsorption of nucleic acid components on rutile (TiO(2)) surfaces.}, journal = {Astrobiology}, volume = {10}, number = {3}, pages = {311-323}, doi = {10.1089/ast.2009.0397}, pmid = {20446871}, issn = {1557-8070}, mesh = {Adsorption ; Deoxyribonucleotides/chemistry ; Hydrogen-Ion Concentration ; Nucleic Acids/*chemistry ; Purines/chemistry ; Pyrimidines/chemistry ; Ribonucleotides/chemistry ; Surface Properties ; Temperature ; Titanium/*chemistry ; }, abstract = {Nucleic acids, the storage molecules of genetic information, are composed of repeating polymers of ribonucleotides (in RNA) or deoxyribonucleotides (in DNA), which are themselves composed of a phosphate moiety, a sugar moiety, and a nitrogenous base. The interactions between these components and mineral surfaces are important because there is a tremendous flux of nucleic acids in the environment due to cell death and horizontal gene transfer. The adsorption of mono-, oligo-, and polynucleotides and their components on mineral surfaces may have been important for the origin of life. We have studied here interactions of nucleic acid components with rutile (TiO(2)), a mineral common in many terrestrial crustal rocks. Our results suggest roles for several nucleic acid functional groups (including sugar hydroxyl groups, the phosphate group, and extracyclic functional groups on the bases) in binding, in agreement with results obtained from studies of other minerals. In contrast with recent studies of nucleotide adsorption on ZnO, aluminum oxides, and hematite, our results suggest a different preferred orientation for the monomers on rutile surfaces. The conformations of the molecules bound to rutile surfaces appear to favor specific interactions, which in turn may allow identification of the most favorable mineral surfaces for nucleic acid adsorption.}, }
@article {pmid20445988, year = {2010}, author = {Dobrindt, U and Chowdary, MG and Krumbholz, G and Hacker, J}, title = {Genome dynamics and its impact on evolution of Escherichia coli.}, journal = {Medical microbiology and immunology}, volume = {199}, number = {3}, pages = {145-154}, pmid = {20445988}, issn = {1432-1831}, mesh = {Adaptation, Biological ; Animals ; Escherichia coli/*genetics/physiology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; Interspersed Repetitive Sequences ; Recombination, Genetic ; }, abstract = {The Escherichia coli genome consists of a conserved part, the so-called core genome, which encodes essential cellular functions and of a flexible, strain-specific part. Genes that belong to the flexible genome code for factors involved in bacterial fitness and adaptation to different environments. Adaptation includes increase in fitness and colonization capacity. Pathogenic as well as non-pathogenic bacteria carry mobile and accessory genetic elements such as plasmids, bacteriophages, genomic islands and others, which code for functions required for proper adaptation. Escherichia coli is a very good example to study the interdependency of genome architecture and lifestyle of bacteria. Thus, these species include pathogenic variants as well as commensal bacteria adapted to different host organisms. In Escherichia coli, various genetic elements encode for pathogenicity factors as well as factors, which increase the fitness of non-pathogenic bacteria. The processes of genome dynamics, such as gene transfer, genome reduction, rearrangements as well as point mutations contribute to the adaptation of the bacteria into particular environments. Using Escherichia coli model organisms, such as uropathogenic strain 536 or commensal strain Nissle 1917, we studied mechanisms of genome dynamics and discuss these processes in the light of the evolution of microbes.}, }
@article {pmid20444286, year = {2010}, author = {Park, HJ and Jin, G and Nakhleh, L}, title = {Bootstrap-based support of HGT inferred by maximum parsimony.}, journal = {BMC evolutionary biology}, volume = {10}, number = {}, pages = {131}, pmid = {20444286}, issn = {1471-2148}, support = {R01LM009494/LM/NLM NIH HHS/United States ; }, mesh = {*Gene Transfer, Horizontal ; Models, Genetic ; Phylogeny ; Plants/*genetics ; Software ; }, abstract = {BACKGROUND: Maximum parsimony is one of the most commonly used criteria for reconstructing phylogenetic trees. Recently, Nakhleh and co-workers extended this criterion to enable reconstruction of phylogenetic networks, and demonstrated its application to detecting reticulate evolutionary relationships. However, one of the major problems with this extension has been that it favors more complex evolutionary relationships over simpler ones, thus having the potential for overestimating the amount of reticulation in the data. An ad hoc solution to this problem that has been used entails inspecting the improvement in the parsimony length as more reticulation events are added to the model, and stopping when the improvement is below a certain threshold.<br><br>RESULTS: In this paper, we address this problem in a more systematic way, by proposing a nonparametric bootstrap-based measure of support of inferred reticulation events, and using it to determine the number of those events, as well as their placements. A number of samples is generated from the given sequence alignment, and reticulation events are inferred based on each sample. Finally, the support of each reticulation event is quantified based on the inferences made over all samples.<br><br>CONCLUSIONS: We have implemented our method in the NEPAL software tool (available publicly at http://bioinfo.cs.rice.edu/), and studied its performance on both biological and simulated data sets. While our studies show very promising results, they also highlight issues that are inherently challenging when applying the maximum parsimony criterion to detect reticulate evolution.}, }
@article {pmid20444106, year = {2010}, author = {Dillon, SC and Cameron, AD and Hokamp, K and Lucchini, S and Hinton, JC and Dorman, CJ}, title = {Genome-wide analysis of the H-NS and Sfh regulatory networks in Salmonella Typhimurium identifies a plasmid-encoded transcription silencing mechanism.}, journal = {Molecular microbiology}, volume = {76}, number = {5}, pages = {1250-1265}, doi = {10.1111/j.1365-2958.2010.07173.x}, pmid = {20444106}, issn = {1365-2958}, support = {BBS/E/F/00042248/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacterial Proteins/genetics/*metabolism ; Base Sequence ; DNA-Binding Proteins/genetics/*metabolism ; Gene Expression Profiling ; *Gene Expression Regulation, Bacterial ; *Gene Regulatory Networks ; *Gene Silencing ; Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; Microarray Analysis ; Molecular Sequence Data ; Plasmids/*genetics/metabolism ; Salmonella typhimurium/*genetics/metabolism ; Transcription, Genetic ; }, abstract = {The conjugative IncHI1 plasmid pSfR27 from Shigella flexneri 2a strain 2457T encodes the Sfh protein, a paralogue of the global transcriptional repressor H-NS. Sfh allows pSfR27 to be transmitted to new bacterial hosts with minimal impact on host fitness, providing a 'stealth' function whose molecular mechanism has yet to be determined. The impact of the Sfh protein on the Salmonella enterica serovar Typhimurium transcriptome was assessed and binding sites for Sfh in the Salmonella Typhimurium genome were identified by chromatin immunoprecipitation. Sfh did not bind uniquely to any sites. Instead, it bound to a subset of the larger H-NS regulatory network. Analysis of Sfh binding in the absence of H-NS revealed a greatly expanded population of Sfh binding sites that included the majority of H-NS target genes. Furthermore, the presence of plasmid pSfR27 caused a decrease in H-NS interactions with the S. Typhimurium chromosome, suggesting that the A + T-rich DNA of this large plasmid acts to titrate H-NS, removing it from chromosomal locations. It is proposed that Sfh acts as a molecular backup for H-NS and that it provides its 'stealth' function by replacing H-NS on the chromosome, thus minimizing disturbances to the H-NS-DNA binding pattern in cells that acquire pSfR27.}, }
@article {pmid20444092, year = {2010}, author = {Chen, B and Bruce, KL and Newnam, GP and Gyoneva, S and Romanyuk, AV and Chernoff, YO}, title = {Genetic and epigenetic control of the efficiency and fidelity of cross-species prion transmission.}, journal = {Molecular microbiology}, volume = {76}, number = {6}, pages = {1483-1499}, pmid = {20444092}, issn = {1365-2958}, support = {R01 GM058763/GM/NIGMS NIH HHS/United States ; R01 GM058763-11/GM/NIGMS NIH HHS/United States ; R01GM58763/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Amyloid/metabolism ; *Gene Expression Regulation, Fungal ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Peptide Termination Factors/*genetics/*metabolism ; *Polymorphism, Genetic ; Saccharomyces cerevisiae/*genetics/*metabolism ; Saccharomyces cerevisiae Proteins/*genetics/*metabolism ; Sequence Alignment ; }, abstract = {Self-perpetuating amyloid-based protein isoforms (prions) transmit neurodegenerative diseases in mammals and phenotypic traits in yeast. Although mechanisms that control species specificity of prion transmission are poorly understood, studies of closely related orthologues of yeast prion protein Sup35 demonstrate that cross-species prion transmission is modulated by both genetic (specific sequence elements) and epigenetic (prion variants, or 'strains') factors. Depending on the prion variant, the species barrier could be controlled at the level of either heterologous co-aggregation or conversion of the aggregate-associated heterologous protein into a prion polymer. Sequence divergence influences cross-species transmission of different prion variants in opposing ways. The ability of a heterologous prion domain to either faithfully reproduce or irreversibly switch the variant-specific prion patterns depends on both sequence divergence and the prion variant. Sequence variations within different modules of prion domains contribute to transmission barriers in different cross-species combinations. Individual amino acid substitutions within short amyloidogenic stretches drastically alter patterns of cross-species prion conversion, implicating these stretches as major determinants of species specificity.}, }
@article {pmid20421328, year = {2010}, author = {Gladyshev, EA and Arkhipova, IR}, title = {Genome structure of bdelloid rotifers: shaped by asexuality or desiccation?.}, journal = {The Journal of heredity}, volume = {101 Suppl 1}, number = {}, pages = {S85-93}, doi = {10.1093/jhered/esq008}, pmid = {20421328}, issn = {1465-7333}, mesh = {Animals ; Cloning, Molecular ; DNA Damage/*genetics ; DNA Primers/genetics ; DNA Transposable Elements/genetics ; Dehydration ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome, Helminth/*genetics ; Reproduction, Asexual/*genetics/physiology ; Rotifera/*genetics/physiology ; }, abstract = {Bdelloid rotifers are microscopic invertebrate animals best known for their ancient asexuality and the ability to survive desiccation at any life stage. Both factors are expected to have a profound influence on their genome structure. Recent molecular studies demonstrated that, although the gene-rich regions of bdelloid genomes are organized as colinear pairs of closely related sequences and depleted in repetitive DNA, subtelomeric regions harbor diverse transposable elements and horizontally acquired genes of foreign origin. Although asexuality is expected to result in depletion of deleterious transposons, only desiccation appears to have the power to produce all the uncovered genomic peculiarities. Repair of desiccation-induced DNA damage would require the presence of a homologous template, maintaining colinear pairs in gene-rich regions and selecting against insertion of repetitive DNA that might cause chromosomal rearrangements. Desiccation may also induce a transient state of competence in recovering animals, allowing them to acquire environmental DNA. Even if bdelloids engage in rare or obscure forms of sexual reproduction, all these features could still be present. The relative contribution of asexuality and desiccation to genome organization may be clarified by analyzing whole-genome sequences and comparing foreign gene and transposon content in species which lost the ability to survive desiccation.}, }
@article {pmid20441541, year = {2010}, author = {Marraffini, LA}, title = {Impact of CRIPSR immunity on the emergence of bacterial pathogens.}, journal = {Future microbiology}, volume = {5}, number = {5}, pages = {693-695}, doi = {10.2217/fmb.10.38}, pmid = {20441541}, issn = {1746-0921}, mesh = {*Adaptation, Biological ; Bacteria/*genetics/*pathogenicity ; Conjugation, Genetic ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Transduction, Genetic ; Transformation, Bacterial ; Virulence Factors/*genetics ; }, }
@article {pmid20437233, year = {2010}, author = {Legat, A and Gruber, C and Zangger, K and Wanner, G and Stan-Lotter, H}, title = {Identification of polyhydroxyalkanoates in Halococcus and other haloarchaeal species.}, journal = {Applied microbiology and biotechnology}, volume = {87}, number = {3}, pages = {1119-1127}, pmid = {20437233}, issn = {1432-0614}, mesh = {Australia ; Geologic Sediments/microbiology ; Halobacteriaceae/*chemistry/isolation &amp; purification/metabolism/ultrastructure ; Halococcus/*chemistry/isolation &amp; purification/metabolism/ultrastructure ; Hydroxybutyrates/*chemistry/metabolism ; Magnetic Resonance Spectroscopy ; Microscopy, Electron, Transmission ; Polyesters/*chemistry/metabolism ; }, abstract = {Polyhydroxyalkanoates (PHAs) are accumulated in many prokaryotes. Several members of the Halobacteriaceae produce poly-3-hydroxybutyrate (PHB), but it is not known if this is a general property of the family. We evaluated identification methods for PHAs with 20 haloarchaeal species, three of them isolates from Permian salt. Staining with Sudan Black B, Nile Blue A, or Nile Red was applied to screen for the presence of PHAs. Transmission electron microscopy and (1)H-nuclear magnetic resonance spectroscopy were used for visualization of PHB granules and chemical confirmation of PHAs in cell extracts, respectively. We report for the first time the production of PHAs by Halococcus sp. (Halococcus morrhuae DSM 1307(T), Halococcus saccharolyticus DSM 5350(T), Halococcus salifodinae DSM 8989(T), Halococcus dombrowskii DSM 14522(T), Halococcus hamelinensis JCM 12892(T), Halococcus qingdaonensis JCM 13587(T)), Halorubrum sp. (Hrr. coriense DSM 10284(T), Halorubrum chaoviator DSM 19316(T), Hrr. chaoviator strains NaxosII and AUS-1), haloalkaliphiles (Natronobacterium gregoryi NCMB 2189(T), Natronococcus occultus DSM 3396(T)) and Halobacterium noricense DSM 9758(T). No PHB was detected in Halobacterium salinarum NRC-1 ATCC 700922, Hbt. salinarum R1 and Haloferax volcanii DSM 3757(T). Most species synthesized PHAs when growing in synthetic as well as in complex medium. The polyesters were generally composed of PHB and poly-ss-hydroxybutyrate-co-3-hydroxyvalerate (PHBV). Available genomic data suggest the absence of PHA synthesis in some haloarchaea and in all other Euryarchaeota and Crenarchaeota. Homologies between haloarchaeal and bacterial PHA synthesizing enzymes had indicated to some authors probable horizontal gene transfer, which, considering the data obtained in this study, may have occurred already before Permian times.}, }
@article {pmid20436956, year = {2010}, author = {Gómez-Consarnau, L and Akram, N and Lindell, K and Pedersen, A and Neutze, R and Milton, DL and González, JM and Pinhassi, J}, title = {Proteorhodopsin phototrophy promotes survival of marine bacteria during starvation.}, journal = {PLoS biology}, volume = {8}, number = {4}, pages = {e1000358}, pmid = {20436956}, issn = {1545-7885}, mesh = {Bacterial Proteins/genetics/*metabolism ; Cell Survival/*physiology ; Chromosome Mapping ; Genome, Bacterial ; Light ; Molecular Sequence Data ; *Phototrophic Processes ; Phylogeny ; RNA, Ribosomal, 16S/classification/genetics ; Rhodopsin/genetics/*metabolism ; Rhodopsins, Microbial ; Seawater/*microbiology ; Vibrio/classification/*metabolism ; }, abstract = {Proteorhodopsins are globally abundant photoproteins found in bacteria in the photic zone of the ocean. Although their function as proton pumps with energy-yielding potential has been demonstrated, the ecological role of proteorhodopsins remains largely unexplored. Here, we report the presence and function of proteorhodopsin in a member of the widespread genus Vibrio, uncovered through whole-genome analysis. Phylogenetic analysis suggests that the Vibrio strain AND4 obtained proteorhodopsin through lateral gene transfer, which could have modified the ecology of this marine bacterium. We demonstrate an increased long-term survival of AND4 when starved in seawater exposed to light rather than held in darkness. Furthermore, mutational analysis provides the first direct evidence, to our knowledge, linking the proteorhodopsin gene and its biological function in marine bacteria. Thus, proteorhodopsin phototrophy confers a fitness advantage to marine bacteria, representing a novel mechanism for bacterioplankton to endure frequent periods of resource deprivation at the ocean's surface.}, }
@article {pmid20433942, year = {2010}, author = {Mogi, T and Kita, K}, title = {Diversity in mitochondrial metabolic pathways in parasitic protists Plasmodium and Cryptosporidium.}, journal = {Parasitology international}, volume = {59}, number = {3}, pages = {305-312}, doi = {10.1016/j.parint.2010.04.005}, pmid = {20433942}, issn = {1873-0329}, mesh = {Animals ; Cryptosporidiosis/parasitology ; Cryptosporidium/enzymology/genetics/*metabolism ; DNA, Mitochondrial/genetics/metabolism ; Humans ; Malaria/parasitology ; *Metabolic Networks and Pathways ; Mitochondria/enzymology/genetics/*metabolism ; Plasmodium/enzymology/genetics/*metabolism ; }, abstract = {Apicomplexans are obligate intracellular parasites and occupy diverse niches. They have remodeled mitochondrial carbon and energy metabolism through reductive evolution. Plasmodium lacks mitochondrial pyruvate dehydrogenase and H(+)-translocating NADH dehydrogenase (Complex I, NDH1). The mitochondorion contains a minimal mtDNA (approximately 6kb) and carries out oxidative phosphorylation in the insect vector stages, by using 2-oxoglutarate as an alternative means of entry into the TCA cycle and a single-subunit flavoprotein as an alternative NADH dehydrogenase (NDH2). In the blood stages of mammalian hosts, mitochondrial enzymes are down-regulated and parasite energy metabolism relies mainly on glycolysis. Mitosomes of Cryptosporidium parvum and Cryptosporidium hominis (human intestine parasites) lack mtDNA, pyruvate dehydrogenase, TCA cycle enzymes except malate-quinone oxidoreductase (MQO), and ATP synthase subunits except alpha and beta. In contrast, mitosomes of Cryptosporidium muris (a rodent gastric parasite) retain all TCA cycle enzymes and functional ATP synthase and carry out oxidative phosphorylation with pyruvate-NADP(+) oxidoreductase (PNO) and a simple and unique respiratory chain consisting of NDH2 and alternative oxidase (AOX). Cryptosporidium and Perkinsus are early branching groups of chromoalveolates (apicomplexa and dinoflagellates, respectively), and both Cryptosporidium mitosome and Perkinsus mitochondrion use PNO, MQO, and AOX. All apicomplexan parasites and dinoflagellates share MQO, which has been acquired from epsilon-proteobacteria via lateral gene transfer. By genome data mining on Plasmodium, Cryptosporidium and Perkinsus, here we summarized their mitochondrial metabolic pathways, which are varied largely from those of mammalian hosts. We hope that our findings will help in understanding the apicomplexan metabolism and development of new chemotherapeutics with novel targets.}, }
@article {pmid20431015, year = {2010}, author = {Moran, NA and Jarvik, T}, title = {Lateral transfer of genes from fungi underlies carotenoid production in aphids.}, journal = {Science (New York, N.Y.)}, volume = {328}, number = {5978}, pages = {624-627}, doi = {10.1126/science.1187113}, pmid = {20431015}, issn = {1095-9203}, mesh = {Animals ; Aphids/*genetics/*metabolism/microbiology ; Carotenoids/analysis/*biosynthesis/genetics ; Crosses, Genetic ; Fungi/genetics ; Gene Duplication ; *Gene Transfer, Horizontal ; *Genes, Fungal ; *Genes, Insect ; Genome, Insect ; Heterozygote ; Molecular Sequence Data ; Mutation ; Oxidoreductases/genetics ; Phylogeny ; Pigmentation/genetics ; Pigments, Biological/chemistry ; Polymorphism, Genetic ; Sequence Analysis, DNA ; }, abstract = {Carotenoids are colored compounds produced by plants, fungi, and microorganisms and are required in the diet of most animals for oxidation control or light detection. Pea aphids display a red-green color polymorphism, which influences their susceptibility to natural enemies, and the carotenoid torulene occurs only in red individuals. Unexpectedly, we found that the aphid genome itself encodes multiple enzymes for carotenoid biosynthesis. Phylogenetic analyses show that these aphid genes are derived from fungal genes, which have been integrated into the genome and duplicated. Red individuals have a 30-kilobase region, encoding a single carotenoid desaturase that is absent from green individuals. A mutation causing an amino acid replacement in this desaturase results in loss of torulene and of red body color. Thus, aphids are animals that make their own carotenoids.}, }
@article {pmid20431000, year = {2010}, author = {Fukatsu, T}, title = {Evolution. A fungal past to insect color.}, journal = {Science (New York, N.Y.)}, volume = {328}, number = {5978}, pages = {574-575}, doi = {10.1126/science.1190417}, pmid = {20431000}, issn = {1095-9203}, mesh = {Animals ; Aphids/*genetics/metabolism/microbiology ; Biological Evolution ; Carotenoids/analysis/*biosynthesis/genetics ; Fungi/genetics ; Gene Duplication ; *Gene Transfer, Horizontal ; *Genes, Fungal ; *Genome, Insect ; Oxidoreductases/genetics ; Phylogeny ; Pigmentation/*genetics ; Pigments, Biological/*chemistry ; }, }
@article {pmid20430903, year = {2010}, author = {Shakil, S and Akram, M and Ali, SM and Khan, AU}, title = {Acquisition of extended-spectrum beta-lactamase producing Escherichia coli strains in male and female infants admitted to a neonatal intensive care unit: molecular epidemiology and analysis of risk factors.}, journal = {Journal of medical microbiology}, volume = {59}, number = {Pt 8}, pages = {948-954}, doi = {10.1099/jmm.0.020214-0}, pmid = {20430903}, issn = {1473-5644}, mesh = {Animals ; *Bacterial Typing Techniques ; Cluster Analysis ; Conjugation, Genetic ; *DNA Fingerprinting ; DNA, Bacterial/genetics ; Escherichia coli/*classification/*enzymology/genetics/isolation &amp; purification ; Escherichia coli Infections/*microbiology ; Escherichia coli Proteins/*genetics ; Female ; Gene Transfer, Horizontal ; Genotype ; Humans ; India ; Infant ; Infant, Newborn ; Intensive Care, Neonatal ; Male ; Molecular Epidemiology ; Risk Factors ; Sequence Analysis, DNA ; beta-Lactamases/*genetics ; }, abstract = {Extended-spectrum beta-lactamases (ESBLs) are bacterial enzymes that confer resistance to advanced generation cephalosporins and can lead to therapeutic failures. There has been no analysis of factors associated with the risk of acquisition of ESBLs in neonates in an intensive care unit from northern India. The CTX-M ESBL enzymes impart resistance against advanced generation cephalosporins (e.g. cefotaxime) and CTX-M variants have become the most prevalent ESBLs worldwide. The CTX-M-15 enzyme in particular is increasingly being reported from Escherichia coli isolates from northern India together with TEM-1. Moreover, E. coli is the most common cause of neonatal sepsis. Accordingly, this study aimed to: (i) characterize the mode of transmission of bla(CTX-M) and bla(TEM) among ESBL-producing E. coli strains isolated from patients admitted to a neonatal intensive care unit (NICU), and (ii) identify factors associated with the acquisition of the said strains in male and female neonates. A total of 97 ESBL-producers was identified among 266 E. coli strains isolated from 238 neonates. The isolates were screened for bla(CTX-M), bla(TEM), armA, rmtA and rmtB, the last three genes being responsible for aminoglycoside resistance. PCR amplified bla(CTX-M) genes were cloned and sequenced. Five bla(CTX-M-15), two rmtB, two bla(TEM-1) and thirteen class1 integrons were detected. All the bla(CTX-M-15) positive isolates, except one, were clonally related. Both univariate and multivariate analyses of factors for the acquisition of the said strains were performed with respect to the sex of the neonates. 'Length of stay in the NICU' was found to be the single independent factor associated with ESBL acquisition. In conclusion, our data suggest that male neonates who are colonized or infected by ESBL-producing E. coli have a longer stay in the NICU compared to their female counterparts. This prolonged stay may be due to male neonates becoming colonized/infected earlier than their female counterparts. Plasmid-mediated-conjugal transfer was found to be the mechanism of transfer of the bla(CTX-M-15) resistance marker in the described setting.}, }
@article {pmid20430808, year = {2010}, author = {Stüken, A and Jakobsen, KS}, title = {The cylindrospermopsin gene cluster of Aphanizomenon sp. strain 10E6: organization and recombination.}, journal = {Microbiology (Reading, England)}, volume = {156}, number = {Pt 8}, pages = {2438-2451}, doi = {10.1099/mic.0.036988-0}, pmid = {20430808}, issn = {1465-2080}, mesh = {Alkaloids ; Aphanizomenon/*genetics ; Bacterial Toxins ; Base Composition ; Comparative Genomic Hybridization ; Cyanobacteria Toxins ; Cylindrospermopsis/genetics ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Molecular Sequence Data ; *Multigene Family ; Phylogeny ; Sequence Analysis, DNA ; Uracil/*analogs &amp; derivatives/biosynthesis ; }, abstract = {Cylindrospermopsin (CYN), a potent hepatoxin, occurs in freshwaters worldwide. Several cyanobacterial species produce the toxin, but the producing species vary between geographical regions. Aphanizomenon flos-aquae, a common algae species in temperate fresh and brackish waters, is one of the three well-documented CYN producers in European waters. So far, no genetic information on the CYN genes of this species has been available. Here, we describe the complete CYN gene cluster, including flanking regions from the German Aphanizomenon sp. strain 10E6 using a full genome sequencing approach by 454 pyrosequencing and bioinformatic identification of the gene cluster. In addition, we have sequenced a approximately 7 kb fragment covering the genes cyrC (partially), cyrA and cyrB (partially) of the same gene cluster in the CYN-producing Aphanizomenon sp. strains 10E9 and 22D11. Comparisons with the orthologous gene clusters of the Australian Cylindrospermopsis raciborskii strains AWT205 and CS505 and the partial gene cluster of the Israeli Aphanizomenon ovalisporum strain ILC-146 revealed a high gene sequence similarity, but also extensive rearrangements of gene order. The high sequence similarity (generally higher than that of 16S rRNA gene fragments from the same strains), atypical GC-content and signs of transposase activities support the suggestion that the CYN genes have been horizontally transferred.}, }
@article {pmid20429715, year = {2010}, author = {Nielsen, KL and Hammerum, AM and Lambertsen, LM and Lester, CH and Arpi, M and Knudsen, JD and Stegger, M and Tolker-Nielsen, T and Frimodt-Møller, N}, title = {Characterization and transfer studies of macrolide resistance genes in Streptococcus pneumoniae from Denmark.}, journal = {Scandinavian journal of infectious diseases}, volume = {42}, number = {8}, pages = {586-593}, doi = {10.3109/00365541003754451}, pmid = {20429715}, issn = {1651-1980}, mesh = {Anti-Bacterial Agents/*pharmacology ; Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; Denmark ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Humans ; Macrolides/*pharmacology ; Microbial Sensitivity Tests ; Pneumococcal Infections/microbiology ; Point Mutation ; Sequence Analysis, DNA ; Streptococcus pneumoniae/*drug effects/*genetics/isolation &amp; purification ; *Transformation, Bacterial ; }, abstract = {Over the last decade, erythromycin resistance has been increasing in frequency in Streptococcus pneumoniae in Denmark. In the present study, 49 non-related erythromycin-resistant S. pneumoniae isolates from invasive sites and 20 isolates from non-invasive sites were collected; antimicrobial susceptibility was tested, and they were genotyped and serotyped. Gene transfer was studied for selected isolates. The frequency of erm(B) was significantly higher in non-invasive isolates compared to invasive isolates (p = 0.001). For the first time, mef(I) was detected in 1 isolate in Denmark. All tested mef(E) isolates had an identical mef(E) sequence, apart from 1 gene with a point mutation, and mef(E) was correlated to 7 different sero-types. The tested erm(B) sequences were 99.3% similar with 5 point mutations at different positions distributed among different serotypes, which did not cause a detectable influence on the protein. Transformation was detectable in 5 out of 13 isolates and transfer of erm(B), mef(I) and mef(E) was detected. To our knowledge, this is the first time mef(I) has been proved transformable. Gene transfer by conjugation was not detectable. Erythromycin resistance in pneumococcal isolates is likely to be caused primarily by horizontal spread of mef(E) and erm(B), as well as clonal spread of a serotype 14 strain carrying mef(A) primarily detected in invasive isolates.}, }
@article {pmid20428170, year = {2010}, author = {Gilbert, C and Schaack, S and Pace, JK and Brindley, PJ and Feschotte, C}, title = {A role for host-parasite interactions in the horizontal transfer of transposons across phyla.}, journal = {Nature}, volume = {464}, number = {7293}, pages = {1347-1350}, pmid = {20428170}, issn = {1476-4687}, support = {R01 GM077582/GM/NIGMS NIH HHS/United States ; R01 GM077582-04/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; DNA Transposable Elements/*genetics ; Disease Vectors ; Evolution, Molecular ; Gene Dosage ; Gene Transfer, Horizontal/*genetics ; Geography ; Host-Parasite Interactions/*genetics ; Lymnaea/genetics/physiology ; Molecular Sequence Data ; Opossums/genetics/parasitology ; Parasites/*classification/*genetics/physiology ; *Phylogeny ; Rhodnius/genetics/physiology ; Saimiri/genetics/parasitology ; }, abstract = {Horizontal transfer (HT), or the passage of genetic material between non-mating species, is increasingly recognized as an important force in the evolution of eukaryotic genomes. Transposons, with their inherent ability to mobilize and amplify within genomes, may be especially prone to HT. However, the means by which transposons can spread across widely diverged species remain elusive. Here we present evidence that host-parasite interactions have promoted the HT of four transposon families between invertebrates and vertebrates. We found that Rhodnius prolixus, a triatomine bug feeding on the blood of various tetrapods and vector of Chagas' disease in humans, carries in its genome four distinct transposon families that also invaded the genomes of a diverse, but overlapping, set of tetrapods. The bug transposons are approximately 98% identical and cluster phylogenetically with those of the opossum and squirrel monkey, two of its preferred mammalian hosts in South America. We also identified one of these transposon families in the pond snail Lymnaea stagnalis, a cosmopolitan vector of trematodes infecting diverse vertebrates, whose ancestral sequence is nearly identical and clusters with those found in Old World mammals. Together these data provide evidence for a previously hypothesized role of host-parasite interactions in facilitating HT among animals. Furthermore, the large amount of DNA generated by the amplification of the horizontally transferred transposons supports the idea that the exchange of genetic material between hosts and parasites influences their genomic evolution.}, }
@article {pmid20421652, year = {2010}, author = {Lieutaud, A and van Lis, R and Duval, S and Capowiez, L and Muller, D and Lebrun, R and Lignon, S and Fardeau, ML and Lett, MC and Nitschke, W and Schoepp-Cothenet, B}, title = {Arsenite oxidase from Ralstonia sp. 22: characterization of the enzyme and its interaction with soluble cytochromes.}, journal = {The Journal of biological chemistry}, volume = {285}, number = {27}, pages = {20433-20441}, pmid = {20421652}, issn = {1083-351X}, mesh = {Amino Acid Sequence ; Arsenates/metabolism ; Arsenic/metabolism ; Cytochromes/chemistry/genetics/*metabolism ; DNA Primers ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Electrophoresis, Polyacrylamide Gel ; Gene Amplification ; Kinetics ; Molecular Sequence Data ; Molecular Weight ; Oxidoreductases/classification/genetics/isolation &amp; purification/*metabolism ; Phylogeny ; Protein Subunits/chemistry/genetics ; Ralstonia/*enzymology ; Sequence Alignment ; Sequence Homology, Amino Acid ; Spheroplasts/enzymology ; }, abstract = {We characterized the aro arsenite oxidation system in the novel strain Ralstonia sp. 22, a beta-proteobacterium isolated from soil samples of the Salsigne mine in southern France. The inducible aro system consists of a heterodimeric membrane-associated enzyme reacting with a dedicated soluble cytochrome c(554). Our biochemical results suggest that the weak association of the enzyme to the membrane probably arises from a still unknown interaction partner. Analysis of the phylogeny of the aro gene cluster revealed that it results from a lateral gene transfer from a species closely related to Achromobacter sp. SY8. This constitutes the first clear cut case of such a transfer in the Aro phylogeny. The biochemical study of the enzyme demonstrates that it can accommodate in vitro various cytochromes, two of which, c(552) and c(554,) are from the parent species. Cytochrome c(552) belongs to the sox and not the aro system. Kinetic studies furthermore established that sulfite and sulfide, substrates of the sox system, are both inhibitors of Aro activity. These results reinforce the idea that sulfur and arsenic metabolism are linked.}, }
@article {pmid20418394, year = {2010}, author = {Filloux, A}, title = {A variety of bacterial pili involved in horizontal gene transfer.}, journal = {Journal of bacteriology}, volume = {192}, number = {13}, pages = {3243-3245}, pmid = {20418394}, issn = {1098-5530}, mesh = {DNA, Bacterial/genetics ; Fimbriae, Bacterial/metabolism/*physiology ; Gene Transfer, Horizontal/*genetics ; }, }
@article {pmid20416045, year = {2010}, author = {Thornton, RF and Kagawa, TF and O'Toole, PW and Cooney, JC}, title = {The dissemination of C10 cysteine protease genes in Bacteroides fragilis by mobile genetic elements.}, journal = {BMC microbiology}, volume = {10}, number = {}, pages = {122}, pmid = {20416045}, issn = {1471-2180}, mesh = {Bacteroides fragilis/*enzymology/*genetics ; Computational Biology ; Cysteine Proteases/*genetics ; DNA, Bacterial/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; *Interspersed Repetitive Sequences ; Prophages/genetics ; Sequence Homology, Amino Acid ; Streptococcus pyogenes/enzymology/genetics ; }, abstract = {BACKGROUND: The C10 family of cysteine proteases includes enzymes that contribute to the virulence of bacterial pathogens, such as SpeB in Streptococcus pyogenes. The presence of homologues of cysteine protease genes in human commensal organisms has not been examined. Bacteroides fragilis is a member of the dominant Bacteroidetes phylum of the human intestinal microbiota, and is a significant opportunistic pathogen.<br><br>RESULTS: Four homologues of the streptococcal virulence factor SpeB were identified in the B. fragilis genome. These four protease genes, two were directly contiguous to open reading frames predicted to encode staphostatin-like inhibitors, with which the protease genes were co-transcribed. Two of these protease genes are unique to B. fragilis 638R and are associated with two large genomic insertions. Gene annotation indicated that one of these insertions was a conjugative Tn-like element and the other was a prophage-like element, which was shown to be capable of excision. Homologues of the B. fragilis C10 protease genes were present in a panel of clinical isolates, and in DNA extracted from normal human faecal microbiota.<br><br>CONCLUSIONS: This study suggests a mechanism for the evolution and dissemination of an important class of protease in major members of the normal human microbiota.}, }
@article {pmid20410933, year = {2010}, author = {Pan, HW and Tan, ZG and Liu, H and Li, ZF and Zhang, CY and Li, CY and Li, J and Li, YZ}, title = {Hdsp, a horizontally transferred gene required for social behavior and halotolerance in salt-tolerant Myxococcus fulvus HW-1.}, journal = {The ISME journal}, volume = {4}, number = {10}, pages = {1282-1289}, doi = {10.1038/ismej.2010.52}, pmid = {20410933}, issn = {1751-7370}, mesh = {Bacterial Proteins/genetics/*physiology ; Cell Division ; DNA Transposable Elements ; DNA, Bacterial/chemistry/genetics ; Environmental Microbiology ; Gene Transfer, Horizontal ; Genomic Islands ; Locomotion ; Molecular Sequence Data ; Mutagenesis, Insertional ; Myxococcus/genetics/growth &amp; development/metabolism/*physiology ; Salts/*metabolism ; Sequence Analysis, DNA ; *Signal Transduction ; Spores, Bacterial/growth &amp; development ; *Stress, Physiological ; }, abstract = {Myxococcus fulvus HW-1, a salt-tolerant bacterial strain, which was isolated from a coastal environment, changes its behavior with different salinities. To study the relationship between behavioral shifts and the adaption to oceanic conditions, the HW-1 strain was randomly mutagenized using transposon insertion, producing a dispersed-growing mutant, designated YLH0401. The mutant did not develop fruiting bodies and myxospores, was deficient in S-motility, produced less extracellular matrix and was less salt tolerant. The YLH0401 strain was determined to be mutated by a single insertion in a large gene of unknown function (7011 bp in size), which is located in a horizontally transferred DNA fragment. The gene is expressed during the vegetative growth stage, as well as highly and stably expressed during the development stage. This horizontally transferred gene may allow Myxococcus to adapt to oceanic conditions.}, }
@article {pmid20409658, year = {2010}, author = {Klenk, HP and Göker, M}, title = {En route to a genome-based classification of Archaea and Bacteria?.}, journal = {Systematic and applied microbiology}, volume = {33}, number = {4}, pages = {175-182}, doi = {10.1016/j.syapm.2010.03.003}, pmid = {20409658}, issn = {1618-0984}, mesh = {Archaea/*classification/*genetics ; Bacteria/*classification/*genetics ; *Genome, Archaeal ; *Genome, Bacterial ; *Phylogeny ; }, abstract = {Given the considerable promise whole-genome sequencing offers for phylogeny and classification, it is surprising that microbial systematics and genomics have not yet been reconciled. This might be due to the intrinsic difficulties in inferring reasonable phylogenies from genomic sequences, particularly in the light of the significant amount of lateral gene transfer in prokaryotic genomes. However, recent studies indicate that the species tree and the hierarchical classification based on it are still meaningful concepts, and that state-of-the-art phylogenetic inference methods are able to provide reliable estimates of the species tree to the benefit of taxonomy. Conversely, we suspect that the current lack of completely sequenced genomes for many of the major lineages of prokaryotes and for most type strains is a major obstacle in progress towards a genome-based classification of microorganisms. We conclude that phylogeny-driven microbial genome sequencing projects such as the Genomic Encyclopaedia of Archaea and Bacteria (GEBA) project are likely to rectify this situation.}, }
@article {pmid20403964, year = {2010}, author = {Amorós-Moya, D and Bedhomme, S and Hermann, M and Bravo, IG}, title = {Evolution in regulatory regions rapidly compensates the cost of nonoptimal codon usage.}, journal = {Molecular biology and evolution}, volume = {27}, number = {9}, pages = {2141-2151}, doi = {10.1093/molbev/msq103}, pmid = {20403964}, issn = {1537-1719}, mesh = {Codon/*genetics ; Drug Resistance, Bacterial/genetics ; Escherichia coli/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/genetics ; Promoter Regions, Genetic/genetics ; }, abstract = {The redundant genetic code contains synonymous codons, whose relative frequencies vary among species. Nonoptimal codon usage lowers gene translation efficiency, potentially leading to a fitness cost. This is particularly relevant for horizontal gene transfer, common among bacteria and a key player in antibiotic resistance propagation. By mimicking the horizontal transfer of an antibiotic resistance gene, we established that a nonoptimal codon usage renders Escherichia coli 10-20 times more sensitive to the antibiotic. After 350 generations of experimental evolution under antibiotic selection pressure, this cost was compensated through both in cis changes in the gene promoter and in trans changes in the host bacterial genome, without introducing mutations in the coding sequence of the resistance gene. Further, we have found experimental evidence for convergent molecular adaptive evolution. The high fitness cost of nonoptimal codon usage remains a minor obstacle to gene fixation upon horizontal transfer. Our results highlight the importance of rapid evolution of regulatory mechanisms in the adaptation to new environmental and genetic situations.}, }
@article {pmid20401627, year = {2010}, author = {Khan, AA and Shrivastava, A}, title = {Bacterial infections associated with cancer: possible implication in etiology with special reference to lateral gene transfer.}, journal = {Cancer metastasis reviews}, volume = {29}, number = {2}, pages = {331-337}, doi = {10.1007/s10555-010-9217-4}, pmid = {20401627}, issn = {1573-7233}, mesh = {Animals ; Bacteria/*genetics ; Bacterial Infections/*complications/genetics ; *Gene Transfer, Horizontal ; Humans ; Neoplasms/*genetics/*microbiology ; }, abstract = {Bacteria are capable of exchanging DNA between each other and even from other organisms including human, but what will be the fate of such exchange? Enigmatic association between bacterial infections and cancer is also demonstrated recently with unknown exact cause and effect mechanism. This enigma may be resolved not in all but in few cases with the view of horizontal DNA transfer. The present article tries to examine this association in the frame of new idea. This article concludes that knowledge of this association may aid in management of cancer in clinical settings.}, }
@article {pmid20400971, year = {2010}, author = {Yue, D and Wang, Y and Ma, P and Li, YY and Chen, H and Wang, P and Ren, CS}, title = {Effects of transferred NK4 gene on proliferation, migration, invasion and apoptosis of human prostate cancer DU145 cells.}, journal = {Asian journal of andrology}, volume = {12}, number = {3}, pages = {381-389}, pmid = {20400971}, issn = {1745-7262}, mesh = {Adenocarcinoma/*genetics/pathology ; Animals ; Apoptosis/genetics ; Autocrine Communication/genetics ; Cell Line, Tumor ; Cell Movement/genetics ; Cell Proliferation ; *Gene Expression Regulation, Neoplastic ; Gene Transfer, Horizontal ; Hepatocyte Growth Factor/*genetics ; Humans ; Male ; Mice ; Mice, Inbred BALB C ; Mice, Nude ; Neoplasm Invasiveness/genetics ; Neoplasm Transplantation ; Prostatic Neoplasms/*genetics/pathology ; Transfection ; Xenograft Model Antitumor Assays ; }, abstract = {We investigated the ability of NK4, an antagonist of human hepatocyte growth factor (HGF), to inhibit the influence of HGF on proliferation, migration, invasion and apoptosis of human prostate cancer cells. Expression vector pBudCE4.1-EGFP-NK4 containing NK4 cDNA was used to transfect human prostate cancer DU145 cells, and the effects of the autocrine NK4 on tumor cell proliferation, migration, invasion and apoptosis were assessed in vitro. In vivo, we subcutaneously implanted DU145 cells, mock-transfected clone (DU145/empty vector) cells and NK4-transfected clone (DU145/NK4) cells into nude mice, and then evaluated tumor growth, cell proliferation and cell apoptosis in vivo. We found that DU145/NK4 cells expressed NK4 protein. In the in vitro study, autocrine NK4 attenuated the HGF-induced tumor cell proliferation, migration and invasion, and stimulated apoptosis. Furthermore, autocrine NK4 effectively inhibited the HGF-induced phosphorylation of c-Met, extracellular signal-regulated kinase-1 (ERK1). and protein kinase B 1/2 (Akt1/2). Histological examination revealed that autocrine NK4 inhibited proliferation and accelerated apoptosis of prostate cancer cells. These results show that genetic modification of DU145 cells with NK4 cDNA yields a significant effect on their proliferation, migration, invasion and apoptosis. Molecular targeting of HGF/c-Met by NK4 could be applied as a novel therapeutic approach to prostate cancer.}, }
@article {pmid20393572, year = {2010}, author = {Auclair, J and Lépine, F and Parent, S and Villemur, R}, title = {Dissimilatory reduction of nitrate in seawater by a Methylophaga strain containing two highly divergent narG sequences.}, journal = {The ISME journal}, volume = {4}, number = {10}, pages = {1302-1313}, doi = {10.1038/ismej.2010.47}, pmid = {20393572}, issn = {1751-7370}, mesh = {Bacterial Proteins/genetics/metabolism ; Biofilms/growth &amp; development ; Carbon Isotopes/metabolism ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Denitrification ; Methanol/metabolism ; Molecular Sequence Data ; Nitrate Reductase/*genetics/*metabolism ; Nitrates/*metabolism ; Nitrites/metabolism ; Oxidation-Reduction ; Oxygen/analysis ; Phylogeny ; Piscirickettsiaceae/*classification/genetics/isolation &amp; purification/*metabolism ; RNA, Ribosomal, 16S/genetics ; Seawater/chemistry/*microbiology ; Sequence Analysis, DNA ; Staining and Labeling/methods ; }, abstract = {Methylophaga spp. are methylotrophs commonly associated with marine environments and have been defined as strict aerobic methylotrophs. They have been shown previously to represent 50-70% of the bacterial population in the biofilm of the methanol-fed denitrification reactor treating a large seawater aquarium at the Montreal Biodome. It was therefore surprising to find such a high concentration of Methylophaga spp. in anoxic conditions. In this study, we showed by cultivation-independent and -dependent approaches that one Methylophaga strain present in the anoxic biofilm is involved in the denitrification process. DNA stable-isotope probing (SIP) experiments in which the biofilm was cultured under denitrifying conditions with (13)C-methanol have revealed the enrichment of one particular taxon. By screening a 16S ribosomal RNA gene library derived from a (13)C-DNA fraction of the SIP gradients, 62% of the library was composed of one sequence affiliated with the genus Methylophaga. One strain, named JAM1, representing this Methylophaga species was isolated. It grows aerobically but also under denitrifying conditions by reducing nitrate into nitrite. The nitrate-reducing activity was correlated with the presence and the expression of two highly divergent narG genes (narG1 and narG2). narG1 showed a high percentage of identity with the corresponding part of narG found in Thiobacillus denitrificans, which suggests a recent acquisition of narG in strain JAM1 by horizontal gene transfer. This study provides the first direct evidence of the adaptation of a Methylophaga species to an oxygen-limited environment.}, }
@article {pmid20393569, year = {2010}, author = {Doroghazi, JR and Buckley, DH}, title = {Widespread homologous recombination within and between Streptomyces species.}, journal = {The ISME journal}, volume = {4}, number = {9}, pages = {1136-1143}, doi = {10.1038/ismej.2010.45}, pmid = {20393569}, issn = {1751-7370}, mesh = {Bacterial Typing Techniques ; DNA Fingerprinting ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; Genetic Linkage ; Genotype ; Geography ; *Recombination, Genetic ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Soil Microbiology ; Streptomyces/*genetics/isolation &amp; purification ; }, abstract = {Horizontal gene transfer (HGT) is widespread in the microbial world, but its impact on the origin and persistence of microbial species remains poorly defined. HGT can result in either acquisition of new genetic material or homologous replacement of existing genes. The evolutionary significance of homologous recombination in a population can be quantified by examining the relative rates at which polymorphisms are introduced from recombination (rho) and mutation (theta(w)). We used multilocus sequence analysis (MLSA) to quantify both intraspecies and interspecies homologous recombination among streptomycetes, multicellular Gram-positive bacteria ubiquitous in soil, which are an important source of antibiotics and bioactive compounds. Intraspecies recombination was examined using strains of Streptomyces flavogriseus isolated from soils at five locations spanning 1000 km. The strains had >99.8% nucleotide identity across the loci examined. We found remarkable levels of gene exchange within S. flavogriseus (rho/theta(w)=27.9), and found that the population was in linkage equilibrium (standardized index of association=0.0018), providing evidence for a freely recombining sexual population structure. We also examined interspecies homologous recombination among different Streptomyces species in an MLSA data set and found that 40% of the species had housekeeping genes acquired through HGT. The recombination rate between these named species (rho/theta(w)=0.21) exceeds that observed within many species of bacteria. Despite widespread gene exchange in the genus, the intraspecies recombination rate exceeded the interspecies rate by two orders of magnitude suggesting that patterns of gene exchange and recombination may shape the evolution of streptomycetes.}, }
@article {pmid20392924, year = {2010}, author = {da Silva Rabello, MC and de Oliveira, RS and Silva, RM and Leao, SC}, title = {Natural occurrence of horizontal transfer of Mycobacterium avium- specific insertion sequence IS1245 to Mycobacterium kansasii.}, journal = {Journal of clinical microbiology}, volume = {48}, number = {6}, pages = {2257-2259}, pmid = {20392924}, issn = {1098-660X}, mesh = {Bacterial Typing Techniques ; DNA Fingerprinting ; *DNA Transposable Elements ; DNA, Bacterial/genetics ; *Gene Transfer, Horizontal ; Humans ; Mycobacterium avium/*genetics/growth &amp; development ; Mycobacterium kansasii/*genetics/growth &amp; development ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; }, abstract = {Mycobacterium kansasii carrying IS1245, a highly prevalent insertion sequence among Mycobacterium avium isolates, was detected in a mixed culture of M. avium and M. kansasii. The insertion sequence was stable and able to transpose by a replicative mechanism in M. kansasii. These findings may have significant implications for molecular diagnosis and treatment outcome.}, }
@article {pmid20386959, year = {2010}, author = {Hale, MC and Jackson, JR and Dewoody, JA}, title = {Discovery and evaluation of candidate sex-determining genes and xenobiotics in the gonads of lake sturgeon (Acipenser fulvescens).}, journal = {Genetica}, volume = {138}, number = {7}, pages = {745-756}, pmid = {20386959}, issn = {1573-6857}, mesh = {Animals ; DNA, Complementary/chemistry/genetics ; Female ; Fish Proteins/*genetics ; Fishes/*genetics ; Gene Library ; Gene Transfer, Horizontal ; Gonads/*metabolism ; Male ; Sequence Analysis, DNA ; Sex Determination Processes/*genetics ; Sex Differentiation/genetics ; Transcription Factors/genetics ; }, abstract = {Modern pyrosequencing has the potential to uncover many interesting aspects of genome evolution, even in lineages where genomic resources are scarce. In particular, 454 pyrosequencing of nonmodel species has been used to characterize expressed sequence tags, xenobiotics, gene ontologies, and relative levels of gene expression. Herein, we use pyrosequencing to study the evolution of genes expressed in the gonads of a polyploid fish, the lake sturgeon (Acipenser fulvescens). Using 454 pyrosequencing of transcribed genes, we produced more than 125 MB of sequence data from 473,577 high-quality sequencing reads. Sequences that passed stringent quality control thresholds were assembled into 12,791 male contigs and 32,629 female contigs. Average depth of coverage was 4.2 x for the male assembly and 5.5x for the female assembly. Analytical rarefaction indicates that our assemblies include most of the genes expressed in lake sturgeon gonads. Over 86,700 sequencing reads were assigned gene ontologies, many to general housekeeping genes like protein, RNA, and ion binding genes. We searched specifically for sex determining genes and documented significant sex differences in the expression of two genes involved in animal sex determination, DMRT1 and TRA-1. DMRT1 is the master sex determining gene in birds and in medaka (Oryzias latipes) whereas TRA-1 helps direct sexual differentiation in nematodes. We also searched the lake sturgeon assembly for evidence of xenobiotic organisms that may exist as endosymbionts. Our results suggest that exogenous parasites (trematodes) and pathogens (protozoans) apparently have infected lake sturgeon gonads, and the trematodes have horizontally transferred some genes to the lake sturgeon genome.}, }
@article {pmid20386741, year = {2010}, author = {Nowrousian, M and Stajich, JE and Chu, M and Engh, I and Espagne, E and Halliday, K and Kamerewerd, J and Kempken, F and Knab, B and Kuo, HC and Osiewacz, HD and Pöggeler, S and Read, ND and Seiler, S and Smith, KM and Zickler, D and Kück, U and Freitag, M}, title = {De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis.}, journal = {PLoS genetics}, volume = {6}, number = {4}, pages = {e1000891}, pmid = {20386741}, issn = {1553-7404}, support = {/WT_/Wellcome Trust/United Kingdom ; BB/F013574/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Base Sequence ; Gene Expression Profiling ; Genome ; *Genome, Fungal ; Genomics/methods ; Models, Biological ; Molecular Sequence Data ; Neurospora crassa/genetics ; Phylogeny ; Sequence Analysis, DNA ; Sordariales/*genetics ; }, abstract = {Filamentous fungi are of great importance in ecology, agriculture, medicine, and biotechnology. Thus, it is not surprising that genomes for more than 100 filamentous fungi have been sequenced, most of them by Sanger sequencing. While next-generation sequencing techniques have revolutionized genome resequencing, e.g. for strain comparisons, genetic mapping, or transcriptome and ChIP analyses, de novo assembly of eukaryotic genomes still presents significant hurdles, because of their large size and stretches of repetitive sequences. Filamentous fungi contain few repetitive regions in their 30-90 Mb genomes and thus are suitable candidates to test de novo genome assembly from short sequence reads. Here, we present a high-quality draft sequence of the Sordaria macrospora genome that was obtained by a combination of Illumina/Solexa and Roche/454 sequencing. Paired-end Solexa sequencing of genomic DNA to 85-fold coverage and an additional 10-fold coverage by single-end 454 sequencing resulted in approximately 4 Gb of DNA sequence. Reads were assembled to a 40 Mb draft version (N50 of 117 kb) with the Velvet assembler. Comparative analysis with Neurospora genomes increased the N50 to 498 kb. The S. macrospora genome contains even fewer repeat regions than its closest sequenced relative, Neurospora crassa. Comparison with genomes of other fungi showed that S. macrospora, a model organism for morphogenesis and meiosis, harbors duplications of several genes involved in self/nonself-recognition. Furthermore, S. macrospora contains more polyketide biosynthesis genes than N. crassa. Phylogenetic analyses suggest that some of these genes may have been acquired by horizontal gene transfer from a distantly related ascomycete group. Our study shows that, for typical filamentous fungi, de novo assembly of genomes from short sequence reads alone is feasible, that a mixture of Solexa and 454 sequencing substantially improves the assembly, and that the resulting data can be used for comparative studies to address basic questions of fungal biology.}, }
@article {pmid20385865, year = {2010}, author = {Merino, M and Acosta, J and Poza, M and Sanz, F and Beceiro, A and Chaves, F and Bou, G}, title = {OXA-24 carbapenemase gene flanked by XerC/XerD-like recombination sites in different plasmids from different Acinetobacter species isolated during a nosocomial outbreak.}, journal = {Antimicrobial agents and chemotherapy}, volume = {54}, number = {6}, pages = {2724-2727}, pmid = {20385865}, issn = {1098-6596}, mesh = {Acinetobacter/drug effects/*enzymology/*genetics/isolation &amp; purification ; Acinetobacter Infections/drug therapy/*epidemiology/*microbiology ; Acinetobacter baumannii/drug effects/enzymology/genetics/isolation &amp; purification ; Acinetobacter calcoaceticus/drug effects/enzymology/genetics/isolation &amp; purification ; Bacterial Proteins/genetics ; Base Sequence ; Cross Infection/drug therapy/*epidemiology/*microbiology ; DNA-Binding Proteins/genetics ; *Disease Outbreaks ; Drug Resistance, Multiple, Bacterial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; In Vitro Techniques ; Molecular Epidemiology ; Molecular Sequence Data ; Plasmids/genetics ; Recombination, Genetic ; Spain/epidemiology ; Species Specificity ; beta-Lactam Resistance/genetics ; beta-Lactamases/*genetics ; }, abstract = {A clinical strain of Acinetobacter calcoaceticus resistant to carbapenems was isolated from a blood culture sample from an inpatient in a hospital in Madrid (Spain) during a large outbreak of infection (affecting more than 300 inpatients), caused by a multidrug-resistant Acinetobacter baumannii clone. The carbapenem resistance in both the A. calcoaceticus and A. baumannii clones was due to a bla(OXA-24) gene harbored in different plasmids. The plasmids were fully sequenced, revealing the presence of site-specific recombination binding sites putatively involved in mobilization of the bla(OXA-24) gene. Comparison of plasmids contained in the two strains revealed possible horizontal transmission of resistance genes between the Acinetobacter species.}, }
@article {pmid21738522, year = {2010}, author = {Betts-Hampikian, HJ and Fields, KA}, title = {The Chlamydial Type III Secretion Mechanism: Revealing Cracks in a Tough Nut.}, journal = {Frontiers in microbiology}, volume = {1}, number = {}, pages = {114}, pmid = {21738522}, issn = {1664-302X}, support = {R01 AI065530/AI/NIAID NIH HHS/United States ; }, abstract = {Present-day members of the Chlamydiaceae contain parasitic bacteria that have been co-evolving with their eukaryotic hosts over hundreds of millions of years. Likewise, a type III secretion system encoded within all genomes has been refined to complement the unique obligate intracellular niche colonized so successfully by Chlamydia spp. All this adaptation has occurred in the apparent absence of the horizontal gene transfer responsible for creating the wide range of diversity in other Gram-negative, type III-expressing bacteria. The result is a system that is, in many ways, uniquely chlamydial. A critical mass of information has been amassed that sheds significant light on how the chlamydial secretion system functions and contributes to an obligate intracellular lifestyle. Although the overall mechanism is certainly similar to homologous systems, an image has emerged where the chlamydial secretion system is essential for both survival and virulence. Numerous apparent differences, some subtle and some profound, differentiate chlamydial type III secretion from others. Herein, we provide a comprehensive review of the current state of knowledge regarding the Chlamydia type III secretion mechanism. We focus on the aspects that are distinctly chlamydial and comment on how this important system influences chlamydial pathogenesis. Gaining a grasp on this fascinating system has been challenging in the absence of a tractable genetic system. However, the surface of this tough nut has been scored and the future promises to be fruitful and revealing.}, }
@article {pmid21798178, year = {2009}, author = {Kinoshita, S and Isu, S and Kaneko, G and Yamada, H and Hara, T and Itoh, Y and Watabe, S}, title = {The occurrence of eukaryotic type III glutamine synthetase in the marine diatom Chaetoceros compressum.}, journal = {Marine genomics}, volume = {2}, number = {2}, pages = {103-111}, doi = {10.1016/j.margen.2009.06.003}, pmid = {21798178}, issn = {1874-7787}, abstract = {Glutamine synthetase (GS) has been described as one of the oldest functioning genes and thus a good molecular clock protein. GS is diverged into three distinct forms, type I (GSI), type II (GSII) and type III (GSIII), the last type of which is a member of the most recently discovered family among GSs and thus has been reported from a limited number of prokaryotes. In the present study, we determined the full-length sequence of GSIII from the marine diatom Chaetoceroscompressum. The 3' untranslated region of the diatom GSIII gene was composed of a polyadenylation signal followed by a poly (A)(+) tail, clearly demonstrating that its mRNA is transcribed from the eukaryotic genome. We also screened available genome databases and identified full-length GSIII sequences from 5 eukaryotic species. These eukaryotic GSIIIs specifically contained regions A-D and a long additional sequence flanking region V toward the C-terminal site, both being specific to GSIII. Phylogenic analysis revealed that eukaryotic GSIIIs are not within a monophyletic relationship with the possible occurrence of lateral gene transfer in GSIII during evolution.}, }
@article {pmid21564726, year = {2009}, author = {Langhoff, P and Authier, A and Buckley, TR and Dugdale, JS and Rodrigo, A and Newcomb, RD}, title = {DNA barcoding of the endemic New Zealand leafroller moth genera, Ctenopseustis and Planotortrix.}, journal = {Molecular ecology resources}, volume = {9}, number = {3}, pages = {691-698}, doi = {10.1111/j.1755-0998.2009.02537.x}, pmid = {21564726}, issn = {1755-098X}, abstract = {Molecular techniques such as DNA barcoding have become popular in assisting species identification especially for cryptic species complexes. We have analysed data from a 468-bp region of the mitochondrial cytochrome oxidase subunit I (COI) gene from 200 specimens of 12 species of endemic New Zealand leafroller moths (Tortricidae) from the genera Planotortrix and Ctenopseustis to assess whether the DNA barcoding region can distinguish these species. Among the 200 sequences analysed, 72 haplotypes were recovered, with each genus forming a separate major clade. Maximum likelihood phylogenetic methods were used to test whether species fell into reciprocally monophyletic clades. The optimal phylogeny showed that four species within the genus Ctenopseustis (C. obliquana, C. herana, C. filicis and C. fraterna) and three within Planotortrix (P. octo, P. excessana and P. avicenniae) are polyphyletic. Shimodaira-Hasegawa tests rejected a null hypothesis of monophyly for the species C. obliquana, C. herana, P. octo and P. excessana. Comparisons of within and between species levels of sequence divergence for the same set of seven species showed cases where maximum levels of within-species divergence were greater than some levels of between-species divergence. DNA barcoding using this region of the COI gene is able to distinguish the two genera and some species within each genus; however, many species cannot be identified using this method. Finally, we discuss the possible reasons for this polyphyly, including incomplete lineage sorting, introgression, horizontal gene transfer and incorrect taxonomy.}, }
@article {pmid20948661, year = {2009}, author = {Langille, MG and Brinkman, FS}, title = {Bioinformatic detection of horizontally transferred DNA in bacterial genomes.}, journal = {F1000 biology reports}, volume = {1}, number = {}, pages = {25}, pmid = {20948661}, issn = {1757-594X}, abstract = {We highlight a selection of recent research on computational methods and associated challenges surrounding the prediction of bacterial horizontal gene transfer. This research area continues to face controversy, but is becoming more critical as the importance of horizontal gene transfer in medically and ecologically important prokaryotic evolution is further appreciated.}, }
@article {pmid20405725, year = {2009}, author = {Boĭko, AG and Labas, IuA and Gordeeva, AV}, title = {[Outline on the phylogenetic history of Metazoa aging phenomenon (to the study of number of dominating pseudo-scientific concepts in biology of aging)].}, journal = {Advances in gerontology = Uspekhi gerontologii}, volume = {22}, number = {4}, pages = {588-595}, pmid = {20405725}, issn = {1561-9125}, mesh = {Aging/*genetics/*physiology ; Animals ; Biology/*methods/trends ; Geriatrics/*methods/trends ; Humans ; *Phylogeny ; }, abstract = {Natural selection is just one of the factors determining genome evolution of Metazoa. But it's not a domineering one along with non-adaptive processes: horizontal gene transfer and input of egoistic genetic elements. That's why in phylogenesis (1) there are more genes of first Metazoa lost than new ones acquired; (2) the appearance of new genes among Metazoa branches is a very rare occasion; (3) genetically Metazoa is a homogeneous group of species with similar set of cellular mechanisms which was established in the course of evolution. The genome of first Metazoa turned to be so successful that evolution connected with organism amplification didn't demand radical changes in the genetic repertoire but it demanded changes in DNA sites regulating genes work. These facts along with the fact of existence of species of Metazoa with negligible aging overturn the core theories of aging biology which consider this or that cellular mechanism to be the initiating factor of organism's aging as sets of cellular mechanisms in aging and non-aging Metazoa forms are practically identical. That's why the basis of aging biology is in essence a collection of theories and dogmas that have never been proved but which are still in use and which have since long ago turned into a dangerous myth standing in the way of progress. If we are interested in progress of biogerontology a number of domineering pseudo scientific dogmas must be revisited. The matter of conservatism in this issue is inappropriate.}, }
@article {pmid21261836, year = {2008}, author = {Burris, K and Mentewab, A and Ripp, S and Stewart, CN}, title = {An Arabidopsis thaliana ABC transporter that confers kanamycin resistance in transgenic plants does not endow resistance to Escherichia coli.}, journal = {Microbial biotechnology}, volume = {1}, number = {2}, pages = {191-195}, pmid = {21261836}, issn = {1751-7915}, mesh = {ATP-Binding Cassette Transporters/genetics/*metabolism ; Anti-Bacterial Agents/pharmacology ; Arabidopsis/drug effects/*genetics/metabolism/microbiology ; Arabidopsis Proteins/genetics/*metabolism ; Escherichia coli/*drug effects/*genetics/physiology ; *Gene Transfer, Horizontal ; Kanamycin/pharmacology ; *Kanamycin Resistance ; Plant Diseases/*microbiology ; Plants, Genetically Modified/drug effects/genetics/metabolism/microbiology ; }, abstract = {Concerns have been raised about potential horizontal gene transfer (HGT) of antibiotic resistance markers (ARMs) from transgenic plants to bacteria of medical and environmental importance. All ARMs used in transgenic plants have been bacterial in origin, but it has been recently shown that an Arabidopsis thaliana ABC transporter, Atwbc19, confers kanamycin resistance when overexpressed in transgenic plants. Atwbc19 was evaluated for its ability to transfer kanamycin resistance to Escherichia coli, a kanamycin-sensitive model bacterium, under simulated HGT, staged by subcloning Atwbc19 under the control of a bacterial promoter, genetically transforming to kanamycin-sensitive bacteria, and assessing if resistance was conferred as compared with bacteria harbouring nptII, the standard kanamycin resistance gene used to produce transgenic plants. NptII provided much greater resistance than Atwbc19 and was significantly different from the no-plasmid control at low concentrations. Atwbc19 was not significantly different from the no-plasmid control at higher concentrations. Even though HGT risks are considered low with nptII, Atwbc19 should have even lower risks, as its encoded protein is possibly mistargeted in bacteria.}, }
@article {pmid21591141, year = {2007}, author = {Phornphisutthimas, S and Thamchaipenet, A and Panijpan, B}, title = {Conjugation in Escherichia coli: A laboratory exercise.}, journal = {Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology}, volume = {35}, number = {6}, pages = {440-445}, doi = {10.1002/bmb.113}, pmid = {21591141}, issn = {1470-8175}, abstract = {Bacterial conjugation is a genetic transfer that involves cell-to-cell between donor and recipient cells. With the current method used to teach students in genetic courses at the undergraduate level, the transconjugants are identified using bacterial physiology and/or antibiotic resistance. Using physiology, however, is difficult for both first-year undergraduates and special science students at the high school levels, who do not have the basic knowledge. We have developed a laboratory exercise that comprises a simple and rapid technique for transferring bacterial DNA by conjugation and examining the transconjuants using only antibiotic resistance on agar. The identity of the right transconjuants is confirmed by agarose gel electrophoresis. This exercise is designed to help students understand how horizontal gene transfer occurs in bacteria by conjugation using Escherichia coli as a hands-on learning model. Students should be able to draw concept maps of three DNA transfer methods on their own after carrying out the experiment and getting some additional information.}, }
@article {pmid20507502, year = {2007}, author = {Stukenbrock, EH and McDonald, BA}, title = {Geographical variation and positive diversifying selection in the host-specific toxin SnToxA.}, journal = {Molecular plant pathology}, volume = {8}, number = {3}, pages = {321-332}, doi = {10.1111/j.1364-3703.2007.00396.x}, pmid = {20507502}, issn = {1364-3703}, abstract = {SUMMARY The host-specific toxin ToxA produced by the wheat pathogens Pyrenophora tritici-repentis and Phaeosphaeria nodorum interacts with the product of the dominant plant gene Tsn1 to induce necrosis. The ToxA gene is thought to have been acquired by Py. tritici-repentis from Ph. nodorum through a recent horizontal gene transfer event. PCR and sequence analysis indicate that the level of ToxA variation, including gene deletion, in Ph. nodorum (SnToxA) is significantly higher than in Py. tritici-repentis (PtrToxA). We PCR-screened 788 isolates of Ph. nodorum originating from eight geographical regions to infer the pattern of SnToxA deletions. The frequency of deletions differed significantly among populations, ranging from 0% (Australia) to 98% (China). Sequence analysis of the SnToxA gene in 123 Ph. nodorum isolates revealed 13 distinct haplotypes. The distribution and diversity of haplotypes varied significantly among populations. The majority of SnToxA mutations were non-synonymous resulting in changes at the protein level. We applied different models of selection to infer the mode of evolution operating at the ToxA locus. Evidence for positive diversifying selection supports the hypothesis that evolution of the ToxA locus is driven by selection imposed by the host. The distribution of SnToxA alleles and deletions may reflect the distribution of different Tsn1 alleles in the corresponding host populations.}, }
@article {pmid20565638, year = {2005}, author = {Joardar, V and Lindeberg, M and Schneider, DJ and Collmer, A and Buell, CR}, title = {Lineage-specific regions in Pseudomonas syringae pv tomato DC3000.}, journal = {Molecular plant pathology}, volume = {6}, number = {1}, pages = {53-64}, doi = {10.1111/j.1364-3703.2004.00263.x}, pmid = {20565638}, issn = {1364-3703}, abstract = {SUMMARY Comparative analyses of the chromosome of Pseudomonas syringae pv tomato DC3000 with the finished, complete genomes of Pseudomonas aeruginosa PAO1, an animal pathogen, and the non-pathogenic soil inhabitant Pseudomonas putida KT2440 revealed a high degree of sequence conservation in genes involved in 'housekeeping functions'. However, divergence is present among these three fluorescent pseudomonads, yielding 'suites' of species-specific genes that may provide the genetic basis for adaptation to an ecological niche and lifestyle. For DC3000, 1053 genes located on the chromosome were specific to DC3000 and not present in PAO1 or KT2440. The majority of these DC3000-specific genes either lack a known function or are mobile genetic elements. However, these genes do share features among themselves such as association with regions of atypical trinucleotides, unusual G+C content and localization within large tracts of DC3000-specific sequence, suggestive of lateral gene transfer events. Indeed, a comparison of syntenic blocks among these three complete Pseudomonas genomes revealed that a substantial portion (533) of the DC3000-specific chromosomal genes (1053) were located in lineage-specific regions (defined as being larger than 2 kb and enriched in mobile genetic elements and/or genes specific to DC3000 in this three-way comparison). A large proportion of mobile genetic elements (199 of 318 genes; 63%), which are highly enriched in DC3000, were present within such regions. Similarly, most of the genes encoding type III secretion system virulence effectors were located in lineage-specific regions. Consistent with the plasticity of the DC3000 genome, a putative chromosomal inversion mediated by identical copies of ISPsy6 involving 2838 kb (44%) of the DC3000 genome was detected. These data suggest that a substantial portion of the differentiation of DC3000, a plant pathogen, from an animal pathogen and a soil inhabitant has involved transfer of a large number of novel genes coupled with amplification of mobile genetic elements.}, }
@article {pmid20569361, year = {2003}, author = {Jones, JT and Furlanetto, C and Bakker, E and Banks, B and Blok, V and Chen, Q and Phillips, M and Prior, A}, title = {Characterization of a chorismate mutase from the potato cyst nematode Globodera pallida.}, journal = {Molecular plant pathology}, volume = {4}, number = {1}, pages = {43-50}, doi = {10.1046/j.1364-3703.2003.00140.x}, pmid = {20569361}, issn = {1364-3703}, abstract = {SUMMARY Some plant endoparasitic nematodes are biotrophic and induce remarkable changes in their hosts in order to ensure a continuous supply of food. Proteins secreted from oesophageal gland cells have been implicated in this pathogenic process. A potentially secreted chorismate mutase has been isolated from the potato cyst nematode Globodera pallida. The gene encoding this protein is expressed in the subventral oesophageal gland cells of the nematode, and the mRNA derived from this gene is only present in the early parasitic stages. Sequence analysis of this gene shows that, like other genes involved in the host-parasite interaction of plant parasitic nematodes, it is likely to have been acquired by horizontal gene transfer from bacteria. The presence of a signal peptide in the deduced amino acid sequence of the G. pallida chorismate mutase and its expression in the subventral oesophageal gland cells suggest that it is secreted from the nematode, pointing to a role for the protein in the host-parasite interaction. The shikimate pathway, of which chorismate mutase is normally a part, is not found in animals but is present in plants and bacteria. In plants it gives rise to a variety of compounds which are important in amino acid synthesis and defence signalling pathways, as well as auxins, which have been implicated in the early development of nematode feeding sites. The potential roles of a nematode chorismate mutase are discussed.}, }
@article {pmid20573011, year = {2001}, author = {Markham, JE and Hille, J}, title = {Host-selective toxins as agents of cell death in plant-fungus interactions.}, journal = {Molecular plant pathology}, volume = {2}, number = {4}, pages = {229-239}, doi = {10.1046/j.1464-6722.2001.00066.x}, pmid = {20573011}, issn = {1364-3703}, abstract = {Summary Host-selective toxins are known determinants of compatibility in plant-fungus interactions and provide a powerful model for understanding the specificity of these associations. The identification of genes required for toxin biosynthesis has shown that the genes are unique to the toxin producing species and are clustered in complex loci. These loci may have been acquired by horizontal gene transfer. Many, if not all, host-selective toxins act by disrupting biochemical processes and in several cases the resulting cell death has the characteristics of programmed cell death. This ability to make dead tissue from living has enabled these facultative saprophytic fungi to become plant pathogens.}, }
@article {pmid21236984, year = {1995}, author = {Gogarten, JP}, title = {The early evolution of cellular life.}, journal = {Trends in ecology &amp; evolution}, volume = {10}, number = {4}, pages = {147-151}, doi = {10.1016/s0169-5347(00)89024-2}, pmid = {21236984}, issn = {0169-5347}, abstract = {Recent progress in data collection and analysis has changed the study of origin of life from an area dominated by speculation into a field abundant with testable hypotheses. This review discusses advances in the following areas: the fossil recordsd; the 'retrodiction' of biochemical pathways; and contradictions between different molecular phylogenies. The latter indicates a limited number of horizontal gene transfers during the early evolution. However, these cases of horizontal gene transfer are so infrequent that they can be detected as exceptions in an otherwise coherent picture. Cases of horizontal gene transfer can be recognized within the background of the majority consensus of molecular markers. The fusion of separate lineages to form new species is revealed by the simultaneous horizontal transfer of several independent genes.}, }
@article {pmid20385859, year = {2010}, author = {Morvan, A and Moubareck, C and Leclercq, A and Hervé-Bazin, M and Bremont, S and Lecuit, M and Courvalin, P and Le Monnier, A}, title = {Antimicrobial resistance of Listeria monocytogenes strains isolated from humans in France.}, journal = {Antimicrobial agents and chemotherapy}, volume = {54}, number = {6}, pages = {2728-2731}, pmid = {20385859}, issn = {1098-6596}, mesh = {Anti-Bacterial Agents/pharmacology ; Base Sequence ; DNA Primers/genetics ; Drug Resistance, Bacterial/*genetics ; Evolution, Molecular ; France/epidemiology ; Gene Transfer, Horizontal ; History, 20th Century ; History, 21st Century ; Humans ; In Vitro Techniques ; Listeria monocytogenes/*drug effects/*genetics/isolation &amp; purification ; Listeriosis/*drug therapy/epidemiology/history/*microbiology ; Microbial Sensitivity Tests ; Molecular Epidemiology ; Time Factors ; }, abstract = {Susceptibility to antibiotics of 4,816 clinical L. monocytogenes strains isolated since 1926 was studied, and the temporal evolution of susceptibility to antibiotics was analyzed through several decades. The mechanisms of resistance in each resistant strain were studied. The prevalence of resistant strains was estimated at 1.27% among isolates from humans. Resistance to tetracyclines+ and fluoroquinolones was more common and has recently emerged. Although acquired resistance in clinical L. monocytogenes did not implicate clinically relevant antibiotics, the possibility of resistance gene transfers, the description of the first clinical isolate with high-level resistance to trimethoprim, and the recent increase in penicillin MICs up to 2 microg/ml reinforce the need for microbiological surveillance.}, }
@article {pmid20383769, year = {2010}, author = {Kang, BG and Ye, X and Osburn, LD and Stewart, CN and Cheng, ZM}, title = {Transgenic hybrid aspen overexpressing the Atwbc19 gene encoding an ATP-binding cassette transporter confers resistance to four aminoglycoside antibiotics.}, journal = {Plant cell reports}, volume = {29}, number = {6}, pages = {643-650}, pmid = {20383769}, issn = {1432-203X}, mesh = {ATP-Binding Cassette Transporters/*genetics/metabolism ; Aminoglycosides/*pharmacology ; Arabidopsis/genetics ; Arabidopsis Proteins/*genetics/metabolism ; DNA, Plant/genetics ; Drug Resistance, Microbial/*genetics ; Gene Expression Regulation, Plant ; Kanamycin/pharmacology ; Plants, Genetically Modified/drug effects/genetics ; Populus/*drug effects/genetics ; Transformation, Genetic ; }, abstract = {Antibiotic-resistance genes of bacterial origin are invaluable markers for plant genetic engineering. However, these genes are feared to pose possible risk to human health by horizontal gene transfer from transgenic plants to bacteria, potentially resulting in antibiotic-resistant pathogenic bacteria; this is a considerable regulatory concern in some countries. The Atwbc19 gene, encoding an Arabidopsis thaliana ATP-binding cassette transporter, has been reported to confer resistance to kanamycin specifically as an alternative to bacterial antibiotic-resistance genes. In this report, we transformed hybrid aspen (Populus canescens x P. grandidentata) with the Atwbc19 gene. Unlike Atwbc19-transgenic tobacco that was only resistant to kanamycin, the transgenic Populus plants also showed resistance to three other aminoglycoside antibiotics (neomycin, geneticin, and paromomycin) at comparable levels to plants containing a CaMV35S-nptII cassette. Although it is unknown why the transgenic Populus with the Atwbc19 gene is resistant to all aminoglycoside antibiotics tested, the broad utility of the Atwbc19 gene as a reporter gene is confirmed here in a second dicot species. Because the Atwbc19 gene is plant-ubiquitous, it might serve as an alternative selectable marker to current bacterial antibiotic-resistance marker genes and alleviate the potential risk for horizontal transfer of bacterial-resistance genes in transgenic plants.}, }
@article {pmid20382218, year = {2010}, author = {Holochová, P and Růzicková, V and Pantůcek, R and Petrás, P and Janisch, R and Doskar, J}, title = {Genomic diversity of two lineages of exfoliative toxin A-converting phages predominating in Staphylococcus aureus strains in the Czech Republic.}, journal = {Research in microbiology}, volume = {161}, number = {4}, pages = {260-267}, doi = {10.1016/j.resmic.2010.03.008}, pmid = {20382218}, issn = {1769-7123}, mesh = {Czech Republic/epidemiology ; Disease Outbreaks ; Exfoliatins/*genetics/metabolism ; Gene Transfer, Horizontal ; *Genetic Variation ; Humans ; Molecular Sequence Data ; Pemphigus/epidemiology/*microbiology ; Staphylococcal Infections/epidemiology/*microbiology ; Staphylococcus Phages/*genetics/*isolation &amp; purification/metabolism ; Staphylococcus aureus/genetics/metabolism/*virology ; }, abstract = {We have isolated and characterized two distinct types of exfoliative toxin A (ETA)-converting bacteriophages originating from Staphylococcus aureus strains responsible for massive outbreaks of pemphigus neonatorum in the Czech Republic. Three induced phages designated as ph iB531, phi B557 and phi B122 were found to be capable of transferring the eta gene into the prophageless non-toxigenic S. aureus strain and converting it into an ETA producer. Comparisons of the phage sequences derived from 12 selected genes and 2 genomic segments (polymorphic P2 and conserved C4) revealed that phi B531 and phi B557 were identical each other, but phi B122 differed from them in 5 gene sequences, the xis gene content and the virion protein profile. Thus, phi B122 represents a new type of still undescribed ETA-converting phage. This study highlights not only the conclusive genomic diversity of eta gene-positive phages, but also their virulence implications in impetigo S. aureus strains.}, }
@article {pmid20376325, year = {2010}, author = {Becq, J and Churlaud, C and Deschavanne, P}, title = {A benchmark of parametric methods for horizontal transfers detection.}, journal = {PloS one}, volume = {5}, number = {4}, pages = {e9989}, pmid = {20376325}, issn = {1932-6203}, mesh = {Base Sequence ; Codon ; Computational Biology/methods ; *Gene Transfer, Horizontal ; Genomics/methods ; Methods ; Models, Genetic ; }, abstract = {Horizontal gene transfer (HGT) has appeared to be of importance for prokaryotic species evolution. As a consequence numerous parametric methods, using only the information embedded in the genomes, have been designed to detect HGTs. Numerous reports of incongruencies in results of the different methods applied to the same genomes were published. The use of artificial genomes in which all HGT parameters are controlled allows testing different methods in the same conditions. The results of this benchmark concerning 16 representative parametric methods showed a great variety of efficiencies. Some methods work very poorly whatever the type of HGTs and some depend on the conditions or on the metrics used. The best methods in terms of total errors were those using tetranucleotides as criterion for the window methods or those using codon usage for gene based methods and the Kullback-Leibler divergence metric. Window methods are very sensitive but less specific and detect badly lone isolated gene. On the other hand gene based methods are often very specific but lack of sensitivity. We propose using two methods in combination to get the best of each category, a gene based one for specificity and a window based one for sensitivity.}, }
@article {pmid20376150, year = {2010}, author = {Hehemann, JH and Correc, G and Barbeyron, T and Helbert, W and Czjzek, M and Michel, G}, title = {Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota.}, journal = {Nature}, volume = {464}, number = {7290}, pages = {908-912}, pmid = {20376150}, issn = {1476-4687}, mesh = {Adaptation, Physiological/physiology ; Bacteroides/*enzymology/genetics ; Biological Evolution ; Crystallography, X-Ray ; Cultural Diversity ; Diet ; Eukaryota/chemistry/metabolism ; Feces/enzymology/microbiology ; *Food Microbiology ; Gene Transfer, Horizontal ; Genome, Bacterial/genetics ; Glycoside Hydrolases/chemistry/isolation &amp; purification/*metabolism ; Humans ; Intestines/*microbiology ; Japan ; *Marine Biology ; *Metagenome ; Models, Molecular ; North America ; Phylogeny ; Porphyra/chemistry/metabolism/microbiology ; Protein Conformation ; Sepharose/*analogs &amp; derivatives/chemistry/metabolism ; Substrate Specificity ; }, abstract = {Gut microbes supply the human body with energy from dietary polysaccharides through carbohydrate active enzymes, or CAZymes, which are absent in the human genome. These enzymes target polysaccharides from terrestrial plants that dominated diet throughout human evolution. The array of CAZymes in gut microbes is highly diverse, exemplified by the human gut symbiont Bacteroides thetaiotaomicron, which contains 261 glycoside hydrolases and polysaccharide lyases, as well as 208 homologues of susC and susD-genes coding for two outer membrane proteins involved in starch utilization. A fundamental question that, to our knowledge, has yet to be addressed is how this diversity evolved by acquiring new genes from microbes living outside the gut. Here we characterize the first porphyranases from a member of the marine Bacteroidetes, Zobellia galactanivorans, active on the sulphated polysaccharide porphyran from marine red algae of the genus Porphyra. Furthermore, we show that genes coding for these porphyranases, agarases and associated proteins have been transferred to the gut bacterium Bacteroides plebeius isolated from Japanese individuals. Our comparative gut metagenome analyses show that porphyranases and agarases are frequent in the Japanese population and that they are absent in metagenome data from North American individuals. Seaweeds make an important contribution to the daily diet in Japan (14.2 g per person per day), and Porphyra spp. (nori) is the most important nutritional seaweed, traditionally used to prepare sushi. This indicates that seaweeds with associated marine bacteria may have been the route by which these novel CAZymes were acquired in human gut bacteria, and that contact with non-sterile food may be a general factor in CAZyme diversity in human gut microbes.}, }
@article {pmid20376136, year = {2010}, author = {Sonnenburg, JL}, title = {Microbiology: Genetic pot luck.}, journal = {Nature}, volume = {464}, number = {7290}, pages = {837-838}, pmid = {20376136}, issn = {1476-4687}, mesh = {Adaptation, Physiological/physiology ; Bacteroides/*enzymology/genetics ; Biological Evolution ; Cultural Diversity ; Diet ; Feces/enzymology/microbiology ; *Food Microbiology ; Gene Transfer, Horizontal ; Glycoside Hydrolases/isolation &amp; purification/*metabolism ; Humans ; Intestines/*microbiology ; Japan ; *Marine Biology ; *Metagenome ; Porphyra/chemistry/metabolism/microbiology ; Sepharose/*analogs &amp; derivatives/metabolism ; United States ; }, }
@article {pmid20368420, year = {2010}, author = {He, M and Sebaihia, M and Lawley, TD and Stabler, RA and Dawson, LF and Martin, MJ and Holt, KE and Seth-Smith, HM and Quail, MA and Rance, R and Brooks, K and Churcher, C and Harris, D and Bentley, SD and Burrows, C and Clark, L and Corton, C and Murray, V and Rose, G and Thurston, S and van Tonder, A and Walker, D and Wren, BW and Dougan, G and Parkhill, J}, title = {Evolutionary dynamics of Clostridium difficile over short and long time scales.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {16}, pages = {7527-7532}, pmid = {20368420}, issn = {1091-6490}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Clostridioides difficile/*genetics ; Computational Biology ; *Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Gene Transfer Techniques ; Genome, Bacterial ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; Recombination, Genetic ; Sequence Analysis, DNA ; Species Specificity ; Time Factors ; Virulence ; }, abstract = {Clostridium difficile has rapidly emerged as the leading cause of antibiotic-associated diarrheal disease, with the transcontinental spread of various PCR ribotypes, including 001, 017, 027 and 078. However, the genetic basis for the emergence of C. difficile as a human pathogen is unclear. Whole genome sequencing was used to analyze genetic variation and virulence of a diverse collection of thirty C. difficile isolates, to determine both macro and microevolution of the species. Horizontal gene transfer and large-scale recombination of core genes has shaped the C. difficile genome over both short and long time scales. Phylogenetic analysis demonstrates C. difficile is a genetically diverse species, which has evolved within the last 1.1-85 million years. By contrast, the disease-causing isolates have arisen from multiple lineages, suggesting that virulence evolved independently in the highly epidemic lineages.}, }
@article {pmid20368407, year = {2010}, author = {Huang, LY and Lu, PL and Chen, TL and Chang, FY and Fung, CP and Siu, LK}, title = {Molecular characterization of beta-lactamase genes and their genetic structures in Acinetobacter genospecies 3 isolates in Taiwan.}, journal = {Antimicrobial agents and chemotherapy}, volume = {54}, number = {6}, pages = {2699-2703}, pmid = {20368407}, issn = {1098-6596}, mesh = {Acinetobacter/drug effects/*enzymology/*genetics/isolation &amp; purification ; Acinetobacter Infections/drug therapy/epidemiology/*microbiology ; Cephalosporinase/genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; In Vitro Techniques ; Integrons/genetics ; Microbial Sensitivity Tests ; Molecular Epidemiology ; Molecular Sequence Data ; Phylogeny ; Taiwan/epidemiology ; beta-Lactam Resistance/genetics ; beta-Lactamases/*genetics ; }, abstract = {The genetic structure of beta-lactamases in Acinetobacter genospecies 3 (AG3) isolates in Taiwan was studied to analyze their high rates of resistance to beta-lactams, including carbapenems (57.9%). bla(IMP-1) and bla(IMP-8) were located in a class 1 integron. bla(OXA-58) was bracketed by ISAba3. A novel TnpF-like integrase gene was identified upstream of bla(VEB-3). Adjacent to the 5' sequence of the bla(ADC) gene, folE was identified. Four new Acinetobacter-derived cephalosporinase (ADC) enzymes were found, which clustered phylogenetically with published AG3 ADC proteins.}, }
@article {pmid20365394, year = {2010}, author = {Park, JM and Muñoz, E and Deem, MW}, title = {Quasispecies theory for finite populations.}, journal = {Physical review. E, Statistical, nonlinear, and soft matter physics}, volume = {81}, number = {1 Pt 1}, pages = {011902}, pmid = {20365394}, issn = {1550-2376}, support = {R90 DK071504/DK/NIDDK NIH HHS/United States ; }, mesh = {Algorithms ; *Biological Evolution ; Computer Simulation ; Gene Transfer, Horizontal ; *Models, Biological ; Mutation ; Probability ; *Stochastic Processes ; Time Factors ; }, abstract = {We present stochastic, finite-population formulations of the Crow-Kimura and Eigen models of quasispecies theory, for fitness functions that depend in an arbitrary way on the number of mutations from the wild type. We include back mutations in our description. We show that the fluctuation of the population numbers about the average values is exceedingly large in these physical models of evolution. We further show that horizontal gene transfer reduces by orders of magnitude the fluctuations in the population numbers and reduces the accumulation of deleterious mutations in the finite population due to Muller's ratchet. Indeed, the population sizes needed to converge to the infinite population limit are often larger than those found in nature for smooth fitness functions in the absence of horizontal gene transfer. These analytical results are derived for the steady state by means of a field-theoretic representation. Numerical results are presented that indicate horizontal gene transfer speeds up the dynamics of evolution as well.}, }
@article {pmid20363801, year = {2010}, author = {Lefèvre, CT and Abreu, F and Lins, U and Bazylinski, DA}, title = {Nonmagnetotactic multicellular prokaryotes from low-saline, nonmarine aquatic environments and their unusual negative phototactic behavior.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {10}, pages = {3220-3227}, pmid = {20363801}, issn = {1098-5336}, mesh = {Bacteriological Techniques/methods ; Deltaproteobacteria/classification/genetics/*physiology/ultrastructure ; Geologic Sediments/*microbiology ; *Light ; Magnetics ; Magnetosomes ; Microscopy, Electron, Transmission ; Molecular Sequence Data ; Nevada ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sodium Chloride/analysis ; *Water Microbiology ; }, abstract = {Magnetotactic multicellular prokaryotes (MMPs) are unique magnetotactic bacteria of the Deltaproteobacteria class and the first found to biomineralize the magnetic mineral greigite (Fe(3)S(4)). Thus far they have been reported only from marine habitats. We questioned whether MMPs exist in low-saline, nonmarine environments. MMPs were observed in samples from shallow springs in the Great Boiling Springs geothermal field and Pyramid Lake, both located in northwestern Nevada. The temperature at all sites was ambient, and salinities ranged from 5 to 11 ppt. These MMPs were not magnetotactic and did not contain magnetosomes (called nMMPs here). nMMPs ranged from 7 to 11 microm in diameter, were composed of about 40 to 60 Gram-negative cells, and were motile by numerous flagella that covered each cell on one side, characteristics similar to those of MMPs. 16S rRNA gene sequences of nMMPs show that they form a separate phylogenetic branch within the MMP group in the Deltaproteobacteria class, probably representing a single species. nMMPs exhibited a negative phototactic behavior to white light and to wavelengths of < or =480 nm (blue). We devised a "light racetrack" to exploit this behavior, which was used to photoconcentrate nMMPs for specific purposes (e.g., DNA extraction) even though their numbers were low in the sample. Our results show that the unique morphology of the MMP is not restricted to marine and magnetotactic prokaryotes. Discovery of nonmagnetotactic forms of the MMP might support the hypothesis that acquisition of the magnetosome genes involves horizontal gene transfer. To our knowledge, this is the first report of phototaxis in bacteria of the Deltaproteobacteria class.}, }
@article {pmid20352493, year = {2010}, author = {Baird, RE and Wadl, PA and Allen, T and McNeill, D and Wang, X and Moulton, JK and Rinehart, TA and Abbas, HK and Shier, T and Trigiano, RN}, title = {Variability of United States isolates of Macrophomina phaseolina based on simple sequence repeats and cross genus transferability to related genera within botryosphaeriaceae.}, journal = {Mycopathologia}, volume = {170}, number = {3}, pages = {169-180}, pmid = {20352493}, issn = {1573-0832}, mesh = {Ascomycota/*genetics/isolation &amp; purification ; Cluster Analysis ; DNA, Fungal/chemistry/*genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; *Gene Transfer, Horizontal ; *Genetic Variation ; Molecular Sequence Data ; Phylogeny ; Plants/microbiology ; *Repetitive Sequences, Nucleic Acid ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; United States ; }, abstract = {Twelve simple sequence repeat (SSRs) loci were used to evaluate genetic diversity of 109 isolates of Macrophomina phaseolina collected from different geographical regions and host species throughout the United States (US). Genetic diversity was assessed using Nei's minimum genetic distance, and the usefulness of each locus was determined by calculating the polymorphism information content (PIC). A total of 98 alleles were detected and of these 31 were unique to individual genotypes. Eight of twelve loci were highly informative with PIC values greater than 0.50. The majority of pairwise comparisons of genetic distance were greater than 0.60 indicating moderate to high genetic diversity. Dendrograms based on the genetic dissimilarities were created for the 109 isolates of which 79 were from soybean. Some clustering by host and geography was noted, but, the dendrograms generally grouped isolates independent of host or geography. Additionally, sequencing of the internal transcribed spacer region (ITS) for 10 isolates revealed that all of these isolates were 99% similar. Three SSR loci from M. phaseolina were cross amplified in other genera in the Botryosphaeriaceae. This was the first study of genotyping and assessing genetic diversity of M. phaseolina isolates collected from a widespread host and geographic range across the US with SSRs. With an additional 34 loci publically available for M. phaseolina, the results indicate that previously developed SSRs from one species can be used in future population, ecological, and genetic studies of M. phaseolina and other genera within the Botryosphaeriaceae.}, }
@article {pmid20347587, year = {2010}, author = {Bornberg-Bauer, E and Huylmans, AK and Sikosek, T}, title = {How do new proteins arise?.}, journal = {Current opinion in structural biology}, volume = {20}, number = {3}, pages = {390-396}, doi = {10.1016/j.sbi.2010.02.005}, pmid = {20347587}, issn = {1879-033X}, mesh = {Animals ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genomics ; Humans ; Protein Folding ; Proteins/chemistry/*genetics/metabolism ; Proteomics ; }, abstract = {Proteins are surreptitious cellular agents: while robust against mutations they are very evolvable; most are marginally stable and dynamic but others form a stable cellular matrix. Some genes seem to have emerged de novo from random pieces of genomic DNA, others may have been around for billions of years, virtually unchanged. Genomic and structural data provide new insights on how proteins came such a long way, probably from an initially very small set of domains and domain arrangements: gene duplicates provide the raw material for adaptive transitions (for example from one fold to another) which are very rare, albeit not impossible. 'New' proteins predominantly arise via tinkering, that is by their underlying genes recruiting and adapting smaller fragments of neighbouring DNA or by modular rearrangements of established domain combinations. Such rearrangements arise predominantly via fusion and terminal loss.}, }
@article {pmid20345890, year = {2010}, author = {Aller, JY and Aller, RC and Kemp, PF and Chistoserdov, AY and Madrid, VM}, title = {Fluidized muds: a novel setting for the generation of biosphere diversity through geologic time.}, journal = {Geobiology}, volume = {8}, number = {3}, pages = {169-178}, doi = {10.1111/j.1472-4669.2010.00234.x}, pmid = {20345890}, issn = {1472-4669}, mesh = {Bacteria/*genetics ; *Biodiversity ; *Evolution, Molecular ; Geologic Sediments/*microbiology ; *Soil Microbiology ; Time ; *Water Microbiology ; }, abstract = {Reworked and fluidized fine-grained deposits in energetic settings are a major modern-day feature of river deltas and estuaries. Similar environments were probably settings for microbial evolution on the early Earth. These sedimentary systems act as efficient biogeochemical reactors with high bacterial phylogenetic diversity and functional redundancy. They are temporally rather than spatially structured, with repeated cycling of redox conditions and successive stages of microbial metabolic processes. Intense reworking of the fluidized bed entrains bacteria from varied habitats providing new, diverse genetic materials to contribute to horizontal gene transfer events and the creation of new bacterial ecotypes. These vast mud environments may act as exporters and promoters of biosphere diversity and novel adaptations, potentially on a globally important scale.}, }
@article {pmid20345811, year = {2010}, author = {Sachs, JL and Ehinger, MO and Simms, EL}, title = {Origins of cheating and loss of symbiosis in wild Bradyrhizobium.}, journal = {Journal of evolutionary biology}, volume = {23}, number = {5}, pages = {1075-1089}, doi = {10.1111/j.1420-9101.2010.01980.x}, pmid = {20345811}, issn = {1420-9101}, support = {GM77892-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Biological/genetics/*physiology ; Base Sequence ; Bayes Theorem ; Bradyrhizobium/genetics/*physiology ; California ; DNA Primers/genetics ; Gene Transfer, Horizontal/*genetics ; Likelihood Functions ; Lotus/*microbiology ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Root Nodules, Plant/*microbiology/physiology ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {Rhizobial bacteria nodulate legume roots and fix nitrogen in exchange for photosynthates. These symbionts are infectiously acquired from the environment and in such cases selection models predict evolutionary spread of uncooperative mutants. Uncooperative rhizobia - including nonfixing and non-nodulating strains - appear common in agriculture, yet their population biology and origins remain unknown in natural soils. Here, a phylogenetically broad sample of 62 wild-collected rhizobial isolates was experimentally inoculated onto Lotus strigosus to assess their nodulation ability and effects on host growth. A cheater strain was discovered that proliferated in host tissue while offering no benefit; its fitness was superior to that of beneficial strains. Phylogenetic reconstruction of Bradyrhizobium rDNA and transmissible symbiosis-island loci suggest that the cheater evolved via symbiotic gene transfer. Many strains were also identified that failed to nodulate L. strigosus, and it appears that nodulation ability on this host has been recurrently lost in the symbiont population. This is the first study to reveal the adaptive nature of rhizobial cheating and to trace the evolutionary origins of uncooperative rhizobial mutants.}, }
@article {pmid20345385, year = {2010}, author = {Ruwandeepika, HA and Defoirdt, T and Bhowmick, PP and Shekar, M and Bossier, P and Karunasagar, I}, title = {Presence of typical and atypical virulence genes in vibrio isolates belonging to the Harveyi clade.}, journal = {Journal of applied microbiology}, volume = {109}, number = {3}, pages = {888-899}, doi = {10.1111/j.1365-2672.2010.04715.x}, pmid = {20345385}, issn = {1365-2672}, mesh = {Animals ; Artemia/microbiology ; Genes, Bacterial ; Polymerase Chain Reaction/methods ; Vibrio/classification/genetics/isolation &amp; purification/*pathogenicity ; Virulence/genetics ; Virulence Factors/*genetics ; }, abstract = {AIMS: The study was aimed at investigating the presence of typical and atypical virulence genes in isolates belonging to the Harveyi clade (Vibrio harveyi and Vibrio campbellii).<br><br>METHODS AND RESULTS: Forty-eight vibrio isolates belonging to the Harveyi clade were screened for the presence of virulence genes that are typical for these bacteria and those found in human pathogenic vibrios such as Vibrio cholerae, Vibrio parahaemolyticus and Vibrio vulnificus and aquatic pathogenic Vibrio anguillarum. The virulence genes were amplified by PCR with specific primers, and the presence further confirmed by dot blot hybridization. The virulence genes vhh, chiA, vhpA, toxR(Vh), luxR and serine protease, typical of Harveyi clade were detected in all the isolates. The haemolysin gene hlyA and the virulence regulator gene toxR(Vc) specific to V. cholerae and the V. anguillarum-specific flagellum gene (flaC) were present in some of the isolates. Challenge tests with gnotobiotic Artemia nauplii did not show any correlation between the presence of the virulence genes and virulence of the isolates.<br><br>CONCLUSION: From our results, there appears a remote possibility that vibrios belonging to the Harveyi clade might acquire virulence genes from other vibrios in the aquatic environment through horizontal gene transfer.<br><br>Vibrios belonging to the Harveyi clade may be an important reservoir of virulence genes of other (human pathogenic) Vibrio species in the aquatic environment. The acquisition of virulence genes by horizontal transfer might increase the ability of Harveyi clade vibrios to infect aquatic organisms by increasing their virulence to a specific host by broadening their host range. The detection of such genes may forewarn the hatchery operators about a potentially virulent pathogen and thus help to develop management measures to handle the problem of vibriosis.}, }
@article {pmid20339871, year = {2010}, author = {Deprá, M and Panzera, Y and Ludwig, A and Valente, VL and Loreto, EL}, title = {Hosimary: a new hAT transposon group involved in horizontal transfer.}, journal = {Molecular genetics and genomics : MGG}, volume = {283}, number = {5}, pages = {451-459}, pmid = {20339871}, issn = {1617-4623}, mesh = {Animals ; Bias ; Blotting, Southern ; Codon/genetics ; DNA Transposable Elements/*genetics ; Drosophila/*genetics ; Evolution, Molecular ; Gene Dosage/genetics ; Gene Transfer, Horizontal/*genetics ; Genome/genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {A PCR screening approach was used to search for sequences homologous to a previously described hAT transposon found in Drosophila simulans and Drosophila sechellia, named here as hosimary. In this study, 52 Drosophilidae species were analyzed and these sequences seem to be restricted to some species of the melanogaster group and Zaprionus indianus. These species present variable number of copies and most of those appear to be putatively encoding. The high hosimary sequences similarity among different species and the patchy distribution presented by this transposon strongly support the hypothesis that hosimary was horizontally transferred between the melanogaster group species and Z. indianus.}, }
@article {pmid20335363, year = {2010}, author = {Sagane, Y and Zech, K and Bouquet, JM and Schmid, M and Bal, U and Thompson, EM}, title = {Functional specialization of cellulose synthase genes of prokaryotic origin in chordate larvaceans.}, journal = {Development (Cambridge, England)}, volume = {137}, number = {9}, pages = {1483-1492}, doi = {10.1242/dev.044503}, pmid = {20335363}, issn = {1477-9129}, mesh = {Animals ; Cellulose/metabolism ; Chordata/classification/*embryology/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Glucosyltransferases/*genetics/*metabolism ; In Situ Hybridization ; Phylogeny ; Prokaryotic Cells/*metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {Extracellular matrices play important, but poorly investigated, roles in morphogenesis. Extracellular cellulose is central to regulation of pattern formation in plants, but among metazoans only tunicates are capable of cellulose biosynthesis. Cellulose synthase (CesA) gene products are present in filter-feeding structures of all tunicates and also regulate metamorphosis in the ascidian Ciona. Ciona CesA is proposed to have been acquired by lateral gene transfer from a prokaryote. We identified two CesA genes in the sister-class larvacean Oikopleura dioica. Each has a mosaic structure of a glycoslyltransferase 2 domain upstream of a glycosyl hydrolase family 6 cellulase-like domain, a signature thus far unique to tunicates. Spatial-temporal expression analysis revealed that Od-CesA1 produces long cellulose fibrils along the larval tail, whereas Od-CesA2 is responsible for the cellulose scaffold of the post-metamorphic filter-feeding house. Knockdown of Od-CesA1 inhibited cellulose production in the extracellular matrix of the larval tail. Notochord cells either failed to align or were misaligned, the tail did not elongate properly and tailbud embryos also exhibited a failure to hatch. Knockdown of Od-CesA2 did not elicit any of these phenotypes and instead caused a mild delay in pre-house formation. Phylogenetic analyses including Od-CesAs indicate that a single lateral gene transfer event from a prokaryote at the base of the lineage conferred biosynthetic capacity in all tunicates. Ascidians possess one CesA gene, whereas duplicated larvacean genes have evolved distinct temporal and functional specializations. Extracellular cellulose microfibrils produced by the pre-metamorphic Od-CesA1 duplicate have a role in notochord and tail morphogenesis.}, }
@article {pmid20333230, year = {2010}, author = {Arbiol, C and Comeau, AM and Kutateladze, M and Adamia, R and Krisch, HM}, title = {Mobile regulatory cassettes mediate modular shuffling in T4-type phage genomes.}, journal = {Genome biology and evolution}, volume = {2}, number = {}, pages = {140-152}, pmid = {20333230}, issn = {1759-6653}, abstract = {Coliphage phi1, which was isolated for phage therapy in the Republic of Georgia, is closely related to the T-like myovirus RB49. The approximately 275 open reading frames encoded by each phage have an average level of amino acid identity of 95.8%. RB49 lacks 7 phi1 genes while 10 phi1 genes are missing from RB49. Most of these unique genes encode functions without known homologs. Many of the insertion, deletion, and replacement events that distinguish the two phages are in the hyperplastic regions (HPRs) of their genomes. The HPRs are rich in both nonessential genes and small regulatory cassettes (promoter(early) stem-loops [PeSLs]) composed of strong sigma(70)-like promoters and stem-loop structures, which are effective transcription terminators. Modular shuffling mediated by recombination between PeSLs has caused much of the sequence divergence between RB49 and phi1. We show that exchanges between nearby PeSLs can also create small circular DNAs that are apparently encapsidated by the virus. Such PeSL "mini-circles" may be important vectors for horizontal gene transfer.}, }
@article {pmid20333218, year = {2009}, author = {Sasaki, NV and Sato, N}, title = {Elucidating genome structure evolution by analysis of isoapostatic gene clusters using statistics of variance of gene distances.}, journal = {Genome biology and evolution}, volume = {2}, number = {}, pages = {1-12}, pmid = {20333218}, issn = {1759-6653}, abstract = {Identifying genomic regions that descended from a common ancestor is important for understanding the function and evolution of genomes. In related genomes, clusters of homologous gene pairs serve as evidence for candidate homologous regions, which make up genomic core. Previous studies on the structural organization of bacterial genomes revealed that basic backbone of genomic core is interrupted by genomic islands. Here, we applied statistics using variance of distances as a measure to classify conserved genes within a set of genomes according to their "isoapostatic" relationship, which keeps nearly identical distances of genes. The results of variance statistics analysis of cyanobacterial genomes including Prochlorococcus, Synechococcus, and Anabaena indicated that the conserved genes are classified into several groups called "virtual linkage groups (VLGs)" according to their positional conservation of orthologs over the genomes analyzed. The VLGs were used to define mosaic domain structure of the genomic core. The current model of mosaic genomic domains can explain global evolution of the genomic core of cyanobacteria. It also visualizes islands of lateral gene transfer. The stability and the robustness of the variance statistics are discussed. This method will also be useful in deciphering the structural organization of genomes in other groups of bacteria.}, }
@article {pmid20332804, year = {2011}, author = {Rankin, DJ and Rocha, EP and Brown, SP}, title = {What traits are carried on mobile genetic elements, and why?.}, journal = {Heredity}, volume = {106}, number = {1}, pages = {1-10}, pmid = {20332804}, issn = {1365-2540}, support = {/WT_/Wellcome Trust/United Kingdom ; 082273/Z/07/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacteria/*genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Interspersed Repetitive Sequences/*genetics ; Plasmids/*genetics ; }, abstract = {Although similar to any other organism, prokaryotes can transfer genes vertically from mother cell to daughter cell, they can also exchange certain genes horizontally. Genes can move within and between genomes at fast rates because of mobile genetic elements (MGEs). Although mobile elements are fundamentally self-interested entities, and thus replicate for their own gain, they frequently carry genes beneficial for their hosts and/or the neighbours of their hosts. Many genes that are carried by mobile elements code for traits that are expressed outside of the cell. Such traits are involved in bacterial sociality, such as the production of public goods, which benefit a cell's neighbours, or the production of bacteriocins, which harm a cell's neighbours. In this study we review the patterns that are emerging in the types of genes carried by mobile elements, and discuss the evolutionary and ecological conditions under which mobile elements evolve to carry their peculiar mix of parasitic, beneficial and cooperative genes.}, }
@article {pmid20308303, year = {2010}, author = {Agnes, JT and Herndon, D and Ueti, MW and Ramabu, SS and Evans, M and Brayton, KA and Palmer, GH}, title = {Association of pathogen strain-specific gene transcription and transmission efficiency phenotype of Anaplasma marginale.}, journal = {Infection and immunity}, volume = {78}, number = {6}, pages = {2446-2453}, pmid = {20308303}, issn = {1098-5522}, support = {AI44005/AI/NIAID NIH HHS/United States ; T32 GM008336-20/GM/NIGMS NIH HHS/United States ; T32 GM008336-21/GM/NIGMS NIH HHS/United States ; R01 AI044005/AI/NIAID NIH HHS/United States ; R37 AI044005/AI/NIAID NIH HHS/United States ; T32 GM008336-19/GM/NIGMS NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; GR075800M/WT_/Wellcome Trust/United Kingdom ; T32 GM008336/GM/NIGMS NIH HHS/United States ; }, mesh = {Anaplasma marginale/*pathogenicity ; Animals ; Genes, Bacterial ; Salivary Glands/microbiology ; Synteny ; Ticks/*microbiology ; *Transcription, Genetic ; Virulence Factors/*biosynthesis ; }, abstract = {Efficient transmission of pathogens by an arthropod vector is influenced by the ability of the pathogen to replicate and develop infectiousness within the arthropod host. While the basic life cycle of development within and transmission from the arthropod vector are known for many bacterial and protozoan pathogens, the determinants of transmission efficiency are largely unknown and represent a significant gap in our knowledge. The St. Maries strain of Anaplasma marginale is a high-transmission-efficiency strain that replicates to a high titer in the tick salivary gland and can be transmitted by <10 ticks. In contrast, A. marginale subsp. centrale (Israel vaccine strain) has an identical life cycle but replicates to a significantly lower level in the salivary gland, with transmission requiring >30-fold more ticks. We hypothesized that strain-specific genes expressed in the tick salivary gland at the time of transmission are linked to the differences in the transmission efficiency phenotype. Using both annotation-dependent and -independent analyses of the complete genome sequences, we identified 58 strain-specific genes. These genes most likely represent divergence from common ancestral genes in one or both strains based on analysis of synteny and lack of statistical support for acquisition as islands by lateral gene transfer. Twenty of the St. Maries strain-specific genes and 16 of the strain-specific genes in the Israel strain were transcribed in the tick salivary gland at the time of transmission. Although associated with the transmission phenotype, the expression levels of strain-specific genes were equal to or less than the expression levels in infected erythrocytes in the mammalian host, suggesting that function is not limited to salivary gland colonization.}, }
@article {pmid20300643, year = {2010}, author = {Tomljenovic-Berube, AM and Mulder, DT and Whiteside, MD and Brinkman, FS and Coombes, BK}, title = {Identification of the regulatory logic controlling Salmonella pathoadaptation by the SsrA-SsrB two-component system.}, journal = {PLoS genetics}, volume = {6}, number = {3}, pages = {e1000875}, pmid = {20300643}, issn = {1553-7404}, support = {MOP-82704//Canadian Institutes of Health Research/Canada ; }, mesh = {Adaptation, Physiological/*genetics ; Bacterial Proteins/*genetics/metabolism ; Base Sequence ; Chromatin Immunoprecipitation ; Conserved Sequence ; DNA, Bacterial/metabolism ; Evolution, Molecular ; Gene Expression Profiling ; *Gene Expression Regulation, Bacterial ; Genetic Loci/genetics ; Genome, Bacterial/genetics ; Genomic Islands/genetics ; Genomics ; Inverted Repeat Sequences/genetics ; Molecular Sequence Data ; Mutation/genetics ; Oligonucleotide Array Sequence Analysis ; Operon/genetics ; Promoter Regions, Genetic/genetics ; Protein Binding ; RNA, Bacterial/*genetics/metabolism ; Regulon/*genetics ; Salmonella/*genetics ; Transcription Factors/*genetics/metabolism ; }, abstract = {Sequence data from the past decade has laid bare the significance of horizontal gene transfer in creating genetic diversity in the bacterial world. Regulatory evolution, in which non-coding DNA is mutated to create new regulatory nodes, also contributes to this diversity to allow niche adaptation and the evolution of pathogenesis. To survive in the host environment, Salmonella enterica uses a type III secretion system and effector proteins, which are activated by the SsrA-SsrB two-component system in response to the host environment. To better understand the phenomenon of regulatory evolution in S. enterica, we defined the SsrB regulon and asked how this transcription factor interacts with the cis-regulatory region of target genes. Using ChIP-on-chip, cDNA hybridization, and comparative genomics analyses, we describe the SsrB-dependent regulon of ancestral and horizontally acquired genes. Further, we used a genetic screen and computational analyses integrating experimental data from S. enterica and sequence data from an orthologous regulatory system in the insect endosymbiont, Sodalis glossinidius, to identify the conserved yet flexible palindrome sequence that defines DNA recognition by SsrB. Mutational analysis of a representative promoter validated this palindrome as the minimal architecture needed for regulatory input by SsrB. These data provide a high-resolution map of a regulatory network and the underlying logic enabling pathogen adaptation to a host.}, }
@article {pmid20299401, year = {2010}, author = {Zilm, PS and Mira, A and Bagley, CJ and Rogers, AH}, title = {Effect of alkaline growth pH on the expression of cell envelope proteins in Fusobacterium nucleatum.}, journal = {Microbiology (Reading, England)}, volume = {156}, number = {Pt 6}, pages = {1783-1794}, doi = {10.1099/mic.0.035881-0}, pmid = {20299401}, issn = {1465-2080}, mesh = {Bacterial Outer Membrane Proteins/*analysis/genetics/*metabolism ; Fusobacterium nucleatum/genetics/*growth &amp; development/*metabolism ; *Gene Expression Regulation, Bacterial ; Gingiva/*microbiology ; Hydrogen-Ion Concentration ; Periplasm/genetics/metabolism ; Proteome/*analysis ; Virulence ; }, abstract = {Fusobacterium nucleatum is a Gram-negative anaerobic organism that plays a central role in the development of periodontal diseases. The progression of periodontitis is associated with a rise in pH of the gingival sulcus which promotes the growth and expression of virulence factors by periodontopathic bacteria. We have previously reported that the expression of specific cytoplasmic proteins is altered by a shift in growth pH. In the present study we have compared cell envelope protein expression of F. nucleatum during chemostat growth at pH 7.2 and 7.8. From a total of 176 proteins resolved from the cell envelope, 15 were found to have altered expression in response to an increase in growth pH and were identified by MS. Upregulated proteins included an outer membrane porin which has been identified as playing a role in virulence, a periplasmic chaperone which assists in the folding of outer membrane proteins, and a transporter thought to be involved with iron uptake. Proteins downregulated at pH 7.8 were consistent with our previous findings that the bacterium reduces its catabolism of energy-yielding substrates in favour of energy-storage pathways. Among the downregulated proteins, two transporters which are involved in the uptake of C4 dicarboxylates and phosphate were identified. A putative protease and an enzyme associated with the metabolism of glutamate were also identified. A high proportion of the cell envelope proteins suggested by these data to play a role in the organism's response to alkaline growth pH may have arisen by lateral gene transfer. This would support the hypothesis that genes that provide an ability to adapt to the changing conditions of the oral environment may be readily shared between oral bacteria.}, }
@article {pmid20237445, year = {2009}, author = {Lee, HL and Aramu, M and Nazni, WA and Selvi, S and Vasan, S}, title = {No evidence for successful interspecific cross-mating of transgenic Aedes aegypti (L.) and wild type Aedes albopictus Skuse.}, journal = {Tropical biomedicine}, volume = {26}, number = {3}, pages = {312-319}, pmid = {20237445}, issn = {0127-5720}, mesh = {Aedes/*genetics/*physiology ; Animals ; Animals, Genetically Modified/physiology ; Chimera/genetics ; Female ; Gene Transfer, Horizontal ; Genotype ; *Insect Vectors/genetics/growth &amp; development/physiology ; Insemination, Artificial ; Larva ; Male ; *Pest Control, Biological ; Reproduction ; *Sexual Behavior, Animal ; Species Specificity ; }, abstract = {The natural and artificial mating of laboratory bred Aedes albopictus and transgenic Aedes aegypti RIDL-513A-Malaysian strain was conducted. The experiment consisted of crossmating of homologous Ae. aegypti RIDL female symbol X Ae. aegypti RIDL male symbol and reciprocal Ae. aegypti RIDL female symbol X Ae. albopictus WT male symbol. The other set comprised homologous Ae. albopictus WT female symbol X Ae. albopictus WT male symbol and reciprocal Ae. albopictus WT female symbol X Ae. aegypti RIDL male symbol. This study demonstrated that reproductive barriers exist between these two species. Cross insemination occurred between A. albopictus male and Ae. aegypti female and their reciprocals. There was 26.67% and 33.33% insemination rate in Ae. aegypti RIDL female cross-mating with A. albopictus WT male and Ae. albopictus female cross-mating with Ae. aegypti RIDL male, respectively. There was 0% hatchability in both directions of the reciprocals. There was also no embryonation of these eggs which were bleached. Although none of the female Ae. albopictus WT was inseminated in the cross-mating with Ae. albopictus WT female symbol X Ae. aegypti RIDL male symbol, a total of 573 eggs were obtained. The homologous mating was very productive resulting in both high insemination rate and hatchability rates. Generally there was a significantly higher insemination rate with artificial mating insemination of homologous than with artificial mating of reciprocal crosses. Interspecific mating between Ae. aegypti RIDL and Ae. albopictus wild type was not productive and no hybrid was obtained, indicating absence of horizontal transfer of introduced RIDL gene in Ae. aegypti to Ae. albopictus.}, }
@article {pmid20236513, year = {2010}, author = {D'Auria, G and Jiménez-Hernández, N and Peris-Bondia, F and Moya, A and Latorre, A}, title = {Legionella pneumophila pangenome reveals strain-specific virulence factors.}, journal = {BMC genomics}, volume = {11}, number = {}, pages = {181}, pmid = {20236513}, issn = {1471-2164}, mesh = {Evolution, Molecular ; *Genome, Bacterial ; Genomic Islands ; Genomics ; Legionella pneumophila/*genetics ; Virulence Factors/*genetics ; }, abstract = {BACKGROUND: Legionella pneumophila subsp. pneumophila is a gram-negative gamma-Proteobacterium and the causative agent of Legionnaires' disease, a form of epidemic pneumonia. It has a water-related life cycle. In industrialized cities L. pneumophila is commonly encountered in refrigeration towers and water pipes. Infection is always via infected aerosols to humans. Although many efforts have been made to eradicate Legionella from buildings, it still contaminates the water systems. The town of Alcoy (Valencian Region, Spain) has had recurrent outbreaks since 1999. The strain "Alcoy 2300/99" is a particularly persistent and recurrent strain that was isolated during one of the most significant outbreaks between the years 1999-2000.<br><br>RESULTS: We have sequenced the genome of the particularly persistent L. pneumophila strain Alcoy 2300/99 and have compared it with four previously sequenced strains known as Philadelphia (USA), Lens (France), Paris (France) and Corby (England).Pangenome analysis facilitated the identification of strain-specific features, as well as some that are shared by two or more strains. We identified: (1) three islands related to anti-drug resistance systems; (2) a system for transport and secretion of heavy metals; (3) three systems related to DNA transfer; (4) two CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) systems, known to provide resistance against phage infections, one similar in the Lens and Alcoy strains, and another specific to the Paris strain; and (5) seven islands of phage-related proteins, five of which seem to be strain-specific and two shared.<br><br>CONCLUSIONS: The dispensable genome disclosed by the pangenomic analysis seems to be a reservoir of new traits that have mainly been acquired by horizontal gene transfer and could confer evolutionary advantages over strains lacking them.}, }
@article {pmid20233933, year = {2010}, author = {Vickerman, MM and Flannagan, SE and Jesionowski, AM and Brossard, KA and Clewell, DB and Sedgley, CM}, title = {A genetic determinant in Streptococcus gordonii Challis encodes a peptide with activity similar to that of enterococcal sex pheromone cAM373, which facilitates intergeneric DNA transfer.}, journal = {Journal of bacteriology}, volume = {192}, number = {10}, pages = {2535-2545}, pmid = {20233933}, issn = {1098-5530}, support = {R01 DE011090/DE/NIDCR NIH HHS/United States ; R29 DE011090/DE/NIDCR NIH HHS/United States ; DE11090/DE/NIDCR NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; DNA, Bacterial/*genetics ; DNA, Intergenic/*genetics ; Enterococcus faecalis/genetics ; Gene Transfer, Horizontal/genetics/physiology ; Molecular Sequence Data ; Mutation ; Oligopeptides/chemistry/genetics/*metabolism ; Polymerase Chain Reaction ; Sequence Homology, Amino Acid ; Streptococcus gordonii/*genetics/*metabolism ; }, abstract = {Enterococcus faecalis strains secrete multiple peptides representing different sex pheromones that induce mating responses by bacteria carrying specific conjugative plasmids. The pheromone cAM373, which induces a response by the enterococcal plasmid pAM373, has been of interest because a similar activity is also secreted by Streptococcus gordonii and Staphylococcus aureus. The potential to facilitate intergeneric DNA transfer from E. faecalis is of concern because of extensive multiple antibiotic resistance, including vancomycin resistance, that has emerged among enterococci in recent years. Here, we characterize the related pheromone determinant in S. gordonii and show that the peptide it encodes, gordonii-cAM373, does indeed induce transfer of plasmid DNA from E. faecalis into S. gordonii. The streptococcal determinant camG encodes a lipoprotein with a leader sequence, the last 7 residues of which represent the gordonii-cAM373 heptapeptide SVFILAA. Synthetic forms of the peptide had activity similar to that of the enterococcal cAM373 AIFILAS. The lipoprotein moiety bore no resemblance to the lipoprotein encoded by E. faecalis. We also identified determinants in S. gordonii encoding a signal peptidase and an Eep-like zinc metalloprotease (lspA and eep, respectively) similar to those involved in processing certain pheromone precursors in E. faecalis. Mutations generated in camG, lspA, and eep each resulted in the ablation of gordonii-cAM373 activity in culture supernatants. This is the first genetic analysis of a potential sex pheromone system in a commensal oral streptococcal species, which may have implications for intergeneric gene acquisition in oral biofilms.}, }
@article {pmid20229224, year = {2010}, author = {Conceição, T and Tavares, A and Miragaia, M and Hyde, K and Aires-de-Sousa, M and de Lencastre, H}, title = {Prevalence and clonality of methicillin-resistant Staphylococcus aureus (MRSA) in the Atlantic Azores islands: predominance of SCCmec types IV, V and VI.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {29}, number = {5}, pages = {543-550}, pmid = {20229224}, issn = {1435-4373}, mesh = {Anti-Bacterial Agents/pharmacology ; Azores/epidemiology ; Bacterial Proteins/*genetics ; Bacterial Toxins/genetics ; Bacterial Typing Techniques/*methods ; Electrophoresis, Gel, Pulsed-Field ; Exotoxins/genetics ; Gene Transfer, Horizontal ; Humans ; Leukocidins/genetics ; Methicillin Resistance/*genetics ; Methicillin-Resistant Staphylococcus aureus/classification/drug effects/genetics/*isolation &amp; purification ; Microbial Sensitivity Tests ; Molecular Diagnostic Techniques/*methods ; Prevalence ; Staphylococcal Infections/epidemiology/*microbiology ; }, abstract = {In order to obtain insights into the methicillin-resistant Staphylococcus aureus (MRSA) population structure in the Azores archipelago, 106 MRSA isolates were collected from patients attending an Azorean central hospital between January 2007 and February 2008. Antimicrobial resistance was determined for all isolates. Molecular typing was performed by pulsed-field gel electrophoresis (PFGE), spa typing, multilocus sequence typing (MLST), staphylococcal chromosome cassette mec (SCCmec) typing and the presence of Panton-Valentine leukocidin (PVL). The majority of the isolates (87%, n = 92) belonged to the EMRSA-15 clone (ST22, SCCmec-IVh), followed by the Pediatric clone (ST5-VI/IVc) (11%, n = 12). The Berlin clone (ST45-IVa) and a new clone (spa type t1839, ST1339 and SCCmec V variant) were represented by single isolates. All of the isolates carried SCCmec types IV, V or VI and a non-multiresistant antibiotic profile, resembling the currently emerging community MRSA. Moreover, PVL was described for the first time to be associated with the Pediatric clone carrying SCCmec type VI. We provided the first description of the population structure of MRSA in the Azores islands, which seems to be shaped by genetic events occurring locally, as well as by the regular population exchange between the islands, continental Portugal, the United Kingdom and the United States.}, }
@article {pmid20228792, year = {2010}, author = {Chapman, JA and Kirkness, EF and Simakov, O and Hampson, SE and Mitros, T and Weinmaier, T and Rattei, T and Balasubramanian, PG and Borman, J and Busam, D and Disbennett, K and Pfannkoch, C and Sumin, N and Sutton, GG and Viswanathan, LD and Walenz, B and Goodstein, DM and Hellsten, U and Kawashima, T and Prochnik, SE and Putnam, NH and Shu, S and Blumberg, B and Dana, CE and Gee, L and Kibler, DF and Law, L and Lindgens, D and Martinez, DE and Peng, J and Wigge, PA and Bertulat, B and Guder, C and Nakamura, Y and Ozbek, S and Watanabe, H and Khalturin, K and Hemmrich, G and Franke, A and Augustin, R and Fraune, S and Hayakawa, E and Hayakawa, S and Hirose, M and Hwang, JS and Ikeo, K and Nishimiya-Fujisawa, C and Ogura, A and Takahashi, T and Steinmetz, PR and Zhang, X and Aufschnaiter, R and Eder, MK and Gorny, AK and Salvenmoser, W and Heimberg, AM and Wheeler, BM and Peterson, KJ and Böttger, A and Tischler, P and Wolf, A and Gojobori, T and Remington, KA and Strausberg, RL and Venter, JC and Technau, U and Hobmayer, B and Bosch, TC and Holstein, TW and Fujisawa, T and Bode, HR and David, CN and Rokhsar, DS and Steele, RE}, title = {The dynamic genome of Hydra.}, journal = {Nature}, volume = {464}, number = {7288}, pages = {592-596}, pmid = {20228792}, issn = {1476-4687}, support = {P 20734/FWF_/Austrian Science Fund FWF/Austria ; P 21108/FWF_/Austrian Science Fund FWF/Austria ; R24 RR015088/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Anthozoa/genetics ; Comamonadaceae/genetics ; DNA Transposable Elements/genetics ; Gene Transfer, Horizontal/genetics ; Genome/*genetics ; Genome, Bacterial/genetics ; Hydra/*genetics/microbiology/ultrastructure ; Molecular Sequence Data ; Neuromuscular Junction/ultrastructure ; }, abstract = {The freshwater cnidarian Hydra was first described in 1702 and has been the object of study for 300 years. Experimental studies of Hydra between 1736 and 1744 culminated in the discovery of asexual reproduction of an animal by budding, the first description of regeneration in an animal, and successful transplantation of tissue between animals. Today, Hydra is an important model for studies of axial patterning, stem cell biology and regeneration. Here we report the genome of Hydra magnipapillata and compare it to the genomes of the anthozoan Nematostella vectensis and other animals. The Hydra genome has been shaped by bursts of transposable element expansion, horizontal gene transfer, trans-splicing, and simplification of gene structure and gene content that parallel simplification of the Hydra life cycle. We also report the sequence of the genome of a novel bacterium stably associated with H. magnipapillata. Comparisons of the Hydra genome to the genomes of other animals shed light on the evolution of epithelia, contractile tissues, developmentally regulated transcription factors, the Spemann-Mangold organizer, pluripotency genes and the neuromuscular junction.}, }
@article {pmid20227783, year = {2010}, author = {Houliston, E and Momose, T and Manuel, M}, title = {Clytia hemisphaerica: a jellyfish cousin joins the laboratory.}, journal = {Trends in genetics : TIG}, volume = {26}, number = {4}, pages = {159-167}, doi = {10.1016/j.tig.2010.01.008}, pmid = {20227783}, issn = {0168-9525}, mesh = {Animals ; Biological Evolution ; Developmental Biology ; Gametogenesis ; Gene Transfer, Horizontal ; Genome ; Hydrozoa/embryology/*genetics ; *Models, Animal ; }, abstract = {Clytia hemisphaerica, a member of the early-branching animal phylum Cnidaria, is emerging rapidly as an experimental model for studies in developmental biology and evolution. Unlike the two existing genome-sequenced cnidarian models Nematostella and Hydra, Clytia has a free-swimming jellyfish form, which like "higher" animals (the Bilateria) has a complex organization including striated musculature, specialized nervous system and structured sensory and reproductive organs. Clytia has proved well suited to laboratory culture and to gene function analysis during early development. Initial studies have shed light on the origins of embryonic polarity and of the nematocyte as a specialized neurosensory cell, and on the regulation of oocyte maturation. With a full genome sequence soon to become available, and a clear potential for genetic approaches, Clytia is well placed to provide invaluable information on core mechanisms in cell and developmental biology, and on the evolution of key features of animal body plans.}, }
@article {pmid20226043, year = {2010}, author = {Mallet, LV and Becq, J and Deschavanne, P}, title = {Whole genome evaluation of horizontal transfers in the pathogenic fungus Aspergillus fumigatus.}, journal = {BMC genomics}, volume = {11}, number = {}, pages = {171}, pmid = {20226043}, issn = {1471-2164}, mesh = {Aspergillus fumigatus/*genetics ; DNA, Fungal/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Fungal ; Genomics/methods ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Numerous cases of horizontal transfers (HTs) have been described for eukaryote genomes, but in contrast to prokaryote genomes, no whole genome evaluation of HTs has been carried out. This is mainly due to a lack of parametric methods specially designed to take the intrinsic heterogeneity of eukaryote genomes into account. We applied a simple and tested method based on local variations of genomic signatures to analyze the genome of the pathogenic fungus Aspergillus fumigatus.<br><br>RESULTS: We detected 189 atypical regions containing 214 genes, accounting for about 1 Mb of DNA sequences. However, the fraction of atypical DNA detected was smaller than the average amount detected in the same conditions in prokaryote genomes (3.1% vs 5.6%). It appeared that about one third of these regions contained no annotated genes, a proportion far greater than in prokaryote genomes. When analyzing the origin of these HTs by comparing their signatures to a home made database of species signatures, 3 groups of donor species emerged: bacteria (40%), fungi (25%), and viruses (22%). It is to be noticed that though inter-domain exchanges are confirmed, we only put in evidence very few exchanges between eukaryotic kingdoms.<br><br>CONCLUSIONS: In conclusion, we demonstrated that HTs are not negligible in eukaryote genomes, bearing in mind that in our stringent conditions this amount is a floor value, though of a lesser extent than in prokaryote genomes. The biological mechanisms underlying those transfers remain to be elucidated as well as the biological functions of the transferred genes.}, }
@article {pmid20222441, year = {2009}, author = {Wang, S and Vongxay, K and Shen, B and Zhou, X and Jin, P and Chen, J and Fang, W}, title = {[Analysis of tdh gene and its adjacent loci of Vibrio parahaemolyticus isolates from seafoods].}, journal = {Wei sheng wu xue bao = Acta microbiologica Sinica}, volume = {49}, number = {12}, pages = {1576-1583}, pmid = {20222441}, issn = {0001-6209}, mesh = {Bacterial Proteins/chemistry/*genetics ; Base Sequence ; Genome, Bacterial ; Molecular Sequence Data ; Seafood/*microbiology ; Sequence Alignment ; Vibrio parahaemolyticus/chemistry/*genetics/*isolation &amp; purification ; }, abstract = {OBJECTIVE: To analyze the structural characteristics of tdh gene and its adjacent loci of Vibrio parahaemolyticus isolates from seafoods.<br><br>METHODS: Long distance PCR and genome walking were used to amplify the DNA sequences flanking the tdh gene, and the sequences were analyzed by blastn against the NCBI database.<br><br>RESULTS: The genetic structure of tdh-adjacent loci (VPA1312-VPA1327) from isolate ZS34 was similar to that of the reference strain RIMD2210633, with the nucleotide identity of 98.3%. The tdh gene of isolates FJ14 and WZ64 was located in the loci different from the reference strain and ZS34, and showed high nucleotide similarity to tdh3 gene. In the genome of isolate FJ14, tdh was 15kb away from the trh- ure cluster, with IS-like elements and transposase genes inserted therein. Isolate WZ64 lacked trh gene, but also harbored IS-like elements upstream of tdh.<br><br>CONCLUSION: The tdh-adjacent loci of V. parahaemolyticus seafood isolates exhibit high diversity, an additional evidence of lateral gene transfer in this particular species.}, }
@article {pmid20221735, year = {2010}, author = {Song, M and Kim, HJ and Ryu, S and Yoon, H and Yun, J and Choy, HE}, title = {ppGpp-mediated stationary phase induction of the genes encoded by horizontally acquired pathogenicity islands and cob/pdu locus in Salmonella enterica serovar Typhimurium.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {48}, number = {1}, pages = {89-95}, pmid = {20221735}, issn = {1976-3794}, mesh = {Bacterial Proteins/biosynthesis/*genetics ; Cell Culture Techniques ; Gene Expression Profiling ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Genetic Loci ; Genomic Islands/*genetics ; Guanosine Tetraphosphate/*genetics/metabolism ; Membrane Proteins/biosynthesis/*genetics ; Oligonucleotide Array Sequence Analysis ; Open Reading Frames ; Salmonella typhimurium/*genetics/metabolism ; }, abstract = {Salmonella enterica is highly diverse in terms of genome structure, which is at least partly due to the horizontal transfer of genetic elements from various sources. In this study, we examined the expression profiles of such genes in Salmonella Pathogenicity Islands (SPIs) and the cob/pdu locus, horizontally acquired large DNA segments, during growth under standard growth conditions. Transcripts from exponentially growing and early stationary phase Salmonellae were compared using various methods including cDNA microarray analysis. Nearly all genes encoded by SPIs and the cob/pdu locus were induced at the onset of the stationary phase in a stringent molecule ppGpp-dependent but stationary phase sigma, sigma38-independent manner. Although, it has been suggested that ppGpp acts in concert with DksA, we found the stationary phase induction of those SPI genes was not DksA dependent. It is suggested that ppGpp stimulates the expression of these stress-inducible genes encoded by horizontally acquired DNA, by itself or in concert with DksA.}, }
@article {pmid20208451, year = {2010}, author = {Youn, JH and Hwang, SY and Kim, SH and Koo, HC and Shin, S and Lim, SK and Park, YH}, title = {mecA gene transferrability and antibiogram of zoonotic Staphylococcus intermedius from animals, staff and the environment in animal hospitals in Korea.}, journal = {Journal of microbiology and biotechnology}, volume = {20}, number = {2}, pages = {425-432}, pmid = {20208451}, issn = {1017-7825}, mesh = {Animals ; Bacterial Proteins/*genetics/metabolism ; Dog Diseases/*microbiology/transmission ; Dogs ; Drug Resistance, Multiple, Bacterial ; *Gene Transfer, Horizontal ; Health Personnel ; Hospitals, Animal ; Humans ; Microbial Sensitivity Tests ; Staphylococcal Infections/*microbiology/transmission/*veterinary ; Staphylococcus/drug effects/*genetics/metabolism ; Zoonoses/microbiology/*transmission ; }, abstract = {Staphylococcus intermedius is a common cause of otitis externa, pyoderma and wound infections in companion animals. Although S. intermedius infections are rare in humans, it is zoonotic, with several case reports describing fatal human infections. Presently, we sought to isolate S. intermedius strains from various sources at animal hospitals nationwide in Korea, examine their antibiotic susceptibilities, and determine the possibility of horizontal transmission between animals and humans. Pulsed field gel electrophoresis (PFGE) was used to compare the mecA gene in S. intermedius strains from humans, animals and the environment in animal hospitals. A total of 119 S. intermedius strains were isolated from 529 samples. Using the disk-diffusion method over 90% of the isolates were susceptible to cephalothin, amoxicillin-clavulanic acid, vancomycin, imipenem, nitroflurantoin and amikacin, whereas 97.5% and 98.3% of the isolates were resistant to penicillin and ampicillin, respectively. Among the 39 S. intermedius strains harbouring mecA, similar PFGE patterns were observed between seven isolates from an animal, two isolates from veterinary staff and the environment in one animal hospital, and single isolates from an animal and a veterinarian at another hospital. This result suggests the possibility of horizontal transmission of S. intermedius containing mecA between humans, animals and the environment in animal hospitals and also emphasizes on the importance of S. intermedius with mecA as a possible emerging threat to public health.}, }
@article {pmid20201981, year = {2010}, author = {Calderón-Cortés, N and Watanabe, H and Cano-Camacho, H and Zavala-Páramo, G and Quesada, M}, title = {cDNA cloning, homology modelling and evolutionary insights into novel endogenous cellulases of the borer beetle Oncideres albomarginata chamela (Cerambycidae).}, journal = {Insect molecular biology}, volume = {19}, number = {3}, pages = {323-336}, doi = {10.1111/j.1365-2583.2010.00991.x}, pmid = {20201981}, issn = {1365-2583}, mesh = {Amino Acid Sequence ; Animals ; Blotting, Southern ; Cellulase/chemistry/*genetics/metabolism ; Cloning, Molecular ; Coleoptera/*enzymology/*genetics ; DNA, Complementary/*genetics ; Enzyme Assays ; *Evolution, Molecular ; *Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Secondary ; Sequence Alignment ; *Structural Homology, Protein ; }, abstract = {Novel endogenous cDNAs of beta-1, 4-endoglucanases (Oa-EGase I and Oa-EGase II) were cloned from the cerambycid beetle Oncideres albomarginata chamela. Oa-EGase I- and Oa-EGase II-deduced proteins and three-dimensional structures possess all features, including general architecture, signature motifs and catalytic domains, of glycosyl hydrolase families 5 and 45 (GHF5 and GHF45) and also share high levels of homology with other beetle cellulases. Total carboxymethylcellulase activity of O. a. chamela was 208.13 U/g of larvae. Phylogenetic analyses suggest that insect GHF5 and GHF45 are very ancient gene families and indicate, at least in the case of GHF5, that this family likely evolved from a common ancestor rather than, as is often reported, via horizontal gene transfer. Beetle GHF45 cellulases did not cluster with other metazoan cellulases. However, the presence of GHF45 cellulases in ancient molluscan taxa puts into question the hypothesis of horizontal gene transfer for the evolution of cellulases in animals.}, }
@article {pmid20122216, year = {2010}, author = {Bansal, MS and Burleigh, JG and Eulenstein, O}, title = {Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models.}, journal = {BMC bioinformatics}, volume = {11 Suppl 1}, number = {Suppl 1}, pages = {S42}, pmid = {20122216}, issn = {1471-2105}, mesh = {Algorithms ; Evolution, Molecular ; *Gene Duplication ; *Genome ; *Phylogeny ; }, abstract = {BACKGROUND: Genomic data provide a wealth of new information for phylogenetic analysis. Yet making use of this data requires phylogenetic methods that can efficiently analyze extremely large data sets and account for processes of gene evolution, such as gene duplication and loss, incomplete lineage sorting (deep coalescence), or horizontal gene transfer, that cause incongruence among gene trees. One such approach is gene tree parsimony, which, given a set of gene trees, seeks a species tree that requires the smallest number of evolutionary events to explain the incongruence of the gene trees. However, the only existing algorithms for gene tree parsimony under the duplication-loss or deep coalescence reconciliation cost are prohibitively slow for large datasets.<br><br>RESULTS: We describe novel algorithms for SPR and TBR based local search heuristics under the duplication-loss cost, and we show how they can be adapted for the deep coalescence cost. These algorithms improve upon the best existing algorithms for these problems by a factor of n, where n is the number of species in the collection of gene trees. We implemented our new SPR based local search algorithm for the duplication-loss cost and demonstrate the tremendous improvement in runtime and scalability it provides compared to existing implementations. We also evaluate the performance of our algorithm on three large-scale genomic data sets.<br><br>CONCLUSION: Our new algorithms enable, for the first time, gene tree parsimony analyses of thousands of genes from hundreds of taxa using the duplication-loss and deep coalescence reconciliation costs. Thus, this work expands both the size of data sets and the range of evolutionary models that can be incorporated into genome-scale phylogenetic analyses.}, }
@article {pmid20195672, year = {2010}, author = {Su, Z and Kong, F and Wang, S and Chen, J and Yin, R and Zhou, C and Zhang, Y and He, Z and Shi, Y and Xue, Y and Shi, X and Lu, L and Shao, Q and Xu, H}, title = {The rag locus of Porphyromonas gingivalis might arise from Bacteroides via horizontal gene transfer.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {29}, number = {4}, pages = {429-437}, pmid = {20195672}, issn = {1435-4373}, mesh = {Adolescent ; Adult ; Aged ; Amino Acid Sequence ; Bacteroides/*genetics ; China ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; *Evolution, Molecular ; Female ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Male ; Middle Aged ; Molecular Sequence Data ; Periodontal Diseases/*microbiology ; Phylogeny ; Polymerase Chain Reaction ; Porphyromonas gingivalis/*genetics ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Young Adult ; }, abstract = {Porphyromonas gingivalis is regarded as one of the risk factors of periodontitis. P. gingivalis exhibits a wide variety of genotypes. Many insertion sequences (ISs), located in their chromosomes, made P. gingivalis differentiate into virulent and avirulent strains. In this research, we investigated the prevalence of P. gingivalis in the gingival crevicular fluid (GCF) among periodontitis patients from Zhenjiang, China, detected the P. gingivalis rag locus distributions by multiplex polymerase chain reaction (PCR), and analyzed the origin of the P. gingivalis rag locus based on evolution. There were three rag locus variants co-existing in Zhenjiang. The results showed that the rag locus may be associated with severe periodontitis. This work also firstly ascertained that the rag locus might arise, in theory, from Bacteroides sp. via horizontal gene transfer.}, }
@article {pmid20195515, year = {2010}, author = {Arsène-Ploetze, F and Koechler, S and Marchal, M and Coppée, JY and Chandler, M and Bonnefoy, V and Brochier-Armanet, C and Barakat, M and Barbe, V and Battaglia-Brunet, F and Bruneel, O and Bryan, CG and Cleiss-Arnold, J and Cruveiller, S and Erhardt, M and Heinrich-Salmeron, A and Hommais, F and Joulian, C and Krin, E and Lieutaud, A and Lièvremont, D and Michel, C and Muller, D and Ortet, P and Proux, C and Siguier, P and Roche, D and Rouy, Z and Salvignol, G and Slyemi, D and Talla, E and Weiss, S and Weissenbach, J and Médigue, C and Bertin, PN}, title = {Structure, function, and evolution of the Thiomonas spp. genome.}, journal = {PLoS genetics}, volume = {6}, number = {2}, pages = {e1000859}, pmid = {20195515}, issn = {1553-7404}, mesh = {Adaptation, Physiological/genetics ; Arsenic/metabolism ; Betaproteobacteria/*genetics ; Carbon/metabolism ; Comparative Genomic Hybridization ; Energy Metabolism/genetics ; Environment ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/genetics ; Genes, Duplicate/genetics ; Genetic Variation ; Genome, Bacterial/*genetics ; Genomic Islands/genetics ; Metabolic Networks and Pathways/genetics ; Plasmids/genetics ; Prophages/genetics ; }, abstract = {Bacteria of the Thiomonas genus are ubiquitous in extreme environments, such as arsenic-rich acid mine drainage (AMD). The genome of one of these strains, Thiomonas sp. 3As, was sequenced, annotated, and examined, revealing specific adaptations allowing this bacterium to survive and grow in its highly toxic environment. In order to explore genomic diversity as well as genetic evolution in Thiomonas spp., a comparative genomic hybridization (CGH) approach was used on eight different strains of the Thiomonas genus, including five strains of the same species. Our results suggest that the Thiomonas genome has evolved through the gain or loss of genomic islands and that this evolution is influenced by the specific environmental conditions in which the strains live.}, }
@article {pmid20195500, year = {2010}, author = {Nikoh, N and McCutcheon, JP and Kudo, T and Miyagishima, SY and Moran, NA and Nakabachi, A}, title = {Bacterial genes in the aphid genome: absence of functional gene transfer from Buchnera to its host.}, journal = {PLoS genetics}, volume = {6}, number = {2}, pages = {e1000827}, pmid = {20195500}, issn = {1553-7404}, support = {K12 GM000708/GM/NIGMS NIH HHS/United States ; 1K 12 GM00708/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Aphids/*genetics/*microbiology ; Bacterial Proteins/genetics ; Buchnera/enzymology/*genetics ; Carboxypeptidases/genetics ; DNA Polymerase III/genetics ; Eukaryotic Cells/metabolism ; Gene Duplication ; Gene Fusion ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/*genetics ; Genome ; Glycoside Hydrolases/chemistry/genetics ; Host-Pathogen Interactions/*genetics ; Molecular Sequence Data ; Muramidase/genetics ; N-Acetylmuramoyl-L-alanine Amidase/chemistry/genetics ; Polymerase Chain Reaction ; Reproducibility of Results ; Rickettsia/genetics ; }, abstract = {Genome reduction is typical of obligate symbionts. In cellular organelles, this reduction partly reflects transfer of ancestral bacterial genes to the host genome, but little is known about gene transfer in other obligate symbioses. Aphids harbor anciently acquired obligate mutualists, Buchnera aphidicola (Gammaproteobacteria), which have highly reduced genomes (420-650 kb), raising the possibility of gene transfer from ancestral Buchnera to the aphid genome. In addition, aphids often harbor other bacteria that also are potential sources of transferred genes. Previous limited sampling of genes expressed in bacteriocytes, the specialized cells that harbor Buchnera, revealed that aphids acquired at least two genes from bacteria. The newly sequenced genome of the pea aphid, Acyrthosiphon pisum, presents the first opportunity for a complete inventory of genes transferred from bacteria to the host genome in the context of an ancient obligate symbiosis. Computational screening of the entire A. pisum genome, followed by phylogenetic and experimental analyses, provided strong support for the transfer of 12 genes or gene fragments from bacteria to the aphid genome: three LD-carboxypeptidases (LdcA1, LdcA2,psiLdcA), five rare lipoprotein As (RlpA1-5), N-acetylmuramoyl-L-alanine amidase (AmiD), 1,4-beta-N-acetylmuramidase (bLys), DNA polymerase III alpha chain (psiDnaE), and ATP synthase delta chain (psiAtpH). Buchnera was the apparent source of two highly truncated pseudogenes (psiDnaE and psiAtpH). Most other transferred genes were closely related to genes from relatives of Wolbachia (Alphaproteobacteria). At least eight of the transferred genes (LdcA1, AmiD, RlpA1-5, bLys) appear to be functional, and expression of seven (LdcA1, AmiD, RlpA1-5) are highly upregulated in bacteriocytes. The LdcAs and RlpAs appear to have been duplicated after transfer. Our results excluded the hypothesis that genome reduction in Buchnera has been accompanied by gene transfer to the host nuclear genome, but suggest that aphids utilize a set of duplicated genes acquired from other bacteria in the context of the Buchnera-aphid mutualism.}, }
@article {pmid20195474, year = {2010}, author = {Vo, AT and van Duijkeren, E and Gaastra, W and Fluit, AC}, title = {Antimicrobial resistance, class 1 integrons, and genomic island 1 in Salmonella isolates from Vietnam.}, journal = {PloS one}, volume = {5}, number = {2}, pages = {e9440}, pmid = {20195474}, issn = {1932-6203}, mesh = {Animals ; Anti-Infective Agents/pharmacology ; Cattle ; Conjugation, Genetic ; Drug Resistance, Multiple, Bacterial/*genetics ; Feces/microbiology ; Gene Transfer, Horizontal ; Genomic Islands/*genetics ; Genotype ; Humans ; Integrons/*genetics ; Molecular Sequence Data ; Mutation ; Phenotype ; Poultry ; Salmonella/drug effects/*genetics/isolation &amp; purification ; Salmonella Infections/microbiology ; Salmonella Infections, Animal/microbiology ; Sequence Analysis, DNA ; Species Specificity ; Swine ; Vietnam ; }, abstract = {BACKGROUND: The objective was to investigate the phenotypic and genotypic resistance and the horizontal transfer of resistance determinants from Salmonella isolates from humans and animals in Vietnam.<br><br>The susceptibility of 297 epidemiologically unrelated non-typhoid Salmonella isolates was investigated by disk diffusion assay. The isolates were screened for the presence of class 1 integrons and Salmonella genomic island 1 by PCR. The potential for the transfer of resistance determinants was investigated by conjugation experiments. Resistance to gentamicin, kanamycin, chloramphenicol, streptomycin, trimethoprim, ampicillin, nalidixic acid, sulphonamides, and tetracycline was found in 13 to 50% of the isolates. Nine distinct integron types were detected in 28% of the isolates belonging to 11 Salmonella serovars including S. Tallahassee. Gene cassettes identified were aadA1, aadA2, aadA5, bla(PSE-1), bla(OXA-30), dfrA1, dfrA12, dfrA17, and sat, as well as open reading frames with unknown functions. Most integrons were located on conjugative plasmids, which can transfer their antimicrobial resistance determinants to Escherichia coli or Salmonella Enteritidis, or with Salmonella Genomic Island 1 or its variants. The resistance gene cluster in serovar Emek identified by PCR mapping and nucleotide sequencing contained SGI1-J3 which is integrated in SGI1 at another position than the majority of SGI1. This is the second report on the insertion of SGI1 at this position. High-level resistance to fluoroquinolones was found in 3 multiresistant S. Typhimurium isolates and was associated with mutations in the gyrA gene leading to the amino acid changes Ser83Phe and Asp87Asn.<br><br>CONCLUSIONS: Resistance was common among Vietnamese Salmonella isolates from different sources. Legislation to enforce a more prudent use of antibiotics in both human and veterinary medicine should be implemented by the authorities in Vietnam.}, }
@article {pmid20194966, year = {2010}, author = {Raz, Y and Tannenbaum, E}, title = {The influence of horizontal gene transfer on the mean fitness of unicellular populations in static environments.}, journal = {Genetics}, volume = {185}, number = {1}, pages = {327-337}, pmid = {20194966}, issn = {1943-2631}, mesh = {Bacteria/*genetics/*growth &amp; development ; Conjugation, Genetic ; *Environment ; Gene Transfer, Horizontal/*genetics ; *Genetic Fitness ; Models, Genetic ; }, abstract = {Horizontal gene transfer (HGT) is believed to be a major source of genetic variation, particularly for prokaryotes. It is believed that horizontal gene transfer plays a major role in shaping bacterial genomes and is also believed to be responsible for the relatively rapid dissemination and acquisition of new, adaptive traits across bacterial strains. Despite the importance of horizontal gene transfer as a major source of genetic variation, the bulk of research on theoretical evolutionary dynamics and population genetics has focused on point mutations (sometimes coupled with gene duplication events) as the main engine of genomic change. Here, we seek to specifically model HGT processes in bacterial cells, by developing a mathematical model describing the influence that conjugation-mediated HGT has on the mutation-selection balance in an asexually reproducing population of unicellular, prokaryotic organisms. It is assumed that mutation-selection balance is reached in the presence of a fixed background concentration of antibiotic, to which the population must become resistant to survive. We find that HGT has a nontrivial effect on the mean fitness of the population. However, one of the central results that emerge from our analysis is that, at mutation-selection balance, conjugation-mediated HGT has a slightly deleterious effect on the mean fitness of a population. Therefore, we conclude that HGT does not confer a selection advantage in static environments. Rather, its advantage must lie in its ability to promote faster adaptation in dynamic environments, an interpretation that is consistent with the observation that HGT can be promoted by environmental stresses on a population.}, }
@article {pmid20194510, year = {2010}, author = {Shaw, FL and Elliott, KA and Kinch, LN and Fuell, C and Phillips, MA and Michael, AJ}, title = {Evolution and multifarious horizontal transfer of an alternative biosynthetic pathway for the alternative polyamine sym-homospermidine.}, journal = {The Journal of biological chemistry}, volume = {285}, number = {19}, pages = {14711-14723}, pmid = {20194510}, issn = {1083-351X}, support = {R01 AI034432/AI/NIAID NIH HHS/United States ; R37 AI034432/AI/NIAID NIH HHS/United States ; R01 AI34432/AI/NIAID NIH HHS/United States ; //Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Alkyl and Aryl Transferases/*metabolism ; Bacteria ; *Biological Evolution ; *Biosynthetic Pathways ; Chromatography, High Pressure Liquid ; Models, Molecular ; Phylogeny ; Polyamines/*metabolism ; Spermidine/*analogs &amp; derivatives/metabolism ; }, abstract = {Polyamines are small flexible organic polycations found in almost all cells. They likely existed in the last universal common ancestor of all extant life, and yet relatively little is understood about their biological function, especially in bacteria and archaea. Unlike eukaryotes, where the predominant polyamine is spermidine, bacteria may contain instead an alternative polyamine, sym-homospermidine. We demonstrate that homospermidine synthase (HSS) has evolved vertically, primarily in the alpha-Proteobacteria, but enzymatically active, diverse HSS orthologues have spread by horizontal gene transfer to other bacteria, bacteriophage, archaea, eukaryotes, and viruses. By expressing diverse HSS orthologues in Escherichia coli, we demonstrate in vivo the production of co-products diaminopropane and N(1)-aminobutylcadaverine, in addition to sym-homospermidine. We show that sym-homospermidine is required for normal growth of the alpha-proteobacterium Rhizobium leguminosarum. However, sym-homospermidine can be replaced, for growth restoration, by the structural analogues spermidine and sym-norspermidine, suggesting that the symmetrical or unsymmetrical form and carbon backbone length are not critical for polyamine function in growth. We found that the HSS enzyme evolved from the alternative spermidine biosynthetic pathway enzyme carboxyspermidine dehydrogenase. The structure of HSS is related to lysine metabolic enzymes, and HSS and carboxyspermidine dehydrogenase evolved from the aspartate family of pathways. Finally, we show that other bacterial phyla such as Cyanobacteria and some alpha-Proteobacteria synthesize sym-homospermidine by an HSS-independent pathway, very probably based on deoxyhypusine synthase orthologues, similar to the alternative homospermidine synthase found in some plants. Thus, bacteria can contain alternative biosynthetic pathways for both spermidine and sym-norspermidine and distinct alternative pathways for sym-homospermidine.}, }
@article {pmid20194428, year = {2010}, author = {Fournier, GP and Gogarten, JP}, title = {Rooting the ribosomal tree of life.}, journal = {Molecular biology and evolution}, volume = {27}, number = {8}, pages = {1792-1801}, doi = {10.1093/molbev/msq057}, pmid = {20194428}, issn = {1537-1719}, mesh = {Amino Acid Sequence ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Code ; Molecular Sequence Data ; Phylogeny ; Ribosomal Proteins/*genetics ; Ribosomes/*genetics ; Sequence Alignment ; }, abstract = {The origin of the genetic code and the rooting of the tree of life (ToL) are two of the most challenging problems in the study of life's early evolution. Although both have been the focus of numerous investigations utilizing a variety of methods, until now, each problem has been addressed independently. Typically, attempts to root the ToL have relied on phylogenies of genes with ancient duplications, which are subject to artifacts of tree reconstruction and horizontal gene transfer, or specific physiological characters believed to be primitive, which are often based on subjective criteria. Here, we demonstrate a unique method for rooting based on the identification of amino acid usage biases comprising the residual signature of a more primitive genetic code. Using a phylogenetic tree of concatenated ribosomal proteins, our analysis of amino acid compositional bias detects a strong and unique signal associated with the early expansion of the genetic code, placing the root of the translation machinery along the bacterial branch.}, }
@article {pmid20194115, year = {2010}, author = {Husain, N and Tkaczuk, KL and Tulsidas, SR and Kaminska, KH and Cubrilo, S and Maravić-Vlahovicek, G and Bujnicki, JM and Sivaraman, J}, title = {Structural basis for the methylation of G1405 in 16S rRNA by aminoglycoside resistance methyltransferase Sgm from an antibiotic producer: a diversity of active sites in m7G methyltransferases.}, journal = {Nucleic acids research}, volume = {38}, number = {12}, pages = {4120-4132}, pmid = {20194115}, issn = {1362-4962}, mesh = {Amino Acid Sequence ; Aminoglycosides/pharmacology ; Anti-Bacterial Agents/biosynthesis/pharmacology ; Bacterial Proteins/*chemistry ; Base Sequence ; Calorimetry ; Catalytic Domain ; Conserved Sequence ; Drug Resistance, Bacterial ; Methylation ; Methyltransferases/*chemistry ; Micromonospora/enzymology ; Models, Molecular ; Molecular Sequence Data ; RNA, Ribosomal, 16S/*chemistry/metabolism ; Ribosome Subunits, Small, Bacterial/chemistry ; S-Adenosylhomocysteine/chemistry ; S-Adenosylmethionine/chemistry ; Sequence Homology, Amino Acid ; }, abstract = {Sgm (Sisomicin-gentamicin methyltransferase) from antibiotic-producing bacterium Micromonospora zionensis is an enzyme that confers resistance to aminoglycosides like gentamicin and sisomicin by specifically methylating G1405 in bacterial 16S rRNA. Sgm belongs to the aminoglycoside resistance methyltransferase (Arm) family of enzymes that have been recently found to spread by horizontal gene transfer among disease-causing bacteria. Structural characterization of Arm enzymes is the key to understand their mechanism of action and to develop inhibitors that would block their activity. Here we report the structure of Sgm in complex with cofactors S-adenosylmethionine (AdoMet) and S-adenosylhomocysteine (AdoHcy) at 2.0 and 2.1 A resolution, respectively, and results of mutagenesis and rRNA footprinting, and protein-substrate docking. We propose the mechanism of methylation of G1405 by Sgm and compare it with other m(7)G methyltransferases, revealing a surprising diversity of active sites and binding modes for the same basic reaction of RNA modification. This analysis can serve as a stepping stone towards developing drugs that would specifically block the activity of Arm methyltransferases and thereby re-sensitize pathogenic bacteria to aminoglycoside antibiotics.}, }
@article {pmid20191269, year = {2010}, author = {Brigulla, M and Wackernagel, W}, title = {Molecular aspects of gene transfer and foreign DNA acquisition in prokaryotes with regard to safety issues.}, journal = {Applied microbiology and biotechnology}, volume = {86}, number = {4}, pages = {1027-1041}, doi = {10.1007/s00253-010-2489-3}, pmid = {20191269}, issn = {1432-0614}, mesh = {Animals ; Bacteria/*genetics ; DNA, Bacterial/*genetics/metabolism ; Food Technology ; Gene Transfer Techniques ; *Gene Transfer, Horizontal ; Humans ; *Interspersed Repetitive Sequences ; Plants, Genetically Modified/genetics ; }, abstract = {Horizontal gene transfer (HGT) is part of prokaryotic life style and a major factor in evolution. In principle, any combinations of genetic information can be explored via HGT for effects on prokaryotic fitness. HGT mechanisms including transformation, conjugation, transduction, and variations of these plus the role of mobile genetic elements are summarized with emphasis on their potential to translocate foreign DNA. Complementarily, we discuss how foreign DNA can be integrated in recipient cells through homologous recombination (HR), illegitimate recombination (IR), and combinations of both, site-specific recombination, and the reconstitution of plasmids. Integration of foreign DNA by IR is very low, and combinations of IR with HR provide intermediate levels compared to the high frequency of homologous integration. A survey of studies on potential HGT from various transgenic plants indicates very rare transfer of foreign DNA. At the same time, in prokaryotic habitats, genes introduced into transgenic plants are abundant, and natural HGT frequencies are relatively high providing a greater chance for direct transfer instead of via transgenic plants. It is concluded that potential HGT from transgenic plants to prokaryotes is not expected to influence prokaryotic evolution and to have negative effects on human or animal health and the environment.}, }
@article {pmid20186266, year = {2010}, author = {, }, title = {Genome sequence of the pea aphid Acyrthosiphon pisum.}, journal = {PLoS biology}, volume = {8}, number = {2}, pages = {e1000313}, pmid = {20186266}, issn = {1545-7885}, support = {BB/F005342/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; K12 GM000708/GM/NIGMS NIH HHS/United States ; U54 HG003273/HG/NHGRI NIH HHS/United States ; 5-U54-HG003273/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Aphids/*genetics/growth &amp; development/microbiology ; Buchnera/genetics ; Gene Transfer, Horizontal/genetics ; Genome, Insect/*genetics ; Symbiosis/genetics/physiology ; }, abstract = {Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.}, }
@article {pmid20182523, year = {2010}, author = {Hemme, CL and Deng, Y and Gentry, TJ and Fields, MW and Wu, L and Barua, S and Barry, K and Tringe, SG and Watson, DB and He, Z and Hazen, TC and Tiedje, JM and Rubin, EM and Zhou, J}, title = {Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community.}, journal = {The ISME journal}, volume = {4}, number = {5}, pages = {660-672}, doi = {10.1038/ismej.2009.154}, pmid = {20182523}, issn = {1751-7370}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification/metabolism ; *Biodiversity ; Fresh Water/*microbiology ; Humans ; *Metagenomics ; Metals, Heavy/toxicity ; Nitric Acid/toxicity ; Organic Chemicals/toxicity ; Water Pollutants, Chemical/*toxicity ; }, abstract = {Understanding adaptation of biological communities to environmental change is a central issue in ecology and evolution. Metagenomic analysis of a stressed groundwater microbial community reveals that prolonged exposure to high concentrations of heavy metals, nitric acid and organic solvents (approximately 50 years) has resulted in a massive decrease in species and allelic diversity as well as a significant loss of metabolic diversity. Although the surviving microbial community possesses all metabolic pathways necessary for survival and growth in such an extreme environment, its structure is very simple, primarily composed of clonal denitrifying gamma- and beta-proteobacterial populations. The resulting community is overabundant in key genes conferring resistance to specific stresses including nitrate, heavy metals and acetone. Evolutionary analysis indicates that lateral gene transfer could have a key function in rapid response and adaptation to environmental contamination. The results presented in this study have important implications in understanding, assessing and predicting the impacts of human-induced activities on microbial communities ranging from human health to agriculture to environmental management, and their responses to environmental changes.}, }
@article {pmid20181243, year = {2010}, author = {Fondi, M and Bacci, G and Brilli, M and Papaleo, MC and Mengoni, A and Vaneechoutte, M and Dijkshoorn, L and Fani, R}, title = {Exploring the evolutionary dynamics of plasmids: the Acinetobacter pan-plasmidome.}, journal = {BMC evolutionary biology}, volume = {10}, number = {}, pages = {59}, pmid = {20181243}, issn = {1471-2148}, mesh = {Acinetobacter/*genetics ; Chromosomes, Bacterial ; Cluster Analysis ; Comparative Genomic Hybridization ; Computational Biology ; DNA, Bacterial/genetics ; *Evolution, Molecular ; Genes, Bacterial ; Genome, Bacterial ; Phylogeny ; Plasmids/*genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Prokaryotic plasmids have a dual importance in the microbial world: first they have a great impact on the metabolic functions of the host cell, providing additional traits that can be accumulated in the cell without altering the gene content of the bacterial chromosome. Additionally and/or alternatively, from a genome perspective, plasmids can provide a basis for genomic rearrangements via homologous recombination and so they can facilitate the loss or acquisition of genes during these events, which eventually may lead to horizontal gene transfer (HGT). Given their importance for conferring adaptive traits to the host organisms, the interest in plasmid sequencing is growing and now many complete plasmid sequences are available online.<br><br>RESULTS: By using the newly developed Blast2Network bioinformatic tool, a comparative analysis was performed on the plasmid and chromosome sequence data available for bacteria belonging to the genus Acinetobacter, an ubiquitous and clinically important group of gamma-proteobacteria. Data obtained showed that, although most of the plasmids lack mobilization and transfer functions, they have probably a long history of rearrangements with other plasmids and with chromosomes. Indeed, traces of transfers between different species can be disclosed.<br><br>CONCLUSIONS: We show that, by combining plasmid and chromosome similarity, identity based, network analysis, an evolutionary scenario can be described even for highly mobile genetic elements that lack extensively shared genes. In particular we found that transposases and selective pressure for mercury resistance seem to have played a pivotal role in plasmid evolution in Acinetobacter genomes sequenced so far.}, }
@article {pmid20180279, year = {2009}, author = {Ragan, MA}, title = {Thinking laterally about genomes.}, journal = {Genome informatics. International Conference on Genome Informatics}, volume = {23}, number = {1}, pages = {221-222}, pmid = {20180279}, issn = {0919-9454}, mesh = {*Gene Transfer, Horizontal ; *Genome ; }, abstract = {Perhaps the most-surprising discovery of the genome era has been the extent to which prokaryotic and many eukaryotic genomes incorporate genetic material from sources other than their parent(s). Lateral genetic transfer (LGT) among bacteria was first observed about 100 years ago, and is now accepted to underlie important phenomena including the spread of antibiotic resistance and ability to degrade xenobiotics. LGT is invoked, perhaps too readily, to explain a breadth of awkward data including compositional heterogeneity of genomes, disagreement among gene-sequence trees, and mismatch between physiology and systematics. At the same time many details of LGT remain unknown or controversial, and some key questions have scarcely been asked. Here I critically review what we think we know about the existence, extent, mechanism and impact of LGT; identify important open questions; and point to research directions that hold particular promise for elucidating the role of LGT in genome evolution. Evidence for LGT in nature is not only inferential but also direct, and potential vectors are ubiquitous. Genetic material can pass between diverse habitats and be significantly altered during residency in viruses, complicating the inference of donors, In prokaryotes about twice as many genes are interrupted by LGT as are transferred intact, and about 5Short protein domains can be privileged units of transfer. Unresolved phylogenetic issues include the correct null hypothesis, and genes as units of analysis. Themes are beginning to emerge regarding the effect of LGT on cellular networks, but I show why generalization is premature. LGT can associate with radical changes in physiology and ecological niche. Better quantitative models of genome evolution are needed, and theoretical frameworks remain to be developed for some observations including chromosome assembly by LGT.}, }
@article {pmid20178587, year = {2010}, author = {Ahmadinejad, N and Dagan, T and Gruenheit, N and Martin, W and Gabaldón, T}, title = {Evolution of spliceosomal introns following endosymbiotic gene transfer.}, journal = {BMC evolutionary biology}, volume = {10}, number = {}, pages = {57}, pmid = {20178587}, issn = {1471-2148}, mesh = {Animals ; Diatoms/genetics ; Eukaryota/genetics ; Gene Transfer, Horizontal ; Introns ; Mitochondria/genetics ; Phylogeny ; Plant Physiological Phenomena ; Plants/genetics ; Spliceosomes/*genetics ; Symbiosis ; }, abstract = {BACKGROUND: Spliceosomal introns are an ancient, widespread hallmark of eukaryotic genomes. Despite much research, many questions regarding the origin and evolution of spliceosomal introns remain unsolved, partly due to the difficulty of inferring ancestral gene structures. We circumvent this problem by using genes originated by endosymbiotic gene transfer, in which an intron-less structure at the time of the transfer can be assumed.<br><br>RESULTS: By comparing the exon-intron structures of 64 mitochondrial-derived genes that were transferred to the nucleus at different evolutionary periods, we can trace the history of intron gains in different eukaryotic lineages. Our results show that the intron density of genes transferred relatively recently to the nuclear genome is similar to that of genes originated by more ancient transfers, indicating that gene structure can be rapidly shaped by intron gain after the integration of the gene into the genome and that this process is mainly determined by forces acting specifically on each lineage. We analyze 12 cases of mitochondrial-derived genes that have been transferred to the nucleus independently in more than one lineage.<br><br>CONCLUSIONS: Remarkably, the proportion of shared intron positions that were gained independently in homologous genes is similar to that proportion observed in genes that were transferred prior to the speciation event and whose shared intron positions might be due to vertical inheritance. A particular case of parallel intron gain in the nad7 gene is discussed in more detail.}, }
@article {pmid20172033, year = {2010}, author = {Thiéry, O and Börstler, B and Ineichen, K and Redecker, D}, title = {Evolutionary dynamics of introns and homing endonuclease ORFs in a region of the large subunit of the mitochondrial rRNA in Glomus species (arbuscular mycorrhizal fungi, Glomeromycota).}, journal = {Molecular phylogenetics and evolution}, volume = {55}, number = {2}, pages = {599-610}, doi = {10.1016/j.ympev.2010.02.013}, pmid = {20172033}, issn = {1095-9513}, mesh = {Endonucleases/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Glomeromycota/classification/*genetics ; *Introns ; *Open Reading Frames ; Phylogeny ; Polymorphism, Genetic ; RNA/genetics ; RNA, Fungal/genetics ; RNA, Mitochondrial ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA ; }, abstract = {The large subunit of the mitochondrial ribosomal RNA genes (mtLSU) has previously been identified as a highly sensitive molecular marker for intraspecies diversity in the arbuscular mycorrhizal fungus Glomus intraradices. In this study, the respective region was analyzed in five species of Glomus (G. mosseae, G. geosporum, G. caledonium, G. clarum, G. coronatum) from the same major clade (Glomus group A), Glomus sp. ISCB 34 from the related Glomus group B and two species of Scutellospora. Results show low level of genetic polymorphism between related morphospecies. Introns homologous to those found in G. intraradices were detected as well as new ones, some of them containing putative ORFs for homing endonucleases (HEs). Introns without ORFs for HEs seem to have been inherited strictly vertically from the ancestors of Glomus groups A and B while other introns indicate occasional horizontal transfer and possibly maintenance, degeneration and loss together with their associated HE ORFs. Overall, we provide first insights into the evolutionary dynamics of introns and HEs in this ecologically important group of fungi, which was previously not analyzed in this respect.}, }
@article {pmid20170524, year = {2010}, author = {Rozhon, W and Petutschnig, E and Khan, M and Summers, DK and Poppenberger, B}, title = {Frequency and diversity of small cryptic plasmids in the genus Rahnella.}, journal = {BMC microbiology}, volume = {10}, number = {}, pages = {56}, pmid = {20170524}, issn = {1471-2180}, mesh = {Bacterial Proteins/genetics ; Base Sequence ; Cloning, Molecular ; Gene Transfer, Horizontal ; Models, Genetic ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Plasmids/chemistry/genetics/*isolation &amp; purification ; Rahnella/*genetics ; Sequence Alignment ; Vegetables/microbiology ; }, abstract = {BACKGROUND: Rahnella is a widely distributed genus belonging to the Enterobacteriaceae and frequently present on vegetables. Although Rahnella has interesting agro-economical and industrial properties and several strains possess antibiotic resistances and toxin genes which might spread within microbial communities, little is known about plasmids of this genus. Thus, we isolated a number of Rahnella strains and investigated their complements of small plasmids.<br><br>RESULTS: In total 53 strains were investigated and 11 plasmids observed. Seven belonged to the ColE1 family; one was ColE2-like and three shared homology to rolling circle plasmids. One of them belonged to the pC194/pUB110 family and two showed similarity to poorly characterised plasmid groups. The G+C content of two rolling circle plasmids deviated considerably from that of Rahnella, indicating that their usual hosts might belong to other genera. Most ColE1-like plasmids formed a subgroup within the ColE1 family that seems to be fairly specific for Rahnella. Intriguingly, the multimer resolution sites of all ColE1-like plasmids had the same orientation with respect to the origin of replication. This arrangement might be necessary to prevent inappropriate synthesis of a small regulatory RNA that regulates cell division. Although the ColE1-like plasmids did not possess any mobilisation system, they shared large parts with high sequence identity in coding and non-coding regions. In addition, highly homologous regions of plasmids isolated from Rahnella and the chromosomes of Erwinia tasmaniensis and Photorhabdus luminescens could be identified.<br><br>CONCLUSIONS: For the genus Rahnella we observed plasmid-containing isolates at a frequency of 19%, which is in the average range for Enterobacteriaceae. These plasmids belonged to different groups with members of the ColE1-family most frequently found. Regions of striking sequence homology of plasmids and bacterial chromosomes highlight the importance of plasmids for lateral gene transfer (including chromosomal sequences) to distinct genera.}, }
@article {pmid20169193, year = {2010}, author = {Hecht, MM and Nitz, N and Araujo, PF and Sousa, AO and Rosa, Ade C and Gomes, DA and Leonardecz, E and Teixeira, AR}, title = {Inheritance of DNA transferred from American trypanosomes to human hosts.}, journal = {PloS one}, volume = {5}, number = {2}, pages = {e9181}, pmid = {20169193}, issn = {1932-6203}, mesh = {Adolescent ; Adult ; Aged ; Animals ; Brazil ; Chagas Disease/*genetics/parasitology ; Child ; DNA, Protozoan/*genetics ; Female ; *Gene Transfer, Horizontal ; Genome, Human/genetics ; Geography ; Host-Parasite Interactions/genetics ; Humans ; In Situ Hybridization, Fluorescence ; Long Interspersed Nucleotide Elements/genetics ; Male ; Middle Aged ; Molecular Sequence Data ; Pedigree ; Recombination, Genetic ; Sequence Analysis, DNA ; Trypanosoma cruzi/*genetics/physiology ; U937 Cells ; Young Adult ; }, abstract = {Interspecies DNA transfer is a major biological process leading to the accumulation of mutations inherited by sexual reproduction among eukaryotes. Lateral DNA transfer events and their inheritance has been challenging to document. In this study we modified a thermal asymmetric interlaced PCR by using additional targeted primers, along with Southern blots, fluorescence techniques, and bioinformatics, to identify lateral DNA transfer events from parasite to host. Instances of naturally occurring human infections by Trypanosoma cruzi are documented, where mitochondrial minicircles integrated mainly into retrotransposable LINE-1 of various chromosomes. The founders of five families show minicircle integrations that were transferred vertically to their progeny. Microhomology end-joining of 6 to 22 AC-rich nucleotide repeats in the minicircles and host DNA mediates foreign DNA integration. Heterogeneous minicircle sequences were distributed randomly among families, with diversity increasing due to subsequent rearrangement of inserted fragments. Mosaic recombination and hitchhiking on retrotransposition events to different loci were more prevalent in germ line as compared to somatic cells. Potential new genes, pseudogenes, and knockouts were identified. A pathway of minicircle integration and maintenance in the host genome is suggested. Thus, infection by T. cruzi has the unexpected consequence of increasing human genetic diversity, and Chagas disease may be a fortuitous share of negative selection. This demonstration of contemporary transfer of eukaryotic DNA to the human genome and its subsequent inheritance by descendants introduces a significant change in the scientific concept of evolutionary biology and medicine.}, }
@article {pmid20167135, year = {2011}, author = {Harris, J}, title = {Taking the "human" out of human rights.}, journal = {Cambridge quarterly of healthcare ethics : CQ : the international journal of healthcare ethics committees}, volume = {20}, number = {1}, pages = {9-20}, doi = {10.1017/S0963180109990570}, pmid = {20167135}, issn = {1469-2147}, support = {087439/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Biological Evolution ; Biomedical Enhancement/*ethics ; *Consciousness ; *Diet ; Food ; *Gene Transfer, Horizontal ; *Human Rights ; Humans ; *Reproduction ; Social Justice ; Transplantation, Heterologous ; Vaccines ; }, }
@article {pmid20163713, year = {2010}, author = {Baldo, L and Desjardins, CA and Russell, JA and Stahlhut, JK and Werren, JH}, title = {Accelerated microevolution in an outer membrane protein (OMP) of the intracellular bacteria Wolbachia.}, journal = {BMC evolutionary biology}, volume = {10}, number = {}, pages = {48}, pmid = {20163713}, issn = {1471-2148}, mesh = {Animals ; Arthropods/immunology/microbiology/physiology ; Bacterial Outer Membrane Proteins/chemistry/*genetics/immunology ; *Evolution, Molecular ; Symbiosis ; Wolbachia/*genetics ; }, abstract = {BACKGROUND: Outer membrane proteins (OMPs) of Gram-negative bacteria are key players in the biology of bacterial-host interactions. However, while considerable attention has been given to OMPs of vertebrate pathogens, relatively little is known about the role of these proteins in bacteria that primarily infect invertebrates. One such OMP is found in the intracellular bacteria Wolbachia, which are widespread symbionts of arthropods and filarial nematodes. Recent experimental studies have shown that the Wolbachia surface protein (WSP) can trigger host immune responses and control cell death programming in humans, suggesting a key role of WSP for establishment and persistence of the symbiosis in arthropods.<br><br>RESULTS: Here we performed an analysis of 515 unique alleles found in 831 Wolbachia isolates, to investigate WSP structure, microevolution and population genetics. WSP shows an eight-strand transmembrane beta-barrel structure with four extracellular loops containing hypervariable regions (HVRs). A clustering approach based upon patterns of HVR haplotype diversity was used to group similar WSP sequences and to estimate the relative contribution of mutation and recombination during early stages of protein divergence. Results indicate that although point mutations generate most of the new protein haplotypes, recombination is a predominant force triggering diversity since the very first steps of protein evolution, causing at least 50% of the total amino acid variation observed in recently diverged proteins. Analysis of synonymous variants indicates that individual WSP protein types are subject to a very rapid turnover and that HVRs can accommodate a virtually unlimited repertoire of peptides. Overall distribution of WSP across hosts supports a non-random association of WSP with the host genus, although extensive horizontal transfer has occurred also in recent times.<br><br>CONCLUSIONS: In OMPs of vertebrate pathogens, large recombination impact, positive selection, reduced structural and compositional constraints, and extensive lateral gene transfer are considered hallmarks of evolution in response to the adaptive immune system. However, Wolbachia do not infect vertebrates. Here we predict that the rapid turnover of WSP loop motifs could aid in evading or inhibiting the invertebrate innate immune response. Overall, these features identify WSP as a strong candidate for future studies of host-Wolbachia interactions that affect establishment and persistence of this widespread endosymbiosis.}, }
@article {pmid20161777, year = {2010}, author = {Rioux, JB and Philippe, N and Pereira, S and Pignol, D and Wu, LF and Ginet, N}, title = {A second actin-like MamK protein in Magnetospirillum magneticum AMB-1 encoded outside the genomic magnetosome island.}, journal = {PloS one}, volume = {5}, number = {2}, pages = {e9151}, pmid = {20161777}, issn = {1932-6203}, mesh = {Actin Cytoskeleton/metabolism/ultrastructure ; Actins/genetics/*metabolism/ultrastructure ; Amino Acid Sequence ; Bacterial Proteins/genetics/*metabolism/ultrastructure ; Blotting, Western ; DNA, Bacterial/genetics ; Gene Expression Regulation, Bacterial ; Genome, Bacterial/genetics ; Genomic Islands/genetics ; Kinetics ; Magnetosomes/genetics/*metabolism ; Magnetospirillum/genetics/*metabolism ; Microscopy, Electron, Transmission ; Molecular Sequence Data ; Mutation ; Operon/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; }, abstract = {Magnetotactic bacteria are able to swim navigating along geomagnetic field lines. They synthesize ferromagnetic nanocrystals that are embedded in cytoplasmic membrane invaginations forming magnetosomes. Regularly aligned in the cytoplasm along cytoskeleton filaments, the magnetosome chain effectively forms a compass needle bestowing on bacteria their magnetotactic behaviour. A large genomic island, conserved among magnetotactic bacteria, contains the genes potentially involved in magnetosome formation. One of the genes, mamK has been described as encoding a prokaryotic actin-like protein which when it polymerizes forms in the cytoplasm filamentous structures that provide the scaffold for magnetosome alignment. Here, we have identified a series of genes highly similar to the mam genes in the genome of Magnetospirillum magneticum AMB-1. The newly annotated genes are clustered in a genomic islet distinct and distant from the known magnetosome genomic island and most probably acquired by lateral gene transfer rather than duplication. We focused on a mamK-like gene whose product shares 54.5% identity with the actin-like MamK. Filament bundles of polymerized MamK-like protein were observed in vitro with electron microscopy and in vivo in E. coli cells expressing MamK-like-Venus fusions by fluorescence microscopy. In addition, we demonstrate that mamK-like is transcribed in AMB-1 wild-type and DeltamamK mutant cells and that the actin-like filamentous structures observed in the DeltamamK strain are probably MamK-like polymers. Thus MamK-like is a new member of the prokaryotic actin-like family. This is the first evidence of a functional mam gene encoded outside the magnetosome genomic island.}, }
@article {pmid20159551, year = {2010}, author = {Kohanski, MA and DePristo, MA and Collins, JJ}, title = {Sublethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis.}, journal = {Molecular cell}, volume = {37}, number = {3}, pages = {311-320}, pmid = {20159551}, issn = {1097-4164}, support = {DP1 OD003644/OD/NIH HHS/United States ; DP1 OD003644-03/OD/NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Amino Acid Sequence ; Anti-Bacterial Agents/*pharmacology ; Base Sequence ; Drug Resistance, Multiple, Bacterial/*drug effects/genetics ; Escherichia coli/*drug effects/genetics/metabolism ; Gene Transfer, Horizontal/drug effects ; Microbial Sensitivity Tests ; Molecular Sequence Data ; *Mutagenesis ; Reactive Oxygen Species/metabolism ; Sequence Alignment ; Sequence Analysis, Protein ; }, abstract = {Antibiotic resistance arises through mechanisms such as selection of naturally occurring resistant mutants and horizontal gene transfer. Recently, oxidative stress has been implicated as one of the mechanisms whereby bactericidal antibiotics kill bacteria. Here, we show that sublethal levels of bactericidal antibiotics induce mutagenesis, resulting in heterogeneous increases in the minimum inhibitory concentration for a range of antibiotics, irrespective of the drug target. This increase in mutagenesis correlates with an increase in ROS and is prevented by the ROS scavenger thiourea and by anaerobic conditions, indicating that sublethal concentrations of antibiotics induce mutagenesis by stimulating the production of ROS. We demonstrate that these effects can lead to mutant strains that are sensitive to the applied antibiotic but resistant to other antibiotics. This work establishes a radical-based molecular mechanism whereby sublethal levels of antibiotics can lead to multidrug resistance, which has important implications for the widespread use and misuse of antibiotics.}, }
@article {pmid20159549, year = {2010}, author = {Kaufmann, BB and Hung, DT}, title = {The fast track to multidrug resistance.}, journal = {Molecular cell}, volume = {37}, number = {3}, pages = {297-298}, doi = {10.1016/j.molcel.2010.01.027}, pmid = {20159549}, issn = {1097-4164}, mesh = {Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Multiple, Bacterial/*drug effects/genetics ; Escherichia coli/*drug effects/genetics ; Gene Transfer, Horizontal/drug effects ; Microbial Sensitivity Tests ; Mutagenesis/drug effects ; }, abstract = {In this issue of Molecular Cell, Kohanski et al. (2010) demonstrate that even subinhibitory concentrations of bactericidal antibiotics result in the generation of reactive oxygen species, leading to an increase in mutation rate and the emergence of multidrug-resistant bacterial strains.}, }
@article {pmid20158921, year = {2010}, author = {Elhaik, E and Graur, D and Josić, K}, title = {'Genome order index' should not be used for defining compositional constraints in nucleotide sequences--a case study of the Z-curve.}, journal = {Biology direct}, volume = {5}, number = {}, pages = {10}, pmid = {20158921}, issn = {1745-6150}, mesh = {Base Composition/*genetics ; Base Sequence/*genetics ; Computer Simulation ; Genome, Bacterial/*genetics ; *Models, Genetic ; }, abstract = {BACKGROUND: The Z-curve is a three dimensional representation of DNA sequences proposed over a decade ago and has been extensively applied to sequence segmentation, horizontal gene transfer detection, and sequence analysis. Based on the Z-curve, a "genome order index," was proposed, which is defined as S = a2+ c2+t2+g2, where a, c, t, and g are the nucleotide frequencies of A, C, T, and G, respectively. This index was found to be smaller than 1/3 for almost all tested genomes, which was taken as support for the existence of a constraint on genome composition. A geometric explanation for this constraint has been suggested. Each genome was represented by a point P whose distance from the four faces of a regular tetrahedron was given by the frequencies a, c, t, and g. They claimed that an inscribed sphere of radius r = 1/ square root 3 contains almost all points corresponding to various genomes, implying that S <r2. The distribution of the points P obtained by S was studied using the Z-curve.<br><br>RESULTS: In this work, we studied the basic properties of the Z-curve using the "genome order index" as a case study. We show that (1) the calculation of the radius of the inscribed sphere of a regular tetrahedron is incorrect, (2) the S index is narrowly distributed, (3) based on the second parity rule, the S index can be derived directly from the Shannon entropy and is, therefore, redundant, and (4) the Z-curve suffers from over dimensionality, and the dimension stands for GC content alone suffices to represent any given genome.<br><br>CONCLUSION: The "genome order index" S does not represent a constraint on nucleotide composition. Moreover, S can be easily computed from the Gini-Simpson index and be directly derived from entropy and is redundant. Overall, the Z-curve and S are over-complicated measures to GC content and Shannon H index, respectively.}, }
@article {pmid20156992, year = {2010}, author = {Fozo, EM and Makarova, KS and Shabalina, SA and Yutin, N and Koonin, EV and Storz, G}, title = {Abundance of type I toxin-antitoxin systems in bacteria: searches for new candidates and discovery of novel families.}, journal = {Nucleic acids research}, volume = {38}, number = {11}, pages = {3743-3759}, pmid = {20156992}, issn = {1362-4962}, support = {//Intramural NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacillus subtilis/genetics ; Bacterial Proteins/chemistry/classification/genetics ; Bacterial Toxins/classification/*genetics ; Enterococcus faecalis/genetics ; Escherichia coli O157/genetics ; Genome, Bacterial ; Genomics ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA, Antisense/chemistry/*genetics ; RNA, Bacterial/chemistry/classification/*genetics ; RNA, Untranslated/chemistry/classification/genetics ; Sequence Homology, Amino Acid ; Streptococcus pneumoniae/genetics ; Tandem Repeat Sequences ; Thermodynamics ; }, abstract = {Small, hydrophobic proteins whose synthesis is repressed by small RNAs (sRNAs), denoted type I toxin-antitoxin modules, were first discovered on plasmids where they regulate plasmid stability, but were subsequently found on a few bacterial chromosomes. We used exhaustive PSI-BLAST and TBLASTN searches across 774 bacterial genomes to identify homologs of known type I toxins. These searches substantially expanded the collection of predicted type I toxins, revealed homology of the Ldr and Fst toxins, and suggested that type I toxin-antitoxin loci are not spread by horizontal gene transfer. To discover novel type I toxin-antitoxin systems, we developed a set of search parameters based on characteristics of known loci including the presence of tandem repeats and clusters of charged and bulky amino acids at the C-termini of short proteins containing predicted transmembrane regions. We detected sRNAs for three predicted toxins from enterohemorrhagic Escherichia coli and Bacillus subtilis, and showed that two of the respective proteins indeed are toxic when overexpressed. We also demonstrated that the local free-energy minima of RNA folding can be used to detect the positions of the sRNA genes. Our results suggest that type I toxin-antitoxin modules are much more widely distributed among bacteria than previously appreciated.}, }
@article {pmid20154113, year = {2010}, author = {Gontang, EA and Gaudêncio, SP and Fenical, W and Jensen, PR}, title = {Sequence-based analysis of secondary-metabolite biosynthesis in marine actinobacteria.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {8}, pages = {2487-2499}, pmid = {20154113}, issn = {1098-5336}, support = {R37 CA044848/CA/NCI NIH HHS/United States ; GM085770/GM/NIGMS NIH HHS/United States ; R01 CA044848/CA/NCI NIH HHS/United States ; R01 GM085770/GM/NIGMS NIH HHS/United States ; CA44848/CA/NCI NIH HHS/United States ; }, mesh = {Actinobacteria/*classification/genetics/*metabolism ; Cluster Analysis ; DNA Primers/genetics ; DNA, Bacterial/*genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genotype ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {A diverse collection of 60 marine-sediment-derived Actinobacteria representing 52 operational taxonomic units was screened by PCR for genes associated with secondary-metabolite biosynthesis. Three primer sets were employed to specifically target adenylation domains associated with nonribosomal peptide synthetases (NRPSs) and ketosynthase (KS) domains associated with type I modular, iterative, hybrid, and enediyne polyketide synthases (PKSs). In total, two-thirds of the strains yielded a sequence-verified PCR product for at least one of these biosynthetic types. Genes associated with enediyne biosynthesis were detected in only two genera, while 88% of the ketosynthase sequences shared greatest homology with modular PKSs. Positive strains included representatives of families not traditionally associated with secondary-metabolite production, including the Corynebacteriaceae, Gordoniaceae, Intrasporangiaceae, and Micrococcaceae. In four of five cases where phylogenetic analyses of KS sequences revealed close evolutionary relationships to genes associated with experimentally characterized biosynthetic pathways, secondary-metabolite production was accurately predicted. Sequence clustering patterns were used to provide an estimate of PKS pathway diversity and to assess the biosynthetic richness of individual strains. The detection of highly similar KS sequences in distantly related strains provided evidence of horizontal gene transfer, while control experiments designed to amplify KS sequences from Salinispora arenicola strain CNS-205, for which a genome sequence is available, led to the detection of 70% of the targeted PKS pathways. The results provide a bioinformatic assessment of secondary-metabolite biosynthetic potential that can be applied in the absence of fully assembled pathways or genome sequences. The rapid identification of strains that possess the greatest potential to produce new secondary metabolites along with those that produce known compounds can be used to improve the process of natural-product discovery by providing a method to prioritize strains for fermentation studies and chemical analysis.}, }
@article {pmid20152048, year = {2010}, author = {Hill, T and Nordström, KJ and Thollesson, M and Säfström, TM and Vernersson, AK and Fredriksson, R and Schiöth, HB}, title = {SPRIT: Identifying horizontal gene transfer in rooted phylogenetic trees.}, journal = {BMC evolutionary biology}, volume = {10}, number = {}, pages = {42}, pmid = {20152048}, issn = {1471-2148}, mesh = {Algorithms ; *Gene Transfer, Horizontal ; *Phylogeny ; *Software ; }, abstract = {BACKGROUND: Phylogenetic trees based on sequences from a set of taxa can be incongruent due to horizontal gene transfer (HGT). By identifying the HGT events, we can reconcile the gene trees and derive a taxon tree that adequately represents the species' evolutionary history. One HGT can be represented by a rooted Subtree Prune and Regraft (RSPR) operation and the number of RSPRs separating two trees corresponds to the minimum number of HGT events. Identifying the minimum number of RSPRs separating two trees is NP-hard, but the problem can be reduced to fixed parameter tractable. A number of heuristic and two exact approaches to identifying the minimum number of RSPRs have been proposed. This is the first implementation delivering an exact solution as well as the intermediate trees connecting the input trees.<br><br>RESULTS: We present the SPR Identification Tool (SPRIT), a novel algorithm that solves the fixed parameter tractable minimum RSPR problem and its GPL licensed Java implementation. The algorithm can be used in two ways, exhaustive search that guarantees the minimum RSPR distance and a heuristic approach that guarantees finding a solution, but not necessarily the minimum one. We benchmarked SPRIT against other software in two different settings, small to medium sized trees i.e. five to one hundred taxa and large trees i.e. thousands of taxa. In the small to medium tree size setting with random artificial incongruence, SPRIT's heuristic mode outperforms the other software by always delivering a solution with a low overestimation of the RSPR distance. In the large tree setting SPRIT compares well to the alternatives when benchmarked on finding a minimum solution within a reasonable time. SPRIT presents both the minimum RSPR distance and the intermediate trees.<br><br>CONCLUSIONS: When used in exhaustive search mode, SPRIT identifies the minimum number of RSPRs needed to reconcile two incongruent rooted trees. SPRIT also performs quick approximations of the minimum RSPR distance, which are comparable to, and often better than, purely heuristic solutions. Put together, SPRIT is an excellent tool for identification of HGT events and pinpointing which taxa have been involved in HGT.}, }
@article {pmid20149099, year = {2010}, author = {Johnsen, PJ and Levin, BR}, title = {Adjusting to alien genes.}, journal = {Molecular microbiology}, volume = {75}, number = {5}, pages = {1061-1063}, doi = {10.1111/j.1365-2958.2010.07075.x}, pmid = {20149099}, issn = {1365-2958}, support = {R01 GM091875/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Biological ; Bacterial Proteins/*genetics ; *Gene Transfer, Horizontal ; Ribosomal Proteins/*genetics ; Salmonella typhimurium/*genetics/physiology ; }, abstract = {From the perspective of a bacterium, higher eukaryotes are oversexed, unadventurous and reproduce in an inconvenient way. Sex, or recombination following horizontal gene transfer (HGT) events, to be less provocative, is a rare event for a bacterium, but a potentially profound one. Through HGT a bacterium can acquire DNA from distant as well as closely related species and, thereby, instantly obtain genes that encode novel functions or replace its existing genes with better ones. While there is an abundance of retrospective evidence for HGT in bacteria, there has been little consideration of the dynamics of the process. In this issue of Molecular Microbiology Lind et al. explore these dynamics theoretically, and then experimentally by substituting Salmonella Typhimurium ribosomal genes with orthologues from various microbial origins. The authors show that the majority of these newly acquired ribosomal proteins reduce fitness in S. Typhimurium, but within short order (40-250 generations) subsequent evolution will mitigate the fitness costs of the alien alleles. The presented results suggest that that at least the initial phase of adapting to alien genes of this informational core ilk is not by changing them but rather by increasing their level of expression by gene amplification. Lind et al. argue that their results provide an explanation as to why duplicated genes are overrepresented among horizontally transferred genes.}, }
@article {pmid20146413, year = {2009}, author = {Suntsov, VV and Suntsova, NI}, title = {[Principles of speciation of the plague causative agent Yersinia pestis: gradualism or saltation?].}, journal = {Izvestiia Akademii nauk. Seriia biologicheskaia}, volume = {}, number = {6}, pages = {645-653}, pmid = {20146413}, issn = {1026-3470}, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial/*physiology ; Humans ; Plague/genetics ; Plasmids/*genetics ; Yersinia pestis/*genetics ; Yersinia pseudotuberculosis/genetics ; }, abstract = {The saltation origin of the causative agent of the plague Yersinia pestis from the pseudotuberculosis microbe Y. pseudotuberculosis O:1b has been proclaimed in recent investigations on molecular genetics. The speciation process in this case is proposed to be connected with horizontal inclusion of exogenous genetic structures (such as specific plasmids pFra and pPst) into the genome of the ancestral form. The alternative "Darwinian" model of the gradual origin of the plague agent is proposed based on ecological factors. The comparison of two evolutionary scenarios, saltation and gradual, is performed; the latter seems more likely.}, }
@article {pmid20145021, year = {2010}, author = {Kaneko, S and Itaya, M}, title = {Designed horizontal transfer of stable giant DNA released from Escherichia coli.}, journal = {Journal of biochemistry}, volume = {147}, number = {6}, pages = {819-822}, doi = {10.1093/jb/mvq012}, pmid = {20145021}, issn = {1756-2651}, mesh = {Bacillus subtilis/*genetics ; Cloning, Molecular/*methods ; Culture Media ; DNA, Bacterial/genetics ; Deoxyribonuclease I/pharmacology ; Escherichia coli/*genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial ; *Plasmids/genetics/metabolism ; *Transformation, Bacterial ; }, abstract = {DNA in the environment is a source to mediate horizontal gene transfer (HGT). Present molecular cloning methods are based on this HGT principle. However, DNA in the extracellular environment, particularly with high molecular-weight, is thought to be prone to shearing or digestion by nucleases. Here we discovered that extracellular plasmid DNA released from lysed Escherichia coli remained intact and stable. Furthermore, it was demonstrated that plasmids up to 100 kb in size were taken up by co-present competent Bacillus subtilis cells. The detailed kinetics of the process together with sensitivity to added DNase I indicated that plasmid DNA released from lysed E. coli into the culture medium was stable enough for quantitative efficacy in the transformation of B. subtilis. Our results will be useful for the development of methods to transfer giant DNAs from general host E. coli without their biochemical purification.}, }
@article {pmid20144182, year = {2010}, author = {Carvalho, FM and Souza, RC and Barcellos, FG and Hungria, M and Vasconcelos, AT}, title = {Genomic and evolutionary comparisons of diazotrophic and pathogenic bacteria of the order Rhizobiales.}, journal = {BMC microbiology}, volume = {10}, number = {}, pages = {37}, pmid = {20144182}, issn = {1471-2180}, mesh = {Alphaproteobacteria/*genetics ; *Evolution, Molecular ; Genes, Bacterial ; Genome, Bacterial ; Models, Genetic ; Multigene Family ; Phylogeny ; Symbiosis/genetics ; Virulence/genetics ; }, abstract = {BACKGROUND: Species belonging to the Rhizobiales are intriguing and extensively researched for including both bacteria with the ability to fix nitrogen when in symbiosis with leguminous plants and pathogenic bacteria to animals and plants. Similarities between the strategies adopted by pathogenic and symbiotic Rhizobiales have been described, as well as high variability related to events of horizontal gene transfer. Although it is well known that chromosomal rearrangements, mutations and horizontal gene transfer influence the dynamics of bacterial genomes, in Rhizobiales, the scenario that determine pathogenic or symbiotic lifestyle are not clear and there are very few studies of comparative genomic between these classes of prokaryotic microorganisms trying to delineate the evolutionary characterization of symbiosis and pathogenesis.<br><br>RESULTS: Non-symbiotic nitrogen-fixing bacteria and bacteria involved in bioremediation closer to symbionts and pathogens in study may assist in the origin and ancestry genes and the gene flow occurring in Rhizobiales. The genomic comparisons of 19 species of Rhizobiales, including nitrogen-fixing, bioremediators and pathogens resulted in 33 common clusters to biological nitrogen fixation and pathogenesis, 15 clusters exclusive to all nitrogen-fixing bacteria and bacteria involved in bioremediation, 13 clusters found in only some nitrogen-fixing and bioremediation bacteria, 01 cluster exclusive to some symbionts, and 01 cluster found only in some pathogens analyzed. In BBH performed to all strains studied, 77 common genes were obtained, 17 of which were related to biological nitrogen fixation and pathogenesis. Phylogenetic reconstructions for Fix, Nif, Nod, Vir, and Trb showed possible horizontal gene transfer events, grouping species of different phenotypes.<br><br>CONCLUSIONS: The presence of symbiotic and virulence genes in both pathogens and symbionts does not seem to be the only determinant factor for lifestyle evolution in these microorganisms, although they may act in common stages of host infection. The phylogenetic analysis for many distinct operons involved in these processes emphasizes the relevance of horizontal gene transfer events in the symbiotic and pathogenic similarity.}, }
@article {pmid20143353, year = {2010}, author = {Huiqun, D and Xiaofeng, C and Jianxin, P and Huazhu, H and Koji, I and Aiying, L}, title = {Practical procedures for genetic manipulation systems for medermycin-producing Streptomyces sp. AM-7161.}, journal = {Journal of basic microbiology}, volume = {50}, number = {3}, pages = {299-301}, doi = {10.1002/jobm.200900240}, pmid = {20143353}, issn = {1521-4028}, mesh = {Anti-Bacterial Agents/*metabolism ; Conjugation, Genetic ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Genetic Engineering/*methods ; Genetic Vectors ; Genetics, Microbial/*methods ; Molecular Biology/*methods ; Naphthoquinones/metabolism ; Plasmids ; Protoplasts ; Streptomyces/*genetics/*metabolism ; Transformation, Bacterial ; }, abstract = {Streptomyces sp. AM-7161 is a producer of an aromatic polyketide medermycin with strong antibacterial and antitumor activity. It has been inefficient to perform genetic manipulations in this strain, which heavily hinders the genetic analysis of some interesting problems concerning tailoring modifications in medermycin biosynthesis. Here, condition optimizations of sporulation and mycelium growth of this strain as well as protoplast preparation and regeneration were conducted systematically. Based on these results, protoplast transformation system was established, and two types of foreign plasmids (integrative and auto-replicating) were efficiently introduced into this strain. Additionally, a conjugation system to mediate plasmid transfer between Escherichia coli and Streptomyces sp. AM-7161 was also optimized and established. These results provide the practical procedures to perform more convenient genetic analysis of medermycin biosynthesis in this strain.}, }
@article {pmid20140207, year = {2010}, author = {Henn, MR and Sullivan, MB and Stange-Thomann, N and Osburne, MS and Berlin, AM and Kelly, L and Yandava, C and Kodira, C and Zeng, Q and Weiand, M and Sparrow, T and Saif, S and Giannoukos, G and Young, SK and Nusbaum, C and Birren, BW and Chisholm, SW}, title = {Analysis of high-throughput sequencing and annotation strategies for phage genomes.}, journal = {PloS one}, volume = {5}, number = {2}, pages = {e9083}, pmid = {20140207}, issn = {1932-6203}, mesh = {Bacteriophages/*genetics ; Computational Biology/methods ; DNA, Viral/chemistry/*genetics/metabolism ; Deoxyribonucleases/metabolism ; Genome, Viral/*genetics ; Molecular Sequence Data ; Open Reading Frames/genetics ; Prochlorococcus/virology ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: Bacterial viruses (phages) play a critical role in shaping microbial populations as they influence both host mortality and horizontal gene transfer. As such, they have a significant impact on local and global ecosystem function and human health. Despite their importance, little is known about the genomic diversity harbored in phages, as methods to capture complete phage genomes have been hampered by the lack of knowledge about the target genomes, and difficulties in generating sufficient quantities of genomic DNA for sequencing. Of the approximately 550 phage genomes currently available in the public domain, fewer than 5% are marine phage.<br><br>To advance the study of phage biology through comparative genomic approaches we used marine cyanophage as a model system. We compared DNA preparation methodologies (DNA extraction directly from either phage lysates or CsCl purified phage particles), and sequencing strategies that utilize either Sanger sequencing of a linker amplification shotgun library (LASL) or of a whole genome shotgun library (WGSL), or 454 pyrosequencing methods. We demonstrate that genomic DNA sample preparation directly from a phage lysate, combined with 454 pyrosequencing, is best suited for phage genome sequencing at scale, as this method is capable of capturing complete continuous genomes with high accuracy. In addition, we describe an automated annotation informatics pipeline that delivers high-quality annotation and yields few false positives and negatives in ORF calling.<br><br>CONCLUSIONS/SIGNIFICANCE: These DNA preparation, sequencing and annotation strategies enable a high-throughput approach to the burgeoning field of phage genomics.}, }
@article {pmid20139183, year = {2010}, author = {Rusniok, C and Couvé, E and Da Cunha, V and El Gana, R and Zidane, N and Bouchier, C and Poyart, C and Leclercq, R and Trieu-Cuot, P and Glaser, P}, title = {Genome sequence of Streptococcus gallolyticus: insights into its adaptation to the bovine rumen and its ability to cause endocarditis.}, journal = {Journal of bacteriology}, volume = {192}, number = {8}, pages = {2266-2276}, pmid = {20139183}, issn = {1098-5530}, mesh = {Animals ; Cattle ; Endocarditis/*microbiology ; Genome, Bacterial/genetics/*physiology ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Polysaccharides/metabolism ; Streptococcus/classification/*genetics/metabolism/*pathogenicity ; Vitamins/metabolism ; }, abstract = {Streptococcus gallolyticus (formerly known as Streptococcus bovis biotype I) is an increasing cause of endocarditis among streptococci and frequently associated with colon cancer. S. gallolyticus is part of the rumen flora but also a cause of disease in ruminants as well as in birds. Here we report the complete nucleotide sequence of strain UCN34, responsible for endocarditis in a patient also suffering from colon cancer. Analysis of the 2,239 proteins encoded by its 2,350-kb-long genome revealed unique features among streptococci, probably related to its adaptation to the rumen environment and its capacity to cause endocarditis. S. gallolyticus has the capacity to use a broad range of carbohydrates of plant origin, in particular to degrade polysaccharides derived from the plant cell wall. Its genome encodes a large repertoire of transporters and catalytic activities, like tannase, phenolic compounds decarboxylase, and bile salt hydrolase, that should contribute to the detoxification of the gut environment. Furthermore, S. gallolyticus synthesizes all 20 amino acids and more vitamins than any other sequenced Streptococcus species. Many of the genes encoding these specific functions were likely acquired by lateral gene transfer from other bacterial species present in the rumen. The surface properties of strain UCN34 may also contribute to its virulence. A polysaccharide capsule might be implicated in resistance to innate immunity defenses, and glucan mucopolysaccharides, three types of pili, and collagen binding proteins may play a role in adhesion to tissues in the course of endocarditis.}, }
@article {pmid20138928, year = {2010}, author = {Mairhofer, J and Cserjan-Puschmann, M and Striedner, G and Nöbauer, K and Razzazi-Fazeli, E and Grabherr, R}, title = {Marker-free plasmids for gene therapeutic applications--lack of antibiotic resistance gene substantially improves the manufacturing process.}, journal = {Journal of biotechnology}, volume = {146}, number = {3}, pages = {130-137}, doi = {10.1016/j.jbiotec.2010.01.025}, pmid = {20138928}, issn = {1873-4863}, mesh = {Drug Resistance, Bacterial/*genetics ; Escherichia coli/*genetics ; Genetic Enhancement/*methods ; Genetic Markers/genetics ; Genetic Therapy/*methods ; Plasmids/*genetics ; Recombinant Proteins/*genetics ; }, abstract = {Plasmid DNA is being considered as a promising alternative to traditional protein vaccines or viral delivery methods for gene therapeutic applications. DNA-based products are highly flexible, stable, are easily stored and can be manufactured on a large scale. Although, much safer than viral approaches, issues have been raised with regard to safety due to possible integration of plasmid DNA into cellular DNA or spread of antibiotic resistance genes to intestinal bacteria by horizontal gene transfer. Accordingly, there is interest in methods for the production of plasmid DNA that lacks the antibiotic resistance gene to further improve their safety profile. Here, we report for the first time the gram-scale manufacturing of a minimized plasmid that is devoid of any additional sequence elements on the plasmid backbone, and merely consists of the target expression cassette and the bacterial origin of replication. Three different host/vector combinations were cultivated in a fed-batch fermentation process, comparing the progenitor strain JM108 to modified strains JM108murselect, hosting a plasmid either containing the aminoglycoside phosphotransferase which provides kanamycin resistance, or a marker-free variant of the same plasmid. The metabolic load exerted by expression of the aminoglycoside phosphotransferase was monitored by measuring ppGpp- and cAMP-levels. Moreover, we revealed that JM108 is deficient of the Lon protease and thereby refined the genotype of JM108. The main consequences of Lon-deficiency with regard to plasmid DNA production are discussed herein. Additionally, we found that the expression of the aminoglycoside phosphotransferase, conferring resistance to kanamycin, was very high in plasmid DNA producing processes that actually inclusion bodies were formed. Thereby, a severe metabolic load on the host cell was imposed, detrimental for overall plasmid yield. Hence, deleting the antibiotic resistance gene from the vector backbone is not only beneficial with regards to safety and potency of the end-product but also regarding the overall process performance.}, }
@article {pmid20134251, year = {2010}, author = {Kim, SE and Moon, JS and Kim, JK and Choi, WS and Lee, SH and Kim, SU}, title = {Investigation of possible horizontal gene transfer from transgenic rice to soil microorganisms in paddy rice field.}, journal = {Journal of microbiology and biotechnology}, volume = {20}, number = {1}, pages = {187-192}, pmid = {20134251}, issn = {1017-7825}, mesh = {*Gene Transfer, Horizontal ; Glucosyltransferases/*genetics/metabolism ; Oryza/enzymology/*genetics ; Plant Proteins/*genetics/metabolism ; Plants, Genetically Modified/enzymology/genetics ; Soil/*analysis ; *Soil Microbiology ; }, abstract = {In order to monitor the possibility of horizontal gene transfer between transgenic rice and microorganisms in paddy rice field, the gene flow from bifunctional fusion (TPSP) rice containing trehalose-6-phosphate synthase and phosphatase to microorganisms in soils was investigated. The soil samples collected every month from the paddy rice field during June, 2004 to March, 2006 were investigated by multiplex PCR, Southern hybridization, and amplified fragment length polymorphism (AFLP). The TPSP gene from soil genomics DNAs was not detected by PCR. Soil genomic DNAs were not shown its homologies on the Southern blotting data, indicating that gene-transfer did not occur during the last two years in paddy rice field. In addition, the AFLP band patterns produced by both soil genomic DNAs extracted from transgenic and non-transgenic rice field appeared similar to each other when analyzed by NTSYSpc program. Thus, these data suggest that transgenic rice does not give a significant impact on the communities of soil microorganisms although long-term observation may be needed.}, }
@article {pmid20133858, year = {2010}, author = {Chayot, R and Montagne, B and Mazel, D and Ricchetti, M}, title = {An end-joining repair mechanism in Escherichia coli.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {5}, pages = {2141-2146}, pmid = {20133858}, issn = {1091-6490}, mesh = {Base Sequence ; DNA Breaks, Double-Stranded ; DNA Repair/*genetics/physiology ; DNA Repair Enzymes/metabolism ; DNA, Bacterial/genetics/metabolism ; Escherichia coli/*genetics/metabolism/pathogenicity ; Gene Transfer, Horizontal ; Humans ; Models, Biological ; Mutagenesis, Insertional ; }, abstract = {Bridging broken DNA ends via nonhomologous end-joining (NHEJ) contributes to the evolution and stability of eukaryote genomes. Although some bacteria possess a simplified NHEJ mechanism, the human commensal Escherichia coli is thought to rely exclusively on homology-directed mechanisms to repair DNA double-strand breaks (DSBs). We show here that laboratory and pathogenic E. coli strains possess a distinct end-joining activity that repairs DSBs and generates genome rearrangements. This mechanism, named alternative end-joining (A-EJ), does not rely on the key NHEJ proteins Ku and Ligase-D which are absent in E. coli. Differently from classical NHEJ, A-EJ is characterized by extensive end-resection largely due to RecBCD, by overwhelming usage of microhomology and extremely rare DNA synthesis. We also show that A-EJ is dependent on the essential Ligase-A and independent on Ligase-B. Importantly, mutagenic repair requires a functional Ligase-A. Although generally mutagenic, accurate A-EJ also occurs and is frequent in some pathogenic bacteria. Furthermore, we show the acquisition of an antibiotic-resistance gene via A-EJ, refuting the notion that bacteria gain exogenous sequences only by recombination-dependent mechanisms. This finding demonstrates that E. coli can integrate unrelated, nonhomologous exogenous sequences by end-joining and it provides an alternative strategy for horizontal gene transfer in the bacterial genome. Thus, A-EJ contributes to bacterial genome evolution and adaptation to environmental challenges. Interestingly, the key features of A-EJ also appear in A-NHEJ, an alternative end-joining mechanism implicated in chromosomal translocations associated with human malignancies, and we propose that this mutagenic repair might have originated in bacteria.}, }
@article {pmid20133735, year = {2010}, author = {Gordon, BR and Li, Y and Wang, L and Sintsova, A and van Bakel, H and Tian, S and Navarre, WW and Xia, B and Liu, J}, title = {Lsr2 is a nucleoid-associated protein that targets AT-rich sequences and virulence genes in Mycobacterium tuberculosis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {11}, pages = {5154-5159}, pmid = {20133735}, issn = {1091-6490}, support = {MOP-15107//Canadian Institutes of Health Research/Canada ; MOP-86683//Canadian Institutes of Health Research/Canada ; }, mesh = {AT Rich Sequence/*genetics ; DNA, Bacterial/*metabolism ; DNA-Binding Proteins/chemistry/*metabolism ; Genes, Bacterial/*genetics ; Models, Molecular ; Mycobacterium tuberculosis/*genetics/immunology/*pathogenicity ; Protein Binding ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Solutions ; Virulence/genetics ; }, abstract = {Bacterial nucleoid-associated proteins play important roles in chromosome organization and global gene regulation. We find that Lsr2 of Mycobacterium tuberculosis is a unique nucleoid-associated protein that binds AT-rich regions of the genome, including genomic islands acquired by horizontal gene transfer and regions encoding major virulence factors, such as the ESX secretion systems, the lipid virulence factors PDIM and PGL, and the PE/PPE families of antigenic proteins. Comparison of genome-wide binding data with expression data indicates that Lsr2 binding results in transcriptional repression. Domain-swapping experiments demonstrate that Lsr2 has an N-terminal dimerization domain and a C-terminal DNA-binding domain. Nuclear magnetic resonance analysis of the DNA-binding domain of Lsr2 and its interaction with DNA reveals a unique structure and a unique mechanism that enables Lsr2 to discriminately target AT-rich sequences through interactions with the minor groove of DNA. Taken together, we provide evidence that mycobacteria have employed a structurally distinct molecule with an apparently different DNA recognition mechanism to achieve a function similar to the Enterobacteriaceae H-NS, likely coordinating global gene regulation and virulence in this group of medically important bacteria.}, }
@article {pmid20133361, year = {2010}, author = {Díez-Villaseñor, C and Almendros, C and García-Martínez, J and Mojica, FJ}, title = {Diversity of CRISPR loci in Escherichia coli.}, journal = {Microbiology (Reading, England)}, volume = {156}, number = {Pt 5}, pages = {1351-1361}, doi = {10.1099/mic.0.036046-0}, pmid = {20133361}, issn = {1465-2080}, mesh = {Base Sequence ; DNA, Bacterial ; DNA, Intergenic ; Escherichia coli/*genetics ; Escherichia coli Proteins/*genetics ; *Genetic Variation ; *Inverted Repeat Sequences ; Molecular Sequence Data ; Species Specificity ; }, abstract = {CRISPR (clustered regularly interspaced short palindromic repeats) and CAS (CRISPR-associated sequence) proteins are constituents of a novel genetic barrier that limits horizontal gene transfer in prokaryotes by means of an uncharacterized mechanism. The fundamental discovery of small RNAs as the guides of the defence apparatus arose as a result of Escherichia coli studies. However, a survey of the system diversity in this species in order to further contribute to the understanding of the CRISPR mode of action has not yet been performed. Here we describe two CRISPR/CAS systems found in E. coli, following the analysis of 100 strains representative of the species' diversity. Our results substantiate different levels of activity between loci of both CRISPR types, as well as different target preferences and CRISPR relevances for particular groups of strains. Interestingly, the data suggest that the degeneration of one CRISPR/CAS system in E. coli ancestors could have been brought about by self-interference.}, }
@article {pmid20132312, year = {2010}, author = {Moliner, C and Fournier, PE and Raoult, D}, title = {Genome analysis of microorganisms living in amoebae reveals a melting pot of evolution.}, journal = {FEMS microbiology reviews}, volume = {34}, number = {3}, pages = {281-294}, doi = {10.1111/j.1574-6976.2010.00209.x}, pmid = {20132312}, issn = {1574-6976}, mesh = {Amoebozoa/*microbiology/*virology ; Bacteria/*genetics/isolation &amp; purification ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome Size ; *Genome, Bacterial ; *Genome, Viral ; Mimiviridae/*genetics/isolation &amp; purification ; Recombination, Genetic ; }, abstract = {Amoebae-resistant microorganisms exhibit a specific lifestyle. Unlike allopatric specialized intracellular pathogens, they have not specialized because they infect the amoebae via amoebal attack and present a sympatric lifestyle with species from different phyla. In this review, we compare the genomes from bacteria (Legionella pneumophila, Legionella drancourtii, Candidatus'Protochlamydia amoebophila,' Rickettsia bellii, Candidatus'Amoebophilus asiaticus') and a virus (mimivirus) that multiply naturally in amoebae. The objective is to highlight the genomic traits characterizing these microorganisms and their niche by comparison with other specialized pathogens. The genome of intra-amoebal microorganisms is significantly larger than that of their relatives, contradicting the genome reduction theory mostly accepted for intracellular pathogens. This is probably due to the fact that they are not specialized and therefore maintain their genome size. Moreover, the presence of many horizontally transferred genes and mobilomes in their genomes suggests that these microorganisms acquired genetic material from their neighbors and amoebal host, thus increasing their genome size. Important features involved in gene transfer and pathogenicity were thus acquired. These characteristics suggest that amoebae constitute a gene melting pot, allowing diverse microorganisms to evolve by the same pathway characterized by gene acquisition, and then either adapt to the intra-amoebal lifestyle or create new pathogens.}, }
@article {pmid20132306, year = {2010}, author = {Rosewarne, CP and Pettigrove, V and Stokes, HW and Parsons, YM}, title = {Class 1 integrons in benthic bacterial communities: abundance, association with Tn402-like transposition modules and evidence for coselection with heavy-metal resistance.}, journal = {FEMS microbiology ecology}, volume = {72}, number = {1}, pages = {35-46}, doi = {10.1111/j.1574-6941.2009.00823.x}, pmid = {20132306}, issn = {1574-6941}, mesh = {Aeromonas/drug effects/genetics ; Bacteria/drug effects/*genetics ; Comamonas testosteroni/drug effects/genetics ; *DNA Transposable Elements ; Drug Resistance, Bacterial/*genetics ; Ecosystem ; Fresh Water ; Gene Transfer, Horizontal ; Geologic Sediments/chemistry/*microbiology ; Integrases/genetics ; *Integrons ; Metals, Heavy/analysis/*pharmacology ; Polymerase Chain Reaction ; Pseudomonas/drug effects/genetics ; *Selection, Genetic ; Sewage ; Victoria ; Water Pollution ; }, abstract = {The integron/gene cassette system contributes to lateral gene transfer of genetic information in bacterial communities, with gene cassette-encoded proteins potentially playing an important role in adaptation to stress. Class 1 integrons are a particularly important class as they themselves seem to be broadly disseminated among the Proteobacteria and have an established role in the spread of antibiotic resistance genes. The abundance and structure of class 1 integrons in freshwater sediment bacterial communities was assessed through sampling of 30 spatially distinct sites encompassing different substrate and catchment types from the Greater Melbourne Area of Victoria, Australia. Real-time PCR was used to demonstrate that the abundance of intI1 was increased as a result of ecosystem perturbation, indicated by classification of sample locations based on the catchment type and a strong positive correlation with the first principal component factor score, comprised primarily of the heavy metals zinc, mercury, lead and copper. Additionally, the abundance of intI1 at sites located downstream from treated sewage outputs was associated with the percentage contribution of the discharge to the basal flow rate. Characterization of class 1 integrons in bacteria cultured from selected sediment samples identified an association with complete Tn402-like transposition modules, and the potential for coselection of heavy-metal and antibiotic resistance mechanisms in benthic environments.}, }
@article {pmid20128113, year = {2010}, author = {Vallenback, P and Bengtsson, BO and Ghatnekar, L}, title = {Geographic and molecular variation in a natural plant transgene.}, journal = {Genetica}, volume = {138}, number = {3}, pages = {355-362}, pmid = {20128113}, issn = {1573-6857}, mesh = {DNA, Chloroplast/analysis/genetics ; Europe ; Evolution, Molecular ; Festuca/enzymology/*genetics ; Gene Frequency ; Gene Transfer, Horizontal ; *Genetic Variation ; Genome, Plant ; *Geography ; Glucose-6-Phosphate Isomerase/genetics ; Oceans and Seas ; Poa/genetics ; Pseudogenes ; Selection, Genetic ; *Transgenes ; }, abstract = {A PCR based survey of Festuca ovina plants from populations around the southern part of the Baltic Sea demonstrates both geographic and molecular variation in the enzyme gene PgiC2, horizontally transferred from a Poa-species. Our results show that PgiC2-a natural functional nuclear transgene-is not a local ephemeral phenomenon but is present in a very large number of individuals. We find also that its frequency is geographically variable and that it appears in more than one molecular form. The chloroplast variation in the region does not indicate any distinct subdivision due to different colonization routes after the last glaciation. Our data illustrate the geographic and molecular variation that may occur in natural populations with a polymorphic, unfixed transgene affected by diverse kinds of mutational and evolutionary processes.}, }
@article {pmid20127470, year = {2009}, author = {Jeong, JH and Shin, KS and Lee, JW and Park, EJ and Son, SY}, title = {Analysis of a novel class 1 integron containing metallo-beta-lactamase gene VIM-2 in Pseudomonas aeruginosa.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {47}, number = {6}, pages = {753-759}, pmid = {20127470}, issn = {1976-3794}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Genotype ; Humans ; Imipenem/pharmacology ; *Integrons ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Plasmids ; Pseudomonas Infections/microbiology ; Pseudomonas aeruginosa/*drug effects/*genetics/isolation &amp; purification ; Republic of Korea ; Sequence Analysis, DNA ; *beta-Lactam Resistance ; beta-Lactamases/*genetics ; }, abstract = {Carbapenems such as imipenem are stable to most beta-lactamases. Recently, increased numbers of carbapenemase producing Gram-negative bacterial strains have been isolated because of the increased use of cabapenems. In this respect, control of these infectious carbapenemase producing Gram-negative bacteria and understanding their resistance mechanism are becoming more important. These carbapenem-hydrolyzing beta-lactamase genes have been reported to exist mostly as gene cassettes in an integron. This implies that antibiotic resistance genes may be transferred to other bacteria via the integron. In the present study, we identified and analyzed an integron containing VIM-2 type metallo-beta-lactamase gene in a carbapenemase producing Pseudomonas aeruginosa. In addition, the possibility of resistance spread by integron located in a plasmid was tested. Among glucose non-fermenting Gram-negative bacilli with reduced imipenem susceptibility (MIC > or = 8 microg/ml) isolated from Korean patients, P. aeruginosa 1082 showed resistance to most beta-lactams, cephalosporin, and aminoglycoside. We found that P. aeruginosa 1082 was inhibited by EDTA in EDTA double disk synergy test which means that this strain produces metallo-beta-lactamase. Class 1 integron containing bla (VIM-2) (carbapenem resistance gene), qacF (quaternary ammonium compound resistance gene), aacA4 (aminoglycoside resistance gene), catB3 (chloramphenicol resistance gene), bla (oxa-30) (extended-spectrum beta-lactam resistance gene), and aadAl (aminoglycoside resistance gene) gene cassettes was detected in P. aeruginosa 1082. The size of the integron was 5,246 bp and the structure and arrangement of the integron was a novel one in comparison with other integrons found in other P. aeruginosa. The integron could be transferred to Escherichia coli JM109 from P. aeruginosa 1082 possibly via self-transferable plasmid DNA. The integron and a bla (VIM-2) gene were detected in the plasmid DNA of the transconjugants whose imipenem resistance was slightly increased as a result of accepting the integron from the donor strain.}, }
@article {pmid20124349, year = {2010}, author = {Martin, W}, title = {Evolutionary origins of metabolic compartmentalization in eukaryotes.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {365}, number = {1541}, pages = {847-855}, pmid = {20124349}, issn = {1471-2970}, mesh = {*Biological Evolution ; Chloroplasts/genetics/metabolism ; Eukaryota/*genetics/*metabolism ; Gene Transfer, Horizontal ; Mitochondria/genetics/metabolism ; Models, Biological ; Organelles/genetics/*metabolism ; Protein Transport ; Symbiosis ; }, abstract = {Many genes in eukaryotes are acquisitions from the free-living antecedents of chloroplasts and mitochondria. But there is no evolutionary 'homing device' that automatically directs the protein product of a transferred gene back to the organelle of its provenance. Instead, the products of genes acquired from endosymbionts can explore all targeting possibilities within the cell. They often replace pre-existing host genes, or even whole pathways. But the transfer of an enzymatic pathway from one compartment to another poses severe problems: over evolutionary time, the enzymes of the pathway acquire their targeting signals for the new compartment individually, not in unison. Until the whole pathway is established in the new compartment, newly routed individual enzymes are useless, and their genes will be lost through mutation. Here it is suggested that pathways attain novel compartmentation variants via a 'minor mistargeting' mechanism. If protein targeting in eukaryotic cells possesses enough imperfection such that small amounts of entire pathways continuously enter novel compartments, selectable units of biochemical function would exist in new compartments, and the genes could become selected. Dual-targeting of proteins is indeed very common within eukaryotic cells, suggesting that targeting variation required for this minor mistargeting mechanism to operate exists in nature.}, }
@article {pmid20124348, year = {2010}, author = {Ginger, ML and McFadden, GI and Michels, PA}, title = {Rewiring and regulation of cross-compartmentalized metabolism in protists.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {365}, number = {1541}, pages = {831-845}, pmid = {20124348}, issn = {1471-2970}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {*Biological Evolution ; Eukaryota/*genetics/*metabolism ; Gene Transfer, Horizontal ; Glycolysis ; *Metabolic Networks and Pathways ; Models, Biological ; Organelles/genetics/metabolism ; Plastids/genetics/metabolism ; Symbiosis ; Systems Biology ; Terpenes/metabolism ; Trypanosomatina/genetics/metabolism ; }, abstract = {Plastid acquisition, endosymbiotic associations, lateral gene transfer, organelle degeneracy or even organelle loss influence metabolic capabilities in many different protists. Thus, metabolic diversity is sculpted through the gain of new metabolic functions and moderation or loss of pathways that are often essential in the majority of eukaryotes. What is perhaps less apparent to the casual observer is that the sub-compartmentalization of ubiquitous pathways has been repeatedly remodelled during eukaryotic evolution, and the textbook pictures of intermediary metabolism established for animals, yeast and plants are not conserved in many protists. Moreover, metabolic remodelling can strongly influence the regulatory mechanisms that control carbon flux through the major metabolic pathways. Here, we provide an overview of how core metabolism has been reorganized in various unicellular eukaryotes, focusing in particular on one near universal catabolic pathway (glycolysis) and one ancient anabolic pathway (isoprenoid biosynthesis). For the example of isoprenoid biosynthesis, the compartmentalization of this process in protists often appears to have been influenced by plastid acquisition and loss, whereas for glycolysis several unexpected modes of compartmentalization have emerged. Significantly, the example of trypanosomatid glycolysis illustrates nicely how mathematical modelling and systems biology can be used to uncover or understand novel modes of pathway regulation.}, }
@article {pmid20124342, year = {2010}, author = {Lim, L and McFadden, GI}, title = {The evolution, metabolism and functions of the apicoplast.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {365}, number = {1541}, pages = {749-763}, pmid = {20124342}, issn = {1471-2970}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {Adenosine Triphosphate/metabolism ; Animals ; Apicomplexa/*genetics/*metabolism/pathogenicity ; *Biological Evolution ; Chloroplasts/metabolism ; Fatty Acids/biosynthesis ; Gene Transfer, Horizontal ; Heme/biosynthesis ; Humans ; Iron-Sulfur Proteins/biosynthesis ; Mitochondria/genetics/metabolism ; Models, Biological ; Plasmodium/genetics/growth &amp; development/metabolism/pathogenicity ; Plastids/*genetics/*metabolism ; Protein Transport ; Symbiosis/genetics/physiology ; Terpenes/metabolism ; }, abstract = {The malaria parasite, Plasmodium falciparum, harbours a relict plastid known as the 'apicoplast'. The discovery of the apicoplast ushered in an exciting new prospect for drug development against the parasite. The eubacterial ancestry of the organelle offers a wealth of opportunities for the development of therapeutic interventions. Morphological, biochemical and bioinformatic studies of the apicoplast have further reinforced its 'plant-like' characteristics and potential as a drug target. However, we are still not sure why the apicoplast is essential for the parasite's survival. This review explores the origins and metabolic functions of the apicoplast. In an attempt to decipher the role of the organelle within the parasite we also take a closer look at the transporters decorating the plastid to better understand the metabolic exchanges between the apicoplast and the rest of the parasite cell.}, }
@article {pmid20124341, year = {2010}, author = {Keeling, PJ}, title = {The endosymbiotic origin, diversification and fate of plastids.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {365}, number = {1541}, pages = {729-748}, pmid = {20124341}, issn = {1471-2970}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {*Biological Evolution ; Chlorophyta/genetics/physiology ; Dinoflagellida/genetics/physiology ; Eukaryota/genetics/physiology ; Gene Transfer, Horizontal ; Mitochondria/genetics/physiology ; Models, Biological ; Phylogeny ; Plastids/*genetics/physiology ; Rhodophyta/genetics/physiology ; Symbiosis/*genetics/physiology ; }, abstract = {Plastids and mitochondria each arose from a single endosymbiotic event and share many similarities in how they were reduced and integrated with their host. However, the subsequent evolution of the two organelles could hardly be more different: mitochondria are a stable fixture of eukaryotic cells that are neither lost nor shuffled between lineages, whereas plastid evolution has been a complex mix of movement, loss and replacement. Molecular data from the past decade have substantially untangled this complex history, and we now know that plastids are derived from a single endosymbiotic event in the ancestor of glaucophytes, red algae and green algae (including plants). The plastids of both red algae and green algae were subsequently transferred to other lineages by secondary endosymbiosis. Green algal plastids were taken up by euglenids and chlorarachniophytes, as well as one small group of dinoflagellates. Red algae appear to have been taken up only once, giving rise to a diverse group called chromalveolates. Additional layers of complexity come from plastid loss, which has happened at least once and probably many times, and replacement. Plastid loss is difficult to prove, and cryptic, non-photosynthetic plastids are being found in many non-photosynthetic lineages. In other cases, photosynthetic lineages are now understood to have evolved from ancestors with a plastid of different origin, so an ancestral plastid has been replaced with a new one. Such replacement has taken place in several dinoflagellates (by tertiary endosymbiosis with other chromalveolates or serial secondary endosymbiosis with a green alga), and apparently also in two rhizarian lineages: chlorarachniophytes and Paulinella (which appear to have evolved from chromalveolate ancestors). The many twists and turns of plastid evolution each represent major evolutionary transitions, and each offers a glimpse into how genomes evolve and how cells integrate through gene transfers and protein trafficking.}, }
@article {pmid20123719, year = {2010}, author = {Cusumano, CK and Hung, CS and Chen, SL and Hultgren, SJ}, title = {Virulence plasmid harbored by uropathogenic Escherichia coli functions in acute stages of pathogenesis.}, journal = {Infection and immunity}, volume = {78}, number = {4}, pages = {1457-1467}, pmid = {20123719}, issn = {1098-5522}, support = {R01 AI029549/AI/NIAID NIH HHS/United States ; R01 AI048689/AI/NIAID NIH HHS/United States ; AI48689/AI/NIAID NIH HHS/United States ; P50 DK064540/DK/NIDDK NIH HHS/United States ; DK51406/DK/NIDDK NIH HHS/United States ; AI029549/AI/NIAID NIH HHS/United States ; DK64540/DK/NIDDK NIH HHS/United States ; R37 AI029549/AI/NIAID NIH HHS/United States ; R01 DK051406/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Colony Count, Microbial ; Disease Models, Animal ; Escherichia coli Infections/microbiology ; Escherichia coli Proteins/genetics/*physiology ; Female ; Gene Knockout Techniques ; Mice ; Mice, Inbred C3H ; Operon ; *Plasmids ; Urinary Bladder/microbiology ; Urinary Tract Infections/microbiology ; Uropathogenic Escherichia coli/*pathogenicity ; Virulence ; Virulence Factors/genetics/*physiology ; }, abstract = {Urinary tract infections (UTIs), the majority of which are caused by uropathogenic Escherichia coli (UPEC), afflict nearly 60% of women within their lifetimes. Studies in mice and humans have revealed that UPEC strains undergo a complex pathogenesis cycle that involves both the formation of intracellular bacterial communities (IBC) and the colonization of extracellular niches. Despite the commonality of the UPEC pathogenesis cycle, no specific urovirulence genetic profile has been determined; this is likely due to the fluid nature of the UPEC genome as the result of horizontal gene transfer and numerous genes of unknown function. UTI89 has a large extrachromosomal element termed pUTI89 with many characteristics of UPEC pathogenicity islands and that likely arose due to horizontal gene transfer. The pUTI89 plasmid has characteristics of both F plasmids and other known virulence plasmids. We sought to determine whether pUTI89 is important for virulence. Both in vitro and in vivo assays were used to examine the function of pUTI89 using plasmid-cured UTI89. No differences were observed between UTI89 and plasmid-cured UTI89 based on growth, type 1 pilus expression, or biofilm formation. However, in a mouse model of UTI, a significant decrease in bacterial invasion, CFU and IBC formation of the pUTI89-cured strain was observed at early time points postinfection compared to the wild type. Through directed deletions of specific operons on pUTI89, the cjr operon was partially implicated in this observed defect. Our findings implicate pUTI89 in the early aspects of infection.}, }
@article {pmid20123713, year = {2010}, author = {Baranowski, E and Guiral, S and Sagné, E and Skapski, A and Citti, C}, title = {Critical role of dispensable genes in Mycoplasma agalactiae interaction with mammalian cells.}, journal = {Infection and immunity}, volume = {78}, number = {4}, pages = {1542-1551}, pmid = {20123713}, issn = {1098-5522}, mesh = {*Bacterial Adhesion ; Bacterial Proteins/genetics/*physiology ; Coculture Techniques ; Colony Count, Microbial ; DNA Transposable Elements ; Epithelial Cells/microbiology ; Gene Knockout Techniques ; Genes, Essential ; Genetic Complementation Test ; HeLa Cells ; Humans ; Mutagenesis, Insertional ; Mycoplasma agalactiae/genetics/growth &amp; development/*pathogenicity ; Virulence Factors/genetics/*physiology ; }, abstract = {Mycoplasmas are minimal bacteria whose genomes barely exceed the smallest amount of information required to sustain autonomous life. Despite this apparent simplicity, several mycoplasmas are successful pathogens of humans and animals, in which they establish intimate interactions with epithelial cells at mucosal surfaces. To identify biological functions mediating mycoplasma interactions with mammalian cells, we produced a library of transposon knockout mutants in the ruminant pathogen Mycoplasma agalactiae and used this library to identify mutants displaying a growth-deficient pheonotype in cell culture. M. agalactiae mutants displaying a 3-fold reduction in CFU titers to nearly complete extinction in coculture with HeLa cells were identified. Mapping of transposon insertion sites revealed 18 genomic regions putatively involved in the interaction of M. agalactiae with HeLa cells. Several of these regions encode proteins with features of membrane lipoproteins and/or were involved in horizontal gene transfer with phylogenetically distant pathogenic mycoplasmas of ruminants. Two mutants with the most extreme phenotype carry a transposon in a genomic region designated the NIF locus which encodes homologues of SufS and SufU, two proteins presumably involved in [Fe-S] cluster biosynthesis in Gram-positive bacteria. Complementation studies confirmed the conditional essentiality of the NIF locus, which was found to be critical for proliferation in the presence of HeLa cells and several other mammalian cell lines but dispensable for axenic growth. While our results raised questions regarding essential functions in mycoplasmas, they also provide a means for studying the role of mycoplasmas as minimal pathogens.}, }
@article {pmid20123152, year = {2010}, author = {Schimith Bier, KE and Luiz, SO and Scheffer, MC and Gales, AC and Paganini, MC and Nascimento, AJ and Carignano, E and Dalla Costa, LM}, title = {Temporal evolution of carbapenem-resistant Acinetobacter baumannii in Curitiba, southern Brazil.}, journal = {American journal of infection control}, volume = {38}, number = {4}, pages = {308-314}, doi = {10.1016/j.ajic.2009.09.012}, pmid = {20123152}, issn = {1527-3296}, mesh = {Acinetobacter Infections/*epidemiology/microbiology ; Acinetobacter baumannii/classification/*drug effects/genetics/isolation &amp; purification ; Adolescent ; Adult ; Aged ; Aged, 80 and over ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics ; *Bacterial Typing Techniques ; Brazil/epidemiology ; Carbapenems/*pharmacology ; Child ; Child, Preschool ; DNA Fingerprinting ; DNA, Bacterial/genetics ; Female ; Gene Transfer, Horizontal ; Humans ; Infant ; Male ; Microbial Sensitivity Tests ; Middle Aged ; Molecular Epidemiology ; Polymerase Chain Reaction ; Young Adult ; *beta-Lactam Resistance ; beta-Lactamases/genetics ; }, abstract = {BACKGROUND: In the last few years, carbapenem-resistant Acinetobacter baumannii isolates (CR-AB) have been identified worldwide. The first description of OXA-23-producing A baumannii in Brazil was from the city of Curitiba in 2003. The aim of the present study was to evaluate the persistence and dissemination of the first OXA-23-producing A baumannii clone isolated from patients in Hospital de Clinicas, Curitiba, Brazil.<br><br>METHODS: An antimicrobial susceptibility profile of the isolates was determined by the standard agar dilution method. Molecular detection of beta-lactamase genes was done by polymerase chain reaction. The clonal relationship of the isolates was analyzed by pulsed-field gel electrophoresis (PFGE). Epidemiologic and clinical features were evaluated as well.<br><br>RESULTS: Genotypic analysis of 172 CR-AB isolates by PFGE identified 3 distinct major PFGE clusters (A, B, and C, accounting for 36, 69, and 65 isolates, respectively). All isolates carried the bla(OXA-23)-like gene and were multidrug-resistant, but were susceptible to tigecycline and polymixin B. The mortality rate related to CR-AB infection was 45.4%, and ventilator-associated pneumonia and bloodstream infections were the most frequent clinical manifestations.<br><br>CONCLUSIONS: The presence of 3 clones among the CR-AB isolates suggests that cross-transmission was the main mechanism responsible for dissemination of OXA-23 producers. PFGE pattern A was genotypically similar to that of the first OXA-23-producing A baumannii clone identified in Curitiba in 1999. This clone persisted in the same hospital until April 2004. The presence of the bla(OXA-)23-like gene was the main mechanism associated with carbapenem resistance among the isolates studied.}, }
@article {pmid20122262, year = {2010}, author = {Nouvel, LX and Sirand-Pugnet, P and Marenda, MS and Sagné, E and Barbe, V and Mangenot, S and Schenowitz, C and Jacob, D and Barré, A and Claverol, S and Blanchard, A and Citti, C}, title = {Comparative genomic and proteomic analyses of two Mycoplasma agalactiae strains: clues to the macro- and micro-events that are shaping mycoplasma diversity.}, journal = {BMC genomics}, volume = {11}, number = {}, pages = {86}, pmid = {20122262}, issn = {1471-2164}, mesh = {Amino Acid Sequence ; Base Sequence ; *Comparative Genomic Hybridization ; DNA, Bacterial/genetics ; *Evolution, Molecular ; Gene Flow ; Gene Pool ; Gene Transfer, Horizontal ; Genome, Bacterial ; Molecular Sequence Data ; Multigene Family ; Mutagenesis, Insertional ; Mycoplasma agalactiae/*genetics ; Polymorphism, Single Nucleotide ; Proteomics/*methods ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: While the genomic era is accumulating a tremendous amount of data, the question of how genomics can describe a bacterial species remains to be fully addressed. The recent sequencing of the genome of the Mycoplasma agalactiae type strain has challenged our general view on mycoplasmas by suggesting that these simple bacteria are able to exchange significant amount of genetic material via horizontal gene transfer. Yet, events that are shaping mycoplasma genomes and that are underlining diversity within this species have to be fully evaluated. For this purpose, we compared two strains that are representative of the genetic spectrum encountered in this species: the type strain PG2 which genome is already available and a field strain, 5632, which was fully sequenced and annotated in this study.<br><br>RESULTS: The two genomes differ by ca. 130 kbp with that of 5632 being the largest (1006 kbp). The make up of this additional genetic material mainly corresponds (i) to mobile genetic elements and (ii) to expanded repertoire of gene families that encode putative surface proteins and display features of highly-variable systems. More specifically, three entire copies of a previously described integrative conjugative element are found in 5632 that accounts for ca. 80 kbp. Other mobile genetic elements, found in 5632 but not in PG2, are the more classical insertion sequences which are related to those found in two other ruminant pathogens, M. bovis and M. mycoides subsp. mycoides SC. In 5632, repertoires of gene families encoding surface proteins are larger due to gene duplication. Comparative proteomic analyses of the two strains indicate that the additional coding capacity of 5632 affects the overall architecture of the surface and suggests the occurrence of new phase variable systems based on single nucleotide polymorphisms.<br><br>CONCLUSION: Overall, comparative analyses of two M. agalactiae strains revealed a very dynamic genome which structure has been shaped by gene flow among ruminant mycoplasmas and expansion-reduction of gene repertoires encoding surface proteins, the expression of which is driven by localized genetic micro-events.}, }
@article {pmid20118370, year = {2010}, author = {Dong, WR and Xiang, LX and Shao, JZ}, title = {Novel antibiotic-free plasmid selection system based on complementation of host auxotrophy in the NAD de novo synthesis pathway.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {7}, pages = {2295-2303}, pmid = {20118370}, issn = {1098-5336}, mesh = {Biosynthetic Pathways/*genetics ; Escherichia coli/genetics ; Genetic Engineering/*methods ; *Genetic Vectors ; Genetics, Microbial/*methods ; NAD/*biosynthesis/*genetics ; Plasmids ; *Selection, Genetic ; }, abstract = {The use of antibiotic resistance genes in plasmids causes potential biosafety and clinical hazards, such as the possibility of horizontal spread of resistance genes or the rapid emergence of multidrug-resistant pathogens. This paper introduces a novel auxotrophy complementation system that allowed plasmids and host cells to be effectively selected and maintained without the use of antibiotics. An Escherichia coli strain carrying a defect in NAD de novo biosynthesis was constructed by knocking out the chromosomal quinolinic acid phosphoribosyltransferase (QAPRTase) gene. The resistance gene in the plasmids was replaced by the QAPRTase gene of E. coli or the mouse. As a result, only expression of the QAPRTase gene from plasmids can complement and rescue E. coli host cells in minimal medium. This is the first time that a vertebrate gene has been used to construct a nonantibiotic selection system, and it can be widely applied in DNA vaccine and gene therapy. As the QAPRTase gene is ubiquitous in species ranging from bacteria to mammals, the potential environmental biosafety problems caused by horizontal gene transfer can be eliminated.}, }
@article {pmid20118250, year = {2010}, author = {Eldholm, V and Gutt, B and Johnsborg, O and Brückner, R and Maurer, P and Hakenbeck, R and Mascher, T and Håvarstein, LS}, title = {The pneumococcal cell envelope stress-sensing system LiaFSR is activated by murein hydrolases and lipid II-interacting antibiotics.}, journal = {Journal of bacteriology}, volume = {192}, number = {7}, pages = {1761-1773}, pmid = {20118250}, issn = {1098-5530}, mesh = {Amino Acid Sequence ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/*metabolism ; Bacteriolysis ; Base Sequence ; Genes, Bacterial ; Molecular Sequence Data ; N-Acetylmuramoyl-L-alanine Amidase/*metabolism ; Regulon ; Sequence Alignment ; *Signal Transduction ; Streptococcus pneumoniae/*drug effects/physiology ; *Stress, Physiological ; Uridine Diphosphate N-Acetylmuramic Acid/*analogs &amp; derivatives/metabolism ; }, abstract = {In the Firmicutes, two-component regulatory systems of the LiaSR type sense and orchestrate the response to various agents that perturb cell envelope functions, in particular lipid II cycle inhibitors. In the current study, we found that the corresponding system in Streptococcus pneumoniae displays similar properties but, in addition, responds to cell envelope stress elicited by murein hydrolases. During competence for genetic transformation, pneumococci attack and lyse noncompetent siblings present in the same environment. This phenomenon, termed fratricide, increases the efficiency of horizontal gene transfer in vitro and is believed to stimulate gene exchange also under natural conditions. Lysis of noncompetent target cells is mediated by the putative murein hydrolase CbpD, the key effector of the fratricide mechanism, and the autolysins LytA and LytC. To avoid succumbing to their own lysins, competent attacker cells must possess a protective mechanism rendering them immune. The most important component of this mechanism is ComM, an integral membrane protein of unknown function that is expressed only in competent cells. Here, we show that a second layer of self-protection is provided by the pneumococcal LiaFSR system, which senses the damage inflicted to the cell wall by CbpD, LytA, and LytC. Two members of the LiaFSR regulon, spr0810 and PcpC (spr0351), were shown to contribute to the LiaFSR-coordinated protection against fratricide-induced self-lysis.}, }
@article {pmid20113208, year = {2010}, author = {Hudson, JA and Bigwood, T and Premaratne, A and Billington, C and Horn, B and McIntyre, L}, title = {Potential to use ultraviolet-treated bacteriophages to control foodborne pathogens.}, journal = {Foodborne pathogens and disease}, volume = {7}, number = {6}, pages = {687-693}, doi = {10.1089/fpd.2009.0453}, pmid = {20113208}, issn = {1556-7125}, mesh = {Animals ; Bacteriolysis ; Bacteriophage T4/physiology/radiation effects ; Bacteriophages/*physiology/*radiation effects ; Cattle ; Colony Count, Microbial ; *DNA Replication ; Escherichia coli/growth &amp; development/virology ; *Food Microbiology ; Foodborne Diseases/*prevention &amp; control ; Kinetics ; Meat/microbiology ; Meat Products/microbiology ; *Microbial Viability ; Pest Control, Biological/*methods ; Temperature ; Time Factors ; *Ultraviolet Rays ; }, abstract = {The use of replication-deficient UV-treated bacteriophages, or phages, presents an alternative to viable phages for food biocontrol applications. Nontransducing UV-treated phages, if used correctly, are unlikely to produce viable progeny phages, which might otherwise mediate undesirable horizontal gene transfer events. Phage T4 and Escherichia coli were used as a model system to examine this possibility. UV-treated phages were able to cause a reduction in the optical density of outer membrane-free cell suspensions and they also killed host cells under conditions not permitting their multiplication, that is, 24 degrees C for 2 h and 37 degrees C for 15 min. Host cell reductions were also demonstrated in broth and on meat at 5 degrees C when high concentrations of phages of 2.3 x 10(9) PFU mL(-1) and 1.8 x 10(8) PFU cm(-2), respectively, were used. At 24 degrees C and 37 degrees C, "lysis from without" was likely to be the mechanism responsible for the reduction in host cell concentrations, but at 5 degrees C this may not have been the case.}, }
@article {pmid20112862, year = {2009}, author = {Shakibaie, MR and Jalilzadeh, KA and Yamakanamardi, SM}, title = {Horizontal transfer of antibiotic resistance genes among gram negative bacteria in sewage and lake water and influence of some physico-chemical parameters of water on conjugation process.}, journal = {Journal of environmental biology}, volume = {30}, number = {1}, pages = {45-49}, pmid = {20112862}, issn = {0254-8704}, mesh = {Conjugation, Genetic/*physiology ; Drug Resistance, Bacterial/*genetics ; Fresh Water/chemistry/*microbiology ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Gram-Negative Bacteria/*genetics/isolation &amp; purification ; Microbial Sensitivity Tests ; Sewage/*microbiology ; }, abstract = {Transfer of antibiotic resistance genes among gram negative bacteria in sewage and lake water and easy access of these bacteria to the community are major environmental and public health concern. The aim of this study was to determine transfer of the antimicrobial resistance genes from resistant to susceptible gram negative bacteria in the sewage and lake water by conjugation process and to determine the influence of some physico-chemical parameters of sewage and lake water on the transfer of these resistance genes. For this reason, we isolated 20 liter of each sewage and lake water from coconut area within university campus and Lingambudi lake respectively in Mysore city, India, during monsoon season and studied different physical parameters of the water samples like pH, temperature, conductivity turbidity and color as well as chemical parameters like BOD, COD, field DO and total chloride ion. The gram negative bacteria were isolated and identified from the above water samples using microbiological and biochemical methods and their sensitivity to different antibiotics was determined by disc diffusion break point assay. Conjugation between two multiple antibiotic resistant isolates Pseudomonas aeuginosa and E. coli as donor and E. coli Rif(r) (sensitive to antibiotics) as recipient were carried out in 5ml sterile sewage and lake water. All isolates were resistant to Am, moderately resistant to Te and E, while majority were sensitive to Cip, Gm and CAZ antibiotics. Horizontal transfer of antibiotic resistance genes by conjugation process revealed transfer of Gm, Te and E resistant genes from Ps. aeruginosa to E. coli Rif(r) recipient with mean frequency of +/- 2.3 x 10(-4) in sewage and +/- 2.6 x 10(-6) in lake water respectively Frequency of conjugation in sewage was two fold more as compared to lake water (p< or =0.05). Co- transfer study revealed simultaneous transfer of above resistant markers together to the recipient cells. As the above results indicate, due to selective pressure in sewage (presence of antibiotics), the isolates from sewage were more resistant to different antibiotics as compared to those from lake water. Furthermore, these resistance genes can transfer to sensitive bacteria by conjugation. Physico-chemical parameters of water may play role in this process.}, }
@article {pmid20107986, year = {2010}, author = {Kampenusa, I and Zikmanis, P}, title = {Distinguishable codon usage and amino acid composition patterns among substrates of leaderless secretory pathways from proteobacteria.}, journal = {Applied microbiology and biotechnology}, volume = {86}, number = {1}, pages = {285-293}, doi = {10.1007/s00253-009-2423-8}, pmid = {20107986}, issn = {1432-0614}, mesh = {Amino Acids/*chemistry/genetics ; Bacterial Proteins/chemistry/genetics/*metabolism ; Base Composition ; Codon/chemistry/*genetics ; Computational Biology ; Discriminant Analysis ; *Proteobacteria/chemistry/genetics/metabolism ; }, abstract = {The combined set of codon usage frequencies (61 sense codons) from the 111 annotated sequences of leaderless secreted type I, type III, type IV, and type VI proteins from proteobacteria were subjected to the forward and backward selection to obtain a combination of most effective predictor variables for classification/prediction purposes. The group of 24 codon frequencies displayed a strong discriminatory power with an accuracy of 100% for originally grouped and 97.3 +/- 1.6% for cross-validated (LOOCV) cases and an acceptable error rate (0.062 +/- 0.012) in k-fold (k = 6) cross-validation (KCV). The summary frequencies of synonymous codons for ten amino acids as the alternative predictor variables revealed a comparable discriminatory power (92.8 +/- 2.5% for LOOCV), however at somewhat lower levels of prediction accuracy (0.106 +/- 0.015 of KCV). A number of significant (p < 0.001) differences were found among indices of codon usage and amino acid composition depending on a definite secretion type. About 60% of secretion substrates were characterized as apparently originated from horizontal gene transfer events or putative alien genes and found to be unequally allocated in respect of groups. The proposed prediction approaches could be used to specify secretome proteins from genomic sequences as well as to assess the compatibility between bacterial secretion pathways and secretion substrates.}, }
@article {pmid20106909, year = {2010}, author = {Mahelka, V and Kopecký, D}, title = {Gene capture from across the grass family in the allohexaploid Elymus repens (L.) Gould (Poaceae, Triticeae) as evidenced by ITS, GBSSI, and molecular cytogenetics.}, journal = {Molecular biology and evolution}, volume = {27}, number = {6}, pages = {1370-1390}, doi = {10.1093/molbev/msq021}, pmid = {20106909}, issn = {1537-1719}, mesh = {Bayes Theorem ; Cytogenetic Analysis/*methods ; DNA, Intergenic ; DNA, Ribosomal ; Databases, Genetic ; Gene Transfer, Horizontal ; *Genes, Plant ; In Situ Hybridization, Fluorescence ; *Models, Genetic ; Phylogeny ; Poaceae/*genetics ; Pseudogenes ; Starch Synthase/*genetics ; Transcription, Genetic ; }, abstract = {Four accessions of hexaploid Elymus repens from its native Central European distribution area were analyzed using sequencing of multicopy (internal transcribed spacer, ITS) and single-copy (granule-bound starch synthase I, GBSSI) DNA in concert with genomic and fluorescent in situ hybridization (GISH and FISH) to disentangle its allopolyploid origin. Despite extensive ITS homogenization, nrDNA in E. repens allowed us to identify at least four distinct lineages. Apart from Pseudoroegneria and Hordeum, representing the major genome constituents, the presence of further unexpected alien genetic material, originating from species outside the Triticeae and close to Panicum (Paniceae) and Bromus (Bromeae), was revealed. GBSSI sequences provided information complementary to the ITS. Apart from Pseudoroegneria and Hordeum, two additional gene variants from within the Triticeae were discovered: One was Taeniatherum-like, but the other did not have a close relationship with any of the diploids sampled. GISH results were largely congruent with the sequence-based markers. GISH clearly confirmed Pseudoroegneria and Hordeum as major genome constituents and further showed the presence of a small chromosome segment corresponding to Panicum. It resided in the Hordeum subgenome and probably represents an old acquisition of a Hordeum progenitor. Spotty hybridization signals across all chromosomes after GISH with Taeniatherum and Bromus probes suggested that gene acquisition from these species is more likely due to common ancestry of the grasses or early introgression than to recent hybridization or allopolyploid origin of E. repens. Physical mapping of rDNA loci using FISH revealed that all rDNA loci except one minor were located on Pseudoroegneria-derived chromosomes, which suggests the loss of all Hordeum-derived loci but one. Because homogenization mechanisms seem to operate effectively among Pseudoroegneria-like copies in this species, incomplete ITS homogenization in our samples is probably due to an interstitial position of an individual minor rDNA locus located within the Hordeum-derived subgenome.}, }
@article {pmid20102721, year = {2010}, author = {Lee, MM and Stock, SP}, title = {A multigene approach for assessing evolutionary relationships of Xenorhabdus spp. (gamma-Proteobacteria), the bacterial symbionts of entomopathogenic Steinernema nematodes.}, journal = {Journal of invertebrate pathology}, volume = {104}, number = {2}, pages = {67-74}, doi = {10.1016/j.jip.2010.01.005}, pmid = {20102721}, issn = {1096-0805}, mesh = {Animals ; Bacterial Proteins/genetics ; *Biological Evolution ; DNA, Bacterial/*analysis ; DNA, Ribosomal/*analysis ; Evolution, Molecular ; Genetic Speciation ; Host-Parasite Interactions ; *Phylogeny ; RNA, Ribosomal/analysis ; Rec A Recombinases/genetics ; Rhabditida/microbiology/parasitology ; Species Specificity ; Symbiosis ; Transaminases/genetics ; Xenorhabdus/*genetics/physiology ; }, abstract = {Xenorhabdus spp., are gram-negative bacterial symbionts of entomopathogenic nematodes in the genus Steinernema. A specialized and intimate relationship exists between nematode and bacteria, affecting many of their life history traits, such as nutrition, dispersal, host-finding, foraging and defense from biotic and abiotic factors. Xenorhabdus currently comprises more than 20 species isolated from Steinernema spp. with diverse host range, host foraging behavior, reproductive modes and environmental tolerance. Xenorhabdus phylogenies have historically been based on 16s rDNA sequence analyses, and only recently has data from housekeeping genes been employed. The prevalence of lateral gene transfer among bacteria calls for a wider perspective when considering their phylogeny. With the increasing number of Xenorhabdus species and strains, various perspectives need to be considered for investigating the evolutionary history of these nematode bacterial symbionts, In this study, we reconstruct the evolutionary histories of 30 species of Xenorhabdus considering the traditional 16s rDNA gene region as well as the housekeeping genes recA and serC. Datasets were analyzed individually and then combined, using a variety of phylogenetic criteria.}, }
@article {pmid20098599, year = {2009}, author = {Hakvåg, S and Fjaervik, E and Klinkenberg, G and Borgos, SE and Josefsen, KD and Ellingsen, TE and Zotchev, SB}, title = {Violacein-producing Collimonas sp. from the sea surface microlayer of costal waters in Trøndelag, Norway.}, journal = {Marine drugs}, volume = {7}, number = {4}, pages = {576-588}, pmid = {20098599}, issn = {1660-3397}, mesh = {Anti-Infective Agents/*isolation &amp; purification/pharmacology ; Base Sequence ; Candida albicans/drug effects ; Enterococcus faecium/drug effects ; Escherichia coli/drug effects ; Genes, Bacterial ; Indoles/*isolation &amp; purification/pharmacology ; Microbial Sensitivity Tests ; Micrococcaceae/drug effects ; Molecular Sequence Data ; Multigene Family ; Norway ; Oxalobacteraceae/genetics/*metabolism ; Phylogeny ; }, abstract = {A new strain belonging to the genus Collimonas was isolated from the sea surface microlayer off the coast of Trøndelag, Norway. The bacterium, designated Collimonas CT, produced an antibacterial compound active against Micrococcus luteus. Subsequent studies using LC-MS identified this antibacterial compound as violacein, known to be produced by several marine-derived bacteria. Fragments of the violacein biosynthesis genes vioA and vioB were amplified by PCR from the Collimonas CT genome and sequenced. Phylogenetic analysis of these sequences demonstrated close relatedness of the Collimonas CT violacein biosynthetic gene cluster to those in Janthinobacterium lividum and Duganella sp., suggesting relatively recent horizontal gene transfer. Considering diverse biological activities of violacein, Collimonas CT shall be further studied as a potential producer of this compound.}, }
@article {pmid20097815, year = {2010}, author = {Lang, P and Lefebure, T and Wang, W and Pavinski Bitar, P and Meinersmann, RJ and Kaya, K and Stanhope, MJ}, title = {Expanded multilocus sequence typing and comparative genomic hybridization of Campylobacter coli isolates from multiple hosts.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {6}, pages = {1913-1925}, pmid = {20097815}, issn = {1098-5336}, support = {N01AI30054/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Birds/microbiology ; Campylobacter coli/*classification/*genetics/isolation &amp; purification ; Cluster Analysis ; *Comparative Genomic Hybridization ; *DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; Environmental Microbiology ; Europe ; Geography ; Humans ; Molecular Sequence Data ; North America ; *Polymorphism, Genetic ; Poultry/microbiology ; Sequence Analysis, DNA ; Swine/microbiology ; United Kingdom ; }, abstract = {The purpose of this work was to evaluate the evolutionary history of Campylobacter coli isolates derived from multiple host sources and to use microarray comparative genomic hybridization to assess whether there are particular genes comprising the dispensable portion of the genome that are more commonly associated with certain host species. Genotyping and ClonalFrame analyses of an expanded 16-gene multilocus sequence typing (MLST) data set involving 85 isolates from 4 different hosts species tentatively supported the development of C. coli host-preferred groups and suggested that recombination has played various roles in their diversification; however, geography could not be excluded as a contributing factor underlying the history of some of the groups. Population genetic analyses of the C. coli pubMLST database by use of STRUCTURE suggested that isolates from swine form a relatively homogeneous genetic group, that chicken and human isolates show considerable genetic overlap, that isolates from ducks and wild birds have similarity with environmental water samples and that turkey isolates have a connection with human infection similar to that observed for chickens. Analysis of molecular variance (AMOVA) was performed on these same data and suggested that host species was a significant factor in explaining genetic variation and that macrogeography (North America, Europe, and the United Kingdom) was not. The microarray comparative genomic hybridization data suggested that there were combinations of genes more commonly associated with isolates derived from particular hosts and, combined with the results on evolutionary history, suggest that this is due to a combination of common ancestry in some cases and lateral gene transfer in others.}, }
@article {pmid20097813, year = {2010}, author = {Baldridge, GD and Burkhardt, NY and Labruna, MB and Pacheco, RC and Paddock, CD and Williamson, PC and Billingsley, PM and Felsheim, RF and Kurtti, TJ and Munderloh, UG}, title = {Wide dispersal and possible multiple origins of low-copy-number plasmids in rickettsia species associated with blood-feeding arthropods.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {6}, pages = {1718-1731}, pmid = {20097813}, issn = {1098-5336}, support = {R01 AI049424/AI/NIAID NIH HHS/United States ; R01 AI081690/AI/NIAID NIH HHS/United States ; R01 AI49424/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacterial Proteins/genetics ; Cluster Analysis ; DNA, Bacterial/chemistry/*genetics ; Heat-Shock Proteins/genetics ; Humans ; Molecular Sequence Data ; Phylogeny ; Plasmids/*genetics ; Rickettsia/*genetics/isolation &amp; purification ; Rickettsia Infections/*microbiology ; Sequence Analysis, DNA ; Sequence Homology ; Ticks/*microbiology ; }, abstract = {Plasmids are mobile genetic elements of bacteria that can impart important adaptive traits, such as increased virulence or antibiotic resistance. We report the existence of plasmids in Rickettsia (Rickettsiales; Rickettsiaceae) species, including Rickettsia akari, "Candidatus Rickettsia amblyommii," R. bellii, R. rhipicephali, and REIS, the rickettsial endosymbiont of Ixodes scapularis. All of the rickettsiae were isolated from humans or North and South American ticks. R. parkeri isolates from both continents did not possess plasmids. We have now demonstrated plasmids in nearly all Rickettsia species that we have surveyed from three continents, which represent three of the four major proposed phylogenetic groups associated with blood-feeding arthropods. Gel-based evidence consistent with the existence of multiple plasmids in some species was confirmed by cloning plasmids with very different sequences from each of two "Ca. Rickettsia amblyommii" isolates. Phylogenetic analysis of rickettsial ParA plasmid partitioning proteins indicated multiple parA gene origins and plasmid incompatibility groups, consistent with possible multiple plasmid origins. Phylogenetic analysis of potentially host-adaptive rickettsial small heat shock proteins showed that hsp2 genes were plasmid specific and that hsp1 genes, found only on plasmids of "Ca. Rickettsia amblyommii," R. felis, R. monacensis, and R. peacockii, were probably acquired independently of the hsp2 genes. Plasmid copy numbers in seven Rickettsia species ranged from 2.4 to 9.2 per chromosomal equivalent, as determined by real-time quantitative PCR. Plasmids may be of significance in rickettsial evolution and epidemiology by conferring genetic plasticity and host-adaptive traits via horizontal gene transfer that counteracts the reductive genome evolution typical of obligate intracellular bacteria.}, }
@article {pmid20097223, year = {2010}, author = {Ferri, L and Gori, A and Biondi, EG and Mengoni, A and Bazzicalupo, M}, title = {Plasmid electroporation of Sinorhizobium strains: The role of the restriction gene hsdR in type strain Rm1021.}, journal = {Plasmid}, volume = {63}, number = {3}, pages = {128-135}, doi = {10.1016/j.plasmid.2010.01.001}, pmid = {20097223}, issn = {1095-9890}, mesh = {Conjugation, Genetic ; DNA/genetics/*metabolism ; DNA Restriction Enzymes/*genetics ; Electroporation/*methods ; Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Genes, Bacterial/*genetics ; Phylogeny ; Plasmids/*genetics/*metabolism ; Sinorhizobium/*classification/*genetics ; Transformation, Genetic ; }, abstract = {Although horizontal gene transfer mediated by plasmids is important to the generation of the genetic variability of Sinorhizobium strains, the barriers which can reduce horizontal gene transfer between bacteria have not yet been studied in Sinorhizobium. We studied the plasmid transfer by electroporation and its restriction in strains of Sinorhizobium meliloti and S. medicae. After conditions for electroporation were established, three S. meliloti strains (including the sequenced type strain Rm1021) and two S. medicae strains were electroporated with plasmid DNA extracted from strains of both species. The efficiency of transformation was found to be variable among different strains. The acquisition of plasmid DNA was found to be donor-dependent in S. meliloti strain Rm1021 that prefers self-DNA more than the DNA from other Sinorhizobium strains. All other strains tested did not show a preference for self-DNA. In strain Rm1021, the inactivation of the hsdR gene, coding for a putative type-I restriction enzyme, increased the efficiency of transformation and conjugation with non-self DNA; the transformation capability was again reduced in hsdR mutant when the cloned hsdR gene was expressed from a lac promoter. Phylogenetic analysis of the hsdR gene clearly indicated that this gene was horizontally transferred to strain Rm1021, explaining its absence in the other strains tested.}, }
@article {pmid20096999, year = {2010}, author = {El Azhari, N and Devers-Lamrani, M and Chatagnier, G and Rouard, N and Martin-Laurent, F}, title = {Molecular analysis of the catechol-degrading bacterial community in a coal wasteland heavily contaminated with PAHs.}, journal = {Journal of hazardous materials}, volume = {177}, number = {1-3}, pages = {593-601}, doi = {10.1016/j.jhazmat.2009.12.074}, pmid = {20096999}, issn = {1873-3336}, mesh = {Actinobacteria ; Bacteria/genetics/*isolation &amp; purification/metabolism ; *Biodegradation, Environmental ; Catechols/*metabolism ; *Coal ; DNA, Bacterial/analysis/genetics ; *Industrial Waste ; *Polycyclic Aromatic Hydrocarbons ; Proteobacteria ; *Soil Pollutants ; }, abstract = {A PCR-based molecular tool was developed to estimate the diversity of the catechol-degrading bacterial community in a coal wasteland heavily contaminated with PAHS. A degenerate primer pair specific to catA sequences was designed by multiple alignment of known sequences coding a key intermediate of the beta-ketoadiapate pathway degrading catechol, namely catechol 1,2-dioxygenase. The specificity of this primer pair was assessed in 21 pure strains by PCR and sequencing. Comparison of the 16S rDNA and catA phylogenies revealed an absence of congruence between these two genes. The primer set was able to amplify catA sequences in DNA extracts from an industrial soil highly contaminated with heavy metals and polycyclic aromatic hydrocarbons (PAHs). RFLP screening of the catA library (95 clones) yielded 32 RFLP families. All of the 43 clone sequences obtained exhibited 86% identity on average to known CatA. Phylogenetic analysis revealed that these CatA sequences were related to Actinobacteria, alpha-, beta- and gamma-Proteobacteria phyla and confirmed the absence of congruence with 16S rDNA sequences, which implies horizontal gene transfer of the cat gene cluster between soil microbiota. Our results suggest that the diversity of the catA bacterial community is maintained in highly contaminated soil.}, }
@article {pmid20095130, year = {2009}, author = {Moore, JE and Maeda, Y and Millar, BC and Goldsmith, CE and Coulter, WA and Mason, C and Elborn, JS}, title = {Long-term antibiotic treatment of patients with cystic fibrosis: a commensal organism's view.}, journal = {British journal of biomedical science}, volume = {66}, number = {4}, pages = {203-205}, doi = {10.1080/09674845.2009.11978169}, pmid = {20095130}, issn = {0967-4845}, mesh = {Adult ; Anti-Bacterial Agents/*pharmacology/therapeutic use ; *Antibiotic Prophylaxis ; Child ; Child, Preschool ; Cystic Fibrosis/complications/*drug therapy/microbiology ; Drug Resistance, Microbial/*genetics ; Drug Therapy, Combination ; Europe ; Gene Transfer, Horizontal ; Humans ; Long-Term Care ; Pseudomonas Infections/drug therapy ; Pseudomonas aeruginosa ; Respiratory System/microbiology ; Respiratory Tract Infections/microbiology/prevention &amp; control ; Sputum/microbiology ; Viridans Streptococci/drug effects ; }, }
@article {pmid20090843, year = {2010}, author = {Zhou, Z and Li, X and Liu, B and Beutin, L and Xu, J and Ren, Y and Feng, L and Lan, R and Reeves, PR and Wang, L}, title = {Derivation of Escherichia coli O157:H7 from its O55:H7 precursor.}, journal = {PloS one}, volume = {5}, number = {1}, pages = {e8700}, pmid = {20090843}, issn = {1932-6203}, support = {R01 AA020703/AA/NIAAA NIH HHS/United States ; R37 AA020703/AA/NIAAA NIH HHS/United States ; }, mesh = {Chromosomes, Bacterial ; Escherichia coli O157/classification/genetics/*isolation &amp; purification ; Genome, Bacterial ; Mutation ; Phylogeny ; Plasmids ; Recombination, Genetic ; Species Specificity ; }, abstract = {There are 29 E. coli genome sequences available, mostly related to studies of species diversity or mode of pathogenicity, including two genomes of the well-known O157:H7 clone. However, there have been no genome studies of closely related clones aimed at exposing the details of evolutionary change. Here we sequenced the genome of an O55:H7 strain, closely related to the major pathogenic O157:H7 clone, with published genome sequences, and undertook comparative genomic and proteomic analysis. We were able to allocate most differences between the genomes to individual mutations, recombination events, or lateral gene transfer events, in specific lineages. Major differences include a type II secretion system present only in the O55:H7 chromosome, fewer type III secretion system effectors in O55:H7, and 19 phage genomes or phagelike elements in O55:H7 compared to 23 in O157:H7, with only three common to both. Many other changes were found in both O55:H7 and O157:H7 lineages, but in general there has been more change in the O157:H7 lineages. For example, we found 50% more synonymous mutational substitutions in O157:H7 compared to O55:H7. The two strains also diverged at the proteomic level. Mutational synonymous SNPs were used to estimate a divergence time of 400 years using a new clock rate, in contrast to 14,000 to 70,000 years using the traditional clock rates. The same approaches were applied to three closely related extraintestinal pathogenic E. coli genomes, and similar levels of mutation and recombination were found. This study revealed for the first time the full range of events involved in the evolution of the O157:H7 clone from its O55:H7 ancestor, and suggested that O157:H7 arose quite recently. Our findings also suggest that E. coli has a much lower frequency of recombination relative to mutation than was observed in a comparable study of a Vibrio cholerae lineage.}, }
@article {pmid20090786, year = {2010}, author = {Kenzaka, T and Tani, K and Nasu, M}, title = {High-frequency phage-mediated gene transfer in freshwater environments determined at single-cell level.}, journal = {The ISME journal}, volume = {4}, number = {5}, pages = {648-659}, doi = {10.1038/ismej.2009.145}, pmid = {20090786}, issn = {1751-7370}, mesh = {Bacteriophage P1/genetics ; Bacteriophage T4/genetics ; Bacteriophages/*genetics ; Enterobacteriaceae/*genetics/*virology ; Fresh Water/*microbiology/*virology ; *Gene Transfer, Horizontal ; In Situ Hybridization, Fluorescence ; Japan ; Nucleic Acid Amplification Techniques ; }, abstract = {Lateral gene transfer by phages has contributed significantly to the genetic diversity of bacteria. To accurately determine the frequency and range of phage-mediated gene transfer, it is important to understand the movement of DNA among microbes. Using an in situ DNA amplification technique (cycling primed in situ amplification-fluorescent in situ hybridization; CPRINS-FISH), we examined the propensity for phage-mediated gene transfer in freshwater environments at the single-cell level. Phage P1, T4 and isolated Escherichia coli phage EC10 were used as vectors. All E. coli phages mediated gene transfer from E. coli to both plaque-forming and non-plaque-forming Enterobacteriaceae strains at frequencies of 0.3-8 x 10(-3) per plaque-forming unit (PFU), whereas culture methods using selective agar media could not detect transductants in non-plaque-forming strains. The DNA transfer frequencies through phage EC10 ranged from undetectable to 9 x 10(-2) per PFU (undetectable to 2 x 10(-3) per total direct count) when natural bacterial communities were recipients. Direct viable counting combined with CPRINS-FISH revealed that more than 20% of the cells carrying the transferred gene retained their viability in most cases. These results indicate that the exchange of DNA sequences among bacteria occurs frequently and in a wide range of bacteria, and may promote rapid evolution of the prokaryotic genome in freshwater environments.}, }
@article {pmid20088865, year = {2010}, author = {Lind, PA and Tobin, C and Berg, OG and Kurland, CG and Andersson, DI}, title = {Compensatory gene amplification restores fitness after inter-species gene replacements.}, journal = {Molecular microbiology}, volume = {75}, number = {5}, pages = {1078-1089}, doi = {10.1111/j.1365-2958.2009.07030.x}, pmid = {20088865}, issn = {1365-2958}, mesh = {Adaptation, Biological ; Bacterial Proteins/*genetics ; Evolution, Molecular ; Gene Amplification ; Gene Duplication ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Ribosomal Proteins/*genetics ; Salmonella typhimurium/*genetics/growth &amp; development/physiology ; }, abstract = {Genes introduced by gene replacements and other types of horizontal gene transfer (HGT) represent a significant presence in many archaeal and eubacterial genomes. Most alien genes are likely to be neutral or deleterious upon arrival and their long-term persistence may require a mechanism that improves their selective contribution. To examine the fate of inter-species gene replacements, we exchanged three native S. typhimurium genes encoding ribosomal proteins with orthologues from various other microbes. The results show that replacement of each of these three genes reduces fitness to such an extent that it would provide an effective barrier against inter-species gene replacements in eubacterial populations. However, these fitness defects could be partially ameliorated by gene amplification that augmented the dosage of the heterologous proteins. This suggests that suboptimal expression is a common fitness constraint for inter-species gene replacements, with fitness costs conferred by either a lower expression level of the alien protein compared with the native protein or a requirement for an increased amount of the alien protein to maintain proper function. Our findings can explain the observation that duplicated genes are over-represented among horizontally transferred genes, and suggest a potential coupling between compensatory gene amplification after HGT and the evolution of new genes.}, }
@article {pmid20087669, year = {2010}, author = {van Iersel, L and Semple, C and Steel, M}, title = {Quantifying the extent of lateral gene transfer required to Avert a 'genome of Eden'.}, journal = {Bulletin of mathematical biology}, volume = {72}, number = {7}, pages = {1783-1798}, doi = {10.1007/s11538-010-9506-7}, pmid = {20087669}, issn = {1522-9602}, mesh = {Algorithms ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome ; *Models, Genetic ; Prokaryotic Cells/*physiology ; }, abstract = {The complex pattern of presence and absence of many genes across different species provides tantalising clues as to how genes evolved through the processes of gene genesis, gene loss, and lateral gene transfer (LGT). The extent of LGT, particularly in prokaryotes, and its implications for creating a 'network of life' rather than a 'tree of life' is controversial. In this paper, we formally model the problem of quantifying LGT, and provide exact mathematical bounds, and new computational results. In particular, we investigate the computational complexity of quantifying the extent of LGT under the simple models of gene genesis, loss, and transfer on which a recent heuristic analysis of biological data relied. Our approach takes advantage of a relationship between LGT optimization and graph-theoretical concepts such as tree width and network flow.}, }
@article {pmid20084283, year = {2010}, author = {Paauw, A and Leverstein-van Hall, MA and Verhoef, J and Fluit, AC}, title = {Evolution in quantum leaps: multiple combinatorial transfers of HPI and other genetic modules in Enterobacteriaceae.}, journal = {PloS one}, volume = {5}, number = {1}, pages = {e8662}, pmid = {20084283}, issn = {1932-6203}, mesh = {Base Sequence ; *Biological Evolution ; DNA Primers ; Enterobacteriaceae/*genetics/pathogenicity ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Phylogeny ; Recombination, Genetic ; Virulence ; }, abstract = {Horizontal gene transfer is a key step in the evolution of Enterobacteriaceae. By acquiring virulence determinants of foreign origin, commensals can evolve into pathogens. In Enterobacteriaceae, horizontal transfer of these virulence determinants is largely dependent on transfer by plasmids, phages, genomic islands (GIs) and genomic modules (GMs). The High Pathogenicity Island (HPI) is a GI encoding virulence genes that can be transferred between different Enterobacteriaceae. We investigated the HPI because it was present in an Enterobacter hormaechei outbreak strain (EHOS). Genome sequence analysis showed that the EHOS contained an integration site for mobile elements and harbored two GIs and three putative GMs, including a new variant of the HPI (HPI-ICEEh1). We demonstrate, for the first time, that combinatorial transfers of GIs and GMs between Enterobacter cloacae complex isolates must have occurred. Furthermore, the excision and circularization of several combinations of the GIs and GMs was demonstrated. Because of its flexibility, the multiple integration site of mobile DNA can be considered an integration hotspot (IHS) that increases the genomic plasticity of the bacterium. Multiple combinatorial transfers of diverse combinations of the HPI and other genomic elements among Enterobacteriaceae may accelerate the generation of new pathogenic strains.}, }
@article {pmid20084095, year = {2010}, author = {Marchetti, M and Capela, D and Glew, M and Cruveiller, S and Chane-Woon-Ming, B and Gris, C and Timmers, T and Poinsot, V and Gilbert, LB and Heeb, P and Médigue, C and Batut, J and Masson-Boivin, C}, title = {Experimental evolution of a plant pathogen into a legume symbiont.}, journal = {PLoS biology}, volume = {8}, number = {1}, pages = {e1000280}, pmid = {20084095}, issn = {1545-7885}, mesh = {Adaptation, Biological ; Chimera ; Directed Molecular Evolution ; Fabaceae/*microbiology ; Gene Transfer, Horizontal ; Nitrogen Fixation ; Plant Root Nodulation/genetics ; Polymorphism, Single Nucleotide ; Rhizobium/*genetics/physiology ; Symbiosis/*genetics ; }, abstract = {Rhizobia are phylogenetically disparate alpha- and beta-proteobacteria that have achieved the environmentally essential function of fixing atmospheric nitrogen in symbiosis with legumes. Ample evidence indicates that horizontal transfer of symbiotic plasmids/islands has played a crucial role in rhizobia evolution. However, adaptive mechanisms that allow the recipient genomes to express symbiotic traits are unknown. Here, we report on the experimental evolution of a pathogenic Ralstonia solanacearum chimera carrying the symbiotic plasmid of the rhizobium Cupriavidus taiwanensis into Mimosa nodulating and infecting symbionts. Two types of adaptive mutations in the hrpG-controlled virulence pathway of R. solanacearum were identified that are crucial for the transition from pathogenicity towards mutualism. Inactivation of the hrcV structural gene of the type III secretion system allowed nodulation and early infection to take place, whereas inactivation of the master virulence regulator hrpG allowed intracellular infection of nodule cells. Our findings predict that natural selection of adaptive changes in the legume environment following horizontal transfer has been a major driving force in rhizobia evolution and diversification and show the potential of experimental evolution to decipher the mechanisms leading to symbiosis.}, }
@article {pmid20082446, year = {2011}, author = {Hrouzek, P and Tomek, P and Lukešová, A and Urban, J and Voloshko, L and Pushparaj, B and Ventura, S and Lukavský, J and Stys, D and Kopecký, J}, title = {Cytotoxicity and secondary metabolites production in terrestrial Nostoc strains, originating from different climatic/geographic regions and habitats: is their cytotoxicity environmentally dependent?.}, journal = {Environmental toxicology}, volume = {26}, number = {4}, pages = {345-358}, doi = {10.1002/tox.20561}, pmid = {20082446}, issn = {1522-7278}, mesh = {*Climate ; Cytotoxins/*metabolism ; Ecosystem ; Nostoc/classification/genetics/*metabolism ; Phylogeny ; Soil Microbiology ; Species Specificity ; Symbiosis ; }, abstract = {Extensive selection of cyanobacterial strains (82 isolates) belonging to the genus Nostoc, isolated from different climatic regions and habitats, were screened for both their secondary metabolite content and their cytotoxic effects to mammalian cell lines. The overall occurrence of cytotoxicity was found to be 33%, which corresponds with previously published data. However, the frequency differs significantly among strains, which originate from different climatic regions and microsites (particular localities). A large fraction of intensely cytotoxic strains were found among symbiotic strains (60%) and temperate and continental climatic isolates (45%); compared with the less significant incidences in strains originating from cold regions (36%), deserts (14%), and tropical habitats (9%). The cytotoxic strains were not randomly distributed; microsites that clearly had a higher occurrence of cytotoxicity were observed. Apparently, certain natural conditions lead to the selection of cytotoxic strains, resulting in a high cytotoxicity occurrence, and vice versa. Moreover, in strains isolated from a particular microsite, the cytotoxic effects were caused by different compounds. This result supports our hypothesis for the environmental dependence of cytotoxicity. It also contradicts the hypothesis that clonality and lateral gene transfer could be the reason for this phenomenon. Enormous variability in the secondary metabolites was detected within the studied Nostoc extracts. According to their molecular masses, only 26% of these corresponded to any known structures; thus, pointing to the high potential for the use of many terrestrial cyanobacteria in both pharmacology and biotechnology.}, }
@article {pmid20079869, year = {2010}, author = {Song, JM and Nam, K and Sun, YU and Kang, MH and Kim, CG and Kwon, ST and Lee, J and Lee, YH}, title = {Molecular and biochemical characterizations of a novel arthropod endo-beta-1,3-glucanase from the Antarctic springtail, Cryptopygus antarcticus, horizontally acquired from bacteria.}, journal = {Comparative biochemistry and physiology. Part B, Biochemistry &amp; molecular biology}, volume = {155}, number = {4}, pages = {403-412}, doi = {10.1016/j.cbpb.2010.01.003}, pmid = {20079869}, issn = {1879-1107}, mesh = {Amino Acid Sequence ; Animals ; Antarctic Regions ; Arthropods/*enzymology ; Base Sequence ; Cellulase/*chemistry/genetics/metabolism ; Cloning, Molecular ; Gene Expression Regulation ; Gene Transfer, Horizontal ; Genes, Bacterial ; Molecular Sequence Data ; Phylogeny ; Recombinant Proteins/chemistry/genetics/metabolism ; Sequence Alignment ; Temperature ; }, abstract = {Collembolan species have been known to have beta-1,3-glucanase activity and yet the genes coding such enzymes have not been demonstrated. We report here a novel arthropod endo-beta-1,3-glucanase gene CaLam from the Antarctic springtail, Cryptopygus antarcticus. The open reading frame consists of 813bp encoding 270 amino acids with a putative signal peptide and a typical motif of glycosyl hydrolase family 16 (GHF16), E-I-D-I-T-E. The recombinant protein expressed in E. coli shows the hydrolytic activity toward laminarin (K(m) approximately 9.98mg/mL) with an optimal temperature 50 degrees C and an optimal pH 6.0. CaLam digests laminarin and laminarioligosaccharides except laminaribiose as an endo-beta-1,3-glucanase, releasing glucose, laminaribiose and laminaritriose as the major products. Analyses of molecular phylogeny of CaLam and its protein structure reveal that CaLam is closely related with bacterial beta-1,3-glucanases more than with the eukaryotic homologues. Even so, the genomic structure of the CaLam gene consisting of six exons interspersed with approximately 57 to 63bp introns confirms that it is endogenous in the genome of the Antarctic springtail. These results suggest that CaLam should have been transferred from bacteria to the lineage of the Collembolan species by horizontal gene transfer.}, }
@article {pmid20078895, year = {2010}, author = {Butler, JE and Young, ND and Lovley, DR}, title = {Evolution of electron transfer out of the cell: comparative genomics of six Geobacter genomes.}, journal = {BMC genomics}, volume = {11}, number = {}, pages = {40}, pmid = {20078895}, issn = {1471-2164}, mesh = {Acetates/metabolism ; Bacterial Proton-Translocating ATPases/genetics ; Citric Acid Cycle ; Cluster Analysis ; *Comparative Genomic Hybridization ; Cytochromes/genetics ; Electron Transport/*genetics ; *Evolution, Molecular ; Gene Duplication ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomics/methods ; Geobacter/*genetics ; NADH Dehydrogenase/genetics ; Oxidation-Reduction ; Phylogeny ; }, abstract = {BACKGROUND: Geobacter species grow by transferring electrons out of the cell--either to Fe(III)-oxides or to man-made substances like energy-harvesting electrodes. Study of Geobacter sulfurreducens has shown that TCA cycle enzymes, inner-membrane respiratory enzymes, and periplasmic and outer-membrane cytochromes are required. Here we present comparative analysis of six Geobacter genomes, including species from the clade that predominates in the subsurface. Conservation of proteins across the genomes was determined to better understand the evolution of Geobacter species and to create a metabolic model applicable to subsurface environments.<br><br>RESULTS: The results showed that enzymes for acetate transport and oxidation, and for proton transport across the inner membrane were well conserved. An NADH dehydrogenase, the ATP synthase, and several TCA cycle enzymes were among the best conserved in the genomes. However, most of the cytochromes required for Fe(III)-reduction were not, including many of the outer-membrane cytochromes. While conservation of cytochromes was poor, an abundance and diversity of cytochromes were found in every genome, with duplications apparent in several species.<br><br>CONCLUSIONS: These results indicate there is a common pathway for acetate oxidation and energy generation across the family and in the last common ancestor. They also suggest that while cytochromes are important for extracellular electron transport, the path of electrons across the periplasm and outer membrane is variable. This combination of abundant cytochromes with weak sequence conservation suggests they may not be specific terminal reductases, but rather may be important in their heme-bearing capacity, as sinks for electrons between the inner-membrane electron transport chain and the extracellular acceptor.}, }
@article {pmid20075255, year = {2010}, author = {Werren, JH and Richards, S and Desjardins, CA and Niehuis, O and Gadau, J and Colbourne, JK and ,  and Werren, JH and Richards, S and Desjardins, CA and Niehuis, O and Gadau, J and Colbourne, JK and Beukeboom, LW and Desplan, C and Elsik, CG and Grimmelikhuijzen, CJ and Kitts, P and Lynch, JA and Murphy, T and Oliveira, DC and Smith, CD and van de Zande, L and Worley, KC and Zdobnov, EM and Aerts, M and Albert, S and Anaya, VH and Anzola, JM and Barchuk, AR and Behura, SK and Bera, AN and Berenbaum, MR and Bertossa, RC and Bitondi, MM and Bordenstein, SR and Bork, P and Bornberg-Bauer, E and Brunain, M and Cazzamali, G and Chaboub, L and Chacko, J and Chavez, D and Childers, CP and Choi, JH and Clark, ME and Claudianos, C and Clinton, RA and Cree, AG and Cristino, AS and Dang, PM and Darby, AC and de Graaf, DC and Devreese, B and Dinh, HH and Edwards, R and Elango, N and Elhaik, E and Ermolaeva, O and Evans, JD and Foret, S and Fowler, GR and Gerlach, D and Gibson, JD and Gilbert, DG and Graur, D and Gründer, S and Hagen, DE and Han, Y and Hauser, F and Hultmark, D and Hunter, HC and Hurst, GD and Jhangian, SN and Jiang, H and Johnson, RM and Jones, AK and Junier, T and Kadowaki, T and Kamping, A and Kapustin, Y and Kechavarzi, B and Kim, J and Kim, J and Kiryutin, B and Koevoets, T and Kovar, CL and Kriventseva, EV and Kucharski, R and Lee, H and Lee, SL and Lees, K and Lewis, LR and Loehlin, DW and Logsdon, JM and Lopez, JA and Lozado, RJ and Maglott, D and Maleszka, R and Mayampurath, A and Mazur, DJ and McClure, MA and Moore, AD and Morgan, MB and Muller, J and Munoz-Torres, MC and Muzny, DM and Nazareth, LV and Neupert, S and Nguyen, NB and Nunes, FM and Oakeshott, JG and Okwuonu, GO and Pannebakker, BA and Pejaver, VR and Peng, Z and Pratt, SC and Predel, R and Pu, LL and Ranson, H and Raychoudhury, R and Rechtsteiner, A and Reese, JT and Reid, JG and Riddle, M and Robertson, HM and Romero-Severson, J and Rosenberg, M and Sackton, TB and Sattelle, DB and Schlüns, H and Schmitt, T and Schneider, M and Schüler, A and Schurko, AM and Shuker, DM and Simões, ZL and Sinha, S and Smith, Z and Solovyev, V and Souvorov, A and Springauf, A and Stafflinger, E and Stage, DE and Stanke, M and Tanaka, Y and Telschow, A and Trent, C and Vattathil, S and Verhulst, EC and Viljakainen, L and Wanner, KW and Waterhouse, RM and Whitfield, JB and Wilkes, TE and Williamson, M and Willis, JH and Wolschin, F and Wyder, S and Yamada, T and Yi, SV and Zecher, CN and Zhang, L and Gibbs, RA}, title = {Functional and evolutionary insights from the genomes of three parasitoid Nasonia species.}, journal = {Science (New York, N.Y.)}, volume = {327}, number = {5963}, pages = {343-348}, pmid = {20075255}, issn = {1095-9203}, support = {5R24GM084917-02/GM/NIGMS NIH HHS/United States ; R01 GM070026-04S1/GM/NIGMS NIH HHS/United States ; R24 GM084917/GM/NIGMS NIH HHS/United States ; R01 GM064864-05A2/GM/NIGMS NIH HHS/United States ; R01 GM070026/GM/NIGMS NIH HHS/United States ; R01 HG000747-14/HG/NHGRI NIH HHS/United States ; U54 HG003273-03/HG/NHGRI NIH HHS/United States ; R01 HG000747/HG/NHGRI NIH HHS/United States ; R01 GM064864/GM/NIGMS NIH HHS/United States ; R01 GM085163-01/GM/NIGMS NIH HHS/United States ; R01GM064864/GM/NIGMS NIH HHS/United States ; R01 GM085233/GM/NIGMS NIH HHS/United States ; R01 AI055624/AI/NIAID NIH HHS/United States ; U54 HG003273/HG/NHGRI NIH HHS/United States ; R24 GM084917-02/GM/NIGMS NIH HHS/United States ; 5R01HG000747-14/HG/NHGRI NIH HHS/United States ; /ImNIH/Intramural NIH HHS/United States ; R01 GM064864-04/GM/NIGMS NIH HHS/United States ; R01 GM085163/GM/NIGMS NIH HHS/United States ; R01 GM079484/GM/NIGMS NIH HHS/United States ; R24 GM084917-01/GM/NIGMS NIH HHS/United States ; 5R01GM070026-04/GM/NIGMS NIH HHS/United States ; AI028309-13A2/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Arthropods/parasitology ; *Biological Evolution ; DNA Methylation ; DNA Transposable Elements ; Female ; Gene Transfer, Horizontal ; Genes, Insect ; Genetic Speciation ; Genetic Variation ; *Genome, Insect ; Host-Parasite Interactions ; Insect Proteins/genetics/metabolism ; Insect Viruses/genetics ; Insecta/genetics ; Male ; Molecular Sequence Data ; Quantitative Trait Loci ; Recombination, Genetic ; Sequence Analysis, DNA ; Wasp Venoms/chemistry/toxicity ; Wasps/*genetics/physiology ; Wolbachia/genetics ; }, abstract = {We report here genome sequences and comparative analyses of three closely related parasitoid wasps: Nasonia vitripennis, N. giraulti, and N. longicornis. Parasitoids are important regulators of arthropod populations, including major agricultural pests and disease vectors, and Nasonia is an emerging genetic model, particularly for evolutionary and developmental genetics. Key findings include the identification of a functional DNA methylation tool kit; hymenopteran-specific genes including diverse venoms; lateral gene transfers among Pox viruses, Wolbachia, and Nasonia; and the rapid evolution of genes involved in nuclear-mitochondrial interactions that are implicated in speciation. Newly developed genome resources advance Nasonia for genetic research, accelerate mapping and cloning of quantitative trait loci, and will ultimately provide tools and knowledge for further increasing the utility of parasitoids as pest insect-control agents.}, }
@article {pmid20074643, year = {2010}, author = {Toomey, N and Bolton, D and Fanning, S}, title = {Characterisation and transferability of antibiotic resistance genes from lactic acid bacteria isolated from Irish pork and beef abattoirs.}, journal = {Research in microbiology}, volume = {161}, number = {2}, pages = {127-135}, doi = {10.1016/j.resmic.2009.12.010}, pmid = {20074643}, issn = {1769-7123}, mesh = {Abattoirs ; Anti-Bacterial Agents/*pharmacology ; Conjugation, Genetic ; DNA, Bacterial/genetics ; *Drug Resistance, Bacterial ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Gram-Positive Bacteria/*drug effects/*genetics/isolation &amp; purification/metabolism ; Ireland ; Lactic Acid/*metabolism ; Microbial Sensitivity Tests ; Polymerase Chain Reaction ; }, abstract = {Lactic acid bacteria isolated from Irish pork and beef abattoirs were analysed for their susceptibility to antimicrobials. Thirty-seven isolates (12 enterococci, 10 lactobacilli, 8 streptococci, 3 lactococci, 2 Leuconostoc, and 2 pediococci) were examined for phenotypic resistance using the E-test and their minimum inhibitory concentration to a panel of six antibiotics (ampicillin, chloramphenicol, erythromycin, streptomycin, tetracycline, and vancomycin) was recorded. The corresponding genetic determinants responsible were characterised by PCR. Also, the transferability of these resistance markers was assessed in filter mating assays. Of the 37 isolates, 33 were found to be resistant to one or more antibiotics. All strains were susceptible to ampicillin and chloramphenicol. The erm(B) and msrA/B genes were detected among the 11 erythromycin-resistant strains of enterococci, lactobacilli, and streptococci. Two tetracycline-resistant strains, Lactobacillus plantarum and Leuconostoc mesenteroides spp., contained tet(M) and tet(S) genes respectively. Intrinsic streptomycin resistance was observed in lactobacilli, streptococci, lactococci and Leuconostoc species; none of the common genetic determinants (strA, strB, aadA, aadE) were identified. Four of 10 strains of Enterococcus faecium were resistant to vancomycin; however, no corresponding genetic determinants for this phenotype were identified. Enterococcus faecalis strains were susceptible to vancomycin. L. plantarum, L. mesenteroides and Pediococcus pentosaceus were intrinsically resistant to vancomycin. Transfer of antibiotic resistance determinants was demonstrated in one strain, wherein the tet(M) gene of L. plantarum (23) isolated from a pork abattoir was transferred to Lactococcus lactis BU-2-60 and to E. faecalis JH2-2. This study identified the presence of antibiotic resistance markers in Irish meat isolates and, in one example, resistance was conjugally transferred to other LAB strains.}, }
@article {pmid20071364, year = {2010}, author = {Juan, C and Zamorano, L and Mena, A and Albertí, S and Pérez, JL and Oliver, A}, title = {Metallo-beta-lactamase-producing Pseudomonas putida as a reservoir of multidrug resistance elements that can be transferred to successful Pseudomonas aeruginosa clones.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {65}, number = {3}, pages = {474-478}, doi = {10.1093/jac/dkp491}, pmid = {20071364}, issn = {1460-2091}, mesh = {Bacterial Typing Techniques ; Blotting, Southern ; Cluster Analysis ; Cross Infection/*epidemiology/microbiology ; DNA, Bacterial/chemistry/genetics ; *Drug Resistance, Multiple, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; *Gene Transfer, Horizontal ; Genotype ; Hospitals ; Humans ; Microbial Sensitivity Tests ; Molecular Epidemiology ; Molecular Sequence Data ; Plasmids ; Polymorphism, Genetic ; Pseudomonas Infections/*epidemiology/microbiology ; Pseudomonas aeruginosa/classification/*enzymology/genetics ; Pseudomonas putida/classification/*enzymology/genetics ; Restriction Mapping ; Sequence Analysis, DNA ; Spain/epidemiology ; beta-Lactamases/*biosynthesis/genetics ; }, abstract = {OBJECTIVES: To study the prevalence, nature, involved genetic elements and epidemiology of metallo-beta-lactamase (MBL)-producing Pseudomonas aeruginosa and Pseudomonas putida isolated in a Spanish hospital between 2005 and 2008.<br><br>METHODS: Etests were used for susceptibility testing and screening for MBLs, confirmed through bla(VIM) PCRs and sequencing. Clonal relatedness was evaluated by PFGE and multilocus sequence typing (MLST). MBL-carrying plasmids were characterized by restriction fragment length polymorphism, Southern blot and electroporation. MBL genetic elements were studied by cloning and sequencing.<br><br>RESULTS: MBL-producing P. putida was detected in eight patients (one clone each; two harbouring bla(VIM-1) and six harbouring bla(VIM-2)), representing 14% of all the infections by the P. putida/fluorescens group. MBLs were detected in only 0.3% of P. aeruginosa infections (11 patients) during the same period. PFGE revealed four P. aeruginosa clones: one producing bla(VIM-13) (two patients); and three producing bla(VIM-2) (two patients, six patients and one patient, respectively). MLST indicated that the VIM-13 clone was the internationally spread sequence type (ST)235, while the major VIM-2 lineage corresponded to ST179, which is associated with chronic respiratory infections. The VIM-1 integron was shown to have both plasmid and chromosomal location, while the VIM-13 integron was only chromosomal. The VIM-2 integron was located in the same transposon (Tn402/Tn5053-like) in all P. aeruginosa and P. putida isolates, suggesting its crucial role in the dissemination of VIM-2.<br><br>CONCLUSIONS: The high diversity and proportion of MBL-positive P. putida suggests an environmental reservoir of these resistance determinants. Dissemination of these multidrug resistance elements to successful P. aeruginosa clones presents a major epidemiological and clinical threat.}, }
@article {pmid20068356, year = {2010}, author = {Sánchez, B and Zúñiga, M and González-Candelas, F and de los Reyes-Gavilán, CG and Margolles, A}, title = {Bacterial and eukaryotic phosphoketolases: phylogeny, distribution and evolution.}, journal = {Journal of molecular microbiology and biotechnology}, volume = {18}, number = {1}, pages = {37-51}, doi = {10.1159/000274310}, pmid = {20068356}, issn = {1660-2412}, mesh = {Aldehyde-Lyases/*genetics ; Bacteria/*enzymology/genetics ; Computational Biology ; Eukaryota/*enzymology/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Phylogeny ; Plasmids ; }, abstract = {Phosphoketolases (XFPs) are glycolytic enzymes present in several organisms belonging to the Eukarya and Bacteria domains. A total of 151 putative xfp genes were detected in 650 complete genomes available in public databases. Elimination of redundant sequences and pseudogenes rendered a final data set of 128 phosphoketolases, which was analyzed by phylogenetic methods. The distribution of xfp genes was uneven in most taxonomic groups, with the exception of the taxonomical division Lactobacillaceae, in which all the species studied harbored a putative xfp gene. Putative xfp genes were also present predominantly in Rhizobiales and Actinobacteria divisions, in which 23 out of 28 genomes and 23 out of 41 genomes contained at least one putative xfp homolog, respectively. Phylogenetic analyses showed clear discordance with the expected order of organismal descent even in groups where xfp is prevalent, such as Lactobacillaceae. The presence of putative paralogs in some organisms cannot account for these discrepancies; instead, these paralogs are most possibly xenologs. The results of the phylogenetic analyses, the distribution of xfp genes and the location of some xfp genes in plasmids are independent pieces of evidence that point to horizontal gene transfer as a major driving force in the evolution of phosphoketolases.}, }
@article {pmid20061483, year = {2010}, author = {Doherty, NC and Shen, F and Halliday, NM and Barrett, DA and Hardie, KR and Winzer, K and Atherton, JC}, title = {In Helicobacter pylori, LuxS is a key enzyme in cysteine provision through a reverse transsulfuration pathway.}, journal = {Journal of bacteriology}, volume = {192}, number = {5}, pages = {1184-1192}, pmid = {20061483}, issn = {1098-5530}, support = {G9219778//Medical Research Council/United Kingdom ; //Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacterial Proteins/genetics/*metabolism ; Carbon-Sulfur Lyases/genetics/*metabolism ; Computational Biology ; Culture Media/chemistry ; Cystathionine/metabolism ; Cysteine/*metabolism ; DNA, Bacterial/genetics ; Gene Knockout Techniques ; Gene Order ; Gene Transfer, Horizontal ; Gram-Positive Bacteria/genetics ; Helicobacter pylori/genetics/growth &amp; development/*metabolism ; Homocysteine/metabolism ; *Metabolic Networks and Pathways ; Sequence Analysis, DNA ; Sulfur/*metabolism ; }, abstract = {In many bacteria, LuxS functions as a quorum-sensing molecule synthase. However, it also has a second, more central metabolic function in the activated methyl cycle (AMC), which generates the S-adenosylmethionine required by methyltransferases and recycles the product via methionine. Helicobacter pylori lacks an enzyme catalyzing homocysteine-to-methionine conversion, rendering the AMC incomplete and thus making any metabolic role of H. pylori LuxS (LuxS(Hp)) unclear. Interestingly, luxS(Hp) is located next to genes annotated as cysK(Hp) and metB(Hp), involved in other bacteria in cysteine and methionine metabolism. We showed that isogenic strains carrying mutations in luxS(Hp), cysK(Hp), and metB(Hp) could not grow without added cysteine (whereas the wild type could), suggesting roles in cysteine synthesis. Growth of the DeltaluxS(Hp) mutant was restored by homocysteine or cystathionine and growth of the DeltacysK(Hp) mutant by cystathionine only. The DeltametB(Hp) mutant had an absolute requirement for cysteine. Metabolite analyses showed that S-ribosylhomocysteine accumulated in the DeltaluxS(Hp) mutant, homocysteine in the DeltacysK(Hp) mutant, and cystathionine in the DeltametB(Hp) mutant. This suggests that S-ribosylhomocysteine is converted by LuxS(Hp) to homocysteine (as in the classic AMC) and thence by CysK(Hp) to cystathionine and by MetB(Hp) to cysteine. In silico analysis suggested that cysK-metB-luxS were acquired by H. pylori from a Gram-positive source. We conclude that cysK-metB-luxS encode the capacity to generate cysteine from products of the incomplete AMC of H. pylori in a process of reverse transsulfuration. We recommend that the misnamed genes cysK(Hp) and metB(Hp) be renamed mccA (methionine-to-cysteine-conversion gene A) and mccB, respectively.}, }
@article {pmid20059637, year = {2010}, author = {Bello-López, JM and Fernández-Rendón, E and Curiel-Quesada, E}, title = {In vivo transfer of plasmid pRAS1 between Aeromonas salmonicida and Aeromonas hydrophila in artificially infected Cyprinus carpio L.}, journal = {Journal of fish diseases}, volume = {33}, number = {3}, pages = {251-259}, doi = {10.1111/j.1365-2761.2009.01118.x}, pmid = {20059637}, issn = {1365-2761}, mesh = {Aeromonas hydrophila/*genetics ; Aeromonas salmonicida/*genetics ; Animals ; Carps/*microbiology ; DNA Transposable Elements ; Fish Diseases/*microbiology ; *Gene Transfer, Horizontal ; Gram-Negative Bacterial Infections/microbiology/*veterinary ; Humans ; Mutagenesis ; Plasmids/*genetics ; }, abstract = {This study investigated the possible in vivo transfer of plasmid pRAS1 between Aeromonas salmonicida and A. hydrophila inhabiting two different organs of Cyprinus carpio L. To distinguish transconjugants from naturally occurring antibiotic resistant bacteria, twelve luminescent transposon-tagged A. hydrophila strains using mini Tn5luxCDABEKm2 transposon were generated. In conjugal transfer experiments, fish were conditioned with the donor bacteria and subsequently immersed in water containing the recipient strain. Bacteria were recovered from gills and intestines and isolated by growth on selective plates. Transconjugants were identified by their resistance to the pRAS1 encoded antimicrobials and by light emission. In vivo transfer frequencies ranged between 10(-3) and 10(-6) and were somewhat lower in intestines, compared to gills. Transfer frequencies were also smaller relative to those obtained in vitro. The minimal amount of donor and recipient bacteria needed to yield detectable transconjugants in vivo was 1 x 10(4) CFU mL(-1). Implications of this plasmid transfer in natural settings and its possible consequences to human health are discussed.}, }
@article {pmid20056882, year = {2010}, author = {Horvath, P and Barrangou, R}, title = {CRISPR/Cas, the immune system of bacteria and archaea.}, journal = {Science (New York, N.Y.)}, volume = {327}, number = {5962}, pages = {167-170}, doi = {10.1126/science.1179555}, pmid = {20056882}, issn = {1095-9203}, mesh = {Archaea/*genetics/immunology/virology ; Archaeal Proteins/metabolism ; Bacteria/*genetics/immunology/virology ; Bacterial Proteins/metabolism ; Bacteriophages/genetics/physiology ; Base Sequence ; Conserved Sequence ; Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; *Genetic Loci ; *Genome, Archaeal ; *Genome, Bacterial ; Genome, Viral ; Mutation ; Plasmids ; RNA Interference ; RNA, Archaeal/genetics/metabolism ; RNA, Bacterial/genetics/metabolism ; *Repetitive Sequences, Nucleic Acid ; }, abstract = {Microbes rely on diverse defense mechanisms that allow them to withstand viral predation and exposure to invading nucleic acid. In many Bacteria and most Archaea, clustered regularly interspaced short palindromic repeats (CRISPR) form peculiar genetic loci, which provide acquired immunity against viruses and plasmids by targeting nucleic acid in a sequence-specific manner. These hypervariable loci take up genetic material from invasive elements and build up inheritable DNA-encoded immunity over time. Conversely, viruses have devised mutational escape strategies that allow them to circumvent the CRISPR/Cas system, albeit at a cost. CRISPR features may be exploited for typing purposes, epidemiological studies, host-virus ecological surveys, building specific immunity against undesirable genetic elements, and enhancing viral resistance in domesticated microbes.}, }
@article {pmid20056688, year = {2010}, author = {Yang, J and Luo, Y and Li, J and Ma, Y and Hu, C and Jin, S and Ye, L and Cui, S}, title = {Characterization of clinical Escherichia coli isolates from China containing transferable quinolone resistance determinants.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {65}, number = {3}, pages = {453-459}, doi = {10.1093/jac/dkp478}, pmid = {20056688}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Typing Techniques ; China ; Cluster Analysis ; DNA Fingerprinting ; DNA Mutational Analysis ; *Drug Resistance, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/*drug effects/isolation &amp; purification ; Escherichia coli Infections/*microbiology ; Escherichia coli Proteins/genetics ; *Gene Transfer, Horizontal ; Genotype ; Humans ; Microbial Sensitivity Tests ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Quinolones/*pharmacology ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The categories of recognized transferable quinolone resistance determinants have been increasing sharply. The rapid horizontal transfer of these quinolone resistance genes has caused concern since they bring new dissemination possibilities for quinolone resistance.<br><br>METHODS: In total, 579 clinical Escherichia coli isolates were subjected to antimicrobial susceptibility testing, screening for qnr alleles, qepA and aac-(6')-Ib-cr by PCR amplification and DNA sequence analysis. Isolates containing transferable quinolone resistance determinants were further characterized by mutation analysis in the quinolone resistance determining regions (QRDRs) of GyrA and ParC, phylogenetic typing and PFGE to determine their genetic relatedness.<br><br>RESULTS: After PCR screening and sequence analysis, transferable quinolone resistance determinants were identified in 74 of 579 E. coli isolates (12.8%). The antimicrobial resistance profiles and phylogenetic groups differed between isolates containing different categories of transferable quinolone resistance determinant. Most of the isolates containing qepA alone were highly resistant to ciprofloxacin (MIC >or= 512 mg/L) and belonged to phylogenetic group D (22/25), while most of the isolates containing aac-(6')-Ib-cr alone belonged to phylogenetic group A (17/35) or D (16/35). Of 74 E. coli isolates containing transferable quinolone resistance determinants, 69 PFGE patterns and 19 clusters were identified.<br><br>CONCLUSIONS: The great genetic variation of E. coli hosts containing transferable quinolone resistance determinants demonstrated the high transmission capacity of these mechanisms. It is urgent to characterize and block their transmission routes in order that the utility of quinolones is preserved.}, }
@article {pmid20049599, year = {2010}, author = {Farajzadeh, D and Aliasgharzad, N and Sokhandan Bashir, N and Yakhchali, B}, title = {Cloning and characterization of a plasmid encoded ACC deaminase from an indigenous Pseudomonas fluorescens FY32.}, journal = {Current microbiology}, volume = {61}, number = {1}, pages = {37-43}, pmid = {20049599}, issn = {1432-0991}, mesh = {Amino Acids, Cyclic/*metabolism ; Anti-Bacterial Agents/pharmacology ; Carbon-Carbon Lyases/*genetics/*metabolism ; Cloning, Molecular ; Drug Resistance, Bacterial ; Escherichia coli/drug effects/genetics ; Ethylenes/metabolism ; Genes, Bacterial ; Molecular Sequence Data ; Phylogeny ; Plasmids/*genetics ; Polymerase Chain Reaction ; Pseudomonas fluorescens/drug effects/*enzymology/*genetics ; Recombinant Fusion Proteins/metabolism ; Sequence Homology, Nucleic Acid ; }, abstract = {In addition to the characterized mechanisms responsible for many direct effects of plant growth promoting bacteria (PGPB) on plants, it has been suggested that a number of PGPB contain the enzyme ACC deaminase that catalyzes degradation of 1-aminocyclopropane-1-carboxylic acid (ACC), the immediate precursor of ethylene, into alpha-ketobutyrate and ammonia. As part of an effort to obtain an ACC deaminase encoding gene from a collection of soil samples, only one bacterial isolate, Pseudomonas fluorescens FY32 was capable of growing on ACC as a sole source of nitrogen. The ACC deaminase gene was amplified from the above isolate by polymerase chain reaction (PCR) giving an expected DNA fragment, 1017 bp. Sequence analysis of the fragment showed that it was highly homologous (94% and 98% identities at nucleotide and amino acid levels, respectively) to the previously characterized acdS gene from Pseudomonas sp. 6G5. Furthermore, fusion of the ACC deaminase ORF with lacZ gene resulted in the expression of active enzyme in Escherichia coli. In addition, further analyses revealed that the acdS gene was plasmid-encoded so that a large plasmid (pFY32) with almost 50 kb in size was identified from this bacterium. Furthermore, transfer of pFY32 into E. coli DH5alpha proved its ACC deaminase activity. This result was in accordance with previous reports suggesting horizontal transfer of the acdS gene. However, it needs more investigation to identify whether this pFY32 plasmid has undergone lateral gene transfer during the evolutionary process.}, }
@article {pmid20047814, year = {2010}, author = {Shen, FT and Young, LS and Hsieh, MF and Lin, SY and Young, CC}, title = {Molecular detection and phylogenetic analysis of the alkane 1-monooxygenase gene from Gordonia spp.}, journal = {Systematic and applied microbiology}, volume = {33}, number = {2}, pages = {53-59}, doi = {10.1016/j.syapm.2009.11.003}, pmid = {20047814}, issn = {1618-0984}, mesh = {Actinobacteria/*classification/*enzymology/genetics/isolation &amp; purification ; Bacterial Proteins/*genetics ; Cluster Analysis ; Cytochrome P-450 CYP4A/*genetics ; DNA Gyrase ; DNA Primers/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/methods ; *Polymorphism, Genetic ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Soil Microbiology ; }, abstract = {The alkB gene encodes for alkane 1-monooxygenase, which is a key enzyme responsible for the initial oxidation of inactivated alkanes. This functional gene can be used as a marker to assess the catabolic potential of bacteria in bioremediation. In the present study, a pair of primers was designed based on the conserved regions of the AlkB amino acid sequences of Actinobacteria, for amplifying the alkB gene from the genus Gordonia (20 Gordonia strains representing 13 species). The amplified alkB genes were then sequenced and analyzed. In the phylogenetic tree based on the translated AlkB amino acid sequences, all the Gordonia segregated clearly from other closely related genera. The sequence identity of the alkB gene in Gordonia ranged from 58.8% to 99.1%, which showed higher sequence variation at the inter-species level compared with other molecular markers, such as the 16S rRNA gene (93.1-99.8%), gyrB gene (77.5-97.3%) or catA gene (72.4-99.5%). The genetic diversity of four selected loci also showed that the alkB gene might have evolved faster than rrn operons, as well as the gyrB or catA genes, in Gordonia. All the available actinobacterial alkB gene sequences derived from the whole genome shotgun sequencing projects are phylogenetically characterized here for the first time, and they exclude the possibility of horizontal gene transfer of the alkB gene in these bacterial groups.}, }
@article {pmid20047140, year = {2010}, author = {Rickard, C}, title = {Response to "Health risks of genetically modified foods".}, journal = {Critical reviews in food science and nutrition}, volume = {50}, number = {1}, pages = {85-91; author reply 92-5}, doi = {10.1080/10408390903467787}, pmid = {20047140}, issn = {1549-7852}, mesh = {Animals ; Food, Genetically Modified/*adverse effects ; Gene Transfer, Horizontal ; *Health Status ; Humans ; Hypersensitivity ; Intestinal Absorption ; Plants/genetics ; Plants, Genetically Modified ; }, }
@article {pmid20047041, year = {2009}, author = {Lubitz, P and Mayr, UB and Lubitz, W}, title = {Applications of bacterial ghosts in biomedicine.}, journal = {Advances in experimental medicine and biology}, volume = {655}, number = {}, pages = {159-170}, doi = {10.1007/978-1-4419-1132-2_12}, pmid = {20047041}, issn = {0065-2598}, mesh = {Bacteria/genetics ; Bacterial Vaccines/*genetics ; Drug Carriers ; Gene Transfer Techniques ; Gene Transfer, Horizontal ; Genetic Techniques ; Gram-Negative Bacteria/genetics/*metabolism ; Humans ; Immune System ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Neoplasms/therapy ; Probiotics ; Vaccines, DNA/genetics ; }, abstract = {Bacterial Ghosts (BG) are empty cell envelopes of Gram-negative bacteria which have been produced by E-mediated lysis. BG are devoid of cytoplasmic content and in combination with the expression of the nuclease SNUC, BG are also devoid of chromosomal and plasmid DNA. Proof of concept and proof of principle studies showed that BG candidate vaccines are highly immunogenic and in many instances induce protective immunity against lethal challenge in animal models. Due to their nature of being bacterial envelope complexes, BG are endowed with intrinsic natural adjuvant activity. BG are able to stimulate the innate and adaptive immune system without any addition of exogenous adjuvants. Although the use of plasmid encoded genetic information is essential for the final make up of BG, BG are not to be considered as genetically manipulated organisms (GMO), as they are nonliving and devoid of genetic information. The latter aspect is of great importance for safety, as no pathogenic islands or antibiotic resistance cassettes can be transferred to other bacteria by horizontal gene transfer. This is an important difference to other chemical-, heat- and pressure- or radiation-inactivated vaccine candidates, which also very often need artificial adjuvants to be added to improve their immunogenicity. The final BG vaccine preparations are freeze dried and are stable for many years at ambient temperature. BG can also be used as carrier and delivery vehicles for drugs or active substances in tumor therapy and due to specific targeting of tumor cells allow a higher specificity of treatment and a reduction of the total amount of drug per application. As carrier of enzymatic activity BG can be used for a new concept of probiotics which can synthesise active compounds from substrates of the environment where they are applied with a certain preference for the gut system. Thus, BG represent a promising technology platform for novel vaccines including combination or DNA vaccines, as drug carriers for therapeutic approaches in tumor treatment and as novel probiotics.}, }
@article {pmid20044792, year = {2010}, author = {Zhu, B and Ma, BL and Blackshaw, RE}, title = {Development of real time PCR assays for detection and quantification of transgene DNA of a Bacillus thuringiensis (Bt) corn hybrid in soil samples.}, journal = {Transgenic research}, volume = {19}, number = {5}, pages = {765-774}, pmid = {20044792}, issn = {1573-9368}, mesh = {Bacillus thuringiensis/*genetics ; *Computer Systems ; Crops, Agricultural/genetics ; DNA, Recombinant/*analysis ; Kanamycin Kinase/genetics ; Kanamycin Resistance/genetics ; Plants, Genetically Modified/*genetics ; Polymerase Chain Reaction/*methods ; Pseudomonas stutzeri/genetics ; Soil/*analysis ; *Soil Microbiology ; Glycine max/genetics/metabolism ; Transformation, Bacterial ; *Transgenes ; Zea mays/*genetics ; }, abstract = {Real time PCR assays were developed to detect and quantify the transgene DNA of a commercially released Bacillus thuringiensis (Bt) corn (Zea mays L.) hybrid (DKC42-23), which was derived from the event MON863 and also carried a neomycin phosphotransferase gene (the nptII gene). We applied the real time PCR assays to investigate the persistence of the transgene DNA in a field trial grown with DKC42-23 over 3 years, in combination with bacterial natural transformation. The results showed that under continuous cultivation of DKC42-23, its transgene DNA was detectable in the field plots all year around. Meanwhile, when soil DNA extracts from DKC42-23 plots were used as donor in bacterial natural transformation, successful recovery of kanamycin resistant (Km(R)) transformants indicated that the nptII gene carried by DKC42-23 could be taken up and integrated into naturally competent Pseudomonas stutzeri pMR7 cells, leading to the restoration of the antibiotic resistance of P. stutzeri pMR7. However, after the cultivation of a soybean line in the same plots for the subsequent growing season, the presence of transgene DNA of DKC42-23 was reduced to undetectable levels at the end of that growing season. Therefore, existing corn-soybean crop rotation practices reduce the availability of transgene DNA in soil and thus minimize the risks that might be attributable to horizontal gene transfer. The real time PCR assays are useful for investigating the persistence of transgene DNA derived from the MON863 event in soil environments.}, }
@article {pmid20041355, year = {2010}, author = {Sachs, RK and Hlatky, L}, title = {A rapid-mutation approximation for cell population dynamics.}, journal = {Bulletin of mathematical biology}, volume = {72}, number = {2}, pages = {359-374}, doi = {10.1007/s11538-009-9450-6}, pmid = {20041355}, issn = {1522-9602}, mesh = {Algorithms ; Aneuploidy ; Animals ; Cell Communication/genetics ; *Cell Proliferation ; Cell Transformation, Neoplastic/*genetics/pathology ; Gene Dosage/genetics ; Gene Transfer, Horizontal/genetics ; Markov Chains ; Mice ; *Models, Genetic ; Mutation/*genetics ; Neoplasms/genetics ; }, abstract = {Carcinogenesis and cancer progression are often modeled using population dynamics equations for a diverse somatic cell population undergoing mutations or other alterations that alter the fitness of a cell and its progeny. Usually it is then assumed, paralleling standard mathematical approaches to evolution, that such alterations are slow compared to selection, i.e., compared to subpopulation frequency changes induced by unequal subpopulation proliferation rates. However, the alterations can be rapid in some cases. For example, results in our lab on in vitro analogues of transformation and progression in carcinogenesis suggest there could be periods where rapid alterations triggered by horizontal intercellular transfer of genetic material occur and quickly result in marked changes of cell population structure.We here initiate a mathematical study of situations where alterations are rapid compared to selection. A classic selection-mutation formalism is generalized to obtain a "proliferation-alteration" system of ordinary differential equations, which we analyze using a rapid-alteration approximation. A system-theoretical estimate of the total-population net growth rate emerges. This rate characterizes the diverse, interacting cell population acting as a single system; it is a weighted average of subpopulation rates, the weights being components of the Perron-Frobenius eigenvector for an ergodic Markov-process matrix that describes alterations by themselves. We give a detailed numerical example to illustrate the rapid-alteration approximation, suggest a possible interpretation of the fact that average aneuploidy during cancer progression often appears to be comparatively stable in time, and briefly discuss possible generalizations as well as weaknesses of our approach.}, }
@article {pmid20041107, year = {2009}, author = {Yang, S and Bourne, PE}, title = {The evolutionary history of protein domains viewed by species phylogeny.}, journal = {PloS one}, volume = {4}, number = {12}, pages = {e8378}, pmid = {20041107}, issn = {1932-6203}, support = {R01 GM078596/GM/NIGMS NIH HHS/United States ; GM 078596/GM/NIGMS NIH HHS/United States ; }, mesh = {Databases, Protein ; *Evolution, Molecular ; Phycobilisomes/chemistry/genetics ; Phycocyanin/chemistry/genetics ; *Phylogeny ; *Protein Structure, Tertiary ; Reproducibility of Results ; Species Specificity ; }, abstract = {BACKGROUND: Protein structural domains are evolutionary units whose relationships can be detected over long evolutionary distances. The evolutionary history of protein domains, including the origin of protein domains, the identification of domain loss, transfer, duplication and combination with other domains to form new proteins, and the formation of the entire protein domain repertoire, are of great interest.<br><br>A methodology is presented for providing a parsimonious domain history based on gain, loss, vertical and horizontal transfer derived from the complete genomic domain assignments of 1015 organisms across the tree of life. When mapped to species trees the evolutionary history of domains and domain combinations is revealed, and the general evolutionary trend of domain and combination is analyzed.<br><br>CONCLUSIONS/SIGNIFICANCE: We show that this approach provides a powerful tool to study how new proteins and functions emerged and to study such processes as horizontal gene transfer among more distant species.}, }
@article {pmid20040589, year = {2010}, author = {Kim, DS and Lee, Y and Hahn, Y}, title = {Evidence for bacterial origin of heat shock RNA-1.}, journal = {RNA (New York, N.Y.)}, volume = {16}, number = {2}, pages = {274-279}, pmid = {20040589}, issn = {1469-9001}, mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins/genetics ; Base Sequence ; Chloride Channels/genetics ; Cricetinae ; DNA-Binding Proteins/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Heat Shock Transcription Factors ; Heat-Shock Response/*genetics ; Humans ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; RNA, Bacterial/*genetics ; RNA, Untranslated/*genetics ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Species Specificity ; Transcription Factors/genetics ; }, abstract = {The heat shock RNA-1 (HSR1) is a noncoding RNA (ncRNA) reported to be involved in mammalian heat shock response. HSR1 was shown to significantly stimulate the heat-shock factor 1 (HSF1) trimerization and DNA binding. The hamster HSR1 sequence was reported to consist of 604 nucleotides (nt) plus a poly(A) tail and to have only a 4-nt difference with the human HSR1. In this study, we present highly convincing evidence for bacterial origin of the HSR1. No HSR1 sequence was found by exhaustive sequence similarity searches of the publicly available eukaryotic nucleotide sequence databases at the NCBI, including the expressed sequence tags, genome survey sequences, and high-throughput genomic sequences divisions of GenBank, as well as the Trace Archive database of whole genome shotgun sequences, and genome assemblies. Instead, a putative open reading frame (ORF) of HSR1 revealed strong similarity to the amino-terminal region of bacterial chloride channel proteins. Furthermore, the 5' flanking region of the putative HSR1 ORF showed similarity to the 5' upstream regions of the bacterial protein genes. We propose that the HSR1 was derived from a bacterial genome fragment either by horizontal gene transfer or by bacterial infection of the cells. The most probable source organism of the HSR1 is a species belonging to the order Burkholderiales.}, }
@article {pmid20039796, year = {2010}, author = {Shahada, F and Chuma, T and Dahshan, H and Akiba, M and Sueyoshi, M and Okamoto, K}, title = {Detection and characterization of extended-spectrum beta-lactamase (TEM-52)-producing Salmonella serotype Infantis from broilers in Japan.}, journal = {Foodborne pathogens and disease}, volume = {7}, number = {5}, pages = {515-521}, doi = {10.1089/fpd.2009.0454}, pmid = {20039796}, issn = {1556-7125}, mesh = {Ampicillin Resistance/genetics ; Animals ; Cecum/microbiology ; Cephalosporin Resistance/genetics ; Chickens/*microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Drug Synergism ; *Food Microbiology ; Gene Transfer, Horizontal ; Genotype ; Integrons/genetics ; Japan ; Microbial Sensitivity Tests ; Phenotype ; Plasmids/genetics ; Salmonella enterica/*drug effects/enzymology/genetics/*isolation &amp; purification ; Serotyping ; beta-Lactamases/*biosynthesis/chemistry/genetics ; }, abstract = {During 2004 and 2006, multidrug-resistant Salmonella enterica subspecies enterica serovar Infantis (Salmonella Infantis) isolates (n = 120) were recovered from broiler cecal samples collected from a meat-processing plant, and the isolates were examined. The study was conducted to detect and characterize extended-spectrum beta-lactamase (ESBL)-producing Salmonella Infantis isolates recovered from broiler chickens and determine the mechanisms of transfer of the resistance traits. Extended-spectrum cephalosporins-resistant Salmonella Infantis isolates producing ESBL TEM-52 were detected. The mutant bla(TEM-52) gene and the wild-type bla(TEM-1) gene that mediated resistance to ampicillin (an extended-spectrum penicillin) and cephalothin (a narrow-spectrum cephalosporin) were located on approximately 50-kb conjugative plasmids among beta-lactam-resistant (n = 29) isolates. The bla(TEM) genes did not cotransfer with aadA1, sul1 (both associated with class 1 integrons), tetA, and dfrA5, signifying a chromosomal location of these non-beta-lactam resistance-encoding genes. This is the first report describing TEM-52-producing S. enterica from food-producing animals in Japan. An emergence of TEM-type ESBL is an important concern to public health because this readily transferable resistance mechanism threatens the value of the third-generation cephalosporins and may reduce the clinical utility of this class of antibiotics against pathogenic Gram-negative bacteria.}, }
@article {pmid20037759, year = {2010}, author = {Linz, S and Semple, C and Stadler, T}, title = {Analyzing and reconstructing reticulation networks under timing constraints.}, journal = {Journal of mathematical biology}, volume = {61}, number = {5}, pages = {715-737}, pmid = {20037759}, issn = {1432-1416}, mesh = {Algorithms ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genes, Plant/genetics ; Hybridization, Genetic/*genetics ; *Models, Genetic ; *Phylogeny ; Poaceae/genetics ; }, abstract = {Reticulation networks are now frequently used to model the history of life for various groups of species whose evolutionary past is likely to include reticulation events such as horizontal gene transfer or hybridization. However, the reconstructed networks are rarely guaranteed to be temporal. If a reticulation network is temporal, then it satisfies the two biologically motivated timing constraints of instantaneously occurring reticulation events and successively occurring speciation events. On the other hand, if a reticulation network is not temporal, it is always possible to make it temporal by adding a number of additional unsampled or extinct taxa. In the first half of the paper, we show that deciding whether a given number of additional taxa is sufficient to transform a non-temporal reticulation network into a temporal one is an NP-complete problem. As one is often given a set of gene trees instead of a network in the context of hybridization, this motivates the second half of the paper which provides an algorithm, called TemporalHybrid, for reconstructing a temporal hybridization network that simultaneously explains the ancestral history of two trees or indicates that no such network exists. We further derive two methods to decide whether or not a temporal hybridization network exists for two given trees and illustrate one of the methods on a grass data set.}, }
@article {pmid20035807, year = {2010}, author = {Peterson, G and Bai, J and Nagaraja, TG and Narayanan, S}, title = {Diagnostic microarray for human and animal bacterial diseases and their virulence and antimicrobial resistance genes.}, journal = {Journal of microbiological methods}, volume = {80}, number = {3}, pages = {223-230}, doi = {10.1016/j.mimet.2009.12.010}, pmid = {20035807}, issn = {1872-8359}, support = {P20 RR016469/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Cattle ; DNA, Bacterial/genetics/isolation &amp; purification ; Drug Resistance, Bacterial/genetics ; Enterococcus faecalis/*genetics/*isolation &amp; purification/pathogenicity ; Enterococcus faecium/*genetics/*isolation &amp; purification/pathogenicity ; Escherichia coli/genetics/isolation &amp; purification/pathogenicity ; Feces/microbiology ; Fusobacterium necrophorum/genetics/isolation &amp; purification/pathogenicity ; Genes, Bacterial ; *Genes, MDR ; Gram-Negative Bacteria/*genetics/*isolation &amp; purification/pathogenicity ; Gram-Negative Bacterial Infections/*diagnosis/microbiology ; Gram-Positive Bacterial Infections/*diagnosis/microbiology ; Humans ; Oligonucleotide Array Sequence Analysis/*methods ; Salmonella typhimurium/genetics/isolation &amp; purification/pathogenicity ; Sensitivity and Specificity ; Soil Microbiology ; Species Specificity ; Virulence ; Virulence Factors/*genetics ; }, abstract = {Rapid diagnosis and treatment of disease is often based on the identification and characterization of causative agents derived from phenotypic characteristics. Current methods can be laborious and time-consuming, often requiring many skilled personnel and a large amount of lab space. The objective of our study was to develop a spotted microarray for rapid identification and characterization of bacterial pathogens and their antimicrobial resistance genes. Our spotted microarray consists of 489 70mer probes that detect 40 bacterial pathogens of medical, veterinary and zoonotic importance (including 15 NIAID Category A, B and C pathogens); associated genes that encode resistance for antimicrobial and metal resistance; and DNA elements that are important for horizontal gene transfer among bacteria. High specificity and reliability of the microarray was achieved for bacterial pathogens of animal and human importance by validating MDR pathogenic bacteria as pure cultures or by following their inoculation in complex and highly organic sample matrices, such as soil and manure.}, }
@article {pmid20035767, year = {2010}, author = {Perlman, SJ and Magnus, SA and Copley, CR}, title = {Pervasive associations between Cybaeus spiders and the bacterial symbiont Cardinium.}, journal = {Journal of invertebrate pathology}, volume = {103}, number = {3}, pages = {150-155}, doi = {10.1016/j.jip.2009.12.009}, pmid = {20035767}, issn = {1096-0805}, mesh = {Animals ; Bacteroidetes/*genetics/pathogenicity ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Female ; Gene Transfer, Horizontal ; Haplotypes ; Male ; Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction ; Spiders/*genetics/*microbiology ; Symbiosis/*genetics ; }, abstract = {Cardinium is a recently discovered maternally transmitted bacterial endosymbiont in the Bacteroidetes that has thus far been documented in five arthropod orders. While its effects on his hosts are largely unknown, a few strains have been shown to manipulate host reproduction in parasitic wasps and in mites, either by transforming males into females, or by causing mating incompatibilities between infected males and uninfected males. Cardinium has recently been reported to be widespread in spiders, and in this study, we document pervasive infections in Cybaeus spiders, which are some of the most abundant yet understudied spiders in the understory of moist Western North American forests. 12/20 species, as well as 96% of individuals in a local population of Cybaeus signifer were infected. Phylogenetic analysis revealed three closely related symbiont haplotypes within Cybaeus. Haplotypes clustered within geographically close species, suggesting that horizontal transmission might be quite high in this symbiont lineage.}, }
@article {pmid20033398, year = {2010}, author = {Tiburcio, RA and Costa, GG and Carazzolle, MF and Mondego, JM and Schuster, SC and Carlson, JE and Guiltinan, MJ and Bailey, BA and Mieczkowski, P and Meinhardt, LW and Pereira, GA}, title = {Genes acquired by horizontal transfer are potentially involved in the evolution of phytopathogenicity in Moniliophthora perniciosa and Moniliophthora roreri, two of the major pathogens of cacao.}, journal = {Journal of molecular evolution}, volume = {70}, number = {1}, pages = {85-97}, pmid = {20033398}, issn = {1432-1432}, mesh = {Basidiomycota/enzymology/*genetics/*pathogenicity ; Bayes Theorem ; *Biological Evolution ; Cacao/*microbiology ; Fungal Proteins/genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Fungal/*genetics ; Hydrolases/genetics ; Necrosis ; Oxidoreductases/genetics ; Phylogeny ; }, abstract = {Moniliophthora perniciosa and Moniliophthora roreri are phytopathogenic basidiomycete species that infect cacao causing two important diseases in this crop: "Witches' Broom" and "Frosty Pod Rot", respectively. The ability of species from this genus (Moniliophthora) to cause disease is exceptional in the family Marasmiaceae. Species in closely related genera including, Marasmius, Crinipellis, and Chaetocalathus, are mainly saprotrophs and are not known to cause disease. In this study, the possibility that this phytopathogenic lifestyle has been acquired by horizontal gene transfer (HGT) was investigated. A stringent genome comparison pipeline was used to identify potential genes that have been obtained by Moniliophthora through HGT. This search led to the identification of three genes: a metallo-dependent hydrolase (MDH), a mannitol phosphate dehydrogenase (MPDH), and a family of necrosis-inducing proteins (NEPs). Phylogenetic analysis of these genes suggests that Moniliophthora acquired NEPs from oomycetes, MDH from actinobacteria and MPDH from firmicutes. Based on the known gene functions and on previous studies of M. perniciosa infection and development, a correlation between gene acquisition and the evolution of the phytopathogenic genus Moniliophthora can be postulated.}, }
@article {pmid20031040, year = {2010}, author = {Mugnier, PD and Poirel, L and Naas, T and Nordmann, P}, title = {Worldwide dissemination of the blaOXA-23 carbapenemase gene of Acinetobacter baumannii.}, journal = {Emerging infectious diseases}, volume = {16}, number = {1}, pages = {35-40}, pmid = {20031040}, issn = {1080-6059}, mesh = {Acinetobacter Infections/diet therapy/epidemiology/microbiology ; Acinetobacter baumannii/drug effects/enzymology/*genetics ; Blotting, Southern ; Cloning, Molecular ; Electrophoresis, Gel, Pulsed-Field ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/genetics ; Humans ; Microbial Sensitivity Tests ; Molecular Sequence Data ; beta-Lactam Resistance/genetics ; beta-Lactamases/*genetics ; }, abstract = {To assess dissemination of OXA-23-producing strains of Acinetobacter baumannii, we obtained 20 carbapenem-resistant, OXA-23-producing isolates from different regions. Their clonal relationship was assessed by pulsed-field gel electrophoresis and multilocus sequence typing. We identified 8 sequence types, including 4 novel types. All except 2 strains belonged to 2 main European clonal lineages. The blaOXA-23 gene was either located on the chromosome or on plasmids and associated with 4 genetic structures.}, }
@article {pmid20030727, year = {2010}, author = {Kumar, P and Wilson, PA and Bhai, R and Thomas, S}, title = {Characterization of an SXT variant Vibrio cholerae O1 Ogawa isolated from a patient in Trivandrum, India.}, journal = {FEMS microbiology letters}, volume = {303}, number = {2}, pages = {132-136}, doi = {10.1111/j.1574-6968.2009.01868.x}, pmid = {20030727}, issn = {1574-6968}, mesh = {Anti-Bacterial Agents/pharmacology ; Attachment Sites, Microbiological ; Cholera/*microbiology ; Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; *Drug Resistance, Multiple, Bacterial ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Humans ; India ; *Interspersed Repetitive Sequences ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Sequence Analysis, DNA ; Vibrio cholerae O1/drug effects/*genetics/*isolation &amp; purification ; }, abstract = {The emerging multiple drug resistance in bacterial pathogens is complicating the treatment of diseases and hence is a major public health concern. In the present study, Vibrio cholerae O1 El Tor Ogawa isolated from a patient was examined for antibiotic susceptibility pattern, presence of SXT and its transmissibility, associated drug resistance genes and variation in the int gene and the attP attachment site of SXT. The strain showed resistance to ampicillin, polymixin B, co-trimoxazole, trimethoprim, streptomycin, spectinomycin, furazolidone, tetracycline, ciprofloxacin and nalidixic acid. The sequencing of int, the SXT-specific integrase and attP attachment site indicated that it possessed a variant of SXT with trimethoprim (dfrA1), sulphamethoxazole (sul2) and streptomycin (strB) resistance genes. Its mobile nature was demonstrated by conjugation with rifampicin-resistant Escherichia coli. The emergence of such an isolate should be closely monitored because it will improve our understanding of the evolution of the multidrug resistance phenotype.}, }
@article {pmid20023016, year = {2010}, author = {Martins, ER and Melo-Cristino, J and Ramirez, M}, title = {Evidence for rare capsular switching in Streptococcus agalactiae.}, journal = {Journal of bacteriology}, volume = {192}, number = {5}, pages = {1361-1369}, pmid = {20023016}, issn = {1098-5530}, mesh = {Adult ; Bacterial Capsules/*genetics/*metabolism ; Bacterial Typing Techniques ; Cluster Analysis ; DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; Electrophoresis, Gel, Pulsed-Field ; Humans ; Infant, Newborn ; Molecular Sequence Data ; *Recombination, Genetic ; Sequence Analysis, DNA ; Serotyping ; Streptococcal Infections/microbiology ; Streptococcus agalactiae/*genetics/*metabolism ; Transformation, Bacterial ; Young Adult ; }, abstract = {The polysaccharide capsule is a major antigenic factor in Streptococcus agalactiae (Lancefield group B streptococcus [GBS]). Previous observations suggest that exchange of capsular loci is likely to occur rather frequently in GBS, even though GBS is not known to be naturally transformable. We sought to identify and characterize putative capsular switching events, by means of a combination of phenotypic and genotypic methods, including pulsed-field gel electrophoretic profiling, multilocus sequence typing, and surface protein and pilus gene profiling. We show that capsular switching by horizontal gene transfer is not as frequent as previously suggested. Serotyping errors may be the main reason behind the overestimation of capsule switching, since phenotypic techniques are prone to errors of interpretation. The identified putative capsular transformants involved the acquisition of the entire capsular locus and were not restricted to the serotype-specific central genes, the previously suggested main mechanism underlying capsular switching. Our data, while questioning the frequency of capsular switching, provide clear evidence for in vivo capsular transformation in S. agalactiae, which may be of critical importance in planning future vaccination strategies against this pathogen.}, }
@article {pmid20022799, year = {2010}, author = {Gelvin, SB}, title = {Finding a way to the nucleus.}, journal = {Current opinion in microbiology}, volume = {13}, number = {1}, pages = {53-58}, doi = {10.1016/j.mib.2009.11.003}, pmid = {20022799}, issn = {1879-0364}, mesh = {Bacterial Proteins/*metabolism ; Cell Nucleus/*metabolism ; DNA, Bacterial/*metabolism ; Eukaryotic Cells/*metabolism ; Gene Transfer, Horizontal ; Models, Biological ; Plants/*microbiology ; Protein Transport ; Rhizobium/*pathogenicity ; Transformation, Genetic ; Virulence Factors/*metabolism ; }, abstract = {Agrobacterium species transfer single-strand DNA and virulence effector proteins to plants. To understand how Agrobacterium achieves interkingdom horizontal gene transfer, scientists have investigated how the interaction of bacterial effector proteins with host proteins directs T-DNA to the plant nucleus. VirE2, a single-strand DNA binding protein, likely plays a key role in T-DNA nuclear targeting. However, subcellular trafficking of VirE2 remains controversial, with reports of both cytoplasmic and nuclear localization. The recent discovery that phosphorylation of the VirE2 interacting protein VIP1 modulates both nuclear targeting and transformation may provide a solution to this conundrum. Novel experimental systems that allow tracking of VirE2 as it exits Agrobacterium and enters the plant cell will also aid in understanding virulence protein/T-DNA cytoplasmic trafficking.}, }
@article {pmid20021636, year = {2009}, author = {Taylor, DJ and Bruenn, J}, title = {The evolution of novel fungal genes from non-retroviral RNA viruses.}, journal = {BMC biology}, volume = {7}, number = {}, pages = {88}, pmid = {20021636}, issn = {1741-7007}, mesh = {Amino Acid Sequence ; Candida/genetics/virology ; Capsid Proteins/genetics ; Computational Biology ; DNA, Fungal ; DNA-Directed RNA Polymerases/genetics ; *Evolution, Molecular ; Fungi/*genetics/virology ; Gene Transfer, Horizontal ; *Genes, Fungal ; Penicillium/genetics/virology ; Polymerase Chain Reaction ; Reverse Transcriptase Polymerase Chain Reaction ; Selection, Genetic ; Sequence Alignment ; Sequence Analysis, DNA ; Totiviridae/*genetics ; *Virus Integration ; }, abstract = {BACKGROUND: Endogenous derivatives of non-retroviral RNA viruses are thought to be absent or rare in eukaryotic genomes because integration of RNA viruses in host genomes is impossible without reverse transcription. However, such derivatives have been proposed for animals, plants and fungi, often based on surrogate bioinformatic evidence. At present, there is little known of the evolution and function of integrated non-retroviral RNA virus genes. Here, we provide direct evidence of integration by sequencing across host-virus gene boundaries and carry out phylogenetic analyses of fungal hosts and totivirids (dsRNA viruses of fungi and protozoans). Further, we examine functionality by tests of neutral evolution, comparison of residues that are necessary for viral capsid functioning and assays for transcripts, dsRNA and viral particles.<br><br>RESULTS: Sequencing evidence from gene boundaries was consistent with integration. We detected previously unknown integrated Totivirus-like sequences in three fungi (Candida parapsilosis, Penicillium marneffei and Uromyces appendiculatus). The phylogenetic evidence strongly indicated that the direction of transfer was from Totivirus to fungus. However, there was evidence of transfer of Totivirus-like sequences among fungi. Tests of selection indicated that integrated genes are maintained by purifying selection. Transcripts were apparent for some gene copies, but, in most cases, the endogenous sequences lacked the residues necessary for normal viral functioning.<br><br>CONCLUSIONS: Our findings reveal that horizontal gene transfer can result in novel gene formation in eukaryotes despite miniaturized genomic targets and a need for co-option of reverse transcriptase.}, }
@article {pmid20021546, year = {2010}, author = {Paz-Y-Miño C, G and Espinosa, A}, title = {Integrating horizontal gene transfer and common descent to depict evolution and contrast it with "common design".}, journal = {The Journal of eukaryotic microbiology}, volume = {57}, number = {1}, pages = {11-18}, pmid = {20021546}, issn = {1550-7408}, support = {P20 GM103430/GM/NIGMS NIH HHS/United States ; P20 RR016457/RR/NCRR NIH HHS/United States ; P20RR16457-04/RR/NCRR NIH HHS/United States ; }, mesh = {Alcohol Dehydrogenase/genetics ; Aldehyde Dehydrogenase/genetics ; Animals ; Biodiversity ; Entamoeba histolytica/enzymology/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Humans ; Models, Genetic ; Phylogeny ; Selection, Genetic ; }, abstract = {Horizontal gene transfer (HGT) and common descent interact in space and time. Because events of HGT co-occur with phylogenetic evolution, it is difficult to depict evolutionary patterns graphically. Tree-like representations of life's diversification are useful, but they ignore the significance of HGT in evolutionary history, particularly of unicellular organisms, ancestors of multicellular life. Here we integrate the reticulated-tree model, ring of life, symbiogenesis whole-organism model, and eliminative pattern pluralism to represent evolution. Using Entamoeba histolytica alcohol dehydrogenase 2 (EhADH2), a bifunctional enzyme in the glycolytic pathway of amoeba, we illustrate how EhADH2 could be the product of both horizontally acquired features from ancestral prokaryotes (i.e. aldehyde dehydrogenase [ALDH] and alcohol dehydrogenase [ADH]), and subsequent functional integration of these enzymes into EhADH2, which is now inherited by amoeba via common descent. Natural selection has driven the evolution of EhADH2 active sites, which require specific amino acids (cysteine 252 in the ALDH domain; histidine 754 in the ADH domain), iron- and NAD(+) as cofactors, and the substrates acetyl-CoA for ALDH and acetaldehyde for ADH. Alternative views invoking "common design" (i.e. the non-naturalistic emergence of major taxa independent from ancestry) to explain the interaction between horizontal and vertical evolution are unfounded.}, }
@article {pmid20021545, year = {2010}, author = {Espinosa, A}, title = {Introduction: protistan biology, horizontal gene transfer, and common descent uncover faulty logic in intelligent design.}, journal = {The Journal of eukaryotic microbiology}, volume = {57}, number = {1}, pages = {1-2}, pmid = {20021545}, issn = {1550-7408}, support = {P20 GM103430/GM/NIGMS NIH HHS/United States ; P20 RR016457/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; Congresses as Topic ; *Gene Transfer, Horizontal ; Humans ; Malaria, Falciparum/parasitology ; Plasmodium falciparum/*physiology ; }, }
@article {pmid20019795, year = {2009}, author = {Matias Rodrigues, JF and Wagner, A}, title = {Evolutionary plasticity and innovations in complex metabolic reaction networks.}, journal = {PLoS computational biology}, volume = {5}, number = {12}, pages = {e1000613}, pmid = {20019795}, issn = {1553-7358}, mesh = {Computational Biology/*methods ; Escherichia coli/genetics/metabolism/*physiology ; *Evolution, Molecular ; *Gene Regulatory Networks ; Genotype ; *Metabolic Networks and Pathways ; Models, Genetic ; Phenotype ; }, abstract = {Genome-scale metabolic networks are highly robust to the elimination of enzyme-coding genes. Their structure can evolve rapidly through mutations that eliminate such genes and through horizontal gene transfer that adds new enzyme-coding genes. Using flux balance analysis we study a vast space of metabolic network genotypes and their relationship to metabolic phenotypes, the ability to sustain life in an environment defined by an available spectrum of carbon sources. Two such networks typically differ in most of their reactions and have few essential reactions in common. Our observations suggest that the robustness of the Escherichia coli metabolic network to mutations is typical of networks with the same phenotype. We also demonstrate that networks with the same phenotype form large sets that can be traversed through single mutations, and that single mutations of different genotypes with the same phenotype can yield very different novel phenotypes. This means that the evolutionary plasticity and robustness of metabolic networks facilitates the evolution of new metabolic abilities. Our approach has broad implications for the evolution of metabolic networks, for our understanding of mutational robustness, for the design of antimetabolic drugs, and for metabolic engineering.}, }
@article {pmid20018208, year = {2010}, author = {Sen, D and Yano, H and Suzuki, H and Król, JE and Rogers, L and Brown, CJ and Top, EM}, title = {Comparative genomics of pAKD4, the prototype IncP-1delta plasmid with a complete backbone.}, journal = {Plasmid}, volume = {63}, number = {2}, pages = {98-107}, pmid = {20018208}, issn = {1095-9890}, support = {P20 RR016448/RR/NCRR NIH HHS/United States ; P20RR016454/RR/NCRR NIH HHS/United States ; P20 RR016448-07/RR/NCRR NIH HHS/United States ; P20RR16448/RR/NCRR NIH HHS/United States ; P20 RR016454-06/RR/NCRR NIH HHS/United States ; P20 RR016454/RR/NCRR NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/metabolism ; DNA Replication/drug effects ; DNA Transposable Elements/genetics ; Evolution, Molecular ; Genes, Bacterial ; *Genomics ; Mercury/toxicity ; Open Reading Frames/genetics ; Phylogeny ; Plasmids/*genetics ; }, abstract = {Plasmids of the incompatibility group IncP-1 are important agents of horizontal gene transfer and contribute to the spread of antibiotic resistance and xenobiotic degradation within bacterial communities. Even though some prototype plasmids have been studied in much detail, the diversity of this plasmid group was still greatly underestimated until recently, as only two of the five currently known divergent sub-groups had been described. To further improve our insight into the diversity and evolutionary history of this family of broad-host-range plasmids, we compared the complete nucleotide sequence of a new IncP-1delta plasmid pAKD4 to the genomes of other IncP-1 plasmids. Plasmid pAKD4 was previously isolated by exogenous plasmid isolation from an agricultural soil in Norway. Its 56,803bp nucleotide sequence shows high similarity in gene sequence and gene order to both plasmids pEST4011 and pIJB1, the only other IncP-1delta plasmids sequenced so far. While all three plasmids have a typical IncP-1 backbone comprising replication, transfer, and stable inheritance/control genes, the low sequence similarity in some regions and presence/absence of some backbone genes compared to other IncP-1 plasmids cluster them in a divergent sub-group. Therefore this study validates the presence of a real IncP-1delta clade with multiple plasmids. Moreover, since both pEST4011 and pIJB1 are missing a portion of their transfer genes, pAKD4 represents the first completely sequenced self-transferable plasmid with a complete IncP-1delta backbone. We therefore propose it to be the prototype IncP-1delta plasmid.}, }
@article {pmid20017754, year = {2010}, author = {Mota, NR and Ludwig, A and Valente, VL and Loreto, EL}, title = {Harrow: new Drosophila hAT transposons involved in horizontal transfer.}, journal = {Insect molecular biology}, volume = {19}, number = {2}, pages = {217-228}, doi = {10.1111/j.1365-2583.2009.00977.x}, pmid = {20017754}, issn = {1365-2583}, mesh = {Animals ; Base Sequence ; DNA Primers/genetics ; DNA Transposable Elements/*genetics ; Drosophila/classification/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Insect ; Molecular Sequence Data ; Phylogeny ; Selection, Genetic ; Species Specificity ; Time Factors ; }, abstract = {In this study we characterize the transposable elements harrow, which belong to the hAT superfamily of DNA transposons. Searches for harrow sequences were performed in 65 Drosophilidae species, mainly representing Neotropical and cosmopolitan groups from the genus Drosophila. The nucleotide divergence among elements found in these species suggests that harrow sequences could be clustered in a subfamily. The patchy distribution throughout the genus Drosophila and the high similarity presented between all harrow sequences indicate that horizontal transfer could play a major role in the evolution of harrow elements. The results obtained suggest an evolutionary scenario in which harrow would have undergone multiple horizontal transfer events in the Neotropics, involving D. tripuncatata, D. mojavensis (Subgenus Drosophila) and several species of the willistoni and saltans groups (subgenus Sophophora).}, }
@article {pmid20011113, year = {2009}, author = {Ramage, HR and Connolly, LE and Cox, JS}, title = {Comprehensive functional analysis of Mycobacterium tuberculosis toxin-antitoxin systems: implications for pathogenesis, stress responses, and evolution.}, journal = {PLoS genetics}, volume = {5}, number = {12}, pages = {e1000767}, pmid = {20011113}, issn = {1553-7404}, support = {K08 AI076620/AI/NIAID NIH HHS/United States ; P01 AI063302/AI/NIAID NIH HHS/United States ; R01 AI051667/AI/NIAID NIH HHS/United States ; }, mesh = {Antitoxins/*metabolism ; Bacterial Toxins/*metabolism ; *Biological Evolution ; Gene Expression ; Genome, Bacterial ; Mycobacterium tuberculosis/genetics/*metabolism/pathogenicity ; }, abstract = {Toxin-antitoxin (TA) systems, stress-responsive genetic elements ubiquitous in microbial genomes, are unusually abundant in the major human pathogen Mycobacterium tuberculosis. Why M. tuberculosis has so many TA systems and what role they play in the unique biology of the pathogen is unknown. To address these questions, we have taken a comprehensive approach to identify and functionally characterize all the TA systems encoded in the M. tuberculosis genome. Here we show that 88 putative TA system candidates are present in M. tuberculosis, considerably more than previously thought. Comparative genomic analysis revealed that the vast majority of these systems are conserved in the M. tuberculosis complex (MTBC), but largely absent from other mycobacteria, including close relatives of M. tuberculosis. We found that many of the M. tuberculosis TA systems are located within discernable genomic islands and were thus likely acquired recently via horizontal gene transfer. We discovered a novel TA system located in the core genome that is conserved across the genus, suggesting that it may fulfill a role common to all mycobacteria. By expressing each of the putative TA systems in M. smegmatis, we demonstrate that 30 encode a functional toxin and its cognate antitoxin. We show that the toxins of the largest family of TA systems, VapBC, act by inhibiting translation via mRNA cleavage. Expression profiling demonstrated that four systems are specifically activated during stresses likely encountered in vivo, including hypoxia and phagocytosis by macrophages. The expansion and maintenance of TA genes in the MTBC, coupled with the finding that a subset is transcriptionally activated by stress, suggests that TA systems are important for M. tuberculosis pathogenesis.}, }
@article {pmid20008390, year = {2010}, author = {Cavalier-Smith, T}, title = {Deep phylogeny, ancestral groups and the four ages of life.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {365}, number = {1537}, pages = {111-132}, pmid = {20008390}, issn = {1471-2970}, mesh = {Cell Membrane/genetics ; Eukaryota/*genetics ; *Evolution, Molecular ; *Genetic Variation ; *Phylogeny ; }, abstract = {Organismal phylogeny depends on cell division, stasis, mutational divergence, cell mergers (by sex or symbiogenesis), lateral gene transfer and death. The tree of life is a useful metaphor for organismal genealogical history provided we recognize that branches sometimes fuse. Hennigian cladistics emphasizes only lineage splitting, ignoring most other major phylogenetic processes. Though methodologically useful it has been conceptually confusing and harmed taxonomy, especially in mistakenly opposing ancestral (paraphyletic) taxa. The history of life involved about 10 really major innovations in cell structure. In membrane topology, there were five successive kinds of cell: (i) negibacteria, with two bounding membranes, (ii) unibacteria, with one bounding and no internal membranes, (iii) eukaryotes with endomembranes and mitochondria, (iv) plants with chloroplasts and (v) finally, chromists with plastids inside the rough endoplasmic reticulum. Membrane chemistry divides negibacteria into the more advanced Glycobacteria (e.g. Cyanobacteria and Proteobacteria) with outer membrane lipolysaccharide and primitive Eobacteria without lipopolysaccharide (deserving intenser study). It also divides unibacteria into posibacteria, ancestors of eukaryotes, and archaebacteria-the sisters (not ancestors) of eukaryotes and the youngest bacterial phylum. Anaerobic eobacteria, oxygenic cyanobacteria, desiccation-resistant posibacteria and finally neomura (eukaryotes plus archaebacteria) successively transformed Earth. Accidents and organizational constraints are as important as adaptiveness in body plan evolution.}, }
@article {pmid20008172, year = {2010}, author = {Mavrodi, DV and Peever, TL and Mavrodi, OV and Parejko, JA and Raaijmakers, JM and Lemanceau, P and Mazurier, S and Heide, L and Blankenfeldt, W and Weller, DM and Thomashow, LS}, title = {Diversity and evolution of the phenazine biosynthesis pathway.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {3}, pages = {866-879}, pmid = {20008172}, issn = {1098-5336}, mesh = {Antifungal Agents/metabolism ; Bacteria/classification/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Base Sequence ; Biosynthetic Pathways/genetics ; DNA, Bacterial/genetics/metabolism ; Escherichia coli/genetics/metabolism ; Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genotype ; Molecular Sequence Data ; Multigene Family ; Phenazines/*metabolism ; Phylogeny ; Plants/genetics/metabolism ; Pseudomonas/genetics/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Soil Microbiology ; Washington ; }, abstract = {Phenazines are versatile secondary metabolites of bacterial origin that function in biological control of plant pathogens and contribute to the ecological fitness and pathogenicity of the producing strains. In this study, we employed a collection of 94 strains having various geographic, environmental, and clinical origins to study the distribution and evolution of phenazine genes in members of the genera Pseudomonas, Burkholderia, Pectobacterium, Brevibacterium, and Streptomyces. Our results confirmed the diversity of phenazine producers and revealed that most of them appear to be soil-dwelling and/or plant-associated species. Genome analyses and comparisons of phylogenies inferred from sequences of the key phenazine biosynthesis (phzF) and housekeeping (rrs, recA, rpoB, atpD, and gyrB) genes revealed that the evolution and dispersal of phenazine genes are driven by mechanisms ranging from conservation in Pseudomonas spp. to horizontal gene transfer in Burkholderia spp. and Pectobacterium spp. DNA extracted from cereal crop rhizospheres and screened for the presence of phzF contained sequences consistent with the presence of a diverse population of phenazine producers in commercial farm fields located in central Washington state, which provided the first evidence of United States soils enriched in indigenous phenazine-producing bacteria.}, }
@article {pmid20008075, year = {2010}, author = {Yasmin, A and Kenny, JG and Shankar, J and Darby, AC and Hall, N and Edwards, C and Horsburgh, MJ}, title = {Comparative genomics and transduction potential of Enterococcus faecalis temperate bacteriophages.}, journal = {Journal of bacteriology}, volume = {192}, number = {4}, pages = {1122-1130}, pmid = {20008075}, issn = {1098-5530}, support = {BB/D003563/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteremia/microbiology ; Bacteriophages/classification/*genetics/isolation &amp; purification ; DNA Fingerprinting ; DNA, Viral/genetics ; Electrophoresis, Gel, Pulsed-Field ; Enterococcus faecalis/drug effects/isolation &amp; purification/radiation effects/*virology ; Gene Order ; *Genome, Viral ; Gram-Positive Bacterial Infections/microbiology ; Humans ; Microscopy, Electron, Transmission ; Mitomycin/pharmacology ; Molecular Sequence Data ; Norfloxacin/pharmacology ; Prophages/*genetics ; Sequence Analysis, DNA ; Sequence Homology ; Synteny ; *Transduction, Genetic ; Ultraviolet Rays ; Virion/ultrastructure ; Virus Activation/drug effects/radiation effects ; }, abstract = {To determine the relative importance of temperate bacteriophage in the horizontal gene transfer of fitness and virulence determinants of Enterococcus faecalis, a panel of 47 bacteremia isolates were treated with the inducing agents mitomycin C, norfloxacin, and UV radiation. Thirty-four phages were purified from culture supernatants and discriminated using pulsed-field gel electrophoresis (PFGE) and restriction mapping. From these analyses the genomes of eight representative phages were pyrosequenced, revealing four distinct groups of phages. Three groups of phages, PhiFL1 to 3, were found to be sequence related, with PhiFL1A to C and PhiFL2A and B sharing the greatest identity (87 to 88%), while PhiFL3A and B share 37 to 41% identity with PhiFL1 and 2. PhiFL4A shares 3 to 12% identity with the phages PhiFL1 to 3. The PhiFL3A and B phages possess a high DNA sequence identity with the morphogenesis and lysis modules of Lactococcus lactis subsp. cremoris prophages. Homologs of the Streptococcus mitis platelet binding phage tail proteins, PblA and PblB, are encoded on each sequenced E. faecalis phage. Few other phage genes encoding potential virulence functions were identified, and there was little evidence of carriage of lysogenic conversion genes distal to endolysin, as has been observed with genomes of many temperate phages from the opportunist pathogens Staphylococcus aureus and Streptococcus pyogenes. E. faecalis JH2-2 lysogens were generated using the eight phages, and these were examined for their relative fitness in Galleria mellonella. Several lysogens exhibited different effects upon survival of G. mellonella compared to their isogenic parent. The eight phages were tested for their ability to package host DNA, and three were shown to be very effective for generalized transduction of naive host cells of the laboratory strains OG1RF and JH2-2.}, }
@article {pmid20007606, year = {2010}, author = {Kaminska, KH and Purta, E and Hansen, LH and Bujnicki, JM and Vester, B and Long, KS}, title = {Insights into the structure, function and evolution of the radical-SAM 23S rRNA methyltransferase Cfr that confers antibiotic resistance in bacteria.}, journal = {Nucleic acids research}, volume = {38}, number = {5}, pages = {1652-1663}, pmid = {20007606}, issn = {1362-4962}, mesh = {Amino Acid Sequence ; Bacterial Proteins/*chemistry/*classification/metabolism ; Drug Resistance, Bacterial ; Evolution, Molecular ; Ligands ; Methylation ; Methyltransferases/*chemistry/*classification/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis ; Phylogeny ; RNA, Ribosomal, 23S/*metabolism ; S-Adenosylmethionine/*chemistry/metabolism ; Sequence Homology, Amino Acid ; }, abstract = {The Cfr methyltransferase confers combined resistance to five classes of antibiotics that bind to the peptidyl tranferase center of bacterial ribosomes by catalyzing methylation of the C-8 position of 23S rRNA nucleotide A2503. The same nucleotide is targeted by the housekeeping methyltransferase RlmN that methylates the C-2 position. Database searches with the Cfr sequence have revealed a large group of closely related sequences from all domains of life that contain the conserved CX(3)CX(2)C motif characteristic of radical S-adenosyl-l-methionine (SAM) enzymes. Phylogenetic analysis of the Cfr/RlmN family suggests that the RlmN subfamily is likely the ancestral form, whereas the Cfr subfamily arose via duplication and horizontal gene transfer. A structural model of Cfr has been calculated and used as a guide for alanine mutagenesis studies that corroborate the model-based predictions of a 4Fe-4S cluster, a SAM molecule coordinated to the iron-sulfur cluster (SAM1) and a SAM molecule that is the putative methyl group donor (SAM2). All mutations at predicted functional sites affect Cfr activity significantly as assayed by antibiotic susceptibility testing and primer extension analysis. The investigation has identified essential amino acids and Cfr variants with altered reaction mechanisms and represents a first step towards understanding the structural basis of Cfr activity.}, }
@article {pmid20007373, year = {2009}, author = {Cordero, OX and Hogeweg, P}, title = {The impact of long-distance horizontal gene transfer on prokaryotic genome size.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {51}, pages = {21748-21753}, pmid = {20007373}, issn = {1091-6490}, mesh = {*Gene Transfer, Horizontal ; *Genome, Bacterial ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Horizontal gene transfer (HGT) is one of the most dominant forces molding prokaryotic gene repertoires. These repertoires can be as small as approximately 200 genes in intracellular organisms or as large as approximately 9,000 genes in large, free-living bacteria. In this article we ask what is the impact of HGT from phylogenetically distant sources, relative to the size of the gene repertoire. Using different approaches for HGT detection and focusing on both cumulative and recent evolutionary histories, we find a surprising pattern of nonlinear enrichment of long-distance transfers in large genomes. Moreover, we find a strong positive correlation between the sizes of the donor and recipient genomes. Our results also show that distant horizontal transfers are biased toward those functional groups that are enriched in large genomes, showing that the trends in functional gene content and the impact of distant transfers are interdependent. These results highlight the intimate relationship between environmental and genomic complexity in microbes and suggest that an ecological, as opposed to phylogenetic, signal in gene content gains relative importance in large-genomed bacteria.}, }
@article {pmid20007369, year = {2009}, author = {Boyer, M and Yutin, N and Pagnier, I and Barrassi, L and Fournous, G and Espinosa, L and Robert, C and Azza, S and Sun, S and Rossmann, MG and Suzan-Monti, M and La Scola, B and Koonin, EV and Raoult, D}, title = {Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {51}, pages = {21848-21853}, pmid = {20007369}, issn = {1091-6490}, support = {R01 AI011219/AI/NIAID NIH HHS/United States ; R37 AI011219/AI/NIAID NIH HHS/United States ; AI11219/AI/NIAID NIH HHS/United States ; /ImNIH/Intramural NIH HHS/United States ; }, mesh = {Amoeba/genetics/*physiology ; *Chimera ; Genome, Viral ; Microscopy, Electron ; Mimiviridae/classification/genetics/*physiology ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Giant viruses such as Mimivirus isolated from amoeba found in aquatic habitats show biological sophistication comparable to that of simple cellular life forms and seem to evolve by similar mechanisms, including extensive gene duplication and horizontal gene transfer (HGT), possibly in part through a viral parasite, the virophage. We report here the isolation of "Marseille" virus, a previously uncharacterized giant virus of amoeba. The virions of Marseillevirus encompass a 368-kb genome, a minimum of 49 proteins, and some messenger RNAs. Phylogenetic analysis of core genes indicates that Marseillevirus is the prototype of a family of nucleocytoplasmic large DNA viruses (NCLDV) of eukaryotes. The genome repertoire of the virus is composed of typical NCLDV core genes and genes apparently obtained from eukaryotic hosts and their parasites or symbionts, both bacterial and viral. We propose that amoebae are "melting pots" of microbial evolution where diverse forms emerge, including giant viruses with complex gene repertoires of various origins.}, }
@article {pmid20006133, year = {2009}, author = {Danchin, A}, title = {A challenge to vaccinology: living organisms trap information.}, journal = {Vaccine}, volume = {27 Suppl 6}, number = {}, pages = {G13-6}, pmid = {20006133}, issn = {1873-2518}, mesh = {Communicable Diseases, Emerging/*prevention &amp; control ; Computational Biology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Models, Genetic ; *Vaccines ; }, abstract = {Life couples reproduction of the cell machinery with replication of the genetic program. Both processes are linked to the expression of some information. Over time, reproduction can enhance the information of the machine. We show that accumulation of valuable information results from degradative processes required to make room for novel entities. Degradation systems act as Maxwell's demons, using energy not to make room per se, but to prevent degradation of what has some functional features. This myopic process will accumulate information, whatever its source, in a ratchet-like manner. The consequence is that genes acquired by horizontal transfer as well as viruses will tend to perpetuate in niches where they are functional, creating recurrent conditions for emergence of diseases.}, }
@article {pmid20005592, year = {2010}, author = {Comunian, R and Daga, E and Dupré, I and Paba, A and Devirgiliis, C and Piccioni, V and Perozzi, G and Zonenschain, D and Rebecchi, A and Morelli, L and De Lorentiis, A and Giraffa, G}, title = {Susceptibility to tetracycline and erythromycin of Lactobacillus paracasei strains isolated from traditional Italian fermented foods.}, journal = {International journal of food microbiology}, volume = {138}, number = {1-2}, pages = {151-156}, doi = {10.1016/j.ijfoodmicro.2009.11.018}, pmid = {20005592}, issn = {1879-3460}, mesh = {Anti-Bacterial Agents/*pharmacology ; Colony Count, Microbial ; Consumer Product Safety ; DNA, Bacterial/analysis ; Dose-Response Relationship, Drug ; Drug Resistance, Bacterial/*genetics ; Erythromycin/pharmacology ; Fermentation ; Food Contamination/*analysis ; Food Microbiology ; *Gene Transfer, Horizontal ; Humans ; Italy ; Lactobacillus/*drug effects/genetics ; Microbial Sensitivity Tests ; Tetracycline/pharmacology ; }, abstract = {The aim of this study was to evaluate the susceptibility of 197 isolates of Lactobacillus paracasei, isolated from Italian fermented products coming from different geographical areas, to tetracycline and erythromycin, two antimicrobials widely used in clinical and animal therapy. Isolation media were supplemented with antibiotics according to the microbiological breakpoints (BPs) defined by European Food Safety Authority (EFSA). Isolates were identified at the species level and were typed by rep-PCR using the (GTG)(5) primer. A total of 121 genotypically different strains were detected and their phenotypic antimicrobial resistance to tetracycline and erythromycin was determined as the minimum inhibitory concentration (MIC) using the broth microdilution method. The presence of the genes ermB, ermC and tetL, tetM, tetS, tetW, in the phenotypically resistant isolates was investigated by PCR. Tetracycline induction of tetM expression on representative resistant strains, grown in medium either lacking or containing the antibiotic, was also analyzed by RT-PCR. Among the 121 tested strains, 77.7% were susceptible to tetracycline (MIC<or=4 microg/ml; BP=4 microg/ml) and 94.2% to erythromycin (MIC<or=1 microg/ml; BP=1 microg/ml). Overall, 27 strains appeared to be resistant to tetracycline (16<or=MIC<or=128 microg/ml) (Tet(R)), and 7 of them were also resistant to erythromycin (MIC>or=1024 microg/ml) (Erm(R)). The tetM and ermB genes were the most frequently detected in the Tet(R) and/or Erm(R) strains. The tetM expression was induced by antibiotic addition to the growth medium. Our study confirmed that L. paracasei is quite sensitive to tetracycline and erythromycin, but the high level of resistance of Erm(R) strains suggested that acquired resistance took place. Further investigations are required to analyze whether the genes identified in L. paracasei isolates might be horizontally transferred to other species. Since "commensal" bacteria, which L. paracasei belongs to, may play an active role in the spreading of antibiotic resistance, a series of measures inspired from a principle of precaution should be taken before they are used as commercial starters or probiotic cultures in food products, complemented by a more prudent use of antibiotics in agriculture, veterinary, and human medicine.}, }
@article {pmid20004590, year = {2010}, author = {Fugmann, SD}, title = {The origins of the Rag genes--from transposition to V(D)J recombination.}, journal = {Seminars in immunology}, volume = {22}, number = {1}, pages = {10-16}, pmid = {20004590}, issn = {1096-3618}, support = {ZIA AG000388-03/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Animals ; *DNA Transposable Elements ; DNA-Binding Proteins/genetics/*immunology ; *Genes, RAG-1 ; Humans ; Transposases/genetics/metabolism ; VDJ Recombinases/*immunology/metabolism ; }, abstract = {The recombination activating genes 1 and 2 (Rag1 and Rag2) encode the key enzyme that is required for the generation of the highly diversified antigen receptor repertoire central to adaptive immunity. The longstanding model proposed that this gene pair was acquired by horizontal gene transfer to explain its abrupt appearance in the vertebrate lineage. The analyses of the enormous amount of sequence data created by many genome sequencing projects now provide the basis for a more refined model as to how this unique gene pair evolved from a selfish DNA transposon into a sophisticated DNA recombinase essential for immunity.}, }
@article {pmid20003527, year = {2009}, author = {Choi, K and Gomez, SM}, title = {Comparison of phylogenetic trees through alignment of embedded evolutionary distances.}, journal = {BMC bioinformatics}, volume = {10}, number = {}, pages = {423}, pmid = {20003527}, issn = {1471-2105}, mesh = {Computational Biology/*methods ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Phylogeny ; Sequence Alignment/*methods ; }, abstract = {BACKGROUND: The understanding of evolutionary relationships is a fundamental aspect of modern biology, with the phylogenetic tree being a primary tool for describing these associations. However, comparison of trees for the purpose of assessing similarity and the quantification of various biological processes remains a significant challenge.<br><br>RESULTS: We describe a novel approach for the comparison of phylogenetic distance information based on the alignment of representative high-dimensional embeddings (xCEED: Comparison of Embedded Evolutionary Distances). The xCEED methodology, which utilizes multidimensional scaling and Procrustes-related superimposition approaches, provides the ability to measure the global similarity between trees as well as incongruities between them. We demonstrate the application of this approach to the prediction of coevolving protein interactions and demonstrate its improved performance over the mirrortree, tol-mirrortree, phylogenetic vector projection, and partial correlation approaches. Furthermore, we show its applicability to both the detection of horizontal gene transfer events as well as its potential use in the prediction of interaction specificity between a pair of multigene families.<br><br>CONCLUSIONS: These approaches provide additional tools for the study of phylogenetic trees and associated evolutionary processes. Source code is available at http://gomezlab.bme.unc.edu/tools.}, }
@article {pmid20002602, year = {2010}, author = {Bontemps, C and Elliott, GN and Simon, MF and Dos Reis Júnior, FB and Gross, E and Lawton, RC and Neto, NE and de Fátima Loureiro, M and De Faria, SM and Sprent, JI and James, EK and Young, JP}, title = {Burkholderia species are ancient symbionts of legumes.}, journal = {Molecular ecology}, volume = {19}, number = {1}, pages = {44-52}, doi = {10.1111/j.1365-294X.2009.04458.x}, pmid = {20002602}, issn = {1365-294X}, mesh = {Brazil ; Burkholderia/classification/*genetics ; DNA, Bacterial/genetics ; Evolution, Molecular ; Genes, Bacterial ; Geography ; Mimosa/*microbiology ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; *Symbiosis ; }, abstract = {Burkholderia has only recently been recognized as a potential nitrogen-fixing symbiont of legumes, but we find that the origins of symbiosis in Burkholderia are much deeper than previously suspected. We sampled 143 symbionts from 47 native species of Mimosa across 1800 km in central Brazil and found that 98% were Burkholderia. Gene sequences defined seven distinct and divergent species complexes within the genus Burkholderia. The symbiosis-related genes formed deep Burkholderia-specific clades, each specific to a species complex, implying that these genes diverged over a long period within Burkholderia without substantial horizontal gene transfer between species complexes.}, }
@article {pmid20000537, year = {2009}, author = {Weyens, N and van der Lelie, D and Artois, T and Smeets, K and Taghavi, S and Newman, L and Carleer, R and Vangronsveld, J}, title = {Bioaugmentation with engineered endophytic bacteria improves contaminant fate in phytoremediation.}, journal = {Environmental science &amp; technology}, volume = {43}, number = {24}, pages = {9413-9418}, doi = {10.1021/es901997z}, pmid = {20000537}, issn = {0013-936X}, mesh = {*Biodegradation, Environmental ; Gene Transfer Techniques ; *Organisms, Genetically Modified/genetics/metabolism ; Plant Transpiration/physiology ; Populus/anatomy &amp; histology/metabolism/microbiology ; *Pseudomonas putida/genetics/metabolism ; RNA, Ribosomal, 16S/genetics/metabolism ; Volatile Organic Compounds/chemistry/metabolism ; Water Pollutants, Chemical/chemistry/*metabolism ; Water Supply/analysis ; }, abstract = {Phytoremediation of volatile organic contaminants often proves not ideal because plants and their rhizosphere microbes only partially degrade these compounds. Consequently, plants undergo evapotranspiration that contaminates the ambient air and, thus, undermines the merits of phytoremediation. Under laboratory conditions, endophytic bacteria equipped with the appropriate degradation pathways can improve in planta degradation of volatile organic contaminants. However, several obstacles must be overcome before engineered endophytes will be successful in field-scale phytoremediation projects. Here we report the first in situ inoculation of poplar trees, growing on a TCE-contaminated site, with the TCE-degrading strain Pseudomonas putida W619-TCE. In situ bioaugmentation with strain W619-TCE reduced TCE evapotranspiration by 90% under field conditions. This encouraging result was achieved after the establishment and enrichment of P. putida W619-TCE as a poplar root endophyte and by further horizontal gene transfer of TCE metabolic activity to members of the poplar's endogenous endophytic population. Since P. putida W619-TCE was engineered via horizontal gene transfer, its deliberate release is not restricted under European genetically modified organisms (GMO) regulations.}, }
@article {pmid19997864, year = {2010}, author = {Egervärn, M and Lindmark, H and Olsson, J and Roos, S}, title = {Transferability of a tetracycline resistance gene from probiotic Lactobacillus reuteri to bacteria in the gastrointestinal tract of humans.}, journal = {Antonie van Leeuwenhoek}, volume = {97}, number = {2}, pages = {189-200}, doi = {10.1007/s10482-009-9401-0}, pmid = {19997864}, issn = {1572-9699}, mesh = {Adult ; Bifidobacterium/drug effects/*genetics ; DNA, Bacterial/genetics ; Enterococcus/drug effects/*genetics ; Feces/microbiology ; Female ; Gastrointestinal Tract/*microbiology ; *Gene Transfer, Horizontal ; Humans ; Limosilactobacillus reuteri/drug effects/*genetics ; Male ; Middle Aged ; Plasmids ; Polymerase Chain Reaction/methods ; Probiotics ; *Tetracycline Resistance ; }, abstract = {The potential of Lactobacillus reuteri as a donor of antibiotic resistance genes in the human gut was investigated by studying the transferability of the tetracycline resistance gene tet(W) to faecal enterococci, bifidobacteria and lactobacilli. In a double-blind clinical study, seven subjects consumed L. reuteri ATCC 55730 harbouring a plasmid-encoded tet(W) gene (tet(W)-reuteri) and an equal number of subjects consumed L. reuteri DSM 17938 derived from the ATCC 55730 strain by the removal of two plasmids, one of which contained the tet(W) gene. Faecal samples were collected before, during and after ingestion of 5 x 10(8) CFU of L. reuteri per day for 14 days. Both L. reuteri strains were detectable at similar levels in faeces after 14 days of intake but neither was detected after a two-week wash-out period. After enrichment and isolation of tetracycline resistant enterococci, bifidobacteria and lactobacilli from each faecal sample, DNA was extracted and analysed for presence of tet(W)-reuteri using a real-time PCR allelic discrimination method developed in this study. No tet(W)-reuteri signal was produced from any of the DNA samples and thus gene transfer to enterococci, bifidobacteria and lactobacilli during intestinal passage of the probiotic strain was non-detectable under the conditions tested, although transfer at low frequencies or to the remaining faecal bacterial population cannot be excluded.}, }
@article {pmid19969386, year = {2010}, author = {Massoudieh, A and Crain, C and Lambertini, E and Nelson, KE and Barkouki, T and L'amoreaux, P and Loge, FJ and Ginn, TR}, title = {Kinetics of conjugative gene transfer on surfaces in granular porous media.}, journal = {Journal of contaminant hydrology}, volume = {112}, number = {1-4}, pages = {91-102}, doi = {10.1016/j.jconhyd.2009.10.009}, pmid = {19969386}, issn = {1873-6009}, mesh = {Conjugation, Genetic ; Culture Media ; Escherichia coli/*genetics ; *Gene Transfer, Horizontal ; Kinetics ; *Models, Biological ; Porosity ; }, abstract = {The transfer of genetic material among bacteria in the environment can occur both in the planktonic and attached state. Given the propensity of organisms to exist in sessile microbial communities in oligotrophic subsurface conditions, and that such conditions typify the subsurface, this study focuses on exploratory modeling of horizontal gene transfer among surface-associated Escherichiacoli in the subsurface. The mathematics so far used to describe the kinetics of conjugation in biofilms are developed largely from experimental observations of planktonic gene transfer, and are absent of lags or plasmid stability that appear experimentally. We develop a model and experimental system to quantify bacterial filtration and gene transfer in the attached state, on granular porous media. We include attachment kinetics described in Nelson et al. (2007) using the filtration theory approach of Nelson and Ginn (2001, 2005) with motility of E. coli described according to Biondi et al. (1998).}, }
@article {pmid19969385, year = {2010}, author = {Marcet-Houben, M and Gabaldón, T}, title = {Acquisition of prokaryotic genes by fungal genomes.}, journal = {Trends in genetics : TIG}, volume = {26}, number = {1}, pages = {5-8}, doi = {10.1016/j.tig.2009.11.007}, pmid = {19969385}, issn = {0168-9525}, mesh = {Fungi/*genetics ; *Gene Transfer, Horizontal ; *Genome, Fungal ; Phylogeny ; *Prokaryotic Cells ; Selection, Genetic ; }, abstract = {The relevance of horizontal gene transfer (HGT) in eukaryotes is a matter of debate. Recent analyses have shown clear examples in some species such as Candida parapsilosis, but broader surveys are lacking. To assess the impact of HGT in the fungal kingdom, we searched for prokaryotic-derived HGTs in 60 fully sequenced genomes. Using strict phylogenomic criteria, we detected 713 transferred genes. HGT affected most fungal clades, with particularly high rates in Pezizomycotina. Transferred genes included bacterial arsenite reductase, catalase, different racemases and peptidoglycan metabolism enzymes. Our results suggest an important role for HGT in fungal evolution.}, }
@article {pmid19968874, year = {2009}, author = {Jackson, AP and Thomas, GH and Parkhill, J and Thomson, NR}, title = {Evolutionary diversification of an ancient gene family (rhs) through C-terminal displacement.}, journal = {BMC genomics}, volume = {10}, number = {}, pages = {584}, pmid = {19968874}, issn = {1471-2164}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/*classification/*genetics ; *Biodiversity ; Enterobacteriaceae/chemistry/*classification/*genetics ; *Evolution, Molecular ; Genetic Loci ; Genome, Bacterial ; Phylogeny ; Sequence Alignment ; }, abstract = {BACKGROUND: Rhs genes are prominent features of bacterial genomes that have previously been implicated in genomic rearrangements in E. coli. By comparing rhs repertoires across the Enterobacteriaceae, this study provides a robust explanation of rhs diversification and evolution, and a mechanistic model of how rhs diversity is gained and lost.<br><br>RESULTS: Rhs genes are ubiquitous and comprise six structurally distinct lineages within the Enterobacteriaceae. There is considerable intergenomic variation in rhs repertoire; for instance, in Salmonella enterica, rhs are restricted to mobile elements, while in Escherichia coli one rhs lineage has diversified through transposition as older lineages have been deleted. Overall, comparative genomics reveals frequent, independent gene gains and losses, as well as occasional lateral gene transfer, in different genera. Furthermore, we demonstrate that Rhs 'core' domains and variable C-termini are evolutionarily decoupled, and propose that rhs diversity is driven by homologous recombination with circular intermediates. Existing C-termini are displaced by laterally acquired alternatives, creating long arrays of dissociated 'tips' that characterize the appearance of rhs loci.<br><br>CONCLUSION: Rhs repertoires are highly dynamic among Enterobacterial genomes, due to repeated gene gains and losses. In contrast, the primary structures of Rhs genes are evolutionarily conserved, indicating that rhs sequence diversity is driven, not by rapid mutation, but by the relatively slow evolution of novel core/tip combinations. Hence, we predict that a large pool of dissociated rhs C-terminal tips exists episomally and these are potentially transmitted across taxonomic boundaries.}, }
@article {pmid19962898, year = {2010}, author = {Al-Khodor, S and Price, CT and Kalia, A and Abu Kwaik, Y}, title = {Functional diversity of ankyrin repeats in microbial proteins.}, journal = {Trends in microbiology}, volume = {18}, number = {3}, pages = {132-139}, pmid = {19962898}, issn = {1878-4380}, support = {R01AI43965/AI/NIAID NIH HHS/United States ; R01 AI069321-03/AI/NIAID NIH HHS/United States ; R01 AI069321/AI/NIAID NIH HHS/United States ; R01AI069321/AI/NIAID NIH HHS/United States ; R01 AI043965/AI/NIAID NIH HHS/United States ; }, mesh = {*Ankyrin Repeat ; Archaeal Proteins/*genetics/metabolism ; Bacterial Proteins/*genetics/metabolism ; *Evolution, Molecular ; Host-Pathogen Interactions ; Protein Binding ; Protein Interaction Domains and Motifs ; Viral Proteins/*genetics/metabolism ; }, abstract = {The ankyrin repeat (ANK) is the most common protein-protein interaction motif in nature, and is predominantly found in eukaryotic proteins. Genome sequencing of various pathogenic or symbiotic bacteria and eukaryotic viruses has identified numerous genes encoding ANK-containing proteins that are proposed to have been acquired from eukaryotes by horizontal gene transfer. However, the recent discovery of additional ANK-containing proteins encoded in the genomes of archaea and free-living bacteria suggests either a more ancient origin of the ANK motif or multiple convergent evolution events. Many bacterial pathogens employ various types of secretion systems to deliver ANK-containing proteins into eukaryotic cells, where they mimic or manipulate various host functions. Studying the molecular and biochemical functions of this family of proteins will enhance our understanding of important host-microbe interactions.}, }
@article {pmid19958081, year = {2009}, author = {McCrow, JP}, title = {Alignment of phylogenetically unambiguous indels in Shewanella.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {16}, number = {11}, pages = {1517-1528}, pmid = {19958081}, issn = {1557-8666}, support = {P50 HG002790-05/HG/NHGRI NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry ; INDEL Mutation/*genetics ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment/*methods ; Sequence Analysis, DNA ; Sequence Analysis, Protein ; Shewanella/*genetics ; }, abstract = {High levels of alignment errors associated with gaps have generally meant their exclusion from phylogenetic analysis. Conserved inserts and deletions (indels) may in some cases be less subject to errors than amino acid substitutions for inferring the history of genomes and identifying recently laterally transferred genes, but alignment error near gaps must be evaluated prior to using indels as phylogenetic characters. A method is presented for evaluating the phylogenetic unambiguity of gaps in multiple sequence alignments by allowing a defined amount of pairwise alignment ambiguity. This work considers the bacterial genus Shewanella, which is of particular interest for applications of bioremediation and environmental engineering. Understanding the genetic history of these species is vital for these applications. A set of pairwise dynamic programming alignments is constructed to test positions in multiple alignments for phylogenetic unambiguity, and a whole genome scan is done on protein sequences from 11 sequenced species of the bacterial genus Shewanella. The splits defined by phylogenetically unambiguous indels are then used as characters for phylogenetic analysis, and results are compared to whole genome Maximum Likelihood phylogeny. A comparable description of the history of the species is found, as well as a set of lateral gene transfer candidates undetectable by traditional analysis of amino acid substitutions. This analysis is applicable to other taxonomic units at all levels and has the potential to allow cataloging of clear genome-wide phylogenetic markers for taxonomic profiling down to the species level.}, }
@article {pmid19956071, year = {2010}, author = {Moskowitz, SM and Wiener-Kronish, JP}, title = {Mechanisms of bacterial virulence in pulmonary infections.}, journal = {Current opinion in critical care}, volume = {16}, number = {1}, pages = {8-12}, pmid = {19956071}, issn = {1531-7072}, support = {R01 AI067653/AI/NIAID NIH HHS/United States ; P50 HL074005/HL/NHLBI NIH HHS/United States ; U01 AI075410/AI/NIAID NIH HHS/United States ; R01 AI067653-04/AI/NIAID NIH HHS/United States ; R01 GM 088416/GM/NIGMS NIH HHS/United States ; P50 HL074005-010002/HL/NHLBI NIH HHS/United States ; R01AI067653/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Toxins/immunology ; Critical Care ; Drug Resistance, Bacterial ; Exotoxins/immunology ; Francisella tularensis/drug effects/immunology/*pathogenicity ; Gene Transfer, Horizontal ; Humans ; Leukocidins/immunology ; Methicillin-Resistant Staphylococcus aureus ; Pneumonia/immunology/*physiopathology ; Staphylococcal Infections/microbiology ; Staphylococcus aureus/drug effects/immunology/*pathogenicity ; }, abstract = {PURPOSE OF REVIEW: To consider the relevance to severe human lung infections of recently discovered virulence mechanisms of Staphylococcus aureus and Francisella tularensis.<br><br>RECENT FINDINGS: S. aureus has long been considered an opportunistic pathogen. However, due to the emergence of community-acquired methicillin-resistant S. aureus (CA-MRSA) strains that can readily infect and kill normal hosts, S. aureus must now be considered a potentially virulent pathogen. The evolution of S. aureus from an organism associated with asymptomatic nasopharyngeal colonization to one associated with community-acquired lethal infections may reflect horizontal acquisition of bacterial genes that enable efficient spread, aggressive host invasion, and effective immune evasion. Alleviating the burden of staphylococcal disease will require better understanding of host susceptibility and of staphylococcal virulence and antibiotic resistance. In contrast to the rapidly evolving staphylococcal virulence strategy, recent genomic analysis of F. tularensis has revealed a small set of bacterial genes associated with the marked virulence of its North American subspecies. This suggests that a relatively stable strategy of immune evasion underlies this pathogen's ability to establish serious life-threatening lung infections from a very small inoculum.<br><br>SUMMARY: Understanding bacterial pathogenesis will require additional research into both host susceptibility factors and bacterial virulence mechanisms, including horizontal gene transfer. Refinements in the molecular detection of bacteria in the clinical setting, as well as whole genome analysis of both pathogens and patients, are expected to aid in the understanding of bacterial-induced lung injury.}, }
@article {pmid19948233, year = {2010}, author = {Alam, MT and Merlo, ME and Takano, E and Breitling, R}, title = {Genome-based phylogenetic analysis of Streptomyces and its relatives.}, journal = {Molecular phylogenetics and evolution}, volume = {54}, number = {3}, pages = {763-772}, doi = {10.1016/j.ympev.2009.11.019}, pmid = {19948233}, issn = {1095-9513}, mesh = {Gene Order ; Genes, Bacterial ; *Genome, Bacterial ; Genomics/*methods ; *Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA ; Streptomyces/*classification/genetics ; }, abstract = {MOTIVATION: Streptomyces is one of the best-studied genera of the order Actinomycetales due to its great importance in medical science, ecology and the biotechnology industry. A comprehensive, detailed and robust phylogeny of Streptomyces and its relatives is needed for understanding how this group emerged and maintained such a vast diversity throughout evolution and how soil-living mycelial forms (e.g., Streptomyces s. str.) are related to parasitic, unicellular pathogens (e.g., Mycobacterium tuberculosis) or marine species (e.g., Salinispora tropica). The most important application area of such a phylogenetic analysis will be in the comparative re-annotation of genome sequences and the reconstruction of Streptomyces metabolic networks for biotechnology.<br><br>METHODS: Classical 16S-rRNA-based phylogenetic reconstruction does not guarantee to produce well-resolved robust trees that reflect the overall relationship between bacterial species with widespread horizontal gene transfer. In our study we therefore combine three whole genome-based phylogenies with eight different, highly informative single-gene phylogenies to determine a new robust consensus tree of 45 Actinomycetales species with completely sequenced genomes.<br><br>RESULTS: None of the individual methods achieved a resolved phylogeny of Streptomyces and its relatives. Single-gene approaches failed to yield a detailed phylogeny; even though the single trees are in good agreement among each other, they show very low resolution of inner branches. The three whole genome-based methods improve resolution considerably. Only by combining the phylogenies from single gene-based and genome-based approaches we finally obtained a consensus tree with well-resolved branches for the entire set of Actinomycetales species. This phylogenetic information is stable and informative enough for application to the system-wide comparative modeling of bacterial physiology.}, }
@article {pmid19946141, year = {2009}, author = {Alvarez-Martinez, CE and Christie, PJ}, title = {Biological diversity of prokaryotic type IV secretion systems.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {73}, number = {4}, pages = {775-808}, pmid = {19946141}, issn = {1098-5557}, support = {R01 GM048746/GM/NIGMS NIH HHS/United States ; GM48746/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacterial Infections/metabolism/microbiology ; Bacterial Proteins/chemistry/metabolism ; *Biodiversity ; Crenarchaeota/chemistry/*physiology ; DNA/metabolism ; Evolution, Molecular ; Gram-Negative Bacteria/chemistry/*physiology ; Gram-Positive Bacteria/chemistry/*physiology ; Humans ; *Secretory Pathway ; }, abstract = {Type IV secretion systems (T4SS) translocate DNA and protein substrates across prokaryotic cell envelopes generally by a mechanism requiring direct contact with a target cell. Three types of T4SS have been described: (i) conjugation systems, operationally defined as machines that translocate DNA substrates intercellularly by a contact-dependent process; (ii) effector translocator systems, functioning to deliver proteins or other macromolecules to eukaryotic target cells; and (iii) DNA release/uptake systems, which translocate DNA to or from the extracellular milieu. Studies of a few paradigmatic systems, notably the conjugation systems of plasmids F, R388, RP4, and pKM101 and the Agrobacterium tumefaciens VirB/VirD4 system, have supplied important insights into the structure, function, and mechanism of action of type IV secretion machines. Information on these systems is updated, with emphasis on recent exciting structural advances. An underappreciated feature of T4SS, most notably of the conjugation subfamily, is that they are widely distributed among many species of gram-negative and -positive bacteria, wall-less bacteria, and the Archaea. Conjugation-mediated lateral gene transfer has shaped the genomes of most if not all prokaryotes over evolutionary time and also contributed in the short term to the dissemination of antibiotic resistance and other virulence traits among medically important pathogens. How have these machines adapted to function across envelopes of distantly related microorganisms? A survey of T4SS functioning in phylogenetically diverse species highlights the biological complexity of these translocation systems and identifies common mechanistic themes as well as novel adaptations for specialized purposes relating to the modulation of the donor-target cell interaction.}, }
@article {pmid19946135, year = {2009}, author = {Lo, CC and Bonner, CA and Xie, G and D'Souza, M and Jensen, RA}, title = {Cohesion group approach for evolutionary analysis of aspartokinase, an enzyme that feeds a branched network of many biochemical pathways.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {73}, number = {4}, pages = {594-651}, pmid = {19946135}, issn = {1098-5557}, support = {Y01 DE006006/DE/NIDCR NIH HHS/United States ; Y1-DE-6006-02/DE/NIDCR NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Amino Acids/biosynthesis ; Animals ; Aspartate Kinase/*analysis/classification/genetics/*metabolism ; Bacteria/genetics/metabolism ; *Biosynthetic Pathways ; *Evolution, Molecular ; Genetic Variation ; Humans ; Phylogeny ; Recombination, Genetic ; }, abstract = {Aspartokinase (Ask) exists within a variable network that supports the synthesis of 9 amino acids and a number of other important metabolites. Lysine, isoleucine, aromatic amino acids, and dipicolinate may arise from the ASK network or from alternative pathways. Ask proteins were subjected to cohesion group analysis, a methodology that sorts a given protein assemblage into groups in which evolutionary continuity is assured. Two subhomology divisions, ASK(alpha) and ASK(beta), have been recognized. The ASK(alpha) subhomology division is the most ancient, being widely distributed throughout the Archaea and Eukarya and in some Bacteria. Within an indel region of about 75 amino acids near the N terminus, ASK(beta) sequences differ from ASK(alpha) sequences by the possession of a proposed ancient deletion. ASK(beta) sequences are present in most Bacteria and usually exhibit an in-frame internal translational start site that can generate a small Ask subunit that is identical to the C-terminal portion of the larger subunit of a heterodimeric unit. Particularly novel are ask genes embedded in gene contexts that imply specialization for ectoine (osmotic agent) or aromatic amino acids. The cohesion group approach is well suited for the easy recognition of relatively recent lateral gene transfer (LGT) events, and many examples of these are described. Given the current density of genome representation for Proteobacteria, it is possible to reconstruct more ancient landmark LGT events. Thus, a plausible scenario in which the three well-studied and iconic Ask homologs of Escherichia coli are not within the vertical genealogy of Gammaproteobacteria, but rather originated via LGT from a Bacteroidetes donor, is supported.}, }
@article {pmid19944380, year = {2009}, author = {Li, C and Wang, Y and Peng, H and Bian, H and Min, M and Chen, L and Liu, Q and Bao, J}, title = {In silico analysis of the potential infection mechanisms of Magnaporthe grisea from horizontal gene transfer hypothesis.}, journal = {Genomics, proteomics &amp; bioinformatics}, volume = {7}, number = {3}, pages = {77-86}, pmid = {19944380}, issn = {2210-3244}, mesh = {*Computational Biology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Fungal/*genetics ; Genome, Fungal ; Magnaporthe/*genetics/*pathogenicity ; Phylogeny ; Plant Diseases/genetics/*microbiology ; }, abstract = {Horizontal gene transfer (HGT) has long been considered as a principal force for an organism to gain novel genes in genome evolution. Homology search, phylogenetic analysis and nucleotide composition analysis are three major objective approaches to arguably determine the occurrence and directionality of HGT. Here, 21 genes that possess the potential to horizontal transfer were acquired from the whole genome of Magnaporthe grisea according to annotation, among which three candidate genes (corresponding protein accession numbers are EAA55123, EAA47200 and EAA52136) were selected for further analysis. According to BLAST homology results, we subsequently conducted phylogenetic analysis of the three candidate HGT genes. Moreover, nucleotide composition analysis was conducted to further validate these HGTs. In addition, the functions of the three candidate genes were searched in COG database. Consequently, we conclude that the gene encoding protein EAA55123 is transferred from Clostridium perfringens. Another HGT event is between EAA52136 and a certain metazoan's corresponding gene, but the direction remains uncertain. Yet, EAA47200 is not a transferred gene.}, }
@article {pmid19927832, year = {2009}, author = {Quan, XC and Tang, H and Hu, LJ and Wang, R and Zhang, N}, title = {[Plasmid pJP4 mediated gene horizontal transfer in a biofilm system and its effect on 2, 4-D degradation].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {30}, number = {9}, pages = {2728-2734}, pmid = {19927832}, issn = {0250-3301}, mesh = {2,4-Dichlorophenoxyacetic Acid/*metabolism ; Biodegradation, Environmental ; Biofilms ; Bioreactors/*microbiology ; *Gene Transfer, Horizontal ; Plasmids/genetics ; Pseudomonas putida/*genetics/metabolism ; Waste Disposal, Fluid/*methods ; }, abstract = {With plasmid pJP4 (which contains functional gene cluster (tfd) encoding 2,4-D degradation) carrying genetic microorganism Pseudomonas putida SM1443:: gfp2x (pJP4:: dsRed) as the donor strain, events of plasmid mediated gene horizontal transfer and its effect on 2,4-D degradation was investigated in a biofilm system operated under fed-batch mode. The surviving status of the functional gene element in the gene-augmented system and effects of gene-augmentation on microbial community structure were also investigated. Results showed that introduction of pJP4 carrying strain to the biofilm system with 2, 4-D (initial concentration at 170 mg/L +/- 10 mg/L) as the sole carbon source could enhance the degradation of 2, 4-D. Enhancement was slight during the initial stage of operation, but it increased with increasing of fed batch runs. Difference in 2, 4-D average degradation rate between gene-augmented system and the control system achieved up to 13.3 mg/(L x h) at most. Through detecting functional gene tfdB and reporter gene gfp, pJP4 mediated gene horizontal transfer to the bacteria on biofilm was further approved. Effects of gene augmentation on microbial community structure was analyzed by PCR-DGGE analysis, and results showed that relatively higher stability of microbial community was maintained for the gene-augmented biofilm system compared to the control system when facing 2,4-D shock loadings.}, }
@article {pmid19922616, year = {2009}, author = {Pearson, T and Giffard, P and Beckstrom-Sternberg, S and Auerbach, R and Hornstra, H and Tuanyok, A and Price, EP and Glass, MB and Leadem, B and Beckstrom-Sternberg, JS and Allan, GJ and Foster, JT and Wagner, DM and Okinaka, RT and Sim, SH and Pearson, O and Wu, Z and Chang, J and Kaul, R and Hoffmaster, AR and Brettin, TS and Robison, RA and Mayo, M and Gee, JE and Tan, P and Currie, BJ and Keim, P}, title = {Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer.}, journal = {BMC biology}, volume = {7}, number = {}, pages = {78}, pmid = {19922616}, issn = {1741-7007}, support = {U54 AI065359/AI/NIAID NIH HHS/United States ; U01AI-075568/AI/NIAID NIH HHS/United States ; U54AI-56359/AI/NIAID NIH HHS/United States ; }, mesh = {Australia ; Burkholderia pseudomallei/*genetics ; DNA, Bacterial/chemistry/genetics ; Gene Transfer, Horizontal/*physiology ; *Genes, Bacterial ; *Genetics, Population ; Genome, Bacterial ; Humans ; Molecular Epidemiology ; Phylogeny ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {BACKGROUND: Phylogeographic reconstruction of some bacterial populations is hindered by low diversity coupled with high levels of lateral gene transfer. A comparison of recombination levels and diversity at seven housekeeping genes for eleven bacterial species, most of which are commonly cited as having high levels of lateral gene transfer shows that the relative contributions of homologous recombination versus mutation for Burkholderia pseudomallei is over two times higher than for Streptococcus pneumoniae and is thus the highest value yet reported in bacteria. Despite the potential for homologous recombination to increase diversity, B. pseudomallei exhibits a relative lack of diversity at these loci. In these situations, whole genome genotyping of orthologous shared single nucleotide polymorphism loci, discovered using next generation sequencing technologies, can provide very large data sets capable of estimating core phylogenetic relationships. We compared and searched 43 whole genome sequences of B. pseudomallei and its closest relatives for single nucleotide polymorphisms in orthologous shared regions to use in phylogenetic reconstruction.<br><br>RESULTS: Bayesian phylogenetic analyses of >14,000 single nucleotide polymorphisms yielded completely resolved trees for these 43 strains with high levels of statistical support. These results enable a better understanding of a separate analysis of population differentiation among >1,700 B. pseudomallei isolates as defined by sequence data from seven housekeeping genes. We analyzed this larger data set for population structure and allele sharing that can be attributed to lateral gene transfer. Our results suggest that despite an almost panmictic population, we can detect two distinct populations of B. pseudomallei that conform to biogeographic patterns found in many plant and animal species. That is, separation along Wallace's Line, a biogeographic boundary between Southeast Asia and Australia.<br><br>CONCLUSION: We describe an Australian origin for B. pseudomallei, characterized by a single introduction event into Southeast Asia during a recent glacial period, and variable levels of lateral gene transfer within populations. These patterns provide insights into mechanisms of genetic diversification in B. pseudomallei and its closest relatives, and provide a framework for integrating the traditionally separate fields of population genetics and phylogenetics for other bacterial species with high levels of lateral gene transfer.}, }
@article {pmid19919719, year = {2009}, author = {Castillo-Ramírez, S and Vázquez-Castellanos, JF and González, V and Cevallos, MA}, title = {Horizontal gene transfer and diverse functional constrains within a common replication-partitioning system in Alphaproteobacteria: the repABC operon.}, journal = {BMC genomics}, volume = {10}, number = {}, pages = {536}, pmid = {19919719}, issn = {1471-2164}, mesh = {Adaptation, Physiological ; Alphaproteobacteria/*genetics ; Bacterial Proteins/*genetics/metabolism ; Bayes Theorem ; Codon/genetics ; *DNA Replication ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Operon/*genetics ; Phylogeny ; Plasmids/*genetics ; Species Specificity ; }, abstract = {BACKGROUND: The repABC plasmid family, which is extensively present within Alphaproteobacteria, and some secondary chromosomes of the Rhizobiales have the particular feature that all the elements involved in replication and partitioning reside within one transcriptional unit, the repABC operon. Given the functional interactions among the elements of the repABC operon, and the fact that they all reside in the same operon, a common evolutionary history would be expected if the entire operon had been horizontally transferred. Here, we tested whether there is a common evolutionary history within the repABC operon. We further examined different incompatibility groups in terms of their differentiation and degree of adaptation to their host.<br><br>RESULTS: We did not find a single evolutionary history within the repABC operon. Each protein had a particular phylogeny, horizontal gene transfer events of the individual genes within the operon were detected, and different functional constraints were found within and between the Rep proteins. When different repABC operons coexisted in the same genome, they were well differentiated from one another. Finally, we found different levels of adaptation to the host genome within and between repABC operons coexisting in the same species.<br><br>CONCLUSION: Horizontal gene transfer with conservation of the repABC operon structure provides a highly dynamic operon in which each member of this operon has its own evolutionary dynamics. In addition, it seems that different incompatibility groups present in the same species have different degrees of adaptation to their host genomes, in proportion to the amount of time the incompatibility group has coexisted with the host genome.}, }
@article {pmid19919536, year = {2010}, author = {Ruimy, R and Brisabois, A and Bernede, C and Skurnik, D and Barnat, S and Arlet, G and Momcilovic, S and Elbaz, S and Moury, F and Vibet, MA and Courvalin, P and Guillemot, D and Andremont, A}, title = {Organic and conventional fruits and vegetables contain equivalent counts of Gram-negative bacteria expressing resistance to antibacterial agents.}, journal = {Environmental microbiology}, volume = {12}, number = {3}, pages = {608-615}, doi = {10.1111/j.1462-2920.2009.02100.x}, pmid = {19919536}, issn = {1462-2920}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics/metabolism ; Drug Resistance, Bacterial/*physiology ; Food Contamination ; Fruit/*microbiology ; Gene Transfer, Horizontal ; Gram-Negative Bacteria/classification/*drug effects/genetics/*physiology ; Humans ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Vegetables/*microbiology ; beta-Lactamases/genetics/metabolism ; }, abstract = {Resistance to antibiotics is a major public health problem which might culminate in outbreaks caused by pathogenic bacteria untreatable by known antibiotics. Most of the genes conferring resistance are acquired horizontally from already resistant commensal or environmental bacteria. Food contamination by resistant bacteria might be a significant source of resistance genes for human bacteria but has never been precisely assessed, nor is it known whether organic products differ in this respect from conventionally produced products. We showed here, on a large year-long constructed sample set containing 399 products that, irrespective of their mode of production, raw fruits and vegetables are heavily contaminated by Gram-negative bacteria (GNB) resistant to multiple antibiotics. Most of these bacteria originate in the soil and environment. We focused on non-oxidative GNB resistant to third-generation cephalosporins, because of their potential impact on human health. Among them, species potentially pathogenic for immunocompetent hosts were rare. Of the products tested, 13% carried bacteria producing extended-spectrum beta-lactamases, all identified as Rahnella sp. which grouped into two phylotypes and all carrying the bla(RAHN) gene. Thus, both organic and conventional fruits and vegetables may constitute significant sources of resistant bacteria and of resistance genes.}, }
@article {pmid19917745, year = {2010}, author = {Ramírez, MS and Piñeiro, S and ,  and Centrón, D}, title = {Novel insights about class 2 integrons from experimental and genomic epidemiology.}, journal = {Antimicrobial agents and chemotherapy}, volume = {54}, number = {2}, pages = {699-706}, pmid = {19917745}, issn = {1098-6596}, mesh = {Acinetobacter Infections/microbiology ; Acinetobacter baumannii/genetics ; DNA Transposable Elements/genetics ; Enterobacter cloacae/genetics ; Enterobacteriaceae Infections/microbiology ; Genome, Bacterial/*genetics ; Humans ; Integrons/*genetics ; Models, Genetic ; Molecular Sequence Data ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {In order to contribute to the knowledge of the architecture and epidemiology of class 2 integrons, we performed a class 2 integron molecular survey in which we analyzed 726 isolates in two bacterial populations from environmental and nonepidemiologically related clinical samples, respectively, collected from 1982 to 2007. We recovered the intI2 gene from 130 of 726 isolates, most of which were clinical isolates, and only 1 (a psychrophilic Pseudomonas sp.) was from a water sample. Unlike the widespread distribution of class 1 integrons within Gram-negative bacilli, only Acinetobacter baumannii and Enterobacter cloacae harbored class 2 integrons at a high frequency in our collection. Class 2 integrons with six novel cassette arrays were documented. Characterization of the transposition module of Tn7, the genetic platform in which class 2 integrons have always been reported, showed tns modules with a mosaic genetic structure. A bioinformatic analysis performed with the tns genes present in sequence databases, the finding of intI2 not associated with tns genes, and the genetic examination of novel tns-like genes found in three isolates indicated the possibility of the independent evolution of the two components related to horizontal gene transfer, the class 2 integrons and the Tn7 transposons.}, }
@article {pmid19917084, year = {2009}, author = {Karim, N and Jones, JT and Okada, H and Kikuchi, T}, title = {Analysis of expressed sequence tags and identification of genes encoding cell-wall-degrading enzymes from the fungivorous nematode Aphelenchus avenae.}, journal = {BMC genomics}, volume = {10}, number = {}, pages = {525}, pmid = {19917084}, issn = {1471-2164}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cell Wall/*metabolism ; Cellulase/genetics ; Cluster Analysis ; Databases, Protein ; Desiccation ; *Expressed Sequence Tags ; Gene Expression Regulation ; Gene Library ; Molecular Sequence Data ; Phylogeny ; Polysaccharide-Lyases/chemistry/genetics ; RNA, Messenger/genetics/metabolism ; Stress, Physiological/genetics ; Tylenchida/cytology/*enzymology/*genetics ; }, abstract = {BACKGROUND: The fungivorus nematode, Aphelenchus avenae is widespread in soil and is found in association with decaying plant material. This nematode is also found in association with plants but its ability to cause plant disease remains largely undetermined. The taxonomic position and intermediate lifestyle of A. avenae make it an important model for studying the evolution of plant parasitism within the Nematoda. In addition, the exceptional capacity of this nematode to survive desiccation makes it an important system for study of anhydrobiosis. Expressed sequence tag (EST) analysis may therefore be useful in providing an initial insight into the poorly understood genetic background of A. avenae.<br><br>RESULTS: We present the generation, analysis and annotation of over 5,000 ESTs from a mixed-stage A. avenae cDNA library. Clustering of 5,076 high-quality ESTs resulted in a set of 2,700 non-redundant sequences comprising 695 contigs and 2,005 singletons. Comparative analyses indicated that 1,567 (58.0%) of the cluster sequences had homologues in Caenorhabditis elegans, 1,750 (64.8%) in other nematodes, 1,321(48.9%) in organisms other than nematodes, and 862 (31.9%) had no significant match to any sequence in current protein or nucleotide databases. In addition, 1,100 (40.7%) of the sequences were functionally classified using Gene Ontology (GO) hierarchy. Similarity searches of the cluster sequences identified a set of genes with significant homology to genes encoding enzymes that degrade plant or fungal cell walls. The full length sequences of two genes encoding glycosyl hydrolase family 5 (GHF5) cellulases and two pectate lyase genes encoding polysaccharide lyase family 3 (PL3) proteins were identified and characterized.<br><br>CONCLUSION: We have described at least 2,214 putative genes from A. avenae and identified a set of genes encoding a range of cell-wall-degrading enzymes. This EST dataset represents a starting point for studies in a number of different fundamental and applied areas. The presence of genes encoding a battery of cell-wall-degrading enzymes in A. avenae and their similarities with genes from other plant parasitic nematodes suggest that this nematode can act not only as a fungal feeder but also a plant parasite. Further studies on genes encoding cell-wall-degrading enzymes in A. avenae will accelerate our understanding of the complex evolutionary histories of plant parasitism and the use of genes obtained by horizontal gene transfer from prokaryotes.}, }
@article {pmid19915034, year = {2010}, author = {Delorme, C and Bartholini, C and Bolotine, A and Ehrlich, SD and Renault, P}, title = {Emergence of a cell wall protease in the Streptococcus thermophilus population.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {2}, pages = {451-460}, pmid = {19915034}, issn = {1098-5336}, mesh = {Bacterial Proteins/*genetics ; Base Sequence ; Cell Wall/enzymology ; Genetic Variation ; Molecular Sequence Data ; Phylogeny ; Serine Endopeptidases/*genetics ; Streptococcus thermophilus/classification/*enzymology/genetics ; }, abstract = {Streptococcus thermophilus is perceived as a recently emerged food bacterium that evolved from a commensal ancestor by loss and gain of functions. Here, we provide data allowing a better understanding of this evolutionary scheme. A multilocus sequence typing approach that we developed showed that S. thermophilus diverges significantly from its potential ancestors of the salivarius group and displays a low level of allelic variability, confirming its likely recent emergence. An analysis of the origin and dissemination of the prtS gene was carried out within this evolutionary scheme. This gene encodes a protease that allows better growth in milk by facilitating casein breakdown to supply amino acids. The S. thermophilus protease exhibits 95% identity to the animal Streptococcus suis protein PrtS. Genomic analysis showed that prtS is part of an island flanked by two tandem insertion sequence elements and containing three other genes which present the best identities and synteny with the S. suis genome. These data indicate a potential origin for this "ecological" island in a species closely related to S. suis. The analysis of the distribution of the prtS gene in S. thermophilus showed that the gene is infrequent in historical collections but frequent in recent industrial ones. Moreover, this "ecological" island conferring an important metabolic trait for milk adaptation appears to have disseminated by lateral transfer in the S. thermophilus population. Taken together, these data support an evolutionary scheme of S. thermophilus where gene acquisition and selection by food producers are determining factors. The source and impact of genes acquired by horizontal gene transfer on the physiology and safety of strains should be addressed.}, }
@article {pmid19910386, year = {2010}, author = {Suzuki, K and Miyagishima, SY}, title = {Eukaryotic and eubacterial contributions to the establishment of plastid proteome estimated by large-scale phylogenetic analyses.}, journal = {Molecular biology and evolution}, volume = {27}, number = {3}, pages = {581-590}, doi = {10.1093/molbev/msp273}, pmid = {19910386}, issn = {1537-1719}, mesh = {Algal Proteins/classification/*genetics ; Arabidopsis/genetics ; Bacteria/genetics ; Bacterial Proteins/classification/genetics ; Cell Nucleus ; Cyanobacteria/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Phylogeny ; Plant Proteins/classification/*genetics ; Plastids/*genetics ; Proteome/*genetics ; Rhodophyta/genetics ; Symbiosis ; }, abstract = {Plastids including chloroplasts arose from a cyanobacterial endosymbiont and have retained their own genome, but the size has been reduced to less than one-tenth of the original bacterial genome. Over time, genes essential to plastid function have been transferred from the ancestral plastid genome to the nucleus, and the gene products are now targeted into the plastid from the host cytosol. However, phylogenetic analyses have suggested that the functions of certain original proteins encoded by the endosymbiont genome have been replaced by nucleus-encoded proteins of noncyanobacterial origin and that several proteins have been newly added to maintain and control plastids. In order to evaluate the rate and origin of noncyanobacterial proteins that have contributed to the establishment of the plastid proteome, we performed phylogenetic analyses of plastid-targeted proteins that are shared by the red alga Cyanidioschyzon merolae (455 proteins) and the Viridiplanta Arabidopsis thaliana (744 proteins). Our results show that approximately 40% of the plastid proteome common to red algae and green plants originated from genes of both the ancestral eukaryotic host and various lineages of bacteria (eubacteria) other than cyanobacteria. The replacement or addition of components was frequently observed for most of the plastid functions except for the light reaction of photosynthesis and the translation and degradation of proteins in the plastid. These results suggest that a considerable amount of bacterial metagenomic material, as well as the genomes of the host and the endosymbiont, has contributed to the establishment of the plastid before the split of the red and green algae.}, }
@article {pmid19910236, year = {2010}, author = {Bock, R}, title = {The give-and-take of DNA: horizontal gene transfer in plants.}, journal = {Trends in plant science}, volume = {15}, number = {1}, pages = {11-22}, doi = {10.1016/j.tplants.2009.10.001}, pmid = {19910236}, issn = {1878-4372}, mesh = {Animals ; DNA/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genetic Engineering ; Plants/*genetics ; }, abstract = {Horizontal gene transfer (HGT) is increasingly being recognized as a significant force in the evolution of eukaryotic genomes. Plants have been both donors and recipients of horizontally mobilized genes and their genetic barter partners include prokaryotes and eukaryotes from all kingdoms. By expanding the gene pool beyond species boundaries, HGT events can drive genomic and phenotypic changes that increase fitness substantially. Accumulating evidence suggests that HGT is particularly prevalent between organisms that are either intimately associated or establish at least occasionally cell-cell contacts (e.g. in mutualistic or parasitic relationships). Here, I summarize current knowledge about HGT in plants, discuss possible molecular mechanisms and adaptive values of HGT events and highlight recent progress made in reconstructing HGT processes in laboratory experiments.}, }
@article {pmid19909380, year = {2010}, author = {Pauchet, Y and Wilkinson, P and Vogel, H and Nelson, DR and Reynolds, SE and Heckel, DG and ffrench-Constant, RH}, title = {Pyrosequencing the Manduca sexta larval midgut transcriptome: messages for digestion, detoxification and defence.}, journal = {Insect molecular biology}, volume = {19}, number = {1}, pages = {61-75}, doi = {10.1111/j.1365-2583.2009.00936.x}, pmid = {19909380}, issn = {1365-2583}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Animals ; Cytochrome P-450 Enzyme System/genetics/metabolism ; Digestion ; Expressed Sequence Tags ; Gastrointestinal Tract/metabolism ; *Gene Expression Profiling ; Gene Transfer, Horizontal ; Inactivation, Metabolic ; Insect Proteins/*metabolism ; Larva/immunology/metabolism ; Molecular Sequence Data ; Moths/genetics/immunology/*metabolism ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; beta-Fructofuranosidase/genetics/*metabolism ; }, abstract = {The tobacco hornworm Manduca sexta is an important model for insect physiology but genomic and transcriptomic data are currently lacking. Following a recent pyrosequencing study generating immune related expressed sequence tags (ESTs), here we use this new technology to define the M. sexta larval midgut transcriptome. We generated over 387,000 midgut ESTs, using a combination of Sanger and 454 sequencing, and classified predicted proteins into those involved in digestion, detoxification and immunity. In many cases the depth of 454 pyrosequencing coverage allowed us to define the entire cDNA sequence of a particular gene. Many new M. sexta genes are described including up to 36 new cytochrome P450s, some of which have been implicated in the metabolism of host plant-derived nicotine. New lepidopteran gene families such as the beta-fructofuranosidases, previously thought to be restricted to Bombyx mori, are also described. An unexpectedly high number of ESTs were involved in immunity, for example 39 contigs encoding serpins, and the increasingly appreciated role of the midgut in insect immunity is discussed. Similar studies of other tissues will allow for a tissue by tissue description of the M. sexta transcriptome and will form an essential complimentary step on the road to genome sequencing and annotation.}, }
@article {pmid19907704, year = {2009}, author = {Lee, SC and Weiss, LM and Heitman, J}, title = {Generation of genetic diversity in microsporidia via sexual reproduction and horizontal gene transfer.}, journal = {Communicative &amp; integrative biology}, volume = {2}, number = {5}, pages = {414-417}, pmid = {19907704}, issn = {1942-0889}, support = {R01 AI031788/AI/NIAID NIH HHS/United States ; R01 AI031788-19/AI/NIAID NIH HHS/United States ; R01 AI050113/AI/NIAID NIH HHS/United States ; }, abstract = {Microsporidia are obligate intracellular pathogens mainly infecting both vertebrate and invertebrate hosts. The group comprises approximately 150 genera with 1,200 species. Due to sequence divergence phylogenic reconstructions that are solely based on DNA sequence have been unprecise for these pathogens. Our previous study identified that three microsporidian genomes contained a putative sex-related locus similar to that of zygomycetes. In a comparison of genome architecture of the microsporidia to other fungi, Rhizopus oryzae, a zygomycete fungus, shared more common gene clusters with Encephalitozoon cuniculi, a microsporidian. This provides evidence supporting the hypothesis that microsporidia and zygomycete fungi may share a more recent common ancestor than other fungal lineages. Genetic recombination is an important outcome of sexual development. We describe genetic markers which will enable tests of whether sex occurs within E. cuniculi populations by analyzing tandem repeat DNA regions in three different isolates. Taken together, the phylogenetic relationship of microsporidia to fungi and the presence of a sex-related locus in their genomes suggest the microsporidia may have an extant sexual cycle. In addition, we describe recently reported evidence of horizontal gene transfer from Chlamydia to the E. cuniculi genome and show that these two obligate intracellular pathogens can infect the same host cells.}, }
@article {pmid19906794, year = {2010}, author = {Chafee, ME and Funk, DJ and Harrison, RG and Bordenstein, SR}, title = {Lateral phage transfer in obligate intracellular bacteria (wolbachia): verification from natural populations.}, journal = {Molecular biology and evolution}, volume = {27}, number = {3}, pages = {501-505}, pmid = {19906794}, issn = {1537-1719}, support = {R01 GM085163/GM/NIGMS NIH HHS/United States ; R01 GM085163-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteriophages/*genetics ; Bayes Theorem ; Coleoptera/genetics/*microbiology/virology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Gryllidae/genetics/*microbiology/virology ; Interspersed Repetitive Sequences ; Phylogeny ; Wolbachia/*genetics/virology ; }, abstract = {Lateral transfer of mobile DNA is a hallmark of bacteria with a free-living replicative stage; however, its significance in obligate intracellular bacteria and other heritable endosymbionts remains controversial. Comparative sequence analyses from laboratory stocks infected with Wolbachia pipientis provide some of the most compelling evidence that bacteriophage WO-B transfers laterally between infections of the same insect host. Lateral transfer between coinfections, however, has been evaluated neither in natural populations nor between closely related Wolbachia strains. Here, we analyze bacterial and phage genes from two pairs of natural sympatric field isolates, of Gryllus pennsylvanicus field crickets and of Neochlamisus bebbianae leaf beetles, to demonstrate WO-B transfers between supergroup B Wolbachia. N. bebbianae revealed the highest number of phage haplotypes yet recorded, hinting that lab lines could underestimate phage haplotype variation and lateral transfer. Finally, using the approximate age of insect host species as the maximum available time for phage transfer between host-associated bacteria, we very conservatively estimate phage WO-B transfer to occur at least once every 0-5.4 My within a host species. Increasing discoveries of mobile elements, intragenic recombination, and bacterial coinfections in host-switching obligate intracellular bacteria specify that mobile element transfer is common in these species.}, }
@article {pmid19906303, year = {2009}, author = {Koonin, EV and Wolf, YI}, title = {Is evolution Darwinian or/and Lamarckian?.}, journal = {Biology direct}, volume = {4}, number = {}, pages = {42}, pmid = {19906303}, issn = {1745-6150}, support = {//Intramural NIH HHS/United States ; }, mesh = {*Biological Evolution ; DNA Transposable Elements/genetics ; Inheritance Patterns/genetics ; *Models, Biological ; Mutagenesis/genetics ; Selection, Genetic ; Stress, Physiological/genetics ; }, abstract = {BACKGROUND: The year 2009 is the 200th anniversary of the publication of Jean-Bapteste Lamarck's Philosophie Zoologique and the 150th anniversary of Charles Darwin's On the Origin of Species. Lamarck believed that evolution is driven primarily by non-randomly acquired, beneficial phenotypic changes, in particular, those directly affected by the use of organs, which Lamarck believed to be inheritable. In contrast, Darwin assigned a greater importance to random, undirected change that provided material for natural selection.<br><br>THE CONCEPT: The classic Lamarckian scheme appears untenable owing to the non-existence of mechanisms for direct reverse engineering of adaptive phenotypic characters acquired by an individual during its life span into the genome. However, various evolutionary phenomena that came to fore in the last few years, seem to fit a more broadly interpreted (quasi)Lamarckian paradigm. The prokaryotic CRISPR-Cas system of defense against mobile elements seems to function via a bona fide Lamarckian mechanism, namely, by integrating small segments of viral or plasmid DNA into specific loci in the host prokaryote genome and then utilizing the respective transcripts to destroy the cognate mobile element DNA (or RNA). A similar principle seems to be employed in the piRNA branch of RNA interference which is involved in defense against transposable elements in the animal germ line. Horizontal gene transfer (HGT), a dominant evolutionary process, at least, in prokaryotes, appears to be a form of (quasi)Lamarckian inheritance. The rate of HGT and the nature of acquired genes depend on the environment of the recipient organism and, in some cases, the transferred genes confer a selective advantage for growth in that environment, meeting the Lamarckian criteria. Various forms of stress-induced mutagenesis are tightly regulated and comprise a universal adaptive response to environmental stress in cellular life forms. Stress-induced mutagenesis can be construed as a quasi-Lamarckian phenomenon because the induced genomic changes, although random, are triggered by environmental factors and are beneficial to the organism.<br><br>CONCLUSION: Both Darwinian and Lamarckian modalities of evolution appear to be important, and reflect different aspects of the interaction between populations and the environment.}, }
@article {pmid19900539, year = {2010}, author = {Gao, J and Chen, LL}, title = {Theoretical methods for identifying important functional genes in bacterial genomes.}, journal = {Research in microbiology}, volume = {161}, number = {1}, pages = {1-8}, doi = {10.1016/j.resmic.2009.10.007}, pmid = {19900539}, issn = {1769-7123}, mesh = {Bacterial Proteins/genetics/*physiology ; Computational Biology/*methods ; Gene Expression ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genes, Essential ; *Genome, Bacterial ; }, abstract = {Some functional genes, such as essential genes, highly expressed genes and horizontally transferred genes, play important roles in the survival and pathogenicity of bacteria. This review attempts to summarize current computational methods in identifying the above functional genes from bacterial genomes, which is of significant importance in exploring the bacterial genomes.}, }
@article {pmid19899641, year = {2009}, author = {Gorbunov, KIu and Liubetskiĭ, VA}, title = {[Reconstructing genes evolution along a species tree].}, journal = {Molekuliarnaia biologiia}, volume = {43}, number = {5}, pages = {946-958}, pmid = {19899641}, issn = {0026-8984}, mesh = {*Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; *Models, Genetic ; *Phylogeny ; }, abstract = {A model and algorithm are proposed to infer evolution of a gene family, given the gene tree, with respect to species evolution, given the species tree. The model describes such evolution using the "nested tree" concept. Performance of the algorithm is verified on several orthologous protein groups. The evolutionary events inferred are: speciation, gene duplication and loss, horizontal gene transfer retaining the original gene copy. A transfer event with the loss of original gene copy is considered a combination of gene transfer and loss. The model maps gene evolution events onto the species phylogeny.}, }
@article {pmid19899625, year = {2009}, author = {Turova, TP and Spiridonova, EM}, title = {[Phylogeny and evolution of RubiCo genes in prokaryotes].}, journal = {Molekuliarnaia biologiia}, volume = {43}, number = {5}, pages = {772-788}, pmid = {19899625}, issn = {0026-8984}, mesh = {*Evolution, Molecular ; Operon/physiology ; Photosynthesis/*physiology ; *Phylogeny ; Prokaryotic Cells/*enzymology ; Ribulose-Bisphosphate Carboxylase/*genetics/*metabolism ; }, abstract = {This paper reviews phylogeny and evolution of ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) protein which is the key enzyme of the autotrophic Kalvin-Benson cycle and the most abundant protein on the planet. It consists of several structural-functional forms which include fully functional forms I, II and III catalyzing carboxylation/oxygenation of ribulose-1,5-bisphosphate and "RubisCO-like" form IV without the carboxylating activity. The genome localization, the operon structure and the copy number of the RubisCO genes varies in different autotrophic organisms. The RubisCO gene phylogeny differs substantially from the phylogeny of other conservative genes including 16S rRNA gene. This is due to commonly occurred duplication/deletion and horizontal gene transfer events happened during evolution of autotrophic organisms.}, }
@article {pmid19897356, year = {2009}, author = {Keeling, PJ}, title = {Functional and ecological impacts of horizontal gene transfer in eukaryotes.}, journal = {Current opinion in genetics &amp; development}, volume = {19}, number = {6}, pages = {613-619}, doi = {10.1016/j.gde.2009.10.001}, pmid = {19897356}, issn = {1879-0380}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Adaptation, Biological ; Animals ; *Biological Evolution ; Eukaryota/*genetics ; *Gene Transfer, Horizontal ; Genome ; Host-Parasite Interactions/genetics ; Humans ; }, abstract = {Horizontal gene transfer (HGT) is known to have contributed to the content of eukaryotic genomes, but the direct effects of HGT on eukaryotic evolution are more obscure because many of the best supported cases involve a new gene replacing a functionally similar homologue. Here, several cases of HGT conferring a plausible adaptive advantage are reviewed to examine emerging trends in such transfer events. In particular, HGT seems to play an important role in adaptation to parasitism and pathogenesis, as well as to other specific environmental conditions such as anaerobiosis or nitrogen and iron limitation in marine environments. Most, but not all, of the functionally significant HGT to eukaryotes comes from bacteria, in part due to chance, but probably also because bacteria have greater metabolic diversity to offer.}, }
@article {pmid19893894, year = {2009}, author = {Blauth, ML and Bruno, RV and Abdelhay, E and Loreto, EL and Valente, VL}, title = {Detection of P element transcripts in embryos of Drosophila melanogaster and D. willistoni.}, journal = {Anais da Academia Brasileira de Ciencias}, volume = {81}, number = {4}, pages = {679-689}, doi = {10.1590/s0001-37652009000400007}, pmid = {19893894}, issn = {1678-2690}, mesh = {Animals ; DNA Transposable Elements/*genetics ; Drosophila/classification/*embryology/genetics ; Drosophila melanogaster/genetics ; Electrophoresis, Agar Gel ; Gene Transfer, Horizontal ; Humans ; Male ; Reverse Transcriptase Polymerase Chain Reaction ; Transcription, Genetic/*genetics ; }, abstract = {The P element is one of the most thoroughly studied transposable elements (TE). Its mobilization causes the hybrid dysgenesis that was first described in Drosophila melanogaster. While studies of the P element have mainly been done in D. melanogaster, it is believed that Drosophila willistoni was the original host species of this TE and that P was transposed to the D. melanogaster genome by horizontal transfer. Our study sought to compare the transcriptional behavior of the P element in embryos of D. melanogaster, which is a recent host, with embryos of two strains of D. willistoni, a species that has contained the P element for a longer time. In both species, potential transcripts of transposase, the enzyme responsible for the TE mobilization, were detected, as were transcripts of the 66-kDa repressor, truncated and antisense sequences, which can have the ability to prevent TEs mobilization. The truncated transcripts reveal the truncated P elements present in the genome strains and whose number seems to be related to the invasion time of the genome by the TE. No qualitative differences in antisense transcripts were observed among the strains, even in the D. willistoni strain with the highest frequency of heterochromatic P elements.}, }
@article {pmid19893622, year = {2009}, author = {McMurdie, PJ and Behrens, SF and Müller, JA and Göke, J and Ritalahti, KM and Wagner, R and Goltsman, E and Lapidus, A and Holmes, S and Löffler, FE and Spormann, AM}, title = {Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides.}, journal = {PLoS genetics}, volume = {5}, number = {11}, pages = {e1000714}, pmid = {19893622}, issn = {1553-7404}, support = {R01 GM086884/GM/NIGMS NIH HHS/United States ; }, mesh = {Chloroflexi/*genetics/metabolism ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Phylogeny ; Vinyl Chloride/*metabolism ; }, abstract = {Vinyl chloride (VC) is a human carcinogen and widespread priority pollutant. Here we report the first, to our knowledge, complete genome sequences of microorganisms able to respire VC, Dehalococcoides sp. strains VS and BAV1. Notably, the respective VC reductase encoding genes, vcrAB and bvcAB, were found embedded in distinct genomic islands (GEIs) with different predicted integration sites, suggesting that these genes were acquired horizontally and independently by distinct mechanisms. A comparative analysis that included two previously sequenced Dehalococcoides genomes revealed a contextually conserved core that is interrupted by two high plasticity regions (HPRs) near the Ori. These HPRs contain the majority of GEIs and strain-specific genes identified in the four Dehalococcoides genomes, an elevated number of repeated elements including insertion sequences (IS), as well as 91 of 96 rdhAB, genes that putatively encode terminal reductases in organohalide respiration. Only three core rdhA orthologous groups were identified, and only one of these groups is supported by synteny. The low number of core rdhAB, contrasted with the high rdhAB numbers per genome (up to 36 in strain VS), as well as their colocalization with GEIs and other signatures for horizontal transfer, suggests that niche adaptation via organohalide respiration is a fundamental ecological strategy in Dehalococccoides. This adaptation has been exacted through multiple mechanisms of recombination that are mainly confined within HPRs of an otherwise remarkably stable, syntenic, streamlined genome among the smallest of any free-living microorganism.}, }
@article {pmid19889369, year = {2009}, author = {Lawrence, JG}, title = {Microbial evolution: enforcing cooperation by partial kin selection.}, journal = {Current biology : CB}, volume = {19}, number = {20}, pages = {R943-5}, doi = {10.1016/j.cub.2009.09.045}, pmid = {19889369}, issn = {1879-0445}, mesh = {*Biological Evolution ; Escherichia coli/genetics/metabolism/*physiology ; Escherichia coli Proteins/metabolism/physiology ; Gene Transfer, Horizontal ; *Microbial Interactions ; }, abstract = {How do bacterial cells mediate effective cooperation? A new paper suggests two routes: converting the uninitiated to their cause by lateral gene transfer, and enforcing cooperative behavior by killing revertants.}, }
@article {pmid19888992, year = {2010}, author = {Maralikova, B and Ali, V and Nakada-Tsukui, K and Nozaki, T and van der Giezen, M and Henze, K and Tovar, J}, title = {Bacterial-type oxygen detoxification and iron-sulfur cluster assembly in amoebal relict mitochondria.}, journal = {Cellular microbiology}, volume = {12}, number = {3}, pages = {331-342}, doi = {10.1111/j.1462-5822.2009.01397.x}, pmid = {19888992}, issn = {1462-5822}, support = {BB/C507145/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/C507145/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bacterial Proteins/*metabolism ; Entamoeba histolytica/*metabolism ; Hemerythrin/metabolism ; Iron/*metabolism ; Microscopy, Fluorescence ; Microscopy, Immunoelectron ; Organelles/*metabolism ; Oxygen/*antagonists &amp; inhibitors ; Peroxidase/metabolism ; Rubredoxins/metabolism ; Sulfur/*metabolism ; }, abstract = {The assembly of vital reactive iron-sulfur (Fe-S) cofactors in eukaryotes is mediated by proteins inherited from the original mitochondrial endosymbiont. Uniquely among eukaryotes, however, Entamoeba and Mastigamoeba lack such mitochondrial-type Fe-S cluster assembly proteins and possess instead an analogous bacterial-type system acquired by lateral gene transfer. Here we demonstrate, using immunomicroscopy and biochemical methods, that beyond their predicted cytosolic distribution the bacterial-type Fe-S cluster assembly proteins NifS and NifU have been recruited to function within the relict mitochondrial organelles (mitosomes) of Entamoeba histolytica. Both Nif proteins are 10-fold more concentrated within mitosomes compared with their cytosolic distribution suggesting that active Fe-S protein maturation occurs in these organelles. Quantitative immunoelectron microscopy showed that amoebal mitosomes are minute but highly abundant cellular structures that occupy up to 2% of the total cell volume. In addition, protein colocalization studies allowed identification of the amoebal hydroperoxide detoxification enzyme rubrerythrin as a mitosomal protein. This protein contains functional Fe-S centres and exhibits peroxidase activity in vitro. Our findings demonstrate the role of analogous protein replacement in mitochondrial organelle evolution and suggest that the relict mitochondrial organelles of Entamoeba are important sites of metabolic activity that function in Fe-S protein-mediated oxygen detoxification.}, }
@article {pmid19886796, year = {2009}, author = {Munoz-Price, LS and Quinn, JP}, title = {The spread of Klebsiella pneumoniae carbapenemases: a tale of strains, plasmids, and transposons.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {49}, number = {11}, pages = {1739-1741}, doi = {10.1086/648078}, pmid = {19886796}, issn = {1537-6591}, mesh = {Bacterial Proteins/*genetics ; Carbapenems/therapeutic use ; DNA Transposable Elements/*genetics ; Drug Resistance, Bacterial/genetics ; Escherichia coli/genetics ; Gene Transfer, Horizontal/*genetics ; Humans ; Klebsiella Infections/*microbiology ; Klebsiella pneumoniae/enzymology/*genetics ; Plasmids/*genetics ; Polymerase Chain Reaction ; Serratia marcescens/genetics ; beta-Lactamases/*genetics ; }, }
@article {pmid19886795, year = {2009}, author = {Sidjabat, HE and Silveira, FP and Potoski, BA and Abu-Elmagd, KM and Adams-Haduch, JM and Paterson, DL and Doi, Y}, title = {Interspecies spread of Klebsiella pneumoniae carbapenemase gene in a single patient.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {49}, number = {11}, pages = {1736-1738}, doi = {10.1086/648077}, pmid = {19886795}, issn = {1537-6591}, mesh = {Adult ; Anti-Bacterial Agents/therapeutic use ; Bacterial Proteins/*genetics ; Carbapenems/therapeutic use ; Drug Resistance, Bacterial/genetics ; Escherichia coli/genetics ; Female ; Gene Transfer, Horizontal/*genetics ; Humans ; Klebsiella Infections/drug therapy/*microbiology ; Klebsiella pneumoniae/enzymology/*genetics ; Plasmids/genetics ; Polymerase Chain Reaction ; Serratia marcescens/genetics ; beta-Lactamases/*genetics ; }, abstract = {Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae, Escherichia coli, and Serratia marcescens were sequentially identified in a patient who underwent small bowel transplantation. Molecular typing and plasmid analysis suggested that the KPC gene was acquired by E. coli, most likely from K. pneumoniae, and was subsequently transferred to S. marcescens.}, }
@article {pmid19883445, year = {2009}, author = {Ma, Y and Jakowitsch, J and Deusch, O and Henze, K and Martin, W and Löffelhardt, W}, title = {Transketolase from Cyanophora paradoxa: in vitro import into cyanelles and pea chloroplasts and a complex history of a gene often, but not always, transferred in the context of secondary endosymbiosis.}, journal = {The Journal of eukaryotic microbiology}, volume = {56}, number = {6}, pages = {568-576}, doi = {10.1111/j.1550-7408.2009.00437.x}, pmid = {19883445}, issn = {1550-7408}, mesh = {Amino Acid Sequence ; Chloroplasts/*enzymology ; Cyanophora/*enzymology/genetics ; DNA, Algal/analysis/genetics ; Euglena gracilis/enzymology/genetics ; *Gene Transfer, Horizontal ; *Genes ; Molecular Sequence Data ; Pisum sativum/metabolism/*microbiology ; Protein Transport ; Sequence Analysis, DNA ; *Symbiosis ; Transketolase/*metabolism ; }, abstract = {The glaucocystophyte Cyanophora paradoxa is an obligatorily photoautotrophic biflagellated protist containing cyanelles, peculiar plastids surrounded by a peptidoglycan layer between their inner and outer envelope membranes. Although the 136-kb cyanelle genome surpasses higher plant chloroplast genomes in coding capacity by about 50 protein genes, these primitive plastids still have to import >2,000 polypeptides across their unique organelle wall. One such protein is transketolase, an essential enzyme of the Calvin cycle. We report the sequence of the pre-transketolase cDNA from C. paradoxa and in vitro import experiments of precursor polypeptides into cyanelles and into pea chloroplasts. The transit sequence clearly indicates the localization of the gene product to cyanelles and is more similar to the transit sequences of the plant homologues than to transit sequences of other cyanelle precursor polypeptides with the exception of a cyanelle consensus sequence at the N-terminus. The mature sequence reveals conservation of the thiamine pyrophosphate binding site. A neighbor-net planar graph suggests that Cyanophora, higher plants, and the photosynthetic protist Euglena gracilis acquired their nuclear-encoded transketolase genes via endosymbiotic gene transfer from the cyanobacterial ancestor of plastids; in the case of Euglena probably entailing two transfers, once from the plastid in the green algal lineage and once again in the secondary endosymbiosis underlying the origin of Euglena's plastids. By contrast, transketolase genes in some eukaryotes with secondary plastids of red algal origin, such as Thalassiosira pseudonana, have retained the pre-existing transketolase gene germane to their secondary host.}, }
@article {pmid19880211, year = {2010}, author = {Boussau, B and Daubin, V}, title = {Genomes as documents of evolutionary history.}, journal = {Trends in ecology &amp; evolution}, volume = {25}, number = {4}, pages = {224-232}, doi = {10.1016/j.tree.2009.09.007}, pmid = {19880211}, issn = {0169-5347}, mesh = {Animals ; *Evolution, Molecular ; Genetic Variation ; *Genome ; Genomics/*methods ; Humans ; *Phylogeny ; }, abstract = {Genomes conceal a vast intricate record of their carriers' descent and evolution. To disclose this information, biologists need phylogenetic models that integrate various levels of organization, ranging from nucleotide sequences to ecological interactions. Rates of duplication and horizontal gene transfer, organism trees and ancestral population sizes can all be inferred through statistical models of gene family evolution and population genetics. Similarly, phylogenomics combined with other fields of natural sciences can reveal the nature of ancient phenotypes and paleoenvironments. These computationally intensive approaches now benefit from progress in statistics and algorithmics. In this article, we review the recent advances and discuss possible developments towards a comprehensive reconstruction of the history of life.}, }
@article {pmid19879348, year = {2010}, author = {Singh, SP and Klisch, M and Sinha, RP and Häder, DP}, title = {Genome mining of mycosporine-like amino acid (MAA) synthesizing and non-synthesizing cyanobacteria: A bioinformatics study.}, journal = {Genomics}, volume = {95}, number = {2}, pages = {120-128}, doi = {10.1016/j.ygeno.2009.10.002}, pmid = {19879348}, issn = {1089-8646}, mesh = {Amino Acids/chemistry ; Bacterial Proteins/genetics/metabolism ; Computational Biology/*methods ; Cyanobacteria/*genetics/metabolism ; Cyclohexanones/*metabolism ; Genes, Bacterial ; *Genome, Bacterial ; Models, Molecular ; Phylogeny ; }, abstract = {Mycosporine-like amino acids (MAAs) are a family of more than 20 compounds having absorption maxima between 310 and 362 nm. These compounds are well known for their UV-absorbing/screening role in various organisms and seem to have evolutionary significance. In the present investigation we tested four cyanobacteria, e.g., Anabaena variabilis PCC 7937, Anabaena sp. PCC 7120, Synechocystis sp. PCC 6803 and Synechococcus sp. PCC 6301, for their ability to synthesize MAA and conducted genomic and phylogenetic analysis to identify the possible set of genes that might be involved in the biosynthesis of these compounds. Out of the four investigated species, only A. variabilis PCC 7937 was able to synthesize MAA. Genome mining identified a combination of genes, YP_324358 (predicted DHQ synthase) and YP_324357 (O-methyltransferase), which were present only in A. variabilis PCC 7937 and missing in the other studied cyanobacteria. Phylogenetic analysis revealed that these two genes are transferred from a cyanobacterial donor to dinoflagellates and finally to metazoa by a lateral gene transfer event. All other cyanobacteria, which have these two genes, also had another copy of the DHQ synthase gene. The predicted protein structure for YP_324358 also suggested that this product is different from the chemically characterized DHQ synthase of Aspergillus nidulans contrary to the YP_324879, which was predicted to be similar to the DHQ synthase. The present study provides a first insight into the genes of cyanobacteria involved in MAA biosynthesis and thus widens the field of research for molecular, bioinformatics and phylogenetic analysis of these evolutionary and industrially important compounds. Based on the results we propose that YP_324358 and YP_324357 gene products are involved in the biosynthesis of the common core (deoxygadusol) of all MAAs.}, }
@article {pmid19878305, year = {2009}, author = {Yadav, VP and Mandal, PK and Rao, DN and Bhattacharya, S}, title = {Characterization of the restriction enzyme-like endonuclease encoded by the Entamoeba histolytica non-long terminal repeat retrotransposon EhLINE1.}, journal = {The FEBS journal}, volume = {276}, number = {23}, pages = {7070-7082}, doi = {10.1111/j.1742-4658.2009.07419.x}, pmid = {19878305}, issn = {1742-4658}, mesh = {Binding Sites ; DNA/chemistry/metabolism ; DNA Restriction Enzymes/*chemistry/*genetics/metabolism ; Entamoeba histolytica/*enzymology/metabolism ; Genome, Protozoan ; Kinetics ; Protein Structure, Tertiary ; Retroelements/*genetics ; Substrate Specificity ; Terminal Repeat Sequences ; }, abstract = {The genome of the human pathogen Entamoeba histolytica, a primitive protist, contains non-long terminal repeat retrotransposable elements called EhLINEs. These encode reverse transcriptase and endonuclease required for retrotransposition. The endonuclease shows sequence similarity with bacterial restriction endonucleases. Here we report the salient enzymatic features of one such endonuclease. The kinetics of an EhLINE1-encoded endonuclease catalyzed reaction, determined under steady-state and single-turnover conditions, revealed a significant burst phase followed by a slower steady-state phase, indicating that release of product could be the slower step in this reaction. For circular supercoiled DNA the K(m) was 2.6 x 10(-8) M and the k(cat) was 1.6 x 10(-2) sec(-1). For linear E. histolytica DNA substrate the K(m) and k(cat) values were 1.3 x 10(-8) M and 2.2 x 10(-4) sec(-1) respectively. Single-turnover reaction kinetics suggested a noncooperative mode of hydrolysis. The enzyme behaved as a monomer. While Mg(2+) was required for activity, 60% activity was seen with Mn(2+) and none with other divalent metal ions. Substitution of PDX(12-14)D (a metal-binding motif) with PAX(12-14)D caused local conformational change in the protein tertiary structure, which could contribute to reduced enzyme activity in the mutated protein. The protein underwent conformational change upon the addition of DNA, which is consistent with the known behavior of restriction endonucleases. The similarities with bacterial restriction endonucleases suggest that the EhLINE1-encoded endonuclease was possibly acquired from bacteria through horizontal gene transfer. The loss of strict sequence specificity for nicking may have been subsequently selected to facilitate spread of the retrotransposon to intergenic regions of the E. histolytica genome.}, }
@article {pmid19875895, year = {2009}, author = {Portillo, MC and Gonzalez, JM}, title = {CRISPR elements in the Thermococcales: evidence for associated horizontal gene transfer in Pyrococcus furiosus.}, journal = {Journal of applied genetics}, volume = {50}, number = {4}, pages = {421-430}, pmid = {19875895}, issn = {1234-1983}, mesh = {Base Composition ; Base Sequence ; Codon/genetics ; DNA, Archaeal/chemistry/genetics ; *Gene Transfer, Horizontal ; Genome, Archaeal ; Phylogeny ; Pyrococcus abyssi/genetics ; Pyrococcus furiosus/*genetics ; Pyrococcus horikoshii/genetics ; Sequence Homology, Nucleic Acid ; Short Interspersed Nucleotide Elements ; Species Specificity ; Thermococcales/*genetics ; Thermococcus/genetics ; }, abstract = {The presence and distribution of CRISPR (clustered regularly interspaced short palindrome repeat) elements in the archaeal order Thermococcales were analyzed. Four complete genome sequences from the species Pyrococcus abyssi, P. furiosus, P. horikoshii, and Thermococcus kodakaraensis were studied. A fragment of the genome of P. furiosus was flanked by CRISPR elements upstream and by a single element downstream. The composition of the gene sequences contained in this genome fragment (positions 699013 to 855319) showed significant differences from the other genes in the P. furiosus genome. Differences were observed in the GC content at the third codon positions and the frequency of codon usage between the genes located in the analyzed fragment and the other genes in the P. furiosus genome. These results represent the first evidence suggesting that repeated CRISPR elements can be involved in horizontal gene transfer and genomic differentiation of hyperthermophilic Archaea.}, }
@article {pmid19875855, year = {2009}, author = {Cardona, G and Rosselló, F and Valiente, G}, title = {Comparison of tree-child phylogenetic networks.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {6}, number = {4}, pages = {552-569}, doi = {10.1109/TCBB.2007.70270}, pmid = {19875855}, issn = {1557-9964}, mesh = {Algorithms ; Computational Biology/*methods ; Computers ; Data Interpretation, Statistical ; Humans ; Internet ; Models, Genetic ; Models, Statistical ; Models, Theoretical ; Phylogeny ; Programming Languages ; Sequence Alignment/methods ; Software ; }, abstract = {Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of nontreelike evolutionary events, like recombination, hybridization, or lateral gene transfer. While much progress has been made to find practical algorithms for reconstructing a phylogenetic network from a set of sequences, all attempts to endorse a class of phylogenetic networks (strictly extending the class of phylogenetic trees) with a well-founded distance measure have, to the best of our knowledge and with the only exception of the bipartition distance on regular networks, failed so far. In this paper, we present and study a new meaningful class of phylogenetic networks, called tree-child phylogenetic networks, and we provide an injective representation of these networks as multisets of vectors of natural numbers, their path multiplicity vectors. We then use this representation to define a distance on this class that extends the well-known Robinson-Foulds distance for phylogenetic trees and to give an alignment method for pairs of networks in this class. Simple polynomial algorithms for reconstructing a tree-child phylogenetic network from its path multiplicity vectors, for computing the distance between two tree-child phylogenetic networks and for aligning a pair of tree-child phylogenetic networks, are provided. They have been implemented as a Perl package and a Java applet, which can be found at http://bioinfo.uib.es/~recerca/phylonetworks/mudistance/.}, }
@article {pmid19865522, year = {2009}, author = {Arnold, ML and Fogarty, ND}, title = {Reticulate evolution and marine organisms: the final frontier?.}, journal = {International journal of molecular sciences}, volume = {10}, number = {9}, pages = {3836-3860}, pmid = {19865522}, issn = {1422-0067}, mesh = {Animals ; Aquatic Organisms/*genetics ; DNA Transposable Elements ; Diatoms/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; Genes, Plant ; Genetic Loci ; Genetic Markers ; }, abstract = {The role that reticulate evolution (i.e., via lateral transfer, viral recombination and/or introgressive hybridization) has played in the origin and adaptation of individual taxa and even entire clades continues to be tested for all domains of life. Though falsified for some groups, the hypothesis of divergence in the face of gene flow is becoming accepted as a major facilitator of evolutionary change for many microorganisms, plants and animals. Yet, the effect of reticulate evolutionary change in certain assemblages has been doubted, either due to an actual dearth of genetic exchange among the lineages belonging to these clades or because of a lack of appropriate data to test alternative hypotheses. Marine organisms represent such an assemblage. In the past half-century, some evolutionary biologists interested in the origin and trajectory of marine organisms, particularly animals, have posited that horizontal transfer, introgression and hybrid speciation have been rare. In this review, we provide examples of such genetic exchange that have come to light largely as a result of analyses of molecular markers. Comparisons among these markers and between these loci and morphological characters have provided numerous examples of marine microorganisms, plants and animals that possess the signature of mosaic genomes.}, }
@article {pmid19864285, year = {2010}, author = {Boto, L}, title = {Horizontal gene transfer in evolution: facts and challenges.}, journal = {Proceedings. Biological sciences}, volume = {277}, number = {1683}, pages = {819-827}, pmid = {19864285}, issn = {1471-2954}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Biological Evolution ; *Gene Transfer, Horizontal ; Phylogeny ; }, abstract = {The contribution of horizontal gene transfer to evolution has been controversial since it was suggested to be a force driving evolution in the microbial world. In this paper, I review the current standpoint on horizontal gene transfer in evolutionary thinking and discuss how important horizontal gene transfer is in evolution in the broad sense, and particularly in prokaryotic evolution. I review recent literature, asking, first, which processes are involved in the evolutionary success of transferred genes and, secondly, about the extent of horizontal gene transfer towards different evolutionary times. Moreover, I discuss the feasibility of reconstructing ancient phylogenetic relationships in the face of horizontal gene transfer. Finally, I discuss how horizontal gene transfer fits in the current neo-Darwinian evolutionary paradigm and conclude there is a need for a new evolutionary paradigm that includes horizontal gene transfer as well as other mechanisms in the explanation of evolution.}, }
@article {pmid19863978, year = {2009}, author = {Brakhage, AA and Thön, M and Spröte, P and Scharf, DH and Al-Abdallah, Q and Wolke, SM and Hortschansky, P}, title = {Aspects on evolution of fungal beta-lactam biosynthesis gene clusters and recruitment of trans-acting factors.}, journal = {Phytochemistry}, volume = {70}, number = {15-16}, pages = {1801-1811}, doi = {10.1016/j.phytochem.2009.09.011}, pmid = {19863978}, issn = {1873-3700}, mesh = {Anti-Bacterial Agents/*biosynthesis ; Bacteria/genetics/metabolism ; *Evolution, Molecular ; Fungi/*genetics/*metabolism ; Gene Expression Regulation, Bacterial ; *Gene Expression Regulation, Fungal ; Molecular Structure ; Transcriptional Activation ; beta-Lactams/*metabolism ; }, abstract = {Penicillins and cephalosporins are beta-lactam antibiotics. The formation of hydrophobic penicillins has been reported in fungi only, notably Penicillium chrysogenum and Aspergillus (Emericella) nidulans, whereas the hydrophilic cephalosporins are produced by both fungi, e.g., Acremonium chrysogenum (cephalosporin C), and bacteria. The producing bacteria include Gram-negatives and Gram-positives, e.g., Streptomyces clavuligerus (cephamycin C) and Lysobacter lactamgenus (cephabacins), respectively. The evolutionary origin of beta-lactam biosynthesis genes has been the subject of discussion for many years, and two main hypotheses have been proposed: (i) horizontal gene transfer (HGT) from bacteria to fungi or (ii) vertical decent. There are strong arguments in favour of HGT, e.g., unlike most other fungal genes, beta-lactam biosynthesis genes are clustered and some of these genes lack introns. In contrast to S. clavuligerus, all regulators of fungal beta-lactam biosynthesis genes represent wide-domain regulators that are not part of the gene cluster. If bacterial regulators were co-transferred with the gene cluster from bacteria to fungi, most likely they would have been non-functional in eukaryotes and lost during evolution. Recently, the penicillin biosynthesis gene aatB was discovered, which is not part of the penicillin biosynthesis gene cluster and is even located on a different chromosome. The aatB gene is regulated by the same regulators AnCF and AnBH1 as the penicillin biosynthesis gene aatA (penDE). Data suggest that aatA and aatB are paralogues derived by duplication of a common ancestor gene. This data supports a model in which part of the beta-lactam biosynthesis gene cluster was transferred to some fungi, i.e., the acvA and ipnA gene without a regulatory gene. We propose that during the assembly of aatA and acvA-ipnA into a single gene cluster, recruitment of transcriptional regulators occurred along with acquisition of the duplicated aatA ancestor gene and its cis-acting sites.}, }
@article {pmid19863689, year = {2010}, author = {Döpfer, D and Sekse, C and Beutin, L and Solheim, H and van der Wal, FJ and de Boer, A and Slettemeås, JS and Wasteson, Y and Urdahl, AM}, title = {Pathogenic potential and horizontal gene transfer in ovine gastrointestinal Escherichia coli.}, journal = {Journal of applied microbiology}, volume = {108}, number = {5}, pages = {1552-1562}, doi = {10.1111/j.1365-2672.2009.04575.x}, pmid = {19863689}, issn = {1365-2672}, mesh = {Animals ; Coliphages/genetics/pathogenicity ; Escherichia coli/classification/*genetics/*pathogenicity ; *Gene Transfer, Horizontal ; Genotype ; Humans ; Minisatellite Repeats/genetics ; Phylogeny ; Serotyping ; Sheep/*microbiology ; Virulence/genetics ; }, abstract = {AIMS: To demonstrate that a thorough characterization and virulotyping of Escherichia coli strains isolated from sheep over time leads to new insights into ovine E. coli potentially becoming human pathogens through horizontal gene transfer.<br><br>METHODS AND RESULTS: One hundred and fifty E. coli isolates from two sheep, sampled over 3 weeks, were characterized by serotyping, virulotyping, genotyping using multiple locus variable number tandem repeats analysis (MLVA) and susceptibility to phage infection in vitro. The 35 MLVA profiles and the serotype and virulotypes of the strains were closely associated. Many MLVA profiles differed in one locus independent of serotypes. Escherichia coli isolates of the same serotype or virulotype had identical or very similar MLVA profiles. No transductants that incorporated the bacteriophages were found in vivo, but six E. coli isolates were susceptible to the phage infection in vitro. Changes in MLVA profiles were seen after acquisition of Stx phages in vitro only.<br><br>CONCLUSIONS: The sheep carried Stx phage susceptible E. coli that possessed virulence markers associated with human pathogenicity. Changes in bacterial genomes by phage transfer may complicate outbreak source investigations. Serotype has to be taken into account when evaluating strain relationships by MLVA.<br><br>Sheep carry E. coli that encode for virulence markers and belong to serogroups known to be human pathogens. In addition, a selection of isolates was found to be susceptible to horizontal transfer of Shiga toxin genes by means of bacteriophages in vitro, and the transfer resulted in a discernible change of the MLVA patterns of E. coli.}, }
@article {pmid19857251, year = {2009}, author = {Lavigne, R and Darius, P and Summer, EJ and Seto, D and Mahadevan, P and Nilsson, AS and Ackermann, HW and Kropinski, AM}, title = {Classification of Myoviridae bacteriophages using protein sequence similarity.}, journal = {BMC microbiology}, volume = {9}, number = {}, pages = {224}, pmid = {19857251}, issn = {1471-2180}, mesh = {Cluster Analysis ; Computational Biology ; *Genome, Viral ; Myoviridae/*classification/genetics ; Phylogeny ; Proteomics/*methods ; Sequence Analysis, Protein ; Sequence Homology, Amino Acid ; Viral Proteins/genetics ; }, abstract = {BACKGROUND: We advocate unifying classical and genomic classification of bacteriophages by integration of proteomic data and physicochemical parameters. Our previous application of this approach to the entirely sequenced members of the Podoviridae fully supported the current phage classification of the International Committee on Taxonomy of Viruses (ICTV). It appears that horizontal gene transfer generally does not totally obliterate evolutionary relationships between phages.<br><br>RESULTS: CoreGenes/CoreExtractor proteome comparison techniques applied to 102 Myoviridae suggest the establishment of three subfamilies (Peduovirinae, Teequatrovirinae, the Spounavirinae) and eight new independent genera (Bcep781, BcepMu, FelixO1, HAP1, Bzx1, PB1, phiCD119, and phiKZ-like viruses). The Peduovirinae subfamily, derived from the P2-related phages, is composed of two distinct genera: the "P2-like viruses", and the "HP1-like viruses". At present, the more complex Teequatrovirinae subfamily has two genera, the "T4-like" and "KVP40-like viruses". In the genus "T4-like viruses" proper, four groups sharing >70% proteins are distinguished: T4-type, 44RR-type, RB43-type, and RB49-type viruses. The Spounavirinae contain the "SPO1-"and "Twort-like viruses."<br><br>CONCLUSION: The hierarchical clustering of these groupings provide biologically significant subdivisions, which are consistent with our previous analysis of the Podoviridae.}, }
@article {pmid19857143, year = {2010}, author = {Bull, L}, title = {Artificial symbiogenesis and differing reproduction rates.}, journal = {Artificial life}, volume = {16}, number = {1}, pages = {65-72}, doi = {10.1162/artl.2009.16.1.16102}, pmid = {19857143}, issn = {1064-5462}, mesh = {Gene Transfer, Horizontal/*physiology ; *Models, Biological ; Reproduction/physiology ; Symbiosis/*physiology ; }, abstract = {Symbiosis is the phenomenon in which organisms of different species live together in close association. Symbiogenesis is the name given to the process by which symbiotic partners combine and unify. This letter reconsiders previous work using the NKCS model of coevolution to explore symbiogenesis. In particular, the role of different replication rates between the coevolving partners is considered. This is shown to provide a broader scope for the emergence of endosymbioses and subsequent horizontal gene transfers.}, }
@article {pmid19853428, year = {2010}, author = {Ibáñez, F and Reinoso, H and Fabra, A}, title = {Experimental evidences of pSym transfer in a native peanut-associated rhizobia.}, journal = {Microbiological research}, volume = {165}, number = {6}, pages = {505-515}, doi = {10.1016/j.micres.2009.08.004}, pmid = {19853428}, issn = {1618-0623}, mesh = {Arachis/*microbiology/physiology ; Bacterial Proteins/*genetics ; *Gene Transfer, Horizontal ; Phaseolus/*microbiology/physiology ; Plasmids/*genetics ; Rhizobium/*genetics/isolation &amp; purification/physiology ; Root Nodules, Plant/microbiology/physiology ; Symbiosis ; }, abstract = {In previous works we have characterized the native bacterial diversity associated with root nodules of peanut grown in Córdoba province, Argentina. Studies performed in the isolate Rhizobium sp. NET30 revealed a phylogenetic incongruence between housekeeping and nodulation genes. This discrepancy could be explained by the horizontal transfer of nodulation genes from the native peanut isolate Rhizobium sp. NCHA22, a bacterium that showed high identity percentages with Rhizobium tropici IIB strains in the basic and symbiotic genes analyzed. In this work, we demonstrate that, in R. sp. NCHA22, genes required for nodule formation in common bean (Phaseolus vulgaris L.) are plasmid-borne. A symbiotic plasmid capable of conjugal transfer to different genetic backgrounds was identified in this isolate. The mechanism involved in the plasmidic transfer differs from that described for R. tropici CIAT899 (R. tropici IIB type strain). The transfer of a symbiotic plasmid, and the subsequent homologous recombination of nodulation genes in R. sp. NET30 genetic background could account for the phylogenetic incongruence determined in this isolate. Results are also indicating that the transfer of the R. tropici NCHA22 pSym may be a frequent event in native conditions.}, }
@article {pmid19850044, year = {2009}, author = {Taviani, E and Grim, CJ and Chun, J and Huq, A and Colwell, RR}, title = {Genomic analysis of a novel integrative conjugative element in Vibrio cholerae.}, journal = {FEBS letters}, volume = {583}, number = {22}, pages = {3630-3636}, doi = {10.1016/j.febslet.2009.10.041}, pmid = {19850044}, issn = {1873-3468}, mesh = {Chromosomes, Bacterial/*genetics ; Conjugation, Genetic/genetics ; DNA Transposable Elements/*genetics ; Gene Order ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; *Genome, Bacterial ; Genomics/methods ; Species Specificity ; Vibrio cholerae/classification/*genetics ; }, abstract = {Integrative conjugative elements (ICEs) are a class of self-transmissible mobile elements that mediate horizontal gene transfer in bacteria, and play an important role in bacterial evolution. Since 1992, ICEs of the SXT/R391 family have been found to be widely distributed among Vibrio cholerae strains isolated in Asian countries. Here we describe ICEVchB33, an ICE found in the genomes of two V. cholerae O1 Eltor strains, one isolated in India, 1994, and the other from Mozambique, 2004. ICEVchB33 revealed a new genetic organization, different from other ICEs of the SXT/R391 family, demonstrating the genomic plasticity of these elements.}, }
@article {pmid19845701, year = {2009}, author = {Salah, IB and Ghigo, E and Drancourt, M}, title = {Free-living amoebae, a training field for macrophage resistance of mycobacteria.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {15}, number = {10}, pages = {894-905}, doi = {10.1111/j.1469-0691.2009.03011.x}, pmid = {19845701}, issn = {1469-0691}, mesh = {Amoeba/*microbiology ; Animals ; DNA, Bacterial/genetics ; Environmental Microbiology ; Evolution, Molecular ; Humans ; Macrophages/*microbiology ; Models, Biological ; Mycobacterium/*pathogenicity ; Mycobacterium Infections/epidemiology ; Phylogeny ; }, abstract = {Mycobacterium species evolved from an environmental recent common ancestor by reductive evolution and lateral gene transfer. Strategies selected through evolution and developed by mycobacteria resulted in resistance to predation by environmental unicellular protists, including free-living amoebae. Indeed, mycobacteria are isolated from the same soil and water environments as are amoebae, and experimental models using Acanthamoeba spp. and Dictyostelium discoideum were exploited to analyse the mechanisms for intracellular survival. Most of these mechanisms have been further reproduced in macrophages for mycobacteria regarded as opportunistic and obligate pathogens. Amoebal cysts may protect intracellular mycobacteria against adverse conditions and may act as a vector for mycobacteria. The latter hypothesis warrants further environmental and clinical studies to better assess the role of free-living amoebae in the epidemiology of infections caused by mycobacteria.}, }
@article {pmid19845634, year = {2009}, author = {Olendzenski, L and Gogarten, JP}, title = {Evolution of genes and organisms: the tree/web of life in light of horizontal gene transfer.}, journal = {Annals of the New York Academy of Sciences}, volume = {1178}, number = {}, pages = {137-145}, doi = {10.1111/j.1749-6632.2009.04998.x}, pmid = {19845634}, issn = {1749-6632}, mesh = {Animals ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome ; Humans ; Phylogeny ; }, abstract = {Gene exchange necessitates expanding the model of the tree of life, impacts the notion of organismal and molecular most recent common ancestors, and provides examples of natural selection working at multiple levels. Gene exchange, whether by horizontal gene transfer (HGT), hybridization of species, or symbiosis, modifies the organismal tree of life into a web. Darwin suggested the tree of life was like a coral, where living surface branches were supported by masses of dead branches. In phylogenetic trees, organismal or molecular lineages coalesce back to a lucky universal ancestor whose descendents are found in current lineages and which coexisted with other, now-extinct lineages. HGT complicates the reconstruction of a universal ancestor; genes in a genome can have different evolutionary histories, and even infrequent gene transfer will cause different molecular lineages to coalesce to molecular ancestors that existed in different organismal lineages and at different times. HGT, as well as symbiosis, provides a mechanism for integrating and expanding the organizational level on which natural selection acts, contributing to selection at the group and community level.}, }
@article {pmid19843217, year = {2009}, author = {Hirtreiter, AM and Calloni, G and Forner, F and Scheibe, B and Puype, M and Vandekerckhove, J and Mann, M and Hartl, FU and Hayer-Hartl, M}, title = {Differential substrate specificity of group I and group II chaperonins in the archaeon Methanosarcina mazei.}, journal = {Molecular microbiology}, volume = {74}, number = {5}, pages = {1152-1168}, doi = {10.1111/j.1365-2958.2009.06924.x}, pmid = {19843217}, issn = {1365-2958}, mesh = {Adenosine Triphosphate/metabolism ; Archaeal Proteins/analysis/chemistry/genetics/*metabolism ; Chaperonin 60/genetics/metabolism ; Eukaryotic Cells/metabolism ; Group I Chaperonins/chemistry/genetics/*metabolism ; Group II Chaperonins/chemistry/genetics/*metabolism ; Methanosarcina/genetics/*metabolism ; Models, Molecular ; Phylogeny ; Protein Binding/genetics ; Protein Folding ; Proteome/analysis ; Substrate Specificity ; Thermosomes/chemistry/genetics/metabolism ; }, abstract = {Chaperonins are macromolecular machines that assist in protein folding. The archaeon Methanosarcina mazei has acquired numerous bacterial genes by horizontal gene transfer. As a result, both the bacterial group I chaperonin, GroEL, and the archaeal group II chaperonin, thermosome, coexist. A proteome-wide analysis of chaperonin interactors was performed to determine the differential substrate specificity of GroEL and thermosome. At least 13% of soluble M. mazei proteins interact with chaperonins, with the two systems having partially overlapping substrate sets. Remarkably, chaperonin selectivity is independent of phylogenetic origin and is determined by distinct structural and biochemical features of proteins. GroEL prefers well-conserved proteins with complex alpha/beta domains. In contrast, thermosome substrates comprise a group of faster-evolving proteins and contain a much wider range of different domain folds, including small all-alpha and all-beta modules, and a greater number of large multidomain proteins. Thus, the group II chaperonins may have facilitated the evolution of the highly complex proteomes characteristic of eukaryotic cells.}, }
@article {pmid19837694, year = {2009}, author = {Yahara, K and Fukuyo, M and Sasaki, A and Kobayashi, I}, title = {Evolutionary maintenance of selfish homing endonuclease genes in the absence of horizontal transfer.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {44}, pages = {18861-18866}, pmid = {19837694}, issn = {1091-6490}, mesh = {Alleles ; Computer Simulation ; Endonucleases/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Models, Genetic ; Repetitive Sequences, Nucleic Acid/*genetics ; Saccharomyces cerevisiae/*genetics ; Stochastic Processes ; Time Factors ; }, abstract = {Homing endonuclease genes are "selfish" mobile genetic elements whose endonuclease promotes the spread of its own gene by creating a break at a specific target site and using the host machinery to repair the break by copying and inserting the gene at this site. Horizontal transfer across the boundary of a species or population within which mating takes place has been thought to be necessary for their evolutionary persistence. This is based on the assumption that they will become fixed in a host population, where opportunities of homing will disappear, and become susceptible to degeneration. To test this hypothesis, we modeled behavior of a homing endonuclease gene that moves during meiosis through double-strand break repair. We mathematically explored conditions for persistence of the homing endonuclease gene and elucidated their parameter dependence as phase diagrams. We found that, if the cost of the pseudogene is lower than that of the homing endonuclease gene, the 2 forms can persist in a population through autonomous periodic oscillation. If the cost of the pseudogene is higher, 2 types of dynamics appear that enable evolutionary persistence: bistability dependent on initial frequency or fixation irrespective of initial frequency. The prediction of long persistence in the absence of horizontal transfer was confirmed by stochastic simulations in finite populations. The average time to extinction of the endonuclease gene was found to be thousands of meiotic generations or more based on realistic parameter values. These results provide a solid theoretical basis for an understanding of these and other extremely selfish elements.}, }
@article {pmid19835890, year = {2010}, author = {Zhong, X and Krol, JE and Top, EM and Krone, SM}, title = {Accounting for mating pair formation in plasmid population dynamics.}, journal = {Journal of theoretical biology}, volume = {262}, number = {4}, pages = {711-719}, pmid = {19835890}, issn = {1095-8541}, support = {P20 RR016448/RR/NCRR NIH HHS/United States ; R01 GM073821-04/GM/NIGMS NIH HHS/United States ; R01 GM73821/GM/NIGMS NIH HHS/United States ; R01 GM073821/GM/NIGMS NIH HHS/United States ; P20 RR16448/RR/NCRR NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/*genetics/metabolism ; Biofilms ; Conjugation, Genetic ; DNA/metabolism ; Fimbriae, Bacterial ; Gene Transfer, Horizontal ; Gram-Negative Bacteria/metabolism ; Kinetics ; Models, Biological ; Models, Theoretical ; Plasmids/*metabolism ; }, abstract = {Plasmids are important vehicles for horizontal gene transfer and rapid adaptation in bacteria, including the spread of antibiotic resistance genes. Conjugative transfer of a plasmid from a plasmid-bearing to a plasmid-free bacterial cell requires contact and attachment of the cells followed by plasmid DNA transfer prior to detachment. We introduce a system of differential equations for plasmid transfer in well-mixed populations that accounts for attachment, DNA transfer, and detachment dynamics. These equations offer advantages over classical mass-action models that combine these three processes into a single "bulk" conjugation rate. By decomposing the process of plasmid transfer into its constituent parts, this new model provides a framework that facilitates meaningful comparisons of plasmid transfer rates in surface and liquid environments. The model also allows one to account for experimental and environmental effects such as mixing intensity. To test the adequacy of the model and further explore the effects of mixing on plasmid transfer, we performed batch culture experiments using three different plasmids and a range of different mixing intensities. The results show that plasmid transfer is optimized at low to moderate shaking speeds and that vigorous shaking negatively affects plasmid transfer. Using reasonable assumptions on attachment and detachment rates, the mathematical model predicts the same behavior.}, }
@article {pmid19835158, year = {2009}, author = {Deng, Y and Zeng, Z and Liu, J and Chen, Z}, title = {[Insertion sequence common region element: a novel gene-capturing system in bacteria--a review].}, journal = {Wei sheng wu xue bao = Acta microbiologica Sinica}, volume = {49}, number = {8}, pages = {987-993}, pmid = {19835158}, issn = {0001-6209}, mesh = {Bacteria/*genetics/metabolism ; *DNA Transposable Elements ; Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Molecular Sequence Data ; }, abstract = {Insertion sequence common region (ISCR) elements are insertion sequences that have similarities to the IS91 family in both structure and function. ISCR elements differ from the insertion sequences by that they lack terminal inverted repeats (IRs), do not generate directly repeated sequence on insertion and are thought to be transposed by a mechanism termed rolling-circle (RC) transposition. ISCR elements, as a novel gene-capturing system, can mobilize any piece of adjacent DNA sequences. This powerful gene mobilization mechanism provides antibiotic resistance genes with a highly mobile genetic vehicle to transfer between different species of bacteria. Nineteen members of the ISCR family have been discovered until now in many Gram-negative pathogens. The majority of these elements are found to be closely associated with antimicrobial resistance genes that are not necessary components of the host genome, suggesting that ISCR elements may be responsible for the rapid transmission of bacterial multi-drug resistance. This review described some important aspects of ISCR elements, including their structure characteristics, classification, mobilization mechanism, origins and evolutions.}, }
@article {pmid19834620, year = {2009}, author = {Lepka, D and Kerrinnes, T and Skiebe, E and Hahn, B and Fruth, A and Wilharm, G}, title = {Adding to Yersinia enterocolitica gene pool diversity: two cryptic plasmids from a biotype 1A isolate.}, journal = {Journal of biomedicine &amp; biotechnology}, volume = {2009}, number = {}, pages = {398434}, pmid = {19834620}, issn = {1110-7251}, mesh = {Amino Acid Sequence ; Animals ; Base Pairing ; Base Sequence ; Cell Adhesion ; Cell Line ; DNA Transposable Elements/genetics ; DNA, Bacterial/chemistry/genetics ; Epitopes ; Escherichia coli/genetics ; *Gene Pool ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genetic Variation ; HeLa Cells ; Humans ; Open Reading Frames ; Plasmids/chemistry/*genetics/isolation &amp; purification ; Rats ; Sequence Homology, Amino Acid ; Swine ; Temperature ; Transformation, Bacterial ; Yersinia enterocolitica/*genetics/*isolation &amp; purification/pathogenicity ; }, abstract = {We report the nucleotide sequence of two novel cryptic plasmids (4357 and 14 662 base pairs) carried by a Yersinia enterocolitica biotype 1A strain isolated from pork. As distinguished from most biotype 1A strains, this isolate, designated 07-04449, exhibited adherence to eukaryotic cells. The smaller plasmid pYe4449-1 carries five attributable open reading frames (ORFs) encoding the first CcdA/CcdB-like antitoxin/toxin system described for a Yersinia plasmid, a RepA-like replication initiation protein, and mobilizing factors MobA and MobC. The deduced amino acid sequences showed highest similarity to proteins described in Salmonella (CcdA/B), Klebsiella (RepA), and Plesiomonas (MobA/C) indicating genomic fluidity among members of the Enterobacteriaceae. One additional ORF with unknown function, termed ORF5, was identified with an ancestry distinct from the rest of the plasmid. While the C+G content of ORF5 is 38.3%, the rest of pYe4449-1 shows a C+G content of 55.7%. The C+G content of the larger plasmid pYe4449-2 (54.9%) was similar to that of pYe4449-1 (53.7%) and differed from that of the Y. enterocolitica genome (47.3%). Of the 14 ORFs identified on pYe4449-2, only six ORFs showed significant similarity to database entries. For three of these ORFs likely functions could be ascribed: a TnpR-like resolvase and a phage replication protein, localized each on a low C+G island, and DNA primase TraC. Two ORFs of pYe4449-2, ORF3 and ORF7, seem to encode secretable proteins. Epitope-tagging of ORF3 revealed protein expression at 4 degrees C but not at or above 27 degrees C suggesting adaptation to a habitat outside swine. The hypothetical protein encoded by ORF7 is the member of a novel repeat protein family sharing the DxxGN(x)(n)DxxGN motif. Our findings illustrate the exceptional gene pool diversity within the species Y. enterocolitica driven by horizontal gene transfer events.}, }
@article {pmid19833774, year = {2010}, author = {Campos, J and Martínez, E and Izquierdo, Y and Fando, R}, title = {VEJ{phi}, a novel filamentous phage of Vibrio cholerae able to transduce the cholera toxin genes.}, journal = {Microbiology (Reading, England)}, volume = {156}, number = {Pt 1}, pages = {108-115}, doi = {10.1099/mic.0.032235-0}, pmid = {19833774}, issn = {1465-2080}, mesh = {Cholera Toxin/*genetics ; Fimbriae Proteins/metabolism ; Gene Transfer, Horizontal ; *Genome, Viral ; Inovirus/*genetics/isolation &amp; purification/metabolism ; Molecular Sequence Data ; Receptors, Virus/metabolism ; Sequence Analysis, DNA ; Transduction, Genetic ; Vibrio cholerae/genetics/*virology ; }, abstract = {A novel filamentous bacteriophage, designated VEJphi, was isolated from strain MO45 of Vibrio cholerae of the O139 serogroup. A molecular characterization of the phage was carried out, which included sequencing of its whole genome, study of the genomic structure, identification of the phage receptor, and determination of the function of some of the genes, such as those encoding the major capsid protein and the single-stranded DNA-binding protein. The genome nucleotide sequence of VEJphi, which consists of 6842 bp, revealed that it is organized in modules of functionally related genes in an array that is characteristic of the genus Inovirus (filamentous phages). VEJphi is closely related to other previously described filamentous phages of V. cholerae, including VGJphi, VSK and fs1. Like these phages, VEJphi uses as a cellular receptor the type IV fimbria called the mannose-sensitive haemagglutinin (MSHA). It was also demonstrated that VEJphi, like phage VGJphi, is able to transmit the genome of phage CTXphi, and therefore the genes encoding the cholera toxin (CT), horizontally among populations of V. cholerae expressing the MSHA receptor fimbria. This suggests that the variety of phages implicated in the horizontal transmission of the CT genes could be more diverse than formerly thought.}, }
@article {pmid19833230, year = {2010}, author = {Hughes, AL and Irausquin, S and Friedman, R}, title = {The evolutionary biology of poxviruses.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {10}, number = {1}, pages = {50-59}, pmid = {19833230}, issn = {1567-7257}, support = {R01 GM043940/GM/NIGMS NIH HHS/United States ; R01 GM043940-20/GM/NIGMS NIH HHS/United States ; GM43940/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Humans ; Poxviridae/*genetics ; Variola virus/genetics ; }, abstract = {The poxviruses (family Poxviridae) are a family of double-stranded viruses including several species that infect humans and their domestic animals, most notably Variola virus (VARV), the causative agent of smallpox. The evolutionary biology of these viruses poses numerous questions, for which we have only partial answers at present. Here we review evidence regarding the origin of poxviruses, the frequency of host transfer in poxvirus history, horizontal transfer of host genes to poxviruses, and the population processes accounting for patterns of nucleotide sequence polymorphism.}, }
@article {pmid19830455, year = {2009}, author = {Zhao, GH and Li, J and Zou, FC and Liu, W and Mo, XH and Lin, RQ and Yuan, ZG and Weng, YB and Song, HQ and Zhu, XQ}, title = {Heterogeneity of class I and class II MHC sequences in Schistosoma japonicum from different endemic regions in mainland China.}, journal = {Parasitology research}, volume = {106}, number = {1}, pages = {201-206}, pmid = {19830455}, issn = {1432-1955}, mesh = {Animals ; Cluster Analysis ; DNA, Helminth/chemistry/genetics ; Female ; *Genes, Helminth ; *Genes, MHC Class I ; *Genes, MHC Class II ; Geography ; Male ; Molecular Sequence Data ; Phylogeny ; *Polymorphism, Genetic ; Rabbits ; Schistosoma japonicum/*drug effects ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {The present study examined sequence variation in class I and class II major histocompatibility complex (MHC) genes among Schistosoma japonicum isolates from different endemic regions in mainland China and assessed the level of horizontal gene transfer and sequence similarity between parasites and their hosts. S. japonicum cercariae were used to infect male adult rabbits to obtain adult S. japonicum samples. A portion of the class I MHC gene (pMHC I) and class II MHC genes (pMHC II) were amplified separately from individual adult trematodes by polymerase chain reaction and sequenced. Among all the examined isolates of S. japonicum, sequence differences between male and female parasites were 0.0-26.6% for pMHC I and 0.0-7.0% for pMHC II. Sequence variations between male and female parasites among different geographical locations from the mountainous areas were 1.1-26.6% for pMHC I and 1.5-3.0% for pMHC II. Sequence variations between samples from Yunnan and those from Sichuan were 2.7-23.5% for pMHC I and 1.1-3.7% for pMHC II. In the lake/marshland areas, sequence variations between male and female parasites among different geographical locations were 0.0-25.0% for pMHC I and 0.0-7.0% for pMHC II. Sequence variations between S. japonicum isolates from mountainous areas, and those from lake/marshland areas were 0.0-26.1% for pMHC I and 0.4-6.1% for pMHC II. BLASTN analysis indicated that all the pMHC II sequences showed high homology to a portion of exon 3 in rabbit MHC class II DP beta gene with more than 89% similarity, and all the pMHC I sequences except isolates in Yunnan (Eryuan) revealed high homology to the portion of exon 2 in rabbit MHC I gene with more than 81% similarity. Phylogenetic analysis showed no specific clustering comprising parasites from single geographical or endemic regions, and the paired parasites were even found in different clusters. These results demonstrated that pMHC I and II of S. japonicum isolates in mainland China existed heterogeneity, but the pMHC I, II, or combined sequences were not suitable markers for examining genetic relationship among different isolates from endemic regions in mainland China.}, }
@article {pmid19825158, year = {2009}, author = {Gazave, E and Lapébie, P and Richards, GS and Brunet, F and Ereskovsky, AV and Degnan, BM and Borchiellini, C and Vervoort, M and Renard, E}, title = {Origin and evolution of the Notch signalling pathway: an overview from eukaryotic genomes.}, journal = {BMC evolutionary biology}, volume = {9}, number = {}, pages = {249}, pmid = {19825158}, issn = {1471-2148}, mesh = {Animals ; Calcium-Binding Proteins/genetics ; Eukaryotic Cells ; *Evolution, Molecular ; Intercellular Signaling Peptides and Proteins/genetics ; Intracellular Signaling Peptides and Proteins ; Membrane Proteins/genetics ; *Phylogeny ; Protein Interaction Domains and Motifs ; Receptors, Notch/*genetics ; Sequence Analysis, DNA ; Serrate-Jagged Proteins ; Signal Transduction/genetics ; }, abstract = {BACKGROUND: Of the 20 or so signal transduction pathways that orchestrate cell-cell interactions in metazoans, seven are involved during development. One of these is the Notch signalling pathway which regulates cellular identity, proliferation, differentiation and apoptosis via the developmental processes of lateral inhibition and boundary induction. In light of this essential role played in metazoan development, we surveyed a wide range of eukaryotic genomes to determine the origin and evolution of the components and auxiliary factors that compose and modulate this pathway.<br><br>RESULTS: We searched for 22 components of the Notch pathway in 35 different species that represent 8 major clades of eukaryotes, performed phylogenetic analyses and compared the domain compositions of the two fundamental molecules: the receptor Notch and its ligands Delta/Jagged. We confirm that a Notch pathway, with true receptors and ligands is specific to the Metazoa. This study also sheds light on the deep ancestry of a number of genes involved in this pathway, while other members are revealed to have a more recent origin. The origin of several components can be accounted for by the shuffling of pre-existing protein domains, or via lateral gene transfer. In addition, certain domains have appeared de novo more recently, and can be considered metazoan synapomorphies.<br><br>CONCLUSION: The Notch signalling pathway emerged in Metazoa via a diversity of molecular mechanisms, incorporating both novel and ancient protein domains during eukaryote evolution. Thus, a functional Notch signalling pathway was probably present in Urmetazoa.}, }
@article {pmid19821008, year = {2010}, author = {Fu, S and Tang, Z and Ren, Z}, title = {Inter- and intra-genomic transfer of small chromosomal segments in wheat-rye allopolyploids.}, journal = {Journal of plant research}, volume = {123}, number = {1}, pages = {97-103}, pmid = {19821008}, issn = {1618-0860}, mesh = {Centromere/genetics ; Chromosomes, Plant/*genetics ; Gene Transfer, Horizontal/*genetics ; Genetic Variation/genetics ; In Situ Hybridization, Fluorescence ; *Polyploidy ; Secale/*genetics ; Telomere/genetics ; Triticum/*genetics ; }, abstract = {Newly synthesized wheat-rye allopolyploids, derived from Triticum aestivum Mianyang11 x S. cereale Kustro, were investigated by sequential fluorescent in situ hybridization (FISH) and genomic in situ hybridization (GISH) using rye tandem repeat pSc200 and rye genomic DNA as probes, respectively, over the first, second and third allopolyploid generations. FISH signals of pSc200 could be observed at both telomeres/subtelomeres of all 14 chromosomes of the parental rye. In the first allopolyploid generation, there were ten rye chromosomes bearing FISH signals at both telomeres/subtelomeres and four rye chromosomes bearing FISH signals at only one telomere/subtelomere. However, in the second and the third allopolyploid generations, there were 12 rye chromosomes bearing FISH signals at both telomeres/subtelomeres and 2 rye chromosomes bearing FISH signals at only one telomere/subtelomere. Rye telomeric segments were transferred to the centromeric region of wheat chromosomes in some cells and small segments derived from non-telomeric regions of rye chromosome were transferred to the telomeric region of wheat chromosomes in some other cells. These observations indicated that the rye telomeric/subtelomeric region was unstable in newly synthesized wheat-rye allopolyploids and allopolyploidization was accompanied by rapid inter/intra-genomic exchange. The inter-genomic exchange may have occurred in somatic cells.}, }
@article {pmid19820094, year = {2009}, author = {Klassen, JL}, title = {Pathway evolution by horizontal transfer and positive selection is accommodated by relaxed negative selection upon upstream pathway genes in purple bacterial carotenoid biosynthesis.}, journal = {Journal of bacteriology}, volume = {191}, number = {24}, pages = {7500-7508}, pmid = {19820094}, issn = {1098-5530}, mesh = {Bacteria/*genetics/*metabolism ; Biosynthetic Pathways/*genetics ; Carotenoids/*biosynthesis ; Computational Biology/methods ; DNA, Bacterial/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Mutation, Missense ; Phylogeny ; Point Mutation ; *Selection, Genetic ; Sequence Analysis, DNA ; }, abstract = {Horizontal gene transfer and selection are major forces driving microbial evolution. However, interactions between them are rarely studied. Phylogenetic analyses of purple bacterial carotenoid biosynthesis genes suggest two lineages: one producing spheroidenone and the other producing spirilloxanthin. Of the latter lineage, Rubrivivax gelatinosus S1 and Hoeflea phototrophica DFL-43 also or instead produce spheroidenone. Evolution of the spheroidenone pathway from that producing spirilloxanthin theoretically requires changes in the substrate specificity of upstream pathway enzymes and acquisition of a terminal ketolase (CrtA). In R. gelatinosus and likely also in H. phototrophica, CrtA was acquired from the Bacteroidetes, in which it functions as a hydroxylase. Estimation of nonsynonymous and synonymous mutations using several pairwise methods indicated positive selection upon both genes, consistent with their functional changes from hydroxylases to ketolases. Relaxed negative selection upon all other carotenoid biosynthetic genes in these organisms was also apparent, likely facilitating changes in their substrate specificities. Furthermore, all genes responsible for terminal carotenoid biosynthetic pathway steps were under reduced negative selection compared to those known to govern biosynthetic pathway specificity. Horizontal transfer of crtA into R. gelatinosus and H. phototrophica has therefore likely been promoted by (i) the apparent selective advantage of spheroidenone production relative to spirilloxanthin production, (ii) reduced negative selection upon other carotenoid biosynthetic genes, facilitating changes in their substrate specificities, and (iii) preexisting low enzyme substrate specificities due to relaxed negative selection. These results highlight the importance and complexity of selection acting upon both a horizontally transferred gene and the biochemical network into which it is integrating.}, }
@article {pmid19819658, year = {2009}, author = {Schleifer, KH}, title = {Classification of Bacteria and Archaea: past, present and future.}, journal = {Systematic and applied microbiology}, volume = {32}, number = {8}, pages = {533-542}, doi = {10.1016/j.syapm.2009.09.002}, pmid = {19819658}, issn = {1618-0984}, mesh = {Archaea/chemistry/*classification/genetics ; Bacteria/chemistry/*classification/genetics ; Classification/*methods ; Genome, Archaeal ; Genome, Bacterial ; }, abstract = {The late 19th century was the beginning of bacterial taxonomy and bacteria were classified on the basis of phenotypic markers. The distinction of prokaryotes and eukaryotes was introduced in the 1960s. Numerical taxonomy improved phenotypic identification but provided little information on the phylogenetic relationships of prokaryotes. Later on, chemotaxonomic and genotypic methods were widely used for a more satisfactory classification. Archaea were first classified as a separate group of prokaryotes in 1977. The current classification of Bacteria and Archaea is based on an operational-based model, the so-called polyphasic approach, comprised of phenotypic, chemotaxonomic and genotypic data, as well as phylogenetic information. The provisional status Candidatus has been established for describing uncultured prokaryotic cells for which their phylogenetic relationship has been determined and their authenticity revealed by in situ probing. The ultimate goal is to achieve a theory-based classification system based on a phylogenetic/evolutionary concept. However, there are currently two contradictory opinions about the future classification of Bacteria and Archaea. A group of mostly molecular biologists posits that the yet-unclear effect of gene flow, in particular lateral gene transfer, makes the line of descent difficult, if not impossible, to describe. However, even in the face of genomic fluidity it seems that the typical geno- and phenotypic characteristics of a taxon are still maintained, and are sufficient for reliable classification and identification of Bacteria and Archaea. There are many well-defined genotypic clusters that are congruent with known species delineated by polyphasic approaches. Comparative sequence analysis of certain core genes, including rRNA genes, may be useful for the characterization of higher taxa, whereas various character genes may be suitable as phylogenetic markers for the delineation of lower taxa. Nevertheless, there may still be a few organisms which escape a reliable classification.}, }
@article {pmid19816563, year = {2009}, author = {Pereyre, S and Sirand-Pugnet, P and Beven, L and Charron, A and Renaudin, H and Barré, A and Avenaud, P and Jacob, D and Couloux, A and Barbe, V and de Daruvar, A and Blanchard, A and Bébéar, C}, title = {Life on arginine for Mycoplasma hominis: clues from its minimal genome and comparison with other human urogenital mycoplasmas.}, journal = {PLoS genetics}, volume = {5}, number = {10}, pages = {e1000677}, pmid = {19816563}, issn = {1553-7404}, mesh = {Arginine/analogs &amp; derivatives/*metabolism ; Carbohydrate Metabolism/genetics ; Cell Adhesion/genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genome, Bacterial ; Humans ; Metabolic Networks and Pathways/genetics ; Models, Biological ; Molecular Sequence Data ; Mycoplasma genitalium/genetics/metabolism ; Mycoplasma hominis/*genetics/growth &amp; development/metabolism ; Ureaplasma/genetics/metabolism ; Virulence/genetics ; }, abstract = {Mycoplasma hominis is an opportunistic human mycoplasma. Two other pathogenic human species, M. genitalium and Ureaplasma parvum, reside within the same natural niche as M. hominis: the urogenital tract. These three species have overlapping, but distinct, pathogenic roles. They have minimal genomes and, thus, reduced metabolic capabilities characterized by distinct energy-generating pathways. Analysis of the M. hominis PG21 genome sequence revealed that it is the second smallest genome among self-replicating free living organisms (665,445 bp, 537 coding sequences (CDSs)). Five clusters of genes were predicted to have undergone horizontal gene transfer (HGT) between M. hominis and the phylogenetically distant U. parvum species. We reconstructed M. hominis metabolic pathways from the predicted genes, with particular emphasis on energy-generating pathways. The Embden-Meyerhoff-Parnas pathway was incomplete, with a single enzyme absent. We identified the three proteins constituting the arginine dihydrolase pathway. This pathway was found essential to promote growth in vivo. The predicted presence of dimethylarginine dimethylaminohydrolase suggested that arginine catabolism is more complex than initially described. This enzyme may have been acquired by HGT from non-mollicute bacteria. Comparison of the three minimal mollicute genomes showed that 247 CDSs were common to all three genomes, whereas 220 CDSs were specific to M. hominis, 172 CDSs were specific to M. genitalium, and 280 CDSs were specific to U. parvum. Within these species-specific genes, two major sets of genes could be identified: one including genes involved in various energy-generating pathways, depending on the energy source used (glucose, urea, or arginine) and another involved in cytadherence and virulence. Therefore, a minimal mycoplasma cell, not including cytadherence and virulence-related genes, could be envisaged containing a core genome (247 genes), plus a set of genes required for providing energy. For M. hominis, this set would include 247+9 genes, resulting in a theoretical minimal genome of 256 genes.}, }
@article {pmid19812028, year = {2010}, author = {Avonce, N and Wuyts, J and Verschooten, K and Vandesteene, L and Van Dijck, P}, title = {The Cytophaga hutchinsonii ChTPSP: First characterized bifunctional TPS-TPP protein as putative ancestor of all eukaryotic trehalose biosynthesis proteins.}, journal = {Molecular biology and evolution}, volume = {27}, number = {2}, pages = {359-369}, doi = {10.1093/molbev/msp241}, pmid = {19812028}, issn = {1537-1719}, mesh = {Arabidopsis Proteins/classification/genetics ; Bacterial Proteins/classification/*genetics ; Cytophaga/*enzymology/genetics ; Gene Transfer, Horizontal ; Glucosyltransferases/classification/genetics ; Models, Biological ; Phosphoric Monoester Hydrolases/classification/*genetics ; Phylogeny ; Trehalose/*biosynthesis/genetics ; }, abstract = {The most widely distributed pathway to synthesize trehalose in nature consists of two consecutive enzymatic reactions with a trehalose-6-P (T6P)-synthase (TPS) enzyme, producing the intermediate T6P, and a T6P-phosphatase (TPP) enzyme, which dephosphorylates T6P to produce trehalose and inorganic phosphate. In plants, these enzymes are called Class I and Class II proteins, respectively, with some Class I proteins being active enzymes. The Class II proteins possess both TPS and TPP consensus regions but appear to have lost enzymatic activity during evolution. Plants also contain an extra group of enzymes of small protein size, of which some members have been characterized as functional TPPs. These Class III proteins have less sequence similarity with the Class I and Class II proteins. Here, we characterize for the first time, by using biochemical analysis and yeast growth complementation assays, the existence of a natural TPS-TPP bifunctional enzyme found in the bacterial species Cytophaga hutchinsonii. Through phylogenetic analysis, we show that prokaryotic genes such as ChTPSP might be the ancestor of the eukaryotic trehalose biosynthesis genes. Second, we show that plants have recruited during evolution, possibly by horizontal transfer from bacteria such as Rhodoferax ferrireducens, a new type of small protein, encoding TPP activity, which have been named Class III proteins. RfTPP has very high TPP activity upon expression in yeast. Finally, we demonstrate that TPS gene duplication, the recruitment of the Class III enzymes, and recruitment of an N-terminal regulatory element, which regulates the Class I enzyme activity in higher plants, were initiated very early in eukaryan evolution as the three classes of trehalose biosynthesis genes are already present in the alga Ostreococcus tauri.}, }
@article {pmid19811538, year = {2010}, author = {Kielak, A and Rodrigues, JL and Kuramae, EE and Chain, PS and van Veen, JA and Kowalchuk, GA}, title = {Phylogenetic and metagenomic analysis of Verrucomicrobia in former agricultural grassland soil.}, journal = {FEMS microbiology ecology}, volume = {71}, number = {1}, pages = {23-33}, doi = {10.1111/j.1574-6941.2009.00785.x}, pmid = {19811538}, issn = {1574-6941}, mesh = {*Agriculture ; Bacteria/classification/*genetics ; Base Sequence ; Cloning, Molecular ; DNA, Bacterial/chemistry/isolation &amp; purification ; *Genome, Bacterial ; *Metagenomics ; Molecular Sequence Data ; *Phylogeny ; Poaceae ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {The bacterial phylum Verrucomicrobia has a widespread distribution, and is known to be one of the most common and diverse phyla in soil habitats. However, members of this phylum have typically been recalcitrant to cultivation methods, hampering the study of this presumably important bacterial group. In this study, we examine the phylogenetic diversity of the Verrucomicrobia in a former agricultural field and gain access to genomic information via a metagenomic approach. We examined Verrucomicrobia-like 16S rRNA gene sequences recovered from general bacterial and phylum-specific libraries, revealing a dominance of subdivisions 1 and 2. A PCR-based screening method was developed to identify inserts containing verrucomicrobial 16S rRNA genes within a large-insert metagenomic library, and on screening of 28,800 clones, four fosmids were identified as containing verrucomicrobial genomic DNA. Full-length sequencing of fosmid inserts and gene annotation identified a total of 98 ORFs, representing a range of functions. No conservation of gene order was observed adjacent to the ribosomal operons. Fosmid inserts were further analyzed for tetranucleotide frequencies to identify remnants of past horizontal gene transfer events. The metagenomic approach utilized proved to be suitable for the recovery of verrucomicrobial genomic DNA, thereby providing a window into the genomes of members of this important, yet poorly characterized, bacterial phylum.}, }
@article {pmid19808865, year = {2010}, author = {Cohen, O and Pupko, T}, title = {Inference and characterization of horizontally transferred gene families using stochastic mapping.}, journal = {Molecular biology and evolution}, volume = {27}, number = {3}, pages = {703-713}, pmid = {19808865}, issn = {1537-1719}, mesh = {Algorithms ; Computer Simulation ; Databases, Genetic ; Eukaryota/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Archaeal ; Genome, Bacterial ; Markov Chains ; *Models, Genetic ; *Models, Statistical ; Phylogeny ; ROC Curve ; Stochastic Processes ; }, abstract = {Macrogenomic events, in which genes are gained and lost, play a pivotal evolutionary role in microbial evolution. Nevertheless, probabilistic-evolutionary models describing such events and methods for their robust inference are considerably less developed than existing methodologies for analyzing site-specific sequence evolution. Here, we present a novel method for the inference of gains and losses of gene families. First, we develop probabilistic-evolutionary models describing the dynamics of gene-family content, which are more biologically realistic than previously suggested models. In our likelihood-based models, gains and losses are represented by transitions between presence and absence, given an underlying phylogeny. We employ a mixture-model approach in which we allow both the gain rate and the loss rate to vary among gene families. Second, we use these models together with the analytic implementation of stochastic mapping to infer branch-specific events. Our novel methodology allows us to infer and quantify horizontal gene transfer (HGT) events. This enables us to rank various gene families and lineages according to their propensity to undergo gains and losses. Applying our methodology to 4,873 gene families shows that: 1) the novel mixture models describe the observed variability in gene-family content among microbes significantly better than previous models; 2) The stochastic mapping approach enables accurate inference of gain and loss events based on simulations; 3) At least 34% of the gene families analyzed are inferred to have experienced HGT at least once during their evolution; and 4) Gene families that were inferred to experience HGT are both enriched and depleted with respect to specific functional categories.}, }
@article {pmid19808864, year = {2010}, author = {Logares, R and Bråte, J and Heinrich, F and Shalchian-Tabrizi, K and Bertilsson, S}, title = {Infrequent transitions between saline and fresh waters in one of the most abundant microbial lineages (SAR11).}, journal = {Molecular biology and evolution}, volume = {27}, number = {2}, pages = {347-357}, doi = {10.1093/molbev/msp239}, pmid = {19808864}, issn = {1537-1719}, mesh = {Bacteria/classification/*genetics/growth &amp; development ; Evolution, Molecular ; Fresh Water/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; }, abstract = {The aquatic bacterial group SAR11 is one of the most abundant organisms on Earth, with an estimated global population size of 2.4 x 10(28) cells in the oceans. Members of SAR11 have also been detected in brackish and fresh waters, but the evolutionary relationships between the species present in the different environments have been ambiguous. In particular, it was not clear how frequently this lineage has crossed the saline-freshwater boundary during its evolutionary diversification. Due to the huge population size of SAR11 and the potential of microbes for long-distance dispersal, we hypothesized that environmental transitions could have occurred repeatedly during the evolutionary diversification of this group. Here, we have constructed extensive 16S rDNA-based molecular phylogenies and undertaken metagenomic data analyses to assess the frequency of saline-freshwater transitions in SAR11 and to investigate the evolutionary implications of this process. Our analyses indicated that very few saline-freshwater transitions occurred during the evolutionary diversification of SAR11, generating genetically distinct saline and freshwater lineages that do not appear to exchange genes extensively via horizontal gene transfer. In contrast to lineages from saline environments, extant freshwater taxa from diverse, and sometimes distant, geographic locations were very closely related. This points to a rapid diversification and dispersal in fresh waters or to slower evolutionary rates in fresh water SAR11 when compared with marine counterparts. In addition, the colonization of both saline and fresh waters appears to have occurred early in the evolution of SAR11. We conclude that the different biogeochemical conditions that prevail in saline and fresh waters have likely prevented the environmental transitions in SAR11, promoting the evolution of clearly distinct lineages in each environment.}, }
@article {pmid19805302, year = {2009}, author = {Novo, M and Bigey, F and Beyne, E and Galeote, V and Gavory, F and Mallet, S and Cambon, B and Legras, JL and Wincker, P and Casaregola, S and Dequin, S}, title = {Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {38}, pages = {16333-16338}, pmid = {19805302}, issn = {1091-6490}, mesh = {Chromosomes, Fungal/genetics ; DNA, Fungal/chemistry/genetics ; Eukaryotic Cells/*metabolism ; Fungal Proteins/classification/genetics ; *Gene Transfer, Horizontal ; Genes, Fungal/genetics ; Genome, Fungal/*genetics ; Phylogeny ; Saccharomyces cerevisiae/*genetics ; Saccharomyces cerevisiae Proteins/classification/genetics ; Sequence Analysis, DNA/methods ; Synteny ; Wine/microbiology ; Yeasts/genetics ; }, abstract = {Saccharomyces cerevisiae has been used for millennia in winemaking, but little is known about the selective forces acting on the wine yeast genome. We sequenced the complete genome of the diploid commercial wine yeast EC1118, resulting in an assembly of 31 scaffolds covering 97% of the S288c reference genome. The wine yeast differed strikingly from the other S. cerevisiae isolates in possessing 3 unique large regions, 2 of which were subtelomeric, the other being inserted within an EC1118 chromosome. These regions encompass 34 genes involved in key wine fermentation functions. Phylogeny and synteny analyses showed that 1 of these regions originated from a species closely related to the Saccharomyces genus, whereas the 2 other regions were of non-Saccharomyces origin. We identified Zygosaccharomyces bailii, a major contaminant of wine fermentations, as the donor species for 1 of these 2 regions. Although natural hybridization between Saccharomyces strains has been described, this report provides evidence that gene transfer may occur between Saccharomyces and non-Saccharomyces species. We show that the regions identified are frequent and differentially distributed among S. cerevisiae clades, being found almost exclusively in wine strains, suggesting acquisition through recent transfer events. Overall, these data show that the wine yeast genome is subject to constant remodeling through the contribution of exogenous genes. Our results suggest that these processes are favored by ecologic proximity and are involved in the molecular adaptation of wine yeasts to conditions of high sugar, low nitrogen, and high ethanol concentrations.}, }
@article {pmid19805231, year = {2009}, author = {Konstantinidis, KT and Serres, MH and Romine, MF and Rodrigues, JL and Auchtung, J and McCue, LA and Lipton, MS and Obraztsova, A and Giometti, CS and Nealson, KH and Fredrickson, JK and Tiedje, JM}, title = {Comparative systems biology across an evolutionary gradient within the Shewanella genus.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {37}, pages = {15909-15914}, pmid = {19805231}, issn = {1091-6490}, mesh = {*Biological Evolution ; Conserved Sequence ; Ecosystem ; Evolution, Molecular ; Gene Expression ; Gene Transfer, Horizontal ; Genome, Bacterial ; Phenotype ; Phylogeny ; Protein Array Analysis ; Proteome ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Shewanella/*classification/*genetics/physiology ; Systems Biology ; Time Factors ; }, abstract = {To what extent genotypic differences translate to phenotypic variation remains a poorly understood issue of paramount importance for several cornerstone concepts of microbiology including the species definition. Here, we take advantage of the completed genomic sequences, expressed proteomic profiles, and physiological studies of 10 closely related Shewanella strains and species to provide quantitative insights into this issue. Our analyses revealed that, despite extensive horizontal gene transfer within these genomes, the genotypic and phenotypic similarities among the organisms were generally predictable from their evolutionary relatedness. The power of the predictions depended on the degree of ecological specialization of the organisms evaluated. Using the gradient of evolutionary relatedness formed by these genomes, we were able to partly isolate the effect of ecology from that of evolutionary divergence and to rank the different cellular functions in terms of their rates of evolution. Our ranking also revealed that whole-cell protein expression differences among these organisms, when the organisms were grown under identical conditions, were relatively larger than differences at the genome level, suggesting that similarity in gene regulation and expression should constitute another important parameter for (new) species description. Collectively, our results provide important new information toward beginning a systems-level understanding of bacterial species and genera.}, }
@article {pmid19800365, year = {2010}, author = {Lioy, VS and Rey, O and Balsa, D and Pellicer, T and Alonso, JC}, title = {A toxin-antitoxin module as a target for antimicrobial development.}, journal = {Plasmid}, volume = {63}, number = {1}, pages = {31-39}, doi = {10.1016/j.plasmid.2009.09.005}, pmid = {19800365}, issn = {1095-9890}, mesh = {Anti-Infective Agents/*pharmacology ; Antitoxins/*metabolism ; Bacillus subtilis/cytology/drug effects ; Biological Assay ; *Drug Design ; Escherichia coli/drug effects/metabolism ; Luminescent Measurements ; Microbial Sensitivity Tests ; Microbial Viability/drug effects ; Molecular Dynamics Simulation ; Mutation/genetics ; Peptides/pharmacology ; Protein Structure, Secondary ; Recombinant Fusion Proteins/metabolism ; Streptococcus pyogenes/drug effects/metabolism ; Toxins, Biological/*metabolism/pharmacology ; }, abstract = {The emergence and spread of pathogenic bacteria that have become resistant to multiple antibiotics through lateral gene transfer have created the need of novel antimicrobials. Toxin-antitoxin (TA) modules, which have been implicated in plasmid maintenance and stress management, are ubiquitous among plasmids from vancomycin or methicillin resistant bacteria. In the Streptococcus pyogenes pSM19035-encoded TA loci, the labile epsilon antitoxin binds to free zeta toxin and neutralizes it. When the zeta toxin is freed from the epsilon antitoxin, it induces a reversible state of growth arrest with a drastic reduction on the rate of replication, transcription and translation. However, upon prolonged zeta toxin action, the cells can no longer be rescued from their stasis state. A compound that disrupts the epsilon.zeta interaction can be considered as an attractive antimicrobial agent. Gene epsilon was fused to luc (Luc-epsilon antitoxin) and zeta to the gfp gene (zeta-GFP). Luc-epsilon or epsilon antitoxin neutralizes the toxic effect of the zeta or zeta-GFP toxin. In the absence of the antitoxin, free zeta or zeta-GFP triggers a reversible loss of cell proliferation, but the zetaK46A-GFP variant fails to block growth. Bioluminescence resonance energy transfer (BRET) assay was developed for high-throughput screening (HTS). To develop the proper controls, molecular dynamics studies were used to predict that the Asp18 and/or Glu22 residues might be relevant for epsilon.zeta interaction. Luc-epsilon efficiently transfers the excited energy to the fluorescent acceptor molecule (zeta-GFP or zetaK46A-GFP) and rendered high bioluminescence BRET signals. The exchange of Asp18 to Ala from zeta (D18A) affects Luc-epsilon.zetaD18A K46A-GFP interaction. In this study, we validate the hypothesis that it is possible to disrupt a TA module and offer a novel and unexploited targets to fight against antibiotic-resistant strains.}, }
@article {pmid19800234, year = {2009}, author = {Nogueira, T and Rankin, DJ and Touchon, M and Taddei, F and Brown, SP and Rocha, EP}, title = {Horizontal gene transfer of the secretome drives the evolution of bacterial cooperation and virulence.}, journal = {Current biology : CB}, volume = {19}, number = {20}, pages = {1683-1691}, pmid = {19800234}, issn = {1879-0445}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Escherichia coli/genetics/pathogenicity/*physiology ; Escherichia coli Proteins/genetics/metabolism ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Microbial Interactions/*genetics ; *Models, Theoretical ; Virulence ; }, abstract = {BACKGROUND: Microbes engage in a remarkable array of cooperative behaviors, secreting shared proteins that are essential for foraging, shelter, microbial warfare, and virulence. These proteins are costly, rendering populations of cooperators vulnerable to exploitation by nonproducing cheaters arising by gene loss or migration. In such conditions, how can cooperation persist?<br><br>RESULTS: Our model predicts that differential gene mobility drives intragenomic variation in investment in cooperative traits. More mobile loci generate stronger among-individual genetic correlations at these loci (higher relatedness) and thereby allow the maintenance of more cooperative traits via kin selection. By analyzing 21 Escherichia genomes, we confirm that genes coding for secreted proteins-the secretome-are very frequently lost and gained and are associated with mobile elements. We show that homologs of the secretome are overrepresented among human gut metagenomics samples, consistent with increased relatedness at secretome loci across multiple species. The biosynthetic cost of secreted proteins is shown to be under intense selective pressure, even more than for highly expressed proteins, consistent with a cost of cooperation driving social dilemmas. Finally, we demonstrate that mobile elements are in conflict with their chromosomal hosts over the chimeric ensemble's social strategy, with mobile elements enforcing cooperation on their otherwise selfish hosts via the cotransfer of secretome genes with "mafia strategy" addictive systems (toxin-antitoxin and restriction-modification).<br><br>CONCLUSION: Our analysis matches the predictions of our model suggesting that horizontal transfer promotes cooperation, as transmission increases local genetic relatedness at mobile loci and enforces cooperation on the resident genes. As a consequence, horizontal transfer promoted by agents such as plasmids, phages, or integrons drives microbial cooperation.}, }
@article {pmid19799525, year = {2009}, author = {Toomey, N and Monaghan, A and Fanning, S and Bolton, DJ}, title = {Assessment of antimicrobial resistance transfer between lactic acid bacteria and potential foodborne pathogens using in vitro methods and mating in a food matrix.}, journal = {Foodborne pathogens and disease}, volume = {6}, number = {8}, pages = {925-933}, doi = {10.1089/fpd.2009.0278}, pmid = {19799525}, issn = {1556-7125}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacillales/genetics/growth &amp; development/pathogenicity ; Conjugation, Genetic ; Cultured Milk Products/microbiology ; DNA Fingerprinting ; DNA Transposable Elements/genetics ; Drug Resistance, Bacterial/*genetics ; Enterobacteriaceae/genetics/growth &amp; development/pathogenicity ; Erythromycin/pharmacology ; *Food Microbiology ; Foodborne Diseases/drug therapy/microbiology ; *Gene Transfer, Horizontal ; Genotype ; Humans ; Lactobacillales/*genetics ; Listeria/*genetics/growth &amp; development/pathogenicity ; Phenotype ; Plasmids/genetics ; Tetracycline Resistance/genetics ; }, abstract = {The transferability of antimicrobial resistance from lactic acid bacteria (LAB) to potential pathogenic strains was studied using in vitro methods and mating in a food matrix. Five LAB donors containing either erythromycin or tetracycline resistance markers on transferable elements were conjugally mated with LAB (Enterococcus faecalis, Lactococcus lactis) and pathogenic strains (Listeria spp., Salmonella ssp., Staphylococcus aureus, and Escherichia coli). In vitro transfer experiments were carried out with the donors and recipients using both the filter and plate mating methods. The food matrix consisted of fermented whole milk (fermented with the LAB donors) with the pathogenic recipients added as contaminants during the production process. All transconjugants were confirmed by phenotypic and molecular methods. Erythromycin resistance transfer from LAB strains to Listeria spp. was observed using both in vitro mating methods at high transfer frequencies of up to 5.1 x 10(-4) transconjugants per recipient. Also, high frequency transfer (ranging from 2.7 x 10(-8) up to 1.1 x 10(-3) transconjugants per recipient) of both erythromycin and tetracycline-resistance was observed between LAB species using in vitro methods. No resistance transfer was observed to Salmonella spp., Staphylococcus aureus, and E. coli. The only conjugal transfer observed in the fermented milk matrix was for tetracycline resistance between two LAB strains (at a transfer frequency of 2.6 x 10(-7) transconjugants per recipients). This study demonstrates the transfer of antimicrobial resistance from LAB to Listeria spp. using in vitro methods and also the transfer of resistance between LAB species in a food matrix. It highlights the involvement of LAB as a potential source of resistance determinants that may be disseminated between LAB and pathogenic strains including Listeria spp. Furthermore, it indicates that food matrices such as fermented milks may provide a suitable environment to support gene exchange.}, }
@article {pmid19798411, year = {2009}, author = {Nan, J and Brostromer, E and Liu, XY and Kristensen, O and Su, XD}, title = {Bioinformatics and structural characterization of a hypothetical protein from Streptococcus mutans: implication of antibiotic resistance.}, journal = {PloS one}, volume = {4}, number = {10}, pages = {e7245}, pmid = {19798411}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Bacterial Proteins/*chemistry/metabolism ; Computational Biology/*methods ; Crystallography, X-Ray/methods ; Databases, Protein ; Dental Caries/microbiology ; *Drug Resistance, Microbial ; Gene Transfer, Horizontal ; Humans ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Secondary ; Sequence Homology, Amino Acid ; Streptococcus mutans/*metabolism ; }, abstract = {As an oral bacterial pathogen, Streptococcus mutans has been known as the aetiologic agent of human dental caries. Among a total of 1960 identified proteins within the genome of this organism, there are about 500 without any known functions. One of these proteins, SMU.440, has very few homologs in the current protein databases and it does not fall into any protein functional families. Phylogenetic studies showed that SMU.440 is related to a particular ecological niche and conserved specifically in some oral pathogens, due to lateral gene transfer. The co-occurrence of a MarR protein within the same operon among these oral pathogens suggests that SMU.440 may be associated with antibiotic resistance. The structure determination of SMU.440 revealed that it shares the same fold and a similar pocket as polyketide cyclases, which indicated that it is very likely to bind some polyketide-like molecules. From the interlinking structural and bioinformatics studies, we have concluded that SMU.440 could be involved in polyketide-like antibiotic resistance, providing a better understanding of this hypothetical protein. Besides, the combination of multiple methods in this study can be used as a general approach for functional studies of a protein with unknown function.}, }
@article {pmid19797437, year = {2009}, author = {Brent, D}, title = {In search of endophenotypes for suicidal behavior.}, journal = {The American journal of psychiatry}, volume = {166}, number = {10}, pages = {1087-1089}, doi = {10.1176/appi.ajp.2009.09081131}, pmid = {19797437}, issn = {1535-7228}, support = {MH-56612/MH/NIMH NIH HHS/United States ; }, mesh = {Adolescent ; Adolescent Behavior/psychology ; Adult ; Aggression/psychology ; Child ; Family ; Female ; Gene Transfer, Horizontal/genetics ; Hostility ; Humans ; Impulsive Behavior/genetics/psychology ; Male ; Personality Disorders/genetics/psychology ; *Phenotype ; Suicide/*psychology ; Suicide, Attempted/prevention &amp; control/psychology ; Suicide Prevention ; }, }
@article {pmid19797358, year = {2010}, author = {Baart, GJE and Langenhof, M and van de Waterbeemd, B and Hamstra, HJ and Zomer, B and van der Pol, LA and Beuvery, EC and Tramper, J and Martens, DE}, title = {Expression of phosphofructokinase in Neisseria meningitidis.}, journal = {Microbiology (Reading, England)}, volume = {156}, number = {Pt 2}, pages = {530-542}, pmid = {19797358}, issn = {1465-2080}, support = {AI38399/AI/NIAID NIH HHS/United States ; }, mesh = {Biomass ; Cloning, Molecular ; Escherichia coli/genetics ; Gene Expression Profiling ; Metabolic Networks and Pathways ; Neisseria meningitidis, Serogroup B/classification/*enzymology/genetics ; Phosphofructokinases/*biosynthesis/genetics ; Phylogeny ; RNA, Bacterial/genetics ; }, abstract = {Neisseria meningitidis serogroup B is a pathogen that can infect diverse sites within the human host. According to the N. meningitidis genomic information and experimental observations, glucose can be completely catabolized through the Entner-Doudoroff pathway and the pentose phosphate pathway. The Embden-Meyerhof-Parnas pathway is not functional, because the gene for phosphofructokinase (PFK) is not present. The phylogenetic distribution of PFK indicates that in most obligate aerobic organisms, PFK is lacking. We conclude that this is because of the limited contribution of PFK to the energy supply in aerobically grown organisms in comparison with the energy generated through oxidative phosphorylation. Under anaerobic or microaerobic conditions, the available energy is limiting, and PFK provides an advantage, which explains the presence of PFK in many (facultatively) anaerobic organisms. In accordance with this, in silico flux balance analysis predicted an increase of biomass yield as a result of PFK expression. However, analysis of a genetically engineered N. meningitidis strain that expressed a heterologous PFK showed that the yield of biomass on substrate decreased in comparison with a pfkA-deficient control strain, which was associated mainly with an increase in CO(2) production, whereas production of by-products was similar in the two strains. This might explain why the pfkA gene has not been obtained by horizontal gene transfer, since it is initially unfavourable for biomass yield. No large effects related to heterologous expression of pfkA were observed in the transcriptome. Although our results suggest that introduction of PFK does not contribute to a more efficient strain in terms of biomass yield, achievement of a robust, optimal metabolic network that enables a higher growth rate or a higher biomass yield might be possible after adaptive evolution of the strain, which remains to be investigated.}, }
@article {pmid19796139, year = {2009}, author = {Li, Q and Zhang, X and Zou, L and Chen, Q and Fewer, DP and Lindström, K}, title = {Horizontal gene transfer and recombination shape mesorhizobial populations in the gene center of the host plants Astragalus luteolus and Astragalus ernestii in Sichuan, China.}, journal = {FEMS microbiology ecology}, volume = {70}, number = {2}, pages = {71-79}, doi = {10.1111/j.1574-6941.2009.00776.x}, pmid = {19796139}, issn = {1574-6941}, mesh = {Amplified Fragment Length Polymorphism Analysis ; Astragalus Plant/*microbiology ; China ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhizobium/classification/*genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Thirty-three rhizobial strains isolated from the root nodules of Astragalus luteolus and Astragalus ernestii growing on the west plateau at two different altitudes in Sichuan province, China, were characterized by amplified rDNA restriction analysis (ARDRA), amplified fragment length polymorphism (AFLP), and by sequencing of rrs, glnA, glnII and nifH. The ARDRA analysis revealed considerable genomic diversity. In AFLP analysis, 20 of 33 Astragalus rhizobia formed three distinct clades, with others dispersed into different groups with the reference strains. Phylogenetic analysis of the rrs gene of six representative strains showed that the isolates were members of the genus Mesorhizobium. Three of the isolates formed a sister clade to Mesorhizobium loti and Mesorhizobium ciceri, whereas the other three formed a sister clade to a clade harboring the species Mesorhizobium huakuii, Mesorhizobium plurifarum, Mesorhizobium septentrionale and Mesorhizobium amorphae, indicating the existence of two new species. Phylogenetic analysis of glnA and glnII confirmed the rrs phylogenies for four strains, but the trees were incongruent. The nifH sequences of the strains formed a monophyletic clade and were typical of those of mesorhizobia forming symbioses with inverted repeat lacking clade legume species. The incongruent phylogenies of the genes studied suggest that horizontal gene transfer and recombination shape mesorhizobial populations in the gene center of the host plants.}, }
@article {pmid19796133, year = {2009}, author = {González-Cerón, G and Miranda-Olivares, OJ and Servín-González, L}, title = {Characterization of the methyl-specific restriction system of Streptomyces coelicolor A3(2) and of the role played by laterally acquired nucleases.}, journal = {FEMS microbiology letters}, volume = {301}, number = {1}, pages = {35-43}, doi = {10.1111/j.1574-6968.2009.01790.x}, pmid = {19796133}, issn = {1574-6968}, mesh = {Amino Acid Sequence ; Cloning, Molecular ; *DNA Methylation ; DNA Restriction Enzymes/genetics/*metabolism ; DNA, Bacterial/metabolism ; Deoxyribonucleases/genetics/*metabolism ; Gene Knockout Techniques ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genomic Islands ; Molecular Sequence Data ; Site-Specific DNA-Methyltransferase (Adenine-Specific)/metabolism ; Streptomyces coelicolor/*enzymology/genetics ; Streptomyces lividans/metabolism ; }, abstract = {The methyl-specific restriction system of Streptomyces coelicolor A3(2) was analyzed by carrying out transformations with unmethylated and methylated pSET152 DNA. Streptomyces coelicolor was found to strongly restrict DNA methylated in vivo by the Dam, Dcm and Hsd modification systems of Escherichia coli. Hsd-modified DNA was restricted as strongly as Dam-modified DNA, even though there are significantly fewer sites on the plasmid; Dcm-modified plasmid was restricted more strongly then either Dam- or Hsd-modified DNA. Restriction of plasmid DNA modified in vitro by different methylases also showed a greater dependence on the methylated sequence than on the number of methylated sites. Streptomyces coelicolor mutants were constructed that lacked genes identified as the likely candidates for encoding methyl-specific restriction nucleases (the products of the SCO4213, SCO4631 and SCO2863 genes, as well as the SCO3261-SCO3262 operon) that are located in the laterally acquired genomic islands of the S. coelicolor chromosome; these mutants showed partial alleviation of methylated DNA restriction. Cloning of these genes in the close relative Streptomyces lividans increased the restriction of methylated DNA by this species, confirming their role as part of the methyl-specific restriction system of S. coelicolor.}, }
@article {pmid19793120, year = {2009}, author = {Moliner, C and Raoult, D and Fournier, PE}, title = {Evidence of horizontal gene transfer between amoeba and bacteria.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {15 Suppl 2}, number = {}, pages = {178-180}, doi = {10.1111/j.1469-0691.2008.02216.x}, pmid = {19793120}, issn = {1469-0691}, mesh = {Acanthamoeba/*genetics ; Bacterial Proteins/genetics ; DNA, Bacterial/chemistry/genetics ; Dictyostelium/*genetics ; *Gene Transfer, Horizontal ; Legionella/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology ; }, }
@article {pmid19788881, year = {2009}, author = {Guttman, DS}, title = {Bacterial evolution: dynamic genomes and the power of transformation.}, journal = {Current biology : CB}, volume = {19}, number = {18}, pages = {R857-9}, doi = {10.1016/j.cub.2009.08.007}, pmid = {19788881}, issn = {1879-0445}, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Phaseolus/microbiology ; Pseudomonas syringae/*genetics/physiology ; Transformation, Bacterial ; Virulence Factors ; }, abstract = {Virulence and avirulence genes carried on large, unstable pathogenicity islands (PAI) strongly influence the course and fate of host-pathogen interactions. A recent study shows how one such PAI can be rapidly transferred between two closely related bacteria via transformation in vivo, and how this horizontal gene transfer affects the fitness of the recipient strain.}, }
@article {pmid19788730, year = {2009}, author = {Koonin, EV and Wolf, YI}, title = {The fundamental units, processes and patterns of evolution, and the tree of life conundrum.}, journal = {Biology direct}, volume = {4}, number = {}, pages = {33}, pmid = {19788730}, issn = {1745-6150}, support = {//Intramural NIH HHS/United States ; }, mesh = {*Biological Evolution ; DNA Replication ; }, abstract = {BACKGROUND: The elucidation of the dominant role of horizontal gene transfer (HGT) in the evolution of prokaryotes led to a severe crisis of the Tree of Life (TOL) concept and intense debates on this subject.<br><br>CONCEPT: Prompted by the crisis of the TOL, we attempt to define the primary units and the fundamental patterns and processes of evolution. We posit that replication of the genetic material is the singular fundamental biological process and that replication with an error rate below a certain threshold both enables and necessitates evolution by drift and selection. Starting from this proposition, we outline a general concept of evolution that consists of three major precepts. 1. The primary agency of evolution consists of Fundamental Units of Evolution (FUEs), that is, units of genetic material that possess a substantial degree of evolutionary independence. The FUEs include both bona fide selfish elements such as viruses, viroids, transposons, and plasmids, which encode some of the information required for their own replication, and regular genes that possess quasi-independence owing to their distinct selective value that provides for their transfer between ensembles of FUEs (genomes) and preferential replication along with the rest of the recipient genome. 2. The history of replication of a genetic element without recombination is isomorphously represented by a directed tree graph (an arborescence, in the graph theory language). Recombination within a FUE is common between very closely related sequences where homologous recombination is feasible but becomes negligible for longer evolutionary distances. In contrast, shuffling of FUEs occurs at all evolutionary distances. Thus, a tree is a natural representation of the evolution of an individual FUE on the macro scale, but not of an ensemble of FUEs such as a genome. 3. The history of life is properly represented by the "forest" of evolutionary trees for individual FUEs (Forest of Life, or FOL). Search for trends and patterns in the FOL is a productive direction of study that leads to the delineation of ensembles of FUEs that evolve coherently for a certain time span owing to a shared history of vertical inheritance or horizontal gene transfer; these ensembles are commonly known as genomes, taxa, or clades, depending on the level of analysis. A small set of genes (the universal genetic core of life) might show a (mostly) coherent evolutionary trend that transcends the entire history of cellular life forms. However, it might not be useful to denote this trend "the tree of life", or organismal, or species tree because neither organisms nor species are fundamental units of life.<br><br>CONCLUSION: A logical analysis of the units and processes of biological evolution suggests that the natural fundamental unit of evolution is a FUE, that is, a genetic element with an independent evolutionary history. Evolution of a FUE on the macro scale is naturally represented by a tree. Only the full compendium of trees for individual FUEs (the FOL) is an adequate depiction of the evolution of life. Coherent evolution of FUEs over extended evolutionary intervals is a crucial aspect of the history of life but a "species" or "organismal" tree is not a fundamental concept.<br><br>REVIEWERS: This articles was reviewed by Valerian Dolja, W. Ford Doolittle, Nicholas Galtier, and William Martin.}, }
@article {pmid19787052, year = {2009}, author = {Matter, AM and Hoot, SB and Anderson, PD and Neves, SS and Cheng, YQ}, title = {Valinomycin biosynthetic gene cluster in Streptomyces: conservation, ecology and evolution.}, journal = {PloS one}, volume = {4}, number = {9}, pages = {e7194}, pmid = {19787052}, issn = {1932-6203}, mesh = {Anti-Bacterial Agents/chemistry/*metabolism ; Bacillus cereus/metabolism ; Bayes Theorem ; Biological Evolution ; Ecology ; Gene Transfer, Horizontal ; Likelihood Functions ; *Multigene Family ; Peptide Synthases/metabolism ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/metabolism ; Sequence Analysis, DNA ; Streptomyces/*genetics/*metabolism ; Valinomycin/chemistry/*metabolism ; }, abstract = {Many Streptomyces strains are known to produce valinomycin (VLM) antibiotic and the VLM biosynthetic gene cluster (vlm) has been characterized in two independent isolates. Here we report the phylogenetic relationships of these strains using both parsimony and likelihood methods, and discuss whether the vlm gene cluster shows evidence of horizontal transmission common in natural product biosynthetic genes. Eight Streptomyces strains from around the world were obtained and sequenced for three regions of the two large nonribosomal peptide synthetase genes (vlm1 and vlm2) involved in VLM biosynthesis. The DNA sequences representing the vlm gene cluster are highly conserved among all eight environmental strains. The geographic distribution pattern of these strains and the strict congruence between the trees of the two vlm genes and the housekeeping genes, 16S rDNA and trpB, suggest vertical transmission of the vlm gene cluster in Streptomyces with no evidence of horizontal gene transfer. We also explored the relationship of the sequence of vlm genes to that of the cereulide biosynthetic genes (ces) found in Bacillus cereus and found them highly divergent from each other at DNA level (genetic distance values >or= 95.6%). It is possible that the vlm gene cluster and the ces gene cluster may share a relatively distant common ancestor but these two gene clusters have since evolved independently.}, }
@article {pmid19784924, year = {2009}, author = {Tank, M and Thiel, V and Imhoff, JF}, title = {Phylogenetic relationship of phototrophic purple sulfur bacteria according to pufL and pufM genes.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {12}, number = {3}, pages = {175-185}, pmid = {19784924}, issn = {1618-1905}, mesh = {Bacterial Proteins/*genetics ; Chromatiaceae/*classification/*genetics ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; Light-Harvesting Protein Complexes/*genetics ; Molecular Sequence Data ; Photosynthetic Reaction Center Complex Proteins/*genetics ; *Phylogeny ; *Polymorphism, Genetic ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; }, abstract = {The phylogenetic relationship of purple sulfur bacteria (PSB), of the order Chromatiales (class Gammaproteobacteria), was analyzed based on photosynthetic gene sequences of the pufL and pufM genes, and the results compared to phylogenetic trees and groupings of the 16S rRNA gene. Primers for pufL and pufM genes were constructed and successfully used to amplify the pufLM genes of members of 16 genera of Chromatiales. In total, pufLM and 16S rRNA gene sequences of 66 PSB strains were analyzed, including 29 type strains and 28 new isolates. The inferred phylogenetic trees of the pufLM and 16S rRNA genes reflected a largely similar phylogenetic development suggesting coevolution of these essential genes within the PSB. It is concluded that horizontal gene transfer of pufLM genes within the PSB is highly unlikely, in contrast to the situation in other groups of anoxygenic phototrophic bacteria belonging to Alpha- and Betaproteobacteria. The phylogeny of pufLM is therefore in good agreement with the current taxonomic classification of PSB. A phylogenetic classification of PSB to the genus level is possible based on their pufL or pufM sequences, and in many cases even to the species level. In addition, our data support a correlation between Puf protein structure and the type of internal photosynthetic membranes (vesicular, lamellar, or tubular).}, }
@article {pmid19784557, year = {2009}, author = {Glansdorff, N and Xu, Y and Labedan, B}, title = {The conflict between horizontal gene transfer and the safeguard of identity: origin of meiotic sexuality.}, journal = {Journal of molecular evolution}, volume = {69}, number = {5}, pages = {470-480}, pmid = {19784557}, issn = {1432-1432}, mesh = {Animals ; Archaea/cytology/*genetics ; Bacteria/cytology/*genetics ; *Biological Evolution ; Carboxyl and Carbamoyl Transferases/genetics ; Computational Biology ; *Eukaryota/cytology/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Humans ; Meiosis/*genetics ; Phylogeny ; Species Specificity ; }, abstract = {Contrary to a widespread opinion, horizontal gene transfer (HGT) between distantly related microorganisms (such as Bacteria and Archaea) has not been demonstrated to occur on a large scale. Except for transfer of mobile elements between closely related organisms, most alleged HGT events reflect phylogenetic discrepancies that can be explained by a variety of artefacts or by the differential loss of paralogous gene copies either originally present in the Last Universal Common Ancestor (LUCA) to the three Domains (a sophisticated, genetically redundant and promiscuous community of protoeukaryotes), or created by duplications having occurred at later times. Besides, (i) there is no experimental evidence for the facile acquisition of foreign DNA between distant taxa and (ii) important biological constraints operate on the phenotypic success of genetic exchange at several levels, including protein-protein interactions involved in metabolic channelling; stable integration and expression of foreign DNA is, therefore, expected to require strong selection. Explaining phylogenetic discrepancies by artefacts or loss of paralogs does not eliminate difficulties in retracing species genealogy but maintains the picture of a universal tree of life, HGT between distant organisms being reduced to a trickle. We illustrate our thesis by the phylogenetic analysis of carbamoyltransferases, a family of paralogous proteins. Among higher eukaryotes HGT appears of limited scope except in asexual organisms. We suggest that meiotic sexuality (a hallmark of eukaryotes) emerged in the genetically redundant and protoeukaryotic LUCA as a molecular identity check providing a defence mechanism against the deleterious effects of HGT.}, }
@article {pmid19781080, year = {2009}, author = {Attia, AS and Sedillo, JL and Hoopman, TC and Liu, W and Liu, L and Brautigam, CA and Hansen, EJ}, title = {Identification of a bacteriocin and its cognate immunity factor expressed by Moraxella catarrhalis.}, journal = {BMC microbiology}, volume = {9}, number = {}, pages = {207}, pmid = {19781080}, issn = {1471-2180}, support = {R01 AI036344-12/AI/NIAID NIH HHS/United States ; AI36344/AI/NIAID NIH HHS/United States ; R01 AI036344-11A2/AI/NIAID NIH HHS/United States ; R01 AI036344-13/AI/NIAID NIH HHS/United States ; AI76365/AI/NIAID NIH HHS/United States ; R01 AI036344/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; *Antibiosis ; Bacteriocins/*genetics/immunology ; Cloning, Molecular ; DNA, Bacterial/genetics ; Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Molecular Sequence Data ; Moraxella catarrhalis/*genetics/immunology ; Multigene Family ; Open Reading Frames ; Plasmids ; Sequence Deletion ; }, abstract = {BACKGROUND: Bacteriocins are antimicrobial proteins and peptides ribosomally synthesized by some bacteria which can effect both intraspecies and interspecies killing.<br><br>RESULTS: Moraxella catarrhalis strain E22 containing plasmid pLQ510 was shown to inhibit the growth of M. catarrhalis strain O35E. Two genes (mcbA and mcbB) in pLQ510 encoded proteins predicted to be involved in the secretion of a bacteriocin. Immediately downstream from these two genes, a very short ORF (mcbC) encoded a protein which had some homology to double-glycine bacteriocins produced by other bacteria. A second very short ORF (mcbI) immediately downstream from mcbC encoded a protein which had no significant similarity to other proteins in the databases. Cloning and expression of the mcbI gene in M. catarrhalis O35E indicated that this gene encoded the cognate immunity factor. Reverse transcriptase-PCR was used to show that the mcbA, mcbB, mcbC, and mcbI ORFs were transcriptionally linked. This four-gene cluster was subsequently shown to be present in the chromosome of several M. catarrhalis strains including O12E. Inactivation of the mcbA, mcbB, or mcbC ORFs in M. catarrhalis O12E eliminated the ability of this strain to inhibit the growth of M. catarrhalis O35E. In co-culture experiments involving a M. catarrhalis strain containing the mcbABCI locus and one which lacked this locus, the former strain became the predominant member of the culture after overnight growth in broth.<br><br>CONCLUSION: This is the first description of a bacteriocin and its cognate immunity factor produced by M. catarrhalis. The killing activity of the McbC protein raises the possibility that it might serve to lyse other M. catarrhalis strains that lack the mcbABCI locus, thereby making their DNA available for lateral gene transfer.}, }
@article {pmid19780824, year = {2009}, author = {Hu, X and Swiecicka, I and Timmery, S and Mahillon, J}, title = {Sympatric soil communities of Bacillus cereus sensu lato: population structure and potential plasmid dynamics of pXO1- and pXO2-like elements.}, journal = {FEMS microbiology ecology}, volume = {70}, number = {3}, pages = {344-355}, doi = {10.1111/j.1574-6941.2009.00771.x}, pmid = {19780824}, issn = {1574-6941}, mesh = {Bacillus cereus/classification/*genetics/*isolation &amp; purification ; Bacterial Typing Techniques ; Belgium ; Computational Biology ; Conjugation, Genetic ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; Genetic Variation ; Plasmids/*genetics ; Replicon ; Sequence Analysis, DNA ; Soil/analysis ; *Soil Microbiology ; }, abstract = {Eighty soil-borne Bacillus cereus group isolates were collected from two neighbouring geographical sites in Belgium. Their genetic relationships and population structure were assessed using Multilocus sequence typing analysis of five chromosomal genes, while the contribution of extrachromosomal elements to the population dynamics was gauged by the presence, diversity and transfer capacity of pXO1- and pXO2-like plasmids. Globally, the bacterial population displayed a broad diversity, including an important subpopulation of psychrotolerant isolates related to Bacillus weihenstephanensis. pXO1- and pXO2-like replicons were present in 12% and 21% of the isolates, but no Bacillus anthracis-related toxin genes were found. Furthermore, only one of the isolates containing a pXO2-related plasmid was shown to be able to mobilize small non-self-conjugative plasmids. Interestingly, several B. cereus sensu lato isolates displaying the same sequence type were observed to have different plasmid contents, suggesting the occurrence of horizontal gene exchange. Similarly, a number of pXO2-like replicons with identical sequences were found in distinct bacterial isolates, therefore strongly arguing for lateral transfers among sympatric bacteria.}, }
@article {pmid19780695, year = {2009}, author = {Sha, HY and Chen, JQ and Chen, J and Zhang, PY and Wang, P and Chen, LP and Cheng, GX and Zhu, JH}, title = {Fates of donor and recipient mitochondrial DNA during generation of interspecies SCNT-derived human ES-like cells.}, journal = {Cloning and stem cells}, volume = {11}, number = {4}, pages = {497-507}, doi = {10.1089/clo.2009.0021}, pmid = {19780695}, issn = {1557-7457}, mesh = {Aborted Fetus ; Animals ; Blastocyst Inner Cell Mass/cytology/metabolism ; Brain/cytology ; Cell Differentiation ; Cellular Reprogramming/genetics ; DNA Polymerase gamma ; DNA, Mitochondrial/*genetics ; DNA-Binding Proteins/genetics ; DNA-Directed DNA Polymerase/genetics ; Electron Transport Complex IV/genetics ; Embryonic Stem Cells/cytology/*metabolism ; Gene Transfer, Horizontal/*genetics ; Goats ; Humans ; Male ; Mitochondrial Proteins/genetics ; Nuclear Transfer Techniques ; Oocytes/cytology/*metabolism ; Species Specificity ; Transcription Factors/genetics ; Transplantation ; }, abstract = {To investigate nuclear donor and cytoplast recipient mitochondria fate and their effects on generation of interspecies somatic cell nuclear transfer (iSCNT)-derived human embryonic stem (ES)-like cells, iSCNT embryos were reconstructed between enucleated goat oocytes and human neural stem cells (hNSCs). A total of 10.74% cleaved embryos (13/121) developed to blastocyst stage. One typical primary ES-like (tpES-like) colony and two nontypical primary ES-like (non-tpES-like) colonies designated as non-tpES-like cell-1 and non-tpES-like cell-2, respectively, were obtained from the inner cell masses of iSCNT blastocysts. The tpES-like cells expressed ESC markers. Both human and goat mtDNA could be detected in the embryos at 2-8-, 16-32-cell, and blastocyst stages, and in tpES-like colony and two non-tpES-like colonies. Human mtDNA copies per cell from embryos at two- to eight-cell stage to the three colonies maintain almost its original level, whereas 2.88 x 10(5) goat mtDNA copies per oocyte decreased to 10.8 copies per tpES-like cell, 493 copies per non-tpES-like cell-1, and 77.6 copies per non-tpES-like cell-2, resulting in 43.75% (8.4/19.2), 1.24% (6.2/499), and 14.63% (13.3/90.9) mtDNA content in tpES-like cell, non-tpES-like cell-1, and non-tpES-like cell-2 was that of nuclear donor, respectively. Human-specific Tfam and Polg mRNA could be detected in cells of the three colonies. However, tpES-like colony failed to be passaged. The mRNA level of CoxIV encoded by nuclear donor in tpES-like cell was higher than that in non-tpES-like cell, but significantly lower than that of human ESC, suggesting proper nuclear-cytoplasmic communication would not be established in tpES-like cells. Thus, the data suggest that (1) goat oocytes could reprogram human neural stem cells (hNSCs) into embryonic state and further support the inner cell mass (ICM) of iSCNT blastocyst to form tpES-like colony; (2) nuclear donor mtDNA could be replicated and maintain its original level during the reduction of recipient mitochondrial DNA copies, (3) nuclear-cytoplasmic communication and recipient mtDNA copies might affect the derivation of iSCNT-derived ES-like cells.}, }
@article {pmid19779832, year = {2009}, author = {Pertseva, MN and Shpakov, AO}, title = {The prokaryotic origin and evolution of eukaryotic chemosignaling systems.}, journal = {Neuroscience and behavioral physiology}, volume = {39}, number = {8}, pages = {793-804}, pmid = {19779832}, issn = {1573-899X}, mesh = {Animals ; Archaea/physiology ; Bacterial Physiological Phenomena ; *Biological Evolution ; Eukaryotic Cells/physiology ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome ; Hormones/*physiology ; Pheromones/*physiology ; Quorum Sensing ; *Signal Transduction ; }, abstract = {Analysis of our own results and data published over the last two decades supports the authors' hypothesis of the prokaryotic origin and endosymbiotic mechanism of appearance of chemosignaling systems in higher eukaryotes. Comparison of the structural-functional organization of these information systems and their component blocks (receptors, GTP-binding proteins, enzymes with cyclase activity, protein kinases, etc.) in bacteria and eukaryotes revealed a whole series of similar characteristics pointing to evolutionary relatedness. This led to the conclusion that eukaryotic signal systems have prokaryotic roots. In terms of their architecture and functional properties, the signal transduction systems seen in unicellular eukaryotes represent a transitional stage in the evolution of chemosignaling systems between prokaryotes and higher eukaryotes. The propagation of chemosignaling systems in three kingdoms - Bacteria, Archaea, and Eukarya - occurred by horizontal transfer of bacterial genes and the coevolution of the components of these systems.}, }
@article {pmid19777734, year = {2009}, author = {Oberpichler-Schwenk, H}, title = {[Antibiotic resistance: a success story? ].}, journal = {Medizinische Monatsschrift fur Pharmazeuten}, volume = {32}, number = {8}, pages = {279}, pmid = {19777734}, issn = {0342-9601}, mesh = {Anti-Bacterial Agents/*pharmacology/*therapeutic use ; Bacteria/*drug effects/*genetics ; Drug Resistance, Bacterial/*drug effects ; Gene Transfer, Horizontal ; }, }
@article {pmid19776768, year = {2010}, author = {Kirkwood, M and Todd, JD and Rypien, KL and Johnston, AW}, title = {The opportunistic coral pathogen Aspergillus sydowii contains dddP and makes dimethyl sulfide from dimethylsulfoniopropionate.}, journal = {The ISME journal}, volume = {4}, number = {1}, pages = {147-150}, doi = {10.1038/ismej.2009.102}, pmid = {19776768}, issn = {1751-7370}, mesh = {Animals ; Anthozoa/*microbiology ; Aspergillus/*genetics/isolation &amp; purification/*metabolism ; Caribbean Region ; DNA, Fungal/chemistry/genetics ; Genes, Fungal ; Molecular Sequence Data ; Sequence Analysis, DNA ; Sulfides/*metabolism ; Sulfonium Compounds/*metabolism ; }, abstract = {The ascomycete Aspergillus sydowii is associated with a serious epizootic of sea fan corals in the Caribbean. Corals are rich in the compatible solute, dimethylsulfoniopropionate (DMSP), produced by their symbionts, the dinoflagellate Symbiodinium. As other Aspergillus species can catabolize DMSP, liberating dimethyl sulfide (DMS) in the process, we tested A. sydowii strains, obtained from diseased corals and other environments, for this Ddd(+) phenotype. All the strains, irrespective of their geographical or environmental origins, made DMS from DMSP, and all of them contained homologs (>87% identical) of the dddP gene, which encodes an enzyme that releases DMS from DMSP and which occurs in other Ddd(+) fungi and in some marine bacteria. The dddP gene was likely acquired by the Aspergillus fungi by inter-domain horizontal gene transfer from alpha-proteobacteria.}, }
@article {pmid19776168, year = {2009}, author = {Ridley, MW}, title = {When ideas have sex: the role of exchange in cultural evolution.}, journal = {Cold Spring Harbor symposia on quantitative biology}, volume = {74}, number = {}, pages = {443-448}, doi = {10.1101/sqb.2009.74.017}, pmid = {19776168}, issn = {1943-4456}, mesh = {Animals ; Commerce ; *Cultural Evolution ; Hominidae ; Humans ; Interpersonal Relations ; Models, Genetic ; Sex ; }, abstract = {Human economic and technological progress has been dominated for the last 100,000 years by natural selection among variants of cultures, rather than among variants of genes. Evidence suggests that cultural evolution depends on exchange and trade to bring together ideas in much the same way that genetic evolution depends on sex to spread genetic mutations, or in the case of bacteria, on horizontal gene transfer. When starved of access to a large "collective brain" by isolation from trade and exchange, people may experience not just less innovation, but even regress. The capacity for ideas to have sex on the Internet is likely to accelerate cultural evolution still further.}, }
@article {pmid19775431, year = {2009}, author = {Bertalan, M and Albano, R and de Pádua, V and Rouws, L and Rojas, C and Hemerly, A and Teixeira, K and Schwab, S and Araujo, J and Oliveira, A and França, L and Magalhães, V and Alquéres, S and Cardoso, A and Almeida, W and Loureiro, MM and Nogueira, E and Cidade, D and Oliveira, D and Simão, T and Macedo, J and Valadão, A and Dreschsel, M and Freitas, F and Vidal, M and Guedes, H and Rodrigues, E and Meneses, C and Brioso, P and Pozzer, L and Figueiredo, D and Montano, H and Junior, J and de Souza Filho, G and Martin Quintana Flores, V and Ferreira, B and Branco, A and Gonzalez, P and Guillobel, H and Lemos, M and Seibel, L and Macedo, J and Alves-Ferreira, M and Sachetto-Martins, G and Coelho, A and Santos, E and Amaral, G and Neves, A and Pacheco, AB and Carvalho, D and Lery, L and Bisch, P and Rössle, SC and Urményi, T and Rael Pereira, A and Silva, R and Rondinelli, E and von Krüger, W and Martins, O and Baldani, JI and Ferreira, PC}, title = {Complete genome sequence of the sugarcane nitrogen-fixing endophyte Gluconacetobacter diazotrophicus Pal5.}, journal = {BMC genomics}, volume = {10}, number = {}, pages = {450}, pmid = {19775431}, issn = {1471-2164}, mesh = {Comparative Genomic Hybridization ; DNA, Bacterial/genetics ; *Genome, Bacterial ; Genomic Islands ; Genomic Library ; Gluconacetobacter/*genetics/metabolism ; Molecular Sequence Data ; Nitrogen Fixation/genetics ; Saccharum/*microbiology ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {BACKGROUND: Gluconacetobacter diazotrophicus Pal5 is an endophytic diazotrophic bacterium that lives in association with sugarcane plants. It has important biotechnological features such as nitrogen fixation, plant growth promotion, sugar metabolism pathways, secretion of organic acids, synthesis of auxin and the occurrence of bacteriocins.<br><br>RESULTS: Gluconacetobacter diazotrophicus Pal5 is the third diazotrophic endophytic bacterium to be completely sequenced. Its genome is composed of a 3.9 Mb chromosome and 2 plasmids of 16.6 and 38.8 kb, respectively. We annotated 3,938 coding sequences which reveal several characteristics related to the endophytic lifestyle such as nitrogen fixation, plant growth promotion, sugar metabolism, transport systems, synthesis of auxin and the occurrence of bacteriocins. Genomic analysis identified a core component of 894 genes shared with phylogenetically related bacteria. Gene clusters for gum-like polysaccharide biosynthesis, tad pilus, quorum sensing, for modulation of plant growth by indole acetic acid and mechanisms involved in tolerance to acidic conditions were identified and may be related to the sugarcane endophytic and plant-growth promoting traits of G. diazotrophicus. An accessory component of at least 851 genes distributed in genome islands was identified, and was most likely acquired by horizontal gene transfer. This portion of the genome has likely contributed to adaptation to the plant habitat.<br><br>CONCLUSION: The genome data offer an important resource of information that can be used to manipulate plant/bacterium interactions with the aim of improving sugarcane crop production and other biotechnological applications.}, }
@article {pmid19775015, year = {2009}, author = {Quan, XC and Tang, H and Wang, YL and He, MC}, title = {[Plasmid pJP4 mediated gene-augmentation in different systems and its effect on 2,4-D biodegradation].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {30}, number = {7}, pages = {2099-2104}, pmid = {19775015}, issn = {0250-3301}, mesh = {2,4-Dichlorophenoxyacetic Acid/isolation &amp; purification/*metabolism ; Bacteria/genetics/metabolism ; Biodegradation, Environmental ; *Conjugation, Genetic ; Gene Transfer, Horizontal ; *Genetic Engineering ; Industrial Microbiology ; Plasmids/*genetics ; Polymerase Chain Reaction ; Pseudomonas putida/*genetics/metabolism ; Sewage/microbiology ; Waste Disposal, Fluid/methods ; }, abstract = {With pJP4 plasmid carrying genetic engineering bacteria Pseudomonas putida SM1443 :: gfp2x (pJP4 :: dsRed) as the donor, horizontal gene transfer of pJP4 plasmid in 4 isolated pure strains was investigated, and effects of the donor bacteria inoculation on the removal of the target pollutant 2,4-dichlorophenoxyacetic acid (2,4-D) was studied through conducting gene augmentation in activated sludge, biofilm, aerobic granular sludge and river sediment system, respectively. Results showed that plasmid pJP4 could transfer from Pseudomonas putida SM1443 to a broad spectrum of bacteria. Inoculation of pJP4 plasmid carrying donor bacterium apparently promoted the degradation of 2,4-D for all the above four systems. For the activated sludge system (2,4-D initial concentration at 450 mg/L), 66% and 54% removal of 2,4-D was achieved after 143.5 h reaction for the gene augmented and control system, respectively. For the biofilm system with 2,4-D initial concentration at 180 mg/L, 2,4-D removal percentage at 113 h was 99% and 61%, respectively. For aerobic granular sludge system (2,4-D initial concentration at 160 mg/L), 2,4-D was nearly completely removed by 62 h in the gene-augmented system, while the control system only degraded 26% at 66 h. For the system with sediment (2,4-D initial concentration at 2 mg/L), 93% and 69% removal of 2,4-D was obtained at 344 h reaction for the gene augmented and control system, respectively. Confocal laser scanning microscopy (CLSM) analysis revealed the formation and presence of transconjugants in different gene augmentation systems.}, }
@article {pmid19773253, year = {2009}, author = {Tseng, SP and Tsai, JC and Teng, LJ and Hsueh, PR}, title = {Dissemination of transposon Tn6001 in carbapenem-non-susceptible and extensively drug-resistant Pseudomonas aeruginosa in Taiwan.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {64}, number = {6}, pages = {1170-1174}, pmid = {19773253}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Typing Techniques ; Carbapenems/*pharmacology ; Cluster Analysis ; DNA Fingerprinting ; *DNA Transposable Elements ; DNA, Bacterial/genetics ; Electrophoresis, Gel, Pulsed-Field ; Gene Order ; Gene Transfer, Horizontal ; Genotype ; Humans ; Molecular Epidemiology ; Polymerase Chain Reaction/methods ; Pseudomonas Infections/*microbiology ; Pseudomonas aeruginosa/classification/*drug effects/*genetics/isolation &amp; purification ; Synteny ; Taiwan ; *beta-Lactam Resistance ; }, abstract = {OBJECTIVES: To investigate the prevalence of metallo-beta-lactamases (MBLs) and Tn6001 in carbapenem-non-susceptible Pseudomonas aeruginosa (CNSPA). The CNSPA included extensively drug-resistant P. aeruginosa (XDRPA) and non-XDRPA isolates in Taiwan.<br><br>METHODS: A total of 308 CNSPA isolates collected at a medical centre from 2000 to 2005 and 26 XDRPA collected from six medical centres in different regions of Taiwan in 2003 were included. MBL genes and Tn6001 were detected by PCR. Clonal relatedness was determined by PFGE.<br><br>RESULTS: Of the 308 CNSPA isolates, 30 (10%) were XDRPA, including 27 (9%) colistin-only-susceptible (COS) and 3 (1%) colistin-only-intermediate (COI) P. aeruginosa. bla(VIM-3) was found in 16 (53%) isolates of the XDRPA (n = 30), whereas only 72 (26%) of the non-XDRPA (n = 278) carried the gene. In450 was higher in COS P. aeruginosa (12/27; 44%) than in non-XDRPA isolates (53/278; 19%). Tn6001 was highest in COS P. aeruginosa (11/27; 41%), followed by COI P. aeruginosa (1/3; 33%), and lowest in non-XDRPA (46/278; 17%). Of 26 XDRPA from six medical centres, higher prevalences of bla(VIM-3) (16/26; 62%), In450 (16/26; 62%) and Tn6001 (12/26; 46%) were found. Genotyping by PFGE revealed 60 pulsotypes. Hybridization of a bla(VIM-3)-specific probe following PFGE suggested that the mobile element Tn6001 might have transferred horizontally.<br><br>CONCLUSIONS: Tn6001 and In450 play an important role in the dissemination of CNSPA and XDRPA. The prevalence of these genetic constituents was higher in XDRPA than in non-XDRPA isolates, suggesting that the mobile element Tn6001 might have transferred horizontally.}, }
@article {pmid19772389, year = {2009}, author = {Heuer, OE and Kruse, H and Grave, K and Collignon, P and Karunasagar, I and Angulo, FJ}, title = {Human health consequences of use of antimicrobial agents in aquaculture.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {49}, number = {8}, pages = {1248-1253}, doi = {10.1086/605667}, pmid = {19772389}, issn = {1537-6591}, mesh = {Animals ; Anti-Infective Agents/*therapeutic use ; Aquaculture/*methods ; Bacteria/*drug effects ; Bacterial Infections/microbiology/veterinary ; *Drug Resistance, Bacterial ; Fish Diseases/microbiology ; *Gene Transfer, Horizontal ; Humans ; *Selection, Genetic ; }, abstract = {Intensive use of antimicrobial agents in aquaculture provides a selective pressure creating reservoirs of drug-resistant bacteria and transferable resistance genes in fish pathogens and other bacteria in the aquatic environment. From these reservoirs, resistance genes may disseminate by horizontal gene transfer and reach human pathogens, or drug-resistant pathogens from the aquatic environment may reach humans directly. Horizontal gene transfer may occur in the aquaculture environment, in the food chain, or in the human intestinal tract. Among the antimicrobial agents commonly used in aquaculture, several are classified by the World Health Organisation as critically important for use in humans. Occurrence of resistance to these antimicrobial agents in human pathogens severely limits the therapeutic options in human infections. Considering the rapid growth and importance of aquaculture industry in many regions of the world and the widespread, intensive, and often unregulated use of antimicrobial agents in this area of animal production, efforts are needed to prevent development and spread of antimicrobial resistance in aquaculture to reduce the risk to human health.}, }
@article {pmid19752375, year = {2009}, author = {Deuse, T and Peter, C and Fedak, PW and Doyle, T and Reichenspurner, H and Zimmermann, WH and Eschenhagen, T and Stein, W and Wu, JC and Robbins, RC and Schrepfer, S}, title = {Hepatocyte growth factor or vascular endothelial growth factor gene transfer maximizes mesenchymal stem cell-based myocardial salvage after acute myocardial infarction.}, journal = {Circulation}, volume = {120}, number = {11 Suppl}, pages = {S247-54}, doi = {10.1161/CIRCULATIONAHA.108.843680}, pmid = {19752375}, issn = {1524-4539}, mesh = {Animals ; Cytokines/biosynthesis ; Gene Transfer, Horizontal ; Genetic Therapy ; Hepatocyte Growth Factor/*genetics ; *Mesenchymal Stem Cell Transplantation ; Mice ; Mice, Inbred BALB C ; Myocardial Infarction/*therapy ; Proto-Oncogene Proteins c-akt/physiology ; Vascular Endothelial Growth Factor A/*genetics ; Ventricular Function, Left ; }, abstract = {BACKGROUND: Mesenchymal stem cell (MSC)-based regenerative strategies were investigated to treat acute myocardial infarction and improve left ventricular function.<br><br>METHODS AND RESULTS: Murine AMI was induced by coronary ligation with subsequent injection of MSCs, hepatocyte growth factor (HGF), vascular endothelial growth factor (VEGF), or MSCs +HGF/VEGF into the border zone. Left ventricular ejection fraction was calculated using micro-computed tomography imaging after 6 months. HGF and VEGF protein injection (with or without concomitant MSC injection) significantly and similarly improved the left ventricular ejection fraction and reduced scar size compared with the MSC group, suggesting that myocardial recovery was due to the cytokines rather than myocardial regeneration. To provide sustained paracrine effects, HGF or VEGF overexpressing MSCs were generated (MSC-HGF, MSC-VEGF). MSC-HGF and MSC-VEGF showed significantly increased in vitro proliferation and increased in vivo proliferation within the border zone. Cytokine production correlated with MSC survival. MSC-HGF- and MSC-VEGF-treated animals showed smaller scar sizes, increased peri-infarct vessel densities, and better preserved left ventricular function when compared with MSCs transfected with empty vector. Murine cardiomyocytes were exposed to hypoxic in vitro conditions. The LDH release was reduced, fewer cardiomyocytes were apoptotic, and Akt activity was increased if cardiomyocytes were maintained in conditioned medium obtained from MSC-HGF or MSC-VEGF cultures.<br><br>CONCLUSIONS: This study showed that (1) elevating the tissue levels of HGF and VEGF after acute myocardial infarction seems to be a promising reparative therapeutic approach, (2) HGF and VEGF are cardioprotective by increasing the tolerance of cardiomyocytes to ischemia, reducing cardiomyocyte apoptosis and increasing prosurvival Akt activation, and (3) MSC-HGF and MSC-VEGF are a valuable source for increased cytokine production and maximize the beneficial effect of MSC-based repair strategies.}, }
@article {pmid19769601, year = {2010}, author = {Elhani, D and Bakir, L and Aouni, M and Passet, V and Arlet, G and Brisse, S and Weill, FX}, title = {Molecular epidemiology of extended-spectrum beta-lactamase-producing Klebsiella pneumoniae strains in a university hospital in Tunis, Tunisia, 1999-2005.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {16}, number = {2}, pages = {157-164}, doi = {10.1111/j.1469-0691.2009.03057.x}, pmid = {19769601}, issn = {1469-0691}, mesh = {*Bacterial Typing Techniques ; Cluster Analysis ; Gene Transfer, Horizontal ; Genotype ; Hospitals, University ; Humans ; Klebsiella Infections/*microbiology ; Klebsiella pneumoniae/*classification/*enzymology/isolation &amp; purification ; Molecular Epidemiology ; Plasmids ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Sequence Analysis, DNA ; Tunisia/epidemiology ; beta-Lactamases/*biosynthesis ; }, abstract = {During a period of 6 years and 5 months (January 1999 to May 2005), 103 extended-spectrum beta-lactamase (ESBL)-producing Klebsiella pneumoniae isolates, each from an individual patient or site, were collected at Mongi Slim University Hospital Centre, Tunis, Tunisia. The objectives of our work were the characterization of the bla genes encoding ESBLs, the investigation of clonal diversity of strains, and identification of the transmission modes of the resistance genes. We carried out detection by PCR and sequencing of the bla(SHV), bla(CTX-M) and bla(TEM) genes, transferability studies, plasmid replicon typing, and analysis by multilocus sequence typing (MLST) on selected isolates. Forty-seven isolates were found to be producers of CTX-M-type ESBLs, of which 43 were CTX-M-15, two CTX-M-14 and two CTX-M-27. Fifty-eight isolates were producers of SHV-12, and three were producers of SHV-2a. More than one ESBL was detected in seven isolates, as five produced both CTX-M-15 and SHV-12, and two produced both CTX-M-27 and SHV-12. By a PCR-based replicon typing method, the plasmids carrying the bla(SHV-2a) or bla(CTX-M-15) genes were assigned to IncFII or, more rarely, to IncL/M types. Of 12 plasmids carrying the bla(SHV-12) gene, only one could be typed: it was positive for the HI2 replicon. The MLST results showed large genetic background diversity in the SHV-12-producing isolates and dissemination of specific clones of the CTX-M-15-producing isolates within the same ward and among wards, and suggested endemicity with horizontal dissemination of the bla(CTX-M-15) and the bla(SHV-12) genes.}, }
@article {pmid19769291, year = {2009}, author = {Polukonova, NV and Demin, AG and Miuge, NS and Shaĭkevich, EV}, title = {[Comparison of Chironomus usenicus and Chironomus curabilis with species of the group plumosus (Diptera) inferred from the mitochondrial DNA gene COI and by the polytene chromosomes banding pattern].}, journal = {Genetika}, volume = {45}, number = {8}, pages = {1029-1035}, pmid = {19769291}, issn = {0016-6758}, mesh = {Animals ; Chironomidae/*genetics ; Chromosome Banding ; Chromosomes/*genetics ; DNA, Mitochondrial/*genetics ; *Gene Transfer, Horizontal ; Genes, Insect/*genetics ; *Phylogeny ; }, abstract = {The sequence of a 595-bp fragment of the mitochondrial COI gene was determined for the species Chironomus usenicus and Chironomus curabilis of the genus Chironomus. Phylogenetic reconstructions based on the analysis of the COI gene sequence coincide on the whole with cytogenetic data, permitting Ch. usenicus and Ch. curabilis to be regarded as members of the group plumosus. Chironomus usenicus and Ch. plumosus have identical COI gene sequences. Two hypotheses explaining this identity are considered: inheritance of mtDNA from one of the parental species during hybridogenesis and horizontal transfer of mitochondrial genes.}, }
@article {pmid19763413, year = {2009}, author = {Kim, BK and Park, YD and Oh, HM and Chun, J}, title = {Identification and characterization of metagenomic fragments from tidal flat sediment.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {47}, number = {4}, pages = {402-410}, pmid = {19763413}, issn = {1976-3794}, mesh = {Archaea/classification/genetics/isolation &amp; purification ; Bacteria/classification/genetics/*isolation &amp; purification ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; *Genome, Archaeal ; *Genome, Bacterial ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Phylogenetic surveys based on cultivation-independent methods have revealed that tidal flat sediments are environments with extensive microbial diversity. Since most of prokaryotes in nature cannot be easily cultivated under general laboratory conditions, our knowledge on prokaryotic dwellers in tidal flat sediment is mainly based on the analysis of metagenomes. Microbial community analysis based on the 16S rRNA gene and other phylogenetic markers has been widely used to provide important information on the role of microorganisms, but it is basically an indirect means, compared with direct sequencing of metagenomic DNAs. In this study, we applied a sequence-based metagenomic approach to characterize uncultivated prokaryotes from tidal flat sediment. Two large-insert genomic libraries based on fosmid were constructed from tidal flat metagenomic DNA. A survey based on end-sequencing of selected fosmid clones resulted in the identification of clones containing 274 bacterial and 16 archaeal homologs in which majority were of proteobacterial origins. Two fosmid clones containing large metagenomic DNAs were completely sequenced using the shotgun method. Both DNA inserts contained more than 20 genes encoding putative proteins which implied their ecological roles in tidal flat sediment. Phylogenetic analyses of evolutionary conserved proteins indicate that these clones are not closely related to known prokaryotes whose genome sequence is known, and genes in tidal flat may be subjected to extensive lateral gene transfer, notably between domains Bacteria and Archaea. This is the first report demonstrating that direct sequencing of metagenomic gene library is useful in underpinning the genetic makeup and functional roles of prokaryotes in tidal flat sediments.}, }
@article {pmid19761790, year = {2010}, author = {Claypool, BM and Yoder, SC and Citron, DM and Finegold, SM and Goldstein, EJ and Haake, SK}, title = {Mobilization and prevalence of a Fusobacterial plasmid.}, journal = {Plasmid}, volume = {63}, number = {1}, pages = {11-19}, pmid = {19761790}, issn = {1095-9890}, support = {R01 DE015348/DE/NIDCR NIH HHS/United States ; R01 DE015348-04/DE/NIDCR NIH HHS/United States ; DE015348/DE/NIDCR NIH HHS/United States ; }, mesh = {Base Sequence ; DNA, Bacterial/genetics/metabolism ; Fusobacterium nucleatum/*genetics ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Plasmids/*genetics/*metabolism ; Sequence Analysis, DNA ; }, abstract = {Fusobacterium nucleatum is a Gram-negative anaerobic rod found in dental plaque biofilms, and is an opportunistic pathogen implicated in periodontitis as well as a wide range of systemic abscesses and infections. Genomic analyses of F. nucleatum indicate considerable genetic diversity and a prominent role for horizontal gene transfer in the evolution of the species. Several plasmids isolated from F. nucleatum, including pFN1, harbor relaxase gene homologs that may function in plasmid mobilization. In this investigation we examined the RP4-mediated mobilization properties of pFN1 and the prevalence of pFN1-related sequences in a panel of F. nucleatum clinical isolates. The fusobacterial plasmid pFN1 was mobilized by RP4 at a high frequency. Deletion analyses were used to delineate the core mobilon of pFN1, which consisted of the relaxase gene (rlx), an upstream open reading frame ORF4 and a region of DNA upstream of ORF4 with potential nic sites. To examine the prevalence of pFN1 in a panel of clinical isolates, total DNA isolated from the strains was hybridized with pFN1 replication (repA) and rlx gene probes. DNA from strains harboring plasmids known to be homologous to pFN1 hybridized with both the repA and rlx probes. Five additional strains were rlx-positive but repA-negative, indicating a greater prevalence of rlx-related genes in comparison with repA-related genes. Plasmid or plasmid-related sequences were identified in 11.5% of the strains examined. These findings demonstrate mobilization properties of a fusobacterial plasmid that may be important in horizontal gene transfer.}, }
@article {pmid19759916, year = {2009}, author = {Okamoto, N and Chantangsi, C and Horák, A and Leander, BS and Keeling, PJ}, title = {Molecular phylogeny and description of the novel katablepharid Roombia truncata gen. et sp. nov., and establishment of the Hacrobia taxon nov.}, journal = {PloS one}, volume = {4}, number = {9}, pages = {e7080}, pmid = {19759916}, issn = {1932-6203}, mesh = {Biological Evolution ; Classification ; Cryptophyta/classification ; Eukaryota/*classification/metabolism ; Evolution, Molecular ; Microscopy, Electron, Scanning ; Phagocytosis ; Phylogeny ; Plastids/*classification/metabolism ; }, abstract = {BACKGROUND: Photosynthetic eukaryotes with a secondary plastid of red algal origin (cryptophytes, haptophytes, stramenopiles, dinoflagellates, and apicomplexans) are hypothesized to share a single origin of plastid acquisition according to Chromalveolate hypothesis. Recent phylogenomic analyses suggest that photosynthetic "chromalveolates" form a large clade with inclusion of several non-photosynthetic protist lineages. Katablepharids are one such non-photosynthetic lineage closely related to cryptophytes. Despite their evolutionary and ecological importance, katablepharids are poorly investigated.<br><br>Here, we report a newly discovered flagellate, Roombia truncata gen. et sp. nov., that is related to katablepharids, but is morphologically distinct from othermembers of the group in the following ways: (1) two flagella emerge from a papilla-like subapical protrusion, (2) conspicuous ejectisomes are aligned in multiple (5-11) rows, (3) each ejectisome increases in size towards the posterior end of the rows, and (4) upon feeding, a part of cytoplasm elastically stretch to engulf whole prey cell. Molecular phylogenies inferred from Hsp90, SSU rDNA, and LSU rDNA sequences consistently and strongly show R. truncata as the sister lineage to all other katablepharids, including lineages known only from environmental sequence surveys. A close association between katablepharids and cryptophytes was also recovered in most analyses. Katablepharids and cryptophytes are together part of a larger, more inclusive, group that also contains haptophytes, telonemids, centrohelids and perhaps biliphytes. The monophyly of this group is supported by several different molecular phylogenetic datasets and one shared lateral gene transfer; therefore, we formally establish this diverse clade as the "Hacrobia."<br><br>CONCLUSIONS/SIGNIFICANCE: Our discovery of R. truncata not only expands our knowledge in the less studied flagellate group, but provide a better understanding of phylogenetic relationship and evolutionary view of plastid acquisition/losses of Hacrobia. Being an ancestral to all katablepharids, and readily cultivable, R. truncata is a good candidate for multiple gene analyses that will contribute to future phylogenetic studies of Hacrobia.}, }
@article {pmid19759494, year = {2009}, author = {Sabra, AH and Araj, GF and Kattar, MM and Abi-Rached, RY and Khairallah, MT and Klena, JD and Matar, GM}, title = {Molecular characterization of ESBL-producing Shigella sonnei isolates from patients with bacilliary dysentery in Lebanon.}, journal = {Journal of infection in developing countries}, volume = {3}, number = {4}, pages = {300-305}, doi = {10.3855/jidc.128}, pmid = {19759494}, issn = {1972-2680}, mesh = {Adult ; Bacterial Proteins/biosynthesis/genetics ; Bacterial Typing Techniques ; Child ; Child, Preschool ; Cluster Analysis ; Conjugation, Genetic ; DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; Dysentery, Bacillary/*microbiology ; Female ; Gene Transfer, Horizontal ; Genotype ; Humans ; Infant ; Lebanon ; Male ; Microbial Sensitivity Tests/methods ; Plasmids ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Shigella sonnei/*enzymology/*isolation &amp; purification ; Young Adult ; beta-Lactamases/*biosynthesis/genetics ; }, abstract = {BACKGROUND: Emergence of extended-spectrum beta-lactamases (ESBLs) in Shigella species imparting resistance to third-generation cephalosporins is a growing concern worldwide. The aim of this study is to molecularly characterize the newly emerging beta-lactam resistant Shigella sonnei, specifically ESBLs in Lebanon, and compare them to beta-lactam sensitive isolates.<br><br>METHODOLOGY: We compared five beta-lactam-resistant S. sonnei isolates to six isolates susceptible to beta-lactams. Presence of ESBLs was established by the combination disk method. PCR amplification and sequence analysis of the beta-lactamase-encoding genes, along with other antimicrobial resistance genes, were performed. The localization of beta-lactamase genes was established by conjugation experiments. Beta-lactamase gene transcription levels were determined by real-time RT-PCR. Molecular typing was performed by pulsed-field gel electrophoresis (PFGE).<br><br>RESULTS: Four of five beta-lactam resistant isolates were extended spectrum beta-lactamase producers. These harbored the bla-CTX-M-15 gene borne on a 70 Kb plasmid and class 2 integron genes on their chromosomes. The bla-CTX-M-15 gene was flanked by an insertion element ISEcp1. A chromosomal bla-TEM-1 gene was detected in one beta-lactam resistant Shigella isolate and two of the ESBL producing isolates. The bla-CTX-M-15 gene transcription levels were increased in EBSL isolates exposed to subinhibitory concentrations of ceftazidime. PFGE analysis revealed that the four bla-CTX-M-15 positive isolates were nonclonal but two of them shared genotypes with -lactam susceptible isolates.<br><br>CONCLUSION: Dissemination of broad-spectrum beta-lactam resistance in Shigella sonnei is mediated by bla-CTX-M-15 through horizontal plasmid transfer rather than by clonal spread of the resistant isolates. Expression of this gene is further induced in the presence of ceftazidime.}, }
@article {pmid19758436, year = {2009}, author = {Rawlings, ND and Bateman, A}, title = {Pepsin homologues in bacteria.}, journal = {BMC genomics}, volume = {10}, number = {}, pages = {437}, pmid = {19758436}, issn = {1471-2164}, support = {/WT_/Wellcome Trust/United Kingdom ; 087656/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Sequence ; Bacterial Proteins/*genetics ; *Evolution, Molecular ; Genome, Bacterial ; Humans ; Molecular Sequence Data ; Pepsin A/*genetics ; Phylogeny ; Proteobacteria/enzymology/*genetics ; Sequence Alignment ; }, abstract = {BACKGROUND: Peptidase family A1, to which pepsin belongs, had been assumed to be restricted to eukaryotes. The tertiary structure of pepsin shows two lobes with similar folds and it has been suggested that the gene has arisen from an ancient duplication and fusion event. The only sequence similarity between the lobes is restricted to the motif around the active site aspartate and a hydrophobic-hydrophobic-Gly motif. Together, these contribute to an essential structural feature known as a psi-loop. There is one such psi-loop in each lobe, and so each lobe presents an active Asp. The human immunodeficiency virus peptidase, retropepsin, from peptidase family A2 also has a similar fold but consists of one lobe only and has to dimerize to be active. All known members of family A1 show the bilobed structure, but it is unclear if the ancestor of family A1 was similar to an A2 peptidase, or if the ancestral retropepsin was derived from a half-pepsin gene. The presence of a pepsin homologue in a prokaryote might give insights into the evolution of the pepsin family.<br><br>RESULTS: Homologues of the aspartic peptidase pepsin have been found in the completed genomic sequences from seven species of bacteria. The bacterial homologues, unlike those from eukaryotes, do not possess signal peptides, and would therefore be intracellular acting at neutral pH. The bacterial homologues have Thr218 replaced by Asp, a change which in renin has been shown to confer activity at neutral pH. No pepsin homologues could be detected in any archaean genome.<br><br>CONCLUSION: The peptidase family A1 is found in some species of bacteria as well as eukaryotes. The bacterial homologues fall into two groups, one from oceanic bacteria and one from plant symbionts. The bacterial homologues are all predicted to be intracellular proteins, unlike the eukaryotic enzymes. The bacterial homologues are bilobed like pepsin, implying that if no horizontal gene transfer has occurred the duplication and fusion event might be very ancient indeed, preceding the divergence of bacteria and eukaryotes. It is unclear whether all the bacterial homologues are derived from horizontal gene transfer, but those from the plant symbionts probably are. The homologues from oceanic bacteria are most closely related to memapsins (or BACE-1 and BACE-2), but are so divergent that they are close to the root of the phylogenetic tree and to the division of the A1 family into two subfamilies.}, }
@article {pmid19756785, year = {2010}, author = {Hsieh, YC and Lee, WS and Ou, TY and Hsueh, PR}, title = {Clonal spread of CC17 vancomycin-resistant Enterococcus faecium with multilocus sequence type 78 (ST78) and a novel ST444 in Taiwan.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {29}, number = {1}, pages = {25-30}, pmid = {19756785}, issn = {1435-4373}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics ; *Bacterial Typing Techniques ; Carbon-Oxygen Ligases/genetics ; Cluster Analysis ; Conjugation, Genetic ; Cross Infection/epidemiology/microbiology/pathology ; DNA Fingerprinting ; DNA Transposable Elements ; Enterococcus faecium/*classification/*drug effects/genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; Genotype ; Gram-Positive Bacterial Infections/*epidemiology/*microbiology/pathology ; Hospitals, University ; Humans ; Microbial Sensitivity Tests ; Molecular Epidemiology ; Sequence Analysis, DNA ; Taiwan/epidemiology ; *Vancomycin Resistance ; }, abstract = {From May 2007 to January 2008, 30 isolates of vancomycin-resistant enterococci (VRE), including 29 Enterococcus faecium (96.7%) and 1 E. faecalis (3.3%) were obtained from various clinical specimens of 30 patients treated at a university hospital in Taiwan. Among these patients, 27 had VRE infections, including urinary tract infection (n = 16), bacteremia (n = 5), wound infection (n = 5), and central nervous system infection (n = 1). Three patients had VRE colonization. All of these isolates belonged to the vanA genotype with vancomycin minimum inhibitory concentrations of 64>or=128 microg/ml. The isolate of E. faecalis had VanB phenotype-vanA genotype. All these isolates were susceptible to linezolid and were inhibited by tigecycline at 0.25 microg/ml. Multilocus sequence typing (MLST) analysis of the E. faecium isolates showed that 82.8% were ST78, which belongs to lineage C1. Transposon typing classified the 30 isolates of VRE into three types and most of the Tn1546-like elements contained an IS1251-like insertion sequence. Mating experiments showed that the vanA gene clusters were transferable at a frequency of about 10(-6) to 10(-7). Our findings indicate that nosocomial spread of VRE resulted from dissemination of lineage C1 E. faecium clones, including a novel E. faecium MLST type (ST444), and the horizontal transfer of Tn1546 elements among enterococci.}, }
@article {pmid19749978, year = {2009}, author = {Than, C and Nakhleh, L}, title = {Species tree inference by minimizing deep coalescences.}, journal = {PLoS computational biology}, volume = {5}, number = {9}, pages = {e1000501}, pmid = {19749978}, issn = {1553-7358}, support = {R01 LM009494/LM/NLM NIH HHS/United States ; R01LM009494/LM/NLM NIH HHS/United States ; }, mesh = {Animals ; Apicomplexa/classification/genetics ; Cluster Analysis ; Computational Biology/*methods ; Databases, Genetic ; *Genetic Speciation ; *Models, Genetic ; *Phylogeny ; Yeasts/classification/genetics ; }, abstract = {In a 1997 seminal paper, W. Maddison proposed minimizing deep coalescences, or MDC, as an optimization criterion for inferring the species tree from a set of incongruent gene trees, assuming the incongruence is exclusively due to lineage sorting. In a subsequent paper, Maddison and Knowles provided and implemented a search heuristic for optimizing the MDC criterion, given a set of gene trees. However, the heuristic is not guaranteed to compute optimal solutions, and its hill-climbing search makes it slow in practice. In this paper, we provide two exact solutions to the problem of inferring the species tree from a set of gene trees under the MDC criterion. In other words, our solutions are guaranteed to find the tree that minimizes the total number of deep coalescences from a set of gene trees. One solution is based on a novel integer linear programming (ILP) formulation, and another is based on a simple dynamic programming (DP) approach. Powerful ILP solvers, such as CPLEX, make the first solution appealing, particularly for very large-scale instances of the problem, whereas the DP-based solution eliminates dependence on proprietary tools, and its simplicity makes it easy to integrate with other genomic events that may cause gene tree incongruence. Using the exact solutions, we analyze a data set of 106 loci from eight yeast species, a data set of 268 loci from eight Apicomplexan species, and several simulated data sets. We show that the MDC criterion provides very accurate estimates of the species tree topologies, and that our solutions are very fast, thus allowing for the accurate analysis of genome-scale data sets. Further, the efficiency of the solutions allow for quick exploration of sub-optimal solutions, which is important for a parsimony-based criterion such as MDC, as we show. We show that searching for the species tree in the compatibility graph of the clusters induced by the gene trees may be sufficient in practice, a finding that helps ameliorate the computational requirements of optimization solutions. Further, we study the statistical consistency and convergence rate of the MDC criterion, as well as its optimality in inferring the species tree. Finally, we show how our solutions can be used to identify potential horizontal gene transfer events that may have caused some of the incongruence in the data, thus augmenting Maddison's original framework. We have implemented our solutions in the PhyloNet software package, which is freely available at: http://bioinfo.cs.rice.edu/phylonet.}, }
@article {pmid19749175, year = {2009}, author = {Akagi, Y and Akamatsu, H and Otani, H and Kodama, M}, title = {Horizontal chromosome transfer, a mechanism for the evolution and differentiation of a plant-pathogenic fungus.}, journal = {Eukaryotic cell}, volume = {8}, number = {11}, pages = {1732-1738}, pmid = {19749175}, issn = {1535-9786}, mesh = {Alternaria/classification/enzymology/*genetics/pathogenicity ; Chromosomes, Fungal/*genetics ; *Evolution, Molecular ; Fungal Proteins/genetics/metabolism ; *Gene Transfer, Horizontal ; Solanum lycopersicum/*microbiology ; Molecular Sequence Data ; Phylogeny ; Plant Diseases/*microbiology ; Polyketide Synthases/genetics/metabolism ; Sphingosine/metabolism ; }, abstract = {The tomato pathotype of Alternaria alternata produces host-specific AAL toxin and causes Alternaria stem canker on tomato. A polyketide synthetase (PKS) gene, ALT1, which is involved in AAL toxin biosynthesis, resides on a 1.0-Mb conditionally dispensable chromosome (CDC) found only in the pathogenic and AAL toxin-producing strains. Genomic sequences of ALT1 and another PKS gene, both of which reside on the CDC in the tomato pathotype strains, were compared to those of tomato pathotype strains collected worldwide. This revealed that the sequences of both CDC genes were identical among five A. alternata tomato pathotype strains having different geographical origins. On the other hand, the sequences of other genes located on chromosomes other than the CDC are not identical in each strain, indicating that the origin of the CDC might be different from that of other chromosomes in the tomato pathotype. Telomere fingerprinting and restriction fragment length polymorphism analyses of the A. alternata strains also indicated that the CDCs in the tomato pathotype strains were identical, although the genetic backgrounds of the strains differed. A hybrid strain between two different pathotypes was shown to harbor the CDCs derived from both parental strains with an expanded range of pathogenicity, indicating that CDCs can be transmitted from one strain to another and stably maintained in the new genome. We propose a hypothesis whereby the ability to produce AAL toxin and to infect a plant could potentially be distributed among A. alternata strains by horizontal transfer of an entire pathogenicity chromosome. This could provide a possible mechanism by which new pathogens arise in nature.}, }
@article {pmid19749048, year = {2009}, author = {Pereira, CS and de Regt, AK and Brito, PH and Miller, ST and Xavier, KB}, title = {Identification of functional LsrB-like autoinducer-2 receptors.}, journal = {Journal of bacteriology}, volume = {191}, number = {22}, pages = {6975-6987}, pmid = {19749048}, issn = {1098-5530}, support = {R15 AI074041/AI/NIAID NIH HHS/United States ; AI074041/AI/NIAID NIH HHS/United States ; }, mesh = {Agrobacterium tumefaciens/genetics/metabolism ; Bacillaceae/genetics/metabolism ; Bacterial Proteins/chemistry/classification/genetics/*metabolism ; Binding Sites ; Enterobacteriaceae/genetics/metabolism ; Escherichia coli/genetics/metabolism ; Genome, Bacterial/genetics/physiology ; Phylogeny ; Protein Binding ; Receptors, Cell Surface/chemistry/classification/genetics/*metabolism ; Rhizobiaceae/genetics/metabolism ; Rhizobium leguminosarum/genetics/metabolism ; Salmonella typhimurium/genetics/metabolism ; Structure-Activity Relationship ; }, abstract = {Although a variety of bacterial species have been reported to use the interspecies communication signal autoinducer-2 (AI-2) to regulate multiple behaviors, the molecular mechanisms of AI-2 recognition and signal transduction remain poorly understood. To date, two types of AI-2 receptors have been identified: LuxP, present in Vibrio spp., and LsrB, first identified in Salmonella enterica serovar Typhimurium. In S. Typhimurium, LsrB is the ligand binding protein of a transport system that enables the internalization of AI-2. Here, using both sequence analysis and structure prediction, we establish a set of criteria for identifying functional AI-2 receptors. We test our predictions experimentally, assaying key species for their abilities to import AI-2 in vivo, and test their LsrB orthologs for AI-2 binding in vitro. Using these experimental approaches, we were able to identify AI-2 receptors in organisms belonging to phylogenetically distinct families such as the Enterobacteriaceae, Rhizobiaceae, and Bacillaceae. Phylogenetic analysis of LsrB orthologs indicates that this pattern could result from one single origin of the functional LsrB gene in a gammaproteobacterium, suggesting possible posterior independent events of lateral gene transfer to the Alphaproteobacteria and Firmicutes. Finally, we used mutagenesis to show that two AI-2-interacting residues are essential for the AI-2 binding ability. These two residues are conserved in the binding sites of all the functional AI-2 binding proteins but not in the non-AI-2-binding orthologs. Together, these results strongly support our ability to identify functional LsrB-type AI-2 receptors, an important step in investigations of this interspecies signal.}, }
@article {pmid19748427, year = {2009}, author = {Chen, LR and Zhou, HW and Cai, JC and Zhang, R and Chen, GX}, title = {Combination of IMP-4 metallo-beta-lactamase production and porin deficiency causes carbapenem resistance in a Klebsiella oxytoca clinical isolate.}, journal = {Diagnostic microbiology and infectious disease}, volume = {65}, number = {2}, pages = {163-167}, doi = {10.1016/j.diagmicrobio.2009.07.002}, pmid = {19748427}, issn = {1879-0070}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/analysis ; Carbapenems/*pharmacology ; China ; Conjugation, Genetic ; Electrophoresis, Polyacrylamide Gel ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Hospitals ; Humans ; Isoelectric Focusing ; Klebsiella Infections/microbiology ; Klebsiella oxytoca/*drug effects/enzymology/genetics/isolation &amp; purification ; Microbial Sensitivity Tests ; Plasmids/analysis ; Porins/*deficiency ; Sequence Analysis, DNA ; *beta-Lactam Resistance ; beta-Lactamases/chemistry/genetics/*metabolism ; }, abstract = {This study shows for the first time the mechanism of carbapenem resistance of a Klebsiella oxytoca clinical isolate ZC101 recovered from a Zhejiang University Hospital in Hangzhou, China. MIC values of imipenem, meropenem, and ertapenem for K. oxytoca ZC101 were 16, 16, and 128 microg/mL, respectively. Conjugation experiments demonstrated the transferability of a resistance determinant from K. oxytoca ZC101 to Escherichia coli EC600. Results from isoelectric focusing, polymerase chain reactions, and DNA sequencing confirmed that K. oxytoca ZC101 produced IMP-4 metallo-beta-lactamase (MBL) and CTX-M-14 extended-spectrum beta-lactamase, whereas E. coli transconjugant only produced the IMP-4. Amplification of integron revealed that bla(IMP-4) gene is located within a class I integron that was carried in a plasmid approximately 55 kb in size. Sodium dodecyl sulfate polyacrylamide gel electrophoresis profiling of outer membrane proteins of K. oxytoca ZC101 indicated lack of expression of the OmpK36 porin. DNA sequence analysis of ompK36 gene of K. oxytoca ZC101 showed the gene was disrupted by an insertion sequence IS5. In all, the results show that plasmid-mediated IMP-4 MBL production combined with the loss of OmpK36 porin caused the resistance in K. oxytoca ZC101 to carbapenems.}, }
@article {pmid19747963, year = {2010}, author = {Novick, P and Smith, J and Ray, D and Boissinot, S}, title = {Independent and parallel lateral transfer of DNA transposons in tetrapod genomes.}, journal = {Gene}, volume = {449}, number = {1-2}, pages = {85-94}, doi = {10.1016/j.gene.2009.08.017}, pmid = {19747963}, issn = {1879-0038}, mesh = {Animals ; Base Sequence ; DNA/*genetics ; DNA Primers ; *DNA Transposable Elements ; Gene Transfer, Horizontal ; *Genome ; }, abstract = {In animals, the mode of transmission of transposable elements is generally vertical. However, recent studies have suggested that lateral transfer has occurred repeatedly in several distantly related tetrapod lineages, including mammals. Using transposons extracted from the genome of the lizard Anolis carolinensis as probes, we identified four novel families of hAT transposons that share extremely high similarity with elements in other genomes including several mammalian lineages (primates, chiropters, marsupials), one amphibian and one flatworm, the planarian Schmidtea mediterranea. The discontinuous phylogenetic distribution of these hAT families, coupled with very low synonymous divergence between species, strongly suggests that these elements were laterally transferred to these different species. This indicates that the horizontal transfer of DNA transposons in vertebrates might be more common than previously thought. Yet, it appears that the transfer of DNA transposons did not occur randomly as the same genomes have been invaded independently by different, unrelated transposon families whereas others seem to be immune to lateral transfer. This suggests that some organisms might be intrinsically more vulnerable to DNA transposon lateral transfer, possibly because of a weakened defense against transposons or because they have developed mechanisms to tolerate their impact.}, }
@article {pmid19747924, year = {2010}, author = {Gehring, R and Schumm, P and Youssef, M and Scoglio, C}, title = {A network-based approach for resistance transmission in bacterial populations.}, journal = {Journal of theoretical biology}, volume = {262}, number = {1}, pages = {97-106}, doi = {10.1016/j.jtbi.2009.09.002}, pmid = {19747924}, issn = {1095-8541}, mesh = {Anti-Bacterial Agents/administration &amp; dosage/pharmacology ; Bacteria/drug effects/*genetics ; Computer Simulation ; Dose-Response Relationship, Drug ; Drug Resistance, Bacterial/drug effects/*genetics/physiology ; Gene Transfer, Horizontal/physiology ; Genes, MDR/genetics ; Microbial Interactions/*drug effects/genetics/physiology ; Microbial Sensitivity Tests ; Models, Biological ; Models, Theoretical ; Transduction, Genetic ; }, abstract = {Horizontal transfer of mobile genetic elements (conjugation) is an important mechanism whereby resistance is spread through bacterial populations. The aim of our work is to develop a mathematical model that quantitatively describes this process, and to use this model to optimize antimicrobial dosage regimens to minimize resistance development. The bacterial population is conceptualized as a compartmental mathematical model to describe changes in susceptible, resistant, and transconjugant bacteria over time. This model is combined with a compartmental pharmacokinetic model to explore the effect of different plasma drug concentration profiles. An agent-based simulation tool is used to account for resistance transfer occurring when two bacteria are adjacent or in close proximity. In addition, a non-linear programming optimal control problem is introduced to minimize bacterial populations as well as the drug dose. Simulation and optimization results suggest that the rapid death of susceptible individuals in the population is pivotal in minimizing the number of transconjugants in a population. This supports the use of potent antimicrobials that rapidly kill susceptible individuals and development of dosage regimens that maintain effective antimicrobial drug concentrations for as long as needed to kill off the susceptible population. Suggestions are made for experiments to test the hypotheses generated by these simulations.}, }
@article {pmid19747826, year = {2009}, author = {Lovell, HC and Mansfield, JW and Godfrey, SA and Jackson, RW and Hancock, JT and Arnold, DL}, title = {Bacterial evolution by genomic island transfer occurs via DNA transformation in planta.}, journal = {Current biology : CB}, volume = {19}, number = {18}, pages = {1586-1590}, doi = {10.1016/j.cub.2009.08.018}, pmid = {19747826}, issn = {1879-0445}, support = {BB/E001998/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/E0011998/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Base Sequence ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Molecular Sequence Data ; Phaseolus/*microbiology ; Pseudomonas syringae/*genetics ; Sequence Alignment ; *Transformation, Bacterial ; Virulence Factors/*genetics ; }, abstract = {Our understanding of the evolution of microbial pathogens has been advanced by the discovery of "islands" of DNA that differ from core genomes and contain determinants of virulence. The acquisition of genomic islands (GIs) by horizontal gene transfer (HGT) is thought to have played a major role in microbial evolution. There are, however, few practical demonstrations of the acquisition of genes that control virulence, and, significantly, all have been achieved outside the animal or plant host. Loss of a GI from the bean pathogen Pseudomonas syringae pv. phaseolicola (Pph) is driven by exposure to the stress imposed by the plant's resistance response. Here, we show that the complete episomal island, which carries pathogenicity genes including the effector avrPphB, transfers between strains of Pph by transformation in planta and inserts at a specific att site in the genome of the recipient. Our results show that the evolution of bacterial pathogens by HGT may be achieved via transformation, the simplest mechanism of DNA exchange. This process is activated by exposure to plant defenses, when the pathogen is in greatest need of acquiring new genetic traits to alleviate the antimicrobial stress imposed by plant innate immunity.}, }
@article {pmid19747541, year = {2010}, author = {Mann, S and Chen, YP}, title = {Bacterial genomic G+C composition-eliciting environmental adaptation.}, journal = {Genomics}, volume = {95}, number = {1}, pages = {7-15}, doi = {10.1016/j.ygeno.2009.09.002}, pmid = {19747541}, issn = {1089-8646}, mesh = {*Adaptation, Biological ; Base Composition ; Computational Biology ; DNA Replication ; DNA, Bacterial/*genetics ; *Environment ; Gene Transfer, Horizontal ; *Genome, Bacterial ; }, abstract = {Bacterial genomes reflect their adaptation strategies through nucleotide usage trends found in their chromosome composition. Bacteria, unlike eukaryotes contain a wide range of genomic G+C. This wide variability may be viewed as a response to environmental adaptation. Two overarching trends are observed across bacterial genomes, the first, correlates genomic G+C to environmental niches and lifestyle, while the other utilizees intra-genomic G+C incongruence to delineate horizontally transferred material. In this review, we focus on the influence of several properties including biochemical, genetic flows, selection biases, and the biochemical-energetic properties shaping genome composition. Outcomes indicate a trend toward high G+C and larger genomes in free-living organisms, as a result of more complex and varied environments (higher chance for horizontal gene transfer). Conversely, nutrient limiting and nutrient poor environments dictate smaller genomes of low GC in attempts to conserve replication expense. Varied processes including translesion repair mechanisms, phage insertion and cytosine degradation has been shown to introduce higher AT in genomic sequences. We conclude the review with an analysis of current bioinformatics tools seeking to elicit compositional variances and highlight the practical implications when using such techniques.}, }
@article {pmid19744990, year = {2009}, author = {Shu, HY and Fung, CP and Liu, YM and Wu, KM and Chen, YT and Li, LH and Liu, TT and Kirby, R and Tsai, SF}, title = {Genetic diversity of capsular polysaccharide biosynthesis in Klebsiella pneumoniae clinical isolates.}, journal = {Microbiology (Reading, England)}, volume = {155}, number = {Pt 12}, pages = {4170-4183}, doi = {10.1099/mic.0.029017-0}, pmid = {19744990}, issn = {1465-2080}, mesh = {Bacterial Capsules/*biosynthesis/*genetics ; Base Sequence ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Variation ; Humans ; Klebsiella Infections/*microbiology ; Klebsiella pneumoniae/classification/*genetics/isolation &amp; purification/metabolism ; Molecular Sequence Data ; Multigene Family ; Recombination, Genetic ; Species Specificity ; }, abstract = {Klebsiella pneumoniae is an enteric pathogen causing community-acquired and hospital-acquired infections in humans. Epidemiological studies have revealed significant diversity in capsular polysaccharide (CPS) type and clinical manifestation of K. pneumoniae infection in different geographical areas of the world. We have sequenced the capsular polysaccharide synthesis (cps) region of seven clinical isolates and compared the sequences with the publicly available cps sequence data of five strains: NTUH-K2044 (K1 serotype), Chedid (K2 serotype), MGH78578 (K52 serotype), A1142 (K57 serotype) and A1517. Among all strains, six genes at the 5' end of the cps clusters that encode proteins for CPS transportation and processing at the bacterial surface are highly similar to each other. The central region of the cps gene clusters, which encodes proteins for polymerization and assembly of the CPS subunits, is highly divergent. Based on the collected sequence, we found that either the wbaP gene or the wcaJ gene exists in a given K. pneumoniae strain, suggesting that there is a major difference in the CPS biosynthesis pathway and that the K. pneumoniae strains can be classified into at least two distinct groups. All isolates contain gnd, encoding gluconate-6-phosphate dehydrogenase, at the 3' end of the cps gene clusters. The rmlBADC genes were found in CPS K9-positive, K14-positive and K52-positive strains, while manC and manB were found in K1, K2, K5, K14, K62 and two undefined strains. Our data indicate that, while overall genomic organization is similar between different pathogenic K. pneumoniae strains, the genetic variation of the sugar moiety and polysaccharide linkage generate the diversity in CPS molecules that could help evade host immune attack.}, }
@article {pmid19743926, year = {2009}, author = {Poole, TL and Edrington, TS and Brichta-Harhay, DM and Carattoli, A and Anderson, RC and Nisbet, DJ}, title = {Conjugative transferability of the A/C plasmids from Salmonella enterica isolates that possess or lack bla(CMY) in the A/C plasmid backbone.}, journal = {Foodborne pathogens and disease}, volume = {6}, number = {10}, pages = {1185-1194}, doi = {10.1089/fpd.2009.0316}, pmid = {19743926}, issn = {1556-7125}, mesh = {Animals ; Cattle ; *Conjugation, Genetic ; Escherichia coli/genetics ; Feces/microbiology ; Female ; *Gene Transfer, Horizontal ; Genes, MDR ; Genotype ; Male ; Microbial Sensitivity Tests ; Phenotype ; Plasmids/chemistry/*genetics ; Polymerase Chain Reaction ; Replicon/genetics ; Salmonella enterica/drug effects/*genetics/isolation &amp; purification/physiology ; Skin/microbiology ; beta-Lactam Resistance/genetics ; beta-Lactamases/*genetics ; }, abstract = {The objective of this study was to understand the conjugative transmissibility of resistance plasmids present in 205 Salmonella enterica isolates from bovine sources. Polymerase chain reaction (PCR)-based replicon typing was used to type plasmid replicons. Conjugation experiments were preformed in triplicate at 30 degrees C and 37 degrees C on solid medium. PCR mapping of the A/C transfer gene operon was done on 17 Salmonella Newport isolates that were only positive for A/C. Eighty-six percent (n = 177) of the Salmonella isolates were multidrug resistant (MDR) with resistance to 3-12 antimicrobial agents. Of these, 82% (n = 146) were resistant to extended-spectrum cephalosporins and possessed a bla(CMY) gene. A/C was the predominant replicon detected, present in 90% (n = 160) of the MDR isolates. Twenty-three percent (n = 37) of the A/C-positive strains were positive for a second replicon. Replicons coresident with A/C included I1, N, B/O, HI1, and HI2. Only 31% (n = 54) of the MDR isolates produced transconjugants, and most of these donors carried multiple replicons. A/C cotransferred with B/O, N, and I1 at both 30 degrees C and 37 degrees C and with HI2 at 30 degrees C. Seven Salmonella Newport isolates that produced transconjugants possessed only the single A/C replicon and lacked bla(CMY). PCR mapping of the A/C transfer gene operon in ten Salmonella Newport isolates that carried bla(CMY) revealed a bla(CMY) inverted repeat element integrated between the traA and traC genes. These results suggest that A/C may have been a conjugative plasmid before the integration of bla(CMY) into the transfer gene operon. Additionally, transfer deficient A/C replicons may be mobilized in the presence of certain compatible conjugative plasmids.}, }
@article {pmid19741736, year = {2010}, author = {Bolhuis, H and Severin, I and Confurius-Guns, V and Wollenzien, UI and Stal, LJ}, title = {Horizontal transfer of the nitrogen fixation gene cluster in the cyanobacterium Microcoleus chthonoplastes.}, journal = {The ISME journal}, volume = {4}, number = {1}, pages = {121-130}, doi = {10.1038/ismej.2009.99}, pmid = {19741736}, issn = {1751-7370}, mesh = {Bacterial Proteins/genetics ; Cluster Analysis ; Cyanobacteria/*genetics ; DNA, Bacterial/chemistry/genetics ; Desulfovibrio/genetics ; Gene Order ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Molecular Sequence Data ; *Multigene Family ; Nitrogen Fixation/*genetics ; Oxidoreductases/genetics ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology ; Synteny ; }, abstract = {The filamentous, non-heterocystous cyanobacterium Microcoleus chthonoplastes is a cosmopolitan organism, known to build microbial mats in a variety of different environments. Although most of these cyanobacterial mats are known for their capacity to fix dinitrogen, M. chthonoplastes has not been assigned as a diazotrophic organism. None of the strains that were correctly identified as M. chthonoplastes has been shown to fix dinitrogen and it has repeatedly been reported that these organisms lacked the cyanobacterial nifH, the structural gene for dinitrogenase reductase. In this study, we show that a complete nif-gene cluster is present in the genome of M. chthonoplastes PCC 7420 and that the three structural nitrogenase genes, nifHDK, are present in a collection of axenic strains of M. chthonoplastes from distant locations. Phylogenetic analysis of nifHDK revealed that they cluster with the Deltaproteobacteria and that they are closely related to Desulfovibrio. The nif operon is flanked by typical cyanobacterial genes, suggesting that it is an integral part of the M. chthonoplastes genome. In this study, we provide evidence that the nif operon of M. chthonoplastes is acquired through horizontal gene transfer. Moreover, the presence of the same nif-cluster in M. chthonoplastes isolates derived from various sites around the world suggests that this horizontal gene transfer event must have occurred early in the evolution of M. chthonoplastes. We have been unable to express nitrogenase in cultures of M. chthonoplastes, but we show that these genes were expressed under natural conditions in the field.}, }
@article {pmid19741735, year = {2010}, author = {Wagner-Döbler, I and Ballhausen, B and Berger, M and Brinkhoff, T and Buchholz, I and Bunk, B and Cypionka, H and Daniel, R and Drepper, T and Gerdts, G and Hahnke, S and Han, C and Jahn, D and Kalhoefer, D and Kiss, H and Klenk, HP and Kyrpides, N and Liebl, W and Liesegang, H and Meincke, L and Pati, A and Petersen, J and Piekarski, T and Pommerenke, C and Pradella, S and Pukall, R and Rabus, R and Stackebrandt, E and Thole, S and Thompson, L and Tielen, P and Tomasch, J and von Jan, M and Wanphrut, N and Wichels, A and Zech, H and Simon, M}, title = {The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea.}, journal = {The ISME journal}, volume = {4}, number = {1}, pages = {61-77}, doi = {10.1038/ismej.2009.94}, pmid = {19741735}, issn = {1751-7370}, mesh = {Aerobiosis ; Anaerobiosis ; Biosynthetic Pathways/genetics ; DNA, Bacterial/*chemistry/*genetics ; Dimethyl Sulfoxide/metabolism ; Eukaryota/growth &amp; development/microbiology ; *Genome, Bacterial ; Molecular Sequence Data ; Nitrates/metabolism ; Plasmids ; Rhodobacteraceae/*genetics/isolation &amp; purification/physiology ; *Sequence Analysis, DNA ; Sequence Homology ; *Symbiosis ; Synteny ; Thiamine/biosynthesis ; Vitamin B 12/biosynthesis ; }, abstract = {Dinoroseobacter shibae DFL12(T), a member of the globally important marine Roseobacter clade, comprises symbionts of cosmopolitan marine microalgae, including toxic dinoflagellates. Its annotated 4 417 868 bp genome sequence revealed a possible advantage of this symbiosis for the algal host. D. shibae DFL12(T) is able to synthesize the vitamins B(1) and B(12) for which its host is auxotrophic. Two pathways for the de novo synthesis of vitamin B(12) are present, one requiring oxygen and the other an oxygen-independent pathway. The de novo synthesis of vitamin B(12) was confirmed to be functional, and D. shibae DFL12(T) was shown to provide the growth-limiting vitamins B(1) and B(12) to its dinoflagellate host. The Roseobacter clade has been considered to comprise obligate aerobic bacteria. However, D. shibae DFL12(T) is able to grow anaerobically using the alternative electron acceptors nitrate and dimethylsulfoxide; it has the arginine deiminase survival fermentation pathway and a complex oxygen-dependent Fnr (fumarate and nitrate reduction) regulon. Many of these traits are shared with other members of the Roseobacter clade. D. shibae DFL12(T) has five plasmids, showing examples for vertical recruitment of chromosomal genes (thiC) and horizontal gene transfer (cox genes, gene cluster of 47 kb) possibly by conjugation (vir gene cluster). The long-range (80%) synteny between two sister plasmids provides insights into the emergence of novel plasmids. D. shibae DFL12(T) shows the most complex viral defense system of all Rhodobacterales sequenced to date.}, }
@article {pmid19735561, year = {2009}, author = {Carrolo, M and Pinto, FR and Melo-Cristino, J and Ramirez, M}, title = {Pherotypes are driving genetic differentiation within Streptococcus pneumoniae.}, journal = {BMC microbiology}, volume = {9}, number = {}, pages = {191}, pmid = {19735561}, issn = {1471-2180}, mesh = {Bacterial Typing Techniques ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; *Evolution, Molecular ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; *Genetics, Population ; Models, Genetic ; Quorum Sensing/genetics ; Streptococcus pneumoniae/classification/*genetics ; }, abstract = {BACKGROUND: The boundaries of bacterial species and the mechanisms underlying bacterial speciation are matters of intense debate. Theoretical studies have shown that recombination acts as a strong cohesive force preventing divergence in bacterial populations. Streptococcus pneumoniae populations have the telltale signs of high recombination with competence implicated as the major driving force behind gene exchange. Competence in S. pneumoniae is triggered by a quorum-sensing mechanism controlled by the competence-stimulating peptide pheromone.<br><br>RESULTS: We studied the distribution of the two major pherotypes in the pneumococcal population and their association with serotype, antimicrobial resistance and genetic lineage. Using multilocus sequence data we evaluated pherotype influence on the dynamics of horizontal gene transfer. We show that pherotype is a clonal property of pneumococci. Standard population genetic analysis and multilocus infinite allele model simulations support the hypothesis that two genetically differentiated populations are defined by the major pherotypes.<br><br>CONCLUSION: Severe limitations to gene flow can therefore occur in bacterial species in the absence of geographical barriers and within highly recombinogenic populations. This departure from panmixia can have important consequences for our understanding of the response of pneumococci to human imposed selective pressures such as vaccination and antibiotic use.}, }
@article {pmid19735324, year = {2010}, author = {Choi, S and Dunams, D and Jiang, SC}, title = {Transfer of cholera toxin genes from O1 to non-O1/O139 strains by vibriophages from California coastal waters.}, journal = {Journal of applied microbiology}, volume = {108}, number = {3}, pages = {1015-1022}, doi = {10.1111/j.1365-2672.2009.04502.x}, pmid = {19735324}, issn = {1365-2672}, mesh = {Bacteriophages/*genetics ; California ; Cholera Toxin/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Viral ; *Transduction, Genetic ; Vibrio cholerae/*genetics/*virology ; *Water Microbiology ; }, abstract = {AIMS: Vibrio cholerae is an important bacterial pathogen that causes global cholera epidemic. Although they are commonly found in coastal waters around the world, most environmental isolates do not contain cholera toxin genes. This study investigates vibriophages in southern California coastal waters and their ability to transfer cholera toxin genes.<br><br>METHODS AND RESULTS: Lytic phages infecting V. cholerae were isolated from Newport Bay, California, between May and November, while none was found in winter. Some of the phage isolates can infect multiple environmental V. cholerae strains and El Tor strains. All phages contained double-stranded DNA. Transduction experiments using kanamycin-resistant gene marked CTXPhi demonstrated that some environmental vibriophages can transfer CTXPhi genes from O1 El Tor strain to environmental non-O1/O139 V. cholerae via generalized transduction.<br><br>CONCLUSIONS: Vibriophages are important components of the natural aquatic ecosystem. They play an important role in influencing the dynamics and evolution of V. cholerae in the environment.<br><br>This study demonstrates the significance of vibriophages in the coastal environment and transduction as one of the mechanisms of pathogenicity evolution among environmental V. cholerae.}, }
@article {pmid19735206, year = {2009}, author = {Huang, SY and Dai, L and Xia, LN and Du, XD and Qi, YH and Liu, HB and Wu, CM and Shen, JZ}, title = {Increased prevalence of plasmid-mediated quinolone resistance determinants in chicken Escherichia coli isolates from 2001 to 2007.}, journal = {Foodborne pathogens and disease}, volume = {6}, number = {10}, pages = {1203-1209}, doi = {10.1089/fpd.2009.0348}, pmid = {19735206}, issn = {1556-7125}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Chickens/*microbiology ; China ; Ciprofloxacin/pharmacology ; Colony Count, Microbial ; Conjugation, Genetic ; DNA, Bacterial/chemistry ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/drug effects/*genetics/isolation &amp; purification ; Escherichia coli Proteins/genetics ; Feces/microbiology ; Fluoroquinolones/*pharmacology ; Food Microbiology ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Plasmids/*genetics ; Polymerase Chain Reaction ; Poultry Diseases/microbiology ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {To evaluate the temporal change in the plasmid-mediated quinolone resistance (PMQR) determinants from 2001 to 2007 in chicken, a total of 532 chicken Escherichia coli isolates were screened for PMQR determinants by polymerase chain reaction and sequencing. The prevalence of qnr genes, aa(6')-Ib-cr, and qepA were 9.8%, 11.7%, and 0.75%, respectively. Among the qnr determinants, qnrA-, qnrB-, and qnrS-type genes were detected in 4 (0.75%), 21 (3.9%), and 27 (5.1%) of the examined isolates, respectively. None of the isolates carried qnrC gene. Ciprofloxacin resistance increased over time (p < 0.01), and a clear trend of increase in the prevalence of qnr and aac(6')-Ib-cr genes among the isolates was shown from 2001 to 2007 (p < 0.01). Pulsed-field gel analysis showed that the PMQR-positive isolates were not clonally related and genetically diverse. Quinolone resistance was transferred by conjugation from qnrB-, qnrS-, and aac(6')-Ib-cr-positive isolates to recipient E. coli. The qnrB and aac(6')-Ib-cr alleles were located on the plasmids with the size of 49 and 50 kb, respectively. However, the qnrS alleles were located on different plasmids with sizes from 57.4 to 88.6 kb, indicating diverse genetic backgrounds. The increasing frequency of ciprofloxacin resistance in E. coli was associated with increasing prevalence of qnr genes and aac(6')-Ib-cr (r(s) = 0.964, p = 0.00045). This survey showed that PMQR determinants were highly prevalent in chicken E. coli isolates in China with a trend of increase from 2001 to 2007. Horizontal transfer and widespread use of quinolone antimicrobials may have contributed to the spread of PMQR determinants in the poultry production system. The widespread dissemination of PMQR could potentially fuel the rapid development of fluoroquinolones resistance.}, }
@article {pmid19730817, year = {2009}, author = {Coffey, L and Clarke, A and Duggan, P and Tambling, K and Horgan, S and Dowling, D and O'Reilly, C}, title = {Isolation of identical nitrilase genes from multiple bacterial strains and real-time PCR detection of the genes from soils provides evidence of horizontal gene transfer.}, journal = {Archives of microbiology}, volume = {191}, number = {10}, pages = {761-771}, doi = {10.1007/s00203-009-0507-6}, pmid = {19730817}, issn = {1432-072X}, mesh = {Acetonitriles/metabolism ; Actinomycetales/*enzymology/genetics ; Amino Acid Sequence ; Base Sequence ; Cloning, Molecular ; DNA, Bacterial/genetics ; Escherichia coli/genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Hydro-Lyases/*genetics/isolation &amp; purification ; Molecular Sequence Data ; Polymerase Chain Reaction ; Recombinant Proteins/genetics/isolation &amp; purification ; Rhodococcus/*enzymology/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Bacterial enzymes capable of nitrile hydrolysis have significant industrial potential. Microbacterium sp. AJ115, Rhodococcus erythropolis AJ270 and AJ300 were isolated from the same location in England and harbour identical nitrile hydratase/amidase gene clusters. Strain AJ270 has been well studied due to its nitrile hydratase and amidase activity. R. erythropolis ITCBP was isolated from Denmark and carries a very similar nitrile hydratase/amidase gene cluster. In this study, an identical nitrilase gene (nit1) was isolated from the four strains, and the nitrilase from strain AJ270 cloned and expressed in Escherichia coli. Analysis of the recombinant nitrilase has shown it to be functional with activity demonstrated towards phenylacetonitrile. A real-time PCR TaqMan assay was developed that allowed nit1 detection directly from soil enrichment cultures without DNA extraction, with nit1 detected in all samples tested. Real-time PCR screening of isolates from these soils resulted in the isolation of nit1 and also very similar nitrilase gene nit2 from a number of Burkholderia sp. The genes nit1 and nit2 have also been detected in many bacteria of different genera but are unstable in these isolates. It is likely that the genes were acquired by horizontal gene transfer and may be wide-spread in the environment.}, }
@article {pmid19730681, year = {2009}, author = {Kidane, D and Carrasco, B and Manfredi, C and Rothmaier, K and Ayora, S and Tadesse, S and Alonso, JC and Graumann, PL}, title = {Evidence for different pathways during horizontal gene transfer in competent Bacillus subtilis cells.}, journal = {PLoS genetics}, volume = {5}, number = {9}, pages = {e1000630}, pmid = {19730681}, issn = {1553-7404}, mesh = {Bacillus subtilis/*genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; DNA/genetics ; *Gene Transfer, Horizontal ; Plasmids/genetics ; }, abstract = {Cytological and genetic evidence suggests that the Bacillus subtilis DNA uptake machinery localizes at a single cell pole and takes up single-stranded (ss) DNA. The integration of homologous donor DNA into the recipient chromosome requires RecA, while plasmid establishment, which is independent of RecA, requires at least RecO and RecU. RecA and RecN colocalize at the polar DNA uptake machinery, from which RecA forms filamentous structures, termed threads, in the presence of chromosomal DNA. We show that the transformation of chromosomal and of plasmid DNA follows distinct pathways. In the absence of DNA, RecU accumulated at a single cell pole in competent cells, dependent on RecA. Upon addition of any kind of DNA, RecA formed highly dynamic thread structures, which rapidly grew and shrank, and RecU dissipated from the pole. RecO visibly accumulated at the cell pole only upon addition of plasmid DNA, and, to a lesser degree, of phage DNA, but not of chromosomal DNA. RecO accumulation was weakly influenced by RecN, but not by RecA. RecO annealed ssDNA complexed with SsbA in vitro, independent of any nucleotide cofactor. The DNA end-joining Ku protein was also found to play a role in viral and plasmid transformation. On the other hand, transfection with SPP1 phage DNA required functions from both chromosomal and plasmid transformation pathways. The findings show that competent bacterial cells possess a dynamic DNA recombination machinery that responds in a differential manner depending if entering DNA shows homology with recipient DNA or has self-annealing potential. Transformation with chromosomal DNA only requires RecA, which forms dynamic filamentous structures that may mediate homology search and DNA strand invasion. Establishment of circular plasmid DNA requires accumulation of RecO at the competence pole, most likely mediating single-strand annealing, and RecU, which possibly down-regulates RecA. Transfection with SPP1 viral DNA follows an intermediate route that contains functions from both chromosomal and plasmid transformation pathways.}, }
@article {pmid19729843, year = {2009}, author = {Musser, JM and Shelburne, SA}, title = {A decade of molecular pathogenomic analysis of group A Streptococcus.}, journal = {The Journal of clinical investigation}, volume = {119}, number = {9}, pages = {2455-2463}, pmid = {19729843}, issn = {1558-8238}, mesh = {Gene Transfer, Horizontal ; Genome, Bacterial ; Genome-Wide Association Study ; Genomics ; Host-Pathogen Interactions ; Humans ; Molecular Epidemiology ; Streptococcal Infections/epidemiology/etiology/microbiology ; Streptococcal Vaccines/isolation &amp; purification ; Streptococcus pyogenes/*genetics/*pathogenicity ; Systems Biology ; Virulence/genetics ; Virulence Factors/biosynthesis/genetics ; }, abstract = {Molecular pathogenomic analysis of the human bacterial pathogen group A Streptococcus has been conducted for a decade. Much has been learned as a consequence of the confluence of low-cost DNA sequencing, microarray technology, high-throughput proteomics, and enhanced bioinformatics. These technical advances, coupled with the availability of unique bacterial strain collections, have facilitated a systems biology investigative strategy designed to enhance and accelerate our understanding of disease processes. Here, we provide examples of the progress made by exploiting an integrated genome-wide research platform to gain new insight into molecular pathogenesis. The studies have provided many new avenues for basic and translational research.}, }
@article {pmid19728837, year = {2010}, author = {Oliver, KM and Degnan, PH and Burke, GR and Moran, NA}, title = {Facultative symbionts in aphids and the horizontal transfer of ecologically important traits.}, journal = {Annual review of entomology}, volume = {55}, number = {}, pages = {247-266}, doi = {10.1146/annurev-ento-112408-085305}, pmid = {19728837}, issn = {1545-4487}, support = {1K 12 GM00708/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Aphids/genetics/*microbiology ; *Gene Transfer, Horizontal ; *Phenotype ; *Symbiosis ; }, abstract = {Aphids engage in symbiotic associations with a diverse assemblage of heritable bacteria. In addition to their obligate nutrient-provisioning symbiont, Buchnera aphidicola, aphids may also carry one or more facultative symbionts. Unlike obligate symbionts, facultative symbionts are not generally required for survival or reproduction and can invade novel hosts, based on both phylogenetic analyses and transfection experiments. Facultative symbionts are mutualistic in the context of various ecological interactions. Experiments on pea aphids (Acyrthosiphon pisum) have demonstrated that facultative symbionts protect against entomopathogenic fungi and parasitoid wasps, ameliorate the detrimental effects of heat, and influence host plant suitability. The protective symbiont, Hamiltonella defensa, has a dynamic genome, exhibiting evidence of recombination, phage-mediated gene uptake, and horizontal gene transfer and containing virulence and toxin-encoding genes. Although transmitted maternally with high fidelity, facultative symbionts occasionally move horizontally within and between species, resulting in the instantaneous acquisition of ecologically important traits, such as parasitoid defense.}, }
@article {pmid19726536, year = {2009}, author = {Rokyta, DR and Wichman, HA}, title = {Genic incompatibilities in two hybrid bacteriophages.}, journal = {Molecular biology and evolution}, volume = {26}, number = {12}, pages = {2831-2839}, pmid = {19726536}, issn = {1537-1719}, support = {P20 RR016448/RR/NCRR NIH HHS/United States ; R01 GM076040/GM/NIGMS NIH HHS/United States ; P20 RR16448/RR/NCRR NIH HHS/United States ; }, mesh = {Amino Acid Substitution/genetics ; Bacteriophages/*genetics ; Evolution, Molecular ; Genes, Viral/*genetics ; Genetic Fitness ; Hybridization, Genetic ; *Recombination, Genetic ; }, abstract = {Horizontal gene transfer and recombination play a major role in microbial evolution and have been detected in diverse groups, including many of medical relevance such as HIV and dengue virus. In the absence of mechanistic barriers, the evolutionary success of a particular recombination event is determined by whether the recombinant genotype suffers a fitness cost through the disruption of favorable epistatic interactions within the genome, and if so, the extent to which this fitness cost might be mitigated by subsequent compensatory evolution. To investigate the importance of epistatic interactions between genes and the evolutionary viability of a homologous recombination event between diverged ancestral genotypes, we constructed two recombinant microvirid bacteriophages by exchanging their alleles of the gene encoding the coat protein. The coding sequences for this gene differ by approximately 8% at the amino acid level and were interchanged between two ancestral phages related to varphiX174 and well adapted to their culture conditions. Because the recombinant phages showed drastically reduced fitnesses, we further explored their evolutionary viability by subjecting replicate lines of each of them to selection. We found that all four lineages achieved fitnesses commensurate with ancestral fitnesses in as few as 60 generations, and on average, the first substitution accounted for more than half of the total fitness recovery. Fitness recovery required three to five substitutions in each lineage, and overall eight of the nine essential phage genes were involved, suggesting extensive epistatic interactions throughout the genome. Interestingly, the proteins with the most extensive and apparent physical interactions with the exchanged protein in the viral capsid did not appear to have much of a role in fitness recovery. This result appears to be a consequence of the conservation of the amino acid residues involved in the interactions. It suggests that strong epistatic interactions are less important than weaker, transient ones in producing genic incompatibilities because they preclude variability in the interacting regions of the proteins.}, }
@article {pmid19725945, year = {2009}, author = {Robertson, M}, title = {Of primordial genomes and cooperative kittens.}, journal = {Journal of biology}, volume = {8}, number = {6}, pages = {52}, pmid = {19725945}, issn = {1475-4924}, mesh = {Gene Transfer, Horizontal ; *Genome ; Hemoglobins/*metabolism ; Oxygen/metabolism ; Phylogeny ; }, }
@article {pmid19721089, year = {2009}, author = {Gazzaniga, F and Stebbins, R and Chang, SZ and McPeek, MA and Brenner, C}, title = {Microbial NAD metabolism: lessons from comparative genomics.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {73}, number = {3}, pages = {529-41, Table of Contents}, pmid = {19721089}, issn = {1098-5557}, mesh = {*Bacteria/genetics/metabolism ; Biosynthetic Pathways ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial ; *Genomics ; NAD/*metabolism ; Sequence Homology, Amino Acid ; }, abstract = {NAD is a coenzyme for redox reactions and a substrate of NAD-consuming enzymes, including ADP-ribose transferases, Sir2-related protein lysine deacetylases, and bacterial DNA ligases. Microorganisms that synthesize NAD from as few as one to as many as five of the six identified biosynthetic precursors have been identified. De novo NAD synthesis from aspartate or tryptophan is neither universal nor strictly aerobic. Salvage NAD synthesis from nicotinamide, nicotinic acid, nicotinamide riboside, and nicotinic acid riboside occurs via modules of different genes. Nicotinamide salvage genes nadV and pncA, found in distinct bacteria, appear to have spread throughout the tree of life via horizontal gene transfer. Biochemical, genetic, and genomic analyses have advanced to the point at which the precursors and pathways utilized by a microorganism can be predicted. Challenges remain in dissecting regulation of pathways.}, }
@article {pmid19720995, year = {2009}, author = {Chun, J and Grim, CJ and Hasan, NA and Lee, JH and Choi, SY and Haley, BJ and Taviani, E and Jeon, YS and Kim, DW and Lee, JH and Brettin, TS and Bruce, DC and Challacombe, JF and Detter, JC and Han, CS and Munk, AC and Chertkov, O and Meincke, L and Saunders, E and Walters, RA and Huq, A and Nair, GB and Colwell, RR}, title = {Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {36}, pages = {15442-15447}, pmid = {19720995}, issn = {1091-6490}, support = {N01AI40001/AI/NIAID NIH HHS/United States ; N01-AI-30001/AI/NIAID NIH HHS/United States ; 1R01A139129-01//PHS HHS/United States ; N01-AI-40001/AI/NIAID NIH HHS/United States ; }, mesh = {Base Sequence ; Cholera Toxin/genetics ; Cluster Analysis ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; *Genetic Variation ; Genomic Islands/genetics ; Genomics ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Vibrio cholerae O1/*genetics ; }, abstract = {Vibrio cholerae, the causative agent of cholera, is a bacterium autochthonous to the aquatic environment, and a serious public health threat. V. cholerae serogroup O1 is responsible for the previous two cholera pandemics, in which classical and El Tor biotypes were dominant in the sixth and the current seventh pandemics, respectively. Cholera researchers continually face newly emerging and reemerging pathogenic clones carrying diverse combinations of phenotypic and genotypic properties, which significantly hampered control of the disease. To elucidate evolutionary mechanisms governing genetic diversity of pandemic V. cholerae, we compared the genome sequences of 23 V. cholerae strains isolated from a variety of sources over the past 98 years. The genome-based phylogeny revealed 12 distinct V. cholerae lineages, of which one comprises both O1 classical and El Tor biotypes. All seventh pandemic clones share nearly identical gene content. Using analogy to influenza virology, we define the transition from sixth to seventh pandemic strains as a "shift" between pathogenic clones belonging to the same O1 serogroup, but from significantly different phyletic lineages. In contrast, transition among clones during the present pandemic period is characterized as a "drift" between clones, differentiated mainly by varying composition of laterally transferred genomic islands, resulting in emergence of variants, exemplified by V. cholerae O139 and V. cholerae O1 El Tor hybrid clones. Based on the comparative genomics it is concluded that V. cholerae undergoes extensive genetic recombination via lateral gene transfer, and, therefore, genome assortment, not serogroup, should be used to define pathogenic V. cholerae clones.}, }
@article {pmid19720753, year = {2009}, author = {Putze, J and Hennequin, C and Nougayrède, JP and Zhang, W and Homburg, S and Karch, H and Bringer, MA and Fayolle, C and Carniel, E and Rabsch, W and Oelschlaeger, TA and Oswald, E and Forestier, C and Hacker, J and Dobrindt, U}, title = {Genetic structure and distribution of the colibactin genomic island among members of the family Enterobacteriaceae.}, journal = {Infection and immunity}, volume = {77}, number = {11}, pages = {4696-4703}, pmid = {19720753}, issn = {1098-5522}, mesh = {Base Sequence ; DNA, Bacterial/*genetics ; Enterobacteriaceae/*genetics ; Escherichia coli Proteins/*genetics ; Flow Cytometry ; Fluorescent Antibody Technique ; Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Genomic Islands/*genetics ; HeLa Cells ; Humans ; Microscopy, Confocal ; Molecular Sequence Data ; Phenotype ; Polymerase Chain Reaction ; }, abstract = {A genomic island encoding the biosynthesis and secretion pathway of putative hybrid nonribosomal peptide-polyketide colibactin has been recently described in Escherichia coli. Colibactin acts as a cyclomodulin and blocks the eukaryotic cell cycle. The origin and prevalence of the colibactin island among enterobacteria are unknown. We therefore screened 1,565 isolates of different genera and species related to the Enterobacteriaceae by PCR for the presence of this DNA element. The island was detected not only in E. coli but also in Klebsiella pneumoniae, Enterobacter aerogenes, and Citrobacter koseri isolates. It was highly conserved among these species and was always associated with the yersiniabactin determinant. Structural variations between individual strains were only observed in an intergenic region containing variable numbers of tandem repeats. In E. coli, the colibactin island was usually restricted to isolates of phylogenetic group B2 and inserted at the asnW tRNA locus. Interestingly, in K. pneumoniae, E. aerogenes, C. koseri, and three E. coli strains of phylogenetic group B1, the functional colibactin determinant was associated with a genetic element similar to the integrative and conjugative elements ICEEc1 and ICEKp1 and to several enterobacterial plasmids. Different asn tRNA genes served as chromosomal insertion sites of the ICE-associated colibactin determinant: asnU in the three E. coli strains of ECOR group B1, and different asn tRNA loci in K. pneumoniae. The detection of the colibactin genes associated with an ICE-like element in several enterobacteria provides new insights into the spread of this gene cluster and its putative mode of transfer. Our results shed light on the mechanisms of genetic exchange between members of the family Enterobacteriaceae.}, }
@article {pmid19719415, year = {2009}, author = {Mooij, MJ and Willemsen, I and Lobbrecht, M and Vandenbroucke-Grauls, C and Kluytmans, J and Savelkoul, PH}, title = {Integron class 1 reservoir among highly resistant gram-negative microorganisms recovered at a Dutch teaching hospital.}, journal = {Infection control and hospital epidemiology}, volume = {30}, number = {10}, pages = {1015-1018}, doi = {10.1086/606039}, pmid = {19719415}, issn = {1559-6834}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Gram-Negative Bacteria/*drug effects/genetics/isolation &amp; purification ; Gram-Negative Bacterial Infections/*epidemiology/microbiology ; Hospitals, Teaching/*statistics &amp; numerical data ; Humans ; Integrases/genetics ; Integrons/*genetics ; Intensive Care Units ; Microbial Sensitivity Tests ; Netherlands/epidemiology ; Prevalence ; }, abstract = {Integrons play an important role in the dissemination of resistance genes among bacteria. Nearly 70% of highly resistant gram-negative bacteria isolated at a tertiary care hospital harbored an integron. Epidemiologic analysis suggests that horizontal gene transfer is an important mechanism of resistance spread and has a greater contribution than cross-transmission to levels of resistance in settings where highly resistant gram-negative bacteria are endemic.}, }
@article {pmid19716201, year = {2009}, author = {Velasco, C and Rodríguez-Baño, J and García, L and Díaz, P and Lupión, C and Durán, L and Pascual, A}, title = {Eradication of an extensive outbreak in a neonatal unit caused by two sequential Klebsiella pneumoniae clones harbouring related plasmids encoding an extended-spectrum beta-lactamase.}, journal = {The Journal of hospital infection}, volume = {73}, number = {2}, pages = {157-163}, doi = {10.1016/j.jhin.2009.06.013}, pmid = {19716201}, issn = {1532-2939}, mesh = {Bacteremia/epidemiology/microbiology/prevention &amp; control ; Cross Infection/epidemiology/microbiology ; *Disease Outbreaks ; Gene Transfer, Horizontal ; Genotype ; Hospitals, University ; Humans ; Infant ; Infant, Newborn ; Infection Control/*methods ; Klebsiella Infections/*epidemiology/microbiology/prevention &amp; control ; Klebsiella pneumoniae/classification/drug effects/*enzymology/genetics ; Molecular Epidemiology ; Plasmids/*genetics ; beta-Lactamases/*genetics/metabolism ; }, abstract = {Outbreaks caused by extended-spectrum beta-lactamase (ESBL)-producing Klebsiella pneumoniae are difficult to control and closure of an affected unit is sometimes necessary. We describe an outbreak of ESBL-producing K. pneumoniae in a 28-bed neonatal unit that began in August 2005 and lasted for seven months. Weekly rectal swabs were taken from all babies admitted throughout the study period. Review of all procedures, contact precautions, thorough environmental cleaning and restriction of cephalosporin use were implemented. ESBL production was investigated according to CLSI recommendations, and characterised by isoelectric focusing and sequencing. Typing of isolates was assessed by pulsed-field gel electrophoresis. Plasmids were also studied. During the outbreak, 32% of 503 admitted babies became colonised and nine babies developed bacteraemia; all the babies recovered. The outbreak was finally terminated in February 2006. Two distinct clones were observed, the first circulating between August and October 2005, and the second between October 2005 and February 2006. Both of these clones carried the non-ESBL SHV-11 and TEM-4 ESBL. Plasmids harbouring TEM-4 from both clones were similar and molecular analysis suggested horizontal dissemination of a single plasmid between the two clones.}, }
@article {pmid19714214, year = {2009}, author = {Coleman, JJ and Rounsley, SD and Rodriguez-Carres, M and Kuo, A and Wasmann, CC and Grimwood, J and Schmutz, J and Taga, M and White, GJ and Zhou, S and Schwartz, DC and Freitag, M and Ma, LJ and Danchin, EG and Henrissat, B and Coutinho, PM and Nelson, DR and Straney, D and Napoli, CA and Barker, BM and Gribskov, M and Rep, M and Kroken, S and Molnár, I and Rensing, C and Kennell, JC and Zamora, J and Farman, ML and Selker, EU and Salamov, A and Shapiro, H and Pangilinan, J and Lindquist, E and Lamers, C and Grigoriev, IV and Geiser, DM and Covert, SF and Temporini, E and Vanetten, HD}, title = {The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion.}, journal = {PLoS genetics}, volume = {5}, number = {8}, pages = {e1000618}, pmid = {19714214}, issn = {1553-7404}, mesh = {Base Composition ; Chromosomes, Fungal/chemistry/*genetics ; Fungi/classification/genetics ; Gene Duplication ; *Genome, Fungal ; Nectria/chemistry/classification/*genetics ; Phylogeny ; }, abstract = {The ascomycetous fungus Nectria haematococca, (asexual name Fusarium solani), is a member of a group of >50 species known as the "Fusarium solani species complex". Members of this complex have diverse biological properties including the ability to cause disease on >100 genera of plants and opportunistic infections in humans. The current research analyzed the most extensively studied member of this complex, N. haematococca mating population VI (MPVI). Several genes controlling the ability of individual isolates of this species to colonize specific habitats are located on supernumerary chromosomes. Optical mapping revealed that the sequenced isolate has 17 chromosomes ranging from 530 kb to 6.52 Mb and that the physical size of the genome, 54.43 Mb, and the number of predicted genes, 15,707, are among the largest reported for ascomycetes. Two classes of genes have contributed to gene expansion: specific genes that are not found in other fungi including its closest sequenced relative, Fusarium graminearum; and genes that commonly occur as single copies in other fungi but are present as multiple copies in N. haematococca MPVI. Some of these additional genes appear to have resulted from gene duplication events, while others may have been acquired through horizontal gene transfer. The supernumerary nature of three chromosomes, 14, 15, and 17, was confirmed by their absence in pulsed field gel electrophoresis experiments of some isolates and by demonstrating that these isolates lacked chromosome-specific sequences found on the ends of these chromosomes. These supernumerary chromosomes contain more repeat sequences, are enriched in unique and duplicated genes, and have a lower G+C content in comparison to the other chromosomes. Although the origin(s) of the extra genes and the supernumerary chromosomes is not known, the gene expansion and its large genome size are consistent with this species' diverse range of habitats. Furthermore, the presence of unique genes on supernumerary chromosomes might account for individual isolates having different environmental niches.}, }
@article {pmid19709369, year = {2009}, author = {Das, A and Saha, D and Pal, J}, title = {Antimicrobial resistance and in vitro gene transfer in bacteria isolated from the ulcers of EUS-affected fish in India.}, journal = {Letters in applied microbiology}, volume = {49}, number = {4}, pages = {497-502}, doi = {10.1111/j.1472-765X.2009.02700.x}, pmid = {19709369}, issn = {1472-765X}, mesh = {Aeromonas/drug effects/*genetics/isolation &amp; purification ; Animals ; Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; *Drug Resistance, Bacterial ; Fish Diseases/*microbiology ; Fishes ; *Gene Transfer, Horizontal ; Gram-Negative Bacterial Infections/microbiology/*veterinary ; Plasmids/genetics ; Ulcer/*microbiology ; }, abstract = {AIMS: The occurrence of drug resistance and plasmid-mediated transferability was investigated in 15 Aeromonas isolates collected from the ulcers of epizootic ulcerative syndrome (EUS)-affected fishes Katla (Catla catla), Mrigel (Cirrhinus mrigala) and Punti (Puntius sp.).<br><br>METHODS AND RESULTS: Disc diffusion assay showed that all the strains were resistant to ampicillin and sensitive to streptomycin. Of the 15 isolates examined, 93.3% isolates were resistant to erythromycin, sulfadiazine and novobiocin, while 66% were resistant to rifampin and 20% to chloramphenicol. All isolates harboured plasmids with sizes ranging from 64 to 23 kbp with a 23-kbp plasmid in common. Plasmids from 11 Aeromonas strains were transferred to Escherichia coli DH5alpha recipient strain along with the transfer of ampicillin, erythromycin and chloramphenicol resistance determinants with frequencies ranging from 7.0 x 10(-6) to 1.8 x 10(-5) transconjugants per recipient cell.<br><br>CONCLUSIONS: The resistance to ampicillin, erythromycin, sulfadiazine, novobiocin and chloramphenicol is prevalent among the bacteria isolated from EUS-affected fish, and resistant determinants of some of these antibiotics have been transferred to the bacteria of other origin.<br><br>The emergence of antibiotic resistance bacteria and gene transfer in vitro suggests that antibiotics should be used more cautiously to treat Aeromonas infections in aquaculture.}, }
@article {pmid19707233, year = {2010}, author = {Liu, YS and Wang, QL and Li, BY}, title = {New insights into plant graft hybridization.}, journal = {Heredity}, volume = {104}, number = {1}, pages = {1-2}, doi = {10.1038/hdy.2009.115}, pmid = {19707233}, issn = {1365-2540}, mesh = {Breeding ; Cell Nucleus/genetics ; Chloroplasts/genetics ; Drug Resistance/genetics ; *Gene Transfer, Horizontal ; Genes, Plant/*genetics ; Plants, Genetically Modified ; Nicotiana/cytology/*genetics ; }, }
@article {pmid19706725, year = {2009}, author = {Deschamps, P and Moreira, D}, title = {Signal conflicts in the phylogeny of the primary photosynthetic eukaryotes.}, journal = {Molecular biology and evolution}, volume = {26}, number = {12}, pages = {2745-2753}, doi = {10.1093/molbev/msp189}, pmid = {19706725}, issn = {1537-1719}, mesh = {Archaea/genetics ; Bayes Theorem ; Cell Nucleus/genetics ; Chloroplasts/genetics ; Eukaryota/*genetics ; Gene Transfer, Horizontal/genetics ; Genetic Markers ; Photosynthesis/*genetics ; *Phylogeny ; Proteins/genetics ; Symbiosis/genetics ; }, abstract = {It is widely accepted that the first photosynthetic eukaryotes arose from a single primary endosymbiosis of a cyanobacterium in a phagotrophic eukaryotic host, which led to the emergence of three major lineages: Chloroplastida (green algae and land plants), Rhodophyta, and Glaucophyta. For a long time, Glaucophyta have been thought to represent the earliest branch among them. However, recent massive phylogenomic analyses of nuclear genes have challenged this view, because most of them suggested a basal position of Rhodophyta, though with moderate statistical support. We have addressed this question by phylogenomic analysis of a large data set of 124 proteins transferred from the chloroplast to the nuclear genome of the three Archaeplastida lineages. In contrast to previous analyses, we found strong support for the basal emergence of the Chloroplastida and the sister-group relationship of Glaucophyta and Rhodophyta. Moreover, the reanalysis of chloroplast gene sequences using methods more robust against compositional and evolutionary rate biases sustained the same result. Finally, we observed that the basal position of Rhodophyta found in the phylogenies based on nuclear genes depended on the sampling of sequences used as outgroup. When eukaryotes supposed to have never had plastids (animals and fungi) were used, the analysis strongly supported the early emergence of Glaucophyta instead of Rhodophyta. Therefore, there is a conflicting signal between genes of different evolutionary origins supporting either the basal branching of Glaucophyta or of Chloroplastida within the Archaeplastida. This second possibility would agree with the existence of the subkingdom Biliphyta, joining Glaucophyta and Rhodophyta.}, }
@article {pmid19706170, year = {2009}, author = {Makarova, KS and Wolf, YI and van der Oost, J and Koonin, EV}, title = {Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements.}, journal = {Biology direct}, volume = {4}, number = {}, pages = {29}, pmid = {19706170}, issn = {1745-6150}, support = {//Intramural NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacteriophages/genetics ; Deoxyribonucleases/metabolism ; Eukaryotic Initiation Factors/*chemistry/*immunology ; Gene Transfer, Horizontal/genetics ; Genome/genetics ; Immune System ; Interspersed Repetitive Sequences/*genetics/*immunology ; Molecular Sequence Data ; Phylogeny ; Prokaryotic Cells/*immunology ; Protein Structure, Tertiary ; Sequence Alignment ; *Sequence Homology, Amino Acid ; }, abstract = {BACKGROUND: In eukaryotes, RNA interference (RNAi) is a major mechanism of defense against viruses and transposable elements as well of regulating translation of endogenous mRNAs. The RNAi systems recognize the target RNA molecules via small guide RNAs that are completely or partially complementary to a region of the target. Key components of the RNAi systems are proteins of the Argonaute-PIWI family some of which function as slicers, the nucleases that cleave the target RNA that is base-paired to a guide RNA. Numerous prokaryotes possess the CRISPR-associated system (CASS) of defense against phages and plasmids that is, in part, mechanistically analogous but not homologous to eukaryotic RNAi systems. Many prokaryotes also encode homologs of Argonaute-PIWI proteins but their functions remain unknown.<br><br>RESULTS: We present a detailed analysis of Argonaute-PIWI protein sequences and the genomic neighborhoods of the respective genes in prokaryotes. Whereas eukaryotic Ago/PIWI proteins always contain PAZ (oligonucleotide binding) and PIWI (active or inactivated nuclease) domains, the prokaryotic Argonaute homologs (pAgos) fall into two major groups in which the PAZ domain is either present or absent. The monophyly of each group is supported by a phylogenetic analysis of the conserved PIWI-domains. Almost all pAgos that lack a PAZ domain appear to be inactivated, and the respective genes are associated with a variety of predicted nucleases in putative operons. An additional, uncharacterized domain that is fused to various nucleases appears to be a unique signature of operons encoding the short (lacking PAZ) pAgo form. By contrast, almost all PAZ-domain containing pAgos are predicted to be active nucleases. Some proteins of this group (e.g., that from Aquifex aeolicus) have been experimentally shown to possess nuclease activity, and are not typically associated with genes for other (putative) nucleases. Given these observations, the apparent extensive horizontal transfer of pAgo genes, and their common, statistically significant over-representation in genomic neighborhoods enriched in genes encoding proteins involved in the defense against phages and/or plasmids, we hypothesize that pAgos are key components of a novel class of defense systems. The PAZ-domain containing pAgos are predicted to directly destroy virus or plasmid nucleic acids via their nuclease activity, whereas the apparently inactivated, PAZ-lacking pAgos could be structural subunits of protein complexes that contain, as active moieties, the putative nucleases that we predict to be co-expressed with these pAgos. All these nucleases are predicted to be DNA endonucleases, so it seems most probable that the putative novel phage/plasmid-defense system targets phage DNA rather than mRNAs. Given that in eukaryotic RNAi systems, the PAZ domain binds a guide RNA and positions it on the complementary region of the target, we further speculate that pAgos function on a similar principle (the guide being either DNA or RNA), and that the uncharacterized domain found in putative operons with the short forms of pAgos is a functional substitute for the PAZ domain.<br><br>CONCLUSION: The hypothesis that pAgos are key components of a novel prokaryotic immune system that employs guide RNA or DNA molecules to degrade nucleic acids of invading mobile elements implies a functional analogy with the prokaryotic CASS and a direct evolutionary connection with eukaryotic RNAi. The predictions of the hypothesis including both the activities of pAgos and those of the associated endonucleases are readily amenable to experimental tests.}, }
@article {pmid19704897, year = {2009}, author = {Gottig, N and Garavaglia, BS and Daurelio, LD and Valentine, A and Gehring, C and Orellano, EG and Ottado, J}, title = {Modulating host homeostasis as a strategy in the plant-pathogen arms race.}, journal = {Communicative &amp; integrative biology}, volume = {2}, number = {2}, pages = {89-90}, pmid = {19704897}, issn = {1942-0889}, abstract = {In plant-pathogen interactions, pathogens aim to overcome host defense responses while plants employ a battery of responses to limit pathogen growth and thus disease. In this "arms race" between hosts and pathogens, horizontal gene transfer is a potent source of 'pathogenic innovation' for viruses and bacteria. However, bacteria rarely acquire 'eukaryotic-like' genes from their hosts, and where they appear to, evidence for a role of the acquired genes remains outstanding. We have recently reported experimental evidence that the citrus canker causing pathogen Xanthomonas axonopodis pv. citri contains a plant natriuretic peptide-like gene (XacPNP) that encodes a protein that modulates host homeostasis to its advantage. We argue that Xanthomonas PNP has been acquired in an ancient horizontal gene transfer, and given that plant and bacterial PNPs trigger a number of similar physiological responses, we make a case of molecular mimicry. Released XacPNP mimics host PNP and results in a suppressed host response, "improved" host tissue health and consequently better pathogen survival in the lesions. Finally, we propose that Xanthomonas axonopodis pv. citri host interactions can serve as model system to study the role of host homeostasis in plant defense against biotrophic pathogens.}, }
@article {pmid19703318, year = {2009}, author = {Isambert, H and Stein, RR}, title = {On the need for widespread horizontal gene transfers under genome size constraint.}, journal = {Biology direct}, volume = {4}, number = {}, pages = {28}, pmid = {19703318}, issn = {1745-6150}, mesh = {Gene Transfer, Horizontal/*genetics/physiology ; Genome, Archaeal/*genetics ; Genome, Bacterial/*genetics ; Prokaryotic Cells/*metabolism ; }, abstract = {BACKGROUND: While eukaryotes primarily evolve by duplication-divergence expansion (and reduction) of their own gene repertoire with only rare horizontal gene transfers, prokaryotes appear to evolve under both gene duplications and widespread horizontal gene transfers over long evolutionary time scales. But, the evolutionary origin of this striking difference in the importance of horizontal gene transfers remains by and large a mystery.<br><br>HYPOTHESIS: We propose that the abundance of horizontal gene transfers in free-living prokaryotes is a simple but necessary consequence of two opposite effects: i) their apparent genome size constraint compared to typical eukaryote genomes and ii) their underlying genome expansion dynamics through gene duplication-divergence evolution, as demonstrated by the presence of many tandem and block repeated genes. In principle, this combination of genome size constraint and underlying duplication expansion should lead to a coalescent-like process with extensive turnover of functional genes. This would, however, imply the unlikely, systematic reinvention of functions from discarded genes within independent phylogenetic lineages. Instead, we propose that the long-term evolutionary adaptation of free-living prokaryotes must have resulted in the emergence of efficient non-phylogenetic pathways to circumvent gene loss.<br><br>IMPLICATIONS: This need for widespread horizontal gene transfers due to genome size constraint implies, in particular, that prokaryotes must remain under strong selection pressure in order to maintain the long-term evolutionary adaptation of their "mutualized" gene pool, beyond the inevitable turnover of individual prokaryote species. By contrast, the absence of genome size constraint for typical eukaryotes has presumably relaxed their need for widespread horizontal gene transfers and strong selection pressure. Yet, the resulting loss of genetic functions, due to weak selection pressure and inefficient gene recovery mechanisms, must have ultimately favored the emergence of more complex life styles and ecological integration of many eukaryotes.<br><br>REVIEWERS: This article was reviewed by Pierre Pontarotti, Eugene V Koonin and Sergei Maslov.}, }
@article {pmid19701742, year = {2009}, author = {Sandhu, S and James, VA and Quesenberry, KH and Altpeter, F}, title = {Risk assessment of transgenic apomictic tetraploid bahiagrass, cytogenetics, breeding behavior and performance of intra-specific hybrids.}, journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik}, volume = {119}, number = {8}, pages = {1383-1395}, pmid = {19701742}, issn = {1432-2242}, mesh = {Flowers/genetics/growth &amp; development ; Gene Flow ; Gene Transfer, Horizontal ; Hybrid Vigor ; *Hybridization, Genetic ; Paspalum/*genetics/growth &amp; development ; Plants, Genetically Modified/growth &amp; development ; Pollen/genetics ; Polymorphism, Restriction Fragment Length ; *Polyploidy ; Transgenes ; }, abstract = {Pollen-mediated gene transfer from stress tolerant or herbicide-resistant transgenic plants may cause environmental or agronomic problems. Apomictic seed production found in some bahiagrass cultivars may serve as a natural transgene containment system. Under greenhouse conditions, the average gene transfer frequency from an herbicide-resistant apomictic tetraploid to a population of sexual diploid bahiagrass genotypes or apomictic tetraploid bahiagrass was 0.16% when the transgenic pollen donor was placed at 0.5-1.5 m distance from the non-transgenic pollen receptors. The herbicide-resistant hybrids were characterized for transgene integration, expression and ploidy, by Southern blot analysis, immuno-chromatography and flow cytometry, respectively. Hybrids resulting from open pollination of non-transgenic diploid female plants with transgenic tetraploid male plants were triploids or near-triploids, with 2n = 26-34. These hybrids displayed a wide range of phenotypic variability, including some non-persistent or non-flowering dwarf-type hybrids with good vigor, or hybrids with vegetative growth similar to non-transgenic plants, but with significantly reduced seed set. Non-flowering aneu-triploids with good vigor/field performance will provide the highest level of transgene containment. Embryo sac analysis of pollinated spikelets confirmed a high proportion of aborted ovules. An apospory-linked RFLP marker was detected in 13 of the 15 near-triploid hybrids. All flowering aneuploid hybrids displayed significantly reduced seed set, and none of the sexual near-triploid hybrids produced any seeds. All tetraploid gene transfer events carried the apospory-linked RFLP marker, suggesting that despite the presence of the aposporus locus, a low degree of sexuality co-exists in apomictic tetraploid cultivars. Thus, tetraploid apomictic bahiagrass does not provide complete transgene containment, although intra-specific gene transfer is drastically reduced compared to sexually reproducing perennial grasses.}, }
@article {pmid19696881, year = {2009}, author = {Pritchard, L and Liu, H and Booth, C and Douglas, E and François, P and Schrenzel, J and Hedley, PE and Birch, PR and Toth, IK}, title = {Microarray comparative genomic hybridisation analysis incorporating genomic organisation, and application to enterobacterial plant pathogens.}, journal = {PLoS computational biology}, volume = {5}, number = {8}, pages = {e1000473}, pmid = {19696881}, issn = {1553-7358}, mesh = {Cluster Analysis ; Comparative Genomic Hybridization/*methods ; Computer Simulation ; Enterobacteriaceae/*genetics ; Gene Transfer, Horizontal ; Genetic Variation ; *Genome, Bacterial ; Genomic Islands ; Markov Chains ; Models, Statistical ; Normal Distribution ; Oligonucleotide Array Sequence Analysis/*methods ; Plant Diseases/*microbiology ; Reproducibility of Results ; }, abstract = {Microarray comparative genomic hybridisation (aCGH) provides an estimate of the relative abundance of genomic DNA (gDNA) taken from comparator and reference organisms by hybridisation to a microarray containing probes that represent sequences from the reference organism. The experimental method is used in a number of biological applications, including the detection of human chromosomal aberrations, and in comparative genomic analysis of bacterial strains, but optimisation of the analysis is desirable in each problem domain.We present a method for analysis of bacterial aCGH data that encodes spatial information from the reference genome in a hidden Markov model. This technique is the first such method to be validated in comparisons of sequenced bacteria that diverge at the strain and at the genus level: Pectobacterium atrosepticum SCRI1043 (Pba1043) and Dickeya dadantii 3937 (Dda3937); and Lactococcus lactis subsp. lactis IL1403 and L. lactis subsp. cremoris MG1363. In all cases our method is found to outperform common and widely used aCGH analysis methods that do not incorporate spatial information. This analysis is applied to comparisons between commercially important plant pathogenic soft-rotting enterobacteria (SRE) Pba1043, P. atrosepticum SCRI1039, P. carotovorum 193, and Dda3937.Our analysis indicates that it should not be assumed that hybridisation strength is a reliable proxy for sequence identity in aCGH experiments, and robustly extends the applicability of aCGH to bacterial comparisons at the genus level. Our results in the SRE further provide evidence for a dynamic, plastic 'accessory' genome, revealing major genomic islands encoding gene products that provide insight into, and may play a direct role in determining, variation amongst the SRE in terms of their environmental survival, host range and aetiology, such as phytotoxin synthesis, multidrug resistance, and nitrogen fixation.}, }
@article {pmid19696498, year = {2009}, author = {Qiu, X and Kulasekara, BR and Lory, S}, title = {Role of Horizontal Gene Transfer in the Evolution of Pseudomonas aeruginosa Virulence.}, journal = {Genome dynamics}, volume = {6}, number = {}, pages = {126-139}, doi = {10.1159/000235767}, pmid = {19696498}, issn = {1660-9263}, mesh = {Evolution, Molecular ; *Gene Transfer, Horizontal ; Genetic Variation ; Host-Pathogen Interactions ; Humans ; Pseudomonas Infections ; *Pseudomonas aeruginosa/genetics ; Sequence Analysis, DNA ; Virulence/genetics ; }, abstract = {The opportunistic pathogen Pseudomonas aeruginosa causes serious infections in immunocompromised patients and individuals with cystic fibrosis (CF). It is one of the most versatile organisms as illustrated by its ability to occupy a wide range of environmental niches. Comparative genomic analysis suggests that horizontal gene transfer (HGT) plays a significant role in determining the genetic repertoire of each strain. Genomic diversity is, in part, due to the acquisition of genetic material that has integrated into the chromosome at a relatively limited number of sites. The resulting genomic islands (GIs) contain genes specifying virulence traits as well as genes that may enhance fitness in a specific environmental niche. Several islands are integrative and conjugative elements (ICEs) that may have evolved from ancestral self-transmissible conjugative plasmids. For some genomic islands, the mechanism of acquisition is not apparent suggesting that the mechanisms utlized are either transformation or bacteriophage-mediated generalized transduction. It appears that HGT takes place primarily in the natural environment of P. aeruginosa and, conceivably, an uncharacterized host-pathogen interaction provides the selective pressures for acquisition and maintenance of the observed virulence phenotypes.}, }
@article {pmid19696497, year = {2009}, author = {Brzuszkiewicz, E and Gottschalk, G and Ron, E and Hacker, J and Dobrindt, U}, title = {Adaptation of Pathogenic E. coli to Various Niches: Genome Flexibility is the Key.}, journal = {Genome dynamics}, volume = {6}, number = {}, pages = {110-125}, doi = {10.1159/000235766}, pmid = {19696497}, issn = {1660-9263}, mesh = {*Escherichia coli/genetics ; Escherichia coli Infections/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; Molecular Sequence Data ; Phylogeny ; }, abstract = {It is a well-known observation and a long-standing hypothesis that pathogen genome dynamics are important in infectious disease processes. Recent achievements in large-scale genome sequencing, comparative genomics and molecular epidemiology help to unravel current challenges of E. coli pathogenomics, i.e. to gain insights into the in vivo relevance of genome dynamics. Data from comparative genomics support the hypothesis of widespread involvement of horizontal gene transfer in the evolution of E. coli, leading to the presence of distinct and variable 'genomic islands' within the conserved 'chromosomal backbone' in several bacterial lineages. Extensive gene acquisition and loss provide different lineages with distinct metabolic, pathogenic and other capabilities. Not only mobile genetic modules but also point mutations facilitate rapid adaptation of E. coli to changing environmental conditions and hence extend the spectrum of sites that can be infected. We report on recent research efforts to analyze pathoadaptive and other genomic alterations of the E. coli genome that affect disease severity and may have consequences for diagnostics and treatment of E. coli infections.}, }
@article {pmid19694552, year = {2009}, author = {Haenni, M and Saras, E and Châtre, P and Meunier, D and Martin, S and Lepage, G and Ménard, MF and Lebreton, P and Rambaud, T and Madec, JY}, title = {vanA in Enterococcus faecium, Enterococcus faecalis, and Enterococcus casseliflavus detected in French cattle.}, journal = {Foodborne pathogens and disease}, volume = {6}, number = {9}, pages = {1107-1111}, doi = {10.1089/fpd.2009.0303}, pmid = {19694552}, issn = {1556-7125}, mesh = {Animal Husbandry/legislation &amp; jurisprudence/methods ; Animals ; Bacterial Proteins/*genetics/metabolism ; Carbon-Oxygen Ligases/*genetics/metabolism ; Cattle/*microbiology ; Cattle Diseases/epidemiology/*microbiology ; Electrophoresis, Gel, Pulsed-Field ; Enterococcus/drug effects/genetics/*isolation &amp; purification ; Enterococcus faecalis/isolation &amp; purification ; Enterococcus faecium/isolation &amp; purification ; Feces/microbiology ; Foodborne Diseases/prevention &amp; control ; France/epidemiology ; Gene Transfer, Horizontal ; Genotype ; Gram-Positive Bacterial Infections/drug therapy/epidemiology/microbiology/*veterinary ; Microbial Sensitivity Tests ; Peptide Synthases/genetics/metabolism ; Phenotype ; Vancomycin Resistance/*genetics ; }, abstract = {The goal of this study was to assess the presence of enterococci species presenting van-mediated glycopeptide resistance in French cattle. Fecal samples were collected from healthy and sick animals, and enterococci were screened for vancomycin resistance. Vancomycin resistance was principally encountered in Enterococcus gallinarum and Enterococcus casseliflavus strains. However, glycopeptide resistance was detected in three different species of enterococci (E. faecalis, E. faecium, and E. casseliflavus). Molecular characterization of the genetic support proved that they all presented the prototypic VanA element. Interestingly, the E. casseliflavus strain displayed a remarkable VanB phenotype/vanA-vanC genotype. Transferability, associated resistances, and factors of vanA cotransfer were sought. This study proved that acquired vanA genes can still be detected in food-producing animals more than a decade after the avoparcin ban. Indeed, calves, which are recurrently exposed to antibiotics in France, may allow the re-emergence of glycopeptide resistance through coselection factors, and this might potentially be concerning for human health.}, }
@article {pmid19689787, year = {2009}, author = {de la Chaux, N and Wagner, A}, title = {Evolutionary dynamics of the LTR retrotransposons roo and rooA inferred from twelve complete Drosophila genomes.}, journal = {BMC evolutionary biology}, volume = {9}, number = {}, pages = {205}, pmid = {19689787}, issn = {1471-2148}, mesh = {Animals ; Drosophila/classification/*genetics ; *Evolution, Molecular ; *Genome, Insect ; *Retroelements ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Roo is the most abundant retrotransposon in the fruit fly Drosophila melanogaster. Its evolutionary origins and dynamics are thus of special interest for understanding the evolutionary history of Drosophila genome organization. We here study the phylogenetic distribution and evolution of roo, and its highly diverged relative rooA in 12 completely sequenced genomes of the genus Drosophila.<br><br>RESULTS: We identify a total of 164 roo copies, 57 of which were previously unidentified copies that occur in 9 of the 12 genomes. Additionally we find 66 rooA copies in four genomes and remnants of this element in two additional genomes. We further increased the number of elements by searching for individual roo/rooA sequence domains. Most of our roo and rooA elements have been recently inserted. Most elements within a genome are highly similar. A comparison of the phylogenetic tree of our roo and rooA elements shows that the split between roo and rooA took place early in Drosophila evolution. Furthermore there is one incongruency between the species tree and the phylogenetic tree of the roo element. This incongruency regards the placement of elements from D. mojavensis, which are more closely related to D. melanogaster than elements from D. willistoni.<br><br>CONCLUSION: Within genomes, the evolutionary dynamics of roo and rooA range from recent transpositional activity to slow decay and extinction. Among genomes, the balance of phylogenetic evidence, sequence divergence distribution, and the occurrence of solo-LTR elements suggests an origin of roo/rooA within the Drosophila clade. We discuss the possibility of a horizontal gene transfer of roo within this clade.}, }
@article {pmid19687238, year = {2009}, author = {Suchland, RJ and Sandoz, KM and Jeffrey, BM and Stamm, WE and Rockey, DD}, title = {Horizontal transfer of tetracycline resistance among Chlamydia spp. in vitro.}, journal = {Antimicrobial agents and chemotherapy}, volume = {53}, number = {11}, pages = {4604-4611}, pmid = {19687238}, issn = {1098-6596}, support = {R01 AI048769/AI/NIAID NIH HHS/United States ; U19 AI031448/AI/NIAID NIH HHS/United States ; AI48769/AI/NIAID NIH HHS/United States ; AI31448/AI/NIAID NIH HHS/United States ; }, mesh = {Chlamydia/*drug effects/genetics ; Fluorescent Antibody Technique ; *Gene Transfer, Horizontal ; Ofloxacin/pharmacology ; Recombination, Genetic ; Rifampin/pharmacology ; Tetracycline Resistance/*genetics ; }, abstract = {There are no examples of stable tetracycline resistance in clinical strains of Chlamydia trachomatis. However, the swine pathogen Chlamydia suis is commonly tetracycline resistant, both in America and in Europe. In tested U.S. strains, this resistance is mediated by a genomic island carrying a tet(C) allele. In the present study, the ability of C. suis to mobilize tet(C) into other chlamydial species was examined. Differently antibiotic resistant strains of C. suis, C. trachomatis, and Chlamydia muridarum were used in coculture experiments to select for multiply antibiotic resistant progeny. Coinfection of mammalian cells with a naturally occurring tetracycline-resistant strain of C. suis and a C. muridarum or C. trachomatis strain containing selected mutations encoding rifampin (rifampicin) or ofloxacin resistance readily produced doubly resistant recombinant clones that demonstrated the acquisition of tetracycline resistance. The resistance phenotype in the progeny from a C. trachomatis L2/ofl(R)-C. suis R19/tet(R) cross resulted from integration of a 40-kb fragment into a single ribosomal operon of a recipient, leading to a merodiploid structure containing three rRNA operons. In contrast, a cross between C. suis R19/tet(R) and C. muridarum MoPn/ofl(R) led to a classical double-crossover event transferring 99 kb of DNA from C. suis R19/tet(R) into C. muridarum MoPn/ofl(R). Tetracycline resistance was also transferred to recent clinical strains of C. trachomatis. Successful crosses were not obtained when a rifampin-resistant Chlamydophila caviae strain was used as a recipient for crosses with C. suis or C. trachomatis. These findings provide a platform for further exploration of the biology of horizontal gene transfer in Chlamydia while bringing to light potential public health concerns generated by the possibility of acquisition of tetracycline resistance by human chlamydial pathogens.}, }
@article {pmid19687234, year = {2009}, author = {Sidjabat, HE and Paterson, DL and Adams-Haduch, JM and Ewan, L and Pasculle, AW and Muto, CA and Tian, GB and Doi, Y}, title = {Molecular epidemiology of CTX-M-producing Escherichia coli isolates at a tertiary medical center in western Pennsylvania.}, journal = {Antimicrobial agents and chemotherapy}, volume = {53}, number = {11}, pages = {4733-4739}, pmid = {19687234}, issn = {1098-6596}, mesh = {Drug Resistance, Bacterial/genetics ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/classification/drug effects/enzymology/*genetics ; Escherichia coli Infections/*microbiology ; Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; Plasmids ; beta-Lactamases/*biosynthesis ; }, abstract = {A combination of phenotypic and genotypic methods was used to investigate 70 unique Escherichia coli clinical isolates identified as producing extended-spectrum beta-lactamases (ESBLs) at a medical center in Pittsburgh, PA, between 2007 and 2008. Fifty-seven isolates (81%) produced CTX-M-type ESBLs, among which CTX-M-15 was predominant (n = 46). Isolates producing CTX-M-2, -9, -14, and -65 were also identified. One CTX-M-producing isolate coproduced CMY-2 cephalosporinase. Ten isolates (14%) produced SHV-type ESBLs, either SHV-5 or SHV-7. Two isolates produced only CMY-2 or -32. Pulsed-field gel electrophoresis revealed the presence of two major clusters of CTX-M-15-producing E. coli isolates, one in phylotype B2 (n = 15) and the other in phylotype A (n = 19). Of four phylotype B2 isolates that were able to transfer the bla(CTX-M-15)-carrying plasmids, three showed fingerprints related (>60%) to those of plasmids from phylotype A isolates. In phylotype B2, all CTX-M-15-producing isolates, as well as three isolates producing CTX-M-14, two producing SHV-5, and one producing SHV-7, belonged to the international epidemic clone defined by serotype O25:H4 and sequence type 131. The plasmids from eight of nine CTX-M-15-producing E. coli isolates of phylotype A that were examined were highly related to each other and were also found in two isolates belonging to phylotype D, suggesting horizontal transfer of this bla(CTX-M-15)-carrying plasmid between phylotypes. Our findings underscore the need to further investigate the epidemiology and virulence of CTX-M-producing E. coli in the United States.}, }
@article {pmid19687197, year = {2009}, author = {Flannery, EL and Mody, L and Mobley, HL}, title = {Identification of a modular pathogenicity island that is widespread among urease-producing uropathogens and shares features with a diverse group of mobile elements.}, journal = {Infection and immunity}, volume = {77}, number = {11}, pages = {4887-4894}, pmid = {19687197}, issn = {1098-5522}, support = {K23 AG022463-05/AG/NIA NIH HHS/United States ; AI59722/AI/NIAID NIH HHS/United States ; K23 AG022463/AG/NIA NIH HHS/United States ; R01 AG032298/AG/NIA NIH HHS/United States ; AI43363/AI/NIAID NIH HHS/United States ; R01 AI059722/AI/NIAID NIH HHS/United States ; R56 AI043363/AI/NIAID NIH HHS/United States ; R01 AI043363/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics ; Comparative Genomic Hybridization ; DNA, Bacterial/genetics ; Enterobacteriaceae Infections/microbiology/urine ; Gene Transfer, Horizontal ; Genomic Islands/*genetics ; Humans ; Interspersed Repetitive Sequences/*genetics ; Molecular Sequence Data ; Morganella morganii/*genetics/pathogenicity ; Oligonucleotide Array Sequence Analysis ; Polymerase Chain Reaction ; Proteus mirabilis/*genetics/pathogenicity ; Providencia/*genetics/pathogenicity ; Sequence Homology, Amino Acid ; Urease/biosynthesis ; Urinary Tract Infections/genetics/microbiology ; Virulence/genetics ; Virulence Factors/genetics ; }, abstract = {Pathogenicity islands (PAIs) are a specific group of genomic islands that contribute to genomic variability and virulence of bacterial pathogens. Using a strain-specific comparative genomic hybridization array, we report the identification of a 94-kb PAI, designated ICEPm1, that is common to Proteus mirabilis, Providencia stuartii, and Morganella morganii. These organisms are highly prevalent etiologic agents of catheter-associated urinary tract infections (caUTI), the most common hospital acquired infection. ICEPm1 carries virulence factors that are important for colonization of the urinary tract, including a known toxin (Proteus toxic agglutinin) and the high pathogenicity island of Yersinia spp. In addition, this PAI shares homology and gene organization similar to the PAIs of other bacterial pathogens, several of which have been classified as mobile integrative and conjugative elements (ICEs). Isolates from this study were cultured from patients with caUTI and show identical sequence similarity at three loci within ICEPm1, suggesting its transfer between bacterial genera. Screening for the presence of ICEPm1 among P. mirabilis colonizing isolates showed that ICEPm1 is more prevalent in urine isolates compared to P. mirabilis strains isolated from other body sites (P<0.0001), further suggesting that it contributes to niche specificity and is positively selected for in the urinary tract.}, }
@article {pmid19687142, year = {2009}, author = {Koonin, EV and Wolf, YI and Puigbò, P}, title = {The phylogenetic forest and the quest for the elusive tree of life.}, journal = {Cold Spring Harbor symposia on quantitative biology}, volume = {74}, number = {}, pages = {205-213}, pmid = {19687142}, issn = {1943-4456}, support = {Z01 LM000073/ImNIH/Intramural NIH HHS/United States ; Z01 LM000073-12/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Biological Evolution ; Gene Transfer, Horizontal ; Metagenomics ; *Models, Genetic ; *Phylogeny ; Prokaryotic Cells ; }, abstract = {Extensive horizontal gene transfer (HGT) among prokaryotes seems to undermine the tree of life (TOL) concept. However, the possibility remains that the TOL can be salvaged as a statistical central trend in the phylogenetic "forest of life" (FOL). A comprehensive comparative analysis of 6901 phylogenetic trees for prokaryotic genes revealed a signal of vertical inheritance that was particularly strong among the 102 nearly universal trees (NUTs), despite the high topological inconsistency among the trees in the FOL, most likely, caused by HGT. The topologies of the NUTs are similar to the topologies of numerous other trees in the FOL; although the NUTs cannot represent the FOL completely, they reflect a significant central trend. Thus, the original TOL concept becomes obsolete but the idea of a "weak" TOL as the dominant trend in the FOL merits further investigation. The totality of gene trees comprising the FOL appears to be a natural representation of the history of life given the inherent tree-like character of the replication process.}, }
@article {pmid19675017, year = {2009}, author = {Hawkey, PM and Jones, AM}, title = {The changing epidemiology of resistance.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {64 Suppl 1}, number = {}, pages = {i3-10}, doi = {10.1093/jac/dkp256}, pmid = {19675017}, issn = {1460-2091}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology/*therapeutic use ; Bacteria/*drug effects/genetics ; Bacterial Infections/*drug therapy/*epidemiology ; *Drug Resistance, Bacterial ; Drug Utilization/trends ; Gene Transfer, Horizontal ; Humans ; Selection, Genetic ; }, abstract = {Antibiotic resistance is now a linked global problem. Dispersion of successful clones of multidrug resistant (MDR) bacteria is common, often via the movement of people. Local evolution of MDR bacteria is also important under the pressure of excessive antibiotic use, with horizontal gene transfer providing the means by which genes such as bla(CTX-M) spread amongst different bacterial species and strains. Beta-lactamase production is a common resistance mechanism in Gram-negative bacteria, and the rapid dissemination of novel genes reflects their evolution under the selective pressure of antibiotic usage. Many Enterobacteriaceae now carry broad-spectrum beta-lactamases such as CTX-M, with particular genotypes associated with different geographical regions. The spread of these enzymes has compromised the clinical utility of a number of beta-lactam classes and with the spread of genes such as bla(KPC), carbapenems may be increasingly compromised in the future. High-level fluoroquinolone resistance (mainly caused by gyrA mutations) has also been shown to be associated with CTX-M and CMY-type enzymes, commonly due to co-carriage on conjugative plasmids of the gene for the aminoglycoside-inactivating enzyme AAC-6(1)-Ib-cr and qnr genes (which confer low-level resistance), allowing the easy selection of gyrA mutants in the host strain. Resistance in Gram-positive bacteria is also widely distributed and increasing, with the emergence of community-associated methicillin-resistant Staphylococcus aureus (MRSA) blurring the distinction between hospital and community strains. Antibiotic use and environmental factors all have a role in the emergence and spread of resistance. This article reviews some of the new mechanisms and recent trends in the global spread of MDR bacteria.}, }
@article {pmid19683039, year = {2009}, author = {Papaleo, MC and Russo, E and Fondi, M and Emiliani, G and Frandi, A and Brilli, M and Pastorelli, R and Fani, R}, title = {Structural, evolutionary and genetic analysis of the histidine biosynthetic "core" in the genus Burkholderia.}, journal = {Gene}, volume = {448}, number = {1}, pages = {16-28}, doi = {10.1016/j.gene.2009.08.002}, pmid = {19683039}, issn = {1879-0038}, mesh = {Bacterial Proteins/*genetics ; Base Sequence ; Biosynthetic Pathways ; Burkholderia/classification/*genetics/metabolism ; Genome, Bacterial ; Histidine/*biosynthesis ; Molecular Sequence Data ; Mutation ; Oligonucleotide Array Sequence Analysis ; *Operon ; *Phylogeny ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Transcription, Genetic ; }, abstract = {In this work a detailed analysis of the structure, the expression and the organization of his genes belonging to the core of histidine biosynthesis (hisBHAF) in 40 newly determined and 13 available sequences of Burkholderia strains was carried out. Data obtained revealed a strong conservation of the structure and organization of these genes through the entire genus. The phylogenetic analysis showed the monophyletic origin of this gene cluster and indicated that it did not undergo horizontal gene transfer events. The analysis of the intergenic regions, based on the substitution rate, entropy plot and bendability suggested the existence of a putative transcription promoter upstream of hisB, that was supported by the genetic analysis that showed that this cluster was able to complement Escherichia colihisA, hisB, and hisF mutations. Moreover, a preliminary transcriptional analysis and the analysis of microarray data revealed that the expression of the his core was constitutive. These findings are in agreement with the fact that the entire Burkholderiahis operon is heterogeneous, in that it contains "alien" genes apparently not involved in histidine biosynthesis. Besides, they also support the idea that the proteobacterial his operon was piece-wisely assembled, i.e. through accretion of smaller units containing only some of the genes (eventually together with their own promoters) involved in this biosynthetic route. The correlation existing between the structure, organization and regulation of his "core" genes and the function(s) they perform in cellular metabolism is discussed.}, }
@article {pmid19682258, year = {2009}, author = {Ramsay, JP and Sullivan, JT and Jambari, N and Ortori, CA and Heeb, S and Williams, P and Barrett, DA and Lamont, IL and Ronson, CW}, title = {A LuxRI-family regulatory system controls excision and transfer of the Mesorhizobium loti strain R7A symbiosis island by activating expression of two conserved hypothetical genes.}, journal = {Molecular microbiology}, volume = {73}, number = {6}, pages = {1141-1155}, doi = {10.1111/j.1365-2958.2009.06843.x}, pmid = {19682258}, issn = {1365-2958}, mesh = {4-Butyrolactone/analogs &amp; derivatives/biosynthesis ; Alphaproteobacteria/genetics/*physiology ; Bacterial Proteins/genetics/*metabolism ; Base Sequence ; Conjugation, Genetic ; DNA, Bacterial/genetics/*metabolism ; *Gene Expression Regulation ; Gene Order ; *Gene Transfer, Horizontal ; *Genomic Islands ; Lotus/microbiology ; Molecular Sequence Data ; Recombination, Genetic ; }, abstract = {The symbiosis island ICEMlSym(R7A) of Mesorhizobium loti R7A is an integrative and conjugative element (ICE) that carries genes required for a nitrogen-fixing symbiosis with Lotus species. ICEMlSym(R7A) encodes homologues (TraR, TraI1 and TraI2) of proteins that regulate plasmid transfer by quorum sensing in rhizobia and agrobacteria. Introduction of traR cloned on a plasmid induced excision of ICEMlSym(R7A) in all cells, a 1000-fold increase in the production of 3-oxo-C6-homoserine lactone (3-oxo-C6-HSL) and a 40-fold increase in conjugative transfer. These effects were dependent on traI1 but not traI2. Induction of expression from the traI1 and traI2 promoters required the presence of plasmid-borne traR and either traI1 or 100 pM 3-oxo-C6-HSL, suggesting that traR expression or TraR activity is repressed in wild-type cells by a mechanism that can be overcome by additional copies of traR. The traI2 gene formed an operon with hypothetical genes msi172 and msi171 that were essential for ICEMlSym(R7A) excision and transfer. Our data suggest that derepressed TraR in conjunction with TraI1-synthesized 3-oxo-C6-HSL regulates excision and transfer of ICEMlSym(R7A) through expression of msi172 and msi171. Homologues of msi172 and msi171 were present on putative ICEs in several alpha-proteobacteria, indicating a conserved role in ICE excision and transfer.}, }
@article {pmid19681690, year = {2009}, author = {Cassone, M and Giordano, A}, title = {Resistance genes traveling the microbial internet: down the drain, up the food chain?.}, journal = {Expert review of anti-infective therapy}, volume = {7}, number = {6}, pages = {637-639}, doi = {10.1586/eri.09.50}, pmid = {19681690}, issn = {1744-8336}, mesh = {Agriculture ; Animals ; *Anti-Bacterial Agents/administration &amp; dosage/therapeutic use ; Drug Resistance, Bacterial/*genetics ; *Food Chain ; Food Microbiology ; Gene Transfer, Horizontal ; Humans ; Soil Microbiology ; Veterinary Drugs ; }, }
@article {pmid19680442, year = {2009}, author = {Levin, BR and Cornejo, OE}, title = {The population and evolutionary dynamics of homologous gene recombination in bacterial populations.}, journal = {PLoS genetics}, volume = {5}, number = {8}, pages = {e1000601}, pmid = {19680442}, issn = {1553-7404}, support = {R01 AI040662/AI/NIAID NIH HHS/United States ; R01 GM091875/GM/NIGMS NIH HHS/United States ; AI40662/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; *Evolution, Molecular ; Models, Genetic ; Mutation ; *Recombination, Genetic ; Selection, Genetic ; }, abstract = {In bacteria, recombination is a rare event, not a part of the reproductive process. Nevertheless, recombination -- broadly defined to include the acquisition of genes from external sources, i.e., horizontal gene transfer (HGT) -- plays a central role as a source of variation for adaptive evolution in many species of bacteria. Much of niche expansion, resistance to antibiotics and other environmental stresses, virulence, and other characteristics that make bacteria interesting and problematic, is achieved through the expression of genes and genetic elements obtained from other populations of bacteria of the same and different species, as well as from eukaryotes and archaea. While recombination of homologous genes among members of the same species has played a central role in the development of the genetics and molecular biology of bacteria, the contribution of homologous gene recombination (HGR) to bacterial evolution is not at all clear. Also, not so clear are the selective pressures responsible for the evolution and maintenance of transformation, the only bacteria-encoded form of HGR. Using a semi-stochastic simulation of mutation, recombination, and selection within bacterial populations and competition between populations, we explore (1) the contribution of HGR to the rate of adaptive evolution in these populations and (2) the conditions under which HGR will provide a bacterial population a selective advantage over non-recombining or more slowly recombining populations. The results of our simulation indicate that, under broad conditions: (1) HGR occurring at rates in the range anticipated for bacteria like Streptococcus pneumoniae, Escherichia coli, Haemophilus influenzae, and Bacillus subtilis will accelerate the rate at which a population adapts to environmental conditions; (2) once established in a population, selection for this capacity to increase rates of adaptive evolution can maintain bacteria-encoded mechanisms of recombination and prevent invasion of non-recombining populations, even when recombination engenders a modest fitness cost; and (3) because of the density- and frequency-dependent nature of HGR in bacteria, this capacity to increase rates of adaptive evolution is not sufficient as a selective force to provide a recombining population a selective advantage when it is rare. Under realistic conditions, homologous gene recombination will increase the rate of adaptive evolution in bacterial populations and, once established, selection for higher rates of evolution will promote the maintenance of bacteria-encoded mechanisms for HGR. On the other hand, increasing rates of adaptive evolution by HGR is unlikely to be the sole or even a dominant selective pressure responsible for the original evolution of transformation.}, }
@article {pmid19678828, year = {2009}, author = {Ceyssens, PJ and Miroshnikov, K and Mattheus, W and Krylov, V and Robben, J and Noben, JP and Vanderschraeghe, S and Sykilinda, N and Kropinski, AM and Volckaert, G and Mesyanzhinov, V and Lavigne, R}, title = {Comparative analysis of the widespread and conserved PB1-like viruses infecting Pseudomonas aeruginosa.}, journal = {Environmental microbiology}, volume = {11}, number = {11}, pages = {2874-2883}, doi = {10.1111/j.1462-2920.2009.02030.x}, pmid = {19678828}, issn = {1462-2920}, mesh = {Conserved Sequence ; DNA, Viral/chemistry/genetics ; Europe ; Gene Expression Profiling ; *Genetic Variation ; Mass Spectrometry ; Protein Processing, Post-Translational ; Pseudomonas Phages/*classification/*genetics/isolation &amp; purification/ultrastructure ; Pseudomonas aeruginosa/*virology ; Sequence Analysis, DNA ; Transcription, Genetic ; Viral Proteins/analysis/genetics ; Virion/chemistry/ultrastructure ; }, abstract = {We examined the genetic diversity of lytic Pseudomonas aeruginosa bacteriophage PB1 and four closely related phages (LBL3, LMA2, 14-1 and SN) isolated throughout Europe. They all encapsulate linear, non-permuted genomes between 64 427 and 66 530 bp within a solid, acid-resistant isometric capsid (diameter: 74 nm) and carry non-flexible, contractile tails of approximately 140 nm. The genomes are organized into at least seven transcriptional blocks, alternating on both strands, and encode between 88 (LBL3) and 95 (LMA2) proteins. Their virion particles are composed of at least 22 different proteins, which were identified using mass spectrometry. Post-translational modifications were suggested for two proteins, and a frameshift hotspot was identified within ORF42, encoding a structural protein. Despite large temporal and spatial separations between phage isolations, very high sequence similarity and limited horizontal gene transfer were found between the individual viruses. These PB1-like viruses constitute a new genus of environmentally very widespread phages within the Myoviridae.}, }
@article {pmid19674339, year = {2009}, author = {Hoang, QT and Cho, SH and McDaniel, SF and Ok, SH and Quatrano, RS and Shin, JS}, title = {An actinoporin plays a key role in water stress in the moss Physcomitrella patens.}, journal = {The New phytologist}, volume = {184}, number = {2}, pages = {502-510}, doi = {10.1111/j.1469-8137.2009.02975.x}, pmid = {19674339}, issn = {1469-8137}, support = {5F32 GM075606-02/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Physiological/*genetics ; Animals ; Biological Evolution ; Bryopsida/*genetics/metabolism ; Dehydration ; Droughts ; Gene Expression Regulation, Plant ; Gene Transfer, Horizontal ; *Genes, Plant ; Hemolysis ; Membrane Proteins/chemistry/*genetics/metabolism ; Sea Anemones/genetics ; Sequence Homology, Nucleic Acid ; Up-Regulation ; }, abstract = {* Modern land plants arose from a green algae-like ancestor c. 480 million years ago. While several novel morphological features were critical for survival in the aerial environment, physiological innovation undoubtedly played a key role in the colonization of terrestrial habitats. Recently, actinoporin genes, a small group of pore-forming toxins from sea anemones, have been found in the bryophyte and lycophyte lineages of land plants where they are upregulated in water-stressed tissues. * The bryoporin gene in the moss Physcomitrella patens (PpBP) was functionally characterized by RNA blot analyses and overexpression in P. patens. In order to examine functional homology between PpBP and sea anemone actinoporins, the recombinant PpBP was subjected to hemolytic analysis of pig blood cells, which is one of the specific activities of actinoporins. * PpBP was upregulated by various abiotic stresses, in particular most strongly by dehydration stress. Overexpression of the bryoporin gene heightens drought tolerance in P. patens significantly. In addition, PpBP shared the highest structural homology with actinoporins in a three-dimensional structural database and showed hemolytic activity. * These results suggest that this phylogenetic distribution may have resulted from an ancient horizontal gene transfer and actinoporins may have played an important role in early land plants.}, }
@article {pmid19669682, year = {2009}, author = {Torruella, G and Suga, H and Riutort, M and Peretó, J and Ruiz-Trillo, I}, title = {The evolutionary history of lysine biosynthesis pathways within eukaryotes.}, journal = {Journal of molecular evolution}, volume = {69}, number = {3}, pages = {240-248}, pmid = {19669682}, issn = {1432-1432}, mesh = {Eukaryota/enzymology/*genetics ; *Evolution, Molecular ; L-Aminoadipate-Semialdehyde Dehydrogenase/genetics ; Lysine/*biosynthesis ; Metabolic Networks and Pathways/*genetics ; Phylogeny ; }, abstract = {Lysine biosynthesis occurs in two ways: the diaminopimelate (DAP) pathway and the alpha-aminoadipate (AAA) pathway. The former is present in eubacteria, plants, and algae, whereas the latter was understood to be almost exclusive to fungi. The recent finding of the alpha-aminoadipate reductase (AAR) gene, one of the core genes of the AAA pathway, in the marine protist Corallochytrium limacisporum was, therefore, believed to be a molecular synapomorphy of fungi and C. limacisporum. To test this hypothesis, we undertook a broader search for the AAR gene in eukaryotes, and also analyzed the distribution of the lysA gene, a core gene of the DAP pathway. We show that the evolutionary history of both genes, AAR and lysA, is much more complex than previously believed. Furthermore, the AAR gene is present in several unicellular opisthokonts, thus rebutting the theory that its presence is a molecular synapomorphy between C. limacisporum and fungi. AAR gene seems to be exclusive of Excavata and Unikonts, whereas the lysA gene is present in several unrelated taxa within all major eukaryotic lineages, indicating a role for several lateral gene transfer (LGT) events. Our data imply that the choanoflagellate Monosiga brevicollis and the "choanozoan" Capsaspora owczarzaki acquired their lysA copies from a proteobacterial ancestor. Overall, these observations represent new evidence that the role of LGT in the evolutionary history of eukaryotes may have been more significant than previously thought.}, }
@article {pmid19666731, year = {2009}, author = {Boguslawska, J and Zycka-Krzesinska, J and Wilcks, A and Bardowski, J}, title = {Intra- and interspecies conjugal transfer of Tn916-like elements from Lactococcus lactis in vitro and in vivo.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {19}, pages = {6352-6360}, pmid = {19666731}, issn = {1098-5336}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Conjugation, Genetic ; *DNA Transposable Elements ; Enterococcus faecalis/drug effects/*genetics ; Feces/microbiology ; Gastrointestinal Tract/microbiology ; *Gene Transfer, Horizontal ; Lactococcus lactis/drug effects/*genetics/isolation &amp; purification ; Male ; Milk/microbiology ; Rats ; Tetracycline/pharmacology/therapeutic use ; *Tetracycline Resistance ; }, abstract = {Tetracycline-resistant Lactococcus lactis strains originally isolated from Polish raw milk were analyzed for the ability to transfer their antibiotic resistance genes in vitro, using filter mating experiments, and in vivo, using germfree rats. Four of six analyzed L. lactis isolates were able to transfer tetracycline resistance determinants in vitro to L. lactis Bu2-60, at frequencies ranging from 10(-5) to 10(-7) transconjugants per recipient. Three of these four strains could also transfer resistance in vitro to Enterococcus faecalis JH2-2, whereas no transfer to Bacillus subtilis YBE01, Pseudomonas putida KT2442, Agrobacterium tumefaciens UBAPF2, or Escherichia coli JE2571 was observed. Rats were initially inoculated with the recipient E. faecalis strain JH2-2, and after a week, the L. lactis IBB477 and IBB487 donor strains were introduced. The first transconjugants were detected in fecal samples 3 days after introduction of the donors. A subtherapeutic concentration of tetracycline did not have any significant effect on the number of transconjugants, but transconjugants were observed earlier in animals dosed with this antibiotic. Molecular analysis of in vivo transconjugants containing the tet(M) gene showed that this gene was identical to tet(M) localized on the conjugative transposon Tn916. Primer-specific PCR confirmed that the Tn916 transposon was complete in all analyzed transconjugants and donors. This is the first study showing in vivo transfer of a Tn916-like antibiotic resistance transposon from L. lactis to E. faecalis. These data suggest that in certain cases food lactococci might be involved in the spread of antibiotic resistance genes to other lactic acid bacteria.}, }
@article {pmid19666579, year = {2009}, author = {Lewis, AL and Desa, N and Hansen, EE and Knirel, YA and Gordon, JI and Gagneux, P and Nizet, V and Varki, A}, title = {Innovations in host and microbial sialic acid biosynthesis revealed by phylogenomic prediction of nonulosonic acid structure.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {32}, pages = {13552-13557}, pmid = {19666579}, issn = {1091-6490}, support = {R01 DK030292/DK/NIDDK NIH HHS/United States ; R01 GM032373/GM/NIGMS NIH HHS/United States ; HL057345/HL/NHLBI NIH HHS/United States ; R01 HD051796/HD/NICHD NIH HHS/United States ; R01-HD051796/HD/NICHD NIH HHS/United States ; DK30292/DK/NIDDK NIH HHS/United States ; P01 HL057345/HL/NHLBI NIH HHS/United States ; R37 DK030292/DK/NIDDK NIH HHS/United States ; }, mesh = {Archaea/*metabolism ; Bacteria/enzymology/*metabolism ; Cluster Analysis ; Evolution, Molecular ; Gastrointestinal Tract/microbiology ; *Genomics ; Glycomics ; *Host-Pathogen Interactions ; Humans ; Metabolic Networks and Pathways ; Methanobrevibacter/genetics ; N-Acetylneuraminic Acid/*biosynthesis ; Photobacterium/genetics ; *Phylogeny ; Reproducibility of Results ; Sialic Acids/*chemistry/metabolism ; Sugar Acids/*chemistry/metabolism ; }, abstract = {Sialic acids (Sias) are nonulosonic acid (NulO) sugars prominently displayed on vertebrate cells and occasionally mimicked by bacterial pathogens using homologous biosynthetic pathways. It has been suggested that Sias were an animal innovation and later emerged in pathogens by convergent evolution or horizontal gene transfer. To better illuminate the evolutionary processes underlying the phenomenon of Sia molecular mimicry, we performed phylogenomic analyses of biosynthetic pathways for Sias and related higher sugars derived from 5,7-diamino-3,5,7,9-tetradeoxynon-2-ulosonic acids. Examination of approximately 1,000 sequenced microbial genomes indicated that such biosynthetic pathways are far more widely distributed than previously realized. Phylogenetic analysis, validated by targeted biochemistry, was used to predict NulO types (i.e., neuraminic, legionaminic, or pseudaminic acids) expressed by various organisms. This approach uncovered previously unreported occurrences of Sia pathways in pathogenic and symbiotic bacteria and identified at least one instance in which a human archaeal symbiont tentatively reported to express Sias in fact expressed the related pseudaminic acid structure. Evaluation of targeted phylogenies and protein domain organization revealed that the "unique" Sia biosynthetic pathway of animals was instead a much more ancient innovation. Pathway phylogenies suggest that bacterial pathogens may have acquired Sia expression via adaptation of pathways for legionaminic acid biosynthesis, one of at least 3 evolutionary paths for de novo Sia synthesis. Together, these data indicate that some of the long-standing paradigms in Sia biology should be reconsidered in a wider evolutionary context of the extended family of NulO sugars.}, }
@article {pmid19665858, year = {2009}, author = {Mnasri, B and Badri, Y and Saïdi, S and de Lajudie, P and Mhamdi, R}, title = {Symbiotic diversity of Ensifer meliloti strains recovered from various legume species in Tunisia.}, journal = {Systematic and applied microbiology}, volume = {32}, number = {8}, pages = {583-592}, doi = {10.1016/j.syapm.2009.07.007}, pmid = {19665858}, issn = {1618-0984}, mesh = {Acyltransferases/genetics ; Bacterial Proteins/genetics ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; Genetic Variation ; Medicago/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Root Nodules, Plant/*microbiology ; Sinorhizobium meliloti/*genetics ; Symbiosis/*genetics ; Tunisia ; }, abstract = {Ensifer meliloti (formerly Sinorhizobium meliloti) was first considered as a specific microsymbiont of Medicago, Melilotus and Trigonella. However, strains of E. meliloti were recovered from root nodules of various legume species and their symbiotic status still remains unclear. Here, we further investigate the specificity of these strains. A collection of 47 E. meliloti strains isolated in Tunisia from root nodules of Medicago truncatula, Medicago sativa, Medicago ciliaris, Medicago laciniata, Medicago marina, Medicago scutellata, Phaseolus vulgaris, Cicer arietinum, Argyrolobium uniflorum, Lotus creticus, Lotus roudairei, Ononis natrix, Retama raetam, Genista saharae, Acacia tortilis, Hedysarum carnosum and Hippocrepis bicontorta were examined by REP-PCR fingerprinting, PCR-RFLPs of the 16S-23S rDNA IGS, the nifH gene and nifD-K intergenic spacer, and sequencing of 16S rRNA and nodA genes. Their nodulation range was also assessed by cross-inoculation experiments. No clear correlation was found between chromosomal backgrounds and host plants of origin. The nodulation polyvalence of the species E. meliloti was associated with a high symbiotic heterogeneity. On the basis of PCR-RFLP data from the nifH gene and nifD-K intergenic spacer, E. meliloti strains isolated from non-Medicago legumes harboured distinct genes and possessed wider host ranges. Some strains did not nodulate Medicago species. On the basis of nodA phylogeny, the majority of the Tunisian strains, including strains from Medicago, harboured distinct nodA alleles more related to those found in E. medicae than those found in E. meliloti. However, more work is still needed to characterize this group further. The diversity observed among M. laciniata isolates, which was supported by nodA phylogeny, nifH typing and the efficiency profile on M. ciliaris, indicated that what was thought to be bv. medicaginis is certainly heterogeneous.}, }
@article {pmid19664294, year = {2009}, author = {Maruyama, S and Matsuzaki, M and Misawa, K and Nozaki, H}, title = {Cyanobacterial contribution to the genomes of the plastid-lacking protists.}, journal = {BMC evolutionary biology}, volume = {9}, number = {}, pages = {197}, pmid = {19664294}, issn = {1471-2148}, mesh = {Animals ; Cyanobacteria/*genetics ; Eukaryota/*genetics ; *Evolution, Molecular ; Fungi/*genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genome, Fungal ; Genome, Protozoan ; Genomics/methods ; Multigene Family ; Phylogeny ; Plastids/genetics ; }, abstract = {BACKGROUND: Eukaryotic genes with cyanobacterial ancestry in plastid-lacking protists have been regarded as important evolutionary markers implicating the presence of plastids in the early evolution of eukaryotes. Although recent genomic surveys demonstrated the presence of cyanobacterial and algal ancestry genes in the genomes of plastid-lacking protists, comparative analyses on the origin and distribution of those genes are still limited.<br><br>RESULTS: We identified 12 gene families with cyanobacterial ancestry in the genomes of a taxonomically wide range of plastid-lacking eukaryotes (Phytophthora [Chromalveolata], Naegleria [Excavata], Dictyostelium [Amoebozoa], Saccharomyces and Monosiga [Opisthokonta]) using a novel phylogenetic pipeline. The eukaryotic gene clades with cyanobacterial ancestry were mostly composed of genes from bikonts (Archaeplastida, Chromalveolata, Rhizaria and Excavata). We failed to find genes with cyanobacterial ancestry in Saccharomyces and Dictyostelium, except for a photorespiratory enzyme conserved among fungi. Meanwhile, we found several Monosiga genes with cyanobacterial ancestry, which were unrelated to other Opisthokonta genes.<br><br>CONCLUSION: Our data demonstrate that a considerable number of genes with cyanobacterial ancestry have contributed to the genome composition of the plastid-lacking protists, especially bikonts. The origins of those genes might be due to lateral gene transfer events, or an ancient primary or secondary endosymbiosis before the diversification of bikonts. Our data also show that all genes identified in this study constitute multi-gene families with punctate distribution among eukaryotes, suggesting that the transferred genes could have survived through rounds of gene family expansion and differential reduction.}, }
@article {pmid19664275, year = {2009}, author = {Veyrier, F and Pletzer, D and Turenne, C and Behr, MA}, title = {Phylogenetic detection of horizontal gene transfer during the step-wise genesis of Mycobacterium tuberculosis.}, journal = {BMC evolutionary biology}, volume = {9}, number = {}, pages = {196}, pmid = {19664275}, issn = {1471-2148}, mesh = {Comparative Genomic Hybridization ; Computational Biology ; DNA, Bacterial/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; Mycobacterium tuberculosis/classification/*genetics/pathogenicity ; *Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: In the past decade, the availability of complete genome sequence data has greatly facilitated comparative genomic research aimed at addressing genetic variability within species. More recently, analysis across species has become feasible, especially in genera where genome sequencing projects of multiple species have been initiated. To understand the genesis of the pathogen Mycobacterium tuberculosis within a genus where the majority of species are harmless environmental organisms, we have used genome sequence data from 16 mycobacteria to look for evidence of horizontal gene transfer (HGT) associated with the emergence of pathogenesis. First, using multi-locus sequence analysis (MLSA) of 20 housekeeping genes across these species, we derived a phylogeny that serves as the basis for HGT assignments. Next, we performed alignment searches for the 3989 proteins of M. tuberculosis H37Rv against 15 other mycobacterial genomes, generating a matrix of 59835 comparisons, to look for genetic elements that were uniquely found in M. tuberculosis and closely-related pathogenic mycobacteria. To assign when foreign genes were likely acquired, we designed a bioinformatic program called mycoHIT (mycobacterial homologue investigation tool) to analyze these data in conjunction with the MLSA-based phylogeny.<br><br>RESULTS: The bioinformatic screen predicted that 137 genes had been acquired by HGT at different phylogenetic strata; these included genes coding for metabolic functions and modification of mycobacterial lipids. For the majority of these genes, corroborating evidence of HGT was obtained, such as presence of phage or plasmid, and an aberrant GC%.<br><br>CONCLUSION: M. tuberculosis emerged through vertical inheritance along with the step-wise addition of genes acquired via HGT events, a process that may more generally describe the evolution of other pathogens.}, }
@article {pmid19664206, year = {2009}, author = {Rodriguez, F and Wu, F and Ané, C and Tanksley, S and Spooner, DM}, title = {Do potatoes and tomatoes have a single evolutionary history, and what proportion of the genome supports this history?.}, journal = {BMC evolutionary biology}, volume = {9}, number = {}, pages = {191}, pmid = {19664206}, issn = {1471-2148}, mesh = {Alleles ; Bayes Theorem ; Cell Nucleus/genetics ; DNA, Plant/genetics ; *Evolution, Molecular ; Genetic Markers ; Genome, Plant ; Solanum lycopersicum/*genetics ; Models, Genetic ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Solanum tuberosum/*genetics ; }, abstract = {BACKGROUND: Phylogenies reconstructed with only one or a few independently inherited loci may be unresolved or incongruent due to taxon and gene sampling, horizontal gene transfer, or differential selection and lineage sorting at individual loci. In an effort to remedy this situation, we examined the utility of conserved orthologous set (COSII) nuclear loci to elucidate the phylogenetic relationships among 29 diploid Solanum species in the sister clades that include tomato and potato, and in Datura inoxia as a far outgroup. We screened 40 COSII markers with intron content over 60% that are mapped in different chromosomes; selected a subset of 19 by the presence of single band amplification of size mostly between 600 and 1200 bp; sequenced these 19 COSII markers, and performed phylogenetic analyses with individual and concatenated datasets. The present study attempts to provide a fully resolved phylogeny among the main clades in potato and tomato that can help to identify the appropriate markers for future studies using additional species.<br><br>RESULTS: Among potatoes, when total evidence is invoked, one single predominant history is highlighted with complete resolution within and among the three main clades. It also supports the hypothesis of the North and Central American B-genome origin of the tuber-bearing members of Solanum sect. Petota and shows a clear division between A genomes in clades 3 and 4, and B genomes in clade 1+2. On the other hand, when a prior agreement approach is invoked other potato evolutionary histories are revealed but with less support. These alternative histories could be explained by past hybridization, or fast rates of speciation. In the case of tomato, the analyses with all sequence data completely resolved 19 of 21 clades, for the first time revealed the monophyly of five clades, and gave further support for the recent segregation of new species from the former Solanum peruvianum. Concordance analyses revealed and summarized the extensive discordance among COSII markers. Some potential reasons for discordance could be methodological, to include systematic errors due to using a wrong model of sequence evolution, coupled with long branches, or mixtures of branch lengths within COSII, or undetected paralogy or alignment bias. Other reasons could be biological processes such as hybridization or lineage sorting.<br><br>CONCLUSION: This study confirms and quantifies the utility of using DNA sequences from different parts of the genome in phylogenetic studies to avoid possible bias in the sampling. It shows that 11-18 loci are enough to get the dominant history in this group of Solanum, but more loci would be needed to discern the distribution of gene genealogies in more depth, and thus detect which mechanism most likely shaped the discordance.}, }
@article {pmid19664165, year = {2009}, author = {Swithers, KS and Gogarten, JP and Fournier, GP}, title = {Trees in the web of life.}, journal = {Journal of biology}, volume = {8}, number = {6}, pages = {54}, pmid = {19664165}, issn = {1475-4924}, mesh = {Bacteria/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, rRNA ; *Genome, Bacterial ; Phylogeny ; Species Specificity ; }, abstract = {Reconstructing the 'Tree of Life' is complicated by extensive horizontal gene transfer between diverse groups of organisms. While numerous conceptual and technical obstacles remain, a report in this issue of Journal of Biology from Koonin and colleagues on the largest-scale prokaryotic genomic reconstruction yet attempted shows that such a tree is discernible, although its branches cannot be traced.}, }
@article {pmid19661396, year = {2009}, author = {Zimmer, C}, title = {Origins. On the origin of eukaryotes.}, journal = {Science (New York, N.Y.)}, volume = {325}, number = {5941}, pages = {666-668}, doi = {10.1126/science.325_666}, pmid = {19661396}, issn = {1095-9203}, mesh = {Animals ; *Archaea/classification/genetics/physiology ; *Bacteria/classification/genetics ; Bacterial Physiological Phenomena ; *Biological Evolution ; Cell Nucleus/genetics/metabolism ; *Eukaryotic Cells/cytology/metabolism/physiology ; Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; Genes, Mitochondrial ; *Genome ; Mitochondria/physiology ; Organelles/physiology ; *Prokaryotic Cells/cytology/metabolism/physiology ; Symbiosis ; }, }
@article {pmid19661281, year = {2009}, author = {Schwarz, R and Seibel, PN and Rahmann, S and Schoen, C and Huenerberg, M and Müller-Reible, C and Dandekar, T and Karchin, R and Schultz, J and Müller, T}, title = {Detecting species-site dependencies in large multiple sequence alignments.}, journal = {Nucleic acids research}, volume = {37}, number = {18}, pages = {5959-5968}, pmid = {19661281}, issn = {1362-4962}, mesh = {Antigens, Bacterial/chemistry/classification ; Bacterial Proteins/chemistry/classification ; Mixed Function Oxygenases/chemistry/classification ; Phylogeny ; Sequence Alignment/*methods ; Sequence Analysis, Protein ; Vitamin K Epoxide Reductases ; }, abstract = {Multiple sequence alignments (MSAs) are one of the most important sources of information in sequence analysis. Many methods have been proposed to detect, extract and visualize their most significant properties. To the same extent that site-specific methods like sequence logos successfully visualize site conservations and sequence-based methods like clustering approaches detect relationships between sequences, both types of methods fail at revealing informational elements of MSAs at the level of sequence-site interactions, i.e. finding clusters of sequences and sites responsible for their clustering, which together account for a high fraction of the overall information of the MSA. To fill this gap, we present here a method that combines the Fisher score-based embedding of sequences from a profile hidden Markov model (pHMM) with correspondence analysis. This method is capable of detecting and visualizing group-specific or conflicting signals in an MSA and allows for a detailed explorative investigation of alignments of any size tractable by pHMMs. Applications of our methods are exemplified on an alignment of the Neisseria surface antigen LP2086, where it is used to detect sites of recombinatory horizontal gene transfer and on the vitamin K epoxide reductase family to distinguish between evolutionary and functional signals.}, }
@article {pmid19659658, year = {2009}, author = {Trucco, F and Tatum, T and Rayburn, AL and Tranel, PJ}, title = {Out of the swamp: unidirectional hybridization with weedy species may explain the prevalence of Amaranthus tuberculatus as a weed.}, journal = {The New phytologist}, volume = {184}, number = {4}, pages = {819-827}, doi = {10.1111/j.1469-8137.2009.02979.x}, pmid = {19659658}, issn = {1469-8137}, mesh = {Agriculture ; Alleles ; Amaranthus/*genetics ; *Gene Transfer, Horizontal ; *Genes, Plant ; Genome, Plant ; Herbicide Resistance/*genetics ; *Hybridization, Genetic ; Pollen ; *Polymorphism, Genetic ; Reproduction ; Seeds ; United States ; }, abstract = {*Amaranthus tuberculatus represents one of the most dramatic cases of weed invasion documented in the midwestern USA. The species is infamous for evolving resistance to multiple herbicides, and predicting whether these resistances may be transferred to widespread weeds of the Amaranthus hybridus aggregate is a matter of epidemiological concern. Here, we explore the patterns of genetic exchange between Amaranthus tuberculatus and A. hybridus in an effort to understand whether allele introgression occurs throughout the genome and if fecundity penalties are associated with genetic exchange. *We evaluated 192 homoploid BC(1)s at 197 amplified fragment length polymorphism (AFLP) loci, as well as two loci associated with herbicide resistance: ALS and PPO. We also assessed the fecundity of each genotype by evaluation of seed production or pollen development. *It was discovered that genetic exchange between the species is unidirectional. Whereas A. hybridus alleles transfer with little or no penalty to A. tuberculatus, the reciprocal exchange is significantly distorted and potentially of limited evolutionary consequence. *Our previous hypothesis suggesting unidirectional introgression at ALS owing to circumstantial linkage is now modified to account for the more generalized distortion of genetic exchange observed in this study.}, }
@article {pmid19659422, year = {2009}, author = {Sanchez, MB and Hernandez, A and Martinez, JL}, title = {Stenotrophomonas maltophilia drug resistance.}, journal = {Future microbiology}, volume = {4}, number = {6}, pages = {655-660}, doi = {10.2217/fmb.09.45}, pmid = {19659422}, issn = {1746-0921}, mesh = {Anti-Bacterial Agents/*pharmacology ; *Drug Resistance, Bacterial ; Evolution, Molecular ; Genes, Bacterial ; Gram-Negative Bacterial Infections/microbiology ; Humans ; Stenotrophomonas maltophilia/*drug effects ; }, abstract = {Stenotrophomonas maltophilia has emerged in recent years as a paradigm of an intrinsically resistant, opportunistic bacterial pathogen with an environmental origin. The recent publication of the sequences of two S. maltophilia genomes has shown that this bacterium contains a large repertoire of antibiotic resistance determinants, probably contributing to its characteristic susceptibility to antibiotics. Among those determinants, the best characterized are a number of multidrug efflux pumps, beta-lactamases and aminoglycoside-inactivating enzymes. Recently, the presence of a gene coding for a Qnr determinant in the genome of S. maltophilia has also been described. Together, these elements confer resistance to several of the drugs currently used for treating infections. Besides these chromosomally encoded determinants, which evolved in S. maltophilia long before the recent human use of antibiotics, this bacterial species is acquiring novel resistance genes by horizontal gene transfer, thereby increasing its resistance. Future studies are required to fully understand the mechanisms of resistance, their regulation and potential crosstalk with S. maltophilia virulence, as well as the population dynamics of the different isolates of this bacterial species.}, }
@article {pmid19658466, year = {2009}, author = {Butler, T and Goldenfeld, N and Mathew, D and Luthey-Schulten, Z}, title = {Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement.}, journal = {Physical review. E, Statistical, nonlinear, and soft matter physics}, volume = {79}, number = {6 Pt 1}, pages = {060901}, doi = {10.1103/PhysRevE.79.060901}, pmid = {19658466}, issn = {1539-3755}, mesh = {Amino Acid Sequence ; Base Sequence ; Computer Simulation ; Genetic Code/*genetics ; *Models, Chemical ; *Models, Genetic ; Molecular Sequence Data ; Proteins/*chemistry/*genetics ; Sequence Analysis, DNA/*methods ; Sequence Analysis, Protein/*methods ; }, abstract = {A molecular dynamics calculation of the amino acid polar requirement is used to score the canonical genetic code. Monte Carlo simulation shows that this computational polar requirement has been optimized by the canonical genetic code, an order of magnitude more than any previously known measure, effectively ruling out a vertical evolution dynamics. The sensitivity of the optimization to the precise metric used in code scoring is consistent with code evolution having proceeded through the communal dynamics of statistical proteins using horizontal gene transfer, as recently proposed. The extreme optimization of the genetic code therefore strongly supports the idea that the genetic code evolved from a communal state of life prior to the last universal common ancestor.}, }
@article {pmid19654869, year = {2009}, author = {Rolland, T and Neuvéglise, C and Sacerdot, C and Dujon, B}, title = {Insertion of horizontally transferred genes within conserved syntenic regions of yeast genomes.}, journal = {PloS one}, volume = {4}, number = {8}, pages = {e6515}, pmid = {19654869}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; *Conserved Sequence ; *Gene Transfer, Horizontal ; *Genome, Fungal ; Kluyveromyces/classification/genetics ; Molecular Sequence Data ; Phylogeny ; Saccharomyces/classification/genetics ; Sequence Homology, Amino Acid ; }, abstract = {Horizontal gene transfer has been occasionally mentioned in eukaryotic genomes, but such events appear much less numerous than in prokaryotes, where they play important functional and evolutionary roles. In yeasts, few independent cases have been described, some of which corresponding to major metabolic functions, but no systematic screening of horizontally transferred genes has been attempted so far. Taking advantage of the synteny conservation among five newly sequenced and annotated genomes of Saccharomycetaceae, we carried out a systematic search for HGT candidates amidst genes present in only one species within conserved synteny blocks. Out of 255 species-specific genes, we discovered 11 candidates for HGT, based on their similarity with bacterial proteins and on reconstructed phylogenies. This corresponds to a minimum of six transfer events because some horizontally acquired genes appear to rapidly duplicate in yeast genomes (e.g. YwqG genes in Kluyveromyces thermotolerans and serine recombinase genes of the IS607 family in Saccharomyces kluyveri). We show that the resulting copies are submitted to a strong functional selective pressure. The mechanisms of DNA transfer and integration are discussed, in relation with the generally small size of HGT candidates. Our results on a limited set of species expand by 50% the number of previously published HGT cases in hemiascomycetous yeasts, suggesting that this type of event is more frequent than usually thought. Our restrictive method does not exclude the possibility that additional HGT events exist. Actually, ancestral events common to several yeast species must have been overlooked, and the absence of homologs in present databases leaves open the question of the origin of the 244 remaining species-specific genes inserted within conserved synteny blocks.}, }
@article {pmid19649313, year = {2009}, author = {Queck, SY and Khan, BA and Wang, R and Bach, TH and Kretschmer, D and Chen, L and Kreiswirth, BN and Peschel, A and Deleo, FR and Otto, M}, title = {Mobile genetic element-encoded cytolysin connects virulence to methicillin resistance in MRSA.}, journal = {PLoS pathogens}, volume = {5}, number = {7}, pages = {e1000533}, pmid = {19649313}, issn = {1553-7374}, support = {//Intramural NIH HHS/United States ; }, mesh = {Animals ; Bacterial Proteins/*genetics/immunology/metabolism ; Bacterial Toxins/*genetics/immunology/metabolism ; Base Sequence ; Biofilms/growth &amp; development ; Chemical Phenomena ; Cysteine/metabolism ; Disease Models, Animal ; Hemolysis ; Humans ; Inflammation/immunology/microbiology ; *Interspersed Repetitive Sequences ; Methicillin-Resistant Staphylococcus aureus/genetics/metabolism/*pathogenicity ; Mice ; Molecular Sequence Data ; Neutrophils/cytology/microbiology ; Penicillin-Binding Proteins ; Perforin/*genetics/metabolism ; Staphylococcus epidermidis/genetics/metabolism/pathogenicity ; }, abstract = {Bacterial virulence and antibiotic resistance have a significant influence on disease severity and treatment options during bacterial infections. Frequently, the underlying genetic determinants are encoded on mobile genetic elements (MGEs). In the leading human pathogen Staphylococcus aureus, MGEs that contain antibiotic resistance genes commonly do not contain genes for virulence determinants. The phenol-soluble modulins (PSMs) are staphylococcal cytolytic toxins with a crucial role in immune evasion. While all known PSMs are core genome-encoded, we here describe a previously unidentified psm gene, psm-mec, within the staphylococcal methicillin resistance-encoding MGE SCCmec. PSM-mec was strongly expressed in many strains and showed the physico-chemical, pro-inflammatory, and cytolytic characteristics typical of PSMs. Notably, in an S. aureus strain with low production of core genome-encoded PSMs, expression of PSM-mec had a significant impact on immune evasion and disease. In addition to providing high-level resistance to methicillin, acquisition of SCCmec elements encoding PSM-mec by horizontal gene transfer may therefore contribute to staphylococcal virulence by substituting for the lack of expression of core genome-encoded PSMs. Thus, our study reveals a previously unknown role of methicillin resistance clusters in staphylococcal pathogenesis and shows that important virulence and antibiotic resistance determinants may be combined in staphylococcal MGEs.}, }
@article {pmid19647074, year = {2009}, author = {Poole, AM}, title = {Horizontal gene transfer and the earliest stages of the evolution of life.}, journal = {Research in microbiology}, volume = {160}, number = {7}, pages = {473-480}, doi = {10.1016/j.resmic.2009.07.009}, pmid = {19647074}, issn = {1769-7123}, mesh = {*Evolution, Molecular ; *Gene Transfer, Horizontal ; Models, Biological ; Selection, Genetic ; }, abstract = {Horizontal gene transfer (HGT) has been suggested to be the dominant hereditary process at the earliest stages of evolution. I examine this suggestion within the context of the problem of genetic parasites and suggest that extreme rates of transfer may in fact negatively impact evolutionary transitions. In regard to the proposal that HGT is Lamarckian, the apparent conflict between HGT and Darwinian evolution is easily avoided by considering HGT at the appropriate level of selection.}, }
@article {pmid19644176, year = {2009}, author = {Jin, G and Nakhleh, L and Snir, S and Tuller, T}, title = {Parsimony score of phylogenetic networks: hardness results and a linear-time heuristic.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {6}, number = {3}, pages = {495-505}, doi = {10.1109/TCBB.2008.119}, pmid = {19644176}, issn = {1557-9964}, mesh = {*Algorithms ; Archaea/genetics ; Cyclooxygenase 2/genetics ; *Models, Genetic ; *Phylogeny ; Plant Proteins/genetics ; Plants/genetics ; Ribosomal Proteins/genetics ; }, abstract = {Phylogenies-the evolutionary histories of groups of organisms-play a major role in representing the interrelationships among biological entities. Many methods for reconstructing and studying such phylogenies have been proposed, almost all of which assume that the underlying history of a given set of species can be represented by a binary tree. Although many biological processes can be effectively modeled and summarized in this fashion, others cannot: recombination, hybrid speciation, and horizontal gene transfer result in networks of relationships rather than trees of relationships. In previous works, we formulated a maximum parsimony (MP) criterion for reconstructing and evaluating phylogenetic networks, and demonstrated its quality on biological as well as synthetic data sets. In this paper, we provide further theoretical results as well as a very fast heuristic algorithm for the MP criterion of phylogenetic networks. In particular, we provide a novel combinatorial definition of phylogenetic networks in terms of "forbidden cycles," and provide detailed hardness and hardness of approximation proofs for the "small" MP problem. We demonstrate the performance of our heuristic in terms of time and accuracy on both biological and synthetic data sets. Finally, we explain the difference between our model and a similar one formulated by Nguyen et al., and describe the implications of this difference on the hardness and approximation results.}, }
@article {pmid19643761, year = {2009}, author = {Naum, M and Brown, EW and Mason-Gamer, RJ}, title = {Phylogenetic evidence for extensive horizontal gene transfer of type III secretion system genes among enterobacterial plant pathogens.}, journal = {Microbiology (Reading, England)}, volume = {155}, number = {Pt 10}, pages = {3187-3199}, doi = {10.1099/mic.0.029892-0}, pmid = {19643761}, issn = {1350-0872}, mesh = {Bacterial Proteins/*genetics ; Cluster Analysis ; Conserved Sequence ; DNA, Bacterial/chemistry/genetics ; Enterobacteriaceae/*genetics/isolation &amp; purification ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Membrane Transport Proteins/*genetics ; Models, Biological ; Molecular Sequence Data ; Phylogeny ; Plant Diseases/*microbiology ; Sequence Analysis, DNA ; Sequence Homology ; Virulence Factors/genetics ; }, abstract = {This study uses sequences from four genes, which are involved in the formation of the type III secretion apparatus, to determine the role of horizontal gene transfer in the evolution of virulence genes for the enterobacterial plant pathogens. Sequences of Erwinia, Brenneria, Pectobacterium, Dickeya and Pantoea were compared (a) with one another, (b) with sequences of enterobacterial animal pathogens, and (c) with sequences of plant pathogenic gamma and beta proteobacteria, to evaluate probable paths of lateral exchange leading to the current distribution of virulence determinants among these micro-organisms. Phylogenies were reconstructed based on hrcC, hrcR, hrcJ and hrcV gene sequences using parsimony and maximum-likelihood algorithms. Virulence gene phylogenies were also compared with several housekeeping gene loci in order to evaluate patterns of lateral versus vertical acquisition. The resulting phylogenies suggest that multiple horizontal gene transfer events have occurred both within and among the enterobacterial plant pathogens and plant pathogenic gamma and beta proteobacteria. hrcJ sequences are the most similar, exhibiting anywhere from 2 to 50 % variation at the nucleotide level, with the highest degree of variation present between plant and animal pathogen sequences. hrcV sequences are conserved among plant and animal pathogens at the N terminus. The C-terminal domain is conserved only among the enterobacterial plant pathogens, as are the hrcC and hrcR sequences. Additionally, hrcJ and hrcV sequence phylogenies suggest that at least some type III secretion system virulence genes from enterobacterial plant pathogens are related more closely to those of the genus Pseudomonas, a conclusion neither supported nor refuted by hrcC or hrcR.}, }
@article {pmid19640295, year = {2009}, author = {Chen, K and Roberts, E and Luthey-Schulten, Z}, title = {Horizontal gene transfer of zinc and non-zinc forms of bacterial ribosomal protein S4.}, journal = {BMC evolutionary biology}, volume = {9}, number = {}, pages = {179}, pmid = {19640295}, issn = {1471-2148}, mesh = {Amino Acid Sequence ; Bacteria/classification/*genetics ; Bacterial Proteins/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Molecular Sequence Data ; Phylogeny ; Ribosomal Proteins/*genetics ; Sequence Alignment ; Zinc ; }, abstract = {BACKGROUND: The universal ribosomal protein S4 is essential for the initiation of small subunit ribosomal assembly and translational accuracy. Being part of the information processing machinery of the cell, the gene for S4 is generally thought of as being inherited vertically and has been used in concatenated gene phylogenies. Here we report the evolution of ribosomal protein S4 in relation to a broad sharing of zinc/non-zinc forms of the gene and study the scope of horizontal gene transfer (HGT) of S4 during bacterial evolution.<br><br>RESULTS: In this study we present the complex evolutionary history of ribosomal protein S4 using 660 bacterial genomes from 16 major bacterial phyla. According to conserved characteristics in the sequences, S4 can be classified into C+ (zinc-binding) and C- (zinc-free) variants, with 26 genomes (mainly from the class Clostridia) containing genes for both. A maximum likelihood phylogenetic tree of the S4 sequences was incongruent with the standard bacterial phylogeny, indicating a departure from strict vertical inheritance. Further analysis using the genome content near the S4 genes, which are usually located in a conserved gene cluster, showed not only that HGT of the C- gene had occurred at various stages of bacterial evolution, but also that both the C- and C+ genes were present before the individual phyla diverged. To explain the latter, we theorize that a gene pool existed early in bacterial evolution from which bacteria could sample S4 gene variants, according to environmental conditions. The distribution of the C+/- variants for seven other zinc-binding ribosomal proteins in these 660 bacterial genomes is consistent with that seen for S4 and may shed light on the evolutionary pressures involved.<br><br>CONCLUSION: The complex history presented for "core" protein S4 suggests the existence of a gene pool before the emergence of bacterial lineages and reflects the pervasive nature of HGT in subsequent bacterial evolution. This has implications for both theoretical models of evolution and practical applications of phylogenetic reconstruction as well as the control of zinc economy in bacterial cells.}, }
@article {pmid19639238, year = {2009}, author = {Swigonová, Z and Mohsen, AW and Vockley, J}, title = {Acyl-CoA dehydrogenases: Dynamic history of protein family evolution.}, journal = {Journal of molecular evolution}, volume = {69}, number = {2}, pages = {176-193}, pmid = {19639238}, issn = {1432-1432}, support = {R01 DK054936/DK/NIDDK NIH HHS/United States ; R01-DK54936/DK/NIDDK NIH HHS/United States ; }, mesh = {Acyl-CoA Dehydrogenases/chemistry/*genetics ; Amino Acid Sequence ; Bayes Theorem ; Conserved Sequence ; *Evolution, Molecular ; Glutaryl-CoA Dehydrogenase/genetics ; Humans ; Molecular Sequence Data ; Multigene Family/*genetics ; Phylogeny ; }, abstract = {The acyl-CoA dehydrogenases (ACADs) are enzymes that catalyze the alpha,beta-dehydrogenation of acyl-CoA esters in fatty acid and amino acid catabolism. Eleven ACADs are now recognized in the sequenced human genome, and several homologs have been reported from bacteria, fungi, plants, and nematodes. We performed a systematic comparative genomic study, integrating homology searches with methods of phylogenetic reconstruction, to investigate the evolutionary history of this family. Sequence analyses indicate origin of the family in the common ancestor of Archaea, Bacteria, and Eukaryota, illustrating its essential role in the metabolism of early life. At least three ACADs were already present at that time: ancestral glutaryl-CoA dehydrogenase (GCD), isovaleryl-CoA dehydrogenase (IVD), and ACAD10/11. Two gene duplications were unique to the eukaryotic domain: one resulted in the VLCAD and ACAD9 paralogs and another in the ACAD10 and ACAD11 paralogs. The overall patchy distribution of specific ACADs across the tree of life is the result of dynamic evolution that includes numerous rounds of gene duplication and secondary losses, interdomain lateral gene transfer events, alteration of cellular localization, and evolution of novel proteins by domain acquisition. Our finding that eukaryotic ACAD species are more closely related to bacterial ACADs is consistent with endosymbiotic origin of ACADs in eukaryotes and further supported by the localization of all nine previously studied ACADs in mitochondria.}, }
@article {pmid19639166, year = {2009}, author = {Sinkovics, JG}, title = {Horizontal gene transfers and cell fusions in microbiology, immunology and oncology (Review).}, journal = {International journal of oncology}, volume = {35}, number = {3}, pages = {441-465}, doi = {10.3892/ijo_00000357}, pmid = {19639166}, issn = {1019-6439}, mesh = {Allergy and Immunology ; Animals ; *Cell Fusion ; Cell Transformation, Neoplastic/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Humans ; Microbiology ; }, abstract = {Evolving young genomes of archaea, prokaryota and unicellular eukaryota were wide open for the acceptance of alien genomic sequences, which they often preserved and vertically transferred to their descendants throughout three billion years of evolution. Established complex large genomes, although seeded with ancestral retroelements, have come to regulate strictly their integrity. However, intruding retroelements, especially the descendents of Ty3/Gypsy, the chromoviruses, continue to find their ways into even the most established genomes. The simian and hominoid-Homo genomes preserved and accommodated a large number of endogenous retroviral genomic segments. These retroelements may mature into exogenous retroviruses, or into functional new genes. Phages and viruses have been instrumental in incorporating and transferring host cell genes. These events profoundly influenced and altered the course of evolution. Horizontal (lateral) gene transfers (HGT) overwhelmed the genomes of the ancient protocells and the evolving unicellular microorganisms, actually leading to their Cambrian explosion. While the rigidly organized genomes of multicellular organisms increasingly resist H/LGT, de-differentiated cells assuming the metabolism of their onto- or phylogenetic ancestors, open up widely to the practice of H/LGT by direct transfer, or to transfers mediated by viruses, or by cell fusions. This activity is intensified in malignantly transformed cells, thus rendering these subjects receptive to therapy with oncolytic viruses and with viral vectors of tumor-suppressive or immunogenic genetic materials. Naturally formed hybrids of dendritic and tumor cells are often tolerogenic, whereas laboratory products of these unisons may be immunogenic in the hosts of origin. As human breast cancer stem cells are induced by a treacherous class of CD8+ T cells to undergo epithelial to mesenchymal (ETM) transition and to yield to malignant transformation by the omnipresent proto-ocogenes (for example, the ras oncogenes), they become defenseless toward oncolytic viruses. Cell fusions and horizontal exchanges of genes are fundamental attributes and inherent characteristics of the living matter.}, }
@article {pmid19638172, year = {2009}, author = {Pagarete, A and Allen, MJ and Wilson, WH and Kimmance, SA and de Vargas, C}, title = {Host-virus shift of the sphingolipid pathway along an Emiliania huxleyi bloom: survival of the fattest.}, journal = {Environmental microbiology}, volume = {11}, number = {11}, pages = {2840-2848}, doi = {10.1111/j.1462-2920.2009.02006.x}, pmid = {19638172}, issn = {1462-2920}, mesh = {Biosynthetic Pathways/*genetics ; DNA, Algal/chemistry/genetics ; Gene Expression Profiling ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Norway ; Oxidoreductases/biosynthesis/genetics ; Phycodnaviridae/*genetics ; Phytoplankton/*metabolism/*virology ; Sequence Analysis, DNA ; Serine C-Palmitoyltransferase/biosynthesis/genetics ; Sphingolipids/*biosynthesis ; Water Microbiology ; }, abstract = {The interactions between viruses and phytoplankton play a key role in shaping the ecological and evolutionary dynamics of oceanic ecosystems. One of the most fascinating examples of horizontal gene transfer between a eukaryotic host and its virus is a de novo sphingolipid biosynthesis pathway (SBP) found in the genomes of both Emiliania huxleyi and its coccolithovirus EhV-86. Here, we focus on a natural E. huxleyi/coccolithovirus system off the coast of Norway and investigate the dynamics of host and virus homologous gene expression for two of the most important sphingolipid biosynthesis enzymes, serine palmitoyl transferase (SPT) and dihydroceramide desaturase (DCD). Transcriptional dynamics display three defined stages along E. huxleyi bloom formation and decline, with the coccolithovirus transcripts taking over and controlling the SBP in stages 2 and 3. The observed patterns fit the hypothesis according to which viral sphingolipids are involved in the timing and physical processes of virion release from the host cells. This study provides a unique insight into the transcriptional interplay of homologous metabolic pathways between virus and host during temporal progression of oceanic E. huxleyi blooms.}, }
@article {pmid19635028, year = {2009}, author = {Brandt, CM and Spellerberg, B}, title = {Human infections due to Streptococcus dysgalactiae subspecies equisimilis.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {49}, number = {5}, pages = {766-772}, doi = {10.1086/605085}, pmid = {19635028}, issn = {1537-6591}, mesh = {Anti-Bacterial Agents/therapeutic use ; Bacterial Typing Techniques ; Drug Resistance, Bacterial ; Humans ; Phylogeny ; Streptococcal Infections/*epidemiology/immunology/*microbiology ; Streptococcus/*classification/genetics/*pathogenicity ; Virulence/genetics ; }, abstract = {Human streptococci that belong to Streptococcus dysgalactiae subspecies equisimilis (SDSE) have long been known under the name of beta-hemolytic groups C and G streptococci. Extensive taxonomic studies during the past years have distinguished most of the veterinary pathogens belonging to Lancefield groups C and G from those of human origin. After being considered nonpathogenic for many years, SDSE is now recognized as an important bacterial pathogen. The clinical spectrum of diseases caused by this species closely resembles Streptococcus pyogenes infections, including the occurrence of poststreptococcal sequelae. In accordance with these observations, many of the virulence factors present in S. pyogenes can also be found in SDSE strains. High nucleotide-sequence identities in virulence genes and the association of these genes with mobile genetic elements support the hypothesis of extensive horizontal gene-transfer events among streptococcal species of the pyogenic group. Recent epidemiological studies have shown increasing numbers of invasive SDSE infections, often among immunocompromised patients, and suggest that this species will probably gain even more clinical importance in the near future. For a better understanding of the changing epidemiology and pathogenicity of SDSE, an increased awareness of these microorganisms as human pathogens and proper identification are mandatory.}, }
@article {pmid19634195, year = {2009}, author = {Snir, S and Tuller, T}, title = {The NET-HMM approach: phylogenetic network inference by combining maximum likelihood and Hidden Markov Models.}, journal = {Journal of bioinformatics and computational biology}, volume = {7}, number = {4}, pages = {625-644}, doi = {10.1142/s021972000900428x}, pmid = {19634195}, issn = {0219-7200}, mesh = {*Algorithms ; Animals ; *Biological Evolution ; Computer Simulation ; Data Interpretation, Statistical ; Gene Transfer, Horizontal/*genetics ; *Genetics, Population ; Humans ; Likelihood Functions ; Markov Chains ; *Models, Genetic ; Models, Statistical ; *Pedigree ; *Phylogeny ; }, abstract = {Horizontal gene transfer (HGT) is the event of transferring genetic material from one lineage in the evolutionary tree to a different lineage. HGT plays a major role in bacterial genome diversification and is a significant mechanism by which bacteria develop resistance to antibiotics. Although the prevailing assumption is of complete HGT, cases of partial HGT (which are also named chimeric HGT) where only part of a gene is horizontally transferred, have also been reported, albeit less frequently. In this work we suggest a new probabilistic model, the NET-HMM, for analyzing and modeling phylogenetic networks. This new model captures the biologically realistic assumption that neighboring sites of DNA or amino acid sequences are not independent, which increases the accuracy of the inference. The model describes the phylogenetic network as a Hidden Markov Model (HMM), where each hidden state is related to one of the network's trees. One of the advantages of the NET-HMM is its ability to infer partial HGT as well as complete HGT. We describe the properties of the NET-HMM, devise efficient algorithms for solving a set of problems related to it, and implement them in software. We also provide a novel complementary significance test for evaluating the fitness of a model (NET-HMM) to a given dataset. Using NET-HMM, we are able to answer interesting biological questions, such as inferring the length of partial HGT's and the affected nucleotides in the genomic sequences, as well as inferring the exact location of HGT events along the tree branches. These advantages are demonstrated through the analysis of synthetical inputs and three different biological inputs.}, }
@article {pmid19634194, year = {2009}, author = {Van Iersel, L and Kelk, S and Mnich, M}, title = {Uniqueness, intractability and exact algorithms: reflections on level-k phylogenetic networks.}, journal = {Journal of bioinformatics and computational biology}, volume = {7}, number = {4}, pages = {597-623}, doi = {10.1142/s0219720009004308}, pmid = {19634194}, issn = {0219-7200}, mesh = {*Algorithms ; Animals ; Computer Simulation ; Gene Transfer, Horizontal/*genetics ; *Genetics, Population ; Humans ; *Models, Genetic ; *Pedigree ; *Phylogeny ; }, abstract = {Phylogenetic networks provide a way to describe and visualize evolutionary histories that have undergone so-called reticulate evolutionary events such as recombination, hybridization or horizontal gene transfer. The level k of a network determines how non-treelike the evolution can be, with level-0 networks being trees. We study the problem of constructing level-k phylogenetic networks from triplets, i.e. phylogenetic trees for three leaves (taxa). We give, for each k, a level-k network that is uniquely defined by its triplets. We demonstrate the applicability of this result by using it to prove that (1) for all k > or = 1 it is NP-hard to construct a level-k network consistent with all input triplets, and (2) for all k > or = 0 it is NP-hard to construct a level-k network consistent with a maximum number of input triplets, even when the input is dense. As a response to this intractability, we give an exact algorithm for constructing level-1 networks consistent with a maximum number of input triplets.}, }
@article {pmid19632175, year = {2009}, author = {Perez, JC and Groisman, EA}, title = {Evolution of transcriptional regulatory circuits in bacteria.}, journal = {Cell}, volume = {138}, number = {2}, pages = {233-244}, pmid = {19632175}, issn = {1097-4172}, support = {/HHMI/Howard Hughes Medical Institute/United States ; 42236//PHS HHS/United States ; 49561//PHS HHS/United States ; }, mesh = {Bacteria/*genetics/*metabolism ; Bacterial Proteins/genetics/metabolism ; *Evolution, Molecular ; *Gene Expression Regulation, Bacterial ; *Gene Regulatory Networks ; Transcription Factors/genetics/metabolism ; }, abstract = {Related organisms typically respond to a given cue by altering the level or activity of orthologous transcription factors, which, paradoxically, often regulate expression of distinct gene sets. Although promoter rewiring of shared genes is primarily responsible for regulatory differences among related eukaryotic species, in bacteria, species-specific genes are often controlled by ancestral transcription factors, and regulatory circuit evolution has been further shaped by horizontal gene transfer. Modifications in transcription factors and in promoter structure also contribute to divergence in bacterial regulatory circuits.}, }
@article {pmid19631737, year = {2009}, author = {Gribaldo, S and Brochier, C}, title = {Phylogeny of prokaryotes: does it exist and why should we care?.}, journal = {Research in microbiology}, volume = {160}, number = {7}, pages = {513-521}, doi = {10.1016/j.resmic.2009.07.006}, pmid = {19631737}, issn = {1769-7123}, mesh = {Archaea/*classification/*genetics ; Bacteria/*classification/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Phylogeny ; Prokaryotic Cells ; }, abstract = {Understanding microbial evolution is essential for gathering information on the most ancient events in the history of Life on our planet. Nevertheless, the idea that it is impossible to reconstruct the evolutionary history of prokaryotes because of horizontal gene transfer has become very popular. We review this important debate and how it can be solved.}, }
@article {pmid19630513, year = {2009}, author = {Mathew, AG and Liamthong, S and Lin, J and Hong, Y}, title = {Evidence of class 1 integron transfer between Escherichia coli and Salmonella spp. on livestock farms.}, journal = {Foodborne pathogens and disease}, volume = {6}, number = {8}, pages = {959-964}, doi = {10.1089/fpd.2009.0263}, pmid = {19630513}, issn = {1556-7125}, mesh = {Animals ; Animals, Domestic/*microbiology ; Chickens/microbiology ; Cloaca/microbiology ; DNA, Bacterial/*genetics/isolation &amp; purification ; Drug Resistance, Bacterial/genetics ; Escherichia coli/*genetics/isolation &amp; purification ; Feces/microbiology ; Female ; *Gene Transfer, Horizontal ; Genetic Variation ; Integrons/*genetics ; Male ; Plasmids/isolation &amp; purification/metabolism ; Polymerase Chain Reaction ; Rectum/microbiology ; Salmonella/*genetics/isolation &amp; purification ; Sus scrofa/microbiology ; Thailand ; United States ; }, abstract = {A study was conducted to determine if homologous integrons occurred in Escherichia coli and Salmonella spp. within livestock production sites in the United States and Thailand suggesting transfer of genetic resistance elements between those organisms. Fecal samples were collected via rectal swabs from live swine in the United States and Thailand, and cloacal swabs from live chickens in Thailand, and killed chickens at a U.S. abattoir. Isolates were derived only from farms harboring both Salmonella and E. coli, resulting in the inclusion of 571 E. coli and 98 Salmonella isolates derived from both livestock species in the United States and Thailand. Class 1 integron variable regions were detected using polymerase chain reaction targeting 5' and 3' conserved sequences. When integron-positive E. coli and Salmonella from the same farm had identical amplicon patterns, polymerase chain reaction products were sequenced to determine homology. Nine integron amplicons, with sizes ranging from 0.5 to 2.5 kb, were observed in bacterial isolates, and we found a single swine farm in Thailand from which identical amplicons were observed in both E. coli and Salmonella. Sequence analysis revealed a 1.0 kb amplicon common to both bacteria contained an aadA1 gene cassette encoding aminoglycoside 3'-adenyltransferase, conferring resistance to streptomycin and spectinomycin. A 2.0 kb amplicon was also found in both types of bacteria from that farm, containing an aadA5 gene encoding aminoglycoside 3'-adenyltransferase, an additional reading frame, orfD, with unknown function, and a dfrA17 gene encoding dihydrofolate reductase, conferring resistance to trimethoprim. Further analyses determined the amplicons were contained on plasmid DNA in both E. coli and Salmonella, and a plasmid of similar size was identified in both species and was found to harbor the class 1 integron. Our results indicate that while in most cases, integrons of coexisting E. coli and Salmonella differed, identical integron amplicons were found in those species from a single swine farm in Thailand, suggesting horizontal transfer between these two organisms may have occurred on-farm.}, }
@article {pmid19594870, year = {2009}, author = {Gu, J and Neary, J and Cai, H and Moshfeghian, A and Rodriguez, SA and Lilburn, TG and Wang, Y}, title = {Genomic and systems evolution in Vibrionaceae species.}, journal = {BMC genomics}, volume = {10 Suppl 1}, number = {Suppl 1}, pages = {S11}, pmid = {19594870}, issn = {1471-2164}, support = {SC1 GM081068/GM/NIGMS NIH HHS/United States ; R21 AI067543/AI/NIAID NIH HHS/United States ; SC1AI080579/AI/NIAID NIH HHS/United States ; SC1 GM081068-01/GM/NIGMS NIH HHS/United States ; 1R21AI067543/AI/NIAID NIH HHS/United States ; SC1GM081068/GM/NIGMS NIH HHS/United States ; T34 GM007717/GM/NIGMS NIH HHS/United States ; GM-07717/GM/NIGMS NIH HHS/United States ; SC1 AI080579-03/AI/NIAID NIH HHS/United States ; SC1 AI080579/AI/NIAID NIH HHS/United States ; SC1 AI080579-02/AI/NIAID NIH HHS/United States ; }, mesh = {Comparative Genomic Hybridization ; *Evolution, Molecular ; *Genome, Bacterial ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; Vibrionaceae/*genetics ; }, abstract = {BACKGROUND: The steadily increasing number of prokaryotic genomes has accelerated the study of genome evolution; in particular, the availability of sets of genomes from closely related bacteria has facilitated the exploration of the mechanisms underlying genome plasticity. The family Vibrionaceae is found in the Gammaproteobacteria and is abundant in aquatic environments. Taxa from the family Vibrionaceae are diversified in their life styles; some species are free living, others are symbiotic, and others are human pathogens. This diversity makes this family a useful set of model organisms for studying bacterial evolution. This evolution is driven by several forces, among them gene duplication and lateral gene transfer, which are believed to provide raw material for functional redundancy and novelty. The resultant gene copy increase in one genome is then detected as lineage-specific expansion (LSE).<br><br>RESULTS: Here we present the results of a detailed comparison of the genomes of eleven Vibrionaceae strains that have distinct life styles and distinct phenotypes. The core genome shared by all eleven strains is composed of 1,882 genes, which make up about 31%-50% of the genome repertoire. We further investigated the distribution and features of genes that have been specifically expanded in one unique lineage of the eleven strains. Abundant duplicate genes have been identified in the eleven Vibrionaceae strains, with 1-11% of the whole genomes composed lineage specific radiations. These LSEs occurred in two distinct patterns: the first type yields one or more copies of a single gene; we call this a single gene expansion. The second pattern has a high evolutionary impact, as the expansion involves two or more gene copies in a block, with the duplicated block located next to the original block (a contiguous block expansion) or at some distance from the original block (a discontiguous block expansion). We showed that LSEs involve genes that are tied to defense and pathogenesis mechanisms as well as in the fundamental life cycle of Vibrionaceae species.<br><br>CONCLUSION: Our results provide evidence of genome plasticity and rapid evolution within the family Vibrionaceae. The comparisons point to sources of genomic variation and candidates for lineage-specific adaptations of each Vibrionaceae pathogen or nonpathogen strain. Such lineage specific expansions could reveal components in bacterial systems that, by their enhanced genetic variability, can be tied to responses to environmental challenges, interesting phenotypes, or adaptive pathogenic responses to host challenges.}, }
@article {pmid19623575, year = {2009}, author = {Tome, Y and Tsuchiya, H and Hayashi, K and Yamauchi, K and Sugimoto, N and Kanaya, F and Tomita, K and Hoffman, RM}, title = {In vivo gene transfer between interacting human osteosarcoma cell lines is associated with acquisition of enhanced metastatic potential.}, journal = {Journal of cellular biochemistry}, volume = {108}, number = {2}, pages = {362-367}, doi = {10.1002/jcb.22259}, pmid = {19623575}, issn = {1097-4644}, mesh = {Animals ; Bone Neoplasms ; Cell Communication ; Cell Line, Tumor ; Drug Resistance, Neoplasm ; Female ; *Gene Transfer, Horizontal ; *Genes, ras ; Germ-Free Life ; Humans ; Luminescent Proteins/biosynthesis/genetics ; Lung Neoplasms/pathology/secondary ; Matched-Pair Analysis ; Mice ; Mice, Nude ; Molecular Imaging/methods ; Neoplasm Metastasis/*genetics/pathology ; Neoplasm Transplantation ; Osteosarcoma/*genetics/pathology ; Retroviridae/genetics ; Tibia ; Transduction, Genetic ; Tumor Burden ; }, abstract = {We report here in vivo gene transfer between cancer cells is associated with acquisition of high metastatic behavior. The 143B-GFP cell line with high metastatic potential and the MNNG/HOS-RFP cell line with low metastatic potential, both derived from the TE85 human osteosarcoma cell line, were either co-transplanted or transplanted alone in the tibia in nude mice. Upon mixed transplantation of the two differently labeled sublines, resulting metastatic colonies are single colored either red or green, thereby demonstrating their clonality and enabling facile color-coded quantification. When MNNG/HOS-RFP and 143B-GFP were co-transplanted in the tibia, the number of lung metastases of MNNG/HOS-RFP increased eight-fold compared to MNNG/HOS-RFP transplanted alone (P < 0.01). In contrast, no enhancement of MNNG/HOS-RFP metastases occurred when MNNG/HOS-RFP and 143B-GFP were transplanted separately in the right and left tibiae, respectively. This result suggests that the presence of 143B-GFP increased the metastatic potential of MNNG/HOS-RFP within the mixed tumor. We observed transfer of the Ki-ras gene from 143B-GFP to MNNG/HOS-RFP after they were co-implanted suggesting the Ki-ras played a role in increasing the metastatic potential of MNNG/HOS-RFP in the presence of 143B-GFP. These data suggest the possible role of in vivo gene transfer in enhancing the metastatic potential of cancer cells. The data also further demonstrated the power of color-coded imaging to visualize cancer-cell/cancer-cell interactions in vivo.}, }
@article {pmid19622749, year = {2009}, author = {Tumbale, P and Brew, K}, title = {Characterization of a metal-independent CAZy family 6 glycosyltransferase from Bacteroides ovatus.}, journal = {The Journal of biological chemistry}, volume = {284}, number = {37}, pages = {25126-25134}, pmid = {19622749}, issn = {1083-351X}, support = {R01 AR040994/AR/NIAMS NIH HHS/United States ; AR40994/AR/NIAMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Antigens, Bacterial/chemistry ; Bacteroides/*enzymology ; Base Sequence ; Carbohydrates/chemistry ; Catalysis ; Catalytic Domain ; Cloning, Molecular ; DNA Mutational Analysis ; Escherichia coli/metabolism ; Glycosyltransferases/*chemistry/metabolism ; Kinetics ; Metals/*chemistry ; Molecular Sequence Data ; Protein Structure, Tertiary ; }, abstract = {The myriad functions of complex carbohydrates include modulating interactions between bacteria and their eukaryotic hosts. In humans and other vertebrates, variations in the activity of glycosyltransferases of CAZy family 6 generate antigenic variation between individuals and species that facilitates resistance to pathogens. The well characterized vertebrate glycosyltransferases of this family are multidomain membrane proteins with C-terminal catalytic domains. Genes for proteins homologous with their catalytic domains are found in at least nine species of anaerobic commensal bacteria and a cyanophage. Although the bacterial proteins are strikingly similar in sequence to the catalytic domains of their eukaryotic relatives, a metal-binding Asp-X-Asp sequence, present in a wide array of metal ion-dependent glycosyltransferases, is replaced by Asn-X-Asn. We have cloned and expressed one of these proteins from Bacteroides ovatus, a bacterium that is linked to inflammatory bowel disease. Functional characterization shows it to be a metal-independent glycosyltransferase with a 200-fold preference for UDP-GalNAc as substrate relative to UDP-Gal. It efficiently catalyzes the synthesis of oligosaccharides similar to human blood group A and may participate in the synthesis of the bacterial O-antigen. The kinetics for GalNAc transfer to 2'-fucosyl lactose are characteristic of a sequential mechanism, as observed previously for this family. Mutational studies indicate that despite the lack of a metal cofactor, there are pronounced similarities in structure-function relationships between the bacterial and vertebrate family 6 glycosyltransferases. These two groups appear to provide an example of horizontal gene transfer involving vertebrates and prokaryotes.}, }
@article {pmid19619625, year = {2009}, author = {Bustos, O and Naik, S and Ayers, G and Casola, C and Perez-Lamigueiro, MA and Chippindale, PT and Pritham, EJ and de la Casa-Esperón, E}, title = {Evolution of the Schlafen genes, a gene family associated with embryonic lethality, meiotic drive, immune processes and orthopoxvirus virulence.}, journal = {Gene}, volume = {447}, number = {1}, pages = {1-11}, pmid = {19619625}, issn = {1879-0038}, mesh = {Animals ; Codon ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Lethal ; Humans ; Immunity ; *Meiosis ; Mice ; Multigene Family/*genetics ; Orthopoxvirus/*genetics/pathogenicity ; Phylogeny ; Virulence/genetics ; }, abstract = {Genes of the Schlafen family, first discovered in mouse, are expressed in hematopoietic cells and are involved in immune processes. Previous results showed that they are candidate genes for two major phenomena: meiotic drive and embryonic lethality (DDK syndrome). However, these genes remain poorly understood, mostly due to the limitations imposed by their similarity, close location and the potential functional redundancy of the gene family members. Here we use genomic and phylogenetic studies to investigate the evolution and role of this family of genes. Our results show that the Schlafen family is widely distributed in mammals, where we recognize four major clades that experienced lineage-specific expansions or contractions in various orders, including primates and rodents. In addition, we identified members of the Schlafen family in Chondrichthyes and Amphibia, indicating an ancient origin of these genes. We find evidence that positive selection has acted on many Schlafen genes. Moreover, our analyses indicate that a member of the Schlafen family was horizontally transferred from murine rodents to orthopoxviruses, where it is hypothesized to play a role in allowing the virus to survive host immune defense mechanisms. The functional relevance of the viral Schlafen sequences is further underscored by our finding that they are evolving under purifying selection. This is of particular importance, since orthopoxviruses infect mammals and include variola, the causative agent of smallpox, and monkeypox, an emerging virus of great concern for human health.}, }
@article {pmid19619164, year = {2009}, author = {Nedelcu, AM and Blakney, AJ and Logue, KD}, title = {Functional replacement of a primary metabolic pathway via multiple independent eukaryote-to-eukaryote gene transfers and selective retention.}, journal = {Journal of evolutionary biology}, volume = {22}, number = {9}, pages = {1882-1894}, doi = {10.1111/j.1420-9101.2009.01797.x}, pmid = {19619164}, issn = {1420-9101}, mesh = {Animals ; *Biological Evolution ; Cation Transport Proteins/genetics ; Choanoflagellata/*genetics ; Eukaryota/genetics ; *Gene Transfer, Horizontal ; Glutamate Synthase/genetics ; Glutamate-Ammonia Ligase/genetics ; Metabolic Networks and Pathways/*genetics ; }, abstract = {Although lateral gene transfer (LGT) is now recognized as a major force in the evolution of prokaryotes, the contribution of LGT to the evolution and diversification of eukaryotes is less understood. Notably, transfers of complete pathways are believed to be less likely between eukaryotes, because the successful transfer of a pathway requires the physical clustering of functionally related genes. Here, we report that in one of the closest unicellular relatives of animals, the choanoflagellate, Monosiga, three genes whose products work together in the glutamate synthase cycle are of algal origin. The concerted retention of these three independently acquired genes is best explained as the consequence of a series of adaptive replacement events. More generally, this study argues that (i) eukaryote-to-eukaryote transfers of entire metabolic pathways are possible, (ii) adaptive functional replacements of primary pathways can occur, and (iii) functional replacements involving eukaryotic genes are likely to have also contributed to the evolution of eukaryotes. Lastly, these data underscore the potential contribution of algal genes to the evolution of nonphotosynthetic lineages.}, }
@article {pmid19617370, year = {2009}, author = {Caro-Quintero, A and Rodriguez-Castaño, GP and Konstantinidis, KT}, title = {Genomic insights into the convergence and pathogenicity factors of Campylobacter jejuni and Campylobacter coli species.}, journal = {Journal of bacteriology}, volume = {191}, number = {18}, pages = {5824-5831}, pmid = {19617370}, issn = {1098-5530}, mesh = {Bacterial Proteins/genetics ; Campylobacter coli/genetics/*pathogenicity ; Campylobacter jejuni/genetics/*pathogenicity ; Databases, Genetic ; *Evolution, Molecular ; Gene Flow ; *Gene Transfer, Horizontal ; Genetic Speciation ; Genome, Bacterial ; *Genomics ; Sequence Analysis, DNA/*methods ; }, abstract = {Whether or not bacteria form coherent evolutionary groups via means of genetic exchange and, hence, elicit distinct species boundaries remains an unsettled issue. A recent report implied that not only may the former be true but also, in fact, the clearly distinct Campylobacter jejuni and Campylobacter coli species may be converging as a consequence of increased interspecies gene flow fostered, presumably, by the recent invasion of an overlapping ecological niche (S. K. Sheppard, N. D. McCarthy, D. Falush, and M. C. Maiden, Science 320:237-239, 2008). We have reanalyzed the Campylobacter multilocus sequence typing database used in the previous study and found that the number of interspecies gene transfer events may actually be too infrequent to account, unequivocally, for species convergence. For instance, only 1 to 2% of the 4,507 Campylobacter isolates examined appeared to have imported gene alleles from another Campylobacter species. Furthermore, by analyzing the available Campylobacter genomic sequences, we show that although there seems to be a slightly higher number of exchanged genes between C. jejuni and C. coli relative to other comparable species (approximately 10% versus 2 to 3% of the total genes in the genome, respectively), the function and spatial distribution in the genome of the exchanged genes are far from random, and hence, inconsistent with the species convergence hypothesis. In fact, the exchanged genes appear to be limited to a few environmentally selected cellular functions. Accordingly, these genes may represent important pathogenic determinants of pathogenic Campylobacter, and convergence of (any) two bacterial species remains to be seen.}, }
@article {pmid19616092, year = {2009}, author = {Ghosh, W and Mallick, S and DasGupta, SK}, title = {Origin of the Sox multienzyme complex system in ancient thermophilic bacteria and coevolution of its constituent proteins.}, journal = {Research in microbiology}, volume = {160}, number = {6}, pages = {409-420}, doi = {10.1016/j.resmic.2009.07.003}, pmid = {19616092}, issn = {1769-7123}, mesh = {Bacteria/classification/*genetics/metabolism ; Bacterial Proteins/*genetics/metabolism ; *Evolution, Molecular ; Hot Temperature ; Multienzyme Complexes ; Phylogeny ; SOX Transcription Factors/*genetics/metabolism ; }, abstract = {The multienzyme complex SoxXABYZ(CD)(2), characteristic of facultatively chemolithotrophic Alphaproteobacteria, oxidizes both sulfone and sulfane sulfur species directly to sulfate, while a truncated SoxXABYZ oxidizes only sulfone sulfur in species of Chromatiaceae and Chlorobi. Here we phylogenetically analyzed SoxXA, SoxYZ and SoxCD sequences, correlated the results with earlier SoxB-based data, and postulated that the system originated in putatively common ancestors of Aquificae and Epsilonproteobacteria, and evolved through extensive horizontal gene transfer, accompanied by gain and/or loss of constituents by different lineages. However, in several Sox systems, particularly those from Alphaproteobacteria (and also Chromatiaceae and Chlorobi), there has been no extra gain or loss of constituents and all their proteins have similar evolutionary paths. This implies that the components of these systems have coevolved parallel to each other without any shuffling with other divergent systems. This, however, holds good only for those Sox systems, which render sulfur oxidation functions equivalent to the typical alphaproteobacterial process. We postulate that coevolution of all the proteins is essential for the typical modular function of Sox. Conversely, mosaic Sox systems (where constituents have disparate phylogenetic paths) are either nonfunctional or with activities deviated from typical systems. Monomeric Sox subunits of the mosaic systems, however, possess almost all the motifs and conserved domains critical for their designated activity and heterodimer formation. So what could be the basis of the functional discrepancies of the mosaic Sox systems? It appears that their discretely evolved heterodimers cannot interact among themselves in the same way as ideally envisaged in the modular Sox system, which in turn, may in some cases lead to novel adventitious reactions.}, }
@article {pmid19615432, year = {2009}, author = {Li, G and Zhang, QJ and Zhong, J and Wang, YQ}, title = {Evolutionary and functional diversity of green fluorescent proteins in cephalochordates.}, journal = {Gene}, volume = {446}, number = {1}, pages = {41-49}, doi = {10.1016/j.gene.2009.07.003}, pmid = {19615432}, issn = {1879-0038}, mesh = {Animals ; Base Sequence ; Chordata, Nonvertebrate/genetics/growth &amp; development/metabolism ; DNA Primers/genetics ; Evolution, Molecular ; Exons ; Female ; Gene Expression Regulation, Developmental ; Green Fluorescent Proteins/*genetics/isolation &amp; purification/metabolism ; Introns ; Multigene Family ; Phylogeny ; Promoter Regions, Genetic ; Recombinant Proteins/genetics/isolation &amp; purification ; Species Specificity ; Spectrometry, Fluorescence ; }, abstract = {Green fluorescent protein (GFP) has been widely used as a molecular marker in modern biological research. Before the recent report of one GFP gene in Branchiostoma floridae, GFP family members were cloned only from other two groups of species: Cnidaria and Copepoda. Here we describe the complete GFP gene repertoire of B. floridae which includes 13 functional genes and 2 pseudogenes, representing the largest GFP family found so far. Coupling with nine other GFP sequences from another two species of genus Branchiostoma and the sequences from Cnidaria and Copepoda, we made a deep-level phylogenetic analysis for GFP genes in cephalochordates and found: 1) GFP genes have experienced a divergent evolution in cephalochordates; 2) all amphioxus GFP genes form four main clades on the tree which had diverged before the radiation of the last common ancestor of all extant cephalochordates; 3) GFP genes in amphioxus shared a common ancestor with that in Copepoda rather than being derived from horizontal gene transfer, which indicates that our ancestor was derived from a fluorescent organism and lost this ability after its separation from Cephalochordata, and also makes GFP a rare gene which has a rather unusual evolutionary path. In addition, we also provided evidence indicating that GFP genes have evolved divergent functions by specializing their expression profile, and different fluorescent spectra by changing their emission peaks. These findings spark two interesting issues: what are GFP in vivo functions in cephalochordates and why they are lost in other examined deuterostomes?}, }
@article {pmid19615092, year = {2009}, author = {Lechner, M and Schmitt, K and Bauer, S and Hot, D and Hubans, C and Levillain, E and Locht, C and Lemoine, Y and Gross, R}, title = {Genomic island excisions in Bordetella petrii.}, journal = {BMC microbiology}, volume = {9}, number = {}, pages = {141}, pmid = {19615092}, issn = {1471-2180}, mesh = {Base Sequence ; Bordetella/*genetics ; Chromosomes, Bacterial/genetics ; DNA Transposable Elements ; DNA, Bacterial/genetics ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomic Instability ; *Genomic Islands ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Phenotype ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Among the members of the genus Bordetella B. petrii is unique, since it is the only species isolated from the environment, while the pathogenic Bordetellae are obligately associated with host organisms. Another feature distinguishing B. petrii from the other sequenced Bordetellae is the presence of a large number of mobile genetic elements including several large genomic regions with typical characteristics of genomic islands collectively known as integrative and conjugative elements (ICEs). These elements mainly encode accessory metabolic factors enabling this bacterium to grow on a large repertoire of aromatic compounds.<br><br>RESULTS: During in vitro culture of Bordetella petrii colony variants appear frequently. We show that this variability can be attributed to the presence of a large number of metastable mobile genetic elements on its chromosome. In fact, the genome sequence of B. petrii revealed the presence of at least seven large genomic islands mostly encoding accessory metabolic functions involved in the degradation of aromatic compounds and detoxification of heavy metals. Four of these islands (termed GI1 to GI3 and GI6) are highly related to ICEclc of Pseudomonas knackmussii sp. strain B13. Here we present first data about the molecular characterization of these islands. We defined the exact borders of each island and we show that during standard culture of the bacteria these islands get excised from the chromosome. For all but one of these islands (GI5) we could detect circular intermediates. For the clc-like elements GI1 to GI3 of B. petrii we provide evidence that tandem insertion of these islands which all encode highly related integrases and attachment sites may also lead to incorporation of genomic DNA which originally was not part of the island and to the formation of huge composite islands. By integration of a tetracycline resistance cassette into GI3 we found this island to be rather unstable and to be lost from the bacterial population within about 100 consecutive generations. Furthermore, we show that GI3 is self transmissible and by conjugation can be transferred to B. bronchiseptica thus proving it to be an active integrative and conjugative element<br><br>CONCLUSION: The results show that phenotypic variation of B. petrii is correlated with the presence of genomic islands. Tandem integration of related islands may contribute to island evolution by the acquisition of genes originally belonging to the bacterial core genome. In conclusion, B. petrii appears to be the first member of the genus in which horizontal gene transfer events have massively shaped its genome structure.}, }
@article {pmid19614596, year = {2009}, author = {Whitaker, JW and McConkey, GA and Westhead, DR}, title = {Prediction of horizontal gene transfers in eukaryotes: approaches and challenges.}, journal = {Biochemical Society transactions}, volume = {37}, number = {Pt 4}, pages = {792-795}, doi = {10.1042/BST0370792}, pmid = {19614596}, issn = {1470-8752}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Eukaryotic Cells/*metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Humans ; Phylogeny ; }, abstract = {HGT (horizontal gene transfer) is recognized as an important force in bacterial evolution. Now that many eukaryotic genomes have been sequenced, it has become possible to carry out studies of HGT in eukaryotes. The present review compares the different approaches that exist for identifying HGT genes and assess them in the context of studying eukaryotic evolution. The metabolic evolution resource metaTIGER is then described, with discussion of its application in identification of HGT in eukaryotes.}, }
@article {pmid19614592, year = {2009}, author = {Zámocký, M and Furtmüller, PG and Obinger, C}, title = {Two distinct groups of fungal catalase/peroxidases.}, journal = {Biochemical Society transactions}, volume = {37}, number = {Pt 4}, pages = {772-777}, pmid = {19614592}, issn = {1470-8752}, support = {P 20996/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Catalase/*classification/genetics ; Computational Biology ; Evolution, Molecular ; Fungal Proteins/*classification/genetics ; Fungi/*enzymology ; Gene Transfer, Horizontal ; Peroxidases/*classification/genetics ; *Phylogeny ; }, abstract = {Catalase/peroxidases (KatGs) are bifunctional haem b-containing (Class I) peroxidases with overwhelming catalase activity and substantial peroxidase activity with various one-electron donors. These unique oxidoreductases evolved in ancestral bacteria revealing a complex gene-duplicated structure. Besides being found in numerous bacteria of all phyla, katG genes were also detected in genomes of lower eukaryotes, most prominently of sac and club fungi. Phylogenetic analysis demonstrates the occurrence of two distinct groups of fungal KatGs that differ in localization, structural and functional properties. Analysis of lateral gene transfer of bacterial katGs into fungal genomes reveals that the most probable progenitor was a katG from a bacteroidetes predecessor. The putative physiological role(s) of both fungal KatG groups is discussed with respect to known structure-function relationships in bacterial KatGs and is related with the acquisition of (phyto)pathogenicity in fungi.}, }
@article {pmid19614583, year = {2009}, author = {Laskowski, RA and Thornton, JM and Sternberg, MJ}, title = {The fine details of evolution.}, journal = {Biochemical Society transactions}, volume = {37}, number = {Pt 4}, pages = {723-726}, doi = {10.1042/BST0370723}, pmid = {19614583}, issn = {1470-8752}, mesh = {Animals ; *Biological Evolution ; Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; Humans ; Phosphorylation ; }, abstract = {Charles Darwin's theory of evolution was based on studies of biology at the species level. In the time since his death, studies at the molecular level have confirmed his ideas about the kinship of all life on Earth and have provided a wealth of detail about the evolutionary relationships between different species and a deeper understanding of the finer workings of natural selection. We now have a wealth of data, including the genome sequences of a wide range of organisms, an even larger number of protein sequences, a significant knowledge of the three-dimensional structures of proteins, DNA and other biological molecules, and a huge body of information about the operation of these molecules as systems in the molecular machinery of all living things. This issue of Biochemical Society Transactions contains papers from oral presentations given at a Biochemical Society Focused Meeting to commemorate the 200th Anniversary of Charles Darwin's birth, held on 26-27 January 2009 at the Wellcome Trust Conference Centre, Cambridge. The talks reported on some of the insights into evolution which have been obtained from the study of protein sequences, structures and systems.}, }
@article {pmid19610199, year = {2009}, author = {Flipphi, M and Sun, J and Robellet, X and Karaffa, L and Fekete, E and Zeng, AP and Kubicek, CP}, title = {Biodiversity and evolution of primary carbon metabolism in Aspergillus nidulans and other Aspergillus spp.}, journal = {Fungal genetics and biology : FG &amp; B}, volume = {46 Suppl 1}, number = {}, pages = {S19-S44}, doi = {10.1016/j.fgb.2008.07.018}, pmid = {19610199}, issn = {1096-0937}, mesh = {Amino Acid Sequence ; Aspergillus nidulans/enzymology/*genetics/*metabolism ; Base Sequence ; *Biodiversity ; Carbohydrate Metabolism ; Carbon/*metabolism ; Enzymes/genetics/metabolism ; *Evolution, Molecular ; *Genes, Fungal ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Some of the Aspergilli are reputed for their versatile and efficient catabolism of soluble carbon sources and related metabolites as well as raw polymeric materials. Here, we present a detailed investigation of the genomic and evolutionary basis for this versatility, using seven Aspergillus and one Neosartorya genome sequences. We manually annotated about 155 genes per genome covering glycolysis, the pentose phosphate cycle, alternative routes of D-glucose metabolism, catabolism of D-galactose and pentoses, and the TCA cycle, as well as the utilization of acetate and ethanol, propionate metabolism, and gluconeogenesis.The annotation reveals that the Aspergilli have re-enforced several areas of their primary metabolism(notably glycolysis, TCA cycle, ethanol utilization, and pentose and polyol metabolism) by gene duplications,horizontal gene transfer or gene clustering. Results from the phylogenetic analysis of several enzymes encoded by duplicated genes also suggests that some gene products may have acquired new(physiological) functions, that render primary carbon metabolism of the Aspergilli more complex than previously thought.}, }
@article {pmid19609255, year = {2009}, author = {Langridge, G}, title = {Testing the water: marine metagenomics.}, journal = {Nature reviews. Microbiology}, volume = {7}, number = {8}, pages = {552}, pmid = {19609255}, issn = {1740-1534}, mesh = {Bacteria/classification/*genetics ; Fresh Water/*microbiology ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genomics ; Nucleic Acid Amplification Techniques ; Seawater/*microbiology ; }, }
@article {pmid19608593, year = {2009}, author = {Weinert, LA and Welch, JJ and Jiggins, FM}, title = {Conjugation genes are common throughout the genus Rickettsia and are transmitted horizontally.}, journal = {Proceedings. Biological sciences}, volume = {276}, number = {1673}, pages = {3619-3627}, pmid = {19608593}, issn = {0962-8452}, mesh = {Animals ; Arthropods/microbiology ; Conjugation, Genetic/*genetics ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Phylogeny ; Rickettsia/*genetics ; Synteny ; }, abstract = {Rickettsia are endosymbionts of arthropods, some of which are vectored to vertebrates where they cause disease. Recently, it has been found that some Rickettsia strains harbour conjugative plasmids and others encode some conjugative machinery within the bacterial genome. We investigated the distribution of these conjugation genes in a phylogenetically diverse collection of Rickettsia isolated from arthropods. We found that these genes are common throughout the genus and, in stark contrast to other genes in the genome, conjugation genes are frequently horizontally transmitted between strains. There is no evidence to suggest that these genes are preferentially transferred between phylogenetically related strains, which is surprising given that closely related strains infect similar host species. In addition to detecting patterns of horizontal transmission between diverse Rickettsia species, these findings have implications for the evolution of pathogenicity, the evolution of Rickettsia genomes and the genetic manipulation of intracellular bacteria.}, }
@article {pmid19603075, year = {2009}, author = {Holden, MT and Hauser, H and Sanders, M and Ngo, TH and Cherevach, I and Cronin, A and Goodhead, I and Mungall, K and Quail, MA and Price, C and Rabbinowitsch, E and Sharp, S and Croucher, NJ and Chieu, TB and Mai, NT and Diep, TS and Chinh, NT and Kehoe, M and Leigh, JA and Ward, PN and Dowson, CG and Whatmore, AM and Chanter, N and Iversen, P and Gottschalk, M and Slater, JD and Smith, HE and Spratt, BG and Xu, J and Ye, C and Bentley, S and Barrell, BG and Schultsz, C and Maskell, DJ and Parkhill, J}, title = {Rapid evolution of virulence and drug resistance in the emerging zoonotic pathogen Streptococcus suis.}, journal = {PloS one}, volume = {4}, number = {7}, pages = {e6072}, pmid = {19603075}, issn = {1932-6203}, support = {/WT_/Wellcome Trust/United Kingdom ; 089472/WT_/Wellcome Trust/United Kingdom ; BB/G019274/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; DNA, Bacterial/genetics ; Disease Outbreaks ; Drug Resistance, Microbial/*genetics ; Genome, Bacterial ; Humans ; Phylogeny ; Streptococcal Infections/epidemiology/microbiology ; Streptococcus suis/classification/drug effects/genetics/*pathogenicity ; Virulence/*genetics ; Zoonoses/*microbiology ; }, abstract = {BACKGROUND: Streptococcus suis is a zoonotic pathogen that infects pigs and can occasionally cause serious infections in humans. S. suis infections occur sporadically in human Europe and North America, but a recent major outbreak has been described in China with high levels of mortality. The mechanisms of S. suis pathogenesis in humans and pigs are poorly understood.<br><br>The sequencing of whole genomes of S. suis isolates provides opportunities to investigate the genetic basis of infection. Here we describe whole genome sequences of three S. suis strains from the same lineage: one from European pigs, and two from human cases from China and Vietnam. Comparative genomic analysis was used to investigate the variability of these strains. S. suis is phylogenetically distinct from other Streptococcus species for which genome sequences are currently available. Accordingly, approximately 40% of the approximately 2 Mb genome is unique in comparison to other Streptococcus species. Finer genomic comparisons within the species showed a high level of sequence conservation; virtually all of the genome is common to the S. suis strains. The only exceptions are three approximately 90 kb regions, present in the two isolates from humans, composed of integrative conjugative elements and transposons. Carried in these regions are coding sequences associated with drug resistance. In addition, small-scale sequence variation has generated pseudogenes in putative virulence and colonization factors.<br><br>CONCLUSIONS/SIGNIFICANCE: The genomic inventories of genetically related S. suis strains, isolated from distinct hosts and diseases, exhibit high levels of conservation. However, the genomes provide evidence that horizontal gene transfer has contributed to the evolution of drug resistance.}, }
@article {pmid19594957, year = {2009}, author = {Puigbò, P and Wolf, YI and Koonin, EV}, title = {Search for a 'Tree of Life' in the thicket of the phylogenetic forest.}, journal = {Journal of biology}, volume = {8}, number = {6}, pages = {59}, pmid = {19594957}, issn = {1475-4924}, support = {//Intramural NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacteria/*genetics ; Conserved Sequence ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Variation ; Models, Theoretical ; *Phylogeny ; Species Specificity ; }, abstract = {BACKGROUND: Comparative genomics has revealed extensive horizontal gene transfer among prokaryotes, a development that is often considered to undermine the 'tree of life' concept. However, the possibility remains that a statistical central trend still exists in the phylogenetic 'forest of life'.<br><br>RESULTS: A comprehensive comparative analysis of a 'forest' of 6,901 phylogenetic trees for prokaryotic genes revealed a consistent phylogenetic signal, particularly among 102 nearly universal trees, despite high levels of topological inconsistency, probably due to horizontal gene transfer. Horizontal transfers seemed to be distributed randomly and did not obscure the central trend. The nearly universal trees were topologically similar to numerous other trees. Thus, the nearly universal trees might reflect a significant central tendency, although they cannot represent the forest completely. However, topological consistency was seen mostly at shallow tree depths and abruptly dropped at the level of the radiation of archaeal and bacterial phyla, suggesting that early phases of evolution could be non-tree-like (Biological Big Bang). Simulations of evolution under compressed cladogenesis or Biological Big Bang yielded a better fit to the observed dependence between tree inconsistency and phylogenetic depth for the compressed cladogenesis model.<br><br>CONCLUSIONS: Horizontal gene transfer is pervasive among prokaryotes: very few gene trees are fully consistent, making the original tree of life concept obsolete. A central trend that most probably represents vertical inheritance is discernible throughout the evolution of archaea and bacteria, although compressed cladogenesis complicates unambiguous resolution of the relationships between the major archaeal and bacterial clades.}, }
@article {pmid19593472, year = {2009}, author = {Rangannan, V and Bansal, M}, title = {Relative stability of DNA as a generic criterion for promoter prediction: whole genome annotation of microbial genomes with varying nucleotide base composition.}, journal = {Molecular bioSystems}, volume = {5}, number = {12}, pages = {1758-1769}, doi = {10.1039/B906535K}, pmid = {19593472}, issn = {1742-2051}, mesh = {Bacillus subtilis/genetics ; Base Composition ; Computer Simulation ; DNA/chemistry/*genetics ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genome, Bacterial ; Genomic Instability ; Models, Statistical ; Mycobacterium tuberculosis/genetics ; *Promoter Regions, Genetic ; RNA, Bacterial/chemistry/genetics ; Reproducibility of Results ; Transcription Initiation Site ; }, abstract = {The rapid increase in genome sequence information has necessitated the annotation of their functional elements, particularly those occurring in the non-coding regions, in the genomic context. Promoter region is the key regulatory region, which enables the gene to be transcribed or repressed, but it is difficult to determine experimentally. Hence an in silico identification of promoters is crucial in order to guide experimental work and to pin point the key region that controls the transcription initiation of a gene. In this analysis, we demonstrate that while the promoter regions are in general less stable than the flanking regions, their average free energy varies depending on the GC composition of the flanking genomic sequence. We have therefore obtained a set of free energy threshold values, for genomic DNA with varying GC content and used them as generic criteria for predicting promoter regions in several microbial genomes, using an in-house developed tool PromPredict. On applying it to predict promoter regions corresponding to the 1144 and 612 experimentally validated TSSs in E. coli (50.8% GC) and B. subtilis (43.5% GC) sensitivity of 99% and 95% and precision values of 58% and 60%, respectively, were achieved. For the limited data set of 81 TSSs available for M. tuberculosis (65.6% GC) a sensitivity of 100% and precision of 49% was obtained.}, }
@article {pmid19593377, year = {2009}, author = {Burstein, D and Zusman, T and Degtyar, E and Viner, R and Segal, G and Pupko, T}, title = {Genome-scale identification of Legionella pneumophila effectors using a machine learning approach.}, journal = {PLoS pathogens}, volume = {5}, number = {7}, pages = {e1000508}, pmid = {19593377}, issn = {1553-7374}, mesh = {Algorithms ; *Artificial Intelligence ; Bacterial Proteins/genetics/metabolism ; Bayes Theorem ; Carrier Proteins/genetics/metabolism ; Cells, Cultured ; Databases, Genetic ; Genes, Bacterial ; *Genome, Bacterial ; Host-Pathogen Interactions ; Humans ; Legionella pneumophila/genetics/metabolism/*physiology ; Membrane Proteins/genetics/metabolism ; Molecular Chaperones/genetics ; Protein Transport ; Reproducibility of Results ; }, abstract = {A large number of highly pathogenic bacteria utilize secretion systems to translocate effector proteins into host cells. Using these effectors, the bacteria subvert host cell processes during infection. Legionella pneumophila translocates effectors via the Icm/Dot type-IV secretion system and to date, approximately 100 effectors have been identified by various experimental and computational techniques. Effector identification is a critical first step towards the understanding of the pathogenesis system in L. pneumophila as well as in other bacterial pathogens. Here, we formulate the task of effector identification as a classification problem: each L. pneumophila open reading frame (ORF) was classified as either effector or not. We computationally defined a set of features that best distinguish effectors from non-effectors. These features cover a wide range of characteristics including taxonomical dispersion, regulatory data, genomic organization, similarity to eukaryotic proteomes and more. Machine learning algorithms utilizing these features were then applied to classify all the ORFs within the L. pneumophila genome. Using this approach we were able to predict and experimentally validate 40 new effectors, reaching a success rate of above 90%. Increasing the number of validated effectors to around 140, we were able to gain novel insights into their characteristics. Effectors were found to have low G+C content, supporting the hypothesis that a large number of effectors originate via horizontal gene transfer, probably from their protozoan host. In addition, effectors were found to cluster in specific genomic regions. Finally, we were able to provide a novel description of the C-terminal translocation signal required for effector translocation by the Icm/Dot secretion system. To conclude, we have discovered 40 novel L. pneumophila effectors, predicted over a hundred additional highly probable effectors, and shown the applicability of machine learning algorithms for the identification and characterization of bacterial pathogenesis determinants.}, }
@article {pmid19592530, year = {2009}, author = {Rayamajhi, N and Cha, SB and Kang, ML and Lee, SI and Lee, HS and Yoo, HS}, title = {Inter- and intraspecies plasmid-mediated transfer of florfenicol resistance in Enterobacteriaceae isolates from swine.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {17}, pages = {5700-5703}, pmid = {19592530}, issn = {1098-5336}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Blotting, Southern ; Conjugation, Genetic ; DNA, Bacterial/genetics ; *Drug Resistance, Bacterial ; Enterobacteriaceae/*drug effects/*genetics/isolation &amp; purification ; *Gene Transfer, Horizontal ; *Plasmids ; Polymerase Chain Reaction ; Swine/*microbiology ; Thiamphenicol/*analogs &amp; derivatives/pharmacology ; }, abstract = {Florfenicol resistance was analyzed in 230 enteric pig isolates collected between 1998 and 2006. PCR, plasmid profiling, Southern blot hybridization, and a mixed-broth conjugation assay suggested the intra- and interspecies plasmid-mediated transfer of florfenicol resistance among the isolates that exhibited MICs for florfenicol between 4 to 128 mg/liter.}, }
@article {pmid19592526, year = {2009}, author = {Käser, M and Hauser, J and Small, P and Pluschke, G}, title = {Large sequence polymorphisms unveil the phylogenetic relationship of environmental and pathogenic mycobacteria related to Mycobacterium ulcerans.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {17}, pages = {5667-5675}, pmid = {19592526}, issn = {1098-5336}, mesh = {Bacterial Toxins/*biosynthesis ; Buruli Ulcer/microbiology ; Cluster Analysis ; DNA Fingerprinting/*methods ; DNA, Bacterial/chemistry/*genetics ; Environmental Microbiology ; Evolution, Molecular ; Gene Order ; Genotype ; INDEL Mutation ; Macrolides ; Molecular Sequence Data ; Mycobacterium/*classification/*genetics/isolation &amp; purification/metabolism ; *Polymorphism, Genetic ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Synteny ; }, abstract = {Mycolactone is an immunosuppressive cytotoxin responsible for the clinical manifestation of Buruli ulcer in humans. It was believed to be confined to its etiologic agent, Mycobacterium ulcerans. However, the identification of other mycolactone-producing mycobacteria (MPMs) in other species, including Mycobacterium marinum, indicated a more complex taxonomic relationship. This highlighted the need for research on the biology, evolution, and distribution of such emerging and potentially infectious strains. The reliable genetic fingerprinting analyses presented here aim at both the unraveling of phylogenetic relatedness and of dispersal between environmental and pathogenic mycolactone producers and the identification of genetic prerequisites that enable lateral gene transfer of such plasmids. This will allow for the identification of environmental reservoirs of virulence plasmids that encode enzymes required for the synthesis of mycolactone. Based on dynamic chromosomal loci identified earlier in M. ulcerans, we characterized large sequence polymorphisms for the phylogenetic analysis of MPMs. Here, we identify new insertional-deletional events and single-nucleotide polymorphisms that confirm and redefine earlier strain differentiation markers. These results support other data showing that all MPMs share a common ancestry. In addition, we found unique genetic features specific for M. marinum strain M, the genome sequence strain which is used widely in research.}, }
@article {pmid19590148, year = {2009}, author = {Cheng, J and Wang, Q and Chen, Y and Ye, Y and Li, H and Li, X and Li, JB}, title = {Phenotypic and molecular characterization of a novel beta-lactamase carried by Klebsiella pneumoniae, CTX-M-72, derived from CTX-M-3.}, journal = {The Journal of general and applied microbiology}, volume = {55}, number = {3}, pages = {207-216}, doi = {10.2323/jgam.55.207}, pmid = {19590148}, issn = {0022-1260}, mesh = {Adult ; Amino Acid Substitution ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/classification/*genetics/metabolism ; Ceftazidime/metabolism ; China/epidemiology ; Clavulanic Acid/pharmacology ; Enzyme Inhibitors/pharmacology ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Humans ; Klebsiella Infections/*epidemiology/microbiology/transmission ; Klebsiella pneumoniae/drug effects/*enzymology/genetics ; Male ; Middle Aged ; Molecular Epidemiology ; Molecular Sequence Data ; Plasmids ; beta-Lactamases/*chemistry/*classification/genetics ; }, abstract = {This study reports phenotypic and molecular characterization of a novel CTX-M beta-lactamase carried by two Klebsiella pneumoniae isolates collected from two hospitals in China. Conjugation experiment, Southern hybridization, susceptibility testing, isoelectric focusing, PCR, and sequencing techniques as well as clone, expression, purification and kinetics were carried out to describe the characterization of the novel CTX-M-type enzyme. The analyses of plasmid profiling and pulsed-field gel electrophoresis of the novel enzyme were performed to investigate epidemiology. The PCR products had 967 nucleotides and a novel CTX-M enzyme with a pI of 8.5 was implicated in this resistance: CTX-M-72. Two strains exhibited a clavulanic acid-inhibited substrate profile that included extended-spectrum cephalosporins. The amino acid sequence of the CTX-M-72 beta-lactamase differed from that of the CTX-M-3 beta-lactamase by the Arg-->Gly change at position 164. The novel enzyme was susceptible to ceftazidime, the same response being observed for other CTX-M enzymes. The substrates of the beta-lactamase were also characterized. Furthermore, two resistant genes of clinical strains were closely related. The emergence of a novel CTX-M-type extended-spectrum beta-lactamase was rarely described in other areas. This study illustrated the importance of molecular surveillance in tracking CTX-M-producing strains in large teaching hospitals, suggested the horizontal transfer of plasmid-borne bla(CTX-M) genes contributed to the dissemination of CTX-M enzymes in hospital environments, and emphasized the need for epidemiological monitoring.}, }
@article {pmid19584142, year = {2009}, author = {Richards, TA and Soanes, DM and Foster, PG and Leonard, G and Thornton, CR and Talbot, NJ}, title = {Phylogenomic analysis demonstrates a pattern of rare and ancient horizontal gene transfer between plants and fungi.}, journal = {The Plant cell}, volume = {21}, number = {7}, pages = {1897-1911}, pmid = {19584142}, issn = {1040-4651}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Evolution, Molecular ; Fungi/*genetics ; Gene Transfer, Horizontal/*genetics ; *Phylogeny ; Plants/*genetics/*microbiology ; }, abstract = {Horizontal gene transfer (HGT) describes the transmission of genetic material across species boundaries and is an important evolutionary phenomenon in the ancestry of many microbes. The role of HGT in plant evolutionary history is, however, largely unexplored. Here, we compare the genomes of six plant species with those of 159 prokaryotic and eukaryotic species and identify 1689 genes that show the highest similarity to corresponding genes from fungi. We constructed a phylogeny for all 1689 genes identified and all homolog groups available from the rice (Oryza sativa) genome (3177 gene families) and used these to define 14 candidate plant-fungi HGT events. Comprehensive phylogenetic analyses of these 14 data sets, using methods that account for site rate heterogeneity, demonstrated support for nine HGT events, demonstrating an infrequent pattern of HGT between plants and fungi. Five HGTs were fungi-to-plant transfers and four were plant-to-fungi HGTs. None of the fungal-to-plant HGTs involved angiosperm recipients. These results alter the current view of organismal barriers to HGT, suggesting that phagotrophy, the consumption of a whole cell by another, is not necessarily a prerequisite for HGT between eukaryotes. Putative functional annotation of the HGT candidate genes suggests that two fungi-to-plant transfers have added phenotypes important for life in a soil environment. Our study suggests that genetic exchange between plants and fungi is exceedingly rare, particularly among the angiosperms, but has occurred during their evolutionary history and added important metabolic traits to plant lineages.}, }
@article {pmid19583791, year = {2009}, author = {Haneda, T and Ishii, Y and Danbara, H and Okada, N}, title = {Genome-wide identification of novel genomic islands that contribute to Salmonella virulence in mouse systemic infection.}, journal = {FEMS microbiology letters}, volume = {297}, number = {2}, pages = {241-249}, doi = {10.1111/j.1574-6968.2009.01686.x}, pmid = {19583791}, issn = {1574-6968}, mesh = {Animals ; Bacterial Proteins/genetics/metabolism ; Disease Models, Animal ; Female ; *Genome, Bacterial ; *Genomic Islands ; Humans ; Mice ; Mice, Inbred BALB C ; Salmonella Infections/*microbiology ; Salmonella typhimurium/genetics/metabolism/*pathogenicity ; Virulence ; }, abstract = {Salmonella pathogenicity islands are inserted into the genome by horizontal gene transfer and are required for expression of full virulence. Here, we performed tRNA scanning of the genome of Salmonella enterica serovar Typhimurium and compared it with that of nonpathogenic Escherichia coli in order to identify genomic islands that contribute to Salmonella virulence. Using deletion analysis, we identified four genomic islands that are required for virulence in the mouse infection model. One of the newly identified pathogenicity islands was the pheV-tRNA-located genomic island, which is comprised of 26 126 bp, and encodes 22 putative genes, including STM3117-STM3138. We also showed that the pheV tRNA-located genomic island is widely distributed among different nontyphoid Salmonella serovars. Furthermore, genes including STM3118-STM3121 were identified as novel virulence-associated genes within the pheV-tRNA-located genomic island. These results indicate that a Salmonella-specific pheV-tRNA genomic island is involved in Salmonella pathogenesis among the nontyphoid Salmonella serovars.}, }
@article {pmid19582169, year = {2009}, author = {Morris, PF and Schlosser, LR and Onasch, KD and Wittenschlaeger, T and Austin, R and Provart, N}, title = {Multiple horizontal gene transfer events and domain fusions have created novel regulatory and metabolic networks in the oomycete genome.}, journal = {PloS one}, volume = {4}, number = {7}, pages = {e6133}, pmid = {19582169}, issn = {1932-6203}, mesh = {*Gene Fusion ; *Gene Transfer, Horizontal ; *Genome, Fungal ; Oomycetes/*genetics/metabolism ; Species Specificity ; }, abstract = {Complex enzymes with multiple catalytic activities are hypothesized to have evolved from more primitive precursors. Global analysis of the Phytophthora sojae genome using conservative criteria for evaluation of complex proteins identified 273 novel multifunctional proteins that were also conserved in P. ramorum. Each of these proteins contains combinations of protein motifs that are not present in bacterial, plant, animal, or fungal genomes. A subset of these proteins were also identified in the two diatom genomes, but the majority of these proteins have formed after the split between diatoms and oomycetes. Documentation of multiple cases of domain fusions that are common to both oomycetes and diatom genomes lends additional support for the hypothesis that oomycetes and diatoms are monophyletic. Bifunctional proteins that catalyze two steps in a metabolic pathway can be used to infer the interaction of orthologous proteins that exist as separate entities in other genomes. We postulated that the novel multifunctional proteins of oomycetes could function as potential Rosetta Stones to identify interacting proteins of conserved metabolic and regulatory networks in other eukaryotic genomes. However ortholog analysis of each domain within our set of 273 multifunctional proteins against 39 sequenced bacterial and eukaryotic genomes, identified only 18 candidate Rosetta Stone proteins. Thus the majority of multifunctional proteins are not Rosetta Stones, but they may nonetheless be useful in identifying novel metabolic and regulatory networks in oomycetes. Phylogenetic analysis of all the enzymes in three pathways with one or more novel multifunctional proteins was conducted to determine the probable origins of individual enzymes. These analyses revealed multiple examples of horizontal transfer from both bacterial genomes and the photosynthetic endosymbiont in the ancestral genome of Stramenopiles. The complexity of the phylogenetic origins of these metabolic pathways and the paucity of Rosetta Stones relative to the total number of multifunctional proteins suggests that the proteome of oomycetes has few features in common with other Kingdoms.}, }
@article {pmid19581466, year = {2009}, author = {Faure, S and Perrin-Guyomard, A and Delmas, JM and Laurentie, M}, title = {Impact of therapeutic treatment with beta-lactam on transfer of the bla(CTX-M-9) resistance gene from Salmonella enterica serovar Virchow to Escherichia coli in gnotobiotic rats.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {17}, pages = {5523-5528}, pmid = {19581466}, issn = {1098-5336}, mesh = {Animals ; Anti-Bacterial Agents/*therapeutic use ; Chickens ; Conjugation, Genetic ; Escherichia coli/*drug effects/genetics ; Escherichia coli Proteins/*genetics ; *Gene Transfer, Horizontal ; Germ-Free Life ; Plasmids ; Rats ; Salmonella Infections, Animal ; Salmonella enterica/*drug effects/genetics/isolation &amp; purification ; *beta-Lactam Resistance ; beta-Lactamases/*genetics ; beta-Lactams/*therapeutic use ; }, abstract = {The conjugative transfer of the plasmid carrying the bla(CTX-M-9) gene from Salmonella enterica serovar Virchow isolated from a chicken farm to a recipient Escherichia coli strain was evaluated in vitro and in axenic rats inoculated with both strains, with or without selective pressure due to therapeutic doses of cefixime. The transfer of the bla(CTX-M-9) gene of S. enterica serovar Virchow to E. coli was confirmed in vitro, at a low frequency of 5.9 x 10(-8) transconjugants/donors. This transfer rate was higher in gnotobiotic rats and reached approximately 10(-5) transconjugants/donors without selective pressure. This frequency was not affected by the addition of therapeutic doses of cefixime. Thus, estimates of in vitro transfer underestimated potential transfer in the digestive tract, and therapeutic doses of cefixime did not increase the selection for transconjugants.}, }
@article {pmid19578403, year = {2009}, author = {Berglund, EC and Frank, AC and Calteau, A and Vinnere Pettersson, O and Granberg, F and Eriksson, AS and Näslund, K and Holmberg, M and Lindroos, H and Andersson, SG}, title = {Run-off replication of host-adaptability genes is associated with gene transfer agents in the genome of mouse-infecting Bartonella grahamii.}, journal = {PLoS genetics}, volume = {5}, number = {7}, pages = {e1000546}, pmid = {19578403}, issn = {1553-7404}, mesh = {Animals ; Bacterial Proteins/genetics/metabolism ; Bacteriophages/genetics/*physiology ; Bartonella/classification/genetics/metabolism/*virology ; Bartonella Infections/*microbiology ; Disease Reservoirs/*microbiology ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Host-Pathogen Interactions ; Humans ; Mice/*microbiology ; Molecular Sequence Data ; Phylogeny ; *Virus Replication ; }, abstract = {The genus Bartonella comprises facultative intracellular bacteria adapted to mammals, including previously recognized and emerging human pathogens. We report the 2,341,328 bp genome sequence of Bartonella grahamii, one of the most prevalent Bartonella species in wild rodents. Comparative genomics revealed that rodent-associated Bartonella species have higher copy numbers of genes for putative host-adaptability factors than the related human-specific pathogens. Many of these gene clusters are located in a highly dynamic region of 461 kb. Using hybridization to a microarray designed for the B. grahamii genome, we observed a massive, putatively phage-derived run-off replication of this region. We also identified a novel gene transfer agent, which packages the bacterial genome, with an over-representation of the amplified DNA, in 14 kb pieces. This is the first observation associating the products of run-off replication with a gene transfer agent. Because of the high concentration of gene clusters for host-adaptation proteins in the amplified region, and since the genes encoding the gene transfer agent and the phage origin are well conserved in Bartonella, we hypothesize that these systems are driven by selection. We propose that the coupling of run-off replication with gene transfer agents promotes diversification and rapid spread of host-adaptability factors, facilitating host shifts in Bartonella.}, }
@article {pmid19577655, year = {2009}, author = {Kamikawa, R and Sanchez-Perez, GF and Sako, Y and Roger, AJ and Inagaki, Y}, title = {Expanded phylogenies of canonical and non-canonical types of methionine adenosyltransferase reveal a complex history of these gene families in eukaryotes.}, journal = {Molecular phylogenetics and evolution}, volume = {53}, number = {2}, pages = {565-570}, doi = {10.1016/j.ympev.2009.06.016}, pmid = {19577655}, issn = {1095-9513}, mesh = {DNA, Algal/genetics ; Diatoms/classification/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Methionine Adenosyltransferase/*genetics ; Models, Genetic ; Multigene Family ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Most eukaryotes possess the highly-conserved enzyme methionine adenosyltransferase (MAT) that produces S-adenosyl-l-methionine, a molecule essential to a variety of cellular processes. However, a recent study revealed that genomes of a very few eukaryote lineages encode a highly divergent type of MAT (called MATX), instead of the canonical MAT enzyme. Since MATX-containing eukaryotes are phylogenetically interspersed with MAT-containing organisms, it is likely that the MATX gene was spread into the MAT-containing groups via multiple eukaryote-to-eukaryote lateral gene transfer events. Here, we further investigate the evolutionary history of these gene families by vastly increasing the sampling of species containing MAT (22 new taxa) and MATX (8 new taxa). Our expanded analyses reveal the first example of lateral transfer of a MAT gene between the pelagophycean alga Aureococcusanophagefferens and a cryptomonad. The increased MATX sampling also provided new insights into the evolution of MATX. Specifically, our MATX phylogeny robustly grouped the haptophyte homologues with the Aureococcus homologue to the exclusion of the diatom homologues, suggesting a transfer of the MATX gene between haptophytes and pelagophytes. Various scenarios of MAT and MATX gene family evolution in diatoms are re-evaluated in light of the new data.}, }
@article {pmid19577594, year = {2009}, author = {Advani, A and Van der Heide, HG and Hallander, HO and Mooi, FR}, title = {Analysis of Swedish Bordetella pertussis isolates with three typing methods: characterization of an epidemic lineage.}, journal = {Journal of microbiological methods}, volume = {78}, number = {3}, pages = {297-301}, doi = {10.1016/j.mimet.2009.06.019}, pmid = {19577594}, issn = {1872-8359}, mesh = {Alleles ; Bacterial Typing Techniques/*methods ; Bordetella pertussis/*classification/*genetics/isolation &amp; purification ; Cluster Analysis ; DNA Fingerprinting/*methods ; DNA, Bacterial/chemistry/genetics ; Electrophoresis, Gel, Pulsed-Field/methods ; Humans ; Minisatellite Repeats ; Molecular Epidemiology/methods ; Molecular Sequence Data ; Polymerase Chain Reaction/methods ; Sensitivity and Specificity ; Sequence Analysis, DNA/methods ; Sweden/epidemiology ; Whooping Cough/*epidemiology/*microbiology ; }, abstract = {Three Bordetella pertussis typing methods, pulsed-field gel electrophoresis (PFGE), multi-locus sequence typing (MLST), and multi-locus variable number tandem repeat analysis (MLVA) were compared using a collection of Swedish strains. Of the three typing methods used, PFGE was found to be the most discriminatory. MLVA and MLST were less discriminatory, but may be valuable for strain discrimination when culture is not possible as they are based on PCR. The combination of MLVA/MLST was found to be equally discriminatory as PFGE and should therefore also be considered. The relationship between predominant lineages in Sweden and The Netherlands, characterized by the PFGE type BpSR11 and the allele for the pertussis toxin promoter ptxP3, respectively, was investigated. Linkage was found between the PFGE type BpSR11 and ptxP3 in that all BpSR11 strains carried ptxP3. On the other hand ptxP3 was found in several other PFGE-types. The presence of the ptxP3 allele in different genetic backgrounds may indicate horizontal gene transfer within B. pertussis or homoplasy. Alternatively, this observation may be due to convergence of PFGE types.}, }
@article {pmid19575565, year = {2009}, author = {Andersson, JO}, title = {Gene transfer and diversification of microbial eukaryotes.}, journal = {Annual review of microbiology}, volume = {63}, number = {}, pages = {177-193}, doi = {10.1146/annurev.micro.091208.073203}, pmid = {19575565}, issn = {1545-3251}, mesh = {*Biodiversity ; Cluster Analysis ; Eukaryotic Cells/*physiology ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Phylogeny ; }, abstract = {The importance of lateral gene transfer in genome evolution of microbial eukaryotes is slowly being appreciated. Acquisitions of genes have led to metabolic adaptation in diverse eukaryotic lineages. In most cases the metabolic genes have originated from prokaryotes, often followed by sequential transfers between eukaryotes. However, the knowledge of gene transfer in eukaryotes is still mainly based on anecdotal evidence. Some of the observed patterns may be biases in experimental approaches and sequence databases rather than evolutionary trends. Rigorous systematic studies of gene acquisitions that allow for the possibility of exchanges of all categories of genes from all sources are needed to get a more objective view of gene transfer in eukaryote evolution. It may be that the role of gene transfer in the diversification process of microbial eukaryotes currently is underestimated.}, }
@article {pmid19571895, year = {2009}, author = {Brazelton, WJ and Baross, JA}, title = {Abundant transposases encoded by the metagenome of a hydrothermal chimney biofilm.}, journal = {The ISME journal}, volume = {3}, number = {12}, pages = {1420-1424}, doi = {10.1038/ismej.2009.79}, pmid = {19571895}, issn = {1751-7370}, mesh = {Atlantic Ocean ; *Biodiversity ; *Biofilms ; Gene Transfer, Horizontal ; Geologic Sediments/*microbiology ; *Hot Springs ; *Metagenome ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Transposases/*genetics ; }, abstract = {The carbonate chimneys of the Lost City Hydrothermal Field on the Mid-Atlantic Ridge are coated in thick microbial biofilms consisting of just a few dominant species. We report a preliminary analysis of a biofilm metagenome that revealed a remarkable abundance and diversity of genes potentially involved in lateral gene transfer (LGT). More than 8% of all metagenomic reads showed significant sequence similarity to transposases; all available metagenomic data sets from other environments contained at least an order of magnitude fewer transposases. Furthermore, the sequence diversity of transposase genes in the biofilm was much greater than that of 16S rRNA genes. The small size and high sequencing coverage of contigs containing transposases indicate that they are located on small but abundant extragenomic molecules. These results suggest that rampant LGT among members of the Lost City biofilm may serve as a generator of phenotypic diversity in a community with very low organismal diversity.}, }
@article {pmid19571247, year = {2009}, author = {Norman, A and Hansen, LH and Sørensen, SJ}, title = {Conjugative plasmids: vessels of the communal gene pool.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {364}, number = {1527}, pages = {2275-2289}, pmid = {19571247}, issn = {1471-2970}, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome, Archaeal/*genetics ; Genome, Bacterial/*genetics ; Interspersed Repetitive Sequences/*genetics ; Plasmids/*genetics/physiology ; }, abstract = {Comparative whole-genome analyses have demonstrated that horizontal gene transfer (HGT) provides a significant contribution to prokaryotic genome innovation. The evolution of specific prokaryotes is therefore tightly linked to the environment in which they live and the communal pool of genes available within that environment. Here we use the term supergenome to describe the set of all genes that a prokaryotic 'individual' can draw on within a particular environmental setting. Conjugative plasmids can be considered particularly successful entities within the communal pool, which have enabled HGT over large taxonomic distances. These plasmids are collections of discrete regions of genes that function as 'backbone modules' to undertake different aspects of overall plasmid maintenance and propagation. Conjugative plasmids often carry suites of 'accessory elements' that contribute adaptive traits to the hosts and, potentially, other resident prokaryotes within specific environmental niches. Insight into the evolution of plasmid modules therefore contributes to our knowledge of gene dissemination and evolution within prokaryotic communities. This communal pool provides the prokaryotes with an important mechanistic framework for obtaining adaptability and functional diversity that alleviates the need for large genomes of specialized 'private genes'.}, }
@article {pmid19571246, year = {2009}, author = {Brüssow, H}, title = {The not so universal tree of life or the place of viruses in the living world.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {364}, number = {1527}, pages = {2263-2274}, pmid = {19571246}, issn = {1471-2970}, mesh = {Classification/*methods ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome, Viral/*genetics ; *Phylogeny ; Viruses/*genetics ; }, abstract = {Darwin provided a great unifying theory for biology; its visual expression is the universal tree of life. The tree concept is challenged by the occurrence of horizontal gene transfer and-as summarized in this review -- by the omission of viruses. Microbial ecologists have demonstrated that viruses are the most numerous biological entities on earth, outnumbering cells by a factor of 10. Viral genomics have revealed an unexpected size and distinctness of the viral DNA sequence space. Comparative genomics has shown elements of vertical evolution in some groups of viruses. Furthermore, structural biology has demonstrated links between viruses infecting the three domains of life pointing to a very ancient origin of viruses. However, presently viruses do not find a place on the universal tree of life, which is thus only a tree of cellular life. In view of the polythetic nature of current life definitions, viruses cannot be dismissed as non-living material. On earth we have therefore at least two large DNA sequence spaces, one represented by capsid-encoding viruses and another by ribosome-encoding cells. Despite their probable distinct evolutionary origin, both spheres were and are connected by intensive two-way gene transfers.}, }
@article {pmid19571244, year = {2009}, author = {Ragan, MA and Beiko, RG}, title = {Lateral genetic transfer: open issues.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {364}, number = {1527}, pages = {2241-2251}, pmid = {19571244}, issn = {1471-2970}, mesh = {*Environment ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome/*genetics ; *Models, Genetic ; *Phylogeny ; }, abstract = {Lateral genetic transfer (LGT) is an important adaptive force in evolution, contributing to metabolic, physiological and ecological innovation in most prokaryotes and some eukaryotes. Genomic sequences and other data have begun to illuminate the processes, mechanisms, quantitative extent and impact of LGT in diverse organisms, populations, taxa and environments; deep questions are being posed, and the provisional answers sometimes challenge existing paradigms. At the same time, there is an enhanced appreciation of the imperfections, biases and blind spots in the data and in analytical approaches. Here we identify and consider significant open questions concerning the role of LGT in genome evolution.}, }
@article {pmid19571243, year = {2009}, author = {Fournier, GP and Huang, J and Gogarten, JP}, title = {Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {364}, number = {1527}, pages = {2229-2239}, pmid = {19571243}, issn = {1471-2970}, mesh = {Chlamydia/*genetics ; Classification/*methods ; Gene Transfer, Horizontal/*genetics ; Methanosarcinaceae/*genetics ; *Phylogeny ; RNA, Ribosomal/genetics ; Thermotoga maritima/genetics ; }, abstract = {Horizontal gene transfer (HGT) is often considered to be a source of error in phylogenetic reconstruction, causing individual gene trees within an organismal lineage to be incongruent, obfuscating the 'true' evolutionary history. However, when identified as such, HGTs between divergent organismal lineages are useful, phylogenetically informative characters that can provide insight into evolutionary history. Here, we discuss several distinct HGT events involving all three domains of life, illustrating the selective advantages that can be conveyed via HGT, and the utility of HGT in aiding phylogenetic reconstruction and in dating the relative sequence of speciation events. We also discuss the role of HGT from extinct lineages, and its impact on our understanding of the evolution of life on Earth. Organismal phylogeny needs to incorporate reticulations; a simple tree does not provide an accurate depiction of the processes that have shaped life's history.}, }
@article {pmid19571242, year = {2009}, author = {Doolittle, WF}, title = {The practice of classification and the theory of evolution, and what the demise of Charles Darwin's tree of life hypothesis means for both of them.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {364}, number = {1527}, pages = {2221-2228}, pmid = {19571242}, issn = {1471-2970}, mesh = {*Biological Evolution ; Classification/*methods ; Gene Transfer, Horizontal/*genetics ; *Models, Theoretical ; *Phylogeny ; }, abstract = {Debates over the status of the tree of life (TOL) often proceed without agreement as to what it is supposed to be: a hierarchical classification scheme, a tracing of genomic and organismal history or a hypothesis about evolutionary processes and the patterns they can generate. I will argue that for Darwin it was a hypothesis, which lateral gene transfer in prokaryotes now shows to be false. I will propose a more general and relaxed evolutionary theory and point out why anti-evolutionists should take no comfort from disproof of the TOL hypothesis.}, }
@article {pmid19571241, year = {2009}, author = {Haggerty, LS and Martin, FJ and Fitzpatrick, DA and McInerney, JO}, title = {Gene and genome trees conflict at many levels.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {364}, number = {1527}, pages = {2209-2219}, pmid = {19571241}, issn = {1471-2970}, mesh = {Base Sequence ; Classification/*methods ; Gammaproteobacteria/*genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/*genetics ; Genome, Bacterial/*genetics ; Likelihood Functions ; Models, Genetic ; *Phylogeny ; RNA, Ribosomal/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Horizontal gene transfer (HGT) plays a significant role in microbial evolution. It can accelerate the adaptation of an organism, it can generate new metabolic pathways and it can completely remodel an organism's genome. We examine 27 closely related genomes from the YESS group of gamma proteobacteria and a variety of four-taxon datasets from a diverse range of prokaryotes in order to explore the kinds of effects HGT has had on these organisms.}, }
@article {pmid19571239, year = {2009}, author = {Dagan, T and Martin, W}, title = {Getting a better picture of microbial evolution en route to a network of genomes.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {364}, number = {1527}, pages = {2187-2196}, pmid = {19571239}, issn = {1471-2970}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Classification/*methods ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome/*genetics ; *Phylogeny ; }, abstract = {Most current thinking about evolution is couched in the concept of trees. The notion of a tree with recursively bifurcating branches representing recurrent divergence events is a plausible metaphor to describe the evolution of multicellular organisms like vertebrates or land plants. But if we try to force the tree metaphor onto the whole of the evolutionary process, things go badly awry, because the more closely we inspect microbial genomes through the looking glass of gene and genome sequence comparisons, the smaller the amount of the data that fits the concept of a bifurcating tree becomes. That is mainly because among microbes, endosymbiosis and lateral gene transfer are important, two mechanisms of natural variation that differ from the kind of natural variation that Darwin had in mind. For such reasons, when it comes to discussing the relationships among all living things, that is, including the microbes and all of their genes rather than just one or a select few, many biologists are now beginning to talk about networks rather than trees in the context of evolutionary relationships among microbial chromosomes. But talk is not enough. If we were to actually construct networks instead of trees to describe the evolutionary process, what would they look like? Here we consider endosymbiosis and an example of a network of genomes involving 181 sequenced prokaryotes and how that squares off with some ideas about early cell evolution.}, }
@article {pmid19571237, year = {2009}, author = {Ragan, MA and McInerney, JO and Lake, JA}, title = {The network of life: genome beginnings and evolution. Introduction.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {364}, number = {1527}, pages = {2169-2175}, pmid = {19571237}, issn = {1471-2970}, mesh = {*Ecosystem ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; *Genetic Variation ; Genome/*genetics ; *Phylogeny ; }, }
@article {pmid19570746, year = {2009}, author = {Csurös, M and Miklós, I}, title = {Streamlining and large ancestral genomes in Archaea inferred with a phylogenetic birth-and-death model.}, journal = {Molecular biology and evolution}, volume = {26}, number = {9}, pages = {2087-2095}, pmid = {19570746}, issn = {1537-1719}, mesh = {Amino Acid Substitution/genetics ; Archaea/*genetics ; Base Sequence ; Computational Biology ; Evolution, Molecular ; Genes, Archaeal ; Genome, Archaeal/*genetics ; *Models, Genetic ; *Phylogeny ; }, abstract = {Homologous genes originate from a common ancestor through vertical inheritance, duplication, or horizontal gene transfer. Entire homolog families spawned by a single ancestral gene can be identified across multiple genomes based on protein sequence similarity. The sequences, however, do not always reveal conclusively the history of large families. To study the evolution of complete gene repertoires, we propose here a mathematical framework that does not rely on resolved gene family histories. We show that so-called phylogenetic profiles, formed by family sizes across multiple genomes, are sufficient to infer principal evolutionary trends. The main novelty in our approach is an efficient algorithm to compute the likelihood of a phylogenetic profile in a model of birth-and-death processes acting on a phylogeny. We examine known gene families in 28 archaeal genomes using a probabilistic model that involves lineage- and family-specific components of gene acquisition, duplication, and loss. The model enables us to consider all possible histories when inferring statistics about archaeal evolution. According to our reconstruction, most lineages are characterized by a net loss of gene families. Major increases in gene repertoire have occurred only a few times. Our reconstruction underlines the importance of persistent streamlining processes in shaping genome composition in Archaea. It also suggests that early archaeal genomes were as complex as typical modern ones, and even show signs, in the case of the methanogenic ancestor, of an extremely large gene repertoire.}, }
@article {pmid19563898, year = {2009}, author = {Wang, X and Wang, Q and Xiao, J and Liu, Q and Wu, H and Xu, L and Zhang, Y}, title = {Edwardsiella tarda T6SS component evpP is regulated by esrB and iron, and plays essential roles in the invasion of fish.}, journal = {Fish &amp; shellfish immunology}, volume = {27}, number = {3}, pages = {469-477}, doi = {10.1016/j.fsi.2009.06.013}, pmid = {19563898}, issn = {1095-9947}, mesh = {Animals ; Bacterial Proteins/chemistry/*metabolism ; Cell Line, Tumor ; Edwardsiella tarda/genetics/*metabolism/*pathogenicity ; Enterobacteriaceae Infections/microbiology/mortality/*veterinary ; Fish Diseases/*microbiology/mortality ; Flatfishes/microbiology ; Hemolysis ; Iron/*metabolism ; Mucus/metabolism ; Sequence Deletion ; Virulence/genetics ; Zebrafish/microbiology ; }, abstract = {Edwardsiella tarda is a gram-negative pathogen for hemorrhagic septicemia in a broad range of hosts. The type VI secretion system (T6SS) has recently been dissected in E. tarda to secrete EvpC, EvpI and a novel effector protein EvpP. In this study, sequencing and genetic alignments showed that evpP genes from different E. tarda isolates were highly similar and an evpP homolog was also found in Aeromonas hydrophila 0865 isolated from a diseased eel, suggesting the possible lateral gene transfer of evpP or the whole T6SS gene island. With reporter strains carrying gfp gene fused to the evpP promoter region, flow cytometric analysis revealed that transcription of evpP was positively regulated by either the two-component system EsrA-EsrB in E. tarda or the iron concentration in media. Compared with the parental strain, in-frame deletion of evpP in E. tarda EIB202 led to the significantly increased 50% lethal doses in zebrafish (Danio rerio) and Japanese flounder (Paralichthys olivaceus), decreased hemolytic activities, failure to adhere to mucus and reduced serum resistance, and complementation of an intact evpP gene restored these phenotypes in the evpP mutant. Investigation of infection kinetics indicated that the evpP deletion mutant was unable to proliferate in vivo, particularly in immune organs of fish. Moreover, the evpP deletion mutant exhibited incapacity to internalize in EPC cell model in vitro, demonstrating that EvpP in T6SS plays critical roles for invasion mechanism of E. tarda and merits as potential target for attenuated live vaccine construction.}, }
@article {pmid19563462, year = {2009}, author = {Franco, IS and Shuman, HA and Charpentier, X}, title = {The perplexing functions and surprising origins of Legionella pneumophila type IV secretion effectors.}, journal = {Cellular microbiology}, volume = {11}, number = {10}, pages = {1435-1443}, doi = {10.1111/j.1462-5822.2009.01351.x}, pmid = {19563462}, issn = {1462-5822}, support = {R01 AI023549/AI/NIAID NIH HHS/United States ; AI023549/AI/NIAID NIH HHS/United States ; AI064481/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacterial Proteins/genetics/*metabolism ; Eukaryota/microbiology ; *Evolution, Molecular ; Humans ; Legionella pneumophila/genetics/*pathogenicity ; Macrophages/microbiology ; Models, Biological ; Phagosomes/microbiology ; Virulence Factors/genetics/*metabolism ; }, abstract = {Only a limited number of bacterial pathogens evade destruction by phagocytic cells such as macrophages. Legionella pneumophila is a Gram-negative gamma-proteobacterial species that can infect and replicate in alveolar macrophages, causing Legionnaires' disease, a severe pneumonia. L. pneumophila uses a complex secretion system to inject host cells with effector proteins capable of disrupting or altering the host cell processes. The L. pneumophila effectors target multiple processes but are essentially aimed at modifying the properties of the L. pneumophila phagosome by altering vesicular trafficking, gradually creating a specialized vacuole in which the bacteria replicate robustly. In nature, L. pneumophila is thought to parasitize free-living protists, which may have selected for traits that promote virulence of L. pneumophila in humans. Indeed, many effector genes encode proteins with eukaryotic domains and are likely to be of protozoan origin. Sustained horizontal gene transfer events within the protozoan niche may have allowed L. pneumophila to become a professional parasite of phagocytes, simultaneously giving rise to its ability to infect macrophages, cells that constitute the first line of cellular defence against bacterial infections.}, }
@article {pmid19562240, year = {2009}, author = {Stelzner, F and von Mallek, D and Ruhlmann, J and Biersack, HJ}, title = {[PET-CT studies of metastasizing cancer of the colon and rectum. Variability of tumor aggressiveness as a micro-evolutionary process of cancer stem cells with predetermined prognosis].}, journal = {Der Chirurg; Zeitschrift fur alle Gebiete der operativen Medizen}, volume = {80}, number = {7}, pages = {645-651}, pmid = {19562240}, issn = {1433-0385}, mesh = {Aged ; Biological Evolution ; Cell Survival/drug effects/genetics/radiation effects ; Cell Transformation, Neoplastic/drug effects/genetics/*pathology/radiation effects ; Chemotherapy, Adjuvant ; Colorectal Neoplasms/drug therapy/genetics/*pathology/radiotherapy/surgery ; Combined Modality Therapy ; Disease Progression ; Drug Resistance, Neoplasm/drug effects/genetics/radiation effects ; Gene Transfer Techniques ; Humans ; *Image Processing, Computer-Assisted ; Liver Neoplasms/genetics/*pathology/*secondary ; Lung Neoplasms/genetics/*pathology/*secondary ; Male ; Middle Aged ; Neoplasm Recurrence, Local/drug therapy/genetics/*pathology/radiotherapy ; Neoplasm Staging ; Neoplastic Cells, Circulating/pathology ; Neoplastic Stem Cells/drug effects/*pathology/radiation effects ; Organ Specificity ; *Positron-Emission Tomography ; Probability Theory ; Prognosis ; Radiotherapy, Adjuvant ; *Tomography, X-Ray Computed ; }, abstract = {Formation of cancer stem cells which are both rare and variably therapy-resistant marks the beginning of a new disease without precursors. Based on molecular changes, these cells are derived from normal cells and exhibit pre-programmed malignant behaviour. In vitro studies have shown that hybrid cancers which behave in a similar way to Dukes A, B or C cancers in vivo can be produce by horizontal gene transfer. The level of aggressiveness follows a Galton curve in the probability distribution. In the current paper we analyzed colorectal cancers by PET-CT in follow-up studies which extended over several years. We conclude that the primary tumors behave differently from distant metastases. Radical exstirpation of the primary tumor is able to cure the malignant process if the homing area is resected. The primary tumor acts as the supplier of cancer stem cells for metastases which appear in different organs. When chemotherapy is administered the distribution of metastases in different organs appears dependent of the response or non-response of cancer stem cells to this therapy. Large numbers of colorectal carcinomas existed for the same time duration before death (15 years) independent of the malignancy grade. The tumor metastasizes immediately after formation. The primary tumor and the metastases appear variably quickly depending on the malignancy grade and are autonomic processes.}, }
@article {pmid19561191, year = {2009}, author = {Wu, J and Xi, C}, title = {Evaluation of different methods for extracting extracellular DNA from the biofilm matrix.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {16}, pages = {5390-5395}, pmid = {19561191}, issn = {1098-5336}, mesh = {Acinetobacter/*genetics/growth &amp; development ; *Biofilms/growth &amp; development ; Cation Exchange Resins/chemistry ; DNA, Bacterial/chemistry/*isolation &amp; purification ; Edetic Acid/chemistry ; Endopeptidase K/metabolism ; Glycoside Hydrolases/metabolism ; Peptide-N4-(N-acetyl-beta-glucosaminyl) Asparagine Amidase/metabolism ; Random Amplified Polymorphic DNA Technique ; Sequence Analysis, DNA ; Sodium Dodecyl Sulfate/chemistry ; }, abstract = {The occurrence of high concentrations of extracellular DNA (eDNA) in the extracellular matrices of biofilms plays an important role in biofilm formation and development and possibly in horizontal gene transfer through natural transformation. Studies have been conducted to characterize the nature of eDNA and its potential function in biofilm development, but it is difficult to extract eDNA from the extracellular matrices of biofilms without any contamination from genomic DNA released by cell lysis during the extraction process. In this report, we compared several different extraction methods in order to obtain highly pure eDNA from different biofilm samples. After different extraction methods were explored, it was concluded that using chemical treatment or enzymatic treatment of biofilm samples may obtain larger amounts of eDNA than using the simple filtration method. There was no detectable cell lysis when the enzymatic treatment methods were used, but substantial cell lysis was observed when the chemical treatment methods were used. These data suggest that eDNA may bind to other extracellular polymers in the biofilm matrix and that enzymatic treatment methods are effective and favorable for extracting eDNA from biofilm samples. Moreover, randomly amplified polymorphic DNA analysis of eDNA in Acinetobacter sp. biofilms and Acinetobacter sp. genomic DNA and DNA sequencing analysis revealed that eDNA originated from genomic DNA but was not structurally identical to the genomic DNA.}, }
@article {pmid19559614, year = {2009}, author = {Walia, H and Josefsson, C and Dilkes, B and Kirkbride, R and Harada, J and Comai, L}, title = {Dosage-dependent deregulation of an AGAMOUS-LIKE gene cluster contributes to interspecific incompatibility.}, journal = {Current biology : CB}, volume = {19}, number = {13}, pages = {1128-1132}, pmid = {19559614}, issn = {1879-0445}, support = {R01 GM076103/GM/NIGMS NIH HHS/United States ; R01 GM076103-03/GM/NIGMS NIH HHS/United States ; 1R01GM076103/GM/NIGMS NIH HHS/United States ; }, mesh = {Arabidopsis/*genetics/metabolism ; Arabidopsis Proteins/*genetics/metabolism ; Gene Dosage ; Gene Expression Regulation, Plant ; *Gene Transfer, Horizontal ; MADS Domain Proteins/*genetics/metabolism ; Microarray Analysis ; *Multigene Family ; Phenotype ; Seeds/physiology ; }, abstract = {Postzygotic lethality of interspecies hybrids can result from differences in gene expression, copy number, or coding sequence and can be overcome by altering parental genome dosage. In crosses between Arabidopsis thaliana and A. arenosa, embryo arrest is associated with endosperm hyperproliferation and delayed development similar to paternal-excess interploidy crosses and polycomb-repressive complex (PRC) mutants. Failure is accompanied by parent-specific loss of gene silencing including the dysregulation of three genes suppressed by PRC. Increasing the maternal genome dosage rescues seed development and gene silencing. A gene set upregulated in the failing seed transcriptome encoded putative AGAMOUS-LIKE MADS domain transcription factors (AGL) that were expressed in normal early endosperm and were shown to interact in a previous yeast 2-hybrid analysis. Suppression of these AGL's expression upon cellularization required PRC. Preceding seed failure, expression of the PRC member FIS2 decreased concomitant with overexpression of the AGL cluster. Inactivating two members, AGL62 and AGL90, attenuated the postzygotic barrier between A. thaliana and A. arenosa. We present a model where dosage-sensitive loss of PRC function results in a dysregulated AGL network, which is detrimental for early seed development.}, }
@article {pmid19558678, year = {2009}, author = {Bertsch, C and Beuve, M and Dolja, VV and Wirth, M and Pelsy, F and Herrbach, E and Lemaire, O}, title = {Retention of the virus-derived sequences in the nuclear genome of grapevine as a potential pathway to virus resistance.}, journal = {Biology direct}, volume = {4}, number = {}, pages = {21}, pmid = {19558678}, issn = {1745-6150}, mesh = {Endogenous Retroviruses/genetics ; Genome, Plant/*genetics ; Immunity, Innate/*genetics/physiology ; Open Reading Frames/genetics ; Plant Diseases/genetics/virology ; Plant Viruses/*genetics ; Plants, Genetically Modified/*genetics/*virology ; Reverse Transcriptase Polymerase Chain Reaction ; Vitis/*genetics/*virology ; }, abstract = {BACKGROUND: Previous studies have revealed a wide-spread occurence of the partial and complete genomes of the reverse-transcribing pararetroviruses in the nuclear genomes of herbaceous plants. Although the absence of the virus-encoded integrases attests to the random and incidental incorporation of the viral sequences, their presence could have functional implications for the virus-host interactions.<br><br>HYPOTHESIS: Analyses of two nuclear genomes of grapevine revealed multiple events of horizontal gene transfer from pararetroviruses. The approximately 200-800 bp inserts that corresponded to partial ORFs encoding reverse transcriptase apparently derived from unknown or extinct caulimoviruses and tungroviruses, were found in 11 grapevine chromosomes. In contrast to the previous reports, no reliable cases of the inserts derived from the positive-strand RNA viruses were found. Because grapevine is known to be infected by the diverse positive-strand RNA viruses, but not pararetroviruses, we hypothesize that pararetroviral inserts have conferred host resistance to these viruses. Furthermore, we propose that such resistance involves RNA interference-related mechanisms acting via small RNA-mediated methylation of pararetroviral DNAs and/or via degradation of the viral mRNAs.<br><br>CONCLUSION: The pararetroviral sequences in plant genomes may be maintained due to the benefits of virus resistance to this class of viruses conferred by their presence. Such resistance could be particularly significant for the woody plants that must withstand years- to centuries-long virus assault. Experimental research into the RNA interference pathways involving the integrated pararetroviral inserts is required to test this hypothesis.<br><br>REVIEWERS: This article was reviewed by Arcady R. Mushegian, I. King Jordan, and Eugene V. Koonin.}, }
@article {pmid19557346, year = {2009}, author = {Han, LL and Wang, ET and Lu, YL and Zhang, YF and Sui, XH and Chen, WF and Chen, WX}, title = {Bradyrhizobium spp. and Sinorhizobium fredii are predominant in root nodules of Vigna angularis, a native legume crop in the subtropical region of China.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {47}, number = {3}, pages = {287-296}, pmid = {19557346}, issn = {1976-3794}, mesh = {Bacterial Proteins/genetics ; Bradyrhizobium/*isolation &amp; purification ; China ; Cluster Analysis ; DNA Fingerprinting/methods ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Evolution, Molecular ; Fabaceae/*microbiology ; Gene Transfer, Horizontal ; Molecular Sequence Data ; N-Acetylglucosaminyltransferases/genetics ; Phylogeny ; Plant Roots/*microbiology ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sinorhizobium fredii/*isolation &amp; purification ; }, abstract = {Adzuki bean (Vigna angularis) is an important legume crop native to China, but its rhizobia have not been well characterized. In the present study, a total of 60 rhizobial strains isolated from eight provinces of China were analyzed with amplified 16S rRNA gene RFLP, IGS-RFLP, and sequencing analyses of 16S rRNA, atpD, recA, and nodC genes. These strains were identified as genomic species within Rhizobium, Sinorhizobium, Mesorhizobium, Bradyrhizobium, and Ochrobactrum. The most abundant groups were Bradyrhizobium species and Sinorhizobium fredii. Diverse nodC genes were found in these strains, which were mainly co-evolved with the housekeeping genes, but a possible lateral transfer of nodC from Sinorhizobium to Rhizobium was found. Analyses of the genomic and symbiotic gene backgrounds showed that adzuki bean shared the same rhizobial gene pool with soybean (legume native to China) and the exotic Vigna species. All of these data demonstrated that nodule formation is the interaction of rhizobia, host plants, and environment characters.}, }
@article {pmid19556510, year = {2009}, author = {Moustafa, A and Beszteri, B and Maier, UG and Bowler, C and Valentin, K and Bhattacharya, D}, title = {Genomic footprints of a cryptic plastid endosymbiosis in diatoms.}, journal = {Science (New York, N.Y.)}, volume = {324}, number = {5935}, pages = {1724-1726}, doi = {10.1126/science.1172983}, pmid = {19556510}, issn = {1095-9203}, support = {R01ES013679/ES/NIEHS NIH HHS/United States ; T32 GM98629/GM/NIGMS NIH HHS/United States ; }, mesh = {Biological Evolution ; Cell Nucleus/genetics ; Chlorophyta/classification/*genetics/physiology ; Diatoms/classification/*genetics/physiology ; Gene Transfer, Horizontal ; Genes ; *Genome ; Phylogeny ; Plastids/*genetics ; Rhodophyta/classification/*genetics/physiology ; *Symbiosis ; }, abstract = {Diatoms and other chromalveolates are among the dominant phytoplankters in the world's oceans. Endosymbiosis was essential to the success of chromalveolates, and it appears that the ancestral plastid in this group had a red algal origin via an ancient secondary endosymbiosis. However, recent analyses have turned up a handful of nuclear genes in chromalveolates that are of green algal derivation. Using a genome-wide approach to estimate the "green" contribution to diatoms, we identified >1700 green gene transfers, constituting 16% of the diatom nuclear coding potential. These genes were probably introduced into diatoms and other chromalveolates from a cryptic endosymbiont related to prasinophyte-like green algae. Chromalveolates appear to have recruited genes from the two major existing algal groups to forge a highly successful, species-rich protist lineage.}, }
@article {pmid19556490, year = {2009}, author = {Dagan, T and Martin, W}, title = {Microbiology. Seeing green and red in diatom genomes.}, journal = {Science (New York, N.Y.)}, volume = {324}, number = {5935}, pages = {1651-1652}, doi = {10.1126/science.1175765}, pmid = {19556490}, issn = {1095-9203}, mesh = {Biological Evolution ; Cell Nucleus/genetics ; Chlorophyta/*genetics/physiology ; Diatoms/*genetics/physiology ; Gene Transfer, Horizontal ; *Genome ; Phylogeny ; Plastids/genetics ; Rhodophyta/*genetics/physiology ; Symbiosis ; }, }
@article {pmid19556291, year = {2009}, author = {Tsai, YL and Wang, MH and Gao, C and Klüsener, S and Baron, C and Narberhaus, F and Lai, EM}, title = {Small heat-shock protein HspL is induced by VirB protein(s) and promotes VirB/D4-mediated DNA transfer in Agrobacterium tumefaciens.}, journal = {Microbiology (Reading, England)}, volume = {155}, number = {Pt 10}, pages = {3270-3280}, pmid = {19556291}, issn = {1350-0872}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Acetophenones/metabolism ; Agrobacterium tumefaciens/*physiology ; Bacterial Proteins/*metabolism ; DNA, Bacterial/*metabolism ; Gene Deletion ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Heat-Shock Proteins, Small/*biosynthesis/genetics ; Transcription Factors/genetics/*metabolism ; }, abstract = {Agrobacterium tumefaciens is a Gram-negative plant-pathogenic bacterium that causes crown gall disease by transferring and integrating its transferred DNA (T-DNA) into the host genome. We characterized the chromosomally encoded alpha-crystallin-type small heat-shock protein (alpha-Hsp) HspL, which was induced by the virulence (vir) gene inducer acetosyringone (AS). The transcription of hspL but not three other alpha-Hsp genes (hspC, hspAT1, hspAT2) was upregulated by AS. Further expression analysis in various vir mutants suggested that AS-induced hspL transcription is not directly activated by the VirG response regulator but rather depends on the expression of VirG-activated virB genes encoding components of the type IV secretion system (T4SS). Among the 11 virB genes encoded by the virB operon, HspL protein levels were reduced in strains with deletions of virB6, virB8 or virB11. VirB protein accumulation but not virB transcription levels were reduced in an hspL deletion mutant early after AS induction, implying that HspL may affect the stability of individual VirB proteins or of the T4S complex directly or indirectly. Tumorigenesis efficiency and the VirB/D4-mediated conjugal transfer of an IncQ plasmid RSF1010 derivative between A. tumefaciens strains were reduced in the absence of HspL. In conclusion, increased HspL abundance is triggered in response to certain VirB protein(s) and plays a role in optimal VirB protein accumulation, VirB/D4-mediated DNA transfer and tumorigenesis.}, }
@article {pmid19553209, year = {2009}, author = {Wu, GA and Jun, SR and Sims, GE and Kim, SH}, title = {Whole-proteome phylogeny of large dsDNA virus families by an alignment-free method.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {31}, pages = {12826-12831}, pmid = {19553209}, issn = {1091-6490}, support = {P50 GM062412/GM/NIGMS NIH HHS/United States ; GM62412/GM/NIGMS NIH HHS/United States ; }, mesh = {Baculoviridae/classification ; DNA Viruses/*classification/genetics ; Gene Transfer, Horizontal ; Herpesviridae/classification ; Phycodnaviridae/classification ; *Phylogeny ; Poxviridae/classification ; *Proteome ; Sequence Alignment ; }, abstract = {The vast sequence divergence among different virus groups has presented a great challenge to alignment-based sequence comparison among different virus families. Using an alignment-free comparison method, we construct the whole-proteome phylogeny for a population of viruses from 11 viral families comprising 142 large dsDNA eukaryote viruses. The method is based on the feature frequency profiles (FFP), where the length of the feature (l-mer) is selected to be optimal for phylogenomic inference. We observe that (i) the FFP phylogeny segregates the population into clades, the membership of each has remarkable agreement with current classification by the International Committee on the Taxonomy of Viruses, with one exception that the mimivirus joins the phycodnavirus family; (ii) the FFP tree detects potential evolutionary relationships among some viral families; (iii) the relative position of the 3 herpesvirus subfamilies in the FFP tree differs from gene alignment-based analysis; (iv) the FFP tree suggests the taxonomic positions of certain "unclassified" viruses; and (v) the FFP method identifies candidates for horizontal gene transfer between virus families.}, }
@article {pmid19548321, year = {2009}, author = {Guixé, V and Merino, F}, title = {The ADP-dependent sugar kinase family: kinetic and evolutionary aspects.}, journal = {IUBMB life}, volume = {61}, number = {7}, pages = {753-761}, doi = {10.1002/iub.217}, pmid = {19548321}, issn = {1521-6551}, mesh = {Adenosine Diphosphate/*metabolism ; Amino Acid Sequence ; Animals ; Cations, Divalent/pharmacology ; Cytidine Diphosphate/metabolism ; Evolution, Molecular ; Glucokinase/genetics/*metabolism ; Kinetics ; Mice ; Phosphotransferases (Alcohol Group Acceptor)/genetics/*metabolism ; Pyrimidines/metabolism ; Substrate Specificity ; }, abstract = {Some archaea of the Euryarchaeota present a unique version of the Embden-Meyerhof pathway where glucose and fructose-6-phosphate are phoshporylated using ADP instead of ATP as the phosphoryl donor. These are the only ADP-dependent kinases known to date. Although initially they were believed to represent a new protein family, they can be classified as members of the ribokinase superfamily, which also include several ATP-dependent kinases. As they were first identified in members of the thermococcales it was proposed that the presence of these ADP-dependent kinases is an adaptation to high temperatures. Later, homologs of these enzymes were identified in the genomes of mesophilic and thermophilic methanogenic archaea and even in the genomes of higher eukaryotes, suggesting that the presence of these proteins is not related to the hyperthermophilic life. The ADP-dependent kinases are very restrictive to their ligands being unable to use triphosphorylated nucleotides such as ATP. However, it has been shown that they can bind ATP by competition kinetic experiments. The hyperthermophilic methanogenic archaeon Methanocaldococcus jannaschii has a homolog of these genes, which can phosphorylate glucose and fructose-6-phosphate. For this reason, it was proposed as an ancestral form for the family. However, recent studies have shown that the ancestral activity in the group is glucokinase, and a combination of gene duplication and lateral gene transfer could have originated the two paralogs in this member of the Euryarchaeota. Interestingly, based on structural comparisons made within the superfamily it has been suggested that the ADP-dependent kinases are the newest in the group. In several members of the superfamily, the presence of divalent metal cations has been shown to be crucial for catalysis, so its role in the ADP-dependent family was investigated through molecular dynamics. The simulation shows that, in fact, the metal coordinates the catalytic ensemble and interacts with crucial residues for catalysis.}, }
@article {pmid19542287, year = {2009}, author = {Cromie, GA}, title = {Phylogenetic ubiquity and shuffling of the bacterial RecBCD and AddAB recombination complexes.}, journal = {Journal of bacteriology}, volume = {191}, number = {16}, pages = {5076-5084}, pmid = {19542287}, issn = {1098-5530}, support = {R01 GM031693/GM/NIGMS NIH HHS/United States ; R56 GM031693/GM/NIGMS NIH HHS/United States ; GM031693/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Proteins/classification/*genetics/physiology ; Computational Biology ; Exodeoxyribonuclease V/classification/*genetics/physiology ; Exodeoxyribonucleases/classification/*genetics/physiology ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/genetics ; *Phylogeny ; Recombination, Genetic/genetics ; }, abstract = {RecBCD and AddAB are bacterial enzymes that share similar helicase and nuclease activities and initiate repair of DNA double-strand breaks by homologous recombination. Examination of the phylogenetic distribution of AddAB and RecBCD revealed that one or the other complex is present in most sequenced bacteria. In addition, horizontal gene transfer (HGT) events involving addAB and recBCD appear to be common, with the genes encoding one complex frequently replacing those encoding the other. HGT may also explain the unexpected identification of archaeal addAB genes. More than 85% of addAB and recBCD genes are clustered on the genome, suggesting operon structures. A few organisms, including the Mycobacteria, encode multiple copies of these complexes of either the same or mixed classes. The possibility that the enzymatic activities of the AddAB and RecBCD enzymes promote their horizontal transfer is discussed, and the distribution of AddAB/RecBCD is compared to that of the RecU/RuvC resolvases. Finally, it appears that two sequence motifs, the Walker A box involved in ATP binding and an iron-sulfur-cysteine cluster, are present only in subsets of AddB proteins, suggesting the existence of mechanistically distinct classes of AddB.}, }
@article {pmid19538505, year = {2009}, author = {Duan, Z and Shang, Y and Gao, Q and Zheng, P and Wang, C}, title = {A phosphoketolase Mpk1 of bacterial origin is adaptively required for full virulence in the insect-pathogenic fungus Metarhizium anisopliae.}, journal = {Environmental microbiology}, volume = {11}, number = {9}, pages = {2351-2360}, doi = {10.1111/j.1462-2920.2009.01961.x}, pmid = {19538505}, issn = {1462-2920}, mesh = {Adaptation, Physiological ; Aldehyde-Lyases/*genetics/metabolism ; Animals ; Base Sequence ; Gene Expression Profiling ; Gene Expression Regulation, Fungal ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Host-Pathogen Interactions ; Insecta/microbiology ; Manduca/pathogenicity ; Metarhizium/enzymology/*pathogenicity ; Molecular Sequence Data ; Pentose Phosphate Pathway ; Pentoses/metabolism ; Phylogeny ; Virulence Factors/*genetics/metabolism ; }, abstract = {Pentose metabolism through the phosphoketolase pathway has been well characterized in bacteria. In this paper, we report the identification of a phosphoketolase homologue Mpk1 in the insect-pathogenic fungus Metarhizium anisopliae. Phylogenetic analysis showed that fungal phosphoketolases are of bacterial origin and diverged into two superfamilies. Frequent gene loss or lack of acquisition is evident in specific fungal lineages or species. The mpk1 gene is highly expressed when grown in trehalose-rich insect haemolymph but poorly induced by insect cuticle or carbohydrate-rich plant root exudate. In addition, mpk1 gene expression and enzyme activity could be upregulated by different sugars including xylose, trehalose, glucose or sucrose. mpk1 null mutants generated by homologous recombination grew similar to the wild type of M. anisopliae on medium amended with xylose as a sole carbon source. However, insect (tobacco hornworm, Manduca sexta) bioassays showed significantly reduced virulence in Deltampk1. The results of this study suggest that the horizontally transferred Mpk1 in M. anisopliae plays an important niche adaptation role for fungal propagation in insect haemocoel. Following the carbohydrate flux from plants to plant-feeding insects and insect pathogenic fungi, a tritrophic relationship is discussed in association with the requirement of fungal phosphoketolase pathway.}, }
@article {pmid19536205, year = {2009}, author = {Schmid, AK and Reiss, DJ and Pan, M and Koide, T and Baliga, NS}, title = {A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability.}, journal = {Molecular systems biology}, volume = {5}, number = {}, pages = {282}, pmid = {19536205}, issn = {1744-4292}, support = {P50GM076547/GM/NIGMS NIH HHS/United States ; 1R01GM077398-01A2/GM/NIGMS NIH HHS/United States ; F32 GM078980/GM/NIGMS NIH HHS/United States ; P50 GM076547/GM/NIGMS NIH HHS/United States ; 5F32GM078980-02/GM/NIGMS NIH HHS/United States ; R01 GM077398/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Archaeal Proteins/*genetics/metabolism ; Binding Sites ; Carbohydrate Metabolism ; Databases, Genetic ; Enhancer Elements, Genetic ; Evolution, Molecular ; Gene Expression Profiling ; Gene Regulatory Networks ; Halobacterium salinarum/*genetics/metabolism ; Metabolic Networks and Pathways/*genetics/physiology ; Molecular Sequence Data ; Oxidation-Reduction ; Phenotype ; Promoter Regions, Genetic ; Sequence Alignment ; Sequence Analysis, Protein ; Signal Transduction/genetics/physiology ; Stress, Physiological ; Transcription Factors/*genetics/metabolism ; }, abstract = {During evolution, enzyme-coding genes are acquired and/or replaced through lateral gene transfer and compiled into metabolic pathways. Gene regulatory networks evolve to fine tune biochemical fluxes through such metabolic pathways, enabling organisms to acclimate to nutrient fluctuations in a competitive environment. Here, we demonstrate that a single TrmB family transcription factor in Halobacterium salinarum NRC-1 globally coordinates functionally linked enzymes of diverse phylogeny in response to changes in carbon source availability. Specifically, during nutritional limitation, TrmB binds a cis-regulatory element to activate or repress 113 promoters of genes encoding enzymes in diverse metabolic pathways. By this mechanism, TrmB coordinates the expression of glycolysis, TCA cycle, and amino-acid biosynthesis pathways with the biosynthesis of their cognate cofactors (e.g. purine and thiamine). Notably, the TrmB-regulated metabolic network includes enzyme-coding genes that are uniquely archaeal as well as those that are conserved across all three domains of life. Simultaneous analysis of metabolic and gene regulatory network architectures suggests an ongoing process of co-evolution in which TrmB integrates the expression of metabolic enzyme-coding genes of diverse origins.}, }
@article {pmid19531707, year = {2009}, author = {Dhanarani, TS and Shankar, C and Park, J and Dexilin, M and Kumar, RR and Thamaraiselvi, K}, title = {Study on acquisition of bacterial antibiotic resistance determinants in poultry litter.}, journal = {Poultry science}, volume = {88}, number = {7}, pages = {1381-1387}, doi = {10.3382/ps.2008-00327}, pmid = {19531707}, issn = {0032-5791}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects ; *Chickens ; Conjugation, Genetic ; *Drug Resistance, Bacterial ; *Floors and Floorcoverings ; Housing, Animal ; Plasmids ; }, abstract = {Antibiotic resistance and the mode of transmission were investigated in bacteria isolated from poultry litter. Total aerobic heterotrophic bacteria were screened and identified for their resistance to different antibiotics such as ampicillin, streptomycin, erythromycin, tetracycline, chloramphenicol, kanamycin, tobramycin, and rifampicin. The distribution of bacteria found in the litter was Staphylococcus (29.1%), which was the predominant group, followed by Streptococcus (25%), Micrococcus (20.8%), Escherichia coli (12.5%), Salmonella (8.3%), and Aeromonas (4.1%). Fifty percent of these isolates were susceptible to ampicillin, 57% to erythromycin, 25% to tetracycline, 4% to chloramphenicol, 40% to kanamycin, 75% to streptomycin, 54% to tobramycin, and 4% to rifampicin. Three randomly selected isolates representing Staphylococcus, Streptococcus, and Micrococcus were examined for plasmids, and plasmid-curing and plasmid-induced transformation studies were conducted. Streptococcus and Micrococcus harbored a plasmid of 4.2 and 5.1 kb, respectively, whereas Staphylococcus did not harbor any plasmids. Plasmids were cured in Streptococcus and Micrococcus at a concentration of 75 and 100 microg/ mL of acridine orange, respectively, and transformation of 4.2- and 5.1-kb plasmids isolated from the Streptococcus and Micrococcus to plasmid-free E. coli DH5alpha strain was possible. In conjugation experiments, the antibiotic resistance profiles of transconjugant cells were found to be the same as the donors with the exception of Staphylococcus. The results of this study suggest that transformation and conjugation could be an important mechanism for horizontal gene transfer between bacteria in poultry litter. An understanding of the mechanism and magnitude of resistance gene transfer may provide a strategy to reduce the potential for dissemination of these genes.}, }
@article {pmid19531232, year = {2009}, author = {Cortez, D and Forterre, P and Gribaldo, S}, title = {A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes.}, journal = {Genome biology}, volume = {10}, number = {6}, pages = {R65}, pmid = {19531232}, issn = {1474-760X}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Base Sequence ; Computer Simulation ; Databases, Nucleic Acid ; *Gene Transfer, Horizontal ; Genome, Archaeal/*genetics ; Genome, Bacterial/*genetics ; Markov Chains ; Models, Genetic ; Multigene Family ; Open Reading Frames/*genetics ; }, abstract = {BACKGROUND: Archaeal and bacterial genomes contain a number of genes of foreign origin that arose from recent horizontal gene transfer, but the role of integrative elements (IEs), such as viruses, plasmids, and transposable elements, in this process has not been extensively quantified. Moreover, it is not known whether IEs play an important role in the origin of ORFans (open reading frames without matches in current sequence databases), whose proportion remains stable despite the growing number of complete sequenced genomes.<br><br>RESULTS: We have performed a large-scale survey of potential recently acquired IEs in 119 archaeal and bacterial genomes. We developed an accurate in silico Markov model-based strategy to identify clusters of genes that show atypical sequence composition (clusters of atypical genes or CAGs) and are thus likely to be recently integrated foreign elements, including IEs. Our method identified a high number of new CAGs. Probabilistic analysis of gene content indicates that 56% of these new CAGs are likely IEs, whereas only 7% likely originated via horizontal gene transfer from distant cellular sources. Thirty-four percent of CAGs remain unassigned, what may reflect a still poor sampling of IEs associated with bacterial and archaeal diversity. Moreover, our study contributes to the issue of the origin of ORFans, because 39% of these are found inside CAGs, many of which likely represent recently acquired IEs.<br><br>CONCLUSIONS: Our results strongly indicate that archaeal and bacterial genomes contain an impressive proportion of recently acquired foreign genes (including ORFans) coming from a still largely unexplored reservoir of IEs.}, }
@article {pmid19530257, year = {2009}, author = {Shivrain, VK and Burgos, NR and Gealy, DR and Sales, MA and Smith, KL}, title = {Gene flow from weedy red rice (Oryza sativa L.) to cultivated rice and fitness of hybrids.}, journal = {Pest management science}, volume = {65}, number = {10}, pages = {1124-1129}, doi = {10.1002/ps.1802}, pmid = {19530257}, issn = {1526-4998}, mesh = {Chimera/*genetics/physiology ; Crops, Agricultural/*genetics/physiology ; *Gene Flow ; Gene Transfer, Horizontal ; Oryza/*genetics/physiology ; }, abstract = {BACKGROUND: Gene transfer from weeds to crops could produce weedy individuals that might impact upon the evolutionary dynamics of weedy populations, the persistence of escaped genes in agroecosystems and approaches to weed management and containment of transgenic crops. The present aim was to quantify the gene flowrate from weedy red rice to cultivated rice, and evaluate the morphology, phenology and fecundity of resulting hybrids. Field experiments were conducted at Stuttgart and Rohwer, Arkansas, USA. Twelve red rice accessions and an imazethapyr-resistant rice (Imi-R; Clearfield) were used.<br><br>RESULTS: Hybrids between Imi-R rice x red rice were 138-150 cm tall and flowered 1-5 days later than the rice parent, regardless of the red rice parent. Hybrids produced 20-50% more seed than the rice parent, but had equivalent seed production to the majority of red rice parents. Seeds of all hybrids were red, pubescent and dehisced at maturity. For the majority of hybrids, seed germination was higher than that of the red rice parent. The gene flowrate from red rice to rice was 0.01-0.2% and differed by red rice biotype. The hybrids had higher fecundity and potential competitive ability than the rice parent, and in some cases also the red rice parent.<br><br>CONCLUSIONS: Red rice plants are vectors of gene flow back to cultivated rice and other weedy populations. The progeny of red rice hybrids from cultivated rice mother plants have higher chances of persistence than those from red rice mother plants. Gene flow mitigation strategies should consider this scenario.}, }
@article {pmid19528223, year = {2009}, author = {Buboltz, AM and Nicholson, TL and Karanikas, AT and Preston, A and Harvill, ET}, title = {Evidence for horizontal gene transfer of two antigenically distinct O antigens in Bordetella bronchiseptica.}, journal = {Infection and immunity}, volume = {77}, number = {8}, pages = {3249-3257}, pmid = {19528223}, issn = {1098-5522}, support = {R01 GM083113-03/GM/NIGMS NIH HHS/United States ; R01 AI053075/AI/NIAID NIH HHS/United States ; R01 GM083113-04/GM/NIGMS NIH HHS/United States ; R01 AI053075-04/AI/NIAID NIH HHS/United States ; R01 AI053075-05/AI/NIAID NIH HHS/United States ; R01 AI053075-03/AI/NIAID NIH HHS/United States ; AI 053075/AI/NIAID NIH HHS/United States ; GM083113/GM/NIGMS NIH HHS/United States ; R56 AI065507/AI/NIAID NIH HHS/United States ; R01 AI053075-01A1/AI/NIAID NIH HHS/United States ; R01 GM083113-01/GM/NIGMS NIH HHS/United States ; AI 065507/AI/NIAID NIH HHS/United States ; R01 GM083113/GM/NIGMS NIH HHS/United States ; R01 GM083113-02/GM/NIGMS NIH HHS/United States ; R01 AI053075-02/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacterial Typing Techniques ; Bordetella Infections/immunology/*microbiology ; Bordetella bronchiseptica/classification/*genetics/immunology/isolation &amp; purification ; Cluster Analysis ; Comparative Genomic Hybridization ; DNA Fingerprinting ; DNA, Bacterial/genetics ; *Gene Transfer, Horizontal ; Genotype ; Mice ; Mice, Inbred C57BL ; O Antigens/*genetics/immunology ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {Host immunity is a major driving force of antigenic diversity, resulting in pathogens that can evade immunity induced by closely related strains. Here we show that two Bordetella bronchiseptica strains, RB50 and 1289, express two antigenically distinct O-antigen serotypes (O1 and O2, respectively). When 18 additional B. bronchiseptica strains were serotyped, all were found to express either the O1 or O2 serotype. Comparative genomic hybridization and PCR screening showed that the expression of either the O1 or O2 serotype correlated with the strain containing either the classical or alternative O-antigen locus, respectively. Multilocus sequence typing analysis of 49 B. bronchiseptica strains was used to build a phylogenetic tree, which revealed that the two O-antigen loci did not associate with a particular lineage, evidence that these loci are horizontally transferred between B. bronchiseptica strains. From experiments using mice vaccinated with purified lipopolysaccharide from strain RB50 (O1), 1289 (O2), or RB50Deltawbm (O antigen deficient), our data indicate that these O antigens do not confer cross-protection in vivo. The lack of cross-immunity between O-antigen serotypes appears to contribute to inefficient antibody-mediated clearance between strains. Together, these data are consistent with the idea that the O-antigen loci of B. bronchiseptica are horizontally transferred between strains and encode antigenically distinct serotypes, resulting in inefficient cross-immunity.}, }
@article {pmid19528170, year = {2009}, author = {Wang, XD and Cai, JC and Zhou, HW and Zhang, R and Chen, GX}, title = {Reduced susceptibility to carbapenems in Klebsiella pneumoniae clinical isolates associated with plasmid-mediated beta-lactamase production and OmpK36 porin deficiency.}, journal = {Journal of medical microbiology}, volume = {58}, number = {Pt 9}, pages = {1196-1202}, doi = {10.1099/jmm.0.008094-0}, pmid = {19528170}, issn = {0022-2615}, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics/*metabolism ; Base Sequence ; Carbapenems/*pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Electrophoresis, Gel, Pulsed-Field ; Gene Expression Regulation, Bacterial/physiology ; Gene Transfer, Horizontal ; Humans ; Klebsiella pneumoniae/*drug effects/*genetics/metabolism ; Molecular Sequence Data ; Plasmids/*metabolism ; Porins/genetics/*metabolism ; beta-Lactamases/genetics/*metabolism ; }, abstract = {Two carbapenem-non-susceptible Klebsiella pneumoniae isolates, Z2554 and Z2110, were collected from a hospital in China and analysed by PFGE. K. pneumoniae Z2554 and Z2110 were genetically unrelated and showed resistance to ertapenem, and reduced susceptibility to imipenem and meropenem. Analysis of their beta-lactamases indicated that K. pneumoniae Z2554 produced TEM-1 and CTX-M-14 beta-lactamases, whilst Z2110 produced a plasmid-mediated AmpC beta-lactamase, DHA-1, in addition to TEM-1 and CTX-M-14. SDS-PAGE analysis of the outer-membrane proteins (OMPs) revealed that both isolates lacked an OMP of approximately 39 kDa (OmpK36), whilst Z2110 had an additional protein with an approximate molecular mass of 26 kDa. Analysis of the OMP-encoding genes demonstrated that the ompK35 sequence of K. pneumoniae Z2554 and Z2110 contained a number of silent mutations. In ompK36, several insertions and deletions of short DNA fragments (1-6 bp) were detected in both isolates. The N-terminal sequence of the approximately 26 kDa protein band identified in Z2110 had no similarity to the sequence of OmpK36. Instead, it shared high similarity with hypothetical protein KPN_03267 originating from K. pneumoniae subsp. pneumoniae MGH 78578. It was concluded that beta-lactamase production combined with OmpK36 deficiency results in ertapenem resistance, and reduced imipenem and meropenem susceptibility, in K. pneumoniae Z2554 and Z2110. OmpK36 may play an important role in the resistance or reduced susceptibility to carbapenems in K. pneumoniae producing AmpC, extended-spectrum beta-lactamase or broad-spectrum beta-lactamase.}, }
@article {pmid19525398, year = {2009}, author = {Ratmann, O and Andrieu, C and Wiuf, C and Richardson, S}, title = {Model criticism based on likelihood-free inference, with an application to protein network evolution.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {26}, pages = {10576-10581}, pmid = {19525398}, issn = {1091-6490}, support = {/WT_/Wellcome Trust/United Kingdom ; BB/C519670/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Algorithms ; Bacterial Proteins/*genetics/metabolism ; Bayes Theorem ; Computational Biology/methods ; Databases, Protein ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Helicobacter pylori/genetics/metabolism ; Likelihood Functions ; *Models, Biological ; Monte Carlo Method ; Protein Interaction Mapping ; Treponema pallidum/genetics/metabolism ; }, abstract = {Mathematical models are an important tool to explain and comprehend complex phenomena, and unparalleled computational advances enable us to easily explore them without any or little understanding of their global properties. In fact, the likelihood of the data under complex stochastic models is often analytically or numerically intractable in many areas of sciences. This makes it even more important to simultaneously investigate the adequacy of these models-in absolute terms, against the data, rather than relative to the performance of other models-but no such procedure has been formally discussed when the likelihood is intractable. We provide a statistical interpretation to current developments in likelihood-free Bayesian inference that explicitly accounts for discrepancies between the model and the data, termed Approximate Bayesian Computation under model uncertainty (ABCmicro). We augment the likelihood of the data with unknown error terms that correspond to freely chosen checking functions, and provide Monte Carlo strategies for sampling from the associated joint posterior distribution without the need of evaluating the likelihood. We discuss the benefit of incorporating model diagnostics within an ABC framework, and demonstrate how this method diagnoses model mismatch and guides model refinement by contrasting three qualitative models of protein network evolution to the protein interaction datasets of Helicobacter pylori and Treponema pallidum. Our results make a number of model deficiencies explicit, and suggest that the T. pallidum network topology is inconsistent with evolution dominated by link turnover or lateral gene transfer alone.}, }
@article {pmid19523153, year = {2009}, author = {Spallek, T and Robatzek, S and Göhre, V}, title = {How microbes utilize host ubiquitination.}, journal = {Cellular microbiology}, volume = {11}, number = {10}, pages = {1425-1434}, doi = {10.1111/j.1462-5822.2009.01346.x}, pmid = {19523153}, issn = {1462-5822}, mesh = {Bacteria/genetics/*metabolism ; Bacterial Proteins/genetics/*metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Host-Pathogen Interactions ; Models, Biological ; *Ubiquitination ; }, abstract = {Activity, abundance and localization of eukaryotic proteins can be regulated through covalent attachment of ubiquitin and ubiquitin-like moieties. Ubiquitination is important in various aspects of immunity. Pathogens utilize host ubiquitination for the suppression of immune signalling and reprogramming host processes to promote microbial life. They deliver so-called effector molecules into host cells, which functionally or structurally resemble components of the host ubiquitination machinery utilizing this enzymatic process or they secrete molecules to inhibit ubiquitin-mediated degradation. Since prokaryotic pathogens lack a classical ubiquitination system, effector mimicry of components of the ubiquitin machinery could be achieved through gene flow. Horizontal gene transfer allows pathogenic bacteria to access ubiquitination enzymes from a potential host, while lateral gene transfer recruits components from another pathogen providing spread within the microbial community. Additionally, convergent evolution can shape bacterial proteins to acquire ubiquitination functions.}, }
@article {pmid19521501, year = {2009}, author = {Baños, RC and Vivero, A and Aznar, S and García, J and Pons, M and Madrid, C and Juárez, A}, title = {Differential regulation of horizontally acquired and core genome genes by the bacterial modulator H-NS.}, journal = {PLoS genetics}, volume = {5}, number = {6}, pages = {e1000513}, pmid = {19521501}, issn = {1553-7404}, mesh = {Bacterial Proteins/genetics/*metabolism ; DNA, Bacterial/genetics ; DNA-Binding Proteins/genetics/*metabolism ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Plasmids/genetics ; Protein Binding ; Salmonella typhimurium/*genetics/*metabolism ; }, abstract = {Horizontal acquisition of DNA by bacteria dramatically increases genetic diversity and hence successful bacterial colonization of several niches, including the human host. A relevant issue is how this newly acquired DNA interacts and integrates in the regulatory networks of the bacterial cell. The global modulator H-NS targets both core genome and HGT genes and silences gene expression in response to external stimuli such as osmolarity and temperature. Here we provide evidence that H-NS discriminates and differentially modulates core and HGT DNA. As an example of this, plasmid R27-encoded H-NS protein has evolved to selectively silence HGT genes and does not interfere with core genome regulation. In turn, differential regulation of both gene lineages by resident chromosomal H-NS requires a helper protein: the Hha protein. Tight silencing of HGT DNA is accomplished by H-NS-Hha complexes. In contrast, core genes are modulated by H-NS homoligomers. Remarkably, the presence of Hha-like proteins is restricted to the Enterobacteriaceae. In addition, conjugative plasmids encoding H-NS variants have hitherto been isolated only from members of the family. Thus, the H-NS system in enteric bacteria presents unique evolutionary features. The capacity to selectively discriminate between core and HGT DNA may help to maintain horizontally transmitted DNA in silent form and may give these bacteria a competitive advantage in adapting to new environments, including host colonization.}, }
@article {pmid19508981, year = {2009}, author = {Zhao, F and Qi, J and Schuster, SC}, title = {Tracking the past: interspersed repeats in an extinct Afrotherian mammal, Mammuthus primigenius.}, journal = {Genome research}, volume = {19}, number = {8}, pages = {1384-1392}, pmid = {19508981}, issn = {1088-9051}, mesh = {Animals ; Chromosome Mapping ; Chromosomes, Mammalian/genetics ; Computer Simulation ; DNA Transposable Elements/genetics ; Evolution, Molecular ; *Extinction, Biological ; Genome/genetics ; Genomics/methods ; Humans ; Interspersed Repetitive Sequences/*genetics ; Mammals/classification/*genetics ; Models, Genetic ; Opossums ; Paleontology ; *Phylogeny ; Retroelements/genetics ; Time Factors ; }, abstract = {The woolly mammoth (Mammuthus primigenius) died out about several thousand years ago, yet recent paleogenomic studies have successfully recovered genetic information from both the mitochondrial and nuclear genomes of this extinct species. Mammoths belong to Afrotheria, a group of mammals exhibiting extreme morphological diversity and large genome sizes. In this study, we found that the mammoth genome contains a larger proportion of interspersed repeats than any other mammalian genome reported so far, in which the proliferation of the RTE family of retrotransposons (covering 12% of the genome) may be the main reason for an increased genome size. Phylogenetic analysis showed that RTEs in mammoth are closely related to the family BovB/RTE. The incongruence of the reconstructed RTE phylogeny indicates that RTEs in mammoth may be acquired through an ancient lateral gene transfer event. A recent proliferation of SINEs was also found in the probocidean lineage, whereas the Afrotherian-wide SINEs in mammoth have undergone a rather flat and stepwise expansion. Comparisons of the transposable elements (TEs) between mammoth and other mammals may shed light on the evolutionary history of TEs in various mammalian lineages.}, }
@article {pmid19502444, year = {2009}, author = {Palmer, K and Drake, HL and Horn, MA}, title = {Genome-derived criteria for assigning environmental narG and nosZ sequences to operational taxonomic units of nitrate reducers.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {15}, pages = {5170-5174}, pmid = {19502444}, issn = {1098-5336}, mesh = {Bacteria/*classification/*genetics ; Bacterial Proteins/*genetics ; Cluster Analysis ; Computational Biology/*methods ; DNA, Ribosomal/genetics ; *Environmental Microbiology ; Nitrate Reductase/*genetics ; Oxidoreductases/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {Ninety percent of cultured bacterial nitrate reducers with a 16S rRNA gene similarity of > or =97% had a narG or nosZ similarity of > or =67% or > or =80%, respectively, suggesting that 67% and 80% could be used as standardized, conservative threshold similarity values for narG and nosZ, respectively (i.e., any two sequences that are less similar than the threshold similarity value have a very high probability of belonging to different species), for estimating species-level operational taxonomic units. Genus-level tree topologies of narG and nosZ were generally similar to those of the corresponding 16S rRNA genes. Although some genomes contained multiple copies of narG, recent horizontal gene transfer of narG was not apparent.}, }
@article {pmid19502430, year = {2009}, author = {Stuart, RK and Dupont, CL and Johnson, DA and Paulsen, IT and Palenik, B}, title = {Coastal strains of marine Synechococcus species exhibit increased tolerance to copper shock and a distinctive transcriptional response relative to those of open-ocean strains.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {15}, pages = {5047-5057}, pmid = {19502430}, issn = {1098-5336}, mesh = {Amino Acid Sequence ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics ; Copper/*pharmacology ; *Drug Resistance, Bacterial ; *Gene Expression Profiling ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Seawater/microbiology ; Sequence Alignment ; *Stress, Physiological ; Synechococcus/*drug effects ; }, abstract = {Copper appears to be influencing the distribution and abundance of phytoplankton in marine environments, and cyanobacteria are thought to be the most sensitive of the phytoplankton groups to copper toxicity. By using growth assays of phylogenetically divergent clades, we found that coastal strains of marine Synechococcus species were more tolerant to copper shock than open-ocean strains. The global transcriptional response to two levels of copper shock were determined for both a coastal strain and an open-ocean strain of marine Synechococcus species using whole-genome expression microarrays. Both strains showed an osmoregulatory-like response, perhaps as a result of increasing membrane permeability. This could have implications for marine carbon cycling if copper shock leads to dissolved organic carbon leakage in Synechococcus species. The two strains additionally showed a common reduction in levels of photosynthesis-related gene transcripts. Contrastingly, the open-ocean strain showed a general stress response, whereas the coastal strain exhibited a more specifically oxidative or heavy-metal acclimation response that may be conferring tolerance. In addition, the coastal strain activated more regulatory elements and transporters, many of which are not conserved in other marine Synechococcus strains and may have been acquired by horizontal gene transfer. Thus, tolerance to copper shock in some marine Synechococcus strains may in part be a result of a generally increased ability to sense and respond in a more stress-specific manner.}, }
@article {pmid19497339, year = {2009}, author = {Arber, W}, title = {Systemic aspects of biological evolution.}, journal = {Journal of biotechnology}, volume = {144}, number = {3}, pages = {242-244}, doi = {10.1016/j.jbiotec.2009.05.010}, pmid = {19497339}, issn = {1873-4863}, mesh = {Animals ; *Biological Evolution ; DNA/genetics ; Gene Rearrangement/genetics ; Genetic Fitness/genetics ; Mutation/genetics ; }, abstract = {In recent years molecular mechanisms and natural strategies have been explored that spontaneously generate genetic variations at low rates without seriously affecting genetic stability at the level of populations. Thereby acquired knowledge suggests systemic aspects of evolutionary interdependences both in the past and in future evolutionary developments. The natural strategy of DNA acquisition by horizontal gene transfer interconnects different branches of the tree of evolution at random times. This makes in principle the entire global gene pool of the biosphere available to any kinds of living beings for their further evolutionary development. The relevance of this knowledge for risk assessments of genetically engineered organisms is discussed.}, }
@article {pmid19492967, year = {2009}, author = {Jensen, SO and Lyon, BR}, title = {Genetics of antimicrobial resistance in Staphylococcus aureus.}, journal = {Future microbiology}, volume = {4}, number = {5}, pages = {565-582}, doi = {10.2217/fmb.09.30}, pmid = {19492967}, issn = {1746-0921}, mesh = {Anti-Bacterial Agents/*pharmacology ; Disinfectants/*pharmacology ; *Drug Resistance, Multiple, Bacterial ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Interspersed Repetitive Sequences ; Mutation ; Staphylococcus aureus/*drug effects/*genetics ; }, abstract = {Strains of Staphylococcus aureus that are resistant to multiple antimicrobial compounds, including most available classes of antibiotics and some antiseptics, are a major threat to patient care owing to their stubborn intransigence to chemotherapy and disinfection. This reality has stimulated extensive efforts to understand the genetic nature of the determinants encoding antimicrobial resistance, together with the mechanisms by which these determinants evolve over time and are spread within bacterial populations. Such studies have benefited from the application of molecular genetics and in recent years, the sequencing of over a dozen complete staphylococcal genomes. It is now evident that the evolution of multiresistance is driven by the acquisition of discrete preformed antimicrobial resistance genes that are exchanged between organisms via horizontal gene transfer. Nonetheless, chromosomal mutation is the catalyst of novel resistance determinants and is likely to have an enhanced influence with the ongoing introduction of synthetic antibiotics.}, }
@article {pmid19487243, year = {2009}, author = {De Riso, V and Raniello, R and Maumus, F and Rogato, A and Bowler, C and Falciatore, A}, title = {Gene silencing in the marine diatom Phaeodactylum tricornutum.}, journal = {Nucleic acids research}, volume = {37}, number = {14}, pages = {e96}, pmid = {19487243}, issn = {1362-4962}, mesh = {Algal Proteins/genetics ; Clone Cells ; Cryptochromes ; Cytosine/metabolism ; DNA Methylation ; Diatoms/*genetics/metabolism ; Flavoproteins/genetics ; *Gene Knockdown Techniques ; *Gene Silencing ; Genes, Reporter ; Genome ; Phenotype ; Phytochrome/genetics ; RNA Interference ; Transgenes ; }, abstract = {Diatoms are a major but poorly understood phytoplankton group. The recent completion of two whole genome sequences has revealed that they contain unique combinations of genes, likely recruited during their history as secondary endosymbionts, as well as by horizontal gene transfer from bacteria. A major limitation for the study of diatom biology and gene function is the lack of tools to generate targeted gene knockout or knockdown mutants. In this work, we have assessed the possibility of triggering gene silencing in Phaeodactylum tricornutum using constructs containing either anti-sense or inverted repeat sequences of selected target genes. We report the successful silencing of a GUS reporter gene expressed in transgenic lines, as well as the knockdown of endogenous phytochrome (DPH1) and cryptochrome (CPF1) genes. To highlight the utility of the approach we also report the first phenotypic characterization of a diatom mutant (cpf1). Our data open the way for reverse genetics in diatoms and represent a major advance for understanding their biology and ecology. Initial molecular analyses reveal that targeted downregulation likely occurs through transcriptional and post-transcriptional gene silencing mechanisms. Interestingly, molecular players involved in RNA silencing in other eukaryotes are only poorly conserved in diatoms.}, }
@article {pmid19485766, year = {2009}, author = {Martínez-Romero, E}, title = {Coevolution in Rhizobium-legume symbiosis?.}, journal = {DNA and cell biology}, volume = {28}, number = {8}, pages = {361-370}, doi = {10.1089/dna.2009.0863}, pmid = {19485766}, issn = {1557-7430}, mesh = {Evolution, Molecular ; Fabaceae/classification/*genetics/microbiology ; Gene Transfer, Horizontal ; Genetic Variation ; Host-Pathogen Interactions ; Rhizobium/classification/*genetics/physiology ; Root Nodules, Plant/genetics/microbiology ; Species Specificity ; Symbiosis/*genetics ; }, abstract = {Legume nodules, specialized structures for nitrogen fixation, are probably the result of coevolution of plants and ancestral rhizobia. Among the evolutionary processes leading to legume radiation and divergence, coevolution with rhizobia might have occurred. Alternatively, bacteria could have been constantly selected by plants, with bacteria slightly influencing plant evolution (required to fulfill the criteria for a coevolutionary hypothesis). Evidence of bacterial effects on plant evolution is scarce but being searched for. Bacterial genetic plasticity may be indicative of the large capacity of Rhizobium to adapt to legumes. Events such as symbiotic replacement, easy recruitment of symbiotic bacteria by legume plants, and lateral transfer of symbiotic genes seem to erase the coevolutionary or selected relationships in rhizobial-legume symbiosis. In particular, the hypotheses proposed are (1) Rhizobium replaced Bradyrhizobium in a few hosts of the Phaseoleae tribe, Phaseolus vulgaris and P. coccineus; (2) Rhizobium etli as a species did not coevolve with bean; and (3) beta-Proteobacteria replaced alpha-Proteobacteria in South American mimosas. Novel results on symbiosis suggest a more complex evolutionary process for nodulation that may include multiple organisms, such as mycorrhiza, nematodes, and other bacteria in addition to rhizobia.}, }
@article {pmid19484299, year = {2009}, author = {Borgo, F and Ricci, G and Arends, K and Schiwon, K and Grohmann, E and Fortina, MG}, title = {Evaluation of plasmid content and tetracycline resistance conjugative transfer in Enterococcus italicus strains of dairy origin.}, journal = {Current microbiology}, volume = {59}, number = {3}, pages = {261-266}, pmid = {19484299}, issn = {1432-0991}, mesh = {Animals ; Blotting, Southern ; Chromosomes, Bacterial ; Conjugation, Genetic ; Dairy Products/*microbiology ; Enterococcus/*drug effects/genetics/*isolation &amp; purification ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Plasmids/*analysis ; *Tetracycline Resistance ; }, abstract = {Five Enterococcus italicus strains harbouring tet genes responsible for the tetracycline resistance were subjected to plasmid profile determination studies. For four strains tested the profiles showed between three and six plasmid bands, the size of which ranged between 1.6 and 18.5 kb. Southern hybridization experiments associated tetS and tetK genes with chromosomal DNA in all strains and tetM gene with plasmids of around the same size (18.5 kb) in two of the tested strains. The ability of the new species to transfer tetM gene was studied by transfer experiments with the tetracycline-susceptible recipient strains E. faecalis JH2-2 and OG1RF; mobilization experiments were performed with E. faecalis JH 2-2 harbouring the conjugative plasmid pIP501as helper plasmid. The results obtained show that the new enterococcal species was able to acquire antibiotic resistance by conjugation, but not to transfer its plasmids to other bacteria. Further PCR and hybridization experiments carried out to assess the presence of mobilization sequences also suggest that the tetM plasmid from E. italicus is a non-mobilizable plasmid.}, }
@article {pmid19482953, year = {2009}, author = {Fourie, G and Steenkamp, ET and Gordon, TR and Viljoen, A}, title = {Evolutionary relationships among the Fusarium oxysporum f. sp. cubense vegetative compatibility groups.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {14}, pages = {4770-4781}, pmid = {19482953}, issn = {1098-5336}, mesh = {Cluster Analysis ; Crosses, Genetic ; DNA, Fungal/chemistry/genetics ; DNA, Mitochondrial/chemistry/genetics ; Evolution, Molecular ; Fusarium/*classification/*genetics/isolation &amp; purification ; Genes, Mating Type, Fungal ; Molecular Sequence Data ; Musa/*microbiology ; Phylogeny ; Plant Diseases/*microbiology ; Recombination, Genetic ; Sequence Analysis, DNA ; }, abstract = {Fusarium oxysporum f. sp. cubense, the causal agent of fusarium wilt of banana (Musa spp.), is one of the most destructive strains of the vascular wilt fungus F. oxysporum. Genetic relatedness among and within vegetative compatibility groups (VCGs) of F. oxysporum f. sp. cubense was studied by sequencing two nuclear and two mitochondrial DNA regions in a collection of 70 F. oxysporum isolates that include representatives of 20 VCGs of F. oxysporum f. sp. cubense, other formae speciales, and nonpathogens. To determine the ability of F. oxysporum f. sp. cubense to sexually recombine, crosses were made between isolates of opposite mating types. Phylogenetic analysis separated the F. oxysporum isolates into two clades and eight lineages. Phylogenetic relationships between F. oxysporum f. sp. cubense and other formae speciales of F. oxysporum and the relationships among VCGs and races of F. oxysporum f. sp. cubense clearly showed that F. oxysporum f. sp. cubense's ability to cause disease on banana has emerged multiple times, independently, and that the ability to cause disease to a specific banana cultivar is also a polyphyletic trait. These analyses further suggest that both coevolution with the host and horizontal gene transfer may have played important roles in the evolutionary history of the pathogen. All examined isolates harbored one of the two mating-type idiomorphs, but never both, which suggests a heterothallic mating system should sexual reproduction occur. Although, no sexual structures were observed, some lineages of F. oxysporum f. sp. cubense harbored MAT-1 and MAT-2 isolates, suggesting a potential that these lineages have a sexual origin that might be more recent than initially anticipated.}, }
@article {pmid19482939, year = {2009}, author = {Lu, J and den Dulk-Ras, A and Hooykaas, PJ and Glover, JN}, title = {Agrobacterium tumefaciens VirC2 enhances T-DNA transfer and virulence through its C-terminal ribbon-helix-helix DNA-binding fold.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {24}, pages = {9643-9648}, pmid = {19482939}, issn = {1091-6490}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {Agrobacterium tumefaciens/genetics/*metabolism/pathogenicity ; Amino Acid Sequence ; Bacterial Proteins/chemistry/*physiology ; Binding Sites ; DNA, Bacterial/*genetics/metabolism ; Electrophoretic Mobility Shift Assay ; Models, Molecular ; Molecular Sequence Data ; Sequence Homology, Amino Acid ; Virulence/*physiology ; }, abstract = {Agrobacterium tumefaciens VirC2 stimulates processing of single-stranded T-DNA that is translocated into plants to induce tumor formation, but how VirC2 functions is unclear. Here, we report the 1.7-A X-ray crystal structure of its trypsin-resistant C-terminal domain, VirC2(82-202), which reveals a form of the ribbon-helix-helix (RHH) DNA-binding fold contained within a single polypeptide chain. DNA-binding assays and mutagenesis indicate that VirC2 uses this RHH fold to bind double-stranded DNA but not single-stranded DNA. Mutations that severely affect VirC2 DNA binding are highly deleterious for both T-DNA transfer into yeast and the virulence of A. tumefaciens in different plants including Nicotiana glauca and Kalanchoe daigremontiana. These data suggest that VirC2 enhances T-DNA transfer and virulence through DNA binding with its RHH fold. The RHH fold of VirC2 is the first crystal structure representing a group of predicted RHH proteins that facilitate endonucleolytic processing of DNA for horizontal gene transfer.}, }
@article {pmid19482938, year = {2009}, author = {Maslov, S and Krishna, S and Pang, TY and Sneppen, K}, title = {Toolbox model of evolution of prokaryotic metabolic networks and their regulation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {24}, pages = {9743-9748}, pmid = {19482938}, issn = {1091-6490}, mesh = {*Biological Evolution ; Gene Expression Regulation ; *Models, Genetic ; *Prokaryotic Cells ; Transcription, Genetic ; }, abstract = {It has been reported that the number of transcription factors encoded in prokaryotic genomes scales approximately quadratically with their total number of genes. We propose a conceptual explanation of this finding and illustrate it using a simple model in which metabolic and regulatory networks of prokaryotes are shaped by horizontal gene transfer of coregulated metabolic pathways. Adapting to a new environmental condition monitored by a new transcription factor (e.g., learning to use another nutrient) involves both acquiring new enzymes and reusing some of the enzymes already encoded in the genome. As the repertoire of enzymes of an organism (its toolbox) grows larger, it can reuse its enzyme tools more often and thus needs to get fewer new ones to master each new task. From this observation, it logically follows that the number of functional tasks and their regulators increases faster than linearly with the total number of genes encoding enzymes. Genomes can also shrink, e.g., because of a loss of a nutrient from the environment, followed by deletion of its regulator and all enzymes that become redundant. We propose several simple models of network evolution elaborating on this toolbox argument and reproducing the empirically observed quadratic scaling. The distribution of lengths of pathway branches in our model agrees with that of the real-life metabolic network of Escherichia coli. Thus, our model provides a qualitative explanation for broad distributions of regulon sizes in prokaryotes.}, }
@article {pmid19478995, year = {2009}, author = {Vinella, D and Brochier-Armanet, C and Loiseau, L and Talla, E and Barras, F}, title = {Iron-sulfur (Fe/S) protein biogenesis: phylogenomic and genetic studies of A-type carriers.}, journal = {PLoS genetics}, volume = {5}, number = {5}, pages = {e1000497}, pmid = {19478995}, issn = {1553-7404}, mesh = {Aerobiosis ; Anaerobiosis ; Carrier Proteins/*genetics/metabolism ; Escherichia coli/*genetics/metabolism ; Escherichia coli Proteins/*genetics/metabolism ; Eukaryotic Cells/classification/metabolism ; *Evolution, Molecular ; Gene Dosage ; Genome, Bacterial ; Iron-Sulfur Proteins/*genetics/metabolism ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Polyisoprenyl Phosphates/metabolism ; Prokaryotic Cells/classification/metabolism ; }, abstract = {Iron sulfur (Fe/S) proteins are ubiquitous and participate in multiple biological processes, from photosynthesis to DNA repair. Iron and sulfur are highly reactive chemical species, and the mechanisms allowing the multiprotein systems ISC and SUF to assist Fe/S cluster formation in vivo have attracted considerable attention. Here, A-Type components of these systems (ATCs for A-Type Carriers) are studied by phylogenomic and genetic analyses. ATCs that have emerged in the last common ancestor of bacteria were conserved in most bacteria and were acquired by eukaryotes and few archaea via horizontal gene transfers. Many bacteria contain multiple ATCs, as a result of gene duplication and/or horizontal gene transfer events. Based on evolutionary considerations, we could define three subfamilies: ATC-I, -II and -III. Escherichia coli, which has one ATC-I (ErpA) and two ATC-IIs (IscA and SufA), was used as a model to investigate functional redundancy between ATCs in vivo. Genetic analyses revealed that, under aerobiosis, E. coli IscA and SufA are functionally redundant carriers, as both are potentially able to receive an Fe/S cluster from IscU or the SufBCD complex and transfer it to ErpA. In contrast, under anaerobiosis, redundancy occurs between ErpA and IscA, which are both potentially able to receive Fe/S clusters from IscU and transfer them to an apotarget. Our combined phylogenomic and genetic study indicates that ATCs play a crucial role in conveying ready-made Fe/S clusters from components of the biogenesis systems to apotargets. We propose a model wherein the conserved biochemical function of ATCs provides multiple paths for supplying Fe/S clusters to apotargets. This model predicts the occurrence of a dynamic network, the structure and composition of which vary with the growth conditions. As an illustration, we depict three ways for a given protein to be matured, which appears to be dependent on the demand for Fe/S biogenesis.}, }
@article {pmid19475445, year = {2009}, author = {Akhtar, M and Hirt, H and Zurek, L}, title = {Horizontal transfer of the tetracycline resistance gene tetM mediated by pCF10 among Enterococcus faecalis in the house fly (Musca domestica L.) alimentary canal.}, journal = {Microbial ecology}, volume = {58}, number = {3}, pages = {509-518}, pmid = {19475445}, issn = {1432-184X}, mesh = {Animals ; Conjugation, Genetic ; Enterococcus faecalis/drug effects/*genetics ; Gastrointestinal Tract/*microbiology ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Houseflies/*microbiology ; Microbial Sensitivity Tests ; Plasmids ; Tetracycline Resistance/drug effects/*genetics ; }, abstract = {The house fly (Musca domestica L.) alimentary canal was evaluated for the potential of horizontal transfer of tetM on plasmid pCF10 among Enterococcus faecalis. Two sets of experiments were conducted: (1) house flies without surface sterilization and (2) surface-sterilized flies. Both sets of flies were exposed to E. faecalis OG1RF:pCF10 as donor for 12 h and then E. faecalis OG1SSp as recipient for 1 h. Another group of flies received the recipient first for 12 h followed by exposure to the donor strain for 1 h. House flies were screened daily to determine the donor, recipient, and transconjugant bacterial load for up to 5 days. In addition, the sponge-like mouth parts used for food uptake (labellum) of surface-sterilized house flies were removed and analyzed for donors, recipients, and transconjugants, separately. In both groups of flies (n = 90 flies/group), transfer occurred within 24 h after exposure with a transconjugant/donor rate from 8.6 x 10(-5) to 4.5 x 10(1). Transconjugants were also isolated from the house fly labellum. Our data suggest that the house fly digestive tract provides a suitable environment for horizontal transfer of conjugative plasmids and antibiotic resistance genes among enterococci. Our results emphasize the importance of this insect as a potential vector of antibiotic-resistant bacterial strains.}, }
@article {pmid19474814, year = {2009}, author = {Penn, K and Jenkins, C and Nett, M and Udwary, DW and Gontang, EA and McGlinchey, RP and Foster, B and Lapidus, A and Podell, S and Allen, EE and Moore, BS and Jensen, PR}, title = {Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria.}, journal = {The ISME journal}, volume = {3}, number = {10}, pages = {1193-1203}, pmid = {19474814}, issn = {1751-7370}, support = {R01 CA127622/CA/NCI NIH HHS/United States ; R01 CA127622-03/CA/NCI NIH HHS/United States ; CA127622/CA/NCI NIH HHS/United States ; }, mesh = {Actinobacteria/genetics/metabolism/*physiology ; *Adaptation, Biological ; *Adaptation, Physiological ; DNA, Bacterial/chemistry/genetics ; Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; Genome, Bacterial ; *Genomic Islands ; Metabolic Networks and Pathways/genetics ; Molecular Sequence Data ; Seawater/microbiology ; Sequence Analysis, DNA ; Synteny ; }, abstract = {Genomic islands have been shown to harbor functional traits that differentiate ecologically distinct populations of environmental bacteria. A comparative analysis of the complete genome sequences of the marine Actinobacteria Salinispora tropica and Salinispora arenicola reveals that 75% of the species-specific genes are located in 21 genomic islands. These islands are enriched in genes associated with secondary metabolite biosynthesis providing evidence that secondary metabolism is linked to functional adaptation. Secondary metabolism accounts for 8.8% and 10.9% of the genes in the S. tropica and S. arenicola genomes, respectively, and represents the major functional category of annotated genes that differentiates the two species. Genomic islands harbor all 25 of the species-specific biosynthetic pathways, the majority of which occur in S. arenicola and may contribute to the cosmopolitan distribution of this species. Genome evolution is dominated by gene duplication and acquisition, which in the case of secondary metabolism provide immediate opportunities for the production of new bioactive products. Evidence that secondary metabolic pathways are exchanged horizontally, coupled with earlier evidence for fixation among globally distributed populations, supports a functional role and suggests that the acquisition of natural product biosynthetic gene clusters represents a previously unrecognized force driving bacterial diversification. Species-specific differences observed in clustered regularly interspaced short palindromic repeat sequences suggest that S. arenicola may possess a higher level of phage immunity, whereas a highly duplicated family of polymorphic membrane proteins provides evidence for a new mechanism of marine adaptation in Gram-positive bacteria.}, }
@article {pmid19474197, year = {2009}, author = {Hao, W and Golding, GB}, title = {Does gene translocation accelerate the evolution of laterally transferred genes?.}, journal = {Genetics}, volume = {182}, number = {4}, pages = {1365-1375}, pmid = {19474197}, issn = {1943-2631}, mesh = {Evolution, Molecular ; Gene Rearrangement ; Genes, Bacterial/genetics ; Genome, Bacterial/*genetics ; *Models, Genetic ; Mutation ; Transformation, Bacterial/*genetics ; }, abstract = {Lateral gene transfer (LGT) and gene rearrangement are essential for shaping bacterial genomes during evolution. Separate attention has been focused on understanding the process of lateral gene transfer and the process of gene translocation. However, little is known about how gene translocation affects laterally transferred genes. Here we have examined gene translocations and lateral gene transfers in closely related genome pairs. The results reveal that translocated genes undergo elevated rates of evolution and gene translocation tends to take place preferentially in recently acquired genes. Translocated genes have a high probability to be truncated, suggesting that translocation followed by truncation/deletion might play an important role in the fast turnover of laterally transferred genes. Furthermore, more recently acquired genes have a higher proportion of genes on the leading strand, suggesting a strong strand bias of lateral gene transfer.}, }
@article {pmid19473381, year = {2009}, author = {Poulsen, M and Fernández-Marín, H and Currie, CR and Boomsma, JJ}, title = {Ephemeral windows of opportunity for horizontal transmission of fungal symbionts in leaf-cutting ants.}, journal = {Evolution; international journal of organic evolution}, volume = {63}, number = {9}, pages = {2235-2247}, doi = {10.1111/j.1558-5646.2009.00704.x}, pmid = {19473381}, issn = {1558-5646}, mesh = {Animals ; Ants/classification/genetics/*microbiology ; Basidiomycota/classification/*genetics/physiology ; Behavior, Animal/physiology ; *Biological Evolution ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; Symbiosis/*genetics ; }, abstract = {Evolutionary theory predicts that hosts are selected to prevent mixing of genetically different symbionts when competition among lineages reduces the productivity of a mutualism. The symbionts themselves may also defend their interests: recent studies of Acromyrmex leaf-cutting ants showed that somatic incompatibility enforces single-clone gardens within mature colonies, thereby constraining horizontal transmission of fungal symbionts. However, phylogenetic analyses indicate that symbiont switches occur frequently enough to remove most signs of host-symbiont cocladogenesis. Here we resolve this paradox by showing that transmission among newly founded Acromyrmex colonies is not constrained. All tested queens of sympatric A. octospinosus and A. echinatior offered a novel fragment of fungus garden accepted the new symbiont. The outcome was unaffected by genetic distance between the novel and the original symbiont, and by the ant species the novel symbiont came from. The colony founding stage may thus provide an efficient but transient window for horizontal transmission, in which the fungus is unable to actively defend its partnership position before the host feeds on it, so that host fecal droplets remain compatible with alternative strains during the early stage of colony founding. We discuss how brief stages of low commitment between partners may increase the evolutionary stability of ancient coevolved mutualisms.}, }
@article {pmid19472510, year = {2009}, author = {Xiong, AS and Peng, RH and Zhuang, J and Gao, F and Zhu, B and Fu, XY and Xue, Y and Jin, XF and Tian, YS and Zhao, W and Yao, QH}, title = {Gene duplication, transfer, and evolution in the chloroplast genome.}, journal = {Biotechnology advances}, volume = {27}, number = {4}, pages = {340-347}, doi = {10.1016/j.biotechadv.2009.01.012}, pmid = {19472510}, issn = {1873-1899}, mesh = {Cell Nucleus/genetics ; Chloroplasts/*genetics ; Eukaryota/genetics ; *Evolution, Molecular ; *Gene Duplication ; *Gene Transfer, Horizontal ; *Genome, Chloroplast ; Genome, Plant ; Models, Biological ; Plants/genetics ; }, abstract = {In addition to the nuclear genome, organisms have organelle genomes. Most of the DNA present in eukaryotic organisms is located in the cell nucleus. Chloroplasts have independent genomes which are inherited from the mother. Duplicated genes are common in the genomes of all organisms. It is believed that gene duplication is the most important step for the origin of genetic variation, leading to the creation of new genes and new gene functions. Despite the fact that extensive gene duplications are rare among the chloroplast genome, gene duplication in the chloroplast genome is an essential source of new genetic functions and a mechanism of neo-evolution. The events of gene transfer between the chloroplast genome and nuclear genome via duplication and subsequent recombination are important processes in evolution. The duplicated gene or genome in the nucleus has been the subject of several recent reviews. In this review, we will briefly summarize gene duplication and evolution in the chloroplast genome. Also, we will provide an overview of gene transfer events between chloroplast and nuclear genomes.}, }
@article {pmid19472367, year = {2009}, author = {Thaler, DS}, title = {The cytoplasmic structure hypothesis for ribosome assembly, vertical inheritance, and phylogeny.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {31}, number = {7}, pages = {774-783}, doi = {10.1002/bies.200800190}, pmid = {19472367}, issn = {1521-1878}, mesh = {Animals ; Cytoplasmic Structures/*genetics ; Gene Transfer, Horizontal ; Inheritance Patterns/*genetics ; *Models, Genetic ; *Phylogeny ; Ribosomes/*genetics ; }, abstract = {Fundamental questions in evolution concern deep divisions in the living world and vertical versus horizontal information transfer. Two contrasting views are: (i) three superkingdoms Archaea, Eubacteria, and Eukarya based on vertical inheritance of genes encoding ribosomes; versus (ii) a prokaryotic/eukaryotic dichotomy with unconstrained horizontal gene transfer (HGT) among prokaryotes. Vertical inheritance implies continuity of cytoplasmic and structural information whereas HGT transfers only DNA. By hypothesis, HGT of the translation machinery is constrained by interaction between new ribosomal gene products and vertically inherited cytoplasmic structure made largely of preexisting ribosomes. Ribosomes differentially enhance the assembly of new ribosomes made from closely related genes and inhibit the assembly of products from more distal genes. This hypothesis suggests experiments for synthetic biology: the ability of synthetic genomes to "boot," i.e., establish hereditary continuity, will be constrained by the phylogenetic closeness of the cell "body" into which genomes are placed.}, }
@article {pmid19470179, year = {2009}, author = {Almagro-Moreno, S and Boyd, EF}, title = {Insights into the evolution of sialic acid catabolism among bacteria.}, journal = {BMC evolutionary biology}, volume = {9}, number = {}, pages = {118}, pmid = {19470179}, issn = {1471-2148}, mesh = {Bacteria/classification/*genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Base Composition ; DNA, Bacterial/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Multigene Family ; N-Acetylneuraminic Acid/*metabolism ; Organic Anion Transporters/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Symporters/genetics ; }, abstract = {BACKGROUND: Sialic acids comprise a family of nine-carbon amino sugars that are prevalent in mucus rich environments. Sialic acids from the human host are used by a number of pathogens as an energy source. Here we explore the evolution of the genes involved in the catabolism of sialic acid.<br><br>RESULTS: The cluster of genes encoding the enzymes N-acetylneuraminate lyase (NanA), epimerase (NanE), and kinase (NanK), necessary for the catabolism of sialic acid (the Nan cluster), are confined 46 bacterial species, 42 of which colonize mammals, 33 as pathogens and 9 as gut commensals. We found a putative sialic acid transporter associated with the Nan cluster in most species. We reconstructed the phylogenetic history of the NanA, NanE, and NanK proteins from the 46 species and compared them to the species tree based on 16S rRNA. Within the NanA phylogeny, Gram-negative and Gram-positive bacteria do not form distinct clades. NanA from Yersinia and Vibrio species was most closely related to the NanA clade from eukaryotes. To examine this further, we reconstructed the phylogeny of all NanA homologues in the databases. In this analysis of 83 NanA sequences, Bacteroidetes, a human commensal group formed a distinct clade with Verrucomicrobia, and branched with the Eukaryotes and the Yersinia/Vibrio clades. We speculate that pathogens such as V. cholerae may have acquired NanA from a commensal aiding their colonization of the human gut. Both the NanE and NanK phylogenies more closely represented the species tree but numerous incidences of incongruence are noted. We confirmed the predicted function of the sialic acid catabolism cluster in members the major intestinal pathogens Salmonella enterica, Vibrio cholerae, V. vulnificus, Yersinia enterocolitica and Y. pestis.<br><br>CONCLUSION: The Nan cluster among bacteria is confined to human pathogens and commensals conferring them the ability to utilize a ubiquitous carbon source in mucus rich surfaces of the human body. The Nan region shows a mosaic evolution with NanA from Bacteroidetes, Vibrio and Yersinia branching closely together with NanA from eukaryotes.}, }
@article {pmid19466576, year = {2009}, author = {Landi, L and Capocasa, F and Costantini, E and Mezzetti, B}, title = {ROLC strawberry plant adaptability, productivity, and tolerance to soil-borne disease and mycorrhizal interactions.}, journal = {Transgenic research}, volume = {18}, number = {6}, pages = {933-942}, pmid = {19466576}, issn = {1573-9368}, mesh = {Fragaria/genetics/microbiology/*physiology ; Fruit/physiology ; Mycorrhizae ; Plant Roots/microbiology ; Plants, Genetically Modified/genetics/microbiology/*physiology ; Rhizobium/genetics ; Symbiosis ; Transformation, Genetic ; }, abstract = {The potential to improve strawberry cultivation was assessed regarding the use the rolC genes from Agrobacterium rhizogenes that can confer higher levels of free cytokinins. Strawberry (cv. Calypso) rolC lines were produced by genetic transformation of Agrobacterium tumefaciens. Yield and fruit quality of the control and transgenic lines were measured under open-field conditions. The effects of the transgenic rolC lines depended on gene copy number: rolC lines with one (Line A) or two gene (Line B) copies showed 30% greater yields than controls, due to 20% more fruit per plant and an increased fruit weight. Line A also differed in terms of the highest fruit quality, due to 10.5% increased soluble solids and 12.7% higher acidity. Moreover, cv. Calypso rolC lines A and B had increased tolerance to greenhouse infection by Phytophthora cactorum. Conversely, for all of these characters, Line F (five rolC copies) was not significantly different from the control line. The same lines were also used to examine their symbiosis with root arbuscular mycorrhizal fungi (AMF) using vital and non-vital staining of roots collected at different stages of plant growth. Control and rolC plants showed similar intensities of AMF infection according to plant phenology and/or physiology. Furthermore, possible horizontal gene transfer of the rolC gene was tested for the AMF spores by PCR, with all AMF samples negative using rolC primers. The use of the rolC gene should be considered for the improvements provided in productivity, fruit quality and disease resistance of cultivated strawberry that show no effects on soil microorganisms.}, }
@article {pmid19466405, year = {2009}, author = {Schmidt, FR}, title = {The RNA interference-virus interplay: tools of nature for gene modulation, morphogenesis, evolution and a possible mean for aflatoxin control.}, journal = {Applied microbiology and biotechnology}, volume = {83}, number = {4}, pages = {611-615}, doi = {10.1007/s00253-009-2007-7}, pmid = {19466405}, issn = {1432-0614}, mesh = {Aflatoxins/biosynthesis ; Evolution, Molecular ; Fungi/virology ; *Gene Expression Regulation ; *Gene Transfer, Horizontal ; *Host-Pathogen Interactions ; *RNA Interference ; RNA Viruses/*genetics ; }, abstract = {This article points out, that viruses, in an interplay with RNA interference and as vehicles for intergenic and interspecies gene transfer, may work as agents for intracellular gene modulation, for steering of individual morphogenesis and as a driving force of evolution in the toolbox of nature. This is illustrated in particular in the light of a fungal double-stranded RNA virus that may be employed as a suitable agent for a biological control of aflatoxins, the most carcinogenic natural substances occurring in food and feedstuff.}, }
@article {pmid19464330, year = {2009}, author = {Odom, MR and Hendrickson, RC and Lefkowitz, EJ}, title = {Poxvirus protein evolution: family wide assessment of possible horizontal gene transfer events.}, journal = {Virus research}, volume = {144}, number = {1-2}, pages = {233-249}, pmid = {19464330}, issn = {1872-7492}, support = {HHSN266200400036C/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Cluster Analysis ; Computational Biology/methods ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Phylogeny ; Poxviridae/classification/*genetics ; Sequence Homology, Amino Acid ; Viral Proteins/classification/*genetics ; }, abstract = {To investigate the evolutionary origins of proteins encoded by the Poxviridae family of viruses, we examined all poxvirus protein coding genes using a method of characterizing and visualizing the similarity between these proteins and taxonomic subsets of proteins in GenBank. Our analysis divides poxvirus proteins into categories based on their relative degree of similarity to two different taxonomic subsets of proteins such as all eukaryote vs. all virus (except poxvirus) proteins. As an example, this allows us to identify, based on high similarity to only eukaryote proteins, poxvirus proteins that may have been obtained by horizontal transfer from their hosts. Although this method alone does not definitively prove horizontal gene transfer, it allows us to provide an assessment of the possibility of horizontal gene transfer for every poxvirus protein. Potential candidates can then be individually studied in more detail during subsequent investigation. Results of our analysis demonstrate that in general, proteins encoded by members of the subfamily Chordopoxvirinae exhibit greater similarity to eukaryote proteins than to proteins of other virus families. In addition, our results reiterate the important role played by host gene capture in poxvirus evolution; highlight the functions of many genes poxviruses share with their hosts; and illustrate which host-like genes are present uniquely in poxviruses and which are also present in other virus families.}, }
@article {pmid19464182, year = {2009}, author = {Roberts, AP and Mullany, P}, title = {A modular master on the move: the Tn916 family of mobile genetic elements.}, journal = {Trends in microbiology}, volume = {17}, number = {6}, pages = {251-258}, doi = {10.1016/j.tim.2009.03.002}, pmid = {19464182}, issn = {1878-4380}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; //Medical Research Council/United Kingdom ; //Wellcome Trust/United Kingdom ; }, mesh = {Bacteriocins/genetics ; *DNA Transposable Elements ; Drug Resistance, Bacterial ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; Gram-Positive Bacteria/*genetics ; Recombination, Genetic ; }, abstract = {The Tn916 family is a group of mobile genetic elements that are widespread among many commensal and pathogenic bacteria. These elements are found primarily, but not exclusively, in the Firmicutes. They are integrated into the bacterial genome and are capable of conjugative transfer to a new host and, often, intracellular transposition to a different genomic site - hence their name: 'conjugative transposons', or 'integrative conjugative elements'. An increasing variety of Tn916 relatives are being reported from different bacteria, harbouring genes coding for resistance to various antibiotics and the potential to encode other functions, such as lantibiotic immunity. This family of mobile genetic elements has an extraordinary ability to acquire accessory genes, making them important vectors in the dissemination of various traits among environmental, commensal and clinical bacteria. These elements are also responsible for genome rearrangements, providing considerable raw material on which natural selection can act. Therefore, the study of this family of mobile genetic elements is essential for a better understanding and control of the current rise of antibiotic resistance among pathogenic bacteria.}, }
@article {pmid19459955, year = {2009}, author = {Petrova, M and Gorlenko, Z and Mindlin, S}, title = {Molecular structure and translocation of a multiple antibiotic resistance region of a Psychrobacter psychrophilus permafrost strain.}, journal = {FEMS microbiology letters}, volume = {296}, number = {2}, pages = {190-197}, doi = {10.1111/j.1574-6968.2009.01635.x}, pmid = {19459955}, issn = {1574-6968}, mesh = {Anti-Bacterial Agents/pharmacology ; DNA Transposable Elements ; DNA, Bacterial/chemistry/genetics ; *Drug Resistance, Multiple, Bacterial ; Gene Order ; Gene Transfer, Horizontal ; Genes, Bacterial ; Molecular Sequence Data ; Plasmids ; Psychrobacter/*genetics/isolation &amp; purification ; *Recombination, Genetic ; Sequence Analysis, DNA ; Siberia ; *Soil Microbiology ; Streptomycin/pharmacology ; Tetracycline/pharmacology ; }, abstract = {A Psychrobacter psychrophilus strain resistant to tetracycline and streptomycin was isolated from a 15,000-35,000-year-old permafrost subsoil sediment sampled from the coast of the Eastern-Siberian Sea. The genes conferring antibiotic resistance were localized on an c. 30-kb pKLH80 plasmid. It was shown that the antibiotic resistance region of this plasmid has a mosaic structure and contains closely linked streptomycin resistance (strA-strB) and tetracycline resistance [tetR-tet(H)] genes, followed by a novel IS element (ISPpy1) belonging to the IS3 family. Both the strA-strB and tetR-tet(H) genes of pKLH80 were highly similar to those found in modern clinical bacterial isolates. It was shown that the ISPpy1 element of pKLH80 can direct translocation of the adjacent antibiotic resistance genes to different target plasmids, either by one-ended transposition or by formation of a composite transposon resulting from the insertion of the ISPpy1 second copy at the other side of the antibiotic resistance region. Thus, our data demonstrate that clinically important antibiotic resistance genes originated long before the introduction of antibiotics into clinical practice and confirm an important role of horizontal gene transfer in the distribution of these genes in natural bacterial populations.}, }
@article {pmid19458346, year = {2009}, author = {Taylor, DE}, title = {Thermosensitive nature of IncHI1 plasmid transfer.}, journal = {Antimicrobial agents and chemotherapy}, volume = {53}, number = {6}, pages = {2703}, pmid = {19458346}, issn = {1098-6596}, mesh = {Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Plasmids/*genetics ; Salmonella typhi/*genetics ; Temperature ; }, }
@article {pmid19457437, year = {2009}, author = {Filée, J}, title = {Lateral gene transfer, lineage-specific gene expansion and the evolution of Nucleo Cytoplasmic Large DNA viruses.}, journal = {Journal of invertebrate pathology}, volume = {101}, number = {3}, pages = {169-171}, doi = {10.1016/j.jip.2009.03.010}, pmid = {19457437}, issn = {1096-0805}, mesh = {Cytoplasm/*virology ; DNA Viruses/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Viral ; Genome, Viral ; }, abstract = {Nucleo Cytoplasmic Large DNA viruses (NCLDVs) are a diverse group that infects a wide range of eukaryotic hosts (for example, vertebrates, insects, protists,...) and also show a huge range in genome size (between 100kb and 1.2Mb). Here I review some recent results that shed light on the origin and genome evolution of these viruses. Current data suggests that NCLDVs could have originated from a simple and ancient viral ancestor with a small subset of 30-35 genes encoding replication and structural proteins. Subsequent lateral gene transfer of both cellular genes and diverse families of Mobile Genetic Elements, followed by massive lineage-specific gene duplications is probably responsible for the huge diversity of genome size and composition found in extant NCLDVs.}, }
@article {pmid19453698, year = {2009}, author = {Yagi, JM and Sims, D and Brettin, T and Bruce, D and Madsen, EL}, title = {The genome of Polaromonas naphthalenivorans strain CJ2, isolated from coal tar-contaminated sediment, reveals physiological and metabolic versatility and evolution through extensive horizontal gene transfer.}, journal = {Environmental microbiology}, volume = {11}, number = {9}, pages = {2253-2270}, doi = {10.1111/j.1462-2920.2009.01947.x}, pmid = {19453698}, issn = {1462-2920}, support = {5T32 ES00752-28./ES/NIEHS NIH HHS/United States ; R21 ES012834/ES/NIEHS NIH HHS/United States ; }, mesh = {Base Sequence ; Biodegradation, Environmental ; Coal Tar/*analysis ; Comamonadaceae/*genetics/isolation &amp; purification/*metabolism ; Evolution, Molecular ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Geologic Sediments/chemistry/*microbiology ; Interspersed Repetitive Sequences ; Molecular Sequence Data ; Naphthalenes/*metabolism ; Oxidative Stress ; Signal Transduction ; Soil Microbiology ; Soil Pollutants/analysis/*metabolism ; }, abstract = {We analysed the genome of the aromatic hydrocarbon-degrading, facultatively chemolithotrophic betaproteobacterium, Polaromonas naphthalenivorans strain CJ2. Recent work has increasingly shown that Polaromonas species are prevalent in a variety of pristine oligotrophic environments, as well as polluted habitats. Besides a circular chromosome of 4.4 Mb, strain CJ2 carries eight plasmids ranging from 353 to 6.4 kb in size. Overall, the genome is predicted to encode 4929 proteins. Comparisons of DNA sequences at the individual gene, gene cluster and whole-genome scales revealed strong trends in shared heredity between strain CJ2 and other members of the Comamonadaceae and Burkholderiaceae. blastp analyses of protein coding sequences across strain CJ2's genome showed that genetic commonalities with other betaproteobacteria diminished significantly in strain CJ2's plasmids compared with the chromosome, especially for the smallest ones. Broad trends in nucleotide characteristics (GC content, GC skew, Karlin signature difference) showed at least six anomalous regions in the chromosome, indicating alteration of genome architecture via horizontal gene transfer. Detailed analysis of one of these anomalous regions (96 kb in size, containing the nag-like naphthalene catabolic operon) indicates that the fragment's insertion site was within a putative MiaB-like tRNA-modifying enzyme coding sequence. The mosaic nature of strain CJ2's genome was further emphasized by the presence of 309 mobile genetic elements scattered throughout the genome, including 131 predicted transposase genes, 178 phage-related genes, and representatives of 12 families of insertion elements. A total of three different terminal oxidase genes were found (putative cytochrome aa(3)-type oxidase, cytochrome cbb(3)-type oxidase and cytochrome bd-type quinol oxidase), suggesting adaptation by strain CJ2 to variable aerobic and microaerobic conditions. Sequence-suggested abilities of strain CJ2 to carry out nitrogen fixation and grow on the aromatic compounds, biphenyl and benzoate, were experimentally verified. These new phenotypes and genotypes set the stage for gaining additional insights into the physiology and biochemistry contributing to strain CJ2's fitness in its native habitat, contaminated sediment.}, }
@article {pmid19451630, year = {2009}, author = {Degnan, PH and Yu, Y and Sisneros, N and Wing, RA and Moran, NA}, title = {Hamiltonella defensa, genome evolution of protective bacterial endosymbiont from pathogenic ancestors.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {22}, pages = {9063-9068}, pmid = {19451630}, issn = {1091-6490}, mesh = {Base Sequence ; Enterobacteriaceae/*classification/*genetics/pathogenicity ; *Evolution, Molecular ; *Genome, Bacterial ; Genomics ; Molecular Sequence Data ; Phylogeny ; Proteome/genetics ; Symbiosis ; }, abstract = {Eukaryotes engage in a multitude of beneficial and deleterious interactions with bacteria. Hamiltonella defensa, an endosymbiont of aphids and other sap-feeding insects, protects its aphid host from attack by parasitoid wasps. Thus H. defensa is only conditionally beneficial to hosts, unlike ancient nutritional symbionts, such as Buchnera, that are obligate. Similar to pathogenic bacteria, H. defensa is able to invade naive hosts and circumvent host immune responses. We have sequenced the genome of H. defensa to identify possible mechanisms that underlie its persistence in healthy aphids and protection from parasitoids. The 2.1-Mb genome has undergone significant reduction in size relative to its closest free-living relatives, which include Yersinia and Serratia species (4.6-5.4 Mb). Auxotrophic for 8 of the 10 essential amino acids, H. defensa is reliant upon the essential amino acids produced by Buchnera. Despite these losses, the H. defensa genome retains more genes and pathways for a variety of cell structures and processes than do obligate symbionts, such as Buchnera. Furthermore, putative pathogenicity loci, encoding type-3 secretion systems, and toxin homologs, which are absent in obligate symbionts, are abundant in the H. defensa genome, as are regulatory genes that likely control the timing of their expression. The genome is also littered with mobile DNA, including phage-derived genes, plasmids, and insertion-sequence elements, highlighting its dynamic nature and the continued role horizontal gene transfer plays in shaping it.}, }
@article {pmid19451591, year = {2009}, author = {Monier, A and Pagarete, A and de Vargas, C and Allen, MJ and Read, B and Claverie, JM and Ogata, H}, title = {Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus.}, journal = {Genome research}, volume = {19}, number = {8}, pages = {1441-1449}, pmid = {19451591}, issn = {1088-9051}, mesh = {Biosynthetic Pathways/genetics ; DNA Viruses/*genetics/physiology ; DNA, Algal/chemistry/genetics ; DNA, Viral/chemistry/genetics ; Eukaryota/*genetics/virology ; Eukaryotic Cells/*metabolism/virology ; *Gene Transfer, Horizontal ; Host-Pathogen Interactions ; Lysophospholipids/chemistry/metabolism ; Molecular Sequence Data ; Molecular Structure ; Mutation ; Oxidoreductases/classification/genetics/metabolism ; Phosphoric Monoester Hydrolases/classification/genetics/metabolism ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Serine C-Palmitoyltransferase/classification/genetics/metabolism ; Sphingolipids/biosynthesis/chemistry ; Sphingosine/analogs &amp; derivatives/chemistry/metabolism ; }, abstract = {Interactions between viruses and phytoplankton, the main primary producers in the oceans, affect global biogeochemical cycles and climate. Recent studies are increasingly revealing possible cases of gene transfers between cyanobacteria and phages, which might have played significant roles in the evolution of cyanobacteria/phage systems. However, little has been documented about the occurrence of horizontal gene transfer in eukaryotic phytoplankton/virus systems. Here we report phylogenetic evidence for the transfer of seven genes involved in the sphingolipid biosynthesis pathway between the cosmopolitan eukaryotic microalga Emiliania huxleyi and its large DNA virus EhV. PCR assays indicate that these genes are prevalent in E. huxleyi and EhV strains isolated from different geographic locations. Patterns of protein and gene sequence conservation support that these genes are functional in both E. huxleyi and EhV. This is the first clear case of horizontal gene transfer of multiple functionally linked enzymes in a eukaryotic phytoplankton-virus system. We examine arguments for the possible direction of the gene transfer. The virus-to-host direction suggests the existence of ancient viruses that controlled the complex metabolic pathway in order to infect primitive eukaryotic cells. In contrast, the host-to-virus direction suggests that the serial acquisition of genes involved in the same metabolic pathway might have been a strategy for the ancestor of EhVs to stay ahead of their closest relatives in the great evolutionary race for survival.}, }
@article {pmid19450709, year = {2009}, author = {Gomez-Valero, L and Rusniok, C and Buchrieser, C}, title = {Legionella pneumophila: population genetics, phylogeny and genomics.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {9}, number = {5}, pages = {727-739}, doi = {10.1016/j.meegid.2009.05.004}, pmid = {19450709}, issn = {1567-7257}, mesh = {Evolution, Molecular ; Genetics, Population ; Genomics ; Humans ; Legionella pneumophila/classification/*genetics ; Legionnaires' Disease/epidemiology/microbiology ; Phylogeny ; }, abstract = {Legionella pneumophila is a human pathogen that was recognized only about 30 years ago. It is the causative agent of Legionnaires' disease, a severe pneumonia that is transmitted through inhalation of aerosols of contaminated water. Shortly after its discovery, the ability of Legionella to multiply intracellularly in fresh water protozoa was discovered. This long lasting co-evolution between the eukaryotic host and Legionella has led to the selection of a panoply of virulence factors, which allow to exploit important cellular processes during infection. Compelling evidence for the importance of protozoa in the evolution of this bacterium comes from analysis of complete genome sequences. A key feature of the L. pneumophila genomes is the presence of a high number and wide variety of eukaryotic like proteins and protein domains probably acquired through horizontal gene transfer and/or convergent evolution. In the last years several different typing methods aiming in investigating the molecular epidemiology of L. pneumophila have been developed. Furthermore, the access to whole genome sequences of several L. pneumophila strains allowed to apply large scale comparative genomic studies using DNA arrays. A higher genetic diversity among environmental isolates with respect to clinical isolates and the presence of specific clones of L. pneumophila overrepresented in human disease or causing legionellosis world wide, were identified. Further studies analyzing the natural populations of Legionella more in detail will allow to gain a better understanding of the population structure and the ecological diversity of this species. This review describes the latest observations about the structure of L. pneumophila populations, the techniques used to study the molecular epidemiology and evolution of L. pneumophila, the knowledge gained from genome analysis, and discusses future perspectives.}, }
@article {pmid19449055, year = {2009}, author = {Quiroga, C and Centrón, D}, title = {Using genomic data to determine the diversity and distribution of target site motifs recognized by class C-attC group II introns.}, journal = {Journal of molecular evolution}, volume = {68}, number = {5}, pages = {539-549}, pmid = {19449055}, issn = {1432-1432}, mesh = {Attachment Sites, Microbiological/*genetics ; Base Composition/genetics ; Base Sequence ; *Genetic Variation ; Genome, Bacterial/*genetics ; Host-Pathogen Interactions/genetics ; Integrases/genetics ; Integrons/genetics ; Introns/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Regulatory Sequences, Nucleic Acid/*genetics ; Sequence Alignment ; }, abstract = {The attC sites are well-known integrase-targeted elements involved in the insertion and excision of gene cassettes from integrons. Recently, functional analysis of Sma.I2, a class C-attC group II intron, showed that this mobile element invades the attC sites through a specific process. The analysis of genomic data indicates that class C-attC group II introns are independently acquired by their bacterial hosts and evolve in the recognition of a variety of target sites, including the attCs. In addition, adaptation of class C-attC group II introns seemed to be favourable for particular genera, such as Shewanella, suggesting a possible niche for the spread of class C-attC group II introns inserted at attC sites. This understanding suggests a functional role of short palindromic DNA sequences, such as the attCs, as important tools for the acquisition of mobile elements associated with horizontal gene transfer.}, }
@article {pmid19447963, year = {2009}, author = {Mardanov, AV and Ravin, NV and Svetlitchnyi, VA and Beletsky, AV and Miroshnichenko, ML and Bonch-Osmolovskaya, EA and Skryabin, KG}, title = {Metabolic versatility and indigenous origin of the archaeon Thermococcus sibiricus, isolated from a siberian oil reservoir, as revealed by genome analysis.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {13}, pages = {4580-4588}, pmid = {19447963}, issn = {1098-5336}, mesh = {Alkanes/metabolism ; Archaeal Proteins/genetics ; Carbohydrate Metabolism ; Cellulose/metabolism ; DNA, Archaeal/chemistry/*genetics ; Enzymes/genetics ; Fuel Oils/*microbiology ; *Genome, Archaeal ; Metabolic Networks and Pathways/genetics ; Molecular Sequence Data ; Sepharose/metabolism ; *Sequence Analysis, DNA ; Thermococcus/*genetics/isolation &amp; purification/*metabolism ; Triglycerides/metabolism ; }, abstract = {Thermococcus species are widely distributed in terrestrial and marine hydrothermal areas, as well as in deep subsurface oil reservoirs. Thermococcus sibiricus is a hyperthermophilic anaerobic archaeon isolated from a well of the never flooded oil-bearing Jurassic horizon of a high-temperature oil reservoir. To obtain insight into the genome of an archaeon inhabiting the oil reservoir, we have determined and annotated the complete 1,845,800-base genome of T. sibiricus. A total of 2,061 protein-coding genes have been identified, 387 of which are absent in other members of the order Thermococcales. Physiological features and genomic data reveal numerous hydrolytic enzymes (e.g., cellulolytic enzymes, agarase, laminarinase, and lipases) and metabolic pathways, support the proposal of the indigenous origin of T. sibiricus in the oil reservoir, and explain its survival over geologic time and its proliferation in this habitat. Indeed, in addition to proteinaceous compounds known previously to be present in oil reservoirs at limiting concentrations, its growth was stimulated by cellulose, agarose, and triacylglycerides, as well as by alkanes. Two polysaccharide degradation loci were probably acquired by T. sibiricus from thermophilic bacteria following lateral gene transfer events. The first, a "saccharolytic gene island" absent in the genomes of other members of the order Thermococcales, contains the complete set of genes responsible for the hydrolysis of cellulose and beta-linked polysaccharides. The second harbors genes for maltose and trehalose degradation. Considering that agarose and laminarin are components of algae, the encoded enzymes and the substrate spectrum of T. sibiricus indicate the ability to metabolize the buried organic matter from the original oceanic sediment.}, }
@article {pmid19447951, year = {2009}, author = {Gao, P and Huang, Y}, title = {Detection, distribution, and organohalogen compound discovery implications of the reduced flavin adenine dinucleotide-dependent halogenase gene in major filamentous actinomycete taxonomic groups.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {14}, pages = {4813-4820}, pmid = {19447951}, issn = {1098-5336}, mesh = {Actinobacteria/*enzymology/genetics ; Anti-Infective Agents/metabolism ; Bacterial Proteins/*genetics/metabolism ; Coenzymes/*pharmacology ; DNA, Bacterial/*genetics ; Flavin-Adenine Dinucleotide/*pharmacology ; Molecular Sequence Data ; Oxidoreductases/*genetics/metabolism ; Peptide Synthases/metabolism ; Phylogeny ; Polyketide Synthases/metabolism ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA ; }, abstract = {Halogenases have been shown to play a significant role in biosynthesis and introducing the bioactivity of many halogenated secondary metabolites. In this study, 54 reduced flavin adenine dinucleotide (FADH(2))-dependent halogenase gene-positive strains were identified after the PCR screening of a large collection of 228 reference strains encompassing all major families and genera of filamentous actinomycetes. The wide distribution of this gene was observed to extend to some rare lineages with higher occurrences and large sequence diversity. Subsequent phylogenetic analyses revealed that strains containing highly homologous halogenases tended to produce halometabolites with similar structures, and halogenase genes are likely to propagate by horizontal gene transfer as well as vertical inheritance within actinomycetes. Higher percentages of halogenase gene-positive strains than those of halogenase gene-negative ones contained polyketide synthase genes and/or nonribosomal peptide synthetase genes or displayed antimicrobial activities in the tests applied, indicating their genetic and physiological potentials for producing secondary metabolites. The robustness of this halogenase gene screening strategy for the discovery of particular biosynthetic gene clusters in rare actinomycetes besides streptomycetes was further supported by genome-walking analysis. The described distribution and phylogenetic implications of the FADH(2)-dependent halogenase gene present a guide for strain selection in the search for novel organohalogen compounds from actinomycetes.}, }
@article {pmid19444186, year = {2009}, author = {Mullard, A}, title = {Microbiology: Tinker, bacteria, eukaryote, spy.}, journal = {Nature}, volume = {459}, number = {7244}, pages = {159-161}, pmid = {19444186}, issn = {1476-4687}, mesh = {Animals ; Apolipoproteins B/genetics/metabolism ; Bacteria/drug effects/genetics/*metabolism/pathogenicity ; Eukaryotic Cells/drug effects/*metabolism/*microbiology ; Gene Transfer, Horizontal ; Host-Pathogen Interactions/drug effects/genetics/*physiology ; Humans ; Methicillin-Resistant Staphylococcus aureus/metabolism/pathogenicity ; Microbiology ; Quorum Sensing/drug effects/physiology ; }, }
@article {pmid19443855, year = {2009}, author = {Roettger, M and Martin, W and Dagan, T}, title = {A machine-learning approach reveals that alignment properties alone can accurately predict inference of lateral gene transfer from discordant phylogenies.}, journal = {Molecular biology and evolution}, volume = {26}, number = {9}, pages = {1931-1939}, doi = {10.1093/molbev/msp105}, pmid = {19443855}, issn = {1537-1719}, mesh = {*Artificial Intelligence ; *Gene Transfer, Horizontal ; Genome/genetics ; *Phylogeny ; Principal Component Analysis ; Proteins/chemistry ; Sequence Alignment/*methods ; }, abstract = {Among the methods currently used in phylogenomic practice to detect the presence of lateral gene transfer (LGT), one of the most frequently employed is the comparison of gene tree topologies for different genes. In cases where the phylogenies for different genes are incompatible, or discordant, for well-supported branches there are three simple interpretations for the result: 1) gene duplications (paralogy) followed by many independent gene losses have occurred, 2) LGT has occurred, or 3) the phylogeny is well supported but for reasons unknown is nonetheless incorrect. Here, we focus on the third possibility by examining the properties of 22,437 published multiple sequence alignments, the Bayesian maximum likelihood trees for which either do or do not suggest the occurrence of LGT by the criterion of discordant branches. The alignments that produce discordant phylogenies differ significantly in several salient alignment properties from those that do not. Using a support vector machine, we were able to predict the inference of discordant tree topologies with up to 80% accuracy from alignment properties alone.}, }
@article {pmid19440984, year = {2009}, author = {del Campo, EM and Casano, LM and Gasulla, F and Barreno, E}, title = {Presence of multiple group I introns closely related to bacteria and fungi in plastid 23S rRNAs of lichen-forming Trebouxia.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {12}, number = {1}, pages = {59-67}, pmid = {19440984}, issn = {1618-1905}, mesh = {Bacteria/genetics ; Chlorophyta/classification/*genetics ; DNA, Chloroplast/*chemistry ; DNA, Ribosomal/chemistry ; Fungi/genetics ; Gene Transfer, Horizontal ; *Introns ; Lichens/genetics ; Plastids ; RNA, Ribosomal, 23S/*genetics ; Symbiosis ; }, abstract = {The chloroplast-encoded large subunit ribosomal RNA gene of several free-living green algae contains group I introns at Escherichia coli genic positions 1917, 1931, 1951, and 2449. Herein we report the presence of group I introns at these positions within the chloroplast-encoded large subunit ribosomal RNA gene of several lichen-forming green algae belonging to the Trebouxia genus. In contrast to the introns inserted at position 2449, all introns inserted at positions 1917, 1931, and 1951 contained LAGLIDADG homing endonuclease genes. Phylogenetic analyses show that: (i) introns inserted at positions 1917, 1931, and 1951 are closely related to introns located at homologous insertion sites in bacterial rDNA genes; and (ii) introns inserted at position 2449 are closely related to fungal introns located at homologous insertion sites in mitochondrial rDNA genes. The symbiogenetic thalli of some lichens are proposed as the likely setting of horizontal transfer of genetic material among distantly related organisms such as bacteria, fungi, and green algae.}, }
@article {pmid19440980, year = {2009}, author = {Leul, M and Normand, P and Sellstedt, A}, title = {The phylogeny of uptake hydrogenases in Frankia.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {12}, number = {1}, pages = {23-28}, pmid = {19440980}, issn = {1618-1905}, mesh = {Bacterial Proteins/*classification ; Frankia/*enzymology/genetics ; Genome, Bacterial ; Geography ; Hydroxyproline/classification ; Nitrogen Fixation ; Oxidoreductases/*classification ; Phylogeny ; }, abstract = {Uptake hydrogenase is an enzyme that is beneficial for nitrogen fixation in bacteria. Recent studies have shown that Frankia sp. has two sets of uptake hydrogenase genes, organized in synton 1 and synton 2. In the present study, phylogenetic analysis of the structural subunits of hydrogenase syntons 1 and 2 showed a distinct clustering pattern between the proteins of Frankia strains that were isolated from different host plants and non-Frankia organisms. The structural subunits of hydrogenase synton 1 of Frankia sp. CpI1, Frankia alni ACN14a, and F. alni AvCI1 were grouped together while those of Frankia spp. CcI3, KB5, UGL140104, and UGL011102 formed another group. The structural subunits of hydrogenase synton 2 of F. alni ACN14a and Frankia spp. CcI3 and BCU110501 grouped together, but those of Frankia spp. KB5 and CpI1, F. alni ArI3, and F. alniAvCI1 comprised a separate group. The structural subunits of hydrogenase syntons 1 and 2 of Frankia sp. EAN1pec were more closely related to those of non-Frankia bacteria, i.e., Streptomyces avermitilis and Anaeromyxobacter sp., respectively, than to those of other Frankia strains, suggesting the occurrence of lateral gene transfer between these organisms. In addition, the accessory Hyp proteins of hydrogenase syntons 1 and 2 of F. alni ACN14a and Frankia sp. CcI3 were shown to be phylogenetically more related to each other than to those of Frankia EAN1pec.}, }
@article {pmid19440514, year = {2008}, author = {Mayo, B and van Sinderen, D and Ventura, M}, title = {Genome analysis of food grade lactic Acid-producing bacteria: from basics to applications.}, journal = {Current genomics}, volume = {9}, number = {3}, pages = {169-183}, pmid = {19440514}, issn = {1389-2029}, abstract = {Whole-genome sequencing has revolutionized and accelerated scientific research that aims to study the genetics, biochemistry and molecular biology of bacteria. Lactic acid-producing bacteria, which include lactic acid bacteria (LAB) and bifidobacteria, are typically Gram-positive, catalase-negative organisms, which occupy a wide range of natural plant- and animal-associated environments. LAB species are frequently involved in the transformation of perishable raw materials into more stable, pleasant, palatable and safe fermented food products. LAB and bifidobacteria are also found among the resident microbiota of the gastrointestinal and/or genitourinary tracts of vertebrates, where they are believed to exert health-promoting effects. At present, the genomes of more than 20 LAB and bifidobacterial species have been completely sequenced. Their genome content reflects its specific metabolism, physiology, biosynthetic capabilities, and adaptability to varying conditions and environments. The typical LAB/bifidobacterial genome is relatively small (from 1.7 to 3.3 Mb) and thus harbors a limited assortment of genes (from around 1,600 to over 3,000). These small genomes code for a broad array of transporters for efficient carbon and nitrogen assimilation from the nutritionally-rich niches they usually inhabit, and specify a rather limited range of biosynthetic and degrading capabilities. The variation in the number of genes suggests that the genome evolution of each of these bacterial groups involved the processes of extensive gene loss from their particular ancestor, diversification of certain common biological activities through gene duplication, and acquisition of key functions via horizontal gene transfer. The availability of genome sequences is expected to revolutionize the exploitation of the metabolic potential of LAB and bifidobacteria, improving their use in bioprocessing and their utilization in biotechnological and health-related applications.}, }
@article {pmid19436929, year = {2009}, author = {Merkl, R and Wiezer, A}, title = {GO4genome: a prokaryotic phylogeny based on genome organization.}, journal = {Journal of molecular evolution}, volume = {68}, number = {5}, pages = {550-562}, pmid = {19436929}, issn = {1432-1432}, mesh = {*Algorithms ; Computational Biology/*methods ; Escherichia coli/genetics ; Gene Order ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Archaeal/*genetics ; Genome, Bacterial/*genetics ; Methanosarcina/genetics ; *Phylogeny ; Prokaryotic Cells/*metabolism ; Streptococcus/genetics ; Yersinia/genetics ; }, abstract = {Determining the phylogeny of closely related prokaryotes may fail in an analysis of rRNA or a small set of sequences. Whole-genome phylogeny utilizes the maximally available sample space. For a precise determination of genome similarity, two aspects have to be considered when developing an algorithm of whole-genome phylogeny: (1) gene order conservation is a more precise signal than gene content; and (2) when using sequence similarity, failures in identifying orthologues or the in situ replacement of genes via horizontal gene transfer may give misleading results. GO4genome is a new paradigm, which is based on a detailed analysis of gene function and the location of the respective genes. For characterization of genes, the algorithm uses gene ontology enabling a comparison of function independent of evolutionary relationship. After the identification of locally optimal series of gene functions, their length distribution is utilized to compute a phylogenetic distance. The outcome is a classification of genomes based on metabolic capabilities and their organization. Thus, the impact of effects on genome organization that are not covered by methods of molecular phylogeny can be studied. Genomes of strains belonging to Escherichia coli, Shigella, Streptococcus, Methanosarcina, and Yersinia were analyzed. Differences from the findings of classical methods are discussed.}, }
@article {pmid19432799, year = {2009}, author = {Sentchilo, V and Czechowska, K and Pradervand, N and Minoia, M and Miyazaki, R and van der Meer, JR}, title = {Intracellular excision and reintegration dynamics of the ICEclc genomic island of Pseudomonas knackmussii sp. strain B13.}, journal = {Molecular microbiology}, volume = {72}, number = {5}, pages = {1293-1306}, doi = {10.1111/j.1365-2958.2009.06726.x}, pmid = {19432799}, issn = {1365-2958}, mesh = {*DNA Transposable Elements ; Gene Targeting ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genomic Islands ; Integrases/genetics ; *Mutagenesis, Insertional ; Pseudomonas/*genetics ; RNA, Bacterial/genetics ; RNA, Transfer, Gly/genetics ; }, abstract = {Genomic islands are DNA elements acquired by horizontal gene transfer that are common to a large number of bacterial genomes, which can contribute specific adaptive functions, e.g. virulence, metabolic capacities or antibiotic resistances. Some genomic islands are still self-transferable and display an intricate life-style, reminiscent of both bacteriophages and conjugative plasmids. Here we studied the dynamical process of genomic island excision and intracellular reintegration using the integrative and conjugative element ICEclc from Pseudomonas knackmussii B13 as model. By using self-transfer of ICEclc from strain B13 to Pseudomonas putida and Cupriavidus necator as recipients, we show that ICEclc can target a number of different tRNA(Gly) genes in a bacterial genome, but only those which carry the GCC anticodon. Two conditional traps were designed for ICEclc based on the attR sequence, and we could show that ICEclc will insert with different frequencies in such traps producing brightly fluorescent cells. Starting from clonal primary transconjugants we demonstrate that ICEclc is excising and reintegrating at detectable frequencies, even in the absence of recipient. Recombination site analysis provided evidence to explain the characteristics of a larger number of genomic island insertions observed in a variety of strains, including Bordetella petri, Pseudomonas aeruginosa and Burkholderia.}, }
@article {pmid19427174, year = {2009}, author = {Rajpara, N and Patel, A and Tiwari, N and Bahuguna, J and Antony, A and Choudhury, I and Ghosh, A and Jain, R and Ghosh, A and Bhardwaj, AK}, title = {Mechanism of drug resistance in a clinical isolate of Vibrio fluvialis: involvement of multiple plasmids and integrons.}, journal = {International journal of antimicrobial agents}, volume = {34}, number = {3}, pages = {220-225}, doi = {10.1016/j.ijantimicag.2009.03.020}, pmid = {19427174}, issn = {1872-7913}, mesh = {Antimalarials/*therapeutic use ; Cholera/*drug therapy/microbiology ; DNA Transposable Elements ; DNA, Bacterial/analysis/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal ; Humans ; *Integrons ; Microbial Sensitivity Tests ; Plasmids/*genetics/isolation &amp; purification ; Sequence Analysis, DNA ; Trimethoprim/therapeutic use ; Vibrio/*drug effects/*genetics/isolation &amp; purification ; }, abstract = {The role of mobile genetic elements in imparting multiple drug resistance to a clinical isolate of Vibrio fluvialis (BD146) was investigated. This isolate showed complete or intermediate resistance to all of the 14 antibiotics tested. Polymerase chain reaction (PCR) revealed the presence of a class 1 integron and the absence of the SXT element in this isolate. The strain harboured a 7.5 kb plasmid and a very low copy number plasmid of unknown molecular size. Transformation of Escherichia coli with plasmid(s) from BD146 generated two kinds of transformants, one that harboured both of these plasmids and the other that harboured only the low copy number plasmid. PCR and antibiogram analysis indicated the association of the class 1 integron with the low copy number plasmid, which also conferred all the transferable resistance traits except trimethoprim to the parent strain. A BLAST search with the sequence of the 7.5kb plasmid showed that it was 99% identical to plasmid pVN84 from Vibrio cholerae O1 in Vietnam, indicating that these two plasmids are probably one and the same. To the best of our knowledge, this is the first report of horizontal transfer of a plasmid between V. fluvialis and V. cholerae.}, }
@article {pmid19425825, year = {2009}, author = {Crippen, TL and Poole, TL}, title = {Conjugative transfer of plasmid-located antibiotic resistance genes within the gastrointestinal tract of lesser mealworm larvae, Alphitobius diaperinus (Coleoptera: Tenebrionidae).}, journal = {Foodborne pathogens and disease}, volume = {6}, number = {7}, pages = {907-915}, doi = {10.1089/fpd.2008.0260}, pmid = {19425825}, issn = {1556-7125}, mesh = {Animals ; Bacterial Typing Techniques ; Chi-Square Distribution ; Coleoptera/*microbiology ; Colony Count, Microbial ; *Conjugation, Genetic ; Disinfection ; Drug Resistance, Multiple, Bacterial/genetics ; Escherichia coli/*genetics/isolation &amp; purification ; Gastrointestinal Tract/growth &amp; development/microbiology ; *Gene Transfer, Horizontal ; *Genes, MDR ; Larva/microbiology ; Microbial Sensitivity Tests ; *Plasmids ; Polymerase Chain Reaction ; Replicon ; Salmonella enterica/*genetics/isolation &amp; purification ; Statistics, Nonparametric ; }, abstract = {The frequency of conjugative transfer of antimicrobial resistance plasmids between bacteria within the gastrointestinal tract of lesser mealworm larvae, a prevalent pest in poultry production facilities, was determined. Lesser mealworm larvae were exposed to a negative bacterial control, a donor Salmonella enterica serotype Newport strain, a recipient Escherichia coli, or both donor and recipient to examine horizontal gene transfer of plasmids. Horizontal gene transfer was validated post external disinfection, via a combination of selective culturing, testing of indole production by spot test, characterization of incompatibility plasmids by polymerase chain reaction, and profiling antibiotic susceptibility by a minimum inhibitory concentration (MIC) assay. Transconjugants were produced in all larvae exposed to both donor and recipient bacteria at frequencies comparable to control in vitro filter mating conjugation studies run concurrently. Transconjugants displayed resistance to seven antibiotics in our MIC panel and, when characterized for incompatibility plasmids, were positive for the N replicon and negative for the A/C replicon. The transconjugants did not display resistance to expanded-spectrum cephalosporins, which were associated with the A/C plasmid. This study demonstrates that lesser mealworm larvae, which infest poultry litter, are capable of supporting the horizontal transfer of antibiotic resistance genes and that this exchange can occur within their gastrointestinal tract and between different species of bacteria under laboratory conditions. This information is essential to science-based risk assessments of industrial antibiotic usage and its impact on animal and human health.}, }
@article {pmid19416510, year = {2009}, author = {Ros, VI and Hurst, GD}, title = {Lateral gene transfer between prokaryotes and multicellular eukaryotes: ongoing and significant?.}, journal = {BMC biology}, volume = {7}, number = {}, pages = {20}, pmid = {19416510}, issn = {1741-7007}, mesh = {Animals ; Eukaryotic Cells/*cytology/*metabolism ; Gene Transfer, Horizontal/*genetics ; Prokaryotic Cells/*metabolism ; Symbiosis/genetics ; }, abstract = {The expansion of genome sequencing projects has produced accumulating evidence for lateral transfer of genes between prokaryotic and eukaryotic genomes. However, it remains controversial whether these genes are of functional importance in their recipient host. Nikoh and Nakabachi, in a recent paper in BMC Biology, take a first step and show that two genes of bacterial origin are highly expressed in the pea aphid Acyrthosiphon pisum. Active gene expression of transferred genes is supported by three other recent studies. Future studies should reveal whether functional proteins are produced and whether and how these are targeted to the appropriate compartment. We argue that the transfer of genes between host and symbiont may occasionally be of great evolutionary importance, particularly in the evolution of the symbiotic interaction itself.}, }
@article {pmid19416011, year = {2009}, author = {Vedantam, G}, title = {Antimicrobial resistance in Bacteroides spp.: occurrence and dissemination.}, journal = {Future microbiology}, volume = {4}, number = {4}, pages = {413-423}, doi = {10.2217/fmb.09.12}, pmid = {19416011}, issn = {1746-0921}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteroides/*drug effects/physiology ; Conjugation, Genetic ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Humans ; Interspersed Repetitive Sequences ; }, abstract = {Bacteroides spp. organisms, though important human commensals, are also opportunistic pathogens when they escape the colonic milieu. Resistance to multiple antibiotics has been increasing in Bacteroides spp. for decades, and is primarily due to horizontal gene transfer of a plethora of mobile elements. The mechanistic aspects of conjugation in Bacteroides spp. are only now being elucidated at a functional level. There appear to be key differences between Bacteroides spp. and non-Bacteroides spp. conjugation systems that may contribute to promiscuous gene transfer within and from this genus. This review summarizes the mechanisms of action and resistance of antibiotics used to treat Bacteroides spp. infections, and highlights current information on conjugation-based DNA exchange.}, }
@article {pmid19413754, year = {2009}, author = {Guan, D and Pettis, GS}, title = {Intergeneric conjugal gene transfer from Escherichia coli to the sweet potato pathogen Streptomyces ipomoeae.}, journal = {Letters in applied microbiology}, volume = {49}, number = {1}, pages = {67-72}, doi = {10.1111/j.1472-765X.2009.02619.x}, pmid = {19413754}, issn = {1472-765X}, mesh = {*Conjugation, Genetic ; Culture Media/chemistry ; Escherichia coli/*genetics/physiology ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Ipomoea batatas/microbiology ; Molecular Biology/*methods ; Plasmids ; Streptomyces/*genetics/physiology ; }, abstract = {AIMS: To develop an effective gene transfer system for Streptomyces ipomoeae, the causative agent of soil rot disease of sweet potatoes.<br><br>METHODS AND RESULTS: Of the several methods investigated, introduction of genes into S. ipomoeae could only be achieved using intergeneric conjugation from Escherichia coli. However, even results for that method varied greatly and were dependent on using particular media for S. ipomoeae spore preparation and conjugation. Transconjugant to recipient ratios as great as 4.1 x 10(-5) were achieved when International Streptomyces Project Medium 4 was used for both sporulation and conjugation protocols. Both site-specifically integrating and autonomously replicating plasmids could be introduced and maintained in S. ipomoeae, and plasmids could be introduced with approximate equivalent frequencies from either methyl-proficient or methyl- deficient E. coli donors; the latter result indicates a likely absence of relevant methyl-specific restriction in S. ipomoeae.<br><br>CONCLUSIONS: Efficient transfer of genes into S. ipomoeae was achieved here by using an optimized intergeneric mating procedure.<br><br>The described protocol will facilitate further genetic manipulation of this agriculturally important pathogen.}, }
@article {pmid19412337, year = {2009}, author = {Asadulghani, M and Ogura, Y and Ooka, T and Itoh, T and Sawaguchi, A and Iguchi, A and Nakayama, K and Hayashi, T}, title = {The defective prophage pool of Escherichia coli O157: prophage-prophage interactions potentiate horizontal transfer of virulence determinants.}, journal = {PLoS pathogens}, volume = {5}, number = {5}, pages = {e1000408}, pmid = {19412337}, issn = {1553-7374}, mesh = {Chloramphenicol Resistance/genetics ; Computer Simulation ; Escherichia coli O157/genetics/pathogenicity/virology ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Interspersed Repetitive Sequences ; Oligonucleotide Array Sequence Analysis ; Polymerase Chain Reaction ; Prophages/*genetics/pathogenicity/physiology ; Recombination, Genetic ; Sequence Alignment ; Shiga Toxin 1/genetics ; Shiga Toxin 2/genetics ; Virion/metabolism/ultrastructure ; Virulence/*genetics ; Virulence Factors/genetics ; }, abstract = {Bacteriophages are major genetic factors promoting horizontal gene transfer (HGT) between bacteria. Their roles in dynamic bacterial genome evolution have been increasingly highlighted by the fact that many sequenced bacterial genomes contain multiple prophages carrying a wide range of genes. Enterohemorrhagic Escherichia coli O157 is the most striking case. A sequenced strain (O157 Sakai) possesses 18 prophages (Sp1-Sp18) that encode numerous genes related to O157 virulence, including those for two potent cytotoxins, Shiga toxins (Stx) 1 and 2. However, most of these prophages appeared to contain multiple genetic defects. To understand whether these defective prophages have the potential to act as mobile genetic elements to spread virulence determinants, we looked closely at the Sp1-Sp18 sequences, defined the genetic defects of each Sp, and then systematically analyzed all Sps for their biological activities. We show that many of the defective prophages, including the Stx1 phage, are inducible and released from O157 cells as particulate DNA. In fact, some prophages can even be transferred to other E. coli strains. We also show that new Stx1 phages are generated by recombination between the Stx1 and Stx2 phage genomes. The results indicate that these defective prophages are not simply genetic remnants generated in the course of O157 evolution, but rather genetic elements with a high potential for disseminating virulence-related genes and other genetic traits to other bacteria. We speculate that recombination and various other types of inter-prophage interactions in the O157 prophage pool potentiate such activities. Our data provide new insights into the potential activities of the defective prophages embedded in bacterial genomes and lead to the formulation of a novel concept of inter-prophage interactions in defective prophage communities.}, }
@article {pmid19411426, year = {2009}, author = {Dam, B and Ghosh, W and Das Gupta, SK}, title = {Conjugative Type 4 secretion system of a novel large plasmid from the chemoautotroph Tetrathiobacter kashmirensis and construction of shuttle vectors for Alcaligenaceae.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {13}, pages = {4362-4373}, pmid = {19411426}, issn = {1098-5336}, mesh = {Alcaligenaceae/*genetics ; Base Sequence ; Conjugation, Genetic ; DNA Repair Enzymes/genetics ; DNA, Bacterial/chemistry/genetics ; Evolution, Molecular ; Gene Order ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genetic Vectors ; Molecular Sequence Data ; Mutagenesis, Insertional ; Phylogeny ; *Plasmids ; Replication Origin ; Replication Protein A/genetics ; Replicon ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {Tetrathiobacter spp. and other members of the Alcaligenaceae are metabolically versatile and environmentally significant. A novel, approximately 60-kb conjugative plasmid, pBTK445, from the sulfur chemolithoautotroph Tetrathiobacter kashmirensis, was identified and characterized. This plasmid exists at a low copy number of 2 to 3 per host chromosome. The portion of pBTK445 sequenced so far (approximately 25 kb) harbors genes putatively involved in replication, transfer functions, partition, and UV damage repair. A 1,373-bp region was identified as the minimal replicon. This region contains a repA gene encoding a protein belonging to the RPA (replication protein A) superfamily and an upstream, iteron-based oriV. A contiguous 11-gene cluster homologous to various type 4 secretion systems (T4SSs) was identified. Insertional inactivation demonstrated that this cluster is involved in the conjugative transfer functions of pBTK445, and thus, it was named the tagB (transfer-associated gene homologous to virB) locus. The core and peripheral TagB components show different phylogenetic affinities, suggesting that this system has evolved by assembling components from evolutionarily divergent T4SSs. A virD4 homolog, putatively involved in nucleoprotein transfer, is also present downstream of the tagB locus. Although pBTK445 resembles IncP plasmids in terms of its genomic organization and the presence of an IncP-specific trbM homolog, it also shows several unique features. Unlike that of IncP, the oriT of pBTK445 is located in close proximity to the oriV, and a traL homolog, which is generally present in the TraI locus of IncP, is present in pBTK445 in isolation, upstream of the tagB locus. A significant outcome of this study is the construction of conjugative shuttle vectors for Tetrathiobacter and related members of the Alkaligenaceae.}, }
@article {pmid19407205, year = {2009}, author = {Stegemann, S and Bock, R}, title = {Exchange of genetic material between cells in plant tissue grafts.}, journal = {Science (New York, N.Y.)}, volume = {324}, number = {5927}, pages = {649-651}, doi = {10.1126/science.1170397}, pmid = {19407205}, issn = {1095-9203}, mesh = {Breeding ; Cell Line ; Cell Nucleus/genetics ; Chloroplasts/genetics ; Drug Resistance/genetics ; *Gene Transfer, Horizontal ; *Genes, Plant ; Genes, Reporter ; Green Fluorescent Proteins/analysis ; Kanamycin/pharmacology ; Luminescent Proteins/analysis ; Plants, Genetically Modified ; Selection, Genetic ; Spectinomycin/pharmacology ; Nicotiana/cytology/*genetics ; }, abstract = {Tissue grafting includes applications ranging from plant breeding to animal organ transplantation. Donor and recipient are generally believed to maintain their genetic integrity, in that the grafted tissues are joined but their genetic materials do not mix. We grafted tobacco plants from two transgenic lines carrying different marker and reporter genes in different cellular compartments, the nucleus and the plastid. Analysis of the graft sites revealed the frequent occurrence of cells harboring both antibiotic resistances and both fluorescent reporters. Our data demonstrate that plant grafting can result in the exchange of genetic information via either large DNA pieces or entire plastid genomes. This observation of novel combinations of genetic material has implications for grafting techniques and also provides a possible path for horizontal gene transfer.}, }
@article {pmid19404327, year = {2009}, author = {Allen, MA and Lauro, FM and Williams, TJ and Burg, D and Siddiqui, KS and De Francisci, D and Chong, KW and Pilak, O and Chew, HH and De Maere, MZ and Ting, L and Katrib, M and Ng, C and Sowers, KR and Galperin, MY and Anderson, IJ and Ivanova, N and Dalin, E and Martinez, M and Lapidus, A and Hauser, L and Land, M and Thomas, T and Cavicchioli, R}, title = {The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: the role of genome evolution in cold adaptation.}, journal = {The ISME journal}, volume = {3}, number = {9}, pages = {1012-1035}, doi = {10.1038/ismej.2009.45}, pmid = {19404327}, issn = {1751-7370}, support = {//Intramural NIH HHS/United States ; }, mesh = {Adaptation, Biological ; Cold Temperature ; DNA, Archaeal/chemistry/*genetics ; Evolution, Molecular ; Genes, Archaeal ; *Genome, Archaeal ; Methanosarcinaceae/*genetics ; Molecular Sequence Data ; *Sequence Analysis, DNA ; }, abstract = {Psychrophilic archaea are abundant and perform critical roles throughout the Earth's expansive cold biosphere. Here we report the first complete genome sequence for a psychrophilic methanogenic archaeon, Methanococcoides burtonii. The genome sequence was manually annotated including the use of a five-tiered evidence rating (ER) system that ranked annotations from ER1 (gene product experimentally characterized from the parent organism) to ER5 (hypothetical gene product) to provide a rapid means of assessing the certainty of gene function predictions. The genome is characterized by a higher level of aberrant sequence composition (51%) than any other archaeon. In comparison to hyper/thermophilic archaea, which are subject to selection of synonymous codon usage, M. burtonii has evolved cold adaptation through a genomic capacity to accommodate highly skewed amino-acid content, while retaining codon usage in common with its mesophilic Methanosarcina cousins. Polysaccharide biosynthesis genes comprise at least 3.3% of protein coding genes in the genome, and Cell wall, membrane, envelope biogenesis COG genes are overrepresented. Likewise, signal transduction (COG category T) genes are overrepresented and M. burtonii has a high 'IQ' (a measure of adaptive potential) compared to many methanogens. Numerous genes in these two overrepresented COG categories appear to have been acquired from epsilon- and delta-Proteobacteria, as do specific genes involved in central metabolism such as a novel B form of aconitase. Transposases also distinguish M. burtonii from other archaea, and their genomic characteristics indicate they have an important role in evolving the M. burtonii genome. Our study reveals a capacity for this model psychrophile to evolve through genome plasticity (including nucleotide skew, horizontal gene transfer and transposase activity) that enables adaptation to the cold, and to the biological and physical changes that have occurred over the last several thousand years as it adapted from a marine to an Antarctic lake environment.}, }
@article {pmid19400792, year = {2009}, author = {Schielke, S and Huebner, C and Spatz, C and Nägele, V and Ackermann, N and Frosch, M and Kurzai, O and Schubert-Unkmeir, A}, title = {Expression of the meningococcal adhesin NadA is controlled by a transcriptional regulator of the MarR family.}, journal = {Molecular microbiology}, volume = {72}, number = {4}, pages = {1054-1067}, doi = {10.1111/j.1365-2958.2009.06710.x}, pmid = {19400792}, issn = {1365-2958}, mesh = {Adhesins, Bacterial/genetics/*metabolism ; Amino Acid Sequence ; Binding Sites ; Cell Line ; Cloning, Molecular ; DNA, Bacterial/genetics ; DNA-Binding Proteins/genetics/*metabolism ; Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Humans ; Molecular Sequence Data ; Mutagenesis, Insertional ; Neisseria meningitidis/*genetics/metabolism ; Promoter Regions, Genetic ; Sequence Alignment ; Sequence Analysis, DNA ; Transcription Factors/genetics/*metabolism ; }, abstract = {Two closely related pathogenic species have evolved in the genus Neisseria: N. meningitidis and N. gonorrhoeae, which occupy different host niches and cause different clinical entities. In contrast to the pathogen N. gonorrhoeae, N. meningitidis is a commensal and only rarely becomes invasive. Little is known about the genetic background of the entirely different lifestyles in these closely related species. Meningococcal NMB1843 encodes a transcriptional regulator of the MarR family. The gonococcal homologue FarR regulates expression of farAB, mediating fatty acid resistance. We show that NmFarR also directly interacts with NmfarAB. Yet, by contrast to N. gonorrhoeae, no significant sensitivity to fatty acids was observed in a DeltafarR mutant due to intrinsic resistance of meningococci. Further analyses identified an NmFarR-repressed protein absent from N. gonorrhoeae. This protein is the meningococcus-specific adhesin and vaccine component NadA that has most likely been acquired by horizontal gene transfer. NmFarR binds to a 16 base pair palindromic repeat within the nadA promoter. De-repression of nadA resulted in significantly higher association of a DeltafarR strain with epithelial cells. Hence NmFarR has gained control over a meningococcus-specific gene involved in host colonization and thus contributed to divergent niche adaptation in pathogenic Neisseriae.}, }
@article {pmid19400643, year = {2009}, author = {Barash, I and Manulis-Sasson, S}, title = {Recent evolution of bacterial pathogens: the gall-forming Pantoea agglomerans case.}, journal = {Annual review of phytopathology}, volume = {47}, number = {}, pages = {133-152}, doi = {10.1146/annurev-phyto-080508-081803}, pmid = {19400643}, issn = {0066-4286}, mesh = {*Biological Evolution ; Gene Transfer, Horizontal ; Genomic Islands/genetics ; Host-Pathogen Interactions ; Pantoea/*genetics/*pathogenicity ; Plant Tumors/genetics/*microbiology ; }, abstract = {Pantoea agglomerans, a widespread epiphyte and commensal bacterium, has evolved into an Hrp-dependent and host-specific tumorigenic pathogen by acquiring a plasmid containing a pathogenicity island (PAI). The PAI was evolved on an iteron plasmid of the IncN family, which is distributed among genetically diverse populations of P. agglomerans. The structure of the PAI supports the premise of a recently evolved pathogen. This review offers insight into a unique model for emergence of new bacterial pathogens. It illustrates how horizontal gene transfer was the major driving force in the creation of the PAI, although a pathoadaptive mechanism might also be involved. It describes the crucial function of plant-produced indole-3-acetic acid (IAA) and cytokinines (CK) in gall initiation as opposed to the significant but secondary role of pathogen-secreted phytohormones. It also unveils the role of type III effectors in determination of host specificity and evolution of the pathogen into pathovars. Finally, it describes how interactions between the quorum sensing system, hrp regulatory genes, and bacterially secreted IAA or CKs affect gall formation and epiphytic fitness.}, }
@article {pmid19400640, year = {2009}, author = {Bird, DM and Williamson, VM and Abad, P and McCarter, J and Danchin, EG and Castagnone-Sereno, P and Opperman, CH}, title = {The genomes of root-knot nematodes.}, journal = {Annual review of phytopathology}, volume = {47}, number = {}, pages = {333-351}, doi = {10.1146/annurev-phyto-080508-081839}, pmid = {19400640}, issn = {0066-4286}, mesh = {Animals ; Biological Evolution ; Gene Transfer, Horizontal ; *Genome, Helminth ; Nematoda/*genetics ; Plant Diseases/genetics ; Plant Roots/genetics ; }, abstract = {Plant-parasitic nematodes are the most destructive group of plant pathogens worldwide and are extremely challenging to control. The recent completion of two root-knot nematode genomes opens the way for a comparative genomics approach to elucidate the success of these parasites. Sequencing revealed that Meloidogyne hapla, a diploid that reproduces by facultative, meiotic parthenogenesis, encodes approximately 14,200 genes in a compact, 54 Mpb genome. Indeed, this is the smallest metazoan genome completed to date. By contrast, the 86 Mbp Meloidogyne incognita genome encodes approximately 19,200 genes. This species reproduces by obligate mitotic parthenogenesis and exhibits a complex pattern of aneuploidy. The genome includes triplicated regions and contains allelic pairs with exceptionally high degrees of sequence divergence, presumably reflecting adaptations to the strictly asexual reproductive mode. Both root-knot nematode genomes have compacted gene families compared with the free-living nematode Caenorhabditis elegans, and both encode large suites of enzymes that uniquely target the host plant. Acquisition of these genes, apparently via horizontal gene transfer, and their subsequent expansion and diversification point to the evolutionary history of these parasites. It also suggests new routes to their control.}, }
@article {pmid19398507, year = {2009}, author = {Chee-Sanford, JC and Mackie, RI and Koike, S and Krapac, IG and Lin, YF and Yannarell, AC and Maxwell, S and Aminov, RI}, title = {Fate and transport of antibiotic residues and antibiotic resistance genes following land application of manure waste.}, journal = {Journal of environmental quality}, volume = {38}, number = {3}, pages = {1086-1108}, doi = {10.2134/jeq2008.0128}, pmid = {19398507}, issn = {0047-2425}, mesh = {Animal Husbandry ; Animals ; Anti-Bacterial Agents/*analysis ; Biological Evolution ; DNA, Bacterial/*analysis ; Drug Resistance, Bacterial/*genetics ; Environment ; Gene Transfer, Horizontal ; Genes, Bacterial ; Manure/*analysis ; Soil/analysis ; *Soil Microbiology ; Waste Management ; }, abstract = {Antibiotics are used in animal livestock production for therapeutic treatment of disease and at subtherapeutic levels for growth promotion and improvement of feed efficiency. It is estimated that approximately 75% of antibiotics are not absorbed by animals and are excreted in waste. Antibiotic resistance selection occurs among gastrointestinal bacteria, which are also excreted in manure and stored in waste holding systems. Land application of animal waste is a common disposal method used in the United States and is a means for environmental entry of both antibiotics and genetic resistance determinants. Concerns for bacterial resistance gene selection and dissemination of resistance genes have prompted interest about the concentrations and biological activity of drug residues and break-down metabolites, and their fate and transport. Fecal bacteria can survive for weeks to months in the environment, depending on species and temperature, however, genetic elements can persist regardless of cell viability. Phylogenetic analyses indicate antibiotic resistance genes have evolved, although some genes have been maintained in bacteria before the modern antibiotic era. Quantitative measurements of drug residues and levels of resistance genes are needed, in addition to understanding the environmental mechanisms of genetic selection, gene acquisition, and the spatiotemporal dynamics of these resistance genes and their bacterial hosts. This review article discusses an accumulation of findings that address aspects of the fate, transport, and persistence of antibiotics and antibiotic resistance genes in natural environments, with emphasis on mechanisms pertaining to soil environments following land application of animal waste effluent.}, }
@article {pmid19396959, year = {2009}, author = {Johnsborg, O and Håvarstein, LS}, title = {Regulation of natural genetic transformation and acquisition of transforming DNA in Streptococcus pneumoniae.}, journal = {FEMS microbiology reviews}, volume = {33}, number = {3}, pages = {627-642}, doi = {10.1111/j.1574-6976.2009.00167.x}, pmid = {19396959}, issn = {1574-6976}, mesh = {Bacterial Proteins/metabolism ; DNA, Bacterial/genetics/*metabolism ; Drug Resistance, Bacterial ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Membrane Transport Proteins/metabolism ; Streptococcus pneumoniae/genetics/*physiology ; *Transformation, Bacterial ; Virulence Factors/genetics ; }, abstract = {The ability of pneumococci to take up naked DNA from the environment and permanently incorporate the DNA into their genome by recombination has been exploited as a valuable research tool for 80 years. From being viewed as a marginal phenomenon, it has become increasingly clear that horizontal gene transfer by natural transformation is a powerful mechanism for generating genetic diversity, and that it has the potential to cause severe problems for future treatment of pneumococcal disease. This process constitutes a highly efficient mechanism for spreading beta-lactam resistance determinants between streptococcal strains and species, and also threatens to undermine the effect of pneumococcal vaccines. Fortunately, great progress has been made during recent decades to elucidate the mechanism behind natural transformation at a molecular level. Increased insight into these matters will be important for future development of therapeutic strategies and countermeasures aimed at reducing the spread of hazardous traits. In this review, we focus on recent developments in our understanding of competence regulation, DNA acquisition and the role of natural transformation in the dissemination of virulence and beta-lactam resistance determinants.}, }
@article {pmid19396949, year = {2009}, author = {Ambur, OH and Davidsen, T and Frye, SA and Balasingham, SV and Lagesen, K and Rognes, T and Tønjum, T}, title = {Genome dynamics in major bacterial pathogens.}, journal = {FEMS microbiology reviews}, volume = {33}, number = {3}, pages = {453-470}, pmid = {19396949}, issn = {1574-6976}, mesh = {Adaptation, Biological ; Bacteria/*genetics/isolation &amp; purification/*pathogenicity ; Bacterial Infections/*microbiology ; DNA Repair ; DNA, Bacterial/*genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; Recombination, Genetic ; }, abstract = {Pathogenic bacteria continuously encounter multiple forms of stress in their hostile environments, which leads to DNA damage. With the new insight into biology offered by genome sequences, the elucidation of the gene content encoding proteins provides clues toward understanding the microbial lifestyle related to habitat and niche. Campylobacter jejuni, Haemophilus influenzae, Helicobacter pylori, Mycobacterium tuberculosis, the pathogenic Neisseria, Streptococcus pneumoniae, Streptococcus pyogenes and Staphylococcus aureus are major human pathogens causing detrimental morbidity and mortality at a global scale. An algorithm for the clustering of orthologs was established in order to identify whether orthologs of selected genes were present or absent in the genomes of the pathogenic bacteria under study. Based on the known genes for the various functions and their orthologs in selected pathogenic bacteria, an overview of the presence of the different types of genes was created. In this context, we focus on selected processes enabling genome dynamics in these particular pathogens, namely DNA repair, recombination and horizontal gene transfer. An understanding of the precise molecular functions of the enzymes participating in DNA metabolism and their importance in the maintenance of bacterial genome integrity has also, in recent years, indicated a future role for these enzymes as targets for therapeutic intervention.}, }
@article {pmid19396940, year = {2009}, author = {Schwarzenlander, C and Haase, W and Averhoff, B}, title = {The role of single subunits of the DNA transport machinery of Thermus thermophilus HB27 in DNA binding and transport.}, journal = {Environmental microbiology}, volume = {11}, number = {4}, pages = {801-808}, doi = {10.1111/j.1462-2920.2008.01801.x}, pmid = {19396940}, issn = {1462-2920}, mesh = {Bacterial Proteins/*metabolism ; DNA/*metabolism ; Membrane Transport Proteins/*metabolism ; Models, Biological ; Protein Binding ; Thermus thermophilus/*metabolism ; }, abstract = {Thermus thermophilus HB27 is well known for its extraordinary trait of high frequencies of natural transformation, which is considered a major mechanism of horizontal gene transfer. We show that the DNA translocator of T. thermophilus binds and transports DNA from members of all three domains. These results, together with the data obtained from genome comparisons, suggest that the DNA translocator of T. thermophilus has a major impact in adaptation of Thermus to thermal stress conditions and interdomain DNA transfer in extreme hot environments. DNA transport in T. thermophilus is mediated by a macromolecular transport machinery that consists of at least 16 subunits and spans the cytoplasmic membrane and the entire cell periphery. Here, we have addressed the role of single subunits in DNA binding and transport. PilQ is involved in DNA binding, ComEA, PilF and PilA4 are involved in transport of DNA through the outer membrane and PilM, PilN, PilO, PilA1-3, PilC and ComEC are essential for the transport of DNA through the thick cell wall layers and/or through the inner membrane. These data are discussed in the light of the subcellular localization of the proteins. A topological model for DNA transport across the cell wall is presented.}, }
@article {pmid19395574, year = {2009}, author = {Devirgiliis, C and Coppola, D and Barile, S and Colonna, B and Perozzi, G}, title = {Characterization of the Tn916 conjugative transposon in a food-borne strain of Lactobacillus paracasei.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {12}, pages = {3866-3871}, pmid = {19395574}, issn = {1098-5336}, mesh = {Bacterial Proteins/genetics ; Bacterial Typing Techniques ; Cluster Analysis ; Conjugation, Genetic ; DNA Fingerprinting ; *DNA Transposable Elements ; DNA, Bacterial/*genetics ; Dairy Products/*microbiology ; Enterococcus faecalis/genetics ; Gene Transfer, Horizontal ; Genotype ; Italy ; Lactobacillus/classification/drug effects/*genetics/isolation &amp; purification ; *Tetracycline Resistance ; }, abstract = {Food-borne antibiotic-resistant lactic acid bacteria have received growing attention in the past few years. We have recently identified tetracycline-resistant Lactobacillus paracasei in samples of milk and natural whey starter cultures employed in the manufacturing process of a typical Italian fermented dairy product, Mozzarella di Bufala Campana. In the present study, we have characterized at the molecular level the genetic context of tetracycline resistance determinants in these natural strains, which we have identified as tet(M). This gene was present in 21 independent isolates, whose fingerprinting profiles were distributed into eight different repetitive extragenic palindromic groups by cluster analysis. We provide evidence that the gene is associated with the broad-host, conjugative transposon Tn916, which had never before been described to occur in L. paracasei. PCR analysis of four independent isolates by use of specifically designed primer pairs detected the presence of a circular intermediate form of the transposon, carrying a coupling sequence (GGCAAA) located between the two termini of Tn916. This novel coupling sequence conferred low conjugation frequency in mating experiments with the recipient strain JH2-2 of Enterococcus faecalis.}, }
@article {pmid19395564, year = {2009}, author = {Liu, M and Siezen, RJ and Nauta, A}, title = {In silico prediction of horizontal gene transfer events in Lactobacillus bulgaricus and Streptococcus thermophilus reveals protocooperation in yogurt manufacturing.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {12}, pages = {4120-4129}, pmid = {19395564}, issn = {1098-5336}, mesh = {Bacterial Proteins/genetics ; Computational Biology ; *Gene Transfer, Horizontal ; Genomics ; Lactobacillus/*genetics/*metabolism ; Multigene Family ; Phylogeny ; Sequence Homology ; Streptococcus thermophilus/*genetics/*metabolism ; Yogurt/*microbiology ; }, abstract = {Lactobacillus bulgaricus and Streptococcus thermophilus, used in yogurt starter cultures, are well known for their stability and protocooperation during their coexistence in milk. In this study, we show that a close interaction between the two species also takes place at the genetic level. We performed an in silico analysis, combining gene composition and gene transfer mechanism-associated features, and predicted horizontally transferred genes in both L. bulgaricus and S. thermophilus. Putative horizontal gene transfer (HGT) events that have occurred between the two bacterial species include the transfer of exopolysaccharide (EPS) biosynthesis genes, transferred from S. thermophilus to L. bulgaricus, and the gene cluster cbs-cblB(cglB)-cysE for the metabolism of sulfur-containing amino acids, transferred from L. bulgaricus or Lactobacillus helveticus to S. thermophilus. The HGT event for the cbs-cblB(cglB)-cysE gene cluster was analyzed in detail, with respect to both evolutionary and functional aspects. It can be concluded that during the coexistence of both yogurt starter species in a milk environment, agonistic coevolution at the genetic level has probably been involved in the optimization of their combined growth and interactions.}, }
@article {pmid19393304, year = {2009}, author = {Elias, M and Archibald, JM}, title = {The RJL family of small GTPases is an ancient eukaryotic invention probably functionally associated with the flagellar apparatus.}, journal = {Gene}, volume = {442}, number = {1-2}, pages = {63-72}, doi = {10.1016/j.gene.2009.04.011}, pmid = {19393304}, issn = {1879-0038}, mesh = {Animals ; Eukaryotic Cells/enzymology ; *Evolution, Molecular ; Flagella/*enzymology ; *Gene Transfer, Horizontal ; HSP40 Heat-Shock Proteins/classification/genetics ; Monomeric GTP-Binding Proteins/*classification/*genetics ; Phylogeny ; Protein Structure, Tertiary ; }, abstract = {A patchily distributed gene family is often taken as evidence for horizontal gene transfer (HGT) events, but it may also result solely from multiple gene losses. The RJL family of uncharacterised Ras-like GTPases was previously suggested to have undergone HGT events between protists and deuterostome metazoans, owing to the apparent absence of RJL in intermediate groups (Nepomuceno-Silva, J.L., de Melo, L.D., Mendonca, S.M., Paixao, J.C., Lopes, U.G., 2004. RJLs: a new family of Ras-related GTP-binding proteins. Gene 327, 221-232). We have reanalysed the phylogenetic distribution and phylogeny of the RJL family, taking advantage of the recent expansion of sequence data available from diverse eukaryotes. We found that RJL orthologs are much more widely distributed than previously assumed. At least one representative encoding an RJL protein could be identified for each of the six major eukaryotic "supergroups" (Opisthokonta, Amoebozoa, Excavata, Archaeplastida, Chromalveolata, and Rhizaria) as well as for a species of Apusomonadida, a deep lineage that may not be specifically related to any of the recognized supergroups. Phylogenetic analyses do not support HGT of RJL genes between the major eukaryotic lineages, indicating that the RJL family was present in the last eukaryotic common ancestor and was lost several times over the course of eukaryotic evolution. Interestingly, RJL was lost from all taxa lacking flagellated cells and from a few lineages that build structurally unusual or reduced flagella, raising the intriguing possibility that RJL proteins are functionally associated with the flagellar apparatus. The RJL GTPase domain has been fused with the DnaJ domain on two separate occasions: in the Holozoa (before the split of Metazoa and choanoflagellates), giving rise to the previously known Rbj type of RJL with the DnaJ domain at the C-terminus, and independently in Alveolata resulting in novel proteins with the DnaJ domain at the N-terminus. These independent fusions suggest that RJL proteins may generally function via regulating the DnaJ-Hsp70 module.}, }
@article {pmid19393086, year = {2009}, author = {Hooper, SD and Mavromatis, K and Kyrpides, NC}, title = {Microbial co-habitation and lateral gene transfer: what transposases can tell us.}, journal = {Genome biology}, volume = {10}, number = {4}, pages = {R45}, pmid = {19393086}, issn = {1474-760X}, mesh = {Bacillus cereus/genetics/growth &amp; development ; Bacteria/classification/*genetics/growth &amp; development ; Bacterial Proteins/genetics ; Databases, Genetic ; *Ecosystem ; Escherichia coli/genetics/growth &amp; development ; Fresh Water/microbiology ; Gene Transfer, Horizontal/*genetics ; Phylogeny ; Proteobacteria/genetics/growth &amp; development ; Salmonella enterica/genetics/growth &amp; development ; Seawater/microbiology ; Soil Microbiology ; Transposases/genetics ; Water Microbiology ; }, abstract = {BACKGROUND: Determining the habitat range for various microbes is not a simple, straightforward matter, as habitats interlace, microbes move between habitats, and microbial communities change over time. In this study, we explore an approach using the history of lateral gene transfer recorded in microbial genomes to begin to answer two key questions: where have you been and who have you been with?<br><br>RESULTS: All currently sequenced microbial genomes were surveyed to identify pairs of taxa that share a transposase that is likely to have been acquired through lateral gene transfer. A microbial interaction network including almost 800 organisms was then derived from these connections. Although the majority of the connections are between closely related organisms with the same or overlapping habitat assignments, numerous examples were found of cross-habitat and cross-phylum connections.<br><br>CONCLUSIONS: We present a large-scale study of the distributions of transposases across phylogeny and habitat, and find a significant correlation between habitat and transposase connections. We observed cases where phylogenetic boundaries are traversed, especially when organisms share habitats; this suggests that the potential exists for genetic material to move laterally between diverse groups via bridging connections. The results presented here also suggest that the complex dynamics of microbial ecology may be traceable in the microbial genomes.}, }
@article {pmid19391971, year = {2009}, author = {He, J and Sun, J and Deem, MW}, title = {Spontaneous emergence of modularity in a model of evolving individuals and in real networks.}, journal = {Physical review. E, Statistical, nonlinear, and soft matter physics}, volume = {79}, number = {3 Pt 1}, pages = {031907}, doi = {10.1103/PhysRevE.79.031907}, pmid = {19391971}, issn = {1539-3755}, mesh = {Bacteria/metabolism ; Environment ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Metabolic Networks and Pathways ; *Models, Biological ; Protein Binding ; Protein Structure, Tertiary ; }, abstract = {We investigate the selective forces that promote the emergence of modularity in nature. We demonstrate the spontaneous emergence of modularity in a population of individuals that evolve in a changing environment. We show that the level of modularity correlates with the rapidity and severity of environmental change. The modularity arises as a synergistic response to the noise in the environment in the presence of horizontal gene transfer. We suggest that the hierarchical structure observed in the natural world may be a broken symmetry state, which generically results from evolution in a changing environment. To support our results, we analyze experimental protein interaction data and show that protein interaction networks became increasingly modular as evolution proceeded over the last four billion years. We also discuss a method to determine the divergence time of a protein.}, }
@article {pmid19390587, year = {2009}, author = {Koenig, JE and Sharp, C and Dlutek, M and Curtis, B and Joss, M and Boucher, Y and Doolittle, WF}, title = {Integron gene cassettes and degradation of compounds associated with industrial waste: the case of the Sydney tar ponds.}, journal = {PloS one}, volume = {4}, number = {4}, pages = {e5276}, pmid = {19390587}, issn = {1932-6203}, mesh = {Algorithms ; Bacterial Proteins/*genetics ; Biodegradation, Environmental ; DNA, Bacterial/chemistry ; Gene Transfer, Horizontal ; Genetic Variation ; *Industrial Waste ; Integrons/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/chemistry ; Sequence Analysis, DNA ; Transcription Factors/*genetics ; Water Microbiology ; }, abstract = {Integrons are genetic platforms that accelerate lateral gene transfer (LGT) among bacteria. They were first detected on plasmids bearing single and multiple drug resistance determinants in human pathogens, and it is abundantly clear that integrons have played a major role in the evolution of this public health menace. Similar genetic elements can be found in nonpathogenic environmental bacteria and in metagenomic environmental DNA samples, and it is reasonable to suppose that integrons have facilitated microbial adaptation through LGT in niches outside infectious disease wards. Here we show that a heavily impacted estuary, exposed for almost a century to products of coal and steel industries, has developed a rich and unique cassette metagenome, containing genes likely to aid in the catabolism of compounds associated with industrial waste found there. In addition, we report that the most abundant cassette recovered in this study is one that encodes a putative LysR protein. This autoregulatory transcriptional regulator is known to activate transcription of linked target genes or unlinked regulons encoding diverse functions including chlorocatechol and dichlorophenol catabolism. Finally, only class 1 integrase genes were amplified in this study despite using different primer sets, and it may be that the cassettes present in the Tar Ponds will prove to be associated with class 1 integrase genes. Nevertheless, our cassette library provides a snapshot of a complex evolutionary process involving integron-meditated LGT likely to be important in natural bioremediation.}, }
@article {pmid19389774, year = {2009}, author = {Ishmael, N and Hotopp, JCD and Ioannidis, P and Biber, S and Sakamoto, J and Siozios, S and Nene, V and Werren, J and Bourtzis, K and Bordenstein, SR and Tettelin, H}, title = {Extensive genomic diversity of closely related Wolbachia strains.}, journal = {Microbiology (Reading, England)}, volume = {155}, number = {Pt 7}, pages = {2211-2222}, pmid = {19389774}, issn = {1350-0872}, support = {R01 GM085163/GM/NIGMS NIH HHS/United States ; R01-GM085163-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Ankyrins/genetics ; Comparative Genomic Hybridization ; DNA, Bacterial/analysis/genetics ; Drosophila melanogaster/*microbiology ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Variation ; Genome, Bacterial ; Interspersed Repetitive Sequences ; Species Specificity ; Wolbachia/*genetics ; }, abstract = {Using microarray-based comparative genome hybridization (mCGH), the genomic content of Wolbachia pipientis wMel from Drosophila melanogaster was compared to the closely related Wolbachia from D. innubila (wInn), D. santomea (wSan), and three strains from D. simulans (wAu, wRi, wSim). A large number of auxiliary genes are identified in these five strains, with most absent/divergent genes being unique to a given strain. Each strain caused an average of approximately 60 genes to be removed from the core genome. As such, these organisms do not appear to have the streamlined genomes expected of obligate intracellular bacteria. Prophage, hypothetical and ankyrin repeat genes are over-represented in the absent/divergent genes, with 21-87% of absent/divergent genes coming from prophage regions. The only wMel region absent/divergent in all five query strains is that containing WD_0509 to WD_0511, including a DNA mismatch repair protein MutL-2, a degenerate RNase, and a conserved hypothetical protein. A region flanked by the two portions of the WO-B prophage in wMel is found in four of the five Wolbachia strains as well as on a plasmid of a rickettsial endosymbiont of Ixodes scapularis, suggesting lateral gene transfer between these two obligate intracellular species. Overall, these insect-associated Wolbachia have highly mosaic genomes, with lateral gene transfer playing an important role in their diversity and evolution.}, }
@article {pmid19386843, year = {2009}, author = {Brugger, SD and Hathaway, LJ and Mühlemann, K}, title = {Detection of Streptococcus pneumoniae strain cocolonization in the nasopharynx.}, journal = {Journal of clinical microbiology}, volume = {47}, number = {6}, pages = {1750-1756}, pmid = {19386843}, issn = {1098-660X}, mesh = {Bacterial Typing Techniques/*methods ; Carrier State/*microbiology ; Child ; Child, Preschool ; Cluster Analysis ; DNA Fingerprinting ; DNA, Bacterial/genetics ; DNA, Intergenic ; Genotype ; Humans ; Infant ; Nasopharynx/*microbiology ; Pneumococcal Infections/epidemiology/*microbiology ; Polymerase Chain Reaction/*methods ; *Polymorphism, Restriction Fragment Length ; Prevalence ; Sensitivity and Specificity ; Streptococcus pneumoniae/*classification/genetics/isolation &amp; purification ; }, abstract = {Colonization with more than one distinct strain of the same species, also termed cocolonization, is a prerequisite for horizontal gene transfer between pneumococcal strains that may lead to change of the capsular serotype. Capsule switch has become an important issue since the introduction of conjugated pneumococcal polysaccharide vaccines. There is, however, a lack of techniques to detect multiple colonization by S. pneumoniae strains directly in nasopharyngeal samples. Two hundred eighty-seven nasopharyngeal swabs collected during the prevaccine era within a nationwide surveillance program were analyzed by a novel technique for the detection of cocolonization, based on PCR amplification of a noncoding region adjacent to the pneumolysin gene (plyNCR) and restriction fragment length polymorphism (RFLP) analysis. The numbers of strains and their relative abundance in cocolonized samples were determined by terminal RFLP. The pneumococcal carriage rate found by PCR was 51.6%, compared to 40.0% found by culture. Cocolonization was present in 9.5% (10/105) of samples, most (9/10) of which contained two strains in a ratio of between 1:1 and 17:1. Five of the 10 cocolonized samples showed combinations of vaccine types only (n = 2) or combinations of nonvaccine types only (n = 3). Carriers of multiple pneumococcal strains had received recent antibiotic treatment more often than those colonized with a single strain (33% versus 9%, P = 0.025). This new technique allows for the rapid and economical study of pneumococcal cocolonization in nasopharyngeal swabs. It will be valuable for the surveillance of S. pneumoniae epidemiology under vaccine selection pressure.}, }
@article {pmid19383137, year = {2009}, author = {Joss, MJ and Koenig, JE and Labbate, M and Polz, MF and Gillings, MR and Stokes, HW and Doolittle, WF and Boucher, Y}, title = {ACID: annotation of cassette and integron data.}, journal = {BMC bioinformatics}, volume = {10}, number = {}, pages = {118}, pmid = {19383137}, issn = {1471-2105}, mesh = {Algorithms ; *Databases, Genetic ; Evolution, Molecular ; Genes, Bacterial ; Genome, Bacterial ; *Integrons ; }, abstract = {BACKGROUND: Although integrons and their associated gene cassettes are present in ~10% of bacteria and can represent up to 3% of the genome in which they are found, very few have been properly identified and annotated in public databases. These genetic elements have been overlooked in comparison to other vectors that facilitate lateral gene transfer between microorganisms.<br><br>DESCRIPTION: By automating the identification of integron integrase genes and of the non-coding cassette-associated attC recombination sites, we were able to assemble a database containing all publicly available sequence information regarding these genetic elements. Specialists manually curated the database and this information was used to improve the automated detection and annotation of integrons and their encoded gene cassettes. ACID (annotation of cassette and integron data) can be searched using a range of queries and the data can be downloaded in a number of formats. Users can readily annotate their own data and integrate it into ACID using the tools provided.<br><br>CONCLUSION: ACID is a community resource providing easy access to annotations of integrons and making tools available to detect them in novel sequence data. ACID also hosts a forum to prompt integron-related discussion, which can hopefully lead to a more universal definition of this genetic element.}, }
@article {pmid19378146, year = {2009}, author = {Zaneveld, J and Hamady, M and Sueoka, N and Knight, R}, title = {CodonExplorer: an interactive online database for the analysis of codon usage and sequence composition.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {537}, number = {}, pages = {207-232}, pmid = {19378146}, issn = {1064-3745}, support = {T32 GM008759/GM/NIGMS NIH HHS/United States ; T32 GM065103-07/GM/NIGMS NIH HHS/United States ; T32 GM 065103/GM/NIGMS NIH HHS/United States ; T32 GM142607/GM/NIGMS NIH HHS/United States ; T32 GM 08759/GM/NIGMS NIH HHS/United States ; T32 GM065103/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Composition ; Base Sequence ; Codon/*genetics ; Computational Biology/*methods ; DNA/*chemistry ; *Databases, Nucleic Acid ; Gene Transfer, Horizontal ; Internet ; Molecular Sequence Data ; *Software ; }, abstract = {The analysis of DNA composition and codon usage reveals many factors that influence the evolution of genes and genomes. In this chapter, we show how to use CodonExplorer, a web tool and interactive database that contains millions of genes, to better understand the principles governing evolution at the single gene and whole-genome level. We present principles and practical procedures for using analyses of GC content and codon usage frequency to identify highly expressed or horizontally transferred genes and to study the relative contribution of different types of mutation to gene and genome composition. CodonExplorer's combination of a user-friendly web interface and a comprehensive genomic database makes these diverse analyses fast and straightforward to perform. CodonExplorer is thus a powerful tool that facilitates and automates a wide range of compositional analyses.}, }
@article {pmid19376926, year = {2009}, author = {Daniels, JB and Call, DR and Hancock, D and Sischo, WM and Baker, K and Besser, TE}, title = {Role of ceftiofur in selection and dissemination of blaCMY-2-mediated cephalosporin resistance in Salmonella enterica and commensal Escherichia coli isolates from cattle.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {11}, pages = {3648-3655}, pmid = {19376926}, issn = {1098-5336}, support = {N01AI30055/AI/NIAID NIH HHS/United States ; T32 AI007025/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Cattle/*microbiology ; *Cephalosporin Resistance ; Cephalosporins/*pharmacology/therapeutic use ; Conjugation, Genetic ; Escherichia coli/*drug effects/isolation &amp; purification ; Gene Transfer, Horizontal ; Plasmids ; Salmonella enterica/*drug effects/isolation &amp; purification ; *Selection, Genetic ; United States ; beta-Lactamases/biosynthesis/*genetics ; }, abstract = {Third-generation cephalosporin resistance of Salmonella and commensal Escherichia coli isolates from cattle in the United States is predominantly conferred by the cephamycinase CMY-2, which inactivates beta-lactam antimicrobial drugs used to treat a wide variety of infections, including pediatric salmonellosis. The emergence and dissemination of bla(CMY-2)(-)-bearing plasmids followed and may in part be the result of selection pressure imposed by the widespread utilization of ceftiofur, a third-generation veterinary cephalosporin. This study assessed the potential effects of ceftiofur on bla(CMY-2) transfer and dissemination by (i) an in vivo experimental study in which calves were inoculated with competent bla(CMY-2)-bearing plasmid donors and susceptible recipients and then subjected to ceftiofur selection and (ii) an observational study to determine whether ceftiofur use in dairy herds is associated with the occurrence and frequency of cephalosporin resistance in Salmonella and commensal E. coli. The first study revealed bla(CMY-2) plasmid transfer in both ceftiofur-treated and untreated calves but detected no enhancement of plasmid transfer associated with ceftiofur treatment. The second study detected no association (P = 0.22) between ceftiofur use and either the occurrence of ceftiofur-resistant salmonellosis or the frequency of cephalosporin resistance in commensal E. coli. However, herds with a history of salmonellosis (including both ceftiofur-resistant and ceftiofur-susceptible Salmonella isolates) used more ceftiofur than herds with no history of salmonellosis (P = 0.03) These findings fail to support a major role for ceftiofur use in the maintenance and dissemination of bla(CMY-2)-bearing plasmid mediated cephalosporin resistance in commensal E. coli and in pathogenic Salmonella in these dairy cattle populations.}, }
@article {pmid19376859, year = {2009}, author = {Nouvel, LX and Marenda, M and Sirand-Pugnet, P and Sagné, E and Glew, M and Mangenot, S and Barbe, V and Barré, A and Claverol, S and Citti, C}, title = {Occurrence, plasticity, and evolution of the vpma gene family, a genetic system devoted to high-frequency surface variation in Mycoplasma agalactiae.}, journal = {Journal of bacteriology}, volume = {191}, number = {13}, pages = {4111-4121}, pmid = {19376859}, issn = {1098-5530}, mesh = {Bacterial Proteins/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Immunoblotting ; Models, Genetic ; Mycoplasma agalactiae/*genetics ; Polymerase Chain Reaction ; Proteomics ; Recombination, Genetic/genetics ; }, abstract = {Mycoplasma agalactiae, an important pathogen of small ruminants, exhibits a very versatile surface architecture by switching multiple, related lipoproteins (Vpmas) on and off. In the type strain, PG2, Vpma phase variation is generated by a cluster of six vpma genes that undergo frequent DNA rearrangements via site-specific recombination. To further comprehend the degree of diversity that can be generated at the M. agalactiae surface, the vpma gene repertoire of a field strain, 5632, was analyzed and shown to contain an extended repertoire of 23 vpma genes distributed between two loci located 250 kbp apart. Loci I and II include 16 and 7 vpma genes, respectively, with all vpma genes of locus II being duplicated at locus I. Several Vpmas displayed a chimeric structure suggestive of homologous recombination, and a global proteomic analysis further indicated that at least 13 of the 16 Vpmas can be expressed by the 5632 strain. Because a single promoter is present in each vpma locus, concomitant Vpma expression can occur in a strain with duplicated loci. Consequently, the number of possible surface combinations is much higher for strain 5632 than for the type strain. Finally, our data suggested that insertion sequences are likely to be involved in 5632 vpma locus duplication at a remote chromosomal position. The role of such mobile genetic elements in chromosomal shuffling of genes encoding major surface components may have important evolutionary and epidemiological consequences for pathogens, such as mycoplasmas, that have a reduced genome and no cell wall.}, }
@article {pmid19375326, year = {2009}, author = {Shapiro, BJ and David, LA and Friedman, J and Alm, EJ}, title = {Looking for Darwin's footprints in the microbial world.}, journal = {Trends in microbiology}, volume = {17}, number = {5}, pages = {196-204}, doi = {10.1016/j.tim.2009.02.002}, pmid = {19375326}, issn = {1878-4380}, mesh = {Bacteria/*genetics ; DNA, Bacterial/*genetics ; *Evolution, Molecular ; *Genome, Bacterial ; *Selection, Genetic ; }, abstract = {As we observe the 200th anniversary of Charles Darwin's birth, microbiologists interested in the application of Darwin's ideas to the microscopic world have a lot to celebrate: an emerging picture of the (mostly microbial) Tree of Life at ever-increasing resolution, an understanding of horizontal gene transfer as a driving force in the evolution of microbes, and thousands of complete genome sequences to help formulate and refine our theories. At the same time, quantitative models of the microevolutionary processes shaping microbial populations remain just out of reach, a point that is perhaps most dramatically illustrated by the lack of consensus on how (or even whether) to define bacterial species. Here, we summarize progress and prospects in bacterial population genetics, with an emphasis on detecting the footprint of positive Darwinian selection in microbial genomes.}, }
@article {pmid19369210, year = {2009}, author = {Baglivo, I and Russo, L and Esposito, S and Malgieri, G and Renda, M and Salluzzo, A and Di Blasio, B and Isernia, C and Fattorusso, R and Pedone, PV}, title = {The structural role of the zinc ion can be dispensable in prokaryotic zinc-finger domains.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {17}, pages = {6933-6938}, pmid = {19369210}, issn = {1091-6490}, mesh = {Alphaproteobacteria/chemistry/genetics/metabolism ; Amino Acid Sequence ; Bacterial Proteins/*chemistry/genetics/*metabolism ; Cations ; Hydrophobic and Hydrophilic Interactions ; Mass Spectrometry ; Molecular Sequence Data ; Nuclear Magnetic Resonance, Biomolecular ; Protein Binding ; Protein Structure, Secondary ; Sequence Alignment ; Sequence Homology, Amino Acid ; Zinc/*chemistry/*metabolism ; *Zinc Fingers ; }, abstract = {The recent characterization of the prokaryotic Cys(2)His(2) zinc-finger domain, identified in Ros protein from Agrobacterium tumefaciens, has demonstrated that, although possessing a similar zinc coordination sphere, this domain is structurally very different from its eukaryotic counterpart. A search in the databases has identified approximately 300 homologues with a high sequence identity to the Ros protein, including the amino acids that form the extensive hydrophobic core in Ros. Surprisingly, the Cys(2)His(2) zinc coordination sphere is generally poorly conserved in the Ros homologues, raising the question of whether the zinc ion is always preserved in these proteins. Here, we present a functional and structural study of a point mutant of Ros protein, Ros(56-142)C82D, in which the second coordinating cysteine is replaced by an aspartate, 5 previously-uncharacterized representative Ros homologues from Mesorhizobium loti, and 2 mutants of the homologues. Our results indicate that the prokaryotic zinc-finger domain, which in Ros protein tetrahedrally coordinates Zn(II) through the typical Cys(2)His(2) coordination, in Ros homologues can either exploit a CysAspHis(2) coordination sphere, previously never described in DNA binding zinc finger domains to our knowledge, or lose the metal, while still preserving the DNA-binding activity. We demonstrate that this class of prokaryotic zinc-finger domains is structurally very adaptable, and surprisingly single mutations can transform a zinc-binding domain into a nonzinc-binding domain and vice versa, without affecting the DNA-binding ability. In light of our findings an evolutionary link between the prokaryotic and eukaryotic zinc-finger domains, based on bacteria-to-eukaryota horizontal gene transfer, is discussed.}, }
@article {pmid19368726, year = {2009}, author = {Whitaker, JW and McConkey, GA and Westhead, DR}, title = {The transferome of metabolic genes explored: analysis of the horizontal transfer of enzyme encoding genes in unicellular eukaryotes.}, journal = {Genome biology}, volume = {10}, number = {4}, pages = {R36}, pmid = {19368726}, issn = {1474-760X}, support = {BB/C52101X/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bacteria/enzymology/genetics ; Bacterial Proteins/genetics/metabolism ; Enzymes/genetics/*metabolism ; Eukaryotic Cells/*metabolism ; *Gene Transfer, Horizontal ; Leishmania/genetics/metabolism ; Lipopolysaccharides/metabolism ; Metabolic Networks and Pathways ; Phytophthora/genetics/metabolism ; Plasmodium/genetics/metabolism ; Saccharomyces/genetics/metabolism ; Xylose/metabolism ; }, abstract = {BACKGROUND: Metabolic networks are responsible for many essential cellular processes, and exhibit a high level of evolutionary conservation from bacteria to eukaryotes. If genes encoding metabolic enzymes are horizontally transferred and are advantageous, they are likely to become fixed. Horizontal gene transfer (HGT) has played a key role in prokaryotic evolution and its importance in eukaryotes is increasingly evident. High levels of endosymbiotic gene transfer (EGT) accompanied the establishment of plastids and mitochondria, and more recent events have allowed further acquisition of bacterial genes. Here, we present the first comprehensive multi-species analysis of E/HGT of genes encoding metabolic enzymes from bacteria to unicellular eukaryotes.<br><br>RESULTS: The phylogenetic trees of 2,257 metabolic enzymes were used to make E/HGT assertions in ten groups of unicellular eukaryotes, revealing the sources and metabolic processes of the transferred genes. Analyses revealed a preference for enzymes encoded by genes gained through horizontal and endosymbiotic transfers to be connected in the metabolic network. Enrichment in particular functional classes was particularly revealing: alongside plastid related processes and carbohydrate metabolism, this highlighted a number of pathways in eukaryotic parasites that are rich in enzymes encoded by transferred genes, and potentially key to pathogenicity. The plant parasites Phytophthora were discovered to have a potential pathway for lipopolysaccharide biosynthesis of E/HGT origin not seen before in eukaryotes outside the Plantae.<br><br>CONCLUSIONS: The number of enzymes encoded by genes gained through E/HGT has been established, providing insight into functional gain during the evolution of unicellular eukaryotes. In eukaryotic parasites, genes encoding enzymes that have been gained through horizontal transfer may be attractive drug targets if they are part of processes not present in the host, or are significantly diverged from equivalent host enzymes.}, }
@article {pmid19361881, year = {2009}, author = {Dieterich, C and Sommer, RJ}, title = {How to become a parasite - lessons from the genomes of nematodes.}, journal = {Trends in genetics : TIG}, volume = {25}, number = {5}, pages = {203-209}, doi = {10.1016/j.tig.2009.03.006}, pmid = {19361881}, issn = {0168-9525}, mesh = {Adaptation, Physiological/genetics ; Animals ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Helminth ; Genomics/*methods ; Helminthiasis, Animal/parasitology ; Humans ; Life Cycle Stages/genetics ; Nematoda/classification/*genetics/growth &amp; development ; Nematode Infections/parasitology ; Phylogeny ; Plant Diseases/parasitology ; }, abstract = {The phylum Nematoda is biologically diverse; it includes parasites of plants and animals in addition to free-living taxa. To date, the genomes of six nematodes have been sequenced. Comparative analyses of these ecologically diverse nematodes are beginning to reveal the mechanisms by which parasites arise and how they evolve. Here, we discuss some emerging principles for the mechanisms and evolution of parasitism. First, horizontal gene transfer represents a common theme in nematode parasites. Second, the human parasite Brugia malayi lost otherwise essential genes most probably owing to the mutualistic relationship with a bacterial endosymbiont. Finally, some parasitic features evolved under free-living conditions. A recent study revealed a conserved endocrine mechanism controlling the formation of dauer and infective larvae in nematodes.}, }
@article {pmid19361343, year = {2009}, author = {Ding, F and Tang, P and Hsu, MH and Cui, P and Hu, S and Yu, J and Chiu, CH}, title = {Genome evolution driven by host adaptations results in a more virulent and antimicrobial-resistant Streptococcus pneumoniae serotype 14.}, journal = {BMC genomics}, volume = {10}, number = {}, pages = {158}, pmid = {19361343}, issn = {1471-2164}, mesh = {Adaptation, Physiological/genetics ; DNA Transposable Elements ; Drug Resistance, Bacterial/*genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; *Genome, Bacterial ; Penicillin-Binding Proteins/genetics ; Streptococcus pneumoniae/classification/drug effects/*genetics/pathogenicity ; Virulence ; }, abstract = {BACKGROUND: Streptococcus pneumoniae serotype 14 is one of the most common pneumococcal serotypes that cause invasive pneumococcal diseases worldwide. Serotype 14 often expresses resistance to a variety of antimicrobial agents, resulting in difficulties in treatment. To gain insight into the evolution of virulence and antimicrobial resistance traits in S. pneumoniae from the genome level, we sequenced the entire genome of a serotype 14 isolate (CGSP14), and carried out comprehensive comparison with other pneumococcal genomes. Multiple serotype 14 clinical isolates were also genotyped by multilocus sequence typing (MLST).<br><br>RESULTS: Comparative genomic analysis revealed that the CGSP14 acquired a number of new genes by horizontal gene transfer (HGT), most of which were associated with virulence and antimicrobial resistance and clustered in mobile genetic elements. The most remarkable feature is the acquisition of two conjugative transposons and one resistance island encoding eight resistance genes. Results of MLST suggested that the major driving force for the genome evolution is the environmental drug pressure.<br><br>CONCLUSION: The genome sequence of S. pneumoniae serotype 14 shows a bacterium with rapid adaptations to its lifecycle in human community. These include a versatile genome content, with a wide range of mobile elements, and chromosomal rearrangement; the latter re-balanced the genome after events of HGT.}, }
@article {pmid19361327, year = {2009}, author = {Ilatovskiy, A and Petukhov, M}, title = {Genome-wide search for local DNA segments with anomalous GC-content.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {16}, number = {4}, pages = {555-564}, doi = {10.1089/cmb.2008.0159}, pmid = {19361327}, issn = {1557-8666}, mesh = {Base Composition/*genetics ; DNA, Bacterial/*genetics ; Escherichia coli/*genetics ; Genome, Bacterial/*genetics ; Statistics, Nonparametric ; }, abstract = {An anomalous (i.e., significantly different from genome-average) GC-content is often used as one of the markers to reveal the events of horizontal gene transfer (HGT). Unfortunately, results obtained by the traditional fixed-length window analysis strongly depend on an arbitrary selection of DNA window length. Here we present a new method for genome-wide statistical analysis of GC-content without that drawback. The method is based on a set of nonparametric statistical tests and is capable of providing reliable estimations of both a local and global GC-content, and thus can identify small local areas (as short as 30 bp) with anomalous GC-content in a bacterial genome. The tests, applied to a well-studied bacterial genome of Escherichia coli K-12, show that approximately 21% of the genome belongs to the anomalous GC-content areas. Among top 23 anomalous GC-content areas, seven correspond to the annotated prophages, four to Rhs elements, and two to IS elements. A remaining 10 areas contain putative horizontally transferred DNA and genes with still unknown functions. Software is available at http://mml.spbstu.ru/gcstat.}, }
@article {pmid19359572, year = {2009}, author = {Archibald, JM}, title = {Genomics. Green evolution, green revolution.}, journal = {Science (New York, N.Y.)}, volume = {324}, number = {5924}, pages = {191-192}, doi = {10.1126/science.1172972}, pmid = {19359572}, issn = {1095-9203}, mesh = {*Biological Evolution ; Chlorophyta/classification/cytology/*genetics/physiology ; Gene Transfer, Horizontal ; Genes ; *Genome ; Introns ; Meiosis/genetics ; Photosynthesis/*genetics ; Plants/*genetics ; Sequence Analysis, DNA ; Transcription Factors/genetics ; }, }
@article {pmid19357771, year = {2009}, author = {Ou, HY and He, X and Shao, Y and Tai, C and Rajakumar, K and Deng, Z}, title = {dndDB: a database focused on phosphorothioation of the DNA backbone.}, journal = {PloS one}, volume = {4}, number = {4}, pages = {e5132}, pmid = {19357771}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Bacteria/classification/*genetics ; Base Sequence ; Computational Biology ; *DNA/chemistry/genetics ; *Databases, Genetic ; Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; *Genomic Islands ; Humans ; Internet ; Molecular Sequence Data ; *Multigene Family ; Phosphates/*chemistry ; Phosphorothioate Oligonucleotides ; Phylogeny ; Sequence Alignment ; Software ; User-Computer Interface ; }, abstract = {BACKGROUND: The Dnd DNA degradation phenotype was first observed during electrophoresis of genomic DNA from Streptomyces lividans more than 20 years ago. It was subsequently shown to be governed by the five-gene dnd cluster. Similar gene clusters have now been found to be widespread among many other distantly related bacteria. Recently the dnd cluster was shown to mediate the incorporation of sulphur into the DNA backbone via a sequence-selective, stereo-specific phosphorothioate modification in Escherichia coli B7A. Intriguingly, to date all identified dnd clusters lie within mobile genetic elements, the vast majority in laterally transferred genomic islands.<br><br>METHODOLOGY: We organized available data from experimental and bioinformatics analyses about the DNA phosphorothioation phenomenon and associated documentation as a dndDB database. It contains the following detailed information: (i) Dnd phenotype; (ii) dnd gene clusters; (iii) genomic islands harbouring dnd genes; (iv) Dnd proteins and conserved domains. As of 25 December 2008, dndDB contained data corresponding to 24 bacterial species exhibiting the Dnd phenotype reported in the scientific literature. In addition, via in silico analysis, dndDB identified 26 syntenic dnd clusters from 25 species of Eubacteria and Archaea, 25 dnd-bearing genomic islands and one dnd plasmid containing 114 dnd genes. A further 397 other genes coding for proteins with varying levels of similarity to Dnd proteins were also included in dndDB. A broad range of similarity search, sequence alignment and phylogenetic tools are readily accessible to allow for to individualized directions of research focused on dnd genes.<br><br>CONCLUSION: dndDB can facilitate efficient investigation of a wide range of aspects relating to dnd DNA modification and other island-encoded functions in host organisms. dndDB version 1.0 is freely available at http://mml.sjtu.edu.cn/dndDB/.}, }
@article {pmid19351897, year = {2009}, author = {Wolf, YI and Novichkov, PS and Karev, GP and Koonin, EV and Lipman, DJ}, title = {The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {18}, pages = {7273-7280}, pmid = {19351897}, issn = {1091-6490}, mesh = {Animals ; Eukaryotic Cells/metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes ; Genome ; Humans ; *Models, Genetic ; Proteins/*genetics ; }, abstract = {The evolutionary rates of protein-coding genes in an organism span, approximately, 3 orders of magnitude and show a universal, approximately log-normal distribution in a broad variety of species from prokaryotes to mammals. This universal distribution implies a steady-state process, with identical distributions of evolutionary rates among genes that are gained and genes that are lost. A mathematical model of such process is developed under the single assumption of the constancy of the distributions of the propensities for gene loss (PGL). This model predicts that genes of different ages, that is, genes with homologs detectable at different phylogenetic depths, substantially differ in those variables that correlate with PGL. We computationally partition protein-coding genes from humans, flies, and Aspergillus fungus into age classes, and show that genes of different ages retain the universal log-normal distribution of evolutionary rates, with a shift toward higher rates in "younger" classes but also with a substantial overlap. The only exception involves human primate-specific genes that show a heavy tail of rapidly evolving genes, probably owing to gene annotation artifacts. As predicted, the gene age classes differ in characteristics correlated with PGL. Compared with "young" genes (e.g., mammal-specific human ones), "old" genes (e.g., eukaryote-specific), on average, are longer, are expressed at a higher level, possess a higher intron density, evolve slower on the short time scale, and are subject to stronger purifying selection. Thus, genome evolution fits a simple model with approximately uniform rates of gene gain and loss, without major bursts of genomic innovation.}, }
@article {pmid19346311, year = {2009}, author = {Wattam, AR and Williams, KP and Snyder, EE and Almeida, NF and Shukla, M and Dickerman, AW and Crasta, OR and Kenyon, R and Lu, J and Shallom, JM and Yoo, H and Ficht, TA and Tsolis, RM and Munk, C and Tapia, R and Han, CS and Detter, JC and Bruce, D and Brettin, TS and Sobral, BW and Boyle, SM and Setubal, JC}, title = {Analysis of ten Brucella genomes reveals evidence for horizontal gene transfer despite a preferred intracellular lifestyle.}, journal = {Journal of bacteriology}, volume = {191}, number = {11}, pages = {3569-3579}, pmid = {19346311}, issn = {1098-5530}, support = {HHSN266200400035C//PHS HHS/United States ; }, mesh = {Adipates/metabolism ; Brucella/classification/*genetics/physiology ; Chromosomes, Bacterial/genetics ; Computational Biology ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial/*genetics ; Models, Genetic ; Phylogeny ; Pseudogenes/genetics ; Signal Transduction/genetics ; }, abstract = {The facultative intracellular bacterial pathogen Brucella infects a wide range of warm-blooded land and marine vertebrates and causes brucellosis. Currently, there are nine recognized Brucella species based on host preferences and phenotypic differences. The availability of 10 different genomes consisting of two chromosomes and representing six of the species allowed for a detailed comparison among themselves and relatives in the order Rhizobiales. Phylogenomic analysis of ortholog families shows limited divergence but distinct radiations, producing four clades as follows: Brucella abortus-Brucella melitensis, Brucella suis-Brucella canis, Brucella ovis, and Brucella ceti. In addition, Brucella phylogeny does not appear to reflect the phylogeny of Brucella species' preferred hosts. About 4.6% of protein-coding genes seem to be pseudogenes, which is a relatively large fraction. Only B. suis 1330 appears to have an intact beta-ketoadipate pathway, responsible for utilization of plant-derived compounds. In contrast, this pathway in the other species is highly pseudogenized and consistent with the "domino theory" of gene death. There are distinct shared anomalous regions (SARs) found in both chromosomes as the result of horizontal gene transfer unique to Brucella and not shared with its closest relative Ochrobactrum, a soil bacterium, suggesting their acquisition occurred in spite of a predominantly intracellular lifestyle. In particular, SAR 2-5 appears to have been acquired by Brucella after it became intracellular. The SARs contain many genes, including those involved in O-polysaccharide synthesis and type IV secretion, which if mutated or absent significantly affect the ability of Brucella to survive intracellularly in the infected host.}, }
@article {pmid19346162, year = {2009}, author = {Kamikawa, R and Masuda, I and Demura, M and Oyama, K and Yoshimatsu, S and Kawachi, M and Sako, Y}, title = {Mitochondrial group II introns in the raphidophycean flagellate Chattonella spp. suggest a diatom-to-Chattonella lateral group II intron transfer.}, journal = {Protist}, volume = {160}, number = {3}, pages = {364-375}, doi = {10.1016/j.protis.2009.02.003}, pmid = {19346162}, issn = {1618-0941}, mesh = {Animals ; DNA, Mitochondrial/chemistry/*genetics ; DNA, Protozoan/chemistry/genetics ; Diatoms/*genetics ; Electron Transport Complex IV/*genetics ; Eukaryota/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Introns ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Protein Structure, Tertiary ; Protozoan Proteins/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {In the cytochrome c oxidase subunit I (cox1) gene of four raphidophycean flagellates Chattonella antiqua, C. marina, C. ovata, and C. minima we found two group II introns described here as Chattonella cox1-i1 and Chattonella cox1-i2 encoding an open reading frame (ORF) comprised of three domains: reverse transcriptase (RT), RNA maturase (Ma) and zinc finger (H-N-H) endonuclease domains. The secondary structures show both Chattonella cox1-i1 and Chattonella cox1-i2 belong to group IIA1, albeit the former possesses a group IIB-like secondary structural character in the epsilon' region of arm I. Our phylogenetic analysis inferred from RT domain sequences of the intronic ORF, comparison of the insertion sites, and the secondary structures of the introns suggests that Chattonella cox1-i1 likely shares an evolutionary origin with the group II introns inserted in cox1 genes of five phylogenetically diverged eukaryotes. In contrast, Chattonella cox1-i2 was suggested to bear a close evolutionary affinity to the group II introns found in diatom cox1 genes. The RT domain-based phylogeny shows a tree topology in which Chattonella cox1-i2 is nested in the diatom sequences suggesting that a diatom-to-Chattonella intron transfer has taken place. Finally, we found no intron in cox1 genes from deeper-branching raphidophyceans. Based on parsimonious discussion, Chattonella cox1-i1 and Chattonella cox1-i2 have invaded into the cox1 gene of an ancestral Chattonella cell after diverging from C. subsalsa.}, }
@article {pmid19345038, year = {2009}, author = {Billal, DS and Hotomi, M and Yan, SS and Fedorko, DP and Shimada, J and Fujihara, K and Yamanaka, N}, title = {Loss of erythromycin resistance genes from strains of Streptococcus pyogenes that have developed resistance to levofloxacin.}, journal = {Diagnostic microbiology and infectious disease}, volume = {64}, number = {2}, pages = {225-228}, doi = {10.1016/j.diagmicrobio.2009.01.034}, pmid = {19345038}, issn = {1879-0070}, mesh = {Anti-Bacterial Agents/*pharmacology ; Conjugation, Genetic ; *Drug Resistance, Bacterial ; Erythromycin/*pharmacology ; *Gene Deletion ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genotype ; Humans ; *Levofloxacin ; Microbial Sensitivity Tests ; Ofloxacin/*pharmacology ; Streptococcus pyogenes/drug effects/*genetics ; }, abstract = {In the past 2 to 3 decades, erythromycin resistance in Streptococcus pyogenes has been decreasing, whereas fluoroquinolone resistance (or reduction in its susceptibility) has been reported often. Although a shift of M-type prevalence and decreased pressure from macrolides have been suggested for the decrease in erythromycin resistance, we hypothesized that this might also be a result of increased antimicrobial pressure from fluoroquinolone use. Levofloxacin resistance for 4 erythromycin-resistant parent strains was induced in vitro. Their mutants became highly resistant to the fluoroquinolones but lost their erythromycin resistance trait. Erythromycin resistance was fully restored by transconjugation with respective parent strains with either mefA- or ermTR-mediated mechanisms.}, }
@article {pmid19341406, year = {2009}, author = {Zhao, Z and Zhu, Y and Erhardt, M and Ruan, Y and Shen, WH}, title = {A non-canonical transferred DNA insertion at the BRI1 locus in Arabidopsis thaliana.}, journal = {Journal of integrative plant biology}, volume = {51}, number = {4}, pages = {367-373}, doi = {10.1111/j.1744-7909.2009.00821.x}, pmid = {19341406}, issn = {1744-7909}, mesh = {Arabidopsis/*genetics ; Arabidopsis Proteins/*genetics ; DNA, Bacterial/*genetics ; Gene Deletion ; Gene Expression Regulation, Plant ; Genetic Loci/*genetics ; Genome, Plant/genetics ; Mutagenesis, Insertional/*genetics ; Mutant Proteins/genetics/isolation &amp; purification ; Mutation/genetics ; Phenotype ; Protein Kinases/*genetics ; }, abstract = {Agrobacterium-mediated transformation is widely used in transgenic plant engineering and has been proven to be a powerful tool for insertional mutagenesis of the plant genome. The transferred DNA (T-DNA) from Agrobacterium is integrated into the plant genome through illegitimate recombination between the T-DNA and the plant DNA. Contrasting to the canonical insertion, here we report on a locus showing a complex mutation associated with T-DNA insertion at the BRI1 gene in Arabidopsis thaliana. We obtained a mutant line, named salade for its phenotype of dwarf stature and proliferating rosette. Molecular characterization of this mutant revealed that in addition to T-DNA a non-T-DNA-localized transposon from bacteria was inserted in the Arabidopsis genome and that a region of more than 11.5 kb of the Arabidopsis genome was deleted at the insertion site. The deleted region contains the brassinosteroid receptor gene BRI1 and the transcription factor gene WRKY13. Our finding reveals non-canonical T-DNA insertion, implicating horizontal gene transfer and cautioning the use of T-DNA as mutagen in transgenic research.}, }
@article {pmid19340086, year = {2009}, author = {Haft, RJ and Mittler, JE and Traxler, B}, title = {Competition favours reduced cost of plasmids to host bacteria.}, journal = {The ISME journal}, volume = {3}, number = {7}, pages = {761-769}, doi = {10.1038/ismej.2009.22}, pmid = {19340086}, issn = {1751-7370}, support = {T32 GM07270/GM/NIGMS NIH HHS/United States ; }, mesh = {*Bacterial Physiological Phenomena ; Coculture Techniques ; Computer Simulation ; Escherichia coli/*genetics/*growth &amp; development ; Escherichia coli Proteins/genetics ; Gene Deletion ; *Gene Transfer, Horizontal ; *Plasmids ; }, abstract = {Conjugative plasmids of Gram-negative bacteria have both vertical and horizontal modes of transmission: they are segregated to daughter cells during division, and transferred between hosts by plasmid-encoded conjugative machinery. Despite maintaining horizontal mobility, many plasmids carry fertility inhibition (fin) systems that repress their own conjugative transfer. To assess the ecological basis of self-transfer repression, we compared the invasion of bacterial populations by fin(+) and fin(-) variants of the plasmid R1 using a computational model and co-culture competitions. We observed that the fin(+) variant had a modest cost to the host (measured by reduction in growth rate), while the fin(-) variant incurred a larger cost. In simulations and empirical competitions the fin(-) plasmid invaded cultures quickly, but was subsequently displaced by the fin(+) plasmid. This indicated a competitive advantage to reducing horizontal transmission and allowing increased host replication. Computational simulations predicted that the advantage associated with reduced cost to the host would be maintained over a wide range of environmental conditions and plasmid costs. We infer that vertical transmission in concert with competitive exclusion favour decreased horizontal mobility of plasmids. Similar dynamics may exert evolutionary pressure on parasites, such as temperate bacteriophages and vertically transmitted animal viruses, to limit their rates of horizontal transfer.}, }
@article {pmid19333776, year = {2009}, author = {Rizzotti, L and La Gioia, F and Dellaglio, F and Torriani, S}, title = {Molecular diversity and transferability of the tetracycline resistance gene tet(M), carried on Tn916-1545 family transposons, in enterococci from a total food chain.}, journal = {Antonie van Leeuwenhoek}, volume = {96}, number = {1}, pages = {43-52}, doi = {10.1007/s10482-009-9334-7}, pmid = {19333776}, issn = {1572-9699}, mesh = {Animals ; Bacterial Proteins/*genetics ; Cluster Analysis ; *DNA Transposable Elements ; DNA, Bacterial/chemistry/genetics ; Enterococcus/*drug effects/*genetics/isolation &amp; purification ; Enterococcus faecalis/drug effects/genetics/isolation &amp; purification ; Enterococcus faecium/drug effects/genetics/isolation &amp; purification ; Feces/microbiology ; *Gene Transfer, Horizontal ; Meat/*microbiology ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology ; Swine/*microbiology ; *Tetracycline Resistance ; }, abstract = {In the present study, 20 enterococci belonging to the species Enterococcus faecalis (12 strains), Enterococcus faecium (4), Enterococcus durans (2), Enterococcus hirae (1) and Enterococcus mundtii (1) and originating from a total production chain of swine meat commodities were analysed to investigate the diversity of their tetracycline resistance gene tet(M). PCR-RFLP and sequence analysis showed that the tet(M) gene of most strains can be correlated with the Tn916 transposon. Conversely, tet(M) of six E. faecalis and the E. hirae strain, all isolated from pig faecal samples, may be associated with previously undescribed members of the Tn916-1545 transposon family. In vitro filter conjugation trials showed the ability of 50% of the enterococcal strains, including E. mundtii, to transfer the tet(M) gene (and the associated Tn916 and new transposons) to E. faecalis or Listeria innocua recipient strains. tet(M) gene transfer to L. innocua recipient was also directly observed in meat food products. Collectively, these sequence and conjugation data indicate that various transposons can be responsible of the spread of tetracycline resistance in enterococci and validate the opinion that Enterococcus species are important sources of antibiotic resistance genes for potentially pathogenic bacteria occurring in the food chain.}, }
@article {pmid19333425, year = {2009}, author = {Al-Karablieh, N and Weingart, H and Ullrich, MS}, title = {Genetic exchange of multidrug efflux pumps among two enterobacterial species with distinctive ecological Niches.}, journal = {International journal of molecular sciences}, volume = {10}, number = {2}, pages = {629-645}, pmid = {19333425}, issn = {1422-0067}, mesh = {Bacterial Outer Membrane Proteins/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; *Ecosystem ; Erwinia amylovora/*genetics/pathogenicity ; Escherichia coli/genetics ; Escherichia coli Proteins/genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Genes, MDR/*genetics ; Genetic Complementation Test ; Lipoproteins/genetics ; Malus/microbiology ; Membrane Transport Proteins/genetics ; Multidrug Resistance-Associated Proteins/genetics ; Mutation ; }, abstract = {AcrAB-TolC is the major multidrug efflux system in Enterobacteriaceae recognizing structurally unrelated molecules including antibiotics, dyes, and detergents. Additionally, in Escherichia coli it mediates resistance to bile salts. In the plant pathogen Erwinia amylovora AcrAB-TolC is required for virulence and phytoalexin resistance. Exchange analysis of AcrAB-TolC was conducted by complementing mutants of both species defective in acrB or tolC with alleles from either species. The acrB and tolC mutants exhibited increased susceptibility profiles for 24 different antibiotics. All mutants were complemented with acrAB or tolC, respectively, regardless of the taxonomic origin of the alleles. Importantly, complementation of E. amylovora mutants with respective E. coli genes restored virulence on apple plants. It was concluded that AcrAB and TolC of both species could interact and that these interactions did not yield in altered functions despite the divergent ecological niches, to which E. coli and E. amylovora have adopted.}, }
@article {pmid19331756, year = {2009}, author = {Cabello, FC}, title = {Aquaculture and florfenicol resistance in Salmonella enterica serovar Typhimurium DT104.}, journal = {Emerging infectious diseases}, volume = {15}, number = {4}, pages = {623; author reply 623-4}, pmid = {19331756}, issn = {1080-6059}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Bacterial/genetics ; *Fisheries ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; R Factors/genetics ; Salmonella typhimurium/*drug effects/genetics ; Thiamphenicol/*analogs &amp; derivatives/pharmacology ; Vibrio/drug effects/genetics ; }, }
@article {pmid19331657, year = {2009}, author = {Mihali, TK and Kellmann, R and Neilan, BA}, title = {Characterisation of the paralytic shellfish toxin biosynthesis gene clusters in Anabaena circinalis AWQC131C and Aphanizomenon sp. NH-5.}, journal = {BMC biochemistry}, volume = {10}, number = {}, pages = {8}, pmid = {19331657}, issn = {1471-2091}, mesh = {Anabaena/classification/*genetics/metabolism ; Aphanizomenon/classification/*genetics/metabolism ; Australia ; Base Sequence ; Biosynthetic Pathways ; Cloning, Molecular ; DNA, Bacterial/chemistry/genetics ; Genes, Bacterial/genetics ; Inverted Repeat Sequences ; Molecular Sequence Data ; Molecular Structure ; *Multigene Family ; Neurotoxins/*biosynthesis/chemistry ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Saxitoxin/*analogs &amp; derivatives/*biosynthesis/chemistry ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Saxitoxin and its analogues collectively known as the paralytic shellfish toxins (PSTs) are neurotoxic alkaloids and are the cause of the syndrome named paralytic shellfish poisoning. PSTs are produced by a unique biosynthetic pathway, which involves reactions that are rare in microbial metabolic pathways. Nevertheless, distantly related organisms such as dinoflagellates and cyanobacteria appear to produce these toxins using the same pathway. Hypothesised explanations for such an unusual phylogenetic distribution of this shared uncommon metabolic pathway, include a polyphyletic origin, an involvement of symbiotic bacteria, and horizontal gene transfer.<br><br>RESULTS: We describe the identification, annotation and bioinformatic characterisation of the putative paralytic shellfish toxin biosynthesis clusters in an Australian isolate of Anabaena circinalis and an American isolate of Aphanizomenon sp., both members of the Nostocales. These putative PST gene clusters span approximately 28 kb and contain genes coding for the biosynthesis and export of the toxin. A putative insertion/excision site in the Australian Anabaena circinalis AWQC131C was identified, and the organization and evolution of the gene clusters are discussed. A biosynthetic pathway leading to the formation of saxitoxin and its analogues in these organisms is proposed.<br><br>CONCLUSION: The PST biosynthesis gene cluster presents a mosaic structure, whereby genes have apparently transposed in segments of varying size, resulting in different gene arrangements in all three sxt clusters sequenced so far. The gene cluster organizational structure and sequence similarity seems to reflect the phylogeny of the producer organisms, indicating that the gene clusters have an ancient origin, or that their lateral transfer was also an ancient event. The knowledge we gain from the characterisation of the PST biosynthesis gene clusters, including the identity and sequence of the genes involved in the biosynthesis, may also afford the identification of these gene clusters in dinoflagellates, the cause of human mortalities and significant financial loss to the tourism and shellfish industries.}, }
@article {pmid19329660, year = {2009}, author = {Pontiroli, A and Rizzi, A and Simonet, P and Daffonchio, D and Vogel, TM and Monier, JM}, title = {Visual evidence of horizontal gene transfer between plants and bacteria in the phytosphere of transplastomic tobacco.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {10}, pages = {3314-3322}, pmid = {19329660}, issn = {1098-5336}, mesh = {Acinetobacter/*genetics/*growth &amp; development ; Artificial Gene Fusion ; DNA, Plant/genetics/*metabolism ; *Gene Transfer, Horizontal ; Genes, Reporter ; Green Fluorescent Proteins/genetics/metabolism ; Plants, Genetically Modified ; Recombination, Genetic ; Nicotiana/*genetics/*microbiology ; }, abstract = {Plant surfaces, colonized by numerous and diverse bacterial species, are often considered hot spots for horizontal gene transfer (HGT) between plants and bacteria. Plant DNA released during the degradation of plant tissues can persist and remain biologically active for significant periods of time, suggesting that soil or plant-associated bacteria could be in direct contact with plant DNA. In addition, nutrients released during the decaying process may provide a copiotrophic environment conducive for opportunistic microbial growth. Using Acinetobacter baylyi strain BD413 and transplastomic tobacco plants harboring the aadA gene as models, the objective of this study was to determine whether specific niches could be shown to foster bacterial growth on intact or decaying plant tissues, to develop a competence state, and to possibly acquire exogenous plant DNA by natural transformation. Visualization of HGT in situ was performed using A. baylyi strain BD413(rbcL-DeltaPaadA::gfp) carrying a promoterless aadA::gfp fusion. Both antibiotic resistance and green fluorescence phenotypes were restored in recombinant bacterial cells after homologous recombination with transgenic plant DNA. Opportunistic growth occurred on decaying plant tissues, and a significant proportion of the bacteria developed a competence state. Quantification of transformants clearly supported the idea that the phytosphere constitutes a hot spot for HGT between plants and bacteria. The nondisruptive approach used to visualize transformants in situ provides new insights into environmental factors influencing HGT for plant tissues.}, }
@article {pmid19329640, year = {2009}, author = {Goerke, C and Pantucek, R and Holtfreter, S and Schulte, B and Zink, M and Grumann, D and Bröker, BM and Doskar, J and Wolz, C}, title = {Diversity of prophages in dominant Staphylococcus aureus clonal lineages.}, journal = {Journal of bacteriology}, volume = {191}, number = {11}, pages = {3462-3468}, pmid = {19329640}, issn = {1098-5530}, support = {HHSN272200700055C/AI/NIAID NIH HHS/United States ; HHSN2722007 00055C//PHS HHS/United States ; }, mesh = {Genome, Bacterial/genetics ; Genotype ; Integrases/genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Prophages/*classification/*genetics ; Sequence Analysis, DNA ; Staphylococcus Phages/*classification/*genetics ; Staphylococcus aureus/*genetics/*virology ; }, abstract = {Temperate bacteriophages play an important role in the pathogenicity of Staphylococcus aureus, for instance, by mediating the horizontal gene transfer of virulence factors. Here we established a classification scheme for staphylococcal prophages of the major Siphoviridae family based on integrase gene polymorphism. Seventy-one published genome sequences of staphylococcal phages were clustered into distinct integrase groups which were related to the chromosomal integration site and to the encoded virulence gene content. Analysis of three marker modules (lysogeny, tail, and lysis) for phage functional units revealed that these phages exhibit different degrees of genome mosaicism. The prevalence of prophages in a representative S. aureus strain collection consisting of 386 isolates of diverse origin was determined. By linking the phage content to dominant S. aureus clonal complexes we could show that the distribution of bacteriophages varied remarkably between lineages, indicating restriction-based barriers. A comparison of colonizing and invasive S. aureus strain populations revealed that hlb-converting phages were significantly more frequent in colonizing strains.}, }
@article {pmid19329507, year = {2009}, author = {Freitas, AR and Novais, C and Ruiz-Garbajosa, P and Coque, TM and Peixe, L}, title = {Clonal expansion within clonal complex 2 and spread of vancomycin-resistant plasmids among different genetic lineages of Enterococcus faecalis from Portugal.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {63}, number = {6}, pages = {1104-1111}, doi = {10.1093/jac/dkp103}, pmid = {19329507}, issn = {1460-2091}, mesh = {Animals ; Bacterial Typing Techniques ; Cluster Analysis ; DNA Fingerprinting ; DNA Transposable Elements ; DNA, Bacterial/genetics ; Electrophoresis, Gel, Pulsed-Field ; Enterococcus faecalis/classification/*drug effects/*genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; Genotype ; Gram-Positive Bacterial Infections/*microbiology ; Humans ; *Plasmids ; Polymorphism, Restriction Fragment Length ; Portugal ; *Vancomycin Resistance ; Virulence Factors/genetics ; }, abstract = {OBJECTIVES: The aim of this study was to assess the diversity of Enterococcus faecalis populations recovered in different regions of Portugal during the last decade (1996-2007) and to analyse their genetic elements associated with vancomycin resistance.<br><br>METHODS: Forty E. faecalis isolates (22 vancomycin-susceptible and 18 vancomycin-resistant) representing disseminated and/or multiresistant strains from different sources (humans, animals and the environment) were characterized by PFGE and multilocus sequence typing. Genes encoding putative virulence markers and the backbone of Tn1546 were investigated by PCR. Plasmid analysis included determination of size, content (S1 hybridization) and comparison of restriction fragment length polymorphism patterns.<br><br>RESULTS: The 40 E. faecalis isolates (22 PFGE types) mostly clustered within the worldwide-spread clonal complexes (CCs) CC2 (13 ST6 mostly corresponding to an epidemic strain, where ST stands for sequence type), CC21 (3 ST21, 1 ST22 and 1 ST224) and ST16 (n = 7), but also comprised ST159, ST35, ST19, ST26, ST30, ST41, ST55, ST59, ST117, ST160 and ST200. CC2 and CC21 were isolated from both hospital and community settings. Similar Tn1546-like elements encoding VanA were found on related plasmids within strains belonging to different clonal lineages and recovered in distinct hospitals over several years.<br><br>CONCLUSIONS: The predominance of E. faecalis CC2 is mainly due to the dissemination of a particular clone persistently recovered for 11 years. The presence in the community of specific strains belonging to major clonal lineages highlights the role of community-associated hosts as possible reservoirs of putative human pathogenic enterococci. Both clonal expansion and dissemination of epidemic conjugative VanA plasmids seem to join forces in the establishment of pathogenic E. faecalis strains.}, }
@article {pmid19326852, year = {2009}, author = {Provorov, NA}, title = {[Plant-microbe symbioses as an evolutionary continuum].}, journal = {Zhurnal obshchei biologii}, volume = {70}, number = {1}, pages = {10-34}, pmid = {19326852}, issn = {0044-4596}, mesh = {Bacteria ; *Bacterial Physiological Phenomena ; *Biological Evolution ; Fungi/*physiology ; Mycorrhizae/*physiology ; *Plant Physiological Phenomena ; *Plants ; Symbiosis/*physiology ; }, abstract = {In spite of enormous taxonomic, structural and functional diversity of plant-microbe interactions, they are characterized by a historical succession which allows us to consider different forms of symbioses as the components of an evolutionary continuum. Their ancestral form is represented by arbuscular mycorrhiza (AM) which originated at the outset of terrestrial flora evolution and constituted a key factor for the land colonization by plants. In the course of AM evolution the plant acquired a basal set of genes for regulating the performance of microbes which colonize the root tissues. Later, these genes were repeatedly reorganized to meet the involvement of novel mutualistic symbionts (N2-fixing bacteria, ectomycorrhizal fungi, endophytes and epiphytes) and pathogens into the symbiotic interactions. Form the microbial side, the evolutionary succession of mutualism and antagonism is restricted to the defensive symbioses formed by plants with the ergot fungi, Clavibacter, Bacillus and Pseudomonas bacteria. Involvement of the similar systems for symbiotic interactions may be related to convergent evolution in the distant microorganisms (adaptation to the conservative host defense/regulatory factors), to molecular mimicry (imitation of the mechanisms of interaction used by the more ancient symbionts) or to the horizontal gene transfer. The hypotheses of the successive substitution of symbionts is suggested to address the relationships between AM and N2-fixing nodular symbioses in dicotyledons plants. AM formation is considered as a source of preadaptations responsible for the substitution of glomalean fungi which occupied the plant symbiotic compartments by the actinomycetes Frankia (in Rosid I plants) which were exchanged for the more competitive root nodule bacteria (in legumes). The development of nutritional symbioses with microbes is considered as an ancestral function of plant roots which were later supplemented or substituted with the function of assimilating the soil nutrients.}, }
@article {pmid19325885, year = {2009}, author = {Van Melderen, L and Saavedra De Bast, M}, title = {Bacterial toxin-antitoxin systems: more than selfish entities?.}, journal = {PLoS genetics}, volume = {5}, number = {3}, pages = {e1000437}, pmid = {19325885}, issn = {1553-7404}, mesh = {Antitoxins/*genetics ; Bacterial Toxins/*genetics ; Escherichia coli Proteins ; Genome, Bacterial ; Operon ; Selection, Genetic ; }, abstract = {Bacterial toxin-antitoxin (TA) systems are diverse and widespread in the prokaryotic kingdom. They are composed of closely linked genes encoding a stable toxin that can harm the host cell and its cognate labile antitoxin, which protects the host from the toxin's deleterious effect. TA systems are thought to invade bacterial genomes through horizontal gene transfer. Some TA systems might behave as selfish elements and favour their own maintenance at the expense of their host. As a consequence, they may contribute to the maintenance of plasmids or genomic islands, such as super-integrons, by post-segregational killing of the cell that loses these genes and so suffers the stable toxin's destructive effect. The function of the chromosomally encoded TA systems is less clear and still open to debate. This Review discusses current hypotheses regarding the biological roles of these evolutionarily successful small operons. We consider the various selective forces that could drive the maintenance of TA systems in bacterial genomes.}, }
@article {pmid19324807, year = {2009}, author = {Puthiyaveetil, S and Allen, JF}, title = {Chloroplast two-component systems: evolution of the link between photosynthesis and gene expression.}, journal = {Proceedings. Biological sciences}, volume = {276}, number = {1665}, pages = {2133-2145}, pmid = {19324807}, issn = {0962-8452}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Chloroplasts/*genetics/*metabolism ; *Evolution, Molecular ; Gene Expression Regulation, Plant/*physiology ; Photosynthesis/*genetics/*physiology ; }, abstract = {Two-component signal transduction, consisting of sensor kinases and response regulators, is the predominant signalling mechanism in bacteria. This signalling system originated in prokaryotes and has spread throughout the eukaryotic domain of life through endosymbiotic, lateral gene transfer from the bacterial ancestors and early evolutionary precursors of eukaryotic, cytoplasmic, bioenergetic organelles-chloroplasts and mitochondria. Until recently, it was thought that two-component systems inherited from an ancestral cyanobacterial symbiont are no longer present in chloroplasts. Recent research now shows that two-component systems have survived in chloroplasts as products of both chloroplast and nuclear genes. Comparative genomic analysis of photosynthetic eukaryotes shows a lineage-specific distribution of chloroplast two-component systems. The components and the systems they comprise have homologues in extant cyanobacterial lineages, indicating their ancient cyanobacterial origin. Sequence and functional characteristics of chloroplast two-component systems point to their fundamental role in linking photosynthesis with gene expression. We propose that two-component systems provide a coupling between photosynthesis and gene expression that serves to retain genes in chloroplasts, thus providing the basis of cytoplasmic, non-Mendelian inheritance of plastid-associated characters. We discuss the role of this coupling in the chronobiology of cells and in the dialogue between nuclear and cytoplasmic genetic systems.}, }
@article {pmid19323823, year = {2009}, author = {Smith, DR and Lee, RW}, title = {The mitochondrial and plastid genomes of Volvox carteri: bloated molecules rich in repetitive DNA.}, journal = {BMC genomics}, volume = {10}, number = {}, pages = {132}, pmid = {19323823}, issn = {1471-2164}, mesh = {Animals ; Base Sequence ; Cell Nucleus/genetics ; Chlamydomonas reinhardtii/genetics ; DNA, Algal/genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; *Genome, Mitochondrial ; *Genome, Plastid ; *Inverted Repeat Sequences ; Mitochondria/genetics ; Molecular Sequence Data ; Plastids/genetics ; Sequence Analysis, DNA ; Volvox/*genetics ; }, abstract = {BACKGROUND: The magnitude of noncoding DNA in organelle genomes can vary significantly; it is argued that much of this variation is attributable to the dissemination of selfish DNA. The results of a previous study indicate that the mitochondrial DNA (mtDNA) of the green alga Volvox carteri abounds with palindromic repeats, which appear to be selfish elements. We became interested in the evolution and distribution of these repeats when, during a cursory exploration of the V. carteri nuclear DNA (nucDNA) and plastid DNA (ptDNA) sequences, we found palindromic repeats with similar structural features to those of the mtDNA. Upon this discovery, we decided to investigate the diversity and evolutionary implications of these palindromic elements by sequencing and characterizing large portions of mtDNA and ptDNA and then comparing these data to the V. carteri draft nuclear genome sequence.<br><br>RESULTS: We sequenced 30 and 420 kilobases (kb) of the mitochondrial and plastid genomes of V. carteri, respectively -- resulting in partial assemblies of these genomes. The mitochondrial genome is the most bloated green-algal mtDNA observed to date: ~61% of the sequence is noncoding, most of which is comprised of short palindromic repeats spread throughout the intergenic and intronic regions. The plastid genome is the largest (>420 kb) and most expanded (>80% noncoding) ptDNA sequence yet discovered, with a myriad of palindromic repeats in the noncoding regions, which have a similar size and secondary structure to those of the mtDNA. We found that 15 kb (~0.01%) of the nuclear genome are homologous to the palindromic elements of the mtDNA, and 50 kb (~0.05%) are homologous to those of the ptDNA.<br><br>CONCLUSION: Selfish elements in the form of short palindromic repeats have propagated in the V. carteri mtDNA and ptDNA, resulting in the distension of these genomes. Copies of these same repeats are also found in a small fraction of the nucDNA, but appear to be inert in this compartment. We conclude that the palindromic repeats in V. carteri represent a single class of selfish DNA and speculate that the derivation of this element involved the lateral gene transfer of an organelle intron that first appeared in the mitochondrial genome, spreading to the ptDNA through mitochondrion-to-plastid DNA migrations, and eventually arrived in the nucDNA through organelle-to-nucleus DNA transfer events. The overall implications of palindromic repeats on the evolution of chlorophyte organelle genomes are discussed.}, }
@article {pmid19321731, year = {2009}, author = {Vrints, M and Mairiaux, E and Van Meervenne, E and Collard, JM and Bertrand, S}, title = {Surveillance of antibiotic susceptibility patterns among Shigella sonnei strains isolated in Belgium during the 18-year period 1990 to 2007.}, journal = {Journal of clinical microbiology}, volume = {47}, number = {5}, pages = {1379-1385}, pmid = {19321731}, issn = {1098-660X}, mesh = {Anti-Bacterial Agents/*pharmacology ; Belgium ; Child, Preschool ; DNA Transposable Elements ; Drug Resistance, Bacterial ; Dysentery, Bacillary/*microbiology ; Gene Transfer, Horizontal ; Humans ; Infant ; Microbial Sensitivity Tests ; R Factors ; Shigella sonnei/*drug effects/isolation &amp; purification ; }, abstract = {This study was conducted to determine the frequency and pattern of antimicrobial susceptibility of Shigella sonnei, the predominant species causing shigellosis in Belgium. Between 1990 and 2007, a total of 7,307 strains, mainly (98.2%) isolated from stools, were diagnosed by peripheral laboratories before being confirmed as Shigella strains by serotyping by the National Reference Center of Salmonella and Shigella. A significant increase in resistances to tetracycline, streptomycin, trimethoprim, sulfonamides, and cotrimoxazole (i.e., trimethoprim in combination with sulfonamides) was observed during this period. Since 1998, resistance to nalidixic acid also increased to reach a peak (12.8%) of resistant isolates in 2004. Concomitantly, multidrug resistance (MDR) in this species emerged in 2007, with 82% of total isolates being MDR. However, during this 18-year period, all isolates remained fully susceptible to ciprofloxacin and gentamicin. The work includes the molecular characterization of mechanisms of resistance to ampicillin, tetracycline, chloramphenicol, and cotrimoxazole and class 1 and class 2 integrons. S. sonnei acquired antimicrobial resistance to traditional antibiotics (ampicillin and tetracycline) by horizontal gene transfer, while the genetic stability of transposons was responsible for a high (89%) proportion of resistance to a commonly prescribed antibiotic (cotrimoxazole). Therefore, cotrimoxazole should no longer be considered appropriate as empirical therapy for treatment of shigellosis in Belgium when antibiotics are indicated. Rates of resistance to nalidixic acid should also be attentively monitored to detect any shift in fluoroquinolone resistance, because it represents the first line among antibiotics used in the treatment of shigellosis.}, }
@article {pmid19319912, year = {2009}, author = {Boucher, Y and Bapteste, E}, title = {Revisiting the concept of lineage in prokaryotes: a phylogenetic perspective.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {31}, number = {5}, pages = {526-536}, doi = {10.1002/bies.200800216}, pmid = {19319912}, issn = {1521-1878}, mesh = {Gene Transfer, Horizontal/genetics/physiology ; Genetic Variation/genetics ; Models, Theoretical ; Mutation/genetics/physiology ; *Phylogeny ; Prokaryotic Cells/*classification/*metabolism ; }, abstract = {Mutation and lateral transfer are two categories of processes generating genetic diversity in prokaryotic genomes. Their relative importance varies between lineages, yet both are complementary rather than independent, separable evolutionary forces. The replication process inevitably merges together their effects on the genome. We develop the concept of "open lineages" to characterize evolutionary lineages that over time accumulate more changes in their genomes by lateral transfer than by mutation. They contrast with "closed lineages," in which most of the changes are caused by mutation. Open and closed lineages are interspersed along the branches of any tree of prokaryotes. This patchy distribution conflicts with the basic assumptions of traditional phylogenetic approaches. As a result, a tree representation including both open and closed lineages is a misrepresentation. The evolution of all prokaryotic lineages cannot be studied under a single model unless new phylogenetic approaches that are more pluralistic about lineage evolution are designed.}, }
@article {pmid19307581, year = {2009}, author = {Klasson, L and Westberg, J and Sapountzis, P and Näslund, K and Lutnaes, Y and Darby, AC and Veneti, Z and Chen, L and Braig, HR and Garrett, R and Bourtzis, K and Andersson, SG}, title = {The mosaic genome structure of the Wolbachia wRi strain infecting Drosophila simulans.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {14}, pages = {5725-5730}, pmid = {19307581}, issn = {1091-6490}, mesh = {Animals ; Ankyrins/genetics ; Drosophila/*microbiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial/*genetics ; Molecular Sequence Data ; Mosaicism ; *Recombination, Genetic ; Wolbachia/*genetics ; }, abstract = {The obligate intracellular bacterium Wolbachia pipientis infects around 20% of all insect species. It is maternally inherited and induces reproductive alterations of insect populations by male killing, feminization, parthenogenesis, or cytoplasmic incompatibility. Here, we present the 1,445,873-bp genome of W. pipientis strain wRi that induces very strong cytoplasmic incompatibility in its natural host Drosophila simulans. A comparison with the previously sequenced genome of W. pipientis strain wMel from Drosophila melanogaster identified 35 breakpoints associated with mobile elements and repeated sequences that are stable in Drosophila lines transinfected with wRi. Additionally, 450 genes with orthologs in wRi and wMel were sequenced from the W. pipientis strain wUni, responsible for the induction of parthenogenesis in the parasitoid wasp Muscidifurax uniraptor. The comparison of these A-group Wolbachia strains uncovered the most highly recombining intracellular bacterial genomes known to date. This was manifested in a 500-fold variation in sequence divergences at synonymous sites, with different genes and gene segments supporting different strain relationships. The substitution-frequency profile resembled that of Neisseria meningitidis, which is characterized by rampant intraspecies recombination, rather than that of Rickettsia, where genes mostly diverge by nucleotide substitutions. The data further revealed diversification of ankyrin repeat genes by short tandem duplications and provided examples of horizontal gene transfer across A- and B-group strains that infect D. simulans. These results suggest that the transmission dynamics of Wolbachia and the opportunity for coinfections have created a freely recombining intracellular bacterial community with mosaic genomes.}, }
@article {pmid19307556, year = {2009}, author = {Zhaxybayeva, O and Swithers, KS and Lapierre, P and Fournier, GP and Bickhart, DM and DeBoy, RT and Nelson, KE and Nesbø, CL and Doolittle, WF and Gogarten, JP and Noll, KM}, title = {On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {14}, pages = {5865-5870}, pmid = {19307556}, issn = {1091-6490}, mesh = {Environment ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Molecular Sequence Data ; *Phylogeny ; Temperature ; Thermotoga maritima/*classification/*genetics ; }, abstract = {Since publication of the first Thermotogales genome, Thermotoga maritima strain MSB8, single- and multi-gene analyses have disagreed on the phylogenetic position of this order of Bacteria. Here we present the genome sequences of 4 additional members of the Thermotogales (Tt. petrophila, Tt. lettingae, Thermosipho melanesiensis, and Fervidobacterium nodosum) and a comprehensive comparative analysis including the original T. maritima genome. While ribosomal protein genes strongly place Thermotogales as a sister group to Aquificales, the majority of genes with sufficient phylogenetic signal show affinities to Archaea and Firmicutes, especially Clostridia. Indeed, on the basis of the majority of genes in their genomes (including genes that are also found in Aquificales), Thermotogales should be considered members of the Firmicutes. This result highlights the conflict between the taxonomic goal of assigning every species to a unique position in an inclusive Linnaean hierarchy and the evolutionary goal of understanding phylogenesis in the presence of pervasive horizontal gene transfer (HGT) within prokaryotes. Amino acid compositions of reconstructed ancestral sequences from 423 gene families suggest an origin of this gene pool even more thermophilic than extant members of this order, followed by adaptation to lower growth temperatures within the Thermotogales.}, }
@article {pmid19307211, year = {2009}, author = {Peigne, C and Bidet, P and Mahjoub-Messai, F and Plainvert, C and Barbe, V and Médigue, C and Frapy, E and Nassif, X and Denamur, E and Bingen, E and Bonacorsi, S}, title = {The plasmid of Escherichia coli strain S88 (O45:K1:H7) that causes neonatal meningitis is closely related to avian pathogenic E. coli plasmids and is associated with high-level bacteremia in a neonatal rat meningitis model.}, journal = {Infection and immunity}, volume = {77}, number = {6}, pages = {2272-2284}, pmid = {19307211}, issn = {1098-5522}, mesh = {Animals ; Animals, Newborn ; Bacteremia/*microbiology ; Colony Count, Microbial ; DNA, Bacterial/chemistry/genetics ; Escherichia coli/*isolation &amp; purification ; Escherichia coli Infections/complications/*microbiology ; Escherichia coli Proteins/genetics ; France ; Gene Transfer, Horizontal ; Humans ; Infant, Newborn ; Infant, Newborn, Diseases/*microbiology ; Meningitis/complications/*microbiology ; Molecular Epidemiology ; Molecular Sequence Data ; Open Reading Frames ; *Plasmids ; Rats ; Sequence Analysis, DNA ; Sequence Homology ; Synteny ; Virulence ; Virulence Factors/genetics ; }, abstract = {A new Escherichia coli virulent clonal group, O45:K1, belonging to the highly virulent subgroup B2(1) was recently identified in France, where it accounts for one-third of E. coli neonatal meningitis cases. Here we describe the sequence, epidemiology and function of the large plasmid harbored by strain S88, which is representative of the O45:K1 clonal group. Plasmid pS88 is 133,853 bp long and contains 144 protein-coding genes. It harbors three different iron uptake systems (aerobactin, salmochelin, and the sitABCD genes) and other putative virulence genes (iss, etsABC, ompT(P), and hlyF). The pS88 sequence is composed of several gene blocks homologous to avian pathogenic E. coli plasmids pAPEC-O2-ColV and pAPEC-O1-ColBM. PCR amplification of 11 open reading frames scattered throughout the plasmid was used to investigate the distribution of pS88 and showed that a pS88-like plasmid is present in other meningitis clonal groups such as O18:K1, O1:K1, and O83:K1. A pS88-like plasmid was also found in avian pathogenic strains and human urosepsis strains belonging to subgroup B2(1). A variant of S88 cured of its plasmid displayed a marked loss of virulence relative to the wild-type strain in a neonatal rat model, with bacteremia more than 2 log CFU/ml lower. The salmochelin siderophore, a known meningovirulence factor, could not alone explain the plasmid's contribution to virulence, as a salmochelin mutant displayed only a minor fall in bacteremia (0.9 log CFU/ml). Thus, pS88 is a major virulence determinant related to avian pathogenic plasmids that has spread not only through meningitis clonal groups but also human urosepsis and avian pathogenic strains.}, }
@article {pmid19304837, year = {2009}, author = {Hu, X and Van der Auwera, G and Timmery, S and Zhu, L and Mahillon, J}, title = {Distribution, diversity, and potential mobility of extrachromosomal elements related to the Bacillus anthracis pXO1 and pXO2 virulence plasmids.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {10}, pages = {3016-3028}, pmid = {19304837}, issn = {1098-5336}, mesh = {Antigens, Bacterial/genetics ; Bacillus cereus/*genetics/isolation &amp; purification ; Bacterial Capsules/genetics ; Bacterial Toxins/genetics ; Blotting, Southern ; Cluster Analysis ; Conjugation, Genetic ; DNA, Bacterial/*genetics ; *Environmental Microbiology ; Gene Order ; Gene Transfer, Horizontal ; Phylogeny ; Plasmids/*analysis ; Sequence Analysis, DNA ; Sequence Homology ; Virulence Factors/*genetics ; }, abstract = {The presence of a pXO1- and/or pXO2-like plasmid(s) in clinical isolates of Bacillus cereus sensu stricto and in strains of the biopesticide Bacillus thuringiensis has been reported recently, and the pXO2-like plasmid pBT9727 and another pXO2-like plasmid, pAW63, were found to be conjugative. In this study, a total of 1,000 B. cereus group isolates were analyzed for the presence of pXO1- and pXO2-like replicons and for the presence of pXO2-related conjugative modules. pXO1- and pXO2-like replicons were present in ca. 6.6% and 7.7% of random environmental samples, respectively, and ca. 1.54% of the strains were positive for pXO2-like transfer module genes. Only the strains harboring a pXO2-like replicon also contained the corresponding transfer genes. For the strains which contained a pXO1- and/or pXO2-like replicon(s), a large plasmid(s) whose size was similar to that of pXO1-like and/or pXO2-like plasmids was also observed, but none of these isolates were found to carry the Bacillus anthracis toxin or capsule virulence genes. Furthermore, 17 of 22 pXO2-like plasmids containing the transfer modules were able to self-transfer and to mobilize small plasmids. No pXO1- or pXO2-like plasmid lacking the cognate transfer modules has been found to have transfer potential. In the strains possessing the putative pXO2-like conjugative apparatus, variations in the presence of the group II introns B.th.I.1 and B.th.I.2 were observed, suggesting that there is important flexibility in the conjugation modules and their regulation. There was no consistent correlation between a pXO2-like repA dendrogram and the presence of the tra region or between a virB4 dendrogram and transfer ability. Discrepancies between pXO2-like repA and virB4 dendrograms were also observed, indicating that the evolution of pXO2 is an active process.}, }
@article {pmid19304835, year = {2009}, author = {Veiga, H and Pinho, MG}, title = {Inactivation of the SauI type I restriction-modification system is not sufficient to generate Staphylococcus aureus strains capable of efficiently accepting foreign DNA.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {10}, pages = {3034-3038}, pmid = {19304835}, issn = {1098-5336}, mesh = {DNA Restriction-Modification Enzymes/*genetics/metabolism ; DNA, Bacterial/*metabolism ; *Gene Deletion ; *Gene Transfer, Horizontal ; Staphylococcus aureus/*enzymology/*genetics ; *Transformation, Bacterial ; }, abstract = {Genetic manipulation of Staphylococcus aureus is limited by the availability of only a single strain, RN4220, that is capable of easily accepting foreign DNA. Inactivation of the hsdR gene of the SauI type I restriction-modification system was shown previously to be responsible for the high transformation efficiency of RN4220 (D. E. Waldron and J. A. Lindsay, J Bacteriol. 188:5578-5585, 2006). However, deletion of this gene in three different S. aureus strains was not sufficient to make them readily transformable, which would be remarkably useful for genetic studies of this pathogenic organism. These results indicate that another unknown factor(s) is required for the transformable phenotype in S. aureus.}, }
@article {pmid19302725, year = {2010}, author = {Nakabachi, A and Koshikawa, S and Miura, T and Miyagishima, S}, title = {Genome size of Pachypsylla venusta (Hemiptera: Psyllidae) and the ploidy of its bacteriocyte, the symbiotic host cell that harbors intracellular mutualistic bacteria with the smallest cellular genome.}, journal = {Bulletin of entomological research}, volume = {100}, number = {1}, pages = {27-33}, doi = {10.1017/S0007485309006737}, pmid = {19302725}, issn = {1475-2670}, mesh = {Animals ; Densitometry ; Flow Cytometry ; Gammaproteobacteria/genetics ; Genome/*genetics ; Genomics ; Hemiptera/*genetics ; *Ploidies ; *Symbiosis ; }, abstract = {Psyllids harbor the primary symbiont, Carsonella ruddii (gamma-Proteobacteria), within the cytoplasm of specialized cells called bacteriocytes. Carsonella has the smallest known cellular genome (160 kb), lacking numerous genes that appear to be essential for bacterial life. This raises the question regarding the genetic mechanisms of the host which supports the survival of Carsonella. Our preceding analyses have indicated that some of the genes that are encoded in the psyllid genome and which are highly expressed in the bacteriocyte are of bacterial origin. This implies that psyllids acquired genes from bacteria by lateral gene transfer (LGT) and are using these genes to maintain the primary symbiont, Carsonella. To reveal the complete picture of LGT from symbiotic bacteria to the genome of psyllids, whole genome analysis of psyllids is essential. In order to assess the feasibility of whole genome analysis of the host psyllid, the genome size of the hackberry petiole gall psyllid, Pachypsylla venusta, was estimated. Feulgen image analysis densitometry and flow cytometry demonstrated that the haploid genome size of P. venusta is 0.74 pg (724 Mb), verifying the feasibility of whole genome analysis. Feulgen image analysis densitometry further revealed that bacteriocytes of P. venusta are invariably 16-ploid. This higher ploidy may be essential to facilitate the symbiotic relationship with bacteria, as it appears to be a feature common to insect bacteriocytes. These results provide a foundation for genomics-based research into host-symbiont interactions.}, }
@article {pmid19302541, year = {2009}, author = {Willner, D and Thurber, RV and Rohwer, F}, title = {Metagenomic signatures of 86 microbial and viral metagenomes.}, journal = {Environmental microbiology}, volume = {11}, number = {7}, pages = {1752-1766}, doi = {10.1111/j.1462-2920.2009.01901.x}, pmid = {19302541}, issn = {1462-2920}, mesh = {Cluster Analysis ; Computational Biology/methods ; *Environmental Microbiology ; *Metagenome ; Metagenomics/*methods ; Microbiological Techniques/*methods ; Phylogeny ; }, abstract = {Previous studies have shown that dinucleotide abundances capture the majority of variation in genome signatures and are useful for quantifying lateral gene transfer and building molecular phylogenies. Metagenomes contain a mixture of individual genomes, and might be expected to lack compositional signatures. In many metagenomic data sets the majority of sequences have no significant similarities to known sequences and are effectively excluded from subsequent analyses. To circumvent this limitation, di-, tri- and tetranucleotide abundances of 86 microbial and viral metagenomes consisting of short pyrosequencing reads were analysed to provide a method which includes all sequences that can be used in combination with other analysis to increase our knowledge about microbial and viral communities. Both principal component analysis and hierarchical clustering showed definitive groupings of metagenomes drawn from similar environments. Together these analyses showed that dinucleotide composition, as opposed to tri- and tetranucleotides, defines a metagenomic signature which can explain up to 80% of the variance between biomes, which is comparable to that obtained by functional genomics. Metagenomes with anomalous content were also identified using dinucleotide abundances. Subsequent analyses determined that these metagenomes were contaminated with exogenous DNA, suggesting that this approach is a useful metric for quality control. The predictive strength of the dinucleotide composition also opens the possibility of assigning ecological classifications to unknown fragments. Environmental selection may be responsible for this dinucleotide signature through direct selection of specific compositional signals; however, simulations suggest that the environment may select indirectly by promoting the increased abundance of a few dominant taxa.}, }
@article {pmid19300486, year = {2009}, author = {Perez, JC and Shin, D and Zwir, I and Latifi, T and Hadley, TJ and Groisman, EA}, title = {Evolution of a bacterial regulon controlling virulence and Mg(2+) homeostasis.}, journal = {PLoS genetics}, volume = {5}, number = {3}, pages = {e1000428}, pmid = {19300486}, issn = {1553-7404}, support = {R01 AI049561/AI/NIAID NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; AI49561/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/*genetics ; Biological Transport/genetics ; Enterobacteriaceae/*genetics ; Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Homeostasis/*genetics ; Magnesium/*metabolism ; Regulon/*genetics/physiology ; Species Specificity ; Virulence/*genetics ; }, abstract = {Related organisms typically rely on orthologous regulatory proteins to respond to a given signal. However, the extent to which (or even if) the targets of shared regulatory proteins are maintained across species has remained largely unknown. This question is of particular significance in bacteria due to the widespread effects of horizontal gene transfer. Here, we address this question by investigating the regulons controlled by the DNA-binding PhoP protein, which governs virulence and Mg(2+) homeostasis in several bacterial species. We establish that the ancestral PhoP protein directs largely different gene sets in ten analyzed species of the family Enterobacteriaceae, reflecting both regulation of species-specific targets and transcriptional rewiring of shared genes. The two targets directly activated by PhoP in all ten species (the most distant of which diverged >200 million years ago), and coding for the most conserved proteins are the phoPQ operon itself and the lipoprotein-encoding slyB gene, which decreases PhoP protein activity. The Mg(2+)-responsive PhoP protein dictates expression of Mg(2+) transporters and of enzymes that modify Mg(2+)-binding sites in the cell envelope in most analyzed species. In contrast to the core PhoP regulon, which determines the amount of active PhoP and copes with the low Mg(2+) stress, the variable members of the regulon contribute species-specific traits, a property shared with regulons controlled by dissimilar regulatory proteins and responding to different signals.}, }
@article {pmid19296042, year = {2009}, author = {Sant'Anna, FH and Trentini, DB and de Souto Weber, S and Cecagno, R and da Silva, SC and Schrank, IS}, title = {The PII superfamily revised: a novel group and evolutionary insights.}, journal = {Journal of molecular evolution}, volume = {68}, number = {4}, pages = {322-336}, pmid = {19296042}, issn = {1432-1432}, mesh = {Amino Acid Sequence ; Azospirillum brasilense/genetics ; Bacteria/*genetics ; Bacterial Proteins/genetics ; *Evolution, Molecular ; Molecular Sequence Data ; PII Nitrogen Regulatory Proteins/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {The PII proteins compose a superfamily of signal transducers with fundamental roles in the nitrogen metabolism of prokaryotic organisms. They act at different cellular targets, such as ammonia transporters, enzymes, and transcriptional factors. These proteins are small, highly conserved, and well distributed among prokaryotes. The current PII classification is based on sequence similarity and genetic linkage. Our work reviewed this classification through an extensive analysis of PII homologues deposited in GenBank. We also investigated evolutionary aspects of this ancient protein superfamily and revised its PROSITE signatures. A new group of PII proteins is described in this work. These PII homologues have a peculiar genetic context, as they are associated with metal transporters and do not contain the canonical PROSITE signatures of PII. Our analysis reveals that horizontal gene transfer could have played an important role in PII evolution. Thus, new insights into PII evolution, a new PII group, and more comprehensive PROSITE signatures are proposed.}, }
@article {pmid19291296, year = {2009}, author = {Roulin, A and Piegu, B and Fortune, PM and Sabot, F and D'Hont, A and Manicacci, D and Panaud, O}, title = {Whole genome surveys of rice, maize and sorghum reveal multiple horizontal transfers of the LTR-retrotransposon Route66 in Poaceae.}, journal = {BMC evolutionary biology}, volume = {9}, number = {}, pages = {58}, pmid = {19291296}, issn = {1471-2148}, mesh = {Computational Biology ; Evolution, Molecular ; Gene Expression Regulation, Plant ; *Gene Transfer, Horizontal ; Genes, Plant ; Genome, Plant ; Oryza/*genetics ; Phylogeny ; *Retroelements ; Sequence Alignment ; Sorghum/*genetics ; *Terminal Repeat Sequences ; Zea mays/*genetics ; }, abstract = {BACKGROUND: Horizontal transfers (HTs) refer to the transmission of genetic material between phylogenetically distant species. Although most of the cases of HTs described so far concern genes, there is increasing evidence that some involve transposable elements (TEs) in Eukaryotes. The availability of the full genome sequence of two cereal species, (i.e. rice and Sorghum), as well as the partial genome sequence of maize, provides the opportunity to carry out genome-wide searches for TE-HTs in Poaceae.<br><br>RESULTS: We have identified an LTR-retrotransposon, that we named Route66, with more than 95% sequence identity between rice and Sorghum. Using a combination of in silico and molecular approaches, we are able to present a substantial phylogenetic evidence that Route66 has been transferred horizontally between Panicoideae and several species of the genus Oryza. In addition, we show that it has remained active after these transfers.<br><br>CONCLUSION: This study constitutes a new case of HTs for an LTR-retrotransposon and we strongly believe that this mechanism could play a major role in the life cycle of transposable elements. We therefore propose to integrate classe I elements into the previous model of transposable element evolution through horizontal transfers.}, }
@article {pmid19286782, year = {2009}, author = {Haaber, J and Moineau, S and Hammer, K}, title = {Activation and transfer of the chromosomal phage resistance mechanism AbiV in Lactococcus lactis.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {10}, pages = {3358-3361}, pmid = {19286782}, issn = {1098-5336}, mesh = {Bacteriophages/*growth &amp; development ; Chromosomes, Bacterial ; Conjugation, Genetic ; Gene Expression Profiling ; Gene Order ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Lactococcus lactis/*genetics/*virology ; Mutation ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {AbiV is a chromosomally encoded phage resistance mechanism that is silent in the wild-type phage-sensitive strain Lactococcus lactis subsp. cremoris MG1363. Spontaneous phage-resistant mutants of L. lactis MG1363 were analyzed by reverse transcriptase PCR and shown to express AbiV. This expression was related to a reorganization in the upstream region of abiV. Transfer of abiV between two lactococcal strains, most likely by conjugation, was also demonstrated. To our knowledge, this is the first report of natural transfer of a chromosomally encoded phage resistance mechanism.}, }
@article {pmid19284580, year = {2009}, author = {Devine, E and Holmqvist, M and Stensjö, K and Lindblad, P}, title = {Diversity and transcription of proteases involved in the maturation of hydrogenases in Nostoc punctiforme ATCC 29133 and Nostoc sp. strain PCC 7120.}, journal = {BMC microbiology}, volume = {9}, number = {}, pages = {53}, pmid = {19284580}, issn = {1471-2180}, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics/*metabolism ; DNA, Bacterial/genetics ; Endopeptidases/genetics/*metabolism ; Gene Expression Regulation, Bacterial ; Hydrogenase/genetics/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Nostoc/enzymology/*genetics ; Phylogeny ; Protein Structure, Tertiary ; Sequence Alignment ; Sequence Analysis, DNA ; Substrate Specificity ; Transcription Initiation Site ; Transcription, Genetic ; }, abstract = {BACKGROUND: The last step in the maturation process of the large subunit of [NiFe]-hydrogenases is a proteolytic cleavage of the C-terminal by a hydrogenase specific protease. Contrary to other accessory proteins these hydrogenase proteases are believed to be specific whereby one type of hydrogenases specific protease only cleaves one type of hydrogenase. In cyanobacteria this is achieved by the gene product of either hupW or hoxW, specific for the uptake or the bidirectional hydrogenase respectively. The filamentous cyanobacteria Nostoc punctiforme ATCC 29133 and Nostoc sp strain PCC 7120 may contain a single uptake hydrogenase or both an uptake and a bidirectional hydrogenase respectively.<br><br>RESULTS: In order to examine these proteases in cyanobacteria, transcriptional analyses were performed of hupW in Nostoc punctiforme ATCC 29133 and hupW and hoxW in Nostoc sp. strain PCC 7120. These studies revealed numerous transcriptional start points together with putative binding sites for NtcA (hupW) and LexA (hoxW). In order to investigate the diversity and specificity among hydrogeanse specific proteases we constructed a phylogenetic tree which revealed several subgroups that showed a striking resemblance to the subgroups previously described for [NiFe]-hydrogenases. Additionally the proteases specificity was also addressed by amino acid sequence analysis and protein-protein docking experiments with 3D-models derived from bioinformatic studies. These studies revealed a so called "HOXBOX"; an amino acid sequence specific for protease of Hox-type which might be involved in docking with the large subunit of the hydrogenase.<br><br>CONCLUSION: Our findings suggest that the hydrogenase specific proteases are under similar regulatory control as the hydrogenases they cleave. The result from the phylogenetic study also indicates that the hydrogenase and the protease have co-evolved since ancient time and suggests that at least one major horizontal gene transfer has occurred. This co-evolution could be the result of a close interaction between the protease and the large subunit of the [NiFe]-hydrogenases, a theory supported by protein-protein docking experiments performed with 3D-models. Finally we present data that may explain the specificity seen among hydrogenase specific proteases, the so called "HOXBOX"; an amino acid sequence specific for proteases of Hox-type. This opens the door for more detailed studies of the specificity found among hydrogenase specific proteases and the structural properties behind it.}, }
@article {pmid19284579, year = {2009}, author = {Butler, JE and Young, ND and Lovley, DR}, title = {Evolution from a respiratory ancestor to fill syntrophic and fermentative niches: comparative fenomics of six Geobacteraceae species.}, journal = {BMC genomics}, volume = {10}, number = {}, pages = {103}, pmid = {19284579}, issn = {1471-2164}, mesh = {Anaerobiosis ; Bacteria, Anaerobic/*genetics/metabolism ; *Biological Evolution ; Cluster Analysis ; DNA, Bacterial/genetics ; Deltaproteobacteria/*genetics/metabolism ; Fermentation/*genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomics ; Multigene Family ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The anaerobic degradation of organic matter in natural environments, and the biotechnical use of anaerobes in energy production and remediation of subsurface environments, both require the cooperative activity of a diversity of microorganisms in different metabolic niches. The Geobacteraceae family contains members with three important anaerobic metabolisms: fermentation, syntrophic degradation of fermentation intermediates, and anaerobic respiration.<br><br>RESULTS: In order to learn more about the evolution of anaerobic microbial communities, the genome sequences of six Geobacteraceae species were analyzed. The results indicate that the last common Geobacteraceae ancestor contained sufficient genes for anaerobic respiration, completely oxidizing organic compounds with the reduction of external electron acceptors, features that are still retained in modern Geobacter and Desulfuromonas species. Evolution of specialization for fermentative growth arose twice, via distinct lateral gene transfer events, in Pelobacter carbinolicus and Pelobacter propionicus. Furthermore, P. carbinolicus gained hydrogenase genes and genes for ferredoxin reduction that appear to permit syntrophic growth via hydrogen production. The gain of new physiological capabilities in the Pelobacter species were accompanied by the loss of several key genes necessary for the complete oxidation of organic compounds and the genes for the c-type cytochromes required for extracellular electron transfer.<br><br>CONCLUSION: The results suggest that Pelobacter species evolved parallel strategies to enhance their ability to compete in environments in which electron acceptors for anaerobic respiration were limiting. More generally, these results demonstrate how relatively few gene changes can dramatically transform metabolic capabilities and expand the range of environments in which microorganisms can compete.}, }
@article {pmid19284544, year = {2009}, author = {Nikoh, N and Nakabachi, A}, title = {Aphids acquired symbiotic genes via lateral gene transfer.}, journal = {BMC biology}, volume = {7}, number = {}, pages = {12}, pmid = {19284544}, issn = {1741-7007}, mesh = {Amino Acid Sequence ; Animal Structures/metabolism/microbiology ; Animals ; Aphids/cytology/*microbiology ; Buchnera/genetics/*physiology ; Carboxypeptidases/chemistry/genetics ; Gene Expression Profiling ; Gene Expression Regulation ; Gene Order ; Gene Transfer, Horizontal/*genetics ; Lipoprotein(a)/chemistry/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Symbiosis/*genetics ; }, abstract = {BACKGROUND: Aphids possess bacteriocytes, which are cells specifically differentiated to harbour the obligate mutualist Buchnera aphidicola (gamma-Proteobacteria). Buchnera has lost many of the genes that appear to be essential for bacterial life. From the bacteriocyte of the pea aphid Acyrthosiphon pisum, we previously identified two clusters of expressed sequence tags that display similarity only to bacterial genes. Southern blot analysis demonstrated that they are encoded in the aphid genome. In this study, in order to assess the possibility of lateral gene transfer, we determined the full-length sequences of these transcripts, and performed detailed structural and phylogenetic analyses. We further examined their expression levels in the bacteriocyte using real-time quantitative RT-PCR.<br><br>RESULTS: Sequence similarity searches demonstrated that these fully sequenced transcripts are significantly similar to the bacterial genes ldcA (product, LD-carboxypeptidase) and rlpA (product, rare lipoprotein A), respectively. Buchnera lacks these genes, whereas many other bacteria, including Escherichia coli, a close relative of Buchnera, possess both ldcA and rlpA. Molecular phylogenetic analysis clearly demonstrated that the aphid ldcA was derived from a rickettsial bacterium closely related to the extant Wolbachia spp. (alpha-Proteobacteria, Rickettsiales), which are intracellular symbionts of various lineages of arthropods. The evolutionary origin of rlpA was not fully resolved, but it was clearly demonstrated that its double-psi beta-barrel domain is of bacterial origin. Real-time quantitative RT-PCR demonstrated that ldcA and rlpA are expressed 11.6 and 154-fold higher in the bacteriocyte than in the whole body, respectively. LdcA is an enzyme required for recycling murein (peptidoglycan), which is a component of the bacterial cell wall. As Buchnera possesses a cell wall composed of murein but lacks ldcA, a high level of expression of the aphid ldcA in the bacteriocyte may be essential to maintain Buchnera. Although the function of RlpA is not well known, conspicuous up-regulation of the aphid rlpA in the bacteriocyte implies that this gene is also essential for Buchnera.<br><br>CONCLUSION: In this study, we obtained several lines of evidence indicating that aphids acquired genes from bacteria via lateral gene transfer and that these genes are used to maintain the obligately mutualistic bacterium, Buchnera.}, }
@article {pmid19281950, year = {2009}, author = {Lopez, P and Bapteste, E}, title = {Molecular phylogeny: reconstructing the forest.}, journal = {Comptes rendus biologies}, volume = {332}, number = {2-3}, pages = {171-182}, doi = {10.1016/j.crvi.2008.07.003}, pmid = {19281950}, issn = {1768-3238}, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal ; Phylogeny ; Trees/*physiology ; }, abstract = {Phylogeny, be it morphological or molecular, has long tried to explain the extant biodiversity by the Tree of Species, which is a logical consequence of strict Darwinian evolutionary principles. Through constant improvement of both methods and data sets, some parts of this diversity have actually been demonstrated to be the result of a tree-like process. For some other parts, and especially for prokaryotes, different molecular markers have, however, produced different evolutionary trees, preventing the reconstruction of such a Tree. While technical artifacts could be blamed for these discrepancies, Lateral Gene Transfers are now largely held for responsible, and their existence requires an extension of the Darwinian framework, since genetic material is not always vertically inherited from parents to offspring. Through a variety of biological processes, sometimes large parts of DNA are exchanged between phylogenetically distant contemporary organisms, especially between those sharing the same environment. While mainly concerning prokaryotes, Lateral Gene Transfers have been also demonstrated to affect eukaryotes, and even multicellular ones, like plants or animals. Most of the time, these transfers allow important adaptations and the colonisation of new niches. The quantitative and qualitative importance of genetic transfers has thus severely challenged the very existence of a universal Tree of Species, since genetic connections, at least for microbes, seem more reticulated than tree-like. Even traditional biological concepts, like the concept of species, need to be re-evaluated in the light of recent discoveries. In short, instead of focusing on a elusive universal tree, biologists are now considering the whole forest corresponding to the multiple processes of inheritance, both vertical and horizontal. This constitutes the major challenge of evolutionary biology for the years to come.}, }
@article {pmid19273337, year = {2009}, author = {Dorman, CJ}, title = {Regulatory integration of horizontally-transferred genes in bacteria.}, journal = {Frontiers in bioscience (Landmark edition)}, volume = {14}, number = {11}, pages = {4103-4112}, doi = {10.2741/3515}, pmid = {19273337}, issn = {2768-6698}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Bacteria/*genetics ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; }, abstract = {Horizontal transfer of genetic material is a fact of microbial life and bacteria can obtain new DNA sequences through the processes of conjugation, transduction and transformation. This offers the bacterium the possibility of evolving rapidly by importing new genes that code for new traits that may assist in environmental adaptation. Research in this area has focused in particular on the role of horizontal transfer in the dissemination through bacterial populations of genes for resistance to antimicrobial agents, including antibiotics. It is becoming clear that many other phenotypic characteristics have been acquired through horizontal routes and that these include traits contributing to pathogenesis and symbiosis. An important corollary to the acquisition of new genes is the problem of how best to integrate them in the existing gene regulatory circuits of the recipient so that fitness is not compromised initially and can be enhanced in the future through optimal expression of the new genes.}, }
@article {pmid19273229, year = {2009}, author = {Waterhouse, M and Themeli, M and Metaxas, Y and Lagadinou, ED and Finke, J and Spyridonidis, A}, title = {Horizontal DNA and mRNA transfer between donor and recipient cells after allogeneic hematopoietic cell transplantation?.}, journal = {Frontiers in bioscience (Landmark edition)}, volume = {14}, number = {7}, pages = {2704-2713}, doi = {10.2741/3407}, pmid = {19273229}, issn = {2768-6698}, mesh = {Chimera ; DNA/*genetics ; *Gene Transfer, Horizontal ; *Hematopoietic Stem Cell Transplantation ; RNA, Messenger/*genetics ; *Tissue Donors ; Transplantation, Homologous ; }, abstract = {Allogeneic hematopoietic cell transplantation in humans results in true biological chimeras. There is now accumulating evidence that besides Graft versus Host Disease (GvHD), there are also other consequences in the co-existence of two genetically distinct populations in the transplant recipient. First, epithelial cells with donor-derived genotype emerge. Second, epithelial tissues of the host acquire genomic alterations. The current review discusses existing data on these recently discovered phenomena and focuses on horizontal gene transfer between donor and recipient cells as a possible mechanism explaining and linking these phenomena.}, }
@article {pmid19271205, year = {2009}, author = {Mitreva, M and Smant, G and Helder, J}, title = {Role of horizontal gene transfer in the evolution of plant parasitism among nematodes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {532}, number = {}, pages = {517-535}, doi = {10.1007/978-1-60327-853-9_30}, pmid = {19271205}, issn = {1064-3745}, support = {AI46593/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Cellulase/genetics ; Ecosystem ; Expressed Sequence Tags ; *Gene Transfer, Horizontal ; Genes, Helminth ; Host-Parasite Interactions/genetics ; Models, Genetic ; Nematoda/*genetics/*pathogenicity ; Phylogeny ; Plants/*parasitology ; Symbiosis/genetics ; }, abstract = {Horizontal gene transfer (HGT) implies the non-sexual exchange of genetic material between species - in some cases even across kingdoms. Although common among Bacteria and Archaea, HGTs from pro- to eukaryotes and between eukaryotes were thought to be extremely rare. Recent studies on intracellular bacteria and their hosts seriously question this view. Recipient organisms could benefit from HGT as new gene packages could allow them to broaden or change their diet, colonize new habitats, or survive conditions that previously would have been lethal.About a decade ago, plant parasitic nematodes were shown to produce and secrete cellulases. Prior to this, animals were thought to fully depend on microbial symbionts for the breakdown of plant cell walls. This discovery prompted Keen and Roberts (1) to hypothesize that the ability of nematodes to parasitize plants was acquired by HGT from soil bacteria to (ancestral) bacterivorous nematodes. Since the identification of the first nematode cellulases, many more plant cell wall-degrading enzymes (CWDE) have been identified in a range of plant parasitic nematode species.Here we discuss a number of criteria that can be used to underpin an HGT claim. HGT requires close physical contact between donor and recipient, and this could be achieved in, for example, a symbiont-host, or a trophic relationship. The former type of relationship was indeed shown to potentially result in the transfer of genetic material (e.g., Brugia malayi and Wolbachia). However, currently known endosymbionts of nematodes may not be the source of CWDEs. Remarkably, all cellulases discovered so far within the order Tylenchida belong to a single glycoside hydrolase family (GHF5). A range of soil bacteria harbours GHF5 cellulases, but of course nothing can be said about the gene content of soil bacteria at the time HGT took place (if at all). We suggest that characterisation of cellulases (and other CWDEs) and their genomic organisation in more basal (facultative) plant parasitic Tylenchida is needed to find out if CWDEs were indeed acquired via HGT from bacteria. A more complete picture about the evolution of CWDEs among plant parasitic Tylenchida will require a detailed characterisation of two - so far - fully unexplored basal suborders, Tylenchina and Criconematina. Finally, we performed a computational high-throughput identification of potential HGT candidates (including ones unrelated to CWDEs) in plant parasitic nematodes using a genomics approach.}, }
@article {pmid19271204, year = {2009}, author = {Keeling, PJ}, title = {Role of horizontal gene transfer in the evolution of photosynthetic eukaryotes and their plastids.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {532}, number = {}, pages = {501-515}, doi = {10.1007/978-1-60327-853-9_29}, pmid = {19271204}, issn = {1064-3745}, mesh = {Biological Evolution ; Chlamydiales/genetics ; Cyanobacteria/genetics ; Eukaryota/genetics ; Gene Flow ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Models, Genetic ; Photosynthesis/*genetics ; Plastids/*genetics ; Symbiosis/genetics ; }, abstract = {Plastids are the organelles derived from a cyanobacterium through endosymbiosis. Unlike mitochondria, plastids are not found in all eukaryotes, but their evolution has an added layer of complexity since plastids have moved between eukaryotic lineages by secondary and tertiary endosymbiotic events. This complex history, together with the genetic integration between plastids and their host, has led to many opportunities for gene flow between phylogenetically distinct lineages. Some intracellular transfers do not lead to a protein functioning in a new environment, but many others do and the protein makeup of many plastids appears to have been influenced by exogenous sources as well. Here, different evolutionary sources and cellular destinations of gene flow that has affected the plastid lineage are reviewed. Most horizontal gene transfer (HGT) affecting the modern plastid has taken place via the host nucleus, in the form of genes for plastid-targeted proteins. The impact of this varies greatly from lineage to lineage, but in some cases such transfers can be as high as one fifth of analyzed genes. More rarely, genes have also been transferred to the plastid genome itself, and plastid genes have also been transferred to other non-plant, non-algal lineages. Overall, the proteome of many plastids has emerged as a mosaic of proteins from many sources, some from within the same cell (e.g., cytosolic genes or genes left over from the replacement of an earlier plastid), some from the plastid of other algal lineages, and some from completely unrelated sources.}, }
@article {pmid19271203, year = {2009}, author = {Alsmark, UC and Sicheritz-Ponten, T and Foster, PG and Hirt, RP and Embley, TM}, title = {Horizontal gene transfer in eukaryotic parasites: a case study of Entamoeba histolytica and Trichomonas vaginalis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {532}, number = {}, pages = {489-500}, doi = {10.1007/978-1-60327-853-9_28}, pmid = {19271203}, issn = {1064-3745}, mesh = {Animals ; Biological Evolution ; Entamoeba histolytica/*genetics/pathogenicity ; Female ; *Gene Transfer, Horizontal ; Genes, Protozoan ; Genome-Wide Association Study ; Humans ; Phylogeny ; Trichomonas vaginalis/*genetics/pathogenicity ; }, abstract = {Over the past few years it has become apparent that horizontal gene transfer (HGT) has played an important role in the evolution of pathogenic prokaryotes. What is less clear is the exact role that HGT has played in shaping the metabolism of eukaryotic organisms. The main problems are the reliable inference of HGT on a genomic scale as well as the functional assignment of genes in these poorly studied organisms. We have screened the completed genomes of the protists Entamoeba histolytica and Trichomonas vaginalis for cases of HGT from prokaryotes. Using a fast primary screen followed by a conservative phylogenetic approach, we found 68 and 153 recent cases of HGT in the respective organisms. The majority of transferred genes that fall into functional categories code for enzymes involved in metabolism. We found a broad range of prokaryotic lineages represented among the donors, but organisms that share similar environmental niches with E. histolytica and T. vaginalis, such as the gut and the vaginal mucosa, dominate.}, }
@article {pmid19271202, year = {2009}, author = {Andersson, JO}, title = {Horizontal gene transfer between microbial eukaryotes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {532}, number = {}, pages = {473-487}, doi = {10.1007/978-1-60327-853-9_27}, pmid = {19271202}, issn = {1064-3745}, mesh = {Biological Evolution ; Eukaryotic Cells ; *Gene Transfer, Horizontal ; *Genetics, Microbial ; Phylogeny ; }, abstract = {Comparative genomics have identified two loosely defined classes of genes: widely distributed core genes that encode proteins for central functions in the cell and accessory genes that are patchily distributed across lineages and encode taxa-specific functions. Studies of microbial eukaryotes show that both categories undergo horizontal gene transfer (HGT) from prokaryotes, but also between eukaryotic organisms. Intra-domain gene transfers of most core genes seem to be relatively infrequent and therefore comparatively easy to detect using phylogenetic methods. In contrast, phylogenies of accessory genes often have complex topologies with little or no resemblance of organismal relationships typically with eukaryotes and prokaryotes intermingled, making detailed evolutionary histories difficult to interpret. Nevertheless, this suggests significant rates of gene transfer between and among the three domains of life for many of these genes, affecting a considerably diversity of eukaryotic microbes, although the current depth of taxonomic sampling usually is insufficient to pin down individual transfer events. The occurrence of intra-domain transfer among microbial eukaryotes has important implications for studies of organismal phylogeny as well as eukaryote genome evolution in general.}, }
@article {pmid19271201, year = {2009}, author = {Sobecky, PA and Coombs, JM}, title = {Horizontal gene transfer in metal and radionuclide contaminated soils.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {532}, number = {}, pages = {455-472}, doi = {10.1007/978-1-60327-853-9_26}, pmid = {19271201}, issn = {1064-3745}, mesh = {Adenosine Triphosphatases/genetics/metabolism ; Arsenate Reductases/genetics/metabolism ; Biodegradation, Environmental ; Ecosystem ; *Gene Transfer, Horizontal ; Genetics, Microbial ; Interspersed Repetitive Sequences ; Metals, Heavy/metabolism ; Plasmids/genetics ; Radioisotopes/metabolism ; *Soil Microbiology ; Soil Pollutants/*metabolism ; Soil Pollutants, Radioactive/*metabolism ; }, abstract = {The horizontal transfer of genes encoded on mobile genetic elements (MGEs) such as plasmids and phage and their associated hitchhiking elements (transposons, integrons, integrative and conjugative elements, and insertion sequences) rapidly accelerate genome diversification of microorganisms, thereby affecting their physiology, metabolism, pathogenicity,and ecological character. The analyses of completed prokaryotic genomes reveal that horizontal gene transfer (HGT) continues to be an important factor contributing to the innovation of microbial genomes. Indeed, microbial genomes are remarkably dynamic and a considerable amount of genetic information is inserted or deleted by HGT mechanisms. Thus, HGT and the vast pool of MGEs provide microbial communities with an unparalleled means by which to respond rapidly to changing environmental conditions and exploit new ecological niches. Metals and radionuclide contamination in soils, the subsurface, and aquifers poses a serious challenge to microbial growth and survival because these contaminants cannot be transformed or biodegraded into non-toxic forms as often occurs with organic xenobiotic contaminants. In this chapter we present cases in which HGT has been demonstrated to contribute to the dissemination of genes that provide adaptation to contaminant stress (i.e., toxic heavy metals and radionuclides). In addition, we present directions for future studies that could provide even greater insights into the contributions of HGT to adaptation for survival in mixed waste sites.}, }
@article {pmid19271200, year = {2009}, author = {Sobecky, PA and Hazen, TH}, title = {Horizontal gene transfer and mobile genetic elements in marine systems.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {532}, number = {}, pages = {435-453}, doi = {10.1007/978-1-60327-853-9_25}, pmid = {19271200}, issn = {1064-3745}, mesh = {Archaea/genetics ; Bacteria/genetics ; Ecosystem ; *Gene Transfer, Horizontal ; Genetic Variation ; Genetics, Microbial ; *Interspersed Repetitive Sequences ; *Marine Biology ; Plasmids/genetics ; Seawater/microbiology/virology ; Virulence/genetics ; Viruses/genetics ; }, abstract = {The pool of mobile genetic elements (MGE) in microbial communities consists of viruses, plasmids, and associated elements (insertion sequences, transposons, and integrons) that are either self-transmissible or use mobile plasmids and viruses as vehicles for their dissemination. This mobilome facilitates the horizontal transfer of genes that promote the evolution and adaptation of microbial communities. Efforts to characterize MGEs from microbial populations resident in a variety of ecological habitats have revealed a surprisingly novel and seemingly untapped biodiversity. To better understand the impact of horizontal gene transfer (HGT), as well as the agents that promote HGT in marine ecosystems and to determine whether or not environmental parameters can effect the composition and structure of the mobilome in marine microbial communities, information on the distribution, diversity, and ecological traits of the marine mobilome is presented. In this chapter we discuss recent insights gained from different methodological approaches used to characterize the biodiversity and ecology of MGE in marine environments and their contributions to HGT. In addition, we present case studies that highlight specific HGT examples in coastal, open-ocean, and deep-sea marine ecosystems.}, }
@article {pmid19271199, year = {2009}, author = {Coombs, JM}, title = {Potential for horizontal gene transfer in microbial communities of the terrestrial subsurface.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {532}, number = {}, pages = {413-433}, doi = {10.1007/978-1-60327-853-9_24}, pmid = {19271199}, issn = {1064-3745}, mesh = {Adenosine Triphosphate/metabolism ; Bacteria/genetics/metabolism ; Bacteriophages/genetics ; Ecosystem ; *Gene Transfer, Horizontal ; Genetics, Microbial ; Genomic Instability ; Interspersed Repetitive Sequences ; Phylogeny ; Plasmids/genetics ; *Soil Microbiology ; }, abstract = {The deep terrestrial subsurface is a vast, largely unexplored environment that is oligotrophic, highly heterogeneous, and may contain extremes of both physical and chemical factors. In spite of harsh conditions, subsurface studies at several widely distributed geographic sites have revealed diverse communities of viable organisms, which have provided evidence of low but detectable metabolic activity. Although much of the terrestrial subsurface may be considered to be distant and isolated, the concept of horizontal gene transfer (HGT) in this environment has far-reaching implications for bioremediation efforts and groundwater quality, industrial harvesting of subsurface natural resources such as petroleum, and accurate assessment of the risks associated with DNA release and transport from genetically modified organisms. This chapter will explore what is known about some of the major mechanisms of HGT, and how the information gained from surface organisms might apply to conditions in the terrestrial subsurface. Evidence for the presence of mobile elements in subsurface bacteria and limited retrospective studies examining genetic signatures of potential past gene transfer events will be discussed.}, }
@article {pmid19271198, year = {2009}, author = {Barlow, M}, title = {What antimicrobial resistance has taught us about horizontal gene transfer.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {532}, number = {}, pages = {397-411}, doi = {10.1007/978-1-60327-853-9_23}, pmid = {19271198}, issn = {1064-3745}, mesh = {Bacteria/drug effects/genetics ; Biological Evolution ; Conjugation, Genetic ; Drug Resistance, Bacterial/*genetics ; Fluoroquinolones/pharmacology ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Models, Genetic ; Multigene Family ; Neisseria/drug effects/genetics ; Phylogeny ; Plasmids/genetics ; Streptococcus/drug effects/genetics ; Transduction, Genetic ; beta-Lactam Resistance/genetics ; beta-Lactamases/genetics ; }, abstract = {Horizontal gene transfer (HGT) has been responsible for the dissemination of numerous antimicrobial-resistance determinants throughout diverse bacterial species. The rapid and broad dissemination of resistance determinants by HGT, and subsequent selection for resistance imposed by the use of antimicrobials, threatens to undermine the usefulness of antimicrobials. However, vigilant surveillance of the emerging antimicrobial resistance in clinical settings and subsequent studies of resistant isolates create a powerful system for studying HGT and detecting rare events. Two of the most closely monitored phenotypes are resistance to beta-lactams and resistance to fluoroquinolones. Studies of resistance to these antimicrobials have revealed that (1) transformation occurs between different species of bacteria including some recipient species that were not previously known to be competent for natural transformation; (2) transduction may be playing an important role in generating novel methicillin-resistant Staphylococcus aureus (MRSA) strains, although the details of transferring the SCCmec element are not yet fully understood; (3) Resistance genes are probably moving to plasmids from chromosomes more rapidly than in the past; and (4) Resistance genes are aggregating upon plasmids. The linkage of numerous resistance genes on individual plasmids may underlie the persistence of resistance to specific antimicrobials even when use of those antimicrobials is discontinued. Further studies of HGT and methods for controlling HGT may be necessary to maintain the usefulness of antimicrobials.}, }
@article {pmid19271197, year = {2009}, author = {Thane Papke, R}, title = {A critique of prokaryotic species concepts.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {532}, number = {}, pages = {379-395}, doi = {10.1007/978-1-60327-853-9_22}, pmid = {19271197}, issn = {1064-3745}, mesh = {Archaea/classification/*genetics ; Bacteria/classification/*genetics ; Biological Evolution ; Gene Transfer, Horizontal ; *Genetic Speciation ; Halorubrum/genetics ; Models, Genetic ; Phylogeny ; Selection, Genetic ; }, abstract = {Developments in DNA sequencing and population genetics analyses have revealed unanticipated complexity in prokaryotic variation. The observation that genetic traits are horizontally inherited at unexpected rates within and between closely related asexually reproducing lineages impacts our comprehension of prokaryotic evolution and ecology. As a result, the concepts that point to species as being discrete clusters or monophyletic lineages are at odds with most of the data, suggesting that taxon circumscription can only proceed by informed compromise, pragmatism, and subjectivity.}, }
@article {pmid19271196, year = {2009}, author = {Riley, MA and Lizotte-Waniewski, M}, title = {Population genomics and the bacterial species concept.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {532}, number = {}, pages = {367-377}, pmid = {19271196}, issn = {1064-3745}, support = {R01 AI064588/AI/NIAID NIH HHS/United States ; R01 AI064588-01A2/AI/NIAID NIH HHS/United States ; R01 GM068657/GM/NIGMS NIH HHS/United States ; R01 GM068657-01A2/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/classification/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genetic Speciation ; Genetics, Population ; Genomics ; Models, Genetic ; Phylogeny ; }, abstract = {In recent years, the importance of horizontal gene transfer (HGT) in bacterial evolution has been elevated to such a degree that many bacteriologists now question the very existence of bacterial species. If gene transfer is as rampant as comparative genomic studies have suggested, how could bacterial species survive such genomic fluidity? And yet, most bacteriologists recognize, and name, as species, clusters of bacterial isolates that share complex phenotypic properties. The Core Genome Hypothesis (CGH) has been proposed to explain this apparent paradox of fluid bacterial genomes associated with stable phenotypic clusters. It posits that there is a core of genes responsible for maintaining the species-specific phenotypic clusters observed throughout bacterial diversity and argues that, even in the face of substantial genomic fluidity, bacterial species can be rationally identified and named.}, }
@article {pmid19271195, year = {2009}, author = {Yerrapragada, S and Siefert, JL and Fox, GE}, title = {Horizontal gene transfer in cyanobacterial signature genes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {532}, number = {}, pages = {339-366}, doi = {10.1007/978-1-60327-853-9_20}, pmid = {19271195}, issn = {1064-3745}, mesh = {Cyanobacteria/classification/*genetics/physiology ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Models, Genetic ; Phenotype ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Comparison of 15 phylogenetically diverse cyanobacterial genomes identified an updated list of 183 signature genes that are widely found in cyanobacteria but absent in non-cyanobacterial species. These signature genes comprise the unique portion of the core cyanobacterial phenotype, and their absence from other lineages implies that if they arose by horizontal gene transfer (HGT), it likely occurred before the last shared cyanobacterial ancestor. A remaining issue is whether or not these signature genes would be relatively immune to HGT within the cyanobacterial lineage. Phylogenetic trees for each signature gene were constructed and compared to cyanobacterial groupings based on 16S rRNA sequences, with clear incongruence considered indicative of HGT. Approximately 18% of the signature genes exhibited such anomalies, indicating that the incidence of inter-lineage HGT has been significant. A preliminary analysis of intra-lineage transfer was conducted using four Synechococcus/Prochlorococcus species. In this case, it was found that 13% of the signature genes had likely been involved in within group HGT. In order to compare this level of likely HGT to other gene types, the analysis was extended to 1380 genes shared by the four Synechococcus/Prochlorococcus species. Successful HGT events appear to be most frequent among genes involved in photosynthesis/respiration and genes of unknown function, many of which are signature genes. This is consistent with the hypothesis that genes that most directly effect competition and adaptation of similar species in neighboring niches would be most usefully transferred. Such genes may be more easily integrated into a new genomic environment due to close similarities in regulatory circuits. In summary, signature genes are not immune from HGT and in fact may be favored candidates for HGT among closely related cyanobacterial strains.}, }
@article {pmid19271194, year = {2009}, author = {Raymond, J}, title = {The role of horizontal gene transfer in photosynthesis, oxygen production, and oxygen tolerance.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {532}, number = {}, pages = {323-338}, doi = {10.1007/978-1-60327-853-9_19}, pmid = {19271194}, issn = {1064-3745}, mesh = {Archaea/genetics/metabolism ; Biological Evolution ; Catalase/genetics/metabolism ; Cyanobacteria/genetics/metabolism ; *Gene Transfer, Horizontal ; History, Ancient ; Oxygen/history/*metabolism ; Photosynthesis/*genetics ; Phylogeny ; Proteobacteria/genetics/metabolism ; Superoxide Dismutase/genetics/metabolism ; }, abstract = {One of the pivotal events during the early evolution of life was the advent of oxygenic photosynthesis, responsible for producing essentially all of the free oxygen in Earth's atmosphere. This molecular innovation required the development of two tandemly linked photosystems that generate a redox potential strong enough to oxidize water and then funnel those electrons ultimately to cellular processes like carbon and nitrogen fixation. The by-product of this reaction, molecular oxygen, spawned an entirely new realm of enzymatic reactions that served to mitigate its potential toxicity, as well as to take advantage of the free energy available from using O(2) as an electron acceptor. These ensuing events ultimately gave rise to aerobic, multicelled eukaryotes and new levels of biological complexity. Remarkably, instances of horizontal gene transfer have been identified at nearly every step in this transformation of the biosphere, from the evolution and radiation of photosynthesis to the development of biological pathways dependent on oxygen. This chapter discusses the evidence and examples of some of these occurrences that have been elucidated in recent years.}, }
@article {pmid19271193, year = {2009}, author = {Noll, KM and Thirangoon, K}, title = {Interdomain transfers of sugar transporters overcome barriers to gene expression.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {532}, number = {}, pages = {309-322}, doi = {10.1007/978-1-60327-853-9_18}, pmid = {19271193}, issn = {1064-3745}, mesh = {ATP-Binding Cassette Transporters/*genetics ; Archaea/genetics ; *Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; Models, Genetic ; Monosaccharide Transport Proteins/genetics ; Operon ; Phylogeny ; Thermotoga maritima/*genetics ; }, abstract = {Horizontal gene transfer (HGT) is nature's mechanism for sharing evolved physiological traits among the members of microbial communities. The extent to which such transfers can be successful is best illustrated by the fact that Archaea-derived genes are found in many bacterial genomes, particularly those in the hyperthermophile Thermotoga maritima. The success of these intergenomic transfers depends upon the successful transcription of the newly acquired archaeal genes using a bacterial transcription machinery that does not recognize archaeal transcriptional signals. To examine how nature solves this problem, we looked to the T. maritima genome for examples of interdomain transfers. Here we lay the groundwork to examine this problem by more clearly delineating the phylogenetic history of Archaea-derived transporter genes in this genome. We find that five of these polysaccharide transporters were derived from the Archaea and one came from the Archaea after that lineage inherited it from the Bacteria. These data can be used for more detailed examinations of the recombinations that allowed these transporters to be expressed in a bacterial host. This work will guide examinations of the genome sequences from other members of the Thermotogales, which will become available.}, }
@article {pmid19271192, year = {2009}, author = {Smets, BF and Lardon, L}, title = {Mass action models describing extant horizontal transfer of plasmids: inferences and parameter sensitivities.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {532}, number = {}, pages = {289-305}, doi = {10.1007/978-1-60327-853-9_17}, pmid = {19271192}, issn = {1064-3745}, mesh = {Computer Simulation ; *Gene Transfer, Horizontal ; Genetics, Microbial ; *Models, Genetic ; Plasmids/*genetics ; Software ; }, abstract = {Predicting the fate of horizontally transmissible elements in extant microbial communities might be facilitated by the availability of suitable mathematical models. Since the mid-1970s, mass action models have been introduced to describe the transfer of conjugal and mobilizable genetic elements. This chapter will summarize and explain the assumptions behind spatially homogenous models, and show the predictions by these models under typical scenarios, such as evaluating existence conditions of conjugal plasmids under chemostat or seasonal growth conditions. Special attention is given to the sensitivity of the outcomes to the various plasmid dynamic parameters. For our analysis, we developed a set of user-friendly MatLab routines, which are deposited in the public domain. We hope that the availability of these routines will encourage the computationally untrained microbiologist to make use of these mathematical models. Finally, further permutations, as well as limitations of these mass action models in view of the structured complexity of most microbial systems are addressed.}, }
@article {pmid19271191, year = {2009}, author = {Larios-Sanz, M and Travisano, M}, title = {Experimental evolution of an essential Bacillus gene in an E. coli host.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {532}, number = {}, pages = {269-287}, doi = {10.1007/978-1-60327-853-9_16}, pmid = {19271191}, issn = {1064-3745}, mesh = {Bacillus/*genetics/metabolism ; *Biological Evolution ; Escherichia coli/*genetics/metabolism ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genetic Techniques ; Models, Genetic ; Plasmids/genetics ; Selection, Genetic ; Sucrose/metabolism ; }, abstract = {The acquisition of foreign genes by HGT potentially greatly speeds up adaptation by allowing faster evolution of beneficial traits. The evolutionary integration of novel genes into host gene expression and physiology is critical for adaptation by HGT, but remains largely unknown. We are exploring the evolutionary consequences of gene acquisition in populations of Escherichia coli in real time. A plasmid bearing the genes necessary for sucrose catabolism was constructed and introduced into a single E. coli genotype. Wild-type E. coli is generally incapable of utilizing sucrose, but E. coli transformants were able to grow on sucrose as a sole carbon and energy source, albeit poorly. Twelve replicate populations were initiated and propagated in sucrose minimal media for 300 generations. Over this time, we observed large fitness improvements in the selected environment. These results demonstrate the potential for HGT to substantially increase microbial niche breadth.}, }
@article {pmid19271189, year = {2009}, author = {Beiko, RG and Ragan, MA}, title = {Untangling hybrid phylogenetic signals: horizontal gene transfer and artifacts of phylogenetic reconstruction.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {532}, number = {}, pages = {241-256}, doi = {10.1007/978-1-60327-853-9_14}, pmid = {19271189}, issn = {1064-3745}, mesh = {Databases, Genetic ; *Gene Transfer, Horizontal ; Models, Genetic ; *Phylogeny ; Software ; }, abstract = {Phylogenomic methods can be used to investigate the tangled evolutionary relationships among genomes. Building 'all the trees of all the genes' can potentially identify common pathways of horizontal gene transfer (HGT) among taxa at varying levels of phylogenetic depth. Phylogenetic affinities can be aggregated and merged with the information about genetic linkage and biochemical function to examine hypotheses of adaptive evolution via HGT. Additionally, the use of many genetic data sets increases the power of statistical tests for phylogenetic artifacts. However, large-scale phylogenetic analyses pose several challenges, including the necessary abandonment of manual validation techniques, the need to translate inferred phylogenetic discordance into inferred HGT events, and the challenges involved in aggregating results from search-based inference methods. In this chapter we describe a tree search procedure to recover the most parsimonious pathways of HGT, and examine some of the assumptions that are made by this method.}, }
@article {pmid19271188, year = {2009}, author = {Poptsova, M}, title = {Testing phylogenetic methods to identify horizontal gene transfer.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {532}, number = {}, pages = {227-240}, doi = {10.1007/978-1-60327-853-9_13}, pmid = {19271188}, issn = {1064-3745}, mesh = {Computer Simulation ; Cyanobacteria/genetics ; Gammaproteobacteria/genetics ; *Gene Transfer, Horizontal ; Genetic Techniques ; Genetics, Microbial ; Models, Genetic ; *Phylogeny ; }, abstract = {The subject of this chapter is to describe the methodology for assessing the power of phylogenetic HGT detection methods. Detection power is defined in the framework of hypothesis testing. Rates of false positives and false negatives can be estimated by testing HGT detection methods on HGT-free orthologous sets, and on the same sets with in silico simulated HGT events. The whole process can be divided into three steps: obtaining HGT-free orthologous sets, in silico simulation of HGT events in the same set, and submitting both sets for evaluation by any of the tested methods.Phylogenetic methods of HGT detection can be roughly divided into three types: likelihood-based tests of topologies (Kishino-Hasegawa (KH), Shimodaira-Hasegawa (SH), and Approximately Unbiased (AU) tests), tree distance methods (symmetrical difference of Robinson and Foulds (RF), and Subtree Pruning and Regrafting (SPR) distances), and genome spectral approaches (bipartition and quartet decomposition analysis). Restrictions that are inherent to phylogenetic methods of HGT detection in general and the power and precision of each method are discussed and comparative analyses of different approaches are provided, as well as some examples of assessing the power of phylogenetic HGT detection methods from a case study of orthologous sets from gamma-proteobacteria (Poptsova and Gogarten, BMC Evol Biol 7, 45, 2007) and cyanobacteria (Zhaxybayeva et al., Genome Res 16, 1099-108, 2006).}, }
@article {pmid19271187, year = {2009}, author = {Cortez, D and Delaye, L and Lazcano, A and Becerra, A}, title = {Composition-based methods to identify horizontal gene transfer.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {532}, number = {}, pages = {215-225}, doi = {10.1007/978-1-60327-853-9_12}, pmid = {19271187}, issn = {1064-3745}, mesh = {Base Composition ; Bayes Theorem ; Codon ; Databases, Nucleic Acid ; Escherichia coli K12/genetics ; *Gene Transfer, Horizontal ; Genetics, Microbial ; Genomics/*methods/statistics &amp; numerical data ; Markov Chains ; Models, Genetic ; Pseudogenes ; }, abstract = {The detection of horizontal gene transfer (HGT) events has become an increasingly important issue in recent years. Here we discuss a simple theoretical analysis based on the in silico artificial addition of known foreign genes from different prokaryotic groups into the genome of Escherichia coli K12 MG1655. Using this dataset as a control, we have tested the efficiency of four methodologies commonly employed to detect HGT, which are based on (a) the codon adaptation index, codon usage, and GC percentage (CAI/GC); (b) the distributional profile (DP) approach with a gene search in the closely related phylogenetic genomes; (c) the Bayesian model (BM); and (d) the first-order Markov model (MM). All methods exhibit limitations as shown here, with BM and MM giving better approximations. The MM has a better detection rate when genes from closely related organisms are evaluated. The application of the MM to detect recently transferred genes in the genomes of E. coli strain K12 MG1655 shows that this organism has undergone a rather significant amount of HGT, several of which have well-defined functions that appear to be involved in the direct interaction of the organisms with their environment.}, }
@article {pmid19271186, year = {2009}, author = {Zhaxybayeva, O}, title = {Detection and quantitative assessment of horizontal gene transfer.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {532}, number = {}, pages = {195-213}, doi = {10.1007/978-1-60327-853-9_11}, pmid = {19271186}, issn = {1064-3745}, mesh = {Computational Biology ; Databases, Genetic/statistics &amp; numerical data ; *Gene Transfer, Horizontal ; Genomics/*methods/statistics &amp; numerical data ; Models, Genetic ; Phylogeny ; }, abstract = {This chapter discusses the pros and cons of the existing computational methods for the detection of horizontal (or lateral) gene transfer and highlights the genome-wide studies utilizing these methods. The impact of horizontal gene transfer (HGT) on prokaryote genome evolution is discussed.}, }
@article {pmid19271185, year = {2009}, author = {Margulis, L}, title = {Genome acquisition in horizontal gene transfer: symbiogenesis and macromolecular sequence analysis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {532}, number = {}, pages = {181-191}, doi = {10.1007/978-1-60327-853-9_10}, pmid = {19271185}, issn = {1064-3745}, mesh = {Animals ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genetic Speciation ; Genetics, Microbial ; *Genome ; Models, Genetic ; Nucleic Acids/genetics ; Phylogeny ; Proteins/genetics ; Replicon ; }, abstract = {Phylogenetic diagrams ("trees of life") based on computer-generated analyses of nucleic acid (DNA, RNA) or protein (amino acid residues) sequences are purported to reconstruct evolutionary history of the living organisms from which the macromolecules were isolated (1). "Horizontal gene transfer", an expression that refers to the ad hoc explanation of anomalous distribution of these macromolecular sequences, is an inferred past event to explain evolution that, even in principle, is not documentable. Although the diagrams ("phylogenies") help establish the details of relationships among important and widely distributed essential components of living systems (e.g., DNA of large and small replicons such as plasmids, viruses, genophores), chromatin, or protein enzymes that have conserved their function throughout the history of the evolutionary lineage (e.g., DNA that codes for polymerases or 16/18S ribosomal RNA), the HGT concept is an Alfred North Whiteheadian fallacy of misplaced concreteness (2). It is deeply flawed because of sets of unstated, unwarranted assumptions accepted as fact by practitioners: genomics and proteomic experts. They tend to be zoocentric and in particular anthropocentric computer scientists. Their relative lack of familiarity with the fossil record, hard-won life histories and transmission-genetics, taxonomy, physiology, metabolism, and ecology of the communities in which the organisms invariably reside, and many other aspects of life have led to codification of systematic errors in analysis of their, often superb, molecular data. Here we point to a prodigious but little-known symbiogenesis literature that contrasts the transfer of sets of genes with HGT taken to mean one or a-very-few-genes at a time.}, }
@article {pmid19271184, year = {2009}, author = {Fournier, G}, title = {Horizontal gene transfer and the evolution of methanogenic pathways.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {532}, number = {}, pages = {163-179}, doi = {10.1007/978-1-60327-853-9_9}, pmid = {19271184}, issn = {1064-3745}, mesh = {*Biological Evolution ; Clostridium/genetics/metabolism ; Euryarchaeota/classification/genetics/metabolism ; *Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; Metabolic Networks and Pathways/genetics ; Methane/*metabolism ; Models, Biological ; Models, Genetic ; Phylogeny ; }, abstract = {Horizontal gene transfer (HGT) is a driving force in the evolution of metabolic pathways, allowing novel enzymatic functions that provide a selective advantage to be rapidly incorporated into an organism's physiology. Here, the role of two HGT events in the evolution of methanogenesis is described. First, the acetoclastic sub-pathway of methanogenesis is shown to have evolved via a transfer of the ackA and pta genes from a cellulolytic clostridia to a family of methanogenic archaea. Second, the system for encoding the amino acid pyrrolysine, used for the synthesis of enzymes for methanogenesis from methylamines, is shown to likely have evolved via transfer from an ancient, unknown, deeply branching organismal lineage.}, }
@article {pmid19271183, year = {2009}, author = {House, CH}, title = {The tree of life viewed through the contents of genomes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {532}, number = {}, pages = {141-161}, doi = {10.1007/978-1-60327-853-9_8}, pmid = {19271183}, issn = {1064-3745}, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal ; Genetics, Microbial ; *Genome ; Genomic Instability ; Phylogeny ; RNA, Ribosomal/genetics ; }, abstract = {A universal Tree of Life has been a longstanding goal of the biosciences. The most common Tree of Life, based on the small subunit rRNA gene, may or may not represent the phylogenetic history of microorganisms. The horizontal transfer of genes from one taxon to another provides a means by which each gene may tell of an independent history. When complete genomes became available, the extent to which horizontal gene transfer (HGT) has occurred became more evident. When using genomic data to study the Tree of Life, one can use any of the four broad approaches: (i) build lots of individual gene trees ("phylogenomics"), (ii) concatenate genes together for an analysis yielding one "supergene" tree, (iii) form a single tree based on the "gene content" within genomes using either orthologs or homologs, or (iv) investigate the order of genes within genomes to discern some aspects of microbial evolution. The application of whole genome tree building has suggested that there is a core tree, that such a core tree can be investigated using these varied methods, and that the results are largely similar to those of the rRNA universal Tree of Life. Some of the most interesting features of the rRNA tree, such as early diverging hyperthermophilic lineages are still uncertain, but remain a possibility. Genomic trees and geologic evidence together suggest that the vertical descent of genes and the horizontal transfer of genes between genetically similar lineages ultimately results in a core Tree of Life with at least some lineages that have phenotypic characteristics recognizable for billions of years.}, }
@article {pmid19271182, year = {2009}, author = {Huang, J and Gogarten, JP}, title = {Ancient gene transfer as a tool in phylogenetic reconstruction.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {532}, number = {}, pages = {127-139}, doi = {10.1007/978-1-60327-853-9_7}, pmid = {19271182}, issn = {1064-3745}, mesh = {Animals ; Archaea/classification/genetics ; Biological Evolution ; Cyanobacteria/classification/genetics ; *Gene Transfer, Horizontal ; Humans ; *Phylogeny ; Plants/classification/genetics ; Rhodophyta/classification/genetics ; Threonine-tRNA Ligase/genetics ; Tyrosine-tRNA Ligase/genetics ; }, abstract = {Although horizontal gene transfer (HGT) is often considered as a disruptive force in reconstructing organismal phylogeny, it can also be a valuable phylogenetic tool. A gene in the net of life is often horizontally transferred to the ancestor of a major lineage. If the gene is retained in the recipient and its descendants, it will constitute a shared derived character and mark the recipient and all descendants as a monophyletic group. Additionally, phylogenetically informative HGTs also provide information about the sequence of emergence of involved taxa, because the donor organism must have emerged at least as early as the recipient. Here we review the recent applications of ancient HGT events in reconstructing organismal phylogeny as well as the promise and potential pitfalls of this approach.}, }
@article {pmid19271181, year = {2009}, author = {Labbate, M and Case, RJ and Stokes, HW}, title = {The integron/gene cassette system: an active player in bacterial adaptation.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {532}, number = {}, pages = {103-125}, doi = {10.1007/978-1-60327-853-9_6}, pmid = {19271181}, issn = {1064-3745}, mesh = {Adaptation, Physiological/genetics ; Bacteria/*genetics ; Bacterial Physiological Phenomena ; Base Sequence ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Integrons ; Sequence Homology, Nucleic Acid ; }, abstract = {The integron includes a site-specific recombination system capable of integrating and expressing genes contained in structures called mobile gene cassettes. Integrons were originally identified on mobile elements from pathogenic bacteria and were found to be a major reservoir of antibiotic-resistance genes. Integrons are now known to be ancient structures that are phylogenetically diverse and, to date, have been found in approximately 9% of sequenced bacterial genomes. Overall, gene diversity in cassettes is extraordinarily high, suggesting that the integron/gene cassette system has a broad role in adaptation rather than being confined to simply conferring resistance to antibiotics. In this chapter, we provide a review of the integron/gene cassette system highlighting characteristics associated with this system, diversity of elements contained within it, and their importance in driving bacterial evolution and consequently adaptation. Ideas on the evolution of gene cassettes and gene cassette arrays are discussed.}, }
@article {pmid19271180, year = {2009}, author = {Bahl, MI and Hansen, LH and Sørensen, SJ}, title = {Persistence mechanisms of conjugative plasmids.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {532}, number = {}, pages = {73-102}, doi = {10.1007/978-1-60327-853-9_5}, pmid = {19271180}, issn = {1064-3745}, mesh = {Antisense Elements (Genetics) ; Bacteria/genetics ; Base Composition ; *Conjugation, Genetic ; DNA Restriction-Modification Enzymes/genetics ; DNA, Bacterial/chemistry/genetics ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genome, Bacterial ; Genomic Instability ; Models, Genetic ; Plasmids/*genetics ; }, abstract = {Are plasmids selfish parasitic DNA molecules or an integrated part of the bacterial genome? This chapter reviews the current understanding of the persistence mechanisms of conjugative plasmids harbored by bacterial cells and populations. The diversity and intricacy of mechanisms affecting the successful propagation and long-term continued existence of these extra-chromosomal elements is extensive. Apart from the accessory genetic elements that may provide plasmid-harboring cells a selective advantage, special focus is placed on the mechanisms conjugative plasmids employ to ensure their stable maintenance in the host cell. These importantly include the ability to self-mobilize in a process termed conjugative transfer, which may occur across species barriers. Other plasmid stabilizing mechanisms include the multimer resolution system, active partitioning, and post-segregational-killing of plasmid-free cells. Finally, various molecular adaptations of plasmids to better match the genetic background of their bacterial host cell will be described.}, }
@article {pmid19271179, year = {2009}, author = {Bapteste, E and Boucher, Y}, title = {Epistemological impacts of horizontal gene transfer on classification in microbiology.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {532}, number = {}, pages = {55-72}, doi = {10.1007/978-1-60327-853-9_4}, pmid = {19271179}, issn = {1064-3745}, mesh = {Biological Evolution ; Classification/*methods ; *Gene Transfer, Horizontal ; Genetic Speciation ; *Genetics, Microbial ; Models, Genetic ; Philosophy ; Phylogeny ; }, abstract = {We describe the reasons why the newly recognized process of horizontal gene transfer (HGT) forces evolutionists who study classification and microbiology to go beyond the classical Darwinian framework. We recall the importance of processes in philosophical definitions of species and for taxonomical purposes in general. More precisely, we present a brief description of a possible transition from a thinking inspired by essentialism to eliminative pluralism in the species debate and we insist on a major philosophical lesson: that processes matter and that, consequently, HGT cannot be overlooked in microbial classification. We then expand the conclusions of eliminative pluralism to microbial classification, namely (i) that species are not real and (ii) that overlapping taxonomies are equally legitimate when they are based on real natural processes. We introduce alternatives to the traditional species concept and describe what we call evolutionary units. Two types of units can be described: coherent and composite. The former are sets of co-evolving genes, pathways, or organisms, which share the same phylogenetic origin, while the latter comprise genes, pathways, or organisms with component parts from multiple phylogenetic origins. These evolutionary units are either "mostly flexible" or "mostly rigid" in their genetic composition and we discuss how this dissimilarity could profoundly affect our systematics practice. In this chapter, we illustrate how much there is to learn from the reconstruction of the complex evolutionary histories of all evolutionary units - large or small - by giving up the notion of species for recombining microbes, and suggest replacing a unique nested hierarchy of life with a comprehensive database including overlapping taxonomical groups.}, }
@article {pmid19271178, year = {2009}, author = {Lawrence, JG and Retchless, AC}, title = {The interplay of homologous recombination and horizontal gene transfer in bacterial speciation.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {532}, number = {}, pages = {29-53}, doi = {10.1007/978-1-60327-853-9_3}, pmid = {19271178}, issn = {1064-3745}, support = {GM078092/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/classification/*genetics ; Biological Evolution ; Ecosystem ; *Gene Transfer, Horizontal ; *Genetic Speciation ; Genome, Bacterial ; Models, Genetic ; Mutation ; *Recombination, Genetic ; Selection, Genetic ; Time Factors ; }, abstract = {Bacteria experience recombination in two ways. In the context of the Biological Species concept, allelic exchange purges genic variability within bacterial populations as gene exchange mediates selective sweeps. In contrast, horizontal gene transfer (HGT) increases the size of the population's pan-genome by providing an influx of novel genetic material. Here we discuss the interplay of these two processes, with an emphasis on how they allow for the maintenance of genotypically cohesive bacterial populations, yet allow for the separation of these populations upon bacterial speciation. In populations that maintain genotypic similarity by frequent allelic exchange, horizontally transferred genes may initiate ecological barriers to genetic exchange. The resulting recombination interference allows for the accumulation of neutral mutations and, consequently, the imposition of a pre-mating barrier to gene transfer.}, }
@article {pmid19271177, year = {2009}, author = {Siefert, JL}, title = {Defining the mobilome.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {532}, number = {}, pages = {13-27}, doi = {10.1007/978-1-60327-853-9_2}, pmid = {19271177}, issn = {1064-3745}, mesh = {Bacteriophages/genetics ; DNA Transposable Elements/genetics ; *Gene Transfer, Horizontal ; Genome ; Inteins ; Interspersed Repetitive Sequences ; Introns ; Phylogeny ; Plasmids/genetics ; }, abstract = {This chapter defines the agents that provide for the movement of genetic material which fuels the adaptive potential of life on our planet. The chapter has been structured to be broadly comprehensive, arbitrarily categorizing the mobilome into four classes: (1) transposons, (2) plasmids, (3) bacteriophage, and (4) self-splicing molecular parasites.Our increasing understanding of the mobilome is as dynamic as the mobilome itself. With continuing discovery, it is clear that nature has not confined these genomic agents of change to neat categories, but rather the classification categories overlap and intertwine. Massive sequencing efforts and their published analyses are continuing to refine our understanding of the extent of the mobilome. This chapter provides a framework to describe our current understanding of the mobilome and a foundation on which appreciation of its impact on genome evolution can be understood.}, }
@article {pmid19271176, year = {2009}, author = {Olendzenski, L and Gogarten, JP}, title = {Gene transfer: who benefits?.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {532}, number = {}, pages = {3-9}, doi = {10.1007/978-1-60327-853-9_1}, pmid = {19271176}, issn = {1064-3745}, mesh = {*Biological Evolution ; *Gene Transfer, Horizontal ; Genetics, Microbial ; Selection, Genetic ; }, abstract = {Horizontal gene and genome transfer forces us to recognize that life evolves by fusion as well as bifurcation of lineages, and necessitates the expansion of traditional views of evolution. This chapter reviews the role that horizontal gene transfer (HGT) may play in integrating selection at the gene, species, and community levels. Additionally, we provide an overview of the structure and content of this book, which reflects current thought in the dynamic field of HGT research.}, }
@article {pmid19270126, year = {2009}, author = {Toomey, N and Monaghan, A and Fanning, S and Bolton, D}, title = {Transfer of antibiotic resistance marker genes between lactic acid bacteria in model rumen and plant environments.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {10}, pages = {3146-3152}, pmid = {19270126}, issn = {1098-5336}, mesh = {Animals ; Cattle ; Conjugation, Genetic ; DNA Transposable Elements ; DNA, Bacterial/genetics ; *Drug Resistance, Bacterial ; *Gene Transfer, Horizontal ; Gram-Positive Bacteria/*genetics/metabolism ; Lactic Acid/*metabolism ; Microbial Sensitivity Tests ; Plants/*microbiology ; Plasmids ; Rumen/*microbiology ; }, abstract = {Three wild-type dairy isolates of lactic acid bacteria (LAB) and one Lactococcus lactis control strain were analyzed for their ability to transfer antibiotic resistance determinants (plasmid or transposon located) to two LAB recipients using both in vitro methods and in vivo models. In vitro transfer experiments were carried out with the donors and recipients using the filter mating method. In vivo mating examined transfer in two natural environments, a rumen model and an alfalfa sprout model. All transconjugants were confirmed by Etest, PCR, pulsed-field gel electrophoresis, and Southern blotting. The in vitro filter mating method demonstrated high transfer frequencies between all LAB pairs, ranging from 1.8 x 10(-5) to 2.2 x 10(-2) transconjugants per recipient. Transconjugants were detected in the rumen model for all mating pairs tested; however, the frequencies of transfer were low and inconsistent over 48 h (ranging from 1.0 x 10(-9) to 8.0 x 10(-6) transconjugants per recipient). The plant model provided an environment that appeared to promote comparatively higher transfer frequencies between all LAB pairs tested over the 9-day period (transfer frequencies ranged from 4.7 x 10(-4) to 3.9 x 10(-1) transconjugants per recipient). In our test models, dairy cultures of LAB can act as a source of mobile genetic elements encoding antibiotic resistance that can spread to other LAB. This observation could have food safety and public health implications.}, }
@article {pmid19270122, year = {2009}, author = {Andeer, PF and Stahl, DA and Bruce, NC and Strand, SE}, title = {Lateral transfer of genes for hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) degradation.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {10}, pages = {3258-3262}, pmid = {19270122}, issn = {1098-5336}, mesh = {Actinomycetales/*genetics/metabolism ; Cytochrome P-450 Enzyme System/*genetics/metabolism ; DNA, Bacterial/chemistry/*genetics ; Gene Transfer, Horizontal ; Molecular Sequence Data ; NADH, NADPH Oxidoreductases/*genetics/metabolism ; Phylogeny ; Plasmids ; Rhodococcus/*genetics ; Sequence Analysis, DNA ; Sequence Homology ; Triazines/*metabolism ; }, abstract = {Recent studies demonstrated that degradation of the military explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) by species of Rhodococcus, Gordonia, and Williamsia is mediated by a novel cytochrome P450 with a fused flavodoxin reductase domain (XplA) in conjunction with a flavodoxin reductase (XplB). Pulse field gel analysis was used to localize xplA to extrachromosomal elements in a Rhodococcus sp. and distantly related Microbacterium sp. strain MA1. Comparison of Rhodococcus rhodochrous 11Y and Microbacterium plasmid sequences in the vicinity of xplB and xplA showed near identity (6,710 of 6,721 bp). Sequencing of the associated 52.2-kb region of the Microbacterium plasmid pMA1 revealed flanking insertion sequence elements and additional genes implicated in RDX uptake and degradation.}, }
@article {pmid19270086, year = {2009}, author = {McBride, SM and Coburn, PS and Baghdayan, AS and Willems, RJ and Grande, MJ and Shankar, N and Gilmore, MS}, title = {Genetic variation and evolution of the pathogenicity island of Enterococcus faecalis.}, journal = {Journal of bacteriology}, volume = {191}, number = {10}, pages = {3392-3402}, pmid = {19270086}, issn = {1098-5530}, support = {F32 DK082156-01/DK/NIDDK NIH HHS/United States ; EY07156/EY/NEI NIH HHS/United States ; EY014104/EY/NEI NIH HHS/United States ; DK082156/DK/NIDDK NIH HHS/United States ; R01 AI072360/AI/NIAID NIH HHS/United States ; AI072360/AI/NIAID NIH HHS/United States ; AI059673/AI/NIAID NIH HHS/United States ; AI41108/AI/NIAID NIH HHS/United States ; T32 EY007156/EY/NEI NIH HHS/United States ; F32 DK082156-02/DK/NIDDK NIH HHS/United States ; F32 DK082156/DK/NIDDK NIH HHS/United States ; R01 AI041108/AI/NIAID NIH HHS/United States ; P30 EY014104/EY/NEI NIH HHS/United States ; R01 AI059673/AI/NIAID NIH HHS/United States ; }, mesh = {Enterococcus faecalis/classification/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genetic Variation/*genetics ; Genomic Islands/*genetics ; Multigene Family/genetics ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; }, abstract = {Enterococcus faecalis is a leading cause of nosocomial infections and is known for its ability to acquire and transfer virulence and antibiotic resistance determinants from other organisms. A 150-kb pathogenicity island (PAI) encoding several genes that contribute to pathogenesis was identified among antibiotic-resistant clinical isolates. In the current study, we examined the structure of the PAI in a collection of isolates from diverse sources in order to gain insight into its genesis and dynamics. Using multilocus sequence typing to assess relatedness at the level of strain background and microarray analysis to identify variations in the PAI, we determined the extent to which structural variations occur within the PAI and also the extent to which these variations occur independently of the chromosome. Our findings provide evidence for a modular gain of defined gene clusters by the PAI. These results support horizontal transfer as the mechanism for accretion of genes into the PAI and highlight a likely role for mobile elements in the evolution of the E. faecalis PAI.}, }
@article {pmid19269603, year = {2009}, author = {Hagi, T and Minagawa, A and Shima, J}, title = {Dynamics of genetically modified Lactococcus lactis in simulated natural environments and impacts on microbial communities.}, journal = {Journal of bioscience and bioengineering}, volume = {107}, number = {3}, pages = {339-343}, doi = {10.1016/j.jbiosc.2008.11.006}, pmid = {19269603}, issn = {1347-4421}, mesh = {*Ecosystem ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Lactococcus lactis/*genetics/physiology ; Soil Microbiology ; Water Microbiology ; }, abstract = {The survival, impacts on microbiota and gene transfer ability of genetically modified (GM) Lactococcus lactis containing ermAM gene in soil and water environments were investigated. After inoculation of GM L. lactis into environments, its DNA remained longer, and the microbial community was changed. No transfer of chromosomal ermAM was observed.}, }
@article {pmid19266030, year = {2009}, author = {Sankar, TS and Neelakanta, G and Sangal, V and Plum, G and Achtman, M and Schnetz, K}, title = {Fate of the H-NS-repressed bgl operon in evolution of Escherichia coli.}, journal = {PLoS genetics}, volume = {5}, number = {3}, pages = {e1000405}, pmid = {19266030}, issn = {1553-7404}, mesh = {Bacterial Proteins/genetics/*metabolism ; DNA-Binding Proteins/genetics/*metabolism ; Down-Regulation ; Enterobacteriaceae/classification/genetics ; Escherichia coli/classification/*genetics/metabolism ; Escherichia coli Proteins/genetics/*metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Operon ; Phylogeny ; }, abstract = {In the enterobacterial species Escherichia coli and Salmonella enterica, expression of horizontally acquired genes with a higher than average AT content is repressed by the nucleoid-associated protein H-NS. A classical example of an H-NS-repressed locus is the bgl (aryl-beta,D-glucoside) operon of E. coli. This locus is "cryptic," as no laboratory growth conditions are known to relieve repression of bgl by H-NS in E. coli K12. However, repression can be relieved by spontaneous mutations. Here, we investigated the phylogeny of the bgl operon. Typing of bgl in a representative collection of E. coli demonstrated that it evolved clonally and that it is present in strains of the phylogenetic groups A, B1, and B2, while it is presumably replaced by a cluster of ORFans in the phylogenetic group D. Interestingly, the bgl operon is mutated in 20% of the strains of phylogenetic groups A and B1, suggesting erosion of bgl in these groups. However, bgl is functional in almost all B2 isolates and, in approximately 50% of them, it is weakly expressed at laboratory growth conditions. Homologs of bgl genes exist in Klebsiella, Enterobacter, and Erwinia species and also in low GC-content Gram-positive bacteria, while absent in E. albertii and Salmonella sp. This suggests horizontal transfer of bgl genes to an ancestral Enterobacterium. Conservation and weak expression of bgl in isolates of phylogenetic group B2 may indicate a functional role of bgl in extraintestinal pathogenic E. coli.}, }
@article {pmid19266023, year = {2009}, author = {Iwasaki, W and Takagi, T}, title = {Rapid pathway evolution facilitated by horizontal gene transfers across prokaryotic lineages.}, journal = {PLoS genetics}, volume = {5}, number = {3}, pages = {e1000402}, pmid = {19266023}, issn = {1553-7404}, mesh = {Bacteria/classification/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Models, Genetic ; Phylogeny ; }, abstract = {The evolutionary history of biological pathways is of general interest, especially in this post-genomic era, because it may provide clues for understanding how complex systems encoded on genomes have been organized. To explain how pathways can evolve de novo, some noteworthy models have been proposed. However, direct reconstruction of pathway evolutionary history both on a genomic scale and at the depth of the tree of life has suffered from artificial effects in estimating the gene content of ancestral species. Recently, we developed an algorithm that effectively reconstructs gene-content evolution without these artificial effects, and we applied it to this problem. The carefully reconstructed history, which was based on the metabolic pathways of 160 prokaryotic species, confirmed that pathways have grown beyond the random acquisition of individual genes. Pathway acquisition took place quickly, probably eliminating the difficulty in holding genes during the course of the pathway evolution. This rapid evolution was due to massive horizontal gene transfers as gene groups, some of which were possibly operon transfers, which would convey existing pathways but not be able to generate novel pathways. To this end, we analyzed how these pathways originally appeared and found that the original acquisition of pathways occurred more contemporaneously than expected across different phylogenetic clades. As a possible model to explain this observation, we propose that novel pathway evolution may be facilitated by bidirectional horizontal gene transfers in prokaryotic communities. Such a model would complement existing pathway evolution models.}, }
@article {pmid19264999, year = {2009}, author = {Leslie, M}, title = {Origins. On the origin of photosynthesis.}, journal = {Science (New York, N.Y.)}, volume = {323}, number = {5919}, pages = {1286-1287}, doi = {10.1126/science.323.5919.1286}, pmid = {19264999}, issn = {1095-9203}, mesh = {Atmosphere ; Bacteria/genetics/*metabolism ; Electrons ; *Evolution, Molecular ; Fossils ; Gene Transfer, Horizontal ; Light ; Oxidation-Reduction ; Oxygen/metabolism ; *Photosynthesis/genetics ; *Photosystem I Protein Complex/chemistry/genetics/metabolism ; *Photosystem II Protein Complex/chemistry/genetics/metabolism ; Ribulose-Bisphosphate Carboxylase/metabolism ; Water/metabolism ; }, }
@article {pmid19262690, year = {2009}, author = {Bellgard, MI and Wanchanthuek, P and La, T and Ryan, K and Moolhuijzen, P and Albertyn, Z and Shaban, B and Motro, Y and Dunn, DS and Schibeci, D and Hunter, A and Barrero, R and Phillips, ND and Hampson, DJ}, title = {Genome sequence of the pathogenic intestinal spirochete brachyspira hyodysenteriae reveals adaptations to its lifestyle in the porcine large intestine.}, journal = {PloS one}, volume = {4}, number = {3}, pages = {e4641}, pmid = {19262690}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; Brachyspira hyodysenteriae/*genetics ; Genome, Bacterial/*genetics ; Intestine, Large/*microbiology ; Metabolic Networks and Pathways ; Swine ; Virulence/genetics ; }, abstract = {Brachyspira hyodysenteriae is an anaerobic intestinal spirochete that colonizes the large intestine of pigs and causes swine dysentery, a disease of significant economic importance. The genome sequence of B. hyodysenteriae strain WA1 was determined, making it the first representative of the genus Brachyspira to be sequenced, and the seventeenth spirochete genome to be reported. The genome consisted of a circular 3,000,694 base pair (bp) chromosome, and a 35,940 bp circular plasmid that has not previously been described. The spirochete had 2,122 protein-coding sequences. Of the predicted proteins, more had similarities to proteins of the enteric Escherichia coli and Clostridium species than they did to proteins of other spirochetes. Many of these genes were associated with transport and metabolism, and they may have been gradually acquired through horizontal gene transfer in the environment of the large intestine. A reconstruction of central metabolic pathways identified a complete set of coding sequences for glycolysis, gluconeogenesis, a non-oxidative pentose phosphate pathway, nucleotide metabolism, lipooligosaccharide biosynthesis, and a respiratory electron transport chain. A notable finding was the presence on the plasmid of the genes involved in rhamnose biosynthesis. Potential virulence genes included those for 15 proteases and six hemolysins. Other adaptations to an enteric lifestyle included the presence of large numbers of genes associated with chemotaxis and motility. B. hyodysenteriae has diverged from other spirochetes in the process of accommodating to its habitat in the porcine large intestine.}, }
@article {pmid19261799, year = {2009}, author = {Wolter, N and du Plessis, M and von Gottberg, A and de Gouveia, L and Klugman, KP}, title = {Molecular characterization of emerging non-levofloxacin-susceptible pneumococci isolated from children in South Africa.}, journal = {Journal of clinical microbiology}, volume = {47}, number = {5}, pages = {1319-1324}, pmid = {19261799}, issn = {1098-660X}, support = {U60/CCU022088//PHS HHS/United States ; U62/PSO022901//PHS HHS/United States ; }, mesh = {Adolescent ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics ; Bacterial Typing Techniques ; Carrier State/microbiology ; Child ; Child, Preschool ; Cluster Analysis ; DNA Fingerprinting ; *Drug Resistance, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Genotype ; Humans ; Infant ; Infant, Newborn ; *Levofloxacin ; Microbial Sensitivity Tests ; Mutation, Missense ; Ofloxacin/*pharmacology ; Pneumococcal Infections/*microbiology ; Sequence Analysis, DNA ; Serotyping ; South Africa ; Streptococcus pneumoniae/*classification/*drug effects/genetics/isolation &amp; purification ; Tuberculosis/complications ; }, abstract = {Fluoroquinolones are not indicated for use for the treatment of pneumonia in children; however, non-levofloxacin-susceptible Streptococcus pneumoniae (NLSSP) has emerged in South Africa among children receiving treatment for multidrug-resistant tuberculosis. This study aimed to genotypically characterize NLSSP isolates. Invasive isolates were collected through active national laboratory-based surveillance for invasive pneumococcal disease (IPD) from 2000 through 2006 (n = 19,404). Carriage studies were conducted at two hospitals for patients with tuberculosis in two provinces. Phenotypic characterization was performed by determination of MICs and serotyping. Fluoroquinolone resistance mutations were identified, and clonality was investigated by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing. Twelve non-levofloxacin-susceptible cases of IPD were identified, and all were in children <15 years of age. Ten isolates were serotype 19F and formed two clusters according to their PFGE profiles, antibiogram types, and fluoroquinolone resistance-conferring mutations. All nine carriage isolates from children in hospital A were NLSSP, serotype 19F, were indistinguishable by PFGE, and were related to invasive isolates in cluster 2. Of 26 child carriers in hospital B, 22 (85%) were colonized with NLSSP. The isolates were indistinguishable by PFGE, although they displayed two serotypes, serotypes 19F and 23F. The isolates were related to invasive isolates in cluster 1; however, higher levofloxacin MICs and different fluoroquinolone resistance mutations were suggestive of horizontal gene transfer. A serotype 23F carriage isolate displayed increased fitness compared with the fitness of an otherwise indistinguishable serotype 19F carriage isolate. These data suggest that a low-level non-levofloxacin-susceptible strain transformed into a highly resistant strain under antibiotic pressure and underwent capsular switching in order to have increased fitness.}, }
@article {pmid19260970, year = {2009}, author = {Couce, A and Blázquez, J}, title = {Side effects of antibiotics on genetic variability.}, journal = {FEMS microbiology reviews}, volume = {33}, number = {3}, pages = {531-538}, doi = {10.1111/j.1574-6976.2009.00165.x}, pmid = {19260970}, issn = {1574-6976}, mesh = {Anti-Bacterial Agents/*adverse effects/*pharmacology ; Bacteria/*drug effects/*genetics ; Gene Transfer, Horizontal/drug effects ; Humans ; Mutation/drug effects ; Recombination, Genetic/drug effects ; *Selection, Genetic ; }, abstract = {In recent years, there has been accumulating evidence that antibiotics, besides their antimicrobial action, potentially have a number of undesired side effects that can, at least in some cases, promote genetic variability of bacteria. In addition to resistant variants, antibiotics have also been shown to select mutator clones, thus stimulating evolution towards further resistance. Furthermore, mutations, recombination and horizontal gene transfer have been reported to be somehow affected when bacteria are exposed to subinhibitory concentrations of certain antibiotics. These findings may have implications for the use of antibiotics, because they may have undesired side effects, such as enhancing antibiotic resistance evolution. Here we present data supporting (or not) this fearsome possibility and discuss whether this potential threat should be taken into consideration.}, }
@article {pmid19259779, year = {2009}, author = {Van der Auwera, GA and Król, JE and Suzuki, H and Foster, B and Van Houdt, R and Brown, CJ and Mergeay, M and Top, EM}, title = {Plasmids captured in C. metallidurans CH34: defining the PromA family of broad-host-range plasmids.}, journal = {Antonie van Leeuwenhoek}, volume = {96}, number = {2}, pages = {193-204}, doi = {10.1007/s10482-009-9316-9}, pmid = {19259779}, issn = {1572-9699}, mesh = {Base Sequence ; Computational Biology ; Conjugation, Genetic ; Cupriavidus/*genetics/metabolism ; DNA Replication ; *DNA Transposable Elements ; DNA, Bacterial/analysis/genetics ; *Gene Transfer, Horizontal ; Genomics ; Molecular Sequence Data ; Plasmids/classification/*genetics ; Sequence Analysis, DNA ; }, abstract = {The self-transmissible, broad-host-range (BHR) plasmid pMOL98 was previously isolated from polluted soil using a triparental plasmid capture approach and shown to possess a replicon similar to that of the BHR plasmids pSB102 and pIPO2. Here, complete sequence analysis and comparative genomics reveal that the 55.5 kb nucleotide sequence of pMOL98 shows extensive sequence similarity and synteny with the BHR plasmid family that now includes pIPO2, pSB102, pTER331, and pMRAD02. They share a plasmid backbone comprising replication, partitioning and conjugative transfer functions. Comparison of the variable accessory regions of these plasmids shows that the majority of natural transposons, as well as the mini-transposon used to mark the plasmids, are inserted in the parA locus. The transposon unique to pMOL98 appears to have inserted from the chromosome of the recipient strain used in the plasmid capture procedure. This demonstrates the necessity for careful screening of plasmids and host chromosomes to avoid mis-interpretation of plasmid genome content. The presence of very similar BHR plasmids with different accessory genes in geographically distinct locations suggests an important role in horizontal gene exchange and bacterial adaptation for this recently defined plasmid group, which we propose to name "PromA".}, }
@article {pmid19258532, year = {2009}, author = {Gutiérrez-Preciado, A and Henkin, TM and Grundy, FJ and Yanofsky, C and Merino, E}, title = {Biochemical features and functional implications of the RNA-based T-box regulatory mechanism.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {73}, number = {1}, pages = {36-61}, pmid = {19258532}, issn = {1098-5557}, support = {R01 GM047823/GM/NIGMS NIH HHS/United States ; R01GM47823/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acids/*genetics ; Amino Acyl-tRNA Synthetases/genetics ; Deltaproteobacteria/genetics ; Evolution, Molecular ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Gram-Positive Bacteria/*genetics/metabolism ; Operon ; Regulatory Sequences, Nucleic Acid ; *Regulon ; Repressor Proteins/genetics/*metabolism ; T-Box Domain Proteins/genetics/*metabolism ; }, abstract = {The T-box mechanism is a common regulatory strategy used for modulating the expression of genes of amino acid metabolism-related operons in gram-positive bacteria, especially members of the Firmicutes. T-box regulation is usually based on a transcription attenuation mechanism in which an interaction between a specific uncharged tRNA and the 5' region of the transcript stabilizes an antiterminator structure in preference to a terminator structure, thereby preventing transcription termination. Although single T-box regulatory elements are common, double or triple T-box arrangements are also observed, expanding the regulatory range of these elements. In the present study, we predict the functional implications of T-box regulation in genes encoding aminoacyl-tRNA synthetases, proteins of amino acid biosynthetic pathways, transporters, and regulatory proteins. We also consider the global impact of the use of this regulatory mechanism on cell physiology. Novel biochemical relationships between regulated genes and their corresponding metabolic pathways were revealed. Some of the genes identified, such as the quorum-sensing gene luxS, in members of the Lactobacillaceae were not previously predicted to be regulated by the T-box mechanism. Our analyses also predict an imbalance in tRNA sensing during the regulation of operons containing multiple aminoacyl-tRNA synthetase genes or biosynthetic genes involved in pathways common to more than one amino acid. Based on the distribution of T-box regulatory elements, we propose that this regulatory mechanism originated in a common ancestor of members of the Firmicutes, Chloroflexi, Deinococcus-Thermus group, and Actinobacteria and was transferred into the Deltaproteobacteria by horizontal gene transfer.}, }
@article {pmid19256882, year = {2008}, author = {Muñoz, E and Park, JM and Deem, MW}, title = {Quasispecies theory for horizontal gene transfer and recombination.}, journal = {Physical review. E, Statistical, nonlinear, and soft matter physics}, volume = {78}, number = {6 Pt 1}, pages = {061921}, pmid = {19256882}, issn = {1539-3755}, support = {R90 DK071504/DK/NIDDK NIH HHS/United States ; }, mesh = {Biophysical Phenomena ; Epistasis, Genetic ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Models, Genetic ; Mutation ; Nonlinear Dynamics ; *Recombination, Genetic ; Stochastic Processes ; }, abstract = {We introduce a generalization of the parallel, or Crow-Kimura, and Eigen models of molecular evolution to represent the exchange of genetic information between individuals in a population. We study the effect of different schemes of genetic recombination on the steady-state mean fitness and distribution of individuals in the population, through an analytic field theoretic mapping. We investigate both horizontal gene transfer from a population and recombination between pairs of individuals. Somewhat surprisingly, these nonlinear generalizations of quasispecies theory to modern biology are analytically solvable. For two-parent recombination, we find two selected phases, one of which is spectrally rigid. We present exact analytical formulas for the equilibrium mean fitness of the population, in terms of a maximum principle, which are generally applicable to any permutation invariant replication rate function. For smooth fitness landscapes, we show that when positive epistatic interactions are present, recombination or horizontal gene transfer introduces a mild load against selection. Conversely, if the fitness landscape exhibits negative epistasis, horizontal gene transfer or recombination introduces an advantage by enhancing selection towards the fittest genotypes. These results prove that the mutational deterministic hypothesis holds for quasispecies models. For the discontinuous single sharp peak fitness landscape, we show that horizontal gene transfer has no effect on the fitness, while recombination decreases the fitness, for both the parallel and the Eigen models. We present numerical and analytical results as well as phase diagrams for the different cases.}, }
@article {pmid19254178, year = {2009}, author = {Jenkins, DJ and Stekel, DJ}, title = {A new model for investigating the evolution of transcription control networks.}, journal = {Artificial life}, volume = {15}, number = {3}, pages = {259-291}, doi = {10.1162/artl.2009.Stekel.006}, pmid = {19254178}, issn = {1064-5462}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Allosteric Site ; Artificial Intelligence ; Bacterial Proteins/metabolism ; Biological Evolution ; Computational Biology/methods ; Computer Simulation ; *Gene Regulatory Networks ; Models, Biological ; Models, Genetic ; Models, Theoretical ; Protein Binding ; Protein Structure, Tertiary ; RNA, Messenger/metabolism ; *Systems Biology ; *Transcription, Genetic ; }, abstract = {Biological systems show unbounded capacity for complex behaviors and responses to their environments. This principally arises from their genetic networks. The processes governing transcription, translation, and gene regulation are well understood, as are the mechanisms of network evolution, such as gene duplication and horizontal gene transfer. However, the evolved networks arising from these simple processes are much more difficult to understand, and it is difficult to perform experiments on the evolution of these networks in living organisms because of the timescales involved. We propose a new framework for modeling and investigating the evolution of transcription networks in realistic, varied environments. The model we introduce contains novel, important, and lifelike features that allow the evolution of arbitrarily complex transcription networks. Molecular interactions are not specified; instead they are determined dynamically based on shape, allowing protein function to freely evolve. Transcriptional logic provides a flexible mechanism for defining genetic regulatory activity. Simulations demonstrate a realistic life cycle as an emergent property, and that even in simple environments lifelike and complex regulation mechanisms are evolved, including stable proteins, unstable mRNA, and repressor activity. This study also highlights the importance of using in silico genetics techniques to investigate evolved model robustness.}, }
@article {pmid19251636, year = {2009}, author = {Perez, JC and Groisman, EA}, title = {Transcription factor function and promoter architecture govern the evolution of bacterial regulons.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {11}, pages = {4319-4324}, pmid = {19251636}, issn = {1091-6490}, support = {R01 AI049561/AI/NIAID NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; AI49561/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; Bacterial Proteins/physiology ; *Biological Evolution ; Gene Regulatory Networks ; Humans ; *Promoter Regions, Genetic ; Regulatory Sequences, Nucleic Acid ; Regulon/*genetics ; Salmonella enterica/genetics ; Transcription Factors/*physiology ; Yersinia pestis/genetics ; }, abstract = {Evolutionary changes in ancestral regulatory circuits can bring about phenotypic differences between related organisms. Studies of regulatory circuits in eukaryotes suggest that these modifications result primarily from changes in cis-regulatory elements (as opposed to alterations in the transcription factors that act upon these sequences). It is presently unclear how the evolution of gene regulatory circuits has proceeded in bacteria, given the rampant effects of horizontal gene transfer, which has significantly altered the composition of bacterial regulons. We now demonstrate that the evolution of the regulons governed by the regulatory protein PhoP in the related human pathogens Salmonella enterica and Yersinia pestis has entailed functional changes in the PhoP protein as well as in the architecture of PhoP-dependent promoters. These changes have resulted in orthologous PhoP proteins that differ both in their ability to promote transcription and in their role as virulence regulators. We posit that these changes allow bacterial transcription factors to incorporate newly acquired genes into ancestral regulatory circuits and yet retain control of the core members of a regulon.}, }
@article {pmid19220348, year = {2009}, author = {Cantón, R}, title = {Antibiotic resistance genes from the environment: a perspective through newly identified antibiotic resistance mechanisms in the clinical setting.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {15 Suppl 1}, number = {}, pages = {20-25}, doi = {10.1111/j.1469-0691.2008.02679.x}, pmid = {19220348}, issn = {1469-0691}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/*genetics ; Bacterial Infections/*microbiology ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; *Soil Microbiology ; }, abstract = {Soil bacteria may contain antibiotic resistance genes responsible for different mechanisms that permit them to overcome the natural antibiotics present in the environment. This gene pool has been recently named the 'resistome', and its components can be mobilized into the microbial community affecting humans because of the participation of genetic platforms that efficiently facilitate the mobilization and maintenance of these resistance genes. Evidence for this transference has been suggested or demonstrated with newly identified widespread genes in multidrug-resistant bacteria. These resistance genes include those responsible for ribosomal methylases affecting aminoglycosides (armA, rtmB), methyltransferases affecting linezolid (cfr) or plasmid-mediated efflux pumps conferring low-level fluoroquinolone resistance (qepA), all of which are associated with antibiotic-producing bacteria. In addition, resistance genes whose ancestors have been identified in environmental isolates that are not recognized as antibiotic producers have also been recently detected. These include the qnr and the bla(CTX) genes compromising the activity of fluoroquinolones and extended-spectrum cephalosporins, respectively. The application of metagenomic tools and phylogenetic analysis will facilitate future identification of other new resistance genes and their corresponding ancestors in environmental bacteria, and will enable further exploration of the concept of the resistome as being a unique reservoir of antibiotic resistance genes and genetic elements participating in resistance gene transfer.}, }
@article {pmid19246754, year = {2009}, author = {Trobos, M and Christensen, H and Sunde, M and Nordentoft, S and Agersø, Y and Simonsen, GS and Hammerum, AM and Olsen, JE}, title = {Characterization of sulphonamide-resistant Escherichia coli using comparison of sul2 gene sequences and multilocus sequence typing.}, journal = {Microbiology (Reading, England)}, volume = {155}, number = {Pt 3}, pages = {831-836}, doi = {10.1099/mic.0.024190-0}, pmid = {19246754}, issn = {1350-0872}, mesh = {Animals ; Bacterial Proteins/*genetics ; Bacterial Typing Techniques ; Base Sequence ; Carrier Proteins/*genetics ; DNA, Bacterial/genetics ; Denmark ; Escherichia coli/classification/*genetics/isolation &amp; purification ; Escherichia coli Proteins/*genetics ; Feces/microbiology ; Food Microbiology ; Gene Transfer, Horizontal ; Humans ; Meat/microbiology ; Molecular Sequence Data ; Norway ; Point Mutation ; Poultry/microbiology ; Sequence Analysis, DNA ; Swine/microbiology ; }, abstract = {The sul2 gene encodes sulphonamide resistance (Sul(R)) and is commonly found in Escherichia coli from different hosts. We typed E. coli isolates by multilocus sequence typing (MLST) and compared the results to sequence variation of sul2, in order to investigate the relation to host origin of pathogenic and commensal E. coli strains and to investigate whether transfer of sul2 into different genomic lineages has happened multiple times. Sixty-eight E. coli isolated in Denmark and Norway from different hosts and years were MLST typed and sul2 PCR products were sequenced and compared. PFGE was performed in a subset of isolates. All isolates were divided into 45 different sequence types (STs), with clonal complexes CC10, CC23, CC168, CC350 and CC69 being the most frequent. The sul2 gene from the majority of E. coli strains had only two point mutations, at positions 159 and 197, leading to a synonymous and a non-synonymous change, respectively. Five strains had extra single mutations. All poultry, poultry meat, and Danish human blood isolates had the same sul2 ST and some of these strains clustered under the same MLST STs, indicating that they shared habitats. Most PFGE profiles clustered according to source, but some included different sources. Sul(R) E. coli from different animals, food, human faeces and infections did not cluster according to their origin, suggesting that these habitats share E. coli and sul2 gene types. However, while pig isolates on one occasion clustered with urinary tract infection isolates, poultry isolates seemed more related to isolates from bloodstream infections in humans. Presence of mainly two types of the sul2 gene in both human and animal isolates, irrespective of date and geography, and the presence of both types in the same clonal lineages, suggest horizontal transfer of sul2.}, }
@article {pmid19246360, year = {2009}, author = {Wu, HM and Harcourt, BH and Hatcher, CP and Wei, SC and Novak, RT and Wang, X and Juni, BA and Glennen, A and Boxrud, DJ and Rainbow, J and Schmink, S and Mair, RD and Theodore, MJ and Sander, MA and Miller, TK and Kruger, K and Cohn, AC and Clark, TA and Messonnier, NE and Mayer, LW and Lynfield, R}, title = {Emergence of ciprofloxacin-resistant Neisseria meningitidis in North America.}, journal = {The New England journal of medicine}, volume = {360}, number = {9}, pages = {886-892}, doi = {10.1056/NEJMoa0806414}, pmid = {19246360}, issn = {1533-4406}, mesh = {Adolescent ; Adult ; Aged ; Anti-Infective Agents/*therapeutic use ; Base Sequence ; Carrier State/microbiology ; Ciprofloxacin/*therapeutic use ; Drug Resistance, Bacterial/*genetics ; Humans ; Infant ; Meningococcal Infections/*drug therapy/microbiology ; Microbial Sensitivity Tests ; Middle Aged ; Neisseria meningitidis/classification/drug effects/*genetics/isolation &amp; purification ; Pharynx/microbiology ; *Point Mutation ; United States ; Young Adult ; }, abstract = {We report on three cases of meningococcal disease caused by ciprofloxacin-resistant Neisseria meningitidis, one in North Dakota and two in Minnesota. The cases were caused by the same serogroup B strain. To assess local carriage of resistant N. meningitidis, we conducted a pharyngeal-carriage survey and isolated the resistant strain from one asymptomatic carrier. Sequencing of the gene encoding subunit A of DNA gyrase (gyrA) revealed a mutation associated with fluoroquinolone resistance and suggests that the resistance was acquired by means of horizontal gene transfer with the commensal N. lactamica. In susceptibility testing of invasive N. meningitidis isolates from the Active Bacterial Core surveillance system between January 2007 and January 2008, an additional ciprofloxacin-resistant isolate was found, in this case from California. Ciprofloxacin-resistant N. meningitidis has emerged in North America.}, }
@article {pmid19245710, year = {2009}, author = {Yutin, N and Wolf, MY and Wolf, YI and Koonin, EV}, title = {The origins of phagocytosis and eukaryogenesis.}, journal = {Biology direct}, volume = {4}, number = {}, pages = {9}, pmid = {19245710}, issn = {1745-6150}, support = {//Intramural NIH HHS/United States ; }, mesh = {Actins/chemistry ; Amino Acid Sequence ; Animals ; Archaea/genetics/metabolism ; Bacteria/enzymology ; Conserved Sequence ; Eukaryotic Cells/*cytology/enzymology ; Microfilament Proteins/chemistry ; Molecular Sequence Data ; Monomeric GTP-Binding Proteins/chemistry/genetics ; *Phagocytosis ; Phylogeny ; Proteomics ; Sequence Homology, Amino Acid ; Symbiosis ; ras Proteins/genetics ; }, abstract = {BACKGROUND: Phagocytosis, that is, engulfment of large particles by eukaryotic cells, is found in diverse organisms and is often thought to be central to the very origin of the eukaryotic cell, in particular, for the acquisition of bacterial endosymbionts including the ancestor of the mitochondrion.<br><br>RESULTS: Comparisons of the sets of proteins implicated in phagocytosis in different eukaryotes reveal extreme diversity, with very few highly conserved components that typically do not possess readily identifiable prokaryotic homologs. Nevertheless, phylogenetic analysis of those proteins for which such homologs do exist yields clues to the possible origin of phagocytosis. The central finding is that a subset of archaea encode actins that are not only monophyletic with eukaryotic actins but also share unique structural features with actin-related proteins (Arp) 2 and 3. All phagocytic processes are strictly dependent on remodeling of the actin cytoskeleton and the formation of branched filaments for which Arp2/3 are responsible. The presence of common structural features in Arp2/3 and the archaeal actins suggests that the common ancestors of the archaeal and eukaryotic actins were capable of forming branched filaments, like modern Arp2/3. The Rho family GTPases that are ubiquitous regulators of phagocytosis in eukaryotes appear to be of bacterial origin, so assuming that the host of the mitochondrial endosymbiont was an archaeon, the genes for these GTPases come via horizontal gene transfer from the endosymbiont or in an earlier event.<br><br>CONCLUSION: The present findings suggest a hypothetical scenario of eukaryogenesis under which the archaeal ancestor of eukaryotes had no cell wall (like modern Thermoplasma) but had an actin-based cytoskeleton including branched actin filaments that allowed this organism to produce actin-supported membrane protrusions. These protrusions would facilitate accidental, occasional engulfment of bacteria, one of which eventually became the mitochondrion. The acquisition of the endosymbiont triggered eukaryogenesis, in particular, the emergence of the endomembrane system that eventually led to the evolution of modern-type phagocytosis, independently in several eukaryotic lineages.}, }
@article {pmid19243440, year = {2009}, author = {Coil, DA and Anné, J}, title = {Twitching motility in Legionella pneumophila.}, journal = {FEMS microbiology letters}, volume = {293}, number = {2}, pages = {271-277}, doi = {10.1111/j.1574-6968.2009.01532.x}, pmid = {19243440}, issn = {1574-6968}, mesh = {Agar ; Charcoal/analysis ; Culture Media/chemistry ; Cysteine/analysis ; Fimbriae, Bacterial/genetics ; Gene Knockout Techniques ; Legionella pneumophila/*physiology ; *Locomotion ; Temperature ; }, abstract = {Twitching motility is a form of bacterial translocation over solid or semi-solid surfaces mediated by the extension, tethering, and subsequent retraction of type IV pili. These pili are also known to be involved in virulence, biofilm formation, formation of fruiting bodies, horizontal gene transfer, and protein secretion. We have characterized the presence of twitching motility on agar plates in Legionella pneumophila, the etiological agent of Legionnaires' disease. By examining twitching motility zones, we have demonstrated that twitching motility was dependent on agar thickness/concentration, the chemical composition of the media, the presence of charcoal and cysteine, proximity to other bacteria, and temperature. A knockout mutant of the pilus subunit, pilE, exhibited a total loss of twitching motility at 37 degrees C, but not at 27 degrees C, suggesting either the existence of a compensating pilus subunit or of another twitching motility system in this organism.}, }
@article {pmid19242532, year = {2009}, author = {Guidot, A and Coupat, B and Fall, S and Prior, P and Bertolla, F}, title = {Horizontal gene transfer between Ralstonia solanacearum strains detected by comparative genomic hybridization on microarrays.}, journal = {The ISME journal}, volume = {3}, number = {5}, pages = {549-562}, doi = {10.1038/ismej.2009.14}, pmid = {19242532}, issn = {1751-7370}, mesh = {*Comparative Genomic Hybridization ; DNA, Bacterial/genetics ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Microarray Analysis ; Ralstonia solanacearum/*genetics ; Recombination, Genetic ; }, abstract = {The plant pathogenic Betaproteobacterium Ralstonia solanacearum is a complex species in that most of the strains share the common characteristic of being naturally transformable. In this study, we used a new approach based on comparative genomic hybridization (CGH) on microarrays to investigate the extent of horizontal gene transfers (HGTs) between different strains of R. solanacearum. Recipient strains from phylotypes I, II and III were naturally transformed in vitro by genomic DNA from the GMI1000 reference strain (phylotype I) and the resulting DNAs were hybridized on a microarray representative of the 5120 predicted genes from the GMI1000 strain. In addition to transfer of the antibiotic resistance marker, in 8 of the 16 tested transformants, CGH on microarrays detected other transferred GMI1000 genes and revealed their number, category, function and localization along the genome. We showed that DNA blocks up to 30 kb and 33 genes could be integrated during a single event. Most of these blocks flanked the marker gene DNA but, interestingly, multiple DNA acquisitions along the genome also occurred in a single recombinant clone in one transformation experiment. The results were confirmed by PCR amplification, cloning and sequencing and Southern blot hybridization. This represents the first comprehensive identification of gene acquisitions and losses along the genome of the recipient bacterial strain during natural transformation experiments. In future studies, this strategy should help to answer many questions related to HGT mechanisms.}, }
@article {pmid19242515, year = {2009}, author = {Sriwiriyanont, P and Hachiya, A and Pickens, WL and Moriwaki, S and Ohuchi, A and Kitahara, T and Takema, Y and Kitzmiller, WJ and Visscher, MO and Bello, A and Tsuboi, R and Kobinger, GP}, title = {Lentiviral vector-mediated gene transfer to human hair follicles.}, journal = {The Journal of investigative dermatology}, volume = {129}, number = {9}, pages = {2296-2299}, doi = {10.1038/jid.2009.33}, pmid = {19242515}, issn = {1523-1747}, mesh = {Animals ; *Gene Transfer, Horizontal ; Genetic Vectors/genetics ; HIV/genetics ; Hair Follicle/*metabolism ; Humans ; Lentivirus/*genetics ; Membrane Glycoproteins/*genetics ; Mice ; Mice, Inbred ICR ; Mice, SCID ; Transduction, Genetic ; Viral Envelope Proteins/*genetics ; beta-Lactamases/genetics ; }, }
@article {pmid19239750, year = {2009}, author = {Krauland, MG and Marsh, JW and Paterson, DL and Harrison, LH}, title = {Integron-mediated multidrug resistance in a global collection of nontyphoidal Salmonella enterica isolates.}, journal = {Emerging infectious diseases}, volume = {15}, number = {3}, pages = {388-396}, pmid = {19239750}, issn = {1080-6059}, support = {K24 AI052788/AI/NIAID NIH HHS/United States ; R56 AI059385/AI/NIAID NIH HHS/United States ; R01-C1322404//PHS HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal ; *Global Health ; Humans ; Integrons/*genetics ; Microbial Sensitivity Tests ; Polymerase Chain Reaction ; Salmonella Infections/microbiology/transmission ; Salmonella enterica/classification/*drug effects/genetics/isolation &amp; purification ; Salmonella typhimurium/drug effects/genetics/isolation &amp; purification ; Sequence Analysis, DNA ; Serotyping ; }, abstract = {Salmonella enterica bacteria have become increasingly resistant to antimicrobial agents, partly as a result of genes carried on integrons. Clonal expansion and horizontal gene transfer may contribute to the spread of antimicrobial drug-resistance integrons in these organisms. We investigated this resistance and integron carriage among 90 isolates with the ACSSuT phenotype (resistance to ampicillin, chloramphenicol, streptomycin, sulfamethoxazole, and tetracycline) in a global collection of S. enterica isolates. Four integrons, dfrA12/orfF/aadA2, dfrA1/aadA1, dfrA7, and arr2/blaOXA30/cmlA5/aadA2, were found in genetically unrelated isolates from 8 countries on 4 continents, which supports a role for horizontal gene transfer in the global dissemination of S. enterica multidrug resistance. Serovar Typhimurium isolates containing identical integrons with the gene cassettes blaPSE1 and aadA2 were found in 4 countries on 3 continents, which supports the role of clonal expansion. This study demonstrates that clonal expansion and horizontal gene transfer contribute to the global dissemination of antimicrobial drug resistance in S. enterica.}, }
@article {pmid19236483, year = {2009}, author = {Guglielmetti, E and Korhonen, JM and Heikkinen, J and Morelli, L and von Wright, A}, title = {Transfer of plasmid-mediated resistance to tetracycline in pathogenic bacteria from fish and aquaculture environments.}, journal = {FEMS microbiology letters}, volume = {293}, number = {1}, pages = {28-34}, doi = {10.1111/j.1574-6968.2009.01512.x}, pmid = {19236483}, issn = {1574-6968}, mesh = {Animals ; *Aquaculture ; Conjugation, Genetic ; Electroporation ; Fish Diseases/*microbiology ; Fishes/microbiology ; *Gene Transfer, Horizontal ; Gram-Positive Bacterial Infections/microbiology/*veterinary ; Humans ; Intestines/microbiology ; Lactococcus/classification/*genetics ; Listeria monocytogenes/*genetics ; Listeriosis/microbiology ; Plasmids/*genetics ; Tetracycline Resistance/*genetics ; }, abstract = {The transferability of a large plasmid that harbors a tetracycline resistance gene tet(S), to fish and human pathogens was assessed using electrotransformation and conjugation. The plasmid, originally isolated from fish intestinal Lactococcus lactis ssp. lactis KYA-7, has potent antagonistic activity against the selected recipients (Lactococcus garvieae and Listeria monocytogenes), preventing conjugation. Therefore the tetracycline resistance determinant was transferred via electroporation to L. garvieae. A transformant clone was used as the donor in conjugation experiments with three different L. monocytogenes strains. To our knowledge, this is the first study showing the transfer of an antibiotic resistance plasmid from fish-associated lactic bacteria to L. monocytogenes, even if the donor L. garvieae was not the original host of the tetracycline resistance but experimentally created by electroporation. These results demonstrate that the antibiotic resistance genes in the fish intestinal bacteria have the potential to spread both to fish and human pathogens, posing a risk to aquaculture and consumer safety.}, }
@article {pmid19234126, year = {2009}, author = {Osborne, SE and Walthers, D and Tomljenovic, AM and Mulder, DT and Silphaduang, U and Duong, N and Lowden, MJ and Wickham, ME and Waller, RF and Kenney, LJ and Coombes, BK}, title = {Pathogenic adaptation of intracellular bacteria by rewiring a cis-regulatory input function.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {10}, pages = {3982-3987}, pmid = {19234126}, issn = {1091-6490}, support = {R01 GM058746/GM/NIGMS NIH HHS/United States ; GM-58746/GM/NIGMS NIH HHS/United States ; }, mesh = {*Adaptation, Physiological ; Animals ; Bacterial Proteins/genetics/metabolism ; Base Sequence ; Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Host-Pathogen Interactions ; Intracellular Space/*microbiology ; Mice ; Molecular Sequence Data ; Mutation/genetics ; Promoter Regions, Genetic/genetics ; Protein Binding ; Regulatory Sequences, Nucleic Acid/*genetics ; Salmonella/*genetics ; Transcription Factors/genetics/metabolism ; Typhoid Fever/metabolism ; }, abstract = {The acquisition of DNA by horizontal gene transfer enables bacteria to adapt to previously unexploited ecological niches. Although horizontal gene transfer and mutation of protein-coding sequences are well-recognized forms of pathogen evolution, the evolutionary significance of cis-regulatory mutations in creating phenotypic diversity through altered transcriptional outputs is not known. We show the significance of regulatory mutation for pathogen evolution by mapping and then rewiring a cis-regulatory module controlling a gene required for murine typhoid. Acquisition of a binding site for the Salmonella pathogenicity island-2 regulator, SsrB, enabled the srfN gene, ancestral to the Salmonella genus, to play a role in pathoadaptation of S. typhimurium to a host animal. We identified the evolved cis-regulatory module and quantified the fitness gain that this regulatory output accrues for the bacterium using competitive infections of host animals. Our findings highlight a mechanism of pathogen evolution involving regulatory mutation that is selected because of the fitness advantage the new regulatory output provides the incipient clones.}, }
@article {pmid19233962, year = {2009}, author = {Mrázek, J}, title = {Phylogenetic signals in DNA composition: limitations and prospects.}, journal = {Molecular biology and evolution}, volume = {26}, number = {5}, pages = {1163-1169}, doi = {10.1093/molbev/msp032}, pmid = {19233962}, issn = {1537-1719}, mesh = {Base Composition ; Base Pairing/genetics ; Base Sequence ; Chromosomes/genetics ; DNA/*genetics ; Genome/genetics ; *Phylogeny ; Principal Component Analysis ; Prokaryotic Cells/*metabolism ; Time Factors ; }, abstract = {The concept of genome signature allows sequence comparisons without alignment. It relies on the premise that oligonucleotide compositions of DNA segments from the same or closely related genomes tend to be more similar than those from distantly related genomes. This concept has been used in detection of lateral gene transfer, phylogenetic classification of metagenome sequences (binning), and in studies of evolution of viruses and plasmids. The goal of this work is to explore limitations of genome signature in phylogenetic classification of DNA sequences and to identify formal representations of genome signature that expose best the phylogenetic relationships among prokaryotes. We found that genome signatures that best represent phylogenetic relationships are those normalized to factor out differences in G + C content and utilizing the standard A-C-G-T alphabet or the degenerate R-Y (purine-pyrimidine) alphabet. The main limitation of all genome signature representations tested is lack of divergence among some distantly related species. "Crowding" of the genome signature space and absence of molecular clock likely contribute to this phenomenon. We introduce "periodicity signatures"--formal representations of periodic sequence patterns related to DNA curvature--which can discriminate between bacterial and archaeal DNA sequences. Interestingly, archaea of the order Halobacteriaceae have periodic signatures similar to bacteria, possibly due to their early divergence from other archaea, extensive lateral gene transfer, or due to their adaptation to high salt environments. Our results have practical implications for development and application of genome signature-based methods for analysis and classification of DNA sequences.}, }
@article {pmid19233952, year = {2009}, author = {Neelakanta, G and Sankar, TS and Schnetz, K}, title = {Characterization of a beta-glucoside operon (bgc) prevalent in septicemic and uropathogenic Escherichia coli strains.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {8}, pages = {2284-2293}, pmid = {19233952}, issn = {1098-5336}, mesh = {Arbutin/metabolism ; Benzyl Alcohols/metabolism ; Cellobiose/metabolism ; Citrobacter/genetics ; Cyclic AMP Receptor Protein/genetics ; Enterobacter/genetics ; Escherichia coli/*enzymology/*genetics/isolation &amp; purification ; Escherichia coli Infections/*microbiology ; Escherichia coli Proteins/genetics ; Glucosides ; Klebsiella/genetics ; *Operon ; Phylogeny ; Repressor Proteins/genetics ; Sepsis/*microbiology ; Sequence Homology ; Synteny ; Urinary Tract Infections/*microbiology ; beta-Glucosidase/*genetics ; }, abstract = {Escherichia coli strains, in general, do not ferment cellobiose and aryl-beta-D-glucosidic sugars, although "cryptic" beta-d-glucoside systems have been characterized. Here we describe an additional cryptic operon (bgc) for the utilization of cellobiose and the aryl-beta-d-glucosides arbutin and salicin at low temperature. The bgc operon was identified by the characterization of beta-glucoside-positive mutants of an E. coli septicemia strain (i484) in which the well-studied bgl (aryl-beta-d-glucoside) operon was deleted. These bgc* mutants appeared after 5 days of incubation on salicin indicator plates at 28 degrees C. The bgc operon codes for proteins homologous to beta-glucoside/cellobiose-specific phosphoenolpyruvate-dependent phosphotransfer system permease subunits IIB (BgcE), IIC (BgcF), and IIA (BgcI); a porin (BgcH); and a phospho-beta-D-glucosidase (BgcA). Next to the bgc operon maps the divergent bgcR gene, which encodes a GntR-type transcriptional regulator. Expression of the bgc operon is dependent on the cyclic-AMP-dependent regulator protein CRP and positively controlled by BgcR. In the bgc* mutants, a single nucleotide exchange enhances the activity of the bgc promoter, rendering it BgcR independent. Typing of a representative collection of E. coli demonstrated the prevalence of bgc in strains of phylogenetic group B2, representing mainly extraintestinal pathogens, while it is rare among commensal E. coli strains. The bgc locus is also present in the closely related species Escherichia albertii. Further, bioinformatic analyses demonstrated that homologs of the bgc genes exist in the enterobacterial Klebsiella, Enterobacter, and Citrobacter spp. and also in gram-positive bacteria, indicative of horizontal gene transfer events.}, }
@article {pmid19232867, year = {2009}, author = {Yu, F and Wang, L and Pan, J and Yao, D and Chen, C and Zhu, T and Lou, Q and Hu, J and Wu, Y and Zhang, X and Chen, Z and Qu, D}, title = {Prevalence of 16S rRNA methylase genes in Klebsiella pneumoniae isolates from a Chinese teaching hospital: coexistence of rmtB and armA genes in the same isolate.}, journal = {Diagnostic microbiology and infectious disease}, volume = {64}, number = {1}, pages = {57-63}, doi = {10.1016/j.diagmicrobio.2009.01.020}, pmid = {19232867}, issn = {1879-0070}, mesh = {Aminoglycosides/*pharmacology ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/*genetics ; Bacterial Typing Techniques ; China ; Chromosomes, Bacterial ; Cluster Analysis ; Conjugation, Genetic ; *Drug Resistance, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/genetics ; Genes, Bacterial ; Hospitals, Teaching ; Humans ; Klebsiella Infections/classification/genetics/*microbiology ; Klebsiella pneumoniae/*enzymology/genetics/isolation &amp; purification ; Methyltransferases/*genetics ; Microbial Sensitivity Tests ; Molecular Epidemiology ; R Factors ; }, abstract = {16S rRNA methylase-mediated high-level resistance to aminoglycosides has been reported recently in clinical isolates of Gram-negative bacilli from several countries. Twenty-one (6.2%, 21/337) of 337 isolates of Klebsiella pneumoniae from a teaching hospital in Wenzhou, China, were positive for 16S rRNA methylase genes (3 for armA, 13 for rmtB, 5 for both armA and rmtB) and highly resistant to gentamicin, amikacin, and tobramycin (MICs, > or =256 microg/mL). Nineteen of 21 isolates harboring 16S rRNA methyalse genes were extended-spectrum beta-lactamase (ESBL) producers. The plasmids harboring 16S rRNA methylase genes from 14 of 21 donors were transferred into the recipients, Escherichia coli J53. The armA and the rmtB usually coexisted with ESBL genes in the same isolate in clinical isolates and cotransferred with ESBL genes on a self-transmissible conjugative plasmid to the recipients. Among 5 isolates harboring both armA and rmtB, the armA genes were located on the chromosomes, and the rmtB genes were located on the plasmids, as determined by Southern hybridization. The result of pulsed-field gel electrophoresis showed that horizontal gene transfer and clonal spread were responsible for the dissemination of the rmtB and the armA genes. 16S rRNA methylase-producing isolates of Klebsiella pneumoniae were commonly identified in the Chinese teaching hospital with coexistence of rmtB and armA genes in the same isolate.}, }
@article {pmid19229493, year = {2009}, author = {Kang, HY and Kim, J and Seol, SY and Lee, YC and Lee, JC and Cho, DT}, title = {Characterization of conjugative plasmids carrying antibiotic resistance genes encoding 16S rRNA methylase, extended-spectrum beta-lactamase, and/or plasmid-mediated AmpC beta-lactamase.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {47}, number = {1}, pages = {68-75}, pmid = {19229493}, issn = {1976-3794}, mesh = {Amikacin/pharmacology ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics/metabolism ; Conjugation, Genetic ; DNA, Bacterial/isolation &amp; purification ; Drug Resistance, Bacterial/*genetics ; Electrophoresis, Gel, Pulsed-Field ; Enterobacteriaceae/drug effects/enzymology/*genetics ; Enterobacteriaceae Infections/microbiology ; Escherichia coli Proteins/*genetics/metabolism ; Gene Transfer, Horizontal ; Gentamicins/pharmacology ; Humans ; Kanamycin/pharmacology ; Methyltransferases/*genetics/metabolism ; Microbial Sensitivity Tests ; Plasmids/*isolation &amp; purification/metabolism ; Polymorphism, Restriction Fragment Length ; Tobramycin/pharmacology ; beta-Lactamases/*genetics/metabolism ; }, abstract = {In this study, we identified extended-spectrum beta-lactamase (ESBL) and plasmid-mediated AmpC beta-lactamase which were associated with 16S rRNA methylase gene on the conjugative plasmid. Among 82 clinical isolates of Enterobacteriaceae that carry 16S rRNA methylase gene (64 strains, armA, and 18 strains, rmtB), bla(SHV-12) was detected either alone or combined with bla(DHA-1), bla(CTX-M-3), and bla(CTX-M-14) in 30 strains carrying armA and 6 strains carrying rmtB. The bla(CTX-M-3) was detected in 13 of 64 strains carrying armA but no strains carrying rmtB. Whereas bla(CTX-M-14) was detected in 15 of 18 strains carrying rmtB but only 2 of 64 strains carrying armA. Overall, bla(SHV-12) and bla(CTX-M-14) was the most common ESBL gene which was associated with armA and rmtB, respectively. In addition, we found that bla(CTX-M-3) localized with armA on the same IncL/M plasmid and bla(CTX-M-14) localized with rmtB on the same IncA/C plasmid. Restriction fragment length polymorphism of conjugative plasmids and pulsed-field gel electrophoresis of genomic DNAs revealed that intercellular horizontal transfer of conjugative plasmid and clonal transmission have been occurred at the same time.}, }
@article {pmid19229489, year = {2009}, author = {Kim, YT and Lee, KS and Kim, MJ and Kim, SB}, title = {Impact of cry1AC-carrying Brassica rapa subsp. pekinensis on leaf bacterial community.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {47}, number = {1}, pages = {33-39}, pmid = {19229489}, issn = {1976-3794}, mesh = {Bacillus thuringiensis Toxins ; Bacterial Proteins/*genetics ; *Brassica rapa/genetics/microbiology ; DNA Fingerprinting ; DNA, Bacterial ; Drug Resistance, Bacterial/genetics ; Endotoxins/*genetics ; Gene Transfer, Horizontal ; Hemolysin Proteins/*genetics ; *Plant Leaves/genetics/microbiology ; *Plants, Genetically Modified/genetics/microbiology ; Pseudomonas syringae/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Transgenes ; }, abstract = {The effects of Chinese cabbage (Brassica rapa subsp. pekinensis) carrying cry1AC derived from Bacillus thuringiensis (Bt) on leaf bacterial community were examined by analyzing the horizontal transfer of trans-gene fragments from plants to bacteria. The effect of plant pathogenic bacteria on the gene transfer was also examined using Pseudomonas syringae pathovar. maculicola. The frequency of hygromycin-resistant bacteria did not alter in Bt leaves, though slight increase was observed in Pseudomonas-infected Bt leaves with no statistical significance. The analysis of bacterial community profiles using the denaturing gradient gel electrophoresis (DGGE) fingerprinting indicated that there were slight differences between Bt and control Chinese cabbage, and also that infected tissues were dominated by P. syringae pv. maculicola. However, the cultured bacterial pools were not found to contain any transgene fragments. Thus, no direct evidence of immediate gene transfer from plant to bacteria or acquisition of hygromycin resistance could be observed. Still, long-term monitoring on the possibility of gene transfer is necessary to correctly assess the environmental effects of the Bt crop on bacteria.}, }
@article {pmid19229488, year = {2009}, author = {Jeong, G and Lee, K and Choi, J and Hwang, S and Park, B and Kim, W and Choi, Y and Park, I and Kim, J}, title = {Incidence of Wolbachia and Cardinium endosymbionts in the Osmia community in Korea.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {47}, number = {1}, pages = {28-32}, pmid = {19229488}, issn = {1976-3794}, mesh = {Animals ; Bacteroidetes/genetics/*isolation &amp; purification ; Bees/genetics/*microbiology/parasitology ; Diptera/genetics/microbiology ; Gene Transfer, Horizontal ; Korea ; Mites/genetics/microbiology ; Pest Control, Biological ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sex Ratio ; *Symbiosis ; Wolbachia/genetics/*isolation &amp; purification ; }, abstract = {Sex ratio distorting endosymbionts induce reproductive anomalies in their arthropod hosts. They have recently been paid much attention as firstly texts of evolution of host-symbiont relationships and secondly potential biological control agents to control arthropod pests. Among such organisms, Wolbachia and Cardinium bacteria are well characterized. This study aims at probing such bacteria in the Osmia community to evaluate their potential utilization to control arthropod pests. Among 17 PCR tested species, Osmia cornifrons and a parasitic fly are infected with Wolbachia and a mite species is infected with Cardinium. Phylogenetic tree analyses suggest that horizontal transfer of the bacteria occurred between phylogenetically distant hosts.}, }
@article {pmid19229333, year = {2009}, author = {Chan, CX and Darling, AE and Beiko, RG and Ragan, MA}, title = {Are protein domains modules of lateral genetic transfer?.}, journal = {PloS one}, volume = {4}, number = {2}, pages = {e4524}, pmid = {19229333}, issn = {1932-6203}, mesh = {Computational Biology/*methods ; Eukaryotic Cells ; Gene Transfer, Horizontal/*genetics ; Genome ; Protein Structure, Tertiary/genetics ; Proteins/*genetics ; Recombination, Genetic ; }, abstract = {BACKGROUND: In prokaryotes and some eukaryotes, genetic material can be transferred laterally among unrelated lineages and recombined into new host genomes, providing metabolic and physiological novelty. Although the process is usually framed in terms of gene sharing (e.g. lateral gene transfer, LGT), there is little reason to imagine that the units of transfer and recombination correspond to entire, intact genes. Proteins often consist of one or more spatially compact structural regions (domains) which may fold autonomously and which, singly or in combination, confer the protein's specific functions. As LGT is frequent in strongly selective environments and natural selection is based on function, we hypothesized that domains might also serve as modules of genetic transfer, i.e. that regions of DNA that are transferred and recombined between lineages might encode intact structural domains of proteins.<br><br>We selected 1,462 orthologous gene sets representing 144 prokaryotic genomes, and applied a rigorous two-stage approach to identify recombination breakpoints within these sequences. Recombination breakpoints are very significantly over-represented in gene sets within which protein domain-encoding regions have been annotated. Within these gene sets, breakpoints significantly avoid the domain-encoding regions (domons), except where these regions constitute most of the sequence length. Recombination breakpoints that fall within longer domons are distributed uniformly at random, but those that fall within shorter domons may show a slight tendency to avoid the domon midpoint. As we find no evidence for differential selection against nucleotide substitutions following the recombination event, any bias against disruption of domains must be a consequence of the recombination event per se.<br><br>CONCLUSIONS/SIGNIFICANCE: This is the first systematic study relating the units of LGT to structural features at the protein level. Many genes have been interrupted by recombination following inter-lineage genetic transfer, during which the regions within these genes that encode protein domains have not been preferentially preserved intact. Protein domains are units of function, but domons are not modules of transfer and recombination. Our results demonstrate that LGT can remodel even the most functionally conservative modules within genomes.}, }
@article {pmid19227143, year = {2008}, author = {Kwiatek, K and Mazur, M and Sieradzki, Z}, title = {Current issues connected with usage of genetically modified crops in production of feed and livestock feeding.}, journal = {Polish journal of veterinary sciences}, volume = {11}, number = {4}, pages = {411-414}, pmid = {19227143}, issn = {1505-1773}, mesh = {Animal Feed/*analysis ; Animal Nutritional Physiological Phenomena ; Animals ; Animals, Domestic/*physiology ; Consumer Product Safety ; Crops, Agricultural/*genetics ; Diet/veterinary ; Nutritive Value ; Plants, Genetically Modified ; }, abstract = {Progress, which is brought by new advances in modern molecular biology, allowed interference in the genome of live organisms and gene manipulation. Introducing new genes to the recipient organism enables to give them new features, absent before. Continuous increase in the area of the biotech crops triggers continuous discussion about safety of genetically modified (GM) crops, including food and feed derived from them. Important issue connected with cultivation of genetically modified crops is a horizontal gene transfer and a bacterial antibiotic resistance. Discussion about safety of GM crops concerns also food allergies caused by eating genetically modified food. The problem of genetic modifications of GM crops used for livestock feeding is widely discussed, taking into account Polish feed law.}, }
@article {pmid19226556, year = {2009}, author = {Aufsatz, W and Nehlin, L and Voronin, V and Schmidt, A and Matzke, AJ and Matzke, M}, title = {A novel strategy for obtaining kanamycin resistance in Arabidopsis thaliana by silencing an endogenous gene encoding a putative chloroplast transporter.}, journal = {Biotechnology journal}, volume = {4}, number = {2}, pages = {224-229}, doi = {10.1002/biot.200800156}, pmid = {19226556}, issn = {1860-7314}, mesh = {Anti-Bacterial Agents/administration &amp; dosage ; Arabidopsis/drug effects/*genetics ; Chloroplast Proteins ; Drug Resistance, Bacterial/*genetics ; Gene Silencing/*physiology ; Genetic Enhancement/*methods ; Kanamycin/*administration &amp; dosage ; Membrane Transport Proteins/*genetics ; Plant Proteins/*genetics ; Plants, Genetically Modified/drug effects/*physiology ; }, abstract = {The use of bacterial antibiotic resistance markers in transgenic plants raises concerns about horizontal gene transfer to soil bacteria. We report here that kanamycin resistance in Arabidopsis thaliana can be achieved by silencing an endogenous gene encoding a putative chloroplast transporter, which presumably imports kanamycin into chloroplasts to interfere with ribosomal RNA. Homologs of the transporter exist in other plant species, suggesting this strategy may be generally useful for selecting transformed plant cells.}, }
@article {pmid19226459, year = {2009}, author = {Bartolomé, C and Bello, X and Maside, X}, title = {Widespread evidence for horizontal transfer of transposable elements across Drosophila genomes.}, journal = {Genome biology}, volume = {10}, number = {2}, pages = {R22}, pmid = {19226459}, issn = {1474-760X}, mesh = {Animals ; Base Sequence ; DNA Transposable Elements/*genetics ; Drosophila/*genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Insect ; Genetic Variation ; Genome/*genetics ; Terminal Repeat Sequences ; }, abstract = {BACKGROUND: Horizontal transfer (HT) could play an important role in the long-term persistence of transposable elements (TEs) because it provides them with the possibility to avoid the checking effects of host-silencing mechanisms and natural selection, which would eventually drive their elimination from the genome. However, despite the increasing evidence for HT of TEs, its rate of occurrence among the TE pools of model eukaryotic organisms is still unknown.<br><br>RESULTS: We have extracted and compared the nucleotide sequences of all potentially functional autonomous TEs present in the genomes of Drosophila melanogaster, D. simulans and D. yakuba - 1,436 insertions classified into 141 distinct families - and show that a large fraction of the families found in two or more species display levels of genetic divergence and within-species diversity that are significantly lower than expected by assuming copy-number equilibrium and vertical transmission, and consistent with a recent origin by HT. Long terminal repeat (LTR) retrotransposons form nearly 90% of the HT cases detected. HT footprints are also frequent among DNA transposons (40% of families compared) but rare among non-LTR retroelements (6%). Our results suggest a genomic rate of 0.04 HT events per family per million years between the three species studied, as well as significant variation between major classes of elements.<br><br>CONCLUSIONS: The genome-wide patterns of sequence diversity of the active autonomous TEs in the genomes of D. melanogaster, D. simulans and D. yakuba suggest that one-third of the TE families originated by recent HT between these species. This result emphasizes the important role of horizontal transmission in the natural history of Drosophila TEs.}, }
@article {pmid19222584, year = {2009}, author = {Wei, M and Zhang, JJ and Liu, H and Wang, SJ and Fu, H and Zhou, NY}, title = {A transposable class I composite transposon carrying mph (methyl parathion hydrolase) from Pseudomonas sp. strain WBC-3.}, journal = {FEMS microbiology letters}, volume = {292}, number = {1}, pages = {85-91}, doi = {10.1111/j.1574-6968.2008.01468.x}, pmid = {19222584}, issn = {1574-6968}, mesh = {Blotting, Southern ; Conjugation, Genetic ; *DNA Transposable Elements ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; Methyl Parathion/metabolism ; Nitrophenols/metabolism ; Phosphoric Monoester Hydrolases/*genetics ; Pseudomonas/*enzymology/*genetics ; Recombination, Genetic ; Sequence Analysis, DNA ; }, abstract = {Pseudomonas sp. strain WBC-3 utilizes methyl parathion (O,O-dimethyl O-p-nitrophenol phosphorothioate) or para-nitrophenol as the sole source of carbon, nitrogen and energy. A gene encoding methyl parathion hydrolase (MPH) had been characterized previously and found to be located on a typical class I composite transposon that comprised IS6100 (Tnmph). In this study, the transposability of this transposon was confirmed by transposition assays in two distinct mating-out systems. Tnmph was demonstrated to transpose efficiently in a random manner in Pseudomonas putida PaW340 by Southern blot and in Ralstonia sp. U2 by sequence analysis of the Tnmph insertion sites, both exhibiting MPH activity. The linkage of the mph-like gene with IS6100, together with the transposability of Tnmph, as well as its capability to transpose in other phylogenetically divergent bacterial species, suggest that Tnmph may contribute to the wide distribution of mph-like genes and the adaptation of bacteria to organophosphorus compounds.}, }
@article {pmid19221094, year = {2009}, author = {Guo, FB and Yuan, JB}, title = {Codon usages of genes on chromosome, and surprisingly, genes in plasmid are primarily affected by strand-specific mutational biases in Lawsonia intracellularis.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {16}, number = {2}, pages = {91-104}, pmid = {19221094}, issn = {1756-1663}, mesh = {Base Composition ; Base Sequence ; Chromosomes, Bacterial/*genetics ; Codon/*genetics ; DNA Replication ; DNA, Bacterial/chemistry/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Genome, Bacterial ; Lawsonia Bacteria/*genetics ; Models, Genetic ; Molecular Sequence Data ; Mutation ; Plasmids/*genetics ; Transcription, Genetic ; }, abstract = {In this study, the factors driving genome-wide patterns of codon usages in Lawsonia intracellularis genome are determined. For genes on the chromosome of the bacterium, it is found that the most important source of variation results from strand-specific mutational biases. A lesser trend of variation is attributable to genes that are presumed as horizontally transferred. These putative alien genes are unusually GC richer than the other genes, whereas horizontally transferred genes have been observed to be AT rich in bacteria with medium and relatively low G + C contents. Hydropathy of encoded protein and expression level are also found to influence codon usage. Therefore, codon usage in L. intracellularis chromosome is the result of a complex balance among the different mutational and selectional factors. When analyzing genes in the largest plasmid, for the first time it is found that the strand-specific mutational biases are responsible for the primary variation of codon usages in plasmid. Genes, particularly highly expressed genes of this plasmid, are mainly located on the leading strands and this supposed to be the effects exerted by replicational-transcriptional selection. These facts suggest that this plasmid adopts the similar mechanism of replication as the chromosome in L. intracellularis. Common characters among the 10 bacteria in whose genomes the strand-specific mutational biases are the primary source of variation of codon usage are also investigated. For example, it is found that genes dnaT and fis that are involved in DNA replication initiation and re-initiation pathways are absent in all of the 10 bacteria.}, }
@article {pmid19220881, year = {2009}, author = {Emiliani, G and Fondi, M and Fani, R and Gribaldo, S}, title = {A horizontal gene transfer at the origin of phenylpropanoid metabolism: a key adaptation of plants to land.}, journal = {Biology direct}, volume = {4}, number = {}, pages = {7}, pmid = {19220881}, issn = {1745-6150}, mesh = {*Adaptation, Biological ; Animals ; *Biological Evolution ; Gene Transfer, Horizontal/*genetics ; Molecular Structure ; Phylogeny ; Plants/*genetics/*metabolism ; *Soil ; }, abstract = {BACKGROUND: The pioneering ancestor of land plants that conquered terrestrial habitats around 500 million years ago had to face dramatic stresses including UV radiation, desiccation, and microbial attack. This drove a number of adaptations, among which the emergence of the phenylpropanoid pathway was crucial, leading to essential compounds such as flavonoids and lignin. However, the origin of this specific land plant secondary metabolism has not been clarified.<br><br>RESULTS: We have performed an extensive analysis of the taxonomic distribution and phylogeny of Phenylalanine Ammonia Lyase (PAL), which catalyses the first and essential step of the general phenylpropanoid pathway, leading from phenylalanine to p-Coumaric acid and p-Coumaroyl-CoA, the entry points of the flavonoids and lignin routes. We obtained robust evidence that the ancestor of land plants acquired a PAL via horizontal gene transfer (HGT) during symbioses with soil bacteria and fungi that are known to have established very early during the first steps of land colonization. This horizontally acquired PAL represented then the basis for further development of the phenylpropanoid pathway and plant radiation on terrestrial environments.<br><br>CONCLUSION: Our results highlight a possible crucial role of HGT from soil bacteria in the path leading to land colonization by plants and their subsequent evolution. The few functional characterizations of sediment/soil bacterial PAL (production of secondary metabolites with powerful antimicrobial activity or production of pigments) suggest that the initial advantage of this horizontally acquired PAL in the ancestor of land plants might have been either defense against an already developed microbial community and/or protection against UV.}, }
@article {pmid19220405, year = {2009}, author = {Jogler, C and Kube, M and Schübbe, S and Ullrich, S and Teeling, H and Bazylinski, DA and Reinhardt, R and Schüler, D}, title = {Comparative analysis of magnetosome gene clusters in magnetotactic bacteria provides further evidence for horizontal gene transfer.}, journal = {Environmental microbiology}, volume = {11}, number = {5}, pages = {1267-1277}, doi = {10.1111/j.1462-2920.2009.01854.x}, pmid = {19220405}, issn = {1462-2920}, mesh = {DNA, Bacterial/chemistry/*genetics ; Gene Order ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Magnetics ; Magnetospirillum/genetics ; Molecular Sequence Data ; *Multigene Family ; Organelles/*genetics ; Sequence Analysis, DNA ; Synteny ; Vibrio/*genetics ; }, abstract = {The organization of magnetosome genes was analysed in all available complete or partial genomic sequences of magnetotactic bacteria (MTB), including the magnetosome island (MAI) of the magnetotactic marine vibrio strain MV-1 determined in this study. The MAI was found to differ in gene content and organization between Magnetospirillum species and strains MV-1 or MC-1. Although a similar organization of magnetosome genes was found in all MTB, distinct variations in gene order and sequence similarity were uncovered that may account for the observed diversity of biomineralization, cell biology and magnetotaxis found in various MTB. While several magnetosome genes were present in all MTB, others were confined to Magnetospirillum species, indicating that the minimal set of genes required for magnetosome biomineralization might be smaller than previously suggested. A number of novel candidate genes were implicated in magnetosome formation by gene cluster comparison. Based on phylogenetic and compositional evidence we present a model for the evolution of magnetotaxis within the Alphaproteobacteria, which suggests the independent horizontal transfer of magnetosome genes from an unknown ancestor of magnetospirilla into strains MC-1 and MV-1.}, }
@article {pmid19219067, year = {2009}, author = {Ehnfors, J and Kost-Alimova, M and Persson, NL and Bergsmedh, A and Castro, J and Levchenko-Tegnebratt, T and Yang, L and Panaretakis, T and Holmgren, L}, title = {Horizontal transfer of tumor DNA to endothelial cells in vivo.}, journal = {Cell death and differentiation}, volume = {16}, number = {5}, pages = {749-757}, doi = {10.1038/cdd.2009.7}, pmid = {19219067}, issn = {1476-5403}, mesh = {Animals ; Antigens, Polyomavirus Transforming/genetics ; DNA, Neoplasm/genetics/*metabolism ; Endothelial Cells/metabolism ; *Gene Transfer, Horizontal ; Humans ; Mice ; Phagocytosis ; Proto-Oncogene Proteins c-myc/genetics ; Rats ; Transplantation, Heterologous ; Tumor Suppressor Protein p53/metabolism ; }, abstract = {Tumor endothelial cells have long been regarded as genomically stable and therefore less likely to develop resistance to antiangiogenic therapies. However, recent findings have challenged this notion. We have shown that DNA can be transferred between cells through phagocytosis of apoptotic bodies by adjacent viable cells. Propagation of the ingested DNA is prevented by the activation of the p53-p21 pathway. In this study, we examined whether concomitant transfer of tumor DNA with genes that inactivate the p53 pathway could overcome the barrier to tumor DNA propagation. Our results demonstrate that fibroblasts and endothelial cells are capable of acquiring and replicating tumor DNA when the apoptotic tumor cells contain the SV40 large T antigen. Analysis of the tumor stroma of xenotransplanted tumors in severe combined immunodeficient mice revealed that a sub-population of the endothelial cells contained tumor DNA. These cells maintained the ability to form functional vessels in an in vivo assay and concurrently express tumor-encoded and endothelial-specific genes.}, }
@article {pmid19217913, year = {2009}, author = {Santoni, D and Romano-Spica, V}, title = {Comparative genomic analysis by microbial COGs self-attraction rate.}, journal = {Journal of theoretical biology}, volume = {258}, number = {4}, pages = {513-520}, doi = {10.1016/j.jtbi.2009.01.035}, pmid = {19217913}, issn = {1095-8541}, mesh = {Archaea/genetics ; Bacteria/genetics ; Cluster Analysis ; *Comparative Genomic Hybridization ; *Genome, Bacterial ; *Models, Genetic ; Phylogeny ; }, abstract = {Whole genome analysis provides new perspectives to determine phylogenetic relationships among microorganisms. The availability of whole nucleotide sequences allows different levels of comparison among genomes by several approaches. In this work, self-attraction rates were considered for each cluster of orthologous groups of proteins (COGs) class in order to analyse gene aggregation levels in physical maps. Phylogenetic relationships among microorganisms were obtained by comparing self-attraction coefficients. Eighteen-dimensional vectors were computed for a set of 168 completely sequenced microbial genomes (19 archea, 149 bacteria). The components of the vector represent the aggregation rate of the genes belonging to each of 18 COGs classes. Genes involved in nonessential functions or related to environmental conditions showed the highest aggregation rates. On the contrary genes involved in basic cellular tasks showed a more uniform distribution along the genome, except for translation genes. Self-attraction clustering approach allowed classification of Proteobacteria, Bacilli and other species belonging to Firmicutes. Rearrangement and Lateral Gene Transfer events may influence divergences from classical taxonomy. Each set of COG classes' aggregation values represents an intrinsic property of the microbial genome. This novel approach provides a new point of view for whole genome analysis and bacterial characterization.}, }
@article {pmid19216943, year = {2009}, author = {Baudry, PJ and Nichol, K and DeCorby, M and Lagacé-Wiens, P and Olivier, E and Boyd, D and Mulvey, MR and Hoban, DJ and Zhanel, GG}, title = {Mechanisms of resistance and mobility among multidrug-resistant CTX-M-producing Escherichia coli from Canadian intensive care units: the 1st report of QepA in North America.}, journal = {Diagnostic microbiology and infectious disease}, volume = {63}, number = {3}, pages = {319-326}, doi = {10.1016/j.diagmicrobio.2008.12.001}, pmid = {19216943}, issn = {1879-0070}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Typing Techniques ; Canada ; Cluster Analysis ; Cross Infection/*microbiology ; DNA Fingerprinting ; DNA, Bacterial/genetics ; *Drug Resistance, Multiple, Bacterial ; Escherichia coli/classification/*drug effects/genetics/isolation &amp; purification ; Escherichia coli Infections/*microbiology ; Escherichia coli Proteins/*genetics ; Gene Transfer, Horizontal ; Genotype ; Humans ; Intensive Care Units ; Plasmids ; beta-Lactamases/*genetics ; }, abstract = {We studied the molecular mechanisms of resistance and mobility of 18 multidrug-resistant CTX-M-producing Escherichia coli isolates isolated from patients in Canadian intensive care units. Fluoroquinolone-resistant isolates (83.3%) had mutations in gyrA and parC. Plasmid-mediated quinolone resistance genes qnr (A, B, and S), qepA, and aac(6')-Ib-cr were detected in 0%, 5.6%, and 44.4%, respectively. Sulfamethoxazole/trimethoprim-resistant isolates (61.1%) carried a dfr gene, and 10 (90.9%) of the 11 carried 1 or more sul genes. Gentamicin-resistant isolates (27.8%) carried the aac(3')-II gene, and doxycycline-resistant isolates (33.3%) carried 1 or more tet efflux genes. Both genetically related and unrelated groups of E. coli harboring extended-spectrum beta-lactamases were observed. The bla(CTX-M) genes were primarily located on diverse IncF plasmids of multiple replicon types downstream of the ISEcp1 element. The spread of the bla(CTX-M) genes among E. coli in Canada occurs through a diversity of different mechanisms and does not correspond to a single CTX-M determinant, or a single clone, or a single plasmid but rather through the combination of clonal spread of virulent strains and acquisition of diverse CTX-M-bearing plasmids. We report the 1st qepA-producing E. coli in North America.}, }
@article {pmid19216728, year = {2009}, author = {Forterre, P and Gribaldo, S and Brochier-Armanet, C}, title = {Happy together: genomic insights into the unique Nanoarchaeum/Ignicoccus association.}, journal = {Journal of biology}, volume = {8}, number = {1}, pages = {7}, pmid = {19216728}, issn = {1475-4924}, mesh = {Desulfurococcaceae/*genetics/physiology ; Gene Transfer, Horizontal ; *Genome, Archaeal ; Genomics ; Multigene Family ; Nanoarchaeota/*genetics/physiology ; Phylogeny ; *Symbiosis ; }, abstract = {The complete genome sequence of the crenarchaeon Ignicoccus hospitalis published recently in Genome Biology provides a great leap forward in the dissection of its unique association with another hyperthermophilic archaeon, Nanoarchaeum equitans.}, }
@article {pmid19213802, year = {2009}, author = {Koonin, EV}, title = {Darwinian evolution in the light of genomics.}, journal = {Nucleic acids research}, volume = {37}, number = {4}, pages = {1011-1034}, pmid = {19213802}, issn = {1362-4962}, support = {//Intramural NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; Genetics/*history ; *Genomics/history/trends ; History, 19th Century ; History, 20th Century ; History, 21st Century ; Humans ; Selection, Genetic ; }, abstract = {Comparative genomics and systems biology offer unprecedented opportunities for testing central tenets of evolutionary biology formulated by Darwin in the Origin of Species in 1859 and expanded in the Modern Synthesis 100 years later. Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected. Major contributions of horizontal gene transfer and diverse selfish genetic elements to genome evolution undermine the Tree of Life concept. An adequate depiction of evolution requires the more complex concept of a network or 'forest' of life. There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a non-adaptive consequence of evolution under weak purifying selection rather than an adaptation. Several universals of genome evolution were discovered including the invariant distributions of evolutionary rates among orthologous genes from diverse genomes and of paralogous gene family sizes, and the negative correlation between gene expression level and sequence evolution rate. Simple, non-adaptive models of evolution explain some of these universals, suggesting that a new synthesis of evolutionary biology might become feasible in a not so remote future.}, }
@article {pmid19212443, year = {2009}, author = {Schmitt, I and Lumbsch, HT}, title = {Ancient horizontal gene transfer from bacteria enhances biosynthetic capabilities of fungi.}, journal = {PloS one}, volume = {4}, number = {2}, pages = {e4437}, pmid = {19212443}, issn = {1932-6203}, mesh = {Animals ; Bacteria/*genetics ; Bacterial Proteins/classification/genetics ; Evolution, Molecular ; Fungal Proteins/classification/genetics ; *Fungi/genetics/metabolism ; Gene Duplication ; *Gene Transfer, Horizontal ; Humans ; Lichens/genetics ; Molecular Sequence Data ; Molecular Structure ; Phylogeny ; Polyketide Synthases/classification/genetics ; Resorcinols/chemistry/metabolism ; Salicylates/chemistry/metabolism ; Symbiosis ; }, abstract = {BACKGROUND: Polyketides are natural products with a wide range of biological functions and pharmaceutical applications. Discovery and utilization of polyketides can be facilitated by understanding the evolutionary processes that gave rise to the biosynthetic machinery and the natural product potential of extant organisms. Gene duplication and subfunctionalization, as well as horizontal gene transfer are proposed mechanisms in the evolution of biosynthetic gene clusters. To explain the amount of homology in some polyketide synthases in unrelated organisms such as bacteria and fungi, interkingdom horizontal gene transfer has been evoked as the most likely evolutionary scenario. However, the origin of the genes and the direction of the transfer remained elusive.<br><br>We used comparative phylogenetics to infer the ancestor of a group of polyketide synthase genes involved in antibiotic and mycotoxin production. We aligned keto synthase domain sequences of all available fungal 6-methylsalicylic acid (6-MSA)-type PKSs and their closest bacterial relatives. To assess the role of symbiotic fungi in the evolution of this gene we generated 24 6-MSA synthase sequence tags from lichen-forming fungi. Our results support an ancient horizontal gene transfer event from an actinobacterial source into ascomycete fungi, followed by gene duplication.<br><br>CONCLUSIONS/SIGNIFICANCE: Given that actinobacteria are unrivaled producers of biologically active compounds, such as antibiotics, it appears particularly promising to study biosynthetic genes of actinobacterial origin in fungi. The large number of 6-MSA-type PKS sequences found in lichen-forming fungi leads us hypothesize that the evolution of typical lichen compounds, such as orsellinic acid derivatives, was facilitated by the gain of this bacterial polyketide synthase.}, }
@article {pmid19207745, year = {2009}, author = {Martinez, JL and Sánchez, MB and Martínez-Solano, L and Hernandez, A and Garmendia, L and Fajardo, A and Alvarez-Ortega, C}, title = {Functional role of bacterial multidrug efflux pumps in microbial natural ecosystems.}, journal = {FEMS microbiology reviews}, volume = {33}, number = {2}, pages = {430-449}, doi = {10.1111/j.1574-6976.2008.00157.x}, pmid = {19207745}, issn = {1574-6976}, mesh = {Animals ; Bacteria/drug effects/growth &amp; development/*metabolism/pathogenicity ; Bacterial Proteins/genetics/metabolism ; *Drug Resistance, Multiple, Bacterial ; *Ecosystem ; *Gene Expression Regulation, Bacterial ; Humans ; Metals, Heavy/pharmacology ; Plant Diseases/microbiology ; Plants/*microbiology ; *Quorum Sensing ; Signal Transduction ; Soil Microbiology ; }, abstract = {Multidrug efflux pumps have emerged as relevant elements in the intrinsic and acquired antibiotic resistance of bacterial pathogens. In contrast with other antibiotic resistance genes that have been obtained by virulent bacteria through horizontal gene transfer, genes coding for multidrug efflux pumps are present in the chromosomes of all living organisms. In addition, these genes are highly conserved (all members of the same species contain the same efflux pumps) and their expression is tightly regulated. Together, these characteristics suggest that the main function of these systems is not resisting the antibiotics used in therapy and that they should have other roles relevant to the behavior of bacteria in their natural ecosystems. Among the potential roles, it has been demonstrated that efflux pumps are important for processes of detoxification of intracellular metabolites, bacterial virulence in both animal and plant hosts, cell homeostasis and intercellular signal trafficking.}, }
@article {pmid19207744, year = {2009}, author = {Averhoff, B}, title = {Shuffling genes around in hot environments: the unique DNA transporter of Thermus thermophilus.}, journal = {FEMS microbiology reviews}, volume = {33}, number = {3}, pages = {611-626}, doi = {10.1111/j.1574-6976.2008.00160.x}, pmid = {19207744}, issn = {1574-6976}, mesh = {Bacterial Proteins/metabolism ; DNA, Bacterial/genetics/*metabolism ; Membrane Transport Proteins/metabolism ; Thermus thermophilus/genetics/*physiology ; *Transformation, Bacterial ; }, abstract = {Natural transformation permits the transport of DNA through bacterial membranes and represents a dominant mode for the transfer of genetic information between bacteria and between microorganisms of distant evolutionary lineages and even between members of different domains. This phenomenon, known as horizontal, or lateral, gene transfer, has been a major force for genome plasticity over evolutionary history, and is largely responsible for the spread of fitness-enhancing traits, including antibiotic resistance and virulence factors. In particular, for adaptation of prokaryotes to extreme environments, lateral gene transfer seems to have played a crucial role. Here, we present a survey of the natural transformation machinery of the thermophile Thermus thermophilus HB27. A tentative model of the transformation machinery comprising of components similar to proteins of type IV pili and type II secretion systems is presented. A comparative discussion of the subunits and the structure of the DNA translocator and the underlying mechanism of transfer of free DNA in T. thermophilus highlights conserved and unique features of the DNA translocator in T. thermophilus. We hypothesize that the extraordinary broad substrate specificity and the high efficiency of the T. thermophilus DNA uptake system is of major importance for thermoadaptation and interdomain DNA transfer in hot environments.}, }
@article {pmid19207739, year = {2009}, author = {Dorman, CJ and Kane, KA}, title = {DNA bridging and antibridging: a role for bacterial nucleoid-associated proteins in regulating the expression of laterally acquired genes.}, journal = {FEMS microbiology reviews}, volume = {33}, number = {3}, pages = {587-592}, doi = {10.1111/j.1574-6976.2008.00155.x}, pmid = {19207739}, issn = {1574-6976}, mesh = {*Bacterial Physiological Phenomena ; Bacterial Proteins/*metabolism ; Chromosomes, Bacterial/*metabolism ; DNA, Bacterial/*metabolism ; DNA-Binding Proteins/*metabolism ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; }, abstract = {Horizontal DNA transfer plays a major role in the evolution of bacteria. It allows them to acquire new traits rapidly and these may confer fitness advantages as the bacteria compete with others in the environment. Historically, the mechanisms of horizontal DNA transfer, chiefly conjugation, transformation and transduction, have received a great deal of attention. Less attention has been focused on the regulatory problems that may accompany the acquisition of new genes by lateral routes. How are these genes integrated into the existing regulatory circuits of the cell? Does a process of 'plug-and-play' operate, or are the new genes silenced pending the evolution of regulatory mechanisms that make their expression not only safe but also beneficial to both the gene and its new host? Recent research shows that bacterial nucleoid-associated proteins such as H-NS, HU and Fis are important contributors to the processes of regulatory integration that accompany horizontal gene transfer. A key emerging theme is the antagonism that exists between the DNA-protein-DNA bridging activity of the H-NS repressor and the DNA-bending and DNA-wrapping activities of regulatory proteins that oppose H-NS.}, }
@article {pmid19207562, year = {2009}, author = {Frickey, T and Kannenberg, E}, title = {Phylogenetic analysis of the triterpene cyclase protein family in prokaryotes and eukaryotes suggests bidirectional lateral gene transfer.}, journal = {Environmental microbiology}, volume = {11}, number = {5}, pages = {1224-1241}, doi = {10.1111/j.1462-2920.2008.01851.x}, pmid = {19207562}, issn = {1462-2920}, support = {AI059577/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/*enzymology ; Cluster Analysis ; Eukaryotic Cells/*enzymology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Intramolecular Transferases/*genetics ; Models, Molecular ; Phylogeny ; Sequence Homology, Amino Acid ; }, abstract = {Functional constraints to modifications in triterpene cyclase amino acid sequences make them good candidates for evolutionary studies on the phylogenetic relatedness of these enzymes in prokaryotes as well as in eukaryotes. In this study, we used a set of identified triterpene cyclases, a group of mainly bacterial squalene cyclases and a group of predominantly eukaryotic oxidosqualene cyclases, as seed sequences to identify 5288 putative triterpene cyclase homologues in publicly available databases. The Cluster Analysis of Sequences software was used to detect groups of sequences with increased pairwise sequence similarity. The sequences fall into two main clusters, a bacterial and a eukaryotic. The conserved, informative regions of a multiple sequence alignment of the family were used to construct a neighbour-joining phylogenetic tree using the AsaturA and maximum likelihood phylogenetic tree using the PhyML software. Both analyses showed that most of the triterpene cyclase sequences were similarly grouped to the accepted taxonomic relationships of the organism the sequences originated from, supporting the idea of vertical transfer of cyclase genes from parent to offspring as the main evolutionary driving force in this protein family. However, a small group of sequences from three bacterial species (Stigmatella, Gemmata and Methylococcus) grouped with an otherwise purely eukaryotic cluster of oxidosqualene cyclases, while a small group of sequences from seven fungal species and a sequence from the fern Adiantum grouped consistently with a cluster of otherwise purely bacterial squalene cyclases. This suggests that lateral gene transfer may have taken place, entailing a transfer of oxidosqualene cyclases from eukaryotes to bacteria and a transfer of squalene cyclase from bacteria to an ancestor of the group of Pezizomycotina fungi.}, }
@article {pmid19205459, year = {2009}, author = {Nagachinta, S and Chen, J}, title = {Integron-mediated antibiotic resistance in Shiga toxin-producing Escherichia coli.}, journal = {Journal of food protection}, volume = {72}, number = {1}, pages = {21-27}, doi = {10.4315/0362-028x-72.1.21}, pmid = {19205459}, issn = {0362-028X}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Base Sequence ; Cattle ; Colony Count, Microbial ; Conjugation, Genetic ; Dose-Response Relationship, Drug ; Drug Resistance, Bacterial/*genetics ; Escherichia coli K12/*drug effects/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Integrons ; Microbial Sensitivity Tests ; Molecular Weight ; Shiga-Toxigenic Escherichia coli/*drug effects/*genetics ; }, abstract = {This study was undertaken to characterize the integrons present in a group of Shiga toxin-producing Escherichia coli (STEC) isolates and the ability of these integrons to transfer antibiotic resistance genes from STEC to E. coli K-12 MG1655. A total of 177 STEC isolates were analyzed for antibiotic susceptibility and the presence of integrons. Class 1 integrons were detected in 14 STEC isolates, and a class 2 integron was identified in 1 STEC isolate. The STEC isolates positive for class 1 integrons were resistant to streptomycin (MICs > 128 microg/ml) and sulfisoxazole (MICs > 1,024 microg/ml), and the isolate positive for the class 2 integron was resistant to streptomycin (MIC of 128 microg/ml), trimethoprim (MIC > 256 microg/ml), and streptothricin (MIC > 32 microg/ml). Results of restriction digestion and nucleotide sequencing revealed that the cassette regions of the class 1 integrons had a uniform size of 1.1 kb and contained a nucleotide sequence identical to that of aadA1. The class 2 integron cassette region was 2.0 kb and carried nucleotide sequences homologous to those of aadA1, sat1, and dfrA1. Results of the conjugation experiments revealed that horizontal transfers of conjugative plasmids are responsible for the dissemination of class 1 integron-mediated antibiotic resistance genes from STEC to E. coli K-12 MG1655. Antibiotic resistance traits not mediated by integrons, such as resistance to tetracycline and oxytetracycline, were cotransferred with the integron-mediated antibiotic resistance genes. The study suggested a possible role of integron and conjugative plasmid in dissemination of genes conferring resistance to antibiotics from pathogenic to generic E. coli cells.}, }
@article {pmid19204812, year = {2008}, author = {Almeida, FC and Leszczyniecka, M and Fisher, PB and Desalle, R}, title = {Examining ancient inter-domain horizontal gene transfer.}, journal = {Evolutionary bioinformatics online}, volume = {4}, number = {}, pages = {109-119}, pmid = {19204812}, issn = {1176-9343}, abstract = {Details of the genomic changes that occurred in the ancestors of Eukarya, Archaea and Bacteria are elusive. Ancient interdomain horizontal gene transfer (IDHGT) amongst the ancestors of these three domains has been difficult to detect and analyze because of the extreme degree of divergence of genes in these three domains and because most evidence for such events are poorly supported. In addition, many researchers have suggested that the prevalence of IDHGT events early in the evolution of life would most likely obscure the patterns of divergence of major groups of organisms let alone allow the tracking of horizontal transfer at this level. In order to approach this problem, we mined the E. coli genome for genes with distinct paralogs. Using the 1,268 E. coli K-12 genes with 40% or higher similarity level to a paralog elsewhere in the E. coli genome we detected 95 genes found exclusively in Bacteria and Archaea and 86 genes found in Bacteria and Eukarya. These genes form the basis for our analysis of IDHGT. We also applied a newly developed statistical test (the node height test), to examine the robustness of these inferences and to corroborate the phylogenetically identified cases of ancient IDHGT. Our results suggest that ancient inter domain HGT is restricted to special cases, mostly involving symbiosis in eukaryotes and specific adaptations in prokaryotes. Only three genes in the Bacteria + Eukarya class (Deoxyxylulose-5-phosphate synthase (DXPS), fructose 1,6-phosphate aldolase class II protein and glucosamine-6-phosphate deaminase) and three genes-in the Bacteria + Archaea class (ABC-type FE3+-siderophore transport system, ferrous iron transport protein B, and dipeptide transport protein) showed evidence of ancient IDHGT. However, we conclude that robust estimates of IDHGT will be very difficult to obtain due to the methodological limitations and the extreme sequence saturation of the genes suspected of being involved in IDHGT.}, }
@article {pmid19204804, year = {2008}, author = {Hickey, G and Dehne, F and Rau-Chaplin, A and Blouin, C}, title = {SPR distance computation for unrooted trees.}, journal = {Evolutionary bioinformatics online}, volume = {4}, number = {}, pages = {17-27}, pmid = {19204804}, issn = {1176-9343}, abstract = {The subtree prune and regraft distance (d(SPR)) between phylogenetic trees is important both as a general means of comparing phylogenetic tree topologies as well as a measure of lateral gene transfer (LGT). Although there has been extensive study on the computation of d(SPR) and similar metrics between rooted trees, much less is known about SPR distances for unrooted trees, which often arise in practice when the root is unresolved. We show that unrooted SPR distance computation is NP-Hard and verify which techniques from related work can and cannot be applied. We then present an efficient heuristic algorithm for this problem and benchmark it on a variety of synthetic datasets. Our algorithm computes the exact SPR distance between unrooted tree, and the heuristic element is only with respect to the algorithm's computation time. Our method is a heuristic version of a fixed parameter tractability (FPT) approach and our experiments indicate that the running time behaves similar to FPT algorithms. For real data sets, our algorithm was able to quickly compute d(SPR) for the majority of trees that were part of a study of LGT in 144 prokaryotic genomes. Our analysis of its performance, especially with respect to searching and reduction rules, is applicable to computing many related distance measures.}, }
@article {pmid19201978, year = {2009}, author = {Ishida, K and Welker, M and Christiansen, G and Cadel-Six, S and Bouchier, C and Dittmann, E and Hertweck, C and Tandeau de Marsac, N}, title = {Plasticity and evolution of aeruginosin biosynthesis in cyanobacteria.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {7}, pages = {2017-2026}, pmid = {19201978}, issn = {1098-5336}, mesh = {Biosynthetic Pathways/*genetics ; DNA, Bacterial/chemistry/genetics ; *Evolution, Molecular ; Gene Order ; Genes, Bacterial ; Microcystis/*genetics/*metabolism ; Molecular Sequence Data ; Multigene Family ; Oligopeptides/*biosynthesis/*genetics ; Peptide Synthases/genetics ; Sequence Analysis, DNA ; Sulfotransferases/genetics ; Synteny ; }, abstract = {Aeruginosins are bioactive oligopeptides that are produced in high structural diversity by strains of the bloom-forming cyanobacterial genera Microcystis and Planktothrix. A hallmark of aeruginosins is the unusual Choi moiety central to the tetrapeptides, while other positions are occupied by variable moieties in individual congeners. Here we report on three aeruginosin synthetase gene clusters (aer) of Microcystis aeruginosa (strains PCC 7806, NIES-98, and NIES-843). The analysis and comparison the aer gene clusters provide the first insight into the molecular basis of biosynthetic and structural plasticity in aeruginosin pathways. Major parts of the aer gene clusters are highly similar in all strains, particularly the genes coding for the first three nonribosomal peptide synthetase (NRPS) modules except for the region coding for the second adenylation domain. However, the gene clusters differ largely in genes coding for tailoring enzymes such as halogenases and sulfotransferases, reflecting structural peculiarities in aeruginosin congeners produced by the individual strains. Significant deviations were further observed in the C-terminal NRPS modules, suggesting two distinct release mechanisms. The architecture of the gene clusters is in agreement with the particular aeruginosin variants that are produced by individual strains, the structures of two of which (aeruginosins 686 A and 686 B) were elucidated. The aer gene clusters of Microcystis and Planktothrix are proposed to originate from a common ancestor and to have evolved to their present-day diversity largely through horizontal gene transfer and recombination events.}, }
@article {pmid19201125, year = {2009}, author = {Rivas, R and Martens, M and de Lajudie, P and Willems, A}, title = {Multilocus sequence analysis of the genus Bradyrhizobium.}, journal = {Systematic and applied microbiology}, volume = {32}, number = {2}, pages = {101-110}, doi = {10.1016/j.syapm.2008.12.005}, pmid = {19201125}, issn = {0723-2020}, mesh = {Bacterial Proteins/*genetics ; *Bacterial Typing Techniques ; Bradyrhizobium/*classification/genetics ; DNA, Bacterial/analysis ; Fabaceae/*microbiology ; Nucleic Acid Hybridization ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {The use of multilocus sequence analysis (MLSA) for the taxonomy of Bradyrhizobium was assessed. We compared partial sequences for atpD, recA, gyrB, rpoB and dnaK for a set of reference strains representing named species and genospecies, and a number of new isolates from Lupinus albus, Arachis hypogaea and Ornithopus compressus from Spain. The phylogenies of the individual genes were compared with previous DNA-DNA hybridization results. High hybridization values were well reflected, but intermediary hybridization values were less clearly apparent. However, the phylogeny of a concatenated dataset of the five genes did reflect all values and thus is more informative of overall genome similarity. Our results indicate that only for the genes gyrB, rpoB and dnaK there is a small gap between the interspecies sequence similarities and the intraspecies similarity, and therefore cut-off levels for species delineation cannot be set, although high sequence similarity (>99%) does permit identification. In a few instances, a reference strain did not group as expected for one of the five genes tested. This may be a result of horizontal gene transfer and recombination events occasionally involving housekeeping genes. This observation indicates it is best to consider more than one gene for taxonomic inferences. The majority of the new isolates from the three host species was identified as Bradyrhizobium canariense. Four strains from L. albus from León, Spain, formed a separate group close to Bradyrhizobium japonicum.}, }
@article {pmid19201124, year = {2009}, author = {Meinersmann, RJ and Phillips, RW and Ladely, SR}, title = {Inter- and intra-genomic heterogeneity of the intervening sequence in the 23S ribosomal RNA gene of Campylobacter jejuni and Campylobacter coli.}, journal = {Systematic and applied microbiology}, volume = {32}, number = {2}, pages = {91-100}, doi = {10.1016/j.syapm.2008.12.004}, pmid = {19201124}, issn = {0723-2020}, mesh = {Animals ; Base Sequence ; Blotting, Southern ; Campylobacter Infections/*microbiology/veterinary ; *Campylobacter coli/classification/genetics/isolation &amp; purification ; *Campylobacter jejuni/classification/genetics/isolation &amp; purification ; Cattle ; Chickens ; DNA, Bacterial/analysis ; DNA, Ribosomal/analysis ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, rRNA ; Genome, Bacterial ; Humans ; *Introns ; Molecular Sequence Data ; Polymerase Chain Reaction ; *Polymorphism, Genetic ; RNA, Ribosomal, 23S/*genetics ; Sequence Analysis, DNA ; Swine ; }, abstract = {An intervening sequence (IVS) can be present or absent in the 23S rRNA of Campylobacter jejuni and Campylobacter coli. As part of a survey, we used a polymerase chain reaction (PCR) assay to detect the presence of the IVS in 43 isolates of C. coli and 82 isolates of C. jejuni. An IVS was present in 40 (93.0%) of the C. coli and only 34 (41.5%) of the C. jejuni isolates. Twelve (27.9%) of the C. coli isolates and seven (8.5%) of the C. jejuni isolates resulted in two polymerase chain reaction products, indicating heterogeneity in the presence of the 23S rRNA IVS. Fourteen of the isolates with two products were evaluated by pulse-field gel electrophoresis; 13 different patterns were observed. The total band size of one isolate was substantially greater than the expected 1.7 Mb, possibly indicating a mixed culture. Southern blot analyses demonstrated the expected three rRNA operons in all tested isolates. Nested PCR reactions with operon-specific primers followed by primers for the IVS confirmed that the strains of interest contained either one or two operons carrying the IVS and the remaining operon(s) did not. Sequence analysis of the IVS and flanking regions of the 23S rRNA genes did not discriminate C. jejuni and C. coli as distinct populations. These results indicate horizontal transfer of 23S rRNA genes or portions of the genes between C. jejuni and C. coli. Also, data showing sequence polymorphisms between the three 23S rRNA loci outside of the IVS region suggest that the isolates with intra-genomic heterogeneity appear to be members of clones that have an ancient defect in gene conversion mechanisms needed for concerted evolution of the ribosomal operons.}, }
@article {pmid19199791, year = {2009}, author = {Johansson, C and Boukharta, L and Eriksson, J and Aqvist, J and Sundström, L}, title = {Mutagenesis and homology modeling of the Tn21 integron integrase IntI1.}, journal = {Biochemistry}, volume = {48}, number = {8}, pages = {1743-1753}, doi = {10.1021/bi8020235}, pmid = {19199791}, issn = {1520-4995}, mesh = {Amino Acid Sequence ; Attachment Sites, Microbiological/genetics ; Autoradiography ; Biocatalysis ; DNA/metabolism ; DNA Transposable Elements/*genetics ; Electrophoresis, Polyacrylamide Gel ; Electrophoretic Mobility Shift Assay ; Hydrogen Bonding ; Integrases/*chemistry ; *Models, Molecular ; Molecular Sequence Data ; *Mutagenesis ; Mutant Proteins/chemistry/metabolism ; Mutation/genetics ; Protein Binding ; Protein Structure, Secondary ; Recombination, Genetic ; Sequence Alignment ; *Structural Homology, Protein ; Vibrio cholerae/*enzymology ; }, abstract = {Horizontal DNA transfer between bacteria is widespread and a major cause of antibiotic resistance. For logistic reasons, single or combined genes are shuttled between vectors such as plasmids and bacterial chromosomes. Special elements termed integrons operate in such shuttling and are therefore vital for horizontal gene transfer. Shorter elements carrying genes, cassettes, are integrated in the integrons, or excised from them, by virtue of a recombination site, attC, positioned in the 3' end of each unit. It is a remarkable and possibly restricting elementary feature of attC that it must be single-stranded while the partner target site, attI, may be double-stranded. The integron integrases belong to the tyrosine recombinase family, and this work reports mutations of the integrase IntI1 from transposon Tn21, chosen within a well-conserved region characteristic of the integron integrases. The mutated proteins were tested for binding to a bottom strand of an attC substrate, by using an electrophoresis mobility shift assay. To aid in interpreting the results, a homology model was constructed on the basis of the crystal structure of integron integrase VchIntIA from Vibrio cholerae bound to its cognate attC substrate VCRbs. The local stability and hydrogen bonding network of key domains of the modeled structure were further examined using molecular dynamics simulations. The homology model allowed us to interpret the roles of several amino acid residues, four of which were clearly binding assay responsive upon mutagenesis. Notably, we also observed features indicating that IntI1 may be more prone to base-specific contacts with VCRbs than VchIntIA.}, }
@article {pmid19197054, year = {2009}, author = {Fraser, C and Alm, EJ and Polz, MF and Spratt, BG and Hanage, WP}, title = {The bacterial species challenge: making sense of genetic and ecological diversity.}, journal = {Science (New York, N.Y.)}, volume = {323}, number = {5915}, pages = {741-746}, doi = {10.1126/science.1159388}, pmid = {19197054}, issn = {1095-9203}, support = {089472/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacteria/*classification/*genetics ; *Biodiversity ; Biological Evolution ; *Ecosystem ; Extinction, Biological ; Genes, Bacterial ; *Genetic Speciation ; *Genetic Variation ; Models, Biological ; Models, Genetic ; Recombination, Genetic ; Selection, Genetic ; }, abstract = {The Bacteria and Archaea are the most genetically diverse superkingdoms of life, and techniques for exploring that diversity are only just becoming widespread. Taxonomists classify these organisms into species in much the same way as they classify eukaryotes, but differences in their biology-including horizontal gene transfer between distantly related taxa and variable rates of homologous recombination-mean that we still do not understand what a bacterial species is. This is not merely a semantic question; evolutionary theory should be able to explain why species exist at all levels of the tree of life, and we need to be able to define species for practical applications in industry, agriculture, and medicine. Recent studies have emphasized the need to combine genetic diversity and distinct ecology in an attempt to define species in a coherent and convincing fashion. The resulting data may help to discriminate among the many theories of prokaryotic species that have been produced to date.}, }
@article {pmid19196269, year = {2009}, author = {Palenik, B and Ren, Q and Tai, V and Paulsen, IT}, title = {Coastal Synechococcus metagenome reveals major roles for horizontal gene transfer and plasmids in population diversity.}, journal = {Environmental microbiology}, volume = {11}, number = {2}, pages = {349-359}, doi = {10.1111/j.1462-2920.2008.01772.x}, pmid = {19196269}, issn = {1462-2920}, mesh = {Amino Acid Sequence ; California ; Codon/genetics ; DNA, Bacterial/chemistry/genetics ; *Gene Transfer, Horizontal ; *Genetic Variation ; Geologic Sediments/*microbiology ; Interspersed Repetitive Sequences ; Molecular Sequence Data ; *Plasmids ; Sequence Alignment ; Sequence Analysis, DNA ; Synechococcus/*classification/*genetics/isolation &amp; purification ; }, abstract = {The extent to which cultured strains represent the genetic diversity of a population of microorganisms is poorly understood. Because they do not require culturing, metagenomic approaches have the potential to reveal the genetic diversity of the microbes actually present in an environment. From coastal California seawater, a complex and diverse environment, the marine cyanobacteria of the genus Synechococcus were enriched by flow cytometry-based sorting and the population metagenome was analysed with 454 sequencing technology. The sequence data were compared with model Synechococcus genomes, including those of two coastal strains, one isolated from the same and one from a very similar environment. The natural population metagenome had high sequence identity to most genes from the coastal model strains but diverged greatly from these genomes in multiple regions of atypical trinucleotide content that encoded diverse functions. These results can be explained by extensive horizontal gene transfer presumably with large differences in horizontally transferred genetic material between different strains. Some assembled contigs showed the presence of novel open reading frames not found in the model genomes, but these could not yet be unambiguously assigned to a Synechococcus clade. At least three distinct mobile DNA elements (plasmids) not found in model strain genomes were detected in the assembled contigs, suggesting for the first time their likely importance in marine cyanobacterial populations and possible role in horizontal gene transfer.}, }
@article {pmid19195810, year = {2009}, author = {Lu, YL and Chen, WF and Wang, ET and Guan, SH and Yan, XR and Chen, WX}, title = {Genetic diversity and biogeography of rhizobia associated with Caragana species in three ecological regions of China.}, journal = {Systematic and applied microbiology}, volume = {32}, number = {5}, pages = {351-361}, doi = {10.1016/j.syapm.2008.10.004}, pmid = {19195810}, issn = {1618-0984}, mesh = {Bacterial Proteins/analysis/genetics ; Caragana/*microbiology ; China ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Electrophoresis, Polyacrylamide Gel ; Gene Transfer, Horizontal ; *Genetic Variation ; Geography ; Molecular Sequence Data ; N-Acetylglucosaminyltransferases/genetics ; Phylogeny ; Proteome/analysis ; RNA, Ribosomal, 16S/genetics ; Rhizobiaceae/chemistry/*classification/genetics/*isolation &amp; purification ; Sequence Analysis, DNA ; }, abstract = {Twenty-two genospecies belonging mainly to Mesorhizobium, and occasionally to Rhizobium and Bradyrhizobium, were defined among the 174 rhizobia strains isolated from Caragana species. Highly similar nodC genes were found in the sole Bradyrhizobium strain and among all the detected Mesorhizobium strains. A clear correlation between rhizobial genospecies and the eco-regions where they were isolated was found using homogeneity analysis. All these results demonstrated that Caragana species had stringently selected the rhizobia symbiotic genotype, but not the genomic background; lateral transfer of symbiotic genes from Mesorhizobium to Bradyrhizobium and among the Mesorhizobium species has happened in the Caragana rhizobia; and biogeography of Caragana rhizobia exists. Furthermore, a combined cluster analysis, based upon the patterns obtained from amplified 16S rRNA gene and 16S-23S intergenic spacer restriction analyses, BOX PCR and SDS-PAGE of proteins, was reported to be an efficient method to define the genospecies.}, }
@article {pmid19191103, year = {2009}, author = {Liu, W and Volpe, MA and Zscheppang, K and Nielsen, HC and Dammann, CE}, title = {ErbB4 regulates surfactant synthesis and proliferation in adult rat pulmonary epithelial cells.}, journal = {Experimental lung research}, volume = {35}, number = {1}, pages = {29-47}, doi = {10.1080/01902140802395757}, pmid = {19191103}, issn = {1521-0499}, support = {P30 DK34928/DK/NIDDK NIH HHS/United States ; HL 037930/HL/NHLBI NIH HHS/United States ; R01 HL085648/HL/NHLBI NIH HHS/United States ; R01 HL037930/HL/NHLBI NIH HHS/United States ; HL 04436/HL/NHLBI NIH HHS/United States ; HD 044784/HD/NICHD NIH HHS/United States ; }, mesh = {Animals ; Cell Count ; Cell Line ; Cell Proliferation ; Culture Media, Conditioned/pharmacology ; Down-Regulation/drug effects ; ErbB Receptors/genetics/*metabolism ; Female ; Gene Expression/drug effects ; Gene Transfer, Horizontal ; Male ; Neuregulin-1/genetics/metabolism ; Phospholipids/antagonists &amp; inhibitors/biosynthesis ; Phosphorylation ; Pulmonary Surfactant-Associated Proteins/*biosynthesis ; RNA, Small Interfering/metabolism ; Rats ; Rats, Sprague-Dawley ; Receptor, ErbB-4 ; Respiratory Mucosa/cytology/drug effects/*metabolism ; }, abstract = {ErbB4 is a predominant heterodimer for other ErbB receptors in late fetal lung development where it participates in regulating type II cell surfactant synthesis. To further elucidate the role of ErbB4 in pulmonary alveolar epithelial cell function, the authors hypothesized that ErbB4 participates in maintaining adult lung type II cell homeostasis. The authors used small interfering RNA (siRNA) to down-regulate endogenous, ErbB4 receptors in the adult rat lung epithelial L2 cell line and measured neuregulin 1beta (NRG1beta)-, and fibroblast conditioned medium (FCM)-induced effects on L2 cell surfactant phospholipid synthesis and proliferation. Under control conditions, total and phosphorylated ErbB4 were significantly increased after both NRG1beta and FCM treatment, as were surfactant phospholipids synthesis and cell proliferation. Down-regulation of ErbB4 with siRNA reduced stimulation of NRG1beta- and FCM-induced ErbB4 phosphorylation, decreased endogenous surfactant phospholipid synthesis, and blocked NRG1beta- and FCM-stimulated surfactant phospholipid synthesis. NRG1beta- and FCM-induced cell proliferation was not affected. The authors conclude that ErbB4 participates in maintaining adult lung alveolar epithelial cell surfactant synthesis and proliferation with development-specific functions.}, }
@article {pmid19189956, year = {2009}, author = {Mine, N and Guglielmini, J and Wilbaux, M and Van Melderen, L}, title = {The decay of the chromosomally encoded ccdO157 toxin-antitoxin system in the Escherichia coli species.}, journal = {Genetics}, volume = {181}, number = {4}, pages = {1557-1566}, pmid = {19189956}, issn = {0016-6731}, mesh = {Amino Acid Sequence ; Antitoxins/*genetics ; Bacterial Toxins/*genetics ; Base Sequence ; Chromosomes, Bacterial ; DNA, Intergenic/genetics ; Escherichia coli/*genetics ; Escherichia coli O157/*genetics ; Escherichia coli Proteins/genetics ; Evolution, Molecular ; Models, Biological ; Molecular Sequence Data ; *Selection, Genetic ; Species Specificity ; }, abstract = {The origin and the evolution of toxin-antitoxin (TA) systems remain to be uncovered. TA systems are abundant in bacterial chromosomes and are thought to be part of the flexible genome that originates from horizontal gene transfer. To gain insight into TA system evolution, we analyzed the distribution of the chromosomally encoded ccdO157 system in 395 natural isolates of Escherichia coli. It was discovered in the E. coli O157:H7 strain in which it constitutes a genomic islet between two core genes (folA and apaH). Our study revealed that the folA-apaH intergenic region is plastic and subject to insertion of foreign DNA. It could be composed (i) of a repetitive extragenic palindromic (REP) sequence, (ii) of the ccdO157 system or subtle variants of it, (iii) of a large DNA piece that contained a ccdAO157 antitoxin remnant in association with ORFs of unknown function, or (iv) of a variant of it containing an insertion sequence in the ccdAO157 remnant. Sequence analysis and functional tests of the ccdO157 variants revealed that 69% of the variants were composed of an active toxin and antitoxin, 29% were composed of an active antitoxin and an inactive toxin, and in 2% of the cases both ORFs were inactive. Molecular evolution analysis showed that ccdBO157 is under neutral evolution, suggesting that this system is devoid of any biological role in the E. coli species.}, }
@article {pmid19189039, year = {2009}, author = {Fitzpatrick, DA}, title = {Lines of evidence for horizontal gene transfer of a phenazine producing operon into multiple bacterial species.}, journal = {Journal of molecular evolution}, volume = {68}, number = {2}, pages = {171-185}, pmid = {19189039}, issn = {1432-1432}, mesh = {Bacteria/*genetics/metabolism ; Bacterial Proteins/*genetics ; Base Composition ; Bayes Theorem ; Codon ; Contraindications ; Databases, Genetic ; Enterobacteriaceae/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Gram-Positive Bacteria/genetics ; Multigene Family ; Operon/*genetics ; Phenazines/*metabolism ; Phylogeny ; Pseudomonas aeruginosa/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Statistics, Nonparametric ; }, abstract = {Phenazines are secondary metabolites with broad-spectrum antibiotic activity against bacteria, fungi, and eukaryotes. In pseudomonad species, a conserved seven-gene phenazine operon (phzABCDEFG) is required for the conversion of chorismic acid to the broad-spectrum antibiotic phenazine-1-carboxylate. Previous analyses of genes involved in phenazine production from nonpseudomonad species uncovered a high degree of sequence similarity to pseudomonad homologues. The analyses undertaken in this study wished to eluciadate the evolutionary history of genes involved in the production of phenazines. Furthermore, I wanted to determine if the phenazine operon has been transferred through horizontal gene transfer. Analyses of GC content, codon usage patterns, frequency of 3:1 dinucleotides, sequence similarities, and phylogenetic reconstructions were undertaken to map the evolutionary history of phenazine genes from multiple bacterial species. Patchy phyletic distribution, high sequence similarities, and phylogenetic evidence infer that pseudomonad, Streptomyces cinnamonensis, Pantoea agglomerans, Burkholderia cepacia, Pectobacterium atrosepticum, Brevibacterium linens, and Mycobacterium abscessus species all contain a phenazine operon which has most likely been transferred among these species through horizontal gene transfer. The acquisition of an antibiotic-associated operon is significant, as it may increase the relative fitness of the recipient species.}, }
@article {pmid19187530, year = {2009}, author = {Weinert, LA and Werren, JH and Aebi, A and Stone, GN and Jiggins, FM}, title = {Evolution and diversity of Rickettsia bacteria.}, journal = {BMC biology}, volume = {7}, number = {}, pages = {6}, pmid = {19187530}, issn = {1741-7007}, mesh = {Animals ; Arthropods/microbiology ; Base Sequence ; Genes, Bacterial/genetics ; *Genetic Variation ; Male ; Molecular Sequence Data ; *Phylogeny ; Recombination, Genetic ; Rickettsia/genetics/*physiology ; Sequence Alignment ; }, abstract = {BACKGROUND: Rickettsia are intracellular symbionts of eukaryotes that are best known for infecting and causing serious diseases in humans and other mammals. All known vertebrate-associated Rickettsia are vectored by arthropods as part of their life-cycle, and many other Rickettsia are found exclusively in arthropods with no known secondary host. However, little is known about the biology of these latter strains. Here, we have identified 20 new strains of Rickettsia from arthropods, and constructed a multi-gene phylogeny of the entire genus which includes these new strains.<br><br>RESULTS: We show that Rickettsia are primarily arthropod-associated bacteria, and identify several novel groups within the genus. Rickettsia do not co-speciate with their hosts but host shifts most often occur between related arthropods. Rickettsia have evolved adaptations including transmission through vertebrates and killing males in some arthropod hosts. We uncovered one case of horizontal gene transfer among Rickettsia, where a strain is a chimera from two distantly related groups, but multi-gene analysis indicates that different parts of the genome tend to share the same phylogeny.<br><br>CONCLUSION: Approximately 150 million years ago, Rickettsia split into two main clades, one of which primarily infects arthropods, and the other infects a diverse range of protists, other eukaryotes and arthropods. There was then a rapid radiation about 50 million years ago, which coincided with the evolution of life history adaptations in a few branches of the phylogeny. Even though Rickettsia are thought to be primarily transmitted vertically, host associations are short lived with frequent switching to new host lineages. Recombination throughout the genus is generally uncommon, although there is evidence of horizontal gene transfer. A better understanding of the evolution of Rickettsia will help in the future to elucidate the mechanisms of pathogenicity, transmission and virulence.}, }
@article {pmid19187282, year = {2009}, author = {Martiny, AC and Huang, Y and Li, W}, title = {Occurrence of phosphate acquisition genes in Prochlorococcus cells from different ocean regions.}, journal = {Environmental microbiology}, volume = {11}, number = {6}, pages = {1340-1347}, doi = {10.1111/j.1462-2920.2009.01860.x}, pmid = {19187282}, issn = {1462-2920}, mesh = {Adaptation, Biological ; Cyanobacteria/classification ; Gene Frequency ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genome, Bacterial ; Geography ; Oceans and Seas ; Phosphates/*analysis/metabolism ; Prochlorococcus/chemistry/*genetics/isolation &amp; purification ; Seawater/chemistry/*microbiology ; }, abstract = {The cyanobacterium Prochlorococcus is the numerically dominant phototroph in oligotrophic parts of the oceans. Recently, it was shown that the distribution of phosphate acquisition genes did not match the 16S rRNA phylogeny among isolates from this group but rather appeared related to phosphate availability where the strains had been isolated. To further understand adaptation to phosphate limitation in Prochlorococcus, the distribution of phosphate acquisition genes was investigated in different ocean regions and related to local ortho-phosphate concentration. In regions characterized by less than 0.1 microM phosphate, most Prochlorococcus cells contain genes involved in phosphate uptake, regulation and utilization of organic phosphates. In contrast, most of these genes are absent in regions with more than 0.1 microM phosphate with the exception of genes involved in transport of phosphate (phoE and pstABCS) and three genes of unknown function. This pattern of phosphate acquisition genes showed no significant correspondence to the distribution of rRNA phylotypes. In addition, it was demonstrated that several genes in a separate genomic island were commonly present in low-P sites while absent in high-P sites. Overall, this study further demonstrates a linkage between environmental conditions in the ocean and genome content of Prochlorococcus.}, }
@article {pmid19187139, year = {2009}, author = {Ghosh, S and Sadowsky, MJ and Roberts, MC and Gralnick, JA and LaPara, TM}, title = {Sphingobacterium sp. strain PM2-P1-29 harbours a functional tet(X) gene encoding for the degradation of tetracycline.}, journal = {Journal of applied microbiology}, volume = {106}, number = {4}, pages = {1336-1342}, doi = {10.1111/j.1365-2672.2008.04101.x}, pmid = {19187139}, issn = {1365-2672}, mesh = {Base Sequence ; *Conjugation, Genetic ; DNA, Bacterial/genetics ; Microbial Sensitivity Tests ; Polymerase Chain Reaction ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sphingobacterium/*genetics/metabolism ; Tetracycline/metabolism/pharmacology ; Tetracycline Resistance/*genetics ; }, abstract = {AIMS: The tet(X) gene has previously been found in obligate anaerobic Bacteroides spp., which is curious because tet(X) encodes for a NADP-dependent monooxygenase that requires oxygen to degrade tetracycline. In this study, we characterized a tetracycline resistant, aerobic, Gram-negative Sphingobacterium sp. strain PM2-P1-29 that harbours a tet(X) gene.<br><br>METHODS AND RESULTS: Sphingobacterium sp. PM2-P1-29 demonstrated the ability to transform tetracycline compared with killed controls. The presence of the tet(X) gene was verified by PCR and nucleotide sequence analysis. Additional nucleotide sequence analysis of regions flanking the tet(X) gene revealed a mobilizable transposon-like element (Tn6031) that shared organizational features and genes with the previously described Bacteroides conjugative transposon CTnDOT. A circular transposition intermediate of the tet(X) region, characteristic of mobilizable transposons, was detected. However, we could not demonstrate the conjugal transfer of the tet(X) gene using three different recipient strains and numerous experimental conditions.<br><br>CONCLUSIONS: This study suggests that Sphingobacterium sp. PM2-P1-29 or a related bacterium may be an ancestral source of the tet(X) gene.<br><br>This study demonstrates the importance of environmental bacteria and lateral gene transfer in the dissemination and proliferation of antibiotic resistance among bacteria.}, }
@article {pmid19181805, year = {2009}, author = {Timmery, S and Modrie, P and Minet, O and Mahillon, J}, title = {Plasmid capture by the Bacillus thuringiensis conjugative plasmid pXO16.}, journal = {Journal of bacteriology}, volume = {191}, number = {7}, pages = {2197-2205}, pmid = {19181805}, issn = {1098-5530}, mesh = {Bacillus thuringiensis/*genetics/metabolism ; *Conjugation, Genetic ; Culture Media/metabolism ; Gene Transfer, Horizontal ; Plasmids/*genetics ; Staphylococcus aureus/genetics/metabolism ; }, abstract = {Conjugation, mobilization, and retromobilization are three related mechanisms of horizontal gene transfer in bacteria. They have been extensively studied in gram-negative species, where retromobilization, the capture of DNA from a recipient by a donor cell, was shown to result from two successive steps: the transfer of the conjugative plasmid from the donor to the recipient followed by the retrotransfer of the mobilizable plasmid to the donor. This successive model was established for gram-negative bacteria but was lacking experimental data from the gram-positive counterparts. In the present work, the mobilization and retromobilization abilities of the conjugative plasmid pXO16 from Bacillus thuringiensis subsp. israelensis were studied using the mobilizable plasmids pUB110 and pE194 and the "nonmobilizable" element pC194 lacking the mob and oriT features (all from Staphylococcus aureus). Experimental data suggested a successive model, since different retromobilization frequencies were observed between the small plasmids. More importantly, retromobilization was shown to be delayed by 50 and 150 min for pUB110 and pE194, respectively, compared to pXO16 conjugation. Natural liquid foods (cow milk, soy milk, and rice milk) were used to evaluate the putative ecological impact of these transfers. In cow and soy milk, conjugation, mobilization, and retromobilization were shown to occur at frequencies of 8.0 x 10(-1), 1.0 x 10(-2), and 1.2 x 10(-4) transconjugants per recipient, respectively. These data are comparable to those obtained with LB medium and about 10-fold lower than in the case of rice milk. Taken together, these results emphasize the potential role of plasmid capture played by B. thuringiensis in natural environments.}, }
@article {pmid19181800, year = {2009}, author = {Bellanger, X and Roberts, AP and Morel, C and Choulet, F and Pavlovic, G and Mullany, P and Decaris, B and Guédon, G}, title = {Conjugative transfer of the integrative conjugative elements ICESt1 and ICESt3 from Streptococcus thermophilus.}, journal = {Journal of bacteriology}, volume = {191}, number = {8}, pages = {2764-2775}, pmid = {19181800}, issn = {1098-5530}, mesh = {Alkylating Agents/pharmacology ; *Conjugation, Genetic ; DNA Damage ; Enterococcus faecalis/genetics ; *Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences ; Lactococcus lactis/genetics ; Mitomycin/pharmacology ; Recombination, Genetic ; Streptococcus pyogenes/genetics ; Streptococcus thermophilus/*genetics ; }, abstract = {Integrative and conjugative elements (ICEs), also called conjugative transposons, are genomic islands that excise, self-transfer by conjugation, and integrate in the genome of the recipient bacterium. The current investigation shows the intraspecies conjugative transfer of the first described ICEs in Streptococcus thermophilus, ICESt1 and ICESt3. Mitomycin C, a DNA-damaging agent, derepresses ICESt3 conjugative transfer almost 25-fold. The ICESt3 host range was determined using various members of the Firmicutes as recipients. Whereas numerous ICESt3 transconjugants of Streptococcus pyogenes and Enterococcus faecalis were recovered, only one transconjugant of Lactococcus lactis was obtained. The newly incoming ICEs, except the one from L. lactis, are site-specifically integrated into the 3' end of the fda gene and are still able to excise in these transconjugants. Furthermore, ICESt3 was retransferred from E. faecalis to S. thermophilus. Recombinant plasmids carrying different parts of the ICESt1 recombination module were used to show that the integrase gene is required for the site-specific integration and excision of the ICEs, whereas the excisionase gene is required for the site-specific excision only.}, }
@article {pmid19180475, year = {2009}, author = {Bianco, NR and Kim, SH and Ruffner, MA and Robbins, PD}, title = {Therapeutic effect of exosomes from indoleamine 2,3-dioxygenase-positive dendritic cells in collagen-induced arthritis and delayed-type hypersensitivity disease models.}, journal = {Arthritis and rheumatism}, volume = {60}, number = {2}, pages = {380-389}, pmid = {19180475}, issn = {0004-3591}, support = {U19 AI056374/AI/NIAID NIH HHS/United States ; U19 AI056374-010002/AI/NIAID NIH HHS/United States ; AI-56374/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Arthritis, Experimental/enzymology/immunology/*therapy ; Bone Marrow Cells ; Dendritic Cells/*enzymology/immunology ; Disease Models, Animal ; Exosomes/genetics/immunology/*transplantation ; Female ; Gene Transfer Techniques ; Gene Transfer, Horizontal ; Hypersensitivity, Delayed/enzymology/immunology/*therapy ; Immunosuppression Therapy ; Immunosuppressive Agents/*administration &amp; dosage ; Indoleamine-Pyrrole 2,3,-Dioxygenase/genetics/*metabolism ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; }, abstract = {OBJECTIVE: We have demonstrated previously that dendritic cells (DCs) modified with immunosuppressive cytokines, and exosomes derived from DCs can suppress the onset of murine collagen-induced arthritis (CIA) and reduce the severity of established arthritis. Indoleamine 2,3-dioxygenase (IDO) is a tryptophan-degrading enzyme that is important for immune regulation and tolerance maintenance. DCs expressing functional IDO can inhibit T cells by depleting them of essential tryptophan and/or by producing toxic metabolites, as well as by generating Treg cells. This study was undertaken to examine the immunosuppressive effects of bone marrow (BM)-derived DCs genetically modified to express IDO, and of exosomes derived from IDO-positive DCs.<br><br>METHODS: BM-derived DCs were adenovirally transduced with IDO or CTLA-4Ig (an inducer of IDO), and the resulting DCs and exosomes were tested for their immunosuppressive ability in the CIA and delayed-type hypersensitivity (DTH) murine models.<br><br>RESULTS: Both DCs and exosomes derived from DCs overexpressing IDO had an antiinflammatory effect in CIA and DTH murine models. The suppressive effects were partially dependent on B7 costimulatory molecules. In addition, gene transfer of CTLA-4Ig to DCs resulted in induction of IDO in the DCs and in exosomes able to reduce inflammation in an IDO-dependent manner.<br><br>CONCLUSION: These results demonstrate that both IDO-expressing DCs and DC-derived exosomes are immunosuppressive and antiinflammatory, and are able to reverse established arthritis. Therefore, exosomes from IDO-positive DCs may represent a novel therapy for rheumatoid arthritis.}, }
@article {pmid19179698, year = {2009}, author = {Cardona, G and Llabrés, M and Rosselló, F and Valiente, G}, title = {Metrics for phylogenetic networks I: generalizations of the Robinson-Foulds metric.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {6}, number = {1}, pages = {46-61}, doi = {10.1109/TCBB.2008.70}, pmid = {19179698}, issn = {1557-9964}, mesh = {Algorithms ; Computational Biology/*methods ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Hybridization, Genetic ; *Models, Genetic ; *Phylogeny ; Recombination, Genetic ; Time Factors ; }, abstract = {The assessment of phylogenetic network reconstruction methods requires the ability to compare phylogenetic networks. This is the first in a series of papers devoted to the analysis and comparison of metrics for tree-child time consistent phylogenetic networks on the same set of taxa. In this paper, we study three metrics that have already been introduced in the literature: the Robinson-Foulds distance, the tripartitions distance and the mu-distance. They generalize to networks the classical Robinson-Foulds or partition distance for phylogenetic trees. We analyze the behavior of these metrics by studying their least and largest values and when they achieve them. As a by-product of this study, we obtain tight bounds on the size of a tree-child time consistent phylogenetic network.}, }
@article {pmid19179697, year = {2009}, author = {Linz, S and Semple, C}, title = {Hybridization in nonbinary trees.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {6}, number = {1}, pages = {30-45}, doi = {10.1109/TCBB.2008.86}, pmid = {19179697}, issn = {1557-9964}, mesh = {Algorithms ; Computational Biology/*methods ; Evolution, Molecular ; *Hybridization, Genetic ; *Models, Genetic ; *Phylogeny ; }, abstract = {Reticulate evolution--the umbrella term for processes like hybridization, horizontal gene transfer, and recombination--plays an important role in the history of life of many species. Although the occurrence of such events is widely accepted, approaches to calculate the extent to which reticulation has influenced evolution are relatively rare. In this paper, we show that the NP-hard problem of calculating the minimum number of reticulation events for two (arbitrary) rooted phylogenetic trees parameterized by this minimum number is fixed-parameter tractable.}, }
@article {pmid19178566, year = {2009}, author = {Juhas, M and van der Meer, JR and Gaillard, M and Harding, RM and Hood, DW and Crook, DW}, title = {Genomic islands: tools of bacterial horizontal gene transfer and evolution.}, journal = {FEMS microbiology reviews}, volume = {33}, number = {2}, pages = {376-393}, pmid = {19178566}, issn = {1574-6976}, support = {G0400039/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Bacteria/drug effects/*genetics/pathogenicity ; Bacterial Infections/microbiology ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Genomic Islands/*genetics ; Humans ; Virulence/genetics ; }, abstract = {Bacterial genomes evolve through mutations, rearrangements or horizontal gene transfer. Besides the core genes encoding essential metabolic functions, bacterial genomes also harbour a number of accessory genes acquired by horizontal gene transfer that might be beneficial under certain environmental conditions. The horizontal gene transfer contributes to the diversification and adaptation of microorganisms, thus having an impact on the genome plasticity. A significant part of the horizontal gene transfer is or has been facilitated by genomic islands (GEIs). GEIs are discrete DNA segments, some of which are mobile and others which are not, or are no longer mobile, which differ among closely related strains. A number of GEIs are capable of integration into the chromosome of the host, excision, and transfer to a new host by transformation, conjugation or transduction. GEIs play a crucial role in the evolution of a broad spectrum of bacteria as they are involved in the dissemination of variable genes, including antibiotic resistance and virulence genes leading to generation of hospital 'superbugs', as well as catabolic genes leading to formation of new metabolic pathways. Depending on the composition of gene modules, the same type of GEIs can promote survival of pathogenic as well as environmental bacteria.}, }
@article {pmid19178544, year = {2009}, author = {Mylvaganam, H and Bruun, T and Vindenes, HA and Langeland, N and Skrede, S}, title = {Molecular epidemiological investigation of an outbreak of invasive beta-haemolytic streptococcal infection in western Norway.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {15}, number = {3}, pages = {245-252}, doi = {10.1111/j.1469-0691.2008.02664.x}, pmid = {19178544}, issn = {1469-0691}, mesh = {Adult ; Aged ; Antigens, Bacterial/genetics ; Bacterial Outer Membrane Proteins/genetics ; Bacterial Typing Techniques ; Carrier Proteins/genetics ; Cluster Analysis ; DNA Fingerprinting ; *Disease Outbreaks ; Female ; Genotype ; Humans ; Male ; Middle Aged ; Molecular Epidemiology ; Norway/epidemiology ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; Serotyping ; Streptococcal Infections/*epidemiology/*microbiology/mortality ; Streptococcus/*classification/genetics/*isolation &amp; purification ; Young Adult ; }, abstract = {During a decade-long, high endemic situation with severe group A streptococcal disease in western Norway, a cluster of 16 patients with invasive streptococcal disease was hospitalized during a period of 11 weeks. A study including clinical characteristics and molecular epidemiology of the outbreak was initiated. Relevant clinical information was obtained from the medical records of the patients. Nine of the 16 patients had soft tissue infection, and seven of these had streptococcal toxic shock syndrome (STSS). Mortality, both overall and among those with STSS, was 25%. Streptococcal isolates from these patients were characterized by serogrouping and emm sequence typing. The emm amplicons were further characterized by sequence analysis and restriction fragment length polymorphism (emm RFLP) analysis. The streptococci were identified as group A streptococcus (GAS) in 11 patients and group G streptococcus (GGS) in four patients. The patients with GGS infection were older than the patients with GAS infection, and all patients infected with GGS had predisposing comorbidities. Isolates from 13 patients were available for emm gene analysis and found to belong to nine different emm types. Similar differentiation was obtained with emm RFLP in GAS. Hence, the outbreak was polyclonal. Results suggestive of horizontal gene transfer and recombination between the emm genes of GAS, group C streptococcus and GGS were found in the isolates from seven patients. Such genetic recombination events suggest a possible role in pathogenesis.}, }
@article {pmid19175679, year = {2009}, author = {Burgos, YK and Pries, K and Pestana de Castro, AF and Beutin, L}, title = {Characterization of the alpha-haemolysin determinant from the human enteropathogenic Escherichia coli O26 plasmid pEO5.}, journal = {FEMS microbiology letters}, volume = {292}, number = {2}, pages = {194-202}, doi = {10.1111/j.1574-6968.2009.01496.x}, pmid = {19175679}, issn = {1574-6968}, mesh = {DNA Transposable Elements ; Enteropathogenic Escherichia coli/*genetics ; Escherichia coli Proteins/*genetics ; Gene Order ; Hemolysin Proteins/*genetics ; Humans ; Molecular Sequence Data ; Nucleic Acid Hybridization ; *Plasmids ; Sequence Analysis, DNA ; Sequence Homology ; Synteny ; }, abstract = {The 157-kb conjugative plasmid pEO5 encoding alpha-haemolysin in strains of human enteropathogenic Escherichia coli (EPEC) O26 was investigated for its relationship with EHEC-haemolysin-encoding plasmids of enterohaemorrhagic E. coli (EHEC) O26 and O157 strains. Plasmid pEO5 was found to be compatible with EHEC-virulence plasmids and did not hybridize in Southern blots with plasmid pO157 from the EHEC O157:H7 strain EDL933, indicating that both plasmids were unrelated. A 9227-bp stretch of pEO5 DNA encompassing the entire alpha-hlyCABD operon was sequenced and compared for similarity to plasmid and chromosomally inherited alpha-hly determinants. The alpha-hly determinant of pEO5 (7252 bp) and its upstream region was most similar to corresponding sequences of the murine E. coli alpha-hly plasmid pHly152, in particular, the structural alpha-hlyCABD genes (99.2% identity) and the regulatory hlyR regions (98.8% identity). pEO5 and alpha-hly plasmids of EPEC O26 strains from humans and cattle were very similar for the regions encompassing the structural alpha-hlyCABD genes. The major difference found between the hly regions of pHly152 and pEO5 is caused by the insertion of an IS2 element upstream of the hlyC gene in pHly152. The presence of transposon-like structures at both ends of the alpha-hly sequence indicates that this pEO5 virulence factor was probably acquired by horizontal gene transfer.}, }
@article {pmid19174147, year = {2009}, author = {Archibald, JM}, title = {The puzzle of plastid evolution.}, journal = {Current biology : CB}, volume = {19}, number = {2}, pages = {R81-8}, doi = {10.1016/j.cub.2008.11.067}, pmid = {19174147}, issn = {1879-0445}, mesh = {Animals ; *Biological Evolution ; Cyanobacteria/cytology/physiology ; Eukaryotic Cells/cytology/physiology ; Gene Transfer, Horizontal ; Photosynthesis ; Phylogeny ; *Plastids/genetics/metabolism ; *Symbiosis/genetics ; }, abstract = {A comprehensive understanding of the origin and spread of plastids remains an important yet elusive goal in the field of eukaryotic evolution. Combined with the discovery of new photosynthetic and non-photosynthetic protist lineages, the results of recent taxonomically broad phylogenomic studies suggest that a re-shuffling of higher-level eukaryote systematics is in order. Consequently, new models of plastid evolution involving ancient secondary and tertiary endosymbioses are needed to explain the full spectrum of photosynthetic eukaryotes.}, }
@article {pmid19172199, year = {2008}, author = {Hakvåg, S and Fjaervik, E and Josefsen, KD and Ian, E and Ellingsen, TE and Zotchev, SB}, title = {Characterization of Streptomyces spp. isolated from the sea surface microlayer in the Trondheim Fjord, Norway.}, journal = {Marine drugs}, volume = {6}, number = {4}, pages = {620-635}, pmid = {19172199}, issn = {1660-3397}, mesh = {Anti-Infective Agents/isolation &amp; purification/*pharmacology ; Base Sequence ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Fungi/drug effects ; Gene Transfer, Horizontal ; Gram-Negative Bacteria/drug effects ; Gram-Positive Bacteria/drug effects ; Norway ; Polyketide Synthases/*genetics/isolation &amp; purification ; Seawater/microbiology ; Streptomyces/*chemistry/genetics/isolation &amp; purification ; Water Microbiology ; }, abstract = {The water surface microlayer is still poorly explored, although it has been shown to contain a high density of metabolically active bacteria, often called bacterioneuston. Actinomycetes from the surface microlayer in the Trondheim fjord, Norway, have been isolated and characterized. A total of 217 isolates from two separate samples morphologically resembling the genus Streptomyces have been further investigated in this study. Antimicrobial assays showed that about 80% of the isolates exhibited antagonistic activity against non-filamentous fungus, Gram-negative, and Gram-positive bacteria. Based on the macroscopic analyses and inhibition patterns from the antimicrobial assays, the sub-grouping of isolates was performed. Partial 16S rDNAs from the candidates from each subgroup were sequenced and phylogenetic analysis performed. 7 isolates with identical 16S rDNA sequences were further studied for the presence of PKS type I genes. Sequencing and phylogenetic analysis of the PKS gene fragments revealed that horizontal gene transfer between closely related species might have taken place. Identification of unique PKS genes in these isolates implies that de-replication can not be performed based solely on the 16S rDNA sequences. The results obtained in this study suggest that streptomycetes from the neuston population may be an interesting source for discovery of new antimicrobial agents.}, }
@article {pmid19170881, year = {2009}, author = {Paulick, A and Koerdt, A and Lassak, J and Huntley, S and Wilms, I and Narberhaus, F and Thormann, KM}, title = {Two different stator systems drive a single polar flagellum in Shewanella oneidensis MR-1.}, journal = {Molecular microbiology}, volume = {71}, number = {4}, pages = {836-850}, doi = {10.1111/j.1365-2958.2008.06570.x}, pmid = {19170881}, issn = {1365-2958}, mesh = {Bacterial Outer Membrane Proteins/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; DNA, Bacterial/genetics ; Flagella/genetics/*metabolism ; Genetic Complementation Test ; Molecular Motor Proteins/genetics/*metabolism ; Phylogeny ; Sequence Deletion ; Shewanella/genetics/*metabolism ; Sodium/*metabolism ; Substrate Specificity ; Transcription, Genetic ; }, abstract = {The Gram-negative metal ion-reducing bacterium Shewanella oneidensis MR-1 is motile by means of a single polar flagellum. We identified two potential stator systems, PomAB and MotAB, each individually sufficient as a force generator to drive flagellar rotation. Physiological studies indicate that PomAB is sodium-dependent while MotAB is powered by the proton motive force. Flagellar function mainly depends on the PomAB stator; however, the presence of both stator systems under low-sodium conditions results in a faster swimming phenotype. Based on stator homology analysis we speculate that MotAB has been acquired by lateral gene transfer as a consequence of adaptation to a low-sodium environment. Expression analysis at the single cell level showed that both stator systems are expressed simultaneously. An active PomB-mCherry fusion protein effectively localized to the flagellated cell pole in 70-80% of the population independent of sodium concentrations. In contrast, polar localization of MotB-mCherry increased with decreasing sodium concentrations. In the absence of the Pom stator, MotB-mCherry localized to the flagellated cell pole independently of the sodium concentration but was rapidly displaced upon expression of PomAB. We propose that selection of the stator occurs at the level of protein localization in response to sodium concentrations.}, }
@article {pmid19168748, year = {2009}, author = {Roitzsch, M and Pyle, AM}, title = {The linear form of a group II intron catalyzes efficient autocatalytic reverse splicing, establishing a potential for mobility.}, journal = {RNA (New York, N.Y.)}, volume = {15}, number = {3}, pages = {473-482}, pmid = {19168748}, issn = {1469-9001}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {*Interspersed Repetitive Sequences ; *Introns ; Mutation ; *RNA Splicing ; RNA, Ribosomal, Self-Splicing/*genetics ; Saccharomyces cerevisiae/*genetics ; }, abstract = {Self-splicing group II introns catalyze their own excision from pre-RNAs, thereby joining the flanking exons. The introns can be released in a lariat or linear form. Lariat introns have been shown to reverse the splicing reaction; in contrast, linear introns are generally believed to perform no or only poor reverse splicing. Here, we show that a linear group II intron derived from ai5gamma can reverse the second step of splicing with unexpectedly high efficiency and precision. Moreover, the linear intron generates dramatically more reverse-splicing product than its lariat equivalent. The finding that linear group II introns can readily undergo the critical first step of mobility by catalyzing efficient reverse splicing into complementary target molecules demonstrates their innate potential for mobility and transposition and raises the possibility that reverse splicing by linear group II introns may have played a significant role in certain forms of intron mobility and lateral gene transfer during evolution.}, }
@article {pmid19168609, year = {2009}, author = {Davies, MR and Shera, J and Van Domselaar, GH and Sriprakash, KS and McMillan, DJ}, title = {A novel integrative conjugative element mediates genetic transfer from group G Streptococcus to other {beta}-hemolytic Streptococci.}, journal = {Journal of bacteriology}, volume = {191}, number = {7}, pages = {2257-2265}, pmid = {19168609}, issn = {1098-5530}, mesh = {Arsenates/pharmacology ; Cadmium/pharmacology ; *Conjugation, Genetic ; Drug Resistance ; *Gene Transfer, Horizontal ; Hemolysis ; *Interspersed Repetitive Sequences ; Molecular Sequence Data ; Multigene Family ; Streptococcal Infections ; Streptococcus/drug effects/*genetics ; }, abstract = {Lateral gene transfer is a significant contributor to the ongoing evolution of many bacterial pathogens, including beta-hemolytic streptococci. Here we provide the first characterization of a novel integrative conjugative element (ICE), ICESde3396, from Streptococcus dysgalactiae subsp. equisimilis (group G streptococcus [GGS]), a bacterium commonly found in the throat and skin of humans. ICESde3396 is 64 kb in size and encodes 66 putative open reading frames. ICESde3396 shares 38 open reading frames with a putative ICE from Streptococcus agalactiae (group B streptococcus [GBS]), ICESa2603. In addition to genes involves in conjugal processes, ICESde3396 also carries genes predicted to be involved in virulence and resistance to various metals. A major feature of ICESde3396 differentiating it from ICESa2603 is the presence of an 18-kb internal recombinogenic region containing four unique gene clusters, which appear to have been acquired from streptococcal and nonstreptococcal bacterial species. The four clusters include two cadmium resistance operons, an arsenic resistance operon, and genes with orthologues in a group A streptococcus (GAS) prophage. Streptococci that naturally harbor ICESde3396 have increased resistance to cadmium and arsenate, indicating the functionality of genes present in the 18-kb recombinogenic region. By marking ICESde3396 with a kanamycin resistance gene, we demonstrate that the ICE is transferable to other GGS isolates as well as GBS and GAS. To investigate the presence of the ICE in clinical streptococcal isolates, we screened 69 isolates (30 GGS, 19 GBS, and 20 GAS isolates) for the presence of three separate regions of ICESde3396. Eleven isolates possessed all three regions, suggesting they harbored ICESde3396-like elements. Another four isolates possessed ICESa2603-like elements. We propose that ICESde3396 is a mobile genetic element that is capable of acquiring DNA from multiple bacterial sources and is a vehicle for dissemination of this DNA through the wider beta-hemolytic streptococcal population.}, }
@article {pmid19165328, year = {2009}, author = {Ninio, S and Celli, J and Roy, CR}, title = {A Legionella pneumophila effector protein encoded in a region of genomic plasticity binds to Dot/Icm-modified vacuoles.}, journal = {PLoS pathogens}, volume = {5}, number = {1}, pages = {e1000278}, pmid = {19165328}, issn = {1553-7374}, support = {R01 AI041699/AI/NIAID NIH HHS/United States ; R01 AI041699-15/AI/NIAID NIH HHS/United States ; /ImNIH/Intramural NIH HHS/United States ; 2R01AI041699-12/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/*genetics/physiology ; Bacterial Translocation ; Carrier Proteins/*genetics/*physiology ; Genome, Bacterial/*genetics ; Legionella pneumophila/*genetics/pathogenicity ; Legionnaires' Disease/genetics ; Membrane Proteins/*physiology ; Molecular Chaperones/*physiology ; Vacuoles/drug effects/*metabolism ; }, abstract = {Legionella pneumophila is an opportunistic pathogen that can cause a severe pneumonia called Legionnaires' disease. In the environment, L. pneumophila is found in fresh water reservoirs in a large spectrum of environmental conditions, where the bacteria are able to replicate within a variety of protozoan hosts. To survive within eukaryotic cells, L. pneumophila require a type IV secretion system, designated Dot/Icm, that delivers bacterial effector proteins into the host cell cytoplasm. In recent years, a number of Dot/Icm substrate proteins have been identified; however, the function of most of these proteins remains unknown, and it is unclear why the bacterium maintains such a large repertoire of effectors to promote its survival. Here we investigate a region of the L. pneumophila chromosome that displays a high degree of plasticity among four sequenced L. pneumophila strains. Analysis of GC content suggests that several genes encoded in this region were acquired through horizontal gene transfer. Protein translocation studies establish that this region of genomic plasticity encodes for multiple Dot/Icm effectors. Ectopic expression studies in mammalian cells indicate that one of these substrates, a protein called PieA, has unique effector activities. PieA is an effector that can alter lysosome morphology and associates specifically with vacuoles that support L. pneumophila replication. It was determined that the association of PieA with vacuoles containing L. pneumophila requires modifications to the vacuole mediated by other Dot/Icm effectors. Thus, the localization properties of PieA reveal that the Dot/Icm system has the ability to spatially and temporally control the association of an effector with vacuoles containing L. pneumophila through activities mediated by other effector proteins.}, }
@article {pmid19161360, year = {2009}, author = {Kado, CI}, title = {Horizontal gene transfer: sustaining pathogenicity and optimizing host-pathogen interactions.}, journal = {Molecular plant pathology}, volume = {10}, number = {1}, pages = {143-150}, pmid = {19161360}, issn = {1364-3703}, mesh = {Bacteria/*genetics/pathogenicity ; *Gene Transfer, Horizontal ; Genes, Plant ; Plants/*microbiology ; Virulence ; }, abstract = {Successful host-pathogen interactions require the presence, maintenance and expression of gene cassettes called 'pathogenicity islands' (PAIs) and 'metabolic islands' (MAIs) in the respective pathogen. The products of these genes confer on the pathogen the means to recognize their host(s) and to efficiently evade host defences in order to colonize, propagate within the host and eventually disseminate from the host. Virulence effectors secreted by type III and type IV secretion systems, among others, play vital roles in sustaining pathogenicity and optimizing host-pathogen interactions. Complete genome sequences of plant pathogenic bacteria have revealed the presence of PAIs and MAIs. The genes of these islands possess mosaic structures with regions displaying differences in nucleotide composition and codon usage in relation to adjacent genome structures, features that are highly suggestive of their acquisition from a foreign donor. These donors can be other bacteria, as well as lower members of the Archaea and Eukarya. Genes that have moved from the domains Archaea and Eukarya to the domain Bacteria are true cases of horizontal gene transfer. They represent interdomain genetic transfer. Genetic exchange between distinct members of the domain Bacteria, however, represents lateral gene transfer, an intradomain event. Both horizontal and lateral gene transfer events have been used to facilitate survival fitness of the pathogen.}, }
@article {pmid19156210, year = {2009}, author = {Mellata, M and Touchman, JW and Curtiss, R}, title = {Full sequence and comparative analysis of the plasmid pAPEC-1 of avian pathogenic E. coli chi7122 (O78:K80:H9).}, journal = {PloS one}, volume = {4}, number = {1}, pages = {e4232}, pmid = {19156210}, issn = {1932-6203}, support = {U01060557//PHS HHS/United States ; }, mesh = {Animals ; Base Sequence ; DNA Primers/chemistry ; Escherichia coli/*genetics ; Escherichia coli Infections/genetics ; Gene Transfer, Horizontal ; Genome ; Genome, Bacterial ; Genomics ; Humans ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Plasmids/*genetics/metabolism ; Virulence/genetics ; }, abstract = {BACKGROUND: Extra-intestinal pathogenic E. coli (ExPEC), including Avian Pathogenic E. coli (APEC), are very diverse. They cause a complex of diseases in Human, animals, and birds. Even though large plasmids are often associated with the virulence of ExPEC, their characterization is still in its infancy.<br><br>We fully sequenced and analyzed the large plasmid pAPEC-1 (103,275-bp) associated with the APEC strain chi7122, from worldwide serogroup O78ratioK80ratioH9. A putative virulence region spanning an 80-kb region of pAPEC-1 possesses four iron acquisition systems (iutA iucABCD, sitABCD, iroBCDN, and temperature-sensitive hemagglutinin tsh), a colicin V operon, increasing serum sensitivity iss, ompT, hlyF, and etsABC. Thirty three ORFs in pAPEC-1 are identified as insertion sequences (ISs) that belong to nine families with diverse origins. The full length of the transfer region in pAPEC-1 (11 kb) is shorter compared to the tra region of other sequenced F plasmids; the absence of some tra genes in pAPEC-1 affects its self-transferability, and the conjugative function of the plasmid was effective only in the presence of other plasmids. Two-replicon systems, repFIIA-repFIC and repFIB, and two post-segregational systems, srnB and hok/sok, are also present in the sequence of pAPEC-1. The comparison of the pAPEC-1 sequence with the two available plasmid sequences reveals more gene loss and reorganization than previously appreciated. The presence of pAPEC-1-associated genes is assessed in human ExPEC by PCR. Many patterns of association between genes are found.<br><br>CONCLUSIONS/SIGNIFICANCE: The pathotype typical of pAPEC-1 was present in some human strains, which indicates a horizontal transfer between strains and the zoonotic risk of APEC strains. ColV plasmids could have common virulence genes that could be acquired by transposition, without sharing genes of plasmid function.}, }
@article {pmid19154594, year = {2009}, author = {Klasson, L and Kambris, Z and Cook, PE and Walker, T and Sinkins, SP}, title = {Horizontal gene transfer between Wolbachia and the mosquito Aedes aegypti.}, journal = {BMC genomics}, volume = {10}, number = {}, pages = {33}, pmid = {19154594}, issn = {1471-2164}, support = {/WT_/Wellcome Trust/United Kingdom ; 079059/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Aedes/*genetics/*microbiology ; Animals ; DNA, Bacterial/genetics ; *Evolution, Molecular ; Female ; *Gene Transfer, Horizontal ; Genes, Insect ; Genome, Bacterial ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Symbiosis/genetics ; Wolbachia/*genetics ; }, abstract = {BACKGROUND: The evolutionary importance of horizontal gene transfer (HGT) from Wolbachia endosymbiotic bacteria to their eukaryotic hosts is a topic of considerable interest and debate. Recent transfers of genome fragments from Wolbachia into insect chromosomes have been reported, but it has been argued that these fragments may be on an evolutionary trajectory to degradation and loss.<br><br>RESULTS: We have discovered a case of HGT, involving two adjacent genes, between the genomes of Wolbachia and the currently Wolbachia-uninfected mosquito Aedes aegypti, an important human disease vector. The lower level of sequence identity between Wolbachia and insect, the transcription of all the genes involved, and the fact that we have identified homologs of the two genes in another Aedes species (Ae. mascarensis), suggest that these genes are being expressed after an extended evolutionary period since horizontal transfer, and therefore that the transfer has functional significance. The association of these genes with Wolbachia prophage regions also provides a mechanism for the transfer.<br><br>CONCLUSION: The data support the argument that HGT between Wolbachia endosymbiotic bacteria and their hosts has produced evolutionary innovation.}, }
@article {pmid19153256, year = {2009}, author = {Cheng, X and Zhang, D and Cheng, Z and Keller, B and Ling, HQ}, title = {A new family of Ty1-copia-like retrotransposons originated in the tomato genome by a recent horizontal transfer event.}, journal = {Genetics}, volume = {181}, number = {4}, pages = {1183-1193}, pmid = {19153256}, issn = {0016-6731}, mesh = {Arabidopsis/genetics ; Base Sequence ; Chromosome Mapping ; Cloning, Molecular ; *Evolution, Molecular ; Gene Dosage ; Gene Transfer, Horizontal/*physiology ; Genome, Plant/physiology ; Solanum lycopersicum/*genetics ; Molecular Sequence Data ; Phylogeny ; Retroelements/*genetics ; Sequence Homology, Nucleic Acid ; Solanaceae/genetics ; Transcription, Genetic ; }, abstract = {Rider is a novel and recently active Ty1-copia-like retrotransposon isolated from the T3238fer mutant of tomato. Structurally, it is delimited by a duplication of target sites and contains two long terminal direct repeats and an internal open reading frame, which encodes a Ty1-copia-type polyprotein with characteristic protein domains required for retrotransposition. The family of Rider elements has an intermediate copy number and is scattered in the chromosomes of tomato. Rider family members in the tomato genome share high sequence similarity, but different structural groups were identified (full-size elements, deletion derivatives, and solo LTRs). Southern blot analysis in Solanaceae species showed that Rider was a Lycopersicon-specific element. Sequence analysis revealed that among other plants, two Arabidopsis elements (named as Rider-like 1 and Rider-like 2) are most similar to Rider in both the coding and noncoding regions. RT-PCR analysis indicates that Rider is constitutively expressed in tomato plants. The phylogeny-based parsimony analysis and the sequence substitution analyses of these data suggest that these Rider-like elements originated from a recent introgression of Rider into the tomato genome by horizontal transfer 1-6 million years ago. Considering its transcriptional activity and the recent insertion of the element into at least two genes, Rider is a recently active retrotransposon in the tomato genome.}, }
@article {pmid19148274, year = {2009}, author = {Blankschien, MD and Potrykus, K and Grace, E and Choudhary, A and Vinella, D and Cashel, M and Herman, C}, title = {TraR, a homolog of a RNAP secondary channel interactor, modulates transcription.}, journal = {PLoS genetics}, volume = {5}, number = {1}, pages = {e1000345}, pmid = {19148274}, issn = {1553-7404}, support = {//Intramural NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Amino Acids ; DNA-Directed RNA Polymerases/chemistry/genetics/*metabolism ; Escherichia coli/*genetics/metabolism ; Escherichia coli Proteins/chemistry/genetics/*metabolism ; *Gene Expression Regulation, Bacterial ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; RNA, Bacterial/metabolism ; Transcription Factors/chemistry/genetics/*metabolism ; *Transcription, Genetic ; }, abstract = {Recent structural and biochemical studies have identified a novel control mechanism of gene expression mediated through the secondary channel of RNA Polymerase (RNAP) during transcription initiation. Specifically, the small nucleotide ppGpp, along with DksA, a RNAP secondary channel interacting factor, modifies the kinetics of transcription initiation, resulting in, among other events, down-regulation of ribosomal RNA synthesis and up-regulation of several amino acid biosynthetic and transport genes during nutritional stress. Until now, this mode of regulation of RNAP was primarily associated with ppGpp. Here, we identify TraR, a DksA homolog that mimics ppGpp/DksA effects on RNAP. First, expression of TraR compensates for dksA transcriptional repression and activation activities in vivo. Second, mutagenesis of a conserved amino acid of TraR known to be critical for DksA function abolishes its activity, implying both structural and functional similarity to DksA. Third, unlike DksA, TraR does not require ppGpp for repression of the rrnB P1 promoter in vivo and in vitro or activation of amino acid biosynthesis/transport genes in vivo. Implications for DksA/ppGpp mechanism and roles of TraR in horizontal gene transfer and virulence are discussed.}, }
@article {pmid19144117, year = {2009}, author = {Rolain, JM and François, P and Hernandez, D and Bittar, F and Richet, H and Fournous, G and Mattenberger, Y and Bosdure, E and Stremler, N and Dubus, JC and Sarles, J and Reynaud-Gaubert, M and Boniface, S and Schrenzel, J and Raoult, D}, title = {Genomic analysis of an emerging multiresistant Staphylococcus aureus strain rapidly spreading in cystic fibrosis patients revealed the presence of an antibiotic inducible bacteriophage.}, journal = {Biology direct}, volume = {4}, number = {}, pages = {1}, pmid = {19144117}, issn = {1745-6150}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteriophages/*drug effects ; Base Sequence ; Cell Proliferation/drug effects ; Cell Wall/ultrastructure ; Cystic Fibrosis/epidemiology/*microbiology ; DNA, Bacterial/genetics/metabolism ; Drug Resistance, Multiple, Bacterial/*genetics ; France/epidemiology ; Gene Expression Profiling ; Genes, Bacterial ; Genome, Bacterial/*genetics ; Humans ; Methicillin Resistance/drug effects/genetics ; Minisatellite Repeats/genetics ; Molecular Sequence Data ; Phenotype ; Phylogeny ; Staphylococcus aureus/*cytology/*genetics/ultrastructure ; Transcription, Genetic/drug effects ; }, abstract = {BACKGROUND: Staphylococcus aureus is a major human pathogen responsible for a variety of nosocomial and community-acquired infections. Recent reports show that the prevalence of Methicillin-Resistant S. aureus (MRSA) infections in cystic fibrosis (CF) patients is increasing. In 2006 in Marseille, France, we have detected an atypical MRSA strain with a specific antibiotic susceptibility profile and a unique growth phenotype. Because of the clinical importance of the spread of such strain among CF patients we decided to sequence the genome of one representative isolate (strain CF-Marseille) to compare this to the published genome sequences. We also conducted a retrospective epidemiological analysis on all S. aureus isolated from 2002 to 2007 in CF patients from our institution.<br><br>RESULTS: CF-Marseille is multidrug resistant, has a hetero-Glycopeptide-Intermediate resistance S. aureus phenotype, grows on Cepacia agar with intense orange pigmentation and has a thickened cell wall. Phylogenetic analyses using Complete Genome Hybridization and Multi Locus VNTR Assay showed that CF-Marseille was closely related to strain Mu50, representing vancomycin-resistant S. aureus. Analysis of CF-Marseille shows a similar core genome to that of previously sequenced MRSA strains but with a different genomic organization due to the presence of specific mobile genetic elements i.e. a new SCCmec type IV mosaic cassette that has integrated the pUB110 plasmid, and a new phage closely related to phiETA3. Moreover this phage could be seen by electron microscopy when mobilized with several antibiotics commonly used in CF patients including, tobramycin, ciprofloxacin, cotrimoxazole, or imipenem. Phylogenetic analysis of phenotypically similar h-GISA in our study also suggests that CF patients are colonized by polyclonal populations of MRSA that represents an incredible reservoir for lateral gene transfer.<br><br>CONCLUSION: In conclusion, we demonstrated the emergence and spreading of a new isolate of MRSA in CF patients in Marseille, France, that has probably been selected in the airways by antibiotic pressure. Antibiotic-mediated phage induction may result in high-frequency transfer and the unintended consequence of promoting the spread of virulence and/or antibiotic resistance determinants. The emergence of well-adapted MRSA is worrying in such population chronically colonized and receiving many antibiotics and represents a model for emergence of uncontrollable super bugs in a specific niche.<br><br>REVIEWERS: This article was reviewed by Eric Bapteste, Pierre Pontarotti, and Igor Zhulin. For the full reviews, please go to the Reviewers' comments section.}, }
@article {pmid19143600, year = {2009}, author = {Large, AT and Goldberg, MD and Lund, PA}, title = {Chaperones and protein folding in the archaea.}, journal = {Biochemical Society transactions}, volume = {37}, number = {Pt 1}, pages = {46-51}, doi = {10.1042/BST0370046}, pmid = {19143600}, issn = {1470-8752}, support = {BB/F002483/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Archaea/*metabolism ; Archaeal Proteins/chemistry/genetics/metabolism ; Chaperonins/chemistry/genetics/metabolism ; HSP70 Heat-Shock Proteins/metabolism ; Molecular Chaperones/chemistry/genetics/*metabolism ; Protein Binding ; *Protein Folding ; }, abstract = {A survey of archaeal genomes for the presence of homologues of bacterial and eukaryotic chaperones reveals several interesting features. All archaea contain chaperonins, also known as Hsp60s (where Hsp is heat-shock protein). These are more similar to the type II chaperonins found in the eukaryotic cytosol than to the type I chaperonins found in bacteria, mitochondria and chloroplasts, although some archaea also contain type I chaperonin homologues, presumably acquired by horizontal gene transfer. Most archaea contain several genes for these proteins. Our studies on the type II chaperonins of the genetically tractable archaeon Haloferax volcanii have shown that only one of the three genes has to be present for the organisms to grow, but that there is some evidence for functional specialization between the different chaperonin proteins. All archaea also possess genes for prefoldin proteins and for small heat-shock proteins, but they generally lack genes for Hsp90 and Hsp100 homologues. Genes for Hsp70 (DnaK) and Hsp40 (DnaJ) homologues are only found in a subset of archaea. Thus chaperone-assisted protein folding in archaea is likely to display some unique features when compared with that in eukaryotes and bacteria, and there may be important differences in the process between euryarchaea and crenarchaea.}, }
@article {pmid19141739, year = {2009}, author = {Hu, Z and Zhao, WH}, title = {Identification of plasmid- and integron-borne blaIMP-1 and blaIMP-10 in clinical isolates of Serratia marcescens.}, journal = {Journal of medical microbiology}, volume = {58}, number = {Pt 2}, pages = {217-221}, doi = {10.1099/jmm.0.006874-0}, pmid = {19141739}, issn = {0022-2615}, mesh = {Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Humans ; *Integrons ; Microbial Sensitivity Tests ; *Plasmids ; Promoter Regions, Genetic ; Serratia Infections/microbiology ; Serratia marcescens/*enzymology/*genetics/isolation &amp; purification ; beta-Lactamases/*genetics ; beta-Lactams/pharmacology ; }, abstract = {The emergence of carbapenem-hydrolysing metallo-beta-lactamases (MBLs) is a serious threat to the clinical utility of carbapenems. This study identified plasmid- and integron-borne bla(IMP-1) and bla(IMP-10) in clinical isolates of Serratia marcescens. The bla(IMP-1) and bla(IMP-10) gene cassettes were carried by a class 1 integron and followed by the aac(6')-IIc gene cassette. The bla(IMP-1) and bla(IMP-10) gene cassettes were preceded by a weak P(ant) promoter, TGGACA(N)(17)TAAGCT, and an inactive P2 promoter, TTGTTA(N)(14)TACAGT. These genes were easily transferred to Escherichia coli by conjugation and transformation, indicating that they are located on transferable plasmids. Due to the acquisition of bla(IMP-1), the susceptibility of E. coli transconjugants to imipenem, meropenem, panipenem and biapenem decreased by 32-, 256-, 64- and 128-fold, respectively. In comparison, after gaining bla(IMP-10), the susceptibility of E. coli transconjugants to the four carbapenems decreased by 64-, 2048-, 256- and 64-fold, respectively. Strains harbouring bla(IMP-10) showed higher-level resistance to imipenem, meropenem and panipenem than the strains harbouring bla(IMP-1), although the nucleotide sequences of the class 1 integrons carrying bla(IMP-10) and bla(IMP-1) were identical except for a single point mutation.}, }
@article {pmid19139236, year = {2009}, author = {Cookson, AL and Bennett, J and Nicol, C and Thomson-Carter, F and Attwood, GT}, title = {Molecular subtyping and distribution of the serine protease from shiga toxin-producing Escherichia coli among atypical enteropathogenic E. coli strains.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {7}, pages = {2246-2249}, pmid = {19139236}, issn = {1098-5336}, mesh = {Cluster Analysis ; DNA Fingerprinting ; Enteropathogenic Escherichia coli/*genetics ; Escherichia coli Proteins/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genotype ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; Sequence Homology ; Serine Endopeptidases/*genetics ; Serotyping ; Shiga-Toxigenic Escherichia coli/enzymology/*genetics ; }, abstract = {Atypical enteropathogenic Escherichia coli (aEPEC) and Shiga toxin-producing E. coli (STEC) were examined to determine the prevalence and sequence of espP, which encodes a serine protease. These analyses indicated shared espP sequence types between the two E. coli pathotypes and thus provide further insights into the evolution of aEPEC and STEC.}, }
@article {pmid19138386, year = {2009}, author = {Hinderhofer, M and Walker, CA and Friemel, A and Stuermer, CA and Möller, HM and Reuter, A}, title = {Evolution of prokaryotic SPFH proteins.}, journal = {BMC evolutionary biology}, volume = {9}, number = {}, pages = {10}, pmid = {19138386}, issn = {1471-2148}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/*genetics ; Conserved Sequence ; Databases, Protein ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial ; Membrane Proteins/chemistry/*genetics ; Molecular Sequence Data ; Operon ; Phylogeny ; Protein Structure, Tertiary ; Sequence Alignment ; Sequence Analysis, Protein ; }, abstract = {BACKGROUND: The SPFH protein superfamily is a diverse family of proteins whose eukaryotic members are involved in the scaffolding of detergent-resistant microdomains. Recently the origin of the SPFH proteins has been questioned. Instead, convergent evolution has been proposed. However, an independent, convergent evolution of three large prokaryotic and three eukaryotic families is highly unlikely, especially when other mechanisms such as lateral gene transfer which could also explain their distribution pattern have not yet been considered.To gain better insight into this very diverse protein family, we have analyzed the genomes of 497 microorganisms and investigated the pattern of occurrence as well as the genomic vicinity of the prokaryotic SPFH members.<br><br>RESULTS: According to sequence and operon structure, a clear division into 12 subfamilies was evident. Three subfamilies (SPFH1, SPFH2 and SPFH5) show a conserved operon structure and two additional subfamilies are linked to those three through functional aspects (SPFH1, SPFH3, SPFH4: interaction with FtsH protease). Therefore these subgroups most likely share common ancestry. The complex pattern of occurrence among the different phyla is indicative of lateral gene transfer. Organisms that do not possess a single SPFH protein are almost exclusively endosymbionts or endoparasites.<br><br>CONCLUSION: The conserved operon structure and functional similarities suggest that at least 5 subfamilies that encompass almost 75% of all prokaryotic SPFH members share a common origin. Their similarity to the different eukaryotic SPFH families, as well as functional similarities, suggests that the eukaryotic SPFH families originated from different prokaryotic SPFH families rather than one. This explains the difficulties in obtaining a consistent phylogenetic tree of the eukaryotic SPFH members. Phylogenetic evidence points towards lateral gene transfer as one source of the very diverse patterns of occurrence in bacterial species.}, }
@article {pmid19136439, year = {2009}, author = {Jacoby, GA}, title = {AmpC beta-lactamases.}, journal = {Clinical microbiology reviews}, volume = {22}, number = {1}, pages = {161-82, Table of Contents}, pmid = {19136439}, issn = {1098-6618}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/*biosynthesis ; Chromosomes, Bacterial ; Enterobacteriaceae/*drug effects/*enzymology ; Enterobacteriaceae Infections/microbiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Plasmids ; *beta-Lactam Resistance ; beta-Lactamases/*biosynthesis ; beta-Lactams/*pharmacology ; }, abstract = {AmpC beta-lactamases are clinically important cephalosporinases encoded on the chromosomes of many of the Enterobacteriaceae and a few other organisms, where they mediate resistance to cephalothin, cefazolin, cefoxitin, most penicillins, and beta-lactamase inhibitor-beta-lactam combinations. In many bacteria, AmpC enzymes are inducible and can be expressed at high levels by mutation. Overexpression confers resistance to broad-spectrum cephalosporins including cefotaxime, ceftazidime, and ceftriaxone and is a problem especially in infections due to Enterobacter aerogenes and Enterobacter cloacae, where an isolate initially susceptible to these agents may become resistant upon therapy. Transmissible plasmids have acquired genes for AmpC enzymes, which consequently can now appear in bacteria lacking or poorly expressing a chromosomal bla(AmpC) gene, such as Escherichia coli, Klebsiella pneumoniae, and Proteus mirabilis. Resistance due to plasmid-mediated AmpC enzymes is less common than extended-spectrum beta-lactamase production in most parts of the world but may be both harder to detect and broader in spectrum. AmpC enzymes encoded by both chromosomal and plasmid genes are also evolving to hydrolyze broad-spectrum cephalosporins more efficiently. Techniques to identify AmpC beta-lactamase-producing isolates are available but are still evolving and are not yet optimized for the clinical laboratory, which probably now underestimates this resistance mechanism. Carbapenems can usually be used to treat infections due to AmpC-producing bacteria, but carbapenem resistance can arise in some organisms by mutations that reduce influx (outer membrane porin loss) or enhance efflux (efflux pump activation).}, }
@article {pmid19136009, year = {2009}, author = {Guogas, LM and Kennedy, SA and Lee, JH and Redinbo, MR}, title = {A novel fold in the TraI relaxase-helicase c-terminal domain is essential for conjugative DNA transfer.}, journal = {Journal of molecular biology}, volume = {386}, number = {2}, pages = {554-568}, pmid = {19136009}, issn = {1089-8638}, support = {R01 AI078924/AI/NIAID NIH HHS/United States ; R01 AI078924-01/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; *Conjugation, Genetic ; Crystallography, X-Ray ; DNA Helicases/*chemistry/*metabolism ; DNA, Bacterial/*metabolism ; Escherichia coli/*physiology ; Escherichia coli Proteins/*chemistry/*metabolism ; Gene Transfer, Horizontal ; Models, Biological ; Models, Molecular ; Molecular Sequence Data ; Protein Structure, Tertiary ; Sequence Alignment ; }, abstract = {TraI relaxase-helicase is the central catalytic component of the multiprotein relaxosome complex responsible for conjugative DNA transfer (CDT) between bacterial cells. CDT is a primary mechanism for the lateral propagation of microbial genetic material, including the spread of antibiotic resistance genes. The 2.4-A resolution crystal structure of the C-terminal domain of the multifunctional Escherichia coli F (fertility) plasmid TraI protein is presented, and specific structural regions essential for CDT are identified. The crystal structure reveals a novel fold composed of a 28-residue N-terminal alpha-domain connected by a proline-rich loop to a compact alpha/beta-domain. Both the globular nature of the alpha/beta-domain and the presence as well as rigidity of the proline-rich loop are required for DNA transfer and single-stranded DNA binding. Taken together, these data establish the specific structural features of this noncatalytic domain that are essential to DNA conjugation.}, }
@article {pmid19135099, year = {2009}, author = {Toomey, N and Monaghan, A and Fanning, S and Bolton, DJ}, title = {Assessment of horizontal gene transfer in Lactic acid bacteria--a comparison of mating techniques with a view to optimising conjugation conditions.}, journal = {Journal of microbiological methods}, volume = {77}, number = {1}, pages = {23-28}, doi = {10.1016/j.mimet.2008.12.002}, pmid = {19135099}, issn = {1872-8359}, mesh = {*Conjugation, Genetic ; *Gene Transfer Techniques ; *Gene Transfer, Horizontal ; Lactococcus lactis/*genetics ; }, abstract = {Plate, filter and broth mating techniques were assessed over a range of pHs using three Lactococcus lactis donor strains (one with an erythromycin resistance marker and two with tetracycline resistance markers, all located on transferable genetic elements) and one L. lactis recipient strain. Transconjugants were confirmed using antibiotic selection, E-tests to determine MICs, PCR assays to detect the corresponding marker genes, DNA fingerprinting by pulsed-field gel electrophoresis (PFGE), and Southern blotting. Horizontal gene transfer (HGT) rates varied (ranging from 1.6 x 10(-1) to 2.3 x 10(-8)). The general trend observed was plate > filter > broth, independent of pH. Our data suggests that standardisation of methodologies to be used to assess HGT, is warranted and would provide a meaningful assessment of the ability of commensal and other bacteria in different environments to transfer relevant markers.}, }
@article {pmid19134215, year = {2009}, author = {Kanhere, A and Vingron, M}, title = {Horizontal Gene Transfers in prokaryotes show differential preferences for metabolic and translational genes.}, journal = {BMC evolutionary biology}, volume = {9}, number = {}, pages = {9}, pmid = {19134215}, issn = {1471-2148}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Computer Simulation ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Likelihood Functions ; Models, Genetic ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Sequence Analysis, Protein ; Sequence Analysis, RNA ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT) is an important process, which contributes in bacterial pathogenesis and drug resistance. A number of methods have been proposed for detection of horizontal gene transfer. One successful approach to the detection of HGT events is due to Novichkov et al. (J. Bacteriology 186, 6575-85), who rely on comparing phylogenetic distances within a gene family with genomic distances of the source organisms. Building on their approach, we introduce outlier detection in the correlation between those two sets of distances. This approach is designed to detect horizontal transfers of core set of genes present in many bacteria. The principle behind method allows detection of xenologous gene displacements as well as acquisition of novel genes.<br><br>RESULTS: Simulations indicated that our method performs better than Novichkov et al's original approach. The approach very efficiently identified HGT between distantly related bacteria and also a limited number of gene transfers between closely related bacteria. In combination with sequence similarity and likelihood tests, it yields a measure robust enough to derive a set of 171 genes deemed likely to have been horizontally transferred. Further analysis of these 171 established horizontal transfer events gave interesting insights in the direction of transfer.<br><br>CONCLUSION: The majority of transfers between archaea and bacteria have occurred in the direction from bacteria to archaea rather than the other way round. Genes transferred between the archaea and bacteria are mostly metabolic genes. On the other hand, genes transferred within the bacterial phyla are mainly involved in translation.}, }
@article {pmid19132082, year = {2009}, author = {Schubert, S and Darlu, P and Clermont, O and Wieser, A and Magistro, G and Hoffmann, C and Weinert, K and Tenaillon, O and Matic, I and Denamur, E}, title = {Role of intraspecies recombination in the spread of pathogenicity islands within the Escherichia coli species.}, journal = {PLoS pathogens}, volume = {5}, number = {1}, pages = {e1000257}, pmid = {19132082}, issn = {1553-7374}, mesh = {Base Sequence ; *Biological Evolution ; Conjugation, Genetic/genetics ; Escherichia coli/genetics/*pathogenicity ; *Gene Transfer, Horizontal ; Genomic Islands/*genetics ; Phylogeny ; Recombination, Genetic ; Virulence/genetics ; }, abstract = {Horizontal gene transfer is a key step in the evolution of bacterial pathogens. Besides phages and plasmids, pathogenicity islands (PAIs) are subjected to horizontal transfer. The transfer mechanisms of PAIs within a certain bacterial species or between different species are still not well understood. This study is focused on the High-Pathogenicity Island (HPI), which is a PAI widely spread among extraintestinal pathogenic Escherichia coli and serves as a model for horizontal transfer of PAIs in general. We applied a phylogenetic approach using multilocus sequence typing on HPI-positive and -negative natural E. coli isolates representative of the species diversity to infer the mechanism of horizontal HPI transfer within the E. coli species. In each strain, the partial nucleotide sequences of 6 HPI-encoded genes and 6 housekeeping genes of the genomic backbone, as well as DNA fragments immediately upstream and downstream of the HPI were compared. This revealed that the HPI is not solely vertically transmitted, but that recombination of large DNA fragments beyond the HPI plays a major role in the spread of the HPI within E. coli species. In support of the results of the phylogenetic analyses, we experimentally demonstrated that HPI can be transferred between different E. coli strains by F-plasmid mediated mobilization. Sequencing of the chromosomal DNA regions immediately upstream and downstream of the HPI in the recipient strain indicated that the HPI was transferred and integrated together with HPI-flanking DNA regions of the donor strain. The results of this study demonstrate for the first time that conjugative transfer and homologous DNA recombination play a major role in horizontal transfer of a pathogenicity island within the species E. coli.}, }
@article {pmid19130745, year = {2008}, author = {Sinkovics, JG}, title = {"Up-dating the monograph." [corrected] Cytolytic immune lymphocytes in the armamentarium of the human host.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {55}, number = {4}, pages = {371-382}, doi = {10.1556/AMicr.55.2008.4.2}, pmid = {19130745}, issn = {1217-8950}, mesh = {Animals ; Biological Evolution ; Gene Transfer, Horizontal ; Herpesviridae/genetics/immunology/physiology ; Host-Pathogen Interactions/*immunology ; Humans ; Immunity, Cellular/genetics ; Immunotherapy, Adoptive ; Interleukin-2 Receptor alpha Subunit/metabolism ; Killer Cells, Natural/*immunology/radiation effects/transplantation ; Lymphocyte Activation ; Membrane Fusion ; Neoplasms/*immunology/therapy/*virology ; Oncolytic Virotherapy ; Oncolytic Viruses/physiology ; Sea Urchins/genetics/virology ; Sharks/genetics/virology ; T-Lymphocytes, Regulatory/immunology/metabolism ; VDJ Recombinases/genetics ; *Virus Physiological Phenomena ; }, abstract = {The author of the monograph "Cytolytic Immune Lymphocytes..." (published in 2008 by Schenk Buchverlag Campus Dialog, Budapest, Passau, Pécs) proposed several research projects and described certain clinical events that require further elaboration and documentation. In this article the author provides what is required and has since become available. The first subject matter in question concerns the fusogenic viruses. The ancient fusogenic viruses might have created the first eukaryotic cell(s) by uniting archaeabacterial and prokaryotic/protobacterial protospheroplasts. Extant fusogenic viruses either produce tumor cell syncytia and lyse them, thus practicing viral oncolysis. Or, create chimaeric fusion products, the so-called "natural hybridomas", of lymphoma cells exhibiting transmembrane budding of retrovirus particles or envelope proteins, and anti-viral specific antibody-producing plasma cells. The second topic concerns the horizontal-lateral mode of acquisition of those genes, which were "present in the waiting" in the amphioxus, sea urchin, and the agnathans, and met in the primitive gnatostomata sharks to encode in unison the entire adaptive immune system. The consensus of opinion is such that these genes derived from newly acquired transposons/retrotransposons. The author points out that the extant Epstein-Barr virus harbors genes displaying sequence homology with those genes from the sharks up to mammals that regulate the somatic hypermutation of specific antibody production. The author proposes that an ancient herpesvirus might have propagated the V(D)J and RAG genes from sea urchins to sharks. The third area is that of lymphocytes cytotoxic/cytolytic to virally infected or malignantly transformed host cells. This discovery led to the adoptive immune lymphocyte therapy of tumors. Installed in the adaptive immune system are regulatory T cells and myeloid-derived suppressor cells for he protection of "self". Tumor cells masquerading as "self" are protected by these cells from attacks launched by immune T cells. The author supports the replacement of IL-2 by IL-15, inasmuch as IL-2 stimulates not only immune T cells, but also regulatory T cells expressing the CD25 IL-2 receptor. The administration of low dose whole body radiotherapy prior to immune lymphocyte therapy increases the efficacy of immune lymphocyte therapy. The author observed this phenomenon in the mid-1960s. The explanation of this phenomenon revealed itself just recently. In pre-irradiated hosts the intestinal wall becomes permeable to the gut flora; the intestinal bacteria activate the entire innate immune system in the mesenteric lymph nodes and a rapid activation of the adaptive immune faculties follows.}, }
@article {pmid19130050, year = {2009}, author = {Zhang, XX and Zhang, T and Fang, HH}, title = {Antibiotic resistance genes in water environment.}, journal = {Applied microbiology and biotechnology}, volume = {82}, number = {3}, pages = {397-414}, doi = {10.1007/s00253-008-1829-z}, pmid = {19130050}, issn = {1432-0614}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/*drug effects/*genetics/isolation &amp; purification/metabolism ; Bacterial Proteins/genetics/metabolism ; *Drug Resistance, Bacterial ; Fresh Water/*microbiology ; Gene Transfer, Horizontal ; Genetic Techniques ; Geography ; Humans ; }, abstract = {The use of antibiotics may accelerate the development of antibiotic resistance genes (ARGs) and bacteria which shade health risks to humans and animals. The emerging of ARGs in the water environment is becoming an increasing worldwide concern. Hundreds of various ARGs encoding resistance to a broad range of antibiotics have been found in microorganisms distributed not only in hospital wastewaters and animal production wastewaters, but also in sewage, wastewater treatment plants, surface water, groundwater, and even in drinking water. This review summarizes recently published information on the types, distributions, and horizontal transfer of ARGs in various aquatic environments, as well as the molecular methods used to detect environmental ARGs, including specific and multiplex PCR (polymerase chain reaction), real-time PCR, DNA sequencing, and hybridization based techniques.}, }
@article {pmid19128515, year = {2009}, author = {Cai, L and Liu, G and Rensing, C and Wang, G}, title = {Genes involved in arsenic transformation and resistance associated with different levels of arsenic-contaminated soils.}, journal = {BMC microbiology}, volume = {9}, number = {}, pages = {4}, pmid = {19128515}, issn = {1471-2180}, mesh = {Actinomycetales/drug effects/genetics/metabolism ; Arsenic/analysis/*metabolism ; Arsenite Transporting ATPases/*genetics/metabolism ; Arsenites/*pharmacology ; Bacteria/classification/drug effects/*genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genes, rRNA ; Gram-Negative Aerobic Rods and Cocci/drug effects/genetics/metabolism ; Molecular Sequence Data ; Oxidoreductases/*genetics/metabolism ; Phylogeny ; Soil Microbiology ; Soil Pollutants/analysis/*metabolism ; }, abstract = {BACKGROUND: Arsenic is known as a toxic metalloid, which primarily exists in inorganic form [As(III) and As(V)] and can be transformed by microbial redox processes in the natural environment. As(III) is much more toxic and mobile than As(V), hence microbial arsenic redox transformation has a major impact on arsenic toxicity and mobility which can greatly influence the human health. Our main purpose was to investigate the distribution and diversity of microbial arsenite-resistant species in three different arsenic-contaminated soils, and further study the As(III) resistance levels and related functional genes of these species.<br><br>RESULTS: A total of 58 arsenite-resistant bacteria were identified from soils with three different arsenic-contaminated levels. Highly arsenite-resistant bacteria (MIC > 20 mM) were only isolated from the highly arsenic-contaminated site and belonged to Acinetobacter, Agrobacterium, Arthrobacter, Comamonas, Rhodococcus, Stenotrophomonas and Pseudomonas. Five arsenite-oxidizing bacteria that belonged to Achromobacter, Agrobacterium and Pseudomonas were identified and displayed a higher average arsenite resistance level than the non-arsenite oxidizers. 5 aoxB genes encoding arsenite oxidase and 51 arsenite transporter genes [18 arsB, 12 ACR3(1) and 21 ACR3(2)] were successfully amplified from these strains using PCR with degenerate primers. The aoxB genes were specific for the arsenite-oxidizing bacteria. Strains containing both an arsenite oxidase gene (aoxB) and an arsenite transporter gene (ACR3 or arsB) displayed a higher average arsenite resistance level than those possessing an arsenite transporter gene only. Horizontal transfer of ACR3(2) and arsB appeared to have occurred in strains that were primarily isolated from the highly arsenic-contaminated soil.<br><br>CONCLUSION: Soils with long-term arsenic contamination may result in the evolution of highly diverse arsenite-resistant bacteria and such diversity was probably caused in part by horizontal gene transfer events. Bacteria capable of both arsenite oxidation and arsenite efflux mechanisms had an elevated arsenite resistance level.}, }
@article {pmid19127608, year = {2009}, author = {Wang, Z and Zhu, XG and Chang, X and Chen, YZ and Li, YX and Liu, L}, title = {Though with constraints imposed by endosymbiosis, preferential attachment is still a plausible mechanism responsible for the evolution of the chloroplast metabolic network.}, journal = {Journal of evolutionary biology}, volume = {22}, number = {1}, pages = {71-79}, doi = {10.1111/j.1420-9101.2008.01621.x}, pmid = {19127608}, issn = {1420-9101}, mesh = {Amino Acids/metabolism ; *Biological Evolution ; Chloroplasts/enzymology/*physiology ; Enzymes/metabolism ; Gene Transfer, Horizontal ; Isoenzymes/metabolism ; Nucleotides/metabolism ; Symbiosis/*physiology ; Synechococcus/enzymology/genetics/metabolism/*physiology ; }, abstract = {Chloroplasts evolved as a result of endosymbiosis, during which sophisticated mechanisms evolved to translocate nucleus-encoded plastid-targeted enzymes into the chloroplast to form the chloroplast metabolic network. Given the constraints and complexity of endosymbiosis, will preferential attachment still be a plausible mechanism for chloroplast metabolic network evolution? We answer this question by analysing the metabolic network properties of the chloroplast and a cyanobacterium, Synechococcus sp. WH8102 (syw). First, we found that enzymes related to more ancient pathways are more connected, and synthetases have the highest connectivity. Most of the enzymes shared by the two densest cores between the chloroplast and syw are synthetases. Second, the highly conserved functional modules mainly consist of highly connected enzymes. Finally, isozymes and enzymes from endosymbiotic gene transfer (EGT) were distributed mainly in conserved modules and showed higher connectivity than nonisozymes or non-EGT enzymes. These results suggest that even with severe evolutionary constraints imposed by endosymbiosis, preferential attachment is still a plausible mechanism responsible for the evolution of the chloroplast metabolic network. However, the current analysis may not completely differentiate whether the chloroplast network properties reflect the evolution of the chloroplast network through preferential attachment or has been inherited from its cyanobacterial ancestor. To fully differentiate these two possibilities, further analyses of the metabolic network structure properties of organisms at various intermediate evolutionary stages between cyanobacteria and the chloroplast are needed.}, }
@article {pmid19124572, year = {2009}, author = {Nesbø, CL and Bapteste, E and Curtis, B and Dahle, H and Lopez, P and Macleod, D and Dlutek, M and Bowman, S and Zhaxybayeva, O and Birkeland, NK and Doolittle, WF}, title = {The genome of Thermosipho africanus TCF52B: lateral genetic connections to the Firmicutes and Archaea.}, journal = {Journal of bacteriology}, volume = {191}, number = {6}, pages = {1974-1978}, pmid = {19124572}, issn = {1098-5530}, mesh = {Archaea/classification/*genetics ; Bacteria/classification/*genetics/isolation &amp; purification ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Lateral gene transfers (LGT) (also called horizontal gene transfers) have been a major force shaping the Thermosipho africanus TCF52B genome, whose sequence we describe here. Firmicutes emerge as the principal LGT partner. Twenty-six percent of phylogenetic trees suggest LGT with this group, while 13% of the open reading frames indicate LGT with Archaea.}, }
@article {pmid19119236, year = {2009}, author = {Chen, J and Novick, RP}, title = {Phage-mediated intergeneric transfer of toxin genes.}, journal = {Science (New York, N.Y.)}, volume = {323}, number = {5910}, pages = {139-141}, doi = {10.1126/science.1164783}, pmid = {19119236}, issn = {1095-9203}, mesh = {Animals ; Attachment Sites, Microbiological/genetics ; Bacterial Toxins/genetics ; Cattle ; Enterotoxins/genetics ; Female ; *Gene Transfer, Horizontal ; Genomic Islands/*genetics ; Gram-Positive Bacteria/genetics ; Interspersed Repetitive Sequences/genetics ; Listeria monocytogenes/*genetics ; Mastitis, Bovine/microbiology/therapy ; Milk/microbiology ; Mutation ; Staphylococcal Infections/microbiology/therapy/veterinary ; Staphylococcus Phages/*genetics/physiology ; Staphylococcus aureus/*genetics/pathogenicity/virology ; Superantigens/genetics ; *Transduction, Genetic ; Viral Plaque Assay ; Virus Activation ; }, abstract = {Because bacteriophages generally parasitize only closely related bacteria, it is assumed that phage-mediated genetic exchange occurs primarily within species. Here we report that staphylococcal pathogenenicity islands, containing superantigen genes, and other mobile elements transferred to Listeria monocytogenes at the same high frequencies as they transfer within Staphylococcus aureus. Several staphylococcal phages transduced L. monocytogenes but could not form plaques. In an experiment modeling phage therapy for bovine mastitis, we observed pathogenicity island transfer between S. aureus and L. monocytogenes in raw milk. Thus, phages may participate in a far more expansive network of genetic information exchange among bacteria of different species than originally thought, with important implications for the evolution of human pathogens.}, }
@article {pmid19118969, year = {2009}, author = {Stucken, K and Murillo, AA and Soto-Liebe, K and Fuentes-Valdés, JJ and Méndez, MA and Vásquez, M}, title = {Toxicity phenotype does not correlate with phylogeny of Cylindrospermopsis raciborskii strains.}, journal = {Systematic and applied microbiology}, volume = {32}, number = {1}, pages = {37-48}, doi = {10.1016/j.syapm.2008.10.002}, pmid = {19118969}, issn = {0723-2020}, mesh = {Alkaloids ; Bacterial Toxins ; Cyanobacteria Toxins ; Cylindrospermopsis/*classification/genetics/*pathogenicity/physiology ; DNA, Bacterial/analysis/genetics ; DNA, Ribosomal Spacer/analysis/genetics ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Peptide Synthases/genetics/metabolism ; Phenotype ; *Phylogeny ; Polyketide Synthases/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Saxitoxin/genetics/*metabolism ; Sequence Analysis, DNA ; Species Specificity ; Uracil/*analogs &amp; derivatives/metabolism ; }, abstract = {Cylindrospermopsis raciborskii is a species of freshwater, bloom-forming cyanobacterium. C. raciborskii produces toxins, including cylindrospermopsin (hepatotoxin) and saxitoxin (neurotoxin), although non toxin-producing strains are also observed. In spite of differences in toxicity, C. raciborskii strains comprise a monophyletic group, based upon 16S rRNA gene sequence identities (greater than 99%). We performed phylogenetic analyses; 16S rRNA gene and 16S-23S rRNA gene internally transcribed spacer (ITS-1) sequence comparisons, and genomic DNA restriction fragment length polymorphism (RFLP), resolved by pulsed-field gel electrophoresis (PFGE), of strains of C. raciborskii, obtained mainly from the Australian phylogeographic cluster. Our results showed no correlation between toxic phenotype and phylogenetic association in the Australian strains. Analyses of the 16S rRNA gene and the respective ITS-1 sequences (long L, and short S) showed an independent evolution of each ribosomal operon. The genes putatively involved in the cylindrospermopsin biosynthetic pathway were present in one locus and only in the hepatotoxic strains, demonstrating a common genomic organization for these genes and the absence of mutated or inactivated biosynthetic genes in the non toxic strains. In summary, our results support the hypothesis that the genes involved in toxicity may have been transferred as an island by processes of gene lateral transfer, rather than convergent evolution.}, }
@article {pmid20333205, year = {2009}, author = {Desmond, E and Gribaldo, S}, title = {Phylogenomics of sterol synthesis: insights into the origin, evolution, and diversity of a key eukaryotic feature.}, journal = {Genome biology and evolution}, volume = {1}, number = {}, pages = {364-381}, pmid = {20333205}, issn = {1759-6653}, abstract = {The availability of complete genomes from a wide sampling of eukaryotic diversity has allowed the application of phylogenomics approaches to study the origin and evolution of unique eukaryotic cellular structures, but these are still poorly applied to study unique eukaryotic metabolic pathways. Sterols are a good example because they are an essential feature of eukaryotic membranes. The sterol pathway has been well dissected in vertebrates, fungi, and land plants. However, although different types of sterols have been identified in other eukaryotic lineages, their pathways have not been fully characterized. We have carried out an extensive analysis of the taxonomic distribution and phylogeny of the enzymes of the sterol pathway in a large sampling of eukaryotic lineages. This allowed us to tentatively indicate features of the sterol pathway in organisms where this has not been characterized and to point out a number of steps for which yet-to-discover enzymes may be at work. We also inferred that the last eukaryotic common ancestor already harbored a large panel of enzymes for sterol synthesis and that subsequent evolution over the eukaryotic tree occurred by tinkering, mainly by gene losses. We highlight a high capacity of sterol synthesis in the myxobacterium Plesiocystis pacifica, and we support the hypothesis that the few bacteria that harbor homologs of the sterol pathway have likely acquired these via horizontal gene transfer from eukaryotes. Finally, we propose a potential candidate for the elusive enzyme performing C-3 ketoreduction (ERG27 equivalent) in land plants and probably in other eukaryotic phyla.}, }
@article {pmid20333202, year = {2009}, author = {Zhaxybayeva, O and Doolittle, WF and Papke, RT and Gogarten, JP}, title = {Intertwined evolutionary histories of marine Synechococcus and Prochlorococcus marinus.}, journal = {Genome biology and evolution}, volume = {1}, number = {}, pages = {325-339}, pmid = {20333202}, issn = {1759-6653}, abstract = {Prochlorococcus is a genus of marine cyanobacteria characterized by small cell and genome size, an evolutionary trend toward low GC content, the possession of chlorophyll b, and the absence of phycobilisomes. Whereas many shared derived characters define Prochlorococcus as a clade, many genome-based analyses recover them as paraphyletic, with some low-light adapted Prochlorococcus spp. grouping with marine Synechococcus. Here, we use 18 Prochlorococcus and marine Synechococcus genomes to analyze gene flow within and between these taxa. We introduce embedded quartet scatter plots as a tool to screen for genes whose phylogeny agrees or conflicts with the plurality phylogenetic signal, with accepted taxonomy and naming, with GC content, and with the ecological adaptation to high and low light intensities. We find that most gene families support high-light adapted Prochlorococcus spp. as a monophyletic clade and low-light adapted Prochlorococcus sp. as a paraphyletic group. But we also detect 16 gene families that were transferred between high-light adapted and low-light adapted Prochlorococcus sp. and 495 gene families, including 19 ribosomal proteins, that do not cluster designated Prochlorococcus and Synechococcus strains in the expected manner. To explain the observed data, we propose that frequent gene transfer between marine Synechococcus spp. and low-light adapted Prochlorococcus spp. has created a "highway of gene sharing" (Beiko RG, Harlow TJ, Ragan MA. 2005. Highways of gene sharing in prokaryotes. Proc Natl Acad Sci USA. 102:14332-14337) that tends to erode genus boundaries without erasing the Prochlorococcus-specific ecological adaptations.}, }
@article {pmid20333176, year = {2009}, author = {Findlay, WA and Redfield, RJ}, title = {Coevolution of DNA uptake sequences and bacterial proteomes.}, journal = {Genome biology and evolution}, volume = {1}, number = {}, pages = {45-55}, pmid = {20333176}, issn = {1759-6653}, support = {R01 GM060715/GM/NIGMS NIH HHS/United States ; }, abstract = {Dramatic examples of repeated sequences occur in the genomes of some naturally competent bacteria, which contain hundreds or thousands of copies of short motifs called DNA uptake signal sequences. Here, we analyze the evolutionary interactions between coding-region uptake sequences and the proteomes of Haemophilus influenzae, Actinobacillus pleuropneumoniae, and Neisseria meningitidis. In all three genomes, uptake sequence accumulation in coding sequences has approximately doubled the frequencies of those tripeptides specified by each species' uptake sequence. The presence of uptake sequences in particular reading frames correlated most strongly with the use of preferred codons at degenerately coded positions, but the density of uptake sequences correlated only poorly with protein functional category. Genes lacking homologs in related genomes also lacked uptake sequences, strengthening the evidence that uptake sequences do not drive lateral gene transfer between distant relatives but instead accumulate after genes have been transferred. Comparison of the uptake sequence-encoded peptides of H. influenzae and N. meningitidis proteins with their homologs from related bacteria without uptake sequences indicated that uptake sequences were also preferentially located in poorly conserved genes and at poorly conserved amino acids. With few exceptions, amino acids at positions encoded by uptake sequences were as well conserved as other amino acids, suggesting that extant uptake sequences impose little or no constraint on coding for protein function. However, this state is likely to be achieved at a substantial cost because of the selective deaths required to eliminate maladaptive mutations that improve uptake sequences.}, }
@article {pmid20210107, year = {2009}, author = {Sapp, J}, title = {Transcending Darwinism thinking laterally on the tree of life.}, journal = {History and philosophy of the life sciences}, volume = {31}, number = {2}, pages = {161-181}, pmid = {20210107}, issn = {0391-9714}, mesh = {*Biological Evolution ; Drug Resistance, Multiple, Bacterial ; Genes, Bacterial ; Genomics/*history ; History, 19th Century ; History, 20th Century ; Humans ; *Symbiosis ; *Transformation, Genetic ; }, abstract = {The scope and significance of lateral gene transfer (LGT) has been discussed periodically since the early twentieth century. In sketching this history here we see that the pendulum of opinion has swung from one extreme that LGT is a rare phenomenon to the other that it is fundamental to evolution. That phages are sources of bacterial evolutionary innovation has been discussed since the 1920s in association with evidence that symbiosis is a major source of evolutionary innovation. Concepts of infectious heredity re-emerged with the rise of bacterial genetics after the Second World War, but LGT was generally discounted as a significant evolutionary force. LGT received increased attention in the 1960s and 1970s because of its role in antibiotic resistance outbreaks. Some speculated that the new molecular approaches to bacterial phylogenetics were ill-conceived because of LGT. With the rise of genomics in the 1990s, it became clear to phylogeneticists that LGT is the principal mode of generating evolutionary novelty in the prokaryotic world. All microbiologists agree today that the Darwinian concept of a bifurcating tree is an inadequate, if not misleading, representation of the evolutionary process in the microbial world. Phages are also reconceived not only as agents of bacterial gene exchange, but also as organisms in their own right, and fundamental in the evolution of new genes.}, }
@article {pmid19112661, year = {2008}, author = {Maderspacher, F}, title = {Sex and the drought.}, journal = {Current biology : CB}, volume = {18}, number = {21}, pages = {R983-5}, doi = {10.1016/j.cub.2008.10.015}, pmid = {19112661}, issn = {0960-9822}, mesh = {Animals ; Droughts ; Female ; Gene Transfer, Horizontal ; Male ; *Parthenogenesis ; Rotifera/genetics/*physiology ; Water/*physiology ; }, }
@article {pmid19105630, year = {2009}, author = {Chen, F and Spano, A and Goodman, BE and Blasier, KR and Sabat, A and Jeffery, E and Norris, A and Shabanowitz, J and Hunt, DF and Lebedev, N}, title = {Proteomic analysis and identification of the structural and regulatory proteins of the Rhodobacter capsulatus gene transfer agent.}, journal = {Journal of proteome research}, volume = {8}, number = {2}, pages = {967-973}, pmid = {19105630}, issn = {1535-3893}, support = {R01 GM037537/GM/NIGMS NIH HHS/United States ; R01 GM037537-23/GM/NIGMS NIH HHS/United States ; GM37537/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacterial Proteins/*chemistry/*genetics/isolation &amp; purification ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Multigene Family ; Multiprotein Complexes/chemistry/ultrastructure ; Peptides/chemistry/genetics/isolation &amp; purification ; Proteome/*analysis ; Recombinant Fusion Proteins/chemistry/genetics/isolation &amp; purification ; *Rhodobacter capsulatus/chemistry/genetics ; }, abstract = {The gene transfer agent of Rhodobacter capsulatus (GTA) is a unique phage-like particle that exchanges genetic information between members of this same species of bacterium. Besides being an excellent tool for genetic mapping, the GTA has a number of advantages for biotechnological and nanoengineering purposes. To facilitate the GTA purification and identify the proteins involved in GTA expression, assembly and regulation, in the present work we construct and transform into R. capsulatus Y262 a gene coding for a C-terminally His-tagged capsid protein. The constructed protein was expressed in the cells, assembled into chimeric GTA particles inside the cells and excreted from the cells into surrounding medium. Transmission electron micrographs of phosphotungstate-stained, NiNTA-purified chimeric GTA confirm that its structure is similar to normal GTA particles, with many particles composed both of a head and a tail. The mass spectrometric proteomic analysis of polypeptides present in the GTA recovered outside the cells shows that GTA is composed of at least 9 proteins represented in the GTA gene cluster including proteins coded for by Orf's 3, 5, 6-9, 11, 13, and 15.}, }
@article {pmid19103931, year = {2009}, author = {Stanton, TB and Humphrey, SB and Bayles, DO and Zuerner, RL}, title = {Identification of a divided genome for VSH-1, the prophage-like gene transfer agent of Brachyspira hyodysenteriae.}, journal = {Journal of bacteriology}, volume = {191}, number = {5}, pages = {1719-1721}, pmid = {19103931}, issn = {1098-5530}, mesh = {Amino Acid Sequence ; Animals ; Bacteriophages/*genetics ; Base Sequence ; Brachyspira hyodysenteriae/*virology ; Gene Transfer, Horizontal ; Genome, Viral/*genetics ; Molecular Sequence Data ; Prophages/*genetics ; Swine ; Viral Proteins/*genetics ; }, abstract = {The Brachyspira hyodysenteriae B204 genome sequence revealed three VSH-1 tail genes, hvp31, hvp60, and hvp37, in a 3.6-kb cluster. The location and transcription direction of these genes relative to those of the previously described VSH-1 16.3-kb gene operon indicate that the gene transfer agent VSH-1 has a noncontiguous, divided genome.}, }
@article {pmid19102787, year = {2008}, author = {Boerlin, P and Reid-Smith, RJ}, title = {Antimicrobial resistance: its emergence and transmission.}, journal = {Animal health research reviews}, volume = {9}, number = {2}, pages = {115-126}, doi = {10.1017/S146625230800159X}, pmid = {19102787}, issn = {1466-2523}, mesh = {Animals ; Anti-Bacterial Agents/*therapeutic use ; Bacteria/*drug effects/genetics/growth &amp; development ; Colony Count, Microbial/veterinary ; Dose-Response Relationship, Drug ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests/*veterinary ; *Mutation ; Plasmids/genetics ; Polymerase Chain Reaction/methods/veterinary ; Sequence Analysis, DNA ; }, abstract = {New concepts have emerged in the past few years that help us to better understand the emergence and spread of antimicrobial resistance (AMR). These include, among others, the discovery of the mutator state and the concept of mutant selection window for resistances emerging primarily through mutations in existing genes. Our understanding of horizontal gene transfer has also evolved significantly in the past few years, and important new mechanisms of AMR transfer have been discovered, including, among others, integrative conjugative elements and ISCR (insertion sequences with common regions) elements. Simultaneously, large-scale studies have helped us to start comprehending the immense and yet untapped reservoir of both AMR genes and mobile genetic elements present in the environment. Finally, new PCR- and DNA sequencing-based techniques are being developed that will allow us to better understand the epidemiology of classical vectors of AMR genes, such as plasmids, and to monitor them in a more global and systematic way.}, }
@article {pmid19101056, year = {2009}, author = {Pavlović-Lazetić, GM and Mitić, NS and Beljanski, MV}, title = {n-Gram characterization of genomic islands in bacterial genomes.}, journal = {Computer methods and programs in biomedicine}, volume = {93}, number = {3}, pages = {241-256}, pmid = {19101056}, issn = {1872-7565}, mesh = {Base Composition/genetics ; Base Sequence/genetics ; Codon/analysis ; Computational Biology/*methods ; Escherichia coli O157/genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial/genetics ; *Genomic Islands ; Genomics/methods ; Markov Chains ; *Models, Statistical ; Molecular Sequence Data ; }, abstract = {The paper presents a novel, n-gram-based method for analysis of bacterial genome segments known as genomic islands (GIs). Identification of GIs in bacterial genomes is an important task since many of them represent inserts that may contribute to bacterial evolution and pathogenesis. In order to characterize and distinguish GIs from rest of the genome, binary classification of islands based on n-gram frequency distribution have been performed. It consists of testing the agreement of islands n-gram frequency distributions with the complete genome and backbone sequence. In addition, a statistic based on the maximal order Markov model is used to identify significantly overrepresented and underrepresented n-grams in islands. The results may be used as a basis for Zipf-like analysis suggesting that some of the n-grams are overrepresented in a subset of islands and underrepresented in the backbone, or vice versa, thus complementing the binary classification. The method is applied to strain-specific regions in the Escherichia coli O157:H7 EDL933 genome (O-islands), resulting in two groups of O-islands with different n-gram characteristics. It refines a characterization based on other compositional features such as G+C content and codon usage, and may help in identification of GIs, and also in research and development of adequate drugs targeting virulence genes in them.}, }
@article {pmid19099604, year = {2008}, author = {Brilli, M and Mengoni, A and Fondi, M and Bazzicalupo, M and Liò, P and Fani, R}, title = {Analysis of plasmid genes by phylogenetic profiling and visualization of homology relationships using Blast2Network.}, journal = {BMC bioinformatics}, volume = {9}, number = {}, pages = {551}, pmid = {19099604}, issn = {1471-2105}, mesh = {Evolution, Molecular ; Gene Regulatory Networks ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Models, Biological ; *Phylogeny ; Plasmids/*genetics ; *Sequence Homology, Amino Acid ; Shigella/genetics ; *Software ; }, abstract = {BACKGROUND: Phylogenetic methods are well-established bioinformatic tools for sequence analysis, allowing to describe the non-independencies of sequences because of their common ancestor. However, the evolutionary profiles of bacterial genes are often complicated by hidden paralogy and extensive and/or (multiple) horizontal gene transfer (HGT) events which make bifurcating trees often inappropriate. In this context, plasmid sequences are paradigms of network-like relationships characterizing the evolution of prokaryotes. Actually, they can be transferred among different organisms allowing the dissemination of novel functions, thus playing a pivotal role in prokaryotic evolution. However, the study of their evolutionary dynamics is complicated by the absence of universally shared genes, a prerequisite for phylogenetic analyses.<br><br>RESULTS: To overcome such limitations we developed a bioinformatic package, named Blast2Network (B2N), allowing the automatic phylogenetic profiling and the visualization of homology relationships in a large number of plasmid sequences. The software was applied to the study of 47 completely sequenced plasmids coming from Escherichia, Salmonella and Shigella spps.<br><br>CONCLUSION: The tools implemented by B2N allow to describe and visualize in a new way some of the evolutionary features of plasmid molecules of Enterobacteriaceae; in particular it helped to shed some light on the complex history of Escherichia, Salmonella and Shigella plasmids and to focus on possible roles of unannotated proteins.The proposed methodology is general enough to be used for comparative genomic analyses of bacteria.}, }
@article {pmid19098098, year = {2008}, author = {Minoia, M and Gaillard, M and Reinhard, F and Stojanov, M and Sentchilo, V and van der Meer, JR}, title = {Stochasticity and bistability in horizontal transfer control of a genomic island in Pseudomonas.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {52}, pages = {20792-20797}, pmid = {19098098}, issn = {1091-6490}, mesh = {Bacterial Proteins/biosynthesis/genetics ; DNA Transposable Elements/*physiology ; *Evolution, Molecular ; Gene Expression Regulation, Bacterial/physiology ; Gene Transfer, Horizontal/*physiology ; Genomic Islands/*physiology ; Integrases/biosynthesis/genetics ; Pseudomonas/enzymology/*genetics ; }, abstract = {Genomic islands (GEI) comprise a recently recognized large family of potentially mobile DNA elements and play an important role in the rapid differentiation and adaptation of bacteria. Most importantly, GEIs have been implicated in the acquisition of virulence factors, antibiotic resistances or toxic compound metabolism. Despite detailed information on coding capacities of GEIs, little is known about the regulatory decisions in individual cells controlling GEI transfer. Here, we show how self-transfer of ICEclc, a GEI in Pseudomonas knackmussii B13 is controlled by a series of stochastic processes, the result of which is that only a few percent of cells in a population will excise ICEclc and launch transfer. Stochastic processes have been implicated before in producing bistable phenotypic transitions, such as sporulation and competence development, but never before in horizontal gene transfer (HGT). Bistability is instigated during stationary phase at the level of expression of an activator protein InrR that lays encoded on ICEclc, and then faithfully propagated to a bistable expression of the IntB13 integrase, the enzyme responsible for excision and integration of the ICEclc. Our results demonstrate how GEI of a very widespread family are likely to control their transfer rates. Furthermore, they help to explain why HGT is typically confined to few members within a population of cells. The finding that, despite apparent stochasticity, HGT rates can be modulated by external environmental conditions provides an explanation as to why selective conditions can promote DNA exchange.}, }
@article {pmid19096720, year = {2008}, author = {Foerstner, KU and Doerks, T and Muller, J and Raes, J and Bork, P}, title = {A nitrile hydratase in the eukaryote Monosiga brevicollis.}, journal = {PloS one}, volume = {3}, number = {12}, pages = {e3976}, pmid = {19096720}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Animals ; Eukaryota/*enzymology/genetics ; Eukaryotic Cells/enzymology ; Hydro-Lyases/chemistry/genetics/*isolation &amp; purification/metabolism ; Models, Biological ; Phylogeny ; Protein Subunits/chemistry ; }, abstract = {Bacterial nitrile hydratase (NHases) are important industrial catalysts and waste water remediation tools. In a global computational screening of conventional and metagenomic sequence data for NHases, we detected the two usually separated NHase subunits fused in one protein of the choanoflagellate Monosiga brevicollis, a recently sequenced unicellular model organism from the closest sister group of Metazoa. This is the first time that an NHase is found in eukaryotes and the first time it is observed as a fusion protein. The presence of an intron, subunit fusion and expressed sequence tags covering parts of the gene exclude contamination and suggest a functional gene. Phylogenetic analyses and genomic context imply a probable ancient horizontal gene transfer (HGT) from proteobacteria. The newly discovered NHase might open biotechnological routes due to its unconventional structure, its new type of host and its apparent integration into eukaryotic protein networks.}, }
@article {pmid19095942, year = {2008}, author = {Marraffini, LA and Sontheimer, EJ}, title = {CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA.}, journal = {Science (New York, N.Y.)}, volume = {322}, number = {5909}, pages = {1843-1845}, pmid = {19095942}, issn = {1095-9203}, support = {R01 GM072830/GM/NIGMS NIH HHS/United States ; R01 GM072830-04/GM/NIGMS NIH HHS/United States ; GM072830/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Sequence ; *Conjugation, Genetic ; DNA, Bacterial/*genetics/metabolism ; Deoxyribonuclease I/genetics/metabolism ; *Gene Silencing ; *Gene Transfer, Horizontal ; Plasmids/genetics ; RNA Splicing ; RNA, Bacterial/*genetics/metabolism ; Repetitive Sequences, Nucleic Acid/*genetics ; Staphylococcus Phages/genetics ; Staphylococcus aureus/genetics ; Staphylococcus epidermidis/*genetics ; *Transformation, Bacterial ; }, abstract = {Horizontal gene transfer (HGT) in bacteria and archaea occurs through phage transduction, transformation, or conjugation, and the latter is particularly important for the spread of antibiotic resistance. Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci confer sequence-directed immunity against phages. A clinical isolate of Staphylococcus epidermidis harbors a CRISPR spacer that matches the nickase gene present in nearly all staphylococcal conjugative plasmids. Here we show that CRISPR interference prevents conjugation and plasmid transformation in S. epidermidis. Insertion of a self-splicing intron into nickase blocks interference despite the reconstitution of the target sequence in the spliced mRNA, which indicates that the interference machinery targets DNA directly. We conclude that CRISPR loci counteract multiple routes of HGT and can limit the spread of antibiotic resistance in pathogenic bacteria.}, }
@article {pmid19095416, year = {2009}, author = {Maltezou, HC}, title = {Metallo-beta-lactamases in Gram-negative bacteria: introducing the era of pan-resistance?.}, journal = {International journal of antimicrobial agents}, volume = {33}, number = {5}, pages = {405.e1-7}, doi = {10.1016/j.ijantimicag.2008.09.003}, pmid = {19095416}, issn = {1872-7913}, mesh = {Anti-Bacterial Agents/*pharmacology ; Cross Infection/drug therapy/epidemiology/microbiology ; Disease Outbreaks ; *Drug Resistance, Multiple, Bacterial ; Gene Transfer, Horizontal ; Gram-Negative Bacteria/*drug effects/*enzymology/isolation &amp; purification ; Gram-Negative Bacterial Infections/drug therapy/epidemiology/*microbiology ; Humans ; Plasmids ; beta-Lactamases/*biosynthesis ; }, abstract = {Metallo-beta-lactamases (MBLs) are being reported with increasing frequency and from several countries worldwide and are becoming the prevalent and most clinically significant determinants of carbapenem resistance. Furthermore, MBL-producing strains that exhibit a pan-resistant phenotype are increasingly detected. Initially MBLs were detected in Pseudomonas aeruginosa, however nowadays they are frequently found in Acinetobacter baumannii, Klebsiella pneumoniae and other Enterobacteriaceae. MBLs spread easily on plasmids and cause nosocomial infections and outbreaks with excess mortality. Such infections mainly concern patients admitted to Intensive Care Units with several co-morbidities and a history of prolonged administration of antibiotics. MBL-producing strains exhibit resistance to almost all currently available antibiotics. In vitro studies reveal that tigecycline and colistin are the only antibacterial agents with consistent activity against MBL-producing strains. Randomised controlled trials are required in order to evaluate the available therapeutic regimens, including treatment combinations. Tigecycline and colistin should be used under appropriate prescribing practices. Surveillance to monitor the emergence of resistance to these agents as well as implementation of infection control measures should be strengthened. MBL inhibitors are urgently needed, however, none is in late pre-clinical development.}, }
@article {pmid19085328, year = {2008}, author = {Beiko, RG and Doolittle, WF and Charlebois, RL}, title = {The impact of reticulate evolution on genome phylogeny.}, journal = {Systematic biology}, volume = {57}, number = {6}, pages = {844-856}, doi = {10.1080/10635150802559265}, pmid = {19085328}, issn = {1076-836X}, mesh = {Classification/*methods ; Computer Simulation ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Speciation ; Genetic Variation ; *Genome ; *Phylogeny ; }, abstract = {Genome phylogenies are used to build tree-like representations of evolutionary relationships among genomes. However, in condensing the phylogenetic signals within a set of genomes down to a single tree, these methods generally do not explicitly take into account discordant signals arising due to lateral genetic transfer. Because conflicting vertical and horizontal signals can produce compromise trees that do not reflect either type of history, it is essential to understand the sensitivity of inferred genome phylogenies to these confounding effects. Using replicated simulations of genome evolution, we show that different scenarios of lateral genetic transfer have significant impacts on the ability to recover the "true" tree of genomes, even when corrections for phylogenetically discordant signals are used.}, }
@article {pmid19082555, year = {2009}, author = {Walsh, DA and Sharma, AK}, title = {Molecular phylogenetics: testing evolutionary hypotheses.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {502}, number = {}, pages = {131-168}, doi = {10.1007/978-1-60327-565-1_9}, pmid = {19082555}, issn = {1064-3745}, mesh = {Bacteriophages/classification/*genetics ; Evolution, Molecular ; Genome, Viral/*genetics ; Models, Genetic ; *Phylogeny ; }, abstract = {A common approach for investigating evolutionary relationships between genes and organisms is to compare extant DNA or protein sequences and infer an evolutionary tree. This methodology is known as molecular phylogenetics and may be the most informative means for exploring phage evolution, since there are few morphological features that can be used to differentiate between these tiny biological entities. In addition, phage genomes can be mosaic, meaning different genes or genomic regions can exhibit conflicting evolutionary histories due to lateral gene transfer or homologous recombination between different phage genomes. Molecular phylogenetics can be used to identify and study such genome mosaicism. This chapter provides a general introduction to the theory and methodology used to reconstruct phylogenetic relationships from molecular data. Also included is a discussion on how the evolutionary history of different genes within the same set of genomes can be compared, using a collection of T4-type phage genomes as an example. A compilation of programs and packages that are available for conducting phylogenetic analyses is supplied as an accompanying appendix.}, }
@article {pmid19081692, year = {2009}, author = {Wei, G and Chen, W and Young, JP and Bontemps, C}, title = {A new clade of Mesorhizobium nodulating Alhagi sparsifolia.}, journal = {Systematic and applied microbiology}, volume = {32}, number = {1}, pages = {8-16}, doi = {10.1016/j.syapm.2008.11.003}, pmid = {19081692}, issn = {0723-2020}, mesh = {Acyltransferases/genetics ; Alphaproteobacteria/*classification/genetics/isolation &amp; purification ; Bacterial Proteins/genetics ; Bacterial Typing Techniques ; China ; DNA, Bacterial/analysis ; DNA, Ribosomal/analysis ; Fabaceae/classification/*microbiology ; Gene Transfer, Horizontal ; Molecular Sequence Data ; N-Acetylglucosaminyltransferases/genetics ; Nitrogen Fixation/genetics ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; *Symbiosis/genetics ; }, abstract = {We isolated 33 nodule bacteria from the legume Alhagi sparsifolia growing in the desert of northwest China. They fell into three groups by restriction analysis of their rrs (small subunit ribosomal RNA) genes, and these, together with dnaK and dnaJ genes, were sequenced from representative isolates to assess their taxonomic position by phylogenetic analysis. The bacteria in each group belonged to different lineages that might represent three different new Mesorhizobium species, two of which form a novel clade very distinct from other species in the genus. Most A. sparsifolia symbionts harboured closely related nodA and nodC genes forming new lineages. The presence of these closely related symbiosis genes in various genomic backgrounds and the incongruence observed between the different gene phylogenies indicate a history of horizontal gene transfer of symbiosis genes between the A. sparsifolia symbionts.}, }
@article {pmid19081010, year = {2008}, author = {Lohtander, K and Pasonen, HL and Aalto, MK and Palva, T and Pappinen, A and Rikkinen, J}, title = {Phylogeny of chitinases and its implications for estimating horizontal gene transfer from chitinase-transgenic silver birch (Betula pendula).}, journal = {Environmental biosafety research}, volume = {7}, number = {4}, pages = {227-239}, doi = {10.1051/ebr:2008019}, pmid = {19081010}, issn = {1635-7922}, mesh = {Amino Acid Sequence ; Beta vulgaris/enzymology/genetics ; Betula/enzymology/*genetics ; Chitinases/*genetics ; Expressed Sequence Tags ; *Gene Transfer, Horizontal ; *Phylogeny ; Plants, Genetically Modified/enzymology/genetics ; Sequence Analysis, DNA ; }, abstract = {Chitinases are hydrolytic enzymes that have been employed in biotechnology in attempts to increase plants' resistance against fungal pathogens. Genetically modified plants have given rise to concerns of the spreading of transgenes into the environment through vertical or horizontal gene transfer (HGT). In this study, chitinase-like sequences from silver birch (Betula pendula) EST-libraries were identified and their phylogenetic relationships to other chitinases were studied. Phylogenetic analyses were used to estimate the frequency of historical gene transfer events of chitinase genes between plants and other organisms, and the usefulness of phylogenetic analyses as a source of information for the risk assessment of transgenic silver birch carrying a sugar beet chitinase IV gene was evaluated. Thirteen partial chitinase-like sequences, with an approximate length of 600 bp, were obtained from the EST-libraries. The sequences belonged to five chitinase classes. Some bacterial chitinases from Streptomyces and Burkholderia, as well as a chitinase from an oomycete, Phytophthora infestans, grouped together with the class IV chitinases of plants, supporting the hypothesis that some class IV chitinases in bacteria have evolved from eukaryotic chitinases via horizontal gene transfer. According to our analyses, HGT of a chitinase IV gene from eukaryotes to bacteria has presumably occurred only once. Based on this, the likelihood for the HGT of chitinase IV gene from transgenic birch to other organisms is extremely low. However, as risk is a function of both the likelihood and consequences of an event, the effects of rare HGT event(s) will finally determine the level of the risk.}, }
@article {pmid19077301, year = {2008}, author = {Cardona, G and Rosselló, F and Valiente, G}, title = {Extended Newick: it is time for a standard representation of phylogenetic networks.}, journal = {BMC bioinformatics}, volume = {9}, number = {}, pages = {532}, pmid = {19077301}, issn = {1471-2105}, mesh = {Computer Graphics/*standards ; Databases, Genetic ; *Gene Transfer, Horizontal ; *Hybridization, Genetic ; *Phylogeny ; *Software ; }, abstract = {BACKGROUND: Phylogenetic trees resulting from molecular phylogenetic analysis are available in Newick format from specialized databases but when it comes to phylogenetic networks, which provide an explicit representation of reticulate evolutionary events such as recombination, hybridization or lateral gene transfer, the lack of a standard format for their representation has hindered the publication of explicit phylogenetic networks in the specialized literature and their incorporation in specialized databases. Two different proposals to represent phylogenetic networks exist: as a single Newick string (where each hybrid node is splitted once for each parent) or as a set of Newick strings (one for each hybrid node plus another one for the phylogenetic network).<br><br>RESULTS: The standard we advocate as extended Newick format describes a whole phylogenetic network with k hybrid nodes as a single Newick string with k repeated nodes, and this representation is unique once the phylogenetic network is drawn or the ordering among children nodes is fixed. The extended Newick format facilitates phylogenetic data sharing and exchange, and also allows for the practical use of phylogenetic networks in computer programs and scripts. This standard has been recently agreed upon by a number of computational biologists, is already supported by several phylogenetic tools, and avoids the different drawbacks of using an a priori unknown number of Newick strings without any additional mark-up to represent a phylogenetic network.<br><br>CONCLUSION: The adoption of the extended Newick format as a standard for the representation of phylogenetic network is an important step towards the publication of explicit phylogenetic networks in peer-reviewed journals and their incorporation in a future database of published phylogenetic networks.}, }
@article {pmid19077245, year = {2008}, author = {Molina, N and van Nimwegen, E}, title = {The evolution of domain-content in bacterial genomes.}, journal = {Biology direct}, volume = {3}, number = {}, pages = {51}, pmid = {19077245}, issn = {1745-6150}, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial/*genetics ; Models, Genetic ; Phylogeny ; Protein Biosynthesis ; Protein Structure, Tertiary/*genetics ; Time Factors ; Transcription, Genetic ; }, abstract = {BACKGROUND: Across all sequenced bacterial genomes, the number of domains nc in different functional categories c scales as a power-law in the total number of domains n, i.e. nc proportional n(alpha)c, with exponents alpha(c) that vary across functional categories. Here we investigate the implications of these scaling laws for the evolution of domain-content in bacterial genomes and derive the simplest evolutionary model consistent with these scaling laws.<br><br>RESULTS: We show that, using only an assumption of time invariance, the scaling laws uniquely determine the relative rates of domain additions and deletions across all functional categories and evolutionary lineages. In particular, the model predicts that the rate of additions and deletions of domains of category c is proportional to the number of domains nc currently in the genome and we discuss the implications of this observation for the role of horizontal transfer in genome evolution. Second, in addition to being proportional to nc, the rate of additions and deletions of domains of category c is proportional to a category-dependent constant rho(c), which is the same for all evolutionary lineages. This 'evolutionary potential' rho(c) represents the relative probability for additions/deletions of domains of category c to be fixed in the population by selection and is predicted to equal the scaling exponent alpha(c). By comparing the domain content of 93 pairs of closely-related genomes from all over the phylogenetic tree of bacteria, we demonstrate that the model's predictions are supported by available genome-sequence data.<br><br>CONCLUSION: Our results establish a direct quantitative connection between the scaling of domain numbers with genome size, and the rate of addition and deletions of domains during short evolutionary time intervals.of domain numbers with genome size, and the rate of addition and deletions of domains during short evolutionary time intervals.}, }
@article {pmid19074602, year = {2009}, author = {Estrella, MJ and Muñoz, S and Soto, MJ and Ruiz, O and Sanjuán, J}, title = {Genetic diversity and host range of rhizobia nodulating Lotus tenuis in typical soils of the Salado River Basin (Argentina).}, journal = {Applied and environmental microbiology}, volume = {75}, number = {4}, pages = {1088-1098}, pmid = {19074602}, issn = {1098-5336}, mesh = {Alphaproteobacteria/*classification/genetics/*isolation &amp; purification ; Argentina ; Bacterial Proteins/genetics ; Cluster Analysis ; Conserved Sequence ; DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Genetic Variation ; Genotype ; Lotus/*microbiology ; Molecular Sequence Data ; N-Acetylglucosaminyltransferases/genetics ; Oxidoreductases/genetics ; Phylogeny ; Plant Roots/microbiology ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; *Soil Microbiology ; }, abstract = {A total of 103 root nodule isolates were used to estimate the diversity of bacteria nodulating Lotus tenuis in typical soils of the Salado River Basin. A high level of genetic diversity was revealed by repetitive extragenic palindromic PCR, and 77 isolates with unique genomic fingerprints were further differentiated into two clusters, clusters A and B, after 16S rRNA restriction fragment length polymorphism analysis. Cluster A strains appeared to be related to the genus Mesorhizobium, whereas cluster B was related to the genus Rhizobium. 16S rRNA sequence and phylogenetic analysis further supported the distribution of most of the symbiotic isolates in either Rhizobium or Mesorhizobium: the only exception was isolate BA135, whose 16S rRNA gene was closely related to the 16S rRNA gene of the genus Aminobacter. Most Mesorhizobium-like isolates were closely related to Mesorhizobium amorphae, Mesorhizobium mediterraneum, Mesorhizobium tianshanense, or the broad-host-range strain NZP2037, but surprisingly few isolates grouped with Mesorhizobium loti type strain NZP2213. Rhizobium-like strains were related to Rhizobium gallicum, Rhizobium etli, or Rhizobium tropici, for which Phaseolus vulgaris is a common host. However, no nodC or nifH genes could be amplified from the L. tenuis isolates, suggesting that they have rather divergent symbiosis genes. In contrast, nodC genes from the Mesorhizobium and Aminobacter strains were closely related to nodC genes from narrow-host-range M. loti strains. Likewise, nifH gene sequences were very highly conserved among the Argentinian isolates and reference Lotus rhizobia. The high levels of conservation of the nodC and nifH genes suggest that there was a common origin of the symbiosis genes in narrow-host-range Lotus symbionts, supporting the hypothesis that both intrageneric horizontal gene transfer and intergeneric horizontal gene transfer are important mechanisms for the spread of symbiotic capacity in the Salado River Basin.}, }
@article {pmid19060088, year = {2008}, author = {Claesson, MJ and van Sinderen, D and O'Toole, PW}, title = {Lactobacillus phylogenomics--towards a reclassification of the genus.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {58}, number = {Pt 12}, pages = {2945-2954}, doi = {10.1099/ijs.0.65848-0}, pmid = {19060088}, issn = {1466-5026}, mesh = {Bacterial Proteins/metabolism ; Genes, Bacterial/genetics ; *Genomics ; Lactobacillus/*classification/genetics ; *Phylogeny ; Species Specificity ; }, abstract = {The extremely diverse genus Lactobacillus is the largest among the lactic acid bacteria, with over 145 recognized species. In this work, which to our knowledge is the largest comparative phylogenomics study of a single genus to date, 12 genomes of Lactobacillus strains were subjected to an array of whole-genome and single-marker phylogenetic approaches, to investigate the case for extracting subgeneric groups and to determine whether a single congruent phylogeny could be identified. We conclude that GroEL is a more robust single-gene phylogenetic marker for the genus Lactobacillus than the 16S rRNA gene, when no whole-genome information is available. Significant incongruence was found, both within a set of trees based on 141 core proteins and within those phylogenies based on numbers of orthologues, concatenated RNA polymerase subunits and single gene/protein markers. This is possibly due to different evolutionary rates, hidden paralogies or horizontal gene transfer. Such phylogenetic ambiguities are efficiently visualized with cluster-networks. Although the genus contains some highly unstable taxa, four subgeneric groups were distinguished. Qualitative and quantitative gene analysis of these groups resulted in three findings: there is a relatively small number of group-specific proteins, the majority of which are poorly characterized; major groupings are functionally better distinguishable by absent genes rather than gained/retained genes; and, finally, a gene cluster possibly involved in purine metabolism is uniquely present in four lactobacilli associated with meat. In conclusion, because of either significantly different branching patterns or the availability of too few members, three of the four identified groups could not serve as the basis for identifying candidate novel genera within the current genus. We therefore suggest targeted sequencing of key taxonomic species identified here, which are likely to add sufficient depth for a future reclassification, followed by phylogenomic analysis involving the core proteins identified here. This will ideally be combined with phenotypic data using a polyphasic approach.}, }
@article {pmid19059164, year = {2008}, author = {Bruzzone, CM and Belcher, JD and Schuld, NJ and Newman, KA and Vineyard, J and Nguyen, J and Chen, C and Beckman, JD and Steer, CJ and Vercellotti, GM}, title = {Quantitative real-time polymerase chain reaction (qRT-PCR) restriction fragment length polymorphism (RFLP) method for monitoring highly conserved transgene expression during gene therapy.}, journal = {Translational research : the journal of laboratory and clinical medicine}, volume = {152}, number = {6}, pages = {290-297}, pmid = {19059164}, issn = {1931-5244}, support = {P01 HL55552/HL/NHLBI NIH HHS/United States ; P01 HL055552-120003/HL/NHLBI NIH HHS/United States ; P01 HL055552/HL/NHLBI NIH HHS/United States ; R01 HL067367-06/HL/NHLBI NIH HHS/United States ; P01 HL055552-129002/HL/NHLBI NIH HHS/United States ; R01 HL067367/HL/NHLBI NIH HHS/United States ; }, mesh = {Amplified Fragment Length Polymorphism Analysis/*methods ; Anemia, Sickle Cell/genetics/*therapy ; Animals ; Disease Models, Animal ; Female ; Gene Expression Profiling/*methods ; Gene Expression Regulation, Enzymologic ; Gene Transfer, Horizontal ; *Genetic Therapy ; Genetic Vectors ; Heme Oxygenase (Decyclizing)/*genetics/metabolism ; Heme Oxygenase-1/*genetics/metabolism ; Hepatocytes/enzymology ; Male ; Membrane Proteins/*genetics/metabolism ; Mice ; Mice, Inbred C57BL ; Polymorphism, Restriction Fragment Length ; RNA, Messenger/metabolism ; Rats ; Rats, Sprague-Dawley ; Reverse Transcriptase Polymerase Chain Reaction ; Transfection ; Transgenes ; }, abstract = {Evaluation of the transfer efficiency of a rat heme oxygenase-1 (HO-1) transgene into mice requires differentiation of rat and mouse HO-1. However, rat and mouse HO-1 have 94% homology; antibodies and enzyme activity cannot adequately distinguish HO-1. We designed a quantitative real-time polymerase chain reaction (qRT-PCR) method to monitor HO-1 transcription relative to a housekeeping gene, GAPDH. The ratio of rat and mouse HO-1 mRNA could be estimated through restriction fragment length polymorphism (RFLP) analysis of the PCR products. In vitro, murine AML12 hepatocytes were transfected with rat HO-1. After 40 h, the total HO-1 mRNA was enriched 2-fold relative to control cells, and rat HO-1 comprised 84% of HO-1 cDNA. In vivo, the rat HO-1 transgene was cloned into a Sleeping Beauty transposase (SB-Tn) construct and was injected hydrodynamically into a mouse model of sickle cell disease (SCD). After 21 days, there was a 32% enrichment of HO-1 mRNA relative to control mice and the rat transgene comprised 88% of HO-1 cDNA. After 21 days, HO-1 protein expression in liver was increased 2.5-fold. In summary, qRT-PCR RFLP is a useful and reliable method to differentiate the transgene from host gene transcription, especially when the host and transgene protein are identical or highly homologous. This method has translational applications to the design, delivery, and monitoring of gene-therapy vectors.}, }
@article {pmid19052629, year = {2009}, author = {Haverkamp, TH and Schouten, D and Doeleman, M and Wollenzien, U and Huisman, J and Stal, LJ}, title = {Colorful microdiversity of Synechococcus strains (picocyanobacteria) isolated from the Baltic Sea.}, journal = {The ISME journal}, volume = {3}, number = {4}, pages = {397-408}, doi = {10.1038/ismej.2008.118}, pmid = {19052629}, issn = {1751-7370}, mesh = {*Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, rRNA ; Molecular Sequence Data ; Oceans and Seas ; Operon ; Phycocyanin/genetics ; Phylogeny ; Pigments, Biological/biosynthesis ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Synechococcus/*classification/genetics/*isolation &amp; purification/physiology ; }, abstract = {Synechococcus is a cosmopolitan genus of picocyanobacteria living in the photic zone of freshwater and marine ecosystems. Here, we describe the isolation of 46 closely related picocyanobacterial strains from the Baltic Sea. The isolates showed considerable variation in their cell size and pigmentation phenotypes, yielding a colorful variety of red, pink and blue-green strains. These pigmentation phenotypes could not be differentiated on the basis of their 16S rRNA-internal transcribed spacer (ITS) sequences. Thirty-nine strains, designated BSea, possessed 16S rRNA-ITS sequences almost identical with Synechococcus strain WH5701. Despite their similar 16S rRNA-ITS sequences, the BSea strains separated into several different clusters when comparing the phycocyanin (cpcBA) operon. This separation was largely consistent with the phycobiliprotein composition of the different BSea strains. The majority of phycocyanin (PC)-rich Bsea strains clustered with WH5701. Remarkably, the phycoerythrin (PE)-rich strains of BSea formed an as yet unidentified cluster within the cpcBA phylogeny, distantly related to other PE-rich groups. Detailed analysis of the cpcBA operon using neighbour-net analysis indicated that the PE-rich BSea strains are probably endemic for the Baltic Sea. Comparison of the phylogenies obtained by the 16S rRNA-ITS, the cpcBA, and the concatenated 16S rRNA-ITS and cpcBA operon sequences revealed possible events of horizontal gene transfer among different Synechococcus lineages. Our results show that microdiversity is important in Synechococcus populations and that it can reflect extensive diversification of different pigmentation phenotypes into different ecological niches.}, }
@article {pmid19049434, year = {2009}, author = {Rice, LB and Lakticová, V and Carias, LL and Rudin, S and Hutton, R and Marshall, SH}, title = {Transferable capacity for gastrointestinal colonization in Enterococcus faecium in a mouse model.}, journal = {The Journal of infectious diseases}, volume = {199}, number = {3}, pages = {342-349}, doi = {10.1086/595986}, pmid = {19049434}, issn = {0022-1899}, support = {R01AI 45626-8/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics/metabolism ; Disease Models, Animal ; Drug Resistance, Bacterial/genetics ; Enterococcus faecium/drug effects/genetics/*physiology ; Female ; Gastrointestinal Diseases/*microbiology ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Gram-Positive Bacterial Infections/*microbiology ; Mice ; Microbial Sensitivity Tests ; Selection, Genetic ; Vancomycin/pharmacology ; }, abstract = {A high level of gastrointestinal colonization frequently precedes invasive infection due to Enterococcus faecium. Factors other than antimicrobial resistance that promote gastrointestinal colonization by E. faecium have not been identified. We tested the ability of a colonization-proficient clinical E. faecium isolate (C68) to transfer colonizing ability to noncolonizing E. faecium recipient strains. Transconjugants derived from matings that used E. faecium D344SRF as a recipient strain colonized mouse gastrointestinal tracts in high numbers under selective pressure from clindamycin or vancomycin, compared with control strains that lacked DNA transferred from C68. We transferred DNA into a second recipient strain (E. faecium GE-1), which also colonized mice in significantly greater numbers under selective pressure from clindamycin, compared with a control strain. These results indicate that E. faecium clinical isolates express transmissible factors other than antimicrobial resistance that promote colonization of the mouse gastrointestinal tract.}, }
@article {pmid19048497, year = {2008}, author = {Cristancho, M and Escobar, C}, title = {Transferability of SSR markers from related Uredinales species to the coffee rust Hemileia vastatrix.}, journal = {Genetics and molecular research : GMR}, volume = {7}, number = {4}, pages = {1186-1192}, doi = {10.4238/vol7-4gmr493}, pmid = {19048497}, issn = {1676-5680}, mesh = {Basidiomycota/*genetics ; Coffea/*microbiology ; Gene Transfer, Horizontal ; Genome, Plant ; Microsatellite Repeats/*genetics ; Plant Diseases/microbiology ; Species Specificity ; }, abstract = {The aim of the present research was to test the transferability of simple sequence repeat (SSR) markers developed in two Uredinales species to Hemileia vastatrix, coffee rust. The development of efficient techniques for the identification of H. vastatrix isolates is imperative, given the continuous development of new races. The transferability of 25 SSR markers developed in the related Uredinales species Puccinia coronata f. sp lolli and Melampsora linii to H. vastatrix was tested. A low level of transferability of SSRs was detected, and only 4 potential markers that can be used to fingerprint the coffee rust races were identified.}, }
@article {pmid19048472, year = {2008}, author = {Pirondini, A and Marmiroli, N}, title = {Environmental risk assessment in GMO analysis.}, journal = {Rivista di biologia}, volume = {101}, number = {2}, pages = {215-246}, pmid = {19048472}, issn = {0035-6050}, mesh = {*Environment ; Gene Transfer, Horizontal ; Organisms, Genetically Modified/*genetics ; Plants, Genetically Modified/*adverse effects/*genetics ; Risk Assessment/methods ; }, abstract = {Genetically modified or engineered organisms (GMOs, GEOs) are utilised in agriculture, expressing traits of interest, such as insect or herbicide resistance. Soybean, maize, cotton and oilseed rape are the GM crops with the largest acreage in the world. The distribution of GM acreage in the different countries is related with the different positions concerning labelling of GMO products: based on the principle of substantial equivalence, or rather based on the precautionary principle. The paper provides an overview on how the risks associated with release of GMO in the environments can be analysed and predicted, in view of a possible coexistence of GM and non-GM organisms in agriculture.Risk assessment procedures, both qualitative and quantitative, are compared in the context of application to GMOs considering also legislation requirements (Directive 2001/18/EC). Criteria and measurable properties to assess harm for human health and environmental safety are listed, and the possible consequences are evaluated in terms of significance.Finally, a mapping of the possible risks deriving from GMO release is reported, focusing on gene transfer to related species, horizontal gene transfer, direct and indirect effects on non target organisms, development of resistance in target organisms, and effects on biodiversity.}, }
@article {pmid19047736, year = {2008}, author = {Gábor, K and Hailesellasse Sene, K and Smidt, H and de Vos, WM and van der Oost, J}, title = {Divergent roles of CprK paralogues from Desulfitobacterium hafniense in activating gene expression.}, journal = {Microbiology (Reading, England)}, volume = {154}, number = {Pt 12}, pages = {3686-3696}, doi = {10.1099/mic.0.2008/021584-0}, pmid = {19047736}, issn = {1350-0872}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/*genetics/metabolism ; Base Sequence ; Cyclic AMP Receptor Protein/chemistry/*genetics/metabolism ; Desulfitobacterium/genetics/*metabolism/physiology ; Escherichia coli/genetics/metabolism ; *Gene Expression Regulation, Bacterial ; Iron-Sulfur Proteins/chemistry/*genetics/metabolism ; Membrane Proteins/genetics/metabolism ; Methyl-Accepting Chemotaxis Proteins ; Molecular Sequence Data ; Transcription Factors/chemistry/*genetics/metabolism ; }, abstract = {Gene duplication and horizontal gene transfer play an important role in the evolution of prokaryotic genomes. We have investigated the role of three CprK paralogues from the cAMP receptor protein-fumarate and nitrate reduction regulator (CRP-FNR) family of transcriptional regulators that are encoded in the genome of Desulfitobacterium hafniense DCB-2 and possibly regulate expression of genes involved in the energy-conserving terminal reduction of organohalides (halorespiration). The results from in vivo and in vitro promoter probe assays show that two regulators (CprK1 and CprK2) have an at least partially overlapping effector specificity, with preference for ortho-chlorophenols, while meta-chlorophenols proved to be effectors for CprK4. The presence of a potential transposase-encoding gene in the vicinity of the cprK genes indicates that their redundancy is probably caused by mobile genetic elements. The CprK paralogues activated transcription from promoters containing a 14 bp inverted repeat (dehalobox) that closely resembles the FNR-box. We found a strong negative correlation between the rate of transcriptional activation and the number of nucleotide changes from the optimal dehalobox sequence (TTAAT-N4-ATTAA). Transcription was initiated by CprK4 from a promoter that is situated upstream of a gene encoding a methyl-accepting chemotaxis protein. This might be the first indication of taxis of an anaerobic bacterium to halogenated aromatic compounds.}, }
@article {pmid19047393, year = {2009}, author = {Leikoski, N and Fewer, DP and Sivonen, K}, title = {Widespread occurrence and lateral transfer of the cyanobactin biosynthesis gene cluster in cyanobacteria.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {3}, pages = {853-857}, pmid = {19047393}, issn = {1098-5336}, mesh = {Cyanobacteria/*genetics/*metabolism ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Metabolic Networks and Pathways/*genetics ; *Multigene Family ; Peptides, Cyclic/*biosynthesis ; }, abstract = {Cyanobactins are small cyclic peptides produced by cyanobacteria. Here we demonstrate the widespread but sporadic occurrence of the cyanobactin biosynthetic pathway. We detected a cyanobactin biosynthetic gene in 48 of the 132 strains included in this study. Our results suggest that cyanobactin biosynthetic genes have a complex evolutionary history in cyanobacteria punctuated by a series of ancient horizontal gene transfer events.}, }
@article {pmid19042975, year = {2009}, author = {Whitfield, CR and Wardle, SJ and Haniford, DB}, title = {The global bacterial regulator H-NS promotes transpososome formation and transposition in the Tn5 system.}, journal = {Nucleic acids research}, volume = {37}, number = {2}, pages = {309-321}, pmid = {19042975}, issn = {1362-4962}, mesh = {Bacterial Proteins/genetics/*metabolism ; Binding Sites ; DNA Footprinting ; *DNA Transposable Elements ; DNA, Bacterial/chemistry/metabolism ; DNA-Binding Proteins/genetics/*metabolism ; Mutation ; }, abstract = {The histone-like nucleoid structuring protein (H-NS) is an important regulator of stress response and virulence genes in gram-negative bacteria. In addition to binding regulatory regions of genes in a structure-specific manner, H-NS also binds in a structure-specific manner to sites in the Tn10 transpososome, allowing it to act as a positive regulator of Tn10 transposition. This is the only example to date of H-NS regulating a transposition system by interacting directly with the transposition machinery. In general, transposition complexes tend to include segments of deformed DNA and given the capacity of H-NS to bind such structures, and the results from the Tn10 system, we asked if H-NS might regulate another transposition system (Tn5) by directly binding the transposition machinery. We show in the current work that H-NS does bind Tn5 transposition complexes and use hydroxyl radical footprinting to characterize the H-NS interaction with the Tn5 transpososome. We also show that H-NS can promote Tn5 transpososome formation in vitro, which correlates with the Tn5 system showing a dependence on H-NS for transposition in vivo. Taken together the results suggest that H-NS might play an important role in the regulation of many different bacterial transposition systems and thereby contribute directly to lateral gene transfer.}, }
@article {pmid19040703, year = {2009}, author = {Strahinic, I and Kojic, M and Tolinacki, M and Fira, D and Topisirovic, L}, title = {Molecular characterization of plasmids pS7a and pS7b from Lactococcus lactis subsp. lactis bv. diacetylactis S50 as a base for the construction of mobilizable cloning vectors.}, journal = {Journal of applied microbiology}, volume = {106}, number = {1}, pages = {78-88}, doi = {10.1111/j.1365-2672.2008.03977.x}, pmid = {19040703}, issn = {1365-2672}, mesh = {Bacteriocins/metabolism ; Conjugation, Genetic/genetics ; Genes, Bacterial/genetics ; Lactococcus lactis/*genetics/metabolism ; Plasmids/*genetics ; Replication Origin ; Sequence Analysis, DNA ; Transformation, Genetic ; }, abstract = {AIMS: Strain Lactococcus lactis subsp. lactis bv. diacetylactis S50 harbours five theta-replicating plasmids (pS6, pS7a, pS7b, pS80 and pS140). The aim of this study was to characterize domains involved in the replication and conjugative mobilization of the small plasmids pS7a and pS7b, which are structurally very similar.<br><br>METHODS AND RESULTS: Complete nucleotide sequences of pS7a and pS7b were determined by cloning DNA fragments of different sizes into Escherichia coli vectors. Linearized plasmids and four EcoRI fragments of the pS7a and pS7b were cloned into an origin probe vector. Constructed plasmids (pSEV10, pSK10, pISE1a and pISE1b) were able to replicate in the strain L. lactis subsp. cremoris MG1363. In addition, experiments showed that plasmids pS7a and pS7b contained oriT sequences and their conjugative transfer directly depended on the presence of pS80 in donor cells.<br><br>CONCLUSIONS: Plasmids pS7a and pS7b contained typical lactococcal theta replication origin and repB gene that enable them to replicate in the strain L. lactis subsp. cremoris MG1363. Plasmid pS80 plays a key role in the conjugative transfer of small plasmids.<br><br>Plasmids pS7a and pS7b-based derivatives could be valuable tools for genetic manipulation, studying processes of plasmid maintenance and horizontal gene transfer in lactococci.}, }
@article {pmid19040477, year = {2008}, author = {Berglund, C and Söderquist, B}, title = {The origin of a methicillin-resistant Staphylococcus aureus isolate at a neonatal ward in Sweden-possible horizontal transfer of a staphylococcal cassette chromosome mec between methicillin-resistant Staphylococcus haemolyticus and Staphylococcus aureus.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {14}, number = {11}, pages = {1048-1056}, doi = {10.1111/j.1469-0691.2008.02090.x}, pmid = {19040477}, issn = {1469-0691}, mesh = {DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; Disease Outbreaks ; *Gene Transfer, Horizontal ; Genotype ; Humans ; Intensive Care Units, Neonatal ; *Methicillin Resistance ; Methicillin-Resistant Staphylococcus aureus/classification/*genetics/*isolation &amp; purification ; Molecular Sequence Data ; Sequence Analysis, DNA ; Staphylococcal Infections/epidemiology/*microbiology ; Staphylococcus haemolyticus/*genetics ; Sweden/epidemiology ; }, abstract = {The first methicillin-resistant Staphylococcus aureus (MRSA) strain originated when a staphylococcal cassette chromosome mec (SCCmec) with the gene mecA was integrated into the chromosome of a susceptible S. aureus cell. The SCCmec elements are common among the coagulase-negative staphylococci, e.g. Staphylococcus haemolyticus, and these are considered to be potential SCCmec donors when new clones of MRSA arise. An outbreak of MRSA occurred at a neonatal intensive-care unit, and the isolates were all of sequence type (ST) 45, as characterized by multilocus sequence typing, but were not typeable with respect to SCCmec types I, II, III or IV. During the same time period, methicillin-resistant S. haemolyticus (MRSH) isolates identified in blood cultures at the same ward were found to be genotypically homogenous by pulsed-field gel electrophoresis, and did not carry a type I, II, III or IV SCCmec either. Thus, the hypothesis was raised that an SCCmec of MRSH had been transferred to a methicillin-susceptible S. aureus strain and thereby created a new clone of MRSA that caused the outbreak. This study showed that MRSA from the outbreak carried a ccrC and a class C mec complex that was also found among MRSH isolates. Partial sequencing of the mec complexes showed more than 99% homology, indicative of a common type V SCCmec. This finding may provide evidence for a recent horizontal transfer of an SCCmec from MRSH to an identified potential recipient, an ST45 methicillin-susceptible S. aureus strain, thereby creating a new clone of MRSA that caused the outbreak.}, }
@article {pmid19040470, year = {2008}, author = {Courvalin, P}, title = {Can pharmacokinetic-pharmacodynamic parameters provide dosing regimens that are less vulnerable to resistance?.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {14}, number = {11}, pages = {989-994}, doi = {10.1111/j.1469-0691.2008.02081.x}, pmid = {19040470}, issn = {1469-0691}, mesh = {Anti-Bacterial Agents/administration &amp; dosage/*pharmacokinetics/pharmacology/*therapeutic use ; Bacteria/*drug effects ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Humans ; Mutation ; Selection, Genetic ; }, abstract = {Dissemination of antibiotic resistance in bacteria is associated with prescription of the corresponding drugs. Various pharmacokinetic-pharmacodynamic parameters have been developed with the intention of reducing the spread of resistance. In this review, it is considered whether dosing regimens based on these parameters can delay this spread. The evolution of bacterial resistance to antibiotics involves two successive but distinct and independent mechanisms. The first occurs by mutation in the genome, including the host chromosome and mobile accessory genetic elements such as plasmids or transposons, or, following acquisition of a resistance determinant from another bacterium, by horizontal gene transfer. These two genetic events happen by chance, which means that they do not rely on the presence of an antibiotic in the environment; that is, they are not induced, but simply revealed and propagated by the drugs. The second step is dissemination of resistance which can be due to the spread of bacteria (clonal epidemics), of replicons (plasmid epidemics) or of resistance determinants (gene epidemics). Resistance dissemination by each one of these three levels which superimpose in nature, is not only infectious but also exponential, since all three are associated with DNA replication (duplication) of the host chromosome, of a plasmid, or of a transposon. As opposed to emergence, dissemination is clearly associated with the selective pressure exerted by antibiotic prescription [1,2]. The consequence of this dual evolutionary pathway is that proper use of antibiotics will, at best, delay the spread of resistance. In this review, the pharmacokinetic-pharmacodynamic (PK-PD) parameters that are intended to lower resistance dissemination are considered exclusively.}, }
@article {pmid19038032, year = {2008}, author = {Tuanyok, A and Leadem, BR and Auerbach, RK and Beckstrom-Sternberg, SM and Beckstrom-Sternberg, JS and Mayo, M and Wuthiekanun, V and Brettin, TS and Nierman, WC and Peacock, SJ and Currie, BJ and Wagner, DM and Keim, P}, title = {Genomic islands from five strains of Burkholderia pseudomallei.}, journal = {BMC genomics}, volume = {9}, number = {}, pages = {566}, pmid = {19038032}, issn = {1471-2164}, support = {U01 AI075568/AI/NIAID NIH HHS/United States ; U54 AI065359/AI/NIAID NIH HHS/United States ; U01AI-075568/AI/NIAID NIH HHS/United States ; U54 AI-065359/AI/NIAID NIH HHS/United States ; }, mesh = {Burkholderia mallei/*genetics ; Gene Transfer, Horizontal ; *Genetic Variation ; *Genomic Islands ; RNA, Transfer/genetics ; Terminology as Topic ; }, abstract = {BACKGROUND: Burkholderia pseudomallei is the etiologic agent of melioidosis, a significant cause of morbidity and mortality where this infection is endemic. Genomic differences among strains of B. pseudomallei are predicted to be one of the major causes of the diverse clinical manifestations observed among patients with melioidosis. The purpose of this study was to examine the role of genomic islands (GIs) as sources of genomic diversity in this species.<br><br>RESULTS: We found that genomic islands (GIs) vary greatly among B. pseudomallei strains. We identified 71 distinct GIs from the genome sequences of five reference strains of B. pseudomallei: K96243, 1710b, 1106a, MSHR668, and MSHR305. The genomic positions of these GIs are not random, as many of them are associated with tRNA gene loci. In particular, the 3' end sequences of tRNA genes are predicted to be involved in the integration of GIs. We propose the term "tRNA-mediated site-specific recombination" (tRNA-SSR) for this mechanism. In addition, we provide a GI nomenclature that is based upon integration hotspots identified here or previously described.<br><br>CONCLUSION: Our data suggest that acquisition of GIs is one of the major sources of genomic diversity within B. pseudomallei and the molecular mechanisms that facilitate horizontally-acquired GIs are common across multiple strains of B. pseudomallei. The differential presence of the 71 GIs across multiple strains demonstrates the importance of these mobile elements for shaping the genetic composition of individual strains and populations within this bacterial species.}, }
@article {pmid19037243, year = {2009}, author = {Marchetti, A and Parker, MS and Moccia, LP and Lin, EO and Arrieta, AL and Ribalet, F and Murphy, ME and Maldonado, MT and Armbrust, EV}, title = {Ferritin is used for iron storage in bloom-forming marine pennate diatoms.}, journal = {Nature}, volume = {457}, number = {7228}, pages = {467-470}, pmid = {19037243}, issn = {1476-4687}, mesh = {Binding Sites ; Ceruloplasmin/metabolism ; Crystallography, X-Ray ; Diatoms/chemistry/genetics/growth &amp; development/*metabolism ; *Eutrophication ; Ferritins/*chemistry/genetics/*metabolism ; Gene Transfer, Horizontal ; Iron/*metabolism ; Iron Deficiencies ; Marine Biology ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; RNA, Messenger/analysis/genetics ; Seawater ; }, abstract = {Primary productivity in 30-40% of the world's oceans is limited by availability of the micronutrient iron. Regions with chronically low iron concentrations are sporadically pulsed with new iron inputs by way of dust or lateral advection from continental margins. Addition of iron to surface waters in these areas induces massive phytoplankton blooms dominated primarily by pennate diatoms. Here we provide evidence that the bloom-forming pennate diatoms Pseudo-nitzschia and Fragilariopsis use the iron-concentrating protein, ferritin, to safely store iron. Ferritin has not been reported previously in any member of the Stramenopiles, a diverse eukaryotic lineage that includes unicellular algae, macroalgae and plant parasites. Phylogenetic analyses suggest that ferritin may have arisen in this small subset of diatoms through a lateral gene transfer. The crystal structure and functional assays of recombinant ferritin derived from Pseudo-nitzschia multiseries reveal a maxi-ferritin that exhibits ferroxidase activity and binds iron. The protein is predicted to be targeted to the chloroplast to control the distribution and storage of iron for proper functioning of the photosynthetic machinery. Abundance of Pseudo-nitzschia ferritin transcripts is regulated by iron nutritional status, and is closely tied to the loss and recovery of photosynthetic competence. Enhanced iron storage with ferritin allows the oceanic diatom Pseudo-nitzschia granii to undergo several more cell divisions in the absence of iron than the comparably sized, oceanic centric diatom Thalassiosira oceanica. Ferritin in pennate diatoms probably contributes to their success in chronically low-iron regions that receive intermittent iron inputs, and provides an explanation for the importance of these organisms in regulating oceanic CO(2) over geological timescales.}, }
@article {pmid19036166, year = {2008}, author = {Reyes, JF and Francis, AR and Tanaka, MM}, title = {Models of deletion for visualizing bacterial variation: an application to tuberculosis spoligotypes.}, journal = {BMC bioinformatics}, volume = {9}, number = {}, pages = {496}, pmid = {19036166}, issn = {1471-2105}, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genotype ; *Models, Genetic ; Mycobacterium tuberculosis/*genetics ; *Polymorphism, Genetic ; Repetitive Sequences, Nucleic Acid/genetics ; }, abstract = {BACKGROUND: Molecular typing methods are commonly used to study genetic relationships among bacterial isolates. Many of these methods have become standardized and produce portable data. A popular approach for analyzing such data is to construct graphs, including phylogenies. Inferences from graph representations of data assist in understanding the patterns of transmission of bacterial pathogens, and basing these graph constructs on biological models of evolution of the molecular marker helps make these inferences. Spoligotyping is a widely used method for genotyping isolates of Mycobacterium tuberculosis that exploits polymorphism in the direct repeat region. Our goal was to examine a range of models describing the evolution of spoligotypes in order to develop a visualization method to represent likely relationships among M. tuberculosis isolates.<br><br>RESULTS: We found that inferred mutations of spoligotypes frequently involve the loss of a single or very few adjacent spacers. Using a second-order variant of Akaike's Information Criterion, we selected the Zipf model as the basis for resolving ambiguities in the ancestry of spoligotypes. We developed a method to construct graphs of spoligotypes (which we call spoligoforests). To demonstrate this method, we applied it to a tuberculosis data set from Cuba and compared the method to some existing methods.<br><br>CONCLUSION: We propose a new approach in analyzing relationships of M. tuberculosis isolates using spoligotypes. The spoligoforest recovers a plausible history of transmission and mutation events based on the selected deletion model. The method may be suitable to study markers based on loci of similar structure from other bacteria. The groupings and relationships in the spoligoforest can be analyzed along with the clinical features of strains to provide an understanding of the evolution of spoligotypes.}, }
@article {pmid19036122, year = {2008}, author = {Filée, J and Pouget, N and Chandler, M}, title = {Phylogenetic evidence for extensive lateral acquisition of cellular genes by Nucleocytoplasmic large DNA viruses.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {320}, pmid = {19036122}, issn = {1471-2148}, mesh = {Animals ; DNA/metabolism ; DNA Viruses/*classification/*genetics ; Eukaryota/virology ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/genetics ; Phycodnaviridae/genetics ; *Phylogeny ; }, abstract = {BACKGROUND: Nucleo-Cytoplasmic Large DNA viruses (NCLDV), a diverse group that infects a wide range of eukaryotic hosts, exhibit a large heterogeneity in genome size (between 100 kb and 1.2 Mb) but have been suggested to form a monophyletic group on the basis of a small subset of approximately 30 conserved genes. NCLDV were proposed to have evolved by simplification from cellular organism although some of the giant NCLDV have clearly grown by gene accretion from a bacterial origin.<br><br>RESULTS: We demonstrate here that many NCLDV lineages appear to have undergone frequent gene exchange in two different ways. Viruses which infect protists directly (Mimivirus) or algae which exist as intracellular protists symbionts (Phycodnaviruses) acquire genes from a bacterial source. Metazoan viruses such as the Poxviruses show a predominant acquisition of host genes. In both cases, the laterally acquired genes show a strong tendency to be positioned at the tip of the genome. Surprisingly, several core genes believed to be ancestral in the family appear to have undergone lateral gene transfers, suggesting that the NCLDV ancestor might have had a smaller genome than previously believed. Moreover, our data show that the larger the genome, the higher is the number of laterally acquired genes. This pattern is incompatible with a genome reduction from a cellular ancestor.<br><br>CONCLUSION: We propose that the NCLDV viruses have evolved by significant growth of a simple DNA virus by gene acquisition from cellular sources.}, }
@article {pmid19032158, year = {2008}, author = {Pundhir, S and Vijayvargiya, H and Kumar, A}, title = {PredictBias: a server for the identification of genomic and pathogenicity islands in prokaryotes.}, journal = {In silico biology}, volume = {8}, number = {3-4}, pages = {223-234}, pmid = {19032158}, issn = {1386-6338}, mesh = {Bacillus subtilis/genetics ; Computational Biology/*methods ; Escherichia coli/genetics ; *Genome ; *Genomic Islands ; Software ; User-Computer Interface ; Virulence/genetics ; }, abstract = {Pathogenicity Islands (PAIs) are the sub-sets of Genomic Islands (GIs) that are acquired by horizontal gene transfer (HGT) and are generally shown to have a significant deviation in G+C, dinucleotide or codon frequency from core genome. Major approaches used for PAI identification are based on composition bias and/or similarity with known PAIs. These approaches either limit the search to GIs or to regions similar to previously annotated PAIs. PredictBias is a web application for the identification of genomic and pathogenicity islands in prokaryotes based on composition bias, presence of insertion elements, proximity with virulence-associated genes and absence in related non-pathogenic species. A profile database of virulence factors (VFPD) has been developed using 213 protein families associated to virulence retrieved from Pfam and PRINTS database. PredictBias performs a RPSBLAST search for regions with significant composition bias against VFPD. If a region encodes for at least one protein related to virulence then it is marked as potential PAI (biased-composition) otherwise as GI. Regions involved in virulence but having unsuspicious composition bias due to ancient HGT are identified by scanning genome segments (8 ORFs) with more than four significant hits to VFPD and are marked as potential PAI (unbiased-composition). The relative absence of potential PAIs in related non-pathogenic species can be investigated using 'compare genome feature' of PredictBias that further aids in validating the results and defining boundaries for PAIs. Performance measure analysis showed that the output of PredictBias is in agreement with the known findings. PredictBias is available at www.davvbiotech.res.in/PredictBias.}, }
@article {pmid19028305, year = {2009}, author = {Coton, E and Coton, M}, title = {Evidence of horizontal transfer as origin of strain to strain variation of the tyramine production trait in Lactobacillus brevis.}, journal = {Food microbiology}, volume = {26}, number = {1}, pages = {52-57}, doi = {10.1016/j.fm.2008.07.009}, pmid = {19028305}, issn = {1095-9998}, mesh = {DNA, Bacterial/analysis/genetics ; DNA, Ribosomal/analysis/genetics ; DNA, Ribosomal Spacer/genetics ; Decarboxylation ; Food Microbiology ; *Gene Transfer, Horizontal ; *Genomic Islands ; Levilactobacillus brevis/*genetics/metabolism/physiology ; Molecular Sequence Data ; Operon ; Polymerase Chain Reaction ; *Polymorphism, Genetic ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Random Amplified Polymorphic DNA Technique ; Sequence Analysis, DNA ; Species Specificity ; Tyramine/*metabolism ; Tyrosine Decarboxylase/metabolism ; }, abstract = {Lactobacillus brevis strains with the ability to decarboxylate tyrosine to tyramine have been described and the involvement of several genes constituting a tyrdc operon at the chromosomal level has been demonstrated in this species. In this study, the existence of Lb. brevis strains unable to form tyramine was observed. In order to evaluate if the tyramine-producing ability was strain-dependent or if it could be correlated to the existence of a new species or subspecies, different isolates were analysed. Analysis by M13-RAPD and sequencing of 16S rDNA, 16S-23S ISR and house-keeping gene recA confirmed that all the isolates belonged to the Lb. brevis species. Analysis of the TyrDC pathway encoding operon region in representative strains indicated the existence of a polymorphism. The genetic differences observed showed that the tyrosine decarboxylating ability is not a Lb. brevis species trait but that it is strain-dependent within this species and suggest that the genes encoding the tyramine-producing pathway constitute a genomic island.}, }
@article {pmid19026976, year = {2008}, author = {Suárez-Díaz, E and Anaya-Muñoz, VH}, title = {History, objectivity, and the construction of molecular phylogenies.}, journal = {Studies in history and philosophy of biological and biomedical sciences}, volume = {39}, number = {4}, pages = {451-468}, doi = {10.1016/j.shpsc.2008.09.002}, pmid = {19026976}, issn = {1369-8486}, mesh = {Amino Acid Substitution ; *Classification ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Code ; History, 20th Century ; Models, Genetic ; Molecular Biology/history ; *Phylogeny ; Sequence Alignment/methods ; }, abstract = {Despite the promises made by molecular evolutionists since the early 1960s that phylogenies would be readily reconstructed using molecular data, the construction of molecular phylogenies has both retained many methodological problems of the past and brought up new ones of considerable epistemic relevance. The field is driven not only by changes in knowledge about the processes of molecular evolution, but also by an ever-present methodological anxiety manifested in the constant search for an increased objectivity-or in its converse, the avoidance of subjectivity. This paper offers an exhaustive account of the methodological and conceptual difficulties embedded in each of the steps required to elaborate molecular phytogenies. The authors adopt a historical perspective on the field in order to follow the development of practices that seek to increase the objectivity of their methods and representations. These include the adoption and development of explicit criteria for evaluation of evidence, and of procedures associated with methods of statistical inference, quantification and automation. All these are linked to an increasing use of computers in research since the mid 1960s. We will show that the practices of objectivity described are highly dependent on the problems and tools of molecular phylogenetics.}, }
@article {pmid19025575, year = {2009}, author = {Santagati, M and Lupo, A and Scillato, M and Di Martino, A and Stefani, S}, title = {Conjugal mobilization of the mega element carrying mef(E) from Streptococcus salivarius to Streptococcus pneumoniae.}, journal = {FEMS microbiology letters}, volume = {290}, number = {1}, pages = {79-84}, doi = {10.1111/j.1574-6968.2008.01408.x}, pmid = {19025575}, issn = {0378-1097}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics ; Child, Preschool ; *Conjugation, Genetic ; *DNA Transposable Elements ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Humans ; Macrolides/*pharmacology ; Microbial Sensitivity Tests ; Streptococcus/classification/drug effects/*genetics/isolation &amp; purification ; Streptococcus pneumoniae/drug effects/*genetics ; Tetracycline Resistance ; }, abstract = {We report the isolation and characterization of an unusual strain of Streptococcus salivarius, 3C30, displaying both the macrolide-lincosamide-streptogramin B and the tetracycline resistance phenotypes. It harbours the mef(E), erm(B), and tet(M) genes carried by different genetic elements. The genetic element carrying mef(E), named mega, was investigated by long PCR and sequencing, while the presence of the Tn3872-like element, carrying tet(M) and erm(B), was demonstrated by sequencing of both the int-xis-Tn and the fragment between the two resistance genes. In strain 3C30 the mega element is 5388 bp in size and its nucleotide sequence is identical to that of the element described previously in S. salivarius, with the exception of a 912 bp deletion at the left end. The composite Tn3872-like element appeared to be nonconjugative while the mega element was transferred by conjugation to Streptococcus pneumoniae. It was, however, impossible to transfer it again from these transconjugants to other strains. In addition, only in the 3C30 strain did mega form circular structures, as identified by real-time PCR. In conclusion, we found a clinical strain of S. salivarius carrying both mega and Tn3872-like genetic elements. Mega is transferable by conjugation to S. pneumoniae but it is not transferable again from the transconjugants, suggesting a possible mobilization by recombinases of the coresident Tn3872-like transposon.}, }
@article {pmid19024377, year = {2008}, author = {Wang, H and Xu, YC and Xie, XL and Wang, P and Zhu, RY and Zhang, XJ and Wang, H and Chen, MJ}, title = {[Molecular characterization of vancomycin-resistant Enterococci].}, journal = {Zhongguo yi xue ke xue yuan xue bao. Acta Academiae Medicinae Sinicae}, volume = {30}, number = {5}, pages = {521-524}, pmid = {19024377}, issn = {1000-503X}, mesh = {Bacterial Proteins/genetics ; Bacterial Typing Techniques ; Drug Resistance, Multiple, Bacterial ; Enterococcus faecium/classification/drug effects/*genetics/isolation &amp; purification ; Gram-Positive Bacterial Infections/*microbiology ; Humans ; *Vancomycin Resistance ; }, abstract = {OBJECTIVE: To investigate the homology and resistant mechanism of vancomycin-resistant Enterococci (VRE) isolates.<br><br>METHODS: A total of 9 VRE isolates were collected from 2006 to 2007 at PUMC hospital. The susceptibility of these isolates to 10 different antibiotics including vancomycin was tested by E-test. These strains were processed by brain heart infusion agar screening in the presence of vancomycin (6 microg/ml), and were analyzed for genotypic characteristics using the multiplex PCR. The homology of the isolates was determined by pulsed-field gel electrophoresis (PFGE).<br><br>RESULTS: All the 9 VRE isolates were identified as Enterococci faecium. The visual analysis of PFGE patterns revealed 6 different PFGE types. The vanA gene was confirmed by PCR and sequencing in 9 VRE isolates, which were consistent between phenotype and genotype for glycopeptides resistance.<br><br>CONCLUSIONS: Only vanA genotype was detected in PUMC hospital. Clonal dissemination, horizontal gene transfer, and the selective pressure of antimicrobial agents may contribute to the increase of VRE.}, }
@article {pmid19022197, year = {2008}, author = {Zhou, Q and Wang, W}, title = {On the origin and evolution of new genes--a genomic and experimental perspective.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {35}, number = {11}, pages = {639-648}, doi = {10.1016/S1673-8527(08)60085-5}, pmid = {19022197}, issn = {1673-8527}, mesh = {Animals ; *Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; *Genes ; Genome ; *Genomics ; Humans ; }, abstract = {The inherent interest on the origin of genetic novelties can be traced back to Darwin. But it was not until recently that we were allowed to investigate the fundamental process of origin of new genes by the studies on newly evolved young genes. Two indispensible steps are involved in this process: origin of new gene copies through various mutational mechanisms and evolution of novel functions, which further more leads to fixation of the new copies within populations. The theoretical framework for the former step formed in 1970s. Ohno proposed gene duplication as the most important mechanism producing new gene copies. He also believed that the most common fate for new gene copies is to become pseudogenes. This classical view was validated and was also challenged by the characterization of the first functional young gene jingwei in Drosophila. Recent genome-wide comparison on young genes of Drosophila has elucidated a comprehensive picture addressing remarkable roles of various mechanisms besides gene duplication during origin of new genes. Case surveys revealed it is not rare that new genes would evolve novel structures and functions to contribute to the adaptive evolution of organisms. Here, we review recent advances in understanding how new genes originated and evolved on the basis of genome-wide results and experimental efforts on cases. We would finally discuss the future directions of this fast-growing research field in the context of functional genomics era.}, }
@article {pmid19019219, year = {2008}, author = {Tripathi, LP and Sowdhamini, R}, title = {Genome-wide survey of prokaryotic serine proteases: analysis of distribution and domain architectures of five serine protease families in prokaryotes.}, journal = {BMC genomics}, volume = {9}, number = {}, pages = {549}, pmid = {19019219}, issn = {1471-2164}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Carboxypeptidases/genetics ; Cluster Analysis ; Endopeptidase Clp/genetics ; Gene Transfer, Horizontal ; *Genome ; Genomics ; Phylogeny ; Prokaryotic Cells ; Protease La/genetics ; Serine Endopeptidases/*genetics ; Subtilisin/genetics ; Trypsin/genetics ; }, abstract = {BACKGROUND: Serine proteases are one of the most abundant groups of proteolytic enzymes found in all the kingdoms of life. While studies have established significant roles for many prokaryotic serine proteases in several physiological processes, such as those associated with metabolism, cell signalling, defense response and development, functional associations for a large number of prokaryotic serine proteases are relatively unknown. Current analysis is aimed at understanding the distribution and probable biological functions of the select serine proteases encoded in representative prokaryotic organisms.<br><br>RESULTS: A total of 966 putative serine proteases, belonging to five families, were identified in the 91 prokaryotic genomes using various sensitive sequence search techniques. Phylogenetic analysis reveals several species-specific clusters of serine proteases suggesting their possible involvement in organism-specific functions. Atypical phylogenetic associations suggest an important role for lateral gene transfer events in facilitating the widespread distribution of the serine proteases in the prokaryotes. Domain organisations of the gene products were analysed, employing sensitive sequence search methods, to infer their probable biological functions. Trypsin, subtilisin and Lon protease families account for a significant proportion of the multi-domain representatives, while the D-Ala-D-Ala carboxypeptidase and the Clp protease families are mostly single-domain polypeptides in prokaryotes. Regulatory domains for protein interaction, signalling, pathogenesis, cell adhesion etc. were found tethered to the serine protease domains. Some domain combinations (such as S1-PDZ; LON-AAA-S16 etc.) were found to be widespread in the prokaryotic lineages suggesting a critical role in prokaryotes.<br><br>CONCLUSION: Domain architectures of many serine proteases and their homologues identified in prokaryotes are very different from those observed in eukaryotes, suggesting distinct roles for serine proteases in prokaryotes. Many domain combinations were found unique to specific prokaryotic species, suggesting functional specialisation in various cellular and physiological processes.}, }
@article {pmid19017544, year = {2009}, author = {Park, AK and Kim, H and Jin, HJ}, title = {Comprehensive phylogenetic analysis of evolutionarily conserved rRNA adenine dimethyltransferase suggests diverse bacterial contributions to the nucleus-encoded plastid proteome.}, journal = {Molecular phylogenetics and evolution}, volume = {50}, number = {2}, pages = {282-289}, doi = {10.1016/j.ympev.2008.10.020}, pmid = {19017544}, issn = {1095-9513}, mesh = {Amino Acid Sequence ; Animals ; Archaea/genetics ; Bacteria/genetics ; Bayes Theorem ; *Biological Evolution ; Conserved Sequence ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Likelihood Functions ; Methyltransferases/*genetics ; *Phylogeny ; Plastids/*genetics ; Proteome/genetics ; RNA, Ribosomal/genetics ; Sequence Alignment ; Sequence Analysis, Protein ; }, abstract = {The KsgA/Dim1 protein family of rRNA adenine dimethyltransferase (rAD) is well conserved throughout evolution. This protein family has been recognized to play multiple additional roles: as a mitochondrial transcription factor (mtTFB); as a yeast pre-rRNA cleavage enzyme (Dim1p); and as a chloroplast developmental protein (PFC1). Comprehensive phylogenetic analysis of rAD led to three main findings. First, rAD sequences were grouped by three domains of life, bacteria, archaea, and eukaryotes. Second, mtTFB shows alpha-proteobacterial endosymbiotic ancestry. Third, plastid-targeted rADs do not show cyanobacterial affiliation. Instead, plastid-targeted homologs from chlorophytes/land plants were clustered with chlamydiae, while those from rhodophytes/red algal lineage grouped with the bacteroides/chlorobi group. These unusual two-bacterial ancestries of plastid-targeted rAD suggest that bacterial genes influenced the evolution of the proteome of eukaryotic plastids in a complex way, involving more diverse bacterial groups than previously believed, and underscoring the importance of eukaryotic acquisition of bacterial functions.}, }
@article {pmid19017057, year = {2008}, author = {Sanchez-Perez, GF and Hampl, V and Simpson, AG and Roger, AJ}, title = {A new divergent type of eukaryotic methionine adenosyltransferase is present in multiple distantly related secondary algal lineages.}, journal = {The Journal of eukaryotic microbiology}, volume = {55}, number = {5}, pages = {374-381}, doi = {10.1111/j.1550-7408.2008.00349.x}, pmid = {19017057}, issn = {1550-7408}, mesh = {Amino Acid Sequence ; Animals ; Catalytic Domain ; Dinoflagellida/*enzymology/genetics ; Euglenida/*enzymology/genetics ; Eukaryota/*enzymology/genetics ; Evolution, Molecular ; Methionine Adenosyltransferase/*genetics ; Models, Biological ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Tertiary ; Sequence Homology, Amino Acid ; }, abstract = {S-adenosylmethionine is one of the most important metabolites in living cells and is synthesized in a single reaction catalyzed by methionine adenosyltransferase (MAT). At the sequence and structural level, this enzyme is one of the most conserved proteins known. Here we show that some representatives of three distantly related eukaryotic lineages--dinoflagellates, haptophytes, and euglenids--possess a highly divergent type of MAT, which we call MATX. Even though MATX contains all the sites known to be involved in catalysis and the association of monomers, it also has four insertions throughout the protein that are not observed in other MAT homologs. The phylogenetic distribution and affinities of MATX suggest that it originated in a single eukaryotic lineage and was spread via multiple events of eukaryote-to-eukaryote lateral gene transfer. We suggest a tentative model in which the origin of MATX is connected with the progression of secondary endosymbiosis.}, }
@article {pmid19014489, year = {2008}, author = {McCann, A and Cotton, JA and McInerney, JO}, title = {The tree of genomes: an empirical comparison of genome-phylogeny reconstruction methods.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {312}, pmid = {19014489}, issn = {1471-2148}, mesh = {Algorithms ; Computational Biology/methods ; Databases, Genetic ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, rRNA ; *Genome, Archaeal ; Genomics/*methods ; Likelihood Functions ; Models, Genetic ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: In the past decade or more, the emphasis for reconstructing species phylogenies has moved from the analysis of a single gene to the analysis of multiple genes and even completed genomes. The simplest method of scaling up is to use familiar analysis methods on a larger scale and this is the most popular approach. However, duplications and losses of genes along with horizontal gene transfer (HGT) can lead to a situation where there is only an indirect relationship between gene and genome phylogenies. In this study we examine five widely-used approaches and their variants to see if indeed they are more-or-less saying the same thing. In particular, we focus on Conditioned Reconstruction as it is a method that is designed to work well even if HGT is present.<br><br>RESULTS: We confirm a previous suggestion that this method has a systematic bias. We show that no two methods produce the same results and most current methods of inferring genome phylogenies produce results that are significantly different to other methods.<br><br>CONCLUSION: We conclude that genome phylogenies need to be interpreted differently, depending on the method used to construct them.}, }
@article {pmid19011035, year = {2009}, author = {Pina, S and Olvera, A and Barceló, A and Bensaid, A}, title = {Trimeric autotransporters of Haemophilus parasuis: generation of an extensive passenger domain repertoire specific for pathogenic strains.}, journal = {Journal of bacteriology}, volume = {191}, number = {2}, pages = {576-587}, pmid = {19011035}, issn = {1098-5530}, mesh = {Adhesins, Bacterial/*chemistry/genetics/metabolism ; Animals ; Base Sequence ; Evolution, Molecular ; Haemophilus Infections/microbiology/*veterinary ; Haemophilus parasuis/*chemistry/classification/genetics/*pathogenicity ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Protein Structure, Tertiary ; Sequence Alignment ; Swine ; Swine Diseases/*microbiology ; Virulence Factors/chemistry/genetics/metabolism ; }, abstract = {Haemophilus parasuis is the agent responsible for causing Glässer's disease, but little is known about the pathogenic determinants of this major pig disease. Here we describe, for the pathogenic strain Nagasaki, the molecular characterization of 13 trimeric autotransporters as assessed by the presence of YadA C-terminal translocator domains which were classified into three groups. All passenger domains possess motifs and repeats characteristic of adhesins, hemagglutinins, and invasins with various centrally located copies of collagen-like repeats. This domain architecture is shared with two trimeric autotransporter proteins of H. somnus 129Pt. Genomic comparison by microarray hybridization demonstrated homologies among H. parasuis virulent strains and high divergence with respect to nonvirulent strains. Therefore, these genes were named vtaA (virulence-associated trimeric autotransporters). The sequencing of 17 homologous vtaA genes of different invasive strains highlighted an extensive mosaic structure. Based also on the presence of DNA uptake signal sequences within the vtaA genes, we propose a mechanism of evolution by which gene duplication and the accumulation of mutations and recombinations, plus the lateral gene transfer of the passenger domain, led to the diversity of this multigene family. This study provides insights to help understand the tissue colonization and invasiveness characteristic of H. parasuis pathogenic strains.}, }
@article {pmid19008450, year = {2008}, author = {Kim, M and Cui, ML and Cubas, P and Gillies, A and Lee, K and Chapman, MA and Abbott, RJ and Coen, E}, title = {Regulatory genes control a key morphological and ecological trait transferred between species.}, journal = {Science (New York, N.Y.)}, volume = {322}, number = {5904}, pages = {1116-1119}, doi = {10.1126/science.1164371}, pmid = {19008450}, issn = {1095-9203}, support = {BB-D017742//Biotechnology and Biological Sciences Research Council/United Kingdom ; G10929//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Biological Evolution ; Crosses, Genetic ; Flowers/anatomy &amp; histology/*genetics/growth &amp; development ; *Gene Transfer, Horizontal ; *Genes, Plant ; *Genes, Regulator ; Genotype ; Haplotypes ; *Hybridization, Genetic ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Polymorphism, Genetic ; Selection, Genetic ; Senecio/*genetics/growth &amp; development ; Sequence Analysis, DNA ; }, abstract = {Hybridization between species can lead to introgression of genes from one species to another, providing a potential mechanism for preserving and recombining key traits during evolution. To determine the molecular basis of such transfers, we analyzed a natural polymorphism for flower-head development in Senecio. We show that the polymorphism arose by introgression of a cluster of regulatory genes, the RAY locus, from the diploid species S. squalidus into the tetraploid S. vulgaris. The RAY genes are expressed in the peripheral regions of the inflorescence meristem, where they promote flower asymmetry and lead to an increase in the rate of outcrossing. Our results highlight how key morphological and ecological traits controlled by regulatory genes may be gained, lost, and regained during evolution.}, }
@article {pmid19007916, year = {2009}, author = {Mokrousov, I}, title = {Corynebacterium diphtheriae: genome diversity, population structure and genotyping perspectives.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {9}, number = {1}, pages = {1-15}, doi = {10.1016/j.meegid.2008.09.011}, pmid = {19007916}, issn = {1567-1348}, mesh = {Corynebacterium diphtheriae/*genetics/isolation &amp; purification/pathogenicity ; Diphtheria/epidemiology/*microbiology ; Disease Outbreaks ; Endemic Diseases ; Genetic Techniques ; *Genetic Variation ; *Genome, Bacterial ; Genotype ; Humans ; Periodicity ; Polymerase Chain Reaction ; Ribotyping ; Risk Factors ; Russia ; USSR ; }, abstract = {The epidemic re-emergence of diphtheria in Russia and the Newly Independent States (NIS) of the former Soviet Union in the 1990s demonstrated the continued threat of this thought to be rare disease. The bacteriophage encoded toxin is a main virulence factor of Corynebacterium diphtheriae, however, an analysis of the first complete genome sequence of C. diphtheriae revealed a recent acquisition of other pathogenicity factors including iron-uptake systems, adhesins and fimbrial proteins as indeed this extracellular pathogen has more possibilities for lateral gene transfer than, e.g., its close relative, mainly intracellular Mycobacterium tuberculosis. C. diphtheriae appears to have a phylogeographical structure mainly represented by area-specific variants whose circulation is under strong influence of human host factors, including health control measures, first of all, vaccination, and social economic conditions. This framework core population structure may be challenged by importation of the endemic and eventually toxigenic strains from new areas thus leading to localized or large epidemics caused directly by imported strains or by bacteriophage-lysogenized indigenous strains converted into toxin production. A feature of C. diphtheriae co-existence with humans is its periodicity: following large epidemic in the 1990s, the present period is marked by increasing heterogeneity of the circulating populations whereas re-emergence of new toxigenic variants along with persistent circulation of invasive non-toxigenic strains appear alarming. To identify and rapidly monitor subtle changes in the genome structure at an infraclonal level during and between epidemics, portable and discriminatory typing methods of C. diphtheriae are still needed. In this view, CRISPRs and minisatellites are promising genomic markers for development of high-resolution typing schemes and databasing of C. diphtheriae.}, }
@article {pmid19005186, year = {2009}, author = {Lima, WC and Varani, AM and Menck, CF}, title = {NAD biosynthesis evolution in bacteria: lateral gene transfer of kynurenine pathway in Xanthomonadales and Flavobacteriales.}, journal = {Molecular biology and evolution}, volume = {26}, number = {2}, pages = {399-406}, doi = {10.1093/molbev/msn261}, pmid = {19005186}, issn = {1537-1719}, mesh = {Bacteroidetes/*genetics/*metabolism ; Biosynthetic Pathways ; *Gene Transfer, Horizontal ; Kynurenine/*metabolism ; Phylogeny ; Quinolinic Acid/metabolism ; Xanthomonas/*genetics/*metabolism ; }, abstract = {The biosynthesis of quinolinate, the de novo precursor of nicotinamide adenine dinucleotide (NAD), may be performed by two distinct pathways, namely, the bacterial aspartate (aspartate-to-quinolinate) and the eukaryotic kynurenine (tryptophan-to-quinolinate). Even though the separation into eukaryotic and bacterial routes is long established, recent genomic surveys have challenged this view, because certain bacterial species also carry the genes for the kynurenine pathway. In this work, both quinolinate biosynthetic pathways were investigated in the Bacteria clade and with special attention to Xanthomonadales and Bacteroidetes, from an evolutionary viewpoint. Genomic screening has revealed that a small number of bacterial species possess some of the genes for the kynurenine pathway, which is complete in the genus Xanthomonas and in the order Flavobacteriales, where the aspartate pathway is absent. The opposite pattern (presence of the aspartate pathway and absence of the kynurenine pathway) in close relatives (Xylella ssp. and the order Bacteroidales, respectively) points to the idea of a recent acquisition of the kynurenine pathway through lateral gene transfer in these bacterial groups. In fact, sequence similarity comparison and phylogenetic reconstruction both suggest that at least part of the genes of the kynurenine pathway in Xanthomonas and Flavobacteriales is shared by eukaryotes. These results reinforce the idea of the role that lateral gene transfer plays in the configuration of bacterial genomes, thereby providing alternative metabolic pathways, even with the replacement of primary and essential cell functions, as exemplified by NAD biosynthesis.}, }
@article {pmid19004808, year = {2008}, author = {Rumpho, ME and Worful, JM and Lee, J and Kannan, K and Tyler, MS and Bhattacharya, D and Moustafa, A and Manhart, JR}, title = {Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {46}, pages = {17867-17871}, pmid = {19004808}, issn = {1091-6490}, support = {R01 ES013679/ES/NIEHS NIH HHS/United States ; T32 GM008629/GM/NIGMS NIH HHS/United States ; R01ES013679/ES/NIEHS NIH HHS/United States ; }, mesh = {Algal Proteins/chemistry/*genetics/metabolism ; Amino Acid Sequence ; Animals ; Cell Nucleus/*genetics ; DNA, Mitochondrial/genetics ; Eukaryota/*genetics ; Gastropoda/*genetics ; Gene Expression Regulation ; Gene Transfer, Horizontal/*genetics ; Molecular Sequence Data ; Oceans and Seas ; Photosynthesis/*genetics ; Plastids/genetics ; Recombination, Genetic ; }, abstract = {The sea slug Elysia chlorotica acquires plastids by ingestion of its algal food source Vaucheria litorea. Organelles are sequestered in the mollusc's digestive epithelium, where they photosynthesize for months in the absence of algal nucleocytoplasm. This is perplexing because plastid metabolism depends on the nuclear genome for >90% of the needed proteins. Two possible explanations for the persistence of photosynthesis in the sea slug are (i) the ability of V. litorea plastids to retain genetic autonomy and/or (ii) more likely, the mollusc provides the essential plastid proteins. Under the latter scenario, genes supporting photosynthesis have been acquired by the animal via horizontal gene transfer and the encoded proteins are retargeted to the plastid. We sequenced the plastid genome and confirmed that it lacks the full complement of genes required for photosynthesis. In support of the second scenario, we demonstrated that a nuclear gene of oxygenic photosynthesis, psbO, is expressed in the sea slug and has integrated into the germline. The source of psbO in the sea slug is V. litorea because this sequence is identical from the predator and prey genomes. Evidence that the transferred gene has integrated into sea slug nuclear DNA comes from the finding of a highly diverged psbO 3' flanking sequence in the algal and mollusc nuclear homologues and gene absence from the mitochondrial genome of E. chlorotica. We demonstrate that foreign organelle retention generates metabolic novelty ("green animals") and is explained by anastomosis of distinct branches of the tree of life driven by predation and horizontal gene transfer.}, }
@article {pmid19004239, year = {2008}, author = {Farshad, S and Japoni, A and Hosseini, M}, title = {Low distribution of integrons among multidrug resistant E. coli strains isolated from children with community-acquired urinary tract infections in Shiraz, Iran.}, journal = {Polish journal of microbiology}, volume = {57}, number = {3}, pages = {193-198}, pmid = {19004239}, issn = {1733-1331}, mesh = {Adolescent ; Anti-Bacterial Agents/pharmacology ; Child ; Child, Preschool ; Community-Acquired Infections/*microbiology ; *Drug Resistance, Multiple, Bacterial ; Escherichia coli/*drug effects/genetics ; Escherichia coli Infections/epidemiology/*microbiology ; Female ; Gene Transfer, Horizontal ; Humans ; Infant ; Integrons/*genetics ; Iran/epidemiology ; Male ; }, abstract = {Although integrons by themselves are not mobile, due to their presence in plasmids and transposons, they can be transferred horizontally. For these reasons integrons are a major mechanism for the spread and maintenance of multidrug resistance (MDR). This study describes the distribution of integron gene cassette classes in a collection of uropathogenic Escherichia coli (UPEC) isolated from children with community acquired urinary tract infection in Jahrom, Iran. E. coli strains isolated from urine samples were tested for susceptibility to 14 different antibiotics using the disk diffusion method and for integron classes by RFLP-PCR. Totally 96 strains of E. coli were isolated from urine samples. High prevalence of resistance to ampicillin (80.2%), co-trimoxazole ((76%) and tetracycline (70.8%) was seen among the UPEC isolates. All isolates were 100% sensitive to imipenem. Sixteen strains (16.6%) had the evidence ofintegron sequences with the prevalence of 6.25% (n = 6) and 10.41% (n = 10) for intI1 and intI2, respectively. No intI3 was detected in the isolates. The presence of integrons was significantly associated with resistance to certain antibiotics including gentamicin and ampicillin. Considering the MDR patterns and the low prevalence ofintegrons among the E. coli strains under the study, we suggest that the antibiotic resistance cassettes in these strains presumably are mostly carried on the other transposable elements rather than integrons.}, }
@article {pmid19000309, year = {2008}, author = {Podar, M and Anderson, I and Makarova, KS and Elkins, JG and Ivanova, N and Wall, MA and Lykidis, A and Mavromatis, K and Sun, H and Hudson, ME and Chen, W and Deciu, C and Hutchison, D and Eads, JR and Anderson, A and Fernandes, F and Szeto, E and Lapidus, A and Kyrpides, NC and Saier, MH and Richardson, PM and Rachel, R and Huber, H and Eisen, JA and Koonin, EV and Keller, M and Stetter, KO}, title = {A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans.}, journal = {Genome biology}, volume = {9}, number = {11}, pages = {R158}, pmid = {19000309}, issn = {1474-760X}, support = {//Intramural NIH HHS/United States ; }, mesh = {Biological Transport ; Desulfurococcaceae/*genetics/physiology ; Energy Metabolism ; Gene Transfer, Horizontal ; Genome, Archaeal ; Nanoarchaeota/*genetics/physiology ; Phylogeny ; Symbiosis ; }, abstract = {BACKGROUND: The relationship between the hyperthermophiles Ignicoccus hospitalis and Nanoarchaeum equitans is the only known example of a specific association between two species of Archaea. Little is known about the mechanisms that enable this relationship.<br><br>RESULTS: We sequenced the complete genome of I. hospitalis and found it to be the smallest among independent, free-living organisms. A comparative genomic reconstruction suggests that the I. hospitalis lineage has lost most of the genes associated with a heterotrophic metabolism that is characteristic of most of the Crenarchaeota. A streamlined genome is also suggested by a low frequency of paralogs and fragmentation of many operons. However, this process appears to be partially balanced by lateral gene transfer from archaeal and bacterial sources.<br><br>CONCLUSIONS: A combination of genomic and cellular features suggests highly efficient adaptation to the low energy yield of sulfur-hydrogen respiration and efficient inorganic carbon and nitrogen assimilation. Evidence of lateral gene exchange between N. equitans and I. hospitalis indicates that the relationship has impacted both genomes. This association is the simplest symbiotic system known to date and a unique model for studying mechanisms of interspecific relationships at the genomic and metabolic levels.}, }
@article {pmid19000033, year = {2009}, author = {Zamocky, M and Furtmüller, PG and Bellei, M and Battistuzzi, G and Stadlmann, J and Vlasits, J and Obinger, C}, title = {Intracellular catalase/peroxidase from the phytopathogenic rice blast fungus Magnaporthe grisea: expression analysis and biochemical characterization of the recombinant protein.}, journal = {The Biochemical journal}, volume = {418}, number = {2}, pages = {443-451}, doi = {10.1042/BJ20081478}, pmid = {19000033}, issn = {1470-8728}, mesh = {Catalase/chemistry/*genetics/*isolation &amp; purification/physiology ; Cloning, Molecular ; Cyanides/metabolism ; Enzyme Stability ; Gene Expression Profiling ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Fungal ; Hydrogen-Ion Concentration ; Intracellular Space/enzymology ; Magnaporthe/enzymology/*genetics/physiology ; Models, Molecular ; Oryza/*parasitology ; Peroxidases/chemistry/genetics/isolation &amp; purification/physiology ; Recombinant Proteins/chemistry/genetics/isolation &amp; purification ; Structure-Activity Relationship ; Thermodynamics ; }, abstract = {Phytopathogenic fungi such as the rice blast fungus Magnaporthe grisea are unique in having two catalase/peroxidase (KatG) paralogues located either intracellularly (KatG1) or extracellularly (KatG2). The coding genes have recently been shown to derive from a lateral gene transfer from a (proteo)bacterial genome followed by gene duplication and diversification. Here we demonstrate that KatG1 is expressed constitutively in M. grisea. It is the first eukaryotic catalase/peroxidase to be expressed heterologously in Escherichia coli in high amounts, with high purity and with almost 100% haem occupancy. Recombinant MagKatG1 is an acidic, mainly homodimeric, oxidoreductase with a predominant five-co-ordinated high-spin haem b. At 25 degrees C and pH 7.0, the E(0)' (standard reduction potential) of the Fe(III)/Fe(II) couple was found to be -186+/-10 mV. It bound cyanide monophasically with an apparent bimolecular rate constant of (9.0+/-0.4)x10(5) M(-1).s(-1) at pH 7.0 and at 25 degrees C and with a K(d) value of 1.5 muM. Its predominantly catalase activity was characterized by a pH optimum at 6.0 and k(cat) and K(m) values of 7010 s(-1) and 4.8 mM respectively. In addition, it acts as a versatile peroxidase with a pH optimum in the range 5.0-5.5 using both one-electron [2,2'-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid) o-dianisidine, pyrogallol or guaiacol] and two-electron (Br(-), I(-) or ethanol) donors. Structure-function relationships are discussed with respect to data reported for prokaryotic KatGs, as is the physiological role of MagKatG1. Phylogenetic analysis suggests that (intracellular) MagKatG1 can be regarded as a typical representative for catalase/peroxidase of both phytopathogenic and saprotrophic fungi.}, }
@article {pmid18993034, year = {2009}, author = {Teo, JW and Ng, KY and Lin, RT}, title = {Detection and genetic characterisation of qnrB in hospital isolates of Klebsiella pneumoniae in Singapore.}, journal = {International journal of antimicrobial agents}, volume = {33}, number = {2}, pages = {177-180}, doi = {10.1016/j.ijantimicag.2008.08.019}, pmid = {18993034}, issn = {0924-8579}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/*genetics ; Blotting, Southern ; Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Hospitals ; Humans ; Interspersed Repetitive Sequences ; Klebsiella Infections/*microbiology ; Klebsiella pneumoniae/*drug effects/genetics/isolation &amp; purification ; Molecular Sequence Data ; Plasmids ; Polymerase Chain Reaction ; Quinolones/*pharmacology ; Sequence Analysis, DNA ; Singapore ; }, abstract = {Polymerase chain reaction (PCR) screening of 116 ciprofloxacin-resistant Klebsiella pneumoniae hospital isolates for the presence of qnr genes that mediate plasmid quinolone resistance revealed that none were positive for qnrA or qnrS. However, qnrB was detected in ca. 5.2% of the isolates. Southern hybridisation demonstrated that the qnrB-hybridising plasmids were large (>70kb) and capable of transferring quinolone resistance by conjugation. Sequence analysis of the qnrB genes detected in this study showed that they were identical to previously identified qnrB1, qnrB4 and qnrB6 genes, although a novel variant designated qnrB20 was also identified. Analysis of the genetic environment around the cloned qnrB genes showed that they were present in diverse plasmid backbones, sometimes within novel genetic contexts, but always associated with mobile or transposable elements.}, }
@article {pmid18988686, year = {2009}, author = {Woolfit, M and Iturbe-Ormaetxe, I and McGraw, EA and O'Neill, SL}, title = {An ancient horizontal gene transfer between mosquito and the endosymbiotic bacterium Wolbachia pipientis.}, journal = {Molecular biology and evolution}, volume = {26}, number = {2}, pages = {367-374}, doi = {10.1093/molbev/msn253}, pmid = {18988686}, issn = {1537-1719}, mesh = {Animals ; Culicidae/*genetics/*microbiology/physiology ; Drosophila melanogaster/microbiology ; Gene Transfer, Horizontal ; Phylogeny ; Symbiosis ; Wolbachia/*genetics/physiology ; }, abstract = {The extent and biological relevance of horizontal gene transfer (HGT) in eukaryotic evolution remain highly controversial. Recent studies have demonstrated frequent and large-scale HGT from endosymbiotic bacteria to their hosts, but the great majority of these transferred genes rapidly become nonfunctional in the recipient genome. Here, we investigate an ancient HGT between a host metazoan and an endosymbiotic bacterium, Wolbachia pipientis. The transferred gene has so far been found only in mosquitoes and Wolbachia. In mosquitoes, it is a member of a gene family encoding candidate receptors required for malaria sporozoite invasion of the mosquito salivary gland. The gene copy in Wolbachia has substantially diverged in sequence from the mosquito homolog, is evolving under purifying selection, and is expressed, suggesting that this gene is also functional in the bacterial genome. Several lines of evidence indicate that the gene may have been transferred from eukaryotic host to bacterial endosymbiont. Regardless of the direction of transfer, however, these results demonstrate that interdomain HGT may give rise to functional, persistent, and possibly evolutionarily significant new genes.}, }
@article {pmid18988685, year = {2009}, author = {Battistuzzi, FU and Hedges, SB}, title = {A major clade of prokaryotes with ancient adaptations to life on land.}, journal = {Molecular biology and evolution}, volume = {26}, number = {2}, pages = {335-343}, doi = {10.1093/molbev/msn247}, pmid = {18988685}, issn = {1537-1719}, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; *Biological Evolution ; Phylogeny ; RNA, Ribosomal/genetics ; }, abstract = {Evolutionary trees of prokaryotes usually define the known classes and phyla but less often agree on the relationships among those groups. This has been attributed to the effects of horizontal gene transfer, biases in sequence change, and large evolutionary distances. Furthermore, higher level clades of prokaryote phyla rarely are supported by information from ecology and cell biology. Nonetheless, common patterns are beginning to emerge as larger numbers of species are analyzed with sophisticated methods. Here, we show how combined evidence from phylogenetic, cytological, and environmental data support the existence of an evolutionary group that appears to have had a common ancestor on land early in Earth's history and includes two-thirds of known prokaryote species. Members of this terrestrial clade (Terrabacteria), which includes Cyanobacteria, the gram-positive phyla (Actinobacteria and Firmicutes), and two phyla with cell walls that differ structurally from typical gram-positive and gram-negative phyla (Chloroflexi and Deinococcus-Thermus), possess important adaptations such as resistance to environmental hazards (e.g., desiccation, ultraviolet radiation, and high salinity) and oxygenic photosynthesis. Moreover, the unique properties of the cell wall in gram-positive taxa, which likely evolved in response to terrestrial conditions, have contributed toward pathogenicity in many species. These results now leave open the possibility that terrestrial adaptations may have played a larger role in prokaryote evolution than currently understood.}, }
@article {pmid18983264, year = {2008}, author = {Parker, MS and Mock, T and Armbrust, EV}, title = {Genomic insights into marine microalgae.}, journal = {Annual review of genetics}, volume = {42}, number = {}, pages = {619-645}, doi = {10.1146/annurev.genet.42.110807.091417}, pmid = {18983264}, issn = {0066-4197}, support = {P50 ES012762/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Carbon/metabolism ; Environment ; Eukaryota/*genetics/metabolism ; Gene Transfer, Horizontal ; Genome ; Iron/metabolism ; Marine Biology ; Models, Genetic ; Nitrogen/metabolism ; Phytoplankton/genetics/metabolism ; Ribulose-Bisphosphate Carboxylase/metabolism ; Symbiosis/genetics ; }, abstract = {Marine eukaryotic photosynthesis is dominated by a diverse group of unicellular organisms collectively called microalgae. Microalgae include cells derived from a primary endosymbiotic event (similar to land plants) and cells derived from subsequent secondary and/or tertiary endosymbiotic events. These latter cells are chimeras of several genomes and dominate primary production in the marine environment. Two consequences of multiple endosymbiotic events include complex targeting mechanisms to allow nuclear-encoded proteins to be imported into the plastid and coordination of enzymes, potentially from disparate originator cells, to form complete metabolic pathways. In this review, we discuss the forces that shaped the genomes of marine microalgae and then discuss some of the metabolic consequences of such a complex evolutionary history. We focus our metabolic discussion on carbon, nitrogen, and iron. We then discuss biomineralization and new evidence for programmed cell death in microalgae. We conclude with a short summary on advances in genetic manipulation of microalgae and thoughts on the future directions of marine algal genomics.}, }
@article {pmid18981247, year = {2009}, author = {Tóth, I and Nougayrède, JP and Dobrindt, U and Ledger, TN and Boury, M and Morabito, S and Fujiwara, T and Sugai, M and Hacker, J and Oswald, E}, title = {Cytolethal distending toxin type I and type IV genes are framed with lambdoid prophage genes in extraintestinal pathogenic Escherichia coli.}, journal = {Infection and immunity}, volume = {77}, number = {1}, pages = {492-500}, pmid = {18981247}, issn = {1098-5522}, mesh = {Bacterial Toxins/*genetics/toxicity ; Cloning, Molecular ; DNA, Bacterial/chemistry/*genetics ; Escherichia coli/*genetics/isolation &amp; purification/*virology ; Evolution, Molecular ; Gene Transfer, Horizontal ; HeLa Cells ; Humans ; Molecular Sequence Data ; Prophages/*genetics ; Sequence Analysis, DNA ; }, abstract = {Five types of cytolethal distending toxin (CDT-I to CDT-V) have been identified in Escherichia coli. In the present study we cloned and sequenced the cdt-IV operon and flanking region from a porcine extraintestinal pathogenic E. coli (ExPEC) strain belonging to serogroup O75. We confirmed that similar to other CDTs, CDT-IV induced phosphorylation of host histone H2AX, a sensitive marker of DNA double-strand breaks, and blocked the HeLa cell cycle at the G(2)-M transition. The cdt-IV genes were framed by lambdoid prophage genes. We cloned and sequenced the cdt-I operon and flanking regions from a human ExPEC O18:K1:H7 strain and observed that cdt-I genes were also flanked by lambdoid prophage genes. PCR studies indicated that a gene coding for a putative protease was always associated with the cdtC-IV gene but was not associated with cdtC genes in strains producing CDT-I, CDT-III, and CDT-V. Our results suggest that the cdt-I and cdt-IV genes might have been acquired from a common ancestor by phage transduction and evolved in their bacterial hosts. The lysogenic bacteriophages have the potential to carry nonessential "cargo" genes or "morons" and therefore play a crucial role in the generation of genetic diversity within ExPEC.}, }
@article {pmid18980666, year = {2008}, author = {Kyndt, T and Haegeman, A and Gheysen, G}, title = {Evolution of GHF5 endoglucanase gene structure in plant-parasitic nematodes: no evidence for an early domain shuffling event.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {305}, pmid = {18980666}, issn = {1471-2148}, mesh = {Animals ; Base Sequence ; Cellulase/chemistry/*genetics ; *Evolution, Molecular ; Helminth Proteins/chemistry/*genetics ; Introns ; Models, Genetic ; Molecular Sequence Data ; Nematoda/chemistry/classification/*enzymology/*genetics ; Phylogeny ; Plants/*parasitology ; Protein Structure, Tertiary ; Sequence Alignment ; }, abstract = {BACKGROUND: Endo-1,4-beta-glucanases or cellulases from the glycosyl hydrolase family 5 (GHF5) have been found in numerous bacteria and fungi, and recently also in higher eukaryotes, particularly in plant-parasitic nematodes (PPN). The origin of these genes has been attributed to horizontal gene transfer from bacteria, although there still is a lot of uncertainty about the origin and structure of the ancestral GHF5 PPN endoglucanase. It is not clear whether this ancestral endoglucanase consisted of the whole gene cassette, containing a catalytic domain and a carbohydrate-binding module (CBM, type 2 in PPN and bacteria) or only of the catalytic domain while the CBM2 was retrieved by domain shuffling later in evolution. Previous studies on the evolution of these genes have focused primarily on data of sedentary nematodes, while in this study, extra data from migratory nematodes were included.<br><br>RESULTS: Two new endoglucanases from the migratory nematodes Pratylenchus coffeae and Ditylenchus africanus were included in this study. The latter one is the first gene isolated from a PPN of a different superfamily (Sphaerularioidea); all previously known nematode endoglucanases belong to the superfamily Tylenchoidea (order Rhabditida). Phylogenetic analyses were conducted with the PPN GHF5 endoglucanases and homologous endoglucanases from bacterial and other eukaryotic lineages such as beetles, fungi and plants. No statistical incongruence between the phylogenetic trees deduced from the catalytic domain and the CBM2 was found, which could suggest that both domains have evolved together. Furthermore, based on gene structure data, we inferred a model for the evolution of the GHF5 endoglucanase gene structure in plant-parasitic nematodes. Our data confirm a close relationship between Pratylenchus spp. and the root knot nematodes, while some Radopholus similis endoglucanases are more similar to cyst nematode genes.<br><br>CONCLUSION: We conclude that the ancestral PPN GHF5 endoglucanase gene most probably consisted of the whole gene cassette, i.e. the GHF5 catalytic domain and the CBM2, rather than that it evolved by domain shuffling. Our evolutionary model for the gene structure in PPN GHF5 endoglucanases implies the occurrence of an early duplication event, and more recent gene duplications at genus or species level.}, }
@article {pmid18974830, year = {2008}, author = {Bellafiore, S and Shen, Z and Rosso, MN and Abad, P and Shih, P and Briggs, SP}, title = {Direct identification of the Meloidogyne incognita secretome reveals proteins with host cell reprogramming potential.}, journal = {PLoS pathogens}, volume = {4}, number = {10}, pages = {e1000192}, pmid = {18974830}, issn = {1553-7374}, mesh = {Animals ; Brugia malayi/genetics ; Chromatography, Liquid ; Computational Biology ; Databases, Protein ; Gene Transfer, Horizontal ; Helminth Proteins/chemistry/genetics/*metabolism ; In Situ Hybridization ; Solanum lycopersicum/parasitology ; Mass Spectrometry ; Plant Diseases/genetics/*parasitology ; Plant Roots/growth &amp; development/parasitology ; Proteome/genetics/metabolism ; Proteomics/methods ; Resorcinols/pharmacology ; Tylenchoidea/drug effects/genetics/*metabolism ; }, abstract = {The root knot nematode, Meloidogyne incognita, is an obligate parasite that causes significant damage to a broad range of host plants. Infection is associated with secretion of proteins surrounded by proliferating cells. Many parasites are known to secrete effectors that interfere with plant innate immunity, enabling infection to occur; they can also release pathogen-associated molecular patterns (PAMPs, e.g., flagellin) that trigger basal immunity through the nematode stylet into the plant cell. This leads to suppression of innate immunity and reprogramming of plant cells to form a feeding structure containing multinucleate giant cells. Effectors have generally been discovered using genetics or bioinformatics, but M. incognita is non-sexual and its genome sequence has not yet been reported. To partially overcome these limitations, we have used mass spectrometry to directly identify 486 proteins secreted by M. incognita. These proteins contain at least segmental sequence identity to those found in our 3 reference databases (published nematode proteins; unpublished M. incognita ESTs; published plant proteins). Several secreted proteins are homologous to plant proteins, which they may mimic, and they contain domains that suggest known effector functions (e.g., regulating the plant cell cycle or growth). Others have regulatory domains that could reprogram cells. Using in situ hybridization we observed that most secreted proteins were produced by the subventral glands, but we found that phasmids also secreted proteins. We annotated the functions of the secreted proteins and classified them according to roles they may play in the development of root knot disease. Our results show that parasite secretomes can be partially characterized without cognate genomic DNA sequence. We observed that the M. incognita secretome overlaps the reported secretome of mammalian parasitic nematodes (e.g., Brugia malayi), suggesting a common parasitic behavior and a possible conservation of function between metazoan parasites of plants and animals.}, }
@article {pmid18974220, year = {2008}, author = {Lisch, D}, title = {A new SPIN on horizontal transfer.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {44}, pages = {16827-16828}, pmid = {18974220}, issn = {1091-6490}, mesh = {Animals ; DNA Transposable Elements ; *Gene Transfer, Horizontal ; Humans ; Phylogeny ; }, }
@article {pmid18971358, year = {2009}, author = {Ibrahem, S and Salmenlinna, S and Virolainen, A and Kerttula, AM and Lyytikäinen, O and Jägerroos, H and Broas, M and Vuopio-Varkila, J}, title = {Carriage of methicillin-resistant Staphylococci and their SCCmec types in a long-term-care facility.}, journal = {Journal of clinical microbiology}, volume = {47}, number = {1}, pages = {32-37}, pmid = {18971358}, issn = {1098-660X}, mesh = {Adult ; Aged ; Aged, 80 and over ; Carrier State/*microbiology ; DNA, Bacterial/genetics ; Disease Outbreaks ; Finland/epidemiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Inpatients ; Long-Term Care ; *Methicillin Resistance ; Methicillin-Resistant Staphylococcus aureus/*classification/genetics/*isolation &amp; purification ; Middle Aged ; Nasal Cavity/*microbiology ; Staphylococcal Infections/epidemiology/*microbiology ; Staphylococcus epidermidis/drug effects/*isolation &amp; purification ; }, abstract = {Following an outbreak caused by staphylococcal cassette chromosome mec (SCCmec) type V methicillin (meticillin)-resistant Staphylococcus aureus (MRSA), a point-prevalence survey of the nasal carriage of staphylococci was conducted in a long-term-care facility in northern Finland in 2004. The focus was directed at methicillin-resistant coagulase-negative staphylococci (MR-CNS) and their SCCmec elements. A nasal swab was taken from 76 of the 80 residents 6 months after the onset of the outbreak. Staphylococcal isolates were identified by conventional methods and the GenoType Staphylococcus test, and their SCCmec elements were analyzed. Of the 76 individuals, 24 (32%) carried S. aureus and 67 (88%) CNS in their nostrils. Of the CNS carriers, 41 (61%) had at least one mecA-positive MR-CNS, and two individuals (3%) had both MRSA and methicillin-resistant Staphylococcus epidermidis (MRSE). Among the 61 MR-CNS isolates identified, 49 (80%) were MRSE. The distribution of the SCCmec types was diverse: 20 (33%) were of type IV, 11 (18%) of type V, 4 (6%) of type I or IA, 3 (4%) of type II, and 23 (38%) of new types (with six different combinations of ccr and other mec genes or only mecA). Both of the individuals with MRSA and MRSE shared SCCmec type V among their isolates. Nasal MR-CNS carriage was common among the residents of this long-term-care facility. A variety of SCCmec types, including many new types, were identified among the MR-CNS strains. The horizontal transfer of SCCmec elements is speculated based on the sharing of SCCmec type V between MRSA and MRSE.}, }
@article {pmid18957394, year = {2009}, author = {Trobos, M and Lester, CH and Olsen, JE and Frimodt-Møller, N and Hammerum, AM}, title = {Natural transfer of sulphonamide and ampicillin resistance between Escherichia coli residing in the human intestine.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {63}, number = {1}, pages = {80-86}, doi = {10.1093/jac/dkn437}, pmid = {18957394}, issn = {1460-2091}, mesh = {Adult ; Ampicillin Resistance/*genetics ; Colony Count, Microbial ; DNA Fingerprinting ; DNA, Bacterial/genetics ; *Drug Resistance, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/*physiology ; Feces/microbiology ; *Gene Transfer, Horizontal ; Human Experimentation ; Humans ; Intestines/*microbiology ; Microbial Sensitivity Tests ; Plasmids ; Sequence Analysis, DNA ; Sulfonamides/*pharmacology ; Time Factors ; }, abstract = {OBJECTIVES: The aim of this study was to investigate whether the sulphonamide resistance gene sul2 could be transferred between Escherichia coli in the human gut.<br><br>METHODS: Nine volunteers ingested a 10(9) cfu suspension of sulphonamide-susceptible, rifampicin-resistant E. coli recipients of human origin. Three hours later, they ingested a 10(7) cfu suspension of a sulphonamide-resistant (MIC>1024 mg/L) E. coli donor of pig origin. Stool samples were collected 24 h prior to ingestion, daily for 7 days and at days 14 and 35. Samples were plated on selective plates and monitored for the acquisition of sulphonamide-resistance by the recipient from the indigenous or administrated donor E. coli. Possible transconjugants were typed by PFGE and tested for the presence of plasmids containing the sul2 gene, which was also sequenced.<br><br>RESULTS: Concentrations of the human and animal E. coli reached a maximum of 7.5x10(6) cfu/g faeces and colonized for more than 7 days, and 2x10(8) cfu/g for more than 14 days, respectively. On day 2, a transconjugant was detected in one volunteer. This volunteer was colonized with sulphonamide-resistant E. coli at day 0. The transconjugant was sul2-positive, had an MIC>1024 mg/L for sulfamethoxazole and the same PFGE profile as the recipient. The resident E. coli transferred a plasmid (>63 kb), containing the sul2 gene, to the recipient. The sul2 sequence of the transconjugant was identical to that of the volunteer's own E. coli from day 0, but differed from the animal strain. Co-transfer of ampicillin resistance was also demonstrated.<br><br>CONCLUSIONS: Transfer of sul2 was observed between E. coli bacteria in the human intestine. The transconjugant's sul2 gene came from the volunteer's own flora. The origin of the E. coli donor is unknown.}, }
@article {pmid18953993, year = {2008}, author = {Pertseva, MN and Shpakov, AO}, title = {[Procaryotic genesis and evolution of chemosignaling systems of eukaryotes].}, journal = {Rossiiskii fiziologicheskii zhurnal imeni I.M. Sechenova}, volume = {94}, number = {9}, pages = {1029-1047}, pmid = {18953993}, issn = {0869-8139}, mesh = {Animals ; Archaea/physiology ; Bacterial Physiological Phenomena ; *Biological Evolution ; Eukaryotic Cells/physiology ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome ; Hormones/*physiology ; Pheromones/*physiology ; Quorum Sensing ; *Signal Transduction ; }, abstract = {The analysis of own and literature data accumulated in the last two decades allowed to check and confirm the author's hypothesis about the prokaryotic origin and endosymbiotic genesis of chemosignalling systems of higher eukaryotes. The comparison of structural-functional organization of these information systems and their components (receptors, GTP-binding proteins, enzymes with cyclase activity, protein kinases etc.) in bacteria and eukaryotes revealed a number of similar features giving evidence for their evolutionary relationship. The conclusion was made that eukaryotic signaling systems have prokaryotic roots. The systems of signal transduction revealed in unicellular eukaryotes according to their architecture and functional properties represent a transient stage in the evolution of chemosignalling systems from prokaryotes to higher eukaryotes. The spreading of signalling systems among three super kingdoms--Bacteria, Archaea and Eukarya occurred as a result of horizontal transfer of bacterial genes and co-evolution of signalling components.}, }
@article {pmid18953415, year = {2008}, author = {Foerstner, KU and Doerks, T and Creevey, CJ and Doerks, A and Bork, P}, title = {A computational screen for type I polyketide synthases in metagenomics shotgun data.}, journal = {PloS one}, volume = {3}, number = {10}, pages = {e3515}, pmid = {18953415}, issn = {1932-6203}, mesh = {Animals ; Biolistics/*methods ; *Computational Biology ; *Databases, Genetic ; Decision Trees ; Gene Transfer, Horizontal ; Genomics/methods ; Humans ; Likelihood Functions ; Markov Chains ; Metabolomics/methods ; Phylogeny ; Polyketide Synthases/analysis/*genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Polyketides are a diverse group of biotechnologically important secondary metabolites that are produced by multi domain enzymes called polyketide synthases (PKS).<br><br>We have estimated frequencies of type I PKS (PKS I) - a PKS subgroup - in natural environments by using Hidden-Markov-Models of eight domains to screen predicted proteins from six metagenomic shotgun data sets. As the complex PKS I have similarities to other multi-domain enzymes (like those for the fatty acid biosynthesis) we increased the reliability and resolution of the dataset by maximum-likelihood trees. The combined information of these trees was then used to discriminate true PKS I domains from evolutionary related but functionally different ones. We were able to identify numerous novel PKS I proteins, the highest density of which was found in Minnesota farm soil with 136 proteins out of 183,536 predicted genes. We also applied the protocol to UniRef database to improve the annotation of proteins with so far unknown function and identified some new instances of horizontal gene transfer.<br><br>CONCLUSIONS/SIGNIFICANCE: The screening approach proved powerful in identifying PKS I sequences in large sequence data sets and is applicable to many other protein families.}, }
@article {pmid18953039, year = {2008}, author = {Suzuki, H and Sota, M and Brown, CJ and Top, EM}, title = {Using Mahalanobis distance to compare genomic signatures between bacterial plasmids and chromosomes.}, journal = {Nucleic acids research}, volume = {36}, number = {22}, pages = {e147}, pmid = {18953039}, issn = {1362-4962}, support = {P20 RR016448/RR/NCRR NIH HHS/United States ; P20RR016454/RR/NCRR NIH HHS/United States ; P20RR16448/RR/NCRR NIH HHS/United States ; }, mesh = {Bacillus anthracis/genetics/pathogenicity ; Chromosomes, Bacterial/*chemistry ; Data Interpretation, Statistical ; Drug Resistance, Multiple, Bacterial/genetics ; Escherichia coli O157/genetics/pathogenicity ; *Genome, Bacterial ; Genomics/*methods ; Plasmids/*chemistry ; Virulence ; }, abstract = {Plasmids are ubiquitous mobile elements that serve as a pool of many host beneficial traits such as antibiotic resistance in bacterial communities. To understand the importance of plasmids in horizontal gene transfer, we need to gain insight into the 'evolutionary history' of these plasmids, i.e. the range of hosts in which they have evolved. Since extensive data support the proposal that foreign DNA acquires the host's nucleotide composition during long-term residence, comparison of nucleotide composition of plasmids and chromosomes could shed light on a plasmid's evolutionary history. The average absolute dinucleotide relative abundance difference, termed delta-distance, has been commonly used to measure differences in dinucleotide composition, or 'genomic signature', between bacterial chromosomes and plasmids. Here, we introduce the Mahalanobis distance, which takes into account the variance-covariance structure of the chromosome signatures. We demonstrate that the Mahalanobis distance is better than the delta-distance at measuring genomic signature differences between plasmids and chromosomes of potential hosts. We illustrate the usefulness of this metric for proposing candidate long-term hosts for plasmids, focusing on the virulence plasmids pXO1 from Bacillus anthracis, and pO157 from Escherichia coli O157:H7, as well as the broad host range multi-drug resistance plasmid pB10 from an unknown host.}, }
@article {pmid18953037, year = {2009}, author = {Whitaker, JW and Letunic, I and McConkey, GA and Westhead, DR}, title = {metaTIGER: a metabolic evolution resource.}, journal = {Nucleic acids research}, volume = {37}, number = {Database issue}, pages = {D531-8}, pmid = {18953037}, issn = {1362-4962}, support = {BB/C52101X/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *Databases, Genetic ; Enzymes/*classification/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genomics ; Metabolic Networks and Pathways/*genetics ; Phylogeny ; User-Computer Interface ; }, abstract = {Metabolic networks are a subject that has received much attention, but existing web resources do not include extensive phylogenetic information. Phylogenomic approaches (phylogenetics on a genomic scale) have been shown to be effective in the study of evolution and processes like horizontal gene transfer (HGT). To address the lack of phylogenomic information relating to eukaryotic metabolism, metaTIGER (www.bioinformatics.leeds.ac.uk/metatiger) has been created, using genomic information from 121 eukaryotes and 404 prokaryotes and sensitive sequence search techniques to predict the presence of metabolic enzymes. These enzyme sequences were used to create a comprehensive database of 2257 maximum-likelihood phylogenetic trees, some containing over 500 organisms. The trees can be viewed using iTOL, an advanced interactive tree viewer, enabling straightforward interpretation of large trees. Complex high-throughput tree analysis is also available through user-defined queries, allowing the rapid identification of trees of interest, e.g. containing putative HGT events. metaTIGER also provides novel and easy-to-use facilities for viewing and comparing the metabolic networks in different organisms via highlighted pathway images and tables. metaTIGER is demonstrated through evolutionary analysis of Plasmodium, including identification of genes horizontally transferred from chlamydia.}, }
@article {pmid18950961, year = {2009}, author = {Motro, Y and La, T and Bellgard, MI and Dunn, DS and Phillips, ND and Hampson, DJ}, title = {Identification of genes associated with prophage-like gene transfer agents in the pathogenic intestinal spirochaetes Brachyspira hyodysenteriae, Brachyspira pilosicoli and Brachyspira intermedia.}, journal = {Veterinary microbiology}, volume = {134}, number = {3-4}, pages = {340-345}, doi = {10.1016/j.vetmic.2008.09.051}, pmid = {18950961}, issn = {0378-1135}, mesh = {Bacterial Proteins/genetics ; Brachyspira/*genetics/virology ; Cloning, Molecular ; DNA, Viral/genetics ; Gene Transfer, Horizontal ; Genome, Bacterial ; Phylogeny ; Prophages/*genetics ; Viral Proteins/genetics ; }, abstract = {VSH-1 is an unusual prophage-like gene transfer agent (GTA) that has been described in the intestinal spirochaete Brachyspira hyodysenteriae. The GTA does not self-propagate, but it assembles into a virus-like particle and transfers random 7.5kb fragments of host DNA to other B. hyodysenteriae cells. To date the GTA VSH-1 has only been analysed in B. hyodysenteriae strain B204, in which 11 late function genes encoding prophage capsid, tail and lysis elements have been described. The aim of the current study was to look for these 11 genes in the near-complete genomes of B. hyodysenteriae WA1, B. pilosicoli 95/1000 and B. intermedia HB60. All 11 genes were found in the three new strains. The GTA genes in WA1 and 95/1000 were contiguous, whilst some of those in HB60 were not-although in all three strains some gene rearrangements were present. A new predicted open reading frame with potential functional importance was found in a consistent position associated with all four GTAs, located between the genes for head protein Hvp24 and tail protein Hvp53, overlapping with the hvp24 sequence. Differences in the nucleotide and predicted amino acid sequences of the GTA genes in the spirochaete strains were consistent with the overall genetic distances between the strains. Hence the GTAs in the two B. hyodysenteriae strains were considered to be strain specific variants, and were designated GTA/Bh-B204 and GTA/Bh-WA1 respectively. The GTAs in the strains of B. intermedia and B. pilosicoli were designated GTA/Bint-HB60 and GTA/Bp-95/1000 respectively. Further work is required to determine the extent to which these GTAs can transfer host genes between different Brachyspira species and strains.}, }
@article {pmid18948295, year = {2008}, author = {Koonin, EV and Wolf, YI}, title = {Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world.}, journal = {Nucleic acids research}, volume = {36}, number = {21}, pages = {6688-6719}, pmid = {18948295}, issn = {1362-4962}, support = {//Intramural NIH HHS/United States ; }, mesh = {Archaea/metabolism ; Bacteria/metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; *Genome, Archaeal ; *Genome, Bacterial ; Genomics ; Signal Transduction ; }, abstract = {The first bacterial genome was sequenced in 1995, and the first archaeal genome in 1996. Soon after these breakthroughs, an exponential rate of genome sequencing was established, with a doubling time of approximately 20 months for bacteria and approximately 34 months for archaea. Comparative analysis of the hundreds of sequenced bacterial and dozens of archaeal genomes leads to several generalizations on the principles of genome organization and evolution. A crucial finding that enables functional characterization of the sequenced genomes and evolutionary reconstruction is that the majority of archaeal and bacterial genes have conserved orthologs in other, often, distant organisms. However, comparative genomics also shows that horizontal gene transfer (HGT) is a dominant force of prokaryotic evolution, along with the loss of genetic material resulting in genome contraction. A crucial component of the prokaryotic world is the mobilome, the enormous collection of viruses, plasmids and other selfish elements, which are in constant exchange with more stable chromosomes and serve as HGT vehicles. Thus, the prokaryotic genome space is a tightly connected, although compartmentalized, network, a novel notion that undermines the 'Tree of Life' model of evolution and requires a new conceptual framework and tools for the study of prokaryotic evolution.}, }
@article {pmid18946957, year = {2008}, author = {Saito, N and Konishi, K and Kato, M and Takeda, H and Asaka, M and Ooi, HK}, title = {Coccoid formation as a mechanism of species-preservation in Helicobacter pylori: an ultrastructural study.}, journal = {[Hokkaido igaku zasshi] The Hokkaido journal of medical science}, volume = {83}, number = {5}, pages = {291-295}, pmid = {18946957}, issn = {0367-6102}, mesh = {Extinction, Biological ; Helicobacter pylori/physiology/*ultrastructure ; }, abstract = {Helicobacter pylori (H. pylorii) changes from a spiral form to coccoid by the aggravation of its surrounding environment. It was believed that the coccoid H. pylori indicated to be dying or becoming dormant. However, the implication of coccoid formation, itself, has not yet been elucidated. In this study, both the ultrastructural changes and the localization of the intracellular DNA were observed during coccoid formation in H. pylori. Some coccoid forms were observed to adhere to each other during transformation from the spiral form. The DNA and Cag A in each bacterium were detected at the boundary area of the aggregate, and then mixed in one new coccoid bacterium formed from the syncytium by plural bacteria. This type of coccoid formation was thought to be a transfer phenomenon of intracellular genetic proteins into neighbor organisms. In other words, the coccoid formation of H. pylori means not only the dying or the dormant condition but also a horizontal gene transfer processes with a positive significance for species-preservation under environmental stress.}, }
@article {pmid18941535, year = {2008}, author = {de Andrade Zanotto, PM and Krakauer, DC}, title = {Complete genome viral phylogenies suggests the concerted evolution of regulatory cores and accessory satellites.}, journal = {PloS one}, volume = {3}, number = {10}, pages = {e3500}, pmid = {18941535}, issn = {1932-6203}, mesh = {*Biological Evolution ; DNA Viruses/*genetics ; DNA, Satellite ; DNA-Directed DNA Polymerase/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Viral ; Kinetics ; Linkage Disequilibrium ; Phylogeny ; }, abstract = {We consider the concerted evolution of viral genomes in four families of DNA viruses. Given the high rate of horizontal gene transfer among viruses and their hosts, it is an open question as to how representative particular genes are of the evolutionary history of the complete genome. To address the concerted evolution of viral genes, we compared genomic evolution across four distinct, extant viral families. For all four viral families we constructed DNA-dependent DNA polymerase-based (DdDp) phylogenies and in addition, whole genome sequence, as quantitative descriptions of inter-genome relationships. We found that the history of the polymerase gene was highly predictive of the history of the genome as a whole, which we explain in terms of repeated, co-divergence events of the core DdDp gene accompanied by a number of satellite, accessory genetic loci. We also found that the rate of gene gain in baculovirus and poxviruses proceeds significantly more quickly than the rate of gene loss and that there is convergent acquisition of satellite functions promoting contextual adaptation when distinct viral families infect related hosts. The congruence of the genome and polymerase trees suggests that a large set of viral genes, including polymerase, derive from a phylogenetically conserved core of genes of host origin, secondarily reinforced by gene acquisition from common hosts or co-infecting viruses within the host. A single viral genome can be thought of as a mutualistic network, with the core genes acting as an effective host and the satellite genes as effective symbionts. Larger virus genomes show a greater departure from linkage equilibrium between core and satellites functions.}, }
@article {pmid18940873, year = {2008}, author = {Suzuki, H and Brown, CJ and Forney, LJ and Top, EM}, title = {Comparison of correspondence analysis methods for synonymous codon usage in bacteria.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {15}, number = {6}, pages = {357-365}, pmid = {18940873}, issn = {1756-1663}, support = {P20 RR016448/RR/NCRR NIH HHS/United States ; R01 GM073821-04/GM/NIGMS NIH HHS/United States ; P20RR016454/RR/NCRR NIH HHS/United States ; P20RR16448/RR/NCRR NIH HHS/United States ; R01 GM073821/GM/NIGMS NIH HHS/United States ; P20 RR016448-05/RR/NCRR NIH HHS/United States ; }, mesh = {Bacteria/classification/*genetics ; Base Composition ; Codon/*genetics ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genetic Code ; Genetic Techniques ; Genome, Bacterial ; Rickettsia prowazekii ; }, abstract = {Synonymous codon usage varies both between organisms and among genes within a genome, and arises due to differences in G + C content, replication strand skew, or gene expression levels. Correspondence analysis (CA) is widely used to identify major sources of variation in synonymous codon usage among genes and provides a way to identify horizontally transferred or highly expressed genes. Four methods of CA have been developed based on three kinds of input data: absolute codon frequency, relative codon frequency, and relative synonymous codon usage (RSCU) as well as within-group CA (WCA). Although different CA methods have been used in the past, no comprehensive comparative study has been performed to evaluate their effectiveness. Here, the four CA methods were evaluated by applying them to 241 bacterial genome sequences. The results indicate that WCA is more effective than the other three methods in generating axes that reflect variations in synonymous codon usage. Furthermore, WCA reveals sources that were previously unnoticed in some genomes; e.g. synonymous codon usage related to replication strand skew was detected in Rickettsia prowazekii. Though CA based on RSCU is widely used, our evaluation indicates that this method does not perform as well as WCA.}, }
@article {pmid18937034, year = {2009}, author = {Alexandrov, NN and Brover, VV and Freidin, S and Troukhan, ME and Tatarinova, TV and Zhang, H and Swaller, TJ and Lu, YP and Bouck, J and Flavell, RB and Feldmann, KA}, title = {Insights into corn genes derived from large-scale cDNA sequencing.}, journal = {Plant molecular biology}, volume = {69}, number = {1-2}, pages = {179-194}, pmid = {18937034}, issn = {0167-4412}, mesh = {Alternative Splicing ; Base Sequence ; DNA Primers ; DNA, Complementary/*genetics ; Expressed Sequence Tags ; *Genes, Plant ; Promoter Regions, Genetic ; Transcription, Genetic ; Zea mays/*genetics ; }, abstract = {We present a large portion of the transcriptome of Zea mays, including ESTs representing 484,032 cDNA clones from 53 libraries and 36,565 fully sequenced cDNA clones, out of which 31,552 clones are non-redundant. These and other previously sequenced transcripts have been aligned with available genome sequences and have provided new insights into the characteristics of gene structures and promoters within this major crop species. We found that although the average number of introns per gene is about the same in corn and Arabidopsis, corn genes have more alternatively spliced isoforms. Examination of the nucleotide composition of coding regions reveals that corn genes, as well as genes of other Poaceae (Grass family), can be divided into two classes according to the GC content at the third position in the amino acid encoding codons. Many of the transcripts that have lower GC content at the third position have dicot homologs but the high GC content transcripts tend to be more specific to the grasses. The high GC content class is also enriched with intronless genes. Together this suggests that an identifiable class of genes in plants is associated with the Poaceae divergence. Furthermore, because many of these genes appear to be derived from ancestral genes that do not contain introns, this evolutionary divergence may be the result of horizontal gene transfer from species not only with different codon usage but possibly that did not have introns, perhaps outside of the plant kingdom. By comparing the cDNAs described herein with the non-redundant set of corn mRNAs in GenBank, we estimate that there are about 50,000 different protein coding genes in Zea. All of the sequence data from this study have been submitted to DDBJ/GenBank/EMBL under accession numbers EU940701-EU977132 (FLI cDNA) and FK944382-FL482108 (EST).}, }
@article {pmid18936483, year = {2008}, author = {Pace, JK and Gilbert, C and Clark, MS and Feschotte, C}, title = {Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {44}, pages = {17023-17028}, pmid = {18936483}, issn = {1091-6490}, support = {R01 GM077582/GM/NIGMS NIH HHS/United States ; R01 GM077582-02/GM/NIGMS NIH HHS/United States ; R01GM77582/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; DNA Transposable Elements/*genetics ; Databases, Genetic ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome ; Humans ; Mammals/genetics ; Mice ; Molecular Sequence Data ; Phylogeny ; Rats ; }, abstract = {Horizontal transfer (HT) is central to the evolution of prokaryotic species. Selfish and mobile genetic elements, such as phages, plasmids, and transposons, are the primary vehicles for HT among prokaryotes. In multicellular eukaryotes, the prevalence and evolutionary significance of HT remain unclear. Here, we identified a set of DNA transposon families dubbed SPACE INVADERS (or SPIN) whose consensus sequences are approximately 96% identical over their entire length (2.9 kb) in the genomes of murine rodents (rat/mouse), bushbaby (prosimian primate), little brown bat (laurasiatherian), tenrec (afrotherian), opossum (marsupial), and two non-mammalian tetrapods (anole lizard and African clawed frog). In contrast, SPIN elements were undetectable in other species represented in the sequence databases, including 19 other mammals with draft whole-genome assemblies. This patchy distribution, coupled with the extreme level of SPIN identity in widely divergent tetrapods and the overall lack of selective constraint acting on these elements, is incompatible with vertical inheritance, but strongly indicative of multiple horizontal introductions. We show that these germline infiltrations likely occurred around the same evolutionary time (15-46 mya) and spawned some of the largest bursts of DNA transposon activity ever recorded in any species lineage (nearly 100,000 SPIN copies per haploid genome in tenrec). The process also led to the emergence of a new gene in the murine lineage derived from a SPIN transposase. In summary, HT of DNA transposons has contributed significantly to shaping and diversifying the genomes of multiple mammalian and tetrapod species.}, }
@article {pmid18927089, year = {2008}, author = {Arenas, M and Valiente, G and Posada, D}, title = {Characterization of reticulate networks based on the coalescent with recombination.}, journal = {Molecular biology and evolution}, volume = {25}, number = {12}, pages = {2517-2520}, pmid = {18927089}, issn = {1537-1719}, mesh = {Biological Evolution ; Classification/*methods ; *Phylogeny ; *Recombination, Genetic ; }, abstract = {Phylogenetic networks aim to represent the evolutionary history of taxa. Within these, reticulate networks are explicitly able to accommodate evolutionary events like recombination, hybridization, or lateral gene transfer. Although several metrics exist to compare phylogenetic networks, they make several assumptions regarding the nature of the networks that are not likely to be fulfilled by the evolutionary process. In order to characterize the potential disagreement between the algorithms and the biology, we have used the coalescent with recombination to build the type of networks produced by reticulate evolution and classified them as regular, tree sibling, tree child, or galled trees. We show that, as expected, the complexity of these reticulate networks is a function of the population recombination rate. At small recombination rates, most of the networks produced are already more complex than regular or tree sibling networks, whereas with moderate and large recombination rates, no network fit into any of the standard classes. We conclude that new metrics still need to be devised in order to properly compare two phylogenetic networks that have arisen from reticulating evolutionary process.}, }
@article {pmid18924096, year = {2008}, author = {Creti, R and Baldassarri, L and Montanaro, L and Arciola, CR}, title = {The Alpha-like surface proteins: an example of an expanding family of adhesins.}, journal = {The International journal of artificial organs}, volume = {31}, number = {9}, pages = {834-840}, doi = {10.1177/039139880803100912}, pmid = {18924096}, issn = {0391-3988}, mesh = {Adhesins, Bacterial/genetics/*metabolism ; Animals ; *Bacterial Adhesion/genetics ; Databases, Genetic ; Evolution, Molecular ; Gastrointestinal Tract/*microbiology ; Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; Mutation ; Virulence Factors/genetics/*metabolism ; }, abstract = {The Alpha-like protein (Alp) family, repeat-containing surface proteins once thought to be important adhesion factors confined to pathogenic streptococci and enterococci, is broader than previously known. Analysis of the annotated microbial genomes has identified new potential members of the Alp family not only in other Gram- positive opportunistic pathogens but also in commensal microflora of the human gut and the skin. This finding has highlighted the importance of genome sequencing projects for unraveling in greater detail lateral gene transfer events involving virulence factors between pathogens and commensals. These should receive constant attention not only as part of infectious disease prevention programs, but also in the food and biotechnology industries.}, }
@article {pmid18923456, year = {2009}, author = {Gillings, MR and Xuejun, D and Hardwick, SA and Holley, MP and Stokes, HW}, title = {Gene cassettes encoding resistance to quaternary ammonium compounds: a role in the origin of clinical class 1 integrons?.}, journal = {The ISME journal}, volume = {3}, number = {2}, pages = {209-215}, doi = {10.1038/ismej.2008.98}, pmid = {18923456}, issn = {1751-7370}, mesh = {Bacteria/drug effects/*genetics ; Disinfectants/*pharmacology ; *Drug Resistance, Bacterial ; *Environmental Microbiology ; Evolution, Molecular ; Gene Transfer, Horizontal ; Humans ; *Integrons ; Quaternary Ammonium Compounds/*pharmacology ; }, abstract = {DNA sequencing, phylogenetic and mapping studies suggest that the class 1 integron found in pathogens arose when one member of the diverse family of environmental class 1 integrons became embedded into a Tn402 transposon. However, the timing of this event and the selective forces that first fixed the newly formed element in a bacterial lineage are still unknown. Biocides have a longer use in clinical practice than antibiotics, and a qac (quaternary ammonium compound) resistance gene, or remnant thereof, is a normal feature of class 1 integrons recovered from clinical isolates. Consequently, it is possible that the initial selective advantage was conferred by resistance to biocides, mediated by qac. Here, we show that diverse qac gene cassettes are a dominant feature of cassette arrays from environmental class 1 integrons, and that they occur in the absence of any antibiotic resistance gene cassettes. They are present in arrays that are dynamic, acquiring and rearranging gene cassettes within the arrays. The abundance of qac gene cassettes makes them a likely candidate for participation in the original insertion into Tn402, and as a source of a readily selectable phenotype. More broadly, the increasing use of qac and other biocides at the present time seems likely to promote the fixation of further novel genetic elements, with unpredictable and potentially adverse consequences for human health and agriculture.}, }
@article {pmid18922764, year = {2009}, author = {Goremykin, VV and Salamini, F and Velasco, R and Viola, R}, title = {Mitochondrial DNA of Vitis vinifera and the issue of rampant horizontal gene transfer.}, journal = {Molecular biology and evolution}, volume = {26}, number = {1}, pages = {99-110}, doi = {10.1093/molbev/msn226}, pmid = {18922764}, issn = {1537-1719}, mesh = {Chloroplasts/genetics ; DNA, Chloroplast/genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Mitochondria/genetics ; Mutagenesis, Insertional ; Protein Biosynthesis ; Vitis/cytology/*genetics ; }, abstract = {The mitochondrial genome of grape (Vitis vinifera), the largest organelle genome sequenced so far, is presented. The genome is 773,279 nt long and has the highest coding capacity among known angiosperm mitochondrial DNAs (mtDNAs). The proportion of promiscuous DNA of plastid origin in the genome is also the largest ever reported for an angiosperm mtDNA, both in absolute and relative terms. In all, 42.4% of chloroplast genome of Vitis has been incorporated into its mitochondrial genome. In order to test if horizontal gene transfer (HGT) has also contributed to the gene content of the grape mtDNA, we built phylogenetic trees with the coding sequences of mitochondrial genes of grape and their homologs from plant mitochondrial genomes. Many incongruent gene tree topologies were obtained. However, the extent of incongruence between these gene trees is not significantly greater than that observed among optimal trees for chloroplast genes, the common ancestry of which has never been in doubt. In both cases, we attribute this incongruence to artifacts of tree reconstruction, insufficient numbers of characters, and gene paralogy. This finding leads us to question the recent phylogenetic interpretation of Bergthorsson et al. (2003, 2004) and Richardson and Palmer (2007) that rampant HGT into the mtDNA of Amborella best explains phylogenetic incongruence between mitochondrial gene trees for angiosperms. The only evidence for HGT into the Vitis mtDNA found involves fragments of two coding sequences stemming from two closteroviruses that cause the leaf roll disease of this plant. We also report that analysis of sequences shared by both chloroplast and mitochondrial genomes provides evidence for a previously unknown gene transfer route from the mitochondrion to the chloroplast.}, }
@article {pmid18852109, year = {2008}, author = {Galtier, N and Daubin, V}, title = {Dealing with incongruence in phylogenomic analyses.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {363}, number = {1512}, pages = {4023-4029}, pmid = {18852109}, issn = {1471-2970}, mesh = {Bacteria/*genetics ; Databases, Genetic ; Gene Transfer, Horizontal/*genetics ; Genomics/*methods ; *Phylogeny ; *Research Design ; }, abstract = {Incongruence between gene trees is the main challenge faced by phylogeneticists in the genomic era. Incongruence can occur for artefactual reasons, when we fail to recover the correct gene trees, or for biological reasons, when true gene trees are actually distinct from each other, and from the species tree. Horizontal gene transfers (HGTs) between genomes are an important process of bacterial evolution resulting in a substantial amount of phylogenetic conflicts between gene trees. We argue that the (bacterial) species tree is still a meaningful scientific concept even in the case of HGTs, and that reconstructing it is still a valid goal. We tentatively assess the amount of phylogenetic incongruence caused by HGTs in bacteria by comparing bacterial datasets to a metazoan dataset in which transfers are presumably very scarce or absent.We review existing phylogenomic methods and their ability to return to the user, both the vertical (speciation/extinction history) and horizontal (gene transfers) phylogenetic signals.}, }
@article {pmid18852099, year = {2008}, author = {Cohen, O and Rubinstein, ND and Stern, A and Gophna, U and Pupko, T}, title = {A likelihood framework to analyse phyletic patterns.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {363}, number = {1512}, pages = {3903-3911}, pmid = {18852099}, issn = {1471-2970}, mesh = {Bayes Theorem ; Computer Simulation ; Data Interpretation, Statistical ; *Evolution, Molecular ; Likelihood Functions ; Markov Chains ; *Models, Genetic ; Multigene Family/genetics ; Mutation/genetics ; *Phylogeny ; Species Specificity ; }, abstract = {Probabilistic evolutionary models revolutionized our capability to extract biological insights from sequence data. While these models accurately describe the stochastic processes of site-specific substitutions, single-base substitutions represent only a fraction of all the events that shape genomes. Specifically, in microbes, events in which entire genes are gained (e.g. via horizontal gene transfer) and lost play a pivotal evolutionary role. In this research, we present a novel likelihood-based evolutionary model for gene gains and losses, and use it to analyse genome-wide patterns of the presence and absence of gene families. The model assumes a Markovian stochastic process, where gains and losses are represented by the transition between presence and absence, respectively, given an underlying phylogenetic tree. To account for differences in the rates of gain and loss of different gene families, we assume among-gene family rate variability, thus allowing for more accurate description of the data. Using the Bayesian approach, we estimated an evolutionary rate for each gene family. Simulation studies demonstrated that our methodology accurately infers these rates. Our methodology was applied to analyse a large corpus of data, consisting of 4873 gene families spanning 63 species and revealed novel insights regarding the evolutionary nature of genome-wide gain and loss dynamics.}, }
@article {pmid18850059, year = {2008}, author = {Kellmann, R and Mihali, TK and Neilan, BA}, title = {Identification of a saxitoxin biosynthesis gene with a history of frequent horizontal gene transfers.}, journal = {Journal of molecular evolution}, volume = {67}, number = {5}, pages = {526-538}, pmid = {18850059}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins/*genetics ; Carboxyl and Carbamoyl Transferases/*genetics ; Cyanobacteria/*genetics/metabolism ; Databases, Genetic ; *Evolution, Molecular ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Marine Toxins/biosynthesis/genetics ; Metabolic Networks and Pathways/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Saxitoxin/*biosynthesis/genetics ; }, abstract = {The paralytic shellfish poisoning (PSP) toxins, saxitoxin, and its derivatives, are produced by a complex and unique biosynthetic pathway. It involves reactions that are rare in other metabolic pathways, however, distantly related organisms, such as dinoflagellates and cyanobacteria, produce these toxins by an identical pathway. Speculative explanations for the unusual phylogenetic distribution of this metabolic pathway have been proposed, including a polyphyletic origin, the involvement of symbiotic bacteria, and horizontal gene transfer. This study describes for the first time the identity of one gene, sxt1, that is involved in the biosynthesis of saxitoxin in cyanobacteria. It encoded an O-carbamoyltransferase (OCTASE) that was proposed to carbamoylate the hydroxymethyl side chain of saxitoxin precursor. Orthologues of sxt1 were exclusively present in PSP-toxic strains of cyanobacteria and had a high sequence similarity to each other. L. wollei had a naturally mutated sxt1 gene that encoded an inactive enzyme, and was incapable of producing carbamoylated PSP-toxin analogues, supporting the proposed function of Sxt1. Phylogenetic analysis revealed that OCATSE genes were present exclusively in prokaryotic organisms and were characterized by a high rate of horizontal gene transfer. OCTASE has most likely evolved from an ancestral O-sialoglycoprotein endopeptidase from proteobacteria, whereas the most likely phylogenetic origin of sxt1 was an ancestral alpha-proteobacterium. The phylogeny of sxt1 suggested that the entire set of genes required for saxitoxin biosynthesis may spread by horizontal gene transfer.}, }
@article {pmid18849060, year = {2009}, author = {Li, MN and Zheng, GH and Wang, L and Xiao, W and Fu, XH and Le, YQ and Ren, DM}, title = {Evaluation of the effectiveness and safety of the thermo-treatment process to dispose of recombinant DNA waste from biological research laboratories.}, journal = {The Science of the total environment}, volume = {407}, number = {2}, pages = {791-797}, doi = {10.1016/j.scitotenv.2008.08.024}, pmid = {18849060}, issn = {0048-9697}, mesh = {China ; DNA, Recombinant/*isolation &amp; purification/metabolism/toxicity ; Electrophoresis ; *Heating ; *Laboratories ; Osmolar Concentration ; Plasmids ; Polymerase Chain Reaction ; *Research ; Safety Management/*methods ; Time Factors ; Waste Management/*methods ; }, abstract = {The discharge of recombinant DNA waste from biological laboratories into the eco-system may be one of the pathways resulting in horizontal gene transfer or "gene pollution". Heating at 100 degrees C for 5-10 min is a common method for treating recombinant DNA waste in biological research laboratories in China. In this study, we evaluated the effectiveness and the safety of the thermo-treatment method in the disposal of recombinant DNA waste. Quantitative PCR, plasmid transformation and electrophoresis technology were used to evaluate the decay/denaturation efficiency during the thermo-treatment process of recombinant plasmid, pET-28b. Results showed that prolonging thermo-treatment time could improve decay efficiency of the plasmid, and its decay half-life was 2.7-4.0 min during the thermo-treatment at 100 degrees C. However, after 30 min of thermo-treatment some transforming activity remained. Higher ionic strength could protect recombinant plasmid from decay during the treatment process. These results indicate that thermo-treatment at 100 degrees C cannot decay and inactivate pET-28b completely. In addition, preliminary results showed that thermo-treated recombinant plasmids were not degraded completely in a short period when they were discharged into an aquatic environment. This implies that when thermo-treated recombinant DNAs are discharged into the eco-system, they may have enough time to re-nature and transform, thus resulting in gene diffusion.}, }
@article {pmid18847408, year = {2008}, author = {Pallecchi, L and Bartoloni, A and Paradisi, F and Rossolini, GM}, title = {Antibiotic resistance in the absence of antimicrobial use: mechanisms and implications.}, journal = {Expert review of anti-infective therapy}, volume = {6}, number = {5}, pages = {725-732}, doi = {10.1586/14787210.6.5.725}, pmid = {18847408}, issn = {1744-8336}, mesh = {Animals ; Animals, Wild/*microbiology ; Chromosomes, Bacterial/genetics ; *Drug Resistance, Bacterial/genetics ; Enterobacteriaceae/drug effects/genetics ; Gene Transfer, Horizontal ; Humans ; Mutation ; Plasmids/genetics ; }, abstract = {The selective pressure generated by the use of antibiotics in clinical, veterinary, husbandry and agricultural practices is considered the major factor responsible for the emergence and spread of antibiotic-resistant bacteria since the beginning of the antibiotic era. However, recent studies have consistently demonstrated that acquired resistance traits can also be found in bacteria isolated from humans and wild animals not subjected to significant antibiotic exposure and living in remote areas of the planet. The scope of this article is to review and discuss the current knowledge on this intriguing phenomenon, which underscores the complexity of the mechanisms involved in the emergence and spread of antibiotic resistance and bears some relevant implications to the design and success of resistance-control strategies.}, }
@article {pmid18844996, year = {2008}, author = {Stabler, RA and Dawson, LF and Oyston, PC and Titball, RW and Wade, J and Hinds, J and Witney, AA and Wren, BW}, title = {Development and application of the active surveillance of pathogens microarray to monitor bacterial gene flux.}, journal = {BMC microbiology}, volume = {8}, number = {}, pages = {177}, pmid = {18844996}, issn = {1471-2180}, support = {062511/WT_/Wellcome Trust/United Kingdom ; G0300020/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Bacteria/*genetics/isolation &amp; purification/*pathogenicity ; Bacterial Infections/*microbiology ; Bacterial Proteins/*genetics/metabolism ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial ; Humans ; Oligonucleotide Array Sequence Analysis/*methods ; Virulence ; Virulence Factors ; }, abstract = {BACKGROUND: Human and animal health is constantly under threat by emerging pathogens that have recently acquired genetic determinants that enhance their survival, transmissibility and virulence. We describe the construction and development of an Active Surveillance of Pathogens (ASP) oligonucleotide microarray, designed to 'actively survey' the genome of a given bacterial pathogen for virulence-associated genes.<br><br>RESULTS: The microarray consists of 4958 reporters from 151 bacterial species and include genes for the identification of individual bacterial species as well as mobile genetic elements (transposons, plasmid and phage), virulence genes and antibiotic resistance genes. The ASP microarray was validated with nineteen bacterial pathogens species, including Francisella tularensis, Clostridium difficile, Staphylococcus aureus, Enterococcus faecium and Stenotrophomonas maltophilia. The ASP microarray identified these bacteria, and provided information on potential antibiotic resistance (eg sufamethoxazole resistance and sulfonamide resistance) and virulence determinants including genes likely to be acquired by horizontal gene transfer (e.g. an alpha-haemolysin).<br><br>CONCLUSION: The ASP microarray has potential in the clinic as a diagnostic tool, as a research tool for both known and emerging pathogens, and as an early warning system for pathogenic bacteria that have been recently modified either naturally or deliberately.}, }
@article {pmid18840511, year = {2008}, author = {Rooney, AP and Ward, TJ}, title = {Birth-and-death evolution of the internalin multigene family in Listeria.}, journal = {Gene}, volume = {427}, number = {1-2}, pages = {124-128}, doi = {10.1016/j.gene.2008.09.007}, pmid = {18840511}, issn = {0378-1119}, mesh = {Bacterial Proteins/*genetics/metabolism ; Evolution, Molecular ; Gene Duplication ; Genes, Bacterial ; *Genetic Techniques ; Genome, Bacterial ; Listeria monocytogenes/*genetics ; Membrane Proteins/genetics/*metabolism ; Models, Biological ; Models, Genetic ; Multigene Family ; Phylogeny ; }, abstract = {The birth-and-death model of multigene family evolution describes patterns of gene origination, diversification and loss within multigene families. Since it was first developed in the 1990s, the model has been found to characterize a large number of eukaryotic multigene families. In this paper, we report for the first time a bacterial multigene family that undergoes birth-and-death evolution. By analyzing the evolutionary relationships among internalins, a relatively large and diverse family of genes associated with key virulence functions in Listeria, we demonstrate the importance of birth-and-death evolution in the diversification of this important bacterial pathogen. We also detected two instances of lateral gene transfer within the internalins, but the estimated frequency would have been much higher had it not been analyzed within the context of birth-and-death evolutionary dynamics and a phenomenon that we term "paralog-sorting", which involves the unequal transmittal of gene duplicates during or subsequent to the speciation process. As such, in addition to providing the first demonstration of birth-and-death evolution within a bacterial multigene family, our results indicate that the extent of lateral transfer in bacterial multigene families should be re-examined in the light of birth-and-death evolution.}, }
@article {pmid18840280, year = {2008}, author = {Podell, S and Gaasterland, T and Allen, EE}, title = {A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm.}, journal = {BMC bioinformatics}, volume = {9}, number = {}, pages = {419}, pmid = {18840280}, issn = {1471-2105}, mesh = {Algorithms ; Amino Acid Sequence ; Base Composition/genetics ; Databases, Genetic ; Evolution, Molecular ; *Gene Transfer, Horizontal/genetics ; *Genome, Archaeal ; *Genome, Bacterial ; Neural Networks, Computer ; *Phylogeny ; Probability ; Proteins/genetics ; Sequence Analysis, DNA ; *User-Computer Interface ; }, abstract = {BACKGROUND: The process of horizontal gene transfer (HGT) is believed to be widespread in Bacteria and Archaea, but little comparative data is available addressing its occurrence in complete microbial genomes. Collection of high-quality, automated HGT prediction data based on phylogenetic evidence has previously been impractical for large numbers of genomes at once, due to prohibitive computational demands. DarkHorse, a recently described statistical method for discovering phylogenetically atypical genes on a genome-wide basis, provides a means to solve this problem through lineage probability index (LPI) ranking scores. LPI scores inversely reflect phylogenetic distance between a test amino acid sequence and its closest available database matches. Proteins with low LPI scores are good horizontal gene transfer candidates; those with high scores are not.<br><br>DESCRIPTION: The DarkHorse algorithm has been applied to 955 microbial genome sequences, and the results organized into a web-searchable relational database, called the DarkHorse HGT Candidate Resource http://darkhorse.ucsd.edu. Users can select individual genomes or groups of genomes to screen by LPI score, search for protein functions by descriptive annotation or amino acid sequence similarity, or select proteins with unusual G+C composition in their underlying coding sequences. The search engine reports LPI scores for match partners as well as query sequences, providing the opportunity to explore whether potential HGT donor sequences are phylogenetically typical or atypical within their own genomes. This information can be used to predict whether or not sufficient information is available to build a well-supported phylogenetic tree using the potential donor sequence.<br><br>CONCLUSION: The DarkHorse HGT Candidate database provides a powerful, flexible set of tools for identifying phylogenetically atypical proteins, allowing researchers to explore both individual HGT events in single genomes, and large-scale HGT patterns among protein families and genome groups. Although the DarkHorse algorithm cannot, by itself, provide definitive proof of horizontal gene transfer, it is a flexible, powerful tool that can be combined with slower, more rigorous methods in situations where these other methods could not otherwise be applied.}, }
@article {pmid18838147, year = {2008}, author = {Serfiotis-Mitsa, D and Roberts, GA and Cooper, LP and White, JH and Nutley, M and Cooper, A and Blakely, GW and Dryden, DT}, title = {The Orf18 gene product from conjugative transposon Tn916 is an ArdA antirestriction protein that inhibits type I DNA restriction-modification systems.}, journal = {Journal of molecular biology}, volume = {383}, number = {5}, pages = {970-981}, doi = {10.1016/j.jmb.2008.06.005}, pmid = {18838147}, issn = {1089-8638}, support = {B20089/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/D001870/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; GR080463MA/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacterial Proteins/chemistry/*metabolism ; Binding, Competitive ; Calorimetry, Differential Scanning ; Chromatography, Gel ; Chromatography, High Pressure Liquid ; Chromosomes, Bacterial/metabolism ; DNA Restriction-Modification Enzymes/*antagonists &amp; inhibitors ; DNA Transposable Elements/*genetics ; DNA, Bacterial/metabolism ; Electrophoresis, Polyacrylamide Gel ; Enterococcus faecalis/*metabolism ; Molecular Weight ; Open Reading Frames/genetics ; Protein Folding ; Protein Structure, Secondary ; Recombinant Proteins/metabolism ; Site-Specific DNA-Methyltransferase (Adenine-Specific)/antagonists &amp; inhibitors ; Spectrometry, Fluorescence ; Thermodynamics ; }, abstract = {Gene orf18, which is situated within the intercellular transposition region of the conjugative transposon Tn916 from the bacterial pathogen Enterococcus faecalis, encodes a putative ArdA (alleviation of restriction of DNA A) protein. Conjugative transposons are generally resistant to DNA restriction upon transfer to a new host. ArdA from Tn916 may be responsible for the apparent immunity of the transposon to DNA restriction and modification (R/M) systems and for ensuring that the transposon has a broad host range. The orf18 gene was engineered for overexpression in Escherichia coli, and the recombinant ArdA protein was purified to homogeneity. The protein appears to exist as a dimer at nanomolar concentrations but can form larger assemblies at micromolar concentrations. R/M assays revealed that ArdA can efficiently inhibit R/M by all four major classes of Type I R/M enzymes both in vivo and in vitro. These R/M systems are present in over 50% of sequenced prokaryotic genomes. Our results suggest that ArdA can overcome the restriction barrier following conjugation and so helps increase the spread of antibiotic resistance genes by horizontal gene transfer.}, }
@article {pmid18834516, year = {2008}, author = {Boussau, B and Guéguen, L and Gouy, M}, title = {Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {272}, pmid = {18834516}, issn = {1471-2148}, mesh = {Bacteria/*classification/*genetics ; Classification/methods ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial/*genetics ; *Phylogeny ; }, abstract = {BACKGROUND: Despite a large agreement between ribosomal RNA and concatenated protein phylogenies, the phylogenetic tree of the bacterial domain remains uncertain in its deepest nodes. For instance, the position of the hyperthermophilic Aquificales is debated, as their commonly observed position close to Thermotogales may proceed from horizontal gene transfers, long branch attraction or compositional biases, and may not represent vertical descent. Indeed, another view, based on the analysis of rare genomic changes, places Aquificales close to epsilon-Proteobacteria.<br><br>RESULTS: To get a whole genome view of Aquifex relationships, all trees containing sequences from Aquifex in the HOGENOM database were surveyed. This study revealed that Aquifex is most often found as a neighbour to Thermotogales. Moreover, informational genes, which appeared to be less often transferred to the Aquifex lineage than non-informational genes, most often placed Aquificales close to Thermotogales. To ensure these results did not come from long branch attraction or compositional artefacts, a subset of carefully chosen proteins from a wide range of bacterial species was selected for further scrutiny. Among these genes, two phylogenetic hypotheses were found to be significantly more likely than the others: the most likely hypothesis placed Aquificales as a neighbour to Thermotogales, and the second one with epsilon-Proteobacteria. We characterized the genes that supported each of these two hypotheses, and found that differences in rates of evolution or in amino-acid compositions could not explain the presence of two incongruent phylogenetic signals in the alignment. Instead, evidence for a large Horizontal Gene Transfer between Aquificales and epsilon-Proteobacteria was found.<br><br>CONCLUSION: Methods based on concatenated informational proteins and methods based on character cladistics led to different conclusions regarding the position of Aquificales because this lineage has undergone many horizontal gene transfers. However, if a tree of vertical descent can be reconstructed for Bacteria, our results suggest Aquificales should be placed close to Thermotogales.}, }
@article {pmid18830745, year = {2009}, author = {Garcia-Migura, L and Hasman, H and Jensen, LB}, title = {Presence of pRI1: a small cryptic mobilizable plasmid isolated from Enterococcus faecium of human and animal origin.}, journal = {Current microbiology}, volume = {58}, number = {2}, pages = {95-100}, pmid = {18830745}, issn = {1432-0991}, mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins/genetics ; Chickens/*microbiology ; Conjugation, Genetic ; Enterococcus faecium/*genetics/isolation &amp; purification ; *Gene Transfer, Horizontal ; Gram-Positive Bacterial Infections/*microbiology ; Humans ; Molecular Sequence Data ; Plasmids/*genetics/isolation &amp; purification ; Replication Origin ; Sequence Homology, Amino Acid ; Swine/*microbiology ; }, abstract = {This study focused on the molecular characterization of a small cryptic, mobilizable plasmid (6038 bp) sequenced from an E. faecium 9631160-1 of poultry origin. Sequence analysis of pRI1 revealed seven open reading frames. pRI1 contained an IS 100% identical to ISEfa4. This insertion element disrupted a putative mobilization gene (mobA) which presented 99% similarity to the one described in plasmid pJS42 (NC_010291). pRI1 harbored a cluster of four coding sequences which exhibited a homology to those described in contig 658 (from nucleotide 8940 to nt 10515) of E. faecium DO. In addition, a rep almost identical to the repA from the pEFNP1 and pKQ10 plasmids from E. faecium was also identified. Presence of the pRI1 replication initiation gene (rep) was analyzed in a panel of 159 E. faecium isolates of human and animal origin from different European countries, of which 60 tested positive for the presence of pRI1-rep. Conjugation experiments verified transfer of the pRI1 together with conjugative plasmids harboring resistance to vancomycin and streptogramin. The presence of pRI1 in enterococcal isolates geographically separated and from different origin demonstrates the ability of enterococci to acquire and transfer mobile genetic elements, emphasizing the need for further studies to reveal the meaning and role that these cryptic plasmids play in nature.}, }
@article {pmid18830684, year = {2009}, author = {von Rozycki, T and Nies, DH}, title = {Cupriavidus metallidurans: evolution of a metal-resistant bacterium.}, journal = {Antonie van Leeuwenhoek}, volume = {96}, number = {2}, pages = {115-139}, doi = {10.1007/s10482-008-9284-5}, pmid = {18830684}, issn = {1572-9699}, mesh = {Bacterial Proteins/genetics ; Cupriavidus/*drug effects/genetics/metabolism ; Drug Resistance, Bacterial/*genetics ; *Evolution, Molecular ; Metals, Heavy/*pharmacology ; }, abstract = {Cupriavidus metallidurans CH34 has gained increasing interest as a model organism for heavy metal detoxification and for biotechnological purposes. Resistance of this bacterium to transition metal cations is predominantly based on metal resistance determinants that contain genes for RND (resistance, nodulation, and cell division protein family) proteins. These are part of transenvelope protein complexes, which seem to detoxify the periplasm by export of toxic metal cations from the periplasm to the outside. Strain CH34 contains 12 predicted RND proteins belonging to a protein family of heavy metal exporters. Together with many efflux systems that detoxify the cytoplasm, regulators and possible metal-binding proteins, RND proteins mediate an efficient defense against transition metal cations. To shed some light into the origin of genes encoding these proteins, the genomes of C. metallidurans CH34 and six related proteobacteria were investigated for occurrence of orthologous and paralogous proteins involved in metal resistance. Strain CH34 was not much different from the other six bacteria when the total content of transport proteins was compared but CH34 had significantly more putative transition metal transport systems than the other bacteria. The genes for these systems are located on its chromosome 2 but especially on plasmids pMOL28 and pMOL30. Cobalt-nickel and chromate resistance determinants located on plasmid pMOL28 evolved by gene duplication and horizontal gene transfer events, leading to a better adaptation of strain CH34 to serpentine-like soils. The czc cobalt-zinc-cadmium resistance determinant, located on plasmid pMOL30 in addition copper, lead and mercury resistance determinants, arose by duplication of a czcICAB core determinant on chromosome 2, plus addition of the czcN gene upstream and the genes czcD, czcRS, czcE downstream of czcICBA. C. metallidurans apparently evolved metal resistance by horizontal acquisition and by duplication of genes for transition metal efflux, mostly on the two plasmids, and decreased the number of uptake systems for those metals.}, }
@article {pmid18822386, year = {2008}, author = {Maiden, MC}, title = {Population genomics: diversity and virulence in the Neisseria.}, journal = {Current opinion in microbiology}, volume = {11}, number = {5}, pages = {467-471}, pmid = {18822386}, issn = {1369-5274}, support = {047072//Wellcome Trust/United Kingdom ; }, mesh = {Base Sequence ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Variation ; Genome, Bacterial ; Genomics ; Humans ; Neisseria gonorrhoeae/*genetics/*pathogenicity ; Neisseria lactamica/*genetics/*pathogenicity ; Neisseria meningitidis/*genetics/*pathogenicity ; Recombination, Genetic ; Virulence Factors/*biosynthesis/genetics ; }, abstract = {Advances in high-throughput nucleotide sequencing and bioinformatics make the study of genomes at the population level feasible. Preliminary population genomic studies have explored the relationships among three closely related bacteria, Neisseria meningitidis, Neisseria gonorrhoeae and Neisseria lactamica, which exhibit very different phenotypes with respect to human colonisation. The data obtained have been especially valuable in the establishing of the role of horizontal genetic exchange in bacterial speciation and shaping population structure. In the meningococcus, they have been used to define invasive genetic types, search for virulence factors and potential vaccine components and investigate the effects of vaccines on population structure. These are generic approaches and their application to the Neisseria provides a foretaste for their application to the wider bacterial world.}, }
@article {pmid18818874, year = {2008}, author = {Blikstad, V and Benachenhou, F and Sperber, GO and Blomberg, J}, title = {Evolution of human endogenous retroviral sequences: a conceptual account.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {65}, number = {21}, pages = {3348-3365}, doi = {10.1007/s00018-008-8495-2}, pmid = {18818874}, issn = {1420-9071}, mesh = {Animals ; DNA, Viral/genetics ; Databases, Genetic ; Endogenous Retroviruses/classification/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome ; Host-Pathogen Interactions/genetics/physiology ; Humans ; RNA, Viral/genetics ; Vertebrates/virology ; Virulence ; Virus Integration ; Virus Replication ; }, abstract = {Endogenous retroviruses (ERVs) most likely are remnants of ancient retroviral infections. ERVs preserve functions of exogenous retroviruses to a varying extent, and can be parasites, symbionts or more or less neutral genetic 'junk'.Their evolution has two facets, pre- and post-endogenization. Although the two are not clearly separated, the first pertains to retroviral evolution in general and the second to the fate of repetitive DNA and the evolution of the host organism and its genome. The study of ERVs provides much material for the understanding of retroviral evolution. This sequence archive reflects the history of successes and shortcomings of antiviral resistance, but also of strategic evolutionary decisions regarding genome organization and new gene acquisition. This review discusses retroviral evolution illustrated through HERVs, bioinformatic prerequisites for ERV studies, the endogenization process and HERV evolution post-endogenization, including relation to disease. (Part of a multi-author review).}, }
@article {pmid18818872, year = {2008}, author = {Stocking, C and Kozak, CA}, title = {Murine endogenous retroviruses.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {65}, number = {21}, pages = {3383-3398}, doi = {10.1007/s00018-008-8497-0}, pmid = {18818872}, issn = {1420-9071}, support = {Z01 AI000300-26//Intramural NIH HHS/United States ; Z99 AI999999//Intramural NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Endogenous Retroviruses/classification/genetics/pathogenicity/*physiology ; Evolution, Molecular ; Gammaretrovirus/classification/genetics ; Gene Transfer, Horizontal ; Genes, Intracisternal A-Particle/genetics ; Genome ; Host-Pathogen Interactions/genetics/*physiology ; Humans ; Membrane Glycoproteins/genetics/physiology ; Mice/*virology ; Models, Biological ; Molecular Sequence Data ; Mutagenesis, Insertional ; Neoplasms/veterinary/virology ; Receptors, Virus/genetics/physiology ; Retroelements/genetics/physiology ; Retroviridae Infections/veterinary/virology ; Retroviridae Proteins/genetics/physiology ; Rodent Diseases/virology ; Tumor Virus Infections/veterinary/virology ; Vertebrates/virology ; }, abstract = {Up to 10% of the mouse genome is comprised of endogenous retrovirus (ERV) sequences, and most represent the remains of ancient germ line infections. Our knowledge of the three distinct classes of ERVs is inversely correlated with their copy number, and their characterization has benefited from the availability of divergent wild mouse species and subspecies, and from ongoing analysis of the Mus genome sequence. In contrast to human ERVs, which are nearly all extinct, active mouse ERVs can still be found in all three ERV classes. The distribution and diversity of ERVs has been shaped by host-virus interactions over the course of evolution, but ERVs have also been pivotal in shaping the mouse genome by altering host genes through insertional mutagenesis, by adding novel regulatory and coding sequences, and by their co-option by host cells as retroviral resistance genes. We review mechanisms by which an adaptive coexistence has evolved. (Part of a multi-author review).}, }
@article {pmid18816395, year = {2008}, author = {Haritha, A and Rodrigue, A and Mohan, PM}, title = {A comparative analysis of metal transportomes from metabolically versatile Pseudomonas.}, journal = {BMC research notes}, volume = {1}, number = {}, pages = {88}, pmid = {18816395}, issn = {1756-0500}, abstract = {BACKGROUND: The availability of complete genome sequences of versatile Pseudomonas occupying remarkably diverse ecological niches enabled to gain insights into their adaptative assets. The objective of this study was to analyze the complete genetic repertoires of metal transporters (metal transportomes) from four representative Pseudomonas species and to identify metal transporters with "Genomic Island" associated features.<br><br>METHODS: A comparative metal transporter inventory was built for the following four Pseudomonas species: P.putida (Ppu) KT2440, P.aeruginosa (Pae) PA01, P.fluorescens (Pfl) Pf-5 and P.syringae (Psy)pv.tomato DC3000 using TIGR-CMR and Transport DB. Genomic analysis of essential and toxic metal ion transporters was accomplished from the above inventory. Metal transporters with "Genomic Island" associated features were identified using Islandpath analysis.<br><br>RESULTS: Dataset cataloguing has been executed for 262 metal transporters from the four spp. Additional metal ion transporters belonging to NiCoT, Ca P-type ATPase, Cu P-type ATPases, ZIP and MgtC families were identified. In Psy DC3000, 48% of metal transporters showed strong GI features while it was 45% in Ppu KT2440. In Pfl Pf-5 and Pae PA01 only 26% of their metal transporters exhibited GI features.<br><br>CONCLUSION: Our comparative inventory of 262 metal transporters from four versatile Pseudomonas spp is the complete suite of metal transportomes analysed till date in a prokaryotic genus. This study identified differences in the basic composition of metal transportomes from Pseudomonas occupying diverse ecological niches and also elucidated their novel features. Based on this inventory we analysed the role of horizontal gene transfer in expansion and variability of metal transporter families.}, }
@article {pmid18812079, year = {2008}, author = {Denker, E and Bapteste, E and Le Guyader, H and Manuel, M and Rabet, N}, title = {Horizontal gene transfer and the evolution of cnidarian stinging cells.}, journal = {Current biology : CB}, volume = {18}, number = {18}, pages = {R858-9}, doi = {10.1016/j.cub.2008.07.031}, pmid = {18812079}, issn = {0960-9822}, mesh = {Animals ; Cnidaria/classification/*genetics ; Cnidarian Venoms ; *Gene Transfer, Horizontal ; Phylogeny ; Snake Bites ; }, }
@article {pmid18810532, year = {2009}, author = {Sabia, C and de Niederhäusern, S and Guerrieri, E and Bondi, M and Anacarso, I and Iseppi, R and Messi, P}, title = {Interference of Lactobacillus plantarum strains in the in vitro conjugative transfer of R-plasmids.}, journal = {Current microbiology}, volume = {58}, number = {2}, pages = {101-105}, pmid = {18810532}, issn = {1432-0991}, mesh = {*Conjugation, Genetic ; *Gene Transfer, Horizontal ; Lactobacillus plantarum/*genetics ; R Factors/*genetics ; Staphylococcus aureus/genetics ; }, abstract = {Probiotic compounds, which are often constituted of lactobacilli, exert a number of health benefits through maintenance of the intestinal ecosystem balance. Among the important interactions that occur in the gut microbiota, plasmid transfer by mating is an increasing cause of concern, particularly when antibiotic-resistant genes are involved. Because lactobacilli seem to be able to influence this mechanism, the aim of the present work was to investigate the in vitro capability of two Lactobacillus plantarum strains (one bacteriocin producer and one nonproducer) to interfere with the conjugation processes. For this purpose different matings were performed adding to the donor and recipient cells L. plantarum 35d bac+ and L. plantarum 396/1 bac- as agents of interference. Conjugations added with a Staphylococcus aureus strain or without any agent of interference were used as controls. The results of our experiments demonstrated that both lactobacillus strains were able to decrease mating frequency. Statistically significant differences in the viable transconjugants were obtained in the presence and in the absence of the lactobacilli. The effect was almost the same with the two L. plantarum independent of bacteriocin production. In the trial performed with S. aureus, no decrease in mating frequency was observed, confirming that the capability to interfere with R-plasmid transfer ability could be a property of the tested L. plantarum strains.}, }
@article {pmid18810317, year = {2009}, author = {Widlak, P and Garrard, WT}, title = {Roles of the major apoptotic nuclease-DNA fragmentation factor-in biology and disease.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {66}, number = {2}, pages = {263-274}, doi = {10.1007/s00018-008-8472-9}, pmid = {18810317}, issn = {1420-9071}, mesh = {Animals ; Apoptosis/*physiology ; *DNA Fragmentation ; Deoxyribonucleases/chemistry/genetics/*metabolism ; Enzyme Activation ; Gene Transfer, Horizontal ; Genetic Predisposition to Disease ; Humans ; Leukemia, Myeloid, Acute/chemically induced/genetics/metabolism ; Lupus Erythematosus, Systemic/genetics ; Mutation ; Neoplasms/genetics/metabolism ; Protein Subunits/chemistry/genetics/metabolism ; }, abstract = {It has now been more than ten years since the discovery of the major apoptotic nuclease, DNA fragmentation factor (DFF), also known as caspase-activated DNase (CAD). Here we review the recent literature that has uncovered new insight into DFF's regulation, and both its positive and negative roles in human disease. Cells from mice deficient in DFF still undergo apoptotic death without significant cell-autonomous DNA degradation. Their corpses' genomes are subsequently degraded by lysosomal DNase II after phagocytosis. However,DFF-deficient mice are more susceptible to cancer. Indeed, several different cancers in humans are associated with defects in DFF expression and it has been proposed that DFF is a p53-independent tumor suppressor. Negative aspects of DFF expression include contributing to susceptibility to acquire systemic lupus erythematosus, to chromosomal translocations that result in mixed lineage leukemias, and in the possible spreading of oncogenes and HIV due to horizontal gene transfer.}, }
@article {pmid18809916, year = {2008}, author = {Opperman, CH and Bird, DM and Williamson, VM and Rokhsar, DS and Burke, M and Cohn, J and Cromer, J and Diener, S and Gajan, J and Graham, S and Houfek, TD and Liu, Q and Mitros, T and Schaff, J and Schaffer, R and Scholl, E and Sosinski, BR and Thomas, VP and Windham, E}, title = {Sequence and genetic map of Meloidogyne hapla: A compact nematode genome for plant parasitism.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {39}, pages = {14802-14807}, pmid = {18809916}, issn = {1091-6490}, mesh = {Animals ; Base Sequence ; Caenorhabditis elegans/genetics ; Chromosome Mapping ; Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; *Genome, Helminth ; Host-Parasite Interactions/*genetics ; Molecular Sequence Data ; Multigene Family ; Operon ; Phylogeny ; Plants/*parasitology ; Synteny ; Tylenchoidea/*genetics ; }, abstract = {We have established Meloidogyne hapla as a tractable model plant-parasitic nematode amenable to forward and reverse genetics, and we present a complete genome sequence. At 54 Mbp, M. hapla represents not only the smallest nematode genome yet completed, but also the smallest metazoan, and defines a platform to elucidate mechanisms of parasitism by what is the largest uncontrolled group of plant pathogens worldwide. The M. hapla genome encodes significantly fewer genes than does the free-living nematode Caenorhabditis elegans (most notably through a reduction of odorant receptors and other gene families), yet it has acquired horizontally from other kingdoms numerous genes suspected to be involved in adaptations to parasitism. In some cases, amplification and tandem duplication have occurred with genes suspected of being acquired horizontally and involved in parasitism of plants. Although M. hapla and C. elegans diverged >500 million years ago, many developmental and biochemical pathways, including those for dauer formation and RNAi, are conserved. Although overall genome organization is not conserved, there are areas of microsynteny that may suggest a primary biological function in nematodes for those genes in these areas. This sequence and map represent a wealth of biological information on both the nature of nematode parasitism of plants and its evolution.}, }
@article {pmid18808704, year = {2008}, author = {Tooming-Klunderud, A and Fewer, DP and Rohrlack, T and Jokela, J and Rouhiainen, L and Sivonen, K and Kristensen, T and Jakobsen, KS}, title = {Evidence for positive selection acting on microcystin synthetase adenylation domains in three cyanobacterial genera.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {256}, pmid = {18808704}, issn = {1471-2148}, mesh = {Amino Acid Sequence ; Bacterial Proteins/*genetics ; Cyanobacteria/*enzymology/*genetics ; DNA, Bacterial/genetics ; Evolution, Molecular ; Genes, Bacterial ; Genetic Variation ; Molecular Sequence Data ; Multigene Family ; Peptide Synthases/*genetics ; Phylogeny ; Protein Interaction Domains and Motifs ; Protein Isoforms ; Recombination, Genetic ; *Selection, Genetic ; Sequence Alignment ; Sequence Analysis, Protein ; Substrate Specificity ; }, abstract = {BACKGROUND: Cyanobacteria produce a wealth of secondary metabolites, including the group of small cyclic heptapeptide hepatotoxins that constitutes the microcystin family. The enzyme complex that directs the biosynthesis of microcystin is encoded in a single large gene cluster (mcy). mcy genes have a widespread distribution among cyanobacteria and are likely to have an ancient origin. The notable diversity within some of the Mcy modules is generated through various recombination events including horizontal gene transfer.<br><br>RESULTS: A comparative analysis of the adenylation domains from the first module of McyB (McyB1) and McyC in the microcystin synthetase complex was performed on a large number of microcystin-producing strains from the Anabaena, Microcystis and Planktothrix genera. We found no decisive evidence for recombination between strains from different genera. However, we detected frequent recombination events in the mcyB and mcyC genes between strains within the same genus. Frequent interdomain recombination events were also observed between mcyB and mcyC sequences in Anabaena and Microcystis. Recombination and mutation rate ratios suggest that the diversification of mcyB and mcyC genes is driven by recombination events as well as point mutations in all three genera. Sequence analysis suggests that generally the adenylation domains of the first domain of McyB and McyC are under purifying selection. However, we found clear evidence for positive selection acting on a number of amino acid residues within these adenylation domains. These include residues important for active site selectivity of the adenylation domain, strongly suggesting selection for novel microcystin variants.<br><br>CONCLUSION: We provide the first clear evidence for positive selection acting on amino acid residues involved directly in the recognition and activation of amino acids incorporated into microcystin, indicating that the microcystin complement of a given strain may influence the ability of a particular strain to interact with its environment.}, }
@article {pmid18806222, year = {2008}, author = {Lozupone, CA and Hamady, M and Cantarel, BL and Coutinho, PM and Henrissat, B and Gordon, JI and Knight, R}, title = {The convergence of carbohydrate active gene repertoires in human gut microbes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {39}, pages = {15076-15081}, pmid = {18806222}, issn = {1091-6490}, support = {P01 DK078669/DK/NIDDK NIH HHS/United States ; R01 DK030292/DK/NIDDK NIH HHS/United States ; T32GM065103/GM/NIGMS NIH HHS/United States ; DK30292/DK/NIDDK NIH HHS/United States ; DK70977/DK/NIDDK NIH HHS/United States ; T32 GM142607/GM/NIGMS NIH HHS/United States ; R37 DK030292/DK/NIDDK NIH HHS/United States ; R01 DK070977/DK/NIDDK NIH HHS/United States ; T32 GM008759/GM/NIGMS NIH HHS/United States ; DK78669/DK/NIDDK NIH HHS/United States ; T32 GM065103/GM/NIGMS NIH HHS/United States ; }, mesh = {Archaea/classification/*genetics/isolation &amp; purification ; Bacteria/classification/*genetics/isolation &amp; purification ; Carbohydrates/biosynthesis/genetics ; Cluster Analysis ; Gene Transfer, Horizontal ; *Genes, Archaeal ; *Genes, Bacterial ; Genetic Variation ; Glycoside Hydrolases/*genetics ; Glycosyltransferases/*genetics ; Humans ; Intestines/*microbiology ; Multigene Family ; Phylogeny ; }, abstract = {The extreme variation in gene content among phylogenetically related microorganisms suggests that gene acquisition, expansion, and loss are important evolutionary forces for adaptation to new environments. Accordingly, phylogenetically disparate organisms that share a habitat may converge in gene content as they adapt to confront shared challenges. This response should be especially pronounced for functional genes that are important for survival in a particular habitat. We illustrate this principle by showing that the repertoires of two different types of carbohydrate-active enzymes, glycoside hydrolases and glycosyltransferases, have converged in bacteria and archaea that live in the human gut and that this convergence is largely due to horizontal gene transfer rather than gene family expansion. We also identify gut microbes that may have more similar dietary niches in the human gut than would be expected based on phylogeny. The techniques used to obtain these results should be broadly applicable to understanding the functional genes and evolutionary processes important for adaptation in many environments and useful for interpreting the large number of reference microbial genome sequences being generated for the International Human Microbiome Project.}, }
@article {pmid18801324, year = {2008}, author = {Keese, P}, title = {Risks from GMOs due to horizontal gene transfer.}, journal = {Environmental biosafety research}, volume = {7}, number = {3}, pages = {123-149}, doi = {10.1051/ebr:2008014}, pmid = {18801324}, issn = {1635-7922}, mesh = {Environmental Monitoring ; Gene Transfer, Horizontal/*genetics ; Plants, Genetically Modified/*genetics ; Risk ; Safety ; }, abstract = {Horizontal gene transfer (HGT) is the stable transfer of genetic material from one organism to another without reproduction or human intervention. Transfer occurs by the passage of donor genetic material across cellular boundaries, followed by heritable incorporation to the genome of the recipient organism. In addition to conjugation, transformation and transduction, other diverse mechanisms of DNA and RNA uptake occur in nature. The genome of almost every organism reveals the footprint of many ancient HGT events. Most commonly, HGT involves the transmission of genes on viruses or mobile genetic elements. HGT first became an issue of public concern in the 1970s through the natural spread of antibiotic resistance genes amongst pathogenic bacteria, and more recently with commercial production of genetically modified (GM) crops. However, the frequency of HGT from plants to other eukaryotes or prokaryotes is extremely low. The frequency of HGT to viruses is potentially greater, but is restricted by stringent selection pressures. In most cases the occurrence of HGT from GM crops to other organisms is expected to be lower than background rates. Therefore, HGT from GM plants poses negligible risks to human health or the environment.}, }
@article {pmid18801176, year = {2008}, author = {Bigot, Y and Samain, S and Augé-Gouillou, C and Federici, BA}, title = {Molecular evidence for the evolution of ichnoviruses from ascoviruses by symbiogenesis.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {253}, pmid = {18801176}, issn = {1471-2148}, mesh = {Amino Acid Sequence ; Animals ; Ascoviridae/classification/*genetics ; Chromosome Mapping ; DNA, Viral/genetics ; Databases, Nucleic Acid ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Viral ; *Genome, Viral ; Models, Genetic ; Molecular Sequence Data ; Open Reading Frames ; Polydnaviridae/classification/*genetics ; Sequence Homology, Amino Acid ; Symbiosis ; Viral Proteins/genetics ; Wasps/virology ; }, abstract = {BACKGROUND: Female endoparasitic ichneumonid wasps inject virus-like particles into their caterpillar hosts to suppress immunity. These particles are classified as ichnovirus virions and resemble ascovirus virions, which are also transmitted by parasitic wasps and attack caterpillars. Ascoviruses replicate DNA and produce virions. Polydnavirus DNA consists of wasp DNA replicated by the wasp from its genome, which also directs particle synthesis. Structural similarities between ascovirus and ichnovirus particles and the biology of their transmission suggest that ichnoviruses evolved from ascoviruses, although molecular evidence for this hypothesis is lacking.<br><br>RESULTS: Here we show that a family of unique pox-D5 NTPase proteins in the Glypta fumiferanae ichnovirus are related to three Diadromus pulchellus ascovirus proteins encoded by ORFs 90, 91 and 93. A new alignment technique also shows that two proteins from a related ichnovirus are orthologs of other ascovirus virion proteins.<br><br>CONCLUSION: Our results provide molecular evidence supporting the origin of ichnoviruses from ascoviruses by lateral transfer of ascoviral genes into ichneumonid wasp genomes, perhaps the first example of symbiogenesis between large DNA viruses and eukaryotic organisms. We also discuss the limits of this evidence through complementary studies, which revealed that passive lateral transfer of viral genes among polydnaviral, bacterial, and wasp genomes may have occurred repeatedly through an intimate coupling of both recombination and replication of viral genomes during evolution. The impact of passive lateral transfers on evolutionary relationships between polydnaviruses and viruses with large double-stranded genomes is considered in the context of the theory of symbiogenesis.}, }
@article {pmid18799744, year = {2008}, author = {Bustamante, VH and Martínez, LC and Santana, FJ and Knodler, LA and Steele-Mortimer, O and Puente, JL}, title = {HilD-mediated transcriptional cross-talk between SPI-1 and SPI-2.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {38}, pages = {14591-14596}, pmid = {18799744}, issn = {1091-6490}, support = {75301-565101//Howard Hughes Medical Institute/United States ; //Intramural NIH HHS/United States ; }, mesh = {Bacterial Proteins/*metabolism ; Blotting, Western ; Culture Media ; Gene Expression Regulation, Bacterial ; Membrane Proteins/*metabolism ; Regulatory Sequences, Nucleic Acid ; Regulon ; Salmonella typhimurium/*genetics/growth &amp; development ; Transcription Factors/*metabolism ; }, abstract = {The acquisition of new genetic traits by horizontal gene transfer and their incorporation into preexisting regulatory networks have been essential events in the evolution of bacterial pathogens. An example of successful assimilation of virulence traits is Salmonella enterica, which acquired, at distinct evolutionary times, Salmonella pathogenicity island 1 (SPI-1), required for efficient invasion of the intestinal epithelium and intestinal disease, and SPI-2, essential for Salmonella replication and survival within macrophages and the progression of a systemic infection. A positive regulatory cascade mainly composed of HilD, HilA, and InvF, encoded in SPI-1, controls the expression of SPI-1 genes, whereas the two-component regulatory system SsrA/B, encoded in SPI-2, controls expression of SPI-2 genes. In this study, we report a previously undescribed transcriptional cross-talk between SPI-1 and SPI-2, where the SPI-1-encoded regulator HilD is essential for the activation of both the SPI-1 and SPI-2 regulons but at different times during the stationary phase of growth in Luria-Bertani medium. Our data indicate that HilD counteracts the H-NS-mediated repression exerted on the OmpR-dependent activation of the ssrAB operon by specifically interacting with its regulatory region. In contrast, HilD is not required for SPI-2 regulon expression under the in vitro growth conditions that are thought to resemble the intracellular environment. Our results suggest that two independent SPI-2 activation pathways evolved to take advantage of the SPI-2-encoded information at different niches and, in consequence, in response to different growth conditions.}, }
@article {pmid18799735, year = {2008}, author = {Chia, N and Woese, CR and Goldenfeld, N}, title = {A collective mechanism for phase variation in biofilms.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {38}, pages = {14597-14602}, pmid = {18799735}, issn = {1091-6490}, mesh = {Bacteria/*genetics/*growth &amp; development ; *Biofilms ; Computer Simulation ; Ecosystem ; Gene Transfer, Horizontal ; Genome, Bacterial ; Models, Biological ; Phenotype ; }, abstract = {Understanding how microbes gather into biofilm communities and maintain diversity remains one of the central questions of microbiology, requiring an understanding of microbes as communal rather then individual organisms. Phase variation plays an integral role in the formation of diverse phenotypes within biofilms. We propose a collective mechanism for phase variation based on gene transfer agents, and apply the theory to predict the population structure and growth dynamics of a biofilm. Our results describe quantitatively recent experiments, with the only adjustable parameter being the rate of intercellular horizontal gene transfer. Our approach derives from a more general picture for the emergence of cooperation between microbes.}, }
@article {pmid18799480, year = {2008}, author = {Baran, RH and Ko, H}, title = {Detecting horizontally transferred and essential genes based on dinucleotide relative abundance.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {15}, number = {5}, pages = {267-276}, pmid = {18799480}, issn = {1756-1663}, mesh = {Bacteria/*genetics ; Base Composition ; Escherichia coli K12/genetics ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; }, abstract = {Various methods have been developed to detect horizontal gene transfer in bacteria, based on anomalous nucleotide composition, assuming that compositional features undergo amelioration in the host genome. Evolutionary theory predicts the inevitability of false positives when essential sequences are strongly conserved. Foreign genes could become more detectable on the basis of their higher order compositions if such features ameliorate more rapidly and uniformly than lower order features. This possibility is tested by comparing the heterogeneities of bacterial genomes with respect to strand-independent first- and second-order features, (i) G + C content and (ii) dinucleotide relative abundance, in 1 kb segments. Although statistical analysis confirms that (ii) is less inhomogeneous than (i) in all 12 species examined, extreme anomalies with respect to (ii) in the Escherichia coli K12 genome are typically co-located with essential genes.}, }
@article {pmid18795953, year = {2008}, author = {Laranjo, M and Alexandre, A and Rivas, R and Velázquez, E and Young, JP and Oliveira, S}, title = {Chickpea rhizobia symbiosis genes are highly conserved across multiple Mesorhizobium species.}, journal = {FEMS microbiology ecology}, volume = {66}, number = {2}, pages = {391-400}, doi = {10.1111/j.1574-6941.2008.00584.x}, pmid = {18795953}, issn = {0168-6496}, mesh = {*Alphaproteobacteria/classification/genetics/isolation &amp; purification ; Bacterial Proteins/genetics ; Cicer/*microbiology ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; N-Acetylglucosaminyltransferases/genetics ; Nitrogen Fixation ; Oxidoreductases/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Symbiosis/*genetics ; }, abstract = {Chickpea has been considered as a restrictive host for nodulation by rhizobia. However, recent studies have reported that several Mesorhizobium species may effectively nodulate chickpea. With the purpose of investigating the evolutionary relationships between these different species with the ability of nodulating the same host, we analysed 21 Portuguese chickpea rhizobial isolates. Symbiosis genes nifH and nodC were sequenced and used for phylogenetic studies. Symbiotic effectiveness was determined to evaluate its relationship with symbiosis genes. The comparison of 16S rRNA gene-based phylogeny with the phylogenies based on symbiosis genes revealed evidence of lateral transfer of symbiosis genes across different species. Chickpea is confirmed as a nonpromiscuous host. Although chickpea is nodulated by many different species, they share common symbiosis genes, suggesting recognition of only a few Nod factors by chickpea. Our results suggest that sequencing of nifH or nodC genes can be used for rapid detection of chickpea mesorhizobia.}, }
@article {pmid18794279, year = {2008}, author = {Castillo, AR and Woodruff, AJ and Connolly, LE and Sause, WE and Ottemann, KM}, title = {Recombination-based in vivo expression technology identifies Helicobacter pylori genes important for host colonization.}, journal = {Infection and immunity}, volume = {76}, number = {12}, pages = {5632-5644}, pmid = {18794279}, issn = {1098-5522}, mesh = {Animals ; Gene Expression Profiling/*methods ; *Gene Expression Regulation, Bacterial ; Gene Library ; *Genes, Bacterial ; Helicobacter Infections/genetics ; Helicobacter pylori/*genetics/*pathogenicity ; Mice ; Promoter Regions, Genetic ; }, abstract = {Here we undertook to identify colonization and gastric disease-promoting factors of the human gastric pathogen Helicobacter pylori as genes that were induced in response to the stomach environment. Using recombination-based in vivo expression technology (RIVET), we identified six promoters induced in the host compared to laboratory conditions. Three of these promoters, designated Pivi10, Pivi66, and Pivi77, regulate genes that H. pylori may use to interact with other microbes or the host. Pivi10 likely regulates the mobA, mobB, and mobD genes, which have potential roles in horizontal gene transfer through plasmid mobilization. Pivi66 occurs in the cytotoxin-associated gene pathogenicity island, a genomic region known to be associated with more severe disease outcomes, and likely regulates cagZ, virB11, and virD4. Pivi77 likely regulates HP0289, an uncharacterized paralogue of the vacA cytotoxin gene. We assessed the roles of a subset of these genes in colonization by creating deletion mutants and analyzing them in single-strain and coinfection experiments. We found that a mobABD mutant was defective for murine host colonization and that a cagZ mutant outcompeted the wild-type strain in a coinfection analysis. Our work supports the conclusion that RIVET is a valuable tool for identifying H. pylori factors with roles in host colonization.}, }
@article {pmid18793737, year = {2008}, author = {Simmons, MP}, title = {Potential use of host-derived genome signatures to root virus phylogenies.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {3}, pages = {969-978}, doi = {10.1016/j.ympev.2008.08.014}, pmid = {18793737}, issn = {1095-9513}, mesh = {Bacteriophages/genetics ; Computational Biology/methods ; DNA Viruses/classification/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Viral ; *Genome, Viral ; Likelihood Functions ; Models, Genetic ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA/*methods ; }, abstract = {Two methods are presented that provide independent evidence with which to test virus-phylogeny roots. The methods may be applied to phages and other viruses in which at least one horizontal transfer between hosts is inferred across the virus phylogeny. The methods are based upon the inference that viral DNA sequences acquire similar genome signatures (or "genomic signatures") to those of their hosts. One of the two methods may be applied to horizontal virus transfers between three or more hosts. Both methods may potentially be extended to rooting plasmid and transposable-element phylogenies. The effect of using different word lengths (2-bp, 3-bp, or 4-bp) to calculate genome signatures, which host genomes (of bacteria) or genome regions (of eukaryotes) were used, which virus sequences were used, and whether distance, counts, or Z-scores are applied were examined using empirical datasets.}, }
@article {pmid18793314, year = {2009}, author = {Costa, R and van Aarle, IM and Mendes, R and van Elsas, JD}, title = {Genomics of pyrrolnitrin biosynthetic loci: evidence for conservation and whole-operon mobility within gram-negative bacteria.}, journal = {Environmental microbiology}, volume = {11}, number = {1}, pages = {159-175}, doi = {10.1111/j.1462-2920.2008.01750.x}, pmid = {18793314}, issn = {1462-2920}, mesh = {Biosynthetic Pathways/*genetics ; Burkholderia/*genetics ; Cluster Analysis ; Conserved Sequence ; DNA, Bacterial/genetics ; Evolution, Molecular ; Gene Order ; Gene Transfer, Horizontal ; Interspersed Repetitive Sequences ; Molecular Sequence Data ; *Operon ; Phylogeny ; Polymorphism, Genetic ; Pseudomonas/*genetics ; Pyrrolnitrin/*biosynthesis ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Serratia/*genetics ; Synteny ; }, abstract = {Pyrrolnitrin (PRN) is a tryptophan-derived secondary metabolite produced by a narrow range of gram-negative bacteria. The PRN biosynthesis by rhizobacteria presumably has a key role in their life strategies and in the biocontrol of plant diseases. The biosynthetic operon that encodes the pathway that converts tryptophan to PRN is composed of four genes, prnA through D, whose diversity, genomic context and spread over bacterial genomes are poorly understood. Therefore, we launched an endeavour aimed at retrieving, by in vitro and in silico means, diverse bacteria carrying the prnABCD biosynthetic loci in their genomes. Analysis of polymorphisms of the prnD gene sequences revealed a high level of conservation between Burkholderia, Pseudomonas and Serratia spp. derived sequences. Whole-operon- and prnD-based phylogeny resulted in tree topologies that are incongruent with the taxonomic status of the evaluated strains as predicted by 16S rRNA gene phylogeny. The genomic composition of c. 20 kb DNA fragments containing the PRN operon varied in different strains. Highly conserved and distinct transposase-encoding genes surrounding the PRN biosynthetic operons of Burkholderia pseudomallei strains were found. A prnABCD-deprived genomic region in B. pseudomallei strain K96243 contained the same gene composition as, and shared high homology with, the flanking regions of the PRN operon in B. pseudomallei strains 668, 1106a and 1710b. Our results strongly suggest that the PRN biosynthetic operon is mobile. The extent, frequency and promiscuity of this mobility remain to be understood.}, }
@article {pmid18793312, year = {2008}, author = {Paerl, RW and Foster, RA and Jenkins, BD and Montoya, JP and Zehr, JP}, title = {Phylogenetic diversity of cyanobacterial narB genes from various marine habitats.}, journal = {Environmental microbiology}, volume = {10}, number = {12}, pages = {3377-3387}, doi = {10.1111/j.1462-2920.2008.01741.x}, pmid = {18793312}, issn = {1462-2920}, mesh = {Atlantic Ocean ; Bacterial Proteins/*genetics ; Cluster Analysis ; Cyanobacteria/*classification/*isolation &amp; purification ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer ; Genes, rRNA ; Molecular Sequence Data ; Nitrate Reductase/*genetics ; Pacific Ocean ; Phylogeny ; *Polymorphism, Genetic ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {Nitrate, the most abundant combined, dissolved form of inorganic nitrogen in global oceans, is a common source of nitrogen (N) for phytoplankton including cyanobacteria. Using a nested polymerase chain reaction (PCR) method, the diversity of the cyanobacterial nitrate reductase gene, narB, was examined in plankton samples from a variety of marine habitats. A total of 480 narB gene fragment sequences were obtained from a coastal coral reef (Heron Island, Australia), open-ocean tropical and subtropical oceanic waters (Atlantic and Pacific Oceans) and a temperate N. Pacific Ocean site (34 degrees N, 129 degrees W). Phylogenetic analyses distinguished eight picocyanobacterial narB clades comprised of DNA sequences derived from the nutrient-replete coastal, nutrient-deplete pelagic and tidally influenced coral reef habitats. The phylogeny of recovered narB gene sequences was consistent with 16S rRNA and ITS sequence phylogenies, suggesting minimal horizontal gene transfer of the narB gene. Depending on sampled habitat, environmental narB sequence types segregated into three divisions: non-picocyanobacterial, coastal picocyanobacterial and open-ocean picocyanobacterial sequences. Using a reverse transcription PCR method, narB mRNA sequences were amplified from Heron Island samples, indicating that narB expression can be detected in environmental samples.}, }
@article {pmid18781358, year = {2008}, author = {Wang, Q and Cheng, J and Chen, Y and Ye, Y and Li, JB and Zhang, XJ}, title = {Characterization of a novel AmpC-type plasmid-mediated beta-lactamase from an Escherichia coli strain isolated in China.}, journal = {Current microbiology}, volume = {57}, number = {6}, pages = {558-563}, pmid = {18781358}, issn = {1432-0991}, mesh = {Aged ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*biosynthesis/chemistry/*genetics/isolation &amp; purification ; Blotting, Southern ; China ; Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/drug effects/*enzymology/isolation &amp; purification ; Escherichia coli Infections/microbiology ; Escherichia coli Proteins/*biosynthesis/chemistry/*genetics/isolation &amp; purification ; Female ; Gene Transfer, Horizontal ; Humans ; Isoelectric Focusing ; Isoelectric Point ; Microbial Sensitivity Tests ; Molecular Sequence Data ; *Plasmids ; Sequence Analysis, DNA ; beta-Lactam Resistance ; beta-Lactamases/*biosynthesis/chemistry/*genetics/isolation &amp; purification ; }, abstract = {The aim of this work was to study the phenotypic and molecular characterization of a novel plasmid-mediated AmpC beta-lactamase from Escherichia coli E384. Conjugation experiments, isoelectric focusing, pulsed-field gel electrophoresis, plasmid profiling, and Southern blot as well as PCR, sequencing techniques, and susceptibility testing were carried out to investigate the underlying mechanism of resistance. The kinetic parameters were determined to characterize the novel enzyme. MIR-4 beta-lactamase, pI 8.2, is a novel variant with four substitutions of amino acids compared with the sequence of MIR-1. E. coli E384 displays resistance to eight beta-lactam antimicrobial agents and three fluoroquinolones. The minimal inhibitory concentrations of beta-lactam in combination with beta-lactamase inhibitors show no significant synergy. Kinetic parameters suggest that the novel enzyme effectively hydrolyzes broad-spectrum beta-lactams. The same hybridization signal was detectable only in the 54-kb plasmid band that hybridized with the bla (CTX-M)- and bla(ampC)-specific probes. This is the first description of a plasmid-mediated MIR-4 enzyme in China. This study illustrates the importance of molecular surveillance in tracking AmpC-producing strains at general hospitals and emphasizes the need for epidemiological monitoring.}, }
@article {pmid18779166, year = {2008}, author = {Li, ZJ and Li, HQ and Diao, XM}, title = {[Methods for the identification of horizontal gene transfer (HGT) events and progress in related fields].}, journal = {Yi chuan = Hereditas}, volume = {30}, number = {9}, pages = {1108-1114}, doi = {10.3724/sp.j.1005.2008.01108}, pmid = {18779166}, issn = {0253-9772}, mesh = {Animals ; Computational Biology/*methods ; Computer Simulation ; Databases, Genetic ; Escherichia coli/genetics ; Eukaryotic Cells ; Gene Transfer, Horizontal/*genetics ; Genome ; Genome, Protozoan/*genetics ; Genomics/*methods ; Humans ; Oceans and Seas ; Phylogeny ; Prokaryotic Cells ; }, abstract = {Horizontal gene transfer is the gene exchange between different organisms or different organelles, which occurs frequently in prokaryotes. Many newly identified horizontal transfer events in eukaryotes indicates that it is a common phenomenon in all organisms. This paper describes the concept of horizontal gene transfer, the standard for judging a horizontal gene transfer events, the character, the mode, the way of horizontal gene transfer, and its impact on gene and genome evolution. The analyses of phylogenetic tree, base composition, selection pressure, intron sequence comparison, inserted special sequence, and biased nucleotide substitution are the most common methods used in previous researches. Evidence accumulated demonstrated that transposable sequences are most likely undergoing horizontal transferring. Transformation, conjugation, and transduction are the main forms of horizontal gene transfer in prokaryotes, but no clear clue was related with the mechanism of horizontal gene transfer in eukaryotes. Horizontal gene transfer plays a special role in genetic, genomic, and the biological evolution.}, }
@article {pmid18775898, year = {2008}, author = {Luque, I and Riera-Alberola, ML and Andújar, A and Ochoa de Alda, JA}, title = {Intraphylum diversity and complex evolution of cyanobacterial aminoacyl-tRNA synthetases.}, journal = {Molecular biology and evolution}, volume = {25}, number = {11}, pages = {2369-2389}, doi = {10.1093/molbev/msn197}, pmid = {18775898}, issn = {1537-1719}, mesh = {Amino Acid Motifs ; Amino Acyl-tRNA Synthetases/*genetics/metabolism ; Arginine-tRNA Ligase/genetics/metabolism ; Aspartate-tRNA Ligase/genetics/metabolism ; Bacterial Proteins/*genetics ; Cyanobacteria/classification/enzymology/*genetics ; *Evolution, Molecular ; Gene Duplication ; Genetic Variation ; Genome, Bacterial ; Glutamate-tRNA Ligase/genetics/metabolism ; Histidine-tRNA Ligase/genetics/metabolism ; Phylogeny ; Protein Structure, Tertiary ; RNA, Bacterial/metabolism ; RNA, Transfer, Amino Acyl/genetics/metabolism ; RNA, Transfer, Asn/metabolism ; RNA, Transfer, Gln/metabolism ; Threonine-tRNA Ligase/genetics/metabolism ; }, abstract = {A comparative genomic analysis of 35 cyanobacterial strains has revealed that the gene complement of aminoacyl-tRNA synthetases (AARSs) and routes for aminoacyl-tRNA synthesis may differ among the species of this phylum. Several genes encoding AARS paralogues were identified in some genomes. In-depth phylogenetic analysis was done for each of these proteins to gain insight into their evolutionary history. GluRS, HisRS, ArgRS, ThrRS, CysRS, and Glu-Q-RS showed evidence of a complex evolutionary course as indicated by a number of inconsistencies with our reference tree for cyanobacterial phylogeny. In addition to sequence data, support for evolutionary hypotheses involving horizontal gene transfer or gene duplication events was obtained from other observations including biased sequence conservation, the presence of indels (insertions or deletions), or vestigial traces of ancestral redundant genes. We present evidences for a novel protein domain with two putative transmembrane helices recruited independently by distinct AARS in particular cyanobacteria.}, }
@article {pmid18772426, year = {2008}, author = {Ogata, H and Claverie, JM}, title = {Microbiology. How to infect a Mimivirus.}, journal = {Science (New York, N.Y.)}, volume = {321}, number = {5894}, pages = {1305-1306}, doi = {10.1126/science.1164839}, pmid = {18772426}, issn = {1095-9203}, mesh = {DNA Viruses/genetics/*physiology ; *Gene Transfer, Horizontal ; Genes, Viral ; *Genome, Viral ; *Virus Physiological Phenomena ; *Virus Replication ; Viruses/genetics ; }, }
@article {pmid18769853, year = {2008}, author = {Abbassi, MS and Bouchami, O and Touati, A and Achour, W and Ben Hassen, A}, title = {Clonality and occurrence of genes encoding antibiotic resistance and biofilm in methicillin-resistant Staphylococcus epidermidis strains isolated from catheters and bacteremia in neutropenic patients.}, journal = {Current microbiology}, volume = {57}, number = {5}, pages = {442-448}, pmid = {18769853}, issn = {0343-8651}, mesh = {Bacteremia/*microbiology ; Bacterial Proteins/*genetics/metabolism ; *Biofilms ; Catheters, Indwelling/*microbiology ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Humans ; Methicillin Resistance ; Neutropenia/*microbiology ; Staphylococcal Infections/microbiology ; Staphylococcus epidermidis/drug effects/*genetics/*isolation &amp; purification/physiology ; }, abstract = {Thirty methicillin-resistant Staphylococcus epidermidis strains isolated from catheters and blood cultures from neutropenic patients were studied. They were classified into 17 multidrug-resistance patterns. Polymerase cahin reaction analysis revealed that methicillin resistance was encoded by the mecA gene in all strains, and aminoglycosides resistance was due to aac(6')-Ie-aph(2'')-Ia (23 strains), ant(4')-Ia (13), and aph(3')-IIIa (1) genes. The aac(6')-Ie-aph(2'')-Ia gene was detected concomitantly with aph(3')-IIIa, and ant(4')-Ia genes in one and nine strains, respectively. Erythromycin resistance was encoded by the ermC (11 strains), ermA (6), and msrA (2) genes. The ermC gene was inducibly expressed in five strains, whereas the ermA was exclusively constitutively expressed. The icaA and icaC genes were detected in 19 strains; however, biofilm production was observed in only 16 strains. Most strains harbored multiple plasmids of variable sizes ranging from 2.2 to 70 kb, and two strains were plasmid-free. PFGE identified 15 distinct PFGE types, and five predominant genotypes were found. Our study showed the occurrence of complex genetic phenomenons. In unrelated strains, evidence of horizontal transfer of antibiotic-encoding genes and/or ica operon, and in indistinguishable strains, there is a quite good likelihood of independent steps of loss and/or gain of these genes. This genome dynamicity might have enhanced the invasiveness power of these methicillin-resistant S epidermidis strains.}, }
@article {pmid18767964, year = {2008}, author = {Rannala, B and Yang, Z}, title = {Phylogenetic inference using whole genomes.}, journal = {Annual review of genomics and human genetics}, volume = {9}, number = {}, pages = {217-231}, doi = {10.1146/annurev.genom.9.081307.164407}, pmid = {18767964}, issn = {1527-8204}, mesh = {Animals ; Data Interpretation, Statistical ; Databases, Genetic/statistics &amp; numerical data ; Gene Transfer, Horizontal ; Genome ; Genomics/*statistics &amp; numerical data ; Humans ; *Phylogeny ; Polymorphism, Genetic ; Recombination, Genetic ; Sequence Alignment/statistics &amp; numerical data ; Software ; }, abstract = {The availability of genome-wide data provides unprecedented opportunities for resolving difficult phylogenetic relationships and for studying population genetic processes of mutation, selection, and recombination on a genomic scale. The use of appropriate statistical models becomes increasingly important when we are faced with very large datasets, which can lead to improved precision but not necessarily improved accuracy if the analytical methods have systematic biases. This review provides a critical examination of methods for analyzing genomic datasets from multiple loci, including concatenation, separate gene-by-gene analyses, and statistical models that accommodate heterogeneity in different aspects of the evolutionary process among data partitions. We discuss factors that may cause the gene tree to differ from the species tree, as well as strategies for estimating species phylogenies in the presence of gene tree conflicts. Genomic datasets provide computational and statistical challenges that are likely to be a focus of research for years to come.}, }
@article {pmid18765693, year = {2008}, author = {Duesberg, CB and Malhotra-Kumar, S and Goossens, H and McGee, L and Klugman, KP and Welte, T and Pletz, MW}, title = {Interspecies recombination occurs frequently in quinolone resistance-determining regions of clinical isolates of Streptococcus pyogenes.}, journal = {Antimicrobial agents and chemotherapy}, volume = {52}, number = {11}, pages = {4191-4193}, pmid = {18765693}, issn = {1098-6596}, mesh = {Anti-Bacterial Agents/*pharmacology ; DNA Topoisomerase IV/genetics ; Drug Resistance, Bacterial/*genetics ; Fluoroquinolones/*pharmacology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Phylogeny ; Recombination, Genetic ; Species Specificity ; Streptococcal Infections/drug therapy/microbiology ; Streptococcus pyogenes/*drug effects/*genetics/isolation &amp; purification ; }, abstract = {Fluoroquinolone resistance in Streptococcus pyogenes has been reported only anecdotally, but a recent Belgian surveillance study found a rate of nonsusceptibility of 5.4%. From an analysis of these isolates, we show that interspecies horizontal gene transfer within the parC quinolone resistance-determining region is a frequent phenomenon that might contribute to fluoroquinolone resistance.}, }
@article {pmid18761693, year = {2008}, author = {Churchward, G}, title = {Back to the future: the new ICE age.}, journal = {Molecular microbiology}, volume = {70}, number = {3}, pages = {554-556}, doi = {10.1111/j.1365-2958.2008.06415.x}, pmid = {18761693}, issn = {1365-2958}, mesh = {Bacillus subtilis/*genetics/metabolism ; Bacterial Proteins/*genetics/metabolism ; Chromosomes, Bacterial/genetics ; Conjugation, Genetic ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences ; Repressor Proteins/*genetics/metabolism ; }, abstract = {The analysis of bacterial genomes has revealed an extraordinary array of conjugal elements (integrative and conjugative element or ICE) that reside in bacterial chromosomes. These elements contribute to the pan-genomes of individual species and confer a wide variety of properties on their bacterial hosts. ICEBs1 is a conjugal element found in Bacillus subtilis that has a remarkable regulatory mechanism that apparently favours conjugation when there are suitable recipient bacteria at high density or when the bacterial host is facing DNA-damaging stresses. In the current issue, Bose et al. dissect the mechanism of induction of transfer of this element, and reveal a new, apparently widespread repressor anti-repressor system and a new mechanism of repressor destruction by proteolysis.}, }
@article {pmid18761623, year = {2008}, author = {Bose, B and Auchtung, JM and Lee, CA and Grossman, AD}, title = {A conserved anti-repressor controls horizontal gene transfer by proteolysis.}, journal = {Molecular microbiology}, volume = {70}, number = {3}, pages = {570-582}, pmid = {18761623}, issn = {1365-2958}, support = {R01 GM050895/GM/NIGMS NIH HHS/United States ; R01 GM050895-12/GM/NIGMS NIH HHS/United States ; GM50895/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacillus Phages/genetics/metabolism ; Bacillus subtilis/*genetics/metabolism ; Bacterial Proteins/*genetics/metabolism ; Chromosomes, Bacterial/genetics ; Cloning, Molecular ; Conjugation, Genetic ; DNA Damage ; DNA, Bacterial/genetics ; Escherichia coli/genetics/metabolism ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences ; Repressor Proteins/*genetics/metabolism ; Sequence Analysis, DNA ; Two-Hybrid System Techniques ; Viral Regulatory and Accessory Proteins/genetics/metabolism ; }, abstract = {The mobile genetic element ICEBs1 is an integrative and conjugative element (a conjugative transposon) found in the Bacillus subtilis chromosome. The SOS response and the RapI-PhrI sensory system activate ICEBs1 gene expression, excision and transfer by inactivating the ICEBs1 repressor protein ImmR. Although ImmR is similar to many characterized phage repressors, we found that, unlike these repressors, inactivation of ImmR requires an ICEBs1-encoded anti-repressor ImmA (YdcM). ImmA was needed for the degradation of ImmR in B. subtilis. Coexpression of ImmA and ImmR in Escherichia coli or co-incubation of purified ImmA and ImmR resulted in site-specific cleavage of ImmR. Homologues of immR and immA are found in many mobile genetic elements. We found that the ImmA homologue encoded by B. subtilis phage phi105 is required for inactivation of the phi105 repressor (an ImmR homologue). ImmA-dependent proteolysis of ImmR repressors may be a conserved mechanism for regulating horizontal gene transfer.}, }
@article {pmid18758448, year = {2008}, author = {Ulker, B and Li, Y and Rosso, MG and Logemann, E and Somssich, IE and Weisshaar, B}, title = {T-DNA-mediated transfer of Agrobacterium tumefaciens chromosomal DNA into plants.}, journal = {Nature biotechnology}, volume = {26}, number = {9}, pages = {1015-1017}, doi = {10.1038/nbt.1491}, pmid = {18758448}, issn = {1546-1696}, mesh = {Agrobacterium tumefaciens/*genetics/metabolism ; Biotechnology/*methods ; Chromosomes/*metabolism ; DNA/genetics/metabolism ; Escherichia coli/metabolism ; Gene Expression Regulation, Plant ; *Gene Transfer Techniques ; Genome, Plant ; Models, Biological ; Mutagenesis ; Plants, Genetically Modified/*genetics/microbiology ; Plasmids/metabolism ; }, abstract = {Besides the well-documented integration of DNA flanked by the transfer DNA borders, occasional insertion of fragments from the tumor-inducing plasmid into plant genomes has also been reported during Agrobacterium tumefaciens-mediated transformation. We demonstrate that large (up to approximately 18 kb) gene-bearing fragments of Agrobacterium chromosomal DNA (AchrDNA) can be integrated into Arabidopsis thaliana genomic DNA during transformation. One in every 250 transgenic plants may carry AchrDNA fragments. This has implications for horizontal gene transfer and indicates a need for greater scrutiny of transgenic plants for undesired bacterial DNA.}, }
@article {pmid18757822, year = {2008}, author = {Viezens, J and Arvand, M}, title = {Simultaneous presence of two different copies of the 16S rRNA gene in Bartonella henselae.}, journal = {Microbiology (Reading, England)}, volume = {154}, number = {Pt 9}, pages = {2881-2886}, doi = {10.1099/mic.0.2008/018630-0}, pmid = {18757822}, issn = {1350-0872}, mesh = {Bacterial Typing Techniques ; Bartonella henselae/classification/*genetics ; Base Sequence ; Blotting, Southern ; Cloning, Molecular ; DNA, Bacterial/genetics ; Gene Dosage ; *Genes, Bacterial ; *Genes, rRNA ; Genotype ; Molecular Sequence Data ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; }, abstract = {Bartonella henselae is an emerging pathogen of increasing medical significance. Previous investigations have revealed two different 16S rRNA gene variants among B. henselae isolates, resulting in delineation of the B. henselae population into 16S RNA type I and type II isolates. While studying 191 B. henselae isolates by multi-locus sequence typing (MLST) we detected three isolates that could not be assigned to a distinct 16S RNA type upon direct sequencing because of ambiguous nucleotides in a distinct region of the 16S rRNA gene. Cloning and sequencing of the target region of the 16S rRNA gene suggested that these atypical isolates contained different 16S rRNA gene copies. Southern blot and hybridization experiments confirmed the presence of two different 16S RNA gene copies in each isolate. The isolates were further analysed by 16S RNA type-specific PCR, which assigned them to both 16S RNA types I and II. These results suggest that a small percentage of B. henselae isolates may harbour two different 16S rRNA gene copies. These isolates, which accounted for 1.6 % of the isolates in our study, have probably emerged by horizontal gene transfer. The implications of these findings for identification and genotyping studies on B. henselae are discussed.}, }
@article {pmid18757540, year = {2008}, author = {McQuiston, JR and Herrera-Leon, S and Wertheim, BC and Doyle, J and Fields, PI and Tauxe, RV and Logsdon, JM}, title = {Molecular phylogeny of the salmonellae: relationships among Salmonella species and subspecies determined from four housekeeping genes and evidence of lateral gene transfer events.}, journal = {Journal of bacteriology}, volume = {190}, number = {21}, pages = {7060-7067}, pmid = {18757540}, issn = {1098-5530}, mesh = {Gene Transfer, Horizontal/*genetics ; Molecular Sequence Data ; *Phylogeny ; Salmonella/*classification/*genetics ; Salmonella enterica/genetics ; Sequence Analysis, DNA ; }, abstract = {The salmonellae are a diverse group of bacteria within the family Enterobacteriaceae that includes two species, Salmonella enterica and Salmonella bongori. In order to characterize the phylogenetic relationships of the species and subspecies of Salmonella, we analyzed four housekeeping genes, gapA, phoP, mdh and recA, comprising 3,459 bp of nucleotide sequence data for each isolate sequenced. Sixty-one isolates representing the most common serotypes of the seven subspecies of Salmonella enterica and six isolates of Salmonella bongori were included in this study. We present a robust phylogeny of the Salmonella species and subspecies that clearly defines the lineages comprising diphasic and monophasic subspecies. Evidence of intersubspecies lateral gene transfer of the housekeeping gene recA, which has not previously been reported, was obtained.}, }
@article {pmid18757181, year = {2008}, author = {Xu, X and Kong, F and Cheng, X and Yan, B and Du, X and Gai, J and Ai, H and Shi, L and Iredell, J}, title = {Integron gene cassettes in Acinetobacter spp. strains from South China.}, journal = {International journal of antimicrobial agents}, volume = {32}, number = {5}, pages = {441-445}, doi = {10.1016/j.ijantimicag.2008.05.014}, pmid = {18757181}, issn = {0924-8579}, mesh = {Acinetobacter/drug effects/*genetics ; Acinetobacter Infections/epidemiology/microbiology ; China/epidemiology ; DNA Fingerprinting ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/drug effects/genetics ; Humans ; Integrons/*genetics ; Microbial Sensitivity Tests ; Mutagenesis, Insertional/*genetics ; Polymorphism, Restriction Fragment Length ; }, abstract = {The epidemiology of emerging antibiotic resistance genes in Asia is inadequately defined and studies within the major pools of transmissible genes such as integron gene cassettes are important. One hundred and twenty-two non-repetitive Acinetobacter spp. isolates were obtained from inpatients of a major hospital in South China. Fifty-three of these isolates contained class 1 integrons, and there is evidence of horizontal gene transfer between unrelated clones. The common pool of gene cassettes was dominated by four cassette arrays: arr3-aacA4 (24 isolates of several unrelated strains); aacC1-orfP-orfQ-aadA1a (11 isolates, probably all the same strain); aacA4-catB8-aadA1 (2 isolates); and dfrVII (1 isolate). We developed a simple restriction fragment length polymorphism (RFLP)-based identification of these and other cassettes reported in China, using readily available enzymes, to facilitate further studies of this type.}, }
@article {pmid18754789, year = {2008}, author = {Old, LA and Russell, RR}, title = {Distribution and activity of IS elements in Streptococcus mutans.}, journal = {FEMS microbiology letters}, volume = {287}, number = {2}, pages = {199-204}, doi = {10.1111/j.1574-6968.2008.01312.x}, pmid = {18754789}, issn = {0378-1097}, mesh = {Base Sequence ; *DNA Transposable Elements ; Genome, Bacterial ; Molecular Sequence Data ; Mutagenesis, Insertional ; Streptococcus mutans/*genetics ; }, abstract = {Insertion sequence (IS) elements are widely distributed selfmobilizing genetic elements that can affect genetic changes by integrating into the chromosome, mediating genetic rearrangements and facilitating horizontal gene transfer. Three members of the IS3 family have been identified in Streptococcus mutans: IS199 was discovered by its transposition while ISSmu1 and ISSmu2 were predicted from the genome sequence of S. mutans UA159. Sixty-eight strains of S. mutans were screened by PCR for carriage of the IS elements IS199, ISSmu1 and ISSmu2. Twenty-seven (30%) of the strains were positive for IS199, 33 (49%) were positive for ISSmu1 and 51 (75%) carried ISSmu2. All three IS were found in 11 strains, two were found in various combinations in 31, one was found in 16, while only 10 strains had none of the three IS for which we screened. ISSmu1 was demonstrated to be capable of transposition at a low frequency but no transposition of ISSmu2 was observed.}, }
@article {pmid18751731, year = {2008}, author = {Wagner, A and de la Chaux, N}, title = {Distant horizontal gene transfer is rare for multiple families of prokaryotic insertion sequences.}, journal = {Molecular genetics and genomics : MGG}, volume = {280}, number = {5}, pages = {397-408}, pmid = {18751731}, issn = {1617-4615}, mesh = {Bacterial Proteins/*genetics ; DNA, Ribosomal/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; *Genome, Bacterial ; *Mutagenesis, Insertional ; Phylogeny ; *Prokaryotic Cells ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Horizontal gene transfer in prokaryotes is rampant on short and intermediate evolutionary time scales. It poses a fundamental problem to our ability to reconstruct the evolutionary tree of life. Is it also frequent over long evolutionary distances? To address this question, we analyzed the evolution of 2,091 insertion sequences from all 20 major families in 438 completely sequenced prokaryotic genomes. Specifically, we mapped insertion sequence occurrence on a 16S rDNA tree of the genomes we analyzed, and we also constructed phylogenetic trees of the insertion sequence transposase coding sequences. We found only 30 cases of likely horizontal transfer among distantly related prokaryotic clades. Most of these horizontal transfer events are ancient. Only seven events are recent. Almost all of these transfer events occur between pairs of human pathogens or commensals. If true also for other, non-mobile DNA, the rarity of distant horizontal transfer increases the odds of reliable phylogenetic inference from sequence data.}, }
@article {pmid18728754, year = {2008}, author = {Brody, T and Yavatkar, AS and Lin, Y and Ross, J and Kuzin, A and Kundu, M and Fann, Y and Odenwald, WF}, title = {Horizontal gene transfers link a human MRSA pathogen to contagious bovine mastitis bacteria.}, journal = {PloS one}, volume = {3}, number = {8}, pages = {e3074}, pmid = {18728754}, issn = {1932-6203}, support = {//Intramural NIH HHS/United States ; }, mesh = {Animals ; Cattle ; Cattle Diseases/microbiology ; Chromosomes, Bacterial/genetics ; Community-Acquired Infections/microbiology/transmission ; Cross Infection/microbiology/transmission ; Female ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial ; Humans ; Mastitis, Bovine/*transmission ; Methicillin Resistance/genetics ; Staphylococcal Infections/*transmission/veterinary ; Staphylococcus aureus/*genetics ; }, abstract = {BACKGROUND: Acquisition of virulence factors and antibiotic resistance by many clinically important bacteria can be traced to horizontal gene transfer (HGT) between related or evolutionarily distant microflora. Comparative genomic analysis has become an important tool for identifying HGT DNA in emerging pathogens. We have adapted the multi-genome alignment tool EvoPrinter to facilitate discovery of HGT DNA sequences within bacterial genomes and within their mobile genetic elements.<br><br>PRINCIPAL FINDINGS: EvoPrinter analysis of 13 different Staphylococcus aureus genomes revealed that one of the human isolates, the hospital epidemic methicillin-resistant MRSA252 strain, uniquely shares multiple putative HGT DNA sequences with different causative agents of bovine mastitis that are not found in the other human S. aureus isolates. MRSA252 shares over 14 different DNA sequence blocks with the bovine mastitis ET3 S. aureus strain RF122, and many of the HGT DNAs encode virulence factors. EvoPrinter analysis of the MRSA252 chromosome also uncovered virulence-factor encoding HGT events with the genome of Listeria monocytogenes and a Staphylococcus saprophyticus associated plasmid. Both bacteria are also causal agents of contagious bovine mastitis.<br><br>CONCLUSIONS: EvoPrinter analysis reveals that the human MRSA252 strain uniquely shares multiple DNA sequence blocks with different causative agents of bovine mastitis, suggesting that HGT events may be occurring between these pathogens. These findings have important implications with regard to animal husbandry practices that inadvertently enhance the contact of human and livestock bacterial pathogens.}, }
@article {pmid18727817, year = {2008}, author = {Rounge, TB and Rohrlack, T and Kristensen, T and Jakobsen, KS}, title = {Recombination and selectional forces in cyanopeptolin NRPS operons from highly similar, but geographically remote Planktothrix strains.}, journal = {BMC microbiology}, volume = {8}, number = {}, pages = {141}, pmid = {18727817}, issn = {1471-2180}, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics ; Conserved Sequence ; Cyanobacteria/*genetics ; DNA, Bacterial/genetics ; Evolution, Molecular ; Genes, Bacterial ; Genetic Variation ; Multigene Family ; *Operon ; Peptide Synthases/*genetics ; Peptides, Cyclic/*genetics ; Phylogeny ; *Recombination, Genetic ; Selection, Genetic ; Sequence Alignment ; Sequence Analysis, Protein ; }, abstract = {BACKGROUND: Cyanopeptolins are nonribosomally produced heptapetides showing a highly variable composition. The cyanopeptolin synthetase operon has previously been investigated in three strains from the genera Microcystis, Planktothrix and Anabaena. Cyanopeptolins are displaying protease inhibitor activity, but the biological function(s) is (are) unknown. Cyanopeptolin gene cluster variability and biological functions of the peptide variants are likely to be interconnected.<br><br>RESULTS: We have investigated two cyanopeptolin gene clusters from highly similar, but geographically remote strains of the same genus. Sequencing of a nonribosomal peptide synthetase (NRPS) cyanopeptolin gene cluster from the Japanese strain Planktothrix NIES 205 (205-oci), showed the 30 kb gene cluster to be highly similar to the oci gene cluster previously described in Planktothrix NIVA CYA 116, isolated in Norway. Both operons contained seven NRPS modules, a sulfotransferase (S) and a glyceric acid loading (GA)-domain. Sequence analyses showed a high degree of conservation, except for the presence of an epimerase domain in NIES 205 and the regions around the epimerase, showing high substitution rates and Ka/Ks values above 1. The two strains produce almost identical cyanopeptolins, cyanopeptolin-1138 and oscillapeptin E respectively, but with slight differences regarding the production of minor cyanopeptolin variants. These variants may be the result of relaxed adenylation (A)-domain specificity in the nonribosomal enzyme complex. Other genetic markers (16S rRNA, ntcA and the phycocyanin cpcBA spacer) were identical, supporting that these geographically separated Planktothrix strains are closely related.<br><br>CONCLUSION: A horizontal gene transfer event resulting in exchange of a whole module-encoding region was observed. Nucleotide statistics indicate that both purifying selection and positive selection forces are operating on the gene cluster. The positive selection forces are acting within and around the epimerase insertion while purifying selection conserves the remaining (major) part of the gene cluster. The presence of an epimerase in the gene cluster is in line with the D-configuration of Htyr, determined experimentally in oscillapeptin E in a previous study.}, }
@article {pmid18725939, year = {2008}, author = {Khaldi, N and Wolfe, KH}, title = {Elusive origins of the extra genes in Aspergillus oryzae.}, journal = {PloS one}, volume = {3}, number = {8}, pages = {e3036}, pmid = {18725939}, issn = {1932-6203}, mesh = {Artifacts ; Aspergillus fumigatus/classification/genetics ; Aspergillus nidulans/classification/genetics ; Aspergillus oryzae/classification/*genetics ; Gene Deletion ; Gene Duplication ; Gene Rearrangement ; *Genes, Fungal ; Models, Genetic ; Phylogeny ; }, abstract = {The genome sequence of Aspergillus oryzae revealed unexpectedly that this species has approximately 20% more genes than its congeneric species A. nidulans and A. fumigatus. Where did these extra genes come from? Here, we evaluate several possible causes of the elevated gene number. Many gene families are expanded in A. oryzae relative to A. nidulans and A. fumigatus, but we find no evidence of ancient whole-genome duplication or other segmental duplications, either in A. oryzae or in the common ancestor of the genus Aspergillus. We show that the presence of divergent pairs of paralogs is a feature peculiar to A. oryzae and is not shared with A. nidulans or A. fumigatus. In phylogenetic trees that include paralog pairs from A. oryzae, we frequently find that one of the genes in a pair from A. oryzae has the expected orthologous relationship with A. nidulans, A. fumigatus and other species in the subphylum Eurotiomycetes, whereas the other A. oryzae gene falls outside this clade but still within the Ascomycota. We identified 456 such gene pairs in A. oryzae. Further phylogenetic analysis did not however indicate a single consistent evolutionary origin for the divergent members of these pairs. Approximately one-third of them showed phylogenies that are suggestive of horizontal gene transfer (HGT) from Sordariomycete species, and these genes are closer together in the A. oryzae genome than expected by chance, but no unique Sordariomycete donor species was identifiable. The postulated HGTs from Sordariomycetes still leave the majority of extra A. oryzae genes unaccounted for. One possible explanation for our observations is that A. oryzae might have been the recipient of many separate HGT events from diverse donors.}, }
@article {pmid18724773, year = {2008}, author = {Wassenaar, TM and Klein, G}, title = {Safety aspects and implications of regulation of probiotic bacteria in food and food supplements.}, journal = {Journal of food protection}, volume = {71}, number = {8}, pages = {1734-1741}, doi = {10.4315/0362-028x-71.8.1734}, pmid = {18724773}, issn = {0362-028X}, mesh = {*Consumer Product Safety ; Dietary Supplements/*standards ; Drug Resistance, Microbial ; *Food Microbiology ; Humans ; Legislation, Food ; *Probiotics/administration &amp; dosage/adverse effects ; Risk Assessment ; Risk Factors ; Virulence/genetics ; }, abstract = {The application of living bacteria as probiotics in food or food supplements requires a careful safety assessment. This review summarizes key issues concerning the safety aspects of bacteria added to particular products marketed for improvement of general health or treatment of (post)infectious symptoms. The bacteria used in such products should be completely safe; however, it can be challenging to provide evidence for absence of all virulence properties. In some cases, virulence factors have been detected in probiotic bacterial strains, and the implications of these traits for safety assessments are discussed. Horizontal gene transfer can result in acquisition of virulence genes or antimicrobial resistance in probiotic bacteria. Antimicrobial resistance in these bacteria can possibly aid the spread of undesired resistance in intestinal bacterial populations. The relative risk of such gene transfers is considered. The generation of complete bacterial genome sequences can both resolve and create safety issues. Current practices of safety assessment procedures in the United States and the European Union are briefly reviewed and a future outlook is provided.}, }
@article {pmid18723649, year = {2008}, author = {White, JR and Escobar-Paramo, P and Mongodin, EF and Nelson, KE and DiRuggiero, J}, title = {Extensive genome rearrangements and multiple horizontal gene transfers in a population of pyrococcus isolates from Vulcano Island, Italy.}, journal = {Applied and environmental microbiology}, volume = {74}, number = {20}, pages = {6447-6451}, pmid = {18723649}, issn = {1098-5336}, mesh = {Adaptation, Biological ; *Chromosomes, Archaeal ; DNA, Archaeal/chemistry/*genetics ; *Gene Rearrangement ; *Gene Transfer, Horizontal ; *Genome, Archaeal ; Hot Springs/*microbiology ; Italy ; Molecular Sequence Data ; Pyrococcus/*genetics/isolation &amp; purification ; Sequence Analysis, DNA ; }, abstract = {The extent of chromosome rearrangements in Pyrococcus isolates from marine hydrothermal vents in Vulcano Island, Italy, was evaluated by high-throughput genomic methods. The results illustrate the dynamic nature of the genomes of the genus Pyrococcus and raise the possibility of a connection between rapidly changing environmental conditions and adaptive genomic properties.}, }
@article {pmid18717747, year = {2008}, author = {Nedelcu, AM and Miles, IH and Fagir, AM and Karol, K}, title = {Adaptive eukaryote-to-eukaryote lateral gene transfer: stress-related genes of algal origin in the closest unicellular relatives of animals.}, journal = {Journal of evolutionary biology}, volume = {21}, number = {6}, pages = {1852-1860}, doi = {10.1111/j.1420-9101.2008.01605.x}, pmid = {18717747}, issn = {1420-9101}, mesh = {Adaptation, Biological/*genetics ; Animals ; Ascorbate Peroxidases ; Caspases/genetics ; Eukaryota/*enzymology/*genetics ; Eukaryotic Cells/*physiology ; Gene Transfer, Horizontal/*genetics ; Peroxidases/genetics ; Phylogeny ; Stress, Physiological/*genetics ; }, abstract = {In addition to mutation, gene duplication and recombination, the transfer of genetic material between unrelated species is now regarded as a potentially significant player in the shaping of extant genomes and the evolution and diversification of life. Although this is probably true for prokaryotes, the extent of such genetic exchanges in eukaryotes (especially eukaryote-to-eukaryote transfers) is more controversial and the selective advantage and evolutionary impact of such events are less documented. A laterally transferred gene could either be added to the gene complement of the recipient or replace the recipient's homologue; whereas gene replacements can be either adaptive or stochastic, gene additions are most likely adaptive. Here, we report the finding of four stress-related genes (two ascorbate peroxidase and two metacaspase genes) of algal origin in the closest unicellular relatives of animals, the choanoflagellates. At least three of these sequences represent additions to the choanoflagellate gene complement, which is consistent with these transfers being adaptive. We suggest that these laterally acquired sequences could have provided the primitive choanoflagellates with additional or more efficient means to cope with stress, especially in relation to adapting to freshwater environments and/or sessile or colonial lifestyles.}, }
@article {pmid18717596, year = {2008}, author = {Rishavy, MA and Berkner, KL}, title = {Insight into the coupling mechanism of the vitamin K-dependent carboxylase: mutation of histidine 160 disrupts glutamic acid carbanion formation and efficient coupling of vitamin K epoxidation to glutamic acid carboxylation.}, journal = {Biochemistry}, volume = {47}, number = {37}, pages = {9836-9846}, pmid = {18717596}, issn = {1520-4995}, support = {R01 HL055666/HL/NHLBI NIH HHS/United States ; R01 HL055666-11/HL/NHLBI NIH HHS/United States ; R01 HL55666/HL/NHLBI NIH HHS/United States ; }, mesh = {Anions/metabolism ; Carbon Dioxide/metabolism ; Carbon-Carbon Ligases/chemistry/*genetics/*metabolism ; Glutamic Acid/*chemistry/metabolism ; Histidine/*genetics/metabolism ; Kinetics ; *Mutation ; Protein Structure, Tertiary ; Substrate Specificity ; Vitamin K/chemistry/*metabolism ; }, abstract = {Vitamin K-dependent (VKD) proteins become activated by the VKD carboxylase, which converts Glu's to carboxylated Glu's (Gla's) in their Gla domains. The carboxylase uses vitamin K epoxidation to drive Glu carboxylation, and the two half-reactions are coupled in 1:1 stoichiometry by an unknown mechanism. We now report the first identification of a residue, His160, required for coupling. A H160A mutant showed wild-type levels of epoxidation but substantially less carboxylation. Monitoring proton abstraction using a peptide with Glu tritiated at the gamma-carbon position revealed that poor coupling was due to impaired carbanion formation. H160A showed a 10-fold lower ratio of tritium release to vitamin K epoxidation than wild-type enzyme (i.e., 0.12 versus 1.14, respectively), which could fully account for the fold decrease in coupling efficiency. The Ala substitution in His160 did not affect the K m for vitamin K and caused only a 2-fold increase in the K m for Glu and 2-fold decrease in the activation of vitamin K epoxidation by Glu. The H160A K m for CO 2 was 5-fold higher than the wild-type enzyme. However, the k cat for H160A carboxylation was 8-9-fold lower than the wild-type enzyme with all three substrates (i.e., Glu, CO 2, and vitamin K), suggesting a catalytic role for His160 in carbanion formation. We propose that His160 facilitates the formation of the transition state for carbanion formation. His160 is highly conserved in metazoan VKD carboxylases but not in some bacterial orthologues (acquired by horizontal gene transfer), which has implications for how bacteria have adapted the carboxylase for novel functions.}, }
@article {pmid18713314, year = {2008}, author = {Skamnioti, P and Furlong, RF and Gurr, SJ}, title = {Evolutionary history of the ancient cutinase family in five filamentous Ascomycetes reveals differential gene duplications and losses and in Magnaporthe grisea shows evidence of sub- and neo-functionalization.}, journal = {The New phytologist}, volume = {180}, number = {3}, pages = {711-721}, doi = {10.1111/j.1469-8137.2008.02598.x}, pmid = {18713314}, issn = {1469-8137}, support = {BB/D009766/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Ascomycota/*genetics/pathogenicity ; Base Composition ; Carboxylic Ester Hydrolases/classification/*genetics ; Evolution, Molecular ; Exons ; *Gene Duplication ; Gene Expression Profiling ; Genes, Fungal ; Introns ; Magnaporthe/*genetics/pathogenicity ; Multigene Family ; Phylogeny ; Plant Diseases ; Plant Structures ; Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis, Protein ; }, abstract = {* The cuticle is the first barrier for fungi that parasitize plants systematically or opportunistically. Here, the evolutionary history is reported of the multimembered cutinase families of the plant pathogenic Ascomycetes Magnaporthe grisea, Fusarium graminearum and Botrytis cinerea and the saprotrophic Ascomycetes Aspergillus nidulans and Neurospora crassa. * Molecular taxonomy of all fungal cutinases demonstrates a clear division into two ancient subfamilies. No evidence was found for lateral gene transfer from prokaryotes. The cutinases in the five Ascomycetes show significant copy number variation, they form six clades and their extreme sequence diversity is highlighted by the lack of consensus intron. The average ratio of gene duplication to loss is 2 : 3, with the exception of M. grisea and N. crassa, which exhibit extreme family expansion and contraction, respectively. * Detailed transcript profiling in vivo, categorizes the M. grisea cutinases into four regulatory patterns. Symmetric or asymmetric expression profiles of phylogenetically related cutinase genes suggest subfunctionalization and neofunctionalization, respectively. * The cutinase family-size per fungal species is discussed in relation to genome characteristics and lifestyle. The ancestry of the cutinase gene family, together with the expression divergence of its individual members provides a first insight into the drivers for niche differentiation in fungi.}, }
@article {pmid18710585, year = {2008}, author = {Honsa, E and Fricke, T and Stephens, AJ and Ko, D and Kong, F and Gilbert, GL and Huygens, F and Giffard, PM}, title = {Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms.}, journal = {BMC microbiology}, volume = {8}, number = {}, pages = {140}, pmid = {18710585}, issn = {1471-2180}, mesh = {Algorithms ; Alleles ; Bacterial Typing Techniques/*methods ; Computational Biology ; DNA, Bacterial/genetics ; Databases, Nucleic Acid ; Genotype ; Humans ; Infant, Newborn ; Polymerase Chain Reaction ; *Polymorphism, Single Nucleotide ; Sensitivity and Specificity ; Sequence Alignment ; Sequence Analysis, DNA ; Streptococcal Infections/microbiology ; Streptococcus agalactiae/*classification/*genetics ; }, abstract = {BACKGROUND: Streptococcus agalactiae (Group B Streptococcus (GBS)) is an important human pathogen, particularly of newborns. Emerging evidence for a relationship between genotype and virulence has accentuated the need for efficient and well-defined typing methods. The objective of this study was to develop a single nucleotide polymorphism (SNP) based method for assigning GBS isolates to multilocus sequence typing (MLST)-defined clonal complexes.<br><br>RESULTS: It was found that a SNP set derived from the MLST database on the basis of maximization of Simpsons Index of Diversity provided poor resolution and did not define groups concordant with the population structure as defined by eBURST analysis of the MLST database. This was interpreted as being a consequence of low diversity and high frequency horizontal gene transfer. Accordingly, a different approach to SNP identification was developed. This entailed use of the "Not-N" bioinformatic algorithm that identifies SNPs diagnostic for groups of known sequence variants, together with an empirical process of SNP testing. This yielded a four member SNP set that divides GBS into 10 groups that are concordant with the population structure. A fifth SNP was identified that increased the sensitivity for the clinically significant clonal complex 17 to 100%. Kinetic PCR methods for the interrogation of these SNPs were developed, and used to genotype 116 well characterized isolates.<br><br>CONCLUSION: A five SNP method for dividing GBS into biologically valid groups has been developed. These SNPs are ideal for high throughput surveillance activities, and combining with more rapidly evolving loci when additional resolution is required.}, }
@article {pmid18707609, year = {2008}, author = {Vogl, K and Wenter, R and Dressen, M and Schlickenrieder, M and Plöscher, M and Eichacker, L and Overmann, J}, title = {Identification and analysis of four candidate symbiosis genes from 'Chlorochromatium aggregatum', a highly developed bacterial symbiosis.}, journal = {Environmental microbiology}, volume = {10}, number = {10}, pages = {2842-2856}, doi = {10.1111/j.1462-2920.2008.01709.x}, pmid = {18707609}, issn = {1462-2920}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Bacterial Proteins/chemistry/*genetics ; Chlorobi/*genetics/physiology ; DNA, Bacterial/genetics/isolation &amp; purification ; *Genes, Bacterial ; Hemagglutinins/genetics ; Hemolysin Proteins/genetics ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Hybridization/methods ; Open Reading Frames ; Phylogeny ; Protein Structure, Tertiary ; Repetitive Sequences, Nucleic Acid ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Symbiosis ; }, abstract = {The consortium 'Chlorochromatium aggregatum' currently represents the most highly developed interspecific association between prokaryotes. It consists of green sulfur bacteria, so-called epibionts, which surround a central, motile, chemotrophic bacterium. Four putative symbiosis genes of the epibiont were recovered by suppression subtractive hybridization and bioinformatics approaches. These genes are transcribed constitutively and do not occur in the free-living relatives of the epibiont. The haemagglutinin-like putative gene products of open reading frames (ORFs) Cag0614 and Cag0616 are unusually large and contain repetitive regions and RGD tripeptides. Cag0616 harbours two betagamma-crystalline Greek key motifs. Cag1920 codes for a putative haemolysin whereas the gene product of Cag1919 is a putative RTX-like protein. Based on detailed analyses of Cag1919, the C-terminal amino acid sequence comprises six repetitions of the motif GGXGXD predicted to form a Ca(2+)-binding beta roll. Intact 'C. aggregatum' consortia disaggregated upon the addition of EGTA or pyrophosphate, but stayed intact in the presence of various lectine-binding sugars or proteolytic enzymes. Unlike other RTX toxins, a gene product of Cag1919 could not be detected by (45)Ca(2+) autoradiography, indicating a low abundance of the corresponding protein in the cells. The RTX-type C-terminus coded by Cag1919 exhibited a significant similarity to RTX modules of various proteobacterial proteins, suggesting that this putative symbiosis gene has been acquired via horizontal gene transfer from a proteobacterium.}, }
@article {pmid18704366, year = {2008}, author = {Lei, X and Wang, ET and Chen, WF and Sui, XH and Chen, WX}, title = {Diverse bacteria isolated from root nodules of wild Vicia species grown in temperate region of China.}, journal = {Archives of microbiology}, volume = {190}, number = {6}, pages = {657-671}, doi = {10.1007/s00203-008-0418-y}, pmid = {18704366}, issn = {1432-072X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Proteins/genetics ; China ; DNA, Ribosomal/genetics/metabolism ; Genetic Variation ; Geography ; Oxidoreductases/genetics ; Phylogeny ; Plant Roots/*microbiology ; Polymorphism, Restriction Fragment Length ; Rhizobium/classification/genetics ; Symbiosis ; Vicia/classification/*microbiology ; }, abstract = {In the present study, a total of 154 bacterial strains isolated from nodules of eighteen Vicia species mainly grown in the temperate Chinese provinces were characterized by ARDRA, ITS PCR-RFLP, BOX-PCR, sequencing of 16S rDNA, nodC, nifH, atpD and glnII, and nodulation tests. The results demonstrated that most of the R. leguminosarum strains were effective microsymbionts of the wild Vicia species, while genomic species related to Rhizobium gallicum, Mesorhizobium huakuii, Ensifer meliloti and Bradyrhizobium spp. were symbiotic bacteria occasionally nodulating with Vicia species. In addition, fourteen strains related to Agrobacterium, Phyllobacterium, Ensifer, Shinella and R. tropici, as well as 22 strains of R. leguminosarum might be nodule endophytes without symbiotic genes. Diverse symbiotic gene lineages were found among the test strains and a strong association was found among the symbiotic gene types and genomic species, indicating the absence of lateral gene transfer. These results greatly enlarged the rhizobial spectrum of Vicia species.}, }
@article {pmid18703526, year = {2008}, author = {Schjørring, S and Struve, C and Krogfelt, KA}, title = {Transfer of antimicrobial resistance plasmids from Klebsiella pneumoniae to Escherichia coli in the mouse intestine.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {62}, number = {5}, pages = {1086-1093}, pmid = {18703526}, issn = {1460-2091}, mesh = {Animals ; Anti-Bacterial Agents/administration &amp; dosage ; Colony Count, Microbial ; *Drug Resistance, Bacterial ; Escherichia coli/drug effects/*genetics ; Female ; *Gene Transfer, Horizontal ; Intestines/*microbiology ; Klebsiella pneumoniae/drug effects/*genetics ; Mice ; *Plasmids ; Selection, Genetic ; }, abstract = {OBJECTIVES AND METHODS: Klebsiella pneumoniae is a nosocomial pathogen and is considered the most common gram-negative bacterium that exhibits multiple antimicrobial resistances. In this study, the transfer of antimicrobial resistance genes from the clinical multiresistant K. pneumoniae MGH75875 isolate was assessed in vitro and in vivo in an intestinal colonization animal model. The ability to colonize and transfer was tested under different antimicrobial treatments. The frequency of the horizontal gene transfer was also examined in vitro.<br><br>RESULTS: The clinical isolate of K. pneumoniae colonized the intestine of mice at levels up to 10(9) cfu/g faeces in antimicrobial-treated mice. In mice without antimicrobial treatment, the strain quickly decreased to below the detection limit due to competitive exclusion by the indigenous mouse flora. Onset of antimicrobial treatment gave immediate rise to detectable levels of the strain in the faeces of up to 10(9) cfu/g faeces. The experiment clearly shows that the treatment selects resistant strains and gives advantages to colonize the gastrointestinal tract. Furthermore, high transfer frequency of different plasmids was observed during colonization of the mouse intestine. The bla(SHV) and bla(TEM) genotypes were transferred to both an indigenous recipient in the in vivo setting and to an MG1655 Escherichia coli recipient strain in vitro.<br><br>CONCLUSIONS: K. pneumoniae is an excellent colonizer of the intestine and is extremely promiscuous with respect to the transferability of its numerous plasmids. Antimicrobial treatment enhances the selection of resistant strains and results in an increase in the resistance gene pool, which ultimately raises the risk of spreading resistance genes.}, }
@article {pmid18701643, year = {2008}, author = {Fu, J and Wenzel, SC and Perlova, O and Wang, J and Gross, F and Tang, Z and Yin, Y and Stewart, AF and Müller, R and Zhang, Y}, title = {Efficient transfer of two large secondary metabolite pathway gene clusters into heterologous hosts by transposition.}, journal = {Nucleic acids research}, volume = {36}, number = {17}, pages = {e113}, pmid = {18701643}, issn = {1362-4962}, mesh = {Conjugation, Genetic ; *DNA Transposable Elements ; Depsipeptides/biosynthesis ; Epothilones/biosynthesis ; *Gene Transfer, Horizontal ; *Genetic Engineering ; Myxococcus xanthus/genetics ; Pseudomonas putida/genetics ; Stigmatella aurantiaca/genetics ; Transformation, Bacterial ; *Transgenes ; }, abstract = {Horizontal gene transfer by transposition has been widely used for transgenesis in prokaryotes. However, conjugation has been preferred for transfer of large transgenes, despite greater restrictions of host range. We examine the possibility that transposons can be used to deliver large transgenes to heterologous hosts. This possibility is particularly relevant to the expression of large secondary metabolite gene clusters in various heterologous hosts. Recently, we showed that the engineering of large gene clusters like type I polyketide/nonribosomal peptide pathways for heterologous expression is no longer a bottleneck. Here, we apply recombineering to engineer either the epothilone (epo) or myxochromide S (mchS) gene cluster for transpositional delivery and expression in heterologous hosts. The 58-kb epo gene cluster was fully reconstituted from two clones by stitching. Then, the epo promoter was exchanged for a promoter active in the heterologous host, followed by engineering into the MycoMar transposon. A similar process was applied to the mchS gene cluster. The engineered gene clusters were transferred and expressed in the heterologous hosts Myxococcus xanthus and Pseudomonas putida. We achieved the largest transposition yet reported for any system and suggest that delivery by transposon will become the method of choice for delivery of large transgenes, particularly not only for metabolic engineering but also for general transgenesis in prokaryotes and eukaryotes.}, }
@article {pmid18701636, year = {2008}, author = {Warren, RL and Freeman, JD and Levesque, RC and Smailus, DE and Flibotte, S and Holt, RA}, title = {Transcription of foreign DNA in Escherichia coli.}, journal = {Genome research}, volume = {18}, number = {11}, pages = {1798-1805}, pmid = {18701636}, issn = {1088-9051}, mesh = {Chromosomes, Artificial, Bacterial/genetics ; DNA, Bacterial/genetics ; DNA, Recombinant/*genetics ; DNA-Directed RNA Polymerases/genetics ; Escherichia coli/*genetics ; Gene Expression Profiling ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Engineering ; Haemophilus influenzae/genetics ; Humans ; Multigene Family ; Oligonucleotide Array Sequence Analysis ; Promoter Regions, Genetic ; Pseudomonas aeruginosa/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sigma Factor/genetics ; Species Specificity ; Transcription, Genetic ; }, abstract = {Propagation of heterologous DNA in E. coli host cells is central to molecular biology. DNA constructs are often engineered for expression of recombinant protein in E. coli, but the extent of incidental transcription arising from natural regulatory sequences in cloned DNA remains underexplored. Here, we have used programmable microarrays and RT-PCR to measure, comprehensively, the transcription of H. influenzae, P. aeruginosa, and human DNA propagating in E. coli as bacterial artificial chromosomes. We find evidence that at least half of all H. influenzae genes are transcribed in E. coli. Highly transcribed genes are principally involved in energy metabolism, and their proximal promoter regions are significantly enriched with E. coli sigma(70) (also known as RpoD) binding sites. H. influenzae genes acquired from an ancient bacteriophage Mu insertion are also highly transcribed. Compared with H. influenzae, a smaller proportion of P. aeruginosa genes are transcribed in E. coli, and in E. coli there is punctuated transcription of human DNA. The presence of foreign DNA in E. coli disturbs the host transcriptional profile, with expression of the E. coli phage shock protein operon and the flagellar gene cluster being particularly strongly up-regulated. While cross-species transcriptional activation is expected to be enabling for horizontal gene transfer in bacteria, incidental expression of toxic genes can be problematic for DNA cloning. Ongoing characterization of cross-expression will help inform the design of biosynthetic gene clusters and synthetic microbial genomes.}, }
@article {pmid18701430, year = {2008}, author = {Soria-Carrasco, V and Castresana, J}, title = {Estimation of phylogenetic inconsistencies in the three domains of life.}, journal = {Molecular biology and evolution}, volume = {25}, number = {11}, pages = {2319-2329}, doi = {10.1093/molbev/msn176}, pmid = {18701430}, issn = {1537-1719}, mesh = {Amino Acid Sequence ; Animals ; Arabidopsis/genetics ; Archaea/*classification/genetics ; Bacillus subtilis/classification/genetics ; Eukaryotic Cells/classification ; Fungi/*classification/genetics ; Gene Transfer, Horizontal ; *Phylogeny ; Proteobacteria/*classification/genetics ; Proteome ; Sequence Alignment ; }, abstract = {Discrepancies in phylogenetic trees of bacteria and archaea are often explained as lateral gene transfer events. However, such discrepancies may also be due to phylogenetic artifacts or orthology assignment problems. A first step that may help to resolve this dilemma is to estimate the extent of phylogenetic inconsistencies in trees of prokaryotes in comparison with those of higher eukaryotes, where no lateral gene transfer is expected. To test this, we used 21 proteomes each of eukaryotes (mainly opisthokonts), proteobacteria, and archaea that spanned equivalent levels of genetic divergence. In each domain of life, we defined a set of putative orthologous sequences using a phylogenetic-based orthology protocol and, as a reference topology, we used a tree constructed with concatenated genes of each domain. Our results show, for most of the tests performed, that the magnitude of topological inconsistencies with respect to the reference tree was very similar in the trees of proteobacteria and eukaryotes. When clade support was taken into account, prokaryotes showed some more inconsistencies, but then all values were very low. Discrepancies were only consistently higher in archaea but, as shown by simulation analysis, this is likely due to the particular tree of the archaeal species used here being more difficult to reconstruct, whereas the trees of proteobacteria and eukaryotes were of similar difficulty. Although these results are based on a relatively small number of genes, it seems that phylogenetic reconstruction problems, including orthology assignment problems, have a similar overall effect over prokaryotic and eukaryotic trees based on single genes. Consequently, lateral gene transfer between distant prokaryotic species may have been more rare than previously thought, which opens the way to obtain the tree of life of bacterial and archaeal species using genomic data and the concatenation of adequate genes, in the same way as it is usually done in eukaryotes.}, }
@article {pmid18698407, year = {2008}, author = {Qu, A and Brulc, JM and Wilson, MK and Law, BF and Theoret, JR and Joens, LA and Konkel, ME and Angly, F and Dinsdale, EA and Edwards, RA and Nelson, KE and White, BA}, title = {Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome.}, journal = {PloS one}, volume = {3}, number = {8}, pages = {e2945}, pmid = {18698407}, issn = {1932-6203}, mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification ; Campylobacter Infections/genetics/veterinary ; Campylobacter jejuni/classification/genetics ; Cecum/*microbiology/physiopathology ; Chickens/*genetics ; DNA, Bacterial/genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; Genomics ; Metagenome ; Phylogeny ; Poultry Diseases/genetics/microbiology ; RNA, Bacterial/genetics ; }, abstract = {BACKGROUND: The complex microbiome of the ceca of chickens plays an important role in nutrient utilization, growth and well-being of these animals. Since we have a very limited understanding of the capabilities of most species present in the cecum, we investigated the role of the microbiome by comparative analyses of both the microbial community structure and functional gene content using random sample pyrosequencing. The overall goal of this study was to characterize the chicken cecal microbiome using a pathogen-free chicken and one that had been challenged with Campylobacter jejuni.<br><br>Comparative metagenomic pyrosequencing was used to generate 55,364,266 bases of random sampled pyrosequence data from two chicken cecal samples. SSU rDNA gene tags and environmental gene tags (EGTs) were identified using SEED subsystems-based annotations. The distribution of phylotypes and EGTs detected within each cecal sample were primarily from the Firmicutes, Bacteroidetes and Proteobacteria, consistent with previous SSU rDNA libraries of the chicken cecum. Carbohydrate metabolism and virulence genes are major components of the EGT content of both of these microbiomes. A comparison of the twelve major pathways in the SEED Virulence Subsystem (metavirulome) represented in the chicken cecum, mouse cecum and human fecal microbiomes showed that the metavirulomes differed between these microbiomes and the metavirulomes clustered by host environment. The chicken cecum microbiomes had the broadest range of EGTs within the SEED Conjugative Transposon Subsystem, however the mouse cecum microbiomes showed a greater abundance of EGTs in this subsystem. Gene assemblies (32 contigs) from one microbiome sample were predominately from the Bacteroidetes, and seven of these showed sequence similarity to transposases, whereas the remaining sequences were most similar to those from catabolic gene families.<br><br>CONCLUSION/SIGNIFICANCE: This analysis has demonstrated that mobile DNA elements are a major functional component of cecal microbiomes, thus contributing to horizontal gene transfer and functional microbiome evolution. Moreover, the metavirulomes of these microbiomes appear to associate by host environment. These data have implications for defining core and variable microbiome content in a host species. Furthermore, this suggests that the evolution of host specific metavirulomes is a contributing factor in disease resistance to zoonotic pathogens.}, }
@article {pmid18695933, year = {2008}, author = {Vigne, E and Marmonier, A and Fuchs, M}, title = {Multiple interspecies recombination events within RNA2 of Grapevine fanleaf virus and Arabis mosaic virus.}, journal = {Archives of virology}, volume = {153}, number = {9}, pages = {1771-1776}, doi = {10.1007/s00705-008-0182-y}, pmid = {18695933}, issn = {0304-8608}, mesh = {Amino Acid Sequence ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Nepovirus/classification/*genetics/isolation &amp; purification ; Phylogeny ; Plant Diseases/*virology ; Sequence Alignment ; Viral Proteins/genetics ; Vitis/virology ; }, abstract = {Sequence alignments and SISCAN analyses inferred multiple interspecies recombination events within RNA2 of strains GHu of Grapevine fanleaf virus (GFLV) and Ta of Arabis mosaic virus (ArMV), two closely related subgroup A nepoviruses in the family Comoviridae. Interspecies recombination events were identified in the 5' untranslated region, the putative homing protein and movement protein genes but not in the coat protein gene and 3' untranslated region. These findings suggest a dynamic relationship between GFLV and ArMV, and a differential selection pressure on RNA2-encoded proteins with constraints in terms of function and co-adaptation that limit interspecies recombination to certain gene segments.}, }
@article {pmid18695325, year = {2008}, author = {Jayanthi, S and Ananthasubramanian, M and Appalaraju, B}, title = {Assessment of pheromone response in biofilm forming clinical isolates of high level gentamicin resistant Enterococcus faecalis.}, journal = {Indian journal of medical microbiology}, volume = {26}, number = {3}, pages = {248-251}, doi = {10.4103/0255-0857.42037}, pmid = {18695325}, issn = {0255-0857}, mesh = {Anti-Bacterial Agents/*pharmacology ; Biofilms/*growth &amp; development ; Conjugation, Genetic ; *Drug Resistance, Multiple, Bacterial ; Enterococcus faecalis/*drug effects/isolation &amp; purification/*physiology ; Gene Transfer, Horizontal ; Gentamicins/*pharmacology ; Gram-Positive Bacterial Infections/microbiology ; Humans ; Pheromones/*metabolism ; Plasmids ; Vancomycin/pharmacology ; }, abstract = {Twenty five clinical isolates of high level gentamicin resistant Enterococcus faecalis were tested for their biofilm formation and pheromone responsiveness. The biofilm assay was carried out using microtiter plate method. Two isolates out of the 25 (8%) were high biofilm formers and 19 (76%) and four (16%) isolates were moderate and weak biofilm formers respectively. All the isolates responded to pheromones of E. faecalis FA2-2 strain. On addition of pheromone producing E. faecalis FA2-2 strain to these isolates, seven of 19 (37%) moderate biofilm formers developed into high biofilm formers. Similarly one of the 4 (25%) weak biofilm formers developed into high level biofilm former. Twelve (48%) of the 25 isolates were transconjugated by cross streak method using gentamicin as selective marker. This proves that the genetic factor for gentamicin resistance is present in the pheromone responsive plasmid. Among these twelve transaconjugants, seven isolates and one isolate were high biofilm formers on addition of E. faecalis FA2-2 and prior to its addition respectively. Out of the total 25 isolates, eight transconjugants for gentamicin resistance could turn to high biofilm formers on addition of the pheromone producing strain. All the isolates were resistant to more than two antibiotics tested. All the isolates were sensitive to vancomycin. The results indicate the significance of this nosocomial pathogen in biofilm formation and the role of pheromone responding clinical isolates of E. faecalis in spread of multidrug resistance genes.}, }
@article {pmid18694346, year = {2008}, author = {Jern, P and Coffin, JM}, title = {Effects of retroviruses on host genome function.}, journal = {Annual review of genetics}, volume = {42}, number = {}, pages = {709-732}, doi = {10.1146/annurev.genet.42.110807.091501}, pmid = {18694346}, issn = {0066-4197}, support = {R37 CA 089441/CA/NCI NIH HHS/United States ; }, mesh = {Alternative Splicing ; Animals ; Biological Evolution ; Endogenous Retroviruses/genetics/pathogenicity ; Enhancer Elements, Genetic ; Gene Transfer, Horizontal ; Host-Pathogen Interactions/*genetics ; Humans ; Models, Biological ; Promoter Regions, Genetic ; Retroviridae/genetics/*pathogenicity ; Retroviridae Infections/genetics/virology ; Retroviridae Proteins/genetics/physiology ; }, abstract = {For millions of years, retroviral infections have challenged vertebrates, occasionally leading to germline integration and inheritance as ERVs, genetic parasites whose remnants today constitute some 7% to 8% of the human genome. Although they have had significant evolutionary side effects, it is useful to view ERVs as fossil representatives of retroviruses extant at the time of their insertion into the germline and not as direct players in the evolutionary process itself. Expression of particular ERVs is associated with several positive physiological functions as well as certain diseases, although their roles in human disease as etiological agents, possible contributing factors, or disease markers-well demonstrated in animal models-remain to be established. Here we discuss ERV contributions to host genome structure and function, including their ability to mediate recombination, and physiological effects on the host transcriptome resulting from their integration, expression, and other events.}, }
@article {pmid18691891, year = {2008}, author = {Briggs, DC and Day, AJ}, title = {A bug in CUB's clothing: similarity between clostridial CBMs and complement CUBs.}, journal = {Trends in microbiology}, volume = {16}, number = {9}, pages = {407-408}, doi = {10.1016/j.tim.2008.06.002}, pmid = {18691891}, issn = {0966-842X}, mesh = {Amino Acid Sequence ; Bacterial Proteins/*chemistry/genetics/metabolism ; Clostridium/*chemistry/genetics/metabolism ; Complement System Proteins/*chemistry ; Gene Transfer, Horizontal ; Humans ; Molecular Sequence Data ; Protein Binding ; Protein Structure, Tertiary ; Receptors, Cell Surface/*chemistry/genetics/metabolism ; Sequence Alignment ; }, }
@article {pmid18690211, year = {2008}, author = {La Scola, B and Desnues, C and Pagnier, I and Robert, C and Barrassi, L and Fournous, G and Merchat, M and Suzan-Monti, M and Forterre, P and Koonin, E and Raoult, D}, title = {The virophage as a unique parasite of the giant mimivirus.}, journal = {Nature}, volume = {455}, number = {7209}, pages = {100-104}, doi = {10.1038/nature07218}, pmid = {18690211}, issn = {1476-4687}, support = {//Intramural NIH HHS/United States ; }, mesh = {Amoeba/*virology ; Animals ; DNA Viruses/genetics/metabolism/*physiology/ultrastructure ; Gene Transfer, Horizontal ; Genes, Viral/genetics ; Genome, Viral/genetics ; Molecular Sequence Data ; Open Reading Frames/genetics ; Parasites/genetics/metabolism/*physiology/ultrastructure ; Viral Proteins/genetics/metabolism ; }, abstract = {Viruses are obligate parasites of Eukarya, Archaea and Bacteria. Acanthamoeba polyphaga mimivirus (APMV) is the largest known virus; it grows only in amoeba and is visible under the optical microscope. Mimivirus possesses a 1,185-kilobase double-stranded linear chromosome whose coding capacity is greater than that of numerous bacteria and archaea1, 2, 3. Here we describe an icosahedral small virus, Sputnik, 50 nm in size, found associated with a new strain of APMV. Sputnik cannot multiply in Acanthamoeba castellanii but grows rapidly, after an eclipse phase, in the giant virus factory found in amoebae co-infected with APMV4. Sputnik growth is deleterious to APMV and results in the production of abortive forms and abnormal capsid assembly of the host virus. The Sputnik genome is an 18.343-kilobase circular double-stranded DNA and contains genes that are linked to viruses infecting each of the three domains of life Eukarya, Archaea and Bacteria. Of the 21 predicted protein-coding genes, eight encode proteins with detectable homologues, including three proteins apparently derived from APMV, a homologue of an archaeal virus integrase, a predicted primase-helicase, a packaging ATPase with homologues in bacteriophages and eukaryotic viruses, a distant homologue of bacterial insertion sequence transposase DNA-binding subunit, and a Zn-ribbon protein. The closest homologues of the last four of these proteins were detected in the Global Ocean Survey environmental data set5, suggesting that Sputnik represents a currently unknown family of viruses. Considering its functional analogy with bacteriophages, we classify this virus as a virophage. The virophage could be a vehicle mediating lateral gene transfer between giant viruses.}, }
@article {pmid18689675, year = {2008}, author = {Udden, SM and Zahid, MS and Biswas, K and Ahmad, QS and Cravioto, A and Nair, GB and Mekalanos, JJ and Faruque, SM}, title = {Acquisition of classical CTX prophage from Vibrio cholerae O141 by El Tor strains aided by lytic phages and chitin-induced competence.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {33}, pages = {11951-11956}, pmid = {18689675}, issn = {1091-6490}, support = {R01 AI070963/AI/NIAID NIH HHS/United States ; R01 GM068851/GM/NIGMS NIH HHS/United States ; AI070963-01A1/AI/NIAID NIH HHS/United States ; 2R01-GM068851-5/GM/NIGMS NIH HHS/United States ; }, mesh = {Chitin/*pharmacology ; DNA, Viral/genetics ; Genome, Viral/genetics ; Microsomes/metabolism ; Prophages/*genetics ; Vibrio cholerae/*drug effects/*virology ; }, abstract = {The El Tor biotype of Vibrio cholerae O1, causing the current seventh pandemic of cholera, has replaced the classical biotype, which caused the sixth pandemic. The CTX prophages encoding cholera toxin in the two biotypes have distinct repressor (rstR) genes. Recently, new variants of El Tor strains that carry the classical type (CTX(class)) prophage have emerged. These "hybrid" strains apparently originate through lateral gene transfer and recombination events. To explore possible donors of the CTX(class) prophage and its mode of transfer, we tested environmental V. cholerae isolates for the presence of CTX(class) prophage and mobility of the phage genome. Of the 272 environmental V. cholerae isolates tested, 6 were found to carry the CTX(class) prophage; all of these belonged to the O141 serogroup. These O141 strains were unable to produce infectious CTX(class) phage or to transmit the prophage to recipient strains in the mouse model of infection; however, the CTX(class) prophage was acquired by El Tor strains when cultured with the O141 strains in microcosms composed of filtered environmental water, a chitin substrate, and a V. cholerae O141-specific bacteriophage. The CTX(class) prophage either coexisted with or replaced the resident CTX(ET) prophage, resulting in El Tor strains with CTX genotypes similar to those of the naturally occurring hybrid strains. Our results support a model involving phages and natural chitin substrate in the emergence of new variants of pathogenic V. cholerae. Furthermore, the O141 strains apparently represent an alternative reservoir of the CTX(class) phage genome, because the classical V. cholerae O1 strains are possibly extinct.}, }
@article {pmid18685665, year = {2008}, author = {Pearson, H}, title = {'Virophage' suggests viruses are alive.}, journal = {Nature}, volume = {454}, number = {7205}, pages = {677}, doi = {10.1038/454677a}, pmid = {18685665}, issn = {1476-4687}, mesh = {DNA Viruses/genetics/isolation &amp; purification/*physiology ; Gene Transfer, Horizontal ; Genes, Viral/genetics ; Genome, Viral ; Host-Parasite Interactions ; *Life ; Marine Biology ; Plankton/virology ; Satellite Viruses/genetics/*pathogenicity ; *Virus Physiological Phenomena ; Virus Replication ; }, }
@article {pmid18684330, year = {2008}, author = {Rogozin, IB and Makarova, KS and Pavlov, YI and Koonin, EV}, title = {A highly conserved family of inactivated archaeal B family DNA polymerases.}, journal = {Biology direct}, volume = {3}, number = {}, pages = {32}, pmid = {18684330}, issn = {1745-6150}, support = {R01 CA129925/CA/NCI NIH HHS/United States ; 1R01CA129925-01A1/CA/NCI NIH HHS/United States ; /ImNIH/Intramural NIH HHS/United States ; }, mesh = {Archaea/*enzymology/*genetics ; Archaeal Proteins/antagonists &amp; inhibitors/chemistry/classification/genetics ; Catalytic Domain/genetics ; *Conserved Sequence ; DNA Replication/genetics ; DNA-Directed DNA Polymerase/chemistry/classification/genetics ; Evolution, Molecular ; *Multigene Family ; *Nucleic Acid Synthesis Inhibitors ; Phylogeny ; Protein Subunits/*antagonists &amp; inhibitors/chemistry/classification/genetics ; Pseudogenes/genetics ; }, abstract = {A widespread and highly conserved family of apparently inactivated derivatives of archaeal B-family DNA polymerases is described. Phylogenetic analysis shows that the inactivated forms comprise a distinct clade among archaeal B-family polymerases and that, within this clade, Euryarchaea and Crenarchaea are clearly separated from each other and from a small group of bacterial homologs. These findings are compatible with an ancient duplication of the DNA polymerase gene followed by inactivation and parallel loss in some of the lineages although contribution of horizontal gene transfer cannot be ruled out. The inactivated derivative of the archaeal DNA polymerase could form a complex with the active paralog and play a structural role in DNA replication.}, }
@article {pmid18682209, year = {2008}, author = {Archibald, JM}, title = {Plastid evolution: remnant algal genes in ciliates.}, journal = {Current biology : CB}, volume = {18}, number = {15}, pages = {R663-R665}, doi = {10.1016/j.cub.2008.06.031}, pmid = {18682209}, issn = {0960-9822}, mesh = {Algal Proteins/*genetics ; Animals ; Eukaryota/*genetics ; Gene Transfer, Horizontal ; Genomics ; Photosynthesis ; *Phylogeny ; Plastids/*genetics ; Symbiosis ; Tetrahymena/cytology/*genetics ; }, abstract = {Determination of the number of times that plastids have been gained and lost during eukaryotic evolution has proven difficult. A recent study has uncovered what could be the molecular signature of a photosynthetic ancestry for an important plastid-lacking lineage of microbial eukaryotes--the ciliates.}, }
@article {pmid18681968, year = {2008}, author = {Borin, S and Crotti, E and Mapelli, F and Tamagnini, I and Corselli, C and Daffonchio, D}, title = {DNA is preserved and maintains transforming potential after contact with brines of the deep anoxic hypersaline lakes of the Eastern Mediterranean Sea.}, journal = {Saline systems}, volume = {4}, number = {}, pages = {10}, pmid = {18681968}, issn = {1746-1448}, abstract = {BACKGROUND: Extracellular dissolved DNA has been demonstrated to be present in many terrestrial and aquatic environments, actively secreted, or released by decaying cells. Free DNA has the genetic potential to be acquired by living competent cells by horizontal gene transfer mediated by natural transformation. The aim of this work is to study the persistence of extracellular DNA and its biological transforming activity in extreme environments like the deep hypersaline anoxic lakes of the Mediterranean Sea. The brine lakes are separated from the upper seawater by a steep chemocline inhabited by stratified prokaryotic networks, where cells sinking through the depth profile encounter increasing salinity values and osmotic stress.<br><br>RESULTS: Seven strains belonging to different taxonomic groups isolated from the seawater-brine interface of four hypersaline lakes were grown at medium salinity and then incubated in the brines. The osmotic stress induced the death of all the inoculated cells in variable time periods, between 2 hours and 144 days, depending on the type of brine rather than the taxonomic group of the strains, i.e. Bacillaceae or gamma-proteobacteria. The Discovery lake confirmed to be the most aggressive environment toward living cells. In all the brines and in deep seawater dissolved plasmid DNA was substantially preserved for a period of 32 days in axenic conditions. L'Atalante and Bannock brines induced a decrease of the supercoiled form up to 70 and 40% respectively; in the other brines only minor changes in plasmid conformation were observed. Plasmid DNA after incubation in the brines maintained the capacity to transform naturally competent cells of Acinetobacter baylii strain BD413.<br><br>CONCLUSION: Free dissolved DNA is likely to be released by the lysis of cells induced by osmotic stress in the deep hypersaline anoxic lakes. Naked DNA was demonstrated to be preserved and biologically active in these extreme environments, and hence could constitute a genetic reservoir of traits acquirable by horizontal gene transfer.}, }
@article {pmid18680424, year = {2008}, author = {Stukenbrock, EH and McDonald, BA}, title = {The origins of plant pathogens in agro-ecosystems.}, journal = {Annual review of phytopathology}, volume = {46}, number = {}, pages = {75-100}, doi = {10.1146/annurev.phyto.010708.154114}, pmid = {18680424}, issn = {0066-4286}, mesh = {*Agriculture ; *Ecosystem ; Host-Parasite Interactions/*physiology ; Plant Diseases/*microbiology ; Plants/*microbiology ; }, abstract = {Plant pathogens can emerge in agricultural ecosystems through several mechanisms, including host-tracking, host jumps, hybridization and horizontal gene transfer. High-throughput DNA sequencing coupled with new analytical approaches make it possible to differentiate among these mechanisms and to infer the time and place where pathogens first emerged. We present several examples to illustrate the different mechanisms and timescales associated with the origins of important plant pathogens. In some cases pathogens were domesticated along with their hosts during the invention of agriculture approximately 10,000 years ago. In other cases pathogens appear to have emerged very recently and almost instantaneously following horizontal gene transfer or hybridization. The predominant unifying feature in these examples is the environmental and genetic uniformity of the agricultural ecosystem in which the pathogens emerged. We conclude that agro-ecosystems will continue to select for new pathogens unless they are re-engineered to make them less conducive to pathogen emergence.}, }
@article {pmid18678909, year = {2008}, author = {Dym, O and Albeck, S and Unger, T and Jacobovitch, J and Branzburg, A and Michael, Y and Frenkiel-Krispin, D and Wolf, SG and Elbaum, M}, title = {Crystal structure of the Agrobacterium virulence complex VirE1-VirE2 reveals a flexible protein that can accommodate different partners.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {32}, pages = {11170-11175}, pmid = {18678909}, issn = {1091-6490}, mesh = {Active Transport, Cell Nucleus/physiology ; Agrobacterium tumefaciens/*chemistry/metabolism ; Bacterial Proteins/*chemistry/metabolism ; Cytoplasm/enzymology ; DNA, Bacterial/chemistry/metabolism ; DNA, Single-Stranded/chemistry/metabolism ; DNA-Binding Proteins/*chemistry/metabolism ; Deoxyribonucleases/metabolism ; Dimerization ; Gene Transfer, Horizontal/physiology ; Ion Channels/*chemistry/metabolism ; Molecular Chaperones/*chemistry/metabolism ; Multiprotein Complexes/*chemistry/metabolism ; Plants/enzymology/genetics/microbiology ; Protein Binding/physiology ; Protein Folding ; Protein Structure, Quaternary/physiology ; Protein Structure, Tertiary/physiology ; Static Electricity ; Virulence Factors/*chemistry/metabolism ; }, abstract = {Agrobacterium tumefaciens infects its plant hosts by a mechanism of horizontal gene transfer. This capability has led to its widespread use in artificial genetic transformation. In addition to DNA, the bacterium delivers an abundant ssDNA binding protein, VirE2, whose roles in the host include protection from cytoplasmic nucleases and adaptation for nuclear import. In Agrobacterium, VirE2 is bound to its acidic chaperone VirE1. When expressed in vitro in the absence of VirE1, VirE2 is prone to oligomerization and forms disordered filamentous aggregates. These filaments adopt an ordered solenoidal form in the presence of ssDNA, which was characterized previously by electron microscopy and three-dimensional image processing. VirE2 coexpressed in vitro with VirE1 forms a soluble heterodimer. VirE1 thus prevents VirE2 oligomerization and competes with its binding to ssDNA. We present here a crystal structure of VirE2 in complex with VirE1, showing that VirE2 is composed of two independent domains presenting a novel fold, joined by a flexible linker. Electrostatic interactions with VirE1 cement the two domains of VirE2 into a locked form. Comparison with the electron microscopy structure indicates that the VirE2 domains adopt different relative orientations. We suggest that the flexible linker between the domains enables VirE2 to accommodate its different binding partners.}, }
@article {pmid18677522, year = {2009}, author = {Novikova, O and Fet, V and Blinov, A}, title = {Non-LTR retrotransposons in fungi.}, journal = {Functional &amp; integrative genomics}, volume = {9}, number = {1}, pages = {27-42}, pmid = {18677522}, issn = {1438-7948}, mesh = {Amino Acid Sequence ; Evolution, Molecular ; Fungi/*genetics ; Gene Transfer, Horizontal ; Genetic Variation ; Genome, Fungal/genetics ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Tertiary ; Retroelements/*genetics ; Ribonuclease H/chemistry ; Sequence Alignment ; Sequence Analysis, DNA ; Terminal Repeat Sequences/*genetics ; }, abstract = {Non-long terminal repeat (non-LTR) retrotransposons have contributed to shaping the structure and function of genomes. Fungi have small genomes, usually with limited amounts of repetitive DNA. In silico approach has been used to survey the non-LTR elements in 57 fungal genomes. More than 100 novel non-LTR retrotransposons were found, which belonged to five diverse clades. The present survey identified two novel clades of fungal non-LTR retrotransposons. The copy number of non-LTR retroelements varied widely. Some of the studied species contained a single copy of non-LTR retrotransposon, whereas others possessed a great number of non-LTR retrotransposon copies per genome. Although evolutionary relationships of most elements are congruent with phylogeny of host species, a new case of possible horizontal transfer was found between Eurotiomycetes and Sordariomycetes.}, }
@article {pmid18676448, year = {2008}, author = {Kim, KM and Sung, S and Caetano-Anollés, G and Han, JY and Kim, H}, title = {An approach of orthology detection from homologous sequences under minimum evolution.}, journal = {Nucleic acids research}, volume = {36}, number = {17}, pages = {e110}, pmid = {18676448}, issn = {1362-4962}, mesh = {*Algorithms ; Confidence Intervals ; DNA/chemistry ; Evolution, Molecular ; Gene Transfer, Horizontal ; Globins/genetics ; *Phylogeny ; Sequence Alignment ; *Sequence Homology, Amino Acid ; *Sequence Homology, Nucleic Acid ; Software ; }, abstract = {In the field of phylogenetics and comparative genomics, it is important to establish orthologous relationships when comparing homologous sequences. Due to the slight sequence dissimilarity between orthologs and paralogs, it is prone to regarding paralogs as orthologs. For this reason, several methods based on evolutionary distance, phylogeny and BLAST have tried to detect orthologs with more precision. Depending on their algorithmic implementations, each of these methods sometimes has increased false negative or false positive rates. Here, we developed a novel algorithm for orthology detection that uses a distance method based on the phylogenetic criterion of minimum evolution. Our algorithm assumes that sets of sequences exhibiting orthologous relationships are evolutionarily less costly than sets that include one or more paralogous relationships. Calculation of evolutionary cost requires the reconstruction of a neighbor-joining (NJ) tree, but calculations are unaffected by the topology of any given NJ tree. Unlike tree reconciliation, our algorithm appears free from the problem of incorrect topologies of species and gene trees. The reliability of the algorithm was tested in a comparative analysis with two other orthology detection methods using 95 manually curated KOG datasets and 21 experimentally verified EXProt datasets. Sensitivity and specificity estimates indicate that the concept of minimum evolution could be valuable for the detection of orthologs.}, }
@article {pmid18675485, year = {2008}, author = {Lampkowska, J and Feld, L and Monaghan, A and Toomey, N and Schjørring, S and Jacobsen, B and van der Voet, H and Andersen, SR and Bolton, D and Aarts, H and Krogfelt, KA and Wilcks, A and Bardowski, J}, title = {A standardized conjugation protocol to asses antibiotic resistance transfer between lactococcal species.}, journal = {International journal of food microbiology}, volume = {127}, number = {1-2}, pages = {172-175}, doi = {10.1016/j.ijfoodmicro.2008.06.017}, pmid = {18675485}, issn = {0168-1605}, mesh = {Anti-Bacterial Agents/pharmacology ; Colony Count, Microbial ; *Conjugation, Genetic ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/*genetics ; Food Microbiology ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Lactococcus lactis/*genetics/*growth &amp; development ; Microbial Sensitivity Tests ; Plasmids/*genetics ; Population Density ; Species Specificity ; }, abstract = {Optimal conditions and a standardized method for conjugation between two model lactococcal strains, Lactococcus lactis SH4174 (pAMbeta1-containing, erythromycin resistant donor) and L. lactis Bu2-60 (plasmid-free, erythromycin sensitive recipient), were developed and tested in a inter-laboratory experiments involving five laboratories from different countries. The ultimate goal of the study was to assess the microbial potential of antibiotic resistance transfer among Lactic Acid Bacteria (LAB). The influence of culture age (various OD values) and ratios of donor and recipient cultures as well as filter, solid and liquid mating techniques, were examined in order to optimize the conjugation protocol. In the result of these studies, we concluded that the donor-to-recipient ratio appear to be important; the most efficient technique for conjugation was filter mating and the optimal conditions for gene transfer were observed when late logarithmic cultures of both donor and recipient were used. Comparison of conjugal transfer frequencies between five partner laboratories showed that results are sufficiently intra-laboratory repeatable and inter-laboratory comparable. This is the first study of this kind, in which a standardized protocol of conjugal mating for testing antibiotic resistance dissemination among LAB was established and validated.}, }
@article {pmid18673073, year = {2008}, author = {Chan, K and Elhanafi, D and Kathariou, S}, title = {Genomic evidence for interspecies acquisition of chromosomal DNA from Campylobacter jejuni by Campylobacter coli strains of a turkey-associated clonal group (cluster II).}, journal = {Foodborne pathogens and disease}, volume = {5}, number = {4}, pages = {387-398}, doi = {10.1089/fpd.2008.0113}, pmid = {18673073}, issn = {1556-7125}, mesh = {Animals ; Bacterial Typing Techniques ; Base Composition ; Campylobacter coli/classification/*genetics ; Campylobacter jejuni/classification/*genetics ; Chromosomes, Bacterial/*genetics ; DNA, Bacterial/*genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; INDEL Mutation ; Molecular Sequence Data ; Open Reading Frames ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; Sequence Alignment ; Sequence Analysis, DNA ; Turkeys/microbiology ; }, abstract = {Previous multilocus sequence typing studies of Campylobacter coli from meat animals identified an unusual cluster of strains, primarily from turkeys, termed "cluster II" and characterized by the presence of the C. jejuni aspA103 allele. To characterize the extent of genomic input from C. jejuni in the aspA region of cluster II C. coli, we sequenced the 6.1 kb genomic region upstream of and including aspA from two turkey-derived cluster II strains (C. coli 6979 and C. coli 7474, of ST-1150 and ST-1161, respectively), as well as from a turkey-derived multidrug-resistant strain (C. coli 6818) representing a major sequence type (ST-1101) outside of cluster II. A gene encoding a putative CRP-family transcriptional regulator (CCO0137) was present in C. coli 6818 and the reference strain C. coli RM2228, whose genome has been sequenced, but not in either cluster II strain evaluated. This gene was also absent from C. jejuni NCTC 11168 and C. jejuni RM1221. Moreover, single nucleotide polymorphism (SNP) analysis revealed that in both cluster II strains, genes encoding subunit II of cytochrome d ubiquinol oxidase (cydB) and a putative aspartate racemase (Cj0085c) harbored numerous C. jejuni-specific SNPs. Interestingly, genes encoding subunit I of cytochrome d ubiquinol oxidase (cydA), uracil-DNA glycosylase (ung), and aspartate ammonia-lyase (aspA) harbored C. coli-specific SNPs in certain portions but C. jejuni-specific SNPs in others, suggesting that these were hybrid genes with C. jejuni-derived segments. Analysis of a ung mutant in C. coli 7474 indicated that the putative hybrid ung of this cluster II strain was functional. Our data suggest the occurrence of recombination events that resulted in genomic import of DNA from C. jejuni in the region between cydA and aspA in cluster II strains of C. coli.}, }
@article {pmid18667942, year = {2008}, author = {Kallman, JC and Phillips, JO and Bramhall, NF and Kelly, JP and Street, VA}, title = {In search of the DFNA11 myosin VIIA low- and mid-frequency auditory genetic modifier.}, journal = {Otology &amp; neurotology : official publication of the American Otological Society, American Neurotology Society [and] European Academy of Otology and Neurotology}, volume = {29}, number = {6}, pages = {860-867}, pmid = {18667942}, issn = {1537-4505}, support = {P30 DC004661/DC/NIDCD NIH HHS/United States ; P30 DC04661/DC/NIDCD NIH HHS/United States ; R01 DC006901-04/DC/NIDCD NIH HHS/United States ; R03 DC004945/DC/NIDCD NIH HHS/United States ; R01 DC006901-05/DC/NIDCD NIH HHS/United States ; DC04945/DC/NIDCD NIH HHS/United States ; }, mesh = {Caloric Tests ; Gene Transfer, Horizontal/genetics ; Hearing Loss, Sensorineural/diagnosis/*genetics ; Humans ; Male ; Membrane Proteins/genetics ; Myosin VIIa ; Myosins/*genetics ; Pedigree ; Plasma Membrane Calcium-Transporting ATPases/genetics ; Point Mutation/genetics ; Polymorphism, Single Nucleotide/genetics ; Severity of Illness Index ; Sex Factors ; Usher Syndromes/diagnosis/*genetics ; Wolfram Syndrome/genetics ; }, abstract = {OBJECTIVES: To evaluate the auditory, vestibular, and retinal characteristics of a large American DFNA11 pedigree with autosomal dominant progressive sensorineural hearing loss that first impacts the low- and mid-frequency auditory range. The pedigree (referred to as the HL2 family) segregates a myosin VIIA (MYO7A) mutation in exon 17 at DNA residue G2164C (MYO7A) that seems to be influenced by a genetic modifier that either rescues or exacerbates the MYO7A alteration. DNA analysis to examine single-nucleotide polymorphisms in 2 candidate modifier genes (ATP2B2 and Wolfram syndrome 1 [WFS1]) is summarized in this report.<br><br>STUDY DESIGN: Family study.<br><br>RESULTS: The degree of low- and mid-frequency hearing loss in HL2 family members segregating the MYO7A mutation varies from mild to more severe, with approximately the same number of HL2 family members falling at each end of the severity spectrum. The extent of hearing loss in HL2 individuals can vary between family generations. Differences in the degree of hearing loss in MYO7A HL2 family members may be mirrored by vestibular function in at least 2 of these same individuals. The single-nucleotide polymorphisms examined within ATP2B2 and WFS1 did not segregate with the mild versus more severe auditory phenotype.<br><br>CONCLUSION: The severity of the auditory and vestibular phenotypes in MYO7A HL2 family members may run in parallel, suggesting a common modifier gene within the inner ear. The putative MYO7A genetic modifier is likely to represent a common polymorphism that is not linked tightly to the MYO7A mutation on the MYO7A allele.}, }
@article {pmid18662388, year = {2008}, author = {Than, C and Ruths, D and Nakhleh, L}, title = {PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships.}, journal = {BMC bioinformatics}, volume = {9}, number = {}, pages = {322}, pmid = {18662388}, issn = {1471-2105}, mesh = {*Biological Evolution ; Chimera ; Gene Transfer, Horizontal ; Genetic Speciation ; *Models, Genetic ; *Phylogeny ; Recombination, Genetic ; *Software ; }, abstract = {BACKGROUND: Phylogenies, i.e., the evolutionary histories of groups of taxa, play a major role in representing the interrelationships among biological entities. Many software tools for reconstructing and evaluating such phylogenies have been proposed, almost all of which assume the underlying evolutionary history to be a tree. While trees give a satisfactory first-order approximation for many families of organisms, other families exhibit evolutionary mechanisms that cannot be represented by trees. Processes such as horizontal gene transfer (HGT), hybrid speciation, and interspecific recombination, collectively referred to as reticulate evolutionary events, result in networks, rather than trees, of relationships. Various software tools have been recently developed to analyze reticulate evolutionary relationships, which include SplitsTree4, LatTrans, EEEP, HorizStory, and T-REX.<br><br>RESULTS: In this paper, we report on the PhyloNet software package, which is a suite of tools for analyzing reticulate evolutionary relationships, or evolutionary networks, which are rooted, directed, acyclic graphs, leaf-labeled by a set of taxa. These tools can be classified into four categories: (1) evolutionary network representation: reading/writing evolutionary networks in a newly devised compact form; (2) evolutionary network characterization: analyzing evolutionary networks in terms of three basic building blocks - trees, clusters, and tripartitions; (3) evolutionary network comparison: comparing two evolutionary networks in terms of topological dissimilarities, as well as fitness to sequence evolution under a maximum parsimony criterion; and (4) evolutionary network reconstruction: reconstructing an evolutionary network from a species tree and a set of gene trees.<br><br>CONCLUSION: The software package, PhyloNet, offers an array of utilities to allow for efficient and accurate analysis of evolutionary networks. The software package will help significantly in analyzing large data sets, as well as in studying the performance of evolutionary network reconstruction methods. Further, the software package supports the proposed eNewick format for compact representation of evolutionary networks, a feature that allows for efficient interoperability of evolutionary network software tools. Currently, all utilities in PhyloNet are invoked on the command line.}, }
@article {pmid18662313, year = {2008}, author = {Coupat, B and Chaumeille-Dole, F and Fall, S and Prior, P and Simonet, P and Nesme, X and Bertolla, F}, title = {Natural transformation in the Ralstonia solanacearum species complex: number and size of DNA that can be transferred.}, journal = {FEMS microbiology ecology}, volume = {66}, number = {1}, pages = {14-24}, doi = {10.1111/j.1574-6941.2008.00552.x}, pmid = {18662313}, issn = {0168-6496}, mesh = {DNA, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; Phylogeny ; Plasmids ; Ralstonia solanacearum/*genetics ; *Transformation, Bacterial ; }, abstract = {Ralstonia solanacearum is a widely distributed phytopathogenic bacterium that is known to invade more than 200 host species, mainly in tropical areas. Reference strain GMI1000 is naturally transformable at in vitro and also in planta conditions and thus has the ability to acquire free exogenous DNA. We tested the ubiquity and variability of natural transformation in the four phylotypes of this species complex using 55 strains isolated from different hosts and geographical regions. Eighty per cent of strains distributed in all the phylotypes were naturally transformable by plasmids and/or genomic DNA. Transformability can be considered as a ubiquitous physiological trait in the R. solanacearum species complex. Transformation performed with two independent DNA donors showed that multiple integration events occurred simultaneously in two distant genomic regions. We also engineered a fourfold-resistant R. solanacearum GMI1000 mutant RS28 to evaluate the size of DNA exchanged during natural transformation. The results demonstrated that this bacterium was able to exchange large DNA fragments ranging from 30 to 90 kb by DNA replacement. The combination of these findings indicated that the natural transformation mechanism could be the main driving force of genetic diversification of the R. solanacearum species complex.}, }
@article {pmid18661249, year = {2008}, author = {Carter, DR}, title = {Plastocyanin-ferredoxin oxidoreduction and endosymbiotic gene transfer.}, journal = {Photosynthesis research}, volume = {97}, number = {3}, pages = {245-253}, pmid = {18661249}, issn = {0166-8595}, mesh = {Cyanobacteria/genetics/metabolism ; DNA, Chloroplast/genetics ; Eukaryota/cytology/genetics ; Evolution, Molecular ; Ferredoxins/*metabolism ; *Gene Transfer, Horizontal ; Oxidation-Reduction ; Plastocyanin/*metabolism ; Symbiosis/genetics ; Synechocystis/genetics/metabolism ; }, abstract = {Sequence similarities of proteins associated with plastocyanin-ferredoxin oxidoreduction (PcFdOR) activity of Photosystem I (PSI) were grouped and compared. PsaA, psaB, psaC, and petG represent genes that have been retained in the chloroplasts of both green- and red-lineage species. PsaD, psaE, psaF, and petF represent genes that have been retained in the chloroplast of red-lineage species, but have been transferred to the nuclear genome of green-lineage species. Translated sequences from red- and green-lineage proteins were compared to that of contemporary cyanobacteria, Synechocystis PCC 6803, and Gloeobacter violaceus PCC 7421. Within the green lineage, a lower level of sequence conservation coincided with gene transfer to the nuclear genome. Surprisingly, a similar pattern of sequence conservation existed for the same set of genes found in the red lineage even though all those genes were retained in their chloroplast genomes. This discrepancy between green and red lineage is discussed in terms of endosymbiotic gene transfer.}, }
@article {pmid18660532, year = {2008}, author = {Deredec, A and Burt, A and Godfray, HC}, title = {The population genetics of using homing endonuclease genes in vector and pest management.}, journal = {Genetics}, volume = {179}, number = {4}, pages = {2013-2026}, pmid = {18660532}, issn = {0016-6731}, mesh = {Animals ; Disease Vectors ; Endonucleases/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genetics, Population ; Models, Theoretical ; Pest Control/*methods ; X Chromosome ; Y Chromosome ; }, abstract = {Homing endonuclease genes (HEGs) encode proteins that in the heterozygous state cause double-strand breaks in the homologous chromosome at the precise position opposite the HEG. If the double-strand break is repaired using the homologous chromosome, the HEG becomes homozygous, and this represents a powerful genetic drive mechanism that might be used as a tool in managing vector or pest populations. HEGs may be used to decrease population fitness to drive down population densities (possibly causing local extinction) or, in disease vectors, to knock out a gene required for pathogen transmission. The relative advantages of HEGs that target viability or fecundity, that are active in one sex or both, and whose target is expressed before or after homing are explored. The conditions under which escape mutants arise are also analyzed. A different strategy is to place HEGs on the Y chromosome that cause one or more breaks on the X chromosome and so disrupt sex ratio. This strategy can cause severe sex-ratio biases with efficiencies that depend on the details of sperm competition and zygote mortality. This strategy is probably less susceptible to escape mutants, especially when multiple X shredders are used.}, }
@article {pmid18657113, year = {2008}, author = {Zhao, CT and Wang, ET and Chen, WF and Chen, WX}, title = {Diverse genomic species and evidences of symbiotic gene lateral transfer detected among the rhizobia associated with Astragalus species grown in the temperate regions of China.}, journal = {FEMS microbiology letters}, volume = {286}, number = {2}, pages = {263-273}, doi = {10.1111/j.1574-6968.2008.01282.x}, pmid = {18657113}, issn = {0378-1097}, mesh = {Astragalus Plant/*microbiology ; Bacterial Proteins/genetics ; China ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; N-Acetylglucosaminyltransferases/genetics ; Oxidoreductases/genetics ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Rhizobiaceae/*classification/genetics/*isolation &amp; purification ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; }, abstract = {Based on the analyses of ribosomal DNA and housekeeping genes, a total of 118 bacterial isolates obtained from 13 Astragalus species grown in the temperate region of China were identified as 19 genomic species of Mesorhizobium, Rhizobium, Sinorhizobium and Bradyrhizobium, two of them being putatively new species. Phylogenetic comparison of symbiotic genes (nodC and nifH) and housekeeping genes showed that the symbiotic genes of the Astragalus rhizobia were maintained by both vertical and horizontal transfer. The results demonstrated that the Astragalus species were very promiscuous hosts for rhizobia and that their rhizobia had very diverse genomic and symbiotic gene backgrounds.}, }
@article {pmid18653732, year = {2008}, author = {Minguet, EG and Vera-Sirera, F and Marina, A and Carbonell, J and Blázquez, MA}, title = {Evolutionary diversification in polyamine biosynthesis.}, journal = {Molecular biology and evolution}, volume = {25}, number = {10}, pages = {2119-2128}, doi = {10.1093/molbev/msn161}, pmid = {18653732}, issn = {1537-1719}, mesh = {Animals ; Evolution, Molecular ; Humans ; Methyltransferases/*metabolism ; Models, Biological ; Models, Chemical ; Models, Genetic ; Phylogeny ; Polyamines/chemistry/*metabolism ; Putrescine/metabolism ; Spermidine/metabolism ; Spermidine Synthase/metabolism ; Spermine/metabolism ; Spermine Synthase/genetics/metabolism ; }, abstract = {Polyamine biosynthesis is an ancient metabolic pathway present in all organisms. Aminopropyltransferases are key enzymes that mediate the synthesis of spermidine, spermine, and thermospermine. The relatively high sequence similarity between aminopropyltransferases and their similarity with putrescine N-methyltransferases (PMT) raises the question of whether they share a common ancestor or have evolved by convergence. Here we show that aminopropyltransferases and PMT are phylogenetically interconnected, and the different activities have been generated by unusually frequent events of diversification of existing functions. Although all spermidine synthases (SPDSs) derive from a common ancestor preceding the separation between prokaryotes and eukaryotes, they have been the origin of a variety of new activities. Among those, spermine synthases (SPMSs) represent a novelty independently arisen at least 3 times, in animals, fungi, and plants. The most parsimonious mechanism would involve the duplication and change of function of preexisting SPDS genes in each phylum. Although spermine is not essential for life, the repeated invention of SPMS and its conservation strongly argues for an evolutionary advantage derived from its presence. Moreover, the appearance of thermospermine synthase (tSPMS) in several genera of Archaea and Bacteria was accompanied by a loss of SPDS, suggesting that the new activity originated as a change of function of this enzyme. Surprisingly, tSPMS was later acquired by plants at an early stage of evolution by horizontal gene transfer and has proven to be essential for vascular development in tracheophytes. Finally, the synthesis of nicotine and tropane alkaloids in Solanales was favored by the origination of a new activity, PMT, as a duplication and change of function from SPDS.}, }
@article {pmid18651922, year = {2008}, author = {Gao, B and Zhu, SY}, title = {Differential potency of drosomycin to Neurospora crassa and its mutant: implications for evolutionary relationship between defensins from insects and plants.}, journal = {Insect molecular biology}, volume = {17}, number = {4}, pages = {405-411}, doi = {10.1111/j.1365-2583.2008.00810.x}, pmid = {18651922}, issn = {1365-2583}, mesh = {Amino Acid Sequence ; Animals ; Antifungal Agents/pharmacology ; *Biological Evolution ; Defensins/*genetics/metabolism ; Drosophila Proteins/genetics/*pharmacology ; Insecta/*genetics/metabolism ; Models, Molecular ; Molecular Sequence Data ; Neurospora crassa/*drug effects ; Plants/*genetics/metabolism ; Protein Conformation ; }, abstract = {Drosomycin, the first inducible antifungal peptide isolated from Drosophila, belongs to the superfamily of CSalphabeta-type defensins. In the present study we report a modified approach for high-level expression of drosomycin, which allows us to evaluate its differential potency on the filamentous fungus Neurospora crassa WT (wild type) and N. crassa MUT16, a specific resistance mutant strain to plant defensins, by using different approaches. The results presented here show for the first time that N. crassa MUT16 is resistant to our recombinant drosomycin. Differential survival rates of Drosophila larvae infected by N. crassa WT and MUT16 further confirm the key antifungal role of drosomycin in vivo. The absence of activity against MUT16 suggests a mechanical commonality between drosomycin and plant defensins, which provides additional evidence in favor of their homologous relationship. Furthermore, the existence of drosomycin-like molecules in fungi suggests that all these peptides could originate from a common ancestry rather than horizontal gene transfer between plants and insects, which is further strengthened by the monophyletic origin of these peptides from plants, fungi and insects.}, }
@article {pmid18647384, year = {2008}, author = {Intra, J and Pavesi, G and Horner, DS}, title = {Phylogenetic analyses suggest multiple changes of substrate specificity within the glycosyl hydrolase 20 family.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {214}, pmid = {18647384}, issn = {1471-2148}, mesh = {Amino Acid Sequence ; Animals ; Eukaryotic Cells/classification ; *Evolution, Molecular ; Gene Order ; Glycoside Hydrolases/chemistry/*genetics/*metabolism ; Humans ; Molecular Sequence Data ; *Phylogeny ; Prokaryotic Cells/classification ; Sequence Alignment ; Sequence Analysis, Protein ; Substrate Specificity ; beta-N-Acetylhexosaminidases/chemistry/genetics ; }, abstract = {BACKGROUND: Beta-N-acetylhexosaminidases belonging to the glycosyl hydrolase 20 (GH20) family are involved in the removal of terminal beta-glycosidacally linked N-acetylhexosamine residues. These enzymes, widely distributed in microorganisms, animals and plants, are involved in many important physiological and pathological processes, such as cell structural integrity, energy storage, pathogen defence, viral penetration, cellular signalling, fertilization, development of carcinomas, inflammatory events and lysosomal storage diseases. Nevertheless, only limited analyses of phylogenetic relationships between GH20 genes have been performed until now.<br><br>RESULTS: Careful phylogenetic analyses of 233 inferred protein sequences from eukaryotes and prokaryotes reveal a complex history for the GH20 family. In bacteria, multiple gene duplications and lineage specific gene loss (and/or horizontal gene transfer) are required to explain the observed taxonomic distribution. The last common ancestor of extant eukaryotes is likely to have possessed at least one GH20 family member. At least one gene duplication before the divergence of animals, plants and fungi as well as other lineage specific duplication events have given rise to multiple paralogous subfamilies in eukaryotes. Phylogenetic analyses also suggest that a second, divergent subfamily of GH20 family genes present in animals derive from an independent prokaryotic source. Our data suggest multiple convergent changes of functional roles of GH20 family members in eukaryotes.<br><br>CONCLUSION: This study represents the first detailed evolutionary analysis of the glycosyl hydrolase GH20 family. Mapping of data concerning physiological function of GH20 family members onto the phylogenetic tree reveals that apparently convergent and highly lineage specific changes in substrate specificity have occurred in multiple GH20 subfamilies.}, }
@article {pmid18646395, year = {2008}, author = {Jagusztyn-Krynicka, EK and Wyszyńska, A}, title = {The decline of antibiotic era--new approaches for antibacterial drug discovery.}, journal = {Polish journal of microbiology}, volume = {57}, number = {2}, pages = {91-98}, pmid = {18646395}, issn = {1733-1331}, mesh = {Amidohydrolases/antagonists &amp; inhibitors ; Anti-Bacterial Agents/*pharmacology ; Antigens, Bacterial/chemistry ; Bacteria/*drug effects/genetics ; Bacterial Adhesion ; Bacterial Toxins/chemistry ; Bacteriophages/chemistry ; *Drug Design ; Drug Resistance, Multiple, Bacterial ; Gene Transfer, Horizontal ; Genome, Bacterial ; Genomics ; Protein Conformation ; Quorum Sensing ; Signal Transduction ; }, abstract = {Infectious diseases still remain the main cause of human premature deaths; especially in developing countries. The emergence and spread of pathogenic bacteria resistant to many antibiotics (multidrug-resistant strains) have created the need for the development of novel therapeutic agents. Only two new classes of antibiotics of novel mechanisms of action (linezolid and daptomycin) have been introduced into the market during the last three decades. The recent progress in molecular biology and bacterial genome analysis has had an enormous impact on antibacterial drug research. This review presents new achievements in searching a new bacterial essential genes, a potential targets for antibacterial drugs. Application of metagenomics strategy is also shown. Some recent technologies aimed at development of anti-pathogenic drugs such as inhibitors of quorum sensing process or histidine kinases are also discussed. Extensive research efforts have provided many details concerning structure of bacterial proteins playing an important role in pathogenesis such as adherence proteins or toxins, what allowed searching for antitoxin drugs or drugs interfering with bacterial adhesion. As an example, the review focuses on anthrax therapies under development. Additionally, the article presents the progress in phage therapy; using bacteriophages or their products such as lysins in antibacterial therapy.}, }
@article {pmid18642884, year = {2008}, author = {Riera, TV and Wang, W and Josephine, HR and Hedstrom, L}, title = {A kinetic alignment of orthologous inosine-5'-monophosphate dehydrogenases.}, journal = {Biochemistry}, volume = {47}, number = {33}, pages = {8689-8696}, pmid = {18642884}, issn = {1520-4995}, support = {AI055268/AI/NIAID NIH HHS/United States ; GM54403/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Binding Sites ; Cryptosporidium parvum/enzymology ; Guanosine Monophosphate/chemistry/metabolism ; IMP Dehydrogenase/*chemistry/*metabolism ; Inosine Monophosphate/chemistry/metabolism ; Kinetics ; Models, Molecular ; Molecular Conformation ; Molecular Sequence Data ; NAD/analogs &amp; derivatives/chemistry/metabolism ; Protein Binding ; Ribonucleotides/chemistry/metabolism ; Xanthine ; }, abstract = {IMP dehydrogenase (IMPDH) catalyzes two very different chemical transformations, a dehydrogenase reaction and a hydrolysis reaction. The enzyme toggles between the open conformation required for the dehydrogenase reaction and the closed conformation of the hydrolase reaction by moving a mobile flap into the NAD site. Despite these multiple functional constraints, the residues of the flap and NAD site are highly diverged, and the equilibrium between open and closed conformations (K c) varies widely. In order to understand how differences in the dynamic properties of the flap influence the catalytic cycle, we have delineated the kinetic mechanism of IMPDH from the pathogenic protozoan parasite Cryptosporidium parvum (CpIMPDH), which was obtained from a bacterial source through horizontal gene transfer, and its host counterpart, human IMPDH type 2 (hIMPDH2). Interestingly, the intrinsic binding energy of NAD (+) differentially distributes across the dinucleotide binding sites of these two enzymes as well as in the previously characterized IMPDH from Tritrichomonas foetus (TfIMPDH). Both the dehydrogenase and hydrolase reactions display significant differences in the host and parasite enzymes, in keeping with the phylogenetic and structural divergence of their active sites. Despite large differences in K c , the catalytic power of both the dehydrogenase and hydrolase conformations are similar in CpIMPDH and TfIMPDH. This observation suggests that the closure of the flap simply sets the stage for catalysis rather than plays a more active role in the chemical transformation. This work provides the essential mechanistic framework for drug discovery.}, }
@article {pmid18641138, year = {2008}, author = {Rajashekara, G and Covert, J and Petersen, E and Eskra, L and Splitter, G}, title = {Genomic island 2 of Brucella melitensis is a major virulence determinant: functional analyses of genomic islands.}, journal = {Journal of bacteriology}, volume = {190}, number = {18}, pages = {6243-6252}, pmid = {18641138}, issn = {1098-5530}, support = {R21-AI-070229/AI/NIAID NIH HHS/United States ; 1-U54-AI-057153/AI/NIAID NIH HHS/United States ; R21 AI070229/AI/NIAID NIH HHS/United States ; U54 AI057153/AI/NIAID NIH HHS/United States ; R01 AI073558/AI/NIAID NIH HHS/United States ; R01-AI-073558/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacterial Outer Membrane Proteins/genetics ; Bacterial Proteins/genetics/metabolism ; Brucella melitensis/*genetics/growth &amp; development/*pathogenicity/physiology ; Brucellosis/*microbiology ; Cell Line ; Female ; Genome, Bacterial ; *Genomic Islands ; Humans ; Lipopolysaccharides/metabolism ; Macrophages/microbiology ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Signal Transduction ; Virulence ; Virulence Factors/genetics/metabolism ; }, abstract = {Brucella genomic islands (GIs) share similarities in their genomic organization to pathogenicity islands from other bacteria and are likely acquired by lateral gene transfer. Here, we report the identification of a GI that is important for the pathogenicity of Brucella melitensis. The deletion of GI-1, GI-5, or GI-6 did not affect bacterial growth in macrophages as well as their virulence in interferon regulatory factor 1-deficient (IRF-1(-/-)) mice, suggesting that these islands do not contribute to Brucella virulence. However, the deletion of GI-2 resulted in the attenuation of bacterial growth in macrophages and virulence in IRF-1(-/-) mice. The GI-2 mutant also displayed a rough lipopolysaccharide (LPS) phenotype indicated by acriflavin agglutination, suggesting that in vitro and in vivo attenuation is a result of LPS alteration. Further, systematic analysis of the entire GI-2 revealed two open reading frames (ORFs), BMEI0997 and I0998, that encode hypothetical sugar transferases and contribute to LPS alteration, as the deletion of either of these ORFs resulted in a rough phenotype similar to that of the GI-2 mutant. Complementation analyses indicated that in addition to I0997 and I0998, I0999 is required to restore the smooth LPS in the GI-2 mutant as well as its full in vitro and in vivo virulence. The I0999 sequence analysis suggested that it might function as a transporter to help facilitate the transport or linking of the O antigen to the LPS. Our study also indicated that the rough LPS resulting from the GI-2 deletion may affect pathogen-associated molecular pattern recognition by Toll-like receptors.}, }
@article {pmid18639605, year = {2009}, author = {Kelly, BG and Vespermann, A and Bolton, DJ}, title = {Gene transfer events and their occurrence in selected environments.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {47}, number = {5}, pages = {978-983}, doi = {10.1016/j.fct.2008.06.012}, pmid = {18639605}, issn = {1873-6351}, mesh = {Animals ; Bacteria/*genetics/metabolism/pathogenicity ; Escherichia coli O157/genetics/metabolism/pathogenicity ; Food Microbiology ; Gastrointestinal Tract/microbiology ; *Gene Transfer, Horizontal ; Host-Pathogen Interactions/*physiology ; Humans ; Mouth/microbiology ; Plants/*genetics/metabolism ; Rumen/microbiology ; Virulence Factors/*genetics ; }, abstract = {Genes encoding virulence determinants are transferred between species in many different environments. In this review we describe gene transfer events to and from different species of bacteria, from bacteria to plants, and from plants to bacteria. Examples of the setting for these transfer events include: the GI tract, the rumen, the oral cavity, and in food matrixes. As a case study, the flux of virulence factors from E.coli O157:H7 is described as an example of gene flow in the environment.}, }
@article {pmid18639483, year = {2008}, author = {Hogenhout, SA and Loria, R}, title = {Virulence mechanisms of Gram-positive plant pathogenic bacteria.}, journal = {Current opinion in plant biology}, volume = {11}, number = {4}, pages = {449-456}, doi = {10.1016/j.pbi.2008.05.007}, pmid = {18639483}, issn = {1369-5266}, mesh = {Gene Transfer, Horizontal ; Gram-Positive Bacteria/genetics/*pathogenicity ; Plant Diseases/microbiology ; Plants/*microbiology ; Virulence ; Virulence Factors/metabolism ; }, abstract = {Actinobacteria and Firmicutes comprise a group of highly divergent prokaryotes known as Gram-positive bacteria, which are ancestral to Gram-negative bacteria. Comparative genomics is revealing that, though plant virulence genes are frequently located on plasmids or in laterally acquired gene clusters, they are rarely shared with Gram-negative bacterial plant pathogens and among Gram-positive genera. Gram-positive bacterial pathogens utilize a variety of virulence strategies to invade their plant hosts, including the production of phytotoxins to allow intracellular and intercellular replication, production of cytokinins to generate gall tissues for invasion, secretion of proteins to induce cankers and the utilization and manipulation of sap-feeding insects for introduction into the phloem sieve cells. Functional analysis of novel virulence genes utilized by Actinobacteria and Firmicutes is revealing how these ancient prokaryotes manipulate plant, and sometimes insect, metabolic processes for their own benefit.}, }
@article {pmid18637201, year = {2008}, author = {Przytycka, TM and Jothi, R and Aravind, L and Lipman, DJ}, title = {Differences in evolutionary pressure acting within highly conserved ortholog groups.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {208}, pmid = {18637201}, issn = {1471-2148}, support = {//Intramural NIH HHS/United States ; }, mesh = {Archaea/*genetics ; Conserved Sequence/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Archaeal/genetics ; Genes, Bacterial/genetics ; Gram-Positive Bacteria/*genetics ; Proteobacteria/*genetics ; }, abstract = {BACKGROUND: In highly conserved widely distributed ortholog groups, the main evolutionary force is assumed to be purifying selection that enforces sequence conservation, with most divergence occurring by accumulation of neutral substitutions. Using a set of ortholog groups from prokaryotes, with a single representative in each studied organism, we asked the question if this evolutionary pressure is acting similarly on different subgroups of orthologs defined as major lineages (e.g. Proteobacteria or Firmicutes).<br><br>RESULTS: Using correlations in entropy measures as a proxy for evolutionary pressure, we observed two distinct behaviors within our ortholog collection. The first subset of ortholog groups, called here informational, consisted mostly of proteins associated with information processing (i.e. translation, transcription, DNA replication) and the second, the non-informational ortholog groups, mostly comprised of proteins involved in metabolic pathways. The evolutionary pressure acting on non-informational proteins is more uniform relative to their informational counterparts. The non-informational proteins show higher level of correlation between entropy profiles and more uniformity across subgroups.<br><br>CONCLUSION: The low correlation of entropy profiles in the informational ortholog groups suggest that the evolutionary pressure acting on the informational ortholog groups is not uniform across different clades considered this study. This might suggest "fine-tuning" of informational proteins in each lineage leading to lineage-specific differences in selection. This, in turn, could make these proteins less exchangeable between lineages. In contrast, the uniformity of the selective pressure acting on the non-informational groups might allow the exchange of the genetic material via lateral gene transfer.}, }
@article {pmid18635792, year = {2008}, author = {Martínez, JL}, title = {Antibiotics and antibiotic resistance genes in natural environments.}, journal = {Science (New York, N.Y.)}, volume = {321}, number = {5887}, pages = {365-367}, doi = {10.1126/science.1159483}, pmid = {18635792}, issn = {1095-9203}, mesh = {Anti-Bacterial Agents/*metabolism/*pharmacology/therapeutic use ; Bacteria/*drug effects/genetics/metabolism ; Bacterial Infections/drug therapy/microbiology ; Drug Resistance, Bacterial/*genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; *Ecosystem ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Mutation ; Soil Microbiology ; }, abstract = {The large majority of antibiotics currently used for treating infections and the antibiotic resistance genes acquired by human pathogens each have an environmental origin. Recent work indicates that the function of these elements in their environmental reservoirs may be very distinct from the "weapon-shield" role they play in clinical settings. Changes in natural ecosystems, including the release of large amounts of antimicrobials, might alter the population dynamics of microorganisms, including selection of resistance, with consequences for human health that are difficult to predict.}, }
@article {pmid18635282, year = {2009}, author = {Horvath, P and Coûté-Monvoisin, AC and Romero, DA and Boyaval, P and Fremaux, C and Barrangou, R}, title = {Comparative analysis of CRISPR loci in lactic acid bacteria genomes.}, journal = {International journal of food microbiology}, volume = {131}, number = {1}, pages = {62-70}, doi = {10.1016/j.ijfoodmicro.2008.05.030}, pmid = {18635282}, issn = {1879-3460}, support = {R01 AI 042399-04/AI/NIAID NIH HHS/United States ; R21 AI64470/AI/NIAID NIH HHS/United States ; }, mesh = {5' Untranslated Regions ; DNA, Intergenic ; *Evolution, Molecular ; *Genes, Bacterial ; *Genome, Bacterial ; Gram-Positive Bacteria/*genetics ; Inverted Repeat Sequences/*genetics ; Lactobacillaceae/*genetics ; }, abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR) are hypervariable loci widely distributed in bacteria and archaea, that provide acquired immunity against foreign genetic elements. Here, we investigate the occurrence of CRISPR loci in the genomes of lactic acid bacteria (LAB), including members of the Firmicutes and Actinobacteria phyla. A total of 102 complete and draft genomes across 11 genera were studied and 66 CRISPR loci were identified in 26 species. We provide a comparative analysis of the CRISPR/cas content and diversity across LAB genera and species for 37 sets of CRISPR loci. We analyzed CRISPR repeats, CRISPR spacers, leader sequences, and cas gene content, sequences and architecture. Interestingly, multiple CRISPR families were identified within Bifidobacterium, Lactobacillus and Streptococcus, and similar CRISPR loci were found in distant organisms. Overall, eight distinct CRISPR families were identified consistently across CRISPR repeats, cas gene content and architecture, and sequences of the universal cas1 gene. Since the clustering of the CRISPR families does not correlate with the classical phylogenetic tree, we hypothesize that CRISPR loci have been subjected to horizontal gene transfer and further evolved independently in select lineages, in part due to selective pressure resulting from phage predation. Globally, we provide additional insights into the origin and evolution of CRISPR loci and discuss their contribution to microbial adaptation.}, }
@article {pmid18632554, year = {2008}, author = {Dagan, T and Artzy-Randrup, Y and Martin, W}, title = {Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {29}, pages = {10039-10044}, pmid = {18632554}, issn = {1091-6490}, mesh = {Archaea/genetics ; Bacteria/genetics ; Bacterial Proteins/genetics ; *Biological Evolution ; *Gene Regulatory Networks ; *Gene Transfer, Horizontal ; Genome, Archaeal ; Genome, Bacterial ; Models, Genetic ; Phylogeny ; Prokaryotic Cells ; }, abstract = {Lateral gene transfer is an important mechanism of natural variation among prokaryotes, but the significance of its quantitative contribution to genome evolution is debated. Here, we report networks that capture both vertical and lateral components of evolutionary history among 539,723 genes distributed across 181 sequenced prokaryotic genomes. Partitioning of these networks by an eigenspectrum analysis identifies community structure in prokaryotic gene-sharing networks, the modules of which do not correspond to a strictly hierarchical prokaryotic classification. Our results indicate that, on average, at least 81 +/- 15% of the genes in each genome studied were involved in lateral gene transfer at some point in their history, even though they can be vertically inherited after acquisition, uncovering a substantial cumulative effect of lateral gene transfer on longer evolutionary time scales.}, }
@article {pmid18632174, year = {2008}, author = {Bezanson, GS and MacInnis, R and Potter, G and Hughes, T}, title = {Presence and potential for horizontal transfer of antibiotic resistance in oxidase-positive bacteria populating raw salad vegetables.}, journal = {International journal of food microbiology}, volume = {127}, number = {1-2}, pages = {37-42}, doi = {10.1016/j.ijfoodmicro.2008.06.008}, pmid = {18632174}, issn = {0168-1605}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria, Aerobic/*drug effects/*enzymology/genetics ; Colony Count, Microbial ; DNA, Bacterial/chemistry/genetics ; Disease Reservoirs ; Dose-Response Relationship, Drug ; *Drug Resistance, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial ; Gene Transfer, Horizontal ; Humans ; Lactuca/microbiology ; Medicago sativa/microbiology ; Microbial Sensitivity Tests ; Oxidoreductases/*metabolism ; Spinacia oleracea/microbiology ; Vegetables/*microbiology ; }, abstract = {To assess whether domestically grown fresh salad vegetables constitute a possible reservoir of antibiotic resistance for Canadian consumers, aerobic bacteria capable of forming colonies at 30 degrees C on nutrient-limited media were recovered from a single sampling of Romaine lettuce, Savoy spinach and alfalfa sprouts, then examined for their susceptibility to ten antibiotics and the carriage of potentially mobile R-plasmids and integrons. Of the 140 isolates resistant to one or more antibiotic, 93.5 and 90.0% were resistant to ampicillin and cephalothin; 35.7% to chloramphenicol, 10.0% to streptomycin, 4.2% to nalidixic acid, 4.2% to kanamycin, and 2.8% to gentamicin. Gram-positive isolates accounted for less than 4% of the antibiotic resistant strains. A small portion (23.1%) of the predominant oxidase-positive, gram-negative isolates was resistant to two or more antimicrobials. Members of the Pseudomonas fluorescens/putida complex were most prevalent among the 34 resistant strains identified. Sphingobacterium spp. and Acinetobacter baumanni also were detected. Ten of 52 resistant strains carried plasmids, 3 of which were self-transmissible and bore resistance to ampicillin and kanamycin. Eighteen of 48 gave PCR evidence for integron DNA. Class 2 type integrons were the most prevalent, followed by class 1. We conclude that the foods examined here carry antibiotic resistant bacteria at the retail level. Further, our determination that resistant strains contain integron-specific DNA sequences and self-transmissible R-plasmids indicates their potential to influence the pool of antibiotic resistance in humans via lateral gene transfer subsequent to ingestion.}, }
@article {pmid18629105, year = {2003}, author = {Allen, JF}, title = {Why chloroplasts and mitochondria contain genomes.}, journal = {Comparative and functional genomics}, volume = {4}, number = {1}, pages = {31-36}, pmid = {18629105}, issn = {1531-6912}, abstract = {Chloroplasts and mitochondria originated as bacterial symbionts. The larger, host cells acquired genetic information from their prokaryotic guests by lateral gene transfer. The prokaryotically-derived genes of the eukaryotic cell nucleus now function to encode the great majority of chloroplast and mitochondrial proteins, as well as many proteins of the nucleus and cytosol. Genes are copied and moved between cellular compartments with relative ease, and there is no established obstacle to successful import of any protein precursor from the cytosol. Yet chloroplasts and mitochondria have not abdicated all genes and gene expression to the nucleus and to cytosolic translation. What, then, do chloroplast- and mitochondrially-encoded proteins have in common that confers a selective advantage on the cytoplasmic location of their genes? The proposal advanced here is that co-location of chloroplast and mitochondrial genes with their gene products is required for rapid and direct regulatory coupling. Redox control of gene expression is suggested as the common feature of those chloroplast and mitochondrial proteins that are encoded in situ. Recent evidence is consistent with this hypothesis, and its underlying assumptions and predictions are described.}, }
@article {pmid18629011, year = {2003}, author = {Davids, W and Fuxelius, HH and Andersson, SG}, title = {The Journey to smORFland.}, journal = {Comparative and functional genomics}, volume = {4}, number = {5}, pages = {537-541}, pmid = {18629011}, issn = {1531-6912}, abstract = {The genome sequences completed so far contain more than 20 000 genes with unknown function and no similarity to genes in other genomes. The origin and evolution of the orphan genes is an enigma. Here, we discuss the suggestion that some orphan genes may represent pseudogenes or short fragments of genes that were functional in the genome of a common ancestor. These may be the remains of unsuccessful duplication or horizontal gene transfer events, in which the acquired sequences have entered the fragmentation process and thereby lost their similarity to genes in other species. This scenario is supported by a recent case study of orphan genes in several closely related species of Rickettsia, where full-length ancestral genes were reconstructed from sets of short, overlapping orphan genes. One of these was found to display similarity to genes encoding proteins with ankyrin-repeat domains.}, }
@article {pmid18627593, year = {2008}, author = {Becker, B and Hoef-Emden, K and Melkonian, M}, title = {Chlamydial genes shed light on the evolution of photoautotrophic eukaryotes.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {203}, pmid = {18627593}, issn = {1471-2148}, mesh = {*Autotrophic Processes ; Bacterial Proteins/genetics ; Chlamydiaceae/*genetics ; Diatoms/genetics ; Eukaryota/classification/*genetics ; Eukaryotic Cells/classification/*metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; *Genes, Bacterial ; Photosynthesis ; Phylogeny ; Plants/classification ; Plastids ; Symbiosis ; }, abstract = {BACKGROUND: Chlamydiae are obligate intracellular bacteria of protists, invertebrates and vertebrates, but have not been found to date in photosynthetic eukaryotes (algae and embryophytes). Genes of putative chlamydial origin, however, are present in significant numbers in sequenced genomes of photosynthetic eukaryotes. It has been suggested that such genes were acquired by an ancient horizontal gene transfer from Chlamydiae to the ancestor of photosynthetic eukaryotes. To further test this hypothesis, an extensive search for proteins of chlamydial origin was performed using several recently sequenced algal genomes and EST databases, and the proteins subjected to phylogenetic analyses.<br><br>RESULTS: A total of 39 proteins of chlamydial origin were retrieved from the photosynthetic eukaryotes analyzed and their identity verified through phylogenetic analyses. The distribution of the chlamydial proteins among four groups of photosynthetic eukaryotes (Viridiplantae, Rhodoplantae, Glaucoplantae, Bacillariophyta) was complex suggesting multiple acquisitions and losses. Evidence is presented that all except one of the chlamydial genes originated from an ancient endosymbiosis of a chlamydial bacterium into the ancestor of the Plantae before their divergence into Viridiplantae, Rhodoplantae and Glaucoplantae, i.e. more than 1.1 BYA. The chlamydial proteins subsequently spread through secondary plastid endosymbioses to other eukaryotes. Of 20 chlamydial proteins recovered from the genomes of two Bacillariophyta, 10 were of rhodoplant, and 10 of viridiplant origin suggesting that they were acquired by two different secondary endosymbioses. Phylogenetic analyses of concatenated sequences demonstrated that the viridiplant secondary endosymbiosis likely occurred before the divergence of Chlorophyta and Streptophyta.<br><br>CONCLUSION: We identified 39 proteins of chlamydial origin in photosynthetic eukaryotes signaling an ancient invasion of the ancestor of the Plantae by a chlamydial bacterium accompanied by horizontal gene transfer. Subsequently, chlamydial proteins spread through secondary endosymbioses to other eukaryotes. We conclude that intracellular chlamydiae likely persisted throughout the early history of the Plantae donating genes to their hosts that replaced their cyanobacterial/plastid homologs thus shaping early algal/plant evolution before they eventually vanished.}, }
@article {pmid18620034, year = {2008}, author = {Ohyanagi, H and Ikeo, K and Gojobori, T}, title = {The origin of nucleus: rebuild from the prokaryotic ancestors of ribosome export factors.}, journal = {Gene}, volume = {423}, number = {2}, pages = {149-152}, doi = {10.1016/j.gene.2008.06.018}, pmid = {18620034}, issn = {0378-1119}, mesh = {Archaea/genetics ; Bacteria/genetics ; Cell Nucleus/*genetics/metabolism ; Eukaryotic Cells/metabolism ; Gene Transfer, Horizontal ; Phylogeny ; Prokaryotic Cells/*metabolism ; Ribosomal Proteins/*metabolism ; Ribosomes/*metabolism ; Saccharomyces cerevisiae/genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {Various hypotheses have been proposed on the evolutionary origin of eukaryotic nucleus. Because one of the major cargoes in the nucleocytoplasmic export in the eukaryotic cell is the ribosome, its stimulating proteins called Ribosome Export Factors (REFs) might have an evolutionary history of inscribing the origin of eukaryotic nucleus. With the aim of understanding the evolutionary origin of the nucleus, here we employed the yeast REFs and searched for their evolutionary origin in more than 500 genomes of archaea and eubacteria by the PSI-BLAST search. Our results showed that the non-membranous REFs (non-mREFs) originated exclusively from eubacterial proteins, whereas the membranous REFs (mREFs) are from both archaeal and eubacterial proteins. Since the non-mREFs just work inside the nucleus while the mREFs shuttle between the nucleus and the cytoplasm, these results suggest that the extant REFs working inside the nucleus have derived exclusively from eubacterial proteins, implying that the nucleus arose in a cell that contained chromosomes possessing a substantial fraction of eubacterial genes, in line with the predictions of several models entailing endosymbiosis at eukaryote origins.}, }
@article {pmid18616601, year = {2008}, author = {González-Fraga, S and Pichel, M and Binsztein, N and Johnson, JA and Morris, JG and Stine, OC}, title = {Lateral gene transfer of O1 serogroup encoding genes of Vibrio cholerae.}, journal = {FEMS microbiology letters}, volume = {286}, number = {1}, pages = {32-38}, doi = {10.1111/j.1574-6968.2008.01251.x}, pmid = {18616601}, issn = {0378-1097}, mesh = {Bacterial Proteins/genetics ; Base Sequence ; Cholera/*microbiology ; DNA, Bacterial/genetics ; *Gene Transfer, Horizontal ; Genetic Linkage ; Humans ; Molecular Sequence Data ; Multigene Family ; O Antigens/*genetics ; Sequence Alignment ; Vibrio cholerae/classification/*genetics/isolation &amp; purification ; }, abstract = {In Gram-negative bacteria, the O-antigen-encoding genes may be transferred between lineages, although mechanisms are not fully understood. To assess possible lateral gene transfer (LGT), 21 Argentinean Vibrio cholerae O-group 1 (O1) isolates were examined using multilocus sequence typing (MLST) to determine the genetic relatedness of housekeeping genes and genes from the O1 gene cluster. MSLT analysis revealed that 4.4% of the nucleotides in the seven housekeeping loci were variable, with six distinct genetic lineages identified among O1 isolates. In contrast, MLST analysis of the eight loci from the O1 serogroup region revealed that 0.24% of the 4943 nucleotides were variable. A putative breakpoint was identified in the JUMPstart sequence. Nine conserved nucleotides differed by a single nucleotide from a DNA uptake signal sequence (USS) also found in Pastuerellaceae. Our data indicate that genes in the O1 biogenesis region are closely related even in distinct genetic lineages, indicative of LGT, with a putative DNA USS identified at the defined boundary for the DNA exchange.}, }
@article {pmid18616581, year = {2008}, author = {Heuer, H and Abdo, Z and Smalla, K}, title = {Patchy distribution of flexible genetic elements in bacterial populations mediates robustness to environmental uncertainty.}, journal = {FEMS microbiology ecology}, volume = {65}, number = {3}, pages = {361-371}, doi = {10.1111/j.1574-6941.2008.00539.x}, pmid = {18616581}, issn = {0168-6496}, mesh = {*Adaptation, Biological ; Bacteria/*genetics ; Conjugation, Genetic ; *Environment ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Variation ; Genetics, Population ; Plasmids/genetics ; }, abstract = {The generation and maintenance of genetic variation seems to be a general ecological strategy of bacterial populations. Thereby they gain robustness to irregular environmental change, which is primarily the result of the dynamic evolution of biotic interactions. A benefit of maintaining population heterogeneity is that only a fraction of the population has to bear the cost of not (yet) beneficial deviation. On evolutionary time frames, an added value of the underlying mechanisms is evolvability, i.e. the heritable ability of an evolutionary lineage to generate and maintain genetic variants that are potentially adaptive in the course of evolution. Horizontal gene transfer is an important mechanism that can lead to differences between individuals within bacterial populations. Broad host-range plasmids foster this heterogeneity because they are typically present in only a fraction of the population and provide individual cells with genetic modules newly acquired from other populations or species. We postulate that the benefit of robustness on population level could balance the cost of transfer and replication functions that plasmids impose on their hosts. Consequently, mechanisms that make a subpopulation conducive to specific conjugative plasmids may have evolved, which could explain the persistence of even cryptic plasmids that do not encode any traits.}, }
@article {pmid18616466, year = {2008}, author = {Margis, R and Dunand, C and Teixeira, FK and Margis-Pinheiro, M}, title = {Glutathione peroxidase family - an evolutionary overview.}, journal = {The FEBS journal}, volume = {275}, number = {15}, pages = {3959-3970}, doi = {10.1111/j.1742-4658.2008.06542.x}, pmid = {18616466}, issn = {1742-464X}, mesh = {Animals ; Bacteria/enzymology ; Eukaryota/enzymology ; *Evolution, Molecular ; Glutathione Peroxidase/classification/*genetics/metabolism ; Humans ; Phylogeny ; Plants/enzymology ; }, abstract = {Glutathione peroxidases (EC 1.11.1.9 and EC 1.11.1.12) catalyze the reduction of H(2)O(2) or organic hydroperoxides to water or corresponding alcohols using reduced glutathione. Some glutathione peroxidase isozymes have a selenium-dependent glutathione peroxidase activity and present a selenocysteine encoded by the opal TGA codon. In the present study, insights into the evolution of the whole glutathione peroxidase gene family were obtained after a comprehensive phylogenetic analysis using the improved number of glutathione peroxidase sequences recorded in the PeroxiBase database (http://peroxidase.isb-sib.ch/index.php). The identification of a common ancestral origin for the diverse glutathione peroxidase clusters was not possible. The complex relationships and evolutionary rates of this gene family suggest that basal glutathione peroxidase classes, present in all kingdoms, have originated from independent evolutionary events such as gene duplication, gene losses, lateral gene transfer among invertebrates and vertebrates or plants. In addition, the present study also emphasizes the possibility of some members being submitted to strong selective forces that probably dictated functional convergences of taxonomically distant groups.}, }
@article {pmid18614527, year = {2008}, author = {Jones, CM and Stres, B and Rosenquist, M and Hallin, S}, title = {Phylogenetic analysis of nitrite, nitric oxide, and nitrous oxide respiratory enzymes reveal a complex evolutionary history for denitrification.}, journal = {Molecular biology and evolution}, volume = {25}, number = {9}, pages = {1955-1966}, doi = {10.1093/molbev/msn146}, pmid = {18614527}, issn = {1537-1719}, mesh = {Archaea/enzymology/genetics ; Chromosome Mapping ; Enzymes/*genetics/metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; Genome, Bacterial ; Likelihood Functions ; Metabolic Networks and Pathways/genetics ; Nitric Oxide/*metabolism ; Nitrites/*metabolism ; Nitrous Oxide/*metabolism ; Phylogeny ; Proteobacteria/enzymology/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; }, abstract = {Denitrification is a facultative respiratory pathway in which nitrite (NO2(-)), nitric oxide (NO), and nitrous oxide (N2O) are successively reduced to nitrogen gas (N(2)), effectively closing the nitrogen cycle. The ability to denitrify is widely dispersed among prokaryotes, and this polyphyletic distribution has raised the possibility of horizontal gene transfer (HGT) having a substantial role in the evolution of denitrification. Comparisons of 16S rRNA and denitrification gene phylogenies in recent studies support this possibility; however, these results remain speculative as they are based on visual comparisons of phylogenies from partial sequences. We reanalyzed publicly available nirS, nirK, norB, and nosZ partial sequences using Bayesian and maximum likelihood phylogenetic inference. Concomitant analysis of denitrification genes with 16S rRNA sequences from the same organisms showed substantial differences between the trees, which were supported by examining the posterior probability of monophyletic constraints at different taxonomic levels. Although these differences suggest HGT of denitrification genes, the presence of structural variants for nirK, norB, and nosZ makes it difficult to determine HGT from other evolutionary events. Additional analysis using phylogenetic networks and likelihood ratio tests of phylogenies based on full-length sequences retrieved from genomes also revealed significant differences in tree topologies among denitrification and 16S rRNA gene phylogenies, with the exception of the nosZ gene phylogeny within the data set of the nirK-harboring genomes. However, inspection of codon usage and G + C content plots from complete genomes gave no evidence for recent HGT. Instead, the close proximity of denitrification gene copies in the genomes of several denitrifying bacteria suggests duplication. Although HGT cannot be ruled out as a factor in the evolution of denitrification genes, our analysis suggests that other phenomena, such gene duplication/divergence and lineage sorting, may have differently influenced the evolution of each denitrification gene.}, }
@article {pmid18614525, year = {2008}, author = {Cadel-Six, S and Dauga, C and Castets, AM and Rippka, R and Bouchier, C and Tandeau de Marsac, N and Welker, M}, title = {Halogenase genes in nonribosomal peptide synthetase gene clusters of Microcystis (cyanobacteria): sporadic distribution and evolution.}, journal = {Molecular biology and evolution}, volume = {25}, number = {9}, pages = {2031-2041}, pmid = {18614525}, issn = {1537-1719}, mesh = {Bacterial Proteins/chemistry/*genetics ; Chlorine/chemistry ; *Evolution, Molecular ; Gene Deletion ; *Genes, Bacterial ; Halogenation ; Mass Spectrometry ; Microcystis/*enzymology/genetics ; *Multigene Family ; Peptide Biosynthesis, Nucleic Acid-Independent ; Peptide Synthases/chemistry/*genetics ; }, abstract = {Cyanobacteria of the genus Microcystis are known to produce secondary metabolites of large structural diversity by nonribosomal peptide synthetase (NRPS) pathways. For a number of such compounds, halogenated congeners have been reported along with nonhalogenated ones. In the present study, chlorinated cyanopeptolin- and/or aeruginosin-type peptides were detected by mass spectrometry in 17 out of 28 axenic strains of Microcystis. In these strains, a halogenase gene was identified between 2 genes coding for NRPS modules in respective gene clusters, whereas it was consistently absent when the strains produced only nonchlorinated corresponding congeners. Nucleotide sequences were obtained for 12 complete halogenase genes and 14 intermodule regions of gene clusters lacking a halogenase gene or containing only fragments of it. When a halogenase gene was found absent, a specific, identical excision pattern was observed for both synthetase gene clusters in most strains. A phylogenetic analysis including other bacterial halogenases showed that the NRPS-related halogenases of Microcystis form a monophyletic group divided into 2 subgroups, corresponding to either the cyanopeptolin or the aeruginosin peptide synthetases. The distribution of these peptide synthetase gene clusters, among the tested Microcystis strains, was found in relative agreement with their phylogeny reconstructed from 16S-23S rDNA intergenic spacer sequences, whereas the distribution of the associated halogenase genes appears to be sporadic. The presented data suggest that in cyanobacteria these prevalent halogenase genes originated from an ancient horizontal gene transfer followed by duplication in the cyanobacterial lineage. We propose an evolutionary scenario implying repeated gene losses to explain the distribution of halogenase genes in 2 NRPS gene clusters that subsequently defines the seemingly erratic production of halogenated and nonhalogenated aeruginosins and cyanopeptolins among Microcystis strains.}, }
@article {pmid18613974, year = {2008}, author = {Glansdorff, N and Xu, Y and Labedan, B}, title = {The last universal common ancestor: emergence, constitution and genetic legacy of an elusive forerunner.}, journal = {Biology direct}, volume = {3}, number = {}, pages = {29}, pmid = {18613974}, issn = {1745-6150}, mesh = {Archaea/cytology/genetics/metabolism/*physiology ; Bacteria/cytology/*genetics/metabolism ; *Biological Evolution ; Eukaryotic Cells/cytology/metabolism/*physiology ; *Phylogeny ; Prokaryotic Cells/cytology/metabolism/*physiology ; }, abstract = {BACKGROUND: Since the reclassification of all life forms in three Domains (Archaea, Bacteria, Eukarya), the identity of their alleged forerunner (Last Universal Common Ancestor or LUCA) has been the subject of extensive controversies: progenote or already complex organism, prokaryote or protoeukaryote, thermophile or mesophile, product of a protracted progression from simple replicators to complex cells or born in the cradle of "catalytically closed" entities? We present a critical survey of the topic and suggest a scenario.<br><br>RESULTS: LUCA does not appear to have been a simple, primitive, hyperthermophilic prokaryote but rather a complex community of protoeukaryotes with a RNA genome, adapted to a broad range of moderate temperatures, genetically redundant, morphologically and metabolically diverse. LUCA's genetic redundancy predicts loss of paralogous gene copies in divergent lineages to be a significant source of phylogenetic anomalies, i.e. instances where a protein tree departs from the SSU-rRNA genealogy; consequently, horizontal gene transfer may not have the rampant character assumed by many. Examining membrane lipids suggest LUCA had sn1,2 ester fatty acid lipids from which Archaea emerged from the outset as thermophilic by "thermoreduction," with a new type of membrane, composed of sn2,3 ether isoprenoid lipids; this occurred without major enzymatic reconversion. Bacteria emerged by reductive evolution from LUCA and some lineages further acquired extreme thermophily by convergent evolution. This scenario is compatible with the hypothesis that the RNA to DNA transition resulted from different viral invasions as proposed by Forterre. Beyond the controversy opposing "replication first" to metabolism first", the predictive arguments of theories on "catalytic closure" or "compositional heredity" heavily weigh in favour of LUCA's ancestors having emerged as complex, self-replicating entities from which a genetic code arose under natural selection.<br><br>CONCLUSION: Life was born complex and the LUCA displayed that heritage. It had the "body "of a mesophilic eukaryote well before maturing by endosymbiosis into an organism adapted to an atmosphere rich in oxygen. Abundant indications suggest reductive evolution of this complex and heterogeneous entity towards the "prokaryotic" Domains Archaea and Bacteria. The word "prokaryote" should be abandoned because epistemologically unsound.<br><br>REVIEWERS: This article was reviewed by Anthony Poole, Patrick Forterre, and Nicolas Galtier.}, }
@article {pmid18612417, year = {2008}, author = {Graham, LA and Lougheed, SC and Ewart, KV and Davies, PL}, title = {Lateral transfer of a lectin-like antifreeze protein gene in fishes.}, journal = {PloS one}, volume = {3}, number = {7}, pages = {e2616}, pmid = {18612417}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Animals ; Antifreeze Proteins/chemistry/*genetics ; Codon/metabolism ; Conserved Sequence ; Fish Proteins/chemistry/*genetics ; Fishes/classification/*genetics ; *Gene Transfer, Horizontal ; Lectins/*chemistry/genetics ; Models, Molecular ; Molecular Sequence Data ; Mutation, Missense ; Phylogeny ; Protein Conformation ; RNA, Ribosomal/metabolism ; Sequence Alignment ; }, abstract = {Fishes living in icy seawater are usually protected from freezing by endogenous antifreeze proteins (AFPs) that bind to ice crystals and stop them from growing. The scattered distribution of five highly diverse AFP types across phylogenetically disparate fish species is puzzling. The appearance of radically different AFPs in closely related species has been attributed to the rapid, independent evolution of these proteins in response to natural selection caused by sea level glaciations within the last 20 million years. In at least one instance the same type of simple repetitive AFP has independently originated in two distant species by convergent evolution. But, the isolated occurrence of three very similar type II AFPs in three distantly related species (herring, smelt and sea raven) cannot be explained by this mechanism. These globular, lectin-like AFPs have a unique disulfide-bonding pattern, and share up to 85% identity in their amino acid sequences, with regions of even higher identity in their genes. A thorough search of current databases failed to find a homolog in any other species with greater than 40% amino acid sequence identity. Consistent with this result, genomic Southern blots showed the lectin-like AFP gene was absent from all other fish species tested. The remarkable conservation of both intron and exon sequences, the lack of correlation between evolutionary distance and mutation rate, and the pattern of silent vs non-silent codon changes make it unlikely that the gene for this AFP pre-existed but was lost from most branches of the teleost radiation. We propose instead that lateral gene transfer has resulted in the occurrence of the type II AFPs in herring, smelt and sea raven and allowed these species to survive in an otherwise lethal niche.}, }
@article {pmid18612393, year = {2008}, author = {Hooper, SD and Raes, J and Foerstner, KU and Harrington, ED and Dalevi, D and Bork, P}, title = {A molecular study of microbe transfer between distant environments.}, journal = {PloS one}, volume = {3}, number = {7}, pages = {e2607}, pmid = {18612393}, issn = {1932-6203}, mesh = {Ecology ; Ecosystem ; *Environment ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Phylogeny ; Water Microbiology ; }, abstract = {BACKGROUND: Environments and their organic content are generally not static and isolated, but in a constant state of exchange and interaction with each other. Through physical or biological processes, organisms, especially microbes, may be transferred between environments whose characteristics may be quite different. The transferred microbes may not survive in their new environment, but their DNA will be deposited. In this study, we compare two environmental sequencing projects to find molecular evidence of transfer of microbes over vast geographical distances.<br><br>METHODOLOGY: By studying synonymous nucleotide composition, oligomer frequency and orthology between predicted genes in metagenomics data from two environments, terrestrial and aquatic, and by correlating with phylogenetic mappings, we find that both environments are likely to contain trace amounts of microbes which have been far removed from their original habitat. We also suggest a bias in direction from soil to sea, which is consistent with the cycles of planetary wind and water.<br><br>CONCLUSIONS: Our findings support the Baas-Becking hypothesis formulated in 1934, which states that due to dispersion and population sizes, microbes are likely to be found in widely disparate environments. Furthermore, the availability of genetic material from distant environments is a possible font of novel gene functions for lateral gene transfer.}, }
@article {pmid18611267, year = {2008}, author = {Huang, J and Gogarten, JP}, title = {Concerted gene recruitment in early plant evolution.}, journal = {Genome biology}, volume = {9}, number = {7}, pages = {R109}, pmid = {18611267}, issn = {1474-760X}, mesh = {*Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Plant ; Phylogeny ; Plants/classification/genetics ; Rhodophyta/classification/genetics ; }, abstract = {BACKGROUND: Horizontal gene transfer occurs frequently in prokaryotes and unicellular eukaryotes. Anciently acquired genes, if retained among descendants, might significantly affect the long-term evolution of the recipient lineage. However, no systematic studies on the scope of anciently acquired genes and their impact on macroevolution are currently available in eukaryotes.<br><br>RESULTS: Analyses of the genome of the red alga Cyanidioschyzon identified 37 genes that were acquired from non-organellar sources prior to the split of red algae and green plants. Ten of these genes are rarely found in cyanobacteria or have additional plastid-derived homologs in plants. These genes most likely provided new functions, often essential for plant growth and development, to the ancestral plant. Many remaining genes may represent replacements of endogenous homologs with a similar function. Furthermore, over 78% of the anciently acquired genes are related to the biogenesis and functionality of plastids, the defining character of plants.<br><br>CONCLUSION: Our data suggest that, although ancient horizontal gene transfer events did occur in eukaryotic evolution, the number of acquired genes does not predict the role of horizontal gene transfer in the adaptation of the recipient organism. Our data also show that multiple independently acquired genes are able to generate and optimize key evolutionary novelties in major eukaryotic groups. In light of these findings, we propose and discuss a general mechanism of horizontal gene transfer in the macroevolution of eukaryotes.}, }
@article {pmid18610833, year = {2008}, author = {Turova, TP and Nazina, TN and Mikhaĭlova, EM and Rodionova, TA and Ekimov, AN and Mashukova, AV and Poltaraus, AB}, title = {[AlkB homologues in thermophilic bacteria of the genus Geobacillus].}, journal = {Molekuliarnaia biologiia}, volume = {42}, number = {2}, pages = {247-257}, pmid = {18610833}, issn = {0026-8984}, mesh = {Amino Acid Sequence/genetics ; Bacillaceae/enzymology/*genetics/growth &amp; development/isolation &amp; purification ; Bacterial Proteins/*genetics/metabolism ; Biomass ; Cytochrome P-450 CYP4A/*genetics/metabolism ; Gene Transfer, Horizontal/*physiology ; Genes, Bacterial/*physiology ; *Phylogeny ; Rhodococcus/enzymology/genetics ; Sequence Analysis, Protein ; Sequence Homology, Amino Acid ; }, abstract = {Screening of alkane hydroxylase genes (alkB) was performed in the thermophilic aerobic bacteria of the genus Geobacillus. Total DNA was extracted from the biomass of 11 strains grown on the mixture of saturated C10-C20 hydrocarbons, PCR amplification of fragments of alkB genes was performed with degenerate oligonucleotide primers, PCR products were cloned and sequenced. For the first time in the genome of thermophilic bacteria the presence of a set of alkB gene homologues was revealed. The strains each contain three to six homologues among which only two are universal for all of the strains. Comparative phylogenetic analysis of the nucleotide sequences and the inferred amino acid sequences showed close relatedness of six of the revealed variants of geobacilli sequences to the alkB4, alkB3, and alkB2 genes that had previously been revealed by other authors in Rhodococcus erythropolis strains NRRL B-16531 and Q15. The rest two variants of alkB sequences were unique. Analysis of the GC composition of all the Geobacillus alkB homologues revealed closer proximity to the rhodococcal chromosomal DNA than to the chromosomal DNA of geobacilli. This may be an indication of the introduction of the alkB genes into the Geobacillus genome by interspecies horizontal transfer; and rhodococci or other representatives of the Actinobacteria phylum were probably the donors of these genes. Analysis of the codon usage in fragments of alkB genes confirms the suggestion that the pool of these genes is common to the majority of Gram-positive and certain Gram-negative bacteria. Formation of a set of several alkB homologues in a genome of a particular microorganism may result from free gene exchange within this pool.}, }
@article {pmid18606739, year = {2008}, author = {Raghavan, R and Hicks, LD and Minnick, MF}, title = {Toxic introns and parasitic intein in Coxiella burnetii: legacies of a promiscuous past.}, journal = {Journal of bacteriology}, volume = {190}, number = {17}, pages = {5934-5943}, pmid = {18606739}, issn = {1098-5530}, support = {U54 AI065357-030023/AI/NIAID NIH HHS/United States ; }, mesh = {Coxiella burnetii/classification/*genetics ; DNA Helicases/genetics/metabolism ; Escherichia coli/genetics/growth &amp; development/metabolism ; Genome, Bacterial ; Inteins/*genetics ; Introns/*genetics ; Models, Biological ; Phylogeny ; Protein Binding ; RNA, Catalytic/genetics/metabolism ; RNA, Ribosomal, 23S/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Ribosomes/metabolism ; Transcription, Genetic ; }, abstract = {The genome of the obligate intracellular pathogen Coxiella burnetii contains a large number of selfish genetic elements, including two group I introns (Cbu.L1917 and Cbu.L1951) and an intervening sequence that interrupts the 23S rRNA gene, an intein (Cbu.DnaB) within dnaB and 29 insertion sequences. Here, we describe the ability of the intron-encoded RNAs (ribozymes) to retard bacterial growth rate (toxicity) and examine the functionality and phylogenetic history of Cbu.DnaB. When expressed in Escherichia coli, both introns repressed growth, with Cbu.L1917 being more inhibitory. Both ribozymes were found to associate with ribosomes of Coxiella and E. coli. In addition, ribozymes significantly reduced in vitro luciferase translation, again with Cbu.L1917 being more inhibitory. We analyzed the relative quantities of ribozymes and genomes throughout a 14-day growth cycle of C. burnetii and found that they were inversely correlated, suggesting that the ribozymes have a negative effect on Coxiella's growth. We determined possible sites for ribozyme associations with 23S rRNA that could explain the observed toxicities. Further research is needed to determine whether the introns are being positively selected because they promote bacterial persistence or whether they were fixed in the population due to genetic drift. The intein, Cbu.DnaB, is able to self-splice, leaving the host protein intact and presumably functional. Similar inteins have been found in two extremophilic bacteria (Alkalilimnicola ehrlichei and Halorhodospira halophila) that are distantly related to Coxiella, making it difficult to determine whether the intein was acquired by horizontal gene transfer or was vertically inherited from a common ancestor.}, }
@article {pmid18606736, year = {2008}, author = {Schmitz-Esser, S and Haferkamp, I and Knab, S and Penz, T and Ast, M and Kohl, C and Wagner, M and Horn, M}, title = {Lawsonia intracellularis contains a gene encoding a functional rickettsia-like ATP/ADP translocase for host exploitation.}, journal = {Journal of bacteriology}, volume = {190}, number = {17}, pages = {5746-5752}, pmid = {18606736}, issn = {1098-5530}, support = {P 19252/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Adenosine Diphosphate/*metabolism ; Adenosine Triphosphate/*metabolism ; Bacterial Proteins/chemistry/genetics/*metabolism ; Biological Transport/physiology ; Chromatography, Thin Layer ; Escherichia coli/genetics/metabolism ; Eukaryotic Cells/microbiology ; Gene Transfer, Horizontal ; Host-Pathogen Interactions ; Kinetics ; Lawsonia Bacteria/*enzymology/genetics/physiology ; Mitochondrial ADP, ATP Translocases/classification/genetics/*metabolism ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Rickettsia/enzymology ; Substrate Specificity ; }, abstract = {ATP/ADP translocases are a hallmark of obligate intracellular pathogens related to chlamydiae and rickettsiae. These proteins catalyze the highly specific exchange of bacterial ADP against host ATP and thus allow bacteria to exploit their hosts' energy pool, a process also referred to as energy parasitism. The genome sequence of the obligate intracellular pathogen Lawsonia intracellularis (Deltaproteobacteria), responsible for one of the most economically important diseases in the swine industry worldwide, revealed the presence of a putative ATP/ADP translocase most similar to known ATP/ADP translocases of chlamydiae and rickettsiae (around 47% amino acid sequence identity). The gene coding for the putative ATP/ADP translocase of L. intracellularis (L. intracellularis nucleotide transporter 1 [NTT1(Li)]) was cloned and expressed in the heterologous host Escherichia coli. The transport properties of NTT1(Li) were determined by measuring the uptake of radioactively labeled substrates by E. coli. NTT1(Li) transported ATP in a counterexchange mode with ADP in a highly specific manner; the substrate affinities determined were 236.3 (+/- 36.5) microM for ATP and 275.2 (+/- 28.1) microM for ADP, identifying this protein as a functional ATP/ADP translocase. NTT1(Li) is the first ATP/ADP translocase from a bacterium not related to Chlamydiae or Rickettsiales, showing that energy parasitism by ATP/ADP translocases is more widespread than previously recognized. The occurrence of an ATP/ADP translocase in L. intracellularis is explained by a relatively recent horizontal gene transfer event with rickettsiae as donors.}, }
@article {pmid18606735, year = {2008}, author = {Letek, M and Ocampo-Sosa, AA and Sanders, M and Fogarty, U and Buckley, T and Leadon, DP and González, P and Scortti, M and Meijer, WG and Parkhill, J and Bentley, S and Vázquez-Boland, JA}, title = {Evolution of the Rhodococcus equi vap pathogenicity island seen through comparison of host-associated vapA and vapB virulence plasmids.}, journal = {Journal of bacteriology}, volume = {190}, number = {17}, pages = {5797-5805}, pmid = {18606735}, issn = {1098-5530}, mesh = {Bacterial Proteins/classification/genetics ; DNA, Bacterial/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genomic Islands/*genetics ; Models, Genetic ; Molecular Sequence Data ; Multigene Family/genetics ; Phylogeny ; Plasmids/*genetics ; Rhodococcus equi/*genetics/pathogenicity ; Sequence Analysis, DNA ; Virulence/genetics ; }, abstract = {The pathogenic actinomycete Rhodococcus equi harbors different types of virulence plasmids associated with specific nonhuman hosts. We determined the complete DNA sequence of a vapB(+) plasmid, typically associated with pig isolates, and compared it with that of the horse-specific vapA(+) plasmid type. pVAPB1593, a circular 79,251-bp element, had the same housekeeping backbone as the vapA(+) plasmid but differed over an approximately 22-kb region. This variable region encompassed the vap pathogenicity island (PAI), was clearly subject to selective pressures different from those affecting the backbone, and showed major genetic rearrangements involving the vap genes. The pVAPB1593 PAI harbored five different vap genes (vapB and vapJ to -M, with vapK present in two copies), which encoded products differing by 24 to 84% in amino acid sequence from the six full-length vapA(+) plasmid-encoded Vap proteins, consistent with a role for the specific vap gene complement in R. equi host tropism. Sequence analyses, including interpolated variable-order motifs for detection of alien DNA and reconstruction of Vap family phylogenetic relationships, suggested that the vap PAI was acquired by an ancestor plasmid via lateral gene transfer, subsequently evolving by vap gene duplication and sequence diversification to give different (host-adapted) plasmids. The R. equi virulence plasmids belong to a new family of actinobacterial circular replicons characterized by an ancient conjugative backbone and a horizontally acquired niche-adaptive plasticity region.}, }
@article {pmid18602102, year = {2008}, author = {Sharp, PJ and Dunn, IC and Waddington, D and Boswell, T}, title = {Chicken leptin.}, journal = {General and comparative endocrinology}, volume = {158}, number = {1}, pages = {2-4}, doi = {10.1016/j.ygcen.2008.05.018}, pmid = {18602102}, issn = {1095-6840}, support = {BBS/E/D/05191130/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Chickens/*genetics ; Databases, Genetic ; Evolution, Molecular ; Gene Transfer, Horizontal/physiology ; Genome ; Leptin/*genetics ; Mice/genetics ; Phylogeny ; Sheep/genetics ; }, }
@article {pmid18601986, year = {2008}, author = {Hao, W and Golding, GB}, title = {High rates of lateral gene transfer are not due to false diagnosis of gene absence.}, journal = {Gene}, volume = {421}, number = {1-2}, pages = {27-31}, doi = {10.1016/j.gene.2008.06.015}, pmid = {18601986}, issn = {0378-1119}, mesh = {Bacillus/*genetics ; *Evolution, Molecular ; Gene Deletion ; *Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; Likelihood Functions ; Sequence Deletion ; }, abstract = {Methods for assessing gene presence and absence have been widely used to study bacterial genome evolution. A recent report by Zhaxybayeva et al. [Zhaxybayeva, O., Nesbo, C. L., and Doolittle, W. F., 2007. Systematic overestimation of gene gain through false diagnosis of gene absence. Genome. Biol. 8, 402] suggests that false diagnosis of gene absence or the presence of undetected truncated genes leads to a systematic overestimation of gene gain. Here (1) we argue that these annotation errors can cause more complicated effects and are not necessarily systematic, (2) we argue that current annotations (supplemented with BLAST searches) are the best way to consistently score gene presence/absence and (3) that genome wide estimates of gene gain/loss are not strongly affected by small differences in gene annotations but that the number of related gene families is strongly affected. We have estimated the rates of gene insertions/deletions using a variety of cutoff thresholds and match lengths as a way in which to alter the recognition of genes and gene fragments. The results reveal that different cutoffs for match length only cause a small variation of the estimated insertion/deletion rates. The rates of gene insertions/deletions on recent branches remain relatively high regardless of the thresholds for match length. Lastly (4), the dynamic process of gene truncation needs to be further considered in genome comparison studies. The data presented suggest that gene truncation tends to take place preferentially in recently transferred genes, which supports a fast turnover of recent laterally transferred genes. The presence of truncated genes or false diagnosis of gene absence therefore does not significantly affect the estimation of gene insertions/deletions rates, but there are several other factors that bias the results toward an under-estimation of the rate of gene insertion/deletion. All of these factors need to be considered.}, }
@article {pmid18599823, year = {2008}, author = {Sung, JM and Lloyd, DH and Lindsay, JA}, title = {Staphylococcus aureus host specificity: comparative genomics of human versus animal isolates by multi-strain microarray.}, journal = {Microbiology (Reading, England)}, volume = {154}, number = {Pt 7}, pages = {1949-1959}, doi = {10.1099/mic.0.2007/015289-0}, pmid = {18599823}, issn = {1350-0872}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Animal Diseases/*microbiology ; Animals ; Animals, Domestic/microbiology ; Bacterial Proteins/genetics ; Camelus ; Cattle ; Gene Expression Profiling ; Gene Transfer, Horizontal ; Genetic Variation ; *Genomics ; Goats ; Horses ; *Host-Pathogen Interactions ; Humans ; Oligonucleotide Array Sequence Analysis ; Sheep ; Species Specificity ; Staphylococcal Infections/*microbiology/*veterinary ; Staphylococcus aureus/classification/*genetics/isolation &amp; purification ; }, abstract = {Staphylococcus aureus is a commensal and pathogen of several mammalian species, particularly humans and cattle. We aimed to (i) identify S. aureus genes associated with host specificity, (ii) determine the relatedness of human and animal isolates, and (iii) identify whether human and animal isolates typically exchanged mobile genetic elements encoding virulence and resistance genes. Using a well-validated seven-strain S. aureus microarray, we compared 56 UK S. aureus isolates that caused infection in cows, horses, goats, sheep and a camel with 161 human S. aureus isolates from healthy carriers and community acquired infections in the UK. We had previously shown that human isolates are clustered into ten dominant and a few minor lineages, each with unique combinations of surface proteins predicted to bind to human proteins. We found that the animal-associated S. aureus clustered into ten lineages, with 61 % assigned to four lineages, ST151, ST771, ST130 and ST873, that were unique to animals. The majority of bovine mastitis was caused by isolates of lineage ST151, ST771 and ST97, but a few human lineages also caused mastitis. S. aureus isolated from horses were more likely to cluster into human-associated lineages, with 54 % of horse-associated S. aureus assigned to the human clusters CC1, CC8 and CC22; along with the presence of some multi-drug resistant strains, this suggests a human origin. This is the most comprehensive genetic comparison of human versus animal S. aureus isolates conducted, and because we used a whole-genome approach we could estimate the key genes with the greatest variability that are associated with host specificity. Several genes conserved in all human isolates were variable or missing in one or more animal lineages, including the well-characterized lineage specific genes fnbA, fnbB and coa. Interestingly, genes carried on mobile genetic elements (MGEs) such as chp, scn and sak were less common in animal S. aureus isolates, and bap was not found. There was a lot of MGE variation within lineages, and some evidence that exchange of MGEs such as bacteriophage and pathogenicity islands between animal and human lineages is feasible, but there was less evidence of antibiotic resistance gene transfer on the staphylococcal cassette chromosomes (SCC) or plasmids. Surprisingly, animal lineages are closely related to human lineages and only a handful of genes or gene combinations may be responsible for host specificity.}, }
@article {pmid18599818, year = {2008}, author = {Tooming-Klunderud, A and Mikalsen, B and Kristensen, T and Jakobsen, KS}, title = {The mosaic structure of the mcyABC operon in Microcystis.}, journal = {Microbiology (Reading, England)}, volume = {154}, number = {Pt 7}, pages = {1886-1899}, doi = {10.1099/mic.0.2007/015875-0}, pmid = {18599818}, issn = {1350-0872}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/*genetics/metabolism ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Microcystins/*biosynthesis ; Microcystis/classification/*enzymology/genetics/metabolism ; Molecular Sequence Data ; Multigene Family ; Mutation ; *Operon ; Phylogeny ; Protein Structure, Tertiary ; *Recombination, Genetic ; Sequence Alignment ; }, abstract = {An extensive study of the mcyABC genes and regions flanking the mcy gene cluster was performed in naturally occurring Microcystis strains. Lack of methylation in strains producing only desmethyl(7)-microcystin was found to be associated with point mutations in substrate-binding sequence motifs of the N-methyltransferase (NMT) domain in McyA. Multiple recombination events giving rise to 'phylogenetic mosaics' were detected within the NMT-domain-encoding mcyA sequences and the adenylation (A) domain sequences of mcyB and mcyC. Recombination leading to exchanges between the mcyB and mcyC regions encoding A domains in modules McyB1 and McyC was also detected. A previously reported replacement of the A domain in McyB1 was found to involve the region between the conserved motifs A3 and A8/A9. In all microcystin-producing strains the mcy gene cluster was flanked by the genes uma1 and dnaN. Clear indications of recombination, an insertion element and footprints of IS elements were found in the dnaN-mcyJ intergenic region. Among the non-microcystin producers, uma1 and dnaN were linked in some, but not all strains. Most non-producing strains lacked all mcy genes, while one strain possessed a partially deleted mcy operon. Our results show that frequent horizontal gene transfer events in addition to point mutations and insertions/deletions contribute to variation in the mcy gene cluster.}, }
@article {pmid18599264, year = {2008}, author = {Morris, RT and Drouin, G}, title = {Similar ectopic gene conversion frequencies in the backbone genome of pathogenic and nonpathogenic Escherichia coli strains.}, journal = {Genomics}, volume = {92}, number = {3}, pages = {168-172}, doi = {10.1016/j.ygeno.2008.05.009}, pmid = {18599264}, issn = {1089-8646}, mesh = {Amino Acid Sequence ; Base Sequence ; Escherichia coli/classification/*genetics/pathogenicity ; Escherichia coli Proteins/genetics ; *Gene Conversion ; Gene Transfer, Horizontal ; Genome, Bacterial ; Molecular Sequence Data ; }, abstract = {We previously showed that gene conversions were more frequent in the genomes of three Escherichia coli pathogenic strains than in the genome of the nonpathogenic K-12 E. coli strain. However, that study did not address whether the more frequent conversions observed in the genes of pathogenic strains occurred between the backbone genes common to these four strains or in the numerous horizontally transferred genes found only in pathogenic strains. Here, we show that ectopic gene conversions are equally frequent in the backbone genes of pathogenic and nonpathogenic strains, that most of these conversions are short, and that the nucleotide changes they generate are probably selectively neutral. Backbone genes are therefore under similar selective constraints in both pathogenic and nonpathogenic E. coli strains. The higher frequency of gene conversions we previously observed in pathogenic strains is therefore due to higher conversion frequencies between the numerous horizontally transferred genes found only in pathogenic strains.}, }
@article {pmid18599103, year = {2008}, author = {Chen, CL and Pan, TY and Kan, SC and Kuan, YC and Hong, LY and Chiu, KR and Sheu, CS and Yang, JS and Hsu, WH and Hu, HY}, title = {Genome sequence of the lytic bacteriophage P1201 from Corynebacterium glutamicum NCHU 87078: evolutionary relationships to phages from Corynebacterineae.}, journal = {Virology}, volume = {378}, number = {2}, pages = {226-232}, doi = {10.1016/j.virol.2008.05.027}, pmid = {18599103}, issn = {1096-0341}, mesh = {Bacteriophages/*genetics/ultrastructure ; Chromatography, Liquid ; Corynebacterium glutamicum/*virology ; DNA/genetics ; DNA, Bacterial/*chemistry/*genetics ; Electrophoresis, Polyacrylamide Gel ; Escherichia coli/genetics ; Gene Order ; Gene Transfer, Horizontal ; *Genome, Viral ; Inteins ; Molecular Sequence Data ; Open Reading Frames ; Protein Splicing ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Tandem Mass Spectrometry ; Viral Proteins/genetics/isolation &amp; purification ; Virion/ultrastructure ; }, abstract = {P1201 is a lytic corynephage of Corynebacterium glutamicum NCHU 87078. Its genome consists of a linear double-stranded DNA molecule of 70,579 base pairs, with 3'-protruding cohesive ends of ten nucleotides. We have identified 69 putative open reading frames, including three apparent genes (thymidylate synthase, terminase, and RNR alpha subunit genes) that are interrupted by an intein. Protein-splicing activities of these inteins were demonstrated in Escherichia coli. Three structural proteins including major capsid and major tail proteins were separated by SDS-PAGE and identified by both LC-MS-MS and N-terminal sequence analyses. Bioinformatics analysis indicated that only about 8.7% of its putative gene products shared substantial protein sequence similarity with the lytic corynephage BFK20 from Brevibacterium flavum, the only corynephage whose genome had been sequenced to date, revealing that the P1201 genome is distinct from BFK20. The mosaic-like genome of P1201 indicates extensive horizontal gene transfer among P1201, Gordonia terrae phage GTE5, mycobacteriophages, and several regions of Corynebacterium spp. genomes.}, }
@article {pmid18595706, year = {2008}, author = {Reyes-Prieto, A and Moustafa, A and Bhattacharya, D}, title = {Multiple genes of apparent algal origin suggest ciliates may once have been photosynthetic.}, journal = {Current biology : CB}, volume = {18}, number = {13}, pages = {956-962}, pmid = {18595706}, issn = {0960-9822}, support = {R01 ES013679/ES/NIEHS NIH HHS/United States ; R01 ES013679-01A2/ES/NIEHS NIH HHS/United States ; T32 GM008629/GM/NIGMS NIH HHS/United States ; R01ES013679/ES/NIEHS NIH HHS/United States ; }, mesh = {Algal Proteins/*genetics ; Animals ; Cyanobacteria/genetics ; *Gene Transfer, Horizontal ; Genome, Protozoan ; Paramecium tetraurelia/genetics ; *Photosynthesis ; Phylogeny ; Protozoan Proteins/genetics ; *Symbiosis ; Tetrahymena thermophila/*genetics ; }, abstract = {Plantae (as defined by Cavalier-Smith, 1981) plastids evolved via primary endosymbiosis whereby a heterotrophic protist enslaved a photosynthetic cyanobacterium. This "primary" plastid spread into other eukaryotes via secondary endosymbiosis. An important but contentious theory in algal evolution is the chromalveolate hypothesis that posits chromists (cryptophytes, haptophytes, and stramenopiles) and alveolates (ciliates, apicomplexans, and dinoflagellates) share a common ancestor that contained a red-algal-derived "secondary" plastid. Under this view, the existence of several later-diverging plastid-lacking chromalveolates such as ciliates and oomycetes would be explained by plastid loss in these lineages. To test the idea of a photosynthetic ancestry for ciliates, we used the 27,446 predicted proteins from the macronuclear genome of Tetrahymena thermophila to query prokaryotic and eukaryotic genomes. We identified 16 proteins of possible algal origin in the ciliates Tetrahymena and Paramecium tetraurelia. Fourteen of these are present in other chromalveolates. Here we compare and contrast the likely scenarios for algal-gene origin in ciliates either via multiple rounds of horizontal gene transfer (HGT) from algal prey or symbionts, or through endosymbiotic gene transfer (EGT) during a putative photosynthetic phase in their evolution.}, }
@article {pmid18593465, year = {2008}, author = {Hou, S and Makarova, KS and Saw, JH and Senin, P and Ly, BV and Zhou, Z and Ren, Y and Wang, J and Galperin, MY and Omelchenko, MV and Wolf, YI and Yutin, N and Koonin, EV and Stott, MB and Mountain, BW and Crowe, MA and Smirnova, AV and Dunfield, PF and Feng, L and Wang, L and Alam, M}, title = {Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia.}, journal = {Biology direct}, volume = {3}, number = {}, pages = {26}, pmid = {18593465}, issn = {1745-6150}, support = {Z99 LM999999/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Base Sequence ; Chlamydiaceae/*genetics/growth &amp; development/*isolation &amp; purification/metabolism ; *Comparative Genomic Hybridization ; *Genome, Bacterial ; Hydrogen-Ion Concentration ; Methane/metabolism ; }, abstract = {BACKGROUND: The phylum Verrucomicrobia is a widespread but poorly characterized bacterial clade. Although cultivation-independent approaches detect representatives of this phylum in a wide range of environments, including soils, seawater, hot springs and human gastrointestinal tract, only few have been isolated in pure culture. We have recently reported cultivation and initial characterization of an extremely acidophilic methanotrophic member of the Verrucomicrobia, strain V4, isolated from the Hell's Gate geothermal area in New Zealand. Similar organisms were independently isolated from geothermal systems in Italy and Russia.<br><br>RESULTS: We report the complete genome sequence of strain V4, the first one from a representative of the Verrucomicrobia. Isolate V4, initially named "Methylokorus infernorum" (and recently renamed Methylacidiphilum infernorum) is an autotrophic bacterium with a streamlined genome of ~2.3 Mbp that encodes simple signal transduction pathways and has a limited potential for regulation of gene expression. Central metabolism of M. infernorum was reconstructed almost completely and revealed highly interconnected pathways of autotrophic central metabolism and modifications of C1-utilization pathways compared to other known methylotrophs. The M. infernorum genome does not encode tubulin, which was previously discovered in bacteria of the genus Prosthecobacter, or close homologs of any other signature eukaryotic proteins. Phylogenetic analysis of ribosomal proteins and RNA polymerase subunits unequivocally supports grouping Planctomycetes, Verrucomicrobia and Chlamydiae into a single clade, the PVC superphylum, despite dramatically different gene content in members of these three groups. Comparative-genomic analysis suggests that evolution of the M. infernorum lineage involved extensive horizontal gene exchange with a variety of bacteria. The genome of M. infernorum shows apparent adaptations for existence under extremely acidic conditions including a major upward shift in the isoelectric points of proteins.<br><br>CONCLUSION: The results of genome analysis of M. infernorum support the monophyly of the PVC superphylum. M. infernorum possesses a streamlined genome but seems to have acquired numerous genes including those for enzymes of methylotrophic pathways via horizontal gene transfer, in particular, from Proteobacteria.<br><br>REVIEWERS: This article was reviewed by John A. Fuerst, Ludmila Chistoserdova, and Radhey S. Gupta.}, }
@article {pmid18591983, year = {2008}, author = {Keeling, PJ and Palmer, JD}, title = {Horizontal gene transfer in eukaryotic evolution.}, journal = {Nature reviews. Genetics}, volume = {9}, number = {8}, pages = {605-618}, doi = {10.1038/nrg2386}, pmid = {18591983}, issn = {1471-0064}, mesh = {Adaptation, Biological/genetics/physiology ; Animals ; *Biological Evolution ; DNA Transposable Elements/physiology ; *Eukaryotic Cells/metabolism/physiology ; Gene Transfer, Horizontal/*physiology ; Genome ; Humans ; Models, Biological ; Phylogeny ; Plants/genetics ; Prokaryotic Cells/metabolism/physiology ; Protein Transport/physiology ; Symbiosis/genetics ; }, abstract = {Horizontal gene transfer (HGT; also known as lateral gene transfer) has had an important role in eukaryotic genome evolution, but its importance is often overshadowed by the greater prevalence and our more advanced understanding of gene transfer in prokaryotes. Recurrent endosymbioses and the generally poor sampling of most nuclear genes from diverse lineages have also complicated the search for transferred genes. Nevertheless, the number of well-supported cases of transfer from both prokaryotes and eukaryotes, many with significant functional implications, is now expanding rapidly. Major recent trends include the important role of HGT in adaptation to certain specialized niches and the highly variable impact of HGT in different lineages.}, }
@article {pmid18590946, year = {2009}, author = {Matveev, V and Okada, N}, title = {Retroposons of salmonoid fishes (Actinopterygii: Salmonoidei) and their evolution.}, journal = {Gene}, volume = {434}, number = {1-2}, pages = {16-28}, doi = {10.1016/j.gene.2008.04.022}, pmid = {18590946}, issn = {1879-0038}, mesh = {Animals ; Base Sequence ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Long Interspersed Nucleotide Elements/*genetics ; Molecular Sequence Data ; Retroelements/*genetics ; Salmoniformes/*genetics ; Short Interspersed Nucleotide Elements/*genetics ; }, abstract = {Short and long retroposons, or non-LTR retrotransposons (SINEs and LINEs, respectively) are two groups of interspersed repetitive elements amplifying in the genome via RNA and cDNA-mediated reverse transcription. In this process, SINEs entirely depend on the enzymatic machinery of autonomous LINEs. The impact of retroposons on the host genome is difficult to overestimate: their sequences account for significant portion of the eukaryotic genome, while propagation of their active copies gradually reshapes it. In this way, the retropositional activity plays a role of important evolutionary factor. More than 100 LINE and nearly 100 SINE families have been described to date from the genomes of various eukaryotes, and it is salmonoid fishes (Actinopterygii: Salmonoidei) that are particularly noticeable for the diversity of transposons they host in their genomes, including two LINE and seven SINE families. Moreover, this group of ray-finned fish represents an excellent opportunity to study such a rare evolutionary phenomenon as lateral gene transfer, due to a great variety of transposons and other sequences salmons share with a blood fluke, Schistosoma japonicum (Trematoda: Strigeiformes)--a parasitic helminth infecting various vertebrates. The aim of the present review is to structure all knowledge accumulated about salmonoid retroposons by now, as well as to complement it with the new data pertaining to the distribution of some SINE families.}, }
@article {pmid18586945, year = {2008}, author = {Chung, GT and Yoo, JS and Oh, HB and Lee, YS and Cha, SH and Kim, SJ and Yoo, CK}, title = {Complete genome sequence of Neisseria gonorrhoeae NCCP11945.}, journal = {Journal of bacteriology}, volume = {190}, number = {17}, pages = {6035-6036}, pmid = {18586945}, issn = {1098-5530}, mesh = {Computational Biology ; DNA, Bacterial/chemistry/*genetics ; Female ; *Genome, Bacterial ; Humans ; Molecular Sequence Data ; Neisseria gonorrhoeae/*genetics/isolation &amp; purification ; Open Reading Frames/genetics ; Sequence Analysis, DNA ; }, abstract = {Neisseria gonorrhoeae is an obligate human pathogen that is the etiological agent of gonorrhea. We explored variations in the genes of a multidrug-resistant N. gonorrhoeae isolate from a Korean patient in an effort to understand the prevalence, antibiotic resistance, and importance of horizontal gene transfer within this important, naturally competent organism. Here, we report the complete annotated genome sequence of N. gonorrhoeae strain NCCP11945.}, }
@article {pmid18586943, year = {2008}, author = {Konczy, P and Ziebell, K and Mascarenhas, M and Choi, A and Michaud, C and Kropinski, AM and Whittam, TS and Wickham, M and Finlay, B and Karmali, MA}, title = {Genomic O island 122, locus for enterocyte effacement, and the evolution of virulent verocytotoxin-producing Escherichia coli.}, journal = {Journal of bacteriology}, volume = {190}, number = {17}, pages = {5832-5840}, pmid = {18586943}, issn = {1098-5530}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Cattle ; Escherichia coli/*genetics/metabolism/pathogenicity ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Genomic Islands/*genetics ; Humans ; Models, Genetic ; Sequence Analysis, DNA ; Shiga Toxins/*metabolism ; Virulence/genetics ; }, abstract = {The locus of enterocyte effacement (LEE) and genomic O island 122 (OI-122) are pathogenicity islands in verocytotoxin-producing Escherichia coli (VTEC) serotypes that are associated with outbreaks and serious disease. Composed of three modules, OI-122 may occur as "complete" (with all three modules) or "incomplete" (with one or two modules) in different strains. OI-122 encodes two non-LEE effector (Nle) molecules that are secreted by the LEE type III secretion system, and LEE and OI-122 are cointegrated in some VTEC strains. Thus, they are functionally linked, but little is known about the patterns of acquisition of these codependent islands. To examine this, we conducted a population genetics analysis, using multilocus sequence typing (MLST), with 72 VTEC strains (classified into seropathotypes A to E) and superimposed on the results the LEE and OI-122 contents of these organisms. The wide distribution of LEE and OI-122 modules among MLST clonal groups corroborates the hypothesis that there has been lateral transfer of both pathogenicity islands. Sequence analysis of a pagC-like gene in OI-122 module 1 also revealed two nonsynonymous single-nucleotide polymorphisms that could help discriminate a subset of seropathotype C strains and determine the presence of the LEE. A nonsense mutation was found in this gene in five less virulent strains, consistent with a decaying or inactive gene. The modular nature of OI-122 could be explained by the acquisition of modules by lateral transfer, either singly or as a group, and by degeneration of genes within modules. Correlations between clonal group, seropathotype, and LEE and OI-122 content provide insight into the role of genomic islands in VTEC evolution.}, }
@article {pmid18586704, year = {2008}, author = {Than, C and Sugino, R and Innan, H and Nakhleh, L}, title = {Efficient inference of bacterial strain trees from genome-scale multilocus data.}, journal = {Bioinformatics (Oxford, England)}, volume = {24}, number = {13}, pages = {i123-31}, pmid = {18586704}, issn = {1367-4811}, mesh = {*Algorithms ; Base Sequence ; *Biological Evolution ; Chromosome Mapping/*methods ; DNA Mutational Analysis/*methods ; *Databases, Genetic ; *Evolution, Molecular ; Genome, Bacterial/*genetics ; Molecular Sequence Data ; Sequence Analysis, DNA/*methods ; Species Specificity ; }, abstract = {MOTIVATION: In bacterial evolution, inferring a strain tree, which is the evolutionary history of different strains of the same bacterium, plays a major role in analyzing and understanding the evolution of strongly isolated populations, population divergence and various evolutionary events, such as horizontal gene transfer and homologous recombination. Inferring a strain tree from multilocus data of these strains is exceptionally hard since, at this scale of evolution, processes such as homologous recombination result in a very high degree of gene tree incongruence.<br><br>RESULTS: In this article we present a novel computational method for inferring the strain tree despite massive gene tree incongruence caused by homologous recombination. Our method operates in three phases, where in phase I a set of candidate strain-tree topologies is computed using the maximal cliques concept, in phase II divergence times for each of the topologies are estimated using mixed integer linear programming (MILP) and in phase III the optimal tree (or trees) is selected based on an optimality criterion. We have analyzed 1898 genes from nine strains of the Staphylococcus aureus bacteria, and identified a fully resolved (binary) strain tree with estimated divergence times, despite the high degrees of sequence identity at the nucleotide level and gene tree incongruence. Our method's efficiency makes it particularly suitable for analysis of genome-scale datasets, including those of strongly isolated populations which are usually very challenging to analyze.<br><br>AVAILABILITY: We have implemented the algorithms in the PhyloNet software package, which is available publicly at http://bioinfo.cs.rice.edu/phylonet/.}, }
@article {pmid18580971, year = {2008}, author = {Konstantinidis, KT and DeLong, EF}, title = {Genomic patterns of recombination, clonal divergence and environment in marine microbial populations.}, journal = {The ISME journal}, volume = {2}, number = {10}, pages = {1052-1065}, doi = {10.1038/ismej.2008.62}, pmid = {18580971}, issn = {1751-7370}, mesh = {Archaea/classification/*genetics/isolation &amp; purification ; Bacteria/classification/*genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; *Genetic Variation ; *Genome, Archaeal ; *Genome, Bacterial ; Pacific Ocean ; Phylogeny ; *Recombination, Genetic ; Seawater/*microbiology ; }, abstract = {Microorganisms represent the largest reservoir of biodiversity on Earth, both in numbers and total genetic diversity, but it remains unclear whether this biodiversity is organized in discrete units that correspond to ecologically coherent species. To further explore this question, we examined patterns of genomic diversity in sympatric microbial populations. Analyses of a total of approximately 200 Mb of microbial community genomic DNA sequence recovered from 4000 m depth in the Pacific Ocean revealed discrete sequence-defined populations of Bacteria and Archaea, with intrapopulation genomic sequence divergence ranging from approximately 1% to approximately 6%. The populations appeared to be maintained, at least in part, by intrapopulation genetic exchange (homologous recombination), although the frequency of recombination was estimated to be about three times lower than that observed previously in thermoacidophilic archaeal biofilm populations. Furthermore, the genotypes of a given population were clearly distinguishable from their closest co-occurring relatives based on their relative abundance in situ. The genetic distinctiveness and the matching sympatric abundances imply that these genotypes share similar ecophysiological properties, and therefore may represent fundamental units of microbial diversity in the deep sea. Comparisons to surface-dwelling relatives of the Sargasso Sea revealed that distinct sequence-based clusters were not always detectable, presumably due to environmental variations, further underscoring the important relationship between environmental contexts and genetic mechanisms, which together shape and sustain microbial population structure.}, }
@article {pmid18578876, year = {2008}, author = {Santos, CL and Vieira, J and Tavares, F and Benson, DR and Tisa, LS and Berry, AM and Moradas-Ferreira, P and Normand, P}, title = {On the nature of fur evolution: a phylogenetic approach in Actinobacteria.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {185}, pmid = {18578876}, issn = {1471-2148}, mesh = {Actinobacteria/classification/*genetics ; Bacterial Proteins/*genetics ; Ecology ; *Evolution, Molecular ; Genome, Bacterial ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Repressor Proteins/*genetics ; }, abstract = {BACKGROUND: An understanding of the evolution of global transcription regulators is essential for comprehending the complex networks of cellular metabolism that have developed among related organisms. The fur gene encodes one of those regulators - the ferric uptake regulator Fur - widely distributed among bacteria and known to regulate different genes committed to varied metabolic pathways. On the other hand, members of the Actinobacteria comprise an ecologically diverse group of bacteria able to inhabit various natural environments, and for which relatively little is currently understood concerning transcriptional regulation.<br><br>RESULTS: BLAST analyses revealed the presence of more than one fur homologue in most members of the Actinobacteria whose genomes have been fully sequenced. We propose a model to explain the evolutionary history of fur within this well-known bacterial phylum: the postulated scenario includes one duplication event from a primitive regulator, which probably had a broad range of co-factors and DNA-binding sites. This duplication predated the appearance of the last common ancestor of the Actinobacteria, while six other duplications occurred later within specific groups of organisms, particularly in two genera: Frankia and Streptomyces. The resulting paralogues maintained main biochemical properties, but became specialised for regulating specific functions, coordinating different metal ions and binding to unique DNA sequences. The presence of syntenic regions surrounding the different fur orthologues supports the proposed model, as do the evolutionary distances and topology of phylogenetic trees built using both Neighbor-Joining and Maximum-Likelihood methods.<br><br>CONCLUSION: The proposed fur evolutionary model, which includes one general duplication and two in-genus duplications followed by divergence and specialization, explains the presence and diversity of fur genes within the Actinobacteria. Although a few rare horizontal gene transfer events have been reported, the model is consistent with the view of gene duplication as a main force of microbial genomes evolution. The parallel study of Fur phylogeny across diverse organisms offers a solid base to guide functional studies and allows the comparison between response mechanisms in relation with the surrounding environment. The survey of regulators among related genomes provides a relevant tool for understanding the evolution of one of the first lines of cellular adaptability, control of DNA transcription.}, }
@article {pmid18577753, year = {2008}, author = {Levy, SB}, title = {Genome size and antibiotic resistance.}, journal = {Antimicrobial agents and chemotherapy}, volume = {52}, number = {7}, pages = {2696}, pmid = {18577753}, issn = {1098-6596}, mesh = {Bacteria/drug effects/genetics ; Bacterial Infections/drug therapy/microbiology ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; Mutation ; Selection, Genetic ; }, }
@article {pmid18577206, year = {2008}, author = {Fitzpatrick, DA and Logue, ME and Butler, G}, title = {Evidence of recent interkingdom horizontal gene transfer between bacteria and Candida parapsilosis.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {181}, pmid = {18577206}, issn = {1471-2148}, mesh = {Amino Acid Isomerases/chemistry/genetics ; Amino Acid Sequence ; Bacteria/enzymology/*genetics ; Candida/enzymology/*genetics ; Codon/genetics ; Databases, Nucleic Acid ; *Evolution, Molecular ; Gene Order ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/genetics ; Genes, Fungal/genetics ; Phylogeny ; Sequence Alignment ; }, abstract = {BACKGROUND: To date very few incidences of interdomain gene transfer into fungi have been identified. Here, we used the emerging genome sequences of Candida albicans WO-1, Candida tropicalis, Candida parapsilosis, Clavispora lusitaniae, Pichia guilliermondii, and Lodderomyces elongisporus to identify recent interdomain HGT events. We refer to these as CTG species because they translate the CTG codon as serine rather than leucine, and share a recent common ancestor.<br><br>RESULTS: Phylogenetic and syntenic information infer that two C. parapsilosis genes originate from bacterial sources. One encodes a putative proline racemase (PR). Phylogenetic analysis also infers that there were independent transfers of bacterial PR enzymes into members of the Pezizomycotina, and protists. The second HGT gene in C. parapsilosis belongs to the phenazine F (PhzF) superfamily. Most CTG species also contain a fungal PhzF homolog. Our phylogeny suggests that the CTG homolog originated from an ancient HGT event, from a member of the proteobacteria. An analysis of synteny suggests that C. parapsilosis has lost the endogenous fungal form of PhzF, and subsequently reacquired it from a proteobacterial source. There is evidence that Schizosaccharomyces pombe and Basidiomycotina also obtained a PhzF homolog through HGT.<br><br>CONCLUSION: Our search revealed two instances of well-supported HGT from bacteria into the CTG clade, both specific to C. parapsilosis. Therefore, while recent interkingdom gene transfer has taken place in the CTG lineage, its occurrence is rare. However, our analysis will not detect ancient gene transfers, and we may have underestimated the global extent of HGT into CTG species.}, }
@article {pmid18573206, year = {2008}, author = {Dessimoz, C and Gil, M}, title = {Covariance of maximum likelihood evolutionary distances between sequences aligned pairwise.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {179}, pmid = {18573206}, issn = {1471-2148}, mesh = {Algorithms ; *Evolution, Molecular ; Models, Statistical ; Phylogeny ; Sequence Alignment/*methods ; Sequence Analysis, Protein/methods ; }, abstract = {BACKGROUND: The estimation of a distance between two biological sequences is a fundamental process in molecular evolution. It is usually performed by maximum likelihood (ML) on characters aligned either pairwise or jointly in a multiple sequence alignment (MSA). Estimators for the covariance of pairs from an MSA are known, but we are not aware of any solution for cases of pairs aligned independently. In large-scale analyses, it may be too costly to compute MSAs every time distances must be compared, and therefore a covariance estimator for distances estimated from pairs aligned independently is desirable. Knowledge of covariances improves any process that compares or combines distances, such as in generalized least-squares phylogenetic tree building, orthology inference, or lateral gene transfer detection.<br><br>RESULTS: In this paper, we introduce an estimator for the covariance of distances from sequences aligned pairwise. Its performance is analyzed through extensive Monte Carlo simulations, and compared to the well-known variance estimator of ML distances. Our covariance estimator can be used together with the ML variance estimator to form covariance matrices.<br><br>CONCLUSION: The estimator performs similarly to the ML variance estimator. In particular, it shows no sign of bias when sequence divergence is below 150 PAM units (i.e. above ~29% expected sequence identity). Above that distance, the covariances tend to be underestimated, but then ML variances are also underestimated.}, }
@article {pmid18572389, year = {2008}, author = {Filée, J and Chandler, M}, title = {Convergent mechanisms of genome evolution of large and giant DNA viruses.}, journal = {Research in microbiology}, volume = {159}, number = {5}, pages = {325-331}, doi = {10.1016/j.resmic.2008.04.012}, pmid = {18572389}, issn = {0923-2508}, mesh = {Animals ; Bacteria/virology ; Bacteriophages/*genetics ; DNA Viruses/*genetics ; Eukaryotic Cells/virology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Viral ; Humans ; }, abstract = {We have taken advantage of the availability of the genome sequences of a collection of large and giant viruses infecting bacteria (T4 family) and eukaryotes (NCLDV group) to assess some of the evolutionary forces which might have shaped their genomes. Despite having apparently different ancestors, these two groups of viruses are affected by convergent evolutionary forces. Both types of virus probably originated from a simple and ancient viral ancestor with a small subset of 30-35 genes encoding replication and structural proteins. The genome size and diversity of the descendants most likely grew progressively by (i) lineage-specific gene duplications, (ii) lateral gene transfers of cellular genes and (iii) accretion of diverse families of mobile genetic elements. These results argue against the hypothesis that giant viruses derive from a regressive cell.}, }
@article {pmid18566777, year = {2008}, author = {Beiko, RG and Ragan, MA}, title = {Detecting lateral genetic transfer : a phylogenetic approach.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {452}, number = {}, pages = {457-469}, doi = {10.1007/978-1-60327-159-2_21}, pmid = {18566777}, issn = {1064-3745}, mesh = {Computational Biology/*methods ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; *Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {Nucleotide sequences of microbial genomes provide evidence that genes have been shared among organisms, a phenomenon known as lateral genetic transfer (LGT). Hypotheses about the importance of LGT in the evolution and diversification of microbes can be tested by analyzing the extensive quantities of sequence data now available. Some analysis methods identify genes with sequence features that differ from those of the surrounding genome, whereas other methods are based on inference and comparison of phylogenetic trees. A large-scale search for LGT in 144 genomes using phylogenetic methods has revealed that although parent-to-offspring ("vertical") inheritance has been the dominant mode of gene transmission, LGT has nonetheless been frequent, especially among organisms that are closely related or share the same habitat. This chapter outlines how bioinformatic and phylogenetic analyses can be built into a workflow to identify LGT among microbial genomes.}, }
@article {pmid18562339, year = {2008}, author = {Cordaux, R and Pichon, S and Ling, A and Pérez, P and Delaunay, C and Vavre, F and Bouchon, D and Grève, P}, title = {Intense transpositional activity of insertion sequences in an ancient obligate endosymbiont.}, journal = {Molecular biology and evolution}, volume = {25}, number = {9}, pages = {1889-1896}, pmid = {18562339}, issn = {1537-1719}, mesh = {Animals ; Crustacea/microbiology ; *DNA Transposable Elements ; *DNA, Bacterial ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Insecta/microbiology ; Molecular Sequence Data ; Sequence Homology, Nucleic Acid ; Symbiosis ; Wolbachia/*genetics ; }, abstract = {The streamlined genomes of ancient obligate endosymbionts generally lack transposable elements, such as insertion sequences (IS). Yet, the genome of Wolbachia, one of the most abundant bacterial endosymbionts on Earth, is littered with IS. Such a paradox raises the question as to why there are so many ISs in the genome of this ancient endosymbiont. To address this question, we investigated IS transpositional activity in the unculturable Wolbachia by tracking the evolutionary dynamics and history of ISWpi1 elements. We show that 1) ISWpi1 is widespread in Wolbachia, being present in at least 55% of the 40 sampled strains, 2) ISWpi1 copies exhibit virtually identical nucleotide sequences both within and among Wolbachia genomes and possess an intact transposase gene, 3) individual ISWpi1 copies are differentially inserted among Wolbachia genomes, and 4) ISWpi1 occurs at variable copy numbers among Wolbachia genomes. Collectively, our results provide compelling evidence for intense ISWpi1 transpositional activity and frequent ISWpi1 horizontal transmission among strains during recent Wolbachia evolution. Thus, the genomes of ancient obligate endosymbionts can carry high loads of functional and transpositionally active transposable elements. Our results also indicate that Wolbachia genomes have experienced multiple and temporally distinct ISWpi1 invasions during their evolutionary history. Such recurrent exposition to new IS invasions may explain, at least partly, the unusually high density of transposable elements found in the genomes of Wolbachia endosymbionts.}, }
@article {pmid18558012, year = {2008}, author = {Brouard, JS and Otis, C and Lemieux, C and Turmel, M}, title = {Chloroplast DNA sequence of the green alga Oedogonium cardiacum (Chlorophyceae): unique genome architecture, derived characters shared with the Chaetophorales and novel genes acquired through horizontal transfer.}, journal = {BMC genomics}, volume = {9}, number = {}, pages = {290}, pmid = {18558012}, issn = {1471-2164}, mesh = {Base Composition ; Base Sequence ; Chlorophyta/*classification/*genetics ; Chromosome Mapping ; Conserved Sequence ; DNA, Algal/chemistry/*genetics ; DNA, Chloroplast/chemistry/*genetics ; Evolution, Molecular ; Gene Order ; Gene Transfer, Horizontal ; Genome ; Introns ; Molecular Sequence Data ; Nucleic Acid Conformation ; Open Reading Frames ; RNA, Algal/chemistry/genetics ; RNA, Chloroplast/chemistry/genetics ; Repetitive Sequences, Nucleic Acid ; Species Specificity ; }, abstract = {BACKGROUND: To gain insight into the branching order of the five main lineages currently recognized in the green algal class Chlorophyceae and to expand our understanding of chloroplast genome evolution, we have undertaken the sequencing of chloroplast DNA (cpDNA) from representative taxa. The complete cpDNA sequences previously reported for Chlamydomonas (Chlamydomonadales), Scenedesmus (Sphaeropleales), and Stigeoclonium (Chaetophorales) revealed tremendous variability in their architecture, the retention of only few ancestral gene clusters, and derived clusters shared by Chlamydomonas and Scenedesmus. Unexpectedly, our recent phylogenies inferred from these cpDNAs and the partial sequences of three other chlorophycean cpDNAs disclosed two major clades, one uniting the Chlamydomonadales and Sphaeropleales (CS clade) and the other uniting the Oedogoniales, Chaetophorales and Chaetopeltidales (OCC clade). Although molecular signatures provided strong support for this dichotomy and for the branching of the Oedogoniales as the earliest-diverging lineage of the OCC clade, more data are required to validate these phylogenies. We describe here the complete cpDNA sequence of Oedogonium cardiacum (Oedogoniales).<br><br>RESULTS: Like its three chlorophycean homologues, the 196,547-bp Oedogonium chloroplast genome displays a distinctive architecture. This genome is one of the most compact among photosynthetic chlorophytes. It has an atypical quadripartite structure, is intron-rich (17 group I and 4 group II introns), and displays 99 different conserved genes and four long open reading frames (ORFs), three of which are clustered in the spacious inverted repeat of 35,493 bp. Intriguingly, two of these ORFs (int and dpoB) revealed high similarities to genes not usually found in cpDNA. At the gene content and gene order levels, the Oedogonium genome most closely resembles its Stigeoclonium counterpart. Characters shared by these chlorophyceans but missing in members of the CS clade include the retention of psaM, rpl32 and trnL(caa), the loss of petA, the disruption of three ancestral clusters and the presence of five derived gene clusters.<br><br>CONCLUSION: The Oedogonium chloroplast genome disclosed additional characters that bolster the evidence for a close alliance between the Oedogoniales and Chaetophorales. Our unprecedented finding of int and dpoB in this cpDNA provides a clear example that novel genes were acquired by the chloroplast genome through horizontal transfers, possibly from a mitochondrial genome donor.}, }
@article {pmid18557937, year = {2008}, author = {Grasselli, E and François, P and Gutacker, M and Gettler, B and Benagli, C and Convert, M and Boerlin, P and Schrenzel, J and Piffaretti, JC}, title = {Evidence of horizontal gene transfer between human and animal commensal Escherichia coli strains identified by microarray.}, journal = {FEMS immunology and medical microbiology}, volume = {53}, number = {3}, pages = {351-358}, doi = {10.1111/j.1574-695X.2008.00434.x}, pmid = {18557937}, issn = {0928-8244}, mesh = {Animals ; Base Composition ; Chromosomes, Bacterial ; DNA, Bacterial/*genetics ; Escherichia coli/*genetics/isolation &amp; purification/physiology ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; *Microarray Analysis ; Multigene Family ; Polymorphism, Genetic ; Synteny ; }, abstract = {Bacteria exchange genetic material by horizontal gene transfer (HGT). To evaluate the impact of HGT on Escherichia coli genome plasticity, 19 commensal strains collected from the intestinal floras of humans and animals were analyzed by microarrays. Strains were hybridized against an oligoarray containing 2700 E. coli K12 chromosomal genes. A core (genes shared among compared genomes) and a flexible gene pool (genes unique for each genome) have been identified. Analysis of hybridization signals evidenced 1015 divergent genes among the 19 strains and each strain showed a specific genomic variability pattern. Four hundred and fifty-eight genes were characterized by higher rates of interstrain variation and were considered hyperdivergent. These genes are not randomly distributed onto the chromosome but are clustered in precise regions. Hyperdivergent genes belong to the flexible gene pool and show a specific GC content, differing from that of the chromosome, indicating acquisition by HGT. Among these genes, those involved in defense mechanisms and cell motility as well as intracellular trafficking and secretion were far more represented than others. The observed genome plasticity contributes to the maintenance of genetic diversity and may therefore be a source of evolutionary adaptation and survival.}, }
@article {pmid18552340, year = {2008}, author = {Minarini, LA and Poirel, L and Cattoir, V and Darini, AL and Nordmann, P}, title = {Plasmid-mediated quinolone resistance determinants among enterobacterial isolates from outpatients in Brazil.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {62}, number = {3}, pages = {474-478}, doi = {10.1093/jac/dkn237}, pmid = {18552340}, issn = {1460-2091}, mesh = {Amino Acid Substitution/genetics ; Anti-Bacterial Agents/*pharmacology ; Brazil ; Citrobacter freundii/drug effects/genetics/isolation &amp; purification ; Conjugation, Genetic ; DNA, Bacterial/genetics ; *Drug Resistance, Bacterial ; Enterobacteriaceae/*drug effects/genetics/*isolation &amp; purification ; Enterobacteriaceae Infections/*microbiology ; Escherichia coli/drug effects/genetics/isolation &amp; purification ; Gene Order ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Klebsiella pneumoniae/drug effects/genetics/isolation &amp; purification ; Microbial Sensitivity Tests ; Mutation, Missense ; *Plasmids ; Polymerase Chain Reaction/methods ; Quinolones/*pharmacology ; Sequence Analysis, DNA ; }, abstract = {OBJECTIVES: The aim of this study was to determine the spread of plasmid-mediated quinolone resistance determinants [qnr-like, aac(6')-Ib-cr and qepA genes] among nalidixic acid-resistant enterobacterial strains isolated from outpatients from Southeast Brazil, their transferability and the genetic structures associated with the qnr genes.<br><br>METHODS: The qnrA, qnrB and qnrS genes were screened by a multiplex PCR-based technique from 257 non-repetitive nalidixic acid-resistant enterobacterial isolates collected from January 2000 to May 2005. Conjugation experiments were performed to determine whether the qnr-carrying plasmids were self-transferable. Genetic structures surrounding the qnr genes were analysed by PCR and cloning. The aac(6')-Ib-cr and qepA genes were screened among qnr-positive strains.<br><br>RESULTS: Six qnrB-like-positive isolates (2.3%) were detected, whereas no qnrA- or qnrS-positive isolates were detected. Three Escherichia coli and two Klebsiella pneumoniae isolates harboured a qnrB2 gene and a single Citrobacter freundii isolate had the qnrB8 gene. One qnrB2-positive isolate also had the extended-spectrum beta-lactamase bla(CTX-M-2) gene. All these isolates also possessed chromosomal substitutions in gyrase- and topoisomerase-encoding genes, explaining their high-level resistance to quinolones.<br><br>CONCLUSIONS: This study constitutes the first epidemiological survey of the three known Qnr determinants among Brazilian isolates and shows their low prevalence in that country, with the qnrB2 gene being mostly identified.}, }
@article {pmid18552189, year = {2008}, author = {Nagachinta, S and Chen, J}, title = {Transfer of class 1 integron-mediated antibiotic resistance genes from shiga toxin-producing Escherichia coli to a susceptible E. coli K-12 strain in storm water and bovine feces.}, journal = {Applied and environmental microbiology}, volume = {74}, number = {16}, pages = {5063-5067}, pmid = {18552189}, issn = {1098-5336}, mesh = {Animals ; Cattle ; *Conjugation, Genetic ; Drug Resistance, Bacterial/*genetics ; Escherichia coli K12/drug effects/*genetics ; Feces/*microbiology ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Georgia ; Hydrogen-Ion Concentration ; Integrons ; Microbial Sensitivity Tests ; Shiga-Toxigenic Escherichia coli/drug effects/*genetics ; Temperature ; Water Microbiology ; }, abstract = {Transfer of class 1 integron-mediated antibiotic resistance genes has been demonstrated under laboratory conditions. However, there is no information concerning the transfer of these genes in an agricultural environment. The present study sought to determine if integron-mediated streptomycin and sulfisoxazole resistance genes could be transferred from Shiga toxin-producing Escherichia coli (STEC) strains 6-20 (O157:H7) and 7-63 (O111:H8) to the susceptible strain E. coli K-12 MG1655 in bovine feces (pH 5.5, 6.0, or 6.5) and storm water (pH 5, 6, 7, or 8) at 4, 15, and 28 degrees C, which are average seasonal temperatures for winter, spring-fall, and summer, respectively, in the Griffin, GA, area. The results indicated that at 28 degrees C, the integron-mediated antibiotic resistance genes were transferred from both of the STEC donors in bovine feces. Higher conjugation efficiencies were, however, observed in the conjugation experiments involving STEC strain 6-20. In storm water, the resistance genes were transferred only from STEC strain 6-20. Greater numbers of transconjugants were recovered in the conjugation experiments performed with pH 6.5 bovine feces and with pH 7 storm water. Antibiotic susceptibility tests confirmed the transfer of integron-mediated streptomycin resistance and sulfisoxazole resistance, as well as the transfer of non-integron-mediated oxytetracycline resistance and tetracycline resistance in the transconjugant cells. These results suggest that the antibiotic resistance genes in STEC could serve as a source of antibiotic resistance genes disseminated via conjugation to susceptible cells of other E. coli strains in an agricultural environment.}, }
@article {pmid18551332, year = {2008}, author = {Blank, LM and Hugenholtz, P and Nielsen, LK}, title = {Evolution of the hyaluronic acid synthesis (has) operon in Streptococcus zooepidemicus and other pathogenic streptococci.}, journal = {Journal of molecular evolution}, volume = {67}, number = {1}, pages = {13-22}, pmid = {18551332}, issn = {0022-2844}, mesh = {Base Sequence ; *Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; Genes, Bacterial ; Hyaluronic Acid/*biosynthesis ; Molecular Sequence Data ; *Operon ; Phylogeny ; Sequence Alignment ; Streptococcus/classification/genetics ; Streptococcus equi/classification/enzymology/*genetics ; }, abstract = {Hyaluronic acid (HA) is a ubiquitous linear polysaccharide in vertebrates and also is the capsule material of some pathogenic bacteria including group A and C streptococci. In bacteria, the HA synthase occurs in an operon (has) coding for enzymes involved in the production of HA precursors. We report two new members of the has operon family from Streptococcus equi subsp. zooepidemicus (S. zooepidemicus) and Streptococcus equi subsp. equi (S. equi). The has operon of S. zooepidemicus contains, in order, hasA, hasB, hasC, glum, and pgi, whereas these genes are separated on two operons in S. equi (hasA, hasB, hasC and hasC, glmU, pgi). The transcription start site and a sigma(70) promoter were experimentally identified 50 bp upstream of hasA in S. zooepidemicus. We performed a phylogenetic analysis of each of the has operon genes to determine the evolutionary origin(s) of the streptococcal has operon. In contrast to other capsular and exopolysaccharide operons, has operons have undergone no detectable interspecies lateral gene transfers in their construction, instead relying on intragenome gene duplication for their assembly. Specifically, hasC and glmU appear to have been duplicated into the S. zooepidemicus has operon from remotely located but near-identical paralogues most likely to improve HA productivity by gene dosage in this streptococcus. The intragene rearrangements appear to be ongoing events and the two has operons of the S. equi subspecies represent two alternatives of the same gene arrangement. A scenario for the evolution of streptococcal has operons is proposed.}, }
@article {pmid18550812, year = {2008}, author = {Zeng, Q and Langereis, MA and van Vliet, AL and Huizinga, EG and de Groot, RJ}, title = {Structure of coronavirus hemagglutinin-esterase offers insight into corona and influenza virus evolution.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {26}, pages = {9065-9069}, pmid = {18550812}, issn = {1091-6490}, mesh = {Animals ; Binding Sites ; *Biological Evolution ; Cattle ; Cell Line ; Conserved Sequence ; Coronavirus/*enzymology/*genetics ; Crystallography, X-Ray ; Hemagglutinins, Viral/*chemistry/isolation &amp; purification ; Humans ; Models, Molecular ; Orthomyxoviridae/*genetics ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Virus/metabolism ; Recombinant Fusion Proteins/chemistry ; Viral Fusion Proteins/*chemistry/isolation &amp; purification ; }, abstract = {The hemagglutinin-esterases (HEs) are a family of viral envelope glycoproteins that mediate reversible attachment to O-acetylated sialic acids by acting both as lectins and as receptor-destroying enzymes (RDEs). Related HEs occur in influenza C, toro-, and coronaviruses, apparently as a result of relatively recent lateral gene transfer events. Here, we report the crystal structure of a coronavirus (CoV) HE in complex with its receptor. We show that CoV HE arose from an influenza C-like HE fusion protein (HEF). In the process, HE was transformed from a trimer into a dimer, whereas remnants of the fusion domain were adapted to establish novel monomer-monomer contacts. Whereas the structural design of the RDE-acetylesterase domain remained unaltered, the HE receptor-binding domain underwent remodeling to such extent that the ligand is now bound in opposite orientation. This is surprising, because the architecture of the HEF site was preserved in influenza A HA over a much larger evolutionary distance, a switch in receptor specificity and extensive antigenic variation notwithstanding. Apparently, HA and HEF are under more stringent selective constraints than HE, limiting their exploration of alternative binding-site topologies. We attribute the plasticity of the CoV HE receptor-binding site to evolutionary flexibility conferred by functional redundancy between HE and its companion spike protein S. Our findings offer unique insights into the structural and functional consequences of independent protein evolution after interviral gene exchange and open potential avenues to broad-spectrum antiviral drug design.}, }
@article {pmid18550618, year = {2008}, author = {Wellner, A and Gophna, U}, title = {Neutrality of foreign complex subunits in an experimental model of lateral gene transfer.}, journal = {Molecular biology and evolution}, volume = {25}, number = {9}, pages = {1835-1840}, doi = {10.1093/molbev/msn131}, pmid = {18550618}, issn = {1537-1719}, mesh = {Acetyl-CoA Carboxylase/genetics ; Cloning, Molecular ; *Directed Molecular Evolution ; Escherichia coli/genetics ; Gene Dosage ; *Gene Transfer, Horizontal ; Genes, Bacterial ; *Models, Genetic ; Protein Subunits/*genetics ; }, abstract = {Lateral gene transfer (LGT) is a powerful force in microbial evolution. However, the barriers that restrict this evolutionary phenomenon are not fully understood. It has long been observed that genes that encode subunits of complexes exhibit relatively compatible phylogenies, implying mostly vertical evolution. This may be explained by the failure of a new gene product to effectively interact with preexisting protein subunits, making its acquisition neutral--a theory termed the "complexity hypothesis." On the other hand, such genes may reduce the fitness of the host by disturbing the stoichiometric balance between complex subunits, resulting in purifying selection against gene retention. To examine these 2 alternative scenarios, we designed an experimental system that mimics the transfer of genes encoding homologs of essential complex subunits into the model bacterium Escherichia coli. In addition, we overexpressed the native E. coli gene in order to examine the contribution of gene dosage effects. We show that accumulation of native or foreign complex subunits in the cell does not result in loss of fitness, except for a minor fitness reduction observed for a single foreign homolog. Indeed, a series of genetic and biochemical assays failed to detect any interaction between the foreign subunits and the native polypeptides of the complex, implying an inability of such transfer events to generate positive selection for gene retention. We conclude that LGT of complex subunits may be mostly neutral and that forces operating against gene retention appear to be moderate.}, }
@article {pmid18550617, year = {2008}, author = {Klasson, L and Walker, T and Sebaihia, M and Sanders, MJ and Quail, MA and Lord, A and Sanders, S and Earl, J and O'Neill, SL and Thomson, N and Sinkins, SP and Parkhill, J}, title = {Genome evolution of Wolbachia strain wPip from the Culex pipiens group.}, journal = {Molecular biology and evolution}, volume = {25}, number = {9}, pages = {1877-1887}, pmid = {18550617}, issn = {1537-1719}, support = {/WT_/Wellcome Trust/United Kingdom ; 079059/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Ankyrin Repeat/genetics ; Bacterial Proteins/genetics/metabolism ; Culex/*microbiology ; DNA, Bacterial ; Drosophila melanogaster/microbiology ; *Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Molecular Sequence Data ; Prophages/genetics ; Symbiosis ; Wolbachia/*genetics ; }, abstract = {The obligate intracellular bacterium Wolbachia pipientis strain wPip induces cytoplasmic incompatibility (CI), patterns of crossing sterility, in the Culex pipiens group of mosquitoes. The complete sequence is presented of the 1.48-Mbp genome of wPip which encodes 1386 coding sequences (CDSs), representing the first genome sequence of a B-supergroup Wolbachia. Comparisons were made with the smaller genomes of Wolbachia strains wMel of Drosophila melanogaster, an A-supergroup Wolbachia that is also a CI inducer, and wBm, a mutualist of Brugia malayi nematodes that belongs to the D-supergroup of Wolbachia. Despite extensive gene order rearrangement, a core set of Wolbachia genes shared between the 3 genomes can be identified and contrasts with a flexible gene pool where rapid evolution has taken place. There are much more extensive prophage and ankyrin repeat encoding (ANK) gene components of the wPip genome compared with wMel and wBm, and both are likely to be of considerable importance in wPip biology. Five WO-B-like prophage regions are present and contain some genes that are identical or highly similar in multiple prophage copies, whereas other genes are unique, and it is likely that extensive recombination, duplication, and insertion have occurred between copies. A much larger number of genes encode ankyrin repeat (ANK) proteins in wPip, with 60 present compared with 23 in wMel, many of which are within or close to the prophage regions. It is likely that this pattern is partly a result of expansions in the wPip lineage, due for example to gene duplication, but their presence is in some cases more ancient. The wPip genome underlines the considerable evolutionary flexibility of Wolbachia, providing clear evidence for the rapid evolution of ANK-encoding genes and of prophage regions. This host-Wolbachia system, with its complex patterns of sterility induced between populations, now provides an excellent model for unraveling the molecular systems underlying host reproductive manipulation.}, }
@article {pmid18549454, year = {2008}, author = {Juhas, M and Crook, DW and Hood, DW}, title = {Type IV secretion systems: tools of bacterial horizontal gene transfer and virulence.}, journal = {Cellular microbiology}, volume = {10}, number = {12}, pages = {2377-2386}, pmid = {18549454}, issn = {1462-5822}, support = {G0400039/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Bacterial Physiological Phenomena ; Bacterial Proteins/*metabolism ; Carrier Proteins/*metabolism ; *Gene Transfer, Horizontal ; Macromolecular Substances/*metabolism ; }, abstract = {Type IV secretion systems (T4SSs) are multisubunit cell-envelope-spanning structures, ancestrally related to bacterial conjugation machines, which transfer proteins and nucleoprotein complexes across membranes. T4SSs mediate horizontal gene transfer, thus contributing to genome plasticity and the evolution of pathogens through dissemination of antibiotic resistance and virulence genes. Moreover, T4SSs are also used for the delivery of bacterial effector proteins across the bacterial membrane and the plasmatic membrane of eukaryotic host cell, thus contributing directly to pathogenicity. T4SSs are usually encoded by multiple genes organized into a single functional unit. Based on a number of features, the organization of genetic determinants, shared homologies and evolutionary relationships, T4SSs have been divided into several groups. Type F and P (type IVA) T4SSs resembling the archetypal VirB/VirD4 system of Agrobacterium tumefaciens are considered to be the paradigm of type IV secretion, while type I (type IVB) T4SSs are found in intracellular bacterial pathogens, Legionella pneumophila and Coxiella burnetii. Several novel T4SSs have been identified recently and their functions await investigation. The most recently described GI type T4SSs play a key role in the horizontal transfer of a wide variety of genomic islands derived from a broad spectrum of bacterial strains.}, }
@article {pmid18544040, year = {2008}, author = {Little, AE and Robinson, CJ and Peterson, SB and Raffa, KF and Handelsman, J}, title = {Rules of engagement: interspecies interactions that regulate microbial communities.}, journal = {Annual review of microbiology}, volume = {62}, number = {}, pages = {375-401}, doi = {10.1146/annurev.micro.030608.101423}, pmid = {18544040}, issn = {0066-4227}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {Biological Evolution ; *Ecosystem ; Gene Transfer, Horizontal ; Genetics, Microbial ; Genomics ; *Microbiological Phenomena ; Species Specificity ; }, abstract = {Microbial communities comprise an interwoven matrix of biological diversity modified by physical and chemical variation over space and time. Although these communities are the major drivers of biosphere processes, relatively little is known about their structure and function, and predictive modeling is limited by a dearth of comprehensive ecological principles that describe microbial community processes. Here we discuss working definitions of central ecological terms that have been used in various fashions in microbial ecology, provide a framework by focusing on different types of interactions within communities, review the status of the interface between evolutionary and ecological study, and highlight important similarities and differences between macro- and microbial ecology. We describe current approaches to study microbial ecology and progress toward predictive modeling.}, }
@article {pmid18539810, year = {2008}, author = {Azcarate-Peril, MA and Altermann, E and Goh, YJ and Tallon, R and Sanozky-Dawes, RB and Pfeiler, EA and O'Flaherty, S and Buck, BL and Dobson, A and Duong, T and Miller, MJ and Barrangou, R and Klaenhammer, TR}, title = {Analysis of the genome sequence of Lactobacillus gasseri ATCC 33323 reveals the molecular basis of an autochthonous intestinal organism.}, journal = {Applied and environmental microbiology}, volume = {74}, number = {15}, pages = {4610-4625}, pmid = {18539810}, issn = {1098-5336}, mesh = {Adult ; Bacterial Adhesion/genetics/physiology ; Bacterial Proteins/genetics ; Child ; DNA Primers ; Gastrointestinal Tract/*microbiology ; Genes, Bacterial ; *Genome, Bacterial ; Humans ; Infant, Newborn ; Intestines/*microbiology ; Lactobacillus/*genetics/isolation &amp; purification/pathogenicity ; Open Reading Frames ; }, abstract = {This study presents the complete genome sequence of Lactobacillus gasseri ATCC 33323, a neotype strain of human origin and a native species found commonly in the gastrointestinal tracts of neonates and adults. The plasmid-free genome was 1,894,360 bp in size and predicted to encode 1,810 genes. The GC content was 35.3%, similar to the GC content of its closest relatives, L. johnsonii NCC 533 (34%) and L. acidophilus NCFM (34%). Two identical copies of the prophage LgaI (40,086 bp), of the Sfi11-like Siphoviridae phage family, were integrated tandomly in the chromosome. A number of unique features were identified in the genome of L. gasseri that were likely acquired by horizontal gene transfer and may contribute to the survival of this bacterium in its ecological niche. L. gasseri encodes two restriction and modification systems, which may limit bacteriophage infection. L. gasseri also encodes an operon for production of heteropolysaccharides of high complexity. A unique alternative sigma factor was present similar to that of B. caccae ATCC 43185, a bacterial species isolated from human feces. In addition, L. gasseri encoded the highest number of putative mucus-binding proteins (14) among lactobacilli sequenced to date. Selected phenotypic characteristics that were compared between ATCC 33323 and other human L. gasseri strains included carbohydrate fermentation patterns, growth and survival in bile, oxalate degradation, and adhesion to intestinal epithelial cells, in vitro. The results from this study indicated high intraspecies variability from a genome encoding traits important for survival and retention in the gastrointestinal tract.}, }
@article {pmid18539053, year = {2008}, author = {Steenkamp, ET and Stepkowski, T and Przymusiak, A and Botha, WJ and Law, IJ}, title = {Cowpea and peanut in southern Africa are nodulated by diverse Bradyrhizobium strains harboring nodulation genes that belong to the large pantropical clade common in Africa.}, journal = {Molecular phylogenetics and evolution}, volume = {48}, number = {3}, pages = {1131-1144}, doi = {10.1016/j.ympev.2008.04.032}, pmid = {18539053}, issn = {1095-9513}, mesh = {Africa ; Arachis/*genetics ; Bradyrhizobium/*genetics ; Fabaceae/*genetics ; Gene Transfer Techniques ; Gene Transfer, Horizontal ; Genes, Plant/*genetics ; Genetic Variation ; Geography ; Models, Genetic ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Species Specificity ; }, abstract = {Cowpea (Vigna unguiculata) and peanut (Arachis hypogaea) in southern Africa are nodulated by a genetically diverse group of Bradyrhizobium strains. To determine the identity of these bacteria, a collection of 22 isolates originating from the root nodules of both hosts in Botswana and South Africa was investigated using the combined sequences for the core genome genes rrs, recA, and glnII. These data separated the majority of the isolates into one of three unique lineages that most likely represent novel Bradyrhizobium species. Some isolates were also conspecific with B. yuanmingense and with B. elkanii, although none grouped with B. japonicum, B. canariense or B. liaoningense. To study the evolution of nodulation genes in these bacteria, the common nodulation gene, nodA, and host-specific nodulation genes, nodZ, noeE, and noeI, were analyzed. The nodA phylogeny showed that the cowpea and peanut Bradyrhizobium isolates represent various locally adapted groups or ecotypes that form part of Clade III of the seven known BradyrhizobiumnodA clades. This large and highly diverse clade comprises all strains from sub-Saharan Africa, as well as some originating from the Americas, Australia, Indonesia, China and Japan. Some similar groupings were supported by the other nodulation genes, although the overall phylogenies for the nodulation genes were incongruent with that inferred from the core genome genes, suggesting that horizontal gene transfer significantly influences the evolution of cowpea and peanut root-nodule bacteria. Furthermore, identification of the nodZ, noeI, and noeE genes in the isolates tested indicates that African Bradyrhizobium species may produce highly decorated nodulation factors, which potentially represent an important adaptation enabling nodulation of a great variety of legumes inhabiting the African continent.}, }
@article {pmid18537840, year = {2008}, author = {Pistorio, M and Giusti, MA and Del Papa, MF and Draghi, WO and Lozano, MJ and Tejerizo, GT and Lagares, A}, title = {Conjugal properties of the Sinorhizobium meliloti plasmid mobilome.}, journal = {FEMS microbiology ecology}, volume = {65}, number = {3}, pages = {372-382}, doi = {10.1111/j.1574-6941.2008.00509.x}, pmid = {18537840}, issn = {0168-6496}, mesh = {Argentina ; Biodiversity ; *Conjugation, Genetic ; DNA Fingerprinting ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; Genetic Variation ; Genetics, Population ; Genotype ; *Plasmids ; Sinorhizobium meliloti/classification/*genetics ; Soil Microbiology ; Symbiosis ; }, abstract = {The biology and biochemistry of plasmid transfer in soil bacteria is currently under active investigation because of its central role in prokaryote adaptation and evolution. In this work, we examined the conjugal properties of the cryptic plasmids present in a collection of the N(2)-fixing legume-symbiont Sinorhizobium meliloti. The study was performed on 65 S. meliloti isolates recovered from 25 humic soils of Argentina, which were grouped into 22 plasmid-profile types [i.e. plasmid operational taxonomic units (OTUs)]. The cumulative Shannon index calculated for the observed plasmid profiles showed a clear saturation plateau, thus indicating an adequate representation of the S. meliloti plasmid-profile types in the isolates studied. The results show that isolates of nearly 14% of the plasmid OTUs hosted transmissible plasmids and that isolates of 29% of the plasmid OTUs were able to retransfer the previously characterized mobilizable-cryptic plasmid pSmeLPU88b to a third recipient strain. It is noteworthy that isolates belonging to 14% of the plasmid OTUs proved to be refractory to the entrance of the model plasmid pSmeLPU88b, suggesting either the presence of surface exclusion phenomena or the occurrence of restriction incompatibility with the incoming replicon. Incompatibility for replication between resident plasmids and plasmid pSmeLPU88b was observed in c. 20% of the OTUs. The results reported here reveal a widespread compatibility among the conjugal functions of the cryptic plasmids in S. meliloti, and this fact, together with the observed high proportion of existing donor genotypes, points to the extrachromosomal compartment of the species as being an extremely active plasmid mobilome.}, }
@article {pmid18535447, year = {2008}, author = {Vrtis, MC}, title = {Is your patient taking the right antimicrobial?.}, journal = {The American journal of nursing}, volume = {108}, number = {6}, pages = {49-55}, doi = {10.1097/01.NAJ.0000324377.09651.c7}, pmid = {18535447}, issn = {1538-7488}, mesh = {Adult ; Anti-Bacterial Agents/therapeutic use ; Bacteroides Infections/diagnosis/drug therapy/etiology ; *Bacteroides fragilis/genetics ; Causality ; Ciprofloxacin/therapeutic use ; Colonic Diseases/complications ; Conjugation, Genetic/genetics ; DNA, Bacterial/genetics ; Diagnostic Errors/adverse effects/nursing/*prevention &amp; control ; Drug Monitoring/nursing ; Drug Resistance, Bacterial ; Fatal Outcome ; Female ; Gene Transfer, Horizontal/genetics ; Humans ; Microbial Sensitivity Tests ; *Nurse's Role ; *Patient Advocacy ; Patient Selection ; Peritoneal Dialysis/adverse effects ; Rupture, Spontaneous ; *Sepsis/diagnosis/drug therapy/etiology ; Transformation, Bacterial/genetics ; }, }
@article {pmid18534838, year = {2008}, author = {Baquero, F and Martínez, JL and Cantón, R}, title = {Antibiotics and antibiotic resistance in water environments.}, journal = {Current opinion in biotechnology}, volume = {19}, number = {3}, pages = {260-265}, doi = {10.1016/j.copbio.2008.05.006}, pmid = {18534838}, issn = {0958-1669}, mesh = {Animals ; Anti-Bacterial Agents/analysis ; Bacteria/drug effects/genetics ; Biotechnology ; *Drug Resistance, Bacterial/genetics ; Ecosystem ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Industrial Waste/analysis ; Risk Assessment ; Soil Pollutants/analysis ; Waste Management ; *Water Microbiology ; Water Pollutants, Chemical/analysis ; }, abstract = {Antibiotic-resistant organisms enter into water environments from human and animal sources. These bacteria are able to spread their genes into water-indigenous microbes, which also contain resistance genes. On the contrary, many antibiotics from industrial origin circulate in water environments, potentially altering microbial ecosystems. Risk assessment protocols for antibiotics and resistant bacteria in water, based on better systems for antibiotics detection and antibiotic-resistance microbial source tracking, are starting to be discussed. Methods to reduce resistant bacterial load in wastewaters, and the amount of antimicrobial agents, in most cases originated in hospitals and farms, include optimization of disinfection procedures and management of wastewater and manure. A policy for preventing mixing human-originated and animal-originated bacteria with environmental organisms seems advisable.}, }
@article {pmid18533837, year = {2008}, author = {Sjöblom, S and Harjunpää, H and Brader, G and Palva, ET}, title = {A novel plant ferredoxin-like protein and the regulator Hor are quorum-sensing targets in the plant pathogen Erwinia carotovora.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {21}, number = {7}, pages = {967-978}, doi = {10.1094/MPMI-21-7-0967}, pmid = {18533837}, issn = {0894-0282}, mesh = {Amino Acid Sequence ; Arabidopsis/genetics/microbiology/physiology ; Bacterial Proteins/genetics/*physiology ; Base Sequence ; DNA Primers/genetics ; DNA, Bacterial/genetics ; DNA, Plant/genetics ; Genes, Bacterial ; Genes, Plant ; Host-Pathogen Interactions/genetics/*physiology ; Models, Biological ; Molecular Sequence Data ; Mutagenesis, Insertional ; Oxidative Stress ; Pectobacterium carotovorum/genetics/*pathogenicity/*physiology ; Plant Diseases/microbiology ; Plant Proteins/genetics/*physiology ; Plants, Genetically Modified ; Quorum Sensing/genetics/physiology ; Sequence Homology, Amino Acid ; Solanum tuberosum/genetics/microbiology/physiology ; Trans-Activators/genetics/physiology ; Virulence/genetics/physiology ; }, abstract = {Quorum sensing (QS), a population-density-sensing mechanism, controls the production of the main virulence determinants, the plant cell-wall-degrading enzymes (PCWDEs) of the soft-rot phytopathogen Erwinia carotovora subsp. carotovora. In this study, we used random transposon mutagenesis with a gusA reporter construct to identify two new QS-controlled genes encoding the regulator Hor and a plant ferredoxin-like protein, FerE. The QS control of the identified genes was executed by the QS regulators ExpR1 and ExpR2 and mediated by the global repressor RsmA. Hor was shown to contribute to bacterial virulence at least partly through its control of PCWDE production. Our results showed that FerE contributes to oxidative stress tolerance and in planta fitness of the bacteria and suggest that QS could be central to control of oxidative stress tolerance. The presence of the FerE protein appears to be rather unique in heterotrophic bacteria and suggests an acquisition of the corresponding gene from plant host by horizontal gene transfer.}, }
@article {pmid18528415, year = {2008}, author = {Fox, RE and Zhong, X and Krone, SM and Top, EM}, title = {Spatial structure and nutrients promote invasion of IncP-1 plasmids in bacterial populations.}, journal = {The ISME journal}, volume = {2}, number = {10}, pages = {1024-1039}, pmid = {18528415}, issn = {1751-7370}, support = {R01 GM073821/GM/NIGMS NIH HHS/United States ; R01 GM073821-03/GM/NIGMS NIH HHS/United States ; R01GM073821/GM/NIGMS NIH HHS/United States ; }, mesh = {Culture Media/metabolism ; Escherichia coli/*genetics/*metabolism ; Escherichia coli Proteins/genetics/metabolism ; *Gene Transfer, Horizontal ; Glucose/*metabolism ; Models, Theoretical ; Plasmids/*genetics/metabolism ; }, abstract = {In spite of the importance of plasmids in bacterial adaptation, we have a poor understanding of their dynamics. It is not known if or how plasmids persist in and spread through (invade) a bacterial population when there is no selection for plasmid-encoded traits. Moreover, the differences in dynamics between spatially structured and mixed populations are poorly understood. Through a joint experimental/theoretical approach, we tested the hypothesis that self-transmissible IncP-1 plasmids can invade a bacterial population in the absence of selection when initially very rare, but only in spatially structured habitats and when nutrients are regularly replenished. Using protocols that differed in the degree of spatial structure and nutrient levels, the invasiveness of plasmid pB10 in Escherichia coli was monitored during at least 15 days, with an initial fraction of plasmid-bearing (p(+)) cells as low as 10(-7). To further explore the mechanisms underlying plasmid dynamics, we developed a spatially explicit mathematical model. When cells were grown on filters and transferred to fresh medium daily, the p(+) fraction increased to 13%, whereas almost complete invasion occurred when the population structure was disturbed daily. The plasmid was unable to invade in liquid. When carbon source levels were lower or not replenished, plasmid invasion was hampered. Simulations of the mathematical model closely matched the experimental results and produced estimates of the effects of alternative experimental parameters. This allowed us to isolate the likely mechanisms most responsible for the observations. In conclusion, spatial structure and nutrient availability can be key determinants in the invasiveness of plasmids.}, }
@article {pmid18524914, year = {2008}, author = {Klockgether, J and Würdemann, D and Wiehlmann, L and Tümmler, B}, title = {Transcript profiling of the Pseudomonas aeruginosa genomic islands PAGI-2 and pKLC102.}, journal = {Microbiology (Reading, England)}, volume = {154}, number = {Pt 6}, pages = {1599-1604}, doi = {10.1099/mic.0.2007/014340-0}, pmid = {18524914}, issn = {1350-0872}, mesh = {Culture Media ; *Gene Expression Profiling ; Genomic Islands/*genetics ; Oligonucleotide Array Sequence Analysis ; Pseudomonas aeruginosa/*genetics/growth &amp; development ; Reverse Transcriptase Polymerase Chain Reaction ; Transcription, Genetic/*genetics ; }, abstract = {The phylogenetically ancient genomic islands of the abundant PAGI-2/pKLC102 family are prone to horizontal gene transfer amongst proteobacteria, and account for most genomic diversity in Pseudomonas aeruginosa. The mRNA expression levels of the sequenced PAGI-2 and pKLC102 islands were determined in P. aeruginosa clone C strains C and SG17M during exponential and stationary growth in Luria broth or Vogel-Bonner mineral medium. Of the 111 ORFs of PAGI-2, only one gene was significantly expressed at a level of more than 0.0001% of total RNA. The individual mRNA transcripts of the 103 pKLC102 ORFs, however, were present in the range of 0.001% to more than 1% in the bacterial RNA population, and amounted altogether to more than 10% of cellular RNA. Homologous genes were strongly transcribed from pKLC102, but not at all from PAGI-2 under the tested conditions. Thus PAGI-2, which was stably captured by its host chromosome, was transcriptionally silent, whereas the mRNA transcripts derived from the mobile and episomally replicating pKLC102 were constitutively more abundant in the cell than the mRNA pool transcribed from the core genome.}, }
@article {pmid18524785, year = {2008}, author = {Sanchez-Puerta, MV and Cho, Y and Mower, JP and Alverson, AJ and Palmer, JD}, title = {Frequent, phylogenetically local horizontal transfer of the cox1 group I Intron in flowering plant mitochondria.}, journal = {Molecular biology and evolution}, volume = {25}, number = {8}, pages = {1762-1777}, pmid = {18524785}, issn = {1537-1719}, support = {F32 GM080079/GM/NIGMS NIH HHS/United States ; R01 GM070612/GM/NIGMS NIH HHS/United States ; R01-GM-70612/GM/NIGMS NIH HHS/United States ; 1F32GM080079/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Sequence ; Cyclooxygenase 1/*genetics ; DNA Primers/genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Introns/*genetics ; Likelihood Functions ; Magnoliopsida/*genetics ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Horizontal gene transfer is surprisingly common among plant mitochondrial genomes. The first well-established case involves a homing group I intron in the mitochondrial cox1 gene shown to have been frequently acquired via horizontal transfer in angiosperms. Here, we report extensive additional sampling of angiosperms, including 85 newly sequenced introns from 30 families. Analysis of all available data leads us to conclude that, among the 640 angiosperms (from 212 families) whose cox1 intron status has been characterized thus far, the intron has been acquired via roughly 70 separate horizontal transfer events. We propose that the intron was originally seeded into angiosperms by a single transfer from fungi, with all subsequent inferred transfers occurring from one angiosperm to another. The pattern of angiosperm-to-angiosperm transfer is biased toward exchanges between plants belonging to the same family. Illegitimate pollination is proposed as one potential factor responsible for this pattern, given that aberrant, cross-species pollination is more likely between close relatives. Other potential factors include shared vectoring agents or common geographic locations. We report the first apparent cases of loss of the cox1 intron; losses are accompanied by retention of the exonic coconversion tract, which is located immediately downstream of the intron and which is a product of the intron's self-insertion mechanism. We discuss the many reasons why the cox1 intron is so frequently and detectably transferred, and rarely lost, and conclude that it should be regarded as the "canary in the coal mine" with respect to horizontal transfer in angiosperm mitochondria.}, }
@article {pmid18523858, year = {2008}, author = {te Poele, EM and Bolhuis, H and Dijkhuizen, L}, title = {Actinomycete integrative and conjugative elements.}, journal = {Antonie van Leeuwenhoek}, volume = {94}, number = {1}, pages = {127-143}, pmid = {18523858}, issn = {0003-6072}, mesh = {Actinobacteria/chemistry/classification/*genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Base Pairing ; Base Sequence ; *Conjugation, Genetic ; DNA Replication ; DNA, Bacterial/chemistry/genetics ; Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genome, Bacterial ; Geography ; Phylogeny ; RNA, Transfer/chemistry/*genetics/metabolism ; }, abstract = {This paper reviews current knowledge on actinomycete integrative and conjugative elements (AICEs). The best characterised AICEs, pSAM2 of Streptomyces ambofaciens (10.9 kb), SLP1 (17.3 kb) of Streptomyces coelicolor and pMEA300 of Amycolatopsis methanolica (13.3 kb), are present as integrative elements in specific tRNA genes, and are capable of conjugative transfer. These AICEs have a highly conserved structural organisation, with functional modules for excision/integration, replication, conjugative transfer, and regulation. Recently, it has been shown that pMEA300 and the related elements pMEA100 of Amycolatopsis mediterranei and pSE211 of Saccharopolyspora erythraea form a novel group of AICEs, the pMEA-elements, based on the unique characteristics of their replication initiator protein RepAM. Evaluation of a large collection of Amycolatopsis isolates has allowed identification of multiple pMEA-like elements. Our data show that, as AICEs, they mainly coevolved with their natural host in an integrated form, rather than being dispersed via horizontal gene transfer. The pMEA-like elements could be separated into two distinct populations from different geographical origins. One group was most closely related to pMEA300 and was found in isolates from Australia and Asia and pMEA100-related sequences were present in European isolates. Genome sequence data have enormously contributed to the recent insight that AICEs are present in many actinomycete genera. The sequence data also provide more insight into their evolutionary relationships, revealing their modular composition and their likely combined descent from bacterial plasmids and bacteriophages. Evidence is accumulating that AICEs act as modulators of host genome diversity and are also involved in the acquisition of secondary metabolite clusters and foreign DNA via horizontal gene transfer. Although still speculative, these AICEs may play a role in the spread of antibiotic resistance factors into pathogenic bacteria. The novel insights on AICE characteristics presented in this review may be used for the effective construction of new vectors that allows us to engineer and optimise strains for the production of commercially and medically interesting secondary metabolites, and bioactive proteins.}, }
@article {pmid18523437, year = {2008}, author = {McGeoch, AT and Bell, SD}, title = {Extra-chromosomal elements and the evolution of cellular DNA replication machineries.}, journal = {Nature reviews. Molecular cell biology}, volume = {9}, number = {7}, pages = {569-574}, doi = {10.1038/nrm2426}, pmid = {18523437}, issn = {1471-0080}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Archaeal Proteins/classification/genetics/metabolism ; Bacterial Proteins/classification/genetics/metabolism ; *Biological Evolution ; Chromosomes/*genetics ; *DNA Replication ; Eukaryotic Cells/physiology ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Multigene Family ; Phylogeny ; Replication Origin ; Replicon ; }, abstract = {DNA replication is fundamental to the propagation of cellular life. Remarkably, the bacterial replication machinery is distinct from that used by archaea and eukaryotes. In this article, we discuss the role that lateral gene transfer by extra-chromosomal elements might have had in shaping the replication machinery and even modulating the manner in which host cellular genomes are replicated.}, }
@article {pmid18522920, year = {2008}, author = {Arnold, ML and Sapir, Y and Martin, NH}, title = {Review. Genetic exchange and the origin of adaptations: prokaryotes to primates.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {363}, number = {1505}, pages = {2813-2820}, pmid = {18522920}, issn = {0962-8436}, mesh = {Adaptation, Physiological/*genetics ; Animals ; Gene Transfer, Horizontal ; *Hybridization, Genetic ; Primates/*genetics ; *Prokaryotic Cells ; }, abstract = {Data supporting the occurrence of adaptive trait transfer (i.e. the transfer of genes and thus the phenotype of an adaptive trait through viral recombination, lateral gene transfer or introgressive hybridization) are provided in this review. Specifically, we discuss examples of lateral gene transfer and introgressive hybridization that have resulted in the transfer or de novo origin of adaptations. The evolutionary clades in which this process has been identified include all types of organisms. However, we restrict our discussion to bacteria, fungi, plants and animals. Each of these examples reflects the same consequence, namely that the transfer of genetic material, through whatever mechanism, may result in adaptive evolution. In particular, each of the events discussed has been inferred to impact adaptations to novel environmental settings in the recipient lineage.}, }
@article {pmid18522807, year = {2009}, author = {Herrmann, JM and Kauff, F and Neuhaus, HE}, title = {Thiol oxidation in bacteria, mitochondria and chloroplasts: common principles but three unrelated machineries?.}, journal = {Biochimica et biophysica acta}, volume = {1793}, number = {1}, pages = {71-77}, doi = {10.1016/j.bbamcr.2008.05.001}, pmid = {18522807}, issn = {0006-3002}, mesh = {Bacterial Proteins/chemistry/*metabolism ; Chloroplasts/*metabolism ; Escherichia coli Proteins/chemistry/*metabolism ; Membrane Proteins/chemistry/*metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins/chemistry/metabolism ; Oxidation-Reduction ; Oxidoreductases/chemistry/*metabolism ; Periplasm/metabolism ; Protein Disulfide-Isomerases/chemistry/*metabolism ; Sulfhydryl Compounds/*metabolism ; Thylakoids/metabolism ; }, abstract = {The intermembrane space of mitochondria and the thylakoid lumen of chloroplasts are evolutionary descendents of the periplasmic space of bacteria. Presumably due to their common ancestry, the active oxidation of cysteinyl thiols is used in these three compartments in order to stabilize protein folding or to regulate protein function. In contrast, compartments of the eukaryotic cell which developed from the bacterial cytosol maintain cysteine residues largely reduced. Whereas the oxidizing machinery of bacteria is well characterized, that of mitochondria was only recently discovered and that of thylakoids still awaits to be identified. In mitochondria, protein oxidation is mediated by the sulfhydryl oxidase Erv1 which is highly conserved among eukaryotes. Erv1 oxidizes its substrate protein Mia40 which serves as an import receptor for proteins destined for the intermembrane space. This review summarizes the current knowledge on the mitochondrial disulfide relay system and compares its features to those of the periplasm and the thylakoid lumen. Although the sulfhydryl oxidases in the intermembrane space, Erv1, and the bacterial periplasm, DsbA-DsbB, share key structural features their primary sequence is not related and the evolutionary origin of Erv1 is unclear. On the basis of phylogenetic analyses of Erv1 sequences we propose that the mitochondrial oxidation machinery originated from a lateral gene transfer from flavobacteria-like prokaryotes early in eukaryotic evolution.}, }
@article {pmid18522759, year = {2008}, author = {Lee, KB and De Backer, P and Aono, T and Liu, CT and Suzuki, S and Suzuki, T and Kaneko, T and Yamada, M and Tabata, S and Kupfer, DM and Najar, FZ and Wiley, GB and Roe, B and Binnewies, TT and Ussery, DW and D'Haeze, W and Herder, JD and Gevers, D and Vereecke, D and Holsters, M and Oyaizu, H}, title = {The genome of the versatile nitrogen fixer Azorhizobium caulinodans ORS571.}, journal = {BMC genomics}, volume = {9}, number = {}, pages = {271}, pmid = {18522759}, issn = {1471-2164}, mesh = {Alphaproteobacteria/classification/genetics ; Azorhizobium caulinodans/classification/*genetics/metabolism ; Base Composition ; DNA, Bacterial/chemistry/genetics ; Fabaceae/microbiology ; *Genome, Bacterial ; Nitrogen Fixation/genetics ; Phylogeny ; Replication Origin ; Symbiosis/genetics/physiology ; Xanthobacter/classification/genetics ; }, abstract = {BACKGROUND: Biological nitrogen fixation is a prokaryotic process that plays an essential role in the global nitrogen cycle. Azorhizobium caulinodans ORS571 has the dual capacity to fix nitrogen both as free-living organism and in a symbiotic interaction with Sesbania rostrata. The host is a fast-growing, submergence-tolerant tropical legume on which A. caulinodans can efficiently induce nodule formation on the root system and on adventitious rootlets located on the stem.<br><br>RESULTS: The 5.37-Mb genome consists of a single circular chromosome with an overall average GC of 67% and numerous islands with varying GC contents. Most nodulation functions as well as a putative type-IV secretion system are found in a distinct symbiosis region. The genome contains a plethora of regulatory and transporter genes and many functions possibly involved in contacting a host. It potentially encodes 4717 proteins of which 96.3% have homologs and 3.7% are unique for A. caulinodans. Phylogenetic analyses show that the diazotroph Xanthobacter autotrophicus is the closest relative among the sequenced genomes, but the synteny between both genomes is very poor.<br><br>CONCLUSION: The genome analysis reveals that A. caulinodans is a diazotroph that acquired the capacity to nodulate most probably through horizontal gene transfer of a complex symbiosis island. The genome contains numerous genes that reflect a strong adaptive and metabolic potential. These combined features and the availability of the annotated genome make A. caulinodans an attractive organism to explore symbiotic biological nitrogen fixation beyond leguminous plants.}, }
@article {pmid18522127, year = {2008}, author = {Hu, J and Shi, J and Chang, H and Li, D and Yang, M and Kamagata, Y}, title = {Phenotyping and genotyping of antibiotic-resistant Escherichia coli isolated from a natural river basin.}, journal = {Environmental science &amp; technology}, volume = {42}, number = {9}, pages = {3415-3420}, doi = {10.1021/es7026746}, pmid = {18522127}, issn = {0013-936X}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Chickens ; China ; Drug Resistance, Bacterial ; *Drug Resistance, Microbial ; Escherichia coli/*genetics/metabolism ; Genotype ; Humans ; *Microbial Sensitivity Tests ; Phenotype ; Rivers ; Sulfonamides/analysis ; Swine ; Tetracycline/analysis ; beta-Lactams/metabolism ; }, abstract = {Scientists have become increasingly concerned about the occurrence of antibacterial resistance in the environment. In this study, Escherichia coli resistant to one or more antibiotics among nine antibiotics was screened from Wenyu River Basin in Beijing, China, with mean frequency of 48.7 +/- 8.7% of 388 isolates in summer and 47 +/- 6% of 236 isolates in winter. The mean multiantibiotic resistance (MAR) index in summer was 0.11 +/- 0.03, slightly lower than that (0.14 +/- 0.04) in winter. Most frequent resistance appeared for sulfonamides, tetracycline, and ampicillin. The distribution of 20 tetracycline, three sulfonamide, and three beta-lactam resistance genes was assessed in the resistant isolates. While 97% of the ampicillin (AMP) resistant mechanism could be explained by the resistance gene TEM, 90% of the tetracycline (TC) and 96% of the sulfonamide (SXT) resistances could be explained by tet(A), tet(B), tet(M), and their combinations and sul(I), sul(II), sul(III), and their combinations, respectively. tet(M), a tetracycline-resistant gene originally detected in Gram-positive bacteria, and its combinations with tet(A) or tet(B) were first detected in E. coli isolated from a natural river basin, suggesting that tet(M) in E. coli might have been transferred from other bacterial species through horizontal gene transfer, which was supported by the fact that no tet(M) was detected in the isolates of human and chicken sources, except for only one isolate from swine. The source of sulfonamide-resistant E. coli in the river was supposed to be mainly from humans, based on a comparison of the sulfonamide resistance genotypes in animals and humans.}, }
@article {pmid18521530, year = {2008}, author = {Layton, BE and D'Souza, AJ and Dampier, W and Zeiger, A and Sabur, A and Jean-Charles, J}, title = {Collagen's triglycine repeat number and phylogeny suggest an interdomain transfer event from a Devonian or Silurian organism into Trichodesmium erythraeum.}, journal = {Journal of molecular evolution}, volume = {66}, number = {6}, pages = {539-554}, pmid = {18521530}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Animals ; Collagen/chemistry/classification/*genetics ; Cyanobacteria/cytology/*genetics/ultrastructure ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Humans ; Microscopy, Atomic Force ; Microscopy, Electron, Scanning ; Molecular Sequence Data ; Oligopeptides/*analysis ; Phylogeny ; Protein Structure, Tertiary ; Repetitive Sequences, Amino Acid ; Sequence Alignment ; }, abstract = {Two competing effects at two vastly different scales may explain collagen's current translation length. The necessity to have long molecules for maintaining mechanical integrity at the organism and supraorganism scales may be limited by the need to have small molecules capable of robust self-assembly at the nanoscale. The triglycine repeat regions of all 556 currently cataloged organisms with collagen-like genes were ranked by length. This revealed a sharp boundary in the GXY transcript number at 1032 amino acids (344 GXY repeats). An anomalous exception, however, is the intron-free Trichodesmium erythraeum collagen gene. Immunogold atomic force microscopy reveals, for the first time, the presence of a collagen-like protein in T. erythraeum. A phylogenetic protein sequence analysis which includes vertebrates, nonvertebrates, shrimp white spot syndrome virus, Streptococcus equi, and Bacillus cereus predicts that the collagen-like sequence may have emerged shortly after the divergence of fibrillar and nonfibrillar collagens. The presence of this anomalously long collagen gene within a prokaryote may represent an interdomain transfer from eukaryotes into prokaryotes that gives T. erythraeum the ability to form blooms that cover hundreds of square kilometers of ocean. We propose that the collagen gene entered the prokaryote intron-free only after it had been molded by years of mechanical selective pressure in larger organisms and only after large, dense food sources such as marine vertebrates became available. This anomalously long collagen-like sequence may explain T. erythraeum's ability to aggregate and thus concentrate its toxin for food-source procurement.}, }
@article {pmid18521076, year = {2008}, author = {Paul, JH}, title = {Prophages in marine bacteria: dangerous molecular time bombs or the key to survival in the seas?.}, journal = {The ISME journal}, volume = {2}, number = {6}, pages = {579-589}, doi = {10.1038/ismej.2008.35}, pmid = {18521076}, issn = {1751-7370}, mesh = {Bacteria/genetics/metabolism/*virology ; *Bacterial Physiological Phenomena ; Gene Transfer, Horizontal ; Genome, Viral ; Lysogeny ; Molecular Sequence Data ; Phenotype ; Prophages/*genetics/isolation &amp; purification/*physiology ; Seawater/*microbiology ; Viral Proteins/genetics/metabolism ; }, abstract = {Bacteriophages are realized to be numerous and important components of oceanic food webs principally because of their lytic capabilities. The subtle changes that temperate phages impart to their hosts in the oceans are far less understood. Occurrences of lysogeny in the oceans correlate well with conditions unfavorable for rapid host growth. In coliphage lambda, phage encoded repressors have been shown to modulate host metabolic gene expression and phenotype, resulting in economizing host energy expenditure. Comparison of lysogenized marine bacteria to the uninfected hosts indicated that prophage acquisition is correlated with host metabolic gene suppression. Screening 113 marine bacterial genomes for prophages yielded 64 prophage-like elements, 21 of which strongly resembled gene transfer agents (GTAs). The remaining 39 putative prophages had a relatively high incidence of transcriptional regulatory and repressor-like proteins (approximately 2/40 kb prophage sequence) compared to lytic marine phages (approximately 0.25/40 kb phage sequence). Here, it has been hypothesized that marine prophages directly contribute to host survival in unfavorable environments by suppression of unneeded metabolic activities. It has been further suggested that such metabolic downshifts are the result of phage-encoded repressors and transcriptional regulators acting directly on host genes. Finally, the widespread occurrence of GTAs may be an efficient mechanism for horizontal gene transfer in the oceans.}, }
@article {pmid18521074, year = {2008}, author = {Souza, V and Eguiarte, LE and Siefert, J and Elser, JJ}, title = {Microbial endemism: does phosphorus limitation enhance speciation?.}, journal = {Nature reviews. Microbiology}, volume = {6}, number = {7}, pages = {559-564}, doi = {10.1038/nrmicro1917}, pmid = {18521074}, issn = {1740-1534}, mesh = {Animals ; Bacteria/*genetics/metabolism/pathogenicity ; *Ecosystem ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Phosphorus/deficiency/*metabolism ; }, abstract = {There is increasing evidence for the existence of unique ecosystems that are dominated by locally adapted microbiota which harbour distinct lineages and biological capabilities, much like the macrobiota of Darwin's Galapagos Islands. As a primary example of such a system, we highlight key discoveries from the Cuatro Ciénegas basin in Mexico. We argue that high microbial endemism requires a combination of geographical isolation, long-term continuity and mechanisms for reducing the intensity of horizontal gene transfer (HGT). We also propose that strong phosphorus limitation has an important role in microbial diversification by reducing the intensity of HGT.}, }
@article {pmid18515416, year = {2008}, author = {Lascols, C and Podglajen, I and Verdet, C and Gautier, V and Gutmann, L and Soussy, CJ and Collatz, E and Cambau, E}, title = {A plasmid-borne Shewanella algae Gene, qnrA3, and its possible transfer in vivo between Kluyvera ascorbata and Klebsiella pneumoniae.}, journal = {Journal of bacteriology}, volume = {190}, number = {15}, pages = {5217-5223}, pmid = {18515416}, issn = {1098-5530}, mesh = {Acetyltransferases/genetics ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Base Sequence ; Conjugation, Genetic ; DNA Transposable Elements ; DNA, Bacterial/chemistry/genetics ; Drug Resistance, Bacterial/*genetics ; Enterobacter cloacae/genetics ; Enterobacteriaceae Infections/microbiology ; Escherichia coli/genetics ; Feces/microbiology ; Gene Order ; *Gene Transfer, Horizontal ; Humans ; Integrons ; Klebsiella pneumoniae/*genetics/isolation &amp; purification ; Kluyvera/*genetics/isolation &amp; purification ; Microbial Sensitivity Tests ; Middle Aged ; Molecular Sequence Data ; *Plasmids ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Shewanella/*genetics ; beta-Lactamases/genetics ; }, abstract = {The plasmid-borne quinolone resistance gene qnrA1 is prevalent in multidrug-resistant Enterobacteriaceae. A chromosomally encoded homologue in Shewanella algae, qnrA3, has been described. We isolated two qnrA3-positive strains, one of Klebsiella pneumoniae (He96) and one of Kluyvera ascorbata (Kas96), from the feces of an immunocompromised outpatient. The qnrA3 allele was identical to that of S. algae except for 5 nucleotides and differed from qnrA1 by 29 nucleotides affecting three amino acids. The analysis of the qnrA3 genetic environment showed that qnrA3 was inserted downstream from an ISCR1 element at a recombination crossover site described for other resistance genes, including qnrA1, and immediately upstream from IS26, a situation not described before. IS26 preceded an incomplete class 1 integron which contained, among other genes, aac(6')-Ib-cr, another transferable quinolone resistance gene, and the beta-lactamase gene bla(OXA-1/30). The 10-kb fragment encompassing qnrA3 was compared to previously described qnrA1-containing plasmids and multidrug-resistant plasmids; it shares identical sequences with pC15a, pHSH2, pQR1, pQKp311H, and pSAL-1 but with rearrangements, deletions, and mutations. Conjugal transfer of qnrA3 was highly efficient (10(-2)) from K. pneumoniae He96 or K. ascorbata Kas96 to Escherichia coli J53 but less so (10(-5)) from either donor to a clinical strain of Enterobacter cloacae. This first description of a plasmid-borne copy and of the in vitro transfer of qnrA3 is taken to illustrate its likely in vivo transfer from S. algae to the Enterobacteriaceae.}, }
@article {pmid18515114, year = {2008}, author = {Jang, J and Becq, J and Gicquel, B and Deschavanne, P and Neyrolles, O}, title = {Horizontally acquired genomic islands in the tubercle bacilli.}, journal = {Trends in microbiology}, volume = {16}, number = {7}, pages = {303-308}, doi = {10.1016/j.tim.2008.04.005}, pmid = {18515114}, issn = {0966-842X}, mesh = {Animals ; Bacterial Proteins/genetics ; Eukaryota/microbiology ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genomic Islands/*genetics ; Humans ; Mycobacterium tuberculosis/*genetics/growth &amp; development/pathogenicity ; Phagocytes/microbiology ; Virulence/genetics ; }, abstract = {Most mycobacteria are environmental species, causing disease only occasionally when they encounter a susceptible human or animal host. A few species, such as Mycobacterium tuberculosis and Mycobacterium avium, have acquired the ability to parasitize host macrophages during the course of evolution and have become major pathogens. Recent genetic studies in these two species have suggested that early episodes of horizontal transfer of genomic islands from surrounding environmental species might have contributed to the evolution towards this virulence phenotype, possibly by helping bacilli to persist in protozoa and, subsequently, in mammalian phagocytes. A better understanding of the function of the proteins encoded by these genomic islands in mycobacterial metabolism might help to define novel targets for the development of future antimicrobials.}, }
@article {pmid18513439, year = {2008}, author = {Nemergut, DR and Robeson, MS and Kysela, RF and Martin, AP and Schmidt, SK and Knight, R}, title = {Insights and inferences about integron evolution from genomic data.}, journal = {BMC genomics}, volume = {9}, number = {}, pages = {261}, pmid = {18513439}, issn = {1471-2164}, mesh = {Bacteria/*genetics ; *Evolution, Molecular ; Genes, Bacterial ; Genetic Variation/genetics ; Genome, Bacterial/genetics ; *Genomics ; Integrons/*genetics ; Phylogeny ; Pseudogenes ; }, abstract = {BACKGROUND: Integrons are mechanisms that facilitate horizontal gene transfer, allowing bacteria to integrate and express foreign DNA. These are important in the exchange of antibiotic resistance determinants, but can also transfer a diverse suite of genes unrelated to pathogenicity. Here, we provide a systematic analysis of the distribution and diversity of integron intI genes and integron-containing bacteria.<br><br>RESULTS: We found integrons in 103 different pathogenic and non-pathogenic bacteria, in six major phyla. Integrons were widely scattered, and their presence was not confined to specific clades within bacterial orders. Nearly 1/3 of the intI genes that we identified were pseudogenes, containing either an internal stop codon or a frameshift mutation that would render the protein product non-functional. Additionally, 20% of bacteria contained more than one integrase gene. dN/dS ratios revealed mutational hotspots in clades of Vibrio and Shewanella intI genes. Finally, we characterized the gene cassettes associated with integrons in Methylobacillus flagellatus KT and Dechloromonas aromatica RCB, and found a heavy metal efflux gene as well as genes involved in protein folding and stability.<br><br>CONCLUSION: Our analysis suggests that the present distribution of integrons is due to multiple losses and gene transfer events. While, in some cases, the ability to integrate and excise foreign DNA may be selectively advantageous, the gain, loss, or rearrangment of gene cassettes could also be deleterious, selecting against functional integrases. Thus, such a high fraction of pseudogenes may suggest that the selective impact of integrons on genomes is variable, oscillating between beneficial and deleterious, possibly depending on environmental conditions.}, }
@article {pmid18512785, year = {2008}, author = {Wang, CR and Shiau, AL and Chen, SY and Lin, LL and Tai, MH and Shieh, GS and Lin, PR and Yo, YT and Lee, CH and Kuo, SM and Liu, MF and Jou, IM and Yang, CY and Shen, PC and Lee, HL and Wu, CL}, title = {Amelioration of collagen-induced arthritis in rats by adenovirus-mediated PTEN gene transfer.}, journal = {Arthritis and rheumatism}, volume = {58}, number = {6}, pages = {1650-1656}, doi = {10.1002/art.23517}, pmid = {18512785}, issn = {0004-3591}, mesh = {Adenoviridae/genetics ; Animals ; Ankle Joint/pathology ; Arthritis, Experimental/pathology/*therapy ; Cells, Cultured ; Fibroblasts/*metabolism ; Gene Transfer, Horizontal ; Genetic Therapy/*methods ; Genetic Vectors ; Humans ; PTEN Phosphohydrolase/*genetics ; Phosphoinositide-3 Kinase Inhibitors ; Proto-Oncogene Proteins c-akt/antagonists &amp; inhibitors ; Rats ; Rats, Sprague-Dawley ; Signal Transduction ; }, abstract = {OBJECTIVE: The phosphatidylinositol 3-kinase (PI 3-kinase)/Akt pathway is known to be activated in rheumatoid arthritis (RA) synovial tissue, which impacts cell growth, proliferation, survival, and migration. Phosphatase and tensin homolog deleted from chromosome 10 (PTEN) functions as a negative regulator of PI 3-kinase signaling, thus blocking Akt activation. The aim of this study was to examine the effect of PTEN gene transfer in rats with collagen-induced arthritis (CIA).<br><br>METHODS: Adenoviral vectors encoding human PTEN (AdPTEN) or beta-galactosidase (AdLacZ) were injected intraarticularly into rats with CIA, and their treatment responses were monitored by measures of clinical, radiographic, and histologic changes. The expression of phosphorylated Akt, total Akt, vascular endothelial growth factor (VEGF), proinflammatory cytokines, and chemokines, as well as the extent of microvessel density in the ankle joints were determined.<br><br>RESULTS: AdPTEN treatment reduced Akt phosphorylation and decreased VEGF production in human RA synovial fibroblasts. Compared with AdLacZ treatment of the rats with CIA, AdPTEN treatment significantly reduced ankle circumference, articular index scores, radiography scores, and histology scores, and also decreased microvessel density and levels of VEGF and interleukin-1beta. Furthermore, PTEN gene transfer led to down-regulation of Akt activation and increased apoptosis in the ankle joints.<br><br>CONCLUSION: This study is the first to demonstrate the in vivo effect of intraarticular gene delivery of PTEN on amelioration of arthritis symptoms in rats with CIA, which involved antiangiogenic, antiproliferative, and antiinflammatory effects of PTEN via inhibition of the PI 3-kinase/Akt signaling pathway. Our findings also implicate the PI 3-kinase/Akt pathway as a therapeutic target for the treatment of RA or other inflammatory diseases.}, }
@article {pmid18511688, year = {2008}, author = {Gladyshev, EA and Meselson, M and Arkhipova, IR}, title = {Massive horizontal gene transfer in bdelloid rotifers.}, journal = {Science (New York, N.Y.)}, volume = {320}, number = {5880}, pages = {1210-1213}, doi = {10.1126/science.1156407}, pmid = {18511688}, issn = {1095-9203}, support = {R01 GM072708/GM/NIGMS NIH HHS/United States ; GM072708/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA Transposable Elements ; DNA, Helminth ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genes, Fungal ; Molecular Sequence Data ; Repetitive Sequences, Nucleic Acid ; Rotifera/*genetics ; Telomere ; }, abstract = {Horizontal gene transfer in metazoans has been documented in only a few species and is usually associated with endosymbiosis or parasitism. By contrast, in bdelloid rotifers we found many genes that appear to have originated in bacteria, fungi, and plants, concentrated in telomeric regions along with diverse mobile genetic elements. Bdelloid proximal gene-rich regions, however, appeared to lack foreign genes, thereby resembling those of model metazoan organisms. Some of the foreign genes were defective, whereas others were intact and transcribed; some of the latter contained functional spliceosomal introns. One such gene, apparently of bacterial origin, was overexpressed in Escherichia coli and yielded an active enzyme. The capture and functional assimilation of exogenous genes may represent an important force in bdelloid evolution.}, }
@article {pmid18511120, year = {2008}, author = {Sletvold, H and Johnsen, PJ and Hamre, I and Simonsen, GS and Sundsfjord, A and Nielsen, KM}, title = {Complete sequence of Enterococcus faecium pVEF3 and the detection of an omega-epsilon-zeta toxin-antitoxin module and an ABC transporter.}, journal = {Plasmid}, volume = {60}, number = {1}, pages = {75-85}, doi = {10.1016/j.plasmid.2008.04.002}, pmid = {18511120}, issn = {0147-619X}, mesh = {ATP-Binding Cassette Transporters/*genetics ; Amino Acid Sequence ; Anti-Bacterial Agents/pharmacology ; Antitoxins/*genetics ; Bacterial Toxins/*genetics/metabolism ; Base Sequence ; Enterococcus faecium/drug effects/*genetics ; Extrachromosomal Inheritance/drug effects/genetics ; Glycopeptides/pharmacology ; Molecular Sequence Data ; Operon/genetics ; Plasmids/*genetics ; Vancomycin/pharmacology ; Vancomycin Resistance/genetics ; }, abstract = {Glycopeptide resistant Enterococcus faecium (GREF) persists on Norwegian poultry farms despite the ban on the growth promoter avoparcin. The biological basis for long-term persistence of avoparcin resistance is not fully understood. This study presents the complete DNA sequence of the E. faecium R-plasmid pVEF3 and functional studies of some plasmid-encoded traits (a toxin-antitoxin (TA) system and an ABC transporter) that may be of importance for plasmid persistence. The pVEF3 (63.1 kbp), isolated from an E. faecium strain of poultry origin sampled in Norway in 1999, has 71 coding sequences including the vanA avoparcin/vancomycin resistance encoding gene cluster. pVEF3 encodes the TA system omega-epsilon-zeta, and plasmid stability tests and transcription analysis show that omega-epsilon-zeta is functional in Enterococcus faecalis OGIX, although with decreasing effect over time. The predicted ABC transporter was not found to confer reduced susceptibility to any of the 28 substances tested. The TA system identified in the pVEF-type plasmids may contribute to vanA plasmid persistence on Norwegian poultry farms. However, size and compositional heterogeneity among E. faecium vanA plasmids suggest that additional plasmid maintenance systems in combination with host specific factors and frequent horizontal gene transfer and rearrangement causes the observed plasmid composition and distribution patterns.}, }
@article {pmid18510552, year = {2008}, author = {Howard, EC and Sun, S and Biers, EJ and Moran, MA}, title = {Abundant and diverse bacteria involved in DMSP degradation in marine surface waters.}, journal = {Environmental microbiology}, volume = {10}, number = {9}, pages = {2397-2410}, doi = {10.1111/j.1462-2920.2008.01665.x}, pmid = {18510552}, issn = {1462-2920}, mesh = {Bacteria/*genetics/metabolism ; Bacterial Proteins/genetics ; Base Composition ; Biodegradation, Environmental ; Biodiversity ; Computational Biology ; DNA, Bacterial/genetics ; Databases, Nucleic Acid ; Genes, Bacterial ; Genome, Bacterial ; Molecular Sequence Data ; Oxidoreductases/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Sulfonium Compounds/*metabolism ; *Water Microbiology ; }, abstract = {An expanded analysis of oceanic metagenomic data indicates that the majority of prokaryotic cells in marine surface waters have the genetic capability to demethylate dimethylsulfoniopropionate (DMSP). The 1701 homologues of the DMSP demethylase gene, dmdA, identified in the (2007) Global Ocean Sampling (GOS) metagenome, are sufficient for 58% (+/-9%) of sampled cells to participate in this critical step in the marine sulfur cycle. This remarkable frequency of DMSP-demethylating cells is in accordance with biogeochemical data indicating that marine phytoplankton direct up to 10% of fixed carbon to DMSP synthesis, and that most of this DMSP is subsequently degraded by bacteria via demethylation. The GOS metagenomic data also revealed a new cluster of dmdA sequences (designated Clade E) that implicates marine gammaproteobacteria in DMSP demethylation, along with previously recognized alphaproteobacterial groups Roseobacter and SAR11. Analyses of G+C content and gene order indicate that lateral gene transfer is likely responsible for the wide distribution of dmdA among diverse taxa, contributing to the homogenization of biogeochemical roles among heterotrophic marine bacterioplankton. Candidate genes for the competing bacterial degradation process that converts DMSP to the climate-active gas dimethylsulfide (DMS) (dddD and dddL) occur infrequently in the (2007) GOS metagenome, suggesting either that the key DMS-producing bacterial genes are yet to be identified or that DMS formation by free-living bacterioplankton is insignificant relative to their demethylation activity.}, }
@article {pmid18510021, year = {2008}, author = {Miller, TA and Lauzon, CR and Lampe, DJ}, title = {Technological advances to enhance agricultural pest management.}, journal = {Advances in experimental medicine and biology}, volume = {627}, number = {}, pages = {141-150}, doi = {10.1007/978-0-387-78225-6_12}, pmid = {18510021}, issn = {0065-2598}, mesh = {*Agriculture ; Bacteria/genetics ; Gene Transfer, Horizontal ; *Pest Control ; Symbiosis ; Transgenes ; }, abstract = {Biotechnology offers new solutions to existing and future pest problems in agriculture including, for the first time, possible tools to use against insect transmitted pathogens causing plant diseases. Here, we describe the strategy first described as Autocidal Biological Control applied for the development of conditional lethal pink bollworm strains. When these strains are mass-reared, the lethal gene expression is suppressed by a tetracycline repressor element, which is activated by the presence of chlorotetracycline, a normal component of the mass-rearing diet. Once removed from the tetracycline diet, the lethal genes are passed on to offspring when ordinary lab-reared pink bollworms mate with special lethal strains. Lethality is dominant (one copy sufficient for lethality), expressed in the egg stage and affects all eggs (100% lethal expression). The initial investment by the California Cotton Pest Control Board is an outstanding example of research partnerships between agriculture industry, the USDA and land grant universities.}, }
@article {pmid18509479, year = {2008}, author = {Hamel, L and Nahar, N and Poptsova, MS and Zhaxybayeva, O and Gogarten, JP}, title = {Unsupervised learning in detection of gene transfer.}, journal = {Journal of biomedicine &amp; biotechnology}, volume = {2008}, number = {}, pages = {472719}, pmid = {18509479}, issn = {1110-7251}, mesh = {Archaeoglobus fulgidus/genetics ; Artificial Intelligence ; Cluster Analysis ; Computational Biology/*methods ; Evolution, Molecular ; Gene Frequency ; *Gene Transfer, Horizontal ; *Genes, Archaeal ; Genomics/methods ; Halobacterium salinarum/genetics ; Methanosarcina/genetics ; Models, Genetic ; Phylogeny ; RNA/classification ; Selection, Genetic ; *Sequence Homology, Nucleic Acid ; Species Specificity ; }, abstract = {The tree representation as a model for organismal evolution has been in use since before Darwin. However, with the recent unprecedented access to biomolecular data, it has been discovered that, especially in the microbial world, individual genes making up the genome of an organism give rise to different and sometimes conflicting evolutionary tree topologies. This discovery calls into question the notion of a single evolutionary tree for an organism and gives rise to the notion of an evolutionary consensus tree based on the evolutionary patterns of the majority of genes in a genome embedded in a network of gene histories. Here, we discuss an approach to the analysis of genomic data of multiple genomes using bipartition spectral analysis and unsupervised learning. An interesting observation is that genes within genomes that have evolutionary tree topologies, which are in substantial conflict with the evolutionary consensus tree of an organism, point to possible horizontal gene transfer events which often delineate significant evolutionary events.}, }
@article {pmid18508537, year = {2008}, author = {Mushegian, A}, title = {Gene content of LUCA, the last universal common ancestor.}, journal = {Frontiers in bioscience : a journal and virtual library}, volume = {13}, number = {}, pages = {4657-4666}, doi = {10.2741/3031}, pmid = {18508537}, issn = {1093-9946}, mesh = {Computational Biology ; Conserved Sequence ; *DNA Replication ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genomics ; Models, Genetic ; Origin of Life ; *Phylogeny ; Protein Biosynthesis ; }, abstract = {Comparative genomics and modern phylogenetic approaches allow us to infer the gene content of LUCA, the Last Universal Common Ancestor of all known currently living cellular organisms. Most of the estimates produce a putative LUCA with 500-1000 protein-coding genes and biochemically coherent metabolism, if the average rates of gene gains (gene emergence plus horizontal gene transfer) and gene losses per family are allowed to be close to each other. This estimate is not strongly sensitive to the topology of the Tree of Life, but the identity of the genes that are placed in LUCA may depend on the position of the deep branches and the root of the tree.}, }
@article {pmid18507822, year = {2008}, author = {Dufresne, A and Ostrowski, M and Scanlan, DJ and Garczarek, L and Mazard, S and Palenik, BP and Paulsen, IT and de Marsac, NT and Wincker, P and Dossat, C and Ferriera, S and Johnson, J and Post, AF and Hess, WR and Partensky, F}, title = {Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria.}, journal = {Genome biology}, volume = {9}, number = {5}, pages = {R90}, pmid = {18507822}, issn = {1474-760X}, mesh = {Gene Transfer, Horizontal ; Genome, Bacterial ; Seawater/*microbiology ; Synechococcus/*classification/*genetics ; }, abstract = {BACKGROUND: The picocyanobacterial genus Synechococcus occurs over wide oceanic expanses, having colonized most available niches in the photic zone. Large scale distribution patterns of the different Synechococcus clades (based on 16S rRNA gene markers) suggest the occurrence of two major lifestyles ('opportunists'/'specialists'), corresponding to two distinct broad habitats ('coastal'/'open ocean'). Yet, the genetic basis of niche partitioning is still poorly understood in this ecologically important group.<br><br>RESULTS: Here, we compare the genomes of 11 marine Synechococcus isolates, representing 10 distinct lineages. Phylogenies inferred from the core genome allowed us to refine the taxonomic relationships between clades by revealing a clear dichotomy within the main subcluster, reminiscent of the two aforementioned lifestyles. Genome size is strongly correlated with the cumulative lengths of hypervariable regions (or 'islands'). One of these, encompassing most genes encoding the light-harvesting phycobilisome rod complexes, is involved in adaptation to changes in light quality and has clearly been transferred between members of different Synechococcus lineages. Furthermore, we observed that two strains (RS9917 and WH5701) that have similar pigmentation and physiology have an unusually high number of genes in common, given their phylogenetic distance.<br><br>CONCLUSION: We propose that while members of a given marine Synechococcus lineage may have the same broad geographical distribution, local niche occupancy is facilitated by lateral gene transfers, a process in which genomic islands play a key role as a repository for transferred genes. Our work also highlights the need for developing picocyanobacterial systematics based on genome-derived parameters combined with ecological and physiological data.}, }
@article {pmid18507680, year = {2008}, author = {Slater, FR and Bailey, MJ and Tett, AJ and Turner, SL}, title = {Progress towards understanding the fate of plasmids in bacterial communities.}, journal = {FEMS microbiology ecology}, volume = {66}, number = {1}, pages = {3-13}, doi = {10.1111/j.1574-6941.2008.00505.x}, pmid = {18507680}, issn = {0168-6496}, mesh = {Bacteria/*genetics ; *Ecology ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; Plasmids/*genetics ; Population Dynamics ; Replicon ; Symbiosis ; }, abstract = {Plasmid-mediated horizontal gene transfer influences bacterial community structure and evolution. However, an understanding of the forces which dictate the fate of plasmids in bacterial populations remains elusive. This is in part due to the enormous diversity of plasmids, in terms of size, structure, transmission, evolutionary history and accessory phenotypes, coupled with the lack of a standard theoretical framework within which to investigate them. This review discusses how ecological factors, such as spatial structure and temporal fluctuations, shape both the population dynamics and the physical features of plasmids. Novel data indicate that larger plasmids are more likely to be harboured by hosts in complex environments. Plasmid size may therefore be determined by environmentally mediated fitness trade-offs. As the correlation between replicon size and complexity of environment is similar for plasmids and chromosomes, plasmids could be used as tractable tools to investigate the influence of ecological factors on chromosomes. Parallels are drawn between plasmids and bacterial facultative symbionts, including the evolution of some members of both groups to a more obligate relationship with their host. The similarity between the influences of ecological factors on plasmids and bacterial symbionts suggests that it may be appropriate to study plasmids within a classical ecological framework.}, }
@article {pmid18506096, year = {2008}, author = {Fujita, K and Ehira, S and Tanaka, K and Asai, K and Ohta, N}, title = {Molecular phylogeny and evolution of the plastid and nuclear encoded cbbX genes in the unicellular red alga Cyanidioschyzon merolae.}, journal = {Genes &amp; genetic systems}, volume = {83}, number = {2}, pages = {127-133}, doi = {10.1266/ggs.83.127}, pmid = {18506096}, issn = {1341-7568}, mesh = {Algal Proteins/chemistry/*classification/*genetics ; Amino Acid Sequence ; Cell Nucleus/genetics ; *Evolution, Molecular ; Gene Expression Regulation ; Molecular Sequence Data ; Phylogeny ; Plastids/genetics ; Rhodophyta/*genetics ; Sequence Homology, Amino Acid ; Transcription, Genetic ; }, abstract = {The cbbX gene is generally encoded in proteobacterial genomes and red-algal plastid genomes. In this study, we found two distinct cbbX genes of Cyanidioschyzon merolae, a unicellular red alga, one encoded in the plastid genome and the other encoded in the cell nucleus. The phylogenetic tree inferred from cbbX genes and strongly conserved gene organization (rbcLS-cbbX) suggests that the plastid-encoded cbbX gene of C. merolae came from an ancestral proteobacterium by horizontal gene transfer. On the other hand, the nuclear-encoded cbbX gene of C. merolae was classified in another cluster together with the nucleomorph-encoded cbbX gene of Guillardia theta. Furthermore, expression of the two cbbX genes were regulated differently in response to extracellular CO(2) concentration. Our results imply that cbbX gene in the plastid genome was copied and transferred to the cell nucleus after horizontal gene transfer of RuBisCo operon from ancestral beta-proteobacteria at comparatively early stage, and that each cbbX evolved in different ways.}, }
@article {pmid18505858, year = {2008}, author = {Jeon, B and Muraoka, W and Sahin, O and Zhang, Q}, title = {Role of Cj1211 in natural transformation and transfer of antibiotic resistance determinants in Campylobacter jejuni.}, journal = {Antimicrobial agents and chemotherapy}, volume = {52}, number = {8}, pages = {2699-2708}, pmid = {18505858}, issn = {1098-6596}, support = {R01 DK063008/DK/NIDDK NIH HHS/United States ; R01DK063008/DK/NIDDK NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacterial Proteins/*genetics ; Base Sequence ; Campylobacter jejuni/*genetics ; Drug Resistance, Microbial/*genetics ; Fluoroquinolones/pharmacology ; Gene Transfer, Horizontal/genetics ; Genetic Complementation Test ; Kanamycin/pharmacology ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Mutation ; Sequence Homology, Amino Acid ; Tetracycline/pharmacology ; Transformation, Bacterial/*genetics ; }, abstract = {Campylobacter jejuni, an important food-borne human pathogen, is increasingly resistant to antimicrobials. Natural transformation is considered to be a main mechanism for mediating the transfer of genetic materials encoding antibiotic resistance determinants in C. jejuni, but direct evidence for this notion is still lacking. In this study, we determined the role of Cj1211 in natural transformation and in the development of antibiotic resistance in C. jejuni. Insertional mutagenesis of Cj1211, a Helicobacter pylori ComH3 homolog, abolished natural transformation in C. jejuni. In vitro coculture of C. jejuni strains carrying either kanamycin or tetracycline resistance markers demonstrated the development of progenies that were resistant to both antibiotics, indicating that the horizontal transfer of antibiotic resistance determinants actively occurs in mixed Campylobacter populations. A mutation of Cj1211 or the addition of DNase I in culture media completely inhibited the formation of progenies that were resistant to both antibiotics, indicating that the horizontal transfer of the resistance determinants is mediated by natural transformation. Interestingly, the mutation of Cj1211 also reduced the frequency of emergence of spontaneous mutants that were resistant to fluoroquinolone (FQ) and streptomycin but did not affect the outcome of FQ resistance development under FQ treatment, suggesting that natural transformation does not play a major role in the emergence of FQ-resistant Campylobacter strains during treatment with FQ antimicrobials. These results define Cj1211 as a competence factor in Campylobacter, prove the role of natural transformation in the horizontal transfer of antibiotic resistance determinants in Campylobacter, and provide new insights into the mechanism underlying the development of FQ-resistant Campylobacter strains.}, }
@article {pmid18504367, year = {2008}, author = {Benavente, E and Cifuentes, M and Dusautoir, JC and David, J}, title = {The use of cytogenetic tools for studies in the crop-to-wild gene transfer scenario.}, journal = {Cytogenetic and genome research}, volume = {120}, number = {3-4}, pages = {384-395}, doi = {10.1159/000121087}, pmid = {18504367}, issn = {1424-859X}, mesh = {Biological Evolution ; Crops, Agricultural/cytology/*genetics ; *Cytogenetic Analysis ; Gene Flow ; *Gene Transfer, Horizontal ; Genetic Speciation ; Hybridization, Genetic ; In Situ Hybridization, Fluorescence ; Karyotyping ; Meiosis/genetics ; Models, Genetic ; Plant Cells ; Plants/*genetics ; Recombination, Genetic ; }, abstract = {Interspecific hybridization in plants is an important evolutionary phenomenon involved in the dynamics of speciation that receives increasing interest in the context of possible gene escapes from transgenic crop varieties. Crops are able to cross-pollinate with a number of wild related species and exchange chromosome segments through homoeologous recombination. In this paper, we review a set of cytogenetic techniques that are appropriate to document the different steps required for the stable introgression of a chromosome segment from a donor species (i.e., the crop) into a recipient species (i.e., the wild). Several examples in hybrids and derivatives are given to illustrate how these approaches may be used to evaluate the potential for gene transfer between crops and wild relatives. Different techniques, from classical chromosome staining methods to recent developments in molecular cytogenetics, can be used to differentiate genomes and identify the chromosome regions eventually involved in genetic exchanges. Some clues are also given for the study of fertility restoration in the interspecific hybrid forms.}, }
@article {pmid18502921, year = {2008}, author = {Kulinska, A and Czeredys, M and Hayes, F and Jagura-Burdzy, G}, title = {Genomic and functional characterization of the modular broad-host-range RA3 plasmid, the archetype of the IncU group.}, journal = {Applied and environmental microbiology}, volume = {74}, number = {13}, pages = {4119-4132}, pmid = {18502921}, issn = {1098-5336}, support = {/WT_/Wellcome Trust/United Kingdom ; G0500588/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics ; *Conjugation, Genetic ; DNA, Bacterial/analysis ; Gene Transfer, Horizontal ; Integrons/genetics ; Molecular Sequence Data ; Plasmids/*genetics ; Proteobacteria/classification/*genetics ; Replication Origin ; }, abstract = {IncU plasmids are a distinctive group of mobile elements with highly conserved backbone functions and variable antibiotic resistance gene cassettes. The IncU archetype is conjugative plasmid RA3, whose sequence (45,909 bp) shows it to be a mosaic, modular replicon with a class I integron different from that of other IncU replicons. Functional analysis demonstrated that RA3 possesses a broad host range and can efficiently self-transfer, replicate, and be maintained stably in alpha-, beta-, and gammaproteobacteria. RA3 contains 50 open reading frames clustered in distinct functional modules. The replication module encompasses the repA and repB genes embedded in long repetitive sequences. RepA, which is homologous to antitoxin proteins from alpha- and gammaproteobacteria, contains a Cro/cI-type DNA-binding domain present in the XRE family of transcriptional regulators. The repA promoter is repressed by RepA and RepB. The minireplicon encompasses repB and the downstream repetitive sequence r1/r2. RepB shows up to 80% similarity to putative replication initiation proteins from environmental plasmids of beta- and gammaproteobacteria, as well as similarity to replication proteins from alphaproteobacteria and Firmicutes. Stable maintenance functions of RA3 are most like those of IncP-1 broad-host-range plasmids and comprise the active partitioning apparatus formed by IncC (ParA) and KorB (ParB), the antirestriction protein KlcA, and accessory stability components KfrA and KfrC. The RA3 origin of transfer was localized experimentally between the maintenance and conjugative-transfer operons. The putative conjugative-transfer module is highly similar in organization and in its products to transfer regions of certain broad-host-range environmental plasmids.}, }
@article {pmid18499493, year = {2008}, author = {Andrews, LD and Graham, J and Snider, MJ and Fraga, D}, title = {Characterization of a novel bacterial arginine kinase from Desulfotalea psychrophila.}, journal = {Comparative biochemistry and physiology. Part B, Biochemistry &amp; molecular biology}, volume = {150}, number = {3}, pages = {312-319}, doi = {10.1016/j.cbpb.2008.03.017}, pmid = {18499493}, issn = {1096-4959}, mesh = {Amino Acid Sequence ; Animals ; Arginine Kinase/classification/genetics/*metabolism ; Bacterial Proteins/classification/genetics/*metabolism ; Deltaproteobacteria/*enzymology ; Eukaryota/enzymology ; Kinetics ; Molecular Sequence Data ; Phylogeny ; RNA, Transfer/metabolism ; Sequence Alignment ; }, abstract = {Phosphagen kinases are found throughout the animal kingdom and catalyze the transfer of a high-energy gamma phosphoryl-group from ATP to a guanidino group on a suitable acceptor molecule such as creatine or arginine. Recent genome sequencing efforts in several proteobacteria, including Desulfotalea psychrophila LSv54, Myxococcus xanthus, Sulfurovum sp. NBC37-1, and Moritella sp. PE36 have revealed what appears to be a phosphagen kinase homolog present in their genomes. Based on sequence comparisons these putative homologs bear a strong resemblance to arginine kinases found in many invertebrates and some protozoa. We describe here a biochemical characterization of one of these homologs from D. psychrophila expressed in E. coli that confirms its ability to reversibly catalyze phosphoryl transfer from ATP to arginine. A phylogenetic analysis suggests that these bacteria homologs are not widely distributed in proteobacteria species. They appear more related to protozoan arginine kinases than to similar proteins seen in some Gram-positive bacteria that share key catalytic residues but encode protein tyrosine kinases. This raises the possibility of horizontal gene transfer as a likely origin of the bacterial arginine kinases.}, }
@article {pmid18497287, year = {2008}, author = {Falkowski, PG and Fenchel, T and Delong, EF}, title = {The microbial engines that drive Earth's biogeochemical cycles.}, journal = {Science (New York, N.Y.)}, volume = {320}, number = {5879}, pages = {1034-1039}, doi = {10.1126/science.1153213}, pmid = {18497287}, issn = {1095-9203}, mesh = {Archaea/genetics/*metabolism ; Archaeal Proteins/chemistry/genetics/metabolism ; Atmosphere ; Bacteria/genetics/*metabolism ; Bacterial Proteins/chemistry/genetics/metabolism ; *Biological Evolution ; *Earth, Planet ; Ecosystem ; Elements ; Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; Genetic Variation ; Geological Phenomena ; Geology ; *Metabolic Networks and Pathways ; Oxidation-Reduction ; Photosynthesis ; Thermodynamics ; }, abstract = {Virtually all nonequilibrium electron transfers on Earth are driven by a set of nanobiological machines composed largely of multimeric protein complexes associated with a small number of prosthetic groups. These machines evolved exclusively in microbes early in our planet's history yet, despite their antiquity, are highly conserved. Hence, although there is enormous genetic diversity in nature, there remains a relatively stable set of core genes coding for the major redox reactions essential for life and biogeochemical cycles. These genes created and coevolved with biogeochemical cycles and were passed from microbe to microbe primarily by horizontal gene transfer. A major challenge in the coming decades is to understand how these machines evolved, how they work, and the processes that control their activity on both molecular and planetary scales.}, }
@article {pmid18497286, year = {2008}, author = {Bohannon, J}, title = {Microbial ecology. Confusing kinships.}, journal = {Science (New York, N.Y.)}, volume = {320}, number = {5879}, pages = {1031-1033}, doi = {10.1126/science.320.5879.1031}, pmid = {18497286}, issn = {1095-9203}, mesh = {Adaptation, Physiological ; Archaea/*classification/genetics/physiology ; Bacteria/*classification/genetics ; Bacterial Physiological Phenomena ; Biodiversity ; Biological Evolution ; Ecology ; *Ecosystem ; Environment ; Gene Transfer, Horizontal ; Genome, Archaeal ; Genome, Bacterial ; Phylogeny ; Recombination, Genetic ; Terminology as Topic ; }, }
@article {pmid18495935, year = {2008}, author = {Yan, Y and Yang, J and Dou, Y and Chen, M and Ping, S and Peng, J and Lu, W and Zhang, W and Yao, Z and Li, H and Liu, W and He, S and Geng, L and Zhang, X and Yang, F and Yu, H and Zhan, Y and Li, D and Lin, Z and Wang, Y and Elmerich, C and Lin, M and Jin, Q}, title = {Nitrogen fixation island and rhizosphere competence traits in the genome of root-associated Pseudomonas stutzeri A1501.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {21}, pages = {7564-7569}, pmid = {18495935}, issn = {1091-6490}, support = {R03 AA020101/AA/NIAAA NIH HHS/United States ; R25 AA021304/AA/NIAAA NIH HHS/United States ; }, mesh = {Base Sequence ; Chromosomes, Bacterial/genetics ; Gene Expression Profiling ; *Genome, Bacterial ; Molecular Sequence Data ; Multigene Family ; Nitrogen Fixation/*genetics ; Nitrogenase/genetics/metabolism ; Plant Roots/*microbiology ; Pseudomonas stutzeri/*genetics/metabolism ; Sequence Analysis, DNA ; }, abstract = {The capacity to fix nitrogen is widely distributed in phyla of Bacteria and Archaea but has long been considered to be absent from the Pseudomonas genus. We report here the complete genome sequencing of nitrogen-fixing root-associated Pseudomonas stutzeri A1501. The genome consists of a single circular chromosome with 4,567,418 bp. Comparative genomics revealed that, among 4,146 protein-encoding genes, 1,977 have orthologs in each of the five other Pseudomonas representative species sequenced to date. The genome contains genes involved in broad utilization of carbon sources, nitrogen fixation, denitrification, degradation of aromatic compounds, biosynthesis of polyhydroxybutyrate, multiple pathways of protection against environmental stress, and other functions that presumably give A1501 an advantage in root colonization. Genetic information on synthesis, maturation, and functioning of nitrogenase is clustered in a 49-kb island, suggesting that this property was acquired by lateral gene transfer. New genes required for the nitrogen fixation process have been identified within the nif island. The genome sequence offers the genetic basis for further study of the evolution of the nitrogen fixation property and identification of rhizosphere competence traits required in the interaction with host plants; moreover, it opens up new perspectives for wider application of root-associated diazotrophs in sustainable agriculture.}, }
@article {pmid18495755, year = {2008}, author = {Niclou, SP and Danzeisen, C and Eikesdal, HP and Wiig, H and Brons, NH and Poli, AM and Svendsen, A and Torsvik, A and Enger, P&#xd8; and Terzis, JA and Bjerkvig, R}, title = {A novel eGFP-expressing immunodeficient mouse model to study tumor-host interactions.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {22}, number = {9}, pages = {3120-3128}, pmid = {18495755}, issn = {1530-6860}, mesh = {Animals ; Cell Communication/physiology ; Green Fluorescent Proteins/*biosynthesis ; Humans ; Mice ; Mice, Inbred NOD ; *Mice, SCID ; Microscopy, Fluorescence, Multiphoton ; Neoplasm Transplantation/immunology/pathology ; Neoplasms/immunology/pathology/*physiopathology ; }, abstract = {A NOD/Scid mouse expressing enhanced green fluorescent protein (eGFP) is described, in which human and mouse tumors marked with red fluorescent protein can be established in vivo, both at subcutaneous and orthotopic locations. Using light microscopy as well as multiphoton confocal microscopy techniques, we visualized in detail the intricate colocalization of tumor and host cells in situ. Moreover, using fluorescence-activated cell sorting (FACS), we were able to completely separate the host cells from the tumor cells, thus providing a system for detailed cellular and molecular analysis of tumor-host cell interactions. The fact that tumor and host cells can be reliably identified also allowed us to detect double-positive cells, possibly arising from cell fusion events or horizontal gene transfer. Similarly, the model can be applied for the detection of circulating metastatic cells and for detailed studies on the vascular compartments within tumors, including vasculogenic mimicry. Thus, the model described should provide significant insight into how tumor cells communicate with their microenvironment.}, }
@article {pmid18493612, year = {2008}, author = {Moustafa, A and Reyes-Prieto, A and Bhattacharya, D}, title = {Chlamydiae has contributed at least 55 genes to Plantae with predominantly plastid functions.}, journal = {PloS one}, volume = {3}, number = {5}, pages = {e2205}, pmid = {18493612}, issn = {1932-6203}, support = {R01 ES013679/ES/NIEHS NIH HHS/United States ; T32 GM008629/GM/NIGMS NIH HHS/United States ; R01ES013679/ES/NIEHS NIH HHS/United States ; }, mesh = {Chlamydia/*genetics ; *Genes, Bacterial ; Plants/genetics/*microbiology ; *Plastids ; }, abstract = {BACKGROUND: The photosynthetic organelle (plastid) originated via primary endosymbiosis in which a phagotrophic protist captured and harnessed a cyanobacterium. The plastid was inherited by the common ancestor of the red, green (including land plants), and glaucophyte algae (together, the Plantae). Despite the critical importance of primary plastid endosymbiosis, its ancient derivation has left behind very few "footprints" of early key events in organelle genesis.<br><br>To gain insights into this process, we conducted an in-depth phylogenomic analysis of genomic data (nuclear proteins) from 17 Plantae species to identify genes of a surprising provenance in these taxa, Chlamydiae bacteria. Previous studies show that Chlamydiae contributed many genes (at least 21 in one study) to Plantae that primarily have plastid functions and were postulated to have played a fundamental role in organelle evolution. Using our comprehensive approach, we identify at least 55 Chlamydiae-derived genes in algae and plants, of which 67% (37/55) are putatively plastid targeted and at least 3 have mitochondrial functions. The remainder of the proteins does not contain a bioinformatically predicted organelle import signal although one has an N-terminal extension in comparison to the Chlamydiae homolog. Our data suggest that environmental Chlamydiae were significant contributors to early Plantae genomes that extend beyond plastid metabolism. The chlamydial gene distribution and protein tree topologies provide evidence for both endosymbiotic gene transfer and a horizontal gene transfer ratchet driven by recurrent endoparasitism as explanations for gene origin.<br><br>CONCLUSIONS/SIGNIFICANCE: Our findings paint a more complex picture of gene origin than can easily be explained by endosymbiotic gene transfer from an organelle-like point source. These data significantly extend the genomic impact of Chlamydiae on Plantae and show that about one-half (30/55) of the transferred genes are most closely related to sequences emanating from the genome of the only environmental isolate that is currently available. This strain, Candidatus Protochlamydia amoebophila UWE25 is an endosymbiont of Acanthamoeba and likely represents the type of endoparasite that contributed the genes to Plantae.}, }
@article {pmid18492663, year = {2008}, author = {Dutilh, BE and Snel, B and Ettema, TJ and Huynen, MA}, title = {Signature genes as a phylogenomic tool.}, journal = {Molecular biology and evolution}, volume = {25}, number = {8}, pages = {1659-1667}, pmid = {18492663}, issn = {1537-1719}, mesh = {Classification/*methods ; Genes/*genetics ; Genome/*genetics ; Genomics/methods ; *Phylogeny ; Species Specificity ; }, abstract = {Gene content has been shown to contain a strong phylogenetic signal, yet its usage for phylogenetic questions is hampered by horizontal gene transfer and parallel gene loss and until now required completely sequenced genomes. Here, we introduce an approach that allows the phylogenetic signal in gene content to be applied to any set of sequences, using signature genes for phylogenetic classification. The hundreds of publicly available genomes allow us to identify signature genes at various taxonomic depths, and we show how the presence of signature genes in an unspecified sample can be used to characterize its taxonomic composition. We identify 8,362 signature genes specific for 112 prokaryotic taxa. We show that these signature genes can be used to address phylogenetic questions on the basis of gene content in cases where classic gene content or sequence analyses provide an ambiguous answer, such as for Nanoarchaeum equitans, and even in cases where complete genomes are not available, such as for metagenomics data. Cross-validation experiments leaving out up to 30% of the species show that approximately 92% of the signature genes correctly place the species in a related clade. Analyses of metagenomics data sets with the signature gene approach are in good agreement with the previously reported species distributions based on phylogenetic analysis of marker genes. Summarizing, signature genes can complement traditional sequence-based methods in addressing taxonomic questions.}, }
@article {pmid18492275, year = {2008}, author = {Hao, W and Golding, GB}, title = {Uncovering rate variation of lateral gene transfer during bacterial genome evolution.}, journal = {BMC genomics}, volume = {9}, number = {}, pages = {235}, pmid = {18492275}, issn = {1471-2164}, mesh = {Bacillus/genetics ; *Evolution, Molecular ; Gene Deletion ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial/*genetics ; Likelihood Functions ; Models, Genetic ; Mutagenesis, Insertional ; Phylogeny ; }, abstract = {BACKGROUND: Large scale genome arrangement, such as whole gene insertion/deletion, plays an important role in bacterial genome evolution. Various methods have been employed to study the dynamic process of gene insertions and deletions, such as parsimony methods and maximum likelihood methods. Previous maximum likelihood studies have assumed that the rate of gene insertions/deletions is constant over different genes. This assumption is unrealistic. For instance, it has been shown that informational genes are less likely to be laterally transferred than non-informational genes. However, how much of the variation in gene transfer rates is due to the difference between informational genes and non-informational genes is unclear. In this study, a Gamma-distribution was incorporated in the likelihood estimation by considering rate variation for gene insertions/deletions between genes. This makes it possible to address whether a difference between informational genes and non-informational genes is the main contributor to rate variation of lateral gene transfers.<br><br>RESULTS: The results show that models incorporating rate variation fit the data better than do constant rate models in many phylogenetic groups. Even though informational genes are less likely to be laterally transferred than non-informational genes, the degree of rate variation for insertions/deletions did not change dramatically and remained high even when informational genes were excluded from the study. This suggests that the variation in rate of insertions/deletions is not due mainly to the simple difference between informational genes and non-informational genes. Among genes that are not classified as informational and among the informational genes themselves, there are still large differences in the rates that these genes are inserted and deleted.<br><br>CONCLUSION: While the difference in informational gene rates contributes to rate variation, it is only a small fraction of the variation present; instead, a substantial amount of rate variation for insertions/deletions remains among both informational genes and among non-informational genes.}, }
@article {pmid18487337, year = {2008}, author = {Gillings, M and Boucher, Y and Labbate, M and Holmes, A and Krishnan, S and Holley, M and Stokes, HW}, title = {The evolution of class 1 integrons and the rise of antibiotic resistance.}, journal = {Journal of bacteriology}, volume = {190}, number = {14}, pages = {5095-5100}, pmid = {18487337}, issn = {1098-5530}, mesh = {Betaproteobacteria/*genetics/isolation &amp; purification ; Chromosomes, Bacterial ; DNA, Bacterial/chemistry/genetics ; Drug Resistance, Microbial/*genetics ; *Evolution, Molecular ; Fresh Water/*microbiology ; Gene Order ; Gene Transfer, Horizontal ; *Integrons ; Molecular Sequence Data ; Phylogeny ; Plasmids ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Class 1 integrons are central players in the worldwide problem of antibiotic resistance, because they can capture and express diverse resistance genes. In addition, they are often embedded in promiscuous plasmids and transposons, facilitating their lateral transfer into a wide range of pathogens. Understanding the origin of these elements is important for the practical control of antibiotic resistance and for exploring how lateral gene transfer can seriously impact on, and be impacted by, human activities. We now show that class 1 integrons can be found on the chromosomes of nonpathogenic soil and freshwater Betaproteobacteria. Here they exhibit structural and sequence diversity, an absence of antibiotic resistance genes, and a phylogenetic signature of lateral transfer. Some examples are almost identical to the core of the class 1 integrons now found in pathogens, leading us to conclude that environmental Betaproteobacteria were the original source of these genetic elements. Because these elements appear to be readily mobilized, their lateral transfer into human commensals and pathogens was inevitable, especially given that Betaproteobacteria carrying class 1 integrons are common in natural environments that intersect with the human food chain. The strong selection pressure imposed by the human use of antimicrobial compounds then ensured their fixation and global spread into new species.}, }
@article {pmid18487127, year = {2008}, author = {Falkowski, PG and Godfrey, LV}, title = {Electrons, life and the evolution of Earth's oxygen cycle.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {363}, number = {1504}, pages = {2705-2716}, pmid = {18487127}, issn = {0962-8436}, mesh = {*Biological Evolution ; Carbon/metabolism ; Earth, Planet ; Electrons ; Eukaryotic Cells ; Feedback, Physiological ; Microbiology ; Models, Biological ; Nitrogen/metabolism ; Oxygen/*metabolism ; Photosynthesis ; }, abstract = {The biogeochemical cycles of H, C, N, O and S are coupled via biologically catalysed electron transfer (redox) reactions. The metabolic processes responsible for maintaining these cycles evolved over the first ca 2.3 Ga of Earth's history in prokaryotes and, through a sequence of events, led to the production of oxygen via the photobiologically catalysed oxidation of water. However, geochemical evidence suggests that there was a delay of several hundred million years before oxygen accumulated in Earth's atmosphere related to changes in the burial efficiency of organic matter and fundamental alterations in the nitrogen cycle. In the latter case, the presence of free molecular oxygen allowed ammonium to be oxidized to nitrate and subsequently denitrified. The interaction between the oxygen and nitrogen cycles in particular led to a negative feedback, in which increased production of oxygen led to decreased fixed inorganic nitrogen in the oceans. This feedback, which is supported by isotopic analyses of fixed nitrogen in sedimentary rocks from the Late Archaean, continues to the present. However, once sufficient oxygen accumulated in Earth's atmosphere to allow nitrification to out-compete denitrification, a new stable electron 'market' emerged in which oxygenic photosynthesis and aerobic respiration ultimately spread via endosymbiotic events and massive lateral gene transfer to eukaryotic host cells, allowing the evolution of complex (i.e. animal) life forms. The resulting network of electron transfers led a gas composition of Earth's atmosphere that is far from thermodynamic equilibrium (i.e. it is an emergent property), yet is relatively stable on geological time scales. The early coevolution of the C, N and O cycles, and the resulting non-equilibrium gaseous by-products can be used as a guide to search for the presence of life on terrestrial planets outside of our Solar System.}, }
@article {pmid18485655, year = {2008}, author = {Marti, S and Sánchez-Céspedes, J and Blasco, MD and Espinal, P and Ruiz, M and Alba, V and Vila, J}, title = {Characterization of the carbapenem-hydrolyzing oxacillinase OXA-58 in an Acinetobacter phenon 6/ct13TU clinical isolate.}, journal = {Diagnostic microbiology and infectious disease}, volume = {61}, number = {4}, pages = {468-470}, doi = {10.1016/j.diagmicrobio.2008.03.014}, pmid = {18485655}, issn = {0732-8893}, mesh = {Acinetobacter/*enzymology/*genetics/isolation &amp; purification ; Acinetobacter Infections/microbiology ; Carbapenems/*metabolism ; DNA, Bacterial/genetics ; Electrophoresis, Agar Gel ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Nucleic Acid Hybridization ; Plasmids/genetics ; Sequence Analysis, DNA ; Sequence Homology ; beta-Lactamases/*genetics/metabolism ; }, abstract = {The bla(OXA-58) gene identified in the Acinetobacter phenon 6/ct13TU clinical isolate presented 100% homology with the same gene in Acinetobacter baumannii. Its location in a plasmid suggests that these resistance genes may be transferred from 1 species to another.}, }
@article {pmid18485266, year = {2009}, author = {Kobayashi, S and Wada, A and Shibasaki, S and Annaka, M and Higuchi, H and Adachi, K and Mori, N and Ishikawa, T and Masuda, Y and Watanabe, H and Yamamoto, N and Yamaoka, S and Inamatsu, T}, title = {Spread of a large plasmid carrying the cpe gene and the tcp locus amongst Clostridium perfringens isolates from nosocomial outbreaks and sporadic cases of gastroenteritis in a geriatric hospital.}, journal = {Epidemiology and infection}, volume = {137}, number = {1}, pages = {108-113}, doi = {10.1017/S0950268808000794}, pmid = {18485266}, issn = {0950-2688}, mesh = {Bacterial Typing Techniques ; Clostridium Infections/*epidemiology/*microbiology ; Clostridium perfringens/*genetics/*isolation &amp; purification ; Cluster Analysis ; DNA Fingerprinting ; DNA, Bacterial/genetics ; *Disease Outbreaks ; Electrophoresis, Gel, Pulsed-Field ; Enterotoxins/genetics ; Feces/microbiology ; Gastroenteritis/*epidemiology/*microbiology ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genotype ; Geriatrics ; Hospitals ; Humans ; *Plasmids ; }, abstract = {SUMMARYTo investigate two clusters of diarrhoea cases observed in our geriatric hospital wards, the faecal specimens were analysed. Reversed passive latex agglutination assay revealed that 63.2% and 41.7% of the faecal specimens from each cluster were positive for Clostridium perfringens enterotoxin. PCR assay revealed that 71.4% and 68.8% of C. perfringens isolates from each cluster were positive for the enterotoxin gene (cpe). These observations suggested that both the clusters were outbreaks caused by enterotoxigenic C. perfringens. Subsequent pulsed-field gel electrophoresis analysis revealed that the two outbreaks were caused by different C. perfringens isolates. However, these outbreak isolates as well as other sporadic diarrhoea isolates shared a 75-kb plasmid on which the cpe gene and the tcp locus were located. The 75-kb plasmid had horizontally spread to various C. perfringens isolates and had caused outbreaks and sporadic infections. However, the site and time of the plasmid transfer are unclear.}, }
@article {pmid18485228, year = {2008}, author = {Maruyama, S and Misawa, K and Iseki, M and Watanabe, M and Nozaki, H}, title = {Origins of a cyanobacterial 6-phosphogluconate dehydrogenase in plastid-lacking eukaryotes.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {151}, pmid = {18485228}, issn = {1471-2148}, mesh = {Bayes Theorem ; Chlorophyta/enzymology/genetics ; Cyanobacteria/*enzymology/*genetics ; DNA, Complementary ; Evolution, Molecular ; Gene Library ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Genome, Plant ; Likelihood Functions ; Phosphogluconate Dehydrogenase/*genetics ; Phylogeny ; Plants/enzymology/genetics ; Plastids/*enzymology/*genetics ; Polymerase Chain Reaction ; Rhodophyta/enzymology/genetics ; }, abstract = {BACKGROUND: Plastids have inherited their own genomes from a single cyanobacterial ancestor, but the majority of cyanobacterial genes, once retained in the ancestral plastid genome, have been lost or transferred into the eukaryotic host nuclear genome via endosymbiotic gene transfer. Although previous studies showed that cyanobacterial gnd genes, which encode 6-phosphogluconate dehydrogenase, are present in several plastid-lacking protists as well as primary and secondary plastid-containing phototrophic eukaryotes, the evolutionary paths of these genes remain elusive.<br><br>RESULTS: Here we show an extended phylogenetic analysis including novel gnd gene sequences from Excavata and Glaucophyta. Our analysis demonstrated the patchy distribution of the excavate genes in the gnd gene phylogeny. The Diplonema gene was related to cytosol-type genes in red algae and Opisthokonta, while heterolobosean genes occupied basal phylogenetic positions with plastid-type red algal genes within the monophyletic eukaryotic group that is sister to cyanobacterial genes. Statistical tests based on exhaustive maximum likelihood analyses strongly rejected that heterolobosean gnd genes were derived from a secondary plastid of green lineage. In addition, the cyanobacterial gnd genes from phototrophic and phagotrophic species in Euglenida were robustly monophyletic with Stramenopiles, and this monophyletic clade was moderately separated from those of red algae. These data suggest that these secondary phototrophic groups might have acquired the cyanobacterial genes independently of secondary endosymbioses.<br><br>CONCLUSION: We propose an evolutionary scenario in which plastid-lacking Excavata acquired cyanobacterial gnd genes via eukaryote-to-eukaryote lateral gene transfer or primary endosymbiotic gene transfer early in eukaryotic evolution, and then lost either their pre-existing or cyanobacterial gene.}, }
@article {pmid18485189, year = {2008}, author = {Comas, I and González-Candelas, F and Zúñiga, M}, title = {Unraveling the evolutionary history of the phosphoryl-transfer chain of the phosphoenolpyruvate:phosphotransferase system through phylogenetic analyses and genome context.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {147}, pmid = {18485189}, issn = {1471-2148}, mesh = {Archaea/*enzymology/genetics ; Bacteria/*enzymology/genetics ; Computational Biology ; Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Gene Expression Regulation, Enzymologic ; *Genome, Archaeal ; *Genome, Bacterial ; Multigene Family ; Phosphoenolpyruvate Sugar Phosphotransferase System/*genetics ; Phosphorylation ; *Phylogeny ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {BACKGROUND: The phosphoenolpyruvate phosphotransferase system (PTS) plays a major role in sugar transport and in the regulation of essential physiological processes in many bacteria. The PTS couples solute transport to its phosphorylation at the expense of phosphoenolpyruvate (PEP) and it consists of general cytoplasmic phosphoryl transfer proteins and specific enzyme II complexes which catalyze the uptake and phosphorylation of solutes. Previous studies have suggested that the evolution of the constituents of the enzyme II complexes has been driven largely by horizontal gene transfer whereas vertical inheritance has been prevalent in the general phosphoryl transfer proteins in some bacterial groups. The aim of this work is to test this hypothesis by studying the evolution of the phosphoryl transfer proteins of the PTS.<br><br>RESULTS: We have analyzed the evolutionary history of the PTS phosphoryl transfer chain (PTS-ptc) components in 222 complete genomes by combining phylogenetic methods and analysis of genomic context. Phylogenetic analyses alone were not conclusive for the deepest nodes but when complemented with analyses of genomic context and functional information, the main evolutionary trends of this system could be depicted.<br><br>CONCLUSION: The PTS-ptc evolved in bacteria after the divergence of early lineages such as Aquificales, Thermotogales and Thermus/Deinococcus. The subsequent evolutionary history of the PTS-ptc varied in different bacterial lineages: vertical inheritance and lineage-specific gene losses mainly explain the current situation in Actinobacteria and Firmicutes whereas horizontal gene transfer (HGT) also played a major role in Proteobacteria. Most remarkably, we have identified a HGT event from Firmicutes or Fusobacteria to the last common ancestor of the Enterobacteriaceae, Pasteurellaceae, Shewanellaceae and Vibrionaceae. This transfer led to extensive changes in the metabolic and regulatory networks of these bacteria including the development of a novel carbon catabolite repression system. Hence, this example illustrates that HGT can drive major physiological modifications in bacteria.}, }
@article {pmid18485065, year = {2008}, author = {Johnsborg, O and Eldholm, V and Bjørnstad, ML and Håvarstein, LS}, title = {A predatory mechanism dramatically increases the efficiency of lateral gene transfer in Streptococcus pneumoniae and related commensal species.}, journal = {Molecular microbiology}, volume = {69}, number = {1}, pages = {245-253}, doi = {10.1111/j.1365-2958.2008.06288.x}, pmid = {18485065}, issn = {1365-2958}, mesh = {Bacterial Proteins/genetics/metabolism ; Bacteriolysis ; Biodiversity ; Coculture Techniques ; DNA, Bacterial/genetics ; *Gene Transfer, Horizontal ; Genes, Reporter ; Models, Biological ; Phenotype ; Pheromones/metabolism ; Streptococcus/*genetics/metabolism ; *Transformation, Bacterial ; beta-Galactosidase/metabolism ; }, abstract = {Bacteria that are competent for natural genetic transformation, such as pneumococci and their commensal relatives Streptococcus mitis and Streptococcus oralis, take up exogenous DNA and incorporate it into their genomes by homologous recombination. Traditionally, it has been assumed that genetic material leaking from dead bacteria constitutes the sole source of external DNA for competent streptococci. Here we describe a mechanism for active acquisition of homologous DNA that dramatically increases the efficiency of gene exchange between and within the streptococcal species mentioned above. This mechanism gives competent streptococci access to a common gene pool that is significantly larger than their own genomes, a property representing a considerable advantage when these bacteria are subjected to external selection pressures, such as vaccination and treatment with antibiotics.}, }
@article {pmid18479346, year = {2008}, author = {Táncsics, A and Szoboszlay, S and Kriszt, B and Kukolya, J and Baka, E and Márialigeti, K and Révész, S}, title = {Applicability of the functional gene catechol 1,2-dioxygenase as a biomarker in the detection of BTEX-degrading Rhodococcus species.}, journal = {Journal of applied microbiology}, volume = {105}, number = {4}, pages = {1026-1033}, doi = {10.1111/j.1365-2672.2008.03832.x}, pmid = {18479346}, issn = {1365-2672}, mesh = {Benzene/metabolism ; Benzene Derivatives/metabolism ; Biodegradation, Environmental ; Catechol 1,2-Dioxygenase/*genetics ; Environmental Monitoring/methods ; Organic Chemicals/*metabolism ; Phylogeny ; Polymerase Chain Reaction/methods ; Rhodococcus/enzymology/genetics/*isolation &amp; purification ; Toluene/metabolism ; *Water Microbiology ; Xylenes/metabolism ; }, abstract = {AIMS: Catechol 1,2-dioxygenase is a key enzyme in the degradation of monoaromatic pollutants. The detection of this gene is in focus today but recently designed degenerate primers are not always suitable. Rhodococcus species are important members of the bacterial community involved in the degradation of aromatic contaminants and their specific detection could help assess functions and activities in the contaminated environments. To reach this aim, specific PCR primer sets were designed for the detection of Rhodococcus related catechol 1,2-dioxygenase genes.<br><br>METHODS AND RESULTS: Primers were tested with genetically well-characterized strains isolated in this study and community DNA samples were used as template for Rhodococcus specific PCR as well. The sequences of the catabolic gene in question were subjected to multiple alignment and a phylogenetic tree was created and compared to a 16S rRNA gene based Rhodococcus tree. A strong coherence was observed between the phylogenetic trees.<br><br>CONCLUSIONS: The results strongly support the opinion that there was no recent lateral gene transfer among Rhodococcus species in the case of catechol 1,2-dioxygenase.<br><br>In gasoline contaminated environments, aromatic hydrocarbon degrading Rhodococcus populations can be identified based upon the detection and sequence analysis of catechol 1,2-dioxygenase gene.}, }
@article {pmid18478535, year = {2008}, author = {Bock, R and Timmis, JN}, title = {Reconstructing evolution: gene transfer from plastids to the nucleus.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {30}, number = {6}, pages = {556-566}, doi = {10.1002/bies.20761}, pmid = {18478535}, issn = {1521-1878}, mesh = {Cell Nucleus/*genetics ; Cyanobacteria/genetics ; DNA/genetics ; *Evolution, Molecular ; Gene Expression Regulation ; Gene Transfer Techniques ; Gene Transfer, Horizontal ; Genome, Bacterial ; Genome, Plant ; Genome, Plastid ; Models, Genetic ; Plants/genetics ; Plants, Genetically Modified ; Plastids/*genetics ; RNA/genetics ; Research Design ; Symbiosis/genetics ; }, abstract = {During evolution, the genomes of eukaryotic cells have undergone major restructuring to meet the new regulatory challenges associated with compartmentalization of the genetic material in the nucleus and the organelles acquired by endosymbiosis (mitochondria and plastids). Restructuring involved the loss of dispensable or redundant genes and the massive translocation of genes from the ancestral organelles to the nucleus. Genomics and bioinformatic data suggest that the process of DNA transfer from organelles to the nucleus still continues, providing raw material for evolutionary tinkering in the nuclear genome. Recent reconstruction of these events in the laboratory has provided a unique tool to observe genome evolution in real time and to study the molecular mechanisms by which plastid genes are converted into functional nuclear genes. Here, we summarize current knowledge about plastid-to-nuclear gene transfer in the context of genome evolution and discuss new insights gained from experiments that recapitulate endosymbiotic gene transfer in the laboratory.}, }
@article {pmid18478120, year = {2008}, author = {Li, Y and Dai, E and Cui, Y and Li, M and Zhang, Y and Wu, M and Zhou, D and Guo, Z and Dai, X and Cui, B and Qi, Z and Wang, Z and Wang, H and Dong, X and Song, Z and Zhai, J and Song, Y and Yang, R}, title = {Different region analysis for genotyping Yersinia pestis isolates from China.}, journal = {PloS one}, volume = {3}, number = {5}, pages = {e2166}, pmid = {18478120}, issn = {1932-6203}, mesh = {Base Sequence ; China ; DNA Primers ; Genes, Bacterial ; Genotype ; Polymerase Chain Reaction ; Yersinia pestis/*genetics ; Yersinia pseudotuberculosis/genetics ; }, abstract = {BACKGROUND: DFR (different region) analysis has been developed for typing Yesinia pestis in our previous study, and in this study, we extended this method by using 23 DFRs to investigate 909 Chinese Y. pestis strains for validating DFR-based genotyping method and better understanding adaptive microevolution of Y. pestis.<br><br>On the basis of PCR and Bionumerics data analysis, 909 Y. pestis strains were genotyped into 32 genomovars according to their DFR profiles. New terms, Major genomovar and Minor genomovar, were coined for illustrating evolutionary relationship between Y. pestis strains from different plague foci and different hosts. In silico DFR profiling of the completed or draft genomes shed lights on the evolutionary scenario of Y. pestis from Y. pseudotuberculosis. Notably, several sequenced Y. pestis strains share the same DFR profiles with Chinese strains, providing data for revealing the global plague foci expansion.<br><br>CONCLUSIONS/SIGNIFICANCE: Distribution of Y. pestis genomovars is plague focus-specific. Microevolution of biovar Orientalis was deduced according to DFR profiles. DFR analysis turns to be an efficient and inexpensive method to portrait the genome plasticity of Y. pestis based on horizontal gene transfer (HGT). DFR analysis can also be used as a tool in comparative and evolutionary genomic research for other bacteria with similar genome plasticity.}, }
@article {pmid18474115, year = {2008}, author = {Mazzoni, CJ and Araki, AS and Ferreira, GE and Azevedo, RV and Barbujani, G and Peixoto, AA}, title = {Multilocus analysis of introgression between two sand fly vectors of leishmaniasis.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {141}, pmid = {18474115}, issn = {1471-2148}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {Animal Migration ; Animals ; Gene Flow ; *Gene Transfer, Horizontal ; Genetic Markers ; Genome, Insect ; Insect Vectors/*genetics ; Leishmaniasis, Cutaneous/transmission ; Phylogeny ; Polymorphism, Genetic ; Psychodidae/classification/*genetics ; Species Specificity ; }, abstract = {BACKGROUND: The phlebotomine sand flies (Diptera:Psychodidae) Lutzomyia (Nyssomyia) intermedia Lutz &amp; Neiva 1912 and Lutzomyia (Nyssomyia) whitmani Antunes &amp; Coutinho 1932 are two very closely related species and important vectors of American cutaneous leishmaniasis. Two single-locus studies have revealed evidence for introgression between the two species in both mitochondrial and nuclear genomes. These findings have prompted the development of a multilocus approach to investigate in more detail the genetic exchanges between the two species.<br><br>RESULTS: We analyzed ten nuclear loci using the "isolation with migration" model implemented in the IM program, finding evidence for introgression from L. intermedia towards L. whitmani in three loci. These results confirm that introgression is occurring between the two species and suggest variation in the effects of gene flow among the different regions of the genome.<br><br>CONCLUSION: The demonstration that these two vectors are not fully reproductively isolated might have important epidemiological consequences as these species could be exchanging genes controlling aspects of their vectorial capacity.}, }
@article {pmid18468982, year = {2008}, author = {Howe, CJ and Barbrook, AC and Nisbet, RE and Lockhart, PJ and Larkum, AW}, title = {The origin of plastids.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {363}, number = {1504}, pages = {2675-2685}, pmid = {18468982}, issn = {0962-8436}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Electron Transport ; Electron Transport Chain Complex Proteins/genetics/metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Models, Biological ; Photosynthesis ; Phylogeny ; Plastids/classification/*genetics/*metabolism ; Symbiosis ; }, abstract = {It is generally accepted that plastids first arose by acquisition of photosynthetic prokaryotic endosymbionts by non-photosynthetic eukaryotic hosts. It is also accepted that photosynthetic eukaryotes were acquired on several occasions as endosymbionts by non-photosynthetic eukaryote hosts to form secondary plastids. In some lineages, secondary plastids were lost and new symbionts were acquired, to form tertiary plastids. Most recent work has been interpreted to indicate that primary plastids arose only once, referred to as a 'monophyletic' origin. We critically assess the evidence for this. We argue that the combination of Ockham's razor and poor taxon sampling will bias studies in favour of monophyly. We discuss possible concerns in phylogenetic reconstruction from sequence data. We argue that improved understanding of lineage-specific substitution processes is needed to assess the reliability of sequence-based trees. Improved understanding of the timing of the radiation of present-day cyanobacteria is also needed. We suggest that acquisition of plastids is better described as the result of a process rather than something occurring at a discrete time, and describe the 'shopping bag' model of plastid origin. We argue that dinoflagellates and other lineages provide evidence in support of this.}, }
@article {pmid18467773, year = {2007}, author = {Sridhar, J and Rafi, ZA}, title = {Identification of novel genomic islands associated with small RNAs.}, journal = {In silico biology}, volume = {7}, number = {6}, pages = {601-611}, pmid = {18467773}, issn = {1386-6338}, mesh = {Base Sequence ; Chromosomes, Bacterial/genetics ; Escherichia coli/genetics ; Genomic Islands/*genetics ; Molecular Sequence Data ; RNA, Bacterial/chemistry/*genetics ; Sequence Analysis, Protein ; Shigella flexneri/genetics ; }, abstract = {Genome evolution in prokaryotes is assisted by integration of gene pools from phages and plasmids. Regions downstream of tRNAs and tmRNAs are considered as hot spots for the integration of these gene pools or genomic islands. Till date, genomic islands have been identified only at tRNA/tmRNA genes in the enterobacterial genomes. Present work reports 10 distinct small RNAs as potent integration sites for genomic islands. A known tool tRNAcc 1.0 has been used to identify genomic islands associated with small RNAs c0362, oxyS, ryaA, rybB, rybD, ryeB, ryeE, rtT, sraE and tmRNA. The coordinates of 25 such small RNA associated genomic islands in three E. coli (strains: CFT073, EDL933 and K12) and Shigella flexneri (strain: 301) genomes are presented. Moreover cross-verification of the genomic sequences encoded within the identified genomic islands in horizontal gene transfer database, GenBank annotation features and atypical sequence compositions support our results. Again, all of the identified 25 genomic integration sites do exhibit genomic block rearrangements with respect to the associated small RNA. Similar to tRNAs/tmRNAs, the downstream regions of the small RNAs are found to be hotspots of integration.}, }
@article {pmid18467308, year = {2008}, author = {Piddock, LJ and Griggs, D and Johnson, MM and Ricci, V and Elviss, NC and Williams, LK and Jørgensen, F and Chisholm, SA and Lawson, AJ and Swift, C and Humphrey, TJ and Owen, RJ}, title = {Persistence of Campylobacter species, strain types, antibiotic resistance and mechanisms of tetracycline resistance in poultry flocks treated with chlortetracycline.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {62}, number = {2}, pages = {303-315}, doi = {10.1093/jac/dkn190}, pmid = {18467308}, issn = {1460-2091}, mesh = {Animals ; Anti-Bacterial Agents/administration &amp; dosage/*pharmacology ; Bacterial Proteins/genetics ; Biological Transport, Active/drug effects ; Campylobacter/classification/*drug effects/isolation &amp; purification ; Carrier Proteins/genetics ; Chlortetracycline/administration &amp; dosage/*pharmacology ; Colony Count, Microbial ; DNA, Bacterial/genetics ; Dipeptides/pharmacology ; Enzyme Inhibitors/pharmacology ; Feces/microbiology ; Flagellin/genetics ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Poultry/*microbiology ; *Tetracycline Resistance ; }, abstract = {OBJECTIVES: The aim of this study was to investigate the persistence of Campylobacter species, strain types, antibiotic resistance and mechanisms of tetracycline resistance in poultry flocks treated with chlortetracycline.<br><br>METHODS: Three commercially reared broiler flocks, naturally colonized with Campylobacter, were treated with chlortetracycline under experimental conditions. The numbers of Campylobacter isolated, and the species, flaA short variable region allele, and antimicrobial resistance of isolates were determined.<br><br>RESULTS: For two of three flocks, tetracycline-resistant strains predominated prior to chlortetracycline exposure. Presence of the antibiotic had no discernible effect on the numbers or types of Campylobacter and the tetracycline-resistant strains persisted in numbers similar to those observed before treatment. With all flocks, some faecal samples were obtained that contained no Campylobacter, irrespective of exposure to chlortetracycline; this was more common as the birds grew older. For the third flock, tetracycline-resistant Campylobacter were in the minority of samples before and during exposure to chlortetracycline, but at sampling times after this, no resistant strains were found in the treated (or untreated) birds, irrespective of exposure to the antibiotic. All tetracycline-resistant isolates (MICs 16 to >128 mg/L) contained tet(O) and, for some isolates, this was transferable to Campylobacter jejuni 81116. The efflux pump inhibitor PAbetaN reduced the MICs of tetracycline for these isolates by 4-fold, suggesting that an intact efflux pump, presumably CmeABC, is required for high-level tetracycline resistance.<br><br>CONCLUSIONS: Our data indicate that chlortetracycline treatment does not eradicate tetracycline-resistant Campylobacter spp. from poultry. However, if a low number of resistant isolates are present, then the antibiotic pressure appears insufficient to select such strains as the dominant population.}, }
@article {pmid18463089, year = {2008}, author = {Yutin, N and Makarova, KS and Mekhedov, SL and Wolf, YI and Koonin, EV}, title = {The deep archaeal roots of eukaryotes.}, journal = {Molecular biology and evolution}, volume = {25}, number = {8}, pages = {1619-1630}, pmid = {18463089}, issn = {1537-1719}, support = {//Intramural NIH HHS/United States ; }, mesh = {Archaea/*genetics ; Computational Biology ; *Eukaryotic Cells ; *Evolution, Molecular ; Likelihood Functions ; Models, Genetic ; Multigene Family/genetics ; *Phylogeny ; Sequence Alignment ; Species Specificity ; }, abstract = {The set of conserved eukaryotic protein-coding genes includes distinct subsets one of which appears to be most closely related to and, by inference, derived from archaea, whereas another one appears to be of bacterial, possibly, endosymbiotic origin. The "archaeal" genes of eukaryotes, primarily, encode components of information-processing systems, whereas the "bacterial" genes are predominantly operational. The precise nature of the archaeo-eukaryotic relationship remains uncertain, and it has been variously argued that eukaryotic informational genes evolved from the homologous genes of Euryarchaeota or Crenarchaeota (the major branches of extant archaea) or that the origin of eukaryotes lies outside the known diversity of archaea. We describe a comprehensive set of 355 eukaryotic genes of apparent archaeal origin identified through ortholog detection and phylogenetic analysis. Phylogenetic hypothesis testing using constrained trees, combined with a systematic search for shared derived characters in the form of homologous inserts in conserved proteins, indicate that, for the majority of these genes, the preferred tree topology is one with the eukaryotic branch placed outside the extant diversity of archaea although small subsets of genes show crenarchaeal and euryarchaeal affinities. Thus, the archaeal genes in eukaryotes appear to descend from a distinct, ancient, and otherwise uncharacterized archaeal lineage that acquired some euryarchaeal and crenarchaeal genes via early horizontal gene transfer.}, }
@article {pmid18462506, year = {2008}, author = {Cattolico, RA and Jacobs, MA and Zhou, Y and Chang, J and Duplessis, M and Lybrand, T and McKay, J and Ong, HC and Sims, E and Rocap, G}, title = {Chloroplast genome sequencing analysis of Heterosigma akashiwo CCMP452 (West Atlantic) and NIES293 (West Pacific) strains.}, journal = {BMC genomics}, volume = {9}, number = {}, pages = {211}, pmid = {18462506}, issn = {1471-2164}, support = {T32 EY007031/EY/NEI NIH HHS/United States ; T32 HG000035/HG/NHGRI NIH HHS/United States ; T32 EY07031/EY/NEI NIH HHS/United States ; T32 HG00035/HG/NHGRI NIH HHS/United States ; }, mesh = {Algal Proteins/genetics ; Amino Acid Sequence ; Atlantic Ocean ; Base Sequence ; Chromosome Mapping ; Cloning, Molecular ; Conserved Sequence ; DNA, Algal/genetics/isolation &amp; purification ; DNA, Chloroplast/genetics/isolation &amp; purification ; Furans ; *Genome, Chloroplast ; Molecular Sequence Data ; Pacific Ocean ; Phaeophyceae/classification/*genetics/isolation &amp; purification ; Polymorphism, Single Nucleotide ; Recombinases/genetics ; Repetitive Sequences, Nucleic Acid ; Sequence Analysis, DNA/methods ; Sequence Homology, Amino Acid ; Species Specificity ; Thiophenes ; }, abstract = {BACKGROUND: Heterokont algae form a monophyletic group within the stramenopile branch of the tree of life. These organisms display wide morphological diversity, ranging from minute unicells to massive, bladed forms. Surprisingly, chloroplast genome sequences are available only for diatoms, representing two (Coscinodiscophyceae and Bacillariophyceae) of approximately 18 classes of algae that comprise this taxonomic cluster. A universal challenge to chloroplast genome sequencing studies is the retrieval of highly purified DNA in quantities sufficient for analytical processing. To circumvent this problem, we have developed a simplified method for sequencing chloroplast genomes, using fosmids selected from a total cellular DNA library. The technique has been used to sequence chloroplast DNA of two Heterosigma akashiwo strains. This raphidophyte has served as a model system for studies of stramenopile chloroplast biogenesis and evolution.<br><br>RESULTS: H. akashiwo strain CCMP452 (West Atlantic) chloroplast DNA is 160,149 bp in size with a 21,822-bp inverted repeat, whereas NIES293 (West Pacific) chloroplast DNA is 159,370 bp in size and has an inverted repeat of 21,665 bp. The fosmid cloning technique reveals that both strains contain an isomeric chloroplast DNA population resulting from an inversion of their single copy domains. Both strains contain multiple small inverted and tandem repeats, non-randomly distributed within the genomes. Although both CCMP452 and NIES293 chloroplast DNAs contains 197 genes, multiple nucleotide polymorphisms are present in both coding and intergenic regions. Several protein-coding genes contain large, in-frame inserts relative to orthologous genes in other plastids. These inserts are maintained in mRNA products. Two genes of interest in H. akashiwo, not previously reported in any chloroplast genome, include tyrC, a tyrosine recombinase, which we hypothesize may be a result of a lateral gene transfer event, and an unidentified 456 amino acid protein, which we hypothesize serves as a G-protein-coupled receptor. The H. akashiwo chloroplast genomes share little synteny with other algal chloroplast genomes sequenced to date.<br><br>CONCLUSION: The fosmid cloning technique eliminates chloroplast isolation, does not require chloroplast DNA purification, and reduces sequencing processing time. Application of this method has provided new insights into chloroplast genome architecture, gene content and evolution within the stramenopile cluster.}, }
@article {pmid18462175, year = {2008}, author = {Tong, SY and McDonald, MI and Holt, DC and Currie, BJ}, title = {Global implications of the emergence of community-associated methicillin-resistant Staphylococcus aureus in Indigenous populations.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {46}, number = {12}, pages = {1871-1878}, doi = {10.1086/588301}, pmid = {18462175}, issn = {1537-6591}, mesh = {Australia/epidemiology ; Community-Acquired Infections/*epidemiology/*microbiology ; Gene Transfer, Horizontal ; Humans ; Methicillin Resistance/*genetics ; Population Groups ; Socioeconomic Factors ; Staphylococcal Infections/*epidemiology/*microbiology ; Staphylococcus aureus/classification/*drug effects/genetics/isolation &amp; purification ; }, abstract = {The emergence of community-associated methicillin-resistant Staphylococcus aureus (MRSA) in Australia may have been facilitated by conditions in socially disadvantaged populations--particularly, remote Australian Aboriginal communities. The appearance of community-associated MRSA was first noticed in Australia during the early 1980s; subsequently, several genetically diverse strains have independently emerged from geographically distinct regions. Molecular and epidemiological studies support the role of genetic transfer of resistance determinants (SCCmecIV) in this process. Conditions in Aboriginal communities--namely, domestic crowding, poor hygiene, and high rates of scabies, pyoderma, and antibiotic use--have facilitated both the clonal expansion and de novo emergence of strains of community-associated MRSA. Combating the worldwide emergence and spread of community-associated MRSA may require novel community-level control strategies targeted at specific groups, such as remote Indigenous populations.}, }
@article {pmid18461135, year = {2008}, author = {Thomas, SH and Wagner, RD and Arakaki, AK and Skolnick, J and Kirby, JR and Shimkets, LJ and Sanford, RA and Löffler, FE}, title = {The mosaic genome of Anaeromyxobacter dehalogenans strain 2CP-C suggests an aerobic common ancestor to the delta-proteobacteria.}, journal = {PloS one}, volume = {3}, number = {5}, pages = {e2103}, pmid = {18461135}, issn = {1932-6203}, mesh = {Bacterial Proteins/genetics ; Deltaproteobacteria/classification/*genetics ; Enzymes/classification/genetics ; *Genome, Bacterial ; Mosaicism ; Myxococcales/classification/*genetics ; Oxygen Consumption ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 18S/genetics ; *Soil Microbiology ; }, abstract = {Anaeromyxobacter dehalogenans strain 2CP-C is a versaphilic delta-Proteobacterium distributed throughout many diverse soil and sediment environments. 16S rRNA gene phylogenetic analysis groups A. dehalogenans together with the myxobacteria, which have distinguishing characteristics including strictly aerobic metabolism, sporulation, fruiting body formation, and surface motility. Analysis of the 5.01 Mb strain 2CP-C genome substantiated that this organism is a myxobacterium but shares genotypic traits with the anaerobic majority of the delta-Proteobacteria (i.e., the Desulfuromonadales). Reflective of its respiratory versatility, strain 2CP-C possesses 68 genes coding for putative c-type cytochromes, including one gene with 40 heme binding motifs. Consistent with its relatedness to the myxobacteria, surface motility was observed in strain 2CP-C and multiple types of motility genes are present, including 28 genes for gliding, adventurous (A-) motility and 17 genes for type IV pilus-based motility (i.e., social (S-) motility) that all have homologs in Myxococcus xanthus. Although A. dehalogenans shares many metabolic traits with the anaerobic majority of the delta-Proteobacteria, strain 2CP-C grows under microaerophilic conditions and possesses detoxification systems for reactive oxygen species. Accordingly, two gene clusters coding for NADH dehydrogenase subunits and two cytochrome oxidase gene clusters in strain 2CP-C are similar to those in M. xanthus. Remarkably, strain 2CP-C possesses a third NADH dehydrogenase gene cluster and a cytochrome cbb(3) oxidase gene cluster, apparently acquired through ancient horizontal gene transfer from a strictly anaerobic green sulfur bacterium. The mosaic nature of the A. dehalogenans strain 2CP-C genome suggests that the metabolically versatile, anaerobic members of the delta-Proteobacteria may have descended from aerobic ancestors with complex lifestyles.}, }
@article {pmid18461076, year = {2008}, author = {Achtman, M and Wagner, M}, title = {Microbial diversity and the genetic nature of microbial species.}, journal = {Nature reviews. Microbiology}, volume = {6}, number = {6}, pages = {431-440}, doi = {10.1038/nrmicro1872}, pmid = {18461076}, issn = {1740-1534}, mesh = {Archaea/*classification/*genetics ; Bacteria/*classification/*genetics/pathogenicity ; Ecosystem ; Environmental Microbiology ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Speciation ; Genetic Variation ; Genetics, Microbial/*methods ; Models, Genetic ; Selection, Genetic ; }, abstract = {The earth contains a huge number of largely uncharacterized Bacteria and Archaea. Microbiologists are struggling to summarize their genetic diversity and classify them, which has resulted in heated debates on methods for defining species, mechanisms that lead to speciation and whether microbial species even exist. This Review proposes that decisions on the existence of species and methods to define them should be guided by a method-free species concept that is based on cohesive evolutionary forces. It summarizes current approaches to defining species and the problems of these approaches, and presents selected examples of the population genetic patterns at and below the species level.}, }
@article {pmid18460604, year = {2008}, author = {Kreimer, A and Borenstein, E and Gophna, U and Ruppin, E}, title = {The evolution of modularity in bacterial metabolic networks.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {19}, pages = {6976-6981}, pmid = {18460604}, issn = {1091-6490}, support = {R01 GM028016/GM/NIGMS NIH HHS/United States ; GM28016/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*metabolism ; *Biological Evolution ; *Metabolic Networks and Pathways ; Proteobacteria/metabolism ; }, abstract = {Deciphering the modular organization of metabolic networks and understanding how modularity evolves have attracted tremendous interest in recent years. Here, we present a comprehensive large scale characterization of modularity across the bacterial tree of life, systematically quantifying the modularity of the metabolic networks of >300 bacterial species. Three main determinants of metabolic network modularity are identified. First, network size is an important topological determinant of network modularity. Second, several environmental factors influence network modularity, with endosymbionts and mammal-specific pathogens having lower modularity scores than bacterial species that occupy a wider range of niches. Moreover, even among the pathogens, those that alternate between two distinct niches, such as insect and mammal, tend to have relatively high metabolic network modularity. Third, horizontal gene transfer is an important force that contributes significantly to metabolic modularity. We additionally reconstruct the metabolic network of ancestral bacterial species and examine the evolution of modularity across the tree of life. This reveals a trend of modularity decrease from ancestors to descendants that is likely the outcome of niche specialization and the incorporation of peripheral metabolic reactions.}, }
@article {pmid18460154, year = {2008}, author = {Sun, GL and Shen, W and Wen, JF}, title = {Triosephosphate isomerase genes in two trophic modes of euglenoids (euglenophyceae) and their phylogenetic analysis.}, journal = {The Journal of eukaryotic microbiology}, volume = {55}, number = {3}, pages = {170-177}, doi = {10.1111/j.1550-7408.2008.00324.x}, pmid = {18460154}, issn = {1066-5234}, mesh = {Algal Proteins/chemistry/*genetics/metabolism ; Amino Acid Sequence ; Animals ; Euglenida/chemistry/classification/*enzymology/genetics ; Evolution, Molecular ; Fungi/genetics ; Molecular Sequence Data ; *Phylogeny ; Plants/genetics ; Protozoan Proteins/chemistry/*genetics/metabolism ; Rhodophyta/genetics ; Sequence Alignment ; Triose-Phosphate Isomerase/chemistry/*genetics/metabolism ; }, abstract = {Two different length cDNAs encoding triosephosphate isomerase (TIM) were identified in the two trophic modes of euglenoids, the phototrophic Euglena gracilis and Euglena intermedia and the saprotrophic Astasia longa. Sequence analyses and presequence prediction indicated that the shorter cDNA encodes a cytosolic TIM and the longer cDNA encodes a plastid TIM (pTIM). The typical presequence of the putative A. longa pTIM and the high sequence similarity between A. longa pTIM and E. gracilis pTIM imply that A. longa pTIM is targeted to plastids. Therefore, although the plastids of A. longa have lost the ability of photosynthesis, they might retain other TIM-related function(s), such as glycolysis and the synthesis of isopentenyl diphosphate or fatty acids. Including the TIM sequences obtained by us from chlorophytes and rhodophytes, our phylogenetic analyses indicated that euglenoid TIMs group neither with TIMs of kinetoplastids, which share the nearest common ancestor with euglenoids, nor are closely related to TIMs of chlorophytes, which are considered to be the donors of euglenoid plastids through secondary endosymbiosis. Instead, they group with TIMs of rhodophytes. In addition, our amino acid sequence alignment and structure modeling showed that TIMs of euglenoids and rhodophytes share a unique 2-aa insertion within their loop-4 areas. Therefore, either tim convergent evolution or lateral gene transfer (more probably) might have occurred between euglenoids and rhodophytes after the divergence of euglenoids with kinetoplastids.}, }
@article {pmid18458344, year = {2008}, author = {Kamikawa, R and Inagaki, Y and Sako, Y}, title = {Direct phylogenetic evidence for lateral transfer of elongation factor-like gene.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {19}, pages = {6965-6969}, pmid = {18458344}, issn = {1091-6490}, mesh = {Diatoms/*genetics ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Peptide Elongation Factor 1/genetics ; Peptide Elongation Factors/*genetics ; *Phylogeny ; Sequence Homology, Nucleic Acid ; }, abstract = {Genes encoding elongation factor-like (EFL) proteins, which show high similarity to elongation factor-1alpha (EF-1alpha), have been found in phylogenetically distantly related eukaryotes. The sporadic distribution of "EFL-containing" lineages within "EF-1alpha-containing" lineages indirectly, but strongly, suggests lateral gene transfer as the principal driving force in EFL evolution. However, one of the most critical aspects in the above hypothesis, the donor lineages in any putative cases of lateral EFL gene transfer, remained unclear. In this study, we provide direct evidence for lateral transfer of an EFL gene through the analyses of 10 diatom EFL genes. All diatom EFL homologues tightly clustered in phylogenetic analyses, suggesting acquisition of the exogenous EFL gene early in diatom evolution. Our survey additionally identified Thalassiosira pseudonana as a eukaryote bearing EF-1alpha and EFL genes and secondary EFL gene loss in Phaeodactylum tricornutum, the complete genome of which encodes only the EF-1alpha gene. Most importantly, the EFL phylogeny recovered a robust grouping of homologues from diatoms, the cercozoan Bigelowiella natans, and the foraminifer Planoglabratella opecularis, with the diatoms nested within the Bigelowiella plus Planoglabratella (Rhizaria) grouping. The particular relationships recovered are further consistent with two characteristic sequence motifs. The best explanation of our data analyses is an EFL gene transfer from a foraminifer to a diatom, the first case in which the donor-recipient relationship was clarified. Finally, based on a reverse transcriptase quantitative PCR assay and the genome information of Thalassiosira and Phaeodactylum, we propose the loss of elongation factor function in Thalassiosira EF-1alpha.}, }
@article {pmid18457000, year = {2008}, author = {Heistad, DD and Watanabe, Y and Chu, Y}, title = {Gene transfer after subarachnoid hemorrhage: a tool and potential therapy.}, journal = {Acta neurochirurgica. Supplement}, volume = {104}, number = {}, pages = {157-159}, doi = {10.1007/978-3-211-75718-5_30}, pmid = {18457000}, issn = {0065-1419}, support = {HL 14388/HL/NHLBI NIH HHS/United States ; HL 16066/HL/NHLBI NIH HHS/United States ; DK 54759/DK/NIDDK NIH HHS/United States ; HL 62984/HL/NHLBI NIH HHS/United States ; P30 DK054759/DK/NIDDK NIH HHS/United States ; NS 24621/NS/NINDS NIH HHS/United States ; }, mesh = {Gene Expression Regulation ; *Gene Transfer, Horizontal ; Humans ; Subarachnoid Hemorrhage/*genetics ; Vasospasm, Intracranial/genetics/*prevention &amp; control ; }, abstract = {This mini-review describes steps towards gene therapy to prevent vasospasm after subarachnoid hemorrhage, and summarizes some remaining obstacles. With recombinant adenoviruses, it is now possible to prevent vasospasm in experimental animals. If an adenoviral or other effective vector is demonstrated to be safe, it is likely that gene therapy will be used in patients to prevent vasospasm.}, }
@article {pmid18452608, year = {2008}, author = {Salzberg, SL and Sommer, DD and Schatz, MC and Phillippy, AM and Rabinowicz, PD and Tsuge, S and Furutani, A and Ochiai, H and Delcher, AL and Kelley, D and Madupu, R and Puiu, D and Radune, D and Shumway, M and Trapnell, C and Aparna, G and Jha, G and Pandey, A and Patil, PB and Ishihara, H and Meyer, DF and Szurek, B and Verdier, V and Koebnik, R and Dow, JM and Ryan, RP and Hirata, H and Tsuyumu, S and Won Lee, S and Seo, YS and Sriariyanum, M and Ronald, PC and Sonti, RV and Van Sluys, MA and Leach, JE and White, FF and Bogdanove, AJ}, title = {Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A.}, journal = {BMC genomics}, volume = {9}, number = {}, pages = {204}, pmid = {18452608}, issn = {1471-2164}, support = {R01 GM083873/GM/NIGMS NIH HHS/United States ; R01-GM083873/GM/NIGMS NIH HHS/United States ; R01 LM006845-09/LM/NLM NIH HHS/United States ; R01 LM006845/LM/NLM NIH HHS/United States ; R01 GM083873-05/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics ; Base Sequence ; DNA Transposable Elements/genetics ; *Evolution, Molecular ; Gene Duplication ; Gene Rearrangement ; Gene Transfer, Horizontal ; Genome, Bacterial/*genetics ; Genomics ; Microsatellite Repeats ; Oryza/*microbiology ; Reproducibility of Results ; Time Factors ; Xanthomonas/*genetics ; }, abstract = {BACKGROUND: Xanthomonas oryzae pv. oryzae causes bacterial blight of rice (Oryza sativa L.), a major disease that constrains production of this staple crop in many parts of the world. We report here on the complete genome sequence of strain PXO99A and its comparison to two previously sequenced strains, KACC10331 and MAFF311018, which are highly similar to one another.<br><br>RESULTS: The PXO99A genome is a single circular chromosome of 5,240,075 bp, considerably longer than the genomes of the other strains (4,941,439 bp and 4,940,217 bp, respectively), and it contains 5083 protein-coding genes, including 87 not found in KACC10331 or MAFF311018. PXO99A contains a greater number of virulence-associated transcription activator-like effector genes and has at least ten major chromosomal rearrangements relative to KACC10331 and MAFF311018. PXO99A contains numerous copies of diverse insertion sequence elements, members of which are associated with 7 out of 10 of the major rearrangements. A rapidly-evolving CRISPR (clustered regularly interspersed short palindromic repeats) region contains evidence of dozens of phage infections unique to the PXO99A lineage. PXO99A also contains a unique, near-perfect tandem repeat of 212 kilobases close to the replication terminus.<br><br>CONCLUSION: Our results provide striking evidence of genome plasticity and rapid evolution within Xanthomonas oryzae pv. oryzae. The comparisons point to sources of genomic variation and candidates for strain-specific adaptations of this pathogen that help to explain the extraordinary diversity of Xanthomonas oryzae pv. oryzae genotypes and races that have been isolated from around the world.}, }
@article {pmid18451043, year = {2008}, author = {Quiroga, C and Roy, PH and Centrón, D}, title = {The S.ma.I2 class C group II intron inserts at integron attC sites.}, journal = {Microbiology (Reading, England)}, volume = {154}, number = {Pt 5}, pages = {1341-1353}, doi = {10.1099/mic.0.2007/016360-0}, pmid = {18451043}, issn = {1350-0872}, mesh = {Base Sequence ; Binding Sites ; DNA, Bacterial/*genetics ; *Integrons ; *Introns ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; RNA Splicing ; RNA, Bacterial/*genetics ; Rec A Recombinases/genetics ; *Recombination, Genetic ; Sequence Homology, Nucleic Acid ; Serratia marcescens/*genetics ; }, abstract = {We previously found the class C S.ma.I2 group II (GII) intron in Serratia marcescens SCH909 inserted into the variable region of a class 1 integron within the attC site of the ant(2'')-Ia gene cassette. Here, we demonstrate that this ant(2'')-Ia : : S.ma.I2 gene cassette is a recombinationally active element despite the presence of the S.ma.I2 intron. In addition, S.ma.I2 is an active GII intron capable of performing self-splicing and invading specific target sites. Intron homing to a DNA target site is RecA-independent and recognizes the intron binding site (IBS)1 and IBS3 regions, formed by the 5' TTGTT 3' consensus sequence located within the inverse core site of attC integrons. Our results also indicate that the process for S.ma.I2 intron mobilization involves a secondary structure provided by the folding of the complete attC site. Moreover, phylogenetic analysis of the class C GII introns showed a clear divergent clade formed by introns that insert within specific sites usually associated with lateral gene transfer.}, }
@article {pmid18442984, year = {2008}, author = {Ménard, A and Danchin, A and Dupouy, S and Mégraud, F and Lehours, P}, title = {A variable gene in a conserved region of the Helicobacter pylori genome: isotopic gene replacement or rapid evolution?.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {15}, number = {3}, pages = {163-168}, pmid = {18442984}, issn = {1340-2838}, mesh = {Base Sequence ; Chromosome Mapping ; *Conserved Sequence ; *Evolution, Molecular ; Gene Transfer, Horizontal/*physiology ; *Genetic Variation ; Genome, Bacterial ; Helicobacter pylori/*genetics ; Phylogeny ; Time Factors ; }, abstract = {The present study concerns the identification of a novel coding sequence in a region of the Helicobacter pylori genome, located between JHP1069/HP1141 and JHP1071/HP1143 according to the numbering of the J99 and 26,695 reference strains, respectively, and spanning three different coding DNA sequences (CDSs). The CDSs located at the centre of this locus were highly polymorphic, as determined by the analysis of 24 European isolates, 3 Asian, and 3 African isolates. Phylogenetic and molecular evolutionary analyses showed that the CDSs were not restricted to the geographical origin of the strains. Despite a very high variability observed in the deduced protein sequences, significant similarity was observed, always with the same protein families, i.e. ATPase and bacteriophage receptor/invasion proteins. Although this variability could be explained by isotopic gene replacement via horizontal transfer of a gene with the same function but coming from a variety of sources, it seems more likely that the very high sequence variation observed at this locus is the result of a strong selection pressure exerted on the corresponding gene product. The CDSs identified in the present study could be used as strain specific markers.}, }
@article {pmid18441063, year = {2008}, author = {Saavedra De Bast, M and Mine, N and Van Melderen, L}, title = {Chromosomal toxin-antitoxin systems may act as antiaddiction modules.}, journal = {Journal of bacteriology}, volume = {190}, number = {13}, pages = {4603-4609}, pmid = {18441063}, issn = {1098-5530}, mesh = {Antitoxins/*genetics ; Bacterial Toxins/*genetics ; Chromosomes, Bacterial/*genetics ; Escherichia coli/genetics ; Escherichia coli Proteins/genetics ; Open Reading Frames/genetics ; Plasmids/genetics ; }, abstract = {Toxin-antitoxin (TA) systems are widespread among bacterial chromosomes and mobile genetic elements. Although in plasmids TA systems have a clear role in their vertical inheritance by selectively killing plasmid-free daughter cells (postsegregational killing or addiction phenomenon), the physiological role of chromosomally encoded ones remains under debate. The assumption that chromosomally encoded TA systems are part of stress response networks and/or programmed cell death machinery has been called into question recently by the observation that none of the five canonical chromosomally encoded TA systems in the Escherichia coli chromosome seem to confer any selective advantage under stressful conditions (V. Tsilibaris, G. Maenhaut-Michel, N. Mine, and L. Van Melderen, J. Bacteriol. 189:6101-6108, 2007). Their prevalence in bacterial chromosomes indicates that they might have been acquired through horizontal gene transfer. Once integrated in chromosomes, they might in turn interfere with their homologues encoded by mobile genetic elements. In this work, we show that the chromosomally encoded Erwinia chrysanthemi ccd (control of cell death) (ccd(Ech)) system indeed protects the cell against postsegregational killing mediated by its F-plasmid ccd (ccd(F)) homologue. Moreover, competition experiments have shown that this system confers a fitness advantage under postsegregational conditions mediated by the ccd(F) system. We propose that ccd(Ech) acts as an antiaddiction module and, more generally, that the integration of TA systems in bacterial chromosomes could drive the evolution of plasmid-encoded ones and select toxins that are no longer recognized by the antiaddiction module.}, }
@article {pmid18440871, year = {2008}, author = {Bafana, A and Chakrabarti, T}, title = {Lateral gene transfer in phylogeny of azoreductase enzyme.}, journal = {Computational biology and chemistry}, volume = {32}, number = {3}, pages = {191-197}, doi = {10.1016/j.compbiolchem.2008.03.003}, pmid = {18440871}, issn = {1476-9271}, mesh = {Amino Acid Sequence ; Animals ; Binding Sites ; Computational Biology/methods ; Computer Simulation ; Databases, Protein ; Enterococcus faecalis/enzymology/genetics ; Escherichia coli/enzymology/genetics ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; NADH, NADPH Oxidoreductases/chemistry/*genetics ; Nitroreductases ; Nucleotides/chemistry ; Phylogeny ; }, abstract = {This paper attempts to reconstruct the phylogeny of azoreductase enzyme from different organisms and compare it with the small subunit rRNA-based phylogeny of the organisms. The two phylogenies were found to be incongruent, indicating several events of lateral transfer of azoreductase gene between phylogenetically diverse organisms. However, the phylogenetic analysis methods have several limitations and a single method may not give the true pattern. Hence, it is necessary to corroborate the results with other complementary analysis tools. We used several tools to test our hypothesis of lateral transfer and found that it was supported not only by the analysis of the whole sequences, but also by the conserved motifs detected in these sequences. There were ample evidences for lateral transfer of azoreductase gene among enteric bacteria. There were also indications that azoreductase probably evolved in prokaryotes and then it was laterally transferred to eukaryotes in multiple events, resulting in some sequence variation among eukaryotic azoreductases. Finally, profile HMMs and conserved motifs extracted from these azoreductase sequences were found to provide sensitive tools for identifying potential azoreductases from the database. The analysis techniques used in this study can be extended to other gene trees to verify their evolutionary histories.}, }
@article {pmid18439362, year = {2008}, author = {Ye, C and Bai, X and Zhang, J and Jing, H and Zheng, H and Du, H and Cui, Z and Zhang, S and Jin, D and Xu, Y and Xiong, Y and Zhao, A and Luo, X and Sun, Q and Gottschalk, M and Xu, J}, title = {Spread of Streptococcus suis sequence type 7, China.}, journal = {Emerging infectious diseases}, volume = {14}, number = {5}, pages = {787-791}, pmid = {18439362}, issn = {1080-6059}, mesh = {Animals ; Bacterial Proteins/genetics ; China/epidemiology ; Conjugation, Genetic ; DNA Transposable Elements ; *Disease Outbreaks ; Gene Transfer, Horizontal ; Humans ; Phylogeny ; Polymerase Chain Reaction ; Streptococcal Infections/epidemiology/microbiology/*transmission ; Streptococcus suis/*classification/*genetics/isolation &amp; purification ; Swine ; Swine Diseases/epidemiology/microbiology ; Tetracycline Resistance/genetics ; }, abstract = {Streptococcus suis sequence type (ST) 7 has been spreading throughout China. To determine events associated with its emergence, we tested 114 isolates. In all 106 ST7 strains responsible for human outbreaks and sporadic infections, the tetracycline-resistance gene, tetM, was detected on the conjugative transposon Tn916. Horizontal transmission of tetM is suspected.}, }
@article {pmid18439288, year = {2008}, author = {Tumapa, S and Holden, MT and Vesaratchavest, M and Wuthiekanun, V and Limmathurotsakul, D and Chierakul, W and Feil, EJ and Currie, BJ and Day, NP and Nierman, WC and Peacock, SJ}, title = {Burkholderia pseudomallei genome plasticity associated with genomic island variation.}, journal = {BMC genomics}, volume = {9}, number = {}, pages = {190}, pmid = {18439288}, issn = {1471-2164}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Burkholderia pseudomallei/*genetics ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genomic Islands ; Humans ; Melioidosis/microbiology ; Molecular Sequence Data ; Sequence Analysis, DNA ; Soil Microbiology ; }, abstract = {BACKGROUND: Burkholderia pseudomallei is a soil-dwelling saprophyte and the cause of melioidosis. Horizontal gene transfer contributes to the genetic diversity of this pathogen and may be an important determinant of virulence potential. The genome contains genomic island (GI) regions that encode a broad array of functions. Although there is some evidence for the variable distribution of genomic islands in B. pseudomallei isolates, little is known about the extent of variation between related strains or their association with disease or environmental survival.<br><br>RESULTS: Five islands from B. pseudomallei strain K96243 were chosen as representatives of different types of genomic islands present in this strain, and their presence investigated in other B. pseudomallei. In silico analysis of 10 B. pseudomallei genome sequences provided evidence for the variable presence of these regions, together with micro-evolutionary changes that generate GI diversity. The diversity of GIs in 186 isolates from NE Thailand (83 environmental and 103 clinical isolates) was investigated using multiplex PCR screening. The proportion of all isolates positive by PCR ranged from 12% for a prophage-like island (GI 9), to 76% for a metabolic island (GI 16). The presence of each of the five GIs did not differ between environmental and disease-associated isolates (p > 0.05 for all five islands). The cumulative number of GIs per isolate for the 186 isolates ranged from 0 to 5 (median 2, IQR 1 to 3). The distribution of cumulative GI number did not differ between environmental and disease-associated isolates (p = 0.27). The presence of GIs was defined for the three largest clones in this collection (each defined as a single sequence type, ST, by multilocus sequence typing); these were ST 70 (n = 15 isolates), ST 54 (n = 11), and ST 167 (n = 9). The rapid loss and/or acquisition of gene islands was observed within individual clones. Comparisons were drawn between isolates obtained from the environment and from patients with melioidosis in order to examine the role of genomic islands in virulence and clinical associations. There was no reproducible association between the individual or cumulative presence of five GIs and a range of clinical features in 103 patients with melioidosis.<br><br>CONCLUSION: Horizontal gene transfer of mobile genetic elements can rapidly alter the gene repertoire of B. pseudomallei. This study confirms the utility of a range of approaches in defining the presence and significance of genomic variation in natural populations of B. pseudomallei.}, }
@article {pmid18436036, year = {2008}, author = {Sedgley, CM and Lee, EH and Martin, MJ and Flannagan, SE}, title = {Antibiotic resistance gene transfer between Streptococcus gordonii and Enterococcus faecalis in root canals of teeth ex vivo.}, journal = {Journal of endodontics}, volume = {34}, number = {5}, pages = {570-574}, doi = {10.1016/j.joen.2008.02.014}, pmid = {18436036}, issn = {1878-3554}, mesh = {Dental Pulp Cavity/*microbiology ; Drug Resistance, Bacterial/*genetics ; Enterococcus faecalis/*genetics ; Erythromycin/*pharmacology ; Gene Transfer, Horizontal/*physiology ; Humans ; Microscopy, Electron, Scanning ; R Factors ; Streptococcus gordonii/*genetics ; }, abstract = {Multiple bacterial species coexisting in infected root canals might interact, but evidence for interspecies gene transfer is lacking. This study tested the hypothesis that horizontal exchange of antibiotic resistance can occur between different bacterial species in root canals. Transfer of the conjugative plasmid pAM81 carrying erythromycin resistance between 2 endodontic infection-associated species, Streptococcus gordonii and Enterococcus faecalis, was investigated in an ex vivo tooth model. Equal numbers of each species (one with pAM81 and the other plasmid-free) were combined in prepared root canals of sterilized teeth and incubated at 37 degrees C. At 24 and 72 hours, bidirectional interspecies antibiotic resistance gene transfer was evident in microorganisms recovered from teeth; average transfer frequencies from S. gordonii to E. faecalis were 10(-3) transconjugants per donor and from E. faecalis to S. gordonii were 10(-6) and 10(-7) transconjugants per donor at 24 and 72 hours, respectively. Microbial accumulations were observed on root canal walls with scanning electron microscopy. Horizontal genetic exchange in endodontic infections might facilitate adoption of an optimal genetic profile for survival.}, }
@article {pmid18434098, year = {2008}, author = {Fuentes, JA and Villagra, N and Castillo-Ruiz, M and Mora, GC}, title = {The Salmonella Typhi hlyE gene plays a role in invasion of cultured epithelial cells and its functional transfer to S. Typhimurium promotes deep organ infection in mice.}, journal = {Research in microbiology}, volume = {159}, number = {4}, pages = {279-287}, doi = {10.1016/j.resmic.2008.02.006}, pmid = {18434098}, issn = {0923-2508}, mesh = {Animals ; Cell Membrane Permeability ; Cells, Cultured ; Epithelial Cells/*microbiology ; *Gene Transfer, Horizontal ; Genomic Islands ; Hemolysin Proteins/genetics/*metabolism ; Humans ; Mice ; Salmonella Infections/*microbiology ; Salmonella enterica/genetics/metabolism ; Salmonella typhi/genetics/metabolism/*pathogenicity/virology ; Salmonella typhimurium/genetics/metabolism/*pathogenicity/virology ; Virulence Factors/genetics/metabolism ; }, abstract = {Comparison of genome sequences of Salmonella enterica serovars Typhi and Typhimurium reveals that S. Typhi has a small 2.3kb genomic island missing in S. Typhimurium, designated Salmonella pathogenicity island 18 (SPI-18), which includes two potential genes. One of these, hlyE, encodes a hemolysin related to the Escherichia coli K12 HlyE hemolysin. PCR assays show that SPI-18 is present in S. Typhi and in many other, but not all, serovars of S. enterica subsp. enterica belonging to the SARB collection. HlyE activity cannot be detected in S. Typhi by means of standard plate assays. Nevertheless, we were able to reveal this activity upon lysis of bacterial cells with phages, in the presence of ampicillin, and in a ompA genetic background, conditions that compromise the integrity of the bacterial envelope. Almost all serovars of the SARB collection shown to cause systemic infections in humans have SPI-18 and hlyE and express an active hemolysin revealed upon bacterial envelope destabilization. S. Typhi hlyE mutants are impaired in invasion of human epithelial cells in vitro, and its heterologous expression in S. Typhimurium improves the colonization of deep organs in mice, demonstrating that the HlyE hemolysin is a new virulence determinant.}, }
@article {pmid18433492, year = {2008}, author = {Gross, J and Meurer, J and Bhattacharya, D}, title = {Evidence of a chimeric genome in the cyanobacterial ancestor of plastids.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {117}, pmid = {18433492}, issn = {1471-2148}, mesh = {Chimera ; Cyanobacteria/*genetics/metabolism ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genome, Plastid ; Markov Chains ; Monte Carlo Method ; Photosystem I Protein Complex/genetics ; Phylogeny ; Plastids/*genetics ; Rhodophyta/*genetics/metabolism ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT) is a vexing fact of life for microbial phylogeneticists. Given the substantial rates of HGT observed in modern-day bacterial chromosomes, it is envisaged that ancient prokaryotic genomes must have been similarly chimeric. But where can one find an ancient prokaryotic genome that has maintained its ancestral condition to address this issue? An excellent candidate is the cyanobacterial endosymbiont that was harnessed over a billion years ago by a heterotrophic protist, giving rise to the plastid. Genetic remnants of the endosymbiont are still preserved in plastids as a highly reduced chromosome encoding 54 - 264 genes. These data provide an ideal target to assess genome chimericism in an ancient cyanobacterial lineage.<br><br>RESULTS: Here we demonstrate that the origin of the plastid-encoded gene cluster for menaquinone/phylloquinone biosynthesis in the extremophilic red algae Cyanidiales contradicts a cyanobacterial genealogy. These genes are relics of an ancestral cluster related to homologs in Chlorobi/Gammaproteobacteria that we hypothesize was established by HGT in the progenitor of plastids, thus providing a 'footprint' of genome chimericism in ancient cyanobacteria. In addition to menB, four components of the original gene cluster (menF, menD, menC, and menH) are now encoded in the nuclear genome of the majority of non-Cyanidiales algae and plants as the unique tetra-gene fusion named PHYLLO. These genes are monophyletic in Plantae and chromalveolates, indicating that loci introduced by HGT into the ancestral cyanobacterium were moved over time into the host nucleus.<br><br>CONCLUSION: Our study provides unambiguous evidence for the existence of genome chimericism in ancient cyanobacteria. In addition we show genes that originated via HGT in the cyanobacterial ancestor of the plastid made their way to the host nucleus via endosymbiotic gene transfer (EGT).}, }
@article {pmid18431505, year = {2008}, author = {Bryan, MJ and Burroughs, NJ and Spence, EM and Clokie, MR and Mann, NH and Bryan, SJ}, title = {Evidence for the intense exchange of MazG in marine cyanophages by horizontal gene transfer.}, journal = {PloS one}, volume = {3}, number = {4}, pages = {e2048}, pmid = {18431505}, issn = {1932-6203}, mesh = {Bacteriophages/*genetics/isolation &amp; purification ; Base Sequence ; Cyanobacteria/genetics/*virology ; *Gene Transfer, Horizontal ; Genes, Viral ; Geography ; Molecular Sequence Data ; Phylogeny ; *Seawater ; Sequence Alignment ; Viral Proteins/*genetics ; }, abstract = {BACKGROUND: S-PM2 is a phage capable of infecting strains of unicellular cyanobacteria belonging to the genus Synechococcus. S-PM2, like other myoviruses infecting marine cyanobacteria, encodes a number of bacterial-like genes. Amongst these genes is one encoding a MazG homologue that is hypothesized to be involved in the adaption of the infected host for production of progeny phage.<br><br>This study focuses on establishing the occurrence of mazG homologues in other cyanophages isolated from different oceanic locations. Degenerate PCR primers were designed using the mazG gene of S-PM2. The mazG gene was found to be widely distributed and highly conserved among Synechococcus myoviruses and podoviruses from diverse oceanic provinces.<br><br>CONCLUSIONS/SIGNIFICANCE: This study provides evidence of a globally connected cyanophage gene pool, the cyanophage mazG gene having a small effective population size indicative of rapid lateral gene transfer despite being present in a substantial fraction of cyanophage. The Prochlorococcus and Synechococcus phage mazG genes do not cluster with the host mazG gene, suggesting that their primary hosts are not the source of the mazG gene.}, }
@article {pmid18431403, year = {2008}, author = {Loreto, EL and Carareto, CM and Capy, P}, title = {Revisiting horizontal transfer of transposable elements in Drosophila.}, journal = {Heredity}, volume = {100}, number = {6}, pages = {545-554}, doi = {10.1038/sj.hdy.6801094}, pmid = {18431403}, issn = {1365-2540}, mesh = {Animals ; DNA Transposable Elements/*genetics ; Drosophila/*genetics ; Drosophila melanogaster/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Phylogeny ; Retroelements/genetics ; Sequence Analysis, DNA ; }, abstract = {Horizontal transfer (HT), defined as the transfer of genetic material between species, is considered to be an essential step in the 'life cycle' of transposable elements. We present a broad overview of suspected cases of HT of transposable elements in Drosophila. Hundred-one putative events of HT have been proposed in Drosophila for 21 different elements (5.0% refer to non-long terminal repeat (LTR) retrotransposons, 42.6% to LTR retrotransposons and 52.4% to DNA transposons). We discuss the methods used to infer HT, their limits and the putative vectors of transposable elements. We outline all the alternative hypotheses and ask how we can be almost certain that phylogenetic inconsistencies are due to HT.}, }
@article {pmid18422620, year = {2008}, author = {Chen, WF and Guan, SH and Zhao, CT and Yan, XR and Man, CX and Wang, ET and Chen, WX}, title = {Different Mesorhizobium species associated with Caragana carry similar symbiotic genes and have common host ranges.}, journal = {FEMS microbiology letters}, volume = {283}, number = {2}, pages = {203-209}, doi = {10.1111/j.1574-6968.2008.01167.x}, pmid = {18422620}, issn = {0378-1097}, mesh = {Alphaproteobacteria/*classification/*genetics/isolation &amp; purification/physiology ; Bacterial Proteins/genetics ; Caragana/*microbiology ; DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/genetics ; Electrophoresis, Polyacrylamide Gel ; *Genes, Bacterial ; Molecular Sequence Data ; N-Acetylglucosaminyltransferases/genetics ; Oxidoreductases/genetics ; Proteome/analysis ; RNA, Ribosomal, 16S/genetics ; Rec A Recombinases/genetics ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; *Symbiosis ; }, abstract = {Fourteen strains representing 11 Caragana-nodulating Mesorhizobium genomic species were identified as representing Mesorhizobium amorphae, Mesorhizobium huakuii, Mesorhizobium septentrionale and groups related to Mesorhizobium plurifarium, Mesorhizobium temperatum, Mesorhizobium tianshanense and Mesorhizobium mediterraneum by sequencing of the 16S rRNA gene, 16S-23S internal transcribed spacer, partial housekeeping recA gene, and previously performed sodium dodecyl sulfate polyacrylamide gel electrophoresis of proteins and BOX-PCR fingerprinting. Despite their different taxonomic affiliation, highly similar symbiotic genes (>93% similarity for nodC and >91.8% similarity for nifH) were found among the Caragana strains and the three type strains for M. tianshanense, M. temperatum and M. septentrionale. Cross nodulation tests revealed that each of these 14 Caragana mesorhizobia and the three type strains mentioned above could effectively infect each of their original host plants, Caragana microphylla, Glycyrrhiza (host for M. tianshanense type strain) and Astragalus adsurgens (host for M. temperatum and M. septentrionale type strains). These results provide evidence that different Mesorhizobium species can nodulate with Caragana, and they have similar symbiotic genes (probably acquired by a phenomenon of lateral gene transfer) and common host ranges.}, }
@article {pmid18420414, year = {2008}, author = {Bapteste, E and Boucher, Y}, title = {Lateral gene transfer challenges principles of microbial systematics.}, journal = {Trends in microbiology}, volume = {16}, number = {5}, pages = {200-207}, doi = {10.1016/j.tim.2008.02.005}, pmid = {18420414}, issn = {0966-842X}, mesh = {Bacteria/*classification/*genetics ; Classification/methods ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Phylogeny ; }, abstract = {Evolutionists strive to learn about the natural historical process that gave rise to various taxa, while also attempting to classify them efficiently and make generalizations about them. The quantitative importance of lateral gene transfer inferred from genomic data, although well acknowledged by microbiologists, is in conflict with the conceptual foundations of the traditional phylogenetic system erected to achieve these goals. To provide a true account of microbial evolution, we suggest developing an alternative conception of natural groups and introduce a new notion--the composite evolutionary unit. Furthermore, we argue that a comprehensive database containing overlapping taxonomical groups would constitute a step forward regarding the classification of microbes in the presence of lateral gene transfer.}, }
@article {pmid18420358, year = {2009}, author = {Takishita, K and Inagaki, Y}, title = {Eukaryotic origin of glyceraldehyde-3-phosphate dehydrogenase genes in Clostridium thermocellum and Clostridium cellulolyticum genomes and putative fates of the exogenous gene in the subsequent genome evolution.}, journal = {Gene}, volume = {441}, number = {1-2}, pages = {22-27}, doi = {10.1016/j.gene.2008.03.001}, pmid = {18420358}, issn = {1879-0038}, mesh = {Archaea/enzymology ; Clostridium cellulolyticum/*genetics ; Clostridium thermocellum/*genetics ; Eukaryotic Cells/enzymology ; *Evolution, Molecular ; Genome, Bacterial ; Glyceraldehyde-3-Phosphate Dehydrogenases/genetics ; *Phylogeny ; }, abstract = {Although lateral gene transfer (LGT) events have been frequently documented in the evolution of glyceraldehyde-3-phosphate dehydrogenase (GAPDH), no eukaryote-to-prokaryote transfer has been reported so far. Here we describe the first case of the GAPDH gene transfer from a eukaryote to a subset of Clostridium species (Bacteria, Firmicutes). A series of phylogenetic analyses of GAPDH homologues revealed that Clostridium thermocellum and Clostridium cellulolyticum homologues have the evolutionary affinity to the eukaryotic homologues, rather than to those of bacterial species closely related to the two Clostridium species in the organismal phylogeny. These results suggest that the GAPDH genes in the two Clostridium species are of eukaryotic origin, which is the first reported case of eukaryote-to-bacterium GAPDH gene transfer. Since a previously published 16S ribosomal DNA phylogeny and our GAPDH phylogeny commonly suggest an intimate evolutionary relationship between C. thermocellum and C. cellulolyticum, a common ancestor of the two species likely acquired the eukaryotic GAPDH gene. In the C. cellulolyticum genome, the exogenous GAPDH gene was physically separated from other glycolytic genes, suggesting that this gene organization was likely achieved by a random insertion of the laterally transferred gene. On the other hand, in the C. thermocellum genome, the laterally transferred GAPDH gene clusters with other bacterial glycolytic genes. We discuss possible scenarios for the evolutionarily chimeric glycolytic gene cluster in the C. thermocellum genome.}, }
@article {pmid18420329, year = {2009}, author = {Kelly, BG and Vespermann, A and Bolton, DJ}, title = {The role of horizontal gene transfer in the evolution of selected foodborne bacterial pathogens.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {47}, number = {5}, pages = {951-968}, doi = {10.1016/j.fct.2008.02.006}, pmid = {18420329}, issn = {1873-6351}, mesh = {Bacteria/*genetics/pathogenicity ; Bacterial Infections/*genetics/*transmission ; Escherichia coli O157/genetics/pathogenicity ; Evolution, Molecular ; Food Microbiology ; *Gene Transfer, Horizontal ; Host-Pathogen Interactions/*physiology ; Listeria monocytogenes/genetics/pathogenicity ; Salmonella/genetics/pathogenicity ; Staphylococcus aureus/genetics/pathogenicity ; }, abstract = {Bacteria use various ways to transfer genetic information. These methods include: conjugation, which requires cell to cell contact between cells, transduction, which is bacteriophage-facilitated transfer of genetic information, and transformation, which is the uptake of free DNA from the environment. Usually the genes to be transferred lie on mobile genetic elements, pieces of DNA that encode proteins important to facilitate movement of DNA within or between genomes. This review highlights the transfer methods and the role of the assorted mobile genetic elements in the evolution of four foodborne bacterial pathogens: Escherichia coli O157:H7, Salmonella, Staphylococcus aureus and Listeria monocytogenes.}, }
@article {pmid18420327, year = {2009}, author = {Kelly, BG and Vespermann, A and Bolton, DJ}, title = {Horizontal gene transfer of virulence determinants in selected bacterial foodborne pathogens.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {47}, number = {5}, pages = {969-977}, doi = {10.1016/j.fct.2008.02.007}, pmid = {18420327}, issn = {1873-6351}, mesh = {Animals ; Bacteria/*genetics/pathogenicity ; Conjugation, Genetic/genetics ; Escherichia coli/genetics/pathogenicity ; *Food Microbiology ; Food Supply ; *Gene Transfer, Horizontal ; Listeria monocytogenes/genetics/pathogenicity ; Mice ; Salmonella/genetics/pathogenicity ; Staphylococcus aureus/genetics/pathogenicity ; Transduction, Genetic ; Transformation, Bacterial/genetics ; Virulence Factors/*genetics ; }, abstract = {This review describes horizontal gene transfer from a historical point of view, with descriptions of the first instances of the different bacterial transfer mechanisms: conjugation, transduction and transformation, as well as examples of some of the early acknowledged transfer events. Gene transfer from four selected foodborne pathogens: Escherichia coli, Listeria monocytogenes,Staphylococcus aureus and Salmonella are highlighted.}, }
@article {pmid18419273, year = {2007}, author = {Keene, JD}, title = {Biological clocks and the coordination theory of RNA operons and regulons.}, journal = {Cold Spring Harbor symposia on quantitative biology}, volume = {72}, number = {}, pages = {157-165}, doi = {10.1101/sqb.2007.72.013}, pmid = {18419273}, issn = {0091-7451}, mesh = {Animals ; Circadian Rhythm/*genetics/physiology ; Gene Expression Regulation ; Gene Transfer, Horizontal ; Genetic Techniques ; MicroRNAs/genetics/metabolism ; Models, Biological ; Models, Genetic ; *Operon ; RNA Processing, Post-Transcriptional ; RNA, Messenger/genetics/metabolism ; RNA-Binding Proteins/genetics/metabolism ; *Regulon ; }, abstract = {One of the regulatory models of circadian rhythms involves the oscillation of transcription and translation. Although transcription factors have been widely examined during circadian processes, posttranscriptional mechanisms are less well-studied. Several laboratories have used microarrays to detect changes in mRNA expression throughout the circadian cycle and have found that mRNAs encoding the RNA-binding proteins (RBPs) nocturnin and butyrate response factor (BRF1) undergo rhythmic changes. Nocturnin is a deadenylation enzyme that removes poly(A) from the 3' ends of mRNAs, whereas BRF1 destabilizes mRNAs encoding early response gene (ERG) transcripts that contain AU-rich sequences in their 3'-untranslated regions (UTRs). Moroni and coworkers proposed that BRF1 functions as an oscillating posttranscriptional RNA operon (PTRO) that diurnally degrades ERG transcripts in peripheral organs (Keene and Tenenbaum 2002; Benjamin et al. 2006). The PTRO model posits that mRNAs can be members of one or more discrete functionally related subsets of mRNAs as determined by cis elements in mRNA and trans-acting RBPs or microRNAs that collectively recognize these cis elements (Keene 2007). This chapter describes the basis of posttranscriptional coordination by RNA operons and their potential for horizontal transfer among cells and discusses the potential for RBPs and microRNAs to participate in coordinating circadian rhythms and other biological clocks.}, }
@article {pmid18415976, year = {2007}, author = {Lashin, SA and Suslov, VV and Kolchanov, NA and Matushkin, YG}, title = {Simulation of coevolution in community by using the "Evolutionary Constructor" program.}, journal = {In silico biology}, volume = {7}, number = {3}, pages = {261-275}, pmid = {18415976}, issn = {1386-6338}, mesh = {Animals ; *Biological Evolution ; Fossils ; Genotype ; *Models, Biological ; *Models, Genetic ; Mutation ; Paleontology ; Software ; }, abstract = {An original modeling tool called Evolutionary Constructor has been proposed and described. Evolutionary Constructor combines the advantages of both generalized and portrait modeling and, additionally, provides an option to modify a current model's structure. The evolution of communities comprising atrophic ring-like network with the horizontal transfer of metabolism genes occurring among the communities has been modeled and presented. It has been demonstrated that a prolonged increase in the fitness of any single population that forms part of that trophic ring-like network of antagonistic communities will eventually lead that system to becoming absolutely dependent on environmental fluctuations. This result challenges the intuitive attitudes that the higher population fitness, the more stability is given to that population. Modeling of a system comprised by symbiotic communities has revealed that horizontal transfer confers a selective advantage not only on the acceptor population (which is up to expectations) but also on the donor population. It has therefore been demonstrated that horizontal transfer can be preserved by selection along evolution even without "selfish genes". Evolutionary Constructor can handle any phenotypic trait that is controlled genetically, epigenetically, etc., which extends the applicability of this tool to various processes of information transduction among populations, provided that these processes resemble horizontal gene transfer.}, }
@article {pmid18412960, year = {2008}, author = {Oren, A}, title = {Microbial life at high salt concentrations: phylogenetic and metabolic diversity.}, journal = {Saline systems}, volume = {4}, number = {}, pages = {2}, pmid = {18412960}, issn = {1746-1448}, abstract = {Halophiles are found in all three domains of life. Within the Bacteria we know halophiles within the phyla Cyanobacteria, Proteobacteria, Firmicutes, Actinobacteria, Spirochaetes, and Bacteroidetes. Within the Archaea the most salt-requiring microorganisms are found in the class Halobacteria. Halobacterium and most of its relatives require over 100-150 g/l salt for growth and structural stability. Also within the order Methanococci we encounter halophilic species. Halophiles and non-halophilic relatives are often found together in the phylogenetic tree, and many genera, families and orders have representatives with greatly different salt requirement and tolerance. A few phylogenetically coherent groups consist of halophiles only: the order Halobacteriales, family Halobacteriaceae (Euryarchaeota) and the anaerobic fermentative bacteria of the order Halanaerobiales (Firmicutes). The family Halomonadaceae (Gammaproteobacteria) almost exclusively contains halophiles. Halophilic microorganisms use two strategies to balance their cytoplasm osmotically with their medium. The first involves accumulation of molar concentrations of KCl. This strategy requires adaptation of the intracellular enzymatic machinery, as proteins should maintain their proper conformation and activity at near-saturating salt concentrations. The proteome of such organisms is highly acidic, and most proteins denature when suspended in low salt. Such microorganisms generally cannot survive in low salt media. The second strategy is to exclude salt from the cytoplasm and to synthesize and/or accumulate organic 'compatible' solutes that do not interfere with enzymatic activity. Few adaptations of the cells' proteome are needed, and organisms using the 'organic-solutes-in strategy' often adapt to a surprisingly broad salt concentration range. Most halophilic Bacteria, but also the halophilic methanogenic Archaea use such organic solutes. A variety of such solutes are known, including glycine betaine, ectoine and other amino acid derivatives, sugars and sugar alcohols. The 'high-salt-in strategy' is not limited to the Halobacteriaceae. The Halanaerobiales (Firmicutes) also accumulate salt rather than organic solutes. A third, phylogenetically unrelated organism accumulates KCl: the red extremely halophilic Salinibacter (Bacteroidetes), recently isolated from saltern crystallizer brines. Analysis of its genome showed many points of resemblance with the Halobacteriaceae, probably resulting from extensive horizontal gene transfer. The case of Salinibacter shows that more unusual types of halophiles may be waiting to be discovered.}, }
@article {pmid18412551, year = {2008}, author = {Dupont, CL and Neupane, K and Shearer, J and Palenik, B}, title = {Diversity, function and evolution of genes coding for putative Ni-containing superoxide dismutases.}, journal = {Environmental microbiology}, volume = {10}, number = {7}, pages = {1831-1843}, doi = {10.1111/j.1462-2920.2008.01604.x}, pmid = {18412551}, issn = {1462-2920}, mesh = {Computational Biology/*methods ; Databases, Genetic ; *Evolution, Molecular ; Marine Biology ; Molecular Sequence Data ; Nickel/chemistry/*metabolism ; Streptomyces/*enzymology/genetics ; Structural Homology, Protein ; Superoxide Dismutase/chemistry/*classification/genetics/metabolism ; }, abstract = {We examined the phylogenetic distribution, functionality and evolution of the sodN gene family, which has been shown to code for a unique Ni-containing isoform of superoxide dismutase (Ni-SOD) in Streptomyces. Many of the putative sodN sequences retrieved from public domain genomic and metagenomic databases are quite divergent from structurally and functionally characterized Ni-SOD. Structural bioinformatics studies verified that the divergent members of the sodN protein family code for similar three-dimensional structures and identified evolutionarily conserved amino acid residues. Structural and biochemical studies of the N-terminus 'Ni-hook' motif coded for by the putative sodN sequences confirmed both Ni (II) ligating and superoxide dismutase activity. Both environmental and organismal genomes expanded the previously noted phylogenetic distribution of sodN, and the sequences form four well-separated clusters, with multiple subclusters. The phylogenetic distribution of sodN suggests that the gene has been acquired via horizontal gene transfer by numerous organisms of diverse phylogenetic background, including both Eukaryotes and Prokaryotes. The presence of sodN correlates with the genomic absence of the gene coding for Fe-SOD, a structurally and evolutionarily distinct isoform of SOD. Given the low levels of Fe found in the marine environment from where many sequences were attained, we suggest that the replacement of Fe-SOD with Ni-SOD may be an evolutionary adaptation to reduce iron requirements.}, }
@article {pmid18411202, year = {2008}, author = {Grant, JR and Stothard, P}, title = {The CGView Server: a comparative genomics tool for circular genomes.}, journal = {Nucleic acids research}, volume = {36}, number = {Web Server issue}, pages = {W181-4}, pmid = {18411202}, issn = {1362-4962}, mesh = {Chromosome Mapping ; Computer Graphics ; DNA, Circular/chemistry ; *Genome, Bacterial ; *Genome, Chloroplast ; *Genome, Mitochondrial ; Genomics ; Internet ; Plasmids/*genetics ; Sequence Alignment ; *Software ; }, abstract = {The CGView Server generates graphical maps of circular genomes that show sequence features, base composition plots, analysis results and sequence similarity plots. Sequences can be supplied in raw, FASTA, GenBank or EMBL format. Additional feature or analysis information can be submitted in the form of GFF (General Feature Format) files. The server uses BLAST to compare the primary sequence to up to three comparison genomes or sequence sets. The BLAST results and feature information are converted to a graphical map showing the entire sequence, or an expanded and more detailed view of a region of interest. Several options are included to control which types of features are displayed and how the features are drawn. The CGView Server can be used to visualize features associated with any bacterial, plasmid, chloroplast or mitochondrial genome, and can aid in the identification of conserved genome segments, instances of horizontal gene transfer, and differences in gene copy number. Because a collection of sequences can be used in place of a comparison genome, maps can also be used to visualize regions of a known genome covered by newly obtained sequence reads. The CGView Server can be accessed at http://stothard.afns.ualberta.ca/cgview_server/}, }
@article {pmid18410603, year = {2008}, author = {Dan, YY and Yeoh, GC}, title = {Liver stem cells: a scientific and clinical perspective.}, journal = {Journal of gastroenterology and hepatology}, volume = {23}, number = {5}, pages = {687-698}, doi = {10.1111/j.1440-1746.2008.05383.x}, pmid = {18410603}, issn = {1440-1746}, mesh = {Animals ; Humans ; Liver Diseases/*therapy ; Stem Cell Transplantation ; *Stem Cells ; Terminology as Topic ; }, abstract = {The promise of liver stem cells lie in their potential to provide a continual and readily available source of liver cells that can be used for gene therapy, cellular transplant, bioartificial liver-assisted devices, drug toxicology testing and use as an in vitro model to understand the developmental biology of the liver. Both the rodent and human embryonic stem cell, bone marrow hematopoietic stem cell, mesenchymal stem cell, umbilical cord blood cell, fetal liver progenitor cell, adult liver progenitor cell as well as the mature hepatocyte have been reported to be capable of self-renewal, giving rise to daughter hepatocytes both in vivo and in vitro. These cells can repopulate livers in animal models of liver injury and seemingly improve liver function. However, significant challenges still exist before these cells can be used in humans. These include lack of consensus in immunophenotype of liver progenitor cells, uncertainty of the physiological role of reported candidate stem/progenitor cell, practicality in obtaining sufficient quantity of cells for clinical use and concerns over ethics, long-term efficacy and safety. Current molecular techniques of stem cell identification are confounded by cell fusion, horizontal gene transfer, incomplete differentiation and fetal microchimerism. Reports of stem cell transplantation and phase 1 trials of bone marrow transplantation in humans for liver diseases are exciting but require more robust verification. We review the evidence for various candidate stem cells, human clinical trials reported to date and highlight the challenges facing clinicians in their quest to use liver stem cells to save lives.}, }
@article {pmid18409383, year = {2008}, author = {Provorov, NA and Vorob'ev, NI and Andronov, EE}, title = {[Macro- and microevolution of bacteria in symbiotic systems].}, journal = {Genetika}, volume = {44}, number = {1}, pages = {12-28}, pmid = {18409383}, issn = {0016-6758}, mesh = {Bacteria/*genetics/metabolism ; *Bacterial Physiological Phenomena ; *Evolution, Molecular ; Genetic Drift ; Genome, Bacterial/physiology ; Genome, Plant/physiology ; *Plant Physiological Phenomena ; Plants/*genetics/metabolism ; Selection, Genetic ; Symbiosis/*physiology ; }, abstract = {Using the examples of diverse interactions among prokaryotes and eukaryotes, the relationships between molecular and population mechanisms of evolution of symbiotic bacteria are addressed. Their circulation in host-environment systems activates microevolutionary factors that direct combinative or reductive genome evolution in facultative, ecologically obligatory, and genetically obligatory symbioses. Due to intense systemic intra-genome rearrangements and horizontal gene transfer, two types of gene systems evolve in these bacteria: (1) controlling the pathogenesis-like processes of host recognition and penetration and (2) responsible for mutualistic interactions that are related to nitrogen fixation and its transfer to the host. The evolution of gene systems of type 1 is directed by individual (Darwinian, frequency-dependent) selection, which is responsible for gene-for-gene interactions between the partners. In the evolution of the type 2 systems, group (interdeme, kin) selection plays the key role, being responsible for the development of bacterial traits beneficial for the host. Using the legume--rhizobia symbiosis as an example, it is shown that evolution of mutualism can be described in terms of biological altruism, whose regularities are common for intraspecific and interspecific relationships. Macroevolutionary rearrangements of bacterial genomes result from the structural changes in their populations, wherein various selection modes are combined with stochastic processes (genetic drift, population waves) induced in the symbiotic systems.}, }
@article {pmid18408155, year = {2008}, author = {Alcaraz, LD and Olmedo, G and Bonilla, G and Cerritos, R and Hernández, G and Cruz, A and Ramírez, E and Putonti, C and Jiménez, B and Martínez, E and López, V and Arvizu, JL and Ayala, F and Razo, F and Caballero, J and Siefert, J and Eguiarte, L and Vielle, JP and Martínez, O and Souza, V and Herrera-Estrella, A and Herrera-Estrella, L}, title = {The genome of Bacillus coahuilensis reveals adaptations essential for survival in the relic of an ancient marine environment.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {15}, pages = {5803-5808}, pmid = {18408155}, issn = {1091-6490}, mesh = {Adaptation, Physiological/*genetics ; Bacillus/*genetics ; Base Sequence ; *Biological Evolution ; Environment ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; Light ; Molecular Sequence Data ; Phosphorus/metabolism ; *Seawater ; }, abstract = {The Cuatro Ciénegas Basin (CCB) in the central part of the Chihuahan desert (Coahuila, Mexico) hosts a wide diversity of microorganisms contained within springs thought to be geomorphological relics of an ancient sea. A major question remaining to be answered is whether bacteria from CCB are ancient marine bacteria that adapted to an oligotrophic system poor in NaCl, rich in sulfates, and with extremely low phosphorus levels (<0.3 microM). Here, we report the complete genome sequence of Bacillus coahuilensis, a sporulating bacterium isolated from the water column of a desiccation lagoon in CCB. At 3.35 Megabases this is the smallest genome sequenced to date of a Bacillus species and provides insights into the origin, evolution, and adaptation of B. coahuilensis to the CCB environment. We propose that the size and complexity of the B. coahuilensis genome reflects the adaptation of an ancient marine bacterium to a novel environment, providing support to a "marine isolation origin hypothesis" that is consistent with the geology of CCB. This genomic adaptation includes the acquisition through horizontal gene transfer of genes involved in phosphorous utilization efficiency and adaptation to high-light environments. The B. coahuilensis genome sequence also revealed important ecological features of the bacterial community in CCB and offers opportunities for a unique glimpse of a microbe-dominated world last seen in the Precambrian.}, }
@article {pmid18408034, year = {2008}, author = {Takarada, H and Sekine, M and Kosugi, H and Matsuo, Y and Fujisawa, T and Omata, S and Kishi, E and Shimizu, A and Tsukatani, N and Tanikawa, S and Fujita, N and Harayama, S}, title = {Complete genome sequence of the soil actinomycete Kocuria rhizophila.}, journal = {Journal of bacteriology}, volume = {190}, number = {12}, pages = {4139-4146}, pmid = {18408034}, issn = {1098-5530}, mesh = {DNA, Bacterial/chemistry/genetics ; *Genome, Bacterial ; Micrococcaceae/classification/*genetics ; Models, Biological ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {The soil actinomycete Kocuria rhizophila belongs to the suborder Micrococcineae, a divergent bacterial group for which only a limited amount of genomic information is currently available. K. rhizophila is also important in industrial applications; e.g., it is commonly used as a standard quality control strain for antimicrobial susceptibility testing. Sequencing and annotation of the genome of K. rhizophila DC2201 (NBRC 103217) revealed a single circular chromosome (2,697,540 bp; G+C content of 71.16%) containing 2,357 predicted protein-coding genes. Most of the predicted proteins (87.7%) were orthologous to actinobacterial proteins, and the genome showed fairly good conservation of synteny with taxonomically related actinobacterial genomes. On the other hand, the genome seems to encode much smaller numbers of proteins necessary for secondary metabolism (one each of nonribosomal peptide synthetase and type III polyketide synthase), transcriptional regulation, and lateral gene transfer, reflecting the small genome size. The presence of probable metabolic pathways for the transformation of phenolic compounds generated from the decomposition of plant materials, and the presence of a large number of genes associated with membrane transport, particularly amino acid transporters and drug efflux pumps, may contribute to the organism's utilization of root exudates, as well as the tolerance to various organic compounds.}, }
@article {pmid18406342, year = {2008}, author = {Hazes, B and Frost, L}, title = {Towards a systems biology approach to study type II/IV secretion systems.}, journal = {Biochimica et biophysica acta}, volume = {1778}, number = {9}, pages = {1839-1850}, doi = {10.1016/j.bbamem.2008.03.011}, pmid = {18406342}, issn = {0006-3002}, mesh = {Bacterial Proteins/*metabolism ; Cell Membrane/metabolism/physiology ; Conjugation, Genetic/physiology ; Fimbriae, Bacterial/metabolism/physiology ; Gram-Negative Bacteria/*metabolism ; Ion Channels/metabolism/physiology ; Metabolic Networks and Pathways/physiology ; Models, Biological ; Multiprotein Complexes/metabolism/physiology ; Systems Biology/*trends ; }, abstract = {Many gram-negative bacteria produce thin protein filaments, named pili, which extend beyond the confines of the outer membrane. The importance of these pili is illustrated by the fact that highly complex, multi-protein pilus-assembly machines have evolved, not once, but several times. Their many functions include motility, adhesion, secretion, and DNA transfer, all of which can contribute to the virulence of bacterial pathogens or to the spread of virulence factors by horizontal gene transfer. The medical importance has stimulated extensive biochemical and genetic studies but the assembly and function of pili remains an enigma. It is clear that progress in this field requires a more holistic approach where the entire molecular apparatus that forms the pilus is studied as a system. In recent years systems biology approaches have started to complement classical studies of pili and their assembly. Moreover, continued progress in structural biology is building a picture of the components that make up the assembly machine. However, the complexity and multiple-membrane spanning nature of these secretion systems pose formidable technical challenges, and it will require a concerted effort before we can create comprehensive and predictive models of these remarkable molecular machines.}, }
@article {pmid18405355, year = {2008}, author = {Hellborg, L and Woolfit, M and Arthursson-Hellborg, M and Piskur, J}, title = {Complex evolution of the DAL5 transporter family.}, journal = {BMC genomics}, volume = {9}, number = {}, pages = {164}, pmid = {18405355}, issn = {1471-2164}, mesh = {Computational Biology ; *Evolution, Molecular ; Fungi/*genetics ; *Gene Duplication ; Likelihood Functions ; Membrane Transport Proteins/*genetics ; Models, Genetic ; Multigene Family/*genetics ; *Phylogeny ; Saccharomyces cerevisiae Proteins/*genetics ; Species Specificity ; }, abstract = {BACKGROUND: Genes continuously duplicate and the duplicated copies remain in the genome or get deleted. The DAL5 subfamily of transmembrane transporter genes has eight known members in S. cerevisiae. All are putative anion:cation symporters of vitamins (such as allantoate, nicotinate, panthotenate and biotin). The DAL5 subfamily is an old and important group since it is represented in both Basidiomycetes ("mushrooms") and Ascomycetes ("yeast"). We studied the complex evolution of this group in species from the kingdom of fungi particularly the Ascomycetes.<br><br>RESULTS: We identified numerous gene duplications creating sets of orthologous and paralogous genes. In different lineages the DAL5 subfamily members expanded or contracted and in some lineages a specific member could not be found at all. We also observed a close relationship between the gene YIL166C and its homologs in the Saccharomyces sensu stricto species and two "wine spoiler" yeasts, Dekkera bruxellensis and Candida guilliermondi, which could possibly be the result of horizontal gene transfer between these distantly related species. In the analyses we detect several well defined groups without S. cerevisiae representation suggesting new gene members in this subfamily with perhaps altered specialization or function.<br><br>CONCLUSION: The transmembrane DAL5 subfamily was found to have a very complex evolution in yeast with intra- and interspecific duplications and unusual relationships indicating specialization, specific deletions and maybe even horizontal gene transfer. We believe that this group will be important in future investigations of evolution in fungi and especially the evolution of transmembrane proteins and their specialization.}, }
@article {pmid18404212, year = {2008}, author = {Fedorova, ND and Khaldi, N and Joardar, VS and Maiti, R and Amedeo, P and Anderson, MJ and Crabtree, J and Silva, JC and Badger, JH and Albarraq, A and Angiuoli, S and Bussey, H and Bowyer, P and Cotty, PJ and Dyer, PS and Egan, A and Galens, K and Fraser-Liggett, CM and Haas, BJ and Inman, JM and Kent, R and Lemieux, S and Malavazi, I and Orvis, J and Roemer, T and Ronning, CM and Sundaram, JP and Sutton, G and Turner, G and Venter, JC and White, OR and Whitty, BR and Youngman, P and Wolfe, KH and Goldman, GH and Wortman, JR and Jiang, B and Denning, DW and Nierman, WC}, title = {Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus.}, journal = {PLoS genetics}, volume = {4}, number = {4}, pages = {e1000046}, pmid = {18404212}, issn = {1553-7404}, support = {N01AI30071/AI/NIAID NIH HHS/United States ; U01-AI48830/AI/NIAID NIH HHS/United States ; R21-AI052236/AI/NIAID NIH HHS/United States ; N01-AI30071/AI/NIAID NIH HHS/United States ; }, mesh = {Allergens/genetics ; Aspergillus/classification/genetics/physiology ; Aspergillus fumigatus/classification/*genetics/pathogenicity/physiology ; Chromosomes, Fungal/genetics ; Eurotiales/classification/genetics/physiology ; Evolution, Molecular ; Fungal Proteins/genetics/immunology ; Genome, Fungal ; *Genomic Islands ; Humans ; Phylogeny ; Species Specificity ; Virulence/genetics ; }, abstract = {We present the genome sequences of a new clinical isolate of the important human pathogen, Aspergillus fumigatus, A1163, and two closely related but rarely pathogenic species, Neosartorya fischeri NRRL181 and Aspergillus clavatus NRRL1. Comparative genomic analysis of A1163 with the recently sequenced A. fumigatus isolate Af293 has identified core, variable and up to 2% unique genes in each genome. While the core genes are 99.8% identical at the nucleotide level, identity for variable genes can be as low 40%. The most divergent loci appear to contain heterokaryon incompatibility (het) genes associated with fungal programmed cell death such as developmental regulator rosA. Cross-species comparison has revealed that 8.5%, 13.5% and 12.6%, respectively, of A. fumigatus, N. fischeri and A. clavatus genes are species-specific. These genes are significantly smaller in size than core genes, contain fewer exons and exhibit a subtelomeric bias. Most of them cluster together in 13 chromosomal islands, which are enriched for pseudogenes, transposons and other repetitive elements. At least 20% of A. fumigatus-specific genes appear to be functional and involved in carbohydrate and chitin catabolism, transport, detoxification, secondary metabolism and other functions that may facilitate the adaptation to heterogeneous environments such as soil or a mammalian host. Contrary to what was suggested previously, their origin cannot be attributed to horizontal gene transfer (HGT), but instead is likely to involve duplication, diversification and differential gene loss (DDL). The role of duplication in the origin of lineage-specific genes is further underlined by the discovery of genomic islands that seem to function as designated "gene dumps" and, perhaps, simultaneously, as "gene factories".}, }
@article {pmid18404206, year = {2008}, author = {van Passel, MW and Marri, PR and Ochman, H}, title = {The emergence and fate of horizontally acquired genes in Escherichia coli.}, journal = {PLoS computational biology}, volume = {4}, number = {4}, pages = {e1000059}, pmid = {18404206}, issn = {1553-7358}, support = {R01 GM056120/GM/NIGMS NIH HHS/United States ; GM56120/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Proteins/*genetics ; Escherichia coli/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genetic Variation/*genetics ; Genomic Instability/*genetics ; Shigella/*genetics ; }, abstract = {Bacterial species, and even strains within species, can vary greatly in their gene contents and metabolic capabilities. We examine the evolution of this diversity by assessing the distribution and ancestry of each gene in 13 sequenced isolates of Escherichia coli and Shigella. We focus on the emergence and demise of two specific classes of genes, ORFans (genes with no homologs in present databases) and HOPs (genes with distant homologs), since these genes, in contrast to most conserved ancestral sequences, are known to be a major source of the novel features in each strain. We find that the rates of gain and loss of these genes vary greatly among strains as well as through time, and that ORFans and HOPs show very different behavior with respect to their emergence and demise. Although HOPs, which mostly represent gene acquisitions from other bacteria, originate more frequently, ORFans are much more likely to persist. This difference suggests that many adaptive traits are conferred by completely novel genes that do not originate in other bacterial genomes. With respect to the demise of these acquired genes, we find that strains of Shigella lose genes, both by disruption events and by complete removal, at accelerated rates.}, }
@article {pmid18403782, year = {2008}, author = {Stinear, TP and Seemann, T and Harrison, PF and Jenkin, GA and Davies, JK and Johnson, PD and Abdellah, Z and Arrowsmith, C and Chillingworth, T and Churcher, C and Clarke, K and Cronin, A and Davis, P and Goodhead, I and Holroyd, N and Jagels, K and Lord, A and Moule, S and Mungall, K and Norbertczak, H and Quail, MA and Rabbinowitsch, E and Walker, D and White, B and Whitehead, S and Small, PL and Brosch, R and Ramakrishnan, L and Fischbach, MA and Parkhill, J and Cole, ST}, title = {Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis.}, journal = {Genome research}, volume = {18}, number = {5}, pages = {729-741}, pmid = {18403782}, issn = {1088-9051}, support = {/WT_/Wellcome Trust/United Kingdom ; R01 AI036396/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics ; Carrier Proteins/genetics ; Cell Wall/chemistry ; *Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Genome, Bacterial/*genetics ; Genomics ; Molecular Sequence Data ; Mycobacterium marinum/*genetics ; Mycobacterium tuberculosis/*genetics ; Phylogeny ; }, abstract = {Mycobacterium marinum, a ubiquitous pathogen of fish and amphibia, is a near relative of Mycobacterium tuberculosis, the etiologic agent of tuberculosis in humans. The genome of the M strain of M. marinum comprises a 6,636,827-bp circular chromosome with 5424 CDS, 10 prophages, and a 23-kb mercury-resistance plasmid. Prominent features are the very large number of genes (57) encoding polyketide synthases (PKSs) and nonribosomal peptide synthases (NRPSs) and the most extensive repertoire yet reported of the mycobacteria-restricted PE and PPE proteins, and related-ESX secretion systems. Some of the NRPS genes comprise a novel family and seem to have been acquired horizontally. M. marinum is used widely as a model organism to study M. tuberculosis pathogenesis, and genome comparisons confirmed the close genetic relationship between these two species, as they share 3000 orthologs with an average amino acid identity of 85%. Comparisons with the more distantly related Mycobacterium avium subspecies paratuberculosis and Mycobacterium smegmatis reveal how an ancestral generalist mycobacterium evolved into M. tuberculosis and M. marinum. M. tuberculosis has undergone genome downsizing and extensive lateral gene transfer to become a specialized pathogen of humans and other primates without retaining an environmental niche. M. marinum has maintained a large genome so as to retain the capacity for environmental survival while becoming a broad host range pathogen that produces disease strikingly similar to M. tuberculosis. The work described herein provides a foundation for using M. marinum to better understand the determinants of pathogenesis of tuberculosis.}, }
@article {pmid18397952, year = {2008}, author = {Khan, H and Archibald, JM}, title = {Lateral transfer of introns in the cryptophyte plastid genome.}, journal = {Nucleic acids research}, volume = {36}, number = {9}, pages = {3043-3053}, pmid = {18397952}, issn = {1362-4962}, mesh = {Algal Proteins/classification/genetics ; Base Sequence ; Cryptophyta/*genetics ; *Gene Transfer, Horizontal ; Genetic Variation ; *Genome, Plastid ; *Introns ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; RNA Splicing ; }, abstract = {Cryptophytes are unicellular eukaryotic algae that acquired photosynthesis secondarily through the uptake and retention of a red-algal endosymbiont. The plastid genome of the cryptophyte Rhodomonas salina CCMP1319 was recently sequenced and found to contain a genetic element similar to a group II intron. Here, we explore the distribution, structure and function of group II introns in the plastid genomes of distantly and closely related cryptophytes. The predicted secondary structures of six introns contained in three different genes were examined and found to be generally similar to group II introns but unusually large in size (including the largest known noncoding intron). Phylogenetic analysis suggests that the cryptophyte group II introns were acquired via lateral gene transfer (LGT) from a euglenid-like species. Unexpectedly, the six introns occupy five distinct genomic locations, suggesting multiple LGT events or recent transposition (or both). Combined with structural considerations, RT-PCR experiments suggest that the transferred introns are degenerate 'twintrons' (i.e. nested group II/group III introns) in which the internal intron has lost its splicing capability, resulting in an amalgamation with the outer intron.}, }
@article {pmid18395130, year = {2008}, author = {Gaze, W and O'Neill, C and Wellington, E and Hawkey, P}, title = {Antibiotic resistance in the environment, with particular reference to MRSA.}, journal = {Advances in applied microbiology}, volume = {63}, number = {}, pages = {249-280}, doi = {10.1016/S0065-2164(07)00007-X}, pmid = {18395130}, issn = {0065-2164}, mesh = {Animals ; Animals, Domestic/microbiology ; Cattle ; Dogs ; Drug Resistance, Bacterial/*genetics ; *Environmental Microbiology ; *Gene Transfer, Horizontal ; Humans ; Methicillin Resistance/*genetics ; Sewage/microbiology ; Soil Microbiology ; Staphylococcal Infections/microbiology ; Staphylococcus aureus/*drug effects/genetics ; }, }
@article {pmid18394957, year = {2008}, author = {Makiuchi, T and Annoura, T and Hashimoto, T and Murata, E and Aoki, T and Nara, T}, title = {Evolutionary analysis of synteny and gene fusion for pyrimidine biosynthetic enzymes in Euglenozoa: an extraordinary gap between kinetoplastids and diplonemids.}, journal = {Protist}, volume = {159}, number = {3}, pages = {459-470}, doi = {10.1016/j.protis.2008.02.002}, pmid = {18394957}, issn = {1434-4610}, mesh = {Amino Acid Sequence ; Animals ; Eukaryota/classification/*enzymology/*genetics/metabolism ; *Evolution, Molecular ; *Gene Fusion ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Protozoan Proteins/*genetics ; Pyrimidines/*biosynthesis ; Sequence Alignment ; *Synteny ; }, abstract = {A unique feature of the genome architecture in the parasitic trypanosomatid protists is large-scale synteny. We addressed the evolutionary trait of synteny in the eukaryotic group, Euglenozoa, which consists of euglenoids (earliest branching), diplonemids, and kinetoplastids (trypanosomatids and bodonids). Synteny of the pyrimidine biosynthetic (pyr) gene cluster, which constitutes part of a large syntenic cluster in trypanosomatids and includes four separate genes (pyr1-pyr4) and one fused gene (pyr6/pyr5 fusion), was conserved in the bodonid, Parabodo caudatus. In the diplonemid, Diplonema papillatum, we identified pyr4 and pyr6 genes. Phylogenetic analyses of pyr4 and pyr6 showed the separate origin of each in kinetoplastids and euglenoids/diplonemids and suggested that kinetoplastids have acquired these genes via lateral gene transfer (LGT). Because replacement of genes by non-orthologs within the syntenic cluster is highly unlikely, we concluded that, after separation of the line leading to diplonemids, the syntenic pyr gene cluster was established in the common ancestor of kinetoplastids, preceded by their acquisition via LGT. Notably, we found that diplonemid pyr6 is a stand-alone gene, inconsistent with both euglenoid pyr5/pyr6 and kinetoplastid pyr6/pyr5 fusions. Our findings provide insights into the evolutionary gaps within Euglenozoa and the evolutionary trait of rearrangement of gene fusion in this lineage.}, }
@article {pmid18393999, year = {2008}, author = {Allen, JW and Jackson, AP and Rigden, DJ and Willis, AC and Ferguson, SJ and Ginger, ML}, title = {Order within a mosaic distribution of mitochondrial c-type cytochrome biogenesis systems?.}, journal = {The FEBS journal}, volume = {275}, number = {10}, pages = {2385-2402}, doi = {10.1111/j.1742-4658.2008.06380.x}, pmid = {18393999}, issn = {1742-464X}, support = {BB/C508118/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; //Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins/genetics/metabolism ; Computational Biology ; Cysteine/chemistry/metabolism ; Cytochromes c/*biosynthesis/chemistry/genetics ; Cytochromes c1/*biosynthesis/chemistry/genetics ; Eukaryotic Cells/classification/physiology ; Evolution, Molecular ; Heme/chemistry/metabolism ; Lyases/genetics/metabolism ; Mitochondria/*metabolism ; Molecular Sequence Data ; Molecular Structure ; Phylogeny ; Plant Proteins/genetics/metabolism ; }, abstract = {Mitochondrial cytochromes c and c(1) are present in all eukaryotes that use oxygen as the terminal electron acceptor in the respiratory chain. Maturation of c-type cytochromes requires covalent attachment of the heme cofactor to the protein, and there are at least five distinct biogenesis systems that catalyze this post-translational modification in different organisms and organelles. In this study, we use biochemical data, comparative genomic and structural bioinformatics investigations to provide a holistic view of mitochondrial c-type cytochrome biogenesis and its evolution. There are three pathways for mitochondrial c-type cytochrome maturation, only one of which is present in prokaryotes. We analyze the evolutionary distribution of these biogenesis systems, which include the Ccm system (System I) and the enzyme heme lyase (System III). We conclude that heme lyase evolved once and, in many lineages, replaced the multicomponent Ccm system (present in the proto-mitochondrial endosymbiont), probably as a consequence of lateral gene transfer. We find no evidence of a System III precursor in prokaryotes, and argue that System III is incompatible with multi-heme cytochromes common to bacteria, but absent from eukaryotes. The evolution of the eukaryotic-specific protein heme lyase is strikingly unusual, given that this protein provides a function (thioether bond formation) that is also ubiquitous in prokaryotes. The absence of any known c-type cytochrome biogenesis system from the sequenced genomes of various trypanosome species indicates the presence of a third distinct mitochondrial pathway. Interestingly, this system attaches heme to mitochondrial cytochromes c that contain only one cysteine residue, rather than the usual two, within the heme-binding motif. The isolation of single-cysteine-containing mitochondrial cytochromes c from free-living kinetoplastids, Euglena and the marine flagellate Diplonema papillatum suggests that this unique form of heme attachment is restricted to, but conserved throughout, the protist phylum Euglenozoa.}, }
@article {pmid18391045, year = {2008}, author = {Juan, C and Gutiérrez, O and Renom, F and Garau, M and Gallegos, C and Albertí, S and Pérez, JL and Oliver, A}, title = {Chronic respiratory infections by mucoid carbapenemase-producing Pseudomonas aeruginosa strains, a new potential public health problem.}, journal = {Antimicrobial agents and chemotherapy}, volume = {52}, number = {6}, pages = {2285-2286}, pmid = {18391045}, issn = {1098-6596}, mesh = {Aged ; Aged, 80 and over ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*biosynthesis/genetics ; Bronchiectasis/complications ; Chronic Disease ; Drug Resistance, Multiple, Bacterial ; Female ; Gene Transfer, Horizontal ; Humans ; Integrons/genetics ; Male ; Pseudomonas Infections/*microbiology ; Pseudomonas aeruginosa/drug effects/enzymology/*pathogenicity/*physiology ; Public Health ; Pulmonary Disease, Chronic Obstructive/complications ; Respiratory Tract Infections/*microbiology ; beta-Lactamases/*biosynthesis/genetics ; }, }
@article {pmid18390661, year = {2008}, author = {Balbontín, R and Figueroa-Bossi, N and Casadesús, J and Bossi, L}, title = {Insertion hot spot for horizontally acquired DNA within a bidirectional small-RNA locus in Salmonella enterica.}, journal = {Journal of bacteriology}, volume = {190}, number = {11}, pages = {4075-4078}, pmid = {18390661}, issn = {1098-5530}, mesh = {Base Sequence ; Centrosome ; DNA, Bacterial/*genetics ; *Gene Transfer, Horizontal ; Genomic Islands/genetics ; Lysogeny/physiology ; Mutagenesis, Insertional ; RNA, Bacterial/*genetics ; Salmonella enterica/*genetics ; }, abstract = {In Escherichia coli and Salmonella enterica, RyeA and RyeB RNAs are encoded on opposite DNA strands at the same locus. We present evidence indicating that the last 23 bp of the ryeB gene, corresponding to an internal portion of the ryeA gene, served repeatedly as the integration site for exogenous DNA during Salmonella evolution and still act as an attachment site for present-day bacteriophages. Interestingly, ryeA sequence and expression are modified upon lysogenization.}, }
@article {pmid18384726, year = {2008}, author = {Brusetti, L and Rizzi, A and Abruzzese, A and Sacchi, GA and Ragg, E and Bazzicalupo, M and Sorlini, C and Daffonchio, D}, title = {Effects of rhizodeposition of non-transgenic and transplastomic tobaccos on the soil bacterial community.}, journal = {Environmental biosafety research}, volume = {7}, number = {1}, pages = {11-24}, doi = {10.1051/ebr:2008002}, pmid = {18384726}, issn = {1635-7922}, mesh = {Bacteria/*genetics/growth &amp; development ; Chromatography, High Pressure Liquid ; DNA, Ribosomal Spacer/genetics ; Gene Transfer, Horizontal/genetics ; Magnetic Resonance Spectroscopy ; Plant Roots/*genetics/metabolism ; Plants, Genetically Modified/*genetics/metabolism ; Polymerase Chain Reaction ; Soil Microbiology ; Nicotiana/*genetics/metabolism ; Transformation, Bacterial/genetics ; Transgenes/genetics ; }, abstract = {The effect of root-released compounds of transplastomic tobacco (Nicotiana tabacum) on the soil bacterial community structure, and their potential to support horizontal gene transfer (HGT) to bacteria have been studied. Soil microcosms were exposed to root-released compounds collected from transplastomic and non-transgenic tobacco cultivars. Cluster analysis of automated ribosomal intergenic spacer analysis (ARISA) profiles of the soil bacterial community after 48 h incubation grouped the transgenic cultivar apart from the non-transgenic, indicating that it had a rhizodeposition pattern different from the parental plants. However, these differences were less than between the two non-transgenic tobacco cultivars studied. NMR characterization of the root-released compounds showed some differences in chemical fingerprinting pattern between the transplastomic and the parental cultivar. However, the effect on bacterial community structure was transient, and tended to disappear after 96 h of incubation. The potential of root-released compounds as a source of transforming DNA for bacteria was investigated by using four potential recipient species. No transformants were obtained following exposure of all the recipients to the root-released compounds. Root-released compounds amended to transgene donor DNA decreased the transformation frequency of Acinetobacter baylyi strain ADP1200, while Azospirillum, Agrobacterium, and Sinorhizobium strains failed to develop competence also in the presence of an external added transgene source. Detection of plastid sequences by PCR suggested that a very low amount of fragmented plastid donor DNA was present in the root-released compounds.}, }
@article {pmid18384660, year = {2008}, author = {Friesen, TL and Faris, JD and Solomon, PS and Oliver, RP}, title = {Host-specific toxins: effectors of necrotrophic pathogenicity.}, journal = {Cellular microbiology}, volume = {10}, number = {7}, pages = {1421-1428}, doi = {10.1111/j.1462-5822.2008.01153.x}, pmid = {18384660}, issn = {1462-5822}, mesh = {Fungal Proteins/genetics/*metabolism ; Fungi/chemistry/genetics/pathogenicity ; *Gene Transfer, Horizontal ; Mycotoxins/genetics/*metabolism ; Plant Diseases/*microbiology ; Quantitative Trait Loci ; Triticum/genetics/microbiology ; }, abstract = {Host-specific toxins (HSTs) are defined as pathogen effectors that induce toxicity and promote disease only in the host species and only in genotypes of that host expressing a specific and often dominant susceptibility gene. They are a feature of a small but well-studied group of fungal plant pathogens. Classical HST pathogens include species of Cochliobolus, Alternaria and Pyrenophora. Recent studies have shown that Stagonospora nodorum produces at least four separate HSTs that interact with four of the many quantitative resistance loci found in the host, wheat. Rationalization of fungal phylogenetics has placed these pathogens in the Pleosporales order of the class Dothideomycetes. It is possible that all HST pathogens lie in this order. Strong evidence of the recent lateral gene transfer of the ToxA gene from S. nodorum to Pyrenophora tritici-repentis has been obtained. Hallmarks of lateral gene transfer are present for all the studied HST genes although definitive proof is lacking. We therefore suggest that the Pleosporales pathogens may have a conserved propensity to acquire HST genes by lateral transfer.}, }
@article {pmid18373588, year = {2008}, author = {Plötner, J and Uzzell, T and Beerli, P and Spolsky, C and Ohst, T and Litvinchuk, SN and Guex, GD and Reyer, HU and Hotz, H}, title = {Widespread unidirectional transfer of mitochondrial DNA: a case in western Palaearctic water frogs.}, journal = {Journal of evolutionary biology}, volume = {21}, number = {3}, pages = {668-681}, pmid = {18373588}, issn = {1420-9101}, support = {R01 GM078985/GM/NIGMS NIH HHS/United States ; R01 GM078985-02/GM/NIGMS NIH HHS/United States ; R01 GM 078985/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Anura/*genetics ; Asia ; Base Sequence ; DNA, Mitochondrial/*genetics ; Ecosystem ; Europe ; Gene Transfer, Horizontal ; Hybridization, Genetic/*genetics ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Interspecies transfer of mitochondrial (mt) DNA is a common phenomenon in plants, invertebrates and vertebrates, normally linked with hybridization of closely related species in zones of sympatry or parapatry. In central Europe, in an area north of 48 degrees N latitude and between 8 degrees and 22 degrees E longitude, western Palaearctic water frogs show massive unidirectional introgression of mtDNA: 33.7% of 407 Rana ridibunda possessed mtDNA specific for Rana lessonae. By contrast, no R. lessonae with R. ridibunda mtDNA was observed. That R. ridibunda with introgressed mitochondrial genomes were found exclusively within the range of the hybrid Rana esculenta and that most hybrids had lessonae mtDNA (90.4% of 335 individuals investigated) is evidence that R. esculenta serves as a vehicle for transfer of lessonae mtDNA into R. ridibunda. Such introgression has occurred several times independently. The abundance and wide distribution of individuals with introgressed mitochondrial genomes show that R. lessonae mt genomes work successfully in a R. ridibunda chromosomal background despite their high sequence divergence from R. ridibunda mtDNAs (14.2-15.2% in the ND2/ND3 genes). Greater effectiveness of enzymes encoded by R. lessonae mtDNA may be advantageous to individuals of R. ridibunda and probably R. esculenta in the northern parts of their ranges.}, }
@article {pmid18371228, year = {2008}, author = {Cardona, G and Rosselló, F and Valiente, G}, title = {A perl package and an alignment tool for phylogenetic networks.}, journal = {BMC bioinformatics}, volume = {9}, number = {}, pages = {175}, pmid = {18371228}, issn = {1471-2105}, mesh = {Algorithms ; Base Sequence ; *Evolution, Molecular ; Gene Expression Profiling/*methods ; Molecular Sequence Data ; Phylogeny ; Programming Languages ; Proteome/*genetics ; Sequence Alignment/*methods ; Sequence Analysis, DNA/*methods ; Signal Transduction/*genetics ; *Software ; }, abstract = {BACKGROUND: Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of evolutionary events acting at the population level, like recombination between genes, hybridization between lineages, and lateral gene transfer. While most phylogenetics tools implement a wide range of algorithms on phylogenetic trees, there exist only a few applications to work with phylogenetic networks, none of which are open-source libraries, and they do not allow for the comparative analysis of phylogenetic networks by computing distances between them or aligning them.<br><br>RESULTS: In order to improve this situation, we have developed a Perl package that relies on the BioPerl bundle and implements many algorithms on phylogenetic networks. We have also developed a Java applet that makes use of the aforementioned Perl package and allows the user to make simple experiments with phylogenetic networks without having to develop a program or Perl script by him or herself.<br><br>CONCLUSION: The Perl package is available as part of the BioPerl bundle, and can also be downloaded. A web-based application is also available (see availability and requirements). The Perl package includes full documentation of all its features.}, }
@article {pmid18367290, year = {2008}, author = {McInerney, JO and Cotton, JA and Pisani, D}, title = {The prokaryotic tree of life: past, present... and future?.}, journal = {Trends in ecology &amp; evolution}, volume = {23}, number = {5}, pages = {276-281}, doi = {10.1016/j.tree.2008.01.008}, pmid = {18367290}, issn = {0169-5347}, mesh = {Biology/*trends ; Genomics ; *Phylogeny ; Prokaryotic Cells/classification ; RNA, Ribosomal/*genetics ; }, abstract = {No accepted phylogenetic scheme for prokaryotes emerged until the late 1970s. Prior to that, it was assumed that there was a phylogenetic tree uniting all prokaryotes, but no suitable data were available for its construction. For 20 years, through the 1980s and 1990s, rRNA phylogenies were the gold standard. However, beginning in the last decade, findings from genomic data have challenged this new consensus. Gene trees can conflict greatly, and strains of the same species can differ enormously in genome content. Horizontal gene transfer is now known to be a significant influence on genome evolution. The next decade is likely to resolve whether or not we retain the centuries-old metaphor of the tree for all of life.}, }
@article {pmid18366724, year = {2008}, author = {Tamames, J and Moya, A}, title = {Estimating the extent of horizontal gene transfer in metagenomic sequences.}, journal = {BMC genomics}, volume = {9}, number = {}, pages = {136}, pmid = {18366724}, issn = {1471-2164}, mesh = {Animals ; Computational Biology/*methods ; Computer Simulation ; Databases, Genetic ; Escherichia coli/genetics ; Eukaryota/classification/*genetics ; Gene Transfer, Horizontal/*genetics ; Genome, Protozoan/*genetics ; Genomics/*methods ; Oceans and Seas ; *Phylogeny ; }, abstract = {BACKGROUND: Although the extent of horizontal gene transfer (HGT) in complete genomes has been widely studied, its influence in the evolution of natural communities of prokaryotes remains unknown. The availability of metagenomic sequences allows us to address the study of global patterns of prokaryotic evolution in samples from natural communities. However, the methods that have been commonly used for the study of HGT are not suitable for metagenomic samples. Therefore it is important to develop new methods or to adapt existing ones to be used with metagenomic sequences.<br><br>RESULTS: We have created two different methods that are suitable for the study of HGT in metagenomic samples. The methods are based on phylogenetic and DNA compositional approaches, and have allowed us to assess the extent of possible HGT events in metagenomes for the first time. The methods are shown to be compatible and quite precise, although they probably underestimate the number of possible events. Our results show that the phylogenetic method detects HGT in between 0.8% and 1.5% of the sequences, while DNA compositional methods identify putative HGT in between 2% and 8% of the sequences. These ranges are very similar to these found in complete genomes by related approaches. Both methods act with a different sensitivity since they probably target HGT events of different ages: the compositional method mostly identifies recent transfers, while the phylogenetic is more suitable for the detections of older events. Nevertheless, the study of the number of HGT events in metagenomic sequences from different communities shows a consistent trend for both methods: the lower amount is found for the sequences of the Sargasso Sea metagenome, while the higher quantity is found in the whale fall metagenome from the bottom of the ocean. The significance of these observations is discussed.<br><br>CONCLUSION: The computational approaches that are used to find possible HGT events in complete genomes can be adapted to work with metagenomic samples, where a level of high performance is shown in different metagenomic samples. The percentage of possible HGT events that were observed is close to that found for complete genomes, and different microbiomes show diverse ratios of putative HGT events. This is probably related with both environmental factors and the composition in the species of each particular community.}, }
@article {pmid18366664, year = {2008}, author = {Xie, J and Fu, Y and Jiang, D and Li, G and Huang, J and Li, B and Hsiang, T and Peng, Y}, title = {Intergeneric transfer of ribosomal genes between two fungi.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {87}, pmid = {18366664}, issn = {1471-2148}, mesh = {Basidiomycota/*genetics ; Blotting, Southern ; DNA Primers ; DNA, Fungal/*genetics ; DNA, Ribosomal Spacer/*genetics ; *Gene Transfer, Horizontal ; *Genes, Fungal ; Oryza/*microbiology ; Polymerase Chain Reaction ; Species Specificity ; }, abstract = {BACKGROUND: Horizontal gene transfer, also called lateral gene transfer, frequently occurs among prokaryotic organisms, and is considered an important force in their evolution. However, there are relatively few reports of transfer to or from fungi, with some notable exceptions in the acquisition of prokaryotic genes. Some fungal species have been found to contain sequences resembling those of bacterial genes, and with such sequences absent in other fungal species, this has been interpreted as horizontal gene transfer. Similarly, a few fungi have been found to contain genes absent in close relatives but present in more distantly related taxa, and horizontal gene transfer has been invoked as a parsimonious explanation. There is a paucity of direct experimental evidence demonstrating the occurrence of horizontal gene transfer in fungi.<br><br>RESULTS: We found a fungal field isolate from rice (Oryzae sativa) that contains ribosomal DNA sequences from two species of fungal rice pathogens (Thanatephorus cucumeris and Ceratobasidium oryzae-sativae). This field isolate has four types of ribosomal DNA internal transcribed spacers (ITS), namely pure ITS of C. oryzae-sativae, which was dominant in this field isolate, pure ITS of T. cucumeris, and two chimeric ITS, with ITS1 derived from C. oryzae-sativae and ITS2 from T. cucumeris, or ITS1 from T. cucumeris and ITS2 from C. oryzae-sativae. The presence of chimeric forms indicates that the intergeneric hybrid was not merely composed of nuclei from the parental species, but that nuclear fusion and crossing over had taken place.<br><br>CONCLUSION: Hyphae of T. cucumeris and C. oryzae-sativae are vegetatively incompatible, and do not successfully anastomose. However, they parasitize the same host, and perhaps under the influence of host enzymes targeted to weaken pathogen cells or in dying host plant tissue, the fungal hyphae lost their integrity, and normal vegetative incompatibility mechanisms were overcome, allowing the hyphae to fuse. Based on the presence of other similarly anomalous isolates from the field, we speculate that these types of intergeneric hybridization events and occurrences of horizontal gene transfer may not be so rare in the field.}, }
@article {pmid18366643, year = {2008}, author = {González Pérez, AD and González González, E and Espinosa Angarica, V and Vasconcelos, AT and Collado-Vides, J}, title = {Impact of Transcription Units rearrangement on the evolution of the regulatory network of gamma-proteobacteria.}, journal = {BMC genomics}, volume = {9}, number = {}, pages = {128}, pmid = {18366643}, issn = {1471-2164}, mesh = {Computational Biology/*methods ; Databases, Genetic ; *Evolution, Molecular ; Gammaproteobacteria/*genetics ; Gene Rearrangement/*genetics ; Gene Regulatory Networks/*genetics ; *Genetic Variation ; Species Specificity ; }, abstract = {BACKGROUND: In the past years, several studies begun to unravel the structure, dynamical properties, and evolution of transcriptional regulatory networks. However, even those comparative studies that focus on a group of closely related organisms are limited by the rather scarce knowledge on regulatory interactions outside a few model organisms, such as E. coli among the prokaryotes.<br><br>RESULTS: In this paper we used the information annotated in Tractor_DB (a database of regulatory networks in gamma-proteobacteria) to calculate a normalized Site Orthology Score (SOS) that quantifies the conservation of a regulatory link across thirty genomes of this subclass. Then we used this SOS to assess how regulatory connections have evolved in this group, and how the variation of basic regulatory connection is reflected on the structure of the chromosome. We found that individual regulatory interactions shift between different organisms, a process that may be described as rewiring the network. At this evolutionary scale (the gamma-proteobacteria subclass) this rewiring process may be an important source of variation of regulatory incoming interactions for individual networks. We also noticed that the regulatory links that form feed forward motifs are conserved in a better correlated manner than triads of random regulatory interactions or pairs of co-regulated genes. Furthermore, the rewiring process that takes place at the most basic level of the regulatory network may be linked to rearrangements of genetic material within bacterial chromosomes, which change the structure of Transcription Units and therefore the regulatory connections between Transcription Factors and structural genes.<br><br>CONCLUSION: The rearrangements that occur in bacterial chromosomes-mostly inversion or horizontal gene transfer events - are important sources of variation of gene regulation at this evolutionary scale.}, }
@article {pmid18365719, year = {2008}, author = {Akhmetov, LI and Filonov, AE and Puntus, IF and Kosheleva, IA and Nechaeva, IA and Yonge, DR and Petersen, JN and Boronin, AM}, title = {[Horizontal transfer of catabolic plasmids in the process of naphthalene biodegradation in model soil systems].}, journal = {Mikrobiologiia}, volume = {77}, number = {1}, pages = {29-39}, pmid = {18365719}, issn = {0026-3656}, mesh = {Biodegradation, Environmental ; Gene Transfer, Horizontal ; Naphthalenes/*metabolism ; Plasmids/*genetics/metabolism ; Pseudomonas fluorescens/*genetics/metabolism ; Pseudomonas putida/*genetics/metabolism ; }, abstract = {The process of naphthalene degradation by indigenous, introduced, and transconjugant strains was studied in laboratory soil microcosms. Conjugation transfer of catabolic plasmids was demonstrated in naphthalene-contaminated soil. Both indigenous microorganisms and an introduced laboratory strain BS394 (pNF142::TnMod-OTc) served as donors of these plasmids. The indigenous bacterial degraders of naphthalene isolated from soil were identified as Pseudomonas putida and Pseudomonas fluorescens. The frequency of plasmid transfer in soil was 10(-5)-10(-4) per donor cell. The activity of the key enzymes of naphthalene biodegradation in indigenous and transconjugant strains was studied. Transconjugant strains harboring indigenous catabolic plasmids possessed high salicylate hydroxylase and low catechol-2,3-dioxygenase activities, in contrast to indigenous degraders, which had a high level of catechol-2,3-dioxygenase activity and a low level of salicylate hydroxylase. Naphthalene degradation in batch culture in liquid mineral medium was shown to accelerate due to cooperation of the indigenous naphthalene degrader P. fluorescens AP1 and the transconjugant strain P. putida KT2442 harboring the indigenous catabolic plasmid pAP35. The role of conjugative transfer of naphthalene biodegradation plasmids in acceleration of naphthalene degradation was demonstrated in laboratory soil microcosms.}, }
@article {pmid18363234, year = {2007}, author = {Wilson, JW and Nickerson, CA}, title = {In vivo excision, cloning, and broad-host-range transfer of large bacterial DNA segments using VEX-Capture.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {394}, number = {}, pages = {105-118}, doi = {10.1007/978-1-59745-512-1_7}, pmid = {18363234}, issn = {1064-3745}, mesh = {*Bacteriological Techniques ; Cloning, Molecular/methods ; DNA, Bacterial/*genetics/*isolation &amp; purification ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; *Genetic Techniques ; Genetic Vectors ; Genome, Bacterial ; Plasmids/genetics ; Salmonella typhimurium/genetics ; }, abstract = {The performance of many bacterial genetic experiments would benefit from a convenient method to clone large sets of genes (20-100+ kb) and transfer these genes to a wide range of other bacterial recipients. The VEX-Capture technique allows such large genomic segments to be cloned in vivo onto a broad-host-range IncP plasmid that is able to self-transfer to a wide variety of Gram-negative bacteria. The advantages of VEX-Capture are its efficiency, specificity, and use of common molecular biological techniques that do not require non-standard equipment and are easily applicable to many types of bacterial species. Here, we describe the VEX-Capture experimental protocol using Salmonella typhimurium as the source of the target DNA segment.}, }
@article {pmid18363232, year = {2007}, author = {Hensel, M}, title = {Genome-based identification and molecular analyses of pathogenicity islands and genomic islands in Salmonella enterica.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {394}, number = {}, pages = {77-88}, doi = {10.1007/978-1-59745-512-1_5}, pmid = {18363232}, issn = {1064-3745}, mesh = {Bacteriological Techniques/statistics &amp; numerical data ; Base Sequence ; Cloning, Molecular ; Computational Biology ; Cosmids ; DNA Primers/genetics ; DNA, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Genetic Techniques/statistics &amp; numerical data ; *Genome, Bacterial ; *Genomic Islands ; Salmonella enterica/drug effects/*genetics/*pathogenicity ; Sequence Deletion ; Virulence/genetics ; }, abstract = {Pathogenicity islands and genomic islands (GI) are key elements in the evolution of bacterial virulence and environmental adaptation. In Salmonella enterica, Salmonella pathogenicity islands ISPI) confer important virulence traits; however, many of these loci have not been characterized in molecular detail. In this chapter, procedures for the identification and molecular characterization of SPI and GI are described. Based on genome sequence data, bioinformatics approaches allow the identification of putative SPI and GI. The role of these loci can be analyzed after the generation of deletion mutant strains using the Red recombination approach. For further analyses, cosmid libraries of S. enterica genomic DNA are screened for clones harboring entire SPI or GI. Such cosmid clones are then used for complementation of SPI or GI deletions as well as for the transfer of these loci to other bacterial species and subsequent functional assays. This set of methods allows the rapid and efficient analyses of the functions of SPI and GI.}, }
@article {pmid18359835, year = {2008}, author = {Stanton, TB and Humphrey, SB and Sharma, VK and Zuerner, RL}, title = {Collateral effects of antibiotics: carbadox and metronidazole induce VSH-1 and facilitate gene transfer among Brachyspira hyodysenteriae strains.}, journal = {Applied and environmental microbiology}, volume = {74}, number = {10}, pages = {2950-2956}, pmid = {18359835}, issn = {1098-5336}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteriophages/drug effects/growth &amp; development/ultrastructure ; Brachyspira hyodysenteriae/*drug effects/*genetics/growth &amp; development/virology ; Carbadox/*pharmacology ; Culture Media/chemistry ; DNA, Viral/analysis ; Drug Resistance, Bacterial/genetics ; Genes, Viral ; Hydrogen Peroxide/pharmacology ; Metronidazole/*pharmacology ; Microscopy, Electron, Transmission ; Mitomycin/pharmacology ; Polymerase Chain Reaction ; Prophages/*drug effects ; RNA, Viral/biosynthesis/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Transcription, Genetic/drug effects ; *Transduction, Genetic ; Viral Proteins/genetics ; }, abstract = {Brachyspira hyodysenteriae is an anaerobic spirochete and the etiologic agent of swine dysentery. The genome of this spirochete contains a mitomycin C-inducible, prophage-like gene transfer agent designated VSH-1. VSH-1 particles package random 7.5-kb fragments of the B. hyodysenteriae genome and transfer genes between B. hyodysenteriae cells. The chemicals and conditions inducing VSH-1 production are largely unknown. Antibiotics used in swine management and stressors inducing traditional prophages might induce VSH-1 and thereby stimulate lateral gene transfer between B. hyodysenteriae cells. In these studies, VSH-1 induction was initially detected by a quantitative real-time reverse transcriptase PCR assay evaluating increased transcription of hvp38 (VSH-1 head protein gene). VSH-1 induction was confirmed by detecting VSH-1-associated 7.5-kb DNA and VSH-1 particles in B. hyodysenteriae cultures. Nine antibiotics (chlortetracycline, lincomycin, tylosin, tiamulin, virginiamycin, ampicillin, ceftriaxone, vancomycin, and florfenicol) at concentrations affecting B. hyodysenteriae growth did not induce VSH-1 production. By contrast, VSH-1 was detected in B. hyodysenteriae cultures treated with mitomycin C (10 microg/ml), carbadox (0.5 microg/ml), metronidazole (0.5 microg/ml), and H(2)O(2) (300 microM). Carbadox- and metronidazole-induced VSH-1 particles transmitted tylosin and chloramphenicol resistance determinants between B. hyodysenteriae strains. The results of these studies suggest that certain antibiotics may induce the production of prophage or prophage-like elements by intestinal bacteria and thereby impact intestinal microbial ecology.}, }
@article {pmid18359833, year = {2008}, author = {Biers, EJ and Wang, K and Pennington, C and Belas, R and Chen, F and Moran, MA}, title = {Occurrence and expression of gene transfer agent genes in marine bacterioplankton.}, journal = {Applied and environmental microbiology}, volume = {74}, number = {10}, pages = {2933-2939}, pmid = {18359833}, issn = {1098-5336}, mesh = {Bacterial Proteins/*biosynthesis ; Bacteriophages/genetics/ultrastructure ; Chromosomes, Bacterial/genetics ; DNA, Bacterial/genetics ; *Gene Expression Profiling ; Gene Order ; Microscopy, Electron, Transmission ; Phylogeny ; Plankton/*genetics ; Prophages/genetics ; Rhodobacteraceae/*genetics ; Sequence Homology, Amino Acid ; *Transduction, Genetic ; }, abstract = {Genes with homology to the transduction-like gene transfer agent (GTA) were observed in genome sequences of three cultured members of the marine Roseobacter clade. A broader search for homologs for this host-controlled virus-like gene transfer system identified likely GTA systems in cultured Alphaproteobacteria, and particularly in marine bacterioplankton representatives. Expression of GTA genes and extracellular release of GTA particles (approximately 50 to 70 nm) was demonstrated experimentally for the Roseobacter clade member Silicibacter pomeroyi DSS-3, and intraspecific gene transfer was documented. GTA homologs are surprisingly infrequent in marine metagenomic sequence data, however, and the role of this lateral gene transfer mechanism in ocean bacterioplankton communities remains unclear.}, }
@article {pmid18359809, year = {2008}, author = {Urbanczyk, H and Ast, JC and Kaeding, AJ and Oliver, JD and Dunlap, PV}, title = {Phylogenetic analysis of the incidence of lux gene horizontal transfer in Vibrionaceae.}, journal = {Journal of bacteriology}, volume = {190}, number = {10}, pages = {3494-3504}, pmid = {18359809}, issn = {1098-5530}, mesh = {Bacterial Proteins/*genetics ; DNA, Bacterial/chemistry/genetics ; *Gene Transfer, Horizontal ; Luminescent Measurements ; Multigene Family ; Operon ; Oxidoreductases/*genetics ; Phylogeny ; Repressor Proteins/*genetics ; Trans-Activators/*genetics ; Vibrionaceae/enzymology/*genetics/physiology ; }, abstract = {Horizontal gene transfer (HGT) is thought to occur frequently in bacteria in nature and to play an important role in bacterial evolution, contributing to the formation of new species. To gain insight into the frequency of HGT in Vibrionaceae and its possible impact on speciation, we assessed the incidence of interspecies transfer of the lux genes (luxCDABEG), which encode proteins involved in luminescence, a distinctive phenotype. Three hundred three luminous strains, most of which were recently isolated from nature and which represent 11 Aliivibrio, Photobacterium, and Vibrio species, were screened for incongruence of phylogenies based on a representative housekeeping gene (gyrB or pyrH) and a representative lux gene (luxA). Strains exhibiting incongruence were then subjected to detailed phylogenetic analysis of horizontal transfer by using multiple housekeeping genes (gyrB, recA, and pyrH) and multiple lux genes (luxCDABEG). In nearly all cases, housekeeping gene and lux gene phylogenies were congruent, and there was no instance in which the lux genes of one luminous species had replaced the lux genes of another luminous species. Therefore, the lux genes are predominantly vertically inherited in Vibrionaceae. The few exceptions to this pattern of congruence were as follows: (i) the lux genes of the only known luminous strain of Vibrio vulnificus, VVL1 (ATCC 43382), were evolutionarily closely related to the lux genes of Vibrio harveyi; (ii) the lux genes of two luminous strains of Vibrio chagasii, 21N-12 and SB-52, were closely related to those of V. harveyi and Vibrio splendidus, respectively; (iii) the lux genes of a luminous strain of Photobacterium damselae, BT-6, were closely related to the lux genes of the lux-rib(2) operon of Photobacterium leiognathi; and (iv) a strain of the luminous bacterium Photobacterium mandapamensis was found to be merodiploid for the lux genes, and the second set of lux genes was closely related to the lux genes of the lux-rib(2) operon of P. leiognathi. In none of these cases of apparent HGT, however, did acquisition of the lux genes correlate with phylogenetic divergence of the recipient strain from other members of its species. The results indicate that horizontal transfer of the lux genes in nature is rare and that horizontal acquisition of the lux genes apparently has not contributed to speciation in recipient taxa.}, }
@article {pmid18356951, year = {2008}, author = {Marri, PR and Golding, GB}, title = {Gene amelioration demonstrated: the journey of nascent genes in bacteria.}, journal = {Genome}, volume = {51}, number = {2}, pages = {164-168}, doi = {10.1139/g07-105}, pmid = {18356951}, issn = {0831-2796}, mesh = {Bacteria/*genetics ; Codon ; *Gene Expression Regulation, Bacterial ; *Genome, Bacterial ; Species Specificity ; Staphylococcus aureus/*genetics ; Streptococcus pyogenes/*genetics ; }, abstract = {Gene amelioration is the hypothesis that genes acquired via lateral gene transfer will, over time, acquire the molecular characteristics of the host genome. Species for which multiple strains have been sequenced permit a demonstration that this hypothesis is correct. We use 7 sequenced genomes of Streptococcus pyogenes and 6 sequenced genomes of Staphylococcus aureus to illustrate the action of amelioration on these genomes.}, }
@article {pmid18356490, year = {2008}, author = {Field, B and Osbourn, AE}, title = {Metabolic diversification--independent assembly of operon-like gene clusters in different plants.}, journal = {Science (New York, N.Y.)}, volume = {320}, number = {5875}, pages = {543-547}, doi = {10.1126/science.1154990}, pmid = {18356490}, issn = {1095-9203}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Acyltransferases/genetics/metabolism ; Arabidopsis/*genetics/*metabolism/microbiology ; Avena/genetics ; Cytochrome P-450 Enzyme System/genetics/metabolism ; Evolution, Molecular ; Gene Expression ; *Genes, Plant ; Intramolecular Transferases/genetics/metabolism ; Metabolic Networks and Pathways/genetics ; *Multigene Family ; Operon ; Plant Diseases ; Plant Epidermis/metabolism ; Plant Roots/metabolism ; Triterpenes/*metabolism ; }, abstract = {Operons are clusters of unrelated genes with related functions that are a feature of prokaryotic genomes. Here, we report on an operon-like gene cluster in the plant Arabidopsis thaliana that is required for triterpene synthesis (the thalianol pathway). The clustered genes are coexpressed, as in bacterial operons. However, despite the resemblance to a bacterial operon, this gene cluster has been assembled from plant genes by gene duplication, neofunctionalization, and genome reorganization, rather than by horizontal gene transfer from bacteria. Furthermore, recent assembly of operon-like gene clusters for triterpene synthesis has occurred independently in divergent plant lineages (Arabidopsis and oat). Thus, selection pressure may act during the formation of certain plant metabolic pathways to drive gene clustering.}, }
@article {pmid18353101, year = {2008}, author = {Ludwig, A and Valente, VL and Loreto, EL}, title = {Multiple invasions of Errantivirus in the genus Drosophila.}, journal = {Insect molecular biology}, volume = {17}, number = {2}, pages = {113-124}, doi = {10.1111/j.1365-2583.2007.00787.x}, pmid = {18353101}, issn = {1365-2583}, mesh = {Animals ; Base Sequence ; DNA/chemistry/genetics ; Drosophilidae/*genetics/*virology ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, env ; *Genome, Insect ; Insect Viruses/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Retroelements/*genetics ; Sequence Alignment ; }, abstract = {Aiming to contribute to the knowledge of the evolutionary history of Errantivirus, a phylogenetic analysis of the env gene sequences of Errantivirus gypsy, gtwin, gypsy2, gypsy3, gypsy4 and gypsy6 was carried out in 33 Drosophilidae species. Most sequences were obtained from in silico searches in the Drosophila genomes. The complex evolutionary pattern reported by other authors for the gypsy retroelement was also observed in the present study, including vertical transmission, ancestral polymorphism, stochastic loss and horizontal transfer. Moreover, the elements gypsy2, gypsy3, gypsy4 and gypsy6 were shown to have followed an evolutionary model that is similar to gypsy. Fifteen new possible cases of horizontal transfer were suggested. The infectious potential of these elements may help elucidate the evolutionary scenario described in the present study.}, }
@article {pmid18351050, year = {2006}, author = {Arber, W}, title = {The evolutionary strategy of DNA acquisition as a possible reason for a universal genetic code.}, journal = {History and philosophy of the life sciences}, volume = {28}, number = {4}, pages = {525-532}, pmid = {18351050}, issn = {0391-9714}, mesh = {DNA, Bacterial/genetics ; *Evolution, Molecular ; *Gene Transfer Techniques ; *Genetic Code ; *Genetic Variation ; Genomic Instability ; Humans ; *Selection, Genetic ; }, abstract = {The evolutionary strategy to generate genetic variants by DNA acquisition involving horizontal gene transfer seems to be widely used by many, if not all, living organisms. A common language between donor and recipient organisms, as provided by the quasi universality of the genetic code, can favor the effectiveness of the DNA acquisition strategy. These considerations are here discussed in the context of our knowledge on the natural strategies of molecular evolution and on the commonly used genetic code.}, }
@article {pmid18347113, year = {2008}, author = {Takahata, S and Kato, Y and Sanbongi, Y and Maebashi, K and Ida, T}, title = {Comparison of the efficacies of oral beta-lactams in selection of Haemophilus influenzae transformants with mutated ftsI genes.}, journal = {Antimicrobial agents and chemotherapy}, volume = {52}, number = {5}, pages = {1880-1883}, pmid = {18347113}, issn = {1098-6596}, mesh = {Ampicillin/pharmacology ; Bacterial Proteins/*genetics ; Carbapenems/pharmacology ; Cefdinir ; Cephalosporins/pharmacology ; Gene Transfer, Horizontal ; Haemophilus influenzae/*drug effects/genetics ; Mutation ; Penicillin-Binding Proteins/*genetics ; beta-Lactams/*pharmacology ; Cefprozil ; }, abstract = {Horizontal transfer of the mutated ftsI gene from beta-lactamase-nonproducing ampicillin-resistant (BLNAR) Haemophilus influenzae to a susceptible strain was examined in vitro under selection with nine oral beta-lactams (ampicillin, amoxicillin, cefprozil, cefuroxime, cefpodoxime, cefdinir, cefcapene, cefditoren, and tebipenem). Compared to the penicillins and the carbapenem, the cephalosporins showed a wide selection window for the genetic transfer.}, }
@article {pmid18343347, year = {2008}, author = {Maravić Vlahovicek, G and Cubrilo, S and Tkaczuk, KL and Bujnicki, JM}, title = {Modeling and experimental analyses reveal a two-domain structure and amino acids important for the activity of aminoglycoside resistance methyltransferase Sgm.}, journal = {Biochimica et biophysica acta}, volume = {1784}, number = {4}, pages = {582-590}, doi = {10.1016/j.bbapap.2007.09.009}, pmid = {18343347}, issn = {0006-3002}, mesh = {Amino Acid Sequence ; Aminoglycosides/*pharmacology ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/chemistry/genetics ; Computational Biology ; *Drug Resistance, Bacterial ; Gentamicins/pharmacology ; Kanamycin/pharmacology ; Methyltransferases/*chemistry/genetics ; Micromonospora/classification/drug effects/genetics ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Phylogeny ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sequence Homology, Amino Acid ; Structure-Activity Relationship ; }, abstract = {Methyltransferases that carry out posttranscriptional N7-methylation of G1405 in 16S rRNA confer bacterial resistance to aminoglycoside antibiotics, including kanamycin and gentamicin. Genes encoding enzymes from this family (hereafter referred to as Arm, for aminoglycoside resistance methyltransferases) have been recently found to spread by horizontal gene transfer between various human pathogens. The knowledge of the Arm protein structure would lay the groundwork for the development of potential resistance inhibitors, which could be used to restore the potential of aminoglycosides to act against the resistant pathogens. We analyzed the sequence-function relationships of Sgm MTase, a member of the Arm family, by limited proteolysis and site-directed and random mutagenesis. We also modeled the structure of Sgm using bioinformatics techniques and used the model to provide a structural context for experimental results. We found that Sgm comprises two domains and we characterized a number of functionally compromised point mutants with substitutions of invariant or conserved residues. Our study provides a low-resolution (residue-level) model of sequence-structure-function relationships in the Arm family of enzymes and reveals the cofactor-binding and substrate-binding sites. These functional regions will be prime targets for further experimental and theoretical studies aimed at defining the reaction mechanism of m7 G1405 methylation, increasing the resolution of the model and developing Arm-specific inhibitors.}, }
@article {pmid18340538, year = {2009}, author = {de Freitas Ortiz, M and Loreto, EL}, title = {Characterization of new hAT transposable elements in 12 Drosophila genomes.}, journal = {Genetica}, volume = {135}, number = {1}, pages = {67-75}, pmid = {18340538}, issn = {1573-6857}, mesh = {Amino Acid Sequence ; Animals ; Codon, Nonsense/analysis ; Consensus Sequence/genetics ; *DNA Transposable Elements ; Drosophila/*genetics ; Drosophila Proteins/analysis/*genetics ; Electronic Data Processing ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Insect ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Terminal Repeat Sequences ; Transposases/analysis/*genetics ; Zinc Fingers/genetics ; }, abstract = {In silico searches for sequences homologous to hAT elements in 12 Drosophila genomes have allowed us to identify 37 new hAT elements (8 in D. ananassae, 11 in D. mojavensis, 2 in D. sechellia, 1 in D. simulans, 2 in D. virilis, 3 in D. yakuba, 3 in D. persimilis, 1 in D. grimshawi, 5 in D. willistoni and 1 in D. pseudobscura). The size of these elements varies from 2,359 to 4,962 bp and the terminal inverted repeats (TIRs) show lengths ranging from 10 to 24 bp. Several elements show intact transposase ORFs, suggesting that they are active. Conserved amino acid motifs were identified that correspond to those important for transposase activity. These elements are highly variable and phylogenetic analysis showed that they can be clustered into four different families. Incongruencies were observed between the phylogenies of the transposable elements and those of their hosts, suggesting that horizontal transfer may have occurred between some of the species.}, }
@article {pmid18339941, year = {2008}, author = {Babic, A and Lindner, AB and Vulic, M and Stewart, EJ and Radman, M}, title = {Direct visualization of horizontal gene transfer.}, journal = {Science (New York, N.Y.)}, volume = {319}, number = {5869}, pages = {1533-1536}, doi = {10.1126/science.1153498}, pmid = {18339941}, issn = {1095-9203}, mesh = {Bacterial Outer Membrane Proteins/genetics/metabolism ; Bacterial Proteins/metabolism ; *Conjugation, Genetic ; DNA, Bacterial/*genetics/metabolism ; DNA-Binding Proteins/genetics/metabolism ; Escherichia coli/*genetics ; Escherichia coli Proteins/genetics/metabolism ; Exodeoxyribonuclease V/metabolism ; *Gene Transfer, Horizontal ; Luminescent Proteins/metabolism ; Microscopy, Fluorescence ; Pili, Sex/physiology ; Recombinant Fusion Proteins/metabolism ; Recombination, Genetic ; }, abstract = {Conjugation allows bacteria to acquire genes for antibiotic resistance, novel virulence attributes, and alternative metabolic pathways. Using a fluorescent protein fusion, SeqA-YFP, we have visualized this process in real time and in single cells of Escherichia coli. We found that the F pilus mediates DNA transfer at considerable cell-to-cell distances. Integration of transferred DNA by recombination occurred in up to 96% of recipients; in the remaining cells, the transferred DNA was fully degraded by the RecBCD helicase/nuclease. The acquired integrated DNA was tracked through successive replication rounds and was found to occasionally split and segregate with different chromosomes, leading to the inheritance of different gene clusters within the cell lineage. The incidence of DNA splitting corresponds to about one crossover per cell generation.}, }
@article {pmid18337685, year = {2008}, author = {Chater, KF and Chandra, G}, title = {The use of the rare UUA codon to define "expression space" for genes involved in secondary metabolism, development and environmental adaptation in streptomyces.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {46}, number = {1}, pages = {1-11}, pmid = {18337685}, issn = {1225-8873}, mesh = {Anti-Bacterial Agents/metabolism ; Bacterial Proteins/*genetics/physiology ; Codon/*genetics/physiology ; Computational Biology ; Gene Expression Regulation, Bacterial ; Oligonucleotide Array Sequence Analysis ; Protein Biosynthesis ; Proteomics ; RNA, Bacterial/*genetics/physiology ; RNA, Messenger/genetics ; RNA, Transfer, Leu/*genetics/physiology ; Streptomyces/*genetics/physiology ; }, abstract = {In Streptomyces coelicolor, bldA encodes the only tRNA for a rare leucine codon, UUA. This tRNA is unnecessary for growth, but is required for some aspects of secondary metabolism and morphological development, as revealed by the phenotypes of bldA mutants in diverse streptomycetes. This article is a comprehensive review of out understanding of this unusual situation. Based on information from four sequenced genomes it now appears that, typically, about 2 approximately 3% of genes in any one streptomycete contain a TTA codon, most having been acquired through species-specific horizontal gene transfer. Among the few widely conserved TTA-containing genes, mutations in just one, the pleiotropic regulatory gene adpA, give an obvious phenotype: such mutants are defective in aerial growth and sporulation, but vary in the extent of their impairment in secondary metabolism in different streptomycetes. The TTA codon in adpA is largely responsible for the morphological phenotype of a bldA mutant of S. coelicolor. AdpA-dependent targets include several genes involved in the integrated action of extracellular proteases that, at least in some species, are involved in the conversion of primary biomass into spores. The effects of bldA mutations on secondary metabolism are mostly attributable to the presence of TTA codons in pathway-specific genes, particularly in transcriptional activator genes. This is not confined to S. coelicolor-it is true for about half of all known antibiotic biosynthetic gene sets from streptomycetes. Combined microarray and proteomic analysis of liquid (and therefore non-sporulating) S. coelicolor bldA mutant cultures revealed effects of the mutation during rapid growth, during transition phase, and in stationary phase. Some of these effects may be secondary consequences of changes in the pattern of ppGpp accumulation. It is argued that the preferential accumulation of the bldA tRNA under conditions in which growth is significantly constrained has evolved to favour the expression of genes that confer adaptive benefits in intermittently encountered sub-optimal environments. The evolution of this system may have been a secondary consequence of the selective pressure exerted by bacteriophage attack. Some biotechnological implications of bldA phenomenology are considered.}, }
@article {pmid19425156, year = {2008}, author = {Moustafa, A and Chan, CX and Danforth, M and Zear, D and Ahmed, H and Jadhav, N and Savage, T and Bhattacharya, D}, title = {A phylogenomic approach for studying plastid endosymbiosis.}, journal = {Genome informatics. International Conference on Genome Informatics}, volume = {21}, number = {}, pages = {165-176}, pmid = {19425156}, issn = {0919-9454}, support = {R01ES013679/ES/NIEHS NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics ; Diatoms/genetics ; Enzymes/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome ; Genome, Bacterial ; Genome, Plant ; *Models, Genetic ; Multigene Family ; *Phylogeny ; Plants/genetics ; Plastids/*genetics ; Rhodophyta/classification/*genetics ; Software ; Symbiosis/*genetics ; }, abstract = {Gene transfer is a major contributing factor to functional innovation in genomes. Endosymbiotic gene transfer (EGT) is a specific instance of lateral gene transfer (LGT) in which genetic materials are acquired by the host genome from an endosymbiont that has been engulfed and retained in the cytoplasm. Here we present a comprehensive approach for detecting gene transfer within a phylogenetic framework. We applied the approach to examine EGT of red algal genes into Thalassiosira pseudonana, a free-living diatom for which a complete genome sequence has recently been determined. Out of 11,390 predicted protein-coding sequences from the genome of T. pseudonana, 124 (1.1%, clustered into 80 gene families) are inferred to be of red algal origin (bootstrap support >or= 75%). Of these 80 gene families, 22 (27.5%) encode novel, unknown functions. We found 21.3% of the gene families to putatively encode non-plastid-targeted proteins. Our results suggest that EGT of red algal genes provides a relatively minor contribution to the nuclear genome of the diatom, but the transferred genes have functions that extend beyond photosynthesis. This assertion awaits experimental validation. Whereas the current study is focused within the context of secondary endosymbiosis, our approach can be applied to large-scale detection of gene transfer in any system.}, }
@article {pmid19381470, year = {2008}, author = {Kiel, JL and Parker, JE and Holwitt, EA and McCreary, RP and Andrews, CJ and De Los Santos, A and Wade, M and Kalns, J and Walker, W}, title = {Geographical distribution of genotypic and phenotypic markers among Bacillus anthracis isolates and related species by historical movement and horizontal transfer.}, journal = {Folia microbiologica}, volume = {53}, number = {6}, pages = {472-478}, pmid = {19381470}, issn = {1874-9356}, mesh = {Animals ; Anthrax/microbiology/veterinary ; Bacillus anthracis/*classification/genetics/isolation &amp; purification/physiology ; Base Sequence ; Cattle ; Cattle Diseases/microbiology ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Markers ; Genotype ; Minisatellite Repeats ; Molecular Sequence Data ; Mutation ; Phenotype ; Plasmids/genetics ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; Recombination, Genetic ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Species Specificity ; Spores, Bacterial ; }, abstract = {The geographical distribution of Bacillus anthracis strains and isolates bearing some of the same genetic markers as the Amerithrax Ames isolate was examined and evaluated. At least one mechanism for the horizontal movement of genetic markers was shown amongst isolates and closely related species and the effect of such mixing was demonstrated on phenotype. The results provided potential mechanisms by which attempts to attribute isolates of Bacillus anthracis to certain geographical and isolate sources may be disrupted.}, }
@article {pmid19704752, year = {2007}, author = {Richards, TA and Talbot, NJ}, title = {Plant parasitic oomycetes such as phytophthora species contain genes derived from three eukaryotic lineages.}, journal = {Plant signaling &amp; behavior}, volume = {2}, number = {2}, pages = {112-114}, pmid = {19704752}, issn = {1559-2316}, abstract = {Fungi and the oomycetes include several groups of plant pathogenic microbes. Although these two eukaryotic groups are unrelated they have a number of phenotypic similarities suggested to have evolved convergently. We have recently shown that gene transfer events have occurred from fungi to the oomycetes. These gene transfer events appear to be only one part of a complex and chimeric ancestry for the oomycete genome, which has also received genes from a red algal endosymbiont.}, }
@article {pmid19468311, year = {2007}, author = {Thuillard, M}, title = {Minimizing contradictions on circular order of phylogenic trees.}, journal = {Evolutionary bioinformatics online}, volume = {3}, number = {}, pages = {267-277}, pmid = {19468311}, issn = {1176-9343}, abstract = {Distance-based approaches to phylogeny use estimations of the evolutionary distance between sequences to reconstruct an evolution tree. If the evolution can be represented by an X-tree, the different sequences can be ordered so that the distance matrix Yi, jn, representing the distance from a leaf n to the path (i, j), is perfectly ordered meaning that Yi, jn >or= Yi, kn and Yk, jn >or= Yk, in for i <or= j <or= k. After ordering of the sequences, the distance matrix Yi, jn permits to visualize phylogenetic relationships between taxa and to localize deviations from perfect order. The effect of perturbations resulting from lateral gene transfer or crossover can be modeled probabilistically. The order is shown to be quite robust against many perturbations. We have developed algorithms to minimize the level of contradiction in the order of the sequences. These algorithms are tested on the SSU rRNA data for Archaea. The degree of contradiction after optimization is for most taxa quite low. Regions in the taxa space with deviations from perfect order were identified.}, }
@article {pmid19455212, year = {2007}, author = {Nikolskaya, AN and Arighi, CN and Huang, H and Barker, WC and Wu, CH}, title = {PIRSF family classification system for protein functional and evolutionary analysis.}, journal = {Evolutionary bioinformatics online}, volume = {2}, number = {}, pages = {197-209}, pmid = {19455212}, issn = {1176-9343}, support = {U01 HG002712/HG/NHGRI NIH HHS/United States ; }, abstract = {The PIRSF protein classification system (http://pir.georgetown.edu/pirsf/) reflects evolutionary relationships of full-length proteins and domains. The primary PIRSF classification unit is the homeomorphic family, whose members are both homologous (evolved from a common ancestor) and homeomorphic (sharing full-length sequence similarity and a common domain architecture). PIRSF families are curated systematically based on literature review and integrative sequence and functional analysis, including sequence and structure similarity, domain architecture, functional association, genome context, and phyletic pattern. The results of classification and expert annotation are summarized in PIRSF family reports with graphical viewers for taxonomic distribution, domain architecture, family hierarchy, and multiple alignment and phylogenetic tree. The PIRSF system provides a comprehensive resource for bioinformatics analysis and comparative studies of protein function and evolution. Domain or fold-based searches allow identification of evolutionarily related protein families sharing domains or structural folds. Functional convergence and functional divergence are revealed by the relationships between protein classification and curated family functions. The taxonomic distribution allows the identification of lineage-specific or broadly conserved protein families and can reveal horizontal gene transfer. Here we demonstrate, with illustrative examples, how to use the web-based PIRSF system as a tool for functional and evolutionary studies of protein families.}, }
@article {pmid19712400, year = {2004}, author = {Badosa, E and Moreno, C and Montesinos, E}, title = {Lack of detection of ampicillin resistance gene transfer from Bt176 transgenic corn to culturable bacteria under field conditions.}, journal = {FEMS microbiology ecology}, volume = {48}, number = {2}, pages = {169-178}, doi = {10.1016/j.femsec.2004.01.005}, pmid = {19712400}, issn = {1574-6941}, mesh = {*Ampicillin Resistance ; Bacteria/*genetics ; DNA, Bacterial/genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Plants, Genetically Modified/*genetics ; Plasmids ; Polymerase Chain Reaction/methods ; Spain ; Zea mays/*genetics ; }, abstract = {Population levels of total and ampicillin-resistant culturable bacteria and the putative horizontal bla gene acquirement from Bt-corn were studied in commercial fields of transgenic corn in Spain during the years 2000-2003. Commercial fields consisting of conventional corn (Dracma) and Bt176 transgenic corn (Compa CB) were located in three climatic regions. The effect of corn type, plant material, field location, stage of sampling and year of study were studied on total and ampicillin resistant bacterial population levels, on median effective dose and on the slope of the dose-response curve to ampicillin. None of the parameters measured were significantly different (P<0.01) between transgenic and non-transgenic cornfields under the diverse conditions studied. However, in population levels of ampicillin resistant bacteria, the minimum difference between sample means to be significant with a likelihood of 80% was 8.9%. Specific detection of putative bacteria harbouring bla TEM-1 ampicillin resistance genes acquired from Bt176 corn was performed with a method based on the extraction of DNA from the culturable bacterial fraction and with PCR. Primers for PCR were targeted to the bla gene and the corresponding flanking regions present in the pUC18 cloning vector or the Bt176 construct. The culturable bacterial fraction of 144 field samples (up to 864 analysis, including ampicillin enrichments) was analysed by PCR. The estimated total number of bacteria analysed was 10(8). The level of detection of a transfer event according to the sensitivity of the methods used was 10(-6). Four samples of transgenic and five of non-transgenic corn gave positive signals. However, the amplification products did not correspond to the ones expected from Bt176 or pUC18. The limitations of the sampling design and of the methods used are discussed.}, }
@article {pmid19719564, year = {2003}, author = {Clokie, MR and Millard, AD and Wilson, WH and Mann, NH}, title = {Encapsidation of host DNA by bacteriophages infecting marine Synechococcus strains.}, journal = {FEMS microbiology ecology}, volume = {46}, number = {3}, pages = {349-352}, doi = {10.1016/S0168-6496(03)00247-2}, pmid = {19719564}, issn = {1574-6941}, abstract = {It has been speculated that horizontal gene transfer might be important in the evolution of strains of the marine cyanobacterium Synechococcus and that phages might mediate this process, but until now there has been no direct evidence to support this idea. We have rigorously purified bacteriophages (cyanomyoviruses) from their Synechococcus host and performed a series of experiments on phage-encapsidated DNA to reveal the presence of chromosomal Synechococcus DNA. Quantitative polymerase chain reaction has shown that approximately 1 in 10(5)Synechococcus phage particles contain a host marker gene in their capsids. This is the first study that has shown that phages infecting marine Synechococcus strains can package host DNA and this provides evidence for the potential importance of these phage in horizontal gene transfer.}, }
@article {pmid19719596, year = {2003}, author = {Hill, KE and Weightman, AJ}, title = {Horizontal transfer of dehalogenase genes on IncP1beta plasmids during bacterial adaptation to degrade alpha-halocarboxylic acids.}, journal = {FEMS microbiology ecology}, volume = {45}, number = {3}, pages = {273-282}, doi = {10.1016/S0168-6496(03)00158-2}, pmid = {19719596}, issn = {1574-6941}, abstract = {The diversity of bacterial alpha-halocarboxylic acid (alphaHA) dehalogenases from a polluted soil was investigated. Polymerase chain reaction (PCR) primers designed to amplify group I and group II dehalogenase (deh) gene sequences were used to screen bacterial isolates, nine beta-Proteobacteria and one gamma-Proteobacterium, from soil enrichments. Primers successfully amplified deh sequences from all 10 alphaHA-utilising isolates. Bacteria isolated at 15 or 30 degrees C on chloroacetic acid or 2-chloropropionic acid from the same polluted soil were shown to contain up to four plasmids, some of these common between isolates. Analysis of deletion mutants and Southern hybridisation showed that each isolate contained an apparently identical IncP1beta plasmid c. 80 kb in size, carrying group I deh genes in addition to an associated insertion sequence element. Moreover, an identical conjugative catabolic plasmid was isolated exogenously in several transconjugants independently selected from biparental matings between Ralstonia eutropha JMP222 and enrichment samples. PCR cloning and sequencing of deh genes directly from enrichment cultures inoculated with the same soil revealed that an identical deh gene was present in both primary, secondary and tertiary enrichment cultures, although this deh could not be amplified directly from soil. Two alphaHA-utilising bacteria isolated at lower temperature were found also to contain group II deh genes. Transfer of the deh catabolic phenotype to R. eutropha strain JMP222 occurred at high frequencies for four strains tested, a result that was consistent with assignment of the plasmids to the IncP1 incompatibility group. The promiscuous nature and broad host range of IncP plasmids make them likely to be involved in horizontal gene transfer during adaptation of bacteria to degrade organohalogens.}, }
@article {pmid19719693, year = {2003}, author = {Souza, JT and Raaijmakers, JM}, title = {Polymorphisms within the prnD and pltC genes from pyrrolnitrin and pyoluteorin-producing Pseudomonas and Burkholderia spp.}, journal = {FEMS microbiology ecology}, volume = {43}, number = {1}, pages = {21-34}, doi = {10.1111/j.1574-6941.2003.tb01042.x}, pmid = {19719693}, issn = {1574-6941}, abstract = {Abstract Pyrrolnitrin (PRN) and pyoluteorin (PLT) are broad-spectrum antibiotics produced by several strains of Pseudomonas and Burkholderia species. Both antibiotics play an important role in the suppression of multiple plant pathogenic fungi. Primers were developed from conserved sequences and amplified prnD and pltC fragments from 18 Pseudomonas and four Burkholderia spp. of worldwide origin that produce either PRN or PLT or both. Subsequent RFLP (restriction fragment length polymorphisms) analysis of the 438-bp pltC fragment showed no polymorphisms among PLT-producing Pseudomonas strains. Polymorphisms within the 786-bp prnD fragment, however, allowed the assessment of the diversity among PRN-producing Pseudomonas and Burkholderia spp. to a level similar to that obtained by three 10-mer primers in random amplified polymorphic DNA analysis. Phylogenetic analysis of 16S rDNA sequences of strains representative of PRN-producing Pseudomonas and Burkholderia species correlated well with their taxonomic status. Phylogenetic relationships inferred from each of the four prn genes and from the complete sequence of the prn biosynthetic locus were similar to 16S rDNA-based phylogeny for most strains, except for Burkholderia pyrrocinia DSM 10685. Both RFLP analysis and comparison of the prn gene sequences showed that B. pyrrocinia DSM 10685 was more closely related to PRN-producing Pseudomonas strains, suggesting that lateral gene transfer may have occurred. Colony hybridization and PCR with PRN- and PLT-specific probes and primers showed that Pseudomonas and Burkholderia spp. harboring the prnD and pltC gene were not present at detectable levels on roots of wheat grown in five agricultural soils collected in The Netherlands, two of them being naturally suppressive to Gaeumannomyces graminis var. tritici. These results suggest that PRN- and PLT-producing Pseudomonas and Burkholderia sp. do not contribute to the natural suppressiveness found in these Dutch take-all decline soils.}, }
@article {pmid19709287, year = {2002}, author = {Tolba, S and Egan, S and Kallifidas, D and Wellington, EM}, title = {Distribution of streptomycin resistance and biosynthesis genes in streptomycetes recovered from different soil sites.}, journal = {FEMS microbiology ecology}, volume = {42}, number = {2}, pages = {269-276}, doi = {10.1111/j.1574-6941.2002.tb01017.x}, pmid = {19709287}, issn = {1574-6941}, abstract = {Streptomycin resistant streptomycetes were isolated from four diverse sites. Two sites in Germany were sampled and included an agricultural experimental plot of apple trees which had a history of streptomycin application (AR) and a control site without antibiotic application (CR). Two sites in the UK were sampled; a pastureland site which had sewage injection (DW) and an agricultural site (CW). The actinomycete counts indicated a high proportion of streptomycin resistant isolates in the CW soil. Streptomycetes were identified by partial sequencing of the 16S rDNA. PCR product of the hypervariable gamma region of 16S rDNA allowed analysis by denaturing gradient gel electrophoresis to assess the diversity within the isolates. The streptomycin and sewage sludge treated sites showed decreased diversity within streptomycete populations. Isolates were screened for the streptomycin resistance gene, strA, and flanking biosynthesis gene, strB1. Distribution of these genes indicated the prevalence of str genes in the streptomycin treated soil. Evidence of horizontal gene transfer was recorded in isolates identified as Streptomyces platensis recovered from CR and AR sites which had acquired a streptomycin resistance gene homologous to that found in Streptomyces griseus. Members of the latter species were the most abundant streptomycin resistant streptomycetes isolated from all soils.}, }
@article {pmid19709286, year = {2002}, author = {Haagensen, JA and Hansen, SK and Johansen, T and Molin, S}, title = {In situ detection of horizontal transfer of mobile genetic elements.}, journal = {FEMS microbiology ecology}, volume = {42}, number = {2}, pages = {261-268}, doi = {10.1111/j.1574-6941.2002.tb01016.x}, pmid = {19709286}, issn = {1574-6941}, abstract = {Plasmid transfer was investigated in microbial populations associated with different types of surfaces. The general strategy behind these investigations was to label the transferable plasmid with a gene encoding a fluorescent protein in order to make it a transfer reporter. This was achieved by fusing the reporter gene with a lac promoter expression cassette and combining this with a donor cell-associated lacI repressor cassette. After construction of a range of strains and plasmids with combinations of genes expressing fluorescent proteins from constitutive (cell tagging) or regulated promoters (transfer reporters) it was thus possible to detect transfer events in situ and correlate these with either the location of donor and recipient cells or with the growth activity of the cells. In some cases, expression of unstable Gfp from a growth-controlled promoter, rrnB from Escherichia coli, was used to monitor bacterial growth activity in situ. Differential tagging of mobilizing and mobilizable plasmids with different genes encoding fluorescent proteins with varying emission wavelengths allowed in situ detection of plasmid mobilization and detection of retro-transfer on agar surfaces. The obtained data show that the several different types of fluorescent reporters, which are now available, allow more informative in situ investigations of horizontal gene transfer to be carried out, and by combining these genes with various expression systems it is possible to simultaneously monitor donor/recipient positioning, cellular activity and appearance of transconjugants.}, }
@article {pmid19709278, year = {2002}, author = {van Elsas, JD and Bailey, MJ}, title = {The ecology of transfer of mobile genetic elements.}, journal = {FEMS microbiology ecology}, volume = {42}, number = {2}, pages = {187-197}, doi = {10.1111/j.1574-6941.2002.tb01008.x}, pmid = {19709278}, issn = {1574-6941}, abstract = {The ecological aspects of the transfer and spread of mobile genetic elements (MGE) are reviewed in the context of the emerging evidence for the dominant role that horizontal gene transfer (HGT) has played in the evolutionary shaping of bacterial communities. Novel tools are described that allow a refined analysis of HGT in natural settings. The occurrence of HGT processes in soil and water, as affected by environmental factors, is then discussed. Examples are provided that illustrate how MGE can influence the behavior of microorganisms in their natural habitats. The occurrence of microorganisms as groups of cells in structured communities, such as those found in biofilms, is used as a framework in order to review the data and pose further questions on the evolutionary role and significance of contemporary gene transfer processes in nature. Selection by the environment is likely to be the dominant force in shaping the genetic make-up of bacterial communities. In fact, selective force can act as an apparent accelerator of gene transfer processes, mainly as a result of the enhancement of survival and persistence of favorably selected products of gene transfer processes (genes, metabolic pathways, microbial cells and communities). However, the current understanding of the triggering and impact of HGT in nature remains limited by our lack of understanding of the very nature and variety of the selective forces that act on microorganisms in situ. Hence, the relevant questions with respect to these triggers acting in natural habitats need to be answered using advanced approaches for studying HGT processes in nature, such as those discussed in this review.}, }
@article {pmid18333509, year = {2007}, author = {Charlton, ND and Cubeta, MA}, title = {Transmission of the M2 double-stranded RNA in Rhizoctonia solani anastomosis group 3 (AG-3).}, journal = {Mycologia}, volume = {99}, number = {6}, pages = {859-867}, doi = {10.3852/mycologia.99.6.859}, pmid = {18333509}, issn = {0027-5514}, mesh = {*Gene Transfer, Horizontal ; Genetic Markers ; Mycelium/genetics ; Polymorphism, Restriction Fragment Length ; RNA, Double-Stranded/*genetics ; RNA, Fungal/*genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Rhizoctonia/*genetics ; Solanaceae/microbiology ; }, abstract = {Horizontal transmission of the 3.57 kb M2 double-stranded RNA (dsRNA) between mycelia of somatically incompatible isolates of Rhizoctonia solani anastomosis group 3 (AG-3), an economically important pathogen of cultivated plants in the family Solanaceae, was investigated. Nine donor isolates of R. solani AG-3 containing the M2 dsRNA were paired on potato-dextrose agar with each of three different recipient isolates where the M2 dsRNA was absent. Reverse-transcription PCR (RT-PCR) was used to detect horizontal transmission of the M2 dsRNA via hyphal anastomosis from donor to recipient isolates by examining hyphal explants taken 3 cm from the hyphal interaction zone. PCR-RFLP genetic-based markers of two nuclear loci and one mitochondrial locus were used to confirm identity and transmission between donor and recipient isolates of R. solani AG-3. The frequency of transmission observed between 72 pairings of the eight donor and three recipient isolates was approximately 4% of the total pairings, and differences in the phenotype of the recipient isolates after acquisition of the M2 dsRNA via horizontal transmission were observed. To our knowledge this represents the first demonstration of transmission of dsRNA between genetically different individuals of R. solani confirmed with nuclear and mitochondrial markers. These results suggest that transmission can occur between somatically incompatible isolates of R. solani AG-3 but that maintenance of the dsRNA in the recipient isolates was not stable after repeated subculturing on nutrient medium.}, }
@article {pmid18326566, year = {2008}, author = {Coros, A and DeConno, E and Derbyshire, KM}, title = {IS6110, a Mycobacterium tuberculosis complex-specific insertion sequence, is also present in the genome of Mycobacterium smegmatis, suggestive of lateral gene transfer among mycobacterial species.}, journal = {Journal of bacteriology}, volume = {190}, number = {9}, pages = {3408-3410}, pmid = {18326566}, issn = {1098-5530}, support = {R01 AI042308/AI/NIAID NIH HHS/United States ; AI 42308/AI/NIAID NIH HHS/United States ; }, mesh = {Base Sequence ; DNA Transposable Elements/*genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Molecular Sequence Data ; Mycobacterium smegmatis/*genetics ; Mycobacterium tuberculosis/*genetics ; }, abstract = {IS6110 is an insertion element found exclusively within the members of the Mycobacterium tuberculosis complex (MTBC), and because of this exclusivity, it has become an important diagnostic tool in the identification of MTBC species. The restriction of IS6110 to the MTBC is hypothesized to arise from the inability of these bacteria to exchange DNA. We have identified an IS6110-related element in a strain of Mycobacterium smegmatis. The presence of IS6110 indicates that lateral gene transfer has occurred among mycobacterial species, suggesting that the mycobacterial gene pool is larger than previously suspected.}, }
@article {pmid18325835, year = {2008}, author = {Witte, W and Cuny, C and Klare, I and Nübel, U and Strommenger, B and Werner, G}, title = {Emergence and spread of antibiotic-resistant Gram-positive bacterial pathogens.}, journal = {International journal of medical microbiology : IJMM}, volume = {298}, number = {5-6}, pages = {365-377}, doi = {10.1016/j.ijmm.2007.10.005}, pmid = {18325835}, issn = {1618-0607}, mesh = {Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Multiple, Bacterial/*genetics ; *Gene Transfer, Horizontal ; Gram-Positive Bacteria/classification/*drug effects/*genetics ; Gram-Positive Bacterial Infections/epidemiology/*microbiology/*transmission ; Humans ; }, abstract = {Development of multiple resistances to antibiotics in staphylococci, enterococci and pneumococci became a health threat during the past 20 years, not only with respect to nosocomial infections. This resistance development is based on acquisition of resistance genes by predominant epidemic subpopulations (clonal complexes). Although emergence and spread of methicillin-resistant Staphylococcus aureus is associated with a limited number of epidemic clones which have been widely disseminated, acquisition of SCCmec elements by susceptible ancestors has taken place at different times and at different locations. Among Staphylococcus epidermidis and Enterococcus faecium, one clonal complex, which had acquired resistance genes at several occasions, is widely disseminated in hospitals. Also in Streptococcus pneumoniae, antibiotic resistance is preferentially associated with clonal lineages which have a capacity for spreading. They became, however, more rare after introduction of the 7-valent conjugate vaccine.}, }
@article {pmid18325257, year = {2008}, author = {Barlow, M and Reik, RA and Jacobs, SD and Medina, M and Meyer, MP and McGowan, JE and Tenover, FC}, title = {High rate of mobilization for blaCTX-Ms.}, journal = {Emerging infectious diseases}, volume = {14}, number = {3}, pages = {423-428}, pmid = {18325257}, issn = {1080-6059}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/*enzymology/genetics ; DNA, Bacterial/*genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genetic Variation ; Phylogeny ; Plasmids/genetics/metabolism ; Protein Transport ; beta-Lactamases/*classification/*metabolism ; }, abstract = {We constructed a phylogenetic analysis of class A beta-lactamases and found that the blaCTX-Ms have been mobilized to plasmids approximately 10 times more frequently than other class A beta-lactamases. We also found that the blaCTX-Ms are descended from a common ancestor that was incorporated in ancient times into the chromosome of the ancestor of Kluyvera species through horizontal transfer. Considerable sequence divergence has occurred among the descendents of that ancestral gene sequence since that gene was inserted. That divergence has mainly occurred in the presence of purifying selection, which indicates a slow rate of evolution for blaCTX-Ms in the pre-antimicrobial drug era.}, }
@article {pmid18322033, year = {2008}, author = {Bonner, CA and Disz, T and Hwang, K and Song, J and Vonstein, V and Overbeek, R and Jensen, RA}, title = {Cohesion group approach for evolutionary analysis of TyrA, a protein family with wide-ranging substrate specificities.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {72}, number = {1}, pages = {13-53, table of contents}, pmid = {18322033}, issn = {1098-5557}, support = {G13 LM008297/LM/NLM NIH HHS/United States ; HHSN266200400042C//PHS HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacteria, Anaerobic/enzymology/genetics ; Bacterial Proteins/*chemistry/*classification/genetics ; Coenzymes/classification/genetics/metabolism ; Computational Biology/*methods ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Multienzyme Complexes/*chemistry/*classification/genetics ; *Phylogeny ; Substrate Specificity ; Tyrosine/biosynthesis/genetics ; }, abstract = {Many enzymes and other proteins are difficult subjects for bioinformatic analysis because they exhibit variant catalytic, structural, regulatory, and fusion mode features within a protein family whose sequences are not highly conserved. However, such features reflect dynamic and interesting scenarios of evolutionary importance. The value of experimental data obtained from individual organisms is instantly magnified to the extent that given features of the experimental organism can be projected upon related organisms. But how can one decide how far along the similarity scale it is reasonable to go before such inferences become doubtful? How can a credible picture of evolutionary events be deduced within the vertical trace of inheritance in combination with intervening events of lateral gene transfer (LGT)? We present a comprehensive analysis of a dehydrogenase protein family (TyrA) as a prototype example of how these goals can be accomplished through the use of cohesion group analysis. With this approach, the full collection of homologs is sorted into groups by a method that eliminates bias caused by an uneven representation of sequences from organisms whose phylogenetic spacing is not optimal. Each sufficiently populated cohesion group is phylogenetically coherent and defined by an overall congruence with a distinct section of the 16S rRNA gene tree. Exceptions that occasionally are found implicate a clearly defined LGT scenario whereby the recipient lineage is apparent and the donor lineage of the gene transferred is localized to those organisms that define the cohesion group. Systematic procedures to manage and organize otherwise overwhelming amounts of data are demonstrated.}, }
@article {pmid18321363, year = {2008}, author = {Oloomi, M and Bouzari, S}, title = {Molecular profile and genetic diversity of cytolethal distending toxin (CDT)-producing Escherichia coli isolates from diarrheal patients.}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {116}, number = {2}, pages = {125-132}, doi = {10.1111/j.1600-0463.2008.00910.x}, pmid = {18321363}, issn = {0903-4641}, mesh = {Bacterial Toxins/biosynthesis/*genetics ; Base Sequence ; Blotting, Southern ; Child ; Cloning, Molecular ; DNA, Bacterial/chemistry/genetics ; Diarrhea/*microbiology ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/*genetics/metabolism ; Escherichia coli Infections/*microbiology ; Genetic Variation ; Humans ; Molecular Sequence Data ; Polymerase Chain Reaction ; RNA, Transfer/chemistry/genetics ; Sequence Analysis, DNA ; }, abstract = {Cytolethal distending toxin (CDT)-producing Escherichia coli strains are considered to be a heterogeneous group of E. coli. In the present investigation, 20 CDT-producing E. coli strains, which had already been shown to be cytotoxic necrotizing factor (cnf) gene positive, were selected by PCR. Since these strains proved to be CDT producers on CHO cells but were partially characterized by PCR, they were subjected to PCR analysis to amplify the complete coding region of cdt genes. Moreover, the genetic relatedness of these strains was examined by pulse field gel electrophoresis (PFGE). To check the extent of homogeneity of these strains at the chromosomal level, tRNA insertion site analysis was performed. The CDT-producing E. coli strains under investigation were shown to be heterogeneous and diverse in regard to their genetic analysis. This observed diversity could be an independent acquisition of virulence genes that might occur through horizontal gene transfer by mobile genetic elements. This conclusion is based on the fact that data shown by tRNA insertion site analysis revealed that there is no common pattern of insertion among these isolates although they do share a common trait of CDT production.}, }
@article {pmid18320344, year = {2008}, author = {Chandra, G and Chater, KF}, title = {Evolutionary flux of potentially bldA-dependent Streptomyces genes containing the rare leucine codon TTA.}, journal = {Antonie van Leeuwenhoek}, volume = {94}, number = {1}, pages = {111-126}, doi = {10.1007/s10482-008-9231-5}, pmid = {18320344}, issn = {0003-6072}, mesh = {Anti-Bacterial Agents/biosynthesis ; Bacterial Proteins/*genetics/metabolism ; Codon/*genetics ; *Evolution, Molecular ; *Gene Expression Regulation, Bacterial ; Genome, Bacterial ; Molecular Sequence Data ; Multigene Family ; RNA, Bacterial/genetics/*metabolism ; RNA, Transfer, Leu/genetics/*metabolism ; Species Specificity ; Streptomyces/*genetics/metabolism ; Streptomyces coelicolor/genetics/metabolism ; }, abstract = {Previous studies have shown that one of the six leucine codons, UUA, is rare in Streptomyces, and that, while the gene for the UUA-specific tRNA, bldA, can generally be inactivated in diverse streptomycetes without impairing vegetative growth, bldA mutants are typically defective in reproductive aerial growth and in antibiotic production. Here, four complete genome sequences and 143 gene clusters for antibiotic biosynthesis from diverse streptomycetes were analysed in order to evaluate the evolution and function of genes whose possession of TTA codons makes them dependent on bldA. It was deduced that the last common ancestor of the four sequenced genomes, possibly 220 million years ago, already possessed the bldA system, together with perhaps 200 TTA-containing target genes. Some 33 of these genes are retained by the modern descendants, though only three of them retain a TTA in all occurrences. Nearly all of these 33, as well as many of the TTA-containing genes with orthologues in two or three of the four genomes, have the same location on the chromosomes as in their common ancestor. However, the majority of TTA-containing genes (61% overall in the four genomes) are species-specific, and were probably acquired by comparatively recent horizontal gene transfer. Most of these genes are of unknown function, and it is likely that many of them confer specialised ecological benefits. On the other hand, one class of species-specific, functionally recognisable, horizontally acquired genes--the gene clusters for antibiotic production--very often contain TTA codons; and nearly half of them have TTA codons in their pathway-specific regulatory genes.}, }
@article {pmid18318843, year = {2008}, author = {Lima, WC and Paquola, AC and Varani, AM and Van Sluys, MA and Menck, CF}, title = {Laterally transferred genomic islands in Xanthomonadales related to pathogenicity and primary metabolism.}, journal = {FEMS microbiology letters}, volume = {281}, number = {1}, pages = {87-97}, doi = {10.1111/j.1574-6968.2008.01083.x}, pmid = {18318843}, issn = {0378-1097}, mesh = {DNA, Bacterial/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genomic Islands ; Metabolic Networks and Pathways/genetics ; Phylogeny ; Sequence Homology, Amino Acid ; Virulence Factors/genetics ; Xanthomonas axonopodis/*genetics/metabolism/pathogenicity ; Xanthomonas campestris/*genetics/metabolism/pathogenicity ; }, abstract = {Lateral gene transfer (LGT) is considered as one of the drivers in bacterial genome evolution, usually associated with increased fitness and/or changes in behavior, especially if one considers pathogenic vs. non-pathogenic bacterial groups. The genomes of two phytopathogens, Xanthomonas campestris pv. campestris and Xanthomonas axonopodis pv. citri, were previously inspected for genome islands originating from LGT events, and, in this work, potentially early and late LGT events were identified according to their altered nucleotide composition. The biological role of the islands was also assessed, and pathogenicity, virulence and secondary metabolism pathways were functions highly represented, especially in islands that were found to be recently transferred. However, old islands are composed of a high proportion of genes related to cell primary metabolic functions. These old islands, normally undetected by traditional atypical composition analysis, but confirmed as product of LGT by atypical phylogenetic reconstruction, reveal the role of LGT events by replacing core metabolic genes normally inherited by vertical processes.}, }
@article {pmid18312397, year = {2008}, author = {van der Does, HC and Lievens, B and Claes, L and Houterman, PM and Cornelissen, BJ and Rep, M}, title = {The presence of a virulence locus discriminates Fusarium oxysporum isolates causing tomato wilt from other isolates.}, journal = {Environmental microbiology}, volume = {10}, number = {6}, pages = {1475-1485}, doi = {10.1111/j.1462-2920.2007.01561.x}, pmid = {18312397}, issn = {1462-2920}, mesh = {Blotting, Southern ; Chromosomes, Fungal ; DNA, Fungal/genetics ; Fungal Proteins/genetics ; Fusarium/*genetics/pathogenicity ; *Genes, Fungal ; Genome, Fungal ; Solanum lycopersicum/*microbiology ; Phylogeny ; Plant Diseases/*microbiology ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA ; Virulence ; Virulence Factors/*genetics ; }, abstract = {Fusarium oxysporum is an asexual fungus that inhabits soils throughout the world. As a species, F. oxysporum can infect a very broad range of plants and cause wilt or root rot disease. Single isolates of F. oxysporum, however, usually infect one or a few plant species only. They have therefore been grouped into formae speciales (f.sp.) based on host specificity. Isolates able to cause tomato wilt (f.sp. lycopersici) do not have a single common ancestor within the F. oxysporum species complex. Here we show that, despite their polyphyletic origin, isolates belonging to f.sp. lycopersici all contain an identical genomic region of at least 8 kb that is absent in other formae speciales and non-pathogenic isolates, and comprises the genes SIX1, SIX2 and SHH1. In addition, SIX3, which lies elsewhere on the same chromosome, is also unique for f.sp. lycopersici. SIX1 encodes a virulence factor towards tomato, and the Six1, Six2 and Six3 proteins are secreted in xylem during colonization of tomato plants. We speculate that these genes may be part of a larger, dispensable region of the genome that confers the ability to cause tomato wilt and has spread among clonal lines of F. oxysporum through horizontal gene transfer. Our findings also have practical implications for the detection and identification of f.sp. lycopersici.}, }
@article {pmid18311156, year = {2008}, author = {Hawkey, PM}, title = {Molecular epidemiology of clinically significant antibiotic resistance genes.}, journal = {British journal of pharmacology}, volume = {153 Suppl 1}, number = {Suppl 1}, pages = {S406-13}, pmid = {18311156}, issn = {0007-1188}, support = {//Department of Health/United Kingdom ; }, mesh = {Animals ; Bacteria/*genetics ; Bacterial Infections/*drug therapy/*genetics/microbiology ; Drug Resistance, Microbial/*genetics ; Genes, Bacterial/*physiology ; Humans ; *Molecular Epidemiology ; }, abstract = {Antimicrobials were first introduced into medical practice a little over 60 years ago and since that time resistant strains of bacteria have arisen in response to the selective pressure of their use. This review uses the paradigm of the evolution and spread of beta-lactamases and in particular beta-lactamases active against antimicrobials used to treat Gram-negative infections. The emergence and evolution particularly of CTX-M extended-spectrum beta-lactamases (ESBLs) is described together with the molecular mechanisms responsible for both primary mutation and horizontal gene transfer. Reference is also made to other significant antibiotic resistance genes, resistance mechanisms in Gram-negative bacteria, such as carbepenamases, and plasmid-mediated fluoroquinolone resistance. The pathogen Staphylococcus aureus is reviewed in detail as an example of a highly successful Gram-positive bacterial pathogen that has acquired and developed resistance to a wide range of antimicrobials. The role of selective pressures in the environment as well as the medical use of antimicrobials together with the interplay of various genetic mechanisms for horizontal gene transfer are considered in the concluding part of this review.}, }
@article {pmid18310418, year = {2008}, author = {Nonaka, S and Sugawara, M and Minamisawa, K and Yuhashi, K and Ezura, H}, title = {1-Aminocyclopropane-1-carboxylate deaminase enhances Agrobacterium tumefaciens-mediated gene transfer into plant cells.}, journal = {Applied and environmental microbiology}, volume = {74}, number = {8}, pages = {2526-2528}, pmid = {18310418}, issn = {1098-5336}, mesh = {Agrobacterium tumefaciens/*genetics ; Arabidopsis/*genetics ; Carbon-Carbon Lyases/*metabolism ; DNA, Bacterial/*metabolism ; Ethylenes/metabolism ; *Gene Transfer Techniques ; *Gene Transfer, Horizontal ; }, abstract = {Agrobacterium-mediated gene transfer is widely used for plant molecular genetics, and efficient techniques are required. Recent studies show that ethylene inhibits the gene transfer. To suppress ethylene evolution, we introduced 1-aminocyclopropane-1-carboxylate (ACC) deaminase into Agrobacterium tumefaciens. The ACC deaminase enhanced A. tumefaciens-mediated gene transfer into plants.}, }
@article {pmid18309263, year = {2008}, author = {Kim, MC and Ahn, JH and Shin, HC and Kim, T and Ryu, TH and Kim, DH and Song, HG and Lee, GH and Ka, JO}, title = {Molecular analysis of bacterial community structures in paddy soils for environmental risk assessment with two varieties of genetically modified rice, Iksan 483 and Milyang 204.}, journal = {Journal of microbiology and biotechnology}, volume = {18}, number = {2}, pages = {207-218}, pmid = {18309263}, issn = {1017-7825}, mesh = {Bacteria/classification/*genetics/*isolation &amp; purification/metabolism ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; *Ecosystem ; Electrophoresis, Polyacrylamide Gel ; Fatty Acids/metabolism ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Oryza/genetics/*microbiology ; Phospholipids/metabolism ; Plants, Genetically Modified/genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; Soil/analysis ; *Soil Microbiology ; Time Factors ; }, abstract = {The impacts of planted transgenic rice varieties on bacterial communities in paddy soils were monitored using both cultivation and molecular methods. The rice field plot consisted of eighteen subplots planted with two genetically modified (GM) rice and four non-GM rice plants in three replicates. Analysis with denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA genes revealed that the bacterial community structures were quite similar to each other in a given month, suggesting that there were no significant differences in bacterial communities between GM and non- GM rice soils. The bacterial community structures appeared to be generally stable with the seasons, as shown by a slight variation of microbial population levels and DGGE banding patterns over the year. Comparison analysis of 16S rDNA clone libraries constructed from soil bacterial DNA showed that there were no significant differences between GM and non-GM soil libraries but revealed seasonal differences of phyla distribution between August and December. The composition profile of phospholipid fatty acids (PLFA) between GM and non-GM soils also was not significantly different to each other. When soil DNAs were analyzed with PCR by using primers for the bar gene, which was introduced into GM rice, positive DNA bands were found in October and December soils. However, no bar gene sequence was detected in PCR analysis with DNAs extracted from both cultured and uncultured soil bacterial fractions. The result of this study suggested that, in spite of seasonal variations of bacterial communities and persistence of the bar gene, the bacterial communities of the experimental rice field were not significantly affected by cultivation of GM rice varieties.}, }
@article {pmid18305979, year = {2008}, author = {Lima, WC and Menck, CF}, title = {Replacement of the arginine biosynthesis operon in Xanthomonadales by lateral gene transfer.}, journal = {Journal of molecular evolution}, volume = {66}, number = {3}, pages = {266-275}, pmid = {18305979}, issn = {0022-2844}, mesh = {Arginine/*biosynthesis/genetics ; *Gene Transfer, Horizontal ; *Operon ; Xanthomonadaceae/*genetics ; }, abstract = {The role of lateral gene transfer (LGT) in prokaryotes has been shown to rapidly change the genome content, providing new gene tools for environmental adaptation. Features related to pathogenesis and resistance to strong selective conditions have been widely shown to be products of gene transfer between bacteria. The genomes of the gamma-proteobacteria from the genus Xanthomonas, composed mainly of phytopathogens, have potential genomic islands that may represent imprints of such evolutionary processes. In this work, the evolution of genes involved in the pathway responsible for arginine biosynthesis in Xanthomonadales was investigated, and several lines of evidence point to the foreign origin of the arg genes clustered within a potential operon. Their presence inside a potential genomic island, bordered by a tRNA gene, the unusual ranking of sequence similarity, and the atypical phylogenies indicate that the metabolic pathway for arginine biosynthesis was acquired through LGT in the Xanthomonadales group. Moreover, although homologues were also found in Bacteroidetes (Flavobacteria group), for many of the genes analyzed close homologues are detected in different life domains (Eukarya and Archaea), indicating that the source of these arg genes may have been outside the Bacteria clade. The possibility of replacement of a complete primary metabolic pathway by LGT events supports the selfish operon hypothesis and may occur only under very special environmental conditions. Such rare events reveal part of the history of these interesting mosaic Xanthomonadales genomes, disclosing the importance of gene transfer modifying primary metabolism pathways and extending the scenario for bacterial genome evolution.}, }
@article {pmid18305156, year = {2008}, author = {Roy, H and Ibba, M}, title = {RNA-dependent lipid remodeling by bacterial multiple peptide resistance factors.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {12}, pages = {4667-4672}, pmid = {18305156}, issn = {1091-6490}, support = {065183//PHS HHS/United States ; }, mesh = {Aminoacylation ; Bacterial Proteins/*metabolism ; Catalysis ; Cell Membrane/metabolism ; Chromatography, Thin Layer ; Clostridium perfringens/*metabolism/pathogenicity ; Evolution, Molecular ; Kinetics ; *Lipid Metabolism ; Peptide Elongation Factor Tu/metabolism ; Phosphatidylglycerols/biosynthesis ; Phylogeny ; RNA/*metabolism ; RNA, Transfer, Amino Acyl/metabolism ; Virulence Factors/*metabolism ; }, abstract = {Multiple peptide resistance (MprF) virulence factors control cellular permeability to cationic antibiotics by aminoacylating inner membrane lipids. It has been shown previously that one class of MprF can use Lys-tRNA(Lys) to modify phosphatidylglycerol (PG), but the mechanism of recognition and possible role of other MprFs are unknown. Here, we used an in vitro reconstituted lipid aminoacylation system to investigate the two phylogenetically distinct MprF paralogs (MprF1 and MprF2) found in the bacterial pathogen Clostridium perfringens. Although both forms of MprF aminoacylate PG, they do so with different amino acids; MprF1 is specific for Ala-tRNA(Ala), and MprF2 utilizes Lys-tRNA(Lys). This provides a mechanism by which the cell can fine tune the charge of the inner membrane by using the neutral amino acid alanine, potentially providing resistance to a broader range of antibiotics than offered by lysine modification alone. Mutation of tRNA(Ala) and tRNA(Lys) had little effect on either MprF activity, indicating that the aminoacyl moiety is the primary determinant for aminoacyl-tRNA recognition. The lack of discrimination of the tRNA is consistent with the role of MprF as a virulence factor, because species-specific differences in tRNA sequence would not present a barrier to horizontal gene transfer. Taken together, our findings reveal how the MprF proteins provide a potent virulence mechanism by which pathogens can readily acquire resistance to chemically diverse antibiotics.}, }
@article {pmid18305155, year = {2008}, author = {Schoen, C and Blom, J and Claus, H and Schramm-Glück, A and Brandt, P and Müller, T and Goesmann, A and Joseph, B and Konietzny, S and Kurzai, O and Schmitt, C and Friedrich, T and Linke, B and Vogel, U and Frosch, M}, title = {Whole-genome comparison of disease and carriage strains provides insights into virulence evolution in Neisseria meningitidis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {9}, pages = {3473-3478}, pmid = {18305155}, issn = {1091-6490}, mesh = {Base Sequence ; *Biological Evolution ; Genes, Bacterial ; *Genome, Bacterial ; Humans ; Meningococcal Infections ; Molecular Sequence Data ; Neisseria meningitidis/*genetics/*pathogenicity ; Phylogeny ; Virulence/genetics ; }, abstract = {Neisseria meningitidis is a leading cause of infectious childhood mortality worldwide. Most research efforts have hitherto focused on disease isolates belonging to only a few hypervirulent clonal lineages. However, up to 10% of the healthy human population is temporarily colonized by genetically diverse strains mostly with little or no pathogenic potential. Currently, little is known about the biology of carriage strains and their evolutionary relationship with disease isolates. The expression of a polysaccharide capsule is the only trait that has been convincingly linked to the pathogenic potential of N. meningitidis. To gain insight into the evolution of virulence traits in this species, whole-genome sequences of three meningococcal carriage isolates were obtained. Gene content comparisons with the available genome sequences from three disease isolates indicate that there is no core pathogenome in N. meningitidis. A comparison of the chromosome structure suggests that a filamentous prophage has mediated large chromosomal rearrangements and the translocation of some candidate virulence genes. Interspecific comparison of the available Neisseria genome sequences and dot blot hybridizations further indicate that the insertion sequence IS1655 is restricted only to N. meningitidis; its low sequence diversity is an indicator of an evolutionarily recent population bottleneck. A genome-based phylogenetic reconstruction provides evidence that N. meningitidis has emerged as an unencapsulated human commensal from a common ancestor with Neisseria gonorrhoeae and Neisseria lactamica and consecutively acquired the genes responsible for capsule synthesis via horizontal gene transfer.}, }
@article {pmid18304319, year = {2008}, author = {Bratke, KA and McLysaght, A}, title = {Identification of multiple independent horizontal gene transfers into poxviruses using a comparative genomics approach.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {67}, pmid = {18304319}, issn = {1471-2148}, mesh = {Deoxyribodipyrimidine Photo-Lyase/genetics ; Gene Transfer, Horizontal/*genetics ; Genomics/*methods ; Glutathione Peroxidase/genetics ; Humans ; Interleukin-10/genetics ; Phylogeny ; Poxviridae/classification/*genetics ; Thymidine Kinase/genetics ; }, abstract = {BACKGROUND: Poxviruses are important pathogens of humans, livestock and wild animals. These large dsDNA viruses have a set of core orthologs whose gene order is extremely well conserved throughout poxvirus genera. They also contain many genes with sequence and functional similarity to host genes which were probably acquired by horizontal gene transfer.Although phylogenetic trees can indicate the occurrence of horizontal gene transfer and even uncover multiple events, their use may be hampered by uncertainties in both the topology and the rooting of the tree. We propose to use synteny conservation around the horizontally transferred gene (HTgene) to distinguish between single and multiple events.<br><br>RESULTS: Here we devise a method that incorporates comparative genomic information into the investigation of horizontal gene transfer, and we apply this method to poxvirus genomes. We examined the synteny conservation around twenty four pox genes that we identified, or which were reported in the literature, as candidate HTgenes. We found support for multiple independent transfers into poxviruses for five HTgenes. Three of these genes are known to be important for the survival of the virus in or out of the host cell and one of them increases susceptibility to some antiviral drugs.<br><br>CONCLUSION: In related genomes conserved synteny information can provide convincing evidence for multiple independent horizontal gene transfer events even in the absence of a robust phylogenetic tree for the HTgene.}, }
@article {pmid18301771, year = {2008}, author = {Kajava, AV and Anisimova, M and Peeters, N}, title = {Origin and evolution of GALA-LRR, a new member of the CC-LRR subfamily: from plants to bacteria?.}, journal = {PloS one}, volume = {3}, number = {2}, pages = {e1694}, pmid = {18301771}, issn = {1932-6203}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacterial Proteins ; *Evolution, Molecular ; F-Box Motifs/genetics ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genes, Plant ; Phylogeny ; Ralstonia solanacearum/chemistry/*genetics/pathogenicity ; Virulence Factors/genetics ; }, abstract = {The phytopathogenic bacterium Ralstonia solanacearum encodes type III effectors, called GALA proteins, which contain F-box and LRR domains. The GALA LRRs do not perfectly fit any of the previously described LRR subfamilies. By applying protein sequence analysis and structural prediction, we clarify this ambiguous case of LRR classification and assign GALA-LRRs to CC-LRR subfamily. We demonstrate that side-by-side packing of LRRs in the 3D structures may control the limits of repeat variability within the LRR subfamilies during evolution. The LRR packing can be used as a criterion, complementing the repeat sequences, to classify newly identified LRR domains. Our phylogenetic analysis of F-box domains proposes the lateral gene transfer of bacterial GALA proteins from host plants. We also present an evolutionary scenario which can explain the transformation of the original plant LRRs into slightly different bacterial LRRs. The examination of the selective evolutionary pressure acting on GALA proteins suggests that the convex side of their horse-shoe shaped LRR domains is more prone to positive selection than the concave side, and we therefore hypothesize that the convex surface might be the site of protein binding relevant to the adaptor function of the F-box GALA proteins. This conclusion provides a strong background for further functional studies aimed at determining the role of these type III effectors in the virulence of R. solanacearum.}, }
@article {pmid18299576, year = {2008}, author = {Martens, C and Vandepoele, K and Van de Peer, Y}, title = {Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {9}, pages = {3427-3432}, pmid = {18299576}, issn = {1091-6490}, mesh = {Animals ; *Biological Evolution ; Eukaryota/*genetics ; Evolution, Molecular ; *Genome ; Genomics ; Phylogeny ; Plasmodium/genetics ; }, abstract = {The chromalveolates form a highly diverse and fascinating assemblage of organisms, ranging from obligatory parasites such as Plasmodium to free-living ciliates and algae such as kelps, diatoms, and dinoflagellates. Many of the species in this monophyletic grouping are of major medical, ecological, and economical importance. Nevertheless, their genome evolution is much less well studied than that of higher plants, animals, or fungi. In the current study, we have analyzed and compared 12 chromalveolate species for which whole-sequence information is available and provide a detailed picture on gene loss and gene gain in the different lineages. As expected, many gene loss and gain events can be directly correlated with the lifestyle and specific adaptations of the organisms studied. For instance, in the obligate intracellular Apicomplexa we observed massive loss of genes that play a role in general basic processes such as amino acid, carbohydrate, and lipid metabolism, reflecting the transition of a free-living to an obligate intracellular lifestyle. In contrast, many gene families show species-specific expansions, such as those in the plant pathogen oomycete Phytophthora that are involved in degrading the plant cell wall polysaccharides to facilitate the pathogen invasion process. In general, chromalveolates show a tremendous difference in genome structure and evolution and in the number of genes they have lost or gained either through duplication or horizontal gene transfer.}, }
@article {pmid18298053, year = {2007}, author = {Eraç, B and Gülay, Z}, title = {Molecular epidemiology of PER-1 extended spectrum beta-lactamase among gram-negative bacteria isolated at a tertiary care hospital.}, journal = {Folia microbiologica}, volume = {52}, number = {5}, pages = {535-541}, pmid = {18298053}, issn = {0015-5632}, mesh = {Acinetobacter Infections/epidemiology/transmission ; Acinetobacter baumannii/drug effects/enzymology/*genetics/isolation &amp; purification ; Anti-Bacterial Agents/pharmacology ; Ceftazidime/pharmacology ; DNA Fingerprinting ; Gene Transfer, Horizontal ; Hospitals, University ; Humans ; Integrons ; Microbial Sensitivity Tests ; Multigene Family ; Polymerase Chain Reaction/methods ; Pseudomonas Infections/epidemiology/transmission ; Pseudomonas aeruginosa/drug effects/enzymology/*genetics/isolation &amp; purification ; Turkey/epidemiology ; beta-Lactam Resistance/drug effects/*genetics ; beta-Lactamases/*genetics ; }, abstract = {The bla(PER-1) presence was sought by PCR in 289 ceftazidime resistant Gram-negative bacteria isolated at Dokuz Eylul University Hospital (Turkey) between 1998 and 2003. PER-1 production rates were 32.3, 33.9, 14.9 and 37.9% in the 1998-2000 period, 2001, 2002 and 2003, respectively. bla(PER-1) was detected in 46.2 and 35.9% of ceftazidime-resistant Pseudomonas aeruginosa and Acinetobacter baumannii isolates, respectively. ERIC-PCR results revealed that dissemination of two endemic clones for both P. aeruginosa (X and Y) and A. baumannii (A and B) was responsible for the high prevalence. Results of the conjugation tests and plasmid curing experiments suggested that bla(PER-1) was located on the chromosome in the representative strains. It was also shown for the first time that bla(PER-1) in a clinical isolate was associated with class-1 integron which could facilitate dissemination of bla(PER-1) among bacteria.}, }
@article {pmid18297656, year = {2008}, author = {Sriramulu, DD}, title = {Adaptive expression of foreign genes in the clonal variants of bacteria: from proteomics to clinical application.}, journal = {Proteomics}, volume = {8}, number = {4}, pages = {882-892}, doi = {10.1002/pmic.200700811}, pmid = {18297656}, issn = {1615-9861}, mesh = {*Adaptation, Physiological ; Bacteria/*genetics/pathogenicity ; Clone Cells/metabolism ; Cystic Fibrosis/microbiology ; DNA, Bacterial/*metabolism ; Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Genetic Variation ; Genomic Islands/genetics ; Humans ; *Proteomics ; Pseudomonas aeruginosa/genetics ; Staphylococcus aureus/drug effects/genetics ; Virulence ; }, abstract = {Clonal variants of bacteria are able to colonize environmental niches and patients. The factors, that determine the interplay between the colonization of diverse habitats and adaptation, are acquired through horizontal gene transfer. Elucidation of mechanisms, which lead to the prevalence of dominant bacterial clones in patients and the environment, requires the knowledge of complex phenotypes. It was found in the genomes of most bacteria, that upon a conserved chromosomal backbone there were regions of plasticity achieved by insertions, deletions and rearrangements of genomic islands and islets as well as large chromosomal inversions. However, it had been shown that environmental and clinical isolates are indistinguishable in certain pathogenic and biodegradative properties. For example, clonal variants of Pseudomonas aeruginosa exhibit convergent phenotypes despite the presence of numerous DNA insertions in the genome. Apart from this feature, expression of a few genes from the acquired genetic material is important for niche-based adaptation of this organism. Protein expression patterns at the cellular and sub-cellular levels showed common virulence factors and novel drug targets among clonal variants of bacteria. This review will give a short overview on proteomics of different clonal variants of bacteria with respect to clinical applications.}, }
@article {pmid18296415, year = {2008}, author = {Csurös, M and Rogozin, IB and Koonin, EV}, title = {Extremely intron-rich genes in the alveolate ancestors inferred with a flexible maximum-likelihood approach.}, journal = {Molecular biology and evolution}, volume = {25}, number = {5}, pages = {903-911}, doi = {10.1093/molbev/msn039}, pmid = {18296415}, issn = {1537-1719}, support = {//Intramural NIH HHS/United States ; }, mesh = {Animals ; Eukaryota/*genetics ; Eukaryotic Cells ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Protozoan ; *Introns ; Likelihood Functions ; Plants/genetics ; }, abstract = {Chromalveolates are a large, diverse supergroup of unicellular eukaryotes that includes Apicomplexa, dinoflagellates, ciliates (three lineages that form the alveolate branch), heterokonts, haptophytes, and cryptomonads (three lineages comprising the chromist branch). All sequenced genomes of chromalveolates have relatively low intron density in protein-coding genes, and few intron positions are shared between chromalveolate lineages. In contrast, genes of different chromalveolates share many intron positions with orthologous genes from other eukaryotic supergroups, in particular, the intron-rich orthologs from animals and plants. Reconstruction of the history of intron gain and loss during the evolution of chromalveolates using a general and flexible maximum-likelihood approach indicates that genes of the ancestors of chromalveolates and, particularly, alveolates had unexpectedly high intron densities. It is estimated that the chromalveolate ancestor had, approximately, two-third of the human intron density, whereas the intron density in the genes of the alveolate ancestor is estimated to be slightly greater than the human intron density. Accordingly, it is inferred that the evolution of chromalveolates was dominated by intron loss. The conclusion that ancestral chromalveolate forms had high intron densities is unexpected because all extant unicellular eukaryotes have relatively few introns and are thought to be unable to maintain numerous introns due to intense purifying selection in their, typically, large populations. It is suggested that, at early stages of evolution, chromalveolates went through major population bottlenecks that were accompanied by intron invasion.}, }
@article {pmid18295883, year = {2008}, author = {te Poele, EM and Samborskyy, M and Oliynyk, M and Leadlay, PF and Bolhuis, H and Dijkhuizen, L}, title = {Actinomycete integrative and conjugative pMEA-like elements of Amycolatopsis and Saccharopolyspora decoded.}, journal = {Plasmid}, volume = {59}, number = {3}, pages = {202-216}, doi = {10.1016/j.plasmid.2008.01.003}, pmid = {18295883}, issn = {0147-619X}, support = {CFB17699/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Actinobacteria/*genetics ; Chromosomes, Bacterial ; Cloning, Molecular ; DNA Replication ; Drug Resistance, Bacterial ; Evolution, Molecular ; Genes, Bacterial/genetics ; Genome, Bacterial ; Models, Biological ; Models, Genetic ; Phenotype ; Phylogeny ; Saccharopolyspora/genetics ; Sequence Analysis, DNA ; }, abstract = {Actinomycete integrative and conjugative elements (AICEs) are present in diverse genera of the actinomycetes, the most important bacterial producers of bioactive secondary metabolites. Comparison of pMEA100 of Amycolatopsis mediterranei, pMEA300 of Amycolatopsis methanolica and pSE211 of Saccharopolyspora erythraea, and other AICEs, revealed a highly conserved structural organisation, consisting of four functional modules (replication, excision/integration, regulation, and conjugative transfer). Features conserved in all elements, or specific for a single element, are discussed and analysed. This study also revealed two novel putative AICEs (named pSE222 and pSE102) in the Sac. erythraea genome, related to the previously described pSE211 and pSE101 elements. Interestingly, pSE102 encodes a putative aminoglycoside phosphotransferase which may confer antibiotic resistance to the host. Furthermore, two of the six pSAM2-like insertions in the Streptomyces coelicolor genome described by Bentley et al. [Bentley, S.D., Chater, K.F., Cerdeno-Tarraga, A.M., et al., 2002. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417, 141-147] could be functional AICEs. Homologues of various AICE proteins were found in other actinomycetes, in Frankia species and in the obligate marine genus Salinispora and may be part of novel AICEs as well. The data presented provide a better understanding of the origin and evolution of these elements, and their functional properties. Several AICEs are able to mobilise chromosomal markers, suggesting that they play an important role in horizontal gene transfer and spread of antibiotic resistance, but also in evolution of genome plasticity.}, }
@article {pmid18291041, year = {2008}, author = {Viljakainen, L and Reuter, M and Pamilo, P}, title = {Wolbachia transmission dynamics in Formica wood ants.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {55}, pmid = {18291041}, issn = {1471-2148}, mesh = {Animals ; Ants/classification/*microbiology ; Bacterial Outer Membrane Proteins/genetics ; DNA, Bacterial/genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genetic Variation ; Haplotypes ; *Host-Pathogen Interactions ; Sequence Analysis, DNA ; Species Specificity ; *Symbiosis ; Wolbachia/classification/*physiology ; }, abstract = {BACKGROUND: The role of Wolbachia endosymbionts in shaping the mitochondrial diversity of their arthropod host depends on the effects they have on host reproduction and on the mode of transmission of the bacteria. We have compared the sequence diversity of wsp (Wolbachia surface protein gene) and the host mtDNA in a group of Formica ant species that have diverged approximately 0.5 million years ago (MYA). The aim was to study the relationship of Wolbachia and its ant hosts in terms of vertical and horizontal transmission of the bacteria.<br><br>RESULTS: All studied ant species were doubly infected with two Wolbachia strains (wFex1 and wFex4) all over their geographical distribution area in Eurasia. The most common haplotypes of these strains were identical with strains previously described from a more distantly related Formica ant, with an estimated divergence time of 3.5 - 4 MYA. Some strain haplotypes were associated to the same or closely related mtDNA haplotypes as expected under vertical transmission. However, in several cases the wsp haplotypes coexisted with distant mtDNA haplotypes, a pattern which is more compatible with horizontal transmission of the bacteria.<br><br>CONCLUSION: Two lines of evidence suggest that the sharing of Wolbachia strains by all F. rufa species is rather due to horizontal than vertical transmission. First, the fact that endosymbiont strains identical to those of F. rufa ants have been found in another species that diverged 3.5-4 MYA strongly suggests that horizontal transfer can and does occur between Formica ants. Second, the frequent sharing of identical Wolbachia strains by distant mitochondrial lineages within the F. rufa group further shows that horizontal transmission has occurred repeatedly. Nevertheless, our dataset also provides some evidence for longer-term persistence of infection, indicating that Wolbachia infection within this host clade has been shaped by both horizontal and vertical transmission of symbionts. The fact that all the ants were infected irrespective of the family structure of their societies gives no support to the proposed hypotheses that the spreading of Wolbachia in ants might be associated to the types of their societies.}, }
@article {pmid18286220, year = {2008}, author = {Carbone, A}, title = {Codon bias is a major factor explaining phage evolution in translationally biased hosts.}, journal = {Journal of molecular evolution}, volume = {66}, number = {3}, pages = {210-223}, pmid = {18286220}, issn = {0022-2844}, mesh = {Bacteria/virology ; Bacteriophages/*genetics ; *Codon ; *Evolution, Molecular ; *Protein Biosynthesis ; }, abstract = {The size and diversity of bacteriophage populations require methodologies to quantitatively study the landscape of phage differences. Statistical approaches are confronted with small genome sizes forbidding significant single-phage analysis, and comparative methods analyzing full phage genomes represent an alternative but they are of difficult interpretation due to lateral gene transfer, which creates a mosaic spectrum of related phage species. Based on a large-scale codon bias analysis of 116 DNA phages hosted by 11 translationally biased bacteria belonging to different phylogenetic families, we observe that phage genomes are almost always under codon selective pressure imposed by translationally biased hosts, and we propose a classification of phages with translationally biased hosts which is based on adaptation patterns. We introduce a computational method for comparing phages sharing homologous proteins, possibly accepted by different hosts. We observe that throughout phages, independently from the host, capsid genes appear to be the most affected by host translational bias. For coliphages, genes involved in virion morphogenesis, host interaction and ssDNA binding are also affected by adaptive pressure. Adaptation affects long and small phages in a significant way. We analyze in more detail the Microviridae phage space to illustrate the potentiality of the approach. The small number of directions in adaptation observed in phages grouped around phi X174 is discussed in the light of functional bias. The adaptation analysis of the set of Microviridae phages defined around phi MH2K shows that phage classification based on adaptation does not reflect bacterial phylogeny.}, }
@article {pmid18281720, year = {2008}, author = {Johnston, AW and Todd, JD and Sun, L and Nikolaidou-Katsaridou, MN and Curson, AR and Rogers, R}, title = {Molecular diversity of bacterial production of the climate-changing gas, dimethyl sulphide, a molecule that impinges on local and global symbioses.}, journal = {Journal of experimental botany}, volume = {59}, number = {5}, pages = {1059-1067}, doi = {10.1093/jxb/erm264}, pmid = {18281720}, issn = {1460-2431}, mesh = {Bacteria/classification/*metabolism ; Bacterial Physiological Phenomena ; Bacterial Proteins/genetics/metabolism ; *Biodiversity ; Climate ; Plant Physiological Phenomena ; Plants/microbiology ; Signal Transduction ; Sulfides/*metabolism ; Sulfonium Compounds/metabolism ; *Symbiosis ; }, abstract = {This paper describes the ddd genes that are involved in the production of the gas dimethyl sulphide from the substrate dimethylsulphoniopropionate (DMSP), an abundant molecule that is a stress protectant in many marine algae and a few genera of angiosperms. What is known of the arrangement of the ddd genes in different bacteria that can undertake this reaction is reviewed here, stressing the fact that these genes are probably subject to horizontal gene transfer and that the same functions (e.g. DMSP transport) may be accomplished by very different mechanisms. A surprising number of DMS-emitting bacteria are associated with the roots of higher plants, these including strains of Rhizobium and some rhizosphere bacteria in the genus Burkholderia. One newly identified strain that is predicted to make DMS is B. phymatum which is a highly unusual beta-proteobacterium that forms N(2)-fixing nodules on some tropical legumes, in this case, the tree Machaerium lunatum, which inhabits mangroves. The importance of DMSP catabolism and DMS production is discussed, not only in terms of nutritional acquisition by the bacteria but also in a speculative scheme (the 'messy eater' model) in which the bacteria may make DMS as an info-chemical to attract other organisms, including invertebrates and other plankton.}, }
@article {pmid18280814, year = {2008}, author = {Zaneveld, J and Turnbaugh, PJ and Lozupone, C and Ley, RE and Hamady, M and Gordon, JI and Knight, R}, title = {Host-bacterial coevolution and the search for new drug targets.}, journal = {Current opinion in chemical biology}, volume = {12}, number = {1}, pages = {109-114}, pmid = {18280814}, issn = {1367-5931}, support = {P01 DK078669/DK/NIDDK NIH HHS/United States ; T32 GM142607/GM/NIGMS NIH HHS/United States ; T32 GM08759/GM/NIGMS NIH HHS/United States ; T32 GM065103/GM/NIGMS NIH HHS/United States ; P01 DK078669-010003/DK/NIDDK NIH HHS/United States ; T32 GM008759/GM/NIGMS NIH HHS/United States ; P01DK078669/DK/NIDDK NIH HHS/United States ; T32GM065103/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacterial Physiological Phenomena/*drug effects ; *Biological Evolution ; Drug Evaluation, Preclinical/*methods ; Gene Transfer, Horizontal ; Host-Pathogen Interactions/*genetics ; Humans ; Symbiosis/genetics ; }, abstract = {Understanding the coevolution between humans and our microbial symbionts and pathogens requires complementary approaches, ranging from community analysis to in-depth analysis of individual genomes. Here we review the evidence for coevolution between symbionts and their hosts, the role of horizontal gene transfer in coevolution, and genomic and metagenomic approaches to identify drug targets. Recent studies have shown that our symbiotic microbes confer many metabolic capabilities that our mammalian genomes lack, and that targeting mechanisms of horizontal gene transfer is a promising new direction for drug discovery. Gnotobiotic ('germ-free') mice are an especially exciting new tool for unraveling the function of microbes, whether individually or in the context of complex communities.}, }
@article {pmid18276190, year = {2008}, author = {Watkins, RF and Gray, MW}, title = {Sampling gene diversity across the supergroup Amoebozoa: large EST data sets from Acanthamoeba castellanii, Hartmannella vermiformis, Physarum polycephalum, Hyperamoeba dachnaya and Hyperamoeba sp.}, journal = {Protist}, volume = {159}, number = {2}, pages = {269-281}, doi = {10.1016/j.protis.2007.12.001}, pmid = {18276190}, issn = {1434-4610}, mesh = {Acanthamoeba castellanii/genetics ; Amoebida/classification/*genetics/physiology ; Animals ; *Biodiversity ; Carbohydrate Metabolism ; DNA, Protozoan/genetics ; Evolution, Molecular ; *Expressed Sequence Tags ; Gene Library ; Gene Transfer, Horizontal ; *Genes, Protozoan ; Genome, Protozoan ; Hartmannella/genetics ; Meiosis ; Physarum polycephalum/classification/*genetics/physiology ; Species Specificity ; }, abstract = {From comparative analysis of EST data for five taxa within the eukaryotic supergroup Amoebozoa, including two free-living amoebae (Acanthamoeba castellanii, Hartmannella vermiformis) and three slime molds (Physarum polycephalum, Hyperamoeba dachnaya and Hyperamoeba sp.), we obtained new broad-range perspectives on the evolution and biosynthetic capacity of this assemblage. Together with genome sequences for the amoebozoans Dictyostelium discoideum and Entamoeba histolytica, and including partial genome sequence available for A. castellanii, we used the EST data to identify genes that appear to be exclusive to the supergroup, and to specific clades therein. Many of these genes are likely involved in cell-cell communication or differentiation. In examining on a broad scale a number of characters that previously have been considered in simpler cross-species comparisons, typically between Dictyostelium and Entamoeba, we find that Amoebozoa as a whole exhibits striking variation in the number and distribution of biosynthetic pathways, for example, ones for certain critical stress-response molecules, including trehalose and mannitol. Finally, we report additional compelling cases of lateral gene transfer within Amoebozoa, further emphasizing that although this process has influenced genome evolution in all examined amoebozoan taxa, it has done so to a variable extent.}, }
@article {pmid18276189, year = {2008}, author = {Dufernez, F and Derelle, E and Noël, C and Sanciu, G and Mantini, C and Dive, D and Soyer-Gobillard, MO and Capron, M and Pierce, RJ and Wintjens, R and Guillebault, D and Viscogliosi, E}, title = {Molecular characterization of iron-containing superoxide dismutases in the heterotrophic dinoflagellate Crypthecodinium cohnii.}, journal = {Protist}, volume = {159}, number = {2}, pages = {223-238}, doi = {10.1016/j.protis.2007.11.005}, pmid = {18276189}, issn = {1434-4610}, mesh = {Amino Acid Sequence ; Animals ; Chlorophyta/classification/enzymology/genetics ; Cloning, Molecular ; Dinoflagellida/classification/*enzymology/genetics/metabolism ; Evolution, Molecular ; Heterotrophic Processes ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Plants/classification/enzymology/genetics ; Protozoan Proteins/chemistry/genetics/isolation &amp; purification/metabolism ; Sequence Alignment ; Superoxide Dismutase/*chemistry/genetics/*isolation &amp; purification/metabolism ; }, abstract = {Superoxide dismutases (SODs) are a family of antioxidant enzymes that catalyse the degradation of toxic superoxide radicals in obligate and facultative aerobic organisms. Here, we report the presence of a multi-copy gene family encoding SODs in the heterotrophic dinoflagellate Crypthecodinium cohnii. All the genes identified (sod1 to sod17) have been cloned and sequenced, and shown to encode potentially functional dimeric iron-containing SOD isozymes. Our data revealed a considerable molecular heterogeneity of this enzyme in C. cohnii at both genomic and transcriptional levels. The C. cohnii SOD1, overexpressed in Escherichia coli, was active and its structure obtained by homology modeling using X-ray crystal structures of homologues exhibited the typical fold of dimeric FeSODs. Phylogenetic studies including 110 other dimeric FeSODs and closely related cambialistic dimeric SOD sequences showed that the C. cohnii SODs form a monophyletic group and have all been acquired by the same event of horizontal gene transfer. It also revealed a dichotomy within the C. cohnii SOD sequences that could be explained by an ancestral sod gene duplication followed by subsequent gene duplications within each of the two groups. Enzyme assays of SOD activity indicated the presence of two FeSOD activities in C. cohnii cell lysate whereas MnSOD and Cu/ZnSOD were not detected. These activities contrasted with the SOD repertoire previously characterized in photosynthetic dinoflagellates. To explain these differences, a hypothetical evolutionary scenario is proposed that suggests gains and losses of sod genes in dinoflagellates.}, }
@article {pmid18273063, year = {2008}, author = {Wright, MS and Baker-Austin, C and Lindell, AH and Stepanauskas, R and Stokes, HW and McArthur, JV}, title = {Influence of industrial contamination on mobile genetic elements: class 1 integron abundance and gene cassette structure in aquatic bacterial communities.}, journal = {The ISME journal}, volume = {2}, number = {4}, pages = {417-428}, doi = {10.1038/ismej.2008.8}, pmid = {18273063}, issn = {1751-7362}, mesh = {Bacteria/classification/genetics ; DNA Transposable Elements ; DNA, Bacterial/analysis/isolation &amp; purification ; *Ecosystem ; Fresh Water/chemistry/microbiology ; Geologic Sediments/chemistry/microbiology ; Georgia ; Industrial Microbiology ; Integrases/*genetics ; Integrons/*genetics ; Metals, Heavy/*analysis ; Molecular Sequence Data ; Polymorphism, Restriction Fragment Length ; Rivers/*chemistry/*microbiology ; Sequence Analysis, DNA ; South Carolina ; Water Pollution/*analysis ; }, abstract = {The acquisition of new genetic material via horizontal gene transfer allows bacteria to rapidly evolve. One key to estimating the contribution of horizontal gene transfer to bacterial evolution is to quantify the abundance of mobile genetic elements (MGEs) in bacterial communities under varying degrees of selective pressure. We quantified class 1 integrase (intI1) gene abundance in total community DNA extracted from contaminated and reference riverine and estuarine microhabitats, and in metal- or antibiotic-amended freshwater microcosms. The intI1 gene was more abundant in all contaminant-exposed communities indicating that relative gene transfer potential is higher in these communities. A second key to assessing the contributions of MGEs to bacterial evolution is to examine the structure and function of the MGE-associated gene pool. We determined that the gene cassette pool is a novel and diverse resource available for bacterial acquisition, but that contamination has no discernible effect on cassette richness. Gene cassette profiles were more similar within sites than among sites, yet bacterial community profiles were not, suggesting that selective pressures can shape the structure of the gene cassette pool. Of the 46 sequenced gene cassette products, 37 were novel sequences, while the 9 gene cassettes with similarity to database sequences were primarily to hypothetical proteins. That class 1 integrons are ubiquitous and abundant in environmental bacterial communities indicates that this group of MGEs can play a substantial role in the acquisition of a diverse array of gene cassettes beyond their demonstrated impact in mediating multidrug resistance in clinical bacteria.}, }
@article {pmid18270203, year = {2008}, author = {Perez, JC and Latifi, T and Groisman, EA}, title = {Overcoming H-NS-mediated transcriptional silencing of horizontally acquired genes by the PhoP and SlyA proteins in Salmonella enterica.}, journal = {The Journal of biological chemistry}, volume = {283}, number = {16}, pages = {10773-10783}, pmid = {18270203}, issn = {0021-9258}, support = {R01 AI049561-16/AI/NIAID NIH HHS/United States ; R01 AI049561/AI/NIAID NIH HHS/United States ; R01 AI042236-10/AI/NIAID NIH HHS/United States ; R01 AI042236/AI/NIAID NIH HHS/United States ; AI49561/AI/NIAID NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Bacterial Proteins/*genetics/*metabolism ; Base Sequence ; Binding Sites ; DNA-Binding Proteins/*genetics/metabolism ; DNA-Directed RNA Polymerases/metabolism ; *Gene Expression Regulation, Bacterial ; Gene Silencing ; Models, Biological ; Molecular Sequence Data ; Plasmids/metabolism ; Protein Binding ; Salmonella enterica/*genetics ; Transcription Factors ; *Transcription, Genetic ; }, abstract = {The acquisition of new traits through horizontal gene transfer depends on the ability of the recipient organism to express the incorporated genes. However, foreign DNA appears to be silenced by the histone-like nucleoid-structuring protein (H-NS) in several enteric pathogens, raising the question of how this silencing is overcome and the acquired genes are expressed at the right time and place. To address this question, we investigated transcription of the horizontally acquired ugtL and pagC genes from Salmonella enterica, which is dependent on the regulatory DNA-binding proteins PhoP and SlyA. We reconstituted transcription of the ugtL and pagC genes in vitro and determined occupancy of their respective promoters by PhoP, H-NS, and RNA polymerase in vivo. The SlyA protein counteracted H-NS-promoted repression in vitro but could not promote gene transcription by itself. PhoP-promoted transcription required SlyA when H-NS was present but not in its absence. In vivo, H-NS remained bound to the ugtL and pagC promoters under inducing conditions that promoted RNA polymerase recruitment and transcription of the ugtL and pagC genes. Our results indicate that relief of H-NS repression and recruitment of RNA polymerase are controlled by different regulatory proteins that act in concert to express horizontally acquired genes.}, }
@article {pmid18268351, year = {2008}, author = {Shi, T and Falkowski, PG}, title = {Genome evolution in cyanobacteria: the stable core and the variable shell.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {7}, pages = {2510-2515}, pmid = {18268351}, issn = {1091-6490}, mesh = {Bacterial Proteins/classification/genetics ; Cyanobacteria/classification/*genetics ; Genome, Bacterial/*genetics ; *Phylogeny ; }, abstract = {Cyanobacteria are the only known prokaryotes capable of oxygenic photosynthesis, the evolution of which transformed the biology and geochemistry of Earth. The rapid increase in published genomic sequences of cyanobacteria provides the first opportunity to reconstruct events in the evolution of oxygenic photosynthesis on the scale of entire genomes. Here, we demonstrate the overall phylogenetic incongruence among 682 orthologous protein families from 13 genomes of cyanobacteria. However, using principal coordinates analysis, we discovered a core set of 323 genes with similar evolutionary trajectories. The core set is highly conserved in amino acid sequence and contains genes encoding the major components in the photosynthetic and ribosomal apparatus. Many of the key proteins are encoded by genome-wide conserved small gene clusters, which often are indicative of protein-protein, protein-prosthetic group, and protein-lipid interactions. We propose that the macromolecular interactions in complex protein structures and metabolic pathways retard the tempo of evolution of the core genes and hence exert a selection pressure that restricts piecemeal horizontal gene transfer of components of the core. Identification of the core establishes a foundation for reconstructing robust organismal phylogeny in genome space. Our phylogenetic trees constructed from 16S rRNA gene sequences, concatenated orthologous proteins, and the core gene set all suggest that the ancestral cyanobacterium did not fix nitrogen and probably was a thermophilic organism.}, }
@article {pmid18268088, year = {2008}, author = {Revilla, C and Garcillán-Barcia, MP and Fernández-López, R and Thomson, NR and Sanders, M and Cheung, M and Thomas, CM and de la Cruz, F}, title = {Different pathways to acquiring resistance genes illustrated by the recent evolution of IncW plasmids.}, journal = {Antimicrobial agents and chemotherapy}, volume = {52}, number = {4}, pages = {1472-1480}, pmid = {18268088}, issn = {0066-4804}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Base Sequence ; Conjugation, Genetic ; DNA Transposable Elements ; Drug Resistance, Bacterial/*genetics ; Enterobacteriaceae/classification/*genetics ; Escherichia coli Proteins/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Integrons/genetics ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis/methods ; Plasmids/*genetics ; Repressor Proteins/genetics ; Sequence Analysis, DNA ; }, abstract = {DNA sequence analysis of five IncW plasmids (R388, pSa, R7K, pIE321, and pIE522) demonstrated that they share a considerable portion of their genomes and allowed us to define the IncW backbone. Among these plasmids, the backbone is stable and seems to have diverged recently, since the overall identity among its members is higher than 95%. The only gene in which significant variation was observed was trwA; the changes in the coding sequence correlated with parallel changes in the corresponding TrwA binding sites at oriT, suggesting a functional connection between both sets of changes. The present IncW plasmid diversity is shaped by the acquisition of antibiotic resistance genes as a consequence of the pressure exerted by antibiotic usage. Sequence comparisons pinpointed the insertion events that differentiated the five plasmids analyzed. Of greatest interest is that a single acquisition of a class I integron platform, into which different gene cassettes were later incorporated, gave rise to plasmids R388, pIE522, and pSa, while plasmids R7K and pIE321 do not contain the integron platform and arose in the antibiotic world because of the insertion of several antibiotic resistance transposons.}, }
@article {pmid18266472, year = {2008}, author = {Shapiro, BJ and Alm, EJ}, title = {Comparing patterns of natural selection across species using selective signatures.}, journal = {PLoS genetics}, volume = {4}, number = {2}, pages = {e23}, pmid = {18266472}, issn = {1553-7404}, mesh = {Bacterial Proteins/genetics ; Ecosystem ; Evolution, Molecular ; Gammaproteobacteria/classification/*genetics/physiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Models, Genetic ; Recombination, Genetic ; *Selection, Genetic ; Species Specificity ; }, abstract = {Comparing gene expression profiles over many different conditions has led to insights that were not obvious from single experiments. In the same way, comparing patterns of natural selection across a set of ecologically distinct species may extend what can be learned from individual genome-wide surveys. Toward this end, we show how variation in protein evolutionary rates, after correcting for genome-wide effects such as mutation rate and demographic factors, can be used to estimate the level and types of natural selection acting on genes across different species. We identify unusually rapidly and slowly evolving genes, relative to empirically derived genome-wide and gene family-specific background rates for 744 core protein families in 30 gamma-proteobacterial species. We describe the pattern of fast or slow evolution across species as the "selective signature" of a gene. Selective signatures represent a profile of selection across species that is predictive of gene function: pairs of genes with correlated selective signatures are more likely to share the same cellular function, and genes in the same pathway can evolve in concert. For example, glycolysis and phenylalanine metabolism genes evolve rapidly in Idiomarina loihiensis, mirroring an ecological shift in carbon source from sugars to amino acids. In a broader context, our results suggest that the genomic landscape is organized into functional modules even at the level of natural selection, and thus it may be easier than expected to understand the complex evolutionary pressures on a cell.}, }
@article {pmid18263725, year = {2008}, author = {Ammann, A and Neve, H and Geis, A and Heller, KJ}, title = {Plasmid transfer via transduction from Streptococcus thermophilus to Lactococcus lactis.}, journal = {Journal of bacteriology}, volume = {190}, number = {8}, pages = {3083-3087}, pmid = {18263725}, issn = {1098-5530}, mesh = {DNA, Bacterial/genetics ; *Gene Transfer, Horizontal ; Lactococcus lactis/*genetics/virology ; *Plasmids ; Streptococcus Phages/genetics ; Streptococcus thermophilus/*genetics/virology ; *Transduction, Genetic ; Virus Attachment ; }, abstract = {Using Streptococcus thermophilus phages, plasmid transduction in Lactococcus lactis was demonstrated. The transduction frequencies were 4 orders of magnitude lower in L. lactis than in S. thermophilus. These results are the first evidence that there is phage-mediated direct transfer of DNA from S. thermophilus to L. lactis. The implications of these results for phage evolution are discussed.}, }
@article {pmid18259879, year = {2008}, author = {Cordeiro, J and Robe, LJ and Loreto, EL and Valente, VL}, title = {The LTR retrotransposon micropia in the cardini group of Drosophila (Diptera: Drosophilidae): a possible case of horizontal transfer.}, journal = {Genetica}, volume = {134}, number = {3}, pages = {335-344}, pmid = {18259879}, issn = {0016-6707}, mesh = {Animals ; Base Sequence ; Blotting, Southern ; Drosophila/*genetics ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; Retroelements/*genetics ; Sequence Alignment ; Terminal Repeat Sequences/*genetics ; }, abstract = {The presence of the micropia retroelement from the Ty1-copia family of LTR retroelements was investigated in three species of the Drosophila cardini group. Southern blot analysis suggested the existence of at least four micropia copies in the genomes of D. cardinoides, D. neocardini and D. polymorpha populations. The high sequence similarity between dhMiF2 and Dm11 clones (micropia retroelements isolated from D. hydei and D. melanogaster, respectively) with micropia sequences amplified from D. cardini group genome supports the hypothesis that this retroelement plays an active role in horizontal transfer events between D. hydei and the D. cardini group.}, }
@article {pmid18257678, year = {2008}, author = {Oliver, RP and Solomon, PS}, title = {Recent fungal diseases of crop plants: is lateral gene transfer a common theme?.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {21}, number = {3}, pages = {287-293}, doi = {10.1094/MPMI-21-3-0287}, pmid = {18257678}, issn = {0894-0282}, mesh = {Fungal Proteins/genetics ; *Gene Transfer, Horizontal ; *Genes, Fungal ; Oomycetes/genetics ; Plant Diseases/*genetics/*microbiology ; Species Specificity ; }, abstract = {A cursory glance at old textbooks of plant pathology reveals that the diseases which are the current scourge of agriculture in many parts of the world are a different set from those that were prominent 50 or 100 years ago. Why have these new diseases arisen? The traditional explanations subscribe to the "nature abhors a vacuum" principle-that control of one disease creates the condition for the emergence of a replacement-but does little to explain why the new pathogen succeeds. The emergence of a new disease requires a series of conditions and steps, including the enhanced fecundity of the new pathogen, enhanced survival from season to season, and spread around the world. Recently, evidence was obtained that wheat tan spot emerged through a lateral gene transfer event some time prior to 1941. Although there have been sporadic and persistent reports of lateral gene transfer between and into fungal plant pathogens, most examples have been dismissed through incomplete evidence. The completion of whole genome sequences of an increasing number of fungal pathogens no longer allows such proposed cases of lateral gene transfer to be dismissed so easily. How frequent are lateral gene transfers involving fungal plant pathogens, and can this process explain the emergence of many of the new diseases of the recent past? Many of the apparently new diseases are dependant on the expression of host-specific toxins. These are enigmatic molecules whose action requires the presence of plant genes with products that specifically encode sensitivity to the toxin and susceptibility to the disease. It is also notable that many new diseases belong to the fungal taxon dothideomycetes. This review explores the coincidence of new diseases, interspecific gene transfer, host-specific toxins, and the dothideomycete class.}, }
@article {pmid18256241, year = {2008}, author = {Cazalet, C and Jarraud, S and Ghavi-Helm, Y and Kunst, F and Glaser, P and Etienne, J and Buchrieser, C}, title = {Multigenome analysis identifies a worldwide distributed epidemic Legionella pneumophila clone that emerged within a highly diverse species.}, journal = {Genome research}, volume = {18}, number = {3}, pages = {431-441}, pmid = {18256241}, issn = {1088-9051}, mesh = {Disease Outbreaks ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genetic Variation ; Genomics ; Humans ; Interspersed Repetitive Sequences ; Legionella/classification/genetics ; Legionella pneumophila/classification/*genetics/pathogenicity ; Legionnaires' Disease/epidemiology/microbiology ; Lipopolysaccharides/biosynthesis ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; }, abstract = {Genomics can provide the basis for understanding the evolution of emerging, lethal human pathogens such as Legionella pneumophila, the causative agent of Legionnaires' disease. This bacterium replicates within amoebae and persists in the environment as a free-living microbe. Among the many Legionella species described, L. pneumophila is associated with 90% of human disease and within the 15 serogroups (Sg), L. pneumophila Sg1 causes over 84% of Legionnaires' disease worldwide. Why L. pneumophila Sg1 is so predominant is unknown. Here, we report the first comprehensive screen of the gene content of 217 L. pneumophila and 32 non-L. pneumophila strains isolated from humans and the environment using a Legionella DNA-array. Strikingly, we uncovered a high conservation of virulence- and eukaryotic-like genes, indicating strong environmental selection pressures for their preservation. No specific hybridization profile differentiated clinical and environmental strains or strains of different serogroups. Surprisingly, the gene cluster coding the determinants of the core and the O side-chain synthesis of the lipopolysaccaride (LPS cluster) determining Sg1 was present in diverse genomic backgrounds, strongly implicating the LPS of Sg1 itself as a principal cause of the high prevalence of Sg1 strains in human disease and suggesting that the LPS cluster can be transferred horizontally. Genomic analysis also revealed that L. pneumophila is a genetically diverse species, in part due to horizontal gene transfer of mobile genetic elements among L. pneumophila strains, but also between different Legionella species. However, the genomic background also plays a role in disease causation as demonstrated by the identification of a globally distributed epidemic strain exhibiting the genotype of the sequenced L. pneumophila strain Paris.}, }
@article {pmid18251664, year = {2008}, author = {Bansal, AK}, title = {Role of bioinformatics in the development of new antibacterial therapy.}, journal = {Expert review of anti-infective therapy}, volume = {6}, number = {1}, pages = {51-65}, doi = {10.1586/14787210.6.1.51}, pmid = {18251664}, issn = {1744-8336}, mesh = {Animals ; Anti-Bacterial Agents/chemistry/*therapeutic use ; Bacterial Infections/drug therapy/genetics ; Computational Biology/methods/*trends ; Drug Resistance, Bacterial/drug effects/physiology ; Humans ; Technology, Pharmaceutical/methods/trends ; }, abstract = {Bacterial virulence and pathogenicity has its genesis in plasmid exchange, horizontal gene transfer, transposons carrying virulent genes, genome rearrangement, missing genes causing gaps in pathways, gene mutations altering gene functionality, pathogenicity islands, efflux pumps, pore-inducing proteins causing cell death and release of exotoxins that can harm the host. In the past, docking based on 3D molecular modeling to identify the compounds that will bind to a protein disrupting the pathway has been used for antibiotic development. However, current hospital practice aided by fast mutation of virulent genes has produced many drug-resistant strains capable of surviving extreme stress conditions caused by antibiotics. Recent bioinformatics research can help remedy the situation by helping to understand the exact functionality of the biomachine inside the bacteria and the host pathogen interaction at the level of individual pathogens, and can reduce the drug-development time in future.}, }
@article {pmid18250311, year = {2008}, author = {Ridley, CP and Lee, HY and Khosla, C}, title = {Evolution of polyketide synthases in bacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {12}, pages = {4595-4600}, pmid = {18250311}, issn = {1091-6490}, support = {R01 CA066736/CA/NCI NIH HHS/United States ; R01 CA077248/CA/NCI NIH HHS/United States ; CA 66736/CA/NCI NIH HHS/United States ; CA 77248/CA/NCI NIH HHS/United States ; }, mesh = {Bacteria/*enzymology ; Base Sequence ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Macrolides/chemistry ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Polyketide Synthases/chemistry/*genetics ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombination, Genetic ; }, abstract = {The emergence of resistant strains of human pathogens to current antibiotics, along with the demonstrated ability of polyketides as antimicrobial agents, provides strong motivation for understanding how polyketide antibiotics have evolved and diversified in nature. Insights into how bacterial polyketide synthases (PKSs) acquire new metabolic capabilities can guide future laboratory efforts in generating the next generation of polyketide antibiotics. Here, we examine phylogenetic and structural evidence to glean answers to two general questions regarding PKS evolution. How did the exceptionally diverse chemistry of present-day PKSs evolve? And what are the take-home messages for the biosynthetic engineer?}, }
@article {pmid18248682, year = {2008}, author = {Patron, NJ and Durnford, DG and Kopriva, S}, title = {Sulfate assimilation in eukaryotes: fusions, relocations and lateral transfers.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {39}, pmid = {18248682}, issn = {1471-2148}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Adenosine Triphosphate/metabolism ; Cyanobacteria/genetics ; Eukaryotic Cells/*metabolism ; Gene Transfer, Horizontal/genetics ; Microscopy, Electron, Transmission ; Oxidoreductases/classification/genetics/metabolism ; Oxidoreductases Acting on Sulfur Group Donors/classification/genetics/metabolism ; Phylogeny ; Plastids/metabolism ; Protein Isoforms/genetics/metabolism ; Sulfate Adenylyltransferase/classification/genetics/metabolism ; Sulfates/*metabolism ; }, abstract = {BACKGROUND: The sulfate assimilation pathway is present in photosynthetic organisms, fungi, and many bacteria, providing reduced sulfur for the synthesis of cysteine and methionine and a range of other metabolites. In photosynthetic eukaryotes sulfate is reduced in the plastids whereas in aplastidic eukaryotes the pathway is cytosolic. The only known exception is Euglena gracilis, where the pathway is localized in mitochondria. To obtain an insight into the evolution of the sulfate assimilation pathway in eukaryotes and relationships of the differently compartmentalized isoforms we determined the locations of the pathway in lineages for which this was unknown and performed detailed phylogenetic analyses of three enzymes involved in sulfate reduction: ATP sulfurylase (ATPS), adenosine 5'-phosphosulfate reductase (APR) and sulfite reductase (SiR).<br><br>RESULTS: The inheritance of ATPS, APR and the related 3'-phosphoadenosine 5'-phosphosulfate reductase (PAPR) are remarkable, with multiple origins in the lineages that comprise the opisthokonts, different isoforms in chlorophytes and streptophytes, gene fusions with other enzymes of the pathway, evidence a eukaryote to prokaryote lateral gene transfer, changes in substrate specificity and two reversals of cellular location of host- and endosymbiont-originating enzymes. We also found that the ATPS and APR active in the mitochondria of Euglena were inherited from its secondary, green algal plastid.<br><br>CONCLUSION: Our results reveal a complex history for the enzymes of the sulfate assimilation pathway. Whilst they shed light on the origin of some characterised novelties, such as a recently described novel isoform of APR from Bryophytes and the origin of the pathway active in the mitochondria of Euglenids, the many distinct and novel isoforms identified here represent an excellent resource for detailed biochemical studies of the enzyme structure/function relationships.}, }
@article {pmid18248422, year = {2008}, author = {Wang, Y and Zeng, F and Hon, CC and Zhang, Y and Leung, FC}, title = {The mitochondrial genome of the Basidiomycete fungus Pleurotus ostreatus (oyster mushroom).}, journal = {FEMS microbiology letters}, volume = {280}, number = {1}, pages = {34-41}, doi = {10.1111/j.1574-6968.2007.01048.x}, pmid = {18248422}, issn = {0378-1097}, mesh = {Amino Acid Sequence ; Basidiomycota/classification/*genetics ; DNA, Fungal/genetics ; DNA, Intergenic/genetics ; DNA, Mitochondrial/genetics ; DNA-Directed RNA Polymerases/chemistry/genetics ; Gene Transfer, Horizontal ; *Genome, Mitochondrial ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; *Physical Chromosome Mapping ; Pleurotus/*genetics ; RNA-Directed DNA Polymerase/chemistry/genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {In this study, the full mitochondrial genome of a basidiomycete fungus, Pleurotus ostreatus, was sequenced and analyzed. It is a circular DNA molecule of 73 242 bp and contains 44 known genes encoding 18 proteins and 26 RNA genes. The protein-coding genes include 14 common mitochondrial genes, one ribosomal small subunit protein 3 gene, one RNA polymerase gene and two DNA polymerase genes. In addition, one RNA and one DNA polymerase genes were identified in a mitochondrial plasmid. These two genes show relatively low similarities to their homologs in the mitochondrial genome but they are nearly identical to the known mitochondrial plasmid genes from another Pleurotus ostreatus strain. This suggests that the plasmid may mediate the horizontal gene transfer of the DNA and RNA polymerase genes into mitochondrial genome, and such a transfer may be an ancient event. Phylogenetic analysis based on the cox1 ORFs verified the traditional classification of Pleurotus ostreatus among fungi. However, the discordances were observed in the phylogenetic trees based on the six cox1 intronic ORFs of Pleurotus ostreatus and their homologs in other species, suggesting that these intronic ORFs are foreign DNA sequences obtained through HGT. In summary, this analysis provides valuable information towards the understanding of the evolution of fungal mtDNA.}, }
@article {pmid18245257, year = {2008}, author = {Coombes, BK and Wickham, ME and Mascarenhas, M and Gruenheid, S and Finlay, BB and Karmali, MA}, title = {Molecular analysis as an aid to assess the public health risk of non-O157 Shiga toxin-producing Escherichia coli strains.}, journal = {Applied and environmental microbiology}, volume = {74}, number = {7}, pages = {2153-2160}, pmid = {18245257}, issn = {1098-5336}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Colon/microbiology ; Escherichia coli Infections/*diagnosis ; Genes, Bacterial ; Genomic Islands/*genetics/physiology ; Hemolytic-Uremic Syndrome/epidemiology/*microbiology ; Humans ; Public Health ; Shiga Toxins/biosynthesis ; Shiga-Toxigenic Escherichia coli/*classification/genetics/isolation &amp; purification ; Virulence Factors/*genetics ; }, abstract = {Shiga toxin-producing Escherichia coli (STEC) strains are commensal bacteria in cattle with high potential for environmental and zoonotic transmission to humans. Although O157:H7 is the most common STEC serotype, there is growing concern over the emergence of more than 200 highly virulent non-O157 STEC serotypes that are globally distributed, several of which are associated with outbreaks and/or severe human illness such as hemolytic-uremic syndrome (HUS) and hemorrhagic colitis. At present, the underlying genetic basis of virulence potential in non-O157 STEC is unknown, although horizontal gene transfer and the acquisition of new pathogenicity islands are an expected origin. We used seropathotype classification as a framework to identify genetic elements that distinguish non-O157 STEC strains posing a serious risk to humans from STEC strains that are not associated with severe and epidemic disease. We report the identification of three genomic islands encoding non-LEE effector (nle) genes and 14 individual nle genes in non-O157 STEC strains that correlate independently with outbreak and HUS potential in humans. The implications for transmissible zoonotic spread and public health are discussed. These results and methods offer a molecular risk assessment strategy to rapidly recognize and respond to non-O157 STEC strains from environmental and animal sources that might pose serious public health risks to humans.}, }
@article {pmid18243021, year = {2008}, author = {Linzer, RE and Otrosina, WJ and Gonthier, P and Bruhn, J and Laflamme, G and Bussières, G and Garbelotto, M}, title = {Inferences on the phylogeography of the fungal pathogen Heterobasidion annosum, including evidence of interspecific horizontal genetic transfer and of human-mediated, long-range dispersal.}, journal = {Molecular phylogenetics and evolution}, volume = {46}, number = {3}, pages = {844-862}, doi = {10.1016/j.ympev.2007.12.010}, pmid = {18243021}, issn = {1055-7903}, mesh = {Basidiomycota/classification/*genetics ; Bayes Theorem ; Cell Nucleus/genetics ; DNA, Fungal/chemistry/genetics ; DNA, Mitochondrial/genetics ; Gene Transfer, Horizontal/*genetics ; Humans ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Fungi in the basidiomycete species complex Heterobasidion annosum are significant root-rot pathogens of conifers throughout the northern hemisphere. We utilize a multilocus phylogenetic approach to examine hypotheses regarding the evolution and divergence of two Heterobasidion taxa associated with pines: the Eurasian H. annosum sensu stricto and the North American H. annosum P intersterility group (ISG). Using DNA sequence information from portions of two nuclear and two mitochondrial loci, we infer phylogenetic relationships via parsimony, Bayesian and median-joining network analysis. Analysis of isolates representative of the entire known geographic range of the two taxa results in monophyletic sister Eurasian and North American lineages, with North America further subdivided into eastern and western clades. Genetically anomalous isolates from the Italian presidential estate of Castelporziano are always part of a North American clade and group with eastern North America, upholding the hypothesis of recent, anthropogenically mediated dispersal. P ISG isolates from Mexico have phylogenetic affinity with both eastern and western North America. Results for an insertion in the mitochondrial rDNA suggest this molecule was obtained from the Heterobasidion S ISG, a taxon sympatric with the P ISG in western North America. These data are compatible with an eastern Eurasian origin of the species, followed by dispersal of two sister taxa into western Eurasia and into eastern North America over a Beringean land bridge, a pattern echoed in the phylogeography of other conifer-associated basidiomycetes.}, }
@article {pmid18242643, year = {2008}, author = {Kumar, GA and Woodhall, MR and Hood, DW and Moxon, ER and Bayliss, CD}, title = {RecJ, ExoI and RecG are required for genome maintenance but not for generation of genetic diversity by repeat-mediated phase variation in Haemophilus influenzae.}, journal = {Mutation research}, volume = {640}, number = {1-2}, pages = {46-53}, doi = {10.1016/j.mrfmmm.2007.12.002}, pmid = {18242643}, issn = {0027-5107}, support = {G0400426/MRC_/Medical Research Council/United Kingdom ; 070123/Z/02/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacterial Proteins/*genetics ; DNA Damage ; DNA Helicases/*genetics ; Exodeoxyribonucleases/*genetics ; Gene Transfer, Horizontal ; *Genetic Variation ; Genomic Instability ; Haemophilus influenzae/*genetics/growth &amp; development ; Mutagenesis ; Sequence Deletion ; *Tandem Repeat Sequences ; }, abstract = {High levels of genetic diversity are generated in Haemophilus influenzae populations through DNA repeat-mediated phase variation and recombination with DNA fragments acquired by uptake from the external milieu. Conversely, multiple pathways for maintenance of the genome sequence are encoded in H. influenzae genomes. In Escherichia coli, mutations in single-stranded-DNA exonucleases destabilise tandem DNA repeats whilst inactivation of recG can stabilise repeat tracts. These enzymes also have varying effects on recombination. Deletion mutations were constructed in H. influenzae genes encoding homologs of ExoI, RecJ and RecG whilst ExoVII was refractory to mutation. Inactivation of RecJ and RecG, but not ExoI, increased sensitivity to irradiation with ultraviolet light. An increase in spontaneous mutation rate was not observed in single mutants but only when both RecJ and ExoI were mutated. None of the single- or double-mutations increased or decreased the rates of slippage in tetranucleotide repeat tracts. Furthermore, the exonuclease mutants did not exhibit significant defects in horizontal gene transfer. We conclude that RecJ, ExoI and RecG are required for maintenance of the H. influenzae genome but none of these enzymes influence the generation of genetic diversity through mutations in the tetranucleotide repeat tracts of this species.}, }
@article {pmid18241920, year = {2008}, author = {Jerke, K and Nakatsu, CH and Beasley, F and Konopka, A}, title = {Comparative analysis of eight Arthrobacter plasmids.}, journal = {Plasmid}, volume = {59}, number = {2}, pages = {73-85}, doi = {10.1016/j.plasmid.2007.12.003}, pmid = {18241920}, issn = {0147-619X}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Arthrobacter/enzymology/*genetics ; Bacterial Proteins/chemistry/genetics ; Base Sequence ; Conjugation, Genetic ; Conserved Sequence ; DNA Nucleotidyltransferases/chemistry ; DNA Replication ; DNA, Concatenated ; Genes, Bacterial ; Molecular Sequence Data ; Phylogeny ; Plasmids/*genetics ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; }, abstract = {Despite the prevalence of Arthrobacter in the environment little is known about their plasmids, or the capacity of Arthrobacter plasmids to mediate horizontal gene transfer. In this study, we compared eight plasmids from five Arthrobacter strains in order to identify putative core maintenance genes for replication, segregation, and conjugation. Iteron like sequences were identified on some of the plasmids; however, no genes with obvious similarity to known replication sequences such as an origin of replication, or rep genes were identified. All eight plasmids contained a putative conjugation system. Genes with similarity to a relaxase, coupling protein, and various components of a type IV secretion system were identified on each plasmid; it appears that three different systems may be present. Putative parA partitioning genes were found in all of the plasmids. Each of the Arthrobacter strains examined contained a putative parB gene; however, of the three plasmids in Arthrobacter strain FB24 only one plasmid had a putative parB gene. Cluster analysis of many of the Arthrobacter genes suggested that they often formed branches within existing families of plasmid maintenance genes. Comparison of a concatenation of all the maintenance genes from each plasmid suggests that the eight Arthrobacter plasmids represent multiple evolutionary pathways.}, }
@article {pmid18238887, year = {2008}, author = {Feld, L and Schjørring, S and Hammer, K and Licht, TR and Danielsen, M and Krogfelt, K and Wilcks, A}, title = {Selective pressure affects transfer and establishment of a Lactobacillus plantarum resistance plasmid in the gastrointestinal environment.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {61}, number = {4}, pages = {845-852}, doi = {10.1093/jac/dkn033}, pmid = {18238887}, issn = {1460-2091}, mesh = {Animals ; Anti-Bacterial Agents/administration &amp; dosage ; Conjugation, Genetic ; Drug Resistance, Bacterial/*genetics ; Enterococcus faecalis/*genetics ; Erythromycin/administration &amp; dosage ; Feces/microbiology ; Female ; Gastrointestinal Tract/*microbiology ; *Gene Transfer, Horizontal ; Germ-Free Life ; Lactobacillus plantarum/*genetics ; Male ; Mice ; *Plasmids ; Rats ; Rats, Sprague-Dawley ; *Selection, Genetic ; Streptomycin/administration &amp; dosage ; }, abstract = {OBJECTIVES AND METHODS: A Lactobacillus plantarum strain recently isolated from French raw-milk cheese was tested for its ability to transfer a small plasmid pLFE1 harbouring the erythromycin resistance gene erm(B) to Enterococcus faecalis. Mating was studied in vitro and in different gastrointestinal environments using gnotobiotic rats as a simple in vivo model and streptomycin-treated mice as a more complex model. Transfer and establishment of transconjugants in the intestine were investigated with and without selective pressure.<br><br>RESULTS: Compared with the relatively low transfer frequency of approximately 5.7 x 10(-8) transconjugants/recipient obtained in vitro by filter mating, a surprisingly high number of transconjugants (10(-4) transconjugants/recipient) was observed in gnotobiotic rats even without antibiotic treatment. When erythromycin was administered, a transfer rate of approximately 100% was observed, i.e. the recipient population turned completely into transconjugants (3 x 10(9) cfu/g faeces). Additionally, the time to reach a stable transconjugant population level was much faster in the erythromycin-treated gnotobiotic rats (1 day) than in the untreated animals (4-5 days). Transconjugants persisted in the gut in relatively stable numbers at least 12 days after termination of antibiotic treatment. In the streptomycin-treated mice, no transfer was observed either with or without erythromycin treatment.<br><br>CONCLUSIONS: The overall results imply that the gastrointestinal tract may comprise a more favourable environment for antibiotic resistance transfer than conditions provided in vitro. However, the indigenous gut microbiota severely restricts transfer, thus minimizing the number of detectable transfer events. Treatment with erythromycin strongly favoured transfer and establishment of pLFE1.}, }
@article {pmid18233336, year = {2007}, author = {Sun, J and Deem, MW}, title = {Spontaneous emergence of modularity in a model of evolving individuals.}, journal = {Physical review letters}, volume = {99}, number = {22}, pages = {228107}, doi = {10.1103/PhysRevLett.99.228107}, pmid = {18233336}, issn = {0031-9007}, mesh = {Adaptation, Biological ; *Biological Evolution ; Environment ; Gene Transfer, Horizontal ; *Models, Genetic ; }, abstract = {We investigate the selective forces that promote the emergence of modularity in nature. We demonstrate the spontaneous emergence of modularity in a population of individuals that evolve in a changing environment. We show that the level of modularity correlates with the rapidity and severity of environmental change. The modularity arises as a synergistic response to the noise in the environment in the presence of horizontal gene transfer. We suggest that the hierarchical structure observed in the natural world may be a broken-symmetry state, which generically results from evolution in a changing environment.}, }
@article {pmid18227242, year = {2008}, author = {Peng, X}, title = {Evidence for the horizontal transfer of an integrase gene from a fusellovirus to a pRN-like plasmid within a single strain of Sulfolobus and the implications for plasmid survival.}, journal = {Microbiology (Reading, England)}, volume = {154}, number = {Pt 2}, pages = {383-391}, doi = {10.1099/mic.0.2007/012963-0}, pmid = {18227242}, issn = {1350-0872}, mesh = {Base Sequence ; Fuselloviridae/enzymology/*genetics/isolation &amp; purification/ultrastructure ; *Gene Transfer, Horizontal ; Genes, Viral ; Genetic Vectors/genetics ; Genome, Viral ; Integrases/*genetics ; Molecular Sequence Data ; Plasmids/chemistry/*genetics ; Recombination, Genetic ; Sequence Alignment ; Sulfolobus/enzymology/*genetics/virology ; Virus Integration ; }, abstract = {A fusellovirus SSV4 and a pRN-like plasmid pXZ1 were co-isolated from a single strain of Sulfolobus. In contrast to the previously characterized virus-plasmid hybrids pSSVx and pSSVi, which can coexist intracellulary with a fusellovirus, pXZ1 is not packaged into viral particles and shows no viral infectivity. The virus and plasmid carry genomes of 15 135 and 6970 bp, respectively. For SSV4, 33 predicted ORFs are compactly organized with a strong preference for UGA stop codons, three-quarters of which overlap with either the Shine-Dalgarno motif or the start codon of the following gene. pXZ1 carries seven ORFs, three of which encode an atypical RepA, a PlrA and a CopG protein. A fourth ORF exhibits a high nucleotide sequence identity to the SSV4 integrase gene, which suggests that it has been transferred to the plasmid from SSV4. A single point mutation within an otherwise identical 500 bp region of the integrase gene occurs in the viral attachment site (attP), which corresponds to the anticodon region of the targeted tRNA gene in the host chromosome. This point mutation confers on pXZ1 the ability to integrate into the tRNA(Glu)[CUC] gene, which differs from the integration site of SSV4, tRNA(Glu)[UUC]. SSV4 and pXZ1 were also shown experimentally to integrate into separate sites on the host chromosome. This is believed to be the first report of a pRN plasmid sharing its natural host with a fusellovirus and carrying a highly similar integrase gene.}, }
@article {pmid18226931, year = {2008}, author = {Simpson, AG and Perley, TA and Lara, E}, title = {Lateral transfer of the gene for a widely used marker, alpha-tubulin, indicated by a multi-protein study of the phylogenetic position of Andalucia (Excavata).}, journal = {Molecular phylogenetics and evolution}, volume = {47}, number = {1}, pages = {366-377}, doi = {10.1016/j.ympev.2007.11.035}, pmid = {18226931}, issn = {1055-7903}, mesh = {*Gene Transfer, Horizontal ; *Phylogeny ; Prokaryotic Cells/*classification ; Proteins/*chemistry ; Tubulin/*genetics ; }, abstract = {alpha-Tubulin is one of the most widely used markers for estimating deep-level phylogenetic relationships amongst eukaryotes. We sequenced 6-7 nuclear protein-coding genes, including alpha-tubulin, from the two described species of the enigmatic jakobid(-like) excavate protist Andalucia. Concatenated protein phylogenies place Andalucia in a clade with other jakobids, Euglenozoa and Heterolobosea. Individual gene trees, except that of alpha-tubulin, do not conflict strongly with this position. In alpha-tubulin trees, Andalucia instead falls in a strongly supported clade with diplomonads, parabasalids and opisthokonts (including animals and fungi), and branches with diplomonads. This clade is robust to changes in taxon sampling, and is unlikely to represent long-branch attraction, compositional heterogeneity artefact, or segmental gene conversion. Phylogenies estimated without alpha-tubulin strongly support the original position for Andalucia, and also reinforce recent studies in placing diplomonads and parabasalids with Preaxostyla, not opisthokonts. alpha-Tubulin seems to have experienced two or more eukaryote-to-eukaryote lateral gene transfer (LGT) events, one perhaps from an ancestral opisthokont to an ancestor of diplomonads and parabasalids, or vice versa, and one probably from the diplomonad lineage to Andalucia. Like EF-1alpha/EFL, alpha-tubulin has a complex history that needs to be taken into account when using this marker for deep-level phylogenetic inference.}, }
@article {pmid18226929, year = {2008}, author = {Vallenback, P and Jaarola, M and Ghatnekar, L and Bengtsson, BO}, title = {Origin and timing of the horizontal transfer of a PgiC gene from Poa to Festuca ovina.}, journal = {Molecular phylogenetics and evolution}, volume = {46}, number = {3}, pages = {890-896}, doi = {10.1016/j.ympev.2007.11.031}, pmid = {18226929}, issn = {1055-7903}, mesh = {Evolution, Molecular ; Festuca/classification/enzymology/*genetics ; *Gene Transfer, Horizontal ; Glucose-6-Phosphate Isomerase/*genetics ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/*genetics ; Poa/classification/enzymology/*genetics ; Time Factors ; }, abstract = {A segregating second locus, PgiC2, for the enzyme phosphoglucose isomerase (PGIC) is found in the grass sheep's fescue, Festuca ovina. We have earlier reported that a phylogenetic analysis indicates that PgiC2 has been horizontally transferred from the reproductively separated grass genus Poa. Here we extend our analysis to include intron and exon information on 27 PgiC sequences from 18 species representing five genera, and confirm our earlier finding. The origin of PgiC2 can be traced to a group of closely interrelated, polyploid and partially asexual Poa species. The sequence most similar to PgiC2 is found in Poa palustris with a divergence, based on synonymous substitutions, of only 0.67%. This value suggests that the transfer took place less than 600,000 years ago (late Pleistocene), at a time when most extant Poa and Festuca species already existed.}, }
@article {pmid18226587, year = {2008}, author = {Lavigne, JP and Blanc-Potard, AB}, title = {Molecular evolution of Salmonella enterica serovar Typhimurium and pathogenic Escherichia coli: from pathogenesis to therapeutics.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {8}, number = {2}, pages = {217-226}, doi = {10.1016/j.meegid.2007.11.005}, pmid = {18226587}, issn = {1567-1348}, mesh = {Biomarkers/analysis ; Disease Transmission, Infectious ; Enterohemorrhagic Escherichia coli/*genetics/immunology/pathogenicity ; Escherichia coli Infections/*etiology/microbiology/*therapy/transmission ; Escherichia coli Vaccines/therapeutic use ; *Evolution, Molecular ; Genes, Bacterial ; Humans ; Immunotherapy, Active/trends ; Salmonella Infections/etiology/therapy/transmission ; Salmonella Vaccines/therapeutic use ; Salmonella typhi/*genetics/immunology ; Typhoid Fever/*etiology/microbiology/*therapy/transmission ; Virulence Factors/genetics ; }, abstract = {Salmonella enterica serovar Typhimurium (S. Typhimurium) and certain Escherichia coli are human pathogens that have evolved through the acquisition of multiple virulence determinants by horizontal gene transfer. Similar genetic elements, as pathogenicity islands and virulence plasmids, have driven molecular evolution of virulence in both species. In addition, the contribution of prophages has been recently highlighted as a reservoir for pathogenic diversity. Characterization of horizontally acquired virulence genes has several clinical implications. First, identification of virulence determinants that have a sporadic distribution and are specifically associated with a pathotype and/or a pathology can be useful markers for risk assessment and diagnosis. Secondly, virulence factors widely distributed in pathogenic strains, but absent from non-pathogenic bacteria, are interesting targets for the development of novel antimicrobial chemotherapies and vaccines. Here, we summarize the horizontally acquired virulence factors of S. Typhimurium, enterohemorrhagic E. coli O157:H7 and uropathogenic E. coli, and we describe their use in novel therapeutic approaches.}, }
@article {pmid18225789, year = {2007}, author = {Smeets, LC and Vandenbroucke-Grauls, CM}, title = {[Horizontal transfer of bacterial genes and its significance for antibiotic resistance and pathogenicity].}, journal = {Nederlands tijdschrift voor geneeskunde}, volume = {151}, number = {49}, pages = {2709-2714}, pmid = {18225789}, issn = {0028-2162}, mesh = {Bacteria/*genetics ; Conjugation, Genetic ; DNA, Bacterial/*genetics ; Drug Resistance, Bacterial/*genetics ; *Gene Transfer, Horizontal ; Transduction, Genetic ; Transformation, Bacterial/genetics ; Transformation, Genetic ; }, abstract = {* Sexual reproduction does not occur in bacteria. The point of departure in bacterial reproduction is always that one individual divides itself into two identical descendants. * In the bacterial world, however, there is certainly exchange of hereditary characteristics (DNA). This type of exchange is called horizontal gene transfer. * There are 3 basic ways for the exchange of DNA between bacteria: conjugation, transduction and natural transformation. Each of these has its specific impact on the species. * During conjugation, a piece of DNA is copied in one bacterium and transferred to another via a temporary connection, a conjugative pilus. In this way, for example, a particular gene that codes for resistance against antibiotics can be transmitted. * In transduction, the transfer of DNA takes place with the aid of bacteriophages. The gene that codes for the toxin produced by Vibrio cholerae is spread by transduction. * In transformation, DNA that is located outside the cell is fragmented and imported into the cell, after which, via recombination, the DNA replaces a piece of original DNA in the chromosome of the host. Transformation is responsible for, among other things, antigen variation in the pneumococcal capsule. Antigen variation helps the pneumococci to resist the immune response leading to the forming of antibodies and adequate opsonisation.}, }
@article {pmid18222943, year = {2008}, author = {Deusch, O and Landan, G and Roettger, M and Gruenheit, N and Kowallik, KV and Allen, JF and Martin, W and Dagan, T}, title = {Genes of cyanobacterial origin in plant nuclear genomes point to a heterocyst-forming plastid ancestor.}, journal = {Molecular biology and evolution}, volume = {25}, number = {4}, pages = {748-761}, doi = {10.1093/molbev/msn022}, pmid = {18222943}, issn = {1537-1719}, mesh = {Amino Acid Sequence ; Animals ; Arabidopsis/genetics ; Bacterial Proteins/chemistry/genetics ; Cell Nucleus/*genetics ; Chlamydomonas/genetics ; Conserved Sequence ; Cyanobacteria/*genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genome, Plant/*genetics ; Molecular Sequence Data ; Nitrogen Fixation/genetics ; Oryza/genetics ; Phylogeny ; Plants/*genetics ; Plastids/*genetics ; Rhodophyta/genetics ; Sequence Alignment ; Symbiosis/genetics ; }, abstract = {Plastids are descended from a cyanobacterial symbiosis which occurred over 1.2 billion years ago. During the course of endosymbiosis, most genes were lost from the cyanobacterium's genome and many were relocated to the host nucleus through endosymbiotic gene transfer (EGT). The issue of how many genes were acquired through EGT in different plant lineages is unresolved. Here, we report the genome-wide frequency of gene acquisitions from cyanobacteria in 4 photosynthetic eukaryotes--Arabidopsis, rice, Chlamydomonas, and the red alga Cyanidioschyzon--by comparison of the 83,138 proteins encoded in their genomes with 851,607 proteins encoded in 9 sequenced cyanobacterial genomes, 215 other reference prokaryotic genomes, and 13 reference eukaryotic genomes. The analyses entail 11,569 phylogenies inferred with both maximum likelihood and Neighbor-Joining approaches. Because each phylogenetic result is dependent not only upon the reconstruction method but also upon the site patterns in the underlying alignment, we investigated how the reliability of site pattern generation via alignment affects our results: if the site patterns in an alignment differ depending upon the order in which amino acids are introduced into multiple sequence alignment--N- to C-terminal versus C- to N-terminal--then the phylogenetic result is likely to be artifactual. Excluding unreliable alignments by this means, we obtain a conservative estimate, wherein about 14% of the proteins examined in each plant genome indicate a cyanobacterial origin for the corresponding nuclear gene, with higher proportions (17-25%) observed among the more reliable alignments. The identification of cyanobacterial genes in plant genomes affords access to an important question: from which type of cyanobacterium did the ancestor of plastids arise? Among the 9 cyanobacterial genomes sampled, Nostoc sp. PCC7120 and Anabaena variabilis ATCC29143 were found to harbor collections of genes which are-in terms of presence/absence and sequence similarity-more like those possessed by the plastid ancestor than those of the other 7 cyanobacterial genomes sampled here. This suggests that the ancestor of plastids might have been an organism more similar to filamentous, heterocyst-forming (nitrogen-fixing) representatives of section IV recognized in Stanier's cyanobacterial classification. Members of section IV are very common partners in contemporary symbiotic associations involving endosymbiotic cyanobacteria, which generally provide nitrogen to their host, consistent with suggestions that fixed nitrogen supplied by the endosymbiont might have played an important role during the origin of plastids.}, }
@article {pmid18222925, year = {2008}, author = {Abe, H and Miyahara, A and Oshima, T and Tashiro, K and Ogura, Y and Kuhara, S and Ogasawara, N and Hayashi, T and Tobe, T}, title = {Global regulation by horizontally transferred regulators establishes the pathogenicity of Escherichia coli.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {15}, number = {1}, pages = {25-38}, pmid = {18222925}, issn = {1756-1663}, mesh = {Escherichia coli O157/*genetics/*pathogenicity ; Escherichia coli Proteins/genetics ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Genomic Islands ; Promoter Regions, Genetic ; Trans-Activators/genetics ; Virulence ; }, abstract = {Enterohemorrhagic Escherichia coli is an emerging pathogen that causes diarrhea and hemolytic uremic syndrome. Much of the genomic information that affects virulence is acquired by horizontal transfer. Genes necessary for attaching and effacing lesions are located in the locus for enterocyte effacement (LEE) pathogenicity island. LEE gene transcription is positively regulated by Ler, which is also encoded by the LEE, and by Pch regulators, which are encoded at other loci. Here we identified genes whose transcription profiles were similar to those of the LEE genes, by comparing the effects of altering ler and pch transcript levels. We assigned these genes into two classes, according to their transcription profiles. By determining the binding profiles for Ler and Pch, we showed that both were involved in regulating one class of genes, but only Pch was involved in regulating the other class. Binding sites were found in the coding region as well as the promoter region of regulated genes, which include genes common to K12 strains as well as 0157-specific genes, suggesting that both act as a global regulator. These results indicate that Ler and Pch orchestrate the transcription of virulence genes, which are captured by horizontal transfer and scattered throughout the chromosome.}, }
@article {pmid18218688, year = {2008}, author = {Fredriksson, R and Hägglund, M and Olszewski, PK and Stephansson, O and Jacobsson, JA and Olszewska, AM and Levine, AS and Lindblom, J and Schiöth, HB}, title = {The obesity gene, FTO, is of ancient origin, up-regulated during food deprivation and expressed in neurons of feeding-related nuclei of the brain.}, journal = {Endocrinology}, volume = {149}, number = {5}, pages = {2062-2071}, doi = {10.1210/en.2007-1457}, pmid = {18218688}, issn = {0013-7227}, mesh = {Alpha-Ketoglutarate-Dependent Dioxygenase FTO ; Amino Acid Sequence ; Animals ; Brain/*metabolism ; Caloric Restriction ; Energy Metabolism/genetics ; Feeding Behavior/physiology ; Female ; Food Deprivation/*physiology ; Homeostasis/genetics ; Male ; Mice ; Molecular Sequence Data ; Neurons/*metabolism ; Obesity/*genetics ; Phylogeny ; Proteins/*genetics/metabolism ; Rats ; Rats, Sprague-Dawley ; Sequence Analysis ; Sequence Homology, Amino Acid ; Tissue Distribution ; Up-Regulation ; }, abstract = {Gene variants of the FTO (fatso) gene have recently been strongly associated with body mass index and obesity. The FTO gene is well conserved and found in a single copy in vertebrate species including fish and chicken, suggesting that the ancestor of this gene was present 450 million years ago. Surprisingly, the FTO gene is present in two species of algae but not in any other invertebrate species. This could indicate that this gene has undergone a horizontal gene transfer. Quantitative real-time PCR showed that the gene is expressed in many peripheral and central rat tissues. Detailed in situ hybridization analysis in the mouse brain showed abundant expression in feeding-related nuclei of the brainstem and hypothalamus, such as the nucleus of the solitary tract, area postrema, and arcuate, paraventricular, and supraoptic nuclei as well as in the bed nucleus of the stria terminalis. Colabeling showed that the FTO gene is predominantly expressed in neurons, whereas it was virtually not found in astrocytes or glia cells. The FTO was significantly up-regulated (41%) in the hypothalamus of rats after 48-h food deprivation. We also found a strong negative correlation of the FTO expression level with the expression of orexigenic galanin-like peptide, which is mainly synthesized in the arcuate nucleus. These results are consistent with the hypothesis that FTO could participate in the central control of energy homeostasis.}, }
@article {pmid18218112, year = {2008}, author = {Davids, W and Zhang, Z}, title = {The impact of horizontal gene transfer in shaping operons and protein interaction networks--direct evidence of preferential attachment.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {23}, pmid = {18218112}, issn = {1471-2148}, mesh = {Escherichia coli/*genetics ; Escherichia coli Proteins/genetics ; *Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal/*genetics ; *Genes, Bacterial ; Metabolic Networks and Pathways ; *Operon ; *Protein Interaction Mapping ; Sequence Alignment ; }, abstract = {BACKGROUND: Despite the prevalence of horizontal gene transfer (HGT) in bacteria, to this date there were few studies on HGT in the context of gene expression, operons and protein-protein interactions. Using the recently available data set on the E. coli protein-protein interaction network, we sought to explore the impact of HGT on genome structure and protein networks.<br><br>RESULTS: We classified the E. coli genes into three categories based on their evolutionary conservation: a set of 2158 Core genes that are shared by all E. coli strains, a set of 1044 Non-core genes that are strain-specific, and a set of 1053 genes that were putatively acquired by horizontal transfer. We observed a clear correlation between gene expressivity (measured by Codon Adaptation Index), evolutionary rates, and node connectivity between these categories of genes. Specifically, we found the Core genes are the most highly expressed and the most slowly evolving, while the HGT genes are expressed at the lowest level and evolve at the highest rate. Core genes are the most likely and HGT genes are the least likely to be member of the operons. In addition, we found the Core genes on average are more highly connected than Non-core and HGT genes in the protein interaction network, however the HGT genes displayed a significantly higher mean node degree than the Core and Non-core genes in the defence COG functional category. Interestingly, HGT genes are more likely to be connected to Core genes than expected by chance, which suggest a model of differential attachment in the expansion of cellular networks.<br><br>CONCLUSION: Results from our analysis shed light on the mode and mechanism of the integration of horizontally transferred genes into operons and protein interaction networks.}, }
@article {pmid18218086, year = {2008}, author = {Khaldi, N and Collemare, J and Lebrun, MH and Wolfe, KH}, title = {Evidence for horizontal transfer of a secondary metabolite gene cluster between fungi.}, journal = {Genome biology}, volume = {9}, number = {1}, pages = {R18}, pmid = {18218086}, issn = {1474-760X}, mesh = {Aspergillus/genetics ; Chaetomium/genetics ; Fungi/*genetics ; *Gene Transfer, Horizontal ; Magnaporthe/genetics ; Metabolism/genetics ; *Multigene Family ; Oryza/microbiology ; Peptide Synthases/genetics ; }, abstract = {BACKGROUND: Filamentous fungi synthesize many secondary metabolites and are rich in genes encoding proteins involved in their biosynthesis. Genes from the same pathway are often clustered and co-expressed in particular conditions. Such secondary metabolism gene clusters evolve rapidly through multiple rearrangements, duplications and losses. It has long been suspected that clusters can be transferred horizontally between species, but few concrete examples have been described so far.<br><br>RESULTS: In the rice blast fungus Magnaporthe grisea, the avirulence gene ACE1 that codes for a hybrid polyketide synthase-nonribosomal peptide synthetase (PKS-NRPS) belongs to a cluster of 15 genes involved in secondary metabolism. Additional related clusters were detected in the ascomycetes Chaetomium globosum, Stagonospora nodorum and Aspergillus clavatus. Gene-by-gene phylogenetic analysis showed that in C. globosum and M. grisea, the evolution of these ACE1-like clusters is characterized by successive complex duplication events including tandem duplication within the M. grisea cluster. The phylogenetic trees also present evidence that at least five of the six genes in the homologous ACE1 gene cluster in A. clavatus originated by horizontal transfer from a donor closely related to M. grisea.<br><br>CONCLUSION: The ACE1 cluster originally identified in M. grisea is shared by only few fungal species. Its sporadic distribution within euascomycetes is mainly explained by multiple events of duplication and losses. However, because A. clavatus contains an ACE1 cluster of only six genes, we propose that horizontal transfer from a relative of M. grisea into an ancestor of A. clavatus provides a much simpler explanation of the observed data than the alternative of multiple events of duplication and losses of parts of the cluster.}, }
@article {pmid18218018, year = {2008}, author = {Wang, J and Steggles, JR and Ellar, DJ}, title = {Molecular characterization of virulence defects in Bacillus thuringiensis mutants.}, journal = {FEMS microbiology letters}, volume = {280}, number = {1}, pages = {127-134}, doi = {10.1111/j.1574-6968.2007.01061.x}, pmid = {18218018}, issn = {0378-1097}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Bacillus thuringiensis/*genetics/*pathogenicity ; Bacterial Proteins/genetics/metabolism ; DNA Transposable Elements ; Manduca/microbiology ; Molecular Sequence Data ; Mutagenesis, Insertional ; *Mutation ; Open Reading Frames ; *Physical Chromosome Mapping ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Transcription, Genetic ; Virulence ; Virulence Factors/genetics/*metabolism ; }, abstract = {Sequence analysis of a virulence-attenuated Bacillus thuringiensis signature tagged mutant 6F8 led to the identification of an 18 182 bp locus encoding 29 potential protein-coding ORFs. Thirteen of the 29 putative ORFs were found to share extensive homology with genes on plasmid pE33L466 of the pathogenic Bacillus cereus E33L strain. Nine ORFs were not only found in a cluster, but also in the same gene order, in both organisms. A number of mobile elements, including a transposon Tn4430, a novel IS231 family insertion sequence ISBth4 and various phage-related proteins, were found flanking this conserved gene cluster. These features of the 6F8 locus suggested that it might have undergone several DNA insertions from different sources by horizontal gene transfer. Transcriptional analyses of the 6F8 locus revealed that ORFs 1-23 were cotranscribed as a single transcript. Null mutants were constructed to investigate the function of the sequences flanking the signature-tagged mutagenesis insertion sites. Competition assays performed with the wild-type and null mutants demonstrated that the Tn4430 transposon element plays an important role in the full virulence of B. thuringiensis during Manduca sexta infection. This study provides the first experimental evidence that a Tn4430 family transposon is directly associated with B. thuringiensis virulence.}, }
@article {pmid18217553, year = {2007}, author = {McDonald, M and Towers, RJ and Andrews, RM and Carapetis, JR and Currie, BJ}, title = {Epidemiology of Streptococcus dysgalactiae subsp. equisimilis in tropical communities, Northern Australia.}, journal = {Emerging infectious diseases}, volume = {13}, number = {11}, pages = {1694-1700}, pmid = {18217553}, issn = {1080-6040}, mesh = {Adolescent ; Australia/epidemiology ; Child ; Humans ; Pharynx/microbiology ; Population Surveillance/methods ; Prospective Studies ; Rheumatic Fever/epidemiology/microbiology ; Rheumatic Heart Disease/epidemiology/microbiology ; Skin/microbiology ; Streptococcal Infections/*epidemiology/microbiology ; Streptococcus/genetics/*isolation &amp; purification ; Tropical Climate ; }, abstract = {Streptococcus dysgalactiae subsp. equisimilis (groups C and G streptococci [GCS/GGS]) is an increasingly recognized human pathogen, although it may follow indirect pathways. Prospective surveillance of selected households in 3 remote Aboriginal communities in Australia provided 337 GCS/GGS isolates that were emm sequence-typed. Lancefield group C isolates (GCS) were localized to specific households and group G isolates (GGS) were more evenly distributed. GCS/GGS was more frequently recovered from the throat than group A streptococci (GAS [S. pyogenes]) but rarely recovered from skin sores, and then only with Staphylococcus aureus or GAS. Symptomatic GGS/GGC pharyngitis was also rare. Specific emm sequence types of GCS/GGS did not appear to cycle through the communities (sequential strain replacement) in a manner suggesting acquisition of type-specific immunity. These communities already have high levels of streptococcal and poststreptococcal disease. GCS/GGS may increase in importance as it acquires key virulence factors from GAS by lateral gene transfer.}, }
@article {pmid18215774, year = {2008}, author = {Umejiego, NN and Gollapalli, D and Sharling, L and Volftsun, A and Lu, J and Benjamin, NN and Stroupe, AH and Riera, TV and Striepen, B and Hedstrom, L}, title = {Targeting a prokaryotic protein in a eukaryotic pathogen: identification of lead compounds against cryptosporidiosis.}, journal = {Chemistry &amp; biology}, volume = {15}, number = {1}, pages = {70-77}, pmid = {18215774}, issn = {1074-5521}, support = {P41 RR001081/RR/NCRR NIH HHS/United States ; R01 AI055268/AI/NIAID NIH HHS/United States ; R01 AI055268-04/AI/NIAID NIH HHS/United States ; P41 RR-01081/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Antiparasitic Agents/chemistry/pharmacology/*therapeutic use ; Binding Sites ; Cryptosporidiosis/*drug therapy/enzymology ; Cryptosporidium parvum/*drug effects/enzymology/pathogenicity ; Eukaryotic Cells/*enzymology ; Guanine Nucleotide Dissociation Inhibitors/chemistry/pharmacology/therapeutic use ; Guanine Nucleotides/metabolism ; Humans ; IMP Dehydrogenase/*antagonists &amp; inhibitors/chemistry/metabolism ; Kinetics ; Paromomycin/chemistry/pharmacology/therapeutic use ; Prokaryotic Cells/*enzymology ; }, abstract = {Cryptosporidium parvum is an important human pathogen and potential bioterrorism agent. No vaccines exist against C. parvum, the drugs currently approved to treat cryptosporidiosis are ineffective, and drug discovery is challenging because the parasite cannot be maintained continuously in cell culture. Mining the sequence of the C. parvum genome has revealed that the only route to guanine nucleotides is via inosine-5'-monophosphate dehydrogenase (IMPDH). Moreover, phylogenetic analysis suggests that the IMPDH gene was obtained from bacteria by lateral gene transfer. Here we exploit the unexpected evolutionary divergence of parasite and host enzymes by designing a high-throughput screen to target the most diverged portion of the IMPDH active site. We have identified four parasite-selective IMPDH inhibitors that display antiparasitic activity with greater potency than paromomycin, the current gold standard for anticryptosporidial activity.}, }
@article {pmid18213396, year = {2008}, author = {Vallès, Y and Halanych, KM and Boore, JL}, title = {Group II introns break new boundaries: presence in a bilaterian's genome.}, journal = {PloS one}, volume = {3}, number = {1}, pages = {e1488}, pmid = {18213396}, issn = {1932-6203}, mesh = {Animals ; Annelida/classification/*genetics ; Base Sequence ; DNA Primers ; DNA, Mitochondrial/genetics ; *Genome ; *Introns ; Phylogeny ; }, abstract = {Group II introns are ribozymes, removing themselves from their primary transcripts, as well as mobile genetic elements, transposing via an RNA intermediate, and are thought to be the ancestors of spliceosomal introns. Although common in bacteria and most eukaryotic organelles, they have never been reported in any bilaterian animal genome, organellar or nuclear. Here we report the first group II intron found in the mitochondrial genome of a bilaterian worm. This location is especially surprising, since animal mitochondrial genomes are generally distinct from those of plants, fungi, and protists by being small and compact, and so are viewed as being highly streamlined, perhaps as a result of strong selective pressures for fast replication while establishing germ plasm during early development. This intron is found in the mtDNA of an annelid worm, (an undescribed species of Nephtys), where the complete sequence revealed a 1819 bp group II intron inside the cox1 gene. We infer that this intron is the result of a recent horizontal gene transfer event from a viral or bacterial vector into the mitochondrial genome of Nephtys sp. Our findings hold implications for understanding mechanisms, constraints, and selective pressures that account for patterns of animal mitochondrial genome evolution.}, }
@article {pmid18213365, year = {2008}, author = {Williamson, SJ and Rusch, DB and Yooseph, S and Halpern, AL and Heidelberg, KB and Glass, JI and Andrews-Pfannkoch, C and Fadrosh, D and Miller, CS and Sutton, G and Frazier, M and Venter, JC}, title = {The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples.}, journal = {PloS one}, volume = {3}, number = {1}, pages = {e1456}, pmid = {18213365}, issn = {1932-6203}, mesh = {Genetic Linkage ; *Genome, Viral ; Oceans and Seas ; Phylogeny ; *Water Microbiology ; }, abstract = {Viruses are the most abundant biological entities on our planet. Interactions between viruses and their hosts impact several important biological processes in the world's oceans such as horizontal gene transfer, microbial diversity and biogeochemical cycling. Interrogation of microbial metagenomic sequence data collected as part of the Sorcerer II Global Ocean Expedition (GOS) revealed a high abundance of viral sequences, representing approximately 3% of the total predicted proteins. Cluster analyses of the viral sequences revealed hundreds to thousands of viral genes encoding various metabolic and cellular functions. Quantitative analyses of viral genes of host origin performed on the viral fraction of aquatic samples confirmed the viral nature of these sequences and suggested that significant portions of aquatic viral communities behave as reservoirs of such genetic material. Distributional and phylogenetic analyses of these host-derived viral sequences also suggested that viral acquisition of environmentally relevant genes of host origin is a more abundant and widespread phenomenon than previously appreciated. The predominant viral sequences identified within microbial fractions originated from tailed bacteriophages and exhibited varying global distributions according to viral family. Recruitment of GOS viral sequence fragments against 27 complete aquatic viral genomes revealed that only one reference bacteriophage genome was highly abundant and was closely related, but not identical, to the cyanomyovirus P-SSM4. The co-distribution across all sampling sites of P-SSM4-like sequences with the dominant ecotype of its host, Prochlorococcus supports the classification of the viral sequences as P-SSM4-like and suggests that this virus may influence the abundance, distribution and diversity of one of the most dominant components of picophytoplankton in oligotrophic oceans. In summary, the abundance and broad geographical distribution of viral sequences within microbial fractions, the prevalence of genes among viral sequences that encode microbial physiological function and their distinct phylogenetic distribution lend strong support to the notion that viral-mediated gene acquisition is a common and ongoing mechanism for generating microbial diversity in the marine environment.}, }
@article {pmid18208393, year = {2008}, author = {Hobel, CF and Albers, SV and Driessen, AJ and Lupas, AN}, title = {The Sulfolobus solfataricus AAA protein Sso0909, a homologue of the eukaryotic ESCRT Vps4 ATPase.}, journal = {Biochemical Society transactions}, volume = {36}, number = {Pt 1}, pages = {94-98}, doi = {10.1042/BST0360094}, pmid = {18208393}, issn = {0300-5127}, mesh = {ATPases Associated with Diverse Cellular Activities ; Adenosine Triphosphatases/*chemistry ; Amino Acid Sequence ; Bacterial Proteins/*chemistry/genetics/isolation &amp; purification ; Endosomal Sorting Complexes Required for Transport ; Gene Expression Regulation, Bacterial ; Gene Targeting ; Humans ; Molecular Sequence Data ; Recombination, Genetic/genetics ; Sequence Alignment ; Sequence Analysis, Protein ; *Sequence Homology, Amino Acid ; Sulfolobus solfataricus/*enzymology/genetics ; Vesicular Transport Proteins/chemistry ; }, abstract = {Sso0909 is a protein of the thermo-acidophilic crenarchaeon Sulfolobus solfataricus, annotated as a p60 katanin-like ATPase. We present here results supporting the hypothesis that Sso0909 is an orthologue of the eukaryotic ESCRT (endosomal sorting complex required for transport) ATPase Vps4 (vacular protein sorting 4). The spectrum of Sso0909 homologues is limited to several orders of Crenarchaea and to three euryarchaeal Thermoplasmata species, where they were presumably acquired by lateral gene transfer. Almost invariably, Sso0909 homologues occur in the genomic vicinity of homologues of eukaryotic ESCRT-III components, which are the targets of disassembly by Vps4, as well as with a creanarchaeal-specific coiled-coil protein. S. solfataricus sso0909 is constitutively expressed under normal growth conditions and appears to be essential, as judged by the failure to obtain stable deletion mutants. We expressed Sso0909 in Escherichia coli and S. solfataricus, but have not obtained preparations with ATPase activity so far.}, }
@article {pmid18205946, year = {2008}, author = {Yin, Y and Fischer, D}, title = {Identification and investigation of ORFans in the viral world.}, journal = {BMC genomics}, volume = {9}, number = {}, pages = {24}, pmid = {18205946}, issn = {1471-2164}, mesh = {Bacteriophages/*classification/genetics ; Base Pairing ; Base Sequence ; DNA, Single-Stranded/genetics ; Databases, Factual ; Gene Transfer, Horizontal ; Genes, Viral/*genetics ; Genetic Variation ; Genome, Viral/genetics ; Models, Genetic ; Molecular Sequence Data ; Open Reading Frames/*genetics ; Phylogeny ; Prokaryotic Cells/virology ; Sequence Analysis, DNA ; Species Specificity ; Viral Proteins/genetics ; }, abstract = {BACKGROUND: Genome-wide studies have already shed light into the evolution and enormous diversity of the viral world. Nevertheless, one of the unresolved mysteries in comparative genomics today is the abundance of ORFans - ORFs with no detectable sequence similarity to any other ORF in the databases. Recently, studies attempting to understand the origin and functions of bacterial ORFans have been reported. Here we present a first genome-wide identification and analysis of ORFans in the viral world, with focus on bacteriophages.<br><br>RESULTS: Almost one-third of all ORFs in 1,456 complete virus genomes correspond to ORFans, a figure significantly larger than that observed in prokaryotes. Like prokaryotic ORFans, viral ORFans are shorter and have a lower GC content than non-ORFans. Nevertheless, a statistically significant lower GC content is found only on a minority of viruses. By focusing on phages, we find that 38.4% of phage ORFs have no homologs in other phages, and 30.1% have no homologs neither in the viral nor in the prokaryotic world. Phages with different host ranges have different percentages of ORFans, reflecting different sampling status and suggesting various diversities. Similarity searches of the phage ORFeome (ORFans and non-ORFans) against prokaryotic genomes shows that almost half of the phage ORFs have prokaryotic homologs, suggesting the major role that horizontal transfer plays in bacterial evolution. Surprisingly, the percentage of phage ORFans with prokaryotic homologs is only 18.7%. This suggests that phage ORFans play a lesser role in horizontal transfer to prokaryotes, but may be among the major players contributing to the vast phage diversity.<br><br>CONCLUSION: Although the current sampling of viral genomes is extremely low, ORFans and near-ORFans are likely to continue to grow in number as more genomes are sequenced. The abundance of phage ORFans may be partially due to the expected vast viral diversity, and may be instrumental in understanding viral evolution. The functions, origins and fates of the majority of viral ORFans remain a mystery. Further computational and experimental studies are likely to shed light on the mechanisms that have given rise to so many bacterial and viral ORFans.}, }
@article {pmid18205905, year = {2008}, author = {Moreira, D and Brochier-Armanet, C}, title = {Giant viruses, giant chimeras: the multiple evolutionary histories of Mimivirus genes.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {12}, pmid = {18205905}, issn = {1471-2148}, mesh = {Acanthamoeba/*virology ; Animals ; Bayes Theorem ; Chimera/*genetics ; DNA Viruses/classification/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Viral ; Host-Pathogen Interactions ; Likelihood Functions ; Open Reading Frames ; Phylogeny ; }, abstract = {BACKGROUND: Although capable to evolve, viruses are generally considered non-living entities because they are acellular and devoid of metabolism. However, the recent publication of the genome sequence of the Mimivirus, a giant virus that parasitises amoebas, strengthened the idea that viruses should be included in the tree of life. In fact, the first phylogenetic analyses of a few Mimivirus genes that are also present in cellular lineages suggested that it could define an independent branch in the tree of life in addition to the three domains, Bacteria, Archaea and Eucarya.<br><br>RESULTS: We tested this hypothesis by carrying out detailed phylogenetic analyses for all the conserved Mimivirus genes that have homologues in cellular organisms. We found no evidence supporting Mimivirus as a new branch in the tree of life. On the contrary, our phylogenetic trees strongly suggest that Mimivirus acquired most of these genes by horizontal gene transfer (HGT) either from its amoebal hosts or from bacteria that parasitise the same hosts. The detection of HGT events involving different eukaryotic donors suggests that the spectrum of hosts of Mimivirus may be larger than currently known.<br><br>CONCLUSION: The large number of genes acquired by Mimivirus from eukaryotic and bacterial sources suggests that HGT has been an important process in the evolution of its genome and the adaptation to parasitism.}, }
@article {pmid18203769, year = {2008}, author = {Birin, H and Gal-Or, Z and Elias, I and Tuller, T}, title = {Inferring horizontal transfers in the presence of rearrangements by the minimum evolution criterion.}, journal = {Bioinformatics (Oxford, England)}, volume = {24}, number = {6}, pages = {826-832}, doi = {10.1093/bioinformatics/btn024}, pmid = {18203769}, issn = {1367-4811}, mesh = {Algorithms ; Bacterial Proteins/*genetics ; Base Sequence ; Chromosome Mapping/*methods ; Computer Simulation ; DNA Mutational Analysis/methods ; *Evolution, Molecular ; Gene Rearrangement, T-Lymphocyte/*genetics ; Gene Transfer, Horizontal/*genetics ; Genetic Variation/genetics ; Models, Genetic ; Molecular Sequence Data ; Plant Proteins/*genetics ; Sequence Alignment/methods ; Sequence Analysis, DNA/*methods ; }, abstract = {MOTIVATION: The evolution of viruses is very rapid and in addition to local point mutations (insertion, deletion, substitution) it also includes frequent recombinations, genome rearrangements and horizontal transfer of genetic materials (HGTS). Evolutionary analysis of viral sequences is therefore a complicated matter for two main reasons: First, due to HGTs and recombinations, the right model of evolution is a network and not a tree. Second, due to genome rearrangements, an alignment of the input sequences is not guaranteed. These facts encourage developing methods for inferring phylogenetic networks that do not require aligned sequences as input.<br><br>RESULTS: In this work, we present the first computational approach which deals with both genome rearrangements and horizontal gene transfers and does not require a multiple alignment as input. We formalize a new set of computational problems which involve analyzing such complex models of evolution. We investigate their computational complexity, and devise algorithms for solving them. Moreover, we demonstrate the viability of our methods on several synthetic datasets as well as four biological datasets.<br><br>AVAILABILITY: The code is available from the authors upon request.}, }
@article {pmid18195030, year = {2008}, author = {Izutsu, K and Kurokawa, K and Tashiro, K and Kuhara, S and Hayashi, T and Honda, T and Iida, T}, title = {Comparative genomic analysis using microarray demonstrates a strong correlation between the presence of the 80-kilobase pathogenicity island and pathogenicity in Kanagawa phenomenon-positive Vibrio parahaemolyticus strains.}, journal = {Infection and immunity}, volume = {76}, number = {3}, pages = {1016-1023}, pmid = {18195030}, issn = {1098-5522}, mesh = {DNA, Bacterial/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; *Genomic Islands ; Humans ; Microarray Analysis ; *Oligonucleotide Array Sequence Analysis ; Polymorphism, Genetic ; Vibrio parahaemolyticus/*genetics ; }, abstract = {Vibrio parahaemolyticus is a gram-negative marine bacterium. A limited population of the organisms causes acute gastroenteritis in humans. Almost all of the clinical V. parahaemolyticus isolates exhibit beta-type hemolysis on Wagatsuma agar, known as the Kanagawa phenomenon (KP). KP is induced by the thermostable direct hemolysin produced by the organism and has been considered a crucial marker to distinguish pathogenic strains from nonpathogenic ones. Since 1996, so-called "pandemic clones," the majority of which belong to serotype O3:K6, have caused worldwide outbreaks of gastroenteritis. In this study, we used a DNA microarray constructed based on the genome sequence of a pandemic V. parahaemolyticus strain, RIMD2210633, to examine the genomic composition of 22 strains of V. parahaemolyticus, including both pathogenic (pandemic and nonpandemic) and nonpathogenic strains. More than 86% of the RIMD2210633 genes were conserved in all of the strains tested. Many variably present genes formed gene clusters on the genome of RIMD2210633 and were probably acquired through lateral gene transfer. At least 65 genes over 11 loci were specifically present in the pandemic strains compared with any of the nonpandemic strains, suggesting that the difference between pandemic and nonpandemic strains is not due to a simple genetic event. Only the genes in the 80-kb pathogenicity island (Vp-PAI) on chromosome II, including two tdh genes and a set of genes for the type III secretion system, were detected only in the KP-positive pathogenic strains. These results strongly suggest that acquisition of this Vp-PAI was crucial for the emergence of V. parahaemolyticus strains that are pathogenic for humans.}, }
@article {pmid18194581, year = {2008}, author = {Moustafa, A and Bhattacharya, D}, title = {PhyloSort: a user-friendly phylogenetic sorting tool and its application to estimating the cyanobacterial contribution to the nuclear genome of Chlamydomonas.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {6}, pmid = {18194581}, issn = {1471-2148}, support = {T32 GM008629/GM/NIGMS NIH HHS/United States ; R01ES013679/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Chlamydomonas reinhardtii/classification/*genetics ; Cyanobacteria/*genetics ; Expressed Sequence Tags ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Genome, Protozoan ; Genomics ; *Phylogeny ; Plastids/*genetics ; Symbiosis/genetics ; User-Computer Interface ; }, abstract = {BACKGROUND: Phylogenomic pipelines generate a large collection of phylogenetic trees that require manual inspection to answer questions about gene or genome evolution. A notable application of phylogenomics is to photosynthetic organelle (plastid) endosymbiosis. In the case of primary endosymbiosis, a heterotrophic protist engulfed a cyanobacterium, giving rise to the first photosynthetic eukaryote. Plastid establishment precipitated extensive gene transfer from the endosymbiont to the nuclear genome of the 'host'. Estimating the magnitude of this endosymbiotic gene transfer (EGT) and determining the functions of the prokaryotic genes remain controversial issues. We used phylogenomics to study EGT in the model green alga Chlamydomonas reinhardtii. To facilitate this procedure, we developed PhyloSort to rapidly search large collection of trees for monophyletic relationships. Here we present PhyloSort and its application to estimating EGT in Chlamydomonas.<br><br>RESULTS: PhyloSort is an open-source tool to sort phylogenetic trees by searching for user specified subtrees that contain a monophyletic group of interest defined by operational taxonomic units in a phylogenomic context. Using PhyloSort, we identified 897 Chlamydomonas genes of putative cyanobacterial origin, of which 531 had bootstrap support values >/= 50% for the grouping of the algal and cyanobacterial homologs.<br><br>CONCLUSION: PhyloSort can be applied to quantify the number of genes that support different evolutionary hypotheses such as a taxonomic classification or endosymbiotic or horizontal gene transfer events. In our application, we demonstrate that cyanobacteria account for 3.5-6% of the protein-coding genes in the nuclear genome of Chlamydomonas.}, }
@article {pmid18194157, year = {2008}, author = {Hülter, N and Wackernagel, W}, title = {Double illegitimate recombination events integrate DNA segments through two different mechanisms during natural transformation of Acinetobacter baylyi.}, journal = {Molecular microbiology}, volume = {67}, number = {5}, pages = {984-995}, doi = {10.1111/j.1365-2958.2007.06096.x}, pmid = {18194157}, issn = {1365-2958}, mesh = {Acinetobacter/*genetics ; Base Sequence ; DNA, Bacterial/chemistry/*genetics ; Electroporation ; Gene Transfer, Horizontal ; Genetic Vectors ; Kanamycin Kinase/genetics ; Kanamycin Resistance ; Models, Genetic ; Molecular Sequence Data ; Plasmids ; Recombinases/metabolism ; *Recombination, Genetic ; Sequence Homology, Nucleic Acid ; *Transformation, Bacterial ; }, abstract = {Acquisition of foreign DNA by horizontal gene transfer is seen as a major source of genetic diversity in prokaryotes. However, strongly divergent DNA is not genomically integrated by homologous recombination and would depend on illegitimate recombination (IR) events which are rare. We show that, by two mechanisms, during natural transformation of Acinetobacter baylyi two IR events can integrate DNA segments. One mechanism is double illegitimate recombination (DIR) acting in the absence of any homology (frequency: 7 x 10(-13) per cell). It occurs about 10(10)-fold less frequent than homologous transformation. The other mechanism is homology-facilitated double illegitimate recombination (HFDIR) being about 440-fold more frequent (3 x 10(-10) per cell) than DIR. HFDIR depends on a homologous sequence located between the IR sites and on recA(+). In HFDIR two IR events act on the same donor DNA molecule as shown by the joint inheritance of molecular DNA tags. While the IR events in HFDIR occurred at microhomologies, in DIR microhomologies were not used. The HFDIR phenomenon indicates that a temporal recA-dependent association of donor DNA at a homology in recipient DNA may facilitate two IR events on the 5' and 3' heterologous parts of the transforming DNA molecule.}, }
@article {pmid18181712, year = {2008}, author = {Snydman, DR}, title = {The safety of probiotics.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {46 Suppl 2}, number = {}, pages = {S104-11; discussion S144-51}, doi = {10.1086/523331}, pmid = {18181712}, issn = {1537-6591}, support = {1R21 AT001892/AT/NCCIH NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*growth &amp; development/pathogenicity ; Clinical Trials as Topic ; Consumer Product Safety/*standards ; Drug Resistance, Microbial/genetics ; Gastrointestinal Tract/microbiology ; Gene Transfer, Horizontal ; Genetic Engineering ; Humans ; Lactobacillus/growth &amp; development/pathogenicity ; Mice ; Probiotics/*adverse effects/standards/therapeutic use ; }, abstract = {Probiotics are generally defined as microorganisms that, when consumed, generally confer a health benefit on humans. There is considerable interest in probiotics for a variety of medical conditions, and millions of people around the world consume probiotics daily for perceived health benefits. Lactobacilli, bifidobacteria, and lactococci have generally been regarded as safe. There are 3 theoretical concerns regarding the safety of probiotics: (1) the occurrence of disease, such as bacteremia or endocarditis; (2) toxic or metabolic effects on the gastrointestinal tract; and (3) the transfer of antibiotic resistance in the gastrointestinal flora. In this review, the evidence for safety of the use of or the study of probiotics is examined. Although there are rare cases of bacteremia or fungemia related to the use of probiotics, epidemiologic evidence suggests no population increase in risk on the basis of usage data. There have been many controlled clinical trials on the use of probiotics that demonstrate safe use. The use of probiotics in clinical trials should be accompanied by the use of a data-safety monitoring board and by knowledge of the antimicrobial susceptibilities of the organism used.}, }
@article {pmid18180362, year = {2008}, author = {Novais, C and Freitas, AR and Sousa, JC and Baquero, F and Coque, TM and Peixe, LV}, title = {Diversity of Tn1546 and its role in the dissemination of vancomycin-resistant enterococci in Portugal.}, journal = {Antimicrobial agents and chemotherapy}, volume = {52}, number = {3}, pages = {1001-1008}, pmid = {18180362}, issn = {0066-4804}, mesh = {Animals ; DNA Transposable Elements/*genetics ; DNA, Bacterial/analysis/genetics ; Electrophoresis, Gel, Pulsed-Field ; *Enterococcus/drug effects/genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; Gram-Positive Bacterial Infections/epidemiology/microbiology/*transmission ; Humans ; Microbial Sensitivity Tests ; Portugal/epidemiology ; Poultry/microbiology ; Sewage/microbiology ; Swine/microbiology ; *Vancomycin Resistance/genetics ; }, abstract = {We characterized the molecular diversity of vanA vancomycin-resistant enterococci (VRE; 176 isolates/87 pulsed-field gel electrophoresis types) from different sources and cities in Portugal (1996 to 2004): (i) food animals (FA; n = 38 isolates out of 31 samples), hospitalized humans (HH; n = 101/101), healthy human volunteers (HV; n = 7/4), and environmental sources (n = 30/10). Some strains were isolated from different hosts and persistently recovered for years. Twenty-four Tn1546 variants were identified, all located on plasmids (30 to 250 kb). Some Tn1546 variants were associated with specific sources such as FA (3 types), HH (11 types), or HV (1 type), while others were recovered from isolates of different origins (8 types). Polymorphisms in the central vanRSHA region of Tn1546 were scarcely detected, while alterations upstream of vanR and downstream of vanA were frequently identified involving mutations (vanS and vanX), deletions (vanY), insertions (IS1216V, ISEf1, and IS19; sequences with or without homology with others available in GenBank databases), and different genetic rearrangements. Most Tn1546 variants contained IS1216V (14 types) or ISEf1 (6 types). IS1216V was found alone or associated with an IS3-like element at different orientations and positions in Tn1546 from human, animal, and environmental samples. ISEf1 was located within vanX-vanY region at nucleotide 9044 of Tn1546 variants mostly associated with clinical isolates, suggesting a common genetic platform. IS19 was observed within the vanX-vanY region in one Tn1546 variant from poultry. Recent spread of VRE in Portugal reflects a complex epidemiology involving both clonal spread and plasmid dissemination containing a variety of Tn1546 types. Apparent Tn1546 heterogeneity among enterococci from human, animal, and environmental sources might reflect frequent genetic exchange events and evolution of particular widely disseminated genetic elements.}, }
@article {pmid18179685, year = {2008}, author = {Price, MN and Dehal, PS and Arkin, AP}, title = {Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli.}, journal = {Genome biology}, volume = {9}, number = {1}, pages = {R4}, pmid = {18179685}, issn = {1474-760X}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {*Biological Evolution ; Escherichia coli/*genetics ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Transcription Factors/genetics ; Transcription, Genetic ; }, abstract = {BACKGROUND: Most bacterial genes were acquired by horizontal gene transfer from other bacteria instead of being inherited by continuous vertical descent from an ancient ancestor. To understand how the regulation of these acquired genes evolved, we examined the evolutionary histories of transcription factors and of regulatory interactions from the model bacterium Escherichia coli K12.<br><br>RESULTS: Although most transcription factors have paralogs, these usually arose by horizontal gene transfer rather than by duplication within the E. coli lineage, as previously believed. In general, most neighbor regulators - regulators that are adjacent to genes that they regulate - were acquired by horizontal gene transfer, whereas most global regulators evolved vertically within the gamma-Proteobacteria. Neighbor regulators were often acquired together with the adjacent operon that they regulate, and so the proximity might be maintained by repeated transfers (like 'selfish operons'). Many of the as yet uncharacterized (putative) regulators have also been acquired together with adjacent genes, and so we predict that these are neighbor regulators as well. When we analyzed the histories of regulatory interactions, we found that the evolution of regulation by duplication was rare, and surprisingly, many of the regulatory interactions that are shared between paralogs result from convergent evolution. Another surprise was that horizontally transferred genes are more likely than other genes to be regulated by multiple regulators, and most of this complex regulation probably evolved after the transfer.<br><br>CONCLUSION: Our findings highlight the rapid evolution of niche-specific gene regulation in bacteria.}, }
@article {pmid18179432, year = {2008}, author = {Baldo, L and Ayoub, NA and Hayashi, CY and Russell, JA and Stahlhut, JK and Werren, JH}, title = {Insight into the routes of Wolbachia invasion: high levels of horizontal transfer in the spider genus Agelenopsis revealed by Wolbachia strain and mitochondrial DNA diversity.}, journal = {Molecular ecology}, volume = {17}, number = {2}, pages = {557-569}, doi = {10.1111/j.1365-294X.2007.03608.x}, pmid = {18179432}, issn = {0962-1083}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Gene Transfer, Horizontal/*genetics ; Genetic Variation ; Geography ; Haplotypes ; Host-Pathogen Interactions ; Phylogeny ; Spiders/classification/*genetics/microbiology ; United States ; Wolbachia/*genetics ; }, abstract = {The pandemic distribution of Wolbachia (alpha-proteobacteria) across arthropods is largely due to the ability of these maternally inherited endosymbionts to successfully shift hosts across species boundaries. Yet it remains unclear whether Wolbachia has preferential routes of transfer among species. Here, we examined populations of eight species of the North American funnel-web spider genus Agelenopsis to evaluate whether Wolbachia show evidence for host specificity and the relative contribution of horizontal vs. vertical transmission of strains within and among related host species. Wolbachia strains were characterized by multilocus sequence typing (MLST) and Wolbachia surface protein (WSP) sequences, and analysed in relation to host phylogeny, mitochondrial diversity and geographical range. Results indicate that at least three sets of divergent Wolbachia strains invaded the genus Agelenopsis. After each invasion, the Wolbachia strains preferentially shuffled across species of this host genus by horizontal transfer rather than cospeciation. Decoupling of Wolbachia and host mitochondrial haplotype (mitotypes) evolutionary histories within single species reveals an extensive contribution of horizontal transfer also in the rapid dispersal of Wolbachia among conspecific host populations. These findings provide some of the strongest evidence to support the association of related Wolbachia strains with related hosts by means of both vertical and horizontal strain transmission. Similar analyses across a broader range of invertebrate taxa are needed, using sensitive methods for strain typing such as MLST, to determine if this pattern of Wolbachia dispersal is peculiar to Agelenopsis (or spiders), or is in fact a general pattern in arthropods.}, }
@article {pmid18179387, year = {2008}, author = {Vojtek, I and Pirzada, ZA and Henriques-Normark, B and Mastny, M and Janapatla, RP and Charpentier, E}, title = {Lysogenic transfer of group A Streptococcus superantigen gene among Streptococci.}, journal = {The Journal of infectious diseases}, volume = {197}, number = {2}, pages = {225-234}, pmid = {18179387}, issn = {0022-1899}, support = {P 17238/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Alleles ; Antigens, Bacterial/*genetics/metabolism ; *Gene Transfer, Horizontal ; Humans ; *Lysogeny ; Recombinant Proteins/genetics/metabolism ; Streptococcus/classification/genetics/immunology/*virology ; Streptococcus Phages/*genetics/*physiology ; Streptococcus pyogenes/classification/genetics/immunology/*virology ; }, abstract = {A group A Streptococcus (GAS) isolate, serotype M12, recovered from a patient with streptococcal toxic shock syndrome was analyzed for superantigen-carrying prophages, revealing phi149, which encodes superantigen SSA. Sequence analysis of the att-L proximal region of phi149 showed that the phage had a mosaic nature. Remarkably, we successfully obtained lysogenic conversion of GAS clinical isolates of various M serotypes (M1, M3, M5, M12, M19, M28, and M94), as well as of group C Streptococcus equisimilis (GCSE) clinical isolates, via transfer of a recombinant phage phi149::Km(r). Phage phi149::Km(r) from selected lysogenized GAS and GCSE strains could be transferred back to M12 GAS strains. Our data indicate that horizontal transfer of lysogenic phages among GAS can occur across the M-type barrier; these data also provide further support for the hypothesis that toxigenic conversion can occur via lysogeny between species. Streptococci might employ this mechanism specifically to allow more efficient adaptation to changing host challenges, potentially leading to fitter and more virulent clones.}, }
@article {pmid18179219, year = {2008}, author = {Kurosawa, K and Ghiviriga, I and Sambandan, TG and Lessard, PA and Barbara, JE and Rha, C and Sinskey, AJ}, title = {Rhodostreptomycins, antibiotics biosynthesized following horizontal gene transfer from Streptomyces padanus to Rhodococcus fascians.}, journal = {Journal of the American Chemical Society}, volume = {130}, number = {4}, pages = {1126-1127}, doi = {10.1021/ja077821p}, pmid = {18179219}, issn = {1520-5126}, mesh = {Anti-Infective Agents/chemistry/*metabolism ; Biotechnology/methods ; Drug Design ; *Gene Transfer Techniques ; *Gene Transfer, Horizontal ; Magnetic Resonance Spectroscopy ; Mass Spectrometry/methods ; Models, Biological ; Models, Chemical ; Molecular Conformation ; Rhodococcus/*metabolism ; Streptomyces/*metabolism ; Streptomycin/*chemistry ; }, }
@article {pmid18178735, year = {2008}, author = {García-Quintanilla, M and Ramos-Morales, F and Casadesús, J}, title = {Conjugal transfer of the Salmonella enterica virulence plasmid in the mouse intestine.}, journal = {Journal of bacteriology}, volume = {190}, number = {6}, pages = {1922-1927}, pmid = {18178735}, issn = {1098-5530}, mesh = {Animals ; Conjugation, Genetic/*genetics ; Feces/microbiology ; Gene Transfer, Horizontal ; Ileum/microbiology ; Intestine, Large/microbiology ; Intestine, Small/microbiology ; Intestines/*microbiology ; Liver/microbiology ; Mice ; Mice, Inbred BALB C ; Plasmids/*genetics ; Salmonella Infections, Animal/microbiology ; Salmonella enterica/*genetics/pathogenicity ; Species Specificity ; Spleen/microbiology ; Virulence/genetics ; }, abstract = {BALB/c mice were infected with two Salmonella enterica serovar Typhimurium strains, one of which lacked the virulence plasmid. Transconjugants were found at high frequencies in the mouse feces and at low frequencies in the liver and the spleen, suggesting that mating occurred in the gut. Laboratory conditions that mimic those of the small intestine (microaerophilic growth in the presence of 0.3 M NaCl) increased the frequency of virulence plasmid transfer. Sodium deoxycholate, which is found at high concentrations in the duodenum, and sodium propionate, which is abundant in the large intestine, reduced the conjugation frequency. Feces inhibited conjugation. Altogether, these observations suggested that transfer of the virulence plasmid occurred in the distal portion of the small intestine. Conjugation trials in ileal loops provided direct evidence that conjugal transfer of the Salmonella virulence plasmid occurs in the ileum in mice.}, }
@article {pmid18177903, year = {2008}, author = {Cardona, G and Rosselló, F and Valiente, G}, title = {Tripartitions do not always discriminate phylogenetic networks.}, journal = {Mathematical biosciences}, volume = {211}, number = {2}, pages = {356-370}, doi = {10.1016/j.mbs.2007.11.003}, pmid = {18177903}, issn = {0025-5564}, mesh = {Evolution, Molecular ; *Models, Genetic ; *Phylogeny ; }, abstract = {Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In a recent series of papers devoted to the study of reconstructibility of phylogenetic networks, Moret, Nakhleh, Warnow and collaborators introduced the so-called tripartition metric for phylogenetic networks. In this paper we show that, in fact, this tripartition metric does not satisfy the separation axiom of distances (zero distance means isomorphism, or, in a more relaxed version, zero distance means indistinguishability in some specific sense) in any of the subclasses of phylogenetic networks where it is claimed to do so. We also present a subclass of phylogenetic networks whose members can be singled out by means of their sets of tripartitions (or even clusters), and hence where the latter can be used to define a meaningful metric.}, }
@article {pmid18177252, year = {2008}, author = {O'Hara, FP and Guex, N and Word, JM and Miller, LA and Becker, JA and Walsh, SL and Scangarella, NE and West, JM and Shawar, RM and Amrine-Madsen, H}, title = {A geographic variant of the Staphylococcus aureus Panton-Valentine leukocidin toxin and the origin of community-associated methicillin-resistant S. aureus USA300.}, journal = {The Journal of infectious diseases}, volume = {197}, number = {2}, pages = {187-194}, doi = {10.1086/524684}, pmid = {18177252}, issn = {0022-1899}, mesh = {Adult ; Amino Acid Substitution ; Bacterial Toxins/chemistry/*genetics ; Child ; Child, Preschool ; Community-Acquired Infections/*microbiology ; Evolution, Molecular ; Exotoxins/chemistry/*genetics ; Gene Transfer, Horizontal ; *Genetic Variation ; Humans ; Leukocidins/chemistry/*genetics ; Methicillin/pharmacology ; *Methicillin Resistance ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Staphylococcal Infections/microbiology ; Staphylococcus aureus/*classification/drug effects/genetics ; }, abstract = {BACKGROUND: The majority of recent community-associated methicillin-resistant Staphylococcus aureus (MRSA) infections in the United States have been caused by a single clone, USA300. USA300 secretes Panton-Valentine leukocidin (PVL) toxin, which is associated with highly virulent infections.<br><br>METHODS: We sequenced the PVL genes of 174 S. aureus isolates from a global clinical sample. We combined phylogenetic reconstruction and protein modeling methods to analyze genetic variation in PVL.<br><br>RESULTS: Nucleotide variation was detected at 12 of 1726 sites. Two PVL sequence variants, the R variant and the H variant, were identified on the basis of a substitution at nt 527. Of sequences obtained in the United States, 96.7% harbor the R variant, whereas 95.6% of sequences obtained outside the United States harbor the H variant; 91.3% of MRSA isolates harbor the R variant, and 91.3% of methicillin-susceptible strains harbor the H variant. A molecular model of PVL shows 3 mechanisms by which the amino acid substitution may affect PVL function.<br><br>CONCLUSIONS: All sampled PVL genes appear to share a recent common ancestor and spread via a combination of clonal expansion and horizontal transfer. US isolates harbor a variant of PVL that is strongly associated with MRSA infections. Protein modeling reveals that this variant may have functional significance. We propose a hypothesis for the origin of USA300.}, }
@article {pmid18176824, year = {2008}, author = {Zhang, Y and Zhang, H and Li, X and Su, Z and Zhang, C}, title = {The cadA gene in cadmium-resistant bacteria from cadmium-polluted soil in the Zhangshi area of Northeast China.}, journal = {Current microbiology}, volume = {56}, number = {3}, pages = {236-239}, pmid = {18176824}, issn = {0343-8651}, mesh = {Adenosine Triphosphatases/chemistry/*genetics/metabolism ; Bacillus/drug effects/enzymology/genetics/isolation &amp; purification ; Bacteria/drug effects/genetics/*isolation &amp; purification ; Cadmium/*pharmacology ; China ; Cloning, Molecular ; DNA, Bacterial/analysis/isolation &amp; purification ; *Drug Resistance, Bacterial ; Flavobacterium/drug effects/enzymology/genetics/isolation &amp; purification ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA ; *Soil Microbiology ; *Soil Pollutants ; }, abstract = {Cadmium-resistant bacteria were isolated from the farmland soil in Zhangshi Irrigation Area in Shenyang of Northeast China, an area has been polluted by heavy metals, especially cadmium, for more than 40 years. The cadA gene was detected in 4 Bacillus strains and for the first time in one Flavobacterium strain. The high sequence identity (93%-99%) of cadA gene, shared indels in different bacterial species and genera, and the phylogenetic incongruence between 16S rDNA gene tree and cadA gene tree suggested that lateral gene transfer (LGT) occurred among Bacillus and Flavobacterium spp. The LGT of cadA gene might play a vital role in promoting the spread of cadmium-resistant phenotypes throughout soil microbial communities.}, }
@article {pmid18174128, year = {2008}, author = {Santos, F and Vera, JL and van der Heijden, R and Valdez, G and de Vos, WM and Sesma, F and Hugenholtz, J}, title = {The complete coenzyme B12 biosynthesis gene cluster of Lactobacillus reuteri CRL1098.}, journal = {Microbiology (Reading, England)}, volume = {154}, number = {Pt 1}, pages = {81-93}, doi = {10.1099/mic.0.2007/011569-0}, pmid = {18174128}, issn = {1350-0872}, mesh = {Aldehydes/metabolism ; Biosynthetic Pathways/*genetics ; Cobamides/*biosynthesis/genetics ; DNA, Bacterial/chemistry/genetics ; Evolution, Molecular ; Feedback, Physiological ; Gene Expression Regulation, Bacterial ; Gene Order ; Glyceraldehyde/analogs &amp; derivatives/metabolism ; Limosilactobacillus reuteri/*genetics ; Listeria/genetics ; Molecular Sequence Data ; *Multigene Family ; Open Reading Frames ; Operon ; Phylogeny ; Propane/metabolism ; RNA Precursors/genetics ; RNA, Bacterial/genetics ; Salmonella/genetics ; Sequence Analysis, DNA ; Transcription, Genetic ; }, abstract = {The coenzyme B(12) production pathway in Lactobacillus reuteri has been deduced using a combination of genetic, biochemical and bioinformatics approaches. The coenzyme B(12) gene cluster of Lb. reuteri CRL1098 has the unique feature of clustering together the cbi, cob and hem genes. It consists of 29 ORFs encoding the complete enzymic machinery necessary for de novo biosynthesis. Transcriptional analysis showed it to be expressed as two tandem transcripts of approximately 22 and 4 kb, carrying cobD, cbiABCDETFGHJ, cobA/hemD, cbiKLMNQOP, sirA, hemACBL, and cobUSC, hemD, cobT, respectively. Both transcripts appear to be similarly regulated, and under the conditions assayed are induced in the late-exponential growth phase. Evidence for a regulatory mechanism of negative feedback inhibition by vitamin B(12) itself was observed. Comparative genomics analysis of the coding sequences showed them to be most similar to those coding for the anaerobic coenzyme B(12) pathways previously characterized in a few representatives of the genera Listeria and Salmonella. This contrasts with the trusted species phylogeny and suggests horizontal gene transfer of the B(12) biosynthesis genes. G+C content and codon adaptation index analysis is suggestive that the postulated transfer of these genes was not a recent event. Additional comparative genomics and transcriptional analysis of the sequences acquired during this study suggests a functional link between coenzyme B(12) biosynthesis and reuterin production, which might be implicated in Lb. reuteri's success in colonizing the gastrointestinal tract. This information on gene organization, gene transcription and gene acquisition is relevant for the development of (fermented) foods and probiotics enriched in B(12).}, }
@article {pmid18174124, year = {2008}, author = {Chen, DE and Podell, S and Sauer, JD and Swanson, MS and Saier, MH}, title = {The phagosomal nutrient transporter (Pht) family.}, journal = {Microbiology (Reading, England)}, volume = {154}, number = {Pt 1}, pages = {42-53}, doi = {10.1099/mic.0.2007/010611-0}, pmid = {18174124}, issn = {1350-0872}, support = {T32 GM145304/GM/NIGMS NIH HHS/United States ; GM077402/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Bacteria/*genetics ; Bacterial Proteins/chemistry/*genetics ; Carrier Proteins/chemistry/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Phagosomes/*microbiology ; Phylogeny ; Protein Structure, Secondary ; Sequence Homology, Amino Acid ; }, abstract = {Phagosomal transporters (Phts), required for intracellular growth of Legionella pneumophila, comprise a novel family of multispanning alpha-helical proteins within the major facilitator superfamily (MFS). The members of this family derive exclusively from bacteria. Multiple paralogues are present in a restricted group of Alpha- and Gammaproteobacteria, but single members were also found in Chlamydia and Cyanobacteria. Their protein sequences were aligned, yielding a phylogenetic tree showing the relations of the proteins to each other. Topological analyses revealed a probable 12 alpha-helical transmembrane segment (TMS) topology. Motif identification and statistical analyses provided convincing evidence that these proteins arose from a six TMS precursor by intragenic duplication. The phylogenetic tree revealed some potential orthologous relationships, suggestive of common function. However, several probable examples of lateral transfer of the encoding genetic material between bacteria were identified and analysed. The Pht family most closely resembles a smaller MFS family (the UMF9 family) with no functionally characterized members. However, the UMF9 family occurs in a broader range of prokaryotic organism types, including Archaea. These two families differ in that organisms bearing members of the Pht family often have numerous paralogues, whereas organisms bearing members of the UMF9 family never have more than two. This work serves to characterize two novel families within the MFS and provides compelling evidence for horizontal transfer of some of the family members.}, }
@article {pmid18174121, year = {2008}, author = {Zaneveld, JR and Nemergut, DR and Knight, R}, title = {Are all horizontal gene transfers created equal? Prospects for mechanism-based studies of HGT patterns.}, journal = {Microbiology (Reading, England)}, volume = {154}, number = {Pt 1}, pages = {1-15}, doi = {10.1099/mic.0.2007/011833-0}, pmid = {18174121}, issn = {1350-0872}, support = {T32 GM008759/GM/NIGMS NIH HHS/United States ; T32 GM142607/GM/NIGMS NIH HHS/United States ; T32 GM08759/GM/NIGMS NIH HHS/United States ; }, mesh = {Computational Biology/*methods ; Gene Transfer, Horizontal/*genetics ; Genomics/*methods ; *Interspersed Repetitive Sequences ; }, abstract = {Detecting patterns of horizontal gene transfer (HGT) in genomic sequences is an important problem, with implications for evolution, ecology, biotechnology and medicine. Extensive genetic, biochemical and genomic studies have provided a good understanding of sequence features that are associated with many (though not all) known mobile elements and mechanisms of gene transfer. This information, however, is not currently incorporated into automated methods for gene transfer detection in genomic data. In this review, we argue that automated annotation of sequence features associated with gene transfer mechanisms could be used both to build more sensitive, mechanism-specific compositional models for the detection of some types of HGT in genomic data, and to ask new questions about the classes of genes most frequently transferred by each mechanism. We then summarize the genes and sequence features associated with different mechanisms of horizontal transfer, emphasizing those that are most useful for distinguishing types of transfer when examining genomic data, and noting those classes of transfers that cannot be distinguished in genomic data using existing techniques. Finally, we describe software, databases and algorithms for identifying particular classes of mobile elements, and outline prospects for better detection of HGT based on specific mechanisms of transfer.}, }
@article {pmid18167190, year = {2007}, author = {Zhong, Q and Shao, SH and Cui, LL and Mu, RH and Ju, XL and Dong, SR}, title = {Type IV secretion system in Helicobacter pylori: a new insight into pathogenicity.}, journal = {Chinese medical journal}, volume = {120}, number = {23}, pages = {2138-2142}, pmid = {18167190}, issn = {0366-6999}, mesh = {Bacterial Proteins/metabolism ; DNA-Binding Proteins ; Gene Transfer, Horizontal ; Helicobacter pylori/genetics/*metabolism/*pathogenicity ; Multigene Family ; }, abstract = {OBJECTIVE: To review the research progress on Type IV secretion system (T4SS) in Helicobacter pylori.<br><br>DATA SOURCES: The data used in this review were identified by searching of PUBMED (1995 - 2007) online resources using the key terms 'Type IV secretion system' and 'Helicobacter pylori'.<br><br>STUDY SELECTION: Mainly original articles and critical reviews written by major pioneer investigators of this field were selected.<br><br>RESULTS: The research progress on T4SS in Helicobacter pylori was summarized. The structure and function was discussed.<br><br>CONCLUSIONS: T4SS is not only involved in toxin secretion and injection of virulence factors into eukaryotic host target cells, but also involved in horizontal DNA transfer to other bacteria and eukaryotic cells, through DNA uptake from or release into the extracellular milieu. It provides a new insight into the pathogenicity of Helicobacter pylori and a novel target for antimicrobials development. However, many challenges remain for us in understanding the biological role of T4SS in Helicobacter pylori.}, }
@article {pmid18165369, year = {2008}, author = {Rizzi, A and Pontiroli, A and Brusetti, L and Borin, S and Sorlini, C and Abruzzese, A and Sacchi, GA and Vogel, TM and Simonet, P and Bazzicalupo, M and Nielsen, KM and Monier, JM and Daffonchio, D}, title = {Strategy for in situ detection of natural transformation-based horizontal gene transfer events.}, journal = {Applied and environmental microbiology}, volume = {74}, number = {4}, pages = {1250-1254}, pmid = {18165369}, issn = {1098-5336}, mesh = {Acinetobacter/*genetics ; Gene Transfer, Horizontal/*genetics ; Genetic Techniques ; Green Fluorescent Proteins/metabolism ; Microscopy, Fluorescence ; Transformation, Bacterial/*genetics ; }, abstract = {A strategy is described that enables the in situ detection of natural transformation in Acinetobacter baylyi BD413 by the expression of a green fluorescent protein. Microscale detection of bacterial transformants growing on plant tissues was shown by fluorescence microscopy and indicated that cultivation-based selection of transformants on antibiotic-containing agar plates underestimates transformation frequencies.}, }
@article {pmid18165364, year = {2008}, author = {Chen, YY and Feng, CW and Chiu, CF and Burne, RA}, title = {cadDX operon of Streptococcus salivarius 57.I.}, journal = {Applied and environmental microbiology}, volume = {74}, number = {5}, pages = {1642-1645}, pmid = {18165364}, issn = {1098-5336}, mesh = {Bacterial Proteins/*genetics ; Base Composition ; Base Sequence ; Cadmium/*metabolism ; DNA Primers/genetics ; Drug Resistance, Bacterial/*genetics ; *Gene Expression Regulation, Bacterial ; Gene Library ; Molecular Sequence Data ; Operon/*genetics ; Plasmids/genetics ; Sequence Analysis, DNA ; Streptococcus/*genetics ; Zinc/*metabolism ; }, abstract = {A CadDX system that confers resistance to Cd(2+) and Zn(2+) was identified in Streptococcus salivarius 57.I. Unlike with other CadDX systems, the expression of the cad promoter was negatively regulated by CadX, and the repression was inducible by Cd(2+) and Zn(2+), similar to what was found for CadCA systems. The lower G+C content of the S. salivarius cadDX genes suggests acquisition by horizontal gene transfer.}, }
@article {pmid18159227, year = {2007}, author = {Goldman, B and Bhat, S and Shimkets, LJ}, title = {Genome evolution and the emergence of fruiting body development in Myxococcus xanthus.}, journal = {PloS one}, volume = {2}, number = {12}, pages = {e1329}, pmid = {18159227}, issn = {1932-6203}, mesh = {*Biological Evolution ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genes, Essential ; *Genome, Bacterial ; Myxococcus xanthus/genetics/*growth &amp; development/metabolism ; Oxygen/metabolism ; }, abstract = {BACKGROUND: Lateral gene transfer (LGT) is thought to promote speciation in bacteria, though well-defined examples have not been put forward.<br><br>We examined the evolutionary history of the genes essential for a trait that defines a phylogenetic order, namely fruiting body development of the Myxococcales. Seventy-eight genes that are essential for Myxococcus xanthus development were examined for LGT. About 73% of the genes exhibit a phylogeny similar to that of the 16S rDNA gene and a codon bias consistent with other M. xanthus genes suggesting vertical transmission. About 22% have an altered codon bias and/or phylogeny suggestive of LGT. The remaining 5% are unique. Genes encoding signal production and sensory transduction were more likely to be transmitted vertically with clear examples of duplication and divergence into multigene families. Genes encoding metabolic enzymes were frequently acquired by LGT. Myxobacteria exhibit aerobic respiration unlike most of the delta Proteobacteria. M. xanthus contains a unique electron transport pathway shaped by LGT of genes for succinate dehydrogenase and three cytochrome oxidase complexes.<br><br>CONCLUSIONS/SIGNIFICANCE: Fruiting body development depends on genes acquired by LGT, particularly those involved in polysaccharide production. We suggest that aerobic growth fostered innovation necessary for development by allowing myxobacteria access to a different gene pool from anaerobic members of the delta Proteobacteria. Habitat destruction and loss of species diversity could restrict the evolution of new bacterial groups by limiting the size of the prospective gene pool.}, }
@article {pmid18158323, year = {2008}, author = {Cusimano, N and Zhang, LB and Renner, SS}, title = {Reevaluation of the cox1 group I intron in Araceae and angiosperms indicates a history dominated by loss rather than horizontal transfer.}, journal = {Molecular biology and evolution}, volume = {25}, number = {2}, pages = {265-276}, doi = {10.1093/molbev/msm241}, pmid = {18158323}, issn = {1537-1719}, mesh = {Araceae/genetics ; Gene Transfer, Horizontal ; *Genes, Plant ; Introns ; Likelihood Functions ; Magnoliopsida/*genetics ; Molecular Sequence Data ; Phylogeny ; Rhizopus/genetics ; }, abstract = {The origin and modes of transmission of introns remain matters of much debate. Previous studies of the group I intron in the angiosperm cox1 gene inferred frequent angiosperm-to-angiosperm horizontal transmission of the intron from apparent incongruence between intron phylogenies and angiosperm phylogenies, patchy distribution of the intron among angiosperms, and differences between cox1 exonic coconversion tracts (the first 22 nt downstream of where the intron inserted). We analyzed the cox1 gene in 179 angiosperms, 110 of them containing the intron (intron(+)) and 69 lacking it (intron(-)). Our taxon sampling in Araceae is especially dense to test hypotheses about vertical and horizontal intron transmission put forward by Cho and Palmer (1999. Multiple acquisitions via horizontal transfer of a group I intron in the mitochondrial coxl gene during evolution of the Araceae family. Mol Biol Evol. 16:1155-1165). Maximum likelihood trees of Araceae cox1 introns, and also of all angiosperm cox1 introns, are largely congruent with known phylogenetic relationships in these taxa. The exceptions can be explained by low signal in the intron and long-branch attraction among a few taxa with high mitochondrial substitution rates. Analysis of the 179 coconversion tracts reveals 20 types of tracts (11 of them only found in single species, all involving silent substitutions). The distribution of these tracts on the angiosperm phylogeny shows a common ancestral type, characterizing most intron(+) and some intron(-) angiosperms, and several derivative tract types arising from gradual back mutation of the coconverted nucleotides. Molecular clock dating of small intron(+) and intron(-) sister clades suggests that coconversion tracts have persisted for 70 Myr in Araceae, whose cox1 sequences evolve comparatively slowly. Sequence similarity among the 110 introns ranges from 91% to identical, whereas putative homologs from fungi are highly different, but sampling in fungi is still sparse. Together, these results suggest that the cox1 intron entered angiosperms once, has largely or entirely been transmitted vertically, and has been lost numerous times, with coconversion tract footprints providing unreliable signal of former intron presence.}, }
@article {pmid18158322, year = {2008}, author = {Lercher, MJ and Pál, C}, title = {Integration of horizontally transferred genes into regulatory interaction networks takes many million years.}, journal = {Molecular biology and evolution}, volume = {25}, number = {3}, pages = {559-567}, doi = {10.1093/molbev/msm283}, pmid = {18158322}, issn = {1537-1719}, mesh = {Escherichia coli/*genetics ; Escherichia coli Proteins/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Phylogeny ; }, abstract = {Adaptation of bacteria to new or changing environments is often associated with the uptake of foreign genes through horizontal gene transfer. However, it has remained unclear how (and how fast) new genes are integrated into their host's cellular networks. Combining the regulatory and protein interaction networks of Escherichia coli with comparative genomics tools, we provide the first systematic analysis of this issue. Genes transferred recently have fewer interaction partners compared to nontransferred genes in both regulatory and protein interaction networks. Thus, horizontally transferred genes involved in complex regulatory and protein-protein interactions are rarely favored by selection. Only few protein-protein interactions are gained after the initial integration of genes following the transfer event. In contrast, transferred genes are gradually integrated into the regulatory network of their host over evolutionary time. During adaptation to the host cellular environment, horizontally transferred genes recruit existing transcription factors of the host, reflected in the fast evolutionary rates of the cis-regulatory regions of transferred genes. Further, genes resulting from increasingly ancient transfer events show increasing numbers of transcriptional regulators as well as improved coregulation with interacting proteins. Fine-tuned integration of horizontally transferred genes into the regulatory network spans more than 8-22 million years and encompasses accelerated evolution of regulatory regions, stabilization of protein-protein interactions, and changes in codon usage.}, }
@article {pmid18154671, year = {2007}, author = {Barkman, TJ and McNeal, JR and Lim, SH and Coat, G and Croom, HB and Young, ND and Depamphilis, CW}, title = {Mitochondrial DNA suggests at least 11 origins of parasitism in angiosperms and reveals genomic chimerism in parasitic plants.}, journal = {BMC evolutionary biology}, volume = {7}, number = {}, pages = {248}, pmid = {18154671}, issn = {1471-2148}, mesh = {Chimera/*genetics ; DNA, Mitochondrial/*genetics ; DNA, Plant/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Plant ; Magnoliopsida/*genetics ; Phylogeny ; Symbiosis ; }, abstract = {BACKGROUND: Some of the most difficult phylogenetic questions in evolutionary biology involve identification of the free-living relatives of parasitic organisms, particularly those of parasitic flowering plants. Consequently, the number of origins of parasitism and the phylogenetic distribution of the heterotrophic lifestyle among angiosperm lineages is unclear.<br><br>RESULTS: Here we report the results of a phylogenetic analysis of 102 species of seed plants designed to infer the position of all haustorial parasitic angiosperm lineages using three mitochondrial genes: atp1, coxI, and matR. Overall, the mtDNA phylogeny agrees with independent studies in terms of non-parasitic plant relationships and reveals at least 11 independent origins of parasitism in angiosperms, eight of which consist entirely of holoparasitic species that lack photosynthetic ability. From these results, it can be inferred that modern-day parasites have disproportionately evolved in certain lineages and that the endoparasitic habit has arisen by convergence in four clades. In addition, reduced taxon, single gene analyses revealed multiple horizontal transfers of atp1 from host to parasite lineage, suggesting that parasites may be important vectors of horizontal gene transfer in angiosperms. Furthermore, in Pilostyles we show evidence for a recent host-to-parasite atp1 transfer based on a chimeric gene sequence that indicates multiple historical xenologous gene acquisitions have occurred in this endoparasite. Finally, the phylogenetic relationships inferred for parasites indicate that the origins of parasitism in angiosperms are strongly correlated with horizontal acquisitions of the invasive coxI group I intron.<br><br>CONCLUSION: Collectively, these results indicate that the parasitic lifestyle has arisen repeatedly in angiosperm evolutionary history and results in increasing parasite genomic chimerism over time.}, }
@article {pmid18096018, year = {2008}, author = {Xu, Z and Shi, L and Alam, MJ and Li, L and Yamasaki, S}, title = {Integron-bearing methicillin-resistant coagulase-negative staphylococci in South China, 2001-2004.}, journal = {FEMS microbiology letters}, volume = {278}, number = {2}, pages = {223-230}, doi = {10.1111/j.1574-6968.2007.00994.x}, pmid = {18096018}, issn = {0378-1097}, mesh = {Bacterial Typing Techniques ; Blotting, Southern ; China ; Coagulase/metabolism ; Cross Infection/microbiology ; DNA Fingerprinting ; Drug Resistance, Bacterial/genetics ; Humans ; Integrons/*genetics ; Methicillin Resistance/*genetics ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Polymerase Chain Reaction ; Staphylococcal Infections/microbiology ; Staphylococcus/classification/drug effects/*genetics ; }, abstract = {A total of 53 methicillin-resistant coagulase-negative staphylococci strains isolated in a hospital in Guangzhou, China, were analyzed to detect class 1 integrons and SCCmec typing. Thirty strains had the class 1 integrase (intI1) gene and 26 strains possessed the 3' conserved region of qacEDelta1-sul1. Four different types of gene cassette arrays were found and a highly prevalent array of dfrA12-orfF-aadA2 gene cassettes was observed. Thirty class 1 integron-positive coagulase-negative staphylococci strains were subjected to Southern hybridization analysis; the result showed that class 1 integrons were located on chromosome, not plasmid. According to the results of SCCmec typing for 30 integron-bearing MRCNS strains, five, 15 and five strains belonged to type I, II and III SCCmec, respectively, and five strains were untypeable. For 23 non-integron-bearing methicillin-resistant coagulase-negative staphylococci strains, four, nine and seven strains belonged to type I, II and III SCCmec, respectively, and three strains were untypeable. None of the strains belonged to type IV or V. Twenty-three coagulase-negative staphylococci isolates of three Staphylococcal species that contained the dfrA12-orfF-aadA2 gene cassette array were phylogenetically unrelated to each other by randomly amplified polymorphic DNA, indicating that the gene cassettes might be disseminated in the clinical strains by a horizontal gene transfer.}, }
@article {pmid18088314, year = {2008}, author = {Roulin, A and Piegu, B and Wing, RA and Panaud, O}, title = {Evidence of multiple horizontal transfers of the long terminal repeat retrotransposon RIRE1 within the genus Oryza.}, journal = {The Plant journal : for cell and molecular biology}, volume = {53}, number = {6}, pages = {950-959}, doi = {10.1111/j.1365-313X.2007.03388.x}, pmid = {18088314}, issn = {1365-313X}, mesh = {Base Sequence ; Gene Expression Regulation, Plant/genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Plant/genetics ; Oryza/*genetics ; Phylogeny ; Plant Proteins/*genetics ; Retroelements/*genetics ; Terminal Repeat Sequences/*genetics ; }, abstract = {Horizontal gene transfer, defined as the transmission of genetic material between reproductively isolated species, has been considered for a long time to be a rare phenomenon. Most well-documented cases of horizontal gene transfer have been described in prokaryotes or in animals and they often involve transposable elements. The most abundant class of transposable elements in plant genomes are the long terminal repeat (LTR) retrotransposons. Because of their propensity to increase their copy number while active, LTR retrotransposons can have a significant impact on genomics changes during evolution. In a previous study, we showed that in the wild rice species Oryza australiensis, 60% of the genome is composed of only three families of LTR retrotransposons named RIRE1, Wallabi and Kangourou. In the present study, using both in silico and experimental approaches, we show that one of these three families, RIRE1, has been transferred horizontally between O. australiensis and seven other reproductively isolated Oryza species. This constitutes a new case of horizontal transfer in plants.}, }
@article {pmid18086210, year = {2008}, author = {Ubeda, C and Maiques, E and Barry, P and Matthews, A and Tormo, MA and Lasa, I and Novick, RP and Penadés, JR}, title = {SaPI mutations affecting replication and transfer and enabling autonomous replication in the absence of helper phage.}, journal = {Molecular microbiology}, volume = {67}, number = {3}, pages = {493-503}, doi = {10.1111/j.1365-2958.2007.06027.x}, pmid = {18086210}, issn = {0950-382X}, support = {R01 AI22159/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteriophages/genetics ; DNA Packaging ; *DNA Replication ; Gene Deletion ; *Gene Transfer, Horizontal ; *Genomic Islands ; Helper Viruses/genetics ; *Mutation ; Open Reading Frames ; Recombination, Genetic ; Repressor Proteins/genetics ; Staphylococcus/*genetics ; Viral Proteins/genetics ; Virus Activation ; }, abstract = {The SaPIs are chromosomal islands in staphylococci and other Gram-positive bacteria that carry genes for superantigens, virulence factors, resistance and certain metabolic functions. They have intimate relationships with certain temperate phages involving phage-induced excision, replication and efficient packaging in special small-headed infective phage-like particles, resulting in very high transfer frequencies. They generally contain 18-22 ORFs. We have systematically inactivated each of these ORFs and determined their functional groupings. In other reports, we have shown that five are involved in excision/integration, replication and packaging. In this report, we summarize the mutational analysis and focus on two key ORFs involved in regulation of the SaPI excision-replication-packaging cycle vis-à-vis phage induction. These two genes are divergently transcribed and define the major transcriptional organization of the SaPI genome. One of them, stl, encodes a master repressor, possibly analogous to the standard cI phage repressor. Mutational inactivation of this gene results in SaPI excision and replication in the absence of any inducing phage. This replicated SaPI DNA is not packaged; however, since the capsid components are provided by the helper phage. We have not yet ascertained any specific function for the second putative regulatory gene, though it is highly conserved among the SaPIs.}, }
@article {pmid18083872, year = {2008}, author = {Cardazzo, B and Negrisolo, E and Carraro, L and Alberghini, L and Patarnello, T and Giaccone, V}, title = {Multiple-locus sequence typing and analysis of toxin genes in Bacillus cereus food-borne isolates.}, journal = {Applied and environmental microbiology}, volume = {74}, number = {3}, pages = {850-860}, pmid = {18083872}, issn = {1098-5336}, mesh = {Algorithms ; Alleles ; Animals ; Bacillus cereus/classification/genetics/isolation &amp; purification/*pathogenicity ; Bacterial Proteins/*genetics ; Bacterial Toxins/*classification/*genetics ; *Bacterial Typing Techniques ; Dairy Products/microbiology ; Evolution, Molecular ; Fishes/microbiology ; *Food Microbiology ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; *Sequence Analysis, DNA ; }, abstract = {In the present study we characterized 47 food-borne isolates of Bacillus cereus using multilocus sequence typing (MLST). Newly determined sequences were combined with sequences available in public data banks in order to produce the largest data set possible. Phylogenetic analysis was performed on a total of 296 strains for which MLST sequence information is available, and three main lineages--I, II, and III--within the B. cereus complex were identified. With few exceptions, all food-borne isolates were in group I. The occurrence of horizontal gene transfer (HGT) among various strains was analyzed by several statistical methods, providing evidence of widespread lateral gene transfer within B. cereus. We also investigated the occurrence of toxin-encoding genes, focusing on their evolutionary history within B. cereus. Several patterns were identified, indicating a pivotal role of HGT in the evolution of toxin-encoding genes. Our results indicate that HGT is an important element in shaping the population structure of the B. cereus complex. The results presented here also provide strong evidence of reticulate evolution within the B. cereus complex.}, }
@article {pmid18083799, year = {2008}, author = {DeMars, R and Weinfurter, J}, title = {Interstrain gene transfer in Chlamydia trachomatis in vitro: mechanism and significance.}, journal = {Journal of bacteriology}, volume = {190}, number = {5}, pages = {1605-1614}, pmid = {18083799}, issn = {1098-5530}, support = {R01 A1 1056124//PHS HHS/United States ; R21 A1 05872801//PHS HHS/United States ; }, mesh = {Chlamydia trachomatis/drug effects/*genetics ; Drug Resistance, Bacterial/genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Models, Genetic ; Molecular Sequence Data ; Ofloxacin/pharmacology ; Polymorphism, Genetic ; Rifampin/pharmacology ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {The high frequency of between-strain genetic recombinants of Chlamydia trachomatis among isolates obtained from human sexually transmitted infections suggests that lateral gene transfer (LGT) is an important means by which C. trachomatis generates variants that have enhanced relative fitness. A mechanism for LGT in C. trachomatis has not been described, and investigation of this phenomenon by experimentation has been hampered by the obligate intracellular development of this pathogen. We describe here experiments that readily detected LGT between strains of C. trachomatis in vitro. Host cells were simultaneously infected with an ofloxacin-resistant (Ofx(r)) mutant of a serovar L1 strain (L1:Ofx(r)-1) and a rifampin-resistant (Rif(r)) mutant of a serovar D strain (D:Rif(r)-1). Development occurred in the absence of antibiotics, and the progeny were subjected to selection for Ofx(r) Rif(r) recombinants. The parental strains differed at many polymorphic nucleotide sites, and DNA sequencing was used to map genetic crossovers and to determine the parental sources of DNA segments in 14 recombinants. Depending on the assumed DNA donor, the estimated minimal length of the transferred DNA was > or = 123 kb in one recombinant but was > or = 336 to > or = 790 kb in all other recombinants. Such trans-DNA lengths have been associated only with conjugation in known microbial LGT systems, but natural DNA transformation remains a conceivable mechanism. LGT studies can now be performed with diverse combinations of C. trachomatis strains, and they could have evolutionary interest and yield useful recombinants for functional analysis of allelic differences between strains.}, }
@article {pmid18083328, year = {2008}, author = {Yu, F and Li, Y and Liu, L and Li, Y}, title = {Comparative genomics of human-like Schistosoma japonicum genes indicates a putative mechanism for host-parasite relationship.}, journal = {Genomics}, volume = {91}, number = {2}, pages = {152-157}, doi = {10.1016/j.ygeno.2007.10.006}, pmid = {18083328}, issn = {1089-8646}, mesh = {Animals ; Expressed Sequence Tags ; *Gene Transfer, Horizontal ; Genes, Helminth ; Genomics/*methods ; Host-Parasite Interactions/*genetics ; Humans ; Phylogeny ; Schistosoma japonicum/*genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {Schistosoma japonicum causes schistosomiasis in humans and livestock in the Asia-Pacific region. We assembled more than 43,700 S. japonicum expressed sequence tags and conducted comparative genomic analyses between S. japonicum and its human host. Some schistosome genes showed exceptionally high similarity in nucleotide sequence to their human homologues, of which five exhibited anomalous phylogeny and human codon usage bias. The most plausible explanation for their presence is horizontal gene transfer from host to parasite. Functional evidence suggests that S. japonicum might exploit host endocrine and immune signals for cell development and maturation via these host-like genes.}, }
@article {pmid18079388, year = {2007}, author = {Thauer, RK}, title = {Microbiology. A fifth pathway of carbon fixation.}, journal = {Science (New York, N.Y.)}, volume = {318}, number = {5857}, pages = {1732-1733}, doi = {10.1126/science.1152209}, pmid = {18079388}, issn = {1095-9203}, mesh = {Anaerobiosis ; Archaea/genetics/metabolism ; *Autotrophic Processes ; Bacteria/genetics/metabolism ; Carbon Dioxide/*metabolism ; Gene Transfer, Horizontal ; Genes, Archaeal ; Hydrogen/metabolism ; Oxygen/metabolism ; Photosynthesis ; Sulfolobaceae/*metabolism ; }, }
@article {pmid18078471, year = {2008}, author = {McCann, HC and Guttman, DS}, title = {Evolution of the type III secretion system and its effectors in plant-microbe interactions.}, journal = {The New phytologist}, volume = {177}, number = {1}, pages = {33-47}, doi = {10.1111/j.1469-8137.2007.02293.x}, pmid = {18078471}, issn = {0028-646X}, mesh = {Bacterial Proteins/*metabolism ; *Biological Evolution ; Plant Diseases/*microbiology ; Plants/*microbiology ; }, abstract = {Many bacterial plant pathogens require the type III secretion system (T3SS) and its effector proteins (T3SEs) to invade and extract nutrients from their hosts successfully. While the molecular function of this system is being studied intensively, we know comparatively little about the evolutionary and ecological pressures governing its fate over time, and even less about the detailed mechanisms underlying and driving complex T3SS-mediated coevolutionary dynamics. In this review we summarize our current understanding of how host-pathogen interactions evolve, with a particular focus on the T3SS of bacterial plant pathogens. We explore the evolutionary origins of the T3SS relative to the closely related flagellar system, and investigate the evolutionary pressures on this secretion and translocation apparatus. We examine the evolutionary forces acting on T3SEs, and compare the support for vertical descent with modification of these virulence-associated systems (pathoadaptation) vs horizontal gene transfer. We address the evolutionary origins of T3SEs from the perspective of both the evolutionary mechanisms that generate new effectors, and the mobile elements that may be the source of novel genetic material. Finally, we propose a number of questions raised by these studies, which may serve to guide our thinking about these complex processes.}, }
@article {pmid18073433, year = {2007}, author = {Hall, C and Dietrich, FS}, title = {The reacquisition of biotin prototrophy in Saccharomyces cerevisiae involved horizontal gene transfer, gene duplication and gene clustering.}, journal = {Genetics}, volume = {177}, number = {4}, pages = {2293-2307}, pmid = {18073433}, issn = {0016-6731}, mesh = {Biotin/*biosynthesis ; *Gene Duplication ; *Gene Transfer, Horizontal ; Metabolic Networks and Pathways/genetics ; Molecular Sequence Data ; *Multigene Family ; Saccharomyces cerevisiae ; Saccharomyces cerevisiae Proteins/*genetics ; }, abstract = {The synthesis of biotin, a vitamin required for many carboxylation reactions, is a variable trait in Saccharomyces cerevisiae. Many S. cerevisiae strains, including common laboratory strains, contain only a partial biotin synthesis pathway. We here report the identification of the first step necessary for the biotin synthesis pathway in S. cerevisiae. The biotin auxotroph strain S288c was able to grow on media lacking biotin when BIO1 and the known biotin synthesis gene BIO6 were introduced together on a plasmid vector. BIO1 is a paralog of YJR154W, a gene of unknown function and adjacent to BIO6. The nature of BIO1 illuminates the remarkable evolutionary history of the biotin biosynthesis pathway in S. cerevisiae. This pathway appears to have been lost in an ancestor of S. cerevisiae and subsequently rebuilt by a combination of horizontal gene transfer and gene duplication followed by neofunctionalization. Unusually, for S. cerevisiae, most of the genes required for biotin synthesis in S. cerevisiae are grouped in two subtelomeric gene clusters. The BIO1-BIO6 functional cluster is an example of a cluster of genes of "dispensable function," one of the few categories of genes in S. cerevisiae that are positionally clustered.}, }
@article {pmid18073380, year = {2008}, author = {Nikoh, N and Tanaka, K and Shibata, F and Kondo, N and Hizume, M and Shimada, M and Fukatsu, T}, title = {Wolbachia genome integrated in an insect chromosome: evolution and fate of laterally transferred endosymbiont genes.}, journal = {Genome research}, volume = {18}, number = {2}, pages = {272-280}, pmid = {18073380}, issn = {1088-9051}, mesh = {Animals ; Base Sequence ; Blotting, Southern ; Chromosome Mapping ; Chromosomes/*genetics ; Coleoptera/genetics/*microbiology ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome/*genetics ; In Situ Hybridization, Fluorescence ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Pseudogenes/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; *Symbiosis ; Wolbachia/*genetics ; }, abstract = {Recent accumulation of microbial genome data has demonstrated that lateral gene transfers constitute an important and universal evolutionary process in prokaryotes, while those in multicellular eukaryotes are still regarded as unusual, except for endosymbiotic gene transfers from mitochondria and plastids. Here we thoroughly investigated the bacterial genes derived from a Wolbachia endosymbiont on the nuclear genome of the beetle Callosobruchus chinensis. Exhaustive PCR detection and Southern blot analysis suggested that approximately 30% of Wolbachia genes, in terms of the gene repertoire of wMel, are present on the insect nuclear genome. Fluorescent in situ hybridization located the transferred genes on the proximal region of the basal short arm of the X chromosome. Molecular evolutionary and other lines of evidence indicated that the transferred genes are probably derived from a single lateral transfer event. The transferred genes were, for the length examined, structurally disrupted, freed from functional constraints, and transcriptionally inactive. Hence, most, if not all, of the transferred genes have been pseudogenized. Notwithstanding this, the transferred genes were ubiquitously detected from Japanese and Taiwanese populations of C. chinensis, while the number of the transferred genes detected differed between the populations. The transferred genes were not detected from congenic beetle species, indicating that the transfer event occurred after speciation of C. chinensis, which was estimated to be one or several million years ago. These features of the laterally transferred endosymbiont genes are compared with the evolutionary patterns of mitochondrial and plastid genome fragments acquired by nuclear genomes through recent endosymbiotic gene transfers.}, }
@article {pmid18070355, year = {2007}, author = {Monier, A and Claverie, JM and Ogata, H}, title = {Horizontal gene transfer and nucleotide compositional anomaly in large DNA viruses.}, journal = {BMC genomics}, volume = {8}, number = {}, pages = {456}, pmid = {18070355}, issn = {1471-2164}, mesh = {*Base Composition ; Bayes Theorem ; DNA Viruses/classification/*genetics ; Databases, Nucleic Acid ; *Gene Transfer, Horizontal ; Genes, Viral ; Genome, Viral ; Phylogeny ; }, abstract = {BACKGROUND: DNA viruses have a wide range of genome sizes (5 kb up to 1.2 Mb, compared to 0.16 Mb to 1.5 Mb for obligate parasitic bacteria) that do not correlate with their virulence or the taxonomic distribution of their hosts. The reasons for such large variation are unclear. According to the traditional view of viruses as gifted "gene pickpockets", large viral genome sizes could originate from numerous gene acquisitions from their hosts. We investigated this hypothesis by studying 67 large DNA viruses with genome sizes larger than 150 kb, including the recently characterized giant mimivirus. Given that horizontally transferred DNA often have anomalous nucleotide compositions differing from the rest of the genome, we conducted a detailed analysis of the inter- and intra-genome compositional properties of these viruses. We then interpreted their compositional heterogeneity in terms of possible causes, including strand asymmetry, gene function/expression, and horizontal transfer.<br><br>RESULTS: We first show that the global nucleotide composition and nucleotide word usage of viral genomes are species-specific and distinct from those of their hosts. Next, we identified compositionally anomalous (cA) genes in viral genomes, using a method based on Bayesian inference. The proportion of cA genes is highly variable across viruses and does not exhibit a significant correlation with genome size. The vast majority of the cA genes were of unknown function, lacking homologs in the databases. For genes with known homologs, we found a substantial enrichment of cA genes in specific functional classes for some of the viruses. No significant association was found between cA genes and compositional strand asymmetry. A possible exogenous origin for a small fraction of the cA genes could be confirmed by phylogenetic reconstruction.<br><br>CONCLUSION: At odds with the traditional dogma, our results argue against frequent genetic transfers to large DNA viruses from their modern hosts. The large genome sizes of these viruses are not simply explained by an increased propensity to acquire foreign genes. This study also confirms that the anomalous nucleotide compositions of the cA genes is sometimes linked to particular biological functions or expression patterns, possibly leading to an overestimation of recent horizontal gene transfers.}, }
@article {pmid18069966, year = {2008}, author = {Urbonavicius, J and Auxilien, S and Walbott, H and Trachana, K and Golinelli-Pimpaneau, B and Brochier-Armanet, C and Grosjean, H}, title = {Acquisition of a bacterial RumA-type tRNA(uracil-54, C5)-methyltransferase by Archaea through an ancient horizontal gene transfer.}, journal = {Molecular microbiology}, volume = {67}, number = {2}, pages = {323-335}, doi = {10.1111/j.1365-2958.2007.06047.x}, pmid = {18069966}, issn = {0950-382X}, mesh = {Archaea/classification/*enzymology/*genetics ; Bacteria/genetics ; Bacterial Proteins/*genetics ; Base Sequence ; Computational Biology ; Conserved Sequence ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Archaeal ; Iron/metabolism ; Magnesium/metabolism ; Methylation ; Molecular Sequence Data ; Nanoarchaeota/genetics ; Phylogeny ; Pyrococcus abyssi/genetics ; RNA, Transfer/metabolism ; Recombinant Fusion Proteins/isolation &amp; purification/metabolism ; Sulfur/metabolism ; Thermococcales/genetics ; Uracil/metabolism ; Uridine/metabolism ; tRNA Methyltransferases/*genetics/metabolism ; }, abstract = {The Pyrococcus abyssi genome displays two genes possibly coding for S-adenosyl-l-methionine-dependent RNA(uracil, C5)-methyltransferases (PAB0719 and PAB0760). Their amino acid sequences are more closely related to Escherichia coli RumA catalysing the formation of 5-methyluridine (m(5)U)-1939 in 23S rRNA than to E. coli TrmA (tRNA methyltransferase A) methylating uridine-54 in tRNA. Comparative genomic and phylogenetic analyses show that homologues of PAB0719 and PAB0760 occur only in a few Archaea, these genes having been acquired via a single horizontal gene transfer from a bacterial donor to the common ancestor of Thermococcales and Nanoarchaea. This transfer event was followed by a duplication event in Thermococcales leading to two closely related genes. None of the gene products of the two P. abyssi paralogues catalyses in vitro the formation of m(5)U in a P. abyssi rRNA fragment homologous to the bacterial RumA substrate. Instead, PAB0719 enzyme (renamed (Pab)TrmU54) displays an identical specificity to TrmA, as it catalyses the in vitro formation of m(5)U-54 in tRNA. Thus, during evolution, at least one of the two P. abyssi RumA-type enzymes has changed of target specificity. This functional shift probably occurred in an ancestor of all Thermococcales. This study also provides new evidence in favour of a close relationship between Thermococcales and Nanoarchaea.}, }
@article {pmid18065487, year = {2008}, author = {Nystedt, B and Frank, AC and Thollesson, M and Andersson, SG}, title = {Diversifying selection and concerted evolution of a type IV secretion system in Bartonella.}, journal = {Molecular biology and evolution}, volume = {25}, number = {2}, pages = {287-300}, doi = {10.1093/molbev/msm252}, pmid = {18065487}, issn = {1537-1719}, mesh = {Bacterial Proteins/*genetics ; Bartonella/*genetics ; Base Sequence ; *Directed Molecular Evolution ; Molecular Sequence Data ; *Phylogeny ; *Selection, Genetic ; }, abstract = {We have studied the evolution of a type IV secretion system (T4SS), in Bartonella, which is thought to have changed function from conjugation to erythrocyte adherence following a recent horizontal gene transfer event. The system, called Trw, is unique among T4SSs in that genes encoding both exo- and intracellular components are located within the same duplicated fragment. This provides an opportunity to study the influence of selection on proteins involved in host-pathogen interactions. We sequenced the trw locus from several strains of Bartonella henselae and investigated its evolutionary history by comparisons to other Bartonella species. Several instances of recombination and gene conversion events where detected in the 2- to 5-fold duplicated gene fragments encompassing trwJIH, explaining the homogenization of the anchoring protein TrwI and the divergence of the minor pilus protein TrwJ. A phylogenetic analysis of the 7- to 8-fold duplicated gene coding for the major pilus protein TrwL displayed 2 distinct clades, likely representing a subfunctionalization event. The analyses of the B. henselae strains also identified a recent horizontal transfer event of almost the complete trwL region. We suggest that the switch in function of the T4SS was mediated by the duplication of the genes encoding pilus components and their diversification by combinatorial sequence shuffling within and among genomes. We suggest that the pilus proteins have evolved by diversifying selection to match a divergent set of erythrocyte surface structures, consistent with the trench warfare coevolutionary model.}, }
@article {pmid18063151, year = {2008}, author = {Ouoba, LI and Lei, V and Jensen, LB}, title = {Resistance of potential probiotic lactic acid bacteria and bifidobacteria of African and European origin to antimicrobials: determination and transferability of the resistance genes to other bacteria.}, journal = {International journal of food microbiology}, volume = {121}, number = {2}, pages = {217-224}, doi = {10.1016/j.ijfoodmicro.2007.11.018}, pmid = {18063151}, issn = {0168-1605}, mesh = {Africa ; Anti-Bacterial Agents/*pharmacology ; Bifidobacterium/*drug effects/genetics ; Colony Count, Microbial ; Drug Resistance, Bacterial/*genetics ; Europe ; Food Microbiology ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Lactobacillus/*drug effects/genetics ; Macrolides/pharmacology ; Microbial Sensitivity Tests ; Probiotics ; Tetracycline Resistance/genetics ; }, abstract = {Probiotic bacteria and starter cultures of Lactobacillus, Weissella and Bifidobacterium of African and European origins were studied and compared for their susceptibility to antimicrobials. The study included, for all isolates, determination of MICs (Minimal Inhibitory Concentration) for 24 antimicrobials, detection of resistance genes by PCR reactions using specific primers and sequencing of positive amplicons. The ability of Lb. reuteri from Africa to transfer the erythromycin resistance gene erm(B) to closely related bacteria was investigated by conjugation. Variations were observed and high levels of intrinsic resistance were found among the tested species. Positive amplicons were obtained for resistance genes encoding aminoglycoside (aph(3')-III, aadA, aadE) and tetracycline (tet(S)) from isolates from Europe and macrolide (erm(B)) from an isolate from Africa. However, only the erm(B) gene found in Lb. reuteri L4: 12002 from Africa contained a homologous sequence to previously published sequences. This gene could be transferred in vitro to enterococci. Higher prevalence of phenotypic resistance for aminoglycoside was found in isolates from Europe.}, }
@article {pmid18062816, year = {2007}, author = {Glazko, G and Makarenkov, V and Liu, J and Mushegian, A}, title = {Evolutionary history of bacteriophages with double-stranded DNA genomes.}, journal = {Biology direct}, volume = {2}, number = {}, pages = {36}, pmid = {18062816}, issn = {1745-6150}, mesh = {Bacteriophages/classification/*genetics ; DNA/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome ; Genome, Viral/*genetics ; Genomics/classification ; Models, Genetic ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Reconstruction of evolutionary history of bacteriophages is a difficult problem because of fast sequence drift and lack of omnipresent genes in phage genomes. Moreover, losses and recombinational exchanges of genes are so pervasive in phages that the plausibility of phylogenetic inference in phage kingdom has been questioned.<br><br>RESULTS: We compiled the profiles of presence and absence of 803 orthologous genes in 158 completely sequenced phages with double-stranded DNA genomes and used these gene content vectors to infer the evolutionary history of phages. There were 18 well-supported clades, mostly corresponding to accepted genera, but in some cases appearing to define new taxonomic groups. Conflicts between this phylogeny and trees constructed from sequence alignments of phage proteins were exploited to infer 294 specific acts of intergenome gene transfer.<br><br>CONCLUSION: A notoriously reticulate evolutionary history of fast-evolving phages can be reconstructed in considerable detail by quantitative comparative genomics.}, }
@article {pmid18059494, year = {2007}, author = {Bhaya, D and Grossman, AR and Steunou, AS and Khuri, N and Cohan, FM and Hamamura, N and Melendrez, MC and Bateson, MM and Ward, DM and Heidelberg, JF}, title = {Population level functional diversity in a microbial community revealed by comparative genomic and metagenomic analyses.}, journal = {The ISME journal}, volume = {1}, number = {8}, pages = {703-713}, doi = {10.1038/ismej.2007.46}, pmid = {18059494}, issn = {1751-7362}, mesh = {Bacterial Proteins/genetics/metabolism ; *Biodiversity ; Cyanobacteria/classification/*genetics/growth &amp; development ; Genetic Variation/genetics ; *Genome, Bacterial ; Genomics/*methods ; Iron/metabolism ; Models, Genetic ; Species Specificity ; Synechococcus/genetics/growth &amp; development ; }, abstract = {In microbial mat communities of Yellowstone hot springs, ribosomal RNA (rRNA) sequence diversity patterns indicate the presence of closely related bacterial populations along environmental gradients of temperature and light. To identify the functional bases for adaptation, we sequenced the genomes of two cyanobacterial (Synechococcus OS-A and OS-B') isolates representing ecologically distinct populations that dominate at different temperatures and are major primary producers in the mat. There was a marked lack of conserved large-scale gene order between the two Synechococcus genomes, indicative of extensive genomic rearrangements. Comparative genomic analyses showed that the isolates shared a large fraction of their gene content at high identity, yet, differences in phosphate and nitrogen utilization pathways indicated that they have adapted differentially to nutrient fluxes, possibly by the acquisition of genes by lateral gene transfer or their loss in certain populations. Comparisons of the Synechococcus genomes to metagenomic sequences derived from mats where these Synechococcus stains were originally isolated, revealed new facets of microbial diversity. First, Synechococcus populations at the lower temperature regions of the mat showed greater sequence diversity than those at high temperatures, consistent with a greater number of ecologically distinct populations at the lower temperature. Second, we found evidence of a specialized population that is apparently very closely related to Synechococcus OS-B', but contains genes that function in the uptake of reduced ferrous iron. In situ expression studies demonstrated that these genes are differentially expressed over the diel cycle, with highest expression when the mats are anoxic and iron may be in the reduced state. Genomic information from these mat-specific isolates and metagenomic information can be coupled to detect naturally occurring populations that are associated with different functionalities, not always represented by isolates, but which may nevertheless be important for niche partitioning and the establishment of microbial community structure.}, }
@article {pmid18055595, year = {2008}, author = {Fournier, GP and Gogarten, JP}, title = {Evolution of acetoclastic methanogenesis in Methanosarcina via horizontal gene transfer from cellulolytic Clostridia.}, journal = {Journal of bacteriology}, volume = {190}, number = {3}, pages = {1124-1127}, pmid = {18055595}, issn = {1098-5530}, mesh = {Acetate Kinase/*genetics ; Acetic Acid/*metabolism ; Cellulose/metabolism ; Clostridium cellulolyticum/enzymology/*genetics ; Clostridium thermocellum/enzymology/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Methane/*metabolism ; Methanosarcina/*genetics/metabolism ; Phosphate Acetyltransferase/*genetics ; Phylogeny ; }, abstract = {Phylogenetic analysis confirmed that two genes required for acetoclastic methanogenesis, ackA and pta, were horizontally transferred to the ancestor of Methanosarcina from a derived cellulolytic organism in the class Clostridia. This event likely occurred within the last 475 million years, causing profound changes in planetary methane biogeochemistry.}, }
@article {pmid18055592, year = {2008}, author = {Hammerl, JA and Klein, I and Lanka, E and Appel, B and Hertwig, S}, title = {Genetic and functional properties of the self-transmissible Yersinia enterocolitica plasmid pYE854, which mobilizes the virulence plasmid pYV.}, journal = {Journal of bacteriology}, volume = {190}, number = {3}, pages = {991-1010}, pmid = {18055592}, issn = {1098-5530}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Bacterial Proteins/genetics/*metabolism ; Base Sequence ; *Conjugation, Genetic ; *Gene Transfer, Horizontal ; Humans ; Molecular Sequence Data ; Mutation ; Plasmids/*genetics ; Replication Origin/genetics ; Sequence Analysis, DNA ; Virulence ; Yersinia enterocolitica/genetics/metabolism/*pathogenicity ; }, abstract = {Yersinia strains frequently harbor plasmids, of which the virulence plasmid pYV, indigenous in pathogenic strains, has been thoroughly characterized during the last decades. Yet, it has been unknown whether the nonconjugative pYV can be transferred by helper plasmids naturally occurring in this genus. We have isolated the conjugative plasmids pYE854 (95.5 kb) and pYE966 (70 kb) from a nonpathogenic and a pathogenic Yersinia enterocolitica strain, respectively, and demonstrate that both plasmids are able to mobilize pYV. The complete sequence of pYE854 has been determined. The transfer proteins and oriT of the plasmid reveal similarities to the F factor. However, the pYE854 replicon does not belong to the IncF group and is more closely related to a plasmid of gram-positive bacteria. Plasmid pYE966 is very similar to pYE854 but lacks two DNA regions of the larger plasmid that are dispensable for conjugation.}, }
@article {pmid18053938, year = {2007}, author = {Cleland, CE}, title = {Epistemological issues in the study of microbial life: alternative terran biospheres?.}, journal = {Studies in history and philosophy of biological and biomedical sciences}, volume = {38}, number = {4}, pages = {847-861}, doi = {10.1016/j.shpsc.2007.09.007}, pmid = {18053938}, issn = {1369-8486}, mesh = {*Earth, Planet ; Evolution, Molecular ; *Exobiology ; Gene Transfer, Horizontal ; *Genetics, Microbial ; Humans ; *Knowledge ; *Life ; Meteoroids ; *Molecular Biology ; Nucleic Acids ; *Origin of Life ; Planets ; Polymerase Chain Reaction ; }, abstract = {The assumption that all life on Earth today shares the same basic molecular architecture and biochemistry is part of the paradigm of modern biology. This paper argues that there is little theoretical or empirical support for this widely held assumption. Scientists know that life could have been at least modestly different at the molecular level and it is clear that alternative molecular building blocks for life were available on the early Earth. If the emergence of life is, like other natural phenomena, highly probable given the right chemical and physical conditions then it seems likely that the early Earth hosted multiple origins of life, some of which produced chemical variations on life as we know it. While these points are often conceded, it is nevertheless maintained that any primitive alternatives to familiar life would have been eliminated long ago, either amalgamated into a single form of life through lateral gene transfer (LGT) or alternatively out-competed by our putatively more evolutionarily robust form of life. Besides, the argument continues, if such life forms still existed, we surely would have encountered telling signs of them by now. These arguments do not hold up well under close scrutiny. They reflect a host of assumptions that are grounded in our experience with large multicellular organisms and, most importantly, do not apply to microbial forms of life, which cannot be easily studied without the aid of sophisticated technologies. Significantly, the most powerful molecular biology techniques available-polymerase chain reaction (PCR) amplification of rRNA genes augmented by metagenomic analysis-could not detect such microbes if they existed. Given the profound philosophical and scientific importance that such a discovery would represent, a dedicated search for 'shadow microbes' (heretofore unrecognized 'alien' forms of terran microbial life) seems in order. The best place to start such a search is with puzzling (anomalous) phenomena, such as desert varnish, that resist classification as 'biological' or 'nonbiological'.}, }
@article {pmid18053934, year = {2007}, author = {Müller-Wille, S}, title = {Hybrids, pure cultures, and pure lines: from nineteenth-century biology to twentieth-century genetics.}, journal = {Studies in history and philosophy of biological and biomedical sciences}, volume = {38}, number = {4}, pages = {796-806}, doi = {10.1016/j.shpsc.2007.09.012}, pmid = {18053934}, issn = {1369-8486}, mesh = {Biochemistry/history ; *Biological Evolution ; Cell Fusion/methods ; *Cell Line ; Genetics/*history ; History, 19th Century ; History, 20th Century ; History, 21st Century ; Humans ; *Hybrid Cells ; Microbiology/history ; Selection, Genetic ; }, abstract = {Prompted by recent recognitions of the omnipresence of horizontal gene transfer among microbial species and the associated emphasis on exchange, rather than isolation, as the driving force of evolution, this essay will reflect on hybridization as one of the central concerns of nineteenth-century biology. I will argue that an emphasis on horizontal exchange was already endorsed by 'biology' when it came into being around 1800 and was brought to full fruition with the emergence of genetics in 1900. The true revolution in nineteenth-century life sciences, I maintain, consisted in a fundamental shift in ontology, which eroded the boundaries between individual and species, and allowed biologists to move up and down the scale of organic complexity. Life became a property extending both 'downwards', to the parts that organisms were composed of, as well as 'upwards', to the collective entities constituted by the relations of exchange and interaction that organisms engage in to reproduce. This mode of thinking was crystallized by Gregor Mendel and consolidated in the late nineteenth-century conjunction of biochemistry, microbiology and breeding in agro-industrial settings. This conjunction and its implications are especially exemplified by Wilhelm Johannsen's and Martinus Beijerinck's work on pure lines and cultures. An understanding of the subsequent constraints imposed by the evolutionary synthesis of the twentieth century on models of genetic systems may require us to rethink the history of biology and displace Darwin's theory of natural selection from that history's centre.}, }
@article {pmid18053933, year = {2007}, author = {Sapp, J}, title = {The structure of microbial evolutionary theory.}, journal = {Studies in history and philosophy of biological and biomedical sciences}, volume = {38}, number = {4}, pages = {780-795}, doi = {10.1016/j.shpsc.2007.09.011}, pmid = {18053933}, issn = {1369-8486}, mesh = {Bacteria ; *Biological Evolution ; Gene Transfer, Horizontal ; Humans ; *Microbiology ; Models, Organizational ; Models, Theoretical ; Phylogeny ; Symbiosis ; }, abstract = {The study of microbial phylogeny and evolution has emerged as an interdisciplinary synthesis, divergent in both methods and concepts from the classical evolutionary biology. The deployment of macromolecular sequencing in microbial classification has provided a deep evolutionary taxonomy hitherto deemed impossible. Microbial phylogenetics has greatly transformed the landscape of evolutionary biology, not only in revitalizing the field in the pursuit of life's history over billions of years, but also in transcending the structure of thought that has shaped evolutionary theory since the time of Darwin. A trio of primary phylogenetic lineages, along with the recognition of symbiosis and lateral gene transfer as fundamental processes of evolutionary innovation, are core principles of microbial evolutionary biology today. Their scope and significance remain contentious among evolutionists.}, }
@article {pmid18053269, year = {2007}, author = {Patil, PB and Bogdanove, AJ and Sonti, RV}, title = {The role of horizontal transfer in the evolution of a highly variable lipopolysaccharide biosynthesis locus in xanthomonads that infect rice, citrus and crucifers.}, journal = {BMC evolutionary biology}, volume = {7}, number = {}, pages = {243}, pmid = {18053269}, issn = {1471-2148}, mesh = {Brassicaceae/microbiology ; Citrus/microbiology ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Lipopolysaccharides/*biosynthesis ; Multigene Family ; Oryza/microbiology ; Repetitive Sequences, Nucleic Acid ; Species Specificity ; Stenotrophomonas maltophilia/*genetics/metabolism/pathogenicity ; Xanthomonas/*genetics/metabolism/pathogenicity ; Xanthomonas campestris/genetics/metabolism/pathogenicity ; }, abstract = {BACKGROUND: Lipopolysaccharide (LPS) is a pathogen associated molecular pattern (PAMP) of animal and plant pathogenic bacteria. Variation at the interstrain level is common in LPS biosynthetic gene clusters of animal pathogenic bacteria. This variation has been proposed to play a role in evading the host immune system. Even though LPS is a modulator of plant defense responses, reports of interstrain variation in LPS gene clusters of plant pathogenic bacteria are rare.<br><br>RESULTS: In this study we report the complete sequence of a variant 19.9 kb LPS locus present in the BXO8 strain of Xanthomonas oryzae pv. oryzae (Xoo), the bacterial blight pathogen of rice. This region is completely different in size, number and organization of genes from the LPS locus present in most other strains of Xoo from India and Asia. Surprisingly, except for one ORF, all the other ORFs at the BXO8 LPS locus are orthologous to the genes present at this locus in a sequenced strain of X. axonopodis pv. citri (Xac; a pathogen of citrus plants). One end of the BXO8 LPS gene cluster, comprised of ten genes, is also present in the related rice pathogen, X. oryzae pv. oryzicola (Xoc). In Xoc, the remainder of the LPS gene cluster, consisting of seven genes, is novel and unrelated to LPS gene clusters of any of the sequenced xanthomonads. We also report substantial interstrain variation suggestive of very recent horizontal gene transfer (HGT) at the LPS biosynthetic locus of Xanthomonas campestris pv. campestris (Xcc), the black rot pathogen of crucifers.<br><br>CONCLUSION: Our analyses indicate that HGT has altered the LPS locus during the evolution of Xanthomonas oryzae pathovars and suggest that the ancestor of all Xanthomonas oryzae pathovars had an Xac type of LPS gene cluster. Our finding of interstrain variation in two major xanthomonad pathogens infecting different hosts suggests that the LPS locus in plant pathogenic bacteria, as in animal pathogens, is under intense diversifying selection.}, }
@article {pmid18052529, year = {2007}, author = {Lefeuvre, P and Lett, JM and Reynaud, B and Martin, DP}, title = {Avoidance of protein fold disruption in natural virus recombinants.}, journal = {PLoS pathogens}, volume = {3}, number = {11}, pages = {e181}, pmid = {18052529}, issn = {1553-7374}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Sequence ; Begomovirus/*genetics ; Gene Transfer, Horizontal/*genetics ; Molecular Sequence Data ; *Protein Folding ; *Protein Structure, Tertiary ; *Selection, Genetic ; Viral Proteins/*chemistry ; }, abstract = {With the development of reliable recombination detection tools and an increasing number of available genome sequences, many studies have reported evidence of recombination in a wide range of virus genera. Recombination is apparently a major mechanism in virus evolution, allowing viruses to evolve more quickly by providing immediate direct access to many more areas of a sequence space than are accessible by mutation alone. Recombination has been widely described amongst the insect-transmitted plant viruses in the genus Begomovirus (family Geminiviridae), with potential recombination hot- and cold-spots also having been identified. Nevertheless, because very little is understood about either the biochemical predispositions of different genomic regions to recombine or what makes some recombinants more viable than others, the sources of the evolutionary and biochemical forces shaping distinctive recombination patterns observed in nature remain obscure. Here we present a detailed analysis of unique recombination events detectable in the DNA-A and DNA-A-like genome components of bipartite and monopartite begomoviruses. We demonstrate both that recombination breakpoint hot- and cold-spots are conserved between the two groups of viruses, and that patterns of sequence exchange amongst the genomes are obviously non-random. Using a computational technique designed to predict structural perturbations in chimaeric proteins, we demonstrate that observed recombination events tend to be less disruptive than sets of simulated ones. Purifying selection acting against natural recombinants expressing improperly folded chimaeric proteins is therefore a major determinant of natural recombination patterns in begomoviruses.}, }
@article {pmid18051853, year = {2007}, author = {Dai, XZ and Jiang, JD and Gu, LF and Pan, RQ and Li, SP}, title = {[Study on the atrazine-degrading genes in Arthrobacter sp. AG1].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {23}, number = {5}, pages = {789-793}, doi = {10.1016/s1872-2075(07)60049-1}, pmid = {18051853}, issn = {1000-3061}, mesh = {Arthrobacter/*genetics ; Atrazine/*metabolism ; Biodegradation, Environmental ; Genes, Bacterial/*genetics ; Herbicides/metabolism ; }, abstract = {Atrazine could be used as the sole carbon, nitrogen and energy sources for growth by strain Arthrobacter sp. AG1, and the atrazine-degrading genes of AG1 were found to be the combination of trzN, atzB and atzC. The atrazine chloride hydrolysase gene trzN was cloned by PCR amplification,whose sequence shared 99% identity with that of Norcardioides sp. C190. Two large plasmids were found in AG1,and trzN and atzB were confirmed to be localized on the larger plasmid pAG1 by the method of southern hybridization. Subculture of AG1 in liquid LB for three generations, 34% of the subsequent cells were found to lose degrading activity, however, neither plasmid was lost. PCR amplification results showed that the mutants had only lost the trzN gene instead of atzB and atzC. It was deduced that mutation might be due to the trzN gene deletion from the plasmid. This study provided new evidence that atrazine metabolic genotypes were resulted from horizontal gene transfer between different bacteria under environmental selective pressure.}, }
@article {pmid18048745, year = {2007}, author = {Young, JM and Park, DC}, title = {Probable synonymy of the nitrogen-fixing genus Azotobacter and the genus Pseudomonas.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {57}, number = {Pt 12}, pages = {2894-2901}, doi = {10.1099/ijs.0.64969-0}, pmid = {18048745}, issn = {1466-5026}, mesh = {Azotobacter/*classification/*genetics/physiology ; Bacterial Proteins/genetics ; Carbon-Nitrogen Ligases/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, rRNA ; Molecular Sequence Data ; *Nitrogen Fixation ; Phylogeny ; Proton-Translocating ATPases/genetics ; Pseudomonas/*classification/*genetics/physiology ; RNA, Ribosomal, 16S/genetics ; Rec A Recombinases/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {The relationships of the genus Azotobacter, Azomonas macrocytogenes and the genus Pseudomonas were revealed by comparative analysis of partial 16S rRNA and atpD, carA and recA gene sequences and as concatenated nucleotide and peptide sequences. Sequence similarities of Azotobacter species and Azomonas macrocytogenes indicated that these may be considered to be synonyms at the molecular level. In addition, these species show an intimate relationship with species of Pseudomonas, especially P. aeruginosa (the type species of the genus). In terms of the current circumscription of the genus Pseudomonas, Azotobacter and Azomonas macrocytogenes should be considered for amalgamation with Pseudomonas. Azotobacter and Azomonas comprise nitrogen-fixing strains with large pleomorphic cells that form cysts, and peritrichous flagella insertion; characteristics not included in the current circumscription of Pseudomonas. The data are discussed in the light of whether lateral transfer of genes could be involved in the determination of significant morphological characteristics, thus leading to a problem that may be encountered more frequently: how to resolve classification of taxa based on conserved sequences with those based on their phenotype. More fundamentally, the results illuminate problems that will increasingly be encountered: by what criteria can taxa be delineated, what are the most appropriate methods for classification, and what are the proper assumptions of bacterial classification?}, }
@article {pmid18048672, year = {2007}, author = {McInerney, JO and Pisani, D}, title = {Genetics. Paradigm for life.}, journal = {Science (New York, N.Y.)}, volume = {318}, number = {5855}, pages = {1390-1391}, doi = {10.1126/science.1151657}, pmid = {18048672}, issn = {1095-9203}, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; *Biological Evolution ; Escherichia coli/classification/*genetics ; *Gene Transfer, Horizontal ; *Genes, Archaeal ; *Genes, Bacterial ; Genetic Speciation ; Phylogeny ; }, }
@article {pmid18047426, year = {2007}, author = {Gusfield, D and Bansal, V and Bafna, V and Song, YS}, title = {A decomposition theory for phylogenetic networks and incompatible characters.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {14}, number = {10}, pages = {1247-1272}, pmid = {18047426}, issn = {1066-5277}, support = {K99 GM080099/GM/NIGMS NIH HHS/United States ; K99 GM080099-01/GM/NIGMS NIH HHS/United States ; 1K99 GM 080099/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Databases, Genetic ; *Models, Genetic ; *Phylogeny ; }, abstract = {Phylogenetic networks are models of evolution that go beyond trees, incorporating non-tree-like biological events such as recombination (or more generally reticulation), which occur either in a single species (meiotic recombination) or between species (reticulation due to lateral gene transfer and hybrid speciation). The central algorithmic problems are to reconstruct a plausible history of mutations and non-tree-like events, or to determine the minimum number of such events needed to derive a given set of binary sequences, allowing one mutation per site. Meiotic recombination, reticulation and recurrent mutation can cause conflict or incompatibility between pairs of sites (or characters) of the input. Previously, we used "conflict graphs" and "incompatibility graphs" to compute lower bounds on the minimum number of recombination nodes needed, and to efficiently solve constrained cases of the minimization problem. Those results exposed the structural and algorithmic importance of the non-trivial connected components of those two graphs. In this paper, we more fully develop the structural importance of non-trivial connected components of the incompatibility and conflict graphs, proving a general decomposition theorem (Gusfield and Bansal, 2005) for phylogenetic networks. The decomposition theorem depends only on the incompatibilities in the input sequences, and hence applies to many types of phylogenetic networks, and to any biological phenomena that causes pairwise incompatibilities. More generally, the proof of the decomposition theorem exposes a maximal embedded tree structure that exists in the network when the sequences cannot be derived on a perfect phylogenetic tree. This extends the theory of perfect phylogeny in a natural and important way. The proof is constructive and leads to a polynomial-time algorithm to find the unique underlying maximal tree structure. We next examine and fully solve the major open question from Gusfield and Bansal (2005): Is it true that for every input there must be a fully decomposed phylogenetic network that minimizes the number of recombination nodes used, over all phylogenetic networks for the input. We previously conjectured that the answer is yes. In this paper, we show that the answer in is no, both for the case that only single-crossover recombination is allowed, and also for the case that unbounded multiple-crossover recombination is allowed. The latter case also resolves a conjecture recently stated in (Huson and Klopper, 2007) in the context of reticulation networks. Although the conjecture from Gusfield and Bansal (2005) is disproved in general, we show that the answer to the conjecture is yes in several natural special cases, and establish necessary combinatorial structure that counterexamples to the conjecture must possess. We also show that counterexamples to the conjecture are rare (for the case of single-crossover recombination) in simulated data.}, }
@article {pmid18045507, year = {2007}, author = {Lee, CN and Hu, RM and Chow, TY and Lin, JW and Chen, HY and Tseng, YH and Weng, SF}, title = {Comparison of genomes of three Xanthomonas oryzae bacteriophages.}, journal = {BMC genomics}, volume = {8}, number = {}, pages = {442}, pmid = {18045507}, issn = {1471-2164}, mesh = {Amino Acid Sequence ; Bacteriophages/*genetics ; Base Composition ; Base Sequence ; Electrophoresis, Polyacrylamide Gel ; Genome, Viral/*genetics ; Mass Spectrometry ; Molecular Sequence Data ; Sequence Analysis, DNA ; Taiwan ; Xanthomonas/*virology ; }, abstract = {BACKGROUND: Xp10 and OP1 are phages of Xanthomonas oryzae pv. oryzae (Xoo), the causative agent of bacterial leaf blight in rice plants, which were isolated in 1967 in Taiwan and in 1954 in Japan, respectively. We recently isolated the Xoo phage Xop411.<br><br>RESULTS: The linear Xop411 genome (44,520 bp, 58 ORFs) sequenced here is 147 bp longer than that of Xp10 (60 ORFs) and 735 bp longer than that of OP1 (59 ORFs). The G+C contents of OP1 (51%) and Xop411 and Xp10 (52% each) are less than that of the host (65%). The 9-bp 3'-overhangs (5'-GGACAGTCT-3') in Xop411 and Xp10 are absent from OP1. More of the deduced Xop411 proteins share higher degrees of identity with Xp10 than with OP1 proteins, while the right end of the genomes of Xp10 and OP1, containing all predicted promoters, share stronger homology. Xop411, Xp10, and OP1 contain 8, 7, and 6 freestanding HNH endonuclease genes, respectively. These genes can be classified into five groups depending on their possession of the HNH domain (HNN or HNH type) and/or AP2 domain in intact or truncated forms. While the HNN-AP2 type endonuclease genes dispersed in the genome, the HNH type endonuclease genes, each with a unique copy, were located within the same genome context. Mass spectrometry and N-terminal sequencing showed nine Xop411 coat proteins, among which three were identified, six were assigned as coat proteins (4) and conserved phage proteins (2) in Xp10. The major coat protein, in which only the N-terminal methionine is removed, appears to exist in oligomeric forms containing 2 to 6 subunits. The three phages exhibit different patterns of domain duplication in the N-terminus of the tail fiber, which are involved in determination of the host range. Many short repeated sequences are present in and around the duplicated domains.<br><br>CONCLUSION: Geographical separation may have confined lateral gene transfer among the Xoo phages. The HNN-AP2 type endonucleases were more likely to transfer their genes randomly in the genome and may degenerate after successful transmission. Some repeated sequences may be involved in duplication/loss of the domains in the tail fiber genes.}, }
@article {pmid18045382, year = {2007}, author = {Gill, EE and Diaz-Triviño, S and Barberà, MJ and Silberman, JD and Stechmann, A and Gaston, D and Tamas, I and Roger, AJ}, title = {Novel mitochondrion-related organelles in the anaerobic amoeba Mastigamoeba balamuthi.}, journal = {Molecular microbiology}, volume = {66}, number = {6}, pages = {1306-1320}, doi = {10.1111/j.1365-2958.2007.05979.x}, pmid = {18045382}, issn = {0950-382X}, mesh = {Amoeba/genetics/*metabolism/ultrastructure ; Anaerobiosis ; Animals ; Chaperonin 60/genetics/metabolism ; Cloning, Molecular ; Electrophoresis, Gel, Two-Dimensional ; Immunoblotting ; Iron-Sulfur Proteins/metabolism ; Microscopy, Electron, Transmission ; Microscopy, Fluorescence ; Mitochondria/*metabolism/ultrastructure ; Organelles/*metabolism/ultrastructure ; Phylogeny ; Protozoan Proteins/classification/genetics/metabolism ; }, abstract = {Unicellular eukaryotes that lack mitochondria typically contain related organelles such as hydrogenosomes or mitosomes. To characterize the evolutionary diversity of these organelles, we conducted an expressed sequence tag (EST) survey on the free-living amoeba Mastigamoeba balamuthi, a relative of the human parasite Entamoeba histolytica. From 19 182 ESTs, we identified 21 putative mitochondrial proteins implicated in protein import, amino acid interconversion and carbohydrate metabolism, two components of the iron-sulphur cluster (Fe-S) assembly apparatus as well as two enzymes characteristic of hydrogenosomes. By immunofluorescence microscopy and subcellular fractionation, we show that mitochondrial chaperonin 60 is targeted to small abundant organelles within Mastigamoeba. In transmission electron micrographs, we identified double-membraned compartments that likely correspond to these mitochondrion-derived organelles, The predicted organellar proteome of the Mastigamoeba organelle indicates a unique spectrum of functions that collectively have never been observed in mitochondrion-related organelles. However, like Entamoeba, the Fe-S cluster assembly proteins in Mastigamoeba were acquired by lateral gene transfer from epsilon-proteobacteria and do not possess obvious organellar targeting peptides. These data indicate that the loss of classical aerobic mitochondrial functions and acquisition of anaerobic enzymes and Fe-S cluster assembly proteins occurred in a free-living member of the eukaryote super-kingdom Amoebozoa.}, }
@article {pmid18043664, year = {2007}, author = {Oregaard, G and Sørensen, SJ}, title = {High diversity of bacterial mercuric reductase genes from surface and sub-surface floodplain soil (Oak Ridge, USA).}, journal = {The ISME journal}, volume = {1}, number = {5}, pages = {453-467}, doi = {10.1038/ismej.2007.56}, pmid = {18043664}, issn = {1751-7362}, mesh = {Bacteria/*enzymology/*genetics ; Base Sequence ; DNA, Bacterial/chemistry ; Genes, Bacterial ; Genetic Variation ; Molecular Sequence Data ; Oxidoreductases/chemistry/*genetics ; Phylogeny ; Sequence Alignment ; *Soil Microbiology ; Tennessee ; }, abstract = {DNA was extracted from different depth soils (0-5, 45-55 and 90-100 cm below surface) sampled at Lower East Fork Poplar Creek floodplain (LEFPCF), Oak Ridge (TN, USA). The presence of merA genes, encoding the mercuric reductase, the key enzyme in detoxification of mercury in bacteria, was examined by PCR targeting Actinobacteria, Firmicutes or beta/gamma-Proteobacteria. beta/gamma-Proteobacteria merA genes were successfully amplified from all soils, whereas Actinobacteria were amplified only from surface soil. merA clone libraries were constructed and sequenced. beta/gamma-Proteobacteria sequences revealed high diversity in all soils, but limited vertical similarity. Less than 20% of the operational taxonomic units (OTU) (DNA sequences > or = 95% identical) were shared between the different soils. Only one of the 62 OTU was > or = 95% identical to a GenBank sequence, highlighting that cultivated bacteria are not representative of what is found in nature. Fewer merA sequences were obtained from the Actinobacteria, but these were also diverse, and all were different from GenBank sequences. A single clone was most closely related to merA of alpha-Proteobacteria. An alignment of putative merA genes of genome sequenced mainly marine alpha-Proteobacteria was used for design of merA primers. PCR amplification of soil alpha-Proteobacteria isolates and sequencing revealed that they were very different from the genome-sequenced bacteria (only 62%-66% identical at the amino-acid level), although internally similar. In light of the high functional diversity of mercury resistance genes and the limited vertical distribution of shared OTU, we discuss the role of horizontal gene transfer as a mechanism of bacterial adaptation to mercury.}, }
@article {pmid18043647, year = {2007}, author = {Stingl, U and Tripp, HJ and Giovannoni, SJ}, title = {Improvements of high-throughput culturing yielded novel SAR11 strains and other abundant marine bacteria from the Oregon coast and the Bermuda Atlantic Time Series study site.}, journal = {The ISME journal}, volume = {1}, number = {4}, pages = {361-371}, doi = {10.1038/ismej.2007.49}, pmid = {18043647}, issn = {1751-7362}, mesh = {Alphaproteobacteria/genetics/growth &amp; development/*isolation &amp; purification ; Bacterial Proteins/genetics/metabolism ; Bermuda ; Culture Media ; DNA, Ribosomal Spacer/genetics ; Marine Biology ; Molecular Sequence Data ; Oceans and Seas ; Oregon ; Phylogeny ; Rhodopsin/genetics/metabolism ; Rhodopsins, Microbial ; Sequence Homology, Nucleic Acid ; *Water Microbiology ; }, abstract = {The introduction of high-throughput dilution-to-extinction culturing (HTC) of marine bacterioplankton using sterilized natural sea water as media yielded isolates of many abundant but previously uncultured marine bacterial clades. In early experiments, bacteria from the SAR11 cluster (class Alphaproteobacteria), which are presumed to be the most abundant prokaryotes on earth, were cultured. Although many additional attempts were made, no further strains of the SAR11 clade were obtained. Here, we describe improvements to the HTC technique, which led to the isolation of 17 new SAR11 strains from the Oregon coast and the Sargasso Sea, accounting for 28% and 31% of all isolates in these experiments. Phylogenetic analysis of the internal transcribed spacer (ITS) region showed that the isolates from the Oregon coast represent three different subclusters of SAR11, while isolates from the Sargasso Sea were more uniform and represented a single ITS cluster. A PCR assay proved the presence of proteorhodopsin (PR) in nearly all SAR11 isolates. Analysis of PR amino-acid sequences indicated that isolates from the Oregon coast were tuned to either green or blue light, while PRs from strains obtained from the Sargasso Sea were exclusively tuned to maximum absorbance in the blue. Interestingly, phylogenies based on PR and ITS did not correlate, suggesting lateral gene transfer. In addition to the new SAR11 strains, many novel strains belonging to clusters of previously uncultured or undescribed species of different bacterial phyla, including the first strain of the highly abundant alphaproteobacterial SAR116 clade, were isolated using the modified methods.}, }
@article {pmid18043630, year = {2007}, author = {Ghosh, S and LaPara, TM}, title = {The effects of subtherapeutic antibiotic use in farm animals on the proliferation and persistence of antibiotic resistance among soil bacteria.}, journal = {The ISME journal}, volume = {1}, number = {3}, pages = {191-203}, doi = {10.1038/ismej.2007.31}, pmid = {18043630}, issn = {1751-7362}, mesh = {Animals ; Animals, Domestic/growth &amp; development/*microbiology ; Anti-Bacterial Agents/*administration &amp; dosage/pharmacology ; Bacteria/classification/*drug effects/growth &amp; development ; Chlortetracycline/pharmacology ; Colony Count, Microbial ; DNA, Bacterial/chemistry/genetics ; Genes, Bacterial ; Manure/*microbiology ; Molecular Sequence Data ; Sequence Analysis, DNA ; *Soil Microbiology ; *Tetracycline Resistance ; }, abstract = {The use of antibiotics at subtherapeutic concentrations for agricultural applications is believed to be an important factor in the proliferation of antibiotic-resistant bacteria. The goal of this study was to determine if the application of manure onto agricultural land would result in the proliferation of antibiotic resistance among soil bacteria. Chlortetracycline-resistant bacteria were enumerated and characterized from soils exposed to the manure of animals fed subtherapeutic concentrations of antibiotics and compared to the chlortetracycline-resistant bacteria from soils at farms with restricted antibiotic use (dairy farms) and from non-agricultural soils. No significant differences were observed at nine different study sites with respect to the numbers and types of cultivated chlortetracycline-resistant bacteria. Genes encoding for tetracycline resistance were rarely detected in the resistant bacteria from these sites. In contrast, soils collected from a tenth farm, which allowed manure to indiscriminately accumulate outside the animal pen, had significantly higher chlortetracycline-resistance levels. These resistant bacteria frequently harbored one of 14 different genes encoding for tetracycline resistance, many of which (especially tet(A) and tet(L)) were detected in numerous different bacterial species. Subsequent bacterial enumerations at this site, following the cessation of farming activity, suggested that this farm remained a hotspot for antibiotic resistance. In conclusion, we speculate that excessive application of animal manure leads to the spread of resistance to soil bacteria (potentially by lateral gene transfer), which then serve as persistent reservoir of antibiotic resistance.}, }
@article {pmid18039769, year = {2008}, author = {Vivero, A and Baños, RC and Mariscotti, JF and Oliveros, JC and García-del Portillo, F and Juárez, A and Madrid, C}, title = {Modulation of horizontally acquired genes by the Hha-YdgT proteins in Salmonella enterica serovar Typhimurium.}, journal = {Journal of bacteriology}, volume = {190}, number = {3}, pages = {1152-1156}, pmid = {18039769}, issn = {1098-5530}, mesh = {Animals ; Bacterial Proteins/genetics/*metabolism ; DNA-Binding Proteins/genetics/*metabolism ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Mice ; Mice, Inbred BALB C ; *Proteome ; Reverse Transcriptase Polymerase Chain Reaction ; Salmonella Infections, Animal/microbiology ; Salmonella typhimurium/genetics/metabolism/*pathogenicity ; Transcription, Genetic ; Virulence ; }, abstract = {We describe a transcriptomic study of the effect of hha and ydgT mutations in Salmonella enterica serovar Typhimurium. A large number of genes showing altered expression are located in AT-rich horizontally acquired DNA sequences. Many of these genes have also been reported to be targets for H-NS. As Hha and YdgT interact with H-NS, our findings strongly suggest that Hha and/or YdgT must form complexes with H-NS when they silence these DNA regions.}, }
@article {pmid18034216, year = {2007}, author = {de Setta, N and Loreto, EL and Carareto, CM}, title = {Is the evolutionary history of the O-type P element in the saltans and willistoni groups of Drosophila similar to that of the canonical P element?.}, journal = {Journal of molecular evolution}, volume = {65}, number = {6}, pages = {715-724}, pmid = {18034216}, issn = {0022-2844}, mesh = {Animals ; DNA Transposable Elements/*genetics ; Drosophila/classification/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Genetic ; Sequence Analysis, DNA ; }, abstract = {We studied the occurrence of O-type P elements in at least one species of each subgroup of the saltans group, in order to better understand the phylogenetic relationships among the elements within the saltans group and with those of species belonging to the willistoni group. We found that the O-type subfamily has a patchy distribution within the saltans group (it does not occur in D. neocordata and D. emarginata), low sequence divergence among species of the saltans group as well as in relation to species of the willistoni group, a lower rate of synonymous substitution for coding sequences compared to Adh, and phylogenetic incongruities. These findings suggest that the evolutionary history of the O-type subfamily within the saltans and willistoni groups follows the same model proposed for the canonical subfamily of P elements, i.e., events of horizontal transfer between species of the saltans and willistoni groups.}, }
@article {pmid18032435, year = {2008}, author = {Nord, D and Sjöberg, BM}, title = {Unconventional GIY-YIG homing endonuclease encoded in group I introns in closely related strains of the Bacillus cereus group.}, journal = {Nucleic acids research}, volume = {36}, number = {1}, pages = {300-310}, pmid = {18032435}, issn = {1362-4962}, mesh = {Amino Acid Sequence ; Bacillus cereus/classification ; Bacillus thuringiensis/classification/*genetics ; Bacterial Proteins/*genetics ; Base Sequence ; Endodeoxyribonucleases/chemistry/classification/*genetics ; *Introns ; Molecular Sequence Data ; Operon ; Phylogeny ; RNA Splicing ; RNA, Bacterial/chemistry ; Ribonucleotide Reductases/*genetics ; Sequence Alignment ; }, abstract = {Several group I introns have been previously found in strains of the Bacillus cereus group at three different insertion sites in the nrdE gene of the essential nrdIEF operon coding for ribonucleotide reductase. Here, we identify an uncharacterized group IA intron in the nrdF gene in 12 strains of the B. cereus group and show that the pre-mRNA is efficiently spliced. The Bacillus thuringiensis ssp. pakistani nrdF intron encodes a homing endonuclease, denoted I-BthII, with an unconventional GIY-(X)8-YIG motif that cleaves an intronless nrdF gene 7 nt upstream of the intron insertion site, producing 2-nt 3' extensions. We also found four additional occurrences of two of the previously reported group I introns in the nrdE gene of 25 sequenced B. thuringiensis and one B. cereus strains, and one non-annotated group I intron at a fourth nrdE insertion site in the B. thuringiensis ssp. Al Hakam sequenced genome. Two strains contain introns in both the nrdE and the nrdF genes. Phylogenetic studies of the nrdIEF operon from 39 strains of the B. cereus group suggest several events of horizontal gene transfer for two of the introns found in this operon.}, }
@article {pmid18025691, year = {2007}, author = {Darling, AE and Treangen, TJ and Messeguer, X and Perna, NT}, title = {Analyzing patterns of microbial evolution using the mauve genome alignment system.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {396}, number = {}, pages = {135-152}, doi = {10.1007/978-1-59745-515-2_10}, pmid = {18025691}, issn = {1064-3745}, support = {5T15LM007359-05/LM/NLM NIH HHS/United States ; GM62004-02/GM/NIGMS NIH HHS/United States ; }, mesh = {*Biological Evolution ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Phylogeny ; *Sequence Alignment ; Yersinia pestis/genetics ; }, abstract = {During the course of evolution, genomes can undergo large-scale mutation events such as rearrangement and lateral transfer. Such mutations can result in significant variations in gene order and gene content among otherwise closely related organisms. The Mauve genome alignment system can successfully identify such rearrangement and lateral transfer events in comparisons of multiple microbial genomes even under high levels of recombination. This chapter outlines the main features of Mauve and provides examples that describe how to use Mauve to conduct a rigorous multiple genome comparison and study evolutionary patterns.}, }
@article {pmid18024004, year = {2008}, author = {Belbahri, L and Calmin, G and Mauch, F and Andersson, JO}, title = {Evolution of the cutinase gene family: evidence for lateral gene transfer of a candidate Phytophthora virulence factor.}, journal = {Gene}, volume = {408}, number = {1-2}, pages = {1-8}, doi = {10.1016/j.gene.2007.10.019}, pmid = {18024004}, issn = {0378-1119}, mesh = {Algal Proteins/genetics ; Carboxylic Ester Hydrolases/*genetics ; DNA, Algal/metabolism ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Multigene Family ; Phylogeny ; Phytophthora/*genetics/pathogenicity ; Virulence Factors/*genetics ; }, abstract = {Lateral gene transfer (LGT) can facilitate the acquisition of new functions in recipient lineages, which may enable them to colonize new environments. Several recent publications have shown that gene transfer between prokaryotes and eukaryotes occurs with appreciable frequency. Here we present a study of interdomain gene transfer of cutinases -- well documented virulence factors in fungi -- between eukaryotic plant pathogens Phytophthora species and prokaryotic bacterial lineages. Two putative cutinase genes were cloned from Phytophthora brassicae and Northern blotting experiments showed that these genes are expressed early during the infection of the host Arabidopsis thaliana and induced during cyst germination of the pathogen. Analysis of the gene organisation of this gene family in Phytophthora ramorum and P. sojae showed three and ten copies in tight succession within a region of 5 and 25 kb, respectively, probably indicating a recent expansion in Phytophthora lineages by gene duplications. Bioinformatic analyses identified orthologues only in three genera of Actinobacteria, and in two distantly related eukaryotic groups: oomycetes and fungi. Together with phylogenetic analyses this limited distribution of the gene in the tree of life strongly support a scenario where cutinase genes originated after the origin of land plants in a microbial lineage living in proximity of plants and subsequently were transferred between distantly related plant-degrading microbes. More precisely, a cutinase gene was likely acquired by an ancestor of P. brassicae, P. sojae, P. infestans and P. ramorum, possibly from an actinobacterial source, suggesting that gene transfer might be an important mechanism in the evolution of their virulence. These findings could indeed provide an interesting model system to study acquisition of virulence factors in these important plant pathogens.}, }
@article {pmid18023150, year = {2007}, author = {Sirand-Pugnet, P and Citti, C and Barré, A and Blanchard, A}, title = {Evolution of mollicutes: down a bumpy road with twists and turns.}, journal = {Research in microbiology}, volume = {158}, number = {10}, pages = {754-766}, doi = {10.1016/j.resmic.2007.09.007}, pmid = {18023150}, issn = {0923-2508}, mesh = {Bacterial Proteins/genetics ; Base Composition ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Tenericutes/classification/*genetics ; }, abstract = {Mollicute evolution has been marked by significant changes in genome structure and use of their genetic information. These include a reduction in their genome G+C content and the use by most mollicutes of the UGA universal stop codon as tryptophan. More striking is the size reduction in their genome which, for some species, is now close to the minimal requirement for sustaining cell life. With the growing body of sequence data, a new picture has recently begun to emerge in which the evolution of these simple bacteria cannot be reduced to a race for the smallest genome.}, }
@article {pmid18021395, year = {2007}, author = {Boxma, B and Ricard, G and van Hoek, AH and Severing, E and Moon-van der Staay, SY and van der Staay, GW and van Alen, TA and de Graaf, RM and Cremers, G and Kwantes, M and McEwan, NR and Newbold, CJ and Jouany, JP and Michalowski, T and Pristas, P and Huynen, MA and Hackstein, JH}, title = {The [FeFe] hydrogenase of Nyctotherus ovalis has a chimeric origin.}, journal = {BMC evolutionary biology}, volume = {7}, number = {}, pages = {230}, pmid = {18021395}, issn = {1471-2148}, mesh = {Animals ; Chimera/*genetics ; Ciliophora/*enzymology/genetics ; Electron Transport Complex I/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Mitochondrial ; Genome, Protozoan ; Hydrogenase/*genetics ; Iron-Sulfur Proteins/*genetics ; Phylogeny ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {BACKGROUND: The hydrogenosomes of the anaerobic ciliate Nyctotherus ovalis show how mitochondria can evolve into hydrogenosomes because they possess a mitochondrial genome and parts of an electron-transport chain on the one hand, and a hydrogenase on the other hand. The hydrogenase permits direct reoxidation of NADH because it consists of a [FeFe] hydrogenase module that is fused to two modules, which are homologous to the 24 kDa and the 51 kDa subunits of a mitochondrial complex I.<br><br>RESULTS: The [FeFe] hydrogenase belongs to a clade of hydrogenases that are different from well-known eukaryotic hydrogenases. The 24 kDa and the 51 kDa modules are most closely related to homologous modules that function in bacterial [NiFe] hydrogenases. Paralogous, mitochondrial 24 kDa and 51 kDa modules function in the mitochondrial complex I in N. ovalis. The different hydrogenase modules have been fused to form a polyprotein that is targeted into the hydrogenosome.<br><br>CONCLUSION: The hydrogenase and their associated modules have most likely been acquired by independent lateral gene transfer from different sources. This scenario for a concerted lateral gene transfer is in agreement with the evolution of the hydrogenosome from a genuine ciliate mitochondrion by evolutionary tinkering.}, }
@article {pmid18006428, year = {2008}, author = {Burghoff, S and Ding, Z and Gödecke, S and Assmann, A and Wirrwar, A and Buchholz, D and Sergeeva, O and Leurs, C and Hanenberg, H and Müller, HW and Bloch, W and Schrader, J}, title = {Horizontal gene transfer from human endothelial cells to rat cardiomyocytes after intracoronary transplantation.}, journal = {Cardiovascular research}, volume = {77}, number = {3}, pages = {534-543}, doi = {10.1093/cvr/cvm071}, pmid = {18006428}, issn = {0008-6363}, mesh = {Animals ; Apoptosis ; Cell Differentiation ; Cells, Cultured ; Endothelial Cells/cytology/*transplantation ; *Gene Transfer, Horizontal ; Green Fluorescent Proteins/genetics ; Humans ; Male ; Myocytes, Cardiac/*metabolism ; Rats ; Rats, Wistar ; Tomography, Emission-Computed, Single-Photon ; }, abstract = {AIMS: Recent studies suggested that human umbilical vein endothelial cells (HUVECs) transdifferentiate into cardiomyocytes and smooth muscle cells in vitro. To test the functional relevance of this observation, we examined the transdifferentiation potential of HUVECs in vivo after intracoronary cell application in Wistar rats.<br><br>METHODS AND RESULTS: SPECT measurements (single photon emission computed tomography) revealed that 18% of (111)In-labelled HUVECs infused by intracoronary delivery stably transplanted to the rat heart. For long-term tracking, HUVECs-expressing enhanced green fluorescent protein (EGFP) were infused. Two days following transplantation, HUVECs were positive for caspase-3. Within 3 days, EGFP was associated with individual cardiomyocytes. No labelling of endothelial and smooth muscle cells was observed. The total number of EGFP-labelled cardiomyocytes accounted for 58% of all initially trapped cells. These EGFP positive cells stained negatively for human mitochondrial proteins, but were positive for rat monocarboxylate transporter-1 protein (MCT-1). Furthermore, EGFP-mRNA was detected in these cells by single-cell RT-PCR (reverse transcription followed by polymerase chain reaction). After 21 days, EGFP positive cells were no longer observed. To investigate the underlying mechanism, we generated in vitro apoptotic bodies from EGFP-labelled HUVECs and found them to contain the genetic information for EGFP. Co-incubation of apoptotic bodies with neonatal rat cardiomyocytes caused cardiomyocytes to express EGFP.<br><br>CONCLUSION: When transplanted into the rat heart by efficient intracoronary delivery, EGFP-expressing HUVECs cause the exclusive but transient labelling of cardiomyocytes. Our in vivo findings suggest that it is not cell fusion and/or transdifferentiation that occurs under these conditions but rather a horizontal gene transfer of the EGFP marker via apoptotic bodies from endothelial cells to cardiomyocytes.}, }
@article {pmid18005738, year = {2007}, author = {Blaxter, M}, title = {Symbiont genes in host genomes: fragments with a future?.}, journal = {Cell host &amp; microbe}, volume = {2}, number = {4}, pages = {211-213}, doi = {10.1016/j.chom.2007.09.008}, pmid = {18005738}, issn = {1934-6069}, mesh = {Animals ; Cell Nucleus/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Nematoda/genetics/physiology ; Plant Roots/parasitology ; Symbiosis ; Wolbachia/*physiology ; }, abstract = {While lateral transfer is the rule in the evolutionary history of bacterial and archaeal genes, events of transfer from prokaryotes to eukaryotes are rare. Germline-transmitted animal symbionts, such as Wolbachia pipientis, are well placed to participate in such transfers. In a recent issue of Science, Dunning Hotopp et al. identified instances of transfer of Wolbachia DNA to host genomes. It is unknown whether these transfers represent innovation in animal evolution.}, }
@article {pmid18004300, year = {2007}, author = {Dunfield, PF and Yuryev, A and Senin, P and Smirnova, AV and Stott, MB and Hou, S and Ly, B and Saw, JH and Zhou, Z and Ren, Y and Wang, J and Mountain, BW and Crowe, MA and Weatherby, TM and Bodelier, PL and Liesack, W and Feng, L and Wang, L and Alam, M}, title = {Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia.}, journal = {Nature}, volume = {450}, number = {7171}, pages = {879-882}, doi = {10.1038/nature06411}, pmid = {18004300}, issn = {1476-4687}, mesh = {Acids/metabolism ; Bacteria/*classification/enzymology/genetics/*metabolism ; Geologic Sediments/microbiology ; Hydrogen-Ion Concentration ; Methane/*metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics ; Oxygen/metabolism ; Oxygenases/genetics ; Partial Pressure ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Temperature ; }, abstract = {Aerobic methanotrophic bacteria consume methane as it diffuses away from methanogenic zones of soil and sediment. They act as a biofilter to reduce methane emissions to the atmosphere, and they are therefore targets in strategies to combat global climate change. No cultured methanotroph grows optimally below pH 5, but some environments with active methane cycles are very acidic. Here we describe an extremely acidophilic methanotroph that grows optimally at pH 2.0-2.5. Unlike the known methanotrophs, it does not belong to the phylum Proteobacteria but rather to the Verrucomicrobia, a widespread and diverse bacterial phylum that primarily comprises uncultivated species with unknown genotypes. Analysis of its draft genome detected genes encoding particulate methane monooxygenase that were homologous to genes found in methanotrophic proteobacteria. However, known genetic modules for methanol and formaldehyde oxidation were incomplete or missing, suggesting that the bacterium uses some novel methylotrophic pathways. Phylogenetic analysis of its three pmoA genes (encoding a subunit of particulate methane monooxygenase) placed them into a distinct cluster from proteobacterial homologues. This indicates an ancient divergence of Verrucomicrobia and Proteobacteria methanotrophs rather than a recent horizontal gene transfer of methanotrophic ability. The findings show that methanotrophy in the Bacteria is more taxonomically, ecologically and genetically diverse than previously thought, and that previous studies have failed to assess the full diversity of methanotrophs in acidic environments.}, }
@article {pmid17997281, year = {2007}, author = {Johnsborg, O and Eldholm, V and Håvarstein, LS}, title = {Natural genetic transformation: prevalence, mechanisms and function.}, journal = {Research in microbiology}, volume = {158}, number = {10}, pages = {767-778}, doi = {10.1016/j.resmic.2007.09.004}, pmid = {17997281}, issn = {0923-2508}, mesh = {Bacteria/*genetics ; DNA, Bacterial/genetics/physiology ; *Gene Transfer, Horizontal ; *Transformation, Bacterial ; }, abstract = {Studies show that gene acquisition through natural transformation has contributed significantly to the adaptation and ecological diversification of several bacterial species. Relatively little is still known, however, about the prevalence and phylogenetic distribution of organisms possessing this property. Thus, whether natural transformation only benefits a limited number of species or has a large impact on lateral gene flow in nature remains a matter of speculation. Here we will review the most recent advances in our understanding of the phenomenon and discuss its possible biological functions.}, }
@article {pmid17997085, year = {2009}, author = {Bautista-Zapanta, JN and Arafat, HH and Tanaka, K and Sawada, H and Suzuki, K}, title = {Variation of 16S-23S internally transcribed spacer sequence and intervening sequence in rDNA among the three major Agrobacterium species.}, journal = {Microbiological research}, volume = {164}, number = {6}, pages = {604-612}, doi = {10.1016/j.micres.2007.08.003}, pmid = {17997085}, issn = {1618-0623}, mesh = {Bacterial Typing Techniques ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; DNA, Ribosomal Spacer/*genetics ; Gene Transfer, Horizontal ; *Genetic Variation ; *Introns ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; RNA, Ribosomal, 23S/*genetics ; Rhizobium/classification/*genetics/isolation &amp; purification ; }, abstract = {We analyzed 16S-23S internally transcribed spacer (ITS) and neighboring sequences among 37 strains belonging to the three major pathogenic Agrobacterium species, in order to know variation in each species and to develop a simple discrimination method. Number of ITS size variation was 9, 4, and 7 in Agrobacterium tumefaciens, Agrobacterium vitis, and Agrobacterium rhizogenes, respectively. The ITS sequence of most strains in each species was distinguishable from that of the other two species. The region surrounded by 16S rRNA gene and trn(Ala) contained information to distinguish between the ITS variants and was easy for sequencing. Intervening sequences (IVSs) in 23S rRNA gene were classified into short and long types in each species. Some long-type IVSs of A. vitis were very similar to that of A. tumefaciens, while the other long-type IVSs of A. vitis were very similar to that of A. rhizogenes. Two A. vitis strains simultaneously contained both types of IVS. Similarly, the two exceptional A. vitis strains possessed A. tumefaciens-type ITS in addition to A. vitis-type ITS. These results suggest horizontal transfer of rDNA and subsequent recombination. Among the three species, A. tumefaciens was most variable based on 16S rRNA gene, ITS and IVS sequences.}, }
@article {pmid17996041, year = {2007}, author = {Juhas, M and Power, PM and Harding, RM and Ferguson, DJ and Dimopoulou, ID and Elamin, AR and Mohd-Zain, Z and Hood, DW and Adegbola, R and Erwin, A and Smith, A and Munson, RS and Harrison, A and Mansfield, L and Bentley, S and Crook, DW}, title = {Sequence and functional analyses of Haemophilus spp. genomic islands.}, journal = {Genome biology}, volume = {8}, number = {11}, pages = {R237}, pmid = {17996041}, issn = {1474-760X}, support = {/WT_/Wellcome Trust/United Kingdom ; G0400039/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Base Sequence ; DNA, Bacterial ; Drug Resistance, Microbial/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Haemophilus/*genetics ; Molecular Sequence Data ; Sequence Homology, Nucleic Acid ; Species Specificity ; }, abstract = {BACKGROUND: A major part of horizontal gene transfer that contributes to the diversification and adaptation of bacteria is facilitated by genomic islands. The evolution of these islands is poorly understood. Some progress was made with the identification of a set of phylogenetically related genomic islands among the Proteobacteria, recognized from the investigation of the evolutionary origins of a Haemophilus influenzae antibiotic resistance island, namely ICEHin1056. More clarity comes from this comparative analysis of seven complete sequences of the ICEHin1056 genomic island subfamily.<br><br>RESULTS: These genomic islands have core and accessory genes in approximately equal proportion, with none demonstrating recent acquisition from other islands. The number of variable sites within core genes is similar to that found in the host bacteria. Furthermore, the GC content of the core genes is similar to that of the host bacteria (38% to 40%). Most of the core gene content is formed by the syntenic type IV secretion system dependent conjugative module and replicative module. GC content and lack of variable sites indicate that the antibiotic resistance genes were acquired relatively recently. An analysis of conjugation efficiency and antibiotic susceptibility demonstrates that phenotypic expression of genomic island-borne genes differs between different hosts.<br><br>CONCLUSION: Genomic islands of the ICEHin1056 subfamily have a longstanding relationship with H. influenzae and H. parainfluenzae and are co-evolving as semi-autonomous genomes within the 'supragenomes' of their host species. They have promoted bacterial diversity and adaptation through becoming efficient vectors of antibiotic resistance by the recent acquisition of antibiotic resistance transposons.}, }
@article {pmid17993669, year = {2007}, author = {Ghai, R and Chakraborty, T}, title = {Comparative microbial genome visualization using GenomeViz.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {395}, number = {}, pages = {97-108}, doi = {10.1007/978-1-59745-514-5_6}, pmid = {17993669}, issn = {1064-3745}, mesh = {*Databases, Genetic ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Sequence Alignment ; }, abstract = {Recent years have brought a tremendous increase in the amount of sequence data from various bacterial genome sequencing projects, an increase that is projected to accelerate over the next years. Comparative genomics of microbial strains has provided us with unprecedented information to describe a bacterial species and examine for microbial diversity. This has allowed us to define core genomes based on genes commonly present in all strains of a species or genus and to identify dispensable regions in the genome harboring genus-, species-, and even strain-specific genes. Nevertheless, the task of organizing and summarizing the data to extract the most informative features remains a challenging yet critical endeavor. Visualization is an effective way of structuring and presenting such information effectively, in a concise and eloquent fashion. The large-scale views unveil commonalities and differences between the genomes that may shed light on their evolutionary relationships and define characteristics that are typical of pathogenicity or other ecological adaptations. We describe GenomeViz, a tool for comparative visualization of bacterial genomes that allows the user to actively create, modify and query a genome plot in a visually compact, user-friendly, and interactive manner.}, }
@article {pmid17993550, year = {2008}, author = {Ghosh, D and Roy, K and Williamson, KE and White, DC and Wommack, KE and Sublette, KL and Radosevich, M}, title = {Prevalence of lysogeny among soil bacteria and presence of 16S rRNA and trzN genes in viral-community DNA.}, journal = {Applied and environmental microbiology}, volume = {74}, number = {2}, pages = {495-502}, pmid = {17993550}, issn = {1098-5336}, mesh = {Actinomycetales/genetics ; Atrazine/pharmacology ; Bacteria/*genetics/ultrastructure/virology ; Bacterial Proteins/*genetics ; Bacteriophages/*genetics/growth &amp; development/ultrastructure ; DNA, Viral/*genetics ; Gene Expression Regulation, Bacterial/drug effects ; Gene Transfer, Horizontal ; Lysogeny/*genetics ; Microscopy, Electron, Transmission ; Mitomycin/pharmacology ; Polymerase Chain Reaction ; Polystyrenes ; RNA, Ribosomal, 16S/*genetics ; Soil Microbiology ; }, abstract = {Bacteriophages are very abundant in the biosphere, and viral infection is believed to affect the activity and genetic diversity of bacterial communities in aquatic environments. Lysogenic conversion, for example, can improve host fitness and lead to phage-mediated horizontal gene transfer. However, little is known about lysogeny and transduction in the soil environment. In this study we employed atrazine-impregnated Bio-Sep beads (a cell immobilization matrix) to sample active microbiota from soils with prior pesticide exposure history. Once recovered from soil, the bead communities were induced with mitomycin C (MC), and viral and bacterial abundances were determined to evaluate the incidence of inducible prophage in soil bacteria. The inducible fraction calculated within bead communities was high (ca. 85%) relative to other studies in aquatic and sedimentary environments. Moreover, the bacterial genes encoding 16S rRNA and trzN, a chlorohydrolase gene responsible for dehalogenation of atrazine, were detected by PCR in the viral DNA fraction purified from MC-induced bead communities. A diverse collection of actinobacterial 16S rRNA gene sequences occurred within the viral DNA fraction of induced, water-equilibrated beads. Similar results were observed in induced atrazine-equilibrated beads, where 77% of the cloned sequences were derived from actinobacterial lineages. Heterogeneous 16S rRNA gene sequences consisting of fragments from two different taxa were detected in the clone libraries. The results suggest that lysogeny is a prevalent reproductive strategy among soil bacteriophages and that the potential for horizontal gene transfer via transduction is significant in soil microbial communities.}, }
@article {pmid17989781, year = {2007}, author = {Laha, T and Loukas, A and Wattanasatitarpa, S and Somprakhon, J and Kewgrai, N and Sithithaworn, P and Kaewkes, S and Mitreva, M and Brindley, PJ}, title = {The bandit, a new DNA transposon from a hookworm-possible horizontal genetic transfer between host and parasite.}, journal = {PLoS neglected tropical diseases}, volume = {1}, number = {1}, pages = {e35}, pmid = {17989781}, issn = {1935-2735}, support = {U01 AI046593/AI/NIAID NIH HHS/United States ; AI 46593/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Ancylostomatoidea/classification/*genetics ; Animals ; Blotting, Southern ; DNA Primers ; DNA Transposable Elements/genetics ; DNA, Helminth/*genetics ; Dog Diseases/*transmission ; Dogs/parasitology ; Gene Library ; Hookworm Infections/*genetics ; Host-Parasite Interactions ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Open Reading Frames ; Phylogeny ; Polymerase Chain Reaction ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {BACKGROUND: An enhanced understanding of the hookworm genome and its resident mobile genetic elements should facilitate understanding of the genome evolution, genome organization, possibly host-parasite co-evolution and horizontal gene transfer, and from a practical perspective, development of transposon-based transgenesis for hookworms and other parasitic nematodes.<br><br>A novel mariner-like element (MLE) was characterized from the genome of the dog hookworm, Ancylostoma caninum, and termed bandit. The consensus sequence of the bandit transposon was 1,285 base pairs (bp) in length. The new transposon was flanked by perfect terminal inverted repeats of 32 nucleotides in length with a common target site duplication TA, and it encoded an open reading frame (ORF) of 342 deduced amino acid residues. Phylogenetic comparisons confirmed that the ORF encoded a mariner-like transposase, which included conserved catalytic domains, and that the bandit transposon belonged to the cecropia subfamily of MLEs. The phylogenetic analysis also indicated that the Hsmar1 transposon from humans was the closest known relative of bandit, and that bandit and Hsmar1 constituted a clade discrete from the Tc1 subfamily of MLEs from the nematode Caenorhabditis elegans. Moreover, homology models based on the crystal structure of Mos1 from Drosophila mauritiana revealed closer identity in active site residues of the catalytic domain including Ser281, Lys289 and Asp293 between bandit and Hsmar1 than between Mos1 and either bandit or Hsmar1. The entire bandit ORF was amplified from genomic DNA and a fragment of the bandit ORF was amplified from RNA, indicating that this transposon is actively transcribed in hookworms.<br><br>CONCLUSIONS/SIGNIFICANCE: A mariner-like transposon termed bandit has colonized the genome of the hookworm A. caninum. Although MLEs exhibit a broad host range, and are identified in other nematodes, the closest phylogenetic relative of bandit is the Hsmar1 element of humans. This surprising finding suggests that bandit was transferred horizontally between hookworm parasites and their mammalian hosts.}, }
@article {pmid17988534, year = {2007}, author = {Lü, P and Xu, XW and Song, WQ and Zhen, JH and Yu, SJ and Yang, YH and Shen, XZ}, title = {[Transfer of erythromycin-resistance among strains and species of bacteria: plasmid conjugation method in enterococcal isolates].}, journal = {Zhonghua yi xue za zhi}, volume = {87}, number = {30}, pages = {2129-2131}, pmid = {17988534}, issn = {0376-2491}, mesh = {Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic/genetics ; DNA, Bacterial/*genetics ; Drug Resistance, Bacterial/*genetics ; Enterococcus/drug effects/*genetics/isolation &amp; purification ; Erythromycin/pharmacology ; *Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Plasmids/genetics ; Species Specificity ; }, abstract = {OBJECTIVE: To study if the resistance to macrolide in Enterococcus can be transferred between strains, and species of the same and different genera.<br><br>METHODS: Agar dilution was used to screen 30 enterococcal isolates that were resistant to erythromycin. Conjugation was performed by filter mating method. The 30 donor bacteria included 13 strains of Enterococcus faecalis, 16 strains of E. faecium, and 1 strain of E. hirae. The recipient bacteria included 1 strain of E. faecalis sensitive to erythromycin and resistant to tetracycline, and 1 strain of Staphylococcus aureus with the MIC against erythromycin of 0.25 approximately 1 microg/ml. Polymerase chain reaction was used to test the existence of ermB gene and the tranposons Tn1545 and Tn917 in the enterococcal isolates before and after filter mating.<br><br>RESULTS: The transfer rate between different strains and species of the same genus were all 100%. The MIC(50) and MIC(90) against erythromycin of 13 conjugates were both 512 microg/ml, and Tn1545 and Tn917 were found in the ermB gene of 12 conjugates. 17 conjugates were obtained from 16 strains of donor E. faecium and 1 strain of E. hirae with the MIC(50) and MIC(90) both of 512 microg/ml. The ermB gene was found in 16 of the 17 conjugates, and 11 of the 16 conjugates showed the existence of Tn1545 and Tn917, Tn1545 existed in the ermB gene of 4 conjugates, and Tn917 existed in the ermB gene of 1 conjugate. 30 conjugates of Staphylococcus aureus were obtained by plasmid conjugation and transfer with a transfer rate of 100% and the MIC(50) and MIC(90) both of 512 microg/ml. The ermB gene was found in 28 of the 30 conjugates. Both Tn1545 and Tn917 were found in the ermB gene of 23 of the 28 conjugates, Tn1545 was found in the ermB gene of 4 conjugates, and Tn917 was found in the ermB gene of 1 conjugate.<br><br>CONCLUSION: The resistance to macrolide of Enterococcus, related with the existence of ermB gene and transposons Tn1545 and Tn917, can be transferred between strains and species of same and different genera.}, }
@article {pmid17983575, year = {2007}, author = {Bordenstein, SR}, title = {Evolutionary genomics: transdomain gene transfers.}, journal = {Current biology : CB}, volume = {17}, number = {21}, pages = {R935-6}, doi = {10.1016/j.cub.2007.09.022}, pmid = {17983575}, issn = {0960-9822}, mesh = {Animals ; Arthropods/*genetics/*microbiology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genomics ; Nematoda/*genetics/*microbiology ; Wolbachia/*genetics ; }, abstract = {Biologists have until now conceded that bacterial gene transfer to multicellular animals is relatively uncommon in Nature. A new study showing promiscuous insertions of bacterial endosymbiont genes into invertebrate genomes ushers in a shift in this paradigm.}, }
@article {pmid17977789, year = {2008}, author = {Werner, G and Klare, I and Fleige, C and Witte, W}, title = {Increasing rates of vancomycin resistance among Enterococcus faecium isolated from German hospitals between 2004 and 2006 are due to wide clonal dissemination of vancomycin-resistant enterococci and horizontal spread of vanA clusters.}, journal = {International journal of medical microbiology : IJMM}, volume = {298}, number = {5-6}, pages = {515-527}, doi = {10.1016/j.ijmm.2007.05.008}, pmid = {17977789}, issn = {1618-0607}, mesh = {Bacterial Proteins/*genetics ; Bacterial Typing Techniques ; Blotting, Southern ; Carbon-Oxygen Ligases/*genetics ; Cluster Analysis ; Cross Infection/*microbiology ; DNA, Bacterial/genetics ; Electrophoresis, Gel, Pulsed-Field ; Enterococcus faecium/*classification/*drug effects/genetics/isolation &amp; purification ; *Gene Transfer, Horizontal ; Genotype ; Germany ; Gram-Positive Bacterial Infections/*microbiology ; Hospitals ; Humans ; Minisatellite Repeats ; Phylogeny ; Polymerase Chain Reaction/methods ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; Vancomycin Resistance/*genetics ; Virulence Factors/genetics ; }, abstract = {Results of national and international surveillance studies revealed increasing rates of vancomycin-resistant Enterococcus faecium (VREF) among German hospital patients since 2003. To investigate the molecular background of vanA-type glycopeptide resistance, 51 clinical VREF isolated between 2004 and 2006 and originating from 19 German hospitals representing 10 Federal States have been investigated. Isolates were characterised by multi-locus sequence typing (MLST), SmaI macrorestriction analysis in pulsed-field gel electrophoresis (PFGE), and multiple-locus variable-number tandem repeat analysis (MLVA). Phylogenetic relatedness between strains was identified using BioNumerics and eBURST software. Distribution of virulence markers esp and hyl(Efm) was investigated by PCR. The structure of the vanA gene clusters was investigated by PCR, long-template PCR, sequencing and Southern hybridisations. The 51 VREF were rather diverse constituting different strain types, different virulence markers and vanA clusters. Within this diversity we found supportive data for a dissemination of related--already vancomycin-resistant--E. faecium among various hospitals and Federal States and for spread of identical vanA gene clusters among clonally different strain types within single hospitals. In conclusion, the increase in the rates of VREF among German hospital patients within the last 2 years might be rather complex and due to different molecular events and scenarios.}, }
@article {pmid17976929, year = {2008}, author = {Gogolevsky, KP and Vassetzky, NS and Kramerov, DA}, title = {Bov-B-mobilized SINEs in vertebrate genomes.}, journal = {Gene}, volume = {407}, number = {1-2}, pages = {75-85}, doi = {10.1016/j.gene.2007.09.021}, pmid = {17976929}, issn = {0378-1119}, mesh = {Animals ; Base Sequence ; *Gene Transfer, Horizontal ; Genome/*genetics ; Molecular Sequence Data ; RNA, Ribosomal, 5S/genetics ; Rodentia/*genetics ; Short Interspersed Nucleotide Elements/*genetics ; }, abstract = {Two new short retroposon families (SINEs) have been found in the genome of springhare Pedetes capensis (Rodentia). One of them, Ped-1, originated from 5S rRNA, while the other one, Ped-2, originated from tRNA-derived SINE ID. In contrast to most currently active mammalian SINEs mobilized by L1 long retrotransposon (LINE), Ped-1 and Ped-2 are mobilized by Bov-B, a LINE family of the widely distributed RTE clade. The 3' part of these SINEs originates from two sequences in the 5' and 3' regions of Bov-B. Such bipartite structure of the LINE-derived part has been revealed in all Bov-B-mobilized SINEs known to date (AfroSINE, Bov-tA, Mar-1, and Ped-1/2), which distinguishes them from other SINEs with only a 3' LINE-derived part. Structural analysis and the distribution of Bov-B LINEs and partner SINEs supports the horizontal transfer of Bov-B, while the SINEs emerged independently in lineages with this LINE.}, }
@article {pmid17976171, year = {2008}, author = {Sutyak, KE and Wirawan, RE and Aroutcheva, AA and Chikindas, ML}, title = {Isolation of the Bacillus subtilis antimicrobial peptide subtilosin from the dairy product-derived Bacillus amyloliquefaciens.}, journal = {Journal of applied microbiology}, volume = {104}, number = {4}, pages = {1067-1074}, pmid = {17976171}, issn = {1365-2672}, support = {R21 AT002897/AT/NCCIH NIH HHS/United States ; R21 AT002897-02/AT/NCCIH NIH HHS/United States ; R21AT002897-01/AT/NCCIH NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/*analysis ; Antibiosis ; Bacillus/*chemistry/genetics/physiology ; Bacteriocins/*analysis ; Chromatography, Liquid/methods ; Dairy Products/*microbiology ; Electrophoresis, Polyacrylamide Gel ; Female ; *Food Microbiology ; Gardnerella vaginalis/physiology ; Humans ; Hydrogen-Ion Concentration ; Microbial Sensitivity Tests ; Microbial Viability ; Peptides, Cyclic/*analysis ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/analysis ; Streptococcus agalactiae/physiology ; Temperature ; Vaginosis, Bacterial/microbiology ; }, abstract = {AIMS: To purify and characterize an antimicrobial protein (bacteriocin) isolated from the dairy product-derived Bacillus amyloliquefaciens.<br><br>METHODS AND RESULTS: An unknown bacterial species cultured from the Yogu Farm probiotic dairy beverage was identified through 16S ribosomal RNA analysis as B. amyloliquefaciens, a phylogenetically close relative of Bacillus subtilis. The cell-free supernatant (CFS) of overnight cultures was active against Listeria monocytogenes and also against clinical isolates of Gardnerella vaginalis and Streptococcus agalactiae. At the same time, several isolates of vaginal probiotic Lactobacilli were resistant to the CFS. The nature of the compound causing inhibitory activity was confirmed as proteinaceous by enzymatic digestion. The protein was isolated using ammonium sulfate precipitation, and further purified via column chromatography. PCR analysis was conducted to determine relatedness to other bacteriocins produced by Bacillus spp.<br><br>CONCLUSION: The antimicrobial protein isolated from B. amyloliquefaciens was shown to be subtilosin, a bacteriocin previously reported as produced only by B. subtilis.<br><br>This is the first report of intra-species horizontal gene transfer for subtilosin and the first fully characterized bacteriocin isolated from B. amyloliquefaciens. Finally, this is the first report on subtilosin's activity against bacterial vaginosis-associated pathogens.}, }
@article {pmid17975096, year = {2007}, author = {Ueno, R and Huss, VAR and Urano, N and Watabe, S}, title = {Direct evidence for redundant segmental replacement between multiple 18S rRNA genes in a single Prototheca strain.}, journal = {Microbiology (Reading, England)}, volume = {153}, number = {Pt 11}, pages = {3879-3893}, doi = {10.1099/mic.0.2007/009365-0}, pmid = {17975096}, issn = {1350-0872}, mesh = {Base Sequence ; *Gene Transfer, Horizontal ; *Genes, rRNA ; Molecular Sequence Data ; Nucleic Acid Conformation ; Prototheca/*classification/*genetics/growth &amp; development ; RNA, Ribosomal, 18S/chemistry/*genetics ; *Recombination, Genetic ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Informational genes such as those encoding rRNAs are related to transcription and translation, and are thus considered to be rarely subject to lateral gene transfer (LGT) between different organisms, compared to operational genes having metabolic functions. However, several lines of evidence have suggested or confirmed the occurrence of LGT of DNA segments encoding evolutionarily variable regions of rRNA genes between different organisms. In the present paper, we show, for the first time to our knowledge, that variable regions of the 18S rRNA gene are segmentally replaced by multiple copies of different sequences in a single strain of the green microalga Prototheca wickerhamii, resulting in at least 17 genotypes, nine of which were actually transcribed. Recombination between different 18S rRNA genes occurred in seven out of eight variable regions (V1-V5 and V7-V9) of eukaryotic small subunit (SSU) rRNAs. While no recombination was observed in V1, one to three different recombination loci were demonstrated for the other regions. Such segmental replacement was also implicated for helix H37, which is defined as V6 of prokaryotic SSU rRNAs. Our observations provide direct evidence for redundant recombination of an informational gene, which encodes a component of mature ribosomes, in a single strain of one organism.}, }
@article {pmid17971860, year = {2007}, author = {Slot, JC and Hibbett, DS}, title = {Horizontal transfer of a nitrate assimilation gene cluster and ecological transitions in fungi: a phylogenetic study.}, journal = {PloS one}, volume = {2}, number = {10}, pages = {e1097}, pmid = {17971860}, issn = {1932-6203}, mesh = {Anion Transport Proteins/chemistry ; *Ecology ; Evolution, Molecular ; Fungal Proteins/*chemistry ; Gene Expression Regulation ; Gene Expression Regulation, Fungal ; *Gene Transfer, Horizontal ; Genome ; Likelihood Functions ; Models, Biological ; *Multigene Family ; Nitrate Transporters ; Nitrates/*chemistry ; Phylogeny ; Phytophthora/metabolism ; Trichoderma/metabolism ; }, abstract = {High affinity nitrate assimilation genes in fungi occur in a cluster (fHANT-AC) that can be coordinately regulated. The clustered genes include nrt2, which codes for a high affinity nitrate transporter; euknr, which codes for nitrate reductase; and NAD(P)H-nir, which codes for nitrite reductase. Homologs of genes in the fHANT-AC occur in other eukaryotes and prokaryotes, but they have only been found clustered in the oomycete Phytophthora (heterokonts). We performed independent and concatenated phylogenetic analyses of homologs of all three genes in the fHANT-AC. Phylogenetic analyses limited to fungal sequences suggest that the fHANT-AC has been transferred horizontally from a basidiomycete (mushrooms and smuts) to an ancestor of the ascomycetous mold Trichoderma reesei. Phylogenetic analyses of sequences from diverse eukaryotes and eubacteria, and cluster structure, are consistent with a hypothesis that the fHANT-AC was assembled in a lineage leading to the oomycetes and was subsequently transferred to the Dikarya (Ascomycota+Basidiomycota), which is a derived fungal clade that includes the vast majority of terrestrial fungi. We propose that the acquisition of high affinity nitrate assimilation contributed to the success of Dikarya on land by allowing exploitation of nitrate in aerobic soils, and the subsequent transfer of a complete assimilation cluster improved the fitness of T. reesei in a new niche. Horizontal transmission of this cluster of functionally integrated genes supports the "selfish operon" hypothesis for maintenance of gene clusters.}, }
@article {pmid17965091, year = {2007}, author = {Lin, Z and Nei, M and Ma, H}, title = {The origins and early evolution of DNA mismatch repair genes--multiple horizontal gene transfers and co-evolution.}, journal = {Nucleic acids research}, volume = {35}, number = {22}, pages = {7591-7603}, pmid = {17965091}, issn = {1362-4962}, support = {R01 GM020293/GM/NIGMS NIH HHS/United States ; R01 GM063871/GM/NIGMS NIH HHS/United States ; GM020293/GM/NIGMS NIH HHS/United States ; GM63871/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *DNA Mismatch Repair ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; Genes, Plant ; Genomics ; Models, Genetic ; *Multigene Family ; MutS DNA Mismatch-Binding Protein/classification/*genetics ; MutS Homolog 2 Protein/classification/genetics ; Phylogeny ; }, abstract = {To understand the evolutionary process of the DNA mismatch repair system, we conducted systematic phylogenetic analysis of its key components, the bacterial MutS and MutL genes and their eukaryotic homologs. Based on genome-wide homolog searches, we identified three new MutS subfamilies (MutS3-5) in addition to the previously studied MutS1 and MutS2 subfamilies. Detailed evolutionary analysis strongly suggests that frequent ancient horizontal gene transfer (HGT) occurred with both MutS and MutL genes from bacteria to eukaryotes and/or archaea. Our results further imply that the origins of mismatch repair system in eukaryotes and archaea are largely attributed to ancient HGT from bacteria instead of vertical evolution. Specifically, the eukaryotic MutS and MutL homologs likely originated from endosymbiotic ancestors of mitochondria or chloroplasts, indicating that not only archaea, but also bacteria are important sources of eukaryotic DNA metabolic genes. The archaeal MutS1 and MutL homologs were also acquired from bacteria simultaneously through HGT. Moreover, the distribution and evolution profiles of the MutS1 and MutL genes suggest that they have undergone long-term coevolution. Our work presents an overall portrait of the evolution of these important genes in DNA metabolism and also provides further understanding about the early evolution of cellular organisms.}, }
@article {pmid17961488, year = {2007}, author = {Nordgård, L and Nguyen, T and Midtvedt, T and Benno, Y and Traavik, T and Nielsen, KM}, title = {Lack of detectable DNA uptake by bacterial gut isolates grown in vitro and by Acinetobacter baylyi colonizing rodents in vivo.}, journal = {Environmental biosafety research}, volume = {6}, number = {1-2}, pages = {149-160}, doi = {10.1051/ebr:2007029}, pmid = {17961488}, issn = {1635-7922}, mesh = {Acinetobacter/*genetics/growth &amp; development/isolation &amp; purification ; Animals ; DNA/*genetics ; Gastrointestinal Tract/*microbiology ; Gene Transfer, Horizontal ; Kanamycin Resistance/genetics ; Mice ; Rats ; Transformation, Bacterial ; }, abstract = {Biological risk assessment of food containing recombinant DNA has exposed knowledge gaps related to the general fate of DNA in the gastrointestinal tract (GIT). Here, a series of experiments is presented that were designed to determine if genetic transformation of the naturally competent bacterium Acinetobacter baylyi BD413 occurs in the GIT of mice and rats, with feed-introduced bacterial DNA containing a kanamycin resistance gene (nptII). Strain BD413 was found in various gut locations in germ-free mice at 10(3)-10(5) CFU per gram GIT content 24-48 h after administration. However, subsequent DNA exposure of the colonized mice did not result in detectable bacterial transformants, with a detection limit of 1 transformant per 10(3)-10(5) bacteria. Further attempts to increase the likelihood of detection by introducing weak positive selection with kanamycin of putative transformants arising in vivo during a 4-week-long feeding experiment (where the mice received DNA and the recipient cells regularly) did not yield transformants either. Moreover, the in vitro exposure of actively growing A. baylyi cells to gut contents from the stomach, small intestine, cecum or colon contents of rats (with a normal microbiota) fed either purified DNA (50 microg) or bacterial cell lysates did not produce bacterial transformants. The presence of gut content of germfree mice was also highly inhibitory to transformation of A. baylyi, indicating that microbially-produced nucleases are not responsible for the sharp 500- to 1,000,000-fold reduction of transformation frequencies seen. Finally, a range of isolates from the genera Enterococcus, Streptococcus and Bifidobacterium spp. was examined for competence expression in vitro, without yielding any transformants. In conclusion, model choice and methodological constraints severely limit the sample size and, hence, transfer frequencies that can be measured experimentally in the GIT. Our observations suggest the contents of the GIT shield or adsorb DNA, preventing detectable exposure of feed-derived DNA fragments to competent bacteria.}, }
@article {pmid17961487, year = {2007}, author = {Ray, JL and Andersen, HK and Young, S and Nielsen, KM and O'Callaghan, M}, title = {An assessment of the potential of herbivorous insect gut bacteria to develop competence for natural transformation.}, journal = {Environmental biosafety research}, volume = {6}, number = {1-2}, pages = {135-147}, doi = {10.1051/ebr:2007032}, pmid = {17961487}, issn = {1635-7922}, mesh = {Acinetobacter/genetics ; Animals ; Drug Resistance, Microbial/genetics ; Feeding Behavior ; Gastrointestinal Tract/*metabolism/microbiology ; *Gene Transfer, Horizontal ; Insecta/*genetics/microbiology/physiology ; Larva/drug effects/genetics ; Poaceae/genetics ; Polymerase Chain Reaction ; Rifampin/pharmacology ; Transformation, Bacterial ; }, abstract = {Whereas the capability of DNA uptake has been well established for numerous species and strains of bacteria grown in vitro, the broader distribution of natural transformability within bacterial communities remains largely unexplored. Here, we investigate the ability of bacterial isolates from the gut of grass grub larvae (Costelytra zealandica (White); Coleoptera: Scarabaeidae) to develop natural genetic competence in vitro. A total of 37 mostly species-divergent strains isolated from the gut of grass grub larvae were selected for spontaneous rifampicin-resistance. Genomic DNA was subsequently isolated from the resistant strains and exposed to sensitive strains grown individually using established filter transformation protocols. DNA isolated from wild-type strains was used as a control. None of the 37 isolates tested exhibited a frequency of conversion to rifampicin-resistance in the presence of DNA at rates that were significantly higher than the rate of spontaneous mutation to rifampicin-resistance in the presence of wild-type DNA (the limit of detection was approximately < 1 culturable transformant per 10(9) exposed bacteria). To further examine if conditions were conducive to bacterial DNA uptake in the grass grubs gut, we employed the competent bacterium Acinetobacter baylyi strain BD413 as a recipient species for in vivo studies. However, no transformants could be detected above the detection limit of 1 transformant per 10(3) cells, possibly due to low population density and limited growth of A. baylyi cells in grass grub guts. PCR analysis indicated that chromosomal Acinetobacter DNA remains detectable by PCR for up to 3 days after direct inoculation into the alimentary tract of grass grub larvae. Nevertheless, neither transforming activity of the DNA recovered from the alimentary tract of grass grubs larvae nor competence of bacterial cells recovered from inoculated larvae could be shown.}, }
@article {pmid17961486, year = {2007}, author = {Brinkmann, N and Tebbe, CC}, title = {Leaf-feeding larvae of Manduca sexta (Insecta, Lepidoptera) drastically reduce copy numbers of aadA antibiotic resistance genes from transplastomic tobacco but maintain intact aadA genes in their feces.}, journal = {Environmental biosafety research}, volume = {6}, number = {1-2}, pages = {121-133}, doi = {10.1051/ebr:2007028}, pmid = {17961486}, issn = {1635-7922}, mesh = {Acinetobacter/genetics ; Animals ; Drug Resistance, Microbial/genetics ; Feces/microbiology ; Feeding Behavior ; Gene Dosage ; Gene Transfer, Horizontal ; Genes, Plant/genetics ; Genome, Chloroplast ; Larva/genetics/physiology ; Manduca/*genetics/physiology ; Plant Leaves/*genetics ; Nicotiana/*genetics ; }, abstract = {The objective of this study was to evaluate the effect of insect larval feeding on the fate and genetic transformability of recombinant DNA from a transplastomic plant. Leaves of tobacco plants with an aadA antibiotic resistance gene inserted into their chloroplast genome were incubated with larvae of the tobacco hornworm Manduca sexta (Lepidoptera). The specifically designed Acinetobacter strain BD413 pBAB(2) was chosen to analyze the functional integrity of the aadA transgene for natural transformation after gut passages. No gene transfer was detected after simultaneous feeding of leaves and the Acinetobacter BD413 pBAB(2) as a recipient, even though 15% of ingested Acinetobacter BD413 cells could be recovered as viable cells from feces 6 h after feeding. Results with real-time PCR indicated that an average of 98.2 to 99.99% of the aadA gene was degraded during the gut passage, but the range in the number of aadA genes in feces of larvae fed with transplastomic leaves was enormous, varying from 5 x 10(6) to 1 x 10(9) copies.g(-1). DNA extracted from feces of larvae fed with transplastomic leaves was still able to transform externally added competent Acinetobacter BD413 pBAB(2) in vitro. Transformation frequencies with concentrated feces DNA were in the same range as those found with leaves (10(-4)-10(-6) transformants per recipient) or purified plasmid DNA (10(-3)-10(-7)). The presence of functionally intact DNA was also qualitatively observed after incubation of 30 mg freshly shed feces directly with competent Acinetobacter BD413 pBAB(2), demonstrating that aadA genes in feces have a potential to undergo further horizontal gene transfer under environmental conditions.}, }
@article {pmid17961484, year = {2007}, author = {Simpson, DJ and Fry, JC and Rogers, HJ and Day, MJ}, title = {Transformation of Acinetobacter baylyi in non-sterile soil using recombinant plant nuclear DNA.}, journal = {Environmental biosafety research}, volume = {6}, number = {1-2}, pages = {101-112}, doi = {10.1051/ebr:2007024}, pmid = {17961484}, issn = {1635-7922}, mesh = {Acinetobacter/*genetics ; DNA, Plant/*genetics ; DNA, Recombinant ; Gene Transfer, Horizontal ; Plant Leaves/genetics ; Plant Roots/genetics ; Seedlings/genetics ; Soil Microbiology ; *Transformation, Bacterial ; }, abstract = {To provide estimates of horizontal gene transfer from transgenic crops to indigenous soil bacteria, transformation frequencies were obtained for naturally transformable Acinetobacter baylyi BD413 using a chromosomally integrated plant transgene. The transgene comprised sequences for two phenotypic markers: kanamycin resistance (npt II) and green fluorescent protein (gfp), expressed from their own bacterial promoters. Recipient bacteria carried a copy of these two genes, with deletions in their 3'-termini abolishing the marker activity, these genes were integrated into a 16S rRNA gene in the bacterial chromosomal genome or carried on a broad host range plasmid. Successful recombination between the plant transgene and the bacterial genome resulted in restoration of the markers, allowing detection through antibiotic selection and fluorescence. Transformation parameters of increasing complexity, without any enrichment steps, were used to approach the field conditions, while still obtaining measurable transformation frequencies. In pure culture filter experiments, transformation was detected using ground, chopped and whole leaves, as well as whole sterile seedlings, and ground roots. In sterile soil microcosms, transformation was detected using pure plant DNA (3.6 x 10(-8) transformants per recipient) and ground leaves (2.5 x 10(-11)). Transformation was also detected for the first time in non-sterile soil using pure plant DNA (5.5 x 10(-11)). Since the same constructs were used throughout, these data allow predictions of even more complex environmental systems where measurable frequencies are not easily obtainable.}, }
@article {pmid17961483, year = {2007}, author = {Richter, B and Smalla, K}, title = {Screening of rhizosphere and soil bacteria for transformability.}, journal = {Environmental biosafety research}, volume = {6}, number = {1-2}, pages = {91-99}, doi = {10.1051/ebr:2007035}, pmid = {17961483}, issn = {1635-7922}, mesh = {Blotting, Southern ; Gene Transfer, Horizontal ; Plant Roots/genetics/*microbiology ; Plasmids/genetics ; Polymerase Chain Reaction ; Soil Microbiology ; Transformation, Bacterial/*genetics ; }, abstract = {Natural transformation is assumed to be the most likely mechanism by which DNA from transgenic plants could be horizontally transferred to bacteria. In order to determine the occurrence of naturally transformable bacteria amongst bulk and rhizosphere soil bacteria, different transformation strategies were employed using either plasmid DNA (IncQ plasmids pSM1890 and pSM1885, conferring GFP, Sm(r), Gm(r) and GFP, Sm(r), Tc(r), respectively) or genomic DNA from rhizosphere isolates, which were chromosomally tagged with mini-Tn5 (GFP, Tc(r)), as transforming DNA. Transformation assays were done in microtiter plates (262 isolates and pSM1890 or pSM1885), on filters (i) with rhizosphere bacterial community mixed with pSM1890 or pSM1885, (ii) with 24 rhizosphere or soil bacterial isolates mixed with genomic DNA of the corresponding mini-Tn5-tagged strains, and in the rhizosphere of tobacco plants inoculated with rifampicin-resistant bacterial isolates and genomic DNA of the corresponding mini-Tn5-tagged strains added. One transformant colony was obtained when Brevundimonas vesicularis was transformed with genomic DNA of the corresponding mini-Tn5-tagged strain. Attempts to reproduce this result were unsuccessful. With this single exception, transformants were neither detected in the collection of isolates nor in the rhizosphere bacterial community. Acinetobacter baylyi BD413 used as a positive control showed drastically reduced transformation frequencies with plasmid pSM1890 as transforming DNA when mixed with the rhizosphere pellet. All transformants were characterized by BOX-PCR fingerprints, and three different BOX patterns were revealed. Sequencing the 16S rRNA gene showed that all transformants could be assigned to Acinetobacter sp. Since transformants were only observed in the positive control, the introduced BD413 either underwent genomic rearrangements, or competence of the Acinetobacter population present in the rhizosphere was stimulated by the introduction of BD413. The various transformation assays performed indicate that the proportion of rhizosphere or bulk soil bacteria which are naturally transformable is negligibly low.}, }
@article {pmid17961481, year = {2007}, author = {Monier, JM and Bernillon, D and Kay, E and Faugier, A and Rybalka, O and Dessaux, Y and Simonet, P and Vogel, TM}, title = {Detection of potential transgenic plant DNA recipients among soil bacteria.}, journal = {Environmental biosafety research}, volume = {6}, number = {1-2}, pages = {71-83}, doi = {10.1051/ebr:2007036}, pmid = {17961481}, issn = {1635-7922}, mesh = {Acinetobacter/genetics ; DNA, Plant/*genetics ; Gene Transfer, Horizontal ; Plants, Genetically Modified/*genetics ; Plasmids/genetics ; *Soil Microbiology ; Nicotiana/genetics ; Transformation, Bacterial ; Transgenes/genetics ; }, abstract = {The likelihood of gene transfer from transgenic plants to bacteria is dependent on gene number and the presence of homologous sequences. The large number of transgene copies in transplastomic (transgenes contained in the chloroplast genome) plant cells as well as the prokaryotic origin of the transgene, may thus significantly increase the likelihood of gene transfer to bacteria that colonize plant tissues. In order to assess the probability of such transfer, the length of homologous DNA sequences required between the transgene and the genome of the bacterial host was assessed. In addition, the probability that bacteria, which co-infect diseased plants, are transformable and have sequences similar to the flanking regions of the transgene was evaluated. Using Acinetobacter baylyi strain BD143 and transplastomic tobacco plants harboring the aadA gene (streptomycin and spectinomycin resistance), we found that sequences identical to the flanking regions containing as few as 55 nucleotides were sufficient for recombination to occur. Consequently, a collection of bacterial isolates able to colonize tobacco plant tissue infected by Ralstonia solanacearum strain K60 was obtained, screened for DNA sequence similarity with the chloroplastic genes accD and rbcL flanking the transgene, and tested for their ability to uptake extracellular DNA (broad host-range pBBR1MCS plasmids) by natural or electro-transformation. Results showed that among the 288 bacterial isolates tested, 8% presented DNA sequence similarity with one or both chloroplastic regions flanking the transgene. Two isolates, identified as Pseudomonas sp. and Acinetobacter sp., were able to integrate exogenous plasmid DNA by electro-transformation and natural transformation, respectively. Our data suggest that transplastomic plant DNA recipients might be present in soil bacterial communities.}, }
@article {pmid17961480, year = {2007}, author = {Simpson, DJ and Dawson, LF and Fry, JC and Rogers, HJ and Day, MJ}, title = {Influence of flanking homology and insert size on the transformation frequency of Acinetobacter baylyi BD413.}, journal = {Environmental biosafety research}, volume = {6}, number = {1-2}, pages = {55-69}, doi = {10.1051/ebr:2007027}, pmid = {17961480}, issn = {1635-7922}, mesh = {Acinetobacter/*genetics ; Gene Transfer, Horizontal ; Models, Genetic ; Plasmids/genetics ; *Transformation, Bacterial ; }, abstract = {RecA-mediated recombination requires regions of homology between donor and recipient DNA for successful integration. This paper investigates the effect of the relationship between the length of gene-sized inserts (434, 733, 2228 and 2400 bp) and flanking sequence homology (100 - ca. 11 000 bp) on transformation frequency in Acinetobacter baylyi strain BD413. Both insert size and size of the homologous region were varied, which improves on previous studies that kept insert size constant and varied only the homologous flank size. Transfer frequency of a non-homologous single small gene for gentamicin resistance (aac(3)I; 773 bp) was increased 18-fold when flanking homology was changed from about 2000 bp to 8000 bp, but was reduced 234-fold when two genes were inserted (nptII-gfp; 2400 bp) between similar homologous regions. To investigate the effect of smaller regions of flanking homology (100 - 2000 bp), a partial nptII-gfp deletion (434 bp) was restored. This confirmed that a minimum of 500 bp on each flank was required for transformation to be affected by flanking homology. The data obtained allowed development of a multiple regression equation to predict transformation frequency from homology, insert size and total fragment size for gene insertions. We also show that the ratio of flanking homology to insert size and not the total size of donor DNA is the most important variable determining transformation frequency. The equation developed was consistent with results previously reported by others, and so will be useful when using A. baylyi as a model for gene transfer by transformation in the laboratory, environment and for biosafety.}, }
@article {pmid17961479, year = {2007}, author = {Nielsen, KM and Johnsen, PJ and Bensasson, D and Daffonchio, D}, title = {Release and persistence of extracellular DNA in the environment.}, journal = {Environmental biosafety research}, volume = {6}, number = {1-2}, pages = {37-53}, doi = {10.1051/ebr:2007031}, pmid = {17961479}, issn = {1635-7922}, mesh = {Bacteria/genetics ; DNA, Bacterial/*analysis/genetics ; DNA, Plant/*analysis/genetics ; *Gene Transfer, Horizontal ; Soil Microbiology ; Water Microbiology ; }, abstract = {The introduction of genetically modified organisms (GMOs) has called for an improved understanding of the fate of DNA in various environments, because extracellular DNA may also be important for transferring genetic information between individuals and species. Accumulating nucleotide sequence data suggest that acquisition of foreign DNA by horizontal gene transfer (HGT) is of considerable importance in bacterial evolution. The uptake of extracellular DNA by natural transformation is one of several ways bacteria can acquire new genetic information given sufficient size, concentration and integrity of the DNA. We review studies on the release, breakdown and persistence of bacterial and plant DNA in soil, sediment and water, with a focus on the accessibility of the extracellular nucleic acids as substrate for competent bacteria. DNA fragments often persist over time in many environments, thereby facilitating their detection and characterization. Nevertheless, the long-term physical persistence of DNA fragments of limited size observed by PCR and Southern hybridization often contrasts with the short-term availability of extracellular DNA to competent bacteria studied in microcosms. The main factors leading to breakdown of extracellular DNA are presented. There is a need for improved methods for accurately determining the degradation routes and the persistence, integrity and potential for horizontal transfer of DNA released from various organisms throughout their lifecycles.}, }
@article {pmid17961478, year = {2007}, author = {Pontiroli, A and Simonet, P and Frostegard, A and Vogel, TM and Monier, JM}, title = {Fate of transgenic plant DNA in the environment.}, journal = {Environmental biosafety research}, volume = {6}, number = {1-2}, pages = {15-35}, doi = {10.1051/ebr:2007037}, pmid = {17961478}, issn = {1635-7922}, mesh = {DNA, Plant/*genetics ; *Gene Transfer, Horizontal ; Models, Biological ; Plants, Genetically Modified/*genetics/microbiology ; Soil Microbiology ; }, abstract = {This review addresses the possible ecological effects of transgenic plants on micro-organisms in the field, hence, in the phytosphere and in the soil matrix. The important steps involved in the interaction between plant DNA and bacteria and the factors that influence the horizontal gene transfer (HGT) process will be discussed. HGT is a process in which two partners are involved, even if indirectly. In the first section, aspects concerning bacteria, such as their physico-chemical, biological and genetic characteristics, are described. Parameters affecting transgenic DNA fate in the environment are described in the second section. Subsequently, terrestrial habitats are evaluated in terms of their capacity to favor horizontal gene transfer. Finally, we focused on several studies in order to evaluate possible perturbations of soil bacterial community composition due to cultivation of transgenic plants in the field.}, }
@article {pmid17961477, year = {2007}, author = {Heuer, H and Smalla, K}, title = {Horizontal gene transfer between bacteria.}, journal = {Environmental biosafety research}, volume = {6}, number = {1-2}, pages = {3-13}, doi = {10.1051/ebr:2007034}, pmid = {17961477}, issn = {1635-7922}, mesh = {Bacteria/*genetics ; Ecosystem ; *Gene Transfer, Horizontal ; Plants/microbiology ; Soil Microbiology ; }, abstract = {Horizontal gene transfer (HGT) refers to the acquisition of foreign genes by organisms. The occurrence of HGT among bacteria in the environment is assumed to have implications in the risk assessment of genetically modified bacteria which are released into the environment. First, introduced genetic sequences from a genetically modified bacterium could be transferred to indigenous micro-organisms and alter their genome and subsequently their ecological niche. Second, the genetically modified bacterium released into the environment might capture mobile genetic elements (MGE) from indigenous micro-organisms which could extend its ecological potential. Thus, for a risk assessment it is important to understand the extent of HGT and genome plasticity of bacteria in the environment. This review summarizes the present state of knowledge on HGT between bacteria as a crucial mechanism contributing to bacterial adaptability and diversity. In view of the use of GM crops and microbes in agricultural settings, in this mini-review we focus particularly on the presence and role of MGE in soil and plant-associated bacteria and the factors affecting gene transfer.}, }
@article {pmid17959756, year = {2008}, author = {Carattoli, A and García-Fernández, A and Varesi, P and Fortini, D and Gerardi, S and Penni, A and Mancini, C and Giordano, A}, title = {Molecular epidemiology of Escherichia coli producing extended-spectrum beta-lactamases isolated in Rome, Italy.}, journal = {Journal of clinical microbiology}, volume = {46}, number = {1}, pages = {103-108}, pmid = {17959756}, issn = {1098-660X}, mesh = {Anti-Bacterial Agents/pharmacology ; Cluster Analysis ; Cross Infection/epidemiology/microbiology/transmission ; DNA Fingerprinting ; DNA, Bacterial/genetics ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/*classification/*drug effects/genetics/isolation &amp; purification ; Escherichia coli Infections/*epidemiology/*microbiology/transmission ; Gene Transfer, Horizontal ; Genomic Islands ; Genotype ; Hospitals, University ; Humans ; Microbial Sensitivity Tests ; Molecular Epidemiology ; Plasmids ; Rome/epidemiology ; beta-Lactamases/*biosynthesis/genetics ; }, abstract = {Escherichia coli strains producing extended-spectrum beta-lactamases (ESBLs) are a major problem in many different hospitals worldwide, causing outbreaks as well as sporadic infections. The prevalence of Escherichia coli ESBL producers was analyzed in a surveillance study performed on the population attending the Policlinico Umberto I, the largest university hospital in Rome, Italy. We also investigated genotypes, pathogenicity islands, and plasmids in the ESBL-positive E. coli isolates as further markers that are useful in describing the epidemiology of the infections. In this survey, 163 nonreplicate isolates of Escherichia coli were isolated from patients from 86 different wards, and 28 were confirmed as ESBL producers. A high prevalence (26/28) of CTX-M-15 producers was observed within the bacterial population circulating in this hospital, and the dissemination of this genetic trait was associated with the spread of related strains; however, these do not have the characteristics of a single epidemic clone spreading. The dissemination was also linked to horizontal transfer among the prevalent E. coli genotypes of multireplicon plasmids showing FIA, FIB, and FII replicons in various combinations, which are well adapted to the E. coli species. The analysis of related bacteria suggests a probable interpatient transmission occurring in several wards, causing small outbreaks.}, }
@article {pmid17958910, year = {2007}, author = {Nascimento, AS and Catalano-Dupuy, DL and Bernardes, A and Neto, Mde O and Santos, MA and Ceccarelli, EA and Polikarpov, I}, title = {Crystal structures of Leptospira interrogans FAD-containing ferredoxin-NADP+ reductase and its complex with NADP+.}, journal = {BMC structural biology}, volume = {7}, number = {}, pages = {69}, pmid = {17958910}, issn = {1472-6807}, mesh = {Amino Acid Sequence ; Aspartic Acid/chemistry ; Bacteria/enzymology ; Binding Sites ; Crystallography, X-Ray ; Escherichia coli/genetics ; Ferredoxin-NADP Reductase/*chemistry/isolation &amp; purification/metabolism ; Flavin-Adenine Dinucleotide/*chemistry/*metabolism ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Kinetics ; Leptospira interrogans/*enzymology ; Models, Molecular ; Molecular Sequence Data ; NADP/*metabolism ; Plants/enzymology ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Scattering, Small Angle ; Sequence Homology, Amino Acid ; Temperature ; X-Ray Diffraction ; }, abstract = {BACKGROUND: Ferredoxin-NADP(H) reductases (FNRs) are flavoenzymes that catalyze the electron transfer between NADP(H) and the proteins ferredoxin or flavodoxin. A number of structural features distinguish plant and bacterial FNRs, one of which is the mode of the cofactor FAD binding. Leptospira interrogans is a spirochaete parasitic bacterium capable of infecting humans and mammals in general. Leptospira interrogans FNR (LepFNR) displays low sequence identity with plant (34% with Zea mays) and bacterial (31% with Escherichia coli) FNRs. However, LepFNR contains all consensus sequences that define the plastidic class FNRs.<br><br>RESULTS: The crystal structures of the FAD-containing LepFNR and the complex of the enzyme with NADP+, were solved and compared to known FNRs. The comparison reveals significant structural similarities of the enzyme with the plastidic type FNRs and differences with the bacterial enzymes. Our small angle X-ray scattering experiments show that LepFNR is a monomeric enzyme. Moreover, our biochemical data demonstrate that the LepFNR has an enzymatic activity similar to those reported for the plastidic enzymes and that is significantly different from bacterial flavoenzymes, which display lower turnover rates.<br><br>CONCLUSION: LepFNR is the first plastidic type FNR found in bacteria and, despite of its low sequence similarity with plastidic FNRs still displays high catalytic turnover rates. The typical structural and biochemical characteristics of plant FNRs unveiled for LepFNR support a notion of a putative lateral gene transfer which presumably offers Leptospira interrogans evolutionary advantages. The wealth of structural information about LepFNR provides a molecular basis for advanced drugs developments against leptospirosis.}, }
@article {pmid17957239, year = {2007}, author = {Fall, S and Mercier, A and Bertolla, F and Calteau, A and Gueguen, L and Perrière, G and Vogel, TM and Simonet, P}, title = {Horizontal gene transfer regulation in bacteria as a "spandrel" of DNA repair mechanisms.}, journal = {PloS one}, volume = {2}, number = {10}, pages = {e1055}, pmid = {17957239}, issn = {1932-6203}, mesh = {Bacteria/genetics ; Computational Biology/methods ; *DNA Repair ; Evolution, Molecular ; *Gene Expression Regulation ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Variation ; *Genome, Bacterial ; Models, Biological ; Models, Genetic ; Phylogeny ; Plasmids/metabolism ; Ralstonia solanacearum/*genetics ; Recombination, Genetic ; }, abstract = {Horizontal gene transfer (HGT) is recognized as the major force for bacterial genome evolution. Yet, numerous questions remain about the transferred genes, their function, quantity and frequency. The extent to which genetic transformation by exogenous DNA has occurred over evolutionary time was initially addressed by an in silico approach using the complete genome sequence of the Ralstonia solanacearum GMI1000 strain. Methods based on phylogenetic reconstruction of prokaryote homologous genes families detected 151 genes (13.3%) of foreign origin in the R. solanacearum genome and tentatively identified their bacterial origin. These putative transfers were analyzed in comparison to experimental transformation tests involving 18 different genomic DNA positions in the genome as sites for homologous or homeologous recombination. Significant transformation frequency differences were observed among these positions tested regardless of the overall genomic divergence of the R. solanacearum strains tested as recipients. The genomic positions containing the putative exogenous DNA were not systematically transformed at the highest frequencies. The two genomic "hot spots", which contain recA and mutS genes, exhibited transformation frequencies from 2 to more than 4 orders of magnitude higher than positions associated with other genes depending on the recipient strain. These results support the notion that the bacterial cell is equipped with active mechanisms to modulate acquisition of new DNA in different genomic positions. Bio-informatics study correlated recombination "hot-spots" to the presence of Chi-like signature sequences with which recombination might be preferentially initiated. The fundamental role of HGT is certainly not limited to the critical impact that the very rare foreign genes acquired mainly by chance can have on the bacterial adaptation potential. The frequency to which HGT with homologous and homeologous DNA happens in the environment might have led the bacteria to hijack DNA repair mechanisms in order to generate genetic diversity without losing too much genomic stability.}, }
@article {pmid17957119, year = {2008}, author = {Mater, DD and Langella, P and Corthier, G and Flores, MJ}, title = {A probiotic Lactobacillus strain can acquire vancomycin resistance during digestive transit in mice.}, journal = {Journal of molecular microbiology and biotechnology}, volume = {14}, number = {1-3}, pages = {123-127}, doi = {10.1159/000106091}, pmid = {17957119}, issn = {1464-1801}, mesh = {Animals ; Bacterial Proteins/genetics ; Carbon-Oxygen Ligases/genetics ; *Conjugation, Genetic ; Enterococcus faecium/*genetics ; Gastrointestinal Tract/*microbiology ; Gene Transfer, Horizontal ; Humans ; Lactobacillus acidophilus/*genetics ; Mice ; Mice, Inbred C3H ; Probiotics/*administration &amp; dosage ; Vancomycin Resistance/*genetics ; }, abstract = {The present study demonstrates for the first time the transfer of vancomycin resistance (vanA cluster) from enterococci to a Lactobacillusacidophilus commercial strain. Transfers were observed in vitro, but also in vivo in the gut of mice (in the absence of antibiotic pressure) where transconjugants arose at relatively high frequencies and could persist in the digestive environment. Since transfer of vancomycin resistance genes might also take place in the human digestive tract, lactobacilli probiotics should be carefully considered especially in either immunocompromised patients or during antibiotherapy. Acquisition and retransfer of resistance genes should be addressed in the safety evaluation of probiotics.}, }
@article {pmid17953777, year = {2007}, author = {Jangid, K and Kong, R and Patole, MS and Shouche, YS}, title = {luxRI homologs are universally present in the genus Aeromonas.}, journal = {BMC microbiology}, volume = {7}, number = {}, pages = {93}, pmid = {17953777}, issn = {1471-2180}, mesh = {Aeromonas/classification/*genetics ; Bacterial Proteins/*genetics ; Base Sequence ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Quorum Sensing/genetics ; Repressor Proteins/*genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Trans-Activators/*genetics ; Transcription Factors/*genetics ; }, abstract = {BACKGROUND: Aeromonas spp. have been regarded as "emerging pathogens". Aeromonads possess multifactorial virulence and the production of many of these virulence determinants is associated with high cell density, a phenomenon that might be regulated by quorum sensing. However, only two species of the genus are reported to possess the luxRI quorum sensing gene homologs. The purpose of this study was to investigate if the luxRI homologs are universally present in the Aeromonas strains collected from various culture collections, clinical laboratories and field studies.<br><br>RESULTS: Of all the 73 Aeromonas strains used in the study, seventy-one strains elicited acyl-homoserine lactone-mediated response in multiple biosensor strains. However, dot blot hybridization revealed that the luxRI homologs are present in all the strains. PCR amplification and sequencing revealed that the luxRI homologs shared a very high percentage sequence similarity. No evidence for lateral gene transfer of the luxRI homologs between aeromonads and other genera was noted.<br><br>CONCLUSION: We propose that the luxRI quorum sensing gene homologs are universally present in the genus Aeromonas independently from their origin. This study is the first genus-wide report of the taxonomic distribution of the luxRI homologs.}, }
@article {pmid17951101, year = {2007}, author = {D'Costa, VM and Griffiths, E and Wright, GD}, title = {Expanding the soil antibiotic resistome: exploring environmental diversity.}, journal = {Current opinion in microbiology}, volume = {10}, number = {5}, pages = {481-489}, doi = {10.1016/j.mib.2007.08.009}, pmid = {17951101}, issn = {1369-5274}, mesh = {Anti-Bacterial Agents/metabolism ; Bacteria/classification/*drug effects/genetics/metabolism ; Biodiversity ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genomics ; Phylogeny ; *Soil Microbiology ; }, abstract = {Antibiotic resistance has largely been studied in the context of failure of the drugs in clinical settings. There is now growing evidence that bacteria that live in the environment (e.g. the soil) are multi-drug-resistant. Recent functional screens and the growing accumulation of metagenomic databases are revealing an unexpected density of resistance genes in the environment: the antibiotic resistome. This challenges our current understanding of antibiotic resistance and provides both barriers and opportunities for antimicrobial drug discovery.}, }
@article {pmid17949441, year = {2007}, author = {Monecke, S and Slickers, P and Ellington, MJ and Kearns, AM and Ehricht, R}, title = {High diversity of Panton-Valentine leukocidin-positive, methicillin-susceptible isolates of Staphylococcus aureus and implications for the evolution of community-associated methicillin-resistant S. aureus.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {13}, number = {12}, pages = {1157-1164}, doi = {10.1111/j.1469-0691.2007.01833.x}, pmid = {17949441}, issn = {1198-743X}, mesh = {Bacterial Toxins/*genetics ; Bacterial Typing Techniques ; Community-Acquired Infections/*microbiology ; *Evolution, Molecular ; Exotoxins/*genetics ; Gene Transfer, Horizontal ; *Genetic Variation ; Genotype ; Germany ; Humans ; Leukocidins/*genetics ; Methicillin Resistance/*genetics ; Microarray Analysis ; Oligonucleotide Array Sequence Analysis ; Staphylococcal Infections/*microbiology ; Staphylococcus aureus/*classification/genetics/isolation &amp; purification ; Virulence Factors/genetics ; }, abstract = {In total, 100 Staphylococcus aureus isolates from diverse cases of skin and soft-tissue infection at a university hospital in Saxony, Germany, were characterised using diagnostic microarrays. Virulence factors, including Panton-Valentine leukocidin (PVL), were detected and the isolates were assigned to clonal groups. Thirty isolates were positive for the genes encoding PVL. Only three PVL-positive methicillin-resistant S. aureus (MRSA) isolates were found, two of which belonged to European clone ST80-MRSA IV and one to USA300 strain ST8-MRSA IV. The remaining methicillin-susceptible PVL-positive isolates belonged to a variety of different multilocus sequence types. The predominant strains were agrI/ST22, agrII/CC5, agrIII/CC30 and agrIV/ST121. In order to check for possible bias caused by regional or local outbreak strains, an additional 18 methicillin-susceptible, PVL-positive isolates from the UK were tested. Approximately two-thirds of the UK isolates belonged to types that also comprised approximately two-thirds of the isolates from Saxony. Some methicillin-susceptible PVL-positive isolates (agrI/ST152, agrIII/ST80 and agrIII/ST96) closely resembled known epidemic community-acquired MRSA (CaMRSA) strains. These findings indicate that the current rise in PVL-positive CaMRSA could be caused by the dissemination of novel SCCmec elements among pre-existing PVL-positive strains, rather than by the spread of PVL phages among MRSA strains.}, }
@article {pmid17947550, year = {2007}, author = {Sorek, R and Zhu, Y and Creevey, CJ and Francino, MP and Bork, P and Rubin, EM}, title = {Genome-wide experimental determination of barriers to horizontal gene transfer.}, journal = {Science (New York, N.Y.)}, volume = {318}, number = {5855}, pages = {1449-1452}, doi = {10.1126/science.1147112}, pmid = {17947550}, issn = {1095-9203}, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; Cloning, Molecular ; Computational Biology ; Escherichia coli/*genetics ; Gene Dosage ; *Gene Transfer, Horizontal ; *Genes, Archaeal ; *Genes, Bacterial ; Genetic Speciation ; Genome, Archaeal ; Genome, Bacterial ; Phylogeny ; }, abstract = {Horizontal gene transfer, in which genetic material is transferred from the genome of one organism to that of another, has been investigated in microbial species mainly through computational sequence analyses. To address the lack of experimental data, we studied the attempted movement of 246,045 genes from 79 prokaryotic genomes into Escherichia coli and identified genes that consistently fail to transfer. We studied the mechanisms underlying transfer inhibition by placing coding regions from different species under the control of inducible promoters. Our data suggest that toxicity to the host inhibited transfer regardless of the species of origin and that increased gene dosage and associated increased expression may be a predominant cause for transfer failure. Although these experimental studies examined transfer solely into E. coli, a computational analysis of gene-transfer rates across available bacterial and archaeal genomes supports that the barriers observed in our study are general across the tree of life.}, }
@article {pmid17947403, year = {2007}, author = {Biedler, JK and Shao, H and Tu, Z}, title = {Evolution and horizontal transfer of a DD37E DNA transposon in mosquitoes.}, journal = {Genetics}, volume = {177}, number = {4}, pages = {2553-2558}, pmid = {17947403}, issn = {0016-6731}, support = {R01 AI042121/AI/NIAID NIH HHS/United States ; R29 AI042121/AI/NIAID NIH HHS/United States ; AI42121/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; Conserved Sequence ; Culicidae/*genetics ; DNA Transposable Elements/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Phylogeny ; }, abstract = {ITmD37E, a unique class II transposable element (TE) with an ancient origin, appears to have been involved in multiple horizontal transfers in mosquitoes as ITmD37E sequences from 10 mosquito species of five genera share high nucleotide (nt) identities. For example, ITmD37E sequences from Aedes aegypti and Anopheles gambiae, which have an estimated common ancestor of 145-200 million years ago, display 92% nt identity. The comparison of ITmD37E and host mosquito phylogenies shows a lack of congruence. The wide distribution of conserved ITmD37Es in mosquitoes and the presence of intact copies suggest that this element may have been recently active.}, }
@article {pmid17943120, year = {2007}, author = {Pallen, MJ and Wren, BW}, title = {Bacterial pathogenomics.}, journal = {Nature}, volume = {449}, number = {7164}, pages = {835-842}, doi = {10.1038/nature06248}, pmid = {17943120}, issn = {1476-4687}, support = {EGA16167/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacteria/*genetics/*pathogenicity ; Gene Deletion ; Gene Transfer, Horizontal ; Genome, Bacterial/*genetics ; *Genomics ; Host-Pathogen Interactions ; Humans ; }, abstract = {Genomes from all of the crucial bacterial pathogens of humans, plants and animals have now been sequenced, as have genomes from many of the important commensal, symbiotic and environmental microorganisms. Analysis of these sequences has revealed the forces that shape pathogen evolution and has brought to light unexpected aspects of pathogen biology. The finding that horizontal gene transfer and genome decay have key roles in the evolution of bacterial pathogens was particularly surprising. It has also become evident that even the definitions for 'pathogen' and 'virulence factor' need to be re-evaluated.}, }
@article {pmid17942681, year = {2007}, author = {Bergthorsson, U and Andersson, DI and Roth, JR}, title = {Ohno's dilemma: evolution of new genes under continuous selection.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {43}, pages = {17004-17009}, pmid = {17942681}, issn = {0027-8424}, support = {P20 RR018754/RR/NCRR NIH HHS/United States ; R01 GM027068/GM/NIGMS NIH HHS/United States ; GM 27068/GM/NIGMS NIH HHS/United States ; P20 RR 18754/RR/NCRR NIH HHS/United States ; }, mesh = {*Biological Evolution ; *Gene Amplification ; Gene Duplication ; Gene Frequency ; Gene Transfer, Horizontal ; Genetic Variation ; *Models, Genetic ; Point Mutation ; Recombination, Genetic ; *Selection, Genetic ; }, abstract = {New genes with novel functions arise by duplication and divergence, but the process poses a problem. After duplication, an extra gene copy must rise to sufficiently high frequency in the population and remain free of common inactivating lesions long enough to acquire the rare mutations that provide a new selectable function. Maintaining a duplicated gene by selection for the original function would restrict the freedom to diverge. (We refer to this problem as Ohno's dilemma). A model is described by which selection continuously favors both maintenance of the duplicate copy and divergence of that copy from the parent gene. Before duplication, the original gene has a trace side activity (the innovation) in addition to its original function. When an altered ecological niche makes the minor innovation valuable, selection favors increases in its level (the amplification), which is most frequently conferred by increased dosage of the parent gene. Selection for the amplified minor function maintains the extra copies and raises the frequency of the amplification in the population. The same selection favors mutational improvement of any of the extra copies, which are not constrained to maintain their original function (the divergence). The rate of mutations (per genome) that improve the new function is increased by the multiplicity of target copies within a genome. Improvement of some copies relaxes selection on others and allows their loss by mutation (becoming pseudogenes). Ultimately one of the extra copies is able to provide all of the new activity.}, }
@article {pmid17942428, year = {2007}, author = {Pilhofer, M and Bauer, AP and Schrallhammer, M and Richter, L and Ludwig, W and Schleifer, KH and Petroni, G}, title = {Characterization of bacterial operons consisting of two tubulins and a kinesin-like gene by the novel Two-Step Gene Walking method.}, journal = {Nucleic acids research}, volume = {35}, number = {20}, pages = {e135}, pmid = {17942428}, issn = {1362-4962}, mesh = {Bacteria/*genetics ; Chromosome Mapping/*methods ; *Genes, Bacterial ; Kinesins ; *Operon ; Polymerase Chain Reaction ; Tubulin/*genetics ; }, abstract = {Tubulins are still considered as typical proteins of Eukaryotes. However, more recently they have been found in the unusual bacteria Prosthecobacter (btubAB). In this study, the genomic organization of the btub-genes and their genomic environment were characterized by using the newly developed Two-Step Gene Walking method. In all investigated Prosthecobacters, btubAB are organized in a typical bacterial operon. Strikingly, all btub-operons comprise a third gene with similarities to kinesin light chain sequences. The genomic environments of the characterized btub-operons are always different. This supports the hypothesis that this group of genes represents an independent functional unit, which was acquired by Prosthecobacter via horizontal gene transfer. The newly developed Two-Step Gene Walking method is based on randomly primed polymerase chain reaction (PCR). It presents a simple workflow, which comprises only two major steps--a Walking-PCR with a single specific outward pointing primer (step 1) and the direct sequencing of its product using a nested specific primer (step 2). Two-Step Gene Walking proved to be highly efficient and was successfully used to characterize over 20 kb of sequence not only in pure culture but even in complex non-pure culture samples.}, }
@article {pmid17938913, year = {2007}, author = {Wang, Y and Xiao, M and Geng, X and Liu, J and Chen, J}, title = {Horizontal transfer of genetic determinants for degradation of phenol between the bacteria living in plant and its rhizosphere.}, journal = {Applied microbiology and biotechnology}, volume = {77}, number = {3}, pages = {733-739}, doi = {10.1007/s00253-007-1187-2}, pmid = {17938913}, issn = {0175-7598}, mesh = {Bacteria/genetics/isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Conjugation, Genetic ; *Gene Transfer, Horizontal ; Phenol/*metabolism ; Phylogeny ; Plant Roots/*microbiology ; *Plasmids ; Soil Microbiology ; Zea mays/*microbiology ; }, abstract = {Phenol and other monocyclic aromatic compounds (MACs) are highly water-soluble and volatile pollutants that plants are unable to completely degrade. Endophytic bacteria with MAC-degrading ability will facilitate phytoremediation, beneficial to plant survival in contaminated soil. Endophytic bacteria, strains FX1-FX3, and rhizosphere bacteria, strains FX0, FX4, and FX5, were isolated from the root tissue of a corn plant (Zea mays) and the corn rhizosphere near a chemical plant, respectively. The strains FX1-FX5 were able to grow on phenol and reduce phenol concentration, but the strain FX0 was unable to. The strains FX1, FX3, and FX4 were classified as Pseudomonas fluorescens and FX0, FX2, and FX5 as Burkholderia cepacia. The plasmids isolated from the strains FX1-FX5 were found to possess similar traits and to be loaded with a gene encoding the catechol 2, 3-dioxygenase (C23O), a key enzyme in the phenol degradation pathway. Alignment and phylogenetic analysis inferred that in situ horizontal transfer of the C23O gene might have occurred. The horizontal transfer of the C23O gene between endophytic and rhizosphere bacteria was proved by using conjugal matings experiment, in which the transconjugants were found to acquire the plasmid with the C23O gene, able to grow on phenol and degrade phenol.}, }
@article {pmid17936488, year = {2008}, author = {Dvorák, J and Mashiyama, ST and Braschi, S and Sajid, M and Knudsen, GM and Hansell, E and Lim, KC and Hsieh, I and Bahgat, M and Mackenzie, B and Medzihradszky, KF and Babbitt, PC and Caffrey, CR and McKerrow, JH}, title = {Differential use of protease families for invasion by schistosome cercariae.}, journal = {Biochimie}, volume = {90}, number = {2}, pages = {345-358}, doi = {10.1016/j.biochi.2007.08.013}, pmid = {17936488}, issn = {0300-9084}, support = {N01-AI-30026/AI/NIAID NIH HHS/United States ; P41 RR01081/RR/NCRR NIH HHS/United States ; R01 AI053247/AI/NIAID NIH HHS/United States ; R01 GM60595/GM/NIGMS NIH HHS/United States ; RR001614/RR/NCRR NIH HHS/United States ; RR015804/RR/NCRR NIH HHS/United States ; RR019934/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Cathepsin B/chemistry/*metabolism ; Chymotrypsin/metabolism ; Gene Transfer, Horizontal ; Larva/enzymology/pathogenicity ; Mass Spectrometry ; Phylogeny ; Proteomics ; Schistosoma japonicum/*enzymology/growth &amp; development/pathogenicity ; Schistosoma mansoni/*enzymology ; Schistosomatidae/enzymology ; Serine Endopeptidases/classification/genetics/*metabolism ; Species Specificity ; }, abstract = {Schistosomes are parasitic platyhelminths (flatworms) of birds and mammals. As a parasitic disease of humans, schistosomiasis ranks second only to malaria in global importance. Schistosome larvae (cercariae) must invade and penetrate skin as an initial step to successful infection of the vertebrate host. Proteolytic enzymes secreted from the acetabular glands of cercariae contribute significantly to the invasion process. In this comparative study, we analyzed protease activities secreted by cercariae of Schistosoma mansoni, Schistosoma japonicum and Schistosomatium douthitti. Using protease-family specific, irreversible active-site probes, fluorogenic peptidyl substrates, immuno-histochemistry and high-resolution mass spectrometry, considerable species differences were noted in the quantity and character of proteases. Serine proteases, the most abundant enzymes secreted by S. mansoni cercariae, were not identified in S. japonicum. In contrast, the acetabular gland contents of S. japonicum cercariae had a 40-fold greater cathepsin B-like activity than those of S. mansoni. Based on the present data and previous reports, we propose that cysteine proteases represent an archetypal tool for tissue invasion among primitive metazoa and the use of serine proteases arose later in schistosome evolution. Computational analysis of serine protease phylogeny revealed an extraordinarily distant relationship between S. mansoni serine proteases and other members of the Clan PA family S1 proteases.}, }
@article {pmid17933912, year = {2008}, author = {Hunt, DE and Gevers, D and Vahora, NM and Polz, MF}, title = {Conservation of the chitin utilization pathway in the Vibrionaceae.}, journal = {Applied and environmental microbiology}, volume = {74}, number = {1}, pages = {44-51}, pmid = {17933912}, issn = {1098-5336}, mesh = {Acetylglucosamine/metabolism ; Bacterial Proteins/genetics ; Chitin/*metabolism ; Chitinases/genetics ; Conserved Sequence ; DNA, Bacterial/chemistry/genetics ; Metabolic Networks and Pathways/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Vibrionaceae/*genetics/growth &amp; development/*metabolism ; }, abstract = {Vibrionaceae are regarded as important marine chitin degraders, and attachment to chitin regulates important biological functions; yet, the degree of chitin pathway conservation in Vibrionaceae is unknown. Here, a core chitin degradation pathway is proposed based on comparison of 19 Vibrio and Photobacterium genomes with a detailed metabolic map assembled for V. cholerae from published biochemical, genomic, and transcriptomic results. Further, to assess whether chitin degradation is a conserved property of Vibrionaceae, a set of 54 strains from 32 taxa were tested for the ability to grow on various forms of chitin. All strains grew on N-acetylglucosamine (GlcNAc), the monomer of chitin. The majority of isolates grew on alpha (crab shell) and beta (squid pen) chitin and contained chitinase A (chiA) genes. chiA sequencing and phylogenetic analysis suggest that this gene is a good indicator of chitin metabolism but appears subject to horizontal gene transfer and duplication. Overall, chitin metabolism appears to be a core function of Vibrionaceae, but individual pathway components exhibit dynamic evolutionary histories.}, }
@article {pmid17933899, year = {2007}, author = {Kim, TJ and Chauhan, S and Motin, VL and Goh, EB and Igo, MM and Young, GM}, title = {Direct transcriptional control of the plasminogen activator gene of Yersinia pestis by the cyclic AMP receptor protein.}, journal = {Journal of bacteriology}, volume = {189}, number = {24}, pages = {8890-8900}, pmid = {17933899}, issn = {1098-5530}, support = {R21 AI067676/AI/NIAID NIH HHS/United States ; AI067676/AI/NIAID NIH HHS/United States ; AI156042/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/*biosynthesis ; Binding Sites/genetics ; Cyclic AMP/metabolism ; Cyclic AMP Receptor Protein/*physiology ; DNA Footprinting ; DNA, Bacterial/genetics/metabolism ; Electrophoretic Mobility Shift Assay ; Gene Deletion ; *Gene Expression Regulation, Bacterial ; Mutagenesis, Insertional ; Plasminogen Activators/*biosynthesis ; Promoter Regions, Genetic ; Protein Binding ; Yersinia pestis/*genetics/metabolism ; }, abstract = {Horizontal gene transfer events followed by proper regulatory integration of a gene drive rapid evolution of bacterial pathogens. A key event in the evolution of the highly virulent plague bacterium Yersinia pestis was the acquisition of plasmid pPCP1, which carries the plasminogen activator gene, pla. This promoted the bubonic form of the disease by increasing bacterial dissemination from flea bite sites and incidentally enhanced replication in respiratory airways during pneumonic infection. We determined that expression of pla is controlled by the global regulator cyclic AMP (cAMP) receptor protein (Crp). This transcription factor is well conserved among distantly related bacteria, where it acts as a soluble receptor for the ubiquitous signaling molecule cAMP and controls a global network of metabolic and stress-protective genes. Crp has a similar physiological role in Y. pestis since loss of its function resulted in an inability to metabolize a variety of nonglucose substrates. Activation of pla expression requires a transcription activation element of the pla promoter that serves as a Crp binding site. Crp interaction with this site was demonstrated to occur only in the presence of cAMP. Alteration of the Crp binding site nucleotide sequence prevented in vitro formation of Crp-DNA complexes and inhibited in vivo expression of pla. The placement of pla under direct regulatory control of Crp highlights how highly adapted pathogens integrate laterally acquired genes to coordinate virulence factor expression with global gene networks to maintain homeostasis through the infectious life cycle.}, }
@article {pmid17933898, year = {2007}, author = {Tuanyok, A and Auerbach, RK and Brettin, TS and Bruce, DC and Munk, AC and Detter, JC and Pearson, T and Hornstra, H and Sermswan, RW and Wuthiekanun, V and Peacock, SJ and Currie, BJ and Keim, P and Wagner, DM}, title = {A horizontal gene transfer event defines two distinct groups within Burkholderia pseudomallei that have dissimilar geographic distributions.}, journal = {Journal of bacteriology}, volume = {189}, number = {24}, pages = {9044-9049}, pmid = {17933898}, issn = {1098-5530}, support = {/WT_/Wellcome Trust/United Kingdom ; U54 AI065359/AI/NIAID NIH HHS/United States ; }, mesh = {Australia/epidemiology ; Burkholderia pseudomallei/*classification/*genetics/isolation &amp; purification ; Chromosomes, Bacterial/genetics ; DNA, Bacterial/chemistry/genetics ; Environmental Microbiology ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genotype ; Humans ; Melioidosis/epidemiology/microbiology ; Molecular Epidemiology ; Molecular Sequence Data ; Multigene Family ; Sequence Analysis, DNA ; Sequence Homology ; Synteny ; Thailand/epidemiology ; }, abstract = {Burkholderia pseudomallei is the etiologic agent of melioidosis. Many disease manifestations are associated with melioidosis, and the mechanisms causing this variation are unknown; genomic differences among strains offer one explanation. We compared the genome sequences of two strains of B. pseudomallei: the original reference strain K96243 from Thailand and strain MSHR305 from Australia. We identified a variable homologous region between the two strains. This region was previously identified in comparisons of the genome of B. pseudomallei strain K96243 with the genome of strain E264 from the closely related B. thailandensis. In that comparison, K96243 was shown to possess a horizontally acquired Yersinia-like fimbrial (YLF) gene cluster. Here, we show that the homologous genomic region in B. pseudomallei strain 305 is similar to that previously identified in B. thailandensis strain E264. We have named this region in B. pseudomallei strain 305 the B. thailandensis-like flagellum and chemotaxis (BTFC) gene cluster. We screened for these different genomic components across additional genome sequences and 571 B. pseudomallei DNA extracts obtained from regions of endemicity. These alternate genomic states define two distinct groups within B. pseudomallei: all strains contained either the BTFC gene cluster (group BTFC) or the YLF gene cluster (group YLF). These two groups have distinct geographic distributions: group BTFC is dominant in Australia, and group YLF is dominant in Thailand and elsewhere. In addition, clinical isolates are more likely to belong to group YLF, whereas environmental isolates are more likely to belong to group BTFC. These groups should be further characterized in an animal model.}, }
@article {pmid17931970, year = {2008}, author = {John, U and Beszteri, B and Derelle, E and Van de Peer, Y and Read, B and Moreau, H and Cembella, A}, title = {Novel insights into evolution of protistan polyketide synthases through phylogenomic analysis.}, journal = {Protist}, volume = {159}, number = {1}, pages = {21-30}, doi = {10.1016/j.protis.2007.08.001}, pmid = {17931970}, issn = {1434-4610}, mesh = {Animals ; Chlamydomonas reinhardtii/enzymology/genetics ; Chlorophyta/classification/enzymology/genetics ; *Evolution, Molecular ; Fatty Acid Synthases/genetics ; Genomics/*methods ; *Phylogeny ; Polyketide Synthases/*genetics ; }, abstract = {Polyketide synthase (PKS) enzymes are large multi-domain complexes that structurally and functionally resemble the fatty acid synthases involved in lipid metabolism. Polyketide biosynthesis of secondary metabolites and hence functional PKS genes are widespread among bacteria, fungi and streptophytes, but the Type I was formerly known only from bacteria and fungi. Recently Type I PKS genes were also uncovered in the genomes of some alveolate protists. Here we show that the newly sequenced genomes of representatives of other protist groups, specifically the chlorophytes Ostreococcus tauri, O. lucimarinus, and Chlamydomonas reinhardtii, and the haptophyte Emiliania huxleyi also contain putative modular Type I PKS genes. Based on the patchy phylogenetic distribution of this gene type among eukaryotic microorganisms, the question arises whether they originate from recent lateral gene transfer from bacteria. Our phylogenetic analyses do not indicate such an evolutionary history. Whether Type I PKS genes originated several times independently during eukaryotic evolution or were rather lost in many extant lineages cannot yet be answered. In any case, we show that environmental genome sequencing projects are likely to be a valuable resource when mining for genes resembling protistan PKS I genes.}, }
@article {pmid17921485, year = {2007}, author = {Snyder, LA and McGowan, S and Rogers, M and Duro, E and O'Farrell, E and Saunders, NJ}, title = {The repertoire of minimal mobile elements in the Neisseria species and evidence that these are involved in horizontal gene transfer in other bacteria.}, journal = {Molecular biology and evolution}, volume = {24}, number = {12}, pages = {2802-2815}, doi = {10.1093/molbev/msm215}, pmid = {17921485}, issn = {0737-4038}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Bacteria/*genetics ; DNA, Intergenic/genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Interspersed Repetitive Sequences/*genetics ; Models, Genetic ; Molecular Sequence Data ; Neisseria/*genetics ; Protein Sorting Signals ; Sequence Analysis, DNA ; }, abstract = {In the Neisseria spp., natural competence for transformation and homologous recombination generate antigenic variants through creation of mosaic genes (such as opas) and through recombination with silent cassettes (such as pilE/pilS) and gene-complement diversity through the horizontal exchange of whole genes or groups of genes, in minimal mobile elements (MMEs). An MME is a region encompassing 2 conserved genes between which different whole-gene cassettes are found in different strains, which are chromosomally incorporated solely through the action of homologous recombination. Comparative analyses of the neisserial genome sequences identified 39 potential MME sites, the contents of which were investigated in 11 neisserial strains. One hundred and eight different MME regions were identified, 20 of which contain novel sequences and these contain 12 newly identified neisserial coding sequences. Neisserial uptake signal sequences are associated with 38 of the 40 MMEs studied. In some sites, divergent dinucleotide signatures of the sequences between the flanking genes suggest relatively recent horizontal acquisition of some cassettes. The neisserial MMEs were used to interrogate all of the other available bacterial genome sequences, revealing frequent conservation of the flanking genes combined with the presence of different gene cassettes between them. In some cases, these sites can definitively be classified as MMEs in these other genera. These findings provide additional evidence for the MME model, indicate that MME-directed investigations are a good basis for the identification of novel strain-specific genes and differences within bacterial populations and demonstrate that these elements are probably ubiquitously involved in genetic exchange, particularly in naturally competent bacteria.}, }
@article {pmid17921483, year = {2007}, author = {Malik, SB and Ramesh, MA and Hulstrand, AM and Logsdon, JM}, title = {Protist homologs of the meiotic Spo11 gene and topoisomerase VI reveal an evolutionary history of gene duplication and lineage-specific loss.}, journal = {Molecular biology and evolution}, volume = {24}, number = {12}, pages = {2827-2841}, doi = {10.1093/molbev/msm217}, pmid = {17921483}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Animals ; Archaeal Proteins ; Conserved Sequence ; DNA Topoisomerases, Type II/chemistry/*genetics ; Endodeoxyribonucleases ; Esterases/chemistry/*genetics ; Eukaryotic Cells/enzymology ; *Evolution, Molecular ; *Gene Duplication ; *Meiosis ; Molecular Sequence Data ; *Phylogeny ; Prokaryotic Cells/enzymology ; Sequence Alignment ; *Sequence Homology, Nucleic Acid ; }, abstract = {Spo11 is a meiotic protein of fundamental importance as it is a conserved meiosis-specific transesterase required for meiotic recombination initiation in fungi, animals, and plants. Spo11 is homologous to the archaebacterial topoisomerase VIA (Top6A) gene, and its homologs are broadly distributed among eukaryotes, with some eukaryotes having more than one homolog. However, the evolutionary relationships among these genes are unclear, with some debate as to whether eukaryotic homologs originated by lateral gene transfer. We have identified and characterized protist Spo11 homologs by degenerate polymerase chain reaction (PCR) and sequencing and by analyses of sequences from public databases. Our phylogenetic analyses show that Spo11 homologs evolved by two ancient eukaryotic gene duplication events prior to the last common ancestor of extant eukaryotes, resulting in three eukaryotic paralogs: Spo11-1, Spo11-2, and Spo11-3. Spo11-1 orthologs encode meiosis-specific proteins and are distributed broadly among eukaryotic lineages, though Spo11-1 is absent from some protists. This absence coincides with the presence of Spo11-2 orthologs, which are meiosis-specific in Arabidopsis and are found in plants, red algae, and some protists but absent in animals and fungi. Spo11-3 encodes a Top6A subunit that interacts with topoisomerase VIB (Top6B) subunits, which together play a role in vegetative growth in Arabidopsis. We identified Spo11-3 (Top6A) and Top6B homologs in plants, red algae, and a few protists, establishing a broader distribution of these genes among eukaryotes, indicating their likely vertical descent followed by lineage-specific loss.}, }
@article {pmid17921289, year = {2007}, author = {Cherif-Zahar, B and Durand, A and Schmidt, I and Hamdaoui, N and Matic, I and Merrick, M and Matassi, G}, title = {Evolution and functional characterization of the RH50 gene from the ammonia-oxidizing bacterium Nitrosomonas europaea.}, journal = {Journal of bacteriology}, volume = {189}, number = {24}, pages = {9090-9100}, pmid = {17921289}, issn = {1098-5530}, mesh = {Ammonia/*metabolism ; Bacterial Proteins/*genetics/*metabolism ; Evolution, Molecular ; Gene Deletion ; Membrane Glycoproteins/*genetics/*metabolism ; Nitrosomonas europaea/*genetics/*physiology ; Phylogeny ; Sequence Homology, Amino Acid ; }, abstract = {The family of ammonia and ammonium channel proteins comprises the Amt proteins, which are present in all three domains of life with the notable exception of vertebrates, and the homologous Rh proteins (Rh50 and Rh30) that have been described thus far only in eukaryotes. The existence of an RH50 gene in bacteria was first revealed by the genome sequencing of the ammonia-oxidizing bacterium Nitrosomonas europaea. Here we have used a phylogenetic approach to study the evolution of the N. europaea RH50 gene, and we show that this gene, probably as a component of an integron cassette, has been transferred to the N. europaea genome by horizontal gene transfer. In addition, by functionally characterizing the Rh50(Ne) protein and the corresponding knockout mutant, we determined that NeRh50 can mediate ammonium uptake. The RH50(Ne) gene may thus have replaced functionally the AMT gene, which is missing in the genome of N. europaea and may be regarded as a case of nonorthologous gene displacement.}, }
@article {pmid17921284, year = {2007}, author = {Rounge, TB and Rohrlack, T and Tooming-Klunderud, A and Kristensen, T and Jakobsen, KS}, title = {Comparison of cyanopeptolin genes in Planktothrix, Microcystis, and Anabaena strains: evidence for independent evolution within each genus.}, journal = {Applied and environmental microbiology}, volume = {73}, number = {22}, pages = {7322-7330}, pmid = {17921284}, issn = {0099-2240}, mesh = {ATP-Binding Cassette Transporters/genetics ; Anabaena/genetics ; Chromatography, Liquid ; Cyanobacteria/classification/*genetics ; Depsipeptides/chemistry/*genetics ; *Evolution, Molecular ; Mass Spectrometry ; Microcystis/genetics ; Molecular Sequence Data ; Molecular Structure ; *Multigene Family ; Peptides, Cyclic/chemistry/*genetics ; Phylogeny ; }, abstract = {The major cyclic peptide cyanopeptolin 1138, produced by Planktothrix strain NIVA CYA 116, was characterized and shown to be structurally very close to the earlier-characterized oscillapeptin E. A cyanopeptolin gene cluster likely to encode the corresponding peptide synthetase was sequenced from the same strain. The 30-kb oci gene cluster contains two novel domains previously not detected in nonribosomal peptide synthetase gene clusters (a putative glyceric acid-activating domain and a sulfotransferase domain), in addition to seven nonribosomal peptide synthetase modules. Unlike in two previously described cyanopeptolin gene clusters from Anabaena and Microcystis, a halogenase gene is not present. The three cyanopeptolin gene clusters show similar gene and domain arrangements, while the binding pocket signatures deduced from the adenylation domain sequences and the additional tailoring domains vary. This suggests loss and gain of tailoring domains within each genus, after the diversification of the three clades, as major events leading to the present diversity. The ABC transporter genes associated with the cyanopeptolin gene clusters form a monophyletic clade and accordingly are likely to have evolved as part of the functional unit. Phylogenetic analyses of adenylation and condensation domains, including domains from cyanopeptolins and microcystins, show a closer similarity between the Planktothrix and Microcystis cyanopeptolin domains than between these and the Anabaena domain. No clear evidence of recombination between cyanopeptolins and microcystins could be detected. There were no strong indications of horizontal gene transfer of cyanopeptolin gene sequences across the three genera, supporting independent evolution within each genus.}, }
@article {pmid17921255, year = {2007}, author = {Chen, G and Jeffrey, PD and Fuqua, C and Shi, Y and Chen, L}, title = {Structural basis for antiactivation in bacterial quorum sensing.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {42}, pages = {16474-16479}, pmid = {17921255}, issn = {0027-8424}, support = {R01 GM065260/GM/NIGMS NIH HHS/United States ; GM065260-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Agrobacterium tumefaciens/*physiology ; Amino Acid Sequence ; Bacterial Proteins/*chemistry/genetics/metabolism ; Crystallography, X-Ray ; Molecular Sequence Data ; Protein Conformation ; *Quorum Sensing ; Repressor Proteins/*chemistry/genetics/metabolism ; }, abstract = {Bacteria can communicate via diffusible signal molecules they generate and release to coordinate their behavior in response to the environment. Signal molecule concentration is often proportional to bacterial population density, and when this reaches a critical concentration, reflecting a bacterial quorum, specific behaviors including virulence, symbiosis, and horizontal gene transfer are activated. Quorum-sensing regulation in many Gram-negative bacteria involves acylated homoserine lactone signals that are perceived through binding to LuxR-type, acylated-homoserine-lactone-responsive transcription factors. Bacteria of the rhizobial group employ the LuxR-type transcriptional activator TraR in quorum sensing, and its activity is further regulated through interactions with the TraM antiactivator. In this study, we have crystallographically determined the 3D structure of the TraR-TraM antiactivation complex from Rhizobium sp. strain NGR234. Unexpectedly, the antiactivator TraM binds to TraR at a site distinct from its DNA-binding motif and induces an allosteric conformational change in the protein, thereby preventing DNA binding. Structural analysis reveals a highly conserved TraR-TraM interface and suggests a mechanism for antiactivation complex formation. This structure may inform alternative strategies to control quorum-sensing-regulated microbial activity including amelioration of infectious disease and antibiotic resistance. In addition, the structural basis of antiactivation presents a regulatory interaction that provides general insights relevant to the field of transcription regulation and signal transduction.}, }
@article {pmid17919288, year = {2007}, author = {Thomas, J and Hecht, DW}, title = {Interaction of Bacteroides fragilis pLV22a relaxase and transfer DNA with Escherichia coli RP4-TraG coupling protein.}, journal = {Molecular microbiology}, volume = {66}, number = {4}, pages = {948-960}, pmid = {17919288}, issn = {0950-382X}, support = {R01 AI050122/AI/NIAID NIH HHS/United States ; R01 AI050122-01A1/AI/NIAID NIH HHS/United States ; AI050122/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/metabolism ; Bacteroides fragilis/genetics/*metabolism ; *Conjugation, Genetic ; DNA Helicases/genetics/*metabolism ; DNA, Bacterial/genetics/*metabolism ; Escherichia coli/genetics/metabolism ; Escherichia coli Proteins/genetics/*metabolism ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genetic Complementation Test ; Immunoprecipitation ; Membrane Proteins/genetics/*metabolism ; Mutation ; Plasmids/genetics ; }, abstract = {Many Bacteroides transfer factors are mobilizable in Escherichia coli when coresident with the IncP conjugative plasmid RP4, but not F. To begin characterization and potential interaction between Bacteroides mobilizable transfer factors and the RP4 mating channel, both mutants and deletions of the DNA processing (dtr), mating pair formation (mpf) and traG coupling genes of RP4 were tested for mobilization of Bacteroides plasmid pLV22a. All 10 mpf but none of the four dtr genes were required for mobilization of pLV22a. The RP4 TraG coupling protein (CP) was also required for mobilization of pLV22a, but could be substituted by a C-terminal deletion mutant of the F TraD CP. Potential interactions of the TraG CP with relaxase protein(s) and transfer DNA of both RP4 and pLV22a were assessed. Overlay assays identified productive interactions between TraG and the relaxase proteins of both MbpB and TraI from pLV22a and RP4 respectively. The Agrobacterium Transfer-ImmunoPrecipitation (TrIP) assay also identified an interaction between TraG and both RP4 and pLV22a transfer DNA. Thus, mobilization of the Bacteroides pLV22a in E. coli utilizes both RP4 Mpf and CP functions including an interaction between the relaxosome and the RP4 CP similar to that of cognate RP4 plasmid.}, }
@article {pmid17918619, year = {2007}, author = {van der Does, HC and Rep, M}, title = {Virulence genes and the evolution of host specificity in plant-pathogenic fungi.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {20}, number = {10}, pages = {1175-1182}, doi = {10.1094/MPMI-20-10-1175}, pmid = {17918619}, issn = {0894-0282}, mesh = {*Evolution, Molecular ; Fungal Proteins/genetics/physiology ; Fungi/genetics/*pathogenicity/physiology ; *Genes, Fungal ; Models, Biological ; Multigene Family ; Plant Diseases/microbiology ; Plants/*microbiology ; Species Specificity ; Virulence Factors/*genetics ; }, abstract = {In the fungal kingdom, the ability to cause disease in plants appears to have arisen multiple times during evolution. In many cases, the ability to infect particular plant species depends on specific genes that distinguish virulent fungi from their sometimes closely related nonvirulent relatives. These genes encode host-determining "virulence factors," including small, secreted proteins and enzymes involved in the synthesis of toxins. These virulence factors typically are involved in evolutionary arms races between plants and pathogens. We briefly summarize current knowledge of these virulence factors from several fungal species in terms of function, phylogenetic distribution, sequence variation, and genomic location. Second, we address some issues that are relevant to the evolution of virulence in fungi toward plants; in particular, horizontal gene transfer and the genomic organization of virulence genes.}, }
@article {pmid17916642, year = {2007}, author = {Blanc, G and Ogata, H and Robert, C and Audic, S and Claverie, JM and Raoult, D}, title = {Lateral gene transfer between obligate intracellular bacteria: evidence from the Rickettsia massiliae genome.}, journal = {Genome research}, volume = {17}, number = {11}, pages = {1657-1664}, pmid = {17916642}, issn = {1088-9051}, mesh = {*Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; Multigene Family ; Phylogeny ; Rickettsia/*genetics ; Rickettsia Infections/genetics ; }, abstract = {Rickettsia massiliae is a tick-borne obligate intracellular alpha-proteobacteria causing spotted fever in humans. Here, we present the sequence of its genome, comprising a 1.3-Mb circular chromosome and a 15.3-kb plasmid. The chromosome exhibits long-range colinearity with the other Spotted Fever Group Rickettsia genomes, except for a large fragment specific to R. massiliae that contains 14 tra genes presumably involved in pilus formation and conjugal DNA transfer. We demonstrate that the tra region was acquired recently by lateral gene transfer (LGT) from a species related to Rickettsia bellii. Further analysis of the genomic sequences identifies additional candidates of LGT between Rickettsia. Our study indicates that recent LGT between obligate intracellular Rickettsia is more common than previously thought.}, }
@article {pmid17916580, year = {2007}, author = {Kurokawa, K and Itoh, T and Kuwahara, T and Oshima, K and Toh, H and Toyoda, A and Takami, H and Morita, H and Sharma, VK and Srivastava, TP and Taylor, TD and Noguchi, H and Mori, H and Ogura, Y and Ehrlich, DS and Itoh, K and Takagi, T and Sakaki, Y and Hayashi, T and Hattori, M}, title = {Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {14}, number = {4}, pages = {169-181}, pmid = {17916580}, issn = {1340-2838}, mesh = {Adult ; Child, Preschool ; Cluster Analysis ; Female ; Gastrointestinal Tract/*metabolism/*microbiology ; *Genes, Bacterial ; *Genomics ; Humans ; Infant ; Intestines ; Male ; Metagenome/*genetics ; Middle Aged ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Numerous microbes inhabit the human intestine, many of which are uncharacterized or uncultivable. They form a complex microbial community that deeply affects human physiology. To identify the genomic features common to all human gut microbiomes as well as those variable among them, we performed a large-scale comparative metagenomic analysis of fecal samples from 13 healthy individuals of various ages, including unweaned infants. We found that, while the gut microbiota from unweaned infants were simple and showed a high inter-individual variation in taxonomic and gene composition, those from adults and weaned children were more complex but showed a high functional uniformity regardless of age or sex. In searching for the genes over-represented in gut microbiomes, we identified 237 gene families commonly enriched in adult-type and 136 families in infant-type microbiomes, with a small overlap. An analysis of their predicted functions revealed various strategies employed by each type of microbiota to adapt to its intestinal environment, suggesting that these gene sets encode the core functions of adult and infant-type gut microbiota. By analysing the orphan genes, 647 new gene families were identified to be exclusively present in human intestinal microbiomes. In addition, we discovered a conjugative transposon family explosively amplified in human gut microbiomes, which strongly suggests that the intestine is a 'hot spot' for horizontal gene transfer between microbes.}, }
@article {pmid17913717, year = {2007}, author = {Machado, E and Coque, TM and Cantón, R and Novais, A and Sousa, JC and Baquero, F and Peixe, L and , }, title = {High diversity of extended-spectrum beta-lactamases among clinical isolates of Enterobacteriaceae from Portugal.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {60}, number = {6}, pages = {1370-1374}, doi = {10.1093/jac/dkm381}, pmid = {17913717}, issn = {0305-7453}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Conjugation, Genetic ; Drug Resistance, Bacterial ; Enterobacteriaceae/drug effects/*enzymology/isolation &amp; purification ; Enterobacteriaceae Infections/*epidemiology/*microbiology ; Gene Transfer, Horizontal ; Humans ; Isoelectric Focusing ; Microbial Sensitivity Tests ; Plasmids ; Polymerase Chain Reaction/methods ; Portugal/epidemiology ; beta-Lactamases/*classification/*genetics ; }, abstract = {OBJECTIVES: To investigate the occurrence and the diversity of Ambler class A ESBLs among Enterobacteriaceae from different Portuguese clinical settings over a 2 year period (2002-04).<br><br>METHODS: One hundred and nine extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae isolates from five geographically distant health institutions in Portugal were studied. ESBLs were characterized by isoelectric focussing, PCR and further sequencing. Antibiotic susceptibility testing, transfer of resistance genes and clonal diversity were determined by standard procedures. Plasmid relatedness was established by comparison of random amplified polymorphic DNA (RAPD) patterns.<br><br>RESULTS: ESBLs were identified as TEM (46%), SHV (30%), CTX-M (22%) and GES (2%) types; TEM-24, TEM-52, SHV-12 and CTX-M-15 enzymes being the most frequently found. Inter-hospital dissemination of epidemic strains harbouring the most prevalent ESBLs was detected, including the TEM-24-producing Enterobacter aerogenes European epidemic clone. Conjugative transfer of ESBLs was achieved for 67% of isolates and epidemic plasmids containing specific bla genes were detected (bla(CTX-M-15) and bla(TEM-24)). We describe two new ESBLs, SHV-90 (A187T, G238S and E240K) and SHV-91 (P20S and E240K), and a new TEM-type enzyme conferring a phenotype resembling that of a complex mutant TEM beta-lactamase, designated as TEM-154 (M69L and R164S). The broad-spectrum beta-lactamases SHV-26, SHV-36 and TEM-110 were first observed in our country.<br><br>CONCLUSIONS: We describe a complex ESBL epidemiology in Portugal, including widespread dissemination of known strains and plasmids coding for TEM-24 and CTX-M-15 enzymes as observed in other European countries.}, }
@article {pmid17913715, year = {2007}, author = {Moura, A and Henriques, I and Ribeiro, R and Correia, A}, title = {Prevalence and characterization of integrons from bacteria isolated from a slaughterhouse wastewater treatment plant.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {60}, number = {6}, pages = {1243-1250}, doi = {10.1093/jac/dkm340}, pmid = {17913715}, issn = {0305-7453}, mesh = {*Abattoirs ; Aeromonas/drug effects/enzymology/genetics/*isolation &amp; purification ; Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; Drug Resistance, Bacterial ; Enterobacteriaceae/drug effects/enzymology/genetics/*isolation &amp; purification ; *Gene Transfer, Horizontal ; Integrases/genetics ; Integrons/*genetics ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Phylogeny ; Prevalence ; Sequence Analysis, DNA ; Waste Disposal, Fluid/*methods ; *Water Microbiology ; }, abstract = {OBJECTIVES: To investigate the presence and distribution of integron-carrying bacteria from a slaughterhouse wastewater treatment plant (WWTP).<br><br>METHODS: Enterobacteriaceae and aeromonads were isolated at different stages of the wastewater treatment process and screened for the presence of integrase genes by dot-blot hybridization. Integrase-positive strains were characterized in terms of phylogenetic affiliation, genetic content of integrons and antimicrobial resistance profiles. Plasmid location of some integrons was established by Southern-blot hybridization. Strains containing integron-carrying plasmids were selected for mating experiments.<br><br>RESULTS: Integrase genes were present in all samples, including the final effluent. The global prevalence was determined to be 35%, higher than in other aquatic environments. Forty-two integrase-positive isolates were further characterized. Nine distinct cassette arrays were found, containing genes encoding resistance to beta-lactams (bla(OXA-30)), aminoglycosides (aadA1, aadA2, aadA13, aadB), streptothricin (sat1, sat2), trimethoprim (dfrA1, dfrA12), a putative esterase (estX) and a protein with unknown function (orfF). Gene cassette arrays aadA1, dfrAI-aadA1 and estX-sat2-aadA1 were common to aeromonads and Enterobacteriaceae. The class 2 integron containing an estX-sat2-aadA1 cassette array was detected for the first time in Aeromonas sp. Nearly 12% (5 out of 43) of intI genes were located in plasmids. intI genes from isolates MM.1.3 and MM.1.5 were successfully conjugated into Escherichia coli at frequencies of 3.79 x 10(-5) and 5.46 x 10(-5) per recipient cell, respectively.<br><br>CONCLUSIONS: Our data support the hypothesis that WWTPs constitute a potential hot spot for horizontal gene transfer and for selection of antimicrobial resistance genes among aquatic bacteria. Moreover, water discharges represent a possible risk for dissemination of undesirable genetic traits.}, }
@article {pmid17913434, year = {2008}, author = {Wu, JJ and Chen, HM and Ko, WC and Wu, HM and Tsai, SH and Yan, JJ}, title = {Prevalence of extended-spectrum beta-lactamases in Proteus mirabilis in a Taiwanese university hospital, 1999 to 2005: identification of a novel CTX-M enzyme (CTX-M-66).}, journal = {Diagnostic microbiology and infectious disease}, volume = {60}, number = {2}, pages = {169-175}, doi = {10.1016/j.diagmicrobio.2007.08.004}, pmid = {17913434}, issn = {0732-8893}, mesh = {Amino Acid Substitution/genetics ; Bacterial Proteins/genetics ; Bacterial Typing Techniques ; DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Electrophoresis, Gel, Pulsed-Field ; Endemic Diseases ; Gene Transfer, Horizontal ; Genotype ; Hospitals ; Humans ; Methyltransferases/genetics ; Molecular Sequence Data ; Proteus Infections/epidemiology/microbiology ; Proteus mirabilis/*enzymology/genetics/isolation &amp; purification ; Sequence Analysis, DNA ; Taiwan/epidemiology ; beta-Lactamases/classification/*genetics ; }, abstract = {A total of 1574 nonduplicate Proteus mirabilis isolates collected at a Taiwanese hospital during 1999 to 2005 were analyzed for production of extended-spectrum beta-lactamases (ESBLs). Forty-four ESBL-producing isolates including 22 CTX-M-14, 18 CTX-M-3, 2 CTX-M-24, and 2 CTX-M-66 producers were detected, and the proportion of ESBL producers increased from 0.7% in 1999 to approximately 6% after 2002. CTX-M-66 is a novel variant of CTX-M ESBLs that differs from CTX-M-3 by a Ser to Asn change at amino acid position 23. Coresistances to aminoglycosides and ciprofloxacin were very common in the CTX-M-3 producers. The presence of ArmA-type or RmtB-type 16S rRNA methylase that confers high-level aminoglycoside resistance was detected in 12 CTX-M-3 producers and 4 CTX-M-14 producers. Twenty-four clones including an endemic CTX-M-14-producing clone were observed among the 44 ESBL producers by pulsed-field gel electrophoresis, suggesting that both horizontal transfer and clonal spread contributed to the increased prevalence of bla(CTX-M) in P. mirabilis.}, }
@article {pmid17909888, year = {2007}, author = {Grudniak, AM and Kraczkiewicz-Dowjat, A and Wolska, KI and Wild, J}, title = {Conjugal transfer of plasmid R6K gamma ori minireplicon derivatives from Escherichia coli to various genera of pathogenic bacteria.}, journal = {Current microbiology}, volume = {55}, number = {6}, pages = {549-553}, pmid = {17909888}, issn = {0343-8651}, mesh = {*Conjugation, Genetic ; Escherichia coli/*genetics ; Gene Dosage ; Gene Transfer, Horizontal ; Gram-Negative Bacteria/genetics ; Listeria monocytogenes/genetics ; Plasmids/*genetics ; Replication Origin/*genetics ; Replicon/*genetics ; }, abstract = {Three R6K-derived gamma ori minireplicons were successfully transferred by conjugation from Escherichia coli to several species of pathogenic bacteria. The pFL129 replicon encodes the wild-type initiation replication protein pi, while plasmids pFL130 and pAG101 encode mutant forms of the pi protein conferring the plasmid copy-up phenotype. Plasmids could be transferred to all recipient species tested, although high efficiency conjugal transfer was only obtained with genera of the Enterobacteriaceae. The efficiency of plasmid transfer to all recipients was lower for the copy-up derivatives, pFL130 and pAG101, than for pFL129. The three gamma ori replicons were stably maintained in all transconjugants except pFL129 in Listeria monocytogenes. The two mutant plasmids retained their copy-up phenotype in the new bacterial hosts.}, }
@article {pmid17906146, year = {2007}, author = {Meyer, B and Kuever, J}, title = {Molecular analysis of the distribution and phylogeny of dissimilatory adenosine-5'-phosphosulfate reductase-encoding genes (aprBA) among sulfur-oxidizing prokaryotes.}, journal = {Microbiology (Reading, England)}, volume = {153}, number = {Pt 10}, pages = {3478-3498}, doi = {10.1099/mic.0.2007/008250-0}, pmid = {17906146}, issn = {1350-0872}, mesh = {Chlorobi/classification/enzymology/*genetics ; Chromatiaceae/classification/enzymology/*genetics ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Oxidoreductases Acting on Sulfur Group Donors/*genetics ; *Phylogeny ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Thiobacillus/classification/enzymology/*genetics ; Thiothrix/classification/enzymology/*genetics ; }, abstract = {Dissimilatory adenosine-5'-phosphosulfate (APS) reductase (AprBA) is a key enzyme of the dissimilatory sulfate-reduction pathway. Homologues have been found in photo- and chemotrophic sulfur-oxidizing prokaryotes (SOP), in which they are postulated to operate in the reverse direction, oxidizing sulfite to APS. Newly developed PCR assays allowed the amplification of 92-93 % (2.1-2.3 kb) of the APS reductase locus aprBA. PCR-based screening of 116 taxonomically divergent SOP reference strains revealed a distribution of aprBA restricted to photo- and chemotrophs with strict anaerobic or at least facultative anaerobic lifestyles, including Chlorobiaceae, Chromatiaceae, Thiobacillus, Thiothrix and invertebrate symbionts. In the AprBA-based tree, the SOP diverge into two distantly related phylogenetic lineages, Apr lineages I and II, with the proteins of lineage II (Chlorobiaceae and others) in closer affiliation to the enzymes of the sulfate-reducing prokaryotes (SRP). This clustering is discordant with the dissimilatory sulfite reductase (DsrAB) phylogeny and indicates putative lateral aprBA gene transfer from SRP to the respective SOB lineages. In support of lateral gene transfer (LGT), several beta- and gammaproteobacterial species harbour both aprBA homologues, the DsrAB-congruent 'authentic' and the SRP-related, LGT-derived gene loci, while some relatives possess exclusively the SRP-related apr genes as a possible result of resident gene displacement by the xenologue. The two-gene state might be an intermediate in the replacement of the resident essential gene. Collected genome data demonstrate the correlation between the AprBA tree topology and the composition/arrangement of the apr gene loci (occurrence of qmoABC or aprM genes) from SRP and SOP of lineages I and II. The putative functional role of the SRP-related APS reductases in photo- and chemotrophic SOP is discussed.}, }
@article {pmid17906123, year = {2007}, author = {Subedi, A and Ubeda, C and Adhikari, RP and Penadés, JR and Novick, RP}, title = {Sequence analysis reveals genetic exchanges and intraspecific spread of SaPI2, a pathogenicity island involved in menstrual toxic shock.}, journal = {Microbiology (Reading, England)}, volume = {153}, number = {Pt 10}, pages = {3235-3245}, doi = {10.1099/mic.0.2007/006932-0}, pmid = {17906123}, issn = {1350-0872}, support = {AI-R01-22159/AI/NIAID NIH HHS/United States ; }, mesh = {Chromosomes, Bacterial/genetics ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; Female ; Gene Order ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genomic Islands/*genetics ; Humans ; *Menstruation ; Molecular Sequence Data ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Shock, Septic/genetics/*microbiology ; Staphylococcal Infections/microbiology ; Staphylococcus aureus/classification/*genetics/isolation &amp; purification ; }, abstract = {SaPIs are a family of homologous phage-related pathogenicity islands in staphylococci that carry superantigen and other virulence genes, and are responsible for a wide variety of superantigen-related diseases. SaPIs are induced to excise and replicate by particular staphylococcal phages and are encapsidated in infectious, small-headed, phage-like particles, which are transmitted at very high frequency among staphylococcal strains and species. SaPI2 is a prototypical member of this family that was identified in a typical menstrual toxic shock syndrome (TSS) strain of Staphylococcus aureus, the so-called Harrisburg strain, and found to be mobilizable by typing phage 80. Most menstrual TSS strains belong to a highly uniform agr group III clone of electrophoretic type (ET) 41, and this study was undertaken to determine whether such strains typically carry SaPI2, and whether it has spread beyond the ET41 clone. We report here the complete sequence of SaPI2, describe its relation to other known SaPIs, and show that it, or a very similar element, is carried by most ET41 strains but that it has disseminated to other strains that have also been implicated in TSS. We show additionally, that SaPIs are widespread among the staphylococci and that most TSS strains carry two or more, including SaPI2.}, }
@article {pmid17905571, year = {2007}, author = {Jackson, CR and Boylan, JA and Frye, JG and Gherardini, FC}, title = {Evidence of a conjugal erythromycin resistance element in the Lyme disease spirochete Borrelia burgdorferi.}, journal = {International journal of antimicrobial agents}, volume = {30}, number = {6}, pages = {496-504}, pmid = {17905571}, issn = {0924-8579}, support = {Z01 AI000906-06/ImNIH/Intramural NIH HHS/United States ; Z99 AI999999/ImNIH/Intramural NIH HHS/United States ; AI33501/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/metabolism/*pharmacology ; Bacillus subtilis/drug effects/genetics ; Bacterial Proteins/genetics/metabolism ; Borrelia burgdorferi/*drug effects/genetics ; Conjugation, Genetic/*genetics ; Drug Resistance, Bacterial/*genetics ; Enterococcus faecalis/drug effects/genetics ; Erythromycin/metabolism/*pharmacology ; *Gene Transfer, Horizontal ; Humans ; Lincosamides ; Macrolides/pharmacology ; Microbial Sensitivity Tests ; Ribosomes/metabolism ; Streptogramin A/pharmacology ; }, abstract = {We report the identification of isolates of Borrelia burgdorferi strain B31 that exhibit an unusual macrolide-lincosamide (ML) or macrolide-lincosamide-streptogramin A (MLS(A)) antibiotic resistance pattern. Low-passage isolates were resistant to high levels (>100 microg/mL) of erythromycin, spiramycin and the lincosamides but were sensitive to dalfopristin, an analogue of streptogramin B. Interestingly, the high-passage erythromycin-resistant strain B31 was resistant to quinupristin, an analogue of streptogramin A (25 microg/mL). Biochemical analysis revealed that resistance was not due to antibiotic inactivation or energy-dependent efflux but was instead due to modification of ribosomes in these isolates. Interestingly, we were able to demonstrate high-frequency transfer of the resistance phenotype via conjugation from B. burgdorferi to Bacillus subtilis (10(-2)-10(-4)) or Enterococcus faecalis (10(-5)). An intergeneric conjugal system in B. burgdorferi suggests that horizontal gene transfer may play a role in its evolution and is a potential tool for developing new genetic systems to study the pathogenesis of Lyme disease.}, }
@article {pmid17905462, year = {2008}, author = {Fu, M and Deng, R and Wang, J and Wang, X}, title = {Detection and analysis of horizontal gene transfer in herpesvirus.}, journal = {Virus research}, volume = {131}, number = {1}, pages = {65-76}, doi = {10.1016/j.virusres.2007.08.009}, pmid = {17905462}, issn = {0168-1702}, mesh = {Computational Biology/*methods ; *Gene Transfer, Horizontal ; Genes, Viral ; Genome, Viral ; Genomics/methods ; *Herpesviridae ; Sequence Analysis, DNA ; }, abstract = {Horizontal gene transfers, where a significant proportion of the coding DNA is contributed by external sources, might give rise to extremely dynamic genomes, which brings impact on the ecological and pathogenic characters of the recipient organisms. Therefore it is important to computationally discriminate between horizontal transferred genes and normal genes. In this paper, we introduce a novel method for identifying horizontal transferred genes. This method, which relies on a gene's nucleotide composition and hence obviates the need for knowledge of codon boundaries, is able to detect the horizontal transferred genes with an accuracy of higher than 90% within a reasonable length of time by using just a common PC. With this method, 141 putative transferred genes in mammalian herpesvirus were identified. Among them, 16 genes had been predicted or reported to have cellular homologues in previous papers, including those involved in immune systems and apoptosis such as GCR in EHV-2, BCL-2 (Bcelllymphoma/leukemia-2) homologue in MuHV-4, etc., and had been suggested being acquired from other organisms. Other 125 genes were identified for the first time. Twelve of the newly identified putative transferred genes had also been reported to participate in immune response, apoptosis, cell proliferation control or virulence determinant. Moreover, 42 of the 141 putative transferred genes were found to have non-virus homologues and so were convincingly revealed as transferred genes. Nine of the 42 transferred genes were phylogenetically analyzed, the origin and the relative origin time of which were discussed.}, }
@article {pmid17901334, year = {2007}, author = {Morrison, HG and McArthur, AG and Gillin, FD and Aley, SB and Adam, RD and Olsen, GJ and Best, AA and Cande, WZ and Chen, F and Cipriano, MJ and Davids, BJ and Dawson, SC and Elmendorf, HG and Hehl, AB and Holder, ME and Huse, SM and Kim, UU and Lasek-Nesselquist, E and Manning, G and Nigam, A and Nixon, JE and Palm, D and Passamaneck, NE and Prabhu, A and Reich, CI and Reiner, DS and Samuelson, J and Svard, SG and Sogin, ML}, title = {Genomic minimalism in the early diverging intestinal parasite Giardia lamblia.}, journal = {Science (New York, N.Y.)}, volume = {317}, number = {5846}, pages = {1921-1926}, doi = {10.1126/science.1143837}, pmid = {17901334}, issn = {1095-9203}, support = {AI43273/AI/NIAID NIH HHS/United States ; R01 HG004164/HG/NHGRI NIH HHS/United States ; AI42488/AI/NIAID NIH HHS/United States ; R01 AI054693/AI/NIAID NIH HHS/United States ; AI51687/AI/NIAID NIH HHS/United States ; R01 AI048082/AI/NIAID NIH HHS/United States ; R01 HG004164-01/HG/NHGRI NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; *Biological Evolution ; DNA Replication/genetics ; *Eukaryotic Cells ; Gene Transfer, Horizontal ; Genes, Protozoan ; *Genome, Protozoan ; Genomics ; Giardia lamblia/classification/*genetics/physiology ; Metabolic Networks and Pathways/genetics ; Molecular Sequence Data ; Phylogeny ; Protein Kinases/genetics/metabolism ; Protozoan Proteins/chemistry/genetics/metabolism ; RNA Processing, Post-Transcriptional ; Signal Transduction ; Transcription, Genetic ; }, abstract = {The genome of the eukaryotic protist Giardia lamblia, an important human intestinal parasite, is compact in structure and content, contains few introns or mitochondrial relics, and has simplified machinery for DNA replication, transcription, RNA processing, and most metabolic pathways. Protein kinases comprise the single largest protein class and reflect Giardia's requirement for a complex signal transduction network for coordinating differentiation. Lateral gene transfer from bacterial and archaeal donors has shaped Giardia's genome, and previously unknown gene families, for example, cysteine-rich structural proteins, have been discovered. Unexpectedly, the genome shows little evidence of heterozygosity, supporting recent speculations that this organism is sexual. This genome sequence will not only be valuable for investigating the evolution of eukaryotes, but will also be applied to the search for new therapeutics for this parasite.}, }
@article {pmid17899790, year = {2007}, author = {Benedek, O and Schubert, S}, title = {Mobility of the Yersinia High-Pathogenicity Island (HPI): transfer mechanisms of pathogenicity islands (PAIS) revisited (a review).}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {54}, number = {2}, pages = {89-105}, doi = {10.1556/AMicr.54.2007.2.1}, pmid = {17899790}, issn = {1217-8950}, mesh = {*Gene Transfer, Horizontal ; Genomic Islands/*genetics ; Humans ; Yersinia/classification/*genetics ; }, abstract = {Horizontal gene transfer (HGT) plays a key role in the evolution of bacterial pathogens. The exchange of genetic material supplies prokaryotes with several fitness traits enhancing their adaptive response to environmental changes. Pathogenicity islands (PAIs) represent an important and in most cases already immobilized subset of the different vehicles for HGT. Encoding several virulence factors PAls represent a major contribution to bacterial pathogenicity. Nonetheless, the transfer mechanisms of PAIs still remain elusive. We summarise the currently available data regarding the major ways of genetic mobilisation with a focus on the transfer of the Yersinia High-Pathogenicity Island (HPI).}, }
@article {pmid17894863, year = {2007}, author = {Nosenko, T and Bhattacharya, D}, title = {Horizontal gene transfer in chromalveolates.}, journal = {BMC evolutionary biology}, volume = {7}, number = {}, pages = {173}, pmid = {17894863}, issn = {1471-2148}, mesh = {Animals ; Cell Line ; Dinoflagellida/enzymology/*genetics/metabolism ; Energy Metabolism ; Expressed Sequence Tags ; *Gene Transfer, Horizontal ; *Genome, Protozoan ; Isoenzymes/genetics ; Mutant Chimeric Proteins/genetics ; Oxidoreductases/genetics ; *Phylogeny ; Protozoan Proteins/*genetics ; Transaminases/genetics ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT), the non-genealogical transfer of genetic material between different organisms, is considered a potentially important mechanism of genome evolution in eukaryotes. Using phylogenomic analyses of expressed sequence tag (EST) data generated from a clonal cell line of a free living dinoflagellate alga Karenia brevis, we investigated the impact of HGT on genome evolution in unicellular chromalveolate protists.<br><br>RESULTS: We identified 16 proteins that have originated in chromalveolates through ancient HGTs before the divergence of the genera Karenia and Karlodinium and one protein that was derived through a more recent HGT. Detailed analysis of the phylogeny and distribution of identified proteins demonstrates that eight have resulted from independent HGTs in several eukaryotic lineages.<br><br>CONCLUSION: Recurring intra- and interdomain gene exchange provides an important source of genetic novelty not only in parasitic taxa as previously demonstrated but as we show here, also in free-living protists. Investigating the tempo and mode of evolution of horizontally transferred genes in protists will therefore advance our understanding of mechanisms of adaptation in eukaryotes.}, }
@article {pmid17890367, year = {2007}, author = {Lili, LN and Britton, NF and Feil, EJ}, title = {The persistence of parasitic plasmids.}, journal = {Genetics}, volume = {177}, number = {1}, pages = {399-405}, pmid = {17890367}, issn = {0016-6731}, mesh = {Bacteria/*classification/*genetics/growth &amp; development ; Bacterial Proteins/genetics ; *Conjugation, Genetic ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; Models, Biological ; Plasmids/*genetics ; Species Specificity ; }, abstract = {The conditions under which plasmids are predicted to persist remain controversial. Here, we reevaluate the ordinary differential equations used previously to model plasmid persistence and conclude that the parameter space required for maintenance is far less stringent than has been supposed. Strikingly, our model demonstrates that purely parasitic plasmids may persist, even in the absence of heterogeneity in the host population, and that this persistence is expressed by oscillations or damped oscillations between the plasmid-bearing and the plasmid-free class.}, }
@article {pmid17888731, year = {2008}, author = {Glöckner, G and Albert-Weissenberger, C and Weinmann, E and Jacobi, S and Schunder, E and Steinert, M and Hacker, J and Heuner, K}, title = {Identification and characterization of a new conjugation/type IVA secretion system (trb/tra) of Legionella pneumophila Corby localized on two mobile genomic islands.}, journal = {International journal of medical microbiology : IJMM}, volume = {298}, number = {5-6}, pages = {411-428}, doi = {10.1016/j.ijmm.2007.07.012}, pmid = {17888731}, issn = {1618-0607}, mesh = {Amino Acid Sequence ; Bacterial Proteins/*genetics ; Base Sequence ; Carrier Proteins/*genetics ; Conjugation, Genetic/*genetics/physiology ; DNA, Bacterial/chemistry/genetics/*metabolism ; Gene Order ; Genes, Bacterial ; Genomic Islands ; Humans ; *Interspersed Repetitive Sequences ; Legionella pneumophila/*genetics/isolation &amp; purification/*metabolism ; Legionnaires' Disease/microbiology ; Models, Biological ; Molecular Sequence Data ; RNA, Bacterial/genetics ; RNA, Transfer, Pro/genetics ; Recombination, Genetic ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Horizontal gene transfer probably contributes to evolution of Legionella pneumophila and its adaptation to different environments. Although horizontal gene transfer was observed in Legionella, the mechanism is still not specified. In this study we identified and analysed a new type of conjugation/type IVA secretion system (trb/tra) of L. pneumophila Corby, a virulent human isolate. Two similar versions of this conjugation system were identified, localized on two different genomic islands (Trb-1, 42,710 bp and Trb-2, 34,434 bp). Trb-1 and Trb-2 are integrated within the tRNA(Pro) gene (lpc2778) and the tmRNA gene (lpc0164), respectively. Both islands exhibit an oriT region and both can be excised from the chromosome forming episomal circles. Trb-1 was analysed in more detail. It is active and can be horizontally transferred to other Legionella strains by conjugation and then integrated into the genome in a site-specific manner within the tRNA(Pro) gene. We characterized the sequence of the excision and integration sites of Trb-1 in three different L. pneumophila strains. Here we demonstrate that L. pneumophila exhibits a functional oriT region and that genomic islands in Legionella can be mobilized and conjugated to other species of Legionella. Thus, we describe for the first time a mechanism that may explain the observed horizontal transfer of chromosomal DNA in Legionella.}, }
@article {pmid17883338, year = {2007}, author = {Phale, PS and Basu, A and Majhi, PD and Deveryshetty, J and Vamsee-Krishna, C and Shrivastava, R}, title = {Metabolic diversity in bacterial degradation of aromatic compounds.}, journal = {Omics : a journal of integrative biology}, volume = {11}, number = {3}, pages = {252-279}, doi = {10.1089/omi.2007.0004}, pmid = {17883338}, issn = {1536-2310}, mesh = {Bacteria, Aerobic/genetics/*metabolism ; Biodegradation, Environmental ; Carbon/chemistry/metabolism ; *Genomics ; Hydrocarbons, Aromatic/chemistry/*metabolism ; Oxidation-Reduction ; Surface-Active Agents/metabolism ; }, abstract = {Aromatic compounds pose a major threat to the environment, being mutagenic, carcinogenic, and recalcitrant. Microbes, however, have evolved the ability to utilize these highly reduced and recalcitrant compounds as a potential source of carbon and energy. Aerobic degradation of aromatics is initiated by oxidizing the aromatic ring, making them more susceptible to cleavage by ring-cleaving dioxygenases. A preponderance of aromatic degradation genes on plasmids, transposons, and integrative genetic elements (and their shuffling through horizontal gene transfer) have lead to the evolution of novel aromatic degradative pathways. This enables the microorganisms to utilize a multitude of aromatics via common routes of degradation leading to metabolic diversity. In this review, we emphasize the exquisiteness and relevance of bacterial degradation of aromatics, interlinked degradative pathways, genetic and metabolic regulation, carbon source preference, and biosurfactant production. We have also explored the avenue of metagenomics, which opens doors to a plethora of uncultured and uncharted microbial genetics and metabolism that can be used effectively for bioremediation.}, }
@article {pmid17881821, year = {2007}, author = {Sato, Y and Maeda, Y and Shimizu, S and Hossain, MT and Ubukata, S and Suzuki, K and Sekiguchi, T and Takénaka, A}, title = {Structure of the nondiscriminating aspartyl-tRNA synthetase from the crenarchaeon Sulfolobus tokodaii strain 7 reveals the recognition mechanism for two different tRNA anticodons.}, journal = {Acta crystallographica. Section D, Biological crystallography}, volume = {63}, number = {Pt 10}, pages = {1042-1047}, doi = {10.1107/S0907444907038292}, pmid = {17881821}, issn = {0907-4449}, mesh = {Anticodon/*chemistry ; Aspartate-tRNA Ligase/chemistry ; Binding Sites ; Escherichia coli/metabolism ; Models, Molecular ; Models, Statistical ; Molecular Conformation ; Protein Structure, Secondary ; Purines/chemistry ; Pyrimidines/chemistry ; RNA, Transfer/*chemistry ; Sulfolobus/*enzymology ; Thermus thermophilus/metabolism ; }, abstract = {In protein synthesis, 20 types of aminoacyl-tRNA synthetase (aaRS) are generally required in order to distinguish between the 20 types of amino acid so that each achieves strict recognition of the cognate amino acid and the cognate tRNA. In the crenarchaeon Sulfolobus tokodaii strain 7 (St), however, asparaginyl-tRNA synthetase (AsnRS) is missing. It is believed that AspRS instead produces Asp-tRNA(Asn) in addition to Asp-tRNA(Asp). In order to reveal the recognition mechanism for the two anticodons, GUC for aspartate and GUU for asparagine, the crystal structure of St-AspRS (nondiscriminating type) has been determined at 2.3 A resolution as the first example of the nondiscriminating type of AspRS from crenarchaea. A structural comparison with structures of discriminating AspRSs indicates that the structures are similar to each other overall and that the catalytic domain is highly conserved as expected. In the N-terminal domain, however, the binding site for the third anticodon nucleotide is modified to accept two pyrimidine bases, C and U, but not purine bases. The C base can bind to form a hydrogen bond to the surrounding main-chain amide group in the discriminating AspRS, while in the nondiscriminating AspRS the corresponding amino-acid residue is replaced by proline, which has no amide H atom for hydrogen-bond formation, thus allowing the U base to be accommodated in this site. In addition, the residues that cover the base plane are missing in the nondiscriminating AspRS. These amino-acid changes make it possible for both C and U to be accepted by the nondiscriminating AspRS. It is speculated that this type of nondiscriminating AspRS has been introduced into Thermus thermophilus through horizontal gene transfer.}, }
@article {pmid17873043, year = {2007}, author = {Hendrickx, AP and van Wamel, WJ and Posthuma, G and Bonten, MJ and Willems, RJ}, title = {Five genes encoding surface-exposed LPXTG proteins are enriched in hospital-adapted Enterococcus faecium clonal complex 17 isolates.}, journal = {Journal of bacteriology}, volume = {189}, number = {22}, pages = {8321-8332}, pmid = {17873043}, issn = {1098-5530}, mesh = {Bacterial Outer Membrane Proteins/*genetics/metabolism ; Bacterial Proteins/*genetics/metabolism ; Cell Wall ; Enterococcus faecium/*classification/*genetics/metabolism ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Variation ; Genome, Bacterial ; Hospitals ; Molecular Sequence Data ; Multigene Family ; Open Reading Frames ; RNA, Bacterial/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; }, abstract = {Most Enterococcus faecium isolates associated with hospital outbreaks and invasive infections belong to a distinct genetic subpopulation called clonal complex 17 (CC17). It has been postulated that the genetic evolution of CC17 involves the acquisition of various genes involved in antibiotic resistance, metabolic pathways, and virulence. To gain insight into additional genes that may have favored the rapid emergence of this nosocomial pathogen, we aimed to identify surface-exposed LPXTG cell wall-anchored proteins (CWAPs) specifically enriched in CC17 E. faecium. Using PCR and Southern and dot blot hybridizations, 131 E. faecium isolates (40 CC17 and 91 non-CC17) were screened for the presence of 22 putative CWAP genes identified from the E. faecium TX0016 genome. Five genes encoding LPXTG surface proteins were specifically enriched in E. faecium CC17 isolates. These five LPXTG surface protein genes were found in 28 to 40 (70 to 100%) of CC17 and in only 7 to 24 (8 to 26%) of non-CC17 isolates (P < 0.05). Three of these CWAP genes clustered together on the E. faecium TX0016 genome, which may comprise a novel enterococcal pathogenicity island covering E. faecium contig 609. Expression at the mRNA level was demonstrated, and immunotransmission electron microscopy revealed an association of the five LPXTG surface proteins with the cell wall. Minimal spanning tree analysis based on the presence and absence of 22 CWAP genes revealed grouping of all 40 CC17 strains together with 18 hospital-derived but evolutionary unrelated non-CC17 isolates in a distinct CWAP-enriched cluster, suggesting horizontal transfer of CWAP genes and a role of these CWAPs in hospital adaptation.}, }
@article {pmid17869068, year = {2007}, author = {Laplana, LM and Cepero, MA and Ruiz, J and Zolezzi, PC and Calvo, MA and Erazo, MC and Gómez-Lus, R}, title = {Molecular typing of Staphylococcus aureus clinical isolates by pulsed-field gel electrophoresis, staphylococcal cassette chromosome mec type determination and dissemination of antibiotic resistance genes.}, journal = {International journal of antimicrobial agents}, volume = {30}, number = {6}, pages = {505-513}, doi = {10.1016/j.ijantimicag.2007.06.020}, pmid = {17869068}, issn = {0924-8579}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics ; *Bacterial Typing Techniques ; Conjugation, Genetic ; Drug Resistance, Bacterial/*genetics ; Electrophoresis, Gel, Pulsed-Field/*methods ; Erythromycin/pharmacology ; *Gene Transfer, Horizontal ; Humans ; Methicillin Resistance/genetics ; Microbial Sensitivity Tests ; Oxacillin/pharmacology ; Penicillin-Binding Proteins ; Polymerase Chain Reaction ; Staphylococcus aureus/*classification/drug effects/genetics ; }, abstract = {Pulsed-field gel electrophoresis (PFGE) of SmaI macrorestriction fragments of genomic DNA as well as staphylococcal cassette chromosome mec (SCCmec) typing for mecA-carrying isolates were used to study the distribution of clonal types among 177 Staphylococcus aureus clinical isolates recovered in a Spanish hospital between 2000 and 2003. Five major clonal types (P1 to P5) were identified by PFGE, with one of them (P1) comprising the majority of strains (47.5%). According to SCCmec typing, SCCmec type IVA was the most prevalent type, showing increasing prevalence in the hospital setting with respect to other pandemic clones. One SCCmec pattern was detected in different PFGE types, which demonstrates that the latter is a major discriminative typing method. Three novel SCCmec elements or variants were found, each in a different PFGE type. Oxacillin (methicillin)-resistant and -susceptible S. aureus (MRSA and MSSA, respectively) strains were detected showing identical PFGE patterns, suggesting horizontal transfer of mecA to MSSA and/or mecA deletion from MRSA. Persistence of several S. aureus clones throughout the years within the same hospital environment was also observed.}, }
@article {pmid17867834, year = {2007}, author = {Djong, TH and Islam, MM and Nishioka, M and Matsui, M and Ota, H and Kuramoto, M and Khan, MM and Alam, MS and Anslem, de S and Khonsue, W and Sumida, M}, title = {Genetic relationships and reproductive-isolation mechanisms among the Fejervarya limnocharis complex from Indonesia (Java) and other Asian countries.}, journal = {Zoological science}, volume = {24}, number = {4}, pages = {360-375}, doi = {10.2108/zsj.24.360}, pmid = {17867834}, issn = {0289-0003}, mesh = {Alleles ; Animals ; Asia ; Crosses, Genetic ; Enzymes/*genetics ; Female ; *Gene Expression Regulation, Enzymologic ; Gene Transfer, Horizontal ; *Genetic Variation ; Indonesia ; Male ; Ranidae/classification/*genetics/*physiology ; Reproduction ; Species Specificity ; }, abstract = {In order to elucidate the genetic relationships and reproductive-isolation mechanisms among the Fejervarya limnocharis complex from Indonesia and other Asian countries, allozyme analyses and crossing experiments were carried out using 208 individuals from 21 localities in eight Asian countries. The allozyme analyses revealed that 17 enzymes examined were controlled by genes at 27 loci, and that 7.9 phenotypes were produced by 5.2 alleles on average. The two species recognized in F. limnocharis sensu lato from Southeast Asia (i.e., F. limnocharis sensu stricto and F. iskandari) were found to occur sympatrically at three localities (Bogor, Cianjur and Malingping), all on Java, Indonesia. Fejervaya iskandari was dominant at each of these localities and showed substantial geographic genetic variation. Laboratory-produced hybrids between F. limnocharis and F. iskandari from Java became underdeveloped and died at the tadpole stage, suggesting that these species are completely isolated by hybrid inviability. Hybrids between topotypic F. limnocharis and the Malaysian and Japanese conspecific populations developed normally to metamorphosis. Likewise, hybrids between topotypic F. iskandari and the Thailand and Bangladesh conspecific populations also showed normal viability throughout larval development. The present allozyme analyses and crossing experiments strongly suggested the presence of two distinct forms, the large type and the small type, in the F. limnocharis complex from Asia, and further subdivision of the large type into the F. limnocharis assemblage and the F. iskandari assemblage. The small type was found in samples from India, Thailand, Bangladesh and Sri Lanka, and included at least three different species. The sample from Pilok, Thailand, was considered to represent an undescribed species.}, }
@article {pmid17867833, year = {2007}, author = {Reimer, JD and Takishita, K and Ono, S and Tsukahara, J and Maruyama, T}, title = {Molecular evidence suggesting interspecific hybridization in Zoanthus spp. (Anthozoa: Hexacorallia).}, journal = {Zoological science}, volume = {24}, number = {4}, pages = {346-359}, doi = {10.2108/zsj.24.346}, pmid = {17867833}, issn = {0289-0003}, mesh = {Animals ; Anthozoa/classification/*genetics/*physiology ; Base Sequence ; *Biodiversity ; DNA, Ribosomal Spacer ; Gene Transfer, Horizontal ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; Species Specificity ; }, abstract = {Interspecific hybridization has been proposed as a possible explanation for the incredible diversity seen in reef-dwelling corals, but until now little proof of such hybridization in other reef-dwelling anthozoans has been reported. Without further observation of hybridization, the question of such a phenomenon being widespread in Anthozoa remains. Here we have examined the mitochondrial cytochrome oxidase I gene (COI) and the nuclear internal transcribed spacer of ribosomal DNA (ITS-rDNA) from three species of the mass-spawning, encrusting anemone genus Zoanthus (Z. sansibaricus, Z. kuroshio, Z. gigantus) to investigate possible hybridization. The three species coexist at two of three sampling locations in southern Japan. Zoanthus spp. ITS-rDNA region spacers (ITS-1 and ITS-2) were shown to have very high rates of divergence. At locations where all three species co-existed, several of our sampled Z. sansibaricus individuals (with identical "sansi" COI sequences) possessed two very divergent (i.e., species-level difference) ITS-rDNA alleles, the expected "sansi" allele and the divergent "B" allele. Additionally, two Z. sansibaricus individuals possessed only "B" alleles despite having "sansi" COI sequences. These results indicate that Z. sansibaricus has possibly experienced interspecific hybridization at least once with a Zoanthus partner possessing the "B" allele, and that these resulting hybrids may also sexually reproduce, demonstrating potential hybridization occurring in the order Zoantharia (Hexacorallia).}, }
@article {pmid17855524, year = {2007}, author = {Abergel, C and Rudinger-Thirion, J and Giegé, R and Claverie, JM}, title = {Virus-encoded aminoacyl-tRNA synthetases: structural and functional characterization of mimivirus TyrRS and MetRS.}, journal = {Journal of virology}, volume = {81}, number = {22}, pages = {12406-12417}, pmid = {17855524}, issn = {0022-538X}, mesh = {Acanthamoeba/*virology ; Animals ; Anticodon/chemistry/metabolism ; Crystallography, X-Ray ; DNA Viruses/*enzymology ; Methionine-tRNA Ligase/*chemistry/classification/genetics ; Phylogeny ; Protein Structure, Secondary ; RNA, Transfer, Met/chemistry/metabolism ; RNA, Transfer, Tyr/chemistry/metabolism ; Tyrosine-tRNA Ligase/*chemistry/classification/genetics ; Viral Proteins/*chemistry/classification/genetics ; }, abstract = {Aminoacyl-tRNA synthetases are pivotal in determining how the genetic code is translated in amino acids and in providing the substrate for protein synthesis. As such, they fulfill a key role in a process universally conserved in all cellular organisms from their most complex to their most reduced parasitic forms. In contrast, even complex viruses were not found to encode much translation machinery, with the exception of isolated components such as tRNAs. In this context, the discovery of four aminoacyl-tRNA synthetases encoded in the genome of mimivirus together with a full set of translation initiation, elongation, and termination factors appeared to blur what was once a clear frontier between the cellular and viral world. Functional studies of two mimivirus tRNA synthetases confirmed the MetRS specificity for methionine and the TyrRS specificity for tyrosine and conformity with the identity rules for tRNA(Tyr) for archea/eukarya. The atomic structure of the mimivirus tyrosyl-tRNA synthetase in complex with tyrosinol exhibits the typical fold and active-site organization of archaeal-type TyrRS. However, the viral enzyme presents a unique dimeric conformation and significant differences in its anticodon binding site. The present work suggests that mimivirus aminoacyl-tRNA synthetases function as regular translation enzymes in infected amoebas. Their phylogenetic classification does not suggest that they have been acquired recently by horizontal gene transfer from a cellular host but rather militates in favor of an intricate evolutionary relationship between large DNA viruses and ancestral eukaryotes.}, }
@article {pmid17851640, year = {2008}, author = {Shintani, M and Fukushima, N and Tezuka, M and Yamane, H and Nojiri, H}, title = {Conjugative transfer of the IncP-7 carbazole degradative plasmid, pCAR1, in river water samples.}, journal = {Biotechnology letters}, volume = {30}, number = {1}, pages = {117-122}, doi = {10.1007/s10529-007-9519-y}, pmid = {17851640}, issn = {1573-6776}, mesh = {Biodegradation, Environmental ; Carbazoles/*metabolism ; Chlortetracycline ; Conjugation, Genetic/*physiology ; Gene Transfer, Horizontal/*genetics ; Plasmids/*genetics ; Pseudomonas putida/*physiology ; Rivers/*microbiology ; Species Specificity ; Stenotrophomonas/*physiology ; *Water Microbiology ; }, abstract = {The transfer of the IncP-7 carbazole degradative plasmid pCAR1 from Pseudomonas putida SM1443 (derived from strain KT2440) into bacteria of river water samples was monitored using a reporter gene encoding red fluorescent protein (RFP). The number of transconjugants drastically increased in the presence of carbazole, and most appeared to belong to the genus Pseudomonas. The results suggest that the presence of carbazole benefits the appearance of transconjugants belonging to the genus Pseudomonas. Intriguingly, we also detected the transfer of pCAR1 into non-Pseudomonas, Stenotrophomonas-like bacteria.}, }
@article {pmid17826337, year = {2007}, author = {Opperdoes, FR and Michels, PA}, title = {Horizontal gene transfer in trypanosomatids.}, journal = {Trends in parasitology}, volume = {23}, number = {10}, pages = {470-476}, doi = {10.1016/j.pt.2007.08.002}, pmid = {17826337}, issn = {1471-4922}, mesh = {Animals ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genes, Plant ; Genes, Viral ; Genome, Protozoan ; Phylogeny ; Trypanosomatina/*genetics ; }, abstract = {Trypanosomes harbour a large number of structural and biochemical peculiarities. Kinetoplast DNA, mitochondrial RNA editing, the sequestration of glycolysis inside glycosomes and unique oxidative-stress protection mechanisms (to name but a few) are found only in the members of the order Kinetoplastida. Thus, it is not surprising that they have provoked much speculation about why and how such oddities have evolved in trypanosomes. However, the true reasons for their existence within the eukaryotic world are still far from clear. Here, Fred Opperdoes and Paul Michels argue that the trypanosome-specific evolution of novel processes and organization could only have been made possible by the acquisition of a large number of foreign genes, which entered a trypanosomatid ancestor through lateral gene transfer. Many different organisms must have served as donors. Some of them were viruses, and others were bacteria, such as cyanobacterial endosymbionts and non-phototrophic bacteria.}, }
@article {pmid17822794, year = {2008}, author = {Delorme, C}, title = {Safety assessment of dairy microorganisms: Streptococcus thermophilus.}, journal = {International journal of food microbiology}, volume = {126}, number = {3}, pages = {274-277}, doi = {10.1016/j.ijfoodmicro.2007.08.014}, pmid = {17822794}, issn = {1879-3460}, mesh = {Bacteriocins/adverse effects/biosynthesis ; Cheese/microbiology ; *Consumer Product Safety ; Cultured Milk Products/*microbiology ; Food Microbiology ; Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; *Phylogeny ; *Risk Assessment ; Species Specificity ; *Streptococcus thermophilus/classification/genetics/metabolism/pathogenicity ; Yogurt/microbiology ; }, abstract = {Streptococcus thermophilus is a major dairy starter used in yogurt and cheese production. In Streptococcus genus, S. thermophilus is the only one food species among commensal and opportunistic pathogen species. Comparative genomics suggest that this species recently emerged and evolved by combination of loss-of-function and horizontal gene transfer events. These gene transfer events detected in S. thermophilus have originated from other dairy species and might contribute to its adaptation to the milk environment.}, }
@article {pmid17804070, year = {2008}, author = {Jakobsen, L and Sandvang, D and Hansen, LH and Bagger-Skjøt, L and Westh, H and Jørgensen, C and Hansen, DS and Pedersen, BM and Monnet, DL and Frimodt-Møller, N and Sørensen, SJ and Hammerum, AM}, title = {Characterisation, dissemination and persistence of gentamicin resistant Escherichia coli from a Danish university hospital to the waste water environment.}, journal = {Environment international}, volume = {34}, number = {1}, pages = {108-115}, doi = {10.1016/j.envint.2007.07.011}, pmid = {17804070}, issn = {0160-4120}, mesh = {Anti-Bacterial Agents/*pharmacology ; Cluster Analysis ; Conjugation, Genetic ; DNA Fingerprinting ; DNA, Bacterial ; Denmark ; *Drug Resistance, Bacterial ; Drug Resistance, Multiple, Bacterial/genetics ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/classification/*drug effects/genetics/*isolation &amp; purification ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genotype ; Gentamicins/*pharmacology ; Hospitals, University ; Humans ; Microbial Sensitivity Tests ; Virulence Factors/genetics ; *Waste Disposal, Fluid ; *Water Microbiology ; }, abstract = {The aim of the study was to investigate the potential spread of gentamicin resistant (GEN(R)) Escherichia coli isolates or GEN(R) determinants from a Danish university hospital to the waste water environment. Waste water samples were collected monthly from the outlets of the hospital bed wards and the inlet of the related waste water treatment plant (WWTP) from October 2002 to August 2003. Waste water samples were also collected monthly from a residential area in the same period to be able to compare the prevalence of GEN(R)E. coli isolates from hospital related and residential waste water. The waste water isolates were compared to GEN(R)E. coli isolates obtained consecutively from September 2002 to September 2003 from patients mainly with urinary tract infections at the hospital with respect to Pulsed Field Gel Electrophoresis (PFGE) profiles. All isolates were investigated for GEN(R) mechanisms (aac(3)-II, aac(3)-IV, ant(2'')-I, armA), phenotypic resistance pattern, and virulence genes (hlyA, chuA, sfaS, fogG, malX, traT, iutA, fyuA, iroN, cnf1) to investigate if the hospital and waste water could be reservoirs of antimicrobial resistance and virulence. The ability for GEN(R) determinants to transfer horizontally was investigated by mating experiments. A total of 38, 15, 21, and two GEN(R)E. coli were isolated from patients, the hospital outlets, the inlet of the WWTP, and the residential area, respectively. GEN(R)E. coli were more prevalent in waste water from the hospital and the WWTP than in waste water from the residential area. PFGE profiling revealed no spread of specific patient isolates to the waste water. The aac(3)-II gene was detected both in patient and waste water isolates. Furthermore horizontal transfer of the aac(3)-II gene of patient origin to a recipient was shown in vitro, indicating a potential spread of the gene from patient isolates to waste water isolates. Regardless of origin, most isolates exhibited multi-resistance and contained several virulence genes. In conclusion, our study showed a possible spread of aac(3)-II from the hospital to the waste water. Most of the GEN(R)E. coli isolates from both patients and waste water had a multi-resistant phenotype and contained virulence genes and should therefore be considered reservoirs of antimicrobial resistance and virulence genes.}, }
@article {pmid17803924, year = {2007}, author = {Guljamow, A and Jenke-Kodama, H and Saumweber, H and Quillardet, P and Frangeul, L and Castets, AM and Bouchier, C and Tandeau de Marsac, N and Dittmann, E}, title = {Horizontal gene transfer of two cytoskeletal elements from a eukaryote to a cyanobacterium.}, journal = {Current biology : CB}, volume = {17}, number = {17}, pages = {R757-9}, doi = {10.1016/j.cub.2007.06.063}, pmid = {17803924}, issn = {0960-9822}, mesh = {Actins/*genetics ; Cytoskeleton/genetics ; Eukaryotic Cells ; *Gene Transfer, Horizontal ; Genomic Islands ; Microcystis/*genetics ; Profilins/*genetics ; *Sequence Homology, Amino Acid ; }, }
@article {pmid17803775, year = {2007}, author = {Nandasena, KG and O'Hara, GW and Tiwari, RP and Sezmiş, E and Howieson, JG}, title = {In situ lateral transfer of symbiosis islands results in rapid evolution of diverse competitive strains of mesorhizobia suboptimal in symbiotic nitrogen fixation on the pasture legume Biserrula pelecinus L.}, journal = {Environmental microbiology}, volume = {9}, number = {10}, pages = {2496-2511}, doi = {10.1111/j.1462-2920.2007.01368.x}, pmid = {17803775}, issn = {1462-2912}, mesh = {Alphaproteobacteria/*genetics/*metabolism ; Base Sequence ; Biological Evolution ; Fabaceae/metabolism/*microbiology ; *Gene Transfer, Horizontal ; Genomic Islands/*genetics ; Molecular Sequence Data ; Nitrogen Fixation/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Root Nodules, Plant/growth &amp; development/metabolism/microbiology ; Soil Microbiology ; }, abstract = {The multi-billion dollar asset attributed to symbiotic nitrogen fixation is often threatened by the nodulation of legumes by rhizobia that are ineffective or poorly effective in N(2) fixation. This study investigated the development of rhizobial diversity for the pasture legume Biserrula pelecinus L., 6 years after its introduction, and inoculation with Mesorhizobium ciceri bv. biserrulae strain WSM1271, to Western Australia. Molecular fingerprinting of 88 nodule isolates indicated seven were distinctive. Two of these were ineffective while five were poorly effective in N(2) fixation on B. pelecinus. Three novel isolates had wider host ranges for nodulation than WSM1271, and four had distinct carbon utilization patterns. Novel isolates were identified as Mesorhizobium sp. using 16S rRNA, dnaK and GSII phylogenies. In a second study, a large number of nodules were collected from commercially grown B. pelecinus from a broader geographical area. These plants were originally inoculated with M. c bv. biserrulae WSM1497 5-6 years prior to isolation of strains for this study. Nearly 50% of isolates from these nodules had distinct molecular fingerprints. At two sites diverse strains dominated nodule occupancy indicating recently evolved strains are highly competitive. All isolates tested were less effective and six were ineffective in N(2) fixation. Twelve randomly selected diverse isolates clustered together, based on dnaK sequences, within Mesorhizobium and distantly to M. c bv. biserrulae. All 12 had identical sequences for the symbiosis island insertion region with WSM1497. This study shows the rapid evolution of competitive, yet suboptimal strains for N(2) fixation on B. pelecinus following the lateral transfer of a symbiosis island from inoculants to other soil bacteria.}, }
@article {pmid17768176, year = {2007}, author = {Karami, N and Martner, A and Enne, VI and Swerkersson, S and Adlerberth, I and Wold, AE}, title = {Transfer of an ampicillin resistance gene between two Escherichia coli strains in the bowel microbiota of an infant treated with antibiotics.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {60}, number = {5}, pages = {1142-1145}, doi = {10.1093/jac/dkm327}, pmid = {17768176}, issn = {0305-7453}, mesh = {Amoxicillin/therapeutic use ; Ampicillin/*pharmacology ; Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/*drug effects/enzymology/*genetics ; Escherichia coli Proteins/genetics ; Feces/microbiology ; Gastrointestinal Tract/*microbiology ; Gene Transfer, Horizontal ; Humans ; Infant, Newborn ; Urinary Tract Infections/drug therapy ; beta-Lactamases/genetics ; }, abstract = {OBJECTIVES: To investigate the presumed acquisition of ampicillin resistance by an Escherichia coli strain residing in the gut of an infant.<br><br>METHODS: E. coli strains were quantified in faecal samples obtained at regular intervals from an infant followed from birth to 12 months of age and their resistance profiles were determined. beta-Lactamases were identified by isoelectric focusing and genes by PCR followed by DNA sequencing. Plasmids were characterized by restriction fragment analysis and Southern-blot hybridization, and tested for conjugative transfer.<br><br>RESULTS: The infant carried two E. coli strains, termed 29A and 29B, simultaneously in the microbiota during the first month of life. All isolates of 29A were resistant to ampicillin, whereas strain 29B, which was initially ampicillin susceptible, acquired resistance following treatment of the infant with ampicillin/amoxicillin because of urinary tract infection. Acquisition of resistance by strain 29B was associated with acquisition of a bla(TEM-1b)-encoding plasmid, pNK29, which was also present in strain 29A. Transfer of plasmid pNK29 could be replicated by conjugation from strain 29A to strain 29B in vitro. Strain 29A also adapted to ampicillin treatment by mutation of the bla(TEM-1b) promoter gene to yield a higher level of resistance.<br><br>CONCLUSIONS: This is an unequivocal demonstration of gene transfer between two strains co-residing in the human gut, as the donor, recipient and transconjugant strains were isolated. The results suggest the dynamic adaptation by commensal bacteria in response to antibiotic treatment may occur readily.}, }
@article {pmid17766449, year = {2007}, author = {Macovei, L and Zurek, L}, title = {Influx of enterococci and associated antibiotic resistance and virulence genes from ready-to-eat food to the human digestive tract.}, journal = {Applied and environmental microbiology}, volume = {73}, number = {21}, pages = {6740-6747}, pmid = {17766449}, issn = {0099-2240}, mesh = {Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; Enterococcus/drug effects/*genetics/*isolation &amp; purification ; *Food Microbiology ; Gastrointestinal Tract/*microbiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Virulence/genetics ; Virulence Factors/*genetics/metabolism ; }, abstract = {The influx of enterococcal antibiotic resistance (AR) and virulence genes from ready-to-eat food (RTEF) to the human digestive tract was assessed. Three RTEFs (chicken salad, chicken burger, and carrot cake) were sampled from five fast-food restaurants five times in summer (SU) and winter (WI). The prevalence of enterococci was significantly higher in SU (92.0% of salad samples and 64.0% of burger samples) than in WI (64.0% of salad samples and 24.0% of burger samples). The overall concentrations of enterococci during the two seasons were similar (approximately 10(3) CFU/g); the most prevalent were Enterococcus casseliflavus (41.5% of isolates) and Enterococcus hirae (41.5%) in WI and Enterococcus faecium (36.8%), E. casseliflavus (27.6%), and Enterococcus faecalis (22.4%) in SU. Resistance in WI was detected primarily to tetracycline (50.8%), ciprofloxacin (13.8%), and erythromycin (4.6%). SU isolates were resistant mainly to tetracycline (22.8%), erythromycin (22.1%), and kanamycin (13.0%). The most common tet gene was tet(M) (35.4% of WI isolates and 11.9% of SU isolates). The prevalence of virulence genes (gelE, asa1, cylA, and esp) and marker genes for clinical isolates (EF_0573, EF_0592, EF_0605, EF_1420, EF_2144, and pathogenicity island EF_0050) was low (< or =12.3%). Genotyping of E. faecalis and E. faecium using pulsed-field gel electrophoresis revealed that the food contamination likely originated from various sources and that it was not clonal. Our conservative estimate (single AR gene copy per cell) for the influx of tet genes alone to the human digestive tract is 3.8 x 10(5) per meal (chicken salad). This AR gene influx is frequent because RTEFs are commonly consumed and that may play a role in the acquisition of AR determinants in the human digestive tract.}, }
@article {pmid17761848, year = {2007}, author = {Dunning Hotopp, JC and Clark, ME and Oliveira, DC and Foster, JM and Fischer, P and Muñoz Torres, MC and Giebel, JD and Kumar, N and Ishmael, N and Wang, S and Ingram, J and Nene, RV and Shepard, J and Tomkins, J and Richards, S and Spiro, DJ and Ghedin, E and Slatko, BE and Tettelin, H and Werren, JH}, title = {Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes.}, journal = {Science (New York, N.Y.)}, volume = {317}, number = {5845}, pages = {1753-1756}, doi = {10.1126/science.1142490}, pmid = {17761848}, issn = {1095-9203}, mesh = {Animals ; Chromosome Mapping ; Crosses, Genetic ; DNA, Bacterial ; Drosophila/genetics/microbiology ; Female ; *Gene Transfer, Horizontal ; Genes, Bacterial ; In Situ Hybridization, Fluorescence ; Insecta/*genetics/microbiology ; Male ; Molecular Sequence Data ; Nematoda/*genetics/microbiology ; Retroelements ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Symbiosis ; Wolbachia/*genetics ; }, abstract = {Although common among bacteria, lateral gene transfer-the movement of genes between distantly related organisms-is thought to occur only rarely between bacteria and multicellular eukaryotes. However, the presence of endosymbionts, such as Wolbachia pipientis, within some eukaryotic germlines may facilitate bacterial gene transfers to eukaryotic host genomes. We therefore examined host genomes for evidence of gene transfer events from Wolbachia bacteria to their hosts. We found and confirmed transfers into the genomes of four insect and four nematode species that range from nearly the entire Wolbachia genome (>1 megabase) to short (<500 base pairs) insertions. Potential Wolbachia-to-host transfers were also detected computationally in three additional sequenced insect genomes. We also show that some of these inserted Wolbachia genes are transcribed within eukaryotic cells lacking endosymbionts. Therefore, heritable lateral gene transfer occurs into eukaryotic hosts from their prokaryote symbionts, potentially providing a mechanism for acquisition of new genes and functions.}, }
@article {pmid17760503, year = {2007}, author = {Mussmann, M and Hu, FZ and Richter, M and de Beer, D and Preisler, A and Jørgensen, BB and Huntemann, M and Glöckner, FO and Amann, R and Koopman, WJ and Lasken, RS and Janto, B and Hogg, J and Stoodley, P and Boissy, R and Ehrlich, GD}, title = {Insights into the genome of large sulfur bacteria revealed by analysis of single filaments.}, journal = {PLoS biology}, volume = {5}, number = {9}, pages = {e230}, pmid = {17760503}, issn = {1545-7885}, support = {R01 DC002148/DC/NIDCD NIH HHS/United States ; R01 DC004173/DC/NIDCD NIH HHS/United States ; DC02148/DC/NIDCD NIH HHS/United States ; DC04173/DC/NIDCD NIH HHS/United States ; }, mesh = {Actin Cytoskeleton/*genetics ; Base Sequence ; Beggiatoa/*genetics ; *Genome, Bacterial ; Hydrogen Sulfide/metabolism ; Metabolic Networks and Pathways/*genetics ; Nitrates/metabolism ; Oxidation-Reduction ; Oxygen/metabolism ; }, abstract = {Marine sediments are frequently covered by mats of the filamentous Beggiatoa and other large nitrate-storing bacteria that oxidize hydrogen sulfide using either oxygen or nitrate, which they store in intracellular vacuoles. Despite their conspicuous metabolic properties and their biogeochemical importance, little is known about their genetic repertoire because of the lack of pure cultures. Here, we present a unique approach to access the genome of single filaments of Beggiatoa by combining whole genome amplification, pyrosequencing, and optical genome mapping. Sequence assemblies were incomplete and yielded average contig sizes of approximately 1 kb. Pathways for sulfur oxidation, nitrate and oxygen respiration, and CO2 fixation confirm the chemolithoautotrophic physiology of Beggiatoa. In addition, Beggiatoa potentially utilize inorganic sulfur compounds and dimethyl sulfoxide as electron acceptors. We propose a mechanism of vacuolar nitrate accumulation that is linked to proton translocation by vacuolar-type ATPases. Comparative genomics indicates substantial horizontal gene transfer of storage, metabolic, and gliding capabilities between Beggiatoa and cyanobacteria. These capabilities enable Beggiatoa to overcome non-overlapping availabilities of electron donors and acceptors while gliding between oxic and sulfidic zones. The first look into the genome of these filamentous sulfur-oxidizing bacteria substantially deepens the understanding of their evolution and their contribution to sulfur and nitrogen cycling in marine sediments.}, }
@article {pmid17722982, year = {2007}, author = {Audic, S and Robert, C and Campagna, B and Parinello, H and Claverie, JM and Raoult, D and Drancourt, M}, title = {Genome analysis of Minibacterium massiliensis highlights the convergent evolution of water-living bacteria.}, journal = {PLoS genetics}, volume = {3}, number = {8}, pages = {e138}, pmid = {17722982}, issn = {1553-7404}, mesh = {Betaproteobacteria/*genetics/metabolism ; *Biological Evolution ; Biological Transport/genetics ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; *Genome, Bacterial ; Iron/metabolism ; Metabolic Networks and Pathways/genetics ; Metals, Heavy/pharmacology ; Molecular Sequence Data ; Phylogeny ; Virulence Factors/genetics ; *Water ; Water Microbiology ; }, abstract = {Filtration usually eliminates water-living bacteria. Here, we report on the complete genome sequence of Minibacterium massiliensis, a beta-proteobacteria that was recovered from 0.22-mum filtered water used for patients in the hospital. The unexpectedly large 4,110,251-nucleotide genome sequence of M. massiliensis was determined using the traditional shotgun sequencing approach. Bioinformatic analyses shows that the M. massiliensis genome sequence illustrates characteristic features of water-living bacteria, including overrepresentation of genes encoding transporters and transcription regulators. Phylogenomic analysis based on the gene content of available bacterial genome sequences displays a congruent evolution of water-living bacteria from various taxonomic origins, principally for genes involved in energy production and conversion, cell division, chromosome partitioning, and lipid metabolism. This phylogenomic clustering partially results from lateral gene transfer, which appears to be more frequent in water than in other environments. The M. massiliensis genome analyses strongly suggest that water-living bacteria are a common source for genes involved in heavy-metal resistance, antibiotics resistance, and virulence factors.}, }
@article {pmid17720348, year = {2007}, author = {Donate-Correa, J and León-Barrios, M and Hernández, M and Pérez-Galdona, R and del Arco-Aguilar, M}, title = {Different Mesorhizobium species sharing the same symbiotic genes nodulate the shrub legume Anagyris latifolia.}, journal = {Systematic and applied microbiology}, volume = {30}, number = {8}, pages = {615-623}, doi = {10.1016/j.syapm.2007.07.002}, pmid = {17720348}, issn = {0723-2020}, mesh = {Alphaproteobacteria/*classification/*genetics/isolation &amp; purification ; Bacterial Proteins/*genetics ; DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer ; Fabaceae/*microbiology ; Genes, Bacterial/genetics ; Genes, rRNA ; Glutamate-Ammonia Ligase/genetics ; Molecular Sequence Data ; N-Acetylglucosaminyltransferases/*genetics ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {The isolation and characterization of six rhizobial strains isolated from Anagyris latifolia, a shrub legume endemic to the Canary Islands, is reported in this study. The isolates were characterized by 16S-ARDRA, and sequencing of the ribosomal 16SrRNA gene, the 16S-23SrDNA intergenic spacer region, and the housekeeping gene for glutamine synthetase II (glnII). The phylogenies based on the three types of sequences matched, showing that the isolates belonged to three distinct lineages within the genus Mesorhizobium that could represent different species. However, the ribosomal and glnII phylogenies revealed some discrepancies in the relationships between the isolates and the named species in this genus. Despite their different taxonomic affiliation, all the isolates showed identical nodC sequences which were closely related (95% similarity) to that of the Mesorhizobium tianshanense type strain, indicating that they must have acquired the nodulation genes by a phenomenon of lateral gene transfer.}, }
@article {pmid17715573, year = {2006}, author = {Rutkowska, J and Olszewski, WL}, title = {DNA transfer in bacteria and animals (humans).}, journal = {Annals of transplantation}, volume = {11}, number = {4}, pages = {16-21}, pmid = {17715573}, issn = {1425-9524}, mesh = {Animals ; Bacteria/*genetics ; *DNA ; *Gene Transfer, Horizontal ; Humans ; Organ Transplantation/*physiology ; }, abstract = {Transplanted vascularized organs shed passenger cells, normal constituents of whole organs, that migrate to recipient lymphoid tissues and produce microchimerism. These cells lysed by recipient cytotoxic cells release cellular organelles into the recipient circulation. In addition, warm and cold ischemia as well as immune rejection of the transplanted organ or tissue bring about destructive changes in the graft parenchymatous cells. Fragments of disintegrated cellular organelles are phagocytized by recipient scavenger cells located in lymph nodes, spleen and liver and digested. Some fragments are incorporated into dendritic cells (DC) and processed. Donor DNA is present in the ingested cellular debris. The allografting with immunosppression is accompanied by microbial infections and host reaction. A large volume of bacterial and viral DNA is shed in the recipient circulation. The fate of the shed DNA remains largely unknown. Does it undergo total disintegration or may be reutilized? What reaction may the non-methylated bacterial DNA evoke in the graft and what is the response of allogeneic recipient to donor DNA remain the unanswered questions.}, }
@article {pmid17714478, year = {2007}, author = {Würdemann, D and Tümmler, B}, title = {In silico comparison of pKLC102-like genomic islands of Pseudomonas aeruginosa.}, journal = {FEMS microbiology letters}, volume = {275}, number = {2}, pages = {244-249}, doi = {10.1111/j.1574-6968.2007.00891.x}, pmid = {17714478}, issn = {0378-1097}, mesh = {Bacterial Proteins/genetics ; Base Sequence ; Computational Biology/*methods ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomic Islands/*genetics ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Open Reading Frames ; Plasmids ; Polymorphism, Single Nucleotide/genetics ; Pseudomonas aeruginosa/*classification/*genetics ; RNA, Transfer, Lys ; Replication Origin ; *Sequence Homology, Nucleic Acid ; Species Specificity ; }, abstract = {The genomic island pKLC102 first detected in Pseudomonas aeruginosa clone C strains can cross species barriers and exhibits the highest mobilization rate of a genomic island known to date. Homologous genomic islands of 81-108 kb in size were identified in the completely sequenced P. aeruginosa strains PA7, PA14, 2192, C3719 and PACS2, but not in strains PAO1 and LES. All pKLC102-like genomic islands are integrated in chromosomal tRNA(Lys) genes and share a syntenic set of more than 70 homologous ORFs, part of which are related to DNA replication or mobility genes. The conserved backbone has predilection sites for the uptake of island-specific gene cassettes. A major difference between the islands is the organization of the origin of replication oriV.}, }
@article {pmid17711596, year = {2007}, author = {Ogura, Y and Ooka, T and Asadulghani,  and Terajima, J and Nougayrède, JP and Kurokawa, K and Tashiro, K and Tobe, T and Nakayama, K and Kuhara, S and Oswald, E and Watanabe, H and Hayashi, T}, title = {Extensive genomic diversity and selective conservation of virulence-determinants in enterohemorrhagic Escherichia coli strains of O157 and non-O157 serotypes.}, journal = {Genome biology}, volume = {8}, number = {7}, pages = {R138}, pmid = {17711596}, issn = {1474-760X}, mesh = {Base Sequence ; Escherichia coli O157/*genetics/pathogenicity ; Evolution, Molecular ; *Genetic Variation ; Genome, Bacterial/*genetics ; Genomics ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Plasmids/genetics ; Prophages/genetics ; Virulence Factors/*genetics ; }, abstract = {BACKGROUND: Enterohemorrhagic Escherichia coli (EHEC) O157 causes severe food-borne illness in humans. The chromosome of O157 consists of 4.1 Mb backbone sequences shared by benign E. coli K-12, and 1.4 Mb O157-specific sequences encoding many virulence determinants, such as Shiga toxin genes (stx genes) and the locus of enterocyte effacement (LEE). Non-O157 EHECs belonging to distinct clonal lineages from O157 also cause similar illness in humans. According to the 'parallel' evolution model, they have independently acquired the major virulence determinants, the stx genes and LEE. However, the genomic differences between O157 and non-O157 EHECs have not yet been systematically analyzed.<br><br>RESULTS: Using microarray and whole genome PCR scanning analyses, we performed a whole genome comparison of 20 EHEC strains of O26, O111, and O103 serotypes with O157. In non-O157 EHEC strains, although genome sizes were similar with or rather larger than O157 and the backbone regions were well conserved, O157-specific regions were very poorly conserved. Around only 20% of the O157-specific genes were fully conserved in each non-O157 serotype. However, the non-O157 EHECs contained a significant number of virulence genes that are found on prophages and plasmids in O157, and also multiple prophages similar to, but significantly divergent from, those in O157.<br><br>CONCLUSION: Although O157 and non-O157 EHECs have independently acquired a huge amount of serotype- or strain-specific genes by lateral gene transfer, they share an unexpectedly large number of virulence genes. Independent infections of similar but distinct bacteriophages carrying these virulence determinants are deeply involved in the evolution of O157 and non-O157 EHECs.}, }
@article {pmid17709750, year = {2007}, author = {Kolesov, G and Wunderlich, Z and Laikova, ON and Gelfand, MS and Mirny, LA}, title = {How gene order is influenced by the biophysics of transcription regulation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {35}, pages = {13948-13953}, pmid = {17709750}, issn = {0027-8424}, mesh = {Bacteria/genetics ; Binding Sites ; Biophysical Phenomena ; Biophysics ; DNA/*chemistry/genetics ; *Gene Expression Regulation ; *Genome ; Homeostasis ; Models, Genetic ; Multigene Family ; Nucleic Acid Conformation ; Protein Biosynthesis ; Proteins/chemistry/genetics ; Transcription Factors/*genetics/metabolism ; *Transcription, Genetic ; }, abstract = {What are the forces that shape the structure of prokaryotic genomes: the order of genes, their proximity, and their orientation? Coregulation and coordinated horizontal gene transfer are believed to promote the proximity of functionally related genes and the formation of operons. However, forces that influence the structure of the genome beyond the level of a single operon remain unknown. Here, we show that the biophysical mechanism by which regulatory proteins search for their sites on DNA can impose constraints on genome structure. Using simulations, we demonstrate that rapid and reliable gene regulation requires that the transcription factor (TF) gene be close to the site on DNA the TF has to bind, thus promoting the colocalization of TF genes and their targets on the genome. We use parameters that have been measured in recent experiments to estimate the relevant length and times scales of this process and demonstrate that the search for a cognate site may be prohibitively slow if a TF has a low copy number and is not colocalized. We also analyze TFs and their sites in a number of bacterial genomes, confirm that they are colocalized significantly more often than expected, and show that this observation cannot be attributed to the pressure for coregulation or formation of selfish gene clusters, thus supporting the role of the biophysical constraint in shaping the structure of prokaryotic genomes. Our results demonstrate how spatial organization can influence timing and noise in gene expression.}, }
@article {pmid17708768, year = {2007}, author = {Koonin, EV}, title = {The Biological Big Bang model for the major transitions in evolution.}, journal = {Biology direct}, volume = {2}, number = {}, pages = {21}, pmid = {17708768}, issn = {1745-6150}, support = {//Intramural NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; Eukaryotic Cells ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Models, Biological ; Prokaryotic Cells ; Recombination, Genetic ; }, abstract = {BACKGROUND: Major transitions in biological evolution show the same pattern of sudden emergence of diverse forms at a new level of complexity. The relationships between major groups within an emergent new class of biological entities are hard to decipher and do not seem to fit the tree pattern that, following Darwin's original proposal, remains the dominant description of biological evolution. The cases in point include the origin of complex RNA molecules and protein folds; major groups of viruses; archaea and bacteria, and the principal lineages within each of these prokaryotic domains; eukaryotic supergroups; and animal phyla. In each of these pivotal nexuses in life's history, the principal "types" seem to appear rapidly and fully equipped with the signature features of the respective new level of biological organization. No intermediate "grades" or intermediate forms between different types are detectable. Usually, this pattern is attributed to cladogenesis compressed in time, combined with the inevitable erosion of the phylogenetic signal.<br><br>HYPOTHESIS: I propose that most or all major evolutionary transitions that show the "explosive" pattern of emergence of new types of biological entities correspond to a boundary between two qualitatively distinct evolutionary phases. The first, inflationary phase is characterized by extremely rapid evolution driven by various processes of genetic information exchange, such as horizontal gene transfer, recombination, fusion, fission, and spread of mobile elements. These processes give rise to a vast diversity of forms from which the main classes of entities at the new level of complexity emerge independently, through a sampling process. In the second phase, evolution dramatically slows down, the respective process of genetic information exchange tapers off, and multiple lineages of the new type of entities emerge, each of them evolving in a tree-like fashion from that point on. This biphasic model of evolution incorporates the previously developed concepts of the emergence of protein folds by recombination of small structural units and origin of viruses and cells from a pre-cellular compartmentalized pool of recombining genetic elements. The model is extended to encompass other major transitions. It is proposed that bacterial and archaeal phyla emerged independently from two distinct populations of primordial cells that, originally, possessed leaky membranes, which made the cells prone to rampant gene exchange; and that the eukaryotic supergroups emerged through distinct, secondary endosymbiotic events (as opposed to the primary, mitochondrial endosymbiosis). This biphasic model of evolution is substantially analogous to the scenario of the origin of universes in the eternal inflation version of modern cosmology. Under this model, universes like ours emerge in the infinite multiverse when the eternal process of exponential expansion, known as inflation, ceases in a particular region as a result of false vacuum decay, a first order phase transition process. The result is the nucleation of a new universe, which is traditionally denoted Big Bang, although this scenario is radically different from the Big Bang of the traditional model of an expanding universe. Hence I denote the phase transitions at the end of each inflationary epoch in the history of life Biological Big Bangs (BBB).<br><br>CONCLUSION: A Biological Big Bang (BBB) model is proposed for the major transitions in life's evolution. According to this model, each transition is a BBB such that new classes of biological entities emerge at the end of a rapid phase of evolution (inflation) that is characterized by extensive exchange of genetic information which takes distinct forms for different BBBs. The major types of new forms emerge independently, via a sampling process, from the pool of recombining entities of the preceding generation. This process is envisaged as being qualitatively different from tree-pattern cladogenesis.}, }
@article {pmid17708761, year = {2007}, author = {Nicolas, P and Bessières, P and Ehrlich, SD and Maguin, E and van de Guchte, M}, title = {Extensive horizontal transfer of core genome genes between two Lactobacillus species found in the gastrointestinal tract.}, journal = {BMC evolutionary biology}, volume = {7}, number = {}, pages = {141}, pmid = {17708761}, issn = {1471-2148}, mesh = {Animals ; Bacterial Proteins/genetics ; Base Composition ; Evolution, Molecular ; Gastrointestinal Tract/microbiology ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Lactobacillus/*genetics ; Lactobacillus acidophilus/genetics ; Lactobacillus delbrueckii/genetics ; Likelihood Functions ; Phylogeny ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {BACKGROUND: While genes that are conserved between related bacterial species are usually thought to have evolved along with the species, phylogenetic trees reconstructed for individual genes may contradict this picture and indicate horizontal gene transfer. Individual trees are often not resolved with high confidence, however, and in that case alternative trees are generally not considered as contradicting the species tree, although not confirming it either. Here we conduct an in-depth analysis of 401 protein phylogenetic trees inferred with varying levels of confidence for three lactobacilli from the acidophilus complex. At present the relationship between these bacteria, isolated from environments as diverse as the gastrointestinal tract (Lactobacillus acidophilus and Lactobacillus johnsonii) and yogurt (Lactobacillus delbrueckii ssp. bulgaricus), is ambiguous due to contradictory phenotypical and 16S rRNA based classifications.<br><br>RESULTS: Among the 401 phylogenetic trees, those that could be reconstructed with high confidence support the 16S-rRNA tree or one alternative topology in an astonishing 3:2 ratio, while the third possible topology is practically absent. Lowering the confidence threshold for trees to be taken into consideration does not significantly affect this ratio, and therefore suggests that gene transfer may have affected as much as 40% of the core genome genes. Gene function bias suggests that the 16S rRNA phylogeny of the acidophilus complex, which indicates that L. acidophilus and L. delbrueckii ssp. bulgaricus are the closest related of these three species, is correct. A novel approach of comparison of interspecies protein divergence data employed in this study allowed to determine that gene transfer most likely took place between the lineages of the two species found in the gastrointestinal tract.<br><br>CONCLUSION: This case-study reports an unprecedented level of phylogenetic incongruence, presumably resulting from extensive horizontal gene transfer. The data give a first indication of the large extent of gene transfer that may take place in the gastrointestinal tract and its accumulated effect. For future studies, our results should encourage a careful weighing of data on phylogenetic tree topology, confidence and distribution to conclude on the absence or presence and extent of horizontal gene transfer.}, }
@article {pmid17702465, year = {2007}, author = {Baldy-Chudzik, K and Stosik, M}, title = {Diversity of fliC gene in commensal Escherichia coli derived from various mammals.}, journal = {Folia microbiologica}, volume = {52}, number = {3}, pages = {261-272}, pmid = {17702465}, issn = {0015-5632}, mesh = {Alleles ; Animals ; Animals, Zoo/*microbiology ; Escherichia coli/*genetics ; Escherichia coli Infections/genetics/transmission/veterinary ; Escherichia coli Proteins/*genetics ; Flagellin ; Gene Transfer, Horizontal ; Genetic Variation/*genetics ; Mammals/*microbiology ; Phylogeny ; Polymorphism, Restriction Fragment Length ; }, abstract = {Relations between the diversity of the fliC gene conditioning flagellum protein in E. coli and the source of the strain origin are presented. The fliC genes have been identified and characterized in commensal E. coli derived from 10 healthy animal species living in Zoo Safari Park (Poland). The fliC gene was found in 150 strains by the PCR method. The amplifiedfliC products revealed single bands within the range 1.26-2.16 kbp. Forty restriction patterns (classed by restriction analysis with the use of RsaI (PCR-RFLP RsaI; R-types) were determined. The neighbor-joining method was employed to illustrate the distribution of the kinds of R-types. There are 3-8 various R-types of a diversified frequency of occurrence in strains. Application of PCR-RFLP RsaI permitted the identification of alleles of fliC genes characteristic for E. coli and the estimation of their diversity among the animal species. The transmission ways of E. coli fliC+ between organisms of different species were determined and confirmed the role of transmission and horizontal gene transfer in the generation of the allelic diversity of fliC gene in natural E. coli populations.}, }
@article {pmid17693723, year = {2007}, author = {Knaust, F and Kube, M and Reinhardt, R and Rabus, R}, title = {Analyses of the vrl gene cluster in Desulfococcus multivorans: homologous to the virulence-associated locus of the ovine footrot pathogen Dichelobacter nodosus strain A198.}, journal = {Journal of molecular microbiology and biotechnology}, volume = {13}, number = {1-3}, pages = {156-164}, doi = {10.1159/000103607}, pmid = {17693723}, issn = {1464-1801}, mesh = {Animals ; Base Sequence ; Deltaproteobacteria/*genetics/pathogenicity ; Dichelobacter nodosus/genetics/pathogenicity ; Foot Rot/microbiology ; Gene Expression Regulation, Bacterial ; Gene Order ; Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Molecular Sequence Data ; *Multigene Family ; Reverse Transcriptase Polymerase Chain Reaction ; Sheep ; Sheep Diseases/microbiology ; Virulence/genetics ; }, abstract = {Major parts of the virulence-associated vrl locus known from the gammaproteobacterium Dichelobacter nodosus, the causative agent of ovine footrot, were analyzed in the genome of the sulfate-reducing deltaproteobacterium Desulfococcus multivorans. In the genome of D. multivorans 13 of the 19 vrl genes described for D. nodosus are present and highly conserved with respect to gene sequence and order. The vrl locus and its flanking regions suggest a bacteriophage-mediated transfer into the genome of D. multivorans. Comparative analysis of the deduced Vrl proteins reveals a wide distribution of parts of the virulence-associated vrl locus in distantly related bacteria. Horizontal transfer is suggested as driving mechanism for the circulation of the vrl genes in bacteria. Except for the vrlBMN genes D. multivorans and Desulfovibrio desulfuricans G20 together contain all vrl genes displaying a high degree of similarity. For D. multivorans it could be shown that guanine plus cytosine (GC) content, GC skew, di-, tri- or tetranucleotide distribution did not differ between the vrl locus and its flanking sequences. This could be a hint that the vrl locus originated from a related organism or at least a genome with similar characteristics. The conspicuous high degree of conservation of the analyzed vrl genes may result from a recent transfer event or reflect a function of the vrl genes, which is still unknown and not necessarily disease associated. The latter is supported by the evidence for expression of the vrl genes in D. multivorans, which has not been described as pathogen or to be associated to any disease pattern before.}, }
@article {pmid17693558, year = {2007}, author = {Abbot, P and Aviles, AE and Eller, L and Durden, LA}, title = {Mixed infections, cryptic diversity, and vector-borne pathogens: evidence from Polygenis fleas and Bartonella species.}, journal = {Applied and environmental microbiology}, volume = {73}, number = {19}, pages = {6045-6052}, pmid = {17693558}, issn = {0099-2240}, mesh = {Animals ; Antigens, Bacterial/metabolism ; Bartonella/classification/*isolation &amp; purification/virology ; Bartonella Infections/transmission ; Disease Reservoirs/veterinary ; Gene Transfer, Horizontal ; Insect Vectors/*microbiology ; Mammals/parasitology ; Molecular Sequence Data ; Phylogeny ; Rodent Diseases/*microbiology/parasitology ; Sigmodontinae ; Siphonaptera/*microbiology ; }, abstract = {Coinfections within hosts present opportunities for horizontal gene transfer between strains and competitive interactions between genotypes and thus can be a critical element of the lifestyles of pathogens. Bartonella spp. are Alphaproteobacteria that parasitize mammalian erythrocytes and endothelial cells. Their vectors are thought to be various biting arthropods, such as fleas, ticks, mites, and lice, and they are commonly cited as agents of various emerging diseases. Coinfections by different Bartonella strains and species can be common in mammals, but little is known about specificity and coinfections in arthropod vectors. We surveyed the rate of mixed infections of Bartonella in flea vectors (Polygenis gwyni) parasitizing cotton rats (Sigmodon hispidus) in which previous surveys indicated high rates of infection. We found that nearly all fleas (20 of 21) harbored one or more strains of Bartonella, with rates of coinfection approaching 90%. A strain previously identified as common in cotton rats was also common in their fleas. However, another common strain in cotton rats was absent from P. gwyni, while a rare cotton rat strain was quite common in P. gwyni. Surprisingly, some samples were also coinfected with a strain phylogenetically related to Bartonella clarridgeiae, which is typically associated with felids and ruminants. Finally, a locus (pap31) that is characteristically borne on phage in Bartonella was successfully sequenced from most samples. However, sequence diversity in pap31 was novel in the P. gwyni samples, relative to other Bartonella previously typed with pap31, emphasizing the likelihood of large reservoirs of cryptic diversity in natural populations of the pathogen.}, }
@article {pmid17693521, year = {2007}, author = {Jeon, B and Zhang, Q}, title = {Cj0011c, a periplasmic single- and double-stranded DNA-binding protein, contributes to natural transformation in Campylobacter jejuni.}, journal = {Journal of bacteriology}, volume = {189}, number = {20}, pages = {7399-7407}, pmid = {17693521}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics/*physiology ; Campylobacter jejuni/genetics/*physiology ; DNA/metabolism ; DNA, Bacterial/metabolism ; DNA, Single-Stranded/metabolism ; DNA-Binding Proteins/genetics/*physiology ; Electrophoretic Mobility Shift Assay ; Gene Deletion ; Membrane Proteins/genetics ; Molecular Sequence Data ; Periplasm/chemistry ; Periplasmic Proteins/genetics/physiology ; Protein Binding ; Sequence Homology, Amino Acid ; Transformation, Bacterial/*physiology ; }, abstract = {Campylobacter jejuni is an important bacterial pathogen causing gastroenteritis in humans. C. jejuni is capable of natural transformation, which is considered a major mechanism mediating horizontal gene transfer and generating genetic diversity. Despite recent efforts to elucidate the transformation mechanisms of C. jejuni, the process of DNA binding and uptake in this organism is still not well understood. In this study, we report a previously unrecognized DNA-binding protein (Cj0011c) in C. jejuni that contributes to natural transformation. Cj0011c is a small protein (79 amino acids) with a partial sequence homology to the C-terminal region of ComEA in Bacillus subtilis. Cj0011c bound to both single- and double-stranded DNA. The DNA-binding activity of Cj0011c was demonstrated with a variety of DNAs prepared from C. jejuni or Escherichia coli, suggesting that the DNA binding of Cj0011c is not sequence dependent. Deletion of the cj0011c gene from C. jejuni resulted in 10- to 50-fold reductions in the natural transformation frequency. Different from the B. subtilis ComEA, which is an integral membrane protein, Cj0011c is localized in the periplasmic space of C. jejuni. These results indicate that Cj0011c functions as a periplasmic DNA receptor contributing to the natural transformation of C. jejuni.}, }
@article {pmid17688696, year = {2007}, author = {Mower, JP and Touzet, P and Gummow, JS and Delph, LF and Palmer, JD}, title = {Extensive variation in synonymous substitution rates in mitochondrial genes of seed plants.}, journal = {BMC evolutionary biology}, volume = {7}, number = {}, pages = {135}, pmid = {17688696}, issn = {1471-2148}, support = {R01 GM070612/GM/NIGMS NIH HHS/United States ; GM-70612/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Substitution ; Cycadopsida/classification/*genetics ; *Evolution, Molecular ; *Genes, Mitochondrial ; Magnoliopsida/classification/*genetics ; Phylogeny ; Sequence Homology, Amino Acid ; }, abstract = {BACKGROUND: It has long been known that rates of synonymous substitutions are unusually low in mitochondrial genes of flowering and other land plants. Although two dramatic exceptions to this pattern have recently been reported, it is unclear how often major increases in substitution rates occur during plant mitochondrial evolution and what the overall magnitude of substitution rate variation is across plants.<br><br>RESULTS: A broad survey was undertaken to evaluate synonymous substitution rates in mitochondrial genes of angiosperms and gymnosperms. Although most taxa conform to the generality that plant mitochondrial sequences evolve slowly, additional cases of highly accelerated rates were found. We explore in detail one of these new cases, within the genus Silene. A roughly 100-fold increase in synonymous substitution rate is estimated to have taken place within the last 5 million years and involves only one of ten species of Silene sampled in this study. Examples of unusually slow sequence evolution were also identified. Comparison of the fastest and slowest lineages shows that synonymous substitution rates vary by four orders of magnitude across seed plants. In other words, some plant mitochondrial lineages accumulate more synonymous change in 10,000 years than do others in 100 million years. Several perplexing cases of gene-to-gene variation in sequence divergence within a plant were uncovered. Some of these probably reflect interesting biological phenomena, such as horizontal gene transfer, mitochondrial-to-nucleus transfer, and intragenomic variation in mitochondrial substitution rates, whereas others are likely the result of various kinds of errors.<br><br>CONCLUSION: The extremes of synonymous substitution rates measured here constitute by far the largest known range of rate variation for any group of organisms. These results highlight the utility of examining absolute substitution rates in a phylogenetic context rather than by traditional pairwise methods. Why substitution rates are generally so low in plant mitochondrial genomes yet occasionally increase dramatically remains mysterious.}, }
@article {pmid17686030, year = {2007}, author = {Scott, AE and Timms, AR and Connerton, PL and El-Shibiny, A and Connerton, IF}, title = {Bacteriophage influence Campylobacter jejuni types populating broiler chickens.}, journal = {Environmental microbiology}, volume = {9}, number = {9}, pages = {2341-2353}, doi = {10.1111/j.1462-2920.2007.01351.x}, pmid = {17686030}, issn = {1462-2912}, support = {BB/C504543/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bacteriophages/*genetics ; Campylobacter jejuni/classification/genetics/*virology ; Carrier State ; Chickens/*microbiology ; *Food Microbiology ; Gastrointestinal Tract/*microbiology ; Gene Transfer, Horizontal/*genetics ; Genetic Variation ; Male ; }, abstract = {The characteristics that allow one Campylobacter jejuni genotype to succeed over another under the influence of bacteriophage predation have been examined in experimental broiler chickens following the observation that this succession appeared to occur in naturally colonized broiler chicken flocks. Examination of three C. jejuni strains from a single flock indicated that horizontal transfer of at least 112 kb of genomic DNA from strain F2C10 (bacteriophage sensitive) to strain F2E1 (bacteriophage insensitive) had created strain F2E3. Transfer of this DNA was associated with acquisition of sensitivity to 6 of 25 lytic bacteriophage isolated from the same flock. All strains tested were capable of colonizing broiler chickens but cocolonization revealed that the bacteriophage sensitive strains F2E3 and F2C10 had a competitive advantage over the bacteriophage insensitive strain F2E1. With the addition of lytic bacteriophage the situation was completely reversed, with F2E1 dominating. The inability to replicate bacteriophage is associated with a significant fitness cost that renders the insensitive strain competitive only in the presence of bacteriophage. We demonstrate that interstrain recombination in vivo can generate genome diversity in C. jejuni and that bacteriophage predation is a strong selective pressure that influences the relative success of emergent strains in broiler chickens.}, }
@article {pmid17678544, year = {2007}, author = {Wellner, A and Lurie, MN and Gophna, U}, title = {Complexity, connectivity, and duplicability as barriers to lateral gene transfer.}, journal = {Genome biology}, volume = {8}, number = {8}, pages = {R156}, pmid = {17678544}, issn = {1474-760X}, mesh = {Escherichia coli/*genetics ; Escherichia coli Proteins/*genetics/*metabolism ; *Evolution, Molecular ; Gene Duplication ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Protein Interaction Mapping ; }, abstract = {BACKGROUND: Lateral gene transfer is a major force in microbial evolution and a great source of genetic innovation in prokaryotes. Protein complexity has been claimed to be a barrier for gene transfer, due to either the inability of a new gene's encoded protein to become a subunit of an existing complex (lack of positive selection), or from a harmful effect exerted by the newcomer on native protein assemblages (negative selection).<br><br>RESULTS: We tested these scenarios using data from the model prokaryote Escherichia coli. Surprisingly, the data did not support an inverse link between membership in protein complexes and gene transfer. As the complexity hypothesis, in its strictest sense, seemed valid only to essential complexes, we broadened its scope to include connectivity in general. Transferred genes are found to be less involved in protein-protein interactions, outside stable complexes, and this is especially true for genes recently transferred to the E. coli genome. Thus, subsequent to transfer, new genes probably integrate slowly into existing protein-interaction networks. We show that a low duplicability of a gene is linked to a lower chance of being horizontally transferred. Notably, many essential genes in E. coli are conserved as singletons across multiple related genomes, have high connectivity and a highly vertical phylogenetic signal.<br><br>CONCLUSION: High complexity and connectivity generally do not impede gene transfer. However, essential genes that exhibit low duplicability and high connectivity do exhibit mostly vertical descent.}, }
@article {pmid17676427, year = {2007}, author = {Baldo, L and Prendini, L and Corthals, A and Werren, JH}, title = {Wolbachia are present in southern african scorpions and cluster with supergroup F.}, journal = {Current microbiology}, volume = {55}, number = {5}, pages = {367-373}, pmid = {17676427}, issn = {0343-8651}, mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins/genetics ; Gene Transfer, Horizontal ; Genetic Variation ; Molecular Sequence Data ; *Phylogeny ; Scorpions/*microbiology ; Sequence Homology, Amino Acid ; South Africa ; Wolbachia/classification/*genetics/growth &amp; development ; }, abstract = {The presence and distribution of the intracellular bacteria Wolbachia in the arthropod subphylum Chelicerata (including class Arachnida) has not been extensively explored. Here we report the discovery of Wolbachia in scorpions. Five strains found in host species of the genus Opistophthalmus (Southern African burrowing scorpions) have been characterized by Multilocus Sequence Typing and by Wolbachia Surface Protein. Phylogenetic analyses indicate clustering in the supergroup F and a high genetic relatedness among all scorpion strains as a result of a potential transmission within the host genus. The F-group is an uncommon lineage compared to the A and B supergroups, although it is present in a broad range of hosts (including insects, filarial nematodes, and now arachnids) and across a large geographical area (e.g., North America, Africa, Europe, and Australia). It also shows no evidence of recombination and has a significantly higher genetic diversity than supergroup A and B. Overall, this pattern suggests an older radiation of F-strains with respect to A and B-strains, followed by limited horizontal transmission across host genera and reduced genetic flux among strains. A more extensive sampling of supergroup F-strains is required to confirm this scenario.}, }
@article {pmid17668884, year = {2007}, author = {Brulport, M and Schormann, W and Bauer, A and Hermes, M and Elsner, C and Hammersen, FJ and Beerheide, W and Spitkovsky, D and Härtig, W and Nussler, A and Horn, LC and Edelmann, J and Pelz-Ackermann, O and Petersen, J and Kamprad, M and von Mach, M and Lupp, A and Zulewski, H and Hengstler, JG}, title = {Fate of extrahepatic human stem and precursor cells after transplantation into mouse livers.}, journal = {Hepatology (Baltimore, Md.)}, volume = {46}, number = {3}, pages = {861-870}, doi = {10.1002/hep.21745}, pmid = {17668884}, issn = {0270-9139}, mesh = {Albumins/analysis ; Animals ; *Cell Differentiation ; Humans ; Liver/*cytology ; Mice ; Mice, Inbred NOD ; Mice, SCID ; *Stem Cell Transplantation ; Stem Cells/chemistry/*cytology/physiology ; *Transplantation, Heterologous ; }, abstract = {UNLABELLED: In recent years, a large number of groups studied the fate of human stem cells in livers of immunodeficient animals. However, the interpretation of the results is quite controversial. We transplanted 4 different types of human extrahepatic precursor cells (derived from cord blood, monocytes, bone marrow, and pancreas) into livers of nonobese diabetic/severe combined immunodeficiency mice. Human hepatocytes were used as positive controls. Tracking of the transplanted human cells could be achieved by in situ hybridization with alu probes. Cells with alu-positive nuclei stained positive for human albumin and glycogen. Both markers were negative before transplantation. However, cells with alu-positive nuclei did not show a hepatocyte-like morphology and did not express cytochrome P450 3A4, and this suggests that these cells represent a mixed cell type possibly resulting from partial transdifferentiation. Using antibodies specific for human albumin, we also observed a second human albumin-positive cell type that could be clearly distinguished from the previously described cells by its hepatocyte-like morphology. Surprisingly, these cells had a mouse and not a human nucleus which is explained by transdifferentiation of human cells. Although it has not yet been formally proven, we suggest horizontal gene transfer as a likely mechanism, especially because we observed small fragments of human nuclei in mouse cells that originated from deteriorating transplanted cells. Qualitatively similar results were obtained with all 4 human precursor cell types through different routes of administration with and without the induction of liver damage.<br><br>CONCLUSION: We observed evidence not for transdifferentiation but instead for a complex situation including partial differentiation and possibly horizontal gene transfer.}, }
@article {pmid17668047, year = {2007}, author = {Karpathy, SE and Qin, X and Gioia, J and Jiang, H and Liu, Y and Petrosino, JF and Yerrapragada, S and Fox, GE and Haake, SK and Weinstock, GM and Highlander, SK}, title = {Genome sequence of Fusobacterium nucleatum subspecies polymorphum - a genetically tractable fusobacterium.}, journal = {PloS one}, volume = {2}, number = {7}, pages = {e659}, pmid = {17668047}, issn = {1932-6203}, support = {R01 DA013759/DA/NIDA NIH HHS/United States ; R01 DE015348/DE/NIDCR NIH HHS/United States ; R01 EY013759/EY/NEI NIH HHS/United States ; R01 DE013759/DE/NIDCR NIH HHS/United States ; }, mesh = {Amino Acids/metabolism ; Base Sequence ; Clostridium/genetics ; DNA, Bacterial/genetics ; Evolution, Molecular ; Fusobacterium nucleatum/classification/*genetics/metabolism ; Gene Transfer Techniques ; *Genome, Bacterial ; Humans ; Infections/microbiology ; Introns ; Multigene Family ; Open Reading Frames ; Peptides/chemistry/genetics ; Plasmids/genetics ; *Polymorphism, Genetic ; Repetitive Sequences, Nucleic Acid ; }, abstract = {Fusobacterium nucleatum is a prominent member of the oral microbiota and is a common cause of human infection. F. nucleatum includes five subspecies: polymorphum, nucleatum, vincentii, fusiforme, and animalis. F. nucleatum subsp. polymorphum ATCC 10953 has been well characterized phenotypically and, in contrast to previously sequenced strains, is amenable to gene transfer. We sequenced and annotated the 2,429,698 bp genome of F. nucleatum subsp. polymorphum ATCC 10953. Plasmid pFN3 from the strain was also sequenced and analyzed. When compared to the other two available fusobacterial genomes (F. nucleatum subsp. nucleatum, and F. nucleatum subsp. vincentii) 627 open reading frames unique to F. nucleatum subsp. polymorphum ATCC 10953 were identified. A large percentage of these mapped within one of 28 regions or islands containing five or more genes. Seventeen percent of the clustered proteins that demonstrated similarity were most similar to proteins from the clostridia, with others being most similar to proteins from other gram-positive organisms such as Bacillus and Streptococcus. A ten kilobase region homologous to the Salmonella typhimurium propanediol utilization locus was identified, as was a prophage and integrated conjugal plasmid. The genome contains five composite ribozyme/transposons, similar to the CdISt IStrons described in Clostridium difficile. IStrons are not present in the other fusobacterial genomes. These findings indicate that F. nucleatum subsp. polymorphum is proficient at horizontal gene transfer and that exchange with the Firmicutes, particularly the Clostridia, is common.}, }
@article {pmid17666765, year = {2007}, author = {Bordewich, M and Semple, C}, title = {Computing the hybridization number of two phylogenetic trees is fixed-parameter tractable.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {4}, number = {3}, pages = {458-466}, doi = {10.1109/tcbb.2007.1019}, pmid = {17666765}, issn = {1545-5963}, mesh = {*Algorithms ; *Biological Evolution ; Computer Simulation ; *Genetics, Population ; Hybridization, Genetic/*genetics ; *Models, Genetic ; *Phylogeny ; }, abstract = {Reticulation processes in evolution mean that the ancestral history of certain groups of present-day species is non-tree-like. These processes include hybridization, lateral gene transfer, and recombination. Despite the existence of reticulation, such events are relatively rare and so a fundamental problem for biologists is the following: Given a collection of rooted binary phylogenetic trees on sets of species that correctly represent the tree-like evolution of different parts of their genomes, what is the smallest number of "reticulation" vertices in any network that explains the evolution of the species under consideration? It has been previously shown that this problem is NP-hard even when the collection consists of only two rooted binary phylogenetic trees. However, in this paper, we show that the problem is fixed-parameter tractable in the two-tree instance, when parameterized by this smallest number of reticulation vertices.}, }
@article {pmid17662722, year = {2007}, author = {Da Lage, JL and Danchin, EG and Casane, D}, title = {Where do animal alpha-amylases come from? An interkingdom trip.}, journal = {FEBS letters}, volume = {581}, number = {21}, pages = {3927-3935}, doi = {10.1016/j.febslet.2007.07.019}, pmid = {17662722}, issn = {0014-5793}, mesh = {Animals ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Humans ; alpha-Amylases/*genetics ; }, abstract = {Alpha-amylases are widely found in eukaryotes and prokaryotes. Few amino acids are conserved among these organisms, but at an intra-kingdom level, conserved protein domains exist. In animals, numerous conserved stretches are considered as typical of animal alpha-amylases. Searching databases, we found no animal-type alpha-amylases outside the Bilateria. Instead, we found in the sponge Reniera sp. and in the sea anemone Nematostella vectensis, alpha-amylases whose most similar cognate was that of the amoeba Dictyostelium discoideum. We found that this "Dictyo-type" alpha-amylase was shared not only by these non-Bilaterian animals, but also by other Amoebozoa, Choanoflagellates, and Fungi. This suggested that the Dictyo-type alpha-amylase was present in the last common ancestor of Unikonts. The additional presence of the Dictyo-type in some Ciliates and Excavates, suggests that horizontal gene transfers may have occurred among Eukaryotes. We have also detected putative interkingdom transfers of amylase genes, which obscured the historical reconstitution. Several alternative scenarii are discussed.}, }
@article {pmid17661706, year = {2007}, author = {Pantosti, A and Sanchini, A and Monaco, M}, title = {Mechanisms of antibiotic resistance in Staphylococcus aureus.}, journal = {Future microbiology}, volume = {2}, number = {3}, pages = {323-334}, doi = {10.2217/17460913.2.3.323}, pmid = {17661706}, issn = {1746-0921}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics/metabolism ; Chromosomes, Bacterial/genetics ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Staphylococcus aureus/*drug effects/genetics/metabolism ; }, abstract = {Staphylococcus aureus can exemplify better than any other human pathogen the adaptive evolution of bacteria in the antibiotic era, as it has demonstrated a unique ability to quickly respond to each new antibiotic with the development of a resistance mechanism, starting with penicillin and methicillin, until the most recent, linezolid and daptomycin. Resistance mechanisms include enzymatic inactivation of the antibiotic (penicillinase and aminoglycoside-modification enzymes), alteration of the target with decreased affinity for the antibiotic (notable examples being penicillin-binding protein 2a of methicillin-resistant S. aureus and D-Ala-D-Lac of peptidoglycan precursors of vancomycin-resistant strains), trapping of the antibiotic (for vancomycin and possibly daptomycin) and efflux pumps (fluoroquinolones and tetracycline). Complex genetic arrays (staphylococcal chromosomal cassette mec elements or the vanA operon) have been acquired by S. aureus through horizontal gene transfer, while resistance to other antibiotics, including some of the most recent ones (e.g., fluoroquinolones, linezolid and daptomycin) have developed through spontaneous mutations and positive selection. Detection of the resistance mechanisms and their genetic basis is an important support to antibiotic susceptibility surveillance in S. aureus.}, }
@article {pmid17661231, year = {2007}, author = {Galtier, N}, title = {A model of horizontal gene transfer and the bacterial phylogeny problem.}, journal = {Systematic biology}, volume = {56}, number = {4}, pages = {633-642}, doi = {10.1080/10635150701546231}, pmid = {17661231}, issn = {1063-5157}, mesh = {Bacteria/*classification/*genetics ; *Gene Transfer, Horizontal ; Models, Genetic ; *Phylogeny ; Stochastic Processes ; }, abstract = {How much horizontal gene transfer (HGT) between species influences bacterial phylogenomics is a controversial issue. This debate, however, lacks any quantitative assessment of the impact of HGT on phylogenies and of the ability of tree-building methods to cope with such events. I introduce a Markov model of genome evolution with HGT, accounting for the constraints on time -- an HGT event can only occur between concomitantly living species. This model is used to simulate multigene sequence data sets with or without HGT. The consequences of HGT on phylogenomic inference are analyzed and compared to other well-known phylogenetic artefacts. It is found that supertree methods are quite robust to HGT, keeping high levels of performance even when gene trees are largely incongruent with each other. Gene tree incongruence per se is not indicative of HGT. HGT, however, removes the (otherwise observed) positive relationship between sequence length and gene tree congruence to the estimated species tree. Surprisingly, when applied to a bacterial and a eukaryotic multigene data set, this criterion rejects the HGT hypothesis for the former, but not the latter data set.}, }
@article {pmid17657536, year = {2007}, author = {de Niederhäusern, S and Sabia, C and Messi, P and Guerrieri, E and Manicardi, G and Bondi, M}, title = {VanA-type vancomycin-resistant enterococci in equine and swine rectal swabs and in human clinical samples.}, journal = {Current microbiology}, volume = {55}, number = {3}, pages = {240-246}, pmid = {17657536}, issn = {0343-8651}, mesh = {Animals ; Bacterial Proteins/*genetics ; Carbon-Oxygen Ligases/*genetics ; Enterococcus/*drug effects/genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; Gram-Positive Bacterial Infections/*microbiology/*veterinary ; Horse Diseases/*microbiology ; Horses ; Humans ; Rectum/*microbiology ; Swine ; Swine Diseases/*microbiology ; Urine/microbiology ; Vancomycin Resistance/*genetics ; Wounds and Injuries/microbiology ; }, abstract = {Vancomycin-resistant enterococci (VRE) in healthy people and in food-producing animals seems to be quite common in Europe. The existence of this community reservoir of VRE has been associated with the massive use of avoparcin in animal husbandry. Eight years after the avoparcin ban in Europe, we investigated the incidence of VanA enterococci, their resistance patterns, and the mobility of their glycopeptide-resistance determinants in a sampling of animal rectal swabs and clinical specimens. A total of 259 enterococci isolated from equine, swine, and clinical samples were subcultured on KF-streptococcus agar (Difco Laboratories, Detroit, MI) supplemented with vancomycin and teicoplanin; 7 (6.7%), 10 (16%), and 8 (8.6%) respectively were found to be glycopeptides resistant (VanA phenotype). Slight differences in antimicrobial resistance patterns resulted among VRE recovered from the different sources. Polymerase chain reaction amplification demonstrated the presence of the vanA gene cluster and its extrachromosomal location in VRE plasmid DNA. VanA resistance was transferred in 7 out of 25 mating experiments, 4 with clinical, 2 with swine, and only 1 with equine donors. The conjugative plasmids of animal strains showed a high homology in the restriction profiles, unlike plasmids of clinical microrganisms. Our observations confirmed the possible horizontal transfer of VanA plasmids across different strains and, consequently, the diffusion of the vancomycin-resistance determinants.}, }
@article {pmid17652520, year = {2007}, author = {Wei, W and McCusker, JH and Hyman, RW and Jones, T and Ning, Y and Cao, Z and Gu, Z and Bruno, D and Miranda, M and Nguyen, M and Wilhelmy, J and Komp, C and Tamse, R and Wang, X and Jia, P and Luedi, P and Oefner, PJ and David, L and Dietrich, FS and Li, Y and Davis, RW and Steinmetz, LM}, title = {Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {31}, pages = {12825-12830}, pmid = {17652520}, issn = {0027-8424}, support = {HG 000205/HG/NHGRI NIH HHS/United States ; GM 068717/GM/NIGMS NIH HHS/United States ; HG 02052/HG/NHGRI NIH HHS/United States ; P01 HG000205/HG/NHGRI NIH HHS/United States ; R01 GM068717/GM/NIGMS NIH HHS/United States ; F32 HG000205/HG/NHGRI NIH HHS/United States ; }, mesh = {Base Sequence ; Chromosome Inversion/genetics ; Gene Transfer, Horizontal/genetics ; Genome, Fungal/*genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Open Reading Frames/genetics ; Phenotype ; Phylogeny ; Polymorphism, Genetic/genetics ; Saccharomyces cerevisiae/*genetics ; Translocation, Genetic/genetics ; }, abstract = {We sequenced the genome of Saccharomyces cerevisiae strain YJM789, which was derived from a yeast isolated from the lung of an AIDS patient with pneumonia. The strain is used for studies of fungal infections and quantitative genetics because of its extensive phenotypic differences to the laboratory reference strain, including growth at high temperature and deadly virulence in mouse models. Here we show that the approximately 12-Mb genome of YJM789 contains approximately 60,000 SNPs and approximately 6,000 indels with respect to the reference S288c genome, leading to protein polymorphisms with a few known cases of phenotypic changes. Several ORFs are found to be unique to YJM789, some of which might have been acquired through horizontal transfer. Localized regions of high polymorphism density are scattered over the genome, in some cases spanning multiple ORFs and in others concentrated within single genes. The sequence of YJM789 contains clues to pathogenicity and spurs the development of more powerful approaches to dissecting the genetic basis of complex hereditary traits.}, }
@article {pmid17652424, year = {2007}, author = {Ogata, H and Claverie, JM}, title = {Unique genes in giant viruses: regular substitution pattern and anomalously short size.}, journal = {Genome research}, volume = {17}, number = {9}, pages = {1353-1361}, pmid = {17652424}, issn = {1088-9051}, mesh = {Base Sequence ; Cell Nucleus/virology ; Computer Simulation ; Cytoplasm/virology ; DNA Viruses/classification/*genetics ; DNA, Viral/*genetics ; *Evolution, Molecular ; *Genome, Viral ; Molecular Sequence Data ; Open Reading Frames ; Proteome/analysis ; Sequence Analysis, Protein ; }, abstract = {Large DNA viruses, including giant mimivirus with a 1.2-Mb genome, exhibit numerous orphan genes possessing no database homologs or genes with homologs solely in close members of the same viral family. Due to their solitary nature, the functions and evolutionary origins of those genes remain obscure. We examined sequence features and evolutionary rates of viral family-specific genes in three nucleo-cytoplasmic large DNA virus (NCLDV) lineages. First, we showed that the proportion of family-specific genes does not correlate with sequence divergence rate. Second, position-dependent nucleotide statistics were similar between family-specific genes and the remaining genes in the genome. Third, we showed that the synonymous-to-nonsynonymous substitution ratios in those viruses are at levels comparable to those estimated for vertebrate proteomes. Thus, the vast majority of family-specific genes do not exhibit an accelerated evolutionary rate, and are thus likely to specify functional polypeptides. On the other hand, these family-specific proteins exhibit several distinct properties: (1) they are shorter, (2) they include a larger fraction of predicted transmembrane proteins, and (3) they are enriched in low-complexity sequences. These results suggest that family-specific genes do not correspond to recent horizontal gene transfer. We propose that their characteristic features are the consequences of the specific evolutionary forces shaping the viral gene repertoires in the context of their parasitic lifestyles.}, }
@article {pmid17650316, year = {2007}, author = {Nie, ZM and Zhang, ZF and Wang, D and He, PA and Jiang, CY and Song, L and Chen, F and Xu, J and Yang, L and Yu, LL and Chen, J and Lv, ZB and Lu, JJ and Wu, XF and Zhang, YZ}, title = {Complete sequence and organization of Antheraea pernyi nucleopolyhedrovirus, a dr-rich baculovirus.}, journal = {BMC genomics}, volume = {8}, number = {}, pages = {248}, pmid = {17650316}, issn = {1471-2164}, mesh = {Animals ; Gene Transfer, Horizontal ; *Genome, Viral ; Lepidoptera/virology ; Nucleopolyhedroviruses/*genetics ; }, abstract = {BACKGROUND: The completion and reporting of baculovirus genomes is extremely important as it advances our understanding of gene function and evolution. Due to the large number of viral genomes now sequenced it is very important that authors present significantly detailed analyses to advance the understanding of the viral genomes. However, there is no report of the Antheraea pernyi nucleopolyhedrovirus (AnpeNPV) genome.<br><br>RESULTS: The genome of AnpeNPV, which infects Chinese tussah silkworm (Antheraea pernyi), was sequenced and analyzed. The genome was 126,629 bp in size. The G+C content of the genome, 53.4%, was higher than that of most of the sequenced baculoviruses. 147 open reading frames (ORFs) that putatively encode proteins of 50 or more amino acid residues with minimal overlap were determined. Of the 147 ORFs, 143 appeared to be homologous to other baculovirus genes, and 4 were unique to AnpeNPV. Furthermore, there are still 29 and 33 conserved genes present in all baculoviruses and all lepidopteran baculoviruses respectively. In addition, the total number of genes common to all lepidopteran NPVs is sill 74, however the 74 genes are somewhat different from the 74 genes identified before because of some new sequenced NPVs. Only 6 genes were found exclusively in all lepidopteran NPVs and 12 genes were found exclusively in all Group I NPVs. AnpeNPV encodes v-trex(Anpe115, a 3' to 5' repair exonuclease), which was observed only in CfMNPV and CfDEFNPV in Group I NPVs. This gene potentially originated by horizontal gene transfer from an ancestral host. In addition, AnpeNPV encodes two conotoxin-like gene homologues (ctls), ctl1 and ctl2, which were observed only in HycuNPV, OpMNPV and LdMNPV. Unlike other baculoviruses, only 3 typical homologous regions (hrs) were identified containing 2~9 repeats of a 30 bp-long palindromic core. However, 24 perfect or imperfect direct repeats (drs) with a high degree of AT content were found within the intergenic spacer regions that may function as non-hr, ori-like regions found in GrleGV, CpGV and AdorGV. 9 drs were also found in intragenic spacer regions of AnpeNPV.<br><br>CONCLUSION: AnpeNPV belongs to Group I NPVs and is most similar to HycuNPV, EppoNPV, OpMNPV and CfMNPV based on gene content, genome arrangement, and amino acid identity. In addition, analysis of genes that flank hrs supported the argument that these regions are involved in the transfer of sequences between the virus and host.}, }
@article {pmid17644584, year = {2007}, author = {Raghavan, R and Miller, SR and Hicks, LD and Minnick, MF}, title = {The unusual 23S rRNA gene of Coxiella burnetii: two self-splicing group I introns flank a 34-base-pair exon, and one element lacks the canonical omegaG.}, journal = {Journal of bacteriology}, volume = {189}, number = {18}, pages = {6572-6579}, pmid = {17644584}, issn = {0021-9193}, support = {U54 AI065357/AI/NIAID NIH HHS/United States ; U54 AI065357-01/AI/NIAID NIH HHS/United States ; U54 AI065357-030023/AI/NIAID NIH HHS/United States ; }, mesh = {Base Sequence ; Coxiella burnetii/*genetics/growth &amp; development/metabolism ; Exons/genetics ; Genes, rRNA/*genetics ; Introns/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Polymerase Chain Reaction ; *RNA Splicing ; RNA, Ribosomal, 23S/*genetics ; Sequence Analysis, DNA ; }, abstract = {We describe the presence and characteristics of two self-splicing group I introns in the sole 23S rRNA gene of Coxiella burnetii. The two group I introns, Cbu.L1917 and Cbu.L1951, are inserted at sites 1917 and 1951 (Escherichia coli numbering), respectively, in the 23S rRNA gene of C. burnetii. Both introns were found to be self-splicing in vivo and in vitro even though the terminal nucleotide of Cbu.L1917 is adenine and not the canonical conserved guanine, termed OmegaG, found in Cbu.L1951 and all other group I introns described to date. Predicted secondary structures for both introns were constructed and revealed that Cbu.L1917 and Cbu.L1951 were group IB2 and group IA3 introns, respectively. We analyzed strains belonging to eight genomic groups of C. burnetii to determine sequence variation and the presence or absence of the elements and found both introns to be highly conserved (>/=99%) among them. Although phylogenetic analysis did not identify the specific identities of donors, it indicates that the introns were likely acquired independently; Cbu.L1917 was acquired from other bacteria like Thermotoga subterranea and Cbu.L1951 from lower eukaryotes like Acanthamoeba castellanii. We also confirmed the fragmented nature of mature 23S rRNA in C. burnetii due to the presence of an intervening sequence. The presence of three selfish elements in C. burnetii's 23S rRNA gene is very unusual for an obligate intracellular bacterium and suggests a recent shift to its current lifestyle from a previous niche with greater opportunities for lateral gene transfer.}, }
@article {pmid17634295, year = {2007}, author = {Zheng, B and Tomita, H and Xiao, YH and Wang, S and Li, Y and Ike, Y}, title = {Molecular characterization of vancomycin-resistant enterococcus faecium isolates from mainland China.}, journal = {Journal of clinical microbiology}, volume = {45}, number = {9}, pages = {2813-2818}, pmid = {17634295}, issn = {0095-1137}, mesh = {Bacterial Typing Techniques/methods ; China/epidemiology ; Conjugation, Genetic ; DNA Transposable Elements/genetics ; DNA, Bacterial/chemistry/genetics ; Enterococcus faecium/*classification/drug effects/*genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; Genotype ; Gram-Positive Bacterial Infections/epidemiology/*microbiology ; Humans ; Molecular Epidemiology ; Plasmids/genetics ; Sequence Analysis, DNA ; Vancomycin Resistance/*genetics ; }, abstract = {Little is known about vancomycin-resistant enterococci in China. Thirteen pulsed-field gel electrophoresis-confirmed heterogeneous VanA-type vancomycin-resistant Enterococcus faecium (VRE) isolates were obtained from five Chinese hospitals from 2001 to 2005. The isolates were typed by multilocus sequence typing into nine different sequence types (STs), including five new STs (ST18, ST25, ST78, ST203, ST320, ST321, ST322, ST323, and ST335). Vancomycin resistance in each isolate was encoded on conjugative plasmids; two of the plasmids, pZB18 (67 kbp) and pZB22 (200 kbp), were highly conjugative and were able to transfer at high frequencies of around 10(-4) and 10(-7) per donor cell in broth mating, respectively. None of the plasmids identified in these isolates carried traA, which is usually conserved in the pMG1-like highly conjugative plasmid for E. faecium, implying that pZB18 and pZB22 were novel types of a highly conjugative plasmid in enterococci. Thirteen Tn1546-like elements encoding VanA-type VRE on the conjugative plasmids were classified into six types (types I to VI), and most of them contained both IS1216V and IS1542 insertions. The isolates carrying the type II element were predominant. The six type elements were different from that of a VanA-type Enterococcus faecalis strain isolated from Chinese chicken meat. The results suggested that the disseminations of VRE in these areas were by Tn1546-like elements being acquired by the conjugative plasmids and transferred among E. faecium strains.}, }
@article {pmid17634101, year = {2007}, author = {Krupovic, M and Bamford, DH}, title = {Putative prophages related to lytic tailless marine dsDNA phage PM2 are widespread in the genomes of aquatic bacteria.}, journal = {BMC genomics}, volume = {8}, number = {}, pages = {236}, pmid = {17634101}, issn = {1471-2164}, mesh = {Bacteria/genetics/virology ; Capsid Proteins/genetics ; Corticoviridae/*genetics ; Databases, Protein ; Evolution, Molecular ; Genome, Bacterial/*genetics ; Genomics/*methods ; Prophages/*genetics ; }, abstract = {BACKGROUND: The origin and evolution of viruses is currently a heavily discussed issue. One element in this discussion is the innate viral "self" concept, which suggests that viral structures and functions can be divided into two categories. The first category consists of genetic determinants that are inherited from a viral ancestor and encode the viral "self". The second group consists of another set of structures and functions, the "nonself", which is interchangeable between different viruses and can be obtained via lateral gene transfer. Comparing the structures and sequences of the "self" elements, we have proposed that viruses can be grouped into lineages regardless of which domain of life (bacteria, archaea, eukarya) they infect. It has also been suggested that viruses are ancient and possibly predate modern cells.<br><br>RESULTS: Here we identified thirteen putative prophages (viral genomes integrated into bacterial chromosome) closely related to the virulent icosahedral tailless lipid-containing bacteriophage PM2. Using the comparative genomics approach, we present evidence to support the viral "self" hypothesis and divide genes of the bacteriophage PM2 and related prophages into "self" and "nonself" categories.<br><br>CONCLUSION: We show here that the previously proposed most conserved viral "self" determinants, the major coat protein and the packaging ATPase, were the only proteins that could be recognized in all detected corticoviral elements. We also argue here that the genes needed for viral genome replication, as well as for host cell lysis, belong to the "nonself" category of genes.Furthermore, we suggest that abundance of PM2-like viruses in the aquatic environment as well as their importance in the ecology of aquatic microorganisms might have been underestimated.}, }
@article {pmid17633442, year = {2007}, author = {Walker, A}, title = {Say hello to our little friends.}, journal = {Nature reviews. Microbiology}, volume = {5}, number = {8}, pages = {572-573}, doi = {10.1038/nrmicro1720}, pmid = {17633442}, issn = {1740-1534}, mesh = {Archaeal Proteins/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; *Bacteroides/genetics/growth &amp; development/isolation &amp; purification/physiology ; Digestive System/*microbiology ; *Ecosystem ; Female ; Gene Transfer, Horizontal ; Genome, Archaeal ; Genome, Bacterial ; Humans ; Male ; Methane/metabolism ; *Methanobacteriaceae/genetics/growth &amp; development/physiology ; *Methanobrevibacter/genetics/growth &amp; development/physiology ; Sequence Analysis, DNA ; }, }
@article {pmid17631633, year = {2007}, author = {Haft, RJ and Gachelet, EG and Nguyen, T and Toussaint, L and Chivian, D and Traxler, B}, title = {In vivo oligomerization of the F conjugative coupling protein TraD.}, journal = {Journal of bacteriology}, volume = {189}, number = {18}, pages = {6626-6634}, pmid = {17631633}, issn = {0021-9193}, support = {T32 GM07270/GM/NIGMS NIH HHS/United States ; T35 HL07763/HL/NHLBI NIH HHS/United States ; T32 GM007270/GM/NIGMS NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; T35 HL007763/HL/NHLBI NIH HHS/United States ; }, mesh = {Cell Membrane/metabolism ; *Conjugation, Genetic ; Cross-Linking Reagents ; Dimerization ; Escherichia coli/genetics/growth &amp; development/metabolism ; Escherichia coli Proteins/chemistry/genetics/*metabolism ; F Factor/*genetics ; Membrane Proteins/chemistry/genetics/*metabolism ; Models, Molecular ; Mutation ; }, abstract = {Type IV secretory systems are a group of bacterial transporters responsible for the transport of proteins and nucleic acids directly into recipient cells. Such systems play key roles in the virulence of some pathogenic organisms and in conjugation-mediated horizontal gene transfer. Many type IV systems require conserved "coupling proteins," transmembrane polypeptides that are critical for transporting secreted substrates across the cytoplasmic membrane of the bacterium. In vitro evidence suggests that the functional form of coupling proteins is a homohexameric, ring-shaped complex. Using a library of tagged mutants, we investigated the structural and functional organization of the F plasmid conjugative coupling protein TraD by coimmunoprecipitation, cross-linking, and genetic means. We present direct evidence that coupling proteins form stable oligomeric complexes in the membranes of bacteria and that the formation of some of these complexes requires other F-encoded functions. Our data also show that different regions of TraD play distinct roles in the oligomerization process. We postulate a model for in vivo oligomerization and discuss the probable participation of individual domains of TraD in each step.}, }
@article {pmid17627781, year = {2007}, author = {Miki, T and Ueki, M and Kawabata, Z and Yamamura, N}, title = {Long-term dynamics of catabolic plasmids introduced to a microbial community in a polluted environment: a mathematical model.}, journal = {FEMS microbiology ecology}, volume = {62}, number = {2}, pages = {211-221}, doi = {10.1111/j.1574-6941.2007.00357.x}, pmid = {17627781}, issn = {0168-6496}, mesh = {Bacteria/genetics/*metabolism ; Computer Simulation ; *Environmental Microbiology ; Gene Transfer, Horizontal ; *Models, Biological ; Plasmids/genetics/*metabolism ; Xenobiotics/*metabolism ; }, abstract = {The long-term dynamics of mobile plasmids in natural environments are unclear. This is the first study of the long-term dynamics of introduced plasmids with xenobiotic degradation abilities using a mathematical model that describes the horizontal gene transfer (HGT) of plasmids into indigenous bacteria via conjugation. We focussed on negative feedback between the spread of plasmids and their selective advantage, i.e. the severe competition between plasmid-bearing and plasmid-free bacteria resulting from a decrease in xenobiotic concentration caused by the gene expression of plasmids, favoring plasmid-free bacteria. Two types of HGT enhanced the persistence of plasmids and the degradation of the xenobiotic in different conditions: a relatively low rate of 'intergeneric HGT' from introduced to indigenous bacteria and a high rate of 'intraindigenous HGT' from indigenous to indigenous bacteria. In addition, when the indigenous resource supply rate was high and when the cost of bearing plasmids was low, both types of HGT made large contributions to xenobiotic degradation compared to the contribution of vertical transfer via plasmid replication within the introduced host population. Initial conditions were also important; a higher initial density of introduced plasmid-bearing bacteria led to a lower degradation rate over a long time scale.}, }
@article {pmid17623783, year = {2007}, author = {Piskurek, O and Okada, N}, title = {Poxviruses as possible vectors for horizontal transfer of retroposons from reptiles to mammals.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {29}, pages = {12046-12051}, pmid = {17623783}, issn = {0027-8424}, mesh = {Animals ; Base Sequence ; Consensus Sequence ; Gene Transfer, Horizontal/*genetics ; *Genetic Vectors ; Geography ; Mammals/*genetics ; Molecular Sequence Data ; Phylogeny ; Poxviridae/*genetics ; Reptiles/*genetics ; Retroelements/*genetics ; Short Interspersed Nucleotide Elements/genetics ; }, abstract = {Poxviruses (Poxviridae) are a family of double-stranded DNA viruses with no RNA stage. Members of the genus Orthopoxvirus (OPV) are highly invasive and virulent. It was recently shown that the taterapox virus (TATV) from a West African rodent is the sister of camelpox virus and therefore belongs to the clade closest to the variola virus (VARV), the etiological agent of smallpox. Although these OPVs are among the most dreaded pathogens on Earth, our current knowledge of their genomes, their origins, and their possible hosts is still very limited. Here, we report the horizontal transfer of a retroposon (known only from reptilian genomes) to the TATV genome. After isolating and analyzing different subfamilies of short interspersed elements (SINEs) from lizards and snakes, we identified a highly poisonous snake (Echis ocellatus) from West Africa as the closest species from which the SINE sequence discovered in the TATV genome (TATV-SINE) was transferred to the virus. We discovered direct repeats derived from the virus flanking the TATV-SINE, and the absence of any snake-derived DNA flanking the SINE. These data provide strong evidence that the TATV-SINE was actually transferred within the snake to the viral genome by retrotransposition and not by any horizontal transfer at the DNA level. We propose that the snake is another host for TATV, suggesting that VARV-related epidemiologically relevant viruses may have derived from our cold-blooded ancestors and that poxviruses are possible vectors for horizontal transfer of retroposons from reptiles to mammals.}, }
@article {pmid17621376, year = {2007}, author = {Scannell, DR and Butler, G and Wolfe, KH}, title = {Yeast genome evolution--the origin of the species.}, journal = {Yeast (Chichester, England)}, volume = {24}, number = {11}, pages = {929-942}, doi = {10.1002/yea.1515}, pmid = {17621376}, issn = {0749-503X}, mesh = {*Evolution, Molecular ; *Gene Duplication ; Gene Order/genetics ; Genes, Fungal/*genetics ; Genome, Fungal/*genetics ; Yeasts/*classification/genetics ; }, abstract = {With almost 20 genomes sequenced from unicellular ascomycetes (Saccharomycotina), and the prospect of many more in the pipeline, we review the patterns and processes of yeast genome evolution. A central core of about 4000 genes is shared by all the sequenced yeast genomes. Gains of genes by horizontal gene transfer seem to be very rare. Gene losses are more frequent, and losses of whole sets of genes in some pathways in some species can be understood in terms of species-specific differences in biology. The wholesale loss of redundant copies of duplicated genes after whole-genome duplication in the ancestor of one clade of yeasts is likely to have caused the emergence of many reproductively isolated lineages of yeasts at that time, but other processes are responsible for species barriers that arose more recently among close relatives of Saccharomyces cerevisiae.}, }
@article {pmid17618225, year = {2007}, author = {Zeng, Y and Jiao, N}, title = {Source environment feature related phylogenetic distribution pattern of anoxygenic photosynthetic bacteria as revealed by pufM analysis.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {45}, number = {3}, pages = {205-212}, pmid = {17618225}, issn = {1225-8873}, mesh = {Bacteria/*classification/*genetics ; Bacterial Proteins/*genetics ; *Environmental Microbiology ; Gene Transfer, Horizontal ; Photosynthesis ; Photosynthetic Reaction Center Complex Proteins/*genetics ; *Phylogeny ; Sequence Homology ; }, abstract = {Anoxygenic photosynthesis, performed primarily by anoxygenic photosynthetic bacteria (APB), has been supposed to arise on Earth more than 3 billion years ago. The long established APB are distributed in almost every corner where light can reach. However, the relationship between APB phylogeny and source environments has been largely unexplored. Here we retrieved the pufM sequences and related source information of 89 pufM containing species from the public database. Phylogenetic analysis revealed that horizontal gene transfer (HGT) most likely occurred within 11 out of a total 21 pufM subgroups, not only among species within the same class but also among species of different phyla or subphyla. A clear source environment feature related phylogenetic distribution pattern was observed, with all species from oxic habitats and those from anoxic habitats clustering into independent subgroups, respectively. HGT among ancient APB and subsequent long term evolution and adaptation to separated niches may have contributed to the coupling of environment and pufM phylogeny.}, }
@article {pmid17618086, year = {2007}, author = {Mercier, A and Bertolla, F and Passelègue-Robe, E and Simonet, P}, title = {Natural transformation-based foreign DNA acquisition in a Ralstonia solanacearum mutS mutant.}, journal = {Research in microbiology}, volume = {158}, number = {6}, pages = {537-544}, doi = {10.1016/j.resmic.2007.05.003}, pmid = {17618086}, issn = {0923-2508}, mesh = {Bacterial Proteins/genetics ; Base Pair Mismatch ; Cell Cycle Proteins/*genetics ; Cloning, Molecular ; DNA, Bacterial/genetics/*metabolism ; DNA, Plant/genetics/*metabolism ; Escherichia coli/genetics ; Mutation ; Plasmids ; Ralstonia solanacearum/*genetics ; Transformation, Bacterial/*genetics ; }, abstract = {Mutator strains with defective methyl-mismatch repair (MMR) systems have been shown to play an important role in adaptation of bacterial populations to changing and stressful environments. In this report, we describe the impact of mutS::aacC3-IV inactivation on foreign DNA acquisition by natural transformation in the phytopathogenic bacterium Ralstonia solanacearum. A mutS mutant of R. solanacearum exhibited 33- to 60-fold greater spontaneous mutation frequencies, in accordance with a mutator phenotype. Transformation experiments indicated that intra- and interspecific DNA transfers increased up to 89-fold. To assess horizontal gene transfer (HGT) from genetically modified plants to R. solanacearum, fitness of the mutator was first evaluated in soil and plant environments. Competitiveness was not modified after 61 days in soil and 8 days in tomato, and the progress of plant decay symptoms was similar to that of the wild-type strain. Despite its survival in soil and in planta, and the powerful capacities of HGT, R. solanacearum was not genetically transformed by transgenic plant DNA in a wide range of in vitro and in planta tests.}, }
@article {pmid17618069, year = {2007}, author = {Liu, Y and Ichige, A and Kobayashi, I}, title = {Regulation of the EcoRI restriction-modification system: Identification of ecoRIM gene promoters and their upstream negative regulators in the ecoRIR gene.}, journal = {Gene}, volume = {400}, number = {1-2}, pages = {140-149}, doi = {10.1016/j.gene.2007.06.006}, pmid = {17618069}, issn = {0378-1119}, mesh = {Base Sequence ; DNA Restriction-Modification Enzymes/*genetics ; Deoxyribonuclease EcoRI/genetics ; Escherichia coli/*genetics ; *Gene Expression Regulation, Bacterial ; *Gene Expression Regulation, Enzymologic ; Genes, Bacterial ; Molecular Sequence Data ; *Promoter Regions, Genetic ; Regulatory Sequences, Nucleic Acid ; Site-Specific DNA-Methyltransferase (Adenine-Specific)/genetics ; Transcription Initiation Site ; }, abstract = {Type II restriction-modification (R-M) systems are composed of linked restriction endonuclease and modification methyltransferase genes and serve as barriers to horizontal gene transfer even though they are mobile in themselves. Their products kill host bacterial cells that have lost the R-M genes, a process that helps to maintain the frequency of the R-M systems in the viable cell population. Their establishment and maintenance in a bacterial host are expected to involve fine regulation of their gene expression. In the present study, we analyzed transcription of the modification gene and its regulation within the EcoRI R-M system. Northern blotting revealed that the downstream ecoRIM gene is transcribed as a monocistronic mRNA and as part of a larger bicistronic mRNA together with the upstream ecoRIR gene. Primer extension, RNase protection, and mutational analysis using lacZ gene fusions identified two overlapping promoters for ecoRIM gene transcription within the ecoRIR gene. Further mutational analysis revealed that two upstream AT-rich elements within the ecoRIR gene, "AATAAA" and "ATTATAAATATA," function as negative regulators of these promoters. Simultaneous substitution of these two elements resulted in a four-fold increase in beta-galactosidase activity and a five-fold increase in transcript levels as measured by RNase protection assay. RNA measurements of the ecoRIM transcript suggested that these elements decreased ecoRIM expression by interfering with transcription initiation of the ecoRIM promoters. Possible roles for these ecoRIM promoters and their negative regulators in the EcoRI R-M system are discussed.}, }
@article {pmid17617713, year = {2007}, author = {Huong, NL and Itoh, K and Miyamoto, M and Suyama, K and Yamamoto, H}, title = {Chlorophenol hydroxylase activity encoded by TfdB from 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading Bradyrhizobium sp. strain RD5-C2.}, journal = {Bioscience, biotechnology, and biochemistry}, volume = {71}, number = {7}, pages = {1691-1696}, doi = {10.1271/bbb.70106}, pmid = {17617713}, issn = {0916-8451}, mesh = {2,4-Dichlorophenoxyacetic Acid/*metabolism ; Bradyrhizobium/*enzymology/genetics ; Chlorophenols/*metabolism ; Mixed Function Oxygenases/*genetics ; Molecular Sequence Data ; }, abstract = {The tfdB gene encoding chlorophenol hydroxylase and its homolog were found in 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading strain RD5-C2, which belongs to Bradyrhizobium sp. of alpha-Proteobacteria. The nucleotide and deduced amino acid sequence identities of the two genes, designated tfdBa and tfdBb, were 60% and 57% respectively. Their nucleotide sequences most closely matched those of previously reported tfdB, which consisted of those from 2,4-D-degrading beta- and gamma-Proteobacteria and Sphingomonas sp. in alpha-Proteobacteria, with 61-67% identity. The TfdBa expressed in Escherichia coli showed the highest activity for 2,4-dichlorophenol but a narrower range of activity for the other chlorophenols than previously reported TfdBs. In the case of TfdBb, however, no observable activity for any chlorophenols or phenol was detected, although production of a protein with an appropriate molecular size was observed. Based on codon usage patterns and the GC content of the genes, it probable that the tfdBa genes in the 2,4-D-degrading Bradyrhizobium sp. were obtained through horizontal gene transfer.}, }
@article {pmid17614791, year = {2007}, author = {Ohradanova, A and Vullo, D and Kopacek, J and Temperini, C and Betakova, T and Pastorekova, S and Pastorek, J and Supuran, CT}, title = {Reconstitution of carbonic anhydrase activity of the cell-surface-binding protein of vaccinia virus.}, journal = {The Biochemical journal}, volume = {407}, number = {1}, pages = {61-67}, pmid = {17614791}, issn = {1470-8728}, mesh = {Acetazolamide/pharmacology ; Amino Acid Sequence ; Binding Sites ; Carbonic Anhydrases/chemistry/*genetics/*metabolism ; HeLa Cells ; Histidine/genetics/metabolism ; Humans ; Molecular Sequence Data ; Mutation ; Phylogeny ; Protein Engineering ; Recombinant Proteins/genetics/isolation &amp; purification/metabolism ; Sequence Alignment ; Transfection ; Vaccinia virus/*enzymology/metabolism ; Viral Proteins/chemistry/*genetics/*metabolism ; }, abstract = {The N-terminal region of a 32 kDa cell-surface-binding protein, encoded by the D8L gene of vaccinia virus, shows sequence homology to CAs (carbonic anhydrases; EC 4.2.1.1). The active CAs catalyse the reversible hydration of CO2 to bicarbonate participating in many physiological processes. The CA-like domain of vaccinia protein [vaccCA (vaccinia virus CA-like protein)] contains one of the three conserved histidine residues required for co-ordination to the catalytic zinc ion and for enzyme activity. In the present study, we report the engineering of catalytically active vaccCA mutants by introduction of the missing histidine residues into the wild-type protein. The wild-type vaccCA was inactive as a catalyst and does not bind sulfonamide CA inhibitors. Its position on a phylogram with other hCAs (human CAs) shows a relationship with the acatalytic isoforms CA X and XI, suggesting that the corresponding viral gene was acquired from the human genome by horizontal gene transfer. The single mutants (vaccCA N92H/Y69H) showed low enzyme activity and low affinity for acetazolamide, a classical sulfonamide CA inhibitor. The activity of the double mutant, vaccCA N92H/Y69H, was much higher, of the same order of magnitude as that of some human isoforms, namely CA VA and CA XII. Moreover, its affinity for acetazolamide was high, comparable with that of the most efficient human isoenzyme, CA II (in the low nanomolar range). Multiplication of vaccinia virus in HeLa cells transfected with the vaccCA N92H/Y69H double mutant was approx. 2-fold more efficient than in wild-type vaccCA transfectants, suggesting that the reconstitution of the enzyme activity improved the virus life cycle.}, }
@article {pmid17610831, year = {2007}, author = {Doolittle, WF and Zhaxybayeva, O}, title = {Evolution: reducible complexity -- the case for bacterial flagella.}, journal = {Current biology : CB}, volume = {17}, number = {13}, pages = {R510-2}, doi = {10.1016/j.cub.2007.05.003}, pmid = {17610831}, issn = {0960-9822}, mesh = {Bacteria/*genetics ; Bacterial Proteins/genetics ; *Biological Evolution ; Flagella/*genetics ; Gene Transfer, Horizontal ; }, abstract = {A recent paper, which will surely figure centrally in the debate between evolutionists and Intelligent Design creationists, proposes a (perhaps too simple) scheme for the evolution of bacterial flagella.}, }
@article {pmid17609597, year = {2007}, author = {Willems, RJ and Bonten, MJ}, title = {Glycopeptide-resistant enterococci: deciphering virulence, resistance and epidemicity.}, journal = {Current opinion in infectious diseases}, volume = {20}, number = {4}, pages = {384-390}, doi = {10.1097/QCO.0b013e32818be63d}, pmid = {17609597}, issn = {0951-7375}, mesh = {Anti-Bacterial Agents/*pharmacology ; Cross Infection/epidemiology/microbiology ; Drug Resistance, Bacterial ; Enterococcus/*drug effects/genetics/*pathogenicity ; Enterococcus faecalis/drug effects/genetics/pathogenicity ; Enterococcus faecium/drug effects/genetics/pathogenicity ; Glycopeptides/*pharmacology ; Gram-Positive Bacterial Infections/epidemiology/*microbiology ; Humans ; Virulence ; }, abstract = {PURPOSE OF REVIEW: Since their first discovery, glycopeptide-resistant enterococci have emerged as important nosocomial pathogens first in the US, followed by the rest of the world. In this review the most recent findings that relate to enterococcal epidemiology, virulence and glycopeptide-resistance maintenance will be discussed.<br><br>RECENT FINDINGS: Frequent horizontal gene transfer and recombination, resulting in high-level genome plasticity, facilitating rapid responsiveness of enterococci to changing environmental conditions may have contributed to the worldwide emergence. For Enterococcus faecium this has resulted in the development of a distinct genetic subspecies, clonal complex 17, responsible for the majority of glycopeptide-resistant enterococci-related hospital burden. Preliminary data also suggest that such high-risk enterococcal clonal complexes may exist within Enterococcus faecalis. The last 2 years have not only disclosed novel determinants implicated in enterococcal pathogenesis, but also showed that enterococci are able to sense their environment and regulate virulence gene expression accordingly. Linkage of glycopeptide resistance in enterococci to plasmid maintenance systems holds a doomed perspective for controlling antibiotic resistance emergence.<br><br>SUMMARY: Recent developments have improved our understanding of enterococcal population structure, pathogenesis and glycopeptide-resistance maintenance. This may contribute to the development of novel intervention strategies to prevent enterococcal infections and contain the spread of glycopeptide-resistant enterococci.}, }
@article {pmid17608697, year = {2007}, author = {Syed, SS and Gilsdorf, JR}, title = {Prevalence of hicAB, lav, traA, and hifBC among Haemophilus influenzae middle ear and throat strains.}, journal = {FEMS microbiology letters}, volume = {274}, number = {2}, pages = {180-183}, doi = {10.1111/j.1574-6968.2007.00822.x}, pmid = {17608697}, issn = {0378-1097}, support = {DC05840/DC/NIDCD NIH HHS/United States ; HD007513/HD/NICHD NIH HHS/United States ; }, mesh = {Bacterial Outer Membrane Proteins/*analysis/genetics ; Bacterial Proteins/*analysis/genetics ; Ear, Middle/*microbiology ; Gene Transfer, Horizontal ; Genome, Bacterial ; Haemophilus Infections/*epidemiology/microbiology ; *Haemophilus influenzae/isolation &amp; purification ; Humans ; Immunoblotting/methods ; Molecular Chaperones/*analysis/genetics ; Pharynx/*microbiology ; *Prevalence ; }, abstract = {Nontypeable Haemophilus influenzae (NTHi) is an important cause of illness among children. To further understand the role of laterally transferred genes in NTHi colonization and otitis media, the prevalence of hicAB, lav, tnaA, and hifBC was determined among 44 middle ear and 35 throat NTHi isolates by dot-blot hybridization.}, }
@article {pmid17605801, year = {2007}, author = {Desmond, E and Brochier-Armanet, C and Gribaldo, S}, title = {Phylogenomics of the archaeal flagellum: rare horizontal gene transfer in a unique motility structure.}, journal = {BMC evolutionary biology}, volume = {7}, number = {}, pages = {106}, pmid = {17605801}, issn = {1471-2148}, mesh = {Archaea/classification/*genetics ; Evolution, Molecular ; Flagella/*genetics ; *Gene Transfer, Horizontal ; Genes, Archaeal ; *Genome, Archaeal ; *Phylogeny ; }, abstract = {BACKGROUND: As bacteria, motile archaeal species swim by means of rotating flagellum structures driven by a proton gradient force. Interestingly, experimental data have shown that the archaeal flagellum is non-homologous to the bacterial flagellum either in terms of overall structure, components and assembly. The growing number of complete archaeal genomes now permits to investigate the evolution of this unique motility system.<br><br>RESULTS: We report here an exhaustive phylogenomic analysis of the components of the archaeal flagellum. In all complete archaeal genomes, the genes coding for flagellum components are co-localized in one or two well-conserved genomic clusters showing two different types of organizations. Despite their small size, these genes harbor a good phylogenetic signal that allows reconstruction of their evolutionary histories. These support a history of mainly vertical inheritance for the components of this unique motility system, and an interesting possible ancient horizontal gene transfer event (HGT) of a whole flagellum-coding gene cluster between Euryarchaeota and Crenarchaeota.<br><br>CONCLUSION: Our study is one of the few exhaustive phylogenomics analyses of a non-informational cell machinery from the third domain of life. We propose an evolutionary scenario for the evolution of the components of the archaeal flagellum. Moreover, we show that the components of the archaeal flagellar system have not been frequently transferred among archaeal species, indicating that gene fixation following HGT can also be rare for genes encoding components of large macromolecular complexes with a structural role.}, }
@article {pmid17600834, year = {2007}, author = {Raman, K and Rajagopalan, P and Chandra, N}, title = {Hallmarks of mycolic acid biosynthesis: a comparative genomics study.}, journal = {Proteins}, volume = {69}, number = {2}, pages = {358-368}, doi = {10.1002/prot.21591}, pmid = {17600834}, issn = {1097-0134}, mesh = {Biosynthetic Pathways/*genetics ; Genome, Bacterial ; Genomics/*methods ; Mycobacterium leprae/enzymology/genetics/metabolism ; Mycobacterium tuberculosis/enzymology/genetics/metabolism ; Mycolic Acids/*metabolism ; Phylogeny ; Protein Interaction Mapping ; Sequence Analysis, Protein ; Sequence Homology, Amino Acid ; }, abstract = {Mycolic acids, which render unique qualities to mycobacteria, are known to be important for mycobacterial growth, survival, and pathogenicity. It is of interest to understand the evolutionary origins of the mycolic acid pathway (MAP), as well as the common minimum principles critical for generating the capability of mycolic acid biosynthesis. The recent curation of a comprehensive model of the MAP in Mycobacterium tuberculosis and the availability of a large number of genome sequences make it feasible to carry out detailed sequence and phylogenetic analyses, to address these questions. A comprehensive phylogenetic pathway profile analysis was carried out for 318 fully sequenced bacterial genomes, for each of the proteins present in the MAP. The organisms were clustered on the basis of co-occurrence of the MAP proteins in their proteome, while the proteins were clustered on the basis of their phylogenetic profiles. The MAP proteins were also searched against the nonredundant sequence database, to identify similar proteins from other phyla. The pathway profiles indicate that four proteins and certain protein domains stand out as more characteristic to mycolate producing organisms. Further analysis leads to the identification of the desaturases DesA1 and DesA2 and certain domains of Fas and Pks13 as hallmarks of the pathway. The roles of these proteins in some other organisms, as well as the distribution of these proteins across all known genome sequences are also briefly discussed. The clustering of organisms, carried out to group organisms with similar profiles, provides a means of obtaining finer classification as compared to the standard taxonomic method. The results indicate that the MAP and hence the capacity of mycolic acid production in mycobacteria is an example of an emergent property that has come about by recruiting enzymes from unrelated pathways in plants, presumably through lateral gene transfer. The understanding of the hallmarks of mycolic acid biosynthesis will also find application in evaluating drug targets.}, }
@article {pmid17600070, year = {2007}, author = {Kickstein, E and Harms, K and Wackernagel, W}, title = {Deletions of recBCD or recD influence genetic transformation differently and are lethal together with a recJ deletion in Acinetobacter baylyi.}, journal = {Microbiology (Reading, England)}, volume = {153}, number = {Pt 7}, pages = {2259-2270}, doi = {10.1099/mic.0.2007/005256-0}, pmid = {17600070}, issn = {1350-0872}, mesh = {Acinetobacter/enzymology/*genetics/*radiation effects ; Bacterial Proteins/metabolism ; DNA Repair ; DNA, Bacterial/genetics/metabolism ; Exodeoxyribonuclease V/*deficiency/*genetics/metabolism/physiology ; Exodeoxyribonucleases/*deficiency/metabolism ; Gene Deletion ; Genes, Bacterial ; Nucleic Acid Heteroduplexes/genetics ; Recombination, Genetic ; *Transformation, Genetic ; Ultraviolet Rays ; }, abstract = {In prokaryotes, homologous recombination is essential for the repair of genomic DNA damage and for the integration of DNA taken up during horizontal gene transfer. In Escherichia coli, the exonucleases RecJ (specific for 5' single-stranded DNA) and RecBCD (degrades duplex DNA) play important roles in recombination and recombinational double-strand break (DSB) repair by the RecF and RecBCD pathways, respectively. The cloned recJ of Acinetobacter baylyi partially complemented an E. coli recJ mutant, suggesting functional similarity of the enzymes. A DeltarecJ mutant of A. baylyi was only slightly altered in transformability and was not affected in UV survival. In contrast, a DeltarecBCD mutant was UV-sensitive, and had a low viability and altered transformation. Compared to wild-type, transformation with large chromosomal DNA fragments was decreased about 5-fold, while transformation with 1.5 kbp DNA fragments was increased 3.3- to 7-fold. A DeltarecD mutation did not affect transformation, viability or UV resistance. However, double mutants recJ recBCD and recJ recD were non-viable, suggesting that the RecJ DNase or the RecBCD DNase (presumably absent in recD) becomes essential for the recombinational repair of spontaneously inactivated replication forks if the other DNase is absent. A model of recombination during genetic transformation is discussed in which the two ends of the single-stranded donor DNA present in the cytoplasm frequently integrate separately and often with a time difference. If replication runs through that genomic region before both ends of the donor DNA are ligated to recipient DNA, a double-strand break (DSB) is formed. In these cases, transformation becomes dependent on DSB repair.}, }
@article {pmid17600052, year = {2007}, author = {McAnulla, C and Edwards, A and Sanchez-Contreras, M and Sawers, RG and Downie, JA}, title = {Quorum-sensing-regulated transcriptional initiation of plasmid transfer and replication genes in Rhizobium leguminosarum biovar viciae.}, journal = {Microbiology (Reading, England)}, volume = {153}, number = {Pt 7}, pages = {2074-2082}, doi = {10.1099/mic.0.2007/007153-0}, pmid = {17600052}, issn = {1350-0872}, mesh = {Conjugation, Genetic ; DNA Replication ; Fabaceae/microbiology ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Plasmids/*genetics ; Quorum Sensing/*physiology ; Rhizobium leguminosarum/*genetics/growth &amp; development ; Transcription, Genetic ; Transcriptional Activation ; }, abstract = {Transfer of the Rhizobium leguminosarum biovar viciae symbiosis plasmid pRL1JI is regulated by a cascade of gene induction involving three LuxR-type quorum-sensing regulators, TraR, BisR and CinR. TraR induces the plasmid transfer traI-trb operon in a population-density-dependent manner in response to N-acylhomoserine lactones (AHLs) made by TraI. Expression of the traR gene is primarily induced by BisR in response to AHLs made by CinI, and expression of cinI is induced by CinR and repressed by BisR. Analysis of transcription initiation of cinI, traR and traI identified potential regulatory domains recognized by the CinR, BisR and TraR regulators. Deletion and mutation of the cinI promoter identified potential recognition motifs for activation by CinR and repression by BisR. Analysis of the DNA sequence upstream of traI and expression of transcriptional gene fusions revealed a predicted TraR-binding (tra-box) domain. Two transcript initiation sites were identified upstream of the plasmid replication gene repA, which is divergently transcribed from traI; one of these repA transcripts requires the quorum-sensing cascade mediated via BisR and TraR, showing that the pRL1JI plasmid replication genes are co-regulated with the plasmid transfer genes.}, }
@article {pmid17600050, year = {2007}, author = {Ihssen, J and Grasselli, E and Bassin, C and François, P and Piffaretti, JC and Köster, W and Schrenzel, J and Egli, T}, title = {Comparative genomic hybridization and physiological characterization of environmental isolates indicate that significant (eco-)physiological properties are highly conserved in the species Escherichia coli.}, journal = {Microbiology (Reading, England)}, volume = {153}, number = {Pt 7}, pages = {2052-2066}, doi = {10.1099/mic.0.2006/002006-0}, pmid = {17600050}, issn = {1350-0872}, mesh = {Environmental Microbiology ; Escherichia coli/genetics/*physiology ; *Escherichia coli Proteins ; Gene Expression Regulation, Bacterial ; Genome, Bacterial ; Glucose/*metabolism ; Molecular Sequence Data ; }, abstract = {Escherichia coli, the common inhabitant of the mammalian intestine, exhibits considerable intraspecies genomic variation, which has been suggested to reflect adaptation to different ecological niches. Also, regulatory trade-offs, e.g. between catabolic versatility and stress protection, are thought to result in significant physiological differences between strains. For these reasons, the relevance of experimental observations made for 'domesticated' E. coli strains with regard to the behaviour of this species in its natural environments is often questioned and doubts are frequently raised on the status of E. coli as a defined species. The variability of important (eco-)physiological functions, such as carbon substrate uptake and breakdown capabilities, as well as stress defence mechanisms, in the genomes of commensal and pathogenic E. coli strains were therefore investigated. Furthermore, (eco-)physiological properties of environmental strains were compared to standard laboratory strain K-12 MG1655. Catabolic, stress protection, and carbon- and energy source transport operons showed a very low intraspecies variability in 57 commensal and pathogenic E. coli. Environmental isolates adapted to glucose-limited growth in a similar way as E. coli MG1655, namely by increasing their catabolic flexibility and by inducing high-affinity substrate uptake systems. The results obtained indicate that significant (eco-)physiological properties are highly conserved in the natural population of E. coli. This questions the proposed dominant role of horizontal gene transfer for niche adaptation.}, }
@article {pmid17600048, year = {2007}, author = {Meyer, B and Kuever, J}, title = {Phylogeny of the alpha and beta subunits of the dissimilatory adenosine-5'-phosphosulfate (APS) reductase from sulfate-reducing prokaryotes--origin and evolution of the dissimilatory sulfate-reduction pathway.}, journal = {Microbiology (Reading, England)}, volume = {153}, number = {Pt 7}, pages = {2026-2044}, doi = {10.1099/mic.0.2006/003152-0}, pmid = {17600048}, issn = {1350-0872}, mesh = {Bacteria, Anaerobic/*genetics/metabolism ; Biological Evolution ; DNA, Bacterial/isolation &amp; purification ; Molecular Sequence Data ; Oxidoreductases Acting on Sulfur Group Donors/*chemistry ; Phylogeny ; Sulfates/metabolism ; Sulfur/metabolism ; Sulfur-Reducing Bacteria/*classification/genetics/metabolism ; }, abstract = {Newly developed PCR assays were used to PCR-amplify and sequence fragments of the dissimilatory adenosine-5'-phosphosulfate (APS) reductase genes (aprBA) comprising nearly the entire gene locus (2.2-2.4 kb, equal to 92-94 % of the protein coding sequence) from 75 sulfate-reducing prokaryotes (SRP) of a taxonomically wide range. Comparative phylogenetic analysis included all determined and publicly available AprBA sequences from SRP and selected homologous sequences of sulfur-oxidizing bacteria (SOB). The almost identical AprB and AprA tree topologies indicated a shared evolutionary path for the aprBA among the investigated SRP by vertical inheritance and concomitant lateral gene transfer (LGT). The topological comparison of AprB/A- and 16S rRNA gene-based phylogenetic trees revealed novel LGT events across the SRP divisions. Compositional gene analysis confirmed Thermacetogenium phaeum to be the first validated strain affected by a recent lateral transfer of aprBA as a putative effect of long-term co-cultivation with a Thermodesulfovibrio species. Interestingly, the Apr proteins of SRP and SOB diverged into two phylogenetic lineages, with the SRP affiliated with the green sulfur bacteria, e.g. Chlorobaculum tepidum, while the Allochromatium vinosum-related sequences formed a distinct group. Analysis of genome data indicated that this phylogenetic separation is also reflected in the differing presence of the putative proteins functionally associated with Apr, QmoABC complex (quinone-interacting membrane-bound oxidoreductase) and AprM (transmembrane protein). Scenarios for the origin and evolution of the dissimilatory APS reductase are discussed within the context of the dissimilatory sulfite reductase (DsrAB) phylogeny, the appearance of QmoABC and AprM in the SRP and SOB genomes, and the geochemical setting of Archean Earth.}, }
@article {pmid17591616, year = {2007}, author = {Azad, RK and Lawrence, JG}, title = {Detecting laterally transferred genes: use of entropic clustering methods and genome position.}, journal = {Nucleic acids research}, volume = {35}, number = {14}, pages = {4629-4639}, pmid = {17591616}, issn = {1362-4962}, mesh = {Cluster Analysis ; Escherichia coli K12/genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Genomics/*methods ; Phylogeny ; }, abstract = {Most parametric methods for detecting foreign genes in bacterial genomes use a scoring function that measures the atypicality of a gene with respect to the bulk of the genome. Genes whose features are sufficiently atypical-lying beyond a threshold value-are deemed foreign. Yet these methods fail when the range of features of donor genomes overlaps with that of the recipient genome, leading to misclassification of foreign and native genes; existing parametric methods choose threshold parameters to balance these error rates. To circumvent this problem, we have developed a two-pronged approach to minimize the misclassification of genes. First, beyond classifying genes as merely atypical, a gene clustering method based on Jensen-Shannon entropic divergence identifies classes of foreign genes that are also similar to each other. Second, genome position is used to reassign genes among classes whose composition features overlap. This process minimizes the misclassification of either native or foreign genes that are weakly atypical. The performance of this approach was assessed using artificial chimeric genomes and then applied to the well-characterized Escherichia coli K12 genome. Not only were foreign genes identified with a high degree of accuracy, but genes originating from the same donor organism were effectively grouped.}, }
@article {pmid17591612, year = {2007}, author = {Tåquist, H and Cui, Y and Ardell, DH}, title = {TFAM 1.0: an online tRNA function classifier.}, journal = {Nucleic acids research}, volume = {35}, number = {Web Server issue}, pages = {W350-3}, pmid = {17591612}, issn = {1362-4962}, mesh = {Alphaproteobacteria/classification/enzymology/*genetics ; Animals ; Computational Biology/*methods ; DNA, Bacterial/classification ; Databases, Nucleic Acid ; Drosophila melanogaster/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genetic Variation ; Internet ; *Models, Statistical ; Phylogeny ; RNA, Transfer/classification/genetics ; Software ; User-Computer Interface ; }, abstract = {We have earlier published an automated statistical classifier of tRNA function called TFAM. Unlike tRNA gene-finders, TFAM uses information from the total sequences of tRNAs and not just their anticodons to predict their function. Therefore TFAM has an advantage in predicting initiator tRNAs, the amino acid charging identity of nonstandard tRNAs such as suppressors, and the former identity of pseudo-tRNAs. In addition, TFAM predictions are robust to sequencing errors and useful for the statistical analysis of tRNA sequence, function and evolution. Earlier versions of TFAM required a complicated installation and running procedure, and only bacterial tRNA identity models were provided. Here we describe a new version of TFAM with both a Web Server interface and simplified standalone installation. New TFAM models are available including a proteobacterial model for the bacterial lysylated isoleucine tRNAs, making it now possible for TFAM to correctly classify all tRNA genes for some bacterial taxa. First-draft eukaryotic and archaeal models are also provided making initiator tRNA prediction easily accessible genes to any researcher or genome sequencing effort. The TFAM Web Server is available at http://tfam.lcb.uu.se.}, }
@article {pmid17588269, year = {2007}, author = {Novikova, O and Sliwińska, E and Fet, V and Settele, J and Blinov, A and Woyciechowski, M}, title = {CR1 clade of non-LTR retrotransposons from Maculinea butterflies (Lepidoptera: Lycaenidae): evidence for recent horizontal transmission.}, journal = {BMC evolutionary biology}, volume = {7}, number = {}, pages = {93}, pmid = {17588269}, issn = {1471-2148}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Bombyx/genetics ; Butterflies/*genetics ; Cloning, Molecular ; Conserved Sequence ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genetic Variation ; Insect Proteins/genetics ; Molecular Sequence Data ; Mutagenesis, Insertional ; Phylogeny ; Polymerase Chain Reaction ; RNA-Directed DNA Polymerase/genetics ; Retroelements/*genetics ; Sequence Alignment ; Sequence Deletion ; Sequence Homology ; Species Specificity ; }, abstract = {BACKGROUND: Non-long terminal repeat (non-LTR) retrotransposons are mobile genetic elements that propagate themselves by reverse transcription of an RNA intermediate. Non-LTR retrotransposons are known to evolve mainly via vertical transmission and random loss. Horizontal transmission is believed to be a very rare event in non-LTR retrotransposons. Our knowledge of distribution and diversity of insect non-LTR retrotransposons is limited to a few species - mainly model organisms such as dipteran genera Drosophila, Anopheles, and Aedes. However, diversity of non-LTR retroelements in arthropods seems to be much richer. The present study extends the analysis of non-LTR retroelements to CR1 clade from four butterfly species of genus Maculinea (Lepidoptera: Lycaenidae).The lycaenid genus Maculinea, the object of interest for evolutionary biologists and also a model group for European biodiversity studies, possesses a unique, specialized myrmecophilous lifestyle at larval stage. Their caterpillars, after three weeks of phytophagous life on specific food plants drop to the ground where they are adopted to the ant nest by Myrmica foraging workers.<br><br>RESULTS: We found that the genome of Maculinea butterflies contains multiple CR1 lineages of non-LTR retrotransposons, including those from MacCR1A, MacCR1B and T1Q families. A comparative analysis of RT nucleotide sequences demonstrated an extremely high similarity among elements both in interspecific and intraspecific comparisons. CR1A-like elements were found only in family Lycaenidae. In contrast, MacCR1B lineage clones were extremely similar to CR1B non-LTR retrotransposons from Bombycidae moths: silkworm Bombyx mori and Oberthueria caeca.<br><br>CONCLUSION: The degree of coding sequence similarity of the studied elements, their discontinuous distribution, and results of divergence-versus-age analysis make it highly unlikely that these sequences diverged at the same time as their host taxa. The only reasonable alternative explanation is horizontal transfer. In addition, phylogenetic markers for population analysis of Maculinea could be developed based on the described non-LTR retrotransposons.}, }
@article {pmid17587582, year = {2007}, author = {De Mot, R}, title = {Actinomycete-like proteasomes in a Gram-negative bacterium.}, journal = {Trends in microbiology}, volume = {15}, number = {8}, pages = {335-338}, doi = {10.1016/j.tim.2007.06.002}, pmid = {17587582}, issn = {0966-842X}, mesh = {Actinobacteria/*enzymology ; *Bacterial Proteins/genetics/metabolism ; Biofilms/*growth &amp; development ; Ecosystem ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial ; Genomics ; Gram-Negative Bacteria/classification/*enzymology/genetics/growth &amp; development ; Hydrogen-Ion Concentration ; *Proteasome Endopeptidase Complex/genetics/metabolism ; Proteome ; }, abstract = {Cultivation-independent proteogenomic exploration of mine-drainage biofilm has revealed proteasomes in Gram-negative bacteria of the Nitrospirae phylum (Leptospirillum group II) dominating this acidophilic community. Most probably, the proteasome genes were acquired from actinobacteria, the only eubacteria previously known to contain proteasomes. In addition, this study shows that the proteasome and the evolutionarily related ATP-dependent protease HslVU (also known as ClpQY) are not mutually exclusive in prokaryotes.}, }
@article {pmid17586666, year = {2007}, author = {Park, M and Jeon, Y and Jang, HH and Ro, HS and Park, W and Madsen, EL and Jeon, CO}, title = {Molecular and biochemical characterization of 3-hydroxybenzoate 6-hydroxylase from Polaromonas naphthalenivorans CJ2.}, journal = {Applied and environmental microbiology}, volume = {73}, number = {16}, pages = {5146-5152}, pmid = {17586666}, issn = {0099-2240}, mesh = {Bacterial Proteins/genetics/*metabolism ; Comamonadaceae/*enzymology/genetics/growth &amp; development ; Dicarboxylic Acids/chemistry/metabolism ; Electrophoresis, Polyacrylamide Gel ; Fumarates/chemistry/metabolism ; Gene Deletion ; Gentisates/chemistry/metabolism ; Hydroxybenzoates/chemistry/metabolism ; Mixed Function Oxygenases/genetics/*metabolism ; Models, Genetic ; Molecular Structure ; Mutation ; Naphthalenes/chemistry/metabolism ; Pimelic Acids/chemistry/metabolism ; Pyruvates/chemistry/metabolism ; Recombinant Proteins/metabolism ; }, abstract = {Prior research revealed that Polaromonas naphthalenivorans CJ2 carries and expresses genes encoding the gentisate metabolic pathway for naphthalene. These metabolic genes are split into two clusters, comprising nagRAaGHAbAcAdBFCQEDJI'-orf1-tnpA and nagR2-orf2I''KL (C. O. Jeon, M. Park, H. Ro, W. Park, and E. L. Madsen, Appl. Environ. Microbiol. 72:1086-1095, 2006). BLAST homology searches of sequences in GenBank indicated that the orf2 gene from the small cluster likely encoded a salicylate 5-hydroxylase, presumed to catalyze the conversion of salicylate into gentisate. Here, we report physiological and genetic evidence that orf2 does not encode salicylate 5-hydroxylase. Instead, we have found that orf2 encodes 3-hydroxybenzoate 6-hydroxylase, the enzyme which catalyzes the NADH-dependent conversion of 3-hydroxybenzoate into gentisate. Accordingly, we have renamed orf2 nagX. After expression in Escherichia coli, the NagX enzyme had an approximate molecular mass of 43 kDa, as estimated by gel filtration, and was probably a monomeric protein. The enzyme was able to convert 3-hydroxybenzoate into gentisate without salicylate 5-hydroxylase activity. Like other 3-hydroxybenzoate 6-hydroxylases, NagX utilized both NADH and NADPH as electron donors and exhibited a yellowish color, indicative of a bound flavin adenine dinucleotide. An engineered mutant of P. naphthalenivorans CJ2 defective in nagX failed to grow on 3-hydroxybenzoate but grew normally on naphthalene. These results indicate that the previously described small catabolic cluster in strain CJ2 may be multifunctional and is essential for the degradation of 3-hydroxybenzoate. Because nagX and an adjacent MarR-type regulatory gene are both closely related to homologues in Azoarcus species, this study raises questions about horizontal gene transfer events that contribute to operon evolution.}, }
@article {pmid17586644, year = {2007}, author = {Ast, JC and Urbanczyk, H and Dunlap, PV}, title = {Natural merodiploidy of the lux-rib operon of Photobacterium leiognathi from coastal waters of Honshu, Japan.}, journal = {Journal of bacteriology}, volume = {189}, number = {17}, pages = {6148-6158}, pmid = {17586644}, issn = {0021-9193}, mesh = {3' Flanking Region/genetics ; 5' Flanking Region/genetics ; Bacterial Proteins/genetics ; DNA, Bacterial/chemistry/genetics ; DNA-Binding Proteins/genetics ; *Diploidy ; Gene Order ; Genes, MDR ; Geography ; Japan ; Luminescent Proteins/genetics ; Membrane Proteins/genetics ; Metabolic Networks and Pathways/genetics ; Molecular Sequence Data ; Operon ; Photobacterium/*genetics/isolation &amp; purification ; Phylogeny ; Riboflavin/biosynthesis ; Sequence Analysis, DNA ; Sequence Homology ; Transcription Factors/genetics ; Transposases/genetics ; Water Microbiology ; }, abstract = {Sequence analysis of the bacterial luminescence (lux) genes has proven effective in helping resolve evolutionary relationships among luminous bacteria. Phylogenetic analysis using lux genes, however, is based on the assumptions that the lux genes are present as single copies on the bacterial chromosome and are vertically inherited. We report here that certain strains of Photobacterium leiognathi carry multiple phylogenetically distinct copies of the entire operon that codes for luminescence and riboflavin synthesis genes, luxCDABEG-ribEBHA. Merodiploid lux-rib strains of P. leiognathi were detected during sequence analysis of luxA. To define the gene content, organization, and sequence of each lux-rib operon, we constructed a fosmid library of genomic DNA from a representative merodiploid strain, lnuch.13.1. Sequence analysis of fosmid clones and genomic analysis of lnuch.13.1 defined two complete, physically separate, and apparently functional operons, designated lux-rib1 and lux-rib2. P. leiognathi strains lelon.2.1 and lnuch.21.1 were also found to carry lux-rib1 and lux-rib2, whereas ATCC 25521T apparently carries only lux-rib1. In lnuch.13.1, lelon.2.1, lnuch.21.1, and ATCC 25521T, lux-rib1 is flanked upstream by lumQ and putA and downstream by a gene for a hypothetical multidrug efflux pump. In contrast, transposase genes flank lux-rib2 of lnuch.13.1, and the chromosomal location of lux-rib2 apparently differs in lnuch.13.1, lelon.2.1, and lnuch.21.1. Phylogenetic analysis demonstrated that lux-rib1 and lux-rib2 are more closely related to each other than either one is to the lux and rib genes of other bacterial species, which rules out interspecies lateral gene transfer as the origin of lux-rib2 in P. leiognathi; lux-rib2 apparently arose within a previously unsampled or extinct P. leiognathi lineage. Analysis of 170 additional strains of P. leiognathi, for a total of 174 strains examined from coastal waters of Japan, Taiwan, the Philippine Islands, and Thailand, identified 106 strains that carry only a single lux-rib operon and 68 that carry multiple lux-rib operons. Strains bearing a single lux-rib operon were obtained throughout the geographic sampling range, whereas lux-rib merodiploid strains were found only in coastal waters of central Honshu. This is the first report of merodiploidy of lux or rib genes in a luminous bacterium and the first indication that a natural merodiploid state in bacteria can correlate with geography.}, }
@article {pmid17584924, year = {2007}, author = {Rogers, MB and Patron, NJ and Keeling, PJ}, title = {Horizontal transfer of a eukaryotic plastid-targeted protein gene to cyanobacteria.}, journal = {BMC biology}, volume = {5}, number = {}, pages = {26}, pmid = {17584924}, issn = {1741-7007}, mesh = {Eukaryotic Cells/cytology/*metabolism ; Evolution, Molecular ; Fructose-Bisphosphate Aldolase/*genetics ; Gene Order/genetics ; Gene Transfer, Horizontal/*genetics ; Likelihood Functions ; Phylogeny ; Plastids/enzymology/*genetics ; Prochlorococcus/*genetics ; Protein Transport ; Regulatory Sequences, Nucleic Acid/genetics ; Synechococcus/*genetics ; }, abstract = {BACKGROUND: Horizontal or lateral transfer of genetic material between distantly related prokaryotes has been shown to play a major role in the evolution of bacterial and archaeal genomes, but exchange of genes between prokaryotes and eukaryotes is not as well understood. In particular, gene flow from eukaryotes to prokaryotes is rarely documented with strong support, which is unusual since prokaryotic genomes appear to readily accept foreign genes.<br><br>RESULTS: Here, we show that abundant marine cyanobacteria in the related genera Synechococcus and Prochlorococcus acquired a key Calvin cycle/glycolytic enzyme from a eukaryote. Two non-homologous forms of fructose bisphosphate aldolase (FBA) are characteristic of eukaryotes and prokaryotes respectively. However, a eukaryotic gene has been inserted immediately upstream of the ancestral prokaryotic gene in several strains (ecotypes) of Synechococcus and Prochlorococcus. In one lineage this new gene has replaced the ancestral gene altogether. The eukaryotic gene is most closely related to the plastid-targeted FBA from red algae. This eukaryotic-type FBA once replaced the plastid/cyanobacterial type in photosynthetic eukaryotes, hinting at a possible functional advantage in Calvin cycle reactions. The strains that now possess this eukaryotic FBA are scattered across the tree of Synechococcus and Prochlorococcus, perhaps because the gene has been transferred multiple times among cyanobacteria, or more likely because it has been selectively retained only in certain lineages.<br><br>CONCLUSION: A gene for plastid-targeted FBA has been transferred from red algae to cyanobacteria, where it has inserted itself beside its non-homologous, functional analogue. Its current distribution in Prochlorococcus and Synechococcus is punctate, suggesting a complex history since its introduction to this group.}, }
@article {pmid17584922, year = {2007}, author = {Kim, N and Lee, C}, title = {Three-Dimensional Phylogeny Explorer: distinguishing paralogs, lateral transfer, and violation of "molecular clock" assumption with 3D visualization.}, journal = {BMC bioinformatics}, volume = {8}, number = {}, pages = {213}, pmid = {17584922}, issn = {1471-2105}, support = {U54 RR021813/RR/NCRR NIH HHS/United States ; }, mesh = {Biological Clocks/*genetics ; Chromosome Mapping/*methods ; Computer Graphics ; Computer Simulation ; *Evolution, Molecular ; Imaging, Three-Dimensional/*methods ; *Models, Genetic ; *Software ; *User-Computer Interface ; }, abstract = {BACKGROUND: Construction and interpretation of phylogenetic trees has been a major research topic for understanding the evolution of genes. Increases in sequence data and complexity are creating a need for more powerful and insightful tree visualization tools.<br><br>RESULTS: We have developed 3D Phylogeny Explorer (3DPE), a novel phylogeny tree viewer that maps trees onto three spatial axes (species on the X-axis; paralogs on Z; evolutionary distance on Y), enabling one to distinguish at a glance evolutionary features such as speciation; gene duplication and paralog evolution; lateral gene transfer; and violation of the "molecular clock" assumption. Users can input any tree on the online 3DPE, then rotate, scroll, rescale, and explore it interactively as "live" 3D views. All objects in 3DPE are clickable to display subtrees, connectivity path highlighting, sequence alignments, and gene summary views, and etc. To illustrate the value of this visualization approach for microbial genomes, we also generated 3D phylogeny analyses for all clusters from the public COG database. We constructed tree views using well-established methods and graph algorithms. We used Scientific Python to generate VRML2 3D views viewable in any web browser.<br><br>CONCLUSION: 3DPE provides a novel phylogenetic tree projection method into 3D space and its web-based implementation with live 3D features for reconstruction of phylogenetic trees of COG database.}, }
@article {pmid17582735, year = {2007}, author = {Albrecht-Buehler, G}, title = {Inversions and inverted transpositions as the basis for an almost universal "format" of genome sequences.}, journal = {Genomics}, volume = {90}, number = {3}, pages = {297-305}, doi = {10.1016/j.ygeno.2007.05.010}, pmid = {17582735}, issn = {0888-7543}, mesh = {*Biological Evolution ; Chromosome Inversion ; Evolution, Molecular ; Gene Deletion ; Gene Transfer, Horizontal ; Genetic Techniques ; Genetic Variation ; *Genome ; Models, Genetic ; Nucleotides/chemistry ; RNA/chemistry ; Stochastic Processes ; Thermodynamics ; Trinucleotide Repeats ; }, abstract = {In genome duplexes that exceed 100 kb the frequency distributions of their trinucleotides (triplet profiles) are the same in both strands. This remarkable symmetry, sometimes called Chargaff's second parity rule, is not the result of base pairing, but can be explained as the result of countless inversions and inverted transpositions that occurred throughout evolution (G. Albrecht-Buehler, 2006, Proc. Natl. Acad. Sci. USA 103, 17828-17833). Furthermore, comparing the triplet profiles of genomes from a large number of different taxa and species revealed that they were not only strand-symmetrical, but even surprisingly similar to one another (majority profile; G. Albrecht-Buehler, 2007, Genomics 89, 596-601). The present article proposes that the same inversion/transposition mechanism(s) that created the strand symmetry may also explain the existence of the majority profile. Thus they may be key factors in the creation of an almost universal "format" in which genome sequences are written. One may speculate that this universality of genome format may facilitate horizontal gene transfer and, thus, accelerate evolution.}, }
@article {pmid17579514, year = {2007}, author = {Xu, J and Mahowald, MA and Ley, RE and Lozupone, CA and Hamady, M and Martens, EC and Henrissat, B and Coutinho, PM and Minx, P and Latreille, P and Cordum, H and Van Brunt, A and Kim, K and Fulton, RS and Fulton, LA and Clifton, SW and Wilson, RK and Knight, RD and Gordon, JI}, title = {Evolution of symbiotic bacteria in the distal human intestine.}, journal = {PLoS biology}, volume = {5}, number = {7}, pages = {e156}, pmid = {17579514}, issn = {1545-7885}, support = {T32 GM008759/GM/NIGMS NIH HHS/United States ; T32 HD07409/HD/NICHD NIH HHS/United States ; T32 GM142607/GM/NIGMS NIH HHS/United States ; T32 HD007409/HD/NICHD NIH HHS/United States ; T32 GM08759/GM/NIGMS NIH HHS/United States ; T32 GM065103/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Physiological ; Bacteriophages/genetics ; Bacteroides/*genetics/physiology/virology ; Conjugation, Genetic ; DNA Transposable Elements ; Ecosystem ; *Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; Genetic Variation ; Genome, Bacterial ; Humans ; Intestines/*microbiology ; Molecular Sequence Data ; Phylogeny ; Polysaccharides, Bacterial/biosynthesis/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; Symbiosis/*genetics ; }, abstract = {The adult human intestine contains trillions of bacteria, representing hundreds of species and thousands of subspecies. Little is known about the selective pressures that have shaped and are shaping this community's component species, which are dominated by members of the Bacteroidetes and Firmicutes divisions. To examine how the intestinal environment affects microbial genome evolution, we have sequenced the genomes of two members of the normal distal human gut microbiota, Bacteroides vulgatus and Bacteroides distasonis, and by comparison with the few other sequenced gut and non-gut Bacteroidetes, analyzed their niche and habitat adaptations. The results show that lateral gene transfer, mobile elements, and gene amplification have played important roles in affecting the ability of gut-dwelling Bacteroidetes to vary their cell surface, sense their environment, and harvest nutrient resources present in the distal intestine. Our findings show that these processes have been a driving force in the adaptation of Bacteroidetes to the distal gut environment, and emphasize the importance of considering the evolution of humans from an additional perspective, namely the evolution of our microbiomes.}, }
@article {pmid17578704, year = {2007}, author = {Chen, Q and Jiang, JG and Wang, F}, title = {Molecular phylogenies and evolution of crt genes in algae.}, journal = {Critical reviews in biotechnology}, volume = {27}, number = {2}, pages = {77-91}, doi = {10.1080/07388550701334378}, pmid = {17578704}, issn = {0738-8551}, mesh = {Carotenoids/biosynthesis/*genetics ; Eukaryota/*genetics ; *Evolution, Molecular ; *Phylogeny ; }, abstract = {The carotenoids constitute the most widespread class of pigments in nature. Most previous work has concentrated on the identification and characterization of their chemical physical properties and bioavailability. In recent years, significant amounts of research have been conducted in an attempt to analyze the genes and the molecular regulation of the genes involved in the biosynthesis of carotenoids. However, it is important not to lose sight of the early evolution of carotenoid biosynthesis. One of the major obstacles in understanding the evolution of the respective enzymes and their patterns of selection is a lack of a well-supported phylogenic analysis. In the present research, a major long-term objective was to provide a clearer picture of the evolutionary history of genes, together with an evaluation of the patterns of selection in algae. These phylogenies will be important in studies characterizing the evolution of algae. The gene sequences of the enzymes involved in the major steps of the carotenoid biosynthetic pathway in algae (cyanobacteria, rhofophyta, chlorophyta) have been analyzed. Phylogenetic relationships among protein-coding DNA sequences were reconstructed by neighbor-joining (NJ) analysis for the respective carotenoid biosynthetic pathway genes (crt) in algae. The analysis also contains an estimation of the rate of nonsynonymous nucleotide substitutions per nonsynonymous site (d(N)), synonymous nucleotide substitution per synonymous site (d(S)), and the ratio of nonsynonmous (d(N)/d(S)) for the test of selection patterns. The phylogenetic trees show that the taxa of some genera have a closer evolutionary relationship with other genera in some gene sequences, which suggests a common ancient origin and that lateral gene transfer has occurred among unrelated genera. The d(N) values of crt genes in the early pathway are relatively low, while those of the following steps are slightly higher, while the d(N) values of crt genes in chlorophyta are higher than those in cyanobacteria. Most of the d(N)/d(S) values exceed 1. The phylogenetic analysis revealed that lateral gene transfer may have taken place across algal genomes and the d(N) values suggest that most of the early crt genes are well conserved compared to the later crt genes. Furthermore, d(N) values also revealed that the crt genes of chlorophyta are more evolutionary than cyanobacteria. The amino acids' changes are mostly adaptive evolution under the influence of positive diversity selection.}, }
@article {pmid17575047, year = {2007}, author = {Navarre, WW and McClelland, M and Libby, SJ and Fang, FC}, title = {Silencing of xenogeneic DNA by H-NS-facilitation of lateral gene transfer in bacteria by a defense system that recognizes foreign DNA.}, journal = {Genes &amp; development}, volume = {21}, number = {12}, pages = {1456-1471}, doi = {10.1101/gad.1543107}, pmid = {17575047}, issn = {0890-9369}, support = {AI34829/AI/NIAID NIH HHS/United States ; AI39557/AI/NIAID NIH HHS/United States ; AI44486/AI/NIAID NIH HHS/United States ; AI52237/AI/NIAID NIH HHS/United States ; AI57733/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/*genetics/*metabolism ; Bacterial Proteins/genetics/*metabolism ; Base Composition ; DNA, Bacterial/genetics/metabolism ; DNA-Binding Proteins/genetics/*metabolism ; Gene Expression Regulation, Bacterial ; *Gene Silencing ; Gene Transfer Techniques ; Gene Transfer, Horizontal ; Genes, Bacterial ; Interspersed Repetitive Sequences ; Models, Genetic ; }, abstract = {Lateral gene transfer has played a prominent role in bacterial evolution, but the mechanisms allowing bacteria to tolerate the acquisition of foreign DNA have been incompletely defined. Recent studies show that H-NS, an abundant nucleoid-associated protein in enteric bacteria and related species, can recognize and selectively silence the expression of foreign DNA with higher adenine and thymine content relative to the resident genome, a property that has made this molecule an almost universal regulator of virulence determinants in enteric bacteria. These and other recent findings challenge the ideas that curvature is the primary determinant recognized by H-NS and that activation of H-NS-silenced genes in response to environmental conditions occurs through a change in the structure of H-NS itself. Derepression of H-NS-silenced genes can occur at specific promoters by several mechanisms including competition with sequence-specific DNA-binding proteins, thereby enabling the regulated expression of foreign genes. The possibility that microorganisms maintain and exploit their characteristic genomic GC ratios for the purpose of self/non-self-discrimination is discussed.}, }
@article {pmid17573802, year = {2007}, author = {Friesen, TL and Meinhardt, SW and Faris, JD}, title = {The Stagonospora nodorum-wheat pathosystem involves multiple proteinaceous host-selective toxins and corresponding host sensitivity genes that interact in an inverse gene-for-gene manner.}, journal = {The Plant journal : for cell and molecular biology}, volume = {51}, number = {4}, pages = {681-692}, doi = {10.1111/j.1365-313X.2007.03166.x}, pmid = {17573802}, issn = {0960-7412}, mesh = {Ascomycota/genetics/*metabolism/pathogenicity ; Chromosome Mapping ; Chromosomes, Plant/genetics ; Fungal Proteins/genetics/metabolism ; Genes, Plant ; Immunity, Innate/genetics ; Mycotoxins/genetics/*metabolism ; Plant Diseases/*genetics/microbiology ; Quantitative Trait Loci ; Triticum/*genetics/microbiology ; }, abstract = {We recently showed that the wheat pathogen Stagonospora nodorum produces proteinaceous host-selective toxins (HSTs). These toxins include SnTox1 as well as SnToxA, a HST first identified from Pyrenophora tritici-repentis that was implicated in a very recent horizontal gene transfer event from S. nodorum to P. tritici-repentis. Compelling evidence implicating SnToxA and SnTox1 in disease development has been obtained. Here, we report the partial purification and characterization of a third HST designated SnTox2, as well as the genetic characterization of the corresponding host-sensitivity gene. SnTox2 was protease sensitive and is estimated between 7 and 10 kDa in size. Sensitivity to SnTox2 was conferred by a single dominant gene designated Snn2, which mapped to the short arm of wheat chromosome 2D. Genetic analysis of reaction to conidial inoculations in a segregating wheat population indicated that both the Snn2-SnTox2 and the Tsn1-SnToxA interactions were involved in disease development, and together they accounted for the majority of the phenotypic variation. Therefore, S. nodorum produces multiple toxins that rely on specific interactions with host gene products to cause disease. The identification of multiple HST-host gene interactions important for disease development and the availability of the S. nodorum whole genome sequence indicate the potential for this pathosystem to serve as a toxin-based, inverse gene-for-gene model.}, }
@article {pmid17573664, year = {2007}, author = {Stehling, EG and Campos, TA and Azevedo, V and Brocchi, M and Silveira, WD}, title = {DNA sequencing of a pathogenicity-related plasmid of an avian septicemic Escherichia coli strain.}, journal = {Genetics and molecular research : GMR}, volume = {6}, number = {2}, pages = {331-337}, pmid = {17573664}, issn = {1676-5680}, mesh = {Animals ; Escherichia coli/*genetics/*pathogenicity ; Escherichia coli Infections/microbiology/*veterinary ; Gene Transfer, Horizontal ; Humans ; *Plasmids ; Poultry/microbiology ; Poultry Diseases/*microbiology ; Sepsis/microbiology/*veterinary ; Virulence/genetics ; }, abstract = {A 43-MDa conjugative plasmid isolated from an avian septicemic Escherichia coli (APEC) strain possessing genes related to the adhesion and invasion capacities of in vitro-cultured cells was sequenced. The results demonstrated that the 43-MDa plasmid harbors bacterial pathogenicity-related sequences which probably allow the wild-type pathogenic strain to adhere to and invade tissues and to cause septicemia in poultry. The existence of homology sequences to sequences belonging to other human pathogenic Enterobacteriaceae like Escherichia coli O157:H7, Shigella and Salmonella was also observed. The presence of these sequences in this plasmid could indicate that there is horizontal genetic transfer between bacterial strains isolated from different host species. In conclusion, the present study suggests that APEC strains harbor high-molecular weight plasmids that present pathogenicity-related sequences and that these are probably responsible for the pathogenicity exhibited by these strains. The presence of human pathogenicity-associated sequences in APEC conjugative plasmids suggests that these strains could represent a zoonotic risk.}, }
@article {pmid17573478, year = {2007}, author = {Tribble, GD and Lamont, GJ and Progulske-Fox, A and Lamont, RJ}, title = {Conjugal transfer of chromosomal DNA contributes to genetic variation in the oral pathogen Porphyromonas gingivalis.}, journal = {Journal of bacteriology}, volume = {189}, number = {17}, pages = {6382-6388}, pmid = {17573478}, issn = {0021-9193}, support = {R03 DE016562/DE/NIDCR NIH HHS/United States ; R03 DE016562-01A1/DE/NIDCR NIH HHS/United States ; DE016562/DE/NIDCR NIH HHS/United States ; }, mesh = {Adaptation, Biological ; Bacteria ; Bacteroides/genetics ; Chromosomes, Bacterial ; *Conjugation, Genetic ; DNA ; DNA, Bacterial/*genetics/metabolism ; Drug Resistance, Bacterial/genetics ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; *Genetic Variation ; Genetic Vectors ; Humans ; Plasmids ; Porphyromonas gingivalis/*genetics ; Recombination, Genetic ; Transfer, Psychology ; }, abstract = {Porphyromonas gingivalis is a major oral pathogen that contributes to the development of periodontal disease. There is a significant degree of genetic variation among strains of P. gingivalis, and the population structure has been predicted to be panmictic, indicating that horizontal DNA transfer and recombination between strains are likely. The molecular events underlying this genetic exchange are not understood, although a putative type IV secretion system is present in the genome sequence of strain W83, implying that DNA conjugation may be responsible for genetic transfer in these bacteria. In this study, we provide in vitro evidence for the horizontal transfer of DNA using plasmid- and chromosome-based assays. In the plasmid assays, Bacteroides-derived shuttle vectors were tested for transfer from P. gingivalis strains into Escherichia coli. Of the eight strains tested, five were able to transfer DNA into E. coli by a mechanism most consistent with conjugation. Additionally, strains W83 and 33277 tested positive for the transfer of chromosomally integrated antibiotic resistance markers. Ten chimeras resulting from the chromosomal transfer assay were further analyzed by Southern hybridization and were shown to have exchanged DNA fragments of between 1.1 and 5.6 kb, but the overall strain identity remained intact. Chimeras showed phenotypic changes in the ability to accrete into biofilms, implying that DNA transfer events are sufficient to generate measurable changes in complex behaviors. This ability to transfer chromosomal DNA between strains may be an adaptation mechanism in the complex environment of the host oral cavity.}, }
@article {pmid17572027, year = {2007}, author = {Than, C and Ruths, D and Innan, H and Nakhleh, L}, title = {Confounding factors in HGT detection: statistical error, coalescent effects, and multiple solutions.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {14}, number = {4}, pages = {517-535}, doi = {10.1089/cmb.2007.A010}, pmid = {17572027}, issn = {1066-5277}, mesh = {*Algorithms ; *Gene Transfer, Horizontal ; *Models, Genetic ; *Phylogeny ; *Prokaryotic Cells ; }, abstract = {Prokaryotic organisms share genetic material across species boundaries by means of a process known as horizontal gene transfer (HGT). This process has great significance for understanding prokaryotic genome diversification and unraveling their complexities. Phylogeny-based detection of HGT is one of the most commonly used methods for this task, and is based on the fundamental fact that HGT may cause gene trees to disagree with one another, as well as with the species phylogeny. Using these methods, we can compare gene and species trees, and infer a set of HGT events to reconcile the differences among these trees. In this paper, we address three factors that confound the detection of the true HGT events, including the donors and recipients of horizontally transferred genes. First, we study experimentally the effects of error in the estimated gene trees (statistical error) on the accuracy of inferred HGT events. Our results indicate that statistical error leads to overestimation of the number of HGT events, and that HGT detection methods should be designed with unresolved gene trees in mind. Second, we demonstrate, both theoretically and empirically, that based on topological comparison alone, the number of HGT scenarios that reconcile a pair of species/gene trees may be exponential. This number may be reduced when branch lengths in both trees are estimated correctly. This set of results implies that in the absence of additional biological information, and/or a biological model of how HGT occurs, multiple HGT scenarios must be sought, and efficient strategies for how to enumerate such solutions must be developed. Third, we address the issue of lineage sorting, how it confounds HGT detection, and how to incorporate it with HGT into a single stochastic framework that distinguishes between the two events by extending population genetics theories. This result is very important, particularly when analyzing closely related organisms, where coalescent effects may not be ignored when reconciling gene trees. In addition to these three confounding factors, we consider the problem of enumerating all valid coalescent scenarios that constitute plausible species/gene tree reconciliations, and develop a polynomial-time dynamic programming algorithm for solving it. This result bears great significance on reducing the search space for heuristics that seek reconciliation scenarios. Finally, we show, empirically, that the locality of incongruence between a pair of trees has an impact on the numbers of HGT and coalescent reconciliation scenarios.}, }
@article {pmid17567566, year = {2007}, author = {Levine, SM and Lin, EA and Emara, W and Kang, J and DiBenedetto, M and Ando, T and Falush, D and Blaser, MJ}, title = {Plastic cells and populations: DNA substrate characteristics in Helicobacter pylori transformation define a flexible but conservative system for genomic variation.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {21}, number = {13}, pages = {3458-3467}, doi = {10.1096/fj.07-8501com}, pmid = {17567566}, issn = {1530-6860}, support = {069662//Wellcome Trust/United Kingdom ; R01 GM63270/GM/NIGMS NIH HHS/United States ; T35 DK007421/DK/NIDDK NIH HHS/United States ; }, mesh = {DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; *Genetic Variation ; *Genome, Bacterial ; Helicobacter pylori/genetics/*physiology ; Point Mutation ; Transformation, Bacterial ; }, abstract = {Helicobacter pylori, bacteria that colonize the human gastric mucosa, are naturally competent for transformation by exogenous DNA, and show a panmictic population structure. To understand the mechanisms involved in its horizontal gene transfer, we sought to define the interval required from exposure to substrate DNA until DNA uptake and expression of a selectable phenotype, as well as the relationship of transforming fragment length, concentration, homology, symmetry, and strandedness, to the transformation frequency. We provide evidence that natural transformation in H. pylori differs in efficiency among wild-type strains but is saturable and varies with substrate DNA length, symmetry, strandedness, and species origin. We show that H. pylori cells can be transformed within one minute of contact with DNA, by DNA fragments as small as 50 bp, and as few as 5 bp on one flank of a selectable single nucleotide mutation is sufficient substrate for recombination of a transforming fragment, and that double-stranded DNA is the preferred (1000-fold >single-stranded) substrate. The high efficiency of double-stranded DNA as transformation substrate, in conjunction with strain-specific restriction endonucleases suggests a model of short-fragment recombination favoring closest relatives, consistent with the observed H. pylori population biology.}, }
@article {pmid17566739, year = {2007}, author = {Boucher, Y and Labbate, M and Koenig, JE and Stokes, HW}, title = {Integrons: mobilizable platforms that promote genetic diversity in bacteria.}, journal = {Trends in microbiology}, volume = {15}, number = {7}, pages = {301-309}, doi = {10.1016/j.tim.2007.05.004}, pmid = {17566739}, issn = {0966-842X}, mesh = {*Biological Evolution ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial/*genetics ; Genetic Variation ; Integrons/*genetics ; Mutagenesis, Insertional/genetics ; *Phylogeny ; Recombinases/genetics ; }, abstract = {Integrons facilitate the capture of potentially adaptive exogenous genetic material by their host genomes. It is now clear that integrons are not limited to the clinical contexts in which they were originally discovered because approximately 10% of bacterial genomes that have been partially or completely sequenced harbour this genetic element. This wealth of sequence information has revealed that integrons are not only much more phylogenetically diverse than previously thought but also more mobilizable, with many integrons having been subjected to frequent lateral gene transfer throughout their evolutionary history. This indicates that the genetic characteristics that make integrons such efficient vectors for the spread of antibiotic resistance genes have been associated with these elements since their earliest origins. Here, we give an overview of the structural and phylogenetic diversity of integrons and describe evolutionary events that have contributed to the success of these genetic elements.}, }
@article {pmid17565956, year = {2007}, author = {Marciano, DC and Karkouti, OY and Palzkill, T}, title = {A fitness cost associated with the antibiotic resistance enzyme SME-1 beta-lactamase.}, journal = {Genetics}, volume = {176}, number = {4}, pages = {2381-2392}, pmid = {17565956}, issn = {0016-6731}, support = {R01 AI032956/AI/NIAID NIH HHS/United States ; R37 AI032956/AI/NIAID NIH HHS/United States ; R56 AI032956/AI/NIAID NIH HHS/United States ; AI 32956/AI/NIAID NIH HHS/United States ; }, mesh = {Base Sequence ; Carbapenems/pharmacology ; DNA Primers/genetics ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; Escherichia coli/enzymology/genetics/growth &amp; development ; Gene Transfer, Horizontal ; Genes, Bacterial ; Molecular Sequence Data ; Plasmids/genetics ; Protein Sorting Signals/genetics ; Serratia marcescens/drug effects/*enzymology/*genetics ; Suppression, Genetic ; beta-Lactamases/*genetics ; }, abstract = {The bla(TEM-1) beta-lactamase gene has become widespread due to the selective pressure of beta-lactam use and its stable maintenance on transferable DNA elements. In contrast, bla(SME-1) is rarely isolated and is confined to the chromosome of carbapenem-resistant Serratia marcescens strains. Dissemination of bla(SME-1) via transfer to a mobile DNA element could hinder the use of carbapenems. In this study, bla(SME-1) was determined to impart a fitness cost upon Escherichia coli in multiple genetic contexts and assays. Genetic screens and designed SME-1 mutants were utilized to identify the source of this fitness cost. These experiments established that the SME-1 protein was required for the fitness cost but also that the enzyme activity of SME-1 was not associated with the fitness cost. The genetic screens suggested that the SME-1 signal sequence was involved in the fitness cost. Consistent with these findings, exchange of the SME-1 signal sequence for the TEM-1 signal sequence alleviated the fitness cost while replacing the TEM-1 signal sequence with the SME-1 signal sequence imparted a fitness cost to TEM-1 beta-lactamase. Taken together, these results suggest that fitness costs associated with some beta-lactamases may limit their dissemination.}, }
@article {pmid17563084, year = {2007}, author = {Vlassov, VV and Laktionov, PP and Rykova, EY}, title = {Extracellular nucleic acids.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {29}, number = {7}, pages = {654-667}, doi = {10.1002/bies.20604}, pmid = {17563084}, issn = {0265-9247}, mesh = {Animals ; Bacteria/genetics/growth &amp; development ; Biofilms/growth &amp; development ; Extracellular Space/*chemistry ; Gene Transfer, Horizontal/genetics ; Humans ; Models, Biological ; Neoplasms/diagnosis/metabolism ; Nucleic Acids/analysis/*physiology ; }, abstract = {Extracellular nucleic acids are found in different biological fluids in the organism and in the environment: DNA is a ubiquitous component of the organic matter pool in the soil and in all marine and freshwater habitats. Data from recent studies strongly suggest that extracellular DNA and RNA play important biological roles in microbial communities and in higher organisms. DNA is an important component of bacterial biofilms and is involved in horizontal gene transfer. In recent years, the circulating extracellular nucleic acids were shown to be associated with some diseases. Attempts are being made to develop noninvasive methods of early tumor diagnostics based on analysis of circulating DNA and RNA. Recent observations demonstrated the possibility of nucleic acids exchange between eukaryotic cells and extracellular space suggesting their participation in so far unidentified biological processes.}, }
@article {pmid17562187, year = {2008}, author = {Carr, M}, title = {Multiple subfamilies of mariner transposable elements are present in stalk-eyed flies (Diptera: Diopsidae).}, journal = {Genetica}, volume = {132}, number = {2}, pages = {113-122}, doi = {10.1007/s10709-007-9157-2}, pmid = {17562187}, issn = {0016-6707}, mesh = {Animals ; Base Sequence ; Consensus Sequence/genetics ; DNA Transposable Elements/*genetics ; Diptera/*genetics ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Multigene Family/*genetics ; Phylogeny ; }, abstract = {The Diopsid stalk-eyed flies are an increasingly well-studied group. Presented here is evidence of the first known transposable elements discovered in these flies. The vertumnana mariner subfamily was identified in the Diopsini tribe, but could not be amplified in species of the Sphyracephalini tribe. PCR screening with degenerate primers revealed that multiple mariner subfamilies are present within the Diopsidae. Most of the sequenced elements appear to be pseudogenes; however two subfamilies are shown to be evolving under purifying selection, raising the possibility that mariner is active in some Diopsid species. Evidence is presented of a possible horizontal transfer event involving an unknown Teleopsis species and the Tephritid fly Bactrocera neohumeralis.}, }
@article {pmid17562012, year = {2007}, author = {Rogers, MB and Watkins, RF and Harper, JT and Durnford, DG and Gray, MW and Keeling, PJ}, title = {A complex and punctate distribution of three eukaryotic genes derived by lateral gene transfer.}, journal = {BMC evolutionary biology}, volume = {7}, number = {}, pages = {89}, pmid = {17562012}, issn = {1471-2148}, mesh = {Animals ; Bacteria/enzymology/genetics ; Bacterial Proteins/genetics ; Carbohydrate Epimerases/*genetics ; Conserved Sequence/*genetics ; DNA/genetics ; Eukaryotic Cells/*enzymology ; *Evolution, Molecular ; Expressed Sequence Tags ; *Gene Transfer, Horizontal ; *Genes ; Genes, Bacterial ; Glyceraldehyde 3-Phosphate Dehydrogenase (NADP+)/*genetics ; Glyceraldehyde-3-Phosphate Dehydrogenase (NADP+)(Phosphorylating)/*genetics ; Molecular Sequence Data ; Species Specificity ; Transketolase/*genetics ; }, abstract = {BACKGROUND: Lateral gene transfer is increasingly invoked to explain phylogenetic results that conflict with our understanding of organismal relationships. In eukaryotes, the most common observation interpreted in this way is the appearance of a bacterial gene (one that is not clearly derived from the mitochondrion or plastid) in a eukaryotic nuclear genome. Ideally such an observation would involve a single eukaryote or a small group of related eukaryotes encoding a gene from a specific bacterial lineage.<br><br>RESULTS: Here we show that several apparently simple cases of lateral transfer are actually more complex than they originally appeared: in these instances we find that two or more distantly related eukaryotic groups share the same bacterial gene, resulting in a punctate distribution. Specifically, we describe phylogenies of three core carbon metabolic enzymes: transketolase, glyceraldehyde-3-phosphate dehydrogenase and ribulose-5-phosphate-3-epimerase. Phylogenetic trees of each of these enzymes includes a strongly-supported clade consisting of several eukaryotes that are distantly related at the organismal level, but whose enzymes are apparently all derived from the same lateral transfer. With less sampling any one of these examples would appear to be a simple case of bacterium-to-eukaryote lateral transfer; taken together, their evolutionary histories cannot be so simple. The distributions of these genes may represent ancient paralogy events or genes that have been transferred from bacteria to an ancient ancestor of the eukaryotes that retain them. They may alternatively have been transferred laterally from a bacterium to a single eukaryotic lineage and subsequently transferred between distantly related eukaryotes.<br><br>CONCLUSION: Determining how complex the distribution of a transferred gene is depends on the sampling available. These results show that seemingly simple cases may be revealed to be more complex with greater sampling, suggesting many bacterial genes found in eukaryotic genomes may have a punctate distribution.}, }
@article {pmid17561946, year = {2007}, author = {Devers, M and El Azhari, N and Kolic, NU and Martin-Laurent, F}, title = {Detection and organization of atrazine-degrading genetic potential of seventeen bacterial isolates belonging to divergent taxa indicate a recent common origin of their catabolic functions.}, journal = {FEMS microbiology letters}, volume = {273}, number = {1}, pages = {78-86}, doi = {10.1111/j.1574-6968.2007.00792.x}, pmid = {17561946}, issn = {0378-1097}, mesh = {Atrazine/*metabolism ; DNA Transposable Elements ; DNA, Bacterial/chemistry/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Gram-Negative Bacteria/*genetics/isolation &amp; purification/metabolism ; Metabolic Networks and Pathways/*genetics ; Molecular Sequence Data ; Plasmids ; Recombination, Genetic ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {A collection of 17 atrazine-degrading bacteria isolated from soils was studied to determine the composition of the atrazine-degrading genetic potential (i.e. trzN, trzD and atz) and the presence of IS1071. The characterization of seven new atrazine-degrading bacteria revealed for the first time the trzN-atzBC gene composition in Gram-negative bacteria such as Sinorhizobium sp. or Polaromonas sp. Three main atrazine-degrading gene combinations (i) trzN-atzBC, (ii) atzABC-trzD and (iii) atzABCDEF were observed. The atz and trz genes were often located on plasmids, suggesting that plasmid conjugation could play an important role in their dispersion. In addition, the observation of these genes (i) on the chromosome, (ii) on the same DNA fragment but on different plasmids and (iii) on DNA fragments also hybridizing with IS1071 suggests that transposition may also contribute to disperse the atrazine-degrading genes.}, }
@article {pmid17561499, year = {2007}, author = {Garcia-Migura, L and Liebana, E and Jensen, LB}, title = {Transposon characterization of vancomycin-resistant Enterococcus faecium (VREF) and dissemination of resistance associated with transferable plasmids.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {60}, number = {2}, pages = {263-268}, doi = {10.1093/jac/dkm186}, pmid = {17561499}, issn = {0305-7453}, mesh = {Animals ; Blotting, Southern ; Chickens/microbiology ; DNA Primers ; DNA Transposable Elements/*genetics ; Enterococcus faecium/*drug effects/*genetics ; Gene Transfer, Horizontal ; Gram-Positive Bacterial Infections/*microbiology/veterinary ; Lincosamides ; Macrolides/pharmacology ; Plasmids/*genetics ; Poultry Diseases/epidemiology/microbiology ; Replicon/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Streptogramin B/pharmacology ; United Kingdom/epidemiology ; Vancomycin Resistance/*genetics ; Virginiamycin/analogs &amp; derivatives/pharmacology ; }, abstract = {OBJECTIVES: VanA glycopeptide resistance has persisted on broiler farms in the UK despite the absence of the antimicrobial selective pressure, avoparcin. This study aimed to investigate the contribution of horizontal gene transfer of Tn1546 versus clonal spread in the dissemination of the resistance.<br><br>METHODS AND RESULTS: One hundred and one vancomycin-resistant Enterococcus faecium isolated from 19 unrelated farms have been investigated. Tn1546 characterization by long PCR and ClaI-digestions of amplicons showed a very low diversity of Tn types (n=4) in comparison to the high genotypic diversity demonstrated by PFGE (n=62). Conjugation experiments were carried out to assess the transfer of vancomycin resistance. Co-transfer of vanA together with erm(B) positioned on the same conjugative plasmid containing a replicon similar to pRE25 was demonstrated and also the presence of different plasmid replicons, associated with antimicrobial resistance on several unrelated farms.<br><br>CONCLUSIONS: Horizontal transfer of vancomycin resistance may play a more important role in the persistence of antimicrobial resistance than clonal spread. The presence of different plasmid replicons, associated with antimicrobial resistance on several unrelated farms, illustrates the ability of these enterococci to acquire and disseminate mobile genetic elements within integrated livestock systems.}, }
@article {pmid17561356, year = {2007}, author = {Passardi, F and Zamocky, M and Favet, J and Jakopitsch, C and Penel, C and Obinger, C and Dunand, C}, title = {Phylogenetic distribution of catalase-peroxidases: are there patches of order in chaos?.}, journal = {Gene}, volume = {397}, number = {1-2}, pages = {101-113}, doi = {10.1016/j.gene.2007.04.016}, pmid = {17561356}, issn = {0378-1119}, support = {P 19793/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Bacteria/enzymology/genetics ; Bacterial Proteins/chemistry/*genetics/metabolism ; Catalytic Domain ; Eukaryotic Cells ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genomic Islands ; Models, Molecular ; Peroxidases/chemistry/*genetics/metabolism ; Phylogeny ; Species Specificity ; Superoxide Dismutase/genetics ; }, abstract = {Hydrogen peroxide features in many biological oxidative processes and must be continuously degraded enzymatically either via a catalatic or a peroxidatic mechanism. For this purpose ancestral bacteria evolved a battery of different heme and non-heme enzymes, among which heme-containing catalase-peroxidases (CP) are one of the most widespread representatives. They are unique since they can follow both H(2)O(2)-degrading mechanisms, the catalase activity being clearly dominant. With the fast increasing amount of genomic data available, we were able to perform an extensive search for CP and found almost 300 sequences covering a large range of microorganisms. Most of them were encoded by bacterial genomes, but we could also find some in eukaryotic organisms other than fungi, which has never been shown until now. Our screen also reveals that approximately 60% of the bacteria do not possess CP genes. Chaotic distribution among species and incongruous phylogenetic reconstruction indicated existence of numerous lateral gene transfers in addition to duplication events and regular speciation. The results obtained show an impressively complex gene transmission pattern, and give some new insights about the role of CP and the origin of life on earth. Finally, we propose for the first time bacterial candidates that may have participated in the transfer of CP from bacteria to eukaryotes.}, }
@article {pmid17556756, year = {2007}, author = {Casola, C and Lawing, AM and Betrán, E and Feschotte, C}, title = {PIF-like transposons are common in drosophila and have been repeatedly domesticated to generate new host genes.}, journal = {Molecular biology and evolution}, volume = {24}, number = {8}, pages = {1872-1888}, doi = {10.1093/molbev/msm116}, pmid = {17556756}, issn = {0737-4038}, support = {GM071813-01/GM/NIGMS NIH HHS/United States ; GM077582/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Base Composition ; Base Sequence ; Codon ; DNA Transposable Elements/*genetics ; Drosophila/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes/*physiology ; *Genetic Variation ; Molecular Sequence Data ; *Phylogeny ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; }, abstract = {The P instability factor or PIF superfamily of DNA transposons constitutes an important group of transposable elements (TEs) in plants, but it is still poorly characterized in metazoans. Taking advantage of the availability of draft genome sequences for twelve Drosophila species, we discovered 4 different lineages of Drosophila PIF-like transposons, named DPLT1-4. These lineages have experienced a complex evolutionary history during the Drosophila radiation, involving differential amplification and retention among species and probable events of horizontal transmission. Like previously described plant and animal PIF transposons, full-length DPLTs encode a putative transposase as well as a second predicted protein containing a Myb/SANT domain. In DPLTs, this domain is most closely related to the MADF DNA-binding domain found in several Drosophila transcription factors. In addition, we identified 7 distinct genes distributed across the Drosophila genus that encode proteins related to PIF transposases, but lack the hallmarks of transposons. Instead, these sequences show features of functional genes, such as an intact coding region evolving under purifying selection, the presence of orthologs in at least 2 Drosophila species, and the conservation of intron/exon structure across orthologs. We also provide evidence that most of these genes are transcribed and that some are developmentally regulated. Together the data indicate that these genes derived from PIF-transposons that have been "domesticated" to serve cellular functions. In one instance the recruitment of the transposase gene was accompanied by the co-recruitment of the adjacent second PIF gene, which raises the hypothesis that both proteins now function in the same pathway. The second PIF gene has retained the capacity to encode a protein with an intact MADF domain, suggesting that it may function as a transcription factor. We conclude that PIF transposons are common in the Drosophila lineage and have been a recurrent source of new genes during Drosophila evolution.}, }
@article {pmid17556529, year = {2007}, author = {Wicker, T and Keller, B}, title = {Genome-wide comparative analysis of copia retrotransposons in Triticeae, rice, and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families.}, journal = {Genome research}, volume = {17}, number = {7}, pages = {1072-1081}, pmid = {17556529}, issn = {1088-9051}, mesh = {Arabidopsis/classification/*genetics ; Gene Transfer Techniques ; *Genome, Plant ; Multigene Family ; Oryza/classification/*genetics ; Phylogeny ; Retroelements/*genetics ; Triticum/classification/*genetics ; }, abstract = {Although copia retrotransposons are major components of all plant genomes, the evolutionary relationships between individual copia families and between elements from different plant species are only poorly studied. We used 20 copia families from the large-genome plants barley and wheat to identify 46 families of homologous copia elements from rice and 22 from Arabidopsis, two plant species with much smaller genomes. In total, 599 copia elements were analyzed. Phylogenetic analysis showed that copia elements from the four species can be classified into six ancient lineages that existed before the divergence of monocots and dicots. The six lineages show a surprising degree of conservation in sequence organization and other characteristics across species. Additionally, the phylogenetic data suggest at least one case of horizontal gene transfer between the Arabidopsis and rice lineages. Insertion time estimates for 522 high-copy elements showed that retrotransposons from rice were active at different times in waves of activity lasting 0.5-2 million years, depending on the family, whereas elements from wheat and barley had longer periods of activity. We estimated that half of the rice copia elements are truncated or otherwise rearranged after approximately 790,000 yr, which is almost twice the half-life of Arabidopsis elements. In contrast, wheat and barley copia elements appear to have a massively longer half-life, beyond our ability to estimate from the available data. These findings suggest that genome size can be explained by the specific rate of DNA removal from the genome and the length of active periods of retrotransposon families.}, }
@article {pmid17553065, year = {2007}, author = {Schlüter, A and Szczepanowski, R and Pühler, A and Top, EM}, title = {Genomics of IncP-1 antibiotic resistance plasmids isolated from wastewater treatment plants provides evidence for a widely accessible drug resistance gene pool.}, journal = {FEMS microbiology reviews}, volume = {31}, number = {4}, pages = {449-477}, doi = {10.1111/j.1574-6976.2007.00074.x}, pmid = {17553065}, issn = {0168-6445}, support = {P20 RR016448/RR/NCRR NIH HHS/United States ; P20 RR16448/RR/NCRR NIH HHS/United States ; R01 GM73821/GM/NIGMS NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/*drug effects/genetics/isolation &amp; purification ; Bacterial Proteins/genetics ; DNA Transposable Elements ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; *Genomics ; Humans ; Integrons ; Plasmids/*genetics ; *Waste Disposal, Fluid ; *Water Microbiology ; }, abstract = {The dramatic spread of antibiotic resistance is a crisis in the treatment of infectious diseases that affect humans. Several studies suggest that wastewater treatment plants (WWTP) are reservoirs for diverse mobile antibiotic resistance elements. This review summarizes findings derived from genomic analysis of IncP-1 resistance plasmids isolated from WWTP bacteria. Plasmids that belong to the IncP-1 group are self-transmissible, and transfer to and replicate in a wide range of hosts. Their backbone functions are described with respect to their impact on vegetative replication, stable maintenance and inheritance, mobility and plasmid control. Accessory genetic modules, mainly representing mobile genetic elements, are integrated in-between functional plasmid backbone modules. These elements carry determinants conferring resistance to nearly all clinically relevant antimicrobial drug classes, to heavy metals, and quaternary ammonium compounds used as disinfectants. All plasmids analysed here contain integrons that potentially facilitate integration, exchange and dissemination of resistance gene cassettes. Comparative genomics of accessory modules located on plasmids from WWTP and corresponding modules previously identified in other bacterial genomes revealed that animal, human and plant pathogens and other bacteria isolated from different habitats share a common pool of resistance determinants.}, }
@article {pmid17552979, year = {2007}, author = {McGrath, CL and Zufall, RA and Katz, LA}, title = {Variation in macronuclear genome content of three ciliates with extensive chromosomal fragmentation: a preliminary analysis.}, journal = {The Journal of eukaryotic microbiology}, volume = {54}, number = {3}, pages = {242-246}, doi = {10.1111/j.1550-7408.2007.00257.x}, pmid = {17552979}, issn = {1066-5234}, mesh = {Animals ; Chromosomes/*genetics ; Ciliophora/*genetics ; Codon/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genes, Protozoan ; Genetic Code ; Genetic Variation ; Genome, Protozoan/*genetics ; Macronucleus/*genetics ; Telomere ; beta-Mannosidase/genetics ; }, abstract = {The genome architecture of ciliates, including features such as nuclear dualism and large-scale genome rearrangements, impacts gene and genome evolution in these organisms. To better understand the structure of macronuclear chromosomes in ciliates with extensively processed chromosomes, a sample of complete macronuclear chromosomes was sequenced from three ciliate species: Metopus es (Class [Cl]: Armophorea), Nyctotherus ovalis (Cl: Armophorea), and Chilodonella uncinata (Cl: Phyllopharyngea). By cloning whole macronuclear chromosomes into a plasmid vector, we generated nine clones from each of M. es and C. uncinata, and 37 clones from N. ovalis. Analysis of these macronuclear chromosomes provides insight into the evolution of genome features such as chromosome content, gene structure, and genetic code. Phylogenetic patterns can be found in telomere structure and codon usage, which are both more similar in M. es and N. ovalis than C. uncinata. In addition, we provide evidence of lateral transfer of a bacterial endo-beta-mannanase gene onto a M. es chromosome and report the discovery of a 42-bp conserved sequence motif within N. ovalis untranslated regions.}, }
@article {pmid17550603, year = {2007}, author = {Marin, B and Nowack, EC and Glöckner, G and Melkonian, M}, title = {The ancestor of the Paulinella chromatophore obtained a carboxysomal operon by horizontal gene transfer from a Nitrococcus-like gamma-proteobacterium.}, journal = {BMC evolutionary biology}, volume = {7}, number = {}, pages = {85}, pmid = {17550603}, issn = {1471-2148}, mesh = {Amino Acid Sequence ; Amoeba/*genetics ; Animals ; Base Sequence ; DNA, Chloroplast ; Evolution, Molecular ; Gammaproteobacteria/*genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Molecular Sequence Data ; *Operon ; *Phylogeny ; RNA, Ribosomal/genetics ; Sequence Alignment ; }, abstract = {BACKGROUND: Paulinella chromatophora is a freshwater filose amoeba with photosynthetic endosymbionts (chromatophores) of cyanobacterial origin that are closely related to free-living Prochlorococcus and Synechococcus species (PS-clade). Members of the PS-clade of cyanobacteria contain a proteobacterial form 1A RubisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) that was acquired by horizontal gene transfer (HGT) of a carboxysomal operon. In rDNA-phylogenies, the Paulinella chromatophore diverged basal to the PS-clade, raising the question whether the HGT occurred before or after the split of the chromatophore ancestor.<br><br>RESULTS: Phylogenetic analyses of the almost complete rDNA operon with an improved taxon sampling containing most known cyanobacterial lineages recovered the Paulinella chromatophore as sister to the complete PS-clade. The sequence of the complete carboxysomal operon of Paulinella was determined. Analysis of RubisCO large subunit (rbcL) sequences revealed that Paulinella shares the proteobacterial form 1A RubisCO with the PS-clade. The gamma-proteobacterium Nitrococcus mobilis was identified as sister of the Paulinella chromatophore and the PS-clade in the RubisCO phylogeny. Gene content and order in the carboxysomal operon correlates well with the RubisCO phylogeny demonstrating that the complete carboxysomal operon was acquired by the common ancestor of the Paulinella chromatophore and the PS-clade through HGT. The carboxysomal operon shows a significantly elevated AT content in Paulinella, which in the rbcL gene is confined to third codon positions. Combined phylogenies using rbcL and the rDNA-operon resulted in a nearly fully resolved tree of the PS-clade.<br><br>CONCLUSION: The HGT of the carboxysomal operon predated the divergence of the chromatophore ancestor from the PS-clade. Following HGT and divergence of the chromatophore ancestor, diversification of the PS-clade into at least three subclades occurred. The gamma-proteobacterium Nitrococcus mobilis represents the closest known relative to the donor of the carboxysomal operon. The isolated position of the Paulinella chromatophore in molecular phylogenies as well as its elevated AT content suggests that the Paulinella chromatophore has already undergone typical steps in the reductive evolution of an endosymbiont.}, }
@article {pmid17548490, year = {2007}, author = {Pallecchi, L and Bartoloni, A and Fiorelli, C and Mantella, A and Di Maggio, T and Gamboa, H and Gotuzzo, E and Kronvall, G and Paradisi, F and Rossolini, GM}, title = {Rapid dissemination and diversity of CTX-M extended-spectrum beta-lactamase genes in commensal Escherichia coli isolates from healthy children from low-resource settings in Latin America.}, journal = {Antimicrobial agents and chemotherapy}, volume = {51}, number = {8}, pages = {2720-2725}, pmid = {17548490}, issn = {0066-4804}, mesh = {Anti-Bacterial Agents/pharmacology ; Bolivia/epidemiology ; Ceftriaxone/pharmacology ; Cephalosporin Resistance ; Child ; Child, Preschool ; Conjugation, Genetic ; Drug Resistance, Bacterial ; Escherichia coli/drug effects/*enzymology/genetics/isolation &amp; purification ; Feces/microbiology ; *Gene Transfer, Horizontal ; *Genetic Variation ; Humans ; Infant ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Peru/epidemiology ; Plasmids/genetics ; *Poverty ; Sequence Analysis, DNA ; Time Factors ; beta-Lactamases/*genetics ; }, abstract = {A survey carried out in 2005 among members of a healthy population of children living in Bolivia and Peru revealed that fecal carriage of Escherichia coli strains resistant to expanded-spectrum cephalosporins was remarkably increased compared to that observed in the same settings in 2002 (1.7% in 2005 versus 0.1% in 2002). In this work, we demonstrated that this phenomenon was mainly related to the dissemination of CTX-M-type extended-spectrum beta-lactamase (ESBL) determinants among commensal E. coli strains. Of 50 ESBL-producing isolates collected in the 2005 survey, 44 harbored a CTX-M-type and 6 an SHV-type (SHV-2 or SHV-12) ESBL. Compared to 2002 results, an increased diversity of CTX-M-type ESBLs was also observed: members of the CTX-M-1 group (CTX-M-15) emerged in Bolivia (where only CTX-M-2 was observed in 2002), while members of the CTX-M-9 group (CTX-M-14 and CTX-M-24) emerged in Peru (where only CTX-M-15 and CTX-M-2 were observed in 2002). A new CTX-M-2 variant named CTX-M-56 was also detected. Molecular characterization of the CTX-M-producing isolates and gene transfer experiments suggested that different mechanisms could be involved in the spreading of different CTX-M group determinants and revealed that additional resistance determinants for non-beta-lactam antibiotics were preferentially carried by plasmids encoding certain CTX-M variants (CTX-M-15 and variants of the CTX-M-2 group). Three CTX-M-15-encoding conjugative plasmids from Peruvian isolates carried the new fluoroquinolone resistance gene aac(6')-Ib-cr. To our best knowledge, this is the first report of the detection of aac(6')-Ib-cr in Latin America.}, }
@article {pmid17548487, year = {2007}, author = {Ip, M and Chau, SS and Chi, F and Tang, J and Chan, PK}, title = {Fluoroquinolone resistance in atypical pneumococci and oral streptococci: evidence of horizontal gene transfer of fluoroquinolone resistance determinants from Streptococcus pneumoniae.}, journal = {Antimicrobial agents and chemotherapy}, volume = {51}, number = {8}, pages = {2690-2700}, pmid = {17548487}, issn = {0066-4804}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Substitution ; Anti-Infective Agents/*pharmacology ; Bacterial Proteins/genetics ; DNA, Bacterial/analysis/isolation &amp; purification ; Drug Resistance, Bacterial/*genetics ; Fluoroquinolones/*pharmacology ; *Gene Transfer, Horizontal ; Genotype ; Humans ; Microbial Sensitivity Tests ; Phenotype ; Phylogeny ; Streptococcus/classification/*drug effects/genetics ; Streptococcus mitis/classification/drug effects/genetics ; Streptococcus oralis/classification/drug effects/genetics ; Streptococcus pneumoniae/classification/drug effects/genetics ; }, abstract = {Atypical strains, presumed to be pneumococcus, with ciprofloxacin MICs of > or =4.0 microg/ml and unique sequence variations within the quinolone resistance-determining regions (QRDRs) of the gyrase and topoisomerase genes in comparison with the Streptococcus pneumoniae R6 strain, were examined. These strains were reidentified using phenotypic methods, including detection of optochin susceptibility, bile solubility, and agglutination by serotype-specific antisera, and genotypic methods, including detection of pneumolysin and autolysin genes by PCR, 16S rRNA sequencing, and multilocus sequence typing (MLST). The analysis based on concatenated sequences of the six MLST loci distinguished the "atypical" strains from pneumococci, and these strains clustered closely with S. mitis. However, all these strains and five of nine strains from the viridans streptococcal group possessed one to three gyrA, gyrB, parC, and parE genes whose QRDR sequences clustered with those of S. pneumoniae, providing evidence of horizontal transfer of the QRDRs of the gyrase and topoisomerase genes from pneumococci into viridans streptococci. These genes also conferred fluoroquinolone resistance to viridans streptococci. In addition, the fluoroquinolone resistance determinants of 32 well-characterized Streptococcus mitis and Streptococcus oralis strains from bacteremic patients were also compared. These strains have unique amino acid substitutions in GyrA and ParC that were distinguishable from those in fluoroquinolone-resistant pneumococci and the "atypical" isolates. Both recombinational events and de novo mutations play an important role in the development of fluoroquinolone resistance.}, }
@article {pmid17547764, year = {2007}, author = {Vernikos, GS and Thomson, NR and Parkhill, J}, title = {Genetic flux over time in the Salmonella lineage.}, journal = {Genome biology}, volume = {8}, number = {6}, pages = {R100}, pmid = {17547764}, issn = {1474-760X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Escherichia coli/classification/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Phylogeny ; Prophages/genetics ; Salmonella/classification/*genetics ; }, abstract = {BACKGROUND: DNA sequences that are shared between closely related organisms while being absent from their common ancestor and from sister lineages of that ancestor are likely to have been acquired by horizontal gene transfer. Over time, the composition of those sequences tends to become more similar to the compositional signature of their host (amelioration).<br><br>RESULTS: From a whole-genome comparative analysis of eleven Salmonella, three Escherichia coli and one Shigella strain, we inferred the relative time of insertion of putative horizontally acquired (PHA) genes in three Salmonella strains on different branches of the S. enterica phylogenetic tree. Compositional analysis suggests that most of the PHA genes are still undergoing an amelioration process and shows a clear correlation between time of insertion and the level of amelioration.<br><br>CONCLUSION: The results show that older insertions include almost all functional classes. However, very recent horizontal transfer events in the Salmonella lineage involve primarily prophage elements that are shared only between very recently diverged lineages; despite this, the prophage sequence composition is close to that of the host, indicating that host adaptation, rather than amelioration, is likely to be the source of the compositional similarity. Almost half of the PHA genes were acquired at the base of the Salmonella lineage, whereas nearly three-quarters are shared between most S. enterica subspecies. The numerical distribution of PHA genes in the Salmonella tree topology correlates well with the divergence of the major Salmonella species, highlighting the major impact of horizontal transfer on the evolution of the salmonellae.}, }
@article {pmid17547748, year = {2007}, author = {Huang, J and Gogarten, JP}, title = {Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids?.}, journal = {Genome biology}, volume = {8}, number = {6}, pages = {R99}, pmid = {17547748}, issn = {1474-760X}, mesh = {Biological Evolution ; Chlamydia/*genetics/physiology ; Cyanobacteria/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Phylogeny ; Plastids/*genetics ; Rhodophyta/*genetics/physiology ; *Symbiosis ; }, abstract = {BACKGROUND: Ancient endosymbioses are responsible for the origins of mitochondria and plastids, and they contribute to the divergence of several major eukaryotic groups. Although chlamydiae, a group of obligate intracellular bacteria, are not found in plants, an unexpected number of chlamydial genes are most similar to plant homologs, which, interestingly, often contain a plastid-targeting signal. This observation has prompted several hypotheses, including gene transfer between chlamydiae and plant-related groups and an ancestral relationship between chlamydiae and cyanobacteria.<br><br>RESULTS: We conducted phylogenomic analyses of the red alga Cyanidioschyzon merolae to identify genes specifically related to chlamydial homologs. We show that at least 21 genes were transferred between chlamydiae and primary photosynthetic eukaryotes, with the donor most similar to the environmental Protochlamydia. Such an unusually high number of transferred genes suggests an ancient chlamydial endosymbiosis with the ancestral primary photosynthetic eukaryote. We hypothesize that three organisms were involved in establishing the primary photosynthetic lineage: the eukaryotic host cell, the cyanobacterial endosymbiont that provided photosynthetic capability, and a chlamydial endosymbiont or parasite that facilitated the establishment of the cyanobacterial endosymbiont.<br><br>CONCLUSION: Our findings provide a glimpse into the complex interactions that were necessary to establish the primary endosymbiotic relationship between plastid and host cytoplasms, and thereby explain the rarity with which long-term successful endosymbiotic relationships between heterotrophs and photoautotrophs were established. Our data also provide strong and independent support for a common origin of all primary photosynthetic eukaryotes and of the plastids they harbor.}, }
@article {pmid17545290, year = {2007}, author = {Maiques, E and Ubeda, C and Tormo, MA and Ferrer, MD and Lasa, I and Novick, RP and Penadés, JR}, title = {Role of staphylococcal phage and SaPI integrase in intra- and interspecies SaPI transfer.}, journal = {Journal of bacteriology}, volume = {189}, number = {15}, pages = {5608-5616}, pmid = {17545290}, issn = {0021-9193}, support = {R01 AI022159/AI/NIAID NIH HHS/United States ; R01-AI-22159/AI/NIAID NIH HHS/United States ; }, mesh = {DNA Packaging ; DNA Replication ; DNA, Bacterial/genetics/metabolism ; *Gene Transfer, Horizontal ; Genetic Complementation Test ; Genomic Islands/*genetics ; Integrases/*genetics/metabolism ; Rec A Recombinases/metabolism ; Recombination, Genetic ; Staphylococcus Phages/*genetics ; Staphylococcus aureus/*genetics/virology ; *Transduction, Genetic ; }, abstract = {SaPIbov2 is a member of the SaPI family of staphylococcal pathogenicity islands and is very closely related to SaPIbov1. Typically, certain temperate phages can induce excision and replication of one or more of these islands and can package them into special small phage-like particles commensurate with their genome sizes (referred to as the excision-replication-packaging [ERP] cycle). We have studied the phage-SaPI interaction in some depth using SaPIbov2, with special reference to the role of its integrase. We demonstrate here that SaPIbov2 can be induced to replicate by different staphylococcal phages. After replication, SaPIbov2 is efficiently encapsidated and transferred to recipient organisms, including different non-Staphylococcus aureus staphylococci, where it integrates at a SaPI-specific attachment site, att(C), by means of a self-coded integrase (Int). Phages that cannot induce the SaPIbov2 ERP cycle can transfer the island by recA-dependent classical generalized transduction and can also transfer it by a novel mechanism that requires the expression of SaPIbov2 int in the recipient but not in the donor. It is suggested that this mechanism involves the encapsidation of standard transducing fragments containing the intact island followed by int-mediated excision, circularization, and integration in the recipient.}, }
@article {pmid17545187, year = {2007}, author = {Becq, J and Gutierrez, MC and Rosas-Magallanes, V and Rauzier, J and Gicquel, B and Neyrolles, O and Deschavanne, P}, title = {Contribution of horizontally acquired genomic islands to the evolution of the tubercle bacilli.}, journal = {Molecular biology and evolution}, volume = {24}, number = {8}, pages = {1861-1871}, doi = {10.1093/molbev/msm111}, pmid = {17545187}, issn = {0737-4038}, mesh = {Blotting, Southern ; Computational Biology ; Evolution, Molecular ; Gene Rearrangement ; *Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; *Genome, Bacterial ; Genomic Islands/*genetics ; Mycobacterium tuberculosis/*genetics/*pathogenicity ; RNA, Transfer/genetics ; Tuberculosis/genetics/pathology ; Virulence ; Virulence Factors/genetics ; }, abstract = {The contribution of horizontal gene transfer (HGT) to the evolution of Mycobacterium tuberculosis -- the main causal agent of tuberculosis in humans -- and closely related members of the M. tuberculosis complex remains poorly understood. Using a combination of genome-wide parametric analyses, we have identified 48 M. tuberculosis chromosomal regions with atypical characteristics, potentially due to HGT. These specific regions account for 4.5% of the genome (199 kb) and include 256 genes. Many display features typical of the genomic islands found in other bacteria, including residual material from mobile genetic elements, flanking direct repeats, insertion in the vicinity of tRNA sequences, and genes with putative or documented virulence functions. Southern blotting analysis of nine of these 48 regions confirmed their presence in "Mycobacterium prototuberculosis," the ancestral species of the M. tuberculosis complex. Finally, our results strongly suggest that the ancestor of the tubercle bacilli was an environmental bacillus that exchanged genetic material with other bacterial species, including Proteobacteria in particular, present in its surroundings. This study describes a rational approach to searching for mycobacterial virulence genes, and highlights the importance of dissecting gene transfer networks to improve our understanding of mycobacterial pathogenicity and evolution.}, }
@article {pmid17544399, year = {2007}, author = {Bergsmedh, A and Ehnfors, J and Spetz, AL and Holmgren, L}, title = {A Cre-loxP based system for studying horizontal gene transfer.}, journal = {FEBS letters}, volume = {581}, number = {16}, pages = {2943-2946}, doi = {10.1016/j.febslet.2007.05.045}, pmid = {17544399}, issn = {0014-5793}, mesh = {Animals ; Cells, Cultured ; Embryo, Mammalian/cytology ; Female ; Gene Silencing ; *Gene Transfer, Horizontal ; HeLa Cells ; Humans ; Immunity, Cellular/genetics ; Influenza A virus/genetics ; Integrases/*genetics ; Lac Operon ; Mice ; Models, Genetic ; Phagocytosis/genetics ; Pregnancy ; Recombination, Genetic ; Transfection/*methods ; Transgenes ; }, abstract = {We have previously shown that DNA can be transferred to phagocytosing cells via the uptake of apoptotic cells. We report a model system that facilitates study of antigen presentation of genes transferred specifically via horizontal gene transfer. Constructs were generated encoding the LacZ gene or the influenza A nucleoprotein silenced by a STOP sequence flanked by two loxP sites. These reporter genes were demonstrated to be silent in donor cells and become activated after phagocytosis of Cre-expressing fibroblasts or macrophages. These results provide a model system for studying the influence of horizontally transferred antigens on activation of the immune system.}, }
@article {pmid17543117, year = {2007}, author = {Pérez-Losada, M and Crandall, KA and Bash, MC and Dan, M and Zenilman, J and Viscidi, RP}, title = {Distinguishing importation from diversification of quinolone-resistant Neisseria gonorrhoeae by molecular evolutionary analysis.}, journal = {BMC evolutionary biology}, volume = {7}, number = {}, pages = {84}, pmid = {17543117}, issn = {1471-2148}, support = {R01 AI050217/AI/NIAID NIH HHS/United States ; R01-AI-50217/AI/NIAID NIH HHS/United States ; }, mesh = {Base Sequence ; Bayes Theorem ; Drug Resistance, Bacterial/*genetics ; *Evolution, Molecular ; Genes, Bacterial/genetics ; *Genetics, Population ; Gonorrhea/*prevention &amp; control ; Humans ; Models, Genetic ; Molecular Sequence Data ; Neisseria gonorrhoeae/*genetics ; *Phylogeny ; Population Dynamics ; *Quinolones ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Distinguishing the recent introduction of quinolone resistant gonococci into a population from diversification of resistant strains already in the population is important for planning effective infection control strategies. We applied molecular evolutionary analyses to DNA sequences from 9 housekeeping genes and gyrA, parC and porB of 24 quinolone resistant N. gonorrhoeae (QRNG) and 24 quinolone sensitive isolates collected in Israel during 2000-2001.<br><br>RESULTS: Phylogenetic and eBURST analyses and estimates of divergence time indicated QRNG were introduced on 3 separate occasions and underwent limited diversification by mutation, deletion and horizontal gene transfer. Reconstruction of N. gonorrhoeae demography showed a slowly declining effective strain population size from 1976 to 1993, rapid decline between 1994 and 1999, and an increase from 1999 to 2001. This is partially attributable to declining gonorrhea case rates from 1973 to 1994. Additional contributing factors are selective sweeps of antibiotic resistant gonococci and increased transmission from sex workers. The abrupt decline in the mid-1990s heralded an increased incidence of gonorrhea from 1997 to the present. The subsequent increase in effective strain population size since 1999 reflects the increased gonococcal census population and introduction of quinolone resistance strains.<br><br>CONCLUSION: Our study demonstrates the effective use of population genetic approaches to assess recent and historical population dynamics of N. gonorrhoeae.}, }
@article {pmid17540514, year = {2007}, author = {Vinogradov, SN and Hoogewijs, D and Bailly, X and Mizuguchi, K and Dewilde, S and Moens, L and Vanfleteren, JR}, title = {A model of globin evolution.}, journal = {Gene}, volume = {398}, number = {1-2}, pages = {132-142}, doi = {10.1016/j.gene.2007.02.041}, pmid = {17540514}, issn = {0378-1119}, mesh = {Animals ; Archaea/classification/genetics ; Bacteria/classification/genetics ; Computational Biology/methods ; Databases, Nucleic Acid ; Eukaryotic Cells/metabolism ; *Evolution, Molecular ; Globins/*genetics ; *Models, Genetic ; Phylogeny ; Time Factors ; }, abstract = {Putative globins have been identified in 426 bacterial, 32 Archaeal and 67 eukaryote genomes. Among these sequences are the hitherto unsuspected presence of single domain sensor globins within Bacteria, Fungi, and a Euryarchaeote. Bayesian phylogenetic trees suggest that their occurrence in the latter two groups could be the result of lateral gene transfer from Bacteria. Iterated psiblast searches based on groups of globin sequences indicate that bacterial flavohemoglobins are closer to metazoan globins than to the other two lineages, the 2-over-2 globins and the globin-coupled sensors. Since Bacteria is the only kingdom to have all the subgroups of the three globin lineages, we propose a working model of globin evolution based on the assumption that all three lineages originated and evolved only in Bacteria. Although the 2-over-2 globins and the globin-coupled sensors recognize flavohemoglobins, there is little recognition between them. Thus, in the first stage of globin evolution, we favor a flavohemoglobin-like single domain protein as the ancestral globin. The next stage comprised the splitting off to single domain 2-over-2 and sensor-like globins, followed by the covalent addition of C-terminal domains resulting in the chimeric flavohemoglobins and globin-coupled sensors. The last stage encompassed the lateral gene transfers of some members of the three globin lineages to specific groups of Archaea and Eukaryotes.}, }
@article {pmid17536935, year = {2007}, author = {Kikuvi, GM and Schwarz, S and Ombui, JN and Mitema, ES and Kehrenberg, C}, title = {Streptomycin and chloramphenicol resistance genes in Escherichia coli isolates from cattle, pigs, and chicken in Kenya.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {13}, number = {1}, pages = {62-68}, doi = {10.1089/mdr.2006.9998}, pmid = {17536935}, issn = {1076-6294}, mesh = {Animal Husbandry ; Animals ; Animals, Domestic/*microbiology ; Anti-Bacterial Agents/*pharmacology ; Bacteriological Techniques ; Cattle/microbiology ; Chickens/microbiology ; Chloramphenicol/pharmacology ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/*drug effects/*genetics ; Food Microbiology ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Integrons ; Kenya/epidemiology ; Plasmids ; Streptomycin/pharmacology ; Swine/microbiology ; }, abstract = {The aims of this study were to determine the genetic basis of streptomycin and chloramphenicol resistance in 30 Escherichia coli isolates from food animals in Kenya and the role of plasmids in the spread of the resistance. Seven of the 29 streptomycin-resistant isolates harbored both the strA and strB genes. Twenty-one of isolates had the strA, strB, and aadA1 genes. The strA gene was disrupted by a functional trimethoprim gene, dfrA14 in 10 of the 21 isolates harboring the three streptomycin resistance genes. Physical linkage of intact strA and sul2 genes was found in two different plasmids from four isolates. Linkage of cassette-borne aadA1 and dfrA1 genes in class 1 integrons was found in two of the isolates. Chloramphenicol resistance was due to the gene catA1 in all the chloramphenicol resistant isolates. The strB, strA, and catA1 genes were transferable by conjugation and this points to the significance of conjugative resistance plasmids in the spread and persistence of streptomycin and chloramphenicol resistance in food animals in Kenya.}, }
@article {pmid17536933, year = {2007}, author = {Srinivasan, V and Nguyen, LT and Headrick, SI and Murinda, SE and Oliver, SP}, title = {Antimicrobial resistance patterns of Shiga toxin-producing Escherichia coli O157:H7 and O157:H7- from different origins.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {13}, number = {1}, pages = {44-51}, doi = {10.1089/mdr.2006.9996}, pmid = {17536933}, issn = {1076-6294}, mesh = {Animals ; Cattle ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli O157/genetics/isolation &amp; purification/*metabolism ; Genotype ; Humans ; Microbial Sensitivity Tests ; Phenotype ; Polymerase Chain Reaction ; Shiga Toxins/*biosynthesis ; }, abstract = {Shiga toxin-producing Escherichia coli (STEC) serotypes including O157:H7 (n = 129) from dairy cows, cull dairy cow feces, cider, salami, human feces, ground beef, bulk tank milk, bovine feces, and lettuce; and O157:H7- (n = 24) isolated from bovine dairy and bovine feedlot cows were evaluated for antimicrobial resistance against 26 antimicrobials and the presence of antimicrobial resistance genes (tetA, tetB, tetC, tetD, tetE, tetG, floR, cmlA, strA, strB, sulI, sulII, and ampC). All E. coli exhibited resistance to five or more antimicrobial agents, and the majority of isolates carried one or more target antimicrobial resistance gene(s) in different combinations. The majority of E. coli showed resistance to ampicillin, aztreonam, cefaclor, cephalothin, cinoxacin, and nalidixic acid, and all isolates were susceptible to chloramphenicol and florfenicol. Many STEC O157:H7 and O157:H7-isolates were susceptible to amikacin, carbenicillin, ceftriaxone, cefuroxime, ciprofloxacin, fosfomycin, moxalactam, norfloxacin, streptomycin, tobramycin, trimethoprim, and tetracycline. The majority of STEC O157:H7 (79.8%) and O157:H7- (91.7%) carried one or more antimicrobial resistance gene(s) regardless of whether phenotypically resistant or susceptible. Four tetracycline resistant STEC O157:H7 isolates carried both tetA and tetC. Other tetracycline resistance genes (tetB, tetD, tetE, and tetG) were not detected in any of the isolates. Among nine streptomycin resistant STEC O157:H7 isolates, eight carried strA-strB along with aadA, whereas the other isolate carried aadA alone. However, the majority of tetracycline and streptomycin susceptible STEC isolates also carried tetA and aadA genes, respectively. Most ampicillin resistant E. coli of both serotypes carried ampC genes. Among sulfonamide resistance genes, sulII was detected only in STEC O157:H7 (4 of 80 sulfonamide-resistant isolates) and sulI was detected in O157:H7- (1 of 16 sulfonamide resistant isolates). The emergence and dissemination of multidrug resistance in STEC can serve as a reservoir for different antimicrobial resistance genes. Dissemination of antimicrobial resistance genes to commensal and pathogenic bacteria could occur through any one of the horizontal gene transfer mechanisms adopted by the bacteria.}, }
@article {pmid17536014, year = {2007}, author = {Deregibus, MC and Cantaluppi, V and Calogero, R and Lo Iacono, M and Tetta, C and Biancone, L and Bruno, S and Bussolati, B and Camussi, G}, title = {Endothelial progenitor cell derived microvesicles activate an angiogenic program in endothelial cells by a horizontal transfer of mRNA.}, journal = {Blood}, volume = {110}, number = {7}, pages = {2440-2448}, doi = {10.1182/blood-2007-03-078709}, pmid = {17536014}, issn = {0006-4971}, mesh = {Apoptosis ; *Cell Differentiation ; Cells, Cultured ; Endothelial Cells/*cytology/*metabolism ; Enzyme Activation ; Gene Transfer, Horizontal ; Humans ; Intracellular Membranes/*metabolism/ultrastructure ; Microscopy, Electron, Scanning ; *Neovascularization, Physiologic ; Nitric Oxide Synthase Type III/metabolism ; Oligonucleotide Array Sequence Analysis ; Proto-Oncogene Proteins c-akt/metabolism ; RNA, Messenger/genetics ; Stem Cells/*cytology/*metabolism ; }, abstract = {Membrane-derived microvesicles (MVs) are released from the cell surface and are implicated in cell-to-cell communication. We evaluated whether MVs derived from endothelial progenitor cells (EPCs) are able to trigger angiogenesis. We found that EPC-derived MVs were incorporated in endothelial cells by interaction with alpha4 and beta1 integrins expressed on the MV surface. In vitro, MVs promoted endothelial cell survival, proliferation, and organization in capillary-like structures. In vivo, in severe combined immunodeficient (SCID) mice, MV-stimulated human endothelial cells organized in patent vessels. When incubated with RNase, despite their internalization into endothelial cells, MVs failed to induce in vitro and in vivo angiogenic effects. mRNA transfer was shown by transduction of GFP protein in endothelial cells by MVs containing GFP-mRNA and the biologic relevance by the angiogenic effect of MV-mRNA extract delivered by lipofectamine. Microarray ana-lysis and quantitative reverse transcription-polymerase chain reaction (RT-PCR) of MV-mRNA extract indicated that MVs were shuttling a specific subset of cellular mRNA, such as mRNA associated with the PI3K/AKT signaling pathway. Protein expression and functional studies showed that PI3K and eNOS play a critical role in the angiogenic effect of MVs. These results suggest that EPCs may activate angiogenesis in endothelial cells by releasing MVs able to trigger an angiogenic program.}, }
@article {pmid17535299, year = {2007}, author = {te Poele, EM and Habets, MN and Tan, GY and Ward, AC and Goodfellow, M and Bolhuis, H and Dijkhuizen, L}, title = {Prevalence and distribution of nucleotide sequences typical for pMEA-like accessory genetic elements in the genus Amycolatopsis.}, journal = {FEMS microbiology ecology}, volume = {61}, number = {2}, pages = {285-294}, doi = {10.1111/j.1574-6941.2007.00334.x}, pmid = {17535299}, issn = {0168-6496}, mesh = {Actinomycetales/*genetics/isolation &amp; purification ; Bacterial Outer Membrane Proteins/chemistry/classification/genetics ; Bacterial Proteins/*chemistry/classification/genetics ; Base Sequence ; Chromosome Mapping ; DNA Helicases/chemistry/classification/genetics ; DNA-Binding Proteins/chemistry/classification/genetics ; Evolution, Molecular ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Trans-Activators/chemistry/classification/genetics ; }, abstract = {The prevalence and distribution of pMEA-like elements in the genus Amycolatopsis was studied. For this purpose, a set of 95 recently isolated Amycolatopsis strains and 16 Amycolatopsis type strains were examined for the presence of two unique pMEA-sequences (repAM and traJ), encoding proteins essential for replication and conjugative transfer. Homologues of repAM and traJ were found in 10 and 26 of 111 investigated strains, respectively, a result which shows that pMEA-like sequences, though not very abundant, can be found in several Amycolatopsis strains. Phylogenetic analysis of the deduced RepAM and TraJ protein sequences revealed clustering with the protein sequences of either pMEA300 or pMEA100. Furthermore, two geographically different populations of pMEA-like elements were distinguished, one originating in Europe and the other in Australia and Asia. Linkage between the distribution of repAM and traJ and the chromosomal identifier, the 16S rRNA gene, indicated that these elements coevolved with their hosts, suggesting that they evolved in an integrated form rather than by horizontal gene transfer of the free replicating form.}, }
@article {pmid17530227, year = {2007}, author = {Gu, CT and Wang, ET and Sui, XH and Chen, WF and Chen, WX}, title = {Diversity and geographical distribution of rhizobia associated with Lespedeza spp. in temperate and subtropical regions of China.}, journal = {Archives of microbiology}, volume = {188}, number = {4}, pages = {355-365}, doi = {10.1007/s00203-007-0256-3}, pmid = {17530227}, issn = {0302-8933}, mesh = {Alphaproteobacteria/*classification/*genetics/isolation &amp; purification ; Bacterial Proteins/analysis/genetics ; China ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Electrophoresis, Polyacrylamide Gel ; Genes, rRNA ; *Geography ; Lespedeza/*microbiology ; Molecular Sequence Data ; N-Acetylglucosaminyltransferases/genetics ; Nucleic Acid Hybridization ; Oxidoreductases/genetics ; Phylogeny ; Plant Roots/microbiology ; *Polymorphism, Genetic ; Polymorphism, Restriction Fragment Length ; Proteome/analysis ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {Eighty-eight root-nodule isolates from Lespedeza spp. grown in temperate and subtropical regions of China were characterized by a polyphasic approach. Nine clusters were defined in numerical taxonomy and SDS-PAGE analysis of whole cell proteins. Based upon further characterizations of amplified 16S rDNA restriction analysis (ARDRA), PCR-based restriction fragment length polymorphism of ribosomal IGS, 16S rDNA sequence analysis and DNA-DNA hybridization, these isolates were identified as Bradyrhizobium japonicum, B. elkanii, B. yuanmingense, Mesorhizobium amorphae, M. huakuii, Sinorhizobium meliloti and three genomic species related to B. yuanmingense, Rhizobium gallicum and R. tropici. The Bradyrhizobium species and R. tropici-related rhizobia were mainly isolated from the subtropical region and the species of Mesorhizobium, S. meliloti and R. gallicum-related species were all isolated from the temperate region. Phylogenetic analyses of nifH and nodC indicated that the symbiotic genes of distinct rhizobial species associated with Lespedeza spp. might have different origins and there was no evidence for lateral gene transfer of symbiotic genes. The results obtained in the present study and in a previous report demonstrated that Lespedeza spp. are nodulated by rhizobia with diverse genomic backgrounds and these Lespedeza-nodulating rhizobia were not specific to the host species, but specific to their geographic origins.}, }
@article {pmid17526501, year = {2007}, author = {Hansen, LH and Jensen, LB and Sørensen, HI and Sørensen, SJ}, title = {Substrate specificity of the OqxAB multidrug resistance pump in Escherichia coli and selected enteric bacteria.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {60}, number = {1}, pages = {145-147}, doi = {10.1093/jac/dkm167}, pmid = {17526501}, issn = {0305-7453}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Anti-Infective Agents, Local/pharmacology ; Bacterial Proteins/genetics/*metabolism ; Detergents/pharmacology ; Disinfectants/pharmacology ; *Drug Resistance, Multiple, Bacterial ; Enterobacteriaceae/classification/*drug effects/genetics ; Escherichia coli/*drug effects/metabolism ; Escherichia coli Proteins/genetics/*metabolism ; Gene Transfer, Horizontal ; Growth Substances/pharmacology ; Microbial Sensitivity Tests ; Plasmids/genetics ; Quinoxalines/*pharmacology ; Substrate Specificity ; }, abstract = {OBJECTIVES: A plasmid-encoded multidrug efflux pump, OqxAB, identified in Escherichia coli of porcine origin, was tested for substrate specificity against selected antibiotics, detergents and disinfectants. The ability of horizontal transfer to food-borne pathogens of the Enterobacteriaceae family was also investigated.<br><br>METHODS: The MICs of selected substrates were determined with a broth dilution assay using two isogenic E. coli strains, except for the presence of the oqxAB operon. A derivative of the plasmid encoding OqxAB (pOLA52) was constructed and horizontal transfer to Salmonella Typhimurium, Klebsiella pneumoniae, Kluyvera sp. and Enterobacter aerogenes was investigated. The effect of the presence of the OqxAB pump on susceptibility for selected compounds was investigated using broth dilution assays.<br><br>RESULTS: The OqxAB pump conferred antimicrobial resistance or reduced susceptibility towards a variety of substrates in E. coli. These included animal growth promoters, antimicrobials, disinfectants and detergents. pOLA52 could readily be transferred to enterobacterial pathogens. Transconjugants showed reduced susceptibility towards chloramphenicol, ciprofloxacin and olaquindox.<br><br>CONCLUSIONS: The plasmid-encoded OqxAB pump has a wide substrate specificity and can be transferred between Enterobacteriaceae conferring reduced susceptibility to a multitude of substrates. These results could indicate some dependence on the outer membrane proteins present in the different species.}, }
@article {pmid17522086, year = {2007}, author = {Khan, H and Parks, N and Kozera, C and Curtis, BA and Parsons, BJ and Bowman, S and Archibald, JM}, title = {Plastid genome sequence of the cryptophyte alga Rhodomonas salina CCMP1319: lateral transfer of putative DNA replication machinery and a test of chromist plastid phylogeny.}, journal = {Molecular biology and evolution}, volume = {24}, number = {8}, pages = {1832-1842}, doi = {10.1093/molbev/msm101}, pmid = {17522086}, issn = {0737-4038}, mesh = {Bacteria/*genetics ; Cryptophyta/*genetics ; *DNA Replication ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Plant ; *Genome ; Phylogeny ; Plastids/*genetics ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {Cryptophytes are a group of unicellular algae with chlorophyll c-containing plastids derived from the uptake of a secondary (i.e., eukaryotic) endosymbiont. Biochemical and molecular data indicate that cryptophyte plastids are derived from red algae, yet the question of whether or not cryptophytes acquired their red algal plastids independent of those in heterokont, haptophyte, and dinoflagellate algae is of long-standing debate. To better understand the origin and evolution of the cryptophyte plastid, we have sequenced the plastid genome of Rhodomonas salina CCMP1319: at 135,854 bp, it is the largest secondary plastid genome characterized thus far. It also possesses interesting features not seen in the distantly related cryptophyte Guillardia theta or in other red secondary plastids, including pseudogenes, introns, and a bacterial-derived gene for the tau/gamma subunit of DNA polymerase III (dnaX), the first time putative DNA replication machinery has been found encoded in any plastid genome. Phylogenetic analyses indicate that dnaX was acquired by lateral gene transfer (LGT) in an ancestor of Rhodomonas, most likely from a firmicute bacterium. A phylogenomic survey revealed no additional cases of LGT, beyond a noncyanobacterial type rpl36 gene similar to that recently characterized in other cryptophytes and haptophytes. Rigorous concatenated analysis of 45 proteins encoded in 15 complete plastid genomes produced trees in which the heterokont, haptophyte, and cryptophyte (i.e., chromist) plastids were monophyletic, and heterokonts and haptophytes were each other's closest relatives. However, statistical support for chromist monophyly disappears when amino acids are recoded according to their chemical properties in order to minimize the impact of composition bias, and a significant fraction of the concatenate appears consistent with a sister-group relationship between cryptophyte and haptophyte plastids.}, }
@article {pmid17521833, year = {2007}, author = {Vo, AT and van Duijkeren, E and Fluit, AC and Gaastra, W}, title = {Characteristics of extended-spectrum cephalosporin-resistant Escherichia coli and Klebsiella pneumoniae isolates from horses.}, journal = {Veterinary microbiology}, volume = {124}, number = {3-4}, pages = {248-255}, doi = {10.1016/j.vetmic.2007.04.027}, pmid = {17521833}, issn = {0378-1135}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; *Cephalosporin Resistance/genetics ; Cephalosporins/pharmacology ; Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Escherichia coli/*drug effects ; Escherichia coli Infections/microbiology/veterinary ; Female ; Gene Transfer, Horizontal ; Horse Diseases/*microbiology ; Horses ; Klebsiella Infections/microbiology/veterinary ; Klebsiella pneumoniae/*drug effects ; Male ; Microbial Sensitivity Tests/veterinary ; Molecular Sequence Data ; beta-Lactamases/*genetics ; }, abstract = {The aim of the present study was to contribute to the knowledge on extended-spectrum beta-lactamases (ESBL's), AmpC beta-lactamases and integrons in Enterobacteriaceae isolated from horses, which is still limited. The susceptibility of 1581 clinical isolates from animals to ceftiofur was tested. Most of these isolates (n=1347) originated from horses. Seven ceftiofur-resistant equine isolates (four Escherichia coli and three Klebsiella pneumoniae) were identified and all seven were multidrug-resistant. These isolates were further studied for the presence of ESBL's, AmpC beta-lactamases and class 1 integrons. The potential for the horizontal transfer of resistance genes among these clinical isolates was also studied. ESBL-type resistance genes were found in five isolates, AmpC-type genes in one isolates and integrons in six isolates. Nucleotide sequence analysis revealed that the isolates carried the bla(CTX-M-1), bla(CMY-2), bla(TEM-1) and/or bla(SHV-1) genes. This is the first report describing the in vitro conjugal transfer of the bla(CTX-M-1) genes from a clinical E. coli isolate to Salmonella isolates. Gene cassettes encoding resistance to aminoglycosides (aadA1, aadA2 and aadA5), and trimethoprim (dfrA1, drfA12 and dfrA17) were found on the integrons present in the isolates. The cassette arrays of the dfrA17-aadA5 and dfrA1-aadA1 genes in the two integrons of a single E. coli isolate have not yet been described before. To our knowledge this is the first report on ESBL's and AmpC beta-lactamases in equine E. coli and Klebsiella isolates.}, }
@article {pmid17521426, year = {2007}, author = {Noble, GP and Rogers, MB and Keeling, PJ}, title = {Complex distribution of EFL and EF-1alpha proteins in the green algal lineage.}, journal = {BMC evolutionary biology}, volume = {7}, number = {}, pages = {82}, pmid = {17521426}, issn = {1471-2148}, mesh = {Algal Proteins/*genetics ; Chlorophyta/*genetics ; *Evolution, Molecular ; GTP Phosphohydrolase-Linked Elongation Factors/*genetics ; Molecular Sequence Data ; Peptide Elongation Factor 1/*genetics ; Phylogeny ; }, abstract = {BACKGROUND: EFL (or elongation factor-like) is a member of the translation superfamily of GTPase proteins. It is restricted to eukaryotes, where it is found in a punctate distribution that is almost mutually exclusive with elongation factor-1 alpha (EF-1alpha). EF-1alpha is a core translation factor previously thought to be essential in eukaryotes, so its relationship to EFL has prompted the suggestion that EFL has spread by horizontal or lateral gene transfer (HGT or LGT) and replaced EF-1alpha multiple times. Among green algae, trebouxiophyceans and chlorophyceans have EFL, but the ulvophycean Acetabularia and the sister group to green algae, land plants, have EF-1alpha. This distribution singles out green algae as a particularly promising group to understand the origin of EFL and the effects of its presence on EF-1alpha.<br><br>RESULTS: We have sampled all major lineages of green algae for both EFL and EF-1alpha. EFL is unexpectedly broad in its distribution, being found in all green algal lineages (chlorophyceans, trebouxiophyceans, ulvophyceans, prasinophyceans, and mesostigmatophyceans), except charophyceans and the genus Acetabularia. The presence of EFL in the genus Mesostigma and EF-1alpha in Acetabularia are of particular interest, since the opposite is true of all their closest relatives. The phylogeny of EFL is poorly resolved, but the Acetabularia EF-1alpha is clearly related to homologues from land plants and charophyceans, demonstrating that EF-1alpha was present in the common ancestor of the green lineage.<br><br>CONCLUSION: The distribution of EFL and EF-1alpha in the green lineage is not consistent with the phylogeny of the organisms, indicating a complex history of both genes. Overall, we suggest that after the introduction of EFL (in the ancestor of green algae or earlier), both genes co-existed in green algal genomes for some time before one or the other was lost on multiple occasions.}, }
@article {pmid17513882, year = {2007}, author = {Slot, JC and Hallstrom, KN and Matheny, PB and Hibbett, DS}, title = {Diversification of NRT2 and the origin of its fungal homolog.}, journal = {Molecular biology and evolution}, volume = {24}, number = {8}, pages = {1731-1743}, doi = {10.1093/molbev/msm098}, pmid = {17513882}, issn = {0737-4038}, mesh = {Anion Transport Proteins/*genetics/metabolism ; Eukaryota/classification/genetics ; Eukaryotic Cells/*physiology ; Evolution, Molecular ; Fungi/*genetics/metabolism ; Gene Expression Regulation, Plant ; Nitrate Transporters ; Nitrates/metabolism ; Phylogeny ; Sequence Alignment ; }, abstract = {We investigated the origin and diversification of the high-affinity nitrate transporter NRT2 in fungi and other eukaryotes using Bayesian and maximum parsimony methods. To assess the higher-level relationships and origins of NRT2 in eukaryotes, we analyzed 200 amino acid sequences from the Nitrate/Nitrite Porter (NNP) Family (to which NRT2 belongs), including 55 fungal, 41 viridiplantae (green plants), 11 heterokonts (stramenopiles), and 87 bacterial sequences. To assess evolution of NRT2 within fungi and other eukaryotes, we analyzed 116 amino acid sequences of NRT2 from 58 fungi, 40 viridiplantae (green plants), 1 rhodophyte, and 5 heterokonts, rooted with 12 bacterial sequences. Our results support a single origin of eukaryotic NRT2 from 1 of several clades of mostly proteobacterial NNP transporters. The phylogeny of bacterial NNP transporters does not directly correspond with bacterial taxonomy, apparently due to ancient duplications and/or horizontal gene transfer events. The distribution of NRT2 in the eukaryotes is patchy, but the NRT2 phylogeny nonetheless supports the monophyly of major groups such as viridiplantae, flowering plants, monocots, and eudicots, as well as fungi, ascomycetes, basidiomycetes, and agaric mushrooms. At least 1 secondary origin of eukaryotic NRT2 via horizontal transfer to the fungi is suggested, possibly from a heterokont donor. Our analyses also suggest that there has been a horizontal transfer of nrt2 from a basidiomycete fungus to an ascomycete fungus and reveal a duplication of nrt2 in the ectomycorrhizal mushroom genus, Hebeloma.}, }
@article {pmid17513584, year = {2007}, author = {Ventura, M and Canchaya, C and Zhang, Z and Fitzgerald, GF and van Sinderen, D}, title = {Molecular characterization of hsp20, encoding a small heat shock protein of bifidobacterium breve UCC2003.}, journal = {Applied and environmental microbiology}, volume = {73}, number = {14}, pages = {4695-4703}, pmid = {17513584}, issn = {0099-2240}, mesh = {Amino Acid Sequence ; Bacterial Proteins/*genetics ; Bifidobacterium/*genetics ; DNA, Bacterial/genetics ; Genome, Bacterial ; HSP20 Heat-Shock Proteins/chemistry/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; }, abstract = {Small heat shock proteins (sHSPs) are members of a diverse family of stress proteins that are important in cells to protect proteins under stressful conditions. Genome analysis of Bifidobacterium breve UCC2003 revealed a single sHSP-encoding gene, which was classified as a hsp20 gene by comparative analyses. Genomic surveillance of available genome sequences indicated that hsp20 homologs are not widely distributed in bacteria. In members of the genus Bifidobacterium, this gene appears to be present in only 7 of the 30 currently described species. Moreover, phylogenetic analysis using all available bacterial and eukaryotic sHSP sequences revealed a close relationship between bifidobacterial HSP20 and the class B sHSPs found in members of the division Firmicutes. The results of this comparative analysis and variation in codon usage content suggest that hsp20 was acquired by certain bifidobacteria through horizontal gene transfer. Analysis by slot blot, Northern blot, and primer extension experiments showed that transcription of hsp20 is strongly induced in response to severe heat shock regimens and by osmotic shock.}, }
@article {pmid17511874, year = {2007}, author = {Sharma, AK and Walsh, DA and Bapteste, E and Rodriguez-Valera, F and Ford Doolittle, W and Papke, RT}, title = {Evolution of rhodopsin ion pumps in haloarchaea.}, journal = {BMC evolutionary biology}, volume = {7}, number = {}, pages = {79}, pmid = {17511874}, issn = {1471-2148}, mesh = {Adenosine Triphosphatases/genetics/metabolism ; Amino Acid Sequence ; Bacteriorhodopsins/genetics/metabolism ; Cell Cycle Proteins/genetics/metabolism ; DNA-Directed RNA Polymerases/*genetics/metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Archaeal ; Genome, Archaeal ; Halobacteriaceae/*genetics/metabolism ; Halorhodopsins/genetics/metabolism ; Ion Pumps/*genetics/metabolism ; Phylogeny ; Rhodopsins, Microbial/*genetics/metabolism ; Valosin Containing Protein ; }, abstract = {BACKGROUND: The type 1 (microbial) rhodopsins are a diverse group of photochemically reactive proteins that display a broad yet patchy distribution among the three domains of life. Recent work indicates that this pattern is likely the result of lateral gene transfer (LGT) of rhodopsin genes between major lineages, and even across domain boundaries. Within the lineage in which the microbial rhodopsins were initially discovered, the haloarchaea, a similar patchy distribution is observed. In this initial study, we assess the roles of LGT and gene loss in the evolution of haloarchaeal rhodopsin ion pump genes, using phylogenetics and comparative genomics approaches.<br><br>RESULTS: Mapping presence/absence of rhodopsins onto the phylogeny of the RNA polymerase B' subunit (RpoB') of the haloarchaea supports previous notions that rhodopsins are patchily distributed. The phylogeny for the bacteriorhodopsin (BR) protein revealed two discrepancies in comparison to the RpoB' marker, while the halorhodopsin (HR) tree showed incongruence to both markers. Comparative analyses of bacteriorhodopsin-linked regions of five haloarchaeal genomes supported relationships observed in the BR tree, and also identified two open reading frames (ORFs) that were more frequently linked to the bacteriorhodopsin gene than those genes previously shown to be important to the function and expression of BR.<br><br>CONCLUSION: The evidence presented here reveals a complex evolutionary history for the haloarchaeal rhodopsins, with both LGT and gene loss contributing to the patchy distribution of rhodopsins within this group. Similarities between the BR and RpoB' phylogenies provide supportive evidence for the presence of bacteriorhodopsin in the last common ancestor of haloarchaea. Furthermore, two loci that we have designated bacterio-opsin associated chaperone (bac) and bacterio-opsin associated protein (bap) are inferred to have important roles in BR biogenesis based on frequent linkage and co-transfer with bacteriorhodopsin genes.}, }
@article {pmid17511520, year = {2007}, author = {Sirand-Pugnet, P and Lartigue, C and Marenda, M and Jacob, D and Barré, A and Barbe, V and Schenowitz, C and Mangenot, S and Couloux, A and Segurens, B and de Daruvar, A and Blanchard, A and Citti, C}, title = {Being pathogenic, plastic, and sexual while living with a nearly minimal bacterial genome.}, journal = {PLoS genetics}, volume = {3}, number = {5}, pages = {e75}, pmid = {17511520}, issn = {1553-7404}, mesh = {Animals ; Bacterial Proteins/genetics ; DNA Restriction-Modification Enzymes ; DNA, Circular/genetics ; DNA, Ribosomal/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Variation ; *Genome, Bacterial/genetics/physiology ; Lipoproteins/genetics ; Molecular Sequence Data ; Mycoplasma agalactiae/*genetics/*physiology ; Mycoplasma mycoides/genetics ; Phylogeny ; Regulatory Sequences, Nucleic Acid/genetics ; Ruminants/microbiology ; }, abstract = {Mycoplasmas are commonly described as the simplest self-replicating organisms, whose evolution was mainly characterized by genome downsizing with a proposed evolutionary scenario similar to that of obligate intracellular bacteria such as insect endosymbionts. Thus far, analysis of mycoplasma genomes indicates a low level of horizontal gene transfer (HGT) implying that DNA acquisition is strongly limited in these minimal bacteria. In this study, the genome of the ruminant pathogen Mycoplasma agalactiae was sequenced. Comparative genomic data and phylogenetic tree reconstruction revealed that approximately 18% of its small genome (877,438 bp) has undergone HGT with the phylogenetically distinct mycoides cluster, which is composed of significant ruminant pathogens. HGT involves genes often found as clusters, several of which encode lipoproteins that usually play an important role in mycoplasma-host interaction. A decayed form of a conjugative element also described in a member of the mycoides cluster was found in the M. agalactiae genome, suggesting that HGT may have occurred by mobilizing a related genetic element. The possibility of HGT events among other mycoplasmas was evaluated with the available sequenced genomes. Our data indicate marginal levels of HGT among Mycoplasma species except for those described above and, to a lesser extent, for those observed in between the two bird pathogens, M. gallisepticum and M. synoviae. This first description of large-scale HGT among mycoplasmas sharing the same ecological niche challenges the generally accepted evolutionary scenario in which gene loss is the main driving force of mycoplasma evolution. The latter clearly differs from that of other bacteria with small genomes, particularly obligate intracellular bacteria that are isolated within host cells. Consequently, mycoplasmas are not only able to subvert complex hosts but presumably have retained sexual competence, a trait that may prevent them from genome stasis and contribute to adaptation to new hosts.}, }
@article {pmid17508406, year = {2007}, author = {Poole, AM and Penny, D}, title = {Response to Dagan and Martin.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {29}, number = {6}, pages = {611-614}, doi = {10.1002/bies.20577}, pmid = {17508406}, issn = {0265-9247}, mesh = {Archaea/*physiology ; *Biological Evolution ; Eukaryotic Cells/*physiology ; Gene Transfer, Horizontal ; *Mitochondria ; *Phagocytosis ; Phylogeny ; }, }
@article {pmid17506902, year = {2007}, author = {Zhang, Y and Laing, C and Steele, M and Ziebell, K and Johnson, R and Benson, AK and Taboada, E and Gannon, VP}, title = {Genome evolution in major Escherichia coli O157:H7 lineages.}, journal = {BMC genomics}, volume = {8}, number = {}, pages = {121}, pmid = {17506902}, issn = {1471-2164}, mesh = {Escherichia coli O157/*genetics/pathogenicity ; *Evolution, Molecular ; Genetic Variation ; *Genome, Bacterial ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Open Reading Frames ; Virulence/genetics ; }, abstract = {BACKGROUND: Genetic analysis of Escherichia coli O157:H7 strains has shown divergence into two distinct lineages, lineages I and II, that appear to have distinct ecological characteristics, with lineage I strains more commonly associated with human disease. In this study, microarray-based comparative genomic hybridization (CGH) was used to identify genomic differences among 31 E. coli O157:H7 strains that belong to various phage types (PTs) and different lineage-specific polymorphism assay (LSPA) types.<br><br>RESULTS: A total of 4,084 out of 6,057 ORFs were detected in all E. coli O157:H7 strains and 1,751 were variably present or absent. Based on this data, E. coli O157:H7 strains were divided into three distinct clusters, which consisted of 15 lineage I (LSPA type 111111), four lineage I/II (designated in this study) (LSPA type 211111) and 12 lineage II strains (LSPA 222222, 222211, 222212, and 222221), respectively. Eleven different genomic regions that were dominant in lineage I strains (present in > or =80% of lineage I and absent from > or = 92% of lineage II strains) spanned segments containing as few as two and up to 25 ORFs each. These regions were identified within E. coli Sakai S-loops # 14, 16, 69, 72, 78, 83, 85, 153 and 286, Sakai phage 10 (S-loops # 91, 92 and 93) and a genomic backbone region. All four lineage I/II strains were of PT 2 and possessed eight of these 11 lineage I-dominant loci. Several differences in virulence-associated loci were noted between lineage I and lineage II strains, including divergence within S-loop 69, which encodes Shiga toxin 2, and absence of the non-LEE encoded effector genes nleF and nleH1-2 and the perC homologue gene pchD in lineage II strains.<br><br>CONCLUSION: CGH data suggest the existence of two dominant lineages as well as LSPA type and PT-related subgroups within E. coli O157:H7. The genomic composition of these subgroups supports the phylogeny that has been inferred from other methods and further suggests that genomic divergence from an ancestral form and lateral gene transfer have contributed to their evolution. The genomic features identified in this study may contribute to apparent differences in the epidemiology and ecology of strains of different E. coli O157:H7 lineages.}, }
@article {pmid17504483, year = {2007}, author = {Cho, JC and Stapels, MD and Morris, RM and Vergin, KL and Schwalbach, MS and Givan, SA and Barofsky, DF and Giovannoni, SJ}, title = {Polyphyletic photosynthetic reaction centre genes in oligotrophic marine Gammaproteobacteria.}, journal = {Environmental microbiology}, volume = {9}, number = {6}, pages = {1456-1463}, doi = {10.1111/j.1462-2920.2007.01264.x}, pmid = {17504483}, issn = {1462-2912}, mesh = {Bacterial Proteins/*genetics ; Gammaproteobacteria/classification/*genetics/isolation &amp; purification ; Marine Biology ; Photosynthesis/*genetics ; Photosynthetic Reaction Center Complex Proteins/*genetics ; Phylogeny ; Seawater/*microbiology ; }, abstract = {Ecological studies indicate that aerobic anoxygenic phototrophic bacteria (AAP) that use bacteriochlorophyll to support phototrophic electron transport are widely distributed in the oceans. All cultivated marine AAP are alpha-3 and alpha-4 Proteobacteria, but metagenomic evidence indicates that uncultured AAP Gammaproteobacteria are important members of ocean surface microbial communities. Here we report the description of obligately oligotrophic, marine Gammaproteobacteria that have genes for aerobic anoxygenic photosynthesis. Three strains belonging to the OM60 clade were isolated in autoclaved seawater media. Polymerase chain reaction assays for the pufM gene show that these strains contain photosynthetic reaction centre genes. DNA sequencing and phylogenetic analysis indicate that the pufM genes are polyphyletic, suggesting multiple instances of lateral gene transfer. Peptide sequences from six photosynthesis genes (pufL, pufM, pufC, pufB, pufA and puhA) were detected by proteomic analyses of strain HTCC2080 cells grown aerobically in seawater. They closely match predicted peptides from an environmental seawater bacterial artificial chromosome clone of gammaproteobacterial origin, thus identifying the OM60 clade as a significant source of gammaproteobacterial AAP genes in marine systems. The cell yield and rate of growth of HTCC2080 in autoclaved, aerobic seawater increased in the light. These findings identify the OM60 clade as a source of Gammaproteobacteria AAP genes in coastal oceans, and demonstrate that aerobic, anoxygenic photosynthetic metabolism can enhance the productivity of marine oligotrophic bacteria that also grow heterotrophically in darkness.}, }
@article {pmid17504243, year = {2007}, author = {O'Halloran, JA and McGrath, BM and Pembroke, JT}, title = {The orf4 gene of the enterobacterial ICE, R391, encodes a novel UV-inducible recombination directionality factor, Jef, involved in excision and transfer of the ICE.}, journal = {FEMS microbiology letters}, volume = {272}, number = {1}, pages = {99-105}, doi = {10.1111/j.1574-6968.2007.00747.x}, pmid = {17504243}, issn = {0378-1097}, mesh = {Amino Acid Sequence ; Bacterial Proteins/biosynthesis/*genetics/*physiology ; Conjugation, Genetic/genetics ; Conserved Sequence/genetics ; DNA, Bacterial/chemistry/genetics ; Enterobacteriaceae/*genetics/physiology/radiation effects ; Gene Deletion ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal/genetics ; *Interspersed Repetitive Sequences ; Isoelectric Point ; Molecular Sequence Data ; Molecular Weight ; Mutagenesis, Insertional ; RNA, Bacterial/biosynthesis/genetics ; RNA, Messenger/biosynthesis/genetics ; *Recombination, Genetic ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sequence Homology ; Ultraviolet Rays ; }, abstract = {The enterobacterial mobile genetic element R391, the prototype ICE (integrating-conjugative element) of the SXT/R391 family, shows increased conjugative transfer following UV irradiation. This is dependent on a functioning R391 orf4 gene, which is adjacent to the element encoded integrase gene, int. orf4 mutants fail to form a detectable circular transfer intermediate, do not show UV induced transfer and show a much reduced general transfer ability. The orf4 gene product, termed Jef (IncJ excision factor), shows little homology to anything currently in the nucleotide or protein databases. It is predicted to encode a 66 amino acid, 8.03 kDa, basic, DNA-binding protein with an iso-electric point of pH 8.1: these characteristics being similar to those of recombinational directionality factors involved in excision. Jef expression is up-regulated upon UV irradiation as demonstrated by real-time reverse transcriptase PCR and is controlled by two element encoded genes orf90 and orf91, which show similarity to the transcriptional activator complex FlhC and FlhD. orf4, orf90 and orf91 are conserved in all the SXT/R391-like elements sequenced to date including SXT, ICESpuPO1 and ICEVchMex1. orf4 is also conserved in other SXT/R391 family members such as R997, R392, R705 and pMERPH as shown by sequencing amplicons from these ICEs generated using orf4 specific primers.}, }
@article {pmid17503372, year = {2006}, author = {Tanaka, M and Yamada, T and Itoh, M and Okuda, S and Goto, S and Kanehisa, M}, title = {Analysis of the differences in metabolic network expansion between prokaryotes and eukaryotes.}, journal = {Genome informatics. International Conference on Genome Informatics}, volume = {17}, number = {1}, pages = {230-239}, pmid = {17503372}, issn = {0919-9454}, mesh = {Animals ; Escherichia coli/metabolism ; Eukaryotic Cells/*metabolism ; Evolution, Molecular ; Metabolic Networks and Pathways/*physiology ; Methanococcaceae/metabolism ; *Models, Biological ; Phylogeny ; Prokaryotic Cells/*metabolism ; Species Specificity ; }, abstract = {Recent evidence points to the existence of scale-free properties in many biological networks. By topological analysis, several models including preferential attachment and hierarchical modules have been proposed to explain how these networks are organized. On the other hand, analyses using dynamics have suggested that gene expression and metabolic networks have been organized with the scale-free property by the other models such as "rich-travel-more" and "log-normal dynamics." Because most of these approaches are based on comparative genomics of extant species, and did not consider evolutionary events such as horizontal gene transfer, gene loss and gene gain, we have analyzed transition of metabolic networks from the vertical point of view of evolution. First, to identify metabolic networks of common ancestors, we applied a parsimony algorithm for the enzymatic reaction set. Then by comparing the estimated metabolic networks among common ancestors, we investigated the transition of metabolic networks along the evolutionary process. As a result, we estimated enzymatic reaction contents of 227 common ancestors from 228 extant species, and found that links of several specific metabolites have frequently changed during the course of evolution.}, }
@article {pmid17500592, year = {2007}, author = {Thomas, JH}, title = {Rapid birth-death evolution specific to xenobiotic cytochrome P450 genes in vertebrates.}, journal = {PLoS genetics}, volume = {3}, number = {5}, pages = {e67}, pmid = {17500592}, issn = {1553-7404}, mesh = {Amino Acid Sequence ; Animals ; Cluster Analysis ; Cytochrome P-450 Enzyme System/chemistry/*genetics ; *Evolution, Molecular ; Gene Duplication ; Genomic Instability ; Humans ; Likelihood Functions ; Macaca/genetics ; Molecular Sequence Data ; Phylogeny ; Selection, Genetic ; Synteny ; Vertebrates/*genetics ; Xenobiotics/*metabolism ; }, abstract = {Genes vary greatly in their long-term phylogenetic stability and there exists no general explanation for these differences. The cytochrome P450 (CYP450) gene superfamily is well suited to investigating this problem because it is large and well studied, and it includes both stable and unstable genes. CYP450 genes encode oxidase enzymes that function in metabolism of endogenous small molecules and in detoxification of xenobiotic compounds. Both types of enzymes have been intensively studied. My analysis of ten nearly complete vertebrate genomes indicates that each genome contains 50-80 CYP450 genes, which are about evenly divided between phylogenetically stable and unstable genes. The stable genes are characterized by few or no gene duplications or losses in species ranging from bony fish to mammals, whereas unstable genes are characterized by frequent gene duplications and losses (birth-death evolution) even among closely related species. All of the CYP450 genes that encode enzymes with known endogenous substrates are phylogenetically stable. In contrast, most of the unstable genes encode enzymes that function as xenobiotic detoxifiers. Nearly all unstable CYP450 genes in the mouse and human genomes reside in a few dense gene clusters, forming unstable gene islands that arose by recurrent local gene duplication. Evidence for positive selection in amino acid sequence is restricted to these unstable CYP450 genes, and sites of selection are associated with substrate-binding regions in the protein structure. These results can be explained by a general model in which phylogenetically stable genes have core functions in development and physiology, whereas unstable genes have accessory functions associated with unstable environmental interactions such as toxin and pathogen exposure. Unstable gene islands in vertebrates share some functional properties with bacterial genomic islands, though they arise by local gene duplication rather than horizontal gene transfer.}, }
@article {pmid17498620, year = {2007}, author = {Zhu, J and Liu, W and Zhou, W and Hu, Y and He, Y}, title = {A Nucleus-encoded topological specificity factor PpMinE in Physcomitrella patens has conserved function similar to its chloroplast-encoded ancestor.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {34}, number = {3}, pages = {229-238}, doi = {10.1016/S1673-8527(07)60024-1}, pmid = {17498620}, issn = {1673-8527}, mesh = {Amino Acid Sequence ; Base Sequence ; Bryopsida/genetics/metabolism ; Cell Cycle Proteins/*genetics/metabolism ; Cell Nucleus/genetics/metabolism ; Chloroplasts/genetics/metabolism ; Cloning, Molecular ; Evolution, Molecular ; Gene Expression Regulation, Plant ; Gene Transfer, Horizontal/*genetics ; Molecular Sequence Data ; Plant Proteins/*genetics/metabolism ; Plants, Genetically Modified ; Sequence Alignment ; }, abstract = {A nucleus-encoded MinE gene, designated PpMinE, from Physcomitrella patens was identified using RT-PCR. The presence of both N- and C-terminal extensions in PpMinE protein suggested its cyanobacterial origin. The transient expression of PpMinE using green fluorescent protein fusion in tobacco (Nicotiana tabacum L.) indicated that the PpMinE was a chloroplast-targeted protein. Overexpression of PpMinE in Escherichia coli caused division site misplacement and minicell formation, suggesting evolutionary functional conservation of MinE during plant phylogenesis. According to the phylogenetic tree, PpMinE protein has a close relationship with the highland plants, which suggests that the transfer events of MinE gene from plastid to nucleus might have occurred before the origin of the land plants.}, }
@article {pmid17497225, year = {2007}, author = {Roberts, K and Granum, E and Leegood, RC and Raven, JA}, title = {Carbon acquisition by diatoms.}, journal = {Photosynthesis research}, volume = {93}, number = {1-3}, pages = {79-88}, pmid = {17497225}, issn = {0166-8595}, mesh = {Carbon/*metabolism ; Cell Respiration/radiation effects ; Diatoms/enzymology/*metabolism/radiation effects ; Light ; Ribulose-Bisphosphate Carboxylase/metabolism ; }, abstract = {Diatoms are responsible for up to 40% of primary productivity in the ocean, and complete genome sequences are available for two species. However, there are very significant gaps in our understanding of how diatoms take up and assimilate inorganic C. Diatom plastids originate from secondary endosymbiosis with a red alga and their Form ID Rubisco (ribulose-1,5-bisphosphate carboxylase-oxygenase) from horizontal gene transfer, which means that embryophyte paradigms can only give general guidance as to their C acquisition mechanisms. Although diatom Rubiscos have relatively high CO(2) affinity and CO(2)/O(2) selectivity, the low diffusion coefficient for CO(2) in water has the potential to restrict the rate of photosynthesis. Diatoms growing in their natural aquatic habitats operate inorganic C concentrating mechanisms (CCMs), which provide a steady-state CO(2) concentration around Rubisco higher than that in the medium. How these CCMs work is still a matter of debate. However, it is known that both CO(2) and HCO (3) (-) are taken up, and an obvious but as yet unproven possibility is that active transport of these species across the plasmalemma and/or the four-membrane plastid envelope is the basis of the CCM. In one marine diatom there is evidence of C(4)-like biochemistry which could act as, or be part of, a CCM. Alternative mechanisms which have not been eliminated include the production of CO(2) from HCO (3) (-) at low pH maintained by a H(+) pump, in a compartment close to that containing Rubisco.}, }
@article {pmid17496100, year = {2007}, author = {Bailly, X and Olivieri, I and Brunel, B and Cleyet-Marel, JC and Béna, G}, title = {Horizontal gene transfer and homologous recombination drive the evolution of the nitrogen-fixing symbionts of Medicago species.}, journal = {Journal of bacteriology}, volume = {189}, number = {14}, pages = {5223-5236}, pmid = {17496100}, issn = {0021-9193}, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial ; Likelihood Functions ; Medicago/*microbiology ; Models, Biological ; Models, Genetic ; Molecular Sequence Data ; Nitrogen Fixation ; Phylogeny ; Polymorphism, Genetic ; Recombination, Genetic/*genetics ; Sinorhizobium/classification/*genetics/metabolism ; }, abstract = {Using nitrogen-fixing Sinorhizobium species that interact with Medicago plants as a model system, we aimed at clarifying how sex has shaped the diversity of bacteria associated with the genus Medicago on the interspecific and intraspecific scales. To gain insights into the diversification of these symbionts, we inferred a topology that includes the different specificity groups which interact with Medicago species, based on sequences of the nodulation gene cluster. Furthermore, 126 bacterial isolates were obtained from two soil samples, using Medicago truncatula and Medicago laciniata as host plants, to study the differentiation between populations of Sinorhizobium medicae, Sinorhizobium meliloti bv. meliloti, and S. meliloti bv. medicaginis. The former two can be associated with M. truncatula (among other species of Medicago), whereas the last organism is the specific symbiont of M. laciniata. These bacteria were characterized using a multilocus sequence analysis of four loci, located on the chromosome and on the two megaplasmids of S. meliloti. The phylogenetic results reveal that several interspecific horizontal gene transfers occurred during the diversification of Medicago symbionts. Within S. meliloti, the analyses show that nod genes specific to different host plants have spread to different genetic backgrounds through homologous recombination, preventing further divergence of the different ecotypes. Thus, specialization to different host plant species does not prevent the occurrence of gene flow among host-specific biovars of S. meliloti, whereas reproductive isolation between S. meliloti bv. meliloti and S. medicae is maintained even though these bacteria can cooccur in sympatry on the same individual host plants.}, }
@article {pmid17494762, year = {2007}, author = {Moran, NA}, title = {Symbiosis as an adaptive process and source of phenotypic complexity.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104 Suppl 1}, number = {Suppl 1}, pages = {8627-8633}, pmid = {17494762}, issn = {0027-8424}, mesh = {Adaptation, Biological/*physiology ; Animals ; Bacteria/genetics/virology ; Bacteriophages/genetics/physiology ; Biological Evolution ; Eukaryotic Cells/physiology ; Gene Transfer, Horizontal ; Genetic Vectors ; Genome/genetics ; Insecta/genetics/physiology ; *Phenotype ; Symbiosis/genetics/*physiology ; }, abstract = {Genomics has revealed that inheritance systems of separate species are often not well segregated: genes and capabilities that evolve in one lineage are often stably acquired by another lineage. Although direct gene transfer between species has occurred at some level in all major groups, it appears to be far more frequent in prokaryotes than in multicellular eukaryotes. An alternative to incorporating novel genes into a recipient genome is acquiring a stable, possibly heritable, symbiotic association and thus enjoying benefits of complementary metabolic capabilities. These kinds of symbioses have arisen frequently in animals; for example, many insect groups have diversified on the basis of symbiotic associations acquired early in their evolutionary histories. The resulting associations are highly complex, often involving specialized cell types and organs, developmental mechanisms that ensure transfer of symbionts between generations, and mechanisms for controlling symbiont proliferation and location. The genomes of long-term obligate symbionts often undergo irreversible gene loss and deterioration even as hosts evolve dependence on them. In some cases, animal genomes may have acquired genes from symbionts, mirroring the gene uptake from mitochondrial and plastid genomes. Multiple symbionts often coexist in the same host, resulting in coadaptation among several phylogenetically distant genomes.}, }
@article {pmid17490428, year = {2007}, author = {Aminov, RI and Mackie, RI}, title = {Evolution and ecology of antibiotic resistance genes.}, journal = {FEMS microbiology letters}, volume = {271}, number = {2}, pages = {147-161}, doi = {10.1111/j.1574-6968.2007.00757.x}, pmid = {17490428}, issn = {0378-1097}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/*genetics/growth &amp; development ; Drug Resistance, Bacterial/*genetics ; *Ecology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Phylogeny ; }, abstract = {A new perspective on the topic of antibiotic resistance is beginning to emerge based on a broader evolutionary and ecological understanding rather than from the traditional boundaries of clinical research of antibiotic-resistant bacterial pathogens. Phylogenetic insights into the evolution and diversity of several antibiotic resistance genes suggest that at least some of these genes have a long evolutionary history of diversification that began well before the 'antibiotic era'. Besides, there is no indication that lateral gene transfer from antibiotic-producing bacteria has played any significant role in shaping the pool of antibiotic resistance genes in clinically relevant and commensal bacteria. Most likely, the primary antibiotic resistance gene pool originated and diversified within the environmental bacterial communities, from which the genes were mobilized and penetrated into taxonomically and ecologically distant bacterial populations, including pathogens. Dissemination and penetration of antibiotic resistance genes from antibiotic producers were less significant and essentially limited to other high G+C bacteria. Besides direct selection by antibiotics, there is a number of other factors that may contribute to dissemination and maintenance of antibiotic resistance genes in bacterial populations.}, }
@article {pmid17488740, year = {2007}, author = {Hackett, JD and Yoon, HS and Li, S and Reyes-Prieto, A and Rümmele, SE and Bhattacharya, D}, title = {Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of rhizaria with chromalveolates.}, journal = {Molecular biology and evolution}, volume = {24}, number = {8}, pages = {1702-1713}, doi = {10.1093/molbev/msm089}, pmid = {17488740}, issn = {0737-4038}, support = {T32 GM98629/GM/NIGMS NIH HHS/United States ; }, mesh = {Algal Proteins/genetics ; Animals ; Cryptophyta/*genetics ; Eukaryota/classification/*genetics ; Expressed Sequence Tags ; Gene Library ; *Gene Transfer, Horizontal ; Genes, Plant ; *Genomics ; Molecular Sequence Data ; *Phylogeny ; Plant Proteins/genetics ; Plastids/chemistry ; Symbiosis ; }, abstract = {Here we use phylogenomics with expressed sequence tag (EST) data from the ecologically important coccolithophore-forming alga Emiliania huxleyi and the plastid-lacking cryptophyte Goniomonas cf. pacifica to establish their phylogenetic positions in the eukaryotic tree. Haptophytes and cryptophytes are members of the putative eukaryotic supergroup Chromalveolata (chromists [cryptophytes, haptophytes, stramenopiles] and alveolates [apicomplexans, ciliates, and dinoflagellates]). The chromalveolates are postulated to be monophyletic on the basis of plastid pigmentation in photosynthetic members, plastid gene and genome relationships, nuclear "host" phylogenies of some chromalveolate lineages, unique gene duplication and replacements shared by these taxa, and the evolutionary history of components of the plastid import and translocation systems. However the phylogenetic position of cryptophytes and haptophytes and the monophyly of chromalveolates as a whole remain to be substantiated. Here we assess chromalveolate monophyly using a multigene dataset of nuclear genes that includes members of all 6 eukaryotic supergroups. An automated phylogenomics pipeline followed by targeted database searches was used to assemble a 16-protein dataset (6,735 aa) from 46 taxa for tree inference. Maximum likelihood and Bayesian analyses of these data support the monophyly of haptophytes and cryptophytes. This relationship is consistent with a gene replacement via horizontal gene transfer of plastid-encoded rpl36 that is uniquely shared by these taxa. The haptophytes + cryptophytes are sister to a clade that includes all other chromalveolates and, surprisingly, two members of the Rhizaria, Reticulomyxa filosa and Bigelowiella natans. The association of the two Rhizaria with chromalveolates is supported by the approximately unbiased (AU)-test and when the fastest evolving amino acid sites are removed from the 16-protein alignment.}, }
@article {pmid17475572, year = {2007}, author = {Stanhope, MJ and Walsh, SL and Becker, JA and Miller, LA and Lefébure, T and Lang, P and Bitar, PD and Amrine-Madsen, H}, title = {The relative frequency of intraspecific lateral gene transfer of penicillin binding proteins 1a, 2b, and 2x, in amoxicillin resistant Streptococcus pneumoniae.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {7}, number = {4}, pages = {520-534}, doi = {10.1016/j.meegid.2007.03.004}, pmid = {17475572}, issn = {1567-1348}, mesh = {Amoxicillin/*pharmacology ; Bacterial Typing Techniques ; Clone Cells ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal/*genetics ; Humans ; Likelihood Functions ; Penicillin-Binding Proteins/*genetics ; Phylogeny ; Streptococcus pneumoniae/classification/*drug effects/*genetics ; }, abstract = {Evidence exists for both interspecific and intraspecific recombination (lateral gene transfer; LGT) involving Streptococcus pneumoniae pbp (penicillin binding protein) loci. LGT of capsular genes, or serotype switching, is also know to occur between S. pneumoniae of different serotype. It is not clear whether intraspecific pbp LGT is relatively common, whether there is a difference in the relative frequency of intraspecific LGT of different pbps, and whether serotype switching is more or less frequent than pbp LGT. The purpose of this study was to use comparative evolutionary biology analysis of 216 international clinical S. pneumoniae isolates, from the Alexander Project collection, to gain insight on these issues, as well as the possible role they might be playing in spreading amoxicillin resistance. All 216 isolates were genotyped using MLST and complete or nearly complete sequences for pbp1a, pbp2b, and pbp2x were determined. Amoxicillin MICs were available for each isolate. pbps were genotyped using phylogenetics and two or more pbp types within a MLST sequence type (ST) or clonal complex were taken as putative cases of pbp LGT; these hypotheses were statistically evaluated using the approximately unbiased (AU) test. Serotypes were determined for 171 of these isolates and the minimum number of switching events necessary to explain the serotype phenotypes for each of the STs and clonal complexes were evaluated. The majority (78%) of the amoxicillin resistant isolates were comprised in 5 clonal complexes. The relative frequency of pbp LGT was greatest for pbp2b and 2x (minimum of 10.2 and 7.8%, respectively, of the isolates consistent with the LGT hypothesis), followed by 1a (3.9%). Serotype switching was more frequent than intraspecific pbp LGT (33% of isolates consistent with serotype switching hypothesis). Although intraspecific LGT of pbps is occurring and has played a role in the spread of amoxicillin resistance in S. pneumoniae, clonal dissemination appears to be more significant.}, }
@article {pmid17475267, year = {2007}, author = {DeMarco, R and Mathieson, W and Dillon, GP and Wilson, RA}, title = {Schistosome albumin is of host, not parasite, origin.}, journal = {International journal for parasitology}, volume = {37}, number = {11}, pages = {1201-1208}, doi = {10.1016/j.ijpara.2007.03.004}, pmid = {17475267}, issn = {0020-7519}, support = {AI54711-02/AI/NIAID NIH HHS/United States ; }, mesh = {Albumins/genetics/*metabolism ; Amino Acid Sequence ; Animals ; Base Sequence ; Blotting, Southern ; Cricetinae ; DNA, Helminth/analysis ; Gene Library ; Gene Transfer, Horizontal ; Host-Parasite Interactions ; Molecular Sequence Data ; Proteomics ; Reverse Transcriptase Polymerase Chain Reaction ; Schistosoma mansoni/*metabolism ; Sequence Alignment ; }, abstract = {Recent work has implicated schistosome albumin as part of a mechanism for neutralizing the oxidative assault by host immune defenses and suggested that the gene had been acquired by horizontal transfer from the mammalian host. In the course of proteomic analyses of Schistosoma mansoni adult worm vomitus and eggs recovered from mice, we identified numerous peptides, largely derived from murine rather than parasite albumin. We therefore conjectured that the supposed S. mansoni albumin sequence deposited on GenBank might be the result of contamination rather than horizontal gene transfer. Based on phylogenetic analysis the most likely source was the Syrian (golden) hamster Mesocricetus auratus. Proteomic analysis of Syrian hamster albumin generated peptide identities to S. mansoni as the top hit, with a high ion score >1,500 and 63% coverage of the translated cDNA sequence. RT-PCR using specific primers permitted amplification of the M. auratus albumin transcript, which is identical to the deposited S. mansoni albumin sequence. PCR amplification of a fragment of the M. auratus albumin gene from genomic DNA suggests a homologous structure to the Mus musculus albumin gene. We were unable to find the S. mansoni albumin gene sequence by in silico searching on either version 3 of the S. mansoni genome assembly or the >3 million shotgun DNA reads. Finally, Southern blotting detected the albumin gene in M. auratus but not in S. mansoni genomic DNA, even when the latter was present in a 10-fold excess. Collectively, our data make the strongest case that the schistosome albumin protein described in previous reports is of host origin and all nucleotide-derived data are the result of contamination with host material. By analogy, we suggest that other reported examples of horizontal gene transfer to schistosomes might similarly be explained by complementary/genomic DNA contamination.}, }
@article {pmid17473884, year = {2006}, author = {Parker, MA and Kennedy, DA}, title = {Diversity and relationships of bradyrhizobia from legumes native to eastern North America.}, journal = {Canadian journal of microbiology}, volume = {52}, number = {12}, pages = {1148-1157}, doi = {10.1139/w06-076}, pmid = {17473884}, issn = {0008-4166}, mesh = {Bradyrhizobium/classification/*genetics ; DNA, Bacterial/chemistry/genetics ; Evolution, Molecular ; Fabaceae/*microbiology ; *Genetic Variation ; Molecular Sequence Data ; North America ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Sequence Analysis, DNA ; }, abstract = {DNA sequencing and polymerase chain reaction (PCR) assays with lineage-specific primers were used to analyze the diversity of 276 isolates of Bradyrhizobium sp. nodule bacteria associated with 13 native legumes species in the northeastern United States, representing eight genera in six legume tribes. A PCR screen with two primer pairs in the rRNA region indicated that seven of the legume species were exclusively associated with strains having markers resembling Bradyrhizobium elkanii, while the remaining six host species harbored strains related to both B. elkanii and Bradyrhizobium japonicum. Sequence analysis of 22 isolates for portions of 16S rRNA and 23S rRNA yielded congruent phylogenetic trees and showed that isolates from different legume genera often shared similar or identical sequences. However, trees inferred from portions of two other genes (alpha-ketoglutarate dioxygenase gene (tfdA), the alpha-subunit of nitrogenase (nifD)) differed significantly from the rRNA phylogeny. Thus, for Bradyrhizobium populations in this region, lateral gene transfer events appear to have altered genealogical relationships of different portions of the genome. These results extend the number of likely cases of gene transfer between divergent taxa of Bradyrhizobium (from members of the B. elkanii lineage to the B. japonicum group) and suggest that transfers have also occurred among separate subgroups of the B. elkanii lineage.}, }
@article {pmid17471262, year = {2007}, author = {de la Cueva-Méndez, G and Pimentel, B}, title = {Gene and cell survival: lessons from prokaryotic plasmid R1.}, journal = {EMBO reports}, volume = {8}, number = {5}, pages = {458-464}, pmid = {17471262}, issn = {1469-221X}, support = {MC_U105365008/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Bacteria/*genetics/metabolism ; Base Sequence ; Drug Resistance, Bacterial ; Gene Dosage ; Gene Transfer, Horizontal ; Molecular Sequence Data ; R Factors/*genetics/metabolism ; Replicon ; }, abstract = {Plasmids are units of extrachromosomal genetic inheritance found in all kingdoms of life. They replicate autonomously and undergo stable propagation in their hosts. Despite their small size, plasmid replication and gene expression constitute a metabolic burden that compromises their stable maintenance in host cells. This pressure has driven the evolution of strategies to increase plasmid stability--a process accelerated by the ability of plasmids to transfer horizontally between cells and to exchange genetic material with their host and other resident episomal DNAs. These abilities drive the adaptability and diversity of plasmids and their host cells. Indeed, survival functions found in plasmids have chromosomal homologues that have an essential role in cellular responses to stress. An analysis of these functions in the prokaryotic plasmid R1, and of their intricate interrelationships, reveals remarkable overall similarities with other gene- and cell-survival strategies found within and beyond the prokaryotic world.}, }
@article {pmid17470660, year = {2007}, author = {Mendes, RE and Castanheira, M and Toleman, MA and Sader, HS and Jones, RN and Walsh, TR}, title = {Characterization of an integron carrying blaIMP-1 and a new aminoglycoside resistance gene, aac(6')-31, and its dissemination among genetically unrelated clinical isolates in a Brazilian hospital.}, journal = {Antimicrobial agents and chemotherapy}, volume = {51}, number = {7}, pages = {2611-2614}, pmid = {17470660}, issn = {0066-4804}, mesh = {Acinetobacter/drug effects/genetics/isolation &amp; purification/pathogenicity ; Amino Acid Sequence ; Aminoglycosides/*pharmacology ; Anti-Bacterial Agents/*pharmacology ; Base Sequence ; Brazil/epidemiology ; Codon, Terminator ; Cross Infection ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Hospitals ; Humans ; Integrons/*genetics ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Open Reading Frames ; Plasmids/genetics ; Pseudomonas putida/drug effects/genetics/isolation &amp; purification/pathogenicity ; Transcription, Genetic ; }, abstract = {Seven bla(IMP-1)-harboring Acinetobacter sp. isolates and one Pseudomonas putida clinical isolate were recovered from hospitalized patients. All isolates possessed a class 1 integron, named In86, carrying the same cassette array [bla(IMP1), aac(6')-31, and aadA1], which was plasmid located in five of the isolates. This report describes the ability of nonfermentative nosocomial pathogens to acquire and disseminate antimicrobial resistance determinants.}, }
@article {pmid17470265, year = {2007}, author = {Hepworth, PJ and Leatherbarrow, H and Hart, CA and Winstanley, C}, title = {Use of suppression subtractive hybridisation to extend our knowledge of genome diversity in Campylobacter jejuni.}, journal = {BMC genomics}, volume = {8}, number = {}, pages = {110}, pmid = {17470265}, issn = {1471-2164}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Bacterial Typing Techniques/*methods ; Campylobacter jejuni/classification/*genetics ; Cattle ; Chickens ; Chromosome Mapping/methods ; DNA, Bacterial/*analysis ; *Genetic Variation ; Genome/*genetics ; Humans ; Nucleic Acid Hybridization/*methods ; Rabbits ; Sequence Analysis, DNA/methods ; Species Specificity ; }, abstract = {BACKGROUND: Previous studies have sought to identify a link between the distribution of variable genes amongst isolates of Campylobacter jejuni and particular host preferences. The genomic sequence data available currently was obtained using only isolates from human or chicken hosts. In order to identify variable genes present in isolates from alternative host species, five subtractions between C. jejuni isolates from different sources (rabbit, cattle, wild bird) were carried out, designed to assess genomic variability within and between common multilocus sequence type (MLST) clonal complexes (ST-21, ST-42, ST-45 and ST-61).<br><br>RESULTS: The vast majority (97%) of the 195 subtracted sequences identified had a best BLASTX match with a Campylobacter protein. However, there was considerable variation within and between the four clonal complexes included in the subtractions. The distributions of eight variable sequences, including four with putative roles in the use of alternative terminal electron acceptors, amongst a panel of C. jejuni isolates representing diverse sources and STs, were determined.<br><br>CONCLUSION: There was a clear correlation between clonal complex and the distribution of the metabolic genes. In contrast, there was no evidence to support the hypothesis that the distribution of such genes may be related to host preference. The other variable genes studied were also generally distributed according to MLST type. Thus, we found little evidence for widespread horizontal gene transfer between clonal complexes involving these genes.}, }
@article {pmid17468768, year = {2007}, author = {Myers, GS and Parker, D and Al-Hasani, K and Kennan, RM and Seemann, T and Ren, Q and Badger, JH and Selengut, JD and Deboy, RT and Tettelin, H and Boyce, JD and McCarl, VP and Han, X and Nelson, WC and Madupu, R and Mohamoud, Y and Holley, T and Fedorova, N and Khouri, H and Bottomley, SP and Whittington, RJ and Adler, B and Songer, JG and Rood, JI and Paulsen, IT}, title = {Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus.}, journal = {Nature biotechnology}, volume = {25}, number = {5}, pages = {569-575}, doi = {10.1038/nbt1302}, pmid = {17468768}, issn = {1087-0156}, mesh = {Animals ; Antigens/genetics/*immunology/*therapeutic use ; Chromosome Mapping/methods ; Dichelobacter nodosus/*genetics/immunology/metabolism/*pathogenicity ; Foot Rot/*immunology/*microbiology/prevention &amp; control ; Genome, Bacterial/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Dichelobacter nodosus causes ovine footrot, a disease that leads to severe economic losses in the wool and meat industries. We sequenced its 1.4-Mb genome, the smallest known genome of an anaerobe. It differs markedly from small genomes of intracellular bacteria, retaining greater biosynthetic capabilities and lacking any evidence of extensive ongoing genome reduction. Comparative genomic microarray studies and bioinformatic analysis suggested that, despite its small size, almost 20% of the genome is derived from lateral gene transfer. Most of these regions seem to be associated with virulence. Metabolic reconstruction indicated unsuspected capabilities, including carbohydrate utilization, electron transfer and several aerobic pathways. Global transcriptional profiling and bioinformatic analysis enabled the prediction of virulence factors and cell surface proteins. Screening of these proteins against ovine antisera identified eight immunogenic proteins that are candidate antigens for a cross-protective vaccine.}, }
@article {pmid17467337, year = {2007}, author = {Steinert, M and Heuner, K and Buchrieser, C and Albert-Weissenberger, C and Glöckner, G}, title = {Legionella pathogenicity: genome structure, regulatory networks and the host cell response.}, journal = {International journal of medical microbiology : IJMM}, volume = {297}, number = {7-8}, pages = {577-587}, doi = {10.1016/j.ijmm.2007.03.009}, pmid = {17467337}, issn = {1438-4221}, mesh = {Animals ; Dictyostelium/genetics/*microbiology ; Gene Expression Regulation, Bacterial ; *Genome, Bacterial ; *Host-Pathogen Interactions ; *Legionella pneumophila/genetics/pathogenicity/physiology ; Legionnaires' Disease/diagnosis/epidemiology/microbiology ; }, abstract = {Legionella spp. the causative agent of Legionnaires' disease is naturally found in fresh water where the bacteria parasitize intracellularly within protozoa. Upon aerosol formation via man-made water systems, Legionella can enter the human lung and cause a severe form of pneumonia. Here we review results from systematic comparative genome analysis of Legionella species with different pathogenic potentials. The complete genomes reveal that horizontal gene transfer has played an important role during the evolution of Legionella and indicate the importance of secretion machineries for the intracellular lifestyle of this pathogen. Moreover, we highlight recent findings on the in vivo transcriptional program of L. pneumophila and the regulatory networks involved in the biphasic life cycle. In order to understand how Legionella effectively subvert host cell functions for its own benefit the transcriptional host cell response upon infection of the model amoeba Dictyostelium discoideum was studied. The use of this model organism made it possible to develop a roadmap of host cell factors which significantly contribute to the uptake of L. pneumophila and the establishment of an ER-associated replicative vacuole.}, }
@article {pmid17467024, year = {2007}, author = {Chopin, A and Deveau, H and Ehrlich, SD and Moineau, S and Chopin, MC}, title = {KSY1, a lactococcal phage with a T7-like transcription.}, journal = {Virology}, volume = {365}, number = {1}, pages = {1-9}, doi = {10.1016/j.virol.2007.03.044}, pmid = {17467024}, issn = {0042-6822}, mesh = {Bacteriophage T7/genetics ; *Genome, Viral ; Lactococcus/*virology ; Molecular Sequence Data ; Open Reading Frames ; Podoviridae/classification/enzymology/*genetics ; Transcription, Genetic ; Viral Proteins/chemistry ; }, abstract = {The virulent lactococcal phage KSY1 possesses a large elongated capsid (223 nm long, 45 nm wide) and a short tail (32 nm). This phage of the Podoviridae group (C3 morphotype) has a linear 79,232-bp double-stranded DNA genome, which encodes 131 putative proteins and 3 tRNAs. This is the first description of the genome of a phage of this morphotype. KSY1 possesses a T7-like transcription system, including an RNA polymerase and a series of specific promoters, showing sequence homology to other known T7-like RNA polymerase promoters. Late stages of KSY1 multiplication are resistant to rifampicin. Otherwise, KSY1 shares limited similarity with other Podoviridae phages. Fourteen KSY1 structural proteins were identified by SDS-PAGE analysis. Among these proteins, those forming the distal tail structure and likely involved in host recognition are encoded by a 5-kb genomic region of KSY1. This region consists of a mosaic of DNA segments highly homologous to DNA of other lactococcal phages, suggesting an horizontal gene transfer.}, }
@article {pmid17464081, year = {2007}, author = {Tanous, C and Chambellon, E and Yvon, M}, title = {Sequence analysis of the mobilizable lactococcal plasmid pGdh442 encoding glutamate dehydrogenase activity.}, journal = {Microbiology (Reading, England)}, volume = {153}, number = {Pt 5}, pages = {1664-1675}, doi = {10.1099/mic.0.2006/002246-0}, pmid = {17464081}, issn = {1350-0872}, mesh = {Amino Acids/metabolism ; Base Sequence ; Conjugation, Genetic ; DNA Replication ; DNA Transposable Elements/genetics ; DNA, Bacterial/*chemistry/*genetics ; Drug Resistance, Bacterial/genetics ; Gene Order ; Gene Transfer, Horizontal ; Genes, Bacterial ; Glutamate Dehydrogenase/biosynthesis/*genetics ; Humans ; Lactococcus lactis/enzymology/*genetics ; Metals/toxicity ; Molecular Sequence Data ; Open Reading Frames ; Plasmids/*genetics/metabolism ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {A novel plasmid named pGdh442 had previously been isolated from a plant Lactococcus lactis strain. This plasmid encodes two interesting properties with applications in the dairy industry: a glutamate dehydrogenase activity that stimulates amino acid conversion to aroma compounds, and cadmium/zinc resistance that can be used as a selectable marker. Moreover, this plasmid can be transferred naturally to other strains, but appears to be incompatible with certain other lactococcal plasmids. During this study, the complete sequence of pGdh442 (68 319 bp) was determined and analysed. This plasmid contains 67 ORFs that include 20 IS elements that may have mediated transfer events between L. lactis and other genera living in the same biotope, such as Streptococcus, Pediococcus and Lactobacillus. Even though it is a low-copy-number plasmid, it is relatively stable due to a theta replication mode and the presence of two genes involved in its maintenance system. However, pGdh442 is incompatible with pSK08-derived protease/lactose plasmids because both possess the same replication and partition system. pGdh442 is not self-transmissible, but can be naturally transmitted via mobilization by conjugative elements carried by the chromosome or by other plasmids, such as the 712-type sex factor, which is widely distributed in L. lactis. In addition to several genes already found on other L. lactis plasmids, such as the oligopeptide transport and utilization genes, pGdh442 also carries several genes not yet identified in L. lactis. Finally, it does not carry genes that would trigger concern over its presence in human food.}, }
@article {pmid17464063, year = {2007}, author = {Labbate, M and Boucher, Y and Joss, MJ and Michael, CA and Gillings, MR and Stokes, HW}, title = {Use of chromosomal integron arrays as a phylogenetic typing system for Vibrio cholerae pandemic strains.}, journal = {Microbiology (Reading, England)}, volume = {153}, number = {Pt 5}, pages = {1488-1498}, doi = {10.1099/mic.0.2006/001065-0}, pmid = {17464063}, issn = {1350-0872}, mesh = {Bacterial Typing Techniques/*methods ; Cholera/epidemiology/*microbiology ; Chromosomes, Bacterial/*genetics ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; Disease Outbreaks ; Evolution, Molecular ; Gene Rearrangement ; Humans ; Integrons/*genetics ; Interspersed Repetitive Sequences/genetics ; Molecular Epidemiology/methods ; Molecular Sequence Data ; Recombination, Genetic ; Sequence Analysis, DNA ; Sequence Deletion ; Vibrio cholerae/*classification/*genetics ; }, abstract = {Approximately 200 serogroups of Vibrio cholerae exist, with only two, O1 and O139, responsible for epidemic and pandemic cholera. Strains from these serogroups have evolved from a common progenitor, with lateral gene transfer largely driving their emergence. These strains are so closely related that separation using single- or multi-locus phylogeny has proven difficult. V. cholerae strains contain a genetic system called the integron that is located in the chromosome and that can integrate and excise DNA elements called mobile gene cassettes (MGCs) by site-specific recombination. Large arrays of MGCs are found in V. cholerae strains. For instance, the O1 El Tor strain N16961 contains 179 MGCs. Since integron arrays are dynamic through recombination and excision of MGCs, it was hypothesized that the MGC composition in a given V. cholerae pandemic strain would be useful as a phylogenetic typing system. To address this, a PCR-based method was used to rapidly characterize the MGC composition of V. cholerae arrays. The results showed that the MGC composition of pandemic V. cholerae cassette arrays is relatively conserved, providing further evidence that these strains have evolved from a common progenitor. Comparison of MGC composition between the V. cholerae pandemic strains was also able to resolve the evolution of O139 from a subgroup of O1 El Tor. This level of differentiation of closely related V. cholerae isolates was more sensitive than conventional single-gene phylogeny or multi-locus sequence analysis. Using this method, novel MGCs from an O1 classical strain and an Argentinian O139 isolate were also identified, and a major deletion in the MGC array in all pandemic O139 strains and a subset of O1 El Tor strains was identified. Analysis of sequenced V. cholerae integron arrays showed that their evolution can proceed by rearrangements and deletions/insertions of large portions of MGCs in addition to the insertion or excision of single MGCs.}, }
@article {pmid17462951, year = {2007}, author = {Bielaszewska, M and Dobrindt, U and Gärtner, J and Gallitz, I and Hacker, J and Karch, H and Müller, D and Schubert, S and Alexander Schmidt, M and Sorsa, LJ and Zdziarski, J}, title = {Aspects of genome plasticity in pathogenic Escherichia coli.}, journal = {International journal of medical microbiology : IJMM}, volume = {297}, number = {7-8}, pages = {625-639}, doi = {10.1016/j.ijmm.2007.03.001}, pmid = {17462951}, issn = {1438-4221}, mesh = {DNA, Bacterial/genetics ; Escherichia coli/*genetics/*pathogenicity ; *Genetic Variation ; *Genome, Bacterial ; Oligonucleotide Array Sequence Analysis/*methods ; Virulence/genetics ; Virulence Factors/*analysis/genetics ; }, abstract = {The species Escherichia coli comprises not only non-pathogenic or commensal variants that belong to the normal intestinal flora of most mammals, but also various pathogenic strains causing diverse intestinal and extraintestinal infections in man and animals. Virulence factors and mechanisms involved in pathogenesis have been successfully analyzed for many years resulting in a wealth of knowledge about many E. coli pathotypes. However, our knowledge on the genome content, diversity and variability between pathogenic and also non-pathogenic subtypes is only slowly accumulating. Pathotypes have been largely defined by the presence or absence of particular DNA segments that in most cases appear to have been acquired via horizontal gene transfer events. As these regions are frequently subjected to excisions, rearrangements, and transfers they contribute to the previously unexpected and underestimated rapid evolution of E. coli variants resulting in the development of novel strains and even pathotypes. In these studies various novel aspects of genome diversity and plasticity in extraintestinal and intestinal pathogenic E. coli pathotypes have been addressed and the results have been directly applied for the improvement of diagnostic methods.}, }
@article {pmid17460045, year = {2007}, author = {Palenik, B and Grimwood, J and Aerts, A and Rouzé, P and Salamov, A and Putnam, N and Dupont, C and Jorgensen, R and Derelle, E and Rombauts, S and Zhou, K and Otillar, R and Merchant, SS and Podell, S and Gaasterland, T and Napoli, C and Gendler, K and Manuell, A and Tai, V and Vallon, O and Piganeau, G and Jancek, S and Heijde, M and Jabbari, K and Bowler, C and Lohr, M and Robbens, S and Werner, G and Dubchak, I and Pazour, GJ and Ren, Q and Paulsen, I and Delwiche, C and Schmutz, J and Rokhsar, D and Van de Peer, Y and Moreau, H and Grigoriev, IV}, title = {The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {18}, pages = {7705-7710}, pmid = {17460045}, issn = {0027-8424}, mesh = {Adaptation, Physiological ; Biological Evolution ; Cell Nucleus/genetics ; Chlorophyta/*genetics/metabolism ; Chromosomes/genetics ; Environment ; Eukaryotic Cells/*classification/*metabolism ; Gene Transfer, Horizontal ; Genome/*genetics ; Metals/metabolism ; Molecular Sequence Data ; Plankton/*classification/*genetics/metabolism ; Selenoproteins/metabolism ; Vitamins/metabolism ; }, abstract = {The smallest known eukaryotes, at approximately 1-mum diameter, are Ostreococcus tauri and related species of marine phytoplankton. The genome of Ostreococcus lucimarinus has been completed and compared with that of O. tauri. This comparison reveals surprising differences across orthologous chromosomes in the two species from highly syntenic chromosomes in most cases to chromosomes with almost no similarity. Species divergence in these phytoplankton is occurring through multiple mechanisms acting differently on different chromosomes and likely including acquisition of new genes through horizontal gene transfer. We speculate that this latter process may be involved in altering the cell-surface characteristics of each species. In addition, the genome of O. lucimarinus provides insights into the unique metal metabolism of these organisms, which are predicted to have a large number of selenocysteine-containing proteins. Selenoenzymes are more catalytically active than similar enzymes lacking selenium, and thus the cell may require less of that protein. As reported here, selenoenzymes, novel fusion proteins, and loss of some major protein families including ones associated with chromatin are likely important adaptations for achieving a small cell size.}, }
@article {pmid17459613, year = {2007}, author = {Kotnova, AP and Glukhov, IA and Karpova, NN and Salenko, VB and Lyubomirskaya, NV and Ilyin, YV}, title = {Evidence for recent horizontal transfer of gypsy-homologous LTR-retrotransposon gtwin into Drosophila erecta followed by its amplification with multiple aberrations.}, journal = {Gene}, volume = {396}, number = {1}, pages = {39-45}, doi = {10.1016/j.gene.2007.02.019}, pmid = {17459613}, issn = {0378-1119}, mesh = {Animals ; Clone Cells ; DNA/isolation &amp; purification ; Drosophila/*classification/*genetics ; *Gene Amplification ; *Gene Transfer, Horizontal ; Genome, Insect/genetics ; Models, Genetic ; Open Reading Frames/genetics ; Phylogeny ; Restriction Mapping ; Retroelements/*genetics ; *Sequence Homology, Nucleic Acid ; Species Specificity ; Terminal Repeat Sequences/*genetics ; }, abstract = {Long terminal repeat (LTR) retrotransposon gtwin was initially discovered in silico, and then it was isolated as gypsy-homologous sequence from Drosophila melanogaster strain, G32. The presence of ORF3 suggests, that gtwin, like gypsy, may be an endogenous retrovirus, which can leave the cell and infect another one. Therefore, in this study we decided to investigate the distribution of gtwin in different species of the melanogaster subgroup in order to find out whether gtwin can be transferred horizontally as well as vertically. Gtwin was found in all 9 species of this subgroup, hence it seems to have inhabited the host genomes for a long time. In addition, we have shown that in the Drosophila erecta genome two gtwin families are present. The first one has 93% of identity to D. melanogaster element and is likely to be a descendant of gtwin that existed in Drosophila before the divergence of the melanogaster subgroup species. The other one has >99% of identity to D. melanogaster gtwin. The most reasonable explanation is that this element has been recently horizontally transferred between D. melanogaster and D. erecta. The number and variety of gtwin copies from the "infectious" family suggest that after the horizontal transfer into D. erecta genome, gtwin underwent amplification and aberrations, leading to the rise of its diverse variants.}, }
@article {pmid17452479, year = {2007}, author = {Daikos, GL and Kosmidis, C and Tassios, PT and Petrikkos, G and Vasilakopoulou, A and Psychogiou, M and Stefanou, I and Avlami, A and Katsilambros, N}, title = {Enterobacteriaceae bloodstream infections: presence of integrons, risk factors, and outcome.}, journal = {Antimicrobial agents and chemotherapy}, volume = {51}, number = {7}, pages = {2366-2372}, pmid = {17452479}, issn = {0066-4804}, mesh = {Bacteremia/epidemiology ; Community-Acquired Infections/blood/microbiology/transmission ; Cross Infection/blood/microbiology/transmission ; DNA, Bacterial/analysis/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Electrophoresis, Gel, Pulsed-Field ; Enterobacteriaceae Infections/*blood/microbiology/*transmission ; Gene Transfer, Horizontal ; Humans ; Infectious Disease Transmission, Professional-to-Patient ; *Integrons ; Microbial Sensitivity Tests ; Nucleic Acid Amplification Techniques ; Polymerase Chain Reaction ; Prospective Studies ; Risk Factors ; Sequence Analysis, DNA ; *Treatment Outcome ; }, abstract = {A prospective observational study was conducted to identify factors associated with bloodstream infections (BSIs) caused by integron-carrying Enterobacteriaceae and to evaluate the clinical significance of integron carriage. Consecutive patients with Enterobacteriaceae BSIs were identified and followed up until discharge or death. Identification of blood isolates and susceptibility testing were performed by the Wider I automated system. int-1-specific PCR, conserved-segment PCR, and DNA sequencing were used to determine the presence, length, and content of integrons. The relatedness among the isolates was examined by pulsed-field gel electrophoresis. Two hundred fifty episodes of Enterobacteriaceae BSI occurred in 233 patients; 109 (43.6%) were nosocomial, 82 (32.8%) were community acquired, and 59 (23.6%) were health care associated. Integrons were detected in 11 (13.4%) community-acquired, 24 (40.7%) health care-associated, and 46 (42.2%) nosocomial isolates. Integron-carrying organisms were more likely to exhibit resistance to three or more classes of antimicrobials (odds ratio [OR], 9.84; 95% confidence interval [95% CI], 5.31 to 18.23; P < 0.001) or to produce extended-spectrum beta-lactamases (OR, 5.75; 95% CI, 2.38 to 13.89; P < 0.001) or a VIM-type metallo-beta-lactamase (P, 0.003). Inter- or intraspecies integron transfer and cross-transmission of integron-carrying clones were observed. Use of cotrimoxazole (OR, 4.77; 95% CI, 1.81 to 12.54; P < 0.001) and a nosocomial or other health care setting (OR, 3.07; 95% CI, 1.30 to 7.22; P, 0.01) were independently associated with BSIs caused by integron-carrying Enterobacteriaceae. Patients with a nonurinary source of bacteremia (OR, 9.46; 95% CI, 2.77 to 32.32; P < 0.001) and a Pitt bacteremia score of > or =4 (OR, 23.36; 95% CI, 7.97 to 68.44; P < 0.001) had a significantly higher 14-day mortality rate, whereas integron carriage did not affect clinical outcomes. These findings may have implications affecting antibiotic policies and infection control measures.}, }
@article {pmid17449831, year = {2007}, author = {Feder, ME}, title = {Evolvability of physiological and biochemical traits: evolutionary mechanisms including and beyond single-nucleotide mutation.}, journal = {The Journal of experimental biology}, volume = {210}, number = {Pt 9}, pages = {1653-1660}, doi = {10.1242/jeb.02725}, pmid = {17449831}, issn = {0022-0949}, mesh = {Adaptation, Biological/*genetics ; *Biological Evolution ; Gene Duplication ; Gene Transfer, Horizontal/genetics ; *Genetic Variation ; Hybridization, Genetic/genetics ; Interspersed Repetitive Sequences/genetics ; *Models, Biological ; Polymorphism, Single Nucleotide/*genetics ; *Selection, Genetic ; Symbiosis/genetics ; Systems Biology/*methods/trends ; }, abstract = {A longstanding challenge for biologists has been to explain not just how organisms are adapted to diverse environments, but how these adaptations arise. Although natural selection is clearly sufficient to act on heritable variation, is this heritable variation sufficient to yield complex adaptations and how does this variation itself arise? Much prior focus has been on mutation of single nucleotides in genes. This process is common and can have dramatic phenotypes, but could be limited in its ability to culminate in complex adaptations for two kinds of reasons: (i) because natural selection is powerful, it can purge genetic variation, and (ii) evolutionary transition from the absence to the presence of a complex adaptation seemingly requires multiple mutations at the right place and time and in the right sequence, with each intermediate stage having increased overall fitness; this seems highly improbable. Because the networks that organisms comprise are hierarchical and redundant and have modular structure, however, single-nucleotide mutations can have large and tolerable impacts. Diverse mechanisms, collectively evolutionary capacitors, can shield genetic variation from the purgative of selection. These features can enable evolution to proceed via single-nucleotide mutation. Importantly, single-nucleotide mutation usually only modifies existing genes rather than creating new ones, and numerous other mechanisms eclipse single-nucleotide mutation in creating genetic variation. These include gene duplication (both segmental and whole-genome), lateral gene transfer, hybridization, mobile genetic elements and symbiosis. Other processes can scramble and reassemble nucleotide sequence. The mechanisms beyond single-gene mutation offer considerable promise in detailing the evolution of complex physiological and biochemical traits, and have already done so for several morphological traits.}, }
@article {pmid17449699, year = {2007}, author = {Miller, MC and Keymer, DP and Avelar, A and Boehm, AB and Schoolnik, GK}, title = {Detection and transformation of genome segments that differ within a coastal population of Vibrio cholerae strains.}, journal = {Applied and environmental microbiology}, volume = {73}, number = {11}, pages = {3695-3704}, pmid = {17449699}, issn = {0099-2240}, mesh = {California ; DNA, Bacterial/*genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; *Genetic Variation ; Genome, Bacterial/*genetics ; Interspersed Repetitive Sequences ; Multigene Family/genetics ; Seawater/*microbiology ; *Transformation, Bacterial ; Vibrio cholerae/*genetics/*isolation &amp; purification ; Vibrio cholerae O1/genetics ; }, abstract = {Vibrio cholerae is an autochthonous member of diverse aquatic ecosystems around the globe. Collectively, the genomes of environmental V. cholerae strains comprise a large repository of encoded functions which can be acquired by individual V. cholerae lineages through uptake and recombination. To characterize the genomic diversity of environmental V. cholerae, we used comparative genome hybridization to study 41 environmental strains isolated from diverse habitats along the central California coast, a region free of endemic cholera. These data were used to classify genes of the epidemic V. cholerae O1 sequenced strain N16961 as conserved, variably present, or absent from the isolates. For the most part, absent genes were restricted to large mobile elements and have known functions in pathogenesis. Conversely, genes present in some, but not all, California isolates were in smaller contiguous clusters and were less likely to be near genes with functions in DNA mobility. Two such clusters of variable genes encoding different selectable metabolic phenotypes (mannose and diglucosamine utilization) were transformed into the genomes of environmental isolates by chitin-dependent competence, indicating that this mechanism of general genetic exchange is conserved among V. cholerae. The transformed DNA had an average size of 22.7 kbp, demonstrating that natural competence can mediate the movement of large chromosome fragments. Thus, whether variable genes arise through the acquisition of new sequences by horizontal gene transfer or by the loss of preexisting DNA though deletion, natural transformation provides a mechanism by which V. cholerae clones can gain access to the V. cholerae pan-genome.}, }
@article {pmid17449198, year = {2007}, author = {Dong, JH and Wen, JF and Tian, HF}, title = {Homologs of eukaryotic Ras superfamily proteins in prokaryotes and their novel phylogenetic correlation with their eukaryotic analogs.}, journal = {Gene}, volume = {396}, number = {1}, pages = {116-124}, doi = {10.1016/j.gene.2007.03.001}, pmid = {17449198}, issn = {0378-1119}, mesh = {Amino Acid Sequence ; Eukaryotic Cells/*chemistry ; Likelihood Functions ; Molecular Sequence Data ; *Multigene Family ; *Phylogeny ; Prokaryotic Cells/*chemistry ; *Sequence Homology, Amino Acid ; ras Proteins/*chemistry ; }, abstract = {Ras superfamily proteins are key regulators in a wide variety of cellular processes. Previously, they were considered to be specific to eukaryotes, and MglA, a group of obviously different prokaryotic proteins, were recognized as their only prokaryotic analogs or even ancestors. Here, taking advantage of quite a current accumulation of prokaryotic genomic databases, we have investigated the existence and taxonomic distribution of Ras superfamily protein homologs in a much wider prokaryotic range, and analyzed their phylogenetic correlation with their eukaryotic analogs. Thirteen unambiguous prokaryotic homologs, which possess the GDP/GTP-binding domain with all the five characteristic motifs of their eukaryotic analogs, were identified in 12 eubacteria and one archaebacterium, respectively. In some other archaebacteria, including four methanogenic archaebacteria and three Thermoplasmales, homologs were also found, but with the GDP/GTP-binding domains not containing all the five characteristic motifs. Many more MglA orthologs were identified than in previous studies mainly in delta-proteobacteria, and all were shown to have common unique features distinct from the Ras superfamily proteins. Our phylogenetic analysis indicated eukaryotic Rab, Ran, Ras, and Rho families have the closest phylogenetic correlation with the 13 unambiguous prokaryotic homologs, whereas the other three eukaryotic protein families (SRbeta, Sar1, and Arf) branch separately from them, but have a relatively close relationship with the methanogenic archaebacterial homologs and MglA. Although homologs were identified in a relative minority of prokaryotes with genomic databases, their presence in a relatively wide variety of lineages, their unique sequence characters distinct from those of eukaryotic analogs, and the topology of our phylogenetic tree altogether do not support their origin from eukaryotes as a result of lateral gene transfer. Therefore, we argue that Ras superfamily proteins might have already emerged at least in some prokaryotic lineages, and that the seven eukaryotic protein families of the Ras superfamily may have two independent prokaryotic origins, probably reflecting the 'fusion' evolutionary history of the eukaryotic cell.}, }
@article {pmid17444411, year = {2007}, author = {Wishart, K and Loughrey, A and McClurg, RB and Goldsmith, CE and Millar, BC and Rao, J and Sengupta, B and Dooley, JS and Rooney, RJ and Moore, JE}, title = {Lack of horizontal gene transfer of methicillin-resistance genetic determinants from PBP2a-positive, coagulase-negative staphylococci to methicillin-sensitive Staphylococcus aureus using transcutaneous electrical nerve stimulation (TENS).}, journal = {British journal of biomedical science}, volume = {64}, number = {1}, pages = {6-9}, doi = {10.1080/09674845.2007.11732747}, pmid = {17444411}, issn = {0967-4845}, mesh = {Anti-Bacterial Agents/*pharmacology ; Electroporation/methods ; Humans ; Methicillin/*pharmacology ; Methicillin Resistance/*genetics ; Northern Ireland ; Staphylococcal Infections/*genetics/microbiology ; Staphylococcus aureus/*genetics/isolation &amp; purification ; Transcutaneous Electric Nerve Stimulation/*methods ; }, abstract = {Previous research shows that approximately half of the coagulase-negative staphylococci (CNS) isolated from patients in the intensive care unit (ICU) at Belfast City Hospital were resistant to methicillin. The presence of this relatively high proportion of methicillin-resistance genetic material gives rise to speculation that these organisms may act as potential reservoirs of methicillin-resistance genetic material to methicillin-sensitive Staphylococcus aureus (MSSA). Mechanisms of horizontal gene transfer from PBP2a-positive CNS to MSSA, potentially transforming MSSA to MRSA, aided by electroporation-type activities such as transcutaneous electrical nerve stimulation (TENS), should be considered. Methicillin-resistant CNS (MR-CNS) isolates are collected over a two-month period from a variety of clinical specimen types, particularly wound swabs. The species of all isolates are confirmed, as well as their resistance to oxacillin by standard disc diffusion assays. In addition, MSSA isolates are collected over the same period and confirmed as PBP2a-negative. Electroporation experiments are designed to mimic the time/voltage combinations used commonly in the clinical application of TENS. No transformed MRSA were isolated and all viable S. aureus cells remained susceptible to oxacillin and PBP2a-negative. Experiments using MSSA pre-exposed to sublethal concentrations of oxacillin (0.25 microg/mL) showed no evidence of methicillin gene transfer and the generation of an MRSA. The study showed no evidence of horizontal transfer of methicillin resistance genetic material from MR-CNS to MSSA. These data support the belief that TENS and the associated time/voltage combinations used do not increase conjugational transposons or facilitate horizontal gene transfer from MR-CNS to MSSA.}, }
@article {pmid17443012, year = {2007}, author = {Grauvogel, C and Brinkmann, H and Petersen, J}, title = {Evolution of the glucose-6-phosphate isomerase: the plasticity of primary metabolism in photosynthetic eukaryotes.}, journal = {Molecular biology and evolution}, volume = {24}, number = {8}, pages = {1611-1621}, doi = {10.1093/molbev/msm075}, pmid = {17443012}, issn = {0737-4038}, mesh = {Biological Evolution ; Cyanophora/*genetics ; DNA, Algal/genetics ; DNA, Plant/genetics ; Eukaryotic Cells/*physiology ; Glucose-6-Phosphate Isomerase/*genetics ; Molecular Sequence Data ; Photosynthesis/*genetics ; Phylogeny ; Plastids/*genetics ; Rhodophyta/*genetics ; Symbiosis ; }, abstract = {Glucose-6-phosphate isomerase (GPI) has an essential function in both catabolic glycolysis and anabolic gluconeogenesis and is universally distributed among Eukaryotes, Bacteria, and some Archaea. In addition to the cytosolic GPI, land plant chloroplasts harbor a nuclear encoded isoenzyme of cyanobacterial origin that is indispensable for the oxidative pentose phosphate pathway (OPPP) and plastid starch accumulation. We established 12 new GPI sequences from rhodophytes, the glaucophyte Cyanophora paradoxa, a ciliate, and all orders of complex algae with red plastids (haptophytes, diatoms, cryptophytes, and dinoflagellates). Our comprehensive phylogenies do not support previous GPI-based speculations about a eukaryote-to-prokaryote horizontal gene transfer from metazoa to gamma-proteobacteria. The evolution of cytosolic GPI is largely in agreement with small subunit analyses, which indicates that it is a specific marker of the host cell. A distinct subtree comprising alveolates (ciliates, apicomplexa, Perkinsus, and dinoflagellates), stramenopiles (diatoms and Phytophthora [oomycete]), and Plantae (green plants, rhodophytes, and Cyanophora) might suggest a common origin of these superensembles. Finally, in contrast to land plants where the plastid GPI is of cyanobacterial origin, chlorophytes and rhodophytes independently recruited a duplicate of the cytosolic GPI that subsequently acquired a transit peptide for plastid import. A secondary loss of the cytosolic isoenzyme and the plastid localization of the single GPI in chlorophycean green algae is compatible with physiological studies. Our findings reveal the fundamental importance of the plastid OPPP for Plantae and document the plasticity of primary metabolism.}, }
@article {pmid17437147, year = {2007}, author = {Larsen, J and Pedersen, AG and Christensen, H and Bisgaard, M and Angen, &#xd8; and Ahrens, P and Olsen, JE}, title = {Evidence for vertical inheritance and loss of the leukotoxin operon in genus Mannheimia.}, journal = {Journal of molecular evolution}, volume = {64}, number = {4}, pages = {423-437}, pmid = {17437147}, issn = {0022-2844}, mesh = {Bacterial Toxins/genetics ; Base Sequence ; DNA, Bacterial/genetics ; Exotoxins/*genetics ; Genes, Bacterial ; Genotype ; Inheritance Patterns/*genetics ; Mannheimia/*genetics ; Operon/*genetics ; Phenotype ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The Mannheimia subclades belong to the same bacterial genus but have taken divergent paths toward their distinct lifestyles. M. haemolytica + M. glucosida are potential pathogens of the respiratory tract in the mammalian suborder Ruminantia, whereas M. ruminalis, the supposed sister group, lives as a commensal in the ovine rumen. We have tested the hypothesis that horizontal gene transfer of the leukotoxin operon has catalyzed pathogenic adaptation and speciation of M. haemolytica + M. glucosida, or other major subclades, by using a strategy that combines compositional and phylogenetic methods. We show that it has been vertically inherited from the last common ancestor of the diverging Mannheimia subclades, although several strains belonging to M. ruminalis have lost the operon. Our analyses support that divergence within M. ruminalis following colonization of the ovine rumen was very rapid and that functional decay of most of the leukotoxin operons occurred early when the adaptation to the rumen was fastest, suggesting that antagonistic pleiotropy was the main contributor to losses in the radiating lineages of M. ruminalis. To sum up, the scenario derived from these analyses reflects two aspects. On one hand, it opposes the hypothesis of horizontal gene transfer as a catalyst of pathogenic adaptation and speciation. On the other hand, it indicates that losses of the leukotoxin operons in the radiating lineages of M. ruminalis have catalyzed their adaptation to a commensal environment and reproductive isolation (speciation).}, }
@article {pmid17434232, year = {2007}, author = {Arnold, DL and Jackson, RW and Waterfield, NR and Mansfield, JW}, title = {Evolution of microbial virulence: the benefits of stress.}, journal = {Trends in genetics : TIG}, volume = {23}, number = {6}, pages = {293-300}, doi = {10.1016/j.tig.2007.03.017}, pmid = {17434232}, issn = {0168-9525}, mesh = {Bacteria/genetics/*pathogenicity ; Bacterial Proteins/*genetics ; *DNA Damage ; Environment ; Gene Rearrangement ; Plant Diseases/*microbiology ; *Virulence ; }, abstract = {Although genome sequencing of microbial pathogens has shed light on the evolution of virulence, the drivers of the gain and loss of genes and of pathogenicity islands (gene clusters), which contribute to the emergence of new disease outbreaks, are unclear. Recent experiments with the bean pathogen Pseudomonas syringae pv. phaseolicola illustrate how exposure to resistance mechanisms acts as the driving force for genome reorganization. Here we argue that the antimicrobial conditions generated by host defences can accelerate the generation of genome rearrangements that provide selective advantages to the invading microbe. Similar exposure to environmental stress outside the host could also drive the horizontal gene transfer that has led to the evolution of pathogenicity towards both animals and plants.}, }
@article {pmid17431169, year = {2007}, author = {Han, K and Konkel, MK and Xing, J and Wang, H and Lee, J and Meyer, TJ and Huang, CT and Sandifer, E and Hebert, K and Barnes, EW and Hubley, R and Miller, W and Smit, AF and Ullmer, B and Batzer, MA}, title = {Mobile DNA in Old World monkeys: a glimpse through the rhesus macaque genome.}, journal = {Science (New York, N.Y.)}, volume = {316}, number = {5822}, pages = {238-240}, doi = {10.1126/science.1139462}, pmid = {17431169}, issn = {1095-9203}, support = {R01 HG002939/HG/NHGRI NIH HHS/United States ; GM59290/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cercopithecidae/*genetics ; *DNA Transposable Elements ; Endogenous Retroviruses/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome ; Genome, Human ; Humans ; Macaca mulatta/*genetics ; Repetitive Sequences, Nucleic Acid ; Retroelements ; }, abstract = {The completion of the draft sequence of the rhesus macaque genome allowed us to study the genomic composition and evolution of transposable elements in this representative of the Old World monkey lineage, a group of diverse primates closely related to humans. The L1 family of long interspersed elements appears to have evolved as a single lineage, and Alu elements have evolved into four currently active lineages. We also found evidence of elevated horizontal transmissions of retroviruses and the absence of DNA transposon activity in the Old World monkey lineage. In addition, approximately 100 precursors of composite SVA (short interspersed element, variable number of tandem repeat, and Alu) elements were identified, with the majority being shared by the common ancestor of humans and rhesus macaques. Mobile elements compose roughly 50% of primate genomes, and our findings illustrate their diversity and strong influence on genome evolution between closely related species.}, }
@article {pmid17428586, year = {2007}, author = {Yan, M and Liu, G and Diao, B and Qiu, H and Zhang, L and Liang, W and Gao, S and Kan, B}, title = {A Vibrio cholerae serogroup O1 vaccine candidate against CTX ET Phi infection.}, journal = {Vaccine}, volume = {25}, number = {20}, pages = {4046-4055}, doi = {10.1016/j.vaccine.2007.02.043}, pmid = {17428586}, issn = {0264-410X}, mesh = {Animals ; Antibodies, Bacterial/biosynthesis/immunology ; Cholera/immunology/microbiology/*prevention &amp; control ; Cholera Vaccines/genetics/*immunology/pharmacology ; Cloning, Molecular ; Cytotoxicity, Immunologic ; Enzyme-Linked Immunosorbent Assay/methods ; Intestines/microbiology ; Rabbits ; Vaccines, Synthetic/genetics/immunology/pharmacology ; Vibrio cholerae O1/genetics/*immunology ; }, abstract = {Cholera is a severe diarrheal disease that may spread rapidly. Vaccination is considered a valid measure against it. We developed a new vaccine candidate, IEM109, against Vibrio cholerae. To generate this candidate, a chromosomal fragment containing the TLC element, attB of the CTX Phi integration site, and RTX cluster responsible for the cytotoxic activity for mammalian cells was deleted through homologous recombination from the previously described El Tor biotype, IEM101. The protective genes ctxB and rstR, which establish resistance to CTX Phi infections, were inserted into that same location on the chromosome of IEM109 to enhance the safety and genetic stability of the vaccine candidate and to prevent horizontal gene transfer. In in vivo tests, cell cultures showed that the cytotoxic effect of IEM109 on Hep-2 was negative. Furthermore, the infection rate of El Tor biotype CTX Phi to that of IEM109 in the rabbit intestine is 3000-fold lower than that of IEM101. Intraintestinal vaccination of rabbits with a single dose of IEM109 elicits high titers of anti-CTB IgG and vibriocidal antibodies. When challenged with 0.5-2 microg CT and 10(5) to 10(8)CFU of four wild toxigenic strains of different biotypes and serogroups, IEM109 conferred full protection. Thus, IEM109 is a stable vaccine candidate that evokes not only antitoxic and vibriocidal immunities, but also resistance to the El Tor biotype CTX Phi infection.}, }
@article {pmid17418306, year = {2007}, author = {Ammor, MS and Flórez, AB and Mayo, B}, title = {Antibiotic resistance in non-enterococcal lactic acid bacteria and bifidobacteria.}, journal = {Food microbiology}, volume = {24}, number = {6}, pages = {559-570}, doi = {10.1016/j.fm.2006.11.001}, pmid = {17418306}, issn = {0740-0020}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bifidobacterium/*drug effects ; Colony Count, Microbial ; Conjugation, Genetic ; *Consumer Product Safety ; Disease Reservoirs/microbiology ; *Drug Resistance, Bacterial/genetics ; Food Microbiology ; Gene Transfer, Horizontal ; Humans ; Lactobacillus/*drug effects ; Microbial Sensitivity Tests ; Mutation ; }, abstract = {Over the last 50 years, human life expectancy and quality of life have increased dramatically due to improvements in nutrition and the use of antibiotics in the fight against infectious diseases. However, the heyday of antibiotic treatment is on the wane due to the appearance and spread of resistance among harmful microorganisms. At present, there is great concern that commensal bacterial populations from food and the gastrointestinal tract (GIT) of humans and animals, such as lactic acid bacteria (LAB) and bifidobacteria, could act as a reservoir for antibiotic resistance genes. Resistances could ultimately be transferred to human pathogenic and opportunistic bacteria hampering the treatment of infections. LAB species have traditionally been used as starter cultures in the production of fermented feed and foodstuffs. Further, LAB and bifidobacteria are normal inhabitants of the GIT where they are known to exert health-promoting effects, and selected strains are currently been used as probiotics. Antibiotic resistance genes carried by LAB and bifidobacteria can be transferred to human pathogenic bacteria either during food manufacture or during passage through the GIT. The aim of this review is to address well-stated and recent knowledge on antibiotic resistance in typical LAB and bifidobacteria species. Therefore, the commonest antibiotic resistance profiles, the distinction between intrinsic and atypical resistances, and some of the genetic determinants already discovered will all be discussed.}, }
@article {pmid17412703, year = {2007}, author = {Pilhofer, M and Rosati, G and Ludwig, W and Schleifer, KH and Petroni, G}, title = {Coexistence of tubulins and ftsZ in different Prosthecobacter species.}, journal = {Molecular biology and evolution}, volume = {24}, number = {7}, pages = {1439-1442}, doi = {10.1093/molbev/msm069}, pmid = {17412703}, issn = {0737-4038}, mesh = {Bacteria/genetics ; Bacterial Proteins/*genetics/physiology ; Cytoskeletal Proteins/*genetics/physiology ; *Evolution, Molecular ; Molecular Sequence Data ; *Phylogeny ; Tubulin/*genetics ; }, abstract = {Prosthecobacter, one of the few cultivable representatives of the bacterial phylum Verrucomicrobia, is of increasing interest to the scientific community due to the presence of tubulin genes in its genome and the apparent absence of the bacterial homologue FtsZ that is normally involved in prokaryotic cell division. These findings suggested the possibility of a vicarious takeover of the FtsZ function through these novel tubulins and opened new scenarios on the possible evolution of bacterial cytoskeleton and cell division. In the present manuscript, we report the characterization of ftsZ and ftsA homologues in different Prosthecobacter species that also possess tubulin genes. Based on these findings, we propose an FtsZ-based cell division mechanism in Verrucomicrobia. The analysis of available genome data of Verrucomicrobia suggests that tubulins are not a feature common to all members of this phylum. Therefore, it can be assumed that Prosthecobacter acquired tubulins through horizontal gene transfer. The functional role of tubulins in Prosthecobacter remains enigmatic.}, }
@article {pmid17408713, year = {2007}, author = {Spano, AJ and Chen, FS and Goodman, BE and Sabat, AE and Simon, MN and Wall, JS and Correia, JJ and McIvor, W and Newcomb, WW and Brown, JC and Schnur, JM and Lebedev, N}, title = {In vitro assembly of a prohead-like structure of the Rhodobacter capsulatus gene transfer agent.}, journal = {Virology}, volume = {364}, number = {1}, pages = {95-102}, doi = {10.1016/j.virol.2007.02.027}, pmid = {17408713}, issn = {0042-6822}, support = {5 P41 EB2181/EB/NIBIB NIH HHS/United States ; }, mesh = {Bacteriophages/genetics/ultrastructure ; Base Sequence ; DNA, Bacterial/genetics ; DNA, Viral/genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genes, Viral ; Microscopy, Electron ; Multigene Family ; Open Reading Frames ; Rhodobacter capsulatus/*genetics/ultrastructure/*virology ; Viral Proteins/genetics/isolation &amp; purification ; Virus Assembly ; }, abstract = {The gene transfer agent (GTA) is a phage-like particle capable of exchanging double-stranded DNA fragments between cells of the photosynthetic bacterium Rhodobacter capsulatus. Here we show that the major capsid protein of GTA, expressed in E. coli, can be assembled into prohead-like structures in the presence of calcium ions in vitro. Transmission electron microscopy (TEM) of uranyl acetate staining material and thin sections of glutaraldehyde-fixed material demonstrates that these associates have spherical structures with diameters in the range of 27-35 nm. The analysis of scanning TEM images revealed particles of mass approximately 4.3 MDa, representing 101+/-11 copies of the monomeric subunit. The establishment of this simple and rapid method to form prohead-like particles permits the GTA system to be used for genome manipulation within the photosynthetic bacterium, for specific targeted drug delivery, and for the construction of biologically based distributed autonomous sensors for environmental monitoring.}, }
@article {pmid17401541, year = {2007}, author = {Chatziefthimiou, AD and Crespo-Medina, M and Wang, Y and Vetriani, C and Barkay, T}, title = {The isolation and initial characterization of mercury resistant chemolithotrophic thermophilic bacteria from mercury rich geothermal springs.}, journal = {Extremophiles : life under extreme conditions}, volume = {11}, number = {3}, pages = {469-479}, pmid = {17401541}, issn = {1431-0651}, mesh = {Bacteria/classification/growth &amp; development/*isolation &amp; purification ; Base Sequence ; Culture Media ; DNA Primers ; Hot Temperature ; Mercury/*pharmacology ; Phylogeny ; *Water Microbiology ; }, abstract = {Mercury rich geothermal springs are likely environments where mercury resistance is critical to microbial life and where microbe-mercury interactions may have evolved. Eleven facultative thermophilic and chemolithoautotrophic, thiosulfate oxidizing bacteria were isolated from thiosulfate enrichments of biofilms from mercury rich hot sulfidic springs in Mount Amiata, Italy. Some strains were highly resistant to mercury (>or=200 muM HgCl(2)) regardless of its presence or absence during primary enrichments, and three reduced ionic mercury to its elemental form. The gene encoding for the mercuric reductase enzyme (MerA), was amplified by PCR from seven strains. However, one highly resistant strain did not reduce mercury nor carried merA, suggesting an alternative resistance mechanism. All strains were members of the order Bacillales and were most closely related to previously described thermophiles belonging to the Firmicutes. Phylogenetic analyses clustered the MerA of the isolates in two supported novel nodes within the Firmicutes lineage and a comparison with the 16S rRNA gene tree suggested at least one case of horizontal gene transfer. Overall, the results show that the thermophilic thiosulfate oxidizing isolates were adapted to life in presence of mercury mostly, but not exclusively, by possessing MerA. These findings suggest that reduction of mercury by chemolithotrophic thermophilic bacteria may mobilize mercury from sulfur and iron deposits in geothermal environments.}, }
@article {pmid17400784, year = {2007}, author = {Bielaszewska, M and Prager, R and Köck, R and Mellmann, A and Zhang, W and Tschäpe, H and Tarr, PI and Karch, H}, title = {Shiga toxin gene loss and transfer in vitro and in vivo during enterohemorrhagic Escherichia coli O26 infection in humans.}, journal = {Applied and environmental microbiology}, volume = {73}, number = {10}, pages = {3144-3150}, pmid = {17400784}, issn = {0099-2240}, support = {R01 AI047499/AI/NIAID NIH HHS/United States ; AI47499/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteriophages/genetics ; Cluster Analysis ; DNA, Bacterial/genetics ; DNA, Viral/genetics ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/classification/*genetics/isolation &amp; purification ; Escherichia coli Infections/*microbiology ; Escherichia coli Proteins/biosynthesis/*genetics ; Feces/microbiology ; *Gene Transfer, Horizontal ; Humans ; Prophages/genetics ; Recombination, Genetic ; Shiga Toxins/biosynthesis/*genetics ; Virulence Factors/biosynthesis/genetics ; }, abstract = {Escherichia coli serogroup O26 consists of enterohemorrhagic E. coli (EHEC) and atypical enteropathogenic E. coli (aEPEC). The former produces Shiga toxins (Stx), major determinants of EHEC pathogenicity, encoded by bacteriophages; the latter is Stx negative. We have isolated EHEC O26 from patient stools early in illness and aEPEC O26 from stools later in illness, and vice versa. Intrapatient EHEC and aEPEC isolates had quite similar pulsed-field gel electrophoresis (PFGE) patterns, suggesting that they might have arisen by conversion between the EHEC and aEPEC pathotypes during infection. To test this hypothesis, we asked whether EHEC O26 can lose stx genes and whether aEPEC O26 can be lysogenized with Stx-encoding phages from EHEC O26 in vitro. The stx2 loss associated with the loss of Stx2-encoding phages occurred in 10% to 14% of colonies tested. Conversely, Stx2- and, to a lesser extent, Stx1-encoding bacteriophages from EHEC O26 lysogenized aEPEC O26 isolates, converting them to EHEC strains. In the lysogens and EHEC O26 donors, Stx2-converting bacteriophages integrated in yecE or wrbA. The loss and gain of Stx-converting bacteriophages diversifies PFGE patterns; this parallels findings of similar but not identical PFGE patterns in the intrapatient EHEC and aEPEC O26 isolates. EHEC O26 and aEPEC O26 thus exist as a dynamic system whose members undergo ephemeral interconversions via loss and gain of Stx-encoding phages to yield different pathotypes. The suggested occurrence of this process in the human intestine has diagnostic, clinical, epidemiological, and evolutionary implications.}, }
@article {pmid17400574, year = {2007}, author = {Cunneen, MM and Reeves, PR}, title = {The Yersinia kristensenii O11 O-antigen gene cluster was acquired by lateral gene transfer and incorporated at a novel chromosomal locus.}, journal = {Molecular biology and evolution}, volume = {24}, number = {6}, pages = {1355-1365}, doi = {10.1093/molbev/msm058}, pmid = {17400574}, issn = {0737-4038}, mesh = {Base Sequence ; Chromosomes, Bacterial/*genetics ; Escherichia coli/genetics ; *Gene Transfer, Horizontal ; Genetic Markers ; Molecular Sequence Data ; *Multigene Family ; O Antigens/*genetics ; Yersinia/*genetics ; }, abstract = {We have sequenced the O-antigen gene clusters for the Escherichia coli O98 and Yersinia kristensenii O11 O antigens. The basic structures of these O antigens are identical, and the sequence data indicate that Y. kristensenii O11 gained its O-antigen gene cluster by lateral gene transfer (LGT). Escherichia coli O98 has a typical O-antigen gene cluster between galF and gnd as is usual in E. coli. However, the O-antigen gene cluster of Y. kristensenii O11 is not located at the traditional Yersinia O-antigen gene cluster locus, between hemH and gsk, but at a novel chromosomal locus between aroA and cmk where it is flanked by remnant galF and gnd genes that indicate the probable source of the gene cluster. Phylogenetic analysis indicated that the source was not E. coli itself but a species in the Escherichia, Salmonella, and Klebsiella group of genera. Although other O-antigen studies imply LGT on the basis of the hypervariability of the loci and GC content, this report also identifies a potential donor and provides evidence for the mechanism involved. Remnant insertion sequence (IS) sequences flank the galF and gnd remnants and suggest that LGT of the gene cluster was IS mediated.}, }
@article {pmid17392430, year = {2007}, author = {Robinson, NP and Bell, SD}, title = {Extrachromosomal element capture and the evolution of multiple replication origins in archaeal chromosomes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {14}, pages = {5806-5811}, pmid = {17392430}, issn = {0027-8424}, mesh = {Aeropyrum/genetics ; Amino Acid Sequence ; Archaeal Proteins/chemistry/genetics/isolation &amp; purification ; Base Sequence ; Cell Cycle Proteins/genetics ; Chromosomes, Archaeal/*genetics ; DNA Footprinting ; DNA Replication/*genetics ; DNA-Binding Proteins/genetics ; *Evolution, Molecular ; Extrachromosomal Inheritance/*genetics ; Genes, Archaeal ; Molecular Sequence Data ; Open Reading Frames/genetics ; Origin Recognition Complex ; Protein Structure, Tertiary/genetics ; Replication Origin/*genetics ; Replicon/genetics ; Restriction Mapping ; Saccharomyces cerevisiae Proteins/genetics ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Sulfolobus acidocaldarius/genetics ; Sulfolobus solfataricus/genetics ; }, abstract = {In all three domains of life, DNA replication begins at specialized loci termed replication origins. In bacteria, replication initiates from a single, clearly defined site. In contrast, eukaryotic organisms exploit a multitude of replication origins, dividing their genomes into an array of short contiguous units. Recently, the multiple replication origin paradigm has also been demonstrated within the archaeal domain of life, with the discovery that the hyperthermophilic archaeon Sulfolobus has three replication origins. However, the evolutionary mechanism driving the progression from single to multiple origin usage remains unclear. Here, we demonstrate that Aeropyrum pernix, a distant relative of Sulfolobus, has two origins. Comparison with the Sulfolobus origins provides evidence for evolution of replicon complexity by capture of extrachromosomal genetic elements. We additionally identify a previously unrecognized candidate archaeal initiator protein that is distantly related to eukaryotic Cdt1. Our data thus provide evidence that horizontal gene transfer, in addition to its well-established role in contributing to the information content of chromosomes, may fundamentally alter the manner in which the host chromosome is replicated.}, }
@article {pmid17384307, year = {2007}, author = {Kenzaka, T and Tani, K and Sakotani, A and Yamaguchi, N and Nasu, M}, title = {High-frequency phage-mediated gene transfer among Escherichia coli cells, determined at the single-cell level.}, journal = {Applied and environmental microbiology}, volume = {73}, number = {10}, pages = {3291-3299}, pmid = {17384307}, issn = {0099-2240}, mesh = {Ampicillin Resistance/genetics ; Bacteriophage P1/genetics/physiology ; Bacteriophage T4/genetics/physiology ; Base Sequence ; Coliphages/*genetics/physiology ; Colony Count, Microbial ; DNA, Viral/chemistry/genetics ; Escherichia coli/*genetics/physiology/*virology ; *Gene Transfer, Horizontal ; Genetic Vectors ; In Situ Hybridization, Fluorescence/methods ; Microbial Viability ; Molecular Sequence Data ; Sequence Analysis ; *Transduction, Genetic ; Viral Plaque Assay ; }, abstract = {Recent whole-genome analysis suggests that lateral gene transfer by bacteriophages has contributed significantly to the genetic diversity of bacteria. To accurately determine the frequency of phage-mediated gene transfer, we employed cycling primed in situ amplification-fluorescent in situ hybridization (CPRINS-FISH) and investigated the movement of the ampicillin resistance gene among Escherichia coli cells mediated by phage at the single-cell level. Phages P1 and T4 and the newly isolated E. coli phage EC10 were used as vectors. The transduction frequencies determined by conventional plating were 3x10(-8) to 2x10(-6), 1x10(-8) to 4x10(-8), and <4x10(-9) to 4x10(-8) per PFU for phages P1, T4, and EC10, respectively. The frequencies of DNA transfer determined by CPRINS-FISH were 7x10(-4) to 1x10(-3), 9x10(-4) to 3x10(-3), and 5x10(-4) to 4x10(-3) for phages P1, T4, and EC10, respectively. Direct viable counting combined with CPRINS-FISH revealed that more than 20% of the cells carrying the transferred gene retained their viabilities. These results revealed that the difference in the number of viable cells carrying the transferred gene and the number of cells capable of growth on the selective medium was 3 to 4 orders of magnitude, indicating that phage-mediated exchange of DNA sequences among bacteria occurs with unexpectedly high frequency.}, }
@article {pmid17384186, year = {2007}, author = {Holt, KE and Thomson, NR and Wain, J and Phan, MD and Nair, S and Hasan, R and Bhutta, ZA and Quail, MA and Norbertczak, H and Walker, D and Dougan, G and Parkhill, J}, title = {Multidrug-resistant Salmonella enterica serovar paratyphi A harbors IncHI1 plasmids similar to those found in serovar typhi.}, journal = {Journal of bacteriology}, volume = {189}, number = {11}, pages = {4257-4264}, pmid = {17384186}, issn = {0021-9193}, support = {/WT_/Wellcome Trust/United Kingdom ; G0600805/MRC_/Medical Research Council/United Kingdom ; }, mesh = {DNA Transposable Elements/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Order ; Gene Transfer, Horizontal/genetics ; Models, Genetic ; Molecular Sequence Data ; Plasmids/chemistry/*genetics ; Polymerase Chain Reaction ; Salmonella paratyphi A/*genetics ; Salmonella typhi/*genetics ; Sequence Analysis, DNA ; }, abstract = {Salmonella enterica serovars Typhi and Paratyphi A cause systemic infections in humans which are referred to as enteric fever. Multidrug-resistant (MDR) serovar Typhi isolates emerged in the 1980s, and in recent years MDR serovar Paratyphi A infections have become established as a significant problem across Asia. MDR in serovar Typhi is almost invariably associated with IncHI1 plasmids, but the genetic basis of MDR in serovar Paratyphi A has remained predominantly undefined. The DNA sequence of an IncHI1 plasmid, pAKU_1, encoding MDR in a serovar Paratyphi A strain has been determined. Significantly, this plasmid shares a common IncHI1-associated DNA backbone with the serovar Typhi plasmid pHCM1 and an S. enterica serovar Typhimurium plasmid pR27. Plasmids pAKU_1 and pHCM1 share 14 antibiotic resistance genes encoded within similar mobile elements, which appear to form a 24-kb composite transposon that has transferred as a single unit into different positions into their IncHI1 backbones. Thus, these plasmids have acquired similar antibiotic resistance genes independently via the horizontal transfer of mobile DNA elements. Furthermore, two IncHI1 plasmids from a Vietnamese isolate of serovar Typhi were found to contain features of the backbone sequence of pAKU_1 rather than pHCM1, with the composite transposon inserted in the same location as in the pAKU_1 sequence. Our data show that these serovar Typhi and Paratyphi A IncHI1 plasmids share highly conserved core DNA and have acquired similar mobile elements encoding antibiotic resistance genes in past decades.}, }
@article {pmid17383832, year = {2007}, author = {Makiuchi, T and Nara, T and Annoura, T and Hashimoto, T and Aoki, T}, title = {Occurrence of multiple, independent gene fusion events for the fifth and sixth enzymes of pyrimidine biosynthesis in different eukaryotic groups.}, journal = {Gene}, volume = {394}, number = {1-2}, pages = {78-86}, doi = {10.1016/j.gene.2007.02.009}, pmid = {17383832}, issn = {0378-1119}, mesh = {Animals ; Cloning, Molecular ; Cyanobacteria/genetics/metabolism ; DNA, Algal/genetics ; DNA, Complementary/genetics ; DNA, Protozoan/genetics ; Euglena gracilis/*genetics/*metabolism ; Evolution, Molecular ; *Gene Fusion ; Gene Transfer, Horizontal ; Genes, Protozoan ; Kinetoplastida/*genetics/*metabolism ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Pyrimidines/*biosynthesis ; Species Specificity ; }, abstract = {The genes encoding orotate phosphoribosyltransferase (OPRT) and orotidine-5'-monophosphate decarboxylase (OMPDC), the fifth and sixth enzymes in the de novo pyrimidine biosynthetic pathway, are fused as OPRT-OMPDC in most eukaryotic groups. On the other hand, the inversely linked OMPDC-OPRT fusion is present in trypanosomatids, belonging to kinetoplastids together with bodonids in a supergroup, Euglenozoa. Here, we show the presence of OMPDC-OPRT in the bodonid, Bodo caudatus, while OPRT-OMPDC in Euglena gracilis, another euglenozoan species belonging to euglenoids. These results suggest that the OMPDC-OPRT fusion event occurred in a common ancestor of kinetoplastids. Genome sequence database searches further revealed the presence of OMPDC-OPRT in stramenopiles and cyanobacteria. Phylogenetic reconstruction of OPRT and OMPDC rejected statistically the monophyly of the OPRT domains of stramenopile and kinetoplastid OMPDC-OPRT, demonstrating that these gene fusions do not share a common evolutionary origin, despite the identical gene order. Thus, the OMPDC-OPRT fusion is likely to have emerged independently in these eukaryotic groups. Phylogenetic analyses also suggested that cyanobacterial OMPDC-OPRT arose via lateral transfer. We conclude that gene fusion events occur more frequently than previously thought and that lateral gene transfer has made a marked contribution to establishment of the rearranged structure of OPRT and OMPDC genes in eukaryotes.}, }
@article {pmid17382590, year = {2007}, author = {Lehmacher, A and Bockemühl, J}, title = {L-Sorbose utilization by virulent Escherichia coli and Shigella: different metabolic adaptation of pathotypes.}, journal = {International journal of medical microbiology : IJMM}, volume = {297}, number = {4}, pages = {245-254}, doi = {10.1016/j.ijmm.2007.01.007}, pmid = {17382590}, issn = {1438-4221}, mesh = {Adaptation, Physiological ; Escherichia coli/classification/genetics/*metabolism ; Feces/microbiology ; Humans ; Klebsiella pneumoniae/genetics/metabolism ; Operon ; Shigella/genetics/*metabolism ; Sorbose/*metabolism ; Transcription, Genetic ; }, abstract = {The frequency of L-Sorbose utilization differs significantly between pathotypes of Escherichia coli and Shigella from 93% to 0%. Among 266 strains tested, this frequency increased in the order Shigella, enterotoxigenic E. coli (ETEC), enteroinvasive E. coli (EIEC), Shiga toxin-producing E. coli (STEC), enteroaggregative E. coli, enteropathogenic E. coli (EPEC), and neonatal bacterial meningitis (NBM) E. coli. This suggests an association of pathomechanism with the capability to degrade L-Sorbose. The use of a selective agar, containing L-Sorbose and antibiotics, facilitated the isolation of L-Sorbose-non-utilizing ETEC from stool specimens of patients. The sor operon, comprising seven genes in the order sorCDFBAME, confers L-Sorbose utilization. Surprisingly, L-Sorbose-non-degrading Shigella harbored all genes of the sor operon indicating L-Sorbose-utilizing E. coli as ancestor. Additionally, strains of several EIEC and STEC serotypes harbored an inactivated sor operon. These L-Sorbose-non-utilizing Shigella, EIEC, and STEC showed significantly reduced amounts of transcripts as examined for sorC and sorD. Common surface antigens, types of intimin gene, and hemolysin gene as well as use of L-Sorbose suggested the relatedness of attaching and effacing O26:H11 and O55:H7 EPEC and STEC, respectively. pepE and yibC genes flank the sor operon of E. coli and Shigella strains. Surprisingly, one O7:K1:H- NBM E. coli harbored an aroE-homologous gene between its sor operon and pepE as in Klebsiella pneumoniae suggesting a horizontal gene transfer. In conclusion, L-Sorbose utilization of virulent E. coli and Shigella is characterized by different adaptation that represents a valuable tool for evolutionary and diagnostic analysis of related patho- and serotypes.}, }
@article {pmid17380051, year = {2007}, author = {Pagamjav, O and Yamada, S and Ibrahim, el-SM and Crandell, RA and Matsumura, T and Yamaguchi, T and Fukushi, H}, title = {Molecular characterization of equine herpesvirus 1 (EHV-1) isolated from cattle indicating no specific mutations associated with the interspecies transmission.}, journal = {Microbiology and immunology}, volume = {51}, number = {3}, pages = {313-319}, doi = {10.1111/j.1348-0421.2007.tb03913.x}, pmid = {17380051}, issn = {0385-5600}, mesh = {Animals ; Base Sequence ; Cattle ; Cattle Diseases/transmission/*virology ; Cricetinae ; DNA Fingerprinting ; Gene Transfer, Horizontal ; Herpesviridae Infections/transmission/*virology ; Herpesvirus 1, Equid/*genetics/isolation &amp; purification/pathogenicity ; Horses ; Molecular Sequence Data ; *Mutation ; Polymerase Chain Reaction/methods ; Polymorphism, Restriction Fragment Length ; Virulence ; }, abstract = {Interspecies trasmission of equine herpesvirus 1 (EHV-1) from horse to cattle was shown by Crandell et al. (1988). Specific mutations related to the transmission were studied by comparison of five EHV-1 isolates in cattle (BH1247, 3M20-3, G118, G1753, and 9BSV4) using polymerase chain reaction and restriction fragment length polymorphism analysis with added sequencing. G118 and 3M20-3 were the genome type EHV-1 P, while G1753 was the genome type EHV-1 B. BH1247 and 9BSV4 might be other genome types. We could not identify specific mutations related to the interspecies transmission.}, }
@article {pmid17376230, year = {2007}, author = {Poptsova, MS and Gogarten, JP}, title = {The power of phylogenetic approaches to detect horizontally transferred genes.}, journal = {BMC evolutionary biology}, volume = {7}, number = {}, pages = {45}, pmid = {17376230}, issn = {1471-2148}, mesh = {Classification/*methods ; Cluster Analysis ; Computational Biology ; Gammaproteobacteria/*genetics ; Gene Transfer, Horizontal/*genetics ; *Genome, Bacterial ; Likelihood Functions ; Models, Genetic ; Multigene Family/*genetics ; *Phylogeny ; }, abstract = {BACKGROUND: Horizontal gene transfer plays an important role in evolution because it sometimes allows recipient lineages to adapt to new ecological niches. High genes transfer frequencies were inferred for prokaryotic and early eukaryotic evolution. Does horizontal gene transfer also impact phylogenetic reconstruction of the evolutionary history of genomes and organisms? The answer to this question depends at least in part on the actual gene transfer frequencies and on the ability to weed out transferred genes from further analyses. Are the detected transfers mainly false positives, or are they the tip of an iceberg of many transfer events most of which go undetected by current methods?<br><br>RESULTS: Phylogenetic detection methods appear to be the method of choice to infer gene transfers, especially for ancient transfers and those followed by orthologous replacement. Here we explore how well some of these methods perform using in silico transfers between the terminal branches of a gamma proteobacterial, genome based phylogeny. For the experiments performed here on average the AU test at a 5% significance level detects 90.3% of the transfers and 91% of the exchanges as significant. Using the Robinson-Foulds distance only 57.7% of the exchanges and 60% of the donations were identified as significant. Analyses using bipartition spectra appeared most successful in our test case. The power of detection was on average 97% using a 70% cut-off and 94.2% with 90% cut-off for identifying conflicting bipartitions, while the rate of false positives was below 4.2% and 2.1% for the two cut-offs, respectively. For all methods the detection rates improved when more intervening branches separated donor and recipient.<br><br>CONCLUSION: Rates of detected transfers should not be mistaken for the actual transfer rates; most analyses of gene transfers remain anecdotal. The method and significance level to identify potential gene transfer events represent a trade-off between the frequency of erroneous identification (false positives) and the power to detect actual transfer events.}, }
@article {pmid17374878, year = {2007}, author = {Linz, S and Radtke, A and von Haeseler, A}, title = {A likelihood framework to measure horizontal gene transfer.}, journal = {Molecular biology and evolution}, volume = {24}, number = {6}, pages = {1312-1319}, doi = {10.1093/molbev/msm052}, pmid = {17374878}, issn = {0737-4038}, mesh = {Bacteria/genetics ; Computational Biology/methods ; *Computer Simulation ; Fungi/genetics ; *Gene Transfer, Horizontal ; Likelihood Functions ; *Models, Genetic ; }, abstract = {We suggest a likelihood-based approach to estimate an overall rate of horizontal gene transfer (HGT) in a simplified setting. To this end, we assume that the number of occurring HGT events within a given time interval follows a Poisson process. To obtain estimates for the rate of HGT, we simulate the distribution of tree topologies for different numbers of HGT events on a clocklike species tree. Using these simulated distributions, we estimate an HGT rate for a collection of gene trees representing a set of taxa. As an illustrative example, we use the "Clusters of Orthologous Groups of proteins" (COGs). We also perform a correction of the estimated rate taking into account the inaccuracies due to gene tree reconstructions. The results suggest a corrected HGT rate of about 0.36 per gene and unit time, in other words 11 HGT events have occurred on average among the 44 taxa of the COG species tree. A software package to estimate an HGT rate is available online (http://www.cibiv.at/software/hgt/).}, }
@article {pmid17374555, year = {2007}, author = {Tysnes, BB and Bjerkvig, R}, title = {Cancer initiation and progression: involvement of stem cells and the microenvironment.}, journal = {Biochimica et biophysica acta}, volume = {1775}, number = {2}, pages = {283-297}, doi = {10.1016/j.bbcan.2007.01.001}, pmid = {17374555}, issn = {0006-3002}, mesh = {Antigens, CD/physiology ; Cell Division ; Cell Fusion ; Centrosome/physiology ; Disease Progression ; Gene Transfer Techniques ; Genomic Instability ; Humans ; Neoplasms/*genetics/pathology/*physiopathology ; Stem Cells/*physiology ; }, abstract = {The molecular events that lead to the cancer-initiating cell involve critical mutations in genes regulating normal cell growth and differentiation. Cancer stem cells, or cancer initiating cells have been described in the context of acute myeloid leukemia, breast, brain, bone, lung, melanoma and prostate. These cells have been shown to be critical in tumor development and should harbor the mutations needed to initiate a tumor. The origin of the cancer stem cells is not clear. They may be derived from stem cell pools, progenitor cells or differentiated cells that undergo trans-differentiation processes. It has been suggested that cell fusion and/or horizontal gene transfer events, which may occur in tissue repair processes, also might play an important role in tumor initiation and progression. Fusion between somatic cells that have undergone a set of specific mutations and normal stem cells might explain the extensive chromosomal derangements seen in early tumors. Centrosome deregulation can be an integrating factor in many of the mechanisms involved in tumor development. The regulation of the balance between cell renewal and cell death is critical in cancer. Increased knowledge of developmental aspects in relation to self-renewal and differentiation, both under normal and deregulated conditions, will probably shed more light on the mechanisms that lead to tumor initiation and progression.}, }
@article {pmid17373739, year = {2007}, author = {Chen, XB and Li, YX and Jiao, Y and Dong, WP and Li, G and Chen, J and Tan, JM}, title = {Influence of heme oxygenase-1 gene transfer on the viability and function of rat islets in in vitro culture.}, journal = {World journal of gastroenterology}, volume = {13}, number = {7}, pages = {1053-1059}, pmid = {17373739}, issn = {1007-9327}, mesh = {Adenoviridae/genetics ; Animals ; Cell Survival/*physiology ; Cells, Cultured ; Dose-Response Relationship, Drug ; Gene Expression Regulation, Enzymologic/physiology ; Gene Transfer, Horizontal/*physiology ; Glucose/pharmacology ; Heme Oxygenase-1/*genetics/physiology ; Insulin/metabolism ; Islets of Langerhans/cytology/*enzymology/*physiology ; Islets of Langerhans Transplantation ; Male ; Rats ; Rats, Sprague-Dawley ; Transfection ; }, abstract = {AIM: To investigate the influence of heme oxygenase-1 (HO-1) gene transfer on the viability and function of cultured rat islets in vitro.<br><br>METHODS: Islets were isolated from the pancreata of Sprague-Dawley rats by intraductal collagenase digestion, and purified by discontinuous Ficoll density gradient centrifugation. Purified rat islets were transfected with adenoviral vectors containing human HO-1 gene (Ad-HO-1) or enhanced green fluorescent protein gene (Ad-EGFP), and then cultured for seven days. Transfection was confirmed by fluorescence microscopy and Western blot. Islet viability was evaluated by acridine orange/propidium iodide fluorescent staining. Glucose-stimulated insulin release was detected using insulin radioimmunoassay kits and was used to assess the function of islets. Stimulation index (SI) was calculated by dividing the insulin release upon high glucose stimulation by the insulin release upon low glucose stimulation.<br><br>RESULTS: After seven days culture, the viability of cultured rat islets decreased significantly (92% +/- 6% vs 52% +/- 13%, P < 0.05), and glucose-stimulated insulin release also decreased significantly (6.47 +/- 0.55 mIU/L/30IEQ vs 4.57 +/- 0.40 mIU/L/30IEQ, 14.93 +/- 1.17 mIU/L/30IEQ vs 9.63 +/- 0.71 mIU/L/30IEQ, P < 0.05). Transfection of rat islets with adenoviral vectors at an MOI of 20 was efficient, and did not impair islet function. At 7 d post-transfection, the viability of Ad-HO-1 transfected islets was higher than that of control islets (71% +/- 15% vs 52% +/- 13%, P < 0.05). There was no significant difference in insulin release upon low glucose stimulation (2.8 mmol/L) among Ad-HO-1 transfected group, Ad-EGFP transfected group, and control group (P > 0.05), while when stimulated by high glucose (16.7 mmol/L) solution, insulin release in Ad-HO-1 transfected group was significantly higher than that in Ad-EGFP transfected group and control group, respectively (12.50 +/- 2.17 mIU/L/30IEQ vs 8.87 +/- 0.65 mIU/L/30IEQ; 12.50 +/- 2.17 mIU/L/30IEQ vs 9.63 +/- 0.71 mIU/L/30IEQ, P < 0.05). The SI of Ad-HO-1 transfected group was also significantly higher than that of Ad-EGFP transfected group and control group, respectively (2.21 +/- 0.02 vs 2.08 +/- 0.05; 2.21 +/- 0.02 vs 2.11 +/- 0.03, P < 0.05).<br><br>CONCLUSION: The viability and function of rat islets decrease over time in in vitro culture, and heme oxygenase-1 gene transfer could improve the viability and function of cultured rat islets.}, }
@article {pmid17372223, year = {2007}, author = {Cosentino Lagomarsino, M and Jona, P and Bassetti, B and Isambert, H}, title = {Hierarchy and feedback in the evolution of the Escherichia coli transcription network.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {13}, pages = {5516-5520}, pmid = {17372223}, issn = {0027-8424}, mesh = {Binding Sites ; DNA/chemistry ; Data Interpretation, Statistical ; Escherichia coli/*metabolism ; Escherichia coli Proteins/*physiology ; Evolution, Molecular ; *Feedback, Physiological ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Models, Biological ; Models, Genetic ; Monte Carlo Method ; Protein Structure, Tertiary ; Transcription Factors/metabolism ; *Transcription, Genetic ; }, abstract = {The Escherichia coli transcription network has an essentially feedforward structure, with abundant feedback at the level of self-regulations. Here, we investigate how these properties emerged during evolution. An assessment of the role of gene duplication based on protein domain architecture shows that (i) transcriptional autoregulators have mostly arisen through duplication, whereas (ii) the expected feedback loops stemming from their initial cross-regulation are strongly selected against. This requires a divergent coevolution of the transcription factor DNA-binding sites and their respective DNA cis-regulatory regions. Moreover, we find that the network tends to grow by expansion of the existing hierarchical layers of computation, rather than by addition of new layers. We also argue that rewiring of regulatory links due to mutation/selection of novel transcription factor/DNA binding interactions appears not to significantly affect the network global hierarchy, and that horizontally transferred genes are mainly added at the bottom, as new target nodes. These findings highlight the important evolutionary roles of both duplication and selective deletion of cross-talks between autoregulators in the emergence of the hierarchical transcription network of E. coli.}, }
@article {pmid17372221, year = {2007}, author = {Martinez, A and Bradley, AS and Waldbauer, JR and Summons, RE and DeLong, EF}, title = {Proteorhodopsin photosystem gene expression enables photophosphorylation in a heterologous host.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {13}, pages = {5590-5595}, pmid = {17372221}, issn = {0027-8424}, mesh = {Adenosine Triphosphate/chemistry ; Archaeal Proteins/chemistry ; Bacterial Proteins/chemistry ; Cell Membrane/metabolism ; Escherichia coli/metabolism ; *Gene Expression Regulation, Plant ; Gene Library ; Gene Transfer, Horizontal ; Light ; Models, Chemical ; Models, Genetic ; Molecular Sequence Data ; Phosphorylation ; Photosynthetic Reaction Center Complex Proteins ; Rhodopsin/*genetics ; Rhodopsins, Microbial ; }, abstract = {Proteorhodopsins (PRs) are retinal-containing proteins that catalyze light-activated proton efflux across the cell membrane. These photoproteins are known to be globally distributed in the ocean's photic zone, and they are found in a diverse array of Bacteria and Archaea. Recently, light-enhanced growth rates and yields have been reported in at least one PR-containing marine bacterium, but the physiological basis of light-activated growth stimulation has not yet been determined. To describe more fully PR photosystem genetics and biochemistry, we functionally surveyed a marine picoplankton large-insert genomic library for recombinant clones expressing PR photosystems in vivo. Our screening approach exploited transient increases in vector copy number that significantly enhanced the sensitivity of phenotypic detection. Two genetically distinct recombinants, initially identified by their orange pigmentation, expressed a small cluster of genes encoding a complete PR-based photosystem. Genetic and biochemical analyses of transposon mutants verified the function of gene products in the photopigment and opsin biosynthetic pathways. Heterologous expression of six genes, five encoding photopigment biosynthetic proteins and one encoding a PR, generated a fully functional PR photosystem that enabled photophosphorylation in recombinant Escherichia coli cells exposed to light. Our results demonstrate that a single genetic event can result in the acquisition of phototrophic capabilities in an otherwise chemoorganotrophic microorganism, and they explain in part the ubiquity of PR photosystems among diverse microbial taxa.}, }
@article {pmid17371826, year = {2007}, author = {Sung, JM and Lindsay, JA}, title = {Staphylococcus aureus strains that are hypersusceptible to resistance gene transfer from enterococci.}, journal = {Antimicrobial agents and chemotherapy}, volume = {51}, number = {6}, pages = {2189-2191}, pmid = {17371826}, issn = {0066-4804}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Cattle ; *Conjugation, Genetic ; Deoxyribonucleases, Type II Site-Specific/genetics ; Enterococcus/drug effects/*genetics ; Female ; *Gene Transfer, Horizontal ; Humans ; Mastitis, Bovine/microbiology ; Molecular Sequence Data ; Mutation ; Sequence Analysis, DNA ; Staphylococcal Infections/microbiology/veterinary ; Staphylococcus aureus/*drug effects/*genetics/isolation &amp; purification ; Vancomycin Resistance/*genetics ; }, abstract = {We identified naturally occurring Staphylococcus aureus mutants of the restriction modification pathway SauI, including bovine lineage ST151. In a model of vancomycin resistance transfer from Enterococcus faecalis, ST151 isolates are 500 times more susceptible than human S. aureus isolates. The eradication of "hyperrecipient" strains may reduce the evolution of vancomycin-resistant S. aureus.}, }
@article {pmid17368985, year = {2007}, author = {Teich, R and Zauner, S and Baurain, D and Brinkmann, H and Petersen, J}, title = {Origin and distribution of Calvin cycle fructose and sedoheptulose bisphosphatases in plantae and complex algae: a single secondary origin of complex red plastids and subsequent propagation via tertiary endosymbioses.}, journal = {Protist}, volume = {158}, number = {3}, pages = {263-276}, doi = {10.1016/j.protis.2006.12.004}, pmid = {17368985}, issn = {1434-4610}, mesh = {Algal Proteins/*genetics ; Animals ; Apicomplexa/genetics ; Ascomycota/genetics ; Ciliophora/genetics ; DNA, Algal/genetics ; DNA, Plant/genetics ; Diatoms/genetics ; Dinoflagellida/genetics ; Emigration and Immigration ; Eukaryota/*enzymology/genetics/physiology ; Evolution, Molecular ; Fructose-Bisphosphatase/*genetics ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Phosphoric Monoester Hydrolases/*genetics ; Phylogeny ; Plant Physiological Phenomena ; Plant Proteins/*genetics ; Plants/*enzymology/genetics ; Plastids/genetics ; Sequence Analysis, DNA ; Sequence Homology ; Symbiosis ; Trypanosoma/genetics ; }, abstract = {Sedoheptulose-1,7-bisphosphatase (SBPase) and fructose-1,6-bisphosphatase (FBPase) are essential nuclear-encoded enzymes involved in land plant Calvin cycle and gluconeogenesis. In this study, we cloned seven SBP and seven FBP cDNAs/genes and established sequences from all lineages of photosynthetic eukaryotes, in order to investigate their origin and evolution. Our data are best explained by a single recruitment of plastid-targeted SBP in Plantae after primary endosymbiosis and a further distribution to algae with complex plastids. While SBP is universally found in photosynthetic lineages, its presence in apicomplexa, ciliates, trypanosomes, and ascomycetes is surprising given that no metabolic function beyond the one in the plastid Calvin cycle is described so far. Sequences of haptophytes, cryptophytes, diatoms, and peridinin-containing dinoflagellates (complex red lineage) strongly group together in the SBP tree and the same assemblage is recovered for plastid-targeted FBP sequences, although this is less supported. Both SBP and plastid-targeted FBP are most likely of red algal origin. Including phosphoribulokinase, fructose bisphosphate aldolase, and glyceraldehyde-3-phosphate dehydrogenase, a total of five independent plastid-related nuclear-encoded markers support a common origin of all complex rhodoplasts via a single secondary endosymbiosis event. However, plastid phylogenies are incongruent with those of the host cell, as illustrated by the cytosolic FBP isoenzyme. These results are discussed in the context of Cavalier-Smith's far-reaching chromalveolate hypothesis. In our opinion, a more plausible evolutionary scenario would be the establishment of a unique secondary rhodoplast and its subsequent spread via tertiary endosymbioses.}, }
@article {pmid17366137, year = {2007}, author = {Holland, B and Conner, G and Huber, K and Moulton, V}, title = {Imputing supertrees and supernetworks from quartets.}, journal = {Systematic biology}, volume = {56}, number = {1}, pages = {57-67}, doi = {10.1080/10635150601167013}, pmid = {17366137}, issn = {1063-5157}, mesh = {*Algorithms ; Classification/*methods ; Computer Simulation ; *Evolution, Molecular ; *Models, Genetic ; *Phylogeny ; }, abstract = {Inferring species phylogenies is an important part of understanding molecular evolution. Even so, it is well known that an accurate phylogenetic tree reconstruction for a single gene does not always necessarily correspond to the species phylogeny. One commonly accepted strategy to cope with this problem is to sequence many genes; the way in which to analyze the resulting collection of genes is somewhat more contentious. Supermatrix and supertree methods can be used, although these can suppress conflicts arising from true differences in the gene trees caused by processes such as lineage sorting, horizontal gene transfer, or gene duplication and loss. In 2004, Huson et al. (IEEE/ACM Trans. Comput. Biol. Bioinformatics 1:151-158) presented the Z-closure method that can circumvent this problem by generating a supernetwork as opposed to a supertree. Here we present an alternative way for generating supernetworks called Q-imputation. In particular, we describe a method that uses quartet information to add missing taxa into gene trees. The resulting trees are subsequently used to generate consensus networks, networks that generalize strict and majority-rule consensus trees. Through simulations and application to real data sets, we compare Q-imputation to the matrix representation with parsimony (MRP) supertree method and Z-closure, and demonstrate that it provides a useful complementary tool.}, }
@article {pmid17361157, year = {2007}, author = {Cavalier-Smith, T}, title = {Concept of a bacterium still valid in prokaryote debate.}, journal = {Nature}, volume = {446}, number = {7133}, pages = {257}, doi = {10.1038/446257c}, pmid = {17361157}, issn = {1476-4687}, mesh = {Bacteria/*classification/cytology/genetics ; *Classification ; Evolution, Molecular ; Gene Transfer, Horizontal ; Prokaryotic Cells/*classification/cytology ; Reproducibility of Results ; Species Specificity ; *Terminology as Topic ; }, }
@article {pmid17360551, year = {2007}, author = {Choi, IG and Kim, SH}, title = {Global extent of horizontal gene transfer.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {11}, pages = {4489-4494}, pmid = {17360551}, issn = {0027-8424}, support = {P50 GM062412/GM/NIGMS NIH HHS/United States ; GM 62412/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Computational Biology/methods ; Databases, Protein ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genetic Techniques ; Genome ; Humans ; Phylogeny ; Protein Structure, Tertiary ; Proteins/chemistry ; Proteomics/methods ; RNA, Ribosomal/chemistry ; }, abstract = {Horizontal gene transfer (HGT) is thought to play an important role in the evolution of species and innovation of genomes. There have been many convincing evidences for HGT for specific genes or gene families, but there has been no estimate of the global extent of HGT. Here, we present a method of identifying HGT events within a given protein family and estimate the global extent of HGT in all curated protein domain families (approximately 8,000) listed in the Pfam database. The results suggest four conclusions: (i) for all protein domain families in Pfam, the fixation of genes horizontally transferred is not a rampant phenomenon between organisms with substantial phylogenetic separations (1.1-9.7% of Pfam families surveyed at three taxonomic ranges studied show indication of HGT); (ii) however, at the level of domains, >50% of Archaea have one or more protein domains acquired by HGT, and nearly 30-50% of Bacteria did the same when examined at three taxonomic ranges. But, the equivalent value for Eukarya is <10%; (iii) HGT will have very little impact in the construction of organism phylogeny, when the construction methods use whole genomes, large numbers of common genes, or SSU rRNAs; and (iv) there appears to be no strong preference of HGT for protein families of particular cellular or molecular functions.}, }
@article {pmid17360276, year = {2007}, author = {Dunny, GM}, title = {The peptide pheromone-inducible conjugation system of Enterococcus faecalis plasmid pCF10: cell-cell signalling, gene transfer, complexity and evolution.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {362}, number = {1483}, pages = {1185-1193}, pmid = {17360276}, issn = {0962-8436}, support = {R01 GM049530/GM/NIGMS NIH HHS/United States ; R01 HL051987/HL/NHLBI NIH HHS/United States ; GM49530/GM/NIGMS NIH HHS/United States ; HL51987/HL/NHLBI NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/*physiology ; Conjugation, Genetic/genetics/*physiology ; Enterococcus faecalis/genetics/*physiology ; Gene Expression Regulation, Bacterial/physiology ; Gene Transfer, Horizontal/genetics/physiology ; Pheromones/genetics/*physiology ; Plasmids/genetics ; Protein Sorting Signals/genetics/*physiology ; Quorum Sensing/genetics/*physiology ; Signal Transduction/genetics/physiology ; }, abstract = {Expression of a large set of gene products required for conjugative transfer of the antibiotic resistance plasmid pCF10 is controlled by cell-cell communication between plasmid-free recipient cells and plasmid-carrying donor cells using a peptide mating pheromone cCF10. Most of the recent experimental analysis of this system has focused on the molecular events involved in initiation of the pheromone response in the donor cells, and on the mechanisms by which the donor cells control self-induction by endogenously produced pheromone. Recently, studies of the molecular machinery of conjugation encoded by the pheromone-inducible genes have been initiated. In addition, the system may serve as a useful bacterial model for addressing the evolution of biological complexity.}, }
@article {pmid17359548, year = {2007}, author = {Gao, L and Qi, J}, title = {Whole genome molecular phylogeny of large dsDNA viruses using composition vector method.}, journal = {BMC evolutionary biology}, volume = {7}, number = {}, pages = {41}, pmid = {17359548}, issn = {1471-2148}, mesh = {Baculoviridae/genetics ; DNA Viruses/*genetics ; DNA, Viral/*genetics ; *Evolution, Molecular ; Gene Duplication ; *Genome, Viral ; Herpesviridae/genetics ; *Phylogeny ; Poxviridae/genetics ; }, abstract = {BACKGROUND: One important mechanism by which large DNA viruses increase their genome size is the addition of modules acquired from other viruses, host genomes or gene duplications. Phylogenetic analysis of large DNA viruses, especially using methods based on alignment, is often difficult due to the presence of horizontal gene transfer events. The recent composition vector approach, not sensitive to such events, is applied here to reconstruct the phylogeny of 124 large DNA viruses.<br><br>RESULTS: The results are mostly consistent with the biologist's systematics with only a few outliers and can also provide some information for those unclassified viruses and cladistic relationships of several families.<br><br>CONCLUSION: With composition vector approach we obtained the phylogenetic tree of large DNA viruses, which not only give results comparable to biologist's systematics but also provide a new way for recovering the phylogeny of viruses.}, }
@article {pmid17359257, year = {2007}, author = {McCarren, J and DeLong, EF}, title = {Proteorhodopsin photosystem gene clusters exhibit co-evolutionary trends and shared ancestry among diverse marine microbial phyla.}, journal = {Environmental microbiology}, volume = {9}, number = {4}, pages = {846-858}, doi = {10.1111/j.1462-2920.2006.01203.x}, pmid = {17359257}, issn = {1462-2912}, mesh = {Bacteria/*classification/genetics ; Carotenoids/classification/genetics/*metabolism ; Classification ; Evolution, Molecular ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; Phytoplankton/*classification/genetics ; Rhodopsin/classification/*genetics/metabolism ; Rhodopsins, Microbial ; Seawater/*microbiology ; }, abstract = {Since the recent discovery of retinylidene proteins in marine bacteria (proteorhodopsins), the estimated abundance and diversity of this gene family has expanded rapidly. To explore proteorhodopsin photosystem evolutionary and distributional trends, we identified and compared 16 different proteorhodopsin-containing genome fragments recovered from naturally occurring bacterioplankton populations. In addition to finding several deep-branching proteorhodopsin sequences, proteorhodopsins were found in novel taxonomic contexts, including a betaproteobacterium and a planctomycete. Approximately one-third of the proteorhodopsin-containing genome fragments analysed, as well as a number of recently reported marine bacterial whole genome sequences, contained a linked set of genes required for biosynthesis of the rhodopsin chromophore, retinal. Phylogenetic analyses of the retinal biosynthetic genes suggested their co-evolution and probable coordinated lateral gene transfer into disparate lineages, including Euryarchaeota, Planctomycetales, and three different proteobacterial lineages. The lateral transfer and retention of genes required to assemble a functional proteorhodopsin photosystem appears to be a coordinated and relatively frequent evolutionary event. Strong selection pressure apparently acts to preserve these light-dependent photosystems in diverse marine microbial lineages.}, }
@article {pmid17358903, year = {2007}, author = {Park, JM and Deem, MW}, title = {Phase diagrams of quasispecies theory with recombination and horizontal gene transfer.}, journal = {Physical review letters}, volume = {98}, number = {5}, pages = {058101}, doi = {10.1103/PhysRevLett.98.058101}, pmid = {17358903}, issn = {0031-9007}, mesh = {Biological Evolution ; Biophysical Phenomena ; Biophysics ; *Gene Transfer, Horizontal ; *Models, Genetic ; Models, Statistical ; Mutation ; *Recombination, Genetic ; }, abstract = {We consider how transfer of genetic information between individuals influences the phase diagram and mean fitness of both the Eigen and the parallel, or Crow-Kimura, models of evolution. In the absence of genetic transfer, these physical models of evolution consider the replication and point mutation of the genomes of independent individuals in a large population. A phase transition occurs, such that below a critical mutation rate an identifiable quasispecies forms. We show how transfer of genetic information changes the phase diagram and mean fitness and introduces metastability in quasispecies theory, via an analytic field theoretic mapping.}, }
@article {pmid17355641, year = {2007}, author = {Serwer, P}, title = {Evolution and the complexity of bacteriophages.}, journal = {Virology journal}, volume = {4}, number = {}, pages = {30}, pmid = {17355641}, issn = {1743-422X}, support = {R01 GM024365/GM/NIGMS NIH HHS/United States ; GM24365/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteriophage T3/*genetics/metabolism ; Bacteriophage T7/*genetics/metabolism ; *Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; Genome, Viral ; Models, Genetic ; Prokaryotic Cells/*virology ; *Selection, Genetic ; Viral Proteins/*genetics/metabolism ; }, abstract = {BACKGROUND: The genomes of both long-genome (> 200 Kb) bacteriophages and long-genome eukaryotic viruses have cellular gene homologs whose selective advantage is not explained. These homologs add genomic and possibly biochemical complexity. Understanding their significance requires a definition of complexity that is more biochemically oriented than past empirically based definitions.<br><br>HYPOTHESIS: Initially, I propose two biochemistry-oriented definitions of complexity: either decreased randomness or increased encoded information that does not serve immediate needs. Then, I make the assumption that these two definitions are equivalent. This assumption and recent data lead to the following four-part hypothesis that explains the presence of cellular gene homologs in long bacteriophage genomes and also provides a pathway for complexity increases in prokaryotic cells: (1) Prokaryotes underwent evolutionary increases in biochemical complexity after the eukaryote/prokaryote splits. (2) Some of the complexity increases occurred via multi-step, weak selection that was both protected from strong selection and accelerated by embedding evolving cellular genes in the genomes of bacteriophages and, presumably, also archaeal viruses (first tier selection). (3) The mechanisms for retaining cellular genes in viral genomes evolved under additional, longer-term selection that was stronger (second tier selection). (4) The second tier selection was based on increased access by prokaryotic cells to improved biochemical systems. This access was achieved when DNA transfer moved to prokaryotic cells both the more evolved genes and their more competitive and complex biochemical systems.<br><br>TESTING THE HYPOTHESIS: I propose testing this hypothesis by controlled evolution in microbial communities to (1) determine the effects of deleting individual cellular gene homologs on the growth and evolution of long genome bacteriophages and hosts, (2) find the environmental conditions that select for the presence of cellular gene homologs, (3) determine which, if any, bacteriophage genes were selected for maintaining the homologs and (4) determine the dynamics of homolog evolution.<br><br>This hypothesis is an explanation of evolutionary leaps in general. If accurate, it will assist both understanding and influencing the evolution of microbes and their communities. Analysis of evolutionary complexity increase for at least prokaryotes should include analysis of genomes of long-genome bacteriophages.}, }
@article {pmid17354607, year = {2007}, author = {Stavskiĭ, EA and Leliak, AI and Larina N M,  and Grishaeva, ON and Serebrov, VV and Gorbunov, IuA and Duben', LG and Timukina, LA and Mit'ko, LV and Koval', RS and Khodyrev, VP}, title = {[Experimental evaluation of the biological risks of introduction of the genetically modified microorganism (GMM) B. subtilis VKPM B-7092 into the environment].}, journal = {Molekuliarnaia genetika, mikrobiologiia i virusologiia}, volume = {}, number = {1}, pages = {35-40}, pmid = {17354607}, issn = {0208-0613}, mesh = {Animals ; Bacillus subtilis/*genetics/*growth &amp; development/isolation &amp; purification ; Cattle/*microbiology ; *Environment ; Gastrointestinal Tract/microbiology ; Gene Transfer, Horizontal ; Genetic Engineering ; Humans ; Interferon-alpha/*genetics ; Risk ; }, abstract = {Experimental evaluation of the biological risks of introducing the genetically modified microorganism (GMM) B. subtilis VKPM B-7092, an active ingredient of the probiotic VETOM 1.1, into an open system was performed. The following features of the GMM were studied: the survival rate of the GMM in bovine gastroenteric tract; its influence on the microbiocenosis; the species composition of microflora of the gastroenteric tract of the animal species; the possibility of transfer of the DNA fragment cloned in the B. subtilis bacterium and containing the gene of human leukocyte alpha2 interferon to the representatives of intestinal microflora of animals fed on the probiotic VETOM 1.1, as well as the GMM transfer to other microorganism species spread in the areas of potential getting of the GMM into the environment (soil). The study revealed no negative effects of the GMM on the animal organism and the environment, including remote aftereffects.}, }
@article {pmid17353219, year = {2007}, author = {Chen, L and Chen, ZL and Liu, JH and Zeng, ZL and Ma, JY and Jiang, HX}, title = {Emergence of RmtB methylase-producing Escherichia coli and Enterobacter cloacae isolates from pigs in China.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {59}, number = {5}, pages = {880-885}, doi = {10.1093/jac/dkm065}, pmid = {17353219}, issn = {0305-7453}, mesh = {Aminoglycosides/pharmacology ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; China ; Drug Resistance, Bacterial/*genetics ; Electrophoresis, Gel, Pulsed-Field ; Enterobacter cloacae/*enzymology/genetics ; Escherichia coli/*enzymology/genetics ; Methyltransferases/*genetics ; Microbial Sensitivity Tests ; Swine/*microbiology ; }, abstract = {OBJECTIVES: To investigate the occurrence of 16S rRNA methylases conferring high-level resistance to aminoglycosides in Enterobacteriaceae isolated from two pig farms in China.<br><br>METHODS: Enterobacteriaceae isolated from 151 pig rectal swab samples and 9 environmental samples were screened for the presence of the rmtA, rmtB, armA and rmtC genes by PCR and sequencing. Conjugation experiments were carried out to study the transferability of the 16S rRNA methylase genes. All isolates and their transconjugants were tested for susceptibility to antimicrobial agents. The clonal relatedness of RmtB-producing Escherichia coli was assessed by PFGE with XbaI.<br><br>RESULTS: Of 152 Enterobacteriaceae isolates recovered from pigs, 49 (32%) were positive for the rmtB gene, including 48 E. coli and a single isolate of Enterobacter cloacae. Of the nine Enterobacteriaceae isolates from environmental samples, no 16S rRNA methylase gene was identified. The 49 rmtB-positive isolates showed resistance to ampicillin, tetracycline and trimethoprim and also carried a bla(TEM) gene. Transfer of the rmtB and bla(TEM) genes by conjugation experiments of all 49 isolates was successful, suggesting that the rmtB-containing plasmids in the E. coli and E. cloacae isolates were self-transmissible. Conjugative transfer frequencies varied from 2.2 x 10(-10) to 1.3 x 10(-6) transconjugants per recipient. The transfer of non-aminoglycoside antimicrobial resistance traits was also observed in most cases. Forty-four rmtB-positive E. coli showed 30 different PFGE types.<br><br>CONCLUSIONS: The rmtB gene was detected on conjugative plasmids of porcine E. coli and E. cloacae isolates. Both horizontal gene transfer and clonal spread were responsible for the dissemination of the rmtB gene. The emergence of 16S rRNA methylases in Enterobacteriaceae isolates is described for the first time in China. This is also the first report of rmtB-positive Enterobacteriaceae among healthy food-producing animals.}, }
@article {pmid17350929, year = {2007}, author = {Brochier-Armanet, C and Forterre, P}, title = {Widespread distribution of archaeal reverse gyrase in thermophilic bacteria suggests a complex history of vertical inheritance and lateral gene transfers.}, journal = {Archaea (Vancouver, B.C.)}, volume = {2}, number = {2}, pages = {83-93}, pmid = {17350929}, issn = {1472-3646}, mesh = {Amino Acid Sequence ; Archaea/classification/enzymology/*genetics ; Archaeal Proteins/*genetics ; Bacteria/classification/enzymology/*genetics ; Bacterial Proteins/*genetics ; DNA Topoisomerases, Type I/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Thermus thermophilus/genetics ; }, abstract = {Reverse gyrase, an enzyme of uncertain funtion, is present in all hyperthermophilic archaea and bacteria. Previous phylogenetic studies have suggested that the gene for reverse gyrase has an archaeal origin and was transferred laterally (LGT) to the ancestors of the two bacterial hyperthermophilic phyla, Thermotogales and Aquificales. Here, we performed an in-depth analysis of the evolutionary history of reverse gyrase in light of genomic progress. We found genes coding for reverse gyrase in the genomes of several thermophilic bacteria that belong to phyla other than Aquificales and Thermotogales. Several of these bacteria are not, strictly speaking, hyperthermophiles because their reported optimal growth temperatures are below 80 degrees C. Furthermore, we detected a reverse gyrase gene in the sequence of the large plasmid of Thermus thermophilus strain HB8, suggesting a possible mechanism of transfer to the T. thermophilus strain HB8 involving plasmids and transposases. The archaeal part of the reverse gyrase tree is congruent with recent phylogenies of the archaeal domain based on ribosomal proteins or RNA polymerase subunits. Although poorly resolved, the complete reverse gyrase phylogeny suggests an ancient acquisition of the gene by bacteria via one or two LGT events, followed by its secondary distribution by LGT within bacteria. Finally, several genes of archaeal origin located in proximity to the reverse gyrase gene in bacterial genomes have bacterial homologues mostly in thermophiles or hyperthermophiles, raising the possibility that they were co-transferred with the reverse gyrase gene. Our new analysis of the reverse gyrase history strengthens the hypothesis that the acquisition of reverse gyrase may have been a crucial evolutionary step in the adaptation of bacteria to high-temperature environments. However, it also questions the role of this enzyme in thermophilic bacteria and the selective advantage its presence could provide.}, }
@article {pmid17350340, year = {2007}, author = {Templeton, TJ}, title = {Whole-genome natural histories of apicomplexan surface proteins.}, journal = {Trends in parasitology}, volume = {23}, number = {5}, pages = {205-212}, doi = {10.1016/j.pt.2007.03.001}, pmid = {17350340}, issn = {1471-4922}, mesh = {Adaptation, Physiological ; Animals ; Apicomplexa/*genetics ; Gene Transfer, Horizontal ; Genes, Protozoan ; Membrane Proteins/*genetics ; Protozoan Proteins/*genetics ; }, abstract = {The natural histories of free-living and pathogenic protozoans have been described in over a century of studies, spanning a range of disciplines such as microscopic, cellular, taxonomic, pathological, clinical and molecular. Only in the last decade has this landscape of work benefited from the availability of whole-genome nucleotide sequence data. For many pathogens, it is now possible to overlay analyses of protein repertoires onto the current spectrum of knowledge. This article illuminates protozoan natural histories, particularly the rapidly evolving and highly adaptive direct physical interface of apicomplexan parasites and their hosts, by providing a brief introduction to the origin and phylogenetic distribution of parasite-encoded surface proteins and their component domains.}, }
@article {pmid17347521, year = {2007}, author = {Filée, J and Siguier, P and Chandler, M}, title = {Insertion sequence diversity in archaea.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {71}, number = {1}, pages = {121-157}, pmid = {17347521}, issn = {1092-2172}, mesh = {Archaea/classification/*genetics ; Base Sequence ; DNA Transposable Elements/*genetics ; *Genetic Variation ; Genome, Archaeal ; *Mutagenesis, Insertional ; Phylogeny ; }, abstract = {Insertion sequences (ISs) can constitute an important component of prokaryotic (bacterial and archaeal) genomes. Over 1,500 individual ISs are included at present in the ISfinder database (www-is.biotoul.fr), and these represent only a small portion of those in the available prokaryotic genome sequences and those that are being discovered in ongoing sequencing projects. In spite of this diversity, the transposition mechanisms of only a few of these ubiquitous mobile genetic elements are known, and these are all restricted to those present in bacteria. This review presents an overview of ISs within the archaeal kingdom. We first provide a general historical summary of the known properties and behaviors of archaeal ISs. We then consider how transposition might be regulated in some cases by small antisense RNAs and by termination codon readthrough. This is followed by an extensive analysis of the IS content in the sequenced archaeal genomes present in the public databases as of June 2006, which provides an overview of their distribution among the major archaeal classes and species. We show that the diversity of archaeal ISs is very great and comparable to that of bacteria. We compare archaeal ISs to known bacterial ISs and find that most are clearly members of families first described for bacteria. Several cases of lateral gene transfer between bacteria and archaea are clearly documented, notably for methanogenic archaea. However, several archaeal ISs do not have bacterial equivalents but can be grouped into Archaea-specific groups or families. In addition to ISs, we identify and list nonautonomous IS-derived elements, such as miniature inverted-repeat transposable elements. Finally, we present a possible scenario for the evolutionary history of ISs in the Archaea.}, }
@article {pmid17345057, year = {2007}, author = {Sola, C and Saka, HA and Vindel, A and Bocco, JL and , }, title = {High frequency of Panton-Valentine leukocidin genes in invasive methicillin-susceptible Staphylococcus aureus strains and the relationship with methicillin-resistant Staphylococcus aureus in Córdoba, Argentina.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {26}, number = {4}, pages = {281-286}, pmid = {17345057}, issn = {0934-9723}, mesh = {Adolescent ; Adult ; Aged ; Argentina/epidemiology ; Bacterial Toxins/*genetics ; Bacterial Typing Techniques ; Child ; Child, Preschool ; Community-Acquired Infections/epidemiology/microbiology ; Cross Infection/epidemiology/microbiology ; Electrophoresis, Gel, Pulsed-Field/methods ; Exotoxins/*genetics ; Gene Transfer, Horizontal/genetics ; Humans ; Infant ; Leukocidins/*genetics ; Methicillin Resistance/*genetics ; Microbial Sensitivity Tests/methods ; Middle Aged ; Staphylococcal Infections/epidemiology/*microbiology ; Staphylococcus aureus/*genetics/isolation &amp; purification ; }, abstract = {In the study presented here, the genetic characteristics of methicillin-susceptible Staphylococcus aureus (MSSA) strains isolated from patients attending hospitals in the city of Córdoba, Argentina, during 1999-2002 were evaluated to determine their genetic relationship with methicillin-resistant S. aureus (MRSA) clones as part of an effort to control the potential emergence of new epidemic MRSA strains. The results showed there is a high frequency of MSSA strains carrying Panton-Valentine leukocidin genes in invasive infections in Córdoba, Argentina, particularly in those occurring in hospital settings. Panton-Valentine leukocidin genes were found in the genomic background of one clone (ST30-N pulsotype) belonging to a successful internationally distributed MSSA lineage (clonal complex 30), which is closely related to the EMRSA-16 pandemic clone. These genes were also detected in the ancestral clone (ST5-M pulsotype) of the most prevalent MRSA epidemic clone causing healthcare-associated infections in this region, known as the Cordobes/Chilean clone. The molecular characterization of circulating MSSA strains, including the detection of Panton-Valentine leukocidin genes, is thus a useful marker for investigating the evolving epidemiology of hospital- and community-acquired MRSA clones.}, }
@article {pmid17339362, year = {2007}, author = {Sayeed, S and Li, J and McClane, BA}, title = {Virulence plasmid diversity in Clostridium perfringens type D isolates.}, journal = {Infection and immunity}, volume = {75}, number = {5}, pages = {2391-2398}, pmid = {17339362}, issn = {0019-9567}, support = {R01 AI056177/AI/NIAID NIH HHS/United States ; T32 AI060525/AI/NIAID NIH HHS/United States ; AI056177-04/AI/NIAID NIH HHS/United States ; T32 AI060525-01A1/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacterial Toxins/*genetics ; Blotting, Southern ; Clostridium perfringens/*classification/genetics/isolation &amp; purification/*pathogenicity ; Conjugation, Genetic ; DNA Transposable Elements ; Electrophoresis, Gel, Pulsed-Field ; Enterotoxins/*genetics ; Gene Transfer, Horizontal ; *Genetic Variation ; Open Reading Frames ; Plasmids/*genetics ; Polymerase Chain Reaction ; Virulence ; }, abstract = {Clostridium perfringens type D isolates are important in biodefense and also cause natural enterotoxemias in sheep, goats, and occasionally cattle. In these isolates, the gene (etx) encoding epsilon-toxin is thought to reside on poorly characterized large plasmids. Type D isolates sometimes also produce other potentially plasmid-encoded toxins, including C. perfringens enterotoxin and beta2 toxin, encoded by the cpe and cbp2 genes, respectively. In the current study we demonstrated that the etx, cpe, and cpb2 genes are carried on plasmids in type D isolates and characterized the toxin-encoding plasmids to obtain insight into their genetic organization, potential transferability, and diversity. Southern blotting of pulsed-field gels showed that the etx gene of type D isolates can be present on at least five different plasmids, whose sizes range from 48 to 110 kb. The etx plasmids also typically carried IS1151 and tcp open reading frames (ORFs) known to mediate conjugative transfer of C. perfringens plasmid pCW3. PCR studies revealed that other than their tcp ORFs, etx plasmids of type D isolates do not carry substantial portions of the conserved or variable regions in the cpe plasmids of type A isolates. Southern blotting also demonstrated that in type D isolates the cpe and cpb2 genes are sometimes present on the etx plasmid. Collectively, these findings confirmed that the virulence of type D isolates is heavily plasmid dependent and indicated that (i) a single type D isolate can carry multiple virulence plasmids, (ii) a single type D virulence plasmid can carry up to three different toxin genes, and (iii) many etx plasmids should be capable of conjugative transfer.}, }
@article {pmid17336933, year = {2007}, author = {Zhao, X and Zhang, Z and Yan, J and Yu, J}, title = {GC content variability of eubacteria is governed by the pol III alpha subunit.}, journal = {Biochemical and biophysical research communications}, volume = {356}, number = {1}, pages = {20-25}, doi = {10.1016/j.bbrc.2007.02.109}, pmid = {17336933}, issn = {0006-291X}, mesh = {Bacteria/classification/enzymology/*genetics ; Base Composition/*genetics ; DNA Polymerase III/*genetics ; Databases, Nucleic Acid ; Genetic Variation ; Phylogeny ; }, abstract = {Eubacterial genomes have highly variable GC content (0.17-0.75) and the primary mechanism of such variability remains unknown. The place to look for is what actually catalyzes the synthesis of DNA, where DNA polymerase III is at the center stage, particularly one of its 10 subunits--the alpha subunit. According to the dimeric combination of alpha subunits, GC contents of eubacterial genomes were partitioned into three groups with distinct GC content variation spectra: dnaE1 (full-spectrum), dnaE2/dnaE1 (high-GC), and polC/dnaE3 (low-GC). Therefore, genomic GC content variability is believed to be governed primarily by the alpha subunit grouping of DNA polymerase III; it is of essence in genome composition analysis to take full account of such a grouping principle. Since horizontal gene transfer is very frequent among bacterial genomes, exceptions of the grouping scheme, a few percents of the total, are readily identifiable and should be excluded from in-depth analyses on nucleotide compositions.}, }
@article {pmid17336013, year = {2007}, author = {Scapoli, C and De Lorenzi, S and Salvatorelli, G and Barrai, I}, title = {Amino acid and codon use: in two influenza viruses and three hosts.}, journal = {Medecine et maladies infectieuses}, volume = {37}, number = {6}, pages = {337-342}, doi = {10.1016/j.medmal.2006.12.005}, pmid = {17336013}, issn = {0399-077X}, mesh = {Alanine/genetics ; Amino Acids/*genetics ; Animals ; Chickens ; Codon/*genetics ; Humans ; Influenza A virus/classification/*genetics ; Influenza B virus/classification/*genetics ; Leucine/genetics ; Proline/genetics ; Swine ; }, abstract = {OBJECTIVE: The aim of this study was to compare the use of amino acids and codons in influenza viruses A and B and in their common hosts, to highlight any relevant difference.<br><br>METHODS: The frequency of the 20 amino acids and of the 61 codons was studied in influenza viruses A, B, and in man, pig, and chicken. The correlation in amino acid and codon use among these hosts was calculated.<br><br>RESULTS: The correlation between the frequency of the 20 amino acids and the molecular weight was also calculated and it was very similar in all studied hosts, ranging from 0.506 to 0.595. The correlation of codon frequency among these organisms was highest between man and chicken (r=0.974), and lowest between pig and virus B (r=0.147).<br><br>CONCLUSIONS: The important correlation in codon use among the three hosts and the two viruses suggests there was a remote lateral gene transfer among the three hosts and the two viruses. The higher use of alanine, leucine, and proline in man versus virus A is significant.}, }
@article {pmid17334710, year = {2007}, author = {Liang, D and Qiao, J}, title = {Phylogenetic analysis of antibiotic glycosyltransferases.}, journal = {Journal of molecular evolution}, volume = {64}, number = {3}, pages = {342-353}, pmid = {17334710}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Anti-Bacterial Agents/*metabolism ; Bacillus/enzymology/genetics ; Bayes Theorem ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Glucosyltransferases ; Glycopeptides/chemistry/metabolism ; Glycosyltransferases/*genetics ; Gram-Positive Bacteria/enzymology/*genetics ; Macrolides/chemistry/metabolism ; Micromonospora/enzymology/genetics ; Molecular Sequence Data ; *Phylogeny ; Streptomyces/enzymology/genetics ; }, abstract = {Catalyzed by a family of enzymes called glycosyltransferases, glycosylation reactions are essential for the bioactivities of secondary metabolites such as antibiotics. Due to the special characters of antibiotic glycosyltransferases (AGts), antibiotics can function by attaching some unusual deoxy-sugars to their aglycons. Comprehensive similarity searches on the amino acid sequences of AGts have been performed. We reconstructed the molecular phylogeny of AGts with neighbor-joining, maximum-likelihood, and Bayesian methods of phylogenetic inference. The phylogenetic trees show a distinct separation of polyene macrolide (PEM) AGts and other polyketide AGts. The former are more like eukaryotic glycosyltransferases and were deduced to be the results of horizontal gene transfer from eukaryotes. Protein tertiary structural comparison also indicated that some glycopeptide AGts (Gtf-proteins) have a close evolutionary relationship with MurGs, essential glycosyltransferases involved in maturation of bacterial cell walls. The evolutionary relationship of glycopeptide antibiotic biosynthetic gene clusters was speculated according to the phylogenetic analysis of Gtf-proteins. Considering the fact that polyketide AGts and Gtf-proteins are all GT Family 1 members and their aglycon acceptor biosynthetic patterns are very similar, we deduced that AGts and the synthases of their aglycon acceptors have some evolutionary relevance. Finally, the evolutionary origins of AGts that do not fall into GT Family 1 are discussed, suggesting that their ancestral proteins appear to be derived from various proteins responsible for primary metabolism.}, }
@article {pmid17332617, year = {2007}, author = {Lim, SJ and Paeng, JC and Kim, SJ and Kim, SY and Lee, H and Moon, DH}, title = {Enhanced expression of adenovirus-mediated sodium iodide symporter gene in MCF-7 breast cancer cells with retinoic acid treatment.}, journal = {Journal of nuclear medicine : official publication, Society of Nuclear Medicine}, volume = {48}, number = {3}, pages = {398-404}, pmid = {17332617}, issn = {0161-5505}, mesh = {Adenoviridae/*genetics ; Breast Neoplasms/*metabolism/pathology ; Cell Line, Tumor ; Cell Proliferation/drug effects ; Female ; Gene Transfer, Horizontal ; Genetic Therapy ; Humans ; Iodine Radioisotopes/pharmacokinetics ; Receptors, Retinoic Acid/physiology ; Retinoid X Receptors/physiology ; Symporters/*genetics ; Tretinoin/*pharmacology ; }, abstract = {UNLABELLED: Increased expression of the sodium iodide symporter (NIS) is required for effective radioiodine treatment and reporter gene imaging of breast cancer. We investigated the effect of retinoic acid on adenovirus-mediated expression of the human NIS gene in the MCF-7 breast cancer cell line.<br><br>METHODS: The MCF-7 cell line was infected with recombinant adenovirus carrying the human NIS gene (Rad-NIS). Levels of NIS messenger RNA (mRNA) and protein expression and radioiodine ((125)I) uptake were measured to evaluate adenovirus-mediated NIS gene expression in wild-type and Rad-NIS-infected MCF-7 cells after treatment with all-trans-retinoic acid (ATRA; 10(-8)-10(-6) mol/L).<br><br>RESULTS: The transduction efficiency of adenovirus in MCF-7 cells at a multiplicity of infection (MOI) of 50 was >60%. After incubation with 10(-6) mol/L ATRA, the mRNA level in Rad-NIS-infected MCF-7 cells increased to 118.5 times that of wild-type MCF-7 cells, whereas the mRNA level in wild-type MCF-7 cells showed only a 2.1-fold increase. Western blot, immunocytochemical staining, and flow cytometry analyses showed that NIS protein expression in MCF-7 cells infected with Rad-NIS increased after ATRA treatment. With ATRA treatment, the amount of (125)I uptake increased in a dose-dependent manner (P < 0.001). The (125)I uptake in wild-type MCF-7 cells increased 3.1-, 5.5-, and 7.6-fold with treatment with 10(-8), 10(-7), and 10(-6) mol/L ATRA, respectively. Rad-NIS-infected cells showed a 4.0-fold increase in (125)I uptake. Treatment of Rad-NIS-infected cells with 10(-8), 10(-7), and 10(-6) mol/L ATRA increased (125)I uptake by 4.9-, 8.2-, and 27.6-fold, respectively, compared with wild-type MCF-7 cells. The level of NIS expression in Rad-NIS-infected MCF-7 cells treated with 10(-6) mol/L ATRA (245.0 +/- 13.7 pmol/10(6) cells) was much greater than the sum of the expression levels seen in ATRA-treated wild-type cells and Rad-NIS-infected wild-type cells.<br><br>CONCLUSION: Retinoic acid increases adenovirus-mediated NIS expression in MCF-7 cells. Our results indicate that improved efficiency of NIS gene therapy or reporter imaging in breast cancer may be possible with retinoic acid treatment.}, }
@article {pmid17331555, year = {2007}, author = {Wang, Y and Duan, Z and Zhu, H and Guo, X and Wang, Z and Zhou, J and She, Q and Huang, L}, title = {A novel Sulfolobus non-conjugative extrachromosomal genetic element capable of integration into the host genome and spreading in the presence of a fusellovirus.}, journal = {Virology}, volume = {363}, number = {1}, pages = {124-133}, doi = {10.1016/j.virol.2007.01.035}, pmid = {17331555}, issn = {0042-6822}, mesh = {Amino Acid Sequence ; Attachment Sites, Microbiological/genetics ; Base Sequence ; Catalytic Domain ; Fuselloviridae/*physiology ; Gene Transfer, Horizontal/genetics ; Integrases/chemistry/metabolism ; Molecular Sequence Data ; Open Reading Frames/genetics ; Recombination, Genetic/*genetics ; Sequence Alignment ; Sulfolobus solfataricus/*genetics ; }, abstract = {An integrative non-conjugative extrachromosomal genetic element, denoted as pSSVi, has been isolated from a Sulfolobus solfataricus P2 strain and was characterized. This genetic element is a double-stranded DNA of 5740 bp in size and contains eight open reading frames (ORFs). It resembles members of the pRN plasmid family in genome organization but shows only weak similarity to the latter in conserved regions. pSSVi has a copG gene similar to that of a pRN plasmid, encodes a large replication protein which, unlike a typical pRN RepA, contains no polymerase/primase domain, and lacks the plrA gene. Interestingly, pSSVi encodes an SSV-type integrase which probably catalyzes the integration of its genome into a specific site (a tRNA(Arg) gene) in the S. solfataricus P2 genome. Like pSSVx, pSSVi can be packaged into a spindle-like viral particle and spread with the help of SSV1 or SSV2. In addition, both SSV1 and SSV2 appeared to replicate more efficiently in the presence of pSSVi. Given the versatile genetic abilities, pSSVi appears to be well suited for a role in horizontal gene transfer.}, }
@article {pmid17328791, year = {2007}, author = {Zhaxybayeva, O and Nesbø, CL and Doolittle, WF}, title = {Systematic overestimation of gene gain through false diagnosis of gene absence.}, journal = {Genome biology}, volume = {8}, number = {2}, pages = {402}, pmid = {17328791}, issn = {1474-760X}, mesh = {Computational Biology/*methods ; Gene Transfer, Horizontal/*genetics ; *Genome, Bacterial ; Genomics/*methods ; Multigene Family/*genetics ; *Research Design ; }, abstract = {The usual BLAST-based methods for assessing gene presence and absence lead to systematic overestimation of within-species gene gain by lateral transfer.}, }
@article {pmid17325223, year = {2007}, author = {Takahata, S and Ida, T and Senju, N and Sanbongi, Y and Miyata, A and Maebashi, K and Hoshiko, S}, title = {Horizontal gene transfer of ftsI, encoding penicillin-binding protein 3, in Haemophilus influenzae.}, journal = {Antimicrobial agents and chemotherapy}, volume = {51}, number = {5}, pages = {1589-1595}, pmid = {17325223}, issn = {0066-4804}, mesh = {Amino Acid Sequence ; Ampicillin Resistance ; Base Sequence ; Electrophoresis, Gel, Pulsed-Field ; *Gene Transfer, Horizontal ; Haemophilus influenzae/classification/*genetics ; Molecular Sequence Data ; Penicillin-Binding Proteins/*genetics ; Recombination, Genetic ; }, abstract = {Horizontal gene transfer has been identified in only a small number of genes in Haemophilus influenzae, an organism which is naturally competent for transformation. This report provides evidence for the genetic transfer of the ftsI gene, which encodes penicillin-binding protein 3, in H. influenzae. Mosaic structures of the ftsI gene were found in several clinical isolates of H. influenzae. To identify the origin of the mosaic sequence, complete sequences of the corresponding gene from seven type strains of Haemophilus species were determined. Comparison of these sequences with mosaic regions identified a homologous recombination of the ftsI gene between H. influenzae and Haemophilus haemolyticus. Subsequently, ampicillin-resistant H. influenzae strains harboring identical ftsI sequences were genotyped by pulsed-field gel electrophoresis (PFGE). Divergent PFGE patterns among beta-lactamase-nonproducing ampicillin-resistant (BLNAR) strains from different hospitals indicated the potential for the genetic transfer of the mutated ftsI gene between these isolates. Moreover, transfer of the ftsI gene from BLNAR strains to beta-lactamase-nonproducing ampicillin-susceptible (BLNAS) H. influenzae strains was evaluated in vitro. Coincubation of a BLNAS strain (a rifampin-resistant mutant of strain Rd) and BLNAR strains resulted in the emergence of rifampin- and cefdinir-resistant clones at frequencies of 5.1 x 10(-7) to 1.5 x 10(-6). Characterization of these doubly resistant mutants by DNA sequencing of the ftsI gene, susceptibility testing, and genotyping by PFGE revealed that the ftsI genes of BLNAR strains had transferred to BLNAS strains during coincubation. In conclusion, horizontal transfer of the ftsI gene in H. influenzae can occur in an intraspecies and an interspecies manner.}, }
@article {pmid17318536, year = {2007}, author = {Vibber, LL and Pressler, MJ and Colores, GM}, title = {Isolation and characterization of novel atrazine-degrading microorganisms from an agricultural soil.}, journal = {Applied microbiology and biotechnology}, volume = {75}, number = {4}, pages = {921-928}, doi = {10.1007/s00253-007-0871-6}, pmid = {17318536}, issn = {0175-7598}, mesh = {Actinomycetales/classification/genetics/*isolation &amp; purification/metabolism ; Arthrobacter/classification/genetics/*isolation &amp; purification/metabolism ; Atrazine/*metabolism ; Bacterial Proteins/genetics/*metabolism ; Biodegradation, Environmental ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Herbicides/metabolism ; Kinetics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {Six previously undescribed microorganisms capable of atrazine degradation were isolated from an agricultural soil that received repeated exposures of the commonly used herbicides atrazine and acetochlor. These isolates are all Gram-positive and group with microorganisms in the genera Nocardioides and Arthrobacter, both of which contain previously described atrazine degraders. All six isolates were capable of utilizing atrazine as a sole nitrogen source when provided with glucose as a separate carbon source. Under the culture conditions used, none of the isolates could utilize atrazine as the sole carbon and nitrogen source. We used several polymerase-chain-reaction-based assays to screen for the presence of a number of atrazine-degrading genes and verified their identity through sequencing. All six isolates contain trzN and atzC, two well-characterized genes involved in the conversion of atrazine to cyanuric acid. An additional atrazine-degrading gene, atzB, was detected in one of the isolates as well, yet none appeared to contain atzA, a commonly encountered gene in atrazine impacted soils and atrazine-degrading isolates. Interestingly, the deoxyribonucleic acid sequences of trzN and atzC were all identical, implying that their presence may be the result of horizontal gene transfer among these isolates.}, }
@article {pmid17318426, year = {2007}, author = {Bolanaki, E and Kottaridi, C and Markoulatos, P and Kyriakopoulou, Z and Margaritis, L and Katsorchis, T}, title = {Partial 3D gene sequences of Coxsackie viruses reveal interspecies exchanges.}, journal = {Virus genes}, volume = {35}, number = {2}, pages = {129-140}, pmid = {17318426}, issn = {0920-8569}, mesh = {Animals ; Cell Line, Tumor ; Enterovirus/classification/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Humans ; Molecular Sequence Data ; Phylogeny ; Recombination, Genetic ; Serotyping ; *Species Specificity ; }, abstract = {The 3D region of 46 clinical Coxsackievirus strains, primarily belonging to the human enterovirus B species (HEV-B), were analyzed using nucleotide distance matrices and phylogeny software. The conclusions from previously analyzed genomic regions (VP1-2A-2B-2C) of the aforementioned strains revealed that enteroviruses' inheritance is being guided by gene adaptation among viruses of different serotypes. In this report the comparison of partial VP1 and 3D gene phylogenies presented an obvious incongruence. Moreover, the phylogeny of 3D sequences of the strains revealed an unexpected (and for the first time reported) homology among strains of different species. The observations of our study indicate that conversion events such as multiple mutations or recombination among strains and unknown donors may occur during the evolution of circulating strains, leading, probably, to viruses with altered genome and virulence.}, }
@article {pmid17308185, year = {2007}, author = {Barcellos, FG and Menna, P and da Silva Batista, JS and Hungria, M}, title = {Evidence of horizontal transfer of symbiotic genes from a Bradyrhizobium japonicum inoculant strain to indigenous diazotrophs Sinorhizobium (Ensifer) fredii and Bradyrhizobium elkanii in a Brazilian Savannah soil.}, journal = {Applied and environmental microbiology}, volume = {73}, number = {8}, pages = {2635-2643}, pmid = {17308185}, issn = {0099-2240}, mesh = {Bradyrhizobium/*genetics/isolation &amp; purification ; Brazil ; DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Genes, rRNA/genetics ; Genomic Islands ; Molecular Sequence Data ; Nitrogen Fixation/genetics ; Phylogeny ; Plant Roots/microbiology ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Homology, Nucleic Acid ; Sinorhizobium fredii/*genetics/isolation &amp; purification ; *Soil Microbiology ; Glycine max/microbiology ; Symbiosis/*genetics ; }, abstract = {The importance of horizontal gene transfer (HGT) in the evolution and speciation of bacteria has been emphasized; however, most studies have focused on genes clustered in pathogenesis and very few on symbiosis islands. Both soybean (Glycine max [L.] Merrill) and compatible Bradyrhizobium japonicum and Bradyrhizobium elkanii strains are exotic to Brazil and have been massively introduced in the country since the early 1960s, occupying today about 45% of the cropped land. For the past 10 years, our group has obtained several isolates showing high diversity in morphological, physiological, genetic, and symbiotic properties in relation to the putative parental inoculant strains. In this study, parental strains and putative natural variants isolated from field-grown soybean nodules were genetically characterized in relation to conserved genes (by repetitive extragenic palindromic PCR using REP and BOX A1R primers, PCR-restriction fragment length polymorphism, and sequencing of the 16SrRNA genes), nodulation, and N(2)-fixation genes (PCR-RFLP and sequencing of nodY-nodA, nodC, and nifH genes). Both genetic variability due to adaptation to the stressful environmental conditions of the Brazilian Cerrados and HGT events were confirmed. One strain (S 127) was identified as an indigenous B. elkanii strain that acquired a nodC gene from the inoculant B. japonicum. Another one (CPAC 402) was identified as an indigenous Sinorhizobium (Ensifer) fredii strain that received the whole symbiotic island from the B. japonicum inoculant strain and maintained an extra copy of the original nifH gene. The results highlight the strategies that bacteria may commonly use to obtain ecological advantages, such as the acquisition of genes to establish effective symbioses with an exotic host legume.}, }
@article {pmid17307855, year = {2007}, author = {Wegmann, U and O'Connell-Motherway, M and Zomer, A and Buist, G and Shearman, C and Canchaya, C and Ventura, M and Goesmann, A and Gasson, MJ and Kuipers, OP and van Sinderen, D and Kok, J}, title = {Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp. cremoris MG1363.}, journal = {Journal of bacteriology}, volume = {189}, number = {8}, pages = {3256-3270}, pmid = {17307855}, issn = {0021-9193}, mesh = {Bacillus Phages/genetics ; Bacterial Proteins/genetics/metabolism ; Base Sequence ; Carbohydrate Metabolism ; *Genome, Bacterial ; Genome, Viral ; Lactococcus lactis/*genetics/metabolism/virology ; Molecular Sequence Data ; Plasmids/genetics ; Prophages/genetics ; }, abstract = {Lactococcus lactis is of great importance for the nutrition of hundreds of millions of people worldwide. This paper describes the genome sequence of Lactococcus lactis subsp. cremoris MG1363, the lactococcal strain most intensively studied throughout the world. The 2,529,478-bp genome contains 81 pseudogenes and encodes 2,436 proteins. Of the 530 unique proteins, 47 belong to the COG (clusters of orthologous groups) functional category "carbohydrate metabolism and transport," by far the largest category of novel proteins in comparison with L. lactis subsp. lactis IL1403. Nearly one-fifth of the 71 insertion elements are concentrated in a specific 56-kb region. This integration hot-spot region carries genes that are typically associated with lactococcal plasmids and a repeat sequence specifically found on plasmids and in the "lateral gene transfer hot spot" in the genome of Streptococcus thermophilus. Although the parent of L. lactis MG1363 was used to demonstrate lysogeny in Lactococcus, L. lactis MG1363 carries four remnant/satellite phages and two apparently complete prophages. The availability of the L. lactis MG1363 genome sequence will reinforce its status as the prototype among lactic acid bacteria through facilitation of further applied and fundamental research.}, }
@article {pmid17307849, year = {2007}, author = {Marrero, J and Waldor, MK}, title = {The SXT/R391 family of integrative conjugative elements is composed of two exclusion groups.}, journal = {Journal of bacteriology}, volume = {189}, number = {8}, pages = {3302-3305}, pmid = {17307849}, issn = {0021-9193}, support = {AI42347/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics ; *Conjugation, Genetic ; Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Genetic Variation ; Gram-Negative Bacteria/drug effects/*genetics ; Molecular Sequence Data ; Sequence Alignment ; }, abstract = {Conjugative elements often encode entry exclusion systems that convert host cells into poor recipients for identical or similar elements. The diversity of exclusion systems within families of conjugative elements has received little attention. We report here the most comprehensive study to date of the diversity of exclusion determinants within a single family of conjugative elements. Unexpectedly, our analyses indicate that there are only two exclusion groups among the diverse members of the SXT/R391 family of integrative conjugative elements.}, }
@article {pmid17303128, year = {2007}, author = {Hohmann-Marriott, MF and Blankenship, RE}, title = {Hypothesis on chlorosome biogenesis in green photosynthetic bacteria.}, journal = {FEBS letters}, volume = {581}, number = {5}, pages = {800-803}, doi = {10.1016/j.febslet.2007.01.078}, pmid = {17303128}, issn = {0014-5793}, mesh = {Bacteria/genetics/*metabolism ; Bacterial Proteins/metabolism ; Bacteriochlorophylls/metabolism ; Membrane Lipids/metabolism ; Membrane Proteins/metabolism ; *Models, Biological ; Organelles/*metabolism ; *Photosynthesis ; }, abstract = {Chlorosomes are specialized compartments that constitute the main light harvesting system of green sulfur bacteria (GSB) and some filamentous anoxygenic phototrophs (FAP). Chlorosome biogenesis promises to be a complex process requiring the generation of a unilayer membrane and the targeting of bacteriochlorophyll, carotenoids, quinones, and proteins to the chlorosome. The biogenesis of chlorosomes as well as their presence in two distinct bacterial groups, GSB and FAP, remains enigmatic. The photosynthetic machinery and overall metabolic characteristics of these two bacterial groups are very different, and horizontal gene transfer has been proposed to explain chlorosome distribution. Chlorosomes have been considered to be unique structures that require a specific assembly machinery. We propose that no special machinery is required for chlorosome assembly. Instead, it is suggested that chlorosomes are a special form of lipid body. We present a model for chlorosome biogenesis that combines aspects of lipid body biogenesis with established chlorosome characteristics and may help explain the presence of chlorosomes in two metabolically diverse organism groups.}, }
@article {pmid17300921, year = {2007}, author = {Wu, TL and Chia, JH and Su, LH and Chiu, CH and Kuo, AJ and Ma, L and Siu, LK}, title = {CMY-2 beta-lactamase-carrying community-acquired urinary tract Escherichia coli: genetic correlation with Salmonella enterica serotypes Choleraesuis and Typhimurium.}, journal = {International journal of antimicrobial agents}, volume = {29}, number = {4}, pages = {410-416}, doi = {10.1016/j.ijantimicag.2006.12.008}, pmid = {17300921}, issn = {0924-8579}, mesh = {Base Sequence ; Cephalosporin Resistance/genetics ; Cephamycins/pharmacology ; Community-Acquired Infections/drug therapy/microbiology ; Conjugation, Genetic ; DNA Transposable Elements ; Escherichia coli/drug effects/*genetics ; Escherichia coli Infections/drug therapy/microbiology ; Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Plasmids/genetics ; Salmonella enterica/*genetics ; Urinary Tract Infections/drug therapy/microbiology ; beta-Lactamases/*genetics ; }, abstract = {Forty-six cephamycin-resistant Escherichia coli isolates from patients diagnosed with community-acquired urinary tract infection were selected in order to study their resistance mechanism. With the exception of one isolate producing CMY-4, all isolates produced a CMY-2 beta-lactamase. Molecular typing showed that the CMY-2-producing isolates were not related. Cephamycin resistance was plasmid encoded and conjugatively transferred. Plasmid digest profiles suggested that the plasmids were different. Thirty-nine of the 45 CMY-2-producing isolates harboured a plasmid containing a specific DNA fragment, ISEcp1-bla(CMY-2)-blc-sugE, which was identical to those previously published in CMY-2-producing Salmonella enterica serotype Choleraesuis (SCB67) and Salmonella enterica serotype Typhimurium (pNF1358) from Taiwan and the USA, respectively. Among the remaining six isolates, insertion of IS1294 and IS1 at different positions was observed in one and five isolates, respectively. The regions surrounding bla(CMY-2) of the six isolates were identical to the other 39 isolates as well as to SCB67 and pNF1358. Since the present identical transmissible bla(CMY-2)-carrying element was observed in food animal sources both in the USA and Taiwan, its possible transmission to humans, as revealed in this study, is of great concern. Awareness of this mobile resistance element is required to prevent introduction into hospitals and to reduce the spread of this emerging resistance within the community.}, }
@article {pmid17298675, year = {2007}, author = {Andersson, JO and Sjögren, AM and Horner, DS and Murphy, CA and Dyal, PL and Svärd, SG and Logsdon, JM and Ragan, MA and Hirt, RP and Roger, AJ}, title = {A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution.}, journal = {BMC genomics}, volume = {8}, number = {}, pages = {51}, pmid = {17298675}, issn = {1471-2164}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Sequence ; Animals ; Base Composition ; Base Sequence ; Codon/genetics ; Databases, Genetic ; Diplomonadida/classification/*genetics ; Eukaryotic Cells/metabolism ; Evolution, Molecular ; Expressed Sequence Tags ; Fishes/*parasitology ; Gene Transfer, Horizontal/*genetics ; Genes, Protozoan/genetics ; *Genome, Protozoan ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Comparative genomic studies of the mitochondrion-lacking protist group Diplomonadida (diplomonads) has been lacking, although Giardia lamblia has been intensively studied. We have performed a sequence survey project resulting in 2341 expressed sequence tags (EST) corresponding to 853 unique clones, 5275 genome survey sequences (GSS), and eleven finished contigs from the diplomonad fish parasite Spironucleus salmonicida (previously described as S. barkhanus).<br><br>RESULTS: The analyses revealed a compact genome with few, if any, introns and very short 3' untranslated regions. Strikingly different patterns of codon usage were observed in genes corresponding to frequently sampled ESTs versus genes poorly sampled, indicating that translational selection is influencing the codon usage of highly expressed genes. Rigorous phylogenomic analyses identified 84 genes--mostly encoding metabolic proteins--that have been acquired by diplomonads or their relatively close ancestors via lateral gene transfer (LGT). Although most acquisitions were from prokaryotes, more than a dozen represent likely transfers of genes between eukaryotic lineages. Many genes that provide novel insights into the genetic basis of the biology and pathogenicity of this parasitic protist were identified including 149 that putatively encode variant-surface cysteine-rich proteins which are candidate virulence factors. A number of genomic properties that distinguish S. salmonicida from its human parasitic relative G. lamblia were identified such as nineteen putative lineage-specific gene acquisitions, distinct mutational biases and codon usage and distinct polyadenylation signals.<br><br>CONCLUSION: Our results highlight the power of comparative genomic studies to yield insights into the biology of parasitic protists and the evolution of their genomes, and suggest that genetic exchange between distantly-related protist lineages may be occurring at an appreciable rate in eukaryote genome evolution.}, }
@article {pmid17298366, year = {2007}, author = {Heuer, H and Smalla, K}, title = {Manure and sulfadiazine synergistically increased bacterial antibiotic resistance in soil over at least two months.}, journal = {Environmental microbiology}, volume = {9}, number = {3}, pages = {657-666}, doi = {10.1111/j.1462-2920.2006.01185.x}, pmid = {17298366}, issn = {1462-2912}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics/isolation &amp; purification ; Bacterial Proteins/genetics ; Carrier Proteins/genetics ; Culture Media ; Dihydropteroate Synthase/genetics ; *Drug Resistance, Bacterial/genetics ; Escherichia coli K12/drug effects/genetics ; Escherichia coli Proteins/genetics ; Gene Transfer, Horizontal/genetics ; Integrons/genetics ; *Manure ; Molecular Sequence Data ; Sequence Analysis, DNA ; *Soil Microbiology ; Sulfadiazine/*pharmacology ; Sulfonamides/*pharmacology ; }, abstract = {Manuring of arable soils may stimulate the spread of resistance genes by introduction of resistant populations and antibiotics. We investigated effects of pig manure and sulfadiazine (SDZ) on bacterial communities in soil microcosms. A silt loam and a loamy sand were mixed with manure containing SDZ (10 or 100 mg per kilogram of soil), and compared with untreated soil and manured soil without SDZ over a 2-month period. In both soils, manure and SDZ positively affected the quotients of total and SDZ-resistant culturable bacteria [most probable number (MPN)], and transfer frequencies of plasmids conferring SDZ resistance in filter matings of soil bacteria and an Escherichia coli recipient. Detection of sulfonamide resistance genes sul1, sul2 and sul3 in community DNA by polymerase chain reaction (PCR) and hybridization revealed a high prevalence of sul1 in manure and manured soils, while sul2 was mainly found in the loamy sand treated with manure and high SDZ amounts, and sul3 was not detected. By PCR quantification of sul1 and bacterial rrn genes, a transient effect of manure alone and a long-term effect of SDZ plus manure on absolute and relative sul1 abundance in soil was shown. The dynamics in soil of class 1 integrons, which are typically associated with sul1, was analysed by amplification of the gene cassette region. Integrons introduced by manure established in both soils. Soil type and SDZ affected the composition of integrons. The synergistic effects of manure and SDZ were still detectable after 2 months. The results suggest that manure from treated pigs enhances spread of antibiotic resistances in soil bacterial communities.}, }
@article {pmid17295320, year = {2007}, author = {Chovancová, E and Kosinski, J and Bujnicki, JM and Damborský, J}, title = {Phylogenetic analysis of haloalkane dehalogenases.}, journal = {Proteins}, volume = {67}, number = {2}, pages = {305-316}, doi = {10.1002/prot.21313}, pmid = {17295320}, issn = {1097-0134}, mesh = {Animals ; Bacterial Proteins ; Binding Sites ; Classification/methods ; Cluster Analysis ; Databases, Protein ; Gene Duplication ; Gene Transfer, Horizontal ; Hydrolases/classification/*genetics ; Mutation ; *Phylogeny ; Sequence Homology, Amino Acid ; Solvents ; Structural Homology, Protein ; Substrate Specificity ; }, abstract = {Haloalkane dehalogenases (HLDs) are enzymes that catalyze the cleavage of carbon-halogen bonds by a hydrolytic mechanism. Although comparative biochemical analyses have been published, no classification system has been proposed for HLDs, to date, that reconciles their phylogenetic and functional relationships. In the study presented here, we have analyzed all sequences and structures of genuine HLDs and their homologs detectable by database searches. Phylogenetic analyses revealed that the HLD family can be divided into three subfamilies denoted HLD-I, HLD-II, and HLD-III, of which HLD-I and HLD-III are predicted to be sister-groups. A mismatch between the HLD protein tree and the tree of species, as well as the presence of more than one HLD gene in a few genomes, suggest that horizontal gene transfers, and perhaps also multiple gene duplications and losses have been involved in the evolution of this family. Most of the biochemically characterized HLDs are found in the HLD-II subfamily. The dehalogenating activity of two members of the newly identified HLD-III subfamily has only recently been confirmed, in a study motivated by this phylogenetic analysis. A novel type of the catalytic pentad (Asp-His-Asp+Asn-Trp) was predicted for members of the HLD-III subfamily. Calculation of the evolutionary rates and lineage-specific innovations revealed a common conserved core as well as a set of residues that characterizes each HLD subfamily. The N-terminal part of the cap domain is one of the most variable regions within the whole family as well as within individual subfamilies, and serves as a preferential site for the location of relatively long insertions. The highest variability of discrete sites was observed among residues that are structural components of the access channels. Mutations at these sites modify the anatomy of the channels, which are important for the exchange of ligands between the buried active site and the bulk solvent, thus creating a structural basis for the molecular evolution of new substrate specificities. Our analysis sheds light on the evolutionary history of HLDs and provides a structural framework for designing enzymes with new specificities.}, }
@article {pmid17293976, year = {2006}, author = {Simões-Barbosa, A and Argañaraz, ER and Barros, AM and Rosa, Ade C and Alves, NP and Louvandini, P and D'Souza-Ault, MR and Nitz, N and Sturm, NR and Nascimento, RJ and Teixeira, AR}, title = {Hitchhiking Trypanosoma cruzi minicircle DNA affects gene expression in human host cells via LINE-1 retrotransposon.}, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {101}, number = {8}, pages = {833-843}, doi = {10.1590/s0074-02762006000800003}, pmid = {17293976}, issn = {0074-0276}, mesh = {Animals ; Base Sequence ; Cell Line/parasitology ; DNA, Kinetoplast/*genetics ; Gene Expression/*genetics ; Gene Transfer, Horizontal ; Host-Parasite Interactions/genetics ; Humans ; Long Interspersed Nucleotide Elements/*genetics ; Macrophages/parasitology ; Molecular Sequence Data ; Retroelements/*genetics ; Trypanosoma cruzi/*genetics/physiology ; }, abstract = {The horizontal transfer of Trypanosoma cruzi mitochondrial minicircle DNA to the genomes of naturally infected humans may play an important role in the pathogenesis of Chagas disease. Minicircle integrations within LINE-1 elements create the potential for foreign DNA mobility within the host genome via the machinery associated with this retrotransposon. Here we document integration of minicircle DNA fragments in clonal human macrophage cell lines and their mobilization over time. The movement of an integration event in a clonal transfected cell line was tracked at three months and three years post-infection. The minicircle sequence integrated into a LINE-1 retrotransposon; one such foreign fragment subsequently relocated to another genomic location in association with associated LINE-1 elements. The p15 locus was altered at three years as a direct effect of minicircle/LINE-1 acquisition, resulting in elimination of p15 mRNA. Here we show for the first time a molecular pathology stemming from mobilization of a kDNA/LINE-1 mutation. These genomic changes and detected transcript variations are consistent with our hypothesis that minicircle integration is a causal component of parasite-independent, autoimmune-driven lesions seen in the heart and other target tissues associated with Chagas disease.}, }
@article {pmid17293429, year = {2007}, author = {Poggio, S and Abreu-Goodger, C and Fabela, S and Osorio, A and Dreyfus, G and Vinuesa, P and Camarena, L}, title = {A complete set of flagellar genes acquired by horizontal transfer coexists with the endogenous flagellar system in Rhodobacter sphaeroides.}, journal = {Journal of bacteriology}, volume = {189}, number = {8}, pages = {3208-3216}, pmid = {17293429}, issn = {0021-9193}, mesh = {Anaerobiosis ; Flagella/*genetics/ultrastructure ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Locomotion ; Microscopy, Electron ; Phylogeny ; Rhodobacter sphaeroides/*physiology/ultrastructure ; }, abstract = {Bacteria swim in liquid environments by means of a complex rotating structure known as the flagellum. Approximately 40 proteins are required for the assembly and functionality of this structure. Rhodobacter sphaeroides has two flagellar systems. One of these systems has been shown to be functional and is required for the synthesis of the well-characterized single subpolar flagellum, while the other was found only after the genome sequence of this bacterium was completed. In this work we found that the second flagellar system of R. sphaeroides can be expressed and produces a functional flagellum. In many bacteria with two flagellar systems, one is required for swimming, while the other allows movement in denser environments by producing a large number of flagella over the entire cell surface. In contrast, the second flagellar system of R. sphaeroides produces polar flagella that are required for swimming. Expression of the second set of flagellar genes seems to be positively regulated under anaerobic growth conditions. Phylogenic analysis suggests that the flagellar system that was initially characterized was in fact acquired by horizontal transfer from a gamma-proteobacterium, while the second flagellar system contains the native genes. Interestingly, other alpha-proteobacteria closely related to R. sphaeroides have also acquired a set of flagellar genes similar to the set found in R. sphaeroides, suggesting that a common ancestor received this gene cluster.}, }
@article {pmid17288581, year = {2007}, author = {Marri, PR and Hao, W and Golding, GB}, title = {The role of laterally transferred genes in adaptive evolution.}, journal = {BMC evolutionary biology}, volume = {7 Suppl 1}, number = {Suppl 1}, pages = {S8}, pmid = {17288581}, issn = {1471-2148}, mesh = {Adaptation, Biological/*genetics ; Corynebacterium/genetics ; *Evolution, Molecular ; Gene Deletion ; Gene Transfer, Horizontal/*physiology ; Genome, Bacterial ; Likelihood Functions ; Mutagenesis, Insertional ; Phylogeny ; Species Specificity ; }, abstract = {BACKGROUND: Bacterial genomes develop new mechanisms to tide them over the imposing conditions they encounter during the course of their evolution. Acquisition of new genes by lateral gene transfer may be one of the dominant ways of adaptation in bacterial genome evolution. Lateral gene transfer provides the bacterial genome with a new set of genes that help it to explore and adapt to new ecological niches.<br><br>METHODS: A maximum likelihood analysis was done on the five sequenced corynebacterial genomes to model the rates of gene insertions/deletions at various depths of the phylogeny.<br><br>RESULTS: The study shows that most of the laterally acquired genes are transient and the inferred rates of gene movement are higher on the external branches of the phylogeny and decrease as the phylogenetic depth increases. The newly acquired genes are under relaxed selection and evolve faster than their older counterparts. Analysis of some of the functionally characterised LGTs in each species has indicated that they may have a possible adaptive role.<br><br>CONCLUSION: The five Corynebacterial genomes sequenced to date have evolved by acquiring between 8-14% of their genomes by LGT and some of these genes may have a role in adaptation.}, }
@article {pmid17284435, year = {2007}, author = {Hou, WG and Lian, B}, title = {[Phylogenetic and genetic analysis of symbiotic nodulation genes within the Bradyrhizobium].}, journal = {Yi chuan = Hereditas}, volume = {29}, number = {1}, pages = {118-126}, doi = {10.1360/yc-007-0118}, pmid = {17284435}, issn = {0253-9772}, mesh = {Bradyrhizobium/classification/*genetics ; *Phylogeny ; Plant Root Nodulation/*genetics ; RNA, Ribosomal, 16S/genetics ; Root Nodules, Plant/genetics ; Sequence Analysis, DNA ; Symbiosis/*genetics ; }, abstract = {Symbiotic nitrogen fixing bacteria-known as rhizobia-harbour a set of nodulation (nod) genes that control the synthesis of modified lipo-chitooligosaccharides, called Nod factors that are required for legume nodulation. The nodA gene, which is essential for symbiosis, is responsible for the attachment of the fatty acid group to the oligosaccharide backbone. The nodZ, nolL, and noeI genes are involved in specific modifications of Nod factors common to bradyrhizobia, i.e., the transfer of a fucosyl group on the Nod factor core, fucose acetylation and fucose methylation, respectively. The distribution of the nodZ, nolL, and noeI genes in the studied strains was found to correlate with the nodA tree topology. Moreover, the nodA, nodZ, and noeI phylogenies were largely congruent, but did not closely follow the taxonomy of the strains shown by the housekeeping 16S rRNA and dnaK genes. Additionally, the distribution of nodZ, noeI, and nolL genes suggested that their presence may be related to the requirements of their legume hosts. These data indicated that the spread and maintenance of nodulation genes within the Bradyrhizobium genus occurred through vertical transmission, although lateral gene transfer also played a significant role.}, }
@article {pmid17283383, year = {2006}, author = {Nambu, T and Inagaki, Y and Kutsukake, K}, title = {Plasticity of the domain structure in FlgJ, a bacterial protein involved in flagellar rod formation.}, journal = {Genes &amp; genetic systems}, volume = {81}, number = {6}, pages = {381-389}, doi = {10.1266/ggs.81.381}, pmid = {17283383}, issn = {1341-7568}, mesh = {Amino Acid Sequence ; Bacteria/*chemistry/classification/genetics ; Bacterial Proteins/*chemistry/genetics/metabolism ; Desulfovibrio/chemistry/classification/genetics ; Flagella/*chemistry ; Gene Transfer, Horizontal ; Molecular Sequence Data ; N-Acetylmuramoyl-L-alanine Amidase/chemistry/genetics/metabolism ; Phylogeny ; Protein Structure, Tertiary ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {Bacterial flagellar rod structure is built across the peptidoglycan (PG) layer. A Salmonella enterica flagellar protein FlgJ is believed to consist of two functional domains, the N-terminal half acting as a scaffold or cap essential for rod assembly and the C-terminal half acting as a PG hydrolase (PGase) that makes a hole in the PG layer to facilitate rod penetration. In this study, molecular data analyses were conducted on FlgJ data sets sampled from a variety of bacterial species, and three types of FlgJ homologs were identified: (i) "canonical dual-domain" type found in beta- and gamma-proteobacteria that has a domain for one of the PGases, acetylmuramidase (Acm), at the C terminus, (ii) "non-canonical dual-domain" type found in the genus Desulfovibrio (delta-proteobacteria) that bears a domain for another PGase, M23/M37-family peptidase (Pep), at the C terminus and (iii) "single-domain" type found in phylogenetically diverged lineages that lacks the Acm or Pep domain. FlgJ phylogeny, together with the domain architecture, suggested that the single-domain type was the original form of FlgJ and the canonical dual-domain type had evolved from the single-domain type by fusion of the Acm domain to its C terminus in the common ancestor of beta- and gamma-proteobacteria. The non-canonical dual-domain type may have been formed by fusion of the Pep domain to the single-domain type in the ancestor of Desulfovibrio. In some lineages of gamma-proteobacteria, the Acm domain appeared to be lost secondarily from the dual-domain type FlgJ to yield again a single-domain type one. To rationalize the underlying mechanism that gave rise to the two different types of dual-domain FlgJ homologs, we propose a model assuming the lineage-specific co-option of flagellum-specific PGase from diverged housekeeping PGases in bacteria.}, }
@article {pmid17277795, year = {2007}, author = {Wright, GD}, title = {The antibiotic resistome: the nexus of chemical and genetic diversity.}, journal = {Nature reviews. Microbiology}, volume = {5}, number = {3}, pages = {175-186}, doi = {10.1038/nrmicro1614}, pmid = {17277795}, issn = {1740-1534}, mesh = {Anti-Bacterial Agents/metabolism/*pharmacology ; Bacteria/*drug effects/enzymology/*genetics/metabolism ; Drug Resistance, Bacterial/*genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Variation ; Humans ; Interspersed Repetitive Sequences/genetics/physiology ; }, abstract = {Over the millennia, microorganisms have evolved evasion strategies to overcome a myriad of chemical and environmental challenges, including antimicrobial drugs. Even before the first clinical use of antibiotics more than 60 years ago, resistant organisms had been isolated. Moreover, the potential problem of the widespread distribution of antibiotic resistant bacteria was recognized by scientists and healthcare specialists from the initial use of these drugs. Why is resistance inevitable and where does it come from? Understanding the molecular diversity that underlies resistance will inform our use of these drugs and guide efforts to develop new efficacious antibiotics.}, }
@article {pmid17277222, year = {2007}, author = {Johnson, TJ and Wannemuehler, YM and Johnson, SJ and Logue, CM and White, DG and Doetkott, C and Nolan, LK}, title = {Plasmid replicon typing of commensal and pathogenic Escherichia coli isolates.}, journal = {Applied and environmental microbiology}, volume = {73}, number = {6}, pages = {1976-1983}, pmid = {17277222}, issn = {0099-2240}, support = {U24 AI 50139/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bird Diseases/microbiology ; Birds/microbiology ; Cluster Analysis ; Colicins/genetics ; DNA, Bacterial/*genetics ; Escherichia coli/*genetics/isolation &amp; purification ; Escherichia coli Infections/microbiology/veterinary ; Feces/microbiology ; Food Microbiology ; Gene Transfer, Horizontal ; Humans ; Meat/microbiology ; Plasmids/*classification/*genetics ; Polymerase Chain Reaction/*methods ; Replicon/*genetics ; Urogenital System/microbiology ; }, abstract = {Despite the critical role of plasmids in horizontal gene transfer, few studies have characterized plasmid relatedness among different bacterial populations. Recently, a multiplex PCR replicon typing protocol was developed for classification of plasmids occurring in members of the Enterobacteriaceae. Here, a simplified version of this replicon typing procedure which requires only three multiplex panels to identify 18 plasmid replicons is described. This method was used to screen 1,015 Escherichia coli isolates of avian, human, and poultry meat origin for plasmid replicon types. Additionally, the isolates were assessed for their content of several colicin-associated genes. Overall, a high degree of plasmid variability was observed, with 221 different profiles occurring among the 1,015 isolates examined. IncFIB plasmids were the most common type identified, regardless of the source type of E. coli. IncFIB plasmids occurred significantly more often in avian pathogenic E. coli (APEC) and retail poultry E. coli (RPEC) than in uropathogenic E. coli (UPEC) and avian and human fecal commensal E. coli isolates (AFEC and HFEC, respectively). APEC and RPEC were also significantly more likely than UPEC, HFEC, and AFEC to possess the colicin-associated genes cvaC, cbi, and/or cma in conjunction with one or more plasmid replicons. The results suggest that E. coli isolates contaminating retail poultry are notably similar to APEC with regard to plasmid profiles, with both generally containing multiple plasmid replicon types in conjunction with colicin-related genes. In contrast, UPEC and human and avian commensal E. coli isolates generally lack the plasmid replicons and colicin-related genes seen in APEC and RPEC, suggesting limited dissemination of such plasmids among these bacterial populations.}, }
@article {pmid17277171, year = {2007}, author = {Woolfit, M and Rozpedowska, E and Piskur, J and Wolfe, KH}, title = {Genome survey sequencing of the wine spoilage yeast Dekkera (Brettanomyces) bruxellensis.}, journal = {Eukaryotic cell}, volume = {6}, number = {4}, pages = {721-733}, pmid = {17277171}, issn = {1535-9778}, mesh = {Base Composition/genetics ; Chromosomes, Fungal/genetics ; DNA, Fungal/genetics ; Fungal Proteins/genetics ; Gene Order ; Gene Transfer, Horizontal ; Genes, Fungal ; Genetic Code ; Genome, Fungal/*genetics ; Introns/genetics ; Multigene Family ; Phylogeny ; *Sequence Analysis, DNA ; Wine/*microbiology ; Yeasts/*genetics ; }, abstract = {The hemiascomycete yeast Dekkera bruxellensis, also known as Brettanomyces bruxellensis, is a major cause of wine spoilage worldwide. Wines infected with D. bruxellensis develop distinctive, unpleasant aromas due to volatile phenols produced by this species, which is highly ethanol tolerant and facultatively anaerobic. Despite its importance, however, D. bruxellensis has been poorly genetically characterized until now. We performed genome survey sequencing of a wine strain of D. bruxellensis to obtain 0.4x coverage of the genome. We identified approximately 3,000 genes, whose products averaged 49% amino acid identity to their Saccharomyces cerevisiae orthologs, with similar intron contents. Maximum likelihood phylogenetic analyses suggest that the relationship between D. bruxellensis, S. cerevisiae, and Candida albicans is close to a trichotomy. The estimated rate of chromosomal rearrangement in D. bruxellensis is slower than that calculated for C. albicans, while its rate of amino acid evolution is somewhat higher. The proteome of D. bruxellensis is enriched for transporters and genes involved in nitrogen and lipid metabolism, among other functions, which may reflect adaptations to its low-nutrient, high-ethanol niche. We also identified an adenyl deaminase gene that has high similarity to a gene in bacteria of the Burkholderia cepacia species complex and appears to be the result of horizontal gene transfer. These data provide a resource for further analyses of the population genetics and evolution of D. bruxellensis and of the genetic bases of its physiological capabilities.}, }
@article {pmid17277061, year = {2007}, author = {Xu, P and Alves, JM and Kitten, T and Brown, A and Chen, Z and Ozaki, LS and Manque, P and Ge, X and Serrano, MG and Puiu, D and Hendricks, S and Wang, Y and Chaplin, MD and Akan, D and Paik, S and Peterson, DL and Macrina, FL and Buck, GA}, title = {Genome of the opportunistic pathogen Streptococcus sanguinis.}, journal = {Journal of bacteriology}, volume = {189}, number = {8}, pages = {3166-3175}, pmid = {17277061}, issn = {0021-9193}, support = {K02 AI054908-05/AI/NIAID NIH HHS/United States ; R01 AI047841/AI/NIAID NIH HHS/United States ; DE12882/DE/NIDCR NIH HHS/United States ; K02 AI054908-01/AI/NIAID NIH HHS/United States ; R01 AI047841-03/AI/NIAID NIH HHS/United States ; R01 AI047841-01A1/AI/NIAID NIH HHS/United States ; AI054908/AI/NIAID NIH HHS/United States ; K02 AI054908-04/AI/NIAID NIH HHS/United States ; K02 AI054908-02/AI/NIAID NIH HHS/United States ; R01 AI047841-02/AI/NIAID NIH HHS/United States ; AI47841/AI/NIAID NIH HHS/United States ; K02 AI054908/AI/NIAID NIH HHS/United States ; R01 AI047841-04A1/AI/NIAID NIH HHS/United States ; R01 AI047841-05/AI/NIAID NIH HHS/United States ; K02 AI054908-03/AI/NIAID NIH HHS/United States ; R01 AI047841-06/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/analysis/metabolism ; Base Composition ; Dental Plaque/microbiology ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; Molecular Sequence Data ; Opportunistic Infections/microbiology ; RNA, Bacterial/metabolism ; RNA, Transfer/metabolism ; Streptococcal Infections/microbiology ; Streptococcus/*genetics/pathogenicity ; rRNA Operon ; }, abstract = {The genome of Streptococcus sanguinis is a circular DNA molecule consisting of 2,388,435 bp and is 177 to 590 kb larger than the other 21 streptococcal genomes that have been sequenced. The G+C content of the S. sanguinis genome is 43.4%, which is considerably higher than the G+C contents of other streptococci. The genome encodes 2,274 predicted proteins, 61 tRNAs, and four rRNA operons. A 70-kb region encoding pathways for vitamin B(12) biosynthesis and degradation of ethanolamine and propanediol was apparently acquired by horizontal gene transfer. The gene complement suggests new hypotheses for the pathogenesis and virulence of S. sanguinis and differs from the gene complements of other pathogenic and nonpathogenic streptococci. In particular, S. sanguinis possesses a remarkable abundance of putative surface proteins, which may permit it to be a primary colonizer of the oral cavity and agent of streptococcal endocarditis and infection in neutropenic patients.}, }
@article {pmid17274820, year = {2007}, author = {Podell, S and Gaasterland, T}, title = {DarkHorse: a method for genome-wide prediction of horizontal gene transfer.}, journal = {Genome biology}, volume = {8}, number = {2}, pages = {R16}, pmid = {17274820}, issn = {1474-760X}, mesh = {Algorithms ; Computational Biology/*methods ; Databases, Genetic ; Gene Transfer, Horizontal/*genetics ; Genomics/*methods ; Phylogeny ; Probability ; *Software ; }, abstract = {A new approach to rapid, genome-wide identification and ranking of horizontal transfer candidate proteins is presented. The method is quantitative, reproducible, and computationally undemanding. It can be combined with genomic signature and/or phylogenetic tree-building procedures to improve accuracy and efficiency. The method is also useful for retrospective assessments of horizontal transfer prediction reliability, recognizing orthologous sequences that may have been previously overlooked or unavailable. These features are demonstrated in bacterial, archaeal, and eukaryotic examples.}, }
@article {pmid17273854, year = {2007}, author = {Mohr, KI and Tebbe, CC}, title = {Field study results on the probability and risk of a horizontal gene transfer from transgenic herbicide-resistant oilseed rape pollen to gut bacteria of bees.}, journal = {Applied microbiology and biotechnology}, volume = {75}, number = {3}, pages = {573-582}, doi = {10.1007/s00253-007-0846-7}, pmid = {17273854}, issn = {0175-7598}, mesh = {Aminobutyrates/pharmacology ; Animals ; Bacteria/classification/*genetics/growth &amp; development ; Bees/*microbiology ; Brassica napus/drug effects/*genetics ; Gene Transfer, Horizontal/*genetics ; Herbicide Resistance/genetics ; Herbicides/pharmacology ; Phylogeny ; Plants, Genetically Modified ; Pollen/*genetics ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Bees are specifically subjected to intimate contacts with transgenic plants due to their feeding activities on pollen. In this study, the probability and ecological risk of a gene transfer from pollen to gut bacteria of bees was investigated with larvae of Apis mellifera (honeybee), Bombus terrestris (bumblebee), and Osmia bicornis (red mason bee), all collected at a flowering transgenic oilseed rape field. The plants were genetically engineered with the pat-gene, conferring resistance against glufosinate (syn. phosphinothricin), a glutamine-synthetase inhibitor in plants and microorganisms. Ninety-six bacterial strains were isolated and characterized by 16S rRNA gene sequencing, revealing that Firmicutes represented 58% of the isolates, Actinobacteria 31%, and Proteobacteria 11%, respectively. Of all isolates, 40% were resistant to 1 mM glufosinate, and 11% even to 10 mM. Resistant phenotypes were found in all phylogenetic groups. None of the resistant phenotypes carried the recombinant pat-gene in its genome. The threshold of detecting gene transfer in this field study was relatively insensitive due to the high background of natural glufosinate resistance. However, the broad occurrence of glufosinate-resistant bacteria from different phylogenetic groups suggests that rare events of horizontal gene transfer will not add significantly to natural bacterial glufosinate resistance.}, }
@article {pmid17265000, year = {2007}, author = {Batista, JS and Hungria, M and Barcellos, FG and Ferreira, MC and Mendes, IC}, title = {Variability in Bradyrhizobium japonicum and B. elkanii seven years after introduction of both the exotic microsymbiont and the soybean host in a cerrados soil.}, journal = {Microbial ecology}, volume = {53}, number = {2}, pages = {270-284}, pmid = {17265000}, issn = {0095-3628}, mesh = {Adaptation, Physiological ; Bradyrhizobium/*physiology ; Brazil ; Genetic Variation ; Genome, Bacterial ; Recombination, Genetic ; Glycine max/*microbiology ; Symbiosis ; }, abstract = {The plasticity of rhizobial genomes is far greater than previously thought, with complex genomic recombination events that may be accelerated by the often stressful environmental conditions of the tropics. This study aimed at evaluating changes in soybean rhizobia due to adaptation to inhospitable environmental conditions (high temperatures, drought, and acid soils) in the Brazilian Cerrados. Both the host plant and combinations of four strains of soybean Bradyrhizobium were introduced in an uncropped soil devoid of rhizobia capable of nodulating soybean. After the third year, seeds were not reinoculated. Two hundred and sixty-three isolates were obtained from nodules of field-grown soybean after the seventh year, and their morphological, physiological, serological, and symbiotic properties determined, followed by genetic analysis of conserved and symbiotic genes. B. japonicum strain CPAC 15 (same serogroup as USDA 123) was characterized as having high saprophytic capacity and competitiveness and by the seventh year represented up to 70% of the cultivable population, in contrast to the poor survival and competitiveness of B. japonicum strain CPAC 7 (same serogroup as CB 1809). In general, adapted strains had increased mucoidy, and up to 43% of the isolates showed no serological reaction. High variability, presumably resulting from the adaptation to the harsh environmental conditions, was verified in rep-PCR (polymerase chain reaction) profiles, being lower in strain CPAC 15, intermediate in B. elkanii, and higher in CPAC 7. Restriction fragment length polymorphism (RFLP)-PCR types of the 16S rDNA corresponded to the following: one type for B. elkanii species, two for B. japonicum, associated to CPAC 15 and CPAC 7, and unknown combinations of profiles. However, when nodC sequences and RFLP-PCR of the nifH region data were considered, only two clusters were observed having full congruence with B. japonicum and B. elkanii species. Combining the results, variability was such that even within a genetically more stable group (such as that of CPAC 15), only 6.4% of the isolates showed high similarity to the inoculant strain, whereas none was similar to CPAC 7. The genetic variability in our study seems to result from a variety and combination of events including strain dispersion, genomic recombination, and horizontal gene transfer. Furthermore, the genetic variability appears to be mainly associated with adaptation, saprophytic capacity, and competitiveness, and not with symbiotic effectiveness, as the similarity of symbiotic genes was higher than that of conserved regions of the DNA.}, }
@article {pmid17263848, year = {2007}, author = {Ryan, RP and Ryan, DJ and Sun, YC and Li, FM and Wang, Y and Dowling, DN}, title = {An acquired efflux system is responsible for copper resistance in Xanthomonas strain IG-8 isolated from China.}, journal = {FEMS microbiology letters}, volume = {268}, number = {1}, pages = {40-46}, doi = {10.1111/j.1574-6968.2006.00592.x}, pmid = {17263848}, issn = {0378-1097}, mesh = {Bacterial Proteins/genetics/*metabolism ; China ; Computational Biology ; Copper/*pharmacology ; *Drug Resistance, Multiple, Bacterial ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Membrane Transport Proteins/genetics/*metabolism ; Microbial Sensitivity Tests ; Molecular Sequence Data ; *Multigene Family ; Sequence Analysis, DNA ; Xanthomonas/*drug effects/genetics/isolation &amp; purification ; }, abstract = {The genus Xanthomonas contains plant pathogens exhibiting innate resistance to a range of antimicrobial agents. In other genera, multidrug resistance is mediated by a synergy between a low-permeability outer membrane and expression of a number of multidrug efflux systems. This report describes the isolation of a novel gene cluster xmeRSA from Xanthomonas strain IG-8 that mediates copper chloride resistance. Subsequent analysis of these genes showed that they were responsible for the high level of multiple resistance in this strain and were homologues of the sme system of Stenotrophomonas maltophilia. Knock-out mutants of this gene cluster indicate that these genes are required for the copper resistance phenotype of strain IG-8. Expression analysis using lacZ fusions indicates that the genes are regulated by copper and other antimicrobials. Bioinformatic analysis suggests that these genes were acquired by horizontal gene transfer.}, }
@article {pmid17261804, year = {2007}, author = {Doolittle, WF and Bapteste, E}, title = {Pattern pluralism and the Tree of Life hypothesis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {7}, pages = {2043-2049}, pmid = {17261804}, issn = {0027-8424}, mesh = {Animals ; *Biological Evolution ; Gene Transfer, Horizontal ; Genetic Variation ; Humans ; *Models, Genetic ; Phylogeny ; }, abstract = {Darwin claimed that a unique inclusively hierarchical pattern of relationships between all organisms based on their similarities and differences [the Tree of Life (TOL)] was a fact of nature, for which evolution, and in particular a branching process of descent with modification, was the explanation. However, there is no independent evidence that the natural order is an inclusive hierarchy, and incorporation of prokaryotes into the TOL is especially problematic. The only data sets from which we might construct a universal hierarchy including prokaryotes, the sequences of genes, often disagree and can seldom be proven to agree. Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true. This is not to say that similarities and differences between organisms are not to be accounted for by evolutionary mechanisms, but descent with modification is only one of these mechanisms, and a single tree-like pattern is not the necessary (or expected) result of their collective operation. Pattern pluralism (the recognition that different evolutionary models and representations of relationships will be appropriate, and true, for different taxa or at different scales or for different purposes) is an attractive alternative to the quixotic pursuit of a single true TOL.}, }
@article {pmid17259616, year = {2007}, author = {De Gelder, L and Ponciano, JM and Joyce, P and Top, EM}, title = {Stability of a promiscuous plasmid in different hosts: no guarantee for a long-term relationship.}, journal = {Microbiology (Reading, England)}, volume = {153}, number = {Pt 2}, pages = {452-463}, doi = {10.1099/mic.0.2006/001784-0}, pmid = {17259616}, issn = {1350-0872}, support = {P20 RR016448/RR/NCRR NIH HHS/United States ; P20 RR16448/RR/NCRR NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics ; *Conjugation, Genetic ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; Models, Biological ; Plasmids/*genetics ; Proteobacteria/*classification/*genetics/growth &amp; development ; Species Specificity ; }, abstract = {Broad-host-range (BHR) IncP-1 plasmids have the ability to transfer between and replicate in nearly all species of the Alpha-, Beta- and Gammaproteobacteria, but surprisingly few data are available on the stability of these plasmids in strains within their host range. Moreover, even though molecular interactions between the bacterial host and its plasmid(s) exist, no systematic study to date has compared the stability of the same plasmid among different hosts. The goal of this study was to examine whether the stability characteristics of an IncP-1 plasmid can be variable between strains within the host range of the plasmid. Therefore, 19 strains within the Alpha-, Beta- or Gammaproteobacteria carrying the IncP-1beta plasmid pB10 were serially propagated in non-selective medium and the fraction of segregants was monitored through replica-picking. Remarkably, a large variation in the stability of pB10 in different strains was found, even between strains within the same genus or species. Ten strains showed no detectable plasmid loss over about 200 generations, and in two strains plasmid-free clones were only sporadically observed. In contrast, three strains, Pseudomonas koreensis R28, Pseudomonas putida H2 and Stenotrophomonas maltophilia P21, exhibited rapid plasmid loss within 80 generations. Parameter estimation after mathematical modelling of these stability data suggested high frequencies of segregation (about 0.04 per generation) or high plasmid cost (i.e. a relative fitness decrease in plasmid-bearing cells of about 15 and 40 %), which was confirmed experimentally. The models also suggested that plasmid reuptake by conjugation only played a significant role in plasmid stability in one of the three strains. Four of the 19 strains lost the plasmid very slowly over about 600 generations. The erratic decrease of the plasmid-containing fraction and simulation of the data with a new mathematical model suggested that plasmid cost was variable over time due to compensatory mutations. The findings of this study demonstrate that the ability of a so-called 'BHR' plasmid to persist in a bacterial population is influenced by strain-specific traits, and therefore observations made for one strain should not be generalized for the entire species or genus.}, }
@article {pmid17257059, year = {2007}, author = {Leavis, HL and Willems, RJ and van Wamel, WJ and Schuren, FH and Caspers, MP and Bonten, MJ}, title = {Insertion sequence-driven diversification creates a globally dispersed emerging multiresistant subspecies of E. faecium.}, journal = {PLoS pathogens}, volume = {3}, number = {1}, pages = {e7}, pmid = {17257059}, issn = {1553-7374}, mesh = {Base Sequence ; *DNA Transposable Elements ; *Drug Resistance, Multiple, Bacterial ; Enterococcus faecium/*classification/drug effects/genetics ; Evolution, Molecular ; Gene Rearrangement ; Genome, Bacterial ; Molecular Sequence Data ; Mosaicism ; Oligonucleotide Array Sequence Analysis ; Open Reading Frames ; Phylogeny ; Recombination, Genetic ; }, abstract = {Enterococcus faecium, an ubiquous colonizer of humans and animals, has evolved in the last 15 years from an avirulent commensal to the third most frequently isolated nosocomial pathogen among intensive care unit patients in the United States. E. faecium combines multidrug resistance with the potential of horizontal resistance gene transfer to even more pathogenic bacteria. Little is known about the evolution and virulence of E. faecium, and genomic studies are hampered by the absence of a completely annotated genome sequence. To further unravel its evolution, we used a mixed whole-genome microarray and hybridized 97 E. faecium isolates from different backgrounds (hospital outbreaks (n = 18), documented infections (n = 34) and asymptomatic carriage of hospitalized patients (n = 15), and healthy persons (n = 15) and animals (n = 21)). Supported by Bayesian posterior probabilities (PP = 1.0), a specific clade containing all outbreak-associated strains and 63% of clinical isolates was identified. Sequencing of 146 of 437 clade-specific inserts revealed mobile elements (n = 74), including insertion sequence (IS) elements (n = 42), phage genes (n = 6) and plasmid sequences (n = 26), hypothetical (n = 58) and membrane proteins (n = 10), and antibiotic resistance (n = 9) and regulatory genes (n = 11), mainly located on two contigs of the unfinished E. faecium DO genome. Split decomposition analysis, varying guanine cytosine content, and aberrant codon adaptation indices all supported acquisition of these genes through horizontal gene transfer with IS16 as the predicted most prominent insert (98% sensitive, 100% specific). These findings suggest that acquisition of IS elements has facilitated niche adaptation of a distinct E. faecium subpopulation by increasing its genome plasticity. Increased genome plasticity was supported by higher diversity indices (ratio of average genetic similarities of pulsed-field gel electrophoresis and multi locus sequence typing) for clade-specific isolates. Interestingly, the previously described multi locus sequence typing-based clonal complex 17 largely overlapped with this clade. The present data imply that the global emergence of E. faecium, as observed since 1990, represents the evolution of a subspecies with a presumably better adaptation than other E. faecium isolates to the constraints of a hospital environment.}, }
@article {pmid17257051, year = {2007}, author = {Wertz, JE and McGregor, KF and Bessen, DE}, title = {Detecting key structural features within highly recombined genes.}, journal = {PLoS computational biology}, volume = {3}, number = {1}, pages = {e14}, pmid = {17257051}, issn = {1553-7358}, support = {GM60793/GM/NIGMS NIH HHS/United States ; R01 AI065572/AI/NIAID NIH HHS/United States ; R01 GM060793/GM/NIGMS NIH HHS/United States ; R21 AI061454/AI/NIAID NIH HHS/United States ; AI061454/AI/NIAID NIH HHS/United States ; AI065572/AI/NIAID NIH HHS/United States ; }, mesh = {*Algorithms ; Base Sequence ; Chromosome Mapping/*methods ; DNA Mutational Analysis/*methods ; Molecular Sequence Data ; Penicillin-Binding Proteins/*genetics ; Phylogeny ; Recombination, Genetic/*genetics ; Sequence Alignment/*methods ; Sequence Analysis, DNA/*methods ; }, abstract = {Many microorganisms exhibit high levels of intragenic recombination following horizontal gene transfer events. Furthermore, many microbial genes are subject to strong diversifying selection as part of the pathogenic process. A multiple sequence alignment is an essential starting point for many of the tools that provide fundamental insights on gene structure and evolution, such as phylogenetics; however, an accurate alignment is not always possible to attain. In this study, a new analytic approach was developed in order to better quantify the genetic organization of highly diversified genes whose alleles do not align. This BLAST-based method, denoted BLAST Miner, employs an iterative process that places short segments of highly similar sequence into discrete datasets that are designated "modules." The relative positions of modules along the length of the genes, and their frequency of occurrence, are used to identify sequence duplications, insertions, and rearrangements. Partial alleles of sof from Streptococcus pyogenes, encoding a surface protein under host immune selection, were analyzed for module content. High-frequency Modules 6 and 13 were identified and examined in depth. Nucleotide sequences corresponding to both modules contain numerous duplications and inverted repeats, whereby many codons form palindromic pairs. Combined with evidence for a strong codon usage bias, data suggest that Module 6 and 13 sequences are under selection to preserve their nucleic acid secondary structure. The concentration of overlapping tandem and inverted repeats within a small region of DNA is highly suggestive of a mechanistic role for Module 6 and 13 sequences in promoting aberrant recombination. Analysis of pbp2X alleles from Streptococcus pneumoniae, encoding cell wall enzymes that confer antibiotic resistance, supports the broad applicability of this tool in deciphering the genetic organization of highly recombined genes. BLAST Miner shares with phylogenetics the important predictive quality that leads to the generation of testable hypotheses based on sequence data.}, }
@article {pmid17253090, year = {2007}, author = {Payandeh, J and Pai, EF}, title = {Enzyme-driven speciation: crystallizing Archaea via lipid capture.}, journal = {Journal of molecular evolution}, volume = {64}, number = {3}, pages = {364-374}, pmid = {17253090}, issn = {0022-2844}, mesh = {Alkyl and Aryl Transferases/*genetics ; Amino Acid Sequence ; Archaea/enzymology/*genetics ; Archaeal Proteins/*genetics ; Archaeoglobus/enzymology/genetics ; *Evolution, Molecular ; Genome, Archaeal ; Membrane Lipids/*biosynthesis/chemistry ; Models, Molecular ; }, abstract = {As the origin(s) of life on Earth remains an open question, detailed characteristics about the "last universal ancestor" (LUA) continue to be obscured. Here we provide arguments that strengthen the bacterial-like nature of the LUA. Our view attempts to recreate the evolution of archaeal lipids, the major components of the distinctive membrane that encapsulates these ancient prokaryotes. We show that (S)- 3-O-geranylgeranylglyceryl phosphate synthase (GGGPS), a TIM-barrel protein that performs the committed step in archaeal lipid synthesis, likely evolved from the duplication and fusion of a (betaalpha)4 half-barrel ancestor. By comparison to the well-characterized HisA and HisF TIM-barrel proteins, we propose a time line for the invention of this diagnostic archaeal biosynthetic pathway. After excluding the possibility of horizontal gene transfer, we conclude that the evolutionary history of GGGPS mirrors the emergence of Archaea from the LUA. We illustrate aspects of this "lipid capture" model that support its likelihood in recreating key evolutionary events and, as our hypothesis is built on a single initiating event, we suggest that the appearance of GGGPS represents an example of enzyme-driven speciation.}, }
@article {pmid17251963, year = {2007}, author = {Goldenfeld, N and Woese, C}, title = {Biology's next revolution.}, journal = {Nature}, volume = {445}, number = {7126}, pages = {369}, doi = {10.1038/445369a}, pmid = {17251963}, issn = {1476-4687}, mesh = {Bacteria/genetics ; Biology/*trends ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; *Models, Biological ; Species Specificity ; Terminology as Topic ; Viruses/genetics ; }, }
@article {pmid17251179, year = {2007}, author = {Touchon, M and Rocha, EP}, title = {Causes of insertion sequences abundance in prokaryotic genomes.}, journal = {Molecular biology and evolution}, volume = {24}, number = {4}, pages = {969-981}, doi = {10.1093/molbev/msm014}, pmid = {17251179}, issn = {0737-4038}, mesh = {Computational Biology ; DNA Transposable Elements/*genetics ; Databases, Nucleic Acid ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Archaeal/*genetics ; Genome, Bacterial/*genetics ; Humans ; Mutagenesis, Insertional ; Prokaryotic Cells/*metabolism ; RNA, Ribosomal, 16S/genetics ; Selection, Genetic ; }, abstract = {Insertion sequences (ISs) are the smallest and most frequent transposable elements in prokaryotes where they play an important evolutionary role by promoting gene inactivation and genome plasticity. Their genomic abundance varies by several orders of magnitude for reasons largely unknown and widely speculated. The current availability of hundreds of genomes renders testable many of these hypotheses, notably that IS abundance correlates positively with the frequency of horizontal gene transfer (HGT), genome size, pathogenicity, nonobligatory ecological associations, and human association. We thus reannotated ISs in 262 prokaryotic genomes and tested these hypotheses showing that when using appropriate controls, there is no empirical basis for IS family specificity, pathogenicity, or human association to influence IS abundance or density. HGT seems necessary for the presence of ISs, but cannot alone explain the absence of ISs in more than 20% of the organisms, some of which showing high rates of HGT. Gene transfer is also not a significant determinant of the abundance of IS elements in genomes, suggesting that IS abundance is controlled at the level of transposition and ensuing natural selection and not at the level of infection. Prokaryotes engaging in obligatory associations have fewer ISs when controlled for genome size, but this may be caused by some being sexually isolated. Surprisingly, genome size is the only significant predictor of IS numbers and density. Alone, it explains over 40% of the variance of IS abundance. Because we find that genome size and IS abundance correlate negatively with minimal doubling times, we conclude that selection for rapid replication cannot account for the few ISs found in small genomes. Instead, we show evidence that IS numbers are controlled by the frequency of highly deleterious insertion targets. Indeed, IS abundance increases quickly with genome size, which is the exact inverse trend found for the density of genes under strong selection such as essential genes. Hence, for ISs, the bigger the genome the better.}, }
@article {pmid17244039, year = {2007}, author = {Wolfe, LM and Blair, AC}, title = {Born to run: competition enhances the spread of genes from crops to wild relatives.}, journal = {The New phytologist}, volume = {173}, number = {3}, pages = {450-452}, doi = {10.1111/j.1469-8137.2007.01982.x}, pmid = {17244039}, issn = {0028-646X}, mesh = {Crops, Agricultural/*genetics ; Fertility ; *Gene Transfer, Horizontal ; *Genes, Plant ; Quantitative Trait, Heritable ; Raphanus/*genetics ; }, }
@article {pmid17241245, year = {2007}, author = {Abe, M and Izumoji, Y and Tanji, Y}, title = {Phenotypic transformation including host-range transition through superinfection of T-even phages.}, journal = {FEMS microbiology letters}, volume = {269}, number = {1}, pages = {145-152}, doi = {10.1111/j.1574-6968.2006.00615.x}, pmid = {17241245}, issn = {0378-1097}, mesh = {Escherichia coli/classification/*virology ; *Gene Transfer, Horizontal ; Genome, Viral ; Phenotype ; T-Phages/*genetics/pathogenicity ; }, abstract = {Mosaic genome design, considered evidence of horizontal gene transfer, is prominent in T-even phage tail fiber genes involved in host recognition. The possibility of direct gene transfer was assessed through superinfection with two virulent phages T2 and PP01, which caused host recognition shift. Two recombinant phages designated as TPr03 and TPr04 were isolated. PCR-restriction fragment length polymorphism analysis and sequence analysis suggested that 18% of the TPr03 and 38% of the TPr04 genome derived from PP01. Both isolates showed host ranges identical to PP01. The results suggested the possibility of generating various recombinant phages by intentional dual infections and of the occasional occurrence in nature of generation of phage showing new characteristics through superinfection, followed by the genomic recombination.}, }
@article {pmid17241242, year = {2007}, author = {Louis, P and McCrae, SI and Charrier, C and Flint, HJ}, title = {Organization of butyrate synthetic genes in human colonic bacteria: phylogenetic conservation and horizontal gene transfer.}, journal = {FEMS microbiology letters}, volume = {269}, number = {2}, pages = {240-247}, doi = {10.1111/j.1574-6968.2006.00629.x}, pmid = {17241242}, issn = {0378-1097}, mesh = {Acyl Coenzyme A/metabolism ; Bacteria, Anaerobic/enzymology/*genetics/growth &amp; development ; Base Sequence ; Butyrates/*metabolism ; Coenzyme A-Transferases/chemistry/*genetics ; Colon/*microbiology ; Conserved Sequence ; *Gene Transfer, Horizontal ; Humans ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Substrate Specificity ; }, abstract = {Butyrate producers constitute an important bacterial group in the human large intestine. Butyryl-CoA is formed from two molecules of acetyl-CoA in a process resembling beta-oxidation in reverse. Three different arrangements of the six genes coding for this pathway have been found in low mol% G+C-content gram-positive human colonic bacteria using DNA sequencing and degenerate PCR. Gene arrangements were strongly conserved within phylogenetic groups defined by 16S rRNA gene sequence relationships. In the case of one of the genes, encoding beta-hydroxybutyryl-CoA dehydrogenase, however, sequence relationships were strongly suggestive of horizontal gene transfer between lineages. The newly identified gene for butyryl-CoA CoA-transferase, which performs the final step in butyrate formation in most known human colonic bacteria, was not closely linked to these central pathway genes.}, }
@article {pmid17240729, year = {2006}, author = {Pigliucci, M}, title = {Evolutionary biology: puzzle solving or paradigm shifting?.}, journal = {The Quarterly review of biology}, volume = {81}, number = {4}, pages = {377-379}, doi = {10.1086/511530}, pmid = {17240729}, issn = {0033-5770}, mesh = {Biological Evolution ; *Gene Transfer, Horizontal ; Humans ; Microbiology ; Models, Theoretical ; *Molecular Biology ; *Phylogeny ; Problem Solving ; *Social Change ; }, }
@article {pmid17238929, year = {2007}, author = {Derbise, A and Chenal-Francisque, V and Pouillot, F and Fayolle, C and Prévost, MC and Médigue, C and Hinnebusch, BJ and Carniel, E}, title = {A horizontally acquired filamentous phage contributes to the pathogenicity of the plague bacillus.}, journal = {Molecular microbiology}, volume = {63}, number = {4}, pages = {1145-1157}, doi = {10.1111/j.1365-2958.2006.05570.x}, pmid = {17238929}, issn = {0950-382X}, mesh = {Animals ; Bacteriophages/*genetics/physiology ; Evolution, Molecular ; Female ; Gene Order ; *Gene Transfer, Horizontal ; Genomic Instability ; Lysogeny ; Mice ; Mice, Inbred C57BL ; Plague/microbiology ; Prophages/genetics ; Siphonaptera/microbiology ; Virulence/genetics ; Yersinia pestis/genetics/*pathogenicity/*virology ; }, abstract = {Yersinia pestis, the plague bacillus, has an exceptional pathogenicity but the factors responsible for its extreme virulence are still unknown. A genome comparison with its less virulent ancestor Yersinia pseudotuberculosis identified a few Y. pestis-specific regions acquired after their divergence. One of them potentially encodes a prophage (YpfPhi), similar to filamentous phages associated with virulence in other pathogens. We show here that YpfPhi forms filamentous phage particles infectious for other Y. pestis isolates. Although it was previously suggested that YpfPhi is restricted to the Orientalis branch, our results indicate that it was acquired by the Y. pestis ancestor. In Antiqua and Medievalis strains, YpfPhi genome forms an unstable episome whereas in Orientalis isolates it is stably integrated as tandem repeats. Deletion of the YpfPhi genome does not affect Y. pestis ability to colonize and block the flea proventriculus, but results in an alteration of Y. pestis pathogenicity in mice. Our results show that transformation of Y. pestis from a classical enteropathogen to the highly virulent plague bacillus was accompanied by the acquisition of an unstable filamentous phage. Continued maintenance of YpfPhi despite its high in vitro instability suggests that it confers selective advantages to Y. pestis under natural conditions.}, }
@article {pmid17238918, year = {2007}, author = {Richmond, GS and Smith, TK}, title = {A novel phospholipase from Trypanosoma brucei.}, journal = {Molecular microbiology}, volume = {63}, number = {4}, pages = {1078-1095}, pmid = {17238918}, issn = {0950-382X}, support = {/WT_/Wellcome Trust/United Kingdom ; 067441/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Catalytic Domain ; Cloning, Molecular ; Cytosol/enzymology ; Evolution, Molecular ; Hydrolysis ; Lysophosphatidylcholines/metabolism ; Molecular Sequence Data ; Mutation ; Phosphatidylcholines/metabolism ; Phospholipases A/*genetics/*metabolism ; Phylogeny ; Recombinant Proteins/genetics/isolation &amp; purification/metabolism ; Sequence Homology, Amino Acid ; Substrate Specificity ; Trypanosoma brucei brucei/*enzymology/genetics ; }, abstract = {Phospholipase A(1) activities have been detected in most cells where they have been sought and yet their characterization lags far behind that of the phospholipases A(2), C and D. The study presented here details the first cloning and characterization of a cytosolic PLA(1) that exhibits preference for phosphatidylcholine (GPCho) substrates. Trypanosoma brucei phospholipase A(1) (TbPLA(1)) is unique from previously identified eukaryotic PLA(1) because it is evolutionarily related to bacterial secreted PLA(1). A T. brucei ancestor most likely acquired the PLA(1) from a horizontal gene transfer of a PLA(1) from Sodalis glossinidius, a bacterial endosymbiont of tsetse flies. Nano-electrospray ionization tandem mass spectrometry analysis of TbPLA(1) mutants established that the enzyme functions in vivo to synthesize lysoGPCho metabolites containing long-chain mostly polyunsaturated and highly unsaturated fatty acids. Analysis of purified mutated recombinant forms of TbPLA(1) revealed that this enzyme is a serine hydrolase whose catalytic mechanism involves a triad consisting of the amino acid residues Ser-131, His-234 and Asp-183. The TbPLA(1) homozygous null mutants generated here constitute the only PLA(1) double knockouts from any organism.}, }
@article {pmid17238916, year = {2007}, author = {Hopwood, DA}, title = {How do antibiotic-producing bacteria ensure their self-resistance before antibiotic biosynthesis incapacitates them?.}, journal = {Molecular microbiology}, volume = {63}, number = {4}, pages = {937-940}, doi = {10.1111/j.1365-2958.2006.05584.x}, pmid = {17238916}, issn = {0950-382X}, mesh = {Anthraquinones/metabolism ; Anti-Bacterial Agents/*biosynthesis/metabolism ; *Bacterial Physiological Phenomena ; Drug Resistance, Bacterial/*physiology ; Gene Expression Regulation, Bacterial ; Mycobacterium tuberculosis/drug effects/physiology ; Streptomyces coelicolor/*drug effects/*physiology ; }, abstract = {Acquired antibiotic resistance among dangerous bacterial pathogens is an increasing medical problem. While in Mycobacterium tuberculosis this occurs by mutation in the genes encoding the targets for antibiotic action, other pathogens have generally gained their resistance genes by horizontal gene transfer from non-pathogenic bacteria. The ultimate source of many of these genes is almost certainly the actinomycetes that make the antibiotics and therefore need self-protective mechanisms to avoid suicide. How do they ensure that they are resistant at the time when intracellular antibiotic concentrations reach potentially lethal levels? In this issue of Molecular Microbiology, Tahlan et al. describe a solution to this problem in which an antibiotically inactive precursor of a Streptomyces coelicolor antibiotic induces resistance -- in this example by means of a trans-membrane export pump -- so that the organism is already primed for resistance at the time when it is needed. The authors generalize their interpretation to other cases where antibiotic resistance depends on export, but it will be interesting to find out whether it could in fact apply more widely, to include the other major mechanisms of resistance: target modification and the synthesis of antibiotics via a series of chemically modified intermediates, with removal of the protective group at the time of secretion into the outside medium.}, }
@article {pmid17237079, year = {2007}, author = {Jin, G and Nakhleh, L and Snir, S and Tuller, T}, title = {Efficient parsimony-based methods for phylogenetic network reconstruction.}, journal = {Bioinformatics (Oxford, England)}, volume = {23}, number = {2}, pages = {e123-8}, doi = {10.1093/bioinformatics/btl313}, pmid = {17237079}, issn = {1367-4811}, mesh = {*Algorithms ; Amino Acid Sequence ; Conserved Sequence/genetics ; *Evolution, Molecular ; Molecular Sequence Data ; *Phylogeny ; Proteome/genetics/*metabolism ; Sequence Alignment/*methods ; Sequence Analysis, Protein/*methods ; Sequence Homology, Amino Acid ; Signal Transduction/*genetics ; }, abstract = {MOTIVATION: Phylogenies--the evolutionary histories of groups of organisms-play a major role in representing relationships among biological entities. Although many biological processes can be effectively modeled as tree-like relationships, others, such as hybrid speciation and horizontal gene transfer (HGT), result in networks, rather than trees, of relationships. Hybrid speciation is a significant evolutionary mechanism in plants, fish and other groups of species. HGT plays a major role in bacterial genome diversification and is a significant mechanism by which bacteria develop resistance to antibiotics. Maximum parsimony is one of the most commonly used criteria for phylogenetic tree inference. Roughly speaking, inference based on this criterion seeks the tree that minimizes the amount of evolution. In 1990, Jotun Hein proposed using this criterion for inferring the evolution of sequences subject to recombination. Preliminary results on small synthetic datasets. Nakhleh et al. (2005) demonstrated the criterion's application to phylogenetic network reconstruction in general and HGT detection in particular. However, the naive algorithms used by the authors are inapplicable to large datasets due to their demanding computational requirements. Further, no rigorous theoretical analysis of computing the criterion was given, nor was it tested on biological data.<br><br>RESULTS: In the present work we prove that the problem of scoring the parsimony of a phylogenetic network is NP-hard and provide an improved fixed parameter tractable algorithm for it. Further, we devise efficient heuristics for parsimony-based reconstruction of phylogenetic networks. We test our methods on both synthetic and biological data (rbcL gene in bacteria) and obtain very promising results.}, }
@article {pmid17237077, year = {2007}, author = {Clemente, JC and Satou, K and Valiente, G}, title = {Phylogenetic reconstruction from non-genomic data.}, journal = {Bioinformatics (Oxford, England)}, volume = {23}, number = {2}, pages = {e110-5}, doi = {10.1093/bioinformatics/btl307}, pmid = {17237077}, issn = {1367-4811}, mesh = {*Algorithms ; Chromosome Mapping ; Computer Simulation ; Databases, Factual ; Evolution, Molecular ; Gene Expression Regulation/*physiology ; Information Storage and Retrieval/methods ; *Models, Biological ; Multienzyme Complexes/*metabolism ; *Phylogeny ; Proteome/*metabolism ; Signal Transduction/*physiology ; }, abstract = {MOTIVATION: Recent results related to horizontal gene transfer suggest that phylogenetic reconstruction cannot be determined conclusively from sequence data, resulting in a shift from approaches based on polymorphism information in DNA or protein sequence to studies aimed at understanding the evolution of complete biological processes. The increasing amount of available information on metabolic pathways for several species makes it of greater relevance to understand the similarities and differences among such pathways. These similarities can then be used to infer phylogenetic trees not based exclusively in sequence data, therefore avoiding the previously mentioned problems.<br><br>RESULTS: In this article, we present a method to assess the structural similarity of metabolic pathways for several organisms. Our algorithms work by using one of the three possible enzyme similarity measures (hierarchical, information content, gene ontology), and one of the two clustering methods (neighbor-joining, unweighted pair group method with arithmetic mean), to produce a phylogenetic tree both in Newick and graphic format. The web server implementing our algorithms is optimized to answer queries in linear time.<br><br>AVAILABILITY: The software is available for free public use on a web server, at the address http://www.jaist.ac.jp/~clemente/cgi-bin/phylo.pl. It is available on demand in source code form for research use to educational institutions, non-profit research institutes, government research laboratories and individuals, for non-exclusive use, without the right of the licensee to further redistribute the source code.}, }
@article {pmid17233752, year = {2007}, author = {Krajmalnik-Brown, R and Sung, Y and Ritalahti, KM and Saunders, FM and Löffler, FE}, title = {Environmental distribution of the trichloroethene reductive dehalogenase gene (tceA) suggests lateral gene transfer among Dehalococcoides.}, journal = {FEMS microbiology ecology}, volume = {59}, number = {1}, pages = {206-214}, doi = {10.1111/j.1574-6941.2006.00243.x}, pmid = {17233752}, issn = {0168-6496}, mesh = {Base Sequence ; Chloroflexi/*enzymology/*genetics ; DNA Transposable Elements/genetics ; *Gene Transfer, Horizontal ; Oxidoreductases/*genetics ; }, abstract = {The trichloroethene reductive dehalogenase gene (tceA) of Dehalococcoides spp. was detected in 12 of 21 trichloroethene-to-ethene dechlorinating enrichment cultures established from aquifer and sediment samples collected from diverse geographic locations in the USA. Analysis of the tceA chromosomal regions indicated that the tceA genes shared greater than 95% sequence identity, and all shared identical tceAB spacer sequences and tceB genes downstream of tceA. A putative transposable element (PTE) was present 1077 bp downstream of the tceB stop codon in three of eight chromosomal regions analyzed. Sequence identity was interrupted downstream of tceB and upstream or downstream of the PTE, suggesting that intrachromosomal or interchromosomal transfer of tceAB had occurred.}, }
@article {pmid17233672, year = {2007}, author = {Maurelli, AT}, title = {Black holes, antivirulence genes, and gene inactivation in the evolution of bacterial pathogens.}, journal = {FEMS microbiology letters}, volume = {267}, number = {1}, pages = {1-8}, doi = {10.1111/j.1574-6968.2006.00526.x}, pmid = {17233672}, issn = {0378-1097}, mesh = {Adaptation, Biological/genetics ; Bacteria/*genetics/*pathogenicity ; *Evolution, Molecular ; Gene Deletion ; *Gene Silencing ; *Genes, Bacterial ; Mutation ; Virulence/*genetics ; }, abstract = {The evolution of bacterial pathogens from nonpathogenic ancestors is marked principally by the acquisition of virulence gene clusters on plasmids and pathogenicity islands via horizontal gene transfer. The flip side of this evolutionary force is the equally important adaptation of the newly minted pathogen to its new host niche. Pathoadaptive mutations take the form of modification of gene expression such that the pathogen is better fit to survive within the new niche. This mini-review describes the concept of pathoadaptation by loss of gene function. In this process, genes that are no longer compatible with the novel lifestyle of the pathogen are selectively inactivated either by point mutation, insertion, or deletion. These genes are called 'antivirulence genes'. Selective pressure sometimes leads to the deletion of large regions of the genome that contain antivirulence genes generating 'black holes' in the pathogen genome. Inactivation of antivirulence genes leads to a pathogen that is highly adapted to its host niche. Identification of antivirulence genes for a particular pathogen can lead to a better understanding of how it became a pathogen and the types of genetic traits that need to be silenced in order for the pathogen to colonize its new host niche successfully.}, }
@article {pmid17233593, year = {2007}, author = {Michell, RH}, title = {Evolution of the diverse biological roles of inositols.}, journal = {Biochemical Society symposium}, volume = {}, number = {74}, pages = {223-246}, doi = {10.1042/BSS0740223}, pmid = {17233593}, issn = {0067-8694}, mesh = {*Biological Evolution ; Models, Biological ; Phosphatidylinositols/chemistry/*metabolism ; }, abstract = {Several of the nine hexahydroxycylohexanes (inositols) have functions in Biology, with myo-inositol (Ins) in most of the starring roles; and Ins polyphosphates are amongst the most abundant organic phosphate constituents on Earth. Many Archaea make Ins and use it as a component of diphytanyl membrane phospholipids and the thermoprotective solute di-L-Ins-1,1'-phosphate. Few bacteria make Ins or use it, other than as a carbon source. Those that do include hyperthermophilic Thermotogales (which also employ di-L-Ins-1,1'-phosphate) and actinomycetes such as Mycobacterium spp. (which use mycothiol, an inositol-containing thiol, as an intracellular redox reagent and have characteristic phosphatidylinositol-linked surface oligosaccharides). Bacteria acquired their Ins3P synthases by lateral gene transfer from Archaea. Many eukaryotes, including stressed plants, insects, deep-sea animals and kidney tubule cells, adapt to environmental variation by making or accumulating diverse inositol derivatives as 'compatible' solutes. Eukaryotes use phosphatidylinositol derivatives for numerous roles in cell signalling and regulation and in protein anchoring at the cell surface. Remarkably, the diradylglycerol cores of archaeal and eukaryote/bacterial glycerophospholipids have mirror image configurations: sn-2,3 and sn-1,2 respectively. Multicellular animals and amoebozoans exhibit the greatest variety of functions for PtdIns derivatives, including the use of PtdIns(3,4,5)P3 as a signal. Evolutionarily, it seems likely that (i) early archaeons first made myo-inositol approx. 3500 Ma (million years) ago; (ii) archeons brought inositol derivatives into early eukaryotes (approx. 2000 Ma?); (iii) soon thereafter, eukaryotes established ubiquitous functions for phosphoinositides in membrane trafficking and Ins polyphosphate synthesis; and (iv) since approx. 1000 Ma, further waves of functional diversification in amoebozoans and metazoans have introduced Ins(1,4,5)P3 receptor Ca2+ channels and the messenger role of PtdIns(3,4,5)P3.}, }
@article {pmid17227414, year = {2007}, author = {Hügler, M and Huber, H and Molyneaux, SJ and Vetriani, C and Sievert, SM}, title = {Autotrophic CO2 fixation via the reductive tricarboxylic acid cycle in different lineages within the phylum Aquificae: evidence for two ways of citrate cleavage.}, journal = {Environmental microbiology}, volume = {9}, number = {1}, pages = {81-92}, doi = {10.1111/j.1462-2920.2006.01118.x}, pmid = {17227414}, issn = {1462-2912}, mesh = {ATP Citrate (pro-S)-Lyase/genetics/metabolism ; *Autotrophic Processes ; Bacteria/*classification/enzymology/genetics/*metabolism ; Carbon Dioxide/*metabolism ; Citric Acid/*metabolism ; *Citric Acid Cycle ; Coenzyme A Ligases/genetics/metabolism ; Evolution, Molecular ; Molecular Sequence Data ; Oxo-Acid-Lyases/genetics/metabolism ; Phylogeny ; }, abstract = {Autotrophic carbon fixation was characterized in representative members of the three lineages of the bacterial phylum Aquificae. Enzyme activity measurements and the detection of key genes demonstrated that Aquificae use the reductive tricarboxylic acid (TCA) cycle for autotrophic CO(2) fixation. This is the first time that strains of the Hydrogenothermaceae and 'Desulfurobacteriaceae' have been investigated for enzymes of autotrophic carbon fixation. Unexpectedly, two different mechanisms of citrate cleavage could be identified within the Aquificae. Aquificaceae use citryl-CoA synthetase and citryl-CoA lyase, whereas Hydrogenothermaceae and 'Desulfurobacteriaceae' use ATP citrate lyase. The first mechanism is likely to represent the ancestral version of the reductive TCA cycle. Sequence analyses further suggest that ATP citrate lyase formed by a gene fusion of citryl-CoA synthetase and citryl-CoA lyase and subsequently became involved in a modified version of this pathway. However, rather than having evolved within the Aquificae, our phylogenetic analyses indicate that Aquificae obtained their ATP citrate lyase through lateral gene transfer. Aquificae play an important role in biogeochemical processes in a variety of high-temperature habitats. Thus, these findings substantiate the hypothesis that autotrophic carbon fixation through the reductive TCA cycle is widespread and contributes significantly to biomass production particularly in hydrothermal habitats.}, }
@article {pmid17220407, year = {2007}, author = {Pallecchi, L and Lucchetti, C and Bartoloni, A and Bartalesi, F and Mantella, A and Gamboa, H and Carattoli, A and Paradisi, F and Rossolini, GM}, title = {Population structure and resistance genes in antibiotic-resistant bacteria from a remote community with minimal antibiotic exposure.}, journal = {Antimicrobial agents and chemotherapy}, volume = {51}, number = {4}, pages = {1179-1184}, pmid = {17220407}, issn = {0066-4804}, mesh = {Anti-Bacterial Agents/pharmacology ; Bolivia ; Conjugation, Genetic ; DNA, Bacterial/*analysis ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/drug effects/*genetics/isolation &amp; purification ; Escherichia coli Infections ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Population Surveillance ; }, abstract = {In a previous study, we detected unexpectedly high levels of acquired antibiotic resistance in commensal Escherichia coli isolates from a remote Guaraní Indian (Bolivia) community with very low levels of antibiotic exposure and limited exchanges with the exterior. Here we analyzed the structure of the resistant E. coli population from that community and the resistance mechanisms. The E. coli population (113 isolates from 72 inhabitants) showed a high degree of genetic heterogeneity, as evidenced by phylogenetic grouping (77% group A, 10% group B1, 8% group D, 5% group B2) and genotyping by randomly amplified polymorphic DNA (RAPD) analysis (44 different RAPD types). The acquired resistance genes were always of the same types as those found in antibiotic-exposed settings [blaTEM, blaPSE-1, catI, cmlA6, tet(A), tet(B), dfrA1, dfrA7, dfrA8, dfrA17, sul1, sul2, aphA1, aadA1, aadA2, aadA5, aadB, and sat-1]. Class 1 and class 2 integrons were found in 12% and 4% of the isolates, respectively, and harbored arrays of gene cassettes similar to those already described. The cotransferability of multiple-resistance traits was observed from selected isolates and was found to be associated with resistance conjugative plasmids of the F, P, and N types. Overall, these data suggest that the resistance observed in this remote community is likely the consequence of the dissemination of resistant bacteria and resistance genes from antibiotic-exposed settings (rather than of an independent in situ selection) which involved both the clonal expansion of resistant strains and the horizontal transfer/recombination of mobile genetic elements harboring resistance genes.}, }
@article {pmid17220258, year = {2007}, author = {El Yacoubi, B and Brunings, AM and Yuan, Q and Shankar, S and Gabriel, DW}, title = {In planta horizontal transfer of a major pathogenicity effector gene.}, journal = {Applied and environmental microbiology}, volume = {73}, number = {5}, pages = {1612-1621}, pmid = {17220258}, issn = {0099-2240}, mesh = {Bacterial Proteins/*genetics ; Citrus/*microbiology ; *Conjugation, Genetic ; *Gene Transfer, Horizontal ; Plant Diseases/microbiology ; Plant Leaves/*microbiology ; Plasmids/genetics ; Transcription Activator-Like Effectors ; Virulence/genetics ; Xanthomonas/genetics/*pathogenicity ; }, abstract = {Xanthomonas citri pv. citri is a clonal group of strains that causes citrus canker disease and appears to have originated in Asia. A phylogenetically distinct clonal group that causes identical disease symptoms on susceptible citrus, X. citri pv. aurantifolii, arose more recently in South America. Genomes of X. citri pv. aurantifolii strains carry two DNA fragments that hybridize to pthA, an X. citri pv. citri gene which encodes a major type III pathogenicity effector protein that is absolutely required to cause citrus canker. Marker interruption mutagenesis and complementation revealed that X. citri pv. aurantifolii strain B69 carried one functional pthA homolog, designated pthB, that was required to cause cankers on citrus. Gene pthB was found among 38 open reading frames on a 37,106-bp plasmid, designated pXcB, which was sequenced and annotated. No additional pathogenicity effectors were found on pXcB, but 11 out of 38 open reading frames appeared to encode a type IV transfer system. pXcB transferred horizontally in planta, without added selection, from B69 to a nonpathogenic X. citri pv. citri (pthA::Tn5) mutant strain, fully restoring canker. In planta transfer efficiencies were very high (>0.1%/recipient) and equivalent to those observed for agar medium with antibiotic selection, indicating that pthB conferred a strong selective advantage to the recipient strain. A single pathogenicity effector that can confer a distinct selective advantage in planta may both facilitate plasmid survival following horizontal gene transfer and account for the origination of phylogenetically distinct groups of strains causing identical disease symptoms.}, }
@article {pmid17219366, year = {2007}, author = {Ochman, H and Liu, R and Rocha, EP}, title = {Erosion of interaction networks in reduced and degraded genomes.}, journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution}, volume = {308}, number = {1}, pages = {97-103}, doi = {10.1002/jez.b.21147}, pmid = {17219366}, issn = {1552-5007}, mesh = {Gammaproteobacteria/*genetics ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genetic Variation ; *Genome, Bacterial ; }, abstract = {Unlike eukaryotes, which often recruit duplicated genes into existing protein-protein interaction (PPI) networks, the low levels of gene duplication coupled with the high probability of lateral transfer of novel genes alters the manner in which PPI networks can evolve in bacteria. By inferring the PPIs present in the ancestor to contemporary Gammaproteobacteria, we were able to trace the changes in gene repertoires, and their consequences on PPI network evolution, in several bacterial lineages that have independently undergone reductions in genome size and genome contents. As genomes degrade, virtually all multi-partner proteins have lost interactors; however, the overall average number of connections increases due to the preferential elimination of proteins that interact with only one other protein partner. We also studied the effect of lateral gene transfer on PPI network evolution by analyzing the connectivity of genes that have been gained along the Escherichia coli lineage, as well as those acquired genes subsequently silenced in Shigella flexneri, since diverging from the gammaproteobacterial ancestor. The situation in PPI networks, in which newly acquired genes preferentially attach to the hubs of the network, contrasts that observed in metabolic networks, which evolve by the peripheral gain and loss of genes, and in regulatory networks, in which high connectivity increases the propensity of loss.}, }
@article {pmid17218529, year = {2007}, author = {Doyle, M and Fookes, M and Ivens, A and Mangan, MW and Wain, J and Dorman, CJ}, title = {An H-NS-like stealth protein aids horizontal DNA transmission in bacteria.}, journal = {Science (New York, N.Y.)}, volume = {315}, number = {5809}, pages = {251-252}, doi = {10.1126/science.1137550}, pmid = {17218529}, issn = {1095-9203}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Bacterial Proteins/*metabolism ; *Conjugation, Genetic ; DNA-Binding Proteins/*metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Movement ; *Plasmids ; Salmonella typhimurium/*genetics/pathogenicity/physiology ; Shigella flexneri/*genetics ; Transcription, Genetic ; Virulence ; }, abstract = {The Sfh protein is encoded by self-transmissible plasmids involved in human typhoid and is closely related to the global regulator H-NS. We have found that Sfh provides a stealth function that allows the plasmids to be transmitted to new bacterial hosts with minimal effects on their fitness. Introducing the plasmid without the sfh gene imposes a mild H-NS(-) phenotype and a severe loss of fitness due to titration of the cellular pool of H-NS by the A+T-rich plasmid. This stealth strategy seems to be used widely to aid horizontal DNA transmission and has important implications for bacterial evolution.}, }
@article {pmid17218520, year = {2007}, author = {Carlton, JM and Hirt, RP and Silva, JC and Delcher, AL and Schatz, M and Zhao, Q and Wortman, JR and Bidwell, SL and Alsmark, UC and Besteiro, S and Sicheritz-Ponten, T and Noel, CJ and Dacks, JB and Foster, PG and Simillion, C and Van de Peer, Y and Miranda-Saavedra, D and Barton, GJ and Westrop, GD and Müller, S and Dessi, D and Fiori, PL and Ren, Q and Paulsen, I and Zhang, H and Bastida-Corcuera, FD and Simoes-Barbosa, A and Brown, MT and Hayes, RD and Mukherjee, M and Okumura, CY and Schneider, R and Smith, AJ and Vanacova, S and Villalvazo, M and Haas, BJ and Pertea, M and Feldblyum, TV and Utterback, TR and Shu, CL and Osoegawa, K and de Jong, PJ and Hrdy, I and Horvathova, L and Zubacova, Z and Dolezal, P and Malik, SB and Logsdon, JM and Henze, K and Gupta, A and Wang, CC and Dunne, RL and Upcroft, JA and Upcroft, P and White, O and Salzberg, SL and Tang, P and Chiu, CH and Lee, YS and Embley, TM and Coombs, GH and Mottram, JC and Tachezy, J and Fraser-Liggett, CM and Johnson, PJ}, title = {Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis.}, journal = {Science (New York, N.Y.)}, volume = {315}, number = {5809}, pages = {207-212}, pmid = {17218520}, issn = {1095-9203}, support = {UO1 AI50913-01/AI/NIAID NIH HHS/United States ; U01 AI050913-01A1/AI/NIAID NIH HHS/United States ; R01 LM006845/LM/NLM NIH HHS/United States ; 072031/WT_/Wellcome Trust/United Kingdom ; R01 LM007938-04/LM/NLM NIH HHS/United States ; U01 AI050913/AI/NIAID NIH HHS/United States ; G0000508/MRC_/Medical Research Council/United Kingdom ; R01 LM006845-08/LM/NLM NIH HHS/United States ; U01 AI050913-02/AI/NIAID NIH HHS/United States ; R01 LM007938/LM/NLM NIH HHS/United States ; G0000508(56841)/MRC_/Medical Research Council/United Kingdom ; G9722968/MRC_/Medical Research Council/United Kingdom ; G9722968(65078)/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Biological Transport/genetics ; DNA Transposable Elements ; DNA, Protozoan/genetics ; Gene Transfer, Horizontal ; Genes, Protozoan ; *Genome, Protozoan ; Humans ; Hydrogen/metabolism ; Metabolic Networks and Pathways/genetics ; Molecular Sequence Data ; Multigene Family ; Organelles/metabolism ; Oxidative Stress/genetics ; Peptide Hydrolases/genetics/metabolism ; Protozoan Proteins/genetics/physiology ; RNA Processing, Post-Transcriptional ; Repetitive Sequences, Nucleic Acid ; *Sequence Analysis, DNA ; Sexually Transmitted Diseases/parasitology ; Trichomonas Infections/parasitology/transmission ; Trichomonas vaginalis/cytology/*genetics/metabolism/pathogenicity ; }, abstract = {We describe the genome sequence of the protist Trichomonas vaginalis, a sexually transmitted human pathogen. Repeats and transposable elements comprise about two-thirds of the approximately 160-megabase genome, reflecting a recent massive expansion of genetic material. This expansion, in conjunction with the shaping of metabolic pathways that likely transpired through lateral gene transfer from bacteria, and amplification of specific gene families implicated in pathogenesis and phagocytosis of host proteins may exemplify adaptations of the parasite during its transition to a urogenital environment. The genome sequence predicts previously unknown functions for the hydrogenosome, which support a common evolutionary origin of this unusual organelle with mitochondria.}, }
@article {pmid17218312, year = {2007}, author = {Jaubert, M and Lavergne, J and Fardoux, J and Hannibal, L and Vuillet, L and Adriano, JM and Bouyer, P and Pignol, D and Giraud, E and Verméglio, A}, title = {A singular bacteriophytochrome acquired by lateral gene transfer.}, journal = {The Journal of biological chemistry}, volume = {282}, number = {10}, pages = {7320-7328}, doi = {10.1074/jbc.M611173200}, pmid = {17218312}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/*genetics ; Bradyrhizobium/*genetics ; Fluorescence ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Phycobilins/metabolism ; Phycocyanin/metabolism ; Phytochrome/chemistry/*genetics ; Temperature ; }, abstract = {Bacteriophytochromes are phytochrome-like proteins that mediate photosensory responses in various bacteria according to their light environment. The genome of the photosynthetic and plant-symbiotic Bradyrhizobium sp. strain ORS278 revealed the presence of a genomic island acquired by lateral transfer harboring a bacteriophytochrome gene, BrBphP3.ORS278, and genes involved in the synthesis of phycocyanobilin and gas vesicles. The corresponding protein BrBphP3.ORS278 is phylogenetically distant from the other (bacterio)phytochromes described thus far and displays a series of unusual properties. It binds phycocyanobilin as a chromophore, a unique feature for a bacteriophytochrome. Moreover, its C-terminal region is short and displays no homology with any known functional domain. Its dark-adapted state absorbs maximally around 610 nm, an unusually short wavelength for (bacterio)phytochromes. This form is designated as Po for orange-absorbing form. Upon illumination, a photo-reversible switch occurs between the Po form and a red (670 nm)-absorbing form (Pr), which rapidly backreacts in the dark. Because of this instability, illumination results in a mixture of the Po and Pr states in proportions that depend on the intensity. These uncommon features suggest that BrBphP3.ORS278 could be fitted to measure light intensity rather than color.}, }
@article {pmid17216168, year = {2007}, author = {Yuan, YM and Hu, XM and Liu, HZ and Hansen, BM and Yan, JP and Yuan, ZM}, title = {Kinetics of plasmid transfer among Bacillus cereus group strains within lepidopteran larvae.}, journal = {Archives of microbiology}, volume = {187}, number = {6}, pages = {425-431}, doi = {10.1007/s00203-006-0206-5}, pmid = {17216168}, issn = {0302-8933}, mesh = {Animals ; Bacillus cereus/*genetics/metabolism ; Bacillus thuringiensis Toxins ; Bacterial Proteins/genetics/metabolism ; Bacterial Toxins/genetics/metabolism ; *Conjugation, Genetic ; Endotoxins/genetics/metabolism ; *Gene Transfer, Horizontal ; Hemolysin Proteins/genetics/metabolism ; Larva/microbiology ; Lepidoptera/classification/growth &amp; development/*microbiology ; Plasmids/*genetics ; }, abstract = {The cry toxin encoding plasmid pHT73 was transferred from Bacillus thuringiensis subspecies kurstaki KT0 to six B. cereus group strains in three lepidopteran (Spodoptera exigua, Plutella xyllostella and Helicoverpa armigera) larvae by conjugation. The conjugation kinetics of the plasmid was precisely studied during the larval infection using a new protocol. The infections were performed with both vegetative and sporulated strains. However, larval death only occurred when infections were made with spore and toxin preparations. Likewise, spore germinations of both donor and recipient strains were only observed in killed larvae, 44-56 h post-infection. Accordingly, kinetics showed that gene transfer between B. thuringiensis strain KT0 and other B. cereus strains only took place in dead larvae among vegetatively growing bacteria. The conjugational transfer ratios varied among different strain combinations and different larvae. The highest transfer ratio reached 5.83 x 10(-6) CFU/donor between the KT0 and the AW05R recipient in Helicoverpa armigera, and all transconjugants gained the ability to produce the insecticidal crystal. These results indicated that horizontal gene transfer among B. cereus group strains might play a key role for the acquisition of extra plasmids and evolution of these strains in toxin susceptible insect larvae.}, }
@article {pmid17214701, year = {2007}, author = {Bisset, LR and Böni, J and Lutz, H and Schüpbach, J}, title = {Lack of evidence for PERV expression after apoptosis-mediated horizontal gene transfer between porcine and human cells.}, journal = {Xenotransplantation}, volume = {14}, number = {1}, pages = {13-24}, doi = {10.1111/j.1399-3089.2006.00351.x}, pmid = {17214701}, issn = {0908-665X}, mesh = {Animals ; Apoptosis/*genetics ; Cell Line ; Coculture Techniques ; DNA, Viral/genetics ; Electron Transport Complex IV/metabolism ; Endogenous Retroviruses/*genetics ; *Gene Expression Regulation ; Gene Expression Regulation, Viral ; Gene Transfer, Horizontal/*genetics ; Glyceraldehyde 3-Phosphate Dehydrogenase (NADP+)/metabolism ; Histocompatibility Antigens Class I/metabolism ; Humans ; Swine ; }, abstract = {Evidence for porcine endogenous retrovirus (PERV) infection of human cells has provoked a public health debate over the proposed use of porcine xenografts to alleviate the worldwide shortage of human allografts. Nevertheless, the potential relevance of PERV transmission by apoptosis-mediated horizontal DNA transfer, a documented means of infection-independent retrovirus delivery, appears to have been overlooked in this discussion. To examine the hypothesis that apoptotic cell death during porcine xenograft rejection is capable of fostering horizontal DNA transfer, we have now assessed in vitro cocultures, consisting of phagocytic human fibroblasts and apoptotic or necrotic porcine B-lymphoblastoid cells, for evidence of cross-species PERV exchange and eventual replication. Using real-time polymerase chain reaction (PCR) assays, designed to differentiate nuclear and cytoplasmic DNA derived from either porcine or human cells, we now report evidence for the presence of porcine DNA, including PERV, in the nucleus of human fibroblasts exposed to apoptotic porcine cells. This novel demonstration of apoptosis-mediated horizontal PERV transfer is characterized by a low efficiency of transfer and a transient nature, being present in only 0.22% of the cocultured human cells and disappearing to undetectable levels within 4 weeks of exposure to apoptotic porcine cells. In contrast, using PERV-specific real-time reverse-transcriptase PCR (RT-PCR) and ultra-sensitive product-enhanced reverse transcriptase (PERT) assays, we find no evidence for human fibroblast-derived cellular PERV RNA or coculture supernatant-based RT-activity, indicating a lack of subsequent PERV replication. Together, these results suggest that apoptosis-mediated horizontal PERV transfer does not present an overt hazard within the framework of porcine xenotransplantation. However, we also present arguments against extrapolation of these in vitro observations directly to clinical circumstances.}, }
@article {pmid17213324, year = {2007}, author = {Dagan, T and Martin, W}, title = {Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {3}, pages = {870-875}, pmid = {17213324}, issn = {0027-8424}, mesh = {Computational Biology ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome/*genetics ; Prokaryotic Cells/*metabolism ; }, abstract = {The amount of lateral gene transfer (LGT) that has occurred in microbial evolution is heavily debated. Efforts to quantify LGT through gene-tree comparisons have delivered estimates that between 2% and 60% of all prokaryotic genes have been affected by LGT, the 30-fold discrepancy reflecting differences among gene samples studied and uncertainties inherent in phylogenetic reconstruction. Here we present a simple method that is independent of gene-tree comparisons to estimate the LGT rate among sequenced prokaryotic genomes. If little or no LGT has occurred during evolution, ancestral genome sizes would become unrealistically large, whereas too much LGT would render them far too small. We determine the amount of LGT that is necessary and sufficient to bring the distribution of inferred ancestral genome sizes into agreement with that observed among modern microbes. Rather than testing for phylogenetic congruence or lack thereof across genes, we assume that all gene trees are compatible; hence, our method delivers very conservative lower-bound estimates of the average LGT rate. The results indicate that among 57,670 gene families distributed across 190 sequenced genomes, at least two-thirds and probably all, have been affected by LGT at some time in their evolutionary past. A component of common ancestry nonetheless remains detectable in gene distribution patterns. We estimate the minimum lower bound for the average LGT rate across all genes as 1.1 LGT events per gene family and gene family lifespan and this minimum rate increases sharply when genes present in only a few genomes are excluded from the analysis.}, }
@article {pmid17210928, year = {2007}, author = {Stinear, TP and Seemann, T and Pidot, S and Frigui, W and Reysset, G and Garnier, T and Meurice, G and Simon, D and Bouchier, C and Ma, L and Tichit, M and Porter, JL and Ryan, J and Johnson, PD and Davies, JK and Jenkin, GA and Small, PL and Jones, LM and Tekaia, F and Laval, F and Daffé, M and Parkhill, J and Cole, ST}, title = {Reductive evolution and niche adaptation inferred from the genome of Mycobacterium ulcerans, the causative agent of Buruli ulcer.}, journal = {Genome research}, volume = {17}, number = {2}, pages = {192-200}, pmid = {17210928}, issn = {1088-9051}, mesh = {Adaptation, Physiological ; Chromosomes, Bacterial/genetics ; DNA Transposable Elements ; *Evolution, Molecular ; *Genome, Bacterial ; Humans ; Molecular Sequence Data ; Mycobacteriophages/isolation &amp; purification ; Mycobacterium Infections, Nontuberculous/microbiology ; Mycobacterium marinum/genetics ; Mycobacterium ulcerans/*genetics/pathogenicity/*physiology/virology ; Pseudogenes ; Skin Ulcer/microbiology ; Species Specificity ; Virulence/genetics ; }, abstract = {Mycobacterium ulcerans is found in aquatic ecosystems and causes Buruli ulcer in humans, a neglected but devastating necrotic disease of subcutaneous tissue that is rampant throughout West and Central Africa. Here, we report the complete 5.8-Mb genome sequence of M. ulcerans and show that it comprises two circular replicons, a chromosome of 5632 kb and a virulence plasmid of 174 kb. The plasmid is required for production of the polyketide toxin mycolactone, which provokes necrosis. Comparisons with the recently completed 6.6-Mb genome of Mycobacterium marinum revealed >98% nucleotide sequence identity and genome-wide synteny. However, as well as the plasmid, M. ulcerans has accumulated 213 copies of the insertion sequence IS2404, 91 copies of IS2606, 771 pseudogenes, two bacteriophages, and multiple DNA deletions and rearrangements. These data indicate that M. ulcerans has recently evolved via lateral gene transfer and reductive evolution from the generalist, more rapid-growing environmental species M. marinum to become a niche-adapted specialist. Predictions based on genome inspection for the production of modified mycobacterial virulence factors, such as the highly abundant phthiodiolone lipids, were confirmed by structural analyses. Similarly, 11 protein-coding sequences identified as M. ulcerans-specific by comparative genomics were verified as such by PCR screening a diverse collection of 33 strains of M. ulcerans and M. marinum. This work offers significant insight into the biology and evolution of mycobacterial pathogens and is an important component of international efforts to counter Buruli ulcer.}, }
@article {pmid17209024, year = {2007}, author = {Abajy, MY and Kopeć, J and Schiwon, K and Burzynski, M and Döring, M and Bohn, C and Grohmann, E}, title = {A type IV-secretion-like system is required for conjugative DNA transport of broad-host-range plasmid pIP501 in gram-positive bacteria.}, journal = {Journal of bacteriology}, volume = {189}, number = {6}, pages = {2487-2496}, pmid = {17209024}, issn = {0021-9193}, mesh = {Bacterial Proteins/*genetics/metabolism ; *Conjugation, Genetic ; DNA Nucleotidyltransferases/genetics ; DNA, Bacterial/*genetics ; Enterococcus faecalis/*genetics ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Open Reading Frames/genetics ; Plasmids/*genetics ; Two-Hybrid System Techniques ; }, abstract = {Plasmid pIP501 has a very broad host range for conjugative transfer among a wide variety of gram-positive bacteria and gram-negative Escherichia coli. Functionality of the pIP501 transfer (tra) genes in E. coli was proven by pIP501 retrotransfer to Enterococcus faecalis (B. Kurenbach, C. Bohn, J. Prabhu, M. Abudukerim, U. Szewzyk, and E. Grohmann, Plasmid 50:86-93, 2003). The 15 pIP501 tra genes are organized in a single operon (B. Kurenbach, J. Kopeć, M. Mägdefrau, K. Andreas, W. Keller, C. Bohn, M. Y. Abajy, and E. Grohmann, Microbiology 152:637-645, 2006). The pIP501 tra operon is negatively autoregulated at the transcriptional level by the conjugative DNA relaxase TraA. Three of the 15 pIP501-encoded Tra proteins show significant sequence similarity to the Agrobacterium type IV secretion system proteins VirB1, VirB4, and VirD4. Here we report a comprehensive protein-protein interaction map of all of the pIP501-encoded Tra proteins determined by the yeast two-hybrid assay. Most of the interactions were verified in vitro by isolation of the protein complexes with pull-down assays. In conjunction with known or postulated functions of the pIP501-encoded Tra proteins and computer-assisted prediction of their cellular location, we propose a model for the first type IV-secretion-like system encoded by a conjugative plasmid from gram-positive bacteria.}, }
@article {pmid17209015, year = {2007}, author = {Dybvig, K and Cao, Z and French, CT and Yu, H}, title = {Evidence for type III restriction and modification systems in Mycoplasma pulmonis.}, journal = {Journal of bacteriology}, volume = {189}, number = {6}, pages = {2197-2202}, pmid = {17209015}, issn = {0021-9193}, support = {R01 AI063909/AI/NIAID NIH HHS/United States ; R01 AR044252/AR/NIAMS NIH HHS/United States ; AI63909/AI/NIAID NIH HHS/United States ; AR44252/AR/NIAMS NIH HHS/United States ; }, mesh = {Animals ; DNA Restriction-Modification Enzymes/*genetics/*metabolism ; DNA Transposable Elements ; Endonucleases/genetics/metabolism ; Gene Transfer, Horizontal ; Mice ; Mutagenesis, Insertional ; Mycoplasma pulmonis/*enzymology/genetics ; Polymerase Chain Reaction ; Transformation, Bacterial ; }, abstract = {Mycoplasma pulmonis possesses a cassette of genes that are predicted to code for type III restriction and modification (R-M) enzymes. Transposon disruption of a gene predicted to code for the endonuclease subunit of the enzyme resulted in loss of R-M activity. Genomic data indicate that the cassette was acquired by horizontal gene transfer and possibly located on a mobile element.}, }
@article {pmid17207587, year = {2007}, author = {Castoe, TA and Stephens, T and Noonan, BP and Calestani, C}, title = {A novel group of type I polyketide synthases (PKS) in animals and the complex phylogenomics of PKSs.}, journal = {Gene}, volume = {392}, number = {1-2}, pages = {47-58}, doi = {10.1016/j.gene.2006.11.005}, pmid = {17207587}, issn = {0378-1119}, mesh = {Animals ; Databases, Genetic ; *Evolution, Molecular ; Molecular Sequence Data ; *Phylogeny ; Polyketide Synthases/chemistry/*genetics ; Protein Structure, Tertiary ; Sequence Alignment ; }, abstract = {Type I polyketide synthases (PKSs), and related fatty acid synthases (FASs), represent a large group of proteins encoded by a diverse gene family that occurs in eubacteria and eukaryotes (mainly in fungi). Collectively, enzymes encoded by this gene family produce a wide array of polyketide compounds that encompass a broad spectrum of biological activity including antibiotic, antitumor, antifungal, immunosuppressive, and predator defense functional roles. We employed a phylogenomics approach to estimate relationships among members of this gene family from eubacterial and eukaryotic genomes. Our results suggest that some animal genomes (sea urchins, birds, and fish) possess a previously unidentified group of pks genes, in addition to possessing fas genes used in fatty acid metabolism. These pks genes in the chicken, fish, and sea urchin genomes do not appear to be closely related to any other animal or fungal genes, and instead are closely related to pks genes from the slime mold Dictyostelium and eubacteria. Continued accumulation of genome sequence data from diverse animal lineages is required to clarify whether the presence of these (non-fas) pks genes in animal genomes owes their origins to horizontal gene transfer (from eubacterial or Dictostelium genomes) or to more conventional patterns of vertical inheritance coupled with massive gene loss in several animal lineages. Additionally, results of our broad-scale phylogenetic analyses bolster the support for previous hypotheses of horizontal gene transfer of pks genes from bacterial to fungal and protozoan lineages.}, }
@article {pmid17204561, year = {2007}, author = {Longstaff, DG and Larue, RC and Faust, JE and Mahapatra, A and Zhang, L and Green-Church, KB and Krzycki, JA}, title = {A natural genetic code expansion cassette enables transmissible biosynthesis and genetic encoding of pyrrolysine.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {3}, pages = {1021-1026}, pmid = {17204561}, issn = {0027-8424}, support = {R01 GM070663/GM/NIGMS NIH HHS/United States ; GM 070663/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Codon, Terminator/genetics ; Escherichia coli/genetics/metabolism ; Gene Expression/genetics ; Genetic Code/*genetics ; Genetic Vectors/genetics ; Lysine/*analogs &amp; derivatives/biosynthesis/genetics ; Mass Spectrometry ; Methanosarcina/chemistry/genetics/metabolism ; Methyltransferases/chemistry/genetics/metabolism ; Molecular Sequence Data ; Protein Biosynthesis/genetics ; Time Factors ; }, abstract = {Pyrrolysine has entered natural genetic codes by the translation of UAG, a canonical stop codon. UAG translation as pyrrolysine requires the pylT gene product, an amber-decoding tRNA(Pyl) that is aminoacylated with pyrrolysine by the pyrrolysyl-tRNA synthetase produced from the pylS gene. The pylTS genes form a gene cluster with pylBCD, whose functions have not been investigated. The pylTSBCD gene order is maintained not only in methanogenic Archaea but also in a distantly related Gram-positive Bacterium, indicating past horizontal gene transfer of all five genes. Here we show that lateral transfer of pylTSBCD introduces biosynthesis and genetic encoding of pyrrolysine into a naïve organism. PylS-based assays demonstrated that pyrrolysine was biosynthesized in Escherichia coli expressing pylBCD from Methanosarcina acetivorans. Production of pyrrolysine did not require tRNA(Pyl) or PylS. However, when pylTSBCD were coexpressed with mtmB1, encoding the methanogen monomethylamine methyltransferase, UAG was translated as pyrrolysine to produce recombinant monomethylamine methyltransferase. Expression of pylTSBCD also suppressed an amber codon introduced into the E. coli uidA gene. Strains lacking one of the pylBCD genes did not produce pyrrolysine or translate UAG as pyrrolysine. These results indicated that pylBCD gene products biosynthesize pyrrolysine using metabolites common to Bacteria and Archaea and, furthermore, that the pyl gene cluster represents a "genetic code expansion cassette," previously unprecedented in natural organisms, whose transfer allows an existing codon to be translated as a novel endogenously synthesized free amino acid. Analogous cassettes may have served similar functions for other amino acids during the evolutionary expansion of the canonical genetic code.}, }
@article {pmid17195478, year = {2007}, author = {Kitano, H}, title = {Biological robustness in complex host-pathogen systems.}, journal = {Progress in drug research. Fortschritte der Arzneimittelforschung. Progres des recherches pharmaceutiques}, volume = {64}, number = {}, pages = {239, 241-63}, doi = {10.1007/978-3-7643-7567-6_10}, pmid = {17195478}, issn = {0071-786X}, mesh = {*Adaptation, Biological ; Animals ; Autoimmune Diseases/immunology ; Humans ; Immune System/*physiology ; Infections/*immunology ; *Symbiosis ; }, abstract = {Infectious diseases are still the number one killer of human beings. Even in developed countries, infectious diseases continue to be a major health threat. This article explores a conceptual framework for understanding infectious diseases in the context of the complex dynamics between microbe and host, and explores theoretical strategies for anti-infectives. The central pillar of this conceptual framework is that biological robustness is a fundamental property of systems that is closely interlinked with the evolution of symbiotic host-pathogen systems. There are specific architectural features of such robust yet evolvable systems and interpretable trade-offs between robustness, fragility, resource demands, and performance. This concept applies equally to both microbes and host. Pathogens have evolved to exploit the host using various strategies as well as effective escape mechanisms. Modular pathogenicity islands (PAI) derived from horizontal gene transfer, highly variable surface molecules, and a range of other countermeasures enhance the robustness of a pathogen against attacks from the host immune system. The host has likewise evolved complex defensive mechanisms to protect itself against pathogenic threats, but the host immune system includes several trade-offs that can be exploited by pathogens and induces undesirable inflammatory reactions. Due to the complexity of the dynamics emerging from the interactions of multiple microbes and a host, effective counter-measures require an in-depth understanding of system dynamics as well as detailed molecular mechanisms of the processes that are involved.}, }
@article {pmid17194795, year = {2007}, author = {Klockgether, J and Würdemann, D and Reva, O and Wiehlmann, L and Tümmler, B}, title = {Diversity of the abundant pKLC102/PAGI-2 family of genomic islands in Pseudomonas aeruginosa.}, journal = {Journal of bacteriology}, volume = {189}, number = {6}, pages = {2443-2459}, pmid = {17194795}, issn = {0021-9193}, mesh = {Gene Transfer, Horizontal ; *Genetic Variation ; Genome, Bacterial ; Genomic Islands/*genetics ; Humans ; Oligonucleotide Array Sequence Analysis/methods ; Plasmids ; Pseudomonas Infections/epidemiology/microbiology ; Pseudomonas aeruginosa/*classification/*genetics/growth &amp; development ; RNA, Transfer, Gly/*genetics ; RNA, Transfer, Lys/*genetics ; }, abstract = {The known genomic islands of Pseudomonas aeruginosa clone C strains are integrated into tRNA(Lys) (pKLC102) or tRNA(Gly) (PAGI-2 and PAGI-3) genes and differ from their core genomes by distinctive tetranucleotide usage patterns. pKLC102 and the related island PAPI-1 from P. aeruginosa PA14 were spontaneously mobilized from their host chromosomes at frequencies of 10% and 0.3%, making pKLC102 the most mobile genomic island known with a copy number of 30 episomal circular pKLC102 molecules per cell. The incidence of islands of the pKLC102/PAGI-2 type was investigated in 71 unrelated P. aeruginosa strains from diverse habitats and geographic origins. pKLC102- and PAGI-2-like islands were identified in 50 and 31 strains, respectively, and 15 and 10 subtypes were differentiated by hybridization on pKLC102 and PAGI-2 macroarrays. The diversity of PAGI-2-type islands was mainly caused by one large block of strain-specific genes, whereas the diversity of pKLC102-type islands was primarily generated by subtype-specific combination of gene cassettes. Chromosomal loss of PAGI-2 could be documented in sequential P. aeruginosa isolates from individuals with cystic fibrosis. PAGI-2 was present in most tested Cupriavidus metallidurans and Cupriavidus campinensis isolates from polluted environments, demonstrating the spread of PAGI-2 across habitats and species barriers. The pKLC102/PAGI-2 family is prevalent in numerous beta- and gammaproteobacteria and is characterized by high asymmetry of the cDNA strands. This evolutionarily ancient family of genomic islands retained its oligonucleotide signature during horizontal spread within and among taxa.}, }
@article {pmid17194592, year = {2007}, author = {Sitkiewicz, I and Stockbauer, KE and Musser, JM}, title = {Secreted bacterial phospholipase A2 enzymes: better living through phospholipolysis.}, journal = {Trends in microbiology}, volume = {15}, number = {2}, pages = {63-69}, doi = {10.1016/j.tim.2006.12.003}, pmid = {17194592}, issn = {0966-842X}, mesh = {Animals ; Bacteria/*enzymology/genetics/*pathogenicity ; Bacterial Infections/microbiology ; Bacterial Proteins/genetics/*metabolism/physiology ; Bacterial Toxins/genetics/metabolism ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Humans ; Phospholipases A/genetics/*metabolism ; Phospholipases A2 ; Pseudomonas aeruginosa/enzymology/pathogenicity ; Streptococcus pyogenes/enzymology/genetics/pathogenicity ; Virulence ; }, abstract = {Phospholipases are ubiquitous and diverse enzymes that induce changes in membrane composition, activate the inflammatory cascade and alter cell signaling pathways. Recent evidence suggests that certain bacterial pathogens have acquired genes encoding secreted phospholipase A2 enzymes through lateral gene transfer events. The two best-studied members of this class of enzyme are ExoU and SlaA, which are produced by Pseudomonas aeruginosa and group A Streptococcus, respectively. These enzymes modulate the host inflammatory response, increase the severity of disease and otherwise alter host-pathogen interactions. We propose that a key function of ExoU and SlaA is to increase the fitness of the subclones expressing these enzymes, thereby increasing the population size of the PLA2-positive strains and enhancing the likelihood of encountering an at-risk host.}, }
@article {pmid17194219, year = {2006}, author = {Ma, W and Dong, FF and Stavrinides, J and Guttman, DS}, title = {Type III effector diversification via both pathoadaptation and horizontal transfer in response to a coevolutionary arms race.}, journal = {PLoS genetics}, volume = {2}, number = {12}, pages = {e209}, pmid = {17194219}, issn = {1553-7404}, mesh = {Adaptation, Biological/*genetics ; Alleles ; Bacterial Adhesion/genetics ; Bacterial Outer Membrane Proteins/*genetics/*metabolism ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genetic Variation ; Multigene Family ; Phylogeny ; Plants/microbiology ; Pseudomonas syringae/*genetics/metabolism/*pathogenicity ; Virulence ; }, abstract = {The concept of the coevolutionary arms race holds a central position in our understanding of pathogen-host interactions. Here we identify the molecular mechanisms and follow the stepwise progression of an arms race in a natural system. We show how the evolution and function of the HopZ family of type III secreted effector proteins carried by the plant pathogen Pseudomonas syringae are influenced by a coevolutionary arms race between pathogen and host. We surveyed 96 isolates of P. syringae and identified three homologs (HopZ1, HopZ2, and HopZ3) distributed among approximately 45% of the strains. All alleles were sequenced and their expression was confirmed. Evolutionary analyses determined that the diverse HopZ1 homologs are ancestral to P. syringae, and have diverged via pathoadaptive mutational changes into three functional and two degenerate forms, while HopZ2 and HopZ3 have been brought into P. syringae via horizontal transfer from other ecologically similar bacteria. A PAML selection analysis revealed that the C terminus of HopZ1 is under strong positive selection. Despite the extensive genetic variation observed in this family, all three homologs have cysteine-protease activity, although their substrate specificity may vary. The introduction of the ancestral hopZ1 allele into strains harboring alternate alleles results in a resistance protein-mediated defense response in their respective hosts, which is not observed with the endogenous allele. These data indicate that the P. syringae HopZ family has undergone allelic diversification via both pathoadaptive mutational changes and horizontal transfer in response to selection imposed by the host defense system. This genetic diversity permits the pathogen to avoid host defenses while still maintaining a virulence-associated protease, thereby allowing it to thrive on its current host, while simultaneously impacting its host range.}, }
@article {pmid17191179, year = {2007}, author = {Seifried, SE and Tice, AD and Eischen, M}, title = {Diversity of community-associated strains of methicillin-resistant Staphylococcus aureus in Hawaii.}, journal = {The Journal of infectious diseases}, volume = {195}, number = {2}, pages = {305; author reply 305-7}, doi = {10.1086/510252}, pmid = {17191179}, issn = {0022-1899}, support = {P50 ES012740/ES/NIEHS NIH HHS/United States ; }, mesh = {Community-Acquired Infections/*epidemiology/*microbiology ; Electrophoresis, Gel, Pulsed-Field ; Environmental Microbiology ; Gene Transfer, Horizontal ; *Genetic Variation ; Hawaii/epidemiology ; Humans ; *Methicillin Resistance ; Staphylococcal Infections/epidemiology/microbiology ; Staphylococcus aureus/*classification/drug effects/genetics/isolation &amp; purification ; Virulence Factors/genetics ; }, }
@article {pmid17191074, year = {2007}, author = {Dorman, CJ}, title = {H-NS, the genome sentinel.}, journal = {Nature reviews. Microbiology}, volume = {5}, number = {2}, pages = {157-161}, doi = {10.1038/nrmicro1598}, pmid = {17191074}, issn = {1740-1534}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {AT Rich Sequence ; Bacterial Proteins/genetics/*metabolism ; Binding Sites ; DNA-Binding Proteins/genetics/*metabolism ; Escherichia coli/*genetics/metabolism ; *Gene Expression Regulation, Bacterial ; *Gene Silencing ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Salmonella typhimurium/*genetics/metabolism ; }, abstract = {Two recent reports have indicated that the H-NS protein in Salmonella enterica serovar Typhimurium has a key role in selectively silencing the transcription of large numbers of horizontally acquired AT-rich genes, including those that make up its major pathogenicity islands. Broadly similar conclusions have emerged from a study of H-NS binding to DNA in Escherichia coli. How do these findings affect our view of H-NS and its ability to influence bacterial evolution?}, }
@article {pmid17185745, year = {2007}, author = {Homma, K and Fukuchi, S and Nakamura, Y and Gojobori, T and Nishikawa, K}, title = {Gene cluster analysis method identifies horizontally transferred genes with high reliability and indicates that they provide the main mechanism of operon gain in 8 species of gamma-Proteobacteria.}, journal = {Molecular biology and evolution}, volume = {24}, number = {3}, pages = {805-813}, doi = {10.1093/molbev/msl206}, pmid = {17185745}, issn = {0737-4038}, mesh = {Cluster Analysis ; Computational Biology ; Databases, Genetic ; *Evolution, Molecular ; Gammaproteobacteria/*genetics ; Gene Transfer, Horizontal/*genetics ; Multigene Family/*genetics ; Operon/*genetics ; *Phylogeny ; Selection, Genetic ; Sequence Alignment/methods ; Species Specificity ; }, abstract = {The formation mechanism of operons remains unresolved: operons may form by rearrangements within a genome or by acquisition of genes from other species, that is, horizontal gene transfer (HGT). One hindrance to its elucidation is the unavailability of a method to accurately identify HGT, although it is generally considered to occur. It is critically important first to select horizontally transferred (HT) genes reliably and then to determine the extent to which HGT is involved in operon formation. For this purpose, we considered indels in terms of gene clusters instead of individual genes and chose candidates of HT genes in 8 species of Escherichia, Shigella, and Salmonella based on the minimization of indels. To select a benchmark set of positively HT genes against which we can evaluate the candidate set, we devised another procedure using intergenetic alignments. Comparison with the benchmark set demonstrated the absence of a significant number of false positives in the candidate set, showing the high reliability of the method. Analyses of Escherichia coli K-12 operons revealed that although approximately 20 operons were probably gained from the last common ancestor of the 8 gamma-proteobacteria, deletion of intervening genes accounts for the formation of no operons, whereas horizontal transfer expanded 2 operons and introduced 4 entire operons. Based on these observations and reasoning, we suggest that the main mechanism of operon gain is HGT rather than intragenomic rearrangements. We propose that genes with related essential functions tend to reside in conserved operons, whereas genes in nonconserved operons mostly confer slight advantage to the organisms and frequently undergo horizontal transfer and decay. HT genes constitute at least 5.5% of the genes in the 8 species and approximately 45% of which originate from other gamma-proteobacteria. Genes involved in viral functions and mobile and extrachromosomal element functions are HT more often than expected. This finding indicates frequent mediation of HGT by bacteriophages. On the other hand, not only informational genes (those involved in transcription, translation, and related processes) but also operational genes (those involved in housekeeping) are HT less frequently than expected.}, }
@article {pmid17185587, year = {2006}, author = {Yeates, TO and Beeby, M}, title = {Biochemistry. Proteins in a small world.}, journal = {Science (New York, N.Y.)}, volume = {314}, number = {5807}, pages = {1882-1883}, doi = {10.1126/science.1137400}, pmid = {17185587}, issn = {1095-9203}, mesh = {Binding Sites ; Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; *Metabolic Networks and Pathways ; Mutation ; Protein Binding ; *Protein Interaction Mapping ; Proteins/*chemistry/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/metabolism ; }, }
@article {pmid17183657, year = {2006}, author = {Goddard, MR and Leigh, J and Roger, AJ and Pemberton, AJ}, title = {Invasion and persistence of a selfish gene in the Cnidaria.}, journal = {PloS one}, volume = {1}, number = {1}, pages = {e3}, pmid = {17183657}, issn = {1932-6203}, mesh = {Animals ; Bayes Theorem ; Cnidaria/classification/*enzymology/*genetics ; DNA Restriction Enzymes/*genetics ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Gene Conversion ; Gene Transfer, Horizontal ; Genes, Mitochondrial ; Genetics, Population ; Models, Genetic ; Phylogeny ; Sea Anemones/enzymology/genetics ; Species Specificity ; United Kingdom ; }, abstract = {BACKGROUND: Homing endonuclease genes (HEGs) are superfluous, but are capable of invading populations that mix alleles by biasing their inheritance patterns through gene conversion. One model suggests that their long-term persistence is achieved through recurrent invasion. This circumvents evolutionary degeneration, but requires reasonable rates of transfer between species to maintain purifying selection. Although HEGs are found in a variety of microbes, we found the previous discovery of this type of selfish genetic element in the mitochondria of a sea anemone surprising.<br><br>METHODS/PRINCIPAL FINDINGS: We surveyed 29 species of Cnidaria for the presence of the COXI HEG. Statistical analyses provided evidence for HEG invasion. We also found that 96 individuals of Metridium senile, from five different locations in the UK, had identical HEG sequences. This lack of sequence divergence illustrates the stable nature of Anthozoan mitochondria. Our data suggests this HEG conforms to the recurrent invasion model of evolution.<br><br>CONCLUSIONS: Ordinarily such low rates of HEG transfer would likely be insufficient to enable major invasion. However, the slow rate of Anthozoan mitochondrial change lengthens greatly the time to HEG degeneration: this significantly extends the periodicity of the HEG life-cycle. We suggest that a combination of very low substitution rates and rare transfers facilitated metazoan HEG invasion.}, }
@article {pmid17182897, year = {2007}, author = {Brindefalk, B and Viklund, J and Larsson, D and Thollesson, M and Andersson, SG}, title = {Origin and evolution of the mitochondrial aminoacyl-tRNA synthetases.}, journal = {Molecular biology and evolution}, volume = {24}, number = {3}, pages = {743-756}, doi = {10.1093/molbev/msl202}, pmid = {17182897}, issn = {0737-4038}, mesh = {Alphaproteobacteria/genetics ; Amino Acyl-tRNA Synthetases/*genetics ; Bayes Theorem ; Cluster Analysis ; Computational Biology ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; *Models, Genetic ; *Phylogeny ; }, abstract = {Many theories favor a fusion of 2 prokaryotic genomes for the origin of the Eukaryotes, but there are disagreements on the origin, timing, and cellular structures of the cells involved. Equally controversial is the source of the nuclear genes for mitochondrial proteins, although the alpha-proteobacterial contribution to the mitochondrial genome is well established. Phylogenetic inferences show that the nuclearly encoded mitochondrial aminoacyl-tRNA synthetases (aaRSs) occupy a position in the tree that is not close to any of the currently sequenced alpha-proteobacterial genomes, despite cohesive and remarkably well-resolved alpha-proteobacterial clades in 12 of the 20 trees. Two or more alpha-proteobacterial clusters were observed in 8 cases, indicative of differential loss of paralogous genes or horizontal gene transfer. Replacement and retargeting events within the nuclear genomes of the Eukaryotes was indicated in 10 trees, 4 of which also show split alpha-proteobacterial groups. A majority of the mitochondrial aaRSs originate from within the bacterial domain, but none specifically from the alpha-Proteobacteria. For some aaRS, the endosymbiotic origin may have been erased by ongoing gene replacements on the bacterial as well as the eukaryotic side. For others that accurately resolve the alpha-proteobacterial divergence patterns, the lack of affiliation with mitochondria is more surprising. We hypothesize that the ancestral eukaryotic gene pool hosted primordial "bacterial-like" genes, to which a limited set of alpha-proteobacterial genes, mostly coding for components of the respiratory chain complexes, were added and selectively maintained.}, }
@article {pmid17180961, year = {2006}, author = {Heinemann, JA and Rosén, H and Savill, M and Burgos-Caraballo, S and Toranzos, GA}, title = {Environment arrays: a possible approach for predicting changes in waterborne bacterial disease potential.}, journal = {Environmental science &amp; technology}, volume = {40}, number = {23}, pages = {7150-7156}, doi = {10.1021/es060331x}, pmid = {17180961}, issn = {0013-936X}, mesh = {Bacteria/*genetics ; Environmental Monitoring/*methods ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial/*genetics ; Genomics/methods ; Integrons/*genetics ; Microarray Analysis/*methods ; Tandem Repeat Sequences/genetics ; *Water Microbiology ; }, abstract = {Current molecular techniques for identifying bacteria in water have proven useful, but they are not reliably predictive of impending disease outbreaks. Genomics-based approaches will help to detect the presence of pathogens quickly and well before they grow into a population that poses a risk to public health. We suggest that genomics is only one component of the toolbox that will be needed to identify emerging waterborne threats. We propose a methodology beyond genomics, based on activity in the mobile genome. This approach makes use of a new device called an environment array. The array will depend upon the same research necessary for genomics-based detection, but will not require an a priori knowledge of virulence genes. Environment arrays are assembled from molecular profiles of the infectious elements that transfer between bacteria. The advantage of the array is that it monitors the activity of the mobile genome, rather than the presence of particular DNA sequences. Environmental arrays should thus be many times more sensitive than traditional hybridization or PCR-based techniques that target already-known DNA sequences. Mobile elements are known to respond to new environmental conditions that may correlate with a chemical contamination or the bloom of bacterial pathogens, potentially allowing for a much broader application in detecting unknown or unanticipated biological and chemical contaminants.}, }
@article {pmid17180960, year = {2006}, author = {Muniesa, M and Jofre, J and García-Aljaro, C and Blanch, AR}, title = {Occurrence of Escherichia coli O157:H7 and other enterohemorrhagic Escherichia coli in the environment.}, journal = {Environmental science &amp; technology}, volume = {40}, number = {23}, pages = {7141-7149}, doi = {10.1021/es060927k}, pmid = {17180960}, issn = {0013-936X}, mesh = {Culture Techniques ; *Disease Outbreaks ; Escherichia coli Infections/*epidemiology ; Escherichia coli O157/*genetics/pathogenicity/*physiology/*virology ; Genomic Islands/genetics ; Humans ; Sewage/*microbiology ; Shiga Toxin 2/genetics ; *Water Microbiology ; }, abstract = {Enterohemorrhagic Escherichia coli (EHEC) (O157 and other serotypes) are zoonotic pathogens linked with severe human illnesses. The main virulence factors of EHEC are the Shiga toxins, among others. Most of the genes coding for these toxins are bacteriophage-encoded. Although ruminants are recognized as their main natural reservoir, water has also been documented as a way of transmission of EHEC. E. coli O157:H7 and other EHEC may contaminate waters (recreational, drinking or irrigation waters) through feces from humans and other animals. Indeed, the occurrence of EHEC carrying the stx2 gene in raw municipal sewage and animal wastewater from several origins has been widely documented. However, the evaluation of the persistence of naturally occurring EHEC in the environment is still difficult due to methodological problems. Methods proposed for the detection and isolation of stx-encoding bacteria, ranging from the classic culture-based methods to molecular approaches, and their application in the environment, are discussed here. Most virulence factors associated with these strains are linked to either plasmids or phages, and consequently they are likely to be subject to horizontal gene transfer between species or serotypes. Moreover, the presence of infectious stx-phages isolated as free particles in the environment and their high persistence in water systems suggest that they may contribute to the spread of stx genes, as they are directly involved in the emergence of new pathogenic strains, which might have important health consequences.}, }
@article {pmid17180746, year = {2007}, author = {Delaye, L and Becerra, A and Orgel, L and Lazcano, A}, title = {Molecular evolution of peptide methionine sulfoxide reductases (MsrA and MsrB): on the early development of a mechanism that protects against oxidative damage.}, journal = {Journal of molecular evolution}, volume = {64}, number = {1}, pages = {15-32}, pmid = {17180746}, issn = {0022-2844}, mesh = {Animals ; Bacterial Proteins/physiology ; *Evolution, Molecular ; Humans ; Methionine Sulfoxide Reductases ; Microfilament Proteins ; Oxidative Stress ; Oxidoreductases/*physiology ; *Phylogeny ; RNA, Ribosomal, 16S ; RNA, Ribosomal, 18S ; Symbiosis ; Transcription Factors ; }, abstract = {Methionine sulfoxide reductases, enzymes that reverse the oxidation of methionine residues, have been described in a wide range of species. The reduction of the diastereoisomers of oxidized methionine is catalyzed by two different monomeric methionine sulfoxide reductases (MsrA and MsrB) and is best understood as an evolutionary response to high levels of oxygen either in the Earth's atmosphere or possibly in more localized environments. Phylogenetic analyses of these proteins suggest that their distribution is the outcome of a complex history including many paralogy and lateral gene transfer events.}, }
@article {pmid17180166, year = {2007}, author = {Leitch, AR}, title = {Conserved gene order belies rapid genome turnover: the dynamic interplay between genomic DNA and the outside world.}, journal = {Heredity}, volume = {98}, number = {2}, pages = {61-62}, doi = {10.1038/sj.hdy.6800924}, pmid = {17180166}, issn = {0018-067X}, mesh = {Animals ; Conserved Sequence ; DNA/metabolism ; Evolution, Molecular ; Gene Order ; *Gene Transfer, Horizontal ; *Genome ; Humans ; *Interspersed Repetitive Sequences ; Synteny ; }, }
@article {pmid17178000, year = {2006}, author = {Avonce, N and Mendoza-Vargas, A and Morett, E and Iturriaga, G}, title = {Insights on the evolution of trehalose biosynthesis.}, journal = {BMC evolutionary biology}, volume = {6}, number = {}, pages = {109}, pmid = {17178000}, issn = {1471-2148}, mesh = {Animals ; *Evolution, Molecular ; Gene Expression Profiling ; Glucosyltransferases/*genetics ; Multigene Family ; Oligonucleotide Array Sequence Analysis ; Phosphoric Monoester Hydrolases/*genetics ; Phylogeny ; Species Specificity ; Trehalose/*biosynthesis/genetics ; }, abstract = {BACKGROUND: The compatible solute trehalose is a non-reducing disaccharide, which accumulates upon heat, cold or osmotic stress. It was commonly accepted that trehalose is only present in extremophiles or cryptobiotic organisms. However, in recent years it has been shown that although higher plants do not accumulate trehalose at significant levels they have actively transcribed genes encoding the corresponding biosynthetic enzymes.<br><br>RESULTS: In this study we show that trehalose biosynthesis ability is present in eubacteria, archaea, plants, fungi and animals. In bacteria there are five different biosynthetic routes, whereas in fungi, plants and animals there is only one. We present phylogenetic analyses of the trehalose-6-phosphate synthase (TPS) and trehalose-phosphatase (TPP) domains and show that there is a close evolutionary relationship between these domains in proteins from diverse organisms. In bacteria TPS and TPP genes are clustered, whereas in eukaryotes these domains are fused in a single protein.<br><br>CONCLUSION: We have demonstrated that trehalose biosynthesis pathways are widely distributed in nature. Interestingly, several eubacterial species have multiple pathways, while eukaryotes have only the TPS/TPP pathway. Vertebrates lack trehalose biosynthetic capacity but can catabolise it. TPS and TPP domains have evolved mainly in parallel and it is likely that they have experienced several instances of gene duplication and lateral gene transfer.}, }
@article {pmid17177781, year = {2006}, author = {Al-Ahmad, H and Dwyer, J and Moloney, M and Gressel, J}, title = {Mitigation of establishment of Brassica napus transgenes in volunteers using a tandem construct containing a selectively unfit gene.}, journal = {Plant biotechnology journal}, volume = {4}, number = {1}, pages = {7-21}, doi = {10.1111/j.1467-7652.2005.00152.x}, pmid = {17177781}, issn = {1467-7652}, mesh = {Brassica napus/drug effects/*genetics/physiology ; Brassica rapa/genetics ; Crosses, Genetic ; Gene Deletion ; Gene Transfer, Horizontal ; *Genes, Plant ; Gibberellins/pharmacology ; Herbicide Resistance/*genetics ; Phenotype ; Plants, Genetically Modified/*genetics/physiology ; *Transgenes ; }, abstract = {Transgenic oilseed rape (Brassica napus) plants may remain as 'volunteer' weeds in following crops, complicating cultivation and contaminating crop yield. Volunteers can become feral as well as act as a genetic bridge for the transfer of transgenes to weedy relatives. Transgenic mitigation using genes that are positive or neutral to the crop, but deleterious to weeds, should prevent volunteer establishment, as previously intimated using a tobacco (Nicotiana tabacum) model. A transgenically mitigated (TM), dwarf, herbicide-resistant construct using a gibberellic acid-insensitive (Deltagai) gene in the B. napus crop was effective in offsetting the risks of transgene establishment in volunteer populations of B. napus. This may be useful in the absence of herbicide, e.g. when wheat is rotated with oilseed rape. The TM dwarf B. napus plants grown alone had a much higher yield than the non-transgenics, but were exceedingly unfit in competition with non-transgenic tall cohorts. The reproductive fitness of TM B. napus was 0% at 2.5-cm and 4% at 5-cm spacing between glasshouse-grown plants relative to non-transgenic B. napus. Under screen-house conditions, the reproductive fitness of TM B. napus relative to non-transgenic B. napus was less than 12%, and the harvest index of the TM plants was less than 40% of that of the non-transgenic competitors. The data clearly indicate that the Deltagai gene greatly enhances the yield in a weed-free transgenic crop, but the dwarf plants can be eliminated when competing with non-transgenic cohorts (and presumably other species) when the selective herbicide is not used.}, }
@article {pmid17175534, year = {2007}, author = {Krause, L and McHardy, AC and Nattkemper, TW and Pühler, A and Stoye, J and Meyer, F}, title = {GISMO--gene identification using a support vector machine for ORF classification.}, journal = {Nucleic acids research}, volume = {35}, number = {2}, pages = {540-549}, pmid = {17175534}, issn = {1362-4962}, mesh = {Algorithms ; *Artificial Intelligence ; Chromosomes, Archaeal ; Chromosomes, Bacterial ; Classification/methods ; Gene Transfer, Horizontal ; *Genes, Archaeal ; *Genes, Bacterial ; Genomics/*methods ; *Open Reading Frames ; Plasmids/genetics ; Reproducibility of Results ; Software ; }, abstract = {We present the novel prokaryotic gene finder GISMO, which combines searches for protein family domains with composition-based classification based on a support vector machine. GISMO is highly accurate; exhibiting high sensitivity and specificity in gene identification. We found that it performs well for complete prokaryotic chromosomes, irrespective of their GC content, and also for plasmids as short as 10 kb, short genes and for genes with atypical sequence composition. Using GISMO, we found several thousand new predictions for the published genomes that are supported by extrinsic evidence, which strongly suggest that these are very likely biologically active genes. The source code for GISMO is freely available under the GPL license.}, }
@article {pmid17173540, year = {2007}, author = {Rawlings, ND}, title = {Unusual phyletic distribution of peptidases as a tool for identifying potential drug targets.}, journal = {The Biochemical journal}, volume = {401}, number = {2}, pages = {e5-7}, pmid = {17173540}, issn = {1470-8728}, mesh = {Animals ; Carboxypeptidases/genetics ; Drug Delivery Systems/methods ; Gene Transfer, Horizontal ; Peptide Hydrolases/*genetics ; Trypanosoma cruzi/*enzymology/genetics ; }, abstract = {Eukaryote homologues of carboxypeptidases Taq have been discovered by Niemirowicz et al. in the protozoan Trypanosoma cruzi, the causative agent of Chagas' disease. This is surprising, because the peptidase family was thought to be restricted to bacteria and archaea. In this issue of the Biochemical Journal, the authors propose that the Trypanosoma carboxypeptidases are potential drug targets for treatment of the disease. The authors also propose that the presence of the genes in the zooflagellates can be explained by a horizontal transfer of an ancestral gene from a prokaryote. Because peptidases are popular drug targets, identifying parasite or pathogen peptidases that have no homologues in their hosts would be a method to select the most promising targets. To understand how unusual this phyletic distribution is among the 183 families of peptidases, several other examples of horizontal transfers are presented, as well as some unusual losses of peptidase genes.}, }
@article {pmid17172342, year = {2007}, author = {Daniel, A and Bonnen, PE and Fischetti, VA}, title = {First complete genome sequence of two Staphylococcus epidermidis bacteriophages.}, journal = {Journal of bacteriology}, volume = {189}, number = {5}, pages = {2086-2100}, pmid = {17172342}, issn = {0021-9193}, support = {R01 AI057472/AI/NIAID NIH HHS/United States ; U19 AI056510/AI/NIAID NIH HHS/United States ; AI-056510/AI/NIAID NIH HHS/United States ; AI-057472/AI/NIAID NIH HHS/United States ; }, mesh = {Base Sequence ; *Genome, Viral ; Introns ; Lysogeny ; Molecular Sequence Data ; Morphogenesis ; Phylogeny ; Staphylococcus Phages/*genetics/physiology/ultrastructure ; Staphylococcus epidermidis/*virology ; Virus Assembly ; }, abstract = {Staphylococcus epidermidis is an important opportunistic pathogen causing nosocomial infections and is often associated with infections in patients with implanted prosthetic devices. A number of virulence determinants have been identified in S. epidermidis, which are typically acquired through horizontal gene transfer. Due to the high recombination potential, bacteriophages play an important role in these transfer events. Knowledge of phage genome sequences provides insights into phage-host biology and evolution. We present the complete genome sequence and a molecular characterization of two S. epidermidis phages, phiPH15 (PH15) and phiCNPH82 (CNPH82). Both phages belonged to the Siphoviridae family and produced stable lysogens. The PH15 and CNPH82 genomes displayed high sequence homology; however, our analyses also revealed important functional differences. The PH15 genome contained two introns, and in vivo splicing of phage mRNAs was demonstrated for both introns. Secondary structures for both introns were also predicted and showed high similarity to those of Streptococcus thermophilus phage 2972 introns. An additional finding was differential superinfection inhibition between the two phages that corresponded with differences in nucleotide sequence and overall gene content within the lysogeny module. We conducted phylogenetic analyses on all known Siphoviridae, which showed PH15 and CNPH82 clustering with Staphylococcus aureus, creating a novel clade within the S. aureus group and providing a higher overall resolution of the siphophage branch of the phage proteomic tree than previous studies. Until now, no S. epidermidis phage genome sequences have been reported in the literature, and thus this study represents the first complete genomic and molecular description of two S. epidermidis phages.}, }
@article {pmid17169972, year = {2007}, author = {Kasai, S and Okada, K and Hoshino, A and Iida, T and Honda, T}, title = {Lateral transfer of the lux gene cluster.}, journal = {Journal of biochemistry}, volume = {141}, number = {2}, pages = {231-237}, doi = {10.1093/jb/mvm023}, pmid = {17169972}, issn = {0021-924X}, mesh = {Bacterial Proteins/*genetics ; Blotting, Southern ; Chromosome Mapping ; Electrophoresis, Gel, Pulsed-Field ; Gammaproteobacteria/*genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Luminescence ; Molecular Sequence Data ; Multigene Family ; *Operon ; Oxidoreductases/*genetics ; Photobacterium/genetics ; Sequence Analysis, DNA ; Shewanella/genetics ; Vibrio/genetics ; }, abstract = {The lux operon is an uncommon gene cluster. To find the pathway through which the operon has been transferred, we sequenced the operon and both flanking regions in four typical luminous species. In Vibrio cholerae NCIMB 41, a five-gene cluster, most genes of which were highly similar to orthologues present in Gram-positive bacteria, along with the lux operon, is inserted between VC1560 and VC1563, on chromosome 1. Because this entire five-gene cluster is present in Photorhabdus luminescens TT01, about 1.5 Mbp upstream of the operon, we deduced that the operon and the gene cluster were transferred from V. cholerae to an ancestor of Pr. luminescens. Because in both V. fischeri and Shewanella hanedai, luxR and luxI were found just upstream of the operon, we concluded that the operon was transferred from either species to the other. Because most of the genes flanking the operon were highly similar to orthologues present on chromosome 2 of vibrios, we speculated that the operon of most species is located on this chromosome. The undigested genomic DNAs of five luminous species were analysed by pulsed-field gel electrophoresis and Southern hybridization. In all the species except V. cholerae, the operons are located on chromosome 2.}, }
@article {pmid17166673, year = {2007}, author = {Pocwierz-Kotus, A and Burzynski, A and Wenne, R}, title = {Family of Tc1-like elements from fish genomes and horizontal transfer.}, journal = {Gene}, volume = {390}, number = {1-2}, pages = {243-251}, doi = {10.1016/j.gene.2006.10.020}, pmid = {17166673}, issn = {0378-1119}, mesh = {Animals ; Base Sequence ; Blotting, Southern ; Cloning, Molecular ; DNA Primers/genetics ; *DNA Transposable Elements ; DNA-Binding Proteins/genetics ; Evolution, Molecular ; Fishes/classification/*genetics ; *Gene Transfer, Horizontal ; Genome ; Phylogeny ; Polymerase Chain Reaction ; Transposases/genetics ; }, abstract = {The involvement of horizontal transfer (HT) in the evolution of vertebrate transposable elements (TEs) is a matter of an ongoing debate. The phylogenetic relationships between Tc1 TEs, based on limited dataset have been previously used to infer a case of Tc1 HT between the genomes of fish and frogs. Here this hypothesis has been critically evaluated by the experimental approach including comparative data on the range of fish species available today. The distribution of a Tc1 subfamily of TE in selected fish species was investigated by PCR with a single primer complementary to ITRs and showed that they are widespread in the studied 17 fish species. They belong to five different subfamilies of Tc1 TEs, as revealed by the comparison with current genomic data for fish and amphibians. The original hypothesis would get much weaker support from the current data, although at least one novel potential and more convincing case of HT was identified between genomes of Perciformes fish. An interesting case of recombination-driven mobilisation of a degenerated TE by distantly related TE from different subfamily was discovered in the genome of pike. The occurrence of such cases widens the range of TE elements identifiable with the employed experimental approach. Further similar studies would help to explain the evolution of the multiple Tc1 lineages including species for which full genome sequences will not be available soon.}, }
@article {pmid17163979, year = {2007}, author = {Coburn, PS and Baghdayan, AS and Dolan, GT and Shankar, N}, title = {Horizontal transfer of virulence genes encoded on the Enterococcus faecalis pathogenicity island.}, journal = {Molecular microbiology}, volume = {63}, number = {2}, pages = {530-544}, doi = {10.1111/j.1365-2958.2006.05520.x}, pmid = {17163979}, issn = {0950-382X}, mesh = {Animals ; Bacterial Proteins/*genetics ; Chloramphenicol Resistance/genetics ; Conjugation, Genetic ; DNA, Bacterial/genetics/metabolism ; Enterococcus faecalis/*genetics/physiology ; Gastrointestinal Tract/microbiology ; *Gene Transfer, Horizontal ; Genes, Reporter ; Genomic Islands/*genetics ; Mice ; Models, Animal ; Plasmids/genetics ; Recombination, Genetic ; Stomach/microbiology ; Virulence Factors/*genetics ; }, abstract = {Enterococcus faecalis, a leading cause of nosocomial antibiotic resistant infections, frequently possesses a 150 kb pathogenicity island (PAI) that carries virulence determinants. The presence of excisionase and integrase genes, conjugative functions and multiple insertion sequence elements suggests that the PAI, or segments thereof, might be capable of horizontal transfer. In this report, the transfer of the E. faecalis PAI is demonstrated and a mechanism for transfer elucidated. In filter matings, chloramphenicol resistance was observed to transfer from strain MMH594b, a clinical isolate possessing the PAI tagged with a cat marker, to OG1RF (pCGC) with a frequency of 3.2 x 10(-10) per donor. Secondary transfer from primary transconjugant TCRFB1 to strain JH2SS in filter and broth matings occurred with a frequency of 1 and 2 x 10(-1) per donor respectively. Analysis of the transconjugants demonstrated that a 27,744 bp internal PAI segment was capable of excision and circularization in the donor, and is mobilized as a cointegrate with a pTEF1-like plasmid. High-frequency transfer also occurred from TCRFB1 to JH2SS during transient colonization of the mouse gastrointestinal tract. This is the first demonstration of the horizontal transfer of PAI-encoded virulence determinants in E. faecalis and has implications for genome evolution and diversity.}, }
@article {pmid17159236, year = {2006}, author = {El-Bondkly, AM}, title = {Gene transfer between different Trichoderma species and Aspergillus niger through intergeneric protoplast fusion to convert ground rice straw to citric acid and cellulases.}, journal = {Applied biochemistry and biotechnology}, volume = {135}, number = {2}, pages = {117-132}, doi = {10.1385/abab:135:2:117}, pmid = {17159236}, issn = {0273-2289}, mesh = {Antifungal Agents/pharmacology ; Aspergillus niger/drug effects/*genetics ; Cell Fusion ; Cellulase/*biosynthesis ; Cellulose/*metabolism ; Citric Acid/*metabolism ; Cobalt/pharmacology ; Copper/pharmacology ; DNA, Fungal/analysis ; Deoxyglucose/pharmacology ; Drug Resistance, Fungal ; *Gene Transfer, Horizontal ; Glycerol/pharmacology ; Haploidy ; Iron/pharmacology ; Mercury/pharmacology ; Oryza/metabolism ; Protoplasts ; Trichoderma/drug effects/*genetics ; Zinc/pharmacology ; }, abstract = {Single-stage direct bioconversion of cellulosic materials to citric acid using intergeneric hybrids obtained from three different Trichoderma species and Aspergillus niger was carried out. The recent results were obtained on the basis of either resistance or sensitivity to one or more of five metal ions, two catabolite repressors, and five antifungal agents, which were used in this study at different concentrations. Sixty-six fusants were isolated after using the three intergeneric protoplast fusion experiments, belonging to two types of intergeneric fusants. Fusants of the first type are heterokaryons (35 fusants). On the other hand, those of the second type are haploids (31 fusants), i.e., they were stable. The present study can be successfully applied in the construction of 14 new genetic fusants, which produced at least 100% more citric acid than the citric acid producer strain A. niger. Out of the fusants, three (1/18, 2/13 and 2/15) showed about a threefold increase of citric acid production in comparison with the parent A. niger strain. Furthermore, studies on DNA content showed that this finding may be submitted on the evidence that citric acid and cellulases production was not correlated with DNA content; however, the productivity depends on specific DNA content.}, }
@article {pmid17159225, year = {2006}, author = {Hotopp, JCD and Grifantini, R and Kumar, N and Tzeng, YL and Fouts, D and Frigimelica, E and Draghi, M and Giuliani, MM and Rappuoli, R and Stephens, DS and Grandi, G and Tettelin, H}, title = {Comparative genomics of Neisseria meningitidis: core genome, islands of horizontal transfer and pathogen-specific genes.}, journal = {Microbiology (Reading, England)}, volume = {152}, number = {Pt 12}, pages = {3733-3749}, doi = {10.1099/mic.0.29261-0}, pmid = {17159225}, issn = {1350-0872}, support = {R01 AI-33517/AI/NIAID NIH HHS/United States ; R01 AI-40247/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Capsules/genetics ; Biological Transport/genetics ; Cluster Analysis ; DNA Transposable Elements ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomic Islands ; *Genomics ; Interspersed Repetitive Sequences ; Neisseria cinerea/genetics ; Neisseria gonorrhoeae/genetics ; Neisseria lactamica/genetics ; Neisseria meningitidis/*genetics/pathogenicity ; Nucleic Acid Hybridization ; Oligonucleotide Array Sequence Analysis ; Prophages/genetics ; Synteny ; Virulence/genetics ; }, abstract = {To better understand Neisseria meningitidis genomes and virulence, microarray comparative genome hybridization (mCGH) data were collected from one Neisseria cinerea, two Neisseria lactamica, two Neisseria gonorrhoeae and 48 Neisseria meningitidis isolates. For N. meningitidis, these isolates are from diverse clonal complexes, invasive and carriage strains, and all major serogroups. The microarray platform represented N. meningitidis strains MC58, Z2491 and FAM18, and N. gonorrhoeae FA1090. By comparing hybridization data to genome sequences, the core N. meningitidis genome and insertions/deletions (e.g. capsule locus, type I secretion system) related to pathogenicity were identified, including further characterization of the capsule locus, bioinformatics analysis of a type I secretion system, and identification of some metabolic pathways associated with intracellular survival in pathogens. Hybridization data clustered meningococcal isolates from similar clonal complexes that were distinguished by the differential presence of six distinct islands of horizontal transfer. Several of these islands contained prophage or other mobile elements, including a novel prophage and a transposon carrying portions of a type I secretion system. Acquisition of some genetic islands appears to have occurred in multiple lineages, including transfer between N. lactamica and N. meningitidis. However, island acquisition occurs infrequently, such that the genomic-level relationship is not obscured within clonal complexes. The N. meningitidis genome is characterized by the horizontal acquisition of multiple genetic islands; the study of these islands reveals important sets of genes varying between isolates and likely to be related to pathogenicity.}, }
@article {pmid17159207, year = {2006}, author = {Kotze, AA and Tuffin, IM and Deane, SM and Rawlings, DE}, title = {Cloning and characterization of the chromosomal arsenic resistance genes from Acidithiobacillus caldus and enhanced arsenic resistance on conjugal transfer of ars genes located on transposon TnAtcArs.}, journal = {Microbiology (Reading, England)}, volume = {152}, number = {Pt 12}, pages = {3551-3560}, doi = {10.1099/mic.0.29247-0}, pmid = {17159207}, issn = {1350-0872}, mesh = {Acidithiobacillus/drug effects/*genetics ; Anti-Bacterial Agents/*pharmacology ; Arsenates/*pharmacology ; Arsenites/*pharmacology ; Chromosomes, Bacterial/genetics ; Cloning, Molecular ; Comamonadaceae/genetics ; Conjugation, Genetic ; DNA Transposable Elements/*genetics ; DNA, Bacterial/chemistry/genetics ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/drug effects/genetics ; Gene Deletion ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genes, Bacterial ; Legionella pneumophila/genetics ; Molecular Sequence Data ; Open Reading Frames ; Operon ; R Factors/genetics ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Transcription, Genetic ; }, abstract = {All strains of the moderately thermophilic, acidophilic, sulphur-oxidizing bacterium Acidithiobacillus caldus that have been tested contain a set of chromosomal arsenic resistance genes. Highly arsenic-resistant strains isolated from commercial arsenopyrite bio-oxidation tanks contain additional transposon-located (TnAtcArs) arsenic resistance genes. The chromosomal At. caldus ars genes were cloned and found to consist of arsR and arsC genes transcribed in one direction, and arsB in the opposite direction. The arsRC genes were co-transcribed with ORF1, and arsB with ORF5 in both At. caldus and Escherichia coli, although deletion of ORFs 1 and 5 did not appear to affect resistance to arsenate or arsenite in E. coli. ORFs 1 and 5 have not previously been reported as part of the ars operons, and had high amino acid identity to hypothetical proteins from Polaromonas naphthalenivorus (76%) and Legionella pneumophila (60%), respectively. Reporter-gene studies showed that the arsenic operon of transposon origin (TnAtcArs) was expressed at a higher level, and was less tightly regulated in E. coli than were the At. caldus ars genes of chromosomal origin. Plasmid pSa-mediated conjugal transfer of TnAtcArs from E. coli to At. caldus strains lacking the transposon was successful, and resulted in greatly increased levels of resistance to arsenite.}, }
@article {pmid17158898, year = {2007}, author = {Coombes, BK and Lowden, MJ and Bishop, JL and Wickham, ME and Brown, NF and Duong, N and Osborne, S and Gal-Mor, O and Finlay, BB}, title = {SseL is a salmonella-specific translocated effector integrated into the SsrB-controlled salmonella pathogenicity island 2 type III secretion system.}, journal = {Infection and immunity}, volume = {75}, number = {2}, pages = {574-580}, pmid = {17158898}, issn = {0019-9567}, mesh = {Animals ; Bacterial Proteins/biosynthesis/genetics/metabolism/*physiology ; Cell Line ; Cytoplasm/chemistry ; Disease Models, Animal ; Epithelial Cells/microbiology ; Flow Cytometry ; Gene Deletion ; Gene Expression Regulation, Bacterial ; Genomic Islands/*genetics ; Humans ; Macrophages/microbiology ; Mice ; Mice, Inbred C57BL ; Mutagenesis, Insertional ; Oligonucleotide Array Sequence Analysis ; *Protein Transport/genetics ; Salmonella Infections, Animal/*microbiology ; Salmonella typhimurium/genetics/*pathogenicity/*physiology ; Transcription Factors/genetics/physiology ; Virulence Factors/biosynthesis/genetics/metabolism/*physiology ; }, abstract = {Bacterial pathogens use horizontal gene transfer to acquire virulence factors that influence host colonization, alter virulence traits, and ultimately shape the outcome of disease following infection. One hallmark of the host-pathogen interaction is the prokaryotic type III secretion system that translocates virulence factors into host cells during infection. Salmonella enterica possesses two type III secretion systems that are utilized during host colonization and intracellular replication. Salmonella pathogenicity island 2 (SPI2) is a genomic island containing approximately 30 contiguous genes required to assemble a functional secretion system including the two-component regulatory system called SsrA-SsrB that positively regulates transcription of the secretion apparatus. We used transcriptional profiling with DNA microarrays to search for genes that coregulate with the SPI2 type III secretion machinery in an SsrB-dependent manner. Here we report the identification of a Salmonella-specific translocated effector called SseL that is required for full virulence during murine typhoid-like disease. Analysis of infected macrophages using fluorescence-activated cell sorting revealed that sseL is induced inside cells and requires SsrB for expression. SseL is retained predominantly in the cytoplasm of infected cells following translocation by the type III system encoded in SPI2. Animal infection experiments with sseL mutant bacteria indicate that integration of SseL into the SsrB response regulatory system contributes to systemic virulence of this pathogen.}, }
@article {pmid17158739, year = {2006}, author = {Mukherjee, M and Brown, MT and McArthur, AG and Johnson, PJ}, title = {Proteins of the glycine decarboxylase complex in the hydrogenosome of Trichomonas vaginalis.}, journal = {Eukaryotic cell}, volume = {5}, number = {12}, pages = {2062-2071}, pmid = {17158739}, issn = {1535-9778}, support = {/WT_/Wellcome Trust/United Kingdom ; T32 AI007323/AI/NIAID NIH HHS/United States ; 2-T32-AI-07323/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Dihydrolipoamide Dehydrogenase/genetics/metabolism ; Genes, Protozoan ; Glycine Decarboxylase Complex/genetics/*metabolism ; Glycine Decarboxylase Complex H-Protein/genetics/metabolism ; Kinetics ; Molecular Sequence Data ; Organelles/enzymology ; Phylogeny ; Protozoan Proteins/genetics/*metabolism ; Recombinant Proteins/genetics/metabolism ; Sequence Homology, Amino Acid ; Trichomonas vaginalis/*enzymology/genetics ; }, abstract = {Trichomonas vaginalis is a unicellular eukaryote that lacks mitochondria and contains a specialized organelle, the hydrogenosome, involved in carbohydrate metabolism and iron-sulfur cluster assembly. We report the identification of two glycine cleavage H proteins and a dihydrolipoamide dehydrogenase (L protein) of the glycine decarboxylase complex in T. vaginalis with predicted N-terminal hydrogenosomal presequences. Immunofluorescence analyses reveal that both H and L proteins are localized in hydrogenosomes, providing the first evidence for amino acid metabolism in this organelle. All three proteins were expressed in Escherichia coli and purified to homogeneity. The experimental Km of L protein for the two H proteins were 2.6 microM and 3.7 microM, consistent with both H proteins serving as substrates of L protein. Analyses using purified hydrogenosomes showed that endogenous H proteins exist as monomers and endogenous L protein as a homodimer in their native states. Phylogenetic analyses of L proteins revealed that the T. vaginalis homologue shares a common ancestry with dihydrolipoamide dehydrogenases from the firmicute bacteria, indicating its acquisition via a horizontal gene transfer event independent of the origins of mitochondria and hydrogenosomes.}, }
@article {pmid17158611, year = {2007}, author = {Jensen, PR and Williams, PG and Oh, DC and Zeigler, L and Fenical, W}, title = {Species-specific secondary metabolite production in marine actinomycetes of the genus Salinispora.}, journal = {Applied and environmental microbiology}, volume = {73}, number = {4}, pages = {1146-1152}, pmid = {17158611}, issn = {0099-2240}, support = {R37 CA044848/CA/NCI NIH HHS/United States ; R01 CA044848/CA/NCI NIH HHS/United States ; P30 CA023100/CA/NCI NIH HHS/United States ; CA44848/CA/NCI NIH HHS/United States ; P50CA23100-16/CA/NCI NIH HHS/United States ; }, mesh = {Micromonosporaceae/*classification/genetics/metabolism ; Molecular Sequence Data ; RNA, Ribosomal, 16S/analysis ; Seawater/*microbiology ; Species Specificity ; }, abstract = {Here we report associations between secondary metabolite production and phylogenetically distinct but closely related marine actinomycete species belonging to the genus Salinispora. The pattern emerged in a study that included global collection sites, and it indicates that secondary metabolite production can be a species-specific, phenotypic trait associated with broadly distributed bacterial populations. Associations between actinomycete phylotype and chemotype revealed an effective, diversity-based approach to natural product discovery that contradicts the conventional wisdom that secondary metabolite production is strain specific. The structural diversity of the metabolites observed, coupled with gene probing and phylogenetic analyses, implicates lateral gene transfer as a source of the biosynthetic genes responsible for compound production. These results conform to a model of selection-driven pathway fixation occurring subsequent to gene acquisition and provide a rare example in which demonstrable physiological traits have been correlated to the fine-scale phylogenetic architecture of an environmental bacterial community.}, }
@article {pmid17151080, year = {2007}, author = {Selengut, JD and Haft, DH and Davidsen, T and Ganapathy, A and Gwinn-Giglio, M and Nelson, WC and Richter, AR and White, O}, title = {TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes.}, journal = {Nucleic acids research}, volume = {35}, number = {Database issue}, pages = {D260-4}, pmid = {17151080}, issn = {1362-4962}, support = {HHSN266200400038C//PHS HHS/United States ; }, mesh = {Archaeal Proteins/classification/genetics/*physiology ; Bacterial Proteins/classification/genetics/*physiology ; *Databases, Protein ; Genome, Bacterial ; Genomics ; Internet ; Phylogeny ; Software ; User-Computer Interface ; }, abstract = {TIGRFAMs is a collection of protein family definitions built to aid in high-throughput annotation of specific protein functions. Each family is based on a hidden Markov model (HMM), where both cutoff scores and membership in the seed alignment are chosen so that the HMMs can classify numerous proteins according to their specific molecular functions. Most TIGRFAMs models describe 'equivalog' families, where both orthology and lateral gene transfer may be part of the evolutionary history, but where a single molecular function has been conserved. The Genome Properties system contains a queriable set of metabolic reconstructions, genome metrics and extractions of information from the scientific literature. Its genome-by-genome assertions of whether or not specific structures, pathways or systems are present provide high-level conceptual descriptions of genomic content. These assertions enable comparative genomics, provide a meaningful biological context to aid in manual annotation, support assignments of Gene Ontology (GO) biological process terms and help validate HMM-based predictions of protein function. The Genome Properties system is particularly useful as a generator of phylogenetic profiles, through which new protein family functions may be discovered. The TIGRFAMs and Genome Properties systems can be accessed at http://www.tigr.org/TIGRFAMs and http://www.tigr.org/Genome_Properties.}, }
@article {pmid17148507, year = {2007}, author = {Alvarez-Venegas, R and Sadder, M and Tikhonov, A and Avramova, Z}, title = {Origin of the bacterial SET domain genes: vertical or horizontal?.}, journal = {Molecular biology and evolution}, volume = {24}, number = {2}, pages = {482-497}, doi = {10.1093/molbev/msl184}, pmid = {17148507}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Archaea/genetics ; Bacteria/*genetics ; Bacterial Proteins/*genetics ; Chlamydia/genetics ; Chromosomes, Bacterial ; Cytophaga/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Leptospira interrogans/genetics ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Tertiary/genetics ; Rhizobium/genetics ; Sequence Alignment ; Spirochaeta/genetics ; }, abstract = {The presence of Supressor of variegation-Enhanser of zeste-Trithorax (SET) domain genes in bacteria is a current paradigm for lateral genetic exchange between eukaryotes and prokaryotes. Because a major function of SET domain proteins is the chemical modification of chromatin and bacteria do not have chromatin, there is no apparent functional requirement for the existence of bacterial SET domain genes. Consequently, their finding in only a small fraction of pathogenic and symbiotic bacteria was taken as evidence that bacteria have obtained the SET domain genes from their hosts. Furthermore, it was proposed that the products of the genes would, most likely, be involved in bacteria-host interactions. The broadened scope of sequenced bacterial genomes to include also free-living and environmental species provided a larger sample to analyze the bacterial SET domain genes. By phylogenetic analysis, examination of individual chromosomal regions for signs of insertion, and evaluating the chromosomal versus SET domain genes' GC contents, we provide evidence that SET domain genes have existed in the bacterial domain of life independently of eukaryotes. The bacterial genes have undergone an evolution of their own unconnected to the evolution of the eukaryotic SET domain genes. Initial finding of SET domain genes in predominantly pathogenic and symbiotic bacteria resulted, most probably, from a biased sample. However, a lateral transfer of SET domain genes may have occurred between some bacteria and a family of Archaea. A model for the evolution and distribution of SET domain genes in bacteria is proposed.}, }
@article {pmid17148431, year = {2006}, author = {Yates, CM and Shaw, DJ and Roe, AJ and Woolhouse, ME and Amyes, SG}, title = {Enhancement of bacterial competitive fitness by apramycin resistance plasmids from non-pathogenic Escherichia coli.}, journal = {Biology letters}, volume = {2}, number = {3}, pages = {463-465}, pmid = {17148431}, issn = {1744-9561}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Anti-Bacterial Agents/metabolism ; Cattle ; Conjugation, Genetic ; *Drug Resistance ; *Drug Resistance, Bacterial ; Escherichia coli/*genetics/metabolism ; Gene Transfer Techniques ; Gene Transfer, Horizontal ; Models, Genetic ; Nebramycin/*analogs &amp; derivatives/pharmacology ; Phenotype ; Plasmids/metabolism ; }, abstract = {The study of antibiotic resistance has in the past focused on organisms that are pathogenic to humans or animals. However, the development of resistance in commensal organisms is of concern because of possible transfer of resistance genes to zoonotic pathogens. Conjugative plasmids are genetic elements capable of such transfer and are traditionally thought to engender a fitness burden on host bacteria. In this study, conjugative apramycin resistance plasmids isolated from newborn calves were characterized. Calves were raised on a farm that had not used apramycin or related aminoglycoside antibiotics for at least 20 months prior to sampling. Of three apramycin resistance plasmids, one was capable of transfer at very high rates and two were found to confer fitness advantages on new Escherichia coli hosts. This is the first identification of natural plasmids isolated from commensal organisms that are able to confer a fitness advantage on a new host. This work indicates that reservoirs of antibiotic resistance genes in commensal organisms might not decrease if antibiotic usage is halted.}, }
@article {pmid17146478, year = {2006}, author = {Yan, B and Wang, H and Li, F and Li, CY}, title = {Regulation of mammalian horizontal gene transfer by apoptotic DNA fragmentation.}, journal = {British journal of cancer}, volume = {95}, number = {12}, pages = {1696-1700}, pmid = {17146478}, issn = {0007-0920}, mesh = {Animals ; Apoptosis/*physiology ; Apoptosis Regulatory Proteins/genetics/metabolism/pharmacology ; Caspases/metabolism ; Cells, Cultured ; *DNA Fragmentation ; Deoxyribonucleases/antagonists &amp; inhibitors/genetics/physiology ; Fibroblasts/metabolism ; Gene Transfer, Horizontal/*genetics ; Mice ; Mice, Knockout/embryology ; Phagocytosis ; Tumor Suppressor Protein p53/genetics/physiology ; }, abstract = {Previously it was shown that horizontal DNA transfer between mammalian cells can occur through the uptake of apoptotic bodies, where genes from the apoptotic cells were transferred to neighbouring cells phagocytosing the apoptotic bodies. The regulation of this process is poorly understood. It was shown that the ability of cells as recipient of horizontally transferred DNA was enhanced by deficiency of p53 or p21. However, little is known with regard to the regulation of DNA from donor apoptotic cells. Here we report that the DNA fragmentation factor/caspase-activated DNase (DFF/CAD), which is the endonuclease responsible for DNA fragmentation during apoptosis, plays a significant role in regulation of horizontal DNA transfer. Cells with inhibited DFF/CAD function are poor donors for horizontal gene transfer (HGT) while their ability of being recipients of HGT is not affected.}, }
@article {pmid17142402, year = {2007}, author = {Berger, B and Pridmore, RD and Barretto, C and Delmas-Julien, F and Schreiber, K and Arigoni, F and Brüssow, H}, title = {Similarity and differences in the Lactobacillus acidophilus group identified by polyphasic analysis and comparative genomics.}, journal = {Journal of bacteriology}, volume = {189}, number = {4}, pages = {1311-1321}, pmid = {17142402}, issn = {0021-9193}, mesh = {*Genetic Variation ; *Genome, Bacterial ; *Genomics ; Lactobacillus acidophilus/*classification/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {A set of lactobacilli were investigated by polyphasic analysis. Multilocus sequence analysis, DNA typing, microarray analysis, and in silico whole-genome alignments provided a remarkably consistent pattern of similarity within the Lactobacillus acidophilus complex. On microarray analysis, 17 and 5% of the genes from Lactobacillus johnsonii strain NCC533 represented variable and strain-specific genes, respectively, when tested against four independent isolates of L. johnsonii. When projected on the NCC533 genome map, about 10 large clusters of variable genes were identified, and they were enriched around the terminus of replication. A quarter of the variable genes and two-thirds of the strain-specific genes were associated with mobile DNA. Signatures for horizontal gene transfer and modular evolution were found in prophages and in DNA from the exopolysaccharide biosynthesis cluster. On microarray hybridizations, Lactobacillus gasseri strains showed a shift to significantly lower fluorescence intensities than the L. johnsonii test strains, and only genes encoding very conserved cellular functions from L. acidophilus hybridized to the L. johnsonii array. In-silico comparative genomics showed extensive protein sequence similarity and genome synteny of L. johnsonii with L. gasseri, L. acidophilus, and Lactobacillus delbrueckii; moderate synteny with Lactobacillus casei; and scattered X-type sharing of protein sequence identity with the other sequenced lactobacilli. The observation of a stepwise decrease in similarity between the members of the L. acidophilus group suggests a strong element of vertical evolution in a natural phylogenetic group. Modern whole-genome-based techniques are thus a useful adjunct to the clarification of taxonomical relationships in problematic bacterial groups.}, }
@article {pmid17142313, year = {2006}, author = {Yuan, J and Palioura, S and Salazar, JC and Su, D and O'Donoghue, P and Hohn, MJ and Cardoso, AM and Whitman, WB and Söll, D}, title = {RNA-dependent conversion of phosphoserine forms selenocysteine in eukaryotes and archaea.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, number = {50}, pages = {18923-18927}, pmid = {17142313}, issn = {0027-8424}, support = {R01 GM022854/GM/NIGMS NIH HHS/United States ; R37 GM022854/GM/NIGMS NIH HHS/United States ; GM 22854/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Escherichia coli/genetics/*metabolism ; Escherichia coli Proteins/genetics/metabolism ; Evolution, Molecular ; Gene Deletion ; Humans ; Methanococcus/genetics/*metabolism ; Phosphoserine/*metabolism ; Phylogeny ; RNA, Archaeal/*genetics ; RNA, Bacterial/*genetics ; RNA, Transfer, Amino Acyl/*genetics ; Selenocysteine/*biosynthesis ; }, abstract = {The trace element selenium is found in proteins as selenocysteine (Sec), the 21st amino acid to participate in ribosome-mediated translation. The substrate for ribosomal protein synthesis is selenocysteinyl-tRNA(Sec). Its biosynthesis from seryl-tRNA(Sec) has been established for bacteria, but the mechanism of conversion from Ser-tRNA(Sec) remained unresolved for archaea and eukarya. Here, we provide evidence for a different route present in these domains of life that requires the tRNA(Sec)-dependent conversion of O-phosphoserine (Sep) to Sec. In this two-step pathway, O-phosphoseryl-tRNA(Sec) kinase (PSTK) converts Ser-tRNA(Sec) to Sep-tRNA(Sec). This misacylated tRNA is the obligatory precursor for a Sep-tRNA:Sec-tRNA synthase (SepSecS); this protein was previously annotated as SLA/LP. The human and archaeal SepSecS genes complement in vivo an Escherichia coli Sec synthase (SelA) deletion strain. Furthermore, purified recombinant SepSecS converts Sep-tRNA(Sec) into Sec-tRNA(Sec) in vitro in the presence of sodium selenite and purified recombinant E. coli selenophosphate synthetase (SelD). Phylogenetic arguments suggest that Sec decoding was present in the last universal common ancestor. SepSecS and PSTK coevolved with the archaeal and eukaryotic lineages, but the history of PSTK is marked by several horizontal gene transfer events, including transfer to non-Sec-decoding Cyanobacteria and fungi.}, }
@article {pmid17141613, year = {2006}, author = {Reyes-Prieto, A and Hackett, JD and Soares, MB and Bonaldo, MF and Bhattacharya, D}, title = {Cyanobacterial contribution to algal nuclear genomes is primarily limited to plastid functions.}, journal = {Current biology : CB}, volume = {16}, number = {23}, pages = {2320-2325}, doi = {10.1016/j.cub.2006.09.063}, pmid = {17141613}, issn = {0960-9822}, mesh = {Cell Nucleus/*metabolism ; Cyanobacteria/*genetics ; Cyanophora/classification/*genetics/physiology ; Gene Transfer, Horizontal ; *Genome ; Phylogeny ; Plastids/*physiology ; Symbiosis ; }, abstract = {A single cyanobacterial primary endosymbiosis that occurred approximately 1.5 billion years ago is believed to have given rise to the plastid in the common ancestor of the Plantae or Archaeplastida--the eukaryotic supergroup comprising red, green (including land plants), and glaucophyte algae. Critical to plastid establishment was the transfer of endosymbiont genes to the host nucleus (i.e., endosymbiotic gene transfer [EGT]). It has been postulated that plastid-derived EGT played a significant role in plant nuclear-genome evolution, with 18% (or 4,500) of all nuclear genes in Arabidopsis thaliana having a cyanobacterial origin with about one-half of these recruited for nonplastid functions. Here, we determine whether the level of cyanobacterial gene recruitment proposed for Arabidopsis is of the same magnitude in the algal sisters of plants by analyzing expressed-sequence tag (EST) data from the glaucophyte alga Cyanophora paradoxa. Bioinformatic analysis of 3,576 Cyanophora nuclear genes shows that 10.8% of these with significant database hits are of cyanobacterial origin and one-ninth of these have nonplastid functions. Our data indicate that unlike plants, early-diverging algal groups appear to retain a smaller number of endosymbiont genes in their nucleus, with only a minor proportion of these recruited for nonplastid functions.}, }
@article {pmid17135441, year = {2007}, author = {Oyarzabal, OA and Rad, R and Backert, S}, title = {Conjugative transfer of chromosomally encoded antibiotic resistance from Helicobacter pylori to Campylobacter jejuni.}, journal = {Journal of clinical microbiology}, volume = {45}, number = {2}, pages = {402-408}, pmid = {17135441}, issn = {0095-1137}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Campylobacter jejuni/drug effects/*genetics ; Chromosomes, Bacterial/*genetics ; *Conjugation, Genetic ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/*genetics ; *Gene Transfer, Horizontal ; Helicobacter pylori/drug effects/*genetics ; Humans ; Streptomycin/pharmacology ; Transformation, Bacterial ; }, abstract = {Many strains of Helicobacter pylori are naturally competent for transformation and able to transfer chromosomal DNA among different isolates using a conjugation-like mechanism. In this study, we sought to determine whether H. pylori can transfer DNA into Campylobacter jejuni, a closely related species of the Campylobacterales group. To monitor the transfer, a chromosomally encoded streptomycin resistance cassette prearranged by a specific mutation in the rpsL gene of H. pylori was used. Mating of the bacteria on plates or in liquid broth medium produced C. jejuni progeny containing the streptomycin marker. DNA transfer was unidirectional, from H. pylori to C. jejuni, and the progeny were genetically identical to C. jejuni recipient strains. DNase I treatment reduced but did not eliminate transfer, and DNase I-treated cell supernatants did not transform, ruling out phage transduction. Recombinants also did not occur when the mating bacteria were separated by a membrane, suggesting that DNA transfer requires cell-to-cell contact. Transfer of the streptomycin marker was independent of the H. pylori comB transformation system, the cag pathogenicity island, and another type IV secretion system called tfs3. These findings indicated that a DNase I-resistant, conjugation-like mechanism may contribute to horizontal DNA transfer between different members of the Campylobacteriales group. The significance of this DNA uptake by C. jejuni in the context of acquiring antibiotic resistance is discussed.}, }
@article {pmid17132163, year = {2006}, author = {Poidevin, L and MacNeill, SA}, title = {Biochemical characterisation of LigN, an NAD+-dependent DNA ligase from the halophilic euryarchaeon Haloferax volcanii that displays maximal in vitro activity at high salt concentrations.}, journal = {BMC molecular biology}, volume = {7}, number = {}, pages = {44}, pmid = {17132163}, issn = {1471-2199}, mesh = {DNA Ligases/chemistry/genetics/isolation &amp; purification/*metabolism ; Haloferax volcanii/classification/*enzymology/genetics ; Potassium Chloride/*pharmacology ; Recombinant Proteins/chemistry/genetics/isolation &amp; purification/metabolism ; Salts ; }, abstract = {BACKGROUND: DNA ligases are required for DNA strand joining in all forms of cellular life. NAD+-dependent DNA ligases are found primarily in eubacteria but also in some eukaryotic viruses, bacteriophage and archaea. Among the archaeal NAD+-dependent DNA ligases is the LigN enzyme of the halophilic euryarchaeon Haloferax volcanii, the gene for which was apparently acquired by Hfx. volcanii through lateral gene transfer (LGT) from a halophilic eubacterium. Genetic studies show that the LGT-acquired LigN enzyme shares an essential function with the native Hfx. volcanii ATP-dependent DNA ligase protein LigA.<br><br>RESULTS: To characterise the enzymatic properties of the LigN protein, wild-type and three mutant forms of the LigN protein were separately expressed in recombinant form in E.coli and purified to apparent homogeneity by immobilised metal ion affinity chromatography (IMAC). Non-isotopic DNA ligase activity assays using lambda DNA restriction fragments with 12 bp cos cohesive ends were used to show that LigN activity was dependent on addition of divalent cations and salt. No activity was detected in the absence of KCl, whereas maximum activity could be detected at 3.2 M KCl, close to the intracellular KCl concentration of Hfx. volcanii cells.<br><br>CONCLUSION: LigN is unique amongst characterised DNA ligase enzymes in displaying maximal DNA strand joining activity at high (> 3 M) salt levels. As such the LigN enzyme has potential both as a novel tool for biotechnology and as a model enzyme for studying the adaptation of proteins to high intracellular salt levels.}, }
@article {pmid17127525, year = {2006}, author = {Salyers, A and Shoemaker, NB}, title = {Reservoirs of antibiotic resistance genes.}, journal = {Animal biotechnology}, volume = {17}, number = {2}, pages = {137-146}, doi = {10.1080/10495390600957076}, pmid = {17127525}, issn = {1049-5398}, mesh = {Animal Husbandry ; Animals ; Anti-Bacterial Agents/*therapeutic use ; Bacteria/*drug effects/*genetics/pathogenicity ; Colon/metabolism/*microbiology ; Conjugation, Genetic ; Drug Resistance, Bacterial/*genetics ; Environmental Microbiology ; Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; }, abstract = {A potential concern about the use of antibiotics in animal husbundary is that, as antibiotic resistant bacteria move from the farm into the human diet, they may pass antibiotic resistance genes to bacteria that normally reside in a the human intestinal tract and from there to bacteria that cause human disease (reservoir hypothesis). In this article various approaches to evaluating the risk of agricultural use of antibiotics are assessed critically. In addition, the potential benefits of applying new technology and using new insights from the field of microbial ecology are explained.}, }
@article {pmid17127524, year = {2006}, author = {Summers, AO}, title = {Genetic linkage and horizontal gene transfer, the roots of the antibiotic multi-resistance problem.}, journal = {Animal biotechnology}, volume = {17}, number = {2}, pages = {125-135}, doi = {10.1080/10495390600957217}, pmid = {17127524}, issn = {1049-5398}, mesh = {Animal Husbandry ; Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/*genetics ; Conjugation, Genetic ; DNA Transposable Elements ; Drug Resistance, Multiple, Bacterial/*genetics ; Environmental Microbiology ; *Gene Transfer, Horizontal ; Genes, Bacterial ; *Genetic Linkage ; Humans ; Integrons ; Metals, Heavy/toxicity ; Transduction, Genetic ; }, abstract = {Bacteria carrying resistance genes for many antibiotics are moving beyond the clinic into the community, infecting otherwise healthy people with untreatable and frequently fatal infections. This state of affairs makes it increasingly important that we understand the sources of this problem in terms of bacterial biology and ecology and also that we find some new targets for drugs that will help control this growing epidemic. This brief and eclectic review takes the perspective that we have too long thought about the problem in terms of treatment with or resistance to a single antibiotic at a time, assuming that dissemination of the resistance gene was affected by simple vertical inheritance. In reality antibiotic resistance genes are readily transferred horizontally, even to and from distantly related bacteria. The common agents of bacterial gene transfer are described and also one of the processes whereby nonantibiotic chemicals, specifically toxic metals, in the environment can select for and enrich bacteria with antibiotic multiresistance. Lastly, some speculation is offered on broadening our perspective on this problem to include drugs directed at compromising the ability of the mobile elements themselves to replicate, transfer, and recombine, that is, the three "infrastructure" processes central to the movement of genes among bacteria.}, }
@article {pmid17123440, year = {2006}, author = {Stechmann, A and Baumgartner, M and Silberman, JD and Roger, AJ}, title = {The glycolytic pathway of Trimastix pyriformis is an evolutionary mosaic.}, journal = {BMC evolutionary biology}, volume = {6}, number = {}, pages = {101}, pmid = {17123440}, issn = {1471-2148}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Eukaryota/enzymology/genetics/*metabolism ; *Expressed Sequence Tags ; *Gene Transfer, Horizontal ; Glycolysis/*genetics ; Molecular Sequence Data ; *Phylogeny ; }, abstract = {BACKGROUND: Glycolysis and subsequent fermentation is the main energy source for many anaerobic organisms. The glycolytic pathway consists of ten enzymatic steps which appear to be universal amongst eukaryotes. However, it has been shown that the origins of these enzymes in specific eukaryote lineages can differ, and sometimes involve lateral gene transfer events. We have conducted an expressed sequence tag (EST) survey of the anaerobic flagellate Trimastix pyriformis to investigate the nature of the evolutionary origins of the glycolytic enzymes in this relatively unstudied organism.<br><br>RESULTS: We have found genes in the Trimastix EST data that encode enzymes potentially catalyzing nine of the ten steps of the glycolytic conversion of glucose to pyruvate. Furthermore, we have found two different enzymes that in principle could catalyze the conversion of phosphoenol pyruvate (PEP) to pyruvate (or the reverse reaction) as part of the last step in glycolysis. Our phylogenetic analyses of all of these enzymes revealed at least four cases where the relationship of the Trimastix genes to homologs from other species is at odds with accepted organismal relationships. Although lateral gene transfer events likely account for these anomalies, with the data at hand we were not able to establish with confidence the bacterial donor lineage that gave rise to the respective Trimastix enzymes.<br><br>CONCLUSION: A number of the glycolytic enzymes of Trimastix have been transferred laterally from bacteria instead of being inherited from the last common eukaryotic ancestor. Thus, despite widespread conservation of the glycolytic biochemical pathway across eukaryote diversity, in a number of protist lineages the enzymatic components of the pathway have been replaced by lateral gene transfer from disparate evolutionary sources. It remains unclear if these replacements result from selectively advantageous properties of the introduced enzymes or if they are neutral outcomes of a gene transfer 'ratchet' from food or endosymbiotic organisms or a combination of both processes.}, }
@article {pmid17122392, year = {2007}, author = {Moubareck, C and Lecso, M and Pinloche, E and Butel, MJ and Doucet-Populaire, F}, title = {Inhibitory impact of bifidobacteria on the transfer of beta-lactam resistance among Enterobacteriaceae in the gnotobiotic mouse digestive tract.}, journal = {Applied and environmental microbiology}, volume = {73}, number = {3}, pages = {855-860}, pmid = {17122392}, issn = {0099-2240}, mesh = {Animals ; *Antibiosis ; Bifidobacterium/*growth &amp; development ; Conjugation, Genetic ; Enterobacteriaceae/drug effects/genetics/*growth &amp; development/metabolism ; Gastrointestinal Tract/*microbiology ; *Gene Transfer, Horizontal ; *Germ-Free Life ; Mice ; beta-Lactam Resistance/*genetics ; beta-Lactamases/genetics ; }, abstract = {While looking for new means to limit the dissemination of antibiotic resistance, we evaluated the role of potentially probiotic bifidobacteria on the transfer of resistance genes between enterobacteria. Transfers of bla genes encoding extended-spectrum beta-lactamases (SHV-5 and CTX-M-15) were studied in the absence or presence of bifidobacteria. In vitro, transfer frequencies of these bla genes decreased significantly in the presence of three of five tested strains, i.e., Bifidobacterium longum CUETM-89-215, Bifidobacterium bifidum CIP-56.7T, and Bifidobacterium pseudocatenulatum CIP-104168T. Four transfer experiments were conducted in the digestive tract of gnotobiotic mice, the first three observing the effect of B. longum CUETM-89-215, B. bifidum CIP-56.7T, and B. pseudocatenulatum CIP-104168T on blaSHV-5 transfer and the fourth experiment studying the effect of B. bifidum CIP-56.7T on blaCTX-M-15 transfer. These experiments revealed significant decreases in the transconjugant levels (up to 3 logs) in mice having received B. bifidum CIP-56.7T or B. pseudocatenulatum CIP-104168T compared to control mice. Bifidobacteria appear to have an inhibitory impact on the transfer of antibiotic resistance genes. The inhibitory effect is associated to specific bifidobacterial strains and may be related to the production of thermostable metabolites by these strains.}, }
@article {pmid17122345, year = {2007}, author = {Demars, R and Weinfurter, J and Guex, E and Lin, J and Potucek, Y}, title = {Lateral gene transfer in vitro in the intracellular pathogen Chlamydia trachomatis.}, journal = {Journal of bacteriology}, volume = {189}, number = {3}, pages = {991-1003}, pmid = {17122345}, issn = {0021-9193}, support = {R01 AI 1056124/AI/NIAID NIH HHS/United States ; R21 AI 05872801/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Chlamydia trachomatis/drug effects/*genetics/growth &amp; development ; Drug Resistance, Bacterial ; Gene Expression Regulation/drug effects ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Complementation Test ; HeLa Cells ; Humans ; Lincomycin/pharmacology ; Microbial Sensitivity Tests ; Microscopy, Phase-Contrast ; *Mutation ; Ofloxacin/pharmacology ; Rifampin/pharmacology ; Trimethoprim/pharmacology ; }, abstract = {Genetic recombinants that resulted from lateral gene transfer (LGT) have been detected in sexually transmitted disease isolates of Chlamydia trachomatis, but a mechanism for LGT in C. trachomatis has not been described. We describe here a system that readily detects C. trachomatis LGT in vitro and that may facilitate discovery of its mechanisms. Host cells were simultaneously infected in the absence of antibiotics with an ofloxacin-resistant mutant and a second mutant that was resistant to lincomycin, trimethoprim, or rifampin. Selection for doubly resistant C. trachomatis isolates in the progeny detected apparent recombinant frequencies of 10(-4) to 10(-3), approximately 10(4) times more frequent than doubly resistant spontaneous mutants in progeny from uniparental control infections. Polyclonal doubly resistant populations and clones isolated from them in the absence of antibiotics had the specific resistance-conferring mutations present in the parental mutants; absence of the corresponding normal nucleotides indicated that they had been replaced by homologous recombination. These results eliminate spontaneous mutation, between-strain complementation, and heterotypic resistance as general explanations of multiply resistant C. trachomatis that originated in mixed infections in our experiments and demonstrate genetic stability of the recombinants. The kind of LGT we observed might be useful for creating new strains for functional studies by creating new alleles or combinations of alleles of polymorphic loci and might also disseminate antibiotic resistance genes in vivo. The apparent absence of phages and conjugative plasmids in C. trachomatis suggests that the LGT may have occurred by means of natural DNA transformation. Therefore, the experimental system may have implications for genetically altering C. trachomatis by means of DNA transfer.}, }
@article {pmid17122343, year = {2007}, author = {Juhas, M and Crook, DW and Dimopoulou, ID and Lunter, G and Harding, RM and Ferguson, DJ and Hood, DW}, title = {Novel type IV secretion system involved in propagation of genomic islands.}, journal = {Journal of bacteriology}, volume = {189}, number = {3}, pages = {761-771}, pmid = {17122343}, issn = {0021-9193}, support = {/WT_/Wellcome Trust/United Kingdom ; G0400039/MRC_/Medical Research Council/United Kingdom ; G0501331/MRC_/Medical Research Council/United Kingdom ; MC_U137761446/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Bacterial Proteins/genetics/*metabolism ; Conjugation, Genetic ; Evolution, Molecular ; Fimbriae, Bacterial/metabolism/ultrastructure ; Gene Expression Regulation, Bacterial ; Genomic Islands/*genetics/physiology ; Haemophilus influenzae/genetics/metabolism ; Microscopy, Electron, Transmission ; *Multigene Family ; Mutation ; Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {Type IV secretion systems (T4SSs) mediate horizontal gene transfer, thus contributing to genome plasticity, evolution of infectious pathogens, and dissemination of antibiotic resistance and other virulence traits. A gene cluster of the Haemophilus influenzae genomic island ICEHin1056 has been identified as a T4SS involved in the propagation of genomic islands. This T4SS is novel and evolutionarily distant from the previously described systems. Mutation analysis showed that inactivation of key genes of this system resulted in a loss of phenotypic traits provided by a T4SS. Seven of 10 mutants with a mutation in this T4SS did not express the type IV secretion pilus. Correspondingly, disruption of the genes resulted in up to 100,000-fold reductions in conjugation frequencies compared to those of the parent strain. Moreover, the expression of this T4SS was found to be positively regulated by one of its components, the tfc24 gene. We concluded that this gene cluster represents a novel family of T4SSs involved in propagation of genomic islands.}, }
@article {pmid17117976, year = {2006}, author = {Xavier, BM and Russell, JB}, title = {Bacterial competition between a bacteriocin-producing and a bacteriocin-negative strain of Streptococcus bovis in batch and continuous culture.}, journal = {FEMS microbiology ecology}, volume = {58}, number = {3}, pages = {317-322}, doi = {10.1111/j.1574-6941.2006.00160.x}, pmid = {17117976}, issn = {0168-6496}, mesh = {Antibiosis/*physiology ; Bacteriocins/*biosynthesis ; Bacteriological Techniques/methods ; Clostridium sticklandii/growth &amp; development/metabolism ; Culture Media ; Gene Transfer, Horizontal ; Streptococcus bovis/classification/*growth &amp; development/*metabolism ; }, abstract = {A bacteriocin-producing Streptococcus bovis strain (HC5) outcompeted a sensitive strain (JB1) before it reached stationary phase (pH 6.4), even though it grew 10% slower and cell-free bovicin HC5 could not yet be detected. The success of bacteriocin-negative S. bovis isolates was enhanced by the presence of another sensitive bacterium (Clostridium sticklandii SR). PCR based on repetitive DNA sequences indicated that S. bovis HC5 was not simply transferring bacteriocin genes to S. bovis JB1. When the two S. bovis strains were coinoculated into minimal medium, bacteriocin-negative isolates predominated, and this effect could be explained by the longer lag time (0.5 vs. 1.5 h) of S. bovis HC5. If the glucose concentration of the minimal medium was increased from 2 to 7 mg mL(-1), the effect of lag time was diminished and bacteriocin-producing isolates once again dominated the coculture. When the competition was examined in continuous culture, it became apparent that batch culture inocula were never able to displace a strain that had already reached steady state, even if the inoculum was large. This result indicated that bacterial selection for substrate affinity was even more important than bacteriocin production.}, }
@article {pmid17116660, year = {2007}, author = {Escudero, JA and San Millan, A and Catalan, A and de la Campa, AG and Rivero, E and Lopez, G and Dominguez, L and Moreno, MA and Gonzalez-Zorn, B}, title = {First characterization of fluoroquinolone resistance in Streptococcus suis.}, journal = {Antimicrobial agents and chemotherapy}, volume = {51}, number = {2}, pages = {777-782}, pmid = {17116660}, issn = {0066-4804}, mesh = {Amino Acid Sequence ; DNA Gyrase/genetics ; DNA Topoisomerase IV/genetics ; *Drug Resistance, Bacterial/genetics ; Female ; Fluoroquinolones/*pharmacology ; Genes, Bacterial ; Humans ; Male ; Molecular Sequence Data ; Point Mutation ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; *Streptococcus suis/drug effects/genetics ; }, abstract = {We have identified and sequenced the genes encoding the quinolone-resistance determining region (QRDR) of ParC and GyrA in fluoroquinolone-susceptible and -resistant Streptococcus suis clinical isolates. Resistance is the consequence of single point mutations in the QRDRs of ParC and GyrA and is not due to clonal spread of resistant strains or horizontal gene transfer with other bacteria.}, }
@article {pmid17116411, year = {2007}, author = {Park, JM and Manen, JF and Schneeweiss, GM}, title = {Horizontal gene transfer of a plastid gene in the non-photosynthetic flowering plants Orobanche and Phelipanche (Orobanchaceae).}, journal = {Molecular phylogenetics and evolution}, volume = {43}, number = {3}, pages = {974-985}, doi = {10.1016/j.ympev.2006.10.011}, pmid = {17116411}, issn = {1055-7903}, mesh = {Amino Acid Sequence ; *Gene Transfer, Horizontal ; Genes, Plant ; Molecular Sequence Data ; Orobanchaceae/*genetics ; Orobanche/*genetics ; Plastids/*genetics ; RNA, Transfer/genetics ; Ribosomal Proteins/genetics ; Ribulose-Bisphosphate Carboxylase/genetics ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; }, abstract = {Plastid sequences are among the most widely used in phylogenetic and phylogeographic studies in flowering plants, where they are usually assumed to evolve like non-recombining, uniparentally transmitted, single-copy genes. Among others, this assumption can be violated by intracellular gene transfer (IGT) within cells or by the exchange of genes across mating barriers (horizontal gene transfer, HGT). We report on HGT of a plastid region including rps2, trnL-F, and rbcL in a group of non-photosynthetic flowering plants. Species of the parasitic broomrape genus Phelipanche harbor two copies of rps2, a plastid ribosomal gene, one corresponding to the phylogenetic position of the respective species, the other being horizontally acquired from the related broomrape genus Orobanche. While the vertically transmitted copies probably reside within the plastid genome, the localization of the horizontally acquired copies is not known. With both donor and recipient being parasitic plants, a possible pathway for the exchange of genetic material is via a commonly attacked host.}, }
@article {pmid17116239, year = {2007}, author = {Madrid, C and Balsalobre, C and García, J and Juárez, A}, title = {The novel Hha/YmoA family of nucleoid-associated proteins: use of structural mimicry to modulate the activity of the H-NS family of proteins.}, journal = {Molecular microbiology}, volume = {63}, number = {1}, pages = {7-14}, doi = {10.1111/j.1365-2958.2006.05497.x}, pmid = {17116239}, issn = {0950-382X}, mesh = {Bacterial Proteins/*metabolism ; DNA-Binding Proteins/*chemistry/*metabolism ; Enterobacteriaceae/*metabolism ; Escherichia coli Proteins ; Gene Expression Regulation, Bacterial ; }, abstract = {The Hha/YmoA family of proteins is a group of conserved, low-molecular-weight proteins involved in the regulation of gene expression. Studies performed in Escherichia coli, Salmonella sp. and Yersinia sp. highlight the contribution of these proteins in regulating bacterial virulence, horizontal gene transfer and cell physiology. Genes encoding such proteins are located on chromosomes and plasmids in different genera of Gram-negative bacteria. Their mode of action is currently being analysed by studying direct binding of Hha to DNA and as a component of protein complexes with regulatory functions. Recent data on the interaction of Hha with the H-NS family of proteins and structural information suggest a physiological role for such protein complexes in many aspects of gene regulation.}, }
@article {pmid17114256, year = {2007}, author = {Hill, KK and Smith, TJ and Helma, CH and Ticknor, LO and Foley, BT and Svensson, RT and Brown, JL and Johnson, EA and Smith, LA and Okinaka, RT and Jackson, PJ and Marks, JD}, title = {Genetic diversity among Botulinum Neurotoxin-producing clostridial strains.}, journal = {Journal of bacteriology}, volume = {189}, number = {3}, pages = {818-832}, pmid = {17114256}, issn = {0021-9193}, support = {U01 AI056493/AI/NIAID NIH HHS/United States ; }, mesh = {Botulinum Toxins/*biosynthesis ; Clostridium botulinum/*genetics/metabolism ; *Genetic Variation ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Serotyping ; }, abstract = {Clostridium botulinum is a taxonomic designation for many diverse anaerobic spore-forming rod-shaped bacteria that have the common property of producing botulinum neurotoxins (BoNTs). The BoNTs are exoneurotoxins that can cause severe paralysis and death in humans and other animal species. A collection of 174 C. botulinum strains was examined by amplified fragment length polymorphism (AFLP) analysis and by sequencing of the 16S rRNA gene and BoNT genes to examine the genetic diversity within this species. This collection contained representatives of each of the seven different serotypes of botulinum neurotoxins (BoNT/A to BoNT/G). Analysis of the16S rRNA gene sequences confirmed previous identifications of at least four distinct genomic backgrounds (groups I to IV), each of which has independently acquired one or more BoNT genes through horizontal gene transfer. AFLP analysis provided higher resolution and could be used to further subdivide the four groups into subgroups. Sequencing of the BoNT genes from multiple strains of serotypes A, B, and E confirmed significant sequence variation within each serotype. Four distinct lineages within each of the BoNT A and B serotypes and five distinct lineages of serotype E strains were identified. The nucleotide sequences of the seven toxin genes of the serotypes were compared and showed various degrees of interrelatedness and recombination, as was previously noted for the nontoxic nonhemagglutinin gene, which is linked to the BoNT gene. These analyses contribute to the understanding of the evolution and phylogeny within this species and assist in the development of improved diagnostics and therapeutics for the treatment of botulism.}, }
@article {pmid17114174, year = {2007}, author = {Chiu, CH and Chen, HL and Kao, LS and Yang, CY and Chu, C and Doublet, B and Praud, K and Cloeckaert, A}, title = {Variant Salmonella genomic island 1 antibiotic resistance gene clusters in Salmonella enterica serovar Derby isolates from humans in Taiwan.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {59}, number = {2}, pages = {325-326}, doi = {10.1093/jac/dkl475}, pmid = {17114174}, issn = {0305-7453}, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genetic Variation ; Genomic Islands/*genetics ; Humans ; *Multigene Family ; Polymerase Chain Reaction ; Salmonella Infections/drug therapy/epidemiology/*microbiology ; Salmonella enterica/*genetics/isolation &amp; purification ; Taiwan/epidemiology ; }, }
@article {pmid17113245, year = {2007}, author = {Kalia, VC and Lal, S and Cheema, S}, title = {Insight in to the phylogeny of polyhydroxyalkanoate biosynthesis: horizontal gene transfer.}, journal = {Gene}, volume = {389}, number = {1}, pages = {19-26}, doi = {10.1016/j.gene.2006.09.010}, pmid = {17113245}, issn = {0378-1119}, mesh = {Biopolymers/*biosynthesis/*genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; *Phylogeny ; }, abstract = {Polyhydroxyalkanoates (PHAs) are gaining more and more importance the world over due to their structural diversity and close analogy to plastics. Their biodegradability makes them extremely desirable substitutes for synthetic plastics. PHAs are produced in organisms under certain stress conditions. Here, we investigated 253 sequenced (completely and unfinished) genomes for the diversity and phylogenetics of the PHA biosynthesis. Discrepancies in the phylogenetic trees for phaA, phaB and phaC genes of the PHA biosynthesis have led to the suggestion that horizontal gene transfer (HGT) may be a major contributor for its evolution. Twenty four organisms belonging to diverse taxa were found to be involved in HGT. Among these, Bacillus cereus ATCC 14579 and Xanthomonas axonopodis pv. citri str. 306 seem to have acquired all the three genes through HGT events and have not been characterized so far as PHA producers. This study also revealed certain potential organisms such as Streptomyces coelicolor A3(2), Staphylococcus epidermidis ATCC 12228, Brucella suis 1330, Burkholderia sp., DSMZ 9242 and Leptospira interrogans serovar lai str. 56601, which can be transformed into novel PHA producers through recombinant DNA technology.}, }
@article {pmid17109990, year = {2007}, author = {Filée, J and Siguier, P and Chandler, M}, title = {I am what I eat and I eat what I am: acquisition of bacterial genes by giant viruses.}, journal = {Trends in genetics : TIG}, volume = {23}, number = {1}, pages = {10-15}, doi = {10.1016/j.tig.2006.11.002}, pmid = {17109990}, issn = {0168-9525}, mesh = {Chromosome Mapping ; Computational Biology ; DNA Viruses/*genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/*genetics ; Genome, Viral/*genetics ; Interspersed Repetitive Sequences/genetics ; *Models, Genetic ; }, abstract = {Giant viruses are nucleocytoplasmic large DNA viruses (NCLDVs) that infect algae (phycodnaviruses) and amoebae (Mimivirus). We report an unexpected abundance in these giant viruses of islands of bacterial-type genes, including apparently intact prokaryotic mobile genetic elements, and hypothesize that NCLDV genomes undergo successive accretions of bacterial genes. The viruses could acquire bacterial genes within their bacteria-feeding eukaryotic hosts, and we suggest that such acquisition is driven by the intimate coupling of recombination and replication in NCLDVs.}, }
@article {pmid17109029, year = {2006}, author = {Williamson, NR and Fineran, PC and Leeper, FJ and Salmond, GP}, title = {The biosynthesis and regulation of bacterial prodiginines.}, journal = {Nature reviews. Microbiology}, volume = {4}, number = {12}, pages = {887-899}, doi = {10.1038/nrmicro1531}, pmid = {17109029}, issn = {1740-1534}, mesh = {Antineoplastic Agents/classification/pharmacology ; Bacteria/*genetics/metabolism ; Cues ; Environment ; Gene Expression Regulation, Bacterial/*physiology ; Gene Order/genetics ; Gene Transfer, Horizontal ; Immunosuppressive Agents/classification/pharmacology ; Multigene Family/genetics ; Prodigiosin/*analogs &amp; derivatives/biosynthesis/classification/pharmacology ; Quorum Sensing/physiology ; Signal Transduction/physiology ; }, abstract = {The red-pigmented prodiginines are bioactive secondary metabolites produced by both Gram-negative and Gram-positive bacteria. Recently, these tripyrrole molecules have received renewed attention owing to reported immunosuppressive and anticancer properties. The enzymes involved in the biosynthetic pathways for the production of two of these molecules, prodigiosin and undecylprodigiosin, are now known. However, the biochemistry of some of the reactions is still poorly understood. The physiology and regulation of prodiginine production in Serratia and Streptomyces are now well understood, although the biological role of these pigments in the producer organisms remains unclear. However, research into the biology of pigment production will stimulate interest in the bioengineering of strains to synthesize useful prodiginine derivatives.}, }
@article {pmid17108068, year = {2007}, author = {Valenzuela, JK and Thomas, L and Partridge, SR and van der Reijden, T and Dijkshoorn, L and Iredell, J}, title = {Horizontal gene transfer in a polyclonal outbreak of carbapenem-resistant Acinetobacter baumannii.}, journal = {Journal of clinical microbiology}, volume = {45}, number = {2}, pages = {453-460}, pmid = {17108068}, issn = {0095-1137}, mesh = {Acinetobacter Infections/*epidemiology/microbiology ; Acinetobacter baumannii/classification/drug effects/*genetics ; Anti-Bacterial Agents/*pharmacology ; Australia/epidemiology ; Bacterial Proteins/genetics ; Carbapenems/*pharmacology ; *Disease Outbreaks ; *Drug Resistance, Bacterial/genetics ; *Gene Transfer, Horizontal ; Humans ; Molecular Sequence Data ; Sequence Analysis, DNA ; }, abstract = {In the last few years, phenotypically carbapenem resistant Acinetobacter strains have been identified throughout the world, including in many of the hospitals and intensive care units (ICUs) of Australia. Genotyping of Australian ICU outbreak-associated isolates by pulsed-field gel electrophoresis of whole genomic DNA indicated that different strains were cocirculating within one hospital. The carbapenem-resistant phenotype of these and other Australian isolates was found to be due to carbapenem-hydrolyzing activity associated with the presence of the blaOXA-23 gene. In all resistant strains examined, the blaOXA-23 gene was adjacent to the insertion sequence ISAba1 in a structure that has been found in Acinetobacter baumannii strains of a similar phenotype from around the world; blaOXA-51-like genes were also found in all A. baumannii strains but were not consistently associated with ISAba1, which is believed to provide the promoter required for expression of linked antibiotic resistance genes. Most isolates were also found to contain additional antibiotic resistance genes within the cassette arrays of class 1 integrons. The same cassette arrays, in addition to the ISAba1-blaOXA-23 structure, were found within unrelated strains, but no common plasmid carrying these accessory genetic elements could be identified. It therefore appears that antibiotic resistance genes are readily exchanged between cocirculating strains in epidemics of phenotypically indistinguishable organisms. Epidemiological investigation of major outbreaks should include whole-genome typing as well as analysis of potentially transmissible resistance genes and their vehicles.}, }
@article {pmid17107661, year = {2007}, author = {Scholten, JC and Culley, DE and Brockman, FJ and Wu, G and Zhang, W}, title = {Evolution of the syntrophic interaction between Desulfovibrio vulgaris and Methanosarcina barkeri: Involvement of an ancient horizontal gene transfer.}, journal = {Biochemical and biophysical research communications}, volume = {352}, number = {1}, pages = {48-54}, doi = {10.1016/j.bbrc.2006.10.164}, pmid = {17107661}, issn = {0006-291X}, mesh = {Amino Acid Sequence/genetics ; *Biological Evolution ; Codon/genetics ; Desulfovibrio vulgaris/*genetics/metabolism ; Gene Expression ; Gene Transfer, Horizontal/*genetics ; Methanosarcina barkeri/*genetics/metabolism ; Sulfur/metabolism ; Time Factors ; }, abstract = {The sulfate reducing bacteria Desulfovibrio vulgaris and the methanogenic archaea Methanosarcina barkeri can grow syntrophically on lactate. In this study, a set of three closely located genes, DVU2103, DVU2104, and DVU2108 of D. vulgaris, was found to be up-regulated 2- to 4-fold following the lifestyle shift from syntroph to sulfate reducer; moreover, none of the genes in this gene set were differentially regulated when comparing gene expression from various D. vulgaris pure culture experiments. Although exact function of this gene set is unknown, the results suggest that it may play roles related to the lifestyle change of D. vulgaris from syntroph to sulfate reducer. This hypothesis is further supported by phylogenomic analyses showing that homologies of this gene set were only narrowly present in several groups of bacteria, most of which are restricted to a syntrophic lifestyle, such as Pelobacter carbinolicus, Syntrophobacter fumaroxidans, Syntrophomonas wolfei, and Syntrophus aciditrophicus. Phylogenetic analysis showed that all three individual genes in the gene set tended to be clustered with their homologies from archaeal genera, and they were rooted on archaeal species in the phylogenetic trees, suggesting that they were horizontally transferred from archaeal methanogens. In addition, no significant bias in codon and amino acid usages was detected between these genes and the rest of the D. vulgaris genome, suggesting the gene transfer may have occurred early in the evolutionary history so that sufficient time has elapsed to allow an adaptation to the codon and amino acid usages of D. vulgaris. This report provides novel insights into the origin and evolution of bacterial genes linked to the lifestyle change of D. vulgaris from a syntrophic to a sulfate-reducing lifestyle.}, }
@article {pmid17103058, year = {2006}, author = {Ludwig, M and Schulz-Friedrich, R and Appel, J}, title = {Occurrence of hydrogenases in cyanobacteria and anoxygenic photosynthetic bacteria: implications for the phylogenetic origin of cyanobacterial and algal hydrogenases.}, journal = {Journal of molecular evolution}, volume = {63}, number = {6}, pages = {758-768}, pmid = {17103058}, issn = {0022-2844}, mesh = {Bacterial Proteins/*genetics ; Cyanobacteria/*enzymology ; Eukaryota/*enzymology ; Hydrogen/metabolism ; Hydrogenase/*genetics ; *Photosynthesis ; Phylogeny ; }, abstract = {Hydrogenases are important enzymes in the energy metabolism of microorganisms. Therefore, they are widespread in prokaryotes. We analyzed the occurrence of hydrogenases in cyanobacteria and deduced a FeFe-hydrogenase in three different heliobacterial strains. This allowed the first phylogenetic analysis of the hydrogenases of all five major groups of photosynthetic bacteria (heliobacteria, green nonsulfur bacteria, green sulfur bacteria, photosynthetic proteobacteria, and cyanobacteria). In the case of both hydrogenases found in cyanobacteria (uptake and bidirectional), the green nonsulfur bacterium Chloroflexus aurantiacus was found to be the closest ancestor. Apart from a close relation between the archaebacterial and the green sulfur bacterial sulfhydrogenase, we could not find any evidence for horizontal gene transfer. Therefore, it would be most parsimonious if a Chloroflexus-like bacterium was the ancestor of Chloroflexus aurantiacus and cyanobacteria. After having transmitted both hydrogenase genes vertically to the different cyanobacterial species, either no, one, or both enzymes were lost, thus producing the current distribution. Our data and the available data from the literature on the occurrence of cyanobacterial hydrogenases show that the cyanobacterial uptake hydrogenase is strictly linked to the occurrence of the nitrogenase. Nevertheless, we did identify a nitrogen-fixing Synechococcus strain without an uptake hydrogenase. Since we could not find genes of a FeFe-hydrogenase in any of the tested cyanobacteria, although strains performing anoxygenic photosynthesis were also included in the analysis, a cyanobacterial origin of the contemporary FeFe-hydrogenase of algal plastids seems unlikely.}, }
@article {pmid17100985, year = {2007}, author = {Garbeva, P and Baggs, EM and Prosser, JI}, title = {Phylogeny of nitrite reductase (nirK) and nitric oxide reductase (norB) genes from Nitrosospira species isolated from soil.}, journal = {FEMS microbiology letters}, volume = {266}, number = {1}, pages = {83-89}, doi = {10.1111/j.1574-6968.2006.00517.x}, pmid = {17100985}, issn = {0378-1097}, mesh = {Gene Transfer, Horizontal ; Molecular Sequence Data ; Nitrite Reductases/*classification/genetics ; Nitrosomonadaceae/*enzymology/genetics/isolation &amp; purification ; Oxidoreductases/*classification/genetics ; Phylogeny ; RNA, Ribosomal, 16S/classification ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Ammonia-oxidizing bacteria are believed to be an important source of the climatically important trace gas nitrous oxide (N(2)O). The genes for nitrite reductase (nirK) and nitric oxide reductase (norB), putatively responsible for nitrous oxide production, have been identified in several ammonia-oxidizing bacteria, but not in Nitrosospira strains that may dominate ammonia-oxidizing communities in soil. In this study, sequences from nirK and norB genes were detected in several cultured Nitrosospira species and the diversity and phylogeny of these genes were compared with those in other ammoniaoxidizing bacteria and in classical denitrifiers. The nirK and norB gene sequences obtained from Nitrosospira spp. were diverse and appeared to be less conserved than 16S rRNA genes and functional ammonia monooxygenase (amoA) genes. The nirK and norB genes from some Nitrosospira spp. were not phylogenetically distinct from those of denitrifiers, and phylogenetic analysis suggests that the nirK and norB genes in ammonia-oxidizing bacteria have been subject to lateral transfer.}, }
@article {pmid17100984, year = {2007}, author = {Johnsen, AR and Kroer, N}, title = {Effects of stress and other environmental factors on horizontal plasmid transfer assessed by direct quantification of discrete transfer events.}, journal = {FEMS microbiology ecology}, volume = {59}, number = {3}, pages = {718-728}, doi = {10.1111/j.1574-6941.2006.00230.x}, pmid = {17100984}, issn = {0168-6496}, mesh = {2,4-Dichlorophenoxyacetic Acid/pharmacology ; Conjugation, Genetic ; Dose-Response Relationship, Drug ; Escherichia coli/*genetics ; *Gene Transfer Techniques ; Gene Transfer, Horizontal/drug effects ; Mercury/pharmacology ; Plasmids/*genetics ; Pseudomonas putida/*metabolism ; Sensitivity and Specificity ; }, abstract = {Selection pressure may affect the horizontal transfer of plasmids. The inability to distinguish between gene transfer and the growth of transconjugants complicates testing. We have developed a method that enables the quantification of discrete transfer events. It uses large numbers of replicate matings (192 or 384) in microtiter wells and the counting of transfer-positive and transfer-negative wells. We applied the method to study the transfer of the IncP1 plasmid pRO103 between Escherichia coli and Pseudomonas putida strains. pRO103 encodes resistance to mercury and tetracycline and partial degradation of 2,4-dichlorophenoxyacetic acid (2,4-D). The results showed positive correlation between transfer and donor metabolic activity, and an optimal temperature for transfer of 29 degrees C. On stimulation of donor activity, the optimal temperature was decreased to 24.5 degrees C. HgCl(2) above 1.0 microg L(-1) negatively affected transfer, whereas 2,4-D up to 0.3 mM had no effect. The negative effect of mercury was shown to be a result of stressing of the recipient. No effects of mercury on transfer could be detected by traditional filter mating. Thus, the method is superior to filter mating and, as the experimental design allows the manipulation of individual parameters, it is ideal for the assessment and comparison of effects of environmental factors on plasmid transfer.}, }
@article {pmid17095536, year = {2007}, author = {Gavotte, L and Henri, H and Stouthamer, R and Charif, D and Charlat, S and Boulétreau, M and Vavre, F}, title = {A Survey of the bacteriophage WO in the endosymbiotic bacteria Wolbachia.}, journal = {Molecular biology and evolution}, volume = {24}, number = {2}, pages = {427-435}, doi = {10.1093/molbev/msl171}, pmid = {17095536}, issn = {0737-4038}, mesh = {Animals ; Bacteriophage Typing ; Bacteriophages/classification/*genetics ; Capsid Proteins/genetics ; DNA, Viral ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Viral ; Insecta/microbiology ; Molecular Sequence Data ; Nematoda/microbiology ; Phylogeny ; Polymerase Chain Reaction ; Wolbachia/classification/genetics/*virology ; }, abstract = {Bacteriophages are common viruses infecting prokaryotes. In addition to their deadly effect, phages are also involved in several evolutionary processes of bacteria, such as coding functional proteins potentially beneficial to them, or favoring horizontal gene transfer through transduction. The particular lifestyle of obligatory intracellular bacteria usually protects them from phage infection. However, Wolbachia, an intracellular alpha-proteobacterium, infecting diverse arthropod and nematode species and best known for the reproductive alterations it induces, harbors a phage named WO, which has recently been proven to be lytic. Here, phage infection was checked in 31 Wolbachia strains, which induce 5 different effects in their hosts and infect 25 insect species and 3 nematodes. Only the Wolbachia infecting nematodes and Trichogramma were found devoid of phage infection. All the 25 detected phages were characterized by the DNA sequence of a minor capsid protein gene. Based on all data currently available, phylogenetic analyses show a lack of congruency between Wolbachia or insect and phage WO phylogenies, indicating numerous horizontal transfers of phage among the different Wolbachia strains. The absence of relation between phage phylogeny and the effects induced by Wolbachia suggests that WO is not directly involved in these effects. Implications on phage WO evolution are discussed.}, }
@article {pmid17086451, year = {2006}, author = {Watkins, RF and Gray, MW}, title = {The frequency of eubacterium-to-eukaryote lateral gene transfers shows significant cross-taxa variation within amoebozoa.}, journal = {Journal of molecular evolution}, volume = {63}, number = {6}, pages = {801-814}, pmid = {17086451}, issn = {0022-2844}, mesh = {Acanthamoeba castellanii/*genetics ; Animals ; Eubacterium/*genetics ; Expressed Sequence Tags ; *Gene Transfer, Horizontal ; *Genetic Variation ; Hartmannella/*genetics ; *Phylogeny ; }, abstract = {Single-celled bacterivorous eukaryotes offer excellent test cases for evaluation of the frequency of prey-to-predator lateral gene transfer (LGT). Here we use analysis of expressed sequence tag (EST) data sets to quantify the extent of LGT from eubacteria to two amoebae, Acanthamoeba castellanii and Hartmannella vermiformis. Stringent screening for LGT proceeded in several steps intended to enrich for authentic events while at the same time minimizing the incidence of false positives due to factors such as limitations in database coverage and ancient paralogy. The results were compared with data obtained when the same methodology was applied to EST libraries from a number of other eukaryotic taxa. Significant differences in the extent of apparent eubacterium-to-eukaryote LGT were found between taxa. Our results indicate that there may be substantial inter-taxon variation in the number of LGT events that become fixed even between amoebozoan species that have similar feeding modalities.}, }
@article {pmid17085557, year = {2007}, author = {Delorme, C and Poyart, C and Ehrlich, SD and Renault, P}, title = {Extent of horizontal gene transfer in evolution of Streptococci of the salivarius group.}, journal = {Journal of bacteriology}, volume = {189}, number = {4}, pages = {1330-1341}, pmid = {17085557}, issn = {0021-9193}, mesh = {Base Sequence ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genomics ; Molecular Sequence Data ; Streptococcus/*classification/*genetics ; }, abstract = {The phylogenetically closely related species Streptococcus salivarius and Streptococcus vestibularis are oral bacteria that are considered commensals, although they can also be found in human infections. The relationship between these two species and the relationship between strains isolated from carriers and strains responsible for invasive infections were investigated by multilocus sequence typing and additional sequence analysis. The clustering of several S. vestibularis alleles and the extent of genomic divergence at certain loci support the conclusion that S. salivarius and S. vestibularis are separate species. The level of sequence diversity in S. salivarius alleles is generally high, whereas that in S. vestibularis alleles is low at certain loci, indicating that the latter species might have evolved recently. Cluster analysis indicated that there has been genetic exchange between S. salivarius and S. vestibularis at three of the nine loci investigated. Horizontal gene transfer between streptococci belonging to the S. salivarius group and other oral streptococci was also detected at several loci. A high level of recombination in S. salivarius was revealed by allele index association and split decomposition sequence analyses. Commensal and infection-associated S. salivarius strains could not be distinguished by cluster analysis, suggesting that the pathogen isolates are opportunistic. Taken together, our results indicate that there is a high level of gene exchange that contributes to the evolution of two streptococcal species from the human oral cavity.}, }
@article {pmid17084894, year = {2007}, author = {Silby, MW and Ferguson, GC and Billington, C and Heinemann, JA}, title = {Localization of the plasmid-encoded proteins TraI and MobA in eukaryotic cells.}, journal = {Plasmid}, volume = {57}, number = {2}, pages = {118-130}, doi = {10.1016/j.plasmid.2006.08.006}, pmid = {17084894}, issn = {0147-619X}, mesh = {Bacterial Proteins/genetics/*metabolism ; Cell Line ; *Conjugation, Genetic ; DNA Helicases/genetics/*metabolism ; DNA, Bacterial/genetics/metabolism ; DNA-Binding Proteins/genetics/*metabolism ; Escherichia coli Proteins/genetics/*metabolism ; Eukaryotic Cells/*metabolism ; Gene Transfer, Horizontal ; Green Fluorescent Proteins/metabolism ; Humans ; Intestines/cytology ; Plasmids/classification/*genetics ; Protein Transport ; Recombinant Fusion Proteins/metabolism ; Saccharomyces cerevisiae/cytology/genetics ; Trans-Activators/genetics/*metabolism ; Transfection ; }, abstract = {Conjugation mediates gene transfer not only between bacterial species but also from bacteria to yeast, plant, and animal cells. DNA transferred by conjugative plasmids from bacteria to eukaryotes must traverse subcellular membranes in the recipient before the transferred genes can be expressed and inherited. This process is most likely facilitated by putative DNA pilot proteins such as VirD2 of the Agrobacterium tumefaciens Ti plasmid. Here, we test this model as a general feature of trans-kingdom conjugation using the DNA-relaxases TraI and MobA of the IncP and IncQ groups. TraI localized unambiguously and uniformly to the nuclei of both yeast and human cells, whereas MobA displayed a range of subcellular localization patterns. The tendency to localize to the nucleus was not correlated with predicted nuclear localization sequence motifs in either protein, suggesting a lack of stringent requirements for nuclear localizing potential in pilot proteins mediating conjugative DNA transfer to eukaryotes. Further, our results indicate that nuclear localization ability may be more commonly associated with conjugative pilot proteins than previously recognized.}, }
@article {pmid17083272, year = {2006}, author = {Alm, E and Huang, K and Arkin, A}, title = {The evolution of two-component systems in bacteria reveals different strategies for niche adaptation.}, journal = {PLoS computational biology}, volume = {2}, number = {11}, pages = {e143}, pmid = {17083272}, issn = {1553-7358}, mesh = {*Adaptation, Physiological ; Bacteria/genetics/*metabolism ; Computational Biology ; *Evolution, Molecular ; Genome, Bacterial ; Genomics ; Histidine Kinase ; Operon/genetics ; Protein Kinases/*genetics/*metabolism ; *Signal Transduction ; }, abstract = {Two-component systems including histidine protein kinases represent the primary signal transduction paradigm in prokaryotic organisms. To understand how these systems adapt to allow organisms to detect niche-specific signals, we analyzed the phylogenetic distribution of nearly 5,000 histidine protein kinases from 207 sequenced prokaryotic genomes. We found that many genomes carry a large repertoire of recently evolved signaling genes, which may reflect selective pressure to adapt to new environmental conditions. Both lineage-specific gene family expansion and horizontal gene transfer play major roles in the introduction of new histidine kinases into genomes; however, there are differences in how these two evolutionary forces act. Genes imported via horizontal transfer are more likely to retain their original functionality as inferred from a similar complement of signaling domains, while gene family expansion accompanied by domain shuffling appears to be a major source of novel genetic diversity. Family expansion is the dominant source of new histidine kinase genes in the genomes most enriched in signaling proteins, and detailed analysis reveals that divergence in domain structure and changes in expression patterns are hallmarks of recent expansions. Finally, while these two modes of gene acquisition are widespread across bacterial taxa, there are clear species-specific preferences for which mode is used.}, }
@article {pmid17081279, year = {2006}, author = {Dagan, T and Martin, W}, title = {The tree of one percent.}, journal = {Genome biology}, volume = {7}, number = {10}, pages = {118}, pmid = {17081279}, issn = {1474-760X}, mesh = {Animals ; Archaea/genetics ; Bacteria/genetics ; *Decision Trees ; *Evolution, Molecular ; Genes, Bacterial ; Genes, Fungal ; Genes, Protozoan ; *Models, Genetic ; Symbiosis ; }, abstract = {Two significant evolutionary processes are fundamentally not tree-like in nature--lateral gene transfer among prokaryotes and endosymbiotic gene transfer (from organelles) among eukaryotes. To incorporate such processes into the bigger picture of early evolution, biologists need to depart from the preconceived notion that all genomes are related by a single bifurcating tree.}, }
@article {pmid17079132, year = {2006}, author = {Gomis-Rüth, FX and Coll, M}, title = {Cut and move: protein machinery for DNA processing in bacterial conjugation.}, journal = {Current opinion in structural biology}, volume = {16}, number = {6}, pages = {744-752}, doi = {10.1016/j.sbi.2006.10.004}, pmid = {17079132}, issn = {0959-440X}, mesh = {Bacteria/*genetics/*metabolism ; Bacterial Proteins/chemistry/metabolism ; *Conjugation, Genetic ; DNA Nucleotidyltransferases/chemistry/metabolism ; DNA, Bacterial/*chemistry/genetics/*metabolism ; Escherichia coli/genetics/metabolism ; Escherichia coli Proteins/chemistry/metabolism ; Macromolecular Substances ; Models, Biological ; Models, Molecular ; Nucleic Acid Conformation ; Protein Conformation ; Transcription, Genetic ; }, abstract = {Conjugation is a paradigmatic example of horizontal or lateral gene transfer, whereby DNA is translocated between bacterial cells. It provides a route for the rapid acquisition of new genetic information. Increased antibiotic resistance among pathogens is a troubling consequence of this microbial capacity. DNA transfer across cell membranes requires a sophisticated molecular machinery that involves the participation of several proteins in DNA processing and replication, cell recruitment, and the transport of DNA and proteins from donor to recipient cells. Although bacterial conjugation was first reported in the 1940s, only now are we beginning to unravel the molecular mechanisms behind this process. In particular, structural biology is revealing the detailed molecular architecture of several of the pieces involved.}, }
@article {pmid17074903, year = {2006}, author = {Osorio, CR and Juiz-Río, S and Lemos, ML}, title = {A siderophore biosynthesis gene cluster from the fish pathogen Photobacterium damselae subsp. piscicida is structurally and functionally related to the Yersinia high-pathogenicity island.}, journal = {Microbiology (Reading, England)}, volume = {152}, number = {Pt 11}, pages = {3327-3341}, doi = {10.1099/mic.0.29190-0}, pmid = {17074903}, issn = {1350-0872}, mesh = {Animals ; Benzethonium/analogs &amp; derivatives/metabolism ; Biological Evolution ; Fish Diseases/microbiology ; Fishes/microbiology ; Gene Transfer, Horizontal ; Genes, Bacterial/*physiology ; Genomic Islands/genetics ; Gram-Negative Bacterial Infections/genetics/metabolism/pathology/*veterinary ; Molecular Sequence Data ; *Multigene Family ; Peptide Synthases/genetics ; Photobacterium/*genetics/metabolism/pathogenicity ; Point Mutation ; Siderophores/*genetics/metabolism ; Virulence ; Virulence Factors/*genetics/metabolism ; Yersinia/genetics/metabolism ; }, abstract = {Photobacterium damselae subsp. piscicida, the causative agent of fish pasteurellosis, produces a siderophore which is distinct from that produced by P. damselae subsp. damselae. Using suppression subtractive hybridization, a subsp. piscicida-specific DNA region of 35 kb was identified in strain DI21, and 11 genes were defined: dahP, araC1, araC2, frpA, irp8, irp2, irp1, irp3, irp4, irp9 and irp5. The sequence of the predicted proteins encoded by these genes showed significant similarity with the proteins responsible for the synthesis and transport of the siderophore yersiniabactin, encoded within the Yersinia high-pathogenicity island (HPI). Southern hybridization demonstrated that this gene cluster is exclusive to some European subsp. piscicida isolates. Database searches revealed that a similar gene cluster is present in Photobacterium profundum SS9 and Vibrio cholerae RC385. An irp1 gene (encoding a putative non-ribosomal peptide synthetase) insertional mutant (CS31) was impaired for growth under iron-limiting conditions and unable to produce siderophores, and showed an approximately 100-fold decrease in degree of virulence for fish. The subsp. piscicida DI21 strain, but not CS31, promoted the growth of a Yersinia enterocolitica irp1 mutant. Furthermore, a yersiniabactin-producing Y. enterocolitica strain as well as purified yersiniabactin were able to cross-feed strains DI21 and CS31, suggesting that the subsp. piscicida siderophore might be functionally and structurally related to yersiniabactin. The differential occurrence among P. damselae strains, and the low sequence similarity to siderophore synthesis genes described in other members of the Vibrionaceae, suggest that this genetic system might have been acquired by horizontal transfer in P. damselae subsp. piscicida, and might have a common evolutionary origin with the Yersinia HPI.}, }
@article {pmid17073777, year = {2006}, author = {Yadav, JS and Doddapaneni, H and Subramanian, V}, title = {P450ome of the white rot fungus Phanerochaete chrysosporium: structure, evolution and regulation of expression of genomic P450 clusters.}, journal = {Biochemical Society transactions}, volume = {34}, number = {Pt 6}, pages = {1165-1169}, doi = {10.1042/BST0341165}, pmid = {17073777}, issn = {0300-5127}, mesh = {Cytochrome P-450 Enzyme System/classification/*genetics ; *Evolution, Molecular ; Fungal Proteins/chemistry/genetics ; Gene Duplication ; *Gene Expression Regulation, Fungal ; Gene Transfer, Horizontal ; Genetic Variation ; Genome, Fungal ; Phanerochaete/enzymology/*genetics ; Translocation, Genetic ; }, abstract = {The model white rot fungus Phanerochaete chrysosporium has the extraordinary ability to degrade (to CO(2)) lignin and detoxify a variety of chemical pollutants. Whole genome sequencing of this fungus has revealed the presence of the largest P450ome in fungi comprising approx. 150 P450 genes, most of which have unknown function. On the basis of our genome-wide structural and evolutionary analysis, these P450 genes could be classified into 12 families and 23 subfamilies and under 11 fungal P450 clans. The analysis further revealed an extensive gene clustering with a total of 16 P450 clusters constituted of up to 11 members per cluster. In particular, evidence and role of gene duplications and horizontal gene transfer in the evolution of these P450 clusters have been discussed using two of the P450 families [CYP63 and CYP505 (where CYP is cytochrome P450)] as examples. In addition, the observed differential transcriptional induction of the clustered members of the CYP63 gene family, in response to different xenobiotic chemicals and carbon sources, indicated functional divergence within the P450 clusters, of this basidiomycete fungus.}, }
@article {pmid17071828, year = {2006}, author = {Liapounova, NA and Hampl, V and Gordon, PM and Sensen, CW and Gedamu, L and Dacks, JB}, title = {Reconstructing the mosaic glycolytic pathway of the anaerobic eukaryote Monocercomonoides.}, journal = {Eukaryotic cell}, volume = {5}, number = {12}, pages = {2138-2146}, pmid = {17071828}, issn = {1535-9778}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Anaerobiosis ; Animals ; Eukaryota/classification/genetics/*metabolism ; Eukaryotic Cells ; Evolution, Molecular ; *Glycolysis/genetics/physiology ; Hexokinase/genetics/metabolism ; Molecular Sequence Data ; Phosphofructokinases/genetics/metabolism ; Phosphoglycerate Mutase/genetics/metabolism ; Phosphopyruvate Hydratase/genetics/metabolism ; Phylogeny ; }, abstract = {All eukaryotes carry out glycolysis, interestingly, not all using the same enzymes. Anaerobic eukaryotes face the challenge of fewer molecules of ATP extracted per molecule of glucose due to their lack of a complete tricarboxylic acid cycle. This may have pressured anaerobic eukaryotes to acquire the more ATP-efficient alternative glycolytic enzymes, such as pyrophosphate-fructose 6-phosphate phosphotransferase and pyruvate orthophosphate dikinase, through lateral gene transfers from bacteria and other eukaryotes. Most studies of these enzymes in eukaryotes involve pathogenic anaerobes; Monocercomonoides, an oxymonad belonging to the eukaryotic supergroup Excavata, is a nonpathogenic anaerobe representing an evolutionarily and ecologically distinct sampling of an anaerobic glycolytic pathway. We sequenced cDNA encoding glycolytic enzymes from a previously established cDNA library of Monocercomonoides and analyzed the relationships of these enzymes to those from other organisms spanning the major groups of Eukaryota, Bacteria, and Archaea. We established that, firstly, Monocercomonoides possesses alternative versions of glycolytic enzymes: fructose-6-phosphate phosphotransferase, both pyruvate kinase and pyruvate orthophosphate dikinase, cofactor-independent phosphoglycerate mutase, and fructose-bisphosphate aldolase (class II, type B). Secondly, we found evidence for the monophyly of oxymonads, kinetoplastids, diplomonads, and parabasalids, the major representatives of the Excavata. We also found several prokaryote-to-eukaryote as well as eukaryote-to-eukaryote lateral gene transfers involving glycolytic enzymes from anaerobic eukaryotes, further suggesting that lateral gene transfer was an important factor in the evolution of this pathway for denizens of this environment.}, }
@article {pmid17071793, year = {2007}, author = {Buckwold, SL and Shoemaker, NB and Sears, CL and Franco, AA}, title = {Identification and characterization of conjugative transposons CTn86 and CTn9343 in Bacteroides fragilis strains.}, journal = {Applied and environmental microbiology}, volume = {73}, number = {1}, pages = {53-63}, pmid = {17071793}, issn = {0099-2240}, support = {R01 AI022383/AI/NIAID NIH HHS/United States ; R56 AI022383/AI/NIAID NIH HHS/United States ; AI/GM 22383/AI/NIAID NIH HHS/United States ; R01 AI 48708/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacterial Proteins/genetics ; Bacterial Toxins/genetics ; Bacteroides fragilis/*classification/*genetics/pathogenicity ; *Conjugation, Genetic ; *DNA Transposable Elements ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; Genomic Islands/genetics ; Humans ; Metalloendopeptidases/genetics ; Nucleic Acid Hybridization/methods ; Polymerase Chain Reaction ; Transposases/genetics ; }, abstract = {The related genetic elements flanking the Bacteroides fragilis pathogenicity island (PAI) in enterotoxigenic B. fragilis (ETBF) 86-5443-2-2 and also present in pattern III nontoxigenic B. fragilis (NTBF) NCTC 9343 were defined as putative conjugative transposons (CTns), designated CTn86 and CTn9343, respectively (A. A. Franco, J. Bacteriol. 181:6623-6633, 2004). CTn86 and CTn9343 have the same basic structures except that their encoded transposases have low similarity and CTn9343 lacks the B. fragilis PAI and contains an extra 7-kb region not present in CTn86. In this study, using DNA hybridization and PCR analysis, we characterized the genetic element flanking the PAI in a collection of ETBF strains and the related genetic elements in a collection of NTBF pattern III strains. We found that in all 123 ETBF strains, the PAI is contained in a genetic element similar to CTn86. Of 73 pattern III strains, 26 (36%) present a genetic element similar to CTn9343, 38 (52%) present a genetic element similar to CTn9343 but lack the 7-kb region that is also absent in CTn86 (CTn9343-like element), and 9 (12%) present a genetic element similar to CTn86 but lacking the PAI (CTn86-like element). In addition to containing CTn86, ETBF strains can also contain CTn9343, CTn9343-like, or CTn86-like elements. CTn86, CTn9343, CTn86-like, and CTn9343-like elements were found exclusively in B. fragilis strains and predominantly in division I, cepA-positive strains.}, }
@article {pmid17069619, year = {2007}, author = {Mølbak, L and Molin, S and Kroer, N}, title = {Root growth and exudate production define the frequency of horizontal plasmid transfer in the Rhizosphere.}, journal = {FEMS microbiology ecology}, volume = {59}, number = {1}, pages = {167-176}, doi = {10.1111/j.1574-6941.2006.00229.x}, pmid = {17069619}, issn = {0168-6496}, mesh = {Gene Transfer, Horizontal/*genetics ; Hordeum/growth &amp; development/*metabolism/*microbiology ; Pisum sativum/growth &amp; development/*metabolism/*microbiology ; Plant Exudates/*biosynthesis ; Plant Roots/growth &amp; development/metabolism/microbiology ; Plasmids/genetics ; }, abstract = {To identify the main drivers of plasmid transfer in the rhizosphere, conjugal transfer was studied in the rhizospheres of pea and barley. The donor Pseudomonas putida KT2442, containing plasmid pKJK5::gfp, was coated onto the seeds, while the recipient P. putida LM24, having a chromosomal insertion of dsRed, was inoculated into the growth medium. Mean transconjugant-to-donor ratios in vermiculite were 4.0+/-0.8 x 10(-2) in the pea and 5.9+/-1.4 x 10(-3) in the barley rhizospheres. In soil, transfer ratios were about 10 times lower. As a result of a 2-times higher root exudation rate in pea, donor densities in pea (1 x 10(6)-2 x 10(9) CFU g(-1) root) were about 10 times higher than in barley. No difference in recipient densities was observed. In situ visualization of single cells on the rhizoplane and macroscopic visualization of the colonization pattern showed that donors and transconjugants were ubiquitously distributed in the pea rhizosphere, while they were only located on the upper parts of the barley roots. Because the barley root elongated about 10 times faster than the pea root, donors were probably outgrown by the elongating barley root. Thus by affecting the cell density and distribution, exudation and root growth appear to be key parameters controlling plasmid transfer in the rhizosphere.}, }
@article {pmid17068107, year = {2007}, author = {Jin, G and Nakhleh, L and Snir, S and Tuller, T}, title = {Inferring phylogenetic networks by the maximum parsimony criterion: a case study.}, journal = {Molecular biology and evolution}, volume = {24}, number = {1}, pages = {324-337}, doi = {10.1093/molbev/msl163}, pmid = {17068107}, issn = {0737-4038}, mesh = {Algorithms ; Bacteria/classification/*genetics ; Classification/*methods ; Computational Biology ; Evolution, Molecular ; Gene Transfer, Horizontal ; Models, Genetic ; *Phylogeny ; Plants/classification/*genetics ; Plastids/genetics ; }, abstract = {Horizontal gene transfer (HGT) may result in genes whose evolutionary histories disagree with each other, as well as with the species tree. In this case, reconciling the species and gene trees results in a network of relationships, known as the "phylogenetic network" of the set of species. A phylogenetic network that incorporates HGT consists of an underlying species tree that captures vertical inheritance and a set of edges which model the "horizontal" transfer of genetic material. In a series of papers, Nakhleh and colleagues have recently formulated a maximum parsimony (MP) criterion for phylogenetic networks, provided an array of computationally efficient algorithms and heuristics for computing it, and demonstrated its plausibility on simulated data. In this article, we study the performance and robustness of this criterion on biological data. Our findings indicate that MP is very promising when its application is extended to the domain of phylogenetic network reconstruction and HGT detection. In all cases we investigated, the MP criterion detected the correct number of HGT events required to map the evolutionary history of a gene data set onto the species phylogeny. Furthermore, our results indicate that the criterion is robust with respect to both incomplete taxon sampling and the use of different site substitution matrices. Finally, our results show that the MP criterion is very promising in detecting HGT in chimeric genes, whose evolutionary histories are a mix of vertical and horizontal evolution. Besides the performance analysis of MP, our findings offer new insights into the evolution of 4 biological data sets and new possible explanations of HGT scenarios in their evolutionary history.}, }
@article {pmid17067382, year = {2006}, author = {Hamady, M and Betterton, MD and Knight, R}, title = {Using the nucleotide substitution rate matrix to detect horizontal gene transfer.}, journal = {BMC bioinformatics}, volume = {7}, number = {}, pages = {476}, pmid = {17067382}, issn = {1471-2105}, support = {T32 GM065103/GM/NIGMS NIH HHS/United States ; }, mesh = {Computational Biology/*methods ; Computer Simulation ; *Gene Transfer, Horizontal ; *Genome, Human ; Humans ; Markov Chains ; Models, Genetic ; Models, Theoretical ; Nucleotides/*chemistry ; Phylogeny ; Reproducibility of Results ; Software ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT) has allowed bacteria to evolve many new capabilities. Because transferred genes perform many medically important functions, such as conferring antibiotic resistance, improved detection of horizontally transferred genes from sequence data would be an important advance. Existing sequence-based methods for detecting HGT focus on changes in nucleotide composition or on differences between gene and genome phylogenies; these methods have high error rates.<br><br>RESULTS: First, we introduce a new class of methods for detecting HGT based on the changes in nucleotide substitution rates that occur when a gene is transferred to a new organism. Our new methods discriminate simulated HGT events with an error rate up to 10 times lower than does GC content. Use of models that are not time-reversible is crucial for detecting HGT. Second, we show that using combinations of multiple predictors of HGT offers substantial improvements over using any single predictor, yielding as much as a factor of 18 improvement in performance (a maximum reduction in error rate from 38% to about 3%). Multiple predictors were combined by using the random forests machine learning algorithm to identify optimal classifiers that separate HGT from non-HGT trees.<br><br>CONCLUSION: The new class of HGT-detection methods introduced here combines advantages of phylogenetic and compositional HGT-detection techniques. These new techniques offer order-of-magnitude improvements over compositional methods because they are better able to discriminate HGT from non-HGT trees under a wide range of simulated conditions. We also found that combining multiple measures of HGT is essential for detecting a wide range of HGT events. These novel indicators of horizontal transfer will be widely useful in detecting HGT events linked to the evolution of important bacterial traits, such as antibiotic resistance and pathogenicity.}, }
@article {pmid17064805, year = {2007}, author = {Weiss, J and Ros-Chumillas, M and Peña, L and Egea-Cortines, M}, title = {Effect of storage and processing on plasmid, yeast and plant genomic DNA stability in juice from genetically modified oranges.}, journal = {Journal of biotechnology}, volume = {128}, number = {1}, pages = {194-203}, doi = {10.1016/j.jbiotec.2006.09.009}, pmid = {17064805}, issn = {0168-1656}, mesh = {Beverages/*analysis ; Citrus sinensis/*genetics ; DNA, Plant/*analysis ; DNA, Recombinant/*analysis ; Food Microbiology ; *Food Preservation ; *Food, Genetically Modified ; Food-Processing Industry/methods ; *Gene Transfer, Horizontal ; Genomic Instability ; Hydrogen-Ion Concentration ; Plants, Genetically Modified/genetics ; Plasmids/analysis/genetics ; }, abstract = {Recombinant DNA technology is an important tool in the development of plant varieties with new favourable features. There is strong opposition towards this technology due to the potential risk of horizontal gene transfer between genetically modified plant material and food-associated bacteria, especially if genes for antibiotic resistance are involved. Since horizontal transfer efficiency depends on size and length of homologous sequences, we investigated the effect of conditions required for orange juice processing on the stability of DNA from three different origins: plasmid DNA, yeast genomic DNA and endogenous genomic DNA from transgenic sweet orange (C. sinensis L. Osb.). Acidic orange juice matrix had a strong degrading effect on plasmid DNA which becomes apparent in a conformation change from supercoiled structure to nicked, linear structure within 5h of storage at 4 degrees C. Genomic yeast DNA was degraded during exposure to acidic orange juice matrix within 4 days, and also the genomic DNA of C. sinensis suffered degradation within 2 days of storage as indicated by amplification results from transgene markers. Standard pasteurization procedures affected DNA integrity depending on the method and time used. Our data show that the current standard industrial procedures to pasteurize orange juice as well as its acidic nature causes a strong degradation of both yeast and endogenous genomic DNA below sizes reported to be suitable for horizontal gene transfer.}, }
@article {pmid17064286, year = {2006}, author = {Marri, PR and Bannantine, JP and Golding, GB}, title = {Comparative genomics of metabolic pathways in Mycobacterium species: gene duplication, gene decay and lateral gene transfer.}, journal = {FEMS microbiology reviews}, volume = {30}, number = {6}, pages = {906-925}, doi = {10.1111/j.1574-6976.2006.00041.x}, pmid = {17064286}, issn = {0168-6445}, mesh = {Amino Acids/biosynthesis ; Animals ; Antigens, Bacterial/genetics ; Bacterial Proteins/genetics/metabolism ; Cell Wall/chemistry ; Energy Metabolism ; Genome, Bacterial ; Humans ; Lipid Metabolism ; Membrane Proteins/genetics ; Mycobacterium/*genetics/metabolism/pathogenicity ; Mycobacterium Infections/microbiology ; Species Specificity ; Virulence ; }, abstract = {The genus Mycobacterium comprises significant pathogenic species that infect both humans and animals. One species within this genus, Mycobacterium tuberculosis, is the primary killer of humans resulting from bacterial infections. Five mycobacterial genomes belonging to four different species (M. tuberculosis, Mycobacterium bovis, Mycobacterium leprae and Mycobacterium avium ssp. paratuberculosis) have been sequenced to date and another 14 mycobacterial genomes are at various stages of completion. A comparative analysis of the gene products of key metabolic pathways revealed that the major differences among these species are in the gene products constituting the cell wall and the gene families encoding the acidic glycine-rich (PE/PPE/PGRS) proteins. Mycobacterium leprae has evolved by retaining a minimal gene set for most of the gene families, whereas M. avium ssp. paratuberculosis has acquired some of the virulence factors by lateral gene transfer.}, }
@article {pmid17061545, year = {2005}, author = {Lloret, L and Martínez-Romero, E}, title = {[Evolution and phylogeny of rhizobia].}, journal = {Revista latinoamericana de microbiologia}, volume = {47}, number = {1-2}, pages = {43-60}, pmid = {17061545}, issn = {0187-4640}, mesh = {Biodiversity ; *Biological Evolution ; Bradyrhizobium/genetics/physiology ; Burkholderia/genetics/physiology ; Cupriavidus/genetics/physiology ; Genes, Bacterial ; Genomic Islands/genetics ; Gram-Negative Aerobic Rods and Cocci/classification/genetics/*physiology ; Magnoliopsida/microbiology ; Nitrogen Fixation/genetics ; Phylogeny ; Plasmids/genetics/physiology ; Rhizobiaceae/genetics/physiology ; Root Nodules, Plant/*microbiology/physiology ; Species Specificity ; Symbiosis/genetics ; }, abstract = {Nitrogen fixation an ancient process that may is have originated in the archaean Eon under the primitive atmosphere anoxygenic conditions. Diazotrophy is an exclusive process of prokaryotes, only Euryarchaeota and 6 of 54 Bacteria phyla have diazotrophs lineages. Some of them coevolved with flowering plants for the establishment of molecular bases of a mutualistic symbiosis relationship. In rhizobia, the nitrogen fixation occurs inside the nodules, special structures on the roots or stems of legumes. Nodule organogenesis starts with the bacterial nodulation factors (Nod factors) codified in large plasmids or symbiotic islands in the bacterial genomes. Nodulation genes had more recent origin than the nitrogen fixation ones because the origin of the nod gene is associated with the origin of the hosts. The 16S rRNA phylogeny groups rhizobia in 7 genuses of the alpha-Proteobacteria: Bradyrhizobium, Mesorhizobium, Rhizobium, Sinorhizobium, Methylobacterium and Devosia, and two genuses recently described in f-Proteobacteria: Burkholderia and Wautersia. The phylogenies obtained with other chromosomal genes are similar at the genus level, but it is incongruent with the symbiotic gene (nif &amp; nod) phylogeny, because horizontal gene transfer has allowed their evolution in function to the legume host fitness.}, }
@article {pmid17059607, year = {2006}, author = {Kondrashov, FA and Koonin, EV and Morgunov, IG and Finogenova, TV and Kondrashova, MN}, title = {Evolution of glyoxylate cycle enzymes in Metazoa: evidence of multiple horizontal transfer events and pseudogene formation.}, journal = {Biology direct}, volume = {1}, number = {}, pages = {31}, pmid = {17059607}, issn = {1745-6150}, abstract = {BACKGROUND: The glyoxylate cycle is thought to be present in bacteria, protists, plants, fungi, and nematodes, but not in other Metazoa. However, activity of the glyoxylate cycle enzymes, malate synthase (MS) and isocitrate lyase (ICL), in animal tissues has been reported. In order to clarify the status of the MS and ICL genes in animals and get an insight into their evolution, we undertook a comparative-genomic study.<br><br>RESULTS: Using sequence similarity searches, we identified MS genes in arthropods, echinoderms, and vertebrates, including platypus and opossum, but not in the numerous sequenced genomes of placental mammals. The regions of the placental mammals' genomes expected to code for malate synthase, as determined by comparison of the gene orders in vertebrate genomes, show clear similarity to the opossum MS sequence but contain stop codons, indicating that the MS gene became a pseudogene in placental mammals. By contrast, the ICL gene is undetectable in animals other than the nematodes that possess a bifunctional, fused ICL-MS gene. Examination of phylogenetic trees of MS and ICL suggests multiple horizontal gene transfer events that probably went in both directions between several bacterial and eukaryotic lineages. The strongest evidence was obtained for the acquisition of the bifunctional ICL-MS gene from an as yet unknown bacterial source with the corresponding operonic organization by the common ancestor of the nematodes.<br><br>CONCLUSION: The distribution of the MS and ICL genes in animals suggests that either they encode alternative enzymes of the glyoxylate cycle that are not orthologous to the known MS and ICL or the animal MS acquired a new function that remains to be characterized. Regardless of the ultimate solution to this conundrum, the genes for the glyoxylate cycle enzymes present a remarkable variety of evolutionary events including unusual horizontal gene transfer from bacteria to animals.}, }
@article {pmid17059480, year = {2007}, author = {Heuer, H and Fox, RE and Top, EM}, title = {Frequent conjugative transfer accelerates adaptation of a broad-host-range plasmid to an unfavorable Pseudomonas putida host.}, journal = {FEMS microbiology ecology}, volume = {59}, number = {3}, pages = {738-748}, doi = {10.1111/j.1574-6941.2006.00223.x}, pmid = {17059480}, issn = {0168-6496}, support = {P20 RR016448/RR/NCRR NIH HHS/United States ; P20 RR16448/RR/NCRR NIH HHS/United States ; }, mesh = {Fresh Water ; *Gene Transfer, Horizontal ; Geologic Sediments/microbiology ; Idaho ; Plasmids/*genetics ; Pseudomonas putida/*genetics ; Species Specificity ; }, abstract = {IncP-1 plasmids are known to be promiscuous, but it is not understood if they are equally well adapted to various species within their host range. Moreover, little is known about their fate in bacterial communities. We determined if the IncP-1beta plasmid pB10 was unstable in some Proteobacteria, and whether plasmid stability was enhanced after long-term carriage in a single host and when regularly switched between isogenic hosts. Plasmid pB10 was found to be very unstable in Pseudomonas putida H2, and conferred a high cost (c. 20% decrease in fitness relative to the plasmid-free host). H2(pB10) was then evolved under conditions that selected for plasmid maintenance, with or without regular plasmid transfer (host-switching). When tested in the ancestral host, the evolved plasmids were more stable and their cost was significantly reduced (9% and 16% for plasmids from host-switched and nonswitched lineages, respectively). Our findings suggest that IncP-1 plasmids can rapidly adapt to an unfavorable host by improving their overall stability, and that regular conjugative transfer accelerates this process.}, }
@article {pmid17058491, year = {2006}, author = {Monceyron Jonassen, C}, title = {SARS/avian coronaviruses.}, journal = {Developments in biologicals}, volume = {126}, number = {}, pages = {161-9; discussion 326-7}, pmid = {17058491}, issn = {1424-6074}, mesh = {Animals ; Animals, Wild/virology ; Base Sequence ; Bird Diseases/*virology ; Birds/*virology ; Chlorocebus aethiops ; Coronavirus/*genetics/*isolation &amp; purification ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Recombination, Genetic ; Severe Acute Respiratory Syndrome/*veterinary/*virology ; Vero Cells ; }, abstract = {In the hunt for the aetiology of the SARS outbreak in 2003, a newly developed virus DNA micro-array was successfully used to hybridise PCR products obtained by random amplification of nucleic acids extracted from a cell culture infected with material from a SARS patient. The SARS agent was found to hybridise with micro-array probes from both coronaviruses and astroviruses, but one of the coronavirus probes and the four astrovirus probes contained redundant sequences, spanning a highly conserved motif, named s2m, found at the 3' end of the genomes of almost all astroviruses, one picornavirus, and the poultry coronaviruses. The three other coronavirus probes, that hybridised with the SARS agent, were located in the replicase gene, and it could be concluded that the SARS agent was a novel coronavirus, harbouring s2m. The presence of this motif in different virus families is probably the result of recombinations between unrelated viruses, but its presence in both poultry and SARS coronaviruses could suggest a bird involvement in the history of the SARS coronavirus. A recent screening of wild birds for the presence of coronaviruses, using a pan-coronavirus RT-PCR, led to the identification of novel coronaviruses in the three species studied. Phylogenetic analyses performed on both replicase gene and nucleocapsid protein could not add support to a close relationship between avian and SARS coronaviruses, but all the novel avian coronaviruses were found to harbour s2m. The motif is inserted at a homologous place in avian and SARS coronavirus genomes, but in a somewhat different context for the SARS coronavirus. If the presence of s2m in these viruses is a result of two separate recombination events, this suggests that its particular position in these genomes is the only one that would not be deleterious for coronaviral replication, or that it is the result of a copy-choice recombination between coronaviruses, following an ancestral introduction in the coronavirus family by an unrelated virus. In conclusion, the relative high frequencies of recombination observed both experimentally and in the natural evolution of RNA viruses, indicate that horizontal gene transfer does occur, even between unrelated viruses. This might represent a challenge in the rapid identification of novel pathogens with DNA micro-array techniques.}, }
@article {pmid17056681, year = {2006}, author = {Marcobal, A and de las Rivas, B and Moreno-Arribas, MV and Muñoz, R}, title = {Evidence for horizontal gene transfer as origin of putrescine production in Oenococcus oeni RM83.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {12}, pages = {7954-7958}, pmid = {17056681}, issn = {0099-2240}, mesh = {Chromosomes, Bacterial/*genetics ; DNA, Bacterial/*genetics ; *Gene Transfer, Horizontal ; Gram-Positive Cocci/*enzymology/*genetics ; Molecular Sequence Data ; Open Reading Frames ; Ornithine Decarboxylase/*genetics ; Putrescine/*biosynthesis ; Recombination, Genetic ; Sequence Analysis, DNA ; Transposases/genetics ; Viral Proteins/genetics ; }, abstract = {The nucleotide sequence of a 17.2-kb chromosomal DNA fragment containing the odc gene encoding ornithine decarboxylase has been determined in the putrescine producer Oenococcus oeni RM83. This DNA fragment contains 13 open reading frames, including genes coding for five transposases and two phage proteins. This description might represent the first evidence of a horizontal gene transfer event as the origin of a biogenic amine biosynthetic locus.}, }
@article {pmid17055108, year = {2006}, author = {Sanders, IR}, title = {Rapid disease emergence through horizontal gene transfer between eukaryotes.}, journal = {Trends in ecology &amp; evolution}, volume = {21}, number = {12}, pages = {656-658}, doi = {10.1016/j.tree.2006.10.006}, pmid = {17055108}, issn = {0169-5347}, mesh = {*Eukaryotic Cells ; Fungi/genetics/*pathogenicity ; *Gene Transfer, Horizontal ; Mycoses/*microbiology ; Plant Diseases/*microbiology ; Virulence ; }, abstract = {Among different species of eukaryotes, the extent and evolutionary significance of horizontal gene transfer remains poorly understood. A newly published study by Friesen and colleagues indicates that a recent gene transfer between two species of fungi has enabled the recipient to rapidly acquire high virulence on wheat. The study highlights a mechanism by which diseases can suddenly emerge, but also brings up the controversial issues of how horizontal gene transfer occurs and whether fungal incompatibility barriers to gene flow are more 'leaky' than was previously thought.}, }
@article {pmid17049238, year = {2006}, author = {Gupta, RS and Griffiths, E}, title = {Chlamydiae-specific proteins and indels: novel tools for studies.}, journal = {Trends in microbiology}, volume = {14}, number = {12}, pages = {527-535}, doi = {10.1016/j.tim.2006.10.002}, pmid = {17049238}, issn = {0966-842X}, mesh = {Bacterial Proteins/*genetics ; Chlamydia/classification/*genetics/metabolism ; Conserved Sequence/genetics ; DNA, Bacterial/analysis/*genetics ; Evolution, Molecular ; Gene Deletion ; Gene Transfer, Horizontal/genetics ; Mutagenesis, Insertional ; Phylogeny ; }, abstract = {Chlamydiae species are important human and animal pathogens. Their obligate intracellular mode of replication has precluded the use of genetic and molecular biological approaches for understanding their biology. Comparative genomics have identified many rare genetic changes consisting of whole proteins and conserved indels (i.e. inserts or deletions) in widely distributed proteins that are distinctive characteristics of either all, or various subgroups within, chlamydiae. Additionally, several interesting cases of the lateral transfer of genes from free-living bacteria to a common ancestor of chlamydiae, and from chlamydiae to Trypanosoma/Leishmania, have been identified. These novel signatures have possible applications for advancing our understanding of the chlamydiae.}, }
@article {pmid17048405, year = {2004}, author = {Moret, BM and Nakhleh, L and Warnow, T and Linder, CR and Tholse, A and Padolina, A and Sun, J and Timme, R}, title = {Phylogenetic networks: modeling, reconstructibility, and accuracy.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {1}, number = {1}, pages = {13-23}, doi = {10.1109/TCBB.2004.10}, pmid = {17048405}, issn = {1545-5963}, mesh = {Algorithms ; Computational Biology/*methods ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; *Models, Genetic ; *Phylogeny ; Recombination, Genetic/genetics ; }, abstract = {Phylogenetic networks model the evolutionary history of sets of organisms when events such as hybrid speciation and horizontal gene transfer occur. In spite of their widely acknowledged importance in evolutionary biology, phylogenetic networks have so far been studied mostly for specific data sets. We present a general definition of phylogenetic networks in terms of directed acyclic graphs (DAGs) and a set of conditions. Further, we distinguish between model networks and reconstructible ones and characterize the effect of extinction and taxon sampling on the reconstructibility of the network. Simulation studies are a standard technique for assessing the performance of phylogenetic methods. A main step in such studies entails quantifying the topological error between the model and inferred phylogenies. While many measures of tree topological accuracy have been proposed, none exist for phylogenetic networks. Previously, we proposed the first such measure, which applied only to a restricted class of networks. In this paper, we extend that measure to apply to all networks, and prove that it is a metric on the space of phylogenetic networks. Our results allow for the systematic study of existing network methods, and for the design of new accurate ones.}, }
@article {pmid17041630, year = {2006}, author = {Kang, J and Blaser, MJ}, title = {Bacterial populations as perfect gases: genomic integrity and diversification tensions in Helicobacter pylori.}, journal = {Nature reviews. Microbiology}, volume = {4}, number = {11}, pages = {826-836}, doi = {10.1038/nrmicro1528}, pmid = {17041630}, issn = {1740-1534}, mesh = {Biological Evolution ; *Genetic Variation ; *Genome, Bacterial ; Helicobacter pylori/*genetics ; }, abstract = {Microorganisms that persist in single hosts face particular challenges. Helicobacter pylori, an obligate bacterial parasite of the human stomach, has evolved a lifestyle that features interstrain competition and intraspecies cooperation, both of which involve horizontal gene transfer. Microbial species must maintain genomic integrity, yet H. pylori has evolved a complex nonlinear system for diversification that exists in dynamic tension with the mechanisms for ensuring fidelity. Here, we review these tensions and propose that they create a dynamic pool of genetic variants that is sufficiently genetically diverse to allow H. pylori to occupy all of the potential niches in the stomach.}, }
@article {pmid17041054, year = {2006}, author = {Diavatopoulos, DA and Cummings, CA and van der Heide, HG and van Gent, M and Liew, S and Relman, DA and Mooi, FR}, title = {Characterization of a highly conserved island in the otherwise divergent Bordetella holmesii and Bordetella pertussis genomes.}, journal = {Journal of bacteriology}, volume = {188}, number = {24}, pages = {8385-8394}, pmid = {17041054}, issn = {0021-9193}, support = {AI054970/AI/NIAID NIH HHS/United States ; R03 AI054970/AI/NIAID NIH HHS/United States ; R21 AI057188/AI/NIAID NIH HHS/United States ; AI057188/AI/NIAID NIH HHS/United States ; R33 AI057188/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/metabolism ; Bordetella/*classification/*genetics/isolation &amp; purification ; Bordetella pertussis/*classification/*genetics/isolation &amp; purification ; Evolution, Molecular ; Genome, Bacterial ; Genomic Islands/*genetics ; Humans ; Hydroxamic Acids/metabolism ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The recently discovered pathogen Bordetella holmesii has been isolated from the airways and blood of diseased humans. Genetic events contributing to the emergence of B. holmesii are not understood, and its phylogenetic position among the bordetellae remains unclear. To address these questions, B. holmesii strains were analyzed by comparative genomic hybridization (CGH) to a Bordetella pertussis microarray and by multilocus sequence typing. Both methods indicated substantial sequence divergence between B. pertussis and B. holmesii. However, CGH identified a putative pathogenicity island of 66 kb that is highly conserved between these species and contains several IS481 elements that may have been laterally transferred from B. pertussis to B. holmesii. This island contains, among other genes, a functional, iron-regulated locus encoding the biosynthesis, export, and uptake of the siderophore alcaligin. The acquisition of this genomic island by B. holmesii may have significantly contributed to its emergence as a human pathogen. Horizontal gene transfer between B. pertussis and B. holmesii may also explain the unusually high sequence identity of their 16S rRNA genes.}, }
@article {pmid17040125, year = {2006}, author = {Fenn, K and Conlon, C and Jones, M and Quail, MA and Holroyd, NE and Parkhill, J and Blaxter, M}, title = {Phylogenetic relationships of the Wolbachia of nematodes and arthropods.}, journal = {PLoS pathogens}, volume = {2}, number = {10}, pages = {e94}, pmid = {17040125}, issn = {1553-7374}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Arthropods/*microbiology ; Base Sequence ; DNA, Bacterial ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Molecular Sequence Data ; Nematoda/*microbiology ; Phylogeny ; Symbiosis/genetics ; Synteny ; Wolbachia/classification/*genetics ; }, abstract = {Wolbachia are well known as bacterial symbionts of arthropods, where they are reproductive parasites, but have also been described from nematode hosts, where the symbiotic interaction has features of mutualism. The majority of arthropod Wolbachia belong to clades A and B, while nematode Wolbachia mostly belong to clades C and D, but these relationships have been based on analysis of a small number of genes. To investigate the evolution and relationships of Wolbachia symbionts we have sequenced over 70 kb of the genome of wOvo, a Wolbachia from the human-parasitic nematode Onchocerca volvulus, and compared the genes identified to orthologues in other sequenced Wolbachia genomes. In comparisons of conserved local synteny, we find that wBm, from the nematode Brugia malayi, and wMel, from Drosophila melanogaster, are more similar to each other than either is to wOvo. Phylogenetic analysis of the protein-coding and ribosomal RNA genes on the sequenced fragments supports reciprocal monophyly of nematode and arthropod Wolbachia. The nematode Wolbachia did not arise from within the A clade of arthropod Wolbachia, and the root of the Wolbachia clade lies between the nematode and arthropod symbionts. Using the wOvo sequence, we identified a lateral transfer event whereby segments of the Wolbachia genome were inserted into the Onchocerca nuclear genome. This event predated the separation of the human parasite O. volvulus from its cattle-parasitic sister species, O. ochengi. The long association between filarial nematodes and Wolbachia symbionts may permit more frequent genetic exchange between their genomes.}, }
@article {pmid17038121, year = {2006}, author = {Kozlowicz, BK and Shi, K and Gu, ZY and Ohlendorf, DH and Earhart, CA and Dunny, GM}, title = {Molecular basis for control of conjugation by bacterial pheromone and inhibitor peptides.}, journal = {Molecular microbiology}, volume = {62}, number = {4}, pages = {958-969}, pmid = {17038121}, issn = {0950-382X}, support = {T32 DE07288/DE/NIDCR NIH HHS/United States ; R01 GM049530-25/GM/NIGMS NIH HHS/United States ; T32 DE007288/DE/NIDCR NIH HHS/United States ; R01 AI057585/AI/NIAID NIH HHS/United States ; AI57585/AI/NIAID NIH HHS/United States ; R01 AI057585-05/AI/NIAID NIH HHS/United States ; GM49530/GM/NIGMS NIH HHS/United States ; R01 GM049530/GM/NIGMS NIH HHS/United States ; T32 GM08347/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Proteins/*physiology ; *Conjugation, Genetic ; DNA, Bacterial ; Enterococcus faecalis/chemistry/genetics/*physiology ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genes, Bacterial ; Lac Operon ; Models, Molecular ; Mutation ; Oligopeptides/antagonists &amp; inhibitors/genetics/*physiology ; Pheromones/antagonists &amp; inhibitors/genetics/*physiology ; Plasmids ; Protein Binding ; Protein Sorting Signals/*physiology ; Receptors, Peptide/physiology ; }, abstract = {In many bacteria expression of lateral gene transfer and of virulence factors is controlled by cell-cell signalling systems. Molecular interactions of microbial signal molecules with their cognate receptors are not well understood. For the Enterococcus faecalis conjugative plasmid pCF10, the PrgX protein serves as a molecular switch controlling expression of conjugation and virulence genes encoded by the plasmid. The induction state of a pCF10-carrying donor cell is determined by the ratio of two signalling peptides, cCF10 pheromone and iCF10 inhibitor. Recent analysis of PrgX/cCF10 interactions suggests a mechanism for conversion to the induced state. However, the means by which iCF10 peptide antagonizes cCF10 activity is unclear, and it has been suggested that inhibitor peptides block import of pheromone peptides. We now show that both of these peptides interact with the same binding pocket of PrgX, but they differentially alter the conformation of the protein and its oligomerization state, resulting in opposing biological activities.}, }
@article {pmid17035353, year = {2007}, author = {Boureux, A and Vignal, E and Faure, S and Fort, P}, title = {Evolution of the Rho family of ras-like GTPases in eukaryotes.}, journal = {Molecular biology and evolution}, volume = {24}, number = {1}, pages = {203-216}, pmid = {17035353}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Animals ; *Evolution, Molecular ; Fungi/genetics ; Gene Duplication ; Humans ; Invertebrates/genetics ; Molecular Sequence Data ; Phylogeny ; Plants/genetics ; Pseudogenes ; Sequence Alignment ; Vertebrates/genetics ; rho GTP-Binding Proteins/*genetics ; }, abstract = {GTPases of the Rho family are molecular switches that play important roles in converting and amplifying external signals into cellular effects. Originally demonstrated to control the dynamics of the F-actin cytoskeleton, Rho GTPases have been implicated in many basic cellular processes that influence cell proliferation, differentiation, motility, adhesion, survival, or secretion. To elucidate the evolutionary history of the Rho family, we have analyzed over 20 species covering major eukaryotic clades from unicellular organisms to mammals, including platypus and opossum, and have reconstructed the ontogeny and the chronology of emergence of the different subfamilies. Our data establish that the 20 mammalian Rho members are structured into 8 subfamilies, among which Rac is the founder of the whole family. Rho, Cdc42, RhoUV, and RhoBTB subfamilies appeared before Coelomates and RhoJQ, Cdc42 isoforms, RhoDF, and Rnd emerged in chordates. In vertebrates, gene duplications and retrotranspositions increased the size of each chordate Rho subfamily, whereas RhoH, the last subfamily, arose probably by horizontal gene transfer. Rac1b, a Rac1 isoform generated by alternative splicing, emerged in amniotes, and RhoD, only in therians. Analysis of Rho mRNA expression patterns in mouse tissues shows that recent subfamilies have tissue-specific and low-level expression that supports their implication only in narrow time windows or in differentiated metabolic functions. These findings give a comprehensive view of the evolutionary canvas of the Rho family and provide guides for future structure and evolution studies of other components of Rho signaling pathways, in particular regulators of the RhoGEF family.}, }
@article {pmid17030797, year = {2006}, author = {Chain, PS and Denef, VJ and Konstantinidis, KT and Vergez, LM and Agulló, L and Reyes, VL and Hauser, L and Córdova, M and Gómez, L and González, M and Land, M and Lao, V and Larimer, F and LiPuma, JJ and Mahenthiralingam, E and Malfatti, SA and Marx, CJ and Parnell, JJ and Ramette, A and Richardson, P and Seeger, M and Smith, D and Spilker, T and Sul, WJ and Tsoi, TV and Ulrich, LE and Zhulin, IB and Tiedje, JM}, title = {Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, number = {42}, pages = {15280-15287}, pmid = {17030797}, issn = {0027-8424}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; P42 ES 04911-12/ES/NIEHS NIH HHS/United States ; }, mesh = {Burkholderia/chemistry/*genetics/metabolism/pathogenicity ; Chromosomes, Bacterial ; Evolution, Molecular ; Gene Expression Profiling ; *Genome, Bacterial ; Molecular Structure ; Oligonucleotide Array Sequence Analysis ; *Replicon ; }, abstract = {Burkholderia xenovorans LB400 (LB400), a well studied, effective polychlorinated biphenyl-degrader, has one of the two largest known bacterial genomes and is the first nonpathogenic Burkholderia isolate sequenced. From an evolutionary perspective, we find significant differences in functional specialization between the three replicons of LB400, as well as a more relaxed selective pressure for genes located on the two smaller vs. the largest replicon. High genomic plasticity, diversity, and specialization within the Burkholderia genus are exemplified by the conservation of only 44% of the genes between LB400 and Burkholderia cepacia complex strain 383. Even among four B. xenovorans strains, genome size varies from 7.4 to 9.73 Mbp. The latter is largely explained by our findings that >20% of the LB400 sequence was recently acquired by means of lateral gene transfer. Although a range of genetic factors associated with in vivo survival and intercellular interactions are present, these genetic factors are likely related to niche breadth rather than determinants of pathogenicity. The presence of at least eleven "central aromatic" and twenty "peripheral aromatic" pathways in LB400, among the highest in any sequenced bacterial genome, supports this hypothesis. Finally, in addition to the experimentally observed redundancy in benzoate degradation and formaldehyde oxidation pathways, the fact that 17.6% of proteins have a better LB400 paralog than an ortholog in a different genome highlights the importance of gene duplication and repeated acquirement, which, coupled with their divergence, raises questions regarding the role of paralogs and potential functional redundancies in large-genome microbes.}, }
@article {pmid17030793, year = {2006}, author = {Makarova, K and Slesarev, A and Wolf, Y and Sorokin, A and Mirkin, B and Koonin, E and Pavlov, A and Pavlova, N and Karamychev, V and Polouchine, N and Shakhova, V and Grigoriev, I and Lou, Y and Rohksar, D and Lucas, S and Huang, K and Goodstein, DM and Hawkins, T and Plengvidhya, V and Welker, D and Hughes, J and Goh, Y and Benson, A and Baldwin, K and Lee, JH and Díaz-Muñiz, I and Dosti, B and Smeianov, V and Wechter, W and Barabote, R and Lorca, G and Altermann, E and Barrangou, R and Ganesan, B and Xie, Y and Rawsthorne, H and Tamir, D and Parker, C and Breidt, F and Broadbent, J and Hutkins, R and O'Sullivan, D and Steele, J and Unlu, G and Saier, M and Klaenhammer, T and Richardson, P and Kozyavkin, S and Weimer, B and Mills, D}, title = {Comparative genomics of the lactic acid bacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, number = {42}, pages = {15611-15616}, pmid = {17030793}, issn = {0027-8424}, support = {R01 GM055434/GM/NIGMS NIH HHS/United States ; R01 GM55434/GM/NIGMS NIH HHS/United States ; //Intramural NIH HHS/United States ; }, mesh = {Animals ; Bacterial Proteins/classification/genetics/metabolism ; Biological Evolution ; Food Microbiology ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genomics ; Lactic Acid/*metabolism ; Lactobacillus/classification/*genetics ; Phylogeny ; Streptococcaceae/classification/*genetics ; }, abstract = {Lactic acid-producing bacteria are associated with various plant and animal niches and play a key role in the production of fermented foods and beverages. We report nine genome sequences representing the phylogenetic and functional diversity of these bacteria. The small genomes of lactic acid bacteria encode a broad repertoire of transporters for efficient carbon and nitrogen acquisition from the nutritionally rich environments they inhabit and reflect a limited range of biosynthetic capabilities that indicate both prototrophic and auxotrophic strains. Phylogenetic analyses, comparison of gene content across the group, and reconstruction of ancestral gene sets indicate a combination of extensive gene loss and key gene acquisitions via horizontal gene transfer during the coevolution of lactic acid bacteria with their habitats.}, }
@article {pmid17030541, year = {2007}, author = {Richardson, AO and Palmer, JD}, title = {Horizontal gene transfer in plants.}, journal = {Journal of experimental botany}, volume = {58}, number = {1}, pages = {1-9}, doi = {10.1093/jxb/erl148}, pmid = {17030541}, issn = {0022-0957}, support = {R01-GM-70612/GM/NIGMS NIH HHS/United States ; }, mesh = {*Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Mitochondrial ; Genes, Plant ; Magnoliopsida/*genetics ; Phylogeny ; Plants/*genetics ; Polymerase Chain Reaction ; }, abstract = {Horizontal gene transfer (HGT) has played a major role in bacterial evolution and is fairly common in certain unicellular eukaryotes. However, the prevalence and importance of HGT in the evolution of multicellular eukaryotes remain unclear. Recent studies indicate that plant mitochondrial genomes are unusually active in HGT relative to all other organellar and nuclear genomes of multicellular eukaryotes. Although little about the mechanisms of plant HGT is known, several studies have implicated parasitic plants as both donors and recipients of mitochondrial genes. Most cases uncovered thus far have involved a single transferred gene per species; however, recent work has uncovered a case of massive HGT in Amborella trichopoda involving acquisition of at least a few dozen and probably hundreds of foreign mitochondrial genes. These foreign genes came from multiple donors, primarily eudicots and mosses. This review will examine the implications of such massive transfer, the potential mechanisms and consequences of plant-to-plant mitochondrial HGT in general, as well as the limited evidence for HGT in plant chloroplast and nuclear genomes.}, }
@article {pmid17029962, year = {2006}, author = {Tounsi, S and Blight, M and Jaoua, S and de Lima Pimenta, A}, title = {From insects to human hosts: Identification of major genomic differences between entomopathogenic strains of Photorhabdus and the emerging human pathogen Photorhabdus asymbiotica.}, journal = {International journal of medical microbiology : IJMM}, volume = {296}, number = {8}, pages = {521-530}, doi = {10.1016/j.ijmm.2006.06.004}, pmid = {17029962}, issn = {1438-4221}, mesh = {Animals ; Bacterial Proteins/genetics ; Communicable Diseases, Emerging/*microbiology ; Enterobacteriaceae Infections/*microbiology ; Genome ; Humans ; Insecta/*microbiology ; Models, Genetic ; Nucleic Acid Hybridization ; Photorhabdus/classification/*genetics/pathogenicity ; Sequence Analysis, DNA ; Symbiosis/genetics ; Virulence Factors/genetics ; }, abstract = {Pathogenic bacteria of the genus Photorhabdus are naturally found in symbiotic association with soil entomopathogenic nematodes, and are of increasing economic interest in view of their potential for the development of novel biopesticides. This bipartite natural system is currently used for the biological control of crop pests in several countries. However, an increasing number of Photorhabdus strains have recently been isolated from human clinical specimens in both the United States and Australia, associated with locally invasive soft tissue infections and disseminated bacteraemia. In view of their growing use in biological control, which increases the potential rate of exposure of humans to these pathogens, we decided to undertake a comparative study of the genomic differences between insect and human pathogenic strains of Photorhabdus, in an attempt to understand the genetic mechanisms involved in the apparent change of host specificity, presumably responsible for their recently acquired capacity to infect humans. The data presented here demonstrates that major genomic differences exist between strains of Photorhabdus exhibiting virulence against insects or humans. Several individual genes, coding for virulence factors, were isolated and shown to be specific to the Photorhabdus asymbiotica human pathogens. One of these genes, sopB, encoding a host cell invasion factor translocated via the type III secretion system, has been cloned and the comparison of its genomic context in different pathogens strongly indicates that horizontal gene transfer is implicated in the acquisition of these virulence factors specific to the human pathogens. The precise role of this and other virulence factors identified here in the pathogenicity of P. asymbiotica towards humans is currently under investigation.}, }
@article {pmid17028434, year = {2006}, author = {Eisold, S and Antolovic, D and Schmidt, J and Wiessner, R and Klar, E and von Knebel-Doeberitz, M and Linnebacher, M}, title = {Effective antitumoral immune responses are not induced by cytosine deaminase suicide gene transfer in a syngeneic rat pancreatic carcinoma model.}, journal = {European surgical research. Europaische chirurgische Forschung. Recherches chirurgicales europeennes}, volume = {38}, number = {6}, pages = {513-521}, doi = {10.1159/000096070}, pmid = {17028434}, issn = {0014-312X}, mesh = {Adenoviridae/genetics ; Animals ; Apoptosis ; CD4-Positive T-Lymphocytes/immunology ; Cytosine Deaminase/*genetics ; *Cytotoxicity, Immunologic ; Disease Models, Animal ; Flucytosine/*therapeutic use ; Gene Transfer, Horizontal ; *Genetic Therapy ; Male ; Pancreatic Neoplasms/immunology/pathology/*therapy ; Rats ; Rats, Inbred Lew ; }, abstract = {BACKGROUND: Experimental gene transfer can make tumors more immunogenic, leading to local regression and inducing immunological memory sufficient to permit resistance to a tumor rechallenge. However, this rarely had any significant impact on large established tumors.<br><br>METHODS: To analyze potential immunological effects, we used weakly immunogenic pancreatic carcinomas in syngeneic, immunocompetent Lewis rats and performed in situ adenoviral mediated cytosine deaminase (CD) gene transfer followed by administration of the prodrug, 5-fluorocytosine (5FC). In order to reflect the clinical situation, such treated tumors were surgically resected and animals were rechallenged with parental DSL6A pancreatic tumor cells. Tumor growth and cytotoxic activity of immune cells were determined.<br><br>RESULTS: CD/5FC treatment of the DSL6A cells revealed significant induction of apoptosis in vitro and slowed down tumor progression in syngeneic hosts. Furthermore, we observed neither significant change in tumor growth nor protective immunity in the rechallenged animals. Analysis of T lymphocytes showed no specific cytotoxic activity against DSL6A cells. There was only a trend towards a minor NK cell activation.<br><br>CONCLUSIONS: Albeit the present study failed to induce protective antitumor immunity, the initial finding of reduced tumor growth argues for the development of multimodal therapeutic options to overcome negative impacts of advanced malignant disease or chemotherapy-related anergy and immunosuppression.}, }
@article {pmid17027337, year = {2006}, author = {Jores, J and Torres, AG and Wagner, S and Tutt, CB and Kaper, JB and Wieler, LH}, title = {Identification and characterization of "pathoadaptive mutations" of the cadBA operon in several intestinal Escherichia coli.}, journal = {International journal of medical microbiology : IJMM}, volume = {296}, number = {8}, pages = {547-552}, doi = {10.1016/j.ijmm.2006.07.002}, pmid = {17027337}, issn = {1438-4221}, support = {R37 AI021657/AI/NIAID NIH HHS/United States ; AI21657/AI/NIAID NIH HHS/United States ; DK58957/DK/NIDDK NIH HHS/United States ; }, mesh = {Amino Acid Transport Systems/*genetics/metabolism ; Antiporters/*genetics/metabolism ; Bacterial Adhesion/physiology ; Carboxy-Lyases/*genetics/metabolism ; Escherichia coli/*genetics/metabolism/*pathogenicity ; Escherichia coli Proteins/*genetics/metabolism ; Genes, Bacterial ; Intestines/microbiology ; Lysine/metabolism ; *Mutation ; Nucleic Acid Hybridization ; *Operon ; Polymerase Chain Reaction ; Shigella/genetics ; }, abstract = {The dysenteric Shigella spp. and enteroinvasive Escherichia coli (EIEC) have evolved from commensal E. coli by the acquisition of a virulence plasmid and inactivation of genes of the cad locus encoding lysine decarboxylase (LDC) by so-called pathoadaptive mutation. As horizontal gene transfer and recombination occurs frequently in E. coli we were interested to see if similar pathoadaptive mutations are commonly present in other intestinal pathotypes. Therefore, we examined 140 intestinal E. coli strains of various pathotypes and the ECOR collection for their ability to decarboxylate lysine, and identified 25 strains that were unable to do so. Complementation of a Shiga toxin-producing E. coli and two enteropathogenic E. coli strains, both LDC-negative, with the intact cad locus restored LDC activity and resulted in a reduction in adherence to tissue culture cells. We investigated the cad locus for possible alterations by using hybridization and PCR techniques and compared the results with the alterations reported for Shigella spp. and EIEC strains. Interestingly, the alterations of the cad genes were similar to those previously reported, pointing towards a parallel evolution of LDC silencing in different intestinal E. coli pathotypes.}, }
@article {pmid17022471, year = {2006}, author = {Markov, AV and Kulikov, AM}, title = {[Hypothesis of "immunological testing" of partners--systems of "friend and foe" recognition in historical prospect].}, journal = {Izvestiia Akademii nauk. Seriia biologicheskaia}, volume = {}, number = {4}, pages = {389-403}, pmid = {17022471}, issn = {1026-3470}, mesh = {Animals ; Autoimmunity ; *Biological Evolution ; Gene Transfer, Horizontal ; Humans ; Reproduction/genetics/*immunology ; Sexual Behavior ; Sexual Behavior, Animal ; Species Specificity ; }, abstract = {The hypothesis of "autoimmune testing" of mating partners assumes formation of individual system of perception on the basis of an immunologic principle, i.e. by lifetime selection of "direct" or "reverse casts" of own key antigens or signal molecules. Such system provides the coordinated change of signaling systems and system of their perception at formation of new adaptations that leads to automatic formation of reproductive isolation within the limited number of generations. Presence of the "friend-foe" recognition systems practically in all living organisms assumes formation of potential mating partners "autoimmune testing" mechanisms at the earliest evolution stages. In this article we analyze possible mechanisms of a "friend and foe" discrimination with MHC-proteins and their homologues in historical prospect--from bacteria to the lower Chordates.}, }
@article {pmid17021929, year = {2006}, author = {Ranea, JA and Sillero, A and Thornton, JM and Orengo, CA}, title = {Protein superfamily evolution and the last universal common ancestor (LUCA).}, journal = {Journal of molecular evolution}, volume = {63}, number = {4}, pages = {513-525}, pmid = {17021929}, issn = {0022-2844}, mesh = {*Evolution, Molecular ; Gene Duplication ; Genetic Variation ; Genome ; Protein Structure, Tertiary ; Proteins/chemistry/*classification/*genetics ; Temperature ; }, abstract = {By exploiting three-dimensional structure comparison, which is more sensitive than conventional sequence-based methods for detecting remote homology, we have identified a set of 140 ancestral protein domains using very restrictive criteria to minimize the potential error introduced by horizontal gene transfer. These domains are highly likely to have been present in the Last Universal Common Ancestor (LUCA) based on their universality in almost all of 114 completed prokaryotic (Bacteria and Archaea) and eukaryotic genomes. Functional analysis of these ancestral domains reveals a genetically complex LUCA with practically all the essential functional systems present in extant organisms, supporting the theory that life achieved its modern cellular status much before the main kingdom separation (Doolittle 2000). In addition, we have calculated different estimations of the genetic and functional versatility of all the superfamilies and functional groups in the prokaryote subsample. These estimations reveal that some ancestral superfamilies have been more versatile than others during evolution allowing more genetic and functional variation. Furthermore, the differences in genetic versatility between protein families are more attributable to their functional nature rather than the time that they have been evolving. These differences in tolerance to mutation suggest that some protein families have eroded their phylogenetic signal faster than others, hiding in many cases, their ancestral origin and suggesting that the calculation of 140 ancestral domains is probably an underestimate.}, }
@article {pmid17021382, year = {2006}, author = {Zaslaver, A and Mayo, A and Ronen, M and Alon, U}, title = {Optimal gene partition into operons correlates with gene functional order.}, journal = {Physical biology}, volume = {3}, number = {3}, pages = {183-189}, doi = {10.1088/1478-3975/3/3/003}, pmid = {17021382}, issn = {1478-3975}, mesh = {Bacteria/*genetics ; *Gene Expression Regulation, Bacterial ; Gene Order ; Gene Transfer, Horizontal ; Genome, Bacterial ; *Models, Genetic ; *Operon ; Time Factors ; }, abstract = {Gene arrangement into operons varies between bacterial species. Genes in a given system can be on one operon in some organisms and on several operons in other organisms. Existing theories explain why genes that work together should be on the same operon, since this allows for advantageous lateral gene transfer and accurate stoichiometry. But what causes the frequent separation into multiple operons of co-regulated genes that act together in a pathway? Here we suggest that separation is due to benefits made possible by differential regulation of each operon. We present a simple mathematical model for the optimal distribution of genes into operons based on a balance of the cost of operons and the benefit of regulation that provides 'just-when-needed' temporal order. The analysis predicts that genes are arranged such that genes on the same operon do not skip functional steps in the pathway. This prediction is supported by genomic data from 137 bacterial genomes. Our work suggests that gene arrangement is not only the result of random historical drift, genome re-arrangement and gene transfer, but has elements that are solutions of an evolutionary optimization problem. Thus gene functional order may be inferred by analyzing the operon structure across different genomes.}, }
@article {pmid17021220, year = {2006}, author = {Musovic, S and Oregaard, G and Kroer, N and Sørensen, SJ}, title = {Cultivation-independent examination of horizontal transfer and host range of an IncP-1 plasmid among gram-positive and gram-negative bacteria indigenous to the barley rhizosphere.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {10}, pages = {6687-6692}, pmid = {17021220}, issn = {0099-2240}, mesh = {Conjugation, Genetic/*genetics ; Gene Transfer, Horizontal ; Gram-Negative Bacteria/genetics ; Gram-Positive Bacteria/genetics ; Hordeum/*microbiology ; Molecular Sequence Data ; Plasmids/*genetics ; RNA, Ribosomal, 16S/analysis/genetics ; Symbiosis/physiology ; Transformation, Bacterial ; }, abstract = {The host range and transfer frequency of an IncP-1 plasmid (pKJK10) among indigenous bacteria in the barley rhizosphere was investigated. A new flow cytometry-based cultivation-independent method for enumeration and sorting of transconjugants for subsequent 16S rRNA gene classification was used. Indigenous transconjugant rhizosphere bacteria were collected by fluorescence-activated cell sorting and identified by cloning and sequencing of 16S rRNA genes from the sorted cells. The host range of the pKJK10 plasmid was exceptionally broad, as it included not only bacteria belonging to the alpha, beta, and gamma subclasses of the Proteobacteria, but also Arthrobacter sp., a gram-positive member of the Actinobacteria. The transfer frequency (transconjugants per donor) from the Pseudomonas putida donor to the indigenous bacteria was 7.03 x 10(-2) +/- 3.84 x 10(-2). This is the first direct documentation of conjugal transfer between gram-negative donor and gram-positive recipient bacteria in situ.}, }
@article {pmid17021219, year = {2006}, author = {Schierack, P and Steinrück, H and Kleta, S and Vahjen, W}, title = {Virulence factor gene profiles of Escherichia coli isolates from clinically healthy pigs.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {10}, pages = {6680-6686}, pmid = {17021219}, issn = {0099-2240}, mesh = {Animals ; Diarrhea/*epidemiology ; Escherichia coli/classification/genetics/*pathogenicity ; Escherichia coli Infections/epidemiology ; Gene Expression Profiling ; Hemolysis ; Polymerase Chain Reaction ; Sus scrofa/*microbiology ; Virulence Factors/*genetics/metabolism ; }, abstract = {Nonpathogenic, intestinal Escherichia coli (commensal E. coli) supports the physiological intestinal balance of the host, whereas pathogenic E. coli with typical virulence factor gene profiles can cause severe outbreaks of diarrhea. In many reports, E. coli isolates from diarrheic animals were classified as putative pathogens. Here we describe a broad variety of virulence gene-positive E. coli isolates from swine with no clinical signs of intestinal disease. The isolation of E. coli from 34 pigs from the same population and the testing of 331 isolates for genes encoding heat-stable enterotoxins I and II, heat-labile enterotoxin I, Shiga toxin 2e, and F4, F5, F6, F18, and F41 fimbriae revealed that 68.6% of the isolates were positive for at least one virulence gene, with a total of 24 different virulence factor gene profiles, implying high rates of horizontal gene transfer in this E. coli population. Additionally, we traced the occurrence of hemolytic E. coli over a period of 1 year in this same pig population. Hemolytic isolates were differentiated into seven clones; only three were found to harbor virulence genes. Hemolytic E. coli isolates without virulence genes or with only the fedA gene were found to be nontypeable by slide agglutination tests with OK antisera intended for screening live cultures against common pathogenic E. coli serogroups. The results appear to indicate that virulence gene-carrying E. coli strains are a normal part of intestinal bacterial populations and that high numbers of E. coli cells harboring virulence genes and/or with hemolytic activity do not necessarily correlate with disease.}, }
@article {pmid17021204, year = {2006}, author = {Lim, SK and Tanimoto, K and Tomita, H and Ike, Y}, title = {Pheromone-responsive conjugative vancomycin resistance plasmids in Enterococcus faecalis isolates from humans and chicken feces.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {10}, pages = {6544-6553}, pmid = {17021204}, issn = {0099-2240}, mesh = {Animals ; Chickens ; Disease Transmission, Infectious ; Drug Resistance, Bacterial ; Enterococcus faecalis/*drug effects/isolation &amp; purification ; Feces/*microbiology ; *Gene Transfer, Horizontal ; Humans ; Molecular Sequence Data ; Pheromones/*pharmacology ; Plasmids/*genetics ; Vancomycin/pharmacology ; *Vancomycin Resistance/genetics ; }, abstract = {The drug resistances and plasmid contents of a total of 85 vancomycin-resistant enterococcus (VRE) strains that had been isolated in Korea were examined. Fifty-four of the strains originated from samples of chicken feces, and 31 were isolated from hospital patients in Korea. Enterococcus faecalis KV1 and KV2, which had been isolated from a patient and a sample of chicken feces, respectively, were found to carry the plasmids pSL1 and pSL2, respectively. The plasmids transferred resistances to vancomycin, gentamicin, kanamycin, streptomycin, and erythromycin to E. faecalis strains at a high frequency of about 10(-3) per donor cell during 4 hours of broth mating. E. faecalis strains containing each of the pSL plasmids formed clumps after 2 hours of incubation in broth containing E. faecalis FA2-2 culture filtrate (i.e., the E. faecalis sex pheromone), and the plasmid subsequently transferred to the recipient strain in a 10-min short mating in broth, indicating that the plasmids are responsive to E. faecalis pheromones. The pSL plasmids did not respond to any of synthetic pheromones for the previously characterized plasmids. The pheromone specific for pSL plasmids has been designated cSL1. Southern hybridization analysis showed that specific FspI fragments from each of the pSL plasmids hybridized with the aggregation substance gene (asa1) of the pheromone-responsive plasmid pAD1, indicating that the plasmids had a gene homologous to asa1. The restriction maps of the plasmids were identical, and the size of the plasmids was estimated to be 128.1 kb. The plasmids carried five drug resistance determinants for vanA, ermB, aph(3'), aph(6'), and aac(6')/aph(2'), which encode resistance to vancomycin, erythromycin, kanamycin, streptomycin, and gentamicin/kanamycin, respectively. Nucleotide sequence analyses of the drug resistance determinants and their flanking regions are described in this report. The results described provide evidence for the exchange of genetic information between human and animal (chicken) VRE reservoirs and suggest the potential for horizontal transmission of multiple drug resistance, including vancomycin resistance, between farm animals and humans via a pheromone-responsive conjugative plasmid.}, }
@article {pmid17021059, year = {2006}, author = {Giske, CG and Libisch, B and Colinon, C and Scoulica, E and Pagani, L and Füzi, M and Kronvall, G and Rossolini, GM}, title = {Establishing clonal relationships between VIM-1-like metallo-beta-lactamase-producing Pseudomonas aeruginosa strains from four European countries by multilocus sequence typing.}, journal = {Journal of clinical microbiology}, volume = {44}, number = {12}, pages = {4309-4315}, pmid = {17021059}, issn = {0095-1137}, mesh = {Bacterial Proteins/genetics ; Bacterial Typing Techniques ; Cluster Analysis ; DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; Electrophoresis, Gel, Pulsed-Field ; Gene Transfer, Horizontal ; Genotype ; Greece/epidemiology ; Humans ; Hungary/epidemiology ; Integrons/genetics ; Italy/epidemiology ; Molecular Epidemiology ; Molecular Sequence Data ; Phylogeny ; Pseudomonas Infections/epidemiology/*microbiology ; Pseudomonas aeruginosa/*classification/*enzymology/genetics/isolation &amp; purification ; Random Amplified Polymorphic DNA Technique ; Recombination, Genetic ; Sequence Analysis, DNA ; Serotyping ; Sweden/epidemiology ; beta-Lactamases/biosynthesis/genetics ; }, abstract = {Ten multidrug-resistant Pseudomonas aeruginosa strains producing VIM-1-like acquired metallo-beta-lactamases (MBLs), isolated from four European countries (Greece, Hungary, Italy, and Sweden), were analyzed for genetic relatedness by several methodologies, including fliC sequence analysis, macrorestriction profiling of genomic DNA by pulsed-field gel electrophoresis (PFGE), random amplification of polymorphic DNA (RAPD), and multilocus sequence typing (MLST). The four approaches yielded consistent results overall but showed different resolution powers in establishing relatedness between isolates (PFGE>RAPD>MLST>fliC typing) and could usefully complement each other to address issues in the molecular epidemiology of P. aeruginosa strains producing acquired MBLs. In particular, the recently developed MLST approach was useful in revealing clonal relatedness between isolates when this was not readily apparent using RAPD and PFGE, and it suggested a common ancestry for some of the VIM-1-like MBL-positive P. aeruginosa strains currently spreading in Europe. The MBL producers belonged in three clonal complexes/burst groups (BGs). Of these, one corresponded to the previously described BG4 and included serotype O12 strains from Hungary and Sweden, while the other two were novel and included serotype O11 or nonserotypable strains from Greece, Sweden, and/or Italy. Comparison of the integrons carrying blaVIM-1-like cassettes of various isolates revealed a remarkable structural heterogeneity, suggesting the possibility that multiple independent events of acquisition of different blaVIM-containing integrons had occurred in members of the same clonal lineage, although a contribution of integrase-mediated cassette shuffling or other recombination mechanisms during the evolution of similar strains could also have played a role in determining this variability.}, }
@article {pmid17020798, year = {2006}, author = {Deshpande, LM and Rhomberg, PR and Sader, HS and Jones, RN}, title = {Emergence of serine carbapenemases (KPC and SME) among clinical strains of Enterobacteriaceae isolated in the United States Medical Centers: report from the MYSTIC Program (1999-2005).}, journal = {Diagnostic microbiology and infectious disease}, volume = {56}, number = {4}, pages = {367-372}, doi = {10.1016/j.diagmicrobio.2006.07.004}, pmid = {17020798}, issn = {0732-8893}, mesh = {Academic Medical Centers ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/*biosynthesis/chemistry ; Enterobacteriaceae/*drug effects/*enzymology/isolation &amp; purification ; Enterobacteriaceae Infections/*microbiology ; Humans ; Imipenem/*pharmacology ; Meropenem ; Microbial Sensitivity Tests ; Population Surveillance ; Serine ; Species Specificity ; Thienamycins/*pharmacology ; United States ; beta-Lactamases/*biosynthesis/chemistry ; }, abstract = {Among 8885 Enterobacteriaceae tested in the 1999 to 2005 period as part of the USA Meropenem Yearly Susceptibility Test Information Collection (MYSTIC) Program, 51 strains with increased imipenem and meropenem MIC values (> or =2 microg/mL) were detected. bla(KPC) was identified from 28 Klebsiella pneumoniae from 3 medical centers in the New York City area (8 ribotypes), 2 Klebsiella oxytoca from Arkansas (same ribotype), 7 Citrobacter freundii (6 from New York [5 ribotypes] and 1 from Delaware), 4 Enterobacter spp. from New York (2 species, different ribotypes), 3 Escherichia coli (2 from New York and 1 from Ohio, same ribotype), and 1 Serratia marcescens (New York). Sequencing confirmed KPC-2 or -3 in all of the strains. S. marcescens strains harboring SME-1 (2 isolates, same ribotype) and SME-2 (1 isolate) were identified from medical centers in Illinois and Washington state, respectively. Our results indicate that bla(KPC-2/3) has emerged widely (New York City area, Arkansas, Delaware, and Ohio) among Enterobacteriaceae isolated in the MYSTIC Program participant sites (2000-2005) and continues to be isolated from multiple species, as a result of clonal expansion and horizontal gene transfer. The escalating occurrence (0.35%) of serine carbapenemases could compromise the role of carbapenems and other beta-lactams in USA clinical practice although observed in only a few locations to date.}, }
@article {pmid17015832, year = {2006}, author = {Goldman, BS and Nierman, WC and Kaiser, D and Slater, SC and Durkin, AS and Eisen, JA and Ronning, CM and Barbazuk, WB and Blanchard, M and Field, C and Halling, C and Hinkle, G and Iartchuk, O and Kim, HS and Mackenzie, C and Madupu, R and Miller, N and Shvartsbeyn, A and Sullivan, SA and Vaudin, M and Wiegand, R and Kaplan, HB}, title = {Evolution of sensory complexity recorded in a myxobacterial genome.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, number = {41}, pages = {15200-15205}, pmid = {17015832}, issn = {0027-8424}, support = {R37 GM023441/GM/NIGMS NIH HHS/United States ; GM23441/GM/NIGMS NIH HHS/United States ; }, mesh = {Deltaproteobacteria/genetics/physiology ; *Evolution, Molecular ; *Genome, Bacterial ; Molecular Sequence Data ; Multigene Family ; Myxococcus xanthus/*genetics/growth &amp; development/physiology ; RNA, Ribosomal, 16S/genetics ; Signal Transduction/genetics/physiology ; }, abstract = {Myxobacteria are single-celled, but social, eubacterial predators. Upon starvation they build multicellular fruiting bodies using a developmental program that progressively changes the pattern of cell movement and the repertoire of genes expressed. Development terminates with spore differentiation and is coordinated by both diffusible and cell-bound signals. The growth and development of Myxococcus xanthus is regulated by the integration of multiple signals from outside the cells with physiological signals from within. A collection of M. xanthus cells behaves, in many respects, like a multicellular organism. For these reasons M. xanthus offers unparalleled access to a regulatory network that controls development and that organizes cell movement on surfaces. The genome of M. xanthus is large (9.14 Mb), considerably larger than the other sequenced delta-proteobacteria. We suggest that gene duplication and divergence were major contributors to genomic expansion from its progenitor. More than 1,500 duplications specific to the myxobacterial lineage were identified, representing >15% of the total genes. Genes were not duplicated at random; rather, genes for cell-cell signaling, small molecule sensing, and integrative transcription control were amplified selectively. Families of genes encoding the production of secondary metabolites are overrepresented in the genome but may have been received by horizontal gene transfer and are likely to be important for predation.}, }
@article {pmid17015669, year = {2006}, author = {Stabler, RA and Gerding, DN and Songer, JG and Drudy, D and Brazier, JS and Trinh, HT and Witney, AA and Hinds, J and Wren, BW}, title = {Comparative phylogenomics of Clostridium difficile reveals clade specificity and microevolution of hypervirulent strains.}, journal = {Journal of bacteriology}, volume = {188}, number = {20}, pages = {7297-7305}, pmid = {17015669}, issn = {0021-9193}, support = {/WT_/Wellcome Trust/United Kingdom ; 062511/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Bacterial Adhesion/genetics ; Bacterial Toxins/genetics ; Clostridioides difficile/*classification/genetics/*pathogenicity/physiology ; Cluster Analysis ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial/genetics ; Genomic Islands ; Humans ; Movement ; Nucleic Acid Hybridization ; Oligonucleotide Array Sequence Analysis ; *Phylogeny ; Virulence ; }, abstract = {Clostridium difficile is the most frequent cause of nosocomial diarrhea worldwide, and recent reports suggested the emergence of a hypervirulent strain in North America and Europe. In this study, we applied comparative phylogenomics (whole-genome comparisons using DNA microarrays combined with Bayesian phylogenies) to model the phylogeny of C. difficile, including 75 diverse isolates comprising hypervirulent, toxin-variable, and animal strains. The analysis identified four distinct statistically supported clusters comprising a hypervirulent clade, a toxin A(-) B(+) clade, and two clades with human and animal isolates. Genetic differences among clades revealed several genetic islands relating to virulence and niche adaptation, including antibiotic resistance, motility, adhesion, and enteric metabolism. Only 19.7% of genes were shared by all strains, confirming that this enteric species readily undergoes genetic exchange. This study has provided insight into the possible origins of C. difficile and its evolution that may have implications in disease control strategies.}, }
@article {pmid17015654, year = {2006}, author = {Jones, CH and Tuckman, M and Murphy, E and Bradford, PA}, title = {Identification and sequence of a tet(M) tetracycline resistance determinant homologue in clinical isolates of Escherichia coli.}, journal = {Journal of bacteriology}, volume = {188}, number = {20}, pages = {7151-7164}, pmid = {17015654}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; Anti-Bacterial Agents/pharmacology ; Base Sequence ; Cloning, Molecular ; Conjugation, Genetic ; DNA Transposable Elements/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Intergenic ; Escherichia coli/drug effects/*genetics/isolation &amp; purification ; Escherichia coli Infections/microbiology ; Escherichia coli Proteins/*genetics ; Gene Expression ; Gene Transfer, Horizontal ; Humans ; Minocycline/pharmacology ; Molecular Sequence Data ; Phylogeny ; Plasmids/genetics ; Promoter Regions, Genetic ; Sequence Homology, Amino Acid ; Tetracycline/pharmacology ; Tetracycline Resistance/*genetics ; }, abstract = {The presence of the tetracycline resistance determinant tet(M) in human clinical isolates of Escherichia coli is described for the first time in this report. The homologue was >99% identical to the tet(M) genes reported to occur in Lactobacillus plantarum, Neisseria meningitidis, and Streptococcus agalactiae, and 3% of the residues in its deduced amino acid sequence diverge from tet(M) of Staphylococcus aureus. Sequence analysis of the regions immediately flanking the gene revealed that sequences upstream of tet(M) in E. coli have homology to Tn916; however, a complete IS26 insertion element was present immediately upstream of the promoter element. Downstream from the termination codon is an insertion sequence that was homologous to the ISVs1 element reported to occur in a plasmid from Vibrio salmonicida that has been associated with another tetracycline resistance determinant, tet(E). Results of mating experiments demonstrated that the E. coli tet(M) gene was on a mobile element so that resistance to tetracycline and minocycline could be transferred to a susceptible strain by conjugation. Expression of the cloned tet(M) gene, under the control of its own promoter, provided tetracycline and minocycline resistance to the E. coli host.}, }
@article {pmid17014680, year = {2007}, author = {Jacobsen, L and Wilcks, A and Hammer, K and Huys, G and Gevers, D and Andersen, SR}, title = {Horizontal transfer of tet(M) and erm(B) resistance plasmids from food strains of Lactobacillus plantarum to Enterococcus faecalis JH2-2 in the gastrointestinal tract of gnotobiotic rats.}, journal = {FEMS microbiology ecology}, volume = {59}, number = {1}, pages = {158-166}, doi = {10.1111/j.1574-6941.2006.00212.x}, pmid = {17014680}, issn = {0168-6496}, mesh = {Animals ; Bacterial Proteins/*genetics ; Blotting, Southern ; Drug Resistance, Bacterial/*genetics ; Enterococcus faecalis/drug effects/*genetics ; Erythromycin/pharmacology ; Female ; *Gene Transfer, Horizontal ; *Germ-Free Life ; Lactobacillus plantarum/drug effects/*genetics ; Male ; Microbial Sensitivity Tests ; Plasmids/genetics ; Rats ; Tetracycline/pharmacology ; Tetracycline Resistance/genetics ; }, abstract = {Two wild-type strains of Lactobacillus plantarum previously isolated from fermented dry sausages were analysed for their ability to transfer antibiotic resistance plasmids in the gastrointestinal tract. For this purpose, we used gnotobiotic rats as an in vivo model. Rats were initially inoculated with the recipient Enterococcus faecalis JH2-2 at a concentration of 10(10) CFU mL(-1). After a week, either of the two donors L. plantarum DG 522 (harbouring a tet(M)-containing plasmid of c. 40 kb) or L. plantarum DG 507 [harbouring a tet(M)-containing plasmid of c. 10 kb and an erm(B)-containing plasmid of c. 8.5 kb] was introduced at concentrations in the range of 10(8)-10(10) CFU mL(-1). Two days after donor introduction, the first transconjugants (TCs) were detected in faecal samples. The detected numbers of tet(M)-TCs were comparable for the two donors. In both cases, this number increased to c. 5 x 10(2) CFU g(-1) faeces towards the end of the experiment. For erm(B)-TCs, the number was significantly higher and increased to c. 10(3) CFU g(-1) faeces. To our knowledge, this is the first study showing in vivo transfer of wild-type antibiotic resistance plasmids from L. plantarum to E. faecalis.}, }
@article {pmid17014499, year = {2006}, author = {Heylen, K and Gevers, D and Vanparys, B and Wittebolle, L and Geets, J and Boon, N and De Vos, P}, title = {The incidence of nirS and nirK and their genetic heterogeneity in cultivated denitrifiers.}, journal = {Environmental microbiology}, volume = {8}, number = {11}, pages = {2012-2021}, doi = {10.1111/j.1462-2920.2006.01081.x}, pmid = {17014499}, issn = {1462-2912}, mesh = {Bacteria/*classification/*genetics/growth &amp; development/metabolism ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genes, rRNA ; Molecular Sequence Data ; Nitrite Reductases/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Gene sequence analysis of nirS and nirK, both encoding nitrite reductases, was performed on cultivated denitrifiers to assess their incidence in different bacterial taxa and their taxonomical value. Almost half of the 227 investigated denitrifying strains did not render an nir amplicon with any of five previously described primers. NirK and nirS were found to be prevalent in Alphaproteobacteria and Betaproteobacteria, respectively, nirK was detected in the Firmicutes and Bacteroidetes and nirS and nirK with equal frequency in the Gammaproteobacteria. These observations deviated from the hitherto reported incidence of nir genes in bacterial taxa. NirS gene phylogeny was congruent with the 16S rRNA gene phylogeny on family or genus level, although some strains did group within clusters of other bacterial classes. Phylogenetic nirK gene sequence analysis was incongruent with the 16S rRNA gene phylogeny. NirK sequences were also found to be significantly more similar to nirK sequences from the same habitat than to nirK sequences retrieved from highly related taxa. This study supports the hypothesis that horizontal gene transfer events of denitrification genes have occurred and underlines that denitrification genes should not be linked with organism diversity of denitrifiers in cultivation-independent studies.}, }
@article {pmid17009867, year = {2006}, author = {Smith, NH}, title = {A re-evaluation of M. prototuberculosis.}, journal = {PLoS pathogens}, volume = {2}, number = {9}, pages = {e98}, pmid = {17009867}, issn = {1553-7374}, mesh = {Animals ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genetic Variation ; Genetics, Population ; Hominidae/*microbiology ; Models, Genetic ; Molecular Sequence Data ; Mycobacterium tuberculosis/classification/*genetics ; Primate Diseases/*microbiology ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; Tuberculosis/*microbiology ; }, }
@article {pmid17008099, year = {2006}, author = {Sharma, AK and Spudich, JL and Doolittle, WF}, title = {Microbial rhodopsins: functional versatility and genetic mobility.}, journal = {Trends in microbiology}, volume = {14}, number = {11}, pages = {463-469}, doi = {10.1016/j.tim.2006.09.006}, pmid = {17008099}, issn = {0966-842X}, mesh = {Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Phylogeny ; Rhodopsins, Microbial/*genetics/physiology ; }, abstract = {The type 1 (microbial) rhodopsins are a diverse group of photochemically reactive proteins that span the three domains of life. Their broad phylogenetic distribution has motivated conjecture that rhodopsin-like functionality was present in the last common ancestor of all life. Here, we discuss the evolution of the type 1 microbial rhodopsins and document five cases of lateral gene transfer (LGT) between domains. We suggest that, thanks to the functional versatility of these retinylidene proteins and the relative ease with which they can complement the existing energy-generating or photosensory repertoires of many organisms, LGT is in fact the principal force that determines their broad but patchy distribution.}, }
@article {pmid17008031, year = {2007}, author = {Park, JM and Schneeweiss, GM and Weiss-Schneeweiss, H}, title = {Diversity and evolution of Ty1-copia and Ty3-gypsy retroelements in the non-photosynthetic flowering plants Orobanche and Phelipanche (Orobanchaceae).}, journal = {Gene}, volume = {387}, number = {1-2}, pages = {75-86}, doi = {10.1016/j.gene.2006.08.012}, pmid = {17008031}, issn = {0378-1119}, mesh = {Chromosome Mapping ; Evolution, Molecular ; *Genetic Variation ; Genome, Plant ; Orobanchaceae/classification/genetics ; Orobanche/*classification/genetics ; Phylogeny ; Repetitive Sequences, Nucleic Acid/*genetics ; Retroelements/*genetics ; Sequence Analysis, DNA ; }, abstract = {We present the first study on the diversity and evolution of Ty1-copia and Ty3-gypsy retroelements in a group of non-photosynthetic flowering plants. To this end partial sequences of the reverse transcriptase (rt) gene were obtained from 20 clones for each retroelement type from seven and six accessions of Orobanche and Phelipanche (Orobanchaceae), respectively. Overall sequence similarity is higher in Ty3-gypsy elements than in Ty1-copia elements in agreement with the results from other angiosperm groups. Higher sequence diversity and stronger phylogenetic structure, especially of Ty1-copia sequences, in Orobanche species compared to Phelipanche species support the previously suggested hypothesis (based on karyological and cytological data) that genomes of Orobanche species are more dynamic than those of Phelipanche species. No evidence was found for intraspecific differences of retroelement diversity nor for differences between pest taxa and their putative wild relatives, e.g., O. crenata and O. owerini. The occurrence of a few sequences from Phelipanche species in clades otherwise comprising sequences from Orobanche species might be due to horizontal gene transfer, but the alternative of vertical transmission cannot be rejected unambiguously.}, }
@article {pmid17007435, year = {2006}, author = {Tóthová, T and Pristas, P and Javorský, P}, title = {Mercuric reductase gene transfer from soil to rumen bacteria.}, journal = {Folia microbiologica}, volume = {51}, number = {4}, pages = {317-319}, pmid = {17007435}, issn = {0015-5632}, mesh = {Animals ; Bacillus subtilis/genetics/metabolism ; Biodegradation, Environmental ; Citrobacter freundii/genetics/metabolism ; *Conjugation, Genetic ; DNA Fingerprinting ; Gene Transfer, Horizontal/*genetics ; Mercury/metabolism ; Oxidoreductases/*genetics/metabolism ; Rumen/*microbiology ; Sheep/metabolism/microbiology ; Slovakia ; *Soil Microbiology ; Soil Pollutants/metabolism ; }, abstract = {Conjugal transfer between soil bacterial population and microorganisms isolated from the rumen of herbivores from mercury-polluted area was investigated. The transfer of merA encoding mercury-resistance plasmids from soil bacteria Enterobacter cloacae and Enterococcus durans into two ruminal isolates Citrobacter freundii and Bacillus subtilis was observed. Approximately the same frequency of mobilization in mating experiments was observed for both Gram-negative (approximately 2.5 x 10(-8), transconjugants-to-recipient ratio) and Gram-positive (approximately 1.3 x 10(-8)) bacteria.}, }
@article {pmid17007421, year = {2006}, author = {Cepeljnik, T and Rincón, MT and Flint, HJ and Marinsek-Logar, R}, title = {Xyn11A, a multidomain multicatalytic enzyme from Pseudobutyrivibrio xylanivorans Mz5T.}, journal = {Folia microbiologica}, volume = {51}, number = {4}, pages = {263-267}, pmid = {17007421}, issn = {0015-5632}, mesh = {Animals ; Bacterial Proteins/*genetics/isolation &amp; purification/metabolism ; Gram-Positive Endospore-Forming Rods/*enzymology/genetics ; Molecular Sequence Data ; Rumen/microbiology ; Xylans/*metabolism ; Xylosidases/*genetics/isolation &amp; purification/metabolism ; }, abstract = {The rumen bacterium Pseudobutyrivibrio xylanivorans Mz5T has a potent xylanolytic enzyme system. A small native peptide (approximately 30-kDa, designated Xyn11A) from the bacterium was first isolated and characterized by Edman degradation. The gene coding for Xyn11A was identified using PCR amplification with consensus primers. It was then fully sequenced to reveal an open reading frame of 1809 bp. The predicted N-terminal domain exhibited xylanolytic activity and was classed to the family 11 of glycosyl hydrolases; it is followed by a region with homology to a family 6 cellulose binding module. The C-terminal domain codes for a putative NodB-like polysaccharide deacetylase which is predicted to be an acetyl esterase implicated in debranching activity in the xylan backbone. As similar domain organization was also found in several other xylanases from a diverse range of bacteria, a common ancestor of such a xylanase is considered to be present and spread, possibly by horizontal gene transfer, to other microorganisms from different ecological niches.}, }
@article {pmid17006816, year = {2006}, author = {Yoo, SJ and Sung, H and Cho, YU and Kim, MN and Pai, CH and Kim, YS}, title = {Role of horizontal transfer of the transposon Tn1546 in the nosocomial spread of vanA vancomycin-resistant enterococci at a tertiary care hospital in Korea.}, journal = {Infection control and hospital epidemiology}, volume = {27}, number = {10}, pages = {1081-1087}, doi = {10.1086/507279}, pmid = {17006816}, issn = {0899-823X}, mesh = {Cross Infection/epidemiology/*microbiology ; DNA Fingerprinting ; DNA Transposable Elements/*genetics ; Electrophoresis, Gel, Pulsed-Field ; Enterococcus/*genetics ; *Gene Transfer, Horizontal ; Genetic Variation ; Gram-Positive Bacterial Infections/epidemiology/*microbiology ; Humans ; Korea ; Polymerase Chain Reaction ; Vancomycin Resistance/*genetics ; }, abstract = {OBJECTIVE: To investigate the epidemiologic characteristics of vancomycin-resistant enterococci (VRE) infection.<br><br>DESIGN: An epidemiologic description by means of chromosomal DNA fingerprinting and transposon typing.<br><br>SETTING: A 2,200-bed tertiary care hospital in Korea.<br><br>PATIENTS: First VRE isolates were obtained from patients hospitalized from April 1997 to December 2001.<br><br>INTERVENTIONS: The van genotypes of isolates were identified by means of multiplex polymerase chain reaction (PCR). The macrorestriction patterns of chromosomal DNA were determined by pulsed-field gel electrophoresis (PFGE). The transposon Tn1546 was typed by means of 2 sets of long PCR restriction fragment-length polymorphism analysis, which were ClaI restriction of a 10.4-kb region from orf1 to vanZ and DdeI restriction of a 4.4-kb region from vanR to vanX.<br><br>RESULTS: VRE isolates were recovered from 215 patients. All were vanA genotype. PFGE analysis of the 215 isolates showed 172 types, including 21 clusters composed of 64 isolates and 151 types of as many isolates. Each type was composed of 2-10 isolates; the isolates within each PFGE cluster were detected within a 10-month period and mostly shared a transposon type. Transposon typing classified 169 strains into 15 types and 158 strains belonged to 4 major transposon clusters. Each of these 4 transposon clusters was isolated from patients treated in 5-22 different wards during a 31-52 month period and consisted of 9-80 PFGE types. Each of the other 11 types were found in only one strain.<br><br>CONCLUSIONS: Our findings suggest that the horizontal transfer of Tn1546 has a major role in the nosocomial spread of vanA VRE. Clonal spread of VRE seemed to contribute to short-term dissemination in limited areas.}, }
@article {pmid17005974, year = {2006}, author = {Ali, H and Scanlan, J and Dumont, MG and Murrell, JC}, title = {Duplication of the mmoX gene in Methylosinus sporium: cloning, sequencing and mutational analysis.}, journal = {Microbiology (Reading, England)}, volume = {152}, number = {Pt 10}, pages = {2931-2942}, doi = {10.1099/mic.0.29031-0}, pmid = {17005974}, issn = {1350-0872}, mesh = {Binding Sites/genetics ; Blotting, Southern ; Cloning, Molecular ; DNA Mutational Analysis ; DNA, Bacterial/chemistry/genetics ; Gene Deletion ; *Gene Duplication ; *Genes, Bacterial ; Genes, Regulator ; Genetic Complementation Test ; Iron/metabolism ; Methylosinus/*enzymology/genetics ; Molecular Sequence Data ; Mutation, Missense ; Operon ; Oxygenases/*genetics ; Phylogeny ; Pigments, Biological/physiology ; Protein Subunits/genetics ; Sequence Analysis, DNA ; }, abstract = {The soluble methane monooxygenase (sMMO) is a key enzyme for methane oxidation, and is found in only some methanotrophs, including Methylosinus sporium 5. sMMO expression is regulated at the level of transcription from a sigma(54) promoter by a copper-switch, and is only expressed when the copper-to-biomass ratio during growth is low. Extensive phylogenetic and genetic analyses of sMMOs and other soluble di-iron monooxygenases reveal that these enzymes have only been acquired relatively recently through horizontal gene transfer. In this study, further evidence of horizontal gene transfer was obtained, through cloning and sequencing of the genes encoding the sMMO enzyme complex plus the regulatory genes mmoG and mmoR, and identification of a duplicate copy of the mmoX gene in Ms. sporium. mmoX encodes the alpha subunit of the hydroxylase of the sMMO enzyme, which constitutes the active site (Prior &amp; Dalton, 1985). The mmoX genes were characterized at the molecular and biochemical levels. Although both copies were transcribed, only mmoX copy 1 was essential for sMMO activity. Construction of an sMMO(-) mutant by marker-exchange mutagenesis gave some possible insights into the role of the water-soluble pigment in siderophore-mediated iron acquisition. Finally, the amenability of Ms. sporium to genetic manipulation was demonstrated by complementing the sMMO(-) mutant by heterologous expression of sMMO genes from Methylosinus trichosporium OB3b and Methylococcus capsulatus (Bath), and it was shown that Ms. sporium could be used as an alternative model organism for molecular analysis of MMO regulation.}, }
@article {pmid17002548, year = {2006}, author = {Wu, TL and Chia, JH and Su, LH and Chu, C and Kuo, AJ and Chiu, CH}, title = {Dissemination of extended-spectrum beta-lactamase-producing Enterobacteriaceae in intensive care units of a medical center in Taiwan.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {12}, number = {3}, pages = {203-209}, doi = {10.1089/mdr.2006.12.203}, pmid = {17002548}, issn = {1076-6294}, mesh = {Enterobacteriaceae/*drug effects/enzymology/genetics/isolation &amp; purification ; Enterobacteriaceae Infections/epidemiology/microbiology/*transmission ; Gene Transfer, Horizontal ; Genotype ; *Hospitals, University ; Humans ; *Intensive Care Units ; Microbial Sensitivity Tests/methods ; Plasmids ; beta-Lactam Resistance ; beta-Lactamases/*biosynthesis/*genetics/metabolism ; }, abstract = {The prevalence of extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae in a tertiary hospital in Taiwan was assessed over a 16-month period. A total of 125 nonrepetitive ESBL-producing isolates of Enterobacter cloacae, Escherichia coli, and Klebsiella pneumoniae were available for investigation using molecular methods. Four predominant intensive care units (ICUs) were identified, and SHV-12 (59%), CTX-M- 3 (36%), and CTX-M-14 (14%) were the three most frequent ESBLs. SHV-12 was predominant among E. cloacae in the burn unit and K. pneumoniae in the other three chest medicine-related ICUs. CTX-M-3 was predominant among E. coli and K. pneumoniae in three other ICUs. The dissemination of ESBL-producing Enterobacteriaceae in four ICUs of a medical center in Taiwan is a consequence of the clonal dissemination of a few epidemic strains along with the horizontal transmission of resistance genes-carrying plasmids among bacterial organisms.}, }
@article {pmid17000138, year = {2007}, author = {Hughes, AL and Langley, KJ}, title = {Nucleotide usage, synonymous substitution pattern, and past recombination in genomes of Streptococcus pyogenes.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {7}, number = {2}, pages = {188-196}, doi = {10.1016/j.meegid.2006.08.003}, pmid = {17000138}, issn = {1567-1348}, support = {R01 GM043940/GM/NIGMS NIH HHS/United States ; R01 GM043940-18/GM/NIGMS NIH HHS/United States ; GM43940/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Substitution ; *Codon ; Discriminant Analysis ; *Evolution, Molecular ; *Genome, Bacterial ; Phylogeny ; *Recombination, Genetic ; Streptococcus pyogenes/*genetics ; }, abstract = {We examined (1) five variables summarizing nucleotide usage at synonymous sites; (2) pairwise patterns of nucleotide substitution among five genomes of Streptococcus pyogenes in order to examine the extent to which these variables are associated with past recombination events. Predicted prophage genes of MGAS10394 were characterized by an average pattern of nucleotide usage at synonymous sites that was distinct from that seen at most other genes. Ribosomal protein genes also showed a distinctive pattern, but one that differed from prophage genes in several key respects. The six most anomalous genes with respect to synonymous substitution in pairwise comparisons among the genomes included four prophage genes; these six genes were characterized by unusually high values of d(S), suggesting that these genes had different evolutionary histories from those of the other shared genes in the genome. This hypothesis was supported by phylogenetic analyses, which revealed phylogenies inconsistent with that of the majority of genes. Eighty-nine genes outside prophage regions were found to resemble prophage genes with respect to nucleotide content and the pattern of synonymous substitution, suggesting that these genes may have been involved in horizontal gene transfers. Although prophage genes do show distinctive patterns of nucleotide composition, the results indicated that those patterns were not in themselves sufficient to distinguish all known prophage genes from other genes. On the other hand, nucleotide content, when suitably measured, can form one of a set of biological indicators that can be used to identify candidate genes for horizontal gene transfer.}, }
@article {pmid16987614, year = {2006}, author = {Waller, RF and Keeling, PJ}, title = {Alveolate and chlorophycean mitochondrial cox2 genes split twice independently.}, journal = {Gene}, volume = {383}, number = {}, pages = {33-37}, doi = {10.1016/j.gene.2006.07.003}, pmid = {16987614}, issn = {0378-1119}, mesh = {Animals ; Apicomplexa/*enzymology/*genetics ; Chlorophyta/*enzymology/*genetics ; Dinoflagellida/enzymology/genetics ; Electron Transport Complex IV/*genetics ; *Evolution, Molecular ; Expressed Sequence Tags ; Gene Transfer, Horizontal ; *Genes, Mitochondrial ; *Genes, Protozoan ; Molecular Sequence Data ; Phylogeny ; Species Specificity ; }, abstract = {The mitochondrial gene for COXII is typically encoded in the organelle genome, however in some members of two unrelated groups, Apicomplexa and Chlorophyceae, cox2 is split into two genes, and both are encoded in the nucleus. Rare genomic changes (RGCs) have acquired popularity as phylogenetic markers, and accordingly this rearrangement of cox2 has been used to infer a possible source of the apicomplexan plastid, the apicoplast, a topic that continues to attract much debate. Accurate interpretation of RGCs, however, is critically dependent on appropriate sampling of the character state of interest amongst relevant taxa. Dinoflagellates form the sister taxon to Apicomplexa, and therefore the state of their cox2 is essential to the interpretation of this apparent RGC. Here we present the first complete cox2 data from dinoflagellates, that suggests despite the remarkable similarity of cox2 seen in Alveolates and Chlorophyceae, this gene reorganization arose independently in these two groups, not through lateral transfer as previously suggested.}, }
@article {pmid16986623, year = {2006}, author = {Ringemann, C and Ebenhöh, O and Heinrich, R and Ginsburg, H}, title = {Can biochemical properties serve as selective pressure for gene selection during inter-species and endosymbiotic lateral gene transfer?.}, journal = {Systems biology}, volume = {153}, number = {4}, pages = {212-222}, doi = {10.1049/ip-syb:20050082}, pmid = {16986623}, issn = {1741-2471}, mesh = {Animals ; Computer Simulation ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Humans ; *Models, Genetic ; Multienzyme Complexes/*genetics ; Phylogeny ; *Selection, Genetic ; Signal Transduction/*genetics ; Species Specificity ; Symbiosis/*genetics ; }, abstract = {During the evolution of endosymbiosis, only one orthologous gene, either from the invader or the invaded genome, is preserved. Genetic and environmental factors are usually invoked to explain this gene preference. How biochemical parameters can play a role in the selection of genes that code for enzymes that constitute a metabolic pathway is explored. Simple Michaelis-Menten-like enzymes are considered whose kinetic parameters are randomly generated to construct two parallel homologous pathways to account for the contributions of the invaded and the invader. Steady-state fluxes as targets of natural selection are focused. Enzymes are eliminated one by one so that the total flux through the pathway is least disturbed. Analysis of the results, done by different criteria, indicate that the maximal velocities, both forward and backward, are more influential in selection than the respective Michaelis constants. This inclination disappears as metabolite concentrations are increased. It is shown that kinetic selection criteria can result in a mosaicism of enzymes in the same pathway in terms of their genetic origin. Analysis of the results using the control coefficient paradigm disclosed an expected robust correlation between flux control coefficients of enzymes and their selective elimination. Similar analyses, performed for the case of single gene transfer or for gene replication with subsequent mutation, yielded essentially similar results. The results conform with the phenomenon of genetic mosaicism found in phylogenetic analyses of single or double endosymbioses and lateral gene transfer.}, }
@article {pmid16986517, year = {2006}, author = {Shen, LM and Wu, YN and Zhang, JZ and Zhou, PP}, title = {[Stability of hpt marker gene in transgenic rice in different food matrices and under varying food-processing conditions].}, journal = {Wei sheng yan jiu = Journal of hygiene research}, volume = {35}, number = {4}, pages = {431-434}, pmid = {16986517}, issn = {1000-8020}, mesh = {Food Handling/*methods ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genes, Plant/genetics ; Genetic Markers ; Methanobacterium/genetics ; Oryza/*genetics ; Phosphotransferases (Alcohol Group Acceptor)/*genetics ; Plants, Genetically Modified/*genetics ; Polymerase Chain Reaction/methods ; }, abstract = {OBJECTIVE: To estimate the likelihood of horizontal gene transfer from transgenic rice to bacteria of the food chain and human gut, the stability of s86 transgenic rice hpt gene in different food matrices and under varying food-processing conditions was studied.<br><br>METHODS: Degradation of DNA was monitored by fragment -multiplex polymerase chain reaction. Integrity of hpt gene in various food samples was tested.<br><br>RESULTS: A PCR system for the hpt gene of genetically modified rice has been established to detect fragments ranging between 236bp and 910bp. Detection of hpt and rbcl gene fragments was carried out in various food-processed samples by this PCR system. The data showed that the fragments up to 500 bp were detected in rice and congee, while the fragment length more than 236bp was not detected in crispy rice and popcorn-like rice.<br><br>CONCLUSION: These results suggested that there are significant differences in DNA degradation by different food-processing methods. The likelihood of the large hpt gene fragments transfer from transgenic rice processed food to bacteria is reduced by food process.}, }
@article {pmid16984631, year = {2006}, author = {Serra-Moreno, R and Acosta, S and Hernalsteens, JP and Jofre, J and Muniesa, M}, title = {Use of the lambda Red recombinase system to produce recombinant prophages carrying antibiotic resistance genes.}, journal = {BMC molecular biology}, volume = {7}, number = {}, pages = {31}, pmid = {16984631}, issn = {1471-2199}, mesh = {Algorithms ; Bacteriophage lambda/enzymology/*genetics ; Cloning, Molecular ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/genetics ; *Gene Transfer Techniques ; Gene Transfer, Horizontal ; Genetic Vectors ; Polymerase Chain Reaction/methods ; Prophages/*genetics/metabolism ; Recombinases/*metabolism ; Recombination, Genetic ; Shiga Toxins/genetics ; Transformation, Bacterial ; }, abstract = {BACKGROUND: The Red recombinase system of bacteriophage lambda has been used to inactivate chromosomal genes in E. coli K-12 through homologous recombination using linear PCR products. The aim of this study was to induce mutations in the genome of some temperate Shiga toxin encoding bacteriophages. When phage genes are in the prophage state, they behave like chromosomal genes. This enables marker genes, such as antibiotic resistance genes, to be incorporated into the stx gene. Once the phages' lytic cycle is activated, recombinant Shiga toxin converting phages are produced. These phages can transfer the marker genes to the bacteria that they infect and convert. As the Red system's effectiveness decreased when used for our purposes, we had to introduce significant variations to the original method. These modifications included: confirming the stability of the target stx gene increasing the number of cells to be transformed and using a three-step PCR method to produce the amplimer containing the antibiotic resistance gene.<br><br>RESULTS: Seven phages carrying two different antibiotic resistance genes were derived from phages that are directly involved in the pathogenesis of Shiga toxin-producing strains, using this modified protocol.<br><br>CONCLUSION: This approach facilitates exploration of the transduction processes and is a valuable tool for studying phage-mediated horizontal gene transfer.}, }
@article {pmid16982535, year = {2006}, author = {Chan, VS}, title = {Use of genetically modified viruses and genetically engineered virus-vector vaccines: environmental effects.}, journal = {Journal of toxicology and environmental health. Part A}, volume = {69}, number = {21}, pages = {1971-1977}, doi = {10.1080/15287390600751405}, pmid = {16982535}, issn = {1528-7394}, mesh = {*Environmental Pollution/adverse effects ; Gene Expression Regulation, Viral ; Gene Transfer, Horizontal ; *Genetic Engineering/adverse effects ; Genetic Vectors/adverse effects/*genetics ; Risk ; Risk Assessment ; Vaccines, DNA/adverse effects/*genetics ; Viral Vaccines/adverse effects/*genetics ; }, abstract = {Despite major therapeutic advances, infectious diseases remain highly problematic. Recent advancements in technology in producing DNA-based vaccines, together with the growing knowledge of the immune system, have provided new insights into the identification of the epitopes needed to target the development of highly targeted vaccines. Genetically modified (GM) viruses and genetically engineered virus-vector vaccines possess significant unpredictability and a number of inherent harmful potential hazards. For all these vaccines, safety assessment concerning unintended and unwanted side effects with regard to targeted vaccinees has always been the main focus. Important questions concerning effects on nontargeted individuals within the same species or other species remain unknown. Horizontal transfer of genes, though lacking supportive experimental or epidemiological investigations, is well established. New hybrid virus progenies resulting from genetic recombination between genetically engineered vaccine viruses and their naturally occurring relatives may possess totally unpredictable characteristics with regard to host preferences and disease-causing potentials. Furthermore, when genetically modified or engineered virus particles break down in the environment, their nuclei acids are released. Appropriate risk management is the key to minimizing any potential risks to humans and environment resulting from the use of these GM vaccines. There is inadequate knowledge to define either the probability of unintended events or the consequences of genetic modifications. The objective of this article is to highlight the limitations in environmental risk assessment and raise awareness of the potential risks involving the use of genetically modified viruses and genetically engineered virus-vector vaccines.}, }
@article {pmid16979565, year = {2006}, author = {Richards, TA and Dacks, JB and Jenkinson, JM and Thornton, CR and Talbot, NJ}, title = {Evolution of filamentous plant pathogens: gene exchange across eukaryotic kingdoms.}, journal = {Current biology : CB}, volume = {16}, number = {18}, pages = {1857-1864}, doi = {10.1016/j.cub.2006.07.052}, pmid = {16979565}, issn = {0960-9822}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Algal Proteins/classification/genetics ; Carrier Proteins/classification/genetics ; Eukaryotic Cells/classification ; *Evolution, Molecular ; Fungal Proteins/classification/genetics ; Fungi/classification/cytology/*genetics ; *Gene Transfer, Horizontal ; Multigene Family ; Oomycetes/classification/cytology/*genetics ; Phylogeny ; Plants/microbiology/parasitology ; }, abstract = {Filamentous fungi and oomycetes are eukaryotic microorganisms that grow by producing networks of thread-like hyphae, which secrete enzymes to break down complex nutrients, such as wood and plant material, and recover the resulting simple sugars and amino acids by osmotrophy. These organisms are extremely similar in both appearance and lifestyle and include some of the most economically important plant pathogens . However, the morphological similarity of fungi and oomycetes is misleading because they represent some of the most distantly related eukaryote evolutionary groupings, and their shared osmotrophic growth habit is interpreted as being the result of convergent evolution . The fungi branch with the animals, whereas the oomycetes branch with photosynthetic algae as part of the Chromalveolata . In this report, we provide strong phylogenetic evidence that multiple horizontal gene transfers (HGT) have occurred from filamentous ascomycete fungi to the distantly related oomycetes. We also present evidence that a subset of the associated gene families was initially the product of prokaryote-to-fungi HGT. The predicted functions of the gene products associated with fungi-to-oomycete HGT suggest that this process has played a significant role in the evolution of the osmotrophic, filamentous lifestyle on two separate branches of the eukaryote tree.}, }
@article {pmid16979549, year = {2006}, author = {Andersson, JO}, title = {Convergent evolution: gene sharing by eukaryotic plant pathogens.}, journal = {Current biology : CB}, volume = {16}, number = {18}, pages = {R804-6}, doi = {10.1016/j.cub.2006.08.042}, pmid = {16979549}, issn = {0960-9822}, mesh = {*Gene Transfer, Horizontal ; Magnaporthe/classification/*genetics ; *Phylogeny ; Phytophthora/classification/*genetics ; Plants/*microbiology/*parasitology ; }, abstract = {Oomycetes and filamentous parasitic fungi are plant pathogens that have undergone convergent evolution. A recent study has shown that these microbial eukaryotes have exchanged metabolic genes, which might explain some of their phenotypic similarities.}, }
@article {pmid16973226, year = {2006}, author = {Ivanetich, KM and Hsu, PH and Wunderlich, KM and Messenger, E and Walkup, WG and Scott, TM and Lukasik, J and Davis, J}, title = {Microbial source tracking by DNA sequence analysis of the Escherichia coli malate dehydrogenase gene.}, journal = {Journal of microbiological methods}, volume = {67}, number = {3}, pages = {507-526}, doi = {10.1016/j.mimet.2006.04.026}, pmid = {16973226}, issn = {0167-7012}, mesh = {Animals ; *Bacterial Typing Techniques ; Base Sequence ; Catalytic Domain/genetics ; Charadriiformes/microbiology ; Deer/microbiology ; Dogs ; Escherichia coli/*classification/*genetics/isolation &amp; purification ; Escherichia coli Infections/*microbiology ; Escherichia coli Proteins/chemistry/genetics ; Feces/microbiology ; Genes, Bacterial ; Horses/microbiology ; Humans ; Malate Dehydrogenase/chemistry/*genetics ; Molecular Epidemiology/*methods ; Molecular Sequence Data ; Mutation ; Polymorphism, Genetic ; Protein Structure, Tertiary ; Reproducibility of Results ; Sensitivity and Specificity ; *Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {Criteria for sub-typing of microbial organisms by DNA sequencing proposed by Olive and Bean were applied to several genes in Escherichia coli to identify targets for the development of microbial source tracking assays. Based on the aforementioned criteria, the icd (isocitrate dehydrogenase), and putP (proline permease) genes were excluded as potential targets due to their high rates of horizontal gene transfer; the rrs (16S rRNA) gene was excluded as a target due to the presence of multiple gene copies, with different sequences in a single genome. Based on the above criteria, the mdh (malate dehydrogenase) gene was selected as a target for development of a microbial source tracking assay. The mdh assay was optimized to analyze a 150 bp fragment corresponding to residues G191 to R240 (helices H10 and H11) of the Mdh catalytic domain. 295 fecal isolates (52 horse, 50 deer, 72 dog, 52 seagull and 69 human isolates) were sequenced and analyzed. Target DNA sequences for isolates from horse, dog plus deer, and seagull formed identifiable groupings. Sequences from human isolates, aside from a low level (ca. 15%) human specific sequence, did not group; nevertheless, other hosts could be distinguished from human. Positive and negative predictive values for two- and three-way host comparisons ranged from 60% to 90% depending on the focus host. False positive rates were below 10%. Multiple E. coli isolates from individual fecal samples exhibited high levels of sequence homogeneity, i.e. typically only one to two mdh sequences were observed per up to five E. coli isolates from a single fecal sample. Among all isolates sequenced from fecal samples from each host, sequence homogeneity decreased in the following order: horse>dog>deer>human and gull. For in-library isolates, blind analysis of fecal isolates (n=12) from four hosts known to contain host specific target sequences was 100% accurate and 100% reproducible for both DNA sequence and host identification. For blind analysis of non-library isolates, 18/19 isolates (94.7%) matched one or more library sequences for the corresponding host. Ten of eleven geographical outlier fecal isolates from Florida had mdh sequences that were identical to in-library sequences for the corresponding host from California. The mdh assay was successfully applied to environmental isolates from an underground telephone vault in California, with 4 of 5 isolates matching sequences in the mdh library. 146 sequences of the 645bp mdh fragment from five host sources were translated into protein sequence and aligned. Seven unique Mdh protein sequences, which contained eight polymorphic sites, were identified. Six of the polymorphic sites were in the NAD+ binding domain and two were in the catalytic domain. All of the polymorphic sites were located in surface exposed regions of the protein. None of the non-silent mutations of the Mdh protein were in the 150bp mdh target. The advantages and disadvantages of the assay compared to established source tracking methods are discussed.}, }
@article {pmid16972986, year = {2006}, author = {Rot, C and Goldfarb, I and Ilan, M and Huchon, D}, title = {Putative cross-kingdom horizontal gene transfer in sponge (Porifera) mitochondria.}, journal = {BMC evolutionary biology}, volume = {6}, number = {}, pages = {71}, pmid = {16972986}, issn = {1471-2148}, mesh = {Animals ; Base Sequence ; Ecosystem ; Electron Transport Complex IV/genetics ; Fungi/*genetics/physiology ; *Gene Transfer, Horizontal ; *Genes, Mitochondrial ; Introns ; Molecular Sequence Data ; Phylogeny ; Porifera/classification/*genetics/*microbiology ; RNA/chemistry/genetics ; RNA, Mitochondrial ; Sequence Alignment ; Symbiosis/*genetics ; }, abstract = {BACKGROUND: The mitochondrial genome of Metazoa is usually a compact molecule without introns. Exceptions to this rule have been reported only in corals and sea anemones (Cnidaria), in which group I introns have been discovered in the cox1 and nad5 genes. Here we show several lines of evidence demonstrating that introns can also be found in the mitochondria of sponges (Porifera).<br><br>RESULTS: A 2,349 bp fragment of the mitochondrial cox1 gene was sequenced from the sponge Tetilla sp. (Spirophorida). This fragment suggests the presence of a 1143 bp intron. Similar to all the cnidarian mitochondrial introns, the putative intron has group I intron characteristics. The intron is present in the cox1 gene and encodes a putative homing endonuclease. In order to establish the distribution of this intron in sponges, the cox1 gene was sequenced from several representatives of the demosponge diversity. The intron was found only in the sponge order Spirophorida. A phylogenetic analysis of the COI protein sequence and of the intron open reading frame suggests that the intron may have been transmitted horizontally from a fungus donor.<br><br>CONCLUSION: Little is known about sponge-associated fungi, although in the last few years the latter have been frequently isolated from sponges. We suggest that the horizontal gene transfer of a mitochondrial intron was facilitated by a symbiotic relationship between fungus and sponge. Ecological relationships are known to have implications at the genomic level. Here, an ecological relationship between sponge and fungus is suggested based on the genomic analysis.}, }
@article {pmid16971639, year = {2006}, author = {Balsalobre, L and Hernández-Madrid, A and Llull, D and Martín-Galiano, AJ and García, E and Fenoll, A and de la Campa, AG}, title = {Molecular characterization of disease-associated streptococci of the mitis group that are optochin susceptible.}, journal = {Journal of clinical microbiology}, volume = {44}, number = {11}, pages = {4163-4171}, pmid = {16971639}, issn = {0095-1137}, mesh = {Alleles ; Base Sequence ; Chromosomes, Bacterial ; Molecular Sequence Data ; Operon ; Quinine/*analogs &amp; derivatives/pharmacology ; Streptococcus mitis/drug effects/*genetics ; }, abstract = {Eight optochin-susceptible (Opt(s)) alpha-hemolytic (viridans) streptococcus isolates were characterized at the molecular level. These isolates showed phenotypic characteristics typical of both viridans streptococci and Streptococcus pneumoniae. Comparison of the sequence of housekeeping genes from these isolates with those of S. pneumoniae, Streptococcus mitis, Streptococcus oralis, and Streptococcus pseudopneumoniae suggested that the Opt(s) isolates corresponded to streptococci of the mitis group. Besides, the Opt(s) streptococci were negative by a Gen-Probe AccuProbe pneumococcus test and hybridized with specific pneumococcal probes (lytA and ply) but also with ant, a gene not present in most S. pneumoniae strains. Moreover, the isolates were insoluble in 1% sodium deoxycholate but completely dissolved in 0.1% deoxycholate. Sequence analysis of the lytA gene revealed that the Opt(s) streptococci carried lytA alleles characteristic of those present in nonpneumococcal streptococci of the mitis group. The determination of the partial nucleotide sequence embracing the atp operon encoding the F(o)F(1) H(+)-ATPase indicated that the optochin susceptibility of the isolates was due to the acquisition of atpC, atpA, and part of atpB from S. pneumoniae by horizontal gene transfer.}, }
@article {pmid16966682, year = {2006}, author = {Marri, PR and Hao, W and Golding, GB}, title = {Gene gain and gene loss in streptococcus: is it driven by habitat?.}, journal = {Molecular biology and evolution}, volume = {23}, number = {12}, pages = {2379-2391}, doi = {10.1093/molbev/msl115}, pmid = {16966682}, issn = {0737-4038}, mesh = {Adaptation, Biological ; *Ecosystem ; Evolution, Molecular ; *Gene Duplication ; Gene Transfer, Horizontal/physiology ; Genes, Bacterial/physiology ; Genome, Bacterial ; Loss of Heterozygosity/*physiology ; Models, Molecular ; Mutagenesis, Insertional ; Phylogeny ; Protein Conformation ; Species Specificity ; Streptococcus/classification/*genetics ; Streptococcus agalactiae/genetics ; Streptococcus mutans/genetics ; Streptococcus pneumoniae/genetics ; Streptococcus pyogenes/genetics ; Streptococcus thermophilus/genetics ; }, abstract = {Bacterial genomes can evolve either by gene gain, gene loss, mutating existing genes, and/or by duplication of existing genes. Recent studies have clearly demonstrated that the acquisition of new genes by lateral gene transfer (LGT) is a predominant force in bacterial evolution. To better understand the significance of LGT, we employed a comparative genomics approach to model species-specific and intraspecies gene insertions/deletions (ins/del among 12 sequenced streptococcal genomes using a maximum likelihood method. This study indicates that the rate of gene ins/del is higher on the external branches and varies dramatically for each species. We have analyzed here some of the experimentally characterized species-specific genes that have been acquired by LGT and conclude that at least a portion of these genes have a role in adaptation.}, }
@article {pmid16966401, year = {2006}, author = {Billington, SJ and Jost, BH}, title = {Multiple genetic elements carry the tetracycline resistance gene tet(W) in the animal pathogen Arcanobacterium pyogenes.}, journal = {Antimicrobial agents and chemotherapy}, volume = {50}, number = {11}, pages = {3580-3587}, pmid = {16966401}, issn = {0066-4804}, mesh = {Actinomycetaceae/*drug effects/*genetics/growth &amp; development ; Alleles ; Base Sequence ; Chromosome Mapping ; Cloning, Molecular ; DNA Transposable Elements/genetics ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Molecular Sequence Data ; Reverse Transcriptase Polymerase Chain Reaction ; Tetracycline Resistance/genetics ; }, abstract = {The tet(W) gene is associated with tetracycline resistance in a wide range of bacterial species, including obligately anaerobic rumen bacteria and isolates from the human gut and oral mucosa. However, little is known about how this gene is disseminated and the types of genetic elements it is carried on. We examined tetracycline-resistant isolates of the animal commensal and opportunistic pathogen Arcanobacterium pyogenes, all of which carried tet(W), and identified three genetic elements designated ATE-1, ATE-2, and ATE-3. These elements were found in 25%, 35%, and 60% of tetracycline-resistant isolates, respectively, with some strains carrying both ATE-2 and ATE-3. ATE-1 shows characteristics of a mobilizable transposon, and the tet(W) genes from strains carrying this element can be transferred at low frequencies between A. pyogenes strains. ATE-2 has characteristics of a simple transposon, carrying only the resistance gene and a transposase, while in ATE-3, the tet(W) gene is associated with a streptomycin resistance gene that is 100% identical at the DNA level with the aadE gene from the Campylobacter jejuni plasmid pCG8245. Both ATE-2 and ATE-3 show evidence of being carried on larger genetic elements, but conjugation to other strains was not observed under the conditions tested. ATE-1 was preferentially associated with A. pyogenes strains of bovine origin, while ATE-2 and ATE-3 elements were primarily found in porcine isolates, suggesting that these elements may circulate in different environments. In addition, four alleles of the tet(W) gene, primarily associated with different elements, were detected among A. pyogenes isolates.}, }
@article {pmid16963634, year = {2006}, author = {Richards, TA and Dacks, JB and Campbell, SA and Blanchard, JL and Foster, PG and McLeod, R and Roberts, CW}, title = {Evolutionary origins of the eukaryotic shikimate pathway: gene fusions, horizontal gene transfer, and endosymbiotic replacements.}, journal = {Eukaryotic cell}, volume = {5}, number = {9}, pages = {1517-1531}, pmid = {16963634}, issn = {1535-9778}, support = {R01 AI43228/AI/NIAID NIH HHS/United States ; AI27530/AI/NIAID NIH HHS/United States ; R01 AI027530/AI/NIAID NIH HHS/United States ; R01 AI043228/AI/NIAID NIH HHS/United States ; //Wellcome Trust/United Kingdom ; }, mesh = {Alcohol Oxidoreductases/genetics/metabolism ; Amino Acids, Aromatic/biosynthesis ; Animals ; Bacteria/genetics/metabolism ; Eukaryota/genetics/metabolism ; Eukaryotic Cells/metabolism ; *Evolution, Molecular ; Fungi/genetics/metabolism ; Gene Fusion/genetics ; Gene Transfer, Horizontal/genetics ; Hydro-Lyases/genetics/metabolism ; Lyases/genetics/metabolism ; Models, Genetic ; Multienzyme Complexes/genetics/metabolism ; Phosphotransferases (Alcohol Group Acceptor)/genetics/metabolism ; *Phylogeny ; Plants/genetics/metabolism ; Prokaryotic Cells/metabolism ; Shikimic Acid/*metabolism ; Symbiosis/genetics ; Transferases/genetics/metabolism ; }, abstract = {Currently the shikimate pathway is reported as a metabolic feature of prokaryotes, ascomycete fungi, apicomplexans, and plants. The plant shikimate pathway enzymes have similarities to prokaryote homologues and are largely active in chloroplasts, suggesting ancestry from the plastid progenitor genome. Toxoplasma gondii, which also possesses an alga-derived plastid organelle, encodes a shikimate pathway with similarities to ascomycete genes, including a five-enzyme pentafunctional arom. These data suggests that the shikimate pathway and the pentafunctional arom either had an ancient origin in the eukaryotes or was conveyed by eukaryote-to-eukaryote horizontal gene transfer (HGT). We expand sampling and analyses of the shikimate pathway genes to include the oomycetes, ciliates, diatoms, basidiomycetes, zygomycetes, and the green and red algae. Sequencing of cDNA from Tetrahymena thermophila confirmed the presence of a pentafused arom, as in fungi and T. gondii. Phylogenies and taxon distribution suggest that the arom gene fusion event may be an ancient eukaryotic innovation. Conversely, the Plantae lineage (represented here by both Viridaeplantae and the red algae) acquired different prokaryotic genes for all seven steps of the shikimate pathway. Two of the phylogenies suggest a derivation of the Plantae genes from the cyanobacterial plastid progenitor genome, but if the full Plantae pathway was originally of cyanobacterial origin, then the five other shikimate pathway genes were obtained from a minimum of two other eubacterial genomes. Thus, the phylogenies demonstrate both separate HGTs and shared derived HGTs within the Plantae clade either by primary HGT transfer or secondarily via the plastid progenitor genome. The shared derived characters support the holophyly of the Plantae lineage and a single ancestral primary plastid endosymbiosis. Our analyses also pinpoints a minimum of 50 gene/domain loss events, demonstrating that loss and replacement events have been an important process in eukaryote genome evolution.}, }
@article {pmid16963556, year = {2006}, author = {Miyazaki, R and Sato, Y and Ito, M and Ohtsubo, Y and Nagata, Y and Tsuda, M}, title = {Complete nucleotide sequence of an exogenously isolated plasmid, pLB1, involved in gamma-hexachlorocyclohexane degradation.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {11}, pages = {6923-6933}, pmid = {16963556}, issn = {0099-2240}, mesh = {Alphaproteobacteria/enzymology/genetics/isolation &amp; purification ; *Base Sequence ; Biodegradation, Environmental ; Conjugation, Genetic ; DNA Transposable Elements ; Gene Transfer, Horizontal ; Hexachlorocyclohexane/*metabolism ; Hydrolases/chemistry/*genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; Plasmids/genetics/*isolation &amp; purification ; Sequence Analysis, DNA ; Soil Microbiology ; Soil Pollutants/*metabolism ; }, abstract = {The alpha-proteobacterial strain Sphingobium japonicum UT26 utilizes a highly chlorinated pesticide, gamma-hexachlorocyclohexane (gamma-HCH), as a sole source of carbon and energy, and haloalkane dehalogenase LinB catalyzes the second step of gamma-HCH degradation in UT26. Functional complementation of a linB mutant of UT26, UT26DB, was performed by the exogenous plasmid isolation technique using HCH-contaminated soil, leading to our successful identification of a plasmid, pLB1, carrying the linB gene. Complete sequencing analysis of pLB1, with a size of 65,998 bp, revealed that it carries (i) 50 totally annotated coding sequences, (ii) an IS6100 composite transposon containing two copies of linB, and (iii) potential genes for replication, maintenance, and conjugative transfer with low levels of similarity to other homologues. A minireplicon assay demonstrated that a 2-kb region containing the predicted repA gene and its upstream region of pLB1 functions as an autonomously replicating unit in UT26. Furthermore, pLB1 was conjugally transferred from UT26DB to other alpha-proteobacterial strains but not to any of the beta- or gamma-proteobacterial strains examined to date. These results suggest that this exogenously isolated novel plasmid contributes to the dissemination of at least some genes for gamma-HCH degradation in the natural environment. To the best of our knowledge, this is the first detailed report of a plasmid involved in gamma-HCH degradation.}, }
@article {pmid16962258, year = {2006}, author = {Ledger, TN and Jaubert, S and Bosselut, N and Abad, P and Rosso, MN}, title = {Characterization of a new beta-1,4-endoglucanase gene from the root-knot nematode Meloidogyne incognita and evolutionary scheme for phytonematode family 5 glycosyl hydrolases.}, journal = {Gene}, volume = {382}, number = {}, pages = {121-128}, doi = {10.1016/j.gene.2006.06.023}, pmid = {16962258}, issn = {0378-1119}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cellulase/*genetics ; Cloning, Molecular ; DNA, Complementary/genetics ; DNA, Helminth/genetics ; *Evolution, Molecular ; Gene Expression ; Gene Transfer, Horizontal ; *Genes, Helminth ; Glycoside Hydrolases/genetics ; Models, Genetic ; Molecular Sequence Data ; Multigene Family ; Nematoda/enzymology/genetics/pathogenicity ; Phylogeny ; Plant Diseases/parasitology ; Sequence Homology, Amino Acid ; Tylenchoidea/*enzymology/*genetics/pathogenicity ; }, abstract = {Cellulases from plant parasitic nematodes are encoded by multiple gene families and are thought to originate from horizontal gene transfer. Unraveling the evolution of these genes in the phylum will help understanding the evolution of plant parasitism in nematodes. Here we describe a new gene, named MI-eng-2, that encodes a family 5 glycosyl hydrolase (GHF5) with a predicted signal peptide and devoid of linker domain and cellulose-binding domain. The beta-1,4-endoglucanase activity of the protein MI-ENG-2 was confirmed in vitro and the transcription of the gene was localized in the secretory oesophageal glands of infective juveniles, suggesting that MI-ENG-2 is involved in plant cell wall degradation during parasitism. Phylogenetic and exon/intron structure analyses of beta-1,4-endoglucanase genes in the order Tylenchida strengthen the hypothesis that nematode GHF5 genes result from horizontal gene transfer of a bacterial gene with a cellulose-binding domain. GHF5 gene families in Tylenchida result from gene duplications associated with occasional loss of the cellulose-binding domain and the linker domain during their evolution.}, }
@article {pmid16957983, year = {2006}, author = {Jeudy, S and Claverie, JM and Abergel, C}, title = {The nucleoside diphosphate kinase from mimivirus: a peculiar affinity for deoxypyrimidine nucleotides.}, journal = {Journal of bioenergetics and biomembranes}, volume = {38}, number = {3-4}, pages = {247-254}, pmid = {16957983}, issn = {0145-479X}, mesh = {Acanthamoeba/*virology ; Amino Acid Sequence ; Animals ; Base Sequence ; DNA Viruses/*enzymology ; Kinetics ; Molecular Sequence Data ; Nucleoside-Diphosphate Kinase/*genetics/*metabolism ; *Phylogeny ; Pyrimidines/metabolism ; Sequence Analysis, DNA ; }, abstract = {The first viral Nucleoside Diphosphate Kinase was recently identified in the giant double-stranded DNA virus Acanthamoeba polyphag a Mimivirus (ApM). Here we report its expression and detailed biochemical characterization. NDK(apm) exhibits unique features such as a shorter Kpn-loop, a structural motif previously reported to be part of the active site and involved in oligomer formation. Enzymatic activity measurements on the recombinant NDK(apm) revealed its preferential affinity for deoxypyrimidine nucleotides. This property might represent an adaptation of NDK(apm) to the production of the limiting TTP deoxynucleotide required for the replication of the large A+T rich (72%) viral genome. The NDK(apm) might also assume a role in dUTP detoxification to compensate for the surprising absence of Mimivirus dUTPase (deoxyuridine triphosphate pyrophosphatase) an important enzyme conserved in most viruses. Although the phylogenetic analysis of NDK sequences sampled through organisms from the three domains of life is only partially informative, it favors an ancestral origin for NDK(apm) over a recent acquisition from a eukaryotic organism by horizontal gene transfer.}, }
@article {pmid16956972, year = {2006}, author = {Choulet, F and Aigle, B and Gallois, A and Mangenot, S and Gerbaud, C and Truong, C and Francou, FX and Fourrier, C and Guérineau, M and Decaris, B and Barbe, V and Pernodet, JL and Leblond, P}, title = {Evolution of the terminal regions of the Streptomyces linear chromosome.}, journal = {Molecular biology and evolution}, volume = {23}, number = {12}, pages = {2361-2369}, doi = {10.1093/molbev/msl108}, pmid = {16956972}, issn = {0737-4038}, mesh = {Chromosome Structures ; *Chromosomes, Bacterial/chemistry ; Conserved Sequence ; *Evolution, Molecular ; Genetic Drift ; Genetic Variation ; Genome, Bacterial ; Streptomyces/*genetics ; Streptomyces coelicolor/genetics ; Synteny ; }, abstract = {Comparative analysis of the Streptomyces chromosome sequences, between Streptomyces coelicolor, Streptomyces avermitilis, and Streptomyces ambofaciens ATCC23877 (whose partial sequence is released in this study), revealed a highly compartmentalized genetic organization of their genome. Indeed, despite the presence of specific genomic islands, the central part of the chromosome appears highly syntenic. In contrast, the chromosome of each species exhibits large species-specific terminal regions (from 753 to 1,393 kb), even when considering closely related species (S. ambofaciens and S. coelicolor). Interestingly, the size of the central conserved region between species decreases as the phylogenetic distance between them increases, whereas the specific terminal fraction reciprocally increases in size. Between highly syntenic central regions and species-specific chromosomal parts, there is a notable degeneration of synteny due to frequent insertions/deletions. This reveals a massive and constant genomic flux (from lateral gene transfer and DNA rearrangements) affecting the terminal contingency regions. We speculate that a gradient of recombination rate (i.e., insertion/deletion events) toward the extremities is the force driving the exclusion of essential genes from the terminal regions (i.e., chromosome compartmentalization) and generating a fast gene turnover for strong adaptation capabilities.}, }
@article {pmid16956407, year = {2006}, author = {Rice, DW and Palmer, JD}, title = {An exceptional horizontal gene transfer in plastids: gene replacement by a distant bacterial paralog and evidence that haptophyte and cryptophyte plastids are sisters.}, journal = {BMC biology}, volume = {4}, number = {}, pages = {31}, pmid = {16956407}, issn = {1741-7007}, support = {R01 GM035087/GM/NIGMS NIH HHS/United States ; R01 GM070612/GM/NIGMS NIH HHS/United States ; GM-35087/GM/NIGMS NIH HHS/United States ; GM-70612/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; *Gene Transfer, Horizontal ; *Genes, Plant ; Oenothera/genetics ; Plants/*genetics ; Plastids/*genetics ; Rhodophyta/genetics ; Symbiosis ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT) to the plant mitochondrial genome has recently been shown to occur at a surprisingly high rate; however, little evidence has been found for HGT to the plastid genome, despite extensive sequencing. In this study, we analyzed all genes from sequenced plastid genomes to unearth any neglected cases of HGT and to obtain a measure of the overall extent of HGT to the plastid.<br><br>RESULTS: Although several genes gave strongly supported conflicting trees under certain conditions, we are confident of HGT in only a single case beyond the rubisco HGT already reported. Most of the conflicts involved near neighbors connected by long branches (e.g. red algae and their secondary hosts), where phylogenetic methods are prone to mislead. However, three genes--clpP, ycf2, and rpl36--provided strong support for taxa moving far from their organismal position. Further taxon sampling of clpP and ycf2 resulted in rejection of HGT due to long-branch attraction and a serious error in the published plastid genome sequence of Oenothera elata, respectively. A single new case, a bacterial rpl36 gene transferred into the ancestor of the cryptophyte and haptophyte plastids, appears to be a true HGT event. Interestingly, this rpl36 gene is a distantly related paralog of the rpl36 type found in other plastids and most eubacteria. Moreover, the transferred gene has physically replaced the native rpl36 gene, yet flanking genes and intergenic regions show no sign of HGT. This suggests that gene replacement somehow occurred by recombination at the very ends of rpl36, without the level and length of similarity normally expected to support recombination.<br><br>CONCLUSION: The rpl36 HGT discovered in this study is of considerable interest in terms of both molecular mechanism and phylogeny. The plastid acquisition of a bacterial rpl36 gene via HGT provides the first strong evidence for a sister-group relationship between haptophyte and cryptophyte plastids to the exclusion of heterokont and alveolate plastids. Moreover, the bacterial gene has replaced the native plastid rpl36 gene by an uncertain mechanism that appears inconsistent with existing models for the recombinational basis of gene conversion.}, }
@article {pmid16955236, year = {2006}, author = {Dohm, JC and Vingron, M and Staub, E}, title = {Horizontal gene transfer in aminoacyl-tRNA synthetases including leucine-specific subtypes.}, journal = {Journal of molecular evolution}, volume = {63}, number = {4}, pages = {437-447}, pmid = {16955236}, issn = {0022-2844}, mesh = {Archaea/enzymology ; Bacteria/enzymology ; Gene Transfer, Horizontal/*genetics ; Isoenzymes/chemistry/genetics ; Leucine/*genetics ; Leucine-tRNA Ligase/chemistry/*genetics/*metabolism ; Phylogeny ; Protein Structure, Tertiary ; Yeasts/enzymology ; }, abstract = {Aminoacyl-tRNA synthetases catalyze a fundamental reaction for the flow of genetic information from RNA to protein. Their presence in all organisms known today highlights their important role in the early evolution of life. We investigated the evolutionary history of aminoacyl-tRNA synthetases on the basis of sequence data from more than 200 Archaea, Bacteria, and Eukaryota. Phylogenetic profiles are in agreement with previous observations that many genes for aminoacyl-tRNA synthetases were transferred horizontally between species from all domains of life. We extended these findings by a detailed analysis of the history of leucyl-tRNA synthetases. Thereby, we identified a previously undetected case of horizontal gene transfer from Bacteria to Archaea based on phylogenetic profiles, trees, and networks. This means that, finally, the last subfamily of aminoacyl-tRNA synthetases has lost its exceptional position as the sole subfamily that is devoid of horizontal gene transfer. Furthermore, the leucyl-tRNA synthetase phylogenetic tree suggests a dichotomy of the archaeal/eukaryotic-cytosolic and bacterial/eukaryotic-mitochondrial proteins. We argue that the traditional division of life into Prokaryota (non-chimeric) and Eukaryota (chimeric) is favorable compared to Woese's trichotomy into Archaea/Bacteria/Eukaryota.}, }
@article {pmid16953419, year = {2006}, author = {Miranda, LM and Murphy, JP and Marshall, D and Leath, S}, title = {Pm34: a new powdery mildew resistance gene transferred from Aegilops tauschii Coss. to common wheat (Triticum aestivum L.).}, journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik}, volume = {113}, number = {8}, pages = {1497-1504}, pmid = {16953419}, issn = {0040-5752}, mesh = {*Ascomycota ; Chromosomes, Plant/genetics ; Gene Transfer, Horizontal ; Genes, Plant/*physiology ; Microsatellite Repeats ; Physical Chromosome Mapping ; Plant Diseases/*genetics/microbiology ; Plants, Genetically Modified/genetics/microbiology ; Poaceae/*genetics ; Triticum/*genetics/microbiology ; }, abstract = {Powdery mildew is a major fungal disease in wheat growing areas worldwide. A novel source of resistance to wheat powdery mildew present in the germplasm line NC97BGTD7 was genetically characterized as a monogenic trait in greenhouse and field trials using F(2) derived lines from a NC97BGTD7 X Saluda cross. Microsatellite markers were used to map and tag this resistance gene, now designated Pm34. Three co-dominant microsatellite markers linked to Pm34 were identified and their most likely order was established as: Xbarc177-5D, 5.4cM, Pm34, 2.6cM, Xbarc144-5D, 14cM, Xgwm272-5D. These microsatellite markers were previously mapped to the long arm of the 5D chromosome and their positions were confirmed using Chinese Spring nullitetrasomic Nulli5D-tetra5A and ditelosomic Dt5DL lines. Pm2, the only other known Pm gene on chromosome 5D, has been mapped to the short arm and its specificity is different from that of Pm34.}, }
@article {pmid16952013, year = {2006}, author = {Uh, M and Khattra, J and Devlin, RH}, title = {Transgene constructs in coho salmon (Oncorhynchus kisutch) are repeated in a head-to-tail fashion and can be integrated adjacent to horizontally-transmitted parasite DNA.}, journal = {Transgenic research}, volume = {15}, number = {6}, pages = {711-727}, pmid = {16952013}, issn = {0962-8819}, mesh = {Animals ; DNA, Helminth/*genetics ; Gene Targeting/*methods ; *Gene Transfer, Horizontal ; Genetic Engineering ; Growth Hormone/genetics ; Microinjections ; Pseudogenes ; Salmon ; Schistosoma japonicum/genetics ; Sequence Analysis, DNA ; Sequence Deletion ; *Tandem Repeat Sequences ; Transgenes/*genetics ; }, abstract = {Currently, little information is available regarding the molecular organization of integrated transgenes in genetically-engineered fish. We performed a detailed structural analysis of an inserted transgene in one strain (M77) of transgenic coho salmon (Oncorhynchus kisutch) containing a salmon growth hormone gene construct (OnMTGH1). Microinjected DNA was found to have inserted into a single site in the coho salmon genome, and was organized with four complete internal copies and two partial terminal copies of the OnMTGH1 construct. All construct copies were organized in a direct-tandem (head-to-tail) repeat fashion in strain M77 and five additional strains (one also possessed a second recombinant junction fragment). For strain M77, the junctions between the transgene insert and the insertion point within the wild-type genome were cloned from strain-specific cosmid libraries and sequenced, revealing that the transgene insertion was accompanied by a deletion of 587 bp of wild-type DNA as well as a small insertion (19 bp) of unknown DNA upstream and a 14 bp direct- tandem duplication of sequence downstream. Upstream and downstream wild-type DNA sequence contained several repetitive sequence elements based on Southern blot analysis and homology to repetitive sequences in GenBank. In the downstream flank, a pseudogene sequence was also identified which has high homology to the CA membrane protein gene from Schistosoma japonicum, a parasite closely related to Sanguinicola sp. parasites which infect salmonids. Whether the presence of an inserted transgene and the presence of potentially horizontally-transmitted DNA are indicative of a genomic region with a predisposition for insertion of foreign DNA requires further study. The information derived from this transgene structure provides information useful for comparison to other transgenic organisms and for determination of the mechanism of transgene integration in lower vertebrates.}, }
@article {pmid16947059, year = {2006}, author = {Saha, MC and Cooper, JD and Mian, MA and Chekhovskiy, K and May, GD}, title = {Tall fescue genomic SSR markers: development and transferability across multiple grass species.}, journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik}, volume = {113}, number = {8}, pages = {1449-1458}, pmid = {16947059}, issn = {0040-5752}, mesh = {Base Sequence ; DNA Primers/genetics ; Festuca/*genetics ; *Gene Transfer, Horizontal ; Genetic Markers ; *Genome, Plant ; Genomic Library ; Minisatellite Repeats/*genetics ; Molecular Sequence Data ; Polymorphism, Genetic ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Simple sequence repeat (SSR) markers are highly informative and widely used for genetic and breeding studies. Currently, a very limited number of SSR markers are available for tall fescue (Festuca arundinacea Schreb.) and other forage grass species. A tall fescue genomic library enriched in (GA/CT)(n) repeats was used to develop primer pairs (PPs) flanking SSRs and assess PP functionality across different forage, cereal, and turf grass species. A total of 511 PPs were developed and assessed for their utility in six different grass species. The parents and a subset of a tall fescue mapping population were used to select PPs for mapping in tall fescue. Survey results revealed that 48% (in rice) to 66% (in tall fescue) of the PPs produced clean SSR-type amplification products in different grass species. Polymorphism rates were higher in tall fescue (68%) compared to other species (46% ryegrass, 39% wheat, and 34% rice). A set of 194 SSR loci (38%) were identified which amplified across all six species. Loci segregating in the tall fescue mapping population were grouped as loci segregating from the female parent (HD28-56, 37%), the male parent (R43-64, 37%), and both parents (26%). Three percent of the loci that were polymorphic between parents were monomorphic in the pseudo F1 mapping population and the remaining loci segregated. Sequencing of amplified products obtained from PP NFFAG428 revealed a very high level of sequence similarity among the grass species under study. Our results are the first report of genomic SSR marker development from tall fescue and they demonstrate the usefulness of these SSRs for genetic linkage mapping in tall fescue and cross-species amplification.}, }
@article {pmid16946263, year = {2006}, author = {Draghi, JA and Turner, PE}, title = {DNA secretion and gene-level selection in bacteria.}, journal = {Microbiology (Reading, England)}, volume = {152}, number = {Pt 9}, pages = {2683-2688}, doi = {10.1099/mic.0.29013-0}, pmid = {16946263}, issn = {1350-0872}, mesh = {Bacteria/*genetics ; Biological Evolution ; DNA, Bacterial/*metabolism ; Gene Transfer, Horizontal ; Genetics, Population ; Models, Genetic ; *Selection, Genetic ; Transformation, Bacterial ; }, abstract = {Natural genetic transformation can facilitate gene transfer in many genera of bacteria and requires the presence of extracellular DNA. Although cell lysis can contribute to this extracellular DNA pool, several studies have suggested that the secretion of DNA from living bacteria may also provide genetic material for transformation. This paper reviews the evidence for specific secretion of DNA from intact bacteria into the extracellular environment and examines this behaviour from a population-genetics perspective. A mathematical model demonstrates that the joint action of DNA secretion and transformation creates a novel type of gene-level natural selection. This model demonstrates that gene-level selection could explain the existence of DNA secretion mechanisms that provide no benefit to individual cells or populations of bacteria. Additionally, the model predicts that any trait affecting DNA secretion will experience selection at the gene level in a transforming population. This analysis confirms that the secretion of DNA from intact bacterial cells is fully explicable with evolutionary theory, and reveals a novel mechanism for bacterial evolution.}, }
@article {pmid16945402, year = {2006}, author = {Zhu, B}, title = {Degradation of plasmid and plant DNA in water microcosms monitored by natural transformation and real-time polymerase chain reaction (PCR).}, journal = {Water research}, volume = {40}, number = {17}, pages = {3231-3238}, doi = {10.1016/j.watres.2006.06.040}, pmid = {16945402}, issn = {0043-1354}, mesh = {Bacillus thuringiensis/metabolism ; Base Sequence ; DNA Primers ; DNA, Plant/*metabolism ; *Ecosystem ; *Environmental Monitoring ; Plants, Genetically Modified/genetics ; Plasmids/*metabolism ; Polymerase Chain Reaction/*methods ; Pseudomonas stutzeri/genetics ; Zea mays/genetics ; }, abstract = {Extracellular DNA exists in the environment and can be taken up by competent bacterial cells, leading to horizontal gene transfer. The persistence of extracellular plasmid and plant DNA in water microcosms was monitored in this study. Water samples were two groundwater (GW1 and GW2) and one river water (RW) samples. Three treatments included: (1) intact, (2) 0.22 microm filter-sterilized, and (3) autoclaved water. DNA from a plasmid (pNS1) and a transgenic Bt (Bacillus thuringiensis) corn line, both carrying a neomycin phosphotransferase gene (nptII gene) conferring kanamycin and neomycin resistance, was inoculated into the microcosms at 0.4 and 0.8 microg/ml, respectively. By monitoring its ability to transform a competent Pseudomonas stutzeri strain harboring plasmid pMR7 (P. stutzeri pMR7), plasmid DNA was degraded to undetectable levels in the intact and/or filter-sterilized water treatments within 48-96 h in GW1, GW2, and RW. Meanwhile, plasmid DNA persisted in the autoclaved treatment throughout the entire incubation period. For plant DNA, a highly sensitive real-time PCR method using SYBR Green I was developed to monitor the degradation dynamics of the nptII gene carried by the transgenic corn line in the microcosms. The results showed that the concentration of plant DNA was reduced by two orders of magnitude (from 0.8-0.008 microg/ml) within 96 h in the intact and filter-sterilized treatments of GW1, GW2, and RW, in contrast to its persistence in the autoclaved treatment. In addition, no kanamycin resistant (Km R) transformants were detected from in situ transformation of P. stutzeri pMR7 with plasmid pNS1 DNA.}, }
@article {pmid16940080, year = {2006}, author = {Robinson, DA and Sutcliffe, JA and Tewodros, W and Manoharan, A and Bessen, DE}, title = {Evolution and global dissemination of macrolide-resistant group A streptococci.}, journal = {Antimicrobial agents and chemotherapy}, volume = {50}, number = {9}, pages = {2903-2911}, pmid = {16940080}, issn = {0066-4804}, support = {AI053826/AI/NIAID NIH HHS/United States ; R01 AI053826/AI/NIAID NIH HHS/United States ; R01 GM060793/GM/NIGMS NIH HHS/United States ; GM060793/GM/NIGMS NIH HHS/United States ; R21 AI061454/AI/NIAID NIH HHS/United States ; AI061454/AI/NIAID NIH HHS/United States ; R56 AI053826/AI/NIAID NIH HHS/United States ; }, mesh = {*Biological Evolution ; Disease Transmission, Infectious ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Genetic Variation ; Humans ; Macrolides/*pharmacology ; Streptococcal Infections/microbiology ; Streptococcus pyogenes/*drug effects/*genetics/isolation &amp; purification/pathogenicity ; Virulence/genetics ; }, abstract = {Macrolide-resistant group A streptococci (MRGAS) have been recovered from many countries worldwide. However, the strain typing information that is available has been insufficient for estimating the total number of macrolide-resistant clones, their geographic distributions, and their evolutionary relationships. In this study, sequence-based strain typing was used to characterize 212 MRGAS isolates from 34 countries. Evaluation of clonal complexes, emm type, and resistance gene content [erm(A), erm(B), mef(A), and undefined] indicate that macrolide resistance was acquired by GAS organisms via > or independent genetic events. In contrast to other collections of mostly susceptible GAS, genetic diversification of MRGAS clones has occurred primarily by mutation rather than by recombination. Twenty-two MRGAS clonal complexes were recovered from more than one continent; intercontinental strains represent nearly 80% of the MRGAS isolates under study. The findings suggest that horizontal transfer of macrolide resistance genes to numerous genetic backgrounds and global dissemination of resistant clones and their descendants are both major components of the present-day macrolide resistance problem found within this species.}, }
@article {pmid16940079, year = {2006}, author = {Mangalappalli-Illathu, AK and Korber, DR}, title = {Adaptive resistance and differential protein expression of Salmonella enterica serovar Enteritidis biofilms exposed to benzalkonium chloride.}, journal = {Antimicrobial agents and chemotherapy}, volume = {50}, number = {11}, pages = {3588-3596}, pmid = {16940079}, issn = {0066-4804}, mesh = {Adaptation, Physiological/genetics ; Anti-Infective Agents, Local/*pharmacology ; Bacterial Proteins/*biosynthesis/genetics ; Benzalkonium Compounds/*pharmacology ; Biofilms/drug effects/*growth &amp; development ; Biomass ; Culture Media ; Drug Resistance, Bacterial/genetics ; Electrophoresis, Polyacrylamide Gel ; Fluorescent Dyes ; Gene Transfer, Horizontal ; Image Processing, Computer-Assisted ; Microbial Sensitivity Tests ; Mutation ; Phenotype ; Salmonella enteritidis/*drug effects/genetics/*metabolism ; }, abstract = {The development of adaptive resistance of Salmonella enterica serovar Enteritidis ATCC 4931 biofilms following exposure to benzalkonium chloride (BC) either continuously (1 microg ml(-1)) or intermittently (10 microg ml(-1) for 10 min daily) was examined. Biofilms adapted to BC over a 144-h period could survive a normally lethal BC challenge (500 microg ml(-1) for 10 min) and then regrow, as determined by increases in biofilm thickness, total biomass, and the ratio of the viable biomass to the nonviable biomass. Exposure of untreated control biofilms to the lethal BC challenge resulted in biofilm erosion and cell death. Proteins found to be up-regulated following BC adaptation were those involved in energy metabolism (TpiA and Eno), amino acid and protein biosynthesis (WrbA, TrxA, RplL, Tsf, Tuf, DsbA, and RpoZ), nutrient binding (FruB), adaptation (CspA), detoxification (Tpx, SodB, and a probable peroxidase), and degradation of 1,2-propanediol (PduJ and PduA). A putative universal stress protein (YnaF) was also found to be up-regulated. Proteins involved in proteolysis (DegQ), cell envelope formation (RfbH), adaptation (UspA), heat shock response (DnaK), and broad regulatory functions (Hns) were found to be down-regulated following adaptation. An overall increase in cellular protein biosynthesis was deduced from the significant up-regulation of ribosomal subunit proteins, translation elongation factors, and amino acid biosynthesis protein and down-regulation of serine endoprotease. The cold shock response, stress response, and detoxification are suggested to play roles in the adaptive resistance of Salmonella serovar Enteritidis biofilms to BC.}, }
@article {pmid16939619, year = {2006}, author = {Schwarzenlander, C and Averhoff, B}, title = {Characterization of DNA transport in the thermophilic bacterium Thermus thermophilus HB27.}, journal = {The FEBS journal}, volume = {273}, number = {18}, pages = {4210-4218}, doi = {10.1111/j.1742-4658.2006.05416.x}, pmid = {16939619}, issn = {1742-464X}, mesh = {Adenosine Triphosphatases/antagonists &amp; inhibitors ; Biological Transport ; Chromosomes, Bacterial/metabolism ; DNA/chemistry/*metabolism ; DNA, Archaeal/metabolism ; DNA, Bacterial/metabolism ; DNA, Plant/metabolism ; Energy Metabolism ; Plasmids/chemistry/metabolism ; Thermus thermophilus/*genetics/*metabolism ; *Transformation, Bacterial ; }, abstract = {Horizontal gene transfer has been a major force for genome plasticity over evolutionary history, and is largely responsible for fitness-enhancing traits, including antibiotic resistance and virulence factors. In particular, for adaptation of prokaryotes to extreme environments, lateral gene transfer seems to have played a crucial role. Recently, by performing a genome-wide mutagenesis approach with Thermus thermophilus HB27, we identified the first genes in a thermophilic bacterium for the uptake of free DNA, a process called natural transformation. Here, we present the first data on the biochemistry and bioenergetics of the DNA transport process in this thermophile. We report that linear and circular plasmid DNA are equally well taken up with a high maximal velocity of 1.5 microg DNA.(mg protein)(-1).min(-1), demonstrating an extremely efficient binding and uptake rate of 40 kb.s(-1).cell(-1). Uncouplers and ATPase inhibitors immediately inhibited DNA uptake, providing clear evidence that DNA translocation in HB27 is an energy-dependent process. DNA uptake studies with genomic DNA of Bacteria, Archaea and Eukarya revealed that Thermus thermophilus HB27 takes up DNA from members of all three domains of life. We propose that the extraordinary broad substrate specificity of the highly efficient Thermus thermophilus HB27 DNA uptake system may contribute significantly to thermoadaptation of Thermus thermophilus HB27 and to interdomain DNA transfer in hot environments.}, }
@article {pmid16939533, year = {2006}, author = {Gal-Mor, O and Finlay, BB}, title = {Pathogenicity islands: a molecular toolbox for bacterial virulence.}, journal = {Cellular microbiology}, volume = {8}, number = {11}, pages = {1707-1719}, doi = {10.1111/j.1462-5822.2006.00794.x}, pmid = {16939533}, issn = {1462-5814}, mesh = {Bacteria/*genetics/pathogenicity ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/genetics ; Genome, Bacterial/genetics ; Genomic Islands/*genetics/physiology ; Models, Biological ; Models, Genetic ; Virulence/genetics ; }, abstract = {Pathogenicity islands (PAIs) are distinct genetic elements on the chromosomes of a large number of bacterial pathogens. PAIs encode various virulence factors and are normally absent from non-pathogenic strains of the same or closely related species. PAIs are considered to be a subclass of genomic islands that are acquired by horizontal gene transfer via transduction, conjugation and transformation, and provide 'quantum leaps' in microbial evolution. Data based on numerous sequenced bacterial genomes demonstrate that PAIs are present in a wide range of both gram-positive and gram-negative bacterial pathogens of humans, animals and plants. Recent research focused on PAIs has not only led to the identification of many novel virulence factors used by these species during infection of their respective hosts, but also dramatically changed our way of thinking about the evolution of bacterial virulence.}, }
@article {pmid16938853, year = {2006}, author = {Palenik, B and Ren, Q and Dupont, CL and Myers, GS and Heidelberg, JF and Badger, JH and Madupu, R and Nelson, WC and Brinkac, LM and Dodson, RJ and Durkin, AS and Daugherty, SC and Sullivan, SA and Khouri, H and Mohamoud, Y and Halpin, R and Paulsen, IT}, title = {Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, number = {36}, pages = {13555-13559}, pmid = {16938853}, issn = {0027-8424}, mesh = {*Adaptation, Physiological ; Base Pairing ; Base Sequence ; Chromosomes, Bacterial ; *Environment ; Frameshift Mutation ; *Genome, Bacterial ; Models, Biological ; Molecular Sequence Data ; Open Reading Frames ; Operon ; Phylogeny ; Point Mutation ; RNA, Transfer ; Synechococcus/*genetics/*physiology ; }, abstract = {Coastal aquatic environments are typically more highly productive and dynamic than open ocean ones. Despite these differences, cyanobacteria from the genus Synechococcus are important primary producers in both types of ecosystems. We have found that the genome of a coastal cyanobacterium, Synechococcus sp. strain CC9311, has significant differences from an open ocean strain, Synechococcus sp. strain WH8102, and these are consistent with the differences between their respective environments. CC9311 has a greater capacity to sense and respond to changes in its (coastal) environment. It has a much larger capacity to transport, store, use, or export metals, especially iron and copper. In contrast, phosphate acquisition seems less important, consistent with the higher concentration of phosphate in coastal environments. CC9311 is predicted to have differences in its outer membrane lipopolysaccharide, and this may be characteristic of the speciation of some cyanobacterial groups. In addition, the types of potentially horizontally transferred genes are markedly different between the coastal and open ocean genomes and suggest a more prominent role for phages in horizontal gene transfer in oligotrophic environments.}, }
@article {pmid16937251, year = {2006}, author = {Vavrova, S and Valkova, D and Drahovska, H and Kokavec, J and Mravec, J and Turna, J}, title = {Analysis of the tellurite resistance determinant on the pNT3B derivative of the pTE53 plasmid from uropathogenic Escherichia coli.}, journal = {Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine}, volume = {19}, number = {5}, pages = {453-460}, doi = {10.1007/s10534-005-4862-8}, pmid = {16937251}, issn = {0966-0844}, mesh = {Computational Biology ; Culture Media/chemistry ; Drug Resistance, Bacterial/*physiology ; *Escherichia coli O157/genetics/metabolism ; Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Open Reading Frames ; Operon ; Plasmids/*genetics ; Tellurium/*metabolism ; }, abstract = {We have found and sequenced a significant part of the previously described tellurite resistance determinant on mini-Mu derivative pPR46, named pNT3B, originally cloned from a large conjugative plasmid pTE53, found in Escherichia coli. This plasmid contains genes essential for tellurite resistance, together with the protective region bearing genes terX, Y, W, and the conserved spacing region bearing several ORFs of unknown function. Computer analysis of obtained sequence revealed a close similarity to the formerly described ter operons found on the Serratia marcescens plasmid R478 and the chromosome of Escherichia coli O157:H7. This finding confirms the presence of a whole region on the large conjugative plasmid that pTE53 originated from a uropathogenic E. coli strain, and suggests its possible role in horizontal gene transfer, resulting in the development of new pathogenic E. coli strains.}, }
@article {pmid16936054, year = {2006}, author = {Nandasena, KG and O'hara, GW and Tiwari, RP and Howieson, JG}, title = {Rapid in situ evolution of nodulating strains for Biserrula pelecinus L. through lateral transfer of a symbiosis island from the original mesorhizobial inoculant.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {11}, pages = {7365-7367}, pmid = {16936054}, issn = {0099-2240}, mesh = {Acyltransferases/genetics ; Bacterial Proteins/genetics ; *Evolution, Molecular ; Fabaceae/*microbiology ; *Gene Transfer, Horizontal ; Genomic Islands/*genetics ; Integrases/genetics ; Oxidoreductases/genetics ; RNA, Transfer, Amino Acyl/genetics ; Rhizobium/*genetics ; Time Factors ; }, abstract = {Diverse rhizobia able to nodulate Biserrula pelecinus evolved following in situ transfer of nodA and nifH from an inoculant to soil bacteria. Transfer of these chromosomal genes and the presence of an identical integrase gene adjacent to a Phe tRNA gene in both the inoculant and recipients indicate that there was lateral transfer of a symbiosis island.}, }
@article {pmid16936040, year = {2006}, author = {Hain, T and Steinweg, C and Kuenne, CT and Billion, A and Ghai, R and Chatterjee, SS and Domann, E and Kärst, U and Goesmann, A and Bekel, T and Bartels, D and Kaiser, O and Meyer, F and Pühler, A and Weisshaar, B and Wehland, J and Liang, C and Dandekar, T and Lampidis, R and Kreft, J and Goebel, W and Chakraborty, T}, title = {Whole-genome sequence of Listeria welshimeri reveals common steps in genome reduction with Listeria innocua as compared to Listeria monocytogenes.}, journal = {Journal of bacteriology}, volume = {188}, number = {21}, pages = {7405-7415}, pmid = {16936040}, issn = {0021-9193}, mesh = {Chromosomes, Bacterial/genetics ; DNA, Bacterial/chemistry/*genetics ; *Evolution, Molecular ; Gene Deletion ; Gene Order ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Listeria/*genetics ; Listeria monocytogenes/genetics ; Mitochondrial Proton-Translocating ATPases/genetics ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; *Sequence Analysis, DNA ; Synteny ; Translocation, Genetic ; }, abstract = {We present the complete genome sequence of Listeria welshimeri, a nonpathogenic member of the genus Listeria. Listeria welshimeri harbors a circular chromosome of 2,814,130 bp with 2,780 open reading frames. Comparative genomic analysis of chromosomal regions between L. welshimeri, Listeria innocua, and Listeria monocytogenes shows strong overall conservation of synteny, with the exception of the translocation of an F(o)F(1) ATP synthase. The smaller size of the L. welshimeri genome is the result of deletions in all of the genes involved in virulence and of "fitness" genes required for intracellular survival, transcription factors, and LPXTG- and LRR-containing proteins as well as 55 genes involved in carbohydrate transport and metabolism. In total, 482 genes are absent from L. welshimeri relative to L. monocytogenes. Of these, 249 deletions are commonly absent in both L. welshimeri and L. innocua, suggesting similar genome evolutionary paths from an ancestor. We also identified 311 genes specific to L. welshimeri that are absent in the other two species, indicating gene expansion in L. welshimeri, including horizontal gene transfer. The species L. welshimeri appears to have been derived from early evolutionary events and an ancestor more compact than L. monocytogenes that led to the emergence of nonpathogenic Listeria spp.}, }
@article {pmid16934869, year = {2007}, author = {Friis, LM and Pin, C and Taylor, DE and Pearson, BM and Wells, JM}, title = {A role for the tet(O) plasmid in maintaining Campylobacter plasticity.}, journal = {Plasmid}, volume = {57}, number = {1}, pages = {18-28}, doi = {10.1016/j.plasmid.2006.06.005}, pmid = {16934869}, issn = {0147-619X}, mesh = {Algorithms ; Campylobacter/*genetics/isolation &amp; purification/physiology ; DNA, Bacterial/genetics/*physiology ; *Gene Transfer, Horizontal ; Oligonucleotide Array Sequence Analysis ; Plasmids/genetics/*physiology ; Tetracycline Resistance ; }, abstract = {Genomic sequencing projects are beginning to reveal regions of extensive DNA homology between bacterial genera. Public fears of the spread of genetically modified organisms into the food chain and the increasing prevalence of multi-drug resistant disease in humans highlight the implications of horizontal gene transfer. The striking DNA sequence similarity between the two uniquely identified tetracycline resistant (Tc(R)) Campylobacter plasmids, pCC31 and pTet, suggests their conserved acquisition and maintenance within Campylobacter [Batchelor, R.A., Pearson, B.M., Friis, L.M., Guerry, P., Wells, J.M. 2004. Nucleotide sequences and comparison of two large conjugative plasmids from different Campylobacter species. Microbiology 150, 3507-3517]. It is thus likely that these and other conjugative plasmids are highly prevalent and broadly distributed across several continents. Microarray technology is now enabling fast and extensive genomic comparisons to be made and allows us to investigate intra- and inter-genetic conservation and variability. This study details the development of a microarray specific for genes from Campylobacter plasmids pCC31, pTet and pVir and its application to the analysis of Campylobacter plasmid gene presence and preservation throughout environmental and clinical isolates. Application of the iterative algorithm GENCOM (freely available at) is used as a rapid and effective way of comparing the content and conservation of plasmids in bacteria and provides details of the Campylobacter flexible gene pool and its contribution to genomic plasticity.}, }
@article {pmid16934344, year = {2006}, author = {Williams, DL and Sayed, AA and Ray, D and McArthur, AG}, title = {Schistosoma mansoni albumin, a major defense against oxidative damage, was acquired by lateral gene transfer from a mammalian host.}, journal = {Molecular and biochemical parasitology}, volume = {150}, number = {2}, pages = {359-363}, doi = {10.1016/j.molbiopara.2006.07.009}, pmid = {16934344}, issn = {0166-6851}, support = {AI054403/AI/NIAID NIH HHS/United States ; AI062845/AI/NIAID NIH HHS/United States ; N01-AI-55270/AI/NIAID NIH HHS/United States ; }, mesh = {Albumins/*genetics/*physiology ; Animals ; *Gene Transfer, Horizontal ; Helminth Proteins/genetics/physiology ; Markov Chains ; Mice ; *Oxidative Stress ; Phylogeny ; Reactive Oxygen Species/metabolism ; Schistosoma mansoni/*genetics/physiology ; }, }
@article {pmid16933988, year = {2006}, author = {Lucchini, S and Rowley, G and Goldberg, MD and Hurd, D and Harrison, M and Hinton, JC}, title = {H-NS mediates the silencing of laterally acquired genes in bacteria.}, journal = {PLoS pathogens}, volume = {2}, number = {8}, pages = {e81}, pmid = {16933988}, issn = {1553-7374}, mesh = {Bacterial Proteins/*genetics/metabolism ; Binding Sites ; Biological Evolution ; DNA, Bacterial/genetics/metabolism ; DNA-Binding Proteins/*genetics/metabolism ; DNA-Directed RNA Polymerases/metabolism ; *Gene Expression Regulation, Bacterial ; *Gene Silencing ; *Gene Transfer, Horizontal ; Salmonella enterica/*genetics/metabolism/pathogenicity ; }, abstract = {Histone-like nucleoid structuring protein (H-NS) is a modular protein that is associated with the bacterial nucleoid. We used chromatin immunoprecipitation to determine the binding sites of H-NS and RNA polymerase on the Salmonella enterica serovar Typhimurium chromosome. We found that H-NS does not bind to actively transcribed genes and does not co-localize with RNA polymerase. This shows that H-NS principally silences gene expression by restricting the access of RNA polymerase to the DNA. H-NS had previously been shown to preferentially bind to curved DNA in vitro. In fact, at the genomic level we discovered that the level of H-NS binding correlates better with the AT-content of DNA. This is likely to have evolutionary consequences because we show that H-NS binds to many Salmonella genes acquired by lateral gene transfer, and functions as a gene silencer. The removal of H-NS from the cell causes un-controlled expression of several Salmonella pathogenicity islands, and we demonstrate that this has deleterious consequences for bacterial fitness. Our discovery of this novel role for H-NS may have implications for the acquisition of foreign genes by enteric bacteria.}, }
@article {pmid16933978, year = {2006}, author = {Swidan, F and Rocha, EP and Shmoish, M and Pinter, RY}, title = {An integrative method for accurate comparative genome mapping.}, journal = {PLoS computational biology}, volume = {2}, number = {8}, pages = {e75}, pmid = {16933978}, issn = {1553-7358}, mesh = {*Algorithms ; Base Sequence ; Chromosome Mapping/*methods ; *Evolution, Molecular ; Molecular Sequence Data ; Sequence Alignment/*methods ; Sequence Analysis, DNA/*methods ; Sequence Homology, Nucleic Acid ; *Software ; Systems Integration ; }, abstract = {We present MAGIC, an integrative and accurate method for comparative genome mapping. Our method consists of two phases: preprocessing for identifying "maximal similar segments," and mapping for clustering and classifying these segments. MAGIC's main novelty lies in its biologically intuitive clustering approach, which aims towards both calculating reorder-free segments and identifying orthologous segments. In the process, MAGIC efficiently handles ambiguities resulting from duplications that occurred before the speciation of the considered organisms from their most recent common ancestor. We demonstrate both MAGIC's robustness and scalability: the former is asserted with respect to its initial input and with respect to its parameters' values. The latter is asserted by applying MAGIC to distantly related organisms and to large genomes. We compare MAGIC to other comparative mapping methods and provide detailed analysis of the differences between them. Our improvements allow a comprehensive study of the diversity of genetic repertoires resulting from large-scale mutations, such as indels and duplications, including explicitly transposable and phagic elements. The strength of our method is demonstrated by detailed statistics computed for each type of these large-scale mutations. MAGIC enabled us to conduct a comprehensive analysis of the different forces shaping prokaryotic genomes from different clades, and to quantify the importance of novel gene content introduced by horizontal gene transfer relative to gene duplication in bacterial genome evolution. We use these results to investigate the breakpoint distribution in several prokaryotic genomes.}, }
@article {pmid16931539, year = {2006}, author = {Sunde, M and Norström, M}, title = {The prevalence of, associations between and conjugal transfer of antibiotic resistance genes in Escherichia coli isolated from Norwegian meat and meat products.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {58}, number = {4}, pages = {741-747}, doi = {10.1093/jac/dkl294}, pmid = {16931539}, issn = {0305-7453}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Cattle ; *Conjugation, Genetic ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/*drug effects/genetics/isolation &amp; purification ; Escherichia coli Proteins/genetics ; Gene Transfer, Horizontal ; Integrons ; Meat/*microbiology ; Meat Products/*microbiology ; Microbial Sensitivity Tests ; Norway ; Polymerase Chain Reaction ; Population Surveillance ; Poultry ; Prevalence ; Sheep ; Swine ; }, abstract = {OBJECTIVES: To investigate the distribution of, associations between and the transferability of antimicrobial resistance genes in resistant Escherichia coli strains isolated from Norwegian meat and meat products.<br><br>METHODS: The 241 strains investigated were collected within the frame of the Norwegian monitoring programme for antimicrobial resistance in bacteria from feed, food and animals (NORM-VET) during the years 2000-2003. PCR was carried out for detection of resistance genes. Conjugation experiments were carried out with the resistant isolates from meat as donor strains and E. coli DH5alpha as the recipient strain. Statistical analyses were performed with the SAS-PC-System version 9.1 for Windows.<br><br>RESULTS: Resistance genes common in pathogenic E. coli were frequently found among the isolates investigated. Strains harbouring several genes encoding resistance to the same antimicrobial agent were significantly (P < 0.0001) more frequently multiresistant than others. Strong positive associations were found between the tet(A) determinant and the genetic elements sul1, dfrA1 and aadA1. Negative associations were found between resistance genes encoding resistance to the same antimicrobial agent: tet(A)/tet(B), sul1/sul2 and strA-strB/aadA1. The resistance genes were successfully transferred from 38% of the isolates. The transfer was more frequent from resistant isolates harbouring class 1 integrons (P < 0.001).<br><br>CONCLUSIONS: Acquired resistance played a major role in conferring resistance among the isolates investigated. The possibility of transferring resistance increases both by increased multiresistance and by the presence of class 1 integrons. The conjugation experiments suggest that tet(A) and class 1 integrons are often located on the same conjugative plasmid.}, }
@article {pmid16930305, year = {2006}, author = {Roberts, AP and Mullany, P}, title = {Genetic basis of horizontal gene transfer among oral bacteria.}, journal = {Periodontology 2000}, volume = {42}, number = {}, pages = {36-46}, doi = {10.1111/j.1600-0757.2006.00149.x}, pmid = {16930305}, issn = {0906-6713}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteriophages/physiology ; Conjugation, Genetic ; DNA Transposable Elements ; Dental Plaque/genetics/*microbiology ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal/drug effects/*genetics ; Humans ; Plasmids ; R Factors ; Transduction, Genetic ; Transformation, Genetic ; }, }
@article {pmid16928736, year = {2006}, author = {Jin, G and Nakhleh, L and Snir, S and Tuller, T}, title = {Maximum likelihood of phylogenetic networks.}, journal = {Bioinformatics (Oxford, England)}, volume = {22}, number = {21}, pages = {2604-2611}, doi = {10.1093/bioinformatics/btl452}, pmid = {16928736}, issn = {1367-4811}, mesh = {*Algorithms ; Chromosome Mapping/*methods ; Computer Simulation ; Evolution, Molecular ; *Genetics, Population ; Likelihood Functions ; *Models, Genetic ; Models, Statistical ; *Phylogeny ; Sequence Alignment/*methods ; Sequence Analysis, DNA/*methods ; }, abstract = {MOTIVATION: Horizontal gene transfer (HGT) is believed to be ubiquitous among bacteria, and plays a major role in their genome diversification as well as their ability to develop resistance to antibiotics. In light of its evolutionary significance and implications for human health, developing accurate and efficient methods for detecting and reconstructing HGT is imperative.<br><br>RESULTS: In this article we provide a new HGT-oriented likelihood framework for many problems that involve phylogeny-based HGT detection and reconstruction. Beside the formulation of various likelihood criteria, we show that most of these problems are NP-hard, and offer heuristics for efficient and accurate reconstruction of HGT under these criteria. We implemented our heuristics and used them to analyze biological as well as synthetic data. In both cases, our criteria and heuristics exhibited very good performance with respect to identifying the correct number of HGT events as well as inferring their correct location on the species tree.<br><br>AVAILABILITY: Implementation of the criteria as well as heuristics and hardness proofs are available from the authors upon request. Hardness proofs can also be downloaded at http://www.cs.tau.ac.il/~tamirtul/MLNET/Supp-ML.pdf}, }
@article {pmid16926853, year = {2006}, author = {Knell, RJ}, title = {Evolution of virulence: new gene, new disease.}, journal = {Heredity}, volume = {97}, number = {5}, pages = {315}, doi = {10.1038/sj.hdy.6800889}, pmid = {16926853}, issn = {0018-067X}, mesh = {Animals ; Ascomycota/*genetics/*pathogenicity ; Fungal Proteins/genetics ; Fungi/genetics/pathogenicity ; Gene Transfer, Horizontal ; Humans ; Mycoses/microbiology ; Mycotoxins/genetics ; Virulence/genetics ; }, }
@article {pmid16926421, year = {2006}, author = {Shen, K and Sayeed, S and Antalis, P and Gladitz, J and Ahmed, A and Dice, B and Janto, B and Dopico, R and Keefe, R and Hayes, J and Johnson, S and Yu, S and Ehrlich, N and Jocz, J and Kropp, L and Wong, R and Wadowsky, RM and Slifkin, M and Preston, RA and Erdos, G and Post, JC and Ehrlich, GD and Hu, FZ}, title = {Extensive genomic plasticity in Pseudomonas aeruginosa revealed by identification and distribution studies of novel genes among clinical isolates.}, journal = {Infection and immunity}, volume = {74}, number = {9}, pages = {5272-5283}, pmid = {16926421}, issn = {0019-9567}, support = {R01 DC002148/DC/NIDCD NIH HHS/United States ; R01 DC004173/DC/NIDCD NIH HHS/United States ; DC 02148/DC/NIDCD NIH HHS/United States ; DC 04173/DC/NIDCD NIH HHS/United States ; }, mesh = {Bacteriophages/isolation &amp; purification ; Base Sequence ; Gene Expression Profiling ; Genes, Bacterial ; Genome, Bacterial/*genetics ; Genomic Library ; Humans ; Molecular Sequence Data ; Open Reading Frames/genetics ; Protein Biosynthesis/genetics ; Pseudomonas Infections/*microbiology ; Pseudomonas aeruginosa/*genetics/*isolation &amp; purification ; Sequence Analysis, DNA ; }, abstract = {The distributed genome hypothesis (DGH) states that each strain within a bacterial species receives a unique distribution of genes from a population-based supragenome that is many times larger than the genome of any given strain. The observations that natural infecting populations are often polyclonal and that most chronic bacterial pathogens have highly developed mechanisms for horizontal gene transfer suggested the DGH and provided the means and the mechanisms to explain how chronic infections persist in the face of a mammalian host's adaptive defense mechanisms. Having previously established the validity of the DGH for obligate pathogens, we wished to evaluate its applicability to an opportunistic bacterial pathogen. This was accomplished by construction and analysis of a highly redundant pooled genomic library containing approximately 216,000 functional clones that was constructed from 12 low-passage clinical isolates of Pseudomonas aeruginosa, 6 otorrheic isolates and 6 from other body sites. Sequence analysis of 3,214 randomly picked clones (mean insert size, approximately 1.4 kb) from this library demonstrated that 348 (10.8%) of the clones were unique with respect to all genomic sequences of the P. aeruginosa prototype strain, PAO1. Hypothetical translations of the open reading frames within these unique sequences demonstrated protein homologies to a number of bacterial virulence factors and other proteins not previously identified in P. aeruginosa. PCR and reverse transcription-PCR-based assays were performed to analyze the distribution and expression patterns of a 70-open reading frame subset of these sequences among 11 of the clinical strains. These sequences were unevenly distributed among the clinical isolates, with nearly half (34/70) of the novel sequences being present in only one or two of the individual strains. Expression profiling revealed that a vast majority of these sequences are expressed, strongly suggesting they encode functional proteins.}, }
@article {pmid16924482, year = {2006}, author = {Sander, J and Engels-Schwarzlose, S and Dahl, C}, title = {Importance of the DsrMKJOP complex for sulfur oxidation in Allochromatium vinosum and phylogenetic analysis of related complexes in other prokaryotes.}, journal = {Archives of microbiology}, volume = {186}, number = {5}, pages = {357-366}, doi = {10.1007/s00203-006-0156-y}, pmid = {16924482}, issn = {0302-8933}, mesh = {Bacterial Proteins/genetics/*metabolism ; Chromatiaceae/genetics/*metabolism ; Cytoplasm/enzymology ; Gene Deletion ; Gene Transfer, Horizontal ; Genes, Bacterial ; Hydrogensulfite Reductase/genetics/*metabolism ; Membrane Proteins/genetics/metabolism ; Multigene Family/physiology ; Oxidation-Reduction ; Phylogeny ; Sulfur/*metabolism ; }, abstract = {In the phototrophic sulfur bacterium Allochromatium vinosum, sulfur of oxidation state zero stored in intracellular sulfur globules is an obligate intermediate during the oxidation of sulfide and thiosulfate. The proteins encoded in the dissimilatory sulfite reductase (dsr) locus are essential for the oxidation of the stored sulfur. DsrMKJOP form a membrane-spanning complex proposed to accept electrons from or to deliver electrons to cytoplasmic sulfur-oxidizing proteins. In frame deletion mutagenesis showed that each individual of the complex-encoding genes is an absolute requirement for the oxidation of the stored sulfur in Alc. vinosum. Complementation of the DeltadsrJ mutant using the conjugative broad host range plasmid pBBR1-MCS2 and the dsr promoter was successful. The importance of the DsrMKJOP complex is underlined by the fact that the respective genes occur in all currently sequenced genomes of sulfur-forming bacteria such as Thiobacillus denitrificans and Chlorobaculum tepidum. Furthermore, closely related genes are present in the genomes of sulfate- and sulfite-reducing prokaryotes. A phylogenetic analysis showed that most dsr genes from sulfide oxidizers are clearly separated of those from sulfate reducers. Surprisingly, the dsrMKJOP genes of the Chlorobiaceae all cluster together with those of the sulfate/sulfite-reducing prokaryotes, indicating a lateral gene transfer at the base of the Chlorobiaceae.}, }
@article {pmid16924432, year = {2006}, author = {Selbitschka, W and Keller, M and Miethling-Graff, R and Dresing, U and Schwieger, F and Krahn, I and Homann, I and Dammann-Kalinowski, T and Pühler, A and Tebbe, CC}, title = {Long-term field release of bioluminescent Sinorhizobium meliloti strains to assess the influence of a recA mutation on the strains' survival.}, journal = {Microbial ecology}, volume = {52}, number = {3}, pages = {583-595}, pmid = {16924432}, issn = {0095-3628}, mesh = {*Air Microbiology ; Biomass ; Carbon/metabolism ; Colony Count, Microbial ; DNA Fingerprinting ; Ecosystem ; Gene Transfer, Horizontal ; Luminescence ; Medicago sativa/microbiology ; *Mutation ; Nitrogen/metabolism ; Organisms, Genetically Modified ; Phenotype ; Polymerase Chain Reaction ; Random Allocation ; Rec A Recombinases/*genetics ; Seasons ; Sinorhizobium meliloti/*genetics/*growth &amp; development ; *Soil Microbiology ; }, abstract = {A field release experiment was carried out to study the fate of the isogenic, firefly luciferase (luc) gene-tagged Sinorhizobium meliloti strains L1 (RecA-) and L33 (RecA+) in the environment. Both strains were released at concentrations of approximately 10(6) cfu g(-1) soil in replicate and randomized field plots, which had been sown with alfalfa (Medicago sativa). The survival of both strains during the following 7 years could be subdivided into three phases: a sharp decline for more than two orders of magnitude within the first 4 months (phase I), followed by fluctuations around an average number of 10(4) cfu g(-1) soil for nearly 4 years (phase II), and a further decline to approximately 60 cfu g(-1) (phase III). At most sampling dates, no significant differences in the survival of both strains were detected, indicating that the recA gene function was dispensable under these environmental conditions. During the field inoculation, both strains were dispersed accidentally by wind in small numbers to noninoculated field plots. Strain L33 established at a concentration of more than 10(3) cfu g(-1) soil with subsequent seasonal fluctuations. Although strain L1 must have been disseminated to a similar extent, it could never be recovered from noninoculated field plots, indicating that the recA mutation interfered with the strain's capability to establish there. At the beginning of the field experiment, an indigenous alfalfa-nodulating population was below the limit of detection. In the following years, however, an indigenous population arose, which finally outcompeted both strains for saprophytic growth and alfalfa nodulation. RecA- strain L1 was outcompeted for alfalfa nodulation slightly faster than its RecA+ counterpart L33. The diversity of the indigenous population was characterized by employing the Enterobacterial Repetitive Intergenic Consensus polymerase chain reaction fingerprint method. Typing of 2731 root nodule isolates revealed a total of 38 fingerprint groups. More than 80% of the isolates could be grouped into six dominant fingerprint groups, indicating that a few dominant bacterial strain types had outcompeted the released strains.}, }
@article {pmid16924101, year = {2006}, author = {Mulkidjanian, AY and Koonin, EV and Makarova, KS and Mekhedov, SL and Sorokin, A and Wolf, YI and Dufresne, A and Partensky, F and Burd, H and Kaznadzey, D and Haselkorn, R and Galperin, MY}, title = {The cyanobacterial genome core and the origin of photosynthesis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, number = {35}, pages = {13126-13131}, pmid = {16924101}, issn = {0027-8424}, support = {Z99 LM999999//Intramural NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics ; Cyanobacteria/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Genome, Bacterial/*genetics ; Molecular Sequence Data ; Multigene Family/genetics ; Photosynthesis/*genetics ; Phylogeny ; Plants/genetics ; }, abstract = {Comparative analysis of 15 complete cyanobacterial genome sequences, including "near minimal" genomes of five strains of Prochlorococcus spp., revealed 1,054 protein families [core cyanobacterial clusters of orthologous groups of proteins (core CyOGs)] encoded in at least 14 of them. The majority of the core CyOGs are involved in central cellular functions that are shared with other bacteria; 50 core CyOGs are specific for cyanobacteria, whereas 84 are exclusively shared by cyanobacteria and plants and/or other plastid-carrying eukaryotes, such as diatoms or apicomplexans. The latter group includes 35 families of uncharacterized proteins, which could also be involved in photosynthesis. Only a few components of cyanobacterial photosynthetic machinery are represented in the genomes of the anoxygenic phototrophic bacteria Chlorobium tepidum, Rhodopseudomonas palustris, Chloroflexus aurantiacus, or Heliobacillus mobilis. These observations, coupled with recent geological data on the properties of the ancient phototrophs, suggest that photosynthesis originated in the cyanobacterial lineage under the selective pressures of UV light and depletion of electron donors. We propose that the first phototrophs were anaerobic ancestors of cyanobacteria ("procyanobacteria") that conducted anoxygenic photosynthesis using a photosystem I-like reaction center, somewhat similar to the heterocysts of modern filamentous cyanobacteria. From procyanobacteria, photosynthesis spread to other phyla by way of lateral gene transfer.}, }
@article {pmid16923532, year = {2006}, author = {Urgun-Demirtas, M and Stark, B and Pagilla, K}, title = {Use of genetically engineered microorganisms (GEMs) for the bioremediation of contaminants.}, journal = {Critical reviews in biotechnology}, volume = {26}, number = {3}, pages = {145-164}, doi = {10.1080/07388550600842794}, pmid = {16923532}, issn = {0738-8551}, mesh = {Bacteria/genetics/*metabolism ; Bacterial Proteins/metabolism ; Bacteriological Techniques ; *Biodegradation, Environmental ; Environmental Pollutants/*metabolism ; Gene Transfer, Horizontal ; Hemoglobins/metabolism ; Metals, Heavy/metabolism ; Organisms, Genetically Modified/*metabolism ; Recombinant Fusion Proteins/metabolism ; Xenobiotics/metabolism ; }, abstract = {This paper presents a critical review of the literature on the application of genetically engineered microorganisms (GEMs) in bioremediation. The important aspects of using GEMs in bioremediation, such as development of novel strains with desirable properties through pathway construction and the modification of enzyme specificity and affinity, are discussed in detail. Particular attention is given to the genetic engineering of bacteria using bacterial hemoglobin (VHb) for the treatment of aromatic organic compounds under hypoxic conditions. The application of VHb technology may advance treatment of contaminated sites, where oxygen availability limits the growth of aerobic bioremediating bacteria, as well as the functioning of oxygenases required for mineralization of many organic pollutants. Despite the many advantages of GEMs, there are still concerns that their introduction into polluted sites to enhance bioremediation may have adverse environmental effects, such as gene transfer. The extent of horizontal gene transfer from GEMs in the environment, compared to that of native organisms including benefits regarding bacterial bioremediation that may occur as a result of such transfer, is discussed. Recent advances in tracking methods and containment strategies for GEMs, including several biological systems that have been developed to detect the fate of GEMs in the environment, are also summarized in this review. Critical research questions pertaining to the development and implementation of GEMs for enhanced bioremediation have been identified and posed for possible future research.}, }
@article {pmid16923165, year = {2006}, author = {Zhao, TY and Zou, SP and Alimova, YV and Wang, G and Hauser, KF and Ghandour, MS and Knapp, PE}, title = {Short interfering RNA-induced gene silencing is transmitted between cells from the mammalian central nervous system.}, journal = {Journal of neurochemistry}, volume = {98}, number = {5}, pages = {1541-1550}, pmid = {16923165}, issn = {0022-3042}, support = {P01 DA019398/DA/NIDA NIH HHS/United States ; R01 NS042089/NS/NINDS NIH HHS/United States ; NS42089/NS/NINDS NIH HHS/United States ; P01DA19398/DA/NIDA NIH HHS/United States ; }, mesh = {Blotting, Northern/methods ; Blotting, Western/methods ; Cell Cycle/drug effects ; Cell Line ; Central Nervous System/cytology/*drug effects/*metabolism ; Chromosomes/metabolism ; Coculture Techniques/methods ; Gene Deletion ; Gene Expression/*drug effects ; Gene Silencing/*drug effects ; Gene Transfer, Horizontal/*drug effects ; Glioblastoma ; Green Fluorescent Proteins/metabolism ; Humans ; Oligodendroglia ; PTEN Phosphohydrolase/genetics/metabolism ; RNA, Messenger/biosynthesis ; RNA, Small Interfering/*pharmacology ; Reverse Transcriptase Polymerase Chain Reaction/methods ; Transfection/methods ; }, abstract = {Although short interfering RNA (siRNA)-induced gene silencing can be transmitted between cells in plants and in Caenorhabditis elegans, this phenomenon has been barely studied in mammalian cells. Both immortalized oligodendrocytes and SNB19 glioblastoma cells were transfected with siRNA constructs for phosphatase and tensin homolog deleted on chromosome 10 (PTEN) or Akt/protein kinase B (Akt). Co-cultures were established between silenced cells and non-silenced cells which were hygromycin resistant and/or expressed green fluorescent protein. After fluorescence sorting or hygromycin selection to remove the silenced cells, the expression of PTEN or Akt genes in the originally unsilenced cells was in all cases significantly decreased. Importantly, silencing did not occur in transwell culture studies, suggesting that transmission of the silencing signal requires a close association between cells. These results provide the first direct demonstration that an siRNA-induced silencing signal can be transmitted between mammalian CNS cells.}, }
@article {pmid16919888, year = {2006}, author = {Gericke, GS}, title = {Is there an emerging endosymbiotic relationship between mycobacteria and the human host based on horizontal transfer of genetic sequences?.}, journal = {Medical hypotheses}, volume = {67}, number = {6}, pages = {1419-1428}, doi = {10.1016/j.mehy.2006.02.057}, pmid = {16919888}, issn = {0306-9877}, mesh = {Gene Transfer, Horizontal/*genetics ; *Genes, Bacterial ; Humans ; *Models, Genetic ; Mycobacterium/*genetics ; Symbiosis/*genetics ; }, abstract = {While not negating the seriousness of tuberculosis and the need to prevent and combat the disease effectively, the large percentage of infected, apparently healthy individuals who harbour latent infections warrants consideration whether an endosymbiotic relationship is being established between mycobacteria and man. By means of a gene decay process eliminating their most metabolically important pathogenic genes associated with an increasing need for host gene products during prolonged intracellular survival, mycobacteria appears to be undergoing a process of establishing a less dangerous relationship with its host. To have tolerated this relationship over time, humans must have benefited. This is suggested to have occurred via changes in DNA higher order structure altering combinatorially regulated gene expression allowing increased cerebrodiversity. It can be expected that, beyond a certain threshold, negative effects ensued, leading to neuropathology and increased susceptibility for certain psychiatric disorders. These processes have probably been happening since the earliest contact with mycobacteria, but recently may have become modified by the emergence of epidemic tuberculosis and waves of increased oxidative stress following the circumstances associated with the Industrial Revolution and the more recent AIDS pandemic. The organism seems to have uniquely exploited the normal stress reaction of the host. Genomic stresses include changes associated with glucocorticoid effects as well as upregulated reactive oxygen species and stress/(heat shock) protein production, the latter two of which result in host cell cycle delay. Subsequently replication dependent chromosomal fragile sites appear in the host genome and together with upregulated chaperonins and mobile element activation, the scene is set for sequence exchange between the organism and host. If proven, these events raise the possibility of modifying chromatin epigenetically to retain the proposed advantages while silencing pathogenicity factors.}, }
@article {pmid16916896, year = {2006}, author = {Pérez-Mendoza, D and Lucas, M and Muñoz, S and Herrera-Cervera, JA and Olivares, J and de la Cruz, F and Sanjuán, J}, title = {The relaxase of the Rhizobium etli symbiotic plasmid shows nic site cis-acting preference.}, journal = {Journal of bacteriology}, volume = {188}, number = {21}, pages = {7488-7499}, pmid = {16916896}, issn = {0021-9193}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Bacterial Proteins/chemistry/genetics/isolation &amp; purification/metabolism ; Cluster Analysis ; Conjugation, Genetic ; DNA Helicases/chemistry/*genetics/isolation &amp; purification/*metabolism ; DNA, Bacterial/*metabolism ; Electrophoretic Mobility Shift Assay ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Oligonucleotides/metabolism ; Phylogeny ; *Plasmids ; Protein Binding ; Protein Structure, Tertiary ; Rhizobium etli/*enzymology/genetics ; Sequence Alignment ; Substrate Specificity ; }, abstract = {Genetic and biochemical characterization of TraA, the relaxase of symbiotic plasmid pRetCFN42d from Rhizobium etli, is described. After purifying the relaxase domain (N265TraA), we demonstrated nic binding and cleavage activity in vitro and thus characterized for the first time the nick site (nic) of a plasmid in the family Rhizobiaceae. We studied the range of N265TraA relaxase specificity in vitro by testing different oligonucleotides in binding and nicking assays. In addition, the ability of pRetCFN42d to mobilize different Rhizobiaceae plasmid origins of transfer (oriT) was examined. Data obtained with these approaches allowed us to establish functional and phylogenetic relationships between different plasmids of this family. Our results suggest novel characteristics of the R. etli pSym relaxase for previously described conjugative systems, with emphasis on the oriT cis-acting preference of this enzyme and its possible biological relevance.}, }
@article {pmid16915928, year = {2006}, author = {Martirosian, IA and Korchagin, VI and Tokarskaia, ON and Darevskiĭ, IS and Ryskov, AP}, title = {[Finding of Bov-B LINE retroelement in parthenogenetic and bisexual lizard species of the genus Darevskia (Lacertidae)].}, journal = {Genetika}, volume = {42}, number = {7}, pages = {963-967}, pmid = {16915928}, issn = {0016-6758}, mesh = {Animals ; Base Sequence ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Lizards/*genetics/physiology ; Molecular Sequence Data ; Parthenogenesis ; Phylogeny ; Reproduction ; *Retroelements ; Species Specificity ; }, abstract = {The Bov-B LINE retrotransposon was first discovered in Ruminantia and was long considered to be specific for this order. Later, this mobile element was described in snakes and some lizard species. Analysis of phylogenetic relationships of Bov-B LINE elements from different ruminants, snakes, and lizard species led to the suggestion on horizontal transfer of this retrotransposon from Squamata to Ruminantia. In the Squamata group, Bov-B LINE element was found in all snakes and some lizard species examined. The element was not detected in the genomes of some species of the genera Lacerta and Podarcis. In the present study, using PCR amplification and sequencing of PCR products, Bov-B LINE element was identified in the genomes of parthenogenetic and bisexual species of the genus Darevskia (Lacertidae), as well as in such species as Lacerta agilis and Zootoca vivipara, where this retrotransposon had not been not detected before.}, }
@article {pmid16914439, year = {2006}, author = {Bayliss, CD and Callaghan, MJ and Moxon, ER}, title = {High allelic diversity in the methyltransferase gene of a phase variable type III restriction-modification system has implications for the fitness of Haemophilus influenzae.}, journal = {Nucleic acids research}, volume = {34}, number = {14}, pages = {4046-4059}, pmid = {16914439}, issn = {1362-4962}, support = {/WT_/Wellcome Trust/United Kingdom ; G0400426/MRC_/Medical Research Council/United Kingdom ; 070123/Z/02/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Alleles ; Amino Acid Sequence ; Bacterial Proteins/chemistry/classification/genetics ; DNA Modification Methylases/chemistry/classification/*genetics ; Deoxyribonucleases, Type III Site-Specific/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Variation ; Haemophilus influenzae/enzymology/*genetics ; Molecular Sequence Data ; Phylogeny ; Selection, Genetic ; Sequence Alignment ; }, abstract = {Phase variable restriction-modification (R-M) systems are widespread in Eubacteria. Haemophilus influenzae encodes a phase variable homolog of Type III R-M systems. Sequence analysis of this system in 22 non-typeable H.influenzae isolates revealed a hypervariable region in the central portion of the mod gene whereas the res gene was conserved. Maximum likelihood (ML) analysis indicated that most sites outside this hypervariable region experienced strong negative selection but evidence of positive selection for a few sites in adjacent regions. A phylogenetic analysis of 61 Type III mod genes revealed clustering of these H.influenzae mod alleles with mod genes from pathogenic Neisseriae and, based on sequence analysis, horizontal transfer of the mod-res complex between these species. Neisserial mod alleles also contained a hypervariable region and all mod alleles exhibited variability in the repeat tract. We propose that this hypervariable region encodes the target recognition domain (TRD) of the Mod protein and that variability results in alterations to the recognition sequence of this R-M system. We argue that the high allelic diversity and phase variable nature of this R-M system have arisen due to selective pressures exerted by diversity in bacteriophage populations but also have implications for other fitness attributes of these bacterial species.}, }
@article {pmid16914045, year = {2006}, author = {Yin, Y and Fischer, D}, title = {On the origin of microbial ORFans: quantifying the strength of the evidence for viral lateral transfer.}, journal = {BMC evolutionary biology}, volume = {6}, number = {}, pages = {63}, pmid = {16914045}, issn = {1471-2148}, mesh = {Bacteria/*genetics/*virology ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genes, Viral/*genetics ; Genome, Viral/genetics ; Models, Genetic ; Open Reading Frames/*genetics ; }, abstract = {BACKGROUND: The origin of microbial ORFans, ORFs having no detectable homology to other ORFs in the databases, is one of the unexplained puzzles of the post-genomic era. Several hypothesis on the origin of ORFans have been suggested in the last few years, most of which based on selected, relatively small, subsets of ORFans. One of the hypotheses for the origin of ORFans is that they have been acquired thru lateral transfer from viruses. Here we carry out a comprehensive, genome-wide study on the origins of ORFans to quantify the strength of current evidence supporting this hypothesis.<br><br>RESULTS: We performed similarity searches by querying all current ORFans against the public virus protein database. Surprisingly, we found that only 2.8% of all microbial ORFans have detectable homologs in viruses, while the percentage of non-ORFans with detectable homologs in viruses is 7.9%, a significantly higher figure. This suggests that the current evidence for the origin of ORFans from lateral transfer from viruses is at best weak. However, an analysis of individual genomes revealed a number of organisms with much higher percentages, many of them belonging to the Firmicutes and Gamma-proteobacteria. We provide evidence suggesting that the current virus database may be biased towards those viruses attacking Firmicutes and Gamma-proteobacteria.<br><br>CONCLUSION: We conclude that as more viral genomes are sequenced, more microbial ORFans will find homologs in viruses, but this trend may vary much for individual genomes. Thus, lateral transfer from viruses alone is unlikely to explain the origin of the majority of ORFans in the majority of prokaryotes and consequently, other, not necessarily exclusive, mechanisms are likely to better explain the origin of the increasing number of ORFans.}, }
@article {pmid16912441, year = {2006}, author = {Subramaniam, G and Palasubramaniam, S and Navaratnam, P}, title = {SHV-5 extended-spectrum beta-lactamases in clinical isolates of Escherichia coli in Malaysia.}, journal = {Indian journal of medical microbiology}, volume = {24}, number = {3}, pages = {205-207}, pmid = {16912441}, issn = {0255-0857}, mesh = {Anti-Bacterial Agents/pharmacology ; Ceftazidime/pharmacology ; DNA, Bacterial ; Drug Resistance, Bacterial ; Escherichia coli/drug effects/*enzymology/genetics/*isolation &amp; purification ; Escherichia coli Infections/*microbiology ; Gene Transfer, Horizontal ; Genotype ; Humans ; Klebsiella pneumoniae/*genetics ; Malaysia ; Microbial Sensitivity Tests ; Phenotype ; Polymerase Chain Reaction ; Polymorphism, Single-Stranded Conformational ; *beta-Lactam Resistance ; beta-Lactamases/*genetics/isolation &amp; purification ; }, abstract = {Escherichia coli isolates resistant to ceftazidime isolated in the University Malaya Medical Center (UMMC) Kuala Lumpur, Malaysia, between the years 1998 and 2000 were studied for extended-spectrum beta-lactamase (ESBL) production. All strains were analysed phenotypically and genotypically and found to be ESBL-producing organisms harbouring SHV-5 beta-lactamase. This was confirmed by PCR-SSCP and nucleotide sequencing of the blaSHV amplified gene. As there was no evidence of ESBL activity in E. coli prior to this, coupled with the fact that there was a predominance of SHV-5 beta-lactamases in Klebsiella pneumoniae isolates in UMMC, we postulate that the E. coli obtained the SHV-5 beta-lactamase genes by plasmid transfer from the ESBL-producing K. pneumoniae.}, }
@article {pmid16907759, year = {2006}, author = {Moussard, H and Moreira, D and Cambon-Bonavita, MA and López-García, P and Jeanthon, C}, title = {Uncultured Archaea in a hydrothermal microbial assemblage: phylogenetic diversity and characterization of a genome fragment from a euryarchaeote.}, journal = {FEMS microbiology ecology}, volume = {57}, number = {3}, pages = {452-469}, doi = {10.1111/j.1574-6941.2006.00128.x}, pmid = {16907759}, issn = {0168-6496}, mesh = {Archaea/*genetics/growth &amp; development ; Biodiversity ; Euryarchaeota/*genetics/growth &amp; development ; Genome Components ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The polychaete Alvinella pompejana lives in organic tubes on the walls of active hydrothermal chimneys along the East Pacific Rise. To examine the diversity of the archaeal community associated with the polychaete tubes, we constructed libraries by direct PCR amplification and cloning of 16S rRNA genes. Almost half of the sequences of the 16S rRNA gene libraries clustered with uncultured archaeal groups. In an effort to access genomic information from uncultured archaeal members we further constructed a fosmid library from the same DNA source. One of the clones, Alv-FOS5, was sequenced completely. Its sequence analysis revealed an incomplete rRNA operon and 32 predicted ORFs. Seventeen of these ORFs have been assigned putative functions, including transcription and translation, cellular processes and signalling, transport systems and metabolic pathways. Phylogenetic analyses of the 16S rRNA gene suggested that Alv-FOS5 formed a new lineage related to members of Deep-Sea Hydrothermal Vent Euryarchaeota group II. Phylogenetic analyses of predicted proteins revealed the existence of likely cases of horizontal gene transfer, both between Crenarchaeota and Euryarchaeota and between Archaea and Bacteria. This study is the first step in using genomics to reveal the physiology of an as yet uncultured group of archaea from deep-sea hydrothermal vents.}, }
@article {pmid16907742, year = {2006}, author = {van Passel, MW and Bart, A and Luyf, AC and van Kampen, AH and van der Ende, A}, title = {Identification of acquired DNA in Neisseria lactamica.}, journal = {FEMS microbiology letters}, volume = {262}, number = {1}, pages = {77-84}, doi = {10.1111/j.1574-6968.2006.00366.x}, pmid = {16907742}, issn = {0378-1097}, mesh = {Adenosine Triphosphatases/genetics ; Adhesins, Bacterial/genetics ; Amino Acid Sequence ; Carrier Proteins/genetics ; Computational Biology ; DNA, Bacterial/chemistry/*genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Molecular Sequence Data ; Neisseria lactamica/*genetics/pathogenicity ; Neisseria meningitidis/genetics ; Operon/genetics ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Serine Endopeptidases/genetics ; Virulence/genetics ; }, abstract = {Anomalous DNA (aDNA) in prokaryotic genomes, identified by its aberrant nucleotide composition, generally represents horizontally acquired DNA. Previous studies showed that frequent DNA transfer occurs between commensal Neisseriae and Neisseria meningitidis. Currently, it is unknown whether aDNA regions are also transferred between these species. The genome of Neisseria lactamica strain 892586 was assessed by a strategy that enables the selective isolation of aDNA, using endonucleases with recognition sites that are overrepresented in aDNA. Of eight regions with aDNA, five displayed similarity to virulence-associated meningococcal sequences. Of three aDNA fragments with limited or no similarity to neisserial sequences, one encodes a novel putative autotransporter/adhesin. The remaining two fragments are adjacent in the N. lactamica genome, and encode a novel putative ATPase/subtilisin-like protease operon. A similar operon is present in the genomes of different respiratory tract pathogens. The identification of aDNA from N. lactamica with similarity to meningococcal aDNA shows that genetic exchange between the Neisseriae is not limited to the neisserial core genome. The discovery of aDNA in N. lactamica similar to a locus in other pathogens substantially expands the neisserial gene pool.}, }
@article {pmid16904374, year = {2006}, author = {Gile, GH and Patron, NJ and Keeling, PJ}, title = {EFL GTPase in cryptomonads and the distribution of EFL and EF-1alpha in chromalveolates.}, journal = {Protist}, volume = {157}, number = {4}, pages = {435-444}, doi = {10.1016/j.protis.2006.06.002}, pmid = {16904374}, issn = {1434-4610}, mesh = {Animals ; Apicomplexa/genetics ; Cryptophyta/*genetics ; Dinoflagellida/*genetics ; Evolution, Molecular ; GTP Phosphohydrolases/*analysis ; Peptide Elongation Factor 1/*analysis ; Peptide Elongation Factors/*analysis ; Phylogeny ; }, abstract = {EFL (EF-like protein) is a member of the GTPase superfamily that includes several translation factors. Because it has only been found in a few eukaryotic lineages and its presence correlates with the absence of the related core translation factor EF-1alpha, its distribution is hypothesized to be the result of lateral gene transfer and replacement of EF-1alpha. In one supergroup of eukaryotes, the chromalveolates, two major lineages were found to contain EFL (dinoflagellates and haptophytes), while the others encode EF-1alpha (apicomplexans, ciliates, heterokonts and cryptomonads). For each of these groups, this distribution was deduced from whole genome sequence or expressed sequence tag (EST) data from several species, with the exception of cryptomonads from which only a single EF-1alpha PCR product from one species was known. By sequencing ESTs from two cryptomonads, Guillardia theta and Rhodomonas salina, and searching for all GTPase translation factors, we revealed that EFL is present in both species, but, contrary to expectations, we found EF-1alpha in neither. On balance, we suggest the previously reported EF-1alpha from Rhodomonas salina is likely an artefact of contamination. We also identified EFL in EST data from two members of the dinoflagellate lineage, Karlodinium micrum and Oxyrrhis marina, and from an ongoing genomic sequence project from a third, Perkinsus marinus. Karlodinium micrum is a symbiotic pairing of two lineages that would have both had EFL (a dinoflagellate and a haptophyte), but only the dinoflagellate gene remains. Oxyrrhis marina and Perkinsus marinus are early diverging sister-groups to dinoflagellates, and together show that EFL originated early in this lineage. Phylogenetic analysis confirmed that these genes are all EFL homologues, and showed that cryptomonad genes are not detectably related to EFL from other chromalveolates, which collectively form several distinct groups. The known distribution of EFL now includes a third group of chromalveolates, cryptomonads. Of the six major subgroups of chromalveolates, EFL is found in half and EF-1alpha in the other half, and none as yet unambiguously possess both genes. Phylogenetic analysis indicates EFL likely arose early within each subgroup where it is found, but suggests it may have originated multiple times within chromalveolates as a whole.}, }
@article {pmid16901777, year = {2006}, author = {VonHoldt, BM and Ostrander, EA}, title = {The singular history of a canine transmissible tumor.}, journal = {Cell}, volume = {126}, number = {3}, pages = {445-447}, doi = {10.1016/j.cell.2006.07.016}, pmid = {16901777}, issn = {0092-8674}, support = {//Intramural NIH HHS/United States ; }, mesh = {Animals ; Canidae/*genetics ; Cell Lineage/genetics ; Clone Cells/cytology/metabolism ; Disease Transmission, Infectious/*veterinary ; Dog Diseases/*genetics/physiopathology/transmission ; Dogs ; Gene Flow/genetics ; Gene Transfer, Horizontal/genetics ; Sarcoma/*genetics/metabolism/physiopathology ; Sexual Behavior, Animal/physiology ; Venereal Tumors, Veterinary/*genetics/physiopathology ; }, abstract = {In this issue of Cell, Murgia et al. (2006) confirm that the infectious agent of canine transmissible venereal tumor is the cancer cell itself and that the tumor is clonal in origin. Their findings have implications for understanding the relationship between genome instability and transmissible cancer and for conservation biology, canine genomics, and companion animal medicine.}, }
@article {pmid16899658, year = {2006}, author = {Zhaxybayeva, O and Gogarten, JP and Charlebois, RL and Doolittle, WF and Papke, RT}, title = {Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events.}, journal = {Genome research}, volume = {16}, number = {9}, pages = {1099-1108}, pmid = {16899658}, issn = {1088-9051}, mesh = {Computational Biology ; Cyanobacteria/cytology/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; *Phylogeny ; Prochlorococcus/classification/genetics ; Synechococcus/classification/genetics ; }, abstract = {Using 1128 protein-coding gene families from 11 completely sequenced cyanobacterial genomes, we attempt to quantify horizontal gene transfer events within cyanobacteria, as well as between cyanobacteria and other phyla. A novel method of detecting and enumerating potential horizontal gene transfer events within a group of organisms based on analyses of "embedded quartets" allows us to identify phylogenetic signal consistent with a plurality of gene families, as well as to delineate cases of conflict to the plurality signal, which include horizontally transferred genes. To infer horizontal gene transfer events between cyanobacteria and other phyla, we added homologs from 168 available genomes. We screened phylogenetic trees reconstructed for each of these extended gene families for highly supported monophyly of cyanobacteria (or lack of it). Cyanobacterial genomes reveal a complex evolutionary history, which cannot be represented by a single strictly bifurcating tree for all genes or even most genes, although a single completely resolved phylogeny was recovered from the quartets' plurality signals. We find more conflicts within cyanobacteria than between cyanobacteria and other phyla. We also find that genes from all functional categories are subject to transfer. However, in interphylum as compared to intraphylum transfers, the proportion of metabolic (operational) gene transfers increases, while the proportion of informational gene transfers decreases.}, }
@article {pmid16897442, year = {2007}, author = {Ludwig, A and Loreto, EL}, title = {Evolutionary pattern of the gtwin retrotransposon in the Drosophila melanogaster subgroup.}, journal = {Genetica}, volume = {130}, number = {2}, pages = {161-168}, doi = {10.1007/s10709-006-9003-y}, pmid = {16897442}, issn = {0016-6707}, mesh = {Animals ; Drosophila/classification/genetics ; Drosophila melanogaster/classification/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Insect ; Phylogeny ; Retroelements/*genetics ; Species Specificity ; }, abstract = {The gtwin retrotransposon was recently discovered in the Drosophila melanogaster genome and it is evolutionarily closer to gypsy endogenous retrovirus. This study has identified gtwin homologous sequences in the genome of D. simulans, D. sechellia, D. erecta and D. yakuba by performing homology searches against the public genome database of Drosophila species. The phylogenetic analyses of the gtwin env gene sequences of these species have shown some incongruities with the host species phylogeny, suggesting some horizontal transfer events for this retroelement. Moreover, we reported the existence of DNA sequences putatively encoding full-length Env proteins in the genomes of Drosophila species other than D. melanogaster. The results suggest that the gtwin element may be an infectious retrovirus able to invade the genome of new species, supporting the gtwin evolutionary picture shown in this work.}, }
@article {pmid16895922, year = {2006}, author = {Makarova, KS and Grishin, NV and Koonin, EV}, title = {The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria.}, journal = {Bioinformatics (Oxford, England)}, volume = {22}, number = {21}, pages = {2581-2584}, doi = {10.1093/bioinformatics/btl418}, pmid = {16895922}, issn = {1367-4811}, support = {//Intramural NIH HHS/United States ; }, mesh = {Antitoxins ; Archaea/genetics/*metabolism ; Bacteria/genetics/*pathogenicity ; Bacterial Toxins/*chemistry/genetics/metabolism ; Binding Sites ; Gene Targeting ; Integrons/genetics ; Protein Binding ; RNA, Archaeal/*chemistry/metabolism ; RNA, Bacterial/*chemistry/metabolism ; RNA-Binding Proteins/*chemistry/genetics/metabolism ; Sequence Analysis, Protein ; }, abstract = {Toxin-antitoxin systems (TAS) are abundant, diverse, horizontally mobile gene modules that encode powerful resistance mechanisms in prokaryotes. We use the comparative-genomic approach to predict a new TAS that consists of a two-gene cassette encoding uncharacterized HicA and HicB proteins. Numerous bacterial and archaeal genomes encode from one to eight HicAB modules which appear to be highly prone to horizontal gene transfer. The HicB protein (COG1598/COG4226) has a partially degraded RNAse H fold, whereas HicA (COG1724) contains a double-stranded RNA-binding domain. The stable combination of these two domains suggests a link to RNA metabolism, possibly, via an RNA interference-type mechanism. In most HicB proteins, the RNAse H-like domain is fused to a DNA-binding domain, either of the ribbon-helix-helix or of the helix-turn-helix class; in other TAS, proteins containing these DNA-binding domains function as antitoxins. Thus, the HicAB module is predicted to be a novel TAS whose mechanism involves RNA-binding and, possibly, cleavage.}, }
@article {pmid16892273, year = {2006}, author = {Bulgakov, VP and Kiselev, KV and Yakovlev, KV and Zhuravlev, YN and Gontcharov, AA and Odintsova, NA}, title = {Agrobacterium-mediated transformation of sea urchin embryos.}, journal = {Biotechnology journal}, volume = {1}, number = {4}, pages = {454-461}, doi = {10.1002/biot.200500045}, pmid = {16892273}, issn = {1860-6768}, mesh = {Animals ; Bacterial Proteins/*genetics ; Embryo, Nonmammalian ; *Gene Transfer Techniques ; Oncogene Proteins/*genetics ; Rhizobium/*genetics ; Sea Urchins/*embryology/*genetics ; Transformation, Genetic/*genetics ; beta-Glucosidase/*genetics ; }, abstract = {Agrobacterium-mediated transformation of higher plants is a well-known and powerful tool for transgene delivery to plant cells. In the present work, we studied whether Agrobacterium can transfer genetic information to animal (sea urchin) embryos. Sea urchin embryos were co-cultivated with A. tumefaciens strains carrying binary vectors containing the nptII marker gene and agrobacterial rolC and rolB oncogenes. Bacterial plasmid T-DNA-sea urchin DNA junction sites were identified in the genome of these embryos, thus indicating successful transformation. The nptII and both rol genes were expressed in the transformed embryos. The processes of transgene integration and transgene expression were suppressed when Agrobacteria contained mutated virA, virB or virG genes, suggesting that Agrobacterium transforms sea urchin cells by a mechanism similar to that which mediates T-DNA transfer to plants. Some of the embryos co-cultivated with Agrobacterium developed teratoma-like structures. The ability of Agrobacterium strains to trigger formation of teratoma-like structures was diminished when they contained the mutated vir genes. In summary, our results demonstrate that Agrobacterium is able to transform animal (sea urchin) embryonic cells, thus indicating a potential of this natural system for gene delivery to animal hosts. We also discuss the possibility of horizontal gene transfer from Agrobacterium to marine invertebrates.}, }
@article {pmid16891499, year = {2006}, author = {Mena, A and Plasencia, V and García, L and Hidalgo, O and Ayestarán, JI and Alberti, S and Borrell, N and Pérez, JL and Oliver, A}, title = {Characterization of a large outbreak by CTX-M-1-producing Klebsiella pneumoniae and mechanisms leading to in vivo carbapenem resistance development.}, journal = {Journal of clinical microbiology}, volume = {44}, number = {8}, pages = {2831-2837}, pmid = {16891499}, issn = {0095-1137}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Outer Membrane Proteins/analysis/isolation &amp; purification ; Bacterial Proteins/genetics/isolation &amp; purification ; Blotting, Western ; DNA Fingerprinting ; DNA Transposable Elements ; DNA, Bacterial/genetics ; *Disease Outbreaks ; *Drug Resistance, Multiple, Bacterial ; Electrophoresis, Polyacrylamide Gel ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Humans ; Isoelectric Focusing ; Klebsiella Infections/*epidemiology/*microbiology ; Klebsiella pneumoniae/classification/*drug effects/enzymology/isolation &amp; purification ; Microbial Sensitivity Tests ; Plasmids/genetics ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Porins/analysis/genetics/isolation &amp; purification ; Transformation, Bacterial ; beta-Lactamases/*biosynthesis/genetics/isolation &amp; purification ; }, abstract = {All extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae isolates from patients admitted to and adult intensive care unit were prospectively documented from 2002 to 2005, when a large outbreak (51 patients affected) of multiresistant ESBL-producing Klebsiella pneumoniae infection was detected. The involvement of a single K. pneumoniae clone was demonstrated by pulsed-field gel electrophoresis. In addition to the ESBL-mediated resistance, the epidemic strain uniformly showed cross-resistance to ciprofloxacin, gentamicin, tobramycin, trimethoprim-sulfamethoxazole, and tetracycline, whereas resistance to the beta-lactam-beta-lactamase inhibitor combinations was variable. The ESBL involved was CTX-M-1, as demonstrated by isoelectric focusing, PCR amplification, and sequencing. CTX-M-1 as well as the aminoglycoside resistance determinants were encoded in a 50-kb plasmid that could be transferred to Escherichia coli only by transformation. In two of the infected patients, carbapenem resistance development (MICs of 8 to 12, 16, and >32 microg/ml for imipenem, meropenem, and ertapenem, respectively) was documented, both in clinical samples and in intestinal colonization studies. The analysis of the outer membrane proteins of the carbapenem-susceptible and -resistant isolates revealed that the former expressed only one of the two major porins, OmpK36, whereas the latter did not express either of them. In one of the cases, the lack of expression of OmpK36 was demonstrated to be mediated by the interruption of the coding sequence by the insertion sequence IS26. This is the first report of a large outbreak of CTX-M-1-producing Enterobacteriaceae and, curiously, the first documented description in the literature of CTX-M-1 in K. pneumoniae, despite the fact that this enzyme has been found in multiple species. Furthermore, we document and characterize for the first time carbapenem resistance development in CTX-M-1-producing Enterobacteriaceae.}, }
@article {pmid16890259, year = {2006}, author = {Provorov, NA and Vorobyov, NI}, title = {Interplay of Darwinian and frequency-dependent selection in the host-associated microbial populations.}, journal = {Theoretical population biology}, volume = {70}, number = {3}, pages = {262-272}, doi = {10.1016/j.tpb.2006.06.002}, pmid = {16890259}, issn = {0040-5809}, mesh = {Colony Count, Microbial ; Ecosystem ; Evolution, Molecular ; Fabaceae/microbiology ; Gene Frequency/*genetics ; Gene Transfer, Horizontal/genetics ; Genetics, Population ; Genotype ; *Models, Genetic ; Mutation/*genetics ; Nitrogen Fixation/genetics ; Polymorphism, Genetic/genetics ; Population Dynamics ; Rhizobium/*genetics ; Root Nodules, Plant/*microbiology ; *Selection, Genetic ; *Soil Microbiology ; Stochastic Processes ; Symbiosis ; Virulence Factors/genetics ; }, abstract = {In order to analyze the microevolutionary processes in host-associated microorganisms, we simulated the dynamics of rhizobia populations composed of a parental strain and its mutants possessing the altered fitness within "plant-soil" system. The population dynamics was presented as a series of cycles (each one involves "soil-->rhizosphere-->nodules-->soil" succession) described using recurrent equations. For representing the selection and mutation pressures, we used a universal approach based on calculating the shifts in the genetic ratios of competing bacterial genotypes within the particular habitats and across several habitats. Analysis of the model demonstrated that a balanced polymorphism may be established in rhizobia population: mutants with an improved fitness do not supplant completely the parental strain while mutants with a decreased fitness may be maintained stably. This polymorphism is caused by a rescue of low-fitted genotypes via negative frequency-dependent selection (FDS) that is implemented during inoculation of nodules and balances the Darwinian selection that occurs during multiplication or extinction of bacteria at different habitats. The most diverse populations are formed if the rhizobia are equally successful in soil and nodules, while a marked preference for any of these habitats results in the decrease of diversity. Our simulation suggests that FDS can maintain the mutualistic rhizobia-legume interactions under the stress conditions deleterious for surviving the bacterial strains capable for intensive N2 fixation. Genetic consequences of releasing the modified rhizobia strains may be addressed using the presented model.}, }
@article {pmid16885440, year = {2006}, author = {Stokes, HW and Nesbø, CL and Holley, M and Bahl, MI and Gillings, MR and Boucher, Y}, title = {Class 1 integrons potentially predating the association with tn402-like transposition genes are present in a sediment microbial community.}, journal = {Journal of bacteriology}, volume = {188}, number = {16}, pages = {5722-5730}, pmid = {16885440}, issn = {0021-9193}, mesh = {Bacteria/*genetics/metabolism ; Base Sequence ; Fresh Water ; Geologic Sediments/*microbiology ; Integrons/*genetics ; Molecular Sequence Data ; *Phylogeny ; }, abstract = {Integrons are genetic elements that contribute to lateral gene transfer in bacteria as a consequence of possessing a site-specific recombination system. This system facilitates the spread of genes when they are part of mobile cassettes. Most integrons are contained within chromosomes and are confined to specific bacterial lineages. However, this is not the case for class 1 integrons, which were the first to be identified and are one of the single biggest contributors to multidrug-resistant nosocomial infections, carrying resistance to many antibiotics in diverse pathogens on a global scale. The rapid spread of class 1 integrons in the last 60 years is partly a result of their association with a specific suite of transposition functions, which has facilitated their recruitment by plasmids and other transposons. The widespread use of antibiotics has acted as a positive selection pressure for bacteria, especially pathogens, which harbor class 1 integrons and their associated antibiotic resistance genes. Here, we have isolated bacteria from soil and sediment in the absence of antibiotic selection. Class 1 integrons were recovered from four different bacterial species not known to be human pathogens or commensals. All four integrons lacked the transposition genes previously considered to be a characteristic of this class. At least two of these integrons were located on a chromosome, and none of them possessed antibiotic resistance genes. We conclude that novel class 1 integrons are present in a sediment environment in various bacteria of the beta-proteobacterial class. These data suggest that the dispersal of this class may have begun before the "antibiotic era."}, }
@article {pmid16884538, year = {2006}, author = {Ledent, V and Vervoort, M}, title = {Comparative genomics of the class 4 histone deacetylase family indicates a complex evolutionary history.}, journal = {BMC biology}, volume = {4}, number = {}, pages = {24}, pmid = {16884538}, issn = {1741-7007}, mesh = {Animals ; Bacteria/enzymology ; Evolution, Molecular ; Histone Deacetylases/*genetics ; *Phylogeny ; Plants/enzymology ; Plasmodium/enzymology ; Protozoan Proteins/genetics ; Viruses/enzymology ; }, abstract = {BACKGROUND: Histone deacetylases are enzymes that modify core histones and play key roles in transcriptional regulation, chromatin assembly, DNA repair, and recombination in eukaryotes. Three types of related histone deacetylases (classes 1, 2, and 4) are widely found in eukaryotes, and structurally related proteins have also been found in some prokaryotes. Here we focus on the evolutionary history of the class 4 histone deacetylase family.<br><br>RESULTS: Through sequence similarity searches against sequenced genomes and expressed sequence tag data, we identified members of the class 4 histone deacetylase family in 45 eukaryotic and 37 eubacterial species representative of very distant evolutionary lineages. Multiple phylogenetic analyses indicate that the phylogeny of these proteins is, in many respects, at odds with the phylogeny of the species in which they are found. In addition, the eukaryotic members of the class 4 histone deacetylase family clearly display an anomalous phyletic distribution.<br><br>CONCLUSION: The unexpected phylogenetic relationships within the class 4 histone deacetylase family and the anomalous phyletic distribution of these proteins within eukaryotes might be explained by two mechanisms: ancient gene duplication followed by differential gene losses and/or horizontal gene transfer. We discuss both possibilities in this report, and suggest that the evolutionary history of the class 4 histone deacetylase family may have been shaped by horizontal gene transfers.}, }
@article {pmid16882701, year = {2006}, author = {Comas, I and Moya, A and Azad, RK and Lawrence, JG and Gonzalez-Candelas, F}, title = {The evolutionary origin of Xanthomonadales genomes and the nature of the horizontal gene transfer process.}, journal = {Molecular biology and evolution}, volume = {23}, number = {11}, pages = {2049-2057}, doi = {10.1093/molbev/msl075}, pmid = {16882701}, issn = {0737-4038}, mesh = {Cluster Analysis ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; *Phylogeny ; Xanthomonadaceae/*genetics ; }, abstract = {Determining the influence of horizontal gene transfer (HGT) on phylogenomic analyses and the retrieval of a tree of life is relevant for our understanding of microbial genome evolution. It is particularly difficult to differentiate between phylogenetic incongruence due to noise and that resulting from HGT. We have performed a large-scale, detailed evolutionary analysis of the different phylogenetic signals present in the genomes of Xanthomonadales, a group of Proteobacteria. We show that the presence of phylogenetic noise is not an obstacle to infer past and present HGTs during their evolution. The scenario derived from this analysis and other recently published reports reflect the confounding effects on bacterial phylogenomics of past and present HGT. Although transfers between closely related species are difficult to detect in genome-scale phylogenetic analyses, past transfers to the ancestor of extant groups appear as conflicting signals that occasionally might make impossible to determine the evolutionary origin of the whole genome.}, }
@article {pmid16879949, year = {2006}, author = {Hopkins, KL and Batchelor, MJ and Liebana, E and Deheer-Graham, AP and Threlfall, EJ}, title = {Characterisation of CTX-M and AmpC genes in human isolates of Escherichia coli identified between 1995 and 2003 in England and Wales.}, journal = {International journal of antimicrobial agents}, volume = {28}, number = {3}, pages = {180-192}, doi = {10.1016/j.ijantimicag.2006.03.027}, pmid = {16879949}, issn = {0924-8579}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics ; Cephalosporins/pharmacology ; Drug Resistance, Bacterial/genetics ; Electrophoresis, Gel, Pulsed-Field ; England ; Escherichia coli/drug effects/*genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Phylogeny ; Plasmids ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Wales ; beta-Lactamases/*genetics ; }, abstract = {CTX-M and AmpC genes in human isolates of Escherichia coli, their genetic environment and their host plasmids were examined. Isolates (n=103) were selected based on resistance (minimum inhibitory concentration (MIC)> or =1 microg/mL) to ceftriaxone and cefotaxime. Polymerase chain reaction (PCR) and sequencing identified 29 isolates containing bla(CTX-M-15), 1 each of bla(CTX-M-2) (a strain originating from Israel) and bla(CTX-M-40), 20 isolates containing bla(CMY-7), 4 bla(CMY-2) and 1 bla(CMY-21). This is the first study of plasmid-mediated AmpC genes in E. coli in the UK. Eleven cefoxitin-resistant, AmpC PCR-negative isolates had ampC promoter region mutations. All bla(CTX-M-15) and 24 of 25 bla(CMY) genes were associated with an ISEcp1-like element. The bla(CTX-M-2) was located in an orf513-bearing class 1 integron. Plasmid restriction digests suggest transfer of genes between different plasmid backbones.}, }
@article {pmid16879637, year = {2006}, author = {Manson, JM and Gilmore, MS}, title = {Pathogenicity island integrase cross-talk: a potential new tool for virulence modulation.}, journal = {Molecular microbiology}, volume = {61}, number = {3}, pages = {555-559}, doi = {10.1111/j.1365-2958.2006.05262.x}, pmid = {16879637}, issn = {0950-382X}, mesh = {Biological Evolution ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genomic Islands/*physiology ; Humans ; Integrases/*metabolism ; Life Style ; }, abstract = {Instability and excision of pathogenicity islands (PAIs) have already been described in Escherichia coli 536. In this edition of Molecular Microbiology, Bianca Hochhut and colleagues from the University of Würzburg in Germany have shown that the instability of four of the E. coli 536 PAIs is mediated by a P4-type integrase encoded within the specific PAI by a site-specific recombination mechanism. The integrase encoded on PAI II(536) is able to mediate excision and integration of both PAI II(536), and also PAI V(536). The att sites of both these PAIs have a region of sequence similarity, which is also found in several other PAIs and in tRNA genes in several bacterial species. The cross-PAI activity of this integrase (Int(PAI II)) suggests that it plays an important role in both genome evolution and horizontal transfer of pathogenicity elements, possibly even across species barriers. Deletion of PAIs that carry genes for adhesins and other traits might lead to a phase variation-like phenomenon. Differential regulation of integrase activity or production might add a further level of fine-tuning during bacterial infection.}, }
@article {pmid16877498, year = {2006}, author = {Nosenko, T and Lidie, KL and Van Dolah, FM and Lindquist, E and Cheng, JF and Bhattacharya, D}, title = {Chimeric plastid proteome in the Florida "red tide" dinoflagellate Karenia brevis.}, journal = {Molecular biology and evolution}, volume = {23}, number = {11}, pages = {2026-2038}, doi = {10.1093/molbev/msl074}, pmid = {16877498}, issn = {0737-4038}, mesh = {Algal Proteins/*genetics ; Animals ; Cell Line ; Chlorophyta/*genetics ; Dinoflagellida/*genetics ; Evolution, Molecular ; Expressed Sequence Tags ; Florida ; Gene Transfer, Horizontal ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Plastids/*genetics ; *Proteome ; Rhodophyta/*genetics ; Symbiosis ; }, abstract = {Current understanding of the plastid proteome comes almost exclusively from studies of plants and red algae. The proteome in these taxa has a relatively simple origin via integration of proteins from a single cyanobacterial primary endosymbiont and the host. However, the most successful algae in marine environments are the chlorophyll c-containing chromalveolates such as diatoms and dinoflagellates that contain a plastid of red algal origin derived via secondary or tertiary endosymbiosis. Virtually nothing is known about the plastid proteome in these taxa. We analyzed expressed sequence tag data from the toxic "Florida red tide" dinoflagellate Karenia brevis that has undergone a tertiary plastid endosymbiosis. Comparative analyses identified 30 nuclear-encoded plastid-targeted proteins in this chromalveolate that originated via endosymbiotic or horizontal gene transfer (HGT) from multiple different sources. We identify a fundamental divide between plant/red algal and chromalveolate plastid proteomes that reflects a history of mixotrophy in the latter group resulting in a highly chimeric proteome. Loss of phagocytosis in the "red" and "green" clades effectively froze their proteomes, whereas chromalveolate lineages retain the ability to engulf prey allowing them to continually recruit new, potentially adaptive genes through subsequent endosymbioses and HGT. One of these genes is an electron transfer protein (plastocyanin) of green algal origin in K. brevis that likely allows this species to thrive under conditions of iron depletion.}, }
@article {pmid16877318, year = {2006}, author = {Ashby, MK}, title = {Distribution, structure and diversity of "bacterial" genes encoding two-component proteins in the Euryarchaeota.}, journal = {Archaea (Vancouver, B.C.)}, volume = {2}, number = {1}, pages = {11-30}, pmid = {16877318}, issn = {1472-3646}, mesh = {Bacterial Proteins/*genetics ; Euryarchaeota/*genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Histidine Kinase ; Open Reading Frames ; Phylogeny ; Protein Kinases/*genetics ; Trans-Activators/*genetics ; }, abstract = {The publicly available annotated archaeal genome sequences (23 complete and three partial annotations, October 2005) were searched for the presence of potential two-component open reading frames (ORFs) using gene category lists and BLASTP. A total of 489 potential two-component genes were identified from the gene category lists and BLASTP. Two-component genes were found in 14 of the 21 Euryarchaeal sequences (October 2005) and in neither the Crenarchaeota nor the Nanoarchaeota. A total of 20 predicted protein domains were identified in the putative two-component ORFs that, in addition to the histidine kinase and receiver domains, also includes sensor and signalling domains. The detailed structure of these putative proteins is shown, as is the distribution of each class of two-component genes in each species. Potential members of orthologous groups have been identified, as have any potential operons containing two or more two-component genes. The number of two-component genes in those Euryarchaeal species which have them seems to be linked more to lifestyle and habitat than to genome complexity, with most examples being found in Methanospirillum hungatei, Haloarcula marismortui, Methanococcoides burtonii and the mesophilic Methanosarcinales group. The large numbers of two-component genes in these species may reflect a greater requirement for internal regulation. Phylogenetic analysis of orthologous groups of five different protein classes, three probably involved in regulating taxis, suggests that most of these ORFs have been inherited vertically from an ancestral Euryarchaeal species and point to a limited number of key horizontal gene transfer events.}, }
@article {pmid16875810, year = {2007}, author = {Zhao, WH and Hu, ZQ and Chen, G and Matsushita, K and Fukuchi, K and Shimamura, T}, title = {Characterization of imipenem-resistant Serratia marcescens producing IMP-type and TEM-type beta-lactamases encoded on a single plasmid.}, journal = {Microbiological research}, volume = {162}, number = {1}, pages = {46-52}, doi = {10.1016/j.micres.2006.06.005}, pmid = {16875810}, issn = {0944-5013}, mesh = {Anti-Bacterial Agents/*pharmacology ; Conjugation, Genetic ; DNA Fingerprinting ; DNA, Bacterial/genetics ; Electrophoresis, Gel, Pulsed-Field ; Gene Transfer, Horizontal ; Genotype ; Humans ; Microbial Sensitivity Tests ; Plasmids/*genetics ; Polymerase Chain Reaction ; Serratia Infections/microbiology ; Serratia marcescens/*drug effects/*enzymology/genetics ; Transformation, Bacterial ; beta-Lactam Resistance/*genetics ; beta-Lactamases/*biosynthesis/classification/genetics ; beta-Lactams/*pharmacology ; }, abstract = {To evaluate the roles of blaIMP and blaTEM genes in the resistance of Serratia marcescens against beta-lactams and to find the spreading ways of these genes, 19 clinical isolates of imipenem-resistant Serratia marcescens were analyzed. Six strains bore blaIMP and blaTEM genes on a single plasmid, as confirmed by transferring resistance determinants via conjugation and transformation, and by detecting bla genes with PCR analysis. The six strains showed two different genomic patterns on pulsed-field gel electrophoresis. All the transconjugants and transformants gained high-level resistance to ampicillin, cephalexin, cefoxitin and cefotaxime, and showed a reduced susceptibility to imipenem, but maintained full susceptibility to aztreonam. In addition, the expressions of blaIMP and blaTEM genes were constitutive, either in Serratia marcescens clinical isolates or in their transconjugants and transformants. These findings may explain the rapid spread of the above resistance determinants among Enterobacteriaceae via transmissible plasmids in the clinical setting.}, }
@article {pmid16872524, year = {2006}, author = {Alvarez, N and Benrey, B and Hossaert-McKey, M and Grill, A and McKey, D and Galtier, N}, title = {Phylogeographic support for horizontal gene transfer involving sympatric bruchid species.}, journal = {Biology direct}, volume = {1}, number = {}, pages = {21}, pmid = {16872524}, issn = {1745-6150}, support = {V 169/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {BACKGROUND: We report on the probable horizontal transfer of a mitochondrial gene, cytb, between species of Neotropical bruchid beetles, in a zone where these species are sympatric. The bruchid beetles Acanthoscelides obtectus, A. obvelatus, A. argillaceus and Zabrotes subfasciatus develop on various bean species in Mexico. Whereas A. obtectus and A. obvelatus develop on Phaseolus vulgaris in the Mexican Altiplano, A. argillaceus feeds on P. lunatus in the Pacific coast. The generalist Z. subfasciatus feeds on both bean species, and is sympatric with A. obtectus and A. obvelatus in the Mexican Altiplano, and with A. argillaceus in the Pacific coast. In order to assess the phylogenetic position of these four species, we amplified and sequenced one nuclear (28S rRNA) and two mitochondrial (cytb, COI) genes.<br><br>RESULTS: Whereas species were well segregated in topologies obtained for COI and 28S rRNA, an unexpected pattern was obtained in the cytb phylogenetic tree. In this tree, individuals from A. obtectus and A. obvelatus, as well as Z. subfasciatus individuals from the Mexican Altiplano, clustered together in a unique little variable monophyletic unit. In contrast, A. argillaceus and Z. subfasciatus individuals from the Pacific coast clustered in two separated clades, identically to the pattern obtained for COI and 28S rRNA. An additional analysis showed that Z. subfasciatus individuals from the Mexican Altiplano also possessed the cytb gene present in individuals of this species from the Pacific coast. Zabrotes subfasciatus individuals from the Mexican Altiplano thus demonstrated two cytb genes, an "original" one and an "infectious" one, showing 25% of nucleotide divergence. The "infectious" cytb gene seems to be under purifying selection and to be expressed in mitochondria.<br><br>CONCLUSION: The high degree of incongruence of the cytb tree with patterns for other genes is discussed in the light of three hypotheses: experimental contamination, hybridization, and pseudogenisation. However, none of these seem able to explain the patterns observed. A fourth hypothesis, involving recent horizontal gene transfer (HGT) between A. obtectus and A. obvelatus, and from one of these species to Z. subfasciatus in the Mexican Altiplano, seems the only plausible explanation. The HGT between our study species seems to have occurred recently, and only in a zone where the three beetles are sympatric and share common host plants. This suggests that transfer could have been effected by some external vector such as a eukaryotic or viral parasite, which might still host the transferred fragment.<br><br>REVIEWERS: This article was reviewed by Eric Bapteste, Adam Eyre-Walker and Alexey Kondrashov.}, }
@article {pmid16871972, year = {2006}, author = {Franiczek, R and Dolna, I and Krzyzanowska, B and Szufnarowski, K and Kowalska-Krochmal, B and Zielińska, M}, title = {[Conjugative transfer frequency of resistance genes from ESBL-producing Enterobacteriaceae strains isolated from patients hospitalized in pediatric wards].}, journal = {Medycyna doswiadczalna i mikrobiologia}, volume = {58}, number = {1}, pages = {41-51}, pmid = {16871972}, issn = {0025-8601}, mesh = {Anti-Bacterial Agents/pharmacology ; Child ; Conjugation, Genetic/*genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Enterobacteriaceae/*drug effects/enzymology/*genetics/isolation &amp; purification ; Gene Transfer, Horizontal/*genetics ; Hospital Departments ; Humans ; Microbial Sensitivity Tests/methods ; Poland ; beta-Lactam Resistance/*genetics ; beta-Lactamases/metabolism ; beta-Lactams/*pharmacology ; }, abstract = {The aim of this study was to evaluate the transfer frequency of plasmids encoding extended-spectrum beta-lactamases (ESBLs) from clinical isolates of Enterobacteriaceae to E. coli K12 C600 recipient strain. Additionally, resistance patterns to antimicrobial drugs of the isolates as well as transconjugants were analyzed. Fifty-four clinical strains belonging to the Enterobacteriaceae family were isolated from children hospitalized in Medical University Hospital in Wrocław. All the strains studied were identified in automatic ATB system using ID32E tests. Besides, they were ESBL-positive as was confirmed by the double-disc synergy test (DDST). The minimal inhibitory concentration (MIC) was determined for twelve selected antibiotics and chemotherapeutics. The majority of the strains (87%) were able to transfer plasmid-mediated ESBL to E. coli K12 C600 recipient strain with a frequencies ranged from 10(-5) to 10(-1) per donor cell. All the isolates studied as well as their transconjugants were susceptible to imipenem, meropenem and norfloxacin (MIC <1mg/L). On the other hand, these strains displayed high level of resistance (MIC 512 - >1024 mg/L) to cefotaxime, ceftriaxone, gentamycin, amikacin and cotrimoxazole. Genetic markers conferring resistance to aminoglycosides and cotrimoxazole were often co-transferred to recipient strain in conjugation process.}, }
@article {pmid16870789, year = {2006}, author = {Ready, D and Pratten, J and Roberts, AP and Bedi, R and Mullany, P and Wilson, M}, title = {Potential role of Veillonella spp. as a reservoir of transferable tetracycline resistance in the oral cavity.}, journal = {Antimicrobial agents and chemotherapy}, volume = {50}, number = {8}, pages = {2866-2868}, pmid = {16870789}, issn = {0066-4804}, mesh = {Bacterial Proteins/genetics ; Conjugation, Genetic ; DNA Transposable Elements/genetics ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Microbial Sensitivity Tests ; Mouth/*microbiology ; Streptococcus/genetics ; Tetracycline Resistance/*genetics ; Veillonella/drug effects/*genetics/isolation &amp; purification ; }, abstract = {Twelve out of 96 Veillonella spp. isolated from oral samples harbored tetracycline resistance genes. The most common resistance gene was tet(M). A tet(M)-positive Veillonella dispar strain was shown to transfer a Tn916-like element to four Streptococcus spp. by conjugation at a frequency of 5.2 x 10(-6) to 4.5 x 10(-5) per recipient.}, }
@article {pmid16870684, year = {2006}, author = {Kavanaugh, LA and Fraser, JA and Dietrich, FS}, title = {Recent evolution of the human pathogen Cryptococcus neoformans by intervarietal transfer of a 14-gene fragment.}, journal = {Molecular biology and evolution}, volume = {23}, number = {10}, pages = {1879-1890}, doi = {10.1093/molbev/msl070}, pmid = {16870684}, issn = {0737-4038}, mesh = {Chromosome Mapping ; Cryptococcus neoformans/classification/*genetics/pathogenicity ; DNA, Fungal/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Fungal ; Genome, Fungal ; Humans ; Hybridization, Genetic ; Multigene Family ; Repetitive Sequences, Nucleic Acid ; Species Specificity ; }, abstract = {The availability of the whole-genome sequence from the 2 known varieties of the human pathogenic fungus Cryptococcus neoformans provides an opportunity to study the relative contribution of divergence and introgression during the process of speciation in a genetically tractable organism. At the genomic level, these varieties are nearly completely syntenic, share approximately 85-90% nucleotide identity, and are believed to have diverged approximately 18 MYA. Via a comparative genomic approach, we identified a 14-gene region (approximately 40 kb) that is nearly identical between the 2 varieties that resulted from a nonreciprocal transfer event from var. grubii to var. neoformans approximately 2 MYA. The majority of clinical and environmental var. neoformans strains from around the world contain this sequence obtained from var. grubii. This introgression event likely occurred via an incomplete intervarietal sexual cycle, creating a hybrid intermediate where mobile elements common to both lineages mediated the exchange. The subsequent duplication in laboratory strains of a fragment of this same genomic region supports evolutionary theories that instabilities in subtelomeric regions promote adaptive evolution through gene amplification and subsequent adaptation. Along with a more ancient predicted transfer event in C. neoformans and a recently reported example from Saccharomyces cerevisiae, these data indicate that DNA exchange between closely related sympatric varieties or species may be a recurrent theme in the evolution of fungal species. It further suggests that although evolutionary divergence is the primary force driving speciation, rare introgression events also play a potentially important role.}, }
@article {pmid16868995, year = {2006}, author = {Luzina, IG and Papadimitriou, JC and Anderson, R and Pochetuhen, K and Atamas, SP}, title = {Induction of prolonged infiltration of T lymphocytes and transient T lymphocyte-dependent collagen deposition in mouse lungs following adenoviral gene transfer of CCL18.}, journal = {Arthritis and rheumatism}, volume = {54}, number = {8}, pages = {2643-2655}, doi = {10.1002/art.21950}, pmid = {16868995}, issn = {0004-3591}, support = {R01-HL-074067/HL/NHLBI NIH HHS/United States ; }, mesh = {Adenoviridae/*genetics ; Animals ; Chemokines, CC/*genetics/metabolism ; Collagen/*metabolism ; Enzyme-Linked Immunosorbent Assay ; Female ; Flow Cytometry ; Gene Expression ; Gene Transfer Techniques ; Gene Transfer, Horizontal ; Genetic Vectors ; Humans ; Immunohistochemistry ; Lung/metabolism/*pathology ; Mice ; Mice, Inbred C57BL ; RNA, Messenger/metabolism ; T-Lymphocytes/immunology/metabolism/*pathology ; }, abstract = {OBJECTIVE: Levels of CCL18 are elevated in patients with scleroderma lung disease and other fibrotic pulmonary diseases associated with T lymphocyte involvement. We sought to determine whether CCL18 alone can induce pulmonary T lymphocytic infiltration and fibrosis in mouse lungs.<br><br>METHODS: An adenovirus vector was constructed and used for CCL18 delivery to mouse lungs in vivo. Immunohistochemical, flow cytometric, and enzyme-linked immunosorbent assay analyses were used to assess the resulting changes.<br><br>RESULTS: Overexpression of CCL18 led to massive perivascular and peribronchial infiltration of T lymphocytes. Although the expression of CCL18 peaked on day 7, the infiltration persisted up to day 64 after infection. The infiltrates were negative for proliferating cell nuclear antigen and TUNEL, suggesting the role of cell trafficking, rather than proliferation and apoptosis, in the infiltration dynamics. Patchy destruction of the alveolar architecture and collagen accumulation in association with the infiltrates were also noticed. These changes were infiltration-dependent, rather than CCL18-dependent, since treatment with antilymphocyte serum completely abrogated the CCL18-induced changes. The infiltrates consisted almost exclusively of T lymphocytes that were minimally activated, with a minimal increase in the expression of CD69 and no changes in the expression of CD25, Fas, FasL, or CD40L. There was no increase in total pulmonary levels of profibrotic cytokines transforming growth factor beta1 (TGFbeta1) or interleukin-13, although active TGFbeta1 was present locally in association with the infiltrates and areas of distorted alveolar architecture. Prestimulation of primary T lymphocytes with CCL18 in vitro caused an up-regulation of TGFbeta1 and collagen production in T lymphocyte/fibroblast cocultures.<br><br>CONCLUSION: CCL18 promotes selective, long-term pulmonary infiltration of T lymphocytes and infiltration-dependent accumulation of collagen through a TGFbeta1-dependent mechanism.}, }
@article {pmid16863784, year = {2006}, author = {Choi, JS and Kim, KB and Han, W and Kim, DS and Park, JS and Lee, JJ and Lee, DS}, title = {Efficacy of therapeutic angiogenesis by intramyocardial injection of pCK-VEGF165 in pigs.}, journal = {The Annals of thoracic surgery}, volume = {82}, number = {2}, pages = {679-686}, doi = {10.1016/j.athoracsur.2006.03.028}, pmid = {16863784}, issn = {1552-6259}, mesh = {Animals ; Echocardiography ; Gene Transfer, Horizontal ; *Genetic Therapy ; Humans ; Male ; Myocardial Contraction ; Myocardial Ischemia/*therapy ; Myocardium/pathology ; *Neovascularization, Physiologic ; Plasmids ; Stroke Volume ; Swine ; Tomography, Emission-Computed, Single-Photon ; Vascular Endothelial Growth Factor A/*genetics ; }, abstract = {BACKGROUND: Intramyocardial injection of vascular endothelial growth factor (VEGF) plasmid DNA was studied to demonstrate improvement of regional myocardial function.<br><br>METHODS: Twenty-one pigs that had undergone ligation of the left anterior descending coronary artery were randomly allocated to one of two treatments: intramyocardial injection of pCK-VEGF165 (VEGF group) or pCK-Null (control group) into the ischemic border zone. Electrocardiogram-gated single-photon emission computed tomography was performed 30 and 60 days after the coronary ligation. Segmental variables of perfusion and function were automatically quantified using a 20-segment model. In the segmental analysis, 119 segments were selected for analysis (71 segments in the VEGF group; 48 segments in the control group). Histologic analysis was also performed in the myocardial tissue of the ischemic border zone.<br><br>RESULTS: At day 30, there were no significant differences in segmental perfusion, wall thickening, and wall motion between the two groups. In the VEGF group, all variables of perfusion, wall thickening, and wall motion were significantly improved at day 60 compared with those at day 30 (p < 0.05), while there were no differences in the control group. At day 60, perfusion (p = 0.018), wall motion (p = 0.004), and wall thickening (p = 0.068) of the VEGF group were improved compared with those of the control group. Histologic analysis showed that microcapillary density was significantly higher in the VEGF group than the control group (p < 0.001).<br><br>CONCLUSIONS: Intramyocardial injection of pCK-VEGF165 significantly augmented neoangiogenesis in the ischemic area and improved regional myocardial function as well as myocardial perfusion.}, }
@article {pmid16861678, year = {2006}, author = {van Passel, MW and van der Ende, A and Bart, A}, title = {Plasmid diversity in neisseriae.}, journal = {Infection and immunity}, volume = {74}, number = {8}, pages = {4892-4899}, pmid = {16861678}, issn = {0019-9567}, mesh = {Bacterial Proteins/genetics ; Base Sequence ; DNA Replication ; DNA, Bacterial/analysis/genetics ; *Genetic Variation ; Humans ; Molecular Sequence Data ; Nasopharynx/microbiology ; Neisseria lactamica/*genetics/isolation &amp; purification ; Neisseria meningitidis/*genetics/isolation &amp; purification ; Plasmids/*genetics ; Sequence Analysis, DNA ; }, abstract = {Horizontal gene transfer constitutes an important force in prokaryotic genome evolution, and it is well-known that plasmids are vehicles for DNA transfer. Chromosomal DNA is frequently exchanged between pathogenic and commensal neisseriae, but relatively little is known about plasmid diversity and prevalence among these nasopharyngeal inhabitants. We investigated the plasmid contents of 18 Neisseria lactamica isolates and 20 nasopharyngeal Neisseria meningitidis isolates. Of 18 N. lactamica strains, 9 harbored one or more plasmids, whereas only one N. meningitidis isolate contained a plasmid. Twelve plasmids were completely sequenced, while five plasmid sequences from the public databases were also included in the analyses. On the basis of nucleic acid sequences, mobilization, and replicase protein alignments, we distinguish six different plasmid groups (I to VI). Three plasmids from N. lactamica appeared to be highly similar on the nucleotide level to the meningococcal plasmids pJS-A (>99%) and pJS-B (>75%). The genetic organizations of two plasmids show a striking resemblance with that of the recently identified meningococcal disease-associated (MDA) phage, while four putative proteins encoded by these plasmids show 25% to 39% protein identity to those encoded by the MDA phage. The putative promoter of the gene encoding the replicase on these plasmids contains a polycytidine tract, suggesting that replication is subjected to phase variation. In conclusion, extensive plasmid diversity is encountered among commensal neisseriae. Members of three plasmid groups are found in both pathogenic and commensal neisseriae, indicating plasmid exchange between these species. Resemblance between plasmids and MDA phage may be indicative of dissemination of phage-related sequences among pathogenic and commensal neisseriae.}, }
@article {pmid16855248, year = {2006}, author = {Waldron, DE and Lindsay, JA}, title = {Sau1: a novel lineage-specific type I restriction-modification system that blocks horizontal gene transfer into Staphylococcus aureus and between S. aureus isolates of different lineages.}, journal = {Journal of bacteriology}, volume = {188}, number = {15}, pages = {5578-5585}, pmid = {16855248}, issn = {0021-9193}, support = {/WT_/Wellcome Trust/United Kingdom ; 062511/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacterial Proteins/genetics ; DNA Restriction-Modification Enzymes/genetics ; Deoxyribonucleases, Type I Site-Specific/genetics/*physiology ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Genetic Variation ; Species Specificity ; Staphylococcus aureus/drug effects/enzymology/*genetics ; Vancomycin Resistance ; }, abstract = {The Sau1 type I restriction-modification system is found on the chromosome of all nine sequenced strains of Staphylococcus aureus and includes a single hsdR (restriction) gene and two copies of hsdM (modification) and hsdS (sequence specificity) genes. The strain S. aureus RN4220 is a vital intermediate for laboratory S. aureus manipulation, as it can accept plasmid DNA from Escherichia coli. We show that it carries a mutation in the sau1hsdR gene and that complementation restored a nontransformable phenotype. Sau1 was also responsible for reduced conjugative transfer from enterococci, a model of vancomycin resistance transfer. This may explain why only four vancomycin-resistant S. aureus strains have been identified despite substantial selective pressure in the clinical setting. Using a multistrain S. aureus microarray, we show that the two copies of sequence specificity genes (sau1hsdS1 and sau1hsdS2) vary substantially between isolates and that the variation corresponds to the 10 dominant S. aureus lineages. Thus, RN4220 complemented with sau1hsdR was resistant to bacteriophage lysis but only if the phage was grown on S. aureus of a different lineage. Similarly, it could be transduced with DNA from its own lineage but not with the phage grown on different S. aureus lineages. Therefore, we propose that Sau1 is the major mechanism for blocking transfer of resistance genes and other mobile genetic elements into S. aureus isolates from other species, as well as for controlling the spread of resistance genes between isolates of different S. aureus lineages. Blocking Sau1 should also allow genetic manipulation of clinical strains of S. aureus.}, }
@article {pmid16850014, year = {2006}, author = {Pflum, MK}, title = {H-NS gives invading DNA the silent treatment.}, journal = {Nature chemical biology}, volume = {2}, number = {8}, pages = {400-401}, doi = {10.1038/nchembio0806-400}, pmid = {16850014}, issn = {1552-4450}, mesh = {Bacterial Proteins/genetics/*metabolism ; Cell Survival/physiology ; DNA/genetics/*metabolism ; DNA-Binding Proteins/genetics/*metabolism ; *Gene Silencing ; *Gene Transfer, Horizontal ; Models, Genetic ; Salmonella typhimurium/genetics ; *Transcription, Genetic ; }, }
@article {pmid16847043, year = {2006}, author = {Roy, SW and Irimia, M and Penny, D}, title = {Very little intron gain in Entamoeba histolytica genes laterally transferred from prokaryotes.}, journal = {Molecular biology and evolution}, volume = {23}, number = {10}, pages = {1824-1827}, doi = {10.1093/molbev/msl061}, pmid = {16847043}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Animals ; Entamoeba histolytica/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Protozoan ; Introns ; Molecular Sequence Data ; Prokaryotic Cells ; Sequence Homology, Amino Acid ; Species Specificity ; }, abstract = {The evolution of spliceosomal introns remains intensely debated. We studied 96 Entamoeba histolytica genes previously identified as having been laterally transferred from prokaryotes, which were presumably intronless at the time of transfer. Ninety out of the 96 are also present in the reptile parasite Entamoeba invadens, indicating lateral transfer before the species' divergence approximately 50 MYA. We find only 2 introns, both shared with E. invadens. Thus, no intron gains have occurred in approximately 50 Myr, implying a very low rate of intron gain of less than one gain per gene per approximately 4.5 billion years. Nine other predicted introns are due to annotation errors reflecting apparent mistakes in the E. histolytica genome assembly. These results underscore the massive differences in intron gain rates through evolution.}, }
@article {pmid16844354, year = {2006}, author = {Jönsson, M and Swedberg, G}, title = {Macrolide resistance can be transferred by conjugation from viridans streptococci to Streptococcus pyogenes.}, journal = {International journal of antimicrobial agents}, volume = {28}, number = {2}, pages = {101-103}, doi = {10.1016/j.ijantimicag.2006.02.023}, pmid = {16844354}, issn = {0924-8579}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics/metabolism ; *Conjugation, Genetic ; Drug Resistance, Bacterial/*genetics ; *Gene Transfer, Horizontal ; Humans ; Macrolides/*pharmacology ; Membrane Proteins/genetics ; Streptococcus mitis/drug effects/genetics ; Streptococcus pyogenes/*drug effects/genetics ; Viridans Streptococci/*drug effects/genetics ; }, abstract = {Efflux pumps encoded by mef genes are among the most common mechanisms of resistance to macrolides. These genes are often located on horizontally transferable elements such as transposons. We present data indicating conjugative transfer of the mef(E) gene from viridans streptococci to the pathogen Streptococcus pyogenes. The mef(E) gene is located on the previously described MEGA (macrolide efflux genetic assembly) element. Of 110 isolates tested, 85% of those that carried the mef(A/E) gene carried it on MEGA, and in all cases of conjugal transfer of the mef(E) gene it was carried on MEGA. It therefore appears reasonable to draw the conclusion that this element is important in the lateral transfer of macrolide resistance between streptococci.}, }
@article {pmid16837528, year = {2006}, author = {Vernikos, GS and Parkhill, J}, title = {Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands.}, journal = {Bioinformatics (Oxford, England)}, volume = {22}, number = {18}, pages = {2196-2203}, doi = {10.1093/bioinformatics/btl369}, pmid = {16837528}, issn = {1367-4811}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {*Algorithms ; Biological Evolution ; DNA, Bacterial/*genetics ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial/genetics ; Genomic Islands/*genetics ; Salmonella/*genetics/*pathogenicity ; Virulence/*genetics ; Virulence Factors/genetics ; }, abstract = {MOTIVATION: There is a growing literature on the detection of Horizontal Gene Transfer (HGT) events by means of parametric, non-comparative methods. Such approaches rely only on sequence information and utilize different low and high order indices to capture compositional deviation from the genome backbone; the superiority of the latter over the former has been shown elsewhere. However even high order k-mers may be poor estimators of HGT, when insufficient information is available, e.g. in short sliding windows. Most of the current HGT prediction methods require pre-existing annotation, which may restrict their application on newly sequenced genomes.<br><br>RESULTS: We introduce a novel computational method, Interpolated Variable Order Motifs (IVOMs), which exploits compositional biases using variable order motif distributions and captures more reliably the local composition of a sequence compared with fixed-order methods. For optimal localization of the boundaries of each predicted region, a second order, two-state hidden Markov model (HMM) is implemented in a change-point detection framework. We applied the IVOM approach to the genome of Salmonella enterica serovar Typhi CT18, a well-studied prokaryote in terms of HGT events, and we show that the IVOMs outperform state-of-the-art low and high order motif methods predicting not only the already characterized Salmonella Pathogenicity Islands (SPI-1 to SPI-10) but also three novel SPIs (SPI-15, SPI-16, SPI-17) and other HGT events.<br><br>AVAILABILITY: The software is available under a GPL license as a standalone application at http://www.sanger.ac.uk/Software/analysis/alien_hunter<br><br>CONTACT: gsv@sanger.ac.uk<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid16835837, year = {2006}, author = {Navarro, F}, title = {Acquisition and horizontal diffusion of beta-lactam resistance among clinically relevant microorganisms.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {9}, number = {2}, pages = {79-81}, pmid = {16835837}, issn = {1139-6709}, mesh = {Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; Gram-Negative Bacteria/*drug effects/*genetics ; Gram-Positive Bacteria/*drug effects/*genetics ; beta-Lactam Resistance/*genetics ; beta-Lactams/pharmacology ; }, }
@article {pmid16834606, year = {2006}, author = {Ciesielski, S and Cydzik-Kwiatkowska, A and Pokoj, T and Klimiuk, E}, title = {Molecular detection and diversity of medium-chain-length polyhydroxyalkanoates-producing bacteria enriched from activated sludge.}, journal = {Journal of applied microbiology}, volume = {101}, number = {1}, pages = {190-199}, doi = {10.1111/j.1365-2672.2006.02973.x}, pmid = {16834606}, issn = {1364-5072}, mesh = {Acyltransferases/genetics ; Bacteria/*genetics/metabolism ; Base Sequence ; DNA, Bacterial/*analysis ; *Ecosystem ; Fermentation ; *Genetic Variation ; Methanol ; Molecular Sequence Data ; Operon ; Phylogeny ; Polymorphism, Restriction Fragment Length ; *Water Microbiology ; }, abstract = {AIMS: Knowledge of the species composition of complex bacterial communities is still very limited. The main objectives of this study were to identify medium-chain-length polyhydroxyalkanoates (mcl-PHAs)-producing bacteria from activated sludge fed with methanol as well as to characterize their PHA operon.<br><br>METHODS AND RESULTS: The identification was based on PCR amplification of mcl-PHA synthase gene fragments. In the analysed sample, four isolates possessing mcl-PHA synthesis systems were distinguished. The results of a 16S rDNA sequence analysis revealed that three strains belonged to Pseudomonas species and the fourth one was characterized as Comamonas testosteroni.<br><br>CONCLUSIONS: The results of this study indicate that the PCR-RFLP approach is an excellent way to identify mcl-PHA-synthesizing micro-organisms. The discovery of 4 genetic variants, among the 20 analysed, demonstrates that microbial diversity of activated sludge is high and thus offers a great opportunity for the discovery of novel gene forms.<br><br>An important discovery of this study is that C. testosteroni could harbour mcl-PHA operon. Moreover, the results obtained indicate that PHAs synthesis ability can be spread by horizontal gene transfer. The results of a comparative phylogenetic analysis revealed that mcl-PHA-synthesizing bacteria can be divided into Pseudomonas fluorescens and Pseudomonas aeruginosa groups.}, }
@article {pmid16832356, year = {2006}, author = {Friesen, TL and Stukenbrock, EH and Liu, Z and Meinhardt, S and Ling, H and Faris, JD and Rasmussen, JB and Solomon, PS and McDonald, BA and Oliver, RP}, title = {Emergence of a new disease as a result of interspecific virulence gene transfer.}, journal = {Nature genetics}, volume = {38}, number = {8}, pages = {953-956}, doi = {10.1038/ng1839}, pmid = {16832356}, issn = {1061-4036}, mesh = {Animals ; Ascomycota/genetics/pathogenicity ; Fungal Proteins/genetics ; *Gene Transfer, Horizontal ; Genes, Fungal ; Genomic Islands/genetics ; Humans ; Molecular Sequence Data ; Mycotoxins/genetics ; Plant Diseases/microbiology ; Species Specificity ; Triticum/microbiology ; Virulence/*genetics ; }, abstract = {New diseases of humans, animals and plants emerge regularly. Enhanced virulence on a new host can be facilitated by the acquisition of novel virulence factors. Interspecific gene transfer is known to be a source of such virulence factors in bacterial pathogens (often manifested as pathogenicity islands in the recipient organism) and it has been speculated that interspecific transfer of virulence factors may occur in fungal pathogens. Until now, no direct support has been available for this hypothesis. Here we present evidence that a gene encoding a critical virulence factor was transferred from one species of fungal pathogen to another. This gene transfer probably occurred just before 1941, creating a pathogen population with significantly enhanced virulence and leading to the emergence of a new damaging disease of wheat.}, }
@article {pmid16830099, year = {2006}, author = {Morales-Hojas, R and Vieira, CP and Vieira, J}, title = {The evolutionary history of the transposable element Penelope in the Drosophila virilis group of species.}, journal = {Journal of molecular evolution}, volume = {63}, number = {2}, pages = {262-273}, pmid = {16830099}, issn = {0022-2844}, mesh = {Animals ; Computational Biology ; DNA Transposable Elements/*genetics ; Drosophila/classification/*genetics ; Gene Transfer, Horizontal ; Genetic Speciation ; *Phylogeny ; Species Specificity ; Time Factors ; }, abstract = {We have used phylogenetic techniques to study the evolutionary history of the Penelope transposable element in the Drosophila virilis species group. Two divergent types of Penelope have been detected, one previously described, clade I, and a new one which we have termed clade III. The phylogeny of some copies of the Penelope clade I element was partially consistent with the species phylogeny of the D. montana subphylad, suggesting cospeciation and allowing the estimation of the evolutionary rate of Penelope. Divergence times of elements found in different species are younger than the age of the species, suggesting horizontal transfer events.}, }
@article {pmid16830093, year = {2006}, author = {Griffiths, E and Gupta, RS}, title = {Lateral transfers of serine hydroxymethyltransferase (glyA) and UDP-N-acetylglucosamine enolpyruvyl transferase (murA) genes from free-living Actinobacteria to the parasitic chlamydiae.}, journal = {Journal of molecular evolution}, volume = {63}, number = {2}, pages = {283-296}, pmid = {16830093}, issn = {0022-2844}, mesh = {Actinobacteria/*genetics ; Amino Acid Sequence ; Chlamydia/*genetics ; DNA, Bacterial/chemistry/genetics ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial/genetics ; Glycine Hydroxymethyltransferase/*genetics ; Molecular Sequence Data ; N-Acetylglucosaminyltransferases/*genetics ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; }, abstract = {The chlamydiae are important human and animal pathogens which form a phylogentically distinct lineage within the Bacteria. There is evidence that some genes in these obligate intracellular parasites have undergone lateral exchange with other free-living organisms. In the present work, we describe two interesting cases of lateral gene transfer between chlamydiae and actinobacteria, which have been identified based on the shared presence of conserved inserts in two important proteins. In the enzyme serine hydroxymethyltransferase (SHMT or GlyA protein), which links amino acid and nucleotide metabolisms by generating the key intermediate for one-carbon transfer reactions, two conserved inserts of 3 and 31 amino acids (aa) are uniquely present in various chlamydiae species as well as in a subset of Actinobacteria and in the Treponema species. Similarly, in the enzyme UDP-N-acetylglucosamine enolpyruvyl transferase (MurA), which is involved in the synthesis of cell wall peptidoglycan, a 16-aa conserved insert is specifically present in various sequenced chlamydiae and a subset of actinobacteria (i.e., Streptomyces, Actinomyces, Tropheryma, Bifidobacterium, Leifsonia, Arthrobacter, and Brevibacterium). To determine the phylogenetic depths of the GlyA and MurA inserts, the fragments of these genes from two chlamydiae-like species, Simkania negevensis and Waddlia chondrophila, were PCR amplified and sequenced. The presence of the corresponding inserts in both these species strongly indicates that these inserts are distinctive characteristics of the Chlamydiales order. In phylogenetic trees based on GlyA and MurA protein sequences, the chlamydiae species (and also the Treponema species in the case of GlyA) branched with a high affinity with various insert-containing actinobacteria within a clade of other actinobacteria. These results provide strong evidence that the shared presence of these indels in these bacteria is very likely a consequence of ancient lateral gene transfers from actinobacteria to chlamydiae. Pairwise sequence identity and the branching pattern of the GlyA homologues in the phylogenetic tree indicates that the glyA gene was initially transferred from an actinobacteria to an ancestor of the Treponema genus and from there it was acquired by the common ancestor of the Chlamydiales.}, }
@article {pmid16829541, year = {2006}, author = {Putonti, C and Luo, Y and Katili, C and Chumakov, S and Fox, GE and Graur, D and Fofanov, Y}, title = {A computational tool for the genomic identification of regions of unusual compositional properties and its utilization in the detection of horizontally transferred sequences.}, journal = {Molecular biology and evolution}, volume = {23}, number = {10}, pages = {1863-1868}, doi = {10.1093/molbev/msl053}, pmid = {16829541}, issn = {0737-4038}, support = {T15 LM007093/LM/NLM NIH HHS/United States ; 5T15LM07093/LM/NLM NIH HHS/United States ; }, mesh = {DNA, Bacterial/genetics ; Escherichia coli K12/genetics ; Escherichia coli O157/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial ; Genomics/*statistics &amp; numerical data ; *Software ; Species Specificity ; Yersinia pseudotuberculosis/genetics ; }, abstract = {Similarity Plot (S-plot) is a Windows-based application for large-scale comparisons and 2-dimensional visualization of compositional similarities between genomic sequences. This application combines 2 approaches widely used in genomics: window analysis of statistical characteristics along genomes and dot-plot visual representation. S-plot is effective in identifying highly similar regions between genomes as well as regions with unusual compositional properties (RUCPs) within a single genome, which may be indicative of horizontal gene transfer or of locus-specific selective forces. We use S-plot to identify regions that may have originated through horizontal gene transfer through a 2-step approach, by first comparing a genomic sequence to itself and, subsequently, comparing it to the genomic sequence of a closely related taxon. Moreover, by comparing these suspect sequences to one another, we can estimate a minimum number of sources for these putative xenologous sequences. We illustrate the uses of S-plot in a comparison involving Escherichia coli K12 and E. coli O157:H7. In O157:H7, we found 145 regions that have most probably originated through horizontal gene transfer. By using S-plot to compare each of these regions with 277 completely sequenced prokaryotic genomes, 1 sequence was found to have similar compositional properties to the Yersinia pseudotuberculosis genome, indicating a transfer from a Yersinia or Yersinia relative. Based upon our analysis of RUCPs in O157:H7, we infer that there were at least 53 sources of horizontally transferred sequences.}, }
@article {pmid16829254, year = {2006}, author = {Larkin, MJ and Kulakov, LA and Allen, CC}, title = {Biodegradation by members of the genus Rhodococcus: biochemistry, physiology, and genetic adaptation.}, journal = {Advances in applied microbiology}, volume = {59}, number = {}, pages = {1-29}, doi = {10.1016/S0065-2164(06)59001-X}, pmid = {16829254}, issn = {0065-2164}, mesh = {Adaptation, Physiological ; Biodegradation, Environmental ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Oxygenases/genetics/*metabolism ; Phylogeny ; Plasmids/genetics ; Recombination, Genetic ; Rhodococcus/classification/genetics/metabolism/*physiology ; Species Specificity ; }, }
@article {pmid16828159, year = {2007}, author = {Chen, CY and Nace, GW and Solow, B and Fratamico, P}, title = {Complete nucleotide sequences of 84.5- and 3.2-kb plasmids in the multi-antibiotic resistant Salmonella enterica serovar Typhimurium U302 strain G8430.}, journal = {Plasmid}, volume = {57}, number = {1}, pages = {29-43}, doi = {10.1016/j.plasmid.2006.05.005}, pmid = {16828159}, issn = {0147-619X}, mesh = {Bacteriophage Typing ; Base Sequence ; DNA Transposable Elements ; *Drug Resistance, Multiple, Bacterial ; Genes, Bacterial ; Genetic Variation ; Plasmids/*genetics ; Salmonella enterica/*genetics/physiology ; Sequence Homology, Nucleic Acid ; }, abstract = {The multi-antibiotic resistant (MR) Salmonella enterica serovar Typhimurium phage type U302 strain G8430 exhibits the penta-resistant ACSSuT-phenotype (ampicillin, chloramphenicol, streptomycin, sulfonamides and tetracycline), and is also resistant to carbenicillin, erythromycin, kanamycin, and gentamicin. Two plasmids, 3.2- and 84.5-kb in size, carrying antibiotic resistance genes were isolated from this strain, and the nucleotide sequences were determined and analyzed. The 3.2-kb plasmid, pU302S, belongs to the ColE1 family and carries the aph(3')-I gene (Kan(R)). The 84.5-kb plasmid, pU302L, is an F-like plasmid and contains 14 complete IS elements and multiple resistance genes including aac3, aph(3')-I, sulII, tetA/R, strA/B, bla(TEM-1), mph, and the mer operon. Sequence analyses of pU302L revealed extensive homology to various plasmids or transposons, including F, R100, pHCM1, pO157, and pCTX-M3 plasmids and TnSF1 transposon, in regions involved in plasmid replication/maintenance functions and/or in antibiotic resistance gene clusters. Though similar to the conjugative plasmids F and R100 in the plasmid replication regions, pU302L does not contain oriT and the tra genes necessary for conjugal transfer. This mosaic pattern of sequence similarities suggests that pU302L acquired the resistance genes from a variety of enteric bacteria and underscores the importance of a further understanding of horizontal gene transfer among the enteric bacteria.}, }
@article {pmid16827551, year = {2005}, author = {Zhang, C and Hampp, R and Nehls, U}, title = {Investigation of horizontal gene transfer in poplar/Amanita muscaria ectomycorrhizas.}, journal = {Environmental biosafety research}, volume = {4}, number = {4}, pages = {235-242}, doi = {10.1051/ebr:2006004}, pmid = {16827551}, issn = {1635-7922}, mesh = {Amanita/*genetics ; DNA, Fungal/analysis ; DNA, Plant/analysis ; *Gene Transfer, Horizontal ; Mycorrhizae ; Plants, Genetically Modified ; Populus/*genetics ; Symbiosis/genetics ; Transformation, Genetic ; }, abstract = {Fine roots of forest trees form together with certain soil fungi symbiotic structures (ectomycorrhizas), where fungal hyphae are in intimate contact with plant cells. Due to root cell degeneration, plant DNA is released and could be taken up by the fungus. The possibility that horizontal gene transfer might result in a risk for the environment should be evaluated before a massive release of genetically engineered trees into nature occurs, even though only a few convincing examples of horizontal gene transfer are known. Transgenic poplars containing a construct of the Streptomyces hygroscopicus bar gene under the control of the Cochliobolus heterostrophus GPD (glyceraldehyde-3-phosphate dehydrogenase) promoter were generated by Agrobacterium-mediated transformation. The functionality of this construct in the ectomycorrhizal model fungus Amanita muscaria was previously verified by protoplast-based fungal transformation. 35,000 ectomycorrhizas, formed between transgenic poplars and non-transgenic A. muscaria hyphae, were isolated and transferred to selective agar plates. Putative herbicide-resistant fungal colonies were obtained after the first round of selection. However, none of these colonies survived a transfer onto fresh selection medium, nor did they contain the bar gene, indicating that no horizontal gene transfer from poplar to A. muscaria occurred during symbiosis under axenic conditions. However, since ectomycorrhizas are associated under natural conditions with viruses, bacteria and other fungi, these additional associations should be evaluated in future.}, }
@article {pmid16827550, year = {2005}, author = {Pettersen, AK and Bøhn, T and Primicerio, R and Shorten, PR and Soboleva, TK and Nielsen, KM}, title = {Modeling suggests frequency estimates are not informative for predicting the long-term effect of horizontal gene transfer in bacteria.}, journal = {Environmental biosafety research}, volume = {4}, number = {4}, pages = {223-233}, doi = {10.1051/ebr:2006008}, pmid = {16827550}, issn = {1635-7922}, mesh = {Bacteria/*genetics ; *Gene Transfer, Horizontal ; Models, Biological ; Population Dynamics ; }, abstract = {Horizontal gene transfer (HGT) is an important mechanism by which bacteria recombine and acquire novel genes and functions. Risk scenarios where novel plant transgenes transfer horizontally into bacteria have been addressed in numerical theoretical assessments and experimental studies. A key outcome of these studies has been that the frequencies of such inter-domain transfer are very low, if occurring at all, suggesting that such transfers would not occur at a level that is biologically significant. The relationship between transfer frequencies and the subsequent selection or genetic drift of transgene carrying bacteria often remains unresolved in these studies and assessments. Here we present a stochastic model to better understand the initial establishment and population dynamics of rare bacterial transformants carrying horizontally acquired (trans)genes. The following key parameters are considered: initial transformant numbers, strength of selection, bacterial population size and bacterial generations (time). We find that the initial number of transformants is important for the subsequent persistence of transformants only in the range of 1 to approximately 50 independent HGT events. Our simulations show that transformant populations under a wide range of HGT rates and selection coefficients undergo stochastic developments where they persist at low frequencies for up to several years (at frequencies that are below detection using available field sampling methodology), after which they eventually may go to fixation. Stochastic variability may thus play a crucial but disregarded role in the design of field monitoring strategies e.g. in biosafety assessments. We also estimate the time required for transformants to reach 0.0002% prevalence in a bacterial population, a threshold that allows experimental detection of transgene carrying bacteria through sampling of the larger bacterial populations.}, }
@article {pmid16822756, year = {2006}, author = {Cavalier-Smith, T}, title = {Origin of mitochondria by intracellular enslavement of a photosynthetic purple bacterium.}, journal = {Proceedings. Biological sciences}, volume = {273}, number = {1596}, pages = {1943-1952}, pmid = {16822756}, issn = {0962-8452}, mesh = {Bacterial Proteins/classification/metabolism/physiology ; *Biological Evolution ; Eukaryotic Cells/ultrastructure ; Gene Transfer, Horizontal ; Genome ; Membrane Proteins/classification/metabolism/physiology ; Mitochondria/genetics/*metabolism/ultrastructure ; Mitochondrial Membrane Transport Proteins/classification/genetics/metabolism ; Mitochondrial Membranes/metabolism/ultrastructure ; Mitochondrial Proteins/classification/metabolism/physiology ; Models, Biological ; Phagocytosis ; Photosynthesis ; Proteobacteria/genetics/*metabolism/ultrastructure ; Symbiosis ; }, abstract = {Mitochondria originated by permanent enslavement of purple non-sulphur bacteria. These endosymbionts became organelles through the origin of complex protein-import machinery and insertion into their inner membranes of protein carriers for extracting energy for the host. A chicken-and-egg problem exists: selective advantages for evolving import machinery were absent until inner membrane carriers were present, but this very machinery is now required for carrier insertion. I argue here that this problem was probably circumvented by conversion of the symbiont protein-export machinery into protein-import machinery, in three phases. I suggest that the first carrier entered the periplasmic space via pre-existing beta-barrel proteins in the bacterial outer membrane that later became Tom40, and inserted into the inner membrane probably helped by a pre-existing inner membrane protein, thereby immediately providing the protoeukaryote host with photosynthesate. This would have created a powerful selective advantage for evolving more efficient carrier import by inserting Tom70 receptors. Massive gene transfer to the nucleus inevitably occurred by mutation pressure. Finally, pressure from harmful, non-selected gene transfer to the nucleus probably caused evolution of the presequence mechanism, and photosynthesis was lost.}, }
@article {pmid16820520, year = {2006}, author = {Mentel, M and Spírek, M and Jørck-Ramberg, D and Piskur, J}, title = {Transfer of genetic material between pathogenic and food-borne yeasts.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {7}, pages = {5122-5125}, pmid = {16820520}, issn = {0099-2240}, mesh = {Candida glabrata/*genetics ; *Conjugation, Genetic ; Food Microbiology ; Fungal Proteins/genetics ; *Gene Transfer, Horizontal ; Humans ; Mycoses/microbiology ; *Plasmids ; Saccharomyces cerevisiae/*genetics ; }, abstract = {Many pathogenic yeast species are asexual and therefore not involved in intra- or interspecies mating. However, high-frequency transfer of plasmid DNA was observed when pathogenic and food-borne yeasts were grown together. This property could play a crucial role in the spread of virulence and drug resistance factors among yeasts.}, }
@article {pmid16820486, year = {2006}, author = {Williams, LE and Detter, C and Barry, K and Lapidus, A and Summers, AO}, title = {Facile recovery of individual high-molecular-weight, low-copy-number natural plasmids for genomic sequencing.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {7}, pages = {4899-4906}, pmid = {16820486}, issn = {0099-2240}, mesh = {Chromosomes, Artificial, Bacterial/genetics ; Corynebacterium/genetics ; DNA, Bacterial/analysis/genetics/*isolation &amp; purification ; Escherichia coli/genetics ; *Genetic Techniques ; Genome, Bacterial/*genetics ; Magnetics ; Microspheres ; Molecular Sequence Data ; Plasmids/analysis/genetics/*isolation &amp; purification ; *Sequence Analysis, DNA ; Staphylococcus/genetics ; }, abstract = {Sequencing of the large (>50 kb), low-copy-number (<5 per cell) plasmids that mediate horizontal gene transfer has been hindered by the difficulty and expense of isolating DNA from individual plasmids of this class. We report here that a kit method previously devised for purification of bacterial artificial chromosomes (BACs) can be adapted for effective preparation of individual plasmids up to 220 kb from wild gram-negative and gram-positive bacteria. Individual plasmid DNA recovered from less than 10 ml of Escherichia coli, Staphylococcus, and Corynebacterium cultures was of sufficient quantity and quality for construction of high-coverage libraries, as shown by sequencing five native plasmids ranging in size from 30 kb to 94 kb. We also report recommendations for vector screening to optimize plasmid sequence assembly, preliminary annotation of novel plasmid genomes, and insights on mobile genetic element biology derived from these sequences. Adaptation of this BAC method for large plasmid isolation removes one major technical hurdle to expanding our knowledge of the natural plasmid gene pool.}, }
@article {pmid16820295, year = {2006}, author = {Martin, B and Quentin, Y and Fichant, G and Claverys, JP}, title = {Independent evolution of competence regulatory cascades in streptococci?.}, journal = {Trends in microbiology}, volume = {14}, number = {8}, pages = {339-345}, doi = {10.1016/j.tim.2006.06.007}, pmid = {16820295}, issn = {0966-842X}, mesh = {DNA, Bacterial/genetics ; *Evolution, Molecular ; Genome, Bacterial/genetics ; Models, Biological ; Phylogeny ; Streptococcus/*genetics ; Streptococcus mutans/genetics ; Streptococcus pneumoniae/genetics ; Transformation, Bacterial/*genetics ; }, abstract = {Natural genetic transformation is a mechanism of horizontal gene transfer that is widely distributed in bacteria and requires assembly of a DNA uptake machinery. Transformable bacteria use fundamentally the same machine, which in most species is assembled only in cells that are developing competence. Competence regulation usually differs between unrelated species. Here, we examine whether related streptococci use the same competence regulatory cascade. Phylogenetic analyses of streptococcal genome sequences reveal the existence of two paralogous two-component regulatory systems, either of which might control competence. This suggests the distribution of streptococci into two groups that use competence regulatory cascades that have at least partly evolved independently. Comparison of data obtained with two transformable streptococci, Streptococcus pneumoniae and Streptococcus mutans, provides support to this suggestion.}, }
@article {pmid16820057, year = {2006}, author = {Legault, BA and Lopez-Lopez, A and Alba-Casado, JC and Doolittle, WF and Bolhuis, H and Rodriguez-Valera, F and Papke, RT}, title = {Environmental genomics of "Haloquadratum walsbyi" in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species.}, journal = {BMC genomics}, volume = {7}, number = {}, pages = {171}, pmid = {16820057}, issn = {1471-2164}, mesh = {Base Composition/genetics ; Chromosomes, Archaeal/genetics ; DNA, Archaeal/chemistry/genetics ; Genome, Archaeal/*genetics ; Genome, Bacterial/genetics ; *Genomic Library ; Genomics/*methods ; Halobacteriaceae/classification/*genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; Sodium Chloride ; Spain ; Water Microbiology ; }, abstract = {BACKGROUND: Mature saturated brine (crystallizers) communities are largely dominated (> 80% of cells) by the square halophilic archaeon "Haloquadratum walsbyi". The recent cultivation of the strain HBSQ001 and the sequencing of its genome allows comparison with the metagenome of this taxonomically simplified environment. Similar studies carried out in other extreme environments have revealed very little diversity in gene content among the cell lineages present.<br><br>RESULTS: The metagenome of the microbial community of a crystallizer pond has been analyzed by end sequencing a 2000 clone fosmid library and comparing the sequences obtained with the genome sequence of "Haloquadratum walsbyi". The genome of the sequenced strain was retrieved nearly complete within this environmental DNA library. However, many ORF's that could be ascribed to the "Haloquadratum" metapopulation by common genome characteristics or scaffolding to the strain genome were not present in the specific sequenced isolate. Particularly, three regions of the sequenced genome were associated with multiple rearrangements and the presence of different genes from the metapopulation. Many transposition and phage related genes were found within this pool which, together with the associated atypical GC content in these areas, supports lateral gene transfer mediated by these elements as the most probable genetic cause of this variability. Additionally, these sequences were highly enriched in putative regulatory and signal transduction functions.<br><br>CONCLUSION: These results point to a large pan-genome (total gene repertoire of the genus/species) even in this highly specialized extremophile and at a single geographic location. The extensive gene repertoire is what might be expected of a population that exploits a diverse nutrient pool, resulting from the degradation of biomass produced at lower salinities.}, }
@article {pmid16818880, year = {2006}, author = {Vetsigian, K and Woese, C and Goldenfeld, N}, title = {Collective evolution and the genetic code.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, number = {28}, pages = {10696-10701}, pmid = {16818880}, issn = {0027-8424}, mesh = {*Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genetic Code ; *Models, Genetic ; Multigene Family ; }, abstract = {A dynamical theory for the evolution of the genetic code is presented, which accounts for its universality and optimality. The central concept is that a variety of collective, but non-Darwinian, mechanisms likely to be present in early communal life generically lead to refinement and selection of innovation-sharing protocols, such as the genetic code. Our proposal is illustrated by using a simplified computer model and placed within the context of a sequence of transitions that early life may have made, before the emergence of vertical descent.}, }
@article {pmid16808974, year = {2006}, author = {Agersø, Y and Wulff, G and Vaclavik, E and Halling-Sørensen, B and Jensen, LB}, title = {Effect of tetracycline residues in pig manure slurry on tetracycline-resistant bacteria and resistance gene tet(M) in soil microcosms.}, journal = {Environment international}, volume = {32}, number = {7}, pages = {876-882}, doi = {10.1016/j.envint.2006.05.008}, pmid = {16808974}, issn = {0160-4120}, mesh = {Animals ; Chlortetracycline/pharmacology ; DNA, Bacterial/analysis ; Enterococcus/*drug effects/*genetics ; Manure/*analysis/microbiology ; Oxytetracycline/pharmacology ; *Soil Microbiology ; Swine ; Tetracycline/*pharmacology ; Tetracycline Resistance/*genetics ; Time Factors ; }, abstract = {Effects of tetracycline residues from pig manure slurry on the prevalence of tetracycline-resistant bacteria and the tetracycline resistance gene, tet(M), were studied in soil microcosms. Four types of soil microcosms were established for a period of 152 days, supplemented with combinations of pig manure slurry and a tetracycline-resistant Enterococcus faecalis, CG110, containing the tetracycline resistance gene tet(M) (on the conjugative transposon, Tn916). The prevalence of both tetracycline-resistant aerobic bacteria and tetracycline-resistant enterococci declined rapidly until day 45 where no significant differences in the levels of tetracycline-resistant bacteria in any of the four types of microcosms could be detected. tet(M) could be detected in microcosms supplemented with either pig manure slurry and/or E. faecalis CG110 (tet(M)) for the whole period (152 days). tet(M) could be detected longer than tetracycline-resistant enterococci could be isolated (limit of detection 100 CFU/g soil) probably due to viable but not culturable (VBNC) bacteria with tet(M), horizontal gene transfer of tet(M) to indigenous soil bacteria or presence of "free" DNA. The concentration of chlortetracycline and oxytetracycline were almost stable through out the experimental period, but the tetracycline concentrations had no effect on prevalence of tetracycline-resistant bacteria. The presented microcosm approach simulated natural farmland conditions well and supported results from previous field studies.}, }
@article {pmid16808834, year = {2006}, author = {Meinicke, P and Brodag, T and Fricke, WF and Waack, S}, title = {P-value based visualization of codon usage data.}, journal = {Algorithms for molecular biology : AMB}, volume = {1}, number = {1}, pages = {10}, pmid = {16808834}, issn = {1748-7188}, abstract = {Two important and not yet solved problems in bacterial genome research are the identification of horizontally transferred genes and the prediction of gene expression levels. Both problems can be addressed by multivariate analysis of codon usage data. In particular dimensionality reduction methods for visualization of multivariate data have shown to be effective tools for codon usage analysis. We here propose a multidimensional scaling approach using a novel similarity measure for codon usage tables. Our probabilistic similarity measure is based on P-values derived from the well-known chi-square test for comparison of two distributions. Experimental results on four microbial genomes indicate that the new method is well-suited for the analysis of horizontal gene transfer and translational selection. As compared with the widely-used correspondence analysis, our method did not suffer from outlier sensitivity and showed a better clustering of putative alien genes in most cases.}, }
@article {pmid16804190, year = {2006}, author = {Takenouchi-Ohkubo, N and Mortensen, LM and Drasbek, KR and Kilian, M and Poulsen, K}, title = {Horizontal transfer of the immunoglobulin A1 protease gene (iga) from Streptococcus to Gemella haemolysans.}, journal = {Microbiology (Reading, England)}, volume = {152}, number = {Pt 7}, pages = {2171-2180}, doi = {10.1099/mic.0.28801-0}, pmid = {16804190}, issn = {1350-0872}, mesh = {Base Sequence ; Blotting, Southern ; Escherichia coli/genetics ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; Serine Endopeptidases/chemistry/*genetics ; Staphylococcaceae/*genetics ; Streptococcus mitis/*genetics ; }, abstract = {Bacterial IgA1 proteases share the ability to cleave human IgA1 at the hinge region. Nature has developed this trait along at least five independent evolutionary lineages. To obtain further insight into the phylogeny and function of IgA1 proteases, the nucleotide sequence of the iga gene that encodes the IgA1 protease was determined from two Streptococcus mitis strains and one Gemella haemolysans strain. Heterologous expression in Escherichia coli confirmed that the genes encode human IgA1-cleaving activity. IgA1 proteases from Streptococcus and G. haemolysans shared structural features, including a motif typical for zinc-dependent metalloproteases of clan MA(E) family M26 and an N-terminal signal sequence followed by an LPXTG cell-wall-anchor motif and two putative membrane-spanning domains. In addition, they all harboured a repeat region preceding the active site of the protease. In the streptococcal IgA1 proteases, a G5 domain, which has been suggested to bind N-acetylglucosamine, was identified. Conservation of these structures in otherwise diverse proteases suggests that they are essential to the biological function of the enzyme. The phylogenetic distribution of homologous iga genes and conservation of gene order in the iga gene region in different Streptococcus species, combined with the sequence homologies, strongly suggest that the iga gene is more ancient in Streptococcus than in G. haemolysans, and therefore that the IgA1 protease gene was transferred from Streptococcus to G. haemolysans.}, }
@article {pmid16804181, year = {2006}, author = {Yost, CK and Rath, AM and Noel, TC and Hynes, MF}, title = {Characterization of genes involved in erythritol catabolism in Rhizobium leguminosarum bv. viciae.}, journal = {Microbiology (Reading, England)}, volume = {152}, number = {Pt 7}, pages = {2061-2074}, doi = {10.1099/mic.0.28938-0}, pmid = {16804181}, issn = {1350-0872}, mesh = {Brucella/genetics ; Chromosome Mapping ; Erythritol/*metabolism ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genome, Bacterial ; Phylogeny ; Plasmids ; Rhizobium leguminosarum/*genetics/metabolism ; }, abstract = {A genetic locus encoding erythritol uptake and catabolism genes was identified in Rhizobium leguminosarum bv. viciae, and shown to be plasmid encoded in a wide range of R. leguminosarum strains. A Tn5-B22 mutant (19B-3) unable to grow on erythritol was isolated from a mutant library of R. leguminosarum strain VF39SM. The mutated gene eryF was cloned and partially sequenced, and determined to have a high homology to permease genes of ABC transporters. A cosmid complementing the mutation (pCos42) was identified and was shown to carry all the genes necessary to restore the ability to grow on erythritol to a VF39SM strain cured of pRleVF39f. In the genomic DNA sequence of strain 3841, the gene linked to the mutation in 19B-3 is flanked by a cluster of genes with high homology to the known erythritol catabolic genes from Brucella spp. Through mutagenesis studies, three distinct operons on pCos42 that are required for growth on erythritol were identified: an ABC-transporter operon (eryEFG), a catabolic operon (eryABCD) and an operon (deoR-tpiA2-rpiB) that encodes a gene with significant homology to triosephosphate isomerase (tpiA2). These genes all share high sequence identity to genes in the erythritol catabolism region of Brucella spp., and clustalw alignments suggest that horizontal transfer of the erythritol locus may have occurred between R. leguminosarum and Brucella. Transcription of the eryABCD operon is repressed by EryD and is induced by the presence of erythritol. Mutant 19B-3 was impaired in its ability to compete against wild-type for nodulation of pea plants but was still capable of forming nitrogen-fixing nodules.}, }
@article {pmid16804166, year = {2006}, author = {Coulthurst, SJ and Williamson, NR and Harris, AKP and Spring, DR and Salmond, GPC}, title = {Metabolic and regulatory engineering of Serratia marcescens: mimicking phage-mediated horizontal acquisition of antibiotic biosynthesis and quorum-sensing capacities.}, journal = {Microbiology (Reading, England)}, volume = {152}, number = {Pt 7}, pages = {1899-1911}, doi = {10.1099/mic.0.28803-0}, pmid = {16804166}, issn = {1350-0872}, mesh = {Anti-Bacterial Agents/*biosynthesis ; Base Sequence ; Genetic Engineering ; Molecular Sequence Data ; Multigene Family ; Phenotype ; Prodigiosin/*biosynthesis ; Serratia marcescens/genetics/*metabolism ; *Signal Transduction ; Virulence ; }, abstract = {Serratia marcescens is an important cause of opportunistic human infections. Many, but not all, strains produce prodigiosin, a secondary metabolic, red-pigment antibiotic, the biosynthesis of which is directed by the pig gene cluster. Quorum sensing (QS) involves the production and detection of chemical signal molecules as a means to regulate gene expression in response to population cell density. Several strains of S. marcescens have previously been shown to possess an N-acyl-L-homoserine lactone (aHSL) QS system. This study aimed to determine the impact of introducing, by phage-mediated horizontal gene transfer, a biosynthetic gene cluster (pig) and a regulatory locus (aHSL QS) into strains lacking the respective trait. The pig cluster from S. marcescens ATCC 274 (Sma 274) was transferred to the non-pigmented strain, S. marcescens strain 12 (Sma 12). In the engineered strain, pigment was expressed and brought under the control of the recipient's native regulatory systems (aHSL QS and luxS). Moreover, transfer of the aHSL locus from Sma 12 to the non-QS Sma 274 resulted in the imposition of aHSL control onto a variety of native traits, including pigment production. In addition, during this study, the QS regulon of the clinical strain, Sma 12, was characterized, and some novel QS-regulated traits in S. marcescens were identified. The results have implications for the evolution and dissemination of biosynthetic and QS loci, illustrating the genetic modularity and ease of acquisition of these traits and the capacity of phages to act as vectors for horizontal gene transfer.}, }
@article {pmid16802857, year = {2006}, author = {Sullivan, MB and Lindell, D and Lee, JA and Thompson, LR and Bielawski, JP and Chisholm, SW}, title = {Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts.}, journal = {PLoS biology}, volume = {4}, number = {8}, pages = {e234}, pmid = {16802857}, issn = {1545-7885}, support = {T32 GM007287/GM/NIGMS NIH HHS/United States ; GM07287-31/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Composition ; Biological Evolution ; Caudovirales/classification/*genetics/pathogenicity ; Gene Transfer, Horizontal ; Genome, Viral ; Molecular Sequence Data ; Photosynthetic Reaction Center Complex Proteins/*genetics ; Photosystem II Protein Complex/genetics ; Phylogeny ; Prochlorococcus/classification/*genetics/*virology ; Synechococcus/classification/*genetics/*virology ; }, abstract = {Cyanophages (cyanobacterial viruses) are important agents of horizontal gene transfer among marine cyanobacteria, the numerically dominant photosynthetic organisms in the oceans. Some cyanophage genomes carry and express host-like photosynthesis genes, presumably to augment the host photosynthetic machinery during infection. To study the prevalence and evolutionary dynamics of this phenomenon, 33 cultured cyanophages of known family and host range and viral DNA from field samples were screened for the presence of two core photosystem reaction center genes, psbA and psbD. Combining this expanded dataset with published data for nine other cyanophages, we found that 88% of the phage genomes contain psbA, and 50% contain both psbA and psbD. The psbA gene was found in all myoviruses and Prochlorococcus podoviruses, but could not be amplified from Prochlorococcus siphoviruses or Synechococcus podoviruses. Nearly all of the phages that encoded both psbA and psbD had broad host ranges. We speculate that the presence or absence of psbA in a phage genome may be determined by the length of the latent period of infection. Whether it also carries psbD may reflect constraints on coupling of viral- and host-encoded PsbA-PsbD in the photosynthetic reaction center across divergent hosts. Phylogenetic clustering patterns of these genes from cultured phages suggest that whole genes have been transferred from host to phage in a discrete number of events over the course of evolution (four for psbA, and two for psbD), followed by horizontal and vertical transfer between cyanophages. Clustering patterns of psbA and psbD from Synechococcus cells were inconsistent with other molecular phylogenetic markers, suggesting genetic exchanges involving Synechococcus lineages. Signatures of intragenic recombination, detected within the cyanophage gene pool as well as between hosts and phages in both directions, support this hypothesis. The analysis of cyanophage psbA and psbD genes from field populations revealed significant sequence diversity, much of which is represented in our cultured isolates. Collectively, these findings show that photosynthesis genes are common in cyanophages and that significant genetic exchanges occur from host to phage, phage to host, and within the phage gene pool. This generates genetic diversity among the phage, which serves as a reservoir for their hosts, and in turn influences photosystem evolution.}, }
@article {pmid16798872, year = {2006}, author = {Lin, Z and Kong, H and Nei, M and Ma, H}, title = {Origins and evolution of the recA/RAD51 gene family: evidence for ancient gene duplication and endosymbiotic gene transfer.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, number = {27}, pages = {10328-10333}, pmid = {16798872}, issn = {0027-8424}, support = {R01 GM020293/GM/NIGMS NIH HHS/United States ; R01 GM063871/GM/NIGMS NIH HHS/United States ; GM020293/GM/NIGMS NIH HHS/United States ; GM63871-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Endocytosis ; *Evolution, Molecular ; *Gene Duplication ; Gene Transfer, Horizontal/*genetics ; Humans ; Multigene Family/*genetics ; Rad51 Recombinase/classification/*genetics/metabolism ; Rec A Recombinases/classification/*genetics/metabolism ; Symbiosis/genetics ; Time Factors ; }, abstract = {The bacterial recA gene and its eukaryotic homolog RAD51 are important for DNA repair, homologous recombination, and genome stability. Members of the recA/RAD51 family have functions that have differentiated during evolution. However, the evolutionary history and relationships of these members remains unclear. Homolog searches in prokaryotes and eukaryotes indicated that most eubacteria contain only one recA. However, many archaeal species have two recA/RAD51 homologs (RADA and RADB), and eukaryotes possess multiple members (RAD51, RAD51B, RAD51C, RAD51D, DMC1, XRCC2, XRCC3, and recA). Phylogenetic analyses indicated that the recA/RAD51 family can be divided into three subfamilies: (i) RADalpha, with highly conserved functions; (ii) RADbeta, with relatively divergent functions; and (iii) recA, functioning in eubacteria and eukaryotic organelles. The RADalpha and RADbeta subfamilies each contain archaeal and eukaryotic members, suggesting that a gene duplication occurred before the archaea/eukaryote split. In the RADalpha subfamily, eukaryotic RAD51 and DMC1 genes formed two separate monophyletic groups when archaeal RADA genes were used as an outgroup. This result suggests that another duplication event occurred in the early stage of eukaryotic evolution, producing the DMC1 clade with meiosis-specific genes. The RADbeta subfamily has a basal archaeal clade and five eukaryotic clades, suggesting that four eukaryotic duplication events occurred before animals and plants diverged. The eukaryotic recA genes were detected in plants and protists and showed strikingly high levels of sequence similarity to recA genes from proteobacteria or cyanobacteria. These results suggest that endosymbiotic transfer of recA genes occurred from mitochondria and chloroplasts to nuclear genomes of ancestral eukaryotes.}, }
@article {pmid16793234, year = {2007}, author = {Dandie, CE and Burton, DL and Zebarth, BJ and Trevors, JT and Goyer, C}, title = {Analysis of denitrification genes and comparison of nosZ, cnorB and 16S rDNA from culturable denitrifying bacteria in potato cropping systems.}, journal = {Systematic and applied microbiology}, volume = {30}, number = {2}, pages = {128-138}, doi = {10.1016/j.syapm.2006.05.002}, pmid = {16793234}, issn = {0723-2020}, mesh = {Bacteria/chemistry/*classification/*genetics/isolation &amp; purification/metabolism ; Bacterial Proteins/*genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fatty Acids/analysis/isolation &amp; purification ; Genes, rRNA ; Metabolic Networks and Pathways/*genetics ; Molecular Sequence Data ; Nitrite Reductases/genetics ; Oxidoreductases/genetics ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Solanum tuberosum/*microbiology ; }, abstract = {Bacterial denitrification in agricultural soils is a major source of nitrous oxide, a potent greenhouse gas. This study examined the culturable bacterial population of denitrifiers in arable field soils in potato (Solanum tuberosum L.) production and denitrification genes (nir, nor and nos) and 16S rDNA in those isolates. Enrichments for culturable denitrifiers yielded 31 diverse isolates that were then analysed for denitrification genes. The nitrous oxide reductase (nosZ) gene was found in all isolates. The majority of isolates (approximately 90%) contained the cnorB nitric oxide reductase gene, with the remainder containing the qnorB gene. Nitrite reductase genes (nirS and nirK) were amplifiable from most of the isolates, and were segregated between species similar to previously isolated denitrifiers. Isolated strains were preliminarily identified using fatty acid methyl ester analysis and further identified using 16S rDNA sequencing. The majority of isolates (21) were classified as Pseudomonas sp., with smaller groups of isolates being most similar to Bosea spp. (4), Achromobacter spp. (4) and two isolates closely related to Sinorhizobium/Ensifer spp. Phylogenetic trees were compared among nosZ, cnorB and 16S rDNA genes for a subset of Pseudomonas strains. The trees were mostly congruent, but some Pseudomonas sp. isolates grouped differently depending on the gene analysed, indicating potential horizontal gene transfer of denitrification genes. Although Bosea spp. are known denitrifiers, to the best of our knowledge this is the first report of isolation and sequencing of denitrification genes from this bacterial genus.}, }
@article {pmid16791790, year = {2006}, author = {Pietramellara, G and Ceccherini, MT and Ascher, J and Nannipieri, P}, title = {Persistence of transgenic and not transgenic extracellular DNA in soil and bacterial transformation.}, journal = {Rivista di biologia}, volume = {99}, number = {1}, pages = {37-68}, pmid = {16791790}, issn = {0035-6050}, mesh = {*DNA/analysis ; Ecology ; Gene Transfer, Horizontal ; *Soil/analysis ; Soil Microbiology ; Transformation, Bacterial/*genetics ; }, abstract = {The study of the fate of transgenic and not transgenic extracellular DNA in soil is of extreme relevance because the soil extracellular DNA pool represents a genetic reservoir that could be utilized as a source of food by any heterotrophic microorganism or genetic information by recipient eukaryotic and prokaryotic cells. Several data have clearly evidenced that extracellular DNA could persist in soil for long time maintaining a sufficient integrity of the molecule. Recent microcosm studies under laboratory conditions have evidenced that extracellular DNA molecule could be leached or raised up by capillarity. The persistence and movement of extracellular DNA molecule in soil suggest that the genetic information of extracellular DNA could be taken up by microorganisms temporarily and spatially separated. Several authors have studied the persistence and transformation efficiency of the extracellular DNA in soil demonstrating that there is a sharp discrepancy between its biological efficiency and its persistence; fragments of target DNA were detected after a long time in soil but no transformations were determined probably because the genetic information originally present in the complete DNA molecule could be lost by degradation. It is also important to underline that the frequency of gene transfer in soil is markedly limited by the few number of bacteria able to develop competence and that this physiological state is reached only under certain conditions. Furthermore the dilution of the transgene in the soil extracellular DNA pool drastically decreases chances for the uptake of the transgene. Anyway the importance of transformation in evolutionary terms, represents a valid reason to continue the investigation on the fate of extracellular DNA in soil.}, }
@article {pmid16790794, year = {2006}, author = {Muniesa, M and Schembri, MA and Hauf, N and Chakraborty, T}, title = {Active genetic elements present in the locus of enterocyte effacement in Escherichia coli O26 and their role in mobility.}, journal = {Infection and immunity}, volume = {74}, number = {7}, pages = {4190-4199}, pmid = {16790794}, issn = {0019-9567}, mesh = {Chromosomes, Bacterial/genetics ; Enterocytes/*microbiology ; Escherichia coli/enzymology/*genetics/*pathogenicity ; Escherichia coli Proteins/*genetics/physiology ; Integrases/genetics/physiology ; Movement/*physiology ; Mutation ; Phosphoproteins/*genetics/physiology ; }, abstract = {The locus of enterocyte effacement (LEE) is a large multigene chromosomal segment encoding gene products responsible for the generation of attaching and effacing lesions in many diarrheagenic Escherichia coli strains. A recently sequenced LEE harboring a pathogenicity island (PAI) from a Shiga toxin E. coli serotype O26 strain revealed a LEE PAI (designated LEE O26) almost identical to that obtained from a rabbit-specific enteropathogenic O15:H- strain. LEE O26 comprises 59,540 bp and is inserted at 94 min within the mature pheU tRNA locus. The LEE O26 PAI is flanked by two direct repeats of 137 and 136 bp (DR1 and DR2), as well as a gene encoding an integrase belonging to the P4 integrase family. We examined LEE O26 for horizontal gene transfer. By generating mini-LEE plasmids harboring only DR1 or DR2 with or without the integrase-like gene, we devised a simple assay to examine recombination processes between these sequences. Recombination was shown to be integrase dependent in a DeltarecA E. coli K-12 strain background. Recombinant plasmids harboring a single direct repeat cloned either with or without the LEE O26 integrase gene were found to insert within the chromosomal pheU locus of E. coli K-12 strains with equal efficiency, suggesting that an endogenous P4-like integrase can substitute for this activity. An integrase with strong homology to the LEE O26 integrase was detected on the K-12 chromosome associated with the leuX tRNA locus at 97 min. Strains deleted for this integrase demonstrated a reduction in the insertion frequency of plasmids harboring only the DR into the pheU locus. These results provide strong evidence that LEE-harboring elements are indeed mobile and suggest that closely related integrases present on the chromosome of E. coli strains contribute to the dynamics of PAI mobility.}, }
@article {pmid16790017, year = {2006}, author = {Eschenlauer, SC and Coombs, GH and Mottram, JC}, title = {PFPI-like genes are expressed in Leishmania major but are pseudogenes in other Leishmania species.}, journal = {FEMS microbiology letters}, volume = {260}, number = {1}, pages = {47-54}, doi = {10.1111/j.1574-6968.2006.00303.x}, pmid = {16790017}, issn = {0378-1097}, support = {G0000508/MRC_/Medical Research Council/United Kingdom ; G0000508(56841)/MRC_/Medical Research Council/United Kingdom ; G9722968/MRC_/Medical Research Council/United Kingdom ; G9722968(65078)/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Animals ; Archaeal Proteins/chemistry/*genetics ; *Genes, Protozoan ; Leishmania/*genetics ; Leishmania major/*genetics ; Molecular Sequence Data ; Open Reading Frames ; Peptide Hydrolases/chemistry/*genetics ; *Pseudogenes ; Recombinant Fusion Proteins/chemistry/*genetics ; }, abstract = {Pyrococcus furiosus protease I (PFPI) is a multimeric cysteine peptidase from P. furiosus. Genome analyses indicate that orthologues are present in rather few other organisms, including Dictyostelium discoideum and several bacteria, Archaea and plants. An open reading frame (ORF) coding for a PFPI-like protein (PFP1) was identified in Leishmania major and Leishmania mexicana and full-length spliced and polyadenylated PFP1 mRNA detected for both species. Vestiges of a PFPI-like gene could also be identified in Leishmania braziliensis and Leishmania infantum, but no ORF remains owing to the presence of frame-shifts and stop codons. No evidence for a PFPI-like gene could be found in the syntenic region of Trypanosoma brucei or Trypanosoma cruzi, raising the possibility that the PFPI-like genes were acquired by a lateral gene transfer event after the divergence of trypanosomes and Leishmania. The gene may have subsequently degenerated into a pseudogene in some Leishmania species, owing to the loss of relevant biological function. However, antibodies raised against L. mexicana recombinant protein detected PFP1 in promastigote extracts of L. major, but not in L. mexicana promastigote or amastigote extracts. The expression of PFP1 in L. major suggests that PFP1 might contribute to the disease tropism that distinguishes this Leishmania species from others.}, }
@article {pmid16788741, year = {2006}, author = {Macario, AJ and Brocchieri, L and Shenoy, AR and Conway de Macario, E}, title = {Evolution of a protein-folding machine: genomic and evolutionary analyses reveal three lineages of the archaeal hsp70(dnaK) gene.}, journal = {Journal of molecular evolution}, volume = {63}, number = {1}, pages = {74-86}, pmid = {16788741}, issn = {0022-2844}, support = {2 R01 GM010452/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; *Evolution, Molecular ; Genes, Archaeal ; Genes, Bacterial ; Genetic Structures ; *Genome, Archaeal ; HSP40 Heat-Shock Proteins/genetics ; HSP70 Heat-Shock Proteins/*genetics ; Internal-External Control ; Molecular Chaperones/genetics ; Phylogeny ; *Protein Folding ; Protein Isoforms/*genetics ; }, abstract = {The stress chaperone protein Hsp70 (DnaK) (abbreviated DnaK) and its co-chaperones Hsp40(DnaJ) (or DnaJ) and GrpE are universal in bacteria and eukaryotes but occur only in some archaea clustered in the order 5'-grpE-dnaK-dnaJ-3' in a locus termed Locus I. Three structural varieties of Locus I, termed Types I, II, and III, were identified, respectively, in Methanosarcinales, in Thermoplasmatales and Methanothermobacter thermoautotrophicus, and in Halobacteriales. These Locus I types corresponded to three groups identified by phylogenetic trees of archaeal DnaK proteins including the same archaeal subdivisions. These archaeal DnaK groups were not significantly interrelated, clustering instead with DnaKs from three bacterial lineages, Methanosarcinales with Firmicutes, Thermoplasmatales and M. thermoautotrophicus with Thermotoga, and Halobacteriales with Actinobacteria, suggesting that the three archaeal types of Locus I were acquired by independent events of lateral gene transfer. These associations, however, lacked strong bootstrap support and were sensitive to dataset choice and tree-reconstruction method. Structural features of dnaK loci in bacteria revealed that Methanosarcinales and Firmicutes shared a similar structure, also common to most other bacterial groups. Structural differences were observed instead in Thermotoga compared to Thermoplasmatales and M. thermoautotrophicus, and in Actinobacteria compared to Halobacteriales. It was also found that the association between the DnaK sequences from Halobacteriales and Actinobacteria likely reflects common biases in their amino acid compositions. Although the loci structural features and the DnaK trees suggested the possibility of lateral gene transfer between Firmicutes and Methanosarcinales, the similarity between the archaeal and the ancestral bacterial loci favors the more parsimonious hypothesis that all archaeal sequences originated from a unique prokaryotic ancestor.}, }
@article {pmid16788724, year = {2006}, author = {Marri, PR and Bannantine, JP and Paustian, ML and Golding, GB}, title = {Lateral gene transfer in Mycobacterium avium subspecies paratuberculosis.}, journal = {Canadian journal of microbiology}, volume = {52}, number = {6}, pages = {560-569}, doi = {10.1139/w06-001}, pmid = {16788724}, issn = {0008-4166}, mesh = {Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/genetics ; Genome, Bacterial/genetics ; Mycobacterium avium/genetics ; Mycobacterium avium subsp. paratuberculosis/classification/*genetics ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA/methods ; }, abstract = {Lateral gene transfer is an integral part of genome evolution in most bacteria. Bacteria can readily change the contents of their genomes to increase adaptability to ever-changing surroundings and to generate evolutionary novelty. Here, we report instances of lateral gene transfer in Mycobacterium avium subsp. paratuberculosis, a pathogenic bacteria that causes Johne's disease in cattle. A set of 275 genes are identified that are likely to have been recently acquired by lateral gene transfer. The analysis indicated that 53 of the 275 genes were acquired after the divergence of M. avium subsp. paratuberculosis from M. avium subsp. avium, whereas the remaining 222 genes were possibly acquired by a common ancestor of M. avium subsp. paratuberculosis and M. avium subsp. avium after its divergence from the ancestor of M. tuberculosis complex. Many of the acquired genes were from proteobacteria or soil dwelling actinobacteria. Prominent among the predicted laterally transferred genes is the gene rsbR, a possible regulator of sigma factor, and the genes designated MAP3614 and MAP3757, which are similar to genes in eukaryotes. The results of this study suggest that like most other bacteria, lateral gene transfers seem to be a common feature in M. avium subsp. paratuberculosis and that the proteobacteria contribute most of these genetic exchanges.}, }
@article {pmid16785718, year = {2006}, author = {Shi, L and Zheng, M and Xiao, Z and Asakura, M and Su, J and Li, L and Yamasaki, S}, title = {Unnoticed spread of class 1 integrons in gram-positive clinical strains isolated in Guangzhou, China.}, journal = {Microbiology and immunology}, volume = {50}, number = {6}, pages = {463-467}, doi = {10.1111/j.1348-0421.2006.tb03815.x}, pmid = {16785718}, issn = {0385-5600}, mesh = {Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Gram-Positive Bacteria/drug effects/*genetics ; Humans ; *Integrons ; Microbial Sensitivity Tests ; }, abstract = {A total of 46 gram-positive bacteria isolated from clinical specimens collected in China were subjected to PCR analysis with the intI1-specific primers, and the intI1-positive strains were further analyzed for their resistance gene cassette. All isolates possessed the class 1 integron in their genomes and the array of gene cassettes was dhfrXII-orfF-aadA2, which is very similar to other organisms except in one isolate carrying an additional copy of the class 1 integron containing the aadA2 gene cassette. Altogether, the results indicate that the class 1 integron is widespread in gram-positive clinical strains isolated in Guangzhou, China.}, }
@article {pmid16782763, year = {2006}, author = {Filée, J and Bapteste, E and Susko, E and Krisch, HM}, title = {A selective barrier to horizontal gene transfer in the T4-type bacteriophages that has preserved a core genome with the viral replication and structural genes.}, journal = {Molecular biology and evolution}, volume = {23}, number = {9}, pages = {1688-1696}, doi = {10.1093/molbev/msl036}, pmid = {16782763}, issn = {0737-4038}, mesh = {Bacteriophage T4/*genetics ; Chromosome Mapping ; Conserved Sequence ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Viral ; *Genome, Viral ; Phylogeny ; Recombination, Genetic ; *Selection, Genetic ; Viral Proteins ; Virus Replication ; }, abstract = {Genomic analysis of bacteriophages frequently reveals a mosaic structure made up from modules that come from disparate sources. This fact has led to the general acceptance of the notion that rampant and promiscuous lateral gene transfer (LGT) plays a critical role in phage evolution. However, recent sequencing of a series of the T4-type phages has revealed that these large and complex genomes all share 2 substantial syntenous blocks of genes encoding the replication and virion structural genes. To analyze the pattern of inheritance of this core T4 genome, we compared the complete genome sequences of 16 T4-type phages. We identified a set of 24 genes present in all these T4-type genomes. Somewhat surprisingly, only one of these genes, that encodes for ribonucleotide reductase (NrdA), displayed evidence of LGT with the bacterial host. We test the congruence of the inheritance of the other 23 markers using heat map analyses and comparison of a reference topology with the 23 individual gene phylogenies. The vast majority of these core genes share a common evolutionary history. In contrast, analyses of all the noncore genes present in the same 16 genomes, located in the hyperplastic regions of the genome, show considerable evidence of frequent LGT. The similar evolution of the core replication and virion structural genes in the T4-type phage genomes suggests that, unlike the situation in many other phage groups, such portions of T4-type genome have been inherited as a block, without significant LGT, from a distant common ancestor. The preservation of the synteny of the core T4 genome could result from several factors acting in synergy, such as the constraints imposed by the sophisticated regulation of the transcription. Moreover, numerous and complex protein-protein interactions during virion morphogenesis could also impose a supplementary barrier against LGT. Finally, there may be some real evolutionary advantage to maintaining large regions of conserved sequence. Such segments could be a sort of genetic glue that maintains the genetic cohesion of the T4-type phages via recombination within the most conserved sequences. This could mediate the swapping of nonconserved sequences that they flank.}, }
@article {pmid16782743, year = {2006}, author = {Peirano, G and Agersø, Y and Aarestrup, FM and dos Reis, EM and dos Prazeres Rodrigues, D}, title = {Occurrence of integrons and antimicrobial resistance genes among Salmonella enterica from Brazil.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {58}, number = {2}, pages = {305-309}, doi = {10.1093/jac/dkl248}, pmid = {16782743}, issn = {0305-7453}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Brazil ; Conjugation, Genetic ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/*genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Integrons/*genetics ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Plasmids ; Polymerase Chain Reaction ; Salmonella enterica/*drug effects/*genetics/isolation &amp; purification ; Sequence Analysis, DNA ; }, abstract = {OBJECTIVES: To determine the occurrence of antimicrobial resistance genes and role of integrons among 135 antimicrobial-resistant Salmonella enterica from Brazil.<br><br>METHODS: The presence of antimicrobial resistance genes, class 1 and 2 integrons and gene cassettes was analysed by PCR and sequencing. The genetic location of class 1 integrons was determined in 25 isolates by hybridization and plasmid transfer experiments.<br><br>RESULTS: Fifty-five of the isolates were positive for class 1 integrons. Integron-positive isolates represented 17 different serovars and were mainly from human (n=28) and animal (n=13) sources. The gene cassette arrangements could be determined in 51 of the positive isolates, which harboured one [dfrA22, aadA1 or orf3 (putative trimethoprim resistance)], two [aadA1-dfrA1, aac(6')-Ib-orf1 (unknown function) or aacA4-aadA1], three [dfrA15b-cmlA4-aadA2, orf2 (unknown function)-dfrA5-orfD] or four [orf4-aacA4-blaOXA-30 (interrupted by an IS1 element)-aadA1] cassettes in their variable region. Only one isolate harboured a class 2 integron with the gene cassette array dfrA1-sat-aadA1. Several integron unrelated resistance genes were also detected in the isolates. Sulphonamide resistance was primarily mediated by sul2 and sul3, tetracycline resistance by tet(B) and tet(A), chloramphenicol resistance by catA1, streptomycin resistance by strA and ampicillin resistance by blaTEM. blaCTX and blaCMY-2 were found in cephalosporin-resistant isolates. Mating and hybridization experiments demonstrated that a high-molecular-weight plasmid mediated the gene transfer of integrons and additional resistance determinants.<br><br>CONCLUSIONS: The present study revealed that integron-mediated resistance genes contributed to the multiresistance phenotype observed in the isolates, but most resistance genes were located outside the integron structure, as independent genes. However, they might be located on the same conjugative plasmid.}, }
@article {pmid16782741, year = {2006}, author = {Antunes, P and Machado, J and Peixe, L}, title = {Characterization of antimicrobial resistance and class 1 and 2 integrons in Salmonella enterica isolates from different sources in Portugal.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {58}, number = {2}, pages = {297-304}, doi = {10.1093/jac/dkl242}, pmid = {16782741}, issn = {0305-7453}, mesh = {Anti-Bacterial Agents/*pharmacology ; Conjugation, Genetic ; DNA, Bacterial/genetics ; *Drug Resistance, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Environmental Microbiology ; Food Microbiology ; Gene Transfer, Horizontal ; Genotype ; Humans ; Integrons/*genetics ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Portugal ; Salmonella Infections/microbiology ; Salmonella enterica/classification/*drug effects/*genetics/isolation &amp; purification ; Sequence Analysis, DNA ; }, abstract = {OBJECTIVES: The antimicrobial resistance profiles of 1183 Salmonella isolates collected during 2002-2003 from several sources (human, food products and environment) were evaluated. The occurrence, distribution and cassette content of class 1 and 2 integrons among the sulphonamide-resistant population, as well as the role of particular clones to the spread of these genetic elements, were investigated.<br><br>METHODS: The isolates were examined for susceptibility to antimicrobial agents. The characterization of class 1 and 2 integrons was investigated using PCR, PCR-RFLP (restriction fragment length polymorphism) and sequencing in the sulphonamide-resistant isolates. Conjugation assays and clonality analysis by PFGE were performed.<br><br>RESULTS: The most common resistance phenotypes were to nalidixic acid, tetracycline, streptomycin, sulfamethoxazole and ampicillin (ranging from 31% to 17%). Resistance to sulphonamides (n=200) was associated with resistance to other antimicrobial agents, with 75% of the isolates carrying one or two class 1 integrons while only 3% simultaneously carried class 1 and 2 integrons. Integrons were observed among at least 11 serotypes (mainly Typhimurium) and in a reduced number of PFGE clones (20). Eight class 1 integron types were found, with the aadA genes (aadA1, aadA2 and aadA5) alone or downstream of a trimethoprim (dfrA1, dfrA12 and dfrA17) or a beta-lactamase resistance gene (blaoxa-30) and the blaPSE-1 gene alone. Most of the class 1 integron types were shared by several clones from the same or different serotypes obtained either from humans or food products of animal origin, especially pork products. However, some Typhimurium-specific integrons were found: aadA2 plus blaPSE-1 and blaoxa-30-aadA1.<br><br>CONCLUSIONS: Apart from the hypothetical contribution of the conjugative transfer of integrons, the incidence of Salmonella carrying these genetic units seems to rely on the ability of certain clones to spread or persist in particular animal niches. Our data suggest that food-producing animals might be simultaneously considered as a reservoir of clones and integrons carrying antibiotic resistance genes, thus making the food chain, especially pork products, a possible source of multidrug-resistant isolates in humans.}, }
@article {pmid16778837, year = {2006}, author = {Telford, JL and Barocchi, MA and Margarit, I and Rappuoli, R and Grandi, G}, title = {Pili in gram-positive pathogens.}, journal = {Nature reviews. Microbiology}, volume = {4}, number = {7}, pages = {509-519}, doi = {10.1038/nrmicro1443}, pmid = {16778837}, issn = {1740-1526}, mesh = {Bacterial Adhesion ; Evolution, Molecular ; Fimbriae Proteins/genetics ; Fimbriae, Bacterial/*genetics/*metabolism/ultrastructure ; Gene Transfer, Horizontal ; Genomic Islands ; Gram-Positive Bacteria/pathogenicity/*physiology/ultrastructure ; Models, Biological ; Protein Subunits/genetics ; }, abstract = {Most bacterial pathogens have long filamentous structures known as pili or fimbriae extending from their surface. These structures are often involved in the initial adhesion of the bacteria to host tissues during colonization. In gram-negative bacteria, pili are typically formed by non-covalent interactions between pilin subunits. By contrast, the recently discovered pili in gram-positive pathogens are formed by covalent polymerization of adhesive pilin subunits. Evidence from studies of pili in the three principal streptococcal pathogens of humans indicates that the genes that encode the pilin subunits and the enzymes that are required for the assembly of these subunits into pili have been acquired en bloc by the horizontal transfer of a pathogenicity island.}, }
@article {pmid16777968, year = {2006}, author = {Levine, MT and Jones, CD and Kern, AD and Lindfors, HA and Begun, DJ}, title = {Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, number = {26}, pages = {9935-9939}, pmid = {16777968}, issn = {0027-8424}, support = {R01 GM071926/GM/NIGMS NIH HHS/United States ; GM 071926/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; DNA Shuffling ; Drosophila melanogaster/*genetics ; Gene Expression ; Genes, Insect/*genetics ; Introns/*genetics ; Male ; Molecular Sequence Data ; RNA, Messenger/analysis/metabolism ; Testis/*metabolism ; X Chromosome/*genetics ; }, abstract = {Descriptions of recently evolved genes suggest several mechanisms of origin including exon shuffling, gene fission/fusion, retrotransposition, duplication-divergence, and lateral gene transfer, all of which involve recruitment of preexisting genes or genetic elements into new function. The importance of noncoding DNA in the origin of novel genes remains an open question. We used the well annotated genome of the genetic model system Drosophila melanogaster and genome sequences of related species to carry out a whole-genome search for new D. melanogaster genes that are derived from noncoding DNA. Here, we describe five such genes, four of which are X-linked. Our RT-PCR experiments show that all five putative novel genes are expressed predominantly in testes. These data support the idea that these novel genes are derived from ancestral noncoding sequence and that new, favored genes are likely to invade populations under selective pressures relating to male reproduction.}, }
@article {pmid16774843, year = {2006}, author = {Rommens, CM}, title = {Kanamycin resistance in plants: an unexpected trait controlled by a potentially multifaceted gene.}, journal = {Trends in plant science}, volume = {11}, number = {7}, pages = {317-319}, doi = {10.1016/j.tplants.2006.05.002}, pmid = {16774843}, issn = {1360-1385}, mesh = {ATP-Binding Cassette Transporters/genetics/*physiology ; Arabidopsis/genetics/*metabolism ; Drug Resistance/*genetics ; Genes, Plant ; Genetic Engineering ; Kanamycin/*metabolism ; Safety ; }, abstract = {Ayalew Mentewab and C. Neal Stewart Jr recently showed that an Arabidopsis kanamycin resistance gene encodes an ATP binding cassette (ABC) transporter. This Atwbc19 protein is hypothesized to prevent ribosome inactivation by translocating kanamycin into the vacuole. Because ABC transporters often recognize multiple exogenous substrates, overexpression of Atwbc19 can result in the accumulation of unexpected compounds in transgenic plants. Another potential safety issue associated with this gene is horizontal gene transfer. Thus, commercial applications are likely to be limited to methods that allow removal of the selectable marker from the transgenic plant genome.}, }
@article {pmid16774784, year = {2006}, author = {Staddon, JH and Bryan, EM and Manias, DA and Chen, Y and Dunny, GM}, title = {Genetic characterization of the conjugative DNA processing system of enterococcal plasmid pCF10.}, journal = {Plasmid}, volume = {56}, number = {2}, pages = {102-111}, pmid = {16774784}, issn = {0147-619X}, support = {T32 GM008347/GM/NIGMS NIH HHS/United States ; T32GM08244/GM/NIGMS NIH HHS/United States ; 1R01-GM49530/GM/NIGMS NIH HHS/United States ; T32GM08347/GM/NIGMS NIH HHS/United States ; R01 GM049530/GM/NIGMS NIH HHS/United States ; R01 GM049530-20/GM/NIGMS NIH HHS/United States ; T32 GM008244/GM/NIGMS NIH HHS/United States ; T32AI07421/AI/NIAID NIH HHS/United States ; T32 AI007421/AI/NIAID NIH HHS/United States ; }, mesh = {Base Sequence ; Chromosome Mapping ; Computational Biology ; Conjugation, Genetic/*genetics ; DNA Primers ; DNA, Bacterial/*genetics ; Electroporation ; Enterococcus faecalis/*genetics ; Gene Transfer Techniques ; Molecular Sequence Data ; Plasmids/*genetics ; Polymerase Chain Reaction ; Replication Origin/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Conjugation is a major contributor to lateral gene transfer in bacteria, and pheromone-inducible conjugation systems in Enterococcus faecalis play an important role in the dissemination of antibiotic resistance and virulence in enterococci and related bacteria. We have genetically dissected the determinants of DNA processing of the enterococcal conjugative plasmid pCF10. Insertional inactivation of a predicted relaxase gene pcfG, via insertion of a splicing-deficient group II intron, severely reduced pCF10 transfer. Restoration of intron splicing ability by genetic complementation restored conjugation. The pCF10 origin of transfer (oriT) was localized to a 40-nucleotide sequence within a non-coding region with sequence similarity to origins of transfer of several other plasmids in gram positive bacteria. Deletion of the oriT reduced pCF10 transfer by more than five orders of magnitude without affecting pCF10-dependent mobilization of co-resident oriT-containing plasmids. Although the host range for pCF10 replication is limited to enterococci, we found that the pCF10 conjugation system promotes mobilization of oriT-containing plasmids to multiple bacterial genera. Therefore, this transfer system may have applications for gene delivery to a variety of poorly-transformed bacteria.}, }
@article {pmid16773828, year = {2005}, author = {Jarzembowski, T and Bryl, E and Witkowski, J}, title = {[Flow cytometric analysis of Enterococcus faecalis aph2"(+) response to aph2" (-) strains with high and low gene transfer rate].}, journal = {Medycyna doswiadczalna i mikrobiologia}, volume = {57}, number = {4}, pages = {355-358}, pmid = {16773828}, issn = {0025-8601}, mesh = {Cell Aggregation/genetics ; Conjugation, Genetic ; DNA/*analysis ; Drug Resistance, Microbial/genetics ; Enterococcus faecalis/*classification/*genetics ; Flow Cytometry/methods ; Gene Transfer, Horizontal/*physiology ; Genes, Bacterial ; Species Specificity ; }, abstract = {Resistance genes, as aph2" are usually encoded on conjugate plasmids and spread with high rate 2 among Gram-positive cocci. The conjugation is inducted by recipient strains by secreting specific pheromone involved in formation of mating aggregates with donor cells. The project aimed to check if strain with lower rate of gene transfer differ also from strains with high gene transfer in ability to aggregate to donor strains. In our study we used two aph2"(+), three aph2"(-) with low transfer e and three aph2"(-) with high transfer strains. Each time one aph2"(+) and one aph2" strains were cultivated for 18h in BHI. The bacteria was washed, stained with carboksyfluorescein, and analyzed by flow cytometry in FACS BD cytometr. Relative fluorescence and size of aggregation was used to compare influence on particular stains. In result of induction of aph2"(+) strains with aph2" recipients with high transfer rate we observed increase of size and number aggregates. Surprisingly, induction with aph2" recipients with low transfer rate result in two different reaction of aph2"(+) donors. In case of one of the , according to expectation we do not observe increase of aggregation. Second of the donors aggregate with induction with aph2" recipients with low transfer rate, but in contrast to reaction to presence of other recipients, fluorescence of such aggregates increased. The results show that strain with lower rate of gene transfer in fact differ from strains with high gene transfer in ability to aggregate to donor strains ant that analysis of aggregation alone is insufficient to distinguish between recipients of high and low transfer rate.}, }
@article {pmid16769896, year = {2006}, author = {Kechris, KJ and Lin, JC and Bickel, PJ and Glazer, AN}, title = {Quantitative exploration of the occurrence of lateral gene transfer by using nitrogen fixation genes as a case study.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, number = {25}, pages = {9584-9589}, pmid = {16769896}, issn = {0027-8424}, support = {R01 GM075312/GM/NIGMS NIH HHS/United States ; R01 GM 075312/GM/NIGMS NIH HHS/United States ; }, mesh = {Codon/genetics ; Computational Biology ; Gene Transfer, Horizontal/*genetics ; Nitrogen Fixation/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Lateral gene transfer (LGT) is now accepted as an important factor in the evolution of prokaryotes. Establishment of the occurrence of LGT is typically attempted by a variety of methods that includes the comparison of reconstructed phylogenetic trees, the search for unusual GC composition or codon usage within a genome, and identification of similarities between distant species as determined by best blast hits. We explore quantitative assessments of these strategies to study the prokaryotic trait of nitrogen fixation, the enzyme-catalyzed reduction of N(2) to ammonia. Phylogenies constructed on nitrogen fixation genes are not in agreement with the tree-of-life based on 16S rRNA but do not conclusively distinguish between gene loss and LGT hypotheses. Using a series of analyses on a set of complete genomes, our results distinguish two structurally distinct classes of MoFe nitrogenases whose distribution cuts across lines of vertical inheritance and makes us believe that a conclusive case for LGT has been made.}, }
@article {pmid16766509, year = {2006}, author = {Azuma, Y and Hirakawa, H and Yamashita, A and Cai, Y and Rahman, MA and Suzuki, H and Mitaku, S and Toh, H and Goto, S and Murakami, T and Sugi, K and Hayashi, H and Fukushi, H and Hattori, M and Kuhara, S and Shirai, M}, title = {Genome sequence of the cat pathogen, Chlamydophila felis.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {13}, number = {1}, pages = {15-23}, doi = {10.1093/dnares/dsi027}, pmid = {16766509}, issn = {1340-2838}, mesh = {Adaptation, Biological ; Animals ; Bacterial Outer Membrane Proteins/genetics ; Bacterial Proteins/genetics ; Base Sequence ; Cat Diseases/*microbiology ; Cats ; Chlamydophila Infections/*veterinary ; Chlamydophila pneumoniae/*genetics ; Evolution, Molecular ; Female ; Gene Frequency ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Models, Genetic ; Molecular Sequence Data ; Phosphoproteins/genetics ; Phylogeny ; Plasmids ; Pneumonia, Bacterial/*microbiology/*veterinary ; Sequence Homology, Nucleic Acid ; Translocation, Genetic ; }, abstract = {Chlamydophila felis (Chlamydia psittaci feline pneumonitis agent) is a worldwide spread pathogen for pneumonia and conjunctivitis in cats. Herein, we determined the entire genomic DNA sequence of the Japanese C. felis strain Fe/C-56 to understand the mechanism of diseases caused by this pathogen. The C. felis genome is composed of a circular 1,166,239 bp chromosome encoding 1005 protein-coding genes and a 7552 bp circular plasmid. Comparison of C. felis gene contents with other Chlamydia species shows that 795 genes are common in the family Chlamydiaceae species and 47 genes are specific to C. felis. Phylogenetic analysis of the common genes reveals that most of the orthologue sets exhibit a similar divergent pattern but 14 C. felis genes accumulate more mutations, implicating that these genes may be involved in the evolutional adaptation to the C. felis-specific niche. Gene distribution and orthologue analyses reveal that two distinctive regions, i.e. the plasticity zone and frequently gene-translocated regions (FGRs), may play important but different roles for chlamydial genome evolution. The genomic DNA sequence of C. felis provides information for comprehension of diseases and elucidation of the chlamydial evolution.}, }
@article {pmid16763111, year = {2006}, author = {Navarre, WW and Porwollik, S and Wang, Y and McClelland, M and Rosen, H and Libby, SJ and Fang, FC}, title = {Selective silencing of foreign DNA with low GC content by the H-NS protein in Salmonella.}, journal = {Science (New York, N.Y.)}, volume = {313}, number = {5784}, pages = {236-238}, doi = {10.1126/science.1128794}, pmid = {16763111}, issn = {1095-9203}, support = {AI034829/AI/NIAID NIH HHS/United States ; AI049417/AI/NIAID NIH HHS/United States ; AI052237/AI/NIAID NIH HHS/United States ; AI057733/AI/NIAID NIH HHS/United States ; AI39557/AI/NIAID NIH HHS/United States ; AI48622/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/*metabolism ; Base Composition ; Binding Sites ; Chromatin Immunoprecipitation ; DNA, Bacterial/*chemistry/*genetics ; DNA-Binding Proteins/genetics/*metabolism ; Gene Expression Regulation, Bacterial ; *Gene Silencing ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Helicobacter pylori/genetics ; Models, Genetic ; Mutation ; Oligonucleotide Array Sequence Analysis ; Repressor Proteins/genetics/*metabolism ; Salmonella typhimurium/*genetics/physiology ; }, abstract = {Horizontal gene transfer plays a major role in microbial evolution. However, newly acquired sequences can decrease fitness unless integrated into preexisting regulatory networks. We found that the histone-like nucleoid structuring protein (H-NS) selectively silences horizontally acquired genes by targeting sequences with GC content lower than the resident genome. Mutations in hns are lethal in Salmonella unless accompanied by compensatory mutations in other regulatory loci. Thus, H-NS provides a previously unrecognized mechanism of bacterial defense against foreign DNA, enabling the acquisition of DNA from exogenous sources while avoiding detrimental consequences from unregulated expression of newly acquired genes. Characteristic GC/AT ratios of bacterial genomes may facilitate discrimination between a cell's own DNA and foreign DNA.}, }
@article {pmid16761366, year = {2006}, author = {Novozhilov, AS and Karev, GP and Koonin, EV}, title = {Biological applications of the theory of birth-and-death processes.}, journal = {Briefings in bioinformatics}, volume = {7}, number = {1}, pages = {70-85}, doi = {10.1093/bib/bbk006}, pmid = {16761366}, issn = {1467-5463}, mesh = {Animals ; Computational Biology/*methods ; *Computer Simulation ; *Evolution, Molecular ; Humans ; *Models, Genetic ; }, abstract = {In this review, we discuss applications of the theory of birth-and-death processes to problems in biology, primarily, those of evolutionary genomics. The mathematical principles of the theory of these processes are briefly described. Birth-and-death processes, with some straightforward additions such as innovation, are a simple, natural and formal framework for modeling a vast variety of biological processes such as population dynamics, speciation, genome evolution, including growth of paralogous gene families and horizontal gene transfer and somatic evolution of cancers. We further describe how empirical data, e.g. distributions of paralogous gene family size, can be used to choose the model that best reflects the actual course of evolution among different versions of birth-death-and-innovation models. We conclude that birth-and-death processes, thanks to their mathematical transparency, flexibility and relevance to fundamental biological processes, are going to be an indispensable mathematical tool for the burgeoning field of systems biology.}, }
@article {pmid16758911, year = {2006}, author = {Zigangirova, NA and Tokarskaia, EA and Narodnitskiĭ, BS and Gintsburg, AL and Tugel'ian, VA}, title = {[Role of lactic acid bacteria in the spread of antibiotic resistant bacteria among healthy persons].}, journal = {Zhurnal mikrobiologii, epidemiologii i immunobiologii}, volume = {}, number = {2}, pages = {106-109}, pmid = {16758911}, issn = {0372-9311}, mesh = {Animal Husbandry/methods ; Animals ; Animals, Domestic/microbiology ; Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Multiple, Bacterial/*genetics ; Enterobacteriaceae/drug effects/*genetics/pathogenicity ; *Food Microbiology ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Humans ; Lactobacillus/genetics/metabolism/*physiology ; Probiotics/metabolism ; Virulence/genetics ; }, abstract = {The wide use of antibiotics in livestock raising has contributed to the selection and accumulation of representatives of commensal microflora, as well as pathogenic bacteria, colonizing livestock and poultry. For this reason the problem of the possible transfer of antibiotic-resistance genes along the chain from bacteria, autochthonous for agricultural animals, to bacteria used for the production of foodstuffs, which are incorporated into normal microflora and may thus participate in the exchange of these genes with bacteria, enteropathogenic for humans, is a highly important task of medical microbiology. The article deals with the review of experimental data, indicative the possibility of the appearance of antibiotic-resistant pathogenic bacteria due to the transfer of antibiotic-resistance genes via alimentary chains.}, }
@article {pmid16757618, year = {2006}, author = {Layer, F and Ghebremedhin, B and König, W and König, B}, title = {Heterogeneity of methicillin-susceptible Staphylococcus aureus strains at a German University Hospital implicates the circulating-strain pool as a potential source of emerging methicillin-resistant S. aureus clones.}, journal = {Journal of clinical microbiology}, volume = {44}, number = {6}, pages = {2179-2185}, pmid = {16757618}, issn = {0095-1137}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Toxins/genetics ; Communicable Diseases, Emerging/microbiology ; Enterotoxins/genetics ; Gene Transfer, Horizontal ; Germany ; *Hospitals, University ; Humans ; Methicillin/*pharmacology ; Methicillin Resistance/*genetics ; Microbial Sensitivity Tests ; Sequence Analysis, DNA ; Staphylococcal Infections/microbiology ; Staphylococcus aureus/classification/*drug effects/genetics/pathogenicity ; Superantigens/genetics ; }, abstract = {Recently, we demonstrated rapid dissemination of different methicillin-resistant Staphylococcus aureus (MRSA) clones at the Institute for Microbiology at the University of Magdeburg (B. Ghebremedhin, W. König, and B. König, Eur. J. Clin. Microbiol. Infect. Dis. 24:388-398, 2005). The majority of them harbored the readily transmissible mec cassette type IV. Thus, theoretically, methicillin-susceptible Staphylococcus aureus (MSSA) might capture the mecA gene from circulating MRSA, or MRSA strains might catch mobile toxin genes from MSSA. Therefore, we characterized MSSA strains circulating at the University Hospital in Magdeburg. Among a total of 84 MSSA strains under study, about 40% possessed the tst (toxic shock syndrome toxin) gene and up to four additional enterotoxin genes. tst-positive MSSA strains belonged to all known agr groups (I to IV) and to 14 different spa types (t008, t012, t015, t019, t024, t056, t065, t127, t133, t162, t271, t287, t399, and t400), and they were classified by multilocus sequence typing (MLST) as ST1, ST8, ST30, ST39, ST45, ST101, ST121, ST395, and ST426. In contrast, simultaneously circulating MRSA strains (n = 24) harbored in general two or three genes of the enterotoxin gene cluster, and the tst-positive MRSA isolates belonged to the well-known epidemic types ST22, ST45, and ST228 and were classified as spa types t001, t028, and t032. From our results, one may conclude that the pool of circulating MSSA strains is an important parameter with regard to the epidemiology of hospital- and community-acquired MRSA clones and their potential virulence.}, }
@article {pmid16757603, year = {2006}, author = {Alix, E and Godreuil, S and Blanc-Potard, AB}, title = {Identification of a Haarlem genotype-specific single nucleotide polymorphism in the mgtC virulence gene of Mycobacterium tuberculosis.}, journal = {Journal of clinical microbiology}, volume = {44}, number = {6}, pages = {2093-2098}, pmid = {16757603}, issn = {0095-1137}, mesh = {Bacterial Proteins/*genetics ; Cation Transport Proteins/*genetics ; Codon/genetics ; Genetic Complementation Test ; Genotype ; Humans ; Mutagenesis, Site-Directed ; Mycobacterium tuberculosis/*classification/genetics/metabolism/*pathogenicity ; Polymerase Chain Reaction/methods ; *Polymorphism, Single Nucleotide ; Species Specificity ; Virulence/genetics ; Virulence Factors/genetics ; }, abstract = {MgtC is a virulence factor common to several intracellular pathogens, including Mycobacterium tuberculosis, that might have been acquired through horizontal gene transfer. In the present study, we investigated the polymorphism of mgtC in clinical isolates representative of the main epidemic groups of M. tuberculosis. MgtC appears to have a low polymorphism rate in M. tuberculosis that consists exclusively of nonsynonymous mutations. We identified a single nucleotide polymorphism (SNP) at mgtC codon 182 (mgtC182) specifically associated with the Haarlem genotype. A simple PCR assay, called the "on/off switch assay," using phosphorothioate-modified primers and Pfu polymerase allowed us to distinguish Haarlem from non-Haarlem strains based on the mgtC182 SNP. The amino acid change (H182R) associated with the mgtC182 SNP in Haarlem strains does not appear to procure a selective advantage. Our results offer a simple and rapid tool to distinguish between Haarlem and non-Haarlem strains. In addition, the on/off switch assay, which allows the detection of SNPs on chromosomal DNA and M. tuberculosis cultures, provides a novel approach for the screening of known SNPs in M. tuberculosis.}, }
@article {pmid16757050, year = {2006}, author = {Hain, T and Steinweg, C and Chakraborty, T}, title = {Comparative and functional genomics of Listeria spp.}, journal = {Journal of biotechnology}, volume = {126}, number = {1}, pages = {37-51}, doi = {10.1016/j.jbiotec.2006.03.047}, pmid = {16757050}, issn = {0168-1656}, mesh = {Chromosomes, Bacterial ; Gene Expression Profiling/methods ; *Genomic Library ; Listeria/classification/*genetics/pathogenicity ; Oligonucleotide Array Sequence Analysis/methods ; Phylogeny ; Proteomics ; Virulence/*genetics ; }, abstract = {The genus Listeria comprises a group of non-sporulating, Gram-positive, soil bacteria belonging to the low G+C group of microorganisms. The genus consists of only six species, L. monocytogenes, L. ivanovii, L. seeligeri, L. innocua, L. welshimeri, and L. grayi.L. monocytogenes and L. ivanovii are the only known pathogens of this group. Comparative whole-genome sequencing of representative strains comprising the entire genus is currently being performed and nearing completion. In the genus Listeria, genome reduction has led to the generation of non-pathogenic species from pathogenic progenitor strains. Indeed, many of the regions absent in the non-pathogenic species represent commonly deleted genes. Speciation and diversity of strains has been achieved by horizontal gene transfer of DNA encoding novel genes probably required for niche specific survival. The sequencing of several listerial genomes has also been accompanied by studies using global strategies involving whole-genome transcriptional profiling and proteomics to examine the adaptative changes of L. monocytogenes to growth in different environments and to catalogue the genes mediating these responses. We review this data and present information on the expression profile of L. monocytogenes EGD-e inside the vacuolar and the cytosolic environments of the host cell using whole-genome microarray analysis. Of the 484 genes regulated during intracellular growth 41 genes are species-specific, being absent from the genome of the non-pathogenic L. innocua CLIP 11262 strain. There were 25 genes that are strain-specific i.e. absent from the genome of the L. monocytogenes F2365 serotype 4b strain suggesting heterogeneity in the gene pool required for intracellular survival of L. monocytogenes in host cells.}, }
@article {pmid16754613, year = {2006}, author = {Roger, AJ and Hug, LA}, title = {The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {361}, number = {1470}, pages = {1039-1054}, pmid = {16754613}, issn = {0962-8436}, mesh = {*Eukaryotic Cells ; *Evolution, Molecular ; Phylogeny ; RNA, Ribosomal/genetics ; Tetrahydrofolate Dehydrogenase/genetics ; Thymidylate Synthase/genetics ; }, abstract = {Determining the relationships among and divergence times for the major eukaryotic lineages remains one of the most important and controversial outstanding problems in evolutionary biology. The sequencing and phylogenetic analyses of ribosomal RNA (rRNA) genes led to the first nearly comprehensive phylogenies of eukaryotes in the late 1980s, and supported a view where cellular complexity was acquired during the divergence of extant unicellular eukaryote lineages. More recently, however, refinements in analytical methods coupled with the availability of many additional genes for phylogenetic analysis showed that much of the deep structure of early rRNA trees was artefactual. Recent phylogenetic analyses of a multiple genes and the discovery of important molecular and ultrastructural phylogenetic characters have resolved eukaryotic diversity into six major hypothetical groups. Yet relationships among these groups remain poorly understood because of saturation of sequence changes on the billion-year time-scale, possible rapid radiations of major lineages, phylogenetic artefacts and endosymbiotic or lateral gene transfer among eukaryotes. Estimating the divergence dates between the major eukaryote lineages using molecular analyses is even more difficult than phylogenetic estimation. Error in such analyses comes from a myriad of sources including: (i) calibration fossil dates, (ii) the assumed phylogenetic tree, (iii) the nucleotide or amino acid substitution model, (iv) substitution number (branch length) estimates, (v) the model of how rates of evolution change over the tree, (vi) error inherent in the time estimates for a given model and (vii) how multiple gene data are treated. By reanalysing datasets from recently published molecular clock studies, we show that when errors from these various sources are properly accounted for, the confidence intervals on inferred dates can be very large. Furthermore, estimated dates of divergence vary hugely depending on the methods used and their assumptions. Accurate dating of divergence times among the major eukaryote lineages will require a robust tree of eukaryotes, a much richer Proterozoic fossil record of microbial eukaryotes assignable to extant groups for calibration, more sophisticated relaxed molecular clock methods and many more genes sampled from the full diversity of microbial eukaryotes.}, }
@article {pmid16754323, year = {2006}, author = {Tamiya, N and Yagi, T}, title = {Evolution without divergence.}, journal = {IUBMB life}, volume = {58}, number = {5-6}, pages = {309-311}, doi = {10.1080/15216540600719648}, pmid = {16754323}, issn = {1521-6543}, mesh = {Animals ; *Biological Evolution ; Evolution, Molecular ; Gene Transfer, Horizontal ; Humans ; Phylogeny ; }, }
@article {pmid16754298, year = {2006}, author = {Koren, A}, title = {Is Saccharomyces cerevisiae apoptotic cell death associated with gene transfer?.}, journal = {IUBMB life}, volume = {58}, number = {4}, pages = {203-207}, doi = {10.1080/15216540600719606}, pmid = {16754298}, issn = {1521-6543}, mesh = {Apoptosis/*genetics ; Caspases/physiology ; Gene Transfer, Horizontal/*genetics ; Saccharomyces cerevisiae/genetics/*physiology ; Saccharomyces cerevisiae Proteins/physiology ; }, abstract = {Programmed cell death in unicellular organisms is difficult to account for in evolutionary terms. In the budding yeast, Saccharomyces cerevisiae, existence of several morphological and biochemical features of apoptosis has been described, and genes responsible for execution of the death program have been identified. It is here suggested that apoptosis of yeast cells could provide direct benefit to the genes of the dying cells, by facilitating DNA transfer to surrounding cells. The biochemical details of yeast apoptotic death are considered in light of a gene transfer hypothesis.}, }
@article {pmid16753962, year = {2006}, author = {Paparini, A and Romano-Spica, V}, title = {Gene transfer and cauliflower mosaic virus promoter 35S activity in mammalian cells.}, journal = {Journal of environmental science and health. Part. B, Pesticides, food contaminants, and agricultural wastes}, volume = {41}, number = {4}, pages = {437-449}, doi = {10.1080/03601230600616957}, pmid = {16753962}, issn = {0360-1234}, mesh = {Animals ; Caulimovirus/*genetics ; Cell Line ; Crops, Agricultural ; DNA, Viral/*analysis ; *Food Technology ; *Gene Transfer Techniques ; Genes, Reporter ; Genetic Vectors ; Mice ; Mice, Inbred BALB C ; Plants, Genetically Modified ; Promoter Regions, Genetic ; Reverse Transcriptase Polymerase Chain Reaction ; Transfection ; Viral Proteins/*genetics ; }, abstract = {The cauliflower mosaic virus 35S promoter (CaMV35s) is extensively used in genetically modified crops for human and animal consumption. Horizontal gene transfer is attracting particular attention, in light of experimental reports, showing the presence of dietary DNA into animal tissues. Health implications may derive from possible activities of the heterologous promoter in mammalian cells after integration in the host genome. To evaluate this hypothesis, in vivo and in vitro experiments were performed using GFP as reporter gene. Recombinant plasmid DNA was fed to Balb/c mice and searched in several tissues by PCR amplification. The activity of the plant virus promoter was assessed by RT-PCR and fluorescence microscopy after liposome-mediated transfection of murine gonadic cells. Obtained data did not highlight evidences of dietary DNA transfer in mice. No CaMV35s transcriptional activity was detected in this experimental model. These findings emphasize the need for further studies and standardized methods.}, }
@article {pmid16751524, year = {2006}, author = {Rohwerder, T and Breuer, U and Benndorf, D and Lechner, U and Müller, RH}, title = {The alkyl tert-butyl ether intermediate 2-hydroxyisobutyrate is degraded via a novel cobalamin-dependent mutase pathway.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {6}, pages = {4128-4135}, pmid = {16751524}, issn = {0099-2240}, mesh = {Amino Acid Sequence ; Bacteria/*metabolism ; Culture Media ; DNA Primers ; Ethyl Ethers/*metabolism ; Gasoline ; Hydroxybutyrates/*metabolism ; Intramolecular Transferases/*metabolism ; Kinetics ; Molecular Sequence Data ; Nocardiaceae/metabolism ; Polymerase Chain Reaction ; Rhodobacter sphaeroides/metabolism ; Streptomyces/enzymology ; Vitamin B 12/*pharmacology ; Xanthobacter/metabolism ; }, abstract = {Fuel oxygenates such as methyl and ethyl tert-butyl ether (MTBE and ETBE, respectively) are degraded only by a limited number of bacterial strains. The aerobic pathway is generally thought to run via tert-butyl alcohol (TBA) and 2-hydroxyisobutyrate (2-HIBA), whereas further steps are unclear. We have now demonstrated for the newly isolated beta-proteobacterial strains L108 and L10, as well as for the closely related strain CIP I-2052, that 2-HIBA was degraded by a cobalamin-dependent enzymatic step. In these strains, growth on substrates containing the tert-butyl moiety, such as MTBE, TBA, and 2-HIBA, was strictly dependent on cobalt, which could be replaced by cobalamin. Tandem mass spectrometry identified a 2-HIBA-induced protein with high similarity to a peptide whose gene sequence was found in the finished genome of the MTBE-degrading strain Methylibium petroleiphilum PM1. Alignment analysis identified it as the small subunit of isobutyryl-coenzyme A (CoA) mutase (ICM; EC 5.4.99.13), which is a cobalamin-containing carbon skeleton-rearranging enzyme, originally described only in Streptomyces spp. Sequencing of the genes of both ICM subunits from strain L108 revealed nearly 100% identity with the corresponding peptide sequences from M. petroleiphilum PM1, suggesting a horizontal gene transfer event to have occurred between these strains. Enzyme activity was demonstrated in crude extracts of induced cells of strains L108 and L10, transforming 2-HIBA into 3-hydroxybutyrate in the presence of CoA and ATP. The physiological and evolutionary aspects of this novel pathway involved in MTBE and ETBE metabolism are discussed.}, }
@article {pmid16751506, year = {2006}, author = {Olvera, A and Calsamiglia, M and Aragon, V}, title = {Genotypic diversity of Haemophilus parasuis field strains.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {6}, pages = {3984-3992}, pmid = {16751506}, issn = {0099-2240}, mesh = {Animals ; Chaperonin 60/genetics ; DNA, Bacterial/genetics/isolation &amp; purification ; *Genetic Variation ; Haemophilus parasuis/*genetics/isolation &amp; purification ; Phylogeny ; RNA, Bacterial/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics/isolation &amp; purification ; Swine/*microbiology ; }, abstract = {Haemophilus parasuis is the cause of Glässer's disease and other clinical disorders in pigs. It can also be isolated from the upper respiratory tracts of healthy pigs, and isolates can have significant differences in virulence. In this work, a partial sequence from the 60-kDa heat shock protein (Hsp60) gene was assessed as an epidemiological marker. We analyzed partial sequences of hsp60 and 16S rRNA genes from 103 strains of H. parasuis and other related species to obtain a better classification of the strains and examine the correlation with virulence. The results were compared with those obtained by enterobacterial repetitive intergenic consensus PCR. Our results showed that hsp60 is a reliable marker for epidemiological studies of H. parasuis and that the analysis of its sequence is a better approach than fingerprinting methods. Furthermore, the analysis of the hsp60 and 16S rRNA gene sequences revealed the presence of a separate lineage of virulent strains and indicated the occurrence of lateral gene transfer among H. parasuis and Actinobacillus strains.}, }
@article {pmid16740275, year = {2006}, author = {Glasner, ME and Fayazmanesh, N and Chiang, RA and Sakai, A and Jacobson, MP and Gerlt, JA and Babbitt, PC}, title = {Evolution of structure and function in the o-succinylbenzoate synthase/N-acylamino acid racemase family of the enolase superfamily.}, journal = {Journal of molecular biology}, volume = {360}, number = {1}, pages = {228-250}, doi = {10.1016/j.jmb.2006.04.055}, pmid = {16740275}, issn = {0022-2836}, support = {GM52594/GM/NIGMS NIH HHS/United States ; GM60595/GM/NIGMS NIH HHS/United States ; P01071790//PHS HHS/United States ; }, mesh = {Actinobacteria/enzymology ; Amidohydrolases/*chemistry ; Amino Acid Sequence ; Bayes Theorem ; Carbon-Carbon Lyases/*chemistry ; Evolution, Molecular ; Genomics ; Molecular Sequence Data ; Phosphopyruvate Hydratase/*chemistry ; Phylogeny ; Racemases and Epimerases/*chemistry ; Sequence Homology, Amino Acid ; Structure-Activity Relationship ; Vitamin K 2/chemistry ; }, abstract = {Understanding how proteins evolve to provide both exquisite specificity and proficient activity is a fundamental problem in biology that has implications for protein function prediction and protein engineering. To study this problem, we analyzed the evolution of structure and function in the o-succinylbenzoate synthase/N-acylamino acid racemase (OSBS/NAAAR) family, part of the mechanistically diverse enolase superfamily. Although all characterized members of the family catalyze the OSBS reaction, this family is extraordinarily divergent, with some members sharing <15% identity. In addition, a member of this family, Amycolatopsis OSBS/NAAAR, is promiscuous, catalyzing both dehydration and racemization. Although the OSBS/NAAAR family appears to have a single evolutionary origin, no sequence or structural motifs unique to this family could be identified; all residues conserved in the family are also found in enolase superfamily members that have different functions. Based on their species distribution, several uncharacterized proteins similar to Amycolatopsis OSBS/NAAAR appear to have been transmitted by lateral gene transfer. Like Amycolatopsis OSBS/NAAAR, these might have additional or alternative functions to OSBS because many are from organisms lacking the pathway in which OSBS is an intermediate. In addition to functional differences, the OSBS/NAAAR family exhibits surprising structural variations, including large differences in orientation between the two domains. These results offer several insights into protein evolution. First, orthologous proteins can exhibit significant structural variation, and specificity can be maintained with little conservation of ligand-contacting residues. Second, the discovery of a set of proteins similar to Amycolatopsis OSBS/NAAAR supports the hypothesis that new protein functions evolve through promiscuous intermediates. Finally, a combination of evolutionary, structural, and sequence analyses identified characteristics that might prime proteins, such as Amycolatopsis OSBS/NAAAR, for the evolution of new activities.}, }
@article {pmid16738125, year = {2006}, author = {Waller, RF and Patron, NJ and Keeling, PJ}, title = {Phylogenetic history of plastid-targeted proteins in the peridinin-containing dinoflagellate Heterocapsa triquetra.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {56}, number = {Pt 6}, pages = {1439-1447}, doi = {10.1099/ijs.0.64061-0}, pmid = {16738125}, issn = {1466-5026}, mesh = {Animals ; Chlorophyta/classification ; Dinoflagellida/*classification ; Expressed Sequence Tags ; Flagella/physiology ; Molecular Sequence Data ; Phylogeny ; Plastids/genetics ; Protozoan Proteins/genetics ; Rhodophyta/classification ; }, abstract = {The evolutionary history and relationship between plastids of dinoflagellate algae and apicomplexan parasites have been controversial both because the organelles are unusual and because their genomes contain few comparable genes. However, most plastid proteins are encoded in the host nucleus and targeted to the organelle, and several of these genes have proved to have interesting and informative evolutionary histories. We have used expressed sequence tag (EST) sequencing to generate gene sequence data from the nuclear genome of the dinoflagellate Heterocapsa triquetra and inferred phylogenies for the complete set of identified plastid-targeted proteins. Overall, dinoflagellate plastid proteins are most consistently related to homologues from the red algal plastid lineage (not green) and, in many of the most robust cases, they branch with other chromalveolate algae. In resolved phylogenies where apicomplexan data are available, dinoflagellates and apicomplexans are related. We also identified two cases of apparent lateral, or horizontal, gene transfer, one from the green plastid lineage and one from a bacterial lineage unrelated to plastids or cyanobacteria.}, }
@article {pmid16737554, year = {2006}, author = {Mau, B and Glasner, JD and Darling, AE and Perna, NT}, title = {Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli.}, journal = {Genome biology}, volume = {7}, number = {5}, pages = {R44}, pmid = {16737554}, issn = {1474-760X}, support = {R01 GM062994/GM/NIGMS NIH HHS/United States ; GM62994-02/GM/NIGMS NIH HHS/United States ; }, mesh = {Alleles ; Base Sequence ; Escherichia coli/*genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; Genomics ; Molecular Sequence Data ; Operon ; Phylogeny ; Polymorphism, Genetic ; *Recombination, Genetic ; Sequence Alignment ; Shigella flexneri/genetics ; }, abstract = {BACKGROUND: Comparisons of complete bacterial genomes reveal evidence of lateral transfer of DNA across otherwise clonally diverging lineages. Some lateral transfer events result in acquisition of novel genomic segments and are easily detected through genome comparison. Other more subtle lateral transfers involve homologous recombination events that result in substitution of alleles within conserved genomic regions. This type of event is observed infrequently among distantly related organisms. It is reported to be more common within species, but the frequency has been difficult to quantify since the sequences under comparison tend to have relatively few polymorphic sites.<br><br>RESULTS: Here we report a genome-wide assessment of homologous recombination among a collection of six complete Escherichia coli and Shigella flexneri genome sequences. We construct a whole-genome multiple alignment and identify clusters of polymorphic sites that exhibit atypical patterns of nucleotide substitution using a random walk-based method. The analysis reveals one large segment (approximately 100 kb) and 186 smaller clusters of single base pair differences that suggest lateral exchange between lineages. These clusters include portions of 10% of the 3,100 genes conserved in six genomes. Statistical analysis of the functional roles of these genes reveals that several classes of genes are over-represented, including those involved in recombination, transport and motility.<br><br>CONCLUSION: We demonstrate that intraspecific recombination in E. coli is much more common than previously appreciated and may show a bias for certain types of genes. The described method provides high-specificity, conservative inference of past recombination events.}, }
@article {pmid16735155, year = {2006}, author = {Rédei, GP and Koncz, C and Phillips, JD}, title = {Changing images of the gene.}, journal = {Advances in genetics}, volume = {56}, number = {}, pages = {53-100}, doi = {10.1016/S0065-2660(06)56002-X}, pmid = {16735155}, issn = {0065-2660}, mesh = {*Alleles ; Animals ; Cytoplasm/genetics ; DNA/*chemistry/genetics ; DNA Transposable Elements ; *Epigenesis, Genetic ; Female ; Gene Dosage ; Gene Transfer, Horizontal ; *Genes ; Genetic Code ; Genomic Imprinting ; Humans ; Male ; Mutation ; Nucleic Acid Conformation ; Prions/genetics ; RNA/genetics ; }, abstract = {During the twentieth century the gene emerged as the major driving force of biology. Initially, even the nature and behavior of gene vehicles, the chromosomes, were subjected to doubts. The basic or standard gene concept, as a unit of function, mutation, and recombination, had to be revised. Half a century was required for reaching a general consensus about the chemical nature of the genetic material, DNA and RNA. The relationship between single genes and individual proteins was a great milestone at the middle of the twentieth century, but within two decades it was realized that the relationship was more complex. Understanding of genetic coding, transcription, and translation during the 1960s laid a firm foundation to the "nucleic doctrine," harking back to the dicta of Lederberg (1959) and meaning that single nucleic acid genes alone were responsible for each separate function within the cell. However, important aspects of gene expression are recognized now as a function of the genome and many genes collaborate in circuits. It has come to light that genes may be mobile, exist in plasmids and cytoplasmic organelles, and can be imported by nonsexual means from other organisms or as synthetic products. Epigenetics has reborn as a new field of developmental genetics. The unorthodox prion proteins can even simulate some gene properties. Genetics was to an extent reincarnated as of the twenty-first century by assimilating the tools of cybernetics and of many formerly distant areas of science. This overview highlights some of the historical milestones that contributed to the development of our image of the gene, extending elements of issues laid down by Rédei (2003).}, }
@article {pmid16732460, year = {2006}, author = {Fegan, N and Barlow, RS and Gobius, KS}, title = {Escherichia coli O157 somatic antigen is present in an isolate of E. fergusonii.}, journal = {Current microbiology}, volume = {52}, number = {6}, pages = {482-486}, pmid = {16732460}, issn = {0343-8651}, mesh = {Animals ; Cattle ; Cross Reactions ; Escherichia/genetics/immunology/*isolation &amp; purification ; Escherichia coli O157/genetics/immunology ; Escherichia coli Proteins/isolation &amp; purification ; Food Microbiology ; Gene Transfer, Horizontal/genetics ; Meat/*microbiology ; O Antigens/genetics/*isolation &amp; purification ; }, abstract = {A bacterium that tested positive with antibodies specific for Escherichia coli O157 was isolated from beef during routine screening procedures. The bacterium was identified as E. fergusonii by biochemical testing and partial sequencing of 16S rRNA. The isolate was tested for the presence of genes encoding Shiga toxins, the E. coli attaching and effacing factor, enterohemolysin, and the O157 O antigen. The isolate tested negative for Shiga toxins and other E. coli O157 virulence markers but was found to harbor the genes encoding the O157 antigen. These results suggest genetic transfer of the O antigen gene cluster between E. coli O157:H7 and E. fergusonii.}, }
@article {pmid16730850, year = {2006}, author = {Huang, J and Gogarten, JP}, title = {Ancient horizontal gene transfer can benefit phylogenetic reconstruction.}, journal = {Trends in genetics : TIG}, volume = {22}, number = {7}, pages = {361-366}, doi = {10.1016/j.tig.2006.05.004}, pmid = {16730850}, issn = {0168-9525}, mesh = {Amino Acid Sequence ; Animals ; Computational Biology ; DNA Topoisomerase IV ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Archaeal ; *Genome, Bacterial ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; }, abstract = {Although horizontal gene transfer (HGT) is usually considered a disruptive force in recovering organismal phylogeny, it creates important phylogenetic information. In the 'net of life', the recipient of an ancient gene transfer can be the ancestor of a lineage that inherits the transferred gene; thus, the transferred gene marks the recipient and its descendants as a monophyletic group. Ancient gene transfer events can also reveal the order of emergence of donor and recipient lineages. In addition, these ancient events can significantly shape the genetic systems of the recipients and can play a part in their long-term evolution. In this article, we discuss the recent progress in phylogenetic application of ancient HGTs and describe two examples of transfer events to the ancestor of red algae and green plants that support a common origin of these two groups. We also address the potential pitfalls of this application.}, }
@article {pmid16729469, year = {2006}, author = {Walther, B and Friedrich, AW and Brunnberg, L and Wieler, LH and Lübke-Becker, A}, title = {[Methicillin-resistant Staphylococcus aureus (MRSA) in veterinary medicine: a "new emerging pathogen"?].}, journal = {Berliner und Munchener tierarztliche Wochenschrift}, volume = {119}, number = {5-6}, pages = {222-232}, pmid = {16729469}, issn = {0005-9366}, mesh = {Animals ; Bacterial Typing Techniques/veterinary ; Communicable Diseases, Emerging/drug therapy/epidemiology/microbiology/*veterinary ; Cross Infection/microbiology/veterinary ; Dogs ; Horses ; Humans ; *Methicillin Resistance/genetics ; Staphylococcal Infections/drug therapy/epidemiology/microbiology/*veterinary ; Staphylococcus aureus/drug effects/genetics/*pathogenicity ; beta-Lactamases/biosynthesis ; }, abstract = {The problem of nosocomial infections is of increasing importance in veterinary medicine. As an example, this review summarizes current knowledge regarding methicillin-resistant Staphylococcus aureus (MRSA) as a typical example, as these pathogens are the most important agents of nosocomial infections in human medicine worldwide and are being increasingly reported in veterinary medicine. MRSA are classified by their ability to be resistant against oxacillin/methicillin, this feature being confered by mecA, a gene which was acquired by horizontal gene transfer of the staphylococcal gene cassette (SCCmec). It is this genetic information that enables MRSA to be resistant against all penicillins, cehalosporins and carbapenems. In addition, MRSA are often resistant against a variety of other antiinfectives, i.e. aminoglycosides, macrolides, lincosamide, streptomycins, tetracyclin, chloramphenicol, but also against fluorquinolones and rifampicin. Presumably, these highly adapted strains are particularly able to acquire resistance genes located on plasmids or transposons. They are also able to develop point mutations, further leading to resistant phenotypes. If these pathogens are leading to infectious diseases, veterinarians may be confronted with a worst-case scenario, being left without any antiinfective therapeutic. As Staphylococcus aureus is highly tenacid, professional hygiene management is of utmost importance. The increasing number of published sporadic MRSA infections, MRSA-infectious diseases as well as MRSA outbreaks in veterinary medicine justifies their recognition as a "New Emerging Pathogen". So far, horses and dogs are mostly affected by MRSA. Although transmission between humans and animals has been reported occasionally, the sources, routes of transmission or the epidemiological relevance of MRSA infections in animals are far from being understood. Therefore, epidemiological investigations utilizing molecular typing tools are mandatory. Typing tools like multilocus-sequence-typing (MLST), pulsefield-gelelectrophoresis (PFGE), sequence analysis of the gene encoding protein A (spa-typing) as well as SCCmec-typing are all at hand.}, }
@article {pmid16723568, year = {2006}, author = {Jansen, WT and Beitsma, MM and Koeman, CJ and van Wamel, WJ and Verhoef, J and Fluit, AC}, title = {Novel mobile variants of staphylococcal cassette chromosome mec in Staphylococcus aureus.}, journal = {Antimicrobial agents and chemotherapy}, volume = {50}, number = {6}, pages = {2072-2078}, pmid = {16723568}, issn = {0066-4804}, mesh = {Anti-Bacterial Agents/*pharmacology ; *Chromosomes, Bacterial ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genetic Variation ; Methicillin/*pharmacology ; Methicillin Resistance/*genetics ; Models, Genetic ; Recombinases/metabolism ; Staphylococcal Infections/microbiology ; Staphylococcus aureus/classification/drug effects/*genetics ; }, abstract = {Staphylococcus aureus staphylococcal cassette chromosome mec type IV (SSCmec IV) is associated with virulent community-acquired methicillin-resistant Staphylococcus aureus (MRSA) and frequent horizontal transfer among staphylococci. To gain insight into the mechanism of transfer, we studied the ccrA/B type 2 recombinase-mediated excision of SCCmec IV (n = 5 strains) and SCCmec II (n = 2). In SCCmec IV- but not SCCmec II-containing strains, spontaneous excision of the cassette was observed. Introduction of ccrA/B type 2 recombinase genes under control of an S. aureus bacterial phage promoter in the different strains yielded excision of SCCmec II and multiple excision variants of SCCmec IV. Sequencing of the alternatively excised products in SCCmec IV strains identified a 100-bp shortened SCCmec' variant and a 5,877-bp, conserved SCC-like element that lacks mecA and ccrA/B recombinases. Excision of the SCC-like element in wild-type S. aureus was dependent on the presence of SCCmec. The element could be excised separately or as part of a novel composite cassette together with SCCmec. The relative abundance of and variety in SCCmec IV excisions may contribute to the frequency of horizontal transfer and genetic plasticity in SCCmec IV MRSA strains.}, }
@article {pmid16723146, year = {2006}, author = {Willms, AR and Roughan, PD and Heinemann, JA}, title = {Static recipient cells as reservoirs of antibiotic resistance during antibiotic therapy.}, journal = {Theoretical population biology}, volume = {70}, number = {4}, pages = {436-451}, doi = {10.1016/j.tpb.2006.04.001}, pmid = {16723146}, issn = {0040-5809}, mesh = {Anti-Bacterial Agents/*therapeutic use ; *Drug Resistance ; Gene Transfer, Horizontal ; Plasmids ; }, abstract = {How does taking the full course of antibiotics prevent antibiotic resistant bacteria establishing in patients? We address this question by testing the possibility that horizontal/lateral gene transfer (HGT) is critical for the accumulation of the antibiotic-resistance phenotype while bacteria are under antibiotic stress. Most antibiotics prevent bacterial reproduction, some by preventing de novo gene expression. Nevertheless, in some cases and at some concentrations, the effects of most antibiotics on gene expression may not be irreversible. If the stress is removed before the bacteria are cleared from the patients by normal turnover, gene expression restarts, converting the residual population to phenotypic resistance. Using mathematical models we investigate how static recipients of resistance genes carried by plasmids accumulate resistance genes, and how specifically an environment cycling between presence and absence of the antibiotic uniquely favors the evolution of horizontally mobile resistance genes. We found that the presence of static recipients can substantially increase the persistence of the plasmid and that this effect is most pronounced when the cost of carriage of the plasmid decreases the cell's growth rate by as much as a half or more. In addition, plasmid persistence can be enhanced even when conjugation rates are as low as half the rate required for the plasmid to persist as a parasite on its own.}, }
@article {pmid16716236, year = {2006}, author = {Nolan, JM and Petrov, V and Bertrand, C and Krisch, HM and Karam, JD}, title = {Genetic diversity among five T4-like bacteriophages.}, journal = {Virology journal}, volume = {3}, number = {}, pages = {30}, pmid = {16716236}, issn = {1743-422X}, mesh = {Aeromonas hydrophila/*virology ; Aeromonas salmonicida/*virology ; Animals ; Bacteriophage T4/*genetics ; Bacteriophages/*classification/genetics ; Base Sequence ; Coliphages/*genetics ; Computational Biology/methods ; *Genetic Variation ; Genome, Viral ; Humans ; Mice ; Molecular Sequence Data ; Open Reading Frames/genetics ; RNA, Transfer/chemistry/genetics ; Sequence Alignment ; Viral Proteins/genetics ; }, abstract = {BACKGROUND: Bacteriophages are an important repository of genetic diversity. As one of the major constituents of terrestrial biomass, they exert profound effects on the earth's ecology and microbial evolution by mediating horizontal gene transfer between bacteria and controlling their growth. Only limited genomic sequence data are currently available for phages but even this reveals an overwhelming diversity in their gene sequences and genomes. The contribution of the T4-like phages to this overall phage diversity is difficult to assess, since only a few examples of complete genome sequence exist for these phages. Our analysis of five T4-like genomes represents half of the known T4-like genomes in GenBank.<br><br>RESULTS: Here, we have examined in detail the genetic diversity of the genomes of five relatives of bacteriophage T4: the Escherichia coli phages RB43, RB49 and RB69, the Aeromonas salmonicida phage 44RR2.8t (or 44RR) and the Aeromonas hydrophila phage Aeh1. Our data define a core set of conserved genes common to these genomes as well as hundreds of additional open reading frames (ORFs) that are nonconserved. Although some of these ORFs resemble known genes from bacterial hosts or other phages, most show no significant similarity to any known sequence in the databases. The five genomes analyzed here all have similarities in gene regulation to T4. Sequence motifs resembling T4 early and late consensus promoters were observed in all five genomes. In contrast, only two of these genomes, RB69 and 44RR, showed similarities to T4 middle-mode promoter sequences and to the T4 motA gene product required for their recognition. In addition, we observed that each phage differed in the number and assortment of putative genes encoding host-like metabolic enzymes, tRNA species, and homing endonucleases.<br><br>CONCLUSION: Our observations suggest that evolution of the T4-like phages has drawn on a highly diverged pool of genes in the microbial world. The T4-like phages harbour a wealth of genetic material that has not been identified previously. The mechanisms by which these genes may have arisen may differ from those previously proposed for the evolution of other bacteriophage genomes.}, }
@article {pmid16707682, year = {2006}, author = {Palchevskiy, V and Finkel, SE}, title = {Escherichia coli competence gene homologs are essential for competitive fitness and the use of DNA as a nutrient.}, journal = {Journal of bacteriology}, volume = {188}, number = {11}, pages = {3902-3910}, pmid = {16707682}, issn = {0021-9193}, support = {T32 AG000093/AG/NIA NIH HHS/United States ; AG 000093/AG/NIA NIH HHS/United States ; }, mesh = {Base Sequence ; Biological Transport ; DNA/*metabolism ; DNA Primers ; Escherichia coli/*genetics/*growth &amp; development ; Kinetics ; Models, Biological ; Phenotype ; }, abstract = {Natural genetic competence is the ability of cells to take up extracellular DNA and is an important mechanism for horizontal gene transfer. Another potential benefit of natural competence is that exogenous DNA can serve as a nutrient source for starving bacteria because the ability to "eat" DNA is necessary for competitive survival in environments containing limited nutrients. We show here that eight Escherichia coli genes, identified as homologs of com genes in Haemophilus influenzae and Neisseria gonorrhoeae, are necessary for the use of extracellular DNA as the sole source of carbon and energy. These genes also confer a competitive advantage to E. coli during long-term stationary-phase incubation. We also show that homologs of these genes are found throughout the proteobacteria, suggesting that the use of DNA as a nutrient may be a widespread phenomenon.}, }
@article {pmid16704357, year = {2006}, author = {Toth, IK and Pritchard, L and Birch, PR}, title = {Comparative genomics reveals what makes an enterobacterial plant pathogen.}, journal = {Annual review of phytopathology}, volume = {44}, number = {}, pages = {305-336}, doi = {10.1146/annurev.phyto.44.070505.143444}, pmid = {16704357}, issn = {0066-4286}, mesh = {Enterobacteriaceae/*genetics ; Genome, Bacterial ; Genomics/*methods ; Plant Diseases/*microbiology ; }, abstract = {The bacterial family Enterobacteriaceae contains some of the most devastating human and animal pathogens, including Escherichia coli, Salmonella enterica and species of Yersinia and Shigella. These are among the best-studied of any organisms, yet there is much to be learned about the nature and evolution of interactions with their hosts and with the wider environment. Comparative and functional genomics have fundamentally improved our understanding of their modes of adaptation to different ecological niches and the genes that determine their pathogenicity. In addition to animal pathogens, Enterobacteriaceae include important plant pathogens, such as Erwinia carotovora subsp. atroseptica (Eca), the first plant-pathogenic enterobacterium to be sequenced. This review focuses on genomic comparisons between Eca and other enterobacteria, with particular emphasis on the differences that exemplify or explain the plant-associated lifestyle(s) of Eca. Horizontal gene transfer in Eca may directly have led to the acquisition of a number of determinants that mediate its interactions, pathogenic or otherwise, with plants, offering a glimpse into its evolutionary divergence from animal-pathogenic enterobacteria.}, }
@article {pmid16701557, year = {2006}, author = {Daimon, T and Katsuma, S and Kang, W and Shimada, T}, title = {Comparative studies of Bombyx mori nucleopolyhedrovirus chitinase and its host ortholog, BmChi-h.}, journal = {Biochemical and biophysical research communications}, volume = {345}, number = {2}, pages = {825-833}, doi = {10.1016/j.bbrc.2006.04.112}, pmid = {16701557}, issn = {0006-291X}, mesh = {Animals ; Baculoviridae/*enzymology/genetics/pathogenicity/physiology ; Blotting, Western ; Bombyx/*virology ; Cells, Cultured ; Chitinases/genetics/*metabolism ; Cloning, Molecular ; Cysteine Endopeptidases/genetics/metabolism ; Nucleopolyhedroviruses/*enzymology/genetics/growth &amp; development ; Occlusion Body Matrix Proteins ; Promoter Regions, Genetic ; Viral Proteins/genetics/metabolism ; Viral Structural Proteins ; }, abstract = {Baculovirus-encoded chitinases (V-CHIAs) were first proposed to be acquired from a bacterium via horizontal gene transfer. However, we have recently reported that lepidopteran hosts also encode v-chiA orthologs. Here we describe comparative studies of Bombyx mori nucleopolyhedrovirus (BmNPV) chitinase and its host ortholog, BmChi-h. We constructed recombinant BmNPVs in which native and modified forms of BmChi-h were driven under the polyhedrin promoter and the authentic v-chiA was deleted. Western blot analysis indicated that BmCHI-h was rapidly secreted from virus-infected BmN cells whereas BmNPV CHIA was localized within the virus-infected cells; probably because of the presence of a C-terminal endoplasmic reticulum retention motif on BmNPV CHIA. Enzymological studies showed that BmNPV CHIA was able to retain much higher chitinolytic activity under alkaline conditions. For B. mori larvae infected with v-chiA-deleted BmNPV, the terminal liquefaction of dead larvae and the activation of baculovirus-encoded cysteine protease were not observed, and the introduction of BmChi-h did not rescue these defects. Our findings show that BmNPV chiA possesses unique features that are not shared by host orthologs, which may reflect functional specialization of baculovirus chitinases.}, }
@article {pmid16701456, year = {2005}, author = {Keeling, PJ and Burger, G and Durnford, DG and Lang, BF and Lee, RW and Pearlman, RE and Roger, AJ and Gray, MW}, title = {The tree of eukaryotes.}, journal = {Trends in ecology &amp; evolution}, volume = {20}, number = {12}, pages = {670-676}, doi = {10.1016/j.tree.2005.09.005}, pmid = {16701456}, issn = {0169-5347}, abstract = {Recent advances in resolving the tree of eukaryotes are converging on a model composed of a few large hypothetical 'supergroups', each comprising a diversity of primarily microbial eukaryotes (protists, or protozoa and algae). The process of resolving the tree involves the synthesis of many kinds of data, including single-gene trees, multigene analyses, and other kinds of molecular and structural characters. Here, we review the recent progress in assembling the tree of eukaryotes, describing the major evidence for each supergroup, and where gaps in our knowledge remain. We also consider other factors emerging from phylogenetic analyses and comparative genomics, in particular lateral gene transfer, and whether such factors confound our understanding of the eukaryotic tree.}, }
@article {pmid16701350, year = {2005}, author = {McInerney, JO and Wilkinson, M}, title = {New methods ring changes for the tree of life.}, journal = {Trends in ecology &amp; evolution}, volume = {20}, number = {3}, pages = {105-107}, doi = {10.1016/j.tree.2005.01.007}, pmid = {16701350}, issn = {0169-5347}, abstract = {Relationships among prokaryotes and the origin of eukaryotes have both proven controversial, with results depending upon the gene sequences and methods used. Extensive horizontal gene transfer is one possible reason why inferring such deep phylogenetic relationships is difficult. In two recent papers, Lake and Rivera introduce new methods that can be used to reconstruct the genomic tree in the presence of horizontal gene transfers, but which suggest that a ring rather than a tree is a better representation of some parts of the history of life on Earth.}, }
@article {pmid16701347, year = {2005}, author = {Crawford, JW and Harris, JA and Ritz, K and Young, IM}, title = {Towards an evolutionary ecology of life in soil.}, journal = {Trends in ecology &amp; evolution}, volume = {20}, number = {2}, pages = {81-87}, doi = {10.1016/j.tree.2004.11.014}, pmid = {16701347}, issn = {0169-5347}, abstract = {The soil-microbe system is one of the most diverse components of the terrestrial ecosystem. The origin of this diversity, and its relation to the life-sustaining processes that are mediated by the resident microbial community, is still poorly understood. The inherent complexities necessitate a theoretical framework that integrates ecological and evolutionary approaches and which embraces the physical heterogeneity of the soil environment. Such a framework is currently lacking, although recent advances in theory and experimentation are beginning to identify the essential ingredients. Here, we review and evaluate the relevance of current modelling approaches, and propose a new synthesis of an evolutionary ecology of life in soil. Key elements include an account of dispersal, horizontal gene transfer, and the consideration of the physical and biological components of soil as an integrated complex adaptive system.}, }
@article {pmid16690328, year = {2006}, author = {Casse, N and Bui, QT and Nicolas, V and Renault, S and Bigot, Y and Laulier, M}, title = {Species sympatry and horizontal transfers of Mariner transposons in marine crustacean genomes.}, journal = {Molecular phylogenetics and evolution}, volume = {40}, number = {2}, pages = {609-619}, doi = {10.1016/j.ympev.2006.02.005}, pmid = {16690328}, issn = {1055-7903}, mesh = {Amino Acid Sequence ; Animals ; Crustacea/*genetics ; DNA Transposable Elements/*genetics ; DNA-Binding Proteins/*genetics ; Gene Transfer, Horizontal/*genetics ; Genome/*genetics ; Molecular Sequence Data ; Oceans and Seas ; Open Reading Frames/genetics ; Phylogeny ; Sequence Alignment ; Transposases ; }, abstract = {Mariner-like elements (MLEs) have been widely detected in terrestrial species. The first complete MLE isolated from a marine invertebrate was detected in the genome of the hydrothermal crab Bythograea thermydron by Halaimia-Toumi et al. [Halaimia-Toumi, N., Casse, N., Demattei, M.V., Renault, S., Pradier, E., Bigot, Y., Laulier, M., 2004. The GC-rich transposon Bytmar1 from the deep-sea hydrothermal crab, Bythograea thermydron, may encode three transposase isoforms from a single ORF. J. Mol. Evol. 59, 747-760] and called Bytmar1. Here, we report the isolation of three new Bytmar1 relatives from the genomes of one hydrothermal amphipod Ventiella sulfuris (Vensmar1) and two coastal crustacea, Maia brachydactila (Maibmar1) and Cancer pagurus (Canpmar1). Like Bytmar1, these MLEs have an unusually high GC content, a high CpG ratio, and a low TpA ratio. Their consensus sequence encodes a transposase that is preceded by an N-flag, as in Bytmar1, which could be a marine feature. Only one of the 19 clones obtained, Vensmar1.3, encoded for a full-length transposase. The phylogenetic analyses revealed that all these Bytmar1-related elements can be differentiated into two clusters, corresponding to the coastal or hydrothermal origin of their hosts. They also confirmed that the irritans sub-family comprises at least four lineages that seem to depend on the taxonomical position and habitat of their hosts. Finally, we observed that elements coding for two potentially complete transposases exhibiting 99.5% similarity, Bytmar1.11 and Vensmar1.3, were present in the genome of two distantly related hydrothermal crustacea, one Amphipod and one Decapod. The hypothesis of horizontal transfers is discussed in the light of the sequence similarities observed.}, }
@article {pmid16689892, year = {2006}, author = {Xu, J}, title = {Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances.}, journal = {Molecular ecology}, volume = {15}, number = {7}, pages = {1713-1731}, doi = {10.1111/j.1365-294X.2006.02882.x}, pmid = {16689892}, issn = {0962-1083}, mesh = {DNA, Ribosomal/analysis ; Ecology/*methods/trends ; Gene Expression Profiling ; Genetics, Microbial/*methods/*trends ; Genomics/*methods/trends ; Microbiological Techniques ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Microbial ecology examines the diversity and activity of micro-organisms in Earth's biosphere. In the last 20 years, the application of genomics tools have revolutionized microbial ecological studies and drastically expanded our view on the previously underappreciated microbial world. This review first introduces the basic concepts in microbial ecology and the main genomics methods that have been used to examine natural microbial populations and communities. In the ensuing three specific sections, the applications of the genomics in microbial ecological research are highlighted. The first describes the widespread application of multilocus sequence typing and representational difference analysis in studying genetic variation within microbial species. Such investigations have identified that migration, horizontal gene transfer and recombination are common in natural microbial populations and that microbial strains can be highly variable in genome size and gene content. The second section highlights and summarizes the use of four specific genomics methods (phylogenetic analysis of ribosomal RNA, DNA-DNA re-association kinetics, metagenomics, and micro-arrays) in analysing the diversity and potential activity of microbial populations and communities from a variety of terrestrial and aquatic environments. Such analyses have identified many unexpected phylogenetic lineages in viruses, bacteria, archaea, and microbial eukaryotes. Functional analyses of environmental DNA also revealed highly prevalent, but previously unknown, metabolic processes in natural microbial communities. In the third section, the ecological implications of sequenced microbial genomes are briefly discussed. Comparative analyses of prokaryotic genomic sequences suggest the importance of ecology in determining microbial genome size and gene content. The significant variability in genome size and gene content among strains and species of prokaryotes indicate the highly fluid nature of prokaryotic genomes, a result consistent with those from multilocus sequence typing and representational difference analyses. The integration of various levels of ecological analyses coupled to the application and further development of high throughput technologies are accelerating the pace of discovery in microbial ecology.}, }
@article {pmid16689874, year = {2006}, author = {Henriques, I and Moura, A and Alves, A and Saavedra, MJ and Correia, A}, title = {Analysing diversity among beta-lactamase encoding genes in aquatic environments.}, journal = {FEMS microbiology ecology}, volume = {56}, number = {3}, pages = {418-429}, doi = {10.1111/j.1574-6941.2006.00073.x}, pmid = {16689874}, issn = {0168-6496}, mesh = {Gene Transfer, Horizontal ; Molecular Sequence Data ; Sequence Analysis, DNA ; Water/*analysis ; beta-Lactam Resistance/*genetics ; beta-Lactamases/classification/*genetics ; }, abstract = {The most common mechanism of resistance to beta-lactam antibiotics is the production of beta-lactamases. These enzymes are encoded by genes that evolve rapidly, thus constituting a group characterized by high levels of molecular diversity. Most of the genetic determinants of resistance to beta-lactam antibiotics characterized until now were obtained from clinical isolates. This study was designed in order to exploit the presence of beta-lactamase gene sequences in an aquatic environment, and to get information on the distinctive features of those sequences when compared to others available on databases. DNA sequences potentially encoding proteins of three different families of clinically relevant beta-lactamases were assessed: TEM, IMP and OXA-2 derivatives. The presence of bla sequences in DNA extracted from water samples from the lagoon Ria de Aveiro was checked by PCR and hybridization. Sequences representing the three families of beta-lactamases studied were detected. The molecular diversity of the amplicons was assessed by cloning and sequence analysis, and denaturing gradient gel electrophoresis (PCR-DGGE) separation. Most of the retrieved sequences (particularly sequences representing bla(TEM)and bla(OXA-2)) were identical or very similar to beta-lactamase gene sequences previously characterized from clinical isolates. Phylogenetic analysis suggests that this aquatic ecosystem is a reservoir of molecular diverse putative bla sequences. The patterns of molecular diversity found within the beta-lactamase gene families studied do not correspond to those reported in studies focussing on clinical isolates.}, }
@article {pmid16675503, year = {2006}, author = {Waller, RF and Slamovits, CH and Keeling, PJ}, title = {Lateral gene transfer of a multigene region from cyanobacteria to dinoflagellates resulting in a novel plastid-targeted fusion protein.}, journal = {Molecular biology and evolution}, volume = {23}, number = {7}, pages = {1437-1443}, doi = {10.1093/molbev/msl008}, pmid = {16675503}, issn = {0737-4038}, mesh = {Animals ; Bacterial Proteins/genetics ; Catechol O-Methyltransferase/genetics/metabolism ; Cyanobacteria/*genetics ; Dinoflagellida/classification/*genetics ; Evolution, Molecular ; Gene Fusion/genetics ; Gene Transfer, Horizontal/*genetics ; Phosphorus-Oxygen Lyases/genetics/metabolism ; Phylogeny ; Plastids/*genetics/metabolism ; Sequence Alignment ; }, abstract = {The number of cases of lateral or horizontal gene transfer in eukaryotic genomes is growing steadily, but in most cases, neither the donor nor the recipient is known, and the biological implications of the transfer are not clear. We describe a relatively well-defined case of transfer from a cyanobacterial source to an ancestor of dinoflagellates that diverged before Oxyrrhis but after Perkinsus. This case is also exceptional in that 2 adjacent genes, a paralogue of the shikimate biosynthetic enzyme AroB and an O-methyltransferase (OMT) were transferred together and formed a fusion protein that was subsequently targeted to the dinoflagellate plastid. Moreover, this fusion subsequently reverted to 2 individual genes in the genus Karlodinium, but both proteins maintained plastid localization with the OMT moiety acquiring its own plastid-targeting peptide. The presence of shikimate biosynthetic enzymes in the plastid is not unprecedented as this is a plastid-based pathway in many eukaryotes, but this species of OMT has not been associated with the plastid previously. It appears that the OMT activity was drawn into the plastid simply by virtue of its attachment to the AroB paralogue resulting from their cotransfer and once in the plastid performed some essential function so that it remained plastid targeted after it separated from AroB. Gene fusion events are considered rare and likely stable, and such an event has recently been used to argue for a root of the eukaryotic tree. Our data, however, show that exact reversals of fusion events do take place, and hence gene fusion data are difficult to interpret without knowledge of the phylogeny of the organisms--therefore their use as phylogenetic markers must be considered carefully.}, }
@article {pmid16672526, year = {2006}, author = {Quinteira, S and Peixe, L}, title = {Multiniche screening reveals the clinically relevant metallo-beta-lactamase VIM-2 in Pseudomonas aeruginosa far from the hospital setting: an ongoing dispersion process?.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {5}, pages = {3743-3745}, pmid = {16672526}, issn = {0099-2240}, mesh = {Animals ; Drug Resistance, Bacterial/genetics ; Ecosystem ; Feces/microbiology ; *Gene Transfer, Horizontal ; *Hospitals ; Humans ; Integrons/genetics ; Microbial Sensitivity Tests ; Portugal ; Pseudomonas aeruginosa/*drug effects/enzymology/genetics/growth &amp; development ; Rivers/*microbiology ; Sewage/*microbiology ; beta-Lactamases/*genetics/metabolism ; beta-Lactams/pharmacology ; }, abstract = {A screening study of the presence of metallo-beta-lactamases (IMP and VIM types and SPM-1) in isolates from different nonhospital sources was conducted, and it revealed the presence of bla(VIM-2), associated with the In58 class 1 integron, in two unrelated Pseudomonas aeruginosa strains from aquatic habitats. The results suggest that the hospital setting was the possible origin of these bla(VIM-2)-carrying strains.}, }
@article {pmid16672510, year = {2006}, author = {Vos, M and Velicer, GJ}, title = {Genetic population structure of the soil bacterium Myxococcus xanthus at the centimeter scale.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {5}, pages = {3615-3625}, pmid = {16672510}, issn = {0099-2240}, mesh = {Bacterial Proteins/genetics ; Bacterial Typing Techniques ; Evolution, Molecular ; *Genetic Variation ; Genotype ; Molecular Sequence Data ; Myxococcus xanthus/*classification/*genetics/growth &amp; development/isolation &amp; purification ; Phylogeny ; Polymorphism, Genetic ; Recombination, Genetic ; Selection, Genetic ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Myxococcus xanthus is a gram-negative soil bacterium best known for its remarkable life history of social swarming, social predation, and multicellular fruiting body formation. Very little is known about genetic diversity within this species or how social strategies might vary among neighboring strains at small spatial scales. To investigate the small-scale population structure of M. xanthus, 78 clones were isolated from a patch of soil (16 by 16 cm) in Tübingen, Germany. Among these isolates, 21 genotypes could be distinguished from a concatemer of three gene fragments: csgA (developmental C signal), fibA (extracellular matrix-associated zinc metalloprotease), and pilA (the pilin subunit of type IV pili). Accumulation curves showed that most of the diversity present at this scale was sampled. The pilA gene contains both conserved and highly variable regions, and two frequency-distribution tests provide evidence for balancing selection on this gene. The functional domains in the csgA gene were found to be conserved. Three instances of lateral gene transfer could be inferred from a comparison of individual gene phylogenies, but no evidence was found for linkage equilibrium, supporting the view that M. xanthus evolution is largely clonal. This study shows that M. xanthus is surrounded by a variety of distinct conspecifics in its natural soil habitat at a spatial scale at which encounters among genotypes are likely.}, }
@article {pmid16672454, year = {2006}, author = {Saile, E and Koehler, TM}, title = {Bacillus anthracis multiplication, persistence, and genetic exchange in the rhizosphere of grass plants.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {5}, pages = {3168-3174}, pmid = {16672454}, issn = {0099-2240}, mesh = {*Bacillus anthracis/genetics/growth &amp; development/physiology ; Colony Count, Microbial ; *Gene Transfer, Horizontal ; Hot Temperature ; Plant Roots/*microbiology ; Plasmids/genetics ; Poaceae/*microbiology ; *Soil Microbiology ; Spores, Bacterial/physiology ; }, abstract = {Bacillus anthracis, the causative agent of anthrax, is known for its rapid proliferation and dissemination in mammalian hosts. In contrast, little information exists regarding the lifestyle of this important pathogen outside of the host. Considering that Bacillus species, including close relatives of B. anthracis, are saprophytic soil organisms, we investigated the capacity of B. anthracis spores to germinate in the rhizosphere and to establish populations of vegetative cells that could support horizontal gene transfer in the soil. Using a simple grass plant-soil model system, we show that B. anthracis strains germinate on and around roots, growing in characteristic long filaments. From 2 to 4 days postinoculation, approximately one-half of the B. anthracis CFU recovered from soil containing grass seedlings arose from heat-sensitive organisms, while B. anthracis CFU retrieved from soil without plants consisted of primarily heat-resistant spores. Co-inoculation of the plant-soil system with spores of a fertile B. anthracis strain carrying the tetracycline resistance plasmid pBC16 and a selectable B. anthracis recipient strain resulted in transfer of pBC16 from the donor to the recipient as early as 3 days postinoculation. Our findings demonstrate that B. anthracis can survive as a saprophyte outside of the host. The data suggest that horizontal gene transfer in the rhizosphere of grass plants may play a role in the evolution of the Bacillus cereus group species.}, }
@article {pmid16672448, year = {2006}, author = {Martinez, RJ and Wang, Y and Raimondo, MA and Coombs, JM and Barkay, T and Sobecky, PA}, title = {Horizontal gene transfer of PIB-type ATPases among bacteria isolated from radionuclide- and metal-contaminated subsurface soils.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {5}, pages = {3111-3118}, pmid = {16672448}, issn = {0099-2240}, mesh = {Adenosine Triphosphatases/*genetics/metabolism ; Arthrobacter/drug effects/enzymology/*genetics ; Bacillus/drug effects/enzymology/*genetics ; DNA, Bacterial/analysis ; DNA, Ribosomal/analysis ; Drug Resistance, Bacterial ; *Gene Transfer, Horizontal ; Lead/pharmacology ; Metals, Heavy/*pharmacology ; Molecular Sequence Data ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; *Soil Microbiology ; Soil Pollutants/*pharmacology ; Uranium/pharmacology ; }, abstract = {Aerobic heterotrophs were isolated from subsurface soil samples obtained from the U.S. Department of Energy's (DOE) Field Research Center (FRC) located at Oak Ridge, Tenn. The FRC represents a unique, extreme environment consisting of highly acidic soils with co-occurring heavy metals, radionuclides, and high nitrate concentrations. Four hundred isolates obtained from contaminated soil were assayed for heavy metal resistance, and a smaller subset was assayed for tolerance to uranium. The vast majority of the isolates were gram-positive bacteria and belonged to the high-G+C- and low-G+C-content genera Arthrobacter and Bacillus, respectively. Genomic DNA from a randomly chosen subset of 50 Pb-resistant (Pb(r)) isolates was amplified with PCR primers specific for P(IB)-type ATPases (i.e., pbrA/cadA/zntA). A total of 10 pbrA/cadA/zntA loci exhibited evidence of acquisition by horizontal gene transfer. A remarkable dissemination of the horizontally acquired P(IB)-type ATPases was supported by unusual DNA base compositions and phylogenetic incongruence. Numerous Pb(r) P(IB)-type ATPase-positive FRC isolates belonging to the genus Arthrobacter tolerated toxic concentrations of soluble U(VI) (UO(2)(2+)) at pH 4. These unrelated, yet synergistic, physiological traits observed in Arthrobacter isolates residing in the contaminated FRC subsurface may contribute to the survival of the organisms in such an extreme environment. This study is, to the best of our knowledge, the first study to report broad horizontal transfer of P(IB)-type ATPases in contaminated subsurface soils and is among the first studies to report uranium tolerance of aerobic heterotrophs obtained from the acidic subsurface at the DOE FRC.}, }
@article {pmid16672386, year = {2006}, author = {Liebana, E and Batchelor, M and Hopkins, KL and Clifton-Hadley, FA and Teale, CJ and Foster, A and Barker, L and Threlfall, EJ and Davies, RH}, title = {Longitudinal farm study of extended-spectrum beta-lactamase-mediated resistance.}, journal = {Journal of clinical microbiology}, volume = {44}, number = {5}, pages = {1630-1634}, pmid = {16672386}, issn = {0095-1137}, mesh = {Animals ; Bacterial Proteins/genetics ; Cattle/*microbiology ; Cattle Diseases/microbiology ; Cefotaxime/pharmacology ; DNA, Bacterial/genetics ; Escherichia coli/drug effects/*enzymology/genetics/isolation &amp; purification ; Escherichia coli Infections/microbiology/veterinary ; Feces/microbiology ; Genes, Bacterial ; Humans ; Longitudinal Studies ; Mutation ; Polymerase Chain Reaction ; Promoter Regions, Genetic ; United Kingdom ; beta-Lactam Resistance/genetics ; beta-Lactamases/genetics/*metabolism ; }, abstract = {Extended-spectrum beta-lactamase (ESBL)-mediated resistance is of considerable importance in human medicine. Recently, such enzymes have been reported in bacteria from animals. We describe a longitudinal study of a dairy farm suffering calf scour with high mortality rates. In November 2004, two Escherichia coli isolates with resistance to a wide range of beta-lactams (including amoxicillin-clavulanate and cefotaxime) were isolated from scouring calves. Testing by PCR and sequence analysis confirmed the isolates as being both bla(CTX-M14/17) and bla(TEM-35) ((IRT-4)) positive. They had indistinguishable plasmid and pulsed-field gel electrophoresis (PFGE) profiles. Transferability studies demonstrated that bla(CTX-M) was located on a conjugative 65-MDa IncK plasmid. Following a farm visit in December 2004, 31/48 calves and 2/60 cows were positive for E. coli with bla(CTX-M). Also, 5/48 calf and 28/60 cow samples yielded bla(CTX)- and bla(TEM)-negative E. coli isolates that were resistant to cefotaxime, and sequence analysis confirmed that these presented mutations in the promoter region of the chromosomal ampC gene. Fingerprinting showed 11 different PFGE types (seven in bla(CTX-M)-positive isolates). Six different PFGE clones conjugated the same bla(CTX-M)-positive IncK plasmid. One clone carried a different-sized, bla(CTX-M)-positive, transformable plasmid. This is the first report of bla(CTX-M) from livestock in the United Kingdom, and this report demonstrates the complexity of ESBL epidemiology. Results indicate that horizontal plasmid transfer between strains as well as horizontal gene transfer between plasmids have contributed to the spread of resistance. We have also shown that some clones can persist for months, suggesting that clonal spread also contributes to the perpetuation of resistance.}, }
@article {pmid16672049, year = {2006}, author = {Hurley, CC and Quirke, A and Reen, FJ and Boyd, EF}, title = {Four genomic islands that mark post-1995 pandemic Vibrio parahaemolyticus isolates.}, journal = {BMC genomics}, volume = {7}, number = {}, pages = {104}, pmid = {16672049}, issn = {1471-2164}, mesh = {Chromosome Deletion ; *Disease Outbreaks ; Gene Transfer, Horizontal ; *Genomic Islands ; Genomics ; Humans ; Vibrio Infections/*epidemiology/microbiology ; Vibrio parahaemolyticus/*genetics/isolation &amp; purification ; }, abstract = {BACKGROUND: Vibrio parahaemolyticus is an aquatic, halophilic, Gram-negative bacterium, first discovered in 1950 in Japan during a food-poisoning outbreak. Infections resulting from consumption of V. parahaemolyticus have increased globally in the last 10 years leading to the bacterium's classification as a newly emerging pathogen. In 1996 the first appearance of a pandemic V. parahaemolyticus clone occurred, a new O3:K6 serotype strain that has now been identified worldwide as a major cause of seafood-borne gastroenteritis.<br><br>RESULTS: We examined the sequenced genome of V. parahaemolyticus RIMD2210633, an O3:K6 serotype strain isolated in Japan in 1996, by bioinformatic analyses to uncover genomic islands (GIs) that may play a role in the emergence and pathogenesis of pandemic strains. We identified 7 regions ranging in size from 10 kb to 81 kb that had the characteristics of GIs such as aberrant base composition compared to the core genome, presence of phage-like integrases, flanked by direct repeats and the absence of these regions from closely related species. Molecular analysis of worldwide clinical isolates of V. parahaemolyticus recovered over the last 33 years demonstrated that a 24 kb region named V. parahaemolyticus island-1 (VPaI-1) encompassing ORFs VP0380 to VP0403 is only present in new O3:K6 and related strains recovered after 1995. We investigated the presence of 3 additional regions, VPaI-4 (VP2131 to VP2144), VPaI-5 (VP2900 to VP2910) and VPaI-6 (VPA1254 to VPA1270) by PCR assays and Southern blot analyses among the same set of V. parahaemolyticus isolates. These 3 VPaI regions also gave similar distribution patterns amongst the 41 strains examined.<br><br>CONCLUSION: The 4 VPaI regions examined may represent DNA acquired by the pandemic group of V. parahaemolyticus isolates that increased their fitness either in the aquatic environment or in their ability to infect humans.}, }
@article {pmid16670965, year = {2006}, author = {Gao, B and Paramanathan, R and Gupta, RS}, title = {Signature proteins that are distinctive characteristics of Actinobacteria and their subgroups.}, journal = {Antonie van Leeuwenhoek}, volume = {90}, number = {1}, pages = {69-91}, doi = {10.1007/s10482-006-9061-2}, pmid = {16670965}, issn = {0003-6072}, mesh = {Actinobacteria/*classification/genetics ; Bacterial Proteins/*classification/genetics/metabolism ; *Genome, Bacterial ; Phylogeny ; }, abstract = {The Actinobacteria constitute one of the main phyla of Bacteria. Presently, no morphological and very few molecular characteristics are known which can distinguish species of this highly diverse group. In this work, we have analyzed the genomes of four actinobacteria (viz. Mycobacterium leprae TN, Leifsonia xyli subsp. xyli str. CTCB07, Bifidobacterium longum NCC2705 and Thermobifida fusca YX) to search for proteins that are unique to Actinobacteria. Our analyses have identified 233 actinobacteria-specific proteins, homologues of which are generally not present in any other bacteria. These proteins can be grouped as follows: (i) 29 proteins uniquely present in most sequenced actinobacterial genomes; (ii) 6 proteins present in almost all actinobacteria except Bifidobacterium longum and another 37 proteins absent in B. longum and few other species; (iii) 11 proteins which are mainly present in Corynebacterium, Mycobacterium and Nocardia (CMN) subgroup as well as Streptomyces, T. fusca and Frankia sp., but they are not found in Bifidobacterium and Micrococcineae; (iv) 8 proteins that are specific for T. fusca and Streptomyces species, plus 2 proteins also present in the Frankia species; (v) 13 proteins that are specific for the Corynebacterineae or the CMN group; (vi) 14 proteins only found in Mycobacterium and Nocardia; (vii) 24 proteins unique to different Mycobacterium species; (viii) 8 proteins specific to the Micrococcineae; (ix) 85 proteins which are distributed sporadically in actinobacterial species. Additionally, many examples of lateral gene transfer from Actinobacteria to Magnetospirillum magnetotacticum have also been identified. The identified proteins provide novel molecular means for defining and circumscribing the Actinobacteria phylum and a number of subgroups within it. The distribution of these proteins also provides useful information regarding interrelationships among the actinobacterial subgroups. Most of these proteins are of unknown function and studies aimed at understanding their cellular functions should reveal common biochemical and physiological characteristics unique to either all actinobacteria or particular subgroups of them. The identified proteins also provide potential targets for development of drugs that are specific for actinobacteria.}, }
@article {pmid16652276, year = {2006}, author = {Diep, BA and Carleton, HA and Chang, RF and Sensabaugh, GF and Perdreau-Remington, F}, title = {Roles of 34 virulence genes in the evolution of hospital- and community-associated strains of methicillin-resistant Staphylococcus aureus.}, journal = {The Journal of infectious diseases}, volume = {193}, number = {11}, pages = {1495-1503}, doi = {10.1086/503777}, pmid = {16652276}, issn = {0022-1899}, support = {5-T32-GM07127-29-30/GM/NIGMS NIH HHS/United States ; N01-AI-95359/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Toxins/genetics ; Community-Acquired Infections/*microbiology ; Cross Infection/*microbiology ; DNA Fingerprinting ; DNA, Bacterial/genetics ; Electrophoresis, Gel, Pulsed-Field ; Enterotoxins/genetics ; *Evolution, Molecular ; Exotoxins/genetics ; Gene Transfer, Horizontal ; Genotype ; Humans ; Leukocidins ; Methicillin Resistance/genetics ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; San Francisco ; Staphylococcal Infections/*microbiology ; Staphylococcus aureus/classification/drug effects/*genetics/isolation &amp; purification ; Superantigens/genetics ; Virulence Factors/*genetics ; }, abstract = {BACKGROUND: The extent to which the horizontal transfer of virulence genes has contributed to the emergence of contemporary virulent strains of methicillin-resistant Staphylococcus aureus (MRSA) in hospital and community settings is poorly understood.<br><br>METHODS: Epidemiologically well-characterized MRSA isolates collected over 8.5 years were genotyped and tested for the presence of 34 virulence genes.<br><br>RESULTS: Six strain types accounted for 88.2% of all MRSA infections. The evolution of contemporary hospital and community phenotypes within the CC8 and CC30 lineages--2 background genomes that produced historical pandemic MRSA clones--were associated with multiple horizontal acquisitions of virulence genes. The epidemic community phenotype of a CC8 strain, designated ST8:USA300, was linked to the acquisition of staphylococcal cassette chromosome (SCC)mec type IV, the genes for Panton-Valentine leukocidin (PVL), and the enterotoxin Q and K genes. Similarly, the epidemic community phenotype of a CC30 strain, ST30:USA1100, was linked to the acquisition of SCCmec type IV and the pvl genes. In contrast, the epidemic hospital phenotype of another CC30 strain, ST36:USA200, was associated with the acquisition of SCCmec type II, the enterotoxin A gene, and the toxic shock syndrome toxin 1 gene. The pvl genes appear not to be essential for the evolution OF other community-associated strains of mrsa, including ST8:USA500 and ST59:USA1000.<br><br>CONCLUSIONS: The horizontal transfer of virulence genes, although infrequent, is epidemiologically associated with the emergence of new virulent strains of MRSA.}, }
@article {pmid16651664, year = {2006}, author = {Hao, W and Golding, GB}, title = {The fate of laterally transferred genes: life in the fast lane to adaptation or death.}, journal = {Genome research}, volume = {16}, number = {5}, pages = {636-643}, pmid = {16651664}, issn = {1088-9051}, mesh = {*Adaptation, Physiological ; Bacillaceae/*genetics ; Bayes Theorem ; *Death ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Likelihood Functions ; Mutagenesis, Insertional ; Phylogeny ; Sequence Deletion ; Species Specificity ; }, abstract = {Large-scale genome arrangement plays an important role in bacterial genome evolution. A substantial number of genes can be inserted into, deleted from, or rearranged within genomes during evolution. Detecting or inferring gene insertions/deletions is of interest because such information provides insights into bacterial genome evolution and speciation. However, efficient inference of genome events is difficult because genome comparisons alone do not generally supply enough information to distinguish insertions, deletions, and other rearrangements. In this study, homologous genes from the complete genomes of 13 closely related bacteria were examined. The presence or absence of genes from each genome was cataloged, and a maximum likelihood method was used to infer insertion/deletion rates according to the phylogenetic history of the taxa. It was found that whole gene insertions/deletions in genomes occur at rates comparable to or greater than the rate of nucleotide substitution and that higher insertion/deletion rates are often inferred to be present at the tips of the phylogeny with lower rates on more ancient interior branches. Recently transferred genes are under faster and relaxed evolution compared with more ancient genes. Together, this implies that many of the lineage-specific insertions are lost quickly during evolution and that perhaps a few of the genes inserted by lateral transfer are niche specific.}, }
@article {pmid16646993, year = {2006}, author = {Wang, Z and Zhu, XG and Chen, Y and Li, Y and Hou, J and Li, Y and Liu, L}, title = {Exploring photosynthesis evolution by comparative analysis of metabolic networks between chloroplasts and photosynthetic bacteria.}, journal = {BMC genomics}, volume = {7}, number = {}, pages = {100}, pmid = {16646993}, issn = {1471-2164}, mesh = {Arabidopsis/metabolism ; *Biological Evolution ; Chloroplasts/*metabolism ; Computer Simulation ; Cyanobacteria/*metabolism ; Databases, Genetic ; Escherichia coli/metabolism ; Photosynthesis/*physiology ; }, abstract = {BACKGROUND: Chloroplasts descended from cyanobacteria and have a drastically reduced genome following an endosymbiotic event. Many genes of the ancestral cyanobacterial genome have been transferred to the plant nuclear genome by horizontal gene transfer. However, a selective set of metabolism pathways is maintained in chloroplasts using both chloroplast genome encoded and nuclear genome encoded enzymes. As an organelle specialized for carrying out photosynthesis, does the chloroplast metabolic network have properties adapted for higher efficiency of photosynthesis? We compared metabolic network properties of chloroplasts and prokaryotic photosynthetic organisms, mostly cyanobacteria, based on metabolic maps derived from genome data to identify features of chloroplast network properties that are different from cyanobacteria and to analyze possible functional significance of those features.<br><br>RESULTS: The properties of the entire metabolic network and the sub-network that consists of reactions directly connected to the Calvin Cycle have been analyzed using hypergraph representation. Results showed that the whole metabolic networks in chloroplast and cyanobacteria both possess small-world network properties. Although the number of compounds and reactions in chloroplasts is less than that in cyanobacteria, the chloroplast's metabolic network has longer average path length, a larger diameter, and is Calvin Cycle -centered, indicating an overall less-dense network structure with specific and local high density areas in chloroplasts. Moreover, chloroplast metabolic network exhibits a better modular organization than cyanobacterial ones. Enzymes involved in the same metabolic processes tend to cluster into the same module in chloroplasts.<br><br>CONCLUSION: In summary, the differences in metabolic network properties may reflect the evolutionary changes during endosymbiosis that led to the improvement of the photosynthesis efficiency in higher plants. Our findings are consistent with the notion that since the light energy absorption, transfer and conversion is highly efficient even in photosynthetic bacteria, the further improvements in photosynthetic efficiency in higher plants may rely on changes in metabolic network properties.}, }
@article {pmid16640777, year = {2006}, author = {Zauner, S and Lockhart, P and Stoebe-Maier, B and Gilson, P and McFadden, GI and Maier, UG}, title = {Differential gene transfers and gene duplications in primary and secondary endosymbioses.}, journal = {BMC evolutionary biology}, volume = {6}, number = {}, pages = {38}, pmid = {16640777}, issn = {1471-2148}, mesh = {Chaperonin 60/*genetics ; Cyanobacteria/*genetics ; Evolution, Molecular ; *Gene Duplication ; *Gene Transfer, Horizontal ; Models, Genetic ; Photosynthesis ; *Phylogeny ; Plastids/genetics ; *Symbiosis ; }, abstract = {BACKGROUND: Most genes introduced into phototrophic eukaryotes during the process of endosymbiosis are either lost or relocated into the host nuclear genome. In contrast, groEL homologues are found in different genome compartments among phototrophic eukaryotes. Comparative sequence analyses of recently available genome data, have allowed us to reconstruct the evolutionary history of these genes and propose a hypothesis that explains the unusual genome distribution of groEL homologues.<br><br>RESULTS: Our analyses indicate that while two distinct groEL genes were introduced into eukaryotes by a progenitor of plastids, these particular homologues have not been maintained in all evolutionary lineages. This is of significant interest, because two chaperone proteins always co-occur in oxygenic photosynthetic organisms. We infer strikingly different lineage specific processes of evolution involving deletion, duplication and targeting of groEL proteins.<br><br>CONCLUSION: The requirement of two groEL homologues for chaperon function in phototrophs has provided a constraint that has shaped convergent evolutionary scenarios in divergent evolutionary lineages. GroEL provides a general evolutionary model for studying gene transfers and convergent evolutionary processes among eukaryotic lineages.}, }
@article {pmid16638804, year = {2006}, author = {Terranova, R and Pereira, CF and Du Roure, C and Merkenschlager, M and Fisher, AG}, title = {Acquisition and extinction of gene expression programs are separable events in heterokaryon reprogramming.}, journal = {Journal of cell science}, volume = {119}, number = {Pt 10}, pages = {2065-2072}, doi = {10.1242/jcs.02945}, pmid = {16638804}, issn = {0021-9533}, support = {MC_U120027516/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Antigens, CD20/biosynthesis/genetics ; B-Lymphocytes/cytology/enzymology/*physiology ; Cell Differentiation/genetics/physiology ; Cell Fusion/methods ; Cell Nucleus/genetics/metabolism ; Cells, Cultured ; Gene Expression ; Gene Silencing ; Gene Transfer, Horizontal ; Heterochromatin/*genetics ; Histone Deacetylase Inhibitors ; Histone Deacetylases/*metabolism ; Humans ; In Situ Hybridization, Fluorescence ; Mice ; Muscle Fibers, Skeletal/cytology/physiology ; Muscles/cytology/enzymology/*physiology ; Neural Cell Adhesion Molecules/biosynthesis/genetics ; }, abstract = {Although differentiated cells normally retain cell-type-specific gene expression patterns throughout their lifetime, cell identity can sometimes be modified or reversed in vivo by transdifferentiation, or experimentally through cell fusion or by nuclear transfer. To examine the epigenetic changes that are required for the dominant conversion of lymphocytes to muscle, we generated heterokaryons between human B lymphocytes and mouse C2C12 myotubes. We show that within 2 days of heterokaryon formation lymphocyte nuclei adopt an architecture resembling that of muscle and then initiate the expression of muscle-specific genes in the same temporal order as developing muscle. The establishment of this muscle-specific program is coordinated with the shutdown of several lymphocyte-associated genes. Interestingly, erasing lymphocyte identity in reprogrammed cells requires histone deacetylase (HDAC) activity. Inhibition of HDAC activity during reprogramming selectively blocks the silencing of lymphocyte-specific genes but does not prevent the establishment of muscle-specific gene expression. Successful reprogramming is therefore shown to be a multi-step process in which the acquisition and extinction of lineage-specific gene programs are separable events.}, }
@article {pmid16635591, year = {2007}, author = {Kelley, ST and Cassirer, EF and Weiser, GC and Safaee, S}, title = {Phylogenetic diversity of Pasteurellaceae and horizontal gene transfer of leukotoxin in wild and domestic sheep.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {7}, number = {1}, pages = {13-23}, doi = {10.1016/j.meegid.2006.03.005}, pmid = {16635591}, issn = {1567-1348}, mesh = {Alleles ; Animals ; Bacterial Proteins/*genetics ; *Gene Transfer, Horizontal ; *Genetic Variation ; Hemolysin Proteins/*genetics ; Pasteurellaceae/classification/*genetics/pathogenicity ; Pasteurellosis, Pneumonic/genetics/*microbiology ; Phylogeny ; Sequence Analysis, DNA ; Sheep Diseases/genetics/microbiology ; Sheep, Domestic ; }, abstract = {Wild and domestic animal populations are known to be sources and reservoirs of emerging diseases. There is also a growing recognition that horizontal genetic transfer (HGT) plays an important role in bacterial pathogenesis. We used molecular phylogenetic methods to assess diversity and cross-transmission rates of Pasteurellaceae bacteria in populations of bighorn sheep, Dall's sheep, domestic sheep and domestic goats. Members of the Pasteurellaceae cause an array of deadly illnesses including bacterial pneumonia known as "pasteurellosis", a particularly devastating disease for bighorn sheep. A phylogenetic analysis of a combined dataset of two RNA genes (16S ribosomal RNA and RNAse P RNA) revealed remarkable evolutionary diversity among Pasteurella trehalosi and Mannheimia (Pasteurella) haemolytica bacteria isolated from sheep and goats. Several phylotypes appeared to associate with particular host species, though we found numerous instances of apparent cross-transmission among species and populations. Statistical analyses revealed that host species, geographic locale and biovariant classification, but not virulence, correlated strongly with Pasteurellaceae phylogeny. Sheep host species correlated with P. trehalosi isolates phylogeny (PTP test; P=0.002), but not with the phylogeny of M. haemolytica isolates, suggesting that P. trehalosi bacteria may be more host specific. With regards to populations within species, we also discovered a strong correlation between geographic locale and isolate phylogeny in the Rocky Mountain bighorn sheep (PTP test; P=0.001). We also investigated the potential for HGT of the leukotoxin A (lktA) gene, which produces a toxin that plays an integral role in causing disease. Comparative analysis of the combined RNA gene phylogeny and the lktA phylogenies revealed considerable incongruence between the phylogenies, suggestive of HGT. Furthermore, we found identical lktA alleles in unrelated bacterial species, some of which had been isolated from sheep in distantly removed populations. For example, lktA sequences from P. trehalosi isolated from remote Alaskan Dall's sheep were 100% identical over a 900-nucleotide stretch to sequences determined from M. haemolytica isolated from domestic sheep in the UK. This extremely high degree of sequence similarity of lktA sequences among distinct bacterial species suggests that HGT has played a role in the evolution of lktA in wild hosts.}, }
@article {pmid16635586, year = {2006}, author = {Kissinger, JC}, title = {A tale of three genomes: the kinetoplastids have arrived.}, journal = {Trends in parasitology}, volume = {22}, number = {6}, pages = {240-243}, doi = {10.1016/j.pt.2006.04.002}, pmid = {16635586}, issn = {1471-4922}, mesh = {Animals ; Gene Transfer Techniques ; Genetic Linkage ; *Genome, Protozoan ; Leishmania major/*genetics ; Protozoan Vaccines ; Trypanosoma brucei brucei/*genetics ; Trypanosoma cruzi/*genetics ; }, abstract = {July 2005 marked a milestone in kinetoplastid biology research. A tour de force effort led by the Tri-Trypanosomatidae "Tritryp" genome consortium yielded the publication of three prominent kinetoplastid parasite genome sequences: Trypanosoma brucei, Trypanosoma cruzi and Leishmania major. The individual and combined comparative analyses of these three genome sequences, combined with proteomic analyses, have yielded insights into topics ranging from genome evolution and horizontal gene transfer to potential new therapeutic and vaccine targets.}, }
@article {pmid16634220, year = {2005}, author = {Raybould, A and Cooper, I}, title = {Tiered tests to assess the environmental risk of fitness changes in hybrids between transgenic crops and wild relatives: the example of virus resistant Brassica napus.}, journal = {Environmental biosafety research}, volume = {4}, number = {3}, pages = {127-140}, doi = {10.1051/ebr:2005018}, pmid = {16634220}, issn = {1635-7922}, mesh = {Brassica/genetics/physiology/*virology ; Chimera/physiology/*virology ; Crops, Agricultural/physiology/virology ; Environment ; Gene Transfer, Horizontal/genetics/physiology ; Immunity, Innate/genetics/physiology ; Plants, Genetically Modified/physiology/*virology ; Potyvirus/*pathogenicity ; Risk Assessment ; United Kingdom ; }, abstract = {Over the last 20 years, there has been much research aimed at improving environmental risk assessment of transgenic crops. Despite large amounts of data, decisions to allow or prohibit the release of transgenic crops remain confused and controversial. We argue that part of the reason for confusion is the lack of clear definitions of components of the environment that should be protected, and, as a consequence, there is no way to judge the relevance of data collected under the auspices of 'environmental risk assessment'. Although this criticism applies to most aspects of environmental risk assessment of transgenic crops, it is most pertinent to effects that might result from an increase in plant fitness, often referred to as increased weediness. Environmental risk assessment of weediness is regarded as complicated: an increase in the fitness of a transgenic plant compared with non-transgenic counterparts will be the result of an interaction between the altered plant phenotype and an enormous number of environmental variables. This has led to the idea that risk assessment of weediness needs to "understand" these interactions, with the implication that exhaustive data are required. Here we argue that environmental risk assessment of the weediness of transgenic plants need not be complicated. Analysis of the conditions that must be met for increased weediness to occur suggests a series of studies that starts with simple tests in the laboratory under "worst case" assumptions, and becomes increasingly complex and realistic should the simpler studies not indicate negligible risk with sufficient certainty. We illustrate how the approach might work for assessing the risks of increased weediness using the example of possible introgression of a gene for Turnip mosaic virus (TuMV) resistance from oilseed rape to certain wild Brassica species.}, }
@article {pmid16631788, year = {2006}, author = {Fraser, JS and Yu, Z and Maxwell, KL and Davidson, AR}, title = {Ig-like domains on bacteriophages: a tale of promiscuity and deceit.}, journal = {Journal of molecular biology}, volume = {359}, number = {2}, pages = {496-507}, doi = {10.1016/j.jmb.2006.03.043}, pmid = {16631788}, issn = {0022-2836}, mesh = {Amino Acid Sequence ; Animals ; Bacteriophages/chemistry/genetics ; *Computational Biology ; Immunoglobulins/*chemistry ; Models, Molecular ; Molecular Sequence Data ; *Protein Conformation ; Protein Folding ; Ribosomes/genetics/metabolism ; Sequence Alignment ; Viral Proteins/chemistry ; }, abstract = {The immunoglobulin (Ig) fold is one of the most important structures in biology, playing essential roles in the vertebrate immune response, cell adhesion, and many other processes. Through bioinformatic analysis, we have discovered that Ig-like domains are often found in the constituent proteins of tailed double-stranded (ds) DNA bacteriophage particles, and are likely displayed on the surface of these viruses. These phage Ig-like domains fall into three distinct sequence families, which are similar to the classic immunoglobulin domain (I-Set), the fibronectin type 3 repeat (FN3), and the bacterial Ig-like domain (Big2). The phage Ig-like domains are very promiscuous. They are attached to more than ten different functional classes of proteins, and found in all three morphogenetic classes of tailed dsDNA phages. In addition, they reside in phages that infect a diverse set of gram negative and gram positive bacteria. These domains are deceptive because many are added to larger proteins through programmed ribosomal frameshifting, so that they are not always detected by standard protein sequence searching procedures. In addition, the presence of unrecognized Ig-like domains in a variety of phage proteins with different functions has led to gene misannotation. Our results demonstrate that horizontal gene transfer involving Ig-like domain encoding DNA has occurred commonly between diverse classes of both lytic and temperate phages, which otherwise display very limited sequence similarities to one another. We suggest that phage may have been an important vector in the spread of Ig-like domains through diverse species of bacteria. While the function of the phage Ig-like domains is unknown, several lines of evidence suggest that they may play an accessory role in phage infection by weakly interacting with carbohydrates on the bacterial cell surface.}, }
@article {pmid16621083, year = {2006}, author = {Angelov, A and Liebl, W}, title = {Insights into extreme thermoacidophily based on genome analysis of Picrophilus torridus and other thermoacidophilic archaea.}, journal = {Journal of biotechnology}, volume = {126}, number = {1}, pages = {3-10}, doi = {10.1016/j.jbiotec.2006.02.017}, pmid = {16621083}, issn = {0168-1656}, mesh = {Acclimatization/*genetics ; Electron Transport/genetics/physiology ; Gene Transfer, Horizontal/*genetics ; Hydrogen-Ion Concentration ; Membrane Transport Proteins/genetics ; Phylogeny ; RNA, Ribosomal, 16S/classification ; Sulfolobus/*genetics/physiology ; Thermoplasmales/*genetics/physiology ; }, abstract = {Thermoacidophiles are prokaryotic microorganisms with the stunning capability to survive and multiply at extremely low pH and simultaneously at high temperatures. The mechanisms by which these organisms, exclusively members of the Archaea, cope with their harsh surroundings are poorly understood. The genome sequences of several representatives of the thermoacidophilic genera Picrophilus, Thermoplasma and Sulfolobus have recently become available. Genome-wide comparison has revealed a number of features as possible facets of the overall acidophilic survival strategy of the most thermoacidophilic organisms known, such as a high ratio of secondary over primary transport systems, the composition of the respiratory chain, and the frequent genetic input via lateral gene transfer (LGT) during evolution.}, }
@article {pmid16619613, year = {2006}, author = {Petridis, M and Bagdasarian, M and Waldor, MK and Walker, E}, title = {Horizontal transfer of Shiga toxin and antibiotic resistance genes among Escherichia coli strains in house fly (Diptera: Muscidae) gut.}, journal = {Journal of medical entomology}, volume = {43}, number = {2}, pages = {288-295}, doi = {10.1603/0022-2585(2006)043[0288:htosta]2.0.co;2}, pmid = {16619613}, issn = {0022-2585}, mesh = {Animals ; Bacteriophages ; Colony Count, Microbial ; Conjugation, Genetic ; DNA Primers/chemistry ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/classification/*genetics ; Gastrointestinal Tract/microbiology ; Gene Transfer, Horizontal/*genetics ; Genetic Markers/genetics ; Houseflies/*microbiology ; Phenotype ; Plasmids ; Polymerase Chain Reaction/methods ; Rifampin ; Shiga Toxin 1/*genetics ; Transduction, Genetic ; }, abstract = {Whether the house fly, Musca domestica L., gut is a permissive environment for horizontal transfer of antibiotic resistance and virulence genes between strains of Escherichia coli is not known. House flies were immobilized and force fed suspensions of defined, donor strains of E. coli containing chloramphenicol resistance genes on a plasmid, or lysogenic, bacteriophage-born Shiga toxin gene stx1 (bacteriophage H-19B::Ap1). Recipient strains were E. coli lacking these mobile elements and genes but having rifampicin as a selectable marker. Plasmid transfer occurred at rates of 10(-2) per donor cell in the fly midgut and 10(-3) in the fly crop after 1 h of incubation postfeeding. Bacteriophage transfer rate was approximately 10(-6) per donor cell without induction, but induction with mitomycin C increased rates of transfer to 10(-2) per donor cell. These findings show that genes encoding antibiotic resistance or toxins will transfer horizontally among bacteria in the house fly gut via plasmid transfer or phage transduction. The house fly gut may provide a favorable environment for the evolution and emergence of pathogenic bacterial strains through acquisition of antibiotic resistance genes or virulence factors.}, }
@article {pmid16617062, year = {2006}, author = {Hasegawa, K and Kobayashi, R and Takada, E and Ono, A and Chiba, N and Morozumi, M and Iwata, S and Sunakawa, K and Ubukata, K and , }, title = {High prevalence of type b beta-lactamase-non-producing ampicillin-resistant Haemophilus influenzae in meningitis: the situation in Japan where Hib vaccine has not been introduced.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {57}, number = {6}, pages = {1077-1082}, doi = {10.1093/jac/dkl142}, pmid = {16617062}, issn = {0305-7453}, mesh = {Amino Acid Substitution ; Ampicillin Resistance/*genetics ; Anti-Bacterial Agents/pharmacology ; Child, Preschool ; DNA, Bacterial/analysis/chemistry/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Haemophilus influenzae type b/*drug effects/enzymology/genetics/isolation &amp; purification ; Humans ; Infant ; Japan ; Meningitis, Haemophilus/*microbiology ; Microbial Sensitivity Tests ; Mutation ; Mutation, Missense ; Penicillin-Binding Proteins/genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Transformation, Bacterial ; beta-Lactamases/*analysis ; beta-Lactams/pharmacology ; }, abstract = {OBJECTIVES: To study yearly changes in resistance and to identify ftsI mutations in beta-lactamase-non-producing ampicillin-resistant (BLNAR) and TEM-1 beta-lactamase-producing amoxicillin/clavulanic acid-resistant (BLPACR) isolates of Haemophilus influenzae from patients with meningitis.<br><br>METHODS: Between January 2000 and December 2004, we received 621 isolates of H. influenzae from 285 member institutions of the Nationwide Surveillance Study Group for Bacterial Meningitis. All isolates were analysed by PCR to identify resistance genes and tested for susceptibility to beta-lactams. The ftsI gene was sequenced in all BLNAR and BLPACR isolates.<br><br>RESULTS: All but four isolates were of serotype b. The isolates could be divided into six classes, namely beta-lactamase-non-producing ampicillin-susceptible (25.0%), TEM-1 beta-lactamase-producing ampicillin-resistant (11.0%), beta-lactamase-non-producing low-level ampicillin-resistant with N526K or R517H substitution in the ftsI gene (30.4%), BLNAR with an S385T substitution together with either N526K or R517H substitution in ftsI (22.2%), BLPACR-I with either a N526K or R517H substitution in ftsI (9.5%) and BLPACR-II with an S385T substitution together with either a N526K or R517H substitution in ftsI (1.9%). The prevalence of BLNAR has increased rapidly, from 5.8% in 2000 to 34.5% in 2004. All BLNAR and BLPACR-II strains were classified into nine subgroups on the basis of substitution patterns in the ftsI gene. The MICs of cephalosporin antibiotics for H. influenzae transformants into which the ftsI genes from BLNAR strains of each of the nine subgroups were introduced increased to varying degrees depending on the mutations.<br><br>CONCLUSIONS: The results suggest that introduction of H. influenzae type b (Hib) vaccination into infants and children is necessary for the prevention of severe Hib infections in Japan.}, }
@article {pmid16615204, year = {2006}, author = {Ghatnekar, L and Jaarola, M and Bengtsson, BO}, title = {The introgression of a functional nuclear gene from Poa to Festuca ovina.}, journal = {Proceedings. Biological sciences}, volume = {273}, number = {1585}, pages = {395-399}, pmid = {16615204}, issn = {0962-8452}, mesh = {Alleles ; Base Sequence ; DNA, Plant/chemistry/genetics ; *Evolution, Molecular ; Festuca/enzymology/*genetics ; Genes, Plant/genetics ; Genetic Variation ; Glucose-6-Phosphate Isomerase/*genetics ; Phylogeny ; Poa/genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {In sheep's fescue, Festuca ovina, genes coding for the cytosolic enzyme phosphoglucose isomerase, PGIC, are not only found at the standard locus, PgiC1, but also at a segregating second locus, PgiC2. We have used PCR-based sequencing to characterize the molecular structure and evolution of five PgiC1 and three PgiC2 alleles in F. ovina. The three PgiC2 alleles were complex in that they carried two gene copies: either two active genes or one active and one pseudogene. All the PgiC2 sequences were very similar to each other but highly diverged from the five PgiC1 sequences. We also sequenced PgiC genes from several other grass species. Phylogenetic analysis of these sequences indicates that PgiC2 has introgressed into F. ovina from the distant genus Poa. Such an introgression may, for example, follow from a non-standard fertilization with more than one pollen grain, or a direct horizontal gene transfer mediated by a plant virus.}, }
@article {pmid16612537, year = {2006}, author = {Godde, JS and Bickerton, A}, title = {The repetitive DNA elements called CRISPRs and their associated genes: evidence of horizontal transfer among prokaryotes.}, journal = {Journal of molecular evolution}, volume = {62}, number = {6}, pages = {718-729}, pmid = {16612537}, issn = {0022-2844}, mesh = {Base Sequence ; Desulfovibrio/genetics ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; *Models, Genetic ; Molecular Sequence Data ; Phylogeny ; *Prokaryotic Cells ; Repetitive Sequences, Nucleic Acid/*genetics ; Sequence Alignment ; Shewanella/genetics ; }, abstract = {We have found direct DNA repeats 21-47 bp in length interspersed with nonrepetitive sequences of similar length, or clustered regularly interspaced short palindromic repeats (CRISPRs) in a wide range of diverse prokaryotes, including many Archaeal and Eubacterial species. A number of cas, CRISPR-associated genes have also been characterized in many of the same organisms. Phylogenetic analysis of these cas genes suggests that the CRISPR loci have been propagated via HGT, horizontal gene transfer. We suggest a mechanism by which this HGT has occurred, namely, that the CRISPR loci can be carried between cells on megaplasmids > or = 40 kb in length.}, }
@article {pmid16610135, year = {2005}, author = {Cortez, DQ and Lazcano, A and Becerra, A}, title = {Comparative analysis of methodologies for the detection of horizontally transferred genes: a reassessment of first-order Markov models.}, journal = {In silico biology}, volume = {5}, number = {5-6}, pages = {581-592}, pmid = {16610135}, issn = {1386-6338}, mesh = {Computer Simulation ; Escherichia coli K12/genetics ; Escherichia coli O157/genetics ; *Gene Transfer, Horizontal ; Genetic Techniques ; Genome, Bacterial ; *Markov Chains ; *Models, Genetic ; Salmonella typhimurium/genetics ; }, abstract = {With the advent of larger genome databases detection of horizontal gene transfer events has been transformed into an increasingly important issue. Here we present a simple theoretical analysis based on the in silico artificial addition of known foreign genes from different prokaryotic groups into the genome of Escherichia coli K12 MG1655. Using this dataset as a control, we have tested the efficiency of four methodologies commonly employed to detect HTG (Horizontally transferred genes), which are based on (a) the codon adaptation index, codon usage, and GC percentage (CAI/GC); (b) a distributional profile (DP) approach made by a gene search in the closely related phylogenetic genomes; (c) a Bayesian model (BM); and (d) a first-order Markov model (MM). All methods exhibit limitations although, as shown here, the BM and the MM are better approximations. Moreover, the MM has demonstrated a more accurate rate of detections when genes from closely related organisms are evaluated. The application of the MM to detect recently transferred genes in the genomes of E. coli strains K12 MG1655, O157 EDL933, and Salmonella typhimurium, shows that these organisms have undergone a rather significant amount of HTG, most of which appear to be pseudogenes. Few of these sequences that have undergone HGT appear to have well defined functions and may be involved in the organism's adaptation.}, }
@article {pmid16610050, year = {2006}, author = {Tsui, TY and Lau, CK and Ma, J and Glockzin, G and Obed, A and Schlitt, HJ and Fan, ST}, title = {Adeno-associated virus-mediated heme oxygenase-1 gene transfer suppresses the progression of micronodular cirrhosis in rats.}, journal = {World journal of gastroenterology}, volume = {12}, number = {13}, pages = {2016-2023}, pmid = {16610050}, issn = {1007-9327}, mesh = {Animals ; Carbon Tetrachloride/toxicity ; Dependovirus/*genetics ; Gene Transfer, Horizontal ; *Genetic Therapy ; Heme Oxygenase-1/*genetics ; Liver/drug effects/enzymology ; Liver Cirrhosis, Experimental/enzymology/*therapy ; RNA, Messenger/analysis ; Rats ; Rats, Inbred Lew ; Transforming Growth Factor beta/genetics ; Transforming Growth Factor beta1 ; }, abstract = {AIM: To test the hypothesis that enhancement of the activity of heme oxygenase can interfere with processes of fibrogenesis associated with recurrent liver injury, we investigated the therapeutic potential of over-expression of heme oxygense-1 in a CCl(4)-induced micronodular cirrhosis model.<br><br>METHODS: Recombinant adeno-associated viruses carrying rat HO-1 or GFP gene were generated. 1x 10(12) vg of adeno-associated viruses were administered through portal injection at the time of the induction of liver fibrosis.<br><br>RESULTS: Conditioning the rat liver with over-expression of HO-1 by rAAV/HO-1 significantly increased the HO enzymatic activities in a stable manner. The development of micronodular cirrhosis was significantly inhibited in rAAV/HO-1-transduced animals as compared to controls. Portal hypertension was markedly diminished in rAAV/HO-1-transduced animals as compared to controls, whereas there are no significant changes in systolic blood pressure. This finding was accompanied with improved liver biochemistry, less infiltrating macrophages and less activated hepatic stellate cells (HSCs) in rAAV/HO-1-transduced livers.<br><br>CONCLUSION: Enhancement of HO activity in the livers suppresses the development of cirrhosis.}, }
@article {pmid16597934, year = {2006}, author = {Cérémonie, H and Buret, F and Simonet, P and Vogel, TM}, title = {Natural Pseudomonas sp. strain N3 in artificial soil microcosms.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {4}, pages = {2385-2389}, pmid = {16597934}, issn = {0099-2240}, mesh = {*Ecosystem ; Gene Transfer, Horizontal ; *Lightning ; Plasmids ; Pseudomonas/*genetics/growth &amp; development ; Soil/analysis ; *Soil Microbiology ; Sterilization ; *Transformation, Bacterial ; }, abstract = {The lightning-competent Pseudomonas sp. strain N3, recently isolated from soil, has been used to study the extent of natural electrotransformation (NET) or lightning transformation as a horizontal gene transfer mechanism in soil. The variation of electrical fields applied to the soil with a laboratory-scale lightning system provides an estimate of the volume of soil affected by NET. Based on the range of the electric field that induces NET of Pseudomonas strain N3, the volume of soil, where NET could occur, ranges from 2 to 950 m(3) per lightning strike. The influence of DNA parameters (amount, size, and purity) and DNA soil residence time were also investigated. NET frequencies (electrotransformants/recipient cells) ranged from 10(-8) for cell lysate after 1 day of residence in soil to 4 x 10(-7) with a purified plasmid added immediately before the lightning. The electrical field gradient (in kilovolts per cm) also played a role as NET frequencies ranging from 1 x 10(-5) at 2.3 kV/cm to 1.7 x 10(-4) at 6.5 kV/cm.}, }
@article {pmid16596396, year = {2006}, author = {Guo, W and Wang, W and Zhou, B and Zhang, T}, title = {Cross-species transferability of G. arboreum-derived EST-SSRs in the diploid species of Gossypium.}, journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik}, volume = {112}, number = {8}, pages = {1573-1581}, pmid = {16596396}, issn = {0040-5752}, mesh = {Alleles ; Base Sequence ; Cluster Analysis ; DNA, Plant/analysis ; Diploidy ; *Expressed Sequence Tags ; Gene Amplification ; Gene Transfer, Horizontal ; Genes, Plant ; Genetic Markers ; Genome, Plant ; Gossypium/*genetics ; *Microsatellite Repeats ; Molecular Sequence Data ; Polymorphism, Genetic ; Recombination, Genetic ; *Repetitive Sequences, Nucleic Acid ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Species Specificity ; }, abstract = {Diploid species with a common Gossypium origin are highly diverse in morphology and have been classified into eight genomic groups designated A-G and K. In this study, the transferability of 207 Gossypium arboreum-derived expressed sequence tag-simple sequence repeat (EST-SSR) primer pairs was examined among 25 different diploid accessions representing 7 genomes and 23 Gossypium species. We found that 124 of the 207 (60%) primer pairs produced amplification products in all 25 accessions. The remaining 83 (40%) primer pairs produced amplification in only a subset of species, ranging from 13 to 22 species, which is consistent with some genome- and species-specific amplification. The cross-species amplification of these EST-SSRs in 22 diploid species was 96.5% in 4,554 combinations (207 SSRsx22 species), indicative of a high transferability among the Gossypium species. Furthermore, a high level of polymorphism with an average number of 6.53 alleles per SSR marker was detected. No correlation was found between the repeat motif type and cross-species amplification. DNA sequencing showed that the high-level polymorphism findings was mainly due to changes in the number of repeat motifs and that the high transferability can be attributed to a higher-level conservation in the flanking regions among these diploid Gossypium species. The transferability among these different diploid species presented here can increase the efficiency of transferring genetic information across species and further enhance their introgression into cultivated cotton species by the molecular tagging of important genes existing in these diploid species using the EST-SSR markers.}, }
@article {pmid16594522, year = {2006}, author = {Singh, A and Billingsley, K and Ward, O}, title = {Composting: a potentially safe process for disposal of genetically modified organisms.}, journal = {Critical reviews in biotechnology}, volume = {26}, number = {1}, pages = {1-16}, doi = {10.1080/07388550500508644}, pmid = {16594522}, issn = {0738-8551}, mesh = {Bacteria/genetics ; Cell Death ; Gene Transfer, Horizontal ; *Organisms, Genetically Modified ; Plants/genetics ; *Soil ; Waste Management/*methods ; }, abstract = {The widespread use of genetically modified organisms (GMOs) may result in the release of GMOs into the environment. The potential risks regarding their use and implementation of disposal methods, especially the possibility of novel genes from GMOs being transferred to natural organisms, need to be evaluated and better understood. There is an increasingly accepted public view that GMO products introduced into the environment should be degradable and should disappear after a limited period of time. Due to the risk of possible horizontal gene transfer, disposal methods for GMOs need to address destruction of both the organism and the genetic material. During the last two decades, we have developed a greater understanding of the biochemical, microbiological and molecular concepts of the composting process, such that maximum decomposition may be achieved in the shortest time with minimal negative impacts to the environment. The conditions created in a properly managed composting process environment may help in destroying GMOs and their genes, thereby reducing the risk of the spread of genetic material. When considering composting as a potential method for the disposal of GMOs, the establishment of controlled conditions providing an essentially homogenous environment appears to be an important requirement. An evaluation of composting as a safe option for disposal of GMOs is provided in this review.}, }
@article {pmid16586364, year = {2006}, author = {Harrison, LH and Jolley, KA and Shutt, KA and Marsh, JW and O'Leary, M and Sanza, LT and Maiden, MC and , }, title = {Antigenic shift and increased incidence of meningococcal disease.}, journal = {The Journal of infectious diseases}, volume = {193}, number = {9}, pages = {1266-1274}, doi = {10.1086/501371}, pmid = {16586364}, issn = {0022-1899}, support = {K24 AI052788/AI/NIAID NIH HHS/United States ; K24 AI52788/AI/NIAID NIH HHS/United States ; //Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Sequence ; Amino Acid Substitution ; Antigenic Variation/*genetics ; Antigens, Bacterial/*genetics ; Bacterial Outer Membrane Proteins/*genetics ; Genes, Bacterial ; Humans ; Incidence ; Meningococcal Infections/*epidemiology/immunology/*microbiology ; Molecular Sequence Data ; Mutation ; Neisseria meningitidis/*genetics/*immunology/isolation &amp; purification ; Porins/genetics ; }, abstract = {BACKGROUND: The incidence of serogroup C and Y meningococcal disease increased in the United States during the 1990s. The cyclical nature of endemic meningococcal disease remains unexplained. The purpose of this study was to investigate the mechanisms associated with the increase in the incidence of meningococcal disease.<br><br>METHODS: We characterized an increasing incidence of invasive serogroup C and Y meningococcal disease using population-based surveillance from 1992 through 2001. Isolates were characterized by multilocus sequence typing and antigen sequence typing of 3 outer membrane protein (OMP) genes: porA variable regions (VRs) 1 and 2, porB, and fetA VR.<br><br>RESULTS: For both serogroups, OMP antigenic shifts were associated with increased incidence of meningococcal disease. For serogroup Y, antigenic shift occurred through amino acid substitutions at all 3 OMPs--PorA VR 1 and 2, PorB, and FetA VR. For serogroup C, antigenic shift involved amino acid substitutions at FetA VR and, in some cases, deletion of the porA gene. On the basis of deduced amino acid sequences, the antigenic changes likely occurred by horizontal gene transfer.<br><br>CONCLUSIONS: Antigenic shifts were associated with increased incidence of serogroup C and serogroup Y meningococcal disease. For serogroup Y, the changes involved all OMP genes that were studied. Increases in the incidence of meningococcal disease may be caused, in part, by antigenic shift.}, }
@article {pmid16585762, year = {2006}, author = {Gerdes, SY and Kurnasov, OV and Shatalin, K and Polanuyer, B and Sloutsky, R and Vonstein, V and Overbeek, R and Osterman, AL}, title = {Comparative genomics of NAD biosynthesis in cyanobacteria.}, journal = {Journal of bacteriology}, volume = {188}, number = {8}, pages = {3012-3023}, pmid = {16585762}, issn = {0021-9193}, support = {R01 AI059146/AI/NIAID NIH HHS/United States ; 1R01 AI 059146-01A2/AI/NIAID NIH HHS/United States ; }, mesh = {Amide Synthases/genetics/metabolism ; Cyanobacteria/*genetics/*metabolism ; Escherichia coli ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Glutamine/metabolism ; Models, Biological ; Multigene Family ; NAD/*biosynthesis ; Niacin/metabolism ; Niacinamide/metabolism ; Nicotinamide Mononucleotide/analogs &amp; derivatives/genetics/metabolism ; Nicotinamide Phosphoribosyltransferase ; Nucleotidyltransferases/genetics/metabolism ; Pentosyltransferases/genetics/metabolism ; Synteny ; }, abstract = {Biosynthesis of NAD(P) cofactors is of special importance for cyanobacteria due to their role in photosynthesis and respiration. Despite significant progress in understanding NAD(P) biosynthetic machinery in some model organisms, relatively little is known about its implementation in cyanobacteria. We addressed this problem by a combination of comparative genome analysis with verification experiments in the model system of Synechocystis sp. strain PCC 6803. A detailed reconstruction of the NAD(P) metabolic subsystem using the SEED genomic platform (http://theseed.uchicago.edu/FIG/index.cgi) helped us accurately annotate respective genes in the entire set of 13 cyanobacterial species with completely sequenced genomes available at the time. Comparative analysis of operational variants implemented in this divergent group allowed us to elucidate both conserved (de novo and universal pathways) and variable (recycling and salvage pathways) aspects of this subsystem. Focused genetic and biochemical experiments confirmed several conjectures about the key aspects of this subsystem. (i) The product of the slr1691 gene, a homolog of Escherichia coli gene nadE containing an additional nitrilase-like N-terminal domain, is a NAD synthetase capable of utilizing glutamine as an amide donor in vitro. (ii) The product of the sll1916 gene, a homolog of E. coli gene nadD, is a nicotinic acid mononucleotide-preferring adenylyltransferase. This gene is essential for survival and cannot be compensated for by an alternative nicotinamide mononucleotide (NMN)-preferring adenylyltransferase (slr0787 gene). (iii) The product of the slr0788 gene is a nicotinamide-preferring phosphoribosyltransferase involved in the first step of the two-step non-deamidating utilization of nicotinamide (NMN shunt). (iv) The physiological role of this pathway encoded by a conserved gene cluster, slr0787-slr0788, is likely in the recycling of endogenously generated nicotinamide, as supported by the inability of this organism to utilize exogenously provided niacin. Positional clustering and the co-occurrence profile of the respective genes across a diverse collection of cellular organisms provide evidence of horizontal transfer events in the evolutionary history of this pathway.}, }
@article {pmid16584645, year = {2006}, author = {Kong, QL and Guan, YZ and Jing, XF and Li, C and Guo, XH and Lü, Z and An, YQ}, title = {BPI700-Fc gamma1(700) chimeric gene expression and its protective effect in a mice model of the lethal E. coli infection.}, journal = {Chinese medical journal}, volume = {119}, number = {6}, pages = {474-481}, pmid = {16584645}, issn = {0366-6999}, mesh = {Animals ; Anti-Bacterial Agents/therapeutic use ; Antimicrobial Cationic Peptides ; Blood Proteins ; CHO Cells ; Cricetinae ; Dependovirus/genetics ; Disease Models, Animal ; Escherichia coli Infections/*therapy ; Gene Transfer, Horizontal ; *Genetic Therapy ; Mice ; Mice, Inbred BALB C ; Proteins/*genetics ; Receptors, IgG/*genetics ; Recombinant Fusion Proteins/*genetics ; }, abstract = {BACKGROUND: Infections caused by gram-negative bacteria (GNB) often lead to high mortality in common clinical settings. The effect of traditional antibiotic therapy is hindered by drug-resistant bacteria and unneutralizable endotoxin. Few effective methods can protect high risk patients from bacterial infection. This study explored the protection of adeno-associated virus 2 (AAV2)-bacteriacidal permeability increasing protein 700 (BPI(700))-fragment crystallizable gamma one 700 (Fc gamma1(700)) chimeric gene transferred mice against the minimal lethal dose (MLD) of E. coli and application of gene therapy for bacterial infection.<br><br>METHODS: After AAV2-BPI(700)-Fc gamma1(700) virus transfection, dot blotting and Western blotting were used to detect the target gene products in Chinese hamster ovary-K1 cells (CHO-K1cells). Reverse transcription-polymerase chain reaction and immunohistochemical assay were carried out to show the target gene expression in mice. Modified BPI-enzyme linked immunosorbent assay was used to identify the target gene products in murine serum. The protection of BPI(700)-Fc gamma1(700) gene transferred mice was examined by survival rate after MLD E. coli challenge. Colony forming unit (CFU) count, limulus amebocyte lysate kit and cytokine kit were used to quantify the bacteria, the level of endotoxin, and proinflammatory cytokine.<br><br>RESULTS: BPI(1-199)-Fc gamma1 protein was identified in the CHO-K1 cell culture supernatant, injected muscles and serum of the gene transferred mice. After MLD E. coli challenge, the survival rate of AAV2-BPI(700)-Fc gamma1(700) gene transferred mice (36.7%) was significantly higher than that of AAV2-enhanced green fluorescent protein (AAV2-EGFP) gene transferred mice (3.3%) and PBS control mice (5.6%). The survival rate of AAV2-BPI(700)-Fc gamma1(700) gene transferred mice treated with cefuroxime sodium was 65.0%. The bacterium number in main viscera, the levels of endotoxin and proinflammatory cytokine (tumor necrosis factor-alpha and interleukin-1beta) in serum of the AAV2-BPI(700)-Fc gamma1(700) gene transferred mice were markedly lower than that of PBS control mice (P < 0.01).<br><br>CONCLUSIONS: AAV2-BPI(700)-Fc gamma1(700) gene transferred mice can resist MLD E. coli infection through expressing BPI(1-199)-Fc gamma1 protein. Our findings suggested that AAV2 mediated BPI(700)-Fc gamma1(700) gene delivery could be used for protection and treatment of clinical GNB infection in high-risk individuals.}, }
@article {pmid16581205, year = {2006}, author = {Chen, LL}, title = {Identification of genomic islands in six plant pathogens.}, journal = {Gene}, volume = {374}, number = {}, pages = {134-141}, doi = {10.1016/j.gene.2006.01.029}, pmid = {16581205}, issn = {0378-1119}, mesh = {Agrobacterium tumefaciens/genetics/pathogenicity ; Base Composition/genetics ; DNA, Bacterial/chemistry ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomic Islands/*genetics ; Gram-Negative Bacteria/classification/*genetics/*pathogenicity ; Plants/*microbiology ; Pseudomonas syringae/genetics/pathogenicity ; Ralstonia solanacearum/genetics/pathogenicity ; Sequence Analysis, DNA ; Xanthomonas/genetics/pathogenicity ; Xanthomonas campestris/genetics/pathogenicity ; Xylella/genetics/pathogenicity ; }, abstract = {Genomic islands (GIs) play important roles in microbial evolution, which are acquired by horizontal gene transfer. In this paper, the GIs of six completely sequenced plant pathogens are identified using a windowless method based on Z curve representation of DNA sequences. Consequently, four, eight, four, one, two and four GIs are recognized with the length greater than 20-Kb in plant pathogens Agrobacterium tumefaciens str. C58, Rolstonia solanacearum GMI1000, Xanthomonas axonopodis pv. citri str. 306 (Xac), Xanthomonas campestris pv. campestris str. ATCC33913 (Xcc), Xylella fastidiosa 9a5c and Pseudomonas syringae pv. tomato str. DC3000, respectively. Most of these regions share a set of conserved features of GIs, including an abrupt change in GC content compared with that of the rest of the genome, the existence of integrase genes at the junction, the use of tRNA as the integration sites, the presence of genetic mobility genes, the difference of codon usage, codon preference and amino acid usage, etc. The identification of these GIs will benefit the research for the six important phytopathogens.}, }
@article {pmid16572170, year = {2006}, author = {Pál, C and Papp, B and Lercher, MJ and Csermely, P and Oliver, SG and Hurst, LD}, title = {Chance and necessity in the evolution of minimal metabolic networks.}, journal = {Nature}, volume = {440}, number = {7084}, pages = {667-670}, doi = {10.1038/nature04568}, pmid = {16572170}, issn = {1476-4687}, support = {E19354/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Biological Evolution ; Buchnera/genetics ; *Computational Biology ; Escherichia coli K12/enzymology/*genetics/*metabolism ; Escherichia coli Proteins/genetics/metabolism ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/genetics ; Genome, Bacterial ; Symbiosis/genetics ; Wigglesworthia/genetics ; }, abstract = {It is possible to infer aspects of an organism's lifestyle from its gene content. Can the reverse also be done? Here we consider this issue by modelling evolution of the reduced genomes of endosymbiotic bacteria. The diversity of gene content in these bacteria may reflect both variation in selective forces and contingency-dependent loss of alternative pathways. Using an in silico representation of the metabolic network of Escherichia coli, we examine the role of contingency by repeatedly simulating the successive loss of genes while controlling for the environment. The minimal networks that result are variable in both gene content and number. Partially different metabolisms can thus evolve owing to contingency alone. The simulation outcomes do preserve a core metabolism, however, which is over-represented in strict intracellular bacteria. Moreover, differences between minimal networks based on lifestyle are predictable: by simulating their respective environmental conditions, we can model evolution of the gene content in Buchnera aphidicola and Wigglesworthia glossinidia with over 80% accuracy. We conclude that, at least for the particular cases considered here, gene content of an organism can be predicted with knowledge of its distant ancestors and its current lifestyle.}, }
@article {pmid16571829, year = {2006}, author = {Kenoutis, C and Efrose, RC and Swevers, L and Lavdas, AA and Gaitanou, M and Matsas, R and Iatrou, K}, title = {Baculovirus-mediated gene delivery into Mammalian cells does not alter their transcriptional and differentiating potential but is accompanied by early viral gene expression.}, journal = {Journal of virology}, volume = {80}, number = {8}, pages = {4135-4146}, pmid = {16571829}, issn = {0022-538X}, mesh = {Animals ; Bombyx/*virology ; *Cell Differentiation ; Cell Line ; Gene Expression ; *Gene Transfer, Horizontal ; *Genes, Immediate-Early ; Green Fluorescent Proteins/genetics ; Humans ; Nucleopolyhedroviruses/*genetics ; Rats ; Schwann Cells/metabolism ; *Transcription, Genetic ; }, abstract = {Gene delivery to neural cells is central to the development of transplantation therapies for neurological diseases. In this study, we used a baculovirus derived from the domesticated silk moth, Bombyx mori, as vector for transducing a human cell line (HEK293) and primary cultures of rat Schwann cells. Under optimal conditions of infection with a recombinant baculovirus containing the reporter green fluorescent protein gene under mammalian promoter control, the infected cells express the transgene with high efficiency. Toxicity assays and transcriptome analyses suggest that baculovirus infection is not cytotoxic and does not induce differential transcriptional responses in HEK293 cells. Infected Schwann cells retain their characteristic morphological and molecular phenotype as determined by immunocytochemistry for the marker proteins S-100, glial fibrillary acidic protein, and p75 nerve growth factor receptor. Moreover, baculovirus-infected Schwann cells are capable of differentiating in vitro and express the P0 myelination marker. However, transcripts for several immediate-early viral genes also accumulate in readily detectable levels in the transduced cells. This transcriptional activity raises concerns regarding the long-term safety of baculovirus vectors for gene therapy applications. Potential approaches for overcoming the identified problem are discussed.}, }
@article {pmid16569761, year = {2006}, author = {Lebrun, E and Santini, JM and Brugna, M and Ducluzeau, AL and Ouchane, S and Schoepp-Cothenet, B and Baymann, F and Nitschke, W}, title = {The Rieske protein: a case study on the pitfalls of multiple sequence alignments and phylogenetic reconstruction.}, journal = {Molecular biology and evolution}, volume = {23}, number = {6}, pages = {1180-1191}, doi = {10.1093/molbev/msk010}, pmid = {16569761}, issn = {0737-4038}, mesh = {Algorithms ; Amino Acid Sequence ; Bacteria/chemistry ; Cytochromes b/genetics ; DNA Transposable Elements ; Electron Transport Complex III/*chemistry/*genetics ; Gene Deletion ; Gene Transfer, Horizontal ; Genes, rRNA ; Iron-Sulfur Proteins/*chemistry/*genetics ; Oxidoreductases/genetics ; *Phylogeny ; Protein Structure, Secondary ; *Sequence Alignment ; Sulfolobus/chemistry ; }, abstract = {Previously published phylogenetic trees reconstructed on "Rieske protein" sequences frequently are at odds with each other, with those of other subunits of the parent enzymes and with small-subunit rRNA trees. These differences are shown to be at least partially if not completely due to problems in the reconstruction procedures. A major source of erroneous Rieske protein trees lies in the presence of a large, poorly conserved domain prone to accommodate very long insertions in well-defined structural hot spots substantially hampering multiple alignments. The remaining smaller domain, in contrast, is too conserved to allow distant phylogenies to be deduced with sufficient confidence. Three-dimensional structures of representatives from this protein family are now available from phylogenetically distant species and from diverse enzymes. Multiple alignments can thus be refined on the basis of these structures. We show that structurally guided alignments of Rieske proteins from Rieske-cytochrome b complexes and arsenite oxidases strongly reduce conflicts between resulting trees and those obtained on their companion enzyme subunits. Further problems encountered during this work, mainly consisting in database errors such as wrong annotations and frameshifts, are described. The obtained results are discussed against the background of hypotheses stipulating pervasive lateral gene transfer in prokaryotes.}, }
@article {pmid16563685, year = {2007}, author = {Hummel, A and Holzapfel, WH and Franz, CM}, title = {Characterisation and transfer of antibiotic resistance genes from enterococci isolated from food.}, journal = {Systematic and applied microbiology}, volume = {30}, number = {1}, pages = {1-7}, doi = {10.1016/j.syapm.2006.02.004}, pmid = {16563685}, issn = {0723-2020}, mesh = {Drug Resistance, Bacterial/*genetics ; Enterococcus faecalis/drug effects/*genetics/isolation &amp; purification ; Enterococcus faecium/drug effects/*genetics/isolation &amp; purification ; *Food Microbiology ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Polymerase Chain Reaction ; Random Amplified Polymorphic DNA Technique ; }, abstract = {The genetic determinants responsible for the resistances against the antibiotics tetracycline [tet(M), tet(O), tet(S), tet(K) and tet(L)], erythromycin (ermA,B,C; mefA,E; msrA/B; and ereA,B) and chloramphenicol (cat) of 38 antibiotic-resistant Enterococcus faecium and Enterococcus faecalis strains from food were characterised. In addition, the transferability of resistance genes was also assessed using filter mating assays. The tet(L) determinant was the most commonly detected among tetracycline-resistant enterococci (94% of the strains), followed by the tet(M) gene, which occurred in 63.0% of the strains. Tet(K) occurred in 56.0% of the resistant strains, while genes for tet(O) and tet(S) could not be detected. The integrase gene of the Tn916-1545 family of transposons was present in 81.3% of the tetracycline resistant strains, indicating that resistance genes might be transferable by transposons. All chloramphenicol-resistant strains carried a cat gene. 81.8% of the erythromycin-resistant strains carried the ermB gene. Two (9.5%) of the 21 erythromycin-resistant strains, which did not contain ermA,B,C, ereA,B and mphA genes harboured the msrC gene encoding an erythromycin efflux pump, which was confirmed by sequencing the PCR amplicon. In addition, all E. faecium strains contained the msrC gene, but none of the E. faecalis strains. Transfer of the genetic determinants for antibiotic resistance could only be demonstrated in one filter mating experiment, where both the tet(M) and tet(L) genes were transferred from E. faecalis FAIR-E 315 to the E. faecalis OG1X recipient strain. Our results show the presence of various types of resistance genes as well as transposon integrase genes associated with transferable resistances in enterococci, indicating a potential for gene transfer in the food environment.}, }
@article {pmid16562379, year = {2005}, author = {Elena, SF and Whittam, TS and Winkworth, CL and Riley, MA and Lenski, RE}, title = {Genomic divergence of Escherichia coli strains: evidence for horizontal transfer and variation in mutation rates.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {8}, number = {4}, pages = {271-278}, pmid = {16562379}, issn = {1139-6709}, mesh = {Codon/genetics ; DNA Repair/genetics ; Escherichia coli/classification/*genetics ; Escherichia coli O157/genetics ; Gene Amplification ; Gene Transfer Techniques ; *Genetic Variation ; Multigene Family ; *Mutation ; Phylogeny ; }, abstract = {This report describes the sequencing in the Escherichia coli B genome of 36 randomly chosen regions that are present in most or all of the fully sequenced E. coli genomes. The phylogenetic relationships among E. coli strains were examined, and evidence for the horizontal gene transfer and variation in mutation rates was determined. The overall phylogenetic tree indicated that E. coli B and K-12 are the most closely related strains, with E. coli O157:H7 being more distantly related, Shigella flexneri 2a even more, and E. coli CFT073 the most distant strain. Within the B, K-12, and O157:H7 clusters, several regions supported alternative topologies. While horizontal transfer may explain these phylogenetic incongruities, faster evolution at synonymous sites along the O157:H7 lineage was also identified. Further interpretation of these results is confounded by an association among genes showing more rapid evolution and results supporting horizontal transfer. Using genes supporting the B and K-12 clusters, an estimate of the genomic mutation rate from a long-term experiment with E. coli B, and an estimate of 200 generations per year, it was estimated that B and K-12 diverged several hundred thousand years ago, while O157:H7 split off from their common ancestor about 1.5-2 million years ago.}, }
@article {pmid16556843, year = {2006}, author = {Coleman, ML and Sullivan, MB and Martiny, AC and Steglich, C and Barry, K and Delong, EF and Chisholm, SW}, title = {Genomic islands and the ecology and evolution of Prochlorococcus.}, journal = {Science (New York, N.Y.)}, volume = {311}, number = {5768}, pages = {1768-1770}, doi = {10.1126/science.1122050}, pmid = {16556843}, issn = {1095-9203}, mesh = {Adaptation, Physiological ; Atlantic Ocean ; Bacteriophages/*genetics/physiology ; *Biological Evolution ; *Ecosystem ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; *Genomic Islands ; Light ; Molecular Sequence Data ; Pacific Ocean ; Phylogeny ; Prochlorococcus/classification/*genetics/isolation &amp; purification/*physiology ; Seawater/*microbiology ; }, abstract = {Prochlorococcus ecotypes are a useful system for exploring the origin and function of diversity among closely related microbes. The genetic variability between phenotypically distinct strains that differ by less that 1% in 16S ribosomal RNA sequences occurs mostly in genomic islands. Island genes appear to have been acquired in part by phage-mediated lateral gene transfer, and some are differentially expressed under light and nutrient stress. Furthermore, genome fragments directly recovered from ocean ecosystems indicate that these islands are variable among cooccurring Prochlorococcus cells. Genomic islands in this free-living photoautotroph share features with pathogenicity islands of parasitic bacteria, suggesting a general mechanism for niche differentiation in microbial species.}, }
@article {pmid16556831, year = {2006}, author = {Falkowski, PG}, title = {Evolution. Tracing oxygen's imprint on earth's metabolic evolution.}, journal = {Science (New York, N.Y.)}, volume = {311}, number = {5768}, pages = {1724-1725}, doi = {10.1126/science.1125937}, pmid = {16556831}, issn = {1095-9203}, mesh = {Animals ; *Biological Evolution ; Computational Biology ; Electron Transport ; Electrons ; Energy Metabolism ; Eukaryotic Cells/metabolism ; *Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; *Metabolism ; Oxidation-Reduction ; Oxygen/*metabolism ; Photosynthesis ; Reactive Oxygen Species/metabolism ; Selection, Genetic ; Water/metabolism ; }, }
@article {pmid16553829, year = {2006}, author = {Wydau, S and Dervyn, R and Anba, J and Dusko Ehrlich, S and Maguin, E}, title = {Conservation of key elements of natural competence in Lactococcus lactis ssp.}, journal = {FEMS microbiology letters}, volume = {257}, number = {1}, pages = {32-42}, doi = {10.1111/j.1574-6968.2006.00141.x}, pmid = {16553829}, issn = {0378-1097}, mesh = {Amino Acid Sequence ; *Bacterial Proteins/chemistry/genetics/metabolism ; Base Sequence ; *Conserved Sequence ; *Gene Expression Regulation, Bacterial ; Genetic Variation ; Lactococcus lactis/*classification/*genetics/metabolism ; Membrane Proteins/chemistry/genetics/metabolism ; Molecular Sequence Data ; Sequence Analysis, DNA ; *Sigma Factor/chemistry/genetics/metabolism ; Transcription Factors/chemistry/genetics/metabolism ; }, abstract = {Natural competence is active in very diverse species of the bacterial kingdom and probably participates in horizontal gene transfer. Recently, the genome sequence of various species, including Lactococcus lactis, revealed the presence of homologues of competence genes in bacteria, which were not previously identified as naturally transformable. We investigated the conservation among lactococcal strains of key components of the natural competence process in streptococci: (i) comX which encodes a sigma factor, allowing the expression of the late competence genes involved in DNA uptake, (ii) its recognition site, the cin-box and (iii) dprA which encodes a protein shown to determine the fate of incoming DNA. The comX and dprA genes and the cin-box appeared conserved among strains, although some L. lactis ssp. lactis strains presented an inactivated dprA gene. We established that ComX controls the expression of the late competence genes in L. lactis. In conclusion, our work strongly suggests that ComX has the same role in streptococci and L. lactis, i.e. the regulation of late competence genes. It also allowed the identification of a set of L. lactis strains and the construction of a comX overexpression system, which should facilitate the investigation of the natural competence activity in lactococci.}, }
@article {pmid16551693, year = {2006}, author = {Ojo, KK and Ruehlen, NL and Close, NS and Luis, H and Bernardo, M and Leitao, J and Roberts, MC}, title = {The presence of a conjugative Gram-positive Tn2009 in Gram-negative commensal bacteria.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {57}, number = {6}, pages = {1065-1069}, doi = {10.1093/jac/dkl094}, pmid = {16551693}, issn = {0305-7453}, support = {N01 DE 72623/DE/NIDCR NIH HHS/United States ; U01 DE 1189/DE/NIDCR NIH HHS/United States ; }, mesh = {Acinetobacter/drug effects/*genetics ; Bacterial Proteins/genetics ; Base Sequence ; Citrobacter/genetics ; Conjugation, Genetic ; DNA Transposable Elements/*genetics ; DNA, Bacterial/chemistry/*genetics ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Homoserine/analogs &amp; derivatives ; Humans ; Membrane Proteins/genetics ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Polymerase Chain Reaction ; Proteus/genetics ; Sequence Analysis, DNA ; Sequence Homology ; Stenotrophomonas/genetics ; Streptococcus pneumoniae/drug effects/*genetics ; }, abstract = {OBJECTIVES: To determine whether mef(A)-msr(D) and tet(M) genes are linked in representative Gram-negative isolates and/or transferred together during conjugation. To molecularly characterize the Acinetobacter junii element and compare the structure and sequence with the non-conjugative Streptococcus pneumoniae Tn2009 element.<br><br>METHODS: PCR assays, DNA-DNA hybridization and sequencing of PCR products were used. Nucleotide sequences were determined at the integration site of the mef(A) element into Tn916 and upstream and downstream flanking regions of the element.<br><br>RESULTS: A total of 10 mef(A)-msr(D)- and tet(M)-positive isolates carried conjugative element(s). The A. junii Tn2009 element was indistinguishable from S. pneumoniae Tn2009. The region upstream of the A. junii Tn2009 contained an orf that was 89-91% identical to an S. pneumoniae spr1206 gene found upstream of the streptococcal Tn2009. In the A. junii, the spr1206 gene was separated by 67 bp from the end of the Tn2009, while 29 bp were found separating spr1206 from the streptococcal Tn2009. The 1201 bp downstream A. junii sequences included 913 unique sequences.<br><br>CONCLUSIONS: A total of 10 different Gram-negative genera were found to carry the tet(M) genes, including the first description in three genera (Citrobacter, Proteus and Stenotrophomonas). All isolates were able to transfer the genes into > or =1 recipient with macrolide selection. Over 3000 bp were sequenced on each side of the insertion mef junction region in the A. junii and were indistinguishable from the streptococcal Tn2009. The A. junii Tn2009 element was flanked by an S. pneumoniae gene upstream and a unique sequence downstream, suggesting that the A. junii Tn2009 could be part of a larger element.}, }
@article {pmid16551352, year = {2006}, author = {Andersson, JO and Hirt, RP and Foster, PG and Roger, AJ}, title = {Evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes.}, journal = {BMC evolutionary biology}, volume = {6}, number = {}, pages = {27}, pmid = {16551352}, issn = {1471-2148}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Alcohol Dehydrogenase/genetics ; Aldehyde Oxidoreductases/genetics ; Aldose-Ketose Isomerases/genetics ; Animals ; Bacterial Proteins/genetics ; Biodiversity ; *Biological Evolution ; DNA, Protozoan/chemistry ; Ecology ; Entamoeba/classification/genetics ; Escherichia coli Proteins ; Eukaryota/classification/*genetics ; Feeding Behavior/physiology ; Gene Transfer, Horizontal/*genetics ; Iron-Sulfur Proteins/genetics ; Markov Chains ; Molecular Sequence Data ; Monte Carlo Method ; Multienzyme Complexes/genetics ; NADH, NADPH Oxidoreductases/genetics ; Naegleria/classification/genetics ; *Phylogeny ; Polymerase Chain Reaction/methods ; Trichomonas vaginalis/classification/genetics ; }, abstract = {BACKGROUND: Lateral gene transfer (LGT) in eukaryotes from non-organellar sources is a controversial subject in need of further study. Here we present gene distribution and phylogenetic analyses of the genes encoding the hybrid-cluster protein, A-type flavoprotein, glucosamine-6-phosphate isomerase, and alcohol dehydrogenase E. These four genes have a limited distribution among sequenced prokaryotic and eukaryotic genomes and were previously implicated in gene transfer events affecting eukaryotes. If our previous contention that these genes were introduced by LGT independently into the diplomonad and Entamoeba lineages were true, we expect that the number of putative transfers and the phylogenetic signal supporting LGT should be stable or increase, rather than decrease, when novel eukaryotic and prokaryotic homologs are added to the analyses.<br><br>RESULTS: The addition of homologs from phagotrophic protists, including several Entamoeba species, the pelobiont Mastigamoeba balamuthi, and the parabasalid Trichomonas vaginalis, and a large quantity of sequences from genome projects resulted in an apparent increase in the number of putative transfer events affecting all three domains of life. Some of the eukaryotic transfers affect a wide range of protists, such as three divergent lineages of Amoebozoa, represented by Entamoeba, Mastigamoeba, and Dictyostelium, while other transfers only affect a limited diversity, for example only the Entamoeba lineage. These observations are consistent with a model where these genes have been introduced into protist genomes independently from various sources over a long evolutionary time.<br><br>CONCLUSION: Phylogenetic analyses of the updated datasets using more sophisticated phylogenetic methods, in combination with the gene distribution analyses, strengthened, rather than weakened, the support for LGT as an important mechanism affecting the evolution of these gene families. Thus, gene transfer seems to be an on-going evolutionary mechanism by which genes are spread between unrelated lineages of all three domains of life, further indicating the importance of LGT from non-organellar sources into eukaryotic genomes.}, }
@article {pmid16549674, year = {2006}, author = {Mazón, G and Campoy, S and Erill, I and Barbé, J}, title = {Identification of the Acidobacterium capsulatum LexA box reveals a lateral acquisition of the Alphaproteobacteria lexA gene.}, journal = {Microbiology (Reading, England)}, volume = {152}, number = {Pt 4}, pages = {1109-1118}, doi = {10.1099/mic.0.28376-0}, pmid = {16549674}, issn = {1350-0872}, mesh = {Alphaproteobacteria/*genetics ; Amino Acid Sequence ; Bacterial Proteins/chemistry/*genetics/isolation &amp; purification/metabolism ; Binding Sites ; DNA Damage ; DNA Repair ; DNA, Bacterial/*genetics/metabolism ; DNA-Binding Proteins ; Electrophoretic Mobility Shift Assay ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; Promoter Regions, Genetic ; Protein Binding ; Rec A Recombinases/analysis ; *SOS Response, Genetics ; Sequence Homology, Amino Acid ; Serine Endopeptidases/chemistry/*genetics/isolation &amp; purification/metabolism ; }, abstract = {Acidobacterium capsulatum is the most thoroughly studied species of a new bacterial phylogenetic group designated the phylum Acidobacteria. Through a tblastn search, the A. capsulatum lexA gene has been identified, and its product purified. Electrophoretic mobility shift assays have shown that A. capsulatum LexA protein binds specifically to the direct repeat GTTCN(7)GTTC motif. Strikingly, this is also the LexA box of the Alphaproteobacteria, but had not previously been described outside this subclass of the Proteobacteria. In addition, a phylogenetic analysis of the LexA protein clusters together Acidobacterium and the Alphaproteobacteria, moving the latter away from their established phylogenetic position as a subclass of the Proteobacteria, and pointing to a lateral gene transfer of the lexA gene from the phylum Acidobacteria, or an immediate ancestor, to the Alphaproteobacteria. Lastly, in vivo experiments demonstrate that the A. capsulatum recA gene is DNA-damage inducible, despite the fact that a LexA-binding sequence is not present in its promoter region.}, }
@article {pmid16549673, year = {2006}, author = {Octavia, S and Lan, R}, title = {Frequent recombination and low level of clonality within Salmonella enterica subspecies I.}, journal = {Microbiology (Reading, England)}, volume = {152}, number = {Pt 4}, pages = {1099-1108}, doi = {10.1099/mic.0.28486-0}, pmid = {16549673}, issn = {1350-0872}, mesh = {Bacterial Proteins/genetics ; DNA, Bacterial/chemistry/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Variation ; Molecular Sequence Data ; MutS DNA Mismatch-Binding Protein/genetics ; Phylogeny ; Polymorphism, Genetic ; *Recombination, Genetic ; Salmonella enterica/classification/*genetics/*physiology ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {The genetic relationship and population structure of Salmonella enterica subspecies I strains were analysed using nucleotide sequences of four genes (mglA, proV, torC and speC). Fifteen strains from the Salmonella reference collection B (SARB), belonging to 13 serovars, were analysed. Sequence data of two housekeeping genes, mdh and mutS, of the same 15 strains reported by Brown et al. (2003) (Proc Natl Acad Sci U S A 100, 15676-15681) were also included in the analyses. Phylogenetic analysis revealed that there was a lack of congruence among the six gene trees. Split decomposition analysis resolved only five strains with a network structure, while others showed a star phylogeny. Compatibility values for the SARB strains were the lowest in comparison to those for strains representing different subspecies of S. enterica. These results showed that the genes studied have undergone frequent recombination, suggesting a low level of clonality within subspecies I of S. enterica.}, }
@article {pmid16549671, year = {2006}, author = {Bodilis, J and Barray, S}, title = {Molecular evolution of the major outer-membrane protein gene (oprF) of Pseudomonas.}, journal = {Microbiology (Reading, England)}, volume = {152}, number = {Pt 4}, pages = {1075-1088}, doi = {10.1099/mic.0.28656-0}, pmid = {16549671}, issn = {1350-0872}, mesh = {Bacterial Outer Membrane Proteins/*genetics ; Base Composition ; Codon/genetics ; *Evolution, Molecular ; Gene Order ; Gene Transfer, Horizontal ; Genome, Bacterial/genetics ; Mutation ; Phylogeny ; Porins/*genetics ; Pseudomonas/classification/*genetics ; Sequence Homology ; }, abstract = {The major outer-membrane protein of Pseudomonas, OprF, is multifunctional. It is a non-specific porin that plays a role in maintenance of cell shape, in growth in a low-osmolarity environment, and in adhesion to various supports or molecules. OprF has been studied extensively for its utility as a vaccine component, its role in antimicrobial drug resistance, and its porin function. The authors have previously shown important differences between the OprF and 16S rDNA phylogenies: Pseudomonas fluorescens isolates split into two quite separate clusters, probably according to their ecological niche. In this study, the evolutionary history of the oprF gene was investigated further. The study of G+C content at the third codon position, synonymous codon usage (codon adaptation index, CAI) and genomic context showed no evidence of horizontal transfer or gene duplication. Similarly, a robust likelihood test of incongruence showed no significant incongruence between the oprF phylogeny and the species phylogeny. In addition, the ratio of nonsynonymous mutations to synonymous mutations (K(a)/K(s)) is high between the different clusters, especially between the two clusters containing P. fluorescens isolates, highlighting important modifications in evolutionary constraints during the history of the oprF gene. Since OprF is known as a pleiotropic protein, modifications in evolutionary constraints could have resulted from variations in cryptic functions, correlated with the ecological fingerprint. Finally, relaxed constraints and/or episodic positive evolution, especially for some P. fluorescens strains, could have led to a phylogeny reconstruction artifact.}, }
@article {pmid16549670, year = {2006}, author = {Mikosa, M and Sochacka-Pietal, M and Baj, J and Bartosik, D}, title = {Identification of a transposable genomic island of Paracoccus pantotrophus DSM 11072 by its transposition to a novel entrapment vector pMMB2.}, journal = {Microbiology (Reading, England)}, volume = {152}, number = {Pt 4}, pages = {1063-1073}, doi = {10.1099/mic.0.28603-0}, pmid = {16549670}, issn = {1350-0872}, mesh = {Base Composition ; Carrier Proteins/genetics ; Chromosome Inversion ; Citric Acid Cycle/genetics ; Conserved Sequence ; DNA Transposable Elements/*genetics ; DNA, Bacterial/chemistry/*genetics ; Evolution, Molecular ; Gene Order ; Gene Transfer, Horizontal ; Genes, Regulator ; Genetic Vectors ; Genomic Islands/*genetics ; Molecular Biology/methods ; Molecular Sequence Data ; Open Reading Frames ; Paracoccus pantotrophus/*genetics ; Repetitive Sequences, Nucleic Acid ; Replicon/genetics ; Rhodobacter sphaeroides/genetics ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; }, abstract = {A novel shuttle entrapment vector, pMMB2, was used to identify a large transposable element, TnPpa1 (44.3 kb), of Paracoccus pantotrophus DSM 11072. TnPpa1 has a composite structure with divergently oriented copies of a cryptic transposon, Tn3434 (Tn3 family), located at both termini. The core region of the element contains a large set of putative genes, whose products show similarity to enzymes involved in central intermediary metabolism (e.g. tricarboxylic acid cycle or 2-methylcitrate cycle), transporters, transcriptional regulators and conserved proteins of unknown function. A 4.2 kb DNA segment of TnPpa1 is homologous to a region of chromosome cII of Rhodobacter sphaeroides 2.4.1, which exemplifies the mosaic structure of this element. TnPpa1 is bordered by 5 bp long directly repeated sequences and is located within a mega-sized replicon, pWKS5, in the DSM 11072 genome. Spontaneous inversion of the core region of TnPpa1 was detected in the host genome. Analysis of the distribution of TnPpa1 in three other strains of P. pantotrophus revealed that this element was present exclusively within DSM 11072, which suggests its relatively recent acquisition by lateral transfer. The identification of TnPpa1 (which may be considered a transposable genomic island) provides evidence for the transposition and lateral transfer of large DNA segments of chromosomal origin (carrying various housekeeping genes), which may have a great impact on the evolution of bacterial genomes.}, }
@article {pmid16547156, year = {2006}, author = {Bergsmedh, A and Ehnfors, J and Kawane, K and Motoyama, N and Nagata, S and Holmgren, L}, title = {DNase II and the Chk2 DNA damage pathway form a genetic barrier blocking replication of horizontally transferred DNA.}, journal = {Molecular cancer research : MCR}, volume = {4}, number = {3}, pages = {187-195}, doi = {10.1158/1541-7786.MCR-05-0262}, pmid = {16547156}, issn = {1541-7786}, mesh = {Animals ; Apoptosis ; Cell Transformation, Neoplastic/*genetics/metabolism ; Cells, Cultured ; Checkpoint Kinase 2 ; Coculture Techniques ; Cyclin-Dependent Kinase Inhibitor p21/metabolism ; *DNA Damage ; DNA Fragmentation ; *DNA Replication ; DNA, Neoplasm/*genetics ; Deoxyribonucleases/metabolism ; Endodeoxyribonucleases/genetics/*metabolism ; *Gene Transfer, Horizontal ; Mice ; Phagocytes/cytology ; Phagocytosis ; Protein Serine-Threonine Kinases/genetics/*metabolism ; Tumor Suppressor Protein p53/metabolism ; }, abstract = {We have previously shown that DNA from dying tumor cells may be transferred to living cells via the uptake of apoptotic bodies and may contribute to tumor progression. DNA encoding H-ras(V12) and c-myc oncogenes may be transferred to the nucleus of the phagocyte but will only integrate and propagate in p53- and p21-deficient mouse embryonic fibroblasts, whereas normal cells are resistant to transformation. Here, we show that this protective mechanism (activation of p53 and p21 after uptake of apoptotic bodies) is dependent on DNA fragmentation, where inhibition of the caspase-activated DNase in the apoptotic cells, in conjunction with genetic ablation of lysosomal DNase II in the phagocytes, completely blocks p53 activation and consequently allows DNA replication of transferred DNA. We, therefore, suggest that there is a causal relationship between DNA degradation during apoptosis and p53 activation. In addition, we could further show that Chk2-/- cells were capable of replicating the hyg(R) gene taken up from engulfed apoptotic cells, suggesting involvement of the DNA damage response. These data show that the phagocytosing cell is sensing the degraded DNA within the apoptotic cell, hence preventing these genes from being replicated, probably through activation of the DNA damage response. We, therefore, hypothesize that DNase II together with the Chk2, p53, and p21 pathway form a genetic barrier blocking the replication of potentially harmful DNA introduced via apoptotic bodies, thereby preventing transformation and malignant development.}, }
@article {pmid16547107, year = {2006}, author = {Bartolomé, C and Charlesworth, B}, title = {Rates and patterns of chromosomal evolution in Drosophila pseudoobscura and D. miranda.}, journal = {Genetics}, volume = {173}, number = {2}, pages = {779-791}, pmid = {16547107}, issn = {0016-6731}, mesh = {Animals ; Chromosome Inversion ; Chromosome Mapping ; Chromosomes/*genetics ; DNA/genetics ; DNA Transposable Elements/genetics ; Drosophila/classification/*genetics ; Drosophila melanogaster/genetics ; *Evolution, Molecular ; Female ; Gene Duplication ; Gene Rearrangement ; Gene Transfer, Horizontal ; Genes, Insect ; In Situ Hybridization ; Male ; Polymorphism, Genetic ; Species Specificity ; Time Factors ; }, abstract = {Comparisons of gene orders between species permit estimation of the rate of chromosomal evolution since their divergence from a common ancestor. We have compared gene orders on three chromosomes of Drosophila pseudoobscura with its close relative, D. miranda, and the distant outgroup species, D. melanogaster, by using the public genome sequences of D. pseudoobscura and D. melanogaster and approximately 50 in situ hybridizations of gene probes in D. miranda. We find no evidence for extensive transfer of genes among chromosomes in D. miranda. The rates of chromosomal rearrangements between D. miranda and D. pseudoobscura are far higher than those found before in Drosophila and approach those for nematodes, the fastest rates among higher eukaryotes. In addition, we find that the D. pseudoobscura chromosome with the highest level of inversion polymorphism (Muller's element C) does not show an unusually fast rate of evolution with respect to chromosome structure, suggesting that this classic case of inversion polymorphism reflects selection rather than mutational processes. On the basis of our results, we propose possible ancestral arrangements for the D. pseudoobscura C chromosome, which are different from those in the current literature. We also describe a new method for correcting for rearrangements that are not detected with a limited set of markers.}, }
@article {pmid16547063, year = {2006}, author = {Maiques, E and Ubeda, C and Campoy, S and Salvador, N and Lasa, I and Novick, RP and Barbé, J and Penadés, JR}, title = {beta-lactam antibiotics induce the SOS response and horizontal transfer of virulence factors in Staphylococcus aureus.}, journal = {Journal of bacteriology}, volume = {188}, number = {7}, pages = {2726-2729}, pmid = {16547063}, issn = {0021-9193}, mesh = {Ampicillin/pharmacology ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal/*drug effects ; Penicillins/pharmacology ; Rec A Recombinases/genetics/metabolism ; SOS Response, Genetics/*drug effects ; Serine Endopeptidases/genetics/metabolism ; Staphylococcus aureus/*drug effects/genetics/metabolism ; Virulence Factors/genetics/*metabolism ; beta-Lactams/*pharmacology ; }, abstract = {Antibiotics that interfere with DNA replication and cell viability activate the SOS response. In Staphylococcus aureus, the antibiotic-induced SOS response promotes replication and high-frequency horizontal transfer of pathogenicity island-encoded virulence factors. Here we report that beta-lactams induce a bona fide SOS response in S. aureus, characterized by the activation of the RecA and LexA proteins, the two master regulators of the SOS response. Moreover, we show that beta-lactams are capable of triggering staphylococcal prophage induction in S. aureus lysogens. Consequently, and as previously described for SOS induction by commonly used fluoroquinolone antibiotics, beta-lactam-mediated phage induction also resulted in replication and high-frequency transfer of the staphylococcal pathogenicity islands, showing that such antibiotics may have the unintended consequence of promoting the spread of bacterial virulence factors.}, }
@article {pmid16542435, year = {2006}, author = {Waack, S and Keller, O and Asper, R and Brodag, T and Damm, C and Fricke, WF and Surovcik, K and Meinicke, P and Merkl, R}, title = {Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models.}, journal = {BMC bioinformatics}, volume = {7}, number = {}, pages = {142}, pmid = {16542435}, issn = {1471-2105}, mesh = {Algorithms ; Bacillus subtilis/genetics ; Base Composition ; Codon ; Computational Biology ; DNA, Bacterial/*genetics ; Escherichia coli K12/genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genomic Islands ; *Markov Chains ; *Models, Genetic ; Software ; Vibrio cholerae/genetics ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT) is considered a strong evolutionary force shaping the content of microbial genomes in a substantial manner. It is the difference in speed enabling the rapid adaptation to changing environmental demands that distinguishes HGT from gene genesis, duplications or mutations. For a precise characterization, algorithms are needed that identify transfer events with high reliability. Frequently, the transferred pieces of DNA have a considerable length, comprise several genes and are called genomic islands (GIs) or more specifically pathogenicity or symbiotic islands.<br><br>RESULTS: We have implemented the program SIGI-HMM that predicts GIs and the putative donor of each individual alien gene. It is based on the analysis of codon usage (CU) of each individual gene of a genome under study. CU of each gene is compared against a carefully selected set of CU tables representing microbial donors or highly expressed genes. Multiple tests are used to identify putatively alien genes, to predict putative donors and to mask putatively highly expressed genes. Thus, we determine the states and emission probabilities of an inhomogeneous hidden Markov model working on gene level. For the transition probabilities, we draw upon classical test theory with the intention of integrating a sensitivity controller in a consistent manner. SIGI-HMM was written in JAVA and is publicly available. It accepts as input any file created according to the EMBL-format.It generates output in the common GFF format readable for genome browsers. Benchmark tests showed that the output of SIGI-HMM is in agreement with known findings. Its predictions were both consistent with annotated GIs and with predictions generated by different methods.<br><br>CONCLUSION: SIGI-HMM is a sensitive tool for the identification of GIs in microbial genomes. It allows to interactively analyze genomes in detail and to generate or to test hypotheses about the origin of acquired genes.}, }
@article {pmid16542428, year = {2006}, author = {DasSarma, S and Berquist, BR and Coker, JA and DasSarma, P and Müller, JA}, title = {Post-genomics of the model haloarchaeon Halobacterium sp. NRC-1.}, journal = {Saline systems}, volume = {2}, number = {}, pages = {3}, pmid = {16542428}, issn = {1746-1448}, abstract = {Halobacteriumsp. NRC-1 is an extremely halophilic archaeon that is easily cultured and genetically tractable. Since its genome sequence was completed in 2000, a combination of genetic, transcriptomic, proteomic, and bioinformatic approaches have provided insights into both its extremophilic lifestyle as well as fundamental cellular processes common to all life forms. Here, we review post-genomic research on this archaeon, including investigations of DNA replication and repair systems, phototrophic, anaerobic, and other physiological capabilities, acidity of the proteome for function at high salinity, and role of lateral gene transfer in its evolution.}, }
@article {pmid16537397, year = {2006}, author = {Inagaki, Y and Susko, E and Roger, AJ}, title = {Recombination between elongation factor 1alpha genes from distantly related archaeal lineages.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, number = {12}, pages = {4528-4533}, pmid = {16537397}, issn = {0027-8424}, mesh = {Archaea/*classification/*genetics ; Base Sequence ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Archaeal/*genetics ; Molecular Sequence Data ; Peptide Elongation Factor 1/*genetics ; Phylogeny ; }, abstract = {Homologous recombination (HR) and lateral gene transfer are major processes in genome evolution. The combination of the two processes, HR between genes in different species, has been documented but is thought to be restricted to very similar sequences in relatively closely related organisms. Here we report two cases of interspecific HR in the gene encoding the core translational protein translation elongation factor 1alpha (EF-1alpha) between distantly related archaeal groups. Maximum-likelihood sliding window analyses indicate that a fragment of the EF-1alpha gene from the archaeal lineage represented by Methanopyrus kandleri was recombined into the orthologous gene in a common ancestor of the Thermococcales. A second recombination event appears to have occurred between the EF-1alpha gene of the genus Methanothermobacter and its ortholog in a common ancestor of the Methanosarcinales, a distantly related euryarchaeal lineage. These findings suggest that HR occurs across a much larger evolutionary distance than generally accepted and affects highly conserved essential "informational" genes. Although difficult to detect by standard whole-gene phylogenetic analyses, interspecific HR in highly conserved genes may occur at an appreciable frequency, potentially confounding deep phylogenetic inference and hypothesis testing.}, }
@article {pmid16534001, year = {2006}, author = {Dam, T and Das, P}, title = {Plasmids -- potential tool for the investigation of gene transfer in Mycobacterium tuberculosis.}, journal = {Journal of medical microbiology}, volume = {55}, number = {Pt 4}, pages = {479-480}, doi = {10.1099/jmm.0.46258-0}, pmid = {16534001}, issn = {0022-2615}, mesh = {Gene Transfer, Horizontal/*genetics ; Mycobacterium tuberculosis/*genetics ; *Plasmids ; }, }
@article {pmid16531508, year = {2006}, author = {Gibbs, MJ and Smeianov, VV and Steele, JL and Upcroft, P and Efimov, BA}, title = {Two families of rep-like genes that probably originated by interspecies recombination are represented in viral, plasmid, bacterial, and parasitic protozoan genomes.}, journal = {Molecular biology and evolution}, volume = {23}, number = {6}, pages = {1097-1100}, doi = {10.1093/molbev/msj122}, pmid = {16531508}, issn = {0737-4038}, mesh = {Animals ; Bifidobacterium/genetics ; Canarypox virus/genetics ; Circovirus/genetics ; DNA Helicases/*genetics ; DNA-Binding Proteins/*genetics ; Databases, Genetic ; Entamoeba histolytica/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genome, Protozoan ; *Genome, Viral ; Lactobacillus acidophilus/genetics ; Lactococcus lactis/genetics ; Phytoplasma/genetics ; Plasmids/*genetics ; Sequence Alignment ; Trans-Activators/*genetics ; }, abstract = {Two families of genes related to, and including, rolling circle replication initiator protein (Rep) genes were defined by sequence similarity and by evidence of intergene family recombination. The Rep genes of circoviruses were the best characterized members of the "RecRep1 family." Other members of the RecRep1 family were Rep-like genes found in the genomes of the Canarypox virus, Entamoeba histolytica, and Giardia duodenalis and in a plasmid, p4M, from the Gram-positive bacterium, Bifidobacterium pseudocatenulatum. The "RecRep2 family" comprised some previously identified Rep-like genes from plasmids of phytoplasmas and similar Rep-like genes from the genomes of Lactobacillus acidophilus, Lactococcus lactis, and Phytoplasma asteris. Both RecRep1 and RecRep2 proteins have a nucleotide-binding domain significantly similar to the helicases (2C proteins) of picorna-like viruses. On the N-terminal side of the nucleotide binding domain, RecRep1 proteins have a domain significantly similar to one found in nanovirus Reps, whereas RecRep2 proteins have a domain significantly similar to one in the Reps of pLS1 plasmids. We speculate that RecRep genes have been transferred from viruses or plasmids to parasitic protozoan and bacterial genomes and that Rep proteins were themselves involved in the original recombination events that generated the ancestral RecRep genes.}, }
@article {pmid16530482, year = {2006}, author = {Schulte-Spechtel, U and Fingerle, V and Goettner, G and Rogge, S and Wilske, B}, title = {Molecular analysis of decorin-binding protein A (DbpA) reveals five major groups among European Borrelia burgdorferi sensu lato strains with impact for the development of serological assays and indicates lateral gene transfer of the dbpA gene.}, journal = {International journal of medical microbiology : IJMM}, volume = {296 Suppl 40}, number = {}, pages = {250-266}, doi = {10.1016/j.ijmm.2006.01.006}, pmid = {16530482}, issn = {1438-4221}, mesh = {Adhesins, Bacterial/*genetics ; Amino Acid Sequence ; Animals ; Antibodies, Monoclonal ; Antigens, Bacterial/genetics ; Antigens, Surface/genetics ; Bacterial Outer Membrane Proteins/*genetics ; Bacterial Vaccines ; Borrelia burgdorferi Group/*genetics ; DNA, Bacterial/analysis ; *Gene Transfer, Horizontal ; Humans ; Immunoblotting ; Lipoproteins/genetics ; Lyme Disease/diagnosis ; Mice ; Molecular Sequence Data ; Sequence Alignment ; Serologic Tests/methods ; }, abstract = {The Borrelia (B.) burgdorferi adhesin DbpA (decorin-binding protein A) is a valuable antigen for serodiagnosis of Lyme borreliosis and a promising candidate for a vaccine. To investigate the heterogeneity of DbpA, we aligned DNA sequences of 83 different dbpA genes (37 from the database, where the majority of sequences belong to B. burgdorferi sensu stricto and 46 were newly sequenced). Analysis of 25 sequences from the species B. burgdorferi s.s., 16 from B. afzelii, 40 from B. garinii, and two from the recently described human pathogenic genospecies A14S revealed five distinct DbpA groups. Group I comprises B. burgdorferi s.s. and group II B. afzelii. B. garinii is divided into groups III and IV, whereas A14S strains form group V. Formation of groups is mainly due to insertions of whole sequence sections. Comparison of dbpA sequences with ospC sequences from a subset of 59 strains revealed all kinds of cross-connections indicating processes of lateral gene transfer among strains. The extent of sequence identity within the dbpA genes decreases from the DNA (67%) to the amino acid (AA) level (44%) by about 23%, in contrast ospC sequence identities differed only by about 10%. This might be an indication that DbpA plays an important role in immune escape. Immunoblots using four recombinant DbpAs representing groups I-IV show that DbpA proteins are sensitive and specific antigens and complement one another in their reactivity. Part of the sera showed group-specific reactivity which could also be demonstrated with monoclonal antibodies.}, }
@article {pmid16530303, year = {2006}, author = {Wang, B and He, J and Liu, C and Chang, LJ}, title = {An effective cancer vaccine modality: lentiviral modification of dendritic cells expressing multiple cancer-specific antigens.}, journal = {Vaccine}, volume = {24}, number = {17}, pages = {3477-3489}, pmid = {16530303}, issn = {0264-410X}, support = {P01 HL059412/HL/NHLBI NIH HHS/United States ; P50 HL059412/HL/NHLBI NIH HHS/United States ; HL59412/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Antigens, Neoplasm/genetics/*immunology ; CD4-Positive T-Lymphocytes/immunology ; CD8-Positive T-Lymphocytes/immunology ; Cancer Vaccines/*immunology ; Cell Line, Tumor ; Cell Movement ; Dendritic Cells/*immunology/metabolism ; Female ; Gene Transfer, Horizontal ; Immunohistochemistry ; Interferon-gamma/biosynthesis ; Lentivirus/*genetics ; Liver Neoplasms, Experimental/immunology/therapy ; Mice ; T-Lymphocytes, Cytotoxic/immunology ; Vaccination ; }, abstract = {Viral modification of dendritic cells (DCs) may deliver a "danger signal" critical to the hypo-reactive DCs in cancer patients. Using three highly differentially expressed hepatoma tumor-associated antigens (TAAs): stem cell antigen-2 (Sca-2), glycoprotein 38 (GP38) and cellular retinoic acid binding protein 1 (RABP1), we explored the therapeutic potential of the DCs modified with lentiviral vectors (LVs). Preventive and therapeutic injection of the LV-TAA-DC vaccine into tumor-bearing mice elicited a strong anti-tumor response and extended survival, which was associated with tumor-specific interferon-gamma and cytotoxic T cell responses. In vivo elimination of the LV-TAA-DCs by a co-expressed thymidine kinase suicide gene abrogated the therapeutic effect. The modification of DCs with LVs encoding multiple TAAs offers a great opportunity in cancer immunotherapy.}, }
@article {pmid16529966, year = {2006}, author = {Brochet, M and Couvé, E and Zouine, M and Vallaeys, T and Rusniok, C and Lamy, MC and Buchrieser, C and Trieu-Cuot, P and Kunst, F and Poyart, C and Glaser, P}, title = {Genomic diversity and evolution within the species Streptococcus agalactiae.}, journal = {Microbes and infection}, volume = {8}, number = {5}, pages = {1227-1243}, doi = {10.1016/j.micinf.2005.11.010}, pmid = {16529966}, issn = {1286-4579}, mesh = {Adult ; Animals ; Bacterial Proteins/genetics ; Cats ; Cattle ; Child, Preschool ; DNA, Bacterial/analysis ; Dogs ; *Evolution, Molecular ; Female ; *Genetic Variation ; Genome, Bacterial ; Guinea Pigs ; Humans ; Infant, Newborn ; Membrane Proteins/genetics ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Rabbits ; Sequence Analysis, DNA ; Serotyping ; Streptococcus agalactiae/*classification/*genetics/pathogenicity ; Virulence/genetics ; }, abstract = {Streptococcus agalactiae is a leading cause of invasive infections in neonates, and responsible for bovine mastitis. It is also a commensal bacterium adapted to asymptomatic colonization of the mammalian gut and of the genitourinary tract. Here, we report the analysis of a collection of 75 strains of human and animal origin by using serotyping, multilocus sequence typing, whole genome DNA-array hybridizations and sequence comparison of putatively virulence-associated loci. Although the most variable parts of the genome are the previously predicted genomic islands, significant genetic variations were present in the genome backbone. Evolution within genes encoding surface and secreted proteins and those involved in the biosynthesis of different capsular types is mainly due to recombination events leading to the replacement of a locus of several genes or to the allelic exchange of the internal part of a gene. These two processes, which led to a broad diversity of surface protein patterns, are probably involved in the diversity of interactions with the host and its immune system. According to gene content comparisons and phylogeny, recent gene replacements by horizontal gene transfer may occur but are rare events. Although specific gene patterns, with respect to the origin of the strains and the epidemiological characteristics, were not identified, we show that the recently described hypervirulent ST-17 lineage is a homogeneous group. The study highlights for the first time that this lineage contains a specific and conserved set of surface proteins, probably accounting for its high capacity to cause infections in newborns.}, }
@article {pmid16529906, year = {2006}, author = {Boocock, GR and Marit, MR and Rommens, JM}, title = {Phylogeny, sequence conservation, and functional complementation of the SBDS protein family.}, journal = {Genomics}, volume = {87}, number = {6}, pages = {758-771}, doi = {10.1016/j.ygeno.2006.01.010}, pmid = {16529906}, issn = {0888-7543}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Sequence ; Animals ; Bone Marrow Diseases/genetics ; Conserved Sequence ; Gene Transfer, Horizontal ; Genetic Complementation Test ; Humans ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Protein Isoforms/chemistry/genetics ; Protein Structure, Tertiary ; Proteins/chemistry/*genetics ; Sequence Homology, Amino Acid ; Species Specificity ; Syndrome ; Zinc Fingers ; }, abstract = {The Shwachman-Bodian-Diamond syndrome (SBDS) protein family occurs widely in nature, although its function has not been determined. Comprehensive database searches revealed SBDS homologues from 159 species, including examples from all sequenced archaeal and eukaryotic genomes and all eukaryotic kingdoms. Sequence alignment with ClustalX and MUSCLE algorithms led to the identification of conserved residues that occurred predominantly in the amino-terminal FYSH domain where they appeared to contribute to protein folding or stability. Only SBDS residue Gly91 was invariant in all species. Four distantly related protists were found to have two divergent SBDS genes in their genomes. In each case, phylogenetic analyses and the identification of shared sequence features suggested that one gene was derived from lateral gene transfer. We also identified a shared C-terminal zinc finger domain fusion in flowering plants and chromalveolates that may shed light on the function of the protein family and the evolutionary histories of these kingdoms. To assess the extent of SBDS functional conservation, we carried out complementation studies of SBDS homologues and interspecies chimeras in Saccharomyces cerevisiae. We determined that the FYSH domain was widely interchangeable among eukaryotes, while domain 2 imparted species specificity to protein function. Domain 3 was largely dispensable for function in our yeast complementation assay. Overall, the phylogeny of SBDS was shared with a group of proteins that were markedly enriched for RNA metabolism and/or ribosome-associated functions. These findings link Shwachman-Diamond syndrome to other bone marrow failure syndromes with defects in nucleolus-associated processes, including Diamond-Blackfan anemia, cartilage-hair hypoplasia, and dyskeratosis congenita.}, }
@article {pmid16529662, year = {2006}, author = {Shaul, S and Nussinov, R and Pupko, T}, title = {Paths of lateral gene transfer of lysyl-aminoacyl-tRNA synthetases with a unique evolutionary transition stage of prokaryotes coding for class I and II varieties by the same organisms.}, journal = {BMC evolutionary biology}, volume = {6}, number = {}, pages = {22}, pmid = {16529662}, issn = {1471-2148}, support = {N01CO12400/CA/NCI NIH HHS/United States ; N01-CO-12400/CO/NCI NIH HHS/United States ; }, mesh = {Alphaproteobacteria/enzymology/genetics ; Archaea/classification/*enzymology/genetics ; Archaeal Proteins/genetics ; Bacteria/classification/*enzymology/genetics ; Bacterial Proteins/genetics ; *Biological Evolution ; Crenarchaeota/enzymology/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal/genetics/physiology ; Genes, Archaeal ; Genes, Bacterial ; Isoenzymes/genetics ; Lysine-tRNA Ligase/classification/*genetics ; Models, Genetic ; Phylogeny ; Prokaryotic Cells/*enzymology ; Species Specificity ; }, abstract = {BACKGROUND: While the premise that lateral gene transfer (LGT) is a dominant evolutionary force is still in considerable dispute, the case for widespread LGT in the family of aminoacyl-tRNA synthetases (aaRS) is no longer contentious. aaRSs are ancient enzymes, guarding the fidelity of the genetic code. They are clustered in two structurally unrelated classes. Only lysine aminoacyl-tRNA synthetase (LysRS) is found both as a class 1 and a class 2 enzyme (LysRS1-2). Remarkably, in several extant prokaryotes both classes of the enzyme coexist, a unique phenomenon that has yet to receive its due attention.<br><br>RESULTS: We applied a phylogenetic approach for determining the extent and origin of LGT in prokaryotic LysRS. Reconstructing species trees for Archaea and Bacteria, and inferring that their last common ancestors encoded LysRS1 and LysRS2, respectively, we studied the gains and losses of both classes. A complex pattern of LGT events emerged. In specific groups of organisms LysRS1 was replaced by LysRS2 (and vice versa). In one occasion, within the alpha proteobacteria, a LysRS2 to LysRS1 LGT was followed by reversal to LysRS2. After establishing the most likely LGT paths, we studied the possible origins of the laterally transferred genes. To this end, we reconstructed LysRS gene trees and evaluated the likely origins of the laterally transferred genes. While the sources of LysRS1 LGTs were readily identified, those for LysRS2 remain, for now, uncertain. The replacement of one LysRS by another apparently transits through a stage simultaneously coding for both synthetases, probably conferring a selective advantage to the affected organisms.<br><br>CONCLUSION: The family of LysRSs features complex LGT events. The currently available data were sufficient for identifying unambiguously the origins of LysRS1 but not of LysRS2 gene transfers. A selective advantage is suggested to organisms encoding simultaneously LysRS1-2.}, }
@article {pmid16527541, year = {2006}, author = {Chatterjee, SS and Otten, S and Hain, T and Lingnau, A and Carl, UD and Wehland, J and Domann, E and Chakraborty, T}, title = {Invasiveness is a variable and heterogeneous phenotype in Listeria monocytogenes serotype strains.}, journal = {International journal of medical microbiology : IJMM}, volume = {296}, number = {4-5}, pages = {277-286}, doi = {10.1016/j.ijmm.2005.10.001}, pmid = {16527541}, issn = {1438-4221}, mesh = {Bacterial Proteins/analysis/genetics/physiology ; Blotting, Western ; Chromosomes, Bacterial/genetics ; DNA, Bacterial/genetics ; Gene Deletion ; Gene Order ; Genetic Complementation Test ; HeLa Cells ; Humans ; Listeria monocytogenes/*genetics/*pathogenicity ; Membrane Proteins/analysis/genetics/physiology ; Molecular Sequence Data ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Serotyping ; Synteny ; Virulence/*genetics ; Virulence Factors/genetics/*physiology ; }, abstract = {The ability of Listeria monocytogenes to breach mucosal and endothelial barriers of the host during infection is a hallmark property mediated by the internalins (Inl) A and B. We examined the invasive property of several L. monocytogenes strains representing 13 serotypes. We found that invasiveness is a heterogeneous phenotype amongst L. monocytogenes serotype strains. Despite this, many of the poorly invasive and non-invasive strains of L. monocytogenes express internalins at levels comparable to those of invasive isolates. Introduction of the inlAB locus from EGD-e into several poorly invasive strains had no effect on their invasive properties. A strain from serotype 4b that exhibits highly invasive properties was further examined. Deletion of the inlAB locus abrogated invasion of this strain while reintroduction of the inlAB locus into this strain restored invasiveness. An analysis of regions flanking the inlAB locus revealed considerable differences in the strains studied. Our results suggest that efficacious entry of L. monocytogenes into eukaryotic cells is complex and requires additional factors apart from internalins. Data presented here also suggest that the inlAB locus was introduced into L. monocytogenes by horizontal gene transfer with subsequent deletion and rearrangements occurring during evolution of this species.}, }
@article {pmid16522219, year = {2006}, author = {Thomason, B and Read, TD}, title = {Shuffling bacterial metabolomes.}, journal = {Genome biology}, volume = {7}, number = {2}, pages = {204}, pmid = {16522219}, issn = {1474-760X}, mesh = {Bacteria/*genetics/*metabolism ; *Gene Transfer, Horizontal ; Genetic Variation ; *Genome, Bacterial ; Genomics ; }, abstract = {Horizontal gene transfer (HGT) has a far more significant role than gene duplication in bacterial evolution. This has recently been illustrated by work demonstrating the importance of HGT in the emergence of bacterial metabolic networks, with horizontally acquired genes being placed in peripheral pathways at the outer branches of the networks.}, }
@article {pmid16520338, year = {2006}, author = {Rosas-Magallanes, V and Deschavanne, P and Quintana-Murci, L and Brosch, R and Gicquel, B and Neyrolles, O}, title = {Horizontal transfer of a virulence operon to the ancestor of Mycobacterium tuberculosis.}, journal = {Molecular biology and evolution}, volume = {23}, number = {6}, pages = {1129-1135}, doi = {10.1093/molbev/msj120}, pmid = {16520338}, issn = {0737-4038}, mesh = {Agrobacterium tumefaciens/genetics ; Computational Biology ; Evolution, Molecular ; Gammaproteobacteria/genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Mycobacterium tuberculosis/*genetics/*pathogenicity ; *Operon ; Virulence Factors/*genetics ; }, abstract = {The contribution of interspecies horizontal gene transfer (HGT) to the evolution and virulence of Mycobacterium tuberculosis, the agent of tuberculosis in humans, has been barely investigated. Here we have studied the evolutionary history of the M. tuberculosis Rv0986-8 virulence operon recently identified, through functional genomics approaches, as playing an important role in parasitism of host phagocytic cells. We showed that among actinobacteria, this operon is specific to the M. tuberculosis complex and to ancestral Mycobacterium prototuberculosis species. These data, together with phylogenetic reconstruction and other in silico analyses, provided strong evidence that this operon has been acquired horizontally by the ancestor of M. tuberculosis, before the recent evolutionary bottleneck that preceded the clonal-like evolution of the M. tuberculosis complex. Genomic signature profiling further suggested that the transfer was plasmid mediated and that the operon originated from a gamma-proteobacterium donor species. Our study points out for the first time the contribution of HGT to the emergence of M. tuberculosis and close relatives as major pathogens. In addition, our data underline the importance of deciphering gene transfer networks in M. tuberculosis in order to better understand the evolutionary mechanisms involved in mycobacterial virulence.}, }
@article {pmid16514144, year = {2006}, author = {Kurenbach, B and Kopeć, J and Mägdefrau, M and Andreas, K and Keller, W and Bohn, C and Abajy, MY and Grohmann, E}, title = {The TraA relaxase autoregulates the putative type IV secretion-like system encoded by the broad-host-range Streptococcus agalactiae plasmid pIP501.}, journal = {Microbiology (Reading, England)}, volume = {152}, number = {Pt 3}, pages = {637-645}, doi = {10.1099/mic.0.28468-0}, pmid = {16514144}, issn = {1350-0872}, mesh = {Bacterial Proteins/genetics/*metabolism ; Base Sequence ; Conjugation, Genetic ; DNA Nucleotidyltransferases/chemistry/genetics/*metabolism ; Enterococcus faecalis/genetics/*metabolism ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Operon ; Plasmids/*genetics ; Promoter Regions, Genetic ; Streptococcus agalactiae/*genetics ; Transcription, Genetic ; }, abstract = {The conjugative multiple antibiotic resistance plasmid pIP501 can be transferred and stably maintained in a variety of Gram-positive genera, including multicellular Streptomyces lividans, as well as in Gram-negative Escherichia coli. The 15 putative pIP501 transfer (tra) genes are organized in an operon-like structure terminating in a strong transcriptional terminator. This paper reports co-transcription of the pIP501 tra genes in exponentially growing Enterococcus faecalis JH2-2 cells, as shown by RT-PCR. The tra genes are expressed throughout the life cycle of Ent. faecalis, and the expression level is independent of the growth phase. Electrophoretic mobility shift assays indicated that the TraA relaxase, the first gene of the tra operon, binds to the tra promoter P(tra), which partially overlaps with the origin of transfer (oriT). DNase I footprinting experiments further delimited the TraA binding region and defined the nucleotides bound by TraA. Beta-Galactosidase assays with P(tra)-lacZ fusions proved P(tra) promoter activity, which was strongly repressed when TraA was supplied in trans. Thus, it is concluded that the pIP501 tra operon is negatively autoregulated at the transcriptional level by the conjugative DNA relaxase TraA.}, }
@article {pmid16513982, year = {2006}, author = {Ciccarelli, FD and Doerks, T and von Mering, C and Creevey, CJ and Snel, B and Bork, P}, title = {Toward automatic reconstruction of a highly resolved tree of life.}, journal = {Science (New York, N.Y.)}, volume = {311}, number = {5765}, pages = {1283-1287}, doi = {10.1126/science.1123061}, pmid = {16513982}, issn = {1095-9203}, mesh = {Amino Acyl-tRNA Synthetases/genetics ; Animals ; Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Biological Evolution ; Computational Biology ; Eukaryotic Cells ; Gene Transfer, Horizontal ; *Genome ; Invertebrates/*classification/genetics ; *Phylogeny ; Plants/*classification/genetics ; Protein Biosynthesis ; Ribosomal Proteins/genetics ; Vertebrates/*classification/genetics ; }, abstract = {We have developed an automatable procedure for reconstructing the tree of life with branch lengths comparable across all three domains. The tree has its basis in a concatenation of 31 orthologs occurring in 191 species with sequenced genomes. It revealed interdomain discrepancies in taxonomic classification. Systematic detection and subsequent exclusion of products of horizontal gene transfer increased phylogenetic resolution, allowing us to confirm accepted relationships and resolve disputed and preliminary classifications. For example, we place the phylum Acidobacteria as a sister group of delta-Proteobacteria, support a Gram-positive origin of Bacteria, and suggest a thermophilic last universal common ancestor.}, }
@article {pmid16513736, year = {2006}, author = {Tendolkar, PM and Baghdayan, AS and Shankar, N}, title = {Putative surface proteins encoded within a novel transferable locus confer a high-biofilm phenotype to Enterococcus faecalis.}, journal = {Journal of bacteriology}, volume = {188}, number = {6}, pages = {2063-2072}, pmid = {16513736}, issn = {0021-9193}, support = {R01 AI059673/AI/NIAID NIH HHS/United States ; AI 059673/AI/NIAID NIH HHS/United States ; }, mesh = {Aminoacyltransferases/genetics ; Bacterial Proteins/genetics/*physiology ; Biofilms/*growth &amp; development ; Blotting, Southern ; Chromosome Mapping ; Conjugation, Genetic ; Cysteine Endopeptidases ; DNA Transposable Elements ; DNA, Bacterial/chemistry/genetics ; Electrophoresis, Agar Gel ; Enterococcus faecalis/genetics/*physiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Membrane Proteins/genetics/*physiology ; Molecular Sequence Data ; Mutagenesis, Insertional ; Mutation ; Phenotype ; Plasmids/genetics ; Sequence Homology, Amino Acid ; }, abstract = {Enterococci are opportunistic pathogens and among the leading causes of nosocomial infections. Enterococcus faecalis, the dominant species among infection-derived isolates, has recently been recognized as capable of forming biofilms on abiotic surfaces in vitro as well as on indwelling medical devices. A few bacterial factors known to contribute to biofilm formation in E. faecalis have been characterized. To identify additional factors which may be important to this process, we utilized a Tn917-based insertional mutagenesis strategy to generate a mutant bank in a high-biofilm-forming E. faecalis strain, E99. The resulting mutant bank was screened for mutants exhibiting a significantly reduced ability to form biofilms. One mutant, P101D12, which showed greater than 70% reduction in its ability to form biofilms compared to the wild-type parent, was further characterized. The single Tn917 insertion in P101D12 was mapped to a gene, bee-2, encoding a probable cell wall-anchored protein. Sequence information for the region flanking bee-2 revealed that this gene was a member of a locus (termed the bee locus for biofilm enhancer in enterococcus) comprised of five genes encoding three putative cell wall-anchored proteins and two probable sortases. Contour-clamped homogeneous electric field gel and Southern hybridization analyses suggested that the bee locus is likely harbored on a large conjugative plasmid. Filter mating assays using wild-type E99 or mutant P101D12 as a donor confirmed that the bee locus could transfer conjugally at high frequency to recipient E. faecalis strains. This represents the first instance of the identification of a mobile genetic element conferring biofilm-forming property in E. faecalis.}, }
@article {pmid16509443, year = {2006}, author = {Licht, TR and Wilcks, A}, title = {Conjugative gene transfer in the gastrointestinal environment.}, journal = {Advances in applied microbiology}, volume = {58}, number = {}, pages = {77-95}, pmid = {16509443}, issn = {0065-2164}, mesh = {Animals ; *Conjugation, Genetic ; DNA Transposable Elements ; Drug Resistance, Bacterial/genetics ; Gastrointestinal Tract/*microbiology ; *Gene Transfer, Horizontal ; Germ-Free Life ; Gram-Negative Bacteria/drug effects/*genetics ; Gram-Positive Bacteria/drug effects/*genetics ; Humans ; Mice ; Mice, Inbred BALB C ; Plasmids/genetics ; Rats ; }, }
@article {pmid16505379, year = {2006}, author = {González, V and Santamaría, RI and Bustos, P and Hernández-González, I and Medrano-Soto, A and Moreno-Hagelsieb, G and Janga, SC and Ramírez, MA and Jiménez-Jacinto, V and Collado-Vides, J and Dávila, G}, title = {The partitioned Rhizobium etli genome: genetic and metabolic redundancy in seven interacting replicons.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, number = {10}, pages = {3834-3839}, pmid = {16505379}, issn = {0027-8424}, mesh = {Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomics ; Molecular Sequence Data ; Multigene Family ; Plasmids/genetics ; Polysaccharides, Bacterial/biosynthesis/genetics ; *Replicon ; Rhizobiaceae/genetics ; Rhizobium etli/*genetics/*metabolism ; Species Specificity ; Symbiosis/genetics ; Transcription, Genetic ; }, abstract = {We report the complete 6,530,228-bp genome sequence of the symbiotic nitrogen fixing bacterium Rhizobium etli. Six large plasmids comprise one-third of the total genome size. The chromosome encodes most functions necessary for cell growth, whereas few essential genes or complete metabolic pathways are located in plasmids. Chromosomal synteny is disrupted by genes related to insertion sequences, phages, plasmids, and cell-surface components. Plasmids do not show synteny, and their orthologs are mostly shared by accessory replicons of species with multipartite genomes. Some nodulation genes are predicted to be functionally related with chromosomal loci encoding for the external envelope of the bacterium. Several pieces of evidence suggest an exogenous origin for the symbiotic plasmid (p42d) and p42a. Additional putative horizontal gene transfer events might have contributed to expand the adaptive repertoire of R. etli, because they include genes involved in small molecule metabolism, transport, and transcriptional regulation. Twenty-three putative sigma factors, numerous isozymes, and paralogous families attest to the metabolic redundancy and the genomic plasticity necessary to sustain the lifestyle of R. etli in symbiosis and in the soil.}, }
@article {pmid16505374, year = {2006}, author = {Fugmann, SD and Messier, C and Novack, LA and Cameron, RA and Rast, JP}, title = {An ancient evolutionary origin of the Rag1/2 gene locus.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, number = {10}, pages = {3728-3733}, pmid = {16505374}, issn = {0027-8424}, support = {//Intramural NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; DNA-Binding Proteins/*genetics ; *Evolution, Molecular ; Gene Expression ; *Genes, RAG-1 ; Genetic Linkage ; Homeodomain Proteins/*genetics ; Mice ; Molecular Sequence Data ; Multigene Family ; Recombinant Fusion Proteins/genetics ; Sequence Homology, Amino Acid ; Strongylocentrotus purpuratus/genetics/immunology ; }, abstract = {The diversity of antigen receptors in the adaptive immune system of jawed vertebrates is generated by a unique process of somatic gene rearrangement known as V(D)J recombination. The Rag1 and Rag2 proteins are the key mediators of this process. They are encoded by a compact gene cluster that has exclusively been identified in animal species displaying V(D)J-mediated immunity, and no homologous gene pair has been identified in other organisms. This distinctly restricted phylogenetic distribution has led to the hypothesis that one or both of the Rag genes were coopted after horizontal gene transfer and assembled into a Rag1/2 gene cluster in a common jawed vertebrate ancestor. Here, we identify and characterize a closely linked pair of genes, SpRag1L and SpRag2L, from an invertebrate, the purple sea urchin (Strongylocentrotus purpuratus) with similarity in both sequence and genomic organization to the vertebrate Rag1 and Rag2 genes. They are coexpressed during development and in adult tissues, and recombinant versions of the proteins form a stable complex with each other as well as with Rag1 and Rag2 proteins from several vertebrate species. We thus conclude that SpRag1L and SpRag2L represent homologs of vertebrate Rag1 and Rag2. In combination with the apparent absence of V(D)J recombination in echinoderms, this finding strongly suggests that linked Rag1- and Rag2-like genes were already present and functioning in a different capacity in the common ancestor of living deuterostomes, and that their specific role in the adaptive immune system was acquired much later in an early jawed vertebrate.}, }
@article {pmid16504553, year = {2006}, author = {Mouhamadou, B and Férandon, C and Barroso, G and Labarère, J}, title = {The mitochondrial apocytochrome b genes of two Agrocybe species suggest lateral transfers of group I homing introns among phylogenetically distant fungi.}, journal = {Fungal genetics and biology : FG &amp; B}, volume = {43}, number = {3}, pages = {135-145}, doi = {10.1016/j.fgb.2005.07.001}, pmid = {16504553}, issn = {1087-1845}, mesh = {Agaricales/*genetics ; Amino Acid Motifs/genetics ; Ascomycota/genetics ; Base Sequence ; Basidiomycota/genetics ; Binding Sites ; Chytridiomycota/genetics ; Cytochromes b/*genetics ; DNA, Fungal/chemistry/genetics ; Endonucleases/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Introns ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Recombination, Genetic ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; }, abstract = {The Agrocybe chaxingu and Agrocybe aegerita mitochondrial apocytochrome b coding sequences are highly similar (97% of nt identity), but have highly different sizes (2312 and 4867nt, respectively), due to the presence of three large group IB introns: two (iAae1 and iAae2) in A. aegerita, one (iAch1) in A. chaxingu. All these introns encode a homing endonuclease (HE) similar to those described in introns of mitochondrial genes (cob, cox1, and nad5) from various organisms. Phylogenetic trees were built with these HE sequences. From these trees, the Agrocybe coding introns argue for recent lateral transfers, i.e., occurring after the separation of the two Agrocybe species, involving phylogenetically distant fungi such as members of the Ascomycota phylum (for iAch1 and iAae2) and, for the first time to our knowledge, a member of the Chytridiomycota phylum (for iAae1). The grouping of the HE gene (HEG) sequences according to the mitochondrial gene (cob, cox1, and nad5) where they are inserted, suggests modifications of the interactions between the HE and the recognized sequences, leading to new target genes. The largest distribution of the iAch1 HE, shared by several cob and cox1 mitochondrial genes from Ascomycota, Basidiomycota, and Chytridiomycota phyla, suggests a higher target flexibility of this HE, perhaps related to the presence of two different LAGLIDADG motifs in the catalytic site of the enzyme.}, }
@article {pmid16503987, year = {2006}, author = {Qvarnstrom, Y and Swedberg, G}, title = {Variations in gene organization and DNA uptake signal sequence in the folP region between commensal and pathogenic Neisseria species.}, journal = {BMC microbiology}, volume = {6}, number = {}, pages = {11}, pmid = {16503987}, issn = {1471-2180}, mesh = {Chromosomes, Bacterial ; DNA, Bacterial/*genetics/*metabolism ; DNA, Intergenic ; Gene Order ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/*genetics ; Genetic Variation/*genetics ; Molecular Sequence Data ; Neisseria/drug effects/*genetics/*pathogenicity/physiology ; Species Specificity ; }, abstract = {BACKGROUND: Horizontal gene transfer is an important source of genetic variation among Neisseria species and has contributed to the spread of resistance to penicillin and sulfonamide drugs in the pathogen Neisseria meningitidis. Sulfonamide resistance in Neisseria meningitidis is mediated by altered chromosomal folP genes. At least some folP alleles conferring resistance have been horizontally acquired from other species, presumably from commensal Neisseriae. In this work, the DNA sequence surrounding folP in commensal Neisseria species was determined and compared to corresponding regions in pathogenic Neisseriae, in order to elucidate the potential for inter-species DNA transfer within this region.<br><br>RESULTS: The upstream region of folP displayed differences in gene order between species, including an insertion of a complete Correia element in Neisseria lactamica and an inversion of a larger genomic segment in Neisseria sicca, Neisseria subflava and Neisseria mucosa. The latter species also had DNA uptake signal sequences (DUS) in this region that were one base different from the DUS in pathogenic Neisseriae. Another interesting finding was evidence of a horizontal transfer event from Neisseria lactamica or Neisseria cinerea that introduced a novel folP allele to the meningococcal population.<br><br>CONCLUSION: Genetic recombination events immediately upstream of folP and horizontal transfer have resulted in sequence differences in the folP region between the Neisseria species. This variability could be a consequence of the selective pressure on this region exerted by the use of sulfonamide drugs.}, }
@article {pmid16503363, year = {2006}, author = {Prangishvili, D and Garrett, RA and Koonin, EV}, title = {Evolutionary genomics of archaeal viruses: unique viral genomes in the third domain of life.}, journal = {Virus research}, volume = {117}, number = {1}, pages = {52-67}, doi = {10.1016/j.virusres.2006.01.007}, pmid = {16503363}, issn = {0168-1702}, support = {//Intramural NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Archaeal Viruses/*genetics ; Crenarchaeota/*virology ; *Evolution, Molecular ; *Genome, Viral ; *Genomics ; Molecular Sequence Data ; Viral Proteins/chemistry/genetics ; }, abstract = {In terms of virion morphology, the known viruses of archaea fall into two distinct classes: viruses of mesophilic and moderately thermophilic Eueryarchaeota closely resemble head-and-tail bacteriophages whereas viruses of hyperthermophilic Crenarchaeota show a variety of unique morphotypes. In accord with this distinction, the sequenced genomes of euryarchaeal viruses encode many proteins homologous to bacteriophage capsid proteins. In contrast, initial analysis of the crenarchaeal viral genomes revealed no relationships with bacteriophages and, generally, very few proteins with detectable homologs. Here we describe a re-analysis of the proteins encoded by archaeal viruses, with an emphasis on comparative genomics of the unique viruses of Crenarchaeota. Detailed examination of conserved domains and motifs uncovered a significant number of previously unnoticed homologous relationships among the proteins of crenarchaeal viruses and between viral proteins and those from cellular life forms and allowed functional predictions for some of these conserved genes. A small pool of genes is shared by overlapping subsets of crenarchaeal viruses, in a general analogy with the metagenome structure of bacteriophages. The proteins encoded by the genes belonging to this pool include predicted transcription regulators, ATPases implicated in viral DNA replication and packaging, enzymes of DNA precursor metabolism, RNA modification enzymes, and glycosylases. In addition, each of the crenarchaeal viruses encodes several proteins with prokaryotic but not viral homologs, some of which, predictably, seem to have been scavenged from the crenarchaeal hosts, but others might have been acquired from bacteria. We conclude that crenarchaeal viruses are, in general, evolutionarily unrelated to other known viruses and, probably, evolved via independent accretion of genes derived from the hosts and, through more complex routes of horizontal gene transfer, from other prokaryotes.}, }
@article {pmid16503196, year = {2006}, author = {Kozlowicz, BK and Dworkin, M and Dunny, GM}, title = {Pheromone-inducible conjugation in Enterococcus faecalis: a model for the evolution of biological complexity?.}, journal = {International journal of medical microbiology : IJMM}, volume = {296}, number = {2-3}, pages = {141-147}, pmid = {16503196}, issn = {1438-4221}, support = {T32 GM008347/GM/NIGMS NIH HHS/United States ; R01 HL051987-12/HL/NHLBI NIH HHS/United States ; HL51987/HL/NHLBI NIH HHS/United States ; GM49530/GM/NIGMS NIH HHS/United States ; R01 GM049530/GM/NIGMS NIH HHS/United States ; R01 GM049530-20/GM/NIGMS NIH HHS/United States ; R01 HL051987/HL/NHLBI NIH HHS/United States ; T32 GM08347/GM/NIGMS NIH HHS/United States ; R01 AI058134/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/physiology ; Biological Evolution ; *Conjugation, Genetic ; Enterococcus faecalis/*genetics/pathogenicity/*physiology ; Gene Transfer, Horizontal ; Models, Biological ; Oligopeptides/genetics/*pharmacology ; Pheromones/genetics/*pharmacology ; Plasmids ; Protein Sorting Signals/physiology ; Virulence ; }, abstract = {Pheromone-inducible transfer of the plasmid pCF10 in Enterococcus faecalis is regulated using a complicated network of proteins and RNAs. The plasmid itself has been assembled from parts garnered from a variety of sources, and many aspects of the system resemble a biological kluge. Recently several new functions of various pCF10 gene products that participate in regulation of plasmid transfer have been identified. The results indicate that selective pressures controlling the evolution of the plasmid have produced a highly complex regulatory network with multiple biological functions that may serve well as a model for the evolution of biological complexity.}, }
@article {pmid16495350, year = {2006}, author = {Susko, E and Leigh, J and Doolittle, WF and Bapteste, E}, title = {Visualizing and assessing phylogenetic congruence of core gene sets: a case study of the gamma-proteobacteria.}, journal = {Molecular biology and evolution}, volume = {23}, number = {5}, pages = {1019-1030}, doi = {10.1093/molbev/msj113}, pmid = {16495350}, issn = {0737-4038}, mesh = {Biological Evolution ; Data Interpretation, Statistical ; Evolution, Molecular ; Gammaproteobacteria/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetics ; Genome, Bacterial ; *Genomics ; Hot Temperature ; Models, Genetic ; Phylogeny ; }, abstract = {Here, we address a much-debated topic: is there or is there not an organismal tree of gamma-proteobacteria that can be unambiguously inferred from a core of shared genes? We apply several recently developed analytical methods to this problem, for the first time. Our heat map analyses of P values and of bootstrap bipartitions show the presence of conflicting phylogenetic signals among these core genes. Our synthesis reconstruction suggests that at least 10% of these genes have been laterally transferred during the divergence of the gamma-proteobacteria, and that for most of the rest, there is too little phylogenetic signal to permit firm conclusions about the mode of inheritance. Although there is clearly a central tendency in this data set (it is far from random), lateral gene transfers cannot be ruled out. Instead of an organismal tree, we propose that these core genes could be used to define a more subtle and partially reticulated pattern of relationships.}, }
@article {pmid16495255, year = {2006}, author = {Pletz, MW and McGee, L and Van Beneden, CA and Petit, S and Bardsley, M and Barlow, M and Klugman, KP}, title = {Fluoroquinolone resistance in invasive Streptococcus pyogenes isolates due to spontaneous mutation and horizontal gene transfer.}, journal = {Antimicrobial agents and chemotherapy}, volume = {50}, number = {3}, pages = {943-948}, pmid = {16495255}, issn = {0066-4804}, mesh = {Adult ; Aged ; Amino Acid Sequence ; Anti-Infective Agents/*pharmacology ; Base Sequence ; Chi-Square Distribution ; Ciprofloxacin/pharmacology ; DNA, Bacterial/analysis/genetics ; Drug Resistance, Bacterial/*genetics ; Female ; Fluoroquinolones/*pharmacology ; Follow-Up Studies ; *Gene Transfer, Horizontal ; Humans ; Male ; Microbial Sensitivity Tests ; Molecular Sequence Data ; *Mutation ; Phylogeny ; Polymerase Chain Reaction ; Recombination, Genetic ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Streptococcus pyogenes/*drug effects/*genetics/isolation &amp; purification ; Time Factors ; Treatment Outcome ; }, abstract = {Fluoroquinolone resistance in Streptococcus pyogenes has been described only anecdotally. In this study we describe two invasive ciprofloxacin-resistant S. pyogenes isolates (ciprofloxacin MICs, 8 mg/liter), one of which shows evidence of interspecies recombination. The quinolone resistance-determining regions of gyrA and parC were sequenced. In both isolates, there was no evidence for an efflux pump and no mutation in gyrA. Both isolates had an S79F mutation in parC that is known to confer fluoroquinolone resistance. In addition, a D91N mutation in parC, which is not related to fluoroquinolone resistance but is a feature of the parC sequence of Streptococcus dysgalactiae, was found in one isolate. The parC nucleotide sequence of that isolate showed greater diversity than that of S. pyogenes. A GenBank search and phylogenetic analysis suggest that this isolate acquired resistance by horizontal gene transfer from S. dysgalactiae. Statistical testing for recombination confirmed interspecies recombination of a 90-bp sequence containing the S79F mutation from S. dysgalactiae. For the other isolate, we could confirm that it acquired resistance by spontaneous mutation by identifying the susceptible ancestor in an outbreak setting.}, }
@article {pmid16494962, year = {2006}, author = {Iyer, LM and Balaji, S and Koonin, EV and Aravind, L}, title = {Evolutionary genomics of nucleo-cytoplasmic large DNA viruses.}, journal = {Virus research}, volume = {117}, number = {1}, pages = {156-184}, doi = {10.1016/j.virusres.2006.01.009}, pmid = {16494962}, issn = {0168-1702}, support = {//Intramural NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Cell Nucleus/*virology ; Cytoplasm/*virology ; DNA Viruses/classification/*genetics ; Eukaryotic Cells/virology ; *Evolution, Molecular ; Genome, Viral ; *Genomics ; Humans ; Molecular Sequence Data ; Phylogeny ; Transcription Factors/chemistry/genetics ; Viral Proteins/chemistry/genetics ; }, abstract = {A previous comparative-genomic study of large nuclear and cytoplasmic DNA viruses (NCLDVs) of eukaryotes revealed the monophyletic origin of four viral families: poxviruses, asfarviruses, iridoviruses, and phycodnaviruses [Iyer, L.M., Aravind, L., Koonin, E.V., 2001. Common origin of four diverse families of large eukaryotic DNA viruses. J. Virol. 75 (23), 11720-11734]. Here we update this analysis by including the recently sequenced giant genome of the mimiviruses and several additional genomes of iridoviruses, phycodnaviruses, and poxviruses. The parsimonious reconstruction of the gene complement of the ancestral NCLDV shows that it was a complex virus with at least 41 genes that encoded the replication machinery, up to four RNA polymerase subunits, at least three transcription factors, capping and polyadenylation enzymes, the DNA packaging apparatus, and structural components of an icosahedral capsid and the viral membrane. The phylogeny of the NCLDVs is reconstructed by cladistic analysis of the viral gene complements, and it is shown that the two principal lineages of NCLDVs are comprised of poxviruses grouped with asfarviruses and iridoviruses grouped with phycodnaviruses-mimiviruses. The phycodna-mimivirus grouping was strongly supported by several derived shared characters, which seemed to rule out the previously suggested basal position of the mimivirus [Raoult, D., Audic, S., Robert, C., Abergel, C., Renesto, P., Ogata, H., La Scola, B., Suzan, M., Claverie, J.M. 2004. The 1.2-megabase genome sequence of Mimivirus. Science 306 (5700), 1344-1350]. These results indicate that the divergence of the major NCLDV families occurred at an early stage of evolution, prior to the divergence of the major eukaryotic lineages. It is shown that subsequent evolution of the NCLDV genomes involved lineage-specific expansion of paralogous gene families and acquisition of numerous genes via horizontal gene transfer from the eukaryotic hosts, other viruses, and bacteria (primarily, endosymbionts and parasites). Amongst the expansions, there are multiple families of predicted virus-specific signaling and regulatory domains. Most NCLDVs have also acquired large arrays of genes related to ubiquitin signaling, and the animal viruses in particular have independently evolved several defenses against apoptosis and immune response, including growth factors and potential inhibitors of cytokine signaling. The mimivirus displays an enormous array of genes of bacterial provenance, including a representative of a new class of predicted papain-like peptidases. It is further demonstrated that a significant number of genes found in NCLDVs also have homologs in bacteriophages, although a vertical relationship between the NCLDVs and a particular bacteriophage group could not be established. On the basis of these observations, two alternative scenarios for the origin of the NCLDVs and other groups of large DNA viruses of eukaryotes are considered. One of these scenarios posits an early assembly of an already large DNA virus precursor from which various large DNA viruses diverged through an ongoing process of displacement of the original genes by xenologous or non-orthologous genes from various sources. The second scenario posits convergent emergence, on multiple occasions, of large DNA viruses from small plasmid-like precursors through independent accretion of similar sets of genes due to strong selective pressures imposed by their life cycles and hosts.}, }
@article {pmid16490276, year = {2006}, author = {Liu, J and Glazko, G and Mushegian, A}, title = {Protein repertoire of double-stranded DNA bacteriophages.}, journal = {Virus research}, volume = {117}, number = {1}, pages = {68-80}, doi = {10.1016/j.virusres.2006.01.015}, pmid = {16490276}, issn = {0168-1702}, mesh = {Bacteriophages/*genetics ; DNA/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Viral ; Viral Proteins/*genetics ; }, abstract = {The complexity and diversity of phage gene sets, which are produced by rapid evolution of phage genomes and rampant gene exchanges among phages, hamper the efforts to decipher the evolutionary relationships between individual phage proteins and reconstruct the complete set of evolutionary events leading to the known phages. To start unraveling the natural history of phages, we built the phage orthologous groups (POGs), a natural system of phage protein families that includes 6378 genes from 164 complete genome sequences of double-stranded DNA bacteriophages. Phage proteomes have high POG coverage: on average, 39 genes per phage genome belong to POGs, which is close to half of all genes in most phages. In an agreement with the notion of phage role in horizontal gene transfer, we see many cases of likely gene exchange between phages and their microbial hosts. At the same time, about 80% of all POGs are highly specific to phage genomes and are not commonly found in microbial genomes, indicating coherence and large degree of evolutionary independence of phage gene sets. The information on orthologous genes is essential for evolutionary classification of known bacteriophages and for reconstruction of ancestral phage genomes.}, }
@article {pmid16489267, year = {2005}, author = {Kleter, GA and Peijnenburg, AA and Aarts, HJ}, title = {Health considerations regarding horizontal transfer of microbial transgenes present in genetically modified crops.}, journal = {Journal of biomedicine &amp; biotechnology}, volume = {2005}, number = {4}, pages = {326-352}, pmid = {16489267}, issn = {1110-7243}, abstract = {The potential effects of horizontal gene transfer on human health are an important item in the safety assessment of genetically modified organisms. Horizontal gene transfer from genetically modified crops to gut microflora most likely occurs with transgenes of microbial origin. The characteristics of microbial transgenes other than antibiotic-resistance genes in market-approved genetically modified crops are reviewed. These characteristics include the microbial source, natural function, function in genetically modified crops, natural prevalence, geographical distribution, similarity to other microbial genes, known horizontal transfer activity, selective conditions and environments for horizontally transferred genes, and potential contribution to pathogenicity and virulence in humans and animals. The assessment of this set of data for each of the microbial genes reviewed does not give rise to health concerns. We recommend including the above-mentioned items into the premarket safety assessment of genetically modified crops carrying transgenes other than those reviewed in the present study.}, }
@article {pmid16483841, year = {2006}, author = {Wei, JR and Lai, HC}, title = {N-acylhomoserine lactone-dependent cell-to-cell communication and social behavior in the genus Serratia.}, journal = {International journal of medical microbiology : IJMM}, volume = {296}, number = {2-3}, pages = {117-124}, doi = {10.1016/j.ijmm.2006.01.033}, pmid = {16483841}, issn = {1438-4221}, mesh = {4-Butyrolactone/*analogs &amp; derivatives/metabolism ; Bacterial Proteins/physiology ; Carbon-Sulfur Lyases ; Cell Communication ; Gene Transfer, Horizontal ; Humans ; Locomotion/physiology ; Serratia/genetics/pathogenicity/*physiology ; Serratia Infections/microbiology ; }, abstract = {Members of the genus Serratia are increasingly responsible for nosocomial infections, the treatment of which may be complicated by the appearance of multi-antibiotic-resistant strains. Some but not all Serratia strains and species produce N-acylhomoserine lactones (AHLs), and possess luxR and luxI homologous genes. Phylogenetic comparisons have provided evidence for the lateral transfer of these quorum-sensing systems, and in at least one strain of S. marcescens, transfer via a complex transposon has been experimentally demonstrated. AHL-dependent quorum sensing in Serratia controls population surface migration, biofilm development, the biosynthesis of a carbapenem antibiotic and production of the red pigment, prodigiosin. Serratia also possesses LuxS and produces autoinducer-2 (AI-2) which appears to function as a second quorum-sensing system controlling many of the same phenotypes as the LuxR/AHL systems.}, }
@article {pmid16482157, year = {2006}, author = {Frigaard, NU and Martinez, A and Mincer, TJ and DeLong, EF}, title = {Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea.}, journal = {Nature}, volume = {439}, number = {7078}, pages = {847-850}, doi = {10.1038/nature04435}, pmid = {16482157}, issn = {1476-4687}, mesh = {Archaea/classification/*genetics ; Bacteria/*genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Archaeal/genetics ; Genes, Bacterial/genetics ; Genes, rRNA/genetics ; Genome ; Genomic Library ; Marine Biology ; Molecular Sequence Data ; Photic Stimulation ; Phylogeny ; Plankton/*genetics ; Rhodopsin/*genetics ; Rhodopsins, Microbial ; Seawater/*microbiology ; Sunlight ; Synteny ; }, abstract = {Planktonic Bacteria, Archaea and Eukarya reside and compete in the ocean's photic zone under the pervasive influence of light. Bacteria in this environment were recently shown to contain photoproteins called proteorhodopsins, thought to contribute to cellular energy metabolism by catalysing light-driven proton translocation across the cell membrane. So far, proteorhodopsin genes have been well documented only in proteobacteria and a few other bacterial groups. Here we report the presence and distribution of proteorhodopsin genes in Archaea affiliated with the order Thermoplasmatales, in the ocean's upper water column. The genomic context and phylogenetic relationships of the archaeal and proteobacterial proteorhodopsins indicate its probable lateral transfer between planktonic Bacteria and Archaea. About 10% of the euryarchaeotes in the photic zone contained the proteorhodopsin gene adjacent to their small-subunit ribosomal RNA. The archaeal proteorhodopsins were also found in other genomic regions, in the same or in different microbial lineages. Although euryarchaeotes were distributed throughout the water column, their proteorhodopsins were found only in the photic zone. The cosmopolitan phylogenetic distribution of proteorhodopsins reflects their significant light-dependent fitness contributions, which drive the photoprotein's lateral acquisition and retention, but constrain its dispersal to the photic zone.}, }
@article {pmid16480495, year = {2006}, author = {van Passel, MW and Bart, A and Luyf, AC and van Kampen, AH and van der Ende, A}, title = {Compositional discordance between prokaryotic plasmids and host chromosomes.}, journal = {BMC genomics}, volume = {7}, number = {}, pages = {26}, pmid = {16480495}, issn = {1471-2164}, mesh = {*Base Composition ; Borrelia burgdorferi/genetics ; Chromosomes/*chemistry/*genetics ; Chromosomes, Bacterial/chemistry/genetics ; DNA/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; Gene Transfer, Horizontal ; Genomics ; Host-Pathogen Interactions/*genetics ; Plasmids/*chemistry/*genetics ; Prokaryotic Cells ; }, abstract = {BACKGROUND: Most plasmids depend on the host replication machinery and possess partitioning genes. These properties confine plasmids to a limited range of hosts, yielding a close and presumably stable relationship between plasmid and host. Hence, it is anticipated that due to amelioration the dinucleotide composition of plasmids is similar to that of the genome of their hosts. However, plasmids are also thought to play a major role in horizontal gene transfer and thus are frequently exchanged between hosts, suggesting dinucleotide composition dissimilarity between plasmid and host genome. We compared the dinucleotide composition of a large collection of plasmids with that of their host genomes to shed more light on this enigma.<br><br>RESULTS: The dinucleotide frequency, coined the genome signature, facilitates the identification of putative horizontally transferred DNA in complete genome sequences, since it was found to be typical for a certain genome, and similar between related species. By comparison of the genome signature of 230 plasmid sequences with that of the genome of each respective host, we found that in general the genome signature of plasmids is dissimilar from that of their host genome.<br><br>CONCLUSION: Our results show that the genome signature of plasmids does not resemble that of their host genome. This indicates either absence of amelioration or a less stable relationship between plasmids and their host. We propose an indiscriminate lifestyle for plasmids preserving the genome signature discordance between these episomes and host chromosomes.}, }
@article {pmid16478452, year = {2006}, author = {Ma, Y and Wang, L and Shao, Z}, title = {Pseudomonas, the dominant polycyclic aromatic hydrocarbon-degrading bacteria isolated from Antarctic soils and the role of large plasmids in horizontal gene transfer.}, journal = {Environmental microbiology}, volume = {8}, number = {3}, pages = {455-465}, doi = {10.1111/j.1462-2920.2005.00911.x}, pmid = {16478452}, issn = {1462-2912}, mesh = {Antarctic Regions ; Blotting, Southern ; Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Dioxygenases ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Multienzyme Complexes/genetics ; Naphthalenes/metabolism ; Oxygenases/genetics ; Phenanthrenes/metabolism ; Phylogeny ; Plasmids/*genetics ; Polycyclic Aromatic Hydrocarbons/*metabolism ; Polymerase Chain Reaction ; Pseudomonas/classification/genetics/*isolation &amp; purification/*metabolism ; RNA, Ribosomal, 16S/genetics ; Rahnella/classification/genetics/isolation &amp; purification/metabolism ; Sequence Analysis, DNA ; Sequence Homology ; *Soil Microbiology ; Temperature ; }, abstract = {Twenty-two polycyclic aromatic hydrocarbon (PAH)-degrading bacterial strains were isolated from Antarctic soils with naphthalene or phenanthrene as a sole carbon source, while no degrader was obtained from an unpolluted sampling site. Phylogenetic analysis showed that all belonged to the genus Pseudomonas except one that was identified as the genus of Rahnella. Some of them were closely related to previously reported cold-tolerant species, while some were separated in deeply rooted branches and represent new strains. All these strains showed a high efficiency to degrade naphthalene at 4 degrees C, and some additionally degraded phenanthrene. Using degenerate primers and polymerase chain reaction (PCR) amplification, ndo gene encoding naphthalene dioxygenase (NDO) was detected from all the isolates. Phylogenetic analysis grouped these genes into two clusters which shared 94% similarity to each other, and showed about 97% similarity within a cluster. However, no obvious difference was observed with mesophilic ndo genes; this indicates that the host cell is pivotal in cold adaptation. In addition, the mismatch between 16S rRNA and NDO phylogenetic trees strongly indicates horizontal gene transfer among these isolates and may have happened in situ. Further, Southern hybridization and plasmid curing confirmed that ndo genes were located on a large self-transmissible plasmid, which can be transferred to a mesophilic strains. The transconjugants acquired the ability to utilize naphthalene and phenanthrene. Results of this article imply that Pseudomonas plays an important role in PAH biodegradation in Antarctic soils, and the related genes might be originally transferred from outside Antarctica and spread among indigenous species.}, }
@article {pmid16477356, year = {2006}, author = {Zhang, R and Cui, Z and Zhang, X and Jiang, J and Gu, JD and Li, S}, title = {Cloning of the organophosphorus pesticide hydrolase gene clusters of seven degradative bacteria isolated from a methyl parathion contaminated site and evidence of their horizontal gene transfer.}, journal = {Biodegradation}, volume = {17}, number = {5}, pages = {465-472}, doi = {10.1007/s10532-005-9018-6}, pmid = {16477356}, issn = {0923-9820}, mesh = {Aryldialkylphosphatase/*genetics ; Biodegradation, Environmental ; Cloning, Molecular ; Environmental Pollution ; Escherichia coli/genetics ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Gram-Negative Aerobic Rods and Cocci/*enzymology/genetics/isolation &amp; purification ; Methyl Parathion/*metabolism ; Multigene Family ; Open Reading Frames ; Pesticides/*metabolism ; }, abstract = {Seven organophosphorus pesticide-degrading bacteria harboring the methyl parathion degrading (mpd) gene were isolated from a methyl parathion contaminated site. In this study, the 4.7 kb mpd gene cluster, conserved in all seven bacteria capable of degrading methyl parathion, was cloned and further analysis revealed that this cluster contained five ORFs and the mpd gene was associated with a mobile element, IS6100. In addition to mpd gene ORF and tnpA ORF, three other ORFs showed high homology to the permease component of ABC-type transport system, the general secretion pathway protein B, and the RNA polymerase sigma 70 factor, respectively. The mpd genes of these 7 strains were subcloned and expressed in E. coli, SDS-PAGE and zymogram analysis showed that two expression products of mpd genes in E. coli were found, but the one without signal peptide showed the hydrolytic activities. Our evidences collectively suggest that mpd gene cluster may be disseminated through horizontal gene transfer based on phylogenetic analysis of the cluster and their host bacterial strains, and comparisons of GC content of the cluster and respective host's chromosome.}, }
@article {pmid16474982, year = {2006}, author = {Hao, W and Golding, GB}, title = {Asymmetrical evolution of cytochrome bd subunits.}, journal = {Journal of molecular evolution}, volume = {62}, number = {2}, pages = {132-142}, pmid = {16474982}, issn = {0022-2844}, mesh = {Bacteria/enzymology/genetics ; Conserved Sequence ; Cytochrome b Group ; Cytochromes/*genetics ; Electron Transport Chain Complex Proteins/*genetics ; Escherichia coli Proteins/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Oxidoreductases/*genetics ; *Phylogeny ; }, abstract = {Functionally linked genes generally evolve at similar rates and the knowledge of this particular feature of genomic evolution has been used as the basis for the phylogenetic profiling method. We illustrate here an exception to this rule in the evolution of the cytochrome bd complex. This is a two-component oxidase complex, with the subunits I and II known to be widely present in bacteria. The subunits within the cytochrome bd complex are under the same evolutionary pressure and most likely behave in the same evolutionary manner. However, the sequence similarity of genes encoding subunit II varies considerably across species. Genes encoding subunit II evolve 1.2 times faster on most of the branches of their phylogeny than subunit I genes. Furthermore, the genes encoding subunit II in Oceanobacillus iheyensis, Bacillus halodurans, and Staphylococcus species do not have detectable homologues within E. coli due to their large divergence. Together, the two subunits of cytochrome bd reveal an interesting example of an asymmetric pattern of evolutionary change.}, }
@article {pmid16474979, year = {2006}, author = {Vuletich, DA and Lecomte, JT}, title = {A phylogenetic and structural analysis of truncated hemoglobins.}, journal = {Journal of molecular evolution}, volume = {62}, number = {2}, pages = {196-210}, pmid = {16474979}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Animals ; Conserved Sequence ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Hemoglobins/*genetics ; Ligands ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Protein Structure, Quaternary ; Sequence Homology, Amino Acid ; Truncated Hemoglobins ; }, abstract = {Truncated hemoglobins (trHbs) are heme proteins found in bacteria, plants, and unicellular eukaryotes. They are distantly related to vertebrate hemoglobins and are typically shorter than these by 20-40 residues. The multiple amino acid deletions, insertions, and replacements result in distinctive alterations of the canonical globin fold and a wide range of chemical properties. An early phylogenetic analysis categorized trHbs into three groups, I (trHbN), II (trHbO), and III (trHbP). Here, we revisit this analysis with 111 trHbs. We find that trHbs are orthologous within each group and paralogous across the groups. Group I globins form the most disparate set and separate into two divergent subgroups. Group II is comparatively homogeneous, whereas Group III displays the highest level of overall conservation. In Group I and Group II globins, for which some ligand binding and structural data are available, an improved description of probable protein-ligand interactions is achieved. Other conservation trends are either confirmed (essential glycines in loops), refined (lining of ligand access tunnel), or newly identified (helix start signal). The Group III globins, so far uncharacterized, exhibit recognizable heme cavity residues while lacking some of the residues thought to be important to the trHb fold. An analysis of the phylogenetic trees of each group provides a plausible scenario for the emergence of trHbs, by which the Group II trHb gene was the original gene, and the Group I trHb and Group III trHb genes were obtained via duplication and transfer events.}, }
@article {pmid16474952, year = {2006}, author = {Kresse, AU and Blöcker, H and Römling, U}, title = {ISPa20 advances the individual evolution of Pseudomonas aeruginosa clone C subclone C13 strains isolated from cystic fibrosis patients by insertional mutagenesis and genomic rearrangements.}, journal = {Archives of microbiology}, volume = {185}, number = {4}, pages = {245-254}, doi = {10.1007/s00203-006-0089-5}, pmid = {16474952}, issn = {0302-8933}, mesh = {*Chromosome Inversion ; Cystic Fibrosis/*microbiology ; *DNA Transposable Elements ; *Evolution, Molecular ; Genome, Bacterial ; Humans ; Lipopolysaccharides/analysis ; Models, Genetic ; *Mutagenesis, Insertional ; Pseudomonas Infections/*microbiology ; Pseudomonas aeruginosa/classification/*genetics/pathogenicity ; }, abstract = {Pseudomonas aeruginosa clone C strains, which chronically colonize the lungs of cystic fibrosis patients reorganize their genome structure. In this study, a novel member of the IS3 subfamily of IS elements, ISPa20, was detected which was specific for clone C subclone C13 strains. ISPa20, which was present in high copy number, mediated events of genomic reorganization. ISPa20 was inserted into P. aeruginosa backbone genes leading to adaptation to the cystic fibrosis lung habitat and into DNA acquired through horizontal gene transfer. Further on, large chromosomal inversions were mediated by ISPa20. In contrast to strains of other subclonal linages high rates of genomic rearrangements of subclone C13 strains were observed in vitro. The acquisition of mobile elements by P. aeruginosa clone C strains in the lungs of cystic fibrosis patients supports the chronic colonization by insertional mutagenesis and chromosome restructuring leading to microevolution within clone C that reflects macroevolution observed on the species level.}, }
@article {pmid16473847, year = {2006}, author = {Ardell, DH and Andersson, SG}, title = {TFAM detects co-evolution of tRNA identity rules with lateral transfer of histidyl-tRNA synthetase.}, journal = {Nucleic acids research}, volume = {34}, number = {3}, pages = {893-904}, pmid = {16473847}, issn = {1362-4962}, mesh = {Alphaproteobacteria/classification/enzymology/*genetics ; DNA, Bacterial/classification ; Databases, Nucleic Acid ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genetic Variation ; Genome, Bacterial ; Genomics ; Histidine-tRNA Ligase/classification/*genetics ; *Models, Statistical ; Phylogeny ; RNA, Transfer/classification/genetics ; RNA, Transfer, His/chemistry/classification/*genetics ; RNA, Transfer, Met/classification ; }, abstract = {We present TFAM, an automated, statistical method to classify the identity of tRNAs. TFAM, currently optimized for bacteria, classifies initiator tRNAs and predicts the charging identity of both typical and atypical tRNAs such as suppressors with high confidence. We show statistical evidence for extensive variation in tRNA identity determinants among bacterial genomes due to variation in overall tDNA base content. With TFAM we have detected the first case of eukaryotic-like tRNA identity rules in bacteria. An alpha-proteobacterial clade encompassing Rhizobiales, Caulobacter crescentus and Silicibacter pomeroyi, unlike a sister clade containing the Rickettsiales, Zymomonas mobilis and Gluconobacter oxydans, uses the eukaryotic identity element A73 instead of the highly conserved prokaryotic element C73. We confirm divergence of bacterial histidylation rules by demonstrating perfect covariation of alpha-proteobacterial tRNA(His) acceptor stems and residues in the motif IIb tRNA-binding pocket of their histidyl-tRNA synthetases (HisRS). Phylogenomic analysis supports lateral transfer of a eukaryotic-like HisRS into the alpha-proteobacteria followed by in situ adaptation of the bacterial tDNA(His) and identity rule divergence. Our results demonstrate that TFAM is an effective tool for the bioinformatics, comparative genomics and evolutionary study of tRNA identity.}, }
@article {pmid16473421, year = {2006}, author = {Lal, R and Dogra, C and Malhotra, S and Sharma, P and Pal, R}, title = {Diversity, distribution and divergence of lin genes in hexachlorocyclohexane-degrading sphingomonads.}, journal = {Trends in biotechnology}, volume = {24}, number = {3}, pages = {121-130}, doi = {10.1016/j.tibtech.2006.01.005}, pmid = {16473421}, issn = {0167-7799}, mesh = {Bacterial Proteins/*genetics/metabolism ; Biodegradation, Environmental ; Gene Transfer, Horizontal/genetics ; Genetic Variation/*genetics ; Gram-Negative Bacteria/enzymology/*genetics ; Hexachlorocyclohexane/*metabolism ; Insecticides/*metabolism ; Lyases/*genetics/metabolism ; Phylogeny ; Plasmids/genetics ; Stereoisomerism ; }, abstract = {Two forms of hexachlorocyclohexane (HCH), gamma-HCH (lindane) and technical HCH (incorporating alpha-, beta-, gamma- and delta- isomers), have been used against agricultural pests and in health programs since the 1940s. Although all the isomers are present in the milieu, delta- and beta-HCH isomers are the most problematic and present a serious environmental problem. Bacteria that degrade HCH isomers have been isolated from HCH contaminated soils from different geographical locations around the world (from the family Sphingomonadaceae). Interestingly, all these bacteria contain nearly identical lin genes (responsible for HCH degradation), which are diverging to perform several catabolic functions. The organization and diversity of lin genes have been studied among several sphingomonads, and they have been found to be associated with plasmids and IS6100, both of which appear to have a significant role in their horizontal transfer. The knowledge of the molecular genetics, diversity and distribution of lin genes, and the potential of sphingomonads to degrade HCH isomers, can now be used for developing bioremediation techniques for the decontamination of HCH contaminated sites.}, }
@article {pmid16472400, year = {2006}, author = {Beiko, RG and Hamilton, N}, title = {Phylogenetic identification of lateral genetic transfer events.}, journal = {BMC evolutionary biology}, volume = {6}, number = {}, pages = {15}, pmid = {16472400}, issn = {1471-2148}, mesh = {*Algorithms ; Computational Biology/methods ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Archaeal ; Genome, Bacterial ; Genomics/methods ; *Phylogeny ; }, abstract = {BACKGROUND: Lateral genetic transfer can lead to disagreements among phylogenetic trees comprising sequences from the same set of taxa. Where topological discordance is thought to have arisen through genetic transfer events, tree comparisons can be used to identify the lineages that may have shared genetic information. An 'edit path' of one or more transfer events can be represented with a series of subtree prune and regraft (SPR) operations, but finding the optimal such set of operations is NP-hard for comparisons between rooted trees, and may be so for unrooted trees as well.<br><br>RESULTS: Efficient Evaluation of Edit Paths (EEEP) is a new tree comparison algorithm that uses evolutionarily reasonable constraints to identify and eliminate many unproductive search avenues, reducing the time required to solve many edit path problems. The performance of EEEP compares favourably to that of other algorithms when applied to strictly bifurcating trees with specified numbers of SPR operations. We also used EEEP to recover edit paths from over 19,000 unrooted, incompletely resolved protein trees containing up to 144 taxa as part of a large phylogenomic study. While inferred protein trees were far more similar to a reference supertree than random trees were to each other, the phylogenetic distance spanned by random versus inferred transfer events was similar, suggesting that real transfer events occur most frequently between closely related organisms, but can span large phylogenetic distances as well. While most of the protein trees examined here were very similar to the reference supertree, requiring zero or one edit operations for reconciliation, some trees implied up to 40 transfer events within a single orthologous set of proteins.<br><br>CONCLUSION: Since sequence trees typically have no implied root and may contain unresolved or multifurcating nodes, the strategy implemented in EEEP is the most appropriate for phylogenomic analyses. The high degree of consistency among inferred protein trees shows that vertical inheritance is the dominant pattern of evolution, at least for the set of organisms considered here. However, the edit paths inferred using EEEP suggest an important role for genetic transfer in the evolution of microbial genomes as well.}, }
@article {pmid16472398, year = {2006}, author = {Ricard, G and McEwan, NR and Dutilh, BE and Jouany, JP and Macheboeuf, D and Mitsumori, M and McIntosh, FM and Michalowski, T and Nagamine, T and Nelson, N and Newbold, CJ and Nsabimana, E and Takenaka, A and Thomas, NA and Ushida, K and Hackstein, JH and Huynen, MA}, title = {Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment.}, journal = {BMC genomics}, volume = {7}, number = {}, pages = {22}, pmid = {16472398}, issn = {1471-2164}, mesh = {Adaptation, Physiological/genetics ; Anaerobiosis ; Animals ; Bacteria/classification/*genetics/metabolism ; Bacteria, Anaerobic ; Carbohydrate Metabolism/genetics ; Ciliophora/classification/*genetics/metabolism ; Expressed Sequence Tags/chemistry ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genes, Protozoan ; Glycoside Hydrolases/genetics ; Phylogeny ; Ruminants/microbiology/parasitology ; }, abstract = {BACKGROUND: The horizontal transfer of expressed genes from Bacteria into Ciliates which live in close contact with each other in the rumen (the foregut of ruminants) was studied using ciliate Expressed Sequence Tags (ESTs). More than 4000 ESTs were sequenced from representatives of the two major groups of rumen Cilates: the order Entodiniomorphida (Entodinium simplex, Entodinium caudatum, Eudiplodinium maggii, Metadinium medium, Diploplastron affine, Polyplastron multivesiculatum and Epidinium ecaudatum) and the order Vestibuliferida, previously called Holotricha (Isotricha prostoma, Isotricha intestinalis and Dasytricha ruminantium).<br><br>RESULTS: A comparison of the sequences with the completely sequenced genomes of Eukaryotes and Prokaryotes, followed by large-scale construction and analysis of phylogenies, identified 148 ciliate genes that specifically cluster with genes from the Bacteria and Archaea. The phylogenetic clustering with bacterial genes, coupled with the absence of close relatives of these genes in the Ciliate Tetrahymena thermophila, indicates that they have been acquired via Horizontal Gene Transfer (HGT) after the colonization of the gut by the rumen Ciliates.<br><br>CONCLUSION: Among the HGT candidates, we found an over-representation (>75%) of genes involved in metabolism, specifically in the catabolism of complex carbohydrates, a rich food source in the rumen. We propose that the acquisition of these genes has greatly facilitated the Ciliates' colonization of the rumen providing evidence for the role of HGT in the adaptation to new niches.}, }
@article {pmid16470417, year = {2006}, author = {Okada, A and Imase, A and Matsuda, H and Ohmae, H and Hata, H and Iwamura, Y}, title = {Heterogeneity of class I and class II MHC sequences in Schistosoma mansoni.}, journal = {Parasitology research}, volume = {99}, number = {1}, pages = {21-27}, pmid = {16470417}, issn = {0932-0113}, mesh = {Animals ; Gene Transfer, Horizontal ; Genes, MHC Class I/*genetics ; Genes, MHC Class II/*genetics ; Genetic Variation ; Host-Parasite Interactions/genetics ; Male ; Mice ; Mice, Inbred BALB C/genetics/parasitology ; Mice, Inbred C57BL/genetics/parasitology ; Schistosoma mansoni/genetics/*physiology ; Species Specificity ; }, abstract = {We investigated the genetic variations in class I and class II major histocompatibility complex (MHC) genes of Schistosoma mansoni and the effects of host MHC genotypes. S. mansoni was maintained in combinations of two mouse strains with different MHC genotypes, and the MHC gene sequences of the cercariae were investigated. The detected class I MHC gene sequences were variable, with high similarity between the H-2D(b) murine host and the parasite. For other combinations, however, the parasite sequence was homologous to those of anthropoids. All class II MHC sequences detected in S. mansoni were homologous to those of anthropoids. Our results suggest that the genetic variation in the MHC sequences of S. mansoni is derived in part from the current host, indicating horizontal transfer of the sequences from mammal to parasite.}, }
@article {pmid16464890, year = {2006}, author = {Blahna, MT and Zalewski, CA and Reuer, J and Kahlmeter, G and Foxman, B and Marrs, CF}, title = {The role of horizontal gene transfer in the spread of trimethoprim-sulfamethoxazole resistance among uropathogenic Escherichia coli in Europe and Canada.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {57}, number = {4}, pages = {666-672}, doi = {10.1093/jac/dkl020}, pmid = {16464890}, issn = {0305-7453}, mesh = {Anti-Bacterial Agents/pharmacology ; Canada/epidemiology ; *Drug Resistance, Bacterial/genetics ; Escherichia coli/*drug effects/genetics ; Escherichia coli Infections/epidemiology/microbiology ; Europe/epidemiology ; *Gene Transfer, Horizontal ; Humans ; Integrons ; Microbial Sensitivity Tests ; Sulfamethoxazole/*pharmacology ; Trimethoprim Resistance ; Trimethoprim, Sulfamethoxazole Drug Combination/*pharmacology ; Urinary Tract Infections/epidemiology/microbiology ; }, abstract = {OBJECTIVES: To describe the distribution of trimethoprim-sulfamethoxazole resistance genes and the role of horizontal gene transfer and clonal expansion in recent increases of antibiotic resistance rates among uropathogenic Escherichia coli in Europe and Canada.<br><br>METHODS: We identified antibiotic resistance alleles sul1, sul2, sul3 and dfr along with type 1 and type 2 integrons among 350 uropathogenic E. coli isolates from a cross-sectional study of acute, uncomplicated, community-acquired urinary tract infections in 16 western European countries and Canada (ECOSENS).<br><br>RESULTS: Trimethoprim resistance gene distributions showed no regional dependency (P = 0.84). The most common trimethoprim resistance gene was dfrA1, which occurred in 37.9% of dfr containing isolates. Similarly, the sulfamethoxazole resistance gene distributions did not vary significantly by region (P = 0.20). sul2, the most common sulfamethoxazole resistance gene, was found in 77.9% of sulfamethoxazole-resistant isolates. The distribution of type 1 and type 2 integrons varied slightly by region (P = 0.04) with type 1 integrons being the more common (85.9%). We observed 34 combinations of the sul genes, dfr genes and integron types; the most common combinations were broadly disseminated across every region examined.<br><br>CONCLUSIONS: Horizontal gene transfer plays a larger role than clonal expansion in the increase of trimethoprim-sulfamethoxazole resistance levels in Europe and Canada.}, }
@article {pmid16464469, year = {2006}, author = {Takushi, Y and Shiraishi, M and Nozato, E and Toyoda, A and Nishimaki, T}, title = {Expression of anti-apoptotic protein, Bcl-2, in liver regeneration after a partial hepatectomy.}, journal = {The Journal of surgical research}, volume = {134}, number = {1}, pages = {93-101}, doi = {10.1016/j.jss.2005.11.586}, pmid = {16464469}, issn = {0022-4804}, mesh = {Adenoviridae/genetics ; Animals ; Gene Transfer, Horizontal ; Hepatectomy ; Hepatocyte Growth Factor/genetics ; Humans ; Immunohistochemistry ; *Liver Regeneration ; Male ; Proliferating Cell Nuclear Antigen/analysis ; Proto-Oncogene Proteins c-bcl-2/analysis/*genetics/physiology ; RNA, Messenger/analysis ; Rats ; Rats, Wistar ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {BACKGROUND: Although Bcl-2 is well known to have anti-apoptotic activities in vitro and in vivo, the role of Bcl-2 relating to liver regeneration remains controversial. The aim of this study was to document the effect of Bcl-2 expression on liver regeneration in rats undergoing a partial hepatectomy.<br><br>MATERIAL AND METHODS: Adult male Wistar rats (n = 4/group) at 72 h before undergoing a 70% partial hepatectomy (PH) were administered 1 x 10(9) plaque-forming units of adenovirus vector encoding either human Bcl-2 (group 1) or LacZ (group 2) intravenously and were sacrificed at 0, 12 h, and at 1, 2, 3, 7, 14, and 21 days postoperatively. In group 3, normal saline was injected instead of adenovirus vector. Liver regeneration was monitored by measuring the restituted liver mass and proliferating cell nuclear antigen (PCNA) immunostaining. The incidence of apoptosis in the liver was analyzed by the immunohistochemical detection of single-stranded DNA at 14 and 21 days postoperatively.<br><br>RESULTS: The restituted liver mass showed significantly higher values in group 1 (26.1 +/- 7.2%) than in group 2 (14.7 +/- 6.8%) and 3 (13.6 +/- 5.0%) at 1 day after PH (P < 0.05). The PCNA labeling index was significantly higher in group 1 (47.2 +/- 9.9%) than in groups 2 (19.0 +/- 7.8%) and 3 (19.2 +/- 15.2%) at 1 day after a partial hepatectomy (P < 0.05). The hepatocyte growth factor (HGF) mRNA expression was significantly lower in group 1 than in group 2 at 12 h after PH (P < 0.05). The number of single-stranded DNA-positive cells decreased significantly more in group 1 (5.67 +/- 1.53 positive cells/10 fields per tissue) than those in group 2 (18.33 +/- 7.57 positive cells/10 fields per tissue) at 14 days after PH.<br><br>CONCLUSIONS: These results thus indicated that an overexpression of anti-apoptotic protein Bcl-2 does not necessarily have an anti-apoptotic effect on liver regeneration but appears to have a pro-proliferative effect in the early phase of liver regeneration.}, }
@article {pmid16463125, year = {2006}, author = {Hens, DK and Chatterjee, NC and Kumar, R}, title = {New temperate DNA phage BcP15 acts as a drug resistance vector.}, journal = {Archives of virology}, volume = {151}, number = {7}, pages = {1345-1353}, doi = {10.1007/s00705-005-0713-8}, pmid = {16463125}, issn = {0304-8608}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteriophages/*genetics ; Blotting, Southern ; Burkholderia cepacia/drug effects/*virology ; DNA Fingerprinting ; DNA, Bacterial/genetics ; DNA, Viral/analysis ; Deoxyribonucleases, Type II Site-Specific ; Drug Resistance, Multiple, Bacterial/*genetics ; Dysentery, Bacillary/microbiology ; Electrophoresis, Gel, Pulsed-Field ; Erythromycin/pharmacology ; *Gene Transfer, Horizontal ; Humans ; India ; Plasmids/genetics ; Polymorphism, Restriction Fragment Length ; Prophages/*genetics ; Shigella flexneri/drug effects/isolation &amp; purification/*virology ; Trimethoprim/pharmacology ; Trimethoprim, Sulfamethoxazole Drug Combination/pharmacology ; Viral Plaque Assay ; }, abstract = {This study was designed to determine the role of a new temperate DNA phage BcP15 in relation to drug resistance. The multidrug resistant Shigella flexneri NK1925 was isolated from a patient of Infectious Diseases Hospital, Kolkata, India. This strain contained five plasmids ranging in size from 3 to 212 kb. After curing of five plasmids, this strain became sensitive to antibiotics. A plasmidless multidrug-resistant strain Burkholderia cepacia DR11 was isolated during the survey of microorganisms from coastal waters of deltaic Sunderbans. This strain always released a temperate phage BcP15 into culture supernatant. Turbid plaque formation was observed on the lawn of a plasmidless version (Pl(-)35) of Shigella flexneri NK1925. A few distinct clones (Pl(-)35R) appeared within the region of each plaque after 18 h incubation. S. flexneri NK1925, Pl(-)35, and Pl(-)35R clones showed the same PFGE band pattern of XbaI-digested chromosomal DNA. However, Pl(-)35R clones were resistant to co-trimoxazole, trimethoprim, and eryth- romycin, to which B. cepacia DR11 was also resistant. Southern hybridization results indicated that these three antibiotic resistances in Pl(-)35R clones were due to a BcP15 phage lysogen in the Pl(-)35 version of S. flexneri NK1925.}, }
@article {pmid16461693, year = {2006}, author = {Tanous, C and Chambellon, E and Le Bars, D and Delespaul, G and Yvon, M}, title = {Glutamate dehydrogenase activity can be transmitted naturally to Lactococcus lactis strains to stimulate amino acid conversion to aroma compounds.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {2}, pages = {1402-1409}, pmid = {16461693}, issn = {0099-2240}, mesh = {Amino Acids/*metabolism ; Base Sequence ; Cadmium/pharmacology ; Cheese/microbiology ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; Gene Expression ; Gene Transfer, Horizontal ; Genes, Bacterial ; Glutamate Decarboxylase/*genetics/*metabolism ; Hydrogen-Ion Concentration ; Lactococcus lactis/drug effects/enzymology/*genetics/*metabolism ; Odorants ; Phenylalanine/metabolism ; Plasmids/genetics ; Zinc/pharmacology ; }, abstract = {Amino acid conversion to aroma compounds by Lactococcus lactis is limited by the low production of alpha-ketoglutarate that is necessary for the first step of conversion. Recently, glutamate dehydrogenase (GDH) activity that catalyzes the reversible glutamate deamination to alpha-ketoglutarate was detected in L. lactis strains isolated from a vegetal source, and the gene responsible for the activity in L. lactis NCDO1867 was identified and characterized. The gene is located on a 70-kb plasmid also encoding cadmium resistance. In this study, gdh gene inactivation and overexpression confirmed the direct impact of GDH activity of L. lactis on amino acid catabolism in a reaction medium at pH 5.5, the pH of cheese. By using cadmium resistance as a selectable marker, the plasmid carrying gdh was naturally transmitted to another L. lactis strain by a mating procedure. The transfer conferred to the host strain GDH activity and the ability to catabolize amino acids in the presence of glutamate in the reaction medium. However, the plasmid appeared unstable in a strain also containing the protease lactose plasmid pLP712, indicating an incompatibility between these two plasmids.}, }
@article {pmid16461685, year = {2006}, author = {Nanavati, DM and Thirangoon, K and Noll, KM}, title = {Several archaeal homologs of putative oligopeptide-binding proteins encoded by Thermotoga maritima bind sugars.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {2}, pages = {1336-1345}, pmid = {16461685}, issn = {0099-2240}, mesh = {ATP-Binding Cassette Transporters/genetics/*metabolism ; Archaea/genetics/metabolism ; Archaeal Proteins/genetics/*metabolism ; Bacterial Proteins/genetics/*metabolism ; Biological Transport, Active ; *Carbohydrate Metabolism ; Gene Expression ; Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; Ligands ; Oligopeptides/metabolism ; Oligosaccharides/metabolism ; Thermotoga maritima/genetics/growth &amp; development/*metabolism ; }, abstract = {The hyperthermophilic bacterium Thermotoga maritima has shared many genes with archaea through horizontal gene transfer. Several of these encode putative oligopeptide ATP binding cassette (ABC) transporters. We sought to test the hypothesis that these transporters actually transport sugars by measuring the substrate affinities of their encoded substrate-binding proteins (SBPs). This information will increase our understanding of the selective pressures that allowed this organism to retain these archaeal homologs. By measuring changes in intrinsic fluorescence of these SBPs in response to exposure to various sugars, we found that five of the eight proteins examined bind to sugars. We could not identify the ligands of the SBPs TM0460, TM1150, and TM1199. The ligands for the archaeal SBPs are TM0031 (BglE), the beta-glucosides cellobiose and laminaribiose; TM0071 (XloE), xylobiose and xylotriose; TM0300 (GloE), large glucose oligosaccharides represented by xyloglucans; TM1223 (ManE), beta-1,4-mannobiose; and TM1226 (ManD), beta-1,4-mannobiose, beta-1,4-mannotriose, beta-1,4-mannotetraose, beta-1,4-galactosyl mannobiose, and cellobiose. For comparison, seven bacterial putative sugar-binding proteins were examined and ligands for three (TM0595, TM0810, and TM1855) were not identified. The ligands for these bacterial SBPs are TM0114 (XylE), xylose; TM0418 (InoE), myo-inositol; TM0432 (AguE), alpha-1,4-digalactouronic acid; and TM0958 (RbsB), ribose. We found that T. maritima does not grow on several complex polypeptide mixtures as sole sources of carbon and nitrogen, so it is unlikely that these archaeal ABC transporters are used primarily for oligopeptide transport. Since these SBPs bind oligosaccharides with micromolar to nanomolar affinities, we propose that they are used primarily for oligosaccharide transport.}, }
@article {pmid16453141, year = {2006}, author = {Lindsay, JA and Holden, MT}, title = {Understanding the rise of the superbug: investigation of the evolution and genomic variation of Staphylococcus aureus.}, journal = {Functional &amp; integrative genomics}, volume = {6}, number = {3}, pages = {186-201}, pmid = {16453141}, issn = {1438-793X}, mesh = {Drug Resistance/*genetics ; *Evolution, Molecular ; Forecasting ; Gene Transfer, Horizontal ; *Genetic Variation ; Genome, Bacterial ; *Genomics ; Humans ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Staphylococcus aureus/*genetics/*pathogenicity ; }, abstract = {The bacterium Staphylococcus aureus is a common cause of human infection, and it is becoming increasingly virulent and resistant to antibiotics. Our understanding of the evolution of this species has been greatly enhanced by the recent sequencing of the genomes of seven strains of S. aureus. Comparative genomic analysis allows us to identify variation in the chromosomes and understand the mechanisms by which this versatile bacterium has accumulated diversity within its genome structure.}, }
@article {pmid16452813, year = {2003}, author = {Hao, B and Qi, J}, title = {Prokaryote phylogeny without sequence alignment: from avoidance signature to composition distance.}, journal = {Proceedings. IEEE Computer Society Bioinformatics Conference}, volume = {2}, number = {}, pages = {375-384}, pmid = {16452813}, issn = {1555-3930}, mesh = {Base Composition ; Base Sequence ; Computer Simulation ; DNA Mutational Analysis/*methods ; DNA, Bacterial/*genetics ; *Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Recombination, Genetic/*genetics ; Sequence Alignment ; Sequence Analysis, DNA/*methods ; Signal Transduction/*genetics ; }, abstract = {A new and essentially simple method to reconstruct prokaryotic phylogenetic trees from their complete genome data without using sequence alignment is proposed. It is based on the appearance frequency of oligopeptides of a fixed length (up to K = 6) in their proteomes. This is a method without fine adjustment and choice of genes. It can incorporate the effect of lateral gene transfer to some extent and leads to results comparable with the bacteriologists' systematics as reflected in the latest 2001 edition of the Bergey's Manual of Systematic Bacteriology [1, 2]. A key point in our approach is subtraction of a random background by using a Markovian model of order K - 1 from the composition vectors to highlight the shaping role of natural selection.}, }
@article {pmid16451411, year = {2006}, author = {Agodi, A and Zarrilli, R and Barchitta, M and Anzaldi, A and Di Popolo, A and Mattaliano, A and Ghiraldi, E and Travali, S}, title = {Alert surveillance of intensive care unit-acquired Acinetobacter infections in a Sicilian hospital.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {12}, number = {3}, pages = {241-247}, doi = {10.1111/j.1469-0691.2005.01339.x}, pmid = {16451411}, issn = {1198-743X}, mesh = {Acinetobacter Infections/*epidemiology ; Acinetobacter baumannii/drug effects/*genetics ; Anti-Bacterial Agents/pharmacology ; Cross Infection/*epidemiology ; Drug Resistance, Microbial ; Electrophoresis, Gel, Pulsed-Field ; Gene Transfer, Horizontal ; Humans ; Imipenem/pharmacology ; Integrons/genetics ; *Intensive Care Units ; Italy/epidemiology ; Meropenem ; Morbidity ; Pneumonia, Bacterial/epidemiology ; Thienamycins/pharmacology ; }, abstract = {The epidemiological impact of Acinetobacter baumannii nosocomial infections in a Sicilian intensive care unit (ICU) was investigated to determine the Acinetobacter-specific infection rates, to estimate the preventable proportion of Acinetobacter infections, i.e., those resulting from cross-transmission, and to investigate the molecular epidemiology of antimicrobial resistance in Acinetobacter. The impact of Acinetobacter nosocomial infection in the ICU was determined to be 3.0 new cases per 100 admissions. Site-specific rates confirmed that ICU-acquired pneumonia was the most important infection type. The incidence rate, adjusted by the number of patient-days, was 3.3 infections/1000 patient-days. The estimated preventable proportion of A. baumannii nosocomial infections in the ICU was 66.7%. A class 1 integron, characterised by its gene cassette content, was present in all A. baumannii isolates of four different pulsed-field gel electrophoresis types, and was associated significantly with clones implicated in cross-transmission episodes. Furthermore, the same integron was detected in two genetically distinct isolates responsible for recurrent infection in the same patient, suggesting the occurrence of horizontal gene transfer in vivo. Even in an endemic setting with low infection rates, spread of A. baumannii was caused mainly by infection control shortcomings that require appropriate surveillance and control policies.}, }
@article {pmid16451182, year = {2006}, author = {Su, J and Shi, L and Yang, L and Xiao, Z and Li, X and Yamasaki, S}, title = {Analysis of integrons in clinical isolates of Escherichia coli in China during the last six years.}, journal = {FEMS microbiology letters}, volume = {254}, number = {1}, pages = {75-80}, doi = {10.1111/j.1574-6968.2005.00025.x}, pmid = {16451182}, issn = {0378-1097}, mesh = {Anti-Bacterial Agents/pharmacology ; China/epidemiology ; Drug Resistance, Bacterial/genetics ; Escherichia coli/drug effects/enzymology/*genetics/isolation &amp; purification ; Escherichia coli Infections/epidemiology/microbiology ; Escherichia coli Proteins/*genetics ; Humans ; Integrases/*genetics ; *Integrons ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA ; }, abstract = {A multiple PCR for the detection of the integrase genes of the three classes of integrons was carried out, and their gene cassettes were characterized in 111 clinical strains of Escherichia coli isolated in Guangzhou City, China during the last 6 years. IntI1 and intI2 genes were detected in 95 isolates (85.6%) and four isolates (3.6%), respectively. No intI3 gene was detected. Six different gene cassettes were found in these strains, and a high prevalence of dfr and aad genes was observed. The E. coli isolates that contained a 1664-bp amplicon of dfrA17-aadA5 in class 1 integron were found to be phylogenetically unrelated to each other by using the enterobacterial repetitive intergenic consensus PCR, as the cassette could be transferred to recipient strains, indicating that the gene cassettes might be disseminated in the clinical strains by a horizontal gene transfer. Therefore, it is important that guidelines for the prudent use of antimicrobial agents are adopted and surveillance programs are established.}, }
@article {pmid16451175, year = {2006}, author = {Bourgeois-Nicolaos, N and Moubareck, C and Mangeney, N and Butel, MJ and Doucet-Populaire, F}, title = {Comparative study of vanA gene transfer from Enterococcus faecium to Enterococcus faecalis and to Enterococcus faecium in the intestine of mice.}, journal = {FEMS microbiology letters}, volume = {254}, number = {1}, pages = {27-33}, doi = {10.1111/j.1574-6968.2005.00004.x}, pmid = {16451175}, issn = {0378-1097}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics ; Carbon-Oxygen Ligases/*genetics ; Conjugation, Genetic ; Enterococcus faecalis/*drug effects/genetics ; Enterococcus faecium/*drug effects/genetics ; Feces/microbiology ; *Gene Transfer, Horizontal ; *Germ-Free Life ; Humans ; Intestines/*microbiology ; Mice ; Microbial Sensitivity Tests ; }, abstract = {Vancomycin-resistant enterococci represent a large reservoir in animals because of the use of avoparcin as a growth promoter in Europe. These strains of animal origin enter the food chain and can either colonize the human gut or transfer their resistance genes to the human microbiota. In this study, we compared the transfer of vancomycin resistance from resistant animal Enterococcus faecium to sensitive human Enterococcus faecalis and E. faecium. We analysed these transfers in dibiotic mice and human faecal flora-associated mice. VanA transfer from animal E. faecium to human E. faecalis occurred in dibiotic mice. The transconjugants appeared rapidly and persisted at levels between 3.0 and 4.0 log10 colony-forming units g(-1) of faeces. In human faecal flora-associated mice, vanA gene transfer was not detected towards E. faecalis but was possible between E. faecium strains. Our experiments revealed the possibility of vanA transfer from animal E. faecium to human E. faecalis in vitro and in vivo in the intestine of dibiotic mice. However, intraspecies transfer of vanA gene seems more common than interspecies transfer among enterococci.}, }
@article {pmid16447967, year = {2005}, author = {Nakhleh, L and Jin, G and Zhao, F and Mellor-Crummey, J}, title = {Reconstructing phylogenetic networks using maximum parsimony.}, journal = {Proceedings. IEEE Computational Systems Bioinformatics Conference}, volume = {}, number = {}, pages = {93-102}, doi = {10.1109/csb.2005.47}, pmid = {16447967}, issn = {1551-7497}, mesh = {*Algorithms ; *Biological Evolution ; Chromosome Mapping/*methods ; Computer Simulation ; DNA Mutational Analysis/*methods ; *Evolution, Molecular ; *Models, Genetic ; *Phylogeny ; }, abstract = {Phylogenies - the evolutionary histories of groups of organisms - are one of the most widely used tools throughout the life sciences, as well as objects of research within systematics, evolutionary biology, epidemiology, etc. Almost every tool devised to date to reconstruct phylogenies produces trees; yet it is widely understood and accepted that trees oversimplify the evolutionary histories of many groups of organims, most prominently bacteria (because of horizontal gene transfer) and plants (because of hybrid speciation). Various methods and criteria have been introduced for phylogenetic tree reconstruction. Parsimony is one of the most widely used and studied criteria, and various accurate and efficient heuristics for reconstructing trees based on parsimony have been devised. Jotun Hein suggested a straightforward extension of the parsimony criterion to phylogenetic networks. In this paper we formalize this concept, and provide the first experimental study of the quality of parsimony as a criterion for constructing and evaluating phylogenetic networks. Our results show that, when extended to phylogenetic networks, the parsimony criterion produces promising results. In a great majority of the cases in our experiments, the parsimony criterion accurately predicts the numbers and placements of non-tree events.}, }
@article {pmid16445749, year = {2006}, author = {Wang, HH and Manuzon, M and Lehman, M and Wan, K and Luo, H and Wittum, TE and Yousef, A and Bakaletz, LO}, title = {Food commensal microbes as a potentially important avenue in transmitting antibiotic resistance genes.}, journal = {FEMS microbiology letters}, volume = {254}, number = {2}, pages = {226-231}, doi = {10.1111/j.1574-6968.2005.00030.x}, pmid = {16445749}, issn = {0378-1097}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/*genetics/growth &amp; development ; Bacterial Proteins/*genetics ; Cheese/microbiology ; Drug Resistance, Bacterial/*genetics ; *Food Microbiology ; *Gene Transfer, Horizontal ; Gram-Positive Cocci/drug effects/genetics ; Humans ; Transformation, Bacterial ; }, abstract = {The rapid emergence of antibiotic-resistant (ART) pathogens is a major threat to public health. While the surfacing of ART food-borne pathogens is alarming, the magnitude of the antibiotic resistance (AR) gene pool in food-borne commensal microbes is yet to be revealed. Incidence of ART commensals in selected retail food products was examined in this study. The presence of 10(2)-10(7) CFU of ART bacteria per gram of foods in many samples, particularly in ready-to-eat, 'healthy' food items, indicates that the ART bacteria are abundant in the food chain. AR-encoding genes were detected in ART isolates, and Streptococcus thermophilus was found to be a major host for AR genes in cheese microbiota. Lactococcus lactis and Leuconostoc sp. isolates were also found carrying AR genes. The data indicate that food could be an important avenue for ART bacterial evolution and dissemination. AR-encoding plasmids from several food-borne commensals were transmitted to Streptococcus mutans via natural gene transformation under laboratory conditions, suggesting the possible transfer of AR genes from food commensals to human residential bacteria via horizontal gene transfer.}, }
@article {pmid16443252, year = {2006}, author = {Bastone, P and Bravo, IG and Löchelt, M}, title = {Feline foamy virus-mediated marker gene transfer: identification of essential genetic elements and influence of truncated and chimeric proteins.}, journal = {Virology}, volume = {348}, number = {1}, pages = {190-199}, doi = {10.1016/j.virol.2005.12.022}, pmid = {16443252}, issn = {0042-6822}, mesh = {5' Untranslated Regions ; Cell Line ; *Gene Transfer Techniques ; *Gene Transfer, Horizontal ; Genes, Reporter ; Genes, pol ; *Genetic Vectors ; Green Fluorescent Proteins/analysis/genetics ; Humans ; Immunoblotting ; RNA, Viral/genetics/*physiology ; Sequence Deletion ; Spumavirus/*genetics ; Viral Proteins/analysis ; beta-Galactosidase/analysis/genetics ; }, abstract = {Retroviral vectors derived from foamy or spumaretroviruses are considered promising tools for targeted gene delivery and vaccination purposes. In order to fully exploit this potential, we identified essential cis-acting sequences on the feline foamy virus (FFV) genome by constructing and analyzing a series of FFV-based replication-deficient vector genomes. Cis-acting sequences essentially required for marker gene transfer were found to be localized at two sites on the FFV genome: (i) in the 5'-untranslated region and close to the gag ATG and (ii) in the central part of the pol gene. The presence of two cis-acting sequences and their relative location on the FFV genome are similar but not identical to the functionally corresponding elements described for simian and primate foamy viruses.}, }
@article {pmid16441461, year = {2006}, author = {Lorino, G and Gherardi, G and Angeletti, S and De Cesaris, M and Graziano, N and Maringhini, S and Merlino, F and Di Bernardo, F and Dicuonzo, G}, title = {Molecular characterisation and clonal analysis of group A streptococci causing pharyngitis among paediatric patients in Palermo, Italy.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {12}, number = {2}, pages = {189-192}, doi = {10.1111/j.1469-0691.2005.01329.x}, pmid = {16441461}, issn = {1198-743X}, mesh = {Adolescent ; Antigens, Bacterial/genetics ; Bacterial Outer Membrane Proteins/genetics ; Bacterial Proteins/genetics ; Carrier Proteins/genetics ; Child ; Child, Preschool ; DNA, Bacterial/analysis/chemistry/genetics ; Drug Resistance, Bacterial/genetics ; Exotoxins/genetics ; Gene Transfer, Horizontal ; Genotype ; Humans ; Italy ; Macrolides/pharmacology ; Membrane Proteins/genetics ; Microbial Sensitivity Tests ; Peptide Hydrolases/genetics ; Pharyngitis/*microbiology ; Phenotype ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Streptococcal Infections/*microbiology ; Streptococcus pyogenes/*classification/*genetics/isolation &amp; purification ; }, abstract = {Group A streptococci (n = 123), isolated consecutively from paediatric patients with pharyngitis from Palermo, Italy, were analysed. The emm and sof genes were sequenced, the presence of the speA and speC genes was investigated, and the macrolide resistance phenotypes and genotypes were determined. A limited number of emm/sof genotypes was found, and the most prevalent types were different from those found in a previous study from Rome. Macrolide resistance was found in the most prevalent clones, suggesting that the spread of mobile antibiotic resistance genes among the fittest clones in the community was the main mechanism influencing macrolide resistance rates in different emm types.}, }
@article {pmid16436707, year = {2006}, author = {Wachino, J and Kurokawa, H and Suzuki, S and Yamane, K and Shibata, N and Kimura, K and Ike, Y and Arakawa, Y}, title = {Horizontal transfer of blaCMY-bearing plasmids among clinical Escherichia coli and Klebsiella pneumoniae isolates and emergence of cefepime-hydrolyzing CMY-19.}, journal = {Antimicrobial agents and chemotherapy}, volume = {50}, number = {2}, pages = {534-541}, pmid = {16436707}, issn = {0066-4804}, mesh = {Amino Acid Sequence ; Blotting, Southern ; Cefepime ; Cephalosporins/*metabolism ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/drug effects/*genetics ; *Gene Transfer, Horizontal ; Humans ; Isoelectric Focusing ; Klebsiella pneumoniae/drug effects/*genetics ; Molecular Sequence Data ; Plasmids ; Structure-Activity Relationship ; beta-Lactam Resistance ; beta-Lactamases/*genetics ; }, abstract = {Nine Escherichia coli and 5 Klebsiella pneumoniae clinical isolates resistant to various cephalosporins and cephamycins were identified in a Japanese general hospital between 1995 and 1997. All nine E. coli isolates and one K. pneumoniae isolate carried bla(CMY-9), while the other four K. pneumoniae isolates harbored a variant of bla(CMY-9), namely, bla(CMY-19). The pulsed-field gel electrophoresis patterns of the nine CMY-9-producing E. coli isolates were almost identical, suggesting their clonal relatedness, while those of the five K. pneumoniae isolates were divergent. Plasmid profiles, Southern hybridization, and conjugation assays revealed that the genes for the CMY-9 and the CMY-19 beta-lactamases were located on very similar conjugative plasmids in E. coli and K. pneumoniae. The genetic environment of bla(CMY-19) was identical to that of bla(CMY-9). A single amino acid substitution, I292S, adjacent to the H-10 helix region was observed between CMY-9 and CMY-19. This substitution was suggested to be responsible for the expansion of the hydrolyzing activity against several broad-spectrum cephalosporins, and this finding was consistent with the kinetic parameters determined with purified enzymes. These findings suggest that the bla(CMY-19) genes found in the four K. pneumoniae isolates might have originated from bla(CMY-9) gene following a point mutation and dispersed among genetically different K. pneumoniae isolates via a large transferable plasmid.}, }
@article {pmid16436438, year = {2006}, author = {Moreira, D and Rodríguez-Valera, F and López-García, P}, title = {Metagenomic analysis of mesopelagic Antarctic plankton reveals a novel deltaproteobacterial group.}, journal = {Microbiology (Reading, England)}, volume = {152}, number = {Pt 2}, pages = {505-517}, doi = {10.1099/mic.0.28254-0}, pmid = {16436438}, issn = {1350-0872}, mesh = {Antarctic Regions ; DNA, Bacterial/analysis ; DNA, Ribosomal/analysis ; Deltaproteobacteria/enzymology/*genetics/growth &amp; development ; Genome, Bacterial ; Molecular Sequence Data ; Plankton ; RNA, Ribosomal, 16S/analysis/genetics ; }, abstract = {Phylogenetic screening of 3200 clones from a metagenomic library of Antarctic mesopelagic picoplankton allowed the identification of two bacterial 16S-rDNA-containing clones belonging to the Deltaproteobacteria, DeepAnt-1F12 and DeepAnt-32C6. These clones were very divergent, forming a monophyletic cluster with the environmental sequence GR-WP33-58 that branched at the base of the myxobacteria. Except for the possession of complete rrn operons without associated tRNA genes, DeepAnt-1F12 and DeepAnt-32C6 were very different in gene content and organization. Gene density was much higher in DeepAnt-32C6, whereas nearly one-third of DeepAnt-1F12 corresponded to intergenic regions. Many of the predicted genes encoded by these metagenomic clones were informational (i.e. involved in replication, transcription, translation and related processes). Despite this, a few putative cases of horizontal gene transfer were detected, including a transposase. DeepAnt-1F12 contained one putative gene encoding a long cysteine-rich protein, probably membrane-bound and Ca2+-binding, with only eukaryotic homologues. DeepAnt-32C6 carried some predicted genes involved in metabolic pathways that suggested this organism may be anaerobic and able to ferment and to degrade complex compounds extracellularly.}, }
@article {pmid16436211, year = {2006}, author = {Griffiths, E and Ventresca, MS and Gupta, RS}, title = {BLAST screening of chlamydial genomes to identify signature proteins that are unique for the Chlamydiales, Chlamydiaceae, Chlamydophila and Chlamydia groups of species.}, journal = {BMC genomics}, volume = {7}, number = {}, pages = {14}, pmid = {16436211}, issn = {1471-2164}, mesh = {Algorithms ; Chlamydia/*genetics ; Chlamydiaceae/*genetics ; Chlamydiales/*genetics ; Chlamydophila/*genetics ; Computational Biology/*methods ; Gene Expression Profiling ; Genome ; *Sequence Analysis, DNA ; Software ; Species Specificity ; }, abstract = {BACKGROUND: Chlamydiae species are of much importance from a clinical viewpoint. Their diversity both in terms of their numbers as well as clinical involvement are presently believed to be significantly underestimated. The obligate intracellular nature of chlamydiae has also limited their genetic and biochemical studies. Thus, it is of importance to develop additional means for their identification and characterization.<br><br>RESULTS: We have carried out analyses of available chlamydiae genomes to identify sets of unique proteins that are either specific for all Chlamydiales genomes, or different Chlamydiaceae family members, or members of the Chlamydia and Chlamydophila genera, or those unique to Protochlamydia amoebophila, but which are not found in any other bacteria. In total, 59 Chlamydiales-specific proteins, 79 Chlamydiaceae-specific proteins, 20 proteins each that are specific for both Chlamydia and Chlamydophila and 445 ORFs that are Protochlamydia-specific were identified. Additionally, 33 cases of possible gene loss or lateral gene transfer were also detected.<br><br>CONCLUSION: The identified chlamydiae-lineage specific proteins, many of which are highly conserved, provide novel biomarkers that should prove of much value in the diagnosis of these bacteria and in exploration of their prevalence and diversity. These conserved protein sequences (CPSs) also provide novel therapeutic targets for drugs that are specific for these bacteria. Lastly, functional studies on these chlamydiae or chlamydiae subgroup-specific proteins should lead to important insights into lineage-specific adaptations with regards to development, infectivity and pathogenicity.}, }
@article {pmid16436070, year = {2006}, author = {Maeda, S and Ito, M and Ando, T and Ishimoto, Y and Fujisawa, Y and Takahashi, H and Matsuda, A and Sawamura, A and Kato, S}, title = {Horizontal transfer of nonconjugative plasmids in a colony biofilm of Escherichia coli.}, journal = {FEMS microbiology letters}, volume = {255}, number = {1}, pages = {115-120}, doi = {10.1111/j.1574-6968.2005.00072.x}, pmid = {16436070}, issn = {0378-1097}, mesh = {Biofilms/*growth &amp; development ; Culture Media ; Escherichia coli/*genetics/growth &amp; development ; *Gene Transfer, Horizontal ; Plasmids/*genetics ; Transformation, Bacterial/*genetics ; }, abstract = {We tested the possibility of nonconjugative lateral DNA transfer in a colony biofilm of mixed Escherichia coli strains. By simply coculturing a plasmid-free F(-) strain and another F(-) strain harboring a nonconjugative plasmid in a colony biofilm on antibiotic-free agar media, transformed cells were produced within 24-48 h at the frequency of 10(-10)-10(-9) per recipient cell. PCR analysis of the transformed cells demonstrated the occurrence of lateral plasmid transfer. These cells survived until at least day 7 under antibiotic-free conditions. Liquid cultures of the same strains in Luria-Bertani broth produced no or few transformants, suggesting the importance of colony-biofilm formation for plasmid transfer. This is a novel line of evidence indicating that nonconjugative, nonviral horizontal gene transfer can occur between E. coli cells.}, }
@article {pmid16431085, year = {2006}, author = {Ouzounis, CA and Kunin, V and Darzentas, N and Goldovsky, L}, title = {A minimal estimate for the gene content of the last universal common ancestor--exobiology from a terrestrial perspective.}, journal = {Research in microbiology}, volume = {157}, number = {1}, pages = {57-68}, doi = {10.1016/j.resmic.2005.06.015}, pmid = {16431085}, issn = {0923-2508}, mesh = {Algorithms ; *Earth, Planet ; *Evolution, Molecular ; *Exobiology ; Gene Transfer, Horizontal ; *Genome ; *Phylogeny ; }, abstract = {Using an algorithm for ancestral state inference of gene content, given a large number of extant genome sequences and a phylogenetic tree, we aim to reconstruct the gene content of the last universal common ancestor (LUCA), a hypothetical life form that presumably was the progenitor of the three domains of life. The method allows for gene loss, previously found to be a major factor in shaping gene content, and thus the estimate of LUCA's gene content appears to be substantially higher than that proposed previously, with a typical number of over 1000 gene families, of which more than 90% are also functionally characterized. More precisely, when only prokaryotes are considered, the number varies between 1006 and 1189 gene families while when eukaryotes are also included, this number increases to between 1344 and 1529 families depending on the underlying phylogenetic tree. Therefore, the common belief that the hypothetical genome of LUCA should resemble those of the smallest extant genomes of obligate parasites is not supported by recent advances in computational genomics. Instead, a fairly complex genome similar to those of free-living prokaryotes, with a variety of functional capabilities including metabolic transformation, information processing, membrane/transport proteins and complex regulation, shared between the three domains of life, emerges as the most likely progenitor of life on Earth, with profound repercussions for planetary exploration and exobiology.}, }
@article {pmid16428786, year = {2006}, author = {Phongsisay, V and Perera, VN and Fry, BN}, title = {Exchange of lipooligosaccharide synthesis genes creates potential Guillain-Barre syndrome-inducible strains of Campylobacter jejuni.}, journal = {Infection and immunity}, volume = {74}, number = {2}, pages = {1368-1372}, pmid = {16428786}, issn = {0019-9567}, mesh = {Bacterial Proteins/*genetics ; Campylobacter jejuni/classification/*genetics/metabolism ; DNA, Bacterial/analysis/genetics ; Electrophoresis, Gel, Pulsed-Field ; G(M1) Ganglioside/metabolism ; *Gene Transfer, Horizontal ; Guillain-Barre Syndrome/etiology/*microbiology ; Humans ; Lipopolysaccharides/*biosynthesis ; Molecular Mimicry ; Multigene Family ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Recombination, Genetic ; *Transformation, Bacterial ; }, abstract = {Human ganglioside-like structures, such as GM1, found on some Campylobacter jejuni strains have been linked to inducing the Guillain-Barré Syndrome (GBS). This study shows that a C. jejuni strain without GM1-like molecules acquired large DNA fragments, including lipooligosaccharide synthesis genes, from a strain expressing GM1-like molecules and consequently transformed into a number of potential GBS-inducible transformants, which exhibited a high degree of genetic and phenotypic diversity.}, }
@article {pmid16428417, year = {2006}, author = {Rokyta, DR and Burch, CL and Caudle, SB and Wichman, HA}, title = {Horizontal gene transfer and the evolution of microvirid coliphage genomes.}, journal = {Journal of bacteriology}, volume = {188}, number = {3}, pages = {1134-1142}, pmid = {16428417}, issn = {0021-9193}, support = {P20 RR016448/RR/NCRR NIH HHS/United States ; P20 RR016454/RR/NCRR NIH HHS/United States ; P20 RR16448/RR/NCRR NIH HHS/United States ; P20 RR16454/RR/NCRR NIH HHS/United States ; }, mesh = {Coliphages/*genetics/pathogenicity ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Viral/genetics ; Genetic Variation/genetics ; *Genome, Viral ; Microviridae/genetics ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Bacteriophage genomic evolution has been largely characterized by rampant, promiscuous horizontal gene transfer involving both homologous and nonhomologous source DNA. This pattern has emerged through study of the tailed double-stranded DNA (dsDNA) phages and is based upon a sparse sampling of the enormous diversity of these phages. The single-stranded DNA phages of the family Microviridae, including phiX174, appear to evolve through qualitatively different mechanisms, possibly as result of their strictly lytic lifestyle and small genome size. However, this apparent difference could reflect merely a dearth of relevant data. We sought to characterize the forces that contributed to the molecular evolution of the Microviridae and to examine the genetic structure of this single family of bacteriophage by sequencing the genomes of microvirid phage isolated on a single bacterial host. Microvirids comprised 3.5% of the detectable phage in our environmental samples, and sequencing yielded 42 new microvirid genomes. Phylogenetic analysis of the genes contained in these and five previously described microvirid phages identified three distinct clades and revealed at least two horizontal transfer events between clades. All members of one clade have a block of five putative genes that are not present in any member of the other two clades. Our data indicate that horizontal transfer does contribute to the evolution of the microvirids but is both quantitatively and qualitatively different from what has been observed for the dsDNA phages.}, }
@article {pmid16428394, year = {2006}, author = {Zhong, J and Skouloubris, S and Dai, Q and Myllykallio, H and Barbour, AG}, title = {Function and evolution of plasmid-borne genes for pyrimidine biosynthesis in Borrelia spp.}, journal = {Journal of bacteriology}, volume = {188}, number = {3}, pages = {909-918}, pmid = {16428394}, issn = {0021-9193}, support = {R01 AI024424/AI/NIAID NIH HHS/United States ; R37 AI024424/AI/NIAID NIH HHS/United States ; AI24424/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Biological Evolution ; Borrelia/classification/*genetics/metabolism ; DNA, Bacterial/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Lyme Disease ; Molecular Sequence Data ; Phylogeny ; Plasmids/*genetics ; Pyrimidines/*biosynthesis/metabolism ; }, abstract = {The thyX gene for thymidylate synthase of the Lyme borreliosis (LB) agent Borrelia burgdorferi is located in a 54-kb linear plasmid. In the present study, we identified an orthologous thymidylate synthase gene in the relapsing fever (RF) agent Borrelia hermsii, located it in a 180-kb linear plasmid, and demonstrated its expression. The functions of the B. hermsii and B. burgdorferi thyX gene products were evaluated both in vivo, by complementation of a thymidylate synthase-deficient Escherichia coli mutant, and in vitro, by testing their activities after purification. The B. hermsii thyX gene complemented the thyA mutation in E. coli, and purified B. hermsii ThyX protein catalyzed the conversion of dTMP from dUMP. In contrast, the B. burgdorferi ThyX protein had only weakly detectable activity in vitro, and the B. burgdorferi thyX gene did not provide complementation in vivo. The lack of activity of B. burgdorferi's ThyX protein was associated with the substitution of a cysteine for a highly conserved arginine at position 91. The B. hermsii thyX locus was further distinguished by the downstream presence in the plasmid of orthologues of nrdI, nrdE, and nrdF, which encode the subunits of ribonucleoside diphosphate reductase and which are not present in the LB agents B. burgdorferi and Borrelia garinii. Phylogenetic analysis suggested that the nrdIEF cluster of B. hermsii was acquired by horizontal gene transfer. These findings indicate that Borrelia spp. causing RF have a greater capability for de novo pyrimidine synthesis than those causing LB, thus providing a basis for some of the biological differences between the two groups of pathogens.}, }
@article {pmid16423843, year = {2006}, author = {Parikh, MR and Greene, DN and Woods, KK and Matsumura, I}, title = {Directed evolution of RuBisCO hypermorphs through genetic selection in engineered E.coli.}, journal = {Protein engineering, design &amp; selection : PEDS}, volume = {19}, number = {3}, pages = {113-119}, pmid = {16423843}, issn = {1741-0126}, support = {R21 AI054602/AI/NIAID NIH HHS/United States ; R21 AI054602-02/AI/NIAID NIH HHS/United States ; T32 GM008367/GM/NIGMS NIH HHS/United States ; 1 R21 AI054602-01/AI/NIAID NIH HHS/United States ; }, mesh = {Blotting, Western ; Carbon Dioxide/metabolism ; Cloning, Molecular ; DNA, Bacterial ; *Directed Molecular Evolution ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Engineering/*methods ; Genetic Variation ; Kinetics ; Mutation ; Ribulose-Bisphosphate Carboxylase/chemistry/*genetics/isolation &amp; purification/*metabolism ; *Selection, Genetic ; Sequence Analysis, DNA ; Species Specificity ; Synechococcus/enzymology/growth &amp; development ; }, abstract = {The Calvin Cycle is the primary conduit for the fixation of carbon dioxide into the biosphere; ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) catalyzes the rate-limiting fixation step. Our goal is to direct the evolution of RuBisCO variants with improved kinetic and biophysical properties. The Calvin Cycle was partially reconstructed in Escherichia coli; the engineered strain requires the Synechococcus PCC6301 RuBisCO for growth in minimal media supplemented with a pentose. We randomly mutated the gene encoding the large subunit of RuBisCO (rbcL), co-expressed the resulting library with the small subunit (rbcS) and the Synechococcus PCC7492 phosphoribulokinase (prkA), and selected hypermorphic variants. The RuBisCO variants that evolved during three rounds of random mutagenesis and selection were over-expressed, and exhibited 5-fold improvement in specific activity relative to the wild-type enzyme. These results demonstrate a new strategy for the artificial selection of RuBisCO and other non-native metabolic enzymes.}, }
@article {pmid16423651, year = {2006}, author = {Lapierre, P and Shial, R and Gogarten, JP}, title = {Distribution of F- and A/V-type ATPases in Thermus scotoductus and other closely related species.}, journal = {Systematic and applied microbiology}, volume = {29}, number = {1}, pages = {15-23}, doi = {10.1016/j.syapm.2005.06.004}, pmid = {16423651}, issn = {0723-2020}, mesh = {Adenosine Triphosphatases/*genetics/metabolism ; Amino Acid Sequence ; Base Sequence ; Blotting, Southern ; DNA, Bacterial/chemistry/genetics ; Evolution, Molecular ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/chemistry/genetics ; Sequence Alignment ; Thermus/*enzymology/genetics ; Vacuolar Proton-Translocating ATPases/genetics/metabolism ; }, abstract = {The presence of an A/V-type ATPase in different Thermus species and in the deeper branching species Meiothermus ruber and Deinococcus radiodurans suggests that the presence of the archaeal-type ATPase is a primitive character of the Deinococci that was acquired through horizontal gene transfer (HGT). However, the presence of a bacterial type F-ATPases was reported in two newly identified Thermus species (Thermus scotoductus DSM 8553 and Thermus filiformis DSM 4687). Two different scenarios can explain this finding, either the recent replacement of the ancestral A/V-type ATPase in Thermus scotoductus and Thermus filiformis with a newly acquired F-type ATPase or a long-term persistence of both F and A type ATPase in the Deinococci, which would imply several independent losses of the F-type ATPase in the Deinococci. Using PCR with redundant primers, sequencing and Southern blot analyses, we tried to confirm the presence of an F-type ATPase in the genome of Thermus scotoductus and Thermus filiformis, and determine its phylogenetic affinities. Initial experiments appeared to confirm the presence of an F-type ATPase in Thermus scotoductus that was similar to the F-ATPases found in Bacillus. However, further experiments revealed that the detection of an F-ATPase was due to a culture contamination. For all the Thermus and Deinococcus species surveyed, including Thermus scotoductus, cultures that were free of contamination only contained an A/V-type ATP synthases.}, }
@article {pmid16423473, year = {2006}, author = {McCuddin, ZP and Carlson, SA and Rasmussen, MA and Franklin, SK}, title = {Klebsiella to Salmonella gene transfer within rumen protozoa: implications for antibiotic resistance and rumen defaunation.}, journal = {Veterinary microbiology}, volume = {114}, number = {3-4}, pages = {275-284}, doi = {10.1016/j.vetmic.2005.12.004}, pmid = {16423473}, issn = {0378-1135}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Base Sequence ; Cattle ; Ceftriaxone/pharmacology ; Cells, Cultured ; Colicins ; Conjugation, Genetic ; Drug Resistance, Bacterial/*genetics ; Eukaryota/*microbiology ; *Gene Transfer, Horizontal ; Goats ; Klebsiella/drug effects/*genetics ; Microbial Sensitivity Tests/veterinary ; Rumen/microbiology/parasitology ; Salmonella/drug effects/*genetics ; Sheep ; Species Specificity ; beta-Lactam Resistance/genetics ; }, abstract = {The rumen has long been thought to be a site of gene transfer for microorganisms. Rumen protozoa (RPz) are active predators of bacteria that can harbor antibiotic resistance genes. In this study, RPz were assessed as sites of gene transfer between two bacterial species, Salmonella and Klebsiella. One Klebsiella isolate carried a plasmid bearing bla(CMY-2), encoding an extended-spectrum beta-lactamase conferring ceftriaxone resistance, while the Salmonella was susceptible to ceftriaxone yet capable of thriving within protozoa. In vitro studies revealed that ceftriaxone-resistant Salmonella could be isolated following co-incubation of Salmonella and Klebsiella with RPz obtained from adult cattle and goats. Ceftriaxone-resistant Salmonella were not recovered in the presence of an inhibitor of protozoa engulfment or when a protozoa-sensitive Salmonella was part of the co-incubation. This transfer event was additionally observed in vitro for protozoa-independent stressors although at a significantly lower frequency. The gene transfer event was related to bacterial conjugation since a conjugation inhibitor, nalidixic acid, perturbed the phenomenon. Ceftriaxone-resistant Salmonella were recovered from calves, sheep, and goats co-challenged with ceftriaxone-resistant Klebsiella and ceftriaxone-sensitive Salmonella. However, the transfer event was not observed in calves and sheep that were defaunated prior to the co-challenge. Moreover, Salmonella transconjugants were isolated from separate bovine in vivo studies involving a Klebsiella donor carrying a plasmid conferring colicin activity while no such transconjugants were obtained from defaunated calves. These results provide an important basis for evaluating and preventing the spread of antibiotic resistance and other selective advantages for pathogens present in ruminants.}, }
@article {pmid16423350, year = {2006}, author = {Fukuda, Y and Okamura, Y and Takeyama, H and Matsunaga, T}, title = {Dynamic analysis of a genomic island in Magnetospirillum sp. strain AMB-1 reveals how magnetosome synthesis developed.}, journal = {FEBS letters}, volume = {580}, number = {3}, pages = {801-812}, doi = {10.1016/j.febslet.2006.01.003}, pmid = {16423350}, issn = {0014-5793}, mesh = {Gene Transfer Techniques ; Genes, Bacterial/*genetics ; Integrases/genetics/metabolism ; Magnetospirillum/*genetics/metabolism ; Repetitive Sequences, Nucleic Acid/*genetics ; *Sequence Analysis, DNA ; *Sequence Deletion ; }, abstract = {The entire structure of a 98 kb genomic region that abounds in genes related to magnetosome synthesis was first described in the Magnetospirillum sp. strain AMB-1. The deletion of this 98 kb genomic region and the circular form after excision from the chromosome was detected by PCR amplification. This strongly suggests that the region has undergone a lateral gene transfer. The region has the characteristics of a genomic island: low GC content, location between two repetitive sequences, and the presence of an integrase in the flanking region of the first repetitive sequence. This 98 kb genomic region has the potential for transfer by the integrase activity. Comparative genome analysis revealed other regions with a high concentration of orthologs in magnetic bacteria besides the 98 kb region, and magnetosome synthesis seemed to need not only the exogenous 98 kb region, but also other orthologs and individually originating genes.}, }
@article {pmid16420738, year = {2005}, author = {Li, Z and Wang, L and Zhong, Y}, title = {Detecting horizontal gene transfer with T-REX and RHOM programs.}, journal = {Briefings in bioinformatics}, volume = {6}, number = {4}, pages = {394-401}, doi = {10.1093/bib/6.4.394}, pmid = {16420738}, issn = {1467-5463}, mesh = {*Algorithms ; Animals ; Chromosome Mapping/*methods ; Computer Graphics ; Conserved Sequence/genetics ; Gene Transfer, Horizontal/*genetics ; Humans ; Programming Languages ; Sequence Alignment/*methods ; Sequence Analysis, DNA/*methods ; Sequence Homology, Nucleic Acid ; *Software ; *User-Computer Interface ; }, abstract = {As the Human Genome Project and other genome projects experience remarkable success and a flood of biological data is produced by means of high-throughout sequencing techniques, detection of horizontal gene transfer (HGT) becomes a promising field in bioinformatics. This review describes two freeware programs: T-REX for MS Windows and RHOM for Linux. T-REX is a graphical user interface program that offers functions to reconstruct the HGT network among the donor and receptor hosts from the gene and species distance matrices. RHOM is a set of command-line driven programs used to detect HGT in genomes. While T-REX impresses with a user-friendly interface and drawing of the reticulation network, the strength of RHOM is an extensive statistical framework of genome and the graphical display of the estimated sequence position probabilities for the candidate horizontally transferred genes.}, }
@article {pmid16420592, year = {2006}, author = {Hanssen, AM and Ericson Sollid, JU}, title = {SCCmec in staphylococci: genes on the move.}, journal = {FEMS immunology and medical microbiology}, volume = {46}, number = {1}, pages = {8-20}, doi = {10.1111/j.1574-695X.2005.00009.x}, pmid = {16420592}, issn = {0928-8244}, mesh = {Chromosomes, Bacterial/*genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genome, Bacterial ; *Interspersed Repetitive Sequences ; Methicillin/pharmacology ; Methicillin Resistance/*genetics ; Staphylococcus aureus/drug effects/*genetics ; }, abstract = {Staphylococcal cassette chromosome (SCC) elements are, so far, the only vectors described for the mecA gene encoding methicillin resistance in staphylococci. SCCmec elements are classified according to the type of recombinase they carry and their general genetic composition. SCCmec types I-V have been described, and SCC elements lacking mecA have also been reported. In this review, we summarize the current knowledge about SCC structure and distribution, including genetic variants and rudiments of the elements. Its origin is still unknown, but one assumes that staphylococcal cassette chromosome is transferred between staphylococci, and mecA-positive coagulase-negative staphylococci may be a potential reservoir for these elements. Staphylococcal genomes seem to change continuously as genetic elements move in and out, but no mechanism of transfer has been found responsible for moving SCC elements between different staphylococcal species. Observations suggesting de novo production of methicillin-resistant staphylococci and horizontal gene transfer of SCCmec will be discussed.}, }
@article {pmid16420365, year = {2006}, author = {Weissman, SJ and Chattopadhyay, S and Aprikian, P and Obata-Yasuoka, M and Yarova-Yarovaya, Y and Stapleton, A and Ba-Thein, W and Dykhuizen, D and Johnson, JR and Sokurenko, EV}, title = {Clonal analysis reveals high rate of structural mutations in fimbrial adhesins of extraintestinal pathogenic Escherichia coli.}, journal = {Molecular microbiology}, volume = {59}, number = {3}, pages = {975-988}, pmid = {16420365}, issn = {0950-382X}, support = {L40 AI057547/AI/NIAID NIH HHS/United States ; P01 DK053369/DK/NIDDK NIH HHS/United States ; R01 DK070906/DK/NIDDK NIH HHS/United States ; K08 AI057737/AI/NIAID NIH HHS/United States ; R01 GM060731-05/GM/NIGMS NIH HHS/United States ; }, mesh = {Adhesins, Escherichia coli/analysis/*genetics ; Alleles ; Clone Cells ; Escherichia coli/genetics/*pathogenicity ; Escherichia coli Infections/*microbiology ; Evolution, Molecular ; Female ; Fimbriae Proteins/analysis/*genetics ; Fimbriae, Bacterial/chemistry/genetics ; Gene Transfer, Horizontal ; *Genetic Variation ; Humans ; Point Mutation ; Vagina/microbiology ; Virulence/genetics ; }, abstract = {Type 1 fimbriae of Escherichia coli mediate mannose-specific adhesion to host epithelial surfaces and consist of a major, antigenically variable pilin subunit, FimA, and a minor, structurally conserved adhesive subunit, FimH, located on the fimbrial tip. We have analysed the variability of fimA and fimH in strains of vaginal and other origin that belong to one of the most prominent clonal groups of extraintestinal pathogenic E. coli, comprised of O1:K1-, O2:K1- and O18:K1-based serotypes. Multiple locus sequence typing (MLST) of this group revealed that the strains have identical (at all but one nucleotide position) eight housekeeping loci around the genome and belong to the ST95 complex defined by the publicly available E. coli MLST database. Multiple highly diverse fimA alleles have been introduced into the ST95 clonal complex via horizontal transfer, at a frequency comparable to that of genes defining the major O- and H-antigens. However, no further significant FimA diversification has occurred via point mutation after the transfers. In contrast, while fimH alleles also move horizontally (along with the fimA loci), they acquire point amino acid replacements at a higher rate than either housekeeping genes or fimA. These FimH mutations enhance binding to monomannose receptors and bacterial tropism for human vaginal epithelium. A similar pattern of rapid within-clonal structural evolution of the adhesive, but not pilin, subunit is also seen, respectively, in papG and papA alleles of the di-galactose-specific P-fimbriae. Thus, while structurally diverse pilin subunits of E. coli fimbriae are under selective pressure for frequent horizontal transfer between clones, the adhesive subunits of extraintestinal E. coli are under strong positive selection (Dn/Ds > 1 for fimH and papG) for functionally adaptive amino acid replacements.}, }
@article {pmid16420348, year = {2006}, author = {Zhao, A and Gray, FC and MacNeill, SA}, title = {ATP- and NAD+-dependent DNA ligases share an essential function in the halophilic archaeon Haloferax volcanii.}, journal = {Molecular microbiology}, volume = {59}, number = {3}, pages = {743-752}, doi = {10.1111/j.1365-2958.2005.04975.x}, pmid = {16420348}, issn = {0950-382X}, mesh = {Archaeal Proteins/classification/genetics/*physiology ; DNA Damage/physiology ; DNA Ligase ATP ; DNA Ligases/classification/genetics/*physiology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Haloferax volcanii/*enzymology/growth &amp; development/radiation effects ; Phylogeny ; }, abstract = {DNA ligases join the ends of DNA molecules during replication, repair and recombination. ATP-dependent ligases are found predominantly in the eukarya and archaea whereas NAD+-dependent DNA ligases are found only in the eubacteria and in entomopoxviruses. Using the genetically tractable halophile Haloferax volcanii as a model system, we describe the first genetic analysis of archaeal DNA ligase function. We show that the Hfx. volcanii ATP-dependent DNA ligase family member, LigA, is non-essential for cell viability, raising the question of how DNA strands are joined in its absence. We show that Hfx. volcanii also encodes an NAD+-dependent DNA ligase family member, LigN, the first such enzyme to be identified in the archaea, and present phylogenetic analysis indicating that the gene encoding this protein has been acquired by lateral gene transfer (LGT) from eubacteria. As with LigA, we show that LigN is also non-essential for cell viability. Simultaneous inactivation of both proteins is lethal, however, indicating that they now share an essential function. Thus the LigN protein acquired by LGT appears to have been co-opted as a back-up for LigA function, perhaps to provide additional ligase activity under conditions of high genotoxic stress.}, }
@article {pmid16417647, year = {2006}, author = {Boucher, Y and Nesbø, CL and Joss, MJ and Robinson, A and Mabbutt, BC and Gillings, MR and Doolittle, WF and Stokes, HW}, title = {Recovery and evolutionary analysis of complete integron gene cassette arrays from Vibrio.}, journal = {BMC evolutionary biology}, volume = {6}, number = {}, pages = {3}, pmid = {16417647}, issn = {1471-2148}, mesh = {DNA, Bacterial/genetics ; *Evolution, Molecular ; *Genes, Bacterial ; Genomic Library ; Integrases/genetics ; *Integrons ; Likelihood Functions ; *Mutagenesis, Insertional ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Vibrio/classification/enzymology/*genetics ; }, abstract = {BACKGROUND: Integrons are genetic elements capable of the acquisition, rearrangement and expression of genes contained in gene cassettes. Gene cassettes generally consist of a promoterless gene associated with a recombination site known as a 59-base element (59-be). Multiple insertion events can lead to the assembly of large integron-associated cassette arrays. The most striking examples are found in Vibrio, where such cassette arrays are widespread and can range from 30 kb to 150 kb. Besides those found in completely sequenced genomes, no such array has yet been recovered in its entirety. We describe an approach to systematically isolate, sequence and annotate large integron gene cassette arrays from bacterial strains.<br><br>RESULTS: The complete Vibrio sp. DAT722 integron cassette array was determined through the streamlined approach described here. To place it in an evolutionary context, we compare the DAT722 array to known vibrio arrays and performed phylogenetic analyses for all of its components (integrase, 59-be sites, gene cassette encoded genes). It differs extensively in terms of genomic context as well as gene cassette content and organization. The phylogenetic tree of the 59-be sites collectively found in the Vibrio gene cassette pool suggests frequent transfer of cassettes within and between Vibrio species, with slower transfer rates between more phylogenetically distant relatives. We also identify multiple cases where non-integron chromosomal genes seem to have been assembled into gene cassettes and others where cassettes have been inserted into chromosomal locations outside integrons.<br><br>CONCLUSION: Our systematic approach greatly facilitates the isolation and annotation of large integrons gene cassette arrays. Comparative analysis of the Vibrio sp. DAT722 integron obtained through this approach to those found in other vibrios confirms the role of this genetic element in promoting lateral gene transfer and suggests a high rate of gene gain/loss relative to most other loci on vibrio chromosomes. We identify a relationship between the phylogenetic distance separating two species and the rate at which they exchange gene cassettes, interactions between the non-mobile portion of bacterial genomes and the vibrio gene cassette pool as well as intragenomic translocation events of integrons in vibrios.}, }
@article {pmid16417203, year = {2005}, author = {Budowle, B and Johnson, MD and Fraser, CM and Leighton, TJ and Murch, RS and Chakraborty, R}, title = {Genetic analysis and attribution of microbial forensics evidence.}, journal = {Critical reviews in microbiology}, volume = {31}, number = {4}, pages = {233-254}, doi = {10.1080/10408410500304082}, pmid = {16417203}, issn = {1040-841X}, mesh = {*Bacterial Typing Techniques ; Bioterrorism ; DNA, Bacterial/*analysis ; *Forensic Medicine ; Humans ; Microbiological Techniques ; *Microbiology ; Nucleic Acid Amplification Techniques ; Oligonucleotide Array Sequence Analysis/instrumentation/methods ; Sequence Analysis, DNA ; }, abstract = {Because of the availability of pathogenic microorganisms and the relatively low cost of preparing and disseminating bioweapons, there is a continuing threat of biocrime and bioterrorism. Thus, enhanced capabilities are needed that enable the full and robust forensic exploitation and interpretation of microbial evidence from acts of bioterrorism or biocrimes. To respond to the need, greater resources and efforts are being applied to the burgeoning field of microbial forensics. Microbial forensics focuses on the characterization, analysis and interpretation of evidence for attributional purposes from a bioterrorism act, biocrime, hoax or inadvertent agent release. To enhance attribution capabilities, a major component of microbial forensics is the analysis of nucleic acids to associate or eliminate putative samples. The degree that attribution can be addressed depends on the context of the case, the available knowledge of the genetics, phylogeny, and ecology of the target microorganism, and technologies applied. The types of genetic markers and features that can impact statistical inferences of microbial forensic evidence include: single nucleotide polymorphisms, repetitive sequences, insertions and deletions, mobile elements, pathogenicity islands, virulence and resistance genes, house keeping genes, structural genes, whole genome sequences, asexual and sexual reproduction, horizontal gene transfer, conjugation, transduction, lysogeny, gene conversion, recombination, gene duplication, rearrangements, and mutational hotspots. Nucleic acid based typing technologies include: PCR, real-time PCR, MLST, MLVA, whole genome sequencing, and microarrays.}, }
@article {pmid16415014, year = {2006}, author = {Jern, P and Sperber, GO and Blomberg, J}, title = {Divergent patterns of recent retroviral integrations in the human and chimpanzee genomes: probable transmissions between other primates and chimpanzees.}, journal = {Journal of virology}, volume = {80}, number = {3}, pages = {1367-1375}, pmid = {16415014}, issn = {0022-538X}, mesh = {Animals ; Endogenous Retroviruses/*genetics/isolation &amp; purification ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome ; *Genome, Human ; Humans ; Macaca/genetics/virology ; Pan troglodytes/*genetics/*virology ; Papio/genetics/virology ; Phylogeny ; Primates/genetics/virology ; }, abstract = {The human genome is littered by endogenous retrovirus sequences (HERVs), which constitute up to 8% of the total genomic sequence. The sequencing of the human (Homo sapiens) and chimpanzee (Pan troglodytes) genomes has facilitated the evolutionary study of ERVs and related sequences. We screened both the human genome (version hg16) and the chimpanzee genome (version PanTro1) for ERVs and conducted a phylogenetic analysis of recent integrations. We found a number of recent integrations within both genomes. They segregated into four groups. Two larger gammaretrovirus-like groups (PtG1 and PtG2) occurred in chimpanzees but not in humans. The PtG sequences were most similar to two baboon ERVs and a macaque sequence but neither to other chimpanzee ERVs nor to any human gammaretrovirus-like ERVs. The pattern was consistent with cross-species transfer via predation. This appears to be an example of horizontal transfer of retroviruses with occasional fixation in the germ line.}, }
@article {pmid16413404, year = {2006}, author = {Dufernez, F and Yernaux, C and Gerbod, D and Noël, C and Chauvenet, M and Wintjens, R and Edgcomb, VP and Capron, M and Opperdoes, FR and Viscogliosi, E}, title = {The presence of four iron-containing superoxide dismutase isozymes in trypanosomatidae: characterization, subcellular localization, and phylogenetic origin in Trypanosoma brucei.}, journal = {Free radical biology &amp; medicine}, volume = {40}, number = {2}, pages = {210-225}, doi = {10.1016/j.freeradbiomed.2005.06.021}, pmid = {16413404}, issn = {0891-5849}, mesh = {Amino Acid Sequence ; Animals ; Chromosome Mapping ; Cloning, Molecular ; Gene Expression Regulation, Enzymologic/genetics ; Iron/*metabolism ; Isoenzymes/chemistry/genetics ; Molecular Sequence Data ; Phylogeny ; Protein Conformation ; Protein Structure, Secondary ; Sequence Alignment ; Sequence Homology, Amino Acid ; Superoxide Dismutase/*chemistry/*genetics ; Trypanosoma brucei brucei/*enzymology ; }, abstract = {Metalloenzymes such as the superoxide dismutases (SODs) form part of a defense mechanism that helps protect obligate and facultative aerobic organisms from oxygen toxicity and damage. Here, we report the presence in the trypanosomatid genomes of four SOD genes: soda, sodb1, sodb2, and a newly identified sodc. All four genes of Trypanosoma brucei have been cloned (Tbsods), sequenced, and overexpressed in Escherichia coli and shown to encode active dimeric FeSOD isozymes. Homology modeling of the structures of all four enzymes using available X-ray crystal structures of homologs showed that the four TbSOD structures were nearly identical. Subcellular localization using GFP-fusion proteins in procyclic insect trypomastigotes shows that TbSODB1 is mainly cytosolic, with a minor glycosomal component, TbSODB2 is mainly glycosomal with some activity in the cytosol, and TbSODA and TbSODC are both mitochondrial isozymes. Phylogenetic studies of all available trypanosomatid SODs and 106 dimeric FeSODs and closely related cambialistic dimeric SOD sequences suggest that the trypanosomatid SODs have all been acquired by more than one event of horizontal gene transfer, followed by events of gene duplication.}, }
@article {pmid16413191, year = {2006}, author = {Gophna, U and Charlebois, RL and Doolittle, WF}, title = {Ancient lateral gene transfer in the evolution of Bdellovibrio bacteriovorus.}, journal = {Trends in microbiology}, volume = {14}, number = {2}, pages = {64-69}, doi = {10.1016/j.tim.2005.12.008}, pmid = {16413191}, issn = {0966-842X}, mesh = {Bdellovibrio/*genetics ; Deltaproteobacteria/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Open Reading Frames/genetics ; Phylogeny ; Sequence Homology, Nucleic Acid ; }, abstract = {The recently sequenced genome of the predatory delta-proteobacterium Bdellovibrio bacteriovorus provides many insights into its metabolism and evolution. Because its genes are reasonably uniform in G+C content, it was suggested that B. bacteriovorus actively resists recombination with foreign DNA and horizontal transfer of DNA from other bacteria. To investigate this further, we carried out a variety of phylogenetic and comparative genomics analyses using data from >200 microbial genomes, including several published delta-proteobacteria. Although there might be little evidence for the extensive recent transfer of genes, we demonstrate that ancient lateral gene acquisition has shaped the B. bacteriovorus genome to a great extent.}, }
@article {pmid16412268, year = {2006}, author = {Zha, XD and Huang, HS and Zhou, LZ and Liu, J and Xu, KS}, title = {Thrombin-like enzymes from venom gland of Deinagkistrodon acutus: cDNA cloning, mechanism of diversity and phylogenetic tree construction.}, journal = {Acta pharmacologica Sinica}, volume = {27}, number = {2}, pages = {184-192}, doi = {10.1111/j.1745-7254.2006.00262.x}, pmid = {16412268}, issn = {1671-4083}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; DNA, Complementary/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Sequence Homology ; Thrombin/*genetics/isolation &amp; purification ; Viper Venoms/*chemistry ; *Viperidae/genetics ; }, abstract = {AIM: To clone cDNAs of thrombin-like enzymes (TLEs) from venom gland of Deinagkistrodon acutus and analyze the mechanisms by which their structural diversity arose.<br><br>METHODS: Reverse transcription-polymerase chain reaction and gene cloning techniques were used, and the cloned sequences were analyzed by using bioinformatics tools.<br><br>RESULTS: Novel cDNAs of snake venom TLEs were cloned. The possibilities of post-transcriptional recombination and horizontal gene transfer are discussed. A phylogenetic tree was constructed.<br><br>CONCLUSION: The cDNAs of snake venom TLEs exhibit great diversification. There are several types of structural variations. These variations may be attributable to certain mechanisms including recombination.}, }
@article {pmid16411919, year = {2006}, author = {Dumke, R and Schröter-Bobsin, U and Jacobs, E and Röske, I}, title = {Detection of phages carrying the Shiga toxin 1 and 2 genes in waste water and river water samples.}, journal = {Letters in applied microbiology}, volume = {42}, number = {1}, pages = {48-53}, doi = {10.1111/j.1472-765X.2005.01809.x}, pmid = {16411919}, issn = {0266-8254}, mesh = {Coliphages/genetics/*isolation &amp; purification ; DNA Primers ; Electrophoresis, Agar Gel/methods ; Escherichia coli/virology ; Gene Transfer, Horizontal/genetics ; Genes, Viral ; Polymerase Chain Reaction/methods ; Rivers/*microbiology ; Shiga Toxin 1/*genetics ; Shiga Toxin 2/*genetics ; Viral Plaque Assay ; *Waste Disposal, Fluid ; Water Microbiology ; }, abstract = {AIMS: To evaluate the occurrence and abundance of phages that carry the stx(1) and stx(2) gene in water samples of different quality.<br><br>METHODS AND RESULTS: Phages growing on the Shiga toxin-negative Escherichia coli O157:H7 (ATCC 43,888) strain were enumerated by a plaque assay in concentrated raw and treated waste water samples and river water samples. Plaques were investigated for the presence of stx(1) and stx(2) genes by a multiplex/nested PCR procedure. An overall number of 805 plaques were tested for the presence of stx-carrying phages. Stx genes could be demonstrated in 2% (stx(1)) and 16% (stx(2)) of the plaques. Stx-phages were eliminated with approximately the same efficiency in comparison with somatic coliphages during the waste water treatment process.<br><br>CONCLUSIONS: Due to the low numbers of phages carrying the stx genes 1 and 2 in treated waste water and river water, the dilution and inactivation of host bacteria and the unsuitable conditions for the transduction of host organisms in aquatic environments, it is difficult to derive from the data the direct evidence for a public health problem.<br><br>The results show the quantitative occurrence of stx-carrying phages in waste and river water and confirm the frequent circulation of these viruses in the aquatic environment.}, }
@article {pmid16408243, year = {2006}, author = {Bachvaroff, TR and Sanchez-Puerta, MV and Delwiche, CF}, title = {Rate variation as a function of gene origin in plastid-derived genes of peridinin-containing dinoflagellates.}, journal = {Journal of molecular evolution}, volume = {62}, number = {1}, pages = {42-52}, pmid = {16408243}, issn = {0022-2844}, mesh = {Animals ; Carotenoids/*genetics ; Dinoflagellida/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Variation ; Plastids/*genetics ; }, abstract = {Peridinin-pigmented dinoflagellates contain secondary plastids that seem to have undergone more nearly complete plastid genome reduction than other eukaryotes. Many typically plastid-encoded genes appear to have been transferred to the nucleus, with a few remaining genes found on minicircles. To understand better the evolution of the dinoflagellate plastid, four categories of plastid-associated genes in dinoflagellates were defined based on their history of transfer and evaluated for rate of sequence evolution, including minicircle genes (presumably plastid-encoded), genes probably transferred from the plastid to the nucleus (plastid-transferred), and genes that were likely acquired directly from the nucleus of the previous plastid host (nuclear-transferred). The fourth category, lateral-transferred genes, are plastid-associated genes that do not appear to have a cyanobacterial origin. The evolutionary rates of these gene categories were compared using relative rate tests and likelihood ratio tests. For comparison with other secondary plastid-containing organisms, rates were calculated for the homologous sequences from the haptophyte Emiliania huxleyi. The evolutionary rate of minicircle and plastid-transferred genes in the dinoflagellate was strikingly higher than that of nuclear-transferred and lateral-transferred genes and, also, substantially higher than that of all plastid-associated genes in the haptophyte. Plastid-transferred genes in the dinoflagellate had an accelerated rate of evolution that was variable but, in most cases, not as extreme as the minicircle genes. Furthermore, the nuclear-transferred and lateral-transferred genes showed rates of evolution that are similar to those of other taxa. Thus, nucleus-to-nucleus transferred genes have a more typical rate of sequence evolution, while those whose history was wholly or partially within the dinoflagellate plastid genome have a markedly accelerated rate of evolution.}, }
@article {pmid16407325, year = {2006}, author = {Erill, I and Campoy, S and Mazon, G and Barbé, J}, title = {Dispersal and regulation of an adaptive mutagenesis cassette in the bacteria domain.}, journal = {Nucleic acids research}, volume = {34}, number = {1}, pages = {66-77}, pmid = {16407325}, issn = {1362-4962}, mesh = {Adaptation, Physiological/genetics ; Bacteria/classification/enzymology/genetics ; Bacterial Proteins/*metabolism ; Betaproteobacteria/classification/genetics ; DNA-Directed DNA Polymerase/genetics/metabolism ; *Evolution, Molecular ; Gammaproteobacteria/classification/genetics ; Gene Duplication ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genomics ; *Mutagenesis, Insertional ; *Operon ; Phylogeny ; Repressor Proteins/*metabolism ; *SOS Response, Genetics ; Serine Endopeptidases/*metabolism ; }, abstract = {Recently, a multiple gene cassette with mutagenic translation synthesis activity was identified and shown to be under LexA regulation in several proteobacteria species. In this work, we have traced down instances of this multiple gene cassette across the bacteria domain. Phylogenetic analyses show that this cassette has undergone several reorganizations since its inception in the actinobacteria, and that it has dispersed across the bacterial domain through a combination of vertical inheritance, lateral gene transfer and duplication. In addition, our analyses show that LexA regulation of this multiple gene cassette is persistent in all the phyla in which it has been detected, and suggest that this regulation is prompted by the combined activity of two of its constituent genes: a polymerase V homolog and an alpha subunit of the DNA polymerase III.}, }
@article {pmid16406369, year = {2006}, author = {Guo, J and Cheng, H and Zhao, S and Yu, L}, title = {GG: a domain involved in phage LTF apparatus and implicated in human MEB and non-syndromic hearing loss diseases.}, journal = {FEBS letters}, volume = {580}, number = {2}, pages = {581-584}, doi = {10.1016/j.febslet.2005.12.076}, pmid = {16406369}, issn = {0014-5793}, mesh = {Amino Acid Sequence ; Animals ; Bacteriophage T4/*metabolism/ultrastructure ; Hearing Loss/*physiopathology ; Humans ; Molecular Sequence Data ; Muscular Dystrophies/*physiopathology ; Phylogeny ; Protein Structure, Tertiary ; Sequence Alignment ; Sequence Homology, Amino Acid ; Viral Tail Proteins/classification/genetics/*metabolism ; }, abstract = {Here, we report the identification of a novel domain--GG (domain in KIAA1199, FAM3, POMGnT1 and Tmem2 proteins, with two well-conserved glycine residues), present in eukaryotic FAM3 superfamily (FAM3A, FAM3B, FAM3C and FAM3D), POMGnT1 (protein O-linked mannose beta-1,2-N-acetylglucosaminyltransferase), TEM2 proteins as well as phage gp35 proteins. GG domain has been revealed to be implicated in muscle-eye-brain disease and non-syndromic hearing loss. The presence of GG domain in Bacteriophage gp35 hinge connector of long tail fiber might reflect the horizontal gene transfer from organisms. And we proposed that GG domain might function as important structural element in phage LTF.}, }
@article {pmid16404955, year = {2006}, author = {Gabriel, DW and Allen, C and Schell, M and Denny, TP and Greenberg, JT and Duan, YP and Flores-Cruz, Z and Huang, Q and Clifford, JM and Presting, G and González, ET and Reddy, J and Elphinstone, J and Swanson, J and Yao, J and Mulholland, V and Liu, L and Farmerie, W and Patnaikuni, M and Balogh, B and Norman, D and Alvarez, A and Castillo, JA and Jones, J and Saddler, G and Walunas, T and Zhukov, A and Mikhailova, N}, title = {Identification of open reading frames unique to a select agent: Ralstonia solanacearum race 3 biovar 2.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {19}, number = {1}, pages = {69-79}, doi = {10.1094/MPMI-19-0069}, pmid = {16404955}, issn = {0894-0282}, mesh = {Arginine ; Genes, Bacterial ; Genome, Bacterial/genetics ; Multigene Family ; Open Reading Frames/*genetics ; Promoter Regions, Genetic ; Prophages ; Protein Transport ; Ralstonia solanacearum/*classification/*genetics/pathogenicity ; Sequence Analysis, DNA ; Species Specificity ; Virulence Factors ; }, abstract = {An 8x draft genome was obtained and annotated for Ralstonia solanacearum race 3 biovar 2 (R3B2) strain UW551, a United States Department of Agriculture Select Agent isolated from geranium. The draft UW551 genome consisted of 80,169 reads resulting in 582 contigs containing 5,925,491 base pairs, with an average 64.5% GC content. Annotation revealed a predicted 4,454 protein coding open reading frames (ORFs), 43 tRNAs, and 5 rRNAs; 2,793 (or 62%) of the ORFs had a functional assignment. The UW551 genome was compared with the published genome of R. solanacearum race 1 biovar 3 tropical tomato strain GMI1000. The two phylogenetically distinct strains were at least 71% syntenic in gene organization. Most genes encoding known pathogenicity determinants, including predicted type III secreted effectors, appeared to be common to both strains. A total of 402 unique UW551 ORFs were identified, none of which had a best hit or >45% amino acid sequence identity with any R. solanacearum predicted protein; 16 had strong (E < 10(-13)) best hits to ORFs found in other bacterial plant pathogens. Many of the 402 unique genes were clustered, including 5 found in the hrp region and 38 contiguous, potential prophage genes. Conservation of some UW551 unique genes among R3B2 strains was examined by polymerase chain reaction among a group of 58 strains from different races and biovars, resulting in the identification of genes that may be potentially useful for diagnostic detection and identification of R3B2 strains. One 22-kb region that appears to be present in GMI1000 as a result of horizontal gene transfer is absent from UW551 and encodes enzymes that likely are essential for utilization of the three sugar alcohols that distinguish biovars 3 and 4 from biovars 1 and 2.}, }
@article {pmid16403873, year = {2006}, author = {Griffiths, E and Gupta, RS}, title = {Molecular signatures in protein sequences that are characteristics of the phylum Aquificae.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {56}, number = {Pt 1}, pages = {99-107}, doi = {10.1099/ijs.0.63927-0}, pmid = {16403873}, issn = {1466-5026}, mesh = {Adenosine Triphosphatases/genetics ; Bacterial Proteins/*genetics ; DNA Polymerase I/genetics ; DNA-Directed RNA Polymerases/genetics ; *Genome, Bacterial ; Gram-Negative Bacteria/chemistry/*classification/enzymology/genetics ; Hot Temperature ; Membrane Transport Proteins/genetics ; Molecular Sequence Data ; Peptide Elongation Factor Tu/genetics ; SEC Translocation Channels ; SecA Proteins ; Species Specificity ; }, abstract = {Species of the phylum Aquificae are of great interest due to their strict extreme thermophilic growth characteristics. Presently, there is no known molecular characteristic which is unique to this group of bacteria. This work describes six conserved inserts and deletions (indels or signature sequences) in four widely distributed proteins that are distinctive features of species from the phylum Aquificae. These include three signatures consisting of a 2 aa insert, a 5-6 aa insert and a 6 aa deletion in DNA polymerase I (PolA), a 6-7 aa insert in glucose-inhibited protein A (GidA), a 52 aa insert in the RNA polymerase beta'-subunit (RpoC) and a 4 aa insert in elongation factor Tu (EF-Tu). Fragments of these genes were amplified in most cases from Hydrogenobacter hydrogenophilus, Hydrogenothermus marinus and Thermocrinis ruber and combined with available sequence data from 'Aquifex aeolicus' and Sulfurihydrogenibium azorense. The presence of the PolA, GidA and RpoC indels in all of the species sequenced provides evidence that they are probably distinctive characteristics of the entire phylum. The indel in EF-Tu, which is shared by Aquifex species and Hydrogenobacter but not Hydrogenothermus and Sulfurihydrogenibium, may provide a molecular marker for the family Aquificaceae. We have also identified a 51 aa insert in SecA preprotein translocase that is commonly shared by various species of the Aquificae as well as two Thermotoga species (Thermotoga maritima and Thermotoga neapolitana) which may be due to lateral gene transfer between these groups. In phylogenetic trees based on a concatenated dataset of fragments from eight different proteins as well as 16S rRNA, the observed branching pattern of these species was very similar and it was consistent with the relationships inferred from various indels. The identified indels provide a novel means for distinguishing species of the Aquificae from all other bacteria in molecular terms and may prove useful for functional studies aimed at understanding the unique biochemical and physiological characteristics of the Aquificae.}, }
@article {pmid16403797, year = {2006}, author = {Dalevi, D and Dubhashi, D and Hermansson, M}, title = {Bayesian classifiers for detecting HGT using fixed and variable order markov models of genomic signatures.}, journal = {Bioinformatics (Oxford, England)}, volume = {22}, number = {5}, pages = {517-522}, doi = {10.1093/bioinformatics/btk029}, pmid = {16403797}, issn = {1367-4803}, mesh = {Artificial Intelligence ; Bayes Theorem ; Chromosome Mapping/*methods ; DNA Fingerprinting/*methods ; DNA, Bacterial/*genetics ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial/*genetics ; Markov Chains ; Models, Genetic ; Models, Statistical ; Pattern Recognition, Automated/*methods ; Sequence Analysis, DNA/*methods ; Species Specificity ; }, abstract = {MOTIVATION: Analyses of genomic signatures are gaining attention as they allow studies of species-specific relationships without involving alignments of homologous sequences. A naïve Bayesian classifier was built to discriminate between different bacterial compositions of short oligomers, also known as DNA words. The classifier has proven successful in identifying foreign genes in Neisseria meningitis. In this study we extend the classifier approach using either a fixed higher order Markov model (Mk) or a variable length Markov model (VLMk).<br><br>RESULTS: We propose a simple algorithm to lock a variable length Markov model to a certain number of parameters and show that the use of Markov models greatly increases the flexibility and accuracy in prediction to that of a na&#xef;ve model. We also test the integrity of classifiers in terms of false-negatives and give estimates of the minimal sizes of training data. We end the report by proposing a method to reject a false hypothesis of horizontal gene transfer.<br><br>AVAILABILITY: Software and Supplementary information available at www.cs.chalmers.se/~dalevi/genetic_sign_classifiers/.}, }
@article {pmid16402664, year = {2005}, author = {Petersen, W and Umbeck, P and Hokanson, K and Halsey, M}, title = {Biosafety considerations for selectable and scorable markers used in cassava (Manihot esculenta Crantz) biotechnology.}, journal = {Environmental biosafety research}, volume = {4}, number = {2}, pages = {89-102}, doi = {10.1051/ebr:2005016}, pmid = {16402664}, issn = {1635-7922}, mesh = {Acetyltransferases/genetics ; Biotechnology/*methods ; Crops, Agricultural/*genetics ; Genes, Reporter/genetics ; Genetic Engineering/*methods ; Genetic Markers/*genetics ; Kanamycin Kinase/genetics ; Manihot/*genetics ; Mannose-6-Phosphate Isomerase/genetics ; Phosphotransferases (Alcohol Group Acceptor)/genetics ; Safety/*standards ; }, abstract = {Cassava is an important subsistence crop grown only in the tropics, and represents a major source of calories for many people in developing countries. Improvements in the areas of resistance to insects and viral diseases, enhanced nutritional qualities, reduced cyanogenic content and modified starch characteristics are urgently needed. Traditional breeding is hampered by the nature of the crop, which has a high degree of heterozygosity, irregular flowering, and poor seed set. Biotechnology has the potential to enhance crop improvement efforts, and genetic engineering techniques for cassava have thus been developed over the past decade. Selectable and scorable markers are critical to efficient transformation technology, and must be evaluated for biosafety, as well as efficiency and cost-effectiveness. In order to facilitate research planning and regulatory submission, the literature on biosafety aspects of the selectable and scorable markers currently used in cassava biotechnology is surveyed. The source, mode of action and current use of each marker gene is described. The potential for toxicity, allergenicity, pleiotropic effects, horizontal gene transfer, and the impact of these on food or feed safety and environmental safety is evaluated. Based on extensive information, the selectable marker genes nptII, hpt, bar/pat, and manA, and the scorable marker gene uidA, all have little risk in terms of biosafety. These appear to represent the safest options for use in cassava biotechnology available at this time.}, }
@article {pmid16391088, year = {2006}, author = {Lee, JH and O'Sullivan, DJ}, title = {Sequence analysis of two cryptic plasmids from Bifidobacterium longum DJO10A and construction of a shuttle cloning vector.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {1}, pages = {527-535}, pmid = {16391088}, issn = {0099-2240}, mesh = {Amino Acid Sequence ; Base Sequence ; Bifidobacterium/*genetics ; Electroporation ; Escherichia coli/genetics ; Genetic Techniques ; Genetic Vectors/*genetics ; Humans ; Molecular Sequence Data ; Plasmids/*genetics ; *Sequence Analysis, DNA ; }, abstract = {Bifidobacterium longum DJO10A is a recent human isolate with probiotic characteristics and contains two plasmids, designated pDOJH10L and pDOJH10S. The complete sequences of both these plasmids have now been determined and consist of two circular DNA molecules of 10,073 and 3,661 bp, with G+C contents of 62.2% and 66.2%, respectively. Plasmid pDOJH10L is a cointegrate plasmid consisting of DNA regions exhibiting very high sequence identity to two other B. longum plasmids, pNAC2 (98%) and pKJ50 (96%), together with another region. Interestingly, the rolling circular replication (RCR) regions of both the pNAC2- and pKJ50-like plasmids were disrupted during the recombination event leading to a further recombination event to acquire a functional replicon. This consists of a new fused rep gene and an RCR-type ori consisting of a conserved DnaA box in an AT-rich region followed by four contiguous repeated sequences consistent with an iteron structure and an inverted repeat. The smaller pDOJH10S had no sequence similarity to any other characterized plasmid from bifidobacteria. In addition, it did not contain any features consistent with RCR, which is the replication mechanism proposed for all the bifidobacteria plasmids characterized to date. It did exhibit sequence similarity with several theta replication-related replication proteins from other gram-positive, high-G+C bacteria, with the closest match from a Rhodococcus rhodochrous plasmid, suggesting a theta mechanism of replication. S1 nuclease analysis of both plasmids in B. longum DJO10A revealed single-strand DNA intermediates for pDOJH10L, which is consistent for RCR, but none were detected for pDOJH10S. As the G+C content of pDOJH10S is similar to that of Rhodococcus rhodochrous (67%) and significantly higher than that of B. longum (60.1%), it may have been acquired through horizontal gene transfer from a Rhodococcus species, as both genera are members of the Actinomycetes and are intestinal inhabitants. An Escherichia coli-B. longum shuttle cloning vector was constructed from pDOJH10S and the E. coli ori region of p15A, a lacZ gene with a multiple cloning site of pUC18, and a chloramphenicol resistance gene (CAT) of pCI372 and was transformed successfully into E. coli and B. longum. It could not be introduced into lactic acid bacteria (Lactococcus and Lactobacillus), showing it was not very promiscuous. It was stably maintained in B. longum in the absence of antibiotic pressure for 92 generations, which is consistent with the segregational stability of theta-replicating plasmids in gram-positive bacteria. This is the first cloning vector for bifidobacteria that does not utilize RCR and should be useful for the stable introduction of heterologous genes into these dominant inhabitants of the large intestine.}, }
@article {pmid16391071, year = {2006}, author = {Susanna, KA and den Hengst, CD and Hamoen, LW and Kuipers, OP}, title = {Expression of transcription activator ComK of Bacillus subtilis in the heterologous host Lactococcus lactis leads to a genome-wide repression pattern: a case study of horizontal gene transfer.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {1}, pages = {404-411}, pmid = {16391071}, issn = {0099-2240}, mesh = {Bacillus subtilis/*genetics/metabolism ; Bacterial Proteins/genetics/*metabolism ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Lactococcus lactis/genetics/growth &amp; development/*metabolism ; Oligonucleotide Array Sequence Analysis ; Transcription Factors/genetics/*metabolism ; Transcription, Genetic ; }, abstract = {Horizontal gene transfer (HGT) is generally considered a possible mechanism by which bacteria acquire new genetic properties. Especially when pathogenicity genes are involved, HGT might have important consequences for humans. In this report we describe a case study of HGT in which a transcriptional activator, ComK of Bacillus subtilis, was introduced into a heterologous host species, Lactococcus lactis. ComK is the central regulator of competence development, activating transcription by binding to a ComK-binding site, a so-called K-box. Interestingly, L. lactis does not contain a comK gene, but it does contain almost 400 putatively functional K-boxes, as well as homologues of a number of competence genes. In this study, the effect of HGT of B. subtilis comK into L. lactis was investigated by determining the effects on the transcription profile using DNA microarray analyses. Production of wild-type ComK was shown to stimulate the transcription of 89 genes and decrease the expression of 114 genes. Notably, potential direct effects (i.e., genes preceded by a K-box) were found mainly among repressed genes, suggesting that ComK functions as a repressor in L. lactis. This is a remarkable difference between L. lactis and B. subtilis, in which ComK almost exclusively activates transcription. Additional DNA microarray analyses with a transcription activation-deficient but DNA-binding ComK variant, ComKDeltaC25, demonstrated that there were similar effects on gene regulation with this variant and with wild-type ComK, confirming that the direct effects of ComK result from interference with normal transcription through binding to available K-boxes. This study demonstrates that horizontal gene transfer can have dramatic effects that are very different than those that are expected on basis of the original functionality of a gene.}, }
@article {pmid16389494, year = {2005}, author = {Zhaxybayeva, O and Lapierre, P and Gogarten, JP}, title = {Ancient gene duplications and the root(s) of the tree of life.}, journal = {Protoplasma}, volume = {227}, number = {1}, pages = {53-64}, pmid = {16389494}, issn = {0033-183X}, mesh = {Carbamoyl-Phosphate Synthase (Ammonia)/metabolism ; Carbon-Nitrogen Ligases/genetics ; *Evolution, Molecular ; *Gene Duplication ; *Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; Phylogeny ; Plant Roots ; }, abstract = {Tracing organismal histories on the timescale of the tree of life remains one of the challenging tasks in evolutionary biology. The hotly debated questions include the evolutionary relationship between the three domains of life (e.g., which of the three domains are sister domains, are the domains para-, poly-, or monophyletic) and the location of the root within the universal tree of life. For the latter, many different points of view have been considered but so far no consensus has been reached. The only widely accepted rationale to root the universal tree of life is to use anciently duplicated paralogous genes that are present in all three domains of life. To date only few anciently duplicated gene families useful for phylogenetic reconstruction have been identified. Here we present results from a systematic search for ancient gene duplications using twelve representative, completely sequenced, archaeal and bacterial genomes. Phylogenetic analyses of identified cases show that the majority of datasets support a root between Archaea and Bacteria; however, some datasets support alternative hypotheses, and all of them suffer from a lack of strong phylogenetic signal. The results are discussed with respect to the impact of horizontal gene transfer on the ability to reconstruct organismal evolution. The exchange of genetic information between divergent organisms gives rise to mosaic genomes, where different genes in a genome have different histories. Simulations show that even low rates of horizontal gene transfer dramatically complicate the reconstruction of organismal evolution, and that the different most recent common molecular ancestors likely existed at different times and in different lineages.}, }
@article {pmid16386964, year = {2006}, author = {Friedman, R and Hughes, AL}, title = {Pattern of gene duplication in the Cotesia congregata Bracovirus.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {6}, number = {4}, pages = {315-322}, doi = {10.1016/j.meegid.2005.10.001}, pmid = {16386964}, issn = {1567-1348}, support = {GM43940/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Evolution, Molecular ; *Gene Duplication ; Gene Transfer, Horizontal ; Phylogeny ; Polydnaviridae/*genetics ; Wasps/*virology ; }, abstract = {Polydnaviruses (PDVs) are a family of double-stranded DNA viruses genetically linked to their wasp hosts. These viruses utilize the transcriptional machinery of the wasp cells to manufacture viral particles which contain circular segments of DNA. The female wasp, hosting the polydnavirus, lays its eggs along with the viral particles inside a caterpillar. Because no replication of the virus occurs while inside the caterpillar, fixed genetic changes occur solely inside the female wasp, as an integrated portion of its genome. Therefore, evolution of the polydnavirus is expected to parallel that of the wasp. Phylogenetic analysis of the polydnavirus genome showed a pattern of gene duplication consistent with the "birth-and-death" process frequently observed in eukaryotic genomes. Phylogenies provided no unequivocal evidence of horizontal gene transfer between the wasp host and the polydnavirus, but in some cases there were suggestions of such gene transfer.}, }
@article {pmid16385040, year = {2006}, author = {Jandle, S and Meyer, R}, title = {Stringent and relaxed recognition of oriT by related systems for plasmid mobilization: implications for horizontal gene transfer.}, journal = {Journal of bacteriology}, volume = {188}, number = {2}, pages = {499-506}, pmid = {16385040}, issn = {0021-9193}, support = {R01 GM037462/GM/NIGMS NIH HHS/United States ; GM37462/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Proteins/metabolism ; DNA, Bacterial/*genetics/metabolism ; *Gene Transfer, Horizontal ; Origin Recognition Complex/metabolism ; Plasmids/*genetics/metabolism ; Replication Origin/genetics ; Species Specificity ; }, abstract = {The plasmids R1162 and pSC101 have origins of conjugative transfer (oriTs) and corresponding relaxases that are closely related. The oriTs are made up of a highly conserved core, where DNA is cleaved by the relaxase prior to transfer, and an inverted repeat that differs in size and sequence. We show that in each case the seven base pairs adjacent to the core and within one arm of the inverted repeat are sufficient to determine specificity. Within this DNA there are three AT base pairs located 4 bp from the core. Mutations in the AT base pairs suggest that the relaxase makes essential contacts at these locations to the minor groove of the DNA. The remaining four bases are different for each oriT and are both necessary and sufficient for stringent recognition of oriT by the pSC101 mobilization proteins. In contrast, the R1162 mobilization proteins have a much more relaxed requirement for the base sequence of this specificity region. As a result, the R1162 mobilization proteins can initiate transfer from a variety of sites, including those derived from the chromosome. The R1162 mobilization proteins could therefore contribute to the horizontal gene transfer of DNA from diverse sources.}, }
@article {pmid16384724, year = {2006}, author = {Ron, EZ}, title = {Host specificity of septicemic Escherichia coli: human and avian pathogens.}, journal = {Current opinion in microbiology}, volume = {9}, number = {1}, pages = {28-32}, doi = {10.1016/j.mib.2005.12.001}, pmid = {16384724}, issn = {1369-5274}, mesh = {Animals ; Bacteremia/*microbiology ; Bird Diseases/*microbiology ; Birds ; Escherichia coli/classification/genetics/*pathogenicity ; Escherichia coli Infections/*microbiology/transmission/veterinary ; Genome, Bacterial ; Humans ; Molecular Epidemiology ; *Virulence Factors/genetics ; Zoonoses ; }, abstract = {Extraintestinal pathogenic Escherichia coli (ExPEC) strains are the cause of a diverse spectrum of invasive human and animal infections, often leading to septicemia. ExPEC strains contain virulence factors that enable them to survive in the host blood and tissues. Most of these virulence factors are distributed in ExPEC strains in a host-independent fashion. Genomic analyses of these strains provide evidence for numerous recombinational events and horizontal gene transfer, as well as for a high diversity of virulence factors. In studies of human and avian septicemic strains of serotypes O2 and O78 it appears that there is a positive correlation between virulence, invasiveness and clonal origin. Yet, it is clear that clonal division in these strains, as well as distribution of virulence factors, is independent of the host and closely related clones reside in different hosts. Although the possibility exists that ExPEC strains do have a certain degree of host specificity, which is not obvious from genomic studies, it is clear that the similarity of virulence factors presents a significant zoonotic risk.}, }
@article {pmid16382899, year = {2005}, author = {Triplett, JW and Herring, BP and Pavalko, FM}, title = {Adenoviral transgene expression enhanced by cotreatment with etoposide in cultured cells.}, journal = {BioTechniques}, volume = {39}, number = {6}, pages = {826, 828, 830, passim}, doi = {10.2144/000112074}, pmid = {16382899}, issn = {0736-6205}, support = {DK61130/DK/NIDDK NIH HHS/United States ; R01 AR049728/AR/NIAMS NIH HHS/United States ; R01 AR49728/AR/NIAMS NIH HHS/United States ; DK65644/DK/NIDDK NIH HHS/United States ; R01 AR049728-03/AR/NIAMS NIH HHS/United States ; R01 HL58571/HL/NHLBI NIH HHS/United States ; }, mesh = {Adenoviridae/*genetics ; Apoptosis/drug effects ; Cell Line, Tumor ; Etoposide/*pharmacology ; Gene Transfer, Horizontal ; Green Fluorescent Proteins/genetics ; Humans ; *Transgenes ; }, }
@article {pmid16380427, year = {2005}, author = {O'Donoghue, P and Sethi, A and Woese, CR and Luthey-Schulten, ZA}, title = {The evolutionary history of Cys-tRNACys formation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {102}, number = {52}, pages = {19003-19008}, pmid = {16380427}, issn = {0027-8424}, mesh = {Amino Acid Sequence ; Amino Acyl-tRNA Synthetases/chemistry ; Archaea ; Bacteria/metabolism ; Binding Sites ; *Biological Evolution ; Cysteine/chemistry ; Dimerization ; Evolution, Molecular ; Imaging, Three-Dimensional ; Methanococcus/metabolism ; Methanosarcina/metabolism ; Molecular Sequence Data ; Phylogeny ; RNA, Transfer, Cys/*chemistry/*genetics ; Sequence Homology, Amino Acid ; }, abstract = {The recent discovery of an alternate pathway for indirectly charging tRNA(Cys) has stimulated a re-examination of the evolutionary history of Cys-tRNA(Cys) formation. In the first step of the pathway, O-phosphoseryl-tRNA synthetase charges tRNA(Cys) with O-phosphoserine (Sep), a precursor of the cognate amino acid. In the following step, Sep-tRNA:Cys-tRNA synthase (SepCysS) converts Sep to Cys in a tRNA-dependent reaction. The existence of such a pathway raises several evolutionary questions, including whether the indirect pathway is a recent evolutionary invention, as might be implied from its localization to the Euryarchaea, or, as evidence presented here indicates, whether this pathway is more ancient, perhaps already in existence at the time of the last universal common ancestral state. A comparative phylogenetic approach is used, combining evolutionary information from protein sequences and structures, that takes both the signature of horizontal gene transfer and the recurrence of the full canonical phylogenetic pattern into account, to document the complete evolutionary history of cysteine coding and understand the nature of this process in the last universal common ancestral state. Resulting from the historical study of tRNA(Cys) aminoacylation and the integrative perspective of sequence, structure, and function are 3D models of O-phosphoseryl-tRNA synthetase and SepCysS, which provide experimentally testable predictions regarding the identity and function of key active-site residues in these proteins. The model of SepCysS is used to suggest a sulfhydrylation reaction mechanism, which is predicted to occur at the interface of a SepCysS dimer.}, }
@article {pmid16378956, year = {2005}, author = {Zhu, XY and Zhang, Y and Zhou, MM}, title = {[Molecular evidence for origin of plastid-like organelle apicoplast: a review].}, journal = {Yi chuan = Hereditas}, volume = {27}, number = {6}, pages = {1020-1024}, pmid = {16378956}, issn = {0253-9772}, mesh = {Animals ; Apicomplexa/*genetics/growth &amp; development ; Dinoflagellida/genetics/growth &amp; development ; Eukaryota/*genetics/growth &amp; development ; *Evolution, Molecular ; Gene Deletion ; Gene Transfer, Horizontal ; Organelles/*genetics ; Plastids/genetics ; Symbiosis/genetics ; }, abstract = {Apicomplexan protozoa contains a highly reduced plastid-like organelle termed apicoplast. The research on evolutionary origin of apicoplast is a topic of long-term intense debate, by far, hasn't still reached congruent conclusion though a variety of molecular technologies were employed, so that it become a typical case in plastid origin field. In this paper , we reviewed the molecular evidence for apicoplast evolutionary origin, predicting the potential source of novel molecular evidence as clues for further studying.}, }
@article {pmid16373421, year = {2006}, author = {Zhang, Z and Dickerson, IM and Russo, AF}, title = {Calcitonin gene-related peptide receptor activation by receptor activity-modifying protein-1 gene transfer to vascular smooth muscle cells.}, journal = {Endocrinology}, volume = {147}, number = {4}, pages = {1932-1940}, doi = {10.1210/en.2005-0918}, pmid = {16373421}, issn = {0013-7227}, support = {R01 DK052328/DK/NIDDK NIH HHS/United States ; DE-016511/DE/NIDCR NIH HHS/United States ; DK-52328/DK/NIDDK NIH HHS/United States ; HL-14388/HL/NHLBI NIH HHS/United States ; }, mesh = {Adenoviridae/genetics ; Animals ; Apoptosis ; Calcitonin Receptor-Like Protein ; Cell Proliferation ; Cells, Cultured ; Cyclic AMP/biosynthesis ; Gene Transfer, Horizontal ; *Genetic Therapy ; Humans ; Intracellular Signaling Peptides and Proteins/*genetics ; Male ; Membrane Proteins/*genetics ; Muscle, Smooth, Vascular/cytology/*metabolism ; Myocytes, Smooth Muscle/*metabolism ; Rats ; Rats, Sprague-Dawley ; Receptor Activity-Modifying Protein 1 ; Receptor Activity-Modifying Proteins ; Receptors, Calcitonin/physiology ; Receptors, Calcitonin Gene-Related Peptide/*physiology ; }, abstract = {The neuropeptide calcitonin gene-related peptide (CGRP) is a potent vasodilator that plays a protective role in the cardiovascular system. The receptor for CGRP is an unusual complex of the G protein-coupled calcitonin-like receptor and an obligate receptor activity modifying protein-1 (RAMP1). In this report we provide the first evidence that RAMP1 is rate limiting in vascular smooth muscle cells. Although cultured rat aorta smooth muscle cells express calcitonin like-receptor and RAMP1, we found that CGRP is not a potent activator of the receptor. After overexpression of RAMP1 by adenoviral gene transfer, there was a striking increase in CGRP-induced production of cAMP, with a 75-fold decrease in the EC(50) and a 1.5-fold increase in the maximal response. The biological consequence of this increased receptor activity was observed in three different paradigms. First, RAMP1 gene transfer caused a CGRP-dependent decrease in cell proliferation. Second, RAMP1 and CGRP treatment led to a 3-fold greater free radical-induced reduction in cell number. Finally, RAMP1 gene transfer resulted in a 5-fold CGRP-dependent increase in terminal deoxynucleotidyltransferase-mediated deoxyuridine triphosphate nick end labeling-positive apoptotic cells upon serum withdrawal. The mechanisms underlying these effects involved cAMP-dependent pathways. We propose that RAMP1 gene transfer may be an effective strategy for increasing the effectiveness of CGRP-induced decrease in restenosis after aortic angioplasty.}, }
@article {pmid16369937, year = {2006}, author = {Lester, L and Meade, A and Pagel, M}, title = {The slow road to the eukaryotic genome.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {28}, number = {1}, pages = {57-64}, doi = {10.1002/bies.20344}, pmid = {16369937}, issn = {0265-9247}, mesh = {Animals ; Eukaryotic Cells/*metabolism ; Evolution, Molecular ; Genome/*genetics ; Phylogeny ; Recombination, Genetic/genetics ; }, abstract = {The eukaryotic genome is a mosaic of eubacterial and archaeal genes in addition to those unique to itself. The mosaic may have arisen as the result of two prokaryotes merging their genomes, or from genes acquired from an endosymbiont of eubacterial origin. A third possibility is that the eukaryotic genome arose from successive events of lateral gene transfer over long periods of time. This theory does not exclude the endosymbiont, but questions whether it is necessary to explain the peculiar set of eukaryotic genes. We use phylogenetic studies and reconstructions of ancestral first appearances of genes on the prokaryotic phylogeny to assess evidence for the lateral gene transfer scenario. We find that phylogenies advanced to support fusion can also arise from a succession of lateral gene transfer events. Our reconstructions of ancestral first appearances of genes reveal that the various genes that make up the eukaryotic mosaic arose at different times and in diverse lineages on the prokaryotic tree, and were not available in a single lineage. Successive events of lateral gene transfer can explain the unusual mosaic structure of the eukaryotic genome, with its content linked to the immediate adaptive value of the genes its acquired. Progress in understanding eukaryotes may come from identifying ancestral features such as the eukaryotic splicesome that could explain why this lineage invaded, or created, the eukaryotic niche.}, }
@article {pmid16367875, year = {2006}, author = {Korochkina, S and Barreau, C and Pradel, G and Jeffery, E and Li, J and Natarajan, R and Shabanowitz, J and Hunt, D and Frevert, U and Vernick, KD}, title = {A mosquito-specific protein family includes candidate receptors for malaria sporozoite invasion of salivary glands.}, journal = {Cellular microbiology}, volume = {8}, number = {1}, pages = {163-175}, doi = {10.1111/j.1462-5822.2005.00611.x}, pmid = {16367875}, issn = {1462-5814}, support = {AI40311/AI/NIAID NIH HHS/United States ; AI44467/AI/NIAID NIH HHS/United States ; AI51656/AI/NIAID NIH HHS/United States ; GM37537/GM/NIGMS NIH HHS/United States ; }, mesh = {Aedes/genetics/*metabolism/parasitology ; Amino Acid Sequence ; Animals ; Anopheles/genetics/*metabolism/parasitology ; Antibodies, Monoclonal ; Insect Proteins/*metabolism ; Molecular Sequence Data ; Plasmodium gallinaceum/*physiology ; Receptors, Cell Surface/*metabolism ; Salivary Glands/immunology/metabolism/parasitology ; Salivary Proteins and Peptides/*metabolism ; Sporozoites/*physiology ; }, abstract = {We describe a previously unrecognized protein family from Aedes and Anopheles mosquitoes, here named SGS proteins. There are no SGS homologues in Drosophila or other eukaryotes, but SGS presence in two mosquito genera suggests that the protein family is widespread among mosquitoes. Ae. aegypti aaSGS1 mRNA and protein are salivary gland specific, and protein is localized in the basal lamina covering the anatomical regions that are preferentially invaded by malaria sporozoites. Anti-aaSGS1 antibodies inhibited sporozoite invasion into the salivary glands in vivo, confirming aaSGS1 as a candidate sporozoite receptor. By homology to aaSGS1 we identified the complete complement of four SGS genes in An. gambiae, which were not recognized in the genome annotation. Two An. gambiae SGS genes display salivary gland specific expression like aaSGS1. Bioinformatic analysis predicts that SGS proteins possess heparin-binding domains, and have among the highest density of tyrosine sulphation sites of all An. gambiae proteins. The major sporozoite surface proteins (CS and TRAP) also bind heparin, and interact with sulphoconjugates during liver cell invasion. Thus, we speculate that sporozoite invasion of mosquito salivary glands and subsequently the vertebrate liver may share similar mechanisms based on sulphation. Phylogenomic analysis suggests that an SGS ancestor was involved in a lateral gene transfer.}, }
@article {pmid16367844, year = {2006}, author = {Paoletti, M and Buck, KW and Brasier, CM}, title = {Selective acquisition of novel mating type and vegetative incompatibility genes via interspecies gene transfer in the globally invading eukaryote Ophiostoma novo-ulmi.}, journal = {Molecular ecology}, volume = {15}, number = {1}, pages = {249-262}, doi = {10.1111/j.1365-294X.2005.02728.x}, pmid = {16367844}, issn = {0962-1083}, mesh = {Ascomycota/*genetics ; Base Sequence ; Chromosome Mapping ; Cluster Analysis ; DNA Primers ; Europe ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genes, Mating Type, Fungal/*genetics ; Geography ; Molecular Sequence Data ; North America ; Nucleic Acid Amplification Techniques ; *Phylogeny ; Polymorphism, Restriction Fragment Length ; Reproduction/genetics ; Sequence Analysis, DNA ; }, abstract = {The Dutch elm disease fungus Ophiostoma novo-ulmi, which has destroyed billions of elm trees worldwide, originally invaded Europe as a series of clonal populations with a single mating type (MAT-2) and a single vegetative incompatibility (vic) type. The populations then rapidly became diverse with the appearance of the MAT-1 type and many vegetative incompatibility types. Here, we have investigated the mechanism using isolates from sites in Portugal at which the rapid evolution of O. novo-ulmi populations from clonality to heterogeneity was well established. We show by genetic mapping of vic and MAT loci with AFLP markers and by sequence analysis of MAT loci that this diversification was due to selective acquisition by O. novo-ulmi of the MAT-1 and vic loci from another species, Ophiostoma ulmi. A global survey showed that interspecies transfer of the MAT-1 locus occurred on many occasions as O. novo-ulmi spread across the world. We discuss the possibility that fixation of the MAT-1 and vic loci occurred in response to spread of deleterious viruses in the originally clonal populations. The process demonstrates the potential of interspecies gene transfer for facilitating rapid adaptation of invasive organisms to a new environment.}, }
@article {pmid16359845, year = {2006}, author = {Liu, SY and Lin, JY and Chu, C and Su, LH and Lin, TY and Chiu, CH}, title = {Integron-associated imipenem resistance in Acinetobacter baumannii isolated from a regional hospital in Taiwan.}, journal = {International journal of antimicrobial agents}, volume = {27}, number = {1}, pages = {81-84}, doi = {10.1016/j.ijantimicag.2005.09.010}, pmid = {16359845}, issn = {0924-8579}, mesh = {Acinetobacter baumannii/drug effects/*genetics/physiology ; Anti-Bacterial Agents/*pharmacology ; Cross Infection/microbiology ; Electrophoresis, Gel, Pulsed-Field ; Gene Order ; Humans ; Imipenem/*pharmacology ; *Integrons ; Plasmids/genetics ; Polymerase Chain Reaction ; Taiwan ; beta-Lactam Resistance/*genetics ; beta-Lactamases/genetics ; }, abstract = {We investigated the genetic properties of imipenem-resistant Acinetobacter baumannii collected from a regional hospital in Taiwan. Pulsed-field gel electrophoresis demonstrated that the isolates were genetically diverse. Polymerase chain reaction, DNA sequencing, and DNA-DNA hybridisation showed that the bla(IMP-1) gene resided as a cassette in a plasmid-borne class 1 integron in two isolates. The majority of the resistant isolates were plasmid-less and carried no bla(IMP), bla(VIM) or bla(CFI) genes, indicating that other uncharacterised metallo-beta-lactamases or mechanisms other than enzyme production are involved in carbapenem resistance in this group of A. baumannii. We conclude that multidrug resistance of A. baumannii was a combined effect of lateral gene transfer and clonal spread of multiple resistant clones. Strict measures should be implemented to control the further spread of resistance.}, }
@article {pmid16359198, year = {2005}, author = {Hansen, LH and Sørensen, SJ and Jørgensen, HS and Jensen, LB}, title = {The prevalence of the OqxAB multidrug efflux pump amongst olaquindox-resistant Escherichia coli in pigs.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {11}, number = {4}, pages = {378-382}, doi = {10.1089/mdr.2005.11.378}, pmid = {16359198}, issn = {1076-6294}, mesh = {ATP Binding Cassette Transporter, Subfamily B/*genetics ; Animals ; Anti-Bacterial Agents/*pharmacology ; Chloramphenicol/pharmacology ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/*drug effects/*genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests/veterinary ; Operon ; Plasmids ; Polymerase Chain Reaction ; Quinoxalines/*pharmacology ; Swine/*microbiology ; }, abstract = {The quinoxaline olaquindox has been used extensively as a growth promoter for pigs. Recently, we isolated a plasmid (pOLA52) conferring resistance to olaquindox from swine manure. On this plasmid, the oqxA and oqxB genes encode an RND-family multidrug efflux pump, OqxAB. It facilitates resistance to olaquindox as well as resistance to other antimicrobials like chloramphenicol. In this study, 10 of the 556 (1.8%) previously isolated Escherichia coli strains were shown to have an MIC >or= 64 microg/ml olaquindox. In nine of the ten strains, the oqxA gene was detected. Sequencing of an internal fragment of oqxA from the oqxA-positive strains showed no variation, indicating highly conserved oqxA genes. All of the oqxA-positive strains contain plasmids with replicons similar to that of pOLA52. It was verified by Southern hybridization that the oqxAB operon was situated on plasmids in most, if not all, resistant strains. Furthermore, horizontal transfer of olaquindox resistance from three olaquindox-resistant isolates was achieved using an olaquindox-sensitive E. coli as recipient.}, }
@article {pmid16357534, year = {2006}, author = {Glinsky, GV and Glinskii, AB and Berezovskaya, O and Smith, BA and Jiang, P and Li, XM and Yang, M and Hoffman, RM}, title = {Dual-color-coded imaging of viable circulating prostate carcinoma cells reveals genetic exchange between tumor cells in vivo, contributing to highly metastatic phenotypes.}, journal = {Cell cycle (Georgetown, Tex.)}, volume = {5}, number = {2}, pages = {191-197}, doi = {10.4161/cc.5.2.2320}, pmid = {16357534}, issn = {1551-4005}, support = {1 R43 CA89779/CA/NCI NIH HHS/United States ; 5R01 CA89827/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Cell Line, Tumor ; Cell Survival ; *Color ; Fluorescence ; Gene Transfer, Horizontal/*genetics ; Genomic Instability/genetics ; Humans ; Lung Neoplasms/blood/genetics/pathology/secondary ; Male ; Mice ; Mice, Nude ; Neoplasm Metastasis/*genetics/*pathology ; Neoplasm Transplantation ; Phenotype ; Prostatic Neoplasms/blood/diagnosis/*genetics/*pathology ; }, abstract = {Color-coded imaging analysis revealed yellow fluorescent metastasis precursor cells that were readily recognized in the blood of tumor-bearing mice after mixtures of red fluorescent protein (RFP)- and green fluorescent protein (GFP)-expressing PC-3 human prostate carcinoma cells were implanted in the nude mouse prostate and metastasized. The yellow fluorescent cells were purified from the blood of nude mice to 99% homogeneity by FACS, expanded in culture, and reimplanted in the prostate of nude mice. The yellow fluorescent phenotype was heritable and stably maintained by tumor cells for many generations in vitro and in vivo. In the animals implanted with the yellow-fluorescing cells, 100% developed aggressive metastatic cancer. Lung metastases were demonstrated in 100% of the animals as early as four weeks after injection of the yellow-fluorescing cells in the mouse prostate. In contrast, when the GFP- and RFP-expressing parental cells were inoculated into the mouse prostate separately, none of the animals developed lung metastasis. All animals had almost exclusively yellow fluorescent cells in the blood and bone marrow. These results are consistent with the idea that spontaneous genetic exchange between tumor cells in vivo contributes to genomic instability and creation of highly metastatic cells.}, }
@article {pmid16357262, year = {2005}, author = {Meibom, KL and Blokesch, M and Dolganov, NA and Wu, CY and Schoolnik, GK}, title = {Chitin induces natural competence in Vibrio cholerae.}, journal = {Science (New York, N.Y.)}, volume = {310}, number = {5755}, pages = {1824-1827}, doi = {10.1126/science.1120096}, pmid = {16357262}, issn = {1095-9203}, support = {AI053706/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacterial Proteins/genetics/metabolism/physiology ; Biofilms/growth &amp; development ; Brachyura/microbiology ; Chitin/metabolism/*physiology ; Culture Media ; DNA-Binding Proteins/genetics/metabolism ; Fimbriae Proteins/biosynthesis/genetics ; Fimbriae, Bacterial/metabolism ; Frameshift Mutation ; Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Models, Biological ; Mutation ; Phenotype ; Regulon ; Sigma Factor/metabolism ; *Transformation, Bacterial ; Vibrio cholerae/*genetics/growth &amp; development/metabolism/physiology ; Vibrio cholerae O1/*genetics/growth &amp; development/metabolism/physiology ; }, abstract = {The mosaic-structured Vibrio cholerae genome points to the importance of horizontal gene transfer (HGT) in the evolution of this human pathogen. We showed that V. cholerae can acquire new genetic material by natural transformation during growth on chitin, a biopolymer that is abundant in aquatic habitats (e.g., from crustacean exoskeletons), where it lives as an autochthonous microbe. Transformation competence was found to require a type IV pilus assembly complex, a putative DNA binding protein, and three convergent regulatory cascades, which are activated by chitin, increasing cell density, and nutrient limitation, a decline in growth rate, or stress.}, }
@article {pmid16357039, year = {2006}, author = {Li, S and Nosenko, T and Hackett, JD and Bhattacharya, D}, title = {Phylogenomic analysis identifies red algal genes of endosymbiotic origin in the chromalveolates.}, journal = {Molecular biology and evolution}, volume = {23}, number = {3}, pages = {663-674}, doi = {10.1093/molbev/msj075}, pmid = {16357039}, issn = {0737-4038}, support = {T 32 GM98629/GM/NIGMS NIH HHS/United States ; }, mesh = {Algal Proteins/genetics ; Animals ; *Gene Transfer, Horizontal ; Genes, Plant ; Molecular Sequence Data ; *Phylogeny ; Plant Proteins/genetics ; Plastids/chemistry ; *Rhodophyta/classification/genetics ; *Symbiosis ; Thylakoids/chemistry ; }, abstract = {Endosymbiosis has spread photosynthesis to many branches of the eukaryotic tree; however, the history of photosynthetic organelle (plastid) gain and loss remains controversial. Fortuitously, endosymbiosis may leave a genomic footprint through the transfer of endosymbiont genes to the "host" nucleus (endosymbiotic gene transfer, EGT). EGT can be detected through comparison of host genomes to uncover the history of past plastid acquisitions. Here we focus on a lineage of chlorophyll c-containing algae and protists ("chromalveolates") that are postulated to share a common red algal secondary endosymbiont. This plastid is originally of cyanobacterial origin through primary endosymbiosis and is closely related among the Plantae (i.e., red, green, and glaucophyte algae). To test these ideas, an automated phylogenomics pipeline was used with a novel unigene data set of 5,081 expressed sequence tags (ESTs) from the haptophyte alga Emiliania huxleyi and genome or EST data from other chromalveolates, red algae, plants, animals, fungi, and bacteria. We focused on nuclear-encoded proteins that are targeted to the plastid to express their function because this group of genes is expected to have phylogenies that are relatively easy to interpret. A total of 708 genes were identified in E. huxleyi that had a significant Blast hit to at least one other taxon in our data set. Forty-six of the alignments that were derived from the 708 genes contained at least one other chromalveolate (i.e., besides E. huxleyi), red and/or green algae (or land plants), and one or more cyanobacteria, whereas 15 alignments contained E. huxleyi, one or more other chromalveolates, and only cyanobacteria. Detailed phylogenetic analyses of these data sets turned up 19 cases of EGT that did not contain significant paralogy and had strong bootstrap support at the internal nodes, allowing us to confidently identify the source of the plastid-targeted gene in E. huxleyi. A total of 17 genes originated from the red algal lineage, whereas 2 genes were of green algal origin. Our data demonstrate the existence of multiple red algal genes that are shared among different chromalveolates, suggesting that at least a subset of this group may share a common origin.}, }
@article {pmid16356716, year = {2006}, author = {Ragan, MA and Harlow, TJ and Beiko, RG}, title = {Do different surrogate methods detect lateral genetic transfer events of different relative ages?.}, journal = {Trends in microbiology}, volume = {14}, number = {1}, pages = {4-8}, doi = {10.1016/j.tim.2005.11.004}, pmid = {16356716}, issn = {0966-842X}, mesh = {Base Composition ; Computational Biology ; Escherichia coli K12/*genetics ; Escherichia coli Proteins/genetics ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial/*genetics ; Markov Chains ; Phylogeny ; }, abstract = {Non-tree-based ("surrogate") methods have been used to identify instances of lateral genetic transfer in microbial genomes but agreement among predictions of different methods can be poor. It has been proposed that this disagreement arises because different surrogate methods are biased towards the detection of certain types of transfer events. This conjecture is supported by a rigorous phylogenetic analysis of 3776 proteins in Escherichia coli K12 MG1655 to map the ages of transfer events relative to one another.}, }
@article {pmid16352842, year = {2006}, author = {Summer, EJ and Gonzalez, CF and Bomer, M and Carlile, T and Embry, A and Kucherka, AM and Lee, J and Mebane, L and Morrison, WC and Mark, L and King, MD and LiPuma, JJ and Vidaver, AK and Young, R}, title = {Divergence and mosaicism among virulent soil phages of the Burkholderia cepacia complex.}, journal = {Journal of bacteriology}, volume = {188}, number = {1}, pages = {255-268}, pmid = {16352842}, issn = {0021-9193}, support = {R01 GM027099/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacteriolysis ; Bacteriophages/classification/*genetics/isolation &amp; purification/*physiology ; Base Sequence ; Burkholderia cepacia complex/*virology ; *Genetic Variation ; Lysogeny ; Molecular Sequence Data ; *Mosaicism ; Sequence Analysis, DNA ; *Soil Microbiology ; Viral Proteins/chemistry/*genetics/metabolism ; }, abstract = {We have determined the genomic sequences of four virulent myophages, Bcep1, Bcep43, BcepB1A, and Bcep781, whose hosts are soil isolates of the Burkholderia cepacia complex. Despite temporal and spatial separations between initial isolations, three of the phages (Bcep1, Bcep43, and Bcep781, designated the Bcep781 group) exhibit 87% to 99% sequence identity to one another and most coding region differences are due to synonymous nucleotide substitutions, a hallmark of neutral genetic drift. Phage BcepB1A has a very different genome organization but is clearly a mosaic with respect to many of the genes of the Bcep781 group, as is a defective prophage element in Photorhabdus luminescens. Functions were assigned to 27 out of 71 predicted genes of Bcep1 despite extreme sequence divergence. Using a lambda repressor fusion technique, 10 Bcep781-encoded proteins were identified for their ability to support homotypic interactions. While head and tail morphogenesis genes have retained canonical gene order despite extreme sequence divergence, genes involved in DNA metabolism and host lysis are not organized as in other phages. This unusual genome arrangement may contribute to the ability of the Bcep781-like phages to maintain a unified genomic type. However, the Bcep781 group phages can also engage in lateral gene transfer events with otherwise unrelated phages, a process that contributes to the broader-scale genomic mosaicism prevalent among the tailed phages.}, }
@article {pmid16352556, year = {2006}, author = {Benarroch, D and Claverie, JM and Raoult, D and Shuman, S}, title = {Characterization of mimivirus DNA topoisomerase IB suggests horizontal gene transfer between eukaryal viruses and bacteria.}, journal = {Journal of virology}, volume = {80}, number = {1}, pages = {314-321}, pmid = {16352556}, issn = {0022-538X}, support = {R01 GM046330/GM/NIGMS NIH HHS/United States ; R37 GM046330/GM/NIGMS NIH HHS/United States ; GM46330/GM/NIGMS NIH HHS/United States ; }, mesh = {Acanthamoeba/virology ; Amino Acid Sequence ; Animals ; Bacteria/genetics/metabolism ; DNA Topoisomerases, Type I/chemistry/genetics/isolation &amp; purification/*metabolism ; DNA, Superhelical/metabolism ; Entomopoxvirinae/chemistry/*enzymology/genetics ; *Gene Transfer, Horizontal ; *Genome, Viral ; Molecular Sequence Data ; Nucleic Acid Conformation ; }, abstract = {Mimivirus, a parasite of Acanthamoeba polyphaga, is the largest DNA virus known; it encodes dozens of proteins with imputed functions in nucleic acid transactions. Here we produced, purified, and characterized mimivirus DNA topoisomerase IB (TopIB), which we find to be a structural and functional homolog of poxvirus TopIB and the poxvirus-like topoisomerases discovered recently in bacteria. Arginine, histidine, and tyrosine side chains responsible for TopIB transesterification are conserved and essential in mimivirus TopIB. Moreover, mimivirus TopIB is capable of incising duplex DNA at the 5'-CCCTT cleavage site recognized by all poxvirus topoisomerases. Based on the available data, mimivirus TopIB appears functionally more akin to poxvirus TopIB than bacterial TopIB, despite its greater primary structure similarity to the bacterial TopIB group. We speculate that the ancestral bacterial/viral TopIB was disseminated by horizontal gene transfer within amoebae, which are permissive hosts for either intracellular growth or persistence of many present-day bacterial species that have a type IB topoisomerase.}, }
@article {pmid16352422, year = {2006}, author = {Giakkoupi, P and Tambic-Andrasevic, A and Vourli, S and Skrlin, J and Sestan-Crnek, S and Tzouvelekis, LS and Vatopoulos, AC}, title = {Transferable DHA-1 cephalosporinase in Escherichia coli.}, journal = {International journal of antimicrobial agents}, volume = {27}, number = {1}, pages = {77-80}, doi = {10.1016/j.ijantimicag.2005.09.013}, pmid = {16352422}, issn = {0924-8579}, mesh = {Bacterial Proteins/genetics ; Cephalosporin Resistance/*genetics ; Cephalosporinase/*genetics ; Cephalosporins/pharmacology ; Conjugation, Genetic ; Croatia ; Escherichia coli/drug effects/*genetics/isolation &amp; purification ; Escherichia coli Infections/microbiology ; Escherichia coli Proteins/*genetics ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Plasmids/genetics ; Polymerase Chain Reaction/methods ; beta-Lactams/pharmacology ; }, abstract = {Three Escherichia coli isolates resistant to third-generation cephalosporins but negative for extended-spectrum beta-lactamase production were isolated from hospitalised patients in Zagreb, Croatia, during June 2003 to February 2004. Resistance was due to the inducible production of a DHA-1 cephalosporinase. Each isolate contained an integron-associated bla(DHA-1)-ampR sequence carried by similar-sized plasmids, of which one was self-transferable. Serotyping and polymerase chain reaction typing using ERIC2 primer indicated that the isolates were distinct. This is the first description of DHA beta-lactamase production in E. coli.}, }
@article {pmid16352412, year = {2006}, author = {Lebuhn, M and Bathe, S and Achouak, W and Hartmann, A and Heulin, T and Schloter, M}, title = {Comparative sequence analysis of the internal transcribed spacer 1 of Ochrobactrum species.}, journal = {Systematic and applied microbiology}, volume = {29}, number = {4}, pages = {265-275}, doi = {10.1016/j.syapm.2005.11.003}, pmid = {16352412}, issn = {0723-2020}, mesh = {Alleles ; DNA, Bacterial/chemistry/genetics ; DNA, Intergenic/*chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Gene Transfer, Horizontal ; *Genes, rRNA ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Ochrobactrum/classification/*genetics ; Phylogeny ; Polymorphism, Genetic ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Statistics as Topic ; }, abstract = {The internal 16S/23S rDNA (rrs/rrl) internal spacer region 1 (ITS1) of 54 Ochrobactrum strains and close relatives was analysed. Separation of ITS1 containing PCR products by gel-electrophoresis, DGGE, cloning and sequencing revealed ITS1 length and sequence heterogeneity. We found up to 5 different allelic ITS1 stretches within a single strain (Ochrobactrum intermedium LMG 3301T), and 2-3 different ITS1 alleles in O. tritici. Within ITS1, ITS1c, being part of the conserved double-stranded rrn processing stem dsPS1, produced the most reliable segment tree. The overall ITS1, ITS1c and rrs phylogenetic tree topologies were generally consistent, but there was evidence for horizontal rrn (segment) transfer in O. tritici LMG 2134 (formerly O. anthropi). Good correlations were found between ITS1, ITS1c and rrs sequence similarity and DNA-DNA hybridization values indicating that phylogenetic analysis of ITS1 and ITS1c both can be used to preliminarily deduce the phylogenetic affiliation if HGT was excluded. Strains sharing > 96.19% ITS1c (> 95.11% ITS1) similarity fell within a species, and < or = 68.42% ITS1c (< or = 70.33% ITS1) similarity outside a genus. Both ITS1 and ITS1c analysis resolved microdiversity more profoundly than rrs analysis and revealed clades (genomovars) within O. anthropi that were also produced in rep cluster analysis. There was no evidence for habitat-specific ITS1 genomovars within Ochrobactrum species. Diversity of Ochrobactrum was higher in soil than at the rhizoplane below and at the species level. Isolates from soil contained only 1 rrn type whereas isolates from human clinical, animal and rhizoplane specimens could contain more.}, }
@article {pmid16351845, year = {2001}, author = {Rumpho, ME and Summer, EJ and Green, BJ and Fox, TC and Manhart, JR}, title = {Mollusc/algal chloroplast symbiosis: how can isolated chloroplasts continue to function for months in the cytosol of a sea slug in the absence of an algal nucleus?.}, journal = {Zoology (Jena, Germany)}, volume = {104}, number = {3-4}, pages = {303-312}, doi = {10.1078/0944-2006-00036}, pmid = {16351845}, issn = {0944-2006}, abstract = {A marine sea slug, Elysia chlorotica, has acquired the ability to carry out photosynthesis as a result of forming an intracellular symbiotic association with chloroplasts of the chromophytic alga, Vaucheria litorea. The symbiont chloroplasts (kleptoplasts) are functional, i.e. they evolve oxygen and fix CO(2) and actively transcribe and translate proteins for several months in the sea slug cytosol. Considering the dependency of plastid function on nuclear genes, the level of kleptoplast activity observed in the animal cell is quite remarkable. Possible factors contributing to this long-lasting functional association that are considered here include: the presence of an algal nuclear genome in the sea slug, autonomous chloroplasts, unusual chloroplast/protein stability, re-directing of animal proteins to the kleptoplast, and lateral gene transfer. Based on our current understanding, the acquisition and incorporation of intact algal plastids by E. chlorotica is aided by the robustness of the plastids and the long-term functional activity of the kleptoplasts appears to be supported by both plastid and protein stability and contributions from the sea slug.}, }
@article {pmid16344004, year = {2006}, author = {Steglich, C and Schaeffer, SW}, title = {The ornithine decarboxylase gene of Trypanosoma brucei: Evidence for horizontal gene transfer from a vertebrate source.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {6}, number = {3}, pages = {205-219}, doi = {10.1016/j.meegid.2005.05.004}, pmid = {16344004}, issn = {1567-1348}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Sequence ; Animals ; Chromosome Mapping ; Chromosomes ; Conserved Sequence ; DNA, Protozoan/chemistry/genetics ; Gene Dosage ; *Gene Transfer, Horizontal ; *Genes, Protozoan ; Genetic Linkage ; Molecular Sequence Data ; Ornithine Decarboxylase/chemistry/*genetics ; Phylogeny ; Protein Structure, Tertiary ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Synteny ; Trypanosoma brucei brucei/*genetics ; Vertebrates/*genetics/*parasitology ; }, abstract = {Kinetoplastid protozoans in the family Trypanosomatidae are parasites, many of them responsible for serious diseases in humans and domestic animals. Ornithine decarboxlyase (ODC), a protein at the core of polyamine metabolism, is a potential target for therapies to overcome these diseases. Eukaryotic phylogenies were constructed from full-length genes for ODC to determine the origin of ODC in the kinetoplastid protozoans. The Odc genes from Trypanosoma brucei and two other African trypanosomes, T. congolense and T. vivax, clustered with Odc genes from vertebrates rather than with Odc genes from other kinetoplastids and other protozoans, making this gene a candidate for horizontal gene transfer from a vertebrate source. This result is unique to the Odc gene from the African trypanosomes as four other genes produced phylogenies consistent with the expected taxonomic relationships for the organisms. Analysis of the genomic regions around the Odc genes in Leishmania major, T. brucei, and Trypanosoma cruzi supports the hypothesis of loss of the Odc gene in the Trypanosoma lineage followed by acquisition of a new copy from a vertebrate host in the African branch of the genus.}, }
@article {pmid16343332, year = {2006}, author = {Hedlund, BP and Staley, JT}, title = {Isolation and characterization of Pseudoalteromonas strains with divergent polycyclic aromatic hydrocarbon catabolic properties.}, journal = {Environmental microbiology}, volume = {8}, number = {1}, pages = {178-182}, doi = {10.1111/j.1462-2920.2005.00871.x}, pmid = {16343332}, issn = {1462-2912}, support = {T32 G07270//PHS HHS/United States ; }, mesh = {Blotting, Southern ; Cluster Analysis ; Dioxygenases ; Gene Transfer, Horizontal ; Multienzyme Complexes/genetics ; Naphthalenes/metabolism ; Oxygenases/genetics ; Phylogeny ; Polycyclic Aromatic Hydrocarbons/*metabolism ; Pseudoalteromonas/*genetics/*metabolism ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Species Specificity ; Washington ; }, abstract = {Fifteen strains of polycyclic aromatic hydrocarbon (PAH)-catabolizing bacteria, identified as Pseudoalteromonas spp. were isolated from Eagle Harbor, Puget Sound, USA, using a most probable number procedure in which naphthalene or phenanthrene was the sole carbon and energy source. Despite having identical 16S rDNA sequences, some catabolized many PAHs, whereas others oxidized only naphthalenes. A putative naphthalene 1,2-dioxygenase gene fragment was polymerase chain reaction-amplified from the naphthalene-degrading strains and shown to be almost identical to a gene present in Neptunomonas naphthovorans, suggesting horizontal transfer.}, }
@article {pmid16342783, year = {2005}, author = {Shao, M and Wang, HM and Liu, ZH and Shen, P and Cai, RX}, title = {[Load of calcium probe Fura -2/AM in Escherichia coli cells].}, journal = {Wei sheng wu xue bao = Acta microbiologica Sinica}, volume = {45}, number = {5}, pages = {805-807}, pmid = {16342783}, issn = {0001-6209}, mesh = {Calcium/*analysis/metabolism ; Escherichia coli/*metabolism ; *Fura-2 ; Spectrometry, Fluorescence ; }, abstract = {The fluorescence characteristics of Fura-2/AM, a kind of calcium probe normally used in analysis of animal cells, were studied in detail in this work. The load of the probe into Escherichia coli cells was elucidated through fluorescence spectra. The combination of Fura-2 with calcium ions inside Escherichiacoli cells was observed, and the transmembrane behaviors of extracellular calcium to Escherichia coli cells were also investigated. The work was aimed at further researches on the calcium-induced horizontal gene transfer in Escherichia coli cells.}, }
@article {pmid16341468, year = {2006}, author = {Merkl, R}, title = {A comparative categorization of protein function encoded in bacterial or archeal genomic islands.}, journal = {Journal of molecular evolution}, volume = {62}, number = {1}, pages = {1-14}, pmid = {16341468}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Archaeal Proteins/genetics/*physiology ; Bacterial Proteins/genetics/*physiology ; *Genomic Islands ; Molecular Sequence Data ; Phylogeny ; Regulatory Elements, Transcriptional ; }, abstract = {Genomes of prokaryotes harbor genomic islands (GIs), which are frequently acquired via horizontal gene transfer (HGT). Here I present an analysis of GIs with respect to gene-encoded functions. GIs were identified by statistical analysis of codon usage and clustering. Genes classified as putatively alien (pA) or putatively native (pN) were categorized according to the COG database. Among pA and pN genes, the distribution of COG functions and classes were studied for different groupings of prokaryotes. Groups were formed according to taxonomical relation or habitats. In all groups, genes related to class L (replication, recombination, and repair) were statistically significantly overrepresented in GIs. GIs of bacteria and archaea showed a distinct pattern of preferences. In archeal GIs, genes belonging to COG class M (cell wall/membrane/envelope biogenesis) or Q (secondary metabolites biosynthesis, transport, and catabolism) were more frequent. In bacterial GIs, genes of classes U (intracellular trafficking, secretion, and vesicular transport), N (cell motility), and V (defense mechanisms) were predominant. Underrepresentation was strongest for genes belonging to class J (translation, ribosomal structure, and biogenesis). Among single COG functions overrepresented in GIs were transferases and transporters. In both superkingdoms, HGT enhances genomic content by meeting demands that are independent of the studied habitats. These findings are in agreement with the complexity theory, which predicts the preferential import of operational genes. However, only specific subsets of operational genes were enriched in GIs. Modification of the cell envelope, cell motility, secretion, and protection of cellular DNA are major issues in HGT.}, }
@article {pmid16336045, year = {2006}, author = {Diao, X and Freeling, M and Lisch, D}, title = {Horizontal transfer of a plant transposon.}, journal = {PLoS biology}, volume = {4}, number = {1}, pages = {e5}, pmid = {16336045}, issn = {1545-7885}, mesh = {Amino Acid Sequence ; Base Sequence ; DNA Transposable Elements/*genetics ; *Gene Transfer, Horizontal ; Introns/genetics ; Molecular Sequence Data ; Oryza/genetics ; Sequence Alignment ; Setaria Plant/*genetics ; Zea mays/genetics ; }, abstract = {The majority of well-documented cases of horizontal transfer between higher eukaryotes involve the movement of transposable elements between animals. Surprisingly, although plant genomes often contain vast numbers of these mobile genetic elements, no evidence of horizontal transfer of a nuclear-encoded transposon between plant species has been detected to date. The most mutagenic known plant transposable element system is the Mutator system in maize. Mu-like elements (MULEs) are widespread among plants, and previous analysis has suggested that the distribution of various subgroups of MULEs is patchy, consistent with horizontal transfer. We have sequenced portions of MULE transposons from a number of species of the genus Setaria and compared them to each other and to publicly available databases. A subset of these elements is remarkably similar to a small family of MULEs in rice. A comparison of noncoding and synonymous sequences revealed that the observed similarity is not due to selection at the amino acid level. Given the amount of time separating Setaria and rice, the degree of similarity between these elements excludes the possibility of simple vertical transmission of this class of MULEs. This is the first well-documented example of horizontal transfer of any nuclear-encoded genes between higher plants.}, }
@article {pmid16333073, year = {2005}, author = {Dogan, B and Schukken, YH and Santisteban, C and Boor, KJ}, title = {Distribution of serotypes and antimicrobial resistance genes among Streptococcus agalactiae isolates from bovine and human hosts.}, journal = {Journal of clinical microbiology}, volume = {43}, number = {12}, pages = {5899-5906}, pmid = {16333073}, issn = {0095-1137}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics ; Cattle ; Cattle Diseases/microbiology ; Drug Resistance, Bacterial/*genetics ; Erythromycin/*pharmacology ; Humans ; Microbial Sensitivity Tests ; Ribotyping ; Serotyping ; Streptococcal Infections/microbiology ; Streptococcus agalactiae/*classification/drug effects/genetics/isolation &amp; purification ; Tetracyclines/*pharmacology ; }, abstract = {To better understand the emergence and transmission of antibiotic-resistant Streptococcus agalactiae, we compared phenotypic and genotypic characteristics of 52 human and 83 bovine S. agalactiae isolates. Serotypes found among isolates from human hosts included V (48.1%), III (19.2%), Ia and Ib (13.5% each), and II (5.8%). Among isolates from bovine hosts, molecular serotypes III and II were predominant (53 and 14.5%, respectively). Four and 21 different ribotypes were found among human and bovine isolates, respectively. A combination of ribotyping and serotyping showed that two bovine isolates were indistinguishable from human isolates. Resistance to tetracycline and erythromycin was more common among human (84.6% and 26.9%, respectively) than bovine (14.5% and 3.6%, respectively) isolates. tetM was found in all tetracycline-resistant human isolates, while tetO was the predominant resistance gene among bovine isolates. tet genes were found among various ribotypes. ermB, ermTR, and mefA were detected among erythromycin-resistant human isolates, while ermB was the only erythromycin resistance determinant among isolates from bovine hosts. For isolates from human hosts, erythromycin resistance genes appeared to be associated with specific ribotypes. We conclude that (i) human and bovine S. agalactiae isolates represent distinct populations; (ii) human host-associated S. agalactiae subtypes may occasionally be transmitted to bovines; (iii) while emergence of erythromycin and tetracycline resistance appears to largely occur independently among human and bovine isolates, occasional cross-species transfer of resistant strains or transmission of resistance genes between human- and bovine-associated subtypes may occur; and (iv) dissemination of antibiotic-resistant S. agalactiae appears to include both clonal spread of resistant strains as well as horizontal gene transfer.}, }
@article {pmid16332840, year = {2005}, author = {Taghavi, S and Barac, T and Greenberg, B and Borremans, B and Vangronsveld, J and van der Lelie, D}, title = {Horizontal gene transfer to endogenous endophytic bacteria from poplar improves phytoremediation of toluene.}, journal = {Applied and environmental microbiology}, volume = {71}, number = {12}, pages = {8500-8505}, pmid = {16332840}, issn = {0099-2240}, mesh = {*Biodegradation, Environmental ; Burkholderia cepacia/*genetics/metabolism ; DNA Primers ; *Gene Transfer, Horizontal ; Plant Leaves/microbiology ; Plant Roots/microbiology ; Plant Stems/microbiology ; Polymerase Chain Reaction ; Populus/growth &amp; development/*microbiology ; Soil Microbiology ; Toluene/*pharmacokinetics ; }, abstract = {Poplar, a plant species frequently used for phytoremediation of groundwater contaminated with organic solvents, was inoculated with the endophyte Burkholderia cepacia VM1468. This strain, whose natural host is yellow lupine, contains the pTOM-Bu61 plasmid coding for constitutively expressed toluene degradation. Noninoculated plants or plants inoculated with the soil bacterium B. cepacia Bu61(pTOM-Bu61) were used as controls. Inoculation of poplar had a positive effect on plant growth in the presence of toluene and reduced the amount of toluene released via evapotranspiration. These effects were more dramatic for VM1468, the endophytic strain, than for Bu61. Remarkably, none of the strains became established at detectable levels in the endophytic community, but there was horizontal gene transfer of pTOM-Bu61 to different members of the endogenous endophytic community, both in the presence and in the absence of toluene. This work is the first report of in planta horizontal gene transfer among plant-associated endophytic bacteria and demonstrates that such transfer could be used to change natural endophytic microbial communities in order to improve the remediation of environmental insults.}, }
@article {pmid16332824, year = {2005}, author = {Siezen, RJ and Renckens, B and van Swam, I and Peters, S and van Kranenburg, R and Kleerebezem, M and de Vos, WM}, title = {Complete sequences of four plasmids of Lactococcus lactis subsp. cremoris SK11 reveal extensive adaptation to the dairy environment.}, journal = {Applied and environmental microbiology}, volume = {71}, number = {12}, pages = {8371-8382}, pmid = {16332824}, issn = {0099-2240}, mesh = {Base Sequence ; Codon, Initiator/genetics ; DNA Replication ; Lactococcus lactis/*genetics/metabolism ; Lactose/metabolism ; Molecular Sequence Data ; Open Reading Frames ; Plasmids/*genetics ; Restriction Mapping ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; }, abstract = {Lactococcus lactis strains are known to carry plasmids encoding industrially important traits. L. lactis subsp. cremoris SK11 is widely used by the dairy industry in cheese making. Its complete plasmid complement was sequenced and found to contain the plasmids pSK11A (10,372 bp), pSK11B (13,332 bp), pSK11L (47,165 bp), and pSK11P (75,814 bp). Six highly homologous repB-containing replicons were found, all belonging to the family of lactococcal theta-type replicons. Twenty-three complete insertion sequence elements segment the plasmids into numerous modules, many of which can be identified as functional units or containing functionally related genes. Plasmid-encoded functions previously known to reside on L. lactis SK11 plasmids were now mapped in detail, e.g., lactose utilization (lacR-lacABCDFEGX), the proteolytic system (prtM-prtP, pepO, pepF), and the oligopeptide permease system (oppDFBCA). Newly identified plasmid-encoded functions could facilitate the uptake of various cations, while the pabA and pabB genes could be essential for folate biosynthesis. A competitive advantage could be obtained by using the putative flavin adenine dinucleotide-dependent d-lactate dehydrogenase and oxalate:formate antiporter for enhanced ATP synthesis, while the activity of the predicted alpha-acetolactate decarboxylase may contribute to the formation of an additional electron sink. Various stress response proteins are plasmid encoded, which could enhance strain robustness. A substantial number of these "adaptation" genes have not been described before on L. lactis plasmids. Moreover, several genes were identified for the first time in L. lactis, possibly reflecting horizontal gene transfer.}, }
@article {pmid16332816, year = {2005}, author = {Beumer, A and Robinson, JB}, title = {A broad-host-range, generalized transducing phage (SN-T) acquires 16S rRNA genes from different genera of bacteria.}, journal = {Applied and environmental microbiology}, volume = {71}, number = {12}, pages = {8301-8304}, pmid = {16332816}, issn = {0099-2240}, mesh = {Bacteriophages/*genetics ; Base Sequence ; DNA Primers ; DNA, Bacterial/genetics ; Genome, Bacterial ; Pseudomonas Phages/genetics ; Pseudomonas aeruginosa/*genetics ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; Serratia marcescens/genetics ; *Transduction, Genetic ; }, abstract = {Genomic analysis has revealed heterogeneity among bacterial 16S rRNA gene sequences within a single species; yet the cause(s) remains uncertain. Generalized transducing bacteriophages have recently gained recognition for their abundance as well as their ability to affect lateral gene transfer and to harbor bacterial 16S rRNA gene sequences. Here, we demonstrate the ability of broad-host-range, generalized transducing phages to acquire 16S rRNA genes and gene sequences. Using PCR and primers specific to conserved regions of the 16S rRNA gene, we have found that generalized transducing phages (D3112, UT1, and SN-T), but not specialized transducing phages (D3), acquired entire bacterial 16S rRNA genes. Furthermore, we show that the broad-host-range, generalized transducing phage SN-T is capable of acquiring the 16S rRNA gene from two different genera: Sphaerotilus natans, the host from which SN-T was originally isolated, and Pseudomonas aeruginosa. In sequential infections, SN-T harbored only 16S rRNA gene sequences of the final host as determined by restriction fragment length polymorphism analysis. The frequency of 16S rRNA gene sequences in SN-T populations was determined to be 1 x 10(-9) transductants/PFU. Our findings further implicate transduction in the horizontal transfer of 16S rRNA genes between different species or genera of bacteria.}, }
@article {pmid16332777, year = {2005}, author = {Russell, JA and Moran, NA}, title = {Horizontal transfer of bacterial symbionts: heritability and fitness effects in a novel aphid host.}, journal = {Applied and environmental microbiology}, volume = {71}, number = {12}, pages = {7987-7994}, pmid = {16332777}, issn = {0099-2240}, mesh = {Animals ; Aphids/classification/*microbiology ; Base Sequence ; DNA Primers ; DNA, Bacterial/genetics ; Female ; Gammaproteobacteria/*genetics/isolation &amp; purification ; Gene Transfer, Horizontal/*genetics ; Polymerase Chain Reaction ; Symbiosis/*genetics ; }, abstract = {Members of several bacterial lineages are known only as symbionts of insects and move among hosts through maternal transmission. Such vertical transfer promotes strong fidelity within these associations, favoring the evolution of microbially mediated effects that improve host fitness. However, phylogenetic evidence indicates occasional horizontal transfer among different insect species, suggesting that some microbial symbionts retain a generalized ability to infect multiple hosts. Here we examine the abilities of three vertically transmitted bacteria from the Gammaproteobacteria to infect and spread within a novel host species, the pea aphid, Acyrthosiphon pisum. Using microinjection, we transferred symbionts from three species of natural aphid hosts into a common host background, comparing transmission efficiencies between novel symbionts and those naturally infecting A. pisum. We also examined the fitness effects of two novel symbionts to determine whether they should persist under natural selection acting at the host level. Our results reveal that these heritable bacteria vary in their capacities to utilize A. pisum as a host. One of three novel symbionts failed to undergo efficient maternal transmission in A. pisum, and one of the two efficiently transmitted bacteria depressed aphid growth rates. Although these findings reveal that negative fitness effects and low transmission efficiency can prevent the establishment of a new infection following horizontal transmission, they also indicate that some symbionts can overcome these obstacles, accounting for their widespread distributions across aphids and related insects.}, }
@article {pmid16332766, year = {2005}, author = {Xiao, X and Yin, X and Lin, J and Sun, L and You, Z and Wang, P and Wang, F}, title = {Chitinase genes in lake sediments of Ardley Island, Antarctica.}, journal = {Applied and environmental microbiology}, volume = {71}, number = {12}, pages = {7904-7909}, pmid = {16332766}, issn = {0099-2240}, mesh = {Antarctic Regions ; Bacteria/classification/enzymology/genetics/*isolation &amp; purification ; Chitinases/*genetics ; Cold Climate ; Conserved Sequence ; DNA Primers ; Fresh Water/*microbiology ; Genetic Variation ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {A sediment core spanning approximately 1,600 years was collected from a lake on Ardley Island, Antarctica. The sediment core had been greatly influenced by penguin guano. Using molecular methods, the chitinolytic bacterial community along the sediment core was studied over its entire length. Primers targeting conserved sequences of the catalytic domains of family 18 subgroup A chitinases detected group A chitinases from a wide taxonomic range of bacteria. Using quantitative competitive PCR (QC-PCR), chitinase gene copies in each 1-cm section of the whole sediment column were quantified. QC-PCR determination of the chitinase gene copies indicated significant correlation with phosphorus and total organic carbon concentration, suggesting a historical connection between chitinase gene copies and the amount of penguin guano input into the lake sediment. Most of the chitinase genes cloned from the historic sediment core were novel. Analysis of the chitinase gene diversity in selected sediment layers and in the fresh penguin deposits indicated frequent shifts in the chitinolytic bacterial community over time. Sequence analysis of the 16S rRNA genes of chitinolytic bacteria isolated from the lake sediment revealed that the isolates belonged to Janthinobacterium species, Stenotrophomonas species of gamma-Proteobacteria, Cytophaga species of the Cytophaga-Flexibacter-Bacteroides group, and Streptomyces and Norcardiopsis species of Actinobacteria. Chitinase gene fragments were cloned and sequenced from these cultivated chitinolytic bacteria. The phylogeny of the chitinase genes obtained from the isolates did not correspond well to that of the isolates, suggesting acquisition via horizontal gene transfer.}, }
@article {pmid16332712, year = {2006}, author = {Cordes, MH and Binford, GJ}, title = {Lateral gene transfer of a dermonecrotic toxin between spiders and bacteria.}, journal = {Bioinformatics (Oxford, England)}, volume = {22}, number = {3}, pages = {264-268}, doi = {10.1093/bioinformatics/bti811}, pmid = {16332712}, issn = {1367-4803}, mesh = {Bacterial Toxins/*chemistry/*genetics/metabolism ; Computer Simulation ; Conserved Sequence ; Dermotoxins/*chemistry/*genetics/metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Models, Chemical ; Models, Genetic ; Models, Molecular ; Sequence Alignment ; Sequence Analysis, Protein ; Sequence Homology, Amino Acid ; Spider Venoms/*chemistry/*genetics/metabolism ; }, abstract = {MOTIVATION: Spiders in the genus Loxosceles, including the notoriously toxic brown recluse, cause severe necrotic skin lesions owing to the presence of a venom enzyme called sphingomyelinase D (SMaseD). This enzyme activity is unknown elsewhere in the animal kingdom but is shared with strains of pathogenic Corynebacteria that cause various illnesses in farm animals. The presence of the same toxic activity only in distantly related organisms poses an interesting and medically important question in molecular evolution.<br><br>RESULTS: We use superpositions of recently determined structures and sequence comparisons to infer that both bacterial and spider SMaseDs originated from a common, broadly conserved domain family, the glycerophosphoryl diester phosphodiesterases. We also identify a unique sequence/structure motif present in both SMaseDs but not in the ancestral family, supporting SMaseD origin through a single divergence event in either bacteria or spiders, followed by lateral gene transfer from one lineage to the other.}, }
@article {pmid16330755, year = {2005}, author = {Mongodin, EF and Nelson, KE and Daugherty, S and Deboy, RT and Wister, J and Khouri, H and Weidman, J and Walsh, DA and Papke, RT and Sanchez Perez, G and Sharma, AK and Nesbø, CL and MacLeod, D and Bapteste, E and Doolittle, WF and Charlebois, RL and Legault, B and Rodriguez-Valera, F}, title = {The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {102}, number = {50}, pages = {18147-18152}, pmid = {16330755}, issn = {0027-8424}, mesh = {Adaptation, Physiological/genetics ; Archaea/*genetics ; Bacteroidetes/enzymology/*genetics ; Base Composition ; Base Sequence ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial/*genetics ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Rhodopsins, Microbial/*genetics ; Sequence Analysis, DNA ; }, abstract = {Saturated thalassic brines are among the most physically demanding habitats on Earth: few microbes survive in them. Salinibacter ruber is among these organisms and has been found repeatedly in significant numbers in climax saltern crystallizer communities. The phenotype of this bacterium is remarkably similar to that of the hyperhalophilic Archaea (Haloarchaea). The genome sequence suggests that this resemblance has arisen through convergence at the physiological level (different genes producing similar overall phenotype) and the molecular level (independent mutations yielding similar sequences or structures). Several genes and gene clusters also derive by lateral transfer from (or may have been laterally transferred to) haloarchaea. S. ruber encodes four rhodopsins. One resembles bacterial proteorhodopsins and three are of the haloarchaeal type, previously uncharacterized in a bacterial genome. The impact of these modular adaptive elements on the cell biology and ecology of S. ruber is substantial, affecting salt adaptation, bioenergetics, and photobiology.}, }
@article {pmid16330169, year = {2006}, author = {Kather, EJ and Marks, SL and Foley, JE}, title = {Determination of the prevalence of antimicrobial resistance genes in canine Clostridium perfringens isolates.}, journal = {Veterinary microbiology}, volume = {113}, number = {1-2}, pages = {97-101}, doi = {10.1016/j.vetmic.2005.10.021}, pmid = {16330169}, issn = {0378-1135}, mesh = {Animals ; Anti-Infective Agents/pharmacology ; Clostridium Infections/epidemiology/microbiology/*veterinary ; Clostridium perfringens/drug effects/*genetics/isolation &amp; purification ; Conjugation, Genetic/genetics/physiology ; Diarrhea/epidemiology/microbiology/*veterinary ; Dog Diseases/epidemiology/*microbiology ; Dogs ; Drug Resistance, Microbial/*genetics ; Gene Transfer, Horizontal/genetics ; Macrolides/pharmacology ; Metronidazole/pharmacology ; Microbial Sensitivity Tests/methods ; Polymerase Chain Reaction/methods ; Prevalence ; Tetracyclines/pharmacology ; }, abstract = {Clostridium perfringens is a well documented cause of a mild self-limiting diarrhea and a potentially fatal acute hemorrhagic diarrheal syndrome in the dog. A recent study documented that 21% of canine C. perfringens isolates had MIC's indicative of resistance to tetracycline, an antimicrobial commonly recommended for treatment of C. perfringens-associated diarrhea. The objective of the present study was to further evaluate the antimicrobial susceptibility profiles of these isolates by determining the prevalence of specific resistance genes, their expression, and ability for transference between bacteria. One hundred and twenty-four canine C. perfringens isolates from 124 dogs were evaluated. Minimum inhibitory concentrations of tetracycline, erythromycin, tylosin, and metronidazole were determined using the CLSI Reference Agar Dilution Method. All isolates were screened for three tetracycline resistance genes: tetA(P), tetB(P) and tetM, and two macrolide resistance genes: ermB and ermQ, via PCR using primer sequences previously described. Ninety-six percent (119/124) of the isolates were positive for the tetA(P) gene, and 41% (51/124) were positive for both the tetA(P) and tetB(P) genes. No isolates were positive for the tetB(P) gene alone. Highly susceptible isolates (MIC< or = 4 microg/ml) were significantly more likely to lack the tetB(P) gene. One isolate (0.8%) was positive for the ermB gene, and one isolate was positive for the ermQ gene. The tetM gene was not found in any of the isolates tested. Two out of 15 tested isolates (13%) demonstrated transfer of tetracycline resistance via bacterial conjugation. Tetracycline should be avoided for the treatment of C. perfringens-associated diarrhea in dogs because of the relatively high prevalence of in vitro resistance, and the potential for conjugative transfer of antimicrobial resistance.}, }
@article {pmid16329851, year = {2004}, author = {Ueki, M and Matsui, K and Choi, K and Kawabata, Z}, title = {The enhancement of conjugal plasmid pBHR1 transfer between bacteria in the presence of extracellular metabolic products produced by Microcystis aeruginosa.}, journal = {FEMS microbiology ecology}, volume = {51}, number = {1}, pages = {1-8}, doi = {10.1016/j.femsec.2004.07.003}, pmid = {16329851}, issn = {0168-6496}, mesh = {Carbon/metabolism ; *Conjugation, Genetic ; Escherichia coli/*genetics ; Gene Transfer, Horizontal ; Microcystis/*metabolism ; Plasmids/*genetics ; Pseudomonas stutzeri/*genetics ; Water Microbiology ; }, abstract = {Conjugal plasmid transfer from Escherichia coli S17-1 (pBHR1) to Pseudomonas stutzeri was investigated in the presence of a cyanophyta Microcystis aeruginosa. The plasmid transfer frequency increased with higher densities of M. aeruginosa. The extracellular metabolic products (EMPs) from M. aeruginosa were found to enhance the plasmid transfer between bacteria. Furthermore, the plasmid transfer frequency in medium containing EMPs was significantly higher than that in culture medium with or without glucose. These results suggest that M. aeruginosa enhances conjugal plasmid transfer between bacteria through its EMPs, and that identity of the carbon source is an important factor affecting conjugal plasmid transfer in aquatic environments.}, }
@article {pmid16327766, year = {2005}, author = {Bjerkvig, R and Tysnes, BB and Aboody, KS and Najbauer, J and Terzis, AJ}, title = {Opinion: the origin of the cancer stem cell: current controversies and new insights.}, journal = {Nature reviews. Cancer}, volume = {5}, number = {11}, pages = {899-904}, doi = {10.1038/nrc1740}, pmid = {16327766}, issn = {1474-175X}, mesh = {Animals ; Cell Fusion ; Cell Transformation, Neoplastic/genetics/*pathology ; Gene Transfer, Horizontal/physiology ; Humans ; Neoplasms/genetics/*pathology ; Stem Cells/*pathology ; }, abstract = {Most tumours are derived from a single cell that is transformed into a cancer-initiating cell (cancer stem cell) that has the capacity to proliferate and form tumours in vivo. However, the origin of the cancer stem cell remains elusive. Interestingly, during development and tissue repair the fusion of genetic and cytoplasmic material between cells of different origins is an important physiological process. Such cell fusion and horizontal gene-transfer events have also been linked to several fundamental features of cancer and could be important in the development of the cancer stem cell.}, }
@article {pmid16323120, year = {2006}, author = {Levine, DP}, title = {Vancomycin: a history.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {42 Suppl 1}, number = {}, pages = {S5-12}, doi = {10.1086/491709}, pmid = {16323120}, issn = {1537-6591}, mesh = {Anti-Bacterial Agents/*history/pharmacology/therapeutic use ; Enterococcus/drug effects ; Gene Transfer, Horizontal/drug effects ; History, 20th Century ; History, 21st Century ; Humans ; Staphylococcus aureus/drug effects ; Vancomycin/*history/pharmacology/therapeutic use ; Vancomycin Resistance/*genetics ; }, abstract = {Vancomycin became available for clinical use >50 years ago but was soon discarded in favor of other antibiotics that were deemed to be more efficacious and less toxic. The advent of pseudomembranous enterocolitis, coupled with the spread of methicillin-resistant Staphylococcus aureus, led to a resurgence in the use of vancomycin. Almost immediately, concerns arose with regard to its therapeutic utility. In addition, resistance to vancomycin developed, first in enterococci and later in staphylococci. Several types of resistance have now been identified, each with a unique effect on infections treated with vancomycin. Recent studies have rekindled interest in the best way to administer the antibiotic. The findings of future studies may result in a return to measuring levels of vancomycin in serum, to assure a successful therapeutic outcome.}, }
@article {pmid16322448, year = {2005}, author = {Chen, I and Christie, PJ and Dubnau, D}, title = {The ins and outs of DNA transfer in bacteria.}, journal = {Science (New York, N.Y.)}, volume = {310}, number = {5753}, pages = {1456-1460}, pmid = {16322448}, issn = {1095-9203}, support = {GM057720/GM/NIGMS NIH HHS/United States ; GM48746/GM/NIGMS NIH HHS/United States ; R01 GM043756/GM/NIGMS NIH HHS/United States ; R01 GM048746-14/GM/NIGMS NIH HHS/United States ; GM43756/GM/NIGMS NIH HHS/United States ; R01 GM048746/GM/NIGMS NIH HHS/United States ; R01 GM057720/GM/NIGMS NIH HHS/United States ; }, mesh = {*Conjugation, Genetic ; DNA, Bacterial/*metabolism ; DNA, Single-Stranded/metabolism ; Gene Transfer, Horizontal ; *Transformation, Bacterial ; }, abstract = {Transformation and conjugation permit the passage of DNA through the bacterial membranes and represent dominant modes for the transfer of genetic information between bacterial cells or between bacterial and eukaryotic cells. As such, they are responsible for the spread of fitness-enhancing traits, including antibiotic resistance. Both processes usually involve the recognition of double-stranded DNA, followed by the transfer of single strands. Elaborate molecular machines are responsible for negotiating the passage of macromolecular DNA through the layers of the cell surface. All or nearly all the machine components involved in transformation and conjugation have been identified, and here we present models for their roles in DNA transport.}, }
@article {pmid16321955, year = {2005}, author = {Scholl, D and Merril, C}, title = {The genome of bacteriophage K1F, a T7-like phage that has acquired the ability to replicate on K1 strains of Escherichia coli.}, journal = {Journal of bacteriology}, volume = {187}, number = {24}, pages = {8499-8503}, pmid = {16321955}, issn = {0021-9193}, support = {//Intramural NIH HHS/United States ; }, mesh = {Bacteriophage T7/genetics ; Base Sequence ; Coliphages/*genetics/physiology ; Escherichia coli/*virology ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Viral ; Molecular Sequence Data ; Neuraminidase/genetics ; Podoviridae/*genetics/physiology ; Sequence Analysis, DNA ; Sequence Homology ; Synteny ; Virus Replication ; }, abstract = {Bacteriophage K1F specifically infects Escherichia coli strains that produce the K1 polysaccharide capsule. Like several other K1 capsule-specific phages, K1F encodes an endo-neuraminidase (endosialidase) that is part of the tail structure which allows the phage to recognize and degrade the polysaccharide capsule. The complete nucleotide sequence of the K1F genome reveals that it is closely related to bacteriophage T7 in both genome organization and sequence similarity. The most striking difference between the two phages is that K1F encodes the endosialidase in the analogous position to the T7 tail fiber gene. This is in contrast with bacteriophage K1-5, another K1-specific phage, which encodes a very similar endosialidase which is part of a tail gene "module" at the end of the phage genome. It appears that diverse phages have acquired endosialidase genes by horizontal gene transfer and that these genes or gene products have adapted to different genome and virion architectures.}, }
@article {pmid16318687, year = {2005}, author = {Courvalin, P}, title = {Antimicrobial drug resistance: "Prediction is very difficult, especially about the future".}, journal = {Emerging infectious diseases}, volume = {11}, number = {10}, pages = {1503-1506}, pmid = {16318687}, issn = {1080-6040}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics ; Bacterial Proteins/genetics ; *Drug Resistance, Bacterial ; Forecasting ; Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; Mutation ; }, abstract = {Evolution of bacteria towards resistance to antimicrobial drugs, including multidrug resistance, is unavoidable because it represents a particular aspect of the general evolution of bacteria that is unstoppable. Therefore, the only means of dealing with this situation is to delay the emergence and subsequent dissemination of resistant bacteria or resistance genes. Resistance to antimicrobial drugs in bacteria can result from mutations in housekeeping structural or regulatory genes. Alternatively, resistance can result from the horizontal acquisition of foreign genetic information. The 2 phenomena are not mutually exclusive and can be associated in the emergence and more efficient spread of resistance. This review discusses the predictable future of the relationship between antimicrobial drugs and bacteria.}, }
@article {pmid16311593, year = {2005}, author = {Pál, C and Papp, B and Lercher, MJ}, title = {Adaptive evolution of bacterial metabolic networks by horizontal gene transfer.}, journal = {Nature genetics}, volume = {37}, number = {12}, pages = {1372-1375}, doi = {10.1038/ng1686}, pmid = {16311593}, issn = {1061-4036}, mesh = {Adaptation, Physiological/*genetics ; Escherichia coli/*genetics/*metabolism ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genomics ; }, abstract = {Numerous studies have considered the emergence of metabolic pathways, but the modes of recent evolution of metabolic networks are poorly understood. Here, we integrate comparative genomics with flux balance analysis to examine (i) the contribution of different genetic mechanisms to network growth in bacteria, (ii) the selective forces driving network evolution and (iii) the integration of new nodes into the network. Most changes to the metabolic network of Escherichia coli in the past 100 million years are due to horizontal gene transfer, with little contribution from gene duplicates. Networks grow by acquiring genes involved in the transport and catalysis of external nutrients, driven by adaptations to changing environments. Accordingly, horizontally transferred genes are integrated at the periphery of the network, whereas central parts remain evolutionarily stable. Genes encoding physiologically coupled reactions are often transferred together, frequently in operons. Thus, bacterial metabolic networks evolve by direct uptake of peripheral reactions in response to changed environments.}, }
@article {pmid16309397, year = {2005}, author = {Nesbø, CL and Boucher, Y and Dlutek, M and Doolittle, WF}, title = {Lateral gene transfer and phylogenetic assignment of environmental fosmid clones.}, journal = {Environmental microbiology}, volume = {7}, number = {12}, pages = {2011-2026}, doi = {10.1111/j.1462-2920.2005.00918.x}, pmid = {16309397}, issn = {1462-2912}, mesh = {Anaerobiosis ; Bacteria/*classification/genetics ; Cosmids ; *Gene Transfer, Horizontal ; Genome, Bacterial/*genetics ; Genomic Library ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Polychlorinated Biphenyls/metabolism ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Species Specificity ; United States ; }, abstract = {Metagenomic data, especially sequence data from large insert clones, are most useful when reasonable inferences about phylogenetic origins of inserts can be made. Often, clones that bear phylotypic markers (usually ribosomal RNA genes) are sought, but sometimes phylogenetic assignments have been based on the preponderance of blast hits obtained with predicted protein coding sequences (CDSs). Here we use a cloning method which greatly enriches for ribosomal RNA-bearing fosmid clones to ask two questions: (i) how reliably can we judge the phylogenetic origin of a clone (that is, its RNA phylotype) from the sequences of its CDSs? and (ii) how much lateral gene transfer (LGT) do we see, as assessed by CDSs of different phylogenetic origins on the same fosmid? We sequenced 12 rRNA containing fosmid clones, obtained from libraries constructed using DNA isolated from Baltimore harbour sediments. Three of the clones are from bacterial candidate divisions for which no cultured representatives are available, and thus represent the first protein coding sequences from these major bacterial lineages. The amount of LGT was assessed by making phylogenetic trees of all the CDSs in the fosmid clones and comparing the phylogenetic position of the CDS to the rRNA phylotype. We find that the majority of CDSs in each fosmid, 57-96%, agree with their respective rRNA genes. However, we also find that a significant fraction of the CDSs in each fosmid, 7-44%, has been acquired by LGT. In several cases, we can infer co-transfer of functionally related genes, and generate hypotheses about mechanism and ecological significance of transfer.}, }
@article {pmid16308675, year = {2006}, author = {Yu, MX and Slater, MR and Ackermann, HW}, title = {Isolation and characterization of Thermus bacteriophages.}, journal = {Archives of virology}, volume = {151}, number = {4}, pages = {663-679}, doi = {10.1007/s00705-005-0667-x}, pmid = {16308675}, issn = {0304-8608}, mesh = {Alkalies ; DNA, Viral/genetics ; *Genome, Viral ; Hydrogen-Ion Concentration ; *Inoviridae/classification/isolation &amp; purification/physiology/ultrastructure ; *Myoviridae/classification/isolation &amp; purification/physiology/ultrastructure ; New Zealand ; Restriction Mapping ; Siberia ; Species Specificity ; Thermus/*virology ; United States ; *Water Microbiology ; }, abstract = {One-hundred-fifteen bacteriophage strains were isolated from alkaline hot springs in Iceland, New Zealand, Russia (Kamchatka), and the U.S.A. The phages belonged to the Myoviridae, Siphoviridae, Tectiviridae, and Inoviridae families. Over 50% of isolates were isometric or filamentous. One type of siphovirus had giant tails of over 800 nm in length. Phages were further characterized by host range, genome size, DNA restriction endonuclease digestion patterns, and temperature and pH sensitivity. Myoviruses and tectiviruses had a worldwide distribution. Most phages were narrowly host-specific and all were highly resistant against heating and alkaline and acidic pH. This is the first time that tectiviruses and filamentous phages are reported for bacteria of the Thermus-Deinococcus phylum. The presence of tectiviruses, inoviruses, and myoviruses is attributed to acquisition from ancestral gamma-proteobacteria by horizontal gene transfer.}, }
@article {pmid16304188, year = {2005}, author = {Spigaglia, P and Barbanti, F and Mastrantonio, P}, title = {Horizontal transfer of erythromycin resistance from Clostridium difficile to Butyrivibrio fibrisolvens.}, journal = {Antimicrobial agents and chemotherapy}, volume = {49}, number = {12}, pages = {5142-5145}, pmid = {16304188}, issn = {0066-4804}, mesh = {Animals ; Bacterial Proteins/*genetics ; Butyrivibrio/drug effects/*genetics ; Cattle ; Clostridioides difficile/drug effects/*genetics ; Drug Resistance/*genetics ; *Gene Transfer, Horizontal ; Methyltransferases/*genetics ; Molecular Sequence Data ; Rumen/microbiology ; }, abstract = {This study demonstrates for the first time the in vitro transfer of the erythromycin resistance gene erm(B) between two obligate anaerobes, the human spore-forming pathogen Clostridium difficile and the rumen commensal Butyrivibrio fibrisolvens, suggesting that this event might occur also in the natural environment.}, }
@article {pmid16303795, year = {2006}, author = {Collyn, F and Guy, L and Marceau, M and Simonet, M and Roten, CA}, title = {Describing ancient horizontal gene transfers at the nucleotide and gene levels by comparative pathogenicity island genometrics.}, journal = {Bioinformatics (Oxford, England)}, volume = {22}, number = {9}, pages = {1072-1079}, doi = {10.1093/bioinformatics/bti793}, pmid = {16303795}, issn = {1367-4803}, mesh = {Chromosome Mapping/*methods ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial ; Genomic Islands/*genetics ; Nucleotides/genetics ; Phylogeny ; Sequence Alignment/methods ; Sequence Analysis, DNA/*methods ; Virulence Factors/*genetics ; Yersinia/*genetics ; }, abstract = {MOTIVATION: Lateral gene transfer is a major mechanism contributing to bacterial genome dynamics and pathovar emergence via pathogenicity island (PAI) spreading. However, since few of these genomic exchanges are experimentally reproducible, it is difficult to establish evolutionary scenarios for the successive PAI transmissions between bacterial genera. Methods initially developed at the gene and/or nucleotide level for genomics, i.e. comparisons of concatenated sequences, ortholog frequency, gene order or dinucleotide usage, were combined and applied here to homologous PAIs: we call this approach comparative PAI genometrics.<br><br>RESULTS: YAPI, a Yersinia PAI, and related islands were compared with measure evolutionary relationships between related modules. Through use of our genometric approach designed for tracking codon usage adaptation and gene phylogeny, an ancient inter-genus PAI transfer was oriented for the first time by characterizing the genomic environment in which the ancestral island emerged and its subsequent transfers to other bacterial genera.}, }
@article {pmid16299387, year = {2006}, author = {Mochizuki, A and Yahara, K and Kobayashi, I and Iwasa, Y}, title = {Genetic addiction: selfish gene's strategy for symbiosis in the genome.}, journal = {Genetics}, volume = {172}, number = {2}, pages = {1309-1323}, pmid = {16299387}, issn = {0016-6731}, mesh = {Bacteria/genetics ; Computer Simulation ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genetics, Population ; *Genome, Bacterial ; *Models, Genetic ; Plasmids/genetics ; Symbiosis/*genetics ; }, abstract = {The evolution and maintenance of the phenomenon of postsegregational host killing or genetic addiction are paradoxical. In this phenomenon, a gene complex, once established in a genome, programs death of a host cell that has eliminated it. The intact form of the gene complex would survive in other members of the host population. It is controversial as to why these genetic elements are maintained, due to the lethal effects of host killing, or perhaps some other properties are beneficial to the host. We analyzed their population dynamics by analytical methods and computer simulations. Genetic addiction turned out to be advantageous to the gene complex in the presence of a competitor genetic element. The advantage is, however, limited in a population without spatial structure, such as that in a well-mixed liquid culture. In contrast, in a structured habitat, such as the surface of a solid medium, the addiction gene complex can increase in frequency, irrespective of its initial density. Our demonstration that genomes can evolve through acquisition of addiction genes has implications for the general question of how a genome can evolve as a community of potentially selfish genes.}, }
@article {pmid16298508, year = {2005}, author = {Celec, P and Kukucková, M and Renczésová, V and Natarajan, S and Pálffy, R and Gardlík, R and Hodosy, J and Behuliak, M and Vlková, B and Minárik, G and Szemes, T and Stuchlík, S and Turna, J}, title = {Biological and biomedical aspects of genetically modified food.}, journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie}, volume = {59}, number = {10}, pages = {531-540}, doi = {10.1016/j.biopha.2005.07.013}, pmid = {16298508}, issn = {0753-3322}, mesh = {Bacteria/*genetics ; Biotechnology ; Consumer Product Safety/legislation &amp; jurisprudence ; Crops, Agricultural/genetics ; European Union ; Food Analysis/legislation &amp; jurisprudence/methods ; Food Hypersensitivity/*etiology ; Food, Fortified ; *Food, Genetically Modified/adverse effects ; Gene Transfer Techniques ; Gene Transfer, Horizontal ; *Genetic Engineering ; Genetic Therapy ; Humans ; Plants, Genetically Modified/genetics ; Probiotics ; Risk Assessment/legislation &amp; jurisprudence ; }, abstract = {Genetically modified (GM) foods are the product of one of the most progressive fields of science-biotechnology. There are major concerns about GM foods in the public; some of them are reasonable, some of them are not. Biomedical risks of GM foods include problems regarding the potential allergenicity, horizontal gene transfer, but environmental side effects on biodiversity must also be recognized. Numerous methods have been developed to assess the potential risk of every GM food type. Benefits of the first generation of GM foods were oriented towards the production process and companies, the second generation of GM foods offers, on contrary, various advantages and added value for the consumer. This includes improved nutritional composition or even therapeutic effects. Recombinant probiotics and the principle of alternative gene therapy represent the latest approach of using GM organisms for biomedical applications. This article tries to summarize and to explain the problematic topic of GM food.}, }
@article {pmid16297239, year = {2005}, author = {van Passel, MW and Bart, A and Thygesen, HH and Luyf, AC and van Kampen, AH and van der Ende, A}, title = {An acquisition account of genomic islands based on genome signature comparisons.}, journal = {BMC genomics}, volume = {6}, number = {}, pages = {163}, pmid = {16297239}, issn = {1471-2164}, mesh = {Algorithms ; Base Sequence ; Chromosome Mapping ; Chromosomes ; Chromosomes, Bacterial ; Cluster Analysis ; Evolution, Molecular ; Gene Expression Profiling/*methods ; *Gene Transfer Techniques ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Linkage ; *Genome ; Genome, Bacterial ; *Genomic Islands ; Genomics ; Plasmids ; Sequence Analysis, DNA ; Vibrio vulnificus/*genetics ; }, abstract = {BACKGROUND: Recent analyses of prokaryotic genome sequences have demonstrated the important force horizontal gene transfer constitutes in genome evolution. Horizontally acquired sequences are detectable by, among others, their dinucleotide composition (genome signature) dissimilarity with the host genome. Genomic islands (GIs) comprise important and interesting horizontally transferred sequences, but information about acquisition events or relatedness between GIs is scarce. In Vibrio vulnificus CMCP6, 10 and 11 GIs have previously been identified in the sequenced chromosomes I and II, respectively. We assessed the compositional similarity and putative acquisition account of these GIs using the genome signature. For this analysis we developed a new algorithm, available as a web application.<br><br>RESULTS: Of 21 GIs, VvI-1 and VvI-10 of chromosome I have similar genome signatures, and while artificially divided due to a linear annotation, they are adjacent on the circular chromosome and therefore comprise one GI. Similarly, GIs VvI-3 and VvI-4 of chromosome I together with the region between these two islands are compositionally similar, suggesting that they form one GI (making a total of 19 GIs in chromosome I + chromosome II). Cluster analysis assigned the 19 GIs to 11 different branches above our conservative threshold. This suggests a limited number of compositionally similar donors or intragenomic dispersion of ancestral acquisitions. Furthermore, 2 GIs of chromosome II cluster with chromosome I, while none of the 19 GIs group with chromosome II, suggesting an unidirectional dispersal of large anomalous gene clusters from chromosome I to chromosome II.<br><br>CONCLUSION: From the results, we infer 10 compositionally dissimilar donors for 19 GIs in the V. vulnificus CMCP6 genome, including chromosome I donating to chromosome II. This suggests multiple transfer events from individual donor types or from donors with similar genome signatures. Applied to other prokaryotes, this approach may elucidate the acquisition account in their genome sequences, and facilitate donor identification of GIs.}, }
@article {pmid16292353, year = {2005}, author = {Azad, RK and Lawrence, JG}, title = {Use of artificial genomes in assessing methods for atypical gene detection.}, journal = {PLoS computational biology}, volume = {1}, number = {6}, pages = {e56}, pmid = {16292353}, issn = {1553-7358}, mesh = {Algorithms ; Base Composition ; Base Sequence ; Chimerism ; Escherichia coli/*genetics ; Genes, Bacterial/*genetics ; Genetic Variation/genetics ; Genome/*genetics ; Genome, Bacterial/genetics ; Markov Chains ; *Models, Genetic ; Open Reading Frames/genetics ; }, abstract = {Parametric methods for identifying laterally transferred genes exploit the directional mutational biases unique to each genome. Yet the development of new, more robust methods--as well as the evaluation and proper implementation of existing methods--relies on an arbitrary assessment of performance using real genomes, where the evolutionary histories of genes are not known. We have used the framework of a generalized hidden Markov model to create artificial genomes modeled after genuine genomes. To model a genome, "core" genes--those displaying patterns of mutational biases shared among large numbers of genes--are identified by a novel gene clustering approach based on the Akaike information criterion. Gene models derived from multiple "core" gene clusters are used to generate an artificial genome that models the properties of a genuine genome. Chimeric artificial genomes--representing those having experienced lateral gene transfer--were created by combining genes from multiple artificial genomes, and the performance of the parametric methods for identifying "atypical" genes was assessed directly. We found that a hidden Markov model that included multiple gene models, each trained on sets of genes representing the range of genotypic variability within a genome, could produce artificial genomes that mimicked the properties of genuine genomes. Moreover, different methods for detecting foreign genes performed differently--i.e., they had different sets of strengths and weaknesses--when identifying atypical genes within chimeric artificial genomes.}, }
@article {pmid16289425, year = {2006}, author = {Lacroix, B and Tzfira, T and Vainstein, A and Citovsky, V}, title = {A case of promiscuity: Agrobacterium's endless hunt for new partners.}, journal = {Trends in genetics : TIG}, volume = {22}, number = {1}, pages = {29-37}, doi = {10.1016/j.tig.2005.10.004}, pmid = {16289425}, issn = {0168-9525}, mesh = {DNA, Bacterial/genetics ; Genetic Engineering ; Humans ; Plant Diseases/genetics/microbiology ; Rhizobium/*genetics/*pathogenicity ; Species Specificity ; Transformation, Genetic ; }, abstract = {Agrobacterium tumefaciens is a phytopathogenic bacterium that induces the 'crown gall' disease in plants by transfer and integration of a segment of its tumor-inducing (Ti) plasmid DNA into the genome of numerous plant species that represent most of the higher plant families. Recently, it has been shown that, under laboratory conditions, the host range of Agrobacterium can be extended to non-plant eukaryotic organisms. These include yeast, filamentous fungi, cultivated mushrooms and human cultured cells. In this article, we present Agrobacterium-mediated transformation of non-plant organisms as a source of new protocols for genetic transformation, as a unique tool for genomic studies (insertional mutagenesis or targeted DNA integration) and as a useful model system to study bacterium-host cell interactions. Moreover, better knowledge of the DNA-transfer mechanisms from bacteria to eukaryotic organisms can also help in understanding horizontal gene transfer--a driving force throughout biological evolution.}, }
@article {pmid16289406, year = {2005}, author = {Mathur, S and Singh, R}, title = {Antibiotic resistance in food lactic acid bacteria--a review.}, journal = {International journal of food microbiology}, volume = {105}, number = {3}, pages = {281-295}, doi = {10.1016/j.ijfoodmicro.2005.03.008}, pmid = {16289406}, issn = {0168-1605}, mesh = {Anti-Bacterial Agents/*pharmacology ; *Conjugation, Genetic ; Consumer Product Safety ; Drug Resistance, Bacterial/*genetics ; *Food Microbiology ; Gene Transfer, Horizontal ; Humans ; Lactobacillus/*drug effects/genetics ; Microbial Sensitivity Tests ; Mutation ; }, abstract = {Antibiotics are a major tool utilized by the health care industry to fight bacterial infections; however, bacteria are highly adaptable creatures and are capable of developing resistance to antibiotics. Consequently, decades of antibiotic use, or rather misuse, have resulted in bacterial resistance to many modern antibiotics. This antibiotic resistance can cause significant danger and suffering for many people with common bacterial infections, those once easily treated with antibiotics. For several decades studies on selection and dissemination of antibiotic resistance have focused mainly on clinically relevant species. However, recently many investigators have speculated that commensal bacteria including lactic acid bacteria (LAB) may act as reservoirs of antibiotic resistance genes similar to those found in human pathogens. The main threat associated with these bacteria is that they can transfer resistance genes to pathogenic bacteria. Genes conferring resistance to tetracycline, erythromycin and vancomycin have been detected and characterized in Lactococcus lactis, Enterococci and, recently, in Lactobacillus species isolated from fermented meat and milk products. A number of initiatives have been recently launched by various organizations across the globe to address the biosafety concerns of starter cultures and probiotic microorganisms. The studies can lead to better understanding of the role played by the dairy starter microorganisms in horizontal transfer of antibiotic resistance genes to intestinal microorganisms and food-associated pathogenic bacteria.}, }
@article {pmid16289358, year = {2006}, author = {Ali, V and Nozaki, T}, title = {Biochemical and functional characterization of phosphoserine aminotransferase from Entamoeba histolytica, which possesses both phosphorylated and non-phosphorylated serine metabolic pathways.}, journal = {Molecular and biochemical parasitology}, volume = {145}, number = {1}, pages = {71-83}, doi = {10.1016/j.molbiopara.2005.09.008}, pmid = {16289358}, issn = {0166-6851}, mesh = {Amino Acid Sequence ; Animals ; Cysteine/metabolism ; Entamoeba histolytica/*enzymology/genetics/metabolism ; Molecular Sequence Data ; Phosphorylation ; Phylogeny ; Recombinant Proteins/chemistry/genetics/isolation &amp; purification/metabolism ; Sequence Alignment ; Serine/*metabolism ; *Transaminases/chemistry/genetics/isolation &amp; purification/metabolism ; }, abstract = {The enteric protozoan parasite Entamoeba histolytica is a unicellular eukaryote that possesses both phosphorylated and non-phosphorylated serine metabolic pathways. In the present study, we described enzymological and functional characterization of phosphoserine aminotransferase (PSAT) from E. histolytica. E. histolytica PSAT (EhPSAT) showed maximum activity for the forward reaction at basic pH, dissimilar to mammalian PSAT, which showed sharp neutral optimum pH. EhPSAT activity was significantly inhibited by substrate analogs, O-phospho-d-serine, O-phospho-l-threonine, and O-acetylserine, suggesting possible regulation of the amoebic PSAT by these metabolic intermediates. Fractionation of the whole parasite lysate and rEhPSAT by anion exchange chromatography verified that EhPSAT represents a dominant PSAT activity. EhPSAT showed a close kinship to PSAT from bacteroides based on amino acid alignment and phylogenetic analyses, suggesting that E. histolytica gained this gene from bacteroides by lateral gene transfer. Comparisons of kinetic properties of recombinant PSAT from E. histolytica and Arabidopsis thaliana showed that EhPSAT possesses significantly higher affinity toward glutamate than the A. thaliana counterpart, which may be explained by significant differences in the isoelectric point and the substitution of arginine, which is involved the binding to the gamma-carboxylate moiety of glutamate, in Escherichia coli PSAT, to serine or threonine in E. histolytica or A. thaliana PSAT, respectively. Heterologous expression of EhPSAT successfully rescued growth defect of a serine-auxotrophic E. coli strain KL282, where serC was deleted, confirming its in vivo role in serine biosynthesis. Together with our previous demonstration of phosphoglycerate dehydrogenase, the present study reinforces physiological significance of the phosphorylated pathway in amoeba.}, }
@article {pmid16282285, year = {2005}, author = {Rand, DM}, title = {Mitochondrial genetics of aging: intergenomic conflict resolution.}, journal = {Science of aging knowledge environment : SAGE KE}, volume = {2005}, number = {45}, pages = {re5}, doi = {10.1126/sageke.2005.45.re5}, pmid = {16282285}, issn = {1539-6150}, mesh = {Aging/*genetics/*physiology ; Archaea ; Cell Nucleus/physiology ; *DNA, Mitochondrial ; Epistasis, Genetic ; Eubacterium ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genetics, Population ; Humans ; Mitochondria/*genetics ; Reactive Oxygen Species ; Symbiosis ; }, abstract = {Mitochondria are the organelles of aerobic respiration. They consume the oxygen we breathe to stay alive and generate energy for cells to function. But oxygen can be dangerous. Indeed, mitochondria generate the majority of reactive oxygen species that are prime suspects among the causes of aging. Mitochondria have been influential elements of evolving eukaryotic cells for perhaps 2 billion years, since a eubacterium fused with an archaebacterium. The picture that has emerged from this long history of genomic fusion is that of a complex network of nuclear-mitochondrial cross-talk. Here, we discuss the biochemical and genetic conflicts between mitochondria and nucleus, which have shaped the role of mitochondria in aging, and point to new paths for further investigations.}, }
@article {pmid16281983, year = {2005}, author = {Light, S and Kraulis, P and Elofsson, A}, title = {Preferential attachment in the evolution of metabolic networks.}, journal = {BMC genomics}, volume = {6}, number = {}, pages = {159}, pmid = {16281983}, issn = {1471-2164}, mesh = {Bacteria/metabolism ; Bacterial Physiological Phenomena ; Escherichia coli/genetics/metabolism ; Escherichia coli Proteins/physiology ; Evolution, Molecular ; *Gene Expression Regulation, Bacterial ; Gene Expression Regulation, Fungal ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Techniques ; Genome, Bacterial ; *Metabolism ; Models, Biological ; Models, Statistical ; Phylogeny ; Protein Interaction Mapping ; Protein Isoforms ; Saccharomyces cerevisiae/metabolism ; Selection, Genetic ; }, abstract = {BACKGROUND: Many biological networks show some characteristics of scale-free networks. Scale-free networks can evolve through preferential attachment where new nodes are preferentially attached to well connected nodes. In networks which have evolved through preferential attachment older nodes should have a higher average connectivity than younger nodes. Here we have investigated preferential attachment in the context of metabolic networks.<br><br>RESULTS: The connectivities of the enzymes in the metabolic network of Escherichia coli were determined and representatives for these enzymes were located in 11 eukaryotes, 17 archaea and 46 bacteria. E. coli enzymes which have representatives in eukaryotes have a higher average connectivity while enzymes which are represented only in the prokaryotes, and especially the enzymes only present in betagamma-proteobacteria, have lower connectivities than expected by chance. Interestingly, the enzymes which have been proposed as candidates for horizontal gene transfer have a higher average connectivity than the other enzymes. Furthermore, It was found that new edges are added to the highly connected enzymes at a faster rate than to enzymes with low connectivities which is consistent with preferential attachment.<br><br>CONCLUSION: Here, we have found indications of preferential attachment in the metabolic network of E. coli. A possible biological explanation for preferential attachment growth of metabolic networks is that novel enzymes created through gene duplication maintain some of the compounds involved in the original reaction, throughout its future evolution. In addition, we found that enzymes which are candidates for horizontal gene transfer have a higher average connectivity than other enzymes. This indicates that while new enzymes are attached preferentially to highly connected enzymes, these highly connected enzymes have sometimes been introduced into the E. coli genome by horizontal gene transfer. We speculate that E. coli has adjusted its metabolic network to a changing environment by replacing the relatively central enzymes for better adapted orthologs from other prokaryotic species.}, }
@article {pmid16280081, year = {2005}, author = {Chapus, C and Dufraigne, C and Edwards, S and Giron, A and Fertil, B and Deschavanne, P}, title = {Exploration of phylogenetic data using a global sequence analysis method.}, journal = {BMC evolutionary biology}, volume = {5}, number = {}, pages = {63}, pmid = {16280081}, issn = {1471-2148}, mesh = {Algorithms ; Animals ; Cluster Analysis ; Computational Biology ; Computer Simulation ; DNA/genetics ; Gammaproteobacteria/genetics ; Gene Transfer, Horizontal ; Genes, Plant ; Genome ; Homeodomain Proteins/genetics ; Humans ; Models, Statistical ; Multigene Family ; *Phylogeny ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Alignment ; Sequence Analysis/*methods ; Sequence Analysis, DNA/*methods ; Software ; }, abstract = {BACKGROUND: Molecular phylogenetic methods are based on alignments of nucleic or peptidic sequences. The tremendous increase in molecular data permits phylogenetic analyses of very long sequences and of many species, but also requires methods to help manage large datasets.<br><br>RESULTS: Here we explore the phylogenetic signal present in molecular data by genomic signatures, defined as the set of frequencies of short oligonucleotides present in DNA sequences. Although violating many of the standard assumptions of traditional phylogenetic analyses--in particular explicit statements of homology inherent in character matrices--the use of the signature does permit the analysis of very long sequences, even those that are unalignable, and is therefore most useful in cases where alignment is questionable. We compare the results obtained by traditional phylogenetic methods to those inferred by the signature method for two genes: RAG1, which is easily alignable, and 18S RNA, where alignments are often ambiguous for some regions. We also apply this method to a multigene data set of 33 genes for 9 bacteria and one archea species as well as to the whole genome of a set of 16 gamma-proteobacteria. In addition to delivering phylogenetic results comparable to traditional methods, the comparison of signatures for the sequences involved in the bacterial example identified putative candidates for horizontal gene transfers.<br><br>CONCLUSION: The signature method is therefore a fast tool for exploring phylogenetic data, providing not only a pretreatment for discovering new sequence relationships, but also for identifying cases of sequence evolution that could confound traditional phylogenetic analysis.}, }
@article {pmid16277676, year = {2005}, author = {Zhang, H and Gao, G and Clayburne, G and Schumacher, HR}, title = {Elimination of rheumatoid synovium in situ using a Fas ligand 'gene scalpel'.}, journal = {Arthritis research &amp; therapy}, volume = {7}, number = {6}, pages = {R1235-43}, pmid = {16277676}, issn = {1478-6362}, support = {T32 AR007442/AR/NIAMS NIH HHS/United States ; 2T32AR07442-12/AR/NIAMS NIH HHS/United States ; R03AR47983/AR/NIAMS NIH HHS/United States ; }, mesh = {Adenoviridae/genetics ; Animals ; Apoptosis/genetics ; Arthritis, Rheumatoid/*pathology/*therapy ; Cartilage, Articular/metabolism/pathology/transplantation ; Cell Count ; Disease Models, Animal ; Fas Ligand Protein ; Gene Transfer Techniques ; Gene Transfer, Horizontal ; *Genetic Therapy ; Humans ; In Situ Nick-End Labeling ; Male ; Membrane Glycoproteins/*genetics/metabolism ; Mice ; Mice, SCID ; RNA, Messenger/metabolism ; Specific Pathogen-Free Organisms ; Synovial Membrane/metabolism/*pathology/transplantation ; Transplantation, Heterologous ; Tumor Necrosis Factors/*genetics/metabolism ; }, abstract = {Surgical synovectomy to remove the inflammatory synovium can temporarily ameliorate rheumatoid inflammation and delay the progress of joint destruction. An efficient medically induced programmed cell death (apoptosis) in the rheumatoid synovium might play a role similar to synovectomy but without surgical tissue damage. Gene transfer of Fas ligand (FasL) has increased the frequency of apoptotic cells in mouse and rabbit arthritic synovium. In this study, we investigated whether repeated FasL gene transfer could remove human inflammatory synovial tissue in situ and function as a molecular synovectomy. Briefly, specimens of human synovium from joint replacement surgeries and synovectomies of rheumatoid arthritis (RA) patients were grafted subcutaneously into male C.B-17 severe combined immunodeficiency (SCID) mice. Injections of a recombinant FasL adenovirus (Ad-FasL) into the grafted synovial tissue at the dosage of 10(11) particles per mouse were performed every two weeks. Three days after the fifth virus injection, the mice were euthanized by CO2 inhalation and the human synovial tissues were collected, weighed and further examined. Compared to the control adenovirus-LacZ (Ad-LacZ) and phosphate buffered saline (PBS) injected RA synovium, the Ad-FasL injected RA synovium was dramatically reduced in size and weight (P < 0.005). The number of both synoviocytes &amp; mononuclear cells was significantly reduced. Interestingly, an approximate 15-fold increased frequency of apoptotic cells was observed in RA synovium three days after Ad-FasL injection, compared with control tissues. In summary, our in vivo investigation of gene transfer to human synovium in SCID mice suggests that repeated intra-articular gene transfer of an apoptosis inducer, such as FasL, may function as a 'gene scalpel' for molecular synovectomy to arrest inflammatory synovium at an early stage of RA.}, }
@article {pmid16277576, year = {2005}, author = {Chen, W and Wang, Y and Chen, C}, title = {Identification of a genomic island of Actinobacillus actinomycetemcomitans.}, journal = {Journal of periodontology}, volume = {76}, number = {11 Suppl}, pages = {2052-2060}, doi = {10.1902/jop.2005.76.11-S.2052}, pmid = {16277576}, issn = {0022-3492}, support = {R01 DE012212/DE/NIDCR NIH HHS/United States ; R01 DE12212/DE/NIDCR NIH HHS/United States ; }, mesh = {Aggregatibacter actinomycetemcomitans/*genetics ; Chromosome Mapping ; GC Rich Sequence/genetics ; Gene Transfer, Horizontal ; Genomic Islands/*genetics ; Sequence Analysis, DNA ; Species Specificity ; Virulence/genetics ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT) is a process by which bacteria acquire genes from organisms of distant taxa. HGT is now recognized as a major driving force in the evolution of bacterial pathogens. Through this process, bacteria may accumulate blocks of DNA such as genomic islands (GEIs) that encode fitness or virulence factors. The periodontal pathogen A. actinomycetemcomitans has been known to exhibit variable virulence potential. It is postulated that GEIs may play a role in modifying the virulence potential of A. actinomycetemcomitans. This study was initiated to identify and determine the distribution of GEIs in A. actinomycetemcomitans.<br><br>METHODS: Forty-seven A. actinomycetemcomitans strains of serotypes a through f were examined. Strain-specific variant DNA in the genomes of A. actinomycetemcomitans was identified by polymerase chain reaction (PCR) genomic mapping and sequenced to identify GEIs. The distribution of the GEIs among test strains of A. actinomycetemcomitans was determined by PCR analysis and Southern hybridization assays.<br><br>RESULTS: An approximately 22 kb GEI of A. actinomycetemcomitans, designated AAI-1, was identified in five serotype b strains. The AAI-1 exhibits low %G+C and encodes proteins of phage, restriction modification systems, mobile elements, and other hypothetical proteins of unknown functions. The insertion of AAI-1 was found to cause truncation of A. actinomycetemcomitans genes at the insertion site.<br><br>CONCLUSIONS: Some A. actinomycetemcomitans strains may harbor GEIs, which were acquired via HGT by the bacteria. The GEIs may increase the gene repertoire of A. actinomycetemcomitans. However, the insertion of the GEIs in A. actinomycetemcomitans may also cause truncation and inactivation of resident genes at the insertion sites. The virulence significance of such gain and loss of genes in A. actinomycetemcomitans remains to be determined.}, }
@article {pmid16275786, year = {2005}, author = {Yang, F and Yang, J and Zhang, X and Chen, L and Jiang, Y and Yan, Y and Tang, X and Wang, J and Xiong, Z and Dong, J and Xue, Y and Zhu, Y and Xu, X and Sun, L and Chen, S and Nie, H and Peng, J and Xu, J and Wang, Y and Yuan, Z and Wen, Y and Yao, Z and Shen, Y and Qiang, B and Hou, Y and Yu, J and Jin, Q}, title = {Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery.}, journal = {Nucleic acids research}, volume = {33}, number = {19}, pages = {6445-6458}, pmid = {16275786}, issn = {1362-4962}, mesh = {DNA Transposable Elements ; Dysentery, Bacillary/microbiology ; Gene Deletion ; Genetic Variation ; *Genome, Bacterial ; Pseudogenes ; Shigella/*genetics/pathogenicity ; Virulence/genetics ; }, abstract = {The Shigella bacteria cause bacillary dysentery, which remains a significant threat to public health. The genus status and species classification appear no longer valid, as compelling evidence indicates that Shigella, as well as enteroinvasive Escherichia coli, are derived from multiple origins of E.coli and form a single pathovar. Nevertheless, Shigella dysenteriae serotype 1 causes deadly epidemics but Shigella boydii is restricted to the Indian subcontinent, while Shigella flexneri and Shigella sonnei are prevalent in developing and developed countries respectively. To begin to explain these distinctive epidemiological and pathological features at the genome level, we have carried out comparative genomics on four representative strains. Each of the Shigella genomes includes a virulence plasmid that encodes conserved primary virulence determinants. The Shigella chromosomes share most of their genes with that of E.coli K12 strain MG1655, but each has over 200 pseudogenes, 300 approximately 700 copies of insertion sequence (IS) elements, and numerous deletions, insertions, translocations and inversions. There is extensive diversity of putative virulence genes, mostly acquired via bacteriophage-mediated lateral gene transfer. Hence, via convergent evolution involving gain and loss of functions, through bacteriophage-mediated gene acquisition, IS-mediated DNA rearrangements and formation of pseudogenes, the Shigella spp. became highly specific human pathogens with variable epidemiological and pathological features.}, }
@article {pmid16275681, year = {2005}, author = {Hurdle, JG and O'Neill, AJ and Mody, L and Chopra, I and Bradley, SF}, title = {In vivo transfer of high-level mupirocin resistance from Staphylococcus epidermidis to methicillin-resistant Staphylococcus aureus associated with failure of mupirocin prophylaxis.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {56}, number = {6}, pages = {1166-1168}, pmid = {16275681}, issn = {0305-7453}, support = {K23 AG022463/AG/NIA NIH HHS/United States ; K23 AG022463-02/AG/NIA NIH HHS/United States ; P60 AG008808/AG/NIA NIH HHS/United States ; AG 08808/AG/NIA NIH HHS/United States ; }, mesh = {Aged ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Antibiotic Prophylaxis ; Bacterial Proteins/genetics ; Carrier State/drug therapy/microbiology ; Conjugation, Genetic ; Drug Resistance, Bacterial/*genetics ; Drug Resistance, Multiple, Bacterial ; *Gene Transfer, Horizontal ; Humans ; Male ; Methicillin Resistance ; Mupirocin/pharmacology/*therapeutic use ; Nuclear Proteins/genetics ; Nursing Homes ; R Factors/genetics/isolation &amp; purification ; Staphylococcal Infections/microbiology/*prevention &amp; control ; Staphylococcus aureus/*drug effects/genetics ; Staphylococcus epidermidis/*drug effects/genetics ; }, abstract = {OBJECTIVES: We examined the molecular basis of the emergence of mupirocin resistance in a methicillin-resistant Staphylococcus aureus (MRSA) strain colonizing a nursing home resident undergoing mupirocin prophylaxis.<br><br>PATIENT AND METHODS: A persistent carrier of mupirocin-susceptible MRSA participated in a trial of mupirocin for nasal decolonization among nursing home residents. During prophylaxis a high-level mupirocin-resistant MRSA emerged in the nasal isolates from this patient. S. aureus and coagulase-negative staphylococci were isolated prior to, during and after 14 days of mupirocin treatment. The staphylococcal isolates and their plasmids were examined by molecular genetic methods.<br><br>RESULTS: All mupirocin-susceptible and -resistant MRSA isolates possessed the same genotype. The patient was also colonized by a single mupirocin-resistant Staphylococcus epidermidis strain. The mupirocin-resistant MRSA and S. epidermidis strains harboured identical plasmids that carried the mupA determinant and genes for conjugative DNA transfer in staphylococci. These plasmids could be transferred in vitro from both clinical isolates to S. aureus RN2677.<br><br>CONCLUSIONS: The MRSA strain contained a conjugative plasmid expressing mupA that was identical with that found in the S. epidermidis strain which colonized the patient. These findings suggest that transfer of mupA from S. epidermidis to MRSA probably occurred during mupirocin prophylaxis.}, }
@article {pmid16274292, year = {2005}, author = {Tolstonog, GV and Belichenko-Weitzmann, IV and Lu, JP and Hartig, R and Shoeman, RL and Traub, U and Traub, P}, title = {Spontaneously immortalized mouse embryo fibroblasts: growth behavior of wild-type and vimentin-deficient cells in relation to mitochondrial structure and activity.}, journal = {DNA and cell biology}, volume = {24}, number = {11}, pages = {680-709}, doi = {10.1089/dna.2005.24.680}, pmid = {16274292}, issn = {1044-5498}, mesh = {Animals ; Cell Adhesion/*physiology ; Cell Line ; Cell Proliferation ; Cell Respiration/physiology ; Cell Survival/physiology ; Contact Inhibition/physiology ; Embryo, Mammalian/cytology ; Fibroblasts/*cytology/physiology/ultrastructure ; Mice ; Mice, Knockout ; Microscopy, Electron, Transmission ; Mitochondria/*physiology/ultrastructure ; Reactive Oxygen Species/metabolism ; Spheroids, Cellular/cytology ; Vimentin/genetics/*physiology ; }, abstract = {Dependent on the presence or absence of vimentin, primary mouse embryo fibroblasts exhibit different growth characteristics in vitro. While most Vim(+/+) fibroblasts stop dividing and die via apoptosis, a substantial fraction of cells immortalize and proliferate almost normally. Vim(-/-) fibroblasts cease to divide earlier, immortalize in vanishingly small numbers and thereafter proliferate extremely slowly. Early after immortalization, Vim(+/+) (imm) fibroblasts appear structurally almost normal, whereas Vim(-/-) (imm) fibroblasts equal postmitotic "crisis" cells, which are characterized by increased cell size, altered cell ultrastructure, nuclear enlargement, genome destabilization, structural degeneration of mitochondria, and diminution of mitochondrial respiratory activity. The differences between immortalized Vim(+/+) (imm) and Vim(-/-) (imm) fibroblasts persist during early cell cloning but disappear during serial subcultivation. At high cell passage, cloned, immortalized vim(-) fibroblasts grow nearly as fast as their cloned vim(+) counterparts, and also resemble them in size, ultrastructure, nuclear volume, and mitochondrial complement; they very likely employ redundancy to cope with the loss of vimentin function when adjusting structure and behavior to that of immortalized vim(+) fibroblasts. Reduction in nuclear size occurs via release of large amounts of filamentous chromatin into extracellular space; because it is complexed with extracellular matrix proteins, it tends to form clusters and to tightly stick to the surface of other cells, thus providing a potential for horizontal gene transfer. On the other hand, cloned vim(+) and vim(-) fibroblasts are equal in showing contact inhibition at young age and becoming anchorage-independent during serial subcultivation, as indicated by the formation of multilayered and -faceted cell sheets and huge spheroids on top of or in soft agar. With this, immortalized vim(-) fibroblasts reduce their adhesiveness to the substratum which, in their precrisis state and early after cloning, is much higher than that of their vim(+) counterparts. In addition, the coupling between the mitochondrial respiratory chain and oxidative phosphorylation is stronger in vim(+) than vim(-) fibroblasts. It appears from these data that after explantation of fibroblasts from the mouse embryo the primary cause of cell and mitochondrial degeneration, including genomic instability, is the mitochondrial production of reactive oxygen species in a vicious circle, and that vimentin provides partial protection from oxidative damage. As a matrix protein with specific in vitro and in vivo affinities for nuclear and mitochondrial, recombinogenic DNA, it may exert this effect preferentially at the genome level via its influence on recombination and repair processes, and in this way also assist the cells in immortalizing. Additional protection of mitochondria by vimentin may occur at the level of mitochondrial fatty acid metabolism.}, }
@article {pmid16272704, year = {2005}, author = {Kuzuhara, T and Suganuma, M and Tsuge, H and Fujiki, H}, title = {Presence of a motif conserved between Helicobacter pylori TNF-alpha inducing protein (Tipalpha) and penicillin-binding proteins.}, journal = {Biological &amp; pharmaceutical bulletin}, volume = {28}, number = {11}, pages = {2133-2137}, doi = {10.1248/bpb.28.2133}, pmid = {16272704}, issn = {0918-6158}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Bacterial Proteins/*chemistry ; Conserved Sequence ; Gene Transfer, Horizontal ; Gram-Positive Bacteria/genetics ; Helicobacter pylori/*chemistry/genetics ; Models, Molecular ; Molecular Sequence Data ; Penicillin-Binding Proteins/*chemistry ; Protein Structure, Tertiary ; Structural Homology, Protein ; }, abstract = {Here we report a primary structure conserved between Helicobacter pylori (H. pylori)-tumor necrosis factor-alpha inducing protein (Tipalpha) and bacterial penicillin-binding proteins. H. pylori is a Gram-negative bacterium which plays a key part in carcinogenesis in the human stomach. We previously reported that Tipalpha has a carcinogenic potential as tumor promoter, and that it has no obvious homologue in other species. To investigate the structure-function relationship of Tipalpha and to predict its ancestral protein, we searched among proteins which have weak homology to Tipalpha in their primary structures, using Psi-Blast, and we identified numerous Gram-positive bacterial penicillin-binding proteins as weakly homologous to Tipalpha. Among these, several unique amino acids are conserved and form a motif-like structure. Phylogenic tree analysis indicated that Tipalpha is closer to the penicillin-binding proteins of Gram-positive bacteria, based on their primary structures, than to H. pylori. This finding suggests that Tipalpha and penicillin-binding proteins are derived from a common ancestral protein, and that Tipalpha gene may be transferred horizontally from Gram-positive bacteria to H. pylori.}, }
@article {pmid16272379, year = {2005}, author = {Alonso, G and Baptista, K and Ngo, T and Taylor, DE}, title = {Transcriptional organization of the temperature-sensitive transfer system from the IncHI1 plasmid R27.}, journal = {Microbiology (Reading, England)}, volume = {151}, number = {Pt 11}, pages = {3563-3573}, doi = {10.1099/mic.0.28256-0}, pmid = {16272379}, issn = {1350-0872}, mesh = {Bacterial Proteins ; Base Sequence ; *Conjugation, Genetic ; DNA-Binding Proteins ; Escherichia coli/genetics/metabolism ; Escherichia coli Proteins/genetics/*metabolism ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Operon ; Promoter Regions, Genetic ; R Factors/*genetics ; *Temperature ; *Transcription, Genetic ; }, abstract = {One of the characteristic features of IncHI1 plasmids is a thermosensitive process of conjugation, which is optimal between 22 degrees C and 30 degrees C but inhibited at 37 degrees C. R27, the prototypical IncHI1 plasmid, contains transfer genes clustered in two regions of the plasmid, Tra1 and Tra2. In the present study, transcriptional analyses of the tra genes were undertaken at both 30 degrees C and 37 degrees C. Screening of 38 tra genes showed that tra genes are transcriptionally linked in six operons, three in each Tra region. RT-PCR analysis showed that gene expression was reduced at 37 degrees C relative to that observed at 30 degrees C. The transcription start sites of the six transcripts were identified, promoters and upstream regions were cloned, and transcription was tested at both temperatures. In cells grown at 37 degrees C, in the presence of R27, the promoters were inhibited, except for promoters of the H operon and AN operon. Conditions that influenced DNA topology, such as osmolarity, anaerobiosis, quorum sensing and acidity, showed no significant influence on transfer frequency. These results should facilitate future understanding of the basis of temperature-sensitive transfer in this large conjugative plasmid.}, }
@article {pmid16272378, year = {2005}, author = {Gunton, JE and Gilmour, MW and Alonso, G and Taylor, DE}, title = {Subcellular localization and functional domains of the coupling protein, TraG, from IncHI1 plasmid R27.}, journal = {Microbiology (Reading, England)}, volume = {151}, number = {Pt 11}, pages = {3549-3561}, doi = {10.1099/mic.0.28255-0}, pmid = {16272378}, issn = {1350-0872}, mesh = {Amino Acid Sequence ; Conjugation, Genetic ; Escherichia coli/genetics/growth &amp; development/metabolism ; Escherichia coli Proteins/*chemistry/genetics/*metabolism ; Gene Expression Regulation, Bacterial ; Immunoprecipitation ; Membrane Proteins/*chemistry/genetics/*metabolism ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; R Factors/*genetics ; Subcellular Fractions/*metabolism ; Temperature ; Transcription, Genetic ; Two-Hybrid System Techniques ; }, abstract = {Bacterial conjugation is a horizontal gene transfer event mediated by the type IV secretion system (T4SS) encoded by bacterial plasmids. Within the T4SS, the coupling protein plays an essential role in linking the membrane-associated pore-forming proteins to the cytoplasmic, DNA-processing proteins. TraG is the coupling protein encoded by the incompatibility group HI plasmids. A hallmark feature of the IncHI plasmids is optimal conjugative transfer at 30 degrees C and an inability to transfer at 37 degrees C. Transcriptional analysis of the transfer region 1 (Tra1) of R27 has revealed that traG is transcribed in a temperature-dependent manner, with significantly reduced levels of expression at 37 degrees C as compared to expression at 30 degrees C. The R27 coupling protein contains nucleoside triphosphate (NTP)-binding domains, the Walker A and Walker B boxes, which are well conserved among this family of proteins. Site-specific mutagenesis within these motifs abrogated the conjugative transfer of R27 into recipient cells. Mutational analysis of the TraG periplasmic-spanning residues, in conjunction with bacterial two-hybrid and immunoprecipitation analysis, determined that this region is essential for a successful interaction with the T4SS protein TrhB. Further characterization of TraG by immunofluorescence studies revealed that the R27 coupling protein forms membrane-associated fluorescent foci independent of R27 conjugative proteins. These foci were found at discrete positions within the cell periphery. These results allow the definition of domains within TraG that are involved in conjugative transfer, and determination of the cellular location of the R27 coupling protein.}, }
@article {pmid16272374, year = {2005}, author = {de Paz, HD and Sangari, FJ and Bolland, S and García-Lobo, JM and Dehio, C and de la Cruz, F and Llosa, M}, title = {Functional interactions between type IV secretion systems involved in DNA transfer and virulence.}, journal = {Microbiology (Reading, England)}, volume = {151}, number = {Pt 11}, pages = {3505-3516}, doi = {10.1099/mic.0.28410-0}, pmid = {16272374}, issn = {1350-0872}, mesh = {Agrobacterium tumefaciens/genetics/metabolism/*pathogenicity ; Animals ; Bacterial Proteins/genetics/*metabolism ; Bartonella/genetics/metabolism/*pathogenicity ; Brucella suis/genetics/metabolism/*pathogenicity ; *Conjugation, Genetic ; DNA, Bacterial/*genetics/metabolism ; DNA-Binding Proteins/genetics/metabolism ; Gene Transfer, Horizontal ; Genetic Complementation Test ; Mutagenesis, Insertional ; Two-Hybrid System Techniques ; Virulence ; }, abstract = {This paper reports an analysis of the functional interactions between type IV secretion systems (T4SS) that are part of the conjugative machinery for horizontal DNA transfer (cT4SS), and T4SS involved in bacterial pathogenicity (pT4SS). The authors' previous work showed that a conjugative coupling protein (T4CP) interacts with the VirB10-type component of the T4SS in order to recruit the protein-DNA complex to the transporter for conjugative DNA transfer. This study now shows by two-hybrid analysis that conjugative T4CPs also interact with the VirB10 element of the pT4SS of Agrobacterium tumefaciens (At), Bartonella tribocorum (Bt) and Brucella suis (Bs). Moreover, the VirB10 component of a cT4SS (protein TrwE of plasmid R388) could be partially substituted by that of a pT4SS (protein TrwE of Bt) for conjugation. This result opens the way for the construction of hybrid T4SS that deliver DNA into animal cells. Interestingly, in the presence of part of the Bs T4SS the R388 T4SS protein levels were decreased and R388 conjugation was strongly inhibited. Complementation assays between the Trw systems of R388 and Bt showed that only individual components from the so-called 'core complex' could be exchanged, supporting the concept that this core is the common scaffold for the transport apparatus while the other 'peripheral components' are largely system-specific.}, }
@article {pmid16272373, year = {2005}, author = {Backert, S and Kwok, T and König, W}, title = {Conjugative plasmid DNA transfer in Helicobacter pylori mediated by chromosomally encoded relaxase and TraG-like proteins.}, journal = {Microbiology (Reading, England)}, volume = {151}, number = {Pt 11}, pages = {3493-3503}, doi = {10.1099/mic.0.28250-0}, pmid = {16272373}, issn = {1350-0872}, mesh = {Bacterial Proteins/genetics/metabolism ; Chromosomes, Bacterial/genetics ; *Conjugation, Genetic ; DNA Nucleotidyltransferases/genetics/metabolism ; DNA, Bacterial/*genetics/metabolism ; Escherichia coli Proteins/genetics/metabolism ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Helicobacter pylori/*enzymology/*genetics ; Humans ; Membrane Proteins/genetics/metabolism ; Plasmids/*genetics ; Transformation, Genetic ; }, abstract = {One of the striking characteristics of Helicobacter pylori is the extensive genetic diversity among clinical isolates. This diversity has been attributed to an elevated mutation rate, impaired DNA repair, DNA transfer and frequent recombination events. Plasmids have also been identified in H. pylori but it remained unknown whether conjugation can contribute to DNA transfer between clinical isolates. To examine whether H. pylori possesses intrinsic capability for conjugative plasmid transfer, shuttle vectors were introduced into H. pylori containing an oriT sequence of the conjugative IncPalpha plasmid RP4 but no mobilization (mob) genes. It was shown that these vectors could stably replicate and be mobilized among clinical H. pylori strains. It was also demonstrated that traG and relaxase (rlx) homologues carried on the H. pylori chromosome were important for plasmid transfer. Primer extension studies and mutagenesis further confirmed that the relaxase homologue rlx1 in H. pylori encodes a functional enzyme capable of acting on the RP4 oriT. Furthermore, the findings of this study indicate that traG and rlx1 act independently of the previously described type IV secretion systems, including that encoded by the cag pathogenicity island and the comB transformation apparatus, in mediating conjugative plasmid DNA transfer between H. pylori strains.}, }
@article {pmid16269802, year = {2005}, author = {Hontzeas, N and Richardson, AO and Belimov, A and Safronova, V and Abu-Omar, MM and Glick, BR}, title = {Evidence for horizontal transfer of 1-aminocyclopropane-1-carboxylate deaminase genes.}, journal = {Applied and environmental microbiology}, volume = {71}, number = {11}, pages = {7556-7558}, pmid = {16269802}, issn = {0099-2240}, mesh = {Carbon-Carbon Lyases/*genetics ; DNA, Bacterial/analysis/genetics ; DNA, Ribosomal/analysis ; *Gene Transfer, Horizontal ; Gram-Negative Bacteria/*enzymology/genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Rhodococcus/*enzymology/genetics ; }, abstract = {PCR was used to rapidly identify and isolate 1-aminocyclopropane-1-carboxylate (ACC) deaminase genes from bacteria. The Shimodaira-Hasegawa test was used to assess whether phylogenetically anomalous gene placements suggestive of horizontal gene transfer (HGT) were significantly favored over vertical transmission. The best maximum likelihood (ML) ACC deaminase tree was significantly more likely than four alternative ML trees, suggesting HGT.}, }
@article {pmid16269744, year = {2005}, author = {Coombs, JM and Barkay, T}, title = {New findings on evolution of metal homeostasis genes: evidence from comparative genome analysis of bacteria and archaea.}, journal = {Applied and environmental microbiology}, volume = {71}, number = {11}, pages = {7083-7091}, pmid = {16269744}, issn = {0099-2240}, mesh = {Adenosine Triphosphatases/*genetics ; Amino Acid Sequence ; Archaea/genetics/metabolism ; Bacteria/genetics/metabolism ; Cation Transport Proteins/genetics ; Copper-Transporting ATPases ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Archaeal ; *Genome, Bacterial ; Genomics ; Homeostasis ; Metals/*metabolism ; Molecular Sequence Data ; Phylogeny ; }, abstract = {In order to examine the natural history of metal homeostasis genes in prokaryotes, open reading frames with homology to characterized P(IB)-type ATPases from the genomes of 188 bacteria and 22 archaea were investigated. Major findings were as follows. First, a high diversity in N-terminal metal binding motifs was observed. These motifs were distributed throughout bacterial and archaeal lineages, suggesting multiple loss and acquisition events. Second, the CopA locus separated into two distinct phylogenetic clusters, CopA1, which contained ATPases with documented Cu(I) influx activity, and CopA2, which contained both efflux and influx transporters and spanned the entire diversity of the bacterial domain, suggesting that CopA2 is the ancestral locus. Finally, phylogentic incongruences between 16S rRNA and P(IB)-type ATPase gene trees identified at least 14 instances of lateral gene transfer (LGT) that had occurred among diverse microbes. Results from bootstrapped supported nodes indicated that (i) a majority of the transfers occurred among proteobacteria, most likely due to the phylogenetic relatedness of these organisms, and (ii) gram-positive bacteria with low moles percent G+C were often involved in instances of LGT. These results, together with our earlier work on the occurrence of LGT in subsurface bacteria (J. M. Coombs and T. Barkay, Appl. Environ. Microbiol. 70:1698-1707, 2004), indicate that LGT has had a minor role in the evolution of P(IB)-type ATPases, unlike other genes that specify survival in metal-stressed environments. This study demonstrates how examination of a specific locus across microbial genomes can contribute to the understanding of phenotypes that are critical to the interactions of microbes with their environment.}, }
@article {pmid16269699, year = {2005}, author = {Crapoulet, N and Robineau, S and Raoult, D and Renesto, P}, title = {Intervening sequence acquired by lateral gene transfer in Tropheryma whipplei results in 23S rRNA fragmentation.}, journal = {Applied and environmental microbiology}, volume = {71}, number = {11}, pages = {6698-6701}, pmid = {16269699}, issn = {0099-2240}, mesh = {Actinomycetales/*genetics/growth &amp; development ; *Gene Transfer, Horizontal ; Introns/*genetics ; Nucleic Acid Conformation ; Phylogeny ; RNA Processing, Post-Transcriptional ; RNA, Bacterial/analysis/genetics/isolation &amp; purification ; RNA, Ribosomal, 23S/genetics/*metabolism ; Ribonuclease III/metabolism ; }, abstract = {Completion of Tropheryma whipplei genome sequencing may provide insights into the evolution of the molecular mechanisms underlying the pathogenicity of this microorganism. The first postgenomic application was the successful design of a comprehensive culture medium that allows axenic growth of this bacterium, which is particularly recalcitrant to cultivation. This achievement in turn permitted analysis of T. whipplei RNA without contaminating eukaryotic nucleic acids. To obtain high-quality RNA, several extraction methods were compared, but under all conditions tested an atypical profile was observed. By using a Northern blot assay we demonstrated that an insertion sequence previously described in T. whipplei 23S rRNA is in fact an intervening sequence excised during maturation. This cleavage could involve an RNase III identified in the genome of this microorganism. Among the bacteria with a 23S rRNA insertion sequence, T. whipplei is the only gram-positive microorganism. We present phylogenetic evidence that this mobile genetic element was acquired by lateral gene transfer from another enteric bacterium.}, }
@article {pmid16269679, year = {2005}, author = {Nordin, K and Unell, M and Jansson, JK}, title = {Novel 4-chlorophenol degradation gene cluster and degradation route via hydroxyquinol in Arthrobacter chlorophenolicus A6.}, journal = {Applied and environmental microbiology}, volume = {71}, number = {11}, pages = {6538-6544}, pmid = {16269679}, issn = {0099-2240}, mesh = {Arthrobacter/genetics/growth &amp; development/*metabolism ; Bacterial Proteins/chemistry/*genetics/metabolism ; Biodegradation, Environmental ; Chlorophenols/*metabolism ; Cloning, Molecular ; Dioxygenases/chemistry/genetics/metabolism ; Hydroquinones/*metabolism ; Molecular Sequence Data ; *Multigene Family ; Mutation ; Sequence Analysis, DNA ; }, abstract = {Arthrobacter chlorophenolicus A6, a previously described 4-chlorophenol-degrading strain, was found to degrade 4-chlorophenol via hydroxyquinol, which is a novel route for aerobic microbial degradation of this compound. In addition, 10 open reading frames exhibiting sequence similarity to genes encoding enzymes involved in chlorophenol degradation were cloned and designated part of a chlorophenol degradation gene cluster (cph genes). Several of the open reading frames appeared to encode enzymes with similar functions; these open reading frames included two genes, cphA-I and cphA-II, which were shown to encode functional hydroxyquinol 1,2-dioxygenases. Disruption of the cphA-I gene yielded a mutant that exhibited negligible growth on 4-chlorophenol, thereby linking the cph gene cluster to functional catabolism of 4-chlorophenol in A. chlorophenolicus A6. The presence of a resolvase pseudogene in the cph gene cluster together with analyses of the G+C content and codon bias of flanking genes suggested that horizontal gene transfer was involved in assembly of the gene cluster during evolution of the ability of the strain to grow on 4-chlorophenol.}, }
@article {pmid16267296, year = {2005}, author = {de Felipe, KS and Pampou, S and Jovanovic, OS and Pericone, CD and Ye, SF and Kalachikov, S and Shuman, HA}, title = {Evidence for acquisition of Legionella type IV secretion substrates via interdomain horizontal gene transfer.}, journal = {Journal of bacteriology}, volume = {187}, number = {22}, pages = {7716-7726}, pmid = {16267296}, issn = {0021-9193}, support = {R01 AI023549/AI/NIAID NIH HHS/United States ; R01 AI064481/AI/NIAID NIH HHS/United States ; AI23549/AI/NIAID NIH HHS/United States ; AI64481/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Motifs/genetics ; Bacterial Proteins/*genetics/metabolism ; Computational Biology ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Legionella pneumophila/*genetics/metabolism ; Open Reading Frames/genetics ; *Protein Transport ; }, abstract = {Intracellular pathogens exploit host cell functions to create a replication niche inside eukaryotic cells. The causative agent of Legionnaires' disease, the gamma-proteobacterium Legionella pneumophila, resides and replicates within a modified vacuole of protozoan and mammalian cells. L. pneumophila translocates effector proteins into host cells through the Icm-Dot complex, a specialized type IVB secretion system that is required for intracellular growth. To find out if some effector proteins may have been acquired through interdomain horizontal gene transfer (HGT), we performed a bioinformatic screen that searched for eukaryotic motifs in all open reading frames of the L. pneumophila Philadelphia-1 genome. We found 44 uncharacterized genes with many distinct eukaryotic motifs. Most of these genes contain G+C biases compared to other L. pneumophila genes, supporting the theory that they were acquired through HGT. Furthermore, we found that several of them are expressed and up-regulated in stationary phase in an RpoS-dependent manner. In addition, at least seven of these gene products are translocated into host cells via the Icm-Dot complex, confirming their role in the intracellular environment. Reminiscent of the case with most Icm-Dot substrates, most of the strains containing mutations in these genes grew comparably to the parent strain intracellularly. Our findings suggest that in L. pneumophila, interdomain HGT may have been a major mechanism for the acquisition of determinants of infection.}, }
@article {pmid16267140, year = {2006}, author = {Baldo, L and Bordenstein, S and Wernegreen, JJ and Werren, JH}, title = {Widespread recombination throughout Wolbachia genomes.}, journal = {Molecular biology and evolution}, volume = {23}, number = {2}, pages = {437-449}, doi = {10.1093/molbev/msj049}, pmid = {16267140}, issn = {0737-4038}, support = {R01 GM62626-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Proteins/*genetics ; Bacteriophages/genetics ; DNA Transposable Elements/genetics ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial/*genetics ; Wolbachia/*genetics ; }, abstract = {Evidence is growing that homologous recombination is a powerful source of genetic variability among closely related free-living bacteria. Here we investigate the extent of recombination among housekeeping genes of the endosymbiotic bacteria Wolbachia. Four housekeeping genes, gltA, dnaA, ftsZ, and groEL, were sequenced from a sample of 22 strains belonging to supergroups A and B. Sequence alignments were searched for recombination within and between genes using phylogenetic inference, analysis of genetic variation, and four recombination detection programs (MaxChi, Chimera, RDP, and Geneconv). Independent analyses indicate no or weak intragenic recombination in ftsZ, dnaA, and groEL. Intragenic recombination affects gltA, with a clear evidence of horizontal DNA transfers within and between divergent Wolbachia supergroups. Intergenic recombination was detected between all pairs of genes, suggesting either a horizontal exchange of a genome portion encompassing several genes or multiple recombination events involving smaller tracts along the genome. Overall, the observed pattern is compatible with pervasive recombination. Such results, combined with previous evidence of recombination in a surface protein, phage, and IS elements, support an unexpected chimeric origin of Wolbachia strains, with important implications for Wolbachia phylogeny and adaptation of these obligate intracellular bacteria in arthropods.}, }
@article {pmid16267088, year = {2005}, author = {Planet, PJ and Sarkar, IN}, title = {mILD: a tool for constructing and analyzing matrices of pairwise phylogenetic character incongruence tests.}, journal = {Bioinformatics (Oxford, England)}, volume = {21}, number = {24}, pages = {4423-4424}, doi = {10.1093/bioinformatics/bti744}, pmid = {16267088}, issn = {1367-4803}, support = {5R01 GM062351-02/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Computational Biology ; Databases, Genetic ; Evolution, Molecular ; Genomics/statistics &amp; numerical data ; *Phylogeny ; *Software ; }, abstract = {Pairwise comparisons of disagreement in phylogenetic datasets offer a powerful tool for isolating historical incongruence for closer analysis. Statistically significant phylogenetic character incongruence may reflect important differences in evolutionary history, such as horizontal gene transfer. Such testing can also be used to specify possible combinations of datasets for further phylogenetic analysis. The process of comparing multiple datasets can be very time consuming, and it is sometimes unclear how to combine data partitions given the observed patterns of incongruence. Here we present an application that automates the process of making pairwise comparisons between large numbers of phylogenetic datasets using the Incongruence Length Difference (ILD) test. The application also implements strategies for data combination based on the patterns of incongruence observed in pairwise comparisons.}, }
@article {pmid16262857, year = {2005}, author = {Silva, C and Vinuesa, P and Eguiarte, LE and Souza, V and Martínez-Romero, E}, title = {Evolutionary genetics and biogeographic structure of Rhizobium gallicum sensu lato, a widely distributed bacterial symbiont of diverse legumes.}, journal = {Molecular ecology}, volume = {14}, number = {13}, pages = {4033-4050}, doi = {10.1111/j.1365-294X.2005.02721.x}, pmid = {16262857}, issn = {0962-1083}, mesh = {Base Sequence ; Cluster Analysis ; *Demography ; Fabaceae/*microbiology ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/genetics ; *Genetics, Population ; Geography ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Rhizobium/classification/*genetics ; Sequence Analysis, DNA ; Species Specificity ; *Symbiosis ; }, abstract = {We used phylogenetic and population genetics approaches to evaluate the importance of the evolutionary forces on shaping the genetic structure of Rhizobium gallicum and related species. We analysed 54 strains from several populations distributed in the Northern Hemisphere, using nucleotide sequences of three 'core' chromosomal genes (rrs, glnII and atpD) and two 'auxiliary' symbiotic genes (nifH and nodB) to elucidate the biogeographic history of the species and symbiotic ecotypes (biovarieties) within species. The analyses revealed that strains classified as Rhizobium mongolense and Rhizobium yanglingense belong to the chromosomal evolutionary lineage of R. gallicum and harbour symbiotic genes corresponding to a new biovar; we propose their reclassification as R. gallicum bv. orientale. The comparison of the chromosomal and symbiotic genes revealed evidence of lateral transfer of symbiotic information within and across species. Genetic differentiation analyses based on the chromosomal protein-coding genes revealed a biogeographic pattern with three main populations, whereas the 16S rDNA sequences did not resolve that biogeographic pattern. Both the phylogenetic and population genetic analyses showed evidence of recombination at the rrs locus. We discuss our results in the light of the contrasting views of bacterial species expressed by microbial taxonomist and evolutionary biologists.}, }
@article {pmid16260446, year = {2005}, author = {Corkill, JE and Anson, JJ and Hart, CA}, title = {High prevalence of the plasmid-mediated quinolone resistance determinant qnrA in multidrug-resistant Enterobacteriaceae from blood cultures in Liverpool, UK.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {56}, number = {6}, pages = {1115-1117}, doi = {10.1093/jac/dki388}, pmid = {16260446}, issn = {0305-7453}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics ; Blood/*microbiology ; Cefotaxime/pharmacology ; Conjugation, Genetic ; DNA Fingerprinting ; Drug Resistance, Multiple, Bacterial/*genetics ; Electrophoresis, Gel, Pulsed-Field ; England ; Enterobacteriaceae/*drug effects/genetics/isolation &amp; purification ; Enterobacteriaceae Infections/*microbiology ; Escherichia coli Proteins/genetics ; Gene Transfer, Horizontal ; Humans ; Integrons/genetics ; Plasmids/*genetics ; Quinolones/*pharmacology ; beta-Lactamases/genetics ; }, abstract = {OBJECTIVES: To determine the prevalence of the plasmid-mediated quinolone resistance qnrA gene in a selected collection of blood culture isolates of Enterobacteriaceae resistant to both ciprofloxacin and cefotaxime.<br><br>METHODS: Over a 29 month period, a total of 47 non-repetitive isolates of Enterobacteriaceae resistant to both ciprofloxacin and cefotaxime were identified. Isolates were screened for the presence of the qnrA gene, class I integrons and bla(ESBL) by PCR. Transferability was examined by conjugation with the sodium azide-resistant Escherichia coli J53. All qnrA-positive isolates were examined for DNA-relatedness by PFGE.<br><br>RESULTS: A total of 15 of the 47 test isolates (32%) were positive for the qnrA gene, and included single isolates of E. coli and Citrobacter freundii, 4 Klebsiella pneumoniae and 9 Enterobacter cloacae. All 15 qnrA-positive isolates carried class 1 integrons, and 11 the extended-spectrum beta-lactamase gene bla(SHV-12). By PFGE two K. pneumoniae and three E. cloacae, respectively, were considered clonally but not temporally related. Plasmid transfer of quinolone resistance was only achieved with single isolates of K. pneumoniae and E. cloacae. Both plasmids carried class 1 integrons with a pSAL-1-like gene cassette arrangement intl1-aadA2-qacEDelta-sul1.<br><br>CONCLUSIONS: In this selected group of ciprofloxacin- and cefotaxime-resistant bacteria, carriage of the qnrA gene was high (32%). This compares with <2.0% as demonstrated in worldwide studies of laboratory collections of ciprofloxacin-resistant bacteria. The majority of qnrA-positive isolates in our study originated from high-dependency care units within our hospital, but were shown not to be clonal by PFGE. This is the first report of qnrA-positive Enterobacteriaceae in the United Kingdom.}, }
@article {pmid16257921, year = {2005}, author = {Zhang, RF and Jiang, JD and Dai, XZ and Gu, LF and Li, SP}, title = {[Horizontal transfer of environmental pollutant-degrading gene and application in bioremediation].}, journal = {Yi chuan = Hereditas}, volume = {27}, number = {5}, pages = {845-851}, pmid = {16257921}, issn = {0253-9772}, mesh = {Adaptation, Physiological/genetics/physiology ; Bacteria/genetics/growth &amp; development/*metabolism ; Bacterial Proteins/genetics/*metabolism ; Environmental Pollutants/*metabolism ; Environmental Restoration and Remediation/methods ; *Gene Transfer, Horizontal ; }, abstract = {Horizontal gene transfer, unlike vertical gene transfer, is a means of genetic communication in bacteria. In the special polluted environment, horizontal transfer of polluted-degrading gene has significant functions. Study on horizontal transfer of degrading gene in polluted environment may deepen our understanding of the mechanism of bacterial adaptation to the organic-polluted environment. In the practical application in bioremediation, horizontal transfer of degrading gene can be regulated to promote degrading ability of microorganisms. In this article, we will review the advances in the study on mechanisms of genetic interactions among bacteria, the effect of degrading gene transfer in contaminated environment on microorganisms'adaptation to contaminated environment and the degradation of the pollutants.}, }
@article {pmid16253442, year = {2005}, author = {Oh, CS and Beer, SV}, title = {Molecular genetics of Erwinia amylovora involved in the development of fire blight.}, journal = {FEMS microbiology letters}, volume = {253}, number = {2}, pages = {185-192}, doi = {10.1016/j.femsle.2005.09.051}, pmid = {16253442}, issn = {0378-1097}, mesh = {Bacterial Proteins/metabolism ; Deferoxamine ; Erwinia amylovora/*genetics/metabolism/*pathogenicity ; Genomic Islands/genetics ; Metalloproteases ; Plant Diseases/genetics/*microbiology ; Protein Transport/*genetics ; Rosaceae/*microbiology ; Sorbitol/metabolism ; Virulence ; }, abstract = {The bacterial plant pathogen, Erwinia amylovora, causes the devastating disease known as fire blight in some Rosaceous plants like apple, pear, quince, raspberry and several ornamentals. Knowledge of the factors affecting the development of fire blight has mushroomed in the last quarter century. On the molecular level, genes encoding a Hrp type III secretion system, genes encoding enzymes involved in synthesis of extracellular polysaccharides and genes facilitating the growth of E. amylovora in its host plants have been characterized. The Hrp pathogenicity island, delimited by genes suggesting horizontal gene transfer, is composed of four distinct regions, the hrp/hrc region, the HEE (Hrp effectors and elicitors) region, the HAE (Hrp-associated enzymes) region, and the IT (Island transfer) region. The Hrp pathogenicity island encodes a Hrp type III secretion system (TTSS), which delivers several proteins from bacteria to plant apoplasts or cytoplasm. E. amylovora produces two exopolysaccharides, amylovoran and levan, which cause the characteristic fire blight wilting symptom in host plants. In addition, other genes, and their encoded proteins, have been characterized as virulence factors of E. amylovora that encode enzymes facilitating sorbitol metabolism, proteolytic activity and iron harvesting. This review summarizes our understanding of the genes and gene products of E. amylovora that are involved in the development of the fire blight disease.}, }
@article {pmid16251307, year = {2005}, author = {Tsuge, K and Inoue, S and Ano, T and Itaya, M and Shoda, M}, title = {Horizontal transfer of iturin A operon, itu, to Bacillus subtilis 168 and conversion into an iturin A producer.}, journal = {Antimicrobial agents and chemotherapy}, volume = {49}, number = {11}, pages = {4641-4648}, pmid = {16251307}, issn = {0066-4804}, mesh = {Bacillus subtilis/*genetics/metabolism ; *Gene Transfer, Horizontal ; *Operon ; Peptides/*genetics/metabolism ; Peptides, Cyclic ; }, abstract = {Iturin A and its derivatives are lipopeptide antibiotics produced by Bacillus subtilis and several closely related bacteria. Three iturin group operons (i.e., iturin A, mycosubtilin, and bacillomycin D) of those antibiotic-producing strains have been cloned and sequenced thus far, strongly implying the horizontal transfer of these operons. To examine the nature of such horizontal transfer in terms of antibiotic production, a 42-kb region of the B. subtilis RB14 genome, which contains a complete 38-kb iturin A operon, was transferred via competent cell transformation to the genome of a non-iturin A producer, B. subtilis 168, using a method based on double-crossover homologous recombination with two short landing pad sequences (LPSs) in the genome. The recombinant was positively selected by confirming the elimination of the cI repressor gene, which was localized between the two LPSs and substituted by the transferred segment. The iturin A operon-transferred strain 168 was then converted into an iturin A producer by the introduction of an sfp gene, which encodes 4'-phosphopantetheinyl transferase and is mutated in strain 168. By inserting the pleiotropic regulator degQ, the productivity of iturin A increased sevenfold and was restored to about half that of the donor strain RB14, without the transfer of additional genes, such as regulatory or self-resistance genes.}, }
@article {pmid16245569, year = {2005}, author = {Provorov, NA}, title = {[Molecular basis of symbiogenic evolution: from free-living bacteria towards organelles].}, journal = {Zhurnal obshchei biologii}, volume = {66}, number = {5}, pages = {371-388}, pmid = {16245569}, issn = {0044-4596}, mesh = {Bacteria/*genetics ; *Bacterial Physiological Phenomena ; Eukaryotic Cells/*cytology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Drift ; Genome, Bacterial ; Organelles ; Plasmids ; Symbiosis ; }, abstract = {Molecular mechanisms of the bacteria evolution are addressed in the context of the theory of symbiogenic origin of eukaryotic cells. In the evolution of symbiotic bacteria two strategies are implemented: (a) combinative, resulted in the formation of symbiotic (sym) gene systems from the genes previously involved in the autonomous life (facultative and ecologically obligatory symbioses); (b) reductive, related to the loss of genes for the autonomous life (genetically obligatory symbioses). Both strategies are based on the increase in genomic plasticity leading: (a) during combinative evolution--to the segregation of sym gene systems into the special plasmids or "islands" (the genome size and complexity increase); (b) during the reductive evolution--to the losses of many metabolic pathways (genome size decreases). These processes are continued during the evolution of mitochondria, hydrogenosomes and plastids in which many genes for the transcription and translation were lost, while the genomes of organelles and nuclei recombined. These reorganizations are related to the peculiarities of the bacteria population dynamics within the symbiotic systems. The bacteria which combine the abilities for symbiotic and autonomous lifestyles are characterized by ecotypic polymorphism (stable coexistence of symbiotic and asymbiotic genotypes). A key role in their evolution is implemented by horizontal transfer of sym genes that in combination with different forms of natural selection (individual, frequency-dependent and group selection) are responsible for the combinative evolution of bacteria genome. In the populations of obligatory symbionts, the genetic drift and group selection dominate that ensure bacteria genome reduction, loss of their biological identity and transformation into organelles.}, }
@article {pmid16242020, year = {2005}, author = {Omelchenko, MV and Wolf, YI and Gaidamakova, EK and Matrosova, VY and Vasilenko, A and Zhai, M and Daly, MJ and Koonin, EV and Makarova, KS}, title = {Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance.}, journal = {BMC evolutionary biology}, volume = {5}, number = {}, pages = {57}, pmid = {16242020}, issn = {1471-2148}, mesh = {Acclimatization ; Archaea/genetics ; DNA Damage ; DNA Repair ; Deinococcus/*genetics ; Escherichia coli/metabolism ; Gamma Rays ; Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; Genome ; *Genome, Archaeal ; Genome, Bacterial ; Hot Temperature ; Iron/chemistry ; Manganese/chemistry ; Models, Genetic ; Multigene Family ; Phenotype ; Phylogeny ; Plasmids/metabolism ; Temperature ; Thermus thermophilus/*genetics ; }, abstract = {BACKGROUND: Thermus thermophilus and Deinococcus radiodurans belong to a distinct bacterial clade but have remarkably different phenotypes. T. thermophilus is a thermophile, which is relatively sensitive to ionizing radiation and desiccation, whereas D. radiodurans is a mesophile, which is highly radiation- and desiccation-resistant. Here we present an in-depth comparison of the genomes of these two related but differently adapted bacteria.<br><br>RESULTS: By reconstructing the evolution of Thermus and Deinococcus after the divergence from their common ancestor, we demonstrate a high level of post-divergence gene flux in both lineages. Various aspects of the adaptation to high temperature in Thermus can be attributed to horizontal gene transfer from archaea and thermophilic bacteria; many of the horizontally transferred genes are located on the single megaplasmid of Thermus. In addition, the Thermus lineage has lost a set of genes that are still present in Deinococcus and many other mesophilic bacteria but are not common among thermophiles. By contrast, Deinococcus seems to have acquired numerous genes related to stress response systems from various bacteria. A comparison of the distribution of orthologous genes among the four partitions of the Deinococcus genome and the two partitions of the Thermus genome reveals homology between the Thermus megaplasmid (pTT27) and Deinococcus megaplasmid (DR177).<br><br>CONCLUSION: After the radiation from their common ancestor, the Thermus and Deinococcus lineages have taken divergent paths toward their distinct lifestyles. In addition to extensive gene loss, Thermus seems to have acquired numerous genes from thermophiles, which likely was the decisive contribution to its thermophilic adaptation. By contrast, Deinococcus lost few genes but seems to have acquired many bacterial genes that apparently enhanced its ability to survive different kinds of environmental stresses. Notwithstanding the accumulation of horizontally transferred genes, we also show that the single megaplasmid of Thermus and the DR177 megaplasmid of Deinococcus are homologous and probably were inherited from the common ancestor of these bacteria.}, }
@article {pmid16240694, year = {2005}, author = {Sabia, C and Bondi, M and Messi, P and De Niederhäusern, S and Manicardi, G}, title = {Study of five penicillinase producing Neisseria gonorrhoeae isolated in Italy.}, journal = {The new microbiologica}, volume = {28}, number = {3}, pages = {223-229}, pmid = {16240694}, issn = {1121-7138}, mesh = {Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; DNA Fingerprinting ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Gonorrhea/*microbiology ; Humans ; Italy ; Male ; Microbial Sensitivity Tests ; Molecular Weight ; Neisseria gonorrhoeae/*drug effects/*enzymology/isolation &amp; purification ; *Penicillin Resistance ; Penicillinase/*biosynthesis ; Plasmids/analysis ; Restriction Mapping ; Urethra/*microbiology ; }, abstract = {Five penicillinase producing Neisseria gonorrhoeae (PPNG) were isolated from urethral specimens of men admitted to the "Santa Chiara" Hospital (Trento, Italy). All strains proved to be resistant to penicillin and ampicillin, and sensitive to cefuroxime, erythromycin, tetracycline, spectinomycin, nalidixic acid and ciprofloxacin. PPNG plasmid profiles showed that four of the isolates carried the 3.2 MDa "Africa" plasmid and one the 4.5 MDa "Asia" plasmid, the two well-known phenotypes reported in the USA and Europe as well as in Asian and African countries. Membrane matings were performed using N. gonorrhoeae carrying the 24.5 MDa conjugative plasmid as donors and E. coli K12 J 53 as recipient. The transfer of beta-lactamic antibiotic resistance was supported by the presence of 4.5 or 3.2 MDa plasmid bands and by beta-lactamase production in the transconjugants. Restriction analysis of Asian and African plasmids is reported.}, }
@article {pmid16239132, year = {2005}, author = {Marcus, E}, title = {Retraction controversy.}, journal = {Cell}, volume = {123}, number = {2}, pages = {173-175}, doi = {10.1016/j.cell.2005.10.007}, pmid = {16239132}, issn = {0092-8674}, mesh = {Animals ; DNA, Kinetoplast/*genetics ; *Editorial Policies ; Ethics Committees/*standards ; Gene Transfer, Horizontal ; Humans ; *Retraction of Publication as Topic ; Trypanosoma cruzi/*genetics ; }, }
@article {pmid16239080, year = {2005}, author = {Baron, C}, title = {From bioremediation to biowarfare: on the impact and mechanism of type IV secretion systems.}, journal = {FEMS microbiology letters}, volume = {253}, number = {2}, pages = {163-170}, doi = {10.1016/j.femsle.2005.09.030}, pmid = {16239080}, issn = {0378-1097}, mesh = {Animals ; Biodegradation, Environmental ; Biological Warfare ; Fimbriae, Bacterial/physiology ; Gram-Negative Bacteria/*pathogenicity/*physiology ; Gram-Negative Bacterial Infections/microbiology ; Humans ; Ion Channels/*physiology ; Mammals/microbiology ; Virulence Factors ; }, abstract = {Type IV secretion systems are employed by a wide variety of Gram-negative microorganisms for the translocation of macromolecules across the cell envelope. The translocated substrates (proteins, protein-DNA complexes and DNA) are as diverse as the organisms on the donor and recipient side of the translocation process. Over the course of evolution, these macromolecular transporters were adapted to many different purposes, but their basic mechanism was conserved. They impact human life in various ways, as there are driving forces of horizontal gene transfer, which spreads biodegradative capabilities of environmental bacteria as well as antibiotic resistance of pathogens in hospitals. Also, they translocate toxins and other effectors, which have an effect on host cell metabolism and are essential for the virulence of bacterial pathogens. We here present recent developments of research on the mechanism of type IV secretion focusing on the energetization of transport and assembly processes, formation of the translocation channel and of surface-exposed pili, which initiate host cell interactions.}, }
@article {pmid16238013, year = {2005}, author = {Dobrindt, U}, title = {(Patho-)Genomics of Escherichia coli.}, journal = {International journal of medical microbiology : IJMM}, volume = {295}, number = {6-7}, pages = {357-371}, doi = {10.1016/j.ijmm.2005.07.009}, pmid = {16238013}, issn = {1438-4221}, mesh = {Bacteriophages/physiology ; *Biological Evolution ; Escherichia coli/*genetics/*pathogenicity/virology ; Escherichia coli Infections/microbiology ; Escherichia coli Proteins/*genetics/metabolism ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Virulence ; }, abstract = {Escherichia coli represents a versatile and diverse enterobacterial species which can be subdivided into (i) nonpathogenic, commensal, (ii) intestinal pathogenic and (iii) extraintestinal pathogenic strains. This classification is mainly based on the presence or absence of DNA regions which are frequently associated with certain pathotypes. In most cases, this genetic information has been horizontally acquired and belongs to the flexible E. coli genome, such as plasmids, bacteriophages and genomic islands. These genomic regions contribute to the rapid evolution of E. coli variants as they are frequently subject to rearrangements, excision and transfer as well as further acquisition of additional DNA thus contributing to the creation of new (pathogenic) variants. Genetic diversity and genome plasticity of E. coli has been underestimated. The accumulating amount of sequence information generated in the era of "genomics" helps to increase our understanding of factors and mechanisms that are involved in diversification of this bacterial species as well as in those that may direct host specificity.}, }
@article {pmid16237032, year = {2005}, author = {Hamilton-Brehm, SD and Schut, GJ and Adams, MW}, title = {Metabolic and evolutionary relationships among Pyrococcus Species: genetic exchange within a hydrothermal vent environment.}, journal = {Journal of bacteriology}, volume = {187}, number = {21}, pages = {7492-7499}, pmid = {16237032}, issn = {0021-9193}, mesh = {DNA Transposable Elements ; DNA, Archaeal/isolation &amp; purification ; Electrophoresis, Gel, Pulsed-Field ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Archaeal ; Hot Springs/*microbiology ; Maltose/metabolism ; Metabolism/genetics ; Multigene Family ; Nitric Oxide/toxicity ; Nucleic Acid Hybridization ; Oligonucleotide Array Sequence Analysis ; Open Reading Frames ; Pyrococcus/*genetics/*metabolism ; Tandem Repeat Sequences ; *Water Microbiology ; }, abstract = {Pyrococcus furiosus and Pyrococcus woesei grow optimally at temperatures near 100 degrees C and were isolated from the same shallow marine volcanic vent system. Hybridization of genomic DNA from P. woesei to a DNA microarray containing all 2,065 open reading frames (ORFs) annotated in the P. furiosus genome, in combination with PCR analysis, indicated that homologs of 105 ORFs present in P. furiosus are absent from the uncharacterized genome of P. woesei. Pulsed-field electrophoresis indicated that the sizes of the two genomes are comparable, and the results were consistent with the hypothesis that P. woesei lacks the 105 ORFs found in P. furiosus. The missing ORFs are present in P. furiosus mainly in clusters. These clusters include one cluster (Mal I, PF1737 to PF1751) involved in maltose metabolism and another cluster (PF0691 to PF0695) whose products are thought to remove toxic reactive nitrogen species. Accordingly, it was found that P. woesei, in contrast to P. furiosus, is unable to utilize maltose as a carbon source for growth, and the growth of P. woesei on starch was inhibited by addition of a nitric oxide generator. In P. furiosus the ORF clusters not present in P. woesei are bracketed by or are in the vicinity of insertion sequences or long clusters of tandem repeats (LCTRs). While the role of LCTRs in lateral gene transfer is not known, the Mal I cluster in P. furiosus is a composite transposon that undergoes replicative transposition. The same locus in P. woesei lacks any evidence of insertion activity, indicating that P. woesei is a sister or even the parent of P. furiosus. P. woesei may have acquired by lateral gene transfer more than 100 ORFs from other organisms living in the same thermophilic environment to produce the type strain of P. furiosus.}, }
@article {pmid16237002, year = {2005}, author = {Flores, M and Morales, L and Avila, A and González, V and Bustos, P and García, D and Mora, Y and Guo, X and Collado-Vides, J and Piñero, D and Dávila, G and Mora, J and Palacios, R}, title = {Diversification of DNA sequences in the symbiotic genome of Rhizobium etli.}, journal = {Journal of bacteriology}, volume = {187}, number = {21}, pages = {7185-7192}, pmid = {16237002}, issn = {0021-9193}, mesh = {DNA, Bacterial/chemistry/*genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Molecular Sequence Data ; Nitrogen Fixation ; Plasmids/*genetics ; *Polymorphism, Single Nucleotide ; Recombination, Genetic ; Rhizobium etli/*genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Symbiosis/*genetics ; }, abstract = {Bacteria of the genus Rhizobium and related genera establish nitrogen-fixing symbioses with the roots of leguminous plants. The genetic elements that participate in the symbiotic process are usually compartmentalized in the genome, either as independent replicons (symbiotic plasmids) or as symbiotic regions or islands in the chromosome. The complete nucleotide sequence of the symbiotic plasmid of Rhizobium etli model strain CFN42, symbiont of the common bean plant, has been reported. To better understand the basis of DNA sequence diversification of this symbiotic compartment, we analyzed the distribution of single-nucleotide polymorphisms in homologous regions from different Rhizobium etli strains. The distribution of polymorphisms is highly asymmetric in each of the different strains, alternating regions containing very few changes with regions harboring an elevated number of substitutions. The regions showing high polymorphism do not correspond with discrete genetic elements and are not the same in the different strains, indicating that they are not hypervariable regions of functional genes. Most interesting, some highly polymorphic regions share exactly the same nucleotide substitutions in more than one strain. Furthermore, in different regions of the symbiotic compartment, different sets of strains share the same substitutions. The data indicate that the majority of nucleotide substitutions are spread in the population by recombination and that the contribution of new mutations to polymorphism is relatively low. We propose that the horizontal transfer of homologous DNA segments among closely related organisms is a major source of genomic diversification.}, }
@article {pmid16235057, year = {2005}, author = {Inal, JM}, title = {Complement C2 receptor inhibitor trispanning: from man to schistosome.}, journal = {Springer seminars in immunopathology}, volume = {27}, number = {3}, pages = {320-331}, pmid = {16235057}, issn = {0344-4325}, mesh = {Amino Acid Sequence ; Animals ; Antigens, Helminth/chemistry/*genetics/immunology ; Carrier Proteins/chemistry/*genetics/immunology ; Complement System Proteins/metabolism ; Gadus morhua/genetics/immunology ; Gene Transfer, Horizontal ; Helminth Proteins/chemistry/*genetics/immunology ; Humans ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Rats ; Receptors, Cell Surface/chemistry/*genetics/immunology ; Schistosoma/genetics/immunology ; Sequence Homology, Amino Acid ; }, abstract = {Horizontal gene transfer (HGT), in relation to genetic transfer between hosts and parasites, is a little described mechanism. Since the complement inhibitor CRIT was first discovered in the human Schistosoma parasite (the causative agent of Bilharzia) and in Trypanosoma cruzi (a parasite causing Chagas' disease), it has been found to be distributed amongst various species, ranging from the early teleost cod to rats and humans. In terms of evolutionary distance, as measured in a phylogenetic analysis of these CRIT genes at nucleotide level, the parasitic species are as removed from their human host as is the rat sequence, suggesting HGT. The hypotheses that CRIT in humans and schistosomes is orthologous and that the presence of CRIT in schistosomes occurs as a result of host-to-parasite HGT are presented in the light of empirical data and the growing body of data on mobile genetic elements in human and schistosome genomes. In summary, these data indicate phylogenetic proximity between Schistosoma and human CRIT, identity of function, high nucleotide/amino acid identity and secondary protein structure, as well as identical genomic organization.}, }
@article {pmid16232353, year = {2005}, author = {Gu, JC and Wang, Y and Zhang, ZT and Xue, JG and Li, JS and Zhou, YZ}, title = {Effects of human interleukin 10 gene transfer on the expression of Bcl-2 Bax and apoptosis of hepatocyte in rats with acute hemorrhagic necrotizing pancreatitis.}, journal = {Chinese medical journal}, volume = {118}, number = {19}, pages = {1658-1660}, pmid = {16232353}, issn = {0366-6999}, mesh = {Animals ; *Apoptosis ; Female ; Gene Transfer, Horizontal ; *Genetic Therapy ; Hemorrhage/pathology/*therapy ; Hepatocytes/*pathology ; Interleukin-10/*genetics ; Male ; Pancreatitis, Acute Necrotizing/pathology/*therapy ; Proto-Oncogene Proteins c-bcl-2/*physiology ; Rats ; Rats, Wistar ; bcl-2-Associated X Protein ; }, }
@article {pmid16232283, year = {2005}, author = {Berg, G and Eberl, L and Hartmann, A}, title = {The rhizosphere as a reservoir for opportunistic human pathogenic bacteria.}, journal = {Environmental microbiology}, volume = {7}, number = {11}, pages = {1673-1685}, doi = {10.1111/j.1462-2920.2005.00891.x}, pmid = {16232283}, issn = {1462-2912}, mesh = {Bacteria/genetics/*pathogenicity ; Bacterial Infections/*microbiology ; *Bacterial Physiological Phenomena ; Humans ; Plant Roots/*microbiology ; *Soil Microbiology ; }, abstract = {During the last years, the number of human infections caused by opportunistic pathogens has increased dramatically. One natural reservoir of opportunistic pathogens is the rhizosphere, the zone around roots that is influenced by the plant. Due to a high content of nutrients, this habitat is a 'microbial hot-spot', where bacterial abundances including those with strong antagonistic traits are enhanced. Various bacterial genera, including Burkholderia, Enterobacter, Herbaspirillum, Ochrobactrum, Pseudomonas, Ralstonia, Staphylococcus and Stenotrophomonas, contain root-associated strains that can encounter bivalent interactions with both plant and human hosts. Mechanisms responsible for colonization of the rhizosphere and antagonistic activity against plant pathogens are similar to those responsible for colonization of human organs and tissues, and pathogenicity. Multiple resistances against antibiotics are not only found with clinical strains but also with strains isolated from the rhizosphere. High competition, the occurrence of diverse antibiotics in the rhizosphere, and enhanced horizontal gene transfer rates in this microenvironment appear to contribute to the high levels of natural resistances. While opportunistic bacteria from the rhizosphere have some properties in common, each of these emerging pathogens has its own features, which are discussed in detail for Burkholderia, Ochrobactrum and Stenotrophomonas.}, }
@article {pmid16229745, year = {2005}, author = {Guerrero, G and Peralta, H and Aguilar, A and Díaz, R and Villalobos, MA and Medrano-Soto, A and Mora, J}, title = {Evolutionary, structural and functional relationships revealed by comparative analysis of syntenic genes in Rhizobiales.}, journal = {BMC evolutionary biology}, volume = {5}, number = {}, pages = {55}, pmid = {16229745}, issn = {1471-2148}, mesh = {Agrobacterium tumefaciens/genetics ; Base Sequence ; Brucella melitensis ; Chromosome Mapping ; Chromosomes, Bacterial ; Codon ; Conserved Sequence ; Evolution, Molecular ; Gene Order ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genetic Linkage ; Genetic Variation ; Genome ; Genome, Bacterial ; Isoelectric Point ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Plasmids/metabolism ; Protein Conformation ; Proteomics/methods ; Recombination, Genetic ; Sinorhizobium meliloti/genetics ; Species Specificity ; Synteny ; }, abstract = {BACKGROUND: Comparative genomics has provided valuable insights into the nature of gene sequence variation and chromosomal organization of closely related bacterial species. However, questions about the biological significance of gene order conservation, or synteny, remain open. Moreover, few comprehensive studies have been reported for rhizobial genomes.<br><br>RESULTS: We analyzed the genomic sequences of four fast growing Rhizobiales (Sinorhizobium meliloti, Agrobacterium tumefaciens, Mesorhizobium loti and Brucella melitensis). We made a comprehensive gene classification to define chromosomal orthologs, genes with homologs in other replicons such as plasmids, and those which were species-specific. About two thousand genes were predicted to be orthologs in each chromosome and about 80% of these were syntenic. A striking gene colinearity was found in pairs of organisms and a large fraction of the microsyntenic regions and operons were similar. Syntenic products showed higher identity levels than non-syntenic ones, suggesting a resistance to sequence variation due to functional constraints; also, an unusually high fraction of syntenic products contained membranal segments. Syntenic genes encode a high proportion of essential cell functions, presented a high level of functional relationships and a very low horizontal gene transfer rate. The sequence variability of the proteins can be considered the species signature in response to specific niche adaptation. Comparatively, an analysis with genomes of Enterobacteriales showed a different gene organization but gave similar results in the synteny conservation, essential role of syntenic genes and higher functional linkage among the genes of the microsyntenic regions.<br><br>CONCLUSION: Syntenic bacterial genes represent a commonly evolved group. They not only reveal the core chromosomal segments present in the last common ancestor and determine the metabolic characteristics shared by these microorganisms, but also show resistance to sequence variation and rearrangement, possibly due to their essential character. In Rhizobiales and Enterobacteriales, syntenic genes encode a high proportion of essential cell functions and presented a high level of functional relationships.}, }
@article {pmid16228576, year = {2003}, author = {Gupta, RS}, title = {Evolutionary relationships among photosynthetic bacteria.}, journal = {Photosynthesis research}, volume = {76}, number = {1-3}, pages = {173-183}, pmid = {16228576}, issn = {1573-5079}, abstract = {To understand the evolution of photosynthetic bacteria it is necessary to understand how the main groups within Bacteria have evolved from a common ancestor, a critical issue that has not been resolved in the past. Recent analysis of shared conserved inserts or deletions (indels) in protein sequences has provided a powerful means to resolve this long-standing problem in microbiology. Based on a set of 25 indels in highly conserved and widely distributed proteins, all main groups within bacteria can now be defined in clear molecular terms and their relative branching orders logically deduced. For the 82 presently completed bacterial genomes, the presence or absence of these signatures in various proteins was found to be almost exactly as predicted by the indel model, with only 11 exceptions observed in 1842 observations. The branching order of different bacterial groups as deduced using this approach is as follows: low G+C Gram-positive (Heliobacterium chlorum) <--> high G+C Gram-positive <--> Clostridium-Fusobacterium-Thermotoga <--> Deinococcus-Thermus <--> green nonsulfur bacteria (Chloroflexus aurantiacus) <--> Cyanobacteria <--> Spirochetes <--> Chlamydia-Cytophaga-Flavobacteria-green sulfur bacteria (Chlorobium tepidum) <--> Aquifex <--> Proteobacteria (delta and in) <--> Proteobacteria (alpha) <--> Proteobacteria (beta) and <--> Proteobacteria (gamma). The Heliobacterium species, which contain an Fe-S type of reaction center (RC 1) and represent the sole photosynthetic phylum from the Gram-positive or monoderm bacteria (i.e., bounded by only a single membrane), is indicated to be the most ancestral of the photosynthetic lineages. Among the Gram-negative or diderm bacteria (containing both inner and outer cell membranes) the green nonsulfur bacteria, which contain a pheophytin-quinone type of reaction center (RC 2), are indicated to have evolved first. The later emerging photosynthetic groups which contain either one or both of these reaction centers could have acquired such genes from the earlier branching lineages by either direct descent or by means of lateral gene transfer.}, }
@article {pmid16227349, year = {2005}, author = {Poirel, L and Liard, A and Rodriguez-Martinez, JM and Nordmann, P}, title = {Vibrionaceae as a possible source of Qnr-like quinolone resistance determinants.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {56}, number = {6}, pages = {1118-1121}, doi = {10.1093/jac/dki371}, pmid = {16227349}, issn = {0305-7453}, mesh = {Amino Acid Sequence ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/drug effects/genetics ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Photobacterium/drug effects/genetics ; Polymerase Chain Reaction ; Quinolones/*pharmacology ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Vibrio parahaemolyticus/drug effects/genetics ; Vibrio vulnificus/drug effects/genetics ; Vibrionaceae/*drug effects/*genetics ; }, abstract = {OBJECTIVES: To gain insight into the functionality of qnr-like genes of several bacterial species of Vibrionaceae that may encode quinolone resistance determinants.<br><br>METHODS: A PCR-based strategy was used to obtain qnr-like genes of reference strains of Vibrio vulnificus CIP103196, Vibrio parahaemolyticus CIP71.2 and Photobacterium profundum CIP106289 that were sequenced, cloned and expressed in Escherichia coli. MICs of quinolones were determined for these reference strains and an E. coli reference strain harbouring recombinant plasmids.<br><br>RESULTS: The Qnr-like proteins of these Vibrionaceae bacterial species shared 40-67% amino acid identity with the plasmid-mediated quinolone resistance determinants QnrA, QnrB and QnrS with a series of highly conserved residues. Once cloned in E. coli they conferred reduced susceptibility to quinolones.<br><br>CONCLUSIONS: This work provides further evidence that water-borne Vibrionaceae may constitute a reservoir for Qnr-like quinolone resistance determinants.}, }
@article {pmid16226338, year = {2005}, author = {Technau, U and Rudd, S and Maxwell, P and Gordon, PM and Saina, M and Grasso, LC and Hayward, DC and Sensen, CW and Saint, R and Holstein, TW and Ball, EE and Miller, DJ}, title = {Maintenance of ancestral complexity and non-metazoan genes in two basal cnidarians.}, journal = {Trends in genetics : TIG}, volume = {21}, number = {12}, pages = {633-639}, doi = {10.1016/j.tig.2005.09.007}, pmid = {16226338}, issn = {0168-9525}, mesh = {Animals ; Anthozoa/*genetics ; Bacterial Proteins/genetics ; Genes, Duplicate ; *Genetics, Population ; Heat-Shock Proteins/genetics ; Humans ; Phylogeny ; }, abstract = {Cnidarians are among the simplest extant animals; however EST analyses reveal that they have a remarkably high level of genetic complexity. In this article, we show that the full diversity of metazoan signaling pathways is represented in this phylum, as are antagonists previously known only in chordates. Many of the cnidarian ESTs match genes previously known only in non-animal kingdoms. At least some of these represent ancient genes lost by all bilaterians examined so far, rather than genes gained by recent lateral gene transfer.}, }
@article {pmid16223881, year = {2005}, author = {Chandler, JR and Hirt, H and Dunny, GM}, title = {A paracrine peptide sex pheromone also acts as an autocrine signal to induce plasmid transfer and virulence factor expression in vivo.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {102}, number = {43}, pages = {15617-15622}, pmid = {16223881}, issn = {0027-8424}, support = {T32 DE007288/DE/NIDCR NIH HHS/United States ; HL 51987/HL/NHLBI NIH HHS/United States ; GM 49530/GM/NIGMS NIH HHS/United States ; T32 DE 07288/DE/NIDCR NIH HHS/United States ; R01 GM049530/GM/NIGMS NIH HHS/United States ; R01 HL051987/HL/NHLBI NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; *Conjugation, Genetic ; Enterococcus faecalis/*genetics ; *Gene Transfer, Horizontal ; Humans ; Molecular Sequence Data ; Oligopeptides/*physiology ; Pheromones/*physiology ; *Plasmids ; Serum Albumin/metabolism ; Signal Transduction ; Virulence Factors/*genetics ; }, abstract = {The peptide pheromone cCF10 of Enterococcus faecalis is an intercellular signal for induction of conjugative transfer of plasmid pCF10 from donor cells to recipient cells. When a donor cell is exposed to recipient-produced cCF10, expression of the pCF10-encoded aggregation substance of pCF10 (Asc10) and other conjugation gene products is activated. Asc10 also increases enterococcal virulence in several models, and when donor cells are grown in animals or in plasma, Asc10 expression is induced by means of the cCF10-sensing machinery. Plasmid pCF10 carries two genes that function to prevent self-induction by endogenous cCF10 in donor cells. The membrane protein PrgY reduces endogenous pheromone activity in donor cells, and the inhibitor peptide iCF10 neutralizes the residual endogenous cCF10 that escapes PrgY. In the current study, we found that E. faecalis strains with allelic replacements abolishing active cCF10 production showed reduced ability to acquire pCF10 by conjugation; prgY-null mutations had no phenotype in the cCF10-negative strains. We observed that expression of the mRNA for iCF10 was reduced in this background and that these mutations also blocked plasma induction of Asc10 expression. These findings support a model in which plasma induction in wild-type donors results from iCF10 inactivation by a plasma component, causing disruption of a precisely maintained balance of iCF10 to cCF10 activity and allowing subsequent induction by endogenous cCF10. Although cCF10 has traditionally been viewed as an intercellular signal, these results show that pCF10 has also adapted cCF10 as an autocrine signal that activates expression of virulence and conjugation functions.}, }
@article {pmid16221896, year = {2006}, author = {Huson, DH and Bryant, D}, title = {Application of phylogenetic networks in evolutionary studies.}, journal = {Molecular biology and evolution}, volume = {23}, number = {2}, pages = {254-267}, doi = {10.1093/molbev/msj030}, pmid = {16221896}, issn = {0737-4038}, mesh = {Animals ; *Evolution, Molecular ; *Models, Genetic ; *Phylogeny ; }, abstract = {The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known that more complex evolutionary scenarios are poorly described by such models. Further, even when evolution proceeds in a tree-like manner, analysis of the data may not be best served by using methods that enforce a tree structure but rather by a richer visualization of the data to evaluate its properties, at least as an essential first step. Thus, phylogenetic networks should be employed when reticulate events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved, and, even in the absence of such events, phylogenetic networks have a useful role to play. This article reviews the terminology used for phylogenetic networks and covers both split networks and reticulate networks, how they are defined, and how they can be interpreted. Additionally, the article outlines the beginnings of a comprehensive statistical framework for applying split network methods. We show how split networks can represent confidence sets of trees and introduce a conservative statistical test for whether the conflicting signal in a network is treelike. Finally, this article describes a new program, SplitsTree4, an interactive and comprehensive tool for inferring different types of phylogenetic networks from sequences, distances, and trees.}, }
@article {pmid16218452, year = {2005}, author = {Tsuda, M and Sota, M}, title = {[Mobile genetic elements for microbial degradation of environmental pollutants].}, journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme}, volume = {50}, number = {12}, pages = {1527-1534}, pmid = {16218452}, issn = {0039-9450}, mesh = {Bacteria/*enzymology/*genetics/metabolism ; Biodegradation, Environmental ; DNA Transposable Elements/genetics/physiology ; Environmental Pollutants/*metabolism ; Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences/genetics/physiology ; Plasmids/genetics/physiology ; }, }
@article {pmid16217547, year = {2005}, author = {Gressmann, H and Linz, B and Ghai, R and Pleissner, KP and Schlapbach, R and Yamaoka, Y and Kraft, C and Suerbaum, S and Meyer, TF and Achtman, M}, title = {Gain and loss of multiple genes during the evolution of Helicobacter pylori.}, journal = {PLoS genetics}, volume = {1}, number = {4}, pages = {e43}, pmid = {16217547}, issn = {1553-7404}, mesh = {*Evolution, Molecular ; *Gene Expression Regulation ; Gene Transfer, Horizontal ; Genome ; Genome, Bacterial ; Helicobacter/genetics ; Helicobacter pylori/*genetics ; Models, Genetic ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; Recombination, Genetic ; Species Specificity ; }, abstract = {Sequence diversity and gene content distinguish most isolates of Helicobacter pylori. Even greater sequence differences differentiate distinct populations of H. pylori from different continents, but it was not clear whether these populations also differ in gene content. To address this question, we tested 56 globally representative strains of H. pylori and four strains of Helicobacter acinonychis with whole genome microarrays. Of the weighted average of 1,531 genes present in the two sequenced genomes, 25% are absent in at least one strain of H. pylori and 21% were absent or variable in H. acinonychis. We extrapolate that the core genome present in all isolates of H. pylori contains 1,111 genes. Variable genes tend to be small and possess unusual GC content; many of them have probably been imported by horizontal gene transfer. Phylogenetic trees based on the microarray data differ from those based on sequences of seven genes from the core genome. These discrepancies are due to homoplasies resulting from independent gene loss by deletion or recombination in multiple strains, which distort phylogenetic patterns. The patterns of these discrepancies versus population structure allow a reconstruction of the timing of the acquisition of variable genes within this species. Variable genes that are located within the cag pathogenicity island were apparently first acquired en bloc after speciation. In contrast, most other variable genes are of unknown function or encode restriction/modification enzymes, transposases, or outer membrane proteins. These seem to have been acquired prior to speciation of H. pylori and were subsequently lost by convergent evolution within individual strains. Thus, the use of microarrays can reveal patterns of gene gain or loss when examined within a phylogenetic context that is based on sequences of core genes.}, }
@article {pmid16217197, year = {2005}, author = {Seed, TM}, title = {Radiation protectants: current status and future prospects.}, journal = {Health physics}, volume = {89}, number = {5}, pages = {531-545}, doi = {10.1097/01.hp.0000175153.19745.25}, pmid = {16217197}, issn = {0017-9078}, mesh = {Combinatorial Chemistry Techniques ; Dietary Supplements ; Electromagnetic Fields ; Gene Transfer, Horizontal ; Genetic Engineering ; Humans ; Radiation Injuries/prevention &amp; control ; *Radiation Protection ; Radiation-Protective Agents/administration &amp; dosage/adverse effects/*pharmacology ; }, abstract = {In today's heightened nuclear/biological/chemical threat environment, there is an increased need to have safe and effective means to protect not only special high-risk service groups, but also the general population at large, from the health hazards of unintended ionizing radiation exposures. An unfulfilled dream has been to have a globally effective pharmacologic that could be easily taken orally without any undue side effects prior to a suspected or impending nuclear/radiological event; such an ideal radioprotective agent has yet to be identified, let alone fully developed and approved for human use. No one would argue against the fact that this is problematic and needs to be corrected, but where might the ultimate solution to this difficult problem be found? Without question, representative species of the aminothiol family [e.g., Amifostine (MedImmune, Gaithersburg, Maryland)] have proven to be potent cytoprotectants for normal tissues subjected to irradiation or to radiomimetic chemicals. Although Amifostine is currently used clinically, drug toxicity, limited times of protection, and unfavorable routes of administration, all serve to limit the drug's utility in nonclinical settings. A full range of research and development strategies is being employed currently in the hunt for new safe and effective radioprotectants. These include: (1) large scale screening of new chemical classes or natural products; (2) restructuring/reformulating older protectants with proven efficacies but unwanted toxicities; (3) using nutraceuticals that are only moderately protective but are essentially nontoxic; (4) using low dose combinations of potentially toxic but efficacious agents that protect through different routes to foster radioprotective synergy; and (5) accepting a lower level of drug efficacy in lieu of reduced toxicity, banking on the premise that the protection afforded can be leveraged by post-exposure therapies. Although it is difficult to predict which of these strategies will ultimately prove to be successful, it is certain that the probability of a useful protectant being fielded is increased significantly. This is due to the resurgence of interest in radiation protection, increased resources being expended by federal agencies, and by the Food and Drug Administration's willingness to innovate relative to new approval guidance.}, }
@article {pmid16216489, year = {2005}, author = {Ouzounis, CA}, title = {Ancestral state reconstructions for genomes.}, journal = {Current opinion in genetics &amp; development}, volume = {15}, number = {6}, pages = {595-600}, doi = {10.1016/j.gde.2005.09.011}, pmid = {16216489}, issn = {0959-437X}, mesh = {*Evolution, Molecular ; Forecasting ; Gene Transfer, Horizontal ; *Genomics/trends ; *Phylogeny ; }, abstract = {The recent expansion of phylogenetic analysis from the traditional field of molecular evolution, analyzing histories of genes, to the nascent field of "genomic evolution", analyzing histories of entire genomes, enables the construction of trees based on genome information, the quantification of the key processes that shape genome content and, ultimately, plausible parsimony reconstructions of ancestral genomes. Thus, when genomes are considered as phylogenetic characters, it is possible to reconstruct not only the history of species but also the ancestral states in terms of genome structure or function. In the future, we might be able to accurately reconstruct--or retrodict--a chain of events that led to the emergence of a specific genome sequence and, ultimately, to synthesize ancestral genomes at will, creating a "Jurassic database" of genomes.}, }
@article {pmid16216105, year = {2005}, author = {Mooij, MJ and Schouten, I and Vos, G and Van Belkum, A and Vandenbroucke-Grauls, CM and Savelkoul, PH and Schultsz, C}, title = {Class 1 integrons in ciprofloxacin-resistant Escherichia coli strains from two Dutch hospitals.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {11}, number = {11}, pages = {898-902}, doi = {10.1111/j.1469-0691.2005.01259.x}, pmid = {16216105}, issn = {1198-743X}, mesh = {Anti-Bacterial Agents/*pharmacology ; Ciprofloxacin/*pharmacology ; Conjugation, Genetic ; DNA Fingerprinting ; DNA Gyrase/genetics ; DNA, Bacterial/analysis/genetics ; Drug Resistance, Bacterial ; Escherichia coli/drug effects/*genetics/*isolation &amp; purification ; Escherichia coli Infections/*microbiology ; Escherichia coli Proteins/genetics ; Gene Transfer, Horizontal ; Hematologic Diseases/complications ; Hospitals ; Humans ; Inpatients ; Integrases/genetics ; *Integrons ; Netherlands ; Nucleic Acid Hybridization ; Polymorphism, Genetic ; }, abstract = {A significant increase in the isolation frequency of ciprofloxacin-resistant Escherichia coli was observed in the haematology departments of two university hospitals in The Netherlands. Amplified fragment length polymorphism analysis revealed that this increase was not caused by the emergence of unique ciprofloxacin-resistant clones. Determination of the presence of class 1 integrons indicated that 81% of the ciprofloxacin-resistant isolates contained an intI1 gene, compared with 11% of the ciprofloxacin-susceptible isolates (p<0.0001). The quinolone resistance gene qnrA was not present in any of the integrons characterised and could not be detected using dot-blot hybridisation of total DNA. In addition, conjugation experiments showed that ciprofloxacin resistance was not co-transferred with class 1 integrons. Ciprofloxacin-resistant isolates harboured mutations in the gyrA gene, which are known to encode ciprofloxacin resistance. In conclusion, an association was observed between ciprofloxacin resistance and the presence of class 1 integrons, which could not be explained by the currently known genetic determinants of quinolone resistance.}, }
@article {pmid16216104, year = {2005}, author = {Wu, LT and Hung, SW and Chuang, YC and Chen, HE and Jones, RN and Yu, WL}, title = {Identification of a novel cephalosporinase (DHA-3) in Klebsiella pneumoniae isolated in Taiwan.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {11}, number = {11}, pages = {893-897}, doi = {10.1111/j.1469-0691.2005.01252.x}, pmid = {16216104}, issn = {1198-743X}, mesh = {Adult ; Amino Acid Sequence ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/analysis/isolation &amp; purification ; Cefoxitin/pharmacology ; Cephalosporinase/*analysis/chemistry/genetics/isolation &amp; purification ; Conjugation, Genetic ; Drug Resistance, Bacterial ; Escherichia coli/drug effects/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Isoelectric Point ; Klebsiella Infections/*microbiology ; Klebsiella pneumoniae/*enzymology/isolation &amp; purification ; Molecular Sequence Data ; Plasmids ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Taiwan ; }, abstract = {A strain of Klebsiella pneumoniae resistant to cefoxitin and oxyimino-cephalosporins, but susceptible to cefepime, was isolated from an adult patient hospitalised in Taichung, Taiwan. Isoelectric focusing revealed three beta-lactamases with isoelectric points of 5.4, 8.2 and 7.9, respectively. Following PCR with plasmid DNA templates and gene sequencing, these enzymes were shown to correspond to TEM-1, SHV-5 and a novel DHA-1-like enzyme (designated DHA-3). The bla genes for TEM-1 and SHV-5 were transferable, but the bla(DHA-3) gene was non-self-transferable in conjugation experiments. All three bla genes were successfully introduced by electrotransformation into an Escherichia coli recipient (DH5alpha), resulting in a similar resistance profile to that observed in the original donor strain. Other K. pneumoniae strains producing DHA-1-like enzymes have been identified previously in Taiwan, and this report suggests that DHA-type beta-lactamases are continuing to emerge in this country.}, }
@article {pmid16211857, year = {2005}, author = {Filonov, AE and Akhmetov, LI and Puntus, IF and Esikova, TZ and Gafarov, AB and Izmalkova, TIu and Sokolov, SL and Kosheleva, IA and Boronin, AM}, title = {[The construction and monitoring of genetically marked, plasmid-containing, naphthalene-degrading strains in soil].}, journal = {Mikrobiologiia}, volume = {74}, number = {4}, pages = {526-532}, pmid = {16211857}, issn = {0026-3656}, mesh = {Biodegradation, Environmental ; DNA Transposable Elements/genetics ; Environmental Pollutants/*metabolism ; Gene Transfer, Horizontal ; Green Fluorescent Proteins/genetics ; Naphthalenes/*metabolism ; Plasmids ; Pseudomonas putida/*genetics/growth &amp; development/*metabolism ; *Soil Microbiology ; Transformation, Bacterial ; }, abstract = {A genetically marked, plasmid-containing, naphthalene-degrading strain, Pseudomonas putida KT2442(pNF142::TnMod-OTc), has been constructed. The presence of the gfp gene (which codes for green fluorescent protein) and the kanamycin and rifampicin resistance genes in the chromosome of this strain allows the strain's fate in model soil systems to be monitored, whereas a minitransposon, built in naphthalene biodegradation plasmid pNF142, contains the tetracycline resistance gene and makes it possible to follow the horizontal transfer of this plasmid between various bacteria. Plasmid pNF142::TnMod-OTc is stable in strain P. putida KT2442 under nonselective conditions. The maximal specific growth rate of this strain on naphthalene was found to be higher than that of the natural host of plasmid pNF142. When introduced into a model soil system, the genetically marked strain is stable and competitive for 40 days. The transfer of marked plasmid pNF142::TnMod-OTc to natural soil bacteria, predominantly fluorescent pseudomonads, has been detected.}, }
@article {pmid16204108, year = {2005}, author = {Pál, C and Papp, B and Lercher, MJ}, title = {Horizontal gene transfer depends on gene content of the host.}, journal = {Bioinformatics (Oxford, England)}, volume = {21 Suppl 2}, number = {}, pages = {ii222-3}, doi = {10.1093/bioinformatics/bti1136}, pmid = {16204108}, issn = {1367-4811}, mesh = {Base Composition/*genetics ; Chromosome Mapping/*methods ; Escherichia coli/*physiology ; Escherichia coli Proteins/*genetics/*metabolism ; Gene Transfer, Horizontal/*genetics ; Genetic Variation/genetics ; Genome, Bacterial/genetics ; Signal Transduction/*genetics ; }, abstract = {Horizontal gene transfer is a major contributor to the evolution of bacterial genomes. We examine this process through a combination of comparative genomics and in silico analysis of the Escherichia coli metabolic network. We validate our horizontal transfer estimates by confirming the predicted gradual amelioration of GC content over time. We find that the chance of acquiring a gene by horizontal transfer is up to six times higher if an enzyme that catalyses a coupled metabolite flux is already encoded in the host genome.}, }
@article {pmid16204096, year = {2005}, author = {Huson, DH and Kloepper, TH}, title = {Computing recombination networks from binary sequences.}, journal = {Bioinformatics (Oxford, England)}, volume = {21 Suppl 2}, number = {}, pages = {ii159-65}, doi = {10.1093/bioinformatics/bti1126}, pmid = {16204096}, issn = {1367-4811}, mesh = {Algorithms ; Chromosome Mapping/*methods ; DNA Mutational Analysis/*methods ; *Evolution, Molecular ; Genetic Variation/*genetics ; *Models, Genetic ; Phylogeny ; Recombination, Genetic/*genetics ; Sequence Analysis, DNA/*methods ; Signal Processing, Computer-Assisted ; Signal Transduction/*genetics ; Software ; Statistical Distributions ; }, abstract = {MOTIVATION: Phylogenetic networks are becoming an important tool in molecular evolution, as the evolutionary role of reticulate events, such as hybridization, horizontal gene transfer and recombination, is becoming more evident, and as the available data is dramatically increasing in quantity and quality.<br><br>RESULTS: This paper addresses the problem of computing a most parsimonious recombination network for an alignment of binary sequences that are assumed to have arisen under the 'infinite sites' model of evolution with recombinations. Using the concept of a splits network as the underlying datastructure, this paper shows how a recent method designed for the computation of hybridization networks can be extended to also compute recombination networks. A robust implementation of the approach is provided and is illustrated using a number of real biological datasets.<br><br>AVAILABILITY: Our implementation of this approach is freely available as part of the SplitsTree4 software, downloadable from www.splitstree.org}, }
@article {pmid16201017, year = {2005}, author = {Gutierrez, MC and Brisse, S and Brosch, R and Fabre, M and Omaïs, B and Marmiesse, M and Supply, P and Vincent, V}, title = {Ancient origin and gene mosaicism of the progenitor of Mycobacterium tuberculosis.}, journal = {PLoS pathogens}, volume = {1}, number = {1}, pages = {e5}, pmid = {16201017}, issn = {1553-7366}, abstract = {The highly successful human pathogen Mycobacterium tuberculosis has an extremely low level of genetic variation, which suggests that the entire population resulted from clonal expansion following an evolutionary bottleneck around 35,000 y ago. Here, we show that this population constitutes just the visible tip of a much broader progenitor species, whose extant representatives are human isolates of tubercle bacilli from East Africa. In these isolates, we detected incongruence among gene phylogenies as well as mosaic gene sequences, whose individual elements are retrieved in classical M. tuberculosis. Therefore, despite its apparent homogeneity, the M. tuberculosis genome appears to be a composite assembly resulting from horizontal gene transfer events predating clonal expansion. The amount of synonymous nucleotide variation in housekeeping genes suggests that tubercle bacilli were contemporaneous with early hominids in East Africa, and have thus been coevolving with their human host much longer than previously thought. These results open novel perspectives for unraveling the molecular bases of M. tuberculosis evolutionary success.}, }
@article {pmid16199583, year = {2005}, author = {Mussmann, M and Richter, M and Lombardot, T and Meyerdierks, A and Kuever, J and Kube, M and Glöckner, FO and Amann, R}, title = {Clustered genes related to sulfate respiration in uncultured prokaryotes support the theory of their concomitant horizontal transfer.}, journal = {Journal of bacteriology}, volume = {187}, number = {20}, pages = {7126-7137}, pmid = {16199583}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; Bacteria/*genetics/*metabolism ; Biological Evolution ; Electron Transport Chain Complex Proteins/genetics/metabolism ; Energy Metabolism/genetics ; Gene Library ; Gene Transfer, Horizontal/*physiology ; Genome, Bacterial ; Molecular Sequence Data ; Multigene Family ; Oxidoreductases Acting on Sulfur Group Donors/genetics/metabolism ; Phylogeny ; Seawater/microbiology ; Sulfates/*metabolism ; }, abstract = {The dissimilatory reduction of sulfate is an ancient metabolic process central to today's biogeochemical cycling of sulfur and carbon in marine sediments. Until now its polyphyletic distribution was most parsimoniously explained by multiple horizontal transfers of single genes rather than by a not-yet-identified "metabolic island." Here we provide evidence that the horizontal transfer of a gene cluster may indeed be responsible for the patchy distribution of sulfate-reducing prokaryotes (SRP) in the phylogenetic tree. We isolated three DNA fragments (32 to 41 kb) from uncultured, closely related SRP from DNA directly extracted from two distinct marine sediments. Fosmid ws39f7, and partially also fosmids ws7f8 and hr42c9, harbored a core set of essential genes for the dissimilatory reduction of sulfate, including enzymes for the reduction of sulfur intermediates and synthesis of the prosthetic group of the dissimilatory sulfite reductase. Genome comparisons suggest that encoded membrane proteins universally present among SRP are critical for electron transfer to cytoplasmic enzymes. In addition, novel, conserved hypothetical proteins that are likely involved in dissimilatory sulfate reduction were identified. Based on comparative genomics and previously published experimental evidence, a more comprehensive model of dissimilatory sulfate reduction is presented. The observed clustering of genes involved in dissimilatory sulfate reduction has not been previously found. These findings strongly support the hypothesis that genes responsible for dissimilatory sulfate reduction were concomitantly transferred in a single event among prokaryotes. The acquisition of an optimized gene set would enormously facilitate a successful implementation of a novel pathway.}, }
@article {pmid16195787, year = {2006}, author = {Dabrowska, K and Switała-Jeleń, K and Opolski, A and Górski, A}, title = {Possible association between phages, Hoc protein, and the immune system.}, journal = {Archives of virology}, volume = {151}, number = {2}, pages = {209-215}, doi = {10.1007/s00705-005-0641-7}, pmid = {16195787}, issn = {0304-8608}, mesh = {Animals ; Bacteriophage T4/genetics/*metabolism ; Capsid Proteins/genetics/*immunology/*metabolism ; Eukaryotic Cells/metabolism ; Gene Transfer, Horizontal ; Immune System/*immunology ; }, abstract = {Mammals have become "an environment" for enterobacterial phage life cycles. Therefore it could be expected that bacteriophages adapt to them. This adaptation must comprise bacteriophage proteins. Gp Hoc seems to have significance neither for phage particle structure nor for phage antibacterial activity. It is evidently not necessary for the "typical" antibacterial actions of bacteriophages. But the rules of evolution make it improbable that gp Hoc really has no function, and non-essential genes of T4-type phages are probably important for phages' adaptation to their particular lifestyle. More interesting is the eukaryotic origin of gp Hoc: a resemblance to immunoglobulin-like proteins that reflects their evolutionary relation. Substantial differences in biological activity between T4 and a mutant that lacks gp Hoc were observed in a mammalian system. Hoc protein seems to be one of the molecules predicted to interact with mammalian organisms and/or modulate these interactions.}, }
@article {pmid16191635, year = {2005}, author = {Davis, CC and Anderson, WR and Wurdack, KJ}, title = {Gene transfer from a parasitic flowering plant to a fern.}, journal = {Proceedings. Biological sciences}, volume = {272}, number = {1578}, pages = {2237-2242}, pmid = {16191635}, issn = {0962-8452}, mesh = {Ferns/*genetics ; Gene Transfer, Horizontal/*genetics ; Geography ; Likelihood Functions ; Loranthaceae/genetics ; Magnoliopsida/*genetics ; Models, Genetic ; *Phylogeny ; }, abstract = {The rattlesnake fern (Botrychium virginianum (L.) Sw.) is obligately mycotrophic and widely distributed across the northern hemisphere. Three mitochondrial gene regions place this species with other ferns in Ophioglossaceae, while two regions place it as a member of the largely parasitic angiosperm order Santalales (sandalwoods and mistletoes). These discordant phylogenetic placements suggest that part of the genome in B. virginianum was acquired by horizontal gene transfer (HGT), perhaps from root-parasitic Loranthaceae. These transgenes are restricted to B. virginianum and occur across the range of the species. Molecular and life-history traits indicate that the transfer preceded the global expansion of B. virginianum, and that the latter may have happened very rapidly. This is the first report of HGT from an angiosperm to a fern, through either direct parasitism or the mediation of interconnecting fungal symbionts.}, }
@article {pmid16189113, year = {2005}, author = {Stanhope, MJ and Walsh, SL and Becker, JA and Italia, MJ and Ingraham, KA and Gwynn, MN and Mathie, T and Poupard, JA and Miller, LA and Brown, JR and Amrine-Madsen, H}, title = {Molecular evolution perspectives on intraspecific lateral DNA transfer of topoisomerase and gyrase loci in Streptococcus pneumoniae, with implications for fluoroquinolone resistance development and spread.}, journal = {Antimicrobial agents and chemotherapy}, volume = {49}, number = {10}, pages = {4315-4326}, pmid = {16189113}, issn = {0066-4804}, mesh = {Amino Acid Sequence ; Anti-Infective Agents/pharmacology ; Base Sequence ; DNA Gyrase/genetics ; DNA Topoisomerases, Type II/*genetics ; Drug Resistance, Bacterial/*genetics ; *Evolution, Molecular ; Fluoroquinolones/pharmacology ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Amino Acid ; Streptococcus pneumoniae/drug effects/enzymology/*genetics/isolation &amp; purification ; }, abstract = {Fluoroquinolones are an important class of antibiotics for the treatment of infections arising from the gram-positive respiratory pathogen Streptococcus pneumoniae. Although there is evidence supporting interspecific lateral DNA transfer of fluoroquinolone target loci, no studies have specifically been designed to assess the role of intraspecific lateral transfer of these genes in the spread of fluoroquinolone resistance. This study involves a comparative evolutionary perspective, in which the evolutionary history of a diverse set of S. pneumoniae clinical isolates is reconstructed from an expanded multilocus sequence typing data set, with putative recombinants excluded. This control history is then assessed against networks of each of the four fluoroquinolone target loci from the same isolates. The results indicate that although the majority of fluoroquinolone target loci from this set of 60 isolates are consistent with a clonal dissemination hypothesis, 3 to 10% of the sequences are consistent with an intraspecific lateral transfer hypothesis. Also evident were examples of interspecific transfer, with two isolates possessing a parE-parC gene region arising from viridans group streptococci. The Spain 23F-1 clone is the most dominant fluoroquinolone-nonsusceptible clone in this set of isolates, and the analysis suggests that its members act as frequent donors of fluoroquinolone-nonsusceptible loci. Although the majority of fluoroquinolone target gene sequences in this set of isolates can be explained on the basis of clonal dissemination, a significant number are more parsimoniously explained by intraspecific lateral DNA transfer, and in situations of high S. pneumoniae population density, such events could be an important means of resistance spread.}, }
@article {pmid16189081, year = {2005}, author = {Alcaine, SD and Sukhnanand, SS and Warnick, LD and Su, WL and McGann, P and McDonough, P and Wiedmann, M}, title = {Ceftiofur-resistant Salmonella strains isolated from dairy farms represent multiple widely distributed subtypes that evolved by independent horizontal gene transfer.}, journal = {Antimicrobial agents and chemotherapy}, volume = {49}, number = {10}, pages = {4061-4067}, pmid = {16189081}, issn = {0066-4804}, mesh = {Alleles ; Animals ; Anti-Bacterial Agents/therapeutic use ; Cattle ; Ceftriaxone/therapeutic use ; Cephalosporin Resistance ; Cephalosporins/*therapeutic use ; Clone Cells ; *Dairying ; *Drug Resistance, Bacterial ; Drug Resistance, Multiple ; Ecosystem ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial ; New York/epidemiology ; Phylogeny ; Salmonella/*genetics/isolation &amp; purification ; Salmonella Infections, Animal/epidemiology/*metabolism/microbiology/transmission ; Sequence Analysis, DNA ; Serologic Tests ; beta-Lactamases/genetics/isolation &amp; purification ; }, abstract = {Salmonella is the leading cause of known food-borne bacterial infections in the United States, with an incidence rate of approximately 15 cases per 100,000 people. The rise of antimicrobial-resistant Salmonella subtypes, including the appearance of subtypes resistant to ceftriaxone, represents a particular concern. Ceftriaxone is used to treat invasive cases of Salmonella in children and is closely related to ceftiofur, an antibiotic commonly used to treat diseases of cattle. In order to develop a better understanding of the evolution and transmission of ceftiofur resistance in Salmonella, we characterized ceftiofur-resistant and -sensitive Salmonella isolates from seven New York dairy farms. A total of 39 isolates from these seven farms were analyzed for evolutionary relatedness (by DNA sequencing of the Salmonella genes fimA, manB, and mdh), antibiotic resistance profiles, and the presence of bla(CMY-2), a beta-lactamase gene associated with resistance to cephalosporins. Our data indicate that (i) resistance to ceftriaxone and ceftiofur was highly correlated with the presence of bla(CMY-2); (ii) ceftiofur-resistant Salmonella strains were geographically widespread, as shown by their isolation from farms located throughout New York State; (iii) ceftiofur-resistant Salmonella strains isolated from farms represent multiple distinct subtypes and evolutionary lineages, as determined by serotyping, DNA sequence typing, and antimicrobial-resistance profiles; and (iv) ceftiofur-resistant Salmonella strains evolved by multiple independent acquisitions of an identical bla(CMY-2) allele and by clonal spread of ceftiofur-resistant subtypes.}, }
@article {pmid16188435, year = {2005}, author = {Dujon, B}, title = {Hemiascomycetous yeasts at the forefront of comparative genomics.}, journal = {Current opinion in genetics &amp; development}, volume = {15}, number = {6}, pages = {614-620}, doi = {10.1016/j.gde.2005.09.005}, pmid = {16188435}, issn = {0959-437X}, mesh = {Adaptation, Physiological/genetics ; Ascomycota/*genetics ; Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; *Genome, Fungal ; *Genomics ; }, abstract = {With more than a dozen species fully sequenced, as many as this partially sequenced, and more in development, yeasts are now used to explore the frontlines of comparative genomics of eukaryotes. Innovative procedures have been developed to compare and annotate genomes at various evolutionary distances, to identify short cis-acting regulatory elements, to map duplications, or to align syntenic blocks. Human and plant pathogens, in addition to yeasts that show a variety of interesting physiological properties, are included in this multidimensional comparative survey, which encompasses a very broad evolutionary range. As major steps of the evolutionary history of hemiascomycetous genomes emerge, precise questions on the general mechanisms of their evolution can be addressed, using both experimental and in silico methods.}, }
@article {pmid16188037, year = {2005}, author = {Pang, A and Smith, AD and Nuin, PA and Tillier, ER}, title = {SIMPROT: using an empirically determined indel distribution in simulations of protein evolution.}, journal = {BMC bioinformatics}, volume = {6}, number = {}, pages = {236}, pmid = {16188037}, issn = {1471-2105}, mesh = {Amino Acid Substitution ; *Computer Simulation ; *Evolution, Molecular ; *Models, Genetic ; Models, Statistical ; Monte Carlo Method ; Phylogeny ; Selection, Genetic ; Sequence Analysis, Protein/*methods ; *Software ; Software Design ; }, abstract = {BACKGROUND: General protein evolution models help determine the baseline expectations for the evolution of sequences, and they have been extensively useful in sequence analysis and for the computer simulation of artificial sequence data sets.<br><br>RESULTS: We have developed a new method of simulating protein sequence evolution, including insertion and deletion (indel) events in addition to amino-acid substitutions. The simulation generates both the simulated sequence family and a true sequence alignment that captures the evolutionary relationships between amino acids from different sequences. Our statistical model for indel evolution is based on the empirical indel distribution determined by Qian and Goldstein. We have parameterized this distribution so that it applies to sequences diverged by varying evolutionary times and generalized it to provide flexibility in simulation conditions. Our method uses a Monte-Carlo simulation strategy, and has been implemented in a C++ program named Simprot.<br><br>CONCLUSION: Simprot will be useful for testing methods of analysis of protein sequence families particularly alignment methods, phylogenetic tree building, detection of recombination and horizontal gene transfer, and homology detection, where knowing the true course of sequence evolution is essential.}, }
@article {pmid16187257, year = {2005}, author = {Gupta, SK and Banerjee, T and Basak, S and Sahu, K and Sau, S and Ghosh, TC}, title = {Studies on codon usage in Thermoplasma acidophilum and its possible implications on the occurrences of lateral gene transfer.}, journal = {Journal of basic microbiology}, volume = {45}, number = {5}, pages = {344-354}, doi = {10.1002/jobm.200510576}, pmid = {16187257}, issn = {0233-111X}, mesh = {Codon/*physiology ; *Gene Transfer, Horizontal ; Multivariate Analysis ; Thermoplasma/*genetics ; }, abstract = {Codon usage studies have been carried out on the coding sequences of Thermoplasma acidophilum, which is an archaeon and grows at very low pH and high temperature. Overall codon usage data analysis indicates that all the four bases are almost equifrequent at the third position of codons, which is expected (since genomic GC % of this genome is about 46%). However, multivariate statistical analysis indicates that there are two major trends in the codon usage variation among the genes in this organism. In the first major trend it is observed that genes having G and C ending codons are clustered at one end while, A and T ending ones are clustered at the other end. We have also found a significant positive correlation between the expressivities of genes and GC contents at the synonymous third codon positions. In the second major trend, it is seen that the genes are clustered into three distinct parts. A comparative analyses of codon usage data of T. acidophilum and Sulfolobus solfataricus reveals that one of the three clusters of genes of T. acidophilum is very similar to a considerable number of S. solfataricus genes, suggesting possible occurrences of lateral gene transfer between these two microorganisms as reported by earlier workers.}, }
@article {pmid16186170, year = {2005}, author = {Mater, DD and Langella, P and Corthier, G and Flores, MJ}, title = {Evidence of vancomycin resistance gene transfer between enterococci of human origin in the gut of mice harbouring human microbiota.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {56}, number = {5}, pages = {975-978}, doi = {10.1093/jac/dki336}, pmid = {16186170}, issn = {0305-7453}, mesh = {Animals ; Bacterial Proteins/genetics ; Carbon-Oxygen Ligases/genetics ; Enterococcus faecalis/drug effects/*genetics ; Enterococcus faecium/drug effects/*genetics ; Feces/microbiology ; Gastrointestinal Tract/*microbiology ; *Gene Transfer, Horizontal ; Gram-Positive Bacterial Infections/microbiology ; Humans ; Mice ; Mice, Inbred C3H ; Models, Animal ; Vancomycin Resistance/*genetics ; }, abstract = {OBJECTIVES: Potential intra- and inter-species transfers of vancomycin resistance genes (vanA gene cluster) between Enterococcus strains were evaluated in the gut of heteroxenic mice harbouring a human microbiota.<br><br>METHODS: Mice colonized with a stable population of E. faecium 64/3 or E. faecalis JH2-2 recipient strain and harbouring an enterococci-free human microbiota were obtained. Donor strain E. faecium HC-VI2 of clinical origin was administered orogastrically to these mice and transfers were evaluated over time in faecal samples.<br><br>RESULTS: Only intraspecies transfers were detected in the digestive tract (DT) of mice harbouring a human microbiota. E. faecium 64/3 transconjugants were detected at several sampling times over the 60 day experiment to levels up to 10(3) cfu/g of faeces, but they did not steadily colonize the DT.<br><br>CONCLUSIONS: Here, we show for the first time that transfer of the vanA gene cluster can occur between Enterococcus strains in the DT colonized with a human microbiota and in the absence of selective pressure. The colonization properties of other enterococci transconjugants and the influence of vancomycin intake should be further investigated since transfers in the DT of animals and humans might contribute to emergence and dissemination of new vancomycin-resistant bacteria.}, }
@article {pmid16186168, year = {2005}, author = {Zarrilli, R and Tripodi, MF and Di Popolo, A and Fortunato, R and Bagattini, M and Crispino, M and Florio, A and Triassi, M and Utili, R}, title = {Molecular epidemiology of high-level aminoglycoside-resistant enterococci isolated from patients in a university hospital in southern Italy.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {56}, number = {5}, pages = {827-835}, doi = {10.1093/jac/dki347}, pmid = {16186168}, issn = {0305-7453}, mesh = {Acetyltransferases/genetics ; Amikacin/pharmacology ; Aminoglycosides/*pharmacology ; Anti-Bacterial Agents/pharmacology ; Chromosomes, Bacterial/genetics/metabolism ; DNA, Bacterial/genetics/metabolism ; Drug Resistance, Bacterial/*genetics ; Electrophoresis, Gel, Pulsed-Field ; Enterococcus faecalis/classification/*drug effects/genetics/isolation &amp; purification ; Enterococcus faecium/classification/*drug effects/genetics/isolation &amp; purification ; Gene Transfer Techniques ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genotype ; Gentamicins/pharmacology ; Gram-Positive Bacterial Infections/*microbiology ; Hospitals, University ; Humans ; Italy ; Microbial Sensitivity Tests ; Molecular Epidemiology ; Phosphotransferases (Alcohol Group Acceptor)/genetics ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; }, abstract = {OBJECTIVES: We evaluated the genetic and molecular basis of high-level resistance to gentamicin and amikacin in 91 clinical isolates of Enterococcus faecalis and Enterococcus faecium in a university hospital in southern Italy from 1987 to 2003.<br><br>METHODS: Antibiotic susceptibility was evaluated by disc diffusion and microdilution methods. Genotyping was performed by PFGE and dendrogram analysis. Aminoglycoside resistance genes were analysed by multiplex PCR. Aminoglycoside resistance gene transfer was performed by filter mating.<br><br>RESULTS: In our strain collection, 44% of E. faecalis and 52% of E. faecium were high-level-resistant to gentamicin. Fifty-two PFGE profiles were identified for E. faecalis and 15 for E. faecium. Although the majority of PFGE patterns were single isolates, four patterns (two for E. faecalis and two for E. faecium) were isolated each in 8 and 4, and 6 and 4 different patients, respectively. The aac(6')-Ie-aph(2'')-Ia gene was responsible for high-level resistance to gentamicin and amikacin in E. faecalis and E. faecium; the aph(2'')-Id gene responsible for resistance to gentamicin was also isolated in E. faecium; the aph(3')-IIIa and ant(4')-Ia genes responsible for resistance to amikacin were also isolated in E. faecalis and E. faecium. High-level resistance to gentamicin, along with the aac(6')-Ie-aph(2'')-Ia gene, was transferred at a frequency of about 10(-5) to 10(-8) per recipient cell in 14 of 17 E. faecalis and 3 of 4 E. faecium different genotypes.<br><br>CONCLUSIONS: The spread of the aac(6')-Ie-aph(2'')-Ia gene was responsible for high-level resistance to gentamicin and amikacin among enterococci isolated from patients in our geographical area.}, }
@article {pmid16184014, year = {2005}, author = {Velkov, VV and Medvinsky, AB and Sokolov, MS and Marchenko, AI}, title = {Will transgenic plants adversely affect the environment?.}, journal = {Journal of biosciences}, volume = {30}, number = {4}, pages = {515-548}, pmid = {16184014}, issn = {0250-5991}, mesh = {Animals ; Bacillus thuringiensis ; Bees ; Biodiversity ; *Environment ; Food Chain ; Herbicides ; *Plants, Genetically Modified/toxicity ; Pollen ; }, abstract = {Transgenic insecticidal plants based on Bacillus thuringiensis (Bt) endotoxins, on proteinase inhibitors and on lectins, and transgenic herbicide tolerant plants are widely used in modern agriculture. The results of the studies on likelihood and non-likelihood of adverse effects of transgenic plants on the environment including: (i) effects on nontarget species; (ii) invasiveness; (iii) potential for transgenes to 'escape' into the environment by horizontal gene transfer; and (iv) adverse effects on soil biota are reviewed. In general, it seems that large-scale implementation of transgenic insecticidal and herbicide tolerant plants do not display considerable negative effects on the environments and, moreover, at least some transgenic plants can improve the corresponding environments and human health because their production considerably reduces the load of chemical insecticides and herbicides.}, }
@article {pmid16179994, year = {2005}, author = {Knoop, V and Groth-Malonek, M and Gebert, M and Eifler, K and Weyand, K}, title = {Transport of magnesium and other divalent cations: evolution of the 2-TM-GxN proteins in the MIT superfamily.}, journal = {Molecular genetics and genomics : MGG}, volume = {274}, number = {3}, pages = {205-216}, pmid = {16179994}, issn = {1617-4615}, mesh = {Amino Acid Motifs/genetics ; Base Sequence ; Biological Transport/genetics ; Cation Transport Proteins/*genetics ; Cluster Analysis ; Computational Biology/*methods ; *Evolution, Molecular ; Genes, Duplicate/genetics ; Magnesium/*metabolism ; Multigene Family/*genetics ; *Phylogeny ; Sequence Alignment ; }, abstract = {In bacteria, magnesium uptake is mainly mediated by the well-characterized CorA type of membrane proteins. In recent years, functional homologues have been characterized in the inner mitochondrial membrane of yeast and mammals (the MRS2/LPE10 type), in the plasma membrane of yeast (the ALR/MNR type) and, as an extended family of proteins, in the model plant Arabidopsis thaliana. Despite generally low sequence similarity, individual proteins can functionally complement each other over large phylogenetic distances. All these proteins are characterized by a universally conserved Gly-Met-Asn (GMN) motif at the end of the first of two conserved transmembrane domains near the C-terminus. Mutations of the GMN motif are known to abolish Mg(2+) transport, but the naturally occurring variants GVN and GIN may be associated with the transport of other divalent cations, such as zinc and cadmium, respectively. We refer to this whole class of proteins as the 2-TM-GxN type. The functional membrane channel is thought to be formed by oligomers containing four or five subunits. The wealth of sequence data now available allows us to explore the evolutionary diversification of the basic 2-TM-GxN model within the so-called metal ion transporter (MIT) superfamily. Here we report phylogenetic analyses on more than 360 homologous protein sequences derived from genomic sequences from representatives of all three domains of life. Independent gene duplications have occurred in fungi, plants and proteobacteria at different phylogenetic depths. Moreover, there is ample evidence for several instances of horizontal gene transfer of members of the 2-TM-GxN superfamily in Eubacteria and Archaea. Only single genes of the MRS2 type have been identified in vertebrate genomes. In contrast, 15 members are found in the model plant Arabidopsis thaliana, which appear to have arisen by at least four independent founder events before the diversification of flowering plants. Phylogenetic clade assignment seems to correlate with alterations in the highly conserved sequence around the GMN motif. This presumably forms an integral part of the pore surface, and changes in its structure may result in altered transport capacities for different divalent cations.}, }
@article {pmid16177341, year = {2005}, author = {Porcella, SF and Raffel, SJ and Anderson, DE and Gilk, SD and Bono, JL and Schrumpf, ME and Schwan, TG}, title = {Variable tick protein in two genomic groups of the relapsing fever spirochete Borrelia hermsii in western North America.}, journal = {Infection and immunity}, volume = {73}, number = {10}, pages = {6647-6658}, pmid = {16177341}, issn = {0019-9567}, mesh = {Amino Acid Sequence ; Animals ; Antigens, Bacterial/chemistry/*genetics ; Bacterial Outer Membrane Proteins/chemistry/classification/*genetics ; Base Sequence ; Borrelia/classification/*genetics/isolation &amp; purification ; Chromosome Mapping ; Conserved Sequence ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomics ; Humans ; Lipoproteins/chemistry/classification/genetics ; Molecular Sequence Data ; North America ; Ornithodoros/microbiology ; Phylogeny ; Plasmids ; Recombination, Genetic ; Relapsing Fever/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Borrelia hermsii is the primary cause of tick-borne relapsing fever in North America. When its tick vector, Ornithodoros hermsi, acquires these spirochetes from the blood of an infected mammal, the bacteria switch their outer surface from one of many bloodstream variable major proteins (Vmps) to a unique protein, Vtp (Vsp33). Vtp may be critical for successful tick transmission of B. hermsii; however, the gene encoding this protein has been described previously in only one isolate. Here we identified and sequenced the vtp gene in 31 isolates of B. hermsii collected over 40 years from localities throughout much of its known geographic distribution. Seven major Vtp types were found. Little or no sequence variation existed within types, but between them significant variation was observed, similar to the pattern of diversity described for the outer surface protein C (OspC) gene in Lyme disease spirochetes. The pattern of sequence relatedness among the Vtp types was incongruent in two branches compared to two genomic groups identified among the isolates by multilocus sequence typing of the 16S rRNA, flaB, gyrB, and glpQ genes. Therefore, both horizontal transfer and recombination within and between the two genomic groups were responsible for some of the variation observed in the vtp gene. O. hermsi ticks were capable of transmitting spirochetes in the newly identified genomic group. Therefore, given the longevity of the tick vector and persistent infection of spirochetes in ticks, these arthropods rather than mammals may be the likely host where the exchange of spirochetal DNA occurs.}, }
@article {pmid16176988, year = {2005}, author = {Beiko, RG and Harlow, TJ and Ragan, MA}, title = {Highways of gene sharing in prokaryotes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {102}, number = {40}, pages = {14332-14337}, pmid = {16176988}, issn = {0027-8424}, mesh = {Bacterial Proteins/genetics ; Base Sequence ; Bayes Theorem ; Computational Biology/methods ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; *Genetic Variation ; Genome, Archaeal/*genetics ; Genome, Bacterial/*genetics ; Models, Genetic ; *Phylogeny ; *Prokaryotic Cells ; Sequence Alignment ; }, abstract = {The extent to which lateral genetic transfer has shaped microbial genomes has major implications for the emergence of community structures. We have performed a rigorous phylogenetic analysis of >220,000 proteins from genomes of 144 prokaryotes to determine the contribution of gene sharing to current prokaryotic diversity, and to identify "highways" of sharing between lineages. The inferred relationships suggest a pattern of inheritance that is largely vertical, but with notable exceptions among closely related taxa, and among distantly related organisms that live in similar environments.}, }
@article {pmid16175684, year = {2005}, author = {Popova, LY and Kargatova, TV and Ganusova, EE and Lobova, TI and Boyandin, AN and Mogilnaya, OA and Pechurkin, NS}, title = {Population dynamics of transgenic strain Escherichia coli Z905/pPHL7 in freshwater and saline lake water microcosms with differing microbial community structures.}, journal = {Advances in space research : the official journal of the Committee on Space Research (COSPAR)}, volume = {35}, number = {9}, pages = {1573-1578}, doi = {10.1016/j.asr.2005.01.037}, pmid = {16175684}, issn = {0273-1177}, mesh = {Ampicillin Resistance/genetics ; *Ecosystem ; Environmental Microbiology ; Escherichia coli/*genetics/*growth &amp; development ; Fresh Water ; Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Micrococcus/genetics/growth &amp; development ; Organisms, Genetically Modified ; Plasmids/genetics ; *Population Dynamics ; Salts ; Water Microbiology ; }, abstract = {Populations of Escherichia coli Z905/pPHL7, a transgenic microorganism, were heterogenic in the expression of plasmid genes when adapting to the conditions of water microcosms of various mineralization levels and structure of microbial community. This TM has formed two subpopulations (ampicillin-resistant and ampicillin-sensitive) in every microcosm. Irrespective of mineralization level of a microcosm, when E. coli Z905/pPHL7 alone was introduced, the ampicillin-resistant subpopulation prevailed, while introduction of the TM together with indigenous bacteria led to the dominance of the ampicillin-sensitive subpopulation. A high level of lux gene expression maintained longer in the freshwater microcosms than in sterile saline lake water microcosms. A horizontal gene transfer has been revealed between the jointly introduced TM and Micrococcus sp. 9/pSH1 in microcosms with the Lake Shira sterile water.}, }
@article {pmid16174872, year = {2005}, author = {Troisfontaines, P and Cornelis, GR}, title = {Type III secretion: more systems than you think.}, journal = {Physiology (Bethesda, Md.)}, volume = {20}, number = {}, pages = {326-339}, doi = {10.1152/physiol.00011.2005}, pmid = {16174872}, issn = {1548-9213}, mesh = {Animals ; Bacterial Proteins/genetics/*metabolism ; Evolution, Molecular ; Gram-Negative Bacteria/*metabolism ; Humans ; Multigene Family ; Plants/microbiology ; }, abstract = {The type III secretion (T3S) pathway allows bacteria to inject effector proteins into the cytosol of target animal or plant cells. T3S systems evolved into seven families that were distributed among Gram-negative bacteria by horizontal gene transfer. There are probably a few hundred effectors interfering with control and signaling in eukaryotic cells and offering a wealth of new tools to cell biologists.}, }
@article {pmid16168051, year = {2005}, author = {Strappe, PM and Hampton, DW and Brown, D and Cachon-Gonzalez, B and Caldwell, M and Fawcett, JW and Lever, AM}, title = {Identification of unique reciprocal and non reciprocal cross packaging relationships between HIV-1, HIV-2 and SIV reveals an efficient SIV/HIV-2 lentiviral vector system with highly favourable features for in vivo testing and clinical usage.}, journal = {Retrovirology}, volume = {2}, number = {}, pages = {55}, pmid = {16168051}, issn = {1742-4690}, support = {G9805564/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Astrocytes/virology ; Cell Line ; Gene Transfer, Horizontal ; Genetic Vectors/*physiology ; HIV-1/genetics/*physiology ; HIV-2/genetics/*physiology ; Humans ; RNA, Viral/physiology ; Rats ; Simian Immunodeficiency Virus/genetics/*physiology ; Stem Cells/virology ; Transduction, Genetic ; *Virus Assembly ; }, abstract = {BACKGROUND: Lentiviral vectors have shown immense promise as vehicles for gene delivery to non-dividing cells particularly to cells of the central nervous system (CNS). Improvements in the biosafety of viral vectors are paramount as lentiviral vectors move into human clinical trials. This study investigates the packaging relationship between gene transfer (vector) and Gag-Pol expression constructs of HIV-1, HIV-2 and SIV. Cross-packaged vectors expressing GFP were assessed for RNA packaging, viral vector titre and their ability to transduce rat primary glial cell cultures and human neural stem cells.<br><br>RESULTS: HIV-1 Gag-Pol demonstrated the ability to cross package both HIV-2 and SIV gene transfer vectors. However both HIV-2 and SIV Gag-Pol showed a reduced ability to package HIV-1 vector RNA with no significant gene transfer to target cells. An unexpected packaging relationship was found to exist between HIV-2 and SIV with SIV Gag-Pol able to package HIV-2 vector RNA and transduce dividing SV2T cells and CNS cell cultures with an efficiency equivalent to the homologous HIV-1 vector however HIV-2 was unable to deliver SIV based vectors.<br><br>CONCLUSION: This new non-reciprocal cross packaging relationship between SIV and HIV-2 provides a novel way of significantly increasing bio-safety with a reduced sequence homology between the HIV-2 gene transfer vector and the SIV Gag-Pol construct thus ensuring that vector RNA packaging is unidirectional.}, }
@article {pmid16166664, year = {2005}, author = {Sikorski, J and Lalucat, J and Wackernagel, W}, title = {Genomovars 11 to 18 of Pseudomonas stutzeri, identified among isolates from soil and marine sediment.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {55}, number = {Pt 5}, pages = {1767-1770}, doi = {10.1099/ijs.0.63535-0}, pmid = {16166664}, issn = {1466-5026}, mesh = {Bacterial Typing Techniques ; DNA, Bacterial/analysis ; DNA, Ribosomal Spacer/analysis ; Genes, rRNA ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Pseudomonas stutzeri/*classification/*genetics/isolation &amp; purification/physiology ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Seawater/*microbiology ; *Soil Microbiology ; }, abstract = {Amongst 440 strains of Pseudomonas stutzeri isolated from soil and marine sediment for a population genetic study, eight strains were each presumed to represent a novel genomic group and were compared with each other and to reference strains of P. stutzeri genomovars 1 to 10 and other Pseudomonas species by DNA-DNA hybridization, 16S rRNA and internally transcribed 16S-23S rRNA spacer region (ITS1) sequences and basic physiological properties defining the species. While 16S rRNA and ITS1 gene sequences positioned the eight strains within the phylogenetic branch of P. stutzeri, the DNA-DNA hybridizations with reference strains of the 10 described genomovars and among the novel strains were generally below 70 %, which is the threshold for species and genomovar differentiation. Since the physiological properties studied in the eight strains fitted the profile of P. stutzeri, eight new genomovars of P. stutzeri, numbered 11 to 18, are proposed, with strains 28a50, 28a39, 28a22, 28a3, 4C29, 24a13, 24a75 and MT-1 being the reference strains. The highly transformable reference strain 28a3 of genomovar 14 had a localized 16S rRNA gene sequence tag characteristic of genomovar strains 2 and 3, suggesting a possible horizontal gene transfer event involving part of the 16S rRNA gene.}, }
@article {pmid16164565, year = {2005}, author = {Wang, J and Karnati, PK and Takacs, CM and Kowalski, JC and Derbyshire, KM}, title = {Chromosomal DNA transfer in Mycobacterium smegmatis is mechanistically different from classical Hfr chromosomal DNA transfer.}, journal = {Molecular microbiology}, volume = {58}, number = {1}, pages = {280-288}, doi = {10.1111/j.1365-2958.2005.04824.x}, pmid = {16164565}, issn = {0950-382X}, support = {R01 AI042308/AI/NIAID NIH HHS/United States ; AI42308/AI/NIAID NIH HHS/United States ; }, mesh = {Blotting, Southern ; Chromosome Mapping ; *Chromosomes, Bacterial ; Conjugation, Genetic ; DNA, Bacterial/analysis/*metabolism ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Linkage ; Mycobacterium smegmatis/*genetics ; }, abstract = {Classical conjugal DNA transfer of chromosomal DNA in bacteria requires the presence of a cis-acting site, oriT, in the chromosome. Acquisition of an oriT occurs if a conjugative plasmid integrates into the chromosome to form an Hfr donor strain, which can transfer extensive regions of chromosomal DNA. Because oriT sequences are unique, and because transfer occurs in a 5' to 3' direction, the frequency with which a particular gene is inherited by the recipient depends on the gene's location: those closest to the 3' side of oriT are transferred most efficiently. In addition, as the entire chromosome must be transferred to regenerate oriT, Hfr transconjugants never become donors. Here we describe novel aspects of a chromosomal DNA transfer system in Mycobacterium smegmatis. We demonstrate that there are multiple transfer initiations from a donor chromosome and, as a result, the inheritance of any gene is location-independent. Transfer is not contiguous; instead, multiple non-linked segments of DNA can be inherited in a recipient. However, we show that, with appropriate selection, segments of DNA at least 266 kb in length can be transferred. In further contrast to Hfr transfer, transconjugants can become donors, suggesting that the recipient chromosome contains multiple cis-acting sequences required for transfer, but lacks the trans-acting transfer functions. We exploit these observations to map a donor-determining locus in the M. smegmatis chromosome using genetic linkage analysis. Together, these studies further underline the unique nature of the M. smegmatis chromosomal transfer system.}, }
@article {pmid16162862, year = {2006}, author = {Gophna, U and Thompson, JR and Boucher, Y and Doolittle, WF}, title = {Complex histories of genes encoding 3-hydroxy-3-methylglutaryl-CoenzymeA reductase.}, journal = {Molecular biology and evolution}, volume = {23}, number = {1}, pages = {168-178}, doi = {10.1093/molbev/msj019}, pmid = {16162862}, issn = {0737-4038}, mesh = {Bacteria/*genetics ; Base Sequence ; DNA Primers ; *Evolution, Molecular ; Gene Order/genetics ; Gene Transfer, Horizontal/*genetics ; Hydroxymethylglutaryl CoA Reductases/*genetics ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; *Selection, Genetic ; Sequence Analysis, DNA ; Signal Transduction/*genetics ; }, abstract = {The mevalonate pathway for the synthesis of isoprenoids can be found in organisms from all domains of life. It has been previously demonstrated that the first gene specific to that pathway, which encodes the enzyme 3-hydroxy-3-methylglutaryl-CoenzymeA reductase (HMGR), has been transferred between domains by lateral gene transfer on several occasions. Here we look within the domain Bacteria at lateral acquisition of HMGR, whether as a single gene or as part of a mevalonate pathway cluster. We observe a complex history of multiple transfer events probably reflecting the fact that HMGR could be beneficial in a variety of physiological and genetic contexts. We demonstrate that even in Vibrio species, where HMGR is not clustered with other genes to form an operon or a metabolic cluster, it is under strong purifying selection.}, }
@article {pmid16162288, year = {2005}, author = {Liang, P and Nair, JR and Song, L and McGuire, JJ and Dolnick, BJ}, title = {Comparative genomic analysis reveals a novel mitochondrial isoform of human rTS protein and unusual phylogenetic distribution of the rTS gene.}, journal = {BMC genomics}, volume = {6}, number = {}, pages = {125}, pmid = {16162288}, issn = {1471-2164}, support = {CA101515/CA/NCI NIH HHS/United States ; EB002116/EB/NIBIB NIH HHS/United States ; P30 CA016056/CA/NCI NIH HHS/United States ; CA16056/CA/NCI NIH HHS/United States ; R01 EB002116/EB/NIBIB NIH HHS/United States ; R03 CA101515/CA/NCI NIH HHS/United States ; CA43500/CA/NCI NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Blotting, Western ; Cell Line ; Codon ; Computational Biology/*methods ; Genome ; Genomics/*methods ; Humans ; Mitochondria/*metabolism ; Models, Biological ; Molecular Sequence Data ; Phylogeny ; Protein Isoforms ; Protein Structure, Tertiary ; Subcellular Fractions ; Thymidylate Synthase/*genetics/metabolism ; }, abstract = {BACKGROUND: The rTS gene (ENOSF1), first identified in Homo sapiens as a gene complementary to the thymidylate synthase (TYMS) mRNA, is known to encode two protein isoforms, rTSalpha and rTSbeta. The rTSbeta isoform appears to be an enzyme responsible for the synthesis of signaling molecules involved in the down-regulation of thymidylate synthase, but the exact cellular functions of rTS genes are largely unknown.<br><br>RESULTS: Through comparative genomic sequence analysis, we predicted the existence of a novel protein isoform, rTS, which has a 27 residue longer N-terminus by virtue of utilizing an alternative start codon located upstream of the start codon in rTSbeta. We observed that a similar extended N-terminus could be predicted in all rTS genes for which genomic sequences are available and the extended regions are conserved from bacteria to human. Therefore, we reasoned that the protein with the extended N-terminus might represent an ancestral form of the rTS protein. Sequence analysis strongly predicts a mitochondrial signal sequence in the extended N-terminal of human rTSgamma, which is absent in rTSbeta. We confirmed the existence of rTS in human mitochondria experimentally by demonstrating the presence of both rTSgamma and rTSbeta proteins in mitochondria isolated by subcellular fractionation. In addition, our comprehensive analysis of rTS orthologous sequences reveals an unusual phylogenetic distribution of this gene, which suggests the occurrence of one or more horizontal gene transfer events.<br><br>CONCLUSION: The presence of two rTS isoforms in mitochondria suggests that the rTS signaling pathway may be active within mitochondria. Our report also presents an example of identifying novel protein isoforms and for improving gene annotation through comparative genomic analysis.}, }
@article {pmid16162145, year = {2005}, author = {Mesrati, LA and Karray, MD and Tounsi, S and Jaoua, S}, title = {Construction of a new high-copy number shuttle vector of Bacillus thuringiensis.}, journal = {Letters in applied microbiology}, volume = {41}, number = {4}, pages = {361-366}, doi = {10.1111/j.1472-765X.2005.01733.x}, pmid = {16162145}, issn = {0266-8254}, mesh = {Animals ; Bacillus thuringiensis/*genetics/growth &amp; development/metabolism ; Bacterial Proteins/genetics/pharmacology ; Escherichia coli/genetics ; *Gene Dosage ; Gene Transfer, Horizontal ; Genetic Vectors/*genetics ; Lepidoptera/drug effects ; Plasmids/*genetics ; Transformation, Bacterial ; }, abstract = {AIMS: Construction and characterization of a new cloning shuttle vector for gene transfer and expression in Bacillus thuringiensis.<br><br>METHODS AND RESULTS: A novel short and high-copy number shuttle vector called pHBLBIV, was constructed for gene transfer and expression in Bacillus thuringiensis. A 1.6-kbp replicon of a relatively high-copy number endogenous plasmid of a selected B. thuringiensis strain was ligated to Escherichia coli pUC18 replicon containing the ampicillin and the erythromycin resistance genes used for the selection of respectively E. coli and B. thuringiensis transformants. The constructed vector was shown to have a high copy number compared with the conventional B. thuringiensis vectors, and used successfully for the transfer of vegetative insecticidal protein-encoding gene (vip) in between B. thuringiensis strains.<br><br>CONCLUSIONS: A new shuttle vector of B. thuringiensis-E. coli named pHBLBIV was constructed. It was characterized by its high copy number, small size and segregational stability. This vector was successfully used for vip gene cloning and transfer in B. thuringiensis.<br><br>A novel shuttle vector has been constructed, which has demonstrated potential for the cloning and expression of genes in B. thuringiensis.}, }
@article {pmid16162143, year = {2005}, author = {Marineo, S and Lecat, E and Cusimano, MG and Giardina, A and Di Caro, V and Puglia, AM}, title = {Identification of SCP2165, a new SCP2-derived plasmid of Streptomyces coelicolor A3(2).}, journal = {Letters in applied microbiology}, volume = {41}, number = {4}, pages = {350-354}, doi = {10.1111/j.1472-765X.2005.01739.x}, pmid = {16162143}, issn = {0266-8254}, mesh = {*Conjugation, Genetic ; Crosses, Genetic ; Electrophoresis, Gel, Pulsed-Field ; Gene Transfer, Horizontal ; *Plasmids ; Recombination, Genetic ; Streptomyces coelicolor/*genetics/physiology ; }, abstract = {AIMS: Characterization of SCP2165, a plasmid identified in the Gram-positive bacterium Streptomyces coelicolor A3(2).<br><br>METHODS AND RESULTS: Pulsed-field gel electrophoresis (PFGE) of mycelia of a S. coelicolor strain embedded in low melting agarose revealed the presence of a plasmid. Restriction enzyme mapping and sequence analysis of a 2.1 kb fragment revealed that this plasmid could be SCP2. SCP2 and its spontaneous derivative SCP2* are self-transmissible plasmids and have chromosome mobilizing ability (c.m.a.). SCP2* has a c. 1000-fold increased c.m.a. compared with SCP2. Interestingly the plasmid, named SCP2165, shows a c.m.a. from 5x10(-2) to 1x10(-1) which is 50-100-fold higher than that described for crosses involving SCP2*.<br><br>CONCLUSIONS: SCP2165 is a SCP2 derivative plasmid with the highest c.m.a. so far described for SCP2 derivative plasmids. PFGE, under conditions we used, seems to be a fast way to identify large circular plasmids in Streptomyces strains.<br><br>Further knowledge of the SCP2 family may allow the construction of improved SCP2-derived cloning vectors. SCP2165 could be a potential tool for conjugational transfer of gene clusters between different Streptomyces species.}, }
@article {pmid16161978, year = {2005}, author = {Mukherjee, S and Bhadra, B and Chakraborty, R and Gurung, A and Some, S and Chakraborty, R}, title = {Unregulated use of antibiotics in Siliguri city vis-a-vis occurrence of MAR bacteria in community waste water and river Mahananda, and their potential for resistance gene transfer.}, journal = {Journal of environmental biology}, volume = {26}, number = {2}, pages = {229-238}, pmid = {16161978}, issn = {0254-8704}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/drug effects/*isolation &amp; purification ; Cities ; Colony Count, Microbial ; Data Collection ; *Drug Resistance, Multiple, Bacterial ; *Gene Transfer, Horizontal ; India ; Plasmids ; Rivers/microbiology ; Sewage/microbiology ; *Water Microbiology ; }, abstract = {The unregulated use of antibiotics, including therapeutic and prophylactic prescribing, in the fastest growing city of West Bengal, Siliguri, was studied indirectly from a random survey conducted on retail medicine sellers at their counters. Ciprofloxacin, ampicillin, norfioxacin and amoxycillin were the highest retailed antibiotics and 58% of the city pharmacies sold antibiotics even without prescriptions. To understand the influence of the extent of antibiotic use by the community on the collective bacterial flora in the aquatic environment, we have determined the fraction(s) of Standard Plate Count (SPC) bacteria resistant to different antibiotics and multiple antibiotic resistance (MAR) profile of resistant SPC isolates from two municipal open drains and Mahananda river water samples of Siliguri. Within the MAR groups of Drain I and Drain II samples, 37.44% and 77.43% respectively were resistant to all seven antibiotics (ampicillin, chloramphenicol, ciprofloxacin, kanamycin, netilmicin, streptomycin and tetracycline) used in the study. Twenty Gram-negative SPC MAR isolates were examined for the presence of plasmids. Antibiotic resistance was shown to be associated with a carriage of a 47 kb (D1QN - 9), 48 kb (D2QN - 14) and 49.4 and 3.6 kb (MR - 1) plasmids, which were transmissible to the Escherichia coli DH5alpha recipient. The rapid spread of antibiotic resistance genes in bacterial population as a consequence of indiscriminate use of antibiotics, which can be partly attributed to plasmid-mediated horizontal transfer was discussed.}, }
@article {pmid16159784, year = {2005}, author = {Froehlich, B and Parkhill, J and Sanders, M and Quail, MA and Scott, JR}, title = {The pCoo plasmid of enterotoxigenic Escherichia coli is a mosaic cointegrate.}, journal = {Journal of bacteriology}, volume = {187}, number = {18}, pages = {6509-6516}, pmid = {16159784}, issn = {0021-9193}, support = {/WT_/Wellcome Trust/United Kingdom ; R01 AI024870/AI/NIAID NIH HHS/United States ; AI24870/AI/NIAID NIH HHS/United States ; }, mesh = {DNA, Bacterial/analysis ; Enterotoxins/genetics/*metabolism ; Escherichia coli/chemistry/*genetics ; Fimbriae Proteins/*genetics ; Gene Transfer, Horizontal ; Plasmids/*genetics ; Recombination, Genetic ; Replication Origin ; Replicon ; }, abstract = {CS1 is the prototype of a class of pili of enterotoxigenic Escherichia coli (ETEC) associated with diarrheal disease in humans. The genes encoding this pilus are carried on a large plasmid, pCoo. We report the sequence of the complete 98,396-bp plasmid. Like many other virulence plasmids, pCoo is a mosaic consisting of regions derived from multiple sources. Complete and fragmented insertion sequences (IS) make up 24% of the total DNA and are scattered throughout the plasmid. The pCoo DNA between these IS elements has a wide range of G+C content (35 to 57%), suggesting that these regions have different ancestries. We find that the pCoo plasmid is a cointegrate of two functional replicons, related to R64 and R100, which are joined at a 1,953-bp direct repeat of IS100. Recombination between these repeats in the cointegrate generates the two smaller replicons which coexist with the cointegrate in the culture. Both of the smaller replicons have plasmid stability genes as well as genes that may be important in pathogenesis. Examination by PCR of 17 other unrelated CS1 ETEC strains with a variety of serotypes demonstrated that all contained at least parts of both replicons of pCoo and that strains of the O6 genotype appear to contain a cointegrate very similar to pCoo. The results suggest that this family of CS1-encoding plasmids is evolving rapidly.}, }
@article {pmid16156724, year = {2005}, author = {Zeidner, G and Bielawski, JP and Shmoish, M and Scanlan, DJ and Sabehi, G and Béjà, O}, title = {Potential photosynthesis gene recombination between Prochlorococcus and Synechococcus via viral intermediates.}, journal = {Environmental microbiology}, volume = {7}, number = {10}, pages = {1505-1513}, doi = {10.1111/j.1462-2920.2005.00833.x}, pmid = {16156724}, issn = {1462-2912}, mesh = {Bacterial Proteins/genetics ; Bacteriophages/genetics/physiology ; Evolution, Molecular ; Photosynthesis/genetics ; Photosystem II Protein Complex/*genetics ; Phylogeny ; Prochlorococcus/genetics/metabolism/*virology ; Prophages/genetics ; *Recombination, Genetic ; Seawater/virology ; Synechococcus/genetics/metabolism/*virology ; }, abstract = {Genes (psbA and psbD) encoding for photosynthetically important proteins were recently found in a number of cultured cyanophage genomes. This phenomenon may be a beneficial trait to the viruses or their photosynthetic cyanobacterial hosts, or may represent an untapped pool of genes involved in the formation of the photosynthetic apparatus that are prone to lateral gene transfer. Here we show analyses of psbA genes from uncultured environmental viruses and prophage populations. We observe a statistically significant separation between viral genes and their potential Synechococcus hosts' genes, and statistical analyses under models of codon evolution indicate that the psbA genes of viruses are evolving under levels of purifying selection that are virtually indistinguishable from their hosts. Furthermore, our data also indicate the possible exchange and reshuffling of psbA genes between Synechococcus and Prochlorococcus via phage intermediates. Overall, these observations raise the possibility that marine viruses serve as a potential genetic pool in shaping the evolution of cyanobacterial photosynthesis.}, }
@article {pmid16153170, year = {2005}, author = {Larrainzar, E and O'Gara, F and Morrissey, JP}, title = {Applications of autofluorescent proteins for in situ studies in microbial ecology.}, journal = {Annual review of microbiology}, volume = {59}, number = {}, pages = {257-277}, doi = {10.1146/annurev.micro.59.030804.121350}, pmid = {16153170}, issn = {0066-4227}, mesh = {*Bacteria/genetics/growth &amp; development/metabolism ; Biofilms/*growth &amp; development ; Biosensing Techniques/*methods ; *Ecosystem ; Luminescent Proteins/genetics/*metabolism ; Plants/*microbiology ; }, abstract = {When autofluorescent proteins (AFPs), such as green fluorescent protein (GFP) and Discosoma striata red fluorescent protein (DsRed), are excited with light of a specific wavelength, they emit light of a longer wavelength, without the further addition of substrates. A range of AFPs have been identified and cloned from marine organisms, and mutagenesis techniques have been employed to develop improved variant AFPs for applications in biological research. In recent years, AFP technology has become an important tool for microbiologists and microbial ecologists studying processes such as microbe-plant interactions, biosensors, biofilm formation, and horizontal gene transfer. The ability to use AFPs with differing fluorescent spectra within a single cell has allowed simultaneous monitoring of several aspects of microbial physiology and gene expression in situ in real time. This provides a tremendous insight into microbial function and behavior in natural environments. Furthermore, the integration of AFP reporters with other markers and technologies is facilitating a systems approach to research in microbial ecology.}, }
@article {pmid16153168, year = {2005}, author = {Snel, B and Huynen, MA and Dutilh, BE}, title = {Genome trees and the nature of genome evolution.}, journal = {Annual review of microbiology}, volume = {59}, number = {}, pages = {191-209}, doi = {10.1146/annurev.micro.59.030804.121233}, pmid = {16153168}, issn = {0066-4227}, mesh = {*Evolution, Molecular ; Gene Order ; Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; *Genome, Archaeal ; *Genome, Bacterial ; Genomics/*methods ; *Phylogeny ; }, abstract = {Genome trees are a means to capture the overwhelming amount of phylogenetic information that is present in genomes. Different formalisms have been introduced to reconstruct genome trees on the basis of various aspects of the genome. On the basis of these aspects, we separate genome trees into five classes: (a) alignment-free trees based on statistic properties of the genome, (b) gene content trees based on the presence and absence of genes, (c) trees based on chromosomal gene order, (d) trees based on average sequence similarity, and (e) phylogenomics-based genome trees. Despite their recent development, genome tree methods have already had some impact on the phylogenetic classification of bacterial species. However, their main impact so far has been on our understanding of the nature of genome evolution and the role of horizontal gene transfer therein. An ideal genome tree method should be capable of using all gene families, including those containing paralogs, in a phylogenomics framework capitalizing on existing methods in conventional phylogenetic reconstruction. We expect such sophisticated methods to help us resolve the branching order between the main bacterial phyla.}, }
@article {pmid16151207, year = {2005}, author = {Pollmann, K and Raff, J and Schnorpfeil, M and Radeva, G and Selenska-Pobell, S}, title = {Novel surface layer protein genes in Bacillus sphaericus associated with unusual insertion elements.}, journal = {Microbiology (Reading, England)}, volume = {151}, number = {Pt 9}, pages = {2961-2973}, doi = {10.1099/mic.0.28201-0}, pmid = {16151207}, issn = {1350-0872}, mesh = {Bacillus/*genetics/growth &amp; development/*metabolism ; Bacterial Proteins/chemistry/genetics/*metabolism ; Binding Sites ; DNA Transposable Elements/*physiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Membrane Glycoproteins/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Transposases/genetics ; }, abstract = {The surface layer (S-layer) protein genes of the uranium mining waste pile isolate Bacillus sphaericus JG-A12 and of its relative B. sphaericus NCTC 9602 were analysed. The almost identical N-termini of the two S-layer proteins possess a unique structure, comprising three N-terminal S-layer homologous (SLH) domains. The central parts of the proteins share a high homology and are related to the S-layer proteins of B. sphaericus CCM 2177 and P-1. In contrast, the C-terminal parts of the S-layer proteins of JG-A12 and NCTC 9602 differ significantly between each other. Surprisingly, the C-terminal part of the S-layer protein of JG-A12 shares a high identity with that of the S-layer protein of B. sphaericus CCM 2177. In both JG-A12 and NCTC 9602 the chromosomal S-layer protein genes are followed by a newly identified putative insertion element comprising three ORFs, which encode a putative transposase, a putative integrase/recombinase and a putative protein containing a DNA binding helix-turn-helix motif, and the S-layer-protein-like gene copies sllA (9602) or sllB (JG-A12). Interestingly, both B. sphaericus strains studied were found to contain an additional, plasmid-located and silent S-layer protein gene with the same sequence as sllA and sllB. The primary structures of the corresponding putative proteins are almost identical in both strains. The N-terminal and central parts of these S-layer proteins share a high identity with those of the chromosomally encoded functional S-layer proteins. Their C-terminal parts, however, differ significantly. These results strongly suggest that the S-layer protein genes have evolved via horizontal transfer of genetic information followed by DNA rearrangements mediated by mobile elements.}, }
@article {pmid16151189, year = {2006}, author = {Paz, A and Kirzhner, V and Nevo, E and Korol, A}, title = {Coevolution of DNA-interacting proteins and genome "dialect".}, journal = {Molecular biology and evolution}, volume = {23}, number = {1}, pages = {56-64}, doi = {10.1093/molbev/msj007}, pmid = {16151189}, issn = {0737-4038}, mesh = {DNA Repair/genetics ; DNA Restriction Enzymes/genetics ; *Evolution, Molecular ; Genome, Bacterial/*genetics ; Proteobacteria/*genetics ; RNA, Ribosomal, 16S/genetics ; Repetitive Sequences, Nucleic Acid/*genetics ; Species Specificity ; }, abstract = {Several species-specific characteristics of genome organization that are superimposed on its coding aspects were proposed earlier, including genome signature (GS), genome accent, and compositional spectrum (CS). These notions could be considered as representatives of genome dialect (GD). We measured within the Proteobacteria some GD representatives, the relative abundance of dinucleotides or GS, the profiles of occurrence of 10 nucleotide words (CS), and the profiles of occurrence of 20 nucleotide words, using a degenerate two-letter alphabet (purine-pyrimidine compositional spectra [PPCS]). Here, we show that the evolutionary distances between DNA repair and recombination orthologous enzymes (especially those of the nucleotide excision repair system) are highly correlated with PPCS and GS distances. Orthologous proteins involved in structural or metabolic processes (control group) have significantly lower correlations of their evolutionary distances with the PPCS and GS distances. We hypothesize that the high correlation of the evolutionary distances of the DNA repair orthologous enzymes with their GD is a result of the coevolution of the DNA repair enzymes' structures and GDs. Species GDs could be substantially influenced by the function of DNA polymerase I (the bacterial major DNA repair polymerase). This might cause the correlation of species GDs differentiation with evolutionary changes of species DNA polymerase I. Simultaneously, the structures of DNA repair-recombination enzymes might be evolutionarily sensitive and responsive to changes in the structure of their substrate-the DNA (including those that are represented by GD differentiation). We further discuss the rationale and mechanisms of the hypothesized coevolution. We suggest that stress might be an important cause of changes in the repair-recombination genes and the GD and the trigger of the aforementioned coevolution process. Other triggers might be massive horizontal gene transfer and ecological selection.}, }
@article {pmid16151187, year = {2006}, author = {Fitzpatrick, DA and Creevey, CJ and McInerney, JO}, title = {Genome phylogenies indicate a meaningful alpha-proteobacterial phylogeny and support a grouping of the mitochondria with the Rickettsiales.}, journal = {Molecular biology and evolution}, volume = {23}, number = {1}, pages = {74-85}, doi = {10.1093/molbev/msj009}, pmid = {16151187}, issn = {0737-4038}, mesh = {Alphaproteobacteria/*genetics ; Base Sequence ; Bayes Theorem ; Computational Biology ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/*genetics ; Mitochondria/*genetics ; Models, Genetic ; *Phylogeny ; Sequence Alignment ; Species Specificity ; }, abstract = {Placement of the mitochondrial branch on the tree of life has been problematic. Sparse sampling, the uncertainty of how lateral gene transfer might overwrite phylogenetic signals, and the uncertainty of phylogenetic inference have all contributed to the issue. Here we address this issue using a supertree approach and completed genomic sequences. We first determine that a sensible alpha-proteobacterial phylogenetic tree exists and that it can confidently be inferred using orthologous genes. We show that congruence across these orthologous gene trees is significantly better than might be expected by random chance. There is some evidence of horizontal gene transfer within the alpha-proteobacteria, but it appears to be restricted to a minority of genes (approximately 23%) most of whom (approximately 74%) can be categorized as operational. This means that placement of the mitochondrion should not be excessively hampered by interspecies gene transfer. We then show that there is a consistently strong signal for placement of the mitochondrion on this tree and that this placement is relatively insensitive to methodological approach or data set. A concatenated alignment was created consisting of 15 mitochondrion-encoded proteins that are unlikely to have undergone any lateral gene transfer in the timeline under consideration. This alignment infers that the sister group of the mitochondria, for the taxa that have been sampled, is the order Rickettsiales.}, }
@article {pmid16151127, year = {2005}, author = {Bergmann, DJ and Hooper, AB and Klotz, MG}, title = {Structure and sequence conservation of hao cluster genes of autotrophic ammonia-oxidizing bacteria: evidence for their evolutionary history.}, journal = {Applied and environmental microbiology}, volume = {71}, number = {9}, pages = {5371-5382}, pmid = {16151127}, issn = {0099-2240}, mesh = {Amino Acid Sequence ; Ammonia/*metabolism ; Betaproteobacteria/enzymology/genetics ; Chromatiaceae/enzymology/genetics ; Conserved Sequence ; *Evolution, Molecular ; Molecular Sequence Data ; *Multigene Family ; Nitrosomonas europaea/enzymology/genetics ; Oxidation-Reduction ; Oxidoreductases/chemistry/*genetics/metabolism ; Phylogeny ; Proteobacteria/*enzymology/genetics ; Sequence Analysis, DNA ; }, abstract = {Comparison of the organization and sequence of the hao (hydroxylamine oxidoreductase) gene clusters from the gammaproteobacterial autotrophic ammonia-oxidizing bacterium (aAOB) Nitrosococcus oceani and the betaproteobacterial aAOB Nitrosospira multiformis and Nitrosomonas europaea revealed a highly conserved gene cluster encoding the following proteins: hao, hydroxylamine oxidoreductase; orf2, a putative protein; cycA, cytochrome c(554); and cycB, cytochrome c(m)(552). The deduced protein sequences of HAO, c(554), and c(m)(552) were highly similar in all aAOB despite their differences in species evolution and codon usage. Phylogenetic inference revealed a broad family of multi-c-heme proteins, including HAO, the pentaheme nitrite reductase, and tetrathionate reductase. The c-hemes of this group also have a nearly identical geometry of heme orientation, which has remained conserved during divergent evolution of function. High sequence similarity is also seen within a protein family, including cytochromes c(m)(552), NrfH/B, and NapC/NirT. It is proposed that the hydroxylamine oxidation pathway evolved from a nitrite reduction pathway involved in anaerobic respiration (denitrification) during the radiation of the Proteobacteria. Conservation of the hydroxylamine oxidation module was maintained by functional pressure, and the module expanded into two separate narrow taxa after a lateral gene transfer event between gamma- and betaproteobacterial ancestors of extant aAOB. HAO-encoding genes were also found in six non-aAOB, either singly or tandemly arranged with an orf2 gene, whereas a c(554) gene was lacking. The conservation of the hao gene cluster in general and the uniqueness of the c(554) gene in particular make it a suitable target for the design of primers and probes useful for molecular ecology approaches to detect aAOB.}, }
@article {pmid16151119, year = {2005}, author = {De Gelder, L and Vandecasteele, FP and Brown, CJ and Forney, LJ and Top, EM}, title = {Plasmid donor affects host range of promiscuous IncP-1beta plasmid pB10 in an activated-sludge microbial community.}, journal = {Applied and environmental microbiology}, volume = {71}, number = {9}, pages = {5309-5317}, pmid = {16151119}, issn = {0099-2240}, support = {P20 RR016448/RR/NCRR NIH HHS/United States ; P20 RR016454/RR/NCRR NIH HHS/United States ; P20 RR 16448/RR/NCRR NIH HHS/United States ; P20 RR 16454/RR/NCRR NIH HHS/United States ; }, mesh = {*Conjugation, Genetic ; DNA, Bacterial/analysis ; Drug Resistance, Multiple, Bacterial/*genetics ; *Ecosystem ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; Plasmids/*genetics ; Proteobacteria/*genetics/growth &amp; development ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/*microbiology ; }, abstract = {Horizontal transfer of multiresistance plasmids in the environment contributes to the growing problem of drug-resistant pathogens. Even though the plasmid host cell is the primary environment in which the plasmid functions, possible effects of the plasmid donor on the range of bacteria to which plasmids spread in microbial communities have not been investigated. In this study we show that the host range of a broad-host-range plasmid within an activated-sludge microbial community was influenced by the donor strain and that various mating conditions and isolation strategies increased the diversity of transconjugants detected. To detect transconjugants, the plasmid pB10 was marked with lacp-rfp, while rfp expression was repressed in the donors by chromosomal lacI(q). The phylogeny of 306 transconjugants obtained was determined by analysis of partial 16S rRNA gene sequences. The transconjugants belonged to 15 genera of the alpha- and gamma-Proteobacteria. The phylogenetic diversity of transconjugants obtained in separate matings with donors Pseudomonas putida SM1443, Ralstonia eutropha JMP228, and Sinorhizobium meliloti RM1021 was significantly different. For example, the transconjugants obtained after matings in sludge with S. meliloti RM1021 included eight genera that were not represented among the transconjugants obtained with the other two donors. Our results indicate that the spectrum of hosts to which a promiscuous plasmid transfers in a microbial community can be strongly influenced by the donor from which it transfers.}, }
@article {pmid16151091, year = {2005}, author = {Suzuki, K and Iijima, K and Ozaki, K and Yamashita, H}, title = {Isolation of a hop-sensitive variant of Lactobacillus lindneri and identification of genetic markers for beer spoilage ability of lactic acid bacteria.}, journal = {Applied and environmental microbiology}, volume = {71}, number = {9}, pages = {5089-5097}, pmid = {16151091}, issn = {0099-2240}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics/metabolism ; Beer/*microbiology ; Drug Resistance, Bacterial/genetics ; Food Contamination ; Food Microbiology ; *Genetic Markers ; *Humulus ; Lactobacillus/*classification/*drug effects/genetics/isolation &amp; purification ; Microbial Sensitivity Tests ; Open Reading Frames/genetics ; Sequence Analysis, DNA ; }, abstract = {We have isolated a hop-sensitive variant of the beer spoilage bacterium Lactobacillus lindneri DSM 20692. The variant lost a plasmid carrying two contiguous open reading frames (ORF s) designated horB(L) and horC(L) that encode a putative regulator and multidrug transporter presumably belonging to the resistance-nodulation-cell division superfamily. The loss of hop resistance ability occurred with the loss of resistance to other drugs, including ethidium bromide, novobiocin, and cetyltrimethylammonium bromide. PCR and Southern blot analysis using 51 beer spoilage strains of various species of lactic acid bacteria (LAB) revealed that 49 strains possessed homologs of horB and horC. No false-positive results have been observed for nonspoilage LAB or frequently encountered brewery isolates. These features are superior to those of horA and ORF 5, previously reported genetic markers for determining the beer spoilage ability of LAB. It was further shown that the combined use of horB/horC and horA is able to detect all 51 beer spoilage strains examined in this study. Furthermore sequence comparison of horB and horC homologs identified in four different beer spoilage species indicates these homologs are 96.6 to 99.5% identical, which is not typical of distinct species. The wide and exclusive distribution of horB and horC homologs among beer spoilage LAB and their sequence identities suggest that the hop resistance ability of beer spoilage LAB has been acquired through horizontal gene transfer. These insights provide a foundation for applying trans-species genetic markers to differentiating beer spoilage LAB including previously unencountered species.}, }
@article {pmid16145755, year = {2005}, author = {Smets, BF and Barkay, T}, title = {Horizontal gene transfer: perspectives at a crossroads of scientific disciplines.}, journal = {Nature reviews. Microbiology}, volume = {3}, number = {9}, pages = {675-678}, doi = {10.1038/nrmicro1253}, pmid = {16145755}, issn = {1740-1526}, mesh = {Archaea/genetics ; Bacteria/genetics ; Gene Transfer Techniques/*trends ; Models, Genetic ; }, }
@article {pmid16145178, year = {2005}, author = {Espedido, B and Iredell, J and Thomas, L and Zelynski, A}, title = {Wide dissemination of a carbapenemase plasmid among gram-negative bacteria: implications of the variable phenotype.}, journal = {Journal of clinical microbiology}, volume = {43}, number = {9}, pages = {4918-4919}, pmid = {16145178}, issn = {0095-1137}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics ; *Conjugation, Genetic ; *Drug Resistance, Bacterial ; *Gene Transfer, Horizontal ; Gram-Negative Bacteria/drug effects/enzymology/*genetics ; Humans ; Microbial Sensitivity Tests ; Phenotype ; Plasmids/*genetics ; beta-Lactamases/*genetics ; }, }
@article {pmid16145160, year = {2005}, author = {Naiemi, NA and Duim, B and Savelkoul, PH and Spanjaard, L and de Jonge, E and Bart, A and Vandenbroucke-Grauls, CM and de Jong, MD}, title = {Widespread transfer of resistance genes between bacterial species in an intensive care unit: implications for hospital epidemiology.}, journal = {Journal of clinical microbiology}, volume = {43}, number = {9}, pages = {4862-4864}, pmid = {16145160}, issn = {0095-1137}, mesh = {Acinetobacter Infections/epidemiology/microbiology ; Acinetobacter baumannii/*drug effects/genetics ; Aminoglycosides/pharmacology ; Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; Cross Infection/epidemiology/microbiology ; Disease Outbreaks ; Drug Resistance, Multiple, Bacterial/*genetics ; Enterobacter cloacae/*drug effects/genetics ; Enterobacteriaceae Infections/epidemiology/microbiology ; *Gene Transfer, Horizontal ; Hospitals ; Humans ; *Intensive Care Units ; Microbial Sensitivity Tests ; Plasmids ; beta-Lactamases/genetics/metabolism ; }, abstract = {A transferable plasmid encoding SHV-12 extended-spectrum beta-lactamase, TEM-116, and aminoglycoside resistance was responsible for two sequential clonal outbreaks of Enterobacter cloacae and Acinetobacter baumannii bacteria. A similar plasmid was present among isolates of four different bacterial species. Recognition of plasmid transfer is crucial for control of outbreaks of multidrug-resistant nosocomial pathogens.}, }
@article {pmid16145137, year = {2005}, author = {Kozitskaya, S and Olson, ME and Fey, PD and Witte, W and Ohlsen, K and Ziebuhr, W}, title = {Clonal analysis of Staphylococcus epidermidis isolates carrying or lacking biofilm-mediating genes by multilocus sequence typing.}, journal = {Journal of clinical microbiology}, volume = {43}, number = {9}, pages = {4751-4757}, pmid = {16145137}, issn = {0095-1137}, support = {R01 AI049311/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Adhesion ; Bacterial Proteins/*genetics/metabolism ; *Bacterial Typing Techniques ; Biofilms/*growth &amp; development ; DNA Transposable Elements ; Humans ; Molecular Sequence Data ; Operon ; Recombination, Genetic ; *Sequence Analysis, DNA ; Staphylococcal Infections/microbiology ; Staphylococcus epidermidis/*classification/genetics/isolation &amp; purification/metabolism ; }, abstract = {Staphylococcus epidermidis is part of the normal microflora of the human skin but is also a leading cause of device-associated infections in critically ill patients. Commensal and clinical S. epidermidis isolates differ in their ability to form biofilms on medical devices; the synthesis of biofilms is mediated by the icaADBC operon. Currently, the epidemiological relatedness between ica-positive and -negative isolates is not known; neither is it known whether the ica genes can spread to biofilm-negative strains through horizontal gene transfer. In this study, multilocus sequence typing (MLST) was employed for the clonal analysis of 118 S. epidermidis ica-positive and -negative strains. MLST revealed that the majority of ica-positive and -negative strains were closely related and formed a single clonal complex. Within this complex one sequence type (ST27) was identified which contained exclusively ica-positive isolates and represented the majority of clinical strains tested. ST27 and related ica-positive clones carried different SCCmec cassettes (conferring methicillin resistance) and the insertion sequence IS256. The findings suggest that the S. epidermidis infections analyzed in this report are mainly caused by a single clone (ST27) which occurs preferentially in hospitals and differs from clones in the community. It is hypothesized that the successful establishment of ST27 within nosocomial environments has been facilitated by the presence of genes encoding biofilm and resistance traits.}, }
@article {pmid16139607, year = {2005}, author = {Lu, F and Shi, D and Wei, J and Yang, S and Wei, Y}, title = {Development of embryos reconstructed by interspecies nuclear transfer of adult fibroblasts between buffalo (Bubalus bubalis) and cattle (Bos indicus).}, journal = {Theriogenology}, volume = {64}, number = {6}, pages = {1309-1319}, doi = {10.1016/j.theriogenology.2005.03.005}, pmid = {16139607}, issn = {0093-691X}, mesh = {Animals ; Blastocyst/cytology/physiology ; *Buffaloes ; *Cattle ; Cleavage Stage, Ovum ; Cloning, Organism ; Embryo, Mammalian/cytology ; Female ; Fibroblasts/cytology/*physiology ; *Gene Transfer, Horizontal ; Karyotyping/veterinary ; Male ; Microinjections/veterinary ; *Nuclear Transfer Techniques ; Oocytes/growth &amp; development/physiology ; Parthenogenesis/physiology ; Species Specificity ; *Transplantation, Heterologous/veterinary ; }, abstract = {The objective of this study was to explore the feasibility of employing adult fibroblasts as donor cells in interspecies nuclear transfer (NT) between buffaloes and cattle. Buffalo and bovine oocytes matured in vitro for 22 h were enucleated by micromanipulation using the Spindle View system. An ear fibroblast, pretreated with 0.1 microg/mL aphidicolin for 24 h, followed by culture for 2-9 days in Dulbecco's Modified Eagle's Media+0.5% fetal bovine serum, was introduced into the cytoplast by microinjection. Reconstructed oocytes were activated by exposure to 5 microM ionomycin for 5 min and 2 mM 6-dimethylaminopurine for 3 h. When buffalo adult fibroblasts were used as donor cells, there were no differences (P < 0.75) in the cleavage rate (66.2% versus 64.0%) between bovine and buffalo recipient oocytes, but more embryos derived from bovine cytoplasts developed to blastocysts than from buffalo cytoplasts (13.3% versus 3.0%, P < 0.05). When bovine adult fibroblasts were used as donor nuclei, both cleavage rate (45.3%) and blastocyst yield (4.5%) of NT embryos derived from buffalo cytoplasts were lower than those of NT embryos derived from bovine cytoplasts (65.5 and 11.9%, P < 0.05). The proportion of parthenogenetic buffalo (29.1%) or bovine (35.6%) oocytes developing to blastocysts was higher than those of NT embryos (P < 0.01). Interspecies NT embryos were derived from the donor cells and 55.0-61.9% of them possessed a normal diploid karyotype. In conclusion, embryos reconstructed by interspecies NT of adult fibroblasts between buffaloes and cattle developed to blastocysts, but bovine cytoplasts may direct embryonic development more effectively than buffalo cytoplasts, regardless of donor cell species.}, }
@article {pmid16138100, year = {2005}, author = {Frost, LS and Leplae, R and Summers, AO and Toussaint, A}, title = {Mobile genetic elements: the agents of open source evolution.}, journal = {Nature reviews. Microbiology}, volume = {3}, number = {9}, pages = {722-732}, doi = {10.1038/nrmicro1235}, pmid = {16138100}, issn = {1740-1526}, mesh = {Conjugation, Genetic/genetics ; DNA, Bacterial/*genetics ; *Evolution, Molecular ; Interspersed Repetitive Sequences/*genetics ; Models, Genetic ; Recombination, Genetic ; }, abstract = {Horizontal genomics is a new field in prokaryotic biology that is focused on the analysis of DNA sequences in prokaryotic chromosomes that seem to have originated from other prokaryotes or eukaryotes. However, it is equally important to understand the agents that effect DNA movement: plasmids, bacteriophages and transposons. Although these agents occur in all prokaryotes, comprehensive genomics of the prokaryotic mobile gene pool or 'mobilome' lags behind other genomics initiatives owing to challenges that are distinct from cellular chromosomal analysis. Recent work shows promise of improved mobile genetic element (MGE) genomics and consequent opportunities to take advantage - and avoid the dangers - of these 'natural genetic engineers'. This review describes MGEs, their properties that are important in horizontal gene transfer, and current opportunities to advance MGE genomics.}, }
@article {pmid16138099, year = {2005}, author = {Thomas, CM and Nielsen, KM}, title = {Mechanisms of, and barriers to, horizontal gene transfer between bacteria.}, journal = {Nature reviews. Microbiology}, volume = {3}, number = {9}, pages = {711-721}, doi = {10.1038/nrmicro1234}, pmid = {16138099}, issn = {1740-1526}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Bacteria/*genetics ; Conjugation, Genetic/genetics ; Evolution, Molecular ; *Gene Transfer Techniques ; Models, Genetic ; Mutation ; Transformation, Bacterial/genetics ; }, abstract = {Bacteria evolve rapidly not only by mutation and rapid multiplication, but also by transfer of DNA, which can result in strains with beneficial mutations from more than one parent. Transformation involves the release of naked DNA followed by uptake and recombination. Homologous recombination and DNA-repair processes normally limit this to DNA from similar bacteria. However, if a gene moves onto a broad-host-range plasmid it might be able to spread without the need for recombination. There are barriers to both these processes but they reduce, rather than prevent, gene acquisition.}, }
@article {pmid16138098, year = {2005}, author = {Sørensen, SJ and Bailey, M and Hansen, LH and Kroer, N and Wuertz, S}, title = {Studying plasmid horizontal transfer in situ: a critical review.}, journal = {Nature reviews. Microbiology}, volume = {3}, number = {9}, pages = {700-710}, doi = {10.1038/nrmicro1232}, pmid = {16138098}, issn = {1740-1526}, mesh = {Bacteria/genetics ; Gene Transfer Techniques/*trends ; Models, Genetic ; Plasmids/*genetics ; Transduction, Genetic ; }, abstract = {This review deals with the prospective, experimental documentation of horizontal gene transfer (HGT) and its role in real-time, local adaptation. We have focused on plasmids and their function as an accessory and/or adaptive gene pool. Studies of the extent of HGT in natural environments have identified certain hot spots, and many of these involve biofilms. Biofilms are uniquely suited for HGT, as they sustain high bacterial density and metabolic activity, even in the harshest environments. Single-cell detection of donor, recipient and transconjugant bacteria in various natural environments, combined with individual-based mathematical models, has provided a new platform for HGT studies.}, }
@article {pmid16348222, year = {1990}, author = {Stewart, GJ and Sinigalliano, CD}, title = {Detection of horizontal gene transfer by natural transformation in native and introduced species of bacteria in marine and synthetic sediments.}, journal = {Applied and environmental microbiology}, volume = {56}, number = {6}, pages = {1818-1824}, pmid = {16348222}, issn = {0099-2240}, abstract = {Both naturally occurring marine sediments and artificial sediments were used as supports for natural transformation of marine bacteria. While transformation of Pseudomonas stutzeri ZoBell suspended in artificial seawater was not detected when recipient cells and rifampin resistance DNA were loaded onto sterile sediment columns, transformation could be detected at frequencies 4 to 20 times that of spontaneous resistance when recipient cells and rifampin resistance DNA were loaded onto sterile sediment columns. Treatment of these columns with DNase I reduced transformation frequencies to levels comparable to those of spontaneous-resistance frequencies. Sediments with higher organic contents supported higher frequencies of transformation than did those with lower amounts of organic matter. Transformation was also detected when recipient cells and DNA were loaded on columns prepared from nonsterile sediments, although the frequencies of transformation were lower than when sterile sediments were used. Finally, nonsterilized sediments that were not supplemented with laboratory strains did not support detectable levels of transformation in sediment columns, but when these same sediments were transferred to filters and placed on complex media, transformation was detected at a frequency three times that for spontaneous resistance. This transformation frequency was partially reduced to levels near that for spontaneous resistance by the addition of DNase I to sediment filters. These results indicate that marine sediments facilitate the uptake and expression of exogenous DNA by transformable marine bacteria and that sediments are a more likely niche for natural transformation than the water column in the marine environment.}, }
@article {pmid16453405, year = {1982}, author = {Busslinger, M and Rusconi, S and Birnstiel, ML}, title = {An unusual evolutionary behaviour of a sea urchin histone gene cluster.}, journal = {The EMBO journal}, volume = {1}, number = {1}, pages = {27-33}, pmid = {16453405}, issn = {0261-4189}, abstract = {DNA sequences of cloned histone coding sequences and spacers of sea urchin species that diverged long ago in evolution were compared. The highly repeated H4 and H3 genes active during early embryogenesis had evolved (in their silent sites) at a rate (0.5-0.6% base changes/Myr) similar to single-copy protein-coding genes and nearly as fast as spacer DNA (0.7% base changes/Myr) and unique DNA. Thus, evolution in the major histone genes conforms to a universal evolutionary clock based on the rate of base sequence change. By contrast, the H4 and H3 coding sequences and a non-transcribed spacer of the DNA clone h19 of Psammechinus miliaris show an exceptionally low rate of sequence evolution only 1/100 to 1/200 that predicted from the clock hypothesis. According to the classical model of gene inheritance, the h19 DNA sequences in the Psammechinus genome require unusual conservation mechanisms by selection at the level of the gene and spacer sequences. An alternative explanation could be recent horizontal gene transfer of a histone gene cluster from the very distantly related Strongylocentrotus dröbachiensis to the P. miliaris genome.}, }
@article {pmid17387892, year = {1968}, author = {Johansen, I and Ustaheim, A}, title = {Enhancement of the viability of irradiated bacteria by chromosome transfer.}, journal = {Radiation research}, volume = {36}, number = {3}, pages = {610-621}, pmid = {17387892}, issn = {0033-7587}, mesh = {Cell Survival/*radiation effects ; Chromosomes, Bacterial/*genetics/radiation effects ; Dose-Response Relationship, Radiation ; Escherichia coli/classification/*genetics/*radiation effects ; Gene Transfer, Horizontal/genetics/radiation effects ; Radiation Dosage ; Species Specificity ; X-Rays ; }, abstract = {The effect of x-irradiating recipient cells of Escherichia coli K-12 before mating on the formation of recombinants and on the distribution of parental genetic material among recombinants was investigated in both the wild-type (Rec+) and a recombination-deficient (Rec-) mutant. In crosses involving Rec- recipients, recombinants selected for a late donor marker were formed in almost normal numbers. Rec- cells exposed to otherwise lethal doses of x-rays were still able to form viable recombinants for a distal male marker. These recombinants had inherited almost all the transferred donor chromosome, as evidenced by the preponderance of male markers in the recombinants. In contrast, the recombinant-forming ability was about as x-ray-sensitive as the colony-forming ability in Rec+ cells. No preference for donor chromosomal material was observed in recombinants from crosses involving x-irradiated Rec+ cells.}, }
@article {pmid16138096, year = {2005}, author = {Gogarten, JP and Townsend, JP}, title = {Horizontal gene transfer, genome innovation and evolution.}, journal = {Nature reviews. Microbiology}, volume = {3}, number = {9}, pages = {679-687}, doi = {10.1038/nrmicro1204}, pmid = {16138096}, issn = {1740-1526}, mesh = {Evolution, Molecular ; Gene Transfer Techniques/*trends ; Genetic Variation ; *Genome ; Models, Genetic ; Phylogeny ; }, abstract = {To what extent is the tree of life the best representation of the evolutionary history of microorganisms? Recent work has shown that, among sets of prokaryotic genomes in which most homologous genes show extremely low sequence divergence, gene content can vary enormously, implying that those genes that are variably present or absent are frequently horizontally transferred. Traditionally, successful horizontal gene transfer was assumed to provide a selective advantage to either the host or the gene itself, but could horizontally transferred genes be neutral or nearly neutral? We suggest that for many prokaryotes, the boundaries between species are fuzzy, and therefore the principles of population genetics must be broadened so that they can be applied to higher taxonomic categories.}, }
@article {pmid16137658, year = {2005}, author = {Fang, SG and Shen, S and Tay, FP and Liu, DX}, title = {Selection of and recombination between minor variants lead to the adaptation of an avian coronavirus to primate cells.}, journal = {Biochemical and biophysical research communications}, volume = {336}, number = {2}, pages = {417-423}, pmid = {16137658}, issn = {0006-291X}, mesh = {Adaptation, Physiological/*genetics ; Amino Acid Sequence ; Animals ; Chickens/*virology ; Chlorocebus aethiops/*virology ; Gene Transfer, Horizontal/genetics ; Genetic Variation/genetics ; Infectious bronchitis virus/*genetics ; Membrane Glycoproteins/chemistry/*genetics ; Molecular Sequence Data ; Primates/virology ; Recombination, Genetic/*genetics ; *Selection, Genetic ; Spike Glycoprotein, Coronavirus ; Vero Cells ; Viral Envelope Proteins/chemistry/*genetics ; }, abstract = {An interesting question posed by the current evidence that severe acute respiratory syndrome coronavirus may be originated from an animal coronavirus is how such an animal coronavirus breaks the host species barrier and becomes zoonotic. In this report, we study the chronological order of genotypic changes in the spike protein of avian coronavirus infectious bronchitis virus (IBV) during its adaptation to a primate cell line. Adaptation of the Beaudette strain of IBV from chicken embryo to Vero cells showed the accumulation of 49 amino acid mutations. Among them, 26 (53.06%) substitutions were located in the S protein. Sequencing analysis and comparison of the S gene demonstrated that the majority of the mutations were accumulated and fixed at passage 7 on Vero cells and minor variants were isolated in several passages. Evidence present suggests that the dominant Vero cell-adapted IBV strain may be derived from the chicken embryo passages by selection of and potential recombination between the minor variants. This may explain why adaptation is a rapid process and the dominant strain, once adapted to a new host cell, becomes relatively stable.}, }
@article {pmid16136351, year = {2005}, author = {Liu, XM and Brown-Guedira, GL and Hatchett, JH and Owuoche, JO and Chen, MS}, title = {Genetic characterization and molecular mapping of a Hessian fly-resistance gene transferred from T. turgidum ssp. dicoccum to common wheat.}, journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik}, volume = {111}, number = {7}, pages = {1308-1315}, pmid = {16136351}, issn = {0040-5752}, mesh = {Animals ; *Chromosome Mapping ; Crosses, Genetic ; *Diptera ; Gene Transfer, Horizontal/*genetics ; Genes, Plant/*genetics ; Immunity, Innate/*genetics ; Minisatellite Repeats/genetics ; Plant Diseases/genetics/*parasitology ; Triticum/*genetics/growth &amp; development ; }, abstract = {A gene (temporarily designated Hdic) conferring resistance to the Hessian fly (Hf) [Mayetiola destructor (Say)] was previously identified from an accession of German cultivated emmer wheat [Triticum turgidum ssp. dicoccum (Schrank ex Schübler) Thell] PI 94641, and was transferred to the Hf-resistant wheat germplasm KS99WGRC42. The inheritance of Hdic resistance exhibited incomplete penetrance because phenotypes of some heterozygous progenies are fully resistant and the others are fully susceptible. Five simple sequence repeat (SSR) markers (Xgwm136,Xcfa2153, Xpsp2999,Xgwm33, and Xbarc263) were linked to the Hdic gene on the short arm of wheat chromosome 1A in the same region as the H9, H10, and H11 loci. Flanking markers Xgwm33 and Xcfa2153 were mapped at distances 0.6 cM proximal and 1.4 cM distal, respectively. Marker analysis revealed that a very small intercalary chromosomal segment containing Hdic was transferred from emmer wheat to KS99WGRC42. This is the first emmer-derived Hf-resistance gene that has been mapped and characterized. The Hdic gene confers a high level of antibiosis to biotypes GP and L, as well as to strains vH9 and vH13 of the Hf, which is different from the biotype reaction patterns of the known Hf-resistance genes on chromosome 1A (H5 and H11 susceptible to biotype L, H9 and H10 susceptible to strain vH9). These results suggested that Hdic is either a new gene or a novel allele of a known H gene on chromosome 1A. The broad spectrum of resistance conferred by the Hdic gene makes it valuable for developing Hf resistant wheat cultivars.}, }
@article {pmid16134896, year = {2005}, author = {Kay, S and Boch, J and Bonas, U}, title = {Characterization of AvrBs3-like effectors from a Brassicaceae pathogen reveals virulence and avirulence activities and a protein with a novel repeat architecture.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {18}, number = {8}, pages = {838-848}, doi = {10.1094/MPMI-18-0838}, pmid = {16134896}, issn = {0894-0282}, mesh = {Amino Acid Sequence ; Bacterial Proteins/*chemistry/genetics/*metabolism ; Brassicaceae/*microbiology ; Gene Transfer, Horizontal ; Solanum lycopersicum/metabolism/microbiology ; Molecular Sequence Data ; Mutation ; Plant Diseases/microbiology ; Plant Leaves/microbiology ; Plant Proteins/metabolism ; Protein Transport ; Terminal Repeat Sequences ; Nicotiana/metabolism/microbiology ; Virulence ; Xanthomonas campestris/genetics/*metabolism/*pathogenicity ; }, abstract = {Xanthomonas campestris pv. armoraciae strain 5 is a Brassicaceae pathogen that expresses three members of the highly related avrBs3 gene family of type III effectors. Here, we report on the isolation and characterization of these genes, designated hax2, hax3, and hax4 (homolog of avrBs3 in Xanthomonas). All three Hax proteins are translocated from Xanthomonas spp. into the plant cell via the type III secretion system. Hax3 and Hax4 show the typical structure of AvrBs3-like effectors and contain a repetitive region in their central part consisting of 34-amino-acid (aa) repeats. By contrast, the Hax2 repeat region is composed of 35-aa repeats that are characterized by an additional proline residue. Hax2, Hax3, and Hax4 contain 21.5, 11.5, and 14.5 repeats, respectively. Genetic studies revealed an additive effect of hax2, hax3, and hax4 on disease symptom formation of X. campestris pv. armoraciae strain 5 on radish. The contribution of individual genes to the aggressiveness of strain 5 is quantitatively different, with hax2 showing the strongest effect on the development of chlorosis and necrosis. In addition, hax3 and hax4, but not hax2, have a Bs4-dependent avirulence activity in tomato and in transgenic Nicotiana benthamiana expressing the Bs4 resistance gene.}, }
@article {pmid16129816, year = {2005}, author = {Leppänen, P and Koota, S and Kholová, I and Koponen, J and Fieber, C and Eriksson, U and Alitalo, K and Ylä-Herttuala, S}, title = {Gene transfers of vascular endothelial growth factor-A, vascular endothelial growth factor-B, vascular endothelial growth factor-C, and vascular endothelial growth factor-D have no effects on atherosclerosis in hypercholesterolemic low-density lipoprotein-receptor/apolipoprotein B48-deficient mice.}, journal = {Circulation}, volume = {112}, number = {9}, pages = {1347-1352}, doi = {10.1161/CIRCULATIONAHA.105.534107}, pmid = {16129816}, issn = {1524-4539}, mesh = {Adenoviridae/genetics ; Animals ; Apolipoprotein B-48 ; Apolipoproteins B/*physiology ; Atherosclerosis/*etiology ; Gene Transfer, Horizontal ; Humans ; Hypercholesterolemia/*complications ; Lipids/blood ; Mice ; Neovascularization, Physiologic ; Receptors, LDL/*physiology ; Vascular Endothelial Growth Factor A/genetics/*physiology ; Vascular Endothelial Growth Factor B/genetics ; Vascular Endothelial Growth Factor C/genetics ; Vascular Endothelial Growth Factor D/genetics ; }, abstract = {BACKGROUND: The role of vascular endothelial growth factors (VEGFs) in large arteries has been proposed to be either vasculoprotective or proatherogenic. Because VEGF family members are used for human therapy, it is important to know whether they could enhance atherogenesis. We tested the effects of the members of the VEGF gene family on atherogenesis in LDL-receptor/apolipoprotein (apo) B48 double-knockout (LDLR/apoB48) mice using systemic adenoviral gene transfer.<br><br>METHODS AND RESULTS: Six groups of LDLR/apoB48-deficient mice (n=110) were kept 3 months on a Western-type diet. After 6 weeks of diet, mice were injected via tail vein with recombinant adenoviruses expressing VEGF-A, -B, -C, or -D or LacZ (1 x 10(9) PFU) or rhVEGF-A protein (2 microg/kg) and euthanized 6 weeks later. Also, older mice (n=36) were injected after 4 months on the diet and euthanized 6 weeks later (total time on the diet, 22 weeks) to evaluate the effects of gene transfers on the development of more mature lesions. Aortas were analyzed for the presence of macroscopic lesions, cross-sectional lesion areas, neovascularization, and cellular composition of the lesions. All groups had equivalent plasma cholesterol and triglyceride levels. Gene transfers with recombinant adenoviruses or administration of rhVEGF-A protein had no statistically significant effects on en face atherosclerotic lesions in the aorta, cross-sectional lesion area, neovascularization, or cellular composition of the lesions.<br><br>CONCLUSIONS: This study shows no proatherogenic effects of adenovirus-mediated gene transfers of VEGF-A, -B, -C, or -D in the LDLR/apoB48-deficient hypercholesterolemic mice, in which lipoprotein profile and atherosclerosis closely resemble those in human disease.}, }
@article {pmid16129810, year = {2005}, author = {Tsutsumi, Y and Losordo, DW}, title = {Double face of VEGF.}, journal = {Circulation}, volume = {112}, number = {9}, pages = {1248-1250}, doi = {10.1161/CIRCULATIONAHA.105.566166}, pmid = {16129810}, issn = {1524-4539}, mesh = {Animals ; Apolipoprotein B-48 ; Apolipoproteins B/*physiology ; Atherosclerosis/*etiology ; Gene Transfer, Horizontal ; Humans ; Hypercholesterolemia/*complications ; Mice ; Neovascularization, Physiologic ; Receptors, LDL/*physiology ; Vascular Endothelial Growth Factor A/genetics/*physiology ; }, }
@article {pmid16128825, year = {2005}, author = {Marsh, PD}, title = {Dental plaque: biological significance of a biofilm and community life-style.}, journal = {Journal of clinical periodontology}, volume = {32 Suppl 6}, number = {}, pages = {7-15}, doi = {10.1111/j.1600-051X.2005.00790.x}, pmid = {16128825}, issn = {0303-6979}, mesh = {*Biofilms ; Dental Plaque/genetics/*microbiology ; Drug Resistance, Bacterial ; Ecosystem ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Humans ; }, abstract = {BACKGROUND: Most microorganisms in nature attach to surfaces and form matrix-embedded biofilms. Biofilms are highly structured and spatially organized, and are often composed of consortia of interacting microorganisms, termed microbial communities, the properties of which are more than the sum of the component species. Microbial gene expression alters markedly in biofilms; organisms communicate by gene transfer and by secretion of diffusible signalling molecules. Cells in biofilms are less susceptible to antimicrobial agents.<br><br>To comprehensively review the literature to determine whether dental plaque displays properties consistent with those of a typical biofilm and microbial community.<br><br>RESULTS: Novel microscopic and molecular techniques have demonstrated that plaque has a structured architecture with an extracellular matrix, and a diverse composition (around 50% of cells are unculturable). The constituent species communicate by gene transfer, by secreted peptides (gram-positive bacteria) and autoinducer-2 (gram-positive and gram-negative bacteria). These organisms are functionally organized for increased metabolic efficiency, greater resistance to stress and for enhanced virulence. Plaque formation has direct and indirect effects on gene expression.<br><br>CONCLUSION: Dental plaque displays properties that are typical of biofilms and microbial communities in general, a clinical consequence of which is a reduced susceptibility to antimicrobial agents as well as pathogenic synergism.}, }
@article {pmid16128397, year = {2005}, author = {Ideses, D and Biran, D and Gophna, U and Levy-Nissenbaum, O and Ron, EZ}, title = {The lpf operon of invasive Escherichia coli.}, journal = {International journal of medical microbiology : IJMM}, volume = {295}, number = {4}, pages = {227-236}, doi = {10.1016/j.ijmm.2005.04.009}, pmid = {16128397}, issn = {1438-4221}, mesh = {Bacterial Adhesion/*genetics/physiology ; Cell Line ; Escherichia coli/classification/*genetics/pathogenicity/physiology ; Escherichia coli Proteins/*genetics/physiology ; Operon ; Virulence ; }, abstract = {Extraintestinal pathogenic Escherichia coli (ExPEC) strains have been shown to code for several virulence factors involved in adherence to host tissues. Here we show the existence of an additional adherence gene cluster, coding for long polar fimbriae--LPF--in several strains of serotype O78 from septicemia and newborn meningitis. The complete gene cluster was sequenced in strain 789 (lpf789), where it is located between the genes glmS and pstS, and contains four ORFs, lpfA to lpfD. The lpf operon is expressed and is important for adherence to epithelial cells. The lpf operon was found only in four of the ExPEC strains tested and is likely to have been acquired by horizontal gene transfer.}, }
@article {pmid16127047, year = {2005}, author = {Sekiguchi, J and Asagi, T and Miyoshi-Akiyama, T and Fujino, T and Kobayashi, I and Morita, K and Kikuchi, Y and Kuratsuji, T and Kirikae, T}, title = {Multidrug-resistant Pseudomonas aeruginosa strain that caused an outbreak in a neurosurgery ward and its aac(6')-Iae gene cassette encoding a novel aminoglycoside acetyltransferase.}, journal = {Antimicrobial agents and chemotherapy}, volume = {49}, number = {9}, pages = {3734-3742}, pmid = {16127047}, issn = {0066-4804}, mesh = {Acetyltransferases/*metabolism ; Amino Acid Sequence ; Anti-Bacterial Agents/pharmacology ; Cross Infection/epidemiology/*microbiology ; DNA, Bacterial/genetics ; Disinfectants/pharmacology ; Drug Resistance, Multiple, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Genotype ; Hospital Units ; Humans ; Integrons ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Neurosurgery ; Phenotype ; Pseudomonas Infections/epidemiology/*microbiology ; Pseudomonas aeruginosa/*drug effects/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {We characterized multidrug-resistant Pseudomonas aeruginosa strains isolated from patients involved in an outbreak of catheter-associated urinary tract infections that occurred in a neurosurgery ward of a hospital in Sendai, Japan. Pulsed-field gel electrophoresis of SpeI-, XbaI-, or HpaI-digested genomic DNAs from the isolates revealed that clonal expansion of a P. aeruginosa strain designated IMCJ2.S1 had occurred in the ward. This strain possessed broad-spectrum resistance to aminoglycosides, beta-lactams, fluoroquinolones, tetracyclines, sulfonamides, and chlorhexidine. Strain IMCJ2.S1 showed a level of resistance to some kinds of disinfectants similar to that of a control strain of P. aeruginosa, ATCC 27853. IMCJ2.S1 contained a novel class 1 integron, In113, in the chromosome but not on a plasmid. In113 contains an array of three gene cassettes of bla(IMP-1), a novel aminoglycoside resistance gene, and the aadA1 gene. The aminoglycoside resistance gene, designated aac(6')-Iae, encoded a 183-amino-acid protein that shared 57.1% identity with AAC(6')-Iq. Recombinant AAC(6')-Iae protein showed aminoglycoside 6'-N-acetyltransferase activity by thin-layer chromatography. Escherichia coli expressing exogenous aac(6')-Iae showed resistance to amikacin, dibekacin, isepamicin, kanamycin, netilmicin, sisomicin, and tobramycin but not to arbekacin, gentamicins, or streptomycin. Alterations of gyrA and parC at the amino acid sequence level were detected in IMCJ2.S1, suggesting that such mutations confer the resistance to fluoroquinolones observed for this strain. These results indicate that P. aeruginosa IMCJ2.S1 has developed multidrug resistance by acquiring resistance determinants, including a novel member of the aac(6')-I family and mutations in drug resistance genes.}, }
@article {pmid16125444, year = {2005}, author = {Eichinger, L and Noegel, AA}, title = {Comparative genomics of Dictyostelium discoideum and Entamoeba histolytica.}, journal = {Current opinion in microbiology}, volume = {8}, number = {5}, pages = {606-611}, doi = {10.1016/j.mib.2005.08.009}, pmid = {16125444}, issn = {1369-5274}, mesh = {Adaptation, Biological/genetics ; Animals ; Dictyostelium/*genetics ; Entamoeba histolytica/*genetics ; Gene Transfer, Horizontal ; Genes, Protozoan ; *Genome, Protozoan ; Genomics ; Humans ; Interspersed Repetitive Sequences/genetics ; Telomere/genetics ; }, abstract = {Amoebozoa represent one of the earliest branches from the last common ancestor of all eukaryotes and contain some of the most dangerous human pathogens. Two amoebozoan genomes -- from the model organism Dictyostelium discoideum and the human pathogen Entamoeba histolytica -- have been published this year. Owing to their high A+T content, both genomes were difficult to sequence. In addition to nine amoebozoan expressed sequence tag projects, efforts are underway for comparative sequencing of four additional Entamoeba species. The completed genome sequences of D. discoideum and E. histolytica revealed unusual telomere structures, a high percentage of repetitive elements and a remarkably high gene content that is close to the one of Drosophila melanogaster. Finally, both organisms are brilliant examples of the influence of the lifestyle of an organism on its genome.}, }
@article {pmid16125007, year = {2005}, author = {Hols, P and Hancy, F and Fontaine, L and Grossiord, B and Prozzi, D and Leblond-Bourget, N and Decaris, B and Bolotin, A and Delorme, C and Dusko Ehrlich, S and Guédon, E and Monnet, V and Renault, P and Kleerebezem, M}, title = {New insights in the molecular biology and physiology of Streptococcus thermophilus revealed by comparative genomics.}, journal = {FEMS microbiology reviews}, volume = {29}, number = {3}, pages = {435-463}, doi = {10.1016/j.femsre.2005.04.008}, pmid = {16125007}, issn = {0168-6445}, mesh = {Bacterial Proteins/*genetics ; Genome, Bacterial ; Genomics ; Streptococcus thermophilus/classification/*genetics/pathogenicity/*physiology ; Virulence Factors/*genetics ; }, abstract = {Streptococcus thermophilus is a major dairy starter used for the manufacture of yoghurt and cheese. The access to three genome sequences, comparative genomics and multilocus sequencing analyses suggests that this species recently emerged and is still undergoing a process of regressive evolution towards a specialised bacterium for growth in milk. Notably, S. thermophilus has maintained a well-developed nitrogen metabolism whereas its sugar catabolism has been subjected to a high level of degeneracy due to a paucity of carbon sources in milk. Furthermore, while pathogenic streptococci are recognised for a high capacity to expose proteins at their cell surface in order to achieve cell adhesion or to escape the host immune system, S. thermophilus has nearly lost this unique feature as well as many virulence-related functions. Although gene decay is obvious in S. thermophilus genome evolution, numerous small genomic islands, which were probably acquired by horizontal gene transfer, comprise important industrial phenotypic traits such as polysaccharide biosynthesis, bacteriocin production, restriction-modification systems or oxygen tolerance.}, }
@article {pmid16122972, year = {2005}, author = {Lawrence, JG and Hendrickson, H}, title = {Genome evolution in bacteria: order beneath chaos.}, journal = {Current opinion in microbiology}, volume = {8}, number = {5}, pages = {572-578}, doi = {10.1016/j.mib.2005.08.005}, pmid = {16122972}, issn = {1369-5274}, mesh = {Bacteria/classification/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Recombination, Genetic ; Sequence Deletion ; }, abstract = {Bacterial genomes have been viewed as collections of genes, with each gene and genome evolving more-or-less independently through the acquisition of mutational changes. This historical view has been overturned by the finding that genomes of even closely-related taxa differ widely in gene content. Yet, genomes are more than ever-shuffling collections of genes. Some genes within a genome are more transient than others, conferring a layer of phenotypic lability over a core of genotypic stability; this core decreases in size as the taxa included become increasingly diverse. In addition, some lineages no longer experience high rates of gene turnover, and gene content alters primarily through slow rates of gene loss. More importantly, the cell and molecular biology of the bacterial cell imposes constraints on chromosome composition, maintaining a stable architecture in the face of gene turnover. As a result, genomes reflect the sum of processes that introduce variability, which is then arbitrated by processes that maintain stability.}, }
@article {pmid16122562, year = {2005}, author = {Jiang, Y and Yang, F and Zhang, X and Yang, J and Chen, L and Yan, Y and Nie, H and Xiong, Z and Wang, J and Dong, J and Xue, Y and Xu, X and Zhu, Y and Chen, S and Jin, Q}, title = {The complete sequence and analysis of the large virulence plasmid pSS of Shigella sonnei.}, journal = {Plasmid}, volume = {54}, number = {2}, pages = {149-159}, doi = {10.1016/j.plasmid.2005.03.002}, pmid = {16122562}, issn = {0147-619X}, mesh = {Bacterial Proteins/genetics ; Base Composition ; DNA Primase ; DNA Replication/genetics ; DNA-Directed RNA Polymerases/genetics ; Endodeoxyribonucleases/genetics ; Escherichia coli Proteins/genetics ; Exodeoxyribonucleases/genetics ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Multigene Family ; O Antigens/genetics ; Open Reading Frames ; Plasmids/*genetics ; Sequence Analysis ; Shigella sonnei/genetics/*pathogenicity ; Virulence/genetics ; }, abstract = {The complete sequence of pSS, which is the large virulence plasmid of Shigella sonnei, was determined. The 214-kb plasmid is composed of segments of virulence-associated genes, the O-antigen gene clusters, a range of replication and maintenance genes, and large numbers of insertion sequence (IS) elements. Two hundred and forty-one open reading frames (ORFs) were identified, of which 117 are highly homologous to IS elements or transposases, 57 are homologous to known pathogenesis-associated proteins, and 30 are related to replication, plasmid maintenance, or other metabolic functions. Thirty-seven ORFs have no similarity to proteins with a known function, including two with no significant similarity to any hypothetical proteins. Interestingly, 10 ORFs encoding O-antigen gene clusters were identified on the plasmid and this is markedly different from most other Shigella spp. virulent plasmids. A novel toxin-antitoxin system, a series of stbDE homologs, was found on the plasmid immediately downstream of the replication region; the sole segregation stability system may be responsible for the instability of pSS. The pSS plasmid is a mixture of genes with different origins and functions. The sequence suggests a remarkable history of IS-mediated recombination and acquisition of DNA across a range of bacterial species.}, }
@article {pmid16122348, year = {2005}, author = {Ge, F and Wang, LS and Kim, J}, title = {The cobweb of life revealed by genome-scale estimates of horizontal gene transfer.}, journal = {PLoS biology}, volume = {3}, number = {10}, pages = {e316}, pmid = {16122348}, issn = {1545-7885}, support = {1-P20-GM-6921-1/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Computational Biology ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; *Genome ; Genome, Archaeal ; Genome, Bacterial ; Genome, Fungal ; Models, Genetic ; }, abstract = {With the availability of increasing amounts of genomic sequences, it is becoming clear that genomes experience horizontal transfer and incorporation of genetic information. However, to what extent such horizontal gene transfer (HGT) affects the core genealogical history of organisms remains controversial. Based on initial analyses of complete genomic sequences, HGT has been suggested to be so widespread that it might be the "essence of phylogeny" and might leave the treelike form of genealogy in doubt. On the other hand, possible biased estimation of HGT extent and the findings of coherent phylogenetic patterns indicate that phylogeny of life is well represented by tree graphs. Here, we reexamine this question by assessing the extent of HGT among core orthologous genes using a novel statistical method based on statistical comparisons of tree topology. We apply the method to 40 microbial genomes in the Clusters of Orthologous Groups database over a curated set of 297 orthologous gene clusters, and we detect significant HGT events in 33 out of 297 clusters over a wide range of functional categories. Estimates of positions of HGT events suggest a low mean genome-specific rate of HGT (2.0%) among the orthologous genes, which is in general agreement with other quantitative of HGT. We propose that HGT events, even when relatively common, still leave the treelike history of phylogenies intact, much like cobwebs hanging from tree branches.}, }
@article {pmid16120264, year = {2005}, author = {O'Malley, MA and Boucher, Y}, title = {Paradigm change in evolutionary microbiology.}, journal = {Studies in history and philosophy of biological and biomedical sciences}, volume = {36}, number = {1}, pages = {183-208}, doi = {10.1016/j.shpsc.2004.12.002}, pmid = {16120264}, issn = {1369-8486}, mesh = {*Biological Evolution ; *Gene Transfer, Horizontal ; Historiography ; History, 20th Century ; Humans ; Microbiology/*history ; Molecular Biology/*history ; *Phylogeny ; Problem Solving ; Social Change ; }, abstract = {Thomas Kuhn had little to say about scientific change in biological science, and biologists are ambivalent about how applicable his framework is for their disciplines. We apply Kuhn's account of paradigm change to evolutionary microbiology, where key Darwinian tenets are being challenged by two decades of findings from molecular phylogenetics. The chief culprit is lateral gene transfer, which undermines the role of vertical descent and the representation of evolutionary history as a tree of life. To assess Kuhn's relevance to this controversy, we add a social analysis of the scientists involved to the historical and philosophical debates. We conclude that while Kuhn's account may capture aspects of the pattern (or outcome) of an episode of scientific change, he has little to say about how the process of generating new understandings is occurring in evolutionary microbiology. Once Kuhn's application is limited to that of an initial investigative probe into how scientific problem-solving occurs, his disciplinary scope becomes broader.}, }
@article {pmid16116418, year = {2005}, author = {Mentewab, A and Stewart, CN}, title = {Overexpression of an Arabidopsis thaliana ABC transporter confers kanamycin resistance to transgenic plants.}, journal = {Nature biotechnology}, volume = {23}, number = {9}, pages = {1177-1180}, doi = {10.1038/nbt1134}, pmid = {16116418}, issn = {1087-0156}, mesh = {ATP-Binding Cassette Transporters/*metabolism ; Arabidopsis/*metabolism ; Arabidopsis Proteins/chemistry/*genetics ; Blotting, Northern ; Blotting, Southern ; Carbohydrate Sequence ; DNA, Bacterial/chemistry ; *Drug Resistance/genetics ; Escherichia coli/metabolism ; Gene Transfer Techniques ; Gene Transfer, Horizontal ; Genes, Plant/*genetics ; Genetic Engineering ; Genetic Markers ; *Genetic Techniques ; Kanamycin/*pharmacology ; Models, Chemical ; Molecular Sequence Data ; *Plants, Genetically Modified ; Streptomyces/metabolism ; }, abstract = {Selectable markers of bacterial origin such as the neomycin phosphotransferase type II gene, which can confer kanamycin resistance to transgenic plants, represent an invaluable tool for plant engineering. However, since all currently used antibiotic-resistance genes are of bacterial origin, there have been concerns about horizontal gene transfer from transgenic plants back to bacteria, which may result in antibiotic resistance. Here we characterize a plant gene, Atwbc19, the gene that encodes an Arabidopsis thaliana ATP binding cassette (ABC) transporter and confers antibiotic resistance to transgenic plants. The mechanism of resistance is novel, and the levels of resistance achieved are comparable to those attained through expression of bacterial antibiotic-resistance genes in transgenic tobacco using the CaMV 35S promoter. Because ABC transporters are endogenous to plants, the use of Atwbc19 as a selectable marker in transgenic plants may provide a practical alternative to current bacterial marker genes in terms of the risk for horizontal transfer of resistance genes.}, }
@article {pmid16113341, year = {2005}, author = {Barbour, AG and Putteet-Driver, AD and Bunikis, J}, title = {Horizontally acquired genes for purine salvage in Borrelia spp. causing relapsing fever.}, journal = {Infection and immunity}, volume = {73}, number = {9}, pages = {6165-6168}, pmid = {16113341}, issn = {0019-9567}, support = {R01 AI024424/AI/NIAID NIH HHS/United States ; R37 AI024424/AI/NIAID NIH HHS/United States ; AI24424/AI/NIAID NIH HHS/United States ; }, mesh = {Adenylosuccinate Lyase/genetics/metabolism ; Adenylosuccinate Synthase/genetics/metabolism ; Animals ; Borrelia/classification/*genetics/metabolism ; DNA, Intergenic ; *Gene Transfer, Horizontal ; Hypoxanthine Phosphoribosyltransferase/genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; Purines/*metabolism ; Relapsing Fever/*metabolism/*microbiology ; }, abstract = {Unlike Borrelia burgdorferi, the relapsing fever agent Borrelia hermsii and the related Borrelia miyamotoi had purA and purB genes of the purine salvage pathway. These were located among the rRNA genes. Phylogenetic analysis indicated that these genes had a different evolutionary history than those of orthologs in other spirochetes.}, }
@article {pmid16113292, year = {2005}, author = {Park, KS and Arita, M and Iida, T and Honda, T}, title = {vpaH, a gene encoding a novel histone-like nucleoid structure-like protein that was possibly horizontally acquired, regulates the biogenesis of lateral flagella in trh-positive Vibrio parahaemolyticus TH3996.}, journal = {Infection and immunity}, volume = {73}, number = {9}, pages = {5754-5761}, pmid = {16113292}, issn = {0019-9567}, mesh = {Amino Acid Sequence ; Bacterial Proteins/*genetics/physiology ; Blotting, Western ; Flagella/*genetics/*metabolism/ultrastructure ; Gene Transfer Techniques ; *Gene Transfer, Horizontal ; HeLa Cells ; Humans ; Microscopy, Electron, Transmission ; Molecular Sequence Data ; Sequence Deletion ; Vibrio parahaemolyticus/*genetics/physiology/ultrastructure ; }, abstract = {A histone-like nucleoid structure (H-NS) is a major component of the bacterial nucleoid and plays a crucial role in the global gene regulation of enteric bacteria. Here, we cloned and characterized the gene for the H-NS-like protein VpaH in Vibrio parahaemolyticus. vpaH encodes a protein of 134 amino acids that shows approximately 55%, 54%, and 41% identities with VicH in Vibrio cholerae, H-NS in V. parahaemolyticus, and H-NS in Escherichia coli, respectively. The vpaH gene was found in only trh-positive V. parahaemolyticus strains and not in Kanagawa-positive or in trh-negative environmental strains. Moreover, the G+C content of the vpaH gene was 38.6%, which is lower than the average G+C content of the whole genome of this bacterium (45.4%). These data suggest that vpaH was transmitted to trh-possessing V. parahaemolyticus strains by lateral transfer. The vpaH gene was located about 2.6 kb downstream of the trh gene, in the convergent direction of the trh transcription. An in-frame deletion mutant of vpaH lacked motility on semisolid motility assay plates. Western blot analysis and electron microscopy observations revealed that the mutant was deficient in lateral flagella biogenesis, whereas there was no defect in the expression of polar flagella. Additionally, the vpaH mutant showed a decreased adherence to HeLa cells and a decrease in biofilm formation compared with the wild-type strain. Introduction of the vpaH gene in the vpaH-negative strain increased the expression of lateral flagella compared with the wild-type strain. In conclusion, our findings suggest that VpaH affects lateral flagellum biogenesis in trh-positive V. parahaemolyticus strain TH3996.}, }
@article {pmid16113272, year = {2005}, author = {Wooldridge, KG and Kizil, M and Wells, DB and Ala'aldeen, DA}, title = {Unusual genetic organization of a functional type I protein secretion system in Neisseria meningitidis.}, journal = {Infection and immunity}, volume = {73}, number = {9}, pages = {5554-5567}, pmid = {16113272}, issn = {0019-9567}, mesh = {Amino Acid Sequence ; Bacterial Outer Membrane Proteins/*genetics/physiology ; Bacterial Proteins/*genetics/metabolism/physiology ; Carrier Proteins/*genetics/physiology ; Escherichia coli Proteins ; Gene Expression Regulation, Bacterial/physiology ; Gene Transfer, Horizontal ; Hemolysin Proteins ; Iron/physiology ; Membrane Proteins/genetics/metabolism/physiology ; Membrane Transport Proteins ; Molecular Sequence Data ; Neisseria gonorrhoeae/genetics ; Neisseria lactamica/genetics ; Neisseria meningitidis/*genetics/physiology ; Proteins/*metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Proteins secreted by Neisseria meningitidis are thought to play important roles in the pathogenesis of meningococcal disease. These proteins include the iron-repressible repeat-in-toxin (RTX) exoprotein FrpC. Related proteins in other pathogens are secreted via a type I secretion system (TOSS), but such a system has not been demonstrated in N. meningitidis. An in silico search of the group B meningococcal genome suggested the presence of a uniquely organized TOSS. Genes encoding homologs of the Escherichia coli HlyB (ATP-binding), HlyD (membrane fusion), and TolC (outer membrane channel) proteins were identified. In contrast to the cistronic organization of the secretion genes in most other rtx operons, the hlyD and tolC genes were adjacent but unlinked to hlyB; neither locus was part of an operon containing genes encoding putative TOSS substrates. Both loci were flanked by genes normally associated with mobile genetic elements. The three genes were shown to be expressed independently. Mutation at either locus resulted in an inability to secrete FrpC and a related protein, here called FrpC2. Successful complementation of these mutations at an ectopic site confirmed the observed phenotypes were caused by loss of function of the putative TOSS genes. We show that genes scattered in the meningococcal genome encode a functional TOSS required for secretion of the meningococcal RTX proteins.}, }
@article {pmid16113222, year = {2005}, author = {Gustavsson, S and Lebrun, AS and Nordén, K and Chaumont, F and Johanson, U}, title = {A novel plant major intrinsic protein in Physcomitrella patens most similar to bacterial glycerol channels.}, journal = {Plant physiology}, volume = {139}, number = {1}, pages = {287-295}, pmid = {16113222}, issn = {0032-0889}, mesh = {Amino Acid Sequence ; Bacterial Proteins/*chemistry/*metabolism ; Bryopsida/*genetics/metabolism ; Cloning, Molecular ; DNA, Complementary/genetics ; Gene Expression Regulation, Plant ; Gene Transfer, Horizontal ; Glycerol/*metabolism ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/*chemistry/genetics/*metabolism ; Sequence Homology, Amino Acid ; Substrate Specificity ; }, abstract = {A gene encoding a novel fifth type of major intrinsic protein (MIP) in plants has been identified in the moss Physcomitrella patens. Phylogenetic analyses show that this protein, GlpF-like intrinsic protein (GIP1;1), is closely related to a subclass of glycerol transporters in bacteria that in addition to glycerol are highly permeable to water. A likely explanation of the occurrence of this bacterial-like MIP in P. patens is horizontal gene transfer. The expressed P. patens GIP1;1 gene contains five introns and encodes a unique C-loop extension of approximately 110 amino acid residues that has no obvious similarity with any other known protein. Based on alignments and structural comparisons with other MIPs, GIP1;1 is suggested to have retained the permeability for glycerol but not for water. Studies on heterologously expressed GIP1;1 in Xenopus laevis oocytes confirm the predicted substrate specificity. Interestingly, proteins of one of the plant-specific subgroups of MIPs, the NOD26-like intrinsic proteins, are also facilitating the transport of glycerol and have previously been suggested to have evolved from a horizontally transferred bacterial gene. Further studies on localization and searches for GIP1;1 homologs in other plants will clarify the function and significance of this new plant MIP.}, }
@article {pmid16110915, year = {2005}, author = {Franiczek, R and Krzyzanowska, B and Dolna, I and Mokracka, G and Szufnarowski, K}, title = {Extended-spectrum beta-lactamase-conferring transferable resistance to different antimicrobial agents in Enterobacteriaceae isolated from bloodstream infections.}, journal = {Folia microbiologica}, volume = {50}, number = {2}, pages = {119-124}, pmid = {16110915}, issn = {0015-5632}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteremia/*microbiology ; Conjugation, Genetic ; Drug Resistance, Bacterial/*genetics ; Enterobacteriaceae/drug effects/enzymology/genetics/*isolation &amp; purification ; Enterobacteriaceae Infections/microbiology ; *Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests/methods ; Polymerase Chain Reaction ; beta-Lactam Resistance/genetics ; beta-Lactamases/*genetics ; beta-Lactams/pharmacology ; }, abstract = {Twenty (18.5%) out of 108 clinical isolates of the family Enterobacteriaceae responsible for bloodstream infection were extended-spectrum beta-lactamase (ESBL)-positive in two screening tests, the double disk synergy test and the Oxoid Combination Disk method. Eleven out of the 20 ESBL-positive isolates transferred oxyimino-beta-lactam resistance to E. coli K12 C600 recipient strain with a frequency of 10(-8) - 10(-1) per donor cell. PCR analysis revealed that the majority of the transconjugants (9 of 11) express CTX-M-type beta-lactamases. Donor strains and their transconjugants displayed susceptibility patterns typical of ESBL producers. They were resistant to oxyimino-beta-lactams but susceptible to clavulanic acid and carbapenems. Resistances to aminoglycosides, tetracycline and mercuric chloride were, in some cases, co-transferred with oxyimino-beta-lactam resistance, suggesting that various resistance determinants were carried by the same conjugative plasmids.}, }
@article {pmid16108914, year = {2005}, author = {Bathe, S and Schwarzenbeck, N and Hausner, M}, title = {Plasmid-mediated bioaugmentation of activated sludge bacteria in a sequencing batch moving bed reactor using pNB2.}, journal = {Letters in applied microbiology}, volume = {41}, number = {3}, pages = {242-247}, doi = {10.1111/j.1472-765X.2005.01754.x}, pmid = {16108914}, issn = {0266-8254}, mesh = {Aniline Compounds/*metabolism ; Biodegradation, Environmental ; Biofilms ; Bioreactors/*microbiology ; Comamonas testosteroni/*genetics/physiology ; Conjugation, Genetic ; Gene Transfer, Horizontal ; Plasmids/*physiology ; Polymerase Chain Reaction ; Pseudomonas putida/genetics/physiology ; Sewage/microbiology ; Water Purification/*methods ; }, abstract = {AIMS: The applicability of plasmid pNB2 for bioaugmentation of bacteria in model wastewater treatment reactors receiving 3-chloroaniline (3-CA) was investigated.<br><br>METHODS AND RESULTS: A setup of three biofilm reactors was studied, all initially inoculated with bacteria from activated sludge. Reactor PB received a Pseudomonas putida pNB2 donor strain not able to degrade 3-CA. Positive control reactor P received a 3-CA degrading Comamonas testosteroni pNB2-transconjugant. The negative control reactor N remained unchanged. Reactor P showed 3-CA degradation from the beginning of the experiment whereas in reactor PB, degradation started after an initial lag period. No degradation was observed in reactor N. PCR analysis showed that the P. putida donor abundance dropped in reactor PB, whereas the plasmid abundance did not, indicating transfer to other bacteria. A number of different 3-CA degrading C. testosteroni strains carrying pNB2 could be isolated from reactor PB.<br><br>CONCLUSIONS: A successful plasmid-mediated bioaugmentation was achieved with C. testosteroni being the dominant 3-CA degrading pNB2 transconjugant species active in reactor PB.<br><br>The study underlines the potential of gene transfer to contribute to establishment and spread of genetic information in general, particularly emphasizing the spread of xenobiotic degrading potential by dissemination of catabolic genes.}, }
@article {pmid16108911, year = {2005}, author = {Baillie, LW}, title = {Bacillus anthracis, a story of nature subverted by man.}, journal = {Letters in applied microbiology}, volume = {41}, number = {3}, pages = {227-229}, doi = {10.1111/j.1472-765X.2005.01786.x}, pmid = {16108911}, issn = {0266-8254}, mesh = {Animals ; Anthrax/*drug therapy/*microbiology/prevention &amp; control ; Anthrax Vaccines/therapeutic use ; Bacillus anthracis/*genetics/*pathogenicity ; *Gene Transfer, Horizontal ; Humans ; }, abstract = {Bacillus anthracis is a pathogen of animals which rarely infects humans. Its use as a bioweapon has stimulated efforts to develop genetic typing methods and therapeutics to respond to an attack. Of particular concern is the transfer of virulence genes from B. anthracis to other closely related strains of bacillus.}, }
@article {pmid16106042, year = {2005}, author = {Makarova, KS and Wolf, YI and Mekhedov, SL and Mirkin, BG and Koonin, EV}, title = {Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell.}, journal = {Nucleic acids research}, volume = {33}, number = {14}, pages = {4626-4638}, pmid = {16106042}, issn = {1362-4962}, support = {//Intramural NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Eukaryotic Cells/*physiology ; *Evolution, Molecular ; *Gene Duplication ; Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; Genomics ; Molecular Sequence Data ; Phylogeny ; Proteins/*genetics ; Sequence Alignment ; }, abstract = {Gene duplication is a crucial mechanism of evolutionary innovation. A substantial fraction of eukaryotic genomes consists of paralogous gene families. We assess the extent of ancestral paralogy, which dates back to the last common ancestor of all eukaryotes, and examine the origins of the ancestral paralogs and their potential roles in the emergence of the eukaryotic cell complexity. A parsimonious reconstruction of ancestral gene repertoires shows that 4137 orthologous gene sets in the last eukaryotic common ancestor (LECA) map back to 2150 orthologous sets in the hypothetical first eukaryotic common ancestor (FECA) [paralogy quotient (PQ) of 1.92]. Analogous reconstructions show significantly lower levels of paralogy in prokaryotes, 1.19 for archaea and 1.25 for bacteria. The only functional class of eukaryotic proteins with a significant excess of paralogous clusters over the mean includes molecular chaperones and proteins with related functions. Almost all genes in this category underwent multiple duplications during early eukaryotic evolution. In structural terms, the most prominent sets of paralogs are superstructure-forming proteins with repetitive domains, such as WD-40 and TPR. In addition to the true ancestral paralogs which evolved via duplication at the onset of eukaryotic evolution, numerous pseudoparalogs were detected, i.e. homologous genes that apparently were acquired by early eukaryotes via different routes, including horizontal gene transfer (HGT) from diverse bacteria. The results of this study demonstrate a major increase in the level of gene paralogy as a hallmark of the early evolution of eukaryotes.}, }
@article {pmid16105942, year = {2005}, author = {Auchtung, JM and Lee, CA and Monson, RE and Lehman, AP and Grossman, AD}, title = {Regulation of a Bacillus subtilis mobile genetic element by intercellular signaling and the global DNA damage response.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {102}, number = {35}, pages = {12554-12559}, pmid = {16105942}, issn = {0027-8424}, support = {R01 GM050895/GM/NIGMS NIH HHS/United States ; GM50895/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacillus/genetics ; Bacillus subtilis/*genetics ; Bacterial Proteins/genetics ; Conjugation, Genetic ; DNA Damage ; DNA, Bacterial/genetics ; Genes, Bacterial ; Intercellular Signaling Peptides and Proteins/genetics ; *Interspersed Repetitive Sequences ; Listeria/genetics ; Oligonucleotide Array Sequence Analysis ; SOS Response, Genetics ; }, abstract = {Horizontal gene transfer contributes to the evolution of bacterial species. Mobile genetic elements play an important role in horizontal gene transfer, and characterization of the regulation of these elements should provide insight into conditions that influence bacterial evolution. We characterized a mobile genetic element, ICEBs1, in the Gram-positive bacterium Bacillus subtilis and found that it is a functional integrative and conjugative element (ICE) capable of transferring to Bacillus and Listeria species. We identified two conditions that promote ICEBs1 transfer: conditions that induce the global DNA damage response and crowding by potential recipients that lack ICEBs1. Transfer of ICEBs1 into cells that already contain the element is inhibited by an intercellular signaling peptide encoded by ICEBs1. The dual regulation of ICEBs1 allows for passive propagation in the host cell until either the potential mating partners lacking ICEBs1 are present or the host cell is in distress.}, }
@article {pmid16104856, year = {2005}, author = {Böltner, D and Moreno-Morillas, S and Ramos, JL}, title = {16S rDNA phylogeny and distribution of lin genes in novel hexachlorocyclohexane-degrading Sphingomonas strains.}, journal = {Environmental microbiology}, volume = {7}, number = {9}, pages = {1329-1338}, doi = {10.1111/j.1462-5822.2005.00820.x}, pmid = {16104856}, issn = {1462-2912}, mesh = {Bacterial Proteins/genetics ; Base Sequence ; Biodegradation, Environmental ; Cloning, Molecular ; DNA, Ribosomal/*genetics ; *Genes, Bacterial ; Hexachlorocyclohexane/*chemistry ; Molecular Sequence Data ; Phylogeny ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; Sequence Alignment ; Soil Microbiology ; Sphingomonas/*genetics/growth &amp; development/isolation &amp; purification ; }, abstract = {Hexachlorocyclohexane (HCH) is a highly recalcitrant pesticide that persists in soils. Three novel HCH-degrading strains (DS2, DS2-2 and DS3-1) were isolated after enrichment from HCH-contaminated soil from Germany. These strains efficiently degraded the alpha-, gamma- and delta-isomers of HCH, while strain DS3-1 also degraded beta-HCH. Based on 16S rDNA analysis, strain DS3-1 was closely related to Sphingomonas taejonensis, while strains DS2 and DS2-2 were closely related to Sphingomonas flava and seven HCH-degrading strains recently isolated from HCH-contaminated Spanish soil. Hence, geographic origin of the strains was not reflected in their phylogenetic affiliation. Subsequently, lin genes involved in HCH degradation, virtually identical to those from Sphingomonas paucimobilis strains UT26 from Japan and B90A from India, were identified in strains DS3-1, DS2, DS2-2 and five of the strains from Spain. The conserved lin gene sequences and structural organization, as well as the close association with IS6100, suggest a shared lin gene origin and recent horizontal gene transfer among phylogenetically diverged Sphingomonas strains in remote geographic locations. The loss of the ability to degrade gamma-HCH was associated with the deletion of the linA gene, probably due to recombination involving IS6100 elements, of which several copies are located in the lin cluster region.}, }
@article {pmid16102417, year = {2005}, author = {Daimon, T and Katsuma, S and Iwanaga, M and Kang, W and Shimada, T}, title = {The BmChi-h gene, a bacterial-type chitinase gene of Bombyx mori, encodes a functional exochitinase that plays a role in the chitin degradation during the molting process.}, journal = {Insect biochemistry and molecular biology}, volume = {35}, number = {10}, pages = {1112-1123}, doi = {10.1016/j.ibmb.2005.05.005}, pmid = {16102417}, issn = {0965-1748}, mesh = {Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Base Sequence ; Bombyx/enzymology/*genetics/growth &amp; development ; Chitin/*metabolism ; Chitinases/*genetics ; Conserved Sequence ; DNA Primers ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Molting/*physiology ; Mutagenesis, Site-Directed ; Polymerase Chain Reaction ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {The silkworm, Bombyx mori, has been recently demonstrated to contain a bacterial-type chitinase gene (BmChi-h) in addition to a well-characterized endochitinase gene (BmChitinase). The deduced amino acid sequence of BmChi-h showed extensive structural similarities with chitinases from bacteria such as Serratia marcescens chiA and baculoviruses (v-CHIA). Bacterial-type chitinase genes have not been found from any eukaryotes and viruses except for lepidopteran insects and lepidopteran baculoviruses. Thus, it was suggested that BmChi-h may be derived from a bacterial or baculovirus chitinase gene via horizontal gene transfer. In this report, we investigated the biological function of BmChi-h. Our enzymological study indicated that a chitinase encoded by BmChi-h has exo-type substrate preference, which is the same as S. marcescens chiA and v-CHIA, and different from BmChitinase, which has endo-type substrate preference. An immunohistochemical study revealed that BmChi-h localizes in the chitin-containing tissues during the molting stages, indicating that it plays a role in chitin degradation during molting. These results suggest that BmChi-h (exochitinase) and BmChitinase (endochitinase) may catalyze a native chitin by a concerted mechanism. Cloning and comparison of BmChi-h orthologues revealed that bacterial-type chitinase genes are highly conserved among lepidopteran insects, suggesting that the utilization of a bacterial-type chitinase during the molting process may be a general feature of lepidopteran insects.}, }
@article {pmid16099532, year = {2005}, author = {Mitreva, M and Blaxter, ML and Bird, DM and McCarter, JP}, title = {Comparative genomics of nematodes.}, journal = {Trends in genetics : TIG}, volume = {21}, number = {10}, pages = {573-581}, doi = {10.1016/j.tig.2005.08.003}, pmid = {16099532}, issn = {0168-9525}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Chromosome Aberrations ; Databases, Genetic ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; *Genetic Variation ; Genome/*genetics ; Genomics/methods/*trends ; Nematoda/*genetics ; *Phylogeny ; Species Specificity ; }, abstract = {Recent transcriptome and genome projects have dramatically expanded the biological data available across the phylum Nematoda. Here we summarize analyses of these sequences, which have revealed multiple unexpected results. Despite a uniform body plan, nematodes are more diverse at the molecular level than was previously recognized, with many species- and group-specific novel genes. In the genus Caenorhabditis, changes in chromosome arrangement, particularly local inversions, are also rapid, with breakpoints occurring at 50-fold the rate in vertebrates. Tylenchid plant parasitic nematode genomes contain several genes closely related to genes in bacteria, implicating horizontal gene transfer events in the origins of plant parasitism. Functional genomics techniques are also moving from Caenorhabditis elegans to application throughout the phylum. Soon, eight more draft nematode genome sequences will be available. This unique resource will underpin both molecular understanding of these most abundant metazoan organisms and aid in the examination of the dynamics of genome evolution in animals.}, }
@article {pmid16098811, year = {2005}, author = {Stanley, SL}, title = {The Entamoeba histolytica genome: something old, something new, something borrowed and sex too?.}, journal = {Trends in parasitology}, volume = {21}, number = {10}, pages = {451-453}, pmid = {16098811}, issn = {1471-4922}, support = {U54 AI057160-03/AI/NIAID NIH HHS/United States ; R01 AI030084-11/AI/NIAID NIH HHS/United States ; R01 AI030084-08/AI/NIAID NIH HHS/United States ; R01 AI030084/AI/NIAID NIH HHS/United States ; R01 AI051621-01/AI/NIAID NIH HHS/United States ; R01 AI051621-02/AI/NIAID NIH HHS/United States ; R01 AI030084-12/AI/NIAID NIH HHS/United States ; R01 AI051621/AI/NIAID NIH HHS/United States ; U54AI57160/AI/NIAID NIH HHS/United States ; U54 AI057160-02/AI/NIAID NIH HHS/United States ; R01 AI030084-10/AI/NIAID NIH HHS/United States ; R01 AI051621-03/AI/NIAID NIH HHS/United States ; R01 AI030084-13/AI/NIAID NIH HHS/United States ; U54 AI057160-01/AI/NIAID NIH HHS/United States ; AI30084/AI/NIAID NIH HHS/United States ; AI51621/AI/NIAID NIH HHS/United States ; U54 AI057160/AI/NIAID NIH HHS/United States ; R01 AI051621-04/AI/NIAID NIH HHS/United States ; R01 AI030084-09/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Entamoeba histolytica/*genetics ; Evolution, Molecular ; Genes, Protozoan ; *Genome, Protozoan ; }, abstract = {The recent publication of the protozoan parasite Entamoeba histolytica genome provides new insights into eukaryotic evolution, the role of lateral gene transfer in amebic biology and the adaptations required for eukaryotes that reside within the human intestine.}, }
@article {pmid16095742, year = {2005}, author = {Blaesing, F and Mühlenweg, A and Vierling, S and Ziegelin, G and Pelzer, S and Lanka, E}, title = {Introduction of DNA into Actinomycetes by bacterial conjugation from E. coli--an evaluation of various transfer systems.}, journal = {Journal of biotechnology}, volume = {120}, number = {2}, pages = {146-161}, doi = {10.1016/j.jbiotec.2005.06.023}, pmid = {16095742}, issn = {0168-1656}, mesh = {Actinobacteria/*genetics ; Base Sequence ; Biotechnology ; Cloning, Molecular ; Conjugation, Genetic ; DNA, Recombinant/genetics ; Escherichia coli/*genetics ; *Gene Transfer Techniques ; Genetic Vectors ; Plasmids/genetics ; Streptomyces/genetics ; }, abstract = {Gene transfer is a basic requirement for optimizing bioactive natural substances produced by an increasing number of industrially used microorganisms. We have analyzed quantitatively horizontal gene transfer from Escherichia coli to Actinomycetes. The efficiencies of DNA transfer of four different systems were compared that consist of conjugative and mobilizable plasmids with a broad-host range. Three novel binary vector set-ups were constructed based on: (i) the IncQ group of mobilizable plasmids (RSF1010), (ii) IncQ-like pTF-FC2 and (iii) pSB102 that belongs to a new class of broad-host-range plasmids. The established system based on the IncPalpha group of conjugative plasmids served as the reference. For all plasmids constructed, we confirmed the functional integrity of the selected transfer machineries by intrageneric matings between E. coli strains. We demonstrate that the transfer systems introduced in this study are efficient in mediating gene transfer from E. coli to Actinomycetes and are possible alternatives for gene transfer into Actinomycetes for which the IncPalpha-based transfer system is not applicable. The use of plasmids that integrate into the recipients' chromosomes compared to that of plasmids replicating autonomously is shown to allow the access to a wider range of hosts.}, }
@article {pmid16093570, year = {2005}, author = {Oborník, M and Green, BR}, title = {Mosaic origin of the heme biosynthesis pathway in photosynthetic eukaryotes.}, journal = {Molecular biology and evolution}, volume = {22}, number = {12}, pages = {2343-2353}, doi = {10.1093/molbev/msi230}, pmid = {16093570}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Chlorophyta/genetics/metabolism ; Diatoms/genetics/metabolism ; Eukaryotic Cells/metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Heme/*biosynthesis/genetics ; Models, Genetic ; Photosynthesis/*genetics ; *Phylogeny ; Plastids ; Rhodophyta/genetics/metabolism ; Symbiosis ; }, abstract = {Heme biosynthesis represents one of the most essential metabolic pathways in living organisms, providing the precursors for cytochrome prosthetic groups, photosynthetic pigments, and vitamin B(12). Using genomic data, we have compared the heme pathway in the diatom Thalassiosira pseudonana and the red alga Cyanidioschyzon merolae to those of green algae and higher plants, as well as to those of heterotrophic eukaryotes (fungi, apicomplexans, and animals). Phylogenetic analyses showed the mosaic character of this pathway in photosynthetic eukaryotes. Although most of the algal and plant enzymes showed the expected plastid (cyanobacterial) origin, at least one of them (porphobilinogen deaminase) appears to have a mitochondrial (alpha-proteobacterial) origin. Another enzyme, glutamyl-tRNA synthase, obviously originated in the eukaryotic nucleus. Because all the plastid-targeted sequences consistently form a well-supported cluster, this suggests that genes were either transferred from the primary endosymbiont (cyanobacteria) to the primary host nucleus shortly after the primary endosymbiotic event or replaced with genes from other sources at an equally early time, i.e., before the formation of three primary plastid lineages. The one striking exception to this pattern is ferrochelatase, the enzyme catalyzing the first committed step to heme and bilin pigments. In this case, two red algal sequences do not cluster either with the other plastid sequences or with cyanobacterial sequences and appear to have a proteobacterial origin like that of the apicomplexan parasites Plasmodium and Toxoplasma. Although the heterokonts also acquired their plastid via secondary endosymbiosis from a red alga, the diatom has a typical plastid-cyanobacterial ferrochelatase. We have not found any remnants of the plastidlike heme pathway in the nonphotosynthetic heterokonts Phytophthora ramorum and Phytophthora sojae.}, }
@article {pmid16088826, year = {2005}, author = {Sumby, P and Porcella, SF and Madrigal, AG and Barbian, KD and Virtaneva, K and Ricklefs, SM and Sturdevant, DE and Graham, MR and Vuopio-Varkila, J and Hoe, NP and Musser, JM}, title = {Evolutionary origin and emergence of a highly successful clone of serotype M1 group a Streptococcus involved multiple horizontal gene transfer events.}, journal = {The Journal of infectious diseases}, volume = {192}, number = {5}, pages = {771-782}, doi = {10.1086/432514}, pmid = {16088826}, issn = {0022-1899}, support = {U01-060595//PHS HHS/United States ; }, mesh = {Antigens, Bacterial/genetics ; Bacterial Outer Membrane Proteins/genetics ; Bacterial Proteins/genetics/metabolism ; Base Sequence ; Carrier Proteins/genetics ; Clone Cells ; DNA, Bacterial/chemistry/genetics ; Gene Transfer, Horizontal/*genetics ; *Genome, Bacterial ; Humans ; Molecular Sequence Data ; NAD+ Nucleosidase/genetics/metabolism ; Nucleic Acid Hybridization ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Sequence Analysis, DNA ; Streptococcal Infections/genetics/*microbiology ; Streptococcus pyogenes/enzymology/*genetics ; Streptolysins/genetics/metabolism ; }, abstract = {To better understand the molecular events involved in the origin of new pathogenic bacteria, we studied the evolution of a highly virulent clone of serotype M1 group A Streptococcus (GAS). Genomic, DNA-DNA microarray, and single-nucleotide polymorphism analyses indicated that this clone evolved through a series of horizontal gene transfer events that involved (1) the acquisition of prophages encoding streptococcal pyrogenic exotoxin A and extracellular DNases and (2) the reciprocal recombination of a 36-kb chromosomal region encoding the extracellular toxins NAD+-glycohydrolase (NADase) and streptolysin O (SLO). These gene transfer events were associated with significantly increased production of SLO and NADase. Virtual identity in the 36-kb region present in contemporary serotype M1 and M12 isolates suggests that a serotype M12 strain served as the donor of this region. Multiple horizontal gene transfer events were a crucial factor in the evolutionary origin and emergence of a very abundant contemporary clone of serotype M1 GAS.}, }
@article {pmid16086848, year = {2005}, author = {Romero, H and Zhang, Y and Gladyshev, VN and Salinas, G}, title = {Evolution of selenium utilization traits.}, journal = {Genome biology}, volume = {6}, number = {8}, pages = {R66}, pmid = {16086848}, issn = {1474-760X}, support = {R01 GM061603/GM/NIGMS NIH HHS/United States ; R03 TW006959/TW/FIC NIH HHS/United States ; GM061603/GM/NIGMS NIH HHS/United States ; TW006959/TW/FIC NIH HHS/United States ; }, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Archaeal/genetics ; Genome, Bacterial/genetics ; Organoselenium Compounds ; Phylogeny ; Selenium/*metabolism ; Uridine/analogs &amp; derivatives/biosynthesis ; }, abstract = {BACKGROUND: The essential trace element selenium is used in a wide variety of biological processes. Selenocysteine (Sec), the 21st amino acid, is co-translationally incorporated into a restricted set of proteins. It is encoded by an UGA codon with the help of tRNASec (SelC), Sec-specific elongation factor (SelB) and a cis-acting mRNA structure (SECIS element). In addition, Sec synthase (SelA) and selenophosphate synthetase (SelD) are involved in the biosynthesis of Sec on the tRNASec. Selenium is also found in the form of 2-selenouridine, a modified base present in the wobble position of certain tRNAs, whose synthesis is catalyzed by YbbB using selenophosphate as a precursor.<br><br>RESULTS: We analyzed completely sequenced genomes for occurrence of the selA, B, C, D and ybbB genes. We found that selB and selC are gene signatures for the Sec-decoding trait. However, selD is also present in organisms that do not utilize Sec, and shows association with either selA, B, C and/or ybbB. Thus, selD defines the overall selenium utilization. A global species map of Sec-decoding and 2-selenouridine synthesis traits is provided based on the presence/absence pattern of selenium-utilization genes. The phylogenies of these genes were inferred and compared to organismal phylogenies, which identified horizontal gene transfer (HGT) events involving both traits.<br><br>CONCLUSION: These results provide evidence for the ancient origin of these traits, their independent maintenance, and a highly dynamic evolutionary process that can be explained as the result of speciation, differential gene loss and HGT. The latter demonstrated that the loss of these traits is not irreversible as previously thought.}, }
@article {pmid16085899, year = {2005}, author = {Wang, Y and Wang, GR and Shoemaker, NB and Whitehead, TR and Salyers, AA}, title = {Distribution of the ermG gene among bacterial isolates from porcine intestinal contents.}, journal = {Applied and environmental microbiology}, volume = {71}, number = {8}, pages = {4930-4934}, pmid = {16085899}, issn = {0099-2240}, support = {R01 AI022383/AI/NIAID NIH HHS/United States ; R56 AI022383/AI/NIAID NIH HHS/United States ; AI/GM 22383/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/*genetics ; Clostridium/drug effects/genetics/isolation &amp; purification ; Conjugation, Genetic ; DNA Transposable Elements ; Drug Resistance, Bacterial/genetics ; Erythromycin/*pharmacology ; Gastrointestinal Contents/*microbiology ; Gene Transfer, Horizontal ; Gram-Positive Bacteria/*drug effects/genetics/isolation &amp; purification ; Molecular Sequence Data ; Staphylococcus/drug effects/genetics/isolation &amp; purification ; Swine/*microbiology ; Tetracycline/pharmacology ; Tetracycline Resistance/genetics ; }, abstract = {The ermG gene was first found in the soil bacterium Bacillus sphaericus. More recently, it was found in several human intestinal Bacteroides species. We report here the first finding of ermG genes in gram-positive bacteria isolated from porcine feces and from under-barn manure pits used to store porcine wastes. The porcine ermG sequences were identical to the sequence of the B. sphaericus ermG gene except that six of the seven ermG-containing strains contained an insertion sequence element insertion in the C-terminal end of the gene. The porcine ermG genes were found in three different gram-positive genera, an indication that it is possible that the gene is being spread by horizontal gene transfer. A segment of a Bacteroides conjugative transposon that carries an ermG gene cross-hybridized with DNA from six of the seven porcine isolates, but the restriction patterns in the porcine strains were different from that of the Bacteroides conjugative transposon.}, }
@article {pmid16085810, year = {2005}, author = {Klieve, AV and Yokoyama, MT and Forster, RJ and Ouwerkerk, D and Bain, PA and Mawhinney, EL}, title = {Naturally occurring DNA transfer system associated with membrane vesicles in cellulolytic Ruminococcus spp. of ruminal origin.}, journal = {Applied and environmental microbiology}, volume = {71}, number = {8}, pages = {4248-4253}, pmid = {16085810}, issn = {0099-2240}, mesh = {Animals ; Cell Membrane/*ultrastructure ; Cellulose/*metabolism ; DNA/genetics/metabolism ; DNA Restriction Enzymes ; DNA, Bacterial/*genetics/metabolism ; *Gene Transfer, Horizontal ; Microscopy, Electron ; Rumen/microbiology ; Ruminococcus/*genetics/isolation &amp; purification/metabolism/ultrastructure ; *Transformation, Genetic ; Transport Vesicles/genetics ; }, abstract = {A genetic transformation system with similarities to those reported for gram-negative bacteria was found to be associated with membrane vesicles of the ruminal cellulolytic genus Ruminococcus. Double-stranded DNA was recovered from the subcellular particulate fraction of all the cellulolytic ruminococci examined. Electron microscopy revealed that the only particles present resembled membrane vesicles. The likelihood that the DNA was associated with membrane vesicles (also known to contain cellulosomes) was further supported by the adherence of the particles associated with the subcellular DNA to cellulose powder added to culture filtrates. The particle-associated DNA comprised a population of linear molecules ranging in size from <20 kb to 49 kb (Ruminococcus sp. strain YE73) and from 23 kb to 90 kb (Ruminococcus albus AR67). Particle-associated DNA from R. albus AR67 represented DNA derived from genomic DNA of the host bacterium having an almost identical HindIII digestion pattern and an identical 16S rRNA gene. Paradoxically, particle-associated DNA was refractory to digestion with EcoRI, while the genomic DNA was susceptible to extensive digestion, suggesting that there is differential restriction modification of genomic DNA and DNA exported from the cell. Transformation using the vesicle-containing fraction of culture supernatant of Ruminococcus sp. strain YE71 was able to restore the ability to degrade crystalline cellulose to two mutants that were otherwise unable to do so. The ability was heritable and transferred to subsequent generations. It appears that membrane-associated transformation plays a role in lateral gene transfer in complex microbial ecosystems, such as the rumen.}, }
@article {pmid16081873, year = {2005}, author = {Paterson, DJ}, title = {Targeting arterial chemoreceptor over-activity in heart failure with a gas.}, journal = {Circulation research}, volume = {97}, number = {3}, pages = {201-203}, doi = {10.1161/01.RES.0000177931.10616.cb}, pmid = {16081873}, issn = {1524-4571}, mesh = {Animals ; Carotid Body/enzymology/*physiology ; Chemoreceptor Cells/*physiology ; Cyclic GMP/physiology ; *Gene Transfer, Horizontal ; Heart Failure/*physiopathology ; Nerve Tissue Proteins/*genetics/physiology ; Nitric Oxide/physiology ; Nitric Oxide Synthase/*genetics/physiology ; Nitric Oxide Synthase Type I ; Rabbits ; }, }
@article {pmid16081870, year = {2005}, author = {Lipskaia, L and del Monte, F and Capiod, T and Yacoubi, S and Hadri, L and Hours, M and Hajjar, RJ and Lompré, AM}, title = {Sarco/endoplasmic reticulum Ca2+-ATPase gene transfer reduces vascular smooth muscle cell proliferation and neointima formation in the rat.}, journal = {Circulation research}, volume = {97}, number = {5}, pages = {488-495}, doi = {10.1161/01.RES.0000180663.42594.aa}, pmid = {16081870}, issn = {1524-4571}, support = {HL 071763/HL/NHLBI NIH HHS/United States ; HL-057623/HL/NHLBI NIH HHS/United States ; }, mesh = {Adenosine Triphosphate/pharmacology ; Animals ; Apoptosis ; Calcineurin Inhibitors ; Calcium/metabolism ; Calcium-Calmodulin-Dependent Protein Kinase Type 2 ; Calcium-Calmodulin-Dependent Protein Kinases/metabolism ; Calcium-Transporting ATPases/genetics/*physiology ; Carotid Artery Diseases/prevention &amp; control ; Cell Proliferation ; Cells, Cultured ; DNA-Binding Proteins/metabolism ; Gene Transfer, Horizontal ; Genetic Therapy ; Male ; Muscle, Smooth, Vascular/*cytology ; NFATC Transcription Factors ; Nuclear Proteins/metabolism ; Phosphorylation ; Rats ; Rats, Sprague-Dawley ; Sarcoplasmic Reticulum Calcium-Transporting ATPases ; Transcription Factors/metabolism ; Tunica Intima/*pathology ; }, abstract = {Proliferation of vascular smooth muscle cells (VSMC) is a primary cause of vascular disorders and is associated with major alterations in Ca2+ handling supported by loss of the sarco/endoplasmic reticulum calcium ATPase, SERCA2a. To determine the importance of SERCA2a in neointima formation, we have prevented loss of its expression by adenoviral gene transfer in a model of balloon injury of the rat carotid artery. Two weeks after injury, the intima/media ratio was significantly lower in SERCA2a-infected than in injured noninfected or injured beta-galactosidase-infected carotids (0.29+/-0.04 versus 0.89+/-0.19 and 0.72+/-0.14, respectively; P<0.05), and was comparable to that observed in control carotids (0.21+/-0.03). The pathways leading to proliferation were analyzed in serum-stimulated VSMC. Forced expression of SERCA2a arrested cell cycle at the G1 phase and prevented apoptosis. SERCA2a inhibits proliferation through inactivation of calcineurin (PP2B) and its target transcription factor NFAT (nuclear factor of activated T-cells) resulting in lowering of cyclin D1 and pRb levels. By using NFAT-competing peptide VIVIT, we showed that NFAT activity is strongly required to promote VSMC proliferation. In conclusion, we provide the first evidence that increasing SERCA2a activity inhibits VSMC proliferation and balloon injury-induced neointima formation.}, }
@article {pmid16079343, year = {2005}, author = {Griffiths, E and Petrich, AK and Gupta, RS}, title = {Conserved indels in essential proteins that are distinctive characteristics of Chlamydiales and provide novel means for their identification.}, journal = {Microbiology (Reading, England)}, volume = {151}, number = {Pt 8}, pages = {2647-2657}, doi = {10.1099/mic.0.28057-0}, pmid = {16079343}, issn = {1350-0872}, mesh = {Chlamydiales/classification/genetics/*isolation &amp; purification ; *Conserved Sequence ; DNA, Bacterial/analysis ; Gene Deletion ; Gene Transfer, Horizontal ; Genome, Bacterial ; Molecular Sequence Data ; RNA, Ribosomal, 16S/analysis/genetics ; }, abstract = {All known chlamydiae are either proven human or animal pathogens or possess such potential. Due to increasing reports of chlamydiae diversity in the environment, it is important to develop reliable means for identifying and characterizing Chlamydiales species. The identification of environmental chlamydiae at present relies on their branching pattern in 16S rRNA trees, as well as 16S/23S consensus motifs which display variability. At present, no reliable molecular signatures are known which are unique to all Chlamydiales species. Besides the rRNAs, sequence information for different Chlamydiales is not available for any other gene sequence. In this report, a number of molecular signatures are described that consist of conserved inserts and deletions (indels), in widely distributed proteins [RNA polymerase alpha subunit (RpoA), elongation factor (EF)-Tu, EF-P, DNA gyrase B subunit (GyrB) and lysyl-tRNA synthetase (LysRS)], that are distinctive characteristics of all available chlamydiae homologues (from Chlamydiaeceae species and Parachlamydiae sp. UWE25) and not found in any other bacteria. Using PCR primers for highly conserved regions in these proteins, the corresponding fragments of these genes from Simkania negevensis, Waddlia chondrophila, and in a number of cases for Neochlamydia hartmanellae, covering all families within the phylum Chlamydiae, have been cloned and sequenced. The shared presence of the identified signatures in these species provides strong evidence that these molecular signatures are distinctive characteristics of the entire order Chlamydiales and can be used to reliably determine the presence of chlamydiae or chlamydia-related organisms in environmental samples. The sequence information for these protein fragments was also used to determine the interrelationships among chlamydiae species. In a phylogenetic tree based on a combined dataset of sequences from RpoA, EF-Tu, EF-P and GyrB, the environmental chlamydiae (i.e. Simkania, Waddlia and Parachlamydia) and the traditional Chlamydiaceae (i.e. Chlamydophila and Chlamydia) formed two distinct clades. Similar relationships were also observed in individual protein phylogenies, as well as in a 16S rRNA tree for the same species. These results provide evidence that the divergence between the traditional Chlamydiaceae species and the other chlamydiae families occurred very early in the evolution of this group of bacteria.}, }
@article {pmid16079338, year = {2005}, author = {Sielaff, B and Andreesen, JR}, title = {Analysis of the nearly identical morpholine monooxygenase-encoding mor genes from different Mycobacterium strains and characterization of the specific NADH : ferredoxin oxidoreductase of this cytochrome P450 system.}, journal = {Microbiology (Reading, England)}, volume = {151}, number = {Pt 8}, pages = {2593-2603}, doi = {10.1099/mic.0.28039-0}, pmid = {16079338}, issn = {1350-0872}, mesh = {Cytochrome P-450 Enzyme System/genetics/isolation &amp; purification/*metabolism ; DNA, Bacterial/chemistry/isolation &amp; purification ; Ferredoxin-NADP Reductase/genetics/isolation &amp; purification/*metabolism ; Ferredoxins/metabolism ; Gene Expression ; Mixed Function Oxygenases/*genetics/metabolism ; Morpholines/*metabolism ; Mycobacterium/classification/*enzymology/genetics/metabolism ; Oxidoreductases/genetics ; }, abstract = {Cloning and sequencing of the morABC operon region revealed the genes encoding the three components of a cytochrome P450 monooxygenase, which is required for the degradation of the N-heterocycle morpholine by Mycobacterium sp. strain HE5. The cytochrome P450 (P450(mor)) and the Fe(3)S(4) ferredoxin (Fd(mor)), encoded by morA and morB, respectively, have been characterized previously, whereas no evidence has hitherto been obtained for a specifically morpholine-induced reductase, which would be required to support the activity of the P450(mor) system. Analysis of the mor operon has now revealed the gene morC, encoding the ferredoxin reductase of this morpholine monooxygenase. The genes morA, morB and morC were identical to the corresponding genes from Mycobacterium sp. strain RP1. Almost identical mor genes in Mycobacterium chlorophenolicum PCP-1, in addition to an inducible cytochrome P450, pointing to horizontal gene transfer, were now identified. No evidence for a circular or linear plasmid was found in Mycobacterium sp. strain HE5. Analysis of the downstream sequences of morC revealed differences in this gene region between Mycobacterium sp. strain HE5 and Mycobacterium sp. strain RP1 on the one hand, and M. chlorophenolicum on the other hand, indicating insertions or deletions after recombination. Downstream of the mor genes, the gene orf1', encoding a putative glutamine synthetase, was identified in all studied strains. The gene morC of Mycobacterium sp. strain HE5 was heterologously expressed. The purified recombinant protein FdR(mor) was characterized as a monomeric 44 kDa protein, being a strictly NADH-dependent, FAD-containing reductase. The K(m) values of FdR(mor) for the substrate NADH (37.7 +/- 4.1 microM) and the artificial electron acceptors potassium ferricyanide (14.2 +/- 1.1 microM) and cytochrome c (28.0 +/- 3.6 microM) were measured. FdR(mor) was shown to interact functionally with its natural redox partner, the Fe(3)S(4) protein Fd(mor), and with the Fe(2)S(2) protein adrenodoxin, albeit with a much lower efficiency, but not with spinach ferredoxin. In contrast, adrenodoxin reductase, the natural redox partner of adrenodoxin, could not use Fd(mor) in activity assays. These results indicated that FdR(mor) can utilize different ferredoxins, but that Fd(mor) requires the specific NADH : ferredoxin oxidoreductase FdR(mor) from the P450(mor) system for efficient catalytic function.}, }
@article {pmid16077904, year = {2005}, author = {Shi, SY and Cai, XH and Ding, DF}, title = {Identification and categorization of horizontally transferred genes in prokaryotic genomes.}, journal = {Acta biochimica et biophysica Sinica}, volume = {37}, number = {8}, pages = {561-566}, doi = {10.1111/j.1745-7270.2005.00075.x}, pmid = {16077904}, issn = {1672-9145}, mesh = {Bacterial Proteins/*genetics/*metabolism ; Chromosome Mapping/*methods ; *Evolution, Molecular ; Gene Expression Profiling/*methods ; Gene Expression Regulation/*genetics ; Gene Transfer, Horizontal/*genetics ; *Genome, Bacterial ; Sequence Analysis, DNA/methods ; Signal Transduction/genetics ; }, abstract = {Horizontal gene transfer (HGT), a process through which genomes acquire genetic materials from distantly related organisms, is believed to be one of the major forces in prokaryotic genome evolution. However, systematic investigation is still scarce to clarify two basic issues about HGT: (1) what types of genes are transferred; and (2) what influence HGT events over the organization and evolution of biological pathways. Genome-scale investigations of these two issues will advance the systematical understanding of HGT in the context of prokaryotic genome evolution. Having investigated 82 genomes, we constructed an HGT database across broad evolutionary timescales. We identified four function categories containing a high proportion of horizontally transferred genes: cell envelope, energy metabolism, regulatory functions, and transport/binding proteins. Such biased function distribution indicates that HGT is not completely random; instead, it is under high selective pressure, required by function restraints in organisms. Furthermore, we mapped the transferred genes onto the connectivity structure map of organism-specific pathways listed in Kyoto Encyclopedia of Genes and Genomes (KEGG). Our results suggest that recruitment of transferred genes into pathways is also selectively constrained because of the tuned interaction between original pathway members. Pathway organization structures still conserve well through evolution even with the recruitment of horizontally transferred genes. Interestingly, in pathways whose organization were significantly affected by HGT events, the operon-like arrangement of transferred genes was found to be prevalent. Such results suggest that operon plays an essential and directional role in the integration of alien genes into pathways.}, }
@article {pmid16077101, year = {2005}, author = {Vasconcelos, AT and Ferreira, HB and Bizarro, CV and Bonatto, SL and Carvalho, MO and Pinto, PM and Almeida, DF and Almeida, LG and Almeida, R and Alves-Filho, L and Assunção, EN and Azevedo, VA and Bogo, MR and Brigido, MM and Brocchi, M and Burity, HA and Camargo, AA and Camargo, SS and Carepo, MS and Carraro, DM and de Mattos Cascardo, JC and Castro, LA and Cavalcanti, G and Chemale, G and Collevatti, RG and Cunha, CW and Dallagiovanna, B and Dambrós, BP and Dellagostin, OA and Falcão, C and Fantinatti-Garboggini, F and Felipe, MS and Fiorentin, L and Franco, GR and Freitas, NS and Frías, D and Grangeiro, TB and Grisard, EC and Guimarães, CT and Hungria, M and Jardim, SN and Krieger, MA and Laurino, JP and Lima, LF and Lopes, MI and Loreto, EL and Madeira, HM and Manfio, GP and Maranhão, AQ and Martinkovics, CT and Medeiros, SR and Moreira, MA and Neiva, M and Ramalho-Neto, CE and Nicolás, MF and Oliveira, SC and Paixão, RF and Pedrosa, FO and Pena, SD and Pereira, M and Pereira-Ferrari, L and Piffer, I and Pinto, LS and Potrich, DP and Salim, AC and Santos, FR and Schmitt, R and Schneider, MP and Schrank, A and Schrank, IS and Schuck, AF and Seuanez, HN and Silva, DW and Silva, R and Silva, SC and Soares, CM and Souza, KR and Souza, RC and Staats, CC and Steffens, MB and Teixeira, SM and Urmenyi, TP and Vainstein, MH and Zuccherato, LW and Simpson, AJ and Zaha, A}, title = {Swine and poultry pathogens: the complete genome sequences of two strains of Mycoplasma hyopneumoniae and a strain of Mycoplasma synoviae.}, journal = {Journal of bacteriology}, volume = {187}, number = {16}, pages = {5568-5577}, pmid = {16077101}, issn = {0021-9193}, mesh = {Animals ; Evolution, Molecular ; Gene Rearrangement ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomics ; Molecular Sequence Data ; Mycoplasma Infections/*microbiology ; Mycoplasma hyopneumoniae/*genetics ; Mycoplasma synoviae/*genetics ; Phylogeny ; Pneumonia of Swine, Mycoplasmal/*microbiology ; Poultry ; Poultry Diseases/*microbiology ; Swine ; }, abstract = {This work reports the results of analyses of three complete mycoplasma genomes, a pathogenic (7448) and a nonpathogenic (J) strain of the swine pathogen Mycoplasma hyopneumoniae and a strain of the avian pathogen Mycoplasma synoviae; the genome sizes of the three strains were 920,079 bp, 897,405 bp, and 799,476 bp, respectively. These genomes were compared with other sequenced mycoplasma genomes reported in the literature to examine several aspects of mycoplasma evolution. Strain-specific regions, including integrative and conjugal elements, and genome rearrangements and alterations in adhesin sequences were observed in the M. hyopneumoniae strains, and all of these were potentially related to pathogenicity. Genomic comparisons revealed that reduction in genome size implied loss of redundant metabolic pathways, with maintenance of alternative routes in different species. Horizontal gene transfer was consistently observed between M. synoviae and Mycoplasma gallisepticum. Our analyses indicated a likely transfer event of hemagglutinin-coding DNA sequences from M. gallisepticum to M. synoviae.}, }
@article {pmid16077098, year = {2005}, author = {Nightingale, KK and Windham, K and Wiedmann, M}, title = {Evolution and molecular phylogeny of Listeria monocytogenes isolated from human and animal listeriosis cases and foods.}, journal = {Journal of bacteriology}, volume = {187}, number = {16}, pages = {5537-5551}, pmid = {16077098}, issn = {0021-9193}, support = {R01 GM063259/GM/NIGMS NIH HHS/United States ; R01GM63259/GM/NIGMS NIH HHS/United States ; }, mesh = {Animal Feed/*microbiology ; Animals ; Bacterial Proteins/genetics ; *Evolution, Molecular ; *Food Microbiology ; Gene Transfer, Horizontal ; Genetic Variation ; Humans ; Listeria monocytogenes/classification/*genetics/isolation &amp; purification ; *Phylogeny ; }, abstract = {To probe the evolution and phylogeny of Listeria monocytogenes from defined host species and environments, L. monocytogenes isolates from human (n = 60) and animal (n = 30) listeriosis cases and food samples (n = 30) were randomly selected from a larger collection of isolates (n = 354) obtained in New York State between 1999 and 2001. Partial sequencing of four housekeeping genes (gap, prs, purM, and ribC), one stress response gene (sigB), and two virulence genes (actA and inlA) revealed between 11 (gap) and 33 (inlA) allelic types as well as 52 sequence types (unique combination of allelic types). actA, ribC, and purM demonstrated the highest levels of nucleotide diversity (pi > 0.05). actA and inlA as well as prs and the hypervariable housekeeping genes ribC and purM showed evidence of horizontal gene transfer and recombination. actA and inlA also showed evidence of positive selection at specific amino acid sites. Maximum likelihood phylogenies for all seven genes confirmed that L. monocytogenes contains two deeply separated evolutionary lineages. Lineage I was found to be highly clonal, while lineage II showed greater diversity and evidence of horizontal gene transfer. Allelic types were exclusive to lineages, except for a single gap allele, and nucleotide distance within lineages was much lower than that between lineages, suggesting that genetic exchange between lineages is rare. Our data show that (i) L. monocytogenes is a highly diverse species with at least two distinct phylogenetic lineages differing in their evolutionary history and population structure and (ii) horizontal gene transfer as well as positive selection contributed to the evolution of L. monocytogenes.}, }
@article {pmid16061481, year = {2005}, author = {Rishavy, MA and Hallgren, KW and Yakubenko, AV and Zuerner, RL and Runge, KW and Berkner, KL}, title = {The vitamin K-dependent carboxylase has been acquired by Leptospira pathogens and shows altered activity that suggests a role other than protein carboxylation.}, journal = {The Journal of biological chemistry}, volume = {280}, number = {41}, pages = {34870-34877}, doi = {10.1074/jbc.M504345200}, pmid = {16061481}, issn = {0021-9258}, support = {R01 AG019960/AG/NIA NIH HHS/United States ; R01 GM050752/GM/NIGMS NIH HHS/United States ; R01 HL055666-08/HL/NHLBI NIH HHS/United States ; HL55666/HL/NHLBI NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Carbon/chemistry ; Carbon-Carbon Ligases/*chemistry ; Dose-Response Relationship, Drug ; Epitopes/chemistry ; Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; Leptospira/*metabolism ; Microsomes/metabolism ; Models, Chemical ; Molecular Sequence Data ; Open Reading Frames ; Oxidoreductases/chemistry ; Phylogeny ; Protein Structure, Tertiary ; Sequence Homology, Amino Acid ; Substrate Specificity ; Vitamin K/chemistry ; }, abstract = {Leptospirosis is an emerging infectious disease whose pathology includes a hemorrhagic response, and sequencing of the Leptospira interrogans genome revealed an ortholog of the vitamin K-dependent (VKD) carboxylase as one of several hemostatic proteins present in the bacterium. Until now, the VKD carboxylase was known to be present only in the animal kingdom (i.e. metazoans that include mammals, fish, snails, and insects), and this restricted distribution and high sequence similarity between metazoan and Leptospira orthologs strongly suggests that Leptospira acquired the VKD carboxylase by horizontal gene transfer. In metazoans, the VKD carboxylase is bifunctional, acting as an epoxidase that oxygenates vitamin K to a strong base and a carboxylase that uses the base to carboxylate Glu residues in VKD proteins, rendering them active in hemostasis and other physiologies. In contrast, the Leptospira ortholog showed epoxidase but not detectable carboxylase activity and divergence in a region of identity in all known metazoan VKD carboxylases that is important to Glu interaction. Furthermore, although the mammalian carboxylase is regulated so that vitamin K epoxidation does not occur unless Glu substrate is present, the Leptospira VKD epoxidase showed unfettered epoxidation in the absence of Glu substrate. Finally, human VKD protein orthologs were not detected in the L. interrogans genome. The combined data, then, suggest that Leptospira exapted the metazoan VKD carboxylase for some use other than VKD protein carboxylation, such as using the strong vitamin K base to drive a new reaction or to promote oxidative damage or depleting vitamin K to indirectly inhibit host VKD protein carboxylation.}, }
@article {pmid16053250, year = {2005}, author = {Hinnebusch, BJ}, title = {The evolution of flea-borne transmission in Yersinia pestis.}, journal = {Current issues in molecular biology}, volume = {7}, number = {2}, pages = {197-212}, pmid = {16053250}, issn = {1467-3037}, mesh = {Animals ; Biofilms ; *Biological Evolution ; Host-Parasite Interactions ; Insect Vectors/anatomy &amp; histology/*parasitology ; Plague/*transmission ; Rodentia/parasitology ; Selection, Genetic ; Siphonaptera/anatomy &amp; histology/*parasitology/physiology ; Virulence/genetics ; Yersinia pestis/*genetics/pathogenicity ; Yersinia pseudotuberculosis/genetics ; Yersinia pseudotuberculosis Infections/transmission ; }, abstract = {Transmission by fleabite is a recent evolutionary adaptation that distinguishes Yersinia pestis, the agent of plague, from Yersinia pseudotuberculosis and all other enteric bacteria. The very close genetic relationship between Y. pestis and Y. pseudotuberculosis indicates that just a few discrete genetic changes were sufficient to give rise to flea-borne transmission. Y. pestis exhibits a distinct infection phenotype in its flea vector, and a transmissible infection depends on genes that are specifically required in the flea, but not the mammal. Transmission factors identified to date suggest that the rapid evolutionary transition of Y. pestis to flea-borne transmission within the last 1,500 to 20,000 years involved at least three steps: acquisition of the two Y. pestis-specific plasmids by horizontal gene transfer; and recruitment of endogenous chromosomal genes for new functions. Perhaps reflective of the recent adaptation, transmission of Y. pestis by fleas is inefficient, and this likely imposed selective pressure favoring the evolution of increased virulence in this pathogen.}, }
@article {pmid16051888, year = {2005}, author = {Amano, H and Hackett, NR and Rafii, S and Crystal, RG}, title = {Thrombopoietin gene transfer-mediated enhancement of angiogenic responses to acute ischemia.}, journal = {Circulation research}, volume = {97}, number = {4}, pages = {337-345}, doi = {10.1161/01.RES.0000179534.17668.f8}, pmid = {16051888}, issn = {1524-4571}, support = {P01 HL59312/HL/NHLBI NIH HHS/United States ; }, mesh = {Acute Disease ; Adenoviridae/genetics ; Animals ; Blood Platelets/physiology ; Cell Differentiation ; Gene Transfer, Horizontal ; *Genetic Therapy ; Hindlimb/blood supply ; Ischemia/physiopathology/*therapy ; Megakaryocytes/cytology ; Mice ; Mice, Inbred C57BL ; *Neovascularization, Physiologic ; Platelet Count ; Platelet Endothelial Cell Adhesion Molecule-1/analysis ; Thrombopoietin/*genetics/physiology ; Vascular Endothelial Growth Factor A/physiology ; Vascular Endothelial Growth Factor Receptor-1/physiology ; }, abstract = {The development of new blood vessels is a complex process, likely requiring the synergy of multiple angiogenic mediators. This study focuses on the proximal angiogenic response using the platelet as a complex carrier of critical mediators of angiogenesis. Platelet levels are controlled by circulating levels of thrombopoietin (TPO) functioning to activate megakaryocyte differentiation and platelet release through the c-mpl receptor. We hypothesized that TPO gene transfer should enhance correction of experimental ischemia by providing increased levels of platelets and hence platelet-derived mediators of angiogenesis. To evaluate this hypothesis, we dissected the role of the TPO-c-mpl-megakaryocyte-platelet pathway in the angiogenic response using a model of acute hindlimb ischemia of wild-type, TPO(-/-), and c-mpl(-/-) mice. The data demonstrate that infusion of platelets will enhance the angiogenic response in wild-type mice and that the endogenous angiogenic response is blunted in TPO(-/-) and c-mpl(-/-) mice. Consistent with this observation, adenovirus (Ad)-mediated transfer of TPO (AdTPO) enhanced the correction of ischemia in wild-type and TPO(-/-), but not c-mpl(-/-), mice. Local versus systemic administration of AdTPO showed that the effect of TPO gene transfer was systemic, not local, and it could be replaced by gene transfer of VEGF, one of the many mediators of angiogenesis carried by the platelets, even in the absence of components in the TPO-c-mpl-megakaryocyte-platelet pathway.}, }
@article {pmid16049560, year = {2005}, author = {Seno, Y and Kariyama, R and Mitsuhata, R and Monden, K and Kumon, H}, title = {Clinical implications of biofilm formation by Enterococcus faecalis in the urinary tract.}, journal = {Acta medica Okayama}, volume = {59}, number = {3}, pages = {79-87}, doi = {10.18926/AMO/31979}, pmid = {16049560}, issn = {0386-300X}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Bacterial Proteins/genetics ; Biofilms/*growth &amp; development ; Child ; Child, Preschool ; Enterococcus faecalis/genetics/*growth &amp; development/pathogenicity ; Female ; Gelatinases/genetics ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Gram-Positive Bacterial Infections/*microbiology ; Hemolysin Proteins/genetics ; Humans ; Infant ; Infant, Newborn ; Male ; Membrane Proteins/genetics ; Middle Aged ; Retrospective Studies ; Urinary Tract Infections/*microbiology ; Virulence ; Virulence Factors/genetics ; }, abstract = {The potential relationships between biofilm formation and pathogenicity of Enterococcus faecalis in urinary tract infections (UTI) were investigated. Over a 12-year period from 1991 through 2002, a total of 352 E.faecalis isolates were collected from patients with complicated UTI (one isolate per patient) at the urology ward of Okayama University Hospital. We analyzed the prevalence and transferability of genes encoding virulence factors(asa1, esp, cylA, gelE /sprE)and antimicrobial resistance(aac(6') /aph(2'')). The production of biofilm, hemolysin and gelatinase by these isolates was also examined and the associated medical records of patients were retrospectively reviewed. Of 352 E. faecalis isolates, 315 possessed and/or genes. Of the 63 hemolysin- and 167 gelatinase-producing isolates, 59 and 94 isolates, respectively, possessed both asa1 and esp genes. E. faecalis isolates with both asa1 and esp genes formed biofilms at significantly higher rates than those with neither gene (P=0.038). The genes encoding asa1, cylA , and aac(6') /(aph(2'') were transferable and appeared to have accumulated in these isolates. The E. faecalis isolates possessing asa1 and/or esp genes were found from both catheter-related or -unrelated UTI. Our study indicates that E. faecalis isolates that have accumulated virulence genes are apt to form persistent biofilms in the urinary tracts.}, }
@article {pmid16049196, year = {2005}, author = {Huang, J and Xu, Y and Gogarten, JP}, title = {The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic.}, journal = {Molecular biology and evolution}, volume = {22}, number = {11}, pages = {2142-2146}, doi = {10.1093/molbev/msi221}, pmid = {16049196}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Animals ; Archaea/*genetics ; Bayes Theorem ; Databases, Nucleic Acid ; Fungi/*genetics ; Gene Transfer, Horizontal/*genetics ; Invertebrates/*genetics ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; Tyrosine-tRNA Ligase/*genetics ; }, abstract = {Lateral gene transfer plays an important role in the evolution of life. Events of ancient gene transfer can transmit genetic novelties to descendent lineages and subsequently shape their genetic systems. We here present the analyses of the gene encoding tyrosyl-tRNA synthetase (tyrRS), which reveal two eukaryotic tyrRS lineages, one including the opisthokonts and the other the remaining eukaryotes. The different origins of tyrRS lineages between the opisthokonts and the remaining eukaryotes indicate a likely case of ancient lateral gene transfer of tyrRS from an archaeon to the opisthokonts, which lends further support for the monophyly of the latter group. Ancient paralogy followed by differential gene loss is an alternative, albeit less parsimonious explanation for the distribution of the two eukaryotic tyrRS types. In either case, the presence of a haloarchaeal tyrRS type in the opisthokonts marks this group as monophyletic. This finding also points to the potential utility of ancient gene transfer events as molecular markers for major organismal lineages.}, }
@article {pmid16048999, year = {2005}, author = {Johnson, EF and Mukhopadhyay, B}, title = {A new type of sulfite reductase, a novel coenzyme F420-dependent enzyme, from the methanarchaeon Methanocaldococcus jannaschii.}, journal = {The Journal of biological chemistry}, volume = {280}, number = {46}, pages = {38776-38786}, doi = {10.1074/jbc.M503492200}, pmid = {16048999}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Catalysis ; Cytochromes/chemistry ; Electrons ; Electrophoresis, Polyacrylamide Gel ; Methane/chemistry ; Methanococcus/*metabolism ; Models, Biological ; Models, Chemical ; Molecular Sequence Data ; Oxidoreductases/chemistry ; Oxidoreductases Acting on Sulfur Group Donors/*chemistry/*physiology ; Peptides/chemistry ; Phylogeny ; Protein Binding ; Protein Structure, Tertiary ; Riboflavin/*analogs &amp; derivatives/chemistry ; Sequence Homology, Amino Acid ; Sulfides/chemistry ; Sulfites/chemistry ; Sulfur/chemistry ; Time Factors ; Ultraviolet Rays ; }, abstract = {Methanocaldococcus jannaschii is a hypertheromphilic, strictly hydrogenotrophic, methanogenic archaeon of ancient lineage isolated from a deep-sea hydrothermal vent. It requires sulfide for growth. Sulfite is inhibitory to the methanogens. Yet, we observed that M. jannaschii grows and produces methane with sulfite as the sole sulfur source. We found that in this organism sulfite induces a novel, highly active, coenzyme F(420)-dependent sulfite reductase (Fsr) with a cell extract specific activity of 0.57 mumol sulfite reduced min(-1) mg(-1) protein. The cellular level of Fsr protein is comparable to that of methyl-coenzyme M reductase, an enzyme essential for methanogenesis and a possible target for sulfite. Purified Fsr reduces sulfite to sulfide using reduced F(420) (H(2)F(420)) as the electron source (K(m): sulfite, 12 microm; H(2)F(420), 21 microm). Therefore, Fsr provides M. jannaschii an anabolic ability and protection from sulfite toxicity. The N-terminal half of the 70-kDa Fsr polypeptide represents a H(2)F(420) dehydrogenase and the C-terminal half a dissimilatory-type siroheme sulfite reductase, and Fsr catalyzes the corresponding partial reactions. Previously described sulfite reductases use nicotinamides and cytochromes as electron carriers. Therefore, this is the first report of a coenzyme F(420)-dependent sulfite reductase. Fsr homologs were found only in Methanopyrus kandleri and Methanothermobacter thermautotrophicus, two strictly hydrogenotrophic thermophilic methanogens. fsr is the likely ancestor of H(2)F(420) dehydrogenases, which serve as electron input units for membrane-based energy transduction systems of certain late evolving archaea, and dissimilatory sulfite reductases of bacteria and archaea. fsr could also have arisen from lateral gene transfer and gene fusion events.}, }
@article {pmid16046084, year = {2005}, author = {Gophna, U and Bapteste, E and Doolittle, WF and Biran, D and Ron, EZ}, title = {Evolutionary plasticity of methionine biosynthesis.}, journal = {Gene}, volume = {355}, number = {}, pages = {48-57}, doi = {10.1016/j.gene.2005.05.028}, pmid = {16046084}, issn = {0378-1119}, mesh = {Arabidopsis/enzymology/genetics/metabolism ; Archaea/enzymology/genetics/metabolism ; Bacteria/enzymology/genetics/metabolism ; *Evolution, Molecular ; Homocysteine/metabolism ; Homoserine/metabolism ; Methionine/*biosynthesis ; Methylation ; Models, Biological ; Saccharomyces/enzymology/genetics/metabolism ; Schizosaccharomyces/enzymology/genetics/metabolism ; }, abstract = {Methionine is an essential cellular constituent, the initiator of protein synthesis and a precursor in many metabolic activities, such as methylation and formylation. Here we investigate the genomic distribution of the methionine biosynthetic pathway and analyze its evolutionary history by reconstructing the phylogeny of its enzymatic components. We demonstrate the evolutionary complexity of methionine synthesis and describe the various mechanisms that have shaped this biosynthetic pathway: gene duplication, functional reassignment, lateral acquisition and gene loss. Lateral gene transfer within and between domains and gene recruitment have played an important role in the evolution of this pathway, especially in its first and third enzymatic steps--homoserine activation and homocysteine methylation. These analyses are also the basis of predictions regarding methionine synthesis in Archaea, where the pathway is yet to be characterized. This study illustrates how diverse molecular solutions can fulfill a conserved function in living beings.}, }
@article {pmid16045617, year = {2005}, author = {Antonenka, U and Nölting, C and Heesemann, J and Rakin, A}, title = {Horizontal transfer of Yersinia high-pathogenicity island by the conjugative RP4 attB target-presenting shuttle plasmid.}, journal = {Molecular microbiology}, volume = {57}, number = {3}, pages = {727-734}, doi = {10.1111/j.1365-2958.2005.04722.x}, pmid = {16045617}, issn = {0950-382X}, mesh = {*Conjugation, Genetic ; *Gene Transfer, Horizontal ; Genetic Vectors ; Genomic Islands/*genetics ; Phenols/metabolism ; Plasmids/*genetics ; *Recombination, Genetic ; Thiazoles/metabolism ; Yersinia enterocolitica/*genetics/growth &amp; development/metabolism ; Yersinia pseudotuberculosis/*genetics/growth &amp; development/metabolism ; }, abstract = {The high-pathogenicity island (HPI) encodes a highly efficient yersiniabactin system of iron acquisition responsible for mouse lethality in Yersinia. Although the HPI is widely disseminated among Enterobacteriaceae it lacks functions necessary for its replication and transmission. Therefore, the mechanism of its horizontal transfer and circulation is completely obscure. On the other hand, the HPI is a genetically active island in the bacterial cell. It encodes a functional recombinase and is able to transpose to new targets on the chromosome. Here we report on a possible mechanism of the HPI dissemination based on site-specific recombination of the excised HPI with the attB-presenting (asn tRNA gene) RP4 promiscuous conjugative shuttle plasmid. The resulting cointegrate can be transferred by conjugation to a new host, where it dissociates, and the released HPI integrates into any unoccupied asn tRNA gene target in the genome. This mechanism has been proven both with the 'mini' island carrying only the attP recognition site and genes coding for recombination enzymes and with the complete HPI labelled with an antibiotic resistance marker. After acquisition of the mobilized complete form of the HPI, the ability of the HPI-cured Yersinia enterocolitica WA-TH(-) strain to produce yersiniabactin has been restored. Such 'trapping' of pathogenicity islands and subsequent shuffling to new hosts by a conjugative replicon carrying a suitable attB site could be applied to other functional integrative elements and explain wide dissemination of PAIs.}, }
@article {pmid16041146, year = {2005}, author = {Nagaya, A and Takeyama, S and Tamegai, H}, title = {Identification of aminotransferase genes for biosynthesis of aminoglycoside antibiotics from soil DNA.}, journal = {Bioscience, biotechnology, and biochemistry}, volume = {69}, number = {7}, pages = {1389-1393}, doi = {10.1271/bbb.69.1389}, pmid = {16041146}, issn = {0916-8451}, mesh = {Amino Acid Sequence ; Aminoglycosides/*biosynthesis ; Anti-Bacterial Agents/*biosynthesis ; Cloning, Molecular ; DNA, Bacterial/chemistry/genetics/*isolation &amp; purification ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Soil/*analysis ; Transaminases/*genetics/metabolism ; }, abstract = {Aminoglycoside has been known as a clinically important antibiotic for a long time, but genetic information for the biosynthesis of aminoglycoside is still insufficient. In this study, we tried to clone aminoglycoside-biosynthetic genes from soil DNA for accumulation of genetic information. We chose the genes encoding L-glutamine:(2-deoxy-)scyllo-inosose aminotransferase as the target, because it is specific for all types of aminoglycoside biosynthesis. By degenerate PCR, we obtained 33 individual clones that were homologous with aminotransferase genes in aminoglycoside biosynthesis. Phylogenetic analysis and alignment of these genes showed that horizontal gene transfer has occurred in the soil. Among these, several quite interesting genes were obtained. Some genes probably originated from non-actinomycetes, and some were far from the known homologs. These genes can be useful markers for the isolation of entire gene clusters and originating organisms.}, }
@article {pmid16041013, year = {2005}, author = {Malott, RJ and Baldwin, A and Mahenthiralingam, E and Sokol, PA}, title = {Characterization of the cciIR quorum-sensing system in Burkholderia cenocepacia.}, journal = {Infection and immunity}, volume = {73}, number = {8}, pages = {4982-4992}, pmid = {16041013}, issn = {0019-9567}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Burkholderia/genetics/*metabolism ; Burkholderia cepacia complex/genetics/metabolism ; Evolution, Molecular ; Gene Expression Regulation, Bacterial/physiology ; Ligases/genetics/*metabolism ; Mutation ; Repressor Proteins/genetics/*metabolism ; Signal Transduction/physiology ; Trans-Activators/genetics/*metabolism ; Transcription, Genetic ; }, abstract = {Several transmissible Burkholderia cenocepacia strains that infect multiple cystic fibrosis patients contain a genomic island designated as the cenocepacia island (cci). The cci contains a predicted N-acylhomoserine lactone (AHL) synthase gene, cciI, and a predicted response regulator gene, cciR. AHL production profiles indicated that CciI catalyzes the synthesis of N-hexanoyl-l-homoserine lactone and minor amounts of N-octanoyl-l-homoserine lactone. The cciI and cciR genes were found to be cotranscribed by reverse transcription-PCR analysis, and the expression of a cciIR::luxCDABE fusion in a cciR mutant suggested that the cciIR system negatively regulates its own expression. B. cenocepacia strains also have a cepIR quorum-sensing system. Expression of cepI::luxCDABE or cepR::luxCDABE fusions in a cciR mutant showed that CciR negatively regulates cepI but does not regulate cepR. Expression of the cciIR::luxCDABE fusion in a cepR mutant indicated that functional CepR is required for cciIR expression. Phylogenetic analysis suggested that the cciIR system was acquired by horizontal gene transfer from a distantly related organism and subsequently incorporated into the ancestral cepIR regulatory network. Mutations in cciI, cciR, cepI cciI, and cepR cciR were constructed in B. cenocepacia K56-2. The cciI mutant had greater protease activity and less swarming motility than the parent strain. The cciR mutant had less protease activity than the parent strain. The phenotypes of the cepI cciI and cepR cciR mutants were similar to cepI or cepR mutants, with less protease activity and swarming motility than the parent strain.}, }
@article {pmid16040994, year = {2005}, author = {Mayr, UB and Haller, C and Haidinger, W and Atrasheuskaya, A and Bukin, E and Lubitz, W and Ignatyev, G}, title = {Bacterial ghosts as an oral vaccine: a single dose of Escherichia coli O157:H7 bacterial ghosts protects mice against lethal challenge.}, journal = {Infection and immunity}, volume = {73}, number = {8}, pages = {4810-4817}, pmid = {16040994}, issn = {0019-9567}, mesh = {Animals ; Cell Membrane/*immunology ; Cell Proliferation ; Colon/immunology ; Escherichia coli Infections/immunology/mortality/*prevention &amp; control ; Escherichia coli O157/*immunology/ultrastructure ; Immunoglobulin A/blood ; Immunoglobulin G/blood ; Interferon-gamma/metabolism ; Mice ; Spleen/immunology/metabolism ; Vaccines, Subunit/immunology ; }, abstract = {Enterohemorrhagic Escherichia coli (EHEC) is a bacterial pathogen that is associated with several life-threatening diseases for humans. The combination of protein E-mediated cell lysis to produce EHEC ghosts and staphylococcal nuclease A to degrade DNA was used for the development of an oral EHEC vaccine. The lack of genetic material in the oral EHEC bacterial-ghost vaccine abolished any hazard of horizontal gene transfer of resistance genes or pathogenic islands to resident gut flora. Intragastric immunization of mice with EHEC ghosts without the addition of any adjuvant induced cellular and humoral immunity. Immunized mice challenged at day 55 showed 86% protection against lethal challenge with a heterologous EHEC strain after single-dose oral immunization and 93.3% protection after one booster at day 28, whereas the controls showed 26.7% and 30% survival, respectively. These results indicate that it is possible to develop an efficacious single-dose oral EHEC bacterial-ghost vaccine.}, }
@article {pmid16033657, year = {2005}, author = {Yoon, SH and Hur, CG and Kang, HY and Kim, YH and Oh, TK and Kim, JF}, title = {A computational approach for identifying pathogenicity islands in prokaryotic genomes.}, journal = {BMC bioinformatics}, volume = {6}, number = {}, pages = {184}, pmid = {16033657}, issn = {1471-2105}, mesh = {Bacteria/*genetics ; Computational Biology/*methods ; Genome ; Genomic Islands/*genetics ; Prokaryotic Cells ; Virulence/*genetics ; }, abstract = {BACKGROUND: Pathogenicity islands (PAIs), distinct genomic segments of pathogens encoding virulence factors, represent a subgroup of genomic islands (GIs) that have been acquired by horizontal gene transfer event. Up to now, computational approaches for identifying PAIs have been focused on the detection of genomic regions which only differ from the rest of the genome in their base composition and codon usage. These approaches often lead to the identification of genomic islands, rather than PAIs.<br><br>RESULTS: We present a computational method for detecting potential PAIs in complete prokaryotic genomes by combining sequence similarities and abnormalities in genomic composition. We first collected 207 GenBank accessions containing either part or all of the reported PAI loci. In sequenced genomes, strips of PAI-homologs were defined based on the proximity of the homologs of genes in the same PAI accession. An algorithm reminiscent of sequence-assembly procedure was then devised to merge overlapping or adjacent genomic strips into a large genomic region. Among the defined genomic regions, PAI-like regions were identified by the presence of homolog(s) of virulence genes. Also, GIs were postulated by calculating G+C content anomalies and codon usage bias. Of 148 prokaryotic genomes examined, 23 pathogenic and 6 non-pathogenic bacteria contained 77 candidate PAIs that partly or entirely overlap GIs.<br><br>CONCLUSION: Supporting the validity of our method, included in the list of candidate PAIs were thirty four PAIs previously identified from genome sequencing papers. Furthermore, in some instances, our method was able to detect entire PAIs for those only partial sequences are available. Our method was proven to be an efficient method for demarcating the potential PAIs in our study. Also, the function(s) and origin(s) of a candidate PAI can be inferred by investigating the PAI queries comprising it. Identification and analysis of potential PAIs in prokaryotic genomes will broaden our knowledge on the structure and properties of PAIs and the evolution of bacterial pathogenesis.}, }
@article {pmid16032656, year = {2005}, author = {Devers, M and Henry, S and Hartmann, A and Martin-Laurent, F}, title = {Horizontal gene transfer of atrazine-degrading genes (atz) from Agrobacterium tumefaciens St96-4 pADP1::Tn5 to bacteria of maize-cultivated soil.}, journal = {Pest management science}, volume = {61}, number = {9}, pages = {870-880}, doi = {10.1002/ps.1098}, pmid = {16032656}, issn = {1526-498X}, mesh = {Agrobacterium tumefaciens/*genetics ; Atrazine/*metabolism ; Biodegradation, Environmental ; Conjugation, Genetic ; *Gene Transfer, Horizontal ; Herbicides/*metabolism ; Organisms, Genetically Modified ; Phylogeny ; *Soil Microbiology ; Zea mays/physiology ; }, abstract = {The plasmid pADP1::Tn5 derived from pADP1[Atr+] carrying a Tn5 transposon conferring kanamycin and streptomycin resistances was constructed and introduced in Agrobacterium tumefaciens St96-4. This genetically modified strain was inoculated (approximately 10(8) cfu g(-1)) in potted soils planted with maize and treated or not with atrazine (1.5 mg kg(-1)). Bulk and maize rhizosphere soils were sampled 39 days after planting to look for soil indigenous bacteria that had acquired pADP1::Tn5. Four transconjugants were isolated from four different soil samples. The estimated transfer frequency of pADP1::Tn5 was 10(-4) per donor. Maize rhizosphere and atrazine treatment had no obvious effect on pADP1::Tn5 transfer frequency. The sequencing of the 16S rDNA sequences of the transconjugants revealed that they were almost identical and highly similar to that of Variovorax spp (97%). In addition, their characterization suggested that the atzA and atzB genes had been transferred from pADP1::Tn5 to the bacterial chromosome in two of the four transconjugants. These data suggest that the atz degrading genes are horizontally transferred in soil and possibly subjected to gene rearrangement.}, }
@article {pmid16030235, year = {2005}, author = {Baldo, L and Lo, N and Werren, JH}, title = {Mosaic nature of the wolbachia surface protein.}, journal = {Journal of bacteriology}, volume = {187}, number = {15}, pages = {5406-5418}, pmid = {16030235}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; Bacterial Outer Membrane Proteins/*genetics ; Molecular Sequence Data ; Phylogeny ; *Recombination, Genetic ; Sequence Alignment ; Wolbachia/*genetics ; }, abstract = {Lateral gene transfer and recombination play important roles in the evolution of many parasitic bacteria. Here we investigate intragenic recombination in Wolbachia bacteria, considered among the most abundant intracellular bacteria on earth. We conduct a detailed analysis of the patterns of variation and recombination within the Wolbachia surface protein, utilizing an extensive set of published and new sequences from five main supergroups of Wolbachia. Analysis of nucleotide and amino acid sequence variations confirms four hypervariable regions (HVRs), separated by regions under strong conservation. Comparison of shared polymorphisms reveals a complex mosaic structure of the gene, characterized by a clear intragenic recombining of segments among several distinct strains, whose major recombination effect is shuffling of a relatively conserved set of amino acid motifs within each of the four HVRs. Exchanges occurred both within and between the arthropod supergroups. Analyses based on phylogenetic methods and a specific recombination detection program (MAXCHI) significantly support this complex partitioning of the gene, indicating a chimeric origin of wsp. Although wsp has been widely used to define macro- and microtaxonomy among Wolbachia strains, these results clearly show that it is not suitable for this purpose. The role of wsp in bacterium-host interactions is currently unknown, but results presented here indicate that exchanges of HVR motifs are favored by natural selection. Identifying host proteins that interact with wsp variants should help reveal how these widespread bacterial parasites affect and evolve in response to the cellular environments of their invertebrate hosts.}, }
@article {pmid16027259, year = {2005}, author = {Song, Y and Jones, JE and Beppu, H and Keaney, JF and Loscalzo, J and Zhang, YY}, title = {Increased susceptibility to pulmonary hypertension in heterozygous BMPR2-mutant mice.}, journal = {Circulation}, volume = {112}, number = {4}, pages = {553-562}, pmid = {16027259}, issn = {1524-4539}, support = {HL58976/HL/NHLBI NIH HHS/United States ; R01 HL061795/HL/NHLBI NIH HHS/United States ; HL55993/HL/NHLBI NIH HHS/United States ; P50 HL055993/HL/NHLBI NIH HHS/United States ; R37 HL061795/HL/NHLBI NIH HHS/United States ; R01 HL058976/HL/NHLBI NIH HHS/United States ; HL61795/HL/NHLBI NIH HHS/United States ; }, mesh = {Adenoviridae/genetics ; Animals ; Arachidonate 5-Lipoxygenase/genetics ; Bone Morphogenetic Protein Receptors, Type II/genetics/*physiology ; Dinoprostone/urine ; Gene Transfer, Horizontal ; Heterozygote ; Hypertension, Pulmonary/*etiology ; Inflammation/physiopathology ; Interleukin-1/pharmacology ; Lung/pathology ; Mice ; Mice, Inbred C57BL ; Mutation ; Platelet Activation ; Systole ; Thromboxane A2/biosynthesis ; }, abstract = {BACKGROUND: Bone morphogenetic protein receptor-2 (BMPR2)-heterozygous, mutant (BMPR2(+/-)) mice have a genetic trait similar to that of certain patients with idiopathic pulmonary arterial hypertension (IPAH). To understand the role of BMPR2 in the development of IPAH, we examined the phenotype of BMPR2(+/-) mice and their response to inflammatory stress.<br><br>METHODS AND RESULTS: BMPR2(+/-) mice were found to have the same life span, right ventricular systolic pressure (RVSP), and lung histology as those of wild-type mice under unstressed conditions. However, when treated with recombinant adenovirus expressing 5-lipoxygenase (Ad5LO), BMPR2(+/-) mice exhibited significantly higher RVSP than wild-type mice. The increase of RVSP occurred in the first 2 weeks after Ad5LO delivery. Modest but significant muscularization of distal pulmonary arterioles appeared in BMPR2(+/-) mice 4 weeks after Ad5LO treatment. Measurement of urinary metabolites of vasoactive molecules showed that cysteinyl leukotrienes, prostacyclin metabolites, and PGE2 were all increased to a similar degree in both BMPR2(+/-) and wild-type mice during 5LO transgene expression, whereas urinary endothelin-1 remained undetectable. Urinary thromboxane A2 metabolites, in contrast, were significantly higher in BMPR2(+/-) than in wild-type mice and paralleled the increase in RVSP. Platelet activation markers, serotonin, and soluble P-selectin showed a trend toward higher concentrations in BMPR2(+/-) than wild-type mice. Cell culture studies found that BMP treatment reduced interleukin-1beta-stimulated thromboxane A2 production in the pulmonary epithelial cell line A549.<br><br>CONCLUSIONS: BMPR2(+/-) mice do not develop pulmonary hypertension spontaneously; however, under inflammatory stress, they are more susceptible to an increase in RVSP, thromboxane A2 production, and vascular remodeling than wild-type mice.}, }
@article {pmid16026964, year = {2005}, author = {Wiezer, A and Merkl, R}, title = {A comparative categorization of gene flux in diverse microbial species.}, journal = {Genomics}, volume = {86}, number = {4}, pages = {462-475}, doi = {10.1016/j.ygeno.2005.05.014}, pmid = {16026964}, issn = {0888-7543}, mesh = {Archaea/*genetics ; Bacteria/genetics ; Codon/genetics ; Databases, Genetic ; Gene Transfer, Horizontal/*genetics ; *Genome, Archaeal ; *Genome, Bacterial ; Genomic Islands/genetics ; Listeria/genetics ; Methanosarcinaceae/genetics ; Species Specificity ; }, abstract = {Microbial genomes harbor genomic islands (GIs), genes presumably acquired via horizontal gene transfer (HGT). We compared GIs of hyperthermophilic, thermophilic, mesophilic, and pathogenic/nonpathogenic species and of small and large genomes. The COG database was used to characterize gene-encoded functions. Putative donors were determined to quantify gene flux between superkingdoms. In hyperthermophiles, more than 10% of the genes were on average acquired across the superkingdom border. For thermophiles and particularly mesophiles, we identified a nearly unidirectional export from bacteria to archaea. Additionally, we analyzed GI composition for Escherichia, and pairs of Listeria, Rhizobiales, Methanosarcinaceae, and Thermus thermophilus/Deinococcus radiodurans. For Escherichia and Listeria, the composition of GIs in pathogenic and nonpathogenic species did not differ significantly with respect to encoded COG classes. The analysis of related genomes showed that the composition of GIs cannot be explained with trends of gene content known to depend on genome size.}, }
@article {pmid16025309, year = {2005}, author = {Tuschak, C and Leung, MM and Beatty, JT and Overmann, J}, title = {The puf operon of the purple sulfur bacterium Amoebobacter purpureus: structure, transcription and phylogenetic analysis.}, journal = {Archives of microbiology}, volume = {183}, number = {6}, pages = {431-443}, doi = {10.1007/s00203-005-0016-1}, pmid = {16025309}, issn = {0302-8933}, mesh = {Amino Acid Sequence ; Base Sequence ; Chromatiaceae/*genetics ; Genes, Bacterial ; Light-Harvesting Protein Complexes/genetics ; Molecular Sequence Data ; *Operon ; Phylogeny ; RNA, Bacterial/analysis ; RNA, Messenger/analysis ; Sequence Alignment ; *Transcription, Genetic ; }, abstract = {The puf operon, encoding photosynthetic reaction center and light-harvesting genes, of the purple sulfur phototrophic bacterium Amoebobacter purpureus was cloned and sequenced. This revealed an unusual operon structure of the genes pufB1 A1 LMCB2 A2 B3 A3. The sequence represents the second complete puf operon available for Chromatiaceae. So far, additional sets of light-harvesting 1 (LH1) genes, pufB2 A2 and pufB3 A3 in the region downstream of pufC have only been described for Allochromatium vinosum. Along with reports of multiple LH1 polypeptides found in some Ectothiorhodospiraceae by direct protein sequencing, our results indicate that multiple LH1 genes may occur frequently in phototrophic gamma-proteobacteria. Phylogenetic analyses suggested a coevolution of the core puf genes pufB1 A1 LM. Separate analysis of the LH1 alpha and beta polypeptides revealed a high intraspecies relatedness for the secondary LH1beta polypeptides, possibly caused by functional constraints. In contrast, LH1alpha subunits of Amb. purpureus and Alc. vinosum are closely related (85% sequence identity) which could reflect horizontal gene transfer. RNA analyses suggested co-transcription of all puf genes in Amb. purpureus as a 5.5 kb primary transcript which appears to be more stable than the puf operon primary transcripts of purple non-sulfur bacteria. The 5' end of the transcript mapped to a putative promoter, which contains a -35 region located in an inverted repeat DNA sequence.}, }
@article {pmid16024162, year = {2005}, author = {Emery, R}, title = {"Bioplutonism" and the evolutionary implications of beneficial genes from another biosphere.}, journal = {Bio Systems}, volume = {82}, number = {1}, pages = {83-92}, doi = {10.1016/j.biosystems.2005.06.001}, pmid = {16024162}, issn = {0303-2647}, mesh = {*Biological Evolution ; *Earth, Planet ; *Ecosystem ; *Evolution, Molecular ; *Evolution, Planetary ; Extraterrestrial Environment ; Gene Transfer, Horizontal/*genetics ; Models, Genetic ; *Origin of Life ; }, abstract = {Could exogenous genes from another biosphere have aided the evolution of life on Earth's surface over the last half-billion years? That possibility was considered by Thomas Gold in 1992, when he hypothesized that a "deep hot biosphere" (DHB) resides independently well below its cooler surface counterpart. And he suggested that "... in the long term ... there may occasionally be beneficial exchanges of genetic material between microbial life at depth and the surface life." Thus, the question: what evidence is there to support Gold's notion that exogenous genes from the DHB--let us call them "bioplutons"--ever bestowed benefits on the evolution of surface life? In pursuit of this question I drafted a null hypothesis: "Nothing beyond our own biosphere, as we know it today, renders any kind of genetic benefits to biological evolution." After objectively analyzing the evidence and arguments pro and con I failed to reject the null hypothesis, given what we know today, especially the fact that no genetic imprint from the DHB has been identified in eukaryotic genomes. But my conclusion is regarded as tentative, because the fundamentals of Gold's argument, collectively referred to herein as "bioplutonism," might be confirmed eventually with successful probes into the DHB, and with the sampling of its alleged genetic material.}, }
@article {pmid16020785, year = {2005}, author = {Jacobson, DJ}, title = {Blocked recombination along the mating-type chromosomes of Neurospora tetrasperma involves both structural heterozygosity and autosomal genes.}, journal = {Genetics}, volume = {171}, number = {2}, pages = {839-843}, pmid = {16020785}, issn = {0016-6731}, mesh = {Chromosomes, Fungal/*genetics ; Crosses, Genetic ; Gene Transfer, Horizontal/*genetics ; Genes, Mating Type, Fungal/*genetics ; Genetic Markers ; Heterozygote ; Neurospora/*genetics ; Recombination, Genetic/*genetics ; Species Specificity ; }, abstract = {The Neurospora tetrasperma mating-type chromosomes have been shown to be structurally heterozygous by reciprocal introgression of these chromosomes between N. tetrasperma and N. crassa. This structural heterozygosity correlates with both a previously described recombination block and cytologically visible unpaired chromosomes at pachytene. Genes on the autosomes are also implicated in blocking recombination.}, }
@article {pmid16020724, year = {2005}, author = {El-Sayed, NM and Myler, PJ and Blandin, G and Berriman, M and Crabtree, J and Aggarwal, G and Caler, E and Renauld, H and Worthey, EA and Hertz-Fowler, C and Ghedin, E and Peacock, C and Bartholomeu, DC and Haas, BJ and Tran, AN and Wortman, JR and Alsmark, UC and Angiuoli, S and Anupama, A and Badger, J and Bringaud, F and Cadag, E and Carlton, JM and Cerqueira, GC and Creasy, T and Delcher, AL and Djikeng, A and Embley, TM and Hauser, C and Ivens, AC and Kummerfeld, SK and Pereira-Leal, JB and Nilsson, D and Peterson, J and Salzberg, SL and Shallom, J and Silva, JC and Sundaram, J and Westenberger, S and White, O and Melville, SE and Donelson, JE and Andersson, B and Stuart, KD and Hall, N}, title = {Comparative genomics of trypanosomatid parasitic protozoa.}, journal = {Science (New York, N.Y.)}, volume = {309}, number = {5733}, pages = {404-409}, doi = {10.1126/science.1112181}, pmid = {16020724}, issn = {1095-9203}, support = {AI45061/AI/NIAID NIH HHS/United States ; AI045039/AI/NIAID NIH HHS/United States ; U01 AI043062/AI/NIAID NIH HHS/United States ; U01 AI045039/AI/NIAID NIH HHS/United States ; AI45038/AI/NIAID NIH HHS/United States ; U01 AI045038/AI/NIAID NIH HHS/United States ; U01 AI040599/AI/NIAID NIH HHS/United States ; R01 AI043062/AI/NIAID NIH HHS/United States ; //Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Biological Evolution ; Chromosomes/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Protozoan ; *Genome, Protozoan ; Genomics ; Leishmania major/chemistry/*genetics/metabolism ; Molecular Sequence Data ; Multigene Family ; Mutation ; Phylogeny ; Plastids/genetics ; *Proteome ; Protozoan Proteins/chemistry/*genetics/physiology ; Recombination, Genetic ; Retroelements ; Species Specificity ; Symbiosis ; Synteny ; Telomere/genetics ; Trypanosoma brucei brucei/chemistry/*genetics/metabolism ; Trypanosoma cruzi/chemistry/*genetics/metabolism ; }, abstract = {A comparison of gene content and genome architecture of Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major, three related pathogens with different life cycles and disease pathology, revealed a conserved core proteome of about 6200 genes in large syntenic polycistronic gene clusters. Many species-specific genes, especially large surface antigen families, occur at nonsyntenic chromosome-internal and subtelomeric regions. Retroelements, structural RNAs, and gene family expansion are often associated with syntenic discontinuities that-along with gene divergence, acquisition and loss, and rearrangement within the syntenic regions-have shaped the genomes of each parasite. Contrary to recent reports, our analyses reveal no evidence that these species are descended from an ancestor that contained a photosynthetic endosymbiont.}, }
@article {pmid16020539, year = {2005}, author = {Nordmann, P and Poirel, L}, title = {Emergence of plasmid-mediated resistance to quinolones in Enterobacteriaceae.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {56}, number = {3}, pages = {463-469}, doi = {10.1093/jac/dki245}, pmid = {16020539}, issn = {0305-7453}, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics/metabolism ; Cephalosporinase/genetics/metabolism ; Drug Resistance, Bacterial/*physiology ; Enterobacteriaceae/*drug effects/*genetics ; Escherichia coli Proteins/genetics ; Gene Transfer, Horizontal ; Integrons ; Molecular Sequence Data ; Plasmids/drug effects/*genetics ; Quinolones/*pharmacology ; beta-Lactamases/genetics ; }, abstract = {Although quinolone resistance results mostly from chromosomal mutations in Enterobacteriaceae, it may also be mediated by plasmid-encoded Qnr determinants. Qnr proteins protect DNA from quinolone binding and compromise the efficacy of quinolones such as nalidixic acid. Qnr proteins (QnrA-like, QnrB and QnrS) have been identified worldwide with a quite high prevalence among Asian isolates with a frequent association with clavulanic acid inhibited expanded-spectrum beta-lactamases and plasmid-mediated cephalosporinases. The qnrA genes are embedded in complex sul1-type integrons. A very recent identification of the origin of QnrA determinants in the water-borne species Shewanella algae underlines the role of the environment as a reservoir for this emerging threat. It may help to determine the location of in vivo transfer of qnrA genes. Further analysis of the role (if any) of quinolones for enhancing this gene transfer may be conducted. This could prevent the spread, if still possible, of this novel antibiotic resistance mechanism.}, }
@article {pmid16018771, year = {2005}, author = {Burton, M and Rose, TM and Faergeman, NJ and Knudsen, J}, title = {Evolution of the acyl-CoA binding protein (ACBP).}, journal = {The Biochemical journal}, volume = {392}, number = {Pt 2}, pages = {299-307}, pmid = {16018771}, issn = {1470-8728}, mesh = {Acyl Coenzyme A/*metabolism ; Amino Acid Sequence ; Animals ; Bacteria/chemistry/genetics ; Carrier Proteins/*chemistry/*genetics/metabolism ; Conserved Sequence ; *Evolution, Molecular ; Fungi/chemistry/genetics ; Humans ; Invertebrates/chemistry/genetics ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Plants/chemistry/genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; Species Specificity ; }, abstract = {Acyl-CoA-binding protein (ACBP) is a 10 kDa protein that binds C12-C22 acyl-CoA esters with high affinity. In vitro and in vivo experiments suggest that it is involved in multiple cellular tasks including modulation of fatty acid biosynthesis, enzyme regulation, regulation of the intracellular acyl-CoA pool size, donation of acyl-CoA esters for beta-oxidation, vesicular trafficking, complex lipid synthesis and gene regulation. In the present study, we delineate the evolutionary history of ACBP to get a complete picture of its evolution and distribution among species. ACBP homologues were identified in all four eukaryotic kingdoms, Animalia, Plantae, Fungi and Protista, and eleven eubacterial species. ACBP homologues were not detected in any other known bacterial species, or in archaea. Nearly all of the ACBP-containing bacteria are pathogenic to plants or animals, suggesting that an ACBP gene could have been acquired from a eukaryotic host by horizontal gene transfer. Many bacterial, fungal and higher eukaryotic species only harbour a single ACBP homologue. However, a number of species, ranging from protozoa to vertebrates, have evolved two to six lineage-specific paralogues through gene duplication and/or retrotransposition events. The ACBP protein is highly conserved across phylums, and the majority of ACBP genes are subjected to strong purifying selection. Experimental evidence indicates that the function of ACBP has been conserved from yeast to humans and that the multiple lineage-specific paralogues have evolved altered functions. The appearance of ACBP very early on in evolution points towards a fundamental role of ACBP in acyl-CoA metabolism, including ceramide synthesis and in signalling.}, }
@article {pmid16013378, year = {2005}, author = {Kim, SH and Wei, CI and An, H}, title = {Molecular characterization of multidrug-resistant Proteus mirabilis isolates from retail meat products.}, journal = {Journal of food protection}, volume = {68}, number = {7}, pages = {1408-1413}, doi = {10.4315/0362-028x-68.7.1408}, pmid = {16013378}, issn = {0362-028X}, mesh = {Anti-Bacterial Agents/*pharmacology ; Conjugation, Genetic ; *Drug Resistance, Multiple, Bacterial/genetics ; Enterobacteriaceae/drug effects/genetics ; Gene Transfer, Horizontal/genetics ; Integrons ; Meat Products/*microbiology ; Microbial Sensitivity Tests ; Mutation ; Plasmids ; Proteus mirabilis/*drug effects/*genetics ; }, abstract = {Sixty-four multidrug-resistant isolates of Proteus mirabilis were collected from retail meat products in Oklahoma. The isolates showed four different patterns of antibiotic resistance based on their resistant phenotype and genotypes. Most of these isolates were resistant to ampicillin, tetracycline, gentamycin, and kanamycin. Class 1 integrons were detected as a common carrier of the antibiotic-resistant genes, such as aadA1, aadB, and aadA2. A few isolates (9%) contained class 2 integrons with three gene cassettes included: dhfr1, sat1, and aadA1. These isolates were even resistant to nalidixic acid due to mutations in gyrA and parC. All ampicillin-resistant isolates contained blaTEM-1. Plasmids that contained class 1 or 2 integrons and blaTEM-1 were able to be transferred from P. mirabilis isolates into Escherichia coli by conjugation, indicating that conjugal transfer could contribute to the dissemination of antibiotic resistance genes between the Enterobacteriaceae species.}, }
@article {pmid16012097, year = {2005}, author = {Hughes, AL and Ekollu, V and Friedman, R and Rose, JR}, title = {Gene family content-based phylogeny of prokaryotes: the effect of criteria for inferring homology.}, journal = {Systematic biology}, volume = {54}, number = {2}, pages = {268-276}, doi = {10.1080/10635150590923335}, pmid = {16012097}, issn = {1063-5157}, support = {GM066710/GM/NIGMS NIH HHS/United States ; }, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Classification/*methods ; Computational Biology ; Data Interpretation, Statistical ; Gene Transfer, Horizontal/genetics ; Multigene Family/*genetics ; *Phylogeny ; }, abstract = {A number of recent papers have suggested that gene family content can be used to resolve phylogenies, particularly in the case of prokaryotes, in which extensive horizontal gene transfer means that individual gene phylogenies may not mirror the organismal phylogeny. However, no study has yet examined how sensitive such analyses are to the criterion of homology assessment used to assemble multigene families. Using data from 99 completely sequenced prokaryotic genomes, we examined the effect of homology criteria in phylogenetic analyses wherein presence or absence of each family in the genome was used as a cladistic character. Different criteria resulted in evidence for contradictory tree topologies, sometimes with high bootstrap support. A moderately strict criterion seemed best for assembling multigene families in a biologically meaningful way, but it was not necessarily preferable for phylogenetic analysis. Instead, a very strict criterion, which broke up gene families into smaller subfamilies, seemed to have advantages for phylogenetic purposes. The poor performance of gene family content-based phylogenetic analysis in the case of prokaryotes appears to reflect high levels of homoplasy resulting not only from horizontal gene transfer but also, more importantly, from extensive parallel loss of gene families in certain bacteria genomes.}, }
@article {pmid16009540, year = {2005}, author = {Langley, RJ and Kenna, D and Bartholdson, J and Campopiano, DJ and Govan, JR}, title = {Temperate bacteriophages DK4 and BcepMu from Burkholderia cenocepacia J2315 are identical.}, journal = {FEMS immunology and medical microbiology}, volume = {45}, number = {2}, pages = {349-350}, doi = {10.1016/j.femsim.2005.06.001}, pmid = {16009540}, issn = {0928-8244}, mesh = {Bacteriophage mu/classification/genetics/isolation &amp; purification ; Bacteriophages/classification/*genetics/isolation &amp; purification ; Burkholderia cepacia complex/pathogenicity/*virology ; Cystic Fibrosis/microbiology ; DNA, Viral/genetics ; Gene Transfer, Horizontal ; Genes, Viral ; Humans ; Virulence ; }, }
@article {pmid16009509, year = {2005}, author = {Aho, EL and Urwin, R and Batcheller, AE and Holmgren, AM and Havig, K and Kulakoski, AM and Vomhof, EE and Longfors, NS and Erickson, CB and Anderson, ZK and Dawlaty, JM and Mueller, JJ}, title = {Neisserial pilin genes display extensive interspecies diversity.}, journal = {FEMS microbiology letters}, volume = {249}, number = {2}, pages = {327-334}, doi = {10.1016/j.femsle.2005.06.035}, pmid = {16009509}, issn = {0378-1097}, mesh = {Amino Acid Sequence ; Chromosome Mapping ; Conserved Sequence ; DNA, Bacterial/genetics ; Fimbriae Proteins/*genetics ; Genetic Variation ; Molecular Sequence Data ; Neisseria/*classification/*genetics ; Phylogeny ; Pili, Sex/genetics ; Polymerase Chain Reaction ; Sequence Alignment ; Sequence Homology, Amino Acid ; Species Specificity ; }, abstract = {All Neisseria live in association with host cells, however, little is known about the genetic potential of nonpathogenic Neisseria species to express attachment factors such as pili. In this study, we demonstrate that type IV pilin-encoding genes are present in a wide range of Neisseria species. N. sicca, N. subflava, and N. elongata each contain two putative pilE genes arranged in tandem, while single genes were identified in N. polysaccharea, N. mucosa, and N. denitrificans. Neisserial pilE genes are highly diverse and display features consistent with a history of horizontal gene transfer.}, }
@article {pmid16006619, year = {2005}, author = {Tsirigos, A and Rigoutsos, I}, title = {A sensitive, support-vector-machine method for the detection of horizontal gene transfers in viral, archaeal and bacterial genomes.}, journal = {Nucleic acids research}, volume = {33}, number = {12}, pages = {3699-3707}, pmid = {16006619}, issn = {1362-4962}, mesh = {*Artificial Intelligence ; Cytomegalovirus/genetics ; *Gene Transfer, Horizontal ; *Genome, Archaeal ; *Genome, Bacterial ; *Genome, Viral ; Genomics/methods ; }, abstract = {In earlier work, we introduced and discussed a generalized computational framework for identifying horizontal transfers. This framework relied on a gene's nucleotide composition, obviated the need for knowledge of codon boundaries and database searches, and was shown to perform very well across a wide range of archaeal and bacterial genomes when compared with previously published approaches, such as Codon Adaptation Index and C + G content. Nonetheless, two considerations remained outstanding: we wanted to further increase the sensitivity of detecting horizontal transfers and also to be able to apply the method to increasingly smaller genomes. In the discussion that follows, we present such a method, Wn-SVM, and show that it exhibits a very significant improvement in sensitivity compared with earlier approaches. Wn-SVM uses a one-class support-vector machine and can learn using rather small training sets. This property makes Wn-SVM particularly suitable for studying small-size genomes, similar to those of viruses, as well as the typically larger archaeal and bacterial genomes. We show experimentally that the new method results in a superior performance across a wide range of organisms and that it improves even upon our own earlier method by an average of 10% across all examined genomes. As a small-genome case study, we analyze the genome of the human cytomegalovirus and demonstrate that Wn-SVM correctly identifies regions that are known to be conserved and prototypical of all beta-herpesvirinae, regions that are known to have been acquired horizontally from the human host and, finally, regions that had not up to now been suspected to be horizontally transferred. Atypical region predictions for many eukaryotic viruses, including the alpha-, beta- and gamma-herpesvirinae, and 123 archaeal and bacterial genomes, have been made available online at http://cbcsrv.watson.ibm.com/HGT_SVM/.}, }
@article {pmid16006479, year = {2005}, author = {Zúñiga, M and Comas, I and Linaje, R and Monedero, V and Yebra, MJ and Esteban, CD and Deutscher, J and Pérez-Martínez, G and González-Candelas, F}, title = {Horizontal gene transfer in the molecular evolution of mannose PTS transporters.}, journal = {Molecular biology and evolution}, volume = {22}, number = {8}, pages = {1673-1685}, doi = {10.1093/molbev/msi163}, pmid = {16006479}, issn = {0737-4038}, mesh = {Bacteria/*genetics ; Bacterial Proteins/*genetics ; Biological Transport, Active/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Monosaccharide Transport Proteins/*genetics ; Multienzyme Complexes/*genetics ; *Phylogeny ; }, abstract = {The phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) represents hitherto the only example of group translocation transport systems. PTS transporters are exclusively found in bacteria and can be grouped on the basis of sequence and structure into six classes. We have analyzed the evolution of mannose-class PTS transporters. These transporters have a limited distribution among bacteria being mostly harbored by species associated to animals. The results obtained indicate that these genes have undergone a complex evolutionary history, including extensive horizontal gene transfer events, duplications, and nonorthologous displacements. The phylogenetic analysis revealed an early diversification to specialize in different transport capabilities, but these events have also occurred relatively recently. In addition, these transporters can be further divided into seven groups and this division correlates with their transport capabilities. Finally, the consideration of the genomic context allowed us to propose putative functional roles for some uncharacterized PTS transporters. The functional role and distribution of mannose-class PTS transporters suggest that their expansion may have played a significant role in the establishment of symbiotic relationships between animals and some bacteria.}, }
@article {pmid16003874, year = {2005}, author = {Naumov, GI}, title = {Domestication of dairy yeast Kluyveromyces lactis: transfer of the beta-galactosidase (LAC4) and lactose permease (LAC12) gene cluster?.}, journal = {Doklady biological sciences : proceedings of the Academy of Sciences of the USSR, Biological sciences sections}, volume = {401}, number = {}, pages = {120-122}, pmid = {16003874}, issn = {0012-4966}, mesh = {Gene Expression Regulation, Fungal ; Gene Transfer, Horizontal/*genetics ; Kluyveromyces/*genetics ; Membrane Transport Proteins/*genetics ; beta-Galactosidase/*genetics ; }, }
@article {pmid16003355, year = {2005}, author = {de Maagd, RA and Bravo, A and Crickmore, N}, title = {Bt toxin not guilty by association.}, journal = {Nature biotechnology}, volume = {23}, number = {7}, pages = {791}, doi = {10.1038/nbt0705-791b}, pmid = {16003355}, issn = {1087-0156}, mesh = {Bacillus thuringiensis/genetics/pathogenicity ; Bacillus thuringiensis Toxins ; Bacterial Proteins/*genetics/metabolism ; Bacterial Toxins/*genetics/metabolism ; Endotoxins/*genetics/metabolism ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/genetics ; Hemolysin Proteins ; *Plants, Genetically Modified ; }, }
@article {pmid16002755, year = {2005}, author = {Davis, ME and Hsieh, PC and Grodzinsky, AJ and Lee, RT}, title = {Custom design of the cardiac microenvironment with biomaterials.}, journal = {Circulation research}, volume = {97}, number = {1}, pages = {8-15}, pmid = {16002755}, issn = {1524-4571}, support = {F32 HL073574/HL/NHLBI NIH HHS/United States ; F32 HL073574-03/HL/NHLBI NIH HHS/United States ; }, mesh = {Angiogenesis Inducing Agents/metabolism ; Animals ; *Biocompatible Materials ; Biodegradation, Environmental ; Cell Adhesion ; Gene Transfer, Horizontal ; Heart Diseases/*therapy ; Humans ; Injections ; Matrix Metalloproteinases/metabolism ; Proteins/metabolism ; Regeneration ; Tissue Engineering/*methods ; }, abstract = {Many strategies for repairing injured myocardium are under active investigation, with some early encouraging results. These strategies include cell therapies, despite little evidence of long-term survival of exogenous cells, and gene or protein therapies, often with incomplete control of locally-delivered dose of the factor. We propose that, ultimately, successful repair and regeneration strategies will require quantitative control of the myocardial microenvironment. This precision control can be engineered through designed biomaterials that provide quantitative adhesion, growth, or migration signals. Quantitative timed release of factors can be regulated by chemical design to direct cellular differentiation pathways such as angiogenesis and vascular maturation. Smart biomaterials respond to the local environment, such as protease activity or mechanical forces, with controlled release or activation. Most of these new biomaterials provide much greater flexibility for regenerating tissues ex vivo, but emerging technologies like self-assembling nanofibers can now establish intramyocardial cellular microenvironments by injection. This may allow percutaneous cardiac regeneration and repair approaches, or injectable-tissue engineering. Finally, materials can be made to multifunction by providing sequential signals with custom design of differential release kinetics for individual factors. Thus, new rationally-designed biomaterials no longer simply coexist with tissues, but can provide precision bioactive control of the microenvironment that may be required for cardiac regeneration and repair.}, }
@article {pmid16002644, year = {2005}, author = {Zhao, R and Daniels, KJ and Lockhart, SR and Yeater, KM and Hoyer, LL and Soll, DR}, title = {Unique aspects of gene expression during Candida albicans mating and possible G(1) dependency.}, journal = {Eukaryotic cell}, volume = {4}, number = {7}, pages = {1175-1190}, pmid = {16002644}, issn = {1535-9778}, support = {R01 DE014158/DE/NIDCR NIH HHS/United States ; AI2392/AI/NIAID NIH HHS/United States ; DE14158/DE/NIDCR NIH HHS/United States ; }, mesh = {Candida albicans/*genetics/metabolism/*physiology ; G1 Phase/*genetics ; *Gene Expression Regulation, Fungal ; Gene Transfer, Horizontal/physiology ; Microarray Analysis/methods ; Models, Biological ; Phenotype ; Time Factors ; }, abstract = {Taking advantage of the high frequency of conjugation tube formation in mating mixtures and alpha-pheromone-treated a/a cells derived from saturation phase cultures of opaque cells of Candida albicans, 56 up-regulated and 30 down-regulated genes were identified employing microarray and Northern analyses. Combining these results with previous profiling studies of pheromone-induced cells, a more comprehensive transcript profile was developed for comparison with Saccharomyces cerevisiae. This comparison revealed the following: (i) that while a majority of mating-associated genes are regulated similarly between the two species, a significant minority are regulated dissimilarly; (ii) that filamentation genes are uniquely up-regulated and opaque-specific genes uniquely down-regulated during C. albicans mating; and (iii) that a newly identified class of genes is selectively down-regulated in opaque, but not white, cells that have entered saturation phase in a growth culture and then are up-regulated by pheromone. The observations that opaque cells are uniquely mating competent, that saturation phase facilitates mating, and that a newly identified group of genes is down-regulated only in opaque cells that have entered saturation phase led us to hypothesize that entering saturation phase may be requisite for mating. A test of this hypothesis revealed, however, that cells, whether in the exponential or saturation phase, may simply have to be in G(1) of the cell cycle to respond to pheromone and that the response includes G(1) arrest. These results add to the lists of similarities and dissimilarities between the mating processes of C. albicans and S. cerevisiae and underscore the unique regulation of filamentation and switching genes in the C. albicans mating process.}, }
@article {pmid16001254, year = {2005}, author = {Gallert, C and Fund, K and Winter, J}, title = {Antibiotic resistance of bacteria in raw and biologically treated sewage and in groundwater below leaking sewers.}, journal = {Applied microbiology and biotechnology}, volume = {69}, number = {1}, pages = {106-112}, doi = {10.1007/s00253-005-0033-7}, pmid = {16001254}, issn = {0175-7598}, mesh = {Actinobacteria/genetics ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/isolation &amp; purification ; *Drug Resistance, Bacterial ; Drug Resistance, Multiple, Bacterial ; Enterobacteriaceae/drug effects/isolation &amp; purification ; Enterococcus/drug effects/isolation &amp; purification ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Pseudomonas/drug effects/isolation &amp; purification ; Sewage/*microbiology ; *Soil Microbiology ; *Water Microbiology ; }, abstract = {More than 750 isolates of faecal coliforms (>200 strains), enterococci (>200 strains) and pseudomonads (>340 strains) from three wastewater treatment plants (WTPs) and from four groundwater wells in the vicinity of leaking sewers were tested for resistance against 14 antibiotics. Most, or at least some, strains of the three bacterial groups, isolated from raw or treated sewage of the three WTPs, were resistant against penicillin G, ampicillin, vancomycin, erythromycin, triple sulfa and trimethoprim/sulfamethoxazole (SXT). Only a few strains of pseudomonads or faecal coliforms were resistant against some of the other tested antibiotics. The antibiotic resistances of pseudomonads, faecal coliforms and enterococci from groundwater varied to a higher extent. In contrast to the faecal coliforms and enterococci, most pseudomonads from all groundwater samples, including those from non-polluted groundwater, were additionally resistant against chloramphenicol and SXT. Pseudomonads from sewage and groundwater had more multiple antibiotic resistances than the faecal coliforms or the enterococci, and many pseudomonads from groundwater were resistant to more antibiotics than those from sewage. The pseudomonads from non-polluted groundwater were the most resistant isolates of all. The few surviving faecal coliforms in groundwater seemed to gain multiple antibiotic resistances, whereas the enterococci lost antibiotic resistances. Pseudomonads, and presumably, other autochthonous soil or groundwater bacteria, such as antibiotic-producing Actinomyces sp., seem to contribute significantly to the gene pool for acquisition of resistances against antibiotics in these environments.}, }
@article {pmid16000737, year = {2005}, author = {Tormo, M&#xc1; and Knecht, E and Götz, F and Lasa, I and Penadés, JR}, title = {Bap-dependent biofilm formation by pathogenic species of Staphylococcus: evidence of horizontal gene transfer?.}, journal = {Microbiology (Reading, England)}, volume = {151}, number = {Pt 7}, pages = {2465-2475}, doi = {10.1099/mic.0.27865-0}, pmid = {16000737}, issn = {1350-0872}, mesh = {Adhesins, Bacterial/chemistry/genetics/metabolism ; Bacterial Proteins/*physiology ; Biofilms/*growth &amp; development ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Staphylococcus aureus/pathogenicity/*physiology ; }, abstract = {The biofilm-associated protein (Bap) is a surface protein implicated in biofilm formation by Staphylococcus aureus isolated from chronic mastitis infections. The bap gene is carried in a putative composite transposon inserted in SaPIbov2, a mobile staphylococcal pathogenicity island. In this study, bap orthologue genes from several staphylococcal species, including Staphylococcus epidermidis, Staphylococcus chromogenes, Staphylococcus xylosus, Staphylococcus simulans and Staphylococcus hyicus, were identified, cloned and sequenced. Sequence analysis comparison of the bap gene from these species revealed a very high sequence similarity, suggesting the horizontal gene transfer of SaPIbov2 amongst them. However, sequence analyses of the flanking region revealed that the bap gene of these species was not contained in the SaPIbov2 pathogenicity island. Although they did not contain the icaADBC operon, all the coagulase-negative staphylococcal isolates harbouring bap were strong biofilm producers. Disruption of the bap gene in S. epidermidis abolished its capacity to form a biofilm, whereas heterologous complementation of a biofilm-negative strain of S. aureus with the Bap protein from S. epidermidis bestowed the capacity to form a biofilm on a polystyrene surface. Altogether, these results demonstrate that Bap orthologues from coagulase-negative staphylococci induce an alternative mechanism of biofilm formation that is independent of the PIA/PNAG exopolysaccharide.}, }
@article {pmid15998462, year = {2005}, author = {Iturbe-Ormaetxe, I and Riegler, M and O'Neill, SL}, title = {New names for old strains? Wolbachia wSim is actually wRi.}, journal = {Genome biology}, volume = {6}, number = {7}, pages = {401; author reply 401}, pmid = {15998462}, issn = {1474-760X}, mesh = {Animals ; Drosophila/microbiology ; Gene Transfer, Horizontal ; Genome ; Genomics ; Phylogeny ; Symbiosis ; Wolbachia/*classification/*genetics/physiology ; }, abstract = {A response to Serendipitous discovery of Wolbachia genomes in multiple Drosophila species by SL Salzberg, JC Dunning Hotopp, AL Delcher, M Pop, DR Smith, MB Eisen and WC Nelson. Genome Biology 2005, 6:R23}, }
@article {pmid15995209, year = {2005}, author = {Mongodin, EF and Hance, IR and Deboy, RT and Gill, SR and Daugherty, S and Huber, R and Fraser, CM and Stetter, K and Nelson, KE}, title = {Gene transfer and genome plasticity in Thermotoga maritima, a model hyperthermophilic species.}, journal = {Journal of bacteriology}, volume = {187}, number = {14}, pages = {4935-4944}, pmid = {15995209}, issn = {0021-9193}, mesh = {Base Sequence ; DNA, Bacterial/genetics ; DNA, Circular/genetics ; Environment ; Gene Expression Regulation, Bacterial ; *Gene Transfer Techniques ; *Genome, Plant ; Geography ; Hot Temperature ; Models, Genetic ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; Thermotoga maritima/*classification/*genetics ; }, abstract = {The genome sequence of the hyperthermophilic bacterium Thermotoga maritima MSB8 presents evidence for lateral gene transfer events between bacterial and archaeal species. To estimate the extent of genomic diversity across the order Thermotogales, a comparative genomic hybridization study was initiated to compare nine Thermotoga strains to the sequenced T. maritima MSB8. Many differences could be associated with substrate utilization patterns, which are most likely a reflection of the environmental niche that these individual species occupy. A detailed analysis of some of the predicted variable regions demonstrates many examples of the deletion/insertion of complete cassettes of genes and of gene rearrangements and insertions of DNA within genes, with the C or N terminus being retained. Although the mechanism for gene transfer in this lineage remains to be elucidated, this analysis suggests possible associations with repetitive elements and highlights the possible benefits of rampant genetic exchange to these species.}, }
@article {pmid15994433, year = {2005}, author = {Li, YL and Li, YF and Liu, D and Cornish, KG and Patel, KP and Zucker, IH and Channon, KM and Schultz, HD}, title = {Gene transfer of neuronal nitric oxide synthase to carotid body reverses enhanced chemoreceptor function in heart failure rabbits.}, journal = {Circulation research}, volume = {97}, number = {3}, pages = {260-267}, doi = {10.1161/01.RES.0000175722.21555.55}, pmid = {15994433}, issn = {1524-4571}, support = {P0-1 HL062222/HL/NHLBI NIH HHS/United States ; }, mesh = {Adenoviridae/genetics ; Animals ; Carotid Body/enzymology/*physiology ; Chemoreceptor Cells/*physiology ; *Gene Transfer, Horizontal ; Heart Failure/*physiopathology ; Kidney/innervation ; Male ; Nerve Tissue Proteins/*genetics/physiology ; Nitric Oxide/physiology ; Nitric Oxide Synthase/*genetics/physiology ; Nitric Oxide Synthase Type I ; Rabbits ; Sympathetic Nervous System/physiopathology ; }, abstract = {Our previous studies showed that decreased nitric oxide (NO) production enhanced carotid body (CB) chemoreceptor activity in chronic heart failure (CHF) rabbits. In the present study, we investigated the effects of neuronal NO synthase (nNOS) gene transfer on CB chemoreceptor activity in CHF rabbits. The nNOS protein expression and NO production were suppressed in CBs (P<0.05) of CHF rabbits, but were increased 3 days after application of an adenovirus expressing nNOS (Ad.nNOS) to the CB. As a control, nNOS and NO levels in CHF CBs were not affected by Ad.EGFP. Baseline single-fiber discharge during normoxia and the response to hypoxia were enhanced (P<0.05) from CB chemoreceptors in CHF versus sham rabbits. Ad.nNOS decreased the baseline discharge (4.5+/-0.3 versus 7.3+/-0.4 imp/s at 105+/-1.9 mm Hg) and the response to hypoxia (18.3+/-1.2 imp/s versus 35.6+/-1.1 at 40+/-2.1 mm Hg) from CB chemoreceptors in CHF rabbits (Ad.nNOS CB versus contralateral noninfected CB respectively, P<0.05). A specific nNOS inhibitor, S-Methyl-L-thiocitrulline (SMTC), fully inhibited the effect of Ad.nNOS on the enhanced CB activity in CHF rabbits. In addition, nNOS gene transfer to the CBs also significantly blunted the baseline renal sympathetic nerve activity (RSNA) and the response of RSNA to hypoxia in CHF rabbits (P<0.05). These results indicate that decreased endogenous nNOS activity in the CB plays an important role in the enhanced activity of the CB chemoreceptors and peripheral chemoreflex function in CHF rabbits.}, }
@article {pmid15990697, year = {2005}, author = {Tetz, VV}, title = {The pangenome concept: a unifying view of genetic information.}, journal = {Medical science monitor : international medical journal of experimental and clinical research}, volume = {11}, number = {7}, pages = {HY24-9}, pmid = {15990697}, issn = {1234-1010}, mesh = {Animals ; *Biological Evolution ; *Gene Transfer, Horizontal ; *Genome ; Humans ; *Recombination, Genetic ; }, abstract = {A way of viewing the genetic information in all organisms on Earth as constituents of the Pangenome is proposed. According to this concept, the Pangenome is the common (collective) genetic system of all living organisms, the organic molecules and their complexes (DNA- and RNA-containing viruses, plasmids, transposons, insertion sequences) involved in the storage and transmission processes of genetic information. Pangenomic stability and variability are discussed. This concept alerts to the inherent fluidity and transmissibility of DNA among organisms of all types, including horizontal gene transfer between closely related and formally unrelated macro- and microorganisms. The roles of death and of all known food chains as universal ways of gene distribution among different organisms are discussed. The contribution of bacteria and viruses in maintaining the circulation of genes within the Pangenome is presented. This concept implies that newly emerging genes are not bound to disappear together with the death of an organism or the extinction of a species and microorganisms are the main pool of genes. Some negative aspects of the intervention of molecular genetics, biotechnology, and ecology, including the spread of transgenic plants and animals, are summarized. It is shown that this concept may be used in medicine for the prognosis of an epidemic situation, particularly newly spreading pathogens, and for the development of new methods for the prophylaxis and early diagnosis of oncologic diseases. This concept can also help to find promising approaches to the discovery of drugs with novel principles of action.}, }
@article {pmid15984554, year = {2003}, author = {Doolittle, WF}, title = {Some thoughts on the tree of life.}, journal = {Harvey lectures}, volume = {99}, number = {}, pages = {111-128}, pmid = {15984554}, issn = {0073-0874}, mesh = {*Biological Evolution ; Gene Transfer, Horizontal ; Genome ; *Models, Genetic ; Multigene Family ; Phylogeny ; Prokaryotic Cells ; Recombination, Genetic ; }, }
@article {pmid15983865, year = {2005}, author = {Calteau, A and Gouy, M and Perrière, G}, title = {Horizontal transfer of two operons coding for hydrogenases between bacteria and archaea.}, journal = {Journal of molecular evolution}, volume = {60}, number = {5}, pages = {557-565}, pmid = {15983865}, issn = {0022-2844}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Computational Biology ; Gene Components ; Gene Transfer, Horizontal/*genetics ; Hydrogenase/*genetics ; Likelihood Functions ; Models, Genetic ; Multigene Family/genetics ; Operon/*genetics ; *Phylogeny ; }, abstract = {Using a phylogenetic approach, we discovered three putative horizontal transfers between bacterial and archaeal species involving large clusters of genes. One transfer involves an operon of 13 genes, called mbx, which probably was transferred into the genome of Thermotoga maritima from a species belonging or close to the Pyrococcus genus. The two others implied an operon of six genes, called ech, transferred independently to the genomes of Thermoanaerobacter tengcongensis and Desulfovibrio gigas, from a species belonging or close to the Methanosarcina genus. All these transfers affected operons coding for multisubunit membrane-bound (NiFe) hydrogenases involved in the energy metabolism of the donor genomes. The functionality of the transferred operons has not been experimentally demonstrated for T. maritima, whereas in D. gigas and T. tengcongensis the encoded multisubunit hydrogenase could have a role in energy conservation. This report adds several cases of horizontal gene transfers among hydrogenases already described.}, }
@article {pmid15983137, year = {2005}, author = {Gladitz, J and Shen, K and Antalis, P and Hu, FZ and Post, JC and Ehrlich, GD}, title = {Codon usage comparison of novel genes in clinical isolates of Haemophilus influenzae.}, journal = {Nucleic acids research}, volume = {33}, number = {11}, pages = {3644-3658}, pmid = {15983137}, issn = {1362-4962}, support = {R01 DC002148/DC/NIDCD NIH HHS/United States ; DC02148/DC/NIDCD NIH HHS/United States ; }, mesh = {Base Sequence ; *Codon ; DNA, Bacterial/chemistry ; Data Interpretation, Statistical ; Gene Expression ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genome, Bacterial ; Genomics ; Haemophilus influenzae/*genetics/isolation &amp; purification/metabolism ; Humans ; Phylogeny ; }, abstract = {A similarity statistic for codon usage was developed and used to compare novel gene sequences found in clinical isolates of Haemophilus influenzae with a reference set of 80 prokaryotic, eukaryotic and viral genomes. These analyses were performed to obtain an indication as to whether individual genes were Haemophilus-like in nature, or if they probably had more recently entered the H.influenzae gene pool via horizontal gene transfer from other species. The average and SD values were calculated for the similarity statistics from a study of the set of all genes in the H.influenzae Rd reference genome that encoded proteins of 100 amino acids or longer. Approximately 80% of Rd genes gave a statistic indicating that they were most like other Rd genes. Genes displaying codon usage statistics >1 SD above this range were either considered part of the highly expressed group of H.influenzae genes, or were considered of foreign origin. An alternative determinant for identifying genes of foreign origin was when the similarity statistics produced a value that was much closer to a non-H.influenzae reference organism than to any of the Haemophilus species contained in the reference set. Approximately 65% of the novel sequences identified in the H.influenzae clinical isolates displayed codon usages most similar to Haemophilus sp. The remaining novel sequences produced similarity statistics closer to one of the other reference genomes thereby suggesting that these sequences may have entered the H.influenzae gene pool more recently via horizontal transfer.}, }
@article {pmid15980893, year = {2005}, author = {Pristas, P and Piknova, M}, title = {Underrepresentation of short palindromes in Selenomonas ruminantium DNA: evidence for horizontal gene transfer of restriction and modification systems?.}, journal = {Canadian journal of microbiology}, volume = {51}, number = {4}, pages = {315-318}, doi = {10.1139/w05-004}, pmid = {15980893}, issn = {0008-4166}, mesh = {Animals ; DNA, Bacterial/genetics ; Deoxyribonucleases, Type II Site-Specific/*genetics ; *Gene Transfer, Horizontal ; Markov Chains ; Rumen/microbiology ; Selenomonas/*genetics ; }, abstract = {Molecular analysis of isolates of the rumen bacterium Selenomonas ruminantium revealed a high variety and frequency of site-specific (restriction) endonucleases. While all known S. ruminantium restriction and modification systems recognize hexanucleotide sequences only, consistently low counts of both 6-bp and 4-bp palindromes were found in DNA sequences of S. ruminantium. Statistical analysis indicated that there is some correlation between the degree of underrepresentation of tetranucleotide words and the number of known restriction endonucleases for a given sequence. Control analysis showed the same correlation in lambda DNA but not in human adenovirus DNA. Based on the data presented, it could be proposed that there is a much higher historical occurrence of restriction and modification systems in S. ruminantium and (or) frequent horizontal gene transfer of restriction and modification gene complexes.}, }
@article {pmid15979391, year = {2005}, author = {Comeau, AM and Krisch, HM}, title = {War is peace--dispatches from the bacterial and phage killing fields.}, journal = {Current opinion in microbiology}, volume = {8}, number = {4}, pages = {488-494}, doi = {10.1016/j.mib.2005.06.004}, pmid = {15979391}, issn = {1369-5274}, mesh = {Bacteria/genetics/*virology ; Bacteriophages/classification/genetics/*pathogenicity ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial ; Genome, Viral ; }, abstract = {Large-scale sequence analyses of phage and bacteria have provided new insights into the diverse and multifaceted interactions of these genomes. Such interactions are important because they determine the partitioning of a large fraction of global biomass. Furthermore, the struggle between phage and bacteria has had a significant impact on the evolution of the biosphere. This competition for resources has created an enormous pool of genetic diversity. Eons of horizontal genetic transfer have permitted the entire biosphere to directly benefit from a bargain-basement source of evolutionary innovation.}, }
@article {pmid15979387, year = {2005}, author = {Hambly, E and Suttle, CA}, title = {The viriosphere, diversity, and genetic exchange within phage communities.}, journal = {Current opinion in microbiology}, volume = {8}, number = {4}, pages = {444-450}, doi = {10.1016/j.mib.2005.06.005}, pmid = {15979387}, issn = {1369-5274}, mesh = {Bacteriophages/*classification/*genetics ; Cyanobacteria/*virology ; Ecosystem ; *Gene Transfer, Horizontal ; *Genetic Variation ; Viral Proteins/genetics ; *Water Microbiology ; }, abstract = {Natural phage communities are reservoirs of the greatest uncharacterized genetic diversity on Earth. Yet, identical phage sequences can be found in extremely different environments, which implies that there is wide circulation of viral genes among distantly related host populations. Further evidence of genetic exchange among phage and host communities is the presence in phage of genes coding for proteins that are essential for photosynthesis. These observations support the idea that a primary role of host populations in phage ecology and evolution is to serve as vectors for genetic exchange.}, }
@article {pmid15978073, year = {2005}, author = {Kreth, J and Merritt, J and Shi, W and Qi, F}, title = {Co-ordinated bacteriocin production and competence development: a possible mechanism for taking up DNA from neighbouring species.}, journal = {Molecular microbiology}, volume = {57}, number = {2}, pages = {392-404}, pmid = {15978073}, issn = {0950-382X}, support = {U01 DE015018/DE/NIDCR NIH HHS/United States ; R01 DE014757/DE/NIDCR NIH HHS/United States ; U01-DE15018/DE/NIDCR NIH HHS/United States ; T32 DE007296/DE/NIDCR NIH HHS/United States ; R01-DE014757/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacterial Proteins/*physiology ; Bacteriocins/*biosynthesis/genetics ; DNA, Bacterial/genetics/*metabolism ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genes, Reporter ; Green Fluorescent Proteins ; Plasmids ; Streptococcus mutans/genetics/*metabolism ; Transformation, Bacterial/*physiology ; }, abstract = {It is important to ensure DNA availability when bacterial cells develop competence. Previous studies in Streptococcus pneumoniae demonstrated that the competence-stimulating peptide (CSP) induced autolysin production and cell lysis of its own non-competent cells, suggesting a possible active mechanism to secure a homologous DNA pool for uptake and recombination. In this study, we found that in Streptococcus mutans CSP induced co-ordinated expression of competence and mutacin production genes. This mutacin (mutacin IV) is a non-lantibiotic bacteriocin which kills closely related Streptococcal species such as S. gordonii. In mixed cultures of S. mutans and S. gordonii harbouring a shuttle plasmid, plasmid DNA transfer from S. gordonii to S. mutans was observed in a CSP and mutacin IV-dependent manner. Further analysis demonstrated an increased DNA release from S. gordonii upon addition of the partially purified mutacin IV extract. On the basis of these findings, we propose that Streptococcus mutans, which resides in a multispecies oral biofilm, may utilize the competence-induced bacteriocin production to acquire transforming DNA from other species living in the same ecological niche. This hypothesis is also consistent with a well-known phenomenon that a large genomic diversity exists among different S. mutans strains. This diversity may have resulted from extensive horizontal gene transfer.}, }
@article {pmid15973534, year = {2005}, author = {Davison, J}, title = {Risk mitigation of genetically modified bacteria and plants designed for bioremediation.}, journal = {Journal of industrial microbiology &amp; biotechnology}, volume = {32}, number = {11-12}, pages = {639-650}, pmid = {15973534}, issn = {1367-5435}, mesh = {Animals ; Bacteria/genetics ; *Biodegradation, Environmental ; Biotechnology/*methods ; *Gene Transfer, Horizontal ; Humans ; *Organisms, Genetically Modified/metabolism ; Plants/genetics ; *Plants, Genetically Modified/metabolism ; *Risk Assessment ; Transgenes ; }, abstract = {While the possible advantages of bioremediation and phytoremediation, by both recombinant microbes and plants, have been extensively reviewed, the biosafety concerns have been less extensively treated. This article reviews the possible risks associated with the use of recombinant bacteria and plants for bioremediation, with particular emphasis on ways in which molecular genetics could contribute to risk mitigation. For example, genetic techniques exist that permit the site-specific excision of unnecessary DNA, so that only the transgenes of interest remain. Other mechanisms exist whereby the recombinant plants or bacteria contain conditional suicide genes that may be activated under certain conditions. These methods act to prevent the spread and survival of the transgenic bacteria or plants in the environment, and to prevent horizontal gene flow to wild or cultivated relatives. Ways in which these genetic technologies may be applied to risk mitigation in bioremediation and phytoremediation are discussed.}, }
@article {pmid15972818, year = {2005}, author = {Díaz-Perales, A and Quesada, V and Peinado, JR and Ugalde, AP and Alvarez, J and Suárez, MF and Gomis-Rüth, FX and López-Otín, C}, title = {Identification and characterization of human archaemetzincin-1 and -2, two novel members of a family of metalloproteases widely distributed in Archaea.}, journal = {The Journal of biological chemistry}, volume = {280}, number = {34}, pages = {30367-30375}, doi = {10.1074/jbc.M504533200}, pmid = {15972818}, issn = {0021-9258}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Archaea ; Base Sequence ; Blotting, Northern ; Catalysis ; Catalytic Domain ; Computational Biology ; DNA, Complementary/metabolism ; Evolution, Molecular ; Gene Expression Regulation, Developmental ; Genome, Archaeal ; Humans ; Hydrogen-Ion Concentration ; Hydrolysis ; Liver/metabolism ; Male ; Mass Spectrometry ; Metalloproteases/*chemistry/physiology ; Molecular Sequence Data ; Myocardium/metabolism ; Peptides/chemistry ; Phylogeny ; Protein Binding ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Testis/metabolism ; Tissue Distribution ; Trypsin/pharmacology ; }, abstract = {Systematic analysis of degradomes, the complete protease repertoires of organisms, has demonstrated the large and growing complexity of proteolytic systems operating in all cells and tissues. We report here the identification of two new human metalloproteases that have been called archaemetzincin-1 (AMZ1) and archaemetzincin-2 (AMZ2) to emphasize their close relationship to putative proteases predicted by bioinformatic analysis of archaeal genomes. Both human proteins contain a catalytic domain with a core motif (HEXXHXXGX3CX4CXMX17CXXC) that includes an archetypal zinc-binding site, the methionine residue characteristic of metzincins, and four conserved cysteine residues that are not present at the equivalent positions of other human metalloproteases. Analysis of genome sequence databases revealed that AMZs are widely distributed in Archaea and vertebrates and contribute to the defining of a new metalloprotease family that has been called archaemetzincin. However, AMZ-like sequences are absent in a number of model organisms from bacteria to nematodes. Phylogenetic analysis showed that these enzymes have undergone a complex evolutionary process involving a series of lateral gene transfer, gene loss, and genetic duplication events that have shaped this novel family of metalloproteases. Northern blot analysis showed that AMZ1 and AMZ2 exhibit distinct expression patterns in human tissues. AMZ1 is mainly detected in liver and heart whereas AMZ2 is predominantly expressed in testis and heart, although both are also detectable at lower levels in other tissues. Both human enzymes were produced in Escherichia coli, and the purified recombinant proteins hydrolyzed synthetic substrates and bioactive peptides, demonstrating that they are functional proteases. Finally, these activities were abolished by inhibitors of metalloproteases, providing further evidence that AMZs belong to this catalytic class of proteolytic enzymes.}, }
@article {pmid15972517, year = {2005}, author = {Hall, LM and Fawell, SC and Shi, X and Faray-Kele, MC and Aduse-Opoku, J and Whiley, RA and Curtis, MA}, title = {Sequence diversity and antigenic variation at the rag locus of Porphyromonas gingivalis.}, journal = {Infection and immunity}, volume = {73}, number = {7}, pages = {4253-4262}, pmid = {15972517}, issn = {0019-9567}, mesh = {Alleles ; Amino Acid Sequence ; Animals ; *Antigenic Variation ; Bacterial Proteins/*genetics ; *Chromosome Mapping ; Genome, Bacterial ; Molecular Sequence Data ; Polymorphism, Genetic ; Porphyromonas gingivalis/genetics/*immunology/pathogenicity ; Rabbits ; Virulence ; }, abstract = {The rag locus of Porphyromonas gingivalis W50 encodes RagA, a predicted tonB-dependent receptor protein, and RagB, a lipoprotein that constitutes an immunodominant outer membrane antigen. The low G+C content of the locus, an association with mobility elements, and an apparent restricted distribution in the species suggested that the locus had arisen by horizontal gene transfer. In the present study, we have demonstrated that there are four divergent alleles of the rag locus. The original rag allele found in W50 was renamed rag-1, while three novel alleles, rag-2 to rag-4, were found in isolates lacking rag-1. The three novel alleles encoded variants of RagA with 63 to 71% amino acid identity to RagA1 and each other and variants of RagB with 43 to 56% amino acid identity. The RagA/B proteins have homology to numerous Bacteroides proteins, including SusC/D, implicated in polysaccharide uptake. Monoclonal and polyclonal antibodies raised against RagB1 of P. gingivalis W50 did not cross-react with proteins from isolates carrying different alleles. In a laboratory collection of 168 isolates, 26% carried rag-1, 36% carried rag-2, 25% carried rag-3, and 14% carried rag-4 (including the type strain, ATCC 33277). Restriction profiles of the locus in different isolates demonstrated polymorphism within each allele, some of which is accounted for by the presence or absence of insertion sequence elements. By reference to a previously published study on virulence in a mouse model (M. L. Laine and A. J. van Winkelhoff, Oral Microbiol. Immunol. 13:322-325, 1998), isolates that caused serious disease in mice were significantly more likely to carry rag-1 than other rag alleles.}, }
@article {pmid15969648, year = {2005}, author = {Lima, WC and Van Sluys, MA and Menck, CF}, title = {Non-gamma-proteobacteria gene islands contribute to the Xanthomonas genome.}, journal = {Omics : a journal of integrative biology}, volume = {9}, number = {2}, pages = {160-172}, doi = {10.1089/omi.2005.9.160}, pmid = {15969648}, issn = {1536-2310}, mesh = {Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genomic Islands ; Multigene Family ; Operon ; Phylogeny ; Plant Diseases/microbiology ; Polysaccharides, Bacterial/biosynthesis/genetics ; Species Specificity ; Virulence/genetics ; Xanthomonas/classification/*genetics/metabolism/pathogenicity ; Xanthomonas campestris/classification/genetics/metabolism/pathogenicity ; }, abstract = {Horizontal gene transfer, a process through which genomes acquire sequences from distantly related organisms, is believed to be a major source of genetic diversity in bacteria. A central question concerning the impact of gene transfer on bacterial genome evolution is the proportion of horizontally transferred sequences within genomes. Through BLAST search, we found that the genomes of two phytopathogens, Xanthomonas campestris pv. campestris and Xanthomonas axonopodis pv. citri, have close to 40% of the genes with the highest similarity to genes from phylogenetically distant organisms (non-gamma-proteobacteria). Most of these genes are found to be contiguous in the genome, forming genome islands, which may have been transferred from other organisms. Overall, the total number of genes within genome islands corresponds to almost one quarter of the entire xanthomonad genomes. Interestingly, many of the genes in these islands are functionally related to plant pathogenesis and virulence. Thus, these results suggest that horizontally transferred genes are clustered in the genome, and may facilitate fitness in new environments, as in the case of plant-bacteria interaction.}, }
@article {pmid15968079, year = {2005}, author = {Tauch, A and Kaiser, O and Hain, T and Goesmann, A and Weisshaar, B and Albersmeier, A and Bekel, T and Bischoff, N and Brune, I and Chakraborty, T and Kalinowski, J and Meyer, F and Rupp, O and Schneiker, S and Viehoever, P and Pühler, A}, title = {Complete genome sequence and analysis of the multiresistant nosocomial pathogen Corynebacterium jeikeium K411, a lipid-requiring bacterium of the human skin flora.}, journal = {Journal of bacteriology}, volume = {187}, number = {13}, pages = {4671-4682}, pmid = {15968079}, issn = {0021-9193}, mesh = {Anti-Bacterial Agents/*pharmacology ; Base Composition ; Corynebacterium/drug effects/genetics/metabolism ; Drug Resistance, Multiple, Bacterial/genetics ; *Genome, Bacterial ; Humans ; *Lipid Metabolism ; Molecular Sequence Data ; Skin/microbiology ; }, abstract = {Corynebacterium jeikeium is a "lipophilic" and multidrug-resistant bacterial species of the human skin flora that has been recognized with increasing frequency as a serious nosocomial pathogen. Here we report the genome sequence of the clinical isolate C. jeikeium K411, which was initially recovered from the axilla of a bone marrow transplant patient. The genome of C. jeikeium K411 consists of a circular chromosome of 2,462,499 bp and the 14,323-bp bacteriocin-producing plasmid pKW4. The chromosome of C. jeikeium K411 contains 2,104 predicted coding sequences, 52% of which were considered to be orthologous with genes in the Corynebacterium glutamicum, Corynebacterium efficiens, and Corynebacterium diphtheriae genomes. These genes apparently represent the chromosomal backbone that is conserved between the four corynebacteria. Among the genes that lack an ortholog in the known corynebacterial genomes, many are located close to transposable elements or revealed an atypical G+C content, indicating that horizontal gene transfer played an important role in the acquisition of genes involved in iron and manganese homeostasis, in multidrug resistance, in bacterium-host interaction, and in virulence. Metabolic analyses of the genome sequence indicated that the "lipophilic" phenotype of C. jeikeium most likely originates from the absence of fatty acid synthase and thus represents a fatty acid auxotrophy. Accordingly, both the complete gene repertoire and the deduced lifestyle of C. jeikeium K411 largely reflect the strict dependence of growth on the presence of exogenous fatty acids. The predicted virulence factors of C. jeikeium K411 are apparently involved in ensuring the availability of exogenous fatty acids by damaging the host tissue.}, }
@article {pmid15967998, year = {2005}, author = {Schlieper, D and Oliva, MA and Andreu, JM and Löwe, J}, title = {Structure of bacterial tubulin BtubA/B: evidence for horizontal gene transfer.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {102}, number = {26}, pages = {9170-9175}, pmid = {15967998}, issn = {0027-8424}, mesh = {Bacterial Proteins/*chemistry/metabolism ; Chlamydiaceae/metabolism ; Crystallography, X-Ray ; Cytoskeletal Proteins/metabolism ; Cytoskeleton/metabolism ; Dimerization ; Escherichia coli/metabolism ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Genome, Bacterial ; Guanosine Triphosphate/chemistry ; Light ; Microscopy, Electron ; Microtubules/chemistry ; Models, Molecular ; Molecular Chaperones ; Nucleotides/chemistry ; Polymers/chemistry ; Protein Binding ; Protein Folding ; Protein Structure, Tertiary ; Scattering, Radiation ; Tubulin/*chemistry/*genetics/metabolism ; Ultracentrifugation ; }, abstract = {alphabeta-Tubulin heterodimers, from which the microtubules of the cytoskeleton are built, have a complex chaperone-dependent folding pathway. They are thought to be unique to eukaryotes, whereas the homologue FtsZ can be found in bacteria. The exceptions are BtubA and BtubB from Prosthecobacter, which have higher sequence homology to eukaryotic tubulin than to FtsZ. Here we show that some of their properties are different from tubulin, such as weak dimerization and chaperone-independent folding. However, their structure is strikingly similar to tubulin including surface loops, and BtubA/B form tubulin-like protofilaments. Presumably, BtubA/B were transferred from a eukaryotic cell by horizontal gene transfer because their high degree of similarity to eukaryotic genes is unique within the Prosthecobacter genome.}, }
@article {pmid15965264, year = {2005}, author = {Llopart, A and Lachaise, D and Coyne, JA}, title = {Multilocus analysis of introgression between two sympatric sister species of Drosophila: Drosophila yakuba and D. santomea.}, journal = {Genetics}, volume = {171}, number = {1}, pages = {197-210}, pmid = {15965264}, issn = {0016-6731}, support = {R01 GM058260/GM/NIGMS NIH HHS/United States ; GM58260/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Chromosome Mapping ; DNA/chemistry/genetics ; DNA, Mitochondrial/chemistry/genetics ; Drosophila/*genetics ; Drosophila Proteins/*genetics ; Female ; Gene Transfer, Horizontal ; Genes, Insect/*genetics ; Genetic Variation ; Male ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Y Chromosome/genetics ; }, abstract = {Drosophila yakuba is widely distributed in sub-Saharan Africa, while D. santomea is endemic to the volcanic island of São Tomé in the Atlantic Ocean, 280 km west of Gabon. On São Tomé, D. yakuba is found mainly in open lowland forests, and D. santomea is restricted to the wet misty forests at higher elevations. At intermediate elevations, the species form a hybrid zone where hybrids occur at a frequency of approximately 1%. To determine the extent of gene flow between these species we studied polymorphism and divergence patterns in 29 regions distributed throughout the genome, including mtDNA and three genes on the Y chromosome. This multilocus approach, together with the comparison to the two allopatric species D. mauritiana and D. sechellia, allowed us to distinguish between forces that should affect all genes and forces that should act on some genes (e.g., introgression). Our results show that D. yakuba mtDNA has replaced that of D. santomea and that there is also significant introgression for two nuclear genes, yellow and salr. The majority of genes, however, has remained distinct. These two species therefore do not form a "hybrid swarm" in which much of the genome shows substantial introgression while disruptive selection maintains distinctness for only a few traits (e.g., pigmentation and male genitalia).}, }
@article {pmid15965028, year = {2005}, author = {Kunin, V and Goldovsky, L and Darzentas, N and Ouzounis, CA}, title = {The net of life: reconstructing the microbial phylogenetic network.}, journal = {Genome research}, volume = {15}, number = {7}, pages = {954-959}, pmid = {15965028}, issn = {1088-9051}, mesh = {Algorithms ; Archaea/*genetics ; Bacteria/*genetics ; Computational Biology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Models, Genetic ; *Phylogeny ; }, abstract = {It has previously been suggested that the phylogeny of microbial species might be better described as a network containing vertical and horizontal gene transfer (HGT) events. Yet, all phylogenetic reconstructions so far have presented microbial trees rather than networks. Here, we present a first attempt to reconstruct such an evolutionary network, which we term the "net of life". We use available tree reconstruction methods to infer vertical inheritance, and use an ancestral state inference algorithm to map HGT events on the tree. We also describe a weighting scheme used to estimate the number of genes exchanged between pairs of organisms. We demonstrate that vertical inheritance constitutes the bulk of gene transfer on the tree of life. We term the bulk of horizontal gene flow between tree nodes as "vines", and demonstrate that multiple but mostly tiny vines interconnect the tree. Our results strongly suggest that the HGT network is a scale-free graph, a finding with important implications for genome evolution. We propose that genes might propagate extremely rapidly across microbial species through the HGT network, using certain organisms as hubs.}, }
@article {pmid15963888, year = {2005}, author = {Doolittle, RF}, title = {Evolutionary aspects of whole-genome biology.}, journal = {Current opinion in structural biology}, volume = {15}, number = {3}, pages = {248-253}, doi = {10.1016/j.sbi.2005.04.001}, pmid = {15963888}, issn = {0959-440X}, mesh = {*Biological Evolution ; Chromosome Mapping/*methods ; *Evolution, Molecular ; Genome ; Genomics/*methods ; Phylogeny ; Sequence Analysis, DNA/*methods ; Systems Biology/*methods ; }, abstract = {A decade of access to whole-genome sequences has been increasingly revealing about the informational network relating all living organisms. Although at one point there was concern that extensive horizontal gene transfer might hopelessly muddle phylogenies, it has not proved a severe hindrance. The melding of sequence and structural information is being used to great advantage, and the prospect exists that some of the earliest aspects of life on Earth can be reconstructed, including the invention of biosynthetic and metabolic pathways. Still, some fundamental phylogenetic problems remain, including determining the root--if there is one--of the historical relationship between Archaea, Bacteria and Eukarya.}, }
@article {pmid15961030, year = {2005}, author = {Dennis, JJ}, title = {The evolution of IncP catabolic plasmids.}, journal = {Current opinion in biotechnology}, volume = {16}, number = {3}, pages = {291-298}, doi = {10.1016/j.copbio.2005.04.002}, pmid = {15961030}, issn = {0958-1669}, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, Viral ; Genome, Viral ; Open Reading Frames ; Plasmids/*genetics ; Pseudomonas/*genetics ; *Recombination, Genetic ; Sequence Homology, Nucleic Acid ; }, abstract = {The recent adoption of whole plasmid genome sequencing as a routine analytical technique has provided the basis for cataloging the historical events through which plasmids are assembled from the available families of modular plasmid components. Horizontal gene transfer mediated by plasmids plays an important role in the adaptation of bacteria to the presence of specific metabolizable compounds, including man-made chemicals, in the surrounding environment. Bacterial plasmid genome sequence comparisons indicate that plasmids have complex genetic histories resulting from transposition, homologous recombination, and illegitimate recombinational events. Evidence from IncP plasmid genome sequences indicates that cryptic plasmid backbones acquire diverse catabolic pathways through gene capture and horizontal gene transfer.}, }
@article {pmid15961029, year = {2005}, author = {Larkin, MJ and Kulakov, LA and Allen, CC}, title = {Biodegradation and Rhodococcus--masters of catabolic versatility.}, journal = {Current opinion in biotechnology}, volume = {16}, number = {3}, pages = {282-290}, doi = {10.1016/j.copbio.2005.04.007}, pmid = {15961029}, issn = {0958-1669}, mesh = {Biodegradation, Environmental ; Conserved Sequence ; Cytochrome P-450 Enzyme System/metabolism ; Dioxygenases/metabolism ; Environmental Pollutants/metabolism ; Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Rhodococcus/*genetics/metabolism ; }, abstract = {The genus Rhodococcus is a very diverse group of bacteria that possesses the ability to degrade a large number of organic compounds, including some of the most difficult compounds with regard to recalcitrance and toxicity. They achieve this through their capacity to acquire a remarkable range of diverse catabolic genes and their robust cellular physiology. Rhodococcus appear to have adopted a strategy of hyper-recombination associated with a large genome. Notably, they harbour large linear plasmids that contribute to their catabolic diversity by acting as 'mass storage' for a large number of catabolic genes. In addition, there is increasing evidence that multiple pathways and gene homologues are present that further increase the catabolic versatility and efficiency of Rhodococcus.}, }
@article {pmid15958783, year = {2005}, author = {Jenke-Kodama, H and Sandmann, A and Müller, R and Dittmann, E}, title = {Evolutionary implications of bacterial polyketide synthases.}, journal = {Molecular biology and evolution}, volume = {22}, number = {10}, pages = {2027-2039}, doi = {10.1093/molbev/msi193}, pmid = {15958783}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Bacteria/*classification/enzymology/genetics ; Bacterial Proteins/chemistry/*genetics ; Genome, Bacterial ; *Phylogeny ; Polyketide Synthases/chemistry/*genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {Polyketide synthases (PKS) perform a stepwise biosynthesis of diverse carbon skeletons from simple activated carboxylic acid units. The products of the complex pathways possess a wide range of pharmaceutical properties, including antibiotic, antitumor, antifungal, and immunosuppressive activities. We have performed a comprehensive phylogenetic analysis of multimodular and iterative PKS of bacteria and fungi and of the distinct types of fatty acid synthases (FAS) from different groups of organisms based on the highly conserved ketoacyl synthase (KS) domains. Apart from enzymes that meet the classification standards we have included enzymes involved in the biosynthesis of mycolic acids, polyunsaturated fatty acids (PUFA), and glycolipids in bacteria. This study has revealed that PKS and FAS have passed through a long joint evolution process, in which modular PKS have a central position. They appear to have derived from bacterial FAS and primary iterative PKS and, in addition, share a common ancestor with animal FAS and secondary iterative PKS. Furthermore, we have carried out a phylogenomic analysis of all modular PKS that are encoded by the complete eubacterial genomes currently available in the database. The phylogenetic distribution of acyltransferase and KS domain sequences revealed that multiple gene duplications, gene losses, as well as horizontal gene transfer (HGT) have contributed to the evolution of PKS I in bacteria. The impact of these factors seems to vary considerably between the bacterial groups. Whereas in actinobacteria and cyanobacteria the majority of PKS I genes may have evolved from a common ancestor, several lines of evidence indicate that HGT has strongly contributed to the evolution of PKS I in proteobacteria. Discovery of new evolutionary links between PKS and FAS and between the different PKS pathways in bacteria may help us in understanding the selective advantage that has led to the evolution of multiple secondary metabolite biosyntheses within individual bacteria.}, }
@article {pmid15958522, year = {2005}, author = {Pajusola, K and Künnapuu, J and Vuorikoski, S and Soronen, J and André, H and Pereira, T and Korpisalo, P and Ylä-Herttuala, S and Poellinger, L and Alitalo, K}, title = {Stabilized HIF-1alpha is superior to VEGF for angiogenesis in skeletal muscle via adeno-associated virus gene transfer.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {19}, number = {10}, pages = {1365-1367}, doi = {10.1096/fj.05-3720fje}, pmid = {15958522}, issn = {1530-6860}, mesh = {Animals ; Capillary Permeability ; Dependovirus/*genetics ; *Gene Transfer, Horizontal ; *Genetic Therapy ; Humans ; Hypoxia-Inducible Factor 1, alpha Subunit/*genetics/metabolism ; Mice ; Muscle, Skeletal/*blood supply ; *Neovascularization, Physiologic ; Perfusion ; Platelet Endothelial Cell Adhesion Molecule-1/analysis ; Proto-Oncogene Proteins c-sis/genetics ; Vascular Endothelial Growth Factor A/*genetics ; }, abstract = {Therapeutic angiogenesis provides a potential alternative for the treatment of cardiovascular ischemic diseases. Vascular endothelial growth factor (VEGF) is an important component of the angiogenic response to ischemia. Here we used adeno-associated virus (AAV) gene delivery to skeletal muscle to examine the effects of VEGF vs. a stabilized form of hypoxia-inducible factor-1alpha (HIF-1alpha). The recombinant AAVs were injected into mouse tibialis anterior muscle, and their effects were analyzed by immunohistochemistry and functional assays. These analyses showed that stabilized HIF-1alpha markedly increase capillary sprouting and proliferation, whereas VEGF164 or VEGF120 induced only proliferation of endothelial cells without formation of proper capillary structures. The Evans Blue permeability assay indicated that, unlike VEGF, HIF-1alpha overexpression did not increase vascular leakiness in the transduced muscle. Doppler ultrasound imaging showed that vascular perfusion in the HIF-1alpha treated muscles was significantly enhanced when compared to the controls and not further improved by co-expression of the arteriogenic growth factors angiopoietin-1 or platelet-derived growth factor-B. Our results show that AAV-mediated transduction of a stabilized form of HIF-1alpha can circumvent the problems associated with overexpression of individual angiogenic growth factors. HIF-1alpha should thus offer a potent alternative for pro-angiogenic gene therapy.}, }
@article {pmid15954096, year = {2005}, author = {Kurland, CG}, title = {What tangled web: barriers to rampant horizontal gene transfer.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {27}, number = {7}, pages = {741-747}, doi = {10.1002/bies.20258}, pmid = {15954096}, issn = {0265-9247}, mesh = {Animals ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome ; Humans ; *Models, Genetic ; Models, Theoretical ; Mutation ; Phylogeny ; }, abstract = {Dawkins in his The Selfish Gene(1) quite aptly applies the term "selfish" to parasitic repetitive DNA sequences endemic to eukaryotic genomes, especially vertebrates. Doolittle and Sapienza(2) as well as Orgel and Crick(3) enlivened this notion of selfish DNA with the identification of such repetitive sequences as remnants of mobile elements such as transposons. In addition, Orgel and Crick(3) associated parasitic DNA with a potential to outgrow their host genomes by propagating both vertically via conventional genome replication as well as infectiously by horizontal gene transfer (HGT) to other genomes. Still later, Doolittle(4) speculated that unchecked HGT between unrelated genomes so complicates phylogeny that the conventional representation of a tree of life would have to be replaced by a thicket or a web of life.(4) In contrast, considerable data now show that reconstructions based on whole genome sequences are consistent with the conventional "tree of life".(5-10) Here, we identify natural barriers that protect modern genome populations from the inroads of rampant HGT.}, }
@article {pmid15950251, year = {2005}, author = {Brakhage, AA and Al-Abdallah, Q and Tüncher, A and Spröte, P}, title = {Evolution of beta-lactam biosynthesis genes and recruitment of trans-acting factors.}, journal = {Phytochemistry}, volume = {66}, number = {11}, pages = {1200-1210}, doi = {10.1016/j.phytochem.2005.02.030}, pmid = {15950251}, issn = {0031-9422}, mesh = {Anti-Bacterial Agents/*biosynthesis ; Bacteria/*genetics/*metabolism ; Evolution, Molecular ; Fungi/genetics/*metabolism ; Gene Expression Regulation, Bacterial ; Gene Expression Regulation, Fungal ; Gene Transfer, Horizontal ; *Transcriptional Activation ; beta-Lactams/*metabolism ; }, abstract = {Penicillins and cephalosporins belong chemically to the group of beta-lactam antibiotics. The formation of hydrophobic penicillins has been reported in fungi only, notably Penicillium chrysogenum and Emericella nidulans, whereas the hydrophilic cephalosporins are produced by both fungi, e.g., Acremonium chrysogenum (cephalosporin C), and bacteria. The producing bacteria include Gram-negatives and Gram-positives, e.g. Lysobacter lactamdurans (cephabacins) and Streptomyces clavuligerus (cephamycin C), respectively. For a long time the evolutionary origin of beta-lactam biosynthesis genes in fungi has been discussed. As often, there are arguments for both hypotheses, i.e., horizontal gene transfer from bacteria to fungi versus vertical descent. There were strong arguments in favour of horizontal gene transfer, e.g., fungal genes were clustered or some genes lack introns. The recent identification and characterisation of cis-/trans-elements involved in the regulation of the beta-lactam biosynthesis genes has provided new arguments in favour of horizontal gene transfer. In contrast to the bacterium S. clavuligerus, all regulators of fungal beta-lactam biosynthesis genes represent wide-domain regulators which were recruited to also regulate the beta-lactam biosynthesis genes. Moreover, the fungal regulatory genes are not part of the gene cluster. If bacterial regulators were co-transferred with the gene cluster from bacteria to fungi, most likely they would have been non-functional in eukaryotes and lost during evolution. Alternatively, it is conceivable that only a part of the beta-lactam biosynthesis gene cluster was transferred to some fungi, e.g., the acvA and ipnA gene without a regulatory gene.}, }
@article {pmid15950129, year = {2005}, author = {Coenye, T and Vandamme, P}, title = {Displacement of epsilon-proteobacterial core genes by horizontally transferred homologous genes.}, journal = {Research in microbiology}, volume = {156}, number = {5-6}, pages = {738-747}, doi = {10.1016/j.resmic.2005.01.016}, pmid = {15950129}, issn = {0923-2508}, mesh = {Computational Biology ; Epsilonproteobacteria/classification/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Operon ; Phylogeny ; *Recombination, Genetic ; }, abstract = {The introduction of novel genes by horizontal gene transfer (HGT) is considered an alternative mechanism for genetic adaptation, leading to diversification and speciation. The goal of this study was to determine which genes that are present in all sequenced epsilon-proteobacterial genomes were acquired by HGT. In our approach we used BLAST analysis to reduce the number of genes that subsequently needed to be analysed using more in-depth phylogenetic methods, including neighbour-joining and maximum likelihood. Among the 991 core genes found in all five completed epsilon-proteobacterial genome sequences, we identified 30 genes that were probably acquired by HGT. It is proposed that these genes displaced an ancestral core gene with a similar function. Although it was not possible to identify putative donor taxa for all acquired genes, it was clear that genes were acquired from a wide range of Bacteria, including Spirochaetes, Firmicutes, Actinobacteria, mycoplasmas and several subdivisions of the Proteobacteria. We did not observe HGT from Archaea to the epsilon-Proteobacteria. The majority of acquired genes were operational genes involved in transport, metabolism, signal transduction and energy production and conversion.}, }
@article {pmid15949858, year = {2006}, author = {Hendrickx, B and Junca, H and Vosahlova, J and Lindner, A and Rüegg, I and Bucheli-Witschel, M and Faber, F and Egli, T and Mau, M and Schlömann, M and Brennerova, M and Brenner, V and Pieper, DH and Top, EM and Dejonghe, W and Bastiaens, L and Springael, D}, title = {Alternative primer sets for PCR detection of genotypes involved in bacterial aerobic BTEX degradation: distribution of the genes in BTEX degrading isolates and in subsurface soils of a BTEX contaminated industrial site.}, journal = {Journal of microbiological methods}, volume = {64}, number = {2}, pages = {250-265}, doi = {10.1016/j.mimet.2005.04.018}, pmid = {15949858}, issn = {0167-7012}, mesh = {Actinobacteria/genetics/metabolism ; Bacteria, Aerobic/*genetics/metabolism ; Bacterial Proteins ; Biodegradation, Environmental ; Carbohydrate Epimerases ; DNA Primers ; Environmental Pollution ; Gene Transfer, Horizontal ; Genes, Bacterial/*physiology ; Hydrocarbons/*metabolism ; Industrial Waste ; Polymerase Chain Reaction/*methods ; Proteobacteria/genetics/metabolism ; *Soil Microbiology ; Soil Pollutants/*metabolism ; Species Specificity ; Substrate Specificity ; }, abstract = {Eight new primer sets were designed for PCR detection of (i) mono-oxygenase and dioxygenase gene sequences involved in initial attack of bacterial aerobic BTEX degradation and of (ii) catechol 2,3-dioxygenase gene sequences responsible for meta-cleavage of the aromatic ring. The new primer sets allowed detection of the corresponding genotypes in soil with a detection limit of 10(3)-10(4) or 10(5)-10(6) gene copies g(-1) soil, assuming one copy of the gene per cell. The primer sets were used in PCR to assess the distribution of the catabolic genes in BTEX degrading bacterial strains and DNA extracts isolated from soils sampled from different locations and depths (vadose, capillary fringe and saturated zone) within a BTEX contaminated site. In both soil DNA and the isolates, tmoA-, xylM- and xylE1-like genes were the most frequently recovered BTEX catabolic genes. xylM and xylE1 were only recovered from material from the contaminated samples while tmoA was detected in material from both the contaminated and non-contaminated samples. The isolates, mainly obtained from the contaminated locations, belonged to the Actinobacteria or Proteobacteria (mainly Pseudomonas). The ability to degrade benzene was the most common BTEX degradation phenotype among them and its distribution was largely congruent with the distribution of the tmoA-like genotype. The presence of tmoA and xylM genes in phylogenetically distant strains indicated the occurrence of horizontal transfer of BTEX catabolic genes in the aquifer. Overall, these results show spatial variation in the composition of the BTEX degradation genes and hence in the type of BTEX degradation activity and pathway, at the examined site. They indicate that bacteria carrying specific pathways and primarily carrying tmoA/xylM/xylE1 genotypes, are being selected upon BTEX contamination.}, }
@article {pmid15948584, year = {2005}, author = {Peuke, AD and Rennenberg, H}, title = {Phytoremediation with transgenic trees.}, journal = {Zeitschrift fur Naturforschung. C, Journal of biosciences}, volume = {60}, number = {3-4}, pages = {199-207}, pmid = {15948584}, issn = {0939-5075}, mesh = {*Biodegradation, Environmental ; Escherichia coli ; Glutamate-Cysteine Ligase/genetics/metabolism ; Glutathione/metabolism ; Metals, Heavy/*pharmacokinetics ; Pesticides/*pharmacokinetics ; *Plants, Genetically Modified ; Populus/*metabolism ; }, abstract = {In the present paper actual trends in the use of transgenic trees for phytoremediation of contaminated soils are reviewed. In this context a current field trial in which transgenic poplars with enhanced GSH synthesis and hence elevated capacity for phytochelatin production are compared with wildtype plants for the removal of heavy metals at different levels of contamination and under different climatic conditions. The studies are carried out with grey poplar (Populus tremula x P. alba), wildtype plants and plants overexpressing the gene for gamma-glutamylcysteine synthetase (gshI) from E. coli in the cytosol. The expression of this gene in poplar leads to two- to four-fold enhanced GSH concentrations in the leaves. In greenhouse experiments under controlled conditions these transgenic poplars showed a high potential for uptake and detoxification of heavy metals and pesticides. This capacity is evaluated in field experiments. Further aims of the project are to elucidate (a) the stability of the transgene under field conditions and (b) the possibility of horizontal gene transfer to microorganisms in the rhizosphere. The results will help to assess the biosafety risk of the use of transgenic poplar for phytoremediation of soils.}, }
@article {pmid15947202, year = {2005}, author = {Hall, C and Brachat, S and Dietrich, FS}, title = {Contribution of horizontal gene transfer to the evolution of Saccharomyces cerevisiae.}, journal = {Eukaryotic cell}, volume = {4}, number = {6}, pages = {1102-1115}, pmid = {15947202}, issn = {1535-9778}, mesh = {Amino Acid Sequence ; Bayes Theorem ; Crosses, Genetic ; Dihydroorotate Dehydrogenase ; *Evolution, Molecular ; Fungal Proteins/chemistry ; *Gene Transfer, Horizontal ; *Genes, Fungal ; Genetic Complementation Test ; Genome, Fungal ; Molecular Sequence Data ; Oxidoreductases Acting on CH-CH Group Donors/genetics ; Phylogeny ; Saccharomyces cerevisiae/*genetics/growth &amp; development ; Saccharomycetales/genetics ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Sulfatases/genetics ; }, abstract = {The genomes of the hemiascomycetes Saccharomyces cerevisiae and Ashbya gossypii have been completely sequenced, allowing a comparative analysis of these two genomes, which reveals that a small number of genes appear to have entered these genomes as a result of horizontal gene transfer from bacterial sources. One potential case of horizontal gene transfer in A. gossypii and 10 potential cases in S. cerevisiae were identified, of which two were investigated further. One gene, encoding the enzyme dihydroorotate dehydrogenase (DHOD), is potentially a case of horizontal gene transfer, as shown by sequencing of this gene from additional bacterial and fungal species to generate sufficient data to construct a well-supported phylogeny. The DHOD-encoding gene found in S. cerevisiae, URA1 (YKL216W), appears to have entered the Saccharomycetaceae after the divergence of the S. cerevisiae lineage from the Candida albicans lineage and possibly since the divergence from the A. gossypii lineage. This gene appears to have come from the Lactobacillales, and following its acquisition the endogenous eukaryotic DHOD gene was lost. It was also shown that the bacterially derived horizontally transferred DHOD is required for anaerobic synthesis of uracil in S. cerevisiae. The other gene discussed in detail is BDS1, an aryl- and alkyl-sulfatase gene of bacterial origin that we have shown allows utilization of sulfate from several organic sources. Among the eukaryotes, this gene is found in S. cerevisiae and Saccharomyces bayanus and appears to derive from the alpha-proteobacteria.}, }
@article {pmid15937755, year = {2005}, author = {Nijssen, S and Florijn, A and Top, J and Willems, R and Fluit, A and Bonten, M}, title = {Unnoticed spread of integron-carrying Enterobacteriaceae in intensive care units.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {41}, number = {1}, pages = {1-9}, doi = {10.1086/430711}, pmid = {15937755}, issn = {1537-6591}, mesh = {Adult ; Aged ; Anti-Bacterial Agents/pharmacology ; Cephalosporins/pharmacology ; Cross Infection/epidemiology/microbiology/transmission ; Drug Resistance, Multiple, Bacterial/*genetics ; Enterobacteriaceae/*drug effects/genetics ; Enterobacteriaceae Infections/*epidemiology/microbiology/*transmission ; Female ; Gene Transfer, Horizontal ; Humans ; Integrases ; Integrons/*genetics ; *Intensive Care Units ; Male ; Microbial Sensitivity Tests ; Middle Aged ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Prevalence ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Integrons are strongly associated with multidrug resistance in Enterobacteriaceae. Little is known about the natural history of integron-associated resistance in hospitals during nonoutbreak periods. The prevalence of integrons and the incidence of cross-transmission and horizontal gene transfer in Enterobacteriaceae with reduced susceptibility to cephalosporins (ERSC) were determined for 2 intensive care units (ICUs).<br><br>METHODS: Microbiological surveillance using rectal swab samples obtained 2 times per week and genotyping using amplified fragment-length polymorphism (AFLP) were used to determine colonization with and genetic relatedness of ERSC. IntI1 integrase polymerase chain reaction (PCR), conserved-segment PCR, restriction fragment-length polymorphism, and DNA sequencing were used to determine the prevalence and contents of integrons.<br><br>RESULTS: Of 457 patients, 121 patients were colonized with ERSC, and 174 isolates underwent AFLP and PCR. In 34 isolates obtained from 31 patients, 11 different integrons were identified; these integrons encoded resistance to streptomycin/spectinomycin, gentamicin/tobramycin/kanamycin, chloramphenicol, and trimethoprim. Integrons could be divided into 7 clusters of > or =2 isolates each. Compared with isolates that were negative for integrons, isolates that were positive for integrons were associated with resistance to piperacillin, cephalosporins, aminoglycosides, and quinolones. Acquisition rates of integron-carrying ERSC were 10 cases per 1000 patient-days in the first ICU and 8 cases per 1000 patient-days in the second ICU, with most cases (26 of 34) being acquired during the ICU stay. Nineteen episodes resulted from cross-transmission. In addition, 2 cases of interspecies transfer and 1 case of intraspecies transfer of integrons were recorded. Younger age was independently associated with acquisition of integron-carrying ERSC (hazard ratio, 0.953; 95% confidence interval, 0.926-0.987).<br><br>CONCLUSION: Surveillance, genotyping, and integron analysis identified previously unnoticed outbreaks of integron-carrying ERSC. Cross-transmission appeared to be the dominant route of transmission. Therefore, barrier precautions are necessary to prevent further spread.}, }
@article {pmid15937190, year = {2005}, author = {Ou, K and Ong, C and Koh, SY and Rodrigues, F and Sim, SH and Wong, D and Ooi, CH and Ng, KC and Jikuya, H and Yau, CC and Soon, SY and Kesuma, D and Lee, MA and Tan, P}, title = {Integrative genomic, transcriptional, and proteomic diversity in natural isolates of the human pathogen Burkholderia pseudomallei.}, journal = {Journal of bacteriology}, volume = {187}, number = {12}, pages = {4276-4285}, pmid = {15937190}, issn = {0021-9193}, mesh = {Bacterial Proteins/genetics ; Burkholderia pseudomallei/*genetics ; *Gene Expression Profiling ; *Genetic Variation ; Genome, Bacterial ; Phenotype ; Protein Isoforms/genetics ; Proteome ; Species Specificity ; *Transcription, Genetic ; }, abstract = {Natural isolates of pathogenic bacteria can exhibit a broad range of phenotypic traits. To investigate the molecular mechanisms contributing to such phenotypic variability, we compared the genomes, transcriptomes, and proteomes of two natural isolates of the gram-negative bacterium Burkholderia pseudomallei, the causative agent of the human disease melioidosis. Significant intrinsic genomic, transcriptional, and proteomic variations were observed between the two strains involving genes of diverse functions. We identified 16 strain-specific regions in the B. pseudomallei K96243 reference genome, and for eight regions their differential presence could be ascribed to either DNA acquisition or loss. A remarkable 43% of the transcriptional differences between the strains could be attributed to genes that were differentially present between K96243 and Bp15682, demonstrating the importance of lateral gene transfer or gene loss events in contributing to pathogen diversity at the gene expression level. Proteins expressed in a strain-specific manner were similarly correlated at the gene expression level, but up to 38% of the global proteomic variation between strains comprised proteins expressed in both strains but associated with strain-specific protein isoforms. Collectively, >65 hypothetical genes were transcriptionally or proteomically expressed, supporting their bona fide biological presence. Our results provide, for the first time, an integrated framework for classifying the repertoire of natural variations existing at distinct molecular levels for an important human pathogen.}, }
@article {pmid15937172, year = {2005}, author = {Faruque, SM and Bin Naser, I and Fujihara, K and Diraphat, P and Chowdhury, N and Kamruzzaman, M and Qadri, F and Yamasaki, S and Ghosh, AN and Mekalanos, JJ}, title = {Genomic sequence and receptor for the Vibrio cholerae phage KSF-1phi: evolutionary divergence among filamentous vibriophages mediating lateral gene transfer.}, journal = {Journal of bacteriology}, volume = {187}, number = {12}, pages = {4095-4103}, pmid = {15937172}, issn = {0021-9193}, support = {R01 GM068851/GM/NIGMS NIH HHS/United States ; GM068851/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteriophages/*genetics/pathogenicity ; *Biological Evolution ; Fimbriae, Bacterial ; *Gene Transfer, Horizontal ; Genome, Viral ; Molecular Sequence Data ; Phylogeny ; Vibrio cholerae/*virology ; }, abstract = {KSF-1phi, a novel filamentous phage of Vibrio cholerae, supports morphogenesis of the RS1 satellite phage by heterologous DNA packaging and facilitates horizontal gene transfer. We analyzed the genomic sequence, morphology, and receptor for KSF-1phi infection, as well as its phylogenetic relationships with other filamentous vibriophages. While strains carrying the mshA gene encoding mannose-sensitive hemagglutinin (MSHA) type IV pilus were susceptible to KSF-1phi infection, naturally occurring MSHA-negative strains and an mshA deletion mutant were resistant. Furthermore, d-mannose as well as a monoclonal antibody against MSHA inhibited infection of MSHA-positive strains by the phage, suggesting that MSHA is the receptor for KSF-1phi. The phage genome comprises 7,107 nucleotides, containing 14 open reading frames, 4 of which have predicted protein products homologous to those of other filamentous phages. Although the overall genetic organization of filamentous phages appears to be preserved in KSF-1phi, the genomic sequence of the phage does not have a high level of identity with that of other filamentous phages and reveals a highly mosaic structure. Separate phylogenetic analysis of genomic sequences encoding putative replication proteins, receptor-binding proteins, and Zot-like proteins of 10 different filamentous vibriophages showed different results, suggesting that the evolution of these phages involved extensive horizontal exchange of genetic material. Filamentous phages which use type IV pili as receptors were found to belong to different branches. While one of these branches is represented by CTXphi, which uses the toxin-coregulated pilus as its receptor, at least four evolutionarily diverged phages share a common receptor MSHA, and most of these phages mediate horizontal gene transfer. Since MSHA is present in a wide variety of V. cholerae strains and is presumed to express in the environment, diverse filamentous phages using this receptor are likely to contribute significantly to V. cholerae evolution.}, }
@article {pmid15936660, year = {2005}, author = {Breitbart, M and Rohwer, F}, title = {Here a virus, there a virus, everywhere the same virus?.}, journal = {Trends in microbiology}, volume = {13}, number = {6}, pages = {278-284}, doi = {10.1016/j.tim.2005.04.003}, pmid = {15936660}, issn = {0966-842X}, mesh = {Bacteriophages/genetics/physiology ; *Biodiversity ; Gene Transfer, Horizontal ; Genes, Viral ; *Genome, Viral ; *Virus Physiological Phenomena ; Viruses/*genetics ; }, abstract = {There are an estimated 10(31) viruses on Earth, most of which are phages that infect bacteria. Metagenomic analyses have shown that environmental viral communities are incredibly diverse. There are an estimated 5000 viral genotypes in 200 liters of seawater and possibly a million different viral genotypes in one kilogram of marine sediment. By contrast, some culturing and molecular studies have found that viruses move between different biomes. Together, these findings suggest that viral diversity could be high on a local scale but relatively limited globally. Also, by moving between environments, viruses can facilitate horizontal gene transfer.}, }
@article {pmid15936656, year = {2005}, author = {Bapteste, E and Walsh, DA}, title = {Does the 'Ring of Life' ring true?.}, journal = {Trends in microbiology}, volume = {13}, number = {6}, pages = {256-261}, doi = {10.1016/j.tim.2005.03.012}, pmid = {15936656}, issn = {0966-842X}, mesh = {*Eukaryotic Cells ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome ; *Models, Genetic ; Phylogeny ; }, abstract = {In a recent stimulating paper, Rivera and Lake applied a new phylogenetic method to study the evolution of genomes, which challenges the classical representation of the Tree of Life. Acknowledging the evolutionary importance of lateral gene transfer, they used the conditioned genome approach to reconstruct the Tree of Life, and in the end proposed a Ring of Life. They explained that the Ring of Life structure is a result of a single fusion event between two prokaryotic genomes at the base of the eukaryotic tree, probably between the ancestors of a photosynthetic bacterium and an archaeon. Because this constitutes an important conclusion with regards to the evolutionary process and origin of the eukaryotic cell, their work deserves further attention before these conclusions can be accepted. Here we question the reconstruction and the meaning of the Ring of Life. In addition to general problems associated with gene-content-based phylogenetic analyses, we discuss some implicit premises and potential weaknesses of the conditioned genome method and conclude that, although Rivera and Lake's conclusions might be right, they have not been established by their current approach.}, }
@article {pmid15935863, year = {2005}, author = {Kim, YH and Cerniglia, CE}, title = {Influence of erythromycin A on the microbial populations in aquaculture sediment microcosms.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {73}, number = {3}, pages = {230-241}, doi = {10.1016/j.aquatox.2005.03.013}, pmid = {15935863}, issn = {0166-445X}, mesh = {Anti-Bacterial Agents/*metabolism/toxicity ; Base Sequence ; Biodegradation, Environmental ; Cluster Analysis ; Colony Count, Microbial ; DNA Primers ; Erythromycin/chemistry/*metabolism/toxicity ; Geologic Sediments/*microbiology ; Kinetics ; *Models, Biological ; Molecular Sequence Data ; Polymorphism, Restriction Fragment Length ; Pseudomonas/drug effects/*genetics/*metabolism ; RNA, Ribosomal, 16S/genetics ; Rivers/*chemistry ; Sequence Analysis, DNA ; Washington ; }, abstract = {Degradation of erythromycin A was studied using two sediment samples obtained from the salmon and trout hatchery sites at Hupp Springs (HS) and Goldendale (GD), Washington, United States. The former site had been treated for 3 years with erythromycin-medicated feed prior to the experiments, and the latter site had not been treated with any antibiotic for at least 6 years. The two sediment microcosms treated with either N-[methyl-14C]erythromycin A or [1,3,5,7,9,11,13-14C]erythromycin A showed S-curves for erythromycin A mineralization with a prolonged lag time of 120 days, except for GD microcosms treated with [1,3,5,7,9,11,13-14C]erythromycin A. We proposed a simplified logistic model to interpret the mineralization curves under the assumption of the low densities of initial populations metabolizing erythromycin A. The model was helpful for knowing the biological potential for erythromycin A degradation in sediments. Although erythromycin A added to the two sediment microcosms did not significantly alter the numbers of total viable aerobic bacteria or erythromycin-resistant bacteria, it affected the bacterial composition. The influence on the bacterial composition appeared to be greater in GD microcosms without pre-exposure to antibiotics. PCR-RFLP and DNA sequence analyses of the 16S ribosomal RNA gene and the erythromycin esterase (ere) gene revealed that ereA type 2 (ereA2) was present in potentially erythromycin-degrading Pseudomonas spp. strains GD100, GD200, HS100, HS200 and HS300, isolated from erythromycin-treated and non-treated GD and HS microcosms. Erythromycin A appeared to influence the development and proliferation of strain GD200, possibly via the lateral gene transfer of ereA2.}, }
@article {pmid15933011, year = {2005}, author = {Zhang, R and Zhang, CT}, title = {Genomic islands in the Corynebacterium efficiens genome.}, journal = {Applied and environmental microbiology}, volume = {71}, number = {6}, pages = {3126-3130}, pmid = {15933011}, issn = {0099-2240}, mesh = {Aspartate Kinase/genetics ; Bacterial Proteins/chemistry/genetics ; Base Composition ; Base Sequence ; Corynebacterium/*enzymology/genetics ; Enzyme Stability ; *Genome, Bacterial ; *Genomic Islands/genetics ; Hot Temperature ; Molecular Sequence Data ; }, abstract = {Corynebacterium efficiens is a gram-positive nonpathogenic bacterium which can grow and produce glutamate at 40 degrees C or above. By using the cumulative GC profile method, we have identified four genomic islands which have many unifying genomic island-specific features in the C. efficiens genome. The presence of the gene encoding an aspartate kinase in a genomic island helps explain the unexpected low thermal stability of this enzyme; i.e., the adaptive mutations have not occurred extensively due to the recent horizontal gene transfer.}, }
@article {pmid15932992, year = {2005}, author = {Luo, H and Wan, K and Wang, HH}, title = {High-frequency conjugation system facilitates biofilm formation and pAMbeta1 transmission by Lactococcus lactis.}, journal = {Applied and environmental microbiology}, volume = {71}, number = {6}, pages = {2970-2978}, pmid = {15932992}, issn = {0099-2240}, mesh = {Bacterial Proteins/genetics ; Biofilms/*growth &amp; development ; *Conjugation, Genetic ; F Factor/genetics ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Lactococcus lactis/*genetics/growth &amp; development ; Microscopy, Electron, Scanning ; Nisin/drug effects ; *Plasmids ; }, abstract = {The importance of conjugation as a mechanism to spread biofilm determinants among microbial populations was illustrated with the gram-positive bacterium Lactococcus lactis. Conjugation triggered the enhanced expression of the clumping protein CluA, which is a main biofilm attribute in lactococci. Clumping transconjugants further transmitted the biofilm-forming elements among the lactococcal population at a much higher frequency than the parental non-clumping donor. This cell-clumping-associated high-frequency conjugation system also appeared to serve as an internal enhancer facilitating the dissemination of the broad-host-range drug resistance gene-encoding plasmid pAMbeta1 within L. lactis, at frequencies more than 10,000 times higher than those for the non-clumping parental donor strain. The implications of this finding for antibiotic resistance gene dissemination are discussed.}, }
@article {pmid15932990, year = {2005}, author = {Regeard, C and Maillard, J and Dufraigne, C and Deschavanne, P and Holliger, C}, title = {Indications for acquisition of reductive dehalogenase genes through horizontal gene transfer by Dehalococcoides ethenogenes strain 195.}, journal = {Applied and environmental microbiology}, volume = {71}, number = {6}, pages = {2955-2961}, pmid = {15932990}, issn = {0099-2240}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/*genetics ; Base Composition ; Chloroflexi/*enzymology/*genetics ; Computational Biology ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Molecular Sequence Data ; Oxidoreductases/chemistry/*genetics ; Recombinases ; }, abstract = {The genome of Dehalococcoides ethenogenes strain 195, an anaerobic dehalorespiring bacterium, contains 18 copies of putative reductive dehalogenase genes, including the well-characterized tceA gene, whose gene product functions as the key enzyme in the environmentally important dehalorespiration process. The genome of D. ethenogenes was analyzed using a bioinformatic tool based on the frequency of oligonucleotides. The results in the form of a genomic signature revealed several local disruptions of the host signature along the genome sequence. These fractures represent DNA segments of potentially foreign origin, so-called atypical regions, which may have been acquired by an ancestor through horizontal gene transfer. Most interestingly, 15 of the 18 reductive dehalogenase genes, including the tceA gene, were found to be located in these regions, strongly indicating the foreign nature of the dehalorespiration activity. The GC content and the presence of recombinase genes within some of these regions corroborate this hypothesis. A hierarchical classification of the atypical regions containing the reductive dehalogenase genes indicated that these regions were probably acquired by several gene transfer events.}, }
@article {pmid15932759, year = {2005}, author = {Koslowski, T and Zehender, F}, title = {Towards a quantitative understanding of horizontal gene transfer: a kinetic model.}, journal = {Journal of theoretical biology}, volume = {237}, number = {1}, pages = {23-29}, doi = {10.1016/j.jtbi.2005.03.028}, pmid = {15932759}, issn = {0022-5193}, mesh = {Animals ; Archaea/genetics ; Cell Membrane Permeability ; Cyanobacteria/genetics ; Eukaryotic Cells/physiology ; Gene Duplication ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; *Models, Genetic ; Mutation ; Symbiosis ; }, abstract = {In this work, we present a simple kinetic model of horizontal gene transfer. It describes the processes of gene duplication, mutation, gene transfer and the regulation of the total size of the genome for genetically homogeneous prokaryotic species or strains. The emerging nonlinear system of first-order differential equations can be linearized at the stationary point. For selected models, we give an analytical solution for the number of foreign and native genes within a species. We identify a regime characterized by a fast gene transfer rate and species with a mixed genome, a slow gene transfer regime with pure organisms, and a crossover region. The data are compared to experiments, and the biological implications of our model are discussed.}, }
@article {pmid15932694, year = {2005}, author = {Wang, CQ and Wang, S and Tang, DM and Lin, X and Ding, HY and Xie, XL and Xu, YM and Wang, BY and Huang, DJ}, title = {[Effects of TIMP-2 gene transfer on atherosclerotic plaque in rabbits].}, journal = {Zhonghua xin xue guan bing za zhi}, volume = {33}, number = {5}, pages = {405-410}, pmid = {15932694}, issn = {0253-3758}, mesh = {Animals ; Atherosclerosis/*enzymology/pathology ; Blotting, Western ; Collagen/analysis ; *Gene Transfer, Horizontal ; *Matrix Metalloproteinase Inhibitors ; RNA, Messenger/analysis ; Rabbits ; Reverse Transcriptase Polymerase Chain Reaction ; Tissue Inhibitor of Metalloproteinase-2/*genetics/physiology ; }, abstract = {OBJECTIVE: To evaluate the effects of TIMP-2 local gene transfer on atherosclerotic plaque.<br><br>METHODS: Atherosclerosis models were induced by denuding femoral artery endothelium plus high lipid diet in rabbits. TIMP-2 gene was transferred locally by balloons eluted with pcDNA3-TIMP-2. RT-PCR and Western blot were performed to verify exogenous genes transfer. MMPs activity in atherosclerotic plaque was evaluated by zymography. HE and VG staining and automatic image analysis system were used for pathological analysis of atherosclerotic femoral arteries. The lumen area of the vessel and the collagen contents in the atherosclerotic plaque were measured.<br><br>RESULTS: The expression of TIMP-2 gene in pcDNA3-TIMP-2 transferred group was significantly higher than control-vector transferred group at the end of week 2 after operation and reached the peak at the end of week 4. Comparing with the control group, the expression of TIMP-2 protein in treated group was also higher at the end of week 2, 4, and 8 after operation. Correspondingly, the MMP-2 and MMP-9 activities were lower in treated group. The thickness of fibrous cap of atherosclerotic plaque and the amount of collagen of the lesion were increased significantly in treated group compared with the control group, but there were no significant differences in vessel lumen area.<br><br>CONCLUSION: TIMP-2 gene transfer locally in atherosclerotic plaque could inhibit the activities of MMP-2 and MMP-9 in the lesion, increase the thickness of fibrous cap and the amount of collagen of the lesion, but may have no effect on the degree of the stenosis.}, }
@article {pmid15931193, year = {2005}, author = {Azeez, G}, title = {Ampicillin threat leads to wider transgene concern.}, journal = {Nature}, volume = {435}, number = {7042}, pages = {561}, doi = {10.1038/435561b}, pmid = {15931193}, issn = {1476-4687}, mesh = {Ampicillin Resistance/*genetics ; Animals ; Escherichia coli/drug effects/genetics ; Food, Genetically Modified ; Gene Transfer, Horizontal/*genetics ; Plants, Genetically Modified/adverse effects/genetics ; Plasmids/genetics ; Risk ; Transgenes/*genetics ; United Kingdom ; United States ; United States Food and Drug Administration ; Zea mays/drug effects/*genetics ; }, }
@article {pmid15930492, year = {2005}, author = {Price, MN and Huang, KH and Arkin, AP and Alm, EJ}, title = {Operon formation is driven by co-regulation and not by horizontal gene transfer.}, journal = {Genome research}, volume = {15}, number = {6}, pages = {809-819}, pmid = {15930492}, issn = {1088-9051}, mesh = {Escherichia coli K12/*genetics ; Escherichia coli Proteins/*genetics ; *Evolution, Molecular ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; *Models, Genetic ; Operon/*genetics ; Promoter Regions, Genetic ; }, abstract = {The organization of bacterial genes into operons was originally ascribed to the benefits of co-regulation. More recently, the "selfish operon" model, in which operons are formed by repeated gain and loss of genes, was proposed. Indeed, operons are often subject to horizontal gene transfer (HGT). On the other hand, non-HGT genes are particularly likely to be in operons. To clarify whether HGT is involved in operon formation, we identified recently formed operons in Escherichia coli K12. We show that genes that have homologs in distantly related bacteria but not in close relatives of E. coli--indicating HGT--form new operons at about the same rates as native genes. Furthermore, genes in new operons are no more likely than other genes to have phylogenetic trees that are inconsistent with the species tree. In contrast, essential genes and ubiquitous genes without paralogs--genes believed to undergo HGT rarely--often form new operons. We conclude that HGT is not a cause of operon formation but instead promotes the prevalence of pre-existing operons. To explain operon formation, we propose that new operons reduce the amount of regulatory information required to specify optimal expression patterns and infer that operons should be more likely to evolve than independent promoters when regulation is complex. Consistent with this hypothesis, operons have greater amounts of conserved regulatory sequences than do individually transcribed genes.}, }
@article {pmid15927057, year = {2005}, author = {Bern, M and Goldberg, D}, title = {Automatic selection of representative proteins for bacterial phylogeny.}, journal = {BMC evolutionary biology}, volume = {5}, number = {}, pages = {34}, pmid = {15927057}, issn = {1471-2148}, mesh = {Algorithms ; Automation ; Bacterial Proteins/*chemistry ; Computational Biology/*methods ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Likelihood Functions ; Models, Statistical ; Models, Theoretical ; Multigene Family ; Phylogeny ; Software ; }, abstract = {BACKGROUND: Although there are now about 200 complete bacterial genomes in GenBank, deep bacterial phylogeny remains a difficult problem, due to confounding horizontal gene transfers and other phylogenetic "noise". Previous methods have relied primarily upon biological intuition or manual curation for choosing genomic sequences unlikely to be horizontally transferred, and have given inconsistent phylogenies with poor bootstrap confidence.<br><br>RESULTS: We describe an algorithm that automatically picks "representative" protein families from entire genomes for use as phylogenetic characters. A representative protein family is one that, taken alone, gives an organismal distance matrix in good agreement with a distance matrix computed from all sufficiently conserved proteins. We then use maximum-likelihood methods to compute phylogenetic trees from a concatenation of representative sequences. We validate the use of representative proteins on a number of small phylogenetic questions with accepted answers. We then use our methodology to compute a robust and well-resolved phylogenetic tree for a diverse set of sequenced bacteria. The tree agrees closely with a recently published tree computed using manually curated proteins, and supports two proposed high-level clades: one containing Actinobacteria, Deinococcus, and Cyanobacteria ("Terrabacteria"), and another containing Planctomycetes and Chlamydiales.<br><br>CONCLUSION: Representative proteins provide an effective solution to the problem of selecting phylogenetic characters.}, }
@article {pmid15921862, year = {2005}, author = {Newbold, CJ and McEwan, NR and Calza, RE and Chareyron, EN and Duval, SM and Eschenlauer, SC and McIntosh, FM and Nelson, N and Travis, AJ and Wallace, RJ}, title = {An NAD(+)-dependent glutamate dehydrogenase cloned from the ruminal ciliate protozoan, Entodinium caudatum.}, journal = {FEMS microbiology letters}, volume = {247}, number = {2}, pages = {113-121}, doi = {10.1016/j.femsle.2005.04.034}, pmid = {15921862}, issn = {0378-1097}, mesh = {Amino Acid Sequence ; Ammonia/metabolism ; Animals ; Bacteroides/genetics ; Base Sequence ; Ciliophora/*enzymology ; Cloning, Molecular ; DNA, Protozoan/chemistry/genetics ; Escherichia coli/genetics/metabolism ; Gene Expression Regulation ; Gene Transfer, Horizontal ; *Genes, Protozoan ; Glutamate Dehydrogenase/*genetics/isolation &amp; purification/*metabolism ; Glutamic Acid/metabolism ; Ketoglutaric Acids/metabolism ; Molecular Sequence Data ; Phylogeny ; RNA, Messenger/analysis ; RNA, Protozoan/analysis ; Recombinant Proteins/metabolism ; Sequence Homology, Amino Acid ; Substrate Specificity ; }, abstract = {An NAD(+)-dependent glutamate dehydrogenase (GDH; EC 1.4.1.24) was cloned from the ruminal ciliate protozoan, Entodinium caudatum. The gene had high sequence similarity to GDH genes from the Bacteroides (class)--a class of bacteria which is highly represented in the rumen. When expressed in Escherichia coli the enzyme had a high affinity for ammonia and alpha-ketoglutarate (apparent K(m) of 2.33 and 0.71 mM, respectively) and a low affinity for glutamate (apparent K(m) of 98 mM). GDH activity and GDH mRNA concentration were increased by incubating washed E. caudatum cells with ammonia and antibiotics. These results suggest that the GDH is an anabolic enzyme catalysing the assimilation of ammonia by E. caudatum in the rumen and that the gene was probably acquired by lateral gene transfer from a ruminal bacterium.}, }
@article {pmid15917552, year = {2005}, author = {Woegerbauer, M and Lagler, H and Graninger, W and Burgmann, H}, title = {DNA in antibiotic preparations: absence of intact resistance genes.}, journal = {Antimicrobial agents and chemotherapy}, volume = {49}, number = {6}, pages = {2490-2494}, pmid = {15917552}, issn = {0066-4804}, mesh = {Animals ; Anti-Bacterial Agents/*chemistry ; Bacterial Proteins/genetics ; DNA, Bacterial/*analysis ; *Drug Contamination ; Drug Resistance, Bacterial/*genetics ; Feces/chemistry ; Female ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Mice ; Mice, Inbred BALB C ; RNA, Ribosomal/genetics ; Species Specificity ; }, abstract = {Fragments of erm(E2), otrA, and aph(6) shorter than 400 bp and producer strain-specific rRNA genes were amplified from various antibiotics. The amount of genetic material and the sizes of amplicons recovered from murine feces after oral administration of a beta-lactamase-encoding plasmid indicated substantial DNA degradation in the mammalian gastrointestinal tract. These observations imply that antibiotics are no major source for horizontal resistance gene transfer in clinical settings.}, }
@article {pmid15917517, year = {2005}, author = {Ferrándiz, MJ and Ardanuy, C and Liñares, J and García-Arenzana, JM and Cercenado, E and Fleites, A and de la Campa, AG and , }, title = {New mutations and horizontal transfer of rpoB among rifampin-resistant Streptococcus pneumoniae from four Spanish hospitals.}, journal = {Antimicrobial agents and chemotherapy}, volume = {49}, number = {6}, pages = {2237-2245}, pmid = {15917517}, issn = {0066-4804}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Sequence ; Anti-Bacterial Agents/*pharmacology ; Base Sequence ; DNA-Directed RNA Polymerases/chemistry/*genetics ; Drug Resistance, Bacterial/*genetics ; *Gene Transfer, Horizontal ; Hospitals ; Humans ; Microbial Sensitivity Tests ; Molecular Sequence Data ; *Mutation ; Phylogeny ; Pneumococcal Infections/epidemiology/microbiology ; Rifampin/*pharmacology ; Sequence Analysis, DNA ; Spain/epidemiology ; Streptococcus pneumoniae/*drug effects/genetics ; }, abstract = {A total of 103 (0.7%) of 14,236 Streptococcus pneumoniae isolates collected in four Spanish hospitals from 1989 to 2003 were resistant to rifampin (MICs, 4 to 512 microg/ml). Only sixty-one (59.2%) of these isolates were available for molecular characterization. Resistance was mostly related to human immunodeficiency virus (HIV) infection in adult patients and to conjunctivitis in children. Thirty-six different pulsed-field gel electrophoresis patterns were identified among resistant isolates, five of which were related to international clones (Spain23F-1, Spain6B-2, Spain9V-3, Spain14-5, and clone C of serotype 19F), and accounted for 49.2% of resistant isolates. Single sense mutations at cluster N or I of the rpoB gene were found in 39 isolates, while double mutations, either at cluster I, at clusters I and II, or at clusters N and III, were found in 14 isolates. The involvement of the mutations in rifampin resistance was confirmed by genetic transformation. Single mutations at clusters N and I conferred MICs of 2 microg/ml and 4 to 32 microg/ml, respectively. Eight isolates showed high degrees of nucleotide sequence variations (2.3 to 10.8%) in rpoB, suggesting a recombinational origin for these isolates, for which viridans group streptococci are their potential gene donors. Although the majority of rifampin-resistant isolates were isolated from individual patients without temporal or geographical relationships, the clonal dissemination of rifampin-resistant isolates was observed among 12 HIV-infected patients in the two hospitals with higher rates of resistance.}, }
@article {pmid15913459, year = {2005}, author = {Bapteste, E and Susko, E and Leigh, J and MacLeod, D and Charlebois, RL and Doolittle, WF}, title = {Do orthologous gene phylogenies really support tree-thinking?.}, journal = {BMC evolutionary biology}, volume = {5}, number = {}, pages = {33}, pmid = {15913459}, issn = {1471-2148}, mesh = {Algorithms ; Alphaproteobacteria/genetics ; Animals ; Biological Evolution ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; Genetic Markers ; Genome ; Models, Biological ; *Models, Genetic ; Models, Statistical ; Models, Theoretical ; Phylogeny ; Software ; }, abstract = {BACKGROUND: Since Darwin's Origin of Species, reconstructing the Tree of Life has been a goal of evolutionists, and tree-thinking has become a major concept of evolutionary biology. Practically, building the Tree of Life has proven to be tedious. Too few morphological characters are useful for conducting conclusive phylogenetic analyses at the highest taxonomic level. Consequently, molecular sequences (genes, proteins, and genomes) likely constitute the only useful characters for constructing a phylogeny of all life. For this reason, tree-makers expect a lot from gene comparisons. The simultaneous study of the largest number of molecular markers possible is sometimes considered to be one of the best solutions in reconstructing the genealogy of organisms. This conclusion is a direct consequence of tree-thinking: if gene inheritance conforms to a tree-like model of evolution, sampling more of these molecules will provide enough phylogenetic signal to build the Tree of Life. The selection of congruent markers is thus a fundamental step in simultaneous analysis of many genes.<br><br>RESULTS: Heat map analyses were used to investigate the congruence of orthologues in four datasets (archaeal, bacterial, eukaryotic and alpha-proteobacterial). We conclude that we simply cannot determine if a large portion of the genes have a common history. In addition, none of these datasets can be considered free of lateral gene transfer.<br><br>CONCLUSION: Our phylogenetic analyses do not support tree-thinking. These results have important conceptual and practical implications. We argue that representations other than a tree should be investigated in this case because a non-critical concatenation of markers could be highly misleading.}, }
@article {pmid15909914, year = {2005}, author = {Semin, BV and Il'in, IuV}, title = {[Diversity of LTR retrotransposons and their role in genome reorganization].}, journal = {Genetika}, volume = {41}, number = {4}, pages = {542-548}, pmid = {15909914}, issn = {0016-6758}, mesh = {Animals ; Gene Transfer, Horizontal/*genetics ; *Genome ; Humans ; Retroelements/*genetics ; Terminal Repeat Sequences/*genetics ; }, abstract = {Current views of retrotransposons possessing long terminal repeats (LTRs) are described. The existing classification and element types isolated by genome organization are considered. Experimental data are summarized to demonstrate that the replicative cycle of a retrotransposon is not restricted to a single cell and that LTR retrotransposons are transferred between somatic cells with a rate comparable with the element transposition rate within the genome of one cell. The major mechanisms mediating the role of LTR retrotransposons in reorganization of the genome are considered with regard to the strategies of their horizontal and vertical transfer.}, }
@article {pmid15909313, year = {2005}, author = {Stolzer, AL and Sadelain, M and Sant'Angelo, DB}, title = {Fulminant experimental autoimmune encephalo-myelitis induced by retrovirally mediated TCR gene transfer.}, journal = {European journal of immunology}, volume = {35}, number = {6}, pages = {1822-1830}, doi = {10.1002/eji.200526123}, pmid = {15909313}, issn = {0014-2980}, support = {P01 CA59350/CA/NCI NIH HHS/United States ; R01 AI041574/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Encephalomyelitis, Autoimmune, Experimental/*etiology/pathology ; *Gene Transfer, Horizontal ; Interferon-gamma/biosynthesis ; Interleukin-4/biosynthesis ; Mice ; Myelin Basic Protein/immunology ; Receptors, Antigen, T-Cell/*genetics/physiology ; Retroviridae/genetics ; Spleen/immunology ; T-Lymphocytes/physiology ; Transduction, Genetic ; }, abstract = {Although some efforts have been made to direct the antigen specificity of developing T cells by retroviral mediated expression of known TCR, it is not clear if the resultant T cells are fully functional. In this study retroviral gene transfer technology was used to introduce a cDNA encoding the TCR from a known encephalitogenic T cell into the bone marrow of mice. Activated T cells expressing this TCR, which is specific for the Ac1-11 peptide from myelin basic protein presented by I-A(u), cause rapid onset of experimental autoimmune encephalomyelitis (EAE). This enabled us to use the onset and progression of the disease as a direct measure of effector functions of T cells generated by this method. The data presented here show that recipients of bone marrow retrovirally transduced with this TCR rapidly develop full-blown EAE that results in paralysis. Therefore, retroviral TCR delivery into the bone marrow supports the development of T cells into fully functional effector cells.}, }
@article {pmid15909225, year = {2005}, author = {Ginolhac, A and Jarrin, C and Robe, P and Perrière, G and Vogel, TM and Simonet, P and Nalin, R}, title = {Type I polyketide synthases may have evolved through horizontal gene transfer.}, journal = {Journal of molecular evolution}, volume = {60}, number = {6}, pages = {716-725}, pmid = {15909225}, issn = {0022-2844}, mesh = {Acyltransferases/genetics ; Amphotericin B/pharmacology ; Bacterial Proteins/metabolism ; *Evolution, Molecular ; *Gene Transfer Techniques ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Macrolides/pharmacology ; Models, Genetic ; Multigene Family ; Natamycin/pharmacology ; Nystatin/pharmacology ; Phylogeny ; Polyketide Synthases/*chemistry/*metabolism ; Protein Structure, Tertiary ; }, abstract = {Type I polyketide synthases (PKSI) are modular multidomain enzymes involved in the biosynthesis of many natural products of industrial interest. PKSI modules are minimally organized in three domains: ketosynthase (KS), acyltransferase (AT), and acyl carrier protein. The KS domain phylogeny of 23 PKSI clusters was determined. The results obtained suggest that many horizontal transfers of PKSI genes have occurred between actinomycetales species. Such gene transfers may explain the homogeneity and the robustness of the actinomycetales group since gene transfers between closely related species could mimic patterns generated by vertical inheritance. We suggest that the linearity and instability of actinomycetales chromosomes associated with their large quantity of genetic mobile elements have favored such horizontal gene transfers.}, }
@article {pmid15908415, year = {2005}, author = {Terry, CE and McGinnis, LM and Madigan, KC and Cao, P and Cover, TL and Liechti, GW and Peek, RM and Forsyth, MH}, title = {Genomic Comparison of cag pathogenicity island (PAI)-positive and -negative Helicobacter pylori strains: identification of novel markers for cag PAI-positive strains.}, journal = {Infection and immunity}, volume = {73}, number = {6}, pages = {3794-3798}, pmid = {15908415}, issn = {0019-9567}, support = {R01 CA077955/CA/NCI NIH HHS/United States ; R29 CA077955/CA/NCI NIH HHS/United States ; R01 DK053623/DK/NIDDK NIH HHS/United States ; R15 AI053062/AI/NIAID NIH HHS/United States ; R01 DK058587/DK/NIDDK NIH HHS/United States ; }, mesh = {Antigens, Bacterial/*genetics ; Bacterial Proteins/*genetics ; Biomarkers ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genomic Islands ; Helicobacter pylori/*genetics/pathogenicity ; Polymerase Chain Reaction ; }, abstract = {In an analysis of Helicobacter pylori genomic DNA by macroarray methodology, genomic DNA from a panel of cag pathogenicity island (PAI)-negative H. pylori clinical isolates failed to hybridize with 27 genes located outside the cag PAI in a cag PAI-positive reference strain. PCR analyses confirmed that HP0217 (encoding a lipopolysaccharide biosynthetic protein) and HP1079 (encoding a protein of unknown function) were present significantly more frequently in cagA-positive strains than in cagA-negative strains. A low G+C content of these two genes suggests they were acquired by horizontal transfer events.}, }
@article {pmid15908390, year = {2005}, author = {McMichael, JW and Maxwell, AI and Hayashi, K and Taylor, K and Wallace, WA and Govan, JR and Dorin, JR and Sallenave, JM}, title = {Antimicrobial activity of murine lung cells against Staphylococcus aureus is increased in vitro and in vivo after elafin gene transfer.}, journal = {Infection and immunity}, volume = {73}, number = {6}, pages = {3609-3617}, pmid = {15908390}, issn = {0019-9567}, mesh = {Adenoviridae/genetics ; Animals ; Female ; Gene Transfer, Horizontal ; *Genetic Therapy ; Immunity, Innate ; Lung/*immunology ; Mice ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; Proteinase Inhibitory Proteins, Secretory ; Proteins/*genetics ; Staphylococcal Infections/*immunology ; Staphylococcus aureus/*immunology ; }, abstract = {Staphylococcus aureus is a pathogen often found in pneumonia and sepsis. In the context of the resistance of this organism to conventional antibiotics, an understanding of the regulation of natural endogenous antimicrobial molecules is of paramount importance. Previous studies have shown that both human and mouse airways express a variety of these molecules, including defensins, cathelicidins, and the four-disulfide core protein secretory leukocyte protease inhibitor. We demonstrate here by culturing mouse tracheal epithelial cells at an air-liquid interface that, despite the production of Defb1, Defb14, and Defr1 in this system, these cells are unable to clear S. aureus when exposed to this respiratory pathogen. Using an adenovirus (Ad)-mediated gene transfer strategy, we show that overexpression of elafin, an anti-elastase/antimicrobial molecule (also a member of the four-disulfide core protein family), dramatically improves the clearance of S. aureus. In addition, we also demonstrate that this overexpression is efficient in vivo and that intratracheal instillation of Ad-elafin significantly reduced the lung bacterial load and demonstrates concomitant anti-inflammatory activity by reducing neutrophil numbers and markers of lung inflammation, such as bronchoalveolar lavage levels of tumor necrosis factor and myeloperoxidase. These findings show that an increased antimicrobial activity phenotype is provided by the elafin molecule and have implications for its use in S. aureus-associated local and systemic infections.}, }
@article {pmid15905464, year = {2005}, author = {Lee, KU and Lee, IK and Han, J and Song, DK and Kim, YM and Song, HS and Kim, HS and Lee, WJ and Koh, EH and Song, KH and Han, SM and Kim, MS and Park, IS and Park, JY}, title = {Effects of recombinant adenovirus-mediated uncoupling protein 2 overexpression on endothelial function and apoptosis.}, journal = {Circulation research}, volume = {96}, number = {11}, pages = {1200-1207}, doi = {10.1161/01.RES.0000170075.73039.5b}, pmid = {15905464}, issn = {1524-4571}, mesh = {Adenoviridae/*genetics ; *Apoptosis ; Arteriosclerosis/*prevention &amp; control ; Calcium/metabolism ; Caspases/metabolism ; Cells, Cultured ; Electron Transport ; Endothelial Cells/*physiology ; Endothelin-1/genetics ; Gene Transfer, Horizontal ; Humans ; Ion Channels ; Linoleic Acid/pharmacology ; Lysophosphatidylcholines/pharmacology ; Membrane Transport Proteins/genetics/*physiology ; Mitochondrial Proteins/genetics/*physiology ; NF-kappa B/metabolism ; Nitric Oxide/analysis ; Nitric Oxide Synthase/genetics ; Nitric Oxide Synthase Type III ; RNA, Messenger/analysis ; Reactive Oxygen Species ; Uncoupling Protein 2 ; }, abstract = {Increased oxidative stress in vascular cells plays a key role in the development of endothelial dysfunction and atherosclerosis. Uncoupling protein 2 (UCP2) is an important regulator of intracellular reactive oxygen species (ROS) production. This study was undertaken to test the hypothesis that, UCP2 functions as an inhibitor of the atherosclerotic process in endothelial cells. Adenovirus-mediated UCP2 (Ad-UCP2) overexpression led to a significant increase in endothelial nitric oxide synthase (eNOS) and decrease in endothelin-1 mRNA expression in human aortic endothelial cells (HAECs). Moreover, UCP2 inhibited the increase in ROS production and NF-kappaB activation, and apoptosis of HAECs induced by lysophophatidylcholine (LPC) and linoleic acid. LPC and linoleic acid caused mitochondrial calcium accumulation and transient mitochondrial membrane hyperpolarization, which was followed by depolarization. UCP2 overexpression prevented these processes. In isolated rat aorta, Ad-UCP2 infection markedly improved impaired vascular relaxation induced by LPC. The data collectively suggest that UCP2, functions as a physiologic regulator of ROS generation in endothelial cells. Thus, measures to increase UCP2 expression in vascular endothelial cells may aid in preventing the development and progression of atherosclerosis in patients with metabolic syndrome.}, }
@article {pmid15905382, year = {2005}, author = {Moreira, D and López-García, P}, title = {Comment on "The 1.2-megabase genome sequence of Mimivirus".}, journal = {Science (New York, N.Y.)}, volume = {308}, number = {5725}, pages = {1114; author reply 1114}, doi = {10.1126/science.1111195}, pmid = {15905382}, issn = {1095-9203}, mesh = {Amino Acyl-tRNA Synthetases/chemistry/genetics ; DNA Viruses/chemistry/classification/*genetics ; DNA-Directed DNA Polymerase/chemistry/genetics ; Evolution, Molecular ; Exonucleases/chemistry/genetics ; Gene Transfer, Horizontal ; Genes, Viral ; *Genome, Viral ; Phylogeny ; RNA Polymerase II/chemistry/genetics ; Sequence Analysis, DNA ; Viral Proteins/chemistry/*genetics ; }, }
@article {pmid15901840, year = {2005}, author = {Novozhilov, AS and Karev, GP and Koonin, EV}, title = {Mathematical modeling of evolution of horizontally transferred genes.}, journal = {Molecular biology and evolution}, volume = {22}, number = {8}, pages = {1721-1732}, doi = {10.1093/molbev/msi167}, pmid = {15901840}, issn = {0737-4038}, mesh = {Bacteria/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/*genetics ; *Models, Genetic ; }, abstract = {We describe a stochastic birth-and-death model of evolution of horizontally transferred genes in microbial populations. The model is a generalization of the stochastic model described by Berg and Kurland and includes five parameters: the rate of mutational inactivation, selection coefficient, invasion rate (i.e., rate of arrival of a novel sequence from outside of the recipient population), within-population horizontal transmission ("infection") rate, and population size. The model of Berg and Kurland included four parameters, namely, mutational inactivation, selection coefficient, population size, and "infection." However, the effect of "infection" was disregarded in the interpretation of the results, and the overall conclusion was that horizontally acquired sequences can be fixed in a population only when they confer a substantial selective advantage onto the recipient and therefore are subject to strong positive selection. Analysis of the present model in different domains of parameter values shows that, as long as the rate of within-population horizontal transmission is comparable to the mutational inactivation rate and there is even a low rate of invasion, horizontally acquired sequences can be fixed in the population or at least persist for a long time in a substantial fraction of individuals in the population even when they are neutral or slightly deleterious. The available biological data strongly suggest that intense within-population and even between-populations gene flows are realistic for at least some prokaryotic species and environments. Therefore, our modeling results are compatible with the notion of a pivotal role of horizontal gene transfer in the evolution of prokaryotes.}, }
@article {pmid15901709, year = {2005}, author = {Gopal, S and Borovok, I and Ofer, A and Yanku, M and Cohen, G and Goebel, W and Kreft, J and Aharonowitz, Y}, title = {A multidomain fusion protein in Listeria monocytogenes catalyzes the two primary activities for glutathione biosynthesis.}, journal = {Journal of bacteriology}, volume = {187}, number = {11}, pages = {3839-3847}, pmid = {15901709}, issn = {0021-9193}, mesh = {Adenosine Triphosphate/metabolism ; Animals ; Bacterial Proteins/chemistry/genetics/metabolism ; Caco-2 Cells ; Catalysis ; Dipeptides/metabolism ; Glutathione/*biosynthesis/metabolism ; Glutathione Synthase/chemistry/*genetics/metabolism ; Humans ; Ligases/chemistry/*genetics/metabolism ; Listeria monocytogenes/*enzymology/*genetics/growth &amp; development ; Listeriosis/*microbiology ; Macrophages/microbiology ; Mice ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Tertiary ; }, abstract = {Glutathione is the predominant low-molecular-weight peptide thiol present in living organisms and plays a key role in protecting cells against oxygen toxicity. Until now, glutathione synthesis was thought to occur solely through the consecutive action of two physically separate enzymes, gamma-glutamylcysteine ligase and glutathione synthetase. In this report we demonstrate that Listeria monocytogenes contains a novel multidomain protein (termed GshF) that carries out complete synthesis of glutathione. Evidence for this comes from experiments which showed that in vitro recombinant GshF directs the formation of glutathione from its constituent amino acids and the in vivo effect of a mutation in GshF that abolishes glutathione synthesis, results in accumulation of the intermediate gamma-glutamylcysteine, and causes hypersensitivity to oxidative agents. We identified GshF orthologs, consisting of a gamma-glutamylcysteine ligase (GshA) domain fused to an ATP-grasp domain, in 20 gram-positive and gram-negative bacteria. Remarkably, 95% of these bacteria are mammalian pathogens. A plausible origin for GshF-dependent glutathione biosynthesis in these bacteria was the recruitment by a GshA ancestor gene of an ATP-grasp gene and the subsequent spread of the fusion gene between mammalian hosts, most likely by horizontal gene transfer.}, }
@article {pmid15901698, year = {2005}, author = {Qi, M and Nelson, KE and Daugherty, SC and Nelson, WC and Hance, IR and Morrison, M and Forsberg, CW}, title = {Novel molecular features of the fibrolytic intestinal bacterium Fibrobacter intestinalis not shared with Fibrobacter succinogenes as determined by suppressive subtractive hybridization.}, journal = {Journal of bacteriology}, volume = {187}, number = {11}, pages = {3739-3751}, pmid = {15901698}, issn = {0021-9193}, mesh = {Bacterial Proteins/genetics/metabolism ; Carbohydrate Metabolism ; Carrier Proteins/genetics ; DNA Restriction Enzymes/genetics/metabolism ; DNA, Bacterial/genetics/metabolism ; Energy Metabolism/genetics ; Fibrobacter/*classification/*genetics/metabolism ; *Gene Expression Profiling ; *Genome, Bacterial ; Hydrolases/genetics/metabolism ; Nucleic Acid Hybridization/*methods ; Transposases/genetics ; }, abstract = {Suppressive subtractive hybridization was conducted to identify unique genes coding for plant cell wall hydrolytic enzymes and other properties of the gastrointestinal bacterium Fibrobacter intestinalis DR7 not shared by Fibrobacter succinogenes S85. Subtractive clones from F. intestinalis were sequenced and assembled to form 712 nonredundant contigs with an average length of 525 bp. Of these, 55 sequences were unique to F. intestinalis. The remaining contigs contained 764 genes with BLASTX similarities to other proteins; of these, 80% had the highest similarities to proteins in F. succinogenes, including 30 that coded for carbohydrate active enzymes. The expression of 17 of these genes was verified by Northern dot blot analysis. Of genes not exhibiting BLASTX similarity to F. succinogenes, 30 encoded putative transposases, 6 encoded restriction modification genes, and 45% had highest similarities to proteins in other species of gastrointestinal bacteria, a finding suggestive of either horizontal gene transfer to F. intestinalis or gene loss from F. succinogenes. Analysis of contigs containing segments of two or more adjacent genes revealed that only 35% exhibited BLASTX similarity and were in the same orientation as those of F. succinogenes, indicating extensive chromosomal rearrangement. The expression of eight transposases, and three restriction-modification genes was confirmed by Northern dot blot analysis. These data clearly document the maintenance of carbohydrate active enzymes in F. intestinalis necessitated by the preponderance of polysaccharide substrates available in the ruminal environment. It also documents substantive changes in the genome from that of F. succinogenes, which may be related to the introduction of the array of transposase and restriction-modification genes.}, }
@article {pmid15893492, year = {2005}, author = {Davies, MR and Tran, TN and McMillan, DJ and Gardiner, DL and Currie, BJ and Sriprakash, KS}, title = {Inter-species genetic movement may blur the epidemiology of streptococcal diseases in endemic regions.}, journal = {Microbes and infection}, volume = {7}, number = {9-10}, pages = {1128-1138}, doi = {10.1016/j.micinf.2005.03.018}, pmid = {15893492}, issn = {1286-4579}, mesh = {Adolescent ; Bacteriophages/genetics ; DNA Transposable Elements/genetics ; DNA, Bacterial/genetics ; Endemic Diseases ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Humans ; Male ; Molecular Epidemiology ; Nucleic Acid Hybridization ; Streptococcal Infections/epidemiology/*microbiology ; Streptococcus/*genetics ; Streptococcus agalactiae/genetics ; Streptococcus pyogenes/genetics ; }, abstract = {Streptococcus dysgalactiae subsp. equisimilis (human group G streptococcus, GGS) is generally regarded as a commensal organism but can cause a spectrum of human diseases very similar to that caused by S. pyogenes (group A streptococcus, GAS). Lateral acquisition of genes between these two phylogenetically closely related species is well documented. However, the extent and mechanisms of lateral acquisitions is not known. We report here genomic subtraction between a pathogenic GGS isolate and a community GGS isolate and analyses of the gene sequences unique to the pathovar. Our results show that cross-species genetic transfers are common between GGS and two closely related human pathogens, GAS and the group B streptococcus. We also demonstrate that mobile genetic elements, such as phages and transposons, play an important role in the ongoing inter-species transfers of genetic traits between extant organisms in the community. Furthermore, lateral gene transfers between GAS and GGS may occur more frequently in geographical regions of high GAS endemicity. These observations may have important implications in understanding the epidemiology of streptococcal diseases in such regions.}, }
@article {pmid15891911, year = {2005}, author = {Cahan, P and Kennell, JC}, title = {Identification and distribution of sequences having similarity to mitochondrial plasmids in mitochondrial genomes of filamentous fungi.}, journal = {Molecular genetics and genomics : MGG}, volume = {273}, number = {6}, pages = {462-473}, pmid = {15891911}, issn = {1617-4615}, mesh = {Base Pairing ; Base Sequence ; Computational Biology ; DNA, Fungal/*chemistry ; DNA, Mitochondrial/*chemistry ; GC Rich Sequence/genetics ; Gene Transfer, Horizontal ; *Genome, Fungal ; Molecular Sequence Data ; Neurospora crassa/*genetics ; Plasmids/*chemistry ; Sequence Analysis, DNA ; }, abstract = {Mitochondrial plasmids are autonomously replicating genetic elements commonly associated with fungal and plant species. Analysis of several plant and fungal mitochondrial genomes has revealed regions that show significant homology to mitochondrial plasmids, suggesting that plasmids have had a long-term association with their mitochondrial hosts. To assess the degree to which plasmids have invaded fungal mitochondrial genomes, BLAST search parameters were modified to identify plasmid sequences within highly AT-rich mtDNAs, and output data were parsed by E value, score, and sequence complexity. High scoring hits were evaluated for the presence of shared repetitive elements and location within plasmids and mtDNAs. Our searches revealed multiple sites of sequence similarity to four distinct plasmids in the wild-type mtDNA of Neurospora crassa, which collectively comprise more than 2% of the mitochondrial genome. Regions of plasmid similarity were not restricted to plasmids known to be associated with senescence, indicating that all mt plasmids can potentially integrate into mitochondrial DNA. Unexpectedly, plasmid-related sequences were found to be clustered in regions that have disproportionately low numbers of PstI palindromic sequences, suggesting that these repetitive elements may play a role in eliminating foreign DNA. A separate class of GC-rich palindromes was identified that appear to be mobile, as indicated by their occurrence within regions of plasmid homology. Sites of sequence similarity to mitochondrial plasmids were also detected in other filamentous fungi, but to a lesser degree. The tools developed here will be useful in assessing the contribution plasmids have made to mitochondrial function and in understanding the co-evolution of mitochondrial plasmids and their hosts.}, }
@article {pmid15885098, year = {2005}, author = {Kurokawa, S and Bessho, Y and Higashijima, K and Shirouzu, M and Yokoyama, S and Watanabe, KI and Ohama, T}, title = {Adaptation of intronic homing endonuclease for successful horizontal transmission.}, journal = {The FEBS journal}, volume = {272}, number = {10}, pages = {2487-2496}, doi = {10.1111/j.1742-4658.2005.04669.x}, pmid = {15885098}, issn = {1742-464X}, mesh = {Algal Proteins/genetics/*metabolism ; Amino Acids/genetics/metabolism ; Animals ; Chlamydomonas/*enzymology/*genetics ; Codon ; DNA Mutational Analysis ; Endodeoxyribonucleases/genetics/*metabolism ; *Gene Transfer, Horizontal ; *Introns ; Mitochondrial Proteins/genetics/metabolism ; Open Reading Frames ; }, abstract = {Group I introns are thought to be self-propagating mobile elements, and are distributed over a wide range of organisms through horizontal transmission. Intron invasion is initiated through cleavage of a target DNA by a homing endonuclease encoded in an open reading frame (ORF) found within the intron. The intron is likely of no benefit to the host cell and is not maintained over time, leading to the accumulation of mutations after intron invasion. Therefore, regular invasional transmission of the intron to a new species at least once before its degeneration is likely essential for its evolutionary long-term existence. In many cases, the target is in a protein-coding region which is well conserved among organisms, but contains ambiguity at the third nucleotide position of the codon. Consequently, the homing endonuclease might be adapted to overcome sequence polymorphisms at the target site. To address whether codon degeneracy affects horizontal transmission, we investigated the recognition properties of a homing enzyme, I-CsmI, that is encoded in the intronic ORF of a group I intron located in the mitochondrial COB gene of the unicellular green alga Chlamydomonas smithii. We successfully expressed and purified three types of N-terminally truncated I-CsmI polypeptides, and assayed the efficiency of cleavage for 81 substrates containing single nucleotide substitutions. We found a slight but significant tendency that I-CsmI cleaves substrates containing a silent or tolerated amino acid change more efficiently than nonsilent or nontolerated ones. The published recognition properties of I-SpomI, I-ScaI, and I-SceII were reconsidered from this point of view, and we detected proficient adaptation of I-SpomI, I-ScaI, and I-SceII for target site sequence degeneracy. Based on the results described above, we propose that intronic homing enzymes are adapted to cleave sequences that might appear at the target region in various species, however, such adaptation becomes less prominent in proportion to the time elapsed after intron invasion into a new host.}, }
@article {pmid15883782, year = {2005}, author = {Kurokawa, T and Sakamoto, J}, title = {Purification and characterization of succinate:menaquinone oxidoreductase from Corynebacterium glutamicum.}, journal = {Archives of microbiology}, volume = {183}, number = {5}, pages = {317-324}, doi = {10.1007/s00203-005-0775-8}, pmid = {15883782}, issn = {0302-8933}, mesh = {Benzoquinones/pharmacology ; Corynebacterium glutamicum/*enzymology ; Electron Transport Complex II/antagonists &amp; inhibitors/*isolation &amp; purification/metabolism ; Heme/analysis ; Hydroxyquinolines/pharmacology ; Phylogeny ; }, abstract = {Succinate:menaquinone oxidoreductase from Corynebacterium glutamicum, a high-G+C, Gram-positive bacterium, was purified to homogeneity. The enzyme contained two heme B molecules and three polypeptides with apparent molecular masses of 67, 29 and 23 kDa, which corresponded to SdhA (flavoprotein), SdhB (iron-sulfur protein), and SdhC (membrane anchor protein), respectively. In non-denaturating polyacrylamide gel electrophoresis, the enzyme migrated as a single band with an apparent molecular mass of 410 kDa, suggesting that it existed as a trimer. The succinate dehydrogenase activity assayed using 2,3-dimethoxy-5-methyl-6-decyl-1,4-benzoquinone and 2,6-dichloroindophenol as the electron acceptor was inhibited by 2-n-heptyl-4-hydroxyquinoline N-oxide (HQNO), and the Dixon plots were biphasic. In contrast, the succinate dehydrogenase activity assayed using phenazine methosulfate and 2,6-dichloroindophenol was inhibited by p-benzoquinone and not by HQNO. These findings suggested that the C. glutamicum succinate:menaquinone oxidoreductase had two quinone binding sites. In the phylogenetic tree of SdhA, Corynebacterium species do not belong to the high-G+C group, which includes Mycobacterium tuberculosis and Streptomyces coelicolor, but are rather close to the group of low-G+C, Gram-positive bacteria such as Bacillus subtilis. This situation may have arisen due to the horizontal gene transfer.}, }
@article {pmid15878987, year = {2005}, author = {Vetsigian, K and Goldenfeld, N}, title = {Global divergence of microbial genome sequences mediated by propagating fronts.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {102}, number = {20}, pages = {7332-7337}, pmid = {15878987}, issn = {0027-8424}, mesh = {Bacillus/*genetics ; Computer Simulation ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genetic Variation ; *Genome, Bacterial ; *Models, Genetic ; Point Mutation/*genetics ; Species Specificity ; }, abstract = {We model the competition between homologous recombination and point mutation in microbial genomes, and present evidence for two distinct phases, one uniform, the other genetically diverse. Depending on the specifics of homologous recombination, we find that global sequence divergence can be mediated by fronts propagating along the genome, whose characteristic signature on genome structure is elucidated, and apparently observed in closely related Bacillus strains. Front propagation provides an emergent, generic mechanism for microbial "speciation," and suggests a classification of microorganisms on the basis of their propensity to support propagating fronts.}, }
@article {pmid15878653, year = {2005}, author = {Andres, P and Petroni, A and Faccone, D and Pasterán, F and Melano, R and Rapoport, M and Martínez, M and Culasso, C and Di Bella, A and Irigoyen, B and Mulki, J and Procopio, A and von Specht, M and Galas, M}, title = {Extended-spectrum beta-lactamases in Shigella flexneri from Argentina: first report of TOHO-1 outside Japan.}, journal = {International journal of antimicrobial agents}, volume = {25}, number = {6}, pages = {501-507}, doi = {10.1016/j.ijantimicag.2005.02.016}, pmid = {15878653}, issn = {0924-8579}, mesh = {Amino Acid Substitution ; Anti-Bacterial Agents/*pharmacology ; Argentina ; Bacterial Typing Techniques ; Conjugation, Genetic ; DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; Dysentery, Bacillary/microbiology ; Electrophoresis, Gel, Pulsed-Field ; Gene Transfer, Horizontal ; Humans ; Isoelectric Focusing ; Molecular Epidemiology ; Molecular Sequence Data ; Mutation, Missense ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Shigella flexneri/*drug effects/*enzymology/isolation &amp; purification ; beta-Lactamases/*genetics/isolation &amp; purification/*metabolism ; beta-Lactams/*pharmacology ; }, abstract = {A 9-year nation-wide survey of the presence of extended-spectrum beta-lactamases (ESBLs) in Shigella flexneri is described. Ten of 9033 (0.1%) isolates produced ESBLs, which were characterized by isoelectric focusing, PCR and DNA sequencing. These were CTX-M-2 (five isolates), TOHO-1 (one isolate), SHV-2 (two isolates) and PER-2 (two isolates, the first report in S. flexneri world wide). The emergence of each ESBL type in S. flexneri was not restricted to a particular region of Argentina. TOHO-1 showed a more basic isoelectric point (8.4) than that previously found (7.8) and its encoding gene (bla(TOHO-1a)) harboured a silent change, G825A, relative to the reported bla(TOHO-1). All the ESBL-encoding genes were transferred to Escherichia coli by conjugation. PFGE analysis indicated that the 10 ESBL-producing S. flexneri isolates were subtypes of a unique clone.}, }
@article {pmid15878127, year = {2005}, author = {de Almeida, LM and Carareto, CM}, title = {Multiple events of horizontal transfer of the Minos transposable element between Drosophila species.}, journal = {Molecular phylogenetics and evolution}, volume = {35}, number = {3}, pages = {583-594}, doi = {10.1016/j.ympev.2004.11.026}, pmid = {15878127}, issn = {1055-7903}, mesh = {Animals ; Base Sequence ; Blotting, Southern ; DNA Transposable Elements/*genetics ; Drosophila/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genetic Variation ; *Models, Genetic ; Molecular Sequence Data ; Mutation/genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Species Specificity ; Transposases/*genetics ; }, abstract = {In this study the Minos element was analyzed in 26 species of the repleta group and seven species of the saltans group of the genus Drosophila. The PCR and Southern blot analysis showed a wide occurrence of the Minos transposable element among species of the repleta and the saltans groups and also a low number of insertions in both genomes. Three different analyses, nucleotide divergence, historical associations, and comparisons between substitution rates (d(N) and d(S)) of Minos and Adh host gene sequences, suggest the occurrence of horizontal transfer between repleta and saltans species. These data reinforce and extend the Arca and Savakis [Genetica 108 (2000) 263] results and suggest five events of horizontal transfer to explain the present Minos distribution: between D. saltans and the ancestor of the mulleri and the mojavensis clusters; between D. hydei and the ancestor of the mulleri and the mojavensis clusters; between D. mojavensis and D. aldrichi; between D. buzzatii and D. serido; and between D. spenceri and D. emarginata. An alternative explanation would be that repeated events of horizontal transfer involving D. hydei, which is a cosmopolitan species that diverged from the others repleta species as long as 14Mya, could have spread Minos within the repleta group and to D. saltans. The data presented in this article support a model in which distribution of Minos transposon among Drosophila species is determined by horizontal transmission balanced by vertical inactivation and extinction.}, }
@article {pmid15876569, year = {2005}, author = {Bapteste, E and Brochier, C and Boucher, Y}, title = {Higher-level classification of the Archaea: evolution of methanogenesis and methanogens.}, journal = {Archaea (Vancouver, B.C.)}, volume = {1}, number = {5}, pages = {353-363}, pmid = {15876569}, issn = {1472-3646}, mesh = {Archaea/*classification/genetics/metabolism ; Archaeal Proteins/*genetics/metabolism ; DNA, Archaeal/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genes, Archaeal/genetics ; Methane/*metabolism ; Phylogeny ; Ribosomal Proteins/*genetics/metabolism ; }, abstract = {We used a phylogenetic approach to analyze the evolution of methanogenesis and methanogens. We show that 23 vertically transmitted ribosomal proteins do not support the monophyly of methanogens, and propose instead that there are two distantly related groups of extant archaea that produce methane, which we have named Class I and Class II. Based on this finding, we subsequently investigated the uniqueness of the origin of methanogenesis by studying both the enzymes of methanogenesis and the proteins that synthesize its specific coenzymes. We conclude that hydrogenotrophic methanogenesis appeared only once during evolution. Genes involved in the seven central steps of the methanogenic reduction of carbon dioxide (CO(2)) are ubiquitous in methanogens and share a common history. This suggests that, although extant methanogens produce methane from various substrates (CO(2), formate, acetate, methylated C-1 compounds), these archaea have a core of conserved enzymes that have undergone little evolutionary change. Furthermore, this core of methanogenesis enzymes seems to originate (as a whole) from the last ancestor of all methanogens and does not appear to have been horizontally transmitted to other organisms or between members of Class I and Class II. The observation of a unique and ancestral form of methanogenesis suggests that it was preserved in two independent lineages, with some instances of specialization or added metabolic flexibility. It was likely lost in the Halobacteriales, Thermoplasmatales and Archaeoglobales. Given that fossil evidence for methanogenesis dates back 2.8 billion years, a unique origin of this process makes the methanogenic archaea a very ancient taxon.}, }
@article {pmid15876483, year = {2006}, author = {Cui, R and Takahashi, K and Takahashi, F and Tanabe, KK and Fukuchi, Y}, title = {Endostatin gene transfer in murine lung carcinoma cells induces vascular endothelial growth factor secretion resulting in up-regulation of in vivo tumorigenecity.}, journal = {Cancer letters}, volume = {232}, number = {2}, pages = {262-271}, doi = {10.1016/j.canlet.2005.02.045}, pmid = {15876483}, issn = {0304-3835}, mesh = {Animals ; Cell Line, Tumor ; Cyclohexanes ; Endostatins/*genetics ; Endothelial Cells/cytology ; *Gene Transfer, Horizontal ; Lung Neoplasms/metabolism/*pathology ; Male ; Mice ; Mice, Inbred C57BL ; O-(Chloroacetylcarbamoyl)fumagillol ; RNA, Messenger/analysis ; Sesquiterpenes/therapeutic use ; Transfection ; Up-Regulation ; Vascular Endothelial Growth Factor A/*biosynthesis/genetics ; }, abstract = {Endostatin (ED) is a carboxyl-terminal fragment of type XVIII collagen with a strong anti-angiogenic activity. The purpose of this study is to determine the effect of ED gene transfer into lung cancer cells on in vivo tumor growth in a murine model. The murine lung cancer cell line, Lewis Lung Carcinoma (LLC), was transfected with ED gene to express and secrete ED. After clones were selected to secrete ED, several stable transfectants with ED gene (LLC/ED) and control transfectants (LLC/Mock) were established. In vitro proliferation of these transfectants demonstrated similar growth speed. In contrast to previous reports, in vivo subcutaneous tumorignecity of LCC/ED transfectants was significantly greater than that of LLC/Mock transfectants. Immunohistochemical staining analysis demonstrated that ED gene transfer induced angiogenesis, suggesting coinduction of another gene implicated for neovascularization. As expected, LLC/ED transfectants secreted not only ED but also vascular endothelial growth factor (VEGF) to a much greater degree than LLC/mock transfectants. Interestingly, culture supernatants of LLC/ED cells enhanced in vitro proliferation of human umbilical vein endothelial cells (HUVEC) to a much greater degree than those of LLC/Mock cells. These results indicate that ED gene transfer in murine lung carcinoma cells induces VEGF secretion, resulting in enhancement of in vivo tumorigenecity in the murine model. More attention should be paid for ED gene therapy into lung cancer cells since it may influence other proteins secretion, which upregulates angiogenesis.}, }
@article {pmid15875012, year = {2005}, author = {Eichinger, L and Pachebat, JA and Glöckner, G and Rajandream, MA and Sucgang, R and Berriman, M and Song, J and Olsen, R and Szafranski, K and Xu, Q and Tunggal, B and Kummerfeld, S and Madera, M and Konfortov, BA and Rivero, F and Bankier, AT and Lehmann, R and Hamlin, N and Davies, R and Gaudet, P and Fey, P and Pilcher, K and Chen, G and Saunders, D and Sodergren, E and Davis, P and Kerhornou, A and Nie, X and Hall, N and Anjard, C and Hemphill, L and Bason, N and Farbrother, P and Desany, B and Just, E and Morio, T and Rost, R and Churcher, C and Cooper, J and Haydock, S and van Driessche, N and Cronin, A and Goodhead, I and Muzny, D and Mourier, T and Pain, A and Lu, M and Harper, D and Lindsay, R and Hauser, H and James, K and Quiles, M and Madan Babu, M and Saito, T and Buchrieser, C and Wardroper, A and Felder, M and Thangavelu, M and Johnson, D and Knights, A and Loulseged, H and Mungall, K and Oliver, K and Price, C and Quail, MA and Urushihara, H and Hernandez, J and Rabbinowitsch, E and Steffen, D and Sanders, M and Ma, J and Kohara, Y and Sharp, S and Simmonds, M and Spiegler, S and Tivey, A and Sugano, S and White, B and Walker, D and Woodward, J and Winckler, T and Tanaka, Y and Shaulsky, G and Schleicher, M and Weinstock, G and Rosenthal, A and Cox, EC and Chisholm, RL and Gibbs, R and Loomis, WF and Platzer, M and Kay, RR and Williams, J and Dear, PH and Noegel, AA and Barrell, B and Kuspa, A}, title = {The genome of the social amoeba Dictyostelium discoideum.}, journal = {Nature}, volume = {435}, number = {7038}, pages = {43-57}, pmid = {15875012}, issn = {1476-4687}, support = {/WT_/Wellcome Trust/United Kingdom ; MC_U105115237/MRC_/Medical Research Council/United Kingdom ; R01 HD035925/HD/NICHD NIH HHS/United States ; }, mesh = {ATP-Binding Cassette Transporters/genetics ; Animals ; Base Composition ; Cell Adhesion/genetics ; Cell Movement/genetics ; Centromere/genetics ; Conserved Sequence/genetics ; DNA Transposable Elements/genetics ; DNA, Ribosomal/genetics ; Dictyostelium/cytology/enzymology/*genetics/metabolism ; Eukaryotic Cells/metabolism ; Gene Duplication ; Gene Transfer, Horizontal/genetics ; *Genome ; *Genomics ; Humans ; Molecular Sequence Data ; Phylogeny ; Proteome ; Protozoan Proteins/chemistry/genetics ; RNA, Transfer/genetics ; Repetitive Sequences, Nucleic Acid/genetics ; Sequence Analysis, DNA ; Signal Transduction/genetics ; *Social Behavior ; Telomere/genetics ; }, abstract = {The social amoebae are exceptional in their ability to alternate between unicellular and multicellular forms. Here we describe the genome of the best-studied member of this group, Dictyostelium discoideum. The gene-dense chromosomes of this organism encode approximately 12,500 predicted proteins, a high proportion of which have long, repetitive amino acid tracts. There are many genes for polyketide synthases and ABC transporters, suggesting an extensive secondary metabolism for producing and exporting small molecules. The genome is rich in complex repeats, one class of which is clustered and may serve as centromeres. Partial copies of the extrachromosomal ribosomal DNA (rDNA) element are found at the ends of each chromosome, suggesting a novel telomere structure and the use of a common mechanism to maintain both the rDNA and chromosomal termini. A proteome-based phylogeny shows that the amoebozoa diverged from the animal-fungal lineage after the plant-animal split, but Dictyostelium seems to have retained more of the diversity of the ancestral genome than have plants, animals or fungi.}, }
@article {pmid15872274, year = {2005}, author = {Zadoks, RN and Schukken, YH and Wiedmann, M}, title = {Multilocus sequence typing of Streptococcus uberis provides sensitive and epidemiologically relevant subtype information and reveals positive selection in the virulence gene pauA.}, journal = {Journal of clinical microbiology}, volume = {43}, number = {5}, pages = {2407-2417}, pmid = {15872274}, issn = {0095-1137}, mesh = {Base Sequence ; DNA Primers ; Humans ; Netherlands/epidemiology ; Reproducibility of Results ; Restriction Mapping ; Ribotyping/methods ; Serotyping ; Streptococcal Infections/*epidemiology ; Streptococcus/*classification/*genetics/isolation &amp; purification/pathogenicity ; United States/epidemiology ; Virulence/*genetics ; }, abstract = {Control of the bovine mastitis pathogen Streptococcus uberis requires sensitive and epidemiologically meaningful subtyping methods that can provide insight into this pathogen's epidemiology and evolution. Development of a multilocus sequence typing (MLST) scheme based on six housekeeping and virulence genes allowed differentiation of 40 sequence types among 50 S. uberis isolates from the United States (n = 30) and The Netherlands (n = 20). MLST was more discriminatory than EcoRI or PvuII ribotyping and provided subtype data with better epidemiological relevance, e.g., by discriminating isolates with identical ribotypes obtained from different farms. Phylogenetic analyses of MLST data revealed indications of reticulate evolution between genes, preventing construction of a core phylogeny based on concatenated DNA sequences. However, all individual gene phylogenies clearly identified a distinct pauA-negative subtaxon of S. uberis for which housekeeping alleles closely resembled those of Streptococcus parauberis. While the average GC content for five genes characterized was between 0.38 and 0.40, pauA showed a considerably lower GC content (0.34), suggesting acquisition through horizontal transfer. pauA also showed a higher nonsynonymous/synonymous rate ratio (dN/dS) (1.2) compared to the other genes sequenced (dN/dS < 0.12), indicating positive selection in this virulence gene. In conclusion, our data show that (i) MLST provides for highly discriminatory and epidemiologically relevant subtyping of S. uberis; (ii) S. uberis has a recombinatorial population structure; (iii) phylogenetic analysis of MLST data reveals an S. uberis subtaxon resembling S. parauberis; and (iv) horizontal gene transfer and positive selection contribute to evolution of certain S. uberis genes, such as the virulence gene pauA.}, }
@article {pmid15868201, year = {2005}, author = {Baroni, M and Grünewald, S and Moulton, V and Semple, C}, title = {Bounding the number of hybridisation events for a consistent evolutionary history.}, journal = {Journal of mathematical biology}, volume = {51}, number = {2}, pages = {171-182}, pmid = {15868201}, issn = {0303-6812}, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal ; *Hybridization, Genetic ; *Models, Genetic ; Phylogeny ; }, abstract = {Evolutionary processes such as hybridisation, lateral gene transfer, and recombination are all key factors in shaping the structure of genes and genomes. However, since such processes are not always best represented by trees, there is now considerable interest in using more general networks instead. For example, in recent studies it has been shown that networks can be used to provide lower bounds on the number of recombination events and also for the number of lateral gene transfers that took place in the evolutionary history of a set of molecular sequences. In this paper we describe the theoretical performance of some related bounds that result when merging pairs of trees into networks.}, }
@article {pmid15866919, year = {2005}, author = {Lesic, B and Carniel, E}, title = {Horizontal transfer of the high-pathogenicity island of Yersinia pseudotuberculosis.}, journal = {Journal of bacteriology}, volume = {187}, number = {10}, pages = {3352-3358}, pmid = {15866919}, issn = {0021-9193}, mesh = {Chromosomes, Bacterial ; Culture Media ; *Disease Transmission, Infectious ; Evolution, Molecular ; *Genomic Islands ; Molecular Epidemiology ; Virulence ; Yersinia pseudotuberculosis/*genetics/growth &amp; development/pathogenicity ; }, abstract = {The horizontal transfer of genetic elements plays a major role in bacterial evolution. The high-pathogenicity island (HPI), which codes for an iron uptake system, is present and highly conserved in various Enterobacteriaceae, suggesting its recent acquisition by lateral gene transfer. The aim of this work was to determine whether the HPI has kept its ability to be transmitted horizontally. We demonstrate here that the HPI is indeed transferable from a donor to a recipient Yersinia pseudotuberculosis strain. This transfer was observable only when the donor and recipient bacteria were cocultured at low temperatures in a liquid medium. When optimized conditions were used (bacteria actively growing in an iron-deprived medium at 4 degrees C), the frequency of HPI transfer reached approximately 10(-8). The island was transferable to various serotype I strains of Y. pseudotuberculosis and to Yersinia pestis, but not to Y. pseudotuberculosis strains of serotypes II and IV or to Yersinia enterocolitica. Upon transfer, the HPI was inserted almost systematically into the asn3 tRNA locus. Acquisition of the HPI resulted in the loss of the resident island, suggesting an incompatibility between two copies of the HPI within the same strain. Transfer of the island did not require a functional HPI-borne insertion-excision machinery and was RecA dependent in the recipient but not the donor strain, suggesting that integration of the island into the recipient chromosome occurs via a mechanism of homologous recombination. This lateral transfer also involved the HPI-adjacent sequences, leading to the mobilization of a chromosomal region at least 46 kb in size.}, }
@article {pmid15865991, year = {2005}, author = {Cotton, JA}, title = {Analytical methods for detecting paralogy in molecular datasets.}, journal = {Methods in enzymology}, volume = {395}, number = {}, pages = {700-724}, doi = {10.1016/S0076-6879(05)95036-2}, pmid = {15865991}, issn = {0076-6879}, mesh = {Animals ; Chromosome Mapping ; *Databases, Genetic ; Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; Humans ; L-Lactate Dehydrogenase/genetics ; Models, Genetic ; Models, Statistical ; Multigene Family ; *Phylogeny ; Rod Opsins/genetics ; Sequence Homology ; Software ; Species Specificity ; }, abstract = {Paralogy (common ancestry through gene duplication rather than speciation) is widely recognized as an important problem for molecular systematists. This chapter introduces the concepts of paralogy and orthology and explains why paralogy can complicate both systematic work and other studies of molecular evolution. The definition of paralogy is explicitly phylogenetic, and phylogenetic methods are crucial in elucidating the pattern of paralogy. In particular, knowledge of the species phylogeny is key. I introduce the theory behind methods for detecting paralogy and briefly discuss two particular software implementations of phylogenetic methods to detect paralogy from molecular data. I also introduce a statistical method for detecting paralogy and some future directions for work on paralogy detection.}, }
@article {pmid15865981, year = {2005}, author = {Ray, JL and Nielsen, KM}, title = {Experimental methods for assaying natural transformation and inferring horizontal gene transfer.}, journal = {Methods in enzymology}, volume = {395}, number = {}, pages = {491-520}, doi = {10.1016/S0076-6879(05)95026-X}, pmid = {15865981}, issn = {0076-6879}, mesh = {Acinetobacter/genetics ; Animal Feed/microbiology ; Animals ; Biofilms ; DNA, Bacterial/genetics ; DNA, Recombinant/genetics ; Digestive System/microbiology ; Ecosystem ; *Gene Transfer Techniques ; *Gene Transfer, Horizontal ; Genetic Markers ; Phylogeny ; Plants, Genetically Modified/genetics/microbiology ; Selection, Genetic ; Soil Microbiology ; *Transformation, Bacterial ; }, abstract = {The observation of frequent lateral acquisitions of genes in sequenced bacterial genomes has spurred experimental investigations to elucidate the factors governing ongoing gene transfer processes in bacteria. The uptake of naked DNA by natural transformation is known to occur in a wide range of bacterial species and in some archaea. We describe a series of protocols designed to dissect the natural genetic transformability of individual bacterial strains under conditions that progress from standard in vitro conditions to purely in situ, or natural, conditions. One of the most important factors in ensuring the success of any transformation assay system is the use of a sensitive, effective, and distinguishable selection regimen. Detailed template protocols for assaying bacterial transformation in vitro are presented using the naturally competent bacterium Acinetobacter baylyi strain BD413 as a model. Factors increasing the complexity of the assay systems are included in the following section describing the incorporation of components of natural systems to the in vitro models, such as in soil and water microcosm experiments. We then present template protocols for the transformation of bacteria in modified natural systems, such as in the presence of host tissues and extracts or in the greenhouse. Clear and ecologically meaningful demonstrations of in situ natural transformation are most desirable but are also the most complex and challenging. Because of the highly variable nature of these experiments, we include a discussion of important factors that should be considered when designing such experiments. Some advantages and disadvantages of the experimental systems with regard to resolving the hypotheses tested are included in each section.}, }
@article {pmid15862598, year = {2005}, author = {Thanos, PK and Rivera, SN and Weaver, K and Grandy, DK and Rubinstein, M and Umegaki, H and Wang, GJ and Hitzemann, R and Volkow, ND}, title = {Dopamine D2R DNA transfer in dopamine D2 receptor-deficient mice: effects on ethanol drinking.}, journal = {Life sciences}, volume = {77}, number = {2}, pages = {130-139}, doi = {10.1016/j.lfs.2004.10.061}, pmid = {15862598}, issn = {0024-3205}, support = {AA 11034/AA/NIAAA NIH HHS/United States ; AA07574/AA/NIAAA NIH HHS/United States ; AA07611/AA/NIAAA NIH HHS/United States ; DA12062/DA/NIDA NIH HHS/United States ; MH66360/MH/NIMH NIH HHS/United States ; MH67497/MH/NIMH NIH HHS/United States ; }, mesh = {*Alcohol Drinking ; Animals ; Conditioning, Psychological ; Gene Transfer, Horizontal ; *Genetic Therapy ; Male ; Mice ; Mice, Inbred C57BL ; Receptors, Dopamine D2/deficiency/*genetics/physiology ; }, abstract = {Dopamine (DA) signals are transmitted via specific receptors including the D2 receptors (D2R). Previous studies have shown that D2R upregulation in the nucleus accumbens (NAc) attenuated alcohol consumption. We hypothesized that upregulation of D2R in the NAc would significantly influence alcohol drinking. We tested this hypothesis by determining the effect that D2R upregulation has on alcohol intake in genetically altered mice lacking D2Rs. After a steady baseline of drinking behavior was established for all mice, a null vector or a genetically modified adenoviral vector containing the rat D2R cDNA was infused into the NAc of wild-type (Drd2+/+), heterozygous (Drd2+/-), and receptor-deficient mice (Drd2-/-). Ethanol intake and preference were then determined using the two-bottle choice paradigm. Our results indicated that Drd2+/+ mice treated with the D2R vector significantly attenuated (58 %) their ethanol intake as well as reduced preference. Drd2+/- and mutant mice showed a similar attenuation, although the change was not as marked (12 %) and did not last as long. In contrast, Drd2-/- mice treated with the D2R vector displayed a temporary but significant increase (46 %) in ethanol intake and preference (consumption). These results supported the notion that the D2R plays an important role in alcohol consumption in mice and suggest that a key threshold range of D2R levels is associated with elevated alcohol consumption. Significant deviations in D2R levels from this range could impact alcohol consumption, and could help to explain possible individual variations in alcohol response, metabolism, sensitivity and consumption.}, }
@article {pmid15853937, year = {2005}, author = {Duncan, MJ}, title = {Oral microbiology and genomics.}, journal = {Periodontology 2000}, volume = {38}, number = {}, pages = {63-71}, doi = {10.1111/j.1600-0757.2005.00111.x}, pmid = {15853937}, issn = {0906-6713}, mesh = {Bacterial Typing Techniques ; Databases, Genetic ; Ecosystem ; Fusobacterium nucleatum/*genetics ; Gene Transfer, Horizontal ; Genome, Bacterial ; *Genomics ; Humans ; Mouth/*microbiology ; Streptococcus mutans/*genetics ; Treponema denticola/*genetics ; }, }
@article {pmid15852975, year = {2005}, author = {Zhou, Q and Sun, M and Li, L and Yang, Z and Yu, Z}, title = {[Construction of Bacillus thuringiensis labeled recombinant strain and horizontal transfer of its cry1Ac10 gene].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {16}, number = {1}, pages = {142-146}, pmid = {15852975}, issn = {1001-9332}, mesh = {Bacillus thuringiensis/*genetics/metabolism ; Bacillus thuringiensis Toxins ; Bacterial Proteins/biosynthesis/*genetics ; Bacterial Toxins/biosynthesis/*genetics ; Endotoxins/biosynthesis/*genetics ; Gene Transfer, Horizontal ; Green Fluorescent Proteins/genetics ; Hemolysin Proteins/biosynthesis/*genetics ; *Pest Control, Biological ; Recombinant Proteins/biosynthesis/genetics ; }, abstract = {A recombinant plasmid pBMBZGC10 was obtained by the ligation of gfp-cry1Ac10 fusion gene and vector plasmid pAD4412, which was then introduced by gene pulser into acrystalliferous strain CryB, and a recombinant strain CryB(pBMBZGC10) was obtained. Different fermentative solutions of recombinant strain were used for multi-spraying on Brassica pekinesis, Ipomoea aquatica and Lycopersicon esculentum leaves. The results of fluorescent detection and PCR amplification revealed that cry1Ac10 gene did not transfer into indigenous bacteria, actinomyces and fungi in test soil, and could not be detected in roots, stems and leaves of test plants.}, }
@article {pmid15851673, year = {2005}, author = {Ochman, H and Lerat, E and Daubin, V}, title = {Examining bacterial species under the specter of gene transfer and exchange.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {102 Suppl 1}, number = {Suppl 1}, pages = {6595-6599}, pmid = {15851673}, issn = {0027-8424}, support = {R01 GM056120/GM/NIGMS NIH HHS/United States ; GM56120/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*classification/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial ; Phylogeny ; }, abstract = {Even in lieu of a dependable species concept for asexual organisms, the classification of bacteria into discrete taxonomic units is considered to be obstructed by the potential for lateral gene transfer (LGT) among lineages at virtually all phylogenetic levels. In most bacterial genomes, large proportions of genes are introduced by LGT, as indicated by their compositional features and/or phylogenetic distributions, and there is also clear evidence of LGT between very distantly related organisms. By adopting a whole-genome approach, which examined the history of every gene in numerous bacterial genomes, we show that LGT does not hamper phylogenetic reconstruction at many of the shallower taxonomic levels. Despite the high levels of gene acquisition, the only taxonomic group for which appreciable amounts of homologous recombination were detected was within bacterial species. Taken as a whole, the results derived from the analysis of complete gene inventories support several of the current means to recognize and define bacterial species.}, }
@article {pmid15851667, year = {2005}, author = {Simonson, AB and Servin, JA and Skophammer, RG and Herbold, CW and Rivera, MC and Lake, JA}, title = {Decoding the genomic tree of life.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {102 Suppl 1}, number = {Suppl 1}, pages = {6608-6613}, pmid = {15851667}, issn = {0027-8424}, support = {T32 HG002536/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; *Genome ; Genomics ; Phylogeny ; }, abstract = {Genomes hold within them the record of the evolution of life on Earth. But genome fusions and horizontal gene transfer (HGT) seem to have obscured sufficiently the gene sequence record such that it is difficult to reconstruct the phylogenetic tree of life. HGT among prokaryotes is not random, however. Some genes (informational genes) are more difficult to transfer than others (operational genes). Furthermore, environmental, metabolic, and genetic differences among organisms restrict HGT, so that prokaryotes preferentially share genes with other prokaryotes having properties in common, including genome size, genome G+C composition, carbon utilization, oxygen utilization/sensitivity, and temperature optima, further complicating attempts to reconstruct the tree of life. A new method of phylogenetic reconstruction based on gene presence and absence, called conditioned reconstruction, has improved our prospects for reconstructing prokaryotic evolution. It is also able to detect past genome fusions, such as the fusion that appears to have created the first eukaryote. This genome fusion between a deep branching eubacterium, possibly an ancestor of the cyanobacterium and a proteobacterium, with an archaeal eocyte (crenarchaea), appears to be the result of an early symbiosis. Given new tools and new genes from relevant organisms, it should soon be possible to test current and future fusion theories for the origin of eukaryotes and to discover the general outlines of the prokaryotic tree of life.}, }
@article {pmid15848187, year = {2005}, author = {Kudla, U and Qin, L and Milac, A and Kielak, A and Maissen, C and Overmars, H and Popeijus, H and Roze, E and Petrescu, A and Smant, G and Bakker, J and Helder, J}, title = {Origin, distribution and 3D-modeling of Gr-EXPB1, an expansin from the potato cyst nematode Globodera rostochiensis.}, journal = {FEBS letters}, volume = {579}, number = {11}, pages = {2451-2457}, doi = {10.1016/j.febslet.2005.03.047}, pmid = {15848187}, issn = {0014-5793}, mesh = {Amino Acid Sequence ; Animals ; Blotting, Southern ; DNA, Complementary/genetics ; Evolution, Molecular ; Genome ; Helminth Proteins/*chemistry/genetics/*metabolism ; *Models, Molecular ; Molecular Sequence Data ; Protein Structure, Tertiary ; Sequence Alignment ; Solanum tuberosum/*parasitology ; Nicotiana/genetics ; Tylenchida/*chemistry/*genetics ; }, abstract = {Southern analysis showed that Gr-EXPB1, a functional expansin from the potato cyst nematode Globodera rostochiensis, is member of a multigene family, and EST data suggest expansins to be present in other plant parasitic nematodes as well. Homology modeling predicted that Gr-EXPB1 domain 1 (D1) has a flat beta-barrel structure with surface-exposed aromatic rings, whereas the 3D structure of Gr-EXPB1-D2 was remarkably similar to plant expansins. Gr-EXPB1 shows highest sequence similarity to two extracellular proteins from saprophytic soil-inhabiting Actinobacteria, and includes a bacterial type II carbohydrate-binding module. These results support the hypothesis that a number of pathogenicity factors of cyst nematodes is of procaryotic origin and were acquired by horizontal gene transfer.}, }
@article {pmid15845517, year = {2005}, author = {Cieslewicz, MJ and Chaffin, D and Glusman, G and Kasper, D and Madan, A and Rodrigues, S and Fahey, J and Wessels, MR and Rubens, CE}, title = {Structural and genetic diversity of group B streptococcus capsular polysaccharides.}, journal = {Infection and immunity}, volume = {73}, number = {5}, pages = {3096-3103}, pmid = {15845517}, issn = {0019-9567}, support = {AI22498/AI/NIAID NIH HHS/United States ; R21 AI042940/AI/NIAID NIH HHS/United States ; R01 AI022498/AI/NIAID NIH HHS/United States ; R01 AI042940/AI/NIAID NIH HHS/United States ; AI42940/AI/NIAID NIH HHS/United States ; R01 AI022498-18/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Capsules/biosynthesis/*chemistry/genetics ; Bacterial Proteins/chemistry/*genetics/metabolism ; Carbohydrate Sequence ; Gene Transfer, Horizontal ; *Genetic Variation ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Recombination, Genetic ; Sequence Analysis, DNA ; Serotyping ; Streptococcal Infections ; Streptococcus agalactiae/*classification/genetics ; }, abstract = {Group B Streptococcus (GBS) is an important pathogen of neonates, pregnant women, and immunocompromised individuals. GBS isolates associated with human infection produce one of nine antigenically distinct capsular polysaccharides which are thought to play a key role in virulence. A comparison of GBS polysaccharide structures of all nine known GBS serotypes together with the predicted amino acid sequences of the proteins that direct their synthesis suggests that the evolution of serotype-specific capsular polysaccharides has proceeded through en bloc replacement of individual glycosyltransferase genes with DNA sequences that encode enzymes with new linkage specificities. We found striking heterogeneity in amino acid sequences of synthetic enzymes with very similar functions, an observation that supports horizontal gene transfer rather than stepwise mutagenesis as a mechanism for capsule variation. Eight of the nine serotypes appear to be closely related both structurally and genetically, whereas serotype VIII is more distantly related. This similarity in polysaccharide structure strongly suggests that the evolutionary pressure toward antigenic variation exerted by acquired immunity is counterbalanced by a survival advantage conferred by conserved structural motifs of the GBS polysaccharides.}, }
@article {pmid15843015, year = {2005}, author = {Coombes, BK and Wickham, ME and Brown, NF and Lemire, S and Bossi, L and Hsiao, WW and Brinkman, FS and Finlay, BB}, title = {Genetic and molecular analysis of GogB, a phage-encoded type III-secreted substrate in Salmonella enterica serovar typhimurium with autonomous expression from its associated phage.}, journal = {Journal of molecular biology}, volume = {348}, number = {4}, pages = {817-830}, doi = {10.1016/j.jmb.2005.03.024}, pmid = {15843015}, issn = {0022-2836}, mesh = {Amino Acid Sequence ; *Gene Expression Regulation, Viral ; HeLa Cells ; Humans ; Molecular Sequence Data ; Mutation/genetics ; Prophages/genetics/metabolism/pathogenicity ; Protein Transport ; Salmonella Phages/*genetics/*metabolism/pathogenicity ; Salmonella typhimurium/chemistry/genetics/*metabolism/*virology ; Sequence Alignment ; Substrate Specificity ; Viral Proteins/chemistry/*genetics/*metabolism ; Virulence Factors/chemistry/genetics/metabolism ; }, abstract = {Salmonella enterica serovar Typhimurium is lysogenized by several temperate bacteriophages that encode lysogenic conversion genes, which can act as virulence factors during infection and contribute to the genetic diversity and pathogenic potential of the lysogen. We have investigated the temperate bacteriophage called Gifsy-1 in S.enterica serovar Typhimurium and show here that the product of the gogB gene encoded within this phage shares similarity with proteins from other Gram-negative pathogens. The amino-terminal portion of GogB shares similarity with leucine-rich repeat-containing virulence-associated proteins from other Gram-negative pathogens, whereas the carboxyl-terminal portion of GogB shares similarity with uncharacterized proteins in other pathogens. We show that GogB is secreted by both type III secretion systems encoded in Salmonella Pathogenicity Island-1 (SPI-1) and SPI-2 but translocation into host cells is a SPI-2-mediated process. Once translocated, GogB localizes to the cytoplasm of infected host cells. The genetic regulation of gogB in Salmonella is influenced by the transcriptional activator, SsrB, under SPI-2-inducing conditions, but the modular nature of the gogB gene allows for autonomous expression and type III secretion following horizontal gene transfer into a heterologous pathogen. These data define the first autonomously expressed lysogenic conversion gene within Gifsy-1 that acts as a modular and promiscuous type III-secreted substrate of the infection process.}, }
@article {pmid15841240, year = {2003}, author = {Shen, Z and Denton, M and Mutti, N and Pappan, K and Kanost, MR and Reese, JC and Reeck, GR}, title = {Polygalacturonase from Sitophilus oryzae: possible horizontal transfer of a pectinase gene from fungi to weevils.}, journal = {Journal of insect science (Online)}, volume = {3}, number = {}, pages = {24}, pmid = {15841240}, issn = {1536-2442}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Fungi/*enzymology/*genetics ; Gene Expression Regulation, Enzymologic ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Polygalacturonase/*genetics ; Weevils/*enzymology/*genetics ; }, abstract = {Endo-polygalacturonase, one of the group of enzymes known collectively as pectinases, is widely distributed in bacteria, plants and fungi. The enzyme has also been found in several weevil species and a few other insects, such as aphids, but not in Drosophila melanogaster, Anopheles gambiae, or Caenorhabditis elegans or, as far as is known, in any more primitive animal species. What, then, is the genetic origin of the polygalacturonases in weevils? Since some weevil species harbor symbiotic microorganisms, it has been suggested, reasonably, that the symbionts' genomes of both aphids and weevils, rather than the insects' genomes, could encode polygalacturonase. We report here the cloning of a cDNA that encodes endo-polygalacturonase in the rice weevil, Sitophilus oryzae (L.), and investigations based on the cloned cDNA. Our results, which include analysis of genes in antibiotic-treated rice weevils, indicate that the enzyme is, in fact, encoded by the insect genome. Given the apparent absence of the gene in much of the rest of the animal kingdom, it is therefore likely that the rice weevil polygalacturonase gene was incorporated into the weevil's genome by horizontal transfer, possibly from a fungus.}, }
@article {pmid15837379, year = {2005}, author = {Thomas, A and Linden, A and Mainil, J and Bischof, DF and Frey, J and Vilei, EM}, title = {Mycoplasma bovis shares insertion sequences with Mycoplasma agalactiae and Mycoplasma mycoides subsp. mycoides SC: Evolutionary and developmental aspects.}, journal = {FEMS microbiology letters}, volume = {245}, number = {2}, pages = {249-255}, doi = {10.1016/j.femsle.2005.03.013}, pmid = {15837379}, issn = {0378-1097}, mesh = {Animals ; Blotting, Southern ; Cattle ; Cattle Diseases/microbiology ; *DNA Transposable Elements ; DNA, Bacterial/chemistry/genetics/isolation &amp; purification ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Mycoplasma Infections/microbiology/veterinary ; Mycoplasma agalactiae/*genetics ; Mycoplasma bovis/*genetics ; Mycoplasma mycoides/*genetics ; Sequence Analysis, DNA ; }, abstract = {Three new insertion elements, ISMbov1, ISMbov2 and ISMbov3, which are closely related to ISMag1 (Mycoplasma agalactiae), ISMmy1 and IS1634 (both Mycoplasma mycoides subsp. mycoides SC), respectively, have been discovered in Mycoplasma bovis, an important pathogen of cattle. Southern blotting showed that the genome of M. bovis harbours 6-12 copies of ISMbov1, 11-15 copies of ISMbov2 and 4-10 copies of ISMbov3, depending on the strain. A fourth insertion element, the IS30-like element, is present in 4-8 copies. This high number of IS elements in M. bovis, which represent a substantial part of its genome, and their relatedness with IS elements of both M. agalactiae and M. mycoides subsp. mycoides SC suggest the occurrence of two evolutionary events: (i) a divergent evolution into M. agalactiae and M. bovis upon infection of different hosts; (ii) a horizontal transfer of IS elements during co-infection with M. mycoides subsp. mycoides SC and M. bovis of a same bovine host.}, }
@article {pmid15823205, year = {2005}, author = {Da Silva, M and Upton, C}, title = {Host-derived pathogenicity islands in poxviruses.}, journal = {Virology journal}, volume = {2}, number = {}, pages = {30}, pmid = {15823205}, issn = {1743-422X}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Computational Biology ; DNA, Viral/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome, Viral ; Genomic Islands/*genetics ; Poxviridae/*genetics ; }, abstract = {BACKGROUND: Poxviruses are important both as pathogens and as vaccine vectors. Poxvirus genomes (150-350 kb) consist of a single linear dsDNA molecule; the two polynucleotide strands are joined by short hairpin loops. The genomes encode highly conserved proteins required for DNA replication and mRNA transcription as well as a variable set of virulence factors; transcription takes place within the cytoplasm of the host cell. We are interested in evolution of poxvirus genomes and especially how these viruses acquire host-derived genes that are believed to function as virulence factors.<br><br>RESULTS: Using a variety of bioinformatics tools, we have identified regions in poxvirus genomes that have unusual nucleotide composition (higher or lower than average A+T content) compared to the genome as a whole; such regions may be several kilobases in length and contain a number of genes. Regions with unusual nucleotide composition may represent genes that have been recently acquired from the host genome. The study of these genomic regions with unusual nucleotide content will help elucidate evolutionary processes in poxviruses.<br><br>CONCLUSION: We have found that dotplots of complete poxvirus genomes can be used to locate regions on the genome that differ significantly in A+T content to the genome as a whole. The genes in these regions may have been acquired relatively recently from the host genome or from another AT-rich poxvirus.}, }
@article {pmid15822923, year = {2005}, author = {Saunders, NF and Goodchild, A and Raftery, M and Guilhaus, M and Curmi, PM and Cavicchioli, R}, title = {Predicted roles for hypothetical proteins in the low-temperature expressed proteome of the Antarctic archaeon Methanococcoides burtonii.}, journal = {Journal of proteome research}, volume = {4}, number = {2}, pages = {464-472}, doi = {10.1021/pr049797+}, pmid = {15822923}, issn = {1535-3893}, mesh = {Adaptation, Physiological ; Chromatography, High Pressure Liquid ; *Cold Temperature ; Mass Spectrometry ; Methanosarcinaceae/genetics/*metabolism/physiology ; Oxidation-Reduction ; *Proteome ; }, abstract = {Using liquid chromatography-mass spectrometry, 528 proteins were identified that are expressed during growth at 4 degrees C in the cold adapted archaeon, Methanococcoides burtonii. Of those, 135 were annotated previously as unique or conserved hypothetical proteins. We have performed a comprehensive, integrated analysis of the latter proteins using threading, InterProScan, predicted subcellular localization and visualization of conserved gene context across multiple prokaryotic genomes. Functional information was obtained for 55 proteins, providing new insight into the physiology of M. burtonii. Many of the proteins were predicted to be involved in DNA/RNA binding or modification and cell signaling, suggesting a complex, uncharacterized regulatory network controlling cellular processes during growth at low-temperature. Novel enzymatic functions were predicted for several proteins, including a putative candidate gene for the posttranslational modification of the key methanogenesis enzyme coenzyme M methyl reductase. A bacterial-like CRISPR locus was identified as a strong candidate for archaeal-bacterial lateral gene transfer. Gene context analysis proved a valuable augmentation to the other predictive methods in several cases, by revealing conserved gene associations and annotations in other microbial genomes. Our results underscore the importance of addressing the "hypothetical protein problem" for a complete understanding of cell physiology.}, }
@article {pmid15819979, year = {2005}, author = {MacLeod, D and Charlebois, RL and Doolittle, F and Bapteste, E}, title = {Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement.}, journal = {BMC evolutionary biology}, volume = {5}, number = {}, pages = {27}, pmid = {15819979}, issn = {1471-2148}, mesh = {Animals ; Computational Biology/methods ; *Evolution, Molecular ; *Gene Rearrangement ; *Gene Transfer, Horizontal ; Genetic Markers ; Likelihood Functions ; Models, Genetic ; Phylogeny ; Programming Languages ; Sequence Analysis, DNA ; Software ; }, abstract = {BACKGROUND: When organismal phylogenies based on sequences of single marker genes are poorly resolved, a logical approach is to add more markers, on the assumption that weak but congruent phylogenetic signal will be reinforced in such multigene trees. Such approaches are valid only when the several markers indeed have identical phylogenies, an issue which many multigene methods (such as the use of concatenated gene sequences or the assembly of supertrees) do not directly address. Indeed, even when the true history is a mixture of vertical descent for some genes and lateral gene transfer (LGT) for others, such methods produce unique topologies.<br><br>RESULTS: We have developed software that aims to extract evidence for vertical and lateral inheritance from a set of gene trees compared against an arbitrary reference tree. This evidence is then displayed as a synthesis showing support over the tree for vertical inheritance, overlaid with explicit lateral gene transfer (LGT) events inferred to have occurred over the history of the tree. Like splits-tree methods, one can thus identify nodes at which conflict occurs. Additionally one can make reasonable inferences about vertical and lateral signal, assigning putative donors and recipients.<br><br>CONCLUSION: A tool such as ours can serve to explore the reticulated dimensionality of molecular evolution, by dissecting vertical and lateral inheritance at high resolution. By this, we mean that individual nodes can be examined not only for congruence, but also for coherence in light of LGT. We assert that our tools will facilitate the comparison of phylogenetic trees, and the interpretation of conflicting data.}, }
@article {pmid15819636, year = {2005}, author = {Ubeda, C and Maiques, E and Knecht, E and Lasa, I and Novick, RP and Penadés, JR}, title = {Antibiotic-induced SOS response promotes horizontal dissemination of pathogenicity island-encoded virulence factors in staphylococci.}, journal = {Molecular microbiology}, volume = {56}, number = {3}, pages = {836-844}, doi = {10.1111/j.1365-2958.2005.04584.x}, pmid = {15819636}, issn = {0950-382X}, mesh = {Anti-Bacterial Agents/*pharmacology ; Base Sequence ; Ciprofloxacin/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Gene Transfer, Horizontal ; Genomic Islands/drug effects/*genetics ; Molecular Sequence Data ; SOS Response, Genetics/*drug effects ; Staphylococcus Phages/drug effects/genetics ; Staphylococcus aureus/drug effects/pathogenicity/*physiology ; Virulence Factors/*genetics ; }, abstract = {Although mobile genetic elements have a crucial role in spreading pathogenicity-determining genes among bacterial populations, environmental and genetic factors involved in the horizontal transfer of these genes are largely unknown. Here we show that SaPIbov1, a Staphylococcus aureus pathogenicity island that belongs to the growing family of these elements that are found in many strains, is induced to excise and replicate after SOS induction of at least three different temperate phages, 80alpha, phi11 and phi147, and is then packaged into phage-like particles and transferred at high frequency. SOS induction by commonly used fluoroquinolone antibiotics, such as ciprofloxacin, also results in replication and high-frequency transfer of this element, as well as of SaPI1, the prototypical island of S. aureus, suggesting that such antibiotics may have the unintended consequence of promoting the spread of bacterial virulence factors. Although the strains containing these prophages do not normally contain SaPIs, we have found that RF122-1, the original SaPIbov1-containing clinical isolate, contains a putative second pathogenicity island that is replicated after SOS induction, by antibiotic treatment, of the prophage(s) present in the strain. Although SaPIbov1 is not induced to replicate after SOS induction in this strain, it is transferred by the antibiotic-activated phages. We conclude that SOS induction by therapeutic agents can promote the spread of staphylococcal virulence genes.}, }
@article {pmid15816921, year = {2005}, author = {Martin, W}, title = {Crystal ball. Getting a better picture of evolution.}, journal = {Environmental microbiology}, volume = {7}, number = {4}, pages = {479-480}, doi = {10.1111/j.1462-2920.2005.803_9.x}, pmid = {15816921}, issn = {1462-2912}, mesh = {*Evolution, Molecular ; *Gene Transfer, Horizontal ; Models, Biological ; Phylogeny ; }, }
@article {pmid15809009, year = {2005}, author = {Butler, MI and Poulter, RT}, title = {The PRP8 inteins in Cryptococcus are a source of phylogenetic and epidemiological information.}, journal = {Fungal genetics and biology : FG &amp; B}, volume = {42}, number = {5}, pages = {452-463}, doi = {10.1016/j.fgb.2005.01.011}, pmid = {15809009}, issn = {1087-1845}, mesh = {Amino Acid Sequence ; Conserved Sequence/genetics ; Cryptococcus/*genetics ; Cryptococcus neoformans/*genetics ; DNA, Fungal/chemistry/genetics ; *Evolution, Molecular ; Fungal Proteins/chemistry/genetics ; Gene Transfer, Horizontal ; *Genes, Fungal ; Inteins/*genetics ; *Molecular Epidemiology ; Molecular Sequence Data ; Phylogeny ; Saccharomyces cerevisiae/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {Only two nuclear encoded inteins have been described. The first, SceVMA, was found in a vacuolar ATPase gene of Saccharomyces cerevisiae and related yeasts. The second, CnePRP8, was found in the PRP8 gene of Cryptococcus neoformans. CnePRP8 contains protein sequences associated with intein splicing but no endonuclease domain. We compared allelic mini-inteins in both varieties of C. neoformans (var. neoformans and var. grubii) and in the related primary pathogen C. gattii to study the evolution of both the mini-intein and the host. We also describe a full-length, endonuclease-containing intein in Cryptococcus laurentii, a moderately distant relation of C. neoformans. We did not detect an intein in the PRP8 gene of other species of Cryptococcus including species closely related to the C. neoformans/C. gattii group. It is therefore probable that the C. neoformans/C. gattii mini-intein was derived from horizontal transfer in which C. laurentii or another intein-containing species was the source.}, }
@article {pmid15808947, year = {2005}, author = {Tobes, R and Pareja, E}, title = {Repetitive extragenic palindromic sequences in the Pseudomonas syringae pv. tomato DC3000 genome: extragenic signals for genome reannotation.}, journal = {Research in microbiology}, volume = {156}, number = {3}, pages = {424-433}, doi = {10.1016/j.resmic.2004.10.014}, pmid = {15808947}, issn = {0923-2508}, mesh = {Base Sequence ; Chromosome Mapping ; Chromosomes, Bacterial/genetics ; *Genome, Bacterial ; Molecular Sequence Data ; Nucleic Acid Conformation ; Pseudomonas syringae/*genetics ; Repetitive Sequences, Nucleic Acid/*genetics ; }, abstract = {Repetitive extragenic palindromic (REPs) sequences were first described in enterobacteriacea and later in Pseudomonas putida. We have detected a new variant (51 base pairs) of REP sequences that appears to be disseminated in more than 300 copies in the Pseudomonas syringae DC3000 genome. The finding of REP sequences in P. syringae confirms the broad presence of this type of repetitive sequence in bacteria. We analyzed the distribution of REP sequences and the structure of the clusters, and we show that palindromy is conserved. REP sequences appear to be allocated to the extragenic space, with a special preference for the intergenic spaces limited by convergent genes, while their presence is scarce between divergent genes. Using REP sequences as markers of extragenicity we re-annotated a set of genes of the P. syringae DC3000 genome demonstrating that REP sequences can be used for refinement of annotation of a genome. The similarity detected between virulence genes from evolutionarily distant pathogenic bacteria suggests the acquisition of clusters of virulence genes by horizontal gene transfer. We did not detect the presence of P. syringae REP elements in the principal pathogenicity gene clusters. This absence suggests that genome fragments lacking REP sequences could point to regions recently acquired from other organisms, and REP sequences might be new tracers for gaining insight into key aspects of bacterial genome evolution, especially when studying pathogenicity acquisition. In addition, as the P. syringae REP sequence is species-specific with respect to the sequenced genomes, it is an exceptional candidate for use as a fingerprint in precise genotyping and epidemiological studies.}, }
@article {pmid15805527, year = {2005}, author = {Davidsen, T and Bjørås, M and Seeberg, EC and Tønjum, T}, title = {Antimutator role of DNA glycosylase MutY in pathogenic Neisseria species.}, journal = {Journal of bacteriology}, volume = {187}, number = {8}, pages = {2801-2809}, pmid = {15805527}, issn = {0021-9193}, mesh = {Base Pair Mismatch/*genetics ; DNA Glycosylases/genetics/*metabolism/physiology ; DNA Mutational Analysis ; DNA Repair ; Guanine/analogs &amp; derivatives/*metabolism ; Neisseria/*enzymology/genetics/metabolism ; Recombinant Fusion Proteins/isolation &amp; purification ; }, abstract = {Genome alterations due to horizontal gene transfer and stress constantly generate strain on the gene pool of Neisseria meningitidis, the causative agent of meningococcal (MC) disease. The DNA glycosylase MutY of the base excision repair pathway is involved in the protection against oxidative stress. MC MutY expressed in Escherichia coli exhibited base excision activity towards DNA substrates containing A:7,8-dihydro-8-oxo-2'-deoxyguanosine and A:C mismatches. Expression in E. coli fully suppressed the elevated spontaneous mutation rate found in the E. coli mutY mutant. An assessment of MutY activity in lysates of neisserial wild-type and mutY mutant strains showed that both MC and gonococcal (GC) MutY is expressed and active in vivo. Strikingly, MC and GC mutY mutants exhibited 60- to 140-fold and 20-fold increases in mutation rates, respectively, compared to the wild-type strains. Moreover, the differences in transitions and transversions in rpoB conferring rifampin resistance observed with the wild type and mutants demonstrated that the neisserial MutY enzyme works in preventing GC-->AT transversions. These findings are important in the context of models linking mutator phenotypes of disease isolates to microbial fitness.}, }
@article {pmid15805016, year = {2005}, author = {Ané, C and Sanderson, M}, title = {Missing the forest for the trees: phylogenetic compression and its implications for inferring complex evolutionary histories.}, journal = {Systematic biology}, volume = {54}, number = {1}, pages = {146-157}, doi = {10.1080/10635150590905984}, pmid = {15805016}, issn = {1063-5157}, mesh = {*Algorithms ; Classification/*methods ; Data Interpretation, Statistical ; *Models, Genetic ; *Phylogeny ; }, abstract = {Phylogenetic tree reconstruction is difficult in the presence of lateral gene transfer and other processes generating conflicting signals. We develop a new approach to this problem using ideas borrowed from algorithmic information theory. It selects the hypothesis that simultaneously minimizes the descriptive complexity of the tree(s) plus the data when encoded using those tree(s). In practice this is the hypothesis that can compress the data the most. We show not only that phylogenetic compression is an efficient method for encoding most phylogenetic data sets and is more efficient than compression schemes designed for single sequences, but also that it provides a clear information theoretic rule for determining when a collection of conflicting trees is a better explanation of the data than a single tree. By casting the parsimony problem in this more general framework, we also conclude that the so-called total-evidence tree--the tree constructed from all the data simultaneously--is not always the most economical explanation of the data.}, }
@article {pmid15803417, year = {2004}, author = {Woloszynska, M and Bocer, T and Mackiewicz, P and Janska, H}, title = {A fragment of chloroplast DNA was transferred horizontally, probably from non-eudicots, to mitochondrial genome of Phaseolus.}, journal = {Plant molecular biology}, volume = {56}, number = {5}, pages = {811-820}, pmid = {15803417}, issn = {0167-4412}, mesh = {Base Sequence ; DNA, Chloroplast/*genetics ; DNA, Mitochondrial/*genetics ; DNA, Plant/genetics ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Phaseolus/*genetics ; Phylogeny ; Plant Proteins/genetics ; RNA, Transfer, Ala/genetics ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; }, abstract = {The mitochondrial genomes of some Phaseolus species contain a fragment of chloroplast trnA gene intron, named pvs-trnA for its location within the Phaseolus vulgaris sterility sequence (pvs). The purpose of this study was to determine the type of transfer (intracellular or horizontal) that gave rise to pvs-trnA. Using a PCR approach we could not find the respective portion of the trnA gene as a part of pvs outside the Phaseolus genus. However, a BLAST search revealed longer fragments of trnA present in the mitochondrial genomes of some Citrus species, Helianthus annuus and Zea mays. Basing on the identity or near-identity between these mitochondrial sequences and their chloroplast counterparts we concluded that they had relocated from chloroplasts to mitochondria via recent, independent, intracellular DNA transfers. In contrast, pvs-trnA displayed a relatively higher sequence divergence when compared with its chloroplast counterpart from Phaseolus vulgaris. Alignment of pvs-trnA with corresponding trnA fragments from 35 plant species as well as phylogenetic analysis revealed that pvs-trnA grouped with non-eudicot sequences and was well separated from all Fabales sequences. In conclusion, we propose that pvs-trnA arose via horizontal transfer of a trnA intron fragment from chloroplast of a non-eudicot plant to Phaseolus mitochondria. This is the first example of horizontal transfer of a chloroplast sequence to the mitochondrial genome in higher plants.}, }
@article {pmid15803388, year = {2005}, author = {O'Mahony, R and Doran, J and Coffey, L and Cahill, OJ and Black, GW and O'Reilly, C}, title = {Characterisation of the nitrile hydratase gene clusters of Rhodococcus erythropolis strains AJ270 and AJ300 and Microbacterium sp. AJ115 indicates horizontal gene transfer and reveals an insertion of IS1166.}, journal = {Antonie van Leeuwenhoek}, volume = {87}, number = {3}, pages = {221-232}, doi = {10.1007/s10482-004-3721-x}, pmid = {15803388}, issn = {0003-6072}, mesh = {ATP-Binding Cassette Transporters/genetics ; Amino Acid Sequence ; Base Sequence ; Chromosomes, Bacterial/genetics ; DNA Transposable Elements ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Evolution, Molecular ; Gene Order ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Hydro-Lyases/*genetics/metabolism ; Molecular Sequence Data ; Multigene Family ; Mycobacteriaceae/enzymology/*genetics/isolation &amp; purification ; Open Reading Frames ; Phylogeny ; Plasmids/genetics ; Polymerase Chain Reaction ; Repetitive Sequences, Nucleic Acid/genetics ; Rhodococcus/enzymology/*genetics/isolation &amp; purification ; Sequence Alignment ; Sequence Homology ; Transposases/genetics ; }, abstract = {The nitrile metabolising strains AJ270, AJ300 and AJ115 were isolated from the same location. The strains have very similar nitrile metabolising profiles. Sequencing of the 16S rRNA gene indicates that strains AJ270 and AJ300 are novel strains of Rhodococcus erythropolis while strain AJ115 is a novel Microbacterium strain very closely related to Microbacterium oxydans and Microbacterium liquefaciens. Analysis of the structure of the nitrile hydratase/amidase gene clusters in the three strains indicates that this region is identical in these strains and that this structure is different to other nitrile hydratase/amidase gene clusters. The major difference seen is the insertion of a complete copy of the insertion sequence IS1166 in the nhr2 gene. This copy of IS1166 generates a 10 bp direct duplication at the point of insertion and has one ORF encoding a protein of 434 amino acids, with 98% homology to the transposase of IS666 from Mycobacterium avium. A gene oxd, encoding aldoxime dehydratase is found upstream of the nitrile hydratase gene cluster and an open reading frame encoding a protein with homology to GlnQ type ABC transporters is found downstream of the nitrile hydratase/amidase genes. The identity of the nitrile hydratase/amidase gene clusters in the three strains suggests horizontal gene transfer of this region. Analysis of the strains for both linear and circular plasmids indicates that both are present in the strains but hybridisation studies indicate that the nitrile hydratase/amidase gene cluster is chromosomally located. The nitrile hydratase/amidase enzymes of strain AJ270 are inducible with acetonitrile or acetamide. Interestingly although a number of Fe-type nitrile hydratases have been shown to be photosensitive, the enzyme from strain AJ270 is not.}, }
@article {pmid15799709, year = {2005}, author = {Lerat, E and Daubin, V and Ochman, H and Moran, NA}, title = {Evolutionary origins of genomic repertoires in bacteria.}, journal = {PLoS biology}, volume = {3}, number = {5}, pages = {e130}, pmid = {15799709}, issn = {1545-7885}, mesh = {Bacteria/classification/*genetics ; Bacterial Proteins/genetics ; *Evolution, Molecular ; Gene Transfer Techniques ; Genetic Variation ; *Genome, Bacterial ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; }, abstract = {Explaining the diversity of gene repertoires has been a major problem in modern evolutionary biology. In eukaryotes, this diversity is believed to result mainly from gene duplication and loss, but in prokaryotes, lateral gene transfer (LGT) can also contribute substantially to genome contents. To determine the histories of gene inventories, we conducted an exhaustive analysis of gene phylogenies for all gene families in a widely sampled group, the gamma-Proteobacteria. We show that, although these bacterial genomes display striking differences in gene repertoires, most gene families having representatives in several species have congruent histories. Other than the few vast multigene families, gene duplication has contributed relatively little to the contents of these genomes; instead, LGT, over time, provides most of the diversity in genomic repertoires. Most such acquired genes are lost, but the majority of those that persist in genomes are transmitted strictly vertically. Although our analyses are limited to the gamma-Proteobacteria, these results resolve a long-standing paradox-i.e., the ability to make robust phylogenetic inferences in light of substantial LGT.}, }
@article {pmid15798778, year = {2005}, author = {Martin, W}, title = {Molecular evolution: lateral gene transfer and other possibilities.}, journal = {Heredity}, volume = {94}, number = {6}, pages = {565-566}, doi = {10.1038/sj.hdy.6800659}, pmid = {15798778}, issn = {0018-067X}, mesh = {DNA, Mitochondrial/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Plants/genetics ; }, }
@article {pmid15797612, year = {2005}, author = {Sánchez-Gracia, A and Maside, X and Charlesworth, B}, title = {High rate of horizontal transfer of transposable elements in Drosophila.}, journal = {Trends in genetics : TIG}, volume = {21}, number = {4}, pages = {200-203}, doi = {10.1016/j.tig.2005.02.001}, pmid = {15797612}, issn = {0168-9525}, mesh = {Animals ; DNA Transposable Elements/*genetics ; Drosophila/*genetics ; Gene Frequency/*genetics ; *Gene Transfer, Horizontal ; *Genetic Variation ; *Genetics, Population ; Phylogeny ; }, abstract = {We have conducted molecular population genetics analyses to understand the relationships among the transposable elements (TEs) in Drosophila melanogaster, in combination with sequence comparisons of TEs from two related species, D. simulans and D. yakuba. We observed much lower than expected genetic differences among elements, clear evidence for departure from expectations for equilibrium copy numbers and little divergence between species. This suggests that a large proportion of TEs in D. melanogaster had a recent origin as a result of interspecies movement.}, }
@article {pmid15790952, year = {2005}, author = {Ziolo, MT and Martin, JL and Bossuyt, J and Bers, DM and Pogwizd, SM}, title = {Adenoviral gene transfer of mutant phospholamban rescues contractile dysfunction in failing rabbit myocytes with relatively preserved SERCA function.}, journal = {Circulation research}, volume = {96}, number = {8}, pages = {815-817}, doi = {10.1161/01.RES.0000163981.97262.3b}, pmid = {15790952}, issn = {1524-4571}, support = {HL30077/HL/NHLBI NIH HHS/United States ; HL46929/HL/NHLBI NIH HHS/United States ; HL73966/HL/NHLBI NIH HHS/United States ; }, mesh = {Adenoviridae/*genetics ; Animals ; Calcium/metabolism ; Calcium-Binding Proteins/*antagonists &amp; inhibitors/genetics ; Calcium-Transporting ATPases/*physiology ; Gene Transfer, Horizontal ; Heart Failure/physiopathology/*therapy ; Mutation ; *Myocardial Contraction ; Myocytes, Cardiac/*physiology ; Rabbits ; Sarcoplasmic Reticulum Calcium-Transporting ATPases ; Ventricular Function, Left ; }, abstract = {In heart failure (HF) a main factor in reduced contractility is reduced SR Ca2+ content and reversed force-frequency response (FFR), ie, from positive to negative. Our arrhythmogenic rabbit HF model exhibits decreased contractility mainly due to an increase in Na/Ca exchange (NCX) activity (with only modest decrease in SR Ca2+-ATPase (SERCA) function), similar to many end-stage HF patients. Here we test whether phospholamban (PLB) inhibition using a dominant-negative mutant PLB adenovirus (K3E/R14E, AdPLB-dn, with beta-galactosidase adenovirus as control) could enhance SERCA function and restore Ca2+ transients and positive FFR in ventricular myocytes from these HF rabbits. HF myocytes infected with AdPLB-dn (versus control) had enhanced Ca2+ transient amplitude (2.0+/-0.1 versus 1.6+/-0.05 F/Fo at 0.5 Hz, P<0.05) and had a positive FFR, whereas acutely isolated HF myocytes or those infected with Adbetagal had negative FFR. Ca2+ transients declined faster in AdPLB-dn versus Adbetagal myocytes (RT50%: 317+/-29 versus 551+/-90 ms at 0.5 Hz, P<0.05) and had an increased SR Ca2+ load (3.5+/-0.3 versus 2.6+/-0.2 F/Fo at 0.5 Hz, P<0.05), indicative of increased SERCA function. Furthermore, this restoration of function was not due to changes in NCX or SERCA expression. Thus, increasing SERCA activity in failing myocytes by AdPLB-dn gene transfer reversed the contractile dysfunction (and restored positive FFR) by increasing SR Ca2+ load. This approach could enhance contractile function in failing hearts of various etiologies, even here where reduced SERCA activity is not the main dysfunction.}, }
@article {pmid15787196, year = {2004}, author = {Wolska, KI and Kraczkiewicz-Dowjat, A and Grudniak, AM and Sajkowska, A and Wiktorowicz, T}, title = {New methods of pathogenic bacteria elimination.}, journal = {Polish journal of microbiology}, volume = {53 Suppl}, number = {}, pages = {39-43}, pmid = {15787196}, issn = {1733-1331}, mesh = {Bacteria/*genetics/*growth &amp; development/metabolism ; Bacterial Infections/*therapy ; Conjugation, Genetic/*physiology ; Gene Transfer, Horizontal/*physiology ; Plasmids/therapeutic use ; Transformation, Bacterial/*physiology ; }, abstract = {The growing bacterial resistance to antibiotics calls for the elaboration of new pathogens elimination strategies. Some of these methods are based on the conjugative transfer of recombinant plasmids able to eliminate pathogenic recipients by plasmid run-away replication or by killing activity of plasmid-encoded bacteriocins. Using live bacteria as donors of plasmid vectors carrying killing determinants requires meeting many safety restrictions in order to eliminate potential biohazard.}, }
@article {pmid15784185, year = {2005}, author = {Gomes, JP and Hsia, RC and Mead, S and Borrego, MJ and Dean, D}, title = {Immunoreactivity and differential developmental expression of known and putative Chlamydia trachomatis membrane proteins for biologically variant serovars representing distinct disease groups.}, journal = {Microbes and infection}, volume = {7}, number = {3}, pages = {410-420}, doi = {10.1016/j.micinf.2004.11.014}, pmid = {15784185}, issn = {1286-4579}, support = {R01-AI39499/AI/NIAID NIH HHS/United States ; R01-EY/AI12219/EY/NEI NIH HHS/United States ; R21-AI51417/AI/NIAID NIH HHS/United States ; }, mesh = {Adolescent ; Animals ; Antibodies, Bacterial/blood ; Bacterial Proteins/*biosynthesis/immunology ; Chlamydia Infections/immunology ; Chlamydia trachomatis/classification/growth &amp; development/immunology/*metabolism ; *Gene Expression Regulation, Bacterial ; *Gene Expression Regulation, Developmental ; HeLa Cells ; Humans ; Membrane Proteins/*biosynthesis/immunology ; }, abstract = {Chlamydia trachomatis is an intracellular bacterium that causes ocular and urogenital diseases worldwide. Membrane proteins have only been partially characterized, and the discovery of a nine-member polymorphic membrane protein gene family has enhanced interest in defining their function. We previously reported two putative insertion sequence-like elements in pmpC for biovariant Ba and one each for G and L2, suggesting horizontal gene transfer. Because of this and the tissue tropism differences for these biovariants, we analyzed by quantitative real-time RT-PCR pmpC expression relative to immunogenic protein genes ompA, groEL and gseA throughout development. Sera from infected adolescents were reacted by immunoblot against recombinant (r)PmpC and rMOMP. ompA and groEL revealed different developmental transcriptome profiles among the biovariants. pmpC expression occurred at 2 h, peaked at 18 for L2 (at 24 for Ba and G), with the highest mRNA levels throughout development for L2. pmpC expression as a function of time paralleled ompA expression with higher mRNA levels compared with groEL later in development. Only sera from D-, E- and G-infected patients reacted to rPmpC; all infected patients reacted to rMOMP. pmpC expression during logarithmic growth suggests a role in membrane building and/or integrity, which is supported by the presence of a signal peptidase and C-terminal phenylalanine in PmpC. Because phylogenetic analyses of pmpC segregate serovars according to tissue tropism, we speculate that biovariant transcriptome differences may contribute to this tropism. The heterogeneous biovariant pmpC expression throughout development and differential PmpC immunoreactivity also suggest a role for pmpC in antigenic variation.}, }
@article {pmid15781714, year = {2005}, author = {Suchard, MA}, title = {Stochastic models for horizontal gene transfer: taking a random walk through tree space.}, journal = {Genetics}, volume = {170}, number = {1}, pages = {419-431}, pmid = {15781714}, issn = {0016-6731}, support = {GM08042/GM/NIGMS NIH HHS/United States ; T32 GM008042/GM/NIGMS NIH HHS/United States ; CA16042/CA/NCI NIH HHS/United States ; R01 GM068955/GM/NIGMS NIH HHS/United States ; GM068955/GM/NIGMS NIH HHS/United States ; P30 CA016042/CA/NCI NIH HHS/United States ; }, mesh = {Archaea/genetics ; Bacteria/genetics ; Data Interpretation, Statistical ; *Gene Transfer, Horizontal ; Markov Chains ; *Models, Genetic ; }, abstract = {Horizontal gene transfer (HGT) plays a critical role in evolution across all domains of life with important biological and medical implications. I propose a simple class of stochastic models to examine HGT using multiple orthologous gene alignments. The models function in a hierarchical phylogenetic framework. The top level of the hierarchy is based on a random walk process in "tree space" that allows for the development of a joint probabilistic distribution over multiple gene trees and an unknown, but estimable species tree. I consider two general forms of random walks. The first form is derived from the subtree prune and regraft (SPR) operator that mirrors the observed effects that HGT has on inferred trees. The second form is based on walks over complete graphs and offers numerically tractable solutions for an increasing number of taxa. The bottom level of the hierarchy utilizes standard phylogenetic models to reconstruct gene trees given multiple gene alignments conditional on the random walk process. I develop a well-mixing Markov chain Monte Carlo algorithm to fit the models in a Bayesian framework. I demonstrate the flexibility of these stochastic models to test competing ideas about HGT by examining the complexity hypothesis. Using 144 orthologous gene alignments from six prokaryotes previously collected and analyzed, Bayesian model selection finds support for (1) the SPR model over the alternative form, (2) the 16S rRNA reconstruction as the most likely species tree, and (3) increased HGT of operational genes compared to informational genes.}, }
@article {pmid15781495, year = {2005}, author = {Chiu, CH and Tang, P and Chu, C and Hu, S and Bao, Q and Yu, J and Chou, YY and Wang, HS and Lee, YS}, title = {The genome sequence of Salmonella enterica serovar Choleraesuis, a highly invasive and resistant zoonotic pathogen.}, journal = {Nucleic acids research}, volume = {33}, number = {5}, pages = {1690-1698}, pmid = {15781495}, issn = {1362-4962}, mesh = {Bacterial Proteins/chemistry ; Base Sequence ; Drug Resistance, Multiple, Bacterial/genetics ; *Genome, Bacterial ; Humans ; Plasmids/genetics ; Pseudogenes ; Salmonella/genetics ; Salmonella Infections/microbiology ; Salmonella enterica/*genetics/pathogenicity ; Sequence Homology, Amino Acid ; Zoonoses/microbiology ; von Willebrand Factor/chemistry ; }, abstract = {Salmonella enterica serovar Choleraesuis (S. Choleraesuis), a highly invasive serovar among non-typhoidal Salmonella, usually causes sepsis or extra-intestinal focal infections in humans. S. Choleraesuis infections have now become particularly difficult to treat because of the emergence of resistance to multiple antimicrobial agents. The 4.7 Mb genome sequence of a multidrug-resistant S. Choleraesuis strain SC-B67 was determined. Genome wide comparison of three sequenced Salmonella genomes revealed that more deletion events occurred in S. Choleraesuis SC-B67 and S.Typhi CT18 relative to S. Typhimurium LT2. S. Choleraesuis has 151 pseudogenes, which, among the three Salmonella genomes, include the highest percentage of pseudogenes arising from the genes involved in bacterial chemotaxis signal-transduction pathways. Mutations in these genes may increase smooth swimming of the bacteria, potentially allowing more effective interactions with and invasion of host cells to occur. A key regulatory gene of TetR/AcrR family, acrR, was inactivated through the introduction of an internal stop codon resulting in overexpression of AcrAB that appears to be associated with ciprofloxacin resistance. While lateral gene transfer providing basic functions to allow niche expansion in the host and environment is maintained during the evolution of different serovars of Salmonella, genes providing little overall selective benefit may be lost rapidly. Our findings suggest that the formation of pseudogenes may provide a simple evolutionary pathway that complements gene acquisition to enhance virulence and antimicrobial resistance in S. Choleraesuis.}, }
@article {pmid15777724, year = {2005}, author = {Magiorkinis, EN and Magiorkinis, GN and Paraskevis, DN and Hatzakis, AE}, title = {Re-analysis of a human hepatitis B virus (HBV) isolate from an East African wild born Pan troglodytes schweinfurthii: evidence for interspecies recombination between HBV infecting chimpanzee and human.}, journal = {Gene}, volume = {349}, number = {}, pages = {165-171}, doi = {10.1016/j.gene.2004.12.021}, pmid = {15777724}, issn = {0378-1119}, mesh = {Africa, Eastern ; Animals ; Animals, Wild/virology ; Base Sequence ; Bayes Theorem ; Cluster Analysis ; Evolution, Molecular ; Gene Transfer, Horizontal ; Hepadnaviridae/classification/genetics ; Hepatitis B virus/classification/*genetics/*isolation &amp; purification ; Humans ; Molecular Sequence Data ; Pan troglodytes/*virology ; Phylogeny ; *Recombination, Genetic ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {According to current estimates, hepatitis B virus (HBV) has infected 2 billion people worldwide and among them, 360 million suffer from chronic HBV infection. Except humans, HBV or HBV-like viruses have also been isolated from different species of apes and mammals. Although recombination has been described to occur extensively between different genotypes within the human HBV lineage, no recombination event has ever been reported between human and non-human primate HBV sequences. It was our objective to perform an exhaustive search for recombination between human and non-human primate HBV strains among all available full-length human and non-human primate HBV sequences, using bootscanning and phylogenetic analyses. Intriguingly, we found that an HBV sequence isolated from a wild born Pan troglodytes schweinfurthii in East Africa-FG-is a recombinant consisting of HBV infecting chimpanzee (ChHBV) and human genotype C. More specifically, in a fragment of approximately 500 nt (positions 551-1050 spanning half of the RT domain of pol, which overlaps with half of the coding region of the small surface protein), FG grouped with HBV genotype C, while in the rest of the genome it grouped with ChHBV sequences. Phylogenetic analyses showed that in the latter region FG was more closely related to the Pan troglodytes troglodytes subspecies, forming an outlier to this group. Moreover, we show evidence that the recombination event occurred after the initial dispersion of HBV genotype C in humans. Finally, our findings point out that although rare recombination between HBV viruses infecting different species occurs.}, }
@article {pmid15774890, year = {2005}, author = {Bishop, AL and Baker, S and Jenks, S and Fookes, M and Gaora, PO and Pickard, D and Anjum, M and Farrar, J and Hien, TT and Ivens, A and Dougan, G}, title = {Analysis of the hypervariable region of the Salmonella enterica genome associated with tRNA(leuX).}, journal = {Journal of bacteriology}, volume = {187}, number = {7}, pages = {2469-2482}, pmid = {15774890}, issn = {0021-9193}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacteriophages ; Chromosome Mapping ; Complementarity Determining Regions/*genetics ; DNA, Circular/genetics ; Escherichia coli/genetics ; Evolution, Molecular ; Genetic Variation ; Genome, Bacterial ; Genomic Islands ; Molecular Sequence Data ; Plasmids/genetics ; RNA, Bacterial/*genetics ; RNA, Transfer, Leu/*genetics ; Salmonella enterica/*genetics ; Species Specificity ; }, abstract = {The divergence of Salmonella enterica and Escherichia coli is estimated to have occurred approximately 140 million years ago. Despite this evolutionary distance, the genomes of these two species still share extensive synteny and homology. However, there are significant differences between the two species in terms of genes putatively acquired via various horizontal transfer events. Here we report on the composition and distribution across the Salmonella genus of a chromosomal region designated SPI-10 in Salmonella enterica serovar Typhi and located adjacent to tRNA(leuX). We find that across the Salmonella genus the tRNA(leuX) region is a hypervariable hot spot for horizontal gene transfer; different isolates from the same S. enterica serovar can exhibit significant variation in this region. Many P4 phage, plasmid, and transposable element-associated genes are found adjacent to tRNA(leuX) in both Salmonella and E. coli, suggesting that these mobile genetic elements have played a major role in driving the variability of this region.}, }
@article {pmid15774886, year = {2005}, author = {Gill, SR and Fouts, DE and Archer, GL and Mongodin, EF and Deboy, RT and Ravel, J and Paulsen, IT and Kolonay, JF and Brinkac, L and Beanan, M and Dodson, RJ and Daugherty, SC and Madupu, R and Angiuoli, SV and Durkin, AS and Haft, DH and Vamathevan, J and Khouri, H and Utterback, T and Lee, C and Dimitrov, G and Jiang, L and Qin, H and Weidman, J and Tran, K and Kang, K and Hance, IR and Nelson, KE and Fraser, CM}, title = {Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain.}, journal = {Journal of bacteriology}, volume = {187}, number = {7}, pages = {2426-2438}, pmid = {15774886}, issn = {0021-9193}, support = {R01-AI43567/AI/NIAID NIH HHS/United States ; U01-AI45667/AI/NIAID NIH HHS/United States ; }, mesh = {Biofilms ; Chromosome Mapping ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomic Islands ; Methicillin Resistance/*genetics ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Staphylococcus aureus/*genetics/metabolism/pathogenicity ; Staphylococcus epidermidis/*genetics/metabolism/pathogenicity ; Virulence/genetics ; }, abstract = {Staphylococcus aureus is an opportunistic pathogen and the major causative agent of numerous hospital- and community-acquired infections. Staphylococcus epidermidis has emerged as a causative agent of infections often associated with implanted medical devices. We have sequenced the approximately 2.8-Mb genome of S. aureus COL, an early methicillin-resistant isolate, and the approximately 2.6-Mb genome of S. epidermidis RP62a, a methicillin-resistant biofilm isolate. Comparative analysis of these and other staphylococcal genomes was used to explore the evolution of virulence and resistance between these two species. The S. aureus and S. epidermidis genomes are syntenic throughout their lengths and share a core set of 1,681 open reading frames. Genome islands in nonsyntenic regions are the primary source of variations in pathogenicity and resistance. Gene transfer between staphylococci and low-GC-content gram-positive bacteria appears to have shaped their virulence and resistance profiles. Integrated plasmids in S. epidermidis carry genes encoding resistance to cadmium and species-specific LPXTG surface proteins. A novel genome island encodes multiple phenol-soluble modulins, a potential S. epidermidis virulence factor. S. epidermidis contains the cap operon, encoding the polyglutamate capsule, a major virulence factor in Bacillus anthracis. Additional phenotypic differences are likely the result of single nucleotide polymorphisms, which are most numerous in cell envelope proteins. Overall differences in pathogenicity can be attributed to genome islands in S. aureus which encode enterotoxins, exotoxins, leukocidins, and leukotoxins not found in S. epidermidis.}, }
@article {pmid15774024, year = {2005}, author = {Salzberg, SL and Dunning Hotopp, JC and Delcher, AL and Pop, M and Smith, DR and Eisen, MB and Nelson, WC}, title = {Serendipitous discovery of Wolbachia genomes in multiple Drosophila species.}, journal = {Genome biology}, volume = {6}, number = {3}, pages = {R23}, pmid = {15774024}, issn = {1474-760X}, support = {R01 LM006845/LM/NLM NIH HHS/United States ; R01 LM007938/LM/NLM NIH HHS/United States ; R01-LM007938/LM/NLM NIH HHS/United States ; R01-LM06845/LM/NLM NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; Drosophila/*microbiology ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomics ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Wolbachia/classification/*genetics ; }, abstract = {BACKGROUND: The Trace Archive is a repository for the raw, unanalyzed data generated by large-scale genome sequencing projects. The existence of this data offers scientists the possibility of discovering additional genomic sequences beyond those originally sequenced. In particular, if the source DNA for a sequencing project came from a species that was colonized by another organism, then the project may yield substantial amounts of genomic DNA, including near-complete genomes, from the symbiotic or parasitic organism.<br><br>RESULTS: By searching the publicly available repository of DNA sequencing trace data, we discovered three new species of the bacterial endosymbiont Wolbachia pipientis in three different species of fruit fly: Drosophila ananassae, D. simulans, and D. mojavensis. We extracted all sequences with partial matches to a previously sequenced Wolbachia strain and assembled those sequences using customized software. For one of the three new species, the data recovered were sufficient to produce an assembly that covers more than 95% of the genome; for a second species the data produce the equivalent of a 'light shotgun' sampling of the genome, covering an estimated 75-80% of the genome; and for the third species the data cover approximately 6-7% of the genome.<br><br>CONCLUSIONS: The results of this study reveal an unexpected benefit of depositing raw data in a central genome sequence repository: new species can be discovered within this data. The differences between these three new Wolbachia genomes and the previously sequenced strain revealed numerous rearrangements and insertions within each lineage and hundreds of novel genes. The three new genomes, with annotation, have been deposited in GenBank.}, }
@article {pmid15772379, year = {2005}, author = {Belda, E and Moya, A and Silva, FJ}, title = {Genome rearrangement distances and gene order phylogeny in gamma-Proteobacteria.}, journal = {Molecular biology and evolution}, volume = {22}, number = {6}, pages = {1456-1467}, doi = {10.1093/molbev/msi134}, pmid = {15772379}, issn = {0737-4038}, mesh = {Biological Evolution ; Escherichia coli/genetics ; Evolution, Molecular ; Gammaproteobacteria/*genetics ; Gene Order ; Gene Transfer, Horizontal ; Genome ; *Genome, Bacterial ; Models, Genetic ; Models, Theoretical ; Phylogeny ; Time Factors ; Yersinia pestis/genetics ; }, abstract = {Genome rearrangements have been studied in 30 gamma-proteobacterial complete genomes by comparing the order of a reduced set of genes on the chromosome. This set included those genes fulfilling several characteristics, the main ones being that an ortholog was present in every genome and that none of them had been acquired by horizontal gene transfer. Genome rearrangement distances were estimated based on either the number of breakpoints or the minimal number of inversions separating two genomes. Breakpoint and inversion distances were highly correlated, indicating that inversions were the main type of rearrangement event in gamma-Proteobacteria. In general, the progressive increase in sequence-based distances between genome pairs was associated with the increase in their rearrangement-based distances but with several groups of distances not following this pattern. Compared with free-living enteric bacteria, the lineages of Pasteurellaceae were evolving, on average, to relatively higher rates of between 2.02 and 1.64, while the endosymbiotic bacterial lineages of Buchnera aphidicola and Wigglesworthia glossinidia were evolving at moderately higher rates of 1.38 and 1.35, respectively. Because we know that the rearrangement rate in the Bu. aphidicola lineage was close to zero during the last 100-150 Myr of evolution, we deduced that a much higher rate took place in the first period of lineage evolution after the divergence of the Escherichia coli lineage. On the other hand, the lineage of the endosymbiont Blochmannia floridanus did present an almost identical rate to free-living enteric bacteria, indicating that the increase in the genome rearrangement rate is not a general change associated with bacterial endosymbiosis. Phylogenetic reconstruction based on rearrangement distances showed a different topology from the one inferred by sequence information. This topology broke the proposed monophyly of the three endosymbiotic lineages and placed Bl. floridanus as a closer relative to E. coli than Yersinia pestis. These results indicate that the phylogeny of these insect endosymbionts is still an open question that will require the development of specific phylogenetic methods to confirm whether the sisterhood of the three endosymbiotic lineages is real or a consequence of a long-branch attraction phenomenon.}, }
@article {pmid15763506, year = {2005}, author = {Kordyum, VA and Shpylova, SP and Andrienko, VI and Sukhorada, OM and Ruban, TA and Deryabina, OG}, title = {Transfer of genetic information in an organism.}, journal = {Cell biology international}, volume = {29}, number = {1}, pages = {95-97}, doi = {10.1016/j.cellbi.2004.11.005}, pmid = {15763506}, issn = {1065-6995}, mesh = {Animals ; CHO Cells ; *Cell Communication ; Cricetinae ; *Gene Transfer, Horizontal ; Liver/embryology ; Mice ; Mutation ; Stem Cells/*physiology ; }, abstract = {New knowledge in biology led us to a better understanding of organization and functioning of living organisms. Today, re-evaluation of our concept of human biology is taking place. Theoretical analysis shows that taking into account the complexity of the organism and frequency of spontaneous mutations, it is impossible to explain the real time of organismal life. Therefore, besides extant systems, other repair systems must also exist. There are three "levels" at which a cell population withstands mutational pressure. First - intracellular (repair), second - intercellular (all forms of informational flows), and third - cellular replacement. Stem cells undertake regenerative functions following damage at the level of the tissue. They are also influenced by mutations, and for stem cells, it is most important that they preserve and support their full activity.}, }
@article {pmid15761667, year = {2005}, author = {Andersson, JO}, title = {Lateral gene transfer in eukaryotes.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {62}, number = {11}, pages = {1182-1197}, doi = {10.1007/s00018-005-4539-z}, pmid = {15761667}, issn = {1420-682X}, mesh = {Animals ; Eukaryotic Cells/*physiology ; Fungi/genetics ; *Gene Transfer, Horizontal ; Models, Biological ; Phylogeny ; Plants/genetics ; }, abstract = {Lateral gene transfer -- the transfer of genetic material between species -- has been acknowledged as a major mechanism in prokaryotic genome evolution for some time. Recently accumulating data indicate that the process also occurs in the evolution of eukaryotic genomes. However, there are large rate variations between groups of eukaryotes; animals and fungi seem to be largely unaffected, with a few exceptions, while lateral gene transfer frequently occurs in protists with phagotrophic lifestyles, possibly with rates comparable to prokaryotic organisms. Gene transfers often facilitate the acquisition of functions encoded in prokaryotic genomes by eukaryotic organisms, which may enable them to colonize new environments. Transfers between eukaryotes also occur, mainly into larger phagotrophic eukaryotes that ingest eukaryotic cells, but also between plant lineages. These findings have implications for eukaryotic genomic research in general, and studies of the origin and phylogeny of eukaryotes in particular.}, }
@article {pmid15752209, year = {2005}, author = {Doublet, B and Boyd, D and Mulvey, MR and Cloeckaert, A}, title = {The Salmonella genomic island 1 is an integrative mobilizable element.}, journal = {Molecular microbiology}, volume = {55}, number = {6}, pages = {1911-1924}, doi = {10.1111/j.1365-2958.2005.04520.x}, pmid = {15752209}, issn = {0950-382X}, mesh = {Amino Acid Sequence ; Attachment Sites, Microbiological/genetics ; Chromosomes, Bacterial/genetics ; Conjugation, Genetic ; DNA, Circular/analysis/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; *Genomic Islands ; Integrases/metabolism ; Molecular Sequence Data ; Plasmids/physiology ; Salmonella enterica/drug effects/*genetics ; Sequence Homology, Amino Acid ; }, abstract = {Salmonella genomic island 1 (SGI1) is a genomic island containing an antibiotic resistance gene cluster identified in several Salmonella enterica serovars. The SGI1 antibiotic resistance gene cluster, which is a complex class 1 integron, confers the common multidrug resistance phenotype of epidemic S. enterica Typhimurium DT104. The SGI1 occurrence in S. enterica serovars Typhimurium, Agona, Paratyphi B, Albany, Meleagridis and Newport indicates the horizontal transfer potential of SGI1. Here, we report that SGI1 could be conjugally transferred from S. enterica donor strains to non-SGI1 S. enterica and Escherichia coli recipient strains where it integrated into the recipient chromosome in a site-specific manner. First, an extrachromosomal circular form of SGI1 was identified by PCR which forms through a specific recombination of the left and right ends of the integrated SGI1. Chromosomal excision of SGI1 was found to require SGI1-encoded integrase which presents similarities to the lambdoid integrase family. Second, the conjugal transfer of SGI1 required the presence of a helper plasmid. The conjugative IncC plasmid R55 could thus mobilize in trans SGI1 which was transferred from the donor to the recipient strains. By this way, the conjugal transfer of SGI1 occurred at a frequency of 10(-5)-10(-6) transconjugants per donor. No transconjugants could be obtained for the SGI1 donor lacking the int integrase gene. Third, chromosomal integration of SGI1 occurred via a site-specific recombination between a 18 bp sequence found in the circular form of SGI1 and a similar 18 bp sequence at the 3' end of thdF gene in the S. enterica and E. coli chromosome. SGI1 appeared to be transmissible only in the presence of additional conjugative functions provided in trans. SGI1 can thus be classified within the group of integrative mobilizable elements (IMEs).}, }
@article {pmid15750634, year = {2005}, author = {DeNap, JC and Hergenrother, PJ}, title = {Bacterial death comes full circle: targeting plasmid replication in drug-resistant bacteria.}, journal = {Organic &amp; biomolecular chemistry}, volume = {3}, number = {6}, pages = {959-966}, doi = {10.1039/b500182j}, pmid = {15750634}, issn = {1477-0520}, support = {R01 GM 68385/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; Base Sequence ; *Cell Death ; *DNA Replication ; Drug Resistance, Bacterial/*genetics ; Molecular Sequence Data ; Plasmids/chemistry/*genetics ; }, abstract = {It is now common for bacterial infections to resist the preferred antibiotic treatment. In particular, hospital-acquired infections that are refractory to multiple antibiotics and ultimately result in death of the patient are prevalent. Many of the bacteria causing these infections have become resistant to antibiotics through the process of lateral gene transfer, with the newly acquired genes encoding a variety of resistance-mediating proteins. These foreign genes often enter the bacteria on plasmids, which are small, circular, extrachromosomal pieces of DNA. This plasmid-encoded resistance has been observed for virtually all classes of antibiotics and in a wide variety of Gram-positive and Gram-negative organisms; many antibiotics are no longer effective due to such plasmid-encoded resistance. The systematic removal of these resistance-mediating plasmids from the bacteria would re-sensitize bacteria to standard antibiotics. As such, plasmids offer novel targets that have heretofore been unexploited clinically. This Perspective details the role of plasmids in multi-drug resistant bacteria, the mechanisms used by plasmids to control their replication, and the potential for small molecules to disrupt plasmid replication and re-sensitize bacteria to antibiotics. An emphasis is placed on plasmid replication that is mediated by small counter-transcript RNAs, and the "plasmid addiction" systems that employ toxins and antitoxins.}, }
@article {pmid15750125, year = {2005}, author = {Albertí, S and García-Rey, C and García-Laorden, MI and Dal-Ré, R and García-de-Lomas, J and , }, title = {Survey of emm-like gene sequences from pharyngeal isolates of group C and group G streptococci collected in Spain.}, journal = {Journal of clinical microbiology}, volume = {43}, number = {3}, pages = {1433-1436}, pmid = {15750125}, issn = {0095-1137}, mesh = {Antigens, Bacterial/*genetics ; Bacterial Outer Membrane Proteins/*genetics ; Base Sequence ; Carrier Proteins/*genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genotype ; Humans ; Molecular Sequence Data ; Pharynx/*microbiology ; Streptococcus/classification/*genetics ; }, abstract = {We conducted a nationwide surveillance of the variable 5' emm-like (M-like protein gene) sequences from 214 pharyngeal group C and group G streptococci. Almost 75% of the isolates exhibited emm or emm-like sequences previously described. We identified six new 5' emm-like regions, and almost 23% of the isolates were nontypeable. Five emm-like sequences accounted for more than 50% of the isolates in group C and group G, suggesting horizontal gene transfer between strains of different species.}, }
@article {pmid15746334, year = {2005}, author = {Trujillo, ME and Willems, A and Abril, A and Planchuelo, AM and Rivas, R and Ludeña, D and Mateos, PF and Martínez-Molina, E and Velázquez, E}, title = {Nodulation of Lupinus albus by strains of Ochrobactrum lupini sp. nov.}, journal = {Applied and environmental microbiology}, volume = {71}, number = {3}, pages = {1318-1327}, pmid = {15746334}, issn = {0099-2240}, mesh = {Base Sequence ; DNA, Bacterial/genetics ; Fatty Acids/analysis ; Genes, Bacterial ; Lupinus/metabolism/*microbiology ; Microscopy, Electron ; Nitrogen Fixation/genetics ; Ochrobactrum/classification/genetics/isolation &amp; purification/*physiology ; Oxidoreductases/genetics ; Phenotype ; Phylogeny ; Plasmids/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; Terminology as Topic ; }, abstract = {The nodulation of legumes has for more than a century been considered an exclusive capacity of a group of microorganisms commonly known as rhizobia and belonging to the alpha-Proteobacteria. However, in the last 3 years four nonrhizobial species, belonging to alpha and beta subclasses of the Proteobacteria, have been described as legume-nodulating bacteria. In the present study, two fast-growing strains, LUP21 and LUP23, were isolated from nodules of Lupinus honoratus. The phylogenetic analysis based on the 16S and 23S rRNA gene sequences showed that the isolates belong to the genus Ochrobactrum. The strains were able to reinfect Lupinus plants. A plasmid profile analysis showed the presence of three plasmids. The nodD and nifH genes were located on these plasmids, and their sequences were obtained. These sequences showed a close resemblance to the nodD and nifH genes of rhizobial species, suggesting that the nodD and nifH genes carried by strain LUP21T were acquired by horizontal gene transfer. A polyphasic study including phenotypic, chemotaxonomic, and molecular features of the strains isolated in this study showed that they belong to a new species of the genus Ochrobactrum for which we propose the name Ochrobactrum lupini sp. nov. Strain LUP21T (LMG 20667T) is the type strain.}, }
@article {pmid15746011, year = {2005}, author = {Frank, AC and Alsmark, CM and Thollesson, M and Andersson, SG}, title = {Functional divergence and horizontal transfer of type IV secretion systems.}, journal = {Molecular biology and evolution}, volume = {22}, number = {5}, pages = {1325-1336}, doi = {10.1093/molbev/msi124}, pmid = {15746011}, issn = {0737-4038}, mesh = {Bacteria/classification/*genetics ; Bacterial Infections/*microbiology ; Bacterial Proteins/genetics/*metabolism ; *Conjugation, Genetic ; DNA, Bacterial/genetics ; Eukaryotic Cells/*microbiology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Phylogeny ; Virulence ; }, abstract = {The type IV secretion system (TFSSs) is a multifunctional family of translocation pathways that mediate the transfer of DNA among bacteria and deliver DNA and proteins to eukaryotic cells during bacterial infections. Horizontal transmission has dominated the evolution of the TFSS, as demonstrated here by a lack of congruence between the tree topology inferred from components of the TFSS and the presumed bacterial species divergence pattern. A parsimony analysis suggests that conjugation represents the ancestral state and that the divergence from conjugation to secretion of effector molecules has occurred independently at multiple sites in the tree. The result shows that the nodes at which functional shifts have occurred coincide with those of horizontal gene transfers among distantly related bacteria. We suggest that it is the transfer between species that paved the way for the divergence of the TFSSs and discuss the general role of horizontal gene transfers for the evolution of novel gene functions.}, }
@article {pmid15743970, year = {2005}, author = {Zverlov, V and Klein, M and Lücker, S and Friedrich, MW and Kellermann, J and Stahl, DA and Loy, A and Wagner, M}, title = {Lateral gene transfer of dissimilatory (bi)sulfite reductase revisited.}, journal = {Journal of bacteriology}, volume = {187}, number = {6}, pages = {2203-2208}, pmid = {15743970}, issn = {0021-9193}, mesh = {Bacteria, Anaerobic/classification/*enzymology/*genetics ; Gene Transfer, Horizontal/*physiology ; Hydrogensulfite Reductase ; Operon/genetics ; Oxidoreductases Acting on Sulfur Group Donors/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In contrast to previous findings, we demonstrate that the dissimilatory (bi)sulfite reductase genes (dsrAB) of Desulfobacula toluolica were vertically inherited. Furthermore, Desulfobacterium anilini and strain mXyS1 were identified, by dsrAB sequencing of 17 reference strains, as members of the donor lineage for those gram-positive Desulfotomaculum species which laterally acquired dsrAB.}, }
@article {pmid15743967, year = {2005}, author = {Gao, R and Lynn, DG}, title = {Environmental pH sensing: resolving the VirA/VirG two-component system inputs for Agrobacterium pathogenesis.}, journal = {Journal of bacteriology}, volume = {187}, number = {6}, pages = {2182-2189}, pmid = {15743967}, issn = {0021-9193}, support = {R01 GM047369/GM/NIGMS NIH HHS/United States ; GM47369/GM/NIGMS NIH HHS/United States ; }, mesh = {Agrobacterium tumefaciens/genetics/*metabolism/*pathogenicity ; Bacterial Proteins/chemistry/genetics/metabolism ; Carbohydrate Metabolism ; DNA-Binding Proteins/genetics/*metabolism ; Environment ; Hydrogen-Ion Concentration ; Membrane Transport Proteins/chemistry/genetics/metabolism ; Mutagenesis ; Periplasmic Binding Proteins/chemistry/genetics/metabolism ; Protein Structure, Tertiary ; Signal Transduction/*physiology ; Transcription Factors/genetics/*metabolism ; Virulence ; Virulence Factors/genetics/*metabolism ; }, abstract = {Agrobacterium tumefaciens stands as one of biotechnology's greatest successes, with all plant genetic engineering building on the strategies of this pathogen. By integrating responses to external pHs, phenols, and monosaccharides, this organism mobilizes oncogenic elements to efficiently transform most dicotyledonous plants. We now show that the complex signaling network used to regulate lateral gene transfer can be resolved as individual signaling modules. While pH and sugar perception are coupled through a common pathway, requiring both low pH and sugar for maximal virulence gene expression, various VirA and ChvE alleles can decouple pH and monosaccharide perception. This VirA and ChvE system may represent a common mechanism that underpins external pH perception in prokaryotes, and the use of these simple genetic elements may now be extended to research on specific responses to changes in environmental pH.}, }
@article {pmid15741510, year = {2005}, author = {Deeds, EJ and Hennessey, H and Shakhnovich, EI}, title = {Prokaryotic phylogenies inferred from protein structural domains.}, journal = {Genome research}, volume = {15}, number = {3}, pages = {393-402}, pmid = {15741510}, issn = {1088-9051}, mesh = {Archaeal Proteins/chemistry/genetics ; Bacterial Proteins/chemistry/genetics ; Evolution, Molecular ; Fungal Proteins/chemistry/genetics ; Gene Transfer, Horizontal ; Genomics ; Models, Genetic ; Phylogeny ; Prokaryotic Cells ; Protein Structure, Tertiary ; Proteins/*chemistry/*genetics ; Proteome ; }, abstract = {The determination of the phylogenetic relationships among microorganisms has long relied primarily on gene sequence information. Given that prokaryotic organisms often lack morphological characteristics amenable to phylogenetic analysis, prokaryotic phylogenies, in particular, are often based on sequence data. In this work, we explore a new source of phylogenetic information, the distribution of protein structural domains within fully sequenced prokaryotic genomes. The evolution of the structural domains we use has been studied extensively, allowing us to base our phylogenetic methods on testable theoretical models of structural evolution. We find that the methods that produce reasonable phylogenetic relationships are indeed the methods that are most consistent with theoretical evolutionary models. This work represents, to our knowledge, the first such theoretically motivated phylogeny, as well as the first application of structural information to phylogeny on this scale. Our results have strong implications for the phylogenetic relationships among prokaryotic organisms and for the understanding of protein evolution as a whole.}, }
@article {pmid15740652, year = {2005}, author = {Zheng, LD and Xiong, ZF and Zhu, JW and Wang, ZH}, title = {Effects of Smac gene over-expression on the radiotherapeutic sensitivities of cervical cancer cell line HeLa.}, journal = {Chinese medical journal}, volume = {118}, number = {3}, pages = {226-230}, pmid = {15740652}, issn = {0366-6999}, mesh = {Apoptosis/radiation effects ; Apoptosis Regulatory Proteins ; Carrier Proteins/genetics/*physiology ; Caspase 3 ; Caspases/metabolism ; Female ; Gene Transfer, Horizontal ; HeLa Cells ; Humans ; Intracellular Signaling Peptides and Proteins ; Mitochondrial Proteins/genetics/*physiology ; Radiation Tolerance ; Uterine Cervical Neoplasms/*drug therapy/enzymology/pathology ; }, abstract = {BACKGROUND: The second mitochondria-derived activator of caspases (Smac) is a novel proapoptotic gene, which plays an important role in the apoptosis-inducing effects of irradiation on tumor cells. The purpose of this study was to investigate the effects of extrinsic Smac gene transfer and its over-expression in radiotherapeutic sensitivities of cervical cancer cells.<br><br>METHODS: After the Smac gene was transferred into the cervical cancer cell line HeLa, subcloned cells were obtained by persistent G418 selection. Cellular Smac gene expression was detected by RT-PCR and Western blot, while in vitro cell viabilities were detected by trypan blue staining assay. After treatment with X-ray irradiation, cellular radiotherapeutic sensitivities were investigated by tetrazolium bromide colorimetry. Cellular apoptosis and its rate were determined by electronic microscopy, annexin V-FITC and propidium iodide staining flow cytometry. The expression and activities of cellular caspase-3 were assayed by Western blot and colorimetry.<br><br>RESULTS: Smac mRNA and protein levels in HeLa/Smac cells and the selected subclone cell line of cervical cancer were significantly higher than those of HeLa (P < 0.01). There was no significant difference in cellular viabilities between them (P > 0.05). However, after irradiation with 8 Gy X-ray, growth activities of HeLa/Smac were reduced by 22.42% (P < 0.01). When compared with those of HeLa, partial HeLa/Smac cells presented characteristic morphological changes of apoptosis under electronic microscope, with higher apoptosis rates (16.4% vs. 6.2%, P < 0.01); the caspase-3 expression levels in HeLa/Smac cells were improved significantly (P < 0.01), while its activities were increased by 3.42 times (P < 0.01).<br><br>CONCLUSIONS: Stable transfer of the extrinsic Smac gene and its over-expression in cervical cancer cell line could significantly enhance the expression and activities of cellular caspase-3 and ameliorate apoptosis-inducing effects of irradiation on cancer cells, which was a novel strategy to improve radiotherapeutic effects on cervical cancer.}, }
@article {pmid15737590, year = {2005}, author = {Hughes, AL and Friedman, R}, title = {Poxvirus genome evolution by gene gain and loss.}, journal = {Molecular phylogenetics and evolution}, volume = {35}, number = {1}, pages = {186-195}, doi = {10.1016/j.ympev.2004.12.008}, pmid = {15737590}, issn = {1055-7903}, support = {GM43940/GM/NIGMS NIH HHS/United States ; }, mesh = {*Evolution, Molecular ; Gene Deletion ; Gene Duplication ; *Genome, Viral ; Phylogeny ; Poxviridae/classification/*genetics ; }, abstract = {The poxviruses (Poxviridae) are a family of viruses with double-stranded DNA genomes and substantial numbers (often >200) of genes per genome. We studied the patterns of gene gain and loss over the evolutionary history of 17 poxvirus complete genomes. A phylogeny based on gene family presence/absence showed good agreement with families based on concatenated amino acid sequences of conserved single-copy genes. Gene duplications in poxviruses were often lineage specific, and the most extensively duplicated viral gene families were found in only a few of the genomes analyzed. A total of 34 gene families were found to include a member in at least one of the poxvirus genomes analyzed and at least one animal genome; in 16 (47%) of these families, there was evidence of recent horizontal gene transfer (HGT) from host to virus. Gene families with evidence of HGT included several involved in host immune defense mechanisms (the MHC class I, interleukin-10, interleukin-24, interleukin-18, the interferon gamma receptor, and tumor necrosis factor receptor II) and others (glutaredoxin and glutathione peroxidase) involved in resistance of cells to oxidative stress. Thus "capture" of host genes by HGT has been a recurrent feature of poxvirus evolution and has played an important role in adapting the virus to survive host antiviral defense mechanisms.}, }
@article {pmid15737398, year = {2005}, author = {Parker, C and Becker, E and Zhang, X and Jandle, S and Meyer, R}, title = {Elements in the co-evolution of relaxases and their origins of transfer.}, journal = {Plasmid}, volume = {53}, number = {2}, pages = {113-118}, doi = {10.1016/j.plasmid.2004.12.007}, pmid = {15737398}, issn = {0147-619X}, support = {GM37462/GM/NIGMS NIH HHS/United States ; }, mesh = {Conjugation, Genetic ; DNA Nucleotidyltransferases/genetics/*physiology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Plasmids ; Replication Origin ; }, abstract = {The central elements in the conjugative mobilization of most plasmids are the relaxase and its cognate origin of transfer (oriT). The relaxase of the plasmid R1162, together with its oriT, belong to a large and widely distributed family of related relaxase/oriT pairs. Several of the properties of these elements are considered for R1162 and for other members of this family with a view to understanding how systems for mobilization might have evolved.}, }
@article {pmid15734556, year = {2005}, author = {Paul, D and Pandey, G and Pandey, J and Jain, RK}, title = {Accessing microbial diversity for bioremediation and environmental restoration.}, journal = {Trends in biotechnology}, volume = {23}, number = {3}, pages = {135-142}, doi = {10.1016/j.tibtech.2005.01.001}, pmid = {15734556}, issn = {0167-7799}, mesh = {Bacteria/*genetics/growth &amp; development ; Biodegradation, Environmental ; Environmental Health/trends ; *Environmental Microbiology ; *Environmental Pollutants/metabolism ; Gene Transfer, Horizontal ; Genetic Engineering/trends ; }, abstract = {Biological methods for decontamination promise an improved substitute for ineffective and costly physico-chemical remediation methods, although so far only a fraction of the total microbial diversity (i.e. the culturable fraction with metabolic potential) has been harnessed for this purpose. Exploring and exploiting the "overlooked" genetic resource might ameliorate concerns associated with the degradation of recalcitrant and xenobiotic pollutants that are not degraded or only poorly degraded by known culturable bacteria. Recent advances in the molecular genetics of biodegradation and in knowledge-based methods of rational protein modification provide insight into the development of "designer biocatalysts" for environmental restoration. The application of such genetically engineered microorganisms (GEMs) in the environment has been limited, however, owing to the risks associated with uncontrolled growth and proliferation of the introduced biocatalyst and horizontal gene transfer. Programming rapid death of the biocatalyst soon after the depletion of the pollutant could minimize the risks in developing these technologies for successful bioremediation.}, }
@article {pmid15731520, year = {2005}, author = {Le Rouzic, A and Capy, P}, title = {The first steps of transposable elements invasion: parasitic strategy vs. genetic drift.}, journal = {Genetics}, volume = {169}, number = {2}, pages = {1033-1043}, pmid = {15731520}, issn = {0016-6731}, mesh = {Animals ; Animals, Outbred Strains ; Computer Simulation ; DNA Transposable Elements/*genetics ; Diploidy ; Evolution, Molecular ; Female ; Gene Dosage ; *Gene Transfer, Horizontal ; *Genetic Drift ; Genetics, Population ; Genome ; Kinetics ; Male ; *Models, Genetic ; Selection, Genetic ; Sequence Analysis, DNA ; }, abstract = {Transposable elements are often considered as selfish DNA sequences able to invade the genome of their host species. Their evolutive dynamics are complex, due to the interaction between their intrinsic amplification capacity, selection at the host level, transposition regulation, and genetic drift. Here, we propose modeling the first steps of TE invasion, i.e., just after a horizontal transfer, when a single copy is present in the genome of one individual. If the element has a constant transposition rate, it will disappear in most cases: the elements with low-transposition rate are frequently lost through genetic drift, while those with high-transposition rate may amplify, leading to the sterility of their host. Elements whose transposition rate is regulated are able to successfully invade the populations, thanks to an initial transposition burst followed by a strong limitation of their activity. Self-regulation or hybrid dysgenesis may thus represent some genome-invasion parasitic strategies.}, }
@article {pmid15729342, year = {2005}, author = {Loftus, B and Anderson, I and Davies, R and Alsmark, UC and Samuelson, J and Amedeo, P and Roncaglia, P and Berriman, M and Hirt, RP and Mann, BJ and Nozaki, T and Suh, B and Pop, M and Duchene, M and Ackers, J and Tannich, E and Leippe, M and Hofer, M and Bruchhaus, I and Willhoeft, U and Bhattacharya, A and Chillingworth, T and Churcher, C and Hance, Z and Harris, B and Harris, D and Jagels, K and Moule, S and Mungall, K and Ormond, D and Squares, R and Whitehead, S and Quail, MA and Rabbinowitsch, E and Norbertczak, H and Price, C and Wang, Z and Guillén, N and Gilchrist, C and Stroup, SE and Bhattacharya, S and Lohia, A and Foster, PG and Sicheritz-Ponten, T and Weber, C and Singh, U and Mukherjee, C and El-Sayed, NM and Petri, WA and Clark, CG and Embley, TM and Barrell, B and Fraser, CM and Hall, N}, title = {The genome of the protist parasite Entamoeba histolytica.}, journal = {Nature}, volume = {433}, number = {7028}, pages = {865-868}, doi = {10.1038/nature03291}, pmid = {15729342}, issn = {1476-4687}, mesh = {Animals ; Entamoeba histolytica/*genetics/metabolism/pathogenicity ; Evolution, Molecular ; Fermentation ; Gene Transfer, Horizontal/genetics ; *Genome, Protozoan ; Glycolysis ; Oxidative Stress/genetics ; Parasites/*genetics/metabolism/pathogenicity ; Phylogeny ; Signal Transduction ; Virulence/genetics ; }, abstract = {Entamoeba histolytica is an intestinal parasite and the causative agent of amoebiasis, which is a significant source of morbidity and mortality in developing countries. Here we present the genome of E. histolytica, which reveals a variety of metabolic adaptations shared with two other amitochondrial protist pathogens: Giardia lamblia and Trichomonas vaginalis. These adaptations include reduction or elimination of most mitochondrial metabolic pathways and the use of oxidative stress enzymes generally associated with anaerobic prokaryotes. Phylogenomic analysis identifies evidence for lateral gene transfer of bacterial genes into the E. histolytica genome, the effects of which centre on expanding aspects of E. histolytica's metabolic repertoire. The presence of these genes and the potential for novel metabolic pathways in E. histolytica may allow for the development of new chemotherapeutic agents. The genome encodes a large number of novel receptor kinases and contains expansions of a variety of gene families, including those associated with virulence. Additional genome features include an abundance of tandemly repeated transfer-RNA-containing arrays, which may have a structural function in the genome. Analysis of the genome provides new insights into the workings and genome evolution of a major human pathogen.}, }
@article {pmid15727561, year = {2005}, author = {Kikuchi, T and Shibuya, H and Jones, JT}, title = {Molecular and biochemical characterization of an endo-beta-1,3-glucanase from the pinewood nematode Bursaphelenchus xylophilus acquired by horizontal gene transfer from bacteria.}, journal = {The Biochemical journal}, volume = {389}, number = {Pt 1}, pages = {117-125}, pmid = {15727561}, issn = {1470-8728}, mesh = {Amino Acid Sequence ; Animals ; Blotting, Southern ; Cloning, Molecular ; Conserved Sequence ; Endo-1,3(4)-beta-Glucanase/chemistry/*genetics/*metabolism ; Enzyme Stability ; Expressed Sequence Tags ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/*genetics ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Nematoda/*enzymology/*genetics ; Phylogeny ; Pinus/*parasitology ; Protein Transport ; Recombinant Proteins/chemistry/genetics/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Substrate Specificity ; Temperature ; }, abstract = {We report the cloning and functional characterization of an endo-beta-1,3-glucanase from the pinewood nematode Bursaphelenchus xylophilus acquired by horizontal gene transfer from bacteria. This is the first gene of this type from any nematode species. We show that a similar cDNA is also present in another closely related species B. mucronatus, but that similar sequences are not present in any other nematode studied to date. The B. xylophilus gene is expressed solely in the oesophageal gland cells of the nematode and the protein is present in the nematode's secretions. The deduced amino acid sequence of the gene is very similar to glycosyl hydrolase family 16 proteins. The recombinant protein, expressed in Escherichia coli, preferentially hydrolysed the beta-1,3-glucan laminarin, and had very low levels of activity on beta-1,3-1,4-glucan, lichenan and barley beta-glucan. Laminarin was degraded in an endoglucanase mode by the enzyme. The optimal temperature and pH for activity of the recombinant enzyme were 65 degrees C and pH 4.9. The protein is probably important in allowing the nematodes to feed on fungi. Sequence comparisons suggest that the gene encoding the endo-beta-1,3-glucanase was acquired by horizontal gene transfer from bacteria. B. xylophilus therefore contains genes that have been acquired by this process from both bacteria and fungi. These findings support the idea that multiple independent horizontal gene transfer events have helped in shaping the evolution of several different life strategies in nematodes.}, }
@article {pmid15723179, year = {2005}, author = {Chen, J and Civerolo, EL and Jarret, RL and Van Sluys, MA and de Oliveira, MC}, title = {Genetic discovery in Xylella fastidiosa through sequence analysis of selected randomly amplified polymorphic DNAs.}, journal = {Current microbiology}, volume = {50}, number = {2}, pages = {78-83}, pmid = {15723179}, issn = {0343-8651}, mesh = {Bacteriophages/genetics/isolation &amp; purification ; Base Sequence ; Conjugation, Genetic ; DNA, Bacterial/*genetics ; Evolution, Molecular ; Gene Rearrangement ; Genes, Bacterial ; Genome, Bacterial ; Molecular Sequence Data ; Plant Diseases/microbiology ; Plasmids/genetics ; Podoviridae/genetics/isolation &amp; purification ; Polymorphism, Single Nucleotide ; Random Amplified Polymorphic DNA Technique ; Xylella/*genetics/pathogenicity/virology ; }, abstract = {Xylella fastidiosa causes many important plant diseases including Pierce's disease (PD) in grape and almond leaf scorch disease (ALSD). DNA-based methodologies, such as randomly amplified polymorphic DNA (RAPD) analysis, have been playing key roles in genetic information collection of the bacterium. This study further analyzed the nucleotide sequences of selected RAPDs from X. fastidiosa strains in conjunction with the available genome sequence databases and unveiled several previously unknown novel genetic traits. These include a sequence highly similar to those in the phage family of Podoviridae. Genome comparisons among X. fastidiosa strains suggested that the "phage" is currently active. Two other RAPDs were also related to horizontal gene transfer: one was part of a broadly distributed cryptic plasmid and the other was associated with conjugal transfer. One RAPD inferred a genomic rearrangement event among X. fastidiosa PD strains and another identified a single nucleotide polymorphism of evolutionary value.}, }
@article {pmid15716432, year = {2005}, author = {Hansen, T and Schlichting, B and Felgendreher, M and Schönheit, P}, title = {Cupin-type phosphoglucose isomerases (Cupin-PGIs) constitute a novel metal-dependent PGI family representing a convergent line of PGI evolution.}, journal = {Journal of bacteriology}, volume = {187}, number = {5}, pages = {1621-1631}, pmid = {15716432}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; Bacteria/*enzymology/genetics ; Euryarchaeota/*enzymology/genetics ; *Evolution, Molecular ; Glucose-6-Phosphate Isomerase/chemistry/genetics/*metabolism ; Metals/*metabolism ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Sequence Homology, Amino Acid ; Temperature ; }, abstract = {Cupin-type phosphoglucose isomerases (cPGIs) were identified in some archaeal and bacterial genomes and the respective coding function of cpgi's from the euryarchaeota Archaeoglobus fulgidus and Methanosarcina mazei, as well as the bacteria Salmonella enterica serovar Typhimurium and Ensifer meliloti, was proven by functional overexpression. These cPGIs and the cPGIs from Pyrococcus and Thermococcus spp. represent the cPGI family and were compared with respect to kinetic, inhibitory, thermophilic, and metal-binding properties. cPGIs showed a high specificity for the substrates fructose-6-phosphate and glucose-6-phosphate and were inhibited by millimolar concentrations of sorbitol-6-phosphate, erythrose-4-phosphate, and 6-phosphogluconate. Treatment of cPGIs with EDTA resulted in a complete loss of catalytic activity, which could be regained by the addition of some divalent cations, most effectively by Fe2+ and Ni2+, indicating a metal dependence of cPGI activity. The motifs TX3PX3GXEX3TXGHXHX6-11EXY and PPX3HX3N were deduced as the two signature patterns of the novel cPGI family. Phylogenetic analysis suggests lateral gene transfer for the bacterial cPGIs from euryarchaeota.}, }
@article {pmid15716310, year = {2005}, author = {Tsirigos, A and Rigoutsos, I}, title = {A new computational method for the detection of horizontal gene transfer events.}, journal = {Nucleic acids research}, volume = {33}, number = {3}, pages = {922-933}, pmid = {15716310}, issn = {1362-4962}, mesh = {Algorithms ; Bacteriophages/genetics ; Computational Biology/*methods ; *Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; Genes, Viral ; Genomics/methods ; Sequence Analysis, DNA/*methods ; }, abstract = {In recent years, the increase in the amounts of available genomic data has made it easier to appreciate the extent by which organisms increase their genetic diversity through horizontally transferred genetic material. Such transfers have the potential to give rise to extremely dynamic genomes where a significant proportion of their coding DNA has been contributed by external sources. Because of the impact of these horizontal transfers on the ecological and pathogenic character of the recipient organisms, methods are continuously sought that are able to computationally determine which of the genes of a given genome are products of transfer events. In this paper, we introduce and discuss a novel computational method for identifying horizontal transfers that relies on a gene's nucleotide composition and obviates the need for knowledge of codon boundaries. In addition to being applicable to individual genes, the method can be easily extended to the case of clusters of horizontally transferred genes. With the help of an extensive and carefully designed set of experiments on 123 archaeal and bacterial genomes, we demonstrate that the new method exhibits significant improvement in sensitivity when compared to previously published approaches. In fact, it achieves an average relative improvement across genomes of between 11 and 41% compared to the Codon Adaptation Index method in distinguishing native from foreign genes. Our method's horizontal gene transfer predictions for 123 microbial genomes are available online at http://cbcsrv.watson.ibm.com/HGT/.}, }
@article {pmid15716108, year = {2005}, author = {Phadwal, K}, title = {Carotenoid biosynthetic pathway: molecular phylogenies and evolutionary behavior of crt genes in eubacteria.}, journal = {Gene}, volume = {345}, number = {1}, pages = {35-43}, doi = {10.1016/j.gene.2004.11.038}, pmid = {15716108}, issn = {0378-1119}, mesh = {Bacteria/enzymology/*genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Carotenoids/*biosynthesis/chemistry/metabolism ; Cyclization ; *Evolution, Molecular ; Farnesyl-Diphosphate Farnesyltransferase/genetics/metabolism ; Lycopene ; Oxidoreductases/genetics/metabolism ; *Phylogeny ; Xanthophylls/chemistry/metabolism ; }, abstract = {Phylogenetic analysis of carotenoid biosynthetic pathway genes and their evolutionary rate variations were studied among eubacterial taxa. The gene sequences for the enzymes involved in this pathway were obtained for major phylogenetic groups of eubacteria (green sulfur bacteria, green nonsulphur bacteria, Gram-positive bacteria, proteobacteria, flavobacteria, cyanobacteria) and archeabacteria. These gene datasets were distributed under five major steps of carotenoid biosynthesis in eubacteria; isoprenoid precursor biosynthesis, phytoene synthesis, dehydrogenation of phytoene, lycopene cyclization, formation of acyclic xanthophylls, formation of cyclic xanthophylls and carotenoid biosynthesis regulation. The NJ algorithm was used on protein coding DNA sequences to deduce the evolutionary relationship for the respective crt genes among different eubacterial lineages. The rate of nonsynonymous nucleotide substitutions per nonsynonymous site (d(N)) and synonymous nucleotide substitutions per synonymous site (d(S)) were calculated for different clades of the respective phylogenetic tree for specific crt genes. The phylogenetic analysis suggests that evolutionary pattern of crt genes in eubacteria is characterized by lateral gene transfer and gene duplication events. The d(N) values indicate that carotenoid biosynthetic genes are more conserved in proteobacteria than in any other eubacterial phyla. Furthermore, of the genes involved in carotenoid biosynthesis pathway, structural genes evolve slowly than the regulatory genes in eubacteria.}, }
@article {pmid15714662, year = {2005}, author = {Threlfall, J and Levent, B and Hopkins, KL and de Pinna, E and Ward, LR and Brown, DJ}, title = {Multidrug-resistant Salmonella Java.}, journal = {Emerging infectious diseases}, volume = {11}, number = {1}, pages = {170-171}, pmid = {15714662}, issn = {1080-6040}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Multiple, Bacterial ; Evolution, Molecular ; Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; Paratyphoid Fever/*epidemiology/microbiology ; Salmonella paratyphi A/*classification/drug effects/*genetics ; United Kingdom/epidemiology ; }, }
@article {pmid15713477, year = {2005}, author = {Robinson, A and Wu, PS and Harrop, SJ and Schaeffer, PM and Dosztányi, Z and Gillings, MR and Holmes, AJ and Nevalainen, KM and Stokes, HW and Otting, G and Dixon, NE and Curmi, PM and Mabbutt, BC}, title = {Integron-associated mobile gene cassettes code for folded proteins: the structure of Bal32a, a new member of the adaptable alpha+beta barrel family.}, journal = {Journal of molecular biology}, volume = {346}, number = {5}, pages = {1229-1241}, doi = {10.1016/j.jmb.2004.12.035}, pmid = {15713477}, issn = {0022-2836}, mesh = {Amino Acid Sequence ; Bacterial Proteins/*chemistry/genetics/metabolism ; Catalytic Domain ; Crystallography, X-Ray ; *DNA Transposable Elements ; Epoxide Hydrolases/chemistry ; Integrons/*physiology ; Ion Transport ; Isomerases/chemistry ; Models, Molecular ; Molecular Sequence Data ; Protein Folding ; *Protein Structure, Secondary ; Sequence Homology, Amino Acid ; Soil/*analysis ; Soil Microbiology ; }, abstract = {The wide-ranging physiology and large genetic variability observed for prokaryotes is largely attributed, not to the prokaryotic genome itself, but rather to mechanisms of lateral gene transfer. Cassette PCR has been used to sample the integron/gene cassette metagenome from different natural environments without laboratory cultivation of the host organism, and without prior knowledge of any target protein sequence. Since over 90% of cassette genes are unrelated to any sequence in the current databases, it is not clear whether these genes code for folded functional proteins. We have selected a sample of eight cassette-encoded genes with no known homologs; five have been isolated as soluble protein products and shown by biophysical techniques to be folded. In solution, at least three of these proteins organise as stable oligomeric assemblies. The tertiary structure of one of these, Bal32a derived from a contaminated soil site, has been solved by X-ray crystallography to 1.8 A resolution. From the three-dimensional structure, Bal32a is found to be a member of the highly adaptable alpha+beta barrel family of transport proteins and enzymes. In Bal32a, the barrel cavity is unusually deep and inaccessible to solvent. Polar side-chains in its interior are reminiscent of catalytic sites of limonene-1,2-epoxide hydrolase and nogalonic acid methyl ester cyclase. These studies demonstrate the viability of direct sampling of mobile DNA as a route for the discovery of novel proteins.}, }
@article {pmid15710748, year = {2005}, author = {Fukui, T and Atomi, H and Kanai, T and Matsumi, R and Fujiwara, S and Imanaka, T}, title = {Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes.}, journal = {Genome research}, volume = {15}, number = {3}, pages = {352-363}, pmid = {15710748}, issn = {1088-9051}, mesh = {Amino Acid Substitution ; Amino Acids/metabolism ; Archaeal Proteins/chemistry/genetics/metabolism ; Chromosome Mapping ; Coenzymes/metabolism ; Energy Metabolism ; *Genome, Archaeal ; Models, Biological ; Nucleotides/metabolism ; Pyrococcus/*genetics/metabolism ; Pyrococcus abyssi/genetics ; Pyrococcus furiosus/genetics ; Pyrococcus horikoshii/genetics ; Thermococcus/*genetics/metabolism ; }, abstract = {The genus Thermococcus, comprised of sulfur-reducing hyperthermophilic archaea, belongs to the order Thermococcales in Euryarchaeota along with the closely related genus Pyrococcus. The members of Thermococcus are ubiquitously present in natural high-temperature environments, and are therefore considered to play a major role in the ecology and metabolic activity of microbial consortia within hot-water ecosystems. To obtain insight into this important genus, we have determined and annotated the complete 2,088,737-base genome of Thermococcus kodakaraensis strain KOD1, followed by a comparison with the three complete genomes of Pyrococcus spp. A total of 2306 coding DNA sequences (CDSs) have been identified, among which half (1165 CDSs) are annotatable, whereas the functions of 41% (936 CDSs) cannot be predicted from the primary structures. The genome contains seven genes for probable transposases and four virus-related regions. Several proteins within these genetic elements show high similarities to those in Pyrococcus spp., implying the natural occurrence of horizontal gene transfer of such mobile elements among the order Thermococcales. Comparative genomics clarified that 1204 proteins, including those for information processing and basic metabolisms, are shared among T. kodakaraensis and the three Pyrococcus spp. On the other hand, among the set of 689 proteins unique to T. kodakaraensis, there are several intriguing proteins that might be responsible for the specific trait of the genus Thermococcus, such as proteins involved in additional pyruvate oxidation, nucleotide metabolisms, unique or additional metal ion transporters, improved stress response system, and a distinct restriction system.}, }
@article {pmid15709366, year = {2005}, author = {Barrett, CF and Parker, MA}, title = {Prevalence of Burkholderia sp. nodule symbionts on four mimosoid legumes from Barro Colorado Island, Panama.}, journal = {Systematic and applied microbiology}, volume = {28}, number = {1}, pages = {57-65}, doi = {10.1016/j.syapm.2004.09.002}, pmid = {15709366}, issn = {0723-2020}, mesh = {Alphaproteobacteria/classification/isolation &amp; purification ; Amidohydrolases/genetics ; Bacterial Proteins/genetics ; Bradyrhizobium/classification/isolation &amp; purification ; Burkholderia/*classification/*isolation &amp; purification ; DNA, Bacterial/chemistry/genetics/isolation &amp; purification ; DNA, Ribosomal/chemistry/isolation &amp; purification ; Fabaceae/*microbiology ; Genes, rRNA ; Molecular Sequence Data ; Nitrogenase/genetics ; Panama ; Phylogeny ; Plant Roots/*microbiology ; Polymerase Chain Reaction ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Rhizobium/classification/isolation &amp; purification ; Sequence Analysis, DNA ; Soil Microbiology ; }, abstract = {Sequences of 16S rRNA and partial 23S rRNA genes and PCR assays with genotype-specific primers indicated that bacteria in the genus Burkholderia were the predominant root nodule symbionts for four mimosoid legumes (Mimosa pigra, M. casta, M. pudica, and Abarema macradenia) on Barro Colorado Island, Panama. Among 51 isolates from these and a fifth mimosoid host (Pithecellobium hymenaeafolium), 44 were Burkholderia strains while the rest were placed in Rhizobium, Mesorhizobium, or Bradyrhizobium. The Burkholderia strains displayed four distinct rRNA sequence types, ranging from 89% to 97% similarity for 23S rRNA and 96.5-98.4% for 16S rRNA. The most common genotype comprised 53% of all isolates sampled and was associated with three legume host species. All Burkholderia genotypes formed nodules on Macroptilium atropurpureum or Mimosa pigra, and sequencing of rRNA genes in strains re-isolated from nodules verified identity with inoculant strains. Sequence analysis of the nitrogenase alpha-subunit gene (nifD) in two of the Burkholderia genotypes indicated that they were most similar to a partial sequence from the nodule-forming strain Burkholderia tuberum STM 678 from South Africa. In addition, a PCR screen with primers specific to Burkholderia nodB genes yielded the expected amplification product in most strains. Comparison of 16S rRNA and partial 23S rRNA phylogenies indicated that tree topologies were significantly incongruent. This implies that relationships across the rRNA region may have been altered by lateral gene transfer events in this Burkholderia population.}, }
@article {pmid15709360, year = {2005}, author = {Schmid, MW and Ng, EY and Lampidis, R and Emmerth, M and Walcher, M and Kreft, J and Goebel, W and Wagner, M and Schleifer, KH}, title = {Evolutionary history of the genus Listeria and its virulence genes.}, journal = {Systematic and applied microbiology}, volume = {28}, number = {1}, pages = {1-18}, doi = {10.1016/j.syapm.2004.09.005}, pmid = {15709360}, issn = {0723-2020}, mesh = {Bacterial Proteins/genetics ; DNA, Bacterial/chemistry ; DNA, Ribosomal/chemistry/genetics ; *Evolution, Molecular ; Gene Deletion ; Genes, Bacterial/genetics ; Genes, rRNA ; Lipoproteins/genetics ; Listeria/*genetics/*pathogenicity ; Molecular Sequence Data ; Multigene Family ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Sequence Analysis, DNA ; Virulence/genetics ; Virulence Factors/*genetics ; }, abstract = {The genus Listeria contains the two pathogenic species Listeria monocytogenes and Listeria ivanovii and the four apparently apathogenic species Listeria innocua, Listeria seeligeri, Listeria welshimeri, and Listeria grayi. Pathogenicity of the former two species is enabled by an approximately 9 kb virulence gene cluster which is also present in a modified form in L. seeligeri. For all Listeria species, the sequence of the virulence gene cluster locus and its flanking regions was either determined in this study or assembled from public databases. Furthermore, some virulence-associated internalin loci were compared among the six species. Phylogenetic analyses were performed on a data set containing the sequences of prs, ldh, vclA, and vclB (all directly flanking the virulence gene cluster), as well as the iap gene and the 16S and 23S-rRNA coding genes which are located at different sites in the listerial chromosomes. L. grayi represents the deepest branch within the genus. The remaining five species form two groupings which have a high bootstrap support and which are consistently found by using different treeing methods. One lineage represents L. monocytogenes and L. innocua, while the other contains L. welshimeri, L. ivanovii and L. seeligeri, with L. welshimeri forming the deepest branch. Based on this perception, we tried to reconstruct the evolution of the virulence gene cluster. Since no traces of lateral gene transfer events could be detected the most parsimonious scenario is that the virulence gene cluster was present in the common ancestor of L. monocytogenes, L. innocua, L. ivanovii, L. seeligeri and L. welshimeri and that the pathogenic capability has been lost in two separate events represented by L. innocua and L. welshimeri. This hypothesis is also supported by the location of the putative deletion breakpoints of the virulence gene cluster within L. innocua and L. welshimeri.}, }
@article {pmid15704333, year = {2004}, author = {Stackebrandt, E}, title = {Will we ever understand? The undescribable diversity of the prokaryotes.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {51}, number = {4}, pages = {449-462}, doi = {10.1556/AMicr.51.2004.4.5}, pmid = {15704333}, issn = {1217-8950}, mesh = {Bacteria/*classification ; *Biodiversity ; Phylogeny ; }, abstract = {This communication will summarize recent estimations on prokaryotic cell numbers, technical aspects of the exploration of the hidden diversity of the as-yet-uncultured prokaryotes and their function in the environment, recognition of novel major lines of descent, elucidation of novel metabolic pathways and attempts to improve the definition of the taxon species. These are some of recent highlights that will reflect only incompletely recent advances of microbiologist and other aspects of diversity at the genomic level, including the tremendous influence of whole genome sequences on the development of DNA macro- and microarrays for rapid identification of genes and specimen, the annotation of gene sequences to gene function by proteomics and the recognition of the extent of lateral gene transfer in the evolution of the genome, hence of contemporary organisms. As an example of modern trends in systematics three new families will be described for recently described genera, namely Thermoleophilaceae, Solirubrobacteraceae and Conexibacteraceae, which are phylogenetically positioned among environmental clone sequences at the root of the class Actinobacteria.}, }
@article {pmid15704225, year = {2005}, author = {Balan, A and Schenberg, AC}, title = {A conditional suicide system for Saccharomyces cerevisiae relying on the intracellular production of the Serratia marcescens nuclease.}, journal = {Yeast (Chichester, England)}, volume = {22}, number = {3}, pages = {203-212}, doi = {10.1002/yea.1203}, pmid = {15704225}, issn = {0749-503X}, mesh = {Blotting, Western ; Chromosomes, Fungal/genetics ; Comet Assay ; DNA, Fungal/chemistry/genetics ; Endodeoxyribonucleases/*biosynthesis/genetics/metabolism ; Endoribonucleases/*biosynthesis/genetics/metabolism ; Genes, Transgenic, Suicide/*genetics ; Glucose/metabolism ; Polymerase Chain Reaction ; Saccharomyces cerevisiae/enzymology/genetics/*growth &amp; development ; Serratia marcescens/*enzymology/*genetics ; Soil Microbiology ; Transformation, Genetic ; }, abstract = {A conditional lethal system for biological containment of genetically modified strains of Saccharomyces cerevisiae is described. This suicide system is based on the intracellular production of the Serratia marcescens nuclease in the yeast cell, aiming at the destruction of the host genetic material. The S. marcescens nuclease, encoded by the nucA gene, is normally secreted by the bacterium into the medium. In the present work, the nucA gene, devoid of its signal peptide coding sequence, was cloned in a yeast expression vector, under control of the glucose-repressed S. cerevisiae alcohol dehydrogenase 2 gene (ADH2) promoter. When transformed into S. cerevisiae, the recombinant plasmid proved to be effective in killing the host cells upon glucose depletion from the medium, and the nuclease activity was found in lysates prepared from the transformants. In addition, the nuclease degrading effect was shown to reach chromosomal DNA in the yeast host. The killing effect of the nucA plasmid was also demonstrated in soil microcosm assays, indicating that whenever the GMM escapes into the environment where glucose is scarce, the nucA gene will be expressed and the resulting nuclease will destroy the genetic material and kill the cells. In contrast to other suicide systems that target the cell envelope, the advantage of the one described here is that it disfavours horizontal gene transfer from recombinant yeast cells to other microorganisms found in the environment.}, }
@article {pmid15703727, year = {2005}, author = {Gelvin, SB}, title = {Agricultural biotechnology: gene exchange by design.}, journal = {Nature}, volume = {433}, number = {7026}, pages = {583-584}, doi = {10.1038/433583a}, pmid = {15703727}, issn = {1476-4687}, mesh = {Biotechnology/methods ; DNA, Bacterial/genetics ; Gene Transfer Techniques ; Gene Transfer, Horizontal/*genetics ; Genetic Vectors/genetics ; Plants/*genetics/*microbiology ; Plants, Genetically Modified ; Rhizobiaceae/classification/*genetics ; Rhizobium/classification/genetics ; Transformation, Genetic/*genetics ; }, }
@article {pmid15703296, year = {2005}, author = {Ostedgaard, LS and Rokhlina, T and Karp, PH and Lashmit, P and Afione, S and Schmidt, M and Zabner, J and Stinski, MF and Chiorini, JA and Welsh, MJ}, title = {A shortened adeno-associated virus expression cassette for CFTR gene transfer to cystic fibrosis airway epithelia.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {102}, number = {8}, pages = {2952-2957}, pmid = {15703296}, issn = {0027-8424}, support = {P01 HL051670/HL/NHLBI NIH HHS/United States ; DK54759/DK/NIDDK NIH HHS/United States ; R01 AI013562/AI/NIAID NIH HHS/United States ; HL51670/HL/NHLBI NIH HHS/United States ; P30 DK054759/DK/NIDDK NIH HHS/United States ; AI-13562/AI/NIAID NIH HHS/United States ; R21 AI013562/AI/NIAID NIH HHS/United States ; }, mesh = {Cells, Cultured ; Chlorides/metabolism ; Cystic Fibrosis/*therapy ; Cystic Fibrosis Transmembrane Conductance Regulator/*genetics ; Dependovirus/*genetics ; Enhancer Elements, Genetic ; Epithelium/metabolism ; Gene Transfer, Horizontal ; *Genetic Therapy ; Genetic Vectors/genetics ; Humans ; Introns ; Ion Transport ; Promoter Regions, Genetic ; Trachea/*metabolism ; }, abstract = {Adeno-associated viruses (AAVs) such as AAV5 that transduce airway epithelia from the apical surface are attractive vectors for gene transfer in cystic fibrosis (CF). However, their utility in CF has been limited because packaging of the insert becomes inefficient when its length exceeds approximately 4,900-5,000 bp. To partially circumvent this size constraint, we previously developed a CF transmembrane conductance regulator (CFTR) transgene that deleted a portion of the R domain (CFTRDeltaR). In this study, we focused on shortening the other elements in the AAV expression cassette. We found that portions of the CMV immediate/early (CMVie) enhancer/promoter could be deleted without abolishing activity. We also tested various intervening sequences, poly(A) signals, and an intron to develop an expression cassette that meets the size restrictions imposed by AAV. We then packaged these shortened elements with the CFTRDeltaR transgene into AAV5 and applied them to the apical surface of differentiated CF airway epithelia. Two to 4 weeks later, the AAV5 vectors partially corrected the CF Cl(-) transport defect. These results demonstrate that a single AAV vector can complement the CF defect in differentiated airway epithelia and thereby further the development of effective CF gene transfer.}, }
@article {pmid15696374, year = {2005}, author = {Annoura, T and Nara, T and Makiuchi, T and Hashimoto, T and Aoki, T}, title = {The origin of dihydroorotate dehydrogenase genes of kinetoplastids, with special reference to their biological significance and adaptation to anaerobic, parasitic conditions.}, journal = {Journal of molecular evolution}, volume = {60}, number = {1}, pages = {113-127}, pmid = {15696374}, issn = {0022-2844}, mesh = {Adaptation, Physiological/genetics ; Amino Acid Sequence ; Anaerobiosis ; Animals ; Aspartate Carbamoyltransferase/genetics ; Blotting, Western ; Cloning, Molecular ; DNA, Complementary/chemistry/genetics ; Dihydroorotate Dehydrogenase ; Euglena gracilis/enzymology/genetics ; *Evolution, Molecular ; Kinetoplastida/enzymology/*genetics/growth &amp; development ; Molecular Sequence Data ; Mutation ; Oxidoreductases Acting on CH-CH Group Donors/*genetics/metabolism ; Phylogeny ; Plasmids/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Transformation, Genetic ; Trypanosoma cruzi/enzymology/genetics ; }, abstract = {Trypanosoma cruzi dihydroorotate dehydrogenase (DHOD), the fourth enzyme of the de novo pyrimidine biosynthetic pathway, is localized in the cytosol and utilizes fumarate as electron acceptor (fumarate reductase activity), while the enzyme from other various eukaryotes is mitochondrial membrane-linked. Here we report that DHOD-knockout T. cruzi did not express the enzyme protein and could not survive even in the presence of pyrimidine nucleosides, substrates for the potentially active salvage pathway, suggesting a vital role of fumarate reductase activity in the regulation of cellular redox balance. Cloning and phylogenetic analysis of euglenozoan DHOD genes showed that the euglenoid Euglena gracilis had a mitochondrial DHOD and that biflagellated bodonids, a sister group of trypanosomatids within kinetoplastids, harbor the cytosolic DHOD. Further, Bodo saliens, a bodonid, had an ACT/DHOD gene fusion encoding aspartate carbamoyltransferase (ACT), the second enzyme of the de novo pyrimidine pathway, and DHOD. This is the first report of this novel gene structure. These results are consistent with suggestions that an ancient common ancestor of Euglenozoa had a mitochondrial DHOD whose descendant exists in E. gracilis and that a common ancestor of kinetoplastids (bodonids and trypanosomatids) subsequently acquired a cytosolic DHOD by horizontal gene transfer. The cytosolic DHOD gene thus acquired may have contributed to adaptation to anaerobiosis in the kinetoplastid lineage and further contributed to the subsequent establishment of parasitism in a trypanosomatid ancestor. Different molecular strategies for anaerobic adaptation in pyrimidine biosynthesis, used by kinetoplastids and by euglenoids, are discussed. Evolutionary implications of the ACT/DHOD gene fusion are also discussed.}, }
@article {pmid15695667, year = {2005}, author = {Beutin, L and Tao, J and Feng, L and Krause, G and Zimmermann, S and Gleier, K and Xia, Q and Wang, L}, title = {Sequence analysis of the Escherichia coli O15 antigen gene cluster and development of a PCR assay for rapid detection of intestinal and extraintestinal pathogenic E. coli O15 strains.}, journal = {Journal of clinical microbiology}, volume = {43}, number = {2}, pages = {703-710}, pmid = {15695667}, issn = {0095-1137}, mesh = {Escherichia coli/classification/genetics/immunology/*pathogenicity ; Escherichia coli Infections/diagnosis/*microbiology ; Escherichia coli Proteins/genetics ; Humans ; Intestinal Diseases/diagnosis/microbiology ; Molecular Sequence Data ; *Multigene Family ; O Antigens/*genetics ; Polymerase Chain Reaction/*methods ; Sensitivity and Specificity ; *Sequence Analysis, DNA ; Serotyping ; Time Factors ; Virulence ; }, abstract = {A collection of 33 Escherichia coli serogroup O15 strains was studied with regard to O:H serotypes and virulence markers and for detection of the O-antigen-specific genes wzx and wzy. The strains were from nine different countries, originated from healthy or diseased humans and animals and from food, and were isolated between 1941 and 2003. On the basis of virulence markers and clinical data the strains could be split into different pathogroups, such as uropathogenic E. coli, enteropathogenic E. coli, Shiga toxin-producing E. coli, and enteroaggregative E. coli. H serotyping and genotyping of the flagellin (fliC) gene revealed 11 different H types and a close association between certain H types, virulence markers, and pathogroups was found. Nucleotide sequence analysis of the O-antigen gene cluster revealed putative genes for biosynthesis of O15 antigen. PCR assays were developed for sensitive and specific detection of the O15-antigen-specific genes wzx and wzy. The high pathotype diversity found in the collection of 33 O15 strains contrasted with the high level of similarity found in the genes specific to the O15 antigen. This might indicate that the O15 determinant has been spread by horizontal gene transfer to a number of genetically unrelated strains of E. coli.}, }
@article {pmid15693614, year = {2004}, author = {Bauer, M and Lombardot, T and Teeling, H and Ward, NL and Amann, RI and Glöckner, FO}, title = {Archaea-like genes for C1-transfer enzymes in Planctomycetes: phylogenetic implications of their unexpected presence in this phylum.}, journal = {Journal of molecular evolution}, volume = {59}, number = {5}, pages = {571-586}, pmid = {15693614}, issn = {0022-2844}, mesh = {Amidohydrolases/chemistry/genetics ; Amino Acid Sequence ; Archaea/*enzymology/*genetics ; Bacteria/*enzymology/*genetics ; Catalysis ; Conserved Sequence ; Genes, Archaeal/*genetics ; Genes, Bacterial/*genetics ; Genome, Bacterial ; Methylobacterium extorquens/chemistry/genetics ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; }, abstract = {The unexpected presence of archaea-like genes for tetrahydromethanopterin (H4MPT)-dependent enzymes in the completely sequence geiome of the aerobic marine planctomycete Pirellula sp. strain 1 ("Rhodopirellula baltica") and in the currently sequenced genome of the aerobic freshwater planctomycete Gemmata obscuriglobus strain UQM2246 revives the discussion on the origin of these genes in the bacterial domain. We compared the genomic arrangement of these genes in Planctomyetes and methylotrophic proteobacteria and perormed a phylogenetic analysis of the encoded protein sequences to address the question whether the genes have been present in the common ancestor of Bacteria and Archaea or were transferred laterally from the archaeal to the bacterial domain and herein. Although this question could not be solved using the data presented here, some constraints on the evolution of the genes involved in archaeal and)acterial H4MPT-dependent C1-transfer may be proposed: (i) lateral gene transfer (LGT) from Archea to a common ancestor of Proteobacteria and Planctomycetes seems more likely than the presence of the genes in the common ancestor of Bacteria and Archaea; (ii) a single event of interdomain LGT can e favored over two independent events; and (iii) the irchacal donor of the genes might have been a repesentative of the Methanosarcinales. In the bacterial domain, the acquired genes evolved according to distinct environmental and metabolic constraints, reflected by specific rearrangements of gene order, gene recruitment, and gene duplication, with subsequent functional specialization. During the course of evolution, genes were lost from some planctomycete genomes or replaced by orthologous genes from proteobacterial lineages.}, }
@article {pmid15689432, year = {2005}, author = {Seif, E and Leigh, J and Liu, Y and Roewer, I and Forget, L and Lang, BF}, title = {Comparative mitochondrial genomics in zygomycetes: bacteria-like RNase P RNAs, mobile elements and a close source of the group I intron invasion in angiosperms.}, journal = {Nucleic acids research}, volume = {33}, number = {2}, pages = {734-744}, pmid = {15689432}, issn = {1362-4962}, mesh = {Bacteria/enzymology/genetics ; Base Sequence ; Conserved Sequence ; DNA Transposable Elements ; DNA, Mitochondrial/*chemistry ; Endonucleases/genetics ; Fungi/classification/*genetics ; Gene Transfer, Horizontal ; Genes, Fungal ; Genetic Code ; *Genome, Fungal ; Introns ; Magnoliopsida/genetics ; Mitochondria/enzymology/*genetics ; Mitochondrial Proteins/classification/genetics ; Molecular Sequence Data ; Phylogeny ; RNA/*chemistry/genetics/metabolism ; RNA, Fungal/chemistry/genetics/metabolism ; RNA, Messenger/chemistry ; RNA, Mitochondrial ; RNA, Ribosomal/chemistry ; Ribonuclease P/*genetics ; }, abstract = {To generate data for comparative analyses of zygomycete mitochondrial gene expression, we sequenced mtDNAs of three distantly related zygomycetes, Rhizopus oryzae, Mortierella verticillata and Smittium culisetae. They all contain the standard fungal mitochondrial gene set, plus rnpB, the gene encoding the RNA subunit of the mitochondrial RNase P (mtP-RNA) and rps3, encoding ribosomal protein S3 (the latter lacking in R.oryzae). The mtP-RNAs of R.oryzae and of additional zygomycete relatives have the most eubacteria-like RNA structures among fungi. Precise mapping of the 5' and 3' termini of the R.oryzae and M.verticillata mtP-RNAs confirms their expression and processing at the exact sites predicted by secondary structure modeling. The 3' RNA processing of zygomycete mitochondrial mRNAs, SSU-rRNA and mtP-RNA occurs at the C-rich sequence motifs similar to those identified in fission yeast and basidiomycete mtDNAs. The C-rich motifs are included in the mature transcripts, and are likely generated by exonucleolytic trimming of RNA 3' termini. Zygomycete mtDNAs feature a variety of insertion elements: (i) mtDNAs of R.oryzae and M.verticillata were subject to invasions by double hairpin elements; (ii) genes of all three species contain numerous mobile group I introns, including one that is closest to an intron that invaded angiosperm mtDNAs; and (iii) at least one additional case of a mobile element, characterized by a homing endonuclease insertion between partially duplicated genes [Paquin,B., Laforest,M.J., Forget,L., Roewer,I., Wang,Z., Longcore,J. and Lang,B.F. (1997) Curr. Genet., 31, 380-395]. The combined mtDNA-encoded proteins contain insufficient phylogenetic signal to demonstrate monophyly of zygomycetes.}, }
@article {pmid15687208, year = {2005}, author = {Ren, CP and Beatson, SA and Parkhill, J and Pallen, MJ}, title = {The Flag-2 locus, an ancestral gene cluster, is potentially associated with a novel flagellar system from Escherichia coli.}, journal = {Journal of bacteriology}, volume = {187}, number = {4}, pages = {1430-1440}, pmid = {15687208}, issn = {0021-9193}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Aeromonas/physiology ; Chromobacterium/genetics/physiology ; Citrobacter rodentium/genetics ; DNA, Bacterial/chemistry/isolation &amp; purification ; DNA-Binding Proteins/physiology ; DNA-Directed RNA Polymerases/physiology ; Escherichia coli/*genetics/physiology ; Escherichia coli Proteins ; Evolution, Molecular ; Flagella/*genetics ; Flagellin/genetics ; Frameshift Mutation ; *Genes, Bacterial ; Molecular Sequence Data ; Movement ; Multigene Family ; Protein Transport/genetics ; Pseudogenes ; RNA Polymerase Sigma 54 ; Salmonella enterica/genetics/physiology ; Sequence Analysis, DNA ; Shigella/genetics ; Sigma Factor/physiology ; Vibrio/physiology ; Yersinia pestis/genetics/physiology ; Yersinia pseudotuberculosis/genetics/physiology ; }, abstract = {Escherichia coli K-12 possesses two adjacent, divergent, promoterless flagellar genes, fhiA-mbhA, that are absent from Salmonella enterica. Through bioinformatics analysis, we found that these genes are remnants of an ancestral 44-gene cluster and are capable of encoding a novel flagellar system, Flag-2. In enteroaggregative E. coli strain 042, there is a frameshift in lfgC that is likely to have inactivated the system in this strain. Tiling path PCR studies showed that the Flag-2 cluster is present in 15 of 72 of the well-characterized ECOR strains. The Flag-2 system resembles the lateral flagellar systems of Aeromonas and Vibrio, particularly in its apparent dependence on RpoN. Unlike the conventional Flag-1 flagellin, the Flag-2 flagellin shows a remarkable lack of sequence polymorphism. The Flag-2 gene cluster encodes a flagellar type III secretion system (including a dedicated flagellar sigma-antisigma combination), thus raising the number of distinct type III secretion systems in Escherichia/Shigella to five. The presence of the Flag-2 cluster at identical sites in E. coli and its close relative Citrobacter rodentium, combined with its absence from S. enterica, suggests that it was acquired by horizontal gene transfer after the former two species diverged from Salmonella. The presence of Flag-2-like gene clusters in Yersinia pestis, Yersinia pseudotuberculosis, and Chromobacterium violaceum suggests that coexistence of two flagellar systems within the same species is more common than previously suspected. The fact that the Flag-2 gene cluster was not discovered in the first 10 Escherichia/Shigella genome sequences studied emphasizes the importance of maintaining an energetic program of genome sequencing for this important taxonomic group.}, }
@article {pmid15676066, year = {2005}, author = {Saunders, NJ and Boonmee, P and Peden, JF and Jarvis, SA}, title = {Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori.}, journal = {BMC genomics}, volume = {6}, number = {}, pages = {9}, pmid = {15676066}, issn = {1471-2164}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Adaptation, Physiological ; Bacteriophages/metabolism ; Conserved Sequence ; DNA Polymerase III/metabolism ; Escherichia coli Proteins/metabolism ; Evolution, Molecular ; Gene Deletion ; Gene Expression Regulation ; *Gene Transfer, Horizontal ; Genes, Bacterial ; *Genetic Variation ; Genome ; Genome, Bacterial ; Helicobacter pylori/*genetics/metabolism ; Integrases/metabolism ; Membrane Proteins/metabolism ; Models, Genetic ; Models, Statistical ; Molecular Sequence Data ; Open Reading Frames ; Protein Structure, Tertiary ; Sequence Analysis, DNA ; Species Specificity ; Virulence ; }, abstract = {BACKGROUND: Horizontal gene transfer is central to evolution in most bacterial species. The detection of exchanged regions is often based upon analysis of compositional characteristics and their comparison to the organism as a whole. In this study we describe a new methodology combining aspects of established signature analysis with textual analysis approaches. This approach has been used to analyze the two available genome sequences of H. pylori.<br><br>RESULTS: This gene-by-gene analysis reveals a wide range of genes related to both virulence behaviour and the strain differences that have been relatively recently acquired from other sequence backgrounds. These frequently involve single genes or small numbers of genes that are not associated with transposases or bacteriophage genes, nor with inverted repeats typically used as markers for horizontal transfer. In addition, clear examples of horizontal exchange in genes associated with 'core' metabolic functions were identified, supported by differences between the sequenced strains, including: ftsK, xerD and polA. In some cases it was possible to determine which strain represented the 'parent' and 'altered' states for insertion-deletion events. Different signature component lengths showed different sensitivities for the detection of some horizontally transferred genes, which may reflect different amelioration rates of sequence components.<br><br>CONCLUSION: New implementations of signature analysis that can be applied on a gene-by-gene basis for the identification of horizontally acquired sequences are described. These findings highlight the central role of the availability of homologous substrates in evolution mediated by horizontal exchange, and suggest that some components of the supposedly stable 'core genome' may actually be favoured targets for integration of foreign sequences because of their degree of conservation.}, }
@article {pmid15673771, year = {2005}, author = {Jones, LA and McIver, CJ and Kim, MJ and Rawlinson, WD and White, PA}, title = {The aadB gene cassette is associated with blaSHV genes in Klebsiella species producing extended-spectrum beta-lactamases.}, journal = {Antimicrobial agents and chemotherapy}, volume = {49}, number = {2}, pages = {794-797}, pmid = {15673771}, issn = {0066-4804}, mesh = {Aminoglycosides/pharmacology ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/*genetics ; Integrases/genetics ; Integrons/genetics ; Klebsiella/*genetics ; Plasmids ; Reverse Transcriptase Polymerase Chain Reaction ; beta-Lactamases/*genetics ; }, abstract = {Integrons were detected in 37 (72.5%) of 51 Klebsiella spp. producing extended-spectrum beta-lactamases by PCR with primers that targeted integrase genes and cassette regions. PCR and amplicon sequencing of the cassette regions revealed aadB and aadA2 gene cassettes that confer resistance to a range of aminoglycosides. aadB was associated with a class 1 integron on a 28-kb plasmid, pES1, that also contained bla(SHV-12) and IS26.}, }
@article {pmid15673766, year = {2005}, author = {Pletz, MW and McGee, L and Beall, B and Whitney, CG and Klugman, KP}, title = {Interspecies recombination in type II topoisomerase genes is not a major cause of fluoroquinolone resistance in invasive Streptococcus pneumoniae isolates in the United States.}, journal = {Antimicrobial agents and chemotherapy}, volume = {49}, number = {2}, pages = {779-780}, pmid = {15673766}, issn = {0066-4804}, mesh = {Anti-Bacterial Agents/*pharmacology ; DNA Topoisomerases, Type II/*genetics ; Drug Resistance, Bacterial ; Fluoroquinolones/*pharmacology ; Gene Transfer, Horizontal ; Levofloxacin ; Ofloxacin/pharmacology ; Pneumococcal Infections/*microbiology ; *Recombination, Genetic ; Streptococcus pneumoniae/*drug effects/*genetics ; United States ; Viridans Streptococci/drug effects/genetics ; }, abstract = {Mutations in the topoisomerase type II enzymes account for fluoroquinolone resistance in Streptococcus pneumoniae. These mutations can arise spontaneously or be transferred by intraspecies or interspecies recombination, primarily with viridans streptococci. We analyzed the nucleotide sequences of the quinolone resistance-determining regions of 49 invasive levofloxacin-resistant pneumococcal isolates and did not find any evidence for interspecies recombination.}, }
@article {pmid15673725, year = {2005}, author = {Gebreyes, WA and Thakur, S}, title = {Multidrug-resistant Salmonella enterica serovar Muenchen from pigs and humans and potential interserovar transfer of antimicrobial resistance.}, journal = {Antimicrobial agents and chemotherapy}, volume = {49}, number = {2}, pages = {503-511}, pmid = {15673725}, issn = {0066-4804}, mesh = {Animals ; Blotting, Southern ; Conjugation, Genetic ; DNA Fingerprinting ; DNA, Bacterial/genetics ; *Disease Reservoirs ; Drug Resistance, Multiple, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Gene Transfer, Horizontal ; Humans ; Integrons/genetics ; Microbial Sensitivity Tests ; Plasmids/genetics ; Salmonella enterica/*drug effects/*genetics ; Salmonella typhimurium/drug effects/genetics ; Swine ; }, abstract = {Salmonella serovars are important reservoirs of antimicrobial resistance. Recently, we reported on multidrug-resistant (MDR) Salmonella enterica serovar Typhimurium strains among pigs with resistance to ampicillin, kanamycin, streptomycin, sulfamethoxazole, and tetracycline (resistance [R] type AKSSuT) and resistance to amoxicillin-clavulanic acid, ampicillin, chloramphenicol, streptomycin, sulfamethoxazole, and tetracycline (R type AxACSSuT). In the present study, 67 isolates (39 from humans and 28 from pigs) of clinically important Salmonella serovar Muenchen were characterized. Among the porcine isolates, 75% showed resistance to seven antimicrobials: ampicillin, chloramphenicol, streptomycin, sulfamethoxazole, tetracycline, amoxicillin-clavulanic acid, and kanamycin (R type ACSSuTAxK). One isolate from humans showed resistance to 10 of the 12 antimicrobials: ampicillin, chloramphenicol, streptomycin, sulfamethoxazole, tetracycline, amoxicillin-clavulanic acid, kanamycin, gentamicin, cephalothin, and ceftriaxone (R type ACSSuTAxKGCfCro). Pulsed-field gel electrophoresis revealed no clonality between the porcine and the human strains. The porcine and the human MDR strains carried class 1 integrons of 2.0 and 1.0 kb, respectively. Genes specific to the porcine strain included aadA2, aphA1-Iab, and tetA(B). DNA sequencing revealed that the porcine isolates carried bla(OXA-30) on a class 1 integron. Genes specific to the human strain included bla(TEM), strA, strB, cmlA, tetA(A), and aadA2. No bla(CMY-2) gene was detected. Serovar Muenchen strains of porcine and human origin were able to transfer resistance genes to laboratory strain Escherichia coli MG1655 by conjugation. Plasmid restriction with four restriction enzymes, EcoRI, BamHI, HindIII, and PstI, showed that the conjugative plasmids from porcine Salmonella serovar Muenchen and Typhimurium R-type MDR strains isolated from the same farms at the same time were similar on the basis of the sizes and the numbers of bands and Southern hybridization. The plasmid profiles among the Salmonella serovar Muenchen isolates from the two host species were different. This is the first report to show a high frequency of MDR Salmonella serovar Muenchen strains from pigs and a human strain that is similar to the MDR isolates with the AmpC enzyme previously reported among Salmonella serovars Newport and Typhimurium strains. The MDR strains from the two host species independently represent public health concerns, as Salmonella serovar Muenchen is among the top 10 causes of salmonellosis in humans.}, }
@article {pmid15668031, year = {2005}, author = {Bischoff, KM and White, DG and Hume, ME and Poole, TL and Nisbet, DJ}, title = {The chloramphenicol resistance gene cmlA is disseminated on transferable plasmids that confer multiple-drug resistance in swine Escherichia coli.}, journal = {FEMS microbiology letters}, volume = {243}, number = {1}, pages = {285-291}, doi = {10.1016/j.femsle.2004.12.017}, pmid = {15668031}, issn = {0378-1097}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Chloramphenicol Resistance/*genetics ; Conjugation, Genetic/*genetics ; Drug Resistance, Multiple, Bacterial ; Escherichia coli/*drug effects/genetics ; Escherichia coli Proteins/*genetics/metabolism ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Integrons/genetics ; Microbial Sensitivity Tests ; Plasmids/*genetics ; Swine ; }, abstract = {A recent study of beta-hemolytic Escherichia coli isolated from diarrheic swine found that 53% were resistant to chloramphenicol, a drug that has been prohibited from use in food animals in the US since the mid-1980s. To identify the factors governing the persistence of chloramphenicol resistance in the absence of specific selection pressure, the location of the chloramphenicol resistance gene cmlA and its linkage to other resistance determinants were investigated. Southern blot analysis of plasmid DNA from 46 swine E. coli isolates indicated that cmlA was present on large plasmids greater than 100 kbp. Fifty-two percent of the isolates were able to transfer chloramphenicol resistance to an E. coli recipient at conjugation frequencies ranging from 10(-3) to 10(-8) per recipient. Antimicrobial susceptibility tests on transconjugant strains demonstrated that resistance to sulfamethoxazole, tetracycline, and kanamycin frequently transferred along with chloramphenicol resistance. The transconjugant strains possessed at least two distinct class 1 integrons that linked cmlA to both aminoglycoside resistance genes aadA1 and aadA2 and either to sul1 or to sul3 sulphonamide resistance genes. These results suggest that in the absence of specific chloramphenicol selection pressure, the cmlA gene is maintained by virtue of gene linkage to genes encoding resistance to antimicrobials that are currently approved for use in food animals.}, }
@article {pmid15667995, year = {2005}, author = {Wilcks, A and Andersen, SR and Licht, TR}, title = {Characterization of transferable tetracycline resistance genes in Enterococcus faecalis isolated from raw food.}, journal = {FEMS microbiology letters}, volume = {243}, number = {1}, pages = {15-19}, doi = {10.1016/j.femsle.2004.11.028}, pmid = {15667995}, issn = {0378-1097}, mesh = {Animals ; Antiporters/genetics ; Cattle ; Chickens ; *Conjugation, Genetic ; Enterococcus faecalis/drug effects/*genetics ; Escherichia coli Proteins/genetics ; Food Microbiology ; *Gene Transfer, Horizontal ; Meat Products/*microbiology ; Membrane Proteins/genetics ; Tetracycline Resistance/*genetics ; }, abstract = {The prevalence of tetracycline resistance, and of specific genetic determinants for this resistance was investigated in 1003 strains of Enterococcus faecalis isolated from various raw food products originating from five categories including chicken meat, other poultry meat, beef, pork, and 'other'. For the 238 resistant isolates identified, the ability to transfer the resistant phenotype to a given recipient in vitro was investigated. New and interesting observations were that the tet(L) resistance determinant was more readily transferred than tet(M), and that the presence of Tn916-like elements known to encode tet(M) did not correlate with increased transferability of the resistant phenotype.}, }
@article {pmid15660951, year = {2005}, author = {Malloch, G and Fenton, B}, title = {Super-infections of Wolbachia in byturid beetles and evidence for genetic transfer between A and B super-groups of Wolbachia.}, journal = {Molecular ecology}, volume = {14}, number = {2}, pages = {627-637}, doi = {10.1111/j.1365-294X.2005.02432.x}, pmid = {15660951}, issn = {0962-1083}, mesh = {Animals ; Bacterial Outer Membrane Proteins/genetics ; Bacterial Proteins/genetics ; Base Sequence ; Cloning, Molecular ; Coleoptera/*genetics/*microbiology ; Cytoskeletal Proteins/genetics ; *Gene Transfer, Horizontal ; *Genetics, Population ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Restriction Mapping ; Sequence Alignment ; Sequence Analysis, DNA ; Wolbachia/*genetics ; }, abstract = {Wolbachia are maternally inherited bacteria responsible for altering host reproduction. The two main groups found in insects, A and B, are based on molecular characterization using ribosomal, ftsZ, wsp (Wolbachia surface protein) or groE genes. We have used the wsp and ftsZ genes to study Wolbachia in byturid beetles. Byturus affinis contained a single copy of the ftsZ gene which grouped with A ftsZ sequences and a single copy of the wsp gene which grouped with B wsp sequences. This suggests that genetic exchange between A and B groups has occurred in the Wolbachia of this beetle. FtsZ and wsp sequences that were identical or nearly identical to those of B. affinis were found in B. tomentosus, suggesting that it also contains the same recombinant Wolbachia genotype. Most other byturids had more than one wsp sequence with at least one from the A and B groups, suggesting multiple copies of bacterial genes or multiple infections. B. ochraceus and B. unicolor both had four distinct wsp gene sequences. All the byturids had a closely related A wsp sequence and most a closely related B wsp sequence. Therefore, there appears to be an association between specific A and B wsp types.}, }
@article {pmid15660210, year = {2005}, author = {Reid, SJ and Abratt, VR}, title = {Sucrose utilisation in bacteria: genetic organisation and regulation.}, journal = {Applied microbiology and biotechnology}, volume = {67}, number = {3}, pages = {312-321}, doi = {10.1007/s00253-004-1885-y}, pmid = {15660210}, issn = {0175-7598}, mesh = {Bacteria/enzymology/*genetics/*metabolism ; DNA Transposable Elements ; Evolution, Molecular ; Genes, Bacterial ; Glucosyltransferases/genetics/metabolism ; Phosphoenolpyruvate Sugar Phosphotransferase System/*genetics/*metabolism ; Phylogeny ; Regulon ; Sucrose/*metabolism ; }, abstract = {Sucrose is the most abundant disaccharide in the environment because of its origin in higher plant tissues, and many Eubacteria possess catalytic enzymes, such as the sucrose-6-phosphate hydrolases and sucrose phosphorylases, that enable them to metabolise this carbohydrate in a regulated manner. This review describes the range of gene architecture, uptake systems, catabolic activity and regulation of the sucrose-utilisation regulons that have been reported in the Eubacteria to date. Evidence is presented that, although there are many common features to these gene clusters and high conservation of the proteins involved, there has been a certain degree of gene shuffling. Phylogenetic analyses of these proteins supports the hypothesis that these clusters have been acquired through horizontal gene transfer via mobile elements and transposons, and this may have enabled the recipient bacteria to colonise sucrose-rich environmental niches.}, }
@article {pmid15659675, year = {2005}, author = {Moore, BC and Leigh, JA}, title = {Markerless mutagenesis in Methanococcus maripaludis demonstrates roles for alanine dehydrogenase, alanine racemase, and alanine permease.}, journal = {Journal of bacteriology}, volume = {187}, number = {3}, pages = {972-979}, pmid = {15659675}, issn = {0021-9193}, support = {R01 GM055255/GM/NIGMS NIH HHS/United States ; R01 GM060403/GM/NIGMS NIH HHS/United States ; GM55255/GM/NIGMS NIH HHS/United States ; GM60403/GM/NIGMS NIH HHS/United States ; }, mesh = {Alanine/metabolism ; Alanine Dehydrogenase ; Alanine Racemase/genetics/*metabolism ; Amino Acid Oxidoreductases/genetics/*metabolism ; Amino Acid Transport Systems/genetics/*metabolism ; Ammonia/metabolism ; Archaeal Proteins/genetics/metabolism ; Base Sequence ; DNA Primers ; Methanococcus/*enzymology/*genetics ; Phylogeny ; Plasmids ; Restriction Mapping ; Stereoisomerism ; }, abstract = {Among the archaea, Methanococcus maripaludis has the unusual ability to use L- or D-alanine as a nitrogen source. To understand how this occurs, we tested the roles of three adjacent genes encoding homologs of alanine dehydrogenase, alanine racemase, and alanine permease. To produce mutations in these genes, we devised a method for markerless mutagenesis that builds on previously established genetic tools for M. maripaludis. The technique uses a negative selection strategy that takes advantage of the ability of the M. maripaludis hpt gene encoding hypoxanthine phosphoribosyltransferase to confer sensitivity to the base analog 8-azahypoxanthine. In addition, we developed a negative selection method to stably incorporate constructs into the genome at the site of the upt gene encoding uracil phosphoribosyltransferase. Mutants with in-frame deletion mutations in the genes for alanine dehydrogenase and alanine permease lost the ability to grow on either isomer of alanine, while a mutant with an in-frame deletion mutation in the gene for alanine racemase lost only the ability to grow on D-alanine. The wild-type gene for alanine dehydrogenase, incorporated into the upt site, complemented the alanine dehydrogenase mutation. Hence, the permease is required for the transport of either isomer, the dehydrogenase is specific for the L isomer, and the racemase converts the D isomer to the L isomer. Phylogenetic analysis indicated that all three genes had been acquired by lateral gene transfer from the low-moles-percent G+C gram-positive bacteria.}, }
@article {pmid15658983, year = {2005}, author = {Favre-Bonté, S and Ranjard, L and Colinon, C and Prigent-Combaret, C and Nazaret, S and Cournoyer, B}, title = {Freshwater selenium-methylating bacterial thiopurine methyltransferases: diversity and molecular phylogeny.}, journal = {Environmental microbiology}, volume = {7}, number = {2}, pages = {153-164}, doi = {10.1111/j.1462-2920.2004.00670.x}, pmid = {15658983}, issn = {1462-2912}, mesh = {Aeromonas ; Bacteria/*enzymology/genetics ; Base Sequence ; Bordetella ; Consensus Sequence ; DNA, Bacterial/chemistry/isolation &amp; purification ; Escherichia coli Proteins/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Variation ; Methyltransferases/*genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Tertiary/genetics ; Selenium/*metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology ; Water Microbiology ; }, abstract = {The diversity of bacterial thiopurine methyltransferases (bTPMT) among five natural Se-methylating freshwaters was investigated by polymerase chain reaction (PCR) screenings and sequencings. DNA sequence analyses confirmed the cloned products' identity and revealed a broad diversity of freshwater TPMTs. Neighbour-joining (NJ) phylogenetic analyses combining these sequences, all GenBank entries closely related to these sequences and deduced TPMTs obtained in this work from selected gamma-proteobacteria showed TPMTs to form a distinct radiation, closely related to UbiG methyltransferases. Inside the TPMT phylogenetic cluster, eukaryote sequences diverged early from the bacterial ones, and all the bacterial database entries belonged to a subgroup of gamma-proteobacteria, with an apparent lateral transfer of a particular allele to beta-proteobacteria of Bordetella. The NJ phylogenetic tree revealed 22 bTPMT lineages, 10 of which harboured freshwater sequences. All lineages showed deep and long branches indicative of major genetic drifts outside regions encoding highly conserved domains. Selected residues among these highly variable domains could reflect adaptations for particular ecological niches. PCR lineage-specific primers differentiated Se-methylating freshwaters according to their 'tpm lineage' signatures. Most freshwater tpm alleles were found to be distinct from those available in the databases, but a group of tpm was found encoding TPMTs identical to an Aeromonas veronii TPMT characterized in this work.}, }
@article {pmid15653627, year = {2005}, author = {Dufraigne, C and Fertil, B and Lespinats, S and Giron, A and Deschavanne, P}, title = {Detection and characterization of horizontal transfers in prokaryotes using genomic signature.}, journal = {Nucleic acids research}, volume = {33}, number = {1}, pages = {e6}, pmid = {15653627}, issn = {1362-4962}, mesh = {Bacillus subtilis/genetics ; Computational Biology ; Escherichia coli/genetics ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomics/*methods ; Haemophilus influenzae/genetics ; }, abstract = {Horizontal DNA transfer is an important factor of evolution and participates in biological diversity. Unfortunately, the location and length of horizontal transfers (HTs) are known for very few species. The usage of short oligonucleotides in a sequence (the so-called genomic signature) has been shown to be species-specific even in DNA fragments as short as 1 kb. The genomic signature is therefore proposed as a tool to detect HTs. Since DNA transfers originate from species with a signature different from those of the recipient species, the analysis of local variations of signature along recipient genome may allow for detecting exogenous DNA. The strategy consists in (i) scanning the genome with a sliding window, and calculating the corresponding local signature (ii) evaluating its deviation from the signature of the whole genome and (iii) looking for similar signatures in a database of genomic signatures. A total of 22 prokaryote genomes are analyzed in this way. It has been observed that atypical regions make up approximately 6% of each genome on the average. Most of the claimed HTs as well as new ones are detected. The origin of putative DNA transfers is looked for among approximately 12 000 species. Donor species are proposed and sometimes strongly suggested, considering similarity of signatures. Among the species studied, Bacillus subtilis, Haemophilus Influenzae and Escherichia coli are investigated by many authors and give the opportunity to perform a thorough comparison of most of the bioinformatics methods used to detect HTs.}, }
@article {pmid15651686, year = {2004}, author = {Zhu, XY}, title = {Phylogenetic analysis indicates bacteria-to-apicoplast lateral gene transfer.}, journal = {Yi chuan xue bao = Acta genetica Sinica}, volume = {31}, number = {11}, pages = {1316-1320}, pmid = {15651686}, issn = {0379-4172}, mesh = {Animals ; Apicomplexa/classification/*genetics ; Bacteria/classification/*genetics ; Bacterial Proteins/genetics ; *Gene Transfer, Horizontal ; Heat-Shock Proteins/genetics ; Phylogeny ; }, abstract = {Apicomplexan protozoa contains a highly reduced plastid-like organelle termed apicoplast. Data from clpC gene in apicoplast and their homologs in other plastids and bacteria were used to reconstruct phylogeny of apicoplast. Trees were reconstructed using neighbor-joining, minimum evolution, maximum parsimony and maximum likelihood. The reconstructions robustly support the monophyly of apicoplast and B. burgdorferi. This result underpins the mixture-genome hypotheses of apicoplast, furthermore, provides a new insight into the origin of this mixture genome.}, }
@article {pmid15651661, year = {2004}, author = {Stavskiĭ, EA and Grishaeva, ON and Leliak, AI and Larina, NM and Timukina, MA and Mit'ko, LV and Koval', RS and Serebrov, VV and Renau, IV and Kul'tenko, OV}, title = {[Experimental evaluation of possible transmission of human alpha-2 interferon artificial gene to the other microorganism species].}, journal = {Vestnik Rossiiskoi akademii meditsinskikh nauk}, volume = {}, number = {11}, pages = {29-32}, pmid = {15651661}, issn = {0869-6047}, mesh = {Agriculture ; Animals ; Bacillus subtilis/*genetics/*isolation &amp; purification ; Cattle ; Cattle Diseases/drug therapy ; *Gene Transfer, Horizontal ; Humans ; Interferon alpha-2 ; Interferon-alpha/*genetics ; Leukocytes/metabolism ; Plasmids/isolation &amp; purification ; Polymerase Chain Reaction ; Probiotics/therapeutic use ; Recombinant Proteins ; Soil/*analysis ; *Soil Microbiology ; }, abstract = {Described within the case study are experimental evaluation data on the remote results of introduction of gene-engineered microorganisms (GEM) of the B-7092 B. subtilis strain into the environment with the follow-up ranging from 1 to 7 years. No bacteria of the above GEM were detected (among selected 19 bacterial cultures) in soil samples from an agricultural farm, where the VETOM 1.1 probiotic was used for the treatment and prevention of cattle; primary and precise identification (two-round PCR with specific primers) was applied. The introduction of the B-7092 B. subtilis strain into the environment did not result in its unlimited growth and proliferation in soil. No transfer of plasmid genes (genes of leukocytic human alpha-2 interferon) from the B-7092 B. subtilis strain GEM to microorganism species available in the environment (soil) was registered. No recombinant plasmid DNA from lysed GEM cells was detected in soil samples.}, }
@article {pmid15648151, year = {2004}, author = {Radchenko, OA}, title = {[Introgressive hybridization off chars of the genus Salvelinus as inferred from mitocchondrial DNA variation].}, journal = {Genetika}, volume = {40}, number = {12}, pages = {1678-1685}, pmid = {15648151}, issn = {0016-6758}, mesh = {Animals ; Cytochromes b/*genetics ; DNA, Mitochondrial/*genetics ; Gene Transfer, Horizontal/*genetics ; *Genetic Variation ; *Hybridization, Genetic ; Phylogeny ; Trout/*genetics ; }, abstract = {Nucleotide sequence analysis of the mitochondrial cyttochrome b gene in the genus Salvelinus revealed hybrids with S. leucomaenis in S. malma malma populations ofthe Northern Okhotsk Sea basin. Hybrids of S. m. malma and S. m. krascheninnikovi were found in S. m. malma populations from the Northern Okhotsk Sea basin and Kamchatka. The findings testify to a secondary contact and mtDNA transfer between these species and forms. It was assumed that introgressive hybridization took place both long ago and relatively recently and occurred in one direction: from S. leucomaenis or S. m. krascheninnikovi to S. m. malma.}, }
@article {pmid15648147, year = {2004}, author = {Mezhzherin, SV and Morozov-leonov, SIu and Nekrasova, OD}, title = {[Natural transfer of nuclear genes in hybrid populations of green frogs Rana esculenta L., 1758 complex: space-time analysis of the phenomenon].}, journal = {Genetika}, volume = {40}, number = {12}, pages = {1646-1653}, pmid = {15648147}, issn = {0016-6758}, mesh = {*Alleles ; Animals ; Biological Evolution ; Chimera/*genetics ; *Crosses, Genetic ; Gene Transfer, Horizontal/*genetics ; Isoenzymes/*genetics ; L-Lactate Dehydrogenase/*genetics ; Rana esculenta ; Rana ridibunda ; }, abstract = {Spatial and temporal analysis of frequency distribution patterns of the Rana esculenta (=lessonae)-specific allele, Ldh-B71, in the populations and individuals of R. ridibunda from the Middle Dnieper region was performed. It was established that the allele was accumulated in the populations of Kiev, where on average 15 to 25% of individuals steadily preserved this allele through at least three to four generations. Furthermore, the allele frequency in juveniles and adults was similar. These findings suggest that the frogs carrying foreign genetic material were not eliminated from the populations, and hence, the observed introduction of foreign genes was adaptively neutral. The transfer of the genetic material from one species to another may be considered as a possible mechanism of the formation of an additional source for population genetic variation, which, however, do not seems to be evolutionary progressive.}, }
@article {pmid15644918, year = {2004}, author = {Chan, YK and McCormick, WA}, title = {Experimental evidence for plasmid-borne nor-nir genes in Sinorhizobium meliloti JJ1c10.}, journal = {Canadian journal of microbiology}, volume = {50}, number = {9}, pages = {657-667}, doi = {10.1139/w04-062}, pmid = {15644918}, issn = {0008-4166}, mesh = {Amino Acid Sequence ; Bacterial Proteins/*genetics/metabolism ; Blotting, Southern ; Conjugation, Genetic ; Escherichia coli/genetics ; Molecular Sequence Data ; Nitric Oxide/metabolism ; Nitrite Reductases/*genetics/metabolism ; Nitrites/metabolism ; Oxidation-Reduction ; Oxidoreductases/*genetics/metabolism ; *Plasmids ; Sequence Analysis, DNA ; Sinorhizobium meliloti/enzymology/genetics ; }, abstract = {In denitrification, nir and nor genes are respectively required for the sequential dissimilatory reduction of nitrite and nitric oxide to form nitrous oxide. Their location on the pSymA megaplasmid of Sinorhizobium meliloti was confirmed by Southern hybridization of its clones with specific structural gene probes for nirK and norCB. A 20-kb region of pSymA containing the nor-nir genes was delineated by nucleotide sequence analysis. These genes were linked to the nap genes encoding periplasmic proteins involved in nitrate reduction. The nor-nir-nap segment is situated within 30 kb downstream from the nos genes encoding nitrous oxide reduction, with a fix cluster intervening between nir and nos. Most of these predicted nor-nir and accessory gene products are highly homologous with those of related proteobacterial denitrifiers. Functional tests of Tn5 mutants confirmed the requirement of the nirV product and 1 unidentified protein for nitrite reduction as well as the norB-D products and another unidentified protein for nitric oxide reduction. Overall comparative analysis of the derived amino acid sequences of the S. meliloti gene products suggested a close relationship between this symbiotic N2 fixer and the free-living non-N2-fixing denitrifier Pseudomonas G-179, despite differences in their genetic organization. This relationship may be due to lateral gene transfer of denitrification genes from a common donor followed by rearrangement and recombination of these genes.}, }
@article {pmid15640200, year = {2005}, author = {Wilson, MM and Metcalf, WW}, title = {Genetic diversity and horizontal transfer of genes involved in oxidation of reduced phosphorus compounds by Alcaligenes faecalis WM2072.}, journal = {Applied and environmental microbiology}, volume = {71}, number = {1}, pages = {290-296}, pmid = {15640200}, issn = {0099-2240}, support = {R01 GM059334/GM/NIGMS NIH HHS/United States ; T32 GM007283/GM/NIGMS NIH HHS/United States ; GM59334/GM/NIGMS NIH HHS/United States ; T32 GM07283/GM/NIGMS NIH HHS/United States ; }, mesh = {Alcaligenes faecalis/enzymology/*genetics/metabolism ; Animals ; Bacterial Proteins/*genetics ; DNA Transposable Elements ; Dioxygenases/genetics/metabolism ; Gene Deletion ; *Gene Transfer, Horizontal ; *Genetic Variation ; Molecular Sequence Data ; Mutagenesis, Insertional ; NADH, NADPH Oxidoreductases/genetics/metabolism ; Oxidation-Reduction ; Phosphites/*metabolism ; Sequence Analysis, DNA ; }, abstract = {Enrichment was performed to isolate organisms that could utilize reduced phosphorus compounds as their sole phosphorus sources. One isolate that grew well with either hypophosphite or phosphite was identified by 16S rRNA gene analysis as a strain of Alcaligenes faecalis. The genes required for oxidation of hypophosphite and phosphite by this organism were identified by using transposon mutagenesis and include homologs of the ptxD and htxA genes of Pseudomonas stutzeri WM88, which encode an NAD-dependent phosphite dehydrogenase (PtxD) and 2-oxoglutarate-dependent hypophosphite dioxygenase (HtxA). This organism also has the htxB, htxC, and htxD genes that comprise an ABC-type transporter, presumably for hypophosphite and phosphite transport. The role of these genes in reduced phosphorus metabolism was confirmed by analyzing the growth of mutants in which these genes were deleted. Sequencing data showed that htxA, htxB, htxC, and htxD are virtually identical to their homologs in P. stutzeri at the DNA level, indicating that horizontal gene transfer occurred. However, A. faecalis ptxD is very different from its P. stutzeri homolog and represents a new ptxD lineage. Therefore, this gene has ancient evolutionary roots in bacteria. These data suggest that there is strong evolutionary selection for the ability of microorganisms to oxidize hypophosphite and phosphite.}, }
@article {pmid15640169, year = {2005}, author = {Pinedo, CA and Smets, BF}, title = {Conjugal TOL transfer from Pseudomonas putida to Pseudomonas aeruginosa: effects of restriction proficiency, toxicant exposure, cell density ratios, and conjugation detection method on observed transfer efficiencies.}, journal = {Applied and environmental microbiology}, volume = {71}, number = {1}, pages = {51-57}, pmid = {15640169}, issn = {0099-2240}, mesh = {Colony Count, Microbial ; *Conjugation, Genetic ; DNA Restriction Enzymes/metabolism ; DNA, Bacterial/genetics/metabolism ; *Gene Transfer, Horizontal ; Green Fluorescent Proteins/genetics/metabolism ; *Plasmids ; Pseudomonas aeruginosa/drug effects/*genetics/growth &amp; development ; Pseudomonas putida/*genetics/growth &amp; development ; Solvents/pharmacology ; Toluene/metabolism/pharmacology ; }, abstract = {The effects of restriction proficiency and premating exposure to toxicants on conjugal transfer of the TOL plasmid between Pseudomonas spp. was investigated by examinations of filter matings. A Pseudomonas putida KT2442-derived strain carrying a gfp-tagged variant of the TOL plasmid was used as a donor, and both restriction-deficient (PAO1162N) and -proficient (PAO2002N) Pseudomonas aeruginosa strains were used as recipients. The in situ enumeration of conjugation events allowed us to obtain frequency estimates that were unbiased by transconjugant growth or plasmid retransfer. We observed a strong dependence of the plasmid transfer frequency on the initial donor-to-recipient ratio of surface matings, which invalidated the use of mass action-based plasmid transfer kinetic estimators. Careful control of the initial parental cell densities permitted evaluations of the true effects of restriction proficiency and toxicant exposure on TOL transfer. At standard donor-to-recipient ratios (10(-3) for PAO1162N and 2 x 10(1) for PAO2002N) and total cell densities (10(5) cells/mm(2) for PAO1162N and 10(6) cells/mm(2) for PAO2002N), plasmid transfer frequencies without toxicant exposure were approximately 10(-7) (events/mm(2))(-1) for PAO1162N and 10(-11) (events/mm(2))(-1) for PAO2002N based on in situ observations of conjugation events. The enumeration of transconjugants via selective plating yielded transfer frequencies that were up to 1 order of magnitude lower. Premating exposure to sodium dodecyl sulfate (1 to 10 mM) significantly increased the transfer frequency for the restriction-proficient strain PAO2002N (P < 0.05) but not for the restriction-deficient strain PAO1162N. On the other hand, premating exposure to ethanol, toluene, or phenol had no positive effect on the plasmid transfer frequency. Clearly, restriction proficiency provides a strong barrier to interspecific transfer of the TOL plasmid, and this barrier was only marginally attenuated by recipient exposure to toxicants within the ranges examined.}, }
@article {pmid15640168, year = {2005}, author = {Corinaldesi, C and Danovaro, R and Dell'Anno, A}, title = {Simultaneous recovery of extracellular and intracellular DNA suitable for molecular studies from marine sediments.}, journal = {Applied and environmental microbiology}, volume = {71}, number = {1}, pages = {46-50}, pmid = {15640168}, issn = {0099-2240}, mesh = {DNA, Bacterial/chemistry/genetics/*isolation &amp; purification ; Genes, rRNA ; Geologic Sediments/*chemistry/*microbiology ; Immunoblotting ; Nucleic Acid Hybridization/methods ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/chemistry/genetics/isolation &amp; purification ; Seawater/chemistry/microbiology ; }, abstract = {The occurrence of high extracellular DNA concentrations in aquatic sediments (concentrations that are 3 to 4 orders of magnitude greater than those in the water column) might play an important role in biogeochemical cycling, as well as in horizontal gene transfer through natural transformation. Since isolation of extracellular DNA from sediments is a difficult and unsolved task, in this study we developed an efficient procedure to recover simultaneously DNA associated with microbial cells and extracellular DNA from the same sediment sample. This procedure is specifically suitable for studying extracellular DNA because it avoids any contamination with DNA released by cell lysis during handling and extraction. Applying this procedure to different sediment types, we obtained extracellular DNA concentrations that were about 10 to 70 times higher than the intracellular DNA concentrations. Using specific targeted prokaryotic primers, we obtained evidence that extracellular DNA recovered from different sediments did not contain amplifiable 16S rRNA genes. By contrast, using DNA extracted from microbial cells as the template, we always amplified 16S rRNA genes. Although 16S rRNA genes were not detected in extracellular DNA, analyses of the sizes of extracellular DNA indicated the presence of high-molecular-weight fragments that might have contained other gene sequences. This protocol allows investigation of extracellular DNA and its possible participation in natural transformation processes.}, }
@article {pmid15639945, year = {2003}, author = {Ou, JH and Xie, ZX and Chen, XD and Ni, LN and Shen, P}, title = {[Horizontal gene transfer].}, journal = {Yi chuan = Hereditas}, volume = {25}, number = {5}, pages = {623-627}, pmid = {15639945}, issn = {0253-9772}, abstract = {In this paper the conception of horizontal gene transfer (HGT) was introduced,and main mode of HGT was also enumerated as follows: HGT by medium such as plasmid and virus etc., and the HGT without any medium. The transfer of genes from one species to another especially between remote species was emphasized by the information from genome sequencing. The problems about evolution phylogenies and safety of GEMs (gene engineered microorganisms) for HGT were discussed.}, }
@article {pmid15639630, year = {2005}, author = {Fux, CA and Costerton, JW and Stewart, PS and Stoodley, P}, title = {Survival strategies of infectious biofilms.}, journal = {Trends in microbiology}, volume = {13}, number = {1}, pages = {34-40}, doi = {10.1016/j.tim.2004.11.010}, pmid = {15639630}, issn = {0966-842X}, support = {R01 GM60052-02/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Physiological ; Bacterial Infections/*microbiology ; Biofilms/drug effects/*growth &amp; development ; Drug Resistance, Bacterial ; Gene Expression Regulation, Bacterial ; Genomics ; Plankton ; Proteomics ; }, abstract = {Modern medicine is facing the spread of biofilm-related infections. Bacterial biofilms are difficult to detect in routine diagnostics and are inherently tolerant to host defenses and antibiotic therapies. In addition, biofilms facilitate the spread of antibiotic resistance by promoting horizontal gene transfer. We review current concepts of biofilm tolerance with special emphasis on the role of the biofilm matrix and the physiology of biofilm-embedded cells. The heterogeneity in metabolic and reproductive activity within a biofilm correlates with a non-uniform susceptibility of enclosed bacteria. Recent studies have documented similar heterogeneity in planktonic cultures. Nutritional starvation and high cell density, two key characteristics of biofilm physiology, also mediate antimicrobial tolerance in stationary-phase planktonic cultures. Advances in characterizing the role of stress response genes, quorum sensing and phase variation in stationary-phase planktonic cultures have shed new light on tolerance mechanisms within biofilm communities.}, }
@article {pmid15638844, year = {2004}, author = {Oelschlaeger, TA and Hacker, J}, title = {Impact of pathogenicity islands in bacterial diagnostics.}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {112}, number = {11-12}, pages = {930-936}, doi = {10.1111/j.1600-0463.2004.apm11211-1214.x}, pmid = {15638844}, issn = {0903-4641}, mesh = {Bacteria/*genetics/isolation &amp; purification/*pathogenicity ; Bacterial Infections/*diagnosis/*microbiology ; Drug Resistance, Bacterial/genetics ; Genome, Bacterial ; *Genomic Islands ; Genomics/methods ; Humans ; Virulence/genetics ; }, abstract = {Pathogenicity islands (PAIs) are a distinct class of genomic islands (GEIs), which are acquired by horizontal gene transfer. PAIs harbour virulence genes and some, in addition, antibiotic resistance genes. More often genes conferring antibiotic resistance are encoded by GEIs not containing virulence genes. Both types of genetic elements are found in genomes of various human, animal and plant pathogens. There are PAIs and GEIs which are specific for a certain serotype(s), strain, or pathotype of a species. Furthermore, there are also PAIs which are more widespread and found in bacterial pathogens causing a certain pathogenic effect in the host. Even the lack of a certain PAI might be characteristic for a defined subspecies. Obviously, PAIs can be used as markers for diagnostic purposes to help identify a certain bacterial pathogen, subtype it, estimate the pathogenic potential, and in some cases predict its antibiotic resistance. This all might be achieved for known PAIs/GEIs without cultivating the microorganism of interest by employing PCR and/or DNA-chip technology. Even yet unknown PAIs can be identified in silico if the genome sequence of the bacterial pathogen under investigation is known. The more PAIs and antibiotic harbouring GEIs are identified and characterized the greater will be the benefits also for diagnostics.}, }
@article {pmid15636742, year = {2005}, author = {Llosa, M and de la Cruz, F}, title = {Bacterial conjugation: a potential tool for genomic engineering.}, journal = {Research in microbiology}, volume = {156}, number = {1}, pages = {1-6}, doi = {10.1016/j.resmic.2004.07.008}, pmid = {15636742}, issn = {0923-2508}, mesh = {Bacteria/*genetics ; *Conjugation, Genetic ; DNA, Bacterial/genetics/metabolism ; *Gene Transfer, Horizontal ; Genetic Engineering/*methods ; }, abstract = {Bacterial conjugation is a mechanism for horizontal DNA transfer with potential for universal DNA delivery. The conjugal machinery can be separated into three functional modules: the relaxosome, the coupling protein, and a type IV protein secretion system. Module interchangeability among different conjugative systems opens up the possibility of "a la carte" engineering of DNA delivery into virtually any cell type.}, }
@article {pmid15631950, year = {2005}, author = {Wegrzyn, G}, title = {What does "plasmid biology" currently mean? Summary of the Plasmid Biology 2004 Meeting.}, journal = {Plasmid}, volume = {53}, number = {1}, pages = {14-22}, doi = {10.1016/j.plasmid.2004.10.002}, pmid = {15631950}, issn = {0147-619X}, mesh = {Biological Evolution ; DNA Replication ; Ecology ; Gene Transfer, Horizontal ; Genomics ; Pathology, Veterinary ; Plasmids/genetics/*physiology ; }, abstract = {Almost 200 scientists from America, Europe, Asia, Australia, and Africa participated in the Plasmid Biology 2004 meeting, which was organized between 15th and 21st September 2004 in Kanoni (Corfu island), Greece. Various aspects of biology of plasmids and other mobile genetic elements were discussed during the meeting, including problems of replication, transfer, stable inheritance, and evolution. Medical and veterinary aspects of plasmids were highlighted as well as other applications of these replicons. It appears that plasmids and other mobile genetic elements are still excellent models in studies of basic biological problems at the molecular level, and their role in medicine and genetic engineering can be enormous. Moreover, studies on ecology of plasmids provide extremely important data that can be used in environment protection as well as in biotechnology. Understanding the importance of studies on plasmids and other mobile genetic elements, participants of the meeting decided to establish the International Society for Plasmid Biology.}, }
@article {pmid15630422, year = {2005}, author = {Allers, T and Mevarech, M}, title = {Archaeal genetics - the third way.}, journal = {Nature reviews. Genetics}, volume = {6}, number = {1}, pages = {58-73}, doi = {10.1038/nrg1504}, pmid = {15630422}, issn = {1471-0056}, mesh = {Archaea/*genetics ; Gene Transfer Techniques ; Gene Transfer, Horizontal ; Genes, Archaeal ; Genetic Markers ; *Genome, Archaeal ; Mutagenesis ; Phylogeny ; Plasmids ; }, abstract = {For decades, archaea were misclassified as bacteria because of their prokaryotic morphology. Molecular phylogeny eventually revealed that archaea, like bacteria and eukaryotes, are a fundamentally distinct domain of life. Genome analyses have confirmed that archaea share many features with eukaryotes, particularly in information processing, and therefore can serve as streamlined models for understanding eukaryotic biology. Biochemists and structural biologists have embraced the study of archaea but geneticists have been more wary, despite the fact that genetic techniques for archaea are quite sophisticated. It is time for geneticists to start asking fundamental questions about our distant relatives.}, }
@article {pmid15629034, year = {2003}, author = {Hu, J and Wang, J and Xu, J and Li, W and Han, Y and Li, Y and Ji, J and Ye, J and Xu, Z and Zhang, Z and Wei, W and Li, S and Wang, J and Wang, J and Yu, J and Yang, H}, title = {Evolution and variation of the SARS-CoV genome.}, journal = {Genomics, proteomics &amp; bioinformatics}, volume = {1}, number = {3}, pages = {216-225}, pmid = {15629034}, issn = {1672-0229}, mesh = {Amino Acid Motifs ; Amino Acid Substitution ; Base Composition ; Codon/genetics ; Computational Biology ; DNA Mutational Analysis ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Variation ; *Genome, Viral ; Phylogeny ; Severe acute respiratory syndrome-related coronavirus/*genetics ; }, abstract = {Knowledge of the evolution of pathogens is of great medical and biological significance to the prevention, diagnosis, and therapy of infectious diseases. In order to understand the origin and evolution of the SARS-CoV (severe acute respiratory syndrome-associated coronavirus), we collected complete genome sequences of all viruses available in GenBank, and made comparative analyses with the SARS-CoV. Genomic signature analysis demonstrates that the coronaviruses all take the TGTT as their richest tetranucleotide except the SARS-CoV. A detailed analysis of the forty-two complete SARS-CoV genome sequences revealed the existence of two distinct genotypes, and showed that these isolates could be classified into four groups. Our manual analysis of the BLASTN results demonstrates that the HE (hemagglutinin-esterase) gene exists in the SARS-CoV, and many mutations made it unfamiliar to us.}, }
@article {pmid15628527, year = {2004}, author = {Ikeda, T and Watanabe, T and Matsumoto, K and Murayama, SY and Koshio, O and Tansho, S and Ono, Y}, title = {[Transferability of vanA gene from vancomycin-resistant Enterococcus faecalis in the digestive tract of specific pathogen-free mice].}, journal = {Kansenshogaku zasshi. The Journal of the Japanese Association for Infectious Diseases}, volume = {78}, number = {11}, pages = {952-958}, doi = {10.11150/kansenshogakuzasshi1970.78.952}, pmid = {15628527}, issn = {0387-5911}, mesh = {Animals ; Bacterial Proteins/*genetics ; Carbon-Oxygen Ligases/*genetics ; Digestive System/microbiology ; Enterococcus faecalis/drug effects/*genetics/isolation &amp; purification ; Female ; *Gene Transfer, Horizontal ; Mice ; Mice, Inbred Strains ; Vancomycin Resistance/*genetics ; }, abstract = {We evaluated the transferability of vanA gene from vancomycin-resistant Enterococcus faecalis (VREF) to vancomycin-sensitive E. faecalis (VSEF) in vitro and in vivo. In vitro conjugal transfer experiment by filter mating, the vanA gene of VREF was transferable at the high frequency to VSEF and a mutant strain which cured vanA gene of VREF. In vivo studies in the digestive tract of specific pathogen-free mice pretreated with oral antibiotics, transconjugants were also detected from the feces of a mouse at the lower frequency. However, the colonization of transconjugants was transient. The vanA gene in the donor and the transconjugant strain was confirmed by using a polymerase chain reaction method. These results suggest that VSEF colonizing in the human digestive tract might be developed to VREF by transferring of the vanA gene.}, }
@article {pmid15621658, year = {2004}, author = {Tamegai, H and Kato, C and Horikoshi, K}, title = {Lateral gene transfer in the deep sea of Mariana Trench: identification of nar gene cluster encoding membrane-bound nitrate reductase from Pseudomonas sp. strain MT-1.}, journal = {DNA sequence : the journal of DNA sequencing and mapping}, volume = {15}, number = {5-6}, pages = {338-343}, doi = {10.1080/10425170400009293}, pmid = {15621658}, issn = {1042-5179}, mesh = {Amino Acid Sequence ; Base Sequence ; Cloning, Molecular ; Cluster Analysis ; Gene Components ; Gene Transfer, Horizontal/*genetics ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Multigene Family/*genetics ; Nitrate Reductase ; Nitrate Reductases/*genetics ; Pacific Ocean ; *Phylogeny ; Pseudomonas/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {The genes encoding membrane-bound nitrate reductase and its locus from Pseudomonas sp. strain MT-1, which is isolated from the sediment of Mariana Trench, were identified. To some extent, the gene organization in the cluster was different from those of other Pseudomonads. Quite interestingly, two genes encoding putative nitrate transporter (narK and narM) showed higher homologies to counterparts of organisms belonging to other genera than those of Pseudomonads. Especially, narM showed no significant homology to the genes for nitrate transporter of Pseudomonads, and was homologous to those of some marine bacteria. Further, arrangements of NarL- and Fnr-binding motifs in the cluster were different from those of P. stutzeri, closely related strain with MT-1. These observations clearly indicated that lateral transfer of genes in nar gene cluster had occurred in deep sea, and it may contribute to bacterial adaptation to environment of there.}, }
@article {pmid15621428, year = {2005}, author = {Coenye, T and Vandamme, P}, title = {Organisation of the S10, spc and alpha ribosomal protein gene clusters in prokaryotic genomes.}, journal = {FEMS microbiology letters}, volume = {242}, number = {1}, pages = {117-126}, doi = {10.1016/j.femsle.2004.10.050}, pmid = {15621428}, issn = {0378-1097}, mesh = {Bacteria/classification/*genetics ; Bacterial Proteins/genetics ; Computational Biology ; Evolution, Molecular ; *Gene Order ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genes, rRNA ; *Genome, Bacterial ; Multigene Family ; *Operon ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Ribosomal Proteins/*genetics ; }, abstract = {Although it is well known that there is no long range colinearity in gene order in bacterial genomes, it is thought that there are several regions that are under strong structural constraints during evolution, in which gene order is extremely conserved. One such region is the str locus, containing the S10-spc-alpha operons. These operons contain genes coding for ribosomal proteins and for a number of housekeeping genes. We compared the organisation of these gene clusters in 111 sequenced prokaryotic genomes (99 bacterial and 12 archaeal genomes). We also compared the organisation to the phylogeny based on 16S ribosomal RNA gene sequences and the sequences of the ribosomal proteins L22, L16 and S14. Our data indicate that there is much variation in gene order and content in these gene clusters, both in bacterial as well as in archaeal genomes. Our data indicate that differential gene loss has occurred on multiple occasions during evolution. We also noted several discrepancies between phylogenetic trees based on 16S rRNA gene sequences and sequences of ribosomal proteins L16, L22 and S14, suggesting that horizontal gene transfer did play a significant role in the evolution of the S10-spc-alpha gene clusters.}, }
@article {pmid15620826, year = {2005}, author = {Corso, A and Faccone, D and Gagetti, P and Togneri, A and Lopardo, H and Melano, R and Rodríguez, V and Rodriguez, M and Galas, M}, title = {First report of VanA Enterococcus gallinarum dissemination within an intensive care unit in Argentina.}, journal = {International journal of antimicrobial agents}, volume = {25}, number = {1}, pages = {51-56}, doi = {10.1016/j.ijantimicag.2004.07.014}, pmid = {15620826}, issn = {0924-8579}, mesh = {Anti-Bacterial Agents/pharmacology ; Argentina/epidemiology ; Bacterial Proteins/*genetics ; Carbon-Oxygen Ligases/*genetics ; *Conjugation, Genetic ; DNA Transposable Elements ; Deoxyribonucleases, Type II Site-Specific/metabolism ; Electrophoresis, Gel, Pulsed-Field ; Enterococcus/classification/*drug effects/genetics ; Gene Transfer, Horizontal ; Gram-Positive Bacterial Infections/*epidemiology/microbiology ; Humans ; *Intensive Care Units ; Male ; Microbial Sensitivity Tests ; Middle Aged ; Peptide Synthases/genetics ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Population Surveillance ; Vancomycin/pharmacology ; *Vancomycin Resistance/genetics ; }, abstract = {Enterococcusgallinarum is intrinsically resistant to low levels of vancomycin and has been described as a colonizing microorganism causing bacteraemia and infection among immunosupresed patients. Between August 2000 and February 2001, 15 highly glycopeptide-resistant E. gallinarum isolates, one from blood and the remaining from rectal swabs, were recovered in a general hospital of Buenos Aires Province, Argentina. All isolates were characterized by biochemical assays, and displayed MICs of vancomycin in the range 16-128 mg/l and MICs of teicoplanin in the range 16-32 mg/l. In all cases, PCR analysis yield positive results for both vanC1 and vanA genes. E. gallinarum isolates were classified as two clonal types by SmaI-PFGE: clone A (n = 8) and clone B (n = 7) and both harboured a transferable vanA element.}, }
@article {pmid15620637, year = {2004}, author = {Nisbet, RE and Kilian, O and McFadden, GI}, title = {Diatom genomics: genetic acquisitions and mergers.}, journal = {Current biology : CB}, volume = {14}, number = {24}, pages = {R1048-50}, doi = {10.1016/j.cub.2004.11.043}, pmid = {15620637}, issn = {0960-9822}, mesh = {Cryptophyta/genetics ; Diatoms/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; *Genome ; Plastids/genetics ; *Symbiosis ; }, abstract = {Diatom algae arose by two-step endosymbiosis. The complete genome of the diatom Thalassiosira pseudonana has now been sequenced, allowing us to reconstruct the remarkable intracellular gene transfers that occurred during this convoluted cellular evolution.}, }
@article {pmid15619448, year = {2005}, author = {Briones, C and Manrubia, SC and Lázaro, E and Lazcano, A and Amils, R}, title = {Reconstructing evolutionary relationships from functional data: a consistent classification of organisms based on translation inhibition response.}, journal = {Molecular phylogenetics and evolution}, volume = {34}, number = {2}, pages = {371-381}, doi = {10.1016/j.ympev.2004.10.020}, pmid = {15619448}, issn = {1055-7903}, mesh = {Archaea/genetics ; Bacteria/genetics ; *Biological Evolution ; Data Interpretation, Statistical ; *Phylogeny ; Protein Biosynthesis/*genetics ; }, abstract = {The last two decades have witnessed an unsurpassed effort aimed at reconstructing the history of life from the genetic information contained in extant organisms. The availability of many sequenced genomes has allowed the reconstruction of phylogenies from gene families and its comparison with traditional single-gene trees. However, the appearance of major discrepancies between both approaches questions whether horizontal gene transfer (HGT) has played a prominent role in shaping the topology of the Tree of Life. Recent attempts at solving this controversy and reaching a consensus tree combine molecular data with additional phylogenetic markers. Translation is a universal cellular function that involves a meaningful, highly conserved set of genes: both rRNA and r-protein operons have an undisputed phylogenetic value and rarely undergo HGT. Ribosomal function reflects the concerted expression of that genetic network and consequently yields information about the evolutionary paths followed by the organisms. Here we report on tree reconstruction using a measure of the performance of the ribosome: antibiotic sensitivity of protein synthesis. A large database has been used where 33 ribosomal systems belonging to the three major cellular lineages were probed against 38 protein synthesis inhibitors. Different definitions of distance between pairs of organisms have been explored, and the classical algorithm of bootstrap evaluation has been adapted to quantify the reliability of the reconstructions obtained. Our analysis returns a consistent phylogeny, where archaea are systematically affiliated to eukarya, in agreement with recent reconstructions which used information-processing systems. The integration of the information derived from relevant functional markers into current phylogenetic reconstructions might facilitate achieving a consensus Tree of Life.}, }
@article {pmid15618503, year = {2004}, author = {Keeling, PJ and Archibald, JM and Fast, NM and Palmer, JD}, title = {Comment on "The evolution of modern eukaryotic phytoplankton".}, journal = {Science (New York, N.Y.)}, volume = {306}, number = {5705}, pages = {2191; author reply 2191}, doi = {10.1126/science.1103879}, pmid = {15618503}, issn = {1095-9203}, mesh = {Biodiversity ; *Biological Evolution ; Chlorophyta/genetics/physiology ; *Eukaryota/genetics/physiology ; Gene Transfer, Horizontal ; Phylogeny ; *Phytoplankton/genetics ; Plastids/genetics/physiology ; Rhodophyta/genetics/physiology ; Symbiosis ; }, }
@article {pmid15615680, year = {2004}, author = {Creevey, CJ and Fitzpatrick, DA and Philip, GK and Kinsella, RJ and O'Connell, MJ and Pentony, MM and Travers, SA and Wilkinson, M and McInerney, JO}, title = {Does a tree-like phylogeny only exist at the tips in the prokaryotes?.}, journal = {Proceedings. Biological sciences}, volume = {271}, number = {1557}, pages = {2551-2558}, pmid = {15615680}, issn = {0962-8452}, mesh = {Bacteria/*genetics ; Classification/*methods ; Gene Transfer, Horizontal/*genetics ; *Genome, Bacterial ; Likelihood Functions ; Models, Genetic ; *Phylogeny ; }, abstract = {The extent to which prokaryotic evolution has been influenced by horizontal gene transfer (HGT) and therefore might be more of a network than a tree is unclear. Here we use supertree methods to ask whether a definitive prokaryotic phylogenetic tree exists and whether it can be confidently inferred using orthologous genes. We analysed an 11-taxon dataset spanning the deepest divisions of prokaryotic relationships, a 10-taxon dataset spanning the relatively recent gamma-proteobacteria and a 61-taxon dataset spanning both, using species for which complete genomes are available. Congruence among gene trees spanning deep relationships is not better than random. By contrast, a strong, almost perfect phylogenetic signal exists in gamma-proteobacterial genes. Deep-level prokaryotic relationships are difficult to infer because of signal erosion, systematic bias, hidden paralogy and/or HGT. Our results do not preclude levels of HGT that would be inconsistent with the notion of a prokaryotic phylogeny. This approach will help decide the extent to which we can say that there is a prokaryotic phylogeny and where in the phylogeny a cohesive genomic signal exists.}, }
@article {pmid15615072, year = {2003}, author = {Smalla, K}, title = {Field releases of genetically modified micro-organisms.}, journal = {Environmental biosafety research}, volume = {2}, number = {1}, pages = {65-68}, pmid = {15615072}, issn = {1635-7922}, mesh = {Agriculture/methods ; Antifungal Agents/metabolism ; Gene Transfer, Horizontal ; Genetic Techniques ; Hybridization, Genetic ; *Organisms, Genetically Modified ; Pest Control, Biological/*methods ; Phenazines/metabolism ; Phloroglucinol/analogs &amp; derivatives/metabolism ; Plant Development ; Plants/*microbiology/parasitology ; Pseudomonas fluorescens/genetics/metabolism ; Pseudomonas putida/genetics/metabolism ; Rhizobium leguminosarum/genetics ; Rhizome/*microbiology/parasitology ; }, }
@article {pmid15615071, year = {2003}, author = {Hoy, MA}, title = {Transgenic insects for pest management programs: status and prospects.}, journal = {Environmental biosafety research}, volume = {2}, number = {1}, pages = {61-64}, pmid = {15615071}, issn = {1635-7922}, mesh = {Africa ; Animals ; *Animals, Genetically Modified ; Central America ; Ceratitis capitata/genetics ; Chagas Disease/prevention &amp; control/transmission ; Culicidae ; Gene Transfer, Horizontal ; Guidelines as Topic ; Insect Vectors ; Insecta/*genetics ; Lepidoptera/genetics ; Malaria/prevention &amp; control/transmission ; Pest Control, Biological/*methods ; Plasmodium/genetics/pathogenicity ; Rhodococcus/genetics ; Risk Assessment/legislation &amp; jurisprudence ; South America ; Transformation, Bacterial ; Trypanosoma cruzi/pathogenicity ; United States ; }, }
@article {pmid15615068, year = {2003}, author = {Alvarez-Morales, A}, title = {Possible implication of the release of transgenic crops in centers of origin or diversity.}, journal = {Environmental biosafety research}, volume = {2}, number = {1}, pages = {47-50}, pmid = {15615068}, issn = {1635-7922}, mesh = {Conservation of Natural Resources ; Crops, Agricultural/*genetics ; *Gene Transfer, Horizontal ; Genetic Variation ; Hybridization, Genetic ; Mexico ; Plants, Genetically Modified/*genetics ; Zea mays/*genetics ; }, }
@article {pmid15615067, year = {2003}, author = {Snow, AA}, title = {Consequences of gene flow.}, journal = {Environmental biosafety research}, volume = {2}, number = {1}, pages = {43-46}, pmid = {15615067}, issn = {1635-7922}, mesh = {Brassica rapa/genetics/physiology ; Crops, Agricultural/*genetics ; Drug Resistance/*genetics ; Environment ; *Gene Transfer, Horizontal ; Helianthus/genetics/physiology ; Herbicides ; Hybridization, Genetic ; Oryza/genetics/physiology ; Plants, Genetically Modified/genetics/*physiology ; Pollen/genetics/physiology ; Seeds/genetics/physiology ; Zea mays/genetics/physiology ; }, }
@article {pmid15615064, year = {2003}, author = {Jenczewski, E and Ronfort, J and Chèvre, AM}, title = {Crop-to-wild gene flow, introgression and possible fitness effects of transgenes.}, journal = {Environmental biosafety research}, volume = {2}, number = {1}, pages = {9-24}, doi = {10.1051/ebr:2003001}, pmid = {15615064}, issn = {1635-7922}, mesh = {Crops, Agricultural/*genetics ; *Gene Transfer, Horizontal ; Hybridization, Genetic ; Phenotype ; Plants, Genetically Modified/*genetics ; Pollen/genetics ; Seeds/genetics ; Transgenes/genetics/*physiology ; }, abstract = {Crop-to-wild gene flow has received close attention over the past ten years in connection with the development and cultivation of transgenic crops. In this paper, we review key examples of crop/wild sympatry and overlapping flowering phenology, pollen and seed dispersal, the barriers to hybridisation and introgression, the evolution and fate of interspecific hybrids, their fitness, and the potential cost of transgenes. We pay particular attention to ways in which the evolution and divergence between crops and their wild relatives may interfere with these successive steps. Our review suggests that crop-to-weed gene flow is highly idiosyncratic and that crop gene dispersion will certainly be very difficult to preclude totally. Future directions for research should thus focus on the long-term establishment and effects of transgenes on natural communities.}, }
@article {pmid15612919, year = {2005}, author = {Karlyshev, AV and Champion, OL and Churcher, C and Brisson, JR and Jarrell, HC and Gilbert, M and Brochu, D and St Michael, F and Li, J and Wakarchuk, WW and Goodhead, I and Sanders, M and Stevens, K and White, B and Parkhill, J and Wren, BW and Szymanski, CM}, title = {Analysis of Campylobacter jejuni capsular loci reveals multiple mechanisms for the generation of structural diversity and the ability to form complex heptoses.}, journal = {Molecular microbiology}, volume = {55}, number = {1}, pages = {90-103}, doi = {10.1111/j.1365-2958.2004.04374.x}, pmid = {15612919}, issn = {0950-382X}, support = {E20372/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacterial Capsules/chemistry/*genetics/metabolism ; Campylobacter jejuni/*genetics/metabolism ; Carbohydrate Epimerases/genetics/physiology ; Carbohydrate Sequence ; DNA, Bacterial ; Gene Duplication ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genetic Variation ; Glycosyltransferases/genetics/physiology ; Heptoses/chemistry/genetics ; Lipopolysaccharides/biosynthesis ; Molecular Sequence Data ; Multigene Family ; Phosphoric Monoester Hydrolases/genetics/physiology ; Recombination, Genetic ; Sequence Analysis, DNA ; Sequence Deletion ; }, abstract = {We recently demonstrated that Campylobacter jejuni produces a capsular polysaccharide (CPS) that is the major antigenic component of the classical Penner serotyping system distinguishing Campylobacter into >60 groups. Although the wide variety of C. jejuni serotypes are suggestive of structural differences in CPS, the genetic mechanisms of such differences are unknown. In this study we sequenced biosynthetic cps regions, ranging in size from 15 to 34 kb, from selected C. jejuni strains of HS:1, HS:19, HS:23, HS:36, HS:23/36 and HS:41 serotypes. Comparison of the determined cps sequences of the HS:1, HS:19 and HS:41 strains with the sequenced strain, NCTC11168 (HS:2), provides evidence for multiple mechanisms of structural variation including exchange of capsular genes and entire clusters by horizontal transfer, gene duplication, deletion, fusion and contingency gene variation. In contrast, the HS:23, HS:36 and HS:23/36 cps sequences were highly conserved. We report the first detailed structural analysis of 81-176 (HS:23/36) and G1 (HS:1) and refine the previous structural interpretations of the HS:19, HS:23, HS:36 and HS:41 serostrains. For the first time, we demonstrate the commonality and function of a second heptose biosynthetic pathway for Campylobacter CPS independent of the pathway for lipooligosaccharide (LOS) biosynthesis and identify a novel heptosyltransferase utilized by this alternate pathway. Furthermore, we show the retention of two functional heptose isomerases in Campylobacter and the sharing of a phosphatase for both LOS and CPS heptose biosynthesis.}, }
@article {pmid15612415, year = {2003}, author = {Alpert, CA and Mater, DD and Muller, MC and Ouriet, MF and Duval-Iflah, Y and Corthier, G}, title = {Worst-case scenarios for horizontal gene transfer from Lactococcus lactis carrying heterologous genes to Enterococcus faecalis in the digestive tract of gnotobiotic mice.}, journal = {Environmental biosafety research}, volume = {2}, number = {3}, pages = {173-180}, doi = {10.1051/ebr:2003010}, pmid = {15612415}, issn = {1635-7922}, mesh = {Animals ; Conjugation, Genetic ; DNA Transposable Elements ; Enterococcus faecalis/*genetics/growth &amp; development ; Gastrointestinal Tract/*microbiology ; *Gene Transfer, Horizontal ; Germ-Free Life ; Lactococcus lactis/*genetics ; Mice ; Mice, Inbred C3H ; Plasmids ; Transformation, Bacterial ; }, abstract = {Since genetically modified (GM) lactic acid bacteria (LAB) might be released in open environments for future nutritional and medical applications, the purpose of this study was to determine an upper limit for the horizontal gene transfer (HGT) in the digestive tract (DT) from Lactococcus lactis carrying heterologous genes (lux genes encoding a bacterial luciferase) to Enterococcus faecalis. Two enterococcal wide host-range conjugative model systems were used: (i) a system composed of a mobilizable plasmid containing the heterologous lux genes and a native conjugative helper plasmid; and (ii) a Tn916-lux transposon. Both systems were tested under the most transfer-prone conditions, i.e. germfree mice mono-associated with the recipient E. faecalis. No transfer was observed with the transposon system. Transfers of the mobilizable plasmid carrying heterologous genes were below 10(2) transconjugants per g of faeces for a single donor dose and reached between 10(3) and 10(4) transconjugants per g of faeces when continuous inoculation of the donor strain was used. Once established in mice, transconjugants persisted at low levels in the mouse DT.}, }
@article {pmid15612351, year = {2004}, author = {Fuchs, M and Chirco, EM and Gonsalves, D}, title = {Movement of coat protein genes from a commercial virus-resistant transgenic squash into a wild relative.}, journal = {Environmental biosafety research}, volume = {3}, number = {1}, pages = {5-16}, doi = {10.1051/ebr:2004003}, pmid = {15612351}, issn = {1635-7922}, mesh = {Capsid Proteins/genetics ; Cucumovirus/genetics/pathogenicity ; Cucurbita/*genetics ; Enzyme-Linked Immunosorbent Assay ; Fertility ; *Gene Transfer, Horizontal ; *Hybridization, Genetic ; Immunity, Innate ; Kanamycin Kinase/genetics ; *Plants, Genetically Modified ; Pollen ; Risk Assessment ; Safety ; }, abstract = {We monitored pollen-mediated transgene dissemination from commercial transgenic squash CZW-3 into its wild relative Cucurbita pepo ssp. ovifera var. texana (C. texana). Transgenic squash CZW-3 expresses the neomycin phosphotransferase II (nptII) gene and the coat protein (CP) genes of Cucumber mosaic virus (CMV), Zucchini yellow mosaic virus (ZYMV), and Watermelon mosaic virus (WMV); thereby, it is resistant to these three aphid-borne viruses. The rate of NPT II and CP transgene introgression increased with overlapping flowering patterns and a high ratio of transgenic F1 hybrids (C. texana x CZW-3) to C. texana. Transgene transfer also readily occurred from transgenic F1 hybrids into C. texana over three generations in field settings where test plants grew sympatrically and viruses were not severely limiting the growth, and fruit and seed production of C. texana. In contrast, introgression of the transgenes into C. texana was not sustained under conditions of high viral disease pressure. As expected, C. texana progeny that acquired the CP transgenes exhibited resistance to CMV, ZYMV, and WMV. This is the first report on transgene dissemination from a transgenic crop that exhibits disease resistance and hybridizes with a wild plant species without loss of fertility.}, }
@article {pmid15611647, year = {2004}, author = {Mans, BJ and Anantharaman, V and Aravind, L and Koonin, EV}, title = {Comparative genomics, evolution and origins of the nuclear envelope and nuclear pore complex.}, journal = {Cell cycle (Georgetown, Tex.)}, volume = {3}, number = {12}, pages = {1612-1637}, doi = {10.4161/cc.3.12.1316}, pmid = {15611647}, issn = {1551-4005}, mesh = {Amino Acid Sequence ; Animals ; Cytoplasm ; DNA-Binding Proteins ; Discoidins ; Eukaryotic Cells/cytology ; *Evolution, Molecular ; *Genomics ; Humans ; Lamins/chemistry ; Lectins/chemistry ; Membrane Proteins/chemistry ; Molecular Sequence Data ; Nuclear Envelope/chemistry/*metabolism ; Nuclear Pore/chemistry/*metabolism ; Nuclear Pore Complex Proteins/chemistry ; Nuclear Proteins/chemistry ; Prokaryotic Cells/cytology ; Protozoan Proteins/chemistry ; Receptors, Cytoplasmic and Nuclear/chemistry ; Ribosomes/metabolism ; Sequence Alignment ; Yeasts/*cytology/*genetics ; Lamin B Receptor ; }, abstract = {The presence of a distinct nucleus, the compartment for confining the genome, transcription and RNA maturation, is a central (and eponymous) feature that distinguishes eukaryotes from prokaryotes. Structural integrity of the nucleus is maintained by the nuclear envelope (NE). A crucial element of this structure is the nuclear pore complex (NPC), a macromolecular machine with over 90 protein components, which mediates nucleo-cytoplasmic communication. We investigated the provenance of the conserved domains found in these perinuclear proteins and reconstructed a parsimonious scenario for NE and NPC evolution by means of comparative-genomic analysis of their components from the available sequences of 28 sequenced eukaryotic genomes. We show that the NE and NPC proteins were tinkered together from diverse domains, which evolved from prokaryotic precursors at different points in eukaryotic evolution, divergence from pre-existing eukaryotic paralogs performing other functions, and de novo. It is shown that several central components of the NPC, in particular, the RanGDP import factor NTF2, the HEH domain of Src1p-Man1, and, probably, also the key domains of karyopherins and nucleoporins, the HEAT/ARM and WD40 repeats, have a bacterial, most likely, endosymbiotic origin. The specialized immunoglobulin (Ig) domain in the globular tail of the animal lamins, and the Ig domains in the nuclear membrane protein GP210 are shown to be related to distinct prokaryotic families of Ig domains. This suggests that independent, late horizontal gene transfer events from bacterial sources might have contributed to the evolution of perinuclear proteins in some of the major eukaryotic lineages. Snurportin 1, one of the highly conserved karyopherins, contains a cap-binding domain which is shown to be an inactive paralog of the guanylyl transferase domain of the mRNA-capping enzyme, exemplifying recruitment of paralogs of pre-exsiting proteins for perinuclear functions. It is shown that several NPC proteins containing super-structure- forming alpha-helical and beta-propeller modules are most closely related to corresponding proteins in the cytoplasmic vesicle biogenesis and coating complexes. From these observations, we infer an autogenous scenario of nuclear evolution in which the nucleus emerged in the primitive eukaryotic ancestor (the "prekaryote") as part of cell compartmentalization triggered by archaeo-bacterial symbiosis. A pivotal event in this process was the radiation of Ras-superfamily GTPases yielding Ran, the key regulator of nuclear transport. A primitive NPC with approximately 20 proteins and a Src1p-Man1-like membrane protein with a DNA-tethering HEH domain are inferred to have been integral perinuclear components in the las common ancestor of modern eukaryotes.}, }
@article {pmid15598737, year = {2004}, author = {Bergthorsson, U and Richardson, AO and Young, GJ and Goertzen, LR and Palmer, JD}, title = {Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, number = {51}, pages = {17747-17752}, pmid = {15598737}, issn = {0027-8424}, support = {R01 GM035087/GM/NIGMS NIH HHS/United States ; R01-GM-35087/GM/NIGMS NIH HHS/United States ; }, mesh = {DNA, Mitochondrial/*genetics ; *Environment ; Gene Transfer, Horizontal/*genetics ; Genes, Plant/*genetics ; Genome, Plant ; Magnoliopsida/*genetics ; Molecular Sequence Data ; Phylogeny ; Plants/*genetics ; }, abstract = {Several plants are known to have acquired a single mitochondrial gene by horizontal gene transfer (HGT), but whether these or any other plants have acquired many foreign genes is entirely unclear. To address this question, we focused on Amborella trichopoda, because it was already known to possess one horizontally acquired gene and because it was found in preliminary analyses to contain several more. We comprehensively sequenced the mitochondrial protein gene set of Amborella, sequenced a variable number of mitochondrial genes from 28 other diverse land plants, and conducted phylogenetic analyses of these sequences plus those already available, including the five sequenced mitochondrial genomes of angiosperms. Results indicate that Amborella has acquired one or more copies of 20 of its 31 known mitochondrial protein genes from other land plants, for a total of 26 foreign genes, whereas no evidence for HGT was found in the five sequenced genomes. Most of the Amborella transfers are from other angiosperms (especially eudicots), whereas others are from nonangiosperms, including six striking cases of transfer from (at least three different) moss donors. Most of the transferred genes are intact, consistent with functionality and/or recency of transfer. Amborella mtDNA has sustained proportionately more HGT than any other eukaryotic, or perhaps even prokaryotic, genome yet examined.}, }
@article {pmid15598528, year = {2004}, author = {Chiu, CM and Thomas, CM}, title = {Evidence for past integration of IncP-1 plasmids into bacterial chromosomes.}, journal = {FEMS microbiology letters}, volume = {241}, number = {2}, pages = {163-169}, doi = {10.1016/j.femsle.2004.10.016}, pmid = {15598528}, issn = {0378-1097}, mesh = {Bacterial Proteins/genetics/metabolism ; Binding Sites ; Chromatin Immunoprecipitation ; Chromosomes, Bacterial/*genetics ; *Conjugation, Genetic ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Gram-Negative Bacteria/*genetics ; Plasmids/*genetics ; }, abstract = {Plasmids of the IncP-1 incompatibility group are self-transmissible between and stably maintained in a very broad range of Gram-negative bacteria. A characteristic feature of IncP-1 genomes is the existence of multiple binding sites (OB) for the KorB protein which plays a dual role in active partitioning of plasmid and coordinate regulation of expression of genes for replication, maintenance and transfer. A search of the available bacterial genome sequences revealed a significant number (70 out of 322) with one or more putative KorB binding sites. Binding of KorB to such a site was demonstrated by chromatin immunoprecipitation (ChIP) for Pseudomonas putida KT2440. While such a site may arise by chance, this is unlikely for Pseudomonas aeruginosa UCBPP-PA14 whose genome sequence contains four clustered OB sites and several regions have more than 80% nucleotide identity to traJ, trbJ and trbL of IncP-1 plasmids. A number of other bacterial genomes also contain integrated partial IncP-1 genomes or their remnants. These data provide evidence for multiple past integration events of IncP-1 plasmids into bacterial chromosomes and provide new evidence for IncP-1 plasmids being important elements in gene mobility.}, }
@article {pmid15597566, year = {2004}, author = {Smirnova, II and Kutyrev, VV}, title = {[Evolution of the cholera agent genome].}, journal = {Molekuliarnaia genetika, mikrobiologiia i virusologiia}, volume = {}, number = {4}, pages = {3-13}, pmid = {15597566}, issn = {0208-0613}, mesh = {Asia/epidemiology ; Cholera/epidemiology/virology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; *Genome, Bacterial ; Humans ; Inoviridae/genetics ; Peru/epidemiology ; Recombination, Genetic ; Saudi Arabia/epidemiology ; Vibrio cholerae/*genetics/pathogenicity ; Vibrio cholerae O139/genetics ; Virulence/genetics ; }, abstract = {"Mikrob" Russian Research Anti-Plague Institute, Saratov Studies of the genomic evolution of pathogenic bacteria became a priority research trend of modern molecular genetics. Vibrio cholerae, whose pathogenic properties are conditioned by the presence of virulence blocks of differing phylogenetic origins in 2 chromosomes, turned out to be a unique model object for studies of evolutionary transformations of genomes that are causative agents of extra dangerous infections. The molecular-and-genetic mechanisms underlying the change of biovariants and the emergence of a cholera agent of a new serogroup are in the focus of attention. Finally, the possibility that the new V. cholerae pathogenic clone originated due to horizontal genetic transfers and recombination phenomena is under discussion in the survey.}, }
@article {pmid15590779, year = {2004}, author = {Handelsman, J}, title = {Metagenomics: application of genomics to uncultured microorganisms.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {68}, number = {4}, pages = {669-685}, pmid = {15590779}, issn = {1092-2172}, mesh = {Biotechnology ; Ecology ; Environmental Microbiology ; *Genetics, Microbial ; Genome, Bacterial ; Genomics/*methods ; }, abstract = {Metagenomics (also referred to as environmental and community genomics) is the genomic analysis of microorganisms by direct extraction and cloning of DNA from an assemblage of microorganisms. The development of metagenomics stemmed from the ineluctable evidence that as-yet-uncultured microorganisms represent the vast majority of organisms in most environments on earth. This evidence was derived from analyses of 16S rRNA gene sequences amplified directly from the environment, an approach that avoided the bias imposed by culturing and led to the discovery of vast new lineages of microbial life. Although the portrait of the microbial world was revolutionized by analysis of 16S rRNA genes, such studies yielded only a phylogenetic description of community membership, providing little insight into the genetics, physiology, and biochemistry of the members. Metagenomics provides a second tier of technical innovation that facilitates study of the physiology and ecology of environmental microorganisms. Novel genes and gene products discovered through metagenomics include the first bacteriorhodopsin of bacterial origin; novel small molecules with antimicrobial activity; and new members of families of known proteins, such as an Na(+)(Li(+))/H(+) antiporter, RecA, DNA polymerase, and antibiotic resistance determinants. Reassembly of multiple genomes has provided insight into energy and nutrient cycling within the community, genome structure, gene function, population genetics and microheterogeneity, and lateral gene transfer among members of an uncultured community. The application of metagenomic sequence information will facilitate the design of better culturing strategies to link genomic analysis with pure culture studies.}, }
@article {pmid15585503, year = {2004}, author = {Nemec, A and Dolzani, L and Brisse, S and van den Broek, P and Dijkshoorn, L}, title = {Diversity of aminoglycoside-resistance genes and their association with class 1 integrons among strains of pan-European Acinetobacter baumannii clones.}, journal = {Journal of medical microbiology}, volume = {53}, number = {Pt 12}, pages = {1233-1240}, doi = {10.1099/jmm.0.45716-0}, pmid = {15585503}, issn = {0022-2615}, mesh = {Acinetobacter baumannii/*drug effects/enzymology/*genetics ; Aminoglycosides/*pharmacology ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/*genetics ; Europe ; Genes, Bacterial ; Genetic Variation ; Genotype ; Integrons/*genetics ; Molecular Sequence Data ; Phenotype ; }, abstract = {The purpose of the present study was to investigate the diversity of the genes encoding aminoglycoside-modifying enzymes and their association with class 1 integrons in three pan-European clones of Acinetobacter baumannii. The study collection included 106 multidrug-resistant strains previously allocated to clone I (n = 56), clone II (n = 36) and clone III (n = 6) and a heterogeneous group of other strains (n = 8), using AFLP fingerprinting and ribotyping. The strains were from hospitals of the Czech Republic (n = 70; collected 1991-2001) and 12 other European countries (n = 36; 1982-1998). Using PCR, at least one of the following aminoglycoside-resistance genes was detected in 101 (95 %) strains: aphA1 (n = 76), aacC1 (n = 68), aadA1 (n = 68), aphA6 (n = 55), aadB (n = 31), aacC2 (n = 7) and aacA4 (n = 3). A combination of two to five different resistance genes was observed in 89 strains (84 %), with a total of 12 different combinations. PCR mapping revealed that aacC1, aadA1 and aacA4 were each associated with a class 1 integron, as was the case with aadB for six strains of clone III. Six different class 1 integron variable regions were detected in 78 strains (74 %), with two predominant regions (2.5 and 3.0 kb) in two sets of 34 strains each. The 3.0 kb region contained five gene cassettes (aacC1, orfX, orfX, orfX', aadA1) and differed from the 2.5 bp region only by one additional orfX cassette. These two integron regions were confined to clones I and II and were found in strains isolated in seven countries between 1982 and 2001. The clone III strains were homogeneous both in resistance genes and in integron variable regions, whereas clones I and II showed a remarkable intraclonal diversity of these properties, with no clear-cut difference between the two clones. Yet, within the Czech clone I and II strains, the diversity of resistance genes and integron structures was limited as compared to those from other countries. The occurrence of identical resistance genes, gene combinations and class 1 integrons associated with these genes in clonally distinct strains indicates that horizontal gene transfer plays a major role in the dissemination of aminoglycoside resistance in A. baumannii.}, }
@article {pmid15585131, year = {2004}, author = {Faruque, SM and Nair, GB and Mekalanos, JJ}, title = {Genetics of stress adaptation and virulence in toxigenic Vibrio cholerae.}, journal = {DNA and cell biology}, volume = {23}, number = {11}, pages = {723-741}, doi = {10.1089/dna.2004.23.723}, pmid = {15585131}, issn = {1044-5498}, support = {GM068851/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Physiological/*genetics ; Cholera Toxin/genetics ; Gene Transfer, Horizontal ; Intestine, Small/microbiology ; Vibrio cholerae/*genetics/pathogenicity/physiology ; Virulence ; }, abstract = {Vibrio cholerae, a Gram-negative bacterium belonging to the gamma-subdivision of the family Proteobacteriaceae is the etiologic agent of cholera, a devastating diarrheal disease which occurs frequently as epidemics. Any bacterial species encountering a broad spectrum of environments during the course of its life cycle is likely to develop complex regulatory systems and stress adaptation mechanisms to best survive in each environment encountered. Toxigenic V. cholerae, which has evolved from environmental nonpathogenic V. cholerae by acquisition of virulence genes, represents a paradigm for this process in that this organism naturally exists in an aquatic environment but infects human beings and cause cholera. The V. cholerae genome, which is comprised of two independent circular mega-replicons, carries the genetic determinants for the bacterium to survive both in an aquatic environment as well as in the human intestinal environment. Pathogenesis of V. cholerae involves coordinated expression of different sets of virulence associated genes, and the synergistic action of their gene products. Although the acquisition of major virulence genes and association between V. cholerae and its human host appears to be recent, and reflects a simple pathogenic strategy, the establishment of a productive infection involves the expression of many more genes that are crucial for survival and adaptation of the bacterium in the host, as well as for its onward transmission and epidemic spread. While a few of the virulence gene clusters involved directly with cholera pathogenesis have been characterized, the potential exists for identification of yet new genes which may influence the stress adaptation, pathogenesis, and epidemiological characteristics of V. cholerae. Coevolution of bacteria and mobile genetic elements (plasmids, transposons, pathogenicity islands, and phages) can determine environmental survival and pathogenic interactions between bacteria and their hosts. Besides horizontal gene transfer mediated by genetic elements and phages, the evolution of pathogenic V. cholerae involves a combination of selection mechanisms both in the host and in the environment. The occurrence of periodic epidemics of cholera in endemic areas appear to enhance this process.}, }
@article {pmid15583313, year = {2004}, author = {Finnan, S and Morrissey, JP and O'Gara, F and Boyd, EF}, title = {Genome diversity of Pseudomonas aeruginosa isolates from cystic fibrosis patients and the hospital environment.}, journal = {Journal of clinical microbiology}, volume = {42}, number = {12}, pages = {5783-5792}, pmid = {15583313}, issn = {0095-1137}, mesh = {Bacterial Proteins/genetics ; Chaperonin 60/genetics ; Cystic Fibrosis/complications/*microbiology ; Environmental Microbiology ; Evolution, Molecular ; *Genetic Variation ; *Genome, Bacterial ; Genotype ; *Hospitals ; Humans ; Malate Dehydrogenase/genetics ; Phenotype ; Pseudomonas Infections/microbiology ; Pseudomonas aeruginosa/*classification/genetics/isolation &amp; purification/pathogenicity ; Virulence/genetics ; }, abstract = {Pseudomonas aeruginosa is a gram-negative rod that is ubiquitous in nature. P. aeruginosa is also the quintessential opportunistic pathogen, causing a wide variety of infections in compromised hosts. In cystic fibrosis patients, P. aeruginosa is the leading cause of death. In this study, the evolutionary genetic relationships among 17 P. aeruginosa isolates were examined by comparative sequence analysis of the housekeeping gene encoding malate dehydrogenase and the chaperone groEL. The P. aeruginosa isolates examined included the sequenced strain PAO1, 11 strains recovered from cystic fibrosis patients in Ireland, 4 environmental isolates recovered from a hospital environment, and 1 isolate recovered from a plant rhizosphere. Phylogenetically, clinical and environmental isolates clustered together with one another on the mdh gene tree. At the groEL locus, among the 17 isolates examined, only two polymorphic sites were observed, highlighting the close genetic relationship between isolates from these different environments. Phenotypic analysis of 12 traits among our isolates, however, found that only clinical isolates produced phenazines and elastase. Furthermore, molecular analysis of the distribution of 15 regions associated with virulence showed that two of the environmental isolates examined lacked the majority of regions. Among the clinical isolates examined, the 15 virulence regions were variably present. The distribution of two prophages (Bacto1, Pf1) was also determined, with most isolates encoding both these regions. Of the four genomic islands (the flagellum island and PAGI-1, -2, and -3) examined, only two isolates contained the flagellum island, and PAGI-1, -2, and -3 were absent from all isolates tested. Our data demonstrate the significant role horizontal gene transfer and recombination, together with gene loss, play in the evolution of this important human pathogen.}, }
@article {pmid15579380, year = {2005}, author = {Vinuesa, P and Silva, C and Werner, D and Martínez-Romero, E}, title = {Population genetics and phylogenetic inference in bacterial molecular systematics: the roles of migration and recombination in Bradyrhizobium species cohesion and delineation.}, journal = {Molecular phylogenetics and evolution}, volume = {34}, number = {1}, pages = {29-54}, doi = {10.1016/j.ympev.2004.08.020}, pmid = {15579380}, issn = {1055-7903}, mesh = {Base Sequence ; Bradyrhizobium/classification/*genetics ; DNA Fingerprinting ; Evolution, Molecular ; Fabaceae/microbiology ; *Genetics, Population ; Likelihood Functions ; Oxidoreductases/genetics ; *Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Rec A Recombinases/genetics ; *Recombination, Genetic ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {A combination of population genetics and phylogenetic inference methods was used to delineate Bradyrhizobium species and to uncover the evolutionary forces acting at the population-species interface of this bacterial genus. Maximum-likelihood gene trees for atpD, glnII, recA, and nifH loci were estimated for diverse strains from all but one of the named Bradyrhizobium species, and three unnamed "genospecies," including photosynthetic isolates. Topological congruence and split decomposition analyses of the three housekeeping loci are consistent with a model of frequent homologous recombination within but not across lineages, whereas strong evidence was found for the consistent lateral gene transfer across lineages of the symbiotic (auxiliary) nifH locus, which grouped strains according to their hosts and not by their species assignation. A well resolved Bayesian species phylogeny was estimated from partially congruent glnII+recA sequences, which is highly consistent with the actual taxonomic scheme of the genus. Population-level analyses of isolates from endemic Canarian genistoid legumes based on REP-PCR genomic fingerprints, allozyme and DNA polymorphism analyses revealed a non-clonal and slightly epidemic population structure for B. canariense isolates of Canarian and Moroccan origin, uncovered recombination and migration as significant evolutionary forces providing the species with internal cohesiveness, and demonstrated its significant genetic differentiation from B. japonicum, its sister species, despite their sympatry and partially overlapped ecological niches. This finding provides strong evidence for the existence of well delineated species in the bacterial world. The results and approaches used herein are discussed in the context of bacterial species concepts and the evolutionary ecology of (brady)rhizobia.}, }
@article {pmid15578178, year = {2005}, author = {Tudzynski, B}, title = {Gibberellin biosynthesis in fungi: genes, enzymes, evolution, and impact on biotechnology.}, journal = {Applied microbiology and biotechnology}, volume = {66}, number = {6}, pages = {597-611}, doi = {10.1007/s00253-004-1805-1}, pmid = {15578178}, issn = {0175-7598}, mesh = {Biotechnology ; Enzymes/genetics/physiology ; *Evolution, Molecular ; Fusarium/enzymology/genetics/*metabolism ; Gene Expression Regulation, Fungal ; *Genes, Fungal ; Gibberellins/*biosynthesis ; }, abstract = {Gibberellins (GAs) constitute a large family of tetracyclic diterpenoid carboxylic acids, some members of which function as growth hormones in higher plants. As well as being phytohormones, GAs are also present in some fungi and bacteria. In recent years, GA biosynthetic genes from Fusarium fujikuroi and Arabidopsis thaliana have been cloned and well characterised. Although higher plants and the fungus both produce structurally identical GAs, there are important differences indicating that GA biosynthetic pathways have evolved independently in higher plants and fungi. The fact that horizontal gene transfer of GA genes from the plant to the fungus can be excluded, and that GA genes are obviously missing in closely related Fusarium species, raises the question of the origin of fungal GA biosynthetic genes. Besides characterisation of F. fujikuroi GA pathway genes, much progress has been made in the molecular analysis of regulatory mechanisms, especially the nitrogen metabolite repression controlling fungal GA biosynthesis. Basic research in this field has been shown to have an impact on biotechnology. Cloning of genes, construction of knock-out mutants, gene amplification, and regulation studies at the molecular level are powerful tools for improvement of production strains. Besides increased yields of the final product, GA3, it is now possible to produce intermediates of the GA biosynthetic pathway, such as ent-kaurene, ent-kaurenoic acid, and GA14, in high amounts using different knock-out mutants. This review concentrates mainly on the fungal biosynthetic pathway, the genes and enzymes involved, the regulation network, the biotechnological relevance of recent studies, and on evolutionary aspects of GA biosynthetic genes.}, }
@article {pmid15576776, year = {2004}, author = {Chibani-Chennoufi, S and Canchaya, C and Bruttin, A and Brüssow, H}, title = {Comparative genomics of the T4-Like Escherichia coli phage JS98: implications for the evolution of T4 phages.}, journal = {Journal of bacteriology}, volume = {186}, number = {24}, pages = {8276-8286}, pmid = {15576776}, issn = {0021-9193}, mesh = {Bacteriophage T4/*genetics ; Escherichia coli/*virology ; *Evolution, Molecular ; *Genome, Viral ; Genomics ; Humans ; Molecular Sequence Data ; Point Mutation ; Sequence Analysis, DNA ; Viral Proteins/genetics ; }, abstract = {About 130 kb of sequence information was obtained from the coliphage JS98 isolated from the stool of a pediatric diarrhea patient in Bangladesh. The DNA shared up to 81% base pair identity with phage T4. The most conserved regions between JS98 and T4 were the structural genes, but their degree of conservation was not uniform. The head genes showed the highest sequence conservation, followed by the tail, baseplate, and tail fiber genes. Many tail fiber genes shared only protein sequence identity. Except for the insertion of endonuclease genes in T4 and gene 24 duplication in JS98, the structural gene maps of the two phages were colinear. The receptor-recognizing tail fiber proteins gp37 and gp38 were only distantly related to T4, but shared up to 83% amino acid identity to other T6-like phages, suggesting lateral gene transfer. A greater degree of variability was seen between JS98 and T4 over DNA replication and DNA transaction genes. While most of these genes came in the same order and shared up to 76% protein sequence identity, a few rearrangements, insertions, and replacements of genes were observed. Many putative gene insertions in the DNA replication module of T4 were flanked by intron-related endonuclease genes, suggesting mobile DNA elements. A hotspot of genome diversification was located downstream of the DNA polymerase gene 43 and the DNA binding gene 32. Comparative genomics of 100-kb genome sequence revealed that T4-like phages diversify more by the accumulation of point mutations and occasional gene duplication events than by modular exchanges.}, }
@article {pmid15576203, year = {2004}, author = {Hiramatsu, K and Watanabe, S and Takeuchi, F and Ito, T and Baba, T}, title = {Genetic characterization of methicillin-resistant Staphylococcus aureus.}, journal = {Vaccine}, volume = {22 Suppl 1}, number = {}, pages = {S5-8}, doi = {10.1016/j.vaccine.2004.08.009}, pmid = {15576203}, issn = {0264-410X}, mesh = {Biological Evolution ; Chromosomes, Bacterial ; Coagulase/genetics ; Humans ; Methicillin Resistance/genetics ; Staphylococcus aureus/*genetics ; }, abstract = {The genome structure of Staphylococcus aureus is analyzed. The genome is composed of two domains. The first domain, descendent from an ancestral bacterial species, contains house-keeping genes that showed highest homology to those of Bacillus species. The second domain contained the genes responsible for virulence and drug-resistance in human infection that seems to have been acquired from other bacterial species via lateral gene transfer. The latter domain constitutes the genetic information that makes S. aureus a notorious hospital pathogen.}, }
@article {pmid15574953, year = {2004}, author = {Rhodes, G and Parkhill, J and Bird, C and Ambrose, K and Jones, MC and Huys, G and Swings, J and Pickup, RW}, title = {Complete nucleotide sequence of the conjugative tetracycline resistance plasmid pFBAOT6, a member of a group of IncU plasmids with global ubiquity.}, journal = {Applied and environmental microbiology}, volume = {70}, number = {12}, pages = {7497-7510}, pmid = {15574953}, issn = {0099-2240}, mesh = {Aeromonas/*genetics ; Amino Acid Sequence ; Bacterial Proteins/chemistry/genetics ; Base Sequence ; *Conjugation, Genetic ; Escherichia coli/*genetics ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Plasmids/*genetics ; *Sequence Analysis, DNA ; Tetracycline Resistance/*genetics ; }, abstract = {This study presents the first complete sequence of an IncU plasmid, pFBAOT6. This plasmid was originally isolated from a strain of Aeromonas caviae from hospital effluent (Westmorland General Hospital, Kendal, United Kingdom) in September 1997 (G. Rhodes, G. Huys, J. Swings, P. McGann, M. Hiney, P. Smith, and R. W. Pickup, Appl. Environ. Microbiol. 66:3883-3890, 2000) and belongs to a group of related plasmids with global ubiquity. pFBAOT6 is 84,748 bp long and has 94 predicted coding sequences, only 12 of which do not have a possible function that has been attributed. Putative replication, maintenance, and transfer functions have been identified and are located in a region in the first 31 kb of the plasmid. The replication region is poorly understood but exhibits some identity at the protein level with replication proteins from the gram-positive bacteria Bacillus and Clostridium. The mating pair formation system is a virB homologue, type IV secretory pathway that is similar in its structural organization to the mating pair formation systems of the related broad-host-range (BHR) environmental plasmids pIPO2, pXF51, and pSB102 from plant-associated bacteria. Partitioning and maintenance genes are homologues of genes in IncP plasmids. The DNA transfer genes and the putative oriT site also exhibit high levels of similarity with those of plasmids pIPO2, pXF51, and pSB102. The genetic load region encompasses 54 kb, comprises the resistance genes, and includes a class I integron, an IS630 relative, and other transposable elements in a 43-kb region that may be a novel Tn1721-flanked composite transposon. This region also contains 24 genes that exhibit the highest levels of identity to chromosomal genes of several plant-associated bacteria. The features of the backbone of pFBAOT6 that are shared with this newly defined group of environmental BHR plasmids suggest that pFBAOT6 may be a relative of this group, but a relative that was isolated from a clinical bacterial environment rather than a plant-associated bacterial environment.}, }
@article {pmid15567133, year = {2005}, author = {Ehrbar, K and Hardt, WD}, title = {Bacteriophage-encoded type III effectors in Salmonella enterica subspecies 1 serovar Typhimurium.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {5}, number = {1}, pages = {1-9}, doi = {10.1016/j.meegid.2004.07.004}, pmid = {15567133}, issn = {1567-1348}, mesh = {Bacterial Proteins/*genetics/physiology ; Evolution, Molecular ; Gene Transfer, Horizontal ; Guanine Nucleotide Exchange Factors/genetics ; Lysogeny/physiology ; Salmonella Phages/*genetics ; Salmonella typhimurium/*genetics/pathogenicity/physiology/virology ; Virulence ; }, abstract = {Salmonella spp. are Gram-negative bacteria which cause infections ranging from mild, self-limiting enterocolitis to systemic (typhoid) disease. Recent work has established that the genetic makeup varies considerably between different Salmonella strains. Phages play an important role in this diversity. In fact, Salmonella has emerged as a prime example for the involvement of virulence factor encoding phages in the emergence of new epidemic strains. Among other virulence factors, Salmonella enterica utilizes two specialized protein secretion systems termed type III secretion systems (TTSS) to deliver effector proteins into host cells which manipulate host cell signaling cascades. These two TTSS and several effectors are encoded within Salmonella pathogenicity islands 1 and 2. Some effectors including SopE, SspH1, SseI and SopE2 are encoded by phages or phage remnants. These phage-encoded effectors seem to be transferred between different Salmonella strains. They have attracted much interest because they might contribute to the evolution of Salmonella spp. Here we will focus on SopEPhi which encodes the SPI-1 effector SopE. It provides an excellent example to illustrate how horizontally transferred effector proteins are integrated into the complex regulatory network of a TTSS in a recipient bacterium. Additional data supporting the hypothesis are presented. This is a prerequisite to allow optimization of the bacterium host cell interaction by reassortment of the phage-encoded effector protein repertoire.}, }
@article {pmid15566569, year = {2004}, author = {Mira, A and Pushker, R and Legault, BA and Moreira, D and Rodríguez-Valera, F}, title = {Evolutionary relationships of Fusobacterium nucleatum based on phylogenetic analysis and comparative genomics.}, journal = {BMC evolutionary biology}, volume = {4}, number = {}, pages = {50}, pmid = {15566569}, issn = {1471-2148}, mesh = {Bacterial Proteins/genetics ; Base Composition/genetics ; Chromosome Mapping/methods ; Chromosomes, Bacterial/genetics ; Enzymes/genetics ; *Evolution, Molecular ; Fusobacterium nucleatum/enzymology/*genetics ; Gene Order/genetics ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/genetics ; Genome, Bacterial ; Genomics/*methods ; Operon/genetics ; *Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 23S/genetics ; Recombinant Fusion Proteins/genetics ; }, abstract = {BACKGROUND: The phylogenetic position and evolutionary relationships of Fusobacteria remain uncertain. Especially intriguing is their relatedness to low G+C Gram positive bacteria (Firmicutes) by ribosomal molecular phylogenies, but their possession of a typical gram negative outer membrane. Taking advantage of the recent completion of the Fusobacterium nucleatum genome sequence we have examined the evolutionary relationships of Fusobacterium genes by phylogenetic analysis and comparative genomics tools.<br><br>RESULTS: The data indicate that Fusobacterium has a core genome of a very different nature to other bacterial lineages, and branches out at the base of Firmicutes. However, depending on the method used, 35-56% of Fusobacterium genes appear to have a xenologous origin from bacteroidetes, proteobacteria, spirochaetes and the Firmicutes themselves. A high number of hypothetical ORFs with unusual codon usage and short lengths were found and hypothesized to be remnants of transferred genes that were discarded. Some proteins and operons are also hypothesized to be of mixed ancestry. A large portion of the Gram-negative cell wall-related genes seems to have been transferred from proteobacteria.<br><br>CONCLUSIONS: Many instances of similarity to other inhabitants of the dental plaque that have been sequenced were found. This suggests that the close physical contact found in this environment might facilitate horizontal gene transfer, supporting the idea of niche-specific gene pools. We hypothesize that at a point in time, probably associated to the rise of mammals, a strong selective pressure might have existed for a cell with a Clostridia-like metabolic apparatus but with the adhesive and immune camouflage features of Proteobacteria.}, }
@article {pmid15563718, year = {2005}, author = {Stoebel, DM}, title = {Lack of evidence for horizontal transfer of the lac operon into Escherichia coli.}, journal = {Molecular biology and evolution}, volume = {22}, number = {3}, pages = {683-690}, doi = {10.1093/molbev/msi056}, pmid = {15563718}, issn = {0737-4038}, support = {GM6073102/GM/NIGMS NIH HHS/United States ; GM6380001/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Biological/*genetics ; Escherichia coli/*genetics ; Escherichia coli Proteins/*genetics ; *Gene Transfer, Horizontal ; Lac Operon/*genetics ; }, abstract = {The idea that Escherichia coli gained the lac operon via horizontal transfer, allowing it to invade a new niche and form a new species, has become a paradigmatic example of bacterial nonpathogenic adaptation and speciation catalyzed by horizontal transfer. Surprisingly, empirical evidence for this event is essentially nonexistent. To see whether horizontal transfer occurred, I compared a phylogeny of 14 Enterobacteriaceae based on two housekeeping genes to a phylogeny of a part of their lac operon. Although several species in this clade appear to have acquired some or all of the operon via horizontal transfer, there is no evidence of horizontal transfer into E. coli. It is not clear whether the horizontal transfer events for which there is evidence were adaptive because those species which have acquired the operon are not thought to live in high lactose environments. I propose that vertical transmission from the common ancestor of the Enterobacteriaceae, with subsequent loss of these genes in many species can explain much of the patchy distribution of lactose use in this clade. Finally, I argue that we need new, well-supported examples of horizontal transfer spurring niche expansion and speciation, particularly in nonpathogenic cases, before we can accept claims that horizontal transfer is a hallmark of bacterial adaptation.}, }
@article {pmid15561838, year = {2004}, author = {Barrow, EW and Bourne, PC and Barrow, WW}, title = {Functional cloning of Bacillus anthracis dihydrofolate reductase and confirmation of natural resistance to trimethoprim.}, journal = {Antimicrobial agents and chemotherapy}, volume = {48}, number = {12}, pages = {4643-4649}, pmid = {15561838}, issn = {0066-4804}, support = {R21 AI055643/AI/NIAID NIH HHS/United States ; R21-AI055643/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacillus anthracis/*enzymology/*genetics ; Base Sequence ; Chromatography, High Pressure Liquid ; Culture Media ; DNA Primers ; Escherichia coli/genetics ; Folic Acid Antagonists/*pharmacology ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Molecular Weight ; Plasmids/genetics ; Recombinant Proteins ; Reverse Transcriptase Polymerase Chain Reaction ; Tetrahydrofolate Dehydrogenase/biosynthesis/*genetics/isolation &amp; purification ; Thrombin/chemistry ; Trimethoprim/*pharmacology ; Trimethoprim Resistance/*genetics ; }, abstract = {Bacillus anthracis is reported to be naturally resistant to trimethoprim (TMP), a drug that inhibits dihydrofolate reductase (DHFR), a key enzyme in the folate pathway. A microdilution broth assay established that the MIC of TMP for B. anthracis Sterne is >2,048 but < or =4,096 microg/ml. A putative DHFR sequence was amplified from B. anthracis Sterne genomic DNA. The PCR product was cloned into the Invitrogen pCRT7/CT-TOPO vector, followed by transformation into Escherichia coli TOP10F' chemically competent cells. Plasmid DNA from a clone showing the correct construct with a thrombin cleavage site attached downstream from the terminus of the cloned PCR product was transformed into E. coli BL21 Star (DE3)pLysS competent cells for expression of the six-histidine-tagged fusion protein and purification on a His-Bind resin column. Functionality of the purified Sterne recombinant DHFR (Sterne rDHFR) was confirmed in an established enzyme assay. The 50% inhibitory concentrations of TMP and methotrexate for the Sterne rDHFR were found to be 77,233 and 12.2 nM, respectively. TMP resistance was observed with E. coli BL21 Star (DE3)pLysS competent cells transformed with the Sterne DHFR gene. Alignment of the amino acid sequence of the Sterne DHFR gene revealed 100% homology with various virulent strains of B. anthracis. These results confirm the natural resistance of B. anthracis to TMP and clarify that the resistance is correlated to a lack of selectivity for the chromosomally encoded gene product. These findings will assist in the development of narrow-spectrum antimicrobial agents for treatment of anthrax.}, }
@article {pmid15561825, year = {2004}, author = {Pallecchi, L and Malossi, M and Mantella, A and Gotuzzo, E and Trigoso, C and Bartoloni, A and Paradisi, F and Kronvall, G and Rossolini, GM}, title = {Detection of CTX-M-type beta-lactamase genes in fecal Escherichia coli isolates from healthy children in Bolivia and Peru.}, journal = {Antimicrobial agents and chemotherapy}, volume = {48}, number = {12}, pages = {4556-4561}, pmid = {15561825}, issn = {0066-4804}, mesh = {Bolivia/epidemiology ; Ceftriaxone/pharmacology ; Cephalosporins/pharmacology ; Conjugation, Genetic ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; Escherichia coli/*enzymology/*genetics ; Feces/*microbiology ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Peru/epidemiology ; Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction ; beta-Lactamases/*genetics ; }, abstract = {A survey was carried out from August to November 2002 to evaluate the antimicrobial susceptibilities of fecal Escherichia coli isolates from 3,208 healthy children from four different urban areas of Latin America, two in Bolivia (Camiri and Villa Montes) and two in Peru (Yurimaguas and Moyobamba). Ceftriaxone-resistant E. coli isolates were detected in four children, one from each of the areas sampled. The isolates exhibited a multidrug-resistant phenotype, including resistance to oxyimino-cephalosporins and aztreonam, and the MICs of ceftazidime for the isolates were lower than those of cefotaxime. By PCR and sequencing, the bla(CTX-M-2) determinant was detected in three isolates and the bla(CTX-M-15) determinant was detected in one isolate (from Peru). The CTX-M-2-producing isolates belonged to three different phylogenetic groups (groups A, B2, and D), while the CTX-M-15-producing isolate belonged to phylogenetic group D. The bla(CTX-M-2) determinants were transferable to E. coli by conjugation, while conjugative transfer of the bla(CTX-M-15) determinant was not detectable. Plasmids harboring the bla(CTX-M-2) determinant exhibited similar restriction profiles, and in all of them the gene was located on a 2.2-kb PstI fragment, suggesting a genetic environment similar to that present in In35 and InS21. The findings of the present study confirm the widespread distribution of CTX-M-type beta-lactamases and underscore the role that commensal E. coli isolates could play as a potential reservoir of these clinically relevant resistance determinants. This is the first report of CTX-M-type enzymes in Bolivia and Peru and also the first report of the detection of CTX-M-15 in Latin America.}, }
@article {pmid15557260, year = {2004}, author = {Sakasegawa, S and Hagemeier, CH and Thauer, RK and Essen, LO and Shima, S}, title = {Structural and functional analysis of the gpsA gene product of Archaeoglobus fulgidus: a glycerol-3-phosphate dehydrogenase with an unusual NADP+ preference.}, journal = {Protein science : a publication of the Protein Society}, volume = {13}, number = {12}, pages = {3161-3171}, pmid = {15557260}, issn = {0961-8368}, mesh = {Amino Acid Sequence ; Animals ; Archaeoglobus fulgidus/*enzymology/genetics ; Binding Sites ; Crystallography, X-Ray ; Glycerolphosphate Dehydrogenase/*chemistry/*physiology ; Leishmania mexicana/enzymology ; Molecular Sequence Data ; NADP/*metabolism ; Protein Conformation ; Sequence Alignment ; }, abstract = {NAD(+)-dependent glycerol-3-phosphate dehydrogenase (G3PDH) is generally absent in archaea, because archaea, unlike eukaryotes and eubacteria, utilize glycerol-1-phosphate instead of glycerol-3-phosphate for the biosynthesis of membrane lipids. Surprisingly, the genome of the hyperthermophilic archaeon Archaeoglobus fulgidus comprises a G3PDH ortholog, gpsA, most likely due to horizontal gene transfer from a eubacterial organism. Biochemical characterization proved G3PDH-like activity of the recombinant gpsA gene product. However, unlike other G3PDHs, the up to 85 degrees C thermostable A. fulgidus G3PDH exerted a 15-fold preference for NADPH over NADH. The A. fulgidus G3PDH bears the hallmarks of adaptation to halotolerance and thermophilicity, because its 1.7-A crystal structure showed a high surface density for negative charges and 10 additional intramolecular salt bridges compared to a mesophilic G3PDH structure. Whereas all amino acid residues required for dihydroxyacetone phosphate binding and reductive catalysis are highly conserved, the binding site for the adenine moiety of the NAD(P) cosubstrate shows a structural variation that reflects the observed NADPH preference, for example, by a putative salt bridge between R49 and the 2'-phosphate.}, }
@article {pmid15556475, year = {2004}, author = {Pérez-Rueda, E and Collado-Vides, J and Segovia, L}, title = {Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea.}, journal = {Computational biology and chemistry}, volume = {28}, number = {5-6}, pages = {341-350}, doi = {10.1016/j.compbiolchem.2004.09.004}, pmid = {15556475}, issn = {1476-9271}, mesh = {Amino Acid Sequence ; Archaea/*genetics/metabolism ; Bacteria/*genetics/metabolism ; DNA/chemistry/*genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Amino Acid ; Transcription Factors, General/genetics/*metabolism ; }, abstract = {We have addressed the distribution and abundance of 75 transcription factor (TF) families in complete genomes from 90 different bacterial and archaeal species. We found that the proportion of TFs increases with genome size. The deficit of TFs in some genomes might be compensated by the presence of proteins organizing and compacting DNA, such as histone-like proteins. Nine families are represented in all the bacteria and archaea we analyzed, whereas 17 families are specific to bacteria, providing evidence for regulon specialization at an early stage of evolution between the bacterial and archeal lineages. Ten of the 17 families identified in bacteria belong exclusively to the proteobacteria defining a specific signature for this taxonomical group. In bacteria, 10 families are lost mostly in intracellular pathogens and endosymbionts, while 9 families seem to have been horizontally transferred to archaea. The winged helix-turn-helix (HTH) is by far the most abundant structure (motif) in prokaryotes, and might have been the earliest HTH motif to appear as shown by its distribution and abundance in both bacterial and archaeal cellular domains. Horizontal gene transfer and lineage-specific gene losses suggest a progressive elimination of TFs in the course of archaeal and bacterial evolution. This analysis provides a framework for discussing the selective forces directing the evolution of the transcriptional machinery in prokaryotes.}, }
@article {pmid15554962, year = {2004}, author = {Atmakuri, K and Cascales, E and Christie, PJ}, title = {Energetic components VirD4, VirB11 and VirB4 mediate early DNA transfer reactions required for bacterial type IV secretion.}, journal = {Molecular microbiology}, volume = {54}, number = {5}, pages = {1199-1211}, pmid = {15554962}, issn = {0950-382X}, support = {R01 GM048746/GM/NIGMS NIH HHS/United States ; GM48746/GM/NIGMS NIH HHS/United States ; }, mesh = {Adenosine Triphosphate/metabolism ; Agrobacterium tumefaciens/genetics/*metabolism ; Amino Acid Motifs ; Bacterial Proteins/genetics/*metabolism ; Binding Sites ; Biological Transport ; DNA, Bacterial/genetics/*metabolism ; DNA-Binding Proteins/genetics/metabolism ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Immunoprecipitation ; Mutagenesis, Site-Directed ; Mutation ; Protein Interaction Mapping ; Protein Subunits/genetics/metabolism ; Virulence Factors/genetics/*metabolism ; }, abstract = {Bacteria use type IV secretion systems (T4SS) to translocate DNA (T-DNA) and protein substrates across the cell envelope. By transfer DNA immunoprecipitation (TrIP), we recently showed that T-DNA translocates through the Agrobacterium tumefaciens VirB/D4 T4SS by forming close contacts sequentially with the VirD4 receptor, VirB11 ATPase, the inner membrane subunits VirB6 and VirB8 and, finally, VirB2 pilin and VirB9. Here, by TrIP, we show that nucleoside triphosphate binding site (Walker A motif) mutations do not disrupt VirD4 substrate binding or transfer to VirB11, suggesting that these early reactions proceed independently of ATP binding or hydrolysis. In contrast, VirD4, VirB11 and VirB4 Walker A mutations each arrest substrate transfer to VirB6 and VirB8, suggesting that these subunits energize this transfer reaction by an ATP-dependent mechanism. By co-immunoprecipitation, we supply evidence for VirD4 interactions with VirB4 and VirB11 independently of other T4SS subunits or intact Walker A motifs, and with the bitopic inner membrane subunit VirB10. We reconstituted substrate transfer from VirD4 to VirB11 and to VirB6 and VirB8 by co-synthesis of previously identified 'core' components of the VirB/D4 T4SS. Our findings define genetic requirements for DNA substrate binding and the early transfer reactions of a bacterial type IV translocation pathway.}, }
@article {pmid15552042, year = {2004}, author = {Cheng, TC and Xia, QY and Liu, C and Zhao, P and Zha, XF and Xu, HF and Xiang, ZH}, title = {[Three Bombyx mori genes, chi, gluE and fruA, encode proteins homologous to microorganism and primary analysis of horizontal gene transfer].}, journal = {Yi chuan xue bao = Acta genetica Sinica}, volume = {31}, number = {10}, pages = {1082-1088}, pmid = {15552042}, issn = {0379-4172}, mesh = {Animals ; Bombyx/*genetics ; Chitinases/*genetics ; *Gene Transfer, Horizontal ; *Genes, Insect ; Phylogeny ; UDPglucose 4-Epimerase/*genetics ; beta-Fructofuranosidase/*genetics ; }, abstract = {According to the analysis of large scale EST sequencing of silkworm, Bombyx mori, we found that chi, glue and fruA of silkworm have very high homology at amino acid level and closely phylogenetic relative with that of microorganism, but lower similarity with genes of eelworm (Caenorhabditis elegans), fruitfly (Drosophila melanogaster), mosquito (Anopheles gambiae) and other relative insects, respectively. It indicates that each of them is likely to have common ancestor with that of microorganism. Namely, microbial genes were likely transferred to silkworm by horizontal gene transfer, instead of the vertical inheritance in evolutionary manner.}, }
@article {pmid15551059, year = {2005}, author = {Rabus, R and Kube, M and Heider, J and Beck, A and Heitmann, K and Widdel, F and Reinhardt, R}, title = {The genome sequence of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1.}, journal = {Archives of microbiology}, volume = {183}, number = {1}, pages = {27-36}, doi = {10.1007/s00203-004-0742-9}, pmid = {15551059}, issn = {0302-8933}, mesh = {Adaptation, Physiological/genetics ; Aerobiosis ; Anaerobiosis ; Azoarcus/genetics ; Bacterial Proteins/genetics ; Betaproteobacteria/classification/*genetics/*metabolism ; Biodegradation, Environmental ; Chromosomes, Bacterial/genetics ; DNA, Bacterial/chemistry ; Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; Hydrocarbons, Aromatic/*metabolism ; Interspersed Repetitive Sequences ; Molecular Sequence Data ; Multigene Family ; Nitrogen Fixation/genetics ; Open Reading Frames ; Plasmids/genetics ; *Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {Recent research on microbial degradation of aromatic and other refractory compounds in anoxic waters and soils has revealed that nitrate-reducing bacteria belonging to the Betaproteobacteria contribute substantially to this process. Here we present the first complete genome of a metabolically versatile representative, strain EbN1, which metabolizes various aromatic compounds, including hydrocarbons. A circular chromosome (4.3 Mb) and two plasmids (0.21 and 0.22 Mb) encode 4603 predicted proteins. Ten anaerobic and four aerobic aromatic degradation pathways were recognized, with the encoding genes mostly forming clusters. The presence of paralogous gene clusters (e.g., for anaerobic phenylacetate oxidation), high sequence similarities to orthologs from other strains (e.g., for anaerobic phenol metabolism) and frequent mobile genetic elements (e.g., more than 200 genes for transposases) suggest high genome plasticity and extensive lateral gene transfer during metabolic evolution of strain EbN1. Metabolic versatility is also reflected by the presence of multiple respiratory complexes. A large number of regulators, including more than 30 two-component and several FNR-type regulators, indicate a finely tuned regulatory network able to respond to the fluctuating availability of organic substrates and electron acceptors in the environment. The absence of genes required for nitrogen fixation and specific interaction with plants separates strain EbN1 ecophysiologically from the closely related nitrogen-fixing plant symbionts of the Azoarcus cluster. Supplementary material on sequence and annotation are provided at the Web page http://www.micro-genomes.mpg.de/ebn1/.}, }
@article {pmid15550939, year = {2004}, author = {Batut, J and Andersson, SG and O'Callaghan, D}, title = {The evolution of chronic infection strategies in the alpha-proteobacteria.}, journal = {Nature reviews. Microbiology}, volume = {2}, number = {12}, pages = {933-945}, doi = {10.1038/nrmicro1044}, pmid = {15550939}, issn = {1740-1526}, mesh = {Alphaproteobacteria/*pathogenicity/*physiology ; Animals ; Biological Evolution ; Chronic Disease ; Eukaryotic Cells/microbiology ; *Genome, Bacterial ; Gram-Negative Bacterial Infections/microbiology ; Humans ; Plants/microbiology ; Symbiosis ; Virulence ; }, abstract = {Many of the alpha-proteobacteria establish long-term, often chronic, interactions with higher eukaryotes. These interactions range from pericellular colonization through facultative intracellular multiplication to obligate intracellular lifestyles. A common feature in this wide range of interactions is modulation of host-cell proliferation, which sometimes leads to the formation of tumour-like structures in which the bacteria can grow. Comparative genome analyses reveal genome reduction by gene loss in the intracellular alpha-proteobacterial lineages, and genome expansion by gene duplication and horizontal gene transfer in the free-living species. In this review, we discuss alpha-proteobacterial genome evolution and highlight strategies and mechanisms used by these bacteria to infect and multiply in eukaryotic cells.}, }
@article {pmid15548986, year = {2004}, author = {Ogata, Y and Fujishiro, J and Kawana, H and Kobayashi, E}, title = {Adenovirus-mediated gene transfer to the rat heart graft.}, journal = {Transplantation}, volume = {78}, number = {9}, pages = {1408; author reply 1408-9}, doi = {10.1097/01.tp.0000137335.73107.5e}, pmid = {15548986}, issn = {0041-1337}, mesh = {Adenoviridae/*genetics ; Animals ; Gene Transfer, Horizontal ; *Genetic Therapy ; Genetic Vectors/genetics ; *Heart Transplantation ; Luciferases/genetics ; Myocardium/metabolism ; Proto-Oncogene Proteins c-bcl-2/*genetics ; Rats ; }, }
@article {pmid15548299, year = {2004}, author = {de Niederhäusern, S and Sabia, C and Messi, P and Guerrieri, E and Manicardi, G and Bondi, M}, title = {Glycopeptide-resistance transferability from vancomycin-resistant enterococci of human and animal source to Listeria spp.}, journal = {Letters in applied microbiology}, volume = {39}, number = {6}, pages = {483-489}, doi = {10.1111/j.1472-765X.2004.01598.x}, pmid = {15548299}, issn = {0266-8254}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics ; Carbon-Oxygen Ligases/genetics ; *Conjugation, Genetic ; DNA, Bacterial/analysis ; Enterococcus/drug effects/*genetics/isolation &amp; purification ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Gram-Positive Bacterial Infections/microbiology ; Humans ; Listeria/drug effects/*genetics ; Microbial Sensitivity Tests ; Plasmids ; Teicoplanin/pharmacology ; Vancomycin/pharmacology ; Vancomycin Resistance/*genetics ; }, abstract = {AIMS: The glycopeptide-resistance transferability from vancomycin-resistant enterococci (VRE) of clinical and animal origin to different species of Listeria was investigated.<br><br>METHODS AND RESULTS: Of 36 matings, performed on membrane filter, the glycopeptide resistance was successfully transferred in six attempts, five with donors of animal origin and only one with donors from clinical source. The acquired glycopeptide resistance in Listeria transconjugants was confirmed by the presence of the conjugative plasmid band and by the amplification of the 732-bp fragment of vanA gene in transferred plasmids.<br><br>CONCLUSIONS: Despite the lower number of bacteria used in this study, the source of enterococci influenced the outcome of mating. Moreover transferred VanA plasmid induced a different expression in Listeria transconjugants, suggesting that gene expression might be influenced by species affiliation of recipients.<br><br>Our data strengthen the opinion that enterococci are an important source of resistance genes for Listeria via the transfer of movable genetic elements. As these strains are commonly found in the same habitats, a horizontal spread of glycopeptide resistance in Listeria spp. could be possible.}, }
@article {pmid15538356, year = {2004}, author = {Mower, JP and Stefanović, S and Young, GJ and Palmer, JD}, title = {Plant genetics: gene transfer from parasitic to host plants.}, journal = {Nature}, volume = {432}, number = {7014}, pages = {165-166}, doi = {10.1038/432165b}, pmid = {15538356}, issn = {1476-4687}, mesh = {Animals ; Cuscuta/classification/cytology/*genetics ; DNA, Mitochondrial/genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Plant/*genetics ; Phylogeny ; Plant Diseases/*genetics/*parasitology ; Plantago/classification/cytology/*genetics/*parasitology ; Pseudogenes/genetics ; }, abstract = {Plant mitochondrial genes are transmitted horizontally across mating barriers with surprising frequency, but the mechanism of transfer is unclear. Here we describe two new cases of horizontal gene transfer, from parasitic flowering plants to their host flowering plants, and present phylogenetic and biogeographic evidence that this occurred as a result of direct physical contact between the two. Our findings complement the discovery that genes can be transferred in the opposite direction, from host to parasite plant.}, }
@article {pmid15535883, year = {2004}, author = {Battistuzzi, FU and Feijao, A and Hedges, SB}, title = {A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land.}, journal = {BMC evolutionary biology}, volume = {4}, number = {}, pages = {44}, pmid = {15535883}, issn = {1471-2148}, mesh = {Bacteria/*genetics ; *Biological Evolution ; Biomass ; Evolution, Molecular ; *Genomics ; Methane/*metabolism ; Photosynthesis/genetics ; *Time ; }, abstract = {BACKGROUND: The timescale of prokaryote evolution has been difficult to reconstruct because of a limited fossil record and complexities associated with molecular clocks and deep divergences. However, the relatively large number of genome sequences currently available has provided a better opportunity to control for potential biases such as horizontal gene transfer and rate differences among lineages. We assembled a data set of sequences from 32 proteins (approximately 7600 amino acids) common to 72 species and estimated phylogenetic relationships and divergence times with a local clock method.<br><br>RESULTS: Our phylogenetic results support most of the currently recognized higher-level groupings of prokaryotes. Of particular interest is a well-supported group of three major lineages of eubacteria (Actinobacteria, Deinococcus, and Cyanobacteria) that we call Terrabacteria and associate with an early colonization of land. Divergence time estimates for the major groups of eubacteria are between 2.5-3.2 billion years ago (Ga) while those for archaebacteria are mostly between 3.1-4.1 Ga. The time estimates suggest a Hadean origin of life (prior to 4.1 Ga), an early origin of methanogenesis (3.8-4.1 Ga), an origin of anaerobic methanotrophy after 3.1 Ga, an origin of phototrophy prior to 3.2 Ga, an early colonization of land 2.8-3.1 Ga, and an origin of aerobic methanotrophy 2.5-2.8 Ga.<br><br>CONCLUSIONS: Our early time estimates for methanogenesis support the consideration of methane, in addition to carbon dioxide, as a greenhouse gas responsible for the early warming of the Earths' surface. Our divergence times for the origin of anaerobic methanotrophy are compatible with highly depleted carbon isotopic values found in rocks dated 2.8-2.6 Ga. An early origin of phototrophy is consistent with the earliest bacterial mats and structures identified as stromatolites, but a 2.6 Ga origin of cyanobacteria suggests that those Archean structures, if biologically produced, were made by anoxygenic photosynthesizers. The resistance to desiccation of Terrabacteria and their elaboration of photoprotective compounds suggests that the common ancestor of this group inhabited land. If true, then oxygenic photosynthesis may owe its origin to terrestrial adaptations.}, }
@article {pmid15535864, year = {2004}, author = {Huang, J and Mullapudi, N and Lancto, CA and Scott, M and Abrahamsen, MS and Kissinger, JC}, title = {Phylogenomic evidence supports past endosymbiosis, intracellular and horizontal gene transfer in Cryptosporidium parvum.}, journal = {Genome biology}, volume = {5}, number = {11}, pages = {R88}, pmid = {15535864}, issn = {1474-760X}, support = {R01 AI045806/AI/NIAID NIH HHS/United States ; U01 AI 46397/AI/NIAID NIH HHS/United States ; AI05093/AI/NIAID NIH HHS/United States ; Z01 AI005093/ImNIH/Intramural NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; 1R01AI045806-01A1/AI/NIAID NIH HHS/United States ; }, mesh = {1,4-alpha-Glucan Branching Enzyme/genetics ; Animals ; Cryptosporidium parvum/*genetics ; Eukaryota/genetics ; Evolution, Molecular ; Gene Expression Profiling/methods ; Gene Expression Regulation/genetics ; Gene Transfer, Horizontal/*genetics ; Genes/genetics ; Genes, Bacterial/genetics ; *Genome, Protozoan ; *Phylogeny ; Symbiosis/*genetics ; }, abstract = {BACKGROUND: The apicomplexan parasite Cryptosporidium parvum is an emerging pathogen capable of causing illness in humans and other animals and death in immunocompromised individuals. No effective treatment is available and the genome sequence has recently been completed. This parasite differs from other apicomplexans in its lack of a plastid organelle, the apicoplast. Gene transfer, either intracellular from an endosymbiont/donor organelle or horizontal from another organism, can provide evidence of a previous endosymbiotic relationship and/or alter the genetic repertoire of the host organism. Given the importance of gene transfers in eukaryotic evolution and the potential implications for chemotherapy, it is important to identify the complement of transferred genes in Cryptosporidium.<br><br>RESULTS: We have identified 31 genes of likely plastid/endosymbiont (n = 7) or prokaryotic (n = 24) origin using a phylogenomic approach. The findings support the hypothesis that Cryptosporidium evolved from a plastid-containing lineage and subsequently lost its apicoplast during evolution. Expression analyses of candidate genes of algal and eubacterial origin show that these genes are expressed and developmentally regulated during the life cycle of C. parvum.<br><br>CONCLUSIONS: Cryptosporidium is the recipient of a large number of transferred genes, many of which are not shared by other apicomplexan parasites. Genes transferred from distant phylogenetic sources, such as eubacteria, may be potential targets for therapeutic drugs owing to their phylogenetic distance or the lack of homologs in the host. The successful integration and expression of the transferred genes in this genome has changed the genetic and metabolic repertoire of the parasite.}, }
@article {pmid15532982, year = {2004}, author = {Franken, C and Brandt, C and Bröker, G and Spellerberg, B}, title = {ISSag1 in streptococcal strains of human and animal origin.}, journal = {International journal of medical microbiology : IJMM}, volume = {294}, number = {4}, pages = {247-254}, doi = {10.1016/j.ijmm.2004.04.002}, pmid = {15532982}, issn = {1438-4221}, mesh = {Adhesins, Bacterial/*genetics ; Animals ; Base Sequence ; Blotting, Southern ; Cattle ; DNA Transposable Elements/*genetics ; DNA, Bacterial/chemistry/genetics ; Endopeptidases/*genetics ; Gene Transfer, Horizontal/*genetics ; Humans ; Molecular Sequence Data ; Polymerase Chain Reaction ; Recombination, Genetic/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Streptococcus agalactiae/enzymology/*genetics ; }, abstract = {The chromosomal region of Streptococcus agalactiae harboring the C5a peptidase and the lmb genes displays the structure of a composite transposon. Its presence in a streptococcal strain is associated with the origin of this strain from a human host. In S. agalactiae it is flanked by two copies of the insertion element ISSag2, and the nucleotide sequence for a third IS element (ISSag1) can be found in this region. Based on amino acid sequence similarity of the deduced transposase ISSag1 belongs to the IS3 family. It is 1251 bp long and flanked by 37 bp imperfect inverted repeats. Horizontal gene transfer among different bacterial species is facilitated by mobile genetic elements. To investigate if ISSag1 homologues are also present in other streptococcal species, various species of pyogenic streptococci from animal and human origin were analyzed by Southern blot hybridization and PCR. Among the different streptococcal species, multiple copies of an ISSag1 homologue could only be detected in S. dysgalactiae subsp. dysgalactiae strains of animal origin. All of the S. agalactiae strains harbored only a single copy, that was always found in strains with the scpB-lmb composite transposon. A single copy of an ISSag1 homologue could also be detected in some of the S. pyogenes and S. dysgalactiae subsp. equisimilis strains. Nucleotide sequencing of the IS element in S. dysgalactiae subsp. dysgalactiae strains revealed several different variants. One of the variants showed the features of a regular IS3 element. The other two variants that were observed displayed a 500-bp deletion and a mosaic structure composed of ISSag1 and ISSag2 homologues. This mosaic structure suggests that recombination and horizontal gene transfer events in S. dysgalactiae strains of bovine origin could have played a role in the assembly of the scpB-lmb composite transposon structure.}, }
@article {pmid15531154, year = {2004}, author = {Burt, A and Koufopanou, V}, title = {Homing endonuclease genes: the rise and fall and rise again of a selfish element.}, journal = {Current opinion in genetics &amp; development}, volume = {14}, number = {6}, pages = {609-615}, doi = {10.1016/j.gde.2004.09.010}, pmid = {15531154}, issn = {0959-437X}, mesh = {Endonucleases/chemistry/*genetics/metabolism ; Evolution, Molecular ; Gene Conversion ; Gene Transfer, Horizontal/*genetics ; *Genes ; }, abstract = {Homing endonuclease genes (HEGs) are selfish genetic elements that spread by first cleaving chromosomes that do not contain them and then getting copied across to the broken chromosome as a byproduct of the repair process. The success of this strategy will depend on the opportunities for homing--in other words, the frequency with which HEG(+) and HEG(-) chromosomes come into contact--which varies widely among host taxa. HEGs are also unusual in that the selection pressure for endonuclease function disappears if they become fixed in a population, which makes them susceptible to degeneration and imposes a need for regular horizontal transmission between species. HEGs will be selected to reduce the harm done to the host organism, and this is expected to influence the evolution of their sequence specificity and maturase functions. HEGs may also be domesticated by their hosts, and are currently being put to human uses.}, }
@article {pmid15530743, year = {2004}, author = {Ewers, C and Janssen, T and Kiessling, S and Philipp, HC and Wieler, LH}, title = {Molecular epidemiology of avian pathogenic Escherichia coli (APEC) isolated from colisepticemia in poultry.}, journal = {Veterinary microbiology}, volume = {104}, number = {1-2}, pages = {91-101}, doi = {10.1016/j.vetmic.2004.09.008}, pmid = {15530743}, issn = {0378-1135}, mesh = {Animals ; *Chickens ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; Electrophoresis, Gel, Pulsed-Field/veterinary ; Escherichia coli/*genetics/isolation &amp; purification/pathogenicity ; Escherichia coli Infections/*epidemiology/microbiology/*veterinary ; Female ; Germany/epidemiology ; Molecular Epidemiology ; Nucleic Acid Hybridization ; O Antigens ; Polymerase Chain Reaction/veterinary ; Poultry Diseases/*epidemiology/*microbiology ; Sepsis/epidemiology/microbiology/veterinary ; Virulence/genetics ; }, abstract = {The molecular biology and epidemiology of 150 avian pathogenic Escherichia coli strains (APEC) isolated from septicemic poultry in Germany was investigated by serotyping, pulsed field gel electrophoresis (PFGE), and polymerase chain reaction (PCR). Only 49.6% of the isolates could be grouped to serogroups O1, O2, and O78. Macrorestriction analyses data revealed two large clonal groups (clusters I and II) among the APEC strains with a similarity of 60.9% to each other. An association between restriction pattern and serogroup or origin of the strains was only present in a few subgroups of each clusters I and II, but was not evident. In contrast, our data revealed distinct combinations of virulence-associated genes in that 51.2% of the O2-strains harboured a combination of the genes fyuA, irp2, iucD, tsh, vat, fimC, and colV and 36.4% of the O78-strains possessed the same gene combination with exception of vat. With 34 different gene combinations the non-O1, -O2, -O78 isolates revealed a higher variability in their virulence gene pattern than O1-, O2-, and O78-strains with 6, 13, and 9 patterns, respectively. Our data indicate only a limited association between the virulence gene pattern and the serogroup of APEC strains and question the sensitivity of O-typing for APEC identification without the application of further diagnostic tools. Although a limited number of APEC clones exist, horizontal gene transfer seems to be common in these pathogens. These findings strengthen further research on the population structure of APEC and may be the reason for the lack of clear definition of this common E. coli pathotype.}, }
@article {pmid15529149, year = {2004}, author = {Davison, J}, title = {Monitoring horizontal gene transfer.}, journal = {Nature biotechnology}, volume = {22}, number = {11}, pages = {1349; author reply 1349-50}, doi = {10.1038/nbt1104-1349a}, pmid = {15529149}, issn = {1087-0156}, mesh = {Ecosystem ; Environmental Monitoring/*methods ; Gene Expression Profiling/*methods ; Gene Transfer, Horizontal/*genetics ; Genetic Engineering/*methods ; Genetic Testing/methods ; Plants, Genetically Modified/*genetics ; Protein Engineering/methods ; Recombinant Proteins/biosynthesis/genetics ; Risk Assessment/*methods ; Risk Factors ; *Soil Microbiology ; }, }
@article {pmid15528742, year = {2004}, author = {Towers, RJ and Gal, D and McMillan, D and Sriprakash, KS and Currie, BJ and Walker, MJ and Chhatwal, GS and Fagan, PK}, title = {Fibronectin-binding protein gene recombination and horizontal transfer between group A and G streptococci.}, journal = {Journal of clinical microbiology}, volume = {42}, number = {11}, pages = {5357-5361}, pmid = {15528742}, issn = {0095-1137}, mesh = {Adhesins, Bacterial/*genetics ; Fibronectins/*metabolism ; *Gene Transfer, Horizontal ; Humans ; Molecular Sequence Data ; *Recombination, Genetic ; Sequence Analysis, DNA ; Streptococcal Infections/microbiology ; Streptococcus/classification/*genetics ; Streptococcus pyogenes/classification/*genetics ; }, abstract = {We report evidence of interspecies gene transfer between the important virulence factor genes sfbI and gfbA. Because the identified group G streptococcus gfbA types possess DNA cassettes that can be identified in a number of group A streptococcus strains, it appears that homologous recombination is occurring between these species.}, }
@article {pmid15528664, year = {2004}, author = {Mazón, G and Erill, I and Campoy, S and Cortés, P and Forano, E and Barbé, J}, title = {Reconstruction of the evolutionary history of the LexA-binding sequence.}, journal = {Microbiology (Reading, England)}, volume = {150}, number = {Pt 11}, pages = {3783-3795}, doi = {10.1099/mic.0.27315-0}, pmid = {15528664}, issn = {1350-0872}, mesh = {Alphaproteobacteria/genetics ; Amino Acid Sequence ; Bacteria/*genetics ; Bacterial Proteins/genetics/isolation &amp; purification/*metabolism ; Binding Sites ; Cyanobacteria ; DNA Footprinting ; DNA-Binding Proteins/metabolism ; Deltaproteobacteria/genetics ; Electrophoretic Mobility Shift Assay ; *Evolution, Molecular ; Fibrobacter/genetics ; Gammaproteobacteria/genetics ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; Protein Binding/*genetics ; Sequence Alignment ; Sequence Homology ; Serine Endopeptidases/genetics/isolation &amp; purification/*metabolism ; }, abstract = {In recent years, the recognition sequence of the SOS repressor LexA protein has been identified for several bacterial clades, such as the Gram-positive, green non-sulfur bacteria and Cyanobacteria phyla, or the 'Alphaproteobacteria', 'Deltaproteobacteria' and 'Gammaproteobacteria' classes. Nevertheless, the evolutionary relationship among these sequences and the proteins that recognize them has not been analysed. Fibrobacter succinogenes is an anaerobic Gram-negative bacterium that branched from a common bacterial ancestor immediately before the Proteobacteria phylum. Taking advantage of its intermediate position in the phylogenetic tree, and in an effort to reconstruct the evolutionary history of LexA-binding sequences, the F. succinogenes lexA gene has been isolated and its product purified to identify its DNA recognition motif through electrophoretic mobility assays and footprinting experiments. After comparing the available LexA DNA-binding sequences with the F. succinogenes one, reported here, directed mutagenesis of the F. succinogenes LexA-binding sequence and phylogenetic analyses of LexA proteins have revealed the existence of two independent evolutionary lanes for the LexA recognition motif that emerged from the Gram-positive box: one generating the Cyanobacteria and 'Alphaproteobacteria' LexA-binding sequences, and the other giving rise to the F. succinogenes and Myxococcus xanthus ones, in a transitional step towards the current 'Gammaproteobacteria' LexA box. The contrast between the results reported here and the phylogenetic data available in the literature suggests that, some time after its emergence as a distinct bacterial class, the 'Alphaproteobacteria' lost its vertically received lexA gene, but received later through lateral gene transfer a new lexA gene belonging to either a cyanobacterium or a bacterial species closely related to this phylum. This constitutes the first report based on experimental evidence of lateral gene transfer in the evolution of a gene governing such a complex regulatory network as the bacterial SOS system.}, }
@article {pmid15525705, year = {2004}, author = {Rigden, DJ}, title = {Archaea recruited D-Tyr-tRNATyr deacylase for editing in Thr-tRNA synthetase.}, journal = {RNA (New York, N.Y.)}, volume = {10}, number = {12}, pages = {1845-1851}, pmid = {15525705}, issn = {1355-8382}, mesh = {Amino Acid Sequence ; Aminoacyltransferases/chemistry/genetics/*metabolism ; Archaea/*genetics/*metabolism ; Computational Biology ; Dimerization ; Evolution, Molecular ; Methanosarcina/genetics/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Structure, Quaternary ; *RNA Editing ; Sequence Homology, Amino Acid ; Threonine-tRNA Ligase/chemistry/genetics/*metabolism ; }, abstract = {Aminoacyl-tRNA synthetases (AARSs) are key players in the maintenance of the genetic code through correct pairing of amino acids with their cognate tRNA molecules. To this end, some AARSs, as well as seeking to recognize the correct amino acid during synthesis of aminoacyl-tRNA, enhance specificity through recognition of mischarged aminoacyl-tRNA molecules in a separate editing reaction. Recently, an editing domain, of uncertain provenance, idiosyncratic to some archaeal ThrRSs has been characterized. Here, sequence analyses and molecular modeling are reported that clearly show a relationship of the archaea-specific ThrRS editing domains with d-Tyr-tRNATyr deacylases (DTDs). The model enables the identification of the catalytic site and other substrate binding residues, as well as the proposal of a likely catalytic mechanism. Interestingly, typical DTD sequences, common in bacteria and eukaryotes, are entirely absent in archaea, consistent with an evolutionary scheme in which DTD was co-opted to serve as a ThrRS editing domain in archaea soon after their divergence from eukaryotes. A group of present-day archaebacteria contain a ThrRS obtained from a bacterium by horizontal gene transfer. In some of these cases a vestigial version of the original archaeal ThrRS, of potentially novel function, is maintained.}, }
@article {pmid15518872, year = {2004}, author = {Espinosa-Urgel, M}, title = {Plant-associated Pseudomonas populations: molecular biology, DNA dynamics, and gene transfer.}, journal = {Plasmid}, volume = {52}, number = {3}, pages = {139-150}, doi = {10.1016/j.plasmid.2004.06.004}, pmid = {15518872}, issn = {0147-619X}, mesh = {Chromosomes, Bacterial/genetics ; DNA, Bacterial/*genetics ; *Gene Transfer Techniques ; Plants/*microbiology ; Pseudomonas/*genetics ; }, abstract = {Bacteria of the genus Pseudomonas are usual colonizers of plant leaves, roots, and seeds, establishing at relatively high cell densities on plant surfaces, where they aggregate and form microcolonies similar to those observed during biofilm development on abiotic surfaces. These plant-associated biofilms undergo chromosomal rearrangements and are hot spots for conjugative plasmid transfer, favored by the close proximity between cells and the constant supply of nutrients coming from the plant in the form of exudates or leachates. The molecular determinants known to be involved in bacterial colonization of the different plant surfaces, and the mechanisms of horizontal gene transfer in plant-associated Pseudomonas populations are summarized in this review.}, }
@article {pmid15516593, year = {2004}, author = {Warren, R and Hsiao, WW and Kudo, H and Myhre, M and Dosanjh, M and Petrescu, A and Kobayashi, H and Shimizu, S and Miyauchi, K and Masai, E and Yang, G and Stott, JM and Schein, JE and Shin, H and Khattra, J and Smailus, D and Butterfield, YS and Siddiqui, A and Holt, R and Marra, MA and Jones, SJ and Mohn, WW and Brinkman, FS and Fukuda, M and Davies, J and Eltis, LD}, title = {Functional characterization of a catabolic plasmid from polychlorinated- biphenyl-degrading Rhodococcus sp. strain RHA1.}, journal = {Journal of bacteriology}, volume = {186}, number = {22}, pages = {7783-7795}, pmid = {15516593}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics ; Base Sequence ; Biodegradation, Environmental ; Cytochrome P-450 Enzyme System/genetics ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Open Reading Frames/genetics ; Phylogeny ; Plasmids/*genetics ; Polychlorinated Biphenyls/*metabolism ; Replication Origin ; Rhodococcus/*genetics/metabolism ; Sequence Analysis, DNA ; Telomere ; }, abstract = {Rhodococcus sp. strain RHA1, a potent polychlorinated-biphenyl (PCB)-degrading strain, contains three linear plasmids ranging in size from 330 to 1,100 kb. As part of a genome sequencing project, we report here the complete sequence and characterization of the smallest and least-well-characterized of the RHA1 plasmids, pRHL3. The plasmid is an actinomycete invertron, containing large terminal inverted repeats with a tightly associated protein and a predicted open reading frame (ORF) that is similar to that of a mycobacterial rep gene. The pRHL3 plasmid has 300 putative genes, almost 21% of which are predicted to have a catabolic function. Most of these are organized into three clusters. One of the catabolic clusters was predicted to include limonene degradation genes. Consistent with this prediction, RHA1 grew on limonene, carveol, or carvone as the sole carbon source. The plasmid carries three cytochrome P450-encoding (CYP) genes, a finding consistent with the high number of CYP genes found in other actinomycetes. Two of the CYP genes appear to belong to novel families; the third belongs to CYP family 116 but appears to belong to a novel class based on the predicted domain structure of its reductase. Analyses indicate that pRHL3 also contains four putative "genomic islands" (likely to have been acquired by horizontal transfer), insertion sequence elements, 19 transposase genes, and a duplication that spans two ORFs. One of the genomic islands appears to encode resistance to heavy metals. The plasmid does not appear to contain any housekeeping genes. However, each of the three catabolic clusters contains related genes that appear to be involved in glucose metabolism.}, }
@article {pmid15516565, year = {2004}, author = {Brom, S and Girard, L and Tun-Garrido, C and García-de los Santos, A and Bustos, P and González, V and Romero, D}, title = {Transfer of the symbiotic plasmid of Rhizobium etli CFN42 requires cointegration with p42a, which may be mediated by site-specific recombination.}, journal = {Journal of bacteriology}, volume = {186}, number = {22}, pages = {7538-7548}, pmid = {15516565}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; Attachment Sites, Microbiological ; Base Sequence ; Conjugation, Genetic ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Integrases/genetics/metabolism ; Molecular Sequence Data ; Phaseolus/microbiology ; Plasmids/*genetics ; *Recombination, Genetic ; Rhizobium etli/*genetics/growth &amp; development/metabolism ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {Plasmid p42a from Rhizobium etli CFN42 is self-transmissible and indispensable for conjugative transfer of the symbiotic plasmid (pSym). Most pSym transconjugants also inherit p42a. pSym transconjugants that lack p42a always contain recombinant pSyms, which we designated RpSyms*. RpSyms* do not contain some pSym segments and instead have p42a sequences, including the replication and transfer regions. These novel recombinant plasmids are compatible with wild-type pSym, incompatible with p42a, and self-transmissible. The symbiotic features of derivatives simultaneously containing a wild-type pSym and an RpSym* were analyzed. Structural analysis of 10 RpSyms* showed that 7 shared one of the two pSym-p42a junctions. Sequencing of this common junction revealed a 53-bp region that was 90% identical in pSym and p42a, including a 5-bp central region flanked by 9- to 11-bp inverted repeats reminiscent of bacterial and phage attachment sites. A gene encoding an integrase-like protein (intA) was localized downstream of the attachment site on p42a. Mutation or the absence of intA abolished pSym transfer from a recA mutant donor. Complementation with the wild-type intA gene restored transfer of pSym. We propose that pSym-p42a cointegration is required for pSym transfer; cointegration may be achieved either through homologous recombination among large reiterated sequences or through IntA-mediated site-specific recombination between the attachment sites. Cointegrates formed through the site-specific system but resolved through RecA-dependent recombination or vice versa generate RpSyms*. A site-specific recombination system for plasmid cointegration is a novel feature of these large plasmids and implies that there is unique regulation which affects the distribution of pSym in nature due to the role of the cointegrate in conjugative transfer.}, }
@article {pmid15508708, year = {2004}, author = {Koga, A}, title = {[DNA-based transposable elements as potential source of genome rearrangements in vertebrates].}, journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme}, volume = {49}, number = {13}, pages = {2103-2110}, pmid = {15508708}, issn = {0039-9450}, mesh = {Animals ; *DNA Transposable Elements/genetics/physiology ; Gene Rearrangement/*genetics ; Gene Transfer, Horizontal/genetics ; *Genome ; Monophenol Monooxygenase/genetics ; Mutation ; Vertebrates/genetics ; }, }
@article {pmid15496784, year = {2005}, author = {Lawrence, JG}, title = {Horizontal and vertical gene transfer: the life history of pathogens.}, journal = {Contributions to microbiology}, volume = {12}, number = {}, pages = {255-271}, doi = {10.1159/000081699}, pmid = {15496784}, issn = {1420-9519}, mesh = {DNA, Bacterial/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; *Genome, Bacterial ; Genomic Islands/genetics ; Gram-Negative Bacteria/*genetics/pathogenicity ; Gram-Negative Bacterial Infections/*microbiology ; Humans ; Virulence ; }, }
@article {pmid15496783, year = {2005}, author = {Hochhut, B and Dobrindt, U and Hacker, J}, title = {Pathogenicity islands and their role in bacterial virulence and survival.}, journal = {Contributions to microbiology}, volume = {12}, number = {}, pages = {234-254}, doi = {10.1159/000081698}, pmid = {15496783}, issn = {1420-9519}, mesh = {Animals ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial ; Genomic Islands/*genetics ; Gram-Negative Bacteria/*genetics/*pathogenicity ; Gram-Negative Bacterial Infections/genetics/*microbiology/pathology ; Gram-Positive Bacteria/*genetics/*pathogenicity ; Gram-Positive Bacterial Infections/genetics/*microbiology/pathology ; Humans ; Virulence ; }, }
@article {pmid15496229, year = {2004}, author = {Nickrent, DL and Blarer, A and Qiu, YL and Vidal-Russell, R and Anderson, FE}, title = {Phylogenetic inference in Rafflesiales: the influence of rate heterogeneity and horizontal gene transfer.}, journal = {BMC evolutionary biology}, volume = {4}, number = {}, pages = {40}, pmid = {15496229}, issn = {1471-2148}, mesh = {Bayes Theorem ; Cell Nucleus/genetics ; Chloroplasts/genetics ; *Gene Transfer, Horizontal ; *Genes, Plant ; Likelihood Functions ; Magnoliopsida/*classification/*genetics ; Mitochondria/genetics ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The phylogenetic relationships among the holoparasites of Rafflesiales have remained enigmatic for over a century. Recent molecular phylogenetic studies using the mitochondrial matR gene placed Rafflesia, Rhizanthes and Sapria (Rafflesiaceae s. str.) in the angiosperm order Malpighiales and Mitrastema (Mitrastemonaceae) in Ericales. These phylogenetic studies did not, however, sample two additional groups traditionally classified within Rafflesiales (Apodantheaceae and Cytinaceae). Here we provide molecular phylogenetic evidence using DNA sequence data from mitochondrial and nuclear genes for representatives of all genera in Rafflesiales.<br><br>RESULTS: Our analyses indicate that the phylogenetic affinities of the large-flowered clade and Mitrastema, ascertained using mitochondrial matR, are congruent with results from nuclear SSU rDNA when these data are analyzed using maximum likelihood and Bayesian methods. The relationship of Cytinaceae to Malvales was recovered in all analyses. Relationships between Apodanthaceae and photosynthetic angiosperms varied depending upon the data partition: Malvales (3-gene), Cucurbitales (matR) or Fabales (atp1). The latter incongruencies suggest that horizontal gene transfer (HGT) may be affecting the mitochondrial gene topologies. The lack of association between Mitrastema and Ericales using atp1 is suggestive of HGT, but greater sampling within eudicots is needed to test this hypothesis further.<br><br>CONCLUSIONS: Rafflesiales are not monophyletic but composed of three or four independent lineages (families): Rafflesiaceae, Mitrastemonaceae, Apodanthaceae and Cytinaceae. Long-branch attraction appears to be misleading parsimony analyses of nuclear small-subunit rDNA data, but model-based methods (maximum likelihood and Bayesian analyses) recover a topology that is congruent with the mitochondrial matR gene tree, thus providing compelling evidence for organismal relationships. Horizontal gene transfer appears to be influencing only some taxa and some mitochondrial genes, thus indicating that the process is acting at the single gene (not whole genome) level.}, }
@article {pmid15493827, year = {2004}, author = {Bröker, G and Spellerberg, B}, title = {Surface proteins of Streptococcus agalactiae and horizontal gene transfer.}, journal = {International journal of medical microbiology : IJMM}, volume = {294}, number = {2-3}, pages = {169-175}, doi = {10.1016/j.ijmm.2004.06.018}, pmid = {15493827}, issn = {1438-4221}, mesh = {Adhesins, Bacterial/genetics ; Antigens, Surface/genetics ; Bacterial Proteins/*genetics ; Chromosomes, Bacterial/genetics ; DNA Transposable Elements ; Endopeptidases/genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Membrane Proteins/*genetics ; Recombination, Genetic ; Streptococcus agalactiae/*genetics/pathogenicity ; Virulence Factors/genetics ; }, abstract = {Streptococcus agalactiae is responsible for serious infectious diseases in neonates, immuno-compromised adult patients and causes bovine mastitis in animal hosts. Genome sequencing projects revealed strong indications for horizontal gene transfer events leading to virulence acquisition and genetic diversity in this species. Bacterial surface proteins establish the first contact with host tissues and represent interesting targets for the exchange of virulence properties among different streptococci. This review will focus on horizontal gene transfer events in characterized S. agalactiae surface proteins, mobile genetic elements adjacent to the corresponding genes and will discuss potential mechanisms of transfer.}, }
@article {pmid15493822, year = {2004}, author = {Eberl, L and Tümmler, B}, title = {Pseudomonas aeruginosa and Burkholderia cepacia in cystic fibrosis: genome evolution, interactions and adaptation.}, journal = {International journal of medical microbiology : IJMM}, volume = {294}, number = {2-3}, pages = {123-131}, doi = {10.1016/j.ijmm.2004.06.022}, pmid = {15493822}, issn = {1438-4221}, mesh = {4-Butyrolactone/*analogs &amp; derivatives/metabolism ; Adaptation, Physiological ; Biofilms/growth &amp; development ; Burkholderia Infections/complications/*microbiology ; Burkholderia cepacia/*genetics/isolation &amp; purification/physiology ; Cystic Fibrosis/complications/*microbiology ; *Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genome, Bacterial ; *Genomic Islands ; Humans ; Lung/microbiology ; Pseudomonas Infections/complications/*microbiology ; Pseudomonas aeruginosa/*genetics/isolation &amp; purification/physiology ; Recombination, Genetic ; Signal Transduction ; Virulence Factors/genetics/physiology ; }, abstract = {The Gram-negative bacteria Pseudomonas aeruginosa and Burkholderia cepacia are opportunistic human pathogens that are responsible for severe nosocomial infections in immunocompromised patients and are the major pathogens in cystic fibrosis (CF). The two bacteria not only inhabit the same environmental niches but can also form mixed biofilms in the lungs of CF patients. Hence, it appears very likely that the two organisms are capable of interacting with each other. Work of the past few years has shown that both bacteria utilize quorum-sensing systems, which rely on N-acyl-homoserine lactone signal molecules, to control the expression of virulence factors and biofilm development. Most importantly, evidence has been presented that these signal molecules also serve as a universal language for communication between the two organisms. Moreover, analyses of the diversity in P. aeruginosa revealed the presence of genome islands that contain genes that are highly homologous to genes identified in strains of Burkholderia sp. This finding suggests that there is a frequent exchange of genetic material between the two organisms.}, }
@article {pmid15493821, year = {2004}, author = {Herold, S and Karch, H and Schmidt, H}, title = {Shiga toxin-encoding bacteriophages--genomes in motion.}, journal = {International journal of medical microbiology : IJMM}, volume = {294}, number = {2-3}, pages = {115-121}, doi = {10.1016/j.ijmm.2004.06.023}, pmid = {15493821}, issn = {1438-4221}, mesh = {Animals ; Bacteriophages/*genetics/physiology ; Citrobacter freundii/*virology ; Enterobacter cloacae/*virology ; Escherichia coli/genetics/*virology ; Gene Expression Regulation, Viral ; Gene Transfer, Horizontal ; Genetic Variation ; Humans ; Lysogeny ; Prophages/*genetics/physiology ; Shiga Toxins/*genetics ; Shigella/genetics/*virology ; Shigella dysenteriae/genetics/virology ; Shigella flexneri/genetics/virology ; Virus Activation ; Virus Integration ; }, abstract = {Shiga toxins (Stx) represent a group of bacterial toxins that are involved in human and animal disease. Stx are mainly produced by Escherichia coli isolated from human and non-human sources, Shigella dysenteriae type 1, and sporadically, by Citrobacter freundii, Enterobacter cloacae and Shigella flexneri. The genes encoding Stx are encoded in the genome of heterogeneous lambdoid prophages (Stx-converting bacteriophages; Stx-phages). They are located in a similar position in the late region of the prophage genome and stx is under control of phage genes. Therefore, induction of Stx-converting prophages triggers increased production of Stx. Following induction, Stx-phages can infect other bacteria in vivo and in vitro. Stx-phages may be considered to represent highly mobile genetic elements that play an important role in the expression of Stx, in horizontal gene transfer, and hence in genome diversification.}, }
@article {pmid15493815, year = {2004}, author = {Heesemann, J}, title = {Darwin's principle of divergence revisited: small steps and quantum leaps set the path of microbial evolution.}, journal = {International journal of medical microbiology : IJMM}, volume = {294}, number = {2-3}, pages = {65-66}, doi = {10.1016/j.ijmm.2004.06.012}, pmid = {15493815}, issn = {1438-4221}, mesh = {Bacteria/*genetics/pathogenicity ; *Biological Evolution ; Ecology ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomic Islands ; Genomics ; *Mutation ; *Recombination, Genetic ; Yersinia pestis/genetics/pathogenicity ; Yersinia pseudotuberculosis/genetics/pathogenicity ; }, }
@article {pmid15492931, year = {2004}, author = {Díaz, E}, title = {Bacterial degradation of aromatic pollutants: a paradigm of metabolic versatility.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {7}, number = {3}, pages = {173-180}, pmid = {15492931}, issn = {1139-6709}, mesh = {Bacteria/*metabolism ; *Biodegradation, Environmental ; *Environmental Pollutants ; Models, Biological ; }, abstract = {Although most organisms have detoxification abilities (i.e mineralization, transformation and/or immobilization of pollutants), microorganisms, particularly bacteria, play a crucial role in biogeochemical cycles and in sustainable development of the biosphere. Next to glucosyl residues, the benzene ring is the most widely distributed unit of chemical structure in nature, and many of the aromatic compounds are major environmental pollutants. Bacteria have developed strategies for obtaining energy from virtually every compound under oxic or anoxic conditions (using alternative final electron acceptors such as nitrate, sulfate, and ferric ions). Clusters of genes coding for the catabolism of aromatic compounds are usually found in mobile genetic elements, such as transposons and plasmids, which facilitate their horizontal gene transfer and, therefore, the rapid adaptation of microorganisms to new pollutants. A successful strategy for in situ bioremediation has been the combination, in a single bacterial strain or in a syntrophic bacterial consortium, of different degrading abilities with genetic traits that provide selective advantages in a given environment. The advent of high-throughput methods for DNA sequencing and analysis of gene expression (genomics) and function (proteomics), as well as advances in modelling microbial metabolism in silico, provide a global, rational approach to unravel the largely unexplored potentials of microorganisms in biotechnological processes thereby facilitating sustainable development.}, }
@article {pmid15492217, year = {2004}, author = {Keeling, PJ and Inagaki, Y}, title = {A class of eukaryotic GTPase with a punctate distribution suggesting multiple functional replacements of translation elongation factor 1alpha.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, number = {43}, pages = {15380-15385}, pmid = {15492217}, issn = {0027-8424}, mesh = {Eukaryotic Cells ; GTP Phosphohydrolases/*metabolism ; Peptide Elongation Factor 1/*metabolism ; Phylogeny ; }, abstract = {Translation elongation factor 1alpha (EF-1alpha, or EF-Tu in bacteria) is a highly conserved core component of the translation machinery that is shared by all cellular life. It is part of a large superfamily of GTPases that are involved in translation initiation, elongation, and termination, as well as several other cellular functions. Eukaryotic EF-1alpha (eEF-1alpha) is well studied and widely sampled and has been used extensively for phylogenetic analyses. It is generally thought that such highly conserved and functionally integrated proteins are unlikely to be involved in events such as lateral gene transfer or ancient duplication and gene sorting, which would undermine phylogenetic reconstruction. Here we describe a GTPase called EF-like (EFL), which is very similar to, but also distinct from, canonical eEF-1alpha. EFL is found in a wide variety of eukaryotes (dinoflagellates, haptophytes, cercozoa, green algae, choanoflagellates, and fungi), but its distribution is punctate: organisms that possess EFL are not closely related to one another, and EFL appears to be absent from the closest relatives of organisms that do possess it. Moreover, in most genomes where EFL is present, canonical eEF-1alpha appears to be absent. Analysis of functional divergence suggests that, whereas EFL is divergent in general, putative functional binding sites involved in translation are not significantly divergent as a whole. Altogether, it appears that EFL has replaced eEF-1alpha several times independently. This finding could be an indication of an ancient paralogy or, more likely, eukaryote-to-eukaryote lateral gene transfer.}, }
@article {pmid15489437, year = {2004}, author = {Lee, LY and Gelvin, SB}, title = {Osa protein constitutes a strong oncogenic suppression system that can block vir-dependent transfer of IncQ plasmids between Agrobacterium cells and the establishment of IncQ plasmids in plant cells.}, journal = {Journal of bacteriology}, volume = {186}, number = {21}, pages = {7254-7261}, pmid = {15489437}, issn = {0021-9193}, mesh = {Agrobacterium tumefaciens/genetics/*pathogenicity ; Bacterial Proteins/genetics/*metabolism ; *Conjugation, Genetic ; DNA-Binding Proteins/genetics/metabolism ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Ion Channels/genetics/metabolism ; Kalanchoe/microbiology ; Plant Leaves/microbiology ; Plant Tumors/*microbiology ; Plasmids/*genetics ; Nicotiana/microbiology ; }, abstract = {The osa (oncogenic suppressive activity) gene of the IncW group plasmid pSa is sufficient to suppress tumorigenesis by Agrobacterium tumefaciens. osa confers oncogenic suppression by inhibiting VirE2 protein export. This result is similar, but not identical, to that of oncogenic suppression by the IncQ plasmid RSF1010. We conducted a series of experiments to compare oncogenic suppression by these two systems. Agrobacterium strains harboring plasmids containing osa are more able to effect oncogenic suppression than are similar strains containing various RSF1010 derivatives. When osa is present within a donor Agrobacterium strain that also carries a derivative of RSF1010, the transfer of RSF1010 derivatives to recipient bacteria and their establishment in plants are blocked. Oncogenic suppression is still effected when the osa gene is integrated into the Agrobacterium chromosome, suggesting that it is the osa gene product that is active in suppression and that suppression does not require a protein-nucleic acid intermediate like that described for IncQ plasmids. Extracellular complementation experiments with tobacco leaf disks indicated that Osa blocks stable transfer of RSF1010 to plant cells by inhibiting transfer of VirE2, which is essential for the transfer of RSF1010 into plant cells, and not by inhibiting the actual transfer of RSF1010 itself. Our results suggest that Osa and RSF1010 cause oncogenic suppression by using different mechanisms.}, }
@article {pmid15487932, year = {2004}, author = {Reams, AB and Neidle, EL}, title = {Selection for gene clustering by tandem duplication.}, journal = {Annual review of microbiology}, volume = {58}, number = {}, pages = {119-142}, doi = {10.1146/annurev.micro.58.030603.123806}, pmid = {15487932}, issn = {0066-4227}, mesh = {Benzoates/metabolism ; Catechols/metabolism ; *Gene Duplication ; Genes, Bacterial/*genetics ; *Genome, Bacterial ; Genomic Islands/genetics ; *Models, Genetic ; Multigene Family/*genetics ; Operon/genetics ; Recombination, Genetic/genetics ; }, abstract = {In prokaryotic genomes, related genes are frequently clustered in operons and higher-order arrangements that reflect functional context. Organization emerges despite rearrangements that constantly shuffle gene and operon order. Evidence is presented that the tandem duplication of related genes acts as a driving evolutionary force in the origin and maintenance of clusters. Gene amplification can be viewed as a dynamic and reversible regulatory mechanism that facilitates adaptation to variable environments. Clustered genes confer selective benefits via their ability to be coamplified. During evolution, rearrangements that bring together related genes can be selected if they increase the fitness of the organism in which they reside. Similarly, the benefits of gene amplification can prevent the dispersal of existing clusters. Examples of frequent and spontaneous amplification of large genomic fragments are provided. The possibility is raised that tandem gene duplication works in concert with horizontal gene transfer as interrelated evolutionary forces for gene clustering.}, }
@article {pmid15483330, year = {2005}, author = {Aris-Brosou, S}, title = {Determinants of adaptive evolution at the molecular level: the extended complexity hypothesis.}, journal = {Molecular biology and evolution}, volume = {22}, number = {2}, pages = {200-209}, doi = {10.1093/molbev/msi006}, pmid = {15483330}, issn = {0737-4038}, mesh = {Adaptation, Biological/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Models, Genetic ; Open Reading Frames ; Protein Structure, Tertiary/*genetics ; }, abstract = {To explain why informational genes (i.e., those involved in transcription, translation, and related processes) are less likely than housekeeping genes to be horizontally transferred, Jain and coworkers proposed the complexity hypothesis. The underlying idea is that informational genes belong to large, complex systems of coevolving genes. Consequently, the likelihood of the successful horizontal transfer of a single gene from such an integrated system is expected to be low. Here, this hypothesis is extended to explain some of the determinants of the mode of evolution of coding sequences. It is proposed that genes belonging to complex systems are relatively less likely to be under adaptive evolution. To evaluate this "extended complexity hypothesis," 2,428 families and protein domains were analyzed. This analysis found that genes whose products are highly connected, located in intracellular components, and involved in complex processes and functions were more conserved and less likely to be under adaptive evolution than are other gene products. The extended complexity hypothesis suggests that both the mode and the rate of evolution of a protein are influenced by its gene ontology (localization, biological process, and molecular function) and by its connectivity.}, }
@article {pmid15483318, year = {2005}, author = {Wenzl, P and Wong, L and Kwang-won, K and Jefferson, RA}, title = {A functional screen identifies lateral transfer of beta-glucuronidase (gus) from bacteria to fungi.}, journal = {Molecular biology and evolution}, volume = {22}, number = {2}, pages = {308-316}, doi = {10.1093/molbev/msi018}, pmid = {15483318}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Ascomycota/genetics ; Bacteria/*genetics ; Fungi/*genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Genes, Fungal/genetics ; Glucuronidase/classification/*genetics ; Gram-Positive Bacteria/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; }, abstract = {Lateral gene transfer (LGT) from prokaryotes to microbial eukaryotes is usually detected by chance through genome-sequencing projects. Here, we explore a different, hypothesis-driven approach. We show that the fitness advantage associated with the transferred gene, typically invoked only in retrospect, can be used to design a functional screen capable of identifying postulated LGT cases. We hypothesized that beta-glucuronidase (gus) genes may be prone to LGT from bacteria to fungi (thought to lack gus) because this would enable fungi to utilize glucuronides in vertebrate urine as a carbon source. Using an enrichment procedure based on a glucose-releasing glucuronide analog (cellobiouronic acid), we isolated two gus(+) ascomycete fungi from soils (Penicillium canescens and Scopulariopsis sp.). A phylogenetic analysis suggested that their gus genes, as well as the gus genes identified in genomic sequences of the ascomycetes Aspergillus nidulans and Gibberella zeae, had been introgressed laterally from high-GC gram(+) bacteria. Two such bacteria (Arthrobacter spp.), isolated together with the gus(+) fungi, appeared to be the descendants of a bacterial donor organism from which gus had been transferred to fungi. This scenario was independently supported by similar substrate affinities of the encoded beta-glucuronidases, the absence of introns from fungal gus genes, and the similarity between the signal peptide-encoding 5' extensions of some fungal gus genes and the Arthrobacter sequences upstream of gus. Differences in the sequences of the fungal 5' extensions suggested at least two separate introgression events after the divergence of the two main Euascomycete classes. We suggest that deposition of glucuronides on soils as a result of the colonization of land by vertebrates may have favored LGT of gus from bacteria to fungi in soils.}, }
@article {pmid15483083, year = {2005}, author = {Kaivo-Oja, N and Mottershead, DG and Mazerbourg, S and Myllymaa, S and Duprat, S and Gilchrist, RB and Groome, NP and Hsueh, AJ and Ritvos, O}, title = {Adenoviral gene transfer allows Smad-responsive gene promoter analyses and delineation of type I receptor usage of transforming growth factor-beta family ligands in cultured human granulosa luteal cells.}, journal = {The Journal of clinical endocrinology and metabolism}, volume = {90}, number = {1}, pages = {271-278}, doi = {10.1210/jc.2004-1288}, pmid = {15483083}, issn = {0021-972X}, support = {U54-HD-31398/HD/NICHD NIH HHS/United States ; }, mesh = {Activin Receptors, Type I/*physiology ; Activins/pharmacology ; Adenoviridae/*genetics ; Bone Morphogenetic Protein 15 ; Cells, Cultured ; DNA-Binding Proteins/*metabolism ; Female ; *Gene Transfer, Horizontal ; Growth Differentiation Factor 9 ; Humans ; Inhibins/biosynthesis ; Intercellular Signaling Peptides and Proteins/pharmacology ; Ligands ; Luteal Cells/*metabolism ; *Promoter Regions, Genetic ; Protein Serine-Threonine Kinases ; Receptor, Transforming Growth Factor-beta Type I ; Receptors, Transforming Growth Factor beta/*physiology ; Smad3 Protein ; Trans-Activators/*metabolism ; Transforming Growth Factor beta/*pharmacology ; }, abstract = {In the human ovary, cell growth and differentiation are regulated by members of the TGF-beta superfamily, including growth differentiation factor-9 (GDF9), TGF-beta, and activin. TGF-beta and activin are known to signal via Smad3 activation, and we have recently shown the involvement of Smad3 in cellular responses to GDF9. Recent studies with Smad3-deficient mice have also indicated a key role for this signaling mediator in ovarian folliculogenesis. We now demonstrate the use of a Smad3 reporter (CAGA-luciferase) adenovirus in primary cultures of human granulosa-luteal (hGL) cells to detect GDF9, TGF-beta, and activin responses. In rodent granulosa cells, TGF-beta and GDF9 signal through the TGF-beta type I receptor or activin receptor-like kinase 5 (Alk5), whereas the effect of activin is mediated though the activin type IB receptor, also known as Alk4. We now show that the GDF9 response in hGL cells is markedly potentiated upon overexpression of Alk5 by adenoviral gene transduction, as measured by the CAGA-luciferase reporter activity. A similar response to Alk5 overexpression was observed for TGF-beta, but not for activin. Adenoviral overexpression of the activin type IB receptor Alk4 in hGL cells specifically potentiated activin signaling, but not GDF9 or TGF-beta signaling. Alk5 overexpression in hGL cells also potentiated the GDF9 response when inhibin B production was used as the read-out. These results indicate that the CAGA-luciferase adenovirus can be used to study Smad3 signaling in primary cultures of human cells, and that adenoviral overexpression of wild-type receptors of the TGF-beta superfamily can be used to amplify the cellular response to ligands such as GDF9, TGF-beta, and activin. Furthermore, these studies indicate the involvement of Alk5 in GDF9 signaling in human cells and therefore, along with other recent studies, highlight how a limited number of type I and II receptors cooperate to generate specificity of action within the TGF-beta superfamily.}, }
@article {pmid15482781, year = {2004}, author = {Chang, KH and Lim, JM and Kang, SK and Lee, BC and Moon, SY and Hwang, WS}, title = {An optimized protocol of a human-to-cattle interspecies somatic cell nuclear transfer.}, journal = {Fertility and sterility}, volume = {82}, number = {4}, pages = {960-962}, doi = {10.1016/j.fertnstert.2004.03.052}, pmid = {15482781}, issn = {0015-0282}, mesh = {Animals ; Cattle/*embryology ; Cell Culture Techniques ; Cell Fusion/*methods ; Culture Media ; Female ; Fibroblasts/*cytology ; Gene Transfer, Horizontal/*genetics ; Humans ; Mammary Glands, Human/cytology ; Oocytes/*cytology ; Prospective Studies ; Random Allocation ; Umbilical Cord/cytology ; }, abstract = {Human somatic cells were transferred into cattle enucleated oocytes, and a prospective, randomized study was designed to optimize donor cell preparation, fusion medium, and culture method. As a result, improved development of interspecies embryos was achieved by employing serum-starved cord fibroblasts, with Ca(2+)/Mg(2+)-free fusion medium and a serum-free medium being used for bovine embryos.}, }
@article {pmid15482780, year = {2004}, author = {Kim, TM and Park, TS and Shin, SS and Han, JY and Moon, SY and Lim, JM}, title = {An interclass nuclear transfer between fowl and mammal: in vitro development of chicken-to-cattle interclass embryos and the detection of chicken genetic complements.}, journal = {Fertility and sterility}, volume = {82}, number = {4}, pages = {957-959}, doi = {10.1016/j.fertnstert.2004.06.019}, pmid = {15482780}, issn = {0015-0282}, mesh = {Animals ; Cattle/*embryology/genetics ; Cell Fusion/*methods ; Cell Nucleus/genetics ; Chick Embryo/*embryology ; Female ; Gene Transfer, Horizontal/*genetics ; *Nuclear Transfer Techniques ; Oocytes/*cytology ; Stem Cells/cytology ; }, abstract = {An attempt was made to develop an interclass somatic cell nuclear transfer method as an alternative means of establishing chicken embryonic stem cells. Chicken-to-cattle interclass embryos that activated calcium ionophore, cycloheximide, and cytochalasin D were developed into blastocysts, and the developing interclass embryos had chicken genetic complements.}, }
@article {pmid15475163, year = {2004}, author = {Harper, JT and Keeling, PJ}, title = {Lateral gene transfer and the complex distribution of insertions in eukaryotic enolase.}, journal = {Gene}, volume = {340}, number = {2}, pages = {227-235}, doi = {10.1016/j.gene.2004.06.048}, pmid = {15475163}, issn = {0378-1119}, mesh = {Amino Acid Sequence ; Animals ; DNA/chemistry/genetics/isolation &amp; purification ; Eukaryotic Cells/classification/*enzymology/metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Molecular Sequence Data ; Phosphopyruvate Hydratase/*genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; }, abstract = {Insertions and deletions in protein-coding genes are relatively rare events compared with sequence substitutions because they are more likely to alter the tertiary structure of the protein. For this reason, insertions and deletions which are clearly homologous are considered to be stable characteristics of the proteins where they are found, and their presence and absence has been used extensively to infer large-scale evolutionary relationships and events. Recently, however, it has been shown that the pattern of highly conserved, clearly homologous insertions at positions with no other detectable homoplasy can be incongruent with the phylogeny of the genes or organisms in which they are found. One case where this has been reported is in the enolase genes of apicomplexan parasites and ciliates, which share homologous insertions in a highly conserved region of the gene with the apparently distantly related enolases of plants. Here we explore the distribution of this character in enolase genes from the third major alveolate group, the dinoflagellates, as well as two groups considered to be closely related to alveolates, haptophytes and heterokonts. With these data, all major groups of the chromalveolates are represented, and the distribution of these insertions is shown to be far more complicated than previously believed. The incongruence between this pattern, the known evolutionary relationships between the organisms, and enolase phylogeny itself cannot be explained by any single event or type of event. Instead, the distribution of enolase insertions is more likely the product of several forces that may have included lateral gene transfer, paralogy, and/or recombination. Of these, lateral gene transfer is the easiest to detect and some well-supported cases of eukaryote-to-eukaryote lateral transfer are evident from the phylogeny.}, }
@article {pmid15473911, year = {2004}, author = {Patil, PB and Sonti, RV}, title = {Variation suggestive of horizontal gene transfer at a lipopolysaccharide (lps) biosynthetic locus in Xanthomonas oryzae pv. oryzae, the bacterial leaf blight pathogen of rice.}, journal = {BMC microbiology}, volume = {4}, number = {}, pages = {40}, pmid = {15473911}, issn = {1471-2180}, mesh = {Base Sequence ; Codon ; DNA, Bacterial/chemistry ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genetic Variation ; Genome, Bacterial ; Lipopolysaccharides/*biosynthesis ; Molecular Sequence Data ; Oryza/microbiology ; Repetitive Sequences, Nucleic Acid ; Virulence Factors/genetics ; Xanthomonas/*genetics/metabolism/pathogenicity ; }, abstract = {BACKGROUND: In animal pathogenic bacteria, horizontal gene transfer events (HGT) have been frequently observed in genomic regions that encode functions involved in biosynthesis of the outer membrane located lipopolysaccharide (LPS). As a result, different strains of the same pathogen can have substantially different lps biosynthetic gene clusters. Since LPS is highly antigenic, the variation at lps loci is attributed to be of advantage in evading the host immune system. Although LPS has been suggested as a potentiator of plant defense responses, interstrain variation at lps biosynthetic gene clusters has not been reported for any plant pathogenic bacterium.<br><br>RESULTS: We report here the complete sequence of a 12.2 kb virulence locus of Xanthomonas oryzae pv. oryzae (Xoo) encoding six genes whose products are homologous to functions involved in LPS biosynthesis and transport. All six open reading frames (ORFs) have atypical G+C content and altered codon usage, which are the hallmarks of genomic islands that are acquired by horizontal gene transfer. The lps locus is flanked by highly conserved genes, metB and etfA, respectively encoding cystathionine gamma lyase and electron transport flavoprotein. Interestingly, two different sets of lps genes are present at this locus in the plant pathogens, Xanthomonas campestris pv. campestris (Xcc) and Xanthomonas axonopodis pv. citri (Xac). The genomic island is present in a number of Xoo strains from India and other Asian countries but is not present in two strains, one from India (BXO8) and another from Nepal (Nepal624) as well as the closely related rice pathogen, Xanthomonas oryzae pv. oryzicola (Xoor). TAIL-PCR analysis indicates that sequences related to Xac are present at the lps locus in both BXO8 and Nepal624. The Xoor strain has a hybrid lps gene cluster, with sequences at the metB and etfA ends, being most closely related to sequences from Xac and the tomato pathogen, Pseudomonas syringae pv. tomato respectively.<br><br>CONCLUSION: This is the first report of hypervariation at an lps locus between different strains of a plant pathogenic bacterium. Our results indicate that multiple HGT events have occurred at this locus in the xanthomonad group of plant pathogens.}, }
@article {pmid15467785, year = {2004}, author = {Hirkala, DL and Germida, JJ}, title = {Field and soil microcosm studies on the survival and conjugation of a Pseudomonas putida strain bearing a recombinant plasmid, pADPTel.}, journal = {Canadian journal of microbiology}, volume = {50}, number = {8}, pages = {595-604}, doi = {10.1139/w04-045}, pmid = {15467785}, issn = {0008-4166}, mesh = {Agriculture ; Brassica napus/*microbiology ; *Conjugation, Genetic ; Drug Resistance, Bacterial/genetics ; Ecosystem ; Gene Transfer, Horizontal ; Plant Roots/microbiology ; Plasmids/*genetics ; Pseudomonas putida/genetics/*growth &amp; development ; *Recombination, Genetic ; Soil/analysis ; *Soil Microbiology ; Tellurium/pharmacology ; }, abstract = {Pseudomonas putida CR30RNS (pADPTel) is an antibiotic-resistant strain with a recombinant plasmid that confers resistance to tellurite and the ability to catabolize atrazine. The survival of this strain as well as its ability to transfer genes for atrazine degradation and tellurite resistance to indigenous soil bacteria were tested in both fallow soil and canola (Brassica napus) rhizosphere by the use of parallel field and laboratory releases. Culturable CR30RNS (pADPTel) were enumerated in field and microcosm soils at 7- to 14-day intervals over 49 d. Strain CR30RNS (pADPTel) survived for up to 7 weeks in microcosm soils at a density of 10(4) CFU/g soil, whereas in field soils the population declined to 10(3) CFU/g soil by the fourth week. In contrast, when CR30RNS (pADPTel) was introduced into the soil as a seed coating of canola (B. napus 'Karoo'), the bacterium established at higher cell densities in the rhizosphere (10(6)-10(5) CFU/g fresh root mass), with no subsequent decrease in numbers. The presence of selective pressure (i.e., atrazine) had no significant effect on the survival of CR30RNS (pADPTel) in either field or microcosm soils. One year postinoculation field sites were examined for the presence of CR30RNS (pADPTel) and no evidence of culturable parental cells was observed when samples were plated onto selective media. However, the atzC and telAB gene segments were amplified from the field soils at that time. Under laboratory conditions, indigenous soil bacteria were capable of receiving and expressing the engineered plasmid construct at frequencies ranging from 1 to 10(-3) transconjugants per donor. However, no plasmid transfer to indigenous soil bacteria was detected in the field or microcosm soils regardless of the presence of canola rhizosphere and (or) the application of atrazine. Our results show that the survival and population size of P. putida CR30RNS (pADPTel) might be sufficient for degradation of environmental pollutants but that the transfer frequency was too low to be detected under the conditions of this study.}, }
@article {pmid15466049, year = {2004}, author = {Hendrickson, EL and Kaul, R and Zhou, Y and Bovee, D and Chapman, P and Chung, J and Conway de Macario, E and Dodsworth, JA and Gillett, W and Graham, DE and Hackett, M and Haydock, AK and Kang, A and Land, ML and Levy, R and Lie, TJ and Major, TA and Moore, BC and Porat, I and Palmeiri, A and Rouse, G and Saenphimmachak, C and Söll, D and Van Dien, S and Wang, T and Whitman, WB and Xia, Q and Zhang, Y and Larimer, FW and Olson, MV and Leigh, JA}, title = {Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis.}, journal = {Journal of bacteriology}, volume = {186}, number = {20}, pages = {6956-6969}, pmid = {15466049}, issn = {0021-9193}, support = {R01 GM060403/GM/NIGMS NIH HHS/United States ; GM60403/GM/NIGMS NIH HHS/United States ; }, mesh = {Archaeal Proteins/genetics/*metabolism ; *Genome, Archaeal ; Hydrogen/*metabolism ; Methane/*metabolism ; Methanococcus/*genetics/metabolism ; Molecular Sequence Data ; Proteome ; *Sequence Analysis, DNA ; }, abstract = {The genome sequence of the genetically tractable, mesophilic, hydrogenotrophic methanogen Methanococcus maripaludis contains 1,722 protein-coding genes in a single circular chromosome of 1,661,137 bp. Of the protein-coding genes (open reading frames [ORFs]), 44% were assigned a function, 48% were conserved but had unknown or uncertain functions, and 7.5% (129 ORFs) were unique to M. maripaludis. Of the unique ORFs, 27 were confirmed to encode proteins by the mass spectrometric identification of unique peptides. Genes for most known functions and pathways were identified. For example, a full complement of hydrogenases and methanogenesis enzymes was identified, including eight selenocysteine-containing proteins, with each being paralogous to a cysteine-containing counterpart. At least 59 proteins were predicted to contain iron-sulfur centers, including ferredoxins, polyferredoxins, and subunits of enzymes with various redox functions. Unusual features included the absence of a Cdc6 homolog, implying a variation in replication initiation, and the presence of a bacterial-like RNase HI as well as an RNase HII typical of the Archaea. The presence of alanine dehydrogenase and alanine racemase, which are uniquely present among the Archaea, explained the ability of the organism to use L- and D-alanine as nitrogen sources. Features that contrasted with the related organism Methanocaldococcus jannaschii included the absence of inteins, even though close homologs of most intein-containing proteins were encoded. Although two-thirds of the ORFs had their highest Blastp hits in Methanocaldococcus jannaschii, lateral gene transfer or gene loss has apparently resulted in genes, which are often clustered, with top Blastp hits in more distantly related groups.}, }
@article {pmid15462566, year = {2004}, author = {Yang, M and Meyer-Rochow, VB}, title = {Fine-structural details of the photoreceptor membranes in the ocellus of the scale-insect parasite Centrodora sp. (Hymenoptera; Aphenelidae): a case of gene transfer between host and parasite?.}, journal = {Biocell : official journal of the Sociedades Latinoamericanas de Microscopia Electronica ... et. al}, volume = {28}, number = {2}, pages = {151-154}, pmid = {15462566}, issn = {0327-9545}, mesh = {Animals ; Cell Membrane/*ultrastructure ; Eye/*ultrastructure ; *Gene Transfer, Horizontal ; Hemiptera/*genetics/physiology ; Host-Parasite Interactions ; Male ; Photoreceptor Cells/*ultrastructure ; Retina/ultrastructure ; Wasps/*anatomy &amp; histology/parasitology ; }, abstract = {Only one insect (the scale insect Eriococcus sp.) is known, in which photoreceptive lamellae appear to have replaced the usual arthropod rhabdom microvilli. We are now reporting the presence of photoreceptive membranes, which also appear to resemble lamellae rather than microvilli, but they are in the ocellus of the tiny wasp Centrodora sp., which parasitizes scale insect eggs. The apparently optically homogenous lens of the Centrodora ocellus measures approximately 10 microm in diameter and, thus, operates at the limits of diffraction. We calculated that the lens is capable of focusing a parallel bundle of rays on the retina of the ocellus.}, }
@article {pmid15461428, year = {2004}, author = {Kilian, O and Kroth, PG}, title = {Presequence acquisition during secondary endocytobiosis and the possible role of introns.}, journal = {Journal of molecular evolution}, volume = {58}, number = {6}, pages = {712-721}, pmid = {15461428}, issn = {0022-2844}, mesh = {Algal Proteins/*genetics/metabolism ; Amino Acid Sequence ; Cell Nucleus/genetics/physiology ; DNA, Complementary/genetics ; Diatoms/*genetics/physiology ; Electrophoresis, Agar Gel ; *Evolution, Molecular ; Gene Library ; Gene Transfer, Horizontal/genetics ; Green Fluorescent Proteins ; Introns/genetics ; Luminescent Proteins/metabolism ; Molecular Sequence Data ; Oligonucleotides ; Phylogeny ; Plastids/genetics ; Polymerase Chain Reaction ; Protein Sorting Signals/genetics/*physiology ; Protein Transport/*physiology ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {Targeting of nucleus-encoded proteins into chloroplasts is mediated by N-terminal presequences. During evolution of plastids from formerly free-living cyanobacteria by endocytobiosis, genes for most plastid proteins have been transferred from the plastid genome to the nucleus and subsequently had to be equipped with such plastid targeting sequences. So far it is unclear how the gene domains coding for presequences and the respective mature proteins may have been assembled. While land plant plastids are supposed to originate from a primary endocytobiosis event (a prokaryotic cyanobacterium was taken up by a eukaryotic cell), organisms with secondary plastids like diatoms experienced a second endocytobiosis step involving a eukaryotic alga taken up by a eukaryotic host cell. In this group of algae, apparently most genes encoding chloroplast proteins have been transferred a second time (from the nucleus of the endosymbiont to the nucleus of the secondary host) and thus must have been equipped with additional targeting signals. We have analyzed cDNAs and the respective genomic DNA fragments of seven plastid preproteins from the diatom Phaeodactylum tricornutum. In all of these genes we found single spliceosomal introns, generally located within the region coding for the N-terminal plastid targeting sequences or shortly downstream of it. The positions of the introns can be related to the putative phylogenetic histories of the respective genes, indicating that the bipartite targeting sequences in these secondary algae might have evolved by recombination events via introns.}, }
@article {pmid15461420, year = {2004}, author = {Tanabe, Y and Kaya, K and Watanabe, MM}, title = {Evidence for recombination in the microcystin synthetase (mcy) genes of toxic cyanobacteria Microcystis spp.}, journal = {Journal of molecular evolution}, volume = {58}, number = {6}, pages = {633-641}, pmid = {15461420}, issn = {0022-2844}, mesh = {Bacterial Proteins ; Base Sequence ; DNA Primers ; Gene Components ; Gene Transfer, Horizontal/*genetics ; *Genetic Variation ; Likelihood Functions ; Microcystis/*genetics ; Models, Genetic ; Molecular Sequence Data ; Multigene Family/genetics ; Peptide Synthases/*genetics ; *Phylogeny ; Recombination, Genetic/*genetics ; Sequence Analysis, DNA ; }, abstract = {Recombination has been suggested to be an important factor for the genetic variation of bacterial genes, but few studies have dealt with intragenic recombination between the same or closely related species of cyanobacteria. Here we provide strong evidence for recombination in the microcystin synthetase (mcy) gene cluster of the toxic cyanobacteria Microcystis spp. This gene cluster contains 10 genes (mcyA to J) that encode a mixed polyketide synthase (PKS)/nonribosomal peptide synthetase (NRPS) complex. mcy gene sequences were determined for four selected regions (within mcyA, D, G, and J) within the mcy gene cluster from 1 Canadian and 10 Asian toxic Microcystis and compared with previously published mcy sequences. Split decomposition analysis indicated a reticulate phylogeny of mcyA, and several potential recombination tracts of mcyA were identified by the RDP analysis and a runs test implemented in GENECONV. In contrast, no recombination was detected in the mcyD, G, and J sequences. However, discrepancies among the four mcy gene genealogies were evident from the results of independent split decomposition analyses, which were further supported by incongruence length difference (ILD) tests. Taken together, these findings suggest that both intragenic and intergenic recombination within the mcy gene cluster contributes to the genetic diversity of the mcy genes of Microcystis spp.}, }
@article {pmid15459293, year = {2004}, author = {Frickey, T and Lupas, AN}, title = {PhyloGenie: automated phylome generation and analysis.}, journal = {Nucleic acids research}, volume = {32}, number = {17}, pages = {5231-5238}, pmid = {15459293}, issn = {1362-4962}, mesh = {Amino Acid Sequence ; Animals ; Gene Transfer, Horizontal ; Genome ; Molecular Sequence Data ; *Phylogeny ; Proteome/*classification/genetics ; Sequence Alignment ; *Software ; Sulfolobus/classification/genetics ; Thermoplasma/classification/genetics ; Zebrafish/genetics ; }, abstract = {Phylogenetic reconstruction is the method of choice to determine the homologous relationships between sequences. Difficulties in producing high-quality alignments, which are the basis of good trees, and in automating the analysis of trees have unfortunately limited the use of phylogenetic reconstruction methods to individual genes or gene families. Due to the large number of sequences involved, phylogenetic analyses of proteomes preclude manual steps and therefore require a high degree of automation in sequence selection, alignment, phylogenetic inference and analysis of the resulting set of trees. We present a set of programs that automates the steps from seed sequence to phylogeny and a utility to extract all phylogenies that match specific topological constraints from a database of trees. Two example applications that show the type of questions that can be answered by phylome analysis are provided. The generation and analysis of the Thermoplasma acidophilum phylome with regard to lateral gene transfer between Thermoplasmata and Sulfolobus, showed best BLAST hits to be far less reliable indicators of lateral transfer than the corresponding protein phylogenies. The generation and analysis of the Danio rerio phylome provided more than twice as many proteins as described previously, supporting the hypothesis of an additional round of genome duplication in the actinopterygian lineage.}, }
@article {pmid15456963, year = {2004}, author = {Roberts, MC}, title = {Resistance to macrolide, lincosamide, streptogramin, ketolide, and oxazolidinone antibiotics.}, journal = {Molecular biotechnology}, volume = {28}, number = {1}, pages = {47-62}, pmid = {15456963}, issn = {1073-6085}, mesh = {Anti-Bacterial Agents/*pharmacology ; Conjugation, Genetic ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Ketolides/pharmacology ; Lincosamides ; Macrolides/*pharmacology ; Mutation/*genetics ; Oxazolidinones/*pharmacology ; Streptogramins/*pharmacology ; }, abstract = {Macrolides have enjoyed a resurgence as new derivatives and related compounds have come to market. These newer compounds have become important in the treatment of community-acquired pneumoniae and nontuberculosis-Mycobacterium diseases. In this review, the bacterial mechanisms of resistance to the macrolide, lincosamide, streptogramin, ketolide, and oxazolidinone antibiotics, the distribution of the various acquired genes that confer resistance, as well as mutations that have been identified in clinical and laboratory strains are examined.}, }
@article {pmid15454934, year = {2004}, author = {Tettelin, H and Parkhill, J}, title = {The use of genome annotation data and its impact on biological conclusions.}, journal = {Nature genetics}, volume = {36}, number = {10}, pages = {1028-1029}, doi = {10.1038/ng1004-1028b}, pmid = {15454934}, issn = {1061-4036}, mesh = {Data Interpretation, Statistical ; Databases, Genetic ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genomics/*statistics &amp; numerical data ; Methyltransferases/genetics ; Neisseria meningitidis/genetics ; Staphylococcus aureus/genetics ; }, }
@article {pmid15454933, year = {2004}, author = {van Passel, M and Bart, A and Pannekoek, Y and van der Ende, A}, title = {Phylogenetic validation of horizontal gene transfer?.}, journal = {Nature genetics}, volume = {36}, number = {10}, pages = {1028}, doi = {10.1038/ng1004-1028a}, pmid = {15454933}, issn = {1061-4036}, mesh = {Bacillus subtilis/genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Methyltransferases/genetics ; Neisseria meningitidis/genetics ; *Phylogeny ; Plasmids/genetics ; Staphylococcus aureus/genetics ; }, }
@article {pmid15448271, year = {2004}, author = {Chien, M and Morozova, I and Shi, S and Sheng, H and Chen, J and Gomez, SM and Asamani, G and Hill, K and Nuara, J and Feder, M and Rineer, J and Greenberg, JJ and Steshenko, V and Park, SH and Zhao, B and Teplitskaya, E and Edwards, JR and Pampou, S and Georghiou, A and Chou, IC and Iannuccilli, W and Ulz, ME and Kim, DH and Geringer-Sameth, A and Goldsberry, C and Morozov, P and Fischer, SG and Segal, G and Qu, X and Rzhetsky, A and Zhang, P and Cayanis, E and De Jong, PJ and Ju, J and Kalachikov, S and Shuman, HA and Russo, JJ}, title = {The genomic sequence of the accidental pathogen Legionella pneumophila.}, journal = {Science (New York, N.Y.)}, volume = {305}, number = {5692}, pages = {1966-1968}, doi = {10.1126/science.1099776}, pmid = {15448271}, issn = {1095-9203}, support = {AI 23549/AI/NIAID NIH HHS/United States ; U01 1 AI 4437/AI/NIAID NIH HHS/United States ; }, mesh = {DNA, Bacterial ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Legionella pneumophila/*genetics/pathogenicity/physiology ; Plasmids ; }, abstract = {We present the genomic sequence of Legionella pneumophila, the bacterial agent of Legionnaires' disease, a potentially fatal pneumonia acquired from aerosolized contaminated fresh water. The genome includes a 45-kilobase pair element that can exist in chromosomal and episomal forms, selective expansions of important gene families, genes for unexpected metabolic pathways, and previously unknown candidate virulence determinants. We highlight the genes that may account for Legionella's ability to survive in protozoa, mammalian macrophages, and inhospitable environmental niches and that may define new therapeutic targets.}, }
@article {pmid15388428, year = {2004}, author = {Leflon-Guibout, V and Jurand, C and Bonacorsi, S and Espinasse, F and Guelfi, MC and Duportail, F and Heym, B and Bingen, E and Nicolas-Chanoine, MH}, title = {Emergence and spread of three clonally related virulent isolates of CTX-M-15-producing Escherichia coli with variable resistance to aminoglycosides and tetracycline in a French geriatric hospital.}, journal = {Antimicrobial agents and chemotherapy}, volume = {48}, number = {10}, pages = {3736-3742}, pmid = {15388428}, issn = {0066-4804}, mesh = {Aged ; Aminoglycosides/*pharmacology ; Cross Infection/*epidemiology/*microbiology ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/drug effects/*enzymology/genetics ; France ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Genotype ; Geriatrics ; Hospitals, Special ; Humans ; Isoelectric Focusing ; Phenotype ; Plasmids/genetics ; Tetracycline/*pharmacology ; Urinary Tract Infections/microbiology ; Virulence Factors/genetics ; beta-Lactamases/*metabolism ; }, abstract = {Three types of multidrug-resistant Escherichia coli isolates, called GEN S, GEN R, and AMG S, according to their three different aminoglycoside resistance patterns, were responsible for urinary tract colonization or infection in 87, 12, and 13 new patients, respectively, in a French 650-bed geriatric hospital over a 13-month period. The three E. coli types belonged to the same clone and phylogenetic group (group B2) and had identical transferable plasmid contents (a 120-kb plasmid), beta-lactam and fluoroquinolone resistance genotypes (bla(TEM-1B), bla(CTX-M-15), and double mutations in both the gyrA and the parC genes), and virulence factor genotypes (aer, fyuA, and irp2). They disseminated in the geriatric hospital, where the antibiotics prescribed most often were fluoroquinolones and ceftriaxone, but not in the affiliated acute-care hospital, where isolation precautions were applied to the transferred patients. Thus, E. coli isolates, both CTX-M-type beta-lactamase producers and fluoroquinolone-resistant isolates, might present a new challenge for French health care settings.}, }
@article {pmid15383907, year = {2004}, author = {Rezen, T and Debeljak, N and Kordis, D and Rozman, D}, title = {New aspects on lanosterol 14alpha-demethylase and cytochrome P450 evolution: lanosterol/cycloartenol diversification and lateral transfer.}, journal = {Journal of molecular evolution}, volume = {59}, number = {1}, pages = {51-58}, pmid = {15383907}, issn = {0022-2844}, support = {1 R03 TW01174-01/TW/FIC NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; Cluster Analysis ; Computational Biology/methods ; Cytochrome P-450 Enzyme System/chemistry/*genetics ; Databases, Nucleic Acid ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; *Genetic Variation ; Oxidoreductases/chemistry/*genetics ; *Phylogeny ; Sterol 14-Demethylase ; }, abstract = {Sterol 14alpha-demethylase (CYP51) is a member of the cytochrome P450 superfamily, widely found in animals, fungi, and plants but present in few prokaryotic groups. CYP51 is currently believed to be the ancestral cytochrome P450 that has been transferred from prokaryotes to eukaryotic kingdoms. We propose an alternate view of CYP51 evolution that has an impact on understanding the evolution of the entire CYP superfamily. Two hundred forty-nine bacterial and four archaeal CYP sequences have been aligned and a bacterial CYP tree designed, showing a separation of two branches. Prokaryotic CYP51s cluster to the minor branch, together with other eukaryote-like CYPs. Mycobacterial and methylococcal CYP51s cluster together (100% bootstrap probability), while Streptomyces CYP51 remains on a distant branch. A CYP51 phylogenetic tree has been constructed from 44 sequences resulting in a ((plant, bacteria),(animal, fungi)) topology (100% bootstrap probability). This is in accordance with the lanosterol/cycloartenol diversification of sterol biosynthesis. The lanosterol branch (nonphotosynthetic lineage) follows the previously proposed topology of animal and fungal orthologues (100% bootstrap probability), while plant and D. discoideum CYP51s belong to the cycloartenol branch (photosynthetic lineage), all in accordance with biochemical data. Bacterial CYP51s cluster within the cycloartenol branch (69% bootstrap probability), which is indicative of a lateral gene transfer of a plant CYP51 to the methylococcal/mycobacterial progenitor, suggesting further that bacterial CYP51s are not the oldest CYP genes. Lateral gene transfer is likely far more important than hitherto thought in the development of the diversified CYP superfamily. Consequently, bacterial CYPs may represent a mixture of genes with prokaryotic and eukaryotic origin.}, }
@article {pmid15383646, year = {2004}, author = {Ueda, K and Yamashita, A and Ishikawa, J and Shimada, M and Watsuji, TO and Morimura, K and Ikeda, H and Hattori, M and Beppu, T}, title = {Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalism.}, journal = {Nucleic acids research}, volume = {32}, number = {16}, pages = {4937-4944}, pmid = {15383646}, issn = {1362-4962}, mesh = {Actinobacteria/*genetics/growth &amp; development/metabolism ; Aerobiosis ; Anaerobiosis ; Bacterial Proteins/genetics/metabolism ; Base Sequence ; DNA Repair ; DNA Replication ; GC Rich Sequence ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Interspersed Repetitive Sequences ; Membrane Transport Proteins/genetics/metabolism ; Molecular Sequence Data ; Protein Biosynthesis ; Recombination, Genetic ; Transcription, Genetic ; }, abstract = {Symbiobacterium thermophilum is an uncultivable bacterium isolated from compost that depends on microbial commensalism. The 16S ribosomal DNA-based phylogeny suggests that this bacterium belongs to an unknown taxon in the Gram-positive bacterial cluster. Here, we describe the 3.57 Mb genome sequence of S.thermophilum. The genome consists of 3338 protein-coding sequences, out of which 2082 have functional assignments. Despite the high G + C content (68.7%), the genome is closest to that of Firmicutes, a phylum consisting of low G + C Gram-positive bacteria. This provides evidence for the presence of an undefined category in the Gram-positive bacterial group. The presence of both spo and related genes and microscopic observation indicate that S.thermophilum is the first high G + C organism that forms endospores. The S.thermophilum genome is also characterized by the widespread insertion of class C group II introns, which are oriented in the same direction as chromosomal replication. The genome has many membrane transporters, a number of which are involved in the uptake of peptides and amino acids. The genes involved in primary metabolism are largely identified, except those that code several biosynthetic enzymes and carbonic anhydrase. The organism also has a variety of respiratory systems including Nap nitrate reductase, which has been found only in Gram-negative bacteria. Overall, these features suggest that S.thermophilum is adaptable to and thus lives in various environments, such that its growth requirement could be a substance or a physiological condition that is generally available in the natural environment rather than a highly specific substance that is present only in a limited niche. The genomic information from S.thermophilum offers new insights into microbial diversity and evolutionary sciences, and provides a framework for characterizing the molecular basis underlying microbial commensalism.}, }
@article {pmid15381435, year = {2004}, author = {Fischer, M and Schott, AK and Römisch, W and Ramsperger, A and Augustin, M and Fidler, A and Bacher, A and Richter, G and Huber, R and Eisenreich, W}, title = {Evolution of vitamin B2 biosynthesis. A novel class of riboflavin synthase in Archaea.}, journal = {Journal of molecular biology}, volume = {343}, number = {1}, pages = {267-278}, doi = {10.1016/j.jmb.2004.08.016}, pmid = {15381435}, issn = {0022-2836}, mesh = {Amino Acid Sequence ; Archaea/*enzymology/*genetics ; Base Sequence ; Codon ; Conserved Sequence ; Evolution, Molecular ; Kinetics ; Magnetic Resonance Spectroscopy ; Methanococcus/enzymology/genetics ; Molecular Sequence Data ; Molecular Weight ; Open Reading Frames ; Phylogeny ; Recombinant Proteins/chemistry/isolation &amp; purification/metabolism ; Riboflavin/*biosynthesis/chemistry/genetics/isolation &amp; purification ; Sequence Analysis, Protein ; Sequence Homology, Amino Acid ; Spectrometry, Mass, Electrospray Ionization ; Substrate Specificity ; Temperature ; Ultracentrifugation ; }, abstract = {The open reading frame MJ1184 of Methanococcus jannaschii with similarity to riboflavin synthase of Methanothermobacter thermoautotrophicus was cloned into an expression vector but was poorly expressed in an Escherichia coli host strain. However, a synthetic open reading frame that was optimized for expression in E.coli directed the synthesis of abundant amounts of a protein with an apparent subunit mass of 17.5 kDa. The protein was purified to apparent homogeneity. Hydrodynamic studies indicated a relative mass of 88 kDa suggesting a homopentamer structure. The enzyme was shown to catalyze the formation of riboflavin from 6,7-dimethyl-8-ribityllumazine at a rate of 24 nmol mg(-1) min(-1) at 40 degrees C. Divalent metal ions, preferably manganese or magnesium, are required for maximum activity. In contrast to pentameric archaeal type riboflavin synthases, orthologs from plants, fungi and eubacteria are trimeric proteins characterized by an internal sequence repeat with similar folding patterns. In these organisms the reaction is achieved by binding the two substrate molecules in an antiparallel orientation. With the enzyme of M.jannaschii, 13C NMR spectroscopy with 13C-labeled 6,7-dimethyl-8-ribityllumazine samples as substrates showed that the regiochemistry of the dismutation reaction is the same as observed in eubacteria and eukaryotes, however, in a non-pseudo-c2 symmetric environment. Whereas the riboflavin synthases of M.jannaschii and M.thermoautotrophicus are devoid of similarity with those of eubacteria and eukaryotes, they have significant sequence similarity with 6,7-dimethyl-8-ribityllumazine synthases catalyzing the penultimate step of riboflavin biosynthesis. 6,7-Dimethyl-8-ribityllumazine synthase and the archaeal riboflavin synthase appear to have diverged early in the evolution of Archaea from a common ancestor. Some Archaea have eubacterial type riboflavin synthases which may have been acquired by lateral gene transfer.}, }
@article {pmid15381417, year = {2004}, author = {Leipe, DD and Koonin, EV and Aravind, L}, title = {STAND, a class of P-loop NTPases including animal and plant regulators of programmed cell death: multiple, complex domain architectures, unusual phyletic patterns, and evolution by horizontal gene transfer.}, journal = {Journal of molecular biology}, volume = {343}, number = {1}, pages = {1-28}, doi = {10.1016/j.jmb.2004.08.023}, pmid = {15381417}, issn = {0022-2836}, mesh = {Adenosine Triphosphatases/chemistry/classification/genetics/physiology ; Animals ; *Apoptosis ; Evolution, Molecular ; Gene Expression Regulation, Enzymologic ; *Gene Transfer, Horizontal ; Humans ; Nucleoside-Triphosphatase/chemistry/*genetics ; *Phylogeny ; Plants/*enzymology ; Protein Structure, Tertiary/genetics ; Sequence Homology, Amino Acid ; }, abstract = {Using sequence profile analysis and sequence-based structure predictions, we define a previously unrecognized, widespread class of P-loop NTPases. The signal transduction ATPases with numerous domains (STAND) class includes the AP-ATPases (animal apoptosis regulators CED4/Apaf-1, plant disease resistance proteins, and bacterial AfsR-like transcription regulators) and NACHT NTPases (e.g. NAIP, TLP1, Het-E-1) that have been studied extensively in the context of apoptosis, pathogen response in animals and plants, and transcriptional regulation in bacteria. We show that, in addition to these well-characterized protein families, the STAND class includes several other groups of (predicted) NTPase domains from diverse signaling and transcription regulatory proteins from bacteria and eukaryotes, and three Archaea-specific families. We identified the STAND domain in several biologically well-characterized proteins that have not been suspected to have NTPase activity, including soluble adenylyl cyclases, nephrocystin 3 (implicated in polycystic kidney disease), and Rolling pebble (a regulator of muscle development); these findings are expected to facilitate elucidation of the functions of these proteins. The STAND class belongs to the additional strand, catalytic E division of P-loop NTPases together with the AAA+ ATPases, RecA/helicase-related ATPases, ABC-ATPases, and VirD4/PilT-like ATPases. The STAND proteins are distinguished from other P-loop NTPases by the presence of unique sequence motifs associated with the N-terminal helix and the core strand-4, as well as a C-terminal helical bundle that is fused to the NTPase domain. This helical module contains a signature GxP motif in the loop between the two distal helices. With the exception of the archaeal families, almost all STAND NTPases are multidomain proteins containing three or more domains. In addition to the NTPase domain, these proteins typically contain DNA-binding or protein-binding domains, superstructure-forming repeats, such as WD40 and TPR, and enzymatic domains involved in signal transduction, including adenylate cyclases and kinases. By analogy to the AAA+ ATPases, it can be predicted that STAND NTPases use the C-terminal helical bundle as a "lever" to transmit the conformational changes brought about by NTP hydrolysis to effector domains. STAND NTPases represent a novel paradigm in signal transduction, whereby adaptor, regulatory switch, scaffolding, and, in some cases, signal-generating moieties are combined into a single polypeptide. The STAND class consists of 14 distinct families, and the evolutionary history of most of these families is riddled with dramatic instances of lineage-specific expansion and apparent horizontal gene transfer. The STAND NTPases are most abundant in developmentally and organizationally complex prokaryotes and eukaryotes. Transfer of genes for STAND NTPases from bacteria to eukaryotes on several occasions might have played a significant role in the evolution of eukaryotic signaling systems.}, }
@article {pmid15381195, year = {2004}, author = {Shackelton, LA and Holmes, EC}, title = {The evolution of large DNA viruses: combining genomic information of viruses and their hosts.}, journal = {Trends in microbiology}, volume = {12}, number = {10}, pages = {458-465}, doi = {10.1016/j.tim.2004.08.005}, pmid = {15381195}, issn = {0966-842X}, mesh = {DNA Viruses/*genetics ; DNA, Viral/*genetics ; *Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal/genetics ; Genomics/*methods ; Phylogeny ; }, }
@article {pmid15378527, year = {2004}, author = {Posta, K and Béki, E and Wilson, DB and Kukolya, J and Hornok, L}, title = {Cloning, characterization and phylogenetic relationships of cel5B, a new endoglucanase encoding gene from Thermobifida fusca.}, journal = {Journal of basic microbiology}, volume = {44}, number = {5}, pages = {383-399}, doi = {10.1002/jobm.200410422}, pmid = {15378527}, issn = {0233-111X}, mesh = {Actinomycetales/*enzymology/genetics ; Amino Acid Sequence/genetics ; Bacterial Proteins/genetics/metabolism ; Base Sequence ; Biological Evolution ; Catalytic Domain ; Cellulase/*genetics/isolation &amp; purification/*metabolism ; Cloning, Molecular ; Conserved Sequence ; DNA, Bacterial/chemistry/isolation &amp; purification ; Enzyme Stability ; Gene Expression ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Tertiary ; Recombinant Proteins/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Streptomyces lividans/genetics/metabolism ; Temperature ; Time Factors ; }, abstract = {Thermobifida fusca, a thermophilic, aerobic, cellulolytic bacterium has a highly complex cellulase system comprising three endoglucanases, two exoglucanases and one processive endoglucanase. Zymogram analysis indicated that additional cellulases may exist in T. fusca strain TM51, therefore a TM51 expression library was prepared in Streptomyces lividans TK24 and screened for hydrolases. A new endoglucanase gene, named Tf cel5B, was identified. Heterologous Cel5B, produced in S. lividans, had temperature and pH optima of 77 degrees C and 8.2, respectively and retained more than 60% of its activity after 24 h incubation at 60 degrees C. Domain analysis revealed an N-terminal catalytic domain with homology to known endoglucanases in family GH5 and a C-terminal cellulose binding module III domain (CBD). Comparing the domain structures of all seven known T. fusca cellulases showed, that the cellulase system of this organism consists of pairs of enzymes from the same GH family, including Cel5A--Cel5B, Cel6A--Cel6B and Cel9A--Cel9B plus a single family GH48 enzyme (Cel48A). Furthermore, the catalytic and substrate binding domains of enzymes, belonging to the same GH family were arranged in opposite orientations. Phylogenetic comparisons of the catalytic domain sequences of the T. fusca cellulases to other family GH5, GH6, GH9 and GH48 cellulases of bacterial origin revealed that the enzyme pairs in the same GH family are not closely related to each other, instead they showed significant similarities to various cellulase enzymes from taxonomically distinct organisms. Therefore, the complex and highly efficient cellulase system of T. fusca seems to be evolved as a result of horizontal gene transfers rather than gene duplication events.}, }
@article {pmid15375152, year = {2004}, author = {Bolotin, A and Quinquis, B and Sorokin, A and Ehrlich, DS}, title = {Recent genetic transfer between Lactococcus lactis and enterobacteria.}, journal = {Journal of bacteriology}, volume = {186}, number = {19}, pages = {6671-6677}, pmid = {15375152}, issn = {0021-9193}, mesh = {Base Sequence ; *Conjugation, Genetic ; Enterobacteriaceae/*genetics ; *Gene Transfer, Horizontal ; Lactococcus lactis/*genetics ; Molecular Sequence Data ; Phylogeny ; }, abstract = {The genome sequence of Lactococcus lactis revealed that the ycdB gene was recently exchanged between lactococci and enterobacteria. The present study of ycdB orthologs suggests that L. lactis was probably the gene donor and reveals three instances of gene transfer to enterobacteria. Analysis of ycdB gene transfer between two L. lactis subspecies, L. lactis subsp. lactis and L. lactis subsp. cremoris, indicates that the gene can be mobilized, possibly by conjugation.}, }
@article {pmid15375139, year = {2004}, author = {Novichkov, PS and Omelchenko, MV and Gelfand, MS and Mironov, AA and Wolf, YI and Koonin, EV}, title = {Genome-wide molecular clock and horizontal gene transfer in bacterial evolution.}, journal = {Journal of bacteriology}, volume = {186}, number = {19}, pages = {6575-6585}, pmid = {15375139}, issn = {0021-9193}, mesh = {*Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Models, Genetic ; Phylogeny ; }, abstract = {We describe a simple theoretical framework for identifying orthologous sets of genes that deviate from a clock-like model of evolution. The approach used is based on comparing the evolutionary distances within a set of orthologs to a standard intergenomic distance, which was defined as the median of the distribution of the distances between all one-to-one orthologs. Under the clock-like model, the points on a plot of intergenic distances versus intergenomic distances are expected to fit a straight line. A statistical technique to identify significant deviations from the clock-like behavior is described. For several hundred analyzed orthologous sets representing three well-defined bacterial lineages, the alpha-Proteobacteria, the gamma-Proteobacteria, and the Bacillus-Clostridium group, the clock-like null hypothesis could not be rejected for approximately 70% of the sets, whereas the rest showed substantial anomalies. Subsequent detailed phylogenetic analysis of the genes with the strongest deviations indicated that over one-half of these genes probably underwent a distinct form of horizontal gene transfer, xenologous gene displacement, in which a gene is displaced by an ortholog from a different lineage. The remaining deviations from the clock-like model could be explained by lineage-specific acceleration of evolution. The results indicate that although xenologous gene displacement is a major force in bacterial evolution, a significant majority of orthologous gene sets in three major bacterial lineages evolved in accordance with the clock-like model. The approach described here allows rapid detection of deviations from this mode of evolution on the genome scale.}, }
@article {pmid15374530, year = {2004}, author = {Hughes, AL}, title = {Evolutionary origin of the Jiv90 gene of Pestivirus.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {4}, number = {4}, pages = {329-333}, doi = {10.1016/j.meegid.2004.04.001}, pmid = {15374530}, issn = {1567-1348}, support = {GM43904/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Artiodactyla/virology ; Base Sequence ; Codon ; *Evolution, Molecular ; Gene Deletion ; Gene Transfer, Horizontal ; *Genome, Viral ; Molecular Sequence Data ; Mutagenesis, Insertional ; Pestivirus/*genetics ; Phylogeny ; Polyproteins/*chemistry ; Sequence Homology, Amino Acid ; }, abstract = {Phylogenetic analyses were used to test the hypothesis that the Jiv90 insert in the genomes of Pestivirus species originated by horizontal transfer from their hosts (mammals in the order Artiodactyla). The results supported this hypothesis because the Jiv90 insert clustered with the corresponding domains of mammalian Jiv proteins and closer to artiodactyl than to rodent or primate genes. A phylogeny of Pestivirus genotypes showed that the Jiv90 insert occurred only in one clade (Pestivirus Type 1), although numerous members of this clade lacked the insert. This pattern is probably most easily explained on the hypothesis that the insert occurred in the common ancestor of the Type 1 clade and that it has been subsequently lost independently by several members of the clade.}, }
@article {pmid15356622, year = {2004}, author = {Rivera, MC and Lake, JA}, title = {The ring of life provides evidence for a genome fusion origin of eukaryotes.}, journal = {Nature}, volume = {431}, number = {7005}, pages = {152-155}, doi = {10.1038/nature02848}, pmid = {15356622}, issn = {1476-4687}, mesh = {Bacteria/genetics ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; DNA, Mitochondrial/genetics ; Eukaryotic Cells/*metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome ; *Genomics/methods ; *Models, Genetic ; Organelles/genetics ; Photosynthesis ; *Phylogeny ; Prokaryotic Cells/metabolism ; Recombination, Genetic/*genetics ; Saccharomyces cerevisiae/genetics ; Schizosaccharomyces/genetics ; }, abstract = {Genomes hold within them the record of the evolution of life on Earth. But genome fusions and horizontal gene transfer seem to have obscured sufficiently the gene sequence record such that it is difficult to reconstruct the phylogenetic tree of life. Here we determine the general outline of the tree using complete genome data from representative prokaryotes and eukaryotes and a new genome analysis method that makes it possible to reconstruct ancient genome fusions and phylogenetic trees. Our analyses indicate that the eukaryotic genome resulted from a fusion of two diverse prokaryotic genomes, and therefore at the deepest levels linking prokaryotes and eukaryotes, the tree of life is actually a ring of life. One fusion partner branches from deep within an ancient photosynthetic clade, and the other is related to the archaeal prokaryotes. The eubacterial organism is either a proteobacterium, or a member of a larger photosynthetic clade that includes the Cyanobacteria and the Proteobacteria.}, }
@article {pmid15356285, year = {2004}, author = {Walsh, DA and Bapteste, E and Kamekura, M and Doolittle, WF}, title = {Evolution of the RNA polymerase B' subunit gene (rpoB') in Halobacteriales: a complementary molecular marker to the SSU rRNA gene.}, journal = {Molecular biology and evolution}, volume = {21}, number = {12}, pages = {2340-2351}, doi = {10.1093/molbev/msh248}, pmid = {15356285}, issn = {0737-4038}, mesh = {Base Sequence ; Classification/methods ; DNA Primers ; DNA-Directed RNA Polymerases/*genetics ; *Genetic Variation ; Halobacteriales/*genetics ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; Mutation/genetics ; *Phylogeny ; RNA, Ribosomal/*genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Many prokaryotes have multiple ribosomal RNA operons. Generally, sequence differences between small subunit (SSU) rRNA genes are minor (<1%) and cause little concern for phylogenetic inference or environmental diversity studies. For Halobacteriales, an order of extremely halophilic, aerobic Archaea, within-genome SSU rRNA sequence divergence can exceed 5%, rendering phylogenetic assignment problematic. The RNA polymerase B' subunit gene (rpoB') is a single-copy conserved gene that may be an appropriate alternative phylogenetic marker for Halobacteriales. We sequenced a fragment of the rpoB' gene from 21 species, encompassing 15 genera of Halobacteriales. To examine the utility of rpoB' as a phylogenetic marker in Halobacteriales, we investigated three properties of rpoB' trees: the variation in resolution between trees inferred from the rpoB' DNA and RpoB' protein alignment, the degree of mutational saturation between taxa, and congruence with the SSU rRNA tree. The rpoB' DNA and protein trees were for the most part congruent and consistently recovered two well-supported monophyletic groups, the clade I and clade II haloarchaea, within a collection of less well resolved Halobacteriales lineages. A comparison of observed versus inferred numbers of substitution revealed mutational saturation in the rpoB' DNA data set, particularly between more distant species. Thus, the RpoB' protein sequence may be more reliable than the rpoB' DNA sequence for inferring Halobacteriales phylogeny. AU tests of tree selection indicated the trees inferred from rpoB' DNA and protein alignments were significantly incongruent with the SSU rRNA tree. We discuss possible explanations for this incongruence, including tree reconstruction artifact, differential paralog sampling, and lateral gene transfer. This is the first study of Halobacteriales evolution based on a marker other than the SSU rRNA gene. In addition, we present a valuable phylogenetic framework encompassing a broad diversity of Halobacteriales, in which novel sequences can be inserted for evolutionary, ecological, or taxonomic investigations.}, }
@article {pmid15356278, year = {2005}, author = {Andersson, JO and Sarchfield, SW and Roger, AJ}, title = {Gene transfers from nanoarchaeota to an ancestor of diplomonads and parabasalids.}, journal = {Molecular biology and evolution}, volume = {22}, number = {1}, pages = {85-90}, doi = {10.1093/molbev/msh254}, pmid = {15356278}, issn = {0737-4038}, mesh = {Alanine-tRNA Ligase/chemistry/*genetics ; Amino Acyl-tRNA Synthetases/chemistry/*genetics ; Animals ; Archaea/genetics ; Cell Lineage ; Diplomonadida/enzymology/*genetics ; Eukaryota/enzymology/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Nanoarchaeota/enzymology/*genetics ; Phylogeny ; }, abstract = {Rare evolutionary events, such as lateral gene transfers and gene fusions, may be useful to pinpoint, and correlate the timing of, key branches across the tree of life. For example, the shared possession of a transferred gene indicates a phylogenetic relationship among organismal lineages by virtue of their shared common ancestral recipient. Here, we present phylogenetic analyses of prolyl-tRNA and alanyl-tRNA synthetase genes that indicate lateral gene transfer events to an ancestor of the diplomonads and parabasalids from lineages more closely related to the newly discovered archaeal hyperthermophile Nanoarchaeum equitans (Nanoarchaeota) than to Crenarchaeota or Euryarchaeota. The support for this scenario is strong from all applied phylogenetic methods for the alanyl-tRNA sequences, whereas the phylogenetic analyses of the prolyl-tRNA sequences show some disagreements between methods, indicating that the donor lineage cannot be identified with a high degree of certainty. However, in both trees, the diplomonads and parabasalids branch together within the Archaea, strongly suggesting that these two groups of unicellular eukaryotes, often regarded as the two earliest independent offshoots of the eukaryotic lineage, share a common ancestor to the exclusion of the eukaryotic root. Unfortunately, the phylogenetic analyses of these two aminoacyl-tRNA synthetase genes are inconclusive regarding the position of the diplomonad/parabasalid group within the eukaryotes. Our results also show that the lineage leading to Nanoarchaeota branched off from Euryarchaeota and Crenarchaeota before the divergence of diplomonads and parabasalids, that this unexplored archaeal diversity, currently only represented by the hyperthermophilic organism Nanoarchaeum equitans, may include members living in close proximity to mesophilic eukaryotes, and that the presence of split genes in the Nanoarchaeum genome is a derived feature.}, }
@article {pmid15355234, year = {2005}, author = {Goldsmith, MR and Shimada, T and Abe, H}, title = {The genetics and genomics of the silkworm, Bombyx mori.}, journal = {Annual review of entomology}, volume = {50}, number = {}, pages = {71-100}, doi = {10.1146/annurev.ento.50.071803.130456}, pmid = {15355234}, issn = {0066-4170}, mesh = {Animals ; Bombyx/*genetics ; Chromosome Mapping ; Databases, Factual ; Expressed Sequence Tags ; Female ; Gene Dosage ; Genetic Engineering ; Genomics ; Male ; Mutation ; Sex Determination Processes ; }, abstract = {We review progress in applying molecular genetic and genomic technologies to studies in the domesticated silkworm, Bombyx mori, highlighting its use as a model for Lepidoptera, and in sericulture and biotechnology. Dense molecular linkage maps are being integrated with classical linkage maps for positional cloning and marker-assisted selection. Classical mutations have been identified by a candidate gene approach. Cytogenetic and sequence analyses show that the W chromosome is composed largely of nested full-length long terminal repeat retrotransposons. Z-chromosome-linked sequences show a lack of dosage compensation. The downstream sex differentiation mechanism has been studied via the silkworm homolog of doublesex. Expressed sequence tagged databases have been used to discover Lepidoptera-specific genes, provide evidence for horizontal gene transfer, and construct microarrays. Physical maps using large-fragment bacterial artificial chromosome libraries have been constructed, and whole-genome shotgun sequencing is underway. Germline transformation and transient expression systems are well established and available for functional studies, high-level protein expression, and gene silencing via RNA interference.}, }
@article {pmid15353570, year = {2004}, author = {Brüssow, H and Canchaya, C and Hardt, WD}, title = {Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {68}, number = {3}, pages = {560-602, table of contents}, pmid = {15353570}, issn = {1092-2172}, mesh = {Bacteria/genetics/*pathogenicity/*virology ; Bacteriophages/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; *Lysogeny ; Prophages/genetics ; }, abstract = {Comparative genomics demonstrated that the chromosomes from bacteria and their viruses (bacteriophages) are coevolving. This process is most evident for bacterial pathogens where the majority contain prophages or phage remnants integrated into the bacterial DNA. Many prophages from bacterial pathogens encode virulence factors. Two situations can be distinguished: Vibrio cholerae, Shiga toxin-producing Escherichia coli, Corynebacterium diphtheriae, and Clostridium botulinum depend on a specific prophage-encoded toxin for causing a specific disease, whereas Staphylococcus aureus, Streptococcus pyogenes, and Salmonella enterica serovar Typhimurium harbor a multitude of prophages and each phage-encoded virulence or fitness factor makes an incremental contribution to the fitness of the lysogen. These prophages behave like "swarms" of related prophages. Prophage diversification seems to be fueled by the frequent transfer of phage material by recombination with superinfecting phages, resident prophages, or occasional acquisition of other mobile DNA elements or bacterial chromosomal genes. Prophages also contribute to the diversification of the bacterial genome architecture. In many cases, they actually represent a large fraction of the strain-specific DNA sequences. In addition, they can serve as anchoring points for genome inversions. The current review presents the available genomics and biological data on prophages from bacterial pathogens in an evolutionary framework.}, }
@article {pmid15351918, year = {2005}, author = {Bjornsdottir, SH and Thorbjarnardottir, SH and Eggertsson, G}, title = {Establishment of a gene transfer system for Rhodothermus marinus.}, journal = {Applied microbiology and biotechnology}, volume = {66}, number = {6}, pages = {675-682}, doi = {10.1007/s00253-004-1730-3}, pmid = {15351918}, issn = {0175-7598}, mesh = {DNA Restriction Enzymes/analysis ; DNA, Bacterial/chemistry ; Electroporation ; Escherichia coli ; *Gene Transfer Techniques ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Vectors ; Molecular Sequence Data ; Plasmids ; Rhodothermus/*genetics ; Selection, Genetic ; Sequence Analysis, DNA ; Transformation, Bacterial ; Tryptophan/biosynthesis/genetics ; }, abstract = {Genetic manipulation of Rhodothermus marinus has been hampered by the lack of a selection system for gene transfer. We report construction of a Rhodothermus/Escherichia coli shuttle plasmid, containing the R. marinus trpB gene, based on pUC18 and the cryptic R. marinus plasmid pRM21. A plasmid-less R. marinus recipient strain was selected on the basis of growth characteristics and absence of restriction activity. The shuttle plasmid, pRM100, was successfully introduced into a TrpB- mutant of the recipient strain using electroporation and was found to transform it to prototrophy. No loss or rearrangement of pRM100 was observed after growth for 80 generations in non-selective medium. The relative copy numbers of pRM100 and of the parental plasmid, pRM21, were determined as 7+/-1 and 42+/-4, respectively. The shuttle plasmid was used to optimize an electroporation protocol, and the maximal number of transformants obtained was 4.3+/8-0.7x10(6) cfu/microg DNA at 22.5 kV/cm, 200 Omega and 25 microF. Transformation failed, however, after chemical preparation of cells according to several protocols. This is the first report of genetic transformation in the genus Rhodothermus.}, }
@article {pmid15347748, year = {2004}, author = {Zhang, XX and Lilley, AK and Bailey, MJ and Rainey, PB}, title = {Functional and phylogenetic analysis of a plant-inducible oligoribonuclease (orn) gene from an indigenous Pseudomonas plasmid.}, journal = {Microbiology (Reading, England)}, volume = {150}, number = {Pt 9}, pages = {2889-2898}, doi = {10.1099/mic.0.27250-0}, pmid = {15347748}, issn = {1350-0872}, mesh = {Amino Acid Sequence ; Beta vulgaris/*microbiology ; Chromosomes, Bacterial/genetics ; Conserved Sequence ; DNA, Bacterial/chemistry/isolation &amp; purification ; Escherichia coli/genetics ; Exoribonucleases/*genetics/metabolism ; Gene Deletion ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Complementation Test ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Plants/microbiology ; *Plasmids ; *Promoter Regions, Genetic ; Protein Structure, Tertiary ; Pseudomonas/*genetics/growth &amp; development/metabolism ; Pseudomonas putida/genetics ; Seeds/microbiology ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Application of a promoter-trapping strategy to identify plant-inducible genes carried on an indigenous Pseudomonas plasmid, pQBR103, revealed the presence of a putative oligoribonuclease (orn) gene that encodes a highly conserved 3' to 5' exoribonuclease specific for small oligoribonucleotides. The deduced amino acid sequence of the plasmid-derived orn (orn(pl)) showed three conserved motifs characteristic of Orn from both prokaryotes and eukaryotes. Deletion of orn(pl) generated no observable phenotype, but inactivation of the chromosomal copy caused slow growth in Pseudomonas putida KT2440. This defect was fully restored by complementation with orn from Escherichia coli (orn(E.coli)). Plasmid-derived orn(pl) was capable of partially complementing the P. putida orn mutant, demonstrating functionality of orn(pl). Phylogenetic analysis showed that plasmid-encoded Orn was distinct from Orn encoded by the chromosome of proteobacteria. A survey of orn(pl) from related Pseudomonas plasmids showed a sporadic distribution but no sequence diversity. These data suggest that the orn(pl) was acquired by pQBR103 in a single gene-transfer event: the donor is unknown, but is unlikely to be a member of the Proteobacteria.}, }
@article {pmid15345390, year = {2004}, author = {Rezzonico, F and Défago, G and Moënne-Loccoz, Y}, title = {Comparison of ATPase-encoding type III secretion system hrcN genes in biocontrol fluorescent Pseudomonads and in phytopathogenic proteobacteria.}, journal = {Applied and environmental microbiology}, volume = {70}, number = {9}, pages = {5119-5131}, pmid = {15345390}, issn = {0099-2240}, mesh = {Adenosine Triphosphatases/*genetics ; Amino Acid Sequence ; Base Sequence ; Genes, Bacterial/genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Proteobacteria/classification/*genetics ; Pseudomonadaceae/classification/*genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; }, abstract = {Type III protein secretion systems play a key role in the virulence of many pathogenic proteobacteria, but they also occur in nonpathogenic, plant-associated bacteria. Certain type III protein secretion genes (e.g., hrcC) have been found in Pseudomonas sp. strain SBW25 (and other biocontrol pseudomonads), but other type III protein secretion genes, such as the ATPase-encoding gene hrcN, have not been found. Using both colony hybridization and a PCR approach, we show here that hrcN is nevertheless present in many biocontrol fluorescent pseudomonads. The phylogeny of biocontrol Pseudomonas strains based on partial hrcN sequences was largely congruent with the phylogenies derived from analyses of rrs (encoding 16S rRNA) and, to a lesser extent, biocontrol genes, such as phlD (for 2,4-diacetylphloroglucinol production) and hcnBC (for HCN production). Most biocontrol pseudomonads clustered separately from phytopathogenic proteobacteria, including pathogenic pseudomonads, in the hrcN tree. The exception was strain KD, which clustered with phytopathogenic pseudomonads, such as Pseudomonas syringae, suggesting that hrcN was acquired from the latter species. Indeed, strain KD (unlike strain SBW25) displayed the same organization of the hrpJ operon, which contains hrcN, as P. syringae. These results indicate that the occurrence of hrcN in most biocontrol pseudomonads is not the result of recent horizontal gene transfer from phytopathogenic bacteria, although such transfer might have occurred for a minority of biocontrol strains.}, }
@article {pmid15345048, year = {2004}, author = {Liu, Y and Harrison, PM and Kunin, V and Gerstein, M}, title = {Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes.}, journal = {Genome biology}, volume = {5}, number = {9}, pages = {R64}, pmid = {15345048}, issn = {1474-760X}, support = {T15 LM007056/LM/NLM NIH HHS/United States ; U54 AI057158/AI/NIAID NIH HHS/United States ; 1U54AI057158-01/AI/NIAID NIH HHS/United States ; T15 LM07056/LM/NLM NIH HHS/United States ; }, mesh = {Escherichia coli K12/genetics ; Gene Dosage ; Gene Duplication ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/genetics ; Genomics/methods ; Models, Genetic ; Multigene Family/genetics ; Mutagenesis/genetics ; Prokaryotic Cells/*chemistry/*metabolism ; Pseudogenes/*genetics ; }, abstract = {BACKGROUND: Pseudogenes often manifest themselves as disabled copies of known genes. In prokaryotes, it was generally believed (with a few well-known exceptions) that they were rare.<br><br>RESULTS: We have carried out a comprehensive analysis of the occurrence of pseudogenes in a diverse selection of 64 prokaryote genomes. Overall, we find a total of around 7,000 candidate pseudogenes. Moreover, in all the genomes surveyed, pseudogenes occur in at least 1 to 5% of all gene-like sequences, with some genomes having considerably higher occurrence. Although many large populations of pseudogenes arise from large, diverse protein families (for example, the ABC transporters), notable numbers of pseudogenes are associated with specific families that do not occur that widely. These include the cytochrome P450 and PPE families (PF00067 and PF00823) and others that have a direct role in DNA transposition.<br><br>CONCLUSIONS: We find suggestive evidence that a large fraction of prokaryote pseudogenes arose from failed horizontal transfer events. In particular, we find that pseudogenes are more than twice as likely as genes to have anomalous codon usage associated with horizontal transfer. Moreover, we found a significant difference in the number of horizontally transferred pseudogenes in pathogenic and non-pathogenic strains of Escherichia coli.}, }
@article {pmid15342577, year = {2004}, author = {Franco, AA}, title = {The Bacteroides fragilis pathogenicity island is contained in a putative novel conjugative transposon.}, journal = {Journal of bacteriology}, volume = {186}, number = {18}, pages = {6077-6092}, pmid = {15342577}, issn = {0021-9193}, support = {R01A148708//PHS HHS/United States ; }, mesh = {Bacterial Proteins/genetics/physiology ; Bacterial Toxins/genetics ; Bacteroides fragilis/drug effects/*genetics/pathogenicity ; *Conjugation, Genetic ; *DNA Transposable Elements ; DNA, Bacterial/chemistry ; Gene Order ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genomic Islands/*genetics ; Integrases/genetics ; Metalloendopeptidases/genetics ; Molecular Sequence Data ; Open Reading Frames ; Recombination, Genetic ; Sequence Analysis, DNA ; Sequence Homology ; Tetracycline/pharmacology ; Transposases/genetics ; }, abstract = {The genetic element flanking the Bacteroides fragilis pathogenicity island (BfPAI) in enterotoxigenic B. fragilis (ETBF) strain 86-5443-2-2 and a related genetic element in NCTC 9343 were characterized. The results suggested that these genetic elements are members of a new family of conjugative transposons (CTns) not described previously. These putative CTns, designated CTn86 and CTn9343 for ETBF 86-5443-2-2 and NCTC 9343, respectively, differ from previously described Bacteroides species CTns in a number of ways. These new transposons do not carry tetQ, and the excision from the chromosome to form a circular intermediate is not regulated by tetracycline; they are predicted to differ in their mechanism of transposition; and their sequences have very limited similarity with CTnDOT or other described CTns. CTn9343 is 64,229 bp in length, contains 61 potential open reading frames, and both ends contain IS21 transposases. Colony blot hybridization, PCR, and sequence analysis indicated that CTn86 has the same structure as CTn9343 except that CTn86 lacks a approximately 7-kb region containing truncated integrase (int2) and rteA genes and it contains the BfPAI integrated between the mob region and the bfmC gene. If these putative CTns were to be demonstrated to be transmissible, this would suggest that the bft gene can be transferred from ETBF to nontoxigenic B. fragilis strains by a mechanism similar to that for the spread of antibiotic resistance genes.}, }
@article {pmid15340481, year = {2004}, author = {Nielsen, KM and Townsend, JP}, title = {Monitoring and modeling horizontal gene transfer.}, journal = {Nature biotechnology}, volume = {22}, number = {9}, pages = {1110-1114}, doi = {10.1038/nbt1006}, pmid = {15340481}, issn = {1087-0156}, mesh = {Ecosystem ; Environmental Monitoring/*methods ; Gene Expression Profiling/*methods ; Gene Transfer, Horizontal/*genetics ; Genetic Engineering/methods ; Genetic Testing/methods ; Intestines/*microbiology ; *Models, Biological ; Plants, Genetically Modified/*genetics ; Protein Engineering/methods ; Recombinant Proteins/biosynthesis/genetics ; Research Design ; Risk Assessment/*methods ; Risk Factors ; *Soil Microbiology ; }, abstract = {Monitoring efforts have failed to identify horizontal gene transfer (HGT) events occurring from transgenic plants into bacterial communities in soil or intestinal environments. The lack of such observations is frequently cited in biosafety literature and by regulatory risk assessment. Our analysis of the sensitivity of current monitoring efforts shows that studies to date have examined potential HGT events occurring in less than 2 g of sample material, when combined. Moreover, a population genetic model predicts that rare bacterial transformants acquiring transgenes require years of growth to out-compete wild-type bacteria. Time of sampling is there-fore crucial to the useful implementation of monitoring. A population genetic approach is advocated for elucidating the necessary sample sizes and times of sampling for monitoring HGT into large bacterial populations. Major changes in current monitoring approaches are needed, including explicit consideration of the population size of exposed bacteria, the bacterial generation time, the strength of selection acting on the transgene-carrying bacteria, and the sample size necessary to verify or falsify the HGT hypotheses tested.}, }
@article {pmid15340480, year = {2004}, author = {Heinemann, JA and Traavik, T}, title = {Problems in monitoring horizontal gene transfer in field trials of transgenic plants.}, journal = {Nature biotechnology}, volume = {22}, number = {9}, pages = {1105-1109}, doi = {10.1038/nbt1009}, pmid = {15340480}, issn = {1087-0156}, mesh = {Ecosystem ; Environmental Monitoring/*methods ; Gene Expression Profiling/*methods ; Gene Transfer, Horizontal/*genetics ; Genetic Engineering/*methods ; Genetic Testing/methods ; Plants, Genetically Modified/*genetics ; Protein Engineering/methods ; Recombinant Proteins/biosynthesis/genetics ; Research Design ; Risk Assessment/*methods ; Risk Factors ; *Soil Microbiology ; }, abstract = {Transgenic crops are approved for release in some countries, while many more countries are wrestling with the issue of how to conduct risk assessments. Controls on field trials often include monitoring of horizontal gene transfer (HGT) from crops to surrounding soil microorganisms. Our analysis of antibiotic-resistant bacteria and of the sensitivity of current techniques for monitoring HGT from transgenic plants to soil microorganisms has two major implications for field trial assessments of transgenic crops: first, HGT from transgenic plants to microbes could still have an environmental impact at a frequency approximately a trillion times lower than the current risk assessment literature estimates the frequency to be; and second, current methods of environmental sampling to capture genes or traits in a recombinant are too insensitive for monitoring evolution by HGT. A model for HGT involving iterative short-patch events explains how HGT can occur at high frequencies but be detected at extremely low frequencies.}, }
@article {pmid15340465, year = {2004}, author = {Gilbert, HJ and O'Donnell, AG and Mathers, JC}, title = {'Informative' horizontal gene transfer.}, journal = {Nature biotechnology}, volume = {22}, number = {9}, pages = {1076}, doi = {10.1038/nbt0904-1076b}, pmid = {15340465}, issn = {1087-0156}, mesh = {Ecosystem ; Gene Expression Profiling/*methods ; Gene Transfer, Horizontal/*genetics ; Genetic Engineering/*methods ; Genetic Testing/*methods ; Humans ; Intestines/*microbiology ; Plants, Genetically Modified/*genetics ; }, }
@article {pmid15338429, year = {2004}, author = {Aoki, S}, title = {Resurrection of an ancestral gene: functional and evolutionary analyses of the Ngrol genes transferred from Agrobacterium to Nicotiana.}, journal = {Journal of plant research}, volume = {117}, number = {4}, pages = {329-337}, pmid = {15338429}, issn = {0918-9440}, mesh = {Biological Evolution ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genes, Plant ; Mutation ; Phenotype ; Phylogeny ; Plant Diseases/genetics ; Plants, Genetically Modified ; Plasmids/genetics ; Rhizobium/*genetics ; Nicotiana/*genetics ; Transformation, Genetic ; }, abstract = {The Ng rol genes, which have high similarity in sequence to the rol genes of Agrobacterium rhizogenes, are present in the genome of untransformed plants of Nicotiana glauca. It is thought that bacterial infection resulted in the transfer of the Ng rol genes to plants early in the evolution of the genus Nicotiana, since several species in this genus contain rol-like sequences but others do not. Plants transformed with the bacterial rol genes exhibit various developmental and morphological changes. The presence of rol-like sequences in plant genomes is therefore thought to have contributed to the evolution of Nicotiana species. This paper focuses on studies of the Ng rol genes in present-day plants and during the evolution of the genus Nicotiana. The functional sequences of several Ng rol genes may have been conserved after their ancient introduction from a bacterium to the plant. Resurrection of an ancestral function of one of the Ng rol genes, as examined by physiological and evolutionary analyses, is also described. The origin of the Ng rol genes is then considered, based on results of molecular phylogenetic analyses. The effects of the horizontal transfer of the Ng rol genes and mutations in the genes are discussed on the plants of the genus Nicotiana during evolution.}, }
@article {pmid15338281, year = {2004}, author = {Mitreva, M and Elling, AA and Dante, M and Kloek, AP and Kalyanaraman, A and Aluru, S and Clifton, SW and Bird, DM and Baum, TJ and McCarter, JP}, title = {A survey of SL1-spliced transcripts from the root-lesion nematode Pratylenchus penetrans.}, journal = {Molecular genetics and genomics : MGG}, volume = {272}, number = {2}, pages = {138-148}, pmid = {15338281}, issn = {1617-4615}, mesh = {Animals ; Caenorhabditis elegans/genetics ; DNA, Helminth/genetics ; Expressed Sequence Tags ; Gene Library ; Gene Transfer, Horizontal ; Genes, Helminth ; Multigene Family ; Phenotype ; Plant Diseases/parasitology ; Plants/*parasitology ; Polymerase Chain Reaction ; RNA Interference ; RNA, Helminth/*genetics ; RNA, Spliced Leader/*genetics ; Species Specificity ; Tylenchoidea/*genetics/growth &amp; development/pathogenicity ; }, abstract = {Plant-parasitic nematodes are important and cosmopolitan pathogens of crops. Here, we describe the generation and analysis of 1928 expressed sequence tags (ESTs) of a splice-leader 1 (SL1) library from mixed life stages of the root-lesion nematode Pratylenchus penetrans. The ESTs were grouped into 420 clusters and classified by function using the Gene Ontology (GO) hierarchy and the Kyoto KEGG database. Approximately 80% of all translated clusters show homology to Caenorhabditis elegans proteins, and 37% of the C. elegans gene homologs had confirmed phenotypes as assessed by RNA interference tests. Use of an SL1-PCR approach, while ensuring the cloning of the 5' ends of mRNAs, has demonstrated bias toward short transcripts. Putative nematode-specific and Pratylenchus -specific genes were identified, and their implications for nematode control strategies are discussed.}, }
@article {pmid15337162, year = {2004}, author = {Salyers, AA and Gupta, A and Wang, Y}, title = {Human intestinal bacteria as reservoirs for antibiotic resistance genes.}, journal = {Trends in microbiology}, volume = {12}, number = {9}, pages = {412-416}, doi = {10.1016/j.tim.2004.07.004}, pmid = {15337162}, issn = {0966-842X}, support = {AI 22383/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; Bacteroides/genetics ; Drug Resistance/*genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Gram-Negative Bacteria/genetics ; Gram-Positive Bacteria/genetics ; Humans ; Intestines/*microbiology ; }, abstract = {Human intestinal bacteria have many roles in human health, most of which are beneficial or neutral for the host. In this review, we explore a more sinister side of intestinal bacteria; their role as traffickers in antibiotic resistance genes. Evidence is accumulating to support the hypothesis that intestinal bacteria not only exchange resistance genes among themselves but might also interact with bacteria that are passing through the colon, causing these bacteria to acquire and transmit antibiotic resistance genes.}, }
@article {pmid15337161, year = {2004}, author = {Bapteste, E and Boucher, Y and Leigh, J and Doolittle, WF}, title = {Phylogenetic reconstruction and lateral gene transfer.}, journal = {Trends in microbiology}, volume = {12}, number = {9}, pages = {406-411}, doi = {10.1016/j.tim.2004.07.002}, pmid = {15337161}, issn = {0966-842X}, mesh = {Biological Evolution ; Gammaproteobacteria/classification/genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial ; *Phylogeny ; }, abstract = {Lateral gene transfer (LGT) is often seen as a form of noise, obscuring the phylogenetic signal with which we might hope to reconstruct the evolution of a group of organisms, or indeed the history of all life (the Tree of Life). Such reconstruction might still be possible if the subset of genes conserved among all genomes in a group (or common to all genomes) comprise a core that is relatively refractory to LGT. Several papers designed to test this notion have recently appeared, and here we re-analyze one, which claims that the core of single-copy orthologs shared by all sequenced genomes of the gammaproteobacteria is essentially free of LGT. This conclusion is unfortunately premature, and it is very hard to determine what fraction of this core has been affected by LGT. We discuss other difficulties with the core concept and suggest that, although the core idea must remain part of our understanding of phylogenetic relationships, it should not be the sole basis for defining such relationships, because these are not exclusively tree-like. We suggest instead a more complex but more natural framework for classification, which we call the Synthesis of Life.}, }
@article {pmid15337159, year = {2004}, author = {Hastings, PJ and Rosenberg, SM and Slack, A}, title = {Antibiotic-induced lateral transfer of antibiotic resistance.}, journal = {Trends in microbiology}, volume = {12}, number = {9}, pages = {401-404}, doi = {10.1016/j.tim.2004.07.003}, pmid = {15337159}, issn = {0966-842X}, support = {R01-GM64022/GM/NIGMS NIH HHS/United States ; R01GM53158/GM/NIGMS NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/drug effects/genetics ; DNA Damage ; Drug Resistance/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; SOS Response, Genetics/*drug effects/*genetics ; }, abstract = {As do many temperate bacteriophages, integrating conjugative elements (ICEs) recruit the SOS DNA damage response to mobilize themselves from the bacterial chromosome and infect other cells. This transfers resistance to multiple antibiotics. Several commonly used antibiotics induce the SOS response, potentially hastening genetic change and the evolution to resistance of pathogenic populations. The use of such antibiotics should be reconsidered.}, }
@article {pmid15333143, year = {2004}, author = {Martins-Pinheiro, M and Galhardo, RS and Lage, C and Lima-Bessa, KM and Aires, KA and Menck, CF}, title = {Different patterns of evolution for duplicated DNA repair genes in bacteria of the Xanthomonadales group.}, journal = {BMC evolutionary biology}, volume = {4}, number = {}, pages = {29}, pmid = {15333143}, issn = {1471-2148}, mesh = {DNA Repair/*genetics ; DNA Repair Enzymes/genetics ; DNA, Bacterial/genetics ; *Evolution, Molecular ; *Gene Duplication ; Genes, Bacterial/*genetics ; Genome, Bacterial ; Phylogeny ; Xanthomonas/enzymology/*genetics ; }, abstract = {BACKGROUND: DNA repair genes encode proteins that protect organisms against genetic damage generated by environmental agents and by-products of cell metabolism. The importance of these genes in life maintenance is supported by their high conservation, and the presence of duplications of such genes may be easily traced, especially in prokaryotic genomes.<br><br>RESULTS: The genome sequences of two Xanthomonas species were used as the basis for phylogenetic analyses of genes related to DNA repair that were found duplicated. Although 16S rRNA phylogenetic analyses confirm their classification at the basis of the gamma proteobacteria subdivision, differences were found in the origin of the various genes investigated. Except for lexA, detected as a recent duplication, most of the genes in more than one copy are represented by two highly divergent orthologs. Basically, one of such duplications is frequently positioned close to other gamma proteobacteria, but the second is often positioned close to unrelated bacteria. These orthologs may have occurred from old duplication events, followed by extensive gene loss, or were originated from lateral gene transfer (LGT), as is the case of the uvrD homolog.<br><br>CONCLUSIONS: Duplications of DNA repair related genes may result in redundancy and also improve the organisms' responses to environmental challenges. Most of such duplications, in Xanthomonas, seem to have arisen from old events and possibly enlarge both functional and evolutionary genome potentiality.}, }
@article {pmid15328112, year = {2004}, author = {Cerdá Zolezzi, P and Laplana, LM and Calvo, CR and Cepero, PG and Erazo, MC and Gómez-Lus, R}, title = {Molecular basis of resistance to macrolides and other antibiotics in commensal viridans group streptococci and Gemella spp. and transfer of resistance genes to Streptococcus pneumoniae.}, journal = {Antimicrobial agents and chemotherapy}, volume = {48}, number = {9}, pages = {3462-3467}, pmid = {15328112}, issn = {0066-4804}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics ; Chloramphenicol Resistance/genetics ; Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Kanamycin/pharmacology ; Kanamycin Kinase/genetics ; Macrolides/*pharmacology ; Microbial Sensitivity Tests ; Staphylococcaceae/*drug effects/*genetics ; Streptococcus pneumoniae/*drug effects/*genetics ; Tetracycline Resistance/genetics ; Viridans Streptococci/*drug effects ; }, abstract = {We assessed the mechanisms of resistance to macrolide-lincosamide-streptogramin B (MLS(B)) antibiotics and related antibiotics in erythromycin-resistant viridans group streptococci (n = 164) and Gemella spp. (n = 28). The macrolide resistance phenotype was predominant (59.38%); all isolates with this phenotype carried the mef(A) or mef(E) gene, with mef(E) being predominant (95.36%). The erm(B) gene was always detected in strains with constitutive and inducible MLS(B) resistance and was combined with the mef(A/E) gene in 47.44% of isolates. None of the isolates carried the erm(A) subclass erm(TR), erm(A), or erm(C) genes. The mel gene was detected in all but four strains carrying the mef(A/E) gene. The tet(M) gene was found in 86.90% of tetracycline-resistant isolates and was strongly associated with the presence of the erm(B) gene. The cat(pC194) gene was detected in seven chloramphenicol-resistant Streptococcus mitis isolates, and the aph(3')-III gene was detected in four viridans group streptococcal isolates with high-level kanamycin resistance. The intTn gene was found in all isolates with the erm(B), tet(M), aph(3')-III, and cat(pC194) gene. The mef(E) and mel genes were successfully transferred from both groups of bacteria to Streptococcus pneumoniae R6 by transformation. Viridans group streptococci and Gemella spp. seem to be important reservoirs of resistance genes.}, }
@article {pmid15322020, year = {2004}, author = {Ko, KS and Kim, JW and Kim, JM and Kim, W and Chung, SI and Kim, IJ and Kook, YH}, title = {Population structure of the Bacillus cereus group as determined by sequence analysis of six housekeeping genes and the plcR Gene.}, journal = {Infection and immunity}, volume = {72}, number = {9}, pages = {5253-5261}, pmid = {15322020}, issn = {0019-9567}, mesh = {Animals ; Bacillus anthracis/*classification/genetics ; Bacillus cereus/*classification/genetics ; Bacillus thuringiensis/*classification/genetics ; Bacterial Proteins/*genetics ; Cattle ; Evolution, Molecular ; Genetic Variation ; Humans ; Molecular Sequence Data ; Phylogeny ; Recombination, Genetic ; *Sequence Analysis, DNA ; Trans-Activators/*genetics ; }, abstract = {The population structure of the Bacillus cereus group (52 strains of B. anthracis, B. cereus, and B. thuringiensis) was investigated by sequencing seven gene fragments (rpoB, gyrB, pycA, mdh, mbl, mutS, and plcR). Most of the strains were classifiable into two large subgroups in six housekeeping gene trees but not in the plcR tree. In addition, several consistent clusters were identified, which were unrelated to species distinction. Moreover, interrelationships among these clusters were incongruent in each gene tree. The incongruence length difference test and split decomposition analyses also showed incongruences between genes, suggesting horizontal gene transfer. The plcR gene was observed to have characteristics that differed from those of the other genes in terms of phylogenetic topology and pattern of sequence diversity. Thus, we suggest that the evolutionary history of the PlcR regulon differs from those of the other chromosomal genes and that recombination of the plcR gene may be frequent. The homogeneity of B. anthracis, which is depicted as an independent lineage in phylogenetic trees, is suggested to be of recent origin or to be due to the narrow taxonomic definition of species.}, }
@article {pmid15321685, year = {2004}, author = {Zhang, X and Gao, P and Chao, Q and Wang, L and Senior, E and Zhao, L}, title = {Microdiversity of phenol hydroxylase genes among phenol-degrading isolates of Alcaligenes sp. from an activated sludge system.}, journal = {FEMS microbiology letters}, volume = {237}, number = {2}, pages = {369-375}, doi = {10.1016/j.femsle.2004.06.057}, pmid = {15321685}, issn = {0378-1097}, mesh = {Alcaligenes/*enzymology/genetics/isolation &amp; purification ; DNA Fingerprinting ; DNA, Bacterial/analysis ; *Genes, Bacterial ; Genes, rRNA ; Genetic Variation ; Mixed Function Oxygenases/classification/*genetics/metabolism ; Nucleic Acid Hybridization ; Phenol/*metabolism ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/*microbiology ; }, abstract = {Enterobacterial repetitive intergenic consensus (ERIC)-PCR fingerprinting classified 97 phenol-degrading isolates with identical amplified ribosomal DNA restriction analysis (ARDRA) patterns into six genotypic groups. The 16S rRNA gene of the representative isolate of each group had higher than 99.47% common identity with each other and higher than 98% identity with the type strain of Alcaligenes faecalis. PCR-TGGE (temperature gradient gel electrophoresis) analysis of the genes of the largest subunit of the multi-component phenol hydroxylase (LmPH) in each isolate followed with sequencing showed that isolates within each ERIC-PCR group had identical LmPH gene sequences. Among the six different ERIC-PCR groups, two were found to harbor two different LmPH genes encoding low- and high-Ks (affinity constants) phenol hydroxylases, and the low-Ks type LmPH was identical in sequence with one predominant LmPH of the parental activated sludge. Three ERIC-PCR groups had only the high-Ks type and one had no sequence similar to the known LmPHs. Our work suggests that there is no correlation between the phylogenetic groupings of phenol-degrading bacteria and their LmPH genotypes possibly due to extensive horizontal gene transfer of this functional gene.}, }
@article {pmid15319480, year = {2004}, author = {Magnani, E and Sjölander, K and Hake, S}, title = {From endonucleases to transcription factors: evolution of the AP2 DNA binding domain in plants.}, journal = {The Plant cell}, volume = {16}, number = {9}, pages = {2265-2277}, pmid = {15319480}, issn = {1040-4651}, mesh = {Animals ; Arabidopsis Proteins/genetics/metabolism ; Bacteriophages/genetics/metabolism ; Conserved Sequence ; Cyanobacteria/genetics/metabolism ; DNA/genetics/*metabolism ; DNA Transposable Elements/genetics ; DNA-Binding Proteins/genetics/*metabolism ; Endonucleases/genetics/*metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Homeodomain Proteins/genetics/*metabolism ; Molecular Sequence Data ; Nuclear Proteins/genetics/*metabolism ; Phylogeny ; Plant Proteins/genetics/*metabolism ; Plants/drug effects/genetics/*metabolism ; Protein Structure, Tertiary/genetics ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Tetrahymena/genetics/metabolism ; Transcription Factors ; }, abstract = {All members of the AP2/ERF family of plant transcription regulators contain at least one copy of a DNA binding domain called the AP2 domain. The AP2 domain has been considered plant specific. Here, we show that homologs are present in the cyanobacterium Trichodesmium erythraeum, the ciliate Tetrahymena thermophila, and the viruses Enterobacteria phage Rb49 and Bacteriophage Felix 01. We demonstrate that the T. erythraeum AP2 domain selectively binds stretches of poly(dG)/poly(dC) showing functional conservation with plant AP2/ERF proteins. The newly discovered nonplant proteins bearing an AP2 domain are predicted to be HNH endonucleases. Sequence conservation extends outside the AP2 domain to include part of the endonuclease domain for the T. erythraeum protein and some plant AP2/ERF proteins. Our phylogenetic analysis of the broader family of AP2 domains supports the possibility of lateral gene transfer. We hypothesize that a horizontal transfer of an HNH-AP2 endonuclease from bacteria or viruses into plants may have led to the origin of the AP2/ERF family of transcription factors via transposition and homing processes.}, }
@article {pmid15317780, year = {2004}, author = {Pérez-Mendoza, D and Domínguez-Ferreras, A and Muñoz, S and Soto, MJ and Olivares, J and Brom, S and Girard, L and Herrera-Cervera, JA and Sanjuán, J}, title = {Identification of functional mob regions in Rhizobium etli: evidence for self-transmissibility of the symbiotic plasmid pRetCFN42d.}, journal = {Journal of bacteriology}, volume = {186}, number = {17}, pages = {5753-5761}, pmid = {15317780}, issn = {0021-9193}, mesh = {Bacterial Proteins/*genetics/physiology ; *Conjugation, Genetic ; Cosmids/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Multigene Family ; *Plasmids ; Replicon ; Rhizobium etli/*genetics/*physiology ; Symbiosis ; }, abstract = {An approach originally designed to identify functional origins of conjugative transfer (oriT or mob) in a bacterial genome (J. A. Herrera-Cervera, J. M. Sanjuán-Pinilla, J. Olivares, and J. Sanjuán, J. Bacteriol. 180:4583-4590, 1998) was modified to improve its reliability and prevent selection of undesired false mob clones. By following this modified approach, we were able to identify two functional mob regions in the genome of Rhizobium etli CFN42. One corresponds to the recently characterized transfer region of the nonsymbiotic, self-transmissible plasmid pRetCFN42a (C. Tun-Garrido, P. Bustos, V. González, and S. Brom, J. Bacteriol. 185:1681-1692, 2003), whereas the second mob region belongs to the symbiotic plasmid pRetCFN42d. The new transfer region identified contains a putative oriT and a typical conjugative (tra) gene cluster organization. Although pRetCFN42d had not previously been shown to be self-transmissible, mobilization of cosmids containing this tra region required the presence of a wild-type pRetCFN42d in the donor cell; the presence of multiple copies of this mob region in CFN42 also promoted conjugal transfer of the Sym plasmid pRetCFN42d. The overexpression of a small open reading frame, named yp028, located downstream of the putative relaxase gene traA, appeared to be responsible for promoting the conjugal transfer of the R. etli pSym under laboratory conditions. This yp028-dependent conjugal transfer required a wild-type pRetCFN42d traA gene. Our results suggest for the first time that the R. etli symbiotic plasmid is self-transmissible and that its transfer is subject to regulation. In wild-type CFN42, pRetCFN42d tra gene expression appears to be insufficient to promote plasmid transfer under standard laboratory conditions; gene yp028 may play some role in the activation of conjugal transfer in response to as-yet-unknown environmental conditions.}, }
@article {pmid15317779, year = {2004}, author = {Davies, RL and Lee, I}, title = {Sequence diversity and molecular evolution of the heat-modifiable outer membrane protein gene (ompA) of Mannheimia(Pasteurella) haemolytica, Mannheimia glucosida, and Pasteurella trehalosi.}, journal = {Journal of bacteriology}, volume = {186}, number = {17}, pages = {5741-5752}, pmid = {15317779}, issn = {0021-9193}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Adaptation, Biological ; Alleles ; Bacterial Outer Membrane Proteins/*genetics ; DNA, Bacterial/chemistry/isolation &amp; purification ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Variation ; Mannheimia/*genetics ; Mannheimia haemolytica/*genetics ; Molecular Sequence Data ; Pasteurella/*genetics ; Phylogeny ; Protein Structure, Tertiary ; Recombination, Genetic ; Selection, Genetic ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {The OmpA (or heat-modifiable) protein is a major structural component of the outer membranes of gram-negative bacteria. The protein contains eight membrane-traversing beta-strands and four surface-exposed loops. The genetic diversity and molecular evolution of OmpA were investigated in 31 Mannheimia (Pasteurella) haemolytica, 6 Mannheimia glucosida, and 4 Pasteurella trehalosi strains by comparative nucleotide sequence analysis. The OmpA proteins of M. haemolytica and M. glucosida contain four hypervariable domains located at the distal ends of the surface-exposed loops. The hypervariable domains of OmpA proteins from bovine and ovine M. haemolytica isolates are very different but are highly conserved among strains from each of these two host species. Fourteen different alleles representing four distinct phylogenetic classes, classes I to IV, were identified in M. haemolytica and M. glucosida. Class I, II, and IV alleles were associated with bovine M. haemolytica, ovine M. haemolytica, and M. glucosida strains, respectively, whereas class III alleles were present in certain M. haemolytica and M. glucosida isolates. Class I and II alleles were associated with divergent lineages of bovine and ovine M. haemolytica strains, respectively, indicating a history of horizontal DNA transfer and assortative (entire gene) recombination. Class III alleles have mosaic structures and were derived by horizontal DNA transfer and intragenic recombination. Our findings suggest that OmpA is under strong selective pressure from the host species and that it plays an important role in host adaptation. It is proposed that the OmpA protein of M. haemolytica acts as a ligand and is involved in binding to specific host cell receptor molecules in cattle and sheep. P. trehalosi expresses two OmpA homologs that are encoded by different tandemly arranged ompA genes. The P. trehalosi ompA genes are highly diverged from those of M. haemolytica and M. glucosida, and evidence is presented to suggest that at least one of these genes was acquired by horizontal DNA transfer.}, }
@article {pmid15317737, year = {2005}, author = {Aquino, RS and Landeira-Fernandez, AM and Valente, AP and Andrade, LR and Mourão, PA}, title = {Occurrence of sulfated galactans in marine angiosperms: evolutionary implications.}, journal = {Glycobiology}, volume = {15}, number = {1}, pages = {11-20}, doi = {10.1093/glycob/cwh138}, pmid = {15317737}, issn = {0959-6658}, mesh = {Alismatales/*chemistry ; *Biological Evolution ; Carbohydrate Sequence ; Cell Wall/chemistry ; Galactans/*analysis/*chemistry/metabolism ; Gene Transfer, Horizontal ; Hydrocharitaceae/*chemistry ; Magnetic Resonance Spectroscopy ; Molecular Sequence Data ; Sulfur/*chemistry ; }, abstract = {We report for the first time that marine angiosperms (seagrasses) possess sulfated polysaccharides, which are absent in terrestrial and freshwater plants. The structure of the sulfated polysaccharide from the seagrass Ruppia maritima was determined. It is a sulfated D-galactan composed of the following regular tetrasaccharide repeating unit: [3-beta-D-Gal-2(OSO3)-1-->4-alpha-D-Gal-1-->4-alpha-D-Gal-1-->3-beta-D-Gal-4(OSO3)-1-->]. Sulfated galactans have been described previously in red algae and in marine invertebrates (ascidians and sea urchins). The sulfated galactan from the marine angiosperm has an intermediate structure when compared with the polysaccharides from these two other groups of organisms. Like marine invertebrate galactan, it expresses a regular repeating unit with a homogenous sulfation pattern. However, seagrass galactan contains the D-enantiomer of galactose instead of the L-isomer found in marine invertebrates. Like red algae, the marine angiosperm polysaccharide contains both alpha and beta units of D-galactose; however, these units are not distributed in an alternating order, as in algal galactan. Sulfated galactan is localized in the plant cell walls, mostly in rhizomes and roots, indicative of a relationship with the absorption of nutrients and of a possible structural function. The occurrence of sulfated galactans in marine organisms may be the result of physiological adaptations, which are not correlated with phylogenetic proximity. We suggest that convergent adaptation, due to environment pressure, may explain the occurrence of sulfated galactans in many marine organisms.}, }
@article {pmid15316277, year = {2004}, author = {Novotny, R and Pfoestl, A and Messner, P and Schäffer, C}, title = {Genetic organization of chromosomal S-layer glycan biosynthesis loci of Bacillaceae.}, journal = {Glycoconjugate journal}, volume = {20}, number = {7-8}, pages = {435-447}, pmid = {15316277}, issn = {0282-0080}, mesh = {Bacillaceae/*genetics ; Bacterial Proteins/*chemistry/genetics/metabolism ; Chromosomes, Bacterial/*genetics/metabolism ; Glycosylation ; Membrane Glycoproteins/*chemistry/genetics/metabolism ; Polysaccharides, Bacterial/*biosynthesis/chemistry ; }, abstract = {S-layer glycoproteins are cell surface glycoconjugates that have been identified in archaea and in bacteria. Usually, S-layer glycoproteins assemble into regular, crystalline arrays covering the entire bacterium. Our research focuses on thermophilic Bacillaceae, which are considered a suitable model system for studying bacterial glycosylation. During the past decade, investigations of S-layer glycoproteins dealt with the elucidation of the highly variable glycan structures by a combination of chemical degradation methods and nuclear magnetic resonance spectroscopy. It was only recently that the molecular characterization of the genes governing the formation of the S-layer glycoprotein glycan chains has been initiated. The S-layer glycosylation (slg) gene clusters of four of the 11 known S-layer glycan structures from members of the Bacillaceae have now been studied. The clusters are approximately 16 to approximately 25 kb in size and transcribed as polycistronic units. They include nucleotide sugar pathway genes that are arranged as operons, sugar transferase genes, glycan processing genes, and transporter genes. So far, the biochemical functions only of the genes required for nucleotide sugar biosynthesis have been demonstrated experimentally. The presence of insertion sequences and the decrease of the G + C content at the slg locus suggest that the investigated organisms have acquired their specific S-layer glycosylation potential by lateral gene transfer. In addition, S-layer protein glycosylation requires the participation of housekeeping genes that map outside the cluster. The gene encoding the respective S-layer target protein is transcribed monocistronically and independently of the slg cluster genes. Its chromosomal location is not necessarily in close vicinity to the slg gene cluster.}, }
@article {pmid15304348, year = {2004}, author = {Kikuchi, T and Jones, JT and Aikawa, T and Kosaka, H and Ogura, N}, title = {A family of glycosyl hydrolase family 45 cellulases from the pine wood nematode Bursaphelenchus xylophilus.}, journal = {FEBS letters}, volume = {572}, number = {1-3}, pages = {201-205}, doi = {10.1016/j.febslet.2004.07.039}, pmid = {15304348}, issn = {0014-5793}, mesh = {Amino Acid Sequence ; Animals ; Botrytis ; Cell Wall/enzymology ; Cellulase/chemistry/genetics/*metabolism ; Cloning, Molecular ; Conserved Sequence ; DNA, Complementary ; Gene Transfer Techniques ; Glycoside Hydrolases/metabolism ; Helminth Proteins/chemistry/genetics/metabolism ; Molecular Sequence Data ; Nematoda/classification/*enzymology/genetics ; Phylogeny ; Plant Diseases/parasitology ; Plants/parasitology ; Sequence Alignment ; Sequence Homology, Amino Acid ; Wood ; }, abstract = {We have characterized a family of GHF45 cellulases from the pine wood nematode Bursaphelenchus xylophilus. The absence of such genes from other nematodes and their similarity to fungal genes suggests that they may have been acquired by horizontal gene transfer (HGT) from fungi. The cell wall degrading enzymes of other plant parasitic nematodes may have been acquired by HGT from bacteria. B. xylophilus is not directly related to other plant parasites and our data therefore suggest that horizontal transfer of cell wall degrading enzymes has played a key role in evolution of plant parasitism by nematodes on more than one occasion.}, }
@article {pmid15303759, year = {2004}, author = {Bathe, S and Mohan, TV and Wuertz, S and Hausner, M}, title = {Bioaugmentation of a sequencing batch biofilm reactor by horizontal gene transfer.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {49}, number = {11-12}, pages = {337-344}, pmid = {15303759}, issn = {0273-1223}, mesh = {2,4-Dichlorophenoxyacetic Acid/*metabolism ; Bacteria/*growth &amp; development ; *Biofilms ; *Bioreactors ; DNA, Bacterial ; *Gene Transfer Techniques ; *Genetic Engineering ; Herbicides/*metabolism ; Plasmids ; Waste Disposal, Fluid/methods ; Water Pollutants, Chemical/metabolism ; }, abstract = {Bioaugmentation by introduction of catabolic genes residing on mobile genetic elements into the microbial community of a soil or wastewater environment might be an alternative to bioaugmentation by addition of bacterial cells with chromosomally encoded catabolic genes. This study investigates the possibility to enhance degradation of the xenobiotic model compound 2,4-dichlorophenoxyacetic acid in a sequencing batch biofilm reactor (SBBR) by using the conjugative plasmid pJP4 carrying genes for 2,4-D degradation. After introduction of a plasmid donor strain to a lab-scale SBBR operated without 2,4-D, the number of plasmid-carrying cells first dropped, and then increased after switching to 2,4-D as the sole carbon source. The donor cells were unable to grow in the applied synthetic wastewater with 2,4-D as the sole carbon source. Transconjugants could be detected both by culture-dependent and culture-independent methods in the 2,4-D degrading biofilm. In contrast to 90% 2,4-D degradation in the bioaugmented reactor within 40 h, a control reactor which had not received the plasmid still contained 60% of the initial 2,4-D concentration after 90 h. This experiment clearly demonstrates the introduction of 2,4-D degradative genes into a microbial biofilm and indicates that horizontal gene transfer is a promising tool for bioaugmentation of reactors treating wastewater.}, }
@article {pmid15303758, year = {2004}, author = {Wuertz, S and Okabe, S and Hausner, M}, title = {Microbial communities and their interactions in biofilm systems: an overview.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {49}, number = {11-12}, pages = {327-336}, pmid = {15303758}, issn = {0273-1223}, mesh = {Bacteria/*growth &amp; development ; *Biofilms ; DNA, Bacterial/analysis ; Genetics, Population ; In Situ Hybridization, Fluorescence ; Oligonucleotide Array Sequence Analysis ; Population Dynamics ; Waste Disposal, Fluid/*methods ; Water Movements ; }, abstract = {Several important advances have been made in the study of biofilm microbial populations relating to their spatial structure (or architecture), their community structure, and their dependence on physicochemical parameters. With the knowledge that hydrodynamic forces influence biofilm architecture came the realization that metabolic processes may be enhanced if certain spatial structures can be forced. An example is the extent of plasmid-mediated horizontal gene transfer in biofilms. Recent in situ work in defined model systems has shown that the biofilm architecture plays a role for genetic transfer by bacterial conjugation in determining how far the donor cells can penetrate the biofilm. Open channels and pores allow for more efficient donor transport and hence more frequent cell collisions leading to rapid spread of the genes by horizontal gene transfer. Such insight into the physical environment of biofilms can be utilized for bioenhancement of catabolic processes by introduction of mobile genetic elements into an existing microbial community. If the donor organisms themselves persist, bioaugmentation can lead to successful establishment of newly introduced species and may be a more successful strategy than biostimulation (the addition of nutrients or specific carbon sources to stimulate the authochthonous population) as shown for an enrichment culture of nitrifying bacteria added to rotating disk biofilm reactors using fluorescent in situ hybridization (FISH) and microelectrode measurements of NH4+, NO2-, NO3-, and O2. However, few studies have been carried out on full-scale systems. Bioaugmentation and bioenhancement are most successful if a constant selective pressure can be maintained favoring the promulgation of the added enrichment culture. Overall, knowledge gain about microbial community interactions in biofilms continues to be driven by the availability of methods for the rapid analysis of microbial communities and their activities. Molecular tools can be grouped into those suitable for ex situ and in situ community analysis. Non-spatial community analysis, in the sense of assessing changes in microbial populations as a function of time or environmental conditions, relies on general fingerprinting methods, like DGGE and T-RFLP, performed on nucleic acids extracted from biofilm. These approaches have been most useful when combined with gene amplification, cloning and sequencing to assemble a phylogenetic inventory of microbial species. It is expected that the use of oligonucleotide microarrays will greatly facilitate the analysis of microbial communities and their activities in biofilms. Structure-activity relationships can be explored using incorporation of 13C-labeled substrates into microbial DNA and RNA to identify metabolically active community members. Finally, based on the DNA sequences in a biofilm, FISH probes can be designed to verify the abundance and spatial location of microbial community members. This in turn allows for in situ structure/function analysis when FISH is combined with microsensors, microautoradiography, and confocal laser scanning microscopy with advanced image analysis.}, }
@article {pmid15292149, year = {2004}, author = {Chen, T and Hosogi, Y and Nishikawa, K and Abbey, K and Fleischmann, RD and Walling, J and Duncan, MJ}, title = {Comparative whole-genome analysis of virulent and avirulent strains of Porphyromonas gingivalis.}, journal = {Journal of bacteriology}, volume = {186}, number = {16}, pages = {5473-5479}, pmid = {15292149}, issn = {0021-9193}, support = {R01 DE12082/DE/NIDCR NIH HHS/United States ; K22 DE14742/DE/NIDCR NIH HHS/United States ; R01 DC012082/DC/NIDCD NIH HHS/United States ; K22 DE014742/DE/NIDCR NIH HHS/United States ; R01 DE010510/DE/NIDCR NIH HHS/United States ; R01DE10510/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacterial Capsules/genetics ; Bacterial Proteins/*genetics/metabolism ; Biological Evolution ; DNA Transposable Elements ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Variation ; *Genome, Bacterial ; Genomic Islands/genetics ; Integrases/genetics ; Oligonucleotide Array Sequence Analysis ; Operon ; Polysaccharides, Bacterial/genetics ; Porphyromonas gingivalis/*genetics/*pathogenicity ; RNA, Transfer/genetics ; Virulence/*genetics ; Virulence Factors/*genetics/metabolism ; }, abstract = {We used Porphyromonas gingivalis gene microarrays to compare the total gene contents of the virulent strain W83 and the avirulent type strain, ATCC 33277. Signal ratios and scatter plots indicated that the chromosomes were very similar, with approximately 93% of the predicted genes in common, while at least 7% of them showed very low or no signals in ATCC 33277. Verification of the array results by PCR indicated that several of the disparate genes were either absent from or variant in ATCC 33277. Divergent features included already reported insertion sequences and ragB, as well as additional hypothetical and functionally assigned genes. Several of the latter were organized in a putative operon in W83 and encoded enzymes involved in capsular polysaccharide synthesis. Another cluster was associated with two paralogous regions of the chromosome with a low G+C content, at 41%, compared to that of the whole genome, at 48%. These regions also contained conserved and species-specific hypothetical genes, transposons, insertion sequences, and integrases and were located adjacent to tRNA genes; thus, they had several characteristics of pathogenicity islands. While this global comparative analysis showed the close relationship between W83 and ATCC 33277, the clustering of genes that are present in W83 but divergent in or absent from ATCC 33277 is suggestive of chromosomal islands that may have been acquired by lateral gene transfer.}, }
@article {pmid15292145, year = {2004}, author = {Grozdanov, L and Raasch, C and Schulze, J and Sonnenborn, U and Gottschalk, G and Hacker, J and Dobrindt, U}, title = {Analysis of the genome structure of the nonpathogenic probiotic Escherichia coli strain Nissle 1917.}, journal = {Journal of bacteriology}, volume = {186}, number = {16}, pages = {5432-5441}, pmid = {15292145}, issn = {0021-9193}, mesh = {Adhesins, Bacterial/genetics/metabolism ; Bacteriocins/genetics/metabolism ; DNA, Bacterial/analysis/isolation &amp; purification ; Endopeptidases/genetics/metabolism ; Enterobactin/metabolism ; Escherichia coli/*genetics ; Escherichia coli Proteins/genetics/metabolism ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomic Islands ; Hemolysin Proteins/genetics/metabolism ; Iron/metabolism ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Polysaccharides, Bacterial/biosynthesis ; Sequence Analysis, DNA ; }, abstract = {Nonpathogenic Escherichia coli strain Nissle 1917 (O6:K5:H1) is used as a probiotic agent in medicine, mainly for the treatment of various gastroenterological diseases. To gain insight on the genetic level into its properties of colonization and commensalism, this strain's genome structure has been analyzed by three approaches: (i) sequence context screening of tRNA genes as a potential indication of chromosomal integration of horizontally acquired DNA, (ii) sequence analysis of 280 kb of genomic islands (GEIs) coding for important fitness factors, and (iii) comparison of Nissle 1917 genome content with that of other E. coli strains by DNA-DNA hybridization. PCR-based screening of 324 nonpathogenic and pathogenic E. coli isolates of different origins revealed that some chromosomal regions are frequently detectable in nonpathogenic E. coli and also among extraintestinal and intestinal pathogenic strains. Many known fitness factor determinants of strain Nissle 1917 are localized on four GEIs which have been partially sequenced and analyzed. Comparison of these data with the available knowledge of the genome structure of E. coli K-12 strain MG1655 and of uropathogenic E. coli O6 strains CFT073 and 536 revealed structural similarities on the genomic level, especially between the E. coli O6 strains. The lack of defined virulence factors (i.e., alpha-hemolysin, P-fimbrial adhesins, and the semirough lipopolysaccharide phenotype) combined with the expression of fitness factors such as microcins, different iron uptake systems, adhesins, and proteases, which may support its survival and successful colonization of the human gut, most likely contributes to the probiotic character of E. coli strain Nissle 1917.}, }
@article {pmid15289485, year = {2004}, author = {Hill, JE and Penny, SL and Crowell, KG and Goh, SH and Hemmingsen, SM}, title = {cpnDB: a chaperonin sequence database.}, journal = {Genome research}, volume = {14}, number = {8}, pages = {1669-1675}, pmid = {15289485}, issn = {1088-9051}, mesh = {Animals ; Bacteria/genetics ; Base Sequence ; Chaperonin 60/*genetics ; Computational Biology ; Databases, Genetic ; Molecular Sequence Data ; Sequence Homology, Nucleic Acid ; }, abstract = {Type I chaperonins are molecular chaperones present in virtually all bacteria, some archaea and the plastids and mitochondria of eukaryotes. Sequences of cpn60 genes, encoding 60-kDa chaperonin protein subunits (CPN60, also known as GroEL or HSP60), are useful for phylogenetic studies and as targets for detection and identification of organisms. Conveniently, a 549-567-bp segment of the cpn60 coding region can be amplified with universal PCR primers. Here, we introduce cpnDB, a curated collection of cpn60 sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic, and microbial ecology studies. The growing database currently contains approximately 2000 records covering over 240 genera of bacteria, eukaryotes, and archaea. The database also contains over 60 sequences for the archaeal Type II chaperonin (thermosome, a homolog of eukaryotic cytoplasmic chaperonin) from 19 archaeal genera. As the largest curated collection of sequences available for a protein-encoding gene, cpnDB provides a resource for researchers interested in exploiting the power of cpn60 as a diagnostic or as a target for phylogenetic or microbial ecology studies, as well as those interested in broader subjects such as lateral gene transfer and codon usage. We built cpnDB from open source tools and it is available at http://cpndb.cbr.nrc.ca.}, }
@article {pmid15289470, year = {2004}, author = {Jaffe, JD and Stange-Thomann, N and Smith, C and DeCaprio, D and Fisher, S and Butler, J and Calvo, S and Elkins, T and FitzGerald, MG and Hafez, N and Kodira, CD and Major, J and Wang, S and Wilkinson, J and Nicol, R and Nusbaum, C and Birren, B and Berg, HC and Church, GM}, title = {The complete genome and proteome of Mycoplasma mobile.}, journal = {Genome research}, volume = {14}, number = {8}, pages = {1447-1461}, pmid = {15289470}, issn = {1088-9051}, support = {R01 AI016478/AI/NIAID NIH HHS/United States ; R37 AI016478/AI/NIAID NIH HHS/United States ; AI16478/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Computational Biology ; *Genome, Bacterial ; Molecular Sequence Data ; Mycoplasma/*genetics ; Phylogeny ; Physical Chromosome Mapping ; Proteome/*genetics ; }, abstract = {Although often considered "minimal" organisms, mycoplasmas show a wide range of diversity with respect to host environment, phenotypic traits, and pathogenicity. Here we report the complete genomic sequence and proteogenomic map for the piscine mycoplasma Mycoplasma mobile, noted for its robust gliding motility. For the first time, proteomic data are used in the primary annotation of a new genome, providing validation of expression for many of the predicted proteins. Several novel features were discovered including a long repeating unit of DNA of approximately 2435 bp present in five complete copies that are shown to code for nearly identical yet uniquely expressed proteins. M. mobile has among the lowest DNA GC contents (24.9%) and most reduced set of tRNAs of any organism yet reported (28). Numerous instances of tandem duplication as well as lateral gene transfer are evident in the genome. The multiple available complete genome sequences for other motile and immotile mycoplasmas enabled us to use comparative genomic and phylogenetic methods to suggest several candidate genes that might be involved in motility. The results of these analyses leave open the possibility that gliding motility might have arisen independently more than once in the mycoplasma lineage.}, }
@article {pmid15288781, year = {2004}, author = {Slamovits, CH and Keeling, PJ}, title = {Class II photolyase in a microsporidian intracellular parasite.}, journal = {Journal of molecular biology}, volume = {341}, number = {3}, pages = {713-721}, doi = {10.1016/j.jmb.2004.06.032}, pmid = {15288781}, issn = {0022-2836}, mesh = {Amino Acid Sequence ; Animals ; DNA Damage ; DNA Repair ; Deoxyribodipyrimidine Photo-Lyase/*chemistry ; Dose-Response Relationship, Radiation ; Escherichia coli/enzymology ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Complementation Test ; Light ; Microsporidia/*enzymology ; Molecular Sequence Data ; Open Reading Frames ; Phenotype ; Phylogeny ; Poly A ; RNA/chemistry ; Sequence Analysis, DNA ; Stress, Physiological ; }, abstract = {Photoreactivation is the repair of DNA damage induced by ultraviolet light radiation using the energy contained in visible-light photons. The process is carried out by a single enzyme, photolyase, which is part of a large and ancient photolyase/cryptochrome gene family. We have characterised a photolyase gene from the microsporidian parasite, Antonospora locustae (formerly Nosema locustae) and show that it encodes a functional photoreactivating enzyme and is expressed in the infectious spore stage of the parasite's life cycle. Sequence and phylogenetic analyses show that it belongs to the class II subfamily of cyclobutane pyrimidine dimer repair enzymes. No photolyase is present in the complete genome sequence of the distantly related microsporidian, Encephalitozoon cuniculi, and this class of photolyase has never yet been described in fungi, the closest relatives of Microsporidia, raising questions about the evolutionary origin of this enzyme. This is the second environmental stress enzyme to be found in A.locustae but absent in E.cuniculi, and in the other case (catalase), the gene is derived by lateral transfer from a bacterium. It appears that A.locustae spores deal with environmental stress differently from E.cuniculi, these results lead to the prediction that they are more robust to environmental damage.}, }
@article {pmid15288311, year = {2004}, author = {van Loon, HJ and Box, AT and Verhoef, J and Fluit, AC}, title = {Evaluation of genetic determinants involved in beta-lactam- and multiresistance in a surgical ICU.}, journal = {International journal of antimicrobial agents}, volume = {24}, number = {2}, pages = {130-134}, doi = {10.1016/j.ijantimicag.2004.01.015}, pmid = {15288311}, issn = {0924-8579}, mesh = {Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Multiple, Bacterial/*genetics ; Enterobacteriaceae/drug effects/enzymology/genetics ; *General Surgery ; Humans ; Integrons ; *Intensive Care Units ; Isoelectric Focusing ; Microbial Sensitivity Tests ; Polymerase Chain Reaction ; Pseudomonas aeruginosa/drug effects/enzymology/genetics ; beta-Lactam Resistance/*genetics ; beta-Lactamases/genetics ; beta-Lactams/pharmacology ; }, abstract = {Antibiotic resistance is a major and well-known problem in intensive care units (ICUs) world-wide and previously susceptible isolates become resistant through the acquisition of resistance determinants from other bacteria or the development of mutations, as is the case in beta-lactam resistance. We evaluated the presence of resistance determinants involved in beta-lactam resistance and multi-resistance in order to establish the contribution of horizontal gene transfer to the spread of resistance in a surgical ICU during an antibiotic rotation study. Pseudomonas aeruginosa and Enterobacteriaceae isolates were selected and iso-electric focusing (IEF), DNA-typing methods such as specific beta-lactamase and specific integron PCRs were performed to determine the presence of beta-lactamases. The PCRs specific for IMP-1, OXA-1, and VIM-type beta-lactamases performed on the selected P. aeruginosa and Enterobacteriaceae isolates with MICs for cephalosporins >1 mg/l did not demonstrate any of these beta-lactamases. IEF for 14 pseudomonads, representing 7 genotypes from 9 patients, showed a beta-lactamase with a pI larger than 8.5 in 13 of the isolates. The integrase PCR was positive for only five isolates from three patients and conserved segment PCR showed integrons of variable sizes (700, 900, 1,400 and 1,500 bp). Each patient had its own integron types. It can be concluded that integrons and associated resistance determinants played only a minor role in the surgical ICU and beta-lactam resistance among P. aeruginosa isolates was most likely due to the derepression of its AmpC gene.}, }
@article {pmid15284843, year = {2004}, author = {Melamed, P and Chong, KL and Johansen, MV}, title = {Evidence for lateral gene transfer from salmonids to two Schistosome species.}, journal = {Nature genetics}, volume = {36}, number = {8}, pages = {786-787}, doi = {10.1038/ng0804-786}, pmid = {15284843}, issn = {1061-4036}, mesh = {Animals ; *Gene Transfer, Horizontal ; Salmonidae/*genetics ; Schistosoma/*genetics ; }, }
@article {pmid15282590, year = {2004}, author = {Giovannoni, S}, title = {Evolutionary biology: oceans of bacteria.}, journal = {Nature}, volume = {430}, number = {6999}, pages = {515-516}, doi = {10.1038/430515a}, pmid = {15282590}, issn = {1476-4687}, mesh = {Bacteria/*classification/*genetics/isolation &amp; purification ; *Biological Evolution ; *Ecosystem ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/genetics ; Genetic Variation/*genetics ; RNA, Ribosomal, 16S/*genetics ; Ribotyping ; Seawater/*microbiology ; }, }
@article {pmid15279959, year = {2004}, author = {Telleria, J and Barnabé, C and Hide, M and Bañuls, AL and Tibayrenc, M}, title = {Predominant clonal evolution leads to a close parity between gene expression profiles and subspecific phylogeny in Trypanosoma cruzi.}, journal = {Molecular and biochemical parasitology}, volume = {137}, number = {1}, pages = {133-141}, doi = {10.1016/j.molbiopara.2004.05.006}, pmid = {15279959}, issn = {0166-6851}, mesh = {Animals ; DNA Fingerprinting ; DNA, Protozoan/analysis ; Electrophoresis ; *Evolution, Molecular ; *Gene Expression Profiling ; Gene Transfer, Horizontal ; *Genetic Variation ; Phylogeny ; *Polymorphism, Genetic ; Protozoan Proteins/genetics/physiology ; Random Amplified Polymorphic DNA Technique ; Recombination, Genetic ; Trypanosoma cruzi/*classification/enzymology/*genetics ; }, abstract = {We investigated the relationships between overall phylogenetic diversity in Trypanosoma cruzi evidenced by multilocus markers (MLEE and RAPD) on the one hand, and gene expression patterns, revealed by mRNA analysis on the other hand. Nineteen laboratory-cloned stocks representative of this parasite's overall phylogenetic diversity and ecogeographical range were analyzed using random amplified differentially expressed sequences (RADES). The bat trypanosome T. cruzi marinkellei was taken as outgroup. The profiles obtained showed that RADES polymorphism cannot be considered as a simple subsample of general RAPD polymorphism. Indeed, many RADES bands were not present in general RAPD profiles, and vice versa. Phylogenies obtained from RADES on the one hand, and MLEE/RAPD on the other hand, were very similar. This suggests that in spite of the recent observation of hybrid genotypes and mosaic genes in T. cruzi, clonal evolution in this parasite has been preponderant enough on an evolutionary scale to carve the polymorphism on all types of DNA sequences, including expressed genes, although these genes are assumed to undergo natural selection pressure contrary to noncoding sequences and neutral polymorphisms.}, }
@article {pmid15273135, year = {2004}, author = {Lau, SK and Woo, PC and To, AP and Lau, AT and Yuen, KY}, title = {Lack of evidence that DNA in antibiotic preparations is a source of antibiotic resistance genes in bacteria from animal or human sources.}, journal = {Antimicrobial agents and chemotherapy}, volume = {48}, number = {8}, pages = {3141-3146}, pmid = {15273135}, issn = {0066-4804}, mesh = {Amino Acids/analysis ; Animals ; Anti-Bacterial Agents/*analysis/biosynthesis ; DNA, Bacterial/*analysis ; DNA-Binding Proteins/genetics ; *Drug Contamination ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Phylogeny ; Tetracycline Resistance ; Transcription Factors/genetics ; }, abstract = {Although DNA encoding antibiotic resistance has been discovered in antibiotic preparations, its significance for the development of antibiotic resistance in bacteria is unknown. No phylogenetic evidence was obtained for recent horizontal transfer of antibiotic resistance genes from antibiotic-producing organisms to bacteria from human or animal sources.}, }
@article {pmid15273090, year = {2004}, author = {Giles, WP and Benson, AK and Olson, ME and Hutkins, RW and Whichard, JM and Winokur, PL and Fey, PD}, title = {DNA sequence analysis of regions surrounding blaCMY-2 from multiple Salmonella plasmid backbones.}, journal = {Antimicrobial agents and chemotherapy}, volume = {48}, number = {8}, pages = {2845-2852}, pmid = {15273090}, issn = {0066-4804}, mesh = {Bacterial Typing Techniques ; Base Sequence ; Blotting, Southern ; DNA Primers ; DNA, Bacterial/*analysis/genetics ; Electrophoresis, Gel, Pulsed-Field ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Plasmids/*genetics ; Polymorphism, Restriction Fragment Length ; Replicon/genetics ; Salmonella/*genetics ; beta-Lactamases/*genetics ; }, abstract = {The emergence in the United States of resistance to expanded-spectrum cephalosporin (e.g., ceftriaxone) within the salmonellae has been associated primarily with three large (>100-kb) plasmids (designated types A, B, and C) and one 10.1-kb plasmid (type D) that carry the blaCMY-2 gene. In the present study, the distribution of these four known blaCMY-2-carrying plasmids among 35 ceftriaxone-resistant Salmonella isolates obtained from 1998 to 2001 was examined. Twenty-three of these isolates were Salmonella enterica serotype Newport, 10 were Salmonella enterica serotype Typhimurium, 1 was Salmonella enterica serotype Agona, and 1 was Salmonella enterica serotype Reading. All 23 serotype Newport isolates carried a type C plasmid, and 5, 4, and 1 serovar Typhimurium isolate carried type B, A, and C plasmids, respectively. Both the serotype Agona and serotype Reading isolates carried type A plasmids. None of the isolates carried a type D plasmid. Hybridization data suggested that plasmid types A and C were highly related replicons. DNA sequencing revealed that the region surrounding blaCMY-2 was highly conserved in all three plasmid types analyzed (types B, C, and D) and was related to a region surrounding blaCMY-5 from the Klebsiella oxytoca plasmid pTKH11. These findings are consistent with a model in which blaCMY-2 has been disseminated primarily through plasmid transfer, and not by mobilization of the gene itself, to multiple Salmonella chromosomal backbones.}, }
@article {pmid15272738, year = {2004}, author = {Imase, A and Ohmae, H and Iwamura, Y and Kirinoki, M and Matsuda, H}, title = {A comparative study on mouse MHC class I sequences detected in Schistosoma japonicum recovered from BALB/c (H-2d) and C57BL/6 (H-2b) mice.}, journal = {The Southeast Asian journal of tropical medicine and public health}, volume = {35}, number = {1}, pages = {10-18}, pmid = {15272738}, issn = {0125-1562}, mesh = {Animals ; Base Sequence ; DNA, Helminth/analysis ; Disease Models, Animal ; Disease Transmission, Infectious/veterinary ; Gene Transfer, Horizontal/genetics ; Genes, MHC Class I/*genetics ; Heterozygote ; Host-Parasite Interactions/genetics ; In Situ Hybridization ; Infectious Disease Transmission, Vertical/veterinary ; Male ; Mice ; Mice, Inbred BALB C/*parasitology ; Mice, Inbred C57BL/*parasitology ; Molecular Sequence Data ; Polymerase Chain Reaction ; Schistosoma japonicum/*genetics ; Schistosomiasis japonica/genetics/*transmission/*veterinary ; Species Specificity ; }, abstract = {The mouse major histocompatibility complex (MHC) class I sequence was detected in all the 8-week-old Schistosoma japonicum recovered from BALB/c (H-2d) and C57BL/6 (H-2b) mice by in situ polymerase chain reaction (in situ PCR). The signals of the mouse class I MHC sequence were observed in the nuclei of the mesenchymal and reproductive cells of 8-week-old S. japonicum. Furthermore, the class I MHC sequence was detected in each DNA extracted from S. japonicum cercariae maintained in BALB/c and C57BL/6 mice by nested PCR. To prove both horizontal and vertical transmission of this sequence in schistosomes, we have used cercariae obtained from parasites maintained in BALB/c mice to infect C57BL/6 and BALB/c mice, and vice versa. The MHC sequences from adult worms were compared to the cercarial MHC and host MHC sequences. Nucleotide sequence comparisons between adult worm DNA, host (H-2d and H-2b mice) DNA and cercarial DNA used for the infection suggested that the sequence of mouse class I MHC was incorporated into schistosome adults and inherited throughout their life-cycle.}, }
@article {pmid15266366, year = {2004}, author = {Michael, CA and Gillings, MR and Holmes, AJ and Hughes, L and Andrew, NR and Holley, MP and Stokes, HW}, title = {Mobile gene cassettes: a fundamental resource for bacterial evolution.}, journal = {The American naturalist}, volume = {164}, number = {1}, pages = {1-12}, doi = {10.1086/421733}, pmid = {15266366}, issn = {1537-5323}, mesh = {Adaptation, Physiological ; Bacteria/*genetics ; DNA, Bacterial/analysis ; Environment ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genetic Variation ; Models, Genetic ; }, abstract = {Horizontal gene transfer increases genetic diversity in prokaryotes to a degree not allowed by the limitations of reproduction by binary fission. The integron/gene cassette system is one of the most recently characterized examples of a system that facilitates horizontal gene transfer. This system, discovered in the context of multidrug resistance, is recognized in a clinical context for its role in allowing pathogens to adapt to the widespread use of antibiotics. Recent studies suggest that gene cassettes are common and encode functions relevant to many adaptive traits. To estimate the diversity of mobile cassettes in a natural environment, a molecular technique was developed to provide representative distributions of cassette populations at points within a sampling area. Subsequently, statistical methods analogous to those used for calculating species diversity were employed to assess the diversity of gene cassettes within the sample area in addition to gaining an estimate of cassette pool size. Results indicated that the number of cassettes within a 5x10-m sample area was large and that the overall mobile cassette metagenome was likely to be orders of magnitude larger again. Accordingly, gene cassettes appear to be capable of mobilizing a significant genetic resource and consequently have a substantial impact on bacterial adaptability.}, }
@article {pmid15263091, year = {2004}, author = {Millard, A and Clokie, MR and Shub, DA and Mann, NH}, title = {Genetic organization of the psbAD region in phages infecting marine Synechococcus strains.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, number = {30}, pages = {11007-11012}, pmid = {15263091}, issn = {0027-8424}, support = {U54 AI057158/AI/NIAID NIH HHS/United States ; AI 57158/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/*genetics ; Bacteriophages/*genetics ; Base Sequence ; Cyanobacteria/*classification/*genetics/isolation &amp; purification/virology ; DNA Primers ; DNA, Bacterial/genetics/isolation &amp; purification ; Geography ; Molecular Sequence Data ; Nucleic Acid Conformation ; Photosystem II Protein Complex/*genetics ; Phylogeny ; Polymerase Chain Reaction ; Seawater/microbiology ; }, abstract = {The discovery of the genes psbA and psbD, encoding the D1 and D2 core components of the photosynthetic reaction center PSII (photosystem II), in the genome of the bacteriophage S-PM2 (a cyanomyovirus) that infects marine cyanobacteria begs the question as to how these genes were acquired. In an attempt to answer this question, it was established that the occurrence of the genes is widespread among marine cyanomyovirus isolates and may even extend to podoviruses. The phage psbA genes fall into a clade that includes the psbA genes from their potential Synechococcus and Prochlorococcus hosts, and thus, this phylogenetic analysis provides evidence to support the idea of the acquisition of these genes by horizontal gene transfer from their cyanobacterial hosts. However, the phage psbA genes form distinct subclades within this lineage, which suggests that their acquisition was not very recent. The psbA genes of two phages contain identical 212-bp insertions that exhibit all of the canonical structural features of a group I self-splicing intron. The different patterns of genetic organization of the psbAD region are consistent with the idea that the psbA and psbD genes were acquired more than once by cyanomyoviruses and that their horizontal transfer between phages via a common phage gene pool, as part of mobile genetic modules, may be a continuing process. In addition, genes were discovered encoding a high-light inducible protein and a putative key enzyme of dark metabolism, transaldolase, extending the areas of host-cell metabolism that may be affected by phage infection.}, }
@article {pmid15262405, year = {2004}, author = {Tautz, D and Lässig, M}, title = {Of statistics and genomes.}, journal = {Trends in genetics : TIG}, volume = {20}, number = {8}, pages = {344-346}, doi = {10.1016/j.tig.2004.06.002}, pmid = {15262405}, issn = {0168-9525}, mesh = {*Algorithms ; Analysis of Variance ; Animals ; *Evolution, Molecular ; *Gene Duplication ; *Gene Transfer, Horizontal ; Genome ; Humans ; }, abstract = {Higher organisms have more genes and larger genomes than simple organisms. This statement sounds almost too trivial to ask the question: why? But there are at least two different answers. Either there is an inherent necessity to increase genome size when more complexity is required or genome size increases because of other reasons that then enable complexity to "latch on". Recently, an article by Lynch and Conery, which used arguments of evolutionary population dynamics, proposed that low population size leads to larger genomes. This then provides the opportunity to generate more complex organisms.}, }
@article {pmid15260988, year = {2004}, author = {Nitz, N and Gomes, C and de Cássia Rosa, A and D'Souza-Ault, MR and Moreno, F and Lauria-Pires, L and Nascimento, RJ and Teixeira, AR}, title = {Heritable integration of kDNA minicircle sequences from Trypanosoma cruzi into the avian genome: insights into human Chagas disease.}, journal = {Cell}, volume = {118}, number = {2}, pages = {175-186}, doi = {10.1016/j.cell.2004.07.001}, pmid = {15260988}, issn = {0092-8674}, mesh = {Animals ; Animals, Newborn ; Autoimmune Diseases/genetics/immunology ; Chagas Disease/*genetics/immunology ; Chick Embryo ; Chickens/*genetics ; DNA, Kinetoplast/*genetics ; Gene Transfer, Horizontal/*genetics ; Genome ; Genome, Human ; Germ-Line Mutation/genetics ; Globins/genetics ; Humans ; Long Interspersed Nucleotide Elements/genetics ; Molecular Sequence Data ; Pluripotent Stem Cells/metabolism ; Rabbits ; Recombination, Genetic/*genetics ; Retroelements/genetics ; Trypanosoma cruzi/*genetics/immunology ; }, abstract = {We demonstrate the genetic transfer of DNA between eukaryotes from different kingdoms. The mitochondrial kinetoplast DNA (kDNA) of the intracellular parasite Trypanosoma cruzi is transferred to human patients with Chagas disease. This transfer was reproduced experimentally in rabbits and chickens. The kDNA is integrated into the host genome. In the human chromosomes, five loci were identified as integration sites, and the beta-globin locus and LINE-1 retrotransposons were frequently targeted. Short repeated sequences in the parasite and the target host DNAs favor kDNA integration by homologous recombination. Introduced kDNA was present in offspring of chronically infected rabbits and in chickens hatched from T. cruzi-inoculated eggs. kDNA incorporated into the chicken germline was inherited through the F2 generation in the absence of persistent infection. kDNA integration represents a potential cause for the autoimmune response that develops in a percentage of chronic Chagas patients, which can now be approached experimentally.}, }
@article {pmid15257457, year = {2004}, author = {Shakeri-Garakani, A and Brinkkötter, A and Schmid, K and Turgut, S and Lengeler, JW}, title = {The genes and enzymes for the catabolism of galactitol, D-tagatose, and related carbohydrates in Klebsiella oxytoca M5a1 and other enteric bacteria display convergent evolution.}, journal = {Molecular genetics and genomics : MGG}, volume = {271}, number = {6}, pages = {717-728}, pmid = {15257457}, issn = {1617-4615}, mesh = {Acetylgalactosamine/*metabolism ; Amino Acid Sequence ; *Biological Evolution ; Enterobacteriaceae/*genetics/metabolism ; Escherichia coli/genetics/metabolism ; Galactitol/*metabolism ; Galactosamine/*metabolism ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Hexoses/*metabolism ; Klebsiella oxytoca/genetics/metabolism ; Molecular Sequence Data ; Phosphotransferases/metabolism ; Recombination, Genetic ; }, abstract = {Enteric bacteria (Enteriobacteriaceae) carry on their single chromosome about 4000 genes that all strains have in common (referred to here as "obligatory genes"), and up to 1300 "facultative" genes that vary from strain to strain and from species to species. In closely related species, obligatory and facultative genes are orthologous genes that are found at similar loci. We have analyzed a set of facultative genes involved in the degradation of the carbohydrates galactitol, D-tagatose, D-galactosamine and N-acetyl-galactosamine in various pathogenic and non-pathogenic strains of these bacteria. The four carbohydrates are transported into the cell by phosphotransferase (PTS) uptake systems, and are metabolized by closely related or even identical catabolic enzymes via pathways that share several intermediates. In about 60% of Escherichia coli strains the genes for galactitol degradation map to a gat operon at 46.8 min. In strains of Salmonella enterica, Klebsiella pneumoniae and K. oxytoca, the corresponding gat genes, although orthologous to their E. coli counterparts, are found at 70.7 min, clustered in a regulon together with three tag genes for the degradation of D-tagatose, an isomer of D-fructose. In contrast, in all the E. coli strains tested, this chromosomal site was found to be occupied by an aga/kba gene cluster for the degradation of D-galactosamine and N-acetyl-galactosamine. The aga/kba and the tag genes were paralogous either to the gat cluster or to the fru genes for degradation of D-fructose. Finally, in more then 90% of strains of both Klebsiella species, and in about 5% of the E. coli strains, two operons were found at 46.8 min that comprise paralogous genes for catabolism of the isomers D-arabinitol (genes atl or dal) and ribitol (genes rtl or rbt). In these strains gat genes were invariably absent from this location, and they were totally absent in S. enterica. These results strongly indicate that these various gene clusters and metabolic pathways have been subject to convergent evolution among the Enterobacteriaceae. This apparently involved recent horizontal gene transfer and recombination events, as indicated by major chromosomal rearrangements found in their immediate vicinity.}, }
@article {pmid15256654, year = {2004}, author = {Pennisi, E}, title = {Microbiology. Researchers trade insights about gene swapping.}, journal = {Science (New York, N.Y.)}, volume = {305}, number = {5682}, pages = {334-335}, doi = {10.1126/science.305.5682.334}, pmid = {15256654}, issn = {1095-9203}, mesh = {Archaea/classification/genetics ; Bacteria/classification/*genetics/metabolism ; Biological Evolution ; Computational Biology ; Conjugation, Genetic ; Ecosystem ; *Gene Transfer, Horizontal ; Genetic Techniques ; Genome, Archaeal ; Genome, Bacterial ; Plasmids ; }, }
@article {pmid15256617, year = {2004}, author = {Davis, CC and Wurdack, KJ}, title = {Host-to-parasite gene transfer in flowering plants: phylogenetic evidence from Malpighiales.}, journal = {Science (New York, N.Y.)}, volume = {305}, number = {5684}, pages = {676-678}, doi = {10.1126/science.1100671}, pmid = {15256617}, issn = {1095-9203}, mesh = {Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Flowers ; *Gene Transfer, Horizontal ; Genes, Plant ; Magnoliopsida/*classification/*genetics ; Mitochondria/genetics ; Mitochondrial Proteins/genetics ; Phylogeny ; Plant Proteins/genetics ; Vitaceae/*classification/*genetics/parasitology ; }, abstract = {Horizontal gene transfer (HGT) between sexually unrelated species has recently been documented for higher plants, but mechanistic explanations for HGTs have remained speculative. We show that a parasitic relationship may facilitate HGT between flowering plants. The endophytic parasites Rafflesiaceae are placed in the diverse order Malpighiales. Our multigene phylogenetic analyses of Malpighiales show that mitochondrial (matR) and nuclear loci (18S ribosomal DNA and PHYC) place Rafflesiaceae in Malpighiales, perhaps near Ochnaceae/Clusiaceae. Mitochondrial nad1B-C, however, groups them within Vitaceae, near their obligate host Tetrastigma. These discordant phylogenetic hypotheses strongly suggest that part of the mitochondrial genome in Rafflesiaceae was acquired via HGT from their hosts.}, }
@article {pmid15256566, year = {2004}, author = {Cantera, JJL and Kawasaki, H and Seki, T}, title = {The nitrogen-fixing gene (nifH) of Rhodopseudomonas palustris: a case of lateral gene transfer?.}, journal = {Microbiology (Reading, England)}, volume = {150}, number = {Pt 7}, pages = {2237-2246}, doi = {10.1099/mic.0.26940-0}, pmid = {15256566}, issn = {1350-0872}, mesh = {Alphaproteobacteria/genetics ; Amino Acid Sequence ; DNA, Ribosomal/analysis ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Molecular Sequence Data ; Nitrogen Fixation/genetics ; Oxidoreductases/chemistry/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhodopseudomonas/enzymology/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Nitrogen fixation is catalysed by some photosynthetic bacteria. This paper presents a phylogenetic comparison of a nitrogen fixation gene (nifH) with the aim of elucidating the processes underlying the evolutionary history of Rhodopseudomonas palustris. In the NifH phylogeny, strains of Rps. palustris were placed in close association with Rhodobacter spp. and other phototrophic purple non-sulfur bacteria belonging to the alpha-Proteobacteria, separated from its close relatives Bradyrhizobium japonicum and the phototrophic rhizobia (Bradyrhizobium spp. IRBG 2, IRBG 228, IRBG 230 and BTAi 1) as deduced from the 16S rRNA phylogeny. The close association of the strains of Rps. palustris with those of Rhodobacter and Rhodovulum, as well as Rhodospirillum rubrum, was supported by the mol% G+C of their nifH gene and by the signature sequences found in the sequence alignment. In contrast, comparison of a number of informational and operational genes common to Rps. palustris CGA009, B. japonicum USDA 110 and Rhodobacter sphaeroides 2.4.1 suggested that the genome of Rps. palustris is more related to that of B. japonicum than to the Rba. sphaeroides genome. These results strongly suggest that the nifH of Rps. palustris is highly related to those of the phototrophic purple non-sulfur bacteria included in this study, and might have come from an ancestral gene common to these phototrophic species through lateral gene transfer. Although this finding complicates the use of nifH to infer the phylogenetic relationships among the phototrophic bacteria in molecular diversity studies, it establishes a framework to resolve the origins and diversification of nitrogen fixation among the phototrophic bacteria in the alpha-Proteobacteria.}, }
@article {pmid15254022, year = {2004}, author = {Guardabassi, L and Schwarz, S and Lloyd, DH}, title = {Pet animals as reservoirs of antimicrobial-resistant bacteria.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {54}, number = {2}, pages = {321-332}, doi = {10.1093/jac/dkh332}, pmid = {15254022}, issn = {0305-7453}, mesh = {Animals ; Animals, Domestic/*microbiology ; Bacteria/*drug effects ; Bacterial Infections/transmission ; Cats ; *Disease Reservoirs ; Disease Transmission, Infectious ; Dogs ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Humans ; Veterinary Medicine ; }, abstract = {Pet animal numbers have substantially increased in modern society and attention is increasingly devoted to pet welfare. Because of these changes, antimicrobial agents are frequently used in small animal veterinary practice, often including antimicrobial preparations used in human medicine, with heavy use of broad-spectrum agents such as aminopenicillins plus clavulanic acid, cephalosporins and fluoroquinolones. Several longitudinal studies conducted at veterinary hospitals have indicated that resistance to various antimicrobial agents has emerged amongst pet animal isolates of Staphylococcus intermedius, Escherichia coli and other bacteria, including species with a potential for zoonotic transmission and resistance phenotypes of clinical interest, such as methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci and multidrug-resistant Salmonella Typhimurium DT104. Based on a review of the current literature, the role of pets in the dissemination of antimicrobial resistance has been given little attention when compared with that of food animals. A marked contrast is evident between the current policies on antimicrobial usage in food and companion animals. Apart from a few countries where limited data on antimicrobial usage and occurrence of resistance in bacteria from pet animals are provided, national surveillance programmes only focus on food animals. However, data on pet animals are clearly needed for guiding antimicrobial use policy in small animal veterinary practice as well as for assessing the risk of transmission of antimicrobial resistance to humans.}, }
@article {pmid15251960, year = {2004}, author = {Anker, P and Zajac, V and Lyautey, J and Lederrey, C and Dunand, C and Lefort, F and Mulcahy, H and Heinemann, J and Stroun, M}, title = {Transcession of DNA from bacteria to human cells in culture: a possible role in oncogenesis.}, journal = {Annals of the New York Academy of Sciences}, volume = {1022}, number = {}, pages = {195-201}, doi = {10.1196/annals.1318.030}, pmid = {15251960}, issn = {0077-8923}, mesh = {Bacillus subtilis/genetics ; Cell Nucleus/chemistry ; Coculture Techniques ; DNA, Bacterial/*analysis/genetics/isolation &amp; purification ; DNA, Circular/*analysis/genetics/isolation &amp; purification ; *Gene Transfer, Horizontal ; Genes, Bacterial ; HL-60 Cells ; Humans ; Neoplasms/*etiology ; Polymerase Chain Reaction ; }, abstract = {The human organism is continuously in close contact with microorganisms, especially bacteria. In the present work, by means of a real-time polymerase chain reaction (PCR) technique, we looked for the presence of a distinct bacterial gene in human cells. To this end, we cultured a human cell line, HL60, in a supernatant in which bacteria (Bacillus subtilis) had been grown. A transient transcession of bacterial DNA into the human cells was observed.}, }
@article {pmid15251204, year = {2004}, author = {Breitbart, M and Miyake, JH and Rohwer, F}, title = {Global distribution of nearly identical phage-encoded DNA sequences.}, journal = {FEMS microbiology letters}, volume = {236}, number = {2}, pages = {249-256}, doi = {10.1016/j.femsle.2004.05.042}, pmid = {15251204}, issn = {0378-1097}, mesh = {Conserved Sequence ; DNA, Viral/*analysis/genetics/isolation &amp; purification ; DNA-Directed DNA Polymerase/*genetics ; Ecosystem ; Environmental Microbiology ; Evolution, Molecular ; Fresh Water/virology ; Genes, Viral ; Geologic Sediments/virology ; Molecular Sequence Data ; Phylogeny ; Podoviridae/enzymology/*genetics/*isolation &amp; purification ; Polymerase Chain Reaction ; Seawater/virology ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {Phages, the most abundant biological entities on the planet, play important roles in biogeochemical cycling, horizontal gene transfer, and defining microbial community composition. However, very little is known about phage diversity or biogeography, and there has not yet been a systematic effort to compare the phages found in different ecosystems. Here, we report that T7-like Podophage DNA polymerase sequences occur in every major biome investigated, including marine, freshwater, sediment, terrestrial, extreme, and metazoan-associated. The majority of these sequences belong to a unique clade that is only distantly related to cultured isolates. Some identical T7-like phage-encoded DNA polymerase genes from this clade were >99% conserved at the nucleotide level in multiple different environments, suggesting that these phages are moving between biomes in recent evolutionary time and that the global genomic pool for T7-like phages may be smaller than previously hypothesized.}, }
@article {pmid15247465, year = {2004}, author = {Olson, MV and Varki, A}, title = {Genomics. The chimpanzee genome--a bittersweet celebration.}, journal = {Science (New York, N.Y.)}, volume = {305}, number = {5681}, pages = {191-192}, doi = {10.1126/science.1100975}, pmid = {15247465}, issn = {1095-9203}, mesh = {Animals ; Behavior, Animal ; Chromosomes, Mammalian/genetics ; Conservation of Natural Resources ; Environment ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; *Genome ; Genome, Human ; Hominidae/genetics ; Humans ; Pan troglodytes/*genetics/physiology ; Primates/genetics ; Proteins/genetics/physiology ; Retroelements ; Selection, Genetic ; *Sequence Analysis, DNA ; Sequence Deletion ; Species Specificity ; }, }
@article {pmid15240837, year = {2004}, author = {Medrano-Soto, A and Moreno-Hagelsieb, G and Vinuesa, P and Christen, JA and Collado-Vides, J}, title = {Successful lateral transfer requires codon usage compatibility between foreign genes and recipient genomes.}, journal = {Molecular biology and evolution}, volume = {21}, number = {10}, pages = {1884-1894}, doi = {10.1093/molbev/msh202}, pmid = {15240837}, issn = {0737-4038}, mesh = {Archaea/genetics ; *Codon ; *Gene Transfer, Horizontal ; Genes/*physiology ; Phylogeny ; Thermotoga maritima/genetics ; }, abstract = {We present evidence supporting the notion that codon usage (CU) compatibility between foreign genes and recipient genomes is an important prerequisite to assess the selective advantage of imported functions, and therefore to increase the fixation probability of horizontal gene transfer (HGT) events. This contrasts with the current tendency in research to predict recent HGTs in prokaryotes by assuming that acquired genes generally display poor CU. By looking at the CU level (poor, typical, or rich) exhibited by putative xenologs still resembling their original CU, we found that most alien genes predominantly present typical CU immediately upon introgression, thereby suggesting that the role of CU amelioration in HGT has been overemphasized. In our strategy, we first scanned a representative set of 103 complete prokaryotic genomes for all pairs of candidate xenologs (exported/imported genes) displaying similar CU. We applied additional filtering criteria, including phylogenetic validations, to enhance the reliability of our predictions. Our approach makes no assumptions about the CU of foreign genes being typical or atypical within the recipient genome, thus providing a novel unbiased framework to study the evolutionary dynamics of HGT.}, }
@article {pmid15231810, year = {2004}, author = {Poly, F and Threadgill, D and Stintzi, A}, title = {Identification of Campylobacter jejuni ATCC 43431-specific genes by whole microbial genome comparisons.}, journal = {Journal of bacteriology}, volume = {186}, number = {14}, pages = {4781-4795}, pmid = {15231810}, issn = {0021-9193}, support = {R01 AI055612/AI/NIAID NIH HHS/United States ; R01 AI055612-04/AI/NIAID NIH HHS/United States ; R01-AI055612/AI/NIAID NIH HHS/United States ; RR15564/RR/NCRR NIH HHS/United States ; P20 RR015564/RR/NCRR NIH HHS/United States ; }, mesh = {Bacterial Capsules/biosynthesis/genetics ; Base Composition ; Biological Transport/genetics ; Campylobacter jejuni/*genetics ; DNA Restriction-Modification Enzymes/genetics ; DNA, Bacterial/chemistry/genetics/isolation &amp; purification ; Gene Library ; Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genetic Variation ; *Genome, Bacterial ; Genomic Islands/genetics ; Helicobacter hepaticus/genetics ; Integrases/genetics ; Lipopolysaccharides/biosynthesis ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Oligonucleotide Array Sequence Analysis ; Open Reading Frames ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {This study describes a novel approach to identify unique genomic DNA sequences from the unsequenced strain C. jejuni ATCC 43431 by comparison with the sequenced strain C. jejuni NCTC 11168. A shotgun DNA microarray was constructed by arraying 9,600 individual DNA fragments from a C. jejuni ATCC 43431 genomic library onto a glass slide. DNA fragments unique to C. jejuni ATCC 43431 were identified by competitive hybridization to the array with genomic DNA of C. jejuni NCTC 11168. The plasmids containing unique DNA fragments were sequenced, allowing the identification of up to 130 complete and incomplete genes. Potential biological roles were assigned to 66% of the unique open reading frames. The mean G+C content of these unique genes (26%) differs significantly from the G+C content of the entire C. jejuni genome (30.6%). This suggests that they may have been acquired through horizontal gene transfer from an organism with a G+C content lower than that of C. jejuni. Because the two C. jejuni strains differ by Penner serotype, a large proportion of the unique ATCC 43431 genes encode proteins involved in lipooligosaccharide and capsular biosynthesis, as expected. Several unique open reading frames encode enzymes which may contribute to genetic variability, i.e., restriction-modification systems and integrases. Interestingly, many of the unique C. jejuni ATCC 43431 genes show identity with a possible pathogenicity island from Helicobacter hepaticus and components of a potential type IV secretion system. In conclusion, this study provides a valuable resource to further investigate Campylobacter diversity and pathogenesis.}, }
@article {pmid15231808, year = {2004}, author = {Franklin, MJ and Douthit, SA and McClure, MA}, title = {Evidence that the algI/algJ gene cassette, required for O acetylation of Pseudomonas aeruginosa alginate, evolved by lateral gene transfer.}, journal = {Journal of bacteriology}, volume = {186}, number = {14}, pages = {4759-4773}, pmid = {15231808}, issn = {0021-9193}, support = {AI-28309/AI/NIAID NIH HHS/United States ; P20/RR-16455-01/RR/NCRR NIH HHS/United States ; R01 AI046588/AI/NIAID NIH HHS/United States ; AI-46588/AI/NIAID NIH HHS/United States ; P20 RR016455/RR/NCRR NIH HHS/United States ; R01 AI028309/AI/NIAID NIH HHS/United States ; }, mesh = {Acetylation ; Alginates/*metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Bacterial Proteins/chemistry/*genetics/metabolism ; Biofilms/growth &amp; development ; Conserved Sequence ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Glucuronic Acid/*metabolism ; Gram-Negative Bacteria/genetics/metabolism ; Gram-Positive Bacteria/genetics/metabolism ; Hexuronic Acids/*metabolism ; Membrane Proteins/genetics/metabolism ; Models, Molecular ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Protein Structure, Secondary ; Pseudomonas aeruginosa/*genetics/metabolism/pathogenicity ; Sequence Alignment ; Sequence Homology ; }, abstract = {Pseudomonas aeruginosa strains, isolated from chronically infected patients with cystic fibrosis, produce the O-acetylated extracellular polysaccharide, alginate, giving these strains a mucoid phenotype. O acetylation of alginate plays an important role in the ability of mucoid P. aeruginosa to form biofilms and to resist complement-mediated phagocytosis. The O-acetylation process is complex, requiring a protein with seven transmembrane domains (AlgI), a type II membrane protein (AlgJ), and a periplasmic protein (AlgF). The cellular localization of these proteins suggests a model wherein alginate is modified at the polymer level after the transport of O-acetyl groups to the periplasm. Here, we demonstrate that this mechanism for polysaccharide esterification may be common among bacteria, since AlgI homologs linked to type II membrane proteins are found in a variety of gram-positive and gram-negative bacteria. In some cases, genes for these homologs have been incorporated into polysaccharide biosynthetic operons other than for alginate biosynthesis. The phylogenies of AlgI do not correlate with the phylogeny of the host bacteria, based on 16S rRNA analysis. The algI homologs and the gene for their adjacent type II membrane protein present a mosaic pattern of gene arrangement, suggesting that individual components of the multigene cassette, as well as the entire cassette, evolved by lateral gene transfer. AlgJ and the other type II membrane proteins, although more diverged than AlgI, contain conserved motifs, including a motif surrounding a highly conserved histidine residue, which is required for alginate O-acetylation activity by AlgJ. The AlgI homologs also contain an ordered series of motifs that included conserved amino acid residues in the cytoplasmic domain CD-4; the transmembrane domains TM-C, TM-D, and TM-E; and the periplasmic domain PD-3. Site-directed mutagenesis studies were used to identify amino acids important for alginate O-acetylation activity, including those likely required for (i) the interaction of AlgI with the O-acetyl precursor in the cytoplasm, (ii) the export of the O-acetyl group across the cytoplasmic membrane, and (iii) the transfer of the O-acetyl group to a periplasmic protein or to alginate. These results indicate that AlgI belongs to a family of membrane proteins required for modification of polysaccharides and that a mechanism requiring an AlgI homolog and a type II membrane protein has evolved by lateral gene transfer for the esterification of many bacterial extracellular polysaccharides.}, }
@article {pmid15231789, year = {2004}, author = {Bacciu, D and Falchi, G and Spazziani, A and Bossi, L and Marogna, G and Leori, GS and Rubino, S and Uzzau, S}, title = {Transposition of the heat-stable toxin astA gene into a gifsy-2-related prophage of Salmonella enterica serovar Abortusovis.}, journal = {Journal of bacteriology}, volume = {186}, number = {14}, pages = {4568-4574}, pmid = {15231789}, issn = {0021-9193}, mesh = {Animals ; Bacterial Proteins/genetics/metabolism ; Bacterial Toxins/*genetics ; Colony Count, Microbial ; *DNA Transposable Elements ; DNA, Bacterial/chemistry/isolation &amp; purification ; Escherichia coli/genetics ; Gene Deletion ; Gene Dosage ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genes, Viral ; Intestines/microbiology ; Liver/microbiology ; Lymph Nodes/microbiology ; Molecular Sequence Data ; Prophages/*genetics/isolation &amp; purification ; Salmonella Infections, Animal/microbiology ; Salmonella enterica/*genetics/isolation &amp; purification/pathogenicity/*virology ; Sheep Diseases/microbiology ; Spleen/microbiology ; Viral Tail Proteins/genetics ; Virulence Factors/*genetics ; }, abstract = {The horizontal transfer and acquisition of virulence genes via mobile genetic elements have been a major driving force in the evolution of Salmonella pathogenicity. Serovars of Salmonella enterica carry variable assortments of phage-encoded virulence genes, suggesting that temperate phages play a pivotal role in this process. Epidemic isolates of S. enterica serovar Typhimurium are consistently lysogenic for two lambdoid phages, Gifsy-1 and Gifsy-2, carrying known virulence genes. Other serovars of S. enterica, including serovars Dublin, Gallinarum, Enteritidis, and Hadar, carry distinct prophages with similarity to the Gifsy phages. In this study, we analyzed Gifsy-related loci from S. enterica serovar Abortusovis, a pathogen associated exclusively with ovine infection. A cryptic prophage, closely related to serovar Typhimurium phage Gifsy-2, was identified. This element, named Gifsy-2AO, was shown to contribute to serovar Abortusovis systemic infection in lambs. Sequence analysis of the prophage b region showed a large deletion which covers genes encoding phage tail fiber proteins and putative virulence factors, including type III secreted effector protein SseI (GtgB, SrfH). This deletion was identified in most of the serovar Abortusovis isolates tested and might be dependent on the replicative transposition of an adjacent insertion sequence, IS1414, previously identified in pathogenic Escherichia coli strains. IS1414 encodes heat-stable toxin EAST1 (astA) and showed multiple genomic copies in isolates of serovar Abortusovis. To our knowledge, this is the first evidence of intergeneric transfer of virulence genes via insertion sequence elements in Salmonella. The acquisition of IS1414 (EAST1) and its frequent transposition within the chromosome might improve the fitness of serovar Abortusovis within its narrow ecological niche.}, }
@article {pmid15231771, year = {2004}, author = {Yates, CM and Pearce, MC and Woolhouse, ME and Amyes, SG}, title = {High frequency transfer and horizontal spread of apramycin resistance in calf faecal Escherichia coli.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {54}, number = {2}, pages = {534-537}, doi = {10.1093/jac/dkh353}, pmid = {15231771}, issn = {0305-7453}, mesh = {Acetyltransferases/genetics ; Animals ; Anti-Bacterial Agents/*pharmacology ; Cattle ; Cluster Analysis ; Conjugation, Genetic ; DNA Primers ; DNA, Bacterial/analysis/genetics ; Drug Resistance, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/*drug effects/*genetics ; Feces/*microbiology ; Gene Transfer, Horizontal ; Genotype ; Microbial Sensitivity Tests ; Nebramycin/*analogs &amp; derivatives/*pharmacology ; Phenotype ; Plasmids/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {OBJECTIVES: The aminoglycoside apramycin has been used extensively in animal husbandry in the UK since 1978. This study aimed to determine both whether calves that had never been treated with aminoglycoside antibiotics harboured apramycin-resistant (apr(R)) commensal Escherichia coli, and the mode of spread of the resistance gene.<br><br>METHODS: Apr(R) E. coli from weekly calf faecal samples were typed by pulsed-field gel electrophoresis, antibiotic resistance phenotype, plasmid restriction profiles and plasmid transfer frequencies.<br><br>RESULTS: During 4 months of weekly sampling, six of 11 calves were found to harbour apr(R) E. coli. All apr(R) E. coli (45) were cross-resistant to gentamicin and tobramycin, which are both used in human medicine. Resistance was conferred by the aac(3)IV gene, present on three different conjugative plasmids. Two of these plasmids also mediated tetracycline and streptomycin resistance. One plasmid demonstrated very high transfer frequencies and was found in three different genotypes.<br><br>CONCLUSIONS: We report the presence of apr(R) commensal E. coli in cattle that have never been treated with aminoglycosides. The presence of one conjugative plasmid in three different genotypes is evidence of horizontal spread of this plasmid. This is the first report of a very high transfer frequency of apr(R) plasmid, demonstrating horizontal spread in the commensal flora of food animals.}, }
@article {pmid15228521, year = {2004}, author = {Piskur, J and Langkjaer, RB}, title = {Yeast genome sequencing: the power of comparative genomics.}, journal = {Molecular microbiology}, volume = {53}, number = {2}, pages = {381-389}, doi = {10.1111/j.1365-2958.2004.04182.x}, pmid = {15228521}, issn = {0950-382X}, mesh = {Biological Evolution ; Gene Expression Regulation, Fungal ; Genes, Fungal ; *Genome, Fungal ; *Genomics ; Phylogeny ; Yeasts/*genetics ; }, abstract = {For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown that the minimum number of genes from each species that need to be compared to produce a reliable phylogeny is about 20. Yeast has also become an attractive model to study speciation in eukaryotes, especially to understand molecular mechanisms behind the establishment of reproductive isolation. Comparison of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide the background to use more yeast species in model studies, to combat pathogens and for efficient manipulation of industrial strains.}, }
@article {pmid15227795, year = {2004}, author = {Malík, R and Pristas, P and Javorský, P}, title = {Occurrence of plasmid-mediated ampicillin resistance among enterobacteria from the ovine rumen.}, journal = {Folia microbiologica}, volume = {49}, number = {2}, pages = {187-190}, pmid = {15227795}, issn = {0015-5632}, mesh = {Ampicillin/pharmacology ; Ampicillin Resistance/*genetics ; Animals ; Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; Enterobacteriaceae/*drug effects/*isolation &amp; purification ; Escherichia coli/genetics ; Feces/microbiology ; Gene Transfer, Horizontal ; *R Factors ; Rumen/*microbiology ; Sheep/*microbiology ; beta-Lactamases/genetics ; }, abstract = {Seasonal samplings of rumen and fecal populations of Enterobacteriacae from sheep digestive tract were done to elucidate potential occurrence and spreading of antibiotic resistance in the environment. Thus 350 rumen and fecal isolates were tested for ampicillin (Amp) resistance in single sampling. Low frequency of Amp resistance (from 0 to 15%) was observed. The occurrence of tem1 encoded Amp resistance confirmed by PCR was observed among both rumen and fecal isolates. The small tem1 carrying plasmid and its transfer (mobilization) was detected and partially characterized after conjugation to laboratory Escherichia coli strain.}, }
@article {pmid15225325, year = {2004}, author = {de Vries, J and Herzfeld, T and Wackernagel, W}, title = {Transfer of plastid DNA from tobacco to the soil bacterium Acinetobacter sp. by natural transformation.}, journal = {Molecular microbiology}, volume = {53}, number = {1}, pages = {323-334}, doi = {10.1111/j.1365-2958.2004.04132.x}, pmid = {15225325}, issn = {0950-382X}, mesh = {Acinetobacter/*genetics ; Base Sequence ; DNA/genetics/*metabolism ; Drug Resistance/genetics ; Genes, Plant/genetics ; Genome, Plant ; Molecular Sequence Data ; Plastids/*genetics ; Recombination, Genetic ; Soil Microbiology ; Nicotiana/*genetics ; Transformation, Bacterial ; *Transformation, Genetic ; }, abstract = {Acquisition of new genetic information by horizontal gene transfer is a major mechanism of genetic adaptation and evolution in prokaryotes. Naturally transformable cells of Acinetobacter sp. were exposed to plant DNA from leaf and root tissue of transplastomic tobacco. With the aadA gene (resistance against spectinomycin and streptomycin) as anchor sequence, the transfer of segments of the tobacco plastid DNA to Acinetobacter by homology-facilitated illegitimate recombination occurred at a frequency of 1.2 x 10(-7) per cell, which was about 0.1% of the frequency of fully homologous transfers. Without anchor sequence, transfer was not detected (</=1.3 x 10(-10)). The integrated plastid DNA segments extended up to 2539 nucleotides and often encompassed tobacco genes (trnL, ycf5). Expression of trnL (leucyl-tRNA) in a transformant was shown by reverse transcription polymerase chain reaction. About 44% of integration events occurred at a single hot-spot and 38% at other multiply used sites. All illegitimate recombination sites were GC-rich microhomologies of 3-6 bp often neighboured by further microhomologies. The sites were located in plant DNA at the ends of distinct larger high-GC regions, which suggests a role for GC-aided association of heterologous sequences in illegitimate DNA end joining. The results show that integration of plant DNA into a bacterial genome by natural transformation is possible and is probably stimulated by hot-spots of illegitimate recombination.}, }
@article {pmid15224914, year = {2004}, author = {Dunfield, KE and Germida, JJ}, title = {Impact of genetically modified crops on soil- and plant-associated microbial communities.}, journal = {Journal of environmental quality}, volume = {33}, number = {3}, pages = {806-815}, doi = {10.2134/jeq2004.0806}, pmid = {15224914}, issn = {0047-2425}, mesh = {Bacteria/genetics ; Ecosystem ; Environment ; Plant Roots/*microbiology ; Plants, Edible/*genetics/growth &amp; development ; *Plants, Genetically Modified ; Population Dynamics ; Risk Factors ; *Soil Microbiology ; Transgenes ; }, abstract = {Transgenic or genetically modified plants possess novel genes that impart beneficial characteristics such as herbicide resistance. One of the least understood areas in the environmental risk assessment of genetically modified crops is their impact on soil- and plant-associated microbial communities. The potential for interaction between transgenic plants and plant residues and the soil microbial community is not well understood. The recognition that these interactions could change microbial biodiversity and affect ecosystem functioning has initiated a limited number of studies in the area. At this time, studies have shown the possibility that transgenes can be transferred to native soil microorganisms through horizontal gene transfer, although there is not evidence of this occurring in the soil. Furthermore, novel proteins have been shown to be released from transgenic plants into the soil ecosystem, and their presence can influence the biodiversity of the microbial community by selectively stimulating the growth of organisms that can use them. Microbial diversity can be altered when associated with transgenic plants; however, these effects are both variable and transient. Soil- and plant-associated microbial communities are influenced not only by plant species and transgene insertion but also by environmental factors such as field site and sampling date. Minor alterations in the diversity of the microbial community could affect soil health and ecosystem functioning, and therefore, the impact that plant variety may have on the dynamics of the rhizosphere microbial populations and in turn plant growth and health and ecosystem sustainability, requires further study.}, }
@article {pmid15223314, year = {2004}, author = {Yang, Z and Shipman, L and Zhang, M and Anton, BP and Roberts, RJ and Cheng, X}, title = {Structural characterization and comparative phylogenetic analysis of Escherichia coli HemK, a protein (N5)-glutamine methyltransferase.}, journal = {Journal of molecular biology}, volume = {340}, number = {4}, pages = {695-706}, pmid = {15223314}, issn = {0022-2836}, support = {GM61355/GM/NIGMS NIH HHS/United States ; R01 GM061355-04/GM/NIGMS NIH HHS/United States ; K12 GM000680/GM/NIGMS NIH HHS/United States ; GM49245/GM/NIGMS NIH HHS/United States ; R01 GM049245/GM/NIGMS NIH HHS/United States ; GM00680/GM/NIGMS NIH HHS/United States ; R01 GM061355/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Binding Sites ; Conserved Sequence ; Crystallography, X-Ray ; Escherichia coli/*enzymology/genetics ; Escherichia coli Proteins/*chemistry ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; *Phylogeny ; Protein Methyltransferases/*chemistry ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sequence Analysis, Protein ; Sequence Homology, Amino Acid ; Synteny ; Thermotoga maritima/enzymology/genetics ; }, abstract = {Protein glutamine methylation at GGQ sites of protein chain release factors plays a pivotal role in the termination of translation. We report here the crystal structure of the Escherichia coli HemK protein (N5)-glutamine methyltransferase (MTase) in a binary complex with the methyl-donor product S-adenosyl-L-homocysteine (AdoHcy). HemK contains two domains: a putative substrate binding domain at the N terminus consisting of a five helix bundle and a seven-stranded catalytic domain at the C terminus that harbors the binding site for AdoHcy. The two domains are linked by a beta-hairpin. Structure-guided sequence analysis of the HemK family revealed 11 invariant residues functioning in methyl-donor binding and catalysis of methyl transfer. The putative substrate-binding domains of HemK from E.coli and Thermotoga maritima are structurally similar, despite the fact that they share very little sequence similarity. When the two proteins are aligned structurally, the helical N-terminal domain is subject to approximately 10 degrees of hinge movement relative to the C-terminal domain. The apparent hinge mobility of the two domains may reflect functional importance during the reaction cycle. Comparative phylogenetic analysis of the hemK gene and its frequent neighbor gene, prfA, which encodes a major substrate, provides evidence for several examples of lateral gene transfer.}, }
@article {pmid15219393, year = {2004}, author = {Iyer, LM and Aravind, L and Coon, SL and Klein, DC and Koonin, EV}, title = {Evolution of cell-cell signaling in animals: did late horizontal gene transfer from bacteria have a role?.}, journal = {Trends in genetics : TIG}, volume = {20}, number = {7}, pages = {292-299}, doi = {10.1016/j.tig.2004.05.007}, pmid = {15219393}, issn = {0168-9525}, mesh = {Animals ; Bacteria/*genetics/*pathogenicity ; Bacteriophages/*physiology ; *Biological Evolution ; *Cell Communication ; Gene Transfer, Horizontal/*physiology ; Phylogeny ; Second Messenger Systems/*physiology ; Signal Transduction ; }, }
@article {pmid15218707, year = {2004}, author = {Stechmann, A and Cavalier-Smith, T}, title = {Evolutionary origins of Hsp90 chaperones and a deep paralogy in their bacterial ancestors.}, journal = {The Journal of eukaryotic microbiology}, volume = {51}, number = {3}, pages = {364-373}, doi = {10.1111/j.1550-7408.2004.tb00580.x}, pmid = {15218707}, issn = {1066-5234}, mesh = {Animals ; Bacteria/classification/*genetics ; Eukaryotic Cells/*metabolism ; *Evolution, Molecular ; HSP90 Heat-Shock Proteins/*genetics ; Phylogeny ; }, abstract = {The 82-90 kD family of molecular chaperone proteins has homologs in eukaryotes (Hsp90) and many eubacteria (HtpG) but not in Archaebacteria. We used representatives of all four different eukaryotic paralogs (cytosolic, endoplasmic reticulum (ER), chloroplast, mitochondrial) together with numerous eubacterial HtpG proteins for phylogenetic analyses to investigate their evolutionary origins. Our trees confirm that none of the organellar Hsp90s derives from the endosymbionts of early eukaryotes. Contrary to previous suggestions of distant origins through lateral gene transfer (LGT) all eukaryote Hsp90s are related to Gram-positive eubacterial HtpG proteins. The nucleocytosolic, ER and chloroplast Hsp90 paralogs are clearly mutually related. The origin of mitochondrial Hsp90 is more obscure, as these sequences are deeply nested within eubacteria. Our trees also reveal a deep split within eubacteria into a group of mainly long-branching sequences (including the eukaryote mitochondrial Hsp90s) and another group comprising exclusively short-branching HtpG proteins, from which the cytosolic/ER versions probably arose. Both versions are present in several eubacterial phyla, suggesting gene duplication very early in eubacterial evolution and multiple independent losses thereafter. We identified one probable case of LGT within eubacteria. However, multiple losses can simply explain the evolutionary pattern of the eubacterial HtpG paralogs and predominate over LGT. We suggest that the actinobacterial ancestor of eukaryotes harbored genes for both eubacterial HtpG paralogs, as the actinobacterium Streptomyces coelicolor still does; one could have given rise to the mitochondrial Hsp90 and the other, following another duplication event in the ancestral eukaryote, to the cytosolic and ER Hsp90 homologs.}, }
@article {pmid15215122, year = {2004}, author = {Doi, Y and Wachino, J and Ishiguro, M and Kurokawa, H and Yamane, K and Shibata, N and Shibayama, K and Yokoyama, K and Kato, H and Yagi, T and Arakawa, Y}, title = {Inhibitor-sensitive AmpC beta-lactamase variant produced by an Escherichia coli clinical isolate resistant to oxyiminocephalosporins and cephamycins.}, journal = {Antimicrobial agents and chemotherapy}, volume = {48}, number = {7}, pages = {2652-2658}, pmid = {15215122}, issn = {0066-4804}, mesh = {Amino Acid Sequence ; Bacterial Proteins/*antagonists &amp; inhibitors/*genetics ; Ceftazidime/pharmacology ; Cephalosporin Resistance ; Cephalosporins/*pharmacology ; Cephamycins/*pharmacology ; Cloning, Molecular ; Culture Media ; Enzyme Inhibitors/*pharmacology ; Escherichia coli/*enzymology/genetics ; Escherichia coli Infections/enzymology/*microbiology ; Gene Deletion ; Gene Transfer, Horizontal ; Isoelectric Focusing ; Microbial Sensitivity Tests ; Models, Molecular ; Molecular Sequence Data ; Plasmids/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Substrate Specificity ; *beta-Lactamase Inhibitors ; beta-Lactamases/*genetics ; }, abstract = {Escherichia coli HKY28, a ceftazidime-resistant strain isolated from a urine specimen in Japan, produced an inhibitor-sensitive AmpC beta-lactamase variant. The deduced amino acid sequence of the enzyme contained a number of substitutions and a tripeptide deletion (Gly286-Ser287-Asp288) compared with the sequence of native AmpC of E. coli. When the deletion was reverted by a 9-base insertion at the relevant site of ampC in the clone, the typical inhibitor-resistant phenotype of AmpC was restored, while at the same time the levels of resistance to ceftazidime, cefpirome, and cefepime were reduced eightfold or more. Molecular modeling studies indicated that a structural change took place in the H-10 helix as a result of the deletion, and this change caused an alteration of the substrate binding site, leading to a unique phenotype analogous to that of inhibitor-sensitive class A extended-spectrum beta-lactamases. The degree of inhibition was greater with sulbactam and tazobactam than with clavulanic acid. To our knowledge, this is the first report to have characterized an E. coli ampC that encodes chromosomal AmpC beta-lactamase sensitive to the available beta-lactamase inhibitors.}, }
@article {pmid15214963, year = {2004}, author = {Xie, G and Bonner, CA and Song, J and Keyhani, NO and Jensen, RA}, title = {Inter-genomic displacement via lateral gene transfer of bacterial trp operons in an overall context of vertical genealogy.}, journal = {BMC biology}, volume = {2}, number = {}, pages = {15}, pmid = {15214963}, issn = {1741-7007}, support = {G13 LM008297/LM/NLM NIH HHS/United States ; }, mesh = {Bacteria/classification/*genetics ; Databases, Factual ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; *Genome, Bacterial ; Operon/*genetics ; Pedigree ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Tryptophan/biosynthesis/*genetics ; }, abstract = {BACKGROUND: The growing conviction that lateral gene transfer plays a significant role in prokaryote genealogy opens up a need for comprehensive evaluations of gene-enzyme systems on a case-by-case basis. Genes of tryptophan biosynthesis are frequently organized as whole-pathway operons, an attribute that is expected to facilitate multi-gene transfer in a single step. We have asked whether events of lateral gene transfer are sufficient to have obscured our ability to track the vertical genealogy that underpins tryptophan biosynthesis.<br><br>RESULTS: In 47 complete-genome Bacteria, the genes encoding the seven catalytic domains that participate in primary tryptophan biosynthesis were distinguished from any paralogs or xenologs engaged in other specialized functions. A reliable list of orthologs with carefully ascertained functional roles has thus been assembled and should be valuable as an annotation resource. The protein domains associated with primary tryptophan biosynthesis were then concatenated, yielding single amino-acid sequence strings that represent the entire tryptophan pathway. Lateral gene transfer of several whole-pathway trp operons was demonstrated by use of phylogenetic analysis. Lateral gene transfer of partial-pathway trp operons was also shown, with newly recruited genes functioning either in primary biosynthesis (rarely) or specialized metabolism (more frequently).<br><br>CONCLUSIONS: (i) Concatenated tryptophan protein trees are congruent with 16S rRNA subtrees provided that the genomes represented are of sufficiently close phylogenetic spacing. There are currently seven tryptophan congruency groups in the Bacteria. Recognition of a succession of others can be expected in the near future, but ultimately these should coalesce to a single grouping that parallels the 16S rRNA tree (except for cases of lateral gene transfer). (ii) The vertical trace of evolution for tryptophan biosynthesis can be deduced. The daunting complexities engendered by paralogy, xenology, and idiosyncrasies of nomenclature at this point in time have necessitated an expert-assisted manual effort to achieve a correct analysis. Once recognized and sorted out, paralogy and xenology can be viewed as features that enrich evolutionary histories.}, }
@article {pmid15214639, year = {2004}, author = {Parker, MA}, title = {RRNA and dnaK relationships of Bradyrhizobium sp. nodule bacteria from four papilionoid legume trees in Costa Rica.}, journal = {Systematic and applied microbiology}, volume = {27}, number = {3}, pages = {334-342}, doi = {10.1078/0723-2020-00266}, pmid = {15214639}, issn = {0723-2020}, mesh = {Bacterial Proteins/*genetics/isolation &amp; purification/metabolism ; Base Sequence ; Bradyrhizobium/*genetics/*isolation &amp; purification/physiology ; Costa Rica ; DNA, Bacterial/chemistry/isolation &amp; purification ; DNA, Ribosomal/chemistry/isolation &amp; purification ; Electrophoresis, Starch Gel ; Fabaceae/*microbiology ; Gene Transfer, Horizontal ; *Genes, rRNA ; Isoenzymes/isolation &amp; purification/metabolism ; Molecular Sequence Data ; Nitrogen Fixation ; Nitrogenase/metabolism ; Nucleic Acid Conformation ; Phylogeny ; Plant Roots/microbiology ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {Enzyme electrophoresis and sequencing of rRNA and dnaK genes revealed high genetic diversity among root nodule bacteria from the Costa Rican trees Andira inermis, Dalbergia retusa, Platymiscium pinnatum (Papilionoideae tribe Dalbergieae) and Lonchocarpus atropurpureus (Papilionoideae tribe Millettieae). A total of 21 distinct multilocus genotypes [ETs (electrophoretic types)] was found among the 36 isolates analyzed, and no ETs were shared in common by isolates from different legume hosts. However, three of the ETs from D. retusa were identical to Bradyrhizobium sp. isolates detected in prior studies of several other legume genera in both Costa Rica and Panama. Nearly full-length 16S rRNA sequences and partial 23S rRNA sequences confirmed that two isolates from D. retusa were highly similar or identical to Bradyrhizobium strains isolated from the legumes Erythrina and Clitoria (Papilionoideae tribe Phaseoleae) in Panama. rRNA sequences for five isolates from L. atropurpureus, P. pinnatum and A. inermis were not closely related to any currently known strains from Central America or elsewhere, but had affinities to the reference strains Bradyrhizobium japonicum USDA 110 (three isolates) or to B. elkanii USDA 76 (two isolates). A phylogenetic tree for 21 Bradyrhizobium strains based on 603 bp of the dnaK gene showed several significant conflicts with the rRNA tree, suggesting that genealogical relationships may have been altered by lateral gene transfer events.}, }
@article {pmid15214638, year = {2004}, author = {Okamoto, T and Maruyama, A and Imura, S and Takeyama, H and Naganuma, T}, title = {Comparative phylogenetic analyses of Halomonas variabilis and related organisms based on 16S rRNA, gyrB and ectBC gene sequences.}, journal = {Systematic and applied microbiology}, volume = {27}, number = {3}, pages = {323-333}, doi = {10.1078/0723-2020-00271}, pmid = {15214638}, issn = {0723-2020}, mesh = {Adaptation, Biological ; Bacterial Typing Techniques ; Cold Temperature ; DNA Gyrase/genetics ; DNA, Bacterial/chemistry/isolation &amp; purification ; DNA, Ribosomal/chemistry/isolation &amp; purification ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genes, rRNA ; Geologic Sediments/microbiology ; Halomonas/*classification/*genetics/isolation &amp; purification/physiology ; Hydro-Lyases/genetics ; Hydrostatic Pressure ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Seawater/microbiology ; Sequence Analysis, DNA ; Sequence Homology ; Sodium Chloride ; Transaminases/genetics ; Water Microbiology ; }, abstract = {Halomonas variabilis and phylogenetically related organisms were isolated from various habitats such as Antarctic terrain and saline ponds, deep-sea sediment, deep-sea waters affected by hydrothermal plumes, and hydrothermal vent fluids. Ten strains were selected for physiological and phylogenetic characterization in detail. All of those strains were found to be piezotolerant and psychrotolerant, as well as euryhaline halophilic or halotolerant. Their stress tolerance may facilitate their wide occurrence, even in so-called extreme environments. The 16S rDNA-based phylogenetic relationship was complemented by analyses of the DNA gyrase subunit B gene (gyrB) and genes involved in the synthesis of the major compatible solute, ectoine: diaminobutyric acid aminotransferase gene (ectB) and ectoine synthase gene (ectC). The phylogenetic relationships of H. variabilis and related organisms were very similar in terms of 16S rDNA, gyrB, and ectB. The ectC-based tree was inconsistent with the other phylogenetic trees. For that reason, ectC was inferred to derive from horizontal transfer.}, }
@article {pmid15213739, year = {2004}, author = {Verma, SC and Chowdhury, SP and Tripathi, AK}, title = {Phylogeny based on 16S rDNA and nifH sequences of Ralstonia taiwanensis strains isolated from nitrogen-fixing nodules of Mimosa pudica, in India.}, journal = {Canadian journal of microbiology}, volume = {50}, number = {5}, pages = {313-322}, doi = {10.1139/w04-020}, pmid = {15213739}, issn = {0008-4166}, mesh = {Bacterial Typing Techniques ; Carbohydrate Metabolism ; Cluster Analysis ; DNA Fingerprinting ; DNA, Bacterial/chemistry/isolation &amp; purification ; DNA, Ribosomal/analysis/chemistry/isolation &amp; purification ; Gene Transfer, Horizontal ; Genes, rRNA ; India ; Mimosa/*microbiology ; Molecular Sequence Data ; *Nitrogen Fixation/genetics ; Oxidoreductases/*genetics/immunology/metabolism ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Ralstonia/*classification/*genetics/isolation &amp; purification ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {Bacterial symbionts present in the indeterminate-type nitrogen (N)-fixing nodules of Mimosa pudica grown in North and South India showed maximum similarity to Ralstonia taiwanensis on the basis of carbon-source utilization patterns and 16S rDNA sequence. Isolates from the nodules of M. pudica from North India and South India showed identical ARDRA (Amplified Ribosomal DNA Restriction Analysis) patterns with Sau3AI and RsaI, but AluI revealed dimorphy between the North Indian and South Indian isolates. Alignment of 16S rDNA sequences revealed similarity of North Indian isolates with an R. taiwanensis strain isolated from M. pudica in Taiwan, whereas South Indian isolates showed closer relatedness with the isolates from Mimosa diplotricha. Alignment of nifH sequences from both North Indian and South Indian isolates with that of the related isolates revealed their closer affinity to alpha-rhizobia, suggesting that nif genes in the beta-rhizobia might have been acquired from alpha-rhizobia via lateral transfer during co-occupancy of nodules by alpha-rhizobia and progenitors of R. taiwanensis, members of the beta-subclass of Proteobacteria. Immunological cross-reaction of the bacteroid preparation of M. pudica nodules showed strong a positive signal with anti-dinitrogenase reductase antibody, whereas a weak positive cross-reaction was observed with free-living R. taiwanensis grown microaerobically in minimal medium with and without NH4Cl. In spite of the expression of dinitrogenase reductase under free-living conditions, acetylene reduction was not observed under N-free conditions even after prolonged incubation.}, }
@article {pmid15212376, year = {2004}, author = {Martin, AP and Costello, EK and Meyer, AF and Nemergut, DR and Schmidt, SK}, title = {The rate and pattern of cladogenesis in microbes.}, journal = {Evolution; international journal of organic evolution}, volume = {58}, number = {5}, pages = {946-955}, doi = {10.1111/j.0014-3820.2004.tb00429.x}, pmid = {15212376}, issn = {0014-3820}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Cluster Analysis ; Databases, Genetic ; Environment ; Gene Transfer, Horizontal/*genetics ; *Genetic Variation ; Geography ; Likelihood Functions ; Models, Genetic ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Time Factors ; }, abstract = {Theories of macroevolution rarely have been extended to include microbes; however, because microbes represent the most ancient and diverse assemblage of organismal diversity, such oversight limits our understanding of evolutionary history. Our analysis of phylogenetic trees for microbes suggests that macroevolution may differ between prokaryotes and both micro- and macroeukaryotes (mainly plants and animals). Phylogenetic trees inferred for prokaryotes and some microbial eukaryotes conformed to expectations assuming a constant rate of cladogenesis over time and among lineages: nevertheless, microbial eukaryote trees exhibited more variation in rates of cladogenesis than prokaryote trees. We hypothesize that the contrast of macroevolutionary dynamics between prokaryotes and many eukaryotes is due, at least in part, to differences in the prevalence of lateral gene transfer (LGT) between the two groups. Inheritance is predominantly, if not wholly, vertical within eukaryotes, a feature that allows for the emergence and maintenance of heritable variation among lineages. By contrast, frequent LGT in prokaryotes may ameliorate heritable variation in rate of cladogenesis resulting from the emergence of key innovations; thus, the inferred difference in macroevolution might reflect exclusivity of key innovations in eukaryotes and their promiscuous nature in prokaryotes.}, }
@article {pmid15208628, year = {2004}, author = {Nakamura, Y and Itoh, T and Matsuda, H and Gojobori, T}, title = {Biased biological functions of horizontally transferred genes in prokaryotic genomes.}, journal = {Nature genetics}, volume = {36}, number = {7}, pages = {760-766}, doi = {10.1038/ng1381}, pmid = {15208628}, issn = {1061-4036}, mesh = {Algorithms ; *Gene Transfer, Horizontal ; Multigene Family ; }, abstract = {Horizontal gene transfer is one of the main mechanisms contributing to microbial genome diversification. To clarify the overall picture of interspecific gene flow among prokaryotes, we developed a new method for detecting horizontally transferred genes and their possible donors by Bayesian inference with training models for nucleotide composition. Our method gives the average posterior probability (horizontal transfer index) for each gene sequence, with a low horizontal transfer index indicating recent horizontal transfer. We found that 14% of open reading frames in 116 prokaryotic complete genomes were subjected to recent horizontal transfer. Based on this data set, we quantitatively determined that the biological functions of horizontally transferred genes, except mobile element genes, are biased to three categories: cell surface, DNA binding and pathogenicity-related functions. Thus, the transferability of genes seems to depend heavily on their functions.}, }
@article {pmid15207870, year = {2004}, author = {Burrus, V and Waldor, MK}, title = {Shaping bacterial genomes with integrative and conjugative elements.}, journal = {Research in microbiology}, volume = {155}, number = {5}, pages = {376-386}, doi = {10.1016/j.resmic.2004.01.012}, pmid = {15207870}, issn = {0923-2508}, mesh = {Attachment Sites, Microbiological/genetics ; Bacteriophages/*genetics ; Base Sequence/genetics ; Conjugation, Genetic/genetics ; DNA Transposable Elements/*genetics ; Drug Resistance, Bacterial/genetics ; F Factor/genetics ; Gene Rearrangement/genetics ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/genetics ; *Genome, Bacterial ; Genomic Instability ; Integration Host Factors/genetics ; Plasmids/*genetics ; }, abstract = {Integrative and conjugative elements (ICEs) are self-transmissible mobile genetic elements that are increasingly recognized to contribute to lateral gene flow in prokaryotes. ICEs, like most temperate bacteriophages integrate into the genome and like conjugative plasmids disseminate by conjugative transfer to new hosts. Thought of schematically, the structure of ICEs is similar to that of other types of the mobile elements; ICEs have a backbone composed of three modules ensuring maintenance, dissemination and regulation. This backbone can acquire additional functions probably through the action of insertion sequences, transposons and specific recombinases. Previously, ICEs were thought of as only vectors for transfer of antibiotic resistance genes, but it is now evident that ICEs can mediate the transfer of a very diverse set of functions. ICEs allow bacteria to rapidly adapt to new environmental conditions and to colonize new niches. Like phages and conjugative plasmids they also likely mediate the transfer of virulence determinants. ICEs shape the bacterial genome, promoting variability between strains of the same species and distributing genes between unrelated bacterial genera. Finally, we propose that by utilizing conserved integration sites, ICEs may promote the mobilization of genomic islands.}, }
@article {pmid15207869, year = {2004}, author = {Rainey, PB and Cooper, TF}, title = {Evolution of bacterial diversity and the origins of modularity.}, journal = {Research in microbiology}, volume = {155}, number = {5}, pages = {370-375}, doi = {10.1016/j.resmic.2004.01.011}, pmid = {15207869}, issn = {0923-2508}, mesh = {Base Composition ; Drug Resistance, Bacterial/genetics ; *Evolution, Molecular ; Gene Expression Regulation, Bacterial/genetics ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/genetics ; *Genetic Variation ; *Genome, Bacterial ; *Models, Biological ; Mutation/genetics ; Plasmids/genetics ; Pseudomonas/genetics ; Regulatory Sequences, Nucleic Acid/genetics ; Signal Transduction/*genetics ; }, abstract = {A characteristic feature of all organisms is modular organisation: the tendency for groups of genes to interact in such a way as to limit the extent of pleiotropic effects among characters belonging to different functional complexes. While the implications of modularity for the evolution of variability have been much discussed the evolutionary origins remain obscure. Here we develop a model, with special reference to signal transduction cascades of bacteria, which predicts that in the face of ecological opportunity and lateral gene transfer, selection will favour modular genome architectures because such architectures minimise the pleiotropic effects associated with accommodation of potentially beneficial foreign DNA.}, }
@article {pmid15207860, year = {2004}, author = {Arber, W}, title = {Biological evolution: lessons to be learned from microbial population biology and genetics.}, journal = {Research in microbiology}, volume = {155}, number = {5}, pages = {297-300}, doi = {10.1016/j.resmic.2004.01.009}, pmid = {15207860}, issn = {0923-2508}, mesh = {*Biological Evolution ; *Ecosystem ; *Environmental Microbiology ; *Evolution, Molecular ; Gene Rearrangement ; Gene Transfer, Horizontal ; Mutation ; }, }
@article {pmid15205695, year = {2004}, author = {Li, PF and Guo, YH and Li, Q and Yao, PY and Chen, GH}, title = {[Adenovirus-mediated gene transfer of rHSG-1 inhibits proliferation of vascular smooth muscle cells from spontaneously hypertensive rats].}, journal = {Beijing da xue xue bao. Yi xue ban = Journal of Peking University. Health sciences}, volume = {36}, number = {3}, pages = {259-262}, pmid = {15205695}, issn = {1671-167X}, mesh = {Adenoviridae/*genetics ; Animals ; Cell Cycle ; Cell Cycle Proteins/analysis ; Cell Division ; Cyclin-Dependent Kinase Inhibitor p27 ; Gene Transfer, Horizontal ; *Genetic Therapy ; Hyperplasia/*prevention &amp; control ; Hypertension/*pathology ; Male ; Muscle, Smooth, Vascular/*pathology ; Proliferating Cell Nuclear Antigen/analysis ; Rats ; Rats, Inbred SHR ; Transfection ; Tumor Suppressor Proteins/analysis ; }, abstract = {OBJECTIVE: To investigate the effect of rat hyperplasia suppressor gene-1(rHSG-1) on the proliferation of aortic vascular smooth muscle cells(VSMCs) from spontaneously hypertensive rats(SHR).<br><br>METHODS: VSMCs were transfected with an adenoviral vector expressing rHSG-1(Ad5rHSG-1). The effect of rHSG-1 on the proliferation of VSMCs was investigated by cell counting, MTT assay and (3)H-thymidine incorporation. We also analyzed the cell-cycle using flow cytometry and detected the expression of p27(Kip1) and p21(Cip1) by Western Blot.<br><br>RESULTS: The proliferation of VSMCs infected with Ad5rHSG-1 was inhibited a 40% reduction compared with the control group(P<0.01). The cell cycle was arrested in G(0)/G(1) phase and the expression of p27(Kip1) and p21(Cip1) was upregulated after the VSMCs transfection with Ad5rHSG-1.<br><br>CONCLUSION: Adenovirus-mediated gene transfer of rHSG-1 inhibits the cell cycle progression and thus the proliferation of VSMCs from SHR.}, }
@article {pmid15205432, year = {2004}, author = {Gomes, JP and Bruno, WJ and Borrego, MJ and Dean, D}, title = {Recombination in the genome of Chlamydia trachomatis involving the polymorphic membrane protein C gene relative to ompA and evidence for horizontal gene transfer.}, journal = {Journal of bacteriology}, volume = {186}, number = {13}, pages = {4295-4306}, pmid = {15205432}, issn = {0021-9193}, support = {R01 AI039499/AI/NIAID NIH HHS/United States ; R01 EY012219/EY/NEI NIH HHS/United States ; AI39499/AI/NIAID NIH HHS/United States ; EY/AI12219/EY/NEI NIH HHS/United States ; }, mesh = {Bacterial Outer Membrane Proteins/*genetics ; Base Composition ; Base Sequence ; Chlamydia trachomatis/*genetics ; DNA Transposable Elements ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Molecular Sequence Data ; Phylogeny ; *Recombination, Genetic ; }, abstract = {Genome sequencing of Chlamydia trachomatis serovar D has identified polymorphic membrane proteins (Pmp) that are a newly recognized protein family unique to the Chlamydiaceae family. Cumulative data suggest that these diverse proteins are expressed on the cell surface and might be immunologically important. We performed phylogenetic analyses and statistical modeling with 18 reference serovars and 1 genovariant of C. trachomatis to examine the evolutionary characteristics and comparative genetics of PmpC and pmpC, the gene that encodes this protein. We also examined 12 recently isolated ocular and urogenital clinical samples, since reference serovars are laboratory adapted and may not represent strains that are presently responsible for human disease. Phylogenetic reconstructions revealed a clear distinction for disease groups, corresponding to levels of tissue specificity and virulence of the organism. Further, the most prevalent serovars, E, F, and Da, formed a distinct clade. According to the results of comparative genetic analyses, these three genital serovars contained two putative insertion sequence (IS)-like elements with 10- and 15-bp direct repeats, respectively, while all other genital serovars contained one IS-like element. Ocular trachoma serovars also contained both insertions. Previously, no IS-like elements have been identified for Chlamydiaceae. Surprisingly, 7 (58%) of 12 clinical isolates revealed pmpC sequences that were identical to the sequences of other serovars, providing clear evidence for a high rate of whole-gene recombination. Recombination and the differential presence of IS-like elements among distinct disease and prevalence groups may contribute to genome plasticity, which may lead to adaptive changes in tissue tropism and pathogenesis over the course of the organism's evolution.}, }
@article {pmid15205409, year = {2004}, author = {Empadinhas, N and Albuquerque, L and Costa, J and Zinder, SH and Santos, MA and Santos, H and da Costa, MS}, title = {A gene from the mesophilic bacterium Dehalococcoides ethenogenes encodes a novel mannosylglycerate synthase.}, journal = {Journal of bacteriology}, volume = {186}, number = {13}, pages = {4075-4084}, pmid = {15205409}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; Base Sequence ; Chloroflexi/*enzymology/genetics ; Escherichia coli/genetics ; *Genes, Bacterial ; Mannosyltransferases/*genetics/isolation &amp; purification/physiology ; Molecular Sequence Data ; Open Reading Frames ; Recombinant Proteins/isolation &amp; purification ; Saccharomyces cerevisiae/genetics ; }, abstract = {Mannosylglycerate (MG) is a common compatible solute found in thermophilic and hyperthermophilic prokaryotes. In this study we characterized a mesophilic and bifunctional mannosylglycerate synthase (MGSD) encoded in the genome of the bacterium Dehalococcoides ethenogenes. mgsD encodes two domains with extensive homology to mannosyl-3-phosphoglycerate synthase (MPGS, EC 2.4.1.217) and to mannosyl-3-phosphoglycerate phosphatase (MPGP, EC 3.1.3.70), which catalyze the consecutive synthesis and dephosphorylation of mannosyl-3-phosphoglycerate to yield MG in Pyrococcus horikoshii, Thermus thermophilus, and Rhodothermus marinus. The bifunctional MGSD was overproduced in Escherichia coli, and we confirmed the combined MPGS and MPGP activities of the recombinant enzyme. The optimum activity of the enzyme was at 50 degrees C. To examine the properties of each catalytic domain of MGSD, we expressed them separately in E. coli. The monofunctional MPGS was unstable, while the MPGP was stable and was characterized. Dehalococcoides ethenogenes cannot be grown sufficiently to identify intracellular compatible solutes, and E. coli harboring MGSD did not accumulate MG. However, Saccharomyces cerevisiae expressing mgsD accumulated MG, confirming that this gene product can synthesize this compatible solute and arguing for a role in osmotic adjustment in the natural host. We did not detect MGSD activity in cell extracts of S. cerevisiae. Here we describe the first gene and enzyme for the synthesis of MG from a mesophilic microorganism and discuss the possible evolution of this bifunctional MGSD by lateral gene transfer from thermophilic and hyperthermophilic organisms.}, }
@article {pmid15199181, year = {2004}, author = {Sheahan, KL and Cordero, CL and Satchell, KJ}, title = {Identification of a domain within the multifunctional Vibrio cholerae RTX toxin that covalently cross-links actin.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, number = {26}, pages = {9798-9803}, pmid = {15199181}, issn = {0027-8424}, support = {F31 AI052490/AI/NIAID NIH HHS/United States ; T32 AI007476/AI/NIAID NIH HHS/United States ; AI051490/AI/NIAID NIH HHS/United States ; R01 AI051490-02/AI/NIAID NIH HHS/United States ; R01 AI051490/AI/NIAID NIH HHS/United States ; T32-AI07476/AI/NIAID NIH HHS/United States ; F31-AI52490/AI/NIAID NIH HHS/United States ; }, mesh = {Actins/*chemistry/*metabolism ; Acyltransferases/*chemistry/genetics/*metabolism ; Animals ; Bacterial Proteins/*chemistry/genetics/*metabolism ; Bacterial Toxins/*chemistry/genetics/*metabolism ; Cell Line ; Cell Size ; Chromosomes, Bacterial/genetics ; Epithelial Cells ; Gene Duplication ; Humans ; Larynx ; Molecular Weight ; Multienzyme Complexes/chemistry/genetics/metabolism ; Protein Structure, Tertiary ; Sequence Deletion/genetics ; Stress Fibers/chemistry/metabolism ; Structure-Activity Relationship ; Vibrio/metabolism ; Vibrio cholerae/*metabolism ; }, abstract = {The Gram-negative pathogen Vibrio cholerae causes diarrheal disease through the export of enterotoxins. The V. cholerae RTX toxin was previously identified and characterized by its ability to round human laryngeal epithelial (HEp-2) cells. Further investigation determined that cell rounding is caused by the depolymerization of actin stress fibers, through the unique mechanism of covalent actin cross-linking. In this study, we identify a domain within the full-length RTX toxin that is capable of mediating the cross-linking reaction when transiently expressed within eukaryotic cells. A structure/function analysis of the actin cross-linking domain (ACD) reveals that a 412-aa, or a 47.8-kDa, region is essential for cross-linking activity. When this domain is deleted from the full-length toxin gene, actin cross-linking, but not cell rounding, is eliminated, indicating that this toxin carries multiple dissociable activities. The ACD shares 59% amino acid identity with a hypothetical protein from V. cholerae, VC1416, and transient expression of the C-terminal domain of VC1416 also results in actin cross-linking in eukaryotic cells. The presence of this second ACD linked to an Rhs-like element suggests that V. cholerae acquired the domain by horizontal gene transfer and the ACD was inserted into the RTX toxin by gene duplication through the evolution of V. cholerae.}, }
@article {pmid15197509, year = {2004}, author = {Hong, SH and Kim, TY and Lee, SY}, title = {Phylogenetic analysis based on genome-scale metabolic pathway reaction content.}, journal = {Applied microbiology and biotechnology}, volume = {65}, number = {2}, pages = {203-210}, doi = {10.1007/s00253-004-1641-3}, pmid = {15197509}, issn = {0175-7598}, mesh = {Archaea/metabolism ; Bacteria/metabolism ; *Computational Biology ; Evolution, Molecular ; Fungi/metabolism ; Genetics, Microbial ; *Genome, Archaeal ; *Genome, Bacterial ; *Genome, Fungal ; *Phylogeny ; }, abstract = {Phylogenetic classifications based on single genes such as rRNA genes do not provide a complete and accurate picture of evolution because they do not account for evolutionary leaps caused by gene transfer, duplication, deletion and functional replacement. Here, we present a whole-genome-scale phylogeny based on metabolic pathway reaction content. From the genome sequences of 42 microorganisms, we deduced the metabolic pathway reactions and used the relatedness of these contents to construct a phylogenetic tree that represents the similarity of metabolic profiles (relatedness) as well as the extent of metabolic pathway similarity (evolutionary distance). This method accounts for horizontal gene transfer and specific gene loss by comparison of whole metabolic subpathways, and allows evaluation of evolutionary relatedness and changes in metabolic pathways. Thus, a tree based on metabolic pathway content represents both the evolutionary time scale (changes in genetic content) and the evolutionary process (changes in metabolism).}, }
@article {pmid15196766, year = {2004}, author = {Hägg, P and de Pohl, JW and Abdulkarim, F and Isaksson, LA}, title = {A host/plasmid system that is not dependent on antibiotics and antibiotic resistance genes for stable plasmid maintenance in Escherichia coli.}, journal = {Journal of biotechnology}, volume = {111}, number = {1}, pages = {17-30}, doi = {10.1016/j.jbiotec.2004.03.010}, pmid = {15196766}, issn = {0168-1656}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*biosynthesis/genetics ; Cell Proliferation ; Drug Resistance, Bacterial/genetics ; Gene Expression Regulation, Bacterial/genetics ; Gene Transfer Techniques ; Genetic Enhancement/methods ; Genomic Instability/genetics ; Plasmids/*genetics ; Prokaryotic Initiation Factor-1/*genetics/*metabolism ; Protein Engineering/*methods ; Recombinant Proteins/*biosynthesis ; Transformation, Bacterial/*genetics ; }, abstract = {Uneven distribution of plasmid-based expression vectors to daughter cells during bacterial cell division results in an increasing proportion of plasmid free cells during growth. This is a major industrial problem leading to reduction of product yields and increased production costs during large-scale cultivation of vector-carrying bacteria. For this reason, a selection must be provided that kills the plasmid free cells. The most conventional method to obtain this desired selection is to insert some gene for antibiotic resistance in the plasmid and then grow the bacteria in the presence of the corresponding antibiotic. We describe here a host/plasmid Escherichia coli system with a totally stable plasmid that can be maintained without the use of antibiotic selection. The plasmid is maintained, since it carries the small essential gene infA (coding for translation initiation factor 1, IF1) in an E. coli strain that has been deleted for its chromosomal infA gene. As a result only plasmid carrying cells can grow, making the strain totally dependent on the maintenance of the plasmid. A selection based on antibiotics is thus not necessary during cultivation, and no antibiotic-resistance genes are present neither in the final strain nor in the final plasmid. Plasmid-free cells do not accumulate even after an extended period of continuous growth. Growth rates of the control and the plasmid harboring strains are indistinguishable from each other in both LB and defined media. The indicated approach can be used to modify existing production strains and plasmids to the described concept. The infA based plasmid stability system should eliminate industrial cultivation problems caused by the loss of expression vector and use of antibiotics in the cultivation medium. Also environmental problems caused by release of antibiotics and antibiotic resistance genes, that potentially can give horizontal gene transfer between bacterial populations, are eliminated.}, }
@article {pmid15194191, year = {2004}, author = {Iyer, LM and Koonin, EV and Aravind, L}, title = {Evolution of bacterial RNA polymerase: implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer.}, journal = {Gene}, volume = {335}, number = {}, pages = {73-88}, doi = {10.1016/j.gene.2004.03.017}, pmid = {15194191}, issn = {0378-1119}, mesh = {Amino Acid Sequence ; Bacteria/classification/*enzymology/genetics ; Binding Sites/genetics ; Catalytic Domain/genetics ; DNA-Directed RNA Polymerases/chemistry/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Protein Conformation ; Protein Subunits/chemistry/genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; Sigma Factor/chemistry/genetics ; }, abstract = {Comparative analysis of the domain architectures of the beta, beta', and sigma(70) subunits of bacterial DNA-dependent RNA polymerases (DdRp), combined with sequence-based phylogenetic analysis, revealed a fundamental split among bacteria. DNA-dependent RNA polymerase subunits of Group I, which includes Proteobacteria, Aquifex, Chlamydia, Spirochaetes, Cytophaga-Chlorobium, and Planctomycetes, are characterized by three distinct inserts, namely a Sandwich Barrel Hybrid Motif domain in the beta subunit, a beta-beta' module (BBM) 1 domain in the beta' subunit, and a distinct helical module in the sigma subunit. The DdRp subunits of remaining bacteria, which comprise Group II, lack these inserts, although some additional inserted domains are present in individual lineages. The separation of bacteria into Group I and Group II is generally compatible with the topologies of phylogenetic trees of the conserved regions of DdRp subunits and concatenated ribosomal proteins and might represent the primary bifurcation in bacterial evolution. A striking deviation from this evolutionary pattern is Aquifex whose DdRp subunits cluster within Group I, whereas phylogenetic analysis of ribosomal proteins identifies Aquifex as grouping with Thermotoga another bacterial hyperthemophile belonging to Group II. The inferred evolutionary scenario for the DdRp subunits includes domain accretion and rearrangement, with some likely horizontal transfer events. Although evolution of bacterial DdRp appeared to be generally dominated by vertical inheritance, horizontal transfer of complete genes for all or some of the subunits, resulting in displacement of the ancestral genes, might have played a role in several lineages, such as Aquifex, Thermotoga, and Fusobacterium.}, }
@article {pmid15194125, year = {2004}, author = {Weldhagen, GF}, title = {Integrons and beta-lactamases--a novel perspective on resistance.}, journal = {International journal of antimicrobial agents}, volume = {23}, number = {6}, pages = {556-562}, doi = {10.1016/j.ijantimicag.2004.03.007}, pmid = {15194125}, issn = {0924-8579}, mesh = {Acinetobacter baumannii/drug effects/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Enterobacteriaceae/drug effects/genetics ; Gene Transfer, Horizontal ; *Integrons ; Pseudomonas aeruginosa/drug effects/genetics ; Selection, Genetic ; beta-Lactam Resistance/*genetics ; beta-Lactamases/biosynthesis/genetics/*metabolism ; }, abstract = {The understanding of microbial resistance to the beta-lactam class of antibiotics in the form of beta-lactamases has come a long way since the early discoveries of narrow-spectrum penicillinases. Integron-borne beta-lactamases co-occurring with a wide array of non-beta-lactam resistance genes, particularly pose an increasing threat to the nosocomial environment, giving rise to multi-drug resistant microbes with complex resistance patterns. Selection of potent beta-lactamases through the use of non-beta-lactam agents may be possible through integron-mediated resistance. It has become imperative that we should continuously strive to understand these complex mechanisms of antimicrobial resistance, not only to overcome them, but to avoid them from evolving further.}, }
@article {pmid15194124, year = {2004}, author = {Miriagou, V and Tassios, PT and Legakis, NJ and Tzouvelekis, LS}, title = {Expanded-spectrum cephalosporin resistance in non-typhoid Salmonella.}, journal = {International journal of antimicrobial agents}, volume = {23}, number = {6}, pages = {547-555}, doi = {10.1016/j.ijantimicag.2004.03.006}, pmid = {15194124}, issn = {0924-8579}, mesh = {Bacterial Proteins/*biosynthesis/genetics/*metabolism ; *Cephalosporin Resistance/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Gene Transfer, Horizontal ; Humans ; Plasmids/genetics ; Salmonella/*drug effects/genetics/isolation &amp; purification ; Salmonella Infections/drug therapy/microbiology ; beta-Lactamases/*biosynthesis/genetics/*metabolism ; beta-Lactams/therapeutic use ; }, abstract = {Expanded-spectrum cephalosporins (ESCs) such as ceftriaxone, together with fluorinated quinolones, are the choice antibiotics in the treatment of invasive salmonella infections. Resistance to ESCs among non-typhoid salmonella has been recognised since the late 1980s. Currently, ESC-resistant salmonella strains are reported world-wide and in some areas their incidence is significant. Resistance is mainly due to acquisition of multi-resistant plasmids encoding a variety of extended-spectrum and AmpC-type beta-lactamases. The origins of ESC-resistant salmonellae are diverse. Exchange of resistance determinants between salmonellae and nosocomial enterobacteria seems to be frequent, at least in developing countries. Also, the use of newer beta-lactams in animal husbandry and veterinary medicine may have facilitated the spread of ESC-resistant salmonella strains in livestock.}, }
@article {pmid15186489, year = {2004}, author = {Budd, A and Blandin, S and Levashina, EA and Gibson, TJ}, title = {Bacterial alpha2-macroglobulins: colonization factors acquired by horizontal gene transfer from the metazoan genome?.}, journal = {Genome biology}, volume = {5}, number = {6}, pages = {R38}, pmid = {15186489}, issn = {1474-760X}, mesh = {Alphaproteobacteria/genetics ; Amino Acid Sequence/genetics ; Bacterial Proteins/genetics ; Bacteroidetes/genetics ; Betaproteobacteria/genetics ; Computational Biology/methods ; Cyanobacteria/genetics ; Databases, Protein ; Fusobacteria/genetics ; Gene Expression Profiling/methods ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/genetics ; *Genome, Bacterial ; Humans ; Magnetospirillum/genetics ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis/methods ; Phylogeny ; Spirochaetales/genetics ; alpha-Macroglobulins/*genetics ; }, abstract = {BACKGROUND: Invasive bacteria are known to have captured and adapted eukaryotic host genes. They also readily acquire colonizing genes from other bacteria by horizontal gene transfer. Closely related species such as Helicobacter pylori and Helicobacter hepaticus, which exploit different host tissues, share almost none of their colonization genes. The protease inhibitor alpha2-macroglobulin provides a major metazoan defense against invasive bacteria, trapping attacking proteases required by parasites for successful invasion.<br><br>RESULTS: Database searches with metazoan alpha2-macroglobulin sequences revealed homologous sequences in bacterial proteomes. The bacterial alpha2-macroglobulin phylogenetic distribution is patchy and violates the vertical descent model. Bacterial alpha2-macroglobulin genes are found in diverse clades, including purple bacteria (proteobacteria), fusobacteria, spirochetes, bacteroidetes, deinococcids, cyanobacteria, planctomycetes and thermotogae. Most bacterial species with bacterial alpha2-macroglobulin genes exploit higher eukaryotes (multicellular plants and animals) as hosts. Both pathogenically invasive and saprophytically colonizing species possess bacterial alpha2-macroglobulins, indicating that bacterial alpha2-macroglobulin is a colonization rather than a virulence factor.<br><br>CONCLUSIONS: Metazoan alpha2-macroglobulins inhibit proteases of pathogens. The bacterial homologs may function in reverse to block host antimicrobial defenses. Alpha2-macroglobulin was probably acquired one or more times from metazoan hosts and has then spread widely through other colonizing bacterial species by more than 10 independent horizontal gene transfers. yfhM-like bacterial alpha2-macroglobulin genes are often found tightly linked with pbpC, encoding an atypical peptidoglycan transglycosylase, PBP1C, that does not function in vegetative peptidoglycan synthesis. We suggest that YfhM and PBP1C are coupled together as a periplasmic defense and repair system. Bacterial alpha2-macroglobulins might provide useful targets for enhancing vaccine efficacy in combating infections.}, }
@article {pmid15186450, year = {2004}, author = {Avrain, L and Vernozy-Rozand, C and Kempf, I}, title = {Evidence for natural horizontal transfer of tetO gene between Campylobacter jejuni strains in chickens.}, journal = {Journal of applied microbiology}, volume = {97}, number = {1}, pages = {134-140}, doi = {10.1111/j.1365-2672.2004.02306.x}, pmid = {15186450}, issn = {1364-5072}, mesh = {Animals ; Bacterial Proteins/*genetics ; Campylobacter jejuni/*genetics/metabolism ; Carrier Proteins/*genetics ; Chickens/*microbiology ; Drug Resistance, Bacterial/*genetics ; Flagellin/genetics ; Gene Transfer, Horizontal ; Intestines/microbiology ; Ribotyping ; Tetracycline Resistance/*genetics ; }, abstract = {AIMS: The transfer of tetO gene conferring resistance to tetracycline was studied between Campylobacter jejuni strains, in the digestive tract of chickens.<br><br>METHODS AND RESULTS: In vitro conjugation experiments were first performed in order to select donor/recipient couples for further in vivo assay. Then, chickens were inoculated with a donor/recipient couple of C. jejuni strains displaying spontaneous in vitro tetracycline resistance gene transfer. The donor was a tetracycline-resistant ampicillin-susceptible strain, and the recipient was a tetracycline-susceptible ampicillin-resistant strain. Chicken droppings were streaked on antimicrobial selective media and bi-resistant Campylobacter isolates were further characterized according to their donor or recipient flaA gene RFLP profile. The acquisition of tetracycline-resistance gene by the recipient C. jejuni strain from the donor C. jejuni strain was confirmed by tetO PCR.<br><br>CONCLUSIONS: The study showed that transfer of tetO gene occurs rapidly and without antimicrobial selection pressure between C. jejuni strains in the digestive tract of chickens.<br><br>The rapid and spontaneous transfer of tetO gene may explain the high prevalence of tetracycline resistance in chicken Campylobacter strains.}, }
@article {pmid15186355, year = {2004}, author = {Espeland, EM and Lipp, EK and Huq, A and Colwell, RR}, title = {Polylysogeny and prophage induction by secondary infection in Vibrio cholerae.}, journal = {Environmental microbiology}, volume = {6}, number = {7}, pages = {760-763}, doi = {10.1111/j.1462-2920.2004.00603.x}, pmid = {15186355}, issn = {1462-2912}, mesh = {Bacterial Typing Techniques ; DNA, Viral/analysis/isolation &amp; purification ; Electrophoresis, Agar Gel ; Gene Transfer, Horizontal ; *Lysogeny ; Microscopy, Electron ; Mitomycin/pharmacology ; Nucleic Acid Synthesis Inhibitors/pharmacology ; Prophages/genetics/*growth &amp; development/ultrastructure ; Vibrio cholerae O1/*virology ; *Virus Activation ; }, abstract = {Strains of Vibrio cholerae O1, biotypes El Tor and classical, were infected with a known temperate phage (PhiP15) and monitored over a 15-day period for prophage induction. Over the course of the experiment two morphologically and three genomically distinct virus-like particles were observed from the phage-infected El Tor strain by transmission electron microscopy and field inversion gel electrophoresis, respectively, whereas only one phage, PhiP15, was observed from the infected classical strain. In the uninfected El Tor culture one prophage was spontaneously induced after 6 days. No induction in either strain was observed after treatment with mitomycin C. Data indicate that El Tor biotypes of V. cholerae may be polylysogenic and that secondary infection can promote multiple prophage induction. These traits may be important in the transfer of genetic material among V. cholerae by providing an environmentally relevant route for multiple prophage propagation and transmission.}, }
@article {pmid15186344, year = {2004}, author = {Trefault, N and De la Iglesia, R and Molina, AM and Manzano, M and Ledger, T and Pérez-Pantoja, D and Sánchez, MA and Stuardo, M and González, B}, title = {Genetic organization of the catabolic plasmid pJP4 from Ralstonia eutropha JMP134 (pJP4) reveals mechanisms of adaptation to chloroaromatic pollutants and evolution of specialized chloroaromatic degradation pathways.}, journal = {Environmental microbiology}, volume = {6}, number = {7}, pages = {655-668}, doi = {10.1111/j.1462-2920.2004.00596.x}, pmid = {15186344}, issn = {1462-2912}, mesh = {*Adaptation, Physiological ; Base Composition ; Biodegradation, Environmental ; Cupriavidus necator/*genetics/*metabolism ; DNA Transposable Elements ; DNA, Bacterial/chemistry/isolation &amp; purification ; Drug Resistance, Bacterial/genetics ; Environmental Pollutants/*metabolism ; Gene Order ; Gene Transfer, Horizontal ; Genes, Bacterial ; Hydrocarbons, Aromatic/*metabolism ; Mercury Compounds/toxicity ; Molecular Sequence Data ; Open Reading Frames ; Operon ; Plasmids/*genetics ; Recombination, Genetic ; Sequence Analysis, DNA ; Transcription, Genetic ; }, abstract = {Ralstonia eutropha JMP134 (pJP4) is a useful model for the study of bacterial degradation of substituted aromatic pollutants. Several key degrading capabilities, encoded by tfd genes, are located in the 88 kb, self-transmissible, IncP-1 beta plasmid pJP4. The complete sequence of the 87,688 nucleotides of pJP4, encoding 83 open reading frames (ORFs), is reported. Most of the coding sequence corresponds to a well-conserved IncP-1 beta backbone and the previously reported tfd genes. In addition, we found hypothetical proteins putatively involved in the transport of aromatic compounds and short-chain fatty acid oxidation. ORFs related to mobile elements, including the Tn501-encoded mercury resistance determinants, an IS1071-based composite transposon and a cryptic class II transposon, are also present in pJP4. These mobile elements are inefficient in transposition and are located in two regions of pJP4 that are rich in remnants of lateral gene transfer events. pJP4 plasmid was able to capture chromosomal genes and form hybrid plasmids with the IncP-1 alpha plasmid RP4. These observations are integrated into a model for the evolution of pJP4, which reveals mechanisms of bacterial adaptation to degrade pollutants.}, }
@article {pmid15185190, year = {2004}, author = {Angulo, FJ and Baker, NL and Olsen, SJ and Anderson, A and Barrett, TJ}, title = {Antimicrobial use in agriculture: controlling the transfer of antimicrobial resistance to humans.}, journal = {Seminars in pediatric infectious diseases}, volume = {15}, number = {2}, pages = {78-85}, doi = {10.1053/j.spid.2004.01.010}, pmid = {15185190}, issn = {1045-1870}, mesh = {Animal Feed ; *Animal Husbandry ; Animals ; Anti-Bacterial Agents/*administration &amp; dosage/*pharmacology/therapeutic use ; Bacterial Infections/*drug therapy/microbiology ; Campylobacter/*drug effects ; Campylobacter Infections/drug therapy ; Drug Resistance, Bacterial/*genetics ; Drug Utilization ; Enterococcus/drug effects/genetics ; Escherichia coli/drug effects/genetics ; Food Microbiology ; Gene Transfer, Horizontal ; Humans ; Salmonella/*drug effects ; Salmonella Infections/drug therapy ; }, abstract = {Salmonella and Campylobacter infections occur commonly in children. Some of these infections are severe, requiring treatment with antimicrobial agents. Many classes of antimicrobial agents that are used in humans also are used in food animals for growth promotion, disease prevention, and therapy. The use of such antimicrobial agents in food animals increases the likelihood that human bacterial pathogens that have food animal reservoirs, such as Salmonella or Campylobacter, will develop cross-resistance to drugs approved for use in human medicine. Resistance determinants also may be transmitted from food animals to humans through the food supply with bacteria that usually are commensal, such as Escherichia coli and enterococci. Clinicians should be aware that antimicrobial resistance is increasing in food-borne pathogens and that patients who are taking antimicrobial agents for any reason are at increased risk for acquiring antimicrobial-resistant food-borne infections. Several European countries have demonstrated that restricting the use of antimicrobial agents in food animals can be followed by a decrease in antimicrobial resistance in humans without compromising animal health or significantly increasing the cost of production. Appropriate use of antimicrobial agents in humans and food animals is an important factor in maintaining their effectiveness.}, }
@article {pmid15184891, year = {2004}, author = {Maier, B and Chen, I and Dubnau, D and Sheetz, MP}, title = {DNA transport into Bacillus subtilis requires proton motive force to generate large molecular forces.}, journal = {Nature structural &amp; molecular biology}, volume = {11}, number = {7}, pages = {643-649}, pmid = {15184891}, issn = {1545-9993}, support = {R01 GM043756/GM/NIGMS NIH HHS/United States ; GM3677/GM/NIGMS NIH HHS/United States ; GM43756/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacillus subtilis/*metabolism ; Biological Transport ; DNA/*metabolism ; Protons ; }, abstract = {Bacteria can acquire genetic diversity, including antibiotic resistance and virulence traits, by horizontal gene transfer. In particular, many bacteria are naturally competent for uptake of naked DNA from the environment in a process called transformation. Here, we used optical tweezers to demonstrate that the DNA transport machinery in Bacillus subtilis is a force-generating motor. Single DNA molecules were processively transported in a linear fashion without observable pausing events. Uncouplers inhibited DNA uptake immediately, suggesting that the transmembrane proton motive force is needed for DNA translocation. We found an uptake rate of 80 +/- 10 bp s(-1) that was force-independent at external forces <40 pN, indicating that a powerful molecular machine supports DNA transport.}, }
@article {pmid15184674, year = {2004}, author = {Fütterer, O and Angelov, A and Liesegang, H and Gottschalk, G and Schleper, C and Schepers, B and Dock, C and Antranikian, G and Liebl, W}, title = {Genome sequence of Picrophilus torridus and its implications for life around pH 0.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, number = {24}, pages = {9091-9096}, pmid = {15184674}, issn = {0027-8424}, mesh = {Base Sequence ; Genome, Archaeal ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Open Reading Frames/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Thermoplasmales/*genetics/metabolism/physiology ; }, abstract = {The euryarchaea Picrophilus torridus and Picrophilus oshimae are able to grow around pH 0 at up to 65 degrees C, thus they represent the most thermoacidophilic organisms known. Several features that may contribute to the thermoacidophilic survival strategy of P. torridus were deduced from analysis of its 1.55-megabase genome. P. torridus has the smallest genome among nonparasitic aerobic microorganisms growing on organic substrates and simultaneously the highest coding density among thermoacidophiles. An exceptionally high ratio of secondary over ATP-consuming primary transport systems demonstrates that the high proton concentration in the surrounding medium is extensively used for transport processes. Certain genes that may be particularly supportive for the extreme lifestyle of P. torridus appear to have been internalized into the genome of the Picrophilus lineage by horizontal gene transfer from crenarchaea and bacteria. Finally, it is noteworthy that the thermoacidophiles from phylogenetically distant branches of the Archaea apparently share an unexpectedly large pool of genes.}, }
@article {pmid15184557, year = {2004}, author = {Krzywinska, E and Krzywinski, J and Schorey, JS}, title = {Naturally occurring horizontal gene transfer and homologous recombination in Mycobacterium.}, journal = {Microbiology (Reading, England)}, volume = {150}, number = {Pt 6}, pages = {1707-1712}, doi = {10.1099/mic.0.27088-0}, pmid = {15184557}, issn = {1350-0872}, mesh = {Animals ; Bacterial Proteins/chemistry/*genetics ; Base Sequence ; *Gene Transfer, Horizontal ; Glycolipids/*biosynthesis ; Glycopeptides/*biosynthesis ; Molecular Sequence Data ; Multigene Family ; Mycobacterium avium/*genetics ; *Recombination, Genetic ; }, abstract = {Acquisition of genetic information through horizontal gene transfer (HGT) is an important evolutionary process by which micro-organisms gain novel phenotypic characteristics. In pathogenic bacteria, for example, it facilitates maintenance and enhancement of virulence and spread of drug resistance. In the genus Mycobacterium, to which several primary human pathogens belong, HGT has not been clearly demonstrated. The few existing reports suggesting this process are based on circumstantial evidence of similarity of sequences found in distantly related species. Here, direct evidence of HGT between strains of Mycobacterium avium representing two different serotypes is presented. Conflicting evolutionary histories of genes encoding elements of the glycopeptidolipid (GPL) biosynthesis pathway led to an analysis of the GPL cluster genomic sequences from four Mycobacterium avium strains. The sequence of M. avium strain 2151 appeared to be a mosaic consisting of three regions having alternating identities to either M. avium strains 724 or 104. Maximum-likelihood estimation of two breakpoints allowed a approximately 4100 bp region horizontally transferred into the strain 2151 genome to be pinpointed with confidence. The maintenance of sequence continuity at both breakpoints and the lack of insertional elements at these sites strongly suggest that the integration of foreign DNA occurred by homologous recombination. To our knowledge, this is the first report to demonstrate naturally occurring homologous recombination in Mycobacterium. This previously undiscovered mechanism of genetic exchange may have major implications for the understanding of Mycobacterium pathogenesis.}, }
@article {pmid15184163, year = {2004}, author = {Bianciotto, V and Genre, A and Jargeat, P and Lumini, E and Bécard, G and Bonfante, P}, title = {Vertical transmission of endobacteria in the arbuscular mycorrhizal fungus Gigaspora margarita through generation of vegetative spores.}, journal = {Applied and environmental microbiology}, volume = {70}, number = {6}, pages = {3600-3608}, pmid = {15184163}, issn = {0099-2240}, mesh = {Bacteria/classification/*genetics/growth &amp; development/isolation &amp; purification ; Culture Media ; Cytoplasm/microbiology ; DNA, Ribosomal/analysis ; Daucus carota/microbiology ; Fungi/*genetics/physiology/ultrastructure ; *Gene Transfer, Horizontal ; Microscopy, Confocal ; Molecular Sequence Data ; *Mycorrhizae ; Plant Roots/microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 23S/genetics ; Soil Microbiology ; Spores, Fungal/*genetics ; Symbiosis ; }, abstract = {Arbuscular mycorrhizal (AM) fungi living in symbiotic association with the roots of vascular plants have also been shown to host endocellular rod-shaped bacteria. Based on their ribosomal sequences, these endobacteria have recently been identified as a new taxon, Candidatus Glomeribacter gigasporarum. In order to investigate the cytoplasmic stability of the endobacteria in their fungal host and their transmission during AM fungal reproduction (asexual), a system based on transformed carrot roots and single-spore inocula of Gigaspora margarita was used. Under these in vitro sterile conditions, with no risk of horizontal contamination, the propagation of endobacteria could be monitored, and it was shown, by using primers designed for both 16S and 23S ribosomal DNAs, to occur through several vegetative spore generations (SG0 to SG4). A method of confocal microscopy for quantifying the density of endobacteria in spore cytoplasm was designed and applied; endobacteria were consistently found in all of the spore generations, although their number rapidly decreased from SG0 to SG4. The study demonstrates that a vertical transmission of endobacteria takes place through the fungal vegetative generations (sporulation) of an AM fungus, indicating that active bacterial proliferation occurs in the coenocytic mycelium of the fungus, and suggests that these bacteria are obligate endocellular components of their AM fungal host.}, }
@article {pmid15184125, year = {2004}, author = {Thacker, RW and Paul, VJ}, title = {Morphological, chemical, and genetic diversity of tropical marine cyanobacteria Lyngbya spp. and Symploca spp. (Oscillatoriales).}, journal = {Applied and environmental microbiology}, volume = {70}, number = {6}, pages = {3305-3312}, pmid = {15184125}, issn = {0099-2240}, mesh = {Bacterial Typing Techniques ; Cyanobacteria/*chemistry/*classification/genetics/ultrastructure ; DNA, Ribosomal/analysis ; *Genetic Variation ; Guam ; Molecular Sequence Data ; Palau ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; *Tropical Climate ; }, abstract = {Although diverse natural products have been isolated from the benthic, filamentous cyanobacterium Lyngbya majuscula, it is unclear whether this chemical variation can be used to establish taxonomic relationships among disparate collections. We compared morphological characteristics, secondary-metabolite compositions, and partial 16S ribosomal DNA (rDNA) sequences among several collections of L. majuscula Gomont, Lyngbya spp., and Symploca spp. from Guam and the Republic of Palau. The morphological characteristics examined were cell length, cell width, and the presence or absence of a calyptra. Secondary metabolites were analyzed by two-dimensional thin-layer chromatography. Each collection possessed a distinct cellular morphology that readily distinguished Lyngbya spp. from Symploca spp. Each collection yielded a unique chemotype, but common chemical characteristics were shared among four collections of L. majuscula. A phylogeny based on secondary-metabolite composition supported the reciprocal monophyly of Lyngbya and Symploca but yielded a basal polytomy for Lyngbya. Pairwise sequence divergence among species ranged from 10 to 14% across 605 bp of 16S rDNA, while collections of L. majuscula showed 0 to 1.3% divergence. Although the phylogeny of 16S rDNA sequences strongly supported the reciprocal monophyly of Lyngbya and Symploca as well as the monophyly of Lyngbya bouillonii and L. majuscula, genetic divergence was not correlated with chemical and morphological differences. These data suggest that 16S rDNA sequence analyses do not predict chemical variability among Lyngbya species. Other mechanisms, including higher rates of evolution for biosynthetic genes, horizontal gene transfer, and interactions between different genotypes and environmental conditions, may play important roles in generating qualitative and quantitative chemical variation within and among Lyngbya species.}, }
@article {pmid15183889, year = {2004}, author = {Lester, CH and Frimodt-Moller, N and Hammerum, AM}, title = {Conjugal transfer of aminoglycoside and macrolide resistance between Enterococcus faecium isolates in the intestine of streptomycin-treated mice.}, journal = {FEMS microbiology letters}, volume = {235}, number = {2}, pages = {385-391}, doi = {10.1016/j.femsle.2004.04.050}, pmid = {15183889}, issn = {0378-1097}, mesh = {Aminoglycosides/*pharmacology ; Animals ; Anti-Bacterial Agents/administration &amp; dosage/*pharmacology ; Bacterial Proteins/genetics ; *Conjugation, Genetic ; Drug Resistance, Multiple, Bacterial/*genetics ; Enterococcus faecium/*drug effects/genetics ; Female ; *Gene Transfer, Horizontal ; Humans ; Intestines/microbiology ; Macrolides/*pharmacology ; Mice ; Microbial Sensitivity Tests ; Streptomycin/administration &amp; dosage/pharmacology ; }, abstract = {The purpose was to study conjugal transfer of resistance genes between a multi-resistant Enterococcus faecium isolate and a sensitive E. faecium isolate. Co-transfer of erm(B)-Tn5405-like element and aac(6')-Ie-aph(2'')-Ia was obtained in both in vivo and in vitro. Plasmid profiles and Southern blots showed that both the erm(B)-Tn5405-like element and aac(6')-Ie-aph(2'')-Ia were placed on the same large plasmid (>147 kb). These data show to our knowledge the first co-transfer of the erm(B)-Tn5405-like element and aac(6')-Ie-aph(2'')-Ia. The in vivo study also indicates that transfer of resistance genes between enterococci might occur under natural conditions in the gut of animals.}, }
@article {pmid15183871, year = {2004}, author = {Bai, X and Zhang, J and Holford, IR and Hogenhout, SA}, title = {Comparative genomics identifies genes shared by distantly related insect-transmitted plant pathogenic mollicutes.}, journal = {FEMS microbiology letters}, volume = {235}, number = {2}, pages = {249-258}, doi = {10.1016/j.femsle.2004.04.043}, pmid = {15183871}, issn = {0378-1097}, mesh = {Animals ; Bacterial Proteins/genetics ; Computational Biology/methods ; *Genome, Bacterial ; *Genomics ; Humans ; Insect Vectors/*microbiology ; Molecular Sequence Data ; Mycoplasma/genetics ; Open Reading Frames/genetics ; Phylogeny ; Phytoplasma/genetics ; Plant Diseases/*microbiology ; Spiroplasma/genetics ; Tenericutes/*genetics/pathogenicity ; }, abstract = {Phytoplasmas and spiroplasmas are distantly related insect-transmitted plant pathogens within the class Mollicutes. Genome sequencing projects of phytoplasma strain Aster Yellows-Witches' Broom (AY-WB) and Spiroplasma kunkelii are near completion. Complete genome sequences of seven obligate animal and human pathogenic mollicutes (Mycoplasma and Ureaplasma spp.), and OY phytoplasma have been reported. Putative ORFs predicted from the genome sequences of AY-WB and S. kunkelii were compared to those of the completed genomes. This resulted in identification of at least three ORFs present in AY-WB, OY and S. kunkelii but not in the obligate animal and human pathogenic mollicutes. Moreover, we identified ORFs that seemed more closely related between AY-WB and S. kunkelii than to their mycoplasma counterparts. Phylogenetic analyses using parsimony were employed to study the origin of these genes, resulting in identification of one gene that may have undergone horizontal gene transfer. The possible involvement of these genes in plant pathogenicity is discussed.}, }
@article {pmid15183058, year = {2004}, author = {Glasgow, JN and Kremer, EJ and Hemminki, A and Siegal, GP and Douglas, JT and Curiel, DT}, title = {An adenovirus vector with a chimeric fiber derived from canine adenovirus type 2 displays novel tropism.}, journal = {Virology}, volume = {324}, number = {1}, pages = {103-116}, doi = {10.1016/j.virol.2004.03.028}, pmid = {15183058}, issn = {0042-6822}, support = {P50 CA89019/CA/NCI NIH HHS/United States ; R01 AG021875/AG/NIA NIH HHS/United States ; R01 CA090547/CA/NCI NIH HHS/United States ; R01 CA86881/CA/NCI NIH HHS/United States ; R01 CA93796/CA/NCI NIH HHS/United States ; R01 HL67962/HL/NHLBI NIH HHS/United States ; T32 CA75930/CA/NCI NIH HHS/United States ; }, mesh = {Adenoviruses, Canine/*physiology ; Adenoviruses, Human/*genetics ; Animals ; CHO Cells ; Cell Line ; Coxsackie and Adenovirus Receptor-Like Membrane Protein ; Cricetinae ; Gene Transfer, Horizontal ; *Genetic Therapy ; *Genetic Vectors ; Humans ; Integrins/physiology ; Luciferases/genetics ; Receptors, Virus/physiology ; Recombinant Fusion Proteins/genetics ; Transduction, Genetic ; Tropism ; }, abstract = {Many clinically relevant tissues are refractory to Ad5 transduction because of negligible levels of the primary Ad5 receptor, the coxsackie and adenovirus receptor (CAR). Thus, development of Ad vectors that display CAR-independent tropism could lead directly to therapeutic gain. The Toronto strain of canine adenovirus type 2 (CAV2) exhibits native tropism that is augmented by, but not fully dependent upon, CAR for cellular transduction. We hypothesized that an Ad5 vector containing the nonhuman CAV2 knob would provide expanded tropism and constructed Ad5Luc1-CK, an E1-deleted Ad5 vector encoding the fiber knob domain from CAV2. Ad5Luc1-CK gene delivery to CAR-deficient cells was augmented up to 30-fold versus the Ad5 control vector, and correlated with increased cell surface binding. Further, we confirmed the importance of cellular integrins to Ad5Luc1-CK transduction. Herein, we present the rationale, design, purification, and characterization of a novel tropism modified, infectivity-enhanced Ad vector.}, }
@article {pmid15175992, year = {2004}, author = {Pong, A and Bradley, JS}, title = {Clinical challenges of nosocomial infections caused by antibiotic-resistant pathogens in pediatrics.}, journal = {Seminars in pediatric infectious diseases}, volume = {15}, number = {1}, pages = {21-29}, doi = {10.1053/j.spid.2004.01.005}, pmid = {15175992}, issn = {1045-1870}, mesh = {Adolescent ; Anti-Bacterial Agents/*therapeutic use ; Bacteremia/drug therapy/microbiology ; Bacteria/*drug effects/genetics ; Bacterial Infections/*drug therapy/*microbiology ; Child ; Cross Infection/*drug therapy/microbiology/*prevention &amp; control ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Humans ; Infant ; Pediatrics ; Pneumonia/drug therapy/microbiology ; Surgical Wound Infection/drug therapy/microbiology ; Urinary Tract Infections/drug therapy/microbiology ; }, abstract = {Antibiotic resistance in nosocomial infections is an ever-increasing problem as health care institutions provide care for children with more complicated medical and surgical problems. Several mechanisms of antibiotic resistance are reviewed for both gram-negative and gram-positive nosocomial pathogens. These adaptive resistance mechanisms allow organisms to survive in an environment of extensive antibiotic use and result in clinically significant infections. Mobile genetic elements have facilitated the rapid spread of antibiotic resistance within and among species. The clinical challenge faced by many practitioners is to understand these mechanisms of antibiotic resistance and to develop strategies for successfully treating infection caused by resistant pathogens. Nosocomial outbreaks caused by resistant organisms are described, and an approach to empiric therapy based on presumed pathogens, site of infection, and local resistance patterns is discussed.}, }
@article {pmid15175416, year = {2004}, author = {Herédia, F and Loreto, EL and Valente, VL}, title = {Complex evolution of gypsy in Drosophilid species.}, journal = {Molecular biology and evolution}, volume = {21}, number = {10}, pages = {1831-1842}, doi = {10.1093/molbev/msh183}, pmid = {15175416}, issn = {0737-4038}, mesh = {Animals ; Drosophilidae/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Phylogeny ; *Retroelements ; }, abstract = {In an endeavor to contribute to the comprehension of the evolution of transposable elements (TEs) in the genome of host species, we investigated the phylogenetic relationships of sequences homologous to the retrotransposon gypsy of Drosophila melanogaster in 19 species of Drosophila, in Scaptodrosophila latifasciaeformis, and in Zaprionus indianus. This phylogenetic study was based on approximately 500 base pairs of the env gene. Our analyses showed considerable discrepancy between the phylogeny of gypsy elements and the relationship of their host species, and they allow us to infer a complex evolutionary pattern that could include ancestral polymorphism, vertical transmission, and several cases of horizontal transmission.}, }
@article {pmid15175300, year = {2004}, author = {Basta, T and Keck, A and Klein, J and Stolz, A}, title = {Detection and characterization of conjugative degradative plasmids in xenobiotic-degrading Sphingomonas strains.}, journal = {Journal of bacteriology}, volume = {186}, number = {12}, pages = {3862-3872}, pmid = {15175300}, issn = {0021-9193}, mesh = {Biodegradation, Environmental ; *Conjugation, Genetic ; DNA, Bacterial/genetics ; Dioxins/metabolism ; Gene Transfer, Horizontal ; Naphthalenesulfonates/metabolism ; Plasmids/*genetics ; Sphingomonas/*genetics/metabolism ; Xenobiotics/*metabolism ; }, abstract = {A systematic survey for the presence of plasmids in 17 different xenobiotic-degrading Sphingomonas strains was performed. In almost all analyzed strains, two to five plasmids with sizes of about 50 to 500 kb were detected by using pulsed-field gel electrophoresis. A comparison of plasmid preparations untreated or treated with S1 nuclease suggested that, in general, Sphingomonas plasmids are circular. Hybridization experiments with labeled gene probes suggested that large plasmids are involved in the degradation of dibenzo-p-dioxin, dibenzofuran, and naphthalenesulfonates in S. wittichii RW1, Sphingomonas sp. HH69, and S. xenophaga BN6, respectively. The plasmids which are responsible for the degradation of naphthalene, biphenyl, and toluene by S. aromaticivorans F199 (pNL1) and of naphthalenesulfonates by S. xenophaga BN6 (pBN6) were site-specifically labeled with a kanamycin resistance cassette. The conjugative transfer of these labeled plasmids was attempted with various bacterial strains as putative recipient strains. Thus, a conjugative transfer of plasmid pBN6 from S. xenophaga BN6 to a cured mutant of strain BN6 and to Sphingomonas sp. SS3 was observed. The conjugation experiments with plasmid pNL1 suggested a broader host range of this plasmid, because it was transferred without any obvious structural changes to S. yanoikuyae B1, Sphingomonas sp. SS3, and S. herbicidovorans. In contrast, major plasmid rearrangements were observed in the transconjugants after the transfer of plasmid pNL1 to Sphingomonas sp. HH69 and of pBN6 to Sphingomonas sp. SS3. No indications for the transfer of a Sphingomonas plasmid to bacteria outside of the Sphingomonadaceae were obtained.}, }
@article {pmid15173110, year = {2004}, author = {Daubin, V and Ochman, H}, title = {Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli.}, journal = {Genome research}, volume = {14}, number = {6}, pages = {1036-1042}, pmid = {15173110}, issn = {1088-9051}, support = {R01 GM056120/GM/NIGMS NIH HHS/United States ; GM56120/GM/NIGMS NIH HHS/United States ; }, mesh = {AT Rich Sequence/genetics ; Base Composition/genetics ; DNA, Bacterial/genetics ; Escherichia coli/*genetics ; Escherichia coli Proteins/genetics/physiology ; Evolution, Molecular ; Genes, Bacterial/*genetics ; *Genome, Bacterial ; Open Reading Frames/*genetics/physiology ; Phylogeny ; }, abstract = {Differences in gene repertoire among bacterial genomes are usually ascribed to gene loss or to lateral gene transfer from unrelated cellular organisms. However, most bacteria contain large numbers of ORFans, that is, annotated genes that are restricted to a particular genome and that possess no known homologs. The uniqueness of ORFans within a genome has precluded the use of a comparative approach to examine their function and evolution. However, by identifying sequences unique to monophyletic groups at increasing phylogenetic depths, we can make direct comparisons of the characteristics of ORFans of different ages in the Escherichia coli genome, and establish their functional status and evolutionary rates. Relative to the genes ancestral to gamma-Proteobacteria and to those genes distributed sporadically in other prokaryotic species, ORFans in the E. coli lineage are short, A+T rich, and evolve quickly. Moreover, most encode functional proteins. Based on these features, ORFans are not attributable to errors in gene annotation, limitations of current databases, or to failure of methods for detecting homology. Rather, ORFans in the genomes of free-living microorganisms apparently derive from bacteriophage and occasionally become established by assuming roles in key cellular functions.}, }
@article {pmid15170386, year = {2004}, author = {Rider, MH and Bertrand, L and Vertommen, D and Michels, PA and Rousseau, GG and Hue, L}, title = {6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase: head-to-head with a bifunctional enzyme that controls glycolysis.}, journal = {The Biochemical journal}, volume = {381}, number = {Pt 3}, pages = {561-579}, pmid = {15170386}, issn = {1470-8728}, mesh = {Amino Acid Sequence ; Animals ; Glycolysis/*physiology ; Humans ; Models, Biological ; Models, Molecular ; Molecular Sequence Data ; Phosphofructokinase-2/chemistry/*physiology ; }, abstract = {Fru-2,6-P2 (fructose 2,6-bisphosphate) is a signal molecule that controls glycolysis. Since its discovery more than 20 years ago, inroads have been made towards the understanding of the structure-function relationships in PFK-2 (6-phosphofructo-2-kinase)/FBPase-2 (fructose-2,6-bisphosphatase), the homodimeric bifunctional enzyme that catalyses the synthesis and degradation of Fru-2,6-P2. The FBPase-2 domain of the enzyme subunit bears sequence, mechanistic and structural similarity to the histidine phosphatase family of enzymes. The PFK-2 domain was originally thought to resemble bacterial PFK-1 (6-phosphofructo-1-kinase), but this proved not to be correct. Molecular modelling of the PFK-2 domain revealed that, instead, it has the same fold as adenylate kinase. This was confirmed by X-ray crystallography. A PFK-2/FBPase-2 sequence in the genome of one prokaryote, the proteobacterium Desulfovibrio desulfuricans, could be the result of horizontal gene transfer from a eukaryote distantly related to all other organisms, possibly a protist. This, together with the presence of PFK-2/FBPase-2 genes in trypanosomatids (albeit with possibly only one of the domains active), indicates that fusion of genes initially coding for separate PFK-2 and FBPase-2 domains might have occurred early in evolution. In the enzyme homodimer, the PFK-2 domains come together in a head-to-head like fashion, whereas the FBPase-2 domains can function as monomers. There are four PFK-2/FBPase-2 isoenzymes in mammals, each coded by a different gene that expresses several isoforms of each isoenzyme. In these genes, regulatory sequences have been identified which account for their long-term control by hormones and tissue-specific transcription factors. One of these, HNF-6 (hepatocyte nuclear factor-6), was discovered in this way. As to short-term control, the liver isoenzyme is phosphorylated at the N-terminus, adjacent to the PFK-2 domain, by PKA (cAMP-dependent protein kinase), leading to PFK-2 inactivation and FBPase-2 activation. In contrast, the heart isoenzyme is phosphorylated at the C-terminus by several protein kinases in different signalling pathways, resulting in PFK-2 activation.}, }
@article {pmid15170264, year = {2004}, author = {Farahi, K and Pusch, GD and Overbeek, R and Whitman, WB}, title = {Detection of lateral gene transfer events in the prokaryotic tRNA synthetases by the ratios of evolutionary distances method.}, journal = {Journal of molecular evolution}, volume = {58}, number = {5}, pages = {615-631}, pmid = {15170264}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Amino Acyl-tRNA Synthetases/*genetics ; Computational Biology/methods ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Archaeal ; *Genes, Bacterial ; Molecular Sequence Data ; *Phylogeny ; Prokaryotic Cells/metabolism ; }, abstract = {The availability of large numbers of genomic sequences has demonstrated the importance of lateral gene transfer (LGT) in prokaryotic evolution. However, considerable uncertainty remains concerning the frequency of LGT compared to other evolutionary processes. To examine LGTs in ancient lineages of prokaryotes a method was developed that utilizes the ratios of evolutionary distances (RED) to distinguish between alternative evolutionary histories. The advantages of this approach are that the variability inherent in comparing protein sequences is transparent, the direction of LGT and the relative rates of evolution are readily identified, and it is possible to detect other types of evolutionary events. This method was standardized using 35 genes encoding ribosomal proteins that were believed to share a vertical evolution. Using RED-T, an original computer program designed to implement the RED method, the evolution of the genes encoding the 20 aminoacyl-tRNA synthetases was examined. Although LGTs were common in the evolution of the aminoacyl-tRNA synthetases, they were not sufficient to obscure the organismal phylogeny. Moreover, much of the apparent complexity of the gene tree was consistent with the formation of the paralogs in the ancestors to the modern lineages followed by more recent loss of one paralog or the other.}, }
@article {pmid15170257, year = {2004}, author = {Mukai, A and Endoh, H}, title = {Presence of a bacterial-like citrate synthase gene in Tetrahymena thermophila: recent lateral gene transfers (LGT) or multiple gene losses subsequent to a single ancient LGT?.}, journal = {Journal of molecular evolution}, volume = {58}, number = {5}, pages = {540-549}, pmid = {15170257}, issn = {0022-2844}, mesh = {Amino Acid Motifs/genetics ; Amino Acid Sequence ; Animals ; Blotting, Southern ; Citrate (si)-Synthase/*genetics ; DNA/analysis ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Molecular Sequence Data ; Peroxisomal Targeting Signal 2 Receptor ; Peroxisome-Targeting Signal 1 Receptor ; Phylogeny ; Receptors, Cytoplasmic and Nuclear/genetics ; Tetrahymena thermophila/*genetics ; }, abstract = {Citrate synthase is the initial enzyme in the tricarboxylic acid cycle of mitochondria. In plants and fungi, it is the second isozyme in the glyoxylate cycle of peroxisomes (or glyoxysomes), and it is also present in bacteria. Some of the biochemical reactions in the glyoxylate cycle of the ciliated protozoan Tetrahymena pyriformis depend upon mitochondrial enzymes, as T. pyriformis lacks some glyoxysome-specific enzymes. Here we demonstrate a new citrate synthase gene from Tetrahymena thermophila that is different from the mitochondrial counterpart. A potential peroxysome-targeted signal was detected in the N-terminus, suggesting the localization of the enzyme in peroxysomes. Phylogenetic analysis placed the Tetrahymena sequence in a clade consisting of a few sequences from eukaryotes such as cellular slime molds and two land plants, near a green sulfur bacterium and many proteobacteria as a sister group but not in a mitochondrial clade. Southern blot analysis revealed that this type of gene was absent from distantly related ciliates and other species of Tetrahymena except for the closest species, T. mallaccensis. The scattered presence of the bacterial-like genes among distantly related eukaryotes suggests three alternative interpretations of acquisition of the novel glyoxysomal citrate synthase gene via lateral gene transfer (LGT). (1). Some eukaryotes independently acquired the gene from a common bacterium or closely related bacteria via LGT. (2). A hypothetical eukaryote once acquired the gene, which was thereafter independently transferred from the eukaryote to other eukaryotes. (3). A single event of LGT (or duplication) occurred in a certain common ancestor of eukaryotes, followed by multiple losses in many eukaryotic lineages during the subsequent evolution. Considering the monophyly of the bacterial-like eukaryotic citrate synthase genes, the first model is somewhat unlikely, even though it is not impossible. The second and third models can rationally explain the present observation, so these models are discussed in some detail.}, }
@article {pmid15170256, year = {2004}, author = {Dutilh, BE and Huynen, MA and Bruno, WJ and Snel, B}, title = {The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise.}, journal = {Journal of molecular evolution}, volume = {58}, number = {5}, pages = {527-539}, pmid = {15170256}, issn = {0022-2844}, mesh = {Computational Biology/methods ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; *Genome ; Genomics/*methods ; *Phylogeny ; }, abstract = {Phylogenetic trees based on gene repertoires are remarkably similar to the current consensus of life history. Yet it has been argued that shared gene content is unreliable for phylogenetic reconstruction because of convergence in gene content due to horizontal gene transfer and parallel gene loss. Here we test this argument, by filtering out as noise those orthologous groups that have an inconsistent phylogenetic distribution, using two independent methods. The resulting phylogenies do indeed contain small but significant improvements. More importantly, we find that the majority of orthologous groups contain some phylogenetic signal and that the resulting phylogeny is the only detectable signal present in the gene distribution across genomes. Horizontal gene transfer or parallel gene loss does not cause systematic biases in the gene content tree.}, }
@article {pmid15168613, year = {2004}, author = {Pereira, MM and Bandeiras, TM and Fernandes, AS and Lemos, RS and Melo, AM and Teixeira, M}, title = {Respiratory chains from aerobic thermophilic prokaryotes.}, journal = {Journal of bioenergetics and biomembranes}, volume = {36}, number = {1}, pages = {93-105}, pmid = {15168613}, issn = {0145-479X}, mesh = {Aerobiosis/physiology ; Archaea/*physiology ; Bacteria, Aerobic/*physiology ; Cell Membrane/*physiology ; Electron Transport/*physiology ; Oxidoreductases/*metabolism ; Signal Transduction/*physiology ; }, abstract = {Thermophiles are organisms that grow optimally above 50 degrees C and up to approximately 120 degrees C. These extreme conditions must have led to specific characteristics of the cellular components. In this paper we extensively analyze the types of respiratory complexes from thermophilic aerobic prokaryotes. The different membrane-bound complexes so far characterized are described, and the genomic data available for thermophilic archaea and bacteria are analyzed. It is observed that no specific characteristics can be associated to thermophilicity as the different types of complexes I-IV are present randomly in thermophilic aerobic organisms, as well as in mesophiles. Rather, the extensive genomic analyses indicate that the differences concerning the several complexes are related to the organism phylogeny, i.e., to evolution and lateral gene transfer events.}, }
@article {pmid15168607, year = {2004}, author = {Averhoff, B}, title = {DNA transport and natural transformation in mesophilic and thermophilic bacteria.}, journal = {Journal of bioenergetics and biomembranes}, volume = {36}, number = {1}, pages = {25-33}, pmid = {15168607}, issn = {0145-479X}, mesh = {Archaea/*physiology ; *Bacterial Physiological Phenomena ; Biological Transport, Active/physiology ; Carrier Proteins/metabolism ; Cell Membrane/*physiology ; DNA/*pharmacokinetics ; Fimbriae Proteins/*metabolism ; Gene Expression Regulation, Archaeal/physiology ; Gene Expression Regulation, Bacterial/physiology ; *Models, Biological ; Signal Transduction/physiology ; Transformation, Genetic/*physiology ; }, abstract = {Comparative genome analyses revealed a massive DNA exchange between microbes of distant evolutionary lineages. This phenomenon known as horizontal, or lateral, gene transfer has a tremendous impact in the evolution of prokaryotes. Here, the process of DNA transport via genetic transformation is discussed. This review will focus on the process of DNA uptake mediated by type IV pilin-like proteins in Gram-positive and Gram-negative bacteria. Three tentative models of transformation machineries comprising components similar to proteins of type IV pili and type II secretion are presented. A comparative discussion of the structure of DNA translocators and the underlying mechanism of transfer of free DNA in mesophilic and extremely thermophilic bacteria highlights conserved and distinctive features of the DNA translocators in mesophilic and thermophilic bacteria.}, }
@article {pmid15166133, year = {2004}, author = {Turner, PE}, title = {Phenotypic plasticity in bacterial plasmids.}, journal = {Genetics}, volume = {167}, number = {1}, pages = {9-20}, pmid = {15166133}, issn = {0016-6731}, mesh = {Analysis of Variance ; Bacteria/*genetics ; *Bacterial Physiological Phenomena ; Cell Culture Techniques/methods ; Escherichia coli/*physiology ; Gene Transfer, Horizontal ; *Models, Genetic ; Phenotype ; Plasmids/*metabolism ; Time Factors ; }, abstract = {Plasmid pB15 was previously shown to evolve increased horizontal (infectious) transfer at the expense of reduced vertical (intergenerational) transfer and vice versa, a key trade-off assumed in theories of parasite virulence. Whereas the models predict that susceptible host abundance should determine which mode of transfer is selectively favored, host density failed to mediate the trade-off in pB15. One possibility is that the plasmid's transfer deviates from the assumption that horizontal spread (conjugation) occurs in direct proportion to cell density. I tested this hypothesis using Escherichia coli/pB15 associations in laboratory serial culture. Contrary to most models of plasmid transfer kinetics, my data show that pB15 invades static (nonshaking) bacterial cultures only at intermediate densities. The results can be explained by phenotypic plasticity in traits governing plasmid transfer. As cells become more numerous, the plasmid's conjugative transfer unexpectedly declines, while the trade-off between transmission routes causes vertical transfer to increase. Thus, at intermediate densities the plasmid's horizontal transfer can offset selection against plasmid-bearing cells, but at high densities pB15 conjugates so poorly that it cannot invade. I discuss adaptive vs. nonadaptive causes for the phenotypic plasticity, as well as potential mechanisms that may lead to complex transfer dynamics of plasmids in liquid environments.}, }
@article {pmid15163767, year = {2004}, author = {Nishio, Y and Nakamura, Y and Usuda, Y and Sugimoto, S and Matsui, K and Kawarabayasi, Y and Kikuchi, H and Gojobori, T and Ikeo, K}, title = {Evolutionary process of amino acid biosynthesis in Corynebacterium at the whole genome level.}, journal = {Molecular biology and evolution}, volume = {21}, number = {9}, pages = {1683-1691}, doi = {10.1093/molbev/msh175}, pmid = {15163767}, issn = {0737-4038}, mesh = {Amino Acids/*biosynthesis ; Base Composition ; Corynebacterium/*genetics/*metabolism/pathogenicity ; Corynebacterium diphtheriae/genetics/metabolism/pathogenicity ; Corynebacterium glutamicum/genetics/metabolism ; DNA, Bacterial/chemistry/genetics ; Evolution, Molecular ; Gene Deletion ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; Humans ; Models, Biological ; Open Reading Frames ; Phylogeny ; Species Specificity ; }, abstract = {Corynebacterium glutamicum, which is the closest relative of Corynebacterium efficiens, is widely used for the large scale production of many kinds of amino acids, particularly glutamic acid and lysine, by fermentation. Corynebacterium diphtheriae, which is well known as a human pathogen, is also closely related to these two species of Corynebacteria, but it lacks such productivity of amino acids. It is an important and interesting question to ask how those closely related bacterial species have undergone such significant functional differentiation in amino acid biosynthesis. The main purpose of the present study is to clarify the evolutionary process of functional differentiation among the three species of Corynebacteria by conducting a comparative analysis of genome sequences. When Mycobacterium and Streptomyces were used as out groups, our comparative study suggested that the common ancestor of Corynebacteria already possessed almost all of the gene sets necessary for amino acid production. However, C. diphtheriae was found to have lost the genes responsible for amino acid production. Moreover, we found that the common ancestor of C. efficiens and C. glutamicum have acquired some of genes responsible for amino acid production by horizontal gene transfer. Thus, we conclude that the evolutionary events of gene loss and horizontal gene transfer must have been responsible for functional differentiation in amino acid biosynthesis of the three species of Corynebacteria.}, }
@article {pmid15162114, year = {2004}, author = {Bensasson, D and Boore, JL and Nielsen, KM}, title = {Genes without frontiers?.}, journal = {Heredity}, volume = {92}, number = {6}, pages = {483-489}, doi = {10.1038/sj.hdy.6800451}, pmid = {15162114}, issn = {0018-067X}, mesh = {Bacteria/*genetics ; Cloning, Molecular ; DNA Transposable Elements/*genetics ; Drug Resistance/genetics ; Gene Transfer, Horizontal/*genetics ; Genes/*genetics ; Genetic Vectors/*genetics ; Guidelines as Topic ; Plasmids/*genetics ; Replication Origin/genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {For bacteria, the primary genetic barrier against the genetic exchange of DNA that is not self-transmissible is dissimilarity in the bacterial DNA sequences concerned. Genetic exchange by homologous recombination is frequent among close bacterial relatives and recent experiments have shown that it can enable the uptake of closely linked nonhomologous foreign DNA. Artificial vectors are mosaics of mobile DNA elements from free-living bacterial isolates and so bear a residual similarity to their ubiquitous natural progenitors. This homology is tightly linked to the multitude of different DNA sequences that are inserted into synthetic vectors. Can homology between vector and bacterial DNA enable the uptake of these foreign DNA inserts? In this review we investigate pUC18 as an example of an artificial vector and consider whether its homology to broad host-range antibiotic resistance transposons and plasmid origins of replication could enable the uptake of insert DNA in the light of studies of homology-facilitated foreign DNA uptake. We also discuss the disposal of recombinant DNA, its persistence in the environment and whether homologies to pUC18 may exist in naturally competent bacteria. Most DNA that is inserted into the cloning site of artificial vectors would be of little use to a bacterium, but perhaps not all.}, }
@article {pmid15160603, year = {2004}, author = {Lewin, A and Tran, TT and Jacob, D and Mayer, M and Freytag, B and Appel, B}, title = {Yeast DNA sequences initiating gene expression in Escherichia coli.}, journal = {Microbiological research}, volume = {159}, number = {1}, pages = {19-28}, doi = {10.1016/j.micres.2004.01.006}, pmid = {15160603}, issn = {0944-5013}, mesh = {Artificial Gene Fusion ; Bacterial Proteins/genetics/physiology ; Base Sequence ; DNA, Fungal/*genetics/isolation &amp; purification ; Escherichia coli/*genetics ; *Gene Expression ; Genes, Bacterial ; Genes, Reporter ; Luciferases/genetics/metabolism ; Luminescent Measurements ; Molecular Sequence Data ; *Promoter Regions, Genetic ; Saccharomyces cerevisiae/genetics ; Transcription Initiation Site ; *Transcription, Genetic ; Transformation, Bacterial ; }, abstract = {DNA transfer between pro- and eukaryotes occurs either during natural horizontal gene transfer or as a result of the employment of gene technology. We analysed the capacity of DNA sequences from a eukaryotic donor organism (Saccharomyces cerevisiae) to serve as promoter region in a prokaryotic recipient (Escherichia coli) by creating fusions between promoterless luxAB genes from Vibrio harveyi and random DNA sequences from S. cerevisiae and measuring the luminescence of transformed E. coli. Fifty-four out of 100 randomly analysed S. cerevisiae DNA sequences caused considerable gene expression in E. coli. Determination of transcription start sites within six selected yeast sequences in E. coli confirmed the existence of bacterial -10 and -35 consensus sequences at appropriate distances upstream from transcription initiation sites. Our results demonstrate that the probability of transcription of transferred eukaryotic DNA in bacteria is extremely high and does not require the insertion of the transferred DNA behind a promoter of the recipient genome.}, }
@article {pmid15159633, year = {2004}, author = {Gray, J and Wardzala, E and Yang, M and Reinbothe, S and Haller, S and Pauli, F}, title = {A small family of LLS1-related non-heme oxygenases in plants with an origin amongst oxygenic photosynthesizers.}, journal = {Plant molecular biology}, volume = {54}, number = {1}, pages = {39-54}, pmid = {15159633}, issn = {0167-4412}, mesh = {Amino Acid Motifs/genetics ; Amino Acid Sequence ; Apoptosis Regulatory Proteins ; Arabidopsis/enzymology/genetics ; Arabidopsis Proteins/*genetics/metabolism ; Bacteria/genetics ; Conserved Sequence/genetics ; Cyanobacteria/genetics ; *Evolution, Molecular ; Genes, Plant/genetics ; Iron-Binding Proteins/genetics ; Molecular Sequence Data ; Oxygen/*metabolism ; Oxygenases/*genetics/metabolism ; Photosynthesis/genetics ; Phylogeny ; Plants/*genetics/metabolism ; Sequence Homology, Amino Acid ; }, abstract = {Conservation of Lethal-leaf spot 1 (Lls1) lesion mimic gene in land plants including moss is consistent with its recently reported function as pheophorbide a oxygenase (Pao) which catalyzes a key step in chlorophyll degradation (Pruzinska et al., 2003). A bioinformatics survey of complete plant genomes reveals that LLS1(PAO) belongs to a small 5-member family of non-heme oxygenases defined by the presence of Rieske and mononuclear iron-binding domains. This gene family includes chlorophyll a oxygenase (Cao), choline monooxygenase (Cmo), the gene for a 55 kDa protein associated with protein transport through the inner chloroplast membrane (Tic 55) and a novel 52 kDa protein isolated from chloroplasts (Ptc 52). Analysis of gene structure reveals that these genes diverged prior to monocot/dicot divergence. Homologues of LLS1(PAO), CAO, TIC55 and PTC52 but not CMO are found in the genomes of several cyanobacteria. LLS1(PAO), PTC52, TIC55 and a set of related cyanobacterial homologues share an extended carboxyl terminus containing a novel F/Y/W-x(2)-H-x(3)-C-x(2)-C motif not present in CAO. These proteins appear to have evolved during the transition to oxygenic photosynthesis to play various roles in chlorophyll metabolism. In contrast, CMO homologues are found only in plants and are most closely related to aromatic ring-hydroxylating enzymes from soil-dwelling bacteria, suggesting a more recent evolution of this enzyme, possibly by horizontal gene transfer. Our phylogenetic analysis of 95 extant non-heme dioxygenases provides a useful framework for the classification of LLS1(PAO)-related non-heme oxygenases.}, }
@article {pmid15158466, year = {2004}, author = {Imamura, H and Jeon, BS and Wakagi, T}, title = {Molecular evolution of the ATPase subunit of three archaeal sugar ABC transporters.}, journal = {Biochemical and biophysical research communications}, volume = {319}, number = {1}, pages = {230-234}, doi = {10.1016/j.bbrc.2004.04.174}, pmid = {15158466}, issn = {0006-291X}, mesh = {ATP-Binding Cassette Transporters/*chemistry/metabolism ; Adenosine Triphosphatases/*chemistry ; Adenosine Triphosphate/chemistry ; Archaea/metabolism ; Archaeal Proteins ; Bacterial Proteins/chemistry ; Biological Transport ; Blotting, Southern ; DNA/chemistry ; Dose-Response Relationship, Drug ; Escherichia coli/metabolism ; Evolution, Molecular ; Gene Transfer Techniques ; Glycoside Hydrolases/chemistry ; Models, Genetic ; Molecular Sequence Data ; Multigene Family ; Open Reading Frames ; Plasmids/metabolism ; Polysaccharides/chemistry ; Thermococcus/metabolism ; Time Factors ; Trehalose/chemistry ; }, abstract = {The sequence of genes encoding extracellular amylopullulanase and putative maltodextrin ATP binding cassette (ABC) transporter of a hyperthermophilic archaeon, Thermococcus litoralis, was determined. The mdxK gene, which encodes an ATPase subunit of the putative maltodextrin ABC transporter, has extraordinarily high similarity with the malK gene, which encodes an ATPase subunit of trehalose/maltose ABC transporter of the same organism. DNA sequence comparison revealed that the malK gene was generated through the duplication of the mdxK gene before lateral gene transfer of the mal gene cluster from T. litoralis to Pyrococcus furiosus.}, }
@article {pmid15157625, year = {2004}, author = {Carroll, IM and Khan, AA and Ahmed, N}, title = {Revisiting the pestilence of Helicobacter pylori: insights into geographical genomics and pathogen evolution.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {4}, number = {2}, pages = {81-90}, doi = {10.1016/j.meegid.2004.01.006}, pmid = {15157625}, issn = {1567-1348}, mesh = {Disease Transmission, Infectious ; Evolution, Molecular ; Forecasting ; *Genomics ; Helicobacter Infections/epidemiology/*transmission ; Helicobacter pylori/*genetics/*pathogenicity ; Humans ; }, abstract = {Helicobacter pylori causes chronic gastritis and plays important roles in peptic ulcer disease, gastric carcinoma, and mucosa-associated lymphoid tissue (MALT) lymphoma. It is believed that H. pylori infects over 50% of the worlds' population. However, only a small subset of infected people experience H. pylori-associated illnesses. Associations with disease-specific factors remain enigmatic. The contribution of comparative genomics to our understanding of the genome organisation and diversity of H. pylori is exemplified herein. The discovery of the cag pathogenicity island has revolutionised our understanding of the molecular pathogenesis of gastroduodenal ulcers. Another type IV secretion system, the comB gene cluster, provides a novel transformation system. Identification of this cluster has boosted our perception of horizontal gene transfer and gene mosaicism in H. pylori as a result of natural competence. Recent discovery of a third type IV secretion system called tfs3 encoding cluster in the so called plasticity zone of the H. pylori has gained significant attention, although its role is not clear. Study of the evolution of polymorphisms and sequence variation in H. pylori populations on a global basis is contributing to understanding of the history of human population migration and co-evolution of this pathogen with its human host. Possible symbiotic relationships were debated since the discovery of this pathogen. The debate has been further intensified as recent studies have posed the intriguing possibility that H. pylori infection may be advantageous in some humans. This analogy is based on increased incidence of diseases like gastro-oesophageal reflux disease (GERD), Barrett's oesophagus and adenocarcinoma of the oesophagus following H. pylori eradication in some patients.}, }
@article {pmid15155937, year = {2004}, author = {Erwin, DH and Krakauer, DC}, title = {Evolution. Insights into innovation.}, journal = {Science (New York, N.Y.)}, volume = {304}, number = {5674}, pages = {1117-1119}, doi = {10.1126/science.1099385}, pmid = {15155937}, issn = {1095-9203}, mesh = {Animals ; *Biological Evolution ; Diffusion of Innovation ; Economics ; Ecosystem ; *Engineering ; Environment ; Epigenesis, Genetic ; Gene Duplication ; Gene Transfer, Horizontal ; Genotype ; Mutation ; Phenotype ; Selection, Genetic ; *Technology ; }, }
@article {pmid15155233, year = {2004}, author = {Poirel, L and Lebessi, E and Castro, M and Fèvre, C and Foustoukou, M and Nordmann, P}, title = {Nosocomial outbreak of extended-spectrum beta-lactamase SHV-5-producing isolates of Pseudomonas aeruginosa in Athens, Greece.}, journal = {Antimicrobial agents and chemotherapy}, volume = {48}, number = {6}, pages = {2277-2279}, pmid = {15155233}, issn = {0066-4804}, mesh = {Adolescent ; Child ; Child, Preschool ; Chromosomes, Bacterial/genetics ; Cross Infection/epidemiology/*microbiology ; DNA, Bacterial/genetics ; Disease Outbreaks ; Electrophoresis, Gel, Pulsed-Field ; Gene Transfer, Horizontal ; Greece/epidemiology ; Humans ; Infant ; Phenotype ; Pseudomonas Infections/epidemiology/*microbiology ; Pseudomonas aeruginosa/*drug effects/enzymology/*genetics ; Reverse Transcriptase Polymerase Chain Reaction ; beta-Lactamases/*metabolism ; }, abstract = {Seven nonrepetitive Pseudomonas aeruginosa isolates producing the clavulanic acid-inhibited extended-spectrum beta-lactamase SHV-5 were isolated in the same hospital in Athens, Greece, from 1998 to 2002. All isolates except one were clonally related, and the bla(SHV-5) gene was chromosomally located. This study underlined that this gene, which is widespread in Enterobacteriaceae in Greece, may disseminate also in P. aeruginosa.}, }
@article {pmid15155202, year = {2004}, author = {Doi, Y and Wachino, J and Yamane, K and Shibata, N and Yagi, T and Shibayama, K and Kato, H and Arakawa, Y}, title = {Spread of novel aminoglycoside resistance gene aac(6')-Iad among Acinetobacter clinical isolates in Japan.}, journal = {Antimicrobial agents and chemotherapy}, volume = {48}, number = {6}, pages = {2075-2080}, pmid = {15155202}, issn = {0066-4804}, mesh = {Acetyltransferases/biosynthesis/*genetics/isolation &amp; purification ; Acinetobacter/*drug effects/genetics ; Acinetobacter Infections/*epidemiology/*microbiology ; Amikacin/pharmacology ; Amino Acid Sequence ; Aminoglycosides/*pharmacology ; Anti-Bacterial Agents/*pharmacology ; Chromatography, High Pressure Liquid ; Cloning, Molecular ; Culture Media ; Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Humans ; Japan/epidemiology ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Plasmids/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {A novel aminoglycoside resistance gene, aac(6')-Iad, encoding aminoglycoside 6'-N-acetyltransferase, was identified in Acinetobacter genospecies 3 strain A-51. The gene encoded a 144-amino-acid protein, which shared modest identity (up to 36.7%) with some of the aminoglycoside 6'-N-acetyltransferases. The results of high-pressure liquid chromatography assays confirmed that the protein is a functional aminoglycoside 6'-N-acetyltransferase. The enzyme conferred resistance to amikacin, tobramycin, sisomicin, and isepamicin but not to gentamicin. The prevalence of this gene among Acinetobacter clinical isolates in Japan was then investigated. Of 264 Acinetobacter sp. strains isolated from geographically diverse areas in Japan in 2002, 16 were not susceptible to amikacin, and aac(6')-Iad was detected in 7. Five of the producers of aminoglycoside 6'-N-acetyltransferase type Iad were identified as Acinetobacter baumannii, and two were identified as Acinetobacter genospecies 3. These results suggest that aac(6')-Iad plays a substantial role in amikacin resistance among Acinetobacter spp. in Japan.}, }
@article {pmid15153690, year = {2004}, author = {Marsh, PD}, title = {Dental plaque as a microbial biofilm.}, journal = {Caries research}, volume = {38}, number = {3}, pages = {204-211}, doi = {10.1159/000077756}, pmid = {15153690}, issn = {0008-6568}, mesh = {Bacterial Adhesion ; Biofilms ; Cell Communication ; Dental Plaque/*microbiology ; Drug Resistance, Bacterial ; Ecosystem ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Humans ; }, abstract = {New technologies have provided novel insights into how dental plaque functions as a biofilm. Confocal microscopy has confirmed that plaque has an open architecture similar to other biofilms, with channels and voids. Gradients develop in areas of dense biomass over short distances in key parameters that influence microbial growth and distribution. Bacteria exhibit an altered pattern of gene expression either as a direct result of being on a surface or indirectly as a response to the local environmental heterogeneity within the biofilm. Bacteria communicate via small diffusible signalling molecules (e.g. competence-stimulating peptide, CSP; autoinducer 2); CSP induces both genetic competence and acid tolerance in recipient sessile cells. Thus, rates of gene transfer increase in biofilm communities, and this is one of several mechanisms (others include: diffusion-reaction, neutralization/inactivation, slow growth rates, novel phenotype) that contribute to the increased antimicrobial resistance exhibited by bacteria in biofilms. Oral bacteria in plaque do not exist as independent entities but function as a co-ordinated, spatially organized and fully metabolically integrated microbial community, the properties of which are greater than the sum of the component species. A greater understanding of the significance of dental plaque as a mixed culture biofilm will lead to novel control strategies.}, }
@article {pmid15153500, year = {2004}, author = {Tsujimura, H and Tamura, T and Kong, HJ and Nishiyama, A and Ishii, KJ and Klinman, DM and Ozato, K}, title = {Toll-like receptor 9 signaling activates NF-kappaB through IFN regulatory factor-8/IFN consensus sequence binding protein in dendritic cells.}, journal = {Journal of immunology (Baltimore, Md. : 1950)}, volume = {172}, number = {11}, pages = {6820-6827}, doi = {10.4049/jimmunol.172.11.6820}, pmid = {15153500}, issn = {0022-1767}, mesh = {Dendritic Cells/*physiology ; Gene Transfer, Horizontal ; Humans ; I-kappa B Kinase ; Interferon Regulatory Factors ; Interleukin-6/biosynthesis ; Membrane Glycoproteins/*physiology ; Mitogen-Activated Protein Kinases/metabolism ; NF-kappa B/*metabolism ; Oligodeoxyribonucleotides/pharmacology ; Phosphorylation ; Protein Serine-Threonine Kinases/metabolism ; Receptors, Cell Surface/*physiology ; Repressor Proteins/genetics/*physiology ; Signal Transduction ; Toll-Like Receptor 4 ; Toll-Like Receptor 9 ; Toll-Like Receptors ; Tumor Necrosis Factor-alpha/biosynthesis ; p38 Mitogen-Activated Protein Kinases ; }, abstract = {Unmethylated CpG DNA binds to the Toll-like receptor 9 (TLR9) and activates NF-kappaB to induce cytokine genes in dendritic cells (DCs). IFN regulatory factor (IRF)-8/IFN consensus sequence binding protein is a transcription factor important for development and activation of DCs. We found that DCs from IRF-8(-/-) mice were unresponsive to CpG and failed to induce TNF-alpha and IL-6, targets of NF-kappaB. Revealing a signaling defect selective for CpG, these cytokines were robustly induced in IRF-8(-/-) DCs in response to LPS that signals through TLR4. IRF-8(-/-) DCs expressed TLR9, adaptor myeloid differentiation factor 88, and other signaling molecules, but CpG failed to activate NF-kappaB in -/- cells. This was due to the selective inability of -/- DCs to activate I-kappaB kinase alphabeta, the kinases required for NF-kappaB in response to CpG. IRF-8 reintroduction fully restored CpG activation of NF-kappaB and cytokine induction in -/- DCs. Together, TLR signals that activate NF-kappaB are diverse among different TLRs, and TLR9 signaling uniquely depends on IRF-8 in DCs.}, }
@article {pmid15149615, year = {2004}, author = {Amábile-Cuevas, CF and Heinemann, JA}, title = {Shooting the messenger of antibiotic resistance: plasmid elimination as a potential counter-evolutionary tactic.}, journal = {Drug discovery today}, volume = {9}, number = {11}, pages = {465-467}, doi = {10.1016/S1359-6446(03)02989-1}, pmid = {15149615}, issn = {1359-6446}, mesh = {Anti-Bacterial Agents/therapeutic use ; Bacteria/drug effects/*genetics ; Bacterial Infections/drug therapy ; Drug Design ; Drug Resistance, Microbial/*genetics ; Drug Resistance, Multiple/*genetics ; Gene Transfer, Horizontal ; Plasmids/*drug effects ; }, }
@article {pmid15149018, year = {2004}, author = {Hacker, J and Hochhut, B and Middendorf, B and Schneider, G and Buchrieser, C and Gottschalk, G and Dobrindt, U}, title = {Pathogenomics of mobile genetic elements of toxigenic bacteria.}, journal = {International journal of medical microbiology : IJMM}, volume = {293}, number = {7-8}, pages = {453-461}, doi = {10.1078/1438-4221-00290}, pmid = {15149018}, issn = {1438-4221}, mesh = {Bacterial Toxins/*genetics ; Enterobacteriaceae/*genetics/*pathogenicity ; Enterobacteriaceae Infections/microbiology ; Gene Transfer, Horizontal/genetics ; Genetic Variation/genetics ; *Genome, Bacterial ; Interspersed Repetitive Sequences/*genetics ; Repetitive Sequences, Nucleic Acid/genetics ; Virulence ; }, abstract = {The growing knowledge of genetic diversity and whole genome organization in bacteria shows that pathogenicity islands (PAIs) represent a subtype of a more general genetic element, termed genomic island (GEI), which is widespread among pathogenic and non-pathogenic microbes. These findings mirror the importance of horizontal gene transfer, genome reduction and recombination events as fundamental mechanisms involved in evolution of bacterial variants. GEIs are part of the flexible gene pool and carry selfish genes, but also determinants which may be beneficial under certain conditions thus increasing bacterial fitness and consequently their survival or transmission. In this review, we focus on the role of mobile genetic elements that may also contain toxin-encoding genes for genome variability and evolution of bacteria.}, }
@article {pmid15147578, year = {2004}, author = {Cherkasov, A and Jones, SJ}, title = {An approach to large scale identification of non-obvious structural similarities between proteins.}, journal = {BMC bioinformatics}, volume = {5}, number = {}, pages = {61}, pmid = {15147578}, issn = {1471-2105}, mesh = {Bacterial Proteins/*chemistry/physiology ; Chlamydia trachomatis/pathogenicity ; Computational Biology/methods ; Genome, Bacterial ; Genome, Human ; Humans ; Models, Biological ; Protein Structure, Quaternary/physiology ; Proteins/*chemistry/physiology ; Sequence Alignment/methods ; Sequence Homology, Amino Acid ; Virulence Factors/classification/physiology ; }, abstract = {BACKGROUND: A new sequence independent bioinformatics approach allowing genome-wide search for proteins with similar three dimensional structures has been developed. By utilizing the numerical output of the sequence threading it establishes putative non-obvious structural similarities between proteins. When applied to the testing set of proteins with known three dimensional structures the developed approach was able to recognize structurally similar proteins with high accuracy.<br><br>RESULTS: The method has been developed to identify pathogenic proteins with low sequence identity and high structural similarity to host analogues. Such protein structure relationships would be hypothesized to arise through convergent evolution or through ancient horizontal gene transfer events, now undetectable using current sequence alignment techniques. The pathogen proteins, which could mimic or interfere with host activities, would represent candidate virulence factors. The developed approach utilizes the numerical outputs from the sequence-structure threading. It identifies the potential structural similarity between a pair of proteins by correlating the threading scores of the corresponding two primary sequences against the library of the standard folds. This approach allowed up to 64% sensitivity and 99.9% specificity in distinguishing protein pairs with high structural similarity.<br><br>CONCLUSION: Preliminary results obtained by comparison of the genomes of Homo sapiens and several strains of Chlamydia trachomatis have demonstrated the potential usefulness of the method in the identification of bacterial proteins with known or potential roles in virulence.}, }
@article {pmid15145575, year = {2004}, author = {Pál, C and Hurst, LD}, title = {Evidence against the selfish operon theory.}, journal = {Trends in genetics : TIG}, volume = {20}, number = {6}, pages = {232-234}, doi = {10.1016/j.tig.2004.04.001}, pmid = {15145575}, issn = {0168-9525}, mesh = {Animals ; Bacteria/*genetics ; Eukaryotic Cells ; *Evolution, Molecular ; *Genes ; *Models, Genetic ; Operon/*genetics ; Selection, Genetic ; }, abstract = {According to the selfish operon hypothesis, the clustering of genes and their subsequent organization into operons is beneficial for the constituent genes because it enables the horizontal gene transfer of weakly selected, functionally coupled genes. The majority of these are expected to be non-essential genes. From our analysis of the Escherichia coli genome, we conclude that the selfish operon hypothesis is unlikely to provide a general explanation for clustering nor can it account for the gene composition of operons. Contrary to expectations, essential genes with related functions have an especially strong tendency to cluster, even if they are not in operons. Moreover, essential genes are particularly abundant in operons.}, }
@article {pmid15140563, year = {2004}, author = {Kobayashi, R and Sekino, Y and Shirao, T and Tanaka, S and Ogura, T and Inada, K and Saji, M}, title = {Antisense knockdown of drebrin A, a dendritic spine protein, causes stronger preference, impaired pre-pulse inhibition, and an increased sensitivity to psychostimulant.}, journal = {Neuroscience research}, volume = {49}, number = {2}, pages = {205-217}, doi = {10.1016/j.neures.2004.02.014}, pmid = {15140563}, issn = {0168-0102}, mesh = {Adaptation, Psychological/physiology ; Amphetamine/pharmacology ; Analysis of Variance ; Animals ; Animals, Genetically Modified ; Behavior, Animal ; Blotting, Western/methods ; Brain/drug effects/metabolism ; Central Nervous System Stimulants/pharmacology ; Gene Transfer, Horizontal ; Genetic Vectors ; Injections, Intraventricular/methods ; Liposomes/metabolism ; Male ; Maze Learning/*drug effects/physiology ; Motor Activity/*drug effects/physiology ; Neural Inhibition/*drug effects/physiology ; Neuropeptides/*antagonists &amp; inhibitors/deficiency/genetics ; Oligonucleotides, Antisense/administration &amp; dosage/*pharmacology ; Rats ; Rats, Wistar ; Reflex, Startle/physiology ; Sendai virus/genetics ; Time Factors ; }, abstract = {Drebrin located in dendritic spines regulates their morphological changes and plays a role in the synaptic plasticity via spine function. Reduced drebrin has been found in the brain of patients with Alzheimer's disease or Down's syndrome. To examine whether the down-regulation of drebrin protein levels causes deficits in higher brain function, such as memory or cognition, we performed antisense-induced knockdown of drebrin A expression in rat brain using an hemagglutinating virus of Japan (HVJ)-liposome gene transfer technique. We investigated the effects of drebrin in vivo knockdown on spatial memory in a water-maze task, sensorimotor gating in a pre-pulse-inhibition test, adaptive behaviors in an open-field test, and sensitivity to psychostimulant in an amphetamine-induced locomotor response. Rats with drebrin A in vivo knockdown displayed a stronger preference for a previous event due to perseverative behavior, impaired pre-pulse inhibition (PPI), increased locomotor activity, anxiety-like behavior, and an increased sensitivity to psychostimulant, suggesting behaviors related to schizophrenia. These findings indicated that decreased drebrin produces deficits in cognitive function but not in spatial memory, probably via hypofunction of dendritic spines.}, }
@article {pmid15140390, year = {2004}, author = {Gassama, A and Aïdara-Kane, A and Chainier, D and Denis, F and Ploy, MC}, title = {Integron-associated antibiotic resistance in enteroaggregative and enteroinvasive Escherichia coli.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {10}, number = {1}, pages = {27-30}, doi = {10.1089/107662904323047763}, pmid = {15140390}, issn = {1076-6294}, mesh = {Chromosome Mapping ; Conjugation, Genetic ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/*genetics/pathogenicity ; Escherichia coli Infections/*genetics/microbiology ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Humans ; Integrons/*genetics ; Microbial Sensitivity Tests ; Polymorphism, Genetic ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {Ten enteroinvasive (EIEC) and 25 enteroaggregative (EaggEC) E. coli strains isolated from Senegalese patients were analyzed for their integron content. All strains were resistant to at least two antibiotics. Four EIEC and 15 EaggEC were found to carry a class 1 integron. An identical integron carrying a single dfrA5 cassette, conferring resistance to trimethoprim, was identified in all four EIEC strains. Five EaggEC strains harbored an integron with a single cassette, dfrA7, while the remaining 10 strains carried two integrons, one with a single cassette, aadA1a conferring resistance to streptomycin and spectinomycin, and the second one bearing two cassettes, dfrA13 and oxa5, the later being a beta-lactam resistance cassette. The presence of these integrons is worrying, because trimethoprim is largely used for diarrheal disease therapy in Africa. Thus, the presence of integrons in diarrheagenic strains is of public health importance because a limited number of antibiotics are available in developing countries.}, }
@article {pmid15137901, year = {2004}, author = {Horner, DS and Pesole, G}, title = {Phylogenetic analyses: a brief introduction to methods and their application.}, journal = {Expert review of molecular diagnostics}, volume = {4}, number = {3}, pages = {339-350}, doi = {10.1586/14737159.4.3.339}, pmid = {15137901}, issn = {1473-7159}, mesh = {Animals ; Base Sequence ; *Clinical Medicine ; Drug Design ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Humans ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; Sequence Homology ; Software ; }, abstract = {Phylogenetic analysis of molecular sequence data plays an increasingly important role in clinical medicine, both in the emerging field of molecular epidemiology and in the rational design of new therapeutic agents. The aims of this review are to introduce some of the methods used to construct phylogenetic trees, to illustrate some of the pitfalls that can introduce artifactual results and to speculate on the long-term importance of this area of computational biology in clinical medicine.}, }
@article {pmid15133093, year = {2004}, author = {Dedysh, SN and Ricke, P and Liesack, W}, title = {NifH and NifD phylogenies: an evolutionary basis for understanding nitrogen fixation capabilities of methanotrophic bacteria.}, journal = {Microbiology (Reading, England)}, volume = {150}, number = {Pt 5}, pages = {1301-1313}, doi = {10.1099/mic.0.26585-0}, pmid = {15133093}, issn = {1350-0872}, mesh = {Bacterial Proteins/*genetics/metabolism ; Beijerinckiaceae/classification/*genetics/growth &amp; development/metabolism ; DNA, Ribosomal/analysis ; Evolution, Molecular ; Methane/*metabolism ; Molecular Sequence Data ; *Nitrogen Fixation ; Nitrogenase/*genetics/metabolism ; Oxidoreductases/*genetics/metabolism ; *Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The ability to utilize dinitrogen as a nitrogen source is an important phenotypic trait in most currently known methanotrophic bacteria (MB). This trait is especially important for acidophilic MB, which inhabit acidic oligotrophic environments, highly depleted in available nitrogen compounds. Phylogenetically, acidophilic MB are most closely related to heterotrophic dinitrogen-fixing bacteria of the genus BEIJERINCKIA: To further explore the phylogenetic linkage between these metabolically different organisms, the sequences of nifH and nifD gene fragments from acidophilic MB of the genera Methylocella and Methylocapsa, and from representatives of Beijerinckia, were determined. For reference, nifH and nifD sequences were also obtained from some type II MB of the alphaproteobacterial Methylosinus/Methylocystis group and from gammaproteobacterial type I MB. The trees constructed for the inferred amino acid sequences of nifH and nifD were highly congruent. The phylogenetic relationships among MB in the NifH and NifD trees also agreed well with the corresponding 16S rRNA-based phylogeny, except for two distinctive features. First, different methods used for phylogenetic analysis grouped the NifH and NifD sequences of strains of the gammaproteobacterial MB Methylococcus capsulatus within a clade mainly characterized by Alphaproteobacteria, including acidophilic MB and type II MB of the Methylosinus/Methylocystis group. From this and other genomic data from Methylococcus capsulatus Bath, it is proposed that an ancient event of lateral gene transfer was responsible for this aberrant branching. Second, the identity values of NifH and NifD sequences between Methylocapsa acidiphila B2 and representatives of Beijerinckia were clearly higher (98.5 and 96.6 %, respectively) than would be expected from their 16S rRNA-based relationships. Possibly, these two bacteria originated from a common acidophilic dinitrogen-fixing ancestor, and were subject to similar evolutionary pressure with regard to nitrogen acquisition. This interpretation is corroborated by the observation that, in contrast to most other diazotrophs, M. acidiphila B2 and Beijerinckia spp. are capable of active growth on nitrogen-free media under fully aerobic conditions.}, }
@article {pmid15130831, year = {2003}, author = {Braun, EL}, title = {Innovation from reduction: gene loss, domain loss and sequence divergence in genome evolution.}, journal = {Applied bioinformatics}, volume = {2}, number = {1}, pages = {13-34}, pmid = {15130831}, issn = {1175-5636}, mesh = {Chromosome Mapping/*methods ; *Evolution, Molecular ; Fungal Proteins/chemistry/*genetics/*metabolism ; Gene Deletion ; Genetic Variation/*genetics ; Genome, Fungal ; Models, Genetic ; Protein Structure, Tertiary ; Proteome/chemistry/*genetics/*metabolism ; Structure-Activity Relationship ; }, abstract = {Analyses of genome sequences have revealed a surprisingly variable distribution of genes, reflecting the generation of novel genes, lateral gene transfer and gene loss. The impact of gene loss on organisms has been difficult to examine, but the loss of protein coding genes, the loss of domains within proteins and the divergence of genes have made surprising contributions to the differences among organisms. This paper reviews surveys of gene loss and divergence in fungal and archaeal genomes that indicate suites of functionally related genes tend to undergo loss and divergence. Instances of fungal gene loss highlighted here suggest that specific cellular systems have changed, such as Ca 2+ biology in Saccharomyces cerevisiae and peroxisome function in Schizosaccharomyces pombe. Analyses of loss and divergence can provide specific predictions regarding protein-protein interactions, and the relationship between networks of protein interactions and loss may form a part of a parametric model of genome evolution.}, }
@article {pmid15130132, year = {2004}, author = {Waters, CM and Hirt, H and McCormick, JK and Schlievert, PM and Wells, CL and Dunny, GM}, title = {An amino-terminal domain of Enterococcus faecalis aggregation substance is required for aggregation, bacterial internalization by epithelial cells and binding to lipoteichoic acid.}, journal = {Molecular microbiology}, volume = {52}, number = {4}, pages = {1159-1171}, doi = {10.1111/j.1365-2958.2004.04045.x}, pmid = {15130132}, issn = {0950-382X}, support = {5 T32 AI07421-5/AI/NIAID NIH HHS/United States ; GM-066751/GM/NIGMS NIH HHS/United States ; HL-51987/HL/NHLBI NIH HHS/United States ; }, mesh = {*Bacterial Adhesion ; Bacterial Proteins/chemistry/*genetics/isolation &amp; purification/*metabolism ; Cell Line ; Enterococcus faecalis/genetics/growth &amp; development/*physiology ; Enterocytes/*microbiology ; Gene Transfer, Horizontal ; HT29 Cells ; Humans ; Lipopolysaccharides/*metabolism ; Membrane Proteins/genetics/isolation &amp; purification/metabolism ; Mutation ; Plasmids ; Protein Binding ; Protein Structure, Tertiary ; Sequence Deletion ; Teichoic Acids/*metabolism ; Virulence/genetics ; }, abstract = {Aggregation substance (AS), a plasmid-encoded surface protein of Enterococcus faecalis, plays important roles in virulence and antibiotic resistance transfer. Previous studies have suggested that AS-mediated aggregation of enterococcal cells could involve the binding of this protein to cell wall lipoteichoic acid (LTA). Here, a method to purify an undegraded form of Asc10, the AS of the plasmid pCF10, is described. Using this purified protein, direct binding of Asc10 to purified E. faecalis LTA was demonstrated. Equivalent binding of Asc10 to LTA purified from INY3000, an E. faecalis strain that is incapable of aggregation, was also observed. Surprisingly, mutations in a previously identified aggregation domain from amino acids 473 to 683 that abolished aggregation had no effect on LTA binding. In frame deletion analysis of Asc10 was used to identify a second aggregation domain located in the N-terminus of the protein from amino acids 156 to 358. A purified Asc10 mutant protein lacking this domain showed reduced LTA binding, while a purified N-terminal fragment from amino acids 44-331 had high LTA binding. Like the previously described aggregation domain, the newly identified Asc10((156-358)) aggregation domain was also required for efficient internalization of E. faecalis into HT-29 enterocytes. Thus, Asc10 possess two distinct domains required for aggregation and eukaryotic cell internalization: an N-terminal domain that promotes binding to LTA and a second domain located near the middle of the protein.}, }
@article {pmid15128574, year = {2004}, author = {Ventura, M and Canchaya, C and van Sinderen, D and Fitzgerald, GF and Zink, R}, title = {Bifidobacterium lactis DSM 10140: identification of the atp (atpBEFHAGDC) operon and analysis of its genetic structure, characteristics, and phylogeny.}, journal = {Applied and environmental microbiology}, volume = {70}, number = {5}, pages = {3110-3121}, pmid = {15128574}, issn = {0099-2240}, mesh = {Bacterial Proteins/chemistry/*genetics ; Bacterial Proton-Translocating ATPases/chemistry/*genetics ; Base Sequence ; Bifidobacterium/*classification/*genetics/growth &amp; development ; DNA, Ribosomal/analysis ; Gene Expression Regulation, Bacterial ; Lactobacillus/classification/genetics/growth &amp; development ; Molecular Sequence Data ; *Operon ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The atp operon is highly conserved among eubacteria, and it has been considered a molecular marker as an alternative to the 16S rRNA gene. PCR primers were designed from the consensus sequences of the atpD gene to amplify partial atpD sequences from 12 Bifidobacterium species and nine Lactobacillus species. All PCR products were sequenced and aligned with other atpD sequences retrieved from public databases. Genes encoding the subunits of the F(1)F(0)-ATPase of Bifidobacterium lactis DSM 10140 (atpBEFHAGDC) were cloned and sequenced. The deduced amino acid sequences of these subunits showed significant homology with the sequences of other organisms. We identified specific sequence signatures for the genus Bifidobacterium and for the closely related taxa Bifidobacterium lactis and Bifidobacterium animalis and Lactobacillus gasseri and Lactobacillus johnsonii, which could provide an alternative to current methods for identification of lactic acid bacterial species. Northern blot analysis showed that there was a transcript at approximately 7.3 kb, which corresponded to the size of the atp operon, and a transcript at 4.5 kb, which corresponded to the atpC, atpD, atpG, and atpA genes. The transcription initiation sites of these two mRNAs were mapped by primer extension, and the results revealed no consensus promoter sequences. Phylogenetic analysis of the atpD genes demonstrated that the Lactobacillus atpD gene clustered with the genera Listeria, Lactococcus, Streptococcus, and Enterococcus and that the higher G+C content and highly biased codon usage with respect to the genome average support the hypothesis that there was probably horizontal gene transfer. The acid inducibility of the atp operon of B. lactis DSM 10140 was verified by slot blot hybridization by using RNA isolated from acid-treated cultures of B. lactis DSM 10140. The rapid increase in the level of atp operon transcripts upon exposure to low pH suggested that the ATPase complex of B. lactis DSM 10140 was regulated at the level of transcription and not at the enzyme assembly step.}, }
@article {pmid15126486, year = {2004}, author = {Froehlich, B and Holtzapple, E and Read, TD and Scott, JR}, title = {Horizontal transfer of CS1 pilin genes of enterotoxigenic Escherichia coli.}, journal = {Journal of bacteriology}, volume = {186}, number = {10}, pages = {3230-3237}, pmid = {15126486}, issn = {0021-9193}, support = {R01 AI024870/AI/NIAID NIH HHS/United States ; AI24870/AI/NIAID NIH HHS/United States ; }, mesh = {Conjugation, Genetic ; DNA Transposable Elements ; Escherichia coli/*genetics ; Fimbriae Proteins/*genetics ; *Gene Transfer, Horizontal ; *Plasmids ; Recombination, Genetic ; Replication Origin ; }, abstract = {CS1 is one of a limited number of serologically distinct pili found in enterotoxigenic Escherichia coli (ETEC) strains associated with disease in people. The genes for the CS1 pilus are on a large plasmid, pCoo. We show that pCoo is not self-transmissible, although our sequence determination for part of pCoo shows regions almost identical to those in the conjugative drug resistance plasmid R64. When we introduced R64 into a strain containing pCoo, we found that pCoo was transferred to a recipient strain in mating. Most of the transconjugant pCoo plasmids result from recombination with R64, leading to acquisition of functional copies of all of the R64 transfer genes. Temporary coresidence of the drug resistance plasmid R64 with pCoo leads to a permanent change in pCoo so that it is now self-transmissible. We conclude that when R64-like plasmids are transmitted to an ETEC strain containing pCoo, their recombination may allow for spread of the pCoo plasmid to other enteric bacteria.}, }
@article {pmid15123384, year = {2004}, author = {van den Eede, G and Aarts, H and Buhk, HJ and Corthier, G and Flint, HJ and Hammes, W and Jacobsen, B and Midtvedt, T and van der Vossen, J and von Wright, A and Wackernagel, W and Wilcks, A}, title = {The relevance of gene transfer to the safety of food and feed derived from genetically modified (GM) plants.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {42}, number = {7}, pages = {1127-1156}, doi = {10.1016/j.fct.2004.02.001}, pmid = {15123384}, issn = {0278-6915}, mesh = {Animal Feed ; Animals ; *Consumer Product Safety ; European Union ; *Food Analysis/methods ; Food Supply ; Gene Transfer Techniques ; *Gene Transfer, Horizontal ; Genetic Engineering ; Humans ; International Cooperation ; Plants, Genetically Modified/adverse effects/*genetics ; Risk Assessment/*methods ; }, abstract = {In 2000, the thematic network ENTRANSFOOD was launched to assess four different topics that are all related to the testing or assessment of food containing or produced from genetically modified organisms (GMOs). Each of the topics was linked to a European Commission (EC)-funded large shared cost action (see http://www.entransfood.com). Since the exchange of genetic information through horizontal (lateral) gene transfer (HGT) might play a more important role, in quantity and quality, than hitherto imagined, a working group dealing with HGT in the context of food and feed safety was established. This working group was linked to the GMOBILITY project (GMOBILITY, 2003) and the results of the deliberations are laid down in this review paper. HGT is reviewed in relation to the potential risks of consuming food or feed derived from transgenic crops. First, the mechanisms for obtaining transgenic crops are described. Next, HGT mechanisms and its possible evolutionary role are described. The use of marker genes is presented in detail as a special case for genes that may pose a risk. Furthermore, the exposure to GMOs and in particular to genetically modified (GM) deoxyribonucleic acid (DNA) is discussed as part of the total risk assessment. The review finishes off with a number of conclusions related to GM food and feed safety. The aim of this paper is to provide a comprehensive overview to assist risk assessors as well as regulators and the general public in understanding the safety issues related to these mechanisms.}, }
@article {pmid15120599, year = {2004}, author = {Aperghis, M and Johnson, IP and Cannon, J and Yang, SY and Goldspink, G}, title = {Different levels of neuroprotection by two insulin-like growth factor-I splice variants.}, journal = {Brain research}, volume = {1009}, number = {1-2}, pages = {213-218}, doi = {10.1016/j.brainres.2004.02.049}, pmid = {15120599}, issn = {0006-8993}, mesh = {*Alternative Splicing ; Animals ; Cell Survival/genetics ; Facial Muscles/cytology ; Facial Nerve Injuries/*metabolism ; Functional Laterality/physiology ; Gene Transfer, Horizontal/physiology ; Injections, Intramuscular ; Insulin-Like Growth Factor I/chemistry/genetics/*physiology ; Male ; Motor Neurons/*metabolism ; Myosin Heavy Chains/genetics ; RNA, Messenger/biosynthesis ; Rabbits ; Rats ; Rats, Sprague-Dawley ; Reverse Transcriptase Polymerase Chain Reaction/methods ; Transfection/methods ; }, abstract = {We compared the neuroprotective effects of a liver-type isoform of insulin-like growth factor-I (IGF-IEa) and its splice variant, mechano-growth factor (MGF), isolated from active skeletal muscle. cDNAs of these peptides were injected into the facial muscle of adult rats prior to facial nerve avulsion. This resulted in significant neuroprotection of 88% and 37%, respectively, of motoneurons compared to control plasmid and avulsion-only groups. MGF is markedly more effective than the liver-type, systemic IGF-I for motoneuron survival, suggesting a major role for the peripheral target in adult neuronal maintenance and survival.}, }
@article {pmid15120140, year = {2004}, author = {Gophna, U and Charlebois, RL and Doolittle, WF}, title = {Have archaeal genes contributed to bacterial virulence?.}, journal = {Trends in microbiology}, volume = {12}, number = {5}, pages = {213-219}, doi = {10.1016/j.tim.2004.03.002}, pmid = {15120140}, issn = {0966-842X}, mesh = {Bacteria/*genetics/*pathogenicity ; Chloride Channels/genetics ; Gene Transfer, Horizontal ; *Genes, Archaeal ; Genome, Bacterial ; Models, Biological ; Mycobacterium tuberculosis/genetics/pathogenicity ; Open Reading Frames ; Phylogeny ; Virulence/genetics ; }, }
@article {pmid15119351, year = {2004}, author = {Ihrmark, K and Stenström, E and Stenlid, J}, title = {Double-stranded RNA transmission through basidiospores of Heterobasidion annosum.}, journal = {Mycological research}, volume = {108}, number = {Pt 2}, pages = {149-153}, doi = {10.1017/s0953756203008839}, pmid = {15119351}, issn = {0953-7562}, mesh = {Agaricales/growth &amp; development/*virology ; *Gene Transfer, Horizontal ; Plant Diseases/microbiology ; RNA Viruses/genetics/*physiology ; RNA, Double-Stranded/*genetics/isolation &amp; purification ; Spores, Fungal/physiology/*virology ; Tracheophyta/microbiology ; Virus Integration ; }, abstract = {A search for double-stranded RNA (dsRNA) was conducted among 106 isolates of the pathogenic basidiomycete Heterobasidion annosum. Of these isolates, 47 were tissue isolates from fruit bodies and 59 were isolated from decayed wood. Nucleic acids were extracted from freeze-dried mycelia and dsRNA was separated by cellulose CF-11 chromatography and confirmed by digestions with specific nucleases. dsRNA was present in 19 and 14% of the tissue and wood isolates, respectively. From five of the fruit bodies containing dsRNA basidiospores were investigated and 10-84% of the germinated basidiospores contained dsRNA. On high nutrient media, the germination frequency of basidiospores was reduced by presence of dsRNA in the fruit body (P < 0.05); germination frequencies were 34 and 78% for spores from fruit bodies with and without dsRNA, respectively. The same trend was present also on low nutrient media, although not statistically significant; germination was 3 and 10% for spores from infected and dsRNA free fruit bodies, respectively. Transmission of dsRNA in H. annosum from mycelia into basidiospores together with the lowered germination frequency are likely to play a significant role in the life cycle of the fungus. The relative importance of different transmission routes for dsRNA in H. annosum is discussed.}, }
@article {pmid15118835, year = {2004}, author = {Temporini, ED and VanEtten, HD}, title = {An analysis of the phylogenetic distribution of the pea pathogenicity genes of Nectria haematococca MPVI supports the hypothesis of their origin by horizontal transfer and uncovers a potentially new pathogen of garden pea: Neocosmospora boniensis.}, journal = {Current genetics}, volume = {46}, number = {1}, pages = {29-36}, pmid = {15118835}, issn = {0172-8083}, mesh = {Ascomycota/genetics/pathogenicity ; Gene Transfer, Horizontal ; *Genes, Fungal ; Multigene Family ; Pisum sativum/*genetics/microbiology ; Phylogeny ; Virulence ; }, abstract = {The filamentous fungus Nectria haematococca mating population VI (MPVI) contains a cluster of genes required to cause disease on pea. This cluster of pea pathogenicity genes (the PEP cluster) is located on a supernumerary chromosome that is dispensable for normal growth in culture. The genes in the PEP cluster have a different G+C content and codon usage compared with the genes located on the other chromosomes and a non-homogeneous distribution within the species. These features suggest that the PEP cluster may have been acquired by N. haematococca MPVI through horizontal gene transfer (HGT). In this work, we show that homologues of the PEP genes are present in another pea pathogen, Fusarium oxysporum f. sp. pisi, but are not common among fungi that are phylogenetically closely related to N. haematococca MPVI. This phylogenetic discontinuity supports the hypothesis that the PEP cluster originated by HGT. Our analysis has also determined that homologues for all the PEP genes are present in Neocosmospora boniensis. A molecular characterization of the PEP homologues in this fungus shows that they are organized as a cluster, which has a different physical organization from the PEP cluster in N. haematococca. In addition, although no reports have been found to show that N. boniensis is a naturally occurring pea pathogen, we show here that this species is able to cause disease on pea.}, }
@article {pmid15115803, year = {2004}, author = {Taoka, M and Yamauchi, Y and Shinkawa, T and Kaji, H and Motohashi, W and Nakayama, H and Takahashi, N and Isobe, T}, title = {Only a small subset of the horizontally transferred chromosomal genes in Escherichia coli are translated into proteins.}, journal = {Molecular &amp; cellular proteomics : MCP}, volume = {3}, number = {8}, pages = {780-787}, doi = {10.1074/mcp.M400030-MCP200}, pmid = {15115803}, issn = {1535-9476}, mesh = {Bacterial Proteins/*genetics/isolation &amp; purification ; Chromatography, Liquid ; Chromosomes, Bacterial/genetics ; Escherichia coli K12/*genetics ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Mass Spectrometry ; Oligonucleotide Array Sequence Analysis ; *Protein Biosynthesis ; }, abstract = {Horizontally transferred genes are believed to play a critical role in the divergence of bacterial strains from a common ancestor, but whether all of these genes express functional proteins in the cell remains unknown. Here, we used an integrated LC-based protein identification technology to analyze the proteome of Escherichia coli strain K12 (JM109) and identified 1,480 expressed proteins, which are equivalent to approximately 35% of the total open reading frames predicted in the genome. This subset contained proteins with cellular abundance of several dozens to hundreds of thousands of copies, and included nearly all types of proteins in terms of chemical characteristics, subcellular distribution, and function. Interestingly, the subset also contained 138 of 164 gene products that are currently known to be essential for bacterial viability (84% coverage). However, the subset contained only a very small population (10%) of protein products from genes mapped within K-loops, which are "hot spots" for the integration of foreign DNAs within the K12 genome. On the other hand, these genes in K-loops appeared to be transcribed to RNAs almost as efficiently as the native genes in the bacterial cell as monitored by DNA microarray analysis, raising the possibility that most of the recently acquired foreign genes are inadequate for the translational machinery for the native genes and do not generate functional proteins within the cell.}, }
@article {pmid15115802, year = {2004}, author = {Hao, W and Golding, GB}, title = {Patterns of bacterial gene movement.}, journal = {Molecular biology and evolution}, volume = {21}, number = {7}, pages = {1294-1307}, doi = {10.1093/molbev/msh129}, pmid = {15115802}, issn = {0737-4038}, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/*genetics ; *Genome, Bacterial ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Lateral gene transfer has emerged as an important force in bacterial evolution. A substantial number of genes can be inserted into or deleted from genomes through the process of lateral transfer. In this study, we looked for atypical occurrence of genes among related organisms to detect laterally transferred genes. We have analyzed 50 bacterial complete genomes from nine groups. For each group we use a 16s rRNA phylogeny and a comparison of protein similarity to map gene insertions/deletions onto their species phylogeny. The results reveal that there is poor correlation of genes inserted, deleted, and duplicated with evolutionary branch length. In addition, the numbers of genes inserted, deleted, or duplicated within the same branch are not always correlated with each other. Nor is there any similarity within groups. For example, in the Rhizobiales group, the ratio of insertions to deletions in the evolutionary branch leading to Agrobacterium tumefaciens str. C58 (Cereon) is 0.52, but it is 39.52 for Mesorhizobium loti. Most strikingly, the number of insertions of foreign genes is much larger in the external branches of the trees. These insertions also greatly outnumber the occurrence of deletions, and yet the genome sizes of these bacteria remain roughly constant. This indicates that many of the insertions are specific to each organism and are lost before related species can evolve. Simulations of the process of insertion and deletion, tailored to each phylogeny, support this conclusion.}, }
@article {pmid15114416, year = {2004}, author = {Rogers, M and Keeling, PJ}, title = {Lateral transfer and recompartmentalization of Calvin cycle enzymes of plants and algae.}, journal = {Journal of molecular evolution}, volume = {58}, number = {4}, pages = {367-375}, pmid = {15114416}, issn = {0022-2844}, mesh = {Eukaryota/*enzymology/genetics ; Fructose-Bisphosphatase/genetics ; Fructose-Bisphosphate Aldolase/genetics ; *Gene Transfer, Horizontal ; Phosphoric Monoester Hydrolases/genetics ; Plants/*enzymology/genetics ; }, abstract = {Certain Calvin cycle enzymes also function in glycolysis or gluconeogenisis, thus photosynthetic eukaryotes would be predicted to have ancestrally possessed cytosolic homologues of these enzymes derived from the eukaryotic host and plastid homologues from the cyanobacterial endosymbiont. In practice, the evolutionary histories of these enzymes are often more complex. Focusing on eukaryotes with secondary plastids, we have examined the evolution of four such genes: class I and II fructose bisphosphate aldolase (FBA), sedoheptulose bisphosphatase (SBPase), and fructose bisphosphatase (FBPase). We show that previously observed distributions of plastid and cytosolic homologues are not always found in algae with secondary plastids: there is evidence for multiple events of both lateral gene transfer and retargeting to a new cellular compartment for both cytosolic and plastid enzymes of plants and algae. In particular, we show that a clade of class II FBAs spans a greater diversity of eukaryotes that previously recognized and contains both plastid-targeted (Phaeodactylum, Odontella) and cytosolic (ascomycetes, oomycetes, Euglena, and Bigelowiella) forms. Lateral transfer events also gave rise to a subset of plant cytosolic FBA, as well as cytosolic FBPase in Toxoplasma and other coccidian apicomplexa. In contrast, it has recently been suggested that the Trypanosoma FBA and SBPase are derived from a plastid, however, greater taxonomic sampling shows that these enzymes provide no evidence for a plastid-containing ancestor of Trypanosoma. Altogether, the evolutionary histories of the FBA and SBPase/FBPase gene families are complex, including extensive paralogy, lateral transfer, and retargeting between cellular compartments.}, }
@article {pmid15113412, year = {2004}, author = {Merkl, R}, title = {SIGI: score-based identification of genomic islands.}, journal = {BMC bioinformatics}, volume = {5}, number = {}, pages = {22}, pmid = {15113412}, issn = {1471-2105}, mesh = {Algorithms ; Base Composition/genetics ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Genes, Archaeal/genetics ; Genes, Bacterial/genetics ; Genome, Archaeal ; Genome, Bacterial ; Genomic Islands/*genetics ; Interspersed Repetitive Sequences/genetics ; Models, Genetic ; Molecular Sequence Data ; Software ; }, abstract = {BACKGROUND: Genomic islands can be observed in many microbial genomes. These stretches of DNA have a conspicuous composition with regard to sequence or encoded functions. Genomic islands are assumed to be frequently acquired via horizontal gene transfer. For the analysis of genome structure and the study of horizontal gene transfer, it is necessary to reliably identify and characterize these islands.<br><br>RESULTS: A scoring scheme on codon frequencies Score_G1G2(cdn) = log(f_G2(cdn) / f_G1(cdn)) was utilized. To analyse genes of a species G1 and to test their relatedness to species G2, scores were determined by applying the formula to log-odds derived from mean codon frequencies of the two genomes. A non-redundant set of nearly 400 codon usage tables comprising microbial species was derived; its members were used alternatively at position G2. Genes having at least one score value above a species-specific and dynamically determined cut-off value were analysed further. By means of cluster analysis, genes were identified that comprise clusters of statistically significant size. These clusters were predicted as genomic islands. Finally and individually for each of these genes, the taxonomical relation among those species responsible for significant scores was interpreted. The validity of the approach and its limitations were made plausible by an extensive analysis of natural genes and synthetic ones aimed at modelling the process of gene amelioration.<br><br>CONCLUSIONS: The method reliably allows to identify genomic island and the likely origin of alien genes.}, }
@article {pmid15112236, year = {2004}, author = {Bazinet, C}, title = {Endosymbiotic origins of sex.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {26}, number = {5}, pages = {558-566}, doi = {10.1002/bies.20023}, pmid = {15112236}, issn = {0265-9247}, support = {HD36498-01/HD/NICHD NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Gene Transfer, Horizontal ; Germ Cells/physiology ; Mitochondria/metabolism ; *Reproduction ; Reproduction, Asexual ; Sperm Motility ; Spermatogenesis/physiology ; *Symbiosis ; }, abstract = {Understanding how complex sexual reproduction arose, and why sexual organisms have been more successful than otherwise similar asexual organisms, is a longstanding problem in evolutionary biology. Within this problem, the potential role of endosymbionts or intracellular pathogens in mediating primitive genetic transfers is a continuing theme. In recent years, several remarkable activities of mitochondria have been observed in the germline cells of complex eukaryotes, and it has been found that bacterial endosymbionts related to mitochondria are capable of manipulating diverse aspects of metazoan gametogenesis. An attempt is made here to rationalize these observations with an endosymbiotic model for the evolutionary origins of sex. It is hypothesized that the contemporary life cycle of germline cells has descended from the life cycle of the endosymbiotic ancestor of the mitochondrion. Through an actin-based motility that drove it from one cell to another, the rickettsial ancestor of mitochondria may have functioned as a primitive transducing particle, the evolutionary progenitor of sperm.}, }
@article {pmid15112225, year = {2004}, author = {Brown, JR and Volker, C}, title = {Phylogeny of gamma-proteobacteria: resolution of one branch of the universal tree?.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {26}, number = {5}, pages = {463-468}, doi = {10.1002/bies.20030}, pmid = {15112225}, issn = {0265-9247}, mesh = {Bacterial Proteins/classification/genetics ; *Biological Evolution ; Gammaproteobacteria/*classification/*genetics ; Gene Transfer, Horizontal ; Genome, Bacterial ; *Phylogeny ; }, abstract = {The reconstruction of bacterial evolutionary relationships has proven to be a daunting task because variable mutation rates and horizontal gene transfer (HGT) among species can cause grave incongruities between phylogenetic trees based on single genes. Recently, a highly robust phylogenetic tree was constructed for 13 gamma-proteobacteria using the combined alignments of 205 conserved orthologous proteins.1 Only two proteins had incongruent tree topologies, which were attributed to HGT between Pseudomonas species and Vibrio cholerae or enterics. While the evolutionary relationships among these species appears to be resolved, further analysis suggests that HGT events with other bacterial partners likely occurred; this alters the implicit assumption of gamma-proteobacteria monophyly. Thus, any thorough reconstruction of bacterial evolution must not only choose a suitable set of molecular markers but also strive to reduce potential bias in the selection of species.}, }
@article {pmid15109941, year = {2004}, author = {Dell, H}, title = {Scavengers beware!.}, journal = {Drug discovery today}, volume = {9}, number = {10}, pages = {425}, doi = {10.1016/S1359-6446(04)03098-3}, pmid = {15109941}, issn = {1359-6446}, mesh = {Animals ; Cryptosporidiosis/parasitology/*therapy ; Cryptosporidium parvum/*genetics ; *Gene Transfer, Horizontal ; Genome, Protozoan ; Host-Parasite Interactions ; In Vitro Techniques ; Public Health ; Pyrimidine Nucleotides/genetics ; }, }
@article {pmid15109780, year = {2004}, author = {Zhaxybayeva, O and Lapierre, P and Gogarten, JP}, title = {Genome mosaicism and organismal lineages.}, journal = {Trends in genetics : TIG}, volume = {20}, number = {5}, pages = {254-260}, doi = {10.1016/j.tig.2004.03.009}, pmid = {15109780}, issn = {0168-9525}, mesh = {Cell Lineage ; Databases as Topic ; *Gene Transfer Techniques ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome ; Models, Genetic ; *Mosaicism ; Phylogeny ; RNA, Ribosomal/metabolism ; }, }
@article {pmid15105882, year = {2004}, author = {Walther-Rasmussen, J and Høiby, N}, title = {Cefotaximases (CTX-M-ases), an expanding family of extended-spectrum beta-lactamases.}, journal = {Canadian journal of microbiology}, volume = {50}, number = {3}, pages = {137-165}, doi = {10.1139/w03-111}, pmid = {15105882}, issn = {0008-4166}, mesh = {Cefotaxime/*metabolism ; Cephalosporins/metabolism ; Clavulanic Acid/pharmacology ; Drug Resistance, Bacterial/*genetics ; Enterobacteriaceae/drug effects/enzymology/genetics ; Enzyme Inhibitors/pharmacology ; Gene Transfer, Horizontal ; Monobactams/metabolism ; Penicillanic Acid/*analogs &amp; derivatives/pharmacology ; Penicillins/metabolism ; Phylogeny ; Sulbactam/pharmacology ; Tazobactam ; beta-Lactamases/*genetics/*metabolism ; }, abstract = {Among the extended-spectrum beta-lactamases, the cefotaximases (CTX-M-ases) constitute a rapidly growing cluster of enzymes that have disseminated geographically. The CTX-M-ases, which hydrolyze cefotaxime efficiently, are mostly encoded by transferable plasmids, and the enzymes have been found predominantly in Enterobacteriaceae, most prevalently in Escherichia coli, Salmonella typhimurium, Klebsiella pneumoniae, and Proteus mirabilis. Isolates of Vibrio cholerae, Acinetobacter baumannii, and Aeromonas hydrophila encoding CTX-M-ases have also been reported. The CTX-M-ases belong to the molecular class A beta-lactamases, and the enzymes are functionally characterized as extended-spectrum beta-lactamases. This group of beta-lactamases confers resistance to penicillins, extended-spectrum cephalosporins, and monobactams, and the enzymes are inhibited by clavulanate, sulbactam, and tazobactam. Typically, the CTX-M-ases hydrolyze cefotaxime more efficiently than ceftazidime, which is reflected in substantially higher MICs to cefotaxime than to ceftazidime. Phylogenetically, the CTX-M-ases are divided into four subfamilies that seem to have descended from chromosomal beta-lactamases of Kluyvera spp. Insertion sequences, especially ISEcp1, have been found adjacent to genes encoding enzymes of all four subfamilies. The class I integron-associated orf513 also seems to be involved in the mobilization of blaCTX-M genes. This review discusses the phylogeny and the hydrolytic properties of the CTX-M-ases, as well as their geographic occurrence and mode of spread.}, }
@article {pmid15100989, year = {2004}, author = {de Almeida, R and Trevilato, PB and Bartoleti, LA and Proença-Módena, JL and Hanna, ES and Gregoracci, GB and Brocchi, M}, title = {Bacteriophages and insertion sequences of Chromobacterium violaceum ATCC 12472.}, journal = {Genetics and molecular research : GMR}, volume = {3}, number = {1}, pages = {76-84}, pmid = {15100989}, issn = {1676-5680}, mesh = {Bacteriophages/*genetics ; Chromobacterium/genetics/*virology ; DNA Transposable Elements/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; }, abstract = {A fluid genome is a great advantage to prokaryotes, enabling quick adaptation to various types of ecological niches and to diverse environmental selective pressures. A substantial portion of these sudden changes is mediated by lateral gene transfer (LGT), through genetic recombination mechanisms, such as transformation, conjugation and transduction. The recent sequencing of several organisms has offered a new approach to the study of LGT, using comparison and analysis of nucleotide sequences dispersed throughout the genome of these species. This analysis in Choromobacterium violaceum has revealed four prophage and 12 insertion sequences, suggesting genetic exchange with several other bacterial species, including Salmonella enterica, Ralstonia and Xanthomonas. An Rhs (recombination hot spot) element (containing a vgr-like gene) was also observed, the function of which remains unknown, but it has a sequence related to species of Acinetobacter and Sphingomonas. These results support the role of LGT in the acquisition of new traits by C. violaceum.}, }
@article {pmid15100694, year = {2004}, author = {Dobrindt, U and Hochhut, B and Hentschel, U and Hacker, J}, title = {Genomic islands in pathogenic and environmental microorganisms.}, journal = {Nature reviews. Microbiology}, volume = {2}, number = {5}, pages = {414-424}, doi = {10.1038/nrmicro884}, pmid = {15100694}, issn = {1740-1526}, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial ; Genomic Islands/*genetics ; Gram-Negative Bacteria/*genetics/pathogenicity ; Gram-Positive Bacteria/*genetics/pathogenicity ; }, }
@article {pmid15090524, year = {2004}, author = {Haake, DA and Suchard, MA and Kelley, MM and Dundoo, M and Alt, DP and Zuerner, RL}, title = {Molecular evolution and mosaicism of leptospiral outer membrane proteins involves horizontal DNA transfer.}, journal = {Journal of bacteriology}, volume = {186}, number = {9}, pages = {2818-2828}, pmid = {15090524}, issn = {0021-9193}, support = {AI 34431/AI/NIAID NIH HHS/United States ; R01 AI034431-07/AI/NIAID NIH HHS/United States ; GM 068955/GM/NIGMS NIH HHS/United States ; R01 GM068955/GM/NIGMS NIH HHS/United States ; R21 AI034431/AI/NIAID NIH HHS/United States ; P30 CA016042/CA/NCI NIH HHS/United States ; CA 16042/CA/NCI NIH HHS/United States ; R01 AI034431/AI/NIAID NIH HHS/United States ; R29 AI034431/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacterial Outer Membrane Proteins/*genetics ; Conserved Sequence ; DNA, Bacterial/chemistry ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Leptospira/classification/*genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Leptospires belong to a genus of parasitic bacterial spirochetes that have adapted to a broad range of mammalian hosts. Mechanisms of leptospiral molecular evolution were explored by sequence analysis of four genes shared by 38 strains belonging to the core group of pathogenic Leptospira species: L. interrogans, L. kirschneri, L. noguchii, L. borgpetersenii, L. santarosai, and L. weilii. The 16S rRNA and lipL32 genes were highly conserved, and the lipL41 and ompL1 genes were significantly more variable. Synonymous substitutions are distributed throughout the ompL1 gene, whereas nonsynonymous substitutions are clustered in four variable regions encoding surface loops. While phylogenetic trees for the 16S, lipL32, and lipL41 genes were relatively stable, 8 of 38 (20%) ompL1 sequences had mosaic compositions consistent with horizontal transfer of DNA between related bacterial species. A novel Bayesian multiple change point model was used to identify the most likely sites of recombination and to determine the phylogenetic relatedness of the segments of the mosaic ompL1 genes. Segments of the mosaic ompL1 genes encoding two of the surface-exposed loops were likely acquired by horizontal transfer from a peregrine allele of unknown ancestry. Identification of the most likely sites of recombination with the Bayesian multiple change point model, an approach which has not previously been applied to prokaryotic gene sequence analysis, serves as a model for future studies of recombination in molecular evolution of genes.}, }
@article {pmid15090503, year = {2004}, author = {Acinas, SG and Marcelino, LA and Klepac-Ceraj, V and Polz, MF}, title = {Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons.}, journal = {Journal of bacteriology}, volume = {186}, number = {9}, pages = {2629-2635}, pmid = {15090503}, issn = {0021-9193}, mesh = {Gene Dosage ; Gene Transfer, Horizontal ; *Genome, Archaeal ; *Genome, Bacterial ; *Operon ; RNA, Ribosomal, 16S/*chemistry/genetics ; }, abstract = {The level of sequence heterogeneity among rrn operons within genomes determines the accuracy of diversity estimation by 16S rRNA-based methods. Furthermore, the occurrence of widespread horizontal gene transfer (HGT) between distantly related rrn operons casts doubt on reconstructions of phylogenetic relationships. For this study, patterns of distribution of rrn copy numbers, interoperonic divergence, and redundancy of 16S rRNA sequences were evaluated. Bacterial genomes display up to 15 operons and operon numbers up to 7 are commonly found, but approximately 40% of the organisms analyzed have either one or two operons. Among the Archaea, a single operon appears to dominate and the highest number of operons is five. About 40% of sequences among 380 operons in 76 bacterial genomes with multiple operons were identical to at least one other 16S rRNA sequence in the same genome, and in 38% of the genomes all 16S rRNAs were invariant. For Archaea, the number of identical operons was only 25%, but only five genomes with 21 operons are currently available. These considerations suggest an upper bound of roughly threefold overestimation of bacterial diversity resulting from cloning and sequencing of 16S rRNA genes from the environment; however, the inclusion of genomes with a single rrn operon may lower this correction factor to approximately 2.5. Divergence among operons appears to be small overall for both Bacteria and Archaea, with the vast majority of 16S rRNA sequences showing <1% nucleotide differences. Only five genomes with operons with a higher level of nucleotide divergence were detected, and Thermoanaerobacter tengcongensis exhibited the highest level of divergence (11.6%) noted to date. Overall, four of the five extreme cases of operon differences occurred among thermophilic bacteria, suggesting a much higher incidence of HGT in these bacteria than in other groups.}, }
@article {pmid15090498, year = {2004}, author = {O'Rourke, EJ and Pinto, AV and Petroni, EA and Tolmasky, ME and Ielpi, L}, title = {Evidence for the active role of a novel nuclease from Helicobacter pylori in the horizontal transfer of genetic information.}, journal = {Journal of bacteriology}, volume = {186}, number = {9}, pages = {2586-2593}, pmid = {15090498}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; Base Sequence ; DNA/metabolism ; Deoxyribonucleases/analysis/chemistry/*physiology ; *Gene Transfer, Horizontal ; Helicobacter pylori/*genetics ; *Transformation, Bacterial ; }, abstract = {Helicobacter pylori is a gram-negative bacterium that colonizes the human stomach, causes gastritis, and is associated with ulcers and gastric cancer. H. pylori is naturally competent for transformation. Natural genetic transformation is believed to be essential for the genetic plasticity observed in this species. While the relevance of horizontal gene transfer in H. pylori adaptiveness and antibiotic resistance is well documented, the DNA transformation machinery components are barely known. No enzymatic activity associated with the transformation process has been determined experimentally and described. We isolated, microsequenced, and cloned a major DNA nuclease from H. pylori. This protein, encoded by the open reading frame hp0323, was expressed in Escherichia coli. The purified protein, NucT, has a cation-independent thermostable nuclease activity that preferentially cleaves single-stranded DNA. NucT is associated with the membrane. NucT-deficient H. pylori strains are one or more orders of magnitude less efficient than the parental strain for transformation with either chromosomal or self-replicating plasmid DNA. To the best of our knowledge, NucT is the first nuclease identified in a gram-negative natural transformation system, and its existence suggests that there is a mechanism of DNA processing and uptake similar to the mechanisms in well-studied gram-positive systems.}, }
@article {pmid15087136, year = {2004}, author = {Brochier, C and López-García, P and Moreira, D}, title = {Horizontal gene transfer and archaeal origin of deoxyhypusine synthase homologous genes in bacteria.}, journal = {Gene}, volume = {330}, number = {}, pages = {169-176}, doi = {10.1016/j.gene.2004.01.018}, pmid = {15087136}, issn = {0378-1119}, mesh = {Amino Acid Sequence ; Archaea/enzymology/*genetics ; Bacteria/enzymology/*genetics ; Eukaryotic Cells/metabolism ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Oxidoreductases Acting on CH-NH Group Donors/*genetics ; Peptide Initiation Factors/genetics ; Phylogeny ; RNA-Binding Proteins/genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; Eukaryotic Translation Initiation Factor 5A ; }, abstract = {The initiation factor 5A (IF-5A) of archaea and eukaryotes undergoes an unusual post-translational modification consisting of the transformation of a specific conserved lysine residue into the amino acid hypusine. This occurs in a two-step reaction catalysed by the enzymes deoxyhypusine synthase (DHS) and deoxyhypusine hydroxylase. Bacteria do not have IF-5A but only a very distant homologue, the elongation factor P (EF-P). Consequently, all bacteria appeared to also lack genes with significant homology to DHS genes. However, we have carried out BLAST searches and found DHS-like genes in a number of bacterial species. The phylogenetic analysis of these sequences strongly suggests that they have been acquired from archaea by horizontal gene transfer (HGT). Our analysis also suggests, although with weaker support, that a single HGT event from archaea, followed by several HGT between bacterial species, accounts for the patchy distribution of DHS-like genes in bacteria. The activity of these genes in bacteria is enigmatic, since we have not found any evidence of interaction between this protein and the bacterial EF-P. Nevertheless, we cannot discard that it exists, since it appears that the interaction between the DHS and its natural substrate, the IF-5A, is rather weak. This is exemplified by the fact that, in archaea, the complex evolutionary history of the DHS is not paralleled by that of the IF-5A, indicating that these proteins do not follow a perfect co-evolution.}, }
@article {pmid15084296, year = {2004}, author = {Steele, RE and Hampson, SE and Stover, NA and Kibler, DF and Bode, HR}, title = {Probable horizontal transfer of a gene between a protist and a cnidarian.}, journal = {Current biology : CB}, volume = {14}, number = {8}, pages = {R298-9}, doi = {10.1016/j.cub.2004.03.047}, pmid = {15084296}, issn = {0960-9822}, mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins/*genetics ; Base Sequence ; DNA, Complementary/genetics ; Gene Transfer, Horizontal/*genetics ; Hydra/*genetics ; Molecular Sequence Data ; RNA, Spliced Leader/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Trichomonas vaginalis/*genetics ; }, }
@article {pmid15080070, year = {2004}, author = {Liu, W and Xin, Z}, title = {[Male reproduction related genes and their function].}, journal = {Zhonghua nan ke xue = National journal of andrology}, volume = {10}, number = {3}, pages = {208-210}, pmid = {15080070}, issn = {1009-3591}, mesh = {Animals ; Gene Targeting ; Gene Transfer, Horizontal ; Genes/*physiology ; Genetic Vectors/genetics ; Humans ; Male ; Models, Animal ; Oligonucleotides, Antisense/therapeutic use ; Reproduction/*genetics ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {With the proceeding of the human genome program(HGP), new genes related to male reproduction have been cloned continuously by different methods. However, investigation of the gene function is still at the rudimentary stage. In spite of the advances in the common methods of studying gene function, some special methods have yet to be developed concerning the study of the genes related to male reproduction. This paper summarizes the current methods of study on gene function relevant to male reproduction.}, }
@article {pmid15073324, year = {2004}, author = {Horn, M and Collingro, A and Schmitz-Esser, S and Beier, CL and Purkhold, U and Fartmann, B and Brandt, P and Nyakatura, GJ and Droege, M and Frishman, D and Rattei, T and Mewes, HW and Wagner, M}, title = {Illuminating the evolutionary history of chlamydiae.}, journal = {Science (New York, N.Y.)}, volume = {304}, number = {5671}, pages = {728-730}, doi = {10.1126/science.1096330}, pmid = {15073324}, issn = {1095-9203}, mesh = {Acanthamoeba/microbiology ; Animals ; Bacterial Proteins/analysis/genetics/metabolism ; *Biological Evolution ; Cell Membrane/chemistry ; Cell Wall/chemistry ; Chlamydia/classification/genetics/metabolism/pathogenicity ; Chlamydiales/*classification/*genetics/metabolism/pathogenicity ; Chlamydophila/classification/genetics/metabolism/pathogenicity ; Electron Transport ; Gene Order ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; Molecular Sequence Data ; Nucleotide Transport Proteins/metabolism ; Phylogeny ; Symbiosis ; Virulence ; Virulence Factors/genetics/metabolism ; }, abstract = {Chlamydiae are the major cause of preventable blindness and sexually transmitted disease. Genome analysis of a chlamydia-related symbiont of free-living amoebae revealed that it is twice as large as any of the pathogenic chlamydiae and had few signs of recent lateral gene acquisition. We showed that about 700 million years ago the last common ancestor of pathogenic and symbiotic chlamydiae was already adapted to intracellular survival in early eukaryotes and contained many virulence factors found in modern pathogenic chlamydiae, including a type III secretion system. Ancient chlamydiae appear to be the originators of mechanisms for the exploitation of eukaryotic cells.}, }
@article {pmid15072696, year = {2004}, author = {Makarenkov, V and Legendre, P}, title = {From a phylogenetic tree to a reticulated network.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {11}, number = {1}, pages = {195-212}, doi = {10.1089/106652704773416966}, pmid = {15072696}, issn = {1066-5277}, mesh = {*Algorithms ; Animals ; Bacteria/genetics ; Computer Simulation ; Eukaryota/genetics ; *Evolution, Molecular ; Humans ; *Models, Genetic ; *Phylogeny ; Plants/genetics ; *Software ; }, abstract = {In many phylogenetic problems, assuming that species have evolved from a common ancestor by a simple branching process is unrealistic. Reticulate phylogenetic models, however, have been largely neglected because the concept of reticulate evolution have not been supported by using appropriate analytical tools and software. The reticulate model can adequately describe such complicated mechanisms as hybridization between species or lateral gene transfer in bacteria. In this paper, we describe a new algorithm for inferring reticulate phylogenies from evolutionary distances among species. The algorithm is capable of detecting contradictory signals encompassed in a phylogenetic tree and identifying possible reticulate events that may have occurred during evolution. The algorithm produces a reticulate phylogeny by gradually improving upon the initial solution provided by a phylogenetic tree model. The new algorithm is compared to the popular SplitsGraph method in a reanalysis of the evolution of photosynthetic organisms. A computer program to construct and visualize reticulate phylogenies, called T-Rex (Tree and Reticulogram Reconstruction), is available to researchers at the following URL: www.fas.umontreal.ca/biol/casgrain/en/labo/t-rex.}, }
@article {pmid15071038, year = {2004}, author = {Baek, JY and Ko, KS and Oh, WS and Jung, SI and Kim, YS and Chang, HH and Lee, H and Kim, SW and Peck, KR and Lee, NY and Song, JH}, title = {Unique variations of pbp2b sequences in penicillin-nonsusceptible Streptococcus pneumoniae isolates from Korea.}, journal = {Journal of clinical microbiology}, volume = {42}, number = {4}, pages = {1746-1750}, pmid = {15071038}, issn = {0095-1137}, mesh = {Amino Acid Sequence ; *Aminoacyltransferases ; Bacterial Proteins/*genetics ; Carrier Proteins/*genetics ; *Genetic Variation ; Hexosyltransferases/*genetics ; Humans ; Korea ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Muramoylpentapeptide Carboxypeptidase/*genetics ; Penicillin Resistance/*genetics ; Penicillin-Binding Proteins ; Penicillins/pharmacology ; Peptidyl Transferases/*genetics ; Pneumococcal Infections/*microbiology ; Polymerase Chain Reaction/methods ; Sequence Alignment ; Sequence Analysis, DNA ; Streptococcus pneumoniae/*drug effects/enzymology/genetics ; }, abstract = {pbp2b gene alterations were analyzed in 102 clinical isolates of Streptococcus pneumoniae (30 penicillin susceptible, 23 intermediate, and 49 resistant) from Korea. On the basis of PBP2B amino acid sequences, penicillin-nonsusceptible isolates of S. pneumoniae belonged to six groups, and 76% of the isolates in groups I to IV showed the same divergent block of amino acid alterations. Thirteen isolates (group II) also possessed a divergent block that was identical to that of Streptococcus oralis. The pbp2b genes of most Korean isolates showed novel mosaic mutations due to horizontal gene transfer. The Thr252 --> Ala substitution, previously thought to be associated only with penicillin-nonsusceptible strains, was also found in three penicillin-susceptible strains. On the basis of their pbp2b nucleotide sequences, all penicillin-nonsusceptible isolates can be detected by multiplex PCR, which can be used as a novel method for detection of antibiotic-resistant pneumococcal strains in clinical specimens.}, }
@article {pmid15068024, year = {2004}, author = {Zechner, EL and Bailey, MJ}, title = {The Horizontal Gene Pool: an ESF workshop summary.}, journal = {Plasmid}, volume = {51}, number = {2}, pages = {67-74}, doi = {10.1016/j.plasmid.2004.01.002}, pmid = {15068024}, issn = {0147-619X}, mesh = {Bacteria/*genetics ; Gene Pool ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Interspersed Repetitive Sequences/*genetics ; Selection, Genetic ; }, abstract = {The European Science Foundation (ESF) funds a limited number of exploratory workshops each year that enable scientists to meet and develop plans for a program of integrated research which would benefit from a coordinated European effort. In summer 2003, the Standing Committee for Life and Environmental Sciences (LESC) sponsored such a workshop called The Horizontal Gene Pool: The Functional Role of Mobile Genetic Information--How Bacteria Perceive, Sample, and Utilize Genetic Elements in evolution and Local Adaptation. The workshop took place at St. Catherine's College, Oxford, UK. Its purpose was to identify how recent advances in the application of genomics and microbial ecology can be harnessed to determine the genetic mechanisms that underpin the biological role of the horizontal gene pool. Scientific excellence at the workshop was contributed by senior scientists and young investigators from research institutes located in nine European countries.}, }
@article {pmid15066813, year = {2004}, author = {Meinersmann, RJ and Phillips, RW and Wiedmann, M and Berrang, ME}, title = {Multilocus sequence typing of Listeria monocytogenes by use of hypervariable genes reveals clonal and recombination histories of three lineages.}, journal = {Applied and environmental microbiology}, volume = {70}, number = {4}, pages = {2193-2203}, pmid = {15066813}, issn = {0099-2240}, support = {R01 GM063259/GM/NIGMS NIH HHS/United States ; R01GM63259/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacterial Typing Techniques ; Base Sequence ; DNA Primers/genetics ; DNA, Bacterial/genetics ; Food Microbiology ; *Genes, Bacterial ; Genetic Variation ; Humans ; Listeria monocytogenes/*classification/*genetics/isolation &amp; purification ; Recombination, Genetic ; Serotyping ; }, abstract = {In an attempt to develop a method to discriminate among isolates of Listeria monocytogenes, the sequences of all of the annotated genes from the fully sequenced strain L. monocytogenes EGD-e (serotype 1/2a) were compared by BLASTn to a file of the unfinished genomic sequence of L. monocytogenes ATCC 19115 (serotype 4b). Approximately 7% of the matching genes demonstrated 90% or lower identity between the two strains, and the lowest observed identity was 80%. Nine genes (hisJ, cbiE, truB, ribC, comEA, purM, aroE, hisC, and addB) in the 80 to 90% identity group and two genes (gyrB and rnhB) with approximately 97% identity were selected for multilocus sequence analysis in two sets of L. monocytogenes isolates (a 15-strain diversity set and a set of 19 isolates from a single food-processing plant). Based on concatenated sequences, a total of 33 allotypes were differentiated among the 34 isolates tested. Population genetics analyses revealed three lineages of L. monocytogenes that differed in their history of apparent recombination. Lineage I appeared to be completely clonal, whereas representatives of the other lineages demonstrated evidence of horizontal gene transfer and recombination. Although most of the gene sequences for lineage II strains were distinct from those of lineage I, a few strains with the majority of genes characteristic of lineage II had some that were characteristic of lineage I. Genes from lineage III organisms were mostly similar to lineage I genes, with instances of genes appearing to be mosaics with lineage II genes. Even though lineage I and lineage II generally demonstrated very distinct sequences, the sequences for the 11 selected genes demonstrated little discriminatory power within each lineage. In the L. monocytogenes isolate set obtained from one food-processing plant, lineage I and lineage II were found to be almost equally prevalent. While it appears that different lineages of L. monocytogenes can share habitats, they appear to differ in their histories of horizontal gene transfer.}, }
@article {pmid15066803, year = {2004}, author = {Itoh, K and Tashiro, Y and Uobe, K and Kamagata, Y and Suyama, K and Yamamoto, H}, title = {Root nodule Bradyrhizobium spp. harbor tfdAalpha and cadA, homologous with genes encoding 2,4-dichlorophenoxyacetic acid-degrading proteins.}, journal = {Applied and environmental microbiology}, volume = {70}, number = {4}, pages = {2110-2118}, pmid = {15066803}, issn = {0099-2240}, mesh = {2,4-Dichlorophenoxyacetic Acid/*metabolism ; Amino Acid Sequence ; Base Composition ; Biodegradation, Environmental ; Bradyrhizobium/classification/*genetics/*metabolism ; Codon/genetics ; DNA, Bacterial/genetics ; *Genes, Bacterial ; Molecular Sequence Data ; Phylogeny ; Plant Roots/microbiology ; Sequence Homology, Amino Acid ; Sphingomonas/classification/genetics/metabolism ; }, abstract = {The distribution of tfdAalpha and cadA, genes encoding 2,4-dichlorophenoxyacetate (2,4-D)-degrading proteins which are characteristic of the 2,4-D-degrading Bradyrhizobium sp. isolated from pristine environments, was examined by PCR and Southern hybridization in several Bradyrhizobium strains including type strains of Bradyrhizobium japonicum USDA110 and Bradyrhizobium elkanii USDA94, in phylogenetically closely related Agromonas oligotrophica and Rhodopseudomonas palustris, and in 2,4-D-degrading Sphingomonas strains. All strains showed positive signals for tfdAalpha, and its phylogenetic tree was congruent with that of 16S rRNA genes in alpha-Proteobacteria, indicating evolution of tfdAalpha without horizontal gene transfer. The nucleotide sequence identities between tfdAalpha and canonical tfdA in beta- and gamma-Proteobacteria were 46 to 57%, and the deduced amino acid sequence of TfdAalpha revealed conserved residues characteristic of the active site of alpha-ketoglutarate-dependent dioxygenases. On the other hand, cadA showed limited distribution in 2,4-D-degrading Bradyrhizobium sp. and Sphingomonas sp. and some strains of non-2,4-D-degrading B. elkanii. The cadA genes were phylogenetically separated between 2,4-D-degrading and nondegrading strains, and the cadA genes of 2,4-D degrading strains were further separated between Bradyrhizobium sp. and Sphingomonas sp., indicating the incongruency of cadA with 16S rRNA genes. The nucleotide sequence identities between cadA and tftA of 2,4,5-trichlorophenoxyacetate-degrading Burkholderia cepacia AC1100 were 46 to 53%. Although all root nodule Bradyrhizobium strains were unable to degrade 2,4-D, three strains carrying cadA homologs degraded 4-chlorophenoxyacetate with the accumulation of 4-chlorophenol as an intermediate, suggesting the involvement of cadA homologs in the cleavage of the aryl ether linkage. Based on codon usage patterns and GC content, it was suggested that the cadA genes of 2,4-D-degrading and nondegrading Bradyrhizobium spp. have different origins and that the genes would be obtained in the former through horizontal gene transfer.}, }
@article {pmid15066037, year = {2004}, author = {Boucher, Y and Kamekura, M and Doolittle, WF}, title = {Origins and evolution of isoprenoid lipid biosynthesis in archaea.}, journal = {Molecular microbiology}, volume = {52}, number = {2}, pages = {515-527}, doi = {10.1111/j.1365-2958.2004.03992.x}, pmid = {15066037}, issn = {0950-382X}, mesh = {Alkyl and Aryl Transferases/genetics/metabolism ; Archaea/chemistry/enzymology/genetics/*metabolism ; Archaeal Proteins/*genetics ; *Biological Evolution ; Genome, Archaeal ; Glycerolphosphate Dehydrogenase/genetics/metabolism ; Glycerophosphates/metabolism ; Lipids/*biosynthesis/chemistry ; Membrane Lipids/*biosynthesis/chemistry/metabolism ; Mevalonic Acid/metabolism ; Molecular Sequence Data ; Phylogeny ; Terpenes/*metabolism ; }, abstract = {A characteristic feature of the domain archaea are the lipids forming the hydrophobic core of their cell membrane. These unique lipids are composed of isoprenoid side-chains stereospecifically ether linked to sn-glycerol-1-phosphate. Recently, considerable progress has been made in characterizing the enzymes responsible for the synthesis of archaeal lipids. However, little is known about their evolution. To better understand how this unique biosynthetic apparatus came to be, large-scale database surveys and phylogenetic analyses were performed. All characterized enzymes involved in the biosynthesis of isoprenoid side-chains and the glycerol phosphate backbone along with their assembly in ether lipids were included in these analyses. The sequence data available in public databases was complemented by an in-depth sampling of isoprenoid lipid biosynthesis genes from multiple genera of the archaeal order Halobacteriales, allowing us to look at the evolution of these enzymes on a smaller phylogenetic scale. This investigation of the isoprenoid biosynthesis apparatus of archaea on small and large phylogenetic scales reveals that it evolved through a combination of evolutionary processes, including the co-option of ancestral enzymes, modification of enzymatic specificity, orthologous and non-orthologous gene displacement, integration of components from eukaryotes and bacteria and lateral gene transfer within and between archaeal orders.}, }
@article {pmid15064399, year = {2004}, author = {Seshadri, R and Myers, GS and Tettelin, H and Eisen, JA and Heidelberg, JF and Dodson, RJ and Davidsen, TM and DeBoy, RT and Fouts, DE and Haft, DH and Selengut, J and Ren, Q and Brinkac, LM and Madupu, R and Kolonay, J and Durkin, SA and Daugherty, SC and Shetty, J and Shvartsbeyn, A and Gebregeorgis, E and Geer, K and Tsegaye, G and Malek, J and Ayodeji, B and Shatsman, S and McLeod, MP and Smajs, D and Howell, JK and Pal, S and Amin, A and Vashisth, P and McNeill, TZ and Xiang, Q and Sodergren, E and Baca, E and Weinstock, GM and Norris, SJ and Fraser, CM and Paulsen, IT}, title = {Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, number = {15}, pages = {5646-5651}, pmid = {15064399}, issn = {0027-8424}, support = {R01-DE12488/DE/NIDCR NIH HHS/United States ; }, mesh = {ATP-Binding Cassette Transporters/genetics ; Bacterial Proteins/genetics ; Base Sequence ; Borrelia burgdorferi/genetics/metabolism ; Genes, Bacterial/genetics ; *Genome, Bacterial ; Leptospira interrogans/genetics/metabolism ; Models, Genetic ; Molecular Sequence Data ; Mouth/*microbiology ; Sequence Homology, Amino Acid ; Treponema/*genetics/metabolism/pathogenicity ; Treponema pallidum/genetics/metabolism ; }, abstract = {We present the complete 2,843,201-bp genome sequence of Treponema denticola (ATCC 35405) an oral spirochete associated with periodontal disease. Analysis of the T. denticola genome reveals factors mediating coaggregation, cell signaling, stress protection, and other competitive and cooperative measures, consistent with its pathogenic nature and lifestyle within the mixed-species environment of subgingival dental plaque. Comparisons with previously sequenced spirochete genomes revealed specific factors contributing to differences and similarities in spirochete physiology as well as pathogenic potential. The T. denticola genome is considerably larger in size than the genome of the related syphilis-causing spirochete Treponema pallidum. The differences in gene content appear to be attributable to a combination of three phenomena: genome reduction, lineage-specific expansions, and horizontal gene transfer. Genes lost due to reductive evolution appear to be largely involved in metabolism and transport, whereas some of the genes that have arisen due to lineage-specific expansions are implicated in various pathogenic interactions, and genes acquired via horizontal gene transfer are largely phage-related or of unknown function.}, }
@article {pmid15064395, year = {2004}, author = {Monaco, C and Andreakos, E and Kiriakidis, S and Mauri, C and Bicknell, C and Foxwell, B and Cheshire, N and Paleolog, E and Feldmann, M}, title = {Canonical pathway of nuclear factor kappa B activation selectively regulates proinflammatory and prothrombotic responses in human atherosclerosis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, number = {15}, pages = {5634-5639}, pmid = {15064395}, issn = {0027-8424}, mesh = {Actins/immunology ; Adenoviridae/genetics ; Arteriosclerosis/immunology/*metabolism/pathology ; CD3 Complex/immunology ; CD40 Ligand/immunology/metabolism ; Cells, Cultured ; Gene Transfer, Horizontal ; Humans ; I-kappa B Kinase ; Inflammation/immunology/metabolism/pathology ; Interleukin-6/biosynthesis ; Interleukin-8/biosynthesis ; Matrix Metalloproteinase Inhibitors ; Matrix Metalloproteinases/biosynthesis ; Myocytes, Smooth Muscle/cytology ; NF-kappa B/antagonists &amp; inhibitors/*metabolism ; NF-kappa B p50 Subunit ; Protein Serine-Threonine Kinases/genetics/metabolism ; Thromboplastin/biosynthesis ; Thrombosis/immunology/*metabolism/pathology ; Tissue Inhibitor of Metalloproteinase-1/biosynthesis ; Transcription Factor RelA ; NF-kappaB-Inducing Kinase ; }, abstract = {Nuclear factor kappa B (NF-kappa B) activation has been observed in human atherosclerotic plaques and is enhanced in unstable coronary plaques, but whether such activation has a protective or pathophysiological role remains to be determined. We addressed this question by developing a short-term culture system of cells isolated from human atherosclerotic tissue, allowing efficient gene transfer to directly investigate signaling pathways in human atherosclerosis. We found that NF-kappa B is activated in these cells and that this activity involves p65, p50, and c-Rel but not p52 or RelB. This NF-kappa B activation can be blocked by overexpression of I kappa B alpha or dominant-negative I kappa B kinase (IKK)-2 but not dominant-negative IKK-1 or NF-kappa B-inducing kinase, resulting in selective inhibition of inflammatory cytokines (tumor necrosis factor alpha, IL-6, and IL-8), tissue factor, and matrix metalloproteinases without affecting the antiinflammatory cytokine IL-10 or tissue inhibitor of matrix metalloproteinases. Our results demonstrate that the canonical pathway of NF-kappa B activation that involves p65, p50, c-Rel, and IKK-2 is activated in human atherosclerosis and results in selective up-regulation of major proinflammatory and prothrombotic mediators of the disease.}, }
@article {pmid15060023, year = {2004}, author = {Dogra, C and Raina, V and Pal, R and Suar, M and Lal, S and Gartemann, KH and Holliger, C and van der Meer, JR and Lal, R}, title = {Organization of lin genes and IS6100 among different strains of hexachlorocyclohexane-degrading Sphingomonas paucimobilis: evidence for horizontal gene transfer.}, journal = {Journal of bacteriology}, volume = {186}, number = {8}, pages = {2225-2235}, pmid = {15060023}, issn = {0021-9193}, mesh = {Bacterial Proteins/genetics/metabolism ; Cloning, Molecular ; *DNA Transposable Elements ; Gene Deletion ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Hexachlorocyclohexane/*metabolism ; Lyases/genetics/metabolism ; Molecular Sequence Data ; Open Reading Frames ; Sphingomonas/*genetics/metabolism ; }, abstract = {The organization of lin genes and IS6100 was studied in three strains of Sphingomonas paucimobilis (B90A, Sp+, and UT26) which degraded hexachlorocyclohexane (HCH) isomers but which had been isolated at different geographical locations. DNA-DNA hybridization data revealed that most of the lin genes in these strains were associated with IS6100, an insertion sequence classified in the IS6 family and initially found in Mycobacterium fortuitum. Eleven, six, and five copies of IS6100 were detected in B90A, Sp+, and UT26, respectively. IS6100 elements in B90A were sequenced from five, one, and one regions of the genomes of B90A, Sp+, and UT26, respectively, and were found to be identical. DNA-DNA hybridization and DNA sequencing of cosmid clones also revealed that S. paucimobilis B90A contains three and two copies of linX and linA, respectively, compared to only one copy of these genes in strains Sp+ and UT26. Although the copy number and the sequence of the remaining genes of the HCH degradative pathway (linB, linC, linD, and linE) were nearly the same in all strains, there were striking differences in the organization of the linA genes as a result of replacement of portions of DNA sequences by IS6100, which gave them a strange mosaic configuration. Spontaneous deletion of linD and linE from B90A and of linA from Sp+ occurred and was associated either with deletion of a copy of IS6100 or changes in IS6100 profiles. The evidence gathered in this study, coupled with the observation that the G+C contents of the linA genes are lower than that of the remaining DNA sequence of S. paucimobilis, strongly suggests that all these strains acquired the linA gene through horizontal gene transfer mediated by IS6100. The association of IS6100 with the rest of the lin genes further suggests that IS6100 played a role in shaping the current lin gene organization.}, }
@article {pmid15059260, year = {2004}, author = {Pushker, R and Mira, A and Rodríguez-Valera, F}, title = {Comparative genomics of gene-family size in closely related bacteria.}, journal = {Genome biology}, volume = {5}, number = {4}, pages = {R27}, pmid = {15059260}, issn = {1474-760X}, mesh = {Chlamydophila pneumoniae/genetics/pathogenicity ; Computational Biology ; Escherichia coli/*genetics/pathogenicity ; Escherichia coli O157/*genetics/pathogenicity ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/genetics/physiology ; *Genome, Bacterial ; Genomics/*methods ; Multigene Family/genetics/physiology ; Staphylococcus aureus/genetics/pathogenicity ; Streptococcus pyogenes/genetics/pathogenicity ; }, abstract = {BACKGROUND: The wealth of genomic data in bacteria is helping microbiologists understand the factors involved in gene innovation. Among these, the expansion and reduction of gene families appears to have a fundamental role in this, but the factors influencing gene family size are unclear.<br><br>RESULTS: The relative content of paralogous genes in bacterial genomes increases with genome size, largely due to the expansion of gene family size in large genomes. Bacteria undergoing genome reduction display a parallel process of redundancy elimination, by which gene families are reduced to one or a few members. Gene family size is also influenced by sequence divergence and physiological function. Large gene families show wider sequence divergence, suggesting they are probably older, and certain functions (such as metabolite transport mechanisms) are overrepresented in large families. The size of a given gene family is remarkably similar in strains of the same species and in closely related species, suggesting that homologous gene families are vertically transmitted and depend little on horizontal gene transfer (HGT).<br><br>CONCLUSIONS: The remarkable preservation of copy numbers in widely different ecotypes indicates a functional role for the different copies rather than simply a back-up role. When different genera are compared, the increase in phylogenetic distance and/or ecological specialization disrupts this preservation, albeit in a gradual manner and maintaining an overall similarity, which also supports this view. HGT can have an important role, however, in nonhomologous gene families, as exemplified by a comparison between saprophytic and enterohemorrhagic strains of Escherichia coli.}, }
@article {pmid15057474, year = {2004}, author = {Gupta, N and Ali, A}, title = {Mercury volatilization by R factor systems in Escherichia coli isolated from aquatic environments of India.}, journal = {Current microbiology}, volume = {48}, number = {2}, pages = {88-96}, doi = {10.1007/s00284-003-4054-0}, pmid = {15057474}, issn = {0343-8651}, mesh = {Biotransformation ; Conjugation, Genetic ; DNA, Bacterial/genetics/isolation &amp; purification ; Drug Resistance, Bacterial ; Escherichia coli/drug effects/*genetics/isolation &amp; purification/*metabolism ; Gene Transfer, Horizontal ; India ; Mercuric Chloride/*metabolism/*pharmacology ; Mercury/analysis ; *R Factors ; Spectrophotometry, Atomic ; Transformation, Bacterial ; Transformation, Genetic ; Volatilization ; *Water Microbiology ; }, abstract = {Ten Escherichia coli strains isolated from five different aquatic environments representing three distinct geographical regions of India showed significantly high levels of tolerance to the inorganic form of mercury, i.e., mercuric chloride (HgCl(2)). MRD14 isolated from the Dal Lake (Kashmir) could tolerate the highest concentration of HgCl(2), i.e., 55 microg/mL, and MRF1 from the flood water of the Yamuna River (Delhi) tolerated the lowest concentration, i.e., 25 microg/mL. All ten strains revealed the presence of a plasmid of approximately 24 kb, and transformation of the isolated plasmids into the mercury-sensitive competent cells of E. coli DH5alpha rendered the transformants resistant to the same concentration of mercury as the wild-type strains. Mating experiments were performed to assess the self-transmissible nature of these promiscuous plasmids. The transfer of mercury resistance from these wild-type strains to the mercury-sensitive, naladixic acid-resistant E. coli K12 (F(-) lac(+)) strain used as a recipient was observed in six of the nine strains tested. Transconjugants revealed the presence of a plasmid of approximately 24 kb. An evaluation of the mechanism of mercury resistance in the three most efficient strains (MRG12, MRD11, and MRD14) encountered in our study was determined by cold vapor atomic absorption spectroscopy (CV-AAS), and it was noted that resistance to HgCl(2) was conferred by conversion of the toxic ionic form of mercury (Hg(++)) to the nontoxic elemental form (Hg(0)) in all three strains. MRD14 volatilized mercury most efficiently.}, }
@article {pmid15057456, year = {2004}, author = {Erbeznik, M and Hudson, SE and Herrman, AB and Strobel, HJ}, title = {Molecular analysis of the xylFGH operon, coding for xylose ABC transport, in Thermoanaerobacter ethanolicus.}, journal = {Current microbiology}, volume = {48}, number = {4}, pages = {295-299}, doi = {10.1007/s00284-003-4202-6}, pmid = {15057456}, issn = {0343-8651}, mesh = {ATP-Binding Cassette Transporters/chemistry/*genetics ; Amino Acid Sequence ; Base Sequence ; Eubacterium/*genetics/metabolism ; Hydrolases/chemistry/*genetics ; Molecular Sequence Data ; Open Reading Frames ; *Operon ; *Proteins ; Xylose/*metabolism ; }, abstract = {A xylose ABC (ATP-binding cassette) transport operon, xylFGH, was cloned from Thermoanaerobacter ethanolicus, a thermophilic ethanol-producing eubacterium. The cistrons code for a periplasmic D-xylose-binding protein (XylF, partial sequence of 250 amino acids), ATP-binding protein (XylG, 505 amino acids), and integral membrane protein (XylH, 388 amino acids). These results, together with previous work, indicate that duplicate copies of both xylF and xylH are present in the T. ethanolicus chromosome, suggesting ancient gene duplication or lateral gene transfer events. XylG resembles other eubacterial monosaccharide ABC-ATPases in that its two nucleotide-binding domains (NBDs) are highly homologous, yet significantly different with respect to putative catalytic residues. Unlike most other integral membrane ABC transport proteins, XylH apparently contains 11 or 12 transmembrane segments (TMS) and is similar to a small group of ABC permeases that defy the "2 x 6" helix paradigm. This is the first report of a monosaccharide ABC transport operon in a thermophilic anaerobic eubacterium.}, }
@article {pmid15056912, year = {2004}, author = {Abe-Yoshizumi, R and Kamei, U and Yamada, A and Kimura, M and Ichihara, S}, title = {The evolution of the phenylacetic acid degradation pathway in bacteria.}, journal = {Bioscience, biotechnology, and biochemistry}, volume = {68}, number = {3}, pages = {746-748}, doi = {10.1271/bbb.68.746}, pmid = {15056912}, issn = {0916-8451}, mesh = {Bacteria/*genetics/metabolism ; Base Sequence ; Biodegradation, Environmental ; Coenzyme A Ligases/*genetics ; Evolution, Molecular ; Molecular Sequence Data ; Phenylacetates/*metabolism ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil Pollutants/metabolism ; }, abstract = {The phenylacetic acid (PhAc) degradation pathway becomes an interesting model for the catabolism of aromatic compounds. To determine the molecular basis for this environmentally important process, we did a phylogenic analysis based on the PhAc CoA ligase gene. It suggests that the PhAc CoA ligase genes are distributing widely and subject to frequent lateral gene transfer within and across bacterial phylum.}, }
@article {pmid15046576, year = {2004}, author = {She, Q and Shen, B and Chen, L}, title = {Archaeal integrases and mechanisms of gene capture.}, journal = {Biochemical Society transactions}, volume = {32}, number = {Pt 2}, pages = {222-226}, doi = {10.1042/bst0320222}, pmid = {15046576}, issn = {0300-5127}, mesh = {Archaea/*enzymology ; Chromosomes, Archaeal/genetics ; Evolution, Molecular ; Gene Transfer Techniques ; Genetic Techniques ; Genome, Archaeal ; Integrases/*chemistry/genetics ; Models, Genetic ; Mutation ; Open Reading Frames ; Plasmids/metabolism ; Protein Structure, Tertiary ; RNA, Transfer/chemistry/genetics ; Sulfolobus/genetics ; }, abstract = {Archaeal integrases facilitate the formation of two distinctive types of integrated element within archaeal chromosomes: the SSV type and pNOB8 type. The former carries a smaller N-terminal and a larger C-terminal integrase gene fragment, and the latter an intact integrase gene. All integrated elements overlap tRNA genes that were target sites for integration. It has been demonstrated that SSV (Sulfolobus spindle virus) viruses, carrying an SSV-type integrase gene, and conjugative plasmids, carrying a pNOB8-type integrase, are integrative elements. Two mechanisms have been proposed for stably maintaining an integrated element within archaeal chromosomes. There is also evidence for changes having occurred in the captured integrated elements present in archaeal genomes. Thus we infer that site-specific integration constitutes an important mechanism for horizontal gene transfer and genome evolution.}, }
@article {pmid15046458, year = {2004}, author = {Kirsch, P and Jores, J and Wieler, LH}, title = {[Plasticity of bacterial genomes: pathogenicity islands and the locus of enterocyte effacement (LEE)].}, journal = {Berliner und Munchener tierarztliche Wochenschrift}, volume = {117}, number = {3-4}, pages = {116-129}, pmid = {15046458}, issn = {0005-9366}, mesh = {Bacteria/*genetics/*pathogenicity ; *Biological Evolution ; *DNA, Bacterial ; Enterocytes/*microbiology ; Gene Transfer, Horizontal ; Genome, Bacterial ; RNA, Transfer/genetics ; Virulence/genetics ; }, abstract = {Many bacterial virulence attributes, like toxins, adhesins, invasins, iron uptake systems, are encoded within specific regions of the bacterial genome. These in size varying regions are termed pathogenicity islands (PAIs) since they confer pathogenic properties to the respective micro-organism. Per definition PAIs are exclusively found in pathogenic strains and are often inserted near transfer-RNA genes. Nevertheless, non-pathogenic bacteria also possess foreign DNA elements that confer advantageous features, leading to improved fitness. These additional DNA elements as well as PAIs are termed genomic islands and were acquired during bacterial evolution. Significant G+C content deviation in pathogenicity islands with respect to the rest of the genome, the presence of direct repeat sequences at the flanking regions, the presence of integrase gene determinants as other mobility features,the particular insertion site (tRNA gene) as well as the observed genetic instability suggests that pathogenicity islands were acquired by horizontal gene transfer. PAIs are the fascinating proof of the plasticity of bacterial genomes. PAIs were originally described in human pathogenic Escherichia (E.) coli strains. In the meantime PAIs have been found in various pathogenic bacteria of humans, animals and even plants. The Locus of Enterocyte Effacement (LEE) is one particular widely distributed PAI of E coli. In addition, it also confers pathogenicity to the related species Citrobacter (C.) rodentium and Escherichia (E.) alvei. The LEE is an important virulence feature of several animal pathogens. It is an obligate PAI of all animal and human enteropathogenic E. coli (EPEC), and most enterohaemorrhegic E. coli (EHEC) also harbor the LEE. The LEE encodes a type III secretion system, an adhesion (intimin) that mediates the intimate contact between the bacterium and the epithelial cell, as well as various proteins which are secreted via the type III secretion system. The LEE encoded virulence features are responsible for the formation of so called attaching and effacing (AE) lesions in the intestinal epithelium. Due to its wide distribution in animal pathogens, LEE encoded antigens are suitable vaccine antigens. Acquisition and structure of the LEE pathogenicity island is the crucial point of numerous investigations. However, the evolution of the LEE, its origin and further spread in E. coli, are far from being resolved.}, }
@article {pmid15045490, year = {2004}, author = {Ruiz-González, MX and Marín, I}, title = {New insights into the evolutionary history of type 1 rhodopsins.}, journal = {Journal of molecular evolution}, volume = {58}, number = {3}, pages = {348-358}, doi = {10.1007/s00239-003-2557-8}, pmid = {15045490}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Archaea/genetics ; Bacteria/genetics ; Chlorophyta/genetics ; Cluster Analysis ; Databases, Nucleic Acid ; *Evolution, Molecular ; Fungi/genetics ; Gene Transfer, Horizontal/*genetics ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; Oryza/genetics ; *Phylogeny ; Rhodopsins, Microbial/*genetics ; Sequence Alignment ; }, abstract = {Type 1 (archaeal) rhodopsins and related rhodopsin-like proteins had been described in a few halophile archaea, gamma-proteobacteria, a single cyanobacteria, some fungi, and a green alga. In exhaustive database searches, we detected rhodopsin-related sequences derived not only from additional fungal species but also from organisms belonging to three groups in which opsins had hitherto not been described: the alpha-proteobacterium Magnetospirillum magnetotacticum, the cryptomonad alga Guillardia theta, and the dinoflagellate Pyrocystis lunula. Putative plant and human type 1 rhodopsin sequences found in the databases are demonstrated to be contaminants of fungal origin. However, a highly diverged sequence supposedly from the plant Oryza sativa was found that is, together with the Pyrocystis sequence, quite similar to gamma-proteobacterial rhodopsins. These close relationships suggest that at least one horizontal gene transfer event involving rhodopsin genes occurred between prokaryotes and eukaryotes. Alternative hypotheses to explain the current phylogenetic range of type 1 rhodopsins are suggested. The broader phylogenetic range found is compatible with an ancient origin of type 1 rhodopsins, their patchy distribution being caused by losses in multiple lineages. However, the possibility of ancient horizontal transfer events between distant relatives cannot be dismissed.}, }
@article {pmid15045489, year = {2004}, author = {Dvornyk, V and Nevo, E}, title = {Evidence for multiple lateral transfers of the circadian clock cluster in filamentous heterocystic cyanobacteria Nostocaceae.}, journal = {Journal of molecular evolution}, volume = {58}, number = {3}, pages = {341-347}, pmid = {15045489}, issn = {0022-2844}, support = {R01 GM60402-01A1/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacterial Proteins/*genetics ; Base Sequence ; Biological Clocks/*genetics ; Circadian Rhythm/*genetics ; Circadian Rhythm Signaling Peptides and Proteins ; Cyanobacteria/*genetics ; DNA Primers ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Israel ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {Cyanobacteria are the first prokaryotes reported to show circadian rhythmicity, which is regulated by a cluster of three genes: kaiA, kaiB, and kaiC. Phylogenetic analysis of the kaiBC cluster in filamentous cyanobacteria of the family Nostocaceae including Nodularia spumigena and Nostoc linckia from Arubotaim Cave, Mt. Sedom, Israel, indicated that this cluster has experienced multiple lateral transfers. The transfers have occurred in different periods of the species' evolution. The data obtained suggest that lateral transfers of the circadian clock cluster in filamentous cyanobacteria have been common and might have adaptive significance.}, }
@article {pmid15041743, year = {2004}, author = {Hirsh, AE and Tsolaki, AG and DeRiemer, K and Feldman, MW and Small, PM}, title = {Stable association between strains of Mycobacterium tuberculosis and their human host populations.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, number = {14}, pages = {4871-4876}, pmid = {15041743}, issn = {0027-8424}, support = {K01 TW000001-05/TW/FIC NIH HHS/United States ; R01 GM028016/GM/NIGMS NIH HHS/United States ; GM 28424/GM/NIGMS NIH HHS/United States ; AI34238/AI/NIAID NIH HHS/United States ; GM 28016/GM/NIGMS NIH HHS/United States ; R01 AI034238/AI/NIAID NIH HHS/United States ; K01 TW000001/TW/FIC NIH HHS/United States ; }, mesh = {Humans ; Mycobacterium tuberculosis/classification/genetics/*physiology ; Phylogeny ; Polymerase Chain Reaction ; Sequence Deletion ; }, abstract = {Mycobacterium tuberculosis is an important human pathogen in virtually every part of the world. Here we investigate whether distinct strains of M. tuberculosis infect different human populations and whether associations between host and pathogen populations are stable despite global traffic and the convergence of diverse strains of the pathogen in cosmopolitan urban centers. The recent global movement and transmission history of 100 M. tuberculosis isolates was inferred from a molecular epidemiologic study of tuberculosis that spans 12 years. Genetic relationships among these isolates were deduced from the distribution of large genomic deletions, which were identified by DNA microarray and confirmed by PCR and sequence analysis. Phylogenetic analysis of these deletions indicates that they are unique event polymorphisms and that horizontal gene transfer is extremely rare in M. tuberculosis. In conjunction with the epidemiological data, phylogenies reveal three large phylogeographic regions. A host's region of origin is predictive of the strain of tuberculosis he or she carries, and this association remains strong even when transmission takes place in a cosmopolitan urban center outside of the region of origin. Approximate dating of the time since divergence of East Asian and Philippine clades of M. tuberculosis suggests that these lineages diverged centuries ago. Thus, associations between host and pathogen populations appear to be highly stable.}, }
@article {pmid15041172, year = {2004}, author = {Zhaxybayeva, O and Gogarten, JP}, title = {Cladogenesis, coalescence and the evolution of the three domains of life.}, journal = {Trends in genetics : TIG}, volume = {20}, number = {4}, pages = {182-187}, doi = {10.1016/j.tig.2004.02.004}, pmid = {15041172}, issn = {0168-9525}, mesh = {Alleles ; Animals ; Archaea/*physiology ; *Bacterial Physiological Phenomena ; Biological Evolution ; Cell Lineage ; Eukaryotic Cells/*physiology ; Extinction, Psychological ; *Gene Transfer, Horizontal ; Humans ; Models, Genetic ; Origin of Life ; Phylogeny ; Time Factors ; }, abstract = {In this article, we explore the large-scale structure of the tree of life by using a simple model with a constant number of species and rates of speciation that equal the rates of extinction. In addition, we discuss the consequences of horizontal gene transfer for the concept of a most recent common ancestor of all living organisms (cenancestor). A simple null hypothesis based on coalescence theory explains some features of the observed topologies of the tree of life. Simulations of genes and organismal lineages suggest that there was no single common ancestor that contained all the genes ancestral to those shared among the three domains of life. Each contemporary molecule has its own history that traces back to an individual molecular cenancestor. However, these molecular ancestors were likely to be present in different organisms and at different times.}, }
@article {pmid15040884, year = {2004}, author = {Hennig, W}, title = {The revolution of the biology of the genome.}, journal = {Cell research}, volume = {14}, number = {1}, pages = {1-7}, pmid = {15040884}, issn = {1001-0602}, mesh = {Animals ; Computational Biology ; Evolution, Molecular ; Gene Duplication ; *Genome ; Genomics ; Humans ; *Molecular Biology ; Polyploidy ; Proteomics ; RNA Interference/physiology ; RNA, Small Interfering/genetics/physiology ; Recombination, Genetic/genetics ; Repetitive Sequences, Nucleic Acid/genetics ; }, abstract = {Sequence data of entire eukaryotic genomes and their detailed comparison have provided new evidence on genome evolution. The major mechanisms involved in the increase of genome sizes are polyploidization and gene duplication. Subsequent gene silencing or mutations, preferentially in regulatory sequences of genes, modify the genome and permit the development of genes with new properties. Mechanisms such as lateral gene transfer, exon shuffling or the creation of new genes by transposition contribute to the evolution of a genome, but remain of relatively restricted relevance. Mechanisms to decrease genome sizes and, in particular, to remove specific DNA sequences, such as blocks of satellite DNAs, appear to involve the action of RNA interference (RNAi). RNAi mechanisms have been proven to be involved in chromatin packaging related with gene inactivation as well as in DNA excision during the macronucleus development in ciliates.}, }
@article {pmid15040816, year = {2004}, author = {van der Giezen, M and Cox, S and Tovar, J}, title = {The iron-sulfur cluster assembly genes iscS and iscU of Entamoeba histolytica were acquired by horizontal gene transfer.}, journal = {BMC evolutionary biology}, volume = {4}, number = {}, pages = {7}, pmid = {15040816}, issn = {1471-2148}, mesh = {5' Flanking Region/genetics ; Amino Acid Sequence ; Animals ; Base Sequence ; DNA, Protozoan/chemistry/genetics ; Entamoeba histolytica/*genetics ; *Gene Transfer, Horizontal ; Iron-Sulfur Proteins/chemistry/*genetics ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Tertiary ; Protozoan Proteins/chemistry/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; }, abstract = {BACKGROUND: Iron-sulfur (FeS) proteins are present in all living organisms and play important roles in electron transport and metalloenzyme catalysis. The maturation of FeS proteins in eukaryotes is an essential function of mitochondria, but little is known about this process in amitochondriate eukaryotes. Here we report on the identification and analysis of two genes encoding critical FeS cluster (Isc) biosynthetic proteins from the amitochondriate human pathogen Entamoeba histolytica.<br><br>RESULTS: E. histolytica IscU and IscS were found to contain all features considered essential for their biological activity, including amino acid residues involved in substrate and/or co-factor binding. The IscU protein differs significantly from other eukaryotic homologs and resembles the long type isoforms encountered in some bacteria. Phylogenetic analyses of E. histolytica IscS and IscU showed a close relationship with homologs from Helicobacter pylori and Campylobacter jejuni, to the exclusion of mitochondrial isoforms.<br><br>CONCLUSIONS: The bacterial-type FeS cluster assembly genes of E. histolytica suggest their lateral acquisition from epsilon proteobacteria. This is a clear example of horizontal gene transfer (HGT) from eubacteria to unicellular eukaryotic organisms, a phenomenon known to contribute significantly to the evolution of eukaryotic genomes.}, }
@article {pmid15040322, year = {2004}, author = {Springael, D and Top, EM}, title = {Horizontal gene transfer and microbial adaptation to xenobiotics: new types of mobile genetic elements and lessons from ecological studies.}, journal = {Trends in microbiology}, volume = {12}, number = {2}, pages = {53-58}, doi = {10.1016/j.tim.2003.12.010}, pmid = {15040322}, issn = {0966-842X}, support = {P20 RR 16448/RR/NCRR NIH HHS/United States ; }, mesh = {Adaptation, Physiological ; Bacteria/*genetics/metabolism ; Biodegradation, Environmental ; Environmental Microbiology ; Environmental Pollutants/metabolism ; *Gene Transfer, Horizontal ; Genomic Islands ; *Interspersed Repetitive Sequences ; Mutation ; Recombination, Genetic ; Xenobiotics/*metabolism ; }, abstract = {The characterization of bacteria that degrade organic xenobiotics has revealed that they can adapt to these compounds by expressing 'novel' catabolic pathways. At least some of them appear to have evolved by patchwork assembly of horizontally transmitted genes and subsequent mutations and gene rearrangements. Recent studies have revealed the existence of new types of xenobiotic catabolic mobile genetic elements, such as catabolic genomic islands, which integrate into the chromosome after transfer. The significance of horizontal gene transfer and patchwork assembly for bacterial adaptation to pollutants under real environmental conditions remains uncertain, but recent publications suggest that these processes do occur in a polluted environment.}, }
@article {pmid15038836, year = {2004}, author = {Nembaware, V and Seoighe, C and Sayed, M and Gehring, C}, title = {A plant natriuretic peptide-like gene in the bacterial pathogen Xanthomonas axonopodis may induce hyper-hydration in the plant host: a hypothesis of molecular mimicry.}, journal = {BMC evolutionary biology}, volume = {4}, number = {}, pages = {10}, pmid = {15038836}, issn = {1471-2148}, mesh = {Amino Acid Sequence ; Arabidopsis Proteins/chemistry/*genetics/physiology ; Bacterial Proteins/chemistry/*genetics/physiology ; Gene Transfer, Horizontal ; Genome, Bacterial ; Genome, Plant ; Models, Molecular ; Models, Theoretical ; Molecular Mimicry ; Molecular Sequence Data ; Phylogeny ; Plant Physiological Phenomena ; Plants/genetics/microbiology ; Protein Folding ; Sequence Alignment ; Sequence Homology, Amino Acid ; Water-Electrolyte Balance/*physiology ; Xanthomonas/*genetics ; }, abstract = {BACKGROUND: Plant natriuretic peptides (PNPs) are systemically mobile molecules that regulate homeostasis at nanomolar concentrations. PNPs are up-regulated under conditions of osmotic stress and PNP-dependent processes include changes in ion transport and increases of H2O uptake into protoplasts and whole tissue.<br><br>The bacterial citrus pathogen Xanthomonas axonopodis pv. Citri str. 306 contains a gene encoding a PNP-like protein. We hypothesise that this bacterial protein can alter plant cell homeostasis and thus is likely to represent an example of molecular mimicry that enables the pathogen to manipulate plant responses in order to bring about conditions favourable to the pathogen such as the induced plant tissue hyper-hydration seen in the wet edged lesions associated with Xanthomonas axonopodis infection.<br><br>TESTING THE HYPOTHESIS: We found a Xanthomonas axonopodis PNP-like protein that shares significant sequence similarity and identical domain organisation with PNPs. We also observed a significant excess of conserved residues between the two proteins within the domain previously identified as being sufficient to induce biological activity. Structural modelling predicts identical six stranded double-psi beta barrel folds for both proteins thus supporting the hypothesis of similar modes of action. No significant similarity between the Xanthomonas axonopodis protein and other bacterial proteins from GenBank was found. Sequence similarity of the Xanthomonas axonopodis PNP-like protein with the Arabidopsis thaliana PNP (AtPNP-A), shared domain organisation and incongruent phylogeny suggest that the PNP-gene may have been acquired by the bacteria in an ancient lateral gene transfer event. Finally, activity of a recombinant Xanthomonas axonopodis protein in plant tissue and changes in symptoms induced by a Xanthomonas axonopodis mutant with a knocked-out PNP-like gene will be experimental proof of molecular mimicry.<br><br>IMPLICATION OF THE HYPOTHESIS: If the hypothesis is true, it could at least in part explain why the citrus pathogen Xanthomonas campestris that does not contain a PNP-like gene produces dry corky lesions while the closely related Xanthomonas axonopodis forms lesions with wet edges. It also suggests that genes typically found in the host, horizontally transferred or heterologous, can help to explain aspects of the physiology of the host-pathogen interactions.}, }
@article {pmid15035042, year = {2003}, author = {Koonin, EV}, title = {Comparative genomics, minimal gene-sets and the last universal common ancestor.}, journal = {Nature reviews. Microbiology}, volume = {1}, number = {2}, pages = {127-136}, doi = {10.1038/nrmicro751}, pmid = {15035042}, issn = {1740-1526}, mesh = {Bacteria/genetics ; Bacterial Proteins/genetics/metabolism ; Computational Biology ; Eukaryotic Cells ; *Evolution, Molecular ; *Genes, Essential ; *Genomics ; Proteins/*genetics/metabolism ; }, abstract = {Comparative genomics, using computational and experimental methods, enables the identification of a minimal set of genes that is necessary and sufficient for sustaining a functional cell. For most essential cellular functions, two or more unrelated or distantly related proteins have evolved; only about 60 proteins, primarily those involved in translation, are common to all cellular life. The reconstruction of ancestral life-forms is based on the principle of evolutionary parsimony, but the size and composition of the reconstructed ancestral gene-repertoires depend on relative rates of gene loss and horizontal gene-transfer. The present estimate suggests a simple last universal common ancestor with only 500-600 genes.}, }
@article {pmid15033867, year = {2004}, author = {Zhang, R and Zhang, CT}, title = {A systematic method to identify genomic islands and its applications in analyzing the genomes of Corynebacterium glutamicum and Vibrio vulnificus CMCP6 chromosome I.}, journal = {Bioinformatics (Oxford, England)}, volume = {20}, number = {5}, pages = {612-622}, doi = {10.1093/bioinformatics/btg453}, pmid = {15033867}, issn = {1367-4803}, mesh = {*Algorithms ; Base Composition/genetics ; Base Sequence ; Chromosome Mapping/methods ; Corynebacterium/*genetics ; Gene Expression Profiling/*methods ; *Genome, Bacterial ; Genomic Islands/*genetics ; Molecular Sequence Data ; Sequence Alignment/methods ; Sequence Analysis, DNA/*methods ; Vibrio vulnificus/*genetics ; }, abstract = {MOTIVATION: Some genomic islands contain horizontally transferred genes, which play critical roles in altering the genotypes and phenotypes of organisms, and horizontal gene transfer has been recognized as a universal event throughout bacterial evolution. A windowless method to display the distribution of genomic GC content, the cumulative GC profile, is proposed to identify genomic islands in genomes whose complete genome sequences are available. Two new indices are proposed to assess the codon usage bias and amino acid usage bias in genomic islands.<br><br>RESULTS: A 211 kb genomic island (CGGI-1) has been identified in the genome of Corynebacterium glutamicum, and three genomic islands VVGI-1, VVGI-2 and VVGI-3, with lengths 167, 40 and 33 kb, respectively, have been identified in the genome of Vibrio vulnificus CMCP6 chromosome I. The CGGI-1 is flanked by two approximately 500 bp direct repeats, and utilizes a Val-tRNA as the integration site. For the VVGI-1 and VVGI-2, each has an integrase gene at 5' junction. All the identified genomic islands show unusual GC content, codon usage and amino acid usage, compared with the rest of the genomes. In addition, it is found that genomic islands are fairly homogenous in terms of GC content variation. An index, h, to quantify the homogeneity of GC content for genomic islands is proposed, and it is shown that h is less than 0.1 for all the genomic islands analyzed. The cumulative GC profile, as well as various indices to assess the codon usage bias, amino acid usage bias and homogeneity of the genomic islands, will be useful in the analysis of other genomes.<br><br>AVAILABILITY: Programs used in this work and numerical results are available upon request.}, }
@article {pmid15033531, year = {2004}, author = {Dolezal, P and Vanácová, S and Tachezy, J and Hrdý, I}, title = {Malic enzymes of Trichomonas vaginalis: two enzyme families, two distinct origins.}, journal = {Gene}, volume = {329}, number = {}, pages = {81-92}, doi = {10.1016/j.gene.2003.12.022}, pmid = {15033531}, issn = {0378-1119}, support = {1 R03 TW05536-01/TW/FIC NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Cloning, Molecular ; Cytosol/enzymology ; DNA, Protozoan/chemistry/genetics ; Isoenzymes/genetics/isolation &amp; purification/metabolism ; Kinetics ; Malate Dehydrogenase/*genetics/isolation &amp; purification/metabolism ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Trichomonas vaginalis/enzymology/*genetics ; }, abstract = {The cytosolic malic enzyme of the amitochondriate protist Trichomonas vaginalis was purified to homogeneity and characterized. The corresponding gene was sequenced and compared with its hydrogenosomal homologue from the same organism. The enzymes were found to differ in coenzyme specificity, molecular mass and physiological role. The cytosolic malic enzyme is a dimer consisting of two 42-kDa subunits with strict specificity for nicotinamide adenine dinucleotide phosphate (NADP(+)), and has a presumed function of pyruvate and NADPH production. The hydrogenosomal malic enzyme is a tetramer of 60-kDa subunits that preferentially utilizes nicotinamide adenine dinucleotide (NAD(+)) to NADP(+). The hydrogenosomal enzyme supplies the hydrogenosome with pyruvate for further catabolic processes linked with substrate-level phosphorylation. Phylogenetic analysis of malic enzymes showed the existence of two distinct families of these enzymes in nature, which differ in subunit size. The trichomonad cytosolic malic enzyme belongs to the small subunit-type family that occurs almost exclusively in prokaryotes. In contrast, the hydrogenosomal malic enzyme displays a close relationship with the large subunit-type family of the enzyme, which is found in mitochondria, plastids and the cytosol of eukaryotes. The eubacterial origin of trichomonad cytosolic malic enzyme suggests an occurrence of horizontal gene transfer from a eubacterium to the ancestor of T. vaginalis. The presence of both prokaryotic and eukaryotic type of malic enzyme in different compartments of a single eukaryotic cell appears to be unique in nature.}, }
@article {pmid15024419, year = {2004}, author = {Wu, M and Sun, LV and Vamathevan, J and Riegler, M and Deboy, R and Brownlie, JC and McGraw, EA and Martin, W and Esser, C and Ahmadinejad, N and Wiegand, C and Madupu, R and Beanan, MJ and Brinkac, LM and Daugherty, SC and Durkin, AS and Kolonay, JF and Nelson, WC and Mohamoud, Y and Lee, P and Berry, K and Young, MB and Utterback, T and Weidman, J and Nierman, WC and Paulsen, IT and Nelson, KE and Tettelin, H and O'Neill, SL and Eisen, JA}, title = {Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements.}, journal = {PLoS biology}, volume = {2}, number = {3}, pages = {E69}, pmid = {15024419}, issn = {1545-7885}, support = {UO1-AI47409-01/AI/NIAID NIH HHS/United States ; }, mesh = {Adenosine Triphosphate/chemistry ; Animals ; Cell Lineage ; DNA/chemistry/genetics ; DNA Primers/chemistry ; Drosophila melanogaster/microbiology ; Evolution, Molecular ; Gene Deletion ; Gene Duplication ; Gene Library ; Genes, Bacterial ; Genome ; Genome, Bacterial ; Genomics/*methods ; Glycolysis ; Interspersed Repetitive Sequences ; Models, Genetic ; Molecular Sequence Data ; Open Reading Frames ; Parasites ; Phylogeny ; Polymerase Chain Reaction ; Protein Structure, Tertiary ; Purines/chemistry ; Wolbachia/*genetics ; }, abstract = {The complete sequence of the 1,267,782 bp genome of Wolbachia pipientis wMel, an obligate intracellular bacteria of Drosophila melanogaster, has been determined. Wolbachia, which are found in a variety of invertebrate species, are of great interest due to their diverse interactions with different hosts, which range from many forms of reproductive parasitism to mutualistic symbioses. Analysis of the wMel genome, in particular phylogenomic comparisons with other intracellular bacteria, has revealed many insights into the biology and evolution of wMel and Wolbachia in general. For example, the wMel genome is unique among sequenced obligate intracellular species in both being highly streamlined and containing very high levels of repetitive DNA and mobile DNA elements. This observation, coupled with multiple evolutionary reconstructions, suggests that natural selection is somewhat inefficient in wMel, most likely owing to the occurrence of repeated population bottlenecks. Genome analysis predicts many metabolic differences with the closely related Rickettsia species, including the presence of intact glycolysis and purine synthesis, which may compensate for an inability to obtain ATP directly from its host, as Rickettsia can. Other discoveries include the apparent inability of wMel to synthesize lipopolysaccharide and the presence of the most genes encoding proteins with ankyrin repeat domains of any prokaryotic genome yet sequenced. Despite the ability of wMel to infect the germline of its host, we find no evidence for either recent lateral gene transfer between wMel and D. melanogaster or older transfers between Wolbachia and any host. Evolutionary analysis further supports the hypothesis that mitochondria share a common ancestor with the alpha-Proteobacteria, but shows little support for the grouping of mitochondria with species in the order Rickettsiales. With the availability of the complete genomes of both species and excellent genetic tools for the host, the wMel-D. melanogaster symbiosis is now an ideal system for studying the biology and evolution of Wolbachia infections.}, }
@article {pmid15022774, year = {2004}, author = {Escobar-Páramo, P and Sabbagh, A and Darlu, P and Pradillon, O and Vaury, C and Denamur, E and Lecointre, G}, title = {Decreasing the effects of horizontal gene transfer on bacterial phylogeny: the Escherichia coli case study.}, journal = {Molecular phylogenetics and evolution}, volume = {30}, number = {1}, pages = {243-250}, doi = {10.1016/s1055-7903(03)00181-7}, pmid = {15022774}, issn = {1055-7903}, mesh = {DNA, Bacterial/genetics/isolation &amp; purification ; Escherichia coli/*classification/*genetics ; Evolution, Molecular ; *Gene Transfer Techniques ; *Phylogeny ; Reproducibility of Results ; }, abstract = {Phylogenetic reconstructions of bacterial species from DNA sequences are hampered by the existence of horizontal gene transfer. One possible way to overcome the confounding influence of such movement of genes is to identify and remove sequences which are responsible for significant character incongruence when compared to a reference dataset free of horizontal transfer (e.g., multilocus enzyme electrophoresis, restriction fragment length polymorphism, or random amplified polymorphic DNA) using the incongruence length difference (ILD) test of Farris et al. [Cladistics 10 (1995) 315]. As obtaining this "whole genome dataset" prior to the reconstruction of a phylogeny is clearly troublesome, we have tested alternative approaches allowing the release from such reference dataset, designed for a species with modest level of horizontal gene transfer, i.e., Escherichia coli. Eleven different genes available or sequenced in this work were studied in a set of 30 E. coli reference (ECOR) strains. Either using ILD to test incongruence between each gene against the all remaining (in this case 10) genes in order to remove sequences responsible for significant incongruence, or using just a simultaneous analysis without removals, gave robust phylogenies with slight topological differences. The use of the ILD test remains a suitable method for estimating the level of horizontal gene transfer in bacterial species. Supertrees also had suitable properties to extract the phylogeny of strains, because the way they summarize taxonomic congruence clearly limits the impact of individual gene transfers on the global topology. Furthermore, this work allowed a significant improvement of the accuracy of the phylogeny within E. coli.}, }
@article {pmid15019620, year = {2004}, author = {Ma, HW and Zeng, AP}, title = {Phylogenetic comparison of metabolic capacities of organisms at genome level.}, journal = {Molecular phylogenetics and evolution}, volume = {31}, number = {1}, pages = {204-213}, doi = {10.1016/j.ympev.2003.08.011}, pmid = {15019620}, issn = {1055-7903}, mesh = {Animals ; Archaea/genetics/metabolism ; Bacteria/genetics/*metabolism ; Enzymes/genetics/metabolism ; Eukaryotic Cells/metabolism ; Gene Transfer, Horizontal ; *Genome ; *Phylogeny ; Plants/genetics/*metabolism ; RNA, Ribosomal, 16S ; }, abstract = {Horizontal gene transfer (HGT) has been shown to widely spread in organisms by comparative genomic studies. However, its effect on the phylogenetic relationship of organisms, especially at a system level of different cellular functions, is still not well understood. In this work, we have constructed phylogenetic trees based on the enzyme, reaction, and gene contents of metabolic networks reconstructed from annotated genome information of 82 sequenced organisms. Results from different phylogenetic distance definitions and based on three different functional subsystems (i.e., metabolism, cellular processes, information storage and processing) were compared. Results based on the three different functional subsystems give different pictures on the phylogenetic relationship of organisms, reflecting the different extents of HGT in the different functional systems. In general, horizontal transfer is prevailing in genes for metabolism, but less in genes for information processing. Nevertheless, the major results of metabolic network-based phylogenetic trees are in good agreement with the tree based on 16S rRNA and genome trees, confirming the three domain classification and the close relationship between eukaryotes and archaea at the level of metabolic networks. These results strongly support the hypothesis that although HGT is widely distributed, it is nevertheless constrained by certain pre-existing metabolic organization principle(s) during the evolution. Further research is needed to identify the organization principle and constraints of metabolic network on HGT which have large impacts on understanding the evolution of life and in purposefully manipulating cellular metabolism.}, }
@article {pmid15014982, year = {2004}, author = {Gojković, Z and Knecht, W and Zameitat, E and Warneboldt, J and Coutelis, JB and Pynyaha, Y and Neuveglise, C and Møller, K and Löffler, M and Piskur, J}, title = {Horizontal gene transfer promoted evolution of the ability to propagate under anaerobic conditions in yeasts.}, journal = {Molecular genetics and genomics : MGG}, volume = {271}, number = {4}, pages = {387-393}, pmid = {15014982}, issn = {1617-4615}, mesh = {*Anaerobiosis ; *Biological Evolution ; Cell Division ; Cytoplasm/enzymology ; DNA, Fungal/genetics/isolation &amp; purification ; Dihydroorotate Dehydrogenase ; Electron Transport ; *Gene Transfer, Horizontal ; Mitochondria/enzymology ; Oxidoreductases Acting on CH-CH Group Donors/metabolism ; Oxygen/metabolism ; Phylogeny ; Pyrimidines/*biosynthesis ; Saccharomyces cerevisiae/*enzymology/genetics/*growth &amp; development ; Subcellular Fractions/enzymology ; }, abstract = {The ability to propagate under anaerobic conditions is an essential and unique trait of brewer's or baker's yeast (Saccharomyces cervisiae). To understand the evolution of facultative anaerobiosis we studied the dependence of de novo pyrimidine biosynthesis, more precisely the fourth enzymic activity catalysed by dihydroorotate dehydrogenase (DHODase), on the enzymes of the respiratory chain in several yeast species. While the majority of yeasts possess a mitochondrial DHODase, Saccharomyces cerevisiae has a cytoplasmatic enzyme, whose activity is independent of the presence of oxygen. From the phylogenetic point of view, this enzyme is closely related to a bacterial DHODase from Lactococcus lactis. Here we show that S. kluyveri, which separated from the S. cerevisiae lineage more than 100 million years ago, represents an evolutionary intermediate, having both cytoplasmic and mitochondrial DHODases. We show that these two S. kluyveri enzymes, and their coding genes, differ in their dependence on the presence of oxygen. Only the cytoplasmic DHODase promotes growth in the absence of oxygen. Apparently a Saccharomyces yeast progenitor which had a eukaryotic-like mitochondrial DHODase acquired a bacterial gene for DHODase, which subsequently allowed cell growth gradually to become independent of oxygen.}, }
@article {pmid15014155, year = {2004}, author = {Canbäck, B and Tamas, I and Andersson, SG}, title = {A phylogenomic study of endosymbiotic bacteria.}, journal = {Molecular biology and evolution}, volume = {21}, number = {6}, pages = {1110-1122}, doi = {10.1093/molbev/msh122}, pmid = {15014155}, issn = {0737-4038}, mesh = {Animals ; Base Composition ; Base Sequence ; Cluster Analysis ; Databases, Genetic ; *Evolution, Molecular ; Gammaproteobacteria/*genetics ; *Genome, Bacterial ; Insecta/microbiology ; Models, Genetic ; *Phylogeny ; Selection, Genetic ; Sequence Alignment ; *Symbiosis ; }, abstract = {Endosymbiotic bacteria of aphids, Buchnera aphidicola, and tsetse flies, Wigglesworthia glossinidia, are descendents of free-living gamma-Proteobacteria. The acceleration of sequence evolution in the endosymbiont genomes is here estimated from a phylogenomic analysis of the gamma-Proteobacteria. The tree topologies associated with the most highly conserved genes suggest that the endosymbionts form a sister group with Escherichia coli, Salmonella sp., and Yersinia pestis. Our results indicate that deviant tree topologies result from high substitution rates and biased nucleotide patterns, rather than from lateral gene transfer, as previously suggested. A reinvestigation of the relative rate increase in the endosymbiont genomes reveals variability among genes that correlate with host-associated metabolic dependencies. The conclusion is that host-level selection has retarded both the loss of genes and the acceleration of sequence evolution in endocellular symbionts.}, }
@article {pmid15014152, year = {2004}, author = {Genschel, U}, title = {Coenzyme A biosynthesis: reconstruction of the pathway in archaea and an evolutionary scenario based on comparative genomics.}, journal = {Molecular biology and evolution}, volume = {21}, number = {7}, pages = {1242-1251}, doi = {10.1093/molbev/msh119}, pmid = {15014152}, issn = {0737-4038}, mesh = {Archaea/enzymology/*genetics ; Carboxy-Lyases/genetics ; Coenzyme A/*biosynthesis/genetics ; Escherichia coli/enzymology/genetics ; *Evolution, Molecular ; *Genomics ; Humans ; Pantothenic Acid/biosynthesis/genetics ; Peptide Synthases/genetics ; *Phylogeny ; }, abstract = {Coenzyme A (CoA) holds a central position in cellular metabolism and therefore can be assumed to be an ancient molecule. Starting from the known E. coli and human enzymes required for the biosynthesis of CoA, phylogenetic profiles and chromosomal proximity methods enabled an almost complete reconstruction of archaeal CoA biosynthesis. This includes the identification of strong candidates for archaeal pantothenate synthetase and pantothenate kinase, which are unrelated to the corresponding bacterial or eukaryotic enzymes. According to this reconstruction, the topology of CoA synthesis from common precursors is essentially conserved across the three domains of life. The CoA pathway is conserved to varying degrees in eukaryotic pathogens like Giardia lamblia or Plasmodium falciparum, indicating that these pathogens have individual uptake-mechanisms for different CoA precursors. Phylogenetic analysis and phyletic distribution of the CoA biosynthetic enzymes suggest that the enzymes required for the synthesis of phosphopantothenate were recruited independently in the bacterial and archaeal lineages by convergent evolution, and that eukaryotes inherited the genes for the synthesis of pantothenate (vitamin B5) from bacteria. Homologues to bacterial enzymes involved in pantothenate biosynthesis are present in a subset of archaeal genomes. The phylogenies of these enzymes indicate that they were acquired from bacterial thermophiles through horizontal gene transfer. Monophyly can be inferred for each of the enzymes catalyzing the four ultimate steps of CoA synthesis, the conversion of phosphopantothenate into CoA. The results support the notion that CoA was initially synthesized from a prebiotic precursor, most likely pantothenate or a related compound.}, }
@article {pmid15013044, year = {2004}, author = {Munday, CJ and Xiong, J and Li, C and Shen, D and Hawkey, PM}, title = {Dissemination of CTX-M type beta-lactamases in Enterobacteriaceae isolates in the People's Republic of China.}, journal = {International journal of antimicrobial agents}, volume = {23}, number = {2}, pages = {175-180}, doi = {10.1016/j.ijantimicag.2003.07.004}, pmid = {15013044}, issn = {0924-8579}, mesh = {Anti-Bacterial Agents/pharmacology ; China/epidemiology ; *Conjugation, Genetic ; DNA, Bacterial/analysis/genetics ; Enterobacteriaceae/classification/*drug effects/enzymology/genetics ; Enterobacteriaceae Infections/epidemiology/microbiology ; *Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; *Plasmids ; Random Amplified Polymorphic DNA Technique ; beta-Lactam Resistance/*genetics ; beta-Lactamases/*genetics/metabolism ; beta-Lactams/pharmacology ; }, abstract = {Previously there have been a number of reports of extended spectrum beta-lactamase (ESBL) producing isolates of the family Enterobacteriaceae in Asia. We first reported the occurrence of bla(CTX-M) in Guangzhou, China, subsequently there have been reports of bla(CTX-M) from a number of other south Asian countries. Initial surveillance study data suggested that bla(CTX-M) might be widely distributed in China. This study examines the type of bla(CTX-M) occurring in other major population centres in China. Initial disk diffusion method susceptibility testing (NCCLS) selected ESBL producing Escherichia coli and Klebsiella pneumoniae isolates from Beijing and near Wuhan, PRC. After screening in both China and the UK, 13 isolates producing CTX-M ESBLs were identified and studied, 11 also produced TEM-1, and 4 also produced SHV-1. Sequence analysis of the bla(CTX-M) containing isolates revealed these isolates contained two different bla(CTX-M), three with bla(CTX-M-3) and 10 with bla(CTX-M-14). After comparison with other previously published studies in the English language, we conclude that the most prevalent bla(CTX-M) so far reported in Asia are bla(CTX-M-14) and bla(CTX-M-3).}, }
@article {pmid15012950, year = {2004}, author = {Moulin, L and Béna, G and Boivin-Masson, C and Stepkowski, T}, title = {Phylogenetic analyses of symbiotic nodulation genes support vertical and lateral gene co-transfer within the Bradyrhizobium genus.}, journal = {Molecular phylogenetics and evolution}, volume = {30}, number = {3}, pages = {720-732}, doi = {10.1016/S1055-7903(03)00255-0}, pmid = {15012950}, issn = {1055-7903}, mesh = {Acyltransferases/genetics ; Bacterial Proteins/genetics ; Blotting, Southern ; Bradyrhizobium/*genetics ; Fabaceae/microbiology ; Fucosyltransferases/genetics ; *Genes, Bacterial ; Nitrogen/metabolism ; Oligonucleotides/genetics ; Oligosaccharides/genetics ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {Symbiotic nitrogen fixing bacteria-known as rhizobia-harbour a set of nodulation (nod) genes that control the synthesis of modified lipo-chitooligosaccharides, called Nod factors that are required for legume nodulation. The nodA gene, which is essential for symbiosis, is responsible for the attachment of the fatty acid group to the oligosaccharide backbone. The nodZ, nolL, and noeI genes are involved in specific modifications of Nod factors common to bradyrhizobia, i.e., the transfer of a fucosyl group on the Nod factor core, fucose acetylation and fucose methylation, respectively. PCR amplification, sequencing and phylogenetic analysis of nodA gene sequences from a collection of diverse Bradyrhizobium strains revealed the monophyletic character with the possible exception of photosynthetic Bradyrhizobium, despite high sequence diversity. The distribution of the nodZ, nolL, and noeI genes in the studied strains, as assessed by gene amplification, hybridization or sequencing, was found to correlate with the nodA tree topology. Moreover, the nodA, nodZ, and noeI phylogenies were largely congruent, but did not closely follow the taxonomy of the strains shown by the housekeeping 16S rRNA and dnaK genes. Additionally, the distribution of nodZ, noeI, and nolL genes suggested that their presence may be related to the requirements of their legume hosts. These data indicated that the spread and maintenance of nodulation genes within the Bradyrhizobium genus occurred through vertical transmission, although lateral gene transfer also played a significant role.}, }
@article {pmid15011140, year = {2003}, author = {Hoenigsberg, H}, title = {Evolution without speciation but with selection: LUCA, the Last Universal Common Ancestor in Gilbert's RNA world.}, journal = {Genetics and molecular research : GMR}, volume = {2}, number = {4}, pages = {366-375}, pmid = {15011140}, issn = {1676-5680}, mesh = {Animals ; *Evolution, Molecular ; *Models, Theoretical ; Phenotype ; *RNA ; *Selection, Genetic ; }, abstract = {This is not an attempt to analyze the Last Universal Common Ancestor (LUCA) to understand the origin of living systems. We do not know what came before Gilberts' RNA world. Our analysis starts with the RNA world and with genes (biological replicators alla Dawkings) made up of RNA proteins with enzymatic catalytic functions within units that are not yet modern cells. We offer a scenario where cellular entities are very simple and without individuality; they are only simple primary units of selection (the first level of selection) in which replicators compete in the most Darwinian manner, totally deprived of cooperation and interactions among genes. The information processing system of this RNA world is inaccurate and inefficient when compared to that found in organisms that came later. Among the "genes" and the entities that harbor them, high mutation rate was the most prevalent source of variability and the only inheritance was through lateral gene transfer of mobile elements. There were no chromosomes or any other genomic organization. As millions of years accumulated, complex and organized biological structures and processes evolved thanks to the variability mustered up mostly by lateral gene transfers and mutations. With micro- and mini-satellites, lateral gene transfers became indispensable devices of selection to mold variability. Competition and Darwinian selection gave way to a new transition in evolution, one I consider ineluctable, in which cooperation among interactive genes prevailed for the sake of higher fitness. Compartmentalization constituted a major transition in evolution that spurted new types of genome organization. Minichromosomes is one of these; cellular membranes and cytoplasmic structures completed the picture of the primitive cell. However, the much talked about phylogenetic tree does not exit in that ancient LUCA. The tree has no organism at its base; only clusters of genes evoke a fragile beginning for the increasingly complex cell types that were to emerge later.}, }
@article {pmid15007099, year = {2004}, author = {Vimr, ER and Kalivoda, KA and Deszo, EL and Steenbergen, SM}, title = {Diversity of microbial sialic acid metabolism.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {68}, number = {1}, pages = {132-153}, pmid = {15007099}, issn = {1092-2172}, mesh = {Amino Acid Sequence ; Animals ; Bacteria/genetics/*metabolism/pathogenicity ; Bacterial Proteins/*genetics/metabolism ; Escherichia coli/genetics/metabolism/pathogenicity ; *Gene Expression Regulation, Bacterial ; Haemophilus influenzae/genetics/metabolism/pathogenicity ; Humans ; Molecular Sequence Data ; N-Acetylneuraminic Acid/chemistry/*metabolism ; }, abstract = {Sialic acids are structurally unique nine-carbon keto sugars occupying the interface between the host and commensal or pathogenic microorganisms. An important function of host sialic acid is to regulate innate immunity, and microbes have evolved various strategies for subverting this process by decorating their surfaces with sialylated oligosaccharides that mimic those of the host. These subversive strategies include a de novo synthetic pathway and at least two truncated pathways that depend on scavenging host-derived intermediates. A fourth strategy involves modification of sialidases so that instead of transferring sialic acid to water (hydrolysis), a second active site is created for binding alternative acceptors. Sialic acids also are excellent sources of carbon, nitrogen, energy, and precursors of cell wall biosynthesis. The catabolic strategies for exploiting host sialic acids as nutritional sources are as diverse as the biosynthetic mechanisms, including examples of horizontal gene transfer and multiple transport systems. Finally, as compounds coating the surfaces of virtually every vertebrate cell, sialic acids provide information about the host environment that, at least in Escherichia coli, is interpreted by the global regulator encoded by nanR. In addition to regulating the catabolism of sialic acids through the nan operon, NanR controls at least two other operons of unknown function and appears to participate in the regulation of type 1 fimbrial phase variation. Sialic acid is, therefore, a host molecule to be copied (molecular mimicry), eaten (nutrition), and interpreted (cell signaling) by diverse metabolic machinery in all major groups of mammalian pathogens and commensals.}, }
@article {pmid15006795, year = {2004}, author = {Coombs, JM and Barkay, T}, title = {Molecular evidence for the evolution of metal homeostasis genes by lateral gene transfer in bacteria from the deep terrestrial subsurface.}, journal = {Applied and environmental microbiology}, volume = {70}, number = {3}, pages = {1698-1707}, pmid = {15006795}, issn = {0099-2240}, mesh = {Bacteria/*genetics/isolation &amp; purification/*metabolism ; Base Sequence ; DNA, Bacterial/genetics ; Ecosystem ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Homeostasis ; Metals/*metabolism ; Molecular Sequence Data ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; *Water Microbiology ; }, abstract = {Lateral gene transfer (LGT) plays a vital role in increasing the genetic diversity of microorganisms and promoting the spread of fitness-enhancing phenotypes throughout microbial communities. To date, LGT has been investigated in surface soils, natural waters, and biofilm communities but not in the deep terrestrial subsurface. Here we used a combination of molecular analyses to investigate the role of LGT in the evolution of metal homeostasis in lead-resistant subsurface bacteria. A nested PCR approach was employed to obtain DNA sequences encoding P(IB)-type ATPases, which are proteins that transport toxic or essential soft metals such as Zn(II), Cd(II), and Pb(II) through the cell wall. Phylogenetic incongruencies between a 16S rRNA gene tree and a tree based on 48 P(IB)-type ATPase amplicons and sequences available for complete bacterial genomes revealed an ancient transfer from a member of the beta subclass of the Proteobacteria (beta-proteobacterium) that may have predated the diversification of the genus Pseudomonas. Four additional phylogenetic incongruencies indicate that LGT has occurred among groups of beta- and gamma-proteobacteria. Two of these transfers appeared to be recent, as indicated by an unusual G+C content of the P(IB)-type ATPase amplicons. This finding provides evidence that LGT plays a distinct role in the evolution of metal homeostasis in deep subsurface bacteria, and it shows that molecular evolutionary approaches may be used for investigation of this process in microbial communities in specific environments.}, }
@article {pmid15003488, year = {2004}, author = {Huang, J and Mullapudi, N and Sicheritz-Ponten, T and Kissinger, JC}, title = {A first glimpse into the pattern and scale of gene transfer in Apicomplexa.}, journal = {International journal for parasitology}, volume = {34}, number = {3}, pages = {265-274}, doi = {10.1016/j.ijpara.2003.11.025}, pmid = {15003488}, issn = {0020-7519}, support = {1R01AI045806-01A1/AI/NIAID NIH HHS/United States ; AI05093/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Apicomplexa/*genetics ; Cryptosporidium parvum/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Protozoan ; Genomics ; Phylogeny ; Plasmodium falciparum/genetics ; Theileria annulata/genetics ; Toxoplasma/genetics ; }, abstract = {Reports of plant-like and bacterial-like genes for a number of parasitic organisms, most notably those within the Apicomplexa and Kinetoplastida, have appeared in the literature over the last few years. Among the apicomplexan organisms, following discovery of the apicomplexan plastid (apicoplast), the discovery of plant-like genes was less surprising although the extent of transfer and the relationship of transferred genes to the apicoplast remained unclear. We used new genome sequence data to begin a systematic examination of the extent and origin of transferred genes in the Apicomplexa combined with a phylogenomic approach to detect potential gene transfers in four apicomplexan genomes. We have detected genes of algal nuclear, chloroplast (cyanobacterial) and proteobacterial origin. Plant-like genes were detected in species not currently harbouring a plastid (e.g. Cryptosporidium parvum) and putatively transferred genes were detected that appear to be unrelated to the function of the apicoplast. While the mechanism of acquisition for many of the identified genes is not certain, it appears that some were most likely acquired via intracellular gene transfer from an algal endosymbiont while others may have been acquired via horizontal gene transfer.}, }
@article {pmid15003123, year = {2004}, author = {Zhaxybayeva, O and Hamel, L and Raymond, J and Gogarten, JP}, title = {Visualization of the phylogenetic content of five genomes using dekapentagonal maps.}, journal = {Genome biology}, volume = {5}, number = {3}, pages = {R20}, pmid = {15003123}, issn = {1474-760X}, mesh = {Archaeoglobus fulgidus/genetics ; Bacillus subtilis/genetics ; Computer Graphics ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; *Genome ; Genome, Archaeal ; Genome, Bacterial ; Genome, Fungal ; *Phylogeny ; Rhodobacter capsulatus/genetics ; Saccharomyces cerevisiae/genetics ; Sulfolobus/genetics ; }, abstract = {The methods presented here summarize phylogenetic relationships of genomes in visually appealing and informative figures. Dekapentagonal maps depict phylogenetic information for orthologous genes present in five genomes, and provide a pre-screen for putatively horizontally transferred genes. If the majority of individual gene phylogenies are unresolved, bipartition histograms provide a means of uncovering and analyzing the plurality consensus. Analyses of genomes representing five photosynthetic bacterial phyla and of the prokaryotic contributions to the eukaryotic cell illustrate the utility of the methods.}, }
@article {pmid15003120, year = {2004}, author = {Brochier, C and Forterre, P and Gribaldo, S}, title = {Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox.}, journal = {Genome biology}, volume = {5}, number = {3}, pages = {R17}, pmid = {15003120}, issn = {1474-760X}, mesh = {Archaea/enzymology/*genetics ; Archaeal Proteins/genetics/*physiology ; DNA, Archaeal/genetics ; DNA-Directed RNA Polymerases/genetics/physiology ; Databases, Genetic ; Euryarchaeota/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genes, Archaeal/genetics ; Genome, Archaeal ; Methanococcus/enzymology/genetics ; *Phylogeny ; Protein Biosynthesis/genetics/*physiology ; Sulfolobales/enzymology/genetics ; Thermoplasmales/enzymology/genetics ; Transcription, Genetic/genetics/*physiology ; }, abstract = {BACKGROUND: Phylogenetic analysis of the Archaea has been mainly established by 16S rRNA sequence comparison. With the accumulation of completely sequenced genomes, it is now possible to test alternative approaches by using large sequence datasets. We analyzed archaeal phylogeny using two concatenated datasets consisting of 14 proteins involved in transcription and 53 ribosomal proteins (3,275 and 6,377 positions, respectively).<br><br>RESULTS: Important relationships were confirmed, notably the dichotomy of the archaeal domain as represented by the Crenarchaeota and Euryarchaeota, the sister grouping of Sulfolobales and Aeropyrum pernix, and the monophyly of a large group comprising Thermoplasmatales, Archaeoglobus fulgidus, Methanosarcinales and Halobacteriales, with the latter two orders forming a robust cluster. The main difference concerned the position of Methanopyrus kandleri, which grouped with Methanococcales and Methanobacteriales in the translation tree, whereas it emerged at the base of the euryarchaeotes in the transcription tree. The incongruent placement of M. kandleri is likely to be the result of a reconstruction artifact due to the high evolutionary rates displayed by the components of its transcription apparatus.<br><br>CONCLUSIONS: We show that two informational systems, transcription and translation, provide a largely congruent signal for archaeal phylogeny. In particular, our analyses support the appearance of methanogenesis after the divergence of the Thermococcales and a late emergence of aerobic respiration from within methanogenic ancestors. We discuss the possible link between the evolutionary acceleration of the transcription machinery in M. kandleri and several unique features of this archaeon, in particular the absence of the elongation transcription factor TFS.}, }
@article {pmid15001188, year = {2004}, author = {Bravo, IG and García-Vallvé, S and Romeu, A and Reglero, A}, title = {Prokaryotic origin of cytidylyltransferases and alpha-ketoacid synthases.}, journal = {Trends in microbiology}, volume = {12}, number = {3}, pages = {120-128}, doi = {10.1016/j.tim.2004.01.004}, pmid = {15001188}, issn = {0966-842X}, mesh = {Bacteria/*enzymology/genetics ; Bacterial Proteins/*genetics/physiology ; Gene Transfer, Horizontal ; Keto Acids/metabolism ; Ketone Oxidoreductases/chemistry/*genetics/physiology ; N-Acylneuraminate Cytidylyltransferase/*genetics/physiology ; Phylogeny ; }, }
@article {pmid14997183, year = {2004}, author = {Pampoulie, C and Gysels, ES and Maes, GE and Hellemans, B and Leentjes, V and Jones, AG and Volckaert, FA}, title = {Evidence for fine-scale genetic structure and estuarine colonisation in a potential high gene flow marine goby (Pomatoschistus minutus).}, journal = {Heredity}, volume = {92}, number = {5}, pages = {434-445}, doi = {10.1038/sj.hdy.6800438}, pmid = {14997183}, issn = {0018-067X}, mesh = {*Alleles ; Animals ; Gene Frequency ; Gene Transfer, Horizontal/*genetics ; *Genotype ; Microsatellite Repeats/*genetics ; North Sea ; Perciformes/*genetics ; Polymorphism, Genetic/*genetics ; Selection, Genetic ; Sequence Analysis, DNA ; }, abstract = {Marine fish seem to experience evolutionary processes that are expected to produce genetically homogeneous populations. We have assessed genetic diversity and differentiation in 15 samples of the sand goby Pomatoschistus minutus (Pallas, 1770) (Gobiidae, Teleostei) from four major habitats within the Southern Bight of the North Sea, using seven microsatellite and 13 allozyme loci. Despite its high dispersal potential, microsatellite loci revealed a moderate level of differentiation (overall F(ST)=0.026; overall R(ST)=0.058). Both hierarchical analysis of molecular variance and multivariate analysis revealed significant differentiation (P<0.01) between estuarine, coastal and marine samples with microsatellites, but not with allozymes. Comparison among the different estimators of differentiation (F(ST) and R(ST)) pointed to possible historical events and contemporary habitat fragmentation. Samples were assigned to two breeding units in the estuary and coastal region. Despite this classification, there were indications of a complex and dynamic spatiotemporal structure, which is, most likely, determined by historical events and local oceanic currents.}, }
@article {pmid14996790, year = {2004}, author = {Gilmour, MW and Taylor, DE}, title = {A subassembly of R27-encoded transfer proteins is dependent on TrhC nucleoside triphosphate-binding motifs for function but not formation.}, journal = {Journal of bacteriology}, volume = {186}, number = {6}, pages = {1606-1613}, pmid = {14996790}, issn = {0021-9193}, mesh = {Coliphages/genetics/physiology ; *Conjugation, Genetic ; Escherichia coli/*genetics/metabolism/virology ; Escherichia coli Proteins/chemistry/genetics/*metabolism ; Gene Transfer, Horizontal ; Green Fluorescent Proteins ; Luminescent Proteins/genetics/metabolism ; Membrane Proteins/chemistry/genetics/*metabolism ; Mutagenesis, Site-Directed ; Mutation ; Nucleotides/*metabolism ; *R Factors ; Recombinant Fusion Proteins/metabolism ; }, abstract = {The transfer of plasmid DNA molecules between bacterial cells is achieved by a large array of conjugative transfer proteins which assemble into both cytoplasmic and membrane-associated complexes. TrhC is a membrane-associated protein that is required for the transfer of the IncHI1 resistance plasmid R27. Homologous proteins are encoded in all known conjugative systems, and each contains characteristic nucleoside triphosphate (NTP)-binding domains. An assembly of R27-encoded proteins was previously visualized by use of a TrhC-green fluorescent protein fusion, which appeared as discrete membrane-associated fluorescent foci. We have utilized this experimental system to determine the requirements for assembly of this TrhC-associated protein complex, and we found that 12 of the other 18 R27 transfer proteins are required for focus formation. An individual focus possibly represents a subassembly comprised of some or all of these transfer proteins. These data support the notion that the transfer apparatus is a multicomponent structure. In contrast, substitutions and deletions within TrhC NTP-binding motifs had minor effects on focus formation, but these mutations did affect plasmid transfer and bacteriophage susceptibility. These results indicate that TrhC requires intact NTP-binding motifs to function during conjugative transfer but that these motifs are not essential for the assembly of TrhC into a complex with other transfer proteins.}, }
@article {pmid14996712, year = {2004}, author = {Tung, CH and Zeng, Q and Shah, K and Kim, DE and Schellingerhout, D and Weissleder, R}, title = {In vivo imaging of beta-galactosidase activity using far red fluorescent switch.}, journal = {Cancer research}, volume = {64}, number = {5}, pages = {1579-1583}, doi = {10.1158/0008-5472.can-03-3226}, pmid = {14996712}, issn = {0008-5472}, support = {P50 CA86355/CA/NCI NIH HHS/United States ; R01 CA99385/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; *Fluorescent Dyes ; Gene Transfer, Horizontal ; Herpesvirus 1, Human/genetics ; Lac Operon ; Mice ; Sensitivity and Specificity ; beta-Galactosidase/*analysis ; }, abstract = {beta-Galactosidase (beta-gal) has been widely used as a transgene reporter enzyme, and several substrates are available for its in vitro detection. The ability to image beta-gal expression in living animals would further extend the use of this reporter. Here we show that DDAOG, a conjugate of beta-galactoside and 7-hydroxy-9H-(1,3-dichloro-9,9-dimethylacridin-2-one) (DDAO), is not only a chromogenic beta-gal substrate but that the cleavage product has far-red fluorescence properties detectable by imaging. Importantly, the cleavage substrate shows a 50-nm red shift, enabling its specific detection in a background of intact probe, a highly desirable feature for in vivo imaging. Specifically, we show that beta-gal-expressing 9L gliomas are readily detectable by red fluorescence imaging in comparison with the native 9L gliomas. We furthermore show that herpes simplex virus amplicon-mediated LacZ gene transfer into tumors can be transiently and thus serially visualized over time. The results indicated that in vivo real-time detection of beta-gal activity is possible by fluorescence imaging technology.}, }
@article {pmid14988930, year = {2004}, author = {Frank, SA and Nowak, MA}, title = {Problems of somatic mutation and cancer.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {26}, number = {3}, pages = {291-299}, doi = {10.1002/bies.20000}, pmid = {14988930}, issn = {0265-9247}, support = {AI24424/AI/NIAID NIH HHS/United States ; }, mesh = {Cell Lineage ; *Cell Transformation, Neoplastic ; Epithelium/physiology ; Gene Transfer, Horizontal ; Humans ; Neoplasms/*genetics/*metabolism/pathology ; *Point Mutation ; Regeneration/physiology ; Stem Cells/physiology ; }, abstract = {Somatic mutation plays a key role in transforming normal cells into cancerous cells. The analysis of cancer progression therefore requires the study of how point mutations and chromosomal mutations accumulate in cellular lineages. The spread of somatic mutations depends on the mutation rate, the number of cell divisions in the history of a cellular lineage, and the nature of competition between different cellular lineages. We consider how various aspects of tissue architecture and cellular competition affect the pace of mutation accumulation. We also discuss the rise and fall of somatic mutation rates during cancer progression.}, }
@article {pmid14985783, year = {2004}, author = {Murad, L and Bielawski, JP and Matyasek, R and Kovarík, A and Nichols, RA and Leitch, AR and Lichtenstein, CP}, title = {The origin and evolution of geminivirus-related DNA sequences in Nicotiana.}, journal = {Heredity}, volume = {92}, number = {4}, pages = {352-358}, doi = {10.1038/sj.hdy.6800431}, pmid = {14985783}, issn = {0018-067X}, mesh = {Base Sequence ; Cytosine/metabolism ; DNA Methylation ; DNA Replication ; DNA, Plant/chemistry/*genetics ; DNA, Viral/chemistry/*genetics ; *Evolution, Molecular ; GC Rich Sequence ; Geminiviridae/*genetics ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; Nicotiana/*genetics ; }, abstract = {A horizontal transmission of a geminiviral DNA sequence, into the germ line of an ancestral Nicotiana, gave rise to multiple repeats of geminivirus-related DNA, GRD, in the genome. We follow GRD evolution in Nicotiana tabacum (tobacco), an allotetraploid, and its diploid relatives, and show GRDs are derived from begomoviruses. GRDs occur in two families: the GRD5 family's ancestor integrated into the common ancestor of three diploid species, Nicotiana kawakamii, Nicotiana tomentosa and Nicotiana tomentosiformis, on homeologous group 4 chromosomes. The GRD3 family was acquired more recently on chromosome 2 in a lineage of N. tomentosiformis, the paternal ancestor of tobacco. Both GRD families include individual members that are methylated and diverged. Using relative rates of synonymous and nonsynonymous nucleotide substitutions, we tested for evidence of selection on GRD units and found none within the GRD3 and GRD5 families. However, the substitutions between GRD3 and GRD5 do show a significant excess of synonymous changes, suggesting purifying selection and hence a period of autonomous evolution between GRD3 and GRD5 integration. We observe in the GRD3 family, features of Helitrons, a major new class of putative rolling-circle replicating eukaryotic transposon, not found in the GRD5 family or geminiviruses. We speculate that the second integration event, resulting in the GRD3 family, involved a free-living geminivirus, a Helitron and perhaps also GRD5. Thus our data point towards recurrent dynamic interplay between geminivirus and plant DNA in evolution.}, }
@article {pmid14982638, year = {2004}, author = {Belhocine, K and Plante, I and Cousineau, B}, title = {Conjugation mediates transfer of the Ll.LtrB group II intron between different bacterial species.}, journal = {Molecular microbiology}, volume = {51}, number = {5}, pages = {1459-1469}, doi = {10.1111/j.1365-2958.2004.03923.x}, pmid = {14982638}, issn = {0950-382X}, mesh = {Base Sequence ; *Conjugation, Genetic ; Enterococcus faecalis/*genetics ; *Gene Transfer, Horizontal ; *Introns ; Lactococcus lactis/*genetics ; RNA, Catalytic/*metabolism ; *Retroelements ; Sequence Alignment ; }, abstract = {Some self-splicing group II introns (ribozymes) are mobile retroelements. These retroelements, which can insert themselves into cognate intronless alleles or ectopic sites by reverse splicing, are thought to be the evolutionary progenitors of the widely distributed eukaryotic spliceosomal introns. Lateral or horizontal transmission of introns (i.e. between species), although never experimentally demonstrated, is a well-accepted model for intron dispersal and evolution. Horizontal transfer of the ancestral bacterial group II introns may have contributed to the dispersal and wide distribution of spliceosomal introns present in modern eukaryotic genomes. Here, the Ll.LtrB group II intron from the Gram-positive bacterium Lactococcus lactis was used as a model system to address the dissemination of introns in the bacterial kingdom. We report the first experimental demonstration of horizontal transfer of a group II intron. We show that the Ll.LtrB group II intron, originally discovered on an L. lactis conjugative plasmid (pRS01) and within a chromosomally located sex factor in L. lactis 712, invades new sites using both retrohoming and retrotransposition pathways after its transfer by conjugation. Ll.LtrB lateral transfer is shown among different L. lactis strains (intraspecies) (retrohoming and retrotransposition) and between L. lactis and Enterococcus faecalis (interspecies) (retrohoming). These results shed light on long-standing questions about intron evolution and propagation, and demonstrate that conjugation is one of the mechanisms by which group II introns are, and probably were, broadly disseminated between widely diverged organisms.}, }
@article {pmid14977960, year = {2004}, author = {Baldwin, A and Sokol, PA and Parkhill, J and Mahenthiralingam, E}, title = {The Burkholderia cepacia epidemic strain marker is part of a novel genomic island encoding both virulence and metabolism-associated genes in Burkholderia cenocepacia.}, journal = {Infection and immunity}, volume = {72}, number = {3}, pages = {1537-1547}, pmid = {14977960}, issn = {0019-9567}, mesh = {Amidohydrolases/genetics ; Base Composition ; Base Sequence ; Burkholderia Infections/complications/epidemiology/microbiology ; Burkholderia cepacia/*genetics/metabolism/pathogenicity ; Burkholderia cepacia complex/*genetics/metabolism/pathogenicity ; Computational Biology ; Cystic Fibrosis/complications/microbiology ; DNA, Bacterial/chemistry/genetics ; Genome, Bacterial ; Genomic Instability ; *Genomic Islands ; Humans ; Ligases/genetics ; Molecular Epidemiology ; Mutagenesis, Site-Directed ; Porins/genetics ; Virulence/genetics ; }, abstract = {The Burkholderia cepacia epidemic strain marker (BCESM) is a useful epidemiological marker for virulent B. cenocepacia strains that infect patients with cystic fibrosis. However, there was no evidence that the original marker, identified by random amplified polymorphic DNA fingerprinting, contributed to pathogenicity. Here we demonstrate that the BCESM is part of a novel genomic island encoding genes linked to both virulence and metabolism. The BCESM was present on a 31.7-kb low-GC-content island that encoded 35 predicted coding sequences (CDSs): an N-acyl homoserine lactone (AHL) synthase gene (cciI) and corresponding transcriptional regulator (cciR), representing the first time cell signaling genes have been found on a genomic island; fatty acid biosynthesis genes; an IS66 family transposase; transcriptional regulator CDSs; amino acid metabolism genes; and a group of hypothetical genes. Mutagenesis of the AHL synthase, amidase (amiI), and porin (opcI) genes on the island was carried out. Testing of the isogenic mutants in a rat model of chronic lung infection demonstrated that the amidase played a role in persistence, while the AHL synthase and porin were both involved in virulence. The island, designated the B. cenocepacia island (cci), is the first genomic island to be defined in the B. cepacia complex and its discovery validates the original epidemiological correlation of the BCESM with virulent CF strains. The features of the cci, which overlap both pathogenicity and metabolism, expand the concept of bacterial pathogenicity islands and illustrate the diversity of accessory functions that can be acquired by lateral gene transfer in bacteria.}, }
@article {pmid14975531, year = {2004}, author = {Francia, MV and Varsaki, A and Garcillán-Barcia, MP and Latorre, A and Drainas, C and de la Cruz, F}, title = {A classification scheme for mobilization regions of bacterial plasmids.}, journal = {FEMS microbiology reviews}, volume = {28}, number = {1}, pages = {79-100}, doi = {10.1016/j.femsre.2003.09.001}, pmid = {14975531}, issn = {0168-6445}, mesh = {Amino Acid Sequence ; Bacteria/*genetics ; Molecular Sequence Data ; Plasmids/*classification/*genetics ; }, abstract = {Transmissible plasmids can be classified according to their mobilization ability, as being conjugative (self-transmissible) or mobilizable (transmissible only in the presence of additional conjugative functions). Naturally occurring mobilizable plasmids carry the genetic information necessary for relaxosome formation and processing, but lack the functions required for mating pair formation. Mobilizable plasmids have a tremendous impact in horizontal gene transfer in nature, including the spread of antibiotic resistance. However, analysis of their promiscuity and diversity has attracted less attention than that of conjugative plasmids. This review will focus on the analysis of the diversity of mobilizable plasmids. For this purpose, we primarily compared the amino acid sequences of their relaxases and, when pertinent, we compared these enzymes with conjugative plasmid relaxases. In this way, we established phylogenetic relationships among the members of each superfamily. We conducted a database and literature analysis that led us to propose a classification system for small mobilizable plasmids in families and superfamilies according to their mobilization regions. This review outlines the genetic organization of each family of mobilization regions, as well as the most relevant properties and relationships among their constituent encoded proteins. In this respect, the present review constitutes a first approach to the characterization of the global gene pool of mobilization regions of small mobilizable plasmids.}, }
@article {pmid14973452, year = {2004}, author = {Whitfield, J}, title = {Origins of life: born in a watery commune.}, journal = {Nature}, volume = {427}, number = {6976}, pages = {674-676}, doi = {10.1038/427674a}, pmid = {14973452}, issn = {1476-4687}, mesh = {Animals ; *Biological Evolution ; Conserved Sequence/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genes ; Genome ; Genomics ; Humans ; *Models, Biological ; Mutagenesis ; *Origin of Life ; Phylogeny ; Water ; }, }
@article {pmid14973196, year = {2004}, author = {Striepen, B and Pruijssers, AJ and Huang, J and Li, C and Gubbels, MJ and Umejiego, NN and Hedstrom, L and Kissinger, JC}, title = {Gene transfer in the evolution of parasite nucleotide biosynthesis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, number = {9}, pages = {3154-3159}, pmid = {14973196}, issn = {0027-8424}, support = {R01 AI045806/AI/NIAID NIH HHS/United States ; 1R01AI45806-01A1/AI/NIAID NIH HHS/United States ; AI05093/AI/NIAID NIH HHS/United States ; }, mesh = {Adenosine/metabolism ; Animals ; Base Sequence ; Cryptosporidium parvum/*genetics/isolation &amp; purification ; DNA Primers ; Databases, Nucleic Acid ; *Evolution, Molecular ; Expressed Sequence Tags ; *Gene Transfer Techniques ; Genes, Protozoan/*genetics ; Host-Parasite Interactions ; Models, Biological ; Molecular Sequence Data ; Nucleotides/*biosynthesis/genetics ; Polymerase Chain Reaction ; Purines/metabolism ; Pyrimidines/metabolism ; }, abstract = {Nucleotide metabolic pathways provide numerous successful targets for antiparasitic chemotherapy, but the human pathogen Cryptosporidium parvum thus far has proved extraordinarily refractory to classical treatments. Given the importance of this protist as an opportunistic pathogen afflicting immunosuppressed individuals, effective treatments are urgently needed. The genome sequence of C. parvum is approaching completion, and we have used this resource to critically assess nucleotide biosynthesis as a target in C. parvum. Genomic analysis indicates that this parasite is entirely dependent on salvage from the host for its purines and pyrimidines. Metabolic pathway reconstruction and experimental validation in the laboratory further suggest that the loss of pyrimidine de novo synthesis is compensated for by possession of three salvage enzymes. Two of these, uridine kinase-uracil phosphoribosyltransferase and thymidine kinase, are unique to C. parvum within the phylum Apicomplexa. Phylogenetic analysis suggests horizontal gene transfer of thymidine kinase from a proteobacterium. We further show that the purine metabolism in C. parvum follows a highly streamlined pathway. Salvage of adenosine provides C. parvum's sole source of purines. This renders the parasite susceptible to inhibition of inosine monophosphate dehydrogenase, the rate-limiting enzyme in the multistep conversion of AMP to GMP. The inosine 5' monophosphate dehydrogenase inhibitors ribavirin and mycophenolic acid, which are already in clinical use, show pronounced anticryptosporidial activity. Taken together, these data help to explain why widely used drugs fail in the treatment of cryptosporidiosis and suggest more promising targets.}, }
@article {pmid14973122, year = {2004}, author = {Piel, J and Höfer, I and Hui, D}, title = {Evidence for a symbiosis island involved in horizontal acquisition of pederin biosynthetic capabilities by the bacterial symbiont of Paederus fuscipes beetles.}, journal = {Journal of bacteriology}, volume = {186}, number = {5}, pages = {1280-1286}, pmid = {14973122}, issn = {0021-9193}, mesh = {Animals ; Bacteria/drug effects/*genetics/metabolism ; Bacterial Proteins/*genetics/metabolism ; Coleoptera/*microbiology ; Drug Resistance, Bacterial ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Multigene Family ; Pyrans/*metabolism ; Sequence Analysis, DNA ; *Symbiosis ; Tellurium/pharmacology ; }, abstract = {Pederin belongs to a group of antitumor compounds found in terrestrial beetles and marine sponges. It is used by apparently all members of the rove beetle genera Paederus and Paederidus as a chemical defense against predators. However, a recent analysis of the putative pederin biosynthesis (ped) gene cluster strongly suggests that pederin is produced by bacterial symbionts. We have sequenced an extended region of the symbiont genome to gain further insight into the biology of this as-yet-unculturable bacterium and the evolution of pederin symbiosis. Our data indicate that the symbiont is a very close relative of Pseudomonas aeruginosa that has acquired several foreign genetic elements by horizontal gene transfer. Besides one functional tellurite resistance operon, the region contains a genomic island spanning 71.6 kb that harbors the putative pederin biosynthetic genes. Several decayed insertion sequence elements and the mosaic-like appearance of the island suggest that the acquisition of the ped symbiosis genes was followed by further insertions and rearrangements. A horizontal transfer of genes for the biosynthesis of protective substances could explain the widespread occurrence of pederin-type compounds in unrelated animals from diverse habitats.}, }
@article {pmid14973054, year = {2004}, author = {Wang, Z and Cook, T and Alber, S and Liu, K and Kovesdi, I and Watkins, SK and Vodovotz, Y and Billiar, TR and Blumberg, D}, title = {Adenoviral gene transfer of the human inducible nitric oxide synthase gene enhances the radiation response of human colorectal cancer associated with alterations in tumor vascularity.}, journal = {Cancer research}, volume = {64}, number = {4}, pages = {1386-1395}, doi = {10.1158/0008-5472.can-03-1307}, pmid = {14973054}, issn = {0008-5472}, mesh = {Adenoviridae/genetics ; Animals ; Apoptosis ; Cell Cycle ; Colorectal Neoplasms/*blood supply/pathology/*radiotherapy ; Gene Transfer, Horizontal ; *Genetic Therapy ; Humans ; Mice ; Mice, Nude ; Nitric Oxide/physiology ; Nitric Oxide Synthase/*genetics ; Nitric Oxide Synthase Type II ; *Radiation Tolerance ; }, abstract = {Nitric oxide is a potent radiosensitizer of tumors, but its use clinically is limited by serious side effects when administered systemically. We have demonstrated previously that gene transfer of the inducible nitric oxide synthase gene (iNOS) into colorectal cancer cells enhances radiation-induced apoptosis in vitro. The objectives of this study were to further characterize the effects of iNOS gene transfer on the radiosensitivity of human colorectal cancer cells in vitro and tumors grown in athymic nude mice. Adenoviral gene transfer of iNOS (AdiNOS) into human colorectal cancer cell lines (HCT-116 and SNU-1040 cells) significantly enhanced the effects of radiation with sensitizing enhancement ratios (0.1) of 1.65 and 1.6, respectively. The radiation enhancement induced by iNOS was associated with increased iNOS expression and nitric oxide production and prevented by L-NIO, an enzymatic inhibitor of iNOS. AdiNOS treatment of HCT-116 tumors combined with radiation (2 Gy x three fractions) led to a 3.4-fold greater (P < 0.005) tumor growth delay compared with radiation (RT) alone. AdiNOS plus RT also caused significant (P < 0.01) tumor regression with 63% of tumors regressing compared with only 6% of tumors treated with RT. AdiNOS plus RT significantly (P < or = 0.001) increased the percentage of apoptotic cells (22 +/- 4%) compared with either tumors treated with control vector plus RT (9 +/- 1%), AdiNOS alone (9 +/- 3%), or no treatment (2 +/- 1%). These radiosensitizing effects of AdiNOS occurred at low infection efficiency (4% of tumor infected), indicating a significant bystander effect.}, }
@article {pmid14973016, year = {2004}, author = {Höppner, C and Liu, Z and Domke, N and Binns, AN and Baron, C}, title = {VirB1 orthologs from Brucella suis and pKM101 complement defects of the lytic transglycosylase required for efficient type IV secretion from Agrobacterium tumefaciens.}, journal = {Journal of bacteriology}, volume = {186}, number = {5}, pages = {1415-1422}, pmid = {14973016}, issn = {0021-9193}, mesh = {Agrobacterium tumefaciens/*enzymology/genetics/growth &amp; development/pathogenicity ; Amino Acid Sequence ; Bacterial Proteins/*genetics/metabolism ; Binding Sites ; Brucella suis/enzymology/*genetics ; Conjugation, Genetic ; Gene Deletion ; Gene Transfer, Horizontal ; *Genetic Complementation Test ; Glycosyltransferases/*genetics/metabolism ; Molecular Sequence Data ; Plant Leaves/microbiology ; Plant Tumors/microbiology ; Plasmids/*genetics ; Nicotiana/microbiology ; Virulence ; Virulence Factors/metabolism ; }, abstract = {Type IV secretion systems mediate conjugative plasmid transfer as well as the translocation of virulence factors from various gram-negative pathogens to eukaryotic host cells. The translocation apparatus consists of 9 to 12 components, and the components from different organisms are believed to have similar functions. However, orthologs to proteins of the prototypical type IV system, VirB of Agrobacterium tumefaciens, typically share only 15 to 30% identical amino acids, and functional complementation between components of different type IV secretion systems has not been achieved. We here report a heterologous complementation in the case of A. tumefaciens virB1 defects with its orthologs from Brucella suis (VirB1s) and the IncN plasmid pKM101 (TraL). In contrast, expression of the genes encoding the VirB1 orthologs from the IncF plasmid (open reading frame 169) and from the Helicobacter pylori cag pathogenicity island (HP0523) did not complement VirB1 functions. The complementation of VirB1 activity was assessed by T-pilus formation, by tumor formation on wounded plants, by IncQ plasmid transfer, and by IncQ plasmid recipient assay. Replacement of the key active-site Glu residue by Ala abolished the complementation by VirB1 from B. suis and by TraL, demonstrating that heterologous complementation requires an intact lytic transglycosylase active site. In contrast, the VirB1 active-site mutant from A. tumefaciens retained considerable residual activity in various activity assays, implying that this protein exerts additional effects during the type IV secretion process.}, }
@article {pmid14970819, year = {2004}, author = {McAdams, HH and Srinivasan, B and Arkin, AP}, title = {The evolution of genetic regulatory systems in bacteria.}, journal = {Nature reviews. Genetics}, volume = {5}, number = {3}, pages = {169-178}, doi = {10.1038/nrg1292}, pmid = {14970819}, issn = {1471-0056}, mesh = {Bacteria/chemistry/*genetics ; Bacterial Proteins ; *Biological Evolution ; DNA-Binding Proteins/genetics/physiology ; Flagella/chemistry/genetics/physiology ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Transcription Factors/genetics/physiology ; }, }
@article {pmid14766976, year = {2004}, author = {Faruque, SM and Chowdhury, N and Kamruzzaman, M and Dziejman, M and Rahman, MH and Sack, DA and Nair, GB and Mekalanos, JJ}, title = {Genetic diversity and virulence potential of environmental Vibrio cholerae population in a cholera-endemic area.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, number = {7}, pages = {2123-2128}, pmid = {14766976}, issn = {0027-8424}, support = {R01 GM068851/GM/NIGMS NIH HHS/United States ; GM068851/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bangladesh/epidemiology ; Cholera/*epidemiology/*microbiology/transmission ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/genetics ; Genetic Variation/*genetics ; Humans ; Mice ; Models, Biological ; Multigene Family/genetics ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal/genetics ; Rabbits ; Ribotyping ; Seasons ; Vibrio cholerae/classification/*genetics/*pathogenicity ; Virulence/genetics ; *Water Microbiology ; }, abstract = {To understand the evolutionary events and possible selection mechanisms involved in the emergence of pathogenic Vibrio cholerae, we analyzed diverse strains of V. cholerae isolated from environmental waters in Bangladesh by direct enrichment in the intestines of adult rabbits and by conventional laboratory culture. Strains isolated by conventional culture were mostly (99.2%) negative for the major virulence gene clusters encoding toxin-coregulated pilus (TCP) and cholera toxin (CT) and were nonpathogenic in animal models. In contrast, all strains selected in rabbits were competent for colonizing infant mice, and 56.8% of these strains carried genes encoding TCP alone or both TCP and CT. Ribotypes of toxigenic O1 and O139 strains from the environment were similar to pandemic strains, whereas ribotypes of non-O1 non-O139 strains and TCP(-) nontoxigenic O1 strains diverged widely from the seventh pandemic O1 and the O139 strains. Results of this study suggest that (i) the environmental V. cholerae population in a cholera-endemic area is highly heterogeneous, (ii) selection in the mammalian intestine can cause enrichment of environmental strains with virulence potential, (iii) pathogenicity of V. cholerae involves more virulence genes than currently appreciated, and (iv) most environmental V. cholerae strains are unlikely to attain a pandemic potential by acquisition of TCP and CT genes alone. Because most of the recorded cholera pandemics originated in the Ganges Delta region, this ecological setting presumably favors extensive genetic exchange among V. cholerae strains and thus promotes the rare, multiple-gene transfer events needed to assemble the critical combination of genes required for pandemic spread.}, }
@article {pmid14766601, year = {2004}, author = {Nemergut, DR and Martin, AP and Schmidt, SK}, title = {Integron diversity in heavy-metal-contaminated mine tailings and inferences about integron evolution.}, journal = {Applied and environmental microbiology}, volume = {70}, number = {2}, pages = {1160-1168}, pmid = {14766601}, issn = {0099-2240}, mesh = {Bacteria/classification/enzymology/*genetics ; DNA, Bacterial/analysis ; Evolution, Molecular ; *Genetic Variation ; Gold ; Integrases/genetics ; Integrons/*genetics ; Metals, Heavy/analysis ; *Mining ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; *Soil Pollutants ; }, abstract = {Integrons are horizontal gene transfer (HGT) systems containing elements necessary for site-specific recombination and expression of foreign DNA. The overall phylogenetic distribution of integrons and range of genes that can be transferred by integrons are unknown. This report contains an exploration of integrons in an environmental microbial community and an investigation of integron evolution. First, using culture-independent techniques, we explored the diversity of integrons and integron-transferred genes in heavy-metal-contaminated mine tailings. Using degenerate primers, we amplified integron integrase genes from the tailings. We discovered 14 previously undescribed integrase genes, including six novel gene lineages. In addition, we found 11 novel gene cassettes in this sample. One of the gene cassettes that we sequenced is similar to a gene that codes for a step in a pathway for nitroaromatic catabolism, a group of compounds associated with mining activity. This suggests that integrons may be important for gene transfer in response to selective pressures other than the presence of antibiotics. We also investigated the evolution of integrons by statistically comparing the phylogenies of 16S rRNA and integrase genes from the same organisms, using sequences from GenBank and various sequencing projects. We found significant differences between the organismal (16S rRNA) and integrase trees, and we suggest that these differences may be due to HGT.}, }
@article {pmid14766598, year = {2004}, author = {Kawase, T and Saito, A and Sato, T and Kanai, R and Fujii, T and Nikaidou, N and Miyashita, K and Watanabe, T}, title = {Distribution and phylogenetic analysis of family 19 chitinases in Actinobacteria.}, journal = {Applied and environmental microbiology}, volume = {70}, number = {2}, pages = {1135-1144}, pmid = {14766598}, issn = {0099-2240}, mesh = {Actinobacteria/*classification/*enzymology/genetics ; Amino Acid Sequence ; *Chitinases/chemistry/genetics/metabolism ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {In organisms other than higher plants, family 19 chitinase was first discovered in Streptomyces griseus HUT6037, and later, the general occurrence of this enzyme in Streptomyces species was demonstrated. In the present study, the distribution of family 19 chitinases in the class Actinobacteria and the phylogenetic relationship of Actinobacteria family 19 chitinases with family 19 chitinases of other organisms were investigated. Forty-nine strains were chosen to cover almost all the suborders of the class Actinobacteria, and chitinase production was examined. Of the 49 strains, 22 formed cleared zones on agar plates containing colloidal chitin and thus appeared to produce chitinases. These 22 chitinase-positive strains were subjected to Southern hybridization analysis by using a labeled DNA fragment corresponding to the catalytic domain of ChiC, and the presence of genes similar to chiC of S. griseus HUT6037 in at least 13 strains was suggested by the results. PCR amplification and sequencing of the DNA fragments corresponding to the major part of the catalytic domains of the family 19 chitinase genes confirmed the presence of family 19 chitinase genes in these 13 strains. The strains possessing family 19 chitinase genes belong to 6 of the 10 suborders in the order Actinomycetales, which account for the greatest part of the Actinobacteria: Phylogenetic analysis suggested that there is a close evolutionary relationship between family 19 chitinases found in Actinobacteria and plant class IV chitinases. The general occurrence of family 19 chitinase genes in Streptomycineae and the high sequence similarity among the genes found in Actinobacteria suggest that the family 19 chitinase gene was first acquired by an ancestor of the Streptomycineae and spread among the Actinobacteria through horizontal gene transfer.}, }
@article {pmid14766590, year = {2004}, author = {Hill, KK and Ticknor, LO and Okinaka, RT and Asay, M and Blair, H and Bliss, KA and Laker, M and Pardington, PE and Richardson, AP and Tonks, M and Beecher, DJ and Kemp, JD and Kolstø, AB and Wong, AC and Keim, P and Jackson, PJ}, title = {Fluorescent amplified fragment length polymorphism analysis of Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis isolates.}, journal = {Applied and environmental microbiology}, volume = {70}, number = {2}, pages = {1068-1080}, pmid = {14766590}, issn = {0099-2240}, mesh = {Animals ; Bacillus anthracis/*classification/genetics ; Bacillus cereus/*classification/genetics ; Bacillus thuringiensis/*classification/genetics ; DNA Fingerprinting/methods ; DNA, Bacterial/analysis/genetics ; Deoxyribonuclease EcoRI/metabolism ; Deoxyribonucleases, Type II Site-Specific/metabolism ; *Fluorescence ; Humans ; Phylogeny ; *Polymorphism, Restriction Fragment Length ; Serotyping ; }, abstract = {DNA from over 300 Bacillus thuringiensis, Bacillus cereus, and Bacillus anthracis isolates was analyzed by fluorescent amplified fragment length polymorphism (AFLP). B. thuringiensis and B. cereus isolates were from diverse sources and locations, including soil, clinical isolates and food products causing diarrheal and emetic outbreaks, and type strains from the American Type Culture Collection, and over 200 B. thuringiensis isolates representing 36 serovars or subspecies were from the U.S. Department of Agriculture collection. Twenty-four diverse B. anthracis isolates were also included. Phylogenetic analysis of AFLP data revealed extensive diversity within B. thuringiensis and B. cereus compared to the monomorphic nature of B. anthracis. All of the B. anthracis strains were more closely related to each other than to any other Bacillus isolate, while B. cereus and B. thuringiensis strains populated the entire tree. Ten distinct branches were defined, with many branches containing both B. cereus and B. thuringiensis isolates. A single branch contained all the B. anthracis isolates plus an unusual B. thuringiensis isolate that is pathogenic in mice. In contrast, B. thuringiensis subsp. kurstaki (ATCC 33679) and other isolates used to prepare insecticides mapped distal to the B. anthracis isolates. The interspersion of B. cereus and B. thuringiensis isolates within the phylogenetic tree suggests that phenotypic traits used to distinguish between these two species do not reflect the genomic content of the different isolates and that horizontal gene transfer plays an important role in establishing the phenotype of each of these microbes. B. thuringiensis isolates of a particular subspecies tended to cluster together.}, }
@article {pmid14766552, year = {2004}, author = {Bahl, MI and Sørensen, SJ and Hansen, LH and Licht, TR}, title = {Effect of tetracycline on transfer and establishment of the tetracycline-inducible conjugative transposon Tn916 in the guts of gnotobiotic rats.}, journal = {Applied and environmental microbiology}, volume = {70}, number = {2}, pages = {758-764}, pmid = {14766552}, issn = {0099-2240}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; *Conjugation, Genetic ; DNA Transposable Elements/*genetics ; Enterococcus faecalis/genetics ; Female ; Gene Transfer, Horizontal/*drug effects ; *Germ-Free Life ; Intestines/*microbiology ; Rats ; Rats, Sprague-Dawley ; Tetracycline/*pharmacology ; Tetracycline Resistance/genetics ; }, abstract = {We have investigated the transfer of Tn916 among strains of Enterococcus faecalis OG1 colonizing in the intestines of gnotobiotic rats. This animal model allows a low limit of detection and efficient colonization of the chosen bacteria. The animals continuously received tetracycline in drinking water. A tetracycline-sensitive recipient strain was allowed to colonize the animals before the resistant donor was introduced. The numbers of donors, recipients, and transconjugants in fecal samples and intestinal segments were estimated. The bioavailable amounts of tetracycline in fecal samples and intestinal segments were monitored by using bacterial biosensors carrying a transcriptional fusion of a tetracycline-regulated promoter and a lacZ reporter gene. Chromosomal locations of Tn916 in transconjugants isolated either from the same animal or from different animals were compared by Southern blot analysis. Our results indicated that selection for the resistant phenotype was the major factor causing higher numbers of transconjugants in the presence of tetracycline. Tetracycline-sensitive E. faecalis cells colonized the intestine even when the concentrations of tetracycline in feces and intestinal luminal contents exceeded growth-inhibitory concentrations. This suggests the existence of tetracycline-depleted microhabitats in the intestinal environment.}, }
@article {pmid14762207, year = {2004}, author = {Sheveleva, EV and Hallick, RB}, title = {Recent horizontal intron transfer to a chloroplast genome.}, journal = {Nucleic acids research}, volume = {32}, number = {2}, pages = {803-810}, pmid = {14762207}, issn = {1362-4962}, support = {GM35665/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Chloroplasts/*genetics ; Cyanobacteria/*genetics ; Euglena/enzymology/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/genetics ; Genes, Protozoan/genetics ; *Genome ; Introns/*genetics ; Molecular Sequence Data ; Photosystem II Protein Complex/genetics ; Phylogeny ; RNA Splicing/genetics ; RNA-Directed DNA Polymerase/genetics ; Time Factors ; }, abstract = {Evidence is presented for the recent, horizontal transfer of a self-splicing, homing group II intron from a cyanobacteria to the chloroplast genome of Euglena myxocylindracea. The psbA gene of E.myxocylindracea was found to contain a single 2566 nt group II intron with a gene in domain 4 for a 575 amino acid maturase. The predicted secondary structure and tertiary interactions of the group II intron, as well as the derived maturase primary sequence, most closely resemble the homing intron of the cyanobacterium Calothrix and the rnl introns of Porphyra purpurea mitochondria, while being only distantly related to all other Euglena plastid introns and maturases. All main functional domains of the intron-encoded proteins of known homing introns are conserved, including reverse transcriptase domains 1-7, the zinc finger domain and domain X. The close relationship with cyanobacterial introns was confirmed by phylogenetic analysis. Both the full-length psbA intron and a Delta-maturase variant self-splice in vitro in two independent assays. The psbA intron is the first example of a self-splicing chloroplast group II intron from any organism. These results support the conclusion that the psbA intron is the result of a recent horizontal transfer into the E.myxocylindracea chloroplast genome from a cyanobacterial donor and should prompt a reconsideration of horizontal transfer mechanisms to account for the origin of other chloroplast genetic elements.}, }
@article {pmid14757765, year = {2004}, author = {Ali, V and Shigeta, Y and Tokumoto, U and Takahashi, Y and Nozaki, T}, title = {An intestinal parasitic protist, Entamoeba histolytica, possesses a non-redundant nitrogen fixation-like system for iron-sulfur cluster assembly under anaerobic conditions.}, journal = {The Journal of biological chemistry}, volume = {279}, number = {16}, pages = {16863-16874}, doi = {10.1074/jbc.M313314200}, pmid = {14757765}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Anaerobiosis ; Animals ; Bacterial Proteins/genetics ; Entamoeba histolytica/genetics/*metabolism ; Iron/*metabolism ; Molecular Sequence Data ; *Nitrogen Fixation/genetics ; Phylogeny ; Sequence Alignment ; Sulfur/*metabolism ; }, abstract = {We have characterized the iron-sulfur (Fe-S) cluster formation in an anaerobic amitochondrial protozoan parasite, Entamoeba histolytica, in which Fe-S proteins play an important role in energy metabolism and electron transfer. A genomewide search showed that E. histolytica apparently possesses a simplified and non-redundant NIF (nitrogen fixation)-like system for the Fe-S cluster formation, composed of only a catalytic component, NifS, and a scaffold component, NifU. Amino acid alignment and phylogenetic analyses revealed that both amebic NifS and NifU (EhNifS and EhNifU, respectively) showed a close kinship to orthologs from epsilon-proteobacteria, suggesting that both of these genes were likely transferred by lateral gene transfer from an ancestor of epsilon-proteobacteria to E. histolytica. The EhNifS protein expressed in E. coli was present as a homodimer, showing cysteine desulfurase activity with a very basic optimum pH compared with NifS from other organisms. Eh-NifU protein existed as a tetramer and contained one stable [2Fe-2S]2+ cluster per monomer, revealed by spectroscopic and iron analyses. Fractionation of the whole parasite lysate by anion exchange chromatography revealed three major cysteine desulfurase activities, one of which corresponded to the EhNifS protein, verified by immunoblot analysis using the specific EhNifS antibody; the other two peaks corresponded to methionine gamma-lyase and cysteine synthase. Finally, ectopic expression of the EhNifS and EhNifU genes successfully complemented, under anaerobic but not aerobic conditions, the growth defect of an Escherichia coli strain, in which both the isc and suf operons were deleted, suggesting that EhNifS and EhNifU are necessary and sufficient for Fe-S clusters of non-nitrogenase Fe-S proteins to form under anaerobic conditions. This is the first demonstration of the presence and biological significance of the NIF-like system in eukaryotes.}, }
@article {pmid14752164, year = {2004}, author = {Rendulic, S and Jagtap, P and Rosinus, A and Eppinger, M and Baar, C and Lanz, C and Keller, H and Lambert, C and Evans, KJ and Goesmann, A and Meyer, F and Sockett, RE and Schuster, SC}, title = {A predator unmasked: life cycle of Bdellovibrio bacteriovorus from a genomic perspective.}, journal = {Science (New York, N.Y.)}, volume = {303}, number = {5658}, pages = {689-692}, doi = {10.1126/science.1093027}, pmid = {14752164}, issn = {1095-9203}, mesh = {Adenosine Triphosphate/metabolism ; Amino Acids/metabolism ; Bacterial Adhesion/genetics ; Bacterial Proteins/biosynthesis/genetics/metabolism ; Bdellovibrio/cytology/*genetics/*growth &amp; development/physiology ; Biological Transport ; Cell Membrane/metabolism ; Computational Biology ; Cytosol/metabolism ; Fimbriae, Bacterial/genetics/physiology ; Flagella/genetics/physiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; Genomics ; Gram-Negative Bacteria ; Hydrolases/genetics/metabolism ; Membrane Transport Proteins/genetics/metabolism ; Open Reading Frames ; Peptidoglycan/metabolism ; Sequence Analysis, DNA ; }, abstract = {Predatory bacteria remain molecularly enigmatic, despite their presence in many microbial communities. Here we report the complete genome of Bdellovibrio bacteriovorus HD100, a predatory Gram-negative bacterium that invades and consumes other Gram-negative bacteria. Its surprisingly large genome shows no evidence of recent gene transfer from its prey. A plethora of paralogous gene families coding for enzymes, such as hydrolases and transporters, are used throughout the life cycle of B. bacteriovorus for prey entry, prey killing, and the uptake of complex molecules.}, }
@article {pmid14747015, year = {2004}, author = {Waller, RF and McConville, MJ and McFadden, GI}, title = {More plastids in human parasites?.}, journal = {Trends in parasitology}, volume = {20}, number = {2}, pages = {54-57}, doi = {10.1016/j.pt.2003.10.018}, pmid = {14747015}, issn = {1471-4922}, mesh = {Animals ; Evolution, Molecular ; Gene Transfer, Horizontal ; Humans ; Microbodies/physiology ; Photosynthesis ; Phylogeny ; Plastids/*physiology ; Trypanosomatina/classification/*genetics ; }, abstract = {Trypanosomatid parasites are disease agents with an extraordinarily broad host range including humans, livestock and plants. Recent work has revealed that trypanosomatids harbour numerous genes sharing apparent common ancestry with plants and/or bacteria. Although there is no evidence of a plastid (chloroplast-like organelle) in trypanosomatids, the presence of such genes suggests lateral gene transfer from some photosynthetic organism(s) during trypanosomatid evolution. Remarkably, many products of these horizontally acquired genes now function in the glycosome, a highly modified peroxisome unique to trypanosomatids and their near relatives.}, }
@article {pmid14746546, year = {2004}, author = {Bischoff, KM and Edrington, TS and Callaway, TR and Genovese, KJ and Nisbet, DJ}, title = {Characterization of antimicrobial resistant Salmonella Kinshasa from dairy calves in Texas.}, journal = {Letters in applied microbiology}, volume = {38}, number = {2}, pages = {140-145}, doi = {10.1111/j.1472-765x.2003.01476.x}, pmid = {14746546}, issn = {0266-8254}, mesh = {Ampicillin/pharmacology ; Animals ; Anti-Bacterial Agents/pharmacology ; Cattle/*microbiology ; Chloramphenicol/pharmacology ; Conjugation, Genetic ; *Drug Resistance, Bacterial ; Drug Resistance, Multiple, Bacterial ; Feces/*microbiology ; Fluoroquinolones/pharmacology ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Nebramycin/*analogs &amp; derivatives/pharmacology ; Neomycin/pharmacology ; Oxytetracycline/pharmacology ; Public Health ; Risk Factors ; Salmonella/classification/*drug effects/genetics/*isolation &amp; purification ; Serotyping ; Spectinomycin/pharmacology ; Streptomycin/pharmacology ; Sulfamethoxazole/pharmacology ; Tetracycline/pharmacology ; Texas ; }, abstract = {AIM: To determine the prevalence of antimicrobial resistance among Salmonella isolated from a central Texas dairy calf farm that raises animals for dairy-beef production.<br><br>METHODS AND RESULTS: Salmonella isolates collected from 50 faecal samples were characterized for susceptibility to 20 antimicrobial agents. Seventy per cent of the faecal samples (35 of 50) tested positive for Salmonella, and high rates of resistance to the following drugs that are commonly used for treatment of bacterial enteritis in livestock were observed: ampicillin (88%), apramycin (83%), neomycin (86%), spectinomycin (91%) and oxytetracycline (90%). No resistance to the fluoroquinolone antibiotics was observed. The most prevalent Salmonella serotype was Kinshasha (22 of 35 samples), followed by Agona (4 of 35), Newport (3 of 35), Infantis (2 of 35), Montevideo (2 of 35), Lille (1 of 35) and Newington (1 of 35). The Kinshasa, Agona, Newport and Infantis serotypes all displayed resistance to ampicillin, chloramphenicol, streptomycin, sulphamethoxazole and tetracycline, and the penta-resistance phenotype was transferable to an Escherichia coli recipient strain.<br><br>SIGNIFICANCE: Multi-drug resistant Salmonella in dairy calves pose a costly animal health problem and a potential risk to the public health. This study emphasizes the need for alternative, non-antimicrobial intervention strategies for the control of zoonotic pathogens.}, }
@article {pmid14745536, year = {2003}, author = {Ortutay, C and Gáspári, Z and Tóth, G and Jáger, E and Vida, G and Orosz, L and Vellai, T}, title = {Speciation in Chlamydia: genomewide phylogenetic analyses identified a reliable set of acquired genes.}, journal = {Journal of molecular evolution}, volume = {57}, number = {6}, pages = {672-680}, pmid = {14745536}, issn = {0022-2844}, mesh = {Base Composition ; Chlamydia/*genetics ; Evolution, Molecular ; Gene Deletion ; Gene Duplication ; Gene Rearrangement ; *Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; *Genome, Bacterial ; Phylogeny ; Species Specificity ; }, abstract = {Horizontal gene transfer (HGT), a process through which genomes acquire sequences from distantly related organisms, is believed to be a major source of genetic diversity in bacteria. A central question concerning the impact of HGT on bacterial genome evolution is the proportion of horizontally transferred sequences within genomes. This issue, however, remains unresolved because the various methods developed to detect potential HGT events identify different sets of genes. The present-day consensus is that phylogenetic analysis of individual genes is still the most objective and accurate approach for determining the occurrence and directionality of HGT. Here we present a genome-scale phylogenetic analysis of protein-encoding genes from five closely related Chlamydia, identifying a reliable set of sequences that have arisen via HGT since the divergence of the Chlamydia lineage. According to our knowledge, this is the first systematic phylogenetic inference-based attempt to establish a reliable set of acquired genes in a bacterial genome. Although Chlamydia are obligate intracellular parasites of higher eukaryotes, and thus suspected to be isolated from HGT more than the free-living species, our results show that their diversification has involved the introduction of foreign sequences into their genome. Furthermore, we also identified a complete set of genes that have undergone deletion, duplication, or rearrangement during this evolutionary period leading to the radiation of Chlamydia species. Our analysis may provide a deeper insight into how these medically important pathogens emerged and evolved from a common ancestor.}, }
@article {pmid14743976, year = {2003}, author = {Wolska, KI}, title = {Horizontal DNA transfer between bacteria in the environment.}, journal = {Acta microbiologica Polonica}, volume = {52}, number = {3}, pages = {233-243}, pmid = {14743976}, issn = {0137-1320}, mesh = {Archaea/genetics ; Bacteria/*genetics ; Conjugation, Genetic/genetics ; DNA, Archaeal/genetics ; DNA, Bacterial/*genetics ; Gene Transfer, Horizontal/*physiology ; Genome, Archaeal ; Genome, Bacterial ; Transduction, Genetic ; Transformation, Bacterial/genetics ; }, abstract = {In the environment horizontal DNA transfer between various bacterial species and genera takes place by transformation, transduction, but mainly by conjugation. Conjugation is responsible for the spread of genes coding for antibiotic resistance and xenobiotic degradation. Transfer events are reported in animal, rhizosphere and phylloplane ecosystems and in non polluted and polluted water and soil. Genetic exchange between Bacteria and Archaea is also observed. Evaluation of the extent of interspecies gene transfer is crucial in view of the deliberate release of a variety of unmodified and genetically modified microorganisms into the natural environments.}, }
@article {pmid14742222, year = {2004}, author = {Yatsuyanagi, J and Saito, S and Harata, S and Suzuki, N and Ito, Y and Amano, K and Enomoto, K}, title = {Class 1 integron containing metallo-beta-lactamase gene blaVIM-2 in Pseudomonas aeruginosa clinical strains isolated in Japan.}, journal = {Antimicrobial agents and chemotherapy}, volume = {48}, number = {2}, pages = {626-628}, pmid = {14742222}, issn = {0066-4804}, mesh = {Blotting, Southern ; DNA Transposable Elements/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Humans ; Integrons/*genetics ; Japan ; Molecular Sequence Data ; Proteins/genetics ; Pseudomonas Infections/*microbiology ; Pseudomonas aeruginosa/*drug effects/enzymology/*genetics ; beta-Lactamases/*genetics ; }, abstract = {Four bla(VIM-2) gene-harboring Pseudomonas aeruginosa strains were identified. These strains possessed a class 1 integron harboring ORF1, bla(VIM-2), and aacA4 gene cassettes. The transposon-mediated horizontal spread of the bla(VIM-2) gene among these strains was suggested, which increases the threat that the bla(VIM-2) gene will disseminate among diverse genera of bacteria.}, }
@article {pmid14739244, year = {2004}, author = {Lake, JA and Rivera, MC}, title = {Deriving the genomic tree of life in the presence of horizontal gene transfer: conditioned reconstruction.}, journal = {Molecular biology and evolution}, volume = {21}, number = {4}, pages = {681-690}, doi = {10.1093/molbev/msh061}, pmid = {14739244}, issn = {0737-4038}, mesh = {Computational Biology ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome ; Genomics/*methods ; Sequence Alignment/methods ; }, abstract = {The horizontal gene transfer (HGT) being inferred within prokaryotic genomes appears to be sufficiently massive that many scientists think it may have effectively obscured much of the history of life recorded in DNA. Here, we demonstrate that the tree of life can be reconstructed even in the presence of extensive HGT, provided the processes of genome evolution are properly modeled. We show that the dynamic deletions and insertions of genes that occur during genome evolution, including those introduced by HGT, may be modeled using techniques similar to those used to model nucleotide substitutions that occur during sequence evolution. In particular, we show that appropriately designed general Markov models are reasonable tools for reconstructing genome evolution. These studies indicate that, provided genomes contain sufficiently many genes and that the Markov assumptions are met, it is possible to reconstruct the tree of life. We also consider the fusion of genomes, a process not encountered in gene sequence evolution, and derive a method for the identification and reconstruction of genome fusion events. Genomic reconstructions of a well-defined classical four-genome problem, the root of the multicellular animals, show that the method, when used in conjunction with paralinear/logdet distances, performs remarkably well and is relatively unaffected by the recently discovered big genome artifact.}, }
@article {pmid14734565, year = {2004}, author = {Giraud, E and Hannibal, L and Fardoux, J and Jaubert, M and Jourand, P and Dreyfus, B and Sturgis, JN and Verméglio, A}, title = {Two distinct crt gene clusters for two different functional classes of carotenoid in Bradyrhizobium.}, journal = {The Journal of biological chemistry}, volume = {279}, number = {15}, pages = {15076-15083}, doi = {10.1074/jbc.M312113200}, pmid = {14734565}, issn = {0021-9258}, mesh = {Bradyrhizobium/*genetics ; Canthaxanthin/*biosynthesis/chemistry ; Carotenoids/chemistry/*genetics/metabolism ; Cell Membrane/metabolism ; Dose-Response Relationship, Drug ; Light ; Lycopene ; Models, Chemical ; Molecular Sequence Data ; *Multigene Family ; Mutation ; Oxidative Stress ; Paraquat/pharmacology ; Phylogeny ; Pigments, Biological ; Reactive Oxygen Species ; Spectrometry, Fluorescence ; Xanthophylls/*analogs &amp; derivatives/*biosynthesis ; }, abstract = {Aerobic photosynthetic bacteria possess the unusual characteristic of producing different classes of carotenoids. In this study, we demonstrate the presence of two distinct crt gene clusters involved in the synthesis of spirilloxanthin and canthaxanthin in a Bradyrhizobium strain. Each cluster contains the genes crtE, crtB, and crtI leading to the common precursor lycopene. We show that spirilloxanthin is associated with the photosynthetic complexes, while canthaxanthin protects the bacteria from oxidative stress. Only the spirilloxanthin crt genes are regulated by light via the control of a bacteriophytochrome. Despite this difference in regulation, the biosyntheses of both carotenoids are strongly interconnected at the level of the common precursors. Phylogenetic analysis suggests that the canthaxanthin crt gene cluster has been acquired by a lateral gene transfer. This acquisition may constitute a major selective advantage for this class of bacteria, which photosynthesize only under conditions where harmful reactive oxygen species are generated.}, }
@article {pmid14734167, year = {2004}, author = {Michaud, L and Di Cello, F and Brilli, M and Fani, R and Lo Giudice, A and Bruni, V}, title = {Biodiversity of cultivable psychrotrophic marine bacteria isolated from Terra Nova Bay (Ross Sea, Antarctica).}, journal = {FEMS microbiology letters}, volume = {230}, number = {1}, pages = {63-71}, doi = {10.1016/S0378-1097(03)00857-7}, pmid = {14734167}, issn = {0378-1097}, mesh = {Antarctic Regions ; Bacteria/*classification/*genetics/growth &amp; development/isolation &amp; purification ; *Biodiversity ; *Cold Temperature ; Culture Media ; DNA, Bacterial/analysis ; DNA, Ribosomal/analysis ; Deoxyribonucleases, Type II Site-Specific ; Molecular Sequence Data ; Phenotype ; RNA, Ribosomal, 16S/genetics ; Random Amplified Polymorphic DNA Technique ; Restriction Mapping ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {A set of 146 Antarctic marine isolates from the Ross Sea was characterized by a combination of molecular techniques in order to determine the degree of inter- and intraspecific variability. Isolates were analyzed by amplified rDNA restriction analysis (ARDRA) using the tetrameric enzyme AluI, resulting in 52 different groups, corresponding to at least 52 different bacterial species, indicating a high degree of interspecific variability. The phylogenetic position of bacteria belonging to some ARDRA groups was obtained by sequencing of 16S rDNA. Random amplified polymorphic DNA (RAPD) analysis, carried out on the largest ARDRA groups, revealed a high intraspecific genetic variability, too. The analysis of plasmid content revealed the existence of horizontal gene transfer between strains belonging to the same and to different species. A comparison of the whole body of morphological, physiological and biochemical data was finally carried out.}, }
@article {pmid14733025, year = {2003}, author = {Jin, S and Zhang, J and Di, J}, title = {[Ecological studies on genetically engineered microorganism in environment].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {14}, number = {9}, pages = {1578-1580}, pmid = {14733025}, issn = {1001-9332}, mesh = {*Ecology ; *Environmental Microbiology ; Gene Transfer, Horizontal ; *Genetic Engineering ; Safety ; }, abstract = {This paper discussed the main problems which should be considered on the environmental release of genetically engineered microorganism (GEM), including GEM construction, gene transfer, fitness, diffusion, translocation, potential eco-influence and so on. Moreover, aiming at the special ecological characteristic and eco-influence of GEM, this paper brought forward the policy of "respective analysis on different problems", and postulated the corresponding projects of GEM ecological research to apply GEM safely and effectively in nature.}, }
@article {pmid14732271, year = {2004}, author = {Corradi, N and Kuhn, G and Sanders, IR}, title = {Monophyly of beta-tubulin and H+-ATPase gene variants in Glomus intraradices: consequences for molecular evolutionary studies of AM fungal genes.}, journal = {Fungal genetics and biology : FG &amp; B}, volume = {41}, number = {2}, pages = {262-273}, doi = {10.1016/j.fgb.2003.11.001}, pmid = {14732271}, issn = {1087-1845}, mesh = {Base Composition/genetics ; DNA, Fungal/chemistry/isolation &amp; purification ; Evolution, Molecular ; Genes, Fungal/genetics ; *Genetic Variation ; Molecular Sequence Data ; Mycorrhizae/classification/*genetics ; *Phylogeny ; Sequence Analysis, DNA ; Tubulin/*genetics ; Vacuolar Proton-Translocating ATPases/*genetics ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) are an ecologically important group of fungi. Previous studies showed the presence of divergent copies of beta-tubulin and V-type vacuolar H+-ATPase genes in AMF genomes and suggested horizontal gene transfer from host plants or mycoparasites to AMF. We sequenced these genes from DNA isolated from an in vitro cultured isolate of Glomus intraradices that was free of any obvious contaminants. We found two highly variable beta-tubulin sequences and variable H+-ATPase sequences. Despite this high variation, comparison of the sequences with those in gene banks supported a glomeromycotan origin of G. intraradices beta-tubulin and H+-ATPase sequences. Thus, our results are in sharp contrast with the previously reported polyphyletic origin of those genes. We present evidence that some highly divergent sequences of beta-tubulin and H+-ATPase deposited in the databases are likely to be contaminants. We therefore reject the prediction of horizontal transfer to AMF genomes. High differences in GC content between glomeromycotan sequences and sequences grouping in other lineages are shown and we suggest they can be used as an indicator to detect such contaminants. H+-ATPase phylogeny gave unexpected results and failed to resolve fungi as a natural group. beta-Tubulin phylogeny supported Glomeromeromycota as sister group of the Chytridiomycota. Contrasts between our results and trees previously generated using rDNA sequences are discussed.}, }
@article {pmid14731283, year = {2004}, author = {Schubert, S and Dufke, S and Sorsa, J and Heesemann, J}, title = {A novel integrative and conjugative element (ICE) of Escherichia coli: the putative progenitor of the Yersinia high-pathogenicity island.}, journal = {Molecular microbiology}, volume = {51}, number = {3}, pages = {837-848}, doi = {10.1046/j.1365-2958.2003.03870.x}, pmid = {14731283}, issn = {0950-382X}, mesh = {Base Sequence ; Escherichia coli/*genetics/metabolism/*pathogenicity ; Gene Transfer, Horizontal ; *Genomic Islands ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Plasmids/genetics/metabolism ; Yersinia/*genetics/metabolism/*pathogenicity ; }, abstract = {Diversification of bacterial species and pathotypes is largely caused by horizontal transfer of diverse DNA elements such as plasmids, phages and genomic islands (e.g. pathogenicity islands, PAIs). A PAI called high-pathogenicity island (HPI) carrying genes involved in siderophore-mediated iron acquisition (yersiniabactin system) has previously been identified in Yersinia pestis, Y. pseudotuberculosis and Y. enterocolitica IB strains, and has been characterized as an essential virulence factor in these species. Strikingly, an orthologous HPI is a widely distributed virulence determinant among Escherichia coli and other Enterobacteriaceae which cause extraintestinal infections. Here we report on the HPI of E. coli strain ECOR31 which is distinct from all other HPIs described to date because the ECOR31 HPI comprises an additional 35 kb fragment at the right border compared to the HPI of other E. coli and Yersinia species. This part encodes for both a functional mating pair formation system and a DNA-processing region related to plasmid CloDF13 of Enterobacter cloacae. Upon induction of the P4-like integrase, the entire HPI of ECOR31 is precisely excised and circularised. The HPI of ECOR31 presented here resembles integrative and conjugative elements termed ICE. It may represent the progenitor of the HPI found in Y. pestis and E. coli, revealing a missing link in the horizontal transfer of an element that contributes to microbial pathogenicity upon acquisition.}, }
@article {pmid14729325, year = {2004}, author = {Schultz, J}, title = {HTTM, a horizontally transferred transmembrane domain.}, journal = {Trends in biochemical sciences}, volume = {29}, number = {1}, pages = {4-7}, doi = {10.1016/j.tibs.2003.11.002}, pmid = {14729325}, issn = {0968-0004}, mesh = {Amino Acid Sequence ; Animals ; Carbon-Carbon Ligases/*chemistry/*genetics ; Gene Transfer, Horizontal ; Humans ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Tertiary ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {Sequence analysis of vitamin K-dependent gamma-carboxylases (VKGC) has revealed the presence of a novel domain, HTTM (for horizontally transferred transmembrane) in its N terminus. In contrast to most known domains, HTTM contains four transmembrane regions. Its occurrence in eukaryotes, bacteria and archaea is probably caused by horizontal gene transfer rather than by early evolution. The conservation of VKGC catalytic sites also indicates an enzymatic function for the other family members.}, }
@article {pmid14729283, year = {2004}, author = {Noto, T and Endoh, H}, title = {A "chimera" theory on the origin of dicyemid mesozoans: evolution driven by frequent lateral gene transfer from host to parasite.}, journal = {Bio Systems}, volume = {73}, number = {1}, pages = {73-83}, doi = {10.1016/j.biosystems.2003.09.002}, pmid = {14729283}, issn = {0303-2647}, mesh = {Animals ; Chimera/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Host-Parasite Interactions/*genetics ; Invertebrates/genetics ; Nematoda/genetics ; }, abstract = {The phylogenetic status of the enigmatic dicyemid mesozoans is still uncertain. Are they primitive multicellular organisms or degenerate triploblastic animals? Presently, the latter view is accepted. A phylogenetic analysis of 18S rDNA sequences placed dicyemids within the animal clade, and this was supported by the discovery of a Hox-type gene with a lophotrochozoan signature sequence. This molecular information suggests that dicyemid mesozoans evolved from an ancestral animal degenerately. Considering their extreme simplicity, which is probably due to parasitism, they might have come from an early embryo via a radical transformation, i.e. neoteny. Irrespective of this molecular information, dicyemid mesozoans retain many protistan-like or extremely primitive features, such as tubular mitochondrial cristae, endocytic ability from the outer surface, and the absence of collagenous tissue, while they do not share noticeable synapomorphy with animals. In addition, the 5S rRNA phylogeny suggests a somewhat closer kinship with protozoan ciliates than with animals. If we accept this clear contradiction, dicyemids should be regarded as a chimera of animals and protistans. Here, we discuss the traditional theory of extreme degeneration via parasitism, and then propose a new "chimera" theory in which dicyemid mesozoans are exposed to a continual flow of genetic information via eating host tissues from the outer surface by endocytosis. Consequently, many of their intrinsic genes have been replaced by host-derived genes through lateral gene transfer (LGT), implying that LGT is a key driving force in the evolution of dicyemid mesozoans.}, }
@article {pmid14726601, year = {2004}, author = {Charkowski, AO}, title = {Making sense of an alphabet soup: the use of a new bioinformatics tool for identification of novel gene islands. Focus on "identification of genomic islands in the genome of Bacillus cereus by comparative analysis with Bacillus anthracis".}, journal = {Physiological genomics}, volume = {16}, number = {2}, pages = {180-181}, doi = {10.1152/physiolgenomics.00199.2003}, pmid = {14726601}, issn = {1531-2267}, mesh = {Algorithms ; Bacillus anthracis/*genetics ; Bacillus cereus/*genetics ; Computational Biology/*methods ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genomic Islands ; }, }
@article {pmid14718552, year = {2004}, author = {Pomati, F and Neilan, BA}, title = {PCR-based positive hybridization to detect genomic diversity associated with bacterial secondary metabolism.}, journal = {Nucleic acids research}, volume = {32}, number = {1}, pages = {e7}, pmid = {14718552}, issn = {1362-4962}, mesh = {Anabaena/classification/*genetics/*metabolism ; Bacterial Toxins/biosynthesis/genetics/toxicity ; Gene Transfer, Horizontal ; *Genetic Variation ; *Genome, Bacterial ; Genomic Library ; Genomics/*methods ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; Polymerase Chain Reaction/*methods ; Reproducibility of Results ; Saxitoxin/*biosynthesis/genetics/toxicity ; }, abstract = {A PCR-based positive hybridization (PPH) method was developed to explore toxic-specific genes in common between toxigenic strains of Anabaena circinalis, a cyanobacterium able to produce saxitoxin (STX). The PPH technique is based on the same principles of suppression subtractive hybridization (SSH), although with the former no driver DNA is required and two tester genomic DNAs are hybridized at high stringency. The aim was to obtain genes associated with cyanobacterial STX production. The genetic diversity within phylogenetically similar strains of A.circinalis was investigated by comparing the results of the standard SSH protocol to the PPH approach by DNA-microarray analysis. SSH allowed the recovery of DNA libraries that were mainly specific for each of the two STX-producing strains used. Several candidate sequences were found by PPH to be in common between both the STX-producing testers. The PPH technique performed using unsubtracted genomic libraries proved to be a powerful tool to identify DNA sequences possibly transferred laterally between two cyanobacterial strains that may be candidate(s) in STX biosynthesis. The approach presented in this study represents a novel and valid tool to study the genetic basis for secondary metabolite production in microorganisms.}, }
@article {pmid14715794, year = {2004}, author = {Chiu, CH and Su, LH and Hung, CC and Chen, KL and Chu, C}, title = {Prevalence and antimicrobial susceptibility of serogroup D nontyphoidal Salmonella in a university hospital in Taiwan.}, journal = {Journal of clinical microbiology}, volume = {42}, number = {1}, pages = {415-417}, pmid = {14715794}, issn = {0095-1137}, mesh = {Drug Resistance, Bacterial ; Hospitals, University ; Microbial Sensitivity Tests ; Plasmids ; Salmonella/*classification/drug effects/isolation &amp; purification ; Serotyping ; Taiwan ; }, abstract = {The incidence of serogroup D Salmonella has been increasing in Taiwan. Most of these isolates belonged to Salmonella enterica serovar Enteritidis and showed a relatively higher rate of resistance to sulfamethoxazole-trimethoprim than to other antimicrobial agents. The results of molecular experiments indicated that genes responsible for the resistance were located on plasmids. The resistance may occur via horizontal gene transfer. Furthermore, the first identification of ciprofloxacin and ceftriaxone resistance in serogroup D Salmonella in our hospital is also than they did to other antimicrobial agents cause for concern.}, }
@article {pmid14711809, year = {2004}, author = {Lin, TL and Shun, CT and Chang, KC and Wang, JT}, title = {Isolation and characterization of a HpyC1I restriction-modification system in Helicobacter pylori.}, journal = {The Journal of biological chemistry}, volume = {279}, number = {12}, pages = {11156-11162}, doi = {10.1074/jbc.M311639200}, pmid = {14711809}, issn = {0021-9258}, mesh = {Base Sequence ; Cell Line, Tumor ; DNA Primers ; DNA Restriction Enzymes/*isolation &amp; purification/metabolism/ultrastructure ; Genetic Complementation Test ; Helicobacter pylori/*enzymology/genetics ; Humans ; Microscopy, Electron ; Molecular Sequence Data ; }, abstract = {Using transposon shuttle mutagenesis, we identified six Helicobacter pylori mutants from the NTUH-C1 strain that exhibited decreased adherence and cell elongation. Inverse polymerase chain reaction and DNA sequencing revealed that the same locus was interrupted in these six mutants. Nucleotide and amino acid sequences showed no homologies with H. pylori 26695 and J99 strains. This novel open reading frame contained 1617 base pairs. The amino acid sequence shared 24% identity with a putative nicking enzyme in Bacillus halodurans and 23 and 20% identity with type IIS restriction endonucleases PleI and MlyI, respectively. The purified protein, HpyC1I, showed endonuclease activity with the recognition and cleavage site 5'-CCATC(4/5)-3'. Two open reading frames were located upstream of the gene encoding HpyC1I. Together, HpyC1I and these two putative methyltransferases (M1.HpyC1I and M2.HpyC1I) function as a restriction-modification (R-M) system. The HpyC1I R-M genes were found in 9 of the 15 H. pylori strains tested. When compared with the full genome, significantly lower G + C content of HpyC1I R-M genes implied that these genes might have been acquired by horizontal gene transfer. Plasmid DNA transformation efficiencies and chromosomal DNA digestion assays demonstrated protection from HpyC1I digestion by the R-M system. In conclusion, we have identified a novel R-M system present in approximately 60% of H. pylori strains. Disruption of this R-M system results in cell elongation and susceptibility to HpyC1I digestion.}, }
@article {pmid14711619, year = {2004}, author = {Chen, S and Zhao, S and White, DG and Schroeder, CM and Lu, R and Yang, H and McDermott, PF and Ayers, S and Meng, J}, title = {Characterization of multiple-antimicrobial-resistant salmonella serovars isolated from retail meats.}, journal = {Applied and environmental microbiology}, volume = {70}, number = {1}, pages = {1-7}, pmid = {14711619}, issn = {0099-2240}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; China ; Conjugation, Genetic ; *Drug Resistance, Multiple, Bacterial/genetics ; Gene Transfer, Horizontal ; Integrons ; Meat/*microbiology ; Microbial Sensitivity Tests ; Salmonella/*classification/*drug effects/genetics/isolation &amp; purification ; Salmonella Infections, Animal/microbiology ; Serotyping ; United States ; }, abstract = {A total of 133 Salmonella isolates recovered from retail meats purchased in the United States and the People's Republic of China were assayed for antimicrobial susceptibility, the presence of integrons and antimicrobial resistance genes, and horizontal transfer of characterized antimicrobial resistance determinants via conjugation. Seventy-three (82%) of these Salmonella isolates were resistant to at least one antimicrobial agent. Resistance to the following antibiotics was common among the United States isolates: tetracycline (68% of the isolates were resistant), streptomycin (61%), sulfamethoxazole (42%), and ampicillin (29%). Eight Salmonella isolates (6%) were resistant to ceftriaxone. Fourteen isolates (11%) from the People's Republic of China were resistant to nalidixic acid and displayed decreased susceptibility to ciprofloxacin. A total of 19 different antimicrobial resistance genes were identified in 30 multidrug-resistant Salmonella isolates. The bla(CMY-2) gene, encoding a class A AmpC beta-lactamase, was detected in all 10 Salmonella isolates resistant to extended-spectrum beta-lactams. Resistance to ampicillin was most often associated with a TEM-1 family beta-lactamase gene. Six aminoglycoside resistance genes, aadA1, aadA2, aacC2, Kn, aph(3)-IIa, and aac(3)-IVa, were commonly present in the Salmonella isolates. Sixteen (54%) of 30 Salmonella isolates tested had integrons ranging in size from 0.75 to 2.7 kb. Conjugation studies demonstrated that there was plasmid-mediated transfer of genes encoding CMY-2 and TEM-1-like beta-lactamases. These data indicate that Salmonella isolates recovered from retail raw meats are commonly resistant to multiple antimicrobials, including those used for treating salmonellosis, such as ceftriaxone. Genes conferring antimicrobial resistance in Salmonella are often carried on integrons and plasmids and could be transmitted through conjugation. These mobile DNA elements have likely played an important role in transmission and dissemination of antimicrobial resistance determinants among Salmonella strains.}, }
@article {pmid14708601, year = {2003}, author = {Woodley, DT and Krueger, GG and Jorgensen, CM and Fairley, JA and Atha, T and Huang, Y and Chan, L and Keene, DR and Chen, M}, title = {Normal and gene-corrected dystrophic epidermolysis bullosa fibroblasts alone can produce type VII collagen at the basement membrane zone.}, journal = {The Journal of investigative dermatology}, volume = {121}, number = {5}, pages = {1021-1028}, doi = {10.1046/j.1523-1747.2003.12571.x}, pmid = {14708601}, issn = {0022-202X}, support = {P01 HD 28528/HD/NICHD NIH HHS/United States ; R01 AR33625/AR/NIAMS NIH HHS/United States ; R01 AR47981/AR/NIAMS NIH HHS/United States ; }, mesh = {Animals ; Basement Membrane/metabolism ; Cell Line ; Collagen Type VII/*biosynthesis/*genetics ; Epidermolysis Bullosa Dystrophica/*genetics/metabolism/therapy ; Fibroblasts/metabolism ; *Gene Transfer, Horizontal ; Genetic Therapy ; Humans ; Mice ; Skin/cytology/*metabolism ; }, abstract = {Type VII collagen is synthesized and secreted by both human keratinocytes and fibroblasts. Although both cell types can secrete type VII collagen, it is thought that keratinocytes account for type VII collagen at the dermal-epidermal junction (DEJ). In this study, we examined if type VII collagen secreted solely by dermal fibroblasts could be transported to the DEJ. We established organotypic, skin-equivalent cultures composed of keratinocytes from patients with recessive dystrophic epidermolysis bullosa (RDEB) and normal dermal fibroblasts. Immuno-labeling of skin equivalent sections with the anti-type VII collagen antibody revealed tight linear staining at the DEJ. RDEB fibroblasts, were gene-corrected to make type VII collagen and used to regenerate human skin on immune-deficient mice. The human skin generated by gene-corrected RDEB fibroblasts or normal human fibroblasts combined with RDEB keratinocytes restored type VII collagen expression at the DEJ in vivo. Further, intradermal injection of normal human or gene-corrected RDEB fibroblasts into mouse skin resulted in the stable expression of human type VII collagen at the mouse DEJ. These data demonstrate that human dermal fibroblasts alone are capable of producing type VII collagen at the DEJ, and it is possible to restore type VII collagen gene expression in RDEB skin in vivo by direct intradermal injection of fibroblasts.}, }
@article {pmid14708580, year = {2003}, author = {Blanc-Potard, AB and Lafay, B}, title = {MgtC as a horizontally-acquired virulence factor of intracellular bacterial pathogens: evidence from molecular phylogeny and comparative genomics.}, journal = {Journal of molecular evolution}, volume = {57}, number = {4}, pages = {479-486}, doi = {10.1007/s00239-003-2496-4}, pmid = {14708580}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Bacterial Proteins/*genetics ; Cation Transport Proteins/*genetics ; Gene Order ; *Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Genome, Bacterial ; Genomics ; Molecular Sequence Data ; Mycobacterium tuberculosis/*genetics/*pathogenicity ; *Phylogeny ; Salmonella typhimurium/*genetics/*pathogenicity ; Sequence Alignment ; Sequence Homology, Amino Acid ; Virulence/genetics ; }, abstract = {MgtC is a virulence factor required for intramacrophage survival and growth in low Mg2+ medium in two pathogens that are not phylogenetically related, Salmonella typhimurium and Mycobacterium tuberculosis. In S. typhimurium, mgtC is carried by the SPI-3 pathogenicity island and hybridization studies have suggested that the distribution of mgtC among enterobacteria is limited. In the present study, we searched for the presence of mgtC-like sequences in eubacterial genomes. Analyses of MgtC-like proteins phylogeny and mgtC-like chromosomal context support the hypothesis that mgtC has been acquired by horizontal gene transfer repeatedly throughout bacterial evolution. In addition, the phylogenetic analysis revealed the existence of a subgroup of proteins, that includes the S. typhimurium and M. tuberculosis MgtC proteins, as well as MgtC-related proteins from other pathogens that are able to survive in macrophages, B. melitensis and Y. pestis. We propose that MgtC has a similar function in all these distantly related pathogens, most likely providing the ability to grow in a low Mg2+ environment.}, }
@article {pmid14708570, year = {2003}, author = {Richer, E and Courville, P and Bergevin, I and Cellier, MF}, title = {Horizontal gene transfer of "prototype" Nramp in bacteria.}, journal = {Journal of molecular evolution}, volume = {57}, number = {4}, pages = {363-376}, pmid = {14708570}, issn = {0022-2844}, mesh = {Bacteria/*genetics ; *Bacterial Proteins ; Biological Transport ; Carrier Proteins/classification/genetics/metabolism ; Cation Transport Proteins/*genetics ; DNA Transposable Elements/genetics ; Escherichia coli/genetics ; *Escherichia coli Proteins ; Eukaryotic Cells/metabolism ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/*genetics ; Genetic Linkage/genetics ; Metals/metabolism ; Open Reading Frames/genetics ; Phylogeny ; Streptococcaceae/genetics ; Wigglesworthia/genetics ; }, abstract = {Eukaryotic Nramp genes encode divalent metal ion permeases important for nutrition and resistance to microbial infection. Bacterial homologs encode proton-dependent transporters of manganese (MntH), and other divalent metal ions. Bacterial MntH were classified in three homology groups (A, B, C) and MntH C further subdivided in Calpha, Cbeta, Cgamma. The proteins from C. tepidum (MntH B) and E. faecalis (MntH Cbeta1, 2), divergent in sequence and hydropathy profile, conferred increased metal sensitivity when expressed in E. coli, suggesting conservation of divalent metal transport function in MntH B and C. Several genomic evidence suggest horizontal gene transfer (HGT) of mntH C genes: (i) The enterobacteria Wigglesworthia mntH Cbeta gene is linked to an Asn t-RNA, and its sequence most conserved with Gram positive bacteria homologs; (ii) all the Cbeta genes identified in oral streptococcaceae are associated with different potentially mobile DNA elements; (iii) Lactococcus lactis and Burkholderia mallei genomes contain an mntH gene prematurely terminated and a novel full-length mntH C gene; (iv) remarkable sequence relatedness between the unicellular alga C. reinhardtii "prototype" Nramp and some MntH Calpha (e.g., Nostoc spp., Listeria spp.) suggests HGT between Eukarya and Bacteria. Other "prototype" Nramp genes (intronless, encoding proteins strongly conserved with MntH A and B proteins) identified in invertebrates represent a possible source for transfer of Nramp genes toward opportunistic bacteria. This study demonstrates complex evolution of MntH in Bacteria. It is proposed that "prototype" Nramp are ancestors of bacterial MntH C proteins, which could facilitate bacterial infection.}, }
@article {pmid14706141, year = {2003}, author = {Bai, X and Fu, JX and Xi, XD and Ruan, CG}, title = {[Establishment of urokinase receptor gene antisense RNA transfer system and its application in leukemia research].}, journal = {Zhongguo shi yan xue ye xue za zhi}, volume = {11}, number = {6}, pages = {591-594}, pmid = {14706141}, issn = {1009-2137}, mesh = {Flow Cytometry ; Gene Transfer, Horizontal ; Humans ; Leukemia/pathology/*therapy ; Matrix Metalloproteinase 9/metabolism ; RNA, Antisense/*genetics/therapeutic use ; Receptors, Cell Surface/analysis/*antagonists &amp; inhibitors/*genetics ; Receptors, Urokinase Plasminogen Activator ; Retroviridae/genetics ; U937 Cells ; }, abstract = {Overexpression of urokinase-type plasminogen activator receptor (uPAR) on tumor cell surface is essential for invasion and metastasis in a variety of tumor cells. To establish a retroviral-mediated antisense RNA transfer system of uPAR gene for exploring its function on down-regulation of uPAR expression in leukemia cells, the retroviral vector LaCD87SN was constructed by inserting uPAR gene into LXSN vector in an antisense orientation. An uPAR gene antisense RNA transfer system was established by liposome-mediated transfection in combination with cross infection with retrovirus. Human leukemia cells U937 were transduced with aCD87 amphotropic retrovirus, expressing uPAR antisense RNA, and the U937/aCD87 cells was obtained by G418 selection. The integration and expression of antisense uPAR gene were analyzed by polymerase chain reaction (PCR) assay. The cell surface expression of CD87 and the activities of matrix metalloproteinase (MMP) were assayed by flow cytometry (FCM) and gelatin zymography, respectively. The results showed that the amphotropic retroviral producers Am12/aCD87, which expressed antisense RNA of uPAR gene with a titer of 6.3 x 10(5) cfu/ml in supernatants, were obtained by means of transfection and superinfection. U937/aCD87 cells were established by continuative G418 selection after retrovirus infection. In U937/aCD87 cells, the integrated provirus and the overexpression of antisense uPAR gene was confirmed. Compared with U937/NeoR cells, FCM analysis revealed that CD87 expression on U937/aCD87 cell surface was not downregulated significantly. However, MMP-9 secretion was significantly suppressed in U937/aCD87 cells. In conclusion, although the retroviral-mediated antisense RNA transfer could not efficiently suppress uPAR expression on leukemic cell surface, it may interfere the uPAR-MMP interactions.}, }
@article {pmid14704857, year = {2004}, author = {Da Lage, JL and Feller, G and Janecek, S}, title = {Horizontal gene transfer from Eukarya to bacteria and domain shuffling: the alpha-amylase model.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {61}, number = {1}, pages = {97-109}, doi = {10.1007/s00018-003-3334-y}, pmid = {14704857}, issn = {1420-682X}, mesh = {Amino Acid Sequence ; Bacteria/*genetics ; Chloroflexus/enzymology/*genetics ; Eukaryotic Cells/enzymology ; Fungi/classification/genetics ; Gammaproteobacteria/enzymology/*genetics ; *Gene Transfer Techniques ; Genome, Bacterial ; Gram-Positive Bacteria/enzymology/*genetics ; Molecular Sequence Data ; Phylogeny ; Plants/*genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; Transfection ; Yeasts/classification/genetics ; alpha-Amylases/chemistry/*genetics ; }, abstract = {Alpha-amylases are present in all kingdoms of the living world. Despite strong conservation of the tertiary structure, only a few amino acids are conserved in interkingdom comparisons. Animal alpha-amylases are characterized by several typical motifs and biochemical properties. A few cases of such alpha-amylases have been previously reported in some eubacterial species. We screened the bacterial genomes available in the sequence databases for new occurrences of animal-like alpha-amylases. Three novel cases were found, which belong to unrelated bacterial phyla: Chloroflexus aurantiacus, Microbulbifer degradans, and Thermobifida fusca. All the animal-like alpha-amylases in Bacteria probably result from repeated horizontal gene transfer from animals. The M. degradans genome also contains bacterial-type and plant-type alpha-amylases in addition to the animal-type one. Thus, this species exhibits alpha-amylases of animal, plant, and bacterial origins. Moreover, the similarities in the extra C-terminal domains (different from both the alpha-amylase domain C and the starch-binding domain), when present, also suggest interkingdom as well as intragenomic shuffling.}, }
@article {pmid14702321, year = {2004}, author = {Klockgether, J and Reva, O and Larbig, K and Tümmler, B}, title = {Sequence analysis of the mobile genome island pKLC102 of Pseudomonas aeruginosa C.}, journal = {Journal of bacteriology}, volume = {186}, number = {2}, pages = {518-534}, pmid = {14702321}, issn = {0021-9193}, mesh = {Gene Transfer, Horizontal ; *Genome, Bacterial ; Operon ; Phenotype ; *Plasmids ; Pseudomonas aeruginosa/*genetics ; RNA, Transfer, Lys/genetics ; Recombination, Genetic ; }, abstract = {The Pseudomonas aeruginosa plasmid pKLC102 coexists as a plasmid and a genome island in clone C strains. Whereas the related plasmid pKLK106 reversibly recombines with P. aeruginosa clone K chromosomes at one of the two tRNA(Lys) genes, pKLC102 is incorporated into the tRNA(Lys) gene only close to the pilA locus. Targeting of the other tRNA(Lys) copy in the chromosome is blocked by a 23,395-bp mosaic of truncated PAO open reading frames, transposons, and pKLC102 homologs. Annotation and phylogenetic analysis of the large 103,532-bp pKLC102 sequence revealed that pKLC102 is a hybrid of plasmid and phage origin. The plasmid lineage conferred oriV and genes for replication, partitioning, and conjugation, including a pil cluster encoding type IV thin sex pili and an 8,524-bp chvB glucan synthetase gene that is known to be a major determinant for host tropism and virulence. The phage lineage conferred integrase, att, and a syntenic set of conserved hypothetical genes also observed in the tRNA(Gly)-associated genome islands of P. aeruginosa clone C chromosomes. In subgroup C isolates from patients with cystic fibrosis, pKLC102 was irreversibly fixed into the chromosome by the insertion of the large 23,061-bp class I transposon TNCP23, which is a composite of plasmid, integron, and IS6100 elements. Intramolecular transposition of a copy of IS6100 led to chromosomal inversions and disruption of plasmid synteny. The case of pKLC102 in P. aeruginosa clone C documents the intraclonal evolution of a genome island from a mobile ancestor via a reversibly integrated state to irreversible incorporation and dissipation in the chromosome.}, }
@article {pmid14702297, year = {2004}, author = {Ly, A and Henderson, J and Lu, A and Culham, DE and Wood, JM}, title = {Osmoregulatory systems of Escherichia coli: identification of betaine-carnitine-choline transporter family member BetU and distributions of betU and trkG among pathogenic and nonpathogenic isolates.}, journal = {Journal of bacteriology}, volume = {186}, number = {2}, pages = {296-306}, pmid = {14702297}, issn = {0021-9193}, mesh = {ATP-Binding Cassette Transporters/physiology ; Betaine/*metabolism ; Biological Transport ; Carnitine/*metabolism ; Choline/*metabolism ; Chromosome Mapping ; Escherichia coli/genetics/*metabolism/pathogenicity ; Escherichia coli Proteins/*analysis ; Membrane Proteins/*analysis ; Potassium/metabolism ; Pyelonephritis/etiology ; Water-Electrolyte Balance ; }, abstract = {Multiple transporters mediate osmoregulatory solute accumulation in Escherichia coli K-12. The larger genomes of naturally occurring strains such as pyelonephritis isolates CFT073 and HU734 may encode additional osmoregulatory systems. CFT073 is more osmotolerant than HU734 in the absence of organic osmoprotectants, yet both strains grew in high osmolality medium at low K(+) (micromolar concentrations) and retained locus trkH, which encodes an osmoregulatory K(+) transporter. Both lacked the trkH homologue trkG. Transporters ProP and ProU account for all glycine-betaine uptake activity in E. coli K-12 and CFT073, but not in HU734, yet elimination of ProP and ProU impairs the growth of HU734, but not CFT073, in high osmolality human urine. No known osmoprotectant stimulated the growth of CFT073 in high osmolality minimal medium, but putative transporters YhjE, YiaMNO, and YehWXYZ may mediate uptake of additional osmoprotectants. Gene betU was isolated from HU734 by functional complementation and shown to encode a betaine uptake system that belongs to the betaine-choline-carnitine transporter family. The incidence of trkG and betU within the ECOR collection, representatives of the E. coli pathotypes (PATH), and additional strains associated with urinary tract infection (UTI) were determined. Gene trkG was present in 66% of the ECOR collection but only in 16% of the PATH and UTI collections. Gene betU was more frequently detected in ECOR groups B2 and D (50% of isolates) than in groups A, B1, and E (20%), but it was similar in overall incidence in the ECOR collection and in the combined UTI and PATH collections (32 and 34%, respectively). Genes trkG and betU may have been acquired by lateral gene transfer, since trkG is part of the rac prophage and betU is flanked by putative insertion sequences. Thus, BetU and TrkG contribute, with other systems, to the osmoregulatory capacity of the species E. coli, but they are not characteristic of a particular phylogenetic group or pathotype.}, }
@article {pmid14701903, year = {2004}, author = {Rantala, A and Fewer, DP and Hisbergues, M and Rouhiainen, L and Vaitomaa, J and Börner, T and Sivonen, K}, title = {Phylogenetic evidence for the early evolution of microcystin synthesis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, number = {2}, pages = {568-573}, pmid = {14701903}, issn = {0027-8424}, mesh = {DNA-Directed RNA Polymerases/genetics ; Microcystins ; Molecular Sequence Data ; Peptides, Cyclic/*biosynthesis ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Cyanobacteria are a prolific source of secondary metabolites, including compounds with toxic and enzyme-inhibiting activities. Microcystins and nodularins are the end products of a secondary metabolic pathway comprised of mixed polyketide synthases and nonribosomal peptide synthetases. Both peptides are potent natural toxins produced by distantly related genera of cyanobacteria. Horizontal gene transfer is thought to play a role in the sporadic distribution of microcystin producers among cyanobacteria. Our phylogenetic analyses indicate a coevolution of housekeeping genes and microcystin synthetase genes for the entire evolutionary history of the toxin. Hence they do not corroborate horizontal transfer of genes for microcystin biosynthesis between the genera. The sporadic distribution of microcystin synthetase genes in modern cyanobacteria suggests that the ability to produce the toxin has been lost repeatedly in the more derived lineages of cyanobacteria. The data we present here strongly suggest that the genes encoding nodularin synthetase are recently derived from those encoding microcystin synthetase.}, }
@article {pmid14700543, year = {2004}, author = {Tønjum, T and Håvarstein, LS and Koomey, M and Seeberg, E}, title = {Transformation and DNA repair: linkage by DNA recombination.}, journal = {Trends in microbiology}, volume = {12}, number = {1}, pages = {1-4}, doi = {10.1016/j.tim.2003.11.008}, pmid = {14700543}, issn = {0966-842X}, mesh = {DNA Damage ; *DNA Repair ; DNA, Bacterial/genetics ; *Genome, Bacterial ; *Recombination, Genetic ; *Transformation, Bacterial ; }, abstract = {The stability of microbial genomes is constantly challenged by horizontal gene transfer, recombination and DNA damage. Mechanisms for rapid genome variation, adaptation and maintenance are a necessity to ensure microbial fitness and survival in changing environments. Indeed, genome sequences reveal that most, if not all, bacterial species have numerous gene functions for DNA repair and recombination. These important topics were addressed at the Second Genome Maintenance Meeting (GMM2).}, }
@article {pmid14694078, year = {2004}, author = {Raymond, J and Siefert, JL and Staples, CR and Blankenship, RE}, title = {The natural history of nitrogen fixation.}, journal = {Molecular biology and evolution}, volume = {21}, number = {3}, pages = {541-554}, doi = {10.1093/molbev/msh047}, pmid = {14694078}, issn = {0737-4038}, mesh = {Amino Acid Motifs ; Bacteria/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Models, Genetic ; Multigene Family ; Nitrogen Fixation/*genetics ; Nitrogenase/genetics ; Phylogeny ; }, abstract = {In recent years, our understanding of biological nitrogen fixation has been bolstered by a diverse array of scientific techniques. Still, the origin and extant distribution of nitrogen fixation has been perplexing from a phylogenetic perspective, largely because of factors that confound molecular phylogeny such as sequence divergence, paralogy, and horizontal gene transfer. Here, we make use of 110 publicly available complete genome sequences to understand how the core components of nitrogenase, including NifH, NifD, NifK, NifE, and NifN proteins, have evolved. These genes are universal in nitrogen fixing organisms-typically found within highly conserved operons-and, overall, have remarkably congruent phylogenetic histories. Additional clues to the early origins of this system are available from two distinct clades of nitrogenase paralogs: a group composed of genes essential to photosynthetic pigment biosynthesis and a group of uncharacterized genes present in methanogens and in some photosynthetic bacteria. We explore the complex genetic history of the nitrogenase family, which is replete with gene duplication, recruitment, fusion, and horizontal gene transfer and discuss these events in light of the hypothesized presence of nitrogenase in the last common ancestor of modern organisms, as well as the additional possibility that nitrogen fixation might have evolved later, perhaps in methanogenic archaea, and was subsequently transferred into the bacterial domain.}, }
@article {pmid14693553, year = {2004}, author = {Hanssen, AM and Kjeldsen, G and Sollid, JU}, title = {Local variants of Staphylococcal cassette chromosome mec in sporadic methicillin-resistant Staphylococcus aureus and methicillin-resistant coagulase-negative Staphylococci: evidence of horizontal gene transfer?.}, journal = {Antimicrobial agents and chemotherapy}, volume = {48}, number = {1}, pages = {285-296}, pmid = {14693553}, issn = {0066-4804}, mesh = {Blotting, Southern ; Coagulase/metabolism ; DNA, Bacterial/chemistry/genetics ; Electrophoresis, Polyacrylamide Gel ; Gene Transfer, Horizontal/*genetics ; Genotype ; Humans ; Methicillin Resistance/*genetics ; Microbial Sensitivity Tests ; Phenotype ; Phylogeny ; RNA, Bacterial/chemistry/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Staphylococcal Infections/microbiology ; Staphylococcus aureus/*drug effects/enzymology/*genetics ; }, abstract = {The mecA gene in Staphylococcus aureus is located on the genetic element staphylococcal cassette chromosome (SCC). Different SCCmecs have been classified according to their putative recombinase genes (ccrA and ccrB) and overall genetic composition. Clinical isolates of coagulase-negative staphylococci (CoNS; n = 39) and S. aureus (n = 20) from Norway, India, Italy, Finland, the United States, and the United Kingdom were analyzed by pulsed-field gel electrophoresis, which showed that most isolates were genetically unrelated. Cluster analyses of 16S rRNA gene and pta sequences confirmed the traditional biochemical species identification. The mecI, mecR1, mecA, and ccrAB genes were detected by PCRs, identifying 19 out of 20 S. aureus and 17 out of 39 CoNS isolates as carriers of one of the three published ccrAB pairs. New variants of SCCmec were identified, as well as CoNS isolates containing ccrAB genes without the mec locus. ccrAB and mec PCRs were verified by hybridization. Sequence alignments of ccrAB genes showed a high level of diversity between the ccrAB alleles from different isolates, i.e., 94 to 100% and 95 to 100% homology for ccrAB1 and ccrAB2, respectively. All of the ccrAB3 genes identified were identical. Genetically unique and sporadic methicillin-resistant S. aureus (MRSA) contained local variants of ccrAB gene pairs identical to those found in MR-CoNS but different from those in MRSA from other regions. Allelic variants of ccrAB in isolates from the same geographic region showed sequence conservation independent of species. The species-independent sequence conservation found suggests that there is a closer genetic relationship between ccrAB2 in Norwegian staphylococci than between ccrAB2 sequences in international MRSA and Norwegian MRSA. This might indicate that different staphylococcal species acquire these genes locally by horizontal gene transfer.}, }
@article {pmid14693379, year = {2004}, author = {Sandoval, P and León, G and Gómez, I and Carmona, R and Figueroa, P and Holuigue, L and Araya, A and Jordana, X}, title = {Transfer of RPS14 and RPL5 from the mitochondrion to the nucleus in grasses.}, journal = {Gene}, volume = {324}, number = {}, pages = {139-147}, doi = {10.1016/j.gene.2003.09.027}, pmid = {14693379}, issn = {0378-1119}, mesh = {Amino Acid Sequence ; Cell Nucleus/*genetics ; DNA, Mitochondrial/*genetics ; DNA, Plant/chemistry/genetics ; *Gene Transfer, Horizontal ; Models, Genetic ; Molecular Sequence Data ; Plant Proteins/genetics ; Poaceae/*genetics ; Pseudogenes/genetics ; RNA Editing ; Ribosomal Proteins/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Transcription, Genetic ; Triticum/genetics ; Zea mays/genetics ; }, abstract = {Gene transfer from the mitochondrion to the nucleus, a process of outstanding importance to the evolution of the eukaryotic cell, is an on-going phenomenon in higher plants. After transfer, the mitochondrial gene has to be adapted to the nuclear context by acquiring a new promoter and targeting information to direct the protein back to the organelle. To better understand the strategies developed by higher plants to transfer organellar genes during evolution, we investigated the fate of the mitochondrial RPL5-RPS14 locus in grasses. While maize mitochondrial genome does not contain RPS14 and RPL5 genes, wheat mitochondrial DNA contains an intact RPL5 gene and a nonfunctional RPS14 pseudogene. RPL5 and PsiRPS14 are co-transcribed and their transcripts are edited. In wheat, the functional RPS14 gene is located in the nucleus, within the intron of the respiratory complex II iron-sulfur subunit gene (SDH2). Its organization and expression mechanisms are similar to those previously described in maize and rice, allowing us to conclude that RPS14 transfer and nuclear activation occurred before divergence of these grasses. Unexpectedly, we found evidence for a more recent RPL5 transfer to the nucleus in wheat. This nuclear wheat RPL5 acquired its targeting information by duplication of an existing targeting presequence for another mitochondrial protein, ribosomal protein L4. Thus, mitochondrial and nuclear functional RPL5 genes appear to be maintained in wheat, supporting the hypothesis that in an intermediate stage of the transfer process, both nuclear and mitochondrial functional genes coexist. Finally, we show that RPL5 has been independently transferred to the nucleus in the maize lineage and has acquired regulatory elements for its expression and a mitochondrial targeting peptide from an unknown source.}, }
@article {pmid14688795, year = {2004}, author = {Beaber, JW and Hochhut, B and Waldor, MK}, title = {SOS response promotes horizontal dissemination of antibiotic resistance genes.}, journal = {Nature}, volume = {427}, number = {6969}, pages = {72-74}, doi = {10.1038/nature02241}, pmid = {14688795}, issn = {1476-4687}, mesh = {Bacterial Proteins/genetics/metabolism ; Chloramphenicol Resistance/drug effects/*genetics ; Ciprofloxacin/pharmacology ; Conjugation, Genetic/drug effects/genetics ; DNA Damage/drug effects ; DNA Transposable Elements/*genetics ; Gene Expression Regulation, Bacterial/drug effects ; Gene Transfer, Horizontal/drug effects/*genetics ; Genes, Bacterial/genetics ; Mitomycin/pharmacology ; Models, Genetic ; Rec A Recombinases/genetics/metabolism ; Repressor Proteins/genetics/metabolism ; SOS Response, Genetics/drug effects/*genetics ; Vibrio cholerae/drug effects/*genetics ; }, abstract = {Mobile genetic elements have a crucial role in spreading antibiotic resistance genes among bacterial populations. Environmental and genetic factors that regulate conjugative transfer of antibiotic resistance genes in bacterial populations are largely unknown. Integrating conjugative elements (ICEs) are a diverse group of mobile elements that are transferred by means of cell-cell contact and integrate into the chromosome of the new host. SXT is a approximately 100-kilobase ICE derived from Vibrio cholerae that encodes genes that confer resistance to chloramphenicol, sulphamethoxazole, trimethoprim and streptomycin. SXT-related elements were not detected in V. cholerae before 1993 but are now present in almost all clinical V. cholerae isolates from Asia. ICEs related to SXT are also present in several other bacterial species and encode a variety of antibiotic and heavy metal resistance genes. Here we show that SetR, an SXT encoded repressor, represses the expression of activators of SXT transfer. The 'SOS response' to DNA damage alleviates this repression, increasing the expression of genes necessary for SXT transfer and hence the frequency of transfer. SOS is induced by a variety of environmental factors and antibiotics, for example ciprofloxacin, and we show that ciprofloxacin induces SXT transfer as well. Thus, we present a mechanism by which therapeutic agents can promote the spread of antibiotic resistance genes.}, }
@article {pmid14686938, year = {2004}, author = {López-García, P and Brochier, C and Moreira, D and Rodríguez-Valera, F}, title = {Comparative analysis of a genome fragment of an uncultivated mesopelagic crenarchaeote reveals multiple horizontal gene transfers.}, journal = {Environmental microbiology}, volume = {6}, number = {1}, pages = {19-34}, doi = {10.1046/j.1462-2920.2003.00533.x}, pmid = {14686938}, issn = {1462-2912}, mesh = {Chromosomes, Archaeal/genetics ; Conserved Sequence ; Crenarchaeota/*genetics ; DNA, Archaeal/chemistry/genetics/isolation &amp; purification ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Gene Order ; *Gene Transfer, Horizontal ; Genes, Archaeal ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Recombination, Genetic ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {Marine planktonic crenarchaeota have escaped all cultivation attempts to date, all crenarchaeota growing in pure culture so far being hyperthermophiles. Here, we present a comparative genomic analysis of a 16S- plus 23S-rDNA-containing fragment of a crenarchaeote retrieved from an environmental genomic library constructed from picoplankton collected at 500 m depth in the Antarctic Polar Front. The clone DeepAnt-EC39 contained an insert of 33.3 kbp, which was completely sequenced. DeepAnt-EC39 appears to represent a lineage specific to deep-sea waters but widespread geographically, as revealed by the analysis of the 16S-23S-rDNA intergenic spacer region. A comparison with previously sequenced marine crenarchaeotal genomic clones also containing an rrn operon (74A4, 4B7 and Cenarchaeum symbiosum strains A and B) revealed a highly variable structure involving gene rearrangements and insertions/deletions. The surroundings of the rrn operon and the contiguous glutamate-1-semialdehyde aminotransferase gene appear hot spots for recombination. Phylogenetic analyses of all individual predicted proteins revealed the existence of several likely cases of horizontal gene transfer both, between the two archaeal kingdoms and between the two prokaryotic domains. The most frequent horizontal transfers appear to involve genes from mesophilic methanogenic euryarchaeota related to Methanosarcinales. We hypothesise that the acquisition of genes from mesophilic bacteria and euryarchaeota has played a major role in the adaptation of Group I crenarchaeota to life at lower temperatures.}, }
@article {pmid14686936, year = {2004}, author = {Weinbauer, MG and Rassoulzadegan, F}, title = {Are viruses driving microbial diversification and diversity?.}, journal = {Environmental microbiology}, volume = {6}, number = {1}, pages = {1-11}, doi = {10.1046/j.1462-2920.2003.00539.x}, pmid = {14686936}, issn = {1462-2912}, mesh = {Bacteria/*genetics/*virology ; Bacteriophages/*genetics/growth &amp; development/*physiology ; Biodiversity ; *Biological Evolution ; Ecosystem ; Gene Transfer, Horizontal ; *Genetic Variation ; Lysogeny ; Transduction, Genetic ; Water Microbiology ; }, abstract = {Viruses can influence the genetic diversity of prokaryotes in various ways. They can affect the community composition of prokaryotes by 'killing the winner' and keeping in check competitive dominants. This may sustain species richness and the amount of information encoded in genomes. Viruses can also transfer (viral and host) genes between species. Such mechanisms have probably influenced the speciation of prokaryotes. Whole-genome sequencing has clearly revealed the importance of (virus-mediated) gene transfer. However, its significance for the ecological performance of aquatic microbial communities is only poorly studied, although the few available reports indicate a large potential. Here, we present data supporting the hypothesis that viral genes and viral activity generate genetic variability of prokaryotes and are a driving force for ecological functioning and evolutionary change.}, }
@article {pmid14677415, year = {2003}, author = {Rollnik, JD and Däuper, J and Wüstefeld, S and Mansouri, S and Karst, M and Fink, M and Kossev, A and Dengler, R}, title = {Repetitive magnetic stimulation for the treatment of chronic pain conditions.}, journal = {Supplements to Clinical neurophysiology}, volume = {56}, number = {}, pages = {390-393}, doi = {10.1016/s1567-424x(09)70242-9}, pmid = {14677415}, issn = {1567-424X}, mesh = {Adult ; Aged ; Chronic Disease ; Electric Stimulation ; *Electric Stimulation Therapy ; Female ; Follow-Up Studies ; Functional Laterality ; Gene Transfer, Horizontal ; Humans ; *Magnetics ; Male ; Middle Aged ; Motor Cortex/physiopathology/radiation effects ; *Pain Management ; Pain Measurement ; Pain Threshold/physiology/radiation effects ; Safety ; Tennis Elbow/physiopathology/therapy ; Time Factors ; }, }
@article {pmid14676319, year = {2003}, author = {Kroken, S and Glass, NL and Taylor, JW and Yoder, OC and Turgeon, BG}, title = {Phylogenomic analysis of type I polyketide synthase genes in pathogenic and saprobic ascomycetes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {100}, number = {26}, pages = {15670-15675}, pmid = {14676319}, issn = {0027-8424}, mesh = {Ascomycota/classification/enzymology/*genetics/pathogenicity ; Bacteria/classification/genetics ; Databases, Nucleic Acid ; Databases, Protein ; Gene Duplication ; Genetic Variation ; Molecular Sequence Data ; Multienzyme Complexes/*genetics ; *Phylogeny ; }, abstract = {Fungal type I polyketides (PKs) are synthesized by PK synthases (PKSs) and include well known secondary metabolites such as the anticholesterol drug lovastatin and the potent natural carcinogen aflatoxin. Other type I PKs are known to be virulence factors for some plant pathogens and pigments such as melanin. In this study, a phylogenomic approach was used to investigate the origin and diversity of fungal genes encoding putative PKSs that are predicted to synthesize type I PKs. The resulting genealogy, constructed by using the highly conserved PKS ketosynthase (KS) domain, indicated that: (i). Species within subphylum Pezizomycotina (phylum Ascomycota) but not early diverging ascomycetes, like Saccharomyces cerevisiae (Saccharomycotina) or Schizosaccharomyces pombe (Taphrinomycotina), had large numbers (7-25) of PKS genes. (ii). Bacteria and fungi had separate groups of PKS genes; the few exceptions are the likely result of horizontal gene transfer from bacteria to various sublineages of fungi. (iii). The bulk of genes encoding fungal PKSs fell into eight groups. Four groups were predicted to synthesize variously reduced PKs, and four groups were predicted to make unreduced PKs. (iv). Species within different classes of Pezizomycotina shared the same groups of PKS genes. (v). Different fungal genomes shared few putative orthologous PKS genes, even between closely related genomes in the same class or genus. (vi) The discontinuous distributions of orthologous PKSs among fungal species can be explained by gene duplication, divergence, and gene loss; horizontal gene transfer among fungi does not need to be invoked.}, }
@article {pmid14676297, year = {2003}, author = {Shibuya, K and Shirakawa, J and Kameyama, T and Honda, S and Tahara-Hanaoka, S and Miyamoto, A and Onodera, M and Sumida, T and Nakauchi, H and Miyoshi, H and Shibuya, A}, title = {CD226 (DNAM-1) is involved in lymphocyte function-associated antigen 1 costimulatory signal for naive T cell differentiation and proliferation.}, journal = {The Journal of experimental medicine}, volume = {198}, number = {12}, pages = {1829-1839}, pmid = {14676297}, issn = {0022-1007}, mesh = {Antigens, Differentiation, T-Lymphocyte/*physiology ; Cell Differentiation ; Cell Division ; Gene Transfer, Horizontal ; Genetic Vectors ; Humans ; Interleukin-12/physiology ; Interleukin-2/pharmacology ; Lentivirus/genetics ; Lymphocyte Activation ; Lymphocyte Function-Associated Antigen-1/*physiology ; Membrane Microdomains/physiology ; T-Lymphocytes/*physiology ; Th1 Cells/physiology ; T Lineage-Specific Activation Antigen 1 ; }, abstract = {Upon antigen recognition by the T cell receptor, lymphocyte function-associated antigen 1 (LFA-1) physically associates with the leukocyte adhesion molecule CD226 (DNAM-1) and the protein tyrosine kinase Fyn. We show that lentiviral vector-mediated mutant (Y-F322) CD226 transferred into naive CD4+ helper T cells (Ths) inhibited interleukin (IL)-12-independent Th1 development initiated by CD3 and LFA-1 ligations. Moreover, proliferation induced by LFA-1 costimulatory signal was suppressed in mutant (Y-F322) CD226-transduced naive CD4+ and CD8+ T cells in the absence of IL-2. These results suggest that CD226 is involved in LFA-1-mediated costimulatory signals for triggering naive T cell differentiation and proliferation. We also demonstrate that although LFA-1, CD226, and Fyn are polarized at the immunological synapse upon stimulation with anti-CD3 in CD4+ and CD8+ T cells, lipid rafts are polarized in CD4+, but not CD8+, T cells. Moreover, proliferation initiated by LFA-1 costimulatory signal is suppressed by lipid raft disruption in CD4+, but not CD8+, T cells, suggesting that the LFA-1 costimulatory signal is independent of lipid rafts in CD8+ T cells.}, }
@article {pmid14671318, year = {2003}, author = {Brown, EW and Mammel, MK and LeClerc, JE and Cebula, TA}, title = {Limited boundaries for extensive horizontal gene transfer among Salmonella pathogens.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {100}, number = {26}, pages = {15676-15681}, pmid = {14671318}, issn = {0027-8424}, mesh = {Base Sequence ; DNA Primers ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal/*genetics ; *Genetic Variation ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; Salmonella/classification/*genetics/*pathogenicity ; }, abstract = {Recombination is thought to be rare within Salmonella, as evidenced by absence of gene transfer among SARC strains that represent the broad genetic diversity of the eight primary subspecies of this common facultative intracellular pathogen. We adopted a phylogenetic approach to assess recombination within the mutS gene of 70 SARB strains, a genetically homogeneous population of Salmonella enterica subspecies I strains, which have in common the ability to infect warm-blooded animals. We report here that SARB strains show evidence for widespread recombinational exchange in contrast to results obtained with strains exhibiting species-level genetic variation. Besides extensive allele shuffling, SARB strains showed notably larger recombinagenic patch sizes for mutS (at least approximately 1.1 kb) than previously reported for S. enterica SARC strains. Explaining these experimental dichotomies provides important insight for understanding microbial evolution, because they suggest likely ecologic and genetic barriers that limit extensive gene transfer in the feral setting.}, }
@article {pmid14667745, year = {2003}, author = {Yokoyama, K and Doi, Y and Yamane, K and Kurokawa, H and Shibata, N and Shibayama, K and Yagi, T and Kato, H and Arakawa, Y}, title = {Acquisition of 16S rRNA methylase gene in Pseudomonas aeruginosa.}, journal = {Lancet (London, England)}, volume = {362}, number = {9399}, pages = {1888-1893}, doi = {10.1016/S0140-6736(03)14959-8}, pmid = {14667745}, issn = {1474-547X}, mesh = {Aminoglycosides/*pharmacology ; Anti-Bacterial Agents/pharmacology ; Cloning, Molecular ; DNA, Bacterial/*genetics ; Drug Resistance/genetics ; Drug Resistance, Microbial/*genetics ; Genes, rRNA/*genetics ; Methyltransferases/*genetics ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Polymerase Chain Reaction ; Pseudomonas aeruginosa/drug effects/enzymology/*genetics ; }, abstract = {BACKGROUND: Bacteria develop resistance to aminoglycosides by producing aminoglycoside-modifying enzymes such as acetyltransferase, phosphorylase, and adenyltransferase. These enzymes, however, cannot confer consistent resistance to various aminoglycosides because of their substrate specificity. Notwithstanding, a Pseudomonas aeruginosa strain AR-2 showing high-level resistance (minimum inhibitory concentration >1024 mg/L) to various aminoglycosides was isolated clinically. We aimed to clone and characterise the genetic determinant of this resistance.<br><br>METHODS: We used conventional methods for DNA manipulation, susceptibility testing, and gene analyses to clone and characterise the genetic determinant of the resistance seen. PCR detection of the gene was also done on a stock of P aeruginosa strains that were isolated clinically since 1997.<br><br>FINDINGS: An aminoglycoside-resistance gene, designated rmtA, was identified in P aeruginosa AR-2. The Escherichia coli transformant and transconjugant harbouring the rmtA gene showed very high-level resistance to various aminoglycosides, including amikacin, tobramycin, isepamicin, arbekacin, kanamycin, and gentamicin. The 756-bp nucleotide rmtA gene encoded a protein, RmtA. This protein showed considerable similarity to the 16S rRNA methylases of aminoglycoside-producing actinomycetes, which protect bacterial 16S rRNA from intrinsic aminoglycosides by methylation. Incorporation of radiolabelled methyl groups into the 30S ribosome was detected in the presence of RmtA. Of 1113 clinically isolated P aeruginosa strains, nine carried the rmtA gene, as shown by PCR analyses.<br><br>INTERPRETATION: Our findings strongly suggest intergeneric lateral gene transfer of 16S rRNA methylase gene from some aminoglycoside-producing microorganisms to P aeruginosa. Further dissemination of the rmtA gene in nosocomial bacteria could be a matter of concern in the future.}, }
@article {pmid14666975, year = {2003}, author = {Kharazmi, M and Bauer, T and Hammes, WP and Hertel, C}, title = {Effect of food processing on the fate of DNA with regard to degradation and transformation capability in Bacillus subtilis.}, journal = {Systematic and applied microbiology}, volume = {26}, number = {4}, pages = {495-501}, doi = {10.1078/072320203770865774}, pmid = {14666975}, issn = {0723-2020}, mesh = {Bacillus subtilis/*genetics ; Bacillus thuringiensis Toxins ; Bacterial Proteins/genetics ; *Bacterial Toxins ; DNA, Plant/*analysis/*genetics/isolation &amp; purification ; Endotoxins/genetics ; *Food Handling ; Gene Deletion ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genes, Plant/genetics ; Hemolysin Proteins ; Kanamycin Kinase/genetics ; Plants, Genetically Modified/chemistry/genetics ; Polymerase Chain Reaction/methods ; Recombination, Genetic ; *Transformation, Bacterial ; }, abstract = {Soymilk, tofu, corn masa, and cooked potato were produced from transgenic raw materials and the effect of processing on the degradation of DNA was studied. Major degrading factors were for soymilk and tofu the mechanical treatment of soaked soybeans and for corn masa and cooked potatoes the thermal treatment. In the processed foods no DNA fragments > 1.1 kb were detected. We included in our studies the effect of the size of donor DNA and length of the homologous sequence on the marker rescue transformation of B. subtilis LTH 5466, which was monitored by restoration of deleted nptII. When DNA fragments (168, 414, 658, and 792 bp) of nptII and linearized plasmid DNA (pGEM-T-1, 3168 bp and pGEM-T-2, 3792 bp) containing the 168 bp or 792 bp fragments, respectively, were used as donor DNA, it was observed that the efficiency of marker rescue decreased with decreasing length of homologous sequence. The use of a larger plasmid (pMR2, 5786 bp) containing the 792 bp fragment revealed higher efficiency of marker rescue compared to pGEM-T-2. The nptII fragments resulted in lower efficiencies compared to plasmid DNA containing the same fragment. For the 792 bp fragment and the linearized plasmid pMR2 a first-order dependency of the frequency of marker rescue transformation on the DNA concentration was observed. Based on the acquired data, the hypothetical frequency of transformation of transgenic DNA to B. subtilis in cooked potatoes was calculated to be equal to 8.5 x 10(-19) and 1.2 x 10(-27) for homologous and illegitimate recombination, respectively. These data permit to roughly estimate the time after which a person (10(8) years) or the world population (15 days) is exposed to one transformant generated by homologous recombination event, when the daily consumption per person is 130 g of cooked potatoes.}, }
@article {pmid14664155, year = {2003}, author = {Il'ina, TS}, title = {[The mechanisms of horizontal gene transfer: the role of bacteriophages and integrons in the evolution of pathogenic bacteria].}, journal = {Molekuliarnaia genetika, mikrobiologiia i virusologiia}, volume = {}, number = {4}, pages = {3-10}, pmid = {14664155}, issn = {0208-0613}, mesh = {Bacteria/*genetics/*pathogenicity ; Bacteriophages/genetics/*physiology ; *Biological Evolution ; DNA Transposable Elements ; Gene Transfer, Horizontal/*physiology ; Virulence/genetics ; }, abstract = {The role of bacteriophages, e.g. filamentous phages, whose single-stranded DNA comprise the coding virulence factors, as well as of certain suspected bacteriophage derivatives like constin-elements, integrons and chromosomal super-integron, played by them in the horizontal gene transfer and in the evolution of bacteria is under discussion.}, }
@article {pmid14663088, year = {2003}, author = {Feldgarden, M and Byrd, N and Cohan, FM}, title = {Gradual evolution in bacteria: evidence from Bacillus systematics.}, journal = {Microbiology (Reading, England)}, volume = {149}, number = {Pt 12}, pages = {3565-3573}, doi = {10.1099/mic.0.26457-0}, pmid = {14663088}, issn = {1350-0872}, mesh = {Adaptation, Physiological ; Bacillus/classification/*genetics/isolation &amp; purification/metabolism ; *Biological Evolution ; Gene Transfer, Horizontal ; Genetic Variation ; Genome, Bacterial ; Sodium Chloride ; Species Specificity ; }, abstract = {The bacterial genome projects have suggested a central role for horizontal transfer in bacterial adaptation, but it is difficult to rule out an adaptive role for ordinary genetic change in existing genes. The bacterial systematics literature can readily address the importance of gene acquisition in adaptive evolution, since phenotypic characterization typically assesses presence versus absence of metabolic capabilities, and metabolic gains and losses are most likely due to horizontal transfer and/or gene loss. Bacterial systematists have not geared their studies toward quantitative differences in metabolic capabilities, which are more likely to involve adjustments of existing genes. Here, quantitative variation in metabolism within and between three closely related Bacillus taxa has been assayed. While these taxa show no qualitative (i.e. presence versus absence) differences in resource utilization, they are quantitatively different in utilization of 8 % of 95 resources tested. Moreover, 93 % of the resources tested showed significant quantitative variation among strains within a single taxon. These results suggest that ordinary genetic changes in existing genes may play an important role in adaptation. If these results are typical, future genomically based assays of quantitative variation in phenotype (e.g. microarray analysis of mRNA concentrations) may identify hundreds of genes whose expression has been modified. A protocol is presented for identifying those modifications of gene expression and those gene acquisitions that are most likely to have played a role in adaptive evolution.}, }
@article {pmid14660793, year = {2003}, author = {Pearson, A and Budin, M and Brocks, JJ}, title = {Phylogenetic and biochemical evidence for sterol synthesis in the bacterium Gemmata obscuriglobus.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {100}, number = {26}, pages = {15352-15357}, pmid = {14660793}, issn = {0027-8424}, mesh = {Animals ; Bacteria/classification/*metabolism ; Genome, Bacterial ; Genome, Plant ; Humans ; Lipids/analysis ; Molecular Sequence Data ; *Phylogeny ; Plankton/classification/*metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Sterols/*biosynthesis ; }, abstract = {Sterol biosynthesis is viewed primarily as a eukaryotic process, and the frequency of its occurrence in bacteria has long been a subject of controversy. Two enzymes, squalene monooxygenase and oxidosqualene cyclase, are the minimum necessary for initial biosynthesis of sterols from squalene. In this work, 19 protein gene sequences for eukaryotic squalene monooxygenase and 12 protein gene sequences for eukaryotic oxidosqualene cyclase were compared with all available complete and partial prokaryotic genomes. The only unequivocal matches for a sterol biosynthetic pathway were in the proteobacterium, Methylococcus capsulatus, in which sterol biosynthesis is known, and in the planctomycete, Gemmata obscuriglobus. The latter species contains the most abbreviated sterol pathway yet identified in any organism. Analysis shows that the major sterols in Gemmata are lanosterol and its uncommon isomer, parkeol. There are no subsequent modifications of these products. In bacteria, the sterol biosynthesis genes occupy a contiguous coding region and possibly comprise a single operon. Phylogenetic trees constructed for both enzymes show that the sterol pathway in bacteria and eukaryotes has a common ancestry. It is likely that this contiguous reading frame was exchanged between bacteria and early eukaryotes via lateral gene transfer or endosymbiotic events. The primitive sterols produced by Gemmata suggest that this genus could retain the most ancient remnants of the sterol biosynthetic pathway.}, }
@article {pmid14658500, year = {2003}, author = {Takishita, K and Ishida, K and Maruyama, T}, title = {An enigmatic GAPDH gene in the symbiotic dinoflagellate genus Symbiodinium and its related species (the order Suessiales): possible lateral gene transfer between two eukaryotic algae, dinoflagellate and euglenophyte.}, journal = {Protist}, volume = {154}, number = {3-4}, pages = {443-454}, doi = {10.1078/143446103322454176}, pmid = {14658500}, issn = {1434-4610}, mesh = {Amino Acid Sequence ; Animals ; Dinoflagellida/classification/*enzymology/*genetics ; *Gene Transfer, Horizontal ; Glyceraldehyde-3-Phosphate Dehydrogenases/*genetics ; Molecular Sequence Data ; Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction ; *Symbiosis ; }, abstract = {A group of unicellular eukaryotic algae, the dinoflagellates, are known to possess two types of gene for glyceraldehyde-3-phosphate dehydrogenase (GAPDH). An enzyme encoded by one type of gene possibly plays a key role in the glycolytic pathway of the cytosol and the other in the Calvin cycle of plastids. In the present study, an additional type of GAPDH gene (GapC3) was found in the symbiotic dinoflagellates, Symbiodinium spp. and their related species, Gymnodinium simplex and Polarella glacialis, all of which belong to the order Suessiales. Since no intracellular translocation signal is found at both amino- and carboxy-termini of its deduced amino acid sequence, the protein is predicted to function in the cytosol. However, it may not be involved in glycolysis due to the presence of an amino acid signature that allows binding for NADP+. It is likely that dinoflagellate species, other than Suessiales investigated in this study, lack this type of GAPDH. Phylogenetic analysis placed GapC3 from the Suessialean species firmly in the clade composed of GAPDH from spirochetes, euglenophytes (cytosolic type) and kinetoplastids (glycosomal type). Specifically, this enigmatic GAPDH gene in dinoflagellates was closely related to its cytosolic counterpart in euglenophytes. It has been previously reported that plastid-targeted (Calvin cycle) GAPDH genes of the dinoflagellates Pyrocystis spp. and that of the euglenophyte Euglena gracilis also seem to share a common ancestor. It appears highly likely that at least two genes (cytosolic and plastid-targeted GAPDH genes) have been laterally transferred between these two eukaryotic algal groups.}, }
@article {pmid14647059, year = {2003}, author = {Moreno, M and Molina, H and Amigo, L and Zanlungo, S and Arrese, M and Rigotti, A and Miquel, JF}, title = {Hepatic overexpression of caveolins increases bile salt secretion in mice.}, journal = {Hepatology (Baltimore, Md.)}, volume = {38}, number = {6}, pages = {1477-1488}, doi = {10.1016/j.hep.2003.09.011}, pmid = {14647059}, issn = {0270-9139}, mesh = {Adenoviridae/genetics ; Animals ; Bile Acids and Salts/*metabolism ; Body Weight ; Caveolin 1 ; Caveolin 2 ; Caveolins/analysis/*physiology ; Cholesterol, HDL/blood ; Gene Transfer, Horizontal ; Immunoblotting ; Immunohistochemistry ; Liver/*metabolism ; Male ; Mice ; Mice, Inbred C57BL ; }, abstract = {Caveolins are cholesterol-binding proteins involved in the regulation of several intracellular processes, including cholesterol transport. Because hepatocytes express caveolin-1 and caveolin-2, these proteins might modulate hepatic lipid metabolism and biliary lipid secretion. Our aim was to investigate the potential physiologic role of caveolins in hepatic cholesterol and bile salt (BS) metabolism and transport using adenoviral gene transfer. C57BL/6 mice were infected with recombinant human caveolin-1 and caveolin-2 adenoviruses. Mice infected with adenovirus lacking the transgene were used as controls. Hepatic caveolin expression was evaluated by immunochemical methods. Reverse-transcription polymerase chain reaction (RT-PCR) and immunoblotting were used to assess messenger RNA (mRNA) levels and protein mass of BS transporters (sodium taurocholate cotransporting polypeptide [Ntcp] and bile salt export pump [Bsep]). Serum, liver, biliary, and fecal biochemical determinations and BS maximal secretory rate (SRm) were performed by standard methods. Ad.Cav-1- and Ad.Cav-2-infected mice exhibited a 10- and 7-fold increase in hepatic caveolin-1 and caveolin-2 protein expression, respectively. Caveolin-1-overexpressing mice had a significant increase in plasma high-density lipoprotein (HDL) cholesterol and hepatic free cholesterol content, whereas total plasma cholesterol and triglyceride levels remained unchanged. Hepatic caveolin-1 and/or caveolin-2 overexpression significantly increased bile flow and secretion of all biliary lipids. Caveolin-1-overexpressing mice showed a 2.5-fold increase in taurocholate (TC) SRm, indicating increased canalicular BS transport capacity. BS pool size and fecal BS excretion remained within the normal range in mice with Cav-1 overexpression. No changes were seen in the protein mass of BS transporters Ntcp and Bsep. In conclusion, our findings indicate that caveolins may play an important role in regulating hepatic BS and cholesterol metabolism.}, }
@article {pmid14645285, year = {2003}, author = {Schouls, LM and Schot, CS and Jacobs, JA}, title = {Horizontal transfer of segments of the 16S rRNA genes between species of the Streptococcus anginosus group.}, journal = {Journal of bacteriology}, volume = {185}, number = {24}, pages = {7241-7246}, pmid = {14645285}, issn = {0021-9193}, mesh = {Amidohydrolases/*genetics ; *Bacterial Proteins ; Base Sequence ; Blotting, Southern ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Mosaicism ; Nucleic Acid Hybridization ; Phenotype ; Sequence Analysis, DNA ; Streptococcus anginosus/classification/*genetics ; }, abstract = {The nature in variation of the 16S rRNA gene of members of the Streptococcus anginosus group was investigated by hybridization and DNA sequencing. A collection of 708 strains was analyzed by reverse line blot hybridization. This revealed the presence of distinct reaction patterns representing 11 different hybridization groups. The 16S rRNA genes of two strains of each hybridization group were sequenced to near-completion, and the sequence data confirmed the reverse line blot hybridization results. Closer inspection of the sequences revealed mosaic-like structures, strongly suggesting horizontal transfer of segments of the 16S rRNA gene between different species belonging to the Streptococcus anginosus group. Southern blot hybridization further showed that within a single strain all copies of the 16S rRNA gene had the same composition, indicating that the apparent mosaic structures were not PCR-induced artifacts. These findings indicate that the highly conserved rRNA genes are also subject to recombination and that these events may be fixed in the population. Such recombination may lead to the construction of incorrect phylogenetic trees based on the 16S rRNA genes.}, }
@article {pmid14645284, year = {2003}, author = {Campos, J and Martínez, E and Marrero, K and Silva, Y and Rodríguez, BL and Suzarte, E and Ledón, T and Fando, R}, title = {Novel type of specialized transduction for CTX phi or its satellite phage RS1 mediated by filamentous phage VGJ phi in Vibrio cholerae.}, journal = {Journal of bacteriology}, volume = {185}, number = {24}, pages = {7231-7240}, pmid = {14645284}, issn = {0021-9193}, mesh = {Bacteriophages/*genetics ; Cholera Toxin/*genetics ; Cholera Vaccines ; Gene Expression Regulation, Viral ; Gene Transfer, Horizontal ; Lysogeny ; Plasmids/genetics ; *Transduction, Genetic ; Vibrio cholerae/*genetics/pathogenicity/*virology ; Virulence ; }, abstract = {The main virulence factor of Vibrio cholerae, the cholera toxin, is encoded by the ctxAB operon, which is contained in the genome of the lysogenic filamentous phage CTX phi. This phage transmits ctxAB genes between V. cholerae bacterial populations that express toxin-coregulated pilus (TCP), the CTX phi receptor. In investigating new forms of ctxAB transmission, we found that V. cholerae filamentous phage VGJ phi, which uses the mannose-sensitive hemagglutinin (MSHA) pilus as a receptor, transmits CTX phi or its satellite phage RS1 by an efficient and highly specific TCP-independent mechanism. This is a novel type of specialized transduction consisting in the site-specific cointegration of VGJ phi and CTX phi (or RS1) replicative forms to produce a single hybrid molecule, which generates a single-stranded DNA hybrid genome that is packaged into hybrid viral particles designated HybP phi (for the VGJ phi/CTX phi hybrid) and HybRS phi (for the VGJ phi/RS1 hybrid). The hybrid phages replicate by using the VGJ phi replicating functions and use the VGJ phi capsid, retaining the ability to infect via MSHA. The hybrid phages infect most tested strains more efficiently than CTX phi, even under in vitro optimal conditions for TCP expression. Infection and lysogenization with HybP phi revert the V. cholerae live attenuated vaccine strain 1333 to virulence. Our results reinforce that TCP is not indispensable for the acquisition of CTX phi. Thus, we discuss an alternative to the current accepted evolutionary model for the emergence of new toxigenic strains of V. cholerae and the importance of our findings for the development of an environmentally safer live attenuated cholera vaccine.}, }
@article {pmid14641594, year = {2003}, author = {Nesbø, CL and Doolittle, WF}, title = {Targeting clusters of transferred genes in Thermotoga maritima.}, journal = {Environmental microbiology}, volume = {5}, number = {11}, pages = {1144-1154}, doi = {10.1046/j.1462-2920.2003.00515.x}, pmid = {14641594}, issn = {1462-2912}, mesh = {Adenosine Triphosphatases/genetics ; Alcohol Dehydrogenase/genetics ; Bacterial Proteins/genetics ; Base Composition ; DNA, Archaeal/chemistry/genetics/isolation &amp; purification ; DNA, Bacterial/chemistry/genetics/isolation &amp; purification ; DNA-Binding Proteins/genetics ; Gene Library ; Gene Order ; Gene Transfer, Horizontal/genetics ; Genes, Archaeal ; Genes, Bacterial ; Genomic Library ; Glycoside Hydrolases/genetics ; Molecular Sequence Data ; MutS DNA Mismatch-Binding Protein ; Phylogeny ; Rhamnose/genetics ; Sequence Analysis, DNA ; Sequence Homology ; Thermotoga maritima/*genetics ; }, abstract = {We screened a Thermotoga sp. strain RQ2 lambda library for genes present in that strain but absent from the closely related completely sequenced relative Thermotoga maritima strain MSB8, by using probes generated in an earlier genomic subtraction study. Five lambda insert fragments were sequenced, containing, respectively, an archaeal type ATPase operon, rhamnose biosynthetic genes, ORFs with similarity to an arabinosidase, a Thermotoga sp. strain RQ2-specific alcohol dehydrogenase and a novel archaeal Mut-S homologue. All but one of these fragments contained additional Thermotoga sp. strain RQ2-specific sequences not screened for, suggesting that many such strain-specific genes will be found clustered in the genome. Moreover, phylogenetic analyses, phylogenetic distribution and/or G + C content suggests that all the Thermotoga sp. strain RQ2 specific sequences in the sequenced lambda clones have been acquired by lateral gene transfer. We suggest that the use of strain-specific small insert clones obtained by subtractive hybridization to target larger inserts for sequencing is an efficient, economical way to identify environmentally (or clinically) relevant interstrain differences and novel gene clusters, and will be invaluable in comparative genomics.}, }
@article {pmid14645288, year = {2003}, author = {Chen, WM and Moulin, L and Bontemps, C and Vandamme, P and Béna, G and Boivin-Masson, C}, title = {Legume symbiotic nitrogen fixation by beta-proteobacteria is widespread in nature.}, journal = {Journal of bacteriology}, volume = {185}, number = {24}, pages = {7266-7272}, pmid = {14645288}, issn = {0021-9193}, mesh = {Acyltransferases/genetics ; Amidohydrolases/genetics ; *Bacterial Proteins ; Burkholderia/*genetics ; Fabaceae/microbiology ; Gene Transfer, Horizontal/genetics ; Mimosa/microbiology ; Molecular Sequence Data ; Nitrogen Fixation/*genetics ; Oxidoreductases/genetics ; *Phylogeny ; Ralstonia/*genetics ; Taiwan ; }, abstract = {Following the initial discovery of two legume-nodulating Burkholderia strains (L. Moulin, A. Munive, B. Dreyfus, and C. Boivin-Masson, Nature 411:948-950, 2001), we identified as nitrogen-fixing legume symbionts at least 50 different strains of Burkholderia caribensis and Ralstonia taiwanensis, all belonging to the beta-subclass of proteobacteria, thus extending the phylogenetic diversity of the rhizobia. R. taiwanensis was found to represent 93% of the Mimosa isolates in Taiwan, indicating that beta-proteobacteria can be the specific symbionts of a legume. The nod genes of rhizobial beta-proteobacteria (beta-rhizobia) are very similar to those of rhizobia from the alpha-subclass (alpha-rhizobia), strongly supporting the hypothesis of the unique origin of common nod genes. The beta-rhizobial nod genes are located on a 0.5-Mb plasmid, together with the nifH gene, in R. taiwanensis and Burkholderia phymatum. Phylogenetic analysis of available nodA gene sequences clustered beta-rhizobial sequences in two nodA lineages intertwined with alpha-rhizobial sequences. On the other hand, the beta-rhizobia were grouped with free-living nitrogen-fixing beta-proteobacteria on the basis of the nifH phylogenetic tree. These findings suggest that beta-rhizobia evolved from diazotrophs through multiple lateral nod gene transfers.}, }
@article {pmid14642748, year = {2003}, author = {Kinsella, RJ and McInerney, JO}, title = {Eukaryotic genes in Mycobacterium tuberculosis? Possible alternative explanations.}, journal = {Trends in genetics : TIG}, volume = {19}, number = {12}, pages = {687-689}, doi = {10.1016/j.tig.2003.10.001}, pmid = {14642748}, issn = {0168-9525}, mesh = {Animals ; Bacterial Proteins/genetics ; Biological Evolution ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Mycobacterium tuberculosis/*genetics/immunology/pathogenicity ; Phylogeny ; Tuberculosis/*genetics ; Virulence/genetics ; }, }
@article {pmid14642119, year = {2003}, author = {Chen, Y and Cui, DX and Yang, YL and Dai, H}, title = {[Adenovirus mediate FGF receptor gene transfer inhibits accelerated graft arteriosclerosis in rat aortic transplants].}, journal = {Zhonghua yi xue za zhi}, volume = {83}, number = {18}, pages = {1607-1610}, pmid = {14642119}, issn = {0376-2491}, mesh = {Adenoviridae/genetics ; Animals ; Aorta, Abdominal/*transplantation ; Arteriosclerosis/*prevention &amp; control ; Base Sequence ; Gene Transfer, Horizontal ; *Genetic Therapy ; Graft Rejection/*prevention &amp; control ; Male ; Molecular Sequence Data ; Rats ; Receptors, Fibroblast Growth Factor/*genetics ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {OBJECTIVE: To evaluate the efficacy of adenovirus mediated fibroblast growth factor (FGF) receptor gene transfer in inhibition of accelerated graft arteriosclerosis (AGA) in rat aorta transplantation model.<br><br>METHODS: The PCR product of rat sFGFR-1 cDNA was cloned into pCMV1-flag vector, then flag-sFGFR was cloned into pAdvs6a to construct recombinant vector pAv3flag-sFGFR1. The abdominal aorta was injected with buffer containing 5 x 10(9) pfu Adv3-sFGFR-1 and then resected in 30 DA rats. A section of abdominal aorta was resected in 30 PVG rats and the abdominal aorta of DA rats was transplanted. Av3-Nall and normal saline of the same volume were injected into the abdominal aortae of and rats as experimental controls and blank controls. Six rats were killed 5, 30, 60, and 90 days after the operation respectively. The transplanted aorta was harvested. RT-PCR was performed to detect the expression of sFGFR-1 gene with pCMV-Flag-sFGFR1 cDNA as positive control and the abdominal aorta RNA of non-transfected rats as negative control. Immunohistochemistry and HE staning were used to detect the localization and expression of sFGFR-1, and the morphology and cytology of the transplanted vessels.<br><br>RESULTS: A construct encoding the FGFR1 ectodomain produced secreted sFGFR1 protein, which bound [(125)I]FGF-2 with high affinity and specificity, and inhibited FGF-2 stimulated 3T3 fibroblast proliferation in vitro. Gene transfer of sFGFR1 into rat aortic grafts, using an adenoviral vector, resulted in expression of sFGFR1 protein in endothelium and adventitia. Neointimal formation 60 and 90 days after transplantation was inhibited (P = 0.013) in aortic allograft transduced with sFGFR1, compared to allograft transduced with Null virus and saline.<br><br>CONCLUSION: FGFs play a causal role in the development of AGA in the rat aortic transplant model and postulate that targeted interruption of FGF function could similarly reduce neointimal formation in transplant setting.}, }
@article {pmid14642101, year = {2003}, author = {Li, J and Chen, G and Gao, QL and Xing, H and Wu, SF and Zhang, AL and Wang, SX and Lu, YP and Ma, D}, title = {[Reversion of ovarian carcinoma metastasis by adeno-associated virus-mediated gene transfer of nm23H1 in orthotopic implantation model].}, journal = {Zhonghua yi xue za zhi}, volume = {83}, number = {19}, pages = {1671-1675}, pmid = {14642101}, issn = {0376-2491}, mesh = {Animals ; Dependovirus/*genetics ; Female ; Gene Transfer, Horizontal ; *Genetic Therapy ; Humans ; Mice ; NM23 Nucleoside Diphosphate Kinases ; Neoplasm Metastasis/*prevention &amp; control ; *Nucleoside-Diphosphate Kinase ; Ovarian Neoplasms/pathology/*therapy ; Polymerase Chain Reaction ; Proteins/*genetics ; }, abstract = {OBJECTIVE: To explore the feasibility of reverse effect of recombinant nm23H(1) adeno-associated virus (rAAV-nm23H(1)) in ovarian carcinoma metastatic orthotopic implantation nude model.<br><br>METHODS: Using DNA recombination technique to construct AAV main plasmid pUF(1)-nm23H(1). rAAV-nm23H(1) and rAAV-Laz were produced by co-transfection of rAAV system in package cell 293 by phosphate-calcium deposit method, and then the transfection efficiency was measured. The titer was measured by dot hybridization. Ovarian carcinoma cell line SW626 was used in the establishment of the ovarian carcinoma orthotopic implantation nude model. The biologic feature of the model was observed and the expression of nm23H(1) in the tumor was measured by Western blot. Three groups of ovarian carcinoma orthotopic implantation nude model were applied by PBS (as control) (12 mice), rAAV-Laz (13 mice), rAAV-nm23H(1) (13 mice) intraperitoneally on the day 10 after transplantation. Then the effect of rAAV-nm23H(1) on survival and liver metastatic incident rates in models were observed.<br><br>RESULTS: rAAV-nm23H(1) and rAAV-Laz were constructed and identified successfully. The titers were both 1 x 10(10) virus particles/ml. The transfection efficiency was 70%. The observation of biological feature showed the orthotopic implantation model was metastatic. The expression of nm23H(1) in AAV-nm23H(1) group was higher significantly than control and rAAV-Laz group (P < 0.05). Survival time of rAAV-nm23H(1) group was 136.67 days, compared with blank control group 106.67 days and rAAV-Laz group 107.06 days. Kaplan-Meier analysis showed rAAV-nm23H(1) group survived longer than control and rAAV-Laz group (P = 0.0051, P = 0.018 P < 0.05). The control and rAAV-Laz groups showed no statistically difference in survival time (P = 0.059 P > 0.05). The metastatic incident rate of control, rAAV-Laz and rAAV-nm23H(1) group was 75%, 61.5%, and 30.8% respectively, the rate of rAAV-nm23H(1) group was lower significantly than that of control and rAAV-Laz group (P = 0.03, P = 0.01). There was no significant difference between control and rAAV-Laz group in liver metastatic rate (P > 0.05).<br><br>CONCLUSION: SW626 line which expressed lower level of nm23H(1) showed high-frequency metastasis properties, rAAV-nm23H(1) could reverse its metastasis in ovarian carcinoma orthotopic transplantation model.}, }
@article {pmid14641578, year = {2003}, author = {Ernst, RK and D'Argenio, DA and Ichikawa, JK and Bangera, MG and Selgrade, S and Burns, JL and Hiatt, P and McCoy, K and Brittnacher, M and Kas, A and Spencer, DH and Olson, MV and Ramsey, BW and Lory, S and Miller, SI}, title = {Genome mosaicism is conserved but not unique in Pseudomonas aeruginosa isolates from the airways of young children with cystic fibrosis.}, journal = {Environmental microbiology}, volume = {5}, number = {12}, pages = {1341-1349}, doi = {10.1111/j.1462-2920.2003.00518.x}, pmid = {14641578}, issn = {1462-2912}, support = {R01AI47938/AI/NIAID NIH HHS/United States ; }, mesh = {Adaptation, Physiological ; Base Composition ; Child ; Child, Preschool ; Cystic Fibrosis/*microbiology ; DNA, Bacterial/chemistry/isolation &amp; purification ; Gene Transfer, Horizontal ; Genetic Variation ; *Genome, Bacterial ; Humans ; Infant ; Melanins/genetics/metabolism ; Oligonucleotide Array Sequence Analysis ; *Oligopeptides ; Pigments, Biological/genetics/metabolism ; Pseudomonas Infections/genetics/*microbiology ; Pseudomonas Phages ; Pseudomonas aeruginosa/*genetics/*isolation &amp; purification/pathogenicity ; Pyocins/metabolism ; RNA, Transfer/genetics ; Sequence Deletion ; }, abstract = {Pseudomonas aeruginosa strains from the chronic lung infections of cystic fibrosis (CF) patients are phenotypically and genotypically diverse. Using strain PAO1 whole genome DNA microarrays, we assessed the genomic variation in P. aeruginosa strains isolated from young children with CF (6 months to 8 years of age) as well as from the environment. Eighty-nine to 97% of the PAO1 open reading frames were detected in 20 strains by microarray analysis, while subsets of 38 gene islands were absent or divergent. No specific pattern of genome mosaicism defined strains associated with CF. Many mosaic regions were distinguished by their low G + C content; their inclusion of phage related or pyocin genes; or by their linkage to a vgr gene or a tRNA gene. Microarray and phenotypic analysis of sequential isolates from individual patients revealed two deletions of greater than 100 kbp formed during evolution in the lung. The gene loss in these sequential isolates raises the possibility that acquisition of pyomelanin production and loss of pyoverdin uptake each may be of adaptive significance. Further characterization of P. aeruginosa diversity within the airways of individual CF patients may reveal common adaptations, perhaps mediated by gene loss, that suggest new opportunities for therapy.}, }
@article {pmid14641569, year = {2003}, author = {Nelson, KE}, title = {The future of microbial genomics.}, journal = {Environmental microbiology}, volume = {5}, number = {12}, pages = {1223-1225}, doi = {10.1111/j.1462-2920.2003.00505.x}, pmid = {14641569}, issn = {1462-2912}, mesh = {Biodiversity ; Computational Biology/methods/trends ; Ecosystem ; Environmental Microbiology ; Gene Transfer, Horizontal ; Genetics, Microbial/methods/*trends ; Genomics/methods/*trends ; Phylogeny ; Sequence Analysis, DNA ; Virulence/genetics ; }, }
@article {pmid14632259, year = {2004}, author = {Silva, JC and Loreto, EL and Clark, JB}, title = {Factors that affect the horizontal transfer of transposable elements.}, journal = {Current issues in molecular biology}, volume = {6}, number = {1}, pages = {57-71}, pmid = {14632259}, issn = {1467-3037}, support = {U01 A1050913-02//PHS HHS/United States ; }, mesh = {Animals ; *DNA Transposable Elements/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genetic Vectors ; Mutagenesis, Insertional ; Phylogeny ; }, abstract = {Transposable elements are characterized by their ability to spread within a host genome. Many are also capable of crossing species boundaries to enter new genomes, a process known as horizontal transfer. Focusing mostly on animal transposable elements, we review the occurrence of horizontal transfer and examine the methods used to detect such transfers. We then discuss factors that affect the frequency of horizontal transfer, with emphasis on the mechanism and regulation of transposition. An intriguing feature of horizontal transfer is that its frequency differs among transposable element families. Evidence summarized in this review indicates that this pattern is due to fundamental differences between Class I and Class II elements. There appears to be a gradient in the incidence of horizontal transfer that reflects the presence of DNA intermediates during transposition. Furthermore, horizontal transfer seems to predominate among families for which copy number is controlled predominantly by self-regulatory mechanisms that limit transposition. We contend that these differences play a major role in the observed predominance of horizontal transfer among Class II transposable elements.}, }
@article {pmid14630923, year = {2004}, author = {Coombs, GH and Westrop, GD and Suchan, P and Puzova, G and Hirt, RP and Embley, TM and Mottram, JC and Müller, S}, title = {The amitochondriate eukaryote Trichomonas vaginalis contains a divergent thioredoxin-linked peroxiredoxin antioxidant system.}, journal = {The Journal of biological chemistry}, volume = {279}, number = {7}, pages = {5249-5256}, doi = {10.1074/jbc.M304359200}, pmid = {14630923}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Animals ; Antioxidants/chemistry ; Blotting, Northern ; Blotting, Western ; Cloning, Molecular ; Cysteine/chemistry ; Electrophoresis, Polyacrylamide Gel ; Gene Transfer Techniques ; Glutathione/metabolism ; Kinetics ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidative Stress ; Oxygen/metabolism ; Peroxidases/*chemistry ; Peroxiredoxins ; Phylogeny ; RNA, Messenger/metabolism ; Recombinant Proteins/metabolism ; Sequence Homology, Amino Acid ; Species Specificity ; Thioredoxin-Disulfide Reductase/chemistry ; Thioredoxins/*chemistry ; Time Factors ; Trichomonas vaginalis/*metabolism ; }, abstract = {Trichomonas is an amitochondriate parasitic protozoon specialized for an anaerobic lifestyle. Nevertheless, it is exposed to oxygen and is able to cope with the resultant oxidative stress. In the absence of glutathione, cysteine has been thought to be the major antioxidant. We now report that the parasite contains thioredoxin reductase, which functions together with thioredoxin and thioredoxin peroxidase to detoxify potentially damaging oxidants. Thioredoxin reductase and thioredoxin also reduce cystine and so may play a role in maintaining the cellular cysteine levels. The importance of the thioredoxin system as one of the major antioxidant defense mechanisms in Trichomonas was confirmed by showing that the parasite responds to environmental changes resulting in increased oxidative stress by up-regulating thioredoxin and thioredoxin peroxidases levels. Sequence data indicate that the thioredoxin reductase of Trichomonas differs fundamentally in structure from that of its human host and thus may represent a useful drug target. The protein is generally similar to thioredoxin reductases present in other lower eukaryotes, all of which probably originated through horizontal gene transfer from a prokaryote. The phylogenetic signal in thioredoxin peroxidase is weak, but evidence from trees suggests that this gene has been subject to repeated horizontal gene transfers from different prokaryotes to different eukaryotes. The data are thus consistent with the complexity hypothesis that predicts that the evolution of simple pathways such as the thioredoxin cascade are likely to be affected by horizontal gene transfer between species.}, }
@article {pmid14629389, year = {2003}, author = {Lilley, AK and Bailey, MJ and Barr, M and Kilshaw, K and Timms-Wilson, TM and Day, MJ and Norris, SJ and Jones, TH and Godfray, HC}, title = {Population dynamics and gene transfer in genetically modified bacteria in a model microcosm.}, journal = {Molecular ecology}, volume = {12}, number = {11}, pages = {3097-3107}, doi = {10.1046/j.1365-294x.2003.01960.x}, pmid = {14629389}, issn = {0962-1083}, mesh = {Bacteriophages/genetics ; Chromosomes, Bacterial/*genetics ; Cluster Analysis ; DNA Primers ; *Ecosystem ; Gene Transfer Techniques ; *Gene Transfer, Horizontal ; Genes, Reporter/genetics ; Phylogeny ; Plasmids/genetics ; Population Dynamics ; Pseudomonas fluorescens/*genetics/physiology ; Sequence Analysis, DNA ; Stellaria/*microbiology ; *Transformation, Bacterial ; }, abstract = {The horizontal transfer and effects on host fitness of a neutral gene cassette inserted into three different genomic loci of a plant-colonizing pseudomonad was assessed in a model ecosystem. The KX reporter cassette (kanamycin resistance, aph, and catechol 2, 3, dioxygenase, xylE) was introduced on the disarmed transposon mini-Tn5 into: (I) the chromosome of a spontaneous rifampicin resistant mutant Pseudomonas fluorescens SBW25R; (II) the chromosome of SBW25R in the presence of a naturally occurring lysogenic-phage (phage Phi101); and (III) a naturally occurring plasmid pQBR11 (330 kbp, tra+, Hgr) introduced into SBW25R. These bacteria were applied to Stellaria media (chickweed) plants as seed dressings [c. 5 x 104 colony-forming units (cfu)/seed] and the seedlings planted in 16 microcosm chambers containing model plant and animal communities. Gene transfer to pseudomonads in the phyllosphere and rhizosphere was found only in the plasmid treatment (III). Bacteria in the phage treatment (II) initially declined in density and free phage was detected, but populations partly recovered as the plants matured. Surprisingly, bacteria in the chromosome insertion treatment (I) consistently achieved higher population densities than the unmanipulated control and other treatments. Plasmids were acquired from indigenous bacterial populations in the control and chromosome insertion treatments. Plasmid acquisition, plasmid transfer from inocula and selection for plasmid carrying inocula coincided with plant maturation.}, }
@article {pmid14625198, year = {2003}, author = {Ouyang, P and Chen, HP and Lai, WY and Yang, WL and Xu, AL}, title = {[Effects of Scatophagus argus apoptosis-related gene on apoptosis of NIH-3T3 cells].}, journal = {Di 1 jun yi da xue xue bao = Academic journal of the first medical college of PLA}, volume = {23}, number = {11}, pages = {1137-1138}, pmid = {14625198}, issn = {1000-2588}, mesh = {Animals ; *Apoptosis/genetics ; DNA, Complementary/*genetics ; Fishes ; *Gene Transfer, Horizontal ; Mice ; NIH 3T3 Cells ; }, abstract = {OBJECTIVE: To observe the effects of Scatophagus argus apoptosis-related (SaAR) gene transfer on the apoptosis of NIH-3T3 cells.<br><br>METHODS: A controlled observation of SaAR gene transfer (at different concentrations) into cultured NIH-3T3 cells via lipofectin was performed, and the rate of cell apoptosis was analyzed by flow cytometry.<br><br>RESULTS: The rate of cell apoptosis was (6.37+/-0.0.56)% in the control group, and was (11.89+/-1.13) %, (18.25+/-1.86) % and (22.34+/-1.08) % respectively in pcDNA3-SaAR gene groups corresponding to pcDNA3-SaAR gene concentrations of 2, 3 and 4 microg/ml respectively. It was shown that SaAR gene significantly induced fibroblast apoptosis when the concentration was above 2 microg/ml (P<0.05), in a dose-dependent manner as compared with the control group (P<0.05).<br><br>CONCLUSION: Transient transfection of SaAR gene can significantly induce apoptosis in NIH-3T3 cells.}, }
@article {pmid14624316, year = {2004}, author = {Cavalca, L and Dell'Amico, E and Andreoni, V}, title = {Intrinsic bioremediability of an aromatic hydrocarbon-polluted groundwater: diversity of bacterial population and toluene monoxygenase genes.}, journal = {Applied microbiology and biotechnology}, volume = {64}, number = {4}, pages = {576-587}, doi = {10.1007/s00253-003-1449-6}, pmid = {14624316}, issn = {0175-7598}, mesh = {Actinomycetales/classification/enzymology/genetics/isolation &amp; purification ; Azoarcus/classification/enzymology/genetics/isolation &amp; purification ; Bacteria/classification/enzymology/genetics/*isolation &amp; purification ; Benzene/metabolism ; Benzene Derivatives/metabolism ; Biodegradation, Environmental ; *Biodiversity ; Bradyrhizobium/classification/enzymology/genetics/isolation &amp; purification ; Catechol 1,2-Dioxygenase ; Catechol 2,3-Dioxygenase ; Catechols/metabolism ; DNA Fingerprinting ; DNA, Bacterial/analysis/chemistry/isolation &amp; purification ; DNA, Ribosomal/chemistry/isolation &amp; purification ; *Dioxygenases ; Gene Transfer, Horizontal ; Hydrocarbons, Aromatic/*metabolism ; Molecular Sequence Data ; Mycobacterium/classification/enzymology/genetics/isolation &amp; purification ; Oxygenases/analysis/*genetics ; Phylogeny ; Pseudomonas/classification/enzymology/genetics/isolation &amp; purification ; Toluene/metabolism ; *Water Microbiology ; Water Pollutants, Chemical/metabolism ; Xylenes/metabolism ; }, abstract = {The functional and phylogenetic biodiversity of bacterial communities in a benzene, toluene, ethylbenzene and xylene (BTEX)-polluted groundwater was analysed. To evaluate the feasibility of using an air sparging treatment to enhance bacterial degradative capabilities, the presence of degrading microorganisms was monitored. The amplification of gene fragments corresponding to toluene monooxygenase (tmo), catechol 1,2-dioxygenase, catechol 2,3-dioxygenase and toluene dioxygenase genes in DNA extracted directly from the groundwater samples was associated with the presence of indigenous degrading bacteria. Five months of air injection reduced species diversity in the cultivable community (as calculated by the Shannon-Weaver index), while little change was noted in the degree of biodiversity in the total bacterial community, as characterised by denaturing gradient gel electrophoresis (DGGE) analysis. BTEX-degrading strains belonged to the genera Pseudomonas, Microbacterium, Azoarcus, Mycobacterium and Bradyrhizobium. The degrading capacities of three strains in batch liquid cultures were also studied. In some of these microorganisms different pathways for toluene degradation seemed to operate simultaneously. Pseudomonas strains of the P24 operational taxonomic unit, able to grow only on catechol and not on BTEX, were the most abundant, and were present in the groundwater community at all stages of treatment, as evidenced both by cultivation approaches and by DGGE profiles. The presence of different tmo-like genes in phylogenetically distant strains of Pseudomonas, Mycobacterium and Bradyrhizobium suggested recent horizontal gene transfer in the groundwater.}, }
@article {pmid14617179, year = {2003}, author = {Quaiser, A and Ochsenreiter, T and Lanz, C and Schuster, SC and Treusch, AH and Eck, J and Schleper, C}, title = {Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics.}, journal = {Molecular microbiology}, volume = {50}, number = {2}, pages = {563-575}, doi = {10.1046/j.1365-2958.2003.03707.x}, pmid = {14617179}, issn = {0950-382X}, mesh = {Bacteria/classification/*genetics ; *Biological Evolution ; Gene Library ; *Genome, Bacterial ; Hydrogen-Ion Concentration ; Phylogeny ; RNA, Bacterial/genetics/*isolation &amp; purification/metabolism ; RNA, Ribosomal, 16S/genetics/*isolation &amp; purification/metabolism ; *Soil Microbiology ; }, abstract = {Acidobacteria have been established as a novel phylum of Bacteria that is consistently detected in many different habitats around the globe by 16S rDNA-based molecular surveys. The phylogenetic diversity, ubiquity and abundance of this group, particularly in soil habitats, suggest an important ecological role and extensive metabolic versatility. However, the genetic and physiological information about Acidobacteria is scarce. In order to gain insight into genome structure, evolution and diversity of these microorganisms we have initiated an environmental genomic approach by constructing large insert libraries directly from DNA of a calcerous grassland soil. Genomic fragments of Acidobacteria were identified with specific 16S rDNA probes and sequence analyses of six independently identified clones were performed, representing in total more than 210,000 bp. The 16S rRNA genes of the genomic fragments differed between 2.3% and 19.9% and were placed into two different subgroups of Acidobacteria (groups III and V). Although partial co-linearity was found between genomic fragments, the gene content around the rRNA operons was generally not conserved. Phylogenetic reconstructions with orthologues that were encoded on two of the six genomic fragments (PurF, PurL, PurB and formamidopyrimidine-DNA glycosylase) confirmed the coherence of the acidobacterial phylum. One genomic fragment harboured a cluster of eight genes which was syntenic and highly homologous to genomic regions in Rhodopseudomonas palustris and Bradyrhizobium japonicum, including a conserved two-component system. Phylogenetic analysis of the putative response regulator confirmed that this similarity between Rhizobiales and Acidobacteria might be due to a horizontal gene transfer. In total, our data give first insight into the genome content and diversity of the ubiquitously distributed but poorly characterized phylum of Acidobacteria. Furthermore they support the phylogenetic inferences made from 16S rRNA gene libraries, suggesting that Acidobacteria form a broad group in the same sense and with a similar diversity as that of many well-studied bacterial phyla.}, }
@article {pmid14617175, year = {2003}, author = {Danino, VE and Wilkinson, A and Edwards, A and Downie, JA}, title = {Recipient-induced transfer of the symbiotic plasmid pRL1JI in Rhizobium leguminosarum bv. viciae is regulated by a quorum-sensing relay.}, journal = {Molecular microbiology}, volume = {50}, number = {2}, pages = {511-525}, doi = {10.1046/j.1365-2958.2003.03699.x}, pmid = {14617175}, issn = {0950-382X}, mesh = {Fabaceae/microbiology ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Plasmids/*genetics ; Rhizobium leguminosarum/genetics/*growth &amp; development ; Signal Transduction ; Symbiosis ; }, abstract = {Analysis of the regulation of plasmid transfer genes on the symbiotic plasmid pRL1JI in Rhizobium leguminosarum bv. viciae has revealed a novel regulatory relay that is specifically poised to detect an N-acyl-homoserine lactone (AHL) made by different cells (potential recipients of pRL1JI). Adjacent to the traI-trbBCDEJKLFGHI plasmid transfer operon on pRL1JI are two regulatory genes, bisR and traR, which encode LuxR-type quorum-sensing regulators required for conjugation. Potential recipients of pRL1JI induce the traI-trb operon and plasmid transfer via a quorum-sensing relay involving BisR, TraR and the traI-trb operon in donor cells. BisR induces expression of traR in response to N-(3-hydroxy-7-cis-tetradecenoyl)-l-homoserine lactone (3-OH-C14:1-HSL), which is produced by CinI in potential recipient strains. In donor strains (carrying pRL1JI), BisR represses the expression of the chromosomal gene cinI; this repression results in a very low level of formation of 3-OH-C14:1-HSL and hence relatively low levels of expression of traR and the traI-trb operon in strains carrying pRL1JI. However, if 3-OH-C14:1-HSL from potential recipients is present, then traR and plasmid transfer are induced. The induction of traR occurs at very low concentrations of 3-OH-C14:1-HSL (around 1 nm). TraR then induces the traI-trb operon in a quorum-sensing dependent manner in re-sponse to the TraI-made AHLs, N-(3-oxo-octanoyl)-l-homoserine lactone and N-(octanoyl)-l-homoserine lactone. The resulting autoinduction results in high levels of expression of the traI-trb operon. Premature expression of the traI-trb operon is reduced by TraM, which probably titres out TraR preventing expression of traI when there are low levels of traR expression. Expression of traR in stationary phase cells is limited by feedback inhibition mediated by TraI-made AHLs.}, }
@article {pmid14617137, year = {2003}, author = {Lawrence, JG and Hendrickson, H}, title = {Lateral gene transfer: when will adolescence end?.}, journal = {Molecular microbiology}, volume = {50}, number = {3}, pages = {739-749}, doi = {10.1046/j.1365-2958.2003.03778.x}, pmid = {14617137}, issn = {0950-382X}, mesh = {Archaea/genetics ; Bacteria/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*physiology ; Genome, Bacterial ; Phylogeny ; RNA, Ribosomal/genetics/physiology ; Ribosomal Proteins/genetics ; }, abstract = {The scope and impact of horizontal gene transfer (HGT) in Bacteria and Archaea has grown from a topic largely ignored by the microbiological community to a hot-button issue gaining staunch supporters (on particular points of view) at a seemingly ever-increasing rate. Opinions range from HGT being a phenomenon with minor impact on overall microbial evolution and diversification to HGT being so rampant as to obfuscate any opportunities for elucidating microbial evolution - especially organismal phylogeny - from sequence comparisons. This contentious issue has been fuelled by the influx of complete genome sequences, which has allowed for a more detailed examination of this question than previously afforded. We propose that the lack of common ground upon which to formulate consensus viewpoints probably stems from the absence of answers to four critical questions. If addressed, they could clarify concepts, reject tenuous speculation and solidify a robust foundation for the integration of HGT into a framework for long-term microbial evolution, regardless of the intellectual camp in which you reside. Here, we examine these issues, why their answers shape the outcome of this debate and the progress being made to address them.}, }
@article {pmid14617135, year = {2003}, author = {Koonin, EV}, title = {Horizontal gene transfer: the path to maturity.}, journal = {Molecular microbiology}, volume = {50}, number = {3}, pages = {725-727}, doi = {10.1046/j.1365-2958.2003.03808.x}, pmid = {14617135}, issn = {0950-382X}, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal/*physiology ; Methanosarcina/genetics ; Models, Genetic ; Phylogeny ; }, }
@article {pmid14616063, year = {2003}, author = {Boucher, Y and Douady, CJ and Papke, RT and Walsh, DA and Boudreau, ME and Nesbø, CL and Case, RJ and Doolittle, WF}, title = {Lateral gene transfer and the origins of prokaryotic groups.}, journal = {Annual review of genetics}, volume = {37}, number = {}, pages = {283-328}, doi = {10.1146/annurev.genet.37.050503.084247}, pmid = {14616063}, issn = {0066-4197}, mesh = {Archaea/*genetics/physiology ; Bacteria/*genetics ; Bacteria, Aerobic/genetics/physiology ; Bacterial Physiological Phenomena ; *Biological Evolution ; *Gene Transfer, Horizontal ; Photosynthesis/genetics/physiology ; Phylogeny ; }, abstract = {Lateral gene transfer (LGT) is now known to be a major force in the evolution of prokaryotic genomes. To date, most analyses have focused on either (a) verifying phylogenies of individual genes thought to have been transferred, or (b) estimating the fraction of individual genomes likely to have been introduced by transfer. Neither approach does justice to the ability of LGT to effect massive and complex transformations in basic biology. In some cases, such transformation will be manifested as the patchy distribution of a seemingly fundamental property (such as aerobiosis or nitrogen fixation) among the members of a group classically defined by the sharing of other properties (metabolic, morphological, or molecular, such as small subunit ribosomal RNA sequence). In other cases, the lineage of recipients so transformed may be seen to comprise a new group of high taxonomic rank ("class" or even "phylum"). Here we review evidence for an important role of LGT in the evolution of photosynthesis, aerobic respiration, nitrogen fixation, sulfate reduction, methylotrophy, isoprenoid biosynthesis, quorum sensing, flotation (gas vesicles), thermophily, and halophily. Sometimes transfer of complex gene clusters may have been involved, whereas other times separate exchanges of many genes must be invoked.}, }
@article {pmid14615592, year = {2003}, author = {Salazar, JC and Ahel, I and Orellana, O and Tumbula-Hansen, D and Krieger, R and Daniels, L and Söll, D}, title = {Coevolution of an aminoacyl-tRNA synthetase with its tRNA substrates.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {100}, number = {24}, pages = {13863-13868}, pmid = {14615592}, issn = {0027-8424}, mesh = {Acidithiobacillus/enzymology/genetics ; Amino Acyl-tRNA Synthetases/*genetics/*metabolism ; Base Sequence ; Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; Genes, Bacterial ; Helicobacter pylori/enzymology/genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; RNA, Bacterial/chemistry/*genetics/*metabolism ; RNA, Transfer, Gln/chemistry/*genetics/*metabolism ; RNA, Transfer, Glu/chemistry/*genetics/*metabolism ; Substrate Specificity ; }, abstract = {Glutamyl-tRNA synthetases (GluRSs) occur in two types, the discriminating and the nondiscriminating enzymes. They differ in their choice of substrates and use either tRNAGlu or both tRNAGlu and tRNAGln. Although most organisms encode only one GluRS, a number of bacteria encode two different GluRS proteins; yet, the tRNA specificity of these enzymes and the reason for such gene duplications are unknown. A database search revealed duplicated GluRS genes in >20 bacterial species, suggesting that this phenomenon is not unusual in the bacterial domain. To determine the tRNA preferences of GluRS, we chose the duplicated enzyme sets from Helicobacter pylori and Acidithiobacillus ferrooxidans. H. pylori contains one tRNAGlu and one tRNAGln species, whereas A. ferrooxidans possesses two of each. We show that the duplicated GluRS proteins are enzyme pairs with complementary tRNA specificities. The H. pylori GluRS1 acylated only tRNAGlu, whereas GluRS2 was specific solely for tRNAGln. The A. ferrooxidans GluRS2 preferentially charged tRNA(UUG)(Gln). Conversely, A. ferrooxidans GluRS1 glutamylated both tRNAGlu isoacceptors and the tRNA(CUG)(Gln) species. These three tRNA species have two structural elements in common, the augmented D-helix and a deletion of nucleotide 47. It appears that the discriminating or nondiscriminating natures of different GluRS enzymes have been derived by the coevolution of protein and tRNA structure. The coexistence of the two GluRS enzymes in one organism may lay the groundwork for the acquisition of the canonical glutaminyl-tRNA synthetase by lateral gene transfer from eukaryotes.}, }
@article {pmid14614262, year = {2003}, author = {Matsukawa, N and Ikenaka, K and Nanmoku, K and Yuasa, H and Hattori, M and Kawano, M and Nakazawa, H and Fujimori, O and Ueda, R and Ojika, K}, title = {Brain malformations caused by retroviral vector-mediated gene transfer of hippocampal cholinergic neurostimulating peptide precursor protein into the CNS via embryonic mice ventricles.}, journal = {Developmental neuroscience}, volume = {25}, number = {5}, pages = {349-356}, doi = {10.1159/000073512}, pmid = {14614262}, issn = {0378-5866}, mesh = {Animals ; Blotting, Western ; Brain/*pathology ; Cerebellum/*pathology/virology ; Embryo, Mammalian ; Gene Transfer, Horizontal ; Hippocampus/*pathology/virology ; Immunohistochemistry ; Injections, Intraventricular ; *MAP Kinase Kinase Kinase 1 ; Mice ; Mitogen-Activated Protein Kinases/metabolism ; Nervous System Malformations/*etiology ; Neuropeptides/genetics/*metabolism ; Protein Serine-Threonine Kinases/metabolism ; Pyramidal Cells/pathology/virology ; Retroviridae ; Transduction, Genetic/methods ; }, abstract = {Hippocampal cholinergic neurostimulating peptide precursor protein (HCNP-pp) is a unique multifunctional protein, being not only the precursor of HCNP, which promotes the phenotype development of septo-hippocampal cholinergic neurons, but also the binding protein of phosphatidylethanolamine, ATP, Raf-1 kinase (known as "Raf-1 kinase inhibitory factor" in peripheral organs), and serine protease. We obtained a high-titer retroviral vector harboring HCNP-pp cDNA by the use of a modified packaging cell line and centrifugation, and by injecting it into embryonic mouse ventricles, we investigated the function of its gene product within the central nervous system (CNS). We found that efficient transduction into hippocampal pyramidal neurons can be achieved by injecting the vector into embryonic brain ventricles on embryonic day 14 (E14). Three days after receiving the intraventricular injection of the high-titer HCNP-pp retrovirus vector on E14, the tissues around the ventricles showed an overexpression of HCNP-pp. This was accompanied by a reduced amount of activated MEK and Erk (as analyzed by histochemical and Western blot methods), suggesting that HCNP-pp also regulates the MAP-kinase cascade within the CNS. Surprisingly, mouse brains that received the HCNP-pp retroviral vector showed massive malformation of the hippocampus and cerebellum when examined 30 days after birth. This shows that strictly regulated HCNP-pp gene expression is necessary for the normal development of the mouse brain, and that the moderate overexpression achieved by retroviral vector-mediated gene transfer is sufficient to cause severe abnormality of entire brain structures.}, }
@article {pmid14613661, year = {2003}, author = {Liu, H and Ye, SL}, title = {[Research on functional localization and cloning of metastasis suppressor genes].}, journal = {Ai zheng = Aizheng = Chinese journal of cancer}, volume = {22}, number = {11}, pages = {1237-1240}, pmid = {14613661}, mesh = {Cloning, Molecular ; Gene Transfer, Horizontal ; *Genes, Tumor Suppressor ; Humans ; Liver Neoplasms/genetics ; Male ; Melanoma/genetics ; Neoplasm Metastasis/genetics/*prevention &amp; control ; Prostatic Neoplasms/genetics ; }, abstract = {Metastasis is the most lethal attribute of cancer, which severely affects the effectiveness and prognosis of cancer patients. The discovery of metastasis suppressor genes will provide important clues for the predictive diagnosis and interferential therapies of metastasis. However, there have been few metastasis suppressor genes discovered till now. And this kind of research has not been reported domestically yet. In order to promote this research, this paper reviewed the theoretical principles and technical approaches for the functional localization and cloning strategy for metastasis suppressor genes, which mainly include microcell mediated chromosome transfer, PCR analysis of site tagged sites, and spontaneous metastasis analysis. The metastasis suppressor genes, KAI-1, KiSS-1, MKK4, and BRMS1, discovered by this technique and the application of this technique in prostate cancer, melanoma, and liver cancer are also reviewed.}, }
@article {pmid14613499, year = {2003}, author = {Hannaert, V and Bringaud, F and Opperdoes, FR and Michels, PA}, title = {Evolution of energy metabolism and its compartmentation in Kinetoplastida.}, journal = {Kinetoplastid biology and disease}, volume = {2}, number = {1}, pages = {11}, pmid = {14613499}, issn = {1475-9292}, abstract = {Kinetoplastida are protozoan organisms that probably diverged early in evolution from other eukaryotes. They are characterized by a number of unique features with respect to their energy and carbohydrate metabolism. These organisms possess peculiar peroxisomes, called glycosomes, which play a central role in this metabolism; the organelles harbour enzymes of several catabolic and anabolic routes, including major parts of the glycolytic and pentosephosphate pathways. The kinetoplastid mitochondrion is also unusual with regard to both its structural and functional properties.In this review, we describe the unique compartmentation of metabolism in Kinetoplastida and the metabolic properties resulting from this compartmentation. We discuss the evidence for our recently proposed hypothesis that a common ancestor of Kinetoplastida and Euglenida acquired a photosynthetic alga as an endosymbiont, contrary to the earlier notion that this event occurred at a later stage of evolution, in the Euglenida lineage alone. The endosymbiont was subsequently lost from the kinetoplastid lineage but, during that process, some of its pathways of energy and carbohydrate metabolism were sequestered in the kinetoplastid peroxisomes, which consequently became glycosomes. The evolution of the kinetoplastid glycosomes and the possible selective advantages of these organelles for Kinetoplastida are discussed. We propose that the possession of glycosomes provided metabolic flexibility that has been important for the organisms to adapt easily to changing environmental conditions. It is likely that metabolic flexibility has been an important selective advantage for many kinetoplastid species during their evolution into the highly successful parasites today found in many divergent taxonomic groups.Also addressed is the evolution of the kinetoplastid mitochondrion, from a supposedly pluripotent organelle, attributed to a single endosymbiotic event that resulted in all mitochondria and hydrogenosomes of extant eukaryotes. Furthermore, indications are presented that Kinetoplastida may have acquired other enzymes of energy and carbohydrate metabolism by various lateral gene transfer events different from those that involved the algal- and alpha-proteobacterial-like endosymbionts responsible for the respective formation of the glycosomes and mitochondria.}, }
@article {pmid14607067, year = {2003}, author = {Faruque, SM and Mekalanos, JJ}, title = {Pathogenicity islands and phages in Vibrio cholerae evolution.}, journal = {Trends in microbiology}, volume = {11}, number = {11}, pages = {505-510}, doi = {10.1016/j.tim.2003.09.003}, pmid = {14607067}, issn = {0966-842X}, mesh = {*Biological Evolution ; Cholera Toxin/genetics ; Humans ; Vibrio cholerae/genetics/*pathogenicity/physiology/*virology ; Virulence/*genetics ; }, abstract = {The identification of accessory genetic elements (plasmids, phages and chromosomal 'pathogenicity islands') encoding virulence-associated genes has facilitated our efforts to understand the origination of pathogenic microorganisms. Toxigenic Vibrio cholerae, the etiologic agent of cholera, represents a paradigm for this process in that this organism evolved from environmental nonpathogenic V. cholerae by acquisition of virulence genes. The major virulence genes in V. cholerae, which are clustered in several chromosomal regions, appear to have been recently acquired from phages or through undefined horizontal gene transfer events. Evidence is accumulating that the interactions of phages with each other can also influence the emergence of pathogenic clones of V. cholerae. Therefore, to track the evolution of pathogens from their nonpathogenic progenitors, it is also crucial to identify and characterize secondary genetic elements that mediate lateral transfer of virulence genes in trans. Understanding the evolutionary events that lead to the emergence of pathogenic clones might provide new approaches to the control of cholera and other infectious diseases.}, }
@article {pmid14605141, year = {2003}, author = {Iredell, J and Blanckenberg, D and Arvand, M and Grauling, S and Feil, EJ and Birtles, RJ}, title = {Characterization of the natural population of Bartonella henselae by multilocus sequence typing.}, journal = {Journal of clinical microbiology}, volume = {41}, number = {11}, pages = {5071-5079}, pmid = {14605141}, issn = {0095-1137}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Bartonella henselae/*classification/genetics/isolation &amp; purification ; Base Sequence ; Cat-Scratch Disease/microbiology ; Cats/microbiology ; DNA Primers ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Genetic Variation ; Genotype ; Humans ; Phylogeny ; Polymerase Chain Reaction/methods ; Polymorphism, Genetic/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Restriction Mapping/methods ; Serotyping/methods ; }, abstract = {Investigations of the population genetics of Bartonella henselae have demonstrated a high level of diversity among strains, and the delineation of isolates into one of two subtypes, type I (Houston) and type II (Marseille), represented by specific 16S ribosomal DNA (rDNA) sequences, has long been considered the most significant genotypic division within the species. This belief is challenged by recent work suggesting a role for horizontal gene exchange in generating intraspecies diversity. We attempted to resolve this issue and extend exploration of the population structure of B. henselae by using multilocus sequence typing (MLST) to examine the distribution of polymorphisms within nine different genes in a sample of 37 human and feline isolates. MLST distinguished seven sequence types (STs) that resolved into three distinct lineages, suggesting a clonal population structure for the species, and support for these divisions was obtained by macrorestriction analysis using pulsed-field gel electrophoresis. The distribution of STs among isolates recovered from human infections was not random, and such isolates were significantly more often associated with one particular ST, lending further support to the suggestion that specific genotypes contribute disproportionately to the disease burden in humans. All but one isolate lay on lineages that bore the representative strain of either the Houston or Marseille subtype. However, the distribution of the two 16S rDNA alleles among the isolates was not entirely congruent with their lineage allocations, indicating that this is not a sensitive marker of the clonal divisions within the species. The inheritances of several of the genes studied could not be reconciled with one another, providing further evidence of horizontal gene transfer among B. henselae strains and suggesting that recombination has a role in shaping the genetic character of bartonellae.}, }
@article {pmid14604803, year = {2003}, author = {Nakamura, Y and Nishio, Y and Ikeo, K and Gojobori, T}, title = {The genome stability in Corynebacterium species due to lack of the recombinational repair system.}, journal = {Gene}, volume = {317}, number = {1-2}, pages = {149-155}, doi = {10.1016/s0378-1119(03)00653-x}, pmid = {14604803}, issn = {0378-1119}, mesh = {Corynebacterium/classification/*genetics ; *DNA Repair ; Gene Order ; Genes, Bacterial/genetics ; Genetic Variation ; *Genome, Bacterial ; Mutation ; Mycobacterium/classification/genetics ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Recombination, Genetic/*genetics ; }, abstract = {Corynebacterium species are members of gram-positive bacteria closely related to Mycobacterium species, both of which are classified into the same taxonomic order Actinomycetales. Recently, three corynebacteria, Corynebacterium efficiens, Corynebacterium glutamicum, and Corynebacterium diphtheriae have been sequenced independently. We found that the order of orthologous genes in these species has been highly conserved though it has been disrupted in Mycobacterium species. This synteny suggests that corynebacteria have rarely undergone extensive genome rearrangements and have maintained ancestral genome structures even after the divergence of corynebacteria and mycobacteria. This is the first report that the genome structures have been conserved in free-living bacteria such as C. efficiens and C. glutamicum, although it has been reported that obligate parasites such as Mycoplasma and Chlamydia have the stable genomes. The comparison of recombinational repair systems among the three corynebacteria and Mycobacterium tuberculosis suggested that the absence of recBCD genes in corynebacteria be responsible for the suppression of genome shuffling in the species. The genome stability in Corynebacterium species will give us hints of the speciation mechanism with the non-shuffled genome, particularly the importance of horizontal gene transfer and nucleotide substitution in the genome.}, }
@article {pmid14604787, year = {2003}, author = {Jeltsch, A}, title = {Maintenance of species identity and controlling speciation of bacteria: a new function for restriction/modification systems?.}, journal = {Gene}, volume = {317}, number = {1-2}, pages = {13-16}, doi = {10.1016/s0378-1119(03)00652-8}, pmid = {14604787}, issn = {0378-1119}, mesh = {Bacteria/enzymology/*genetics ; DNA Restriction-Modification Enzymes/*metabolism ; DNA, Bacterial/genetics/metabolism ; Gene Transfer, Horizontal ; Species Specificity ; }, abstract = {Bacteria frequently exchange DNA among each other by horizontal gene transfer. However, maintenance of species identity and in particular speciation requires a certain barrier against an unregulated uptake of foreign DNA. Here it is suggested that formation of such a barrier is one important biological function of restriction/modification systems, in addition to the classical function of protection of bacteria against bacteriophage infection. This model explains the extreme variability and wide distribution of restriction/modification systems among prokaryotes, the prevalence of RM-systems in pathogenic bacteria and the existence of several RM-systems in single bacterial strains.}, }
@article {pmid14604786, year = {2003}, author = {Arber, W}, title = {Elements for a theory of molecular evolution.}, journal = {Gene}, volume = {317}, number = {1-2}, pages = {3-11}, doi = {10.1016/s0378-1119(03)00654-1}, pmid = {14604786}, issn = {0378-1119}, mesh = {*Evolution, Molecular ; Gene Rearrangement ; Genetic Variation/*genetics ; Genome ; Mutation ; }, abstract = {Biological evolution is known to be driven by the availability of genetic variants. Spontaneous genetic variation can be the result of a number of specific molecular mechanisms. These can be grouped into three qualitatively different natural strategies of generating genetic variations, namely local sequence changes, DNA rearrangement within the genome and horizontal gene transfer, which is referred to here as DNA acquisition. All of these strategies bring about alterations in the DNA sequences of the genome, thus corresponding to the molecular genetic definition of the term mutation. A detailed inspection of specific mechanisms of mutagenesis reveals on the one hand the impact of non-genetic internal and environmental factors, and on the other hand the specific involvement of gene products. The underlying so-called evolution genes can be classified into generators of genetic variations and into modulators of the frequency of genetic variation. These evolution genes are postulated to have themselves undergone biological evolution under the pressure of second-order selection. On the basis of a few selected examples of mutagenesis, elements for a theory of molecular evolution are collected without a claim for completeness. Philosophical dimensions as well as practical aspects of the advanced knowledge on specific molecular mechanisms involved in molecular evolution are also briefly discussed.}, }
@article {pmid14604302, year = {2003}, author = {Bhakta, M and Arora, S and Bal, M}, title = {Intraspecies transfer of a chloramphenicol-resistance plasmid of staphylococcal origin.}, journal = {The Indian journal of medical research}, volume = {117}, number = {}, pages = {146-151}, pmid = {14604302}, issn = {0971-5916}, mesh = {Chloramphenicol Resistance/*genetics ; Conjugation, Genetic ; *Gene Transfer, Horizontal ; R Factors/genetics/*metabolism ; Staphylococcus aureus/*genetics ; }, abstract = {BACKGROUND &amp; OBJECTIVES: The emergence of antibiotic-resistant bacteria is a phenomenon of concern to the clinician as well as to the pharmaceutical industry, because it is the major cause of failure in the treatment of infectious diseases. The genetic exchange of plasmids containing antibiotic resistant determinants (R-plasmids) between organisms of the same or different species is believed to play a crucial role in the evolution of antibiotic resistant bacteria. Staphylococcus aureus is well known for its multi-drug resistance (MDR). This work was undertaken to study the intraspecies transfer of a chloramphenicol (C) resistance staphylococcal R-plasmid among different clinical isolates of S. aureus.<br><br>METHODS: From a MDR S. aureus MC524 strain, a small plasmid pMC524/MBM was isolated. Lysostaphin lysis and sucrose mediated detergent lysis were used for plasmid preparation. Agarose gel electrophoresis, transformation experiments, Southern blotting and hybridization were done. Restriction endonuclease (RE) digestions were performed.<br><br>RESULTS: pMC524/MBM, which codes for C resistance could be transferred into some C sensitive clinical strains of S. aureus. The size and the RE digestion patterns of the plasmids isolated from the S. aureus transformants were identical to those of pMC524/MBM.<br><br>These results suggest that pMC524/MBM, without any modification is capable of transferring, maintaining, replicating and expressing itself in different clinical strains of S. aureus and hence may be responsible for the spread of C resistance.}, }
@article {pmid14602600, year = {2003}, author = {Gupta, A and Vlamakis, H and Shoemaker, N and Salyers, AA}, title = {A new Bacteroides conjugative transposon that carries an ermB gene.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {11}, pages = {6455-6463}, pmid = {14602600}, issn = {0099-2240}, support = {R01 AI022383/AI/NIAID NIH HHS/United States ; R56 AI022383/AI/NIAID NIH HHS/United States ; AI22383/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteroides/*genetics ; *Conjugation, Genetic ; *DNA Transposable Elements ; *Gene Transfer, Horizontal ; Humans ; Methyltransferases/*genetics ; Molecular Sequence Data ; Plasmids/genetics ; Sequence Analysis, DNA ; }, abstract = {The erythromycin resistance gene ermB has been found in a variety of gram-positive bacteria. This gene has also been found in Bacteroides species but only in six recently isolated strains; thus, the gene seems to have entered this genus only recently. One of the six Bacteroides ermB-containing isolates, WH207, could transfer ermB to Bacteroides thetaiotaomicron strain BT4001 by conjugation. WH207 was identified as a Bacteroides uniformis strain based on the sequence of its 16S rRNA gene. Results of pulsed-field gel electrophoresis experiments demonstrated that the transferring element was normally integrated into the Bacteroides chromosome. The element was estimated from pulsed-field gel data to be about 100 kb in size. Since the element appeared to be a conjugative transposon (CTn), it was designated CTnBST. CTnBST was able to mobilize coresident plasmids and the circular form of the mobilizable transposon NBU1 to Bacteroides and Escherichia coli recipients. A 13-kb segment that contained ermB was cloned and sequenced. Most of the open reading frames in this region had little similarity at the amino acid sequence level to any proteins in the sequence databases, but a 1,723-bp DNA segment that included a 950-bp segment downstream of ermB had a DNA sequence that was virtually identical to that of a segment of DNA found previously in a Clostridium perfringens strain. This finding, together with the finding that ermB is located on a CTn, supports the hypothesis that CTnBST could have entered Bacteroides from some other genus, possibly from gram-positive bacteria. Moreover, this finding supports the hypothesis that many transmissible antibiotic resistance genes in Bacteroides are carried on CTns.}, }
@article {pmid14600214, year = {2003}, author = {Zhang, R and Zhang, CT}, title = {Identification of genomic islands in the genome of Bacillus cereus by comparative analysis with Bacillus anthracis.}, journal = {Physiological genomics}, volume = {16}, number = {1}, pages = {19-23}, doi = {10.1152/physiolgenomics.00170.2003}, pmid = {14600214}, issn = {1531-2267}, mesh = {Bacillus anthracis/*genetics ; Bacillus cereus/*genetics ; Base Composition ; *Genome, Bacterial ; Genomic Islands/*genetics ; Genomics ; }, abstract = {Horizontal gene transfer has been recognized as a universal event throughout bacterial evolution. The availability of both complete genome sequences of Bacillus cereus and B. anthracis provides the possibility to perform comparative analysis based on their genomes. By using a windowless method to display the distribution of the genomic GC content of B. cereus and B. anthracis, we have found three genomic islands in the genome of B. cereus, i.e., BCGI-1, BCGI-2, and BCGI-3, respectively, which are absent in the genome of B. anthracis. All the genomic islands have abrupt changes in GC content compared with that of surrounding regions. BCGI-1 has many conserved features of genomic islands, e.g., a Val-tRNA gene is utilized as the integration site, and a site-specific recombinase gene is located at the 3' end. BCGI-2 has a large percentage of phage protein, suggesting a phage-related recombination is involved. BCGI-3 contains a ferric anguibactin transport system, which is likely to be involved in the iron transport that enables the bacterium to overcome the iron limitation in the host. In addition, BCGI-3 also contains a cluster of genes related to lantibiotics, which may play a role during the evolution of the genome. Furthermore, the integrations of the genomic islands, BCGI-1 and BCGI-3, result in deletions of DNA sequence fragments; therefore, such integrations lead to both gene gain and gene loss simultaneously.}, }
@article {pmid14595899, year = {2003}, author = {Giovannetti, M}, title = {The ecological risks of transgenic plants.}, journal = {Rivista di biologia}, volume = {96}, number = {2}, pages = {207-223}, pmid = {14595899}, issn = {0035-6050}, mesh = {Biotechnology/methods ; *Ecology ; Gene Transfer, Horizontal ; *Plants, Genetically Modified ; Pollen ; Risk ; Seeds ; }, abstract = {Biotechnologies have been utilized "ante litteram" for thousands of years to produce food and drink and genetic engineering techniques have been widely applied to produce many compounds for human use, from insulin to other medicines. The debate on genetically modified (GM) organisms broke out all over the world only when GM crops were released into the field. Plant ecologists, microbiologists and population geneticists carried out experiments aimed at evaluating the environmental impact of GM crops. The most significant findings concern: the spread of transgenes through GM pollen diffusion and its environmental impact after hybridisation with closely related wild species or subspecies; horizontal gene transfer from transgenic plants to soil microbes; the impact of insecticide proteins released into the soil by transformed plants on non-target microbial soil communities. Recent developments in genetic engineering produced a technology, dubbed "Terminator", which protects patented genes introduced in transgenic plants by killing the seeds in the second generation. This genetic construct, which interferes so heavily with fundamental life processes, is considered dangerous and should be ex-ante evaluated taking into account the data on "unexpected events", as here discussed, instead of relying on the "safe until proven otherwise" claim. Awareness that scientists, biotechnologists and genetic engineers cannot answer the fundamental question "how likely is that transgenes will be transferred from cultivated plants into the natural environment?" should foster long-term studies on the ecological risks and benefits of transgenic crops.}, }
@article {pmid14595556, year = {2003}, author = {Lopez, JV}, title = {Naturally mosaic operons for secondary metabolite biosynthesis: variability and putative horizontal transfer of discrete catalytic domains of the epothilone polyketide synthase locus.}, journal = {Molecular genetics and genomics : MGG}, volume = {270}, number = {5}, pages = {420-431}, pmid = {14595556}, issn = {1617-4615}, mesh = {*Catalytic Domain ; *Gene Transfer, Horizontal ; *Mosaicism ; Multienzyme Complexes/*genetics/metabolism ; *Operon ; Phylogeny ; }, abstract = {A putative instance of horizontal gene transfer (HGT) involving adjacent, discrete beta-ketoacyl synthase (KS), acyl carrier protein (ACP) and nonribosomal peptide synthase (NRPS) domains of the epothilone Type I polyketide biosynthetic gene cluster from the myxobacterium Sorangium cellulosom was identified using molecular phylogenetics and sequence analyses. The specific KS domain of the module EPO B fails to cluster phylogenetically with other epothilone KS sequences present at this locus, in contrast to what is typically observed in many other Type I polyketide synthase (PKS) biosynthetic loci. Furthermore, the GC content of the epoB KS, epoA ACP and NRPS domains differs significantly from the base composition of other epothilone domain sequences. In addition, the putatively transferred epothilone loci are located near previously identified transposon-like sequences. Lastly, comparison with other KS loci revealed another possible case of horizontal transfer of secondary metabolite genes in the genus Pseudomonas. This study emphasizes the use of several lines of concordant evidence (phylogenetics, base composition, transposon sequences) to infer the evolutionary history of particular gene and enzyme sequences, and the results support the idea that genes coding for adaptive traits, e.g. defensive natural products, may be prone to transposition between divergent prokaryotic taxa and genomes.}, }
@article {pmid14594847, year = {2003}, author = {Miyamoto, H and Yoshida, S and Taniguchi, H and Shuman, HA}, title = {Virulence conversion of Legionella pneumophila by conjugal transfer of chromosomal DNA.}, journal = {Journal of bacteriology}, volume = {185}, number = {22}, pages = {6712-6718}, pmid = {14594847}, issn = {0021-9193}, support = {R01 AI023549/AI/NIAID NIH HHS/United States ; AI-23549/AI/NIAID NIH HHS/United States ; }, mesh = {Acanthamoeba/microbiology ; Animals ; Bacterial Proteins/*genetics/metabolism ; Chromosomes, Bacterial ; *Conjugation, Genetic ; *Gene Transfer, Horizontal ; Guinea Pigs ; Humans ; Legionella pneumophila/genetics/growth &amp; development/*pathogenicity ; Legionnaires' Disease/microbiology ; Macrophages, Peritoneal/microbiology ; Virulence/genetics ; }, abstract = {In this study, we examined whether virulence conversion occurs in Legionella pneumophila by conjugal transfer of chromosomal DNA. A virulent strain, K6, which has the genes for Kmr and LacZ+ transposed in the chromosome of strain Philadelphia-1, which belongs to serogroup 1, was used as one parent, and an avirulent strain, Chicago-2S, which is a spontaneous streptomycin-resistant derivative of strain Chicago-2 belonging to serogroup 6, was used as the other parent. Experiments in which K6 (approximately 2.6 x 10(9) CFU) and Chicago-2S (approximately 8.9 x 10(9) CFU) were mated typically yielded 10(3) Kmr Smr LacZ+ transconjugants. Thirty-two (about 2.8%) of 1,152 transconjugants belonging to serogroup 6 acquired the ability to grow intracellularly in Acanthamoeba castellanii and guinea pig macrophages. When guinea pigs were infected with sublethal doses of Legionella aerosols generated from one of these transconjugants (HM1011), they developed a severe pneumonia similar to that caused by donor strain K6. These results show that avirulent strain Chicago-2S changed into virulent strain HM1011 through conjugation with virulent strain K6. Furthermore, we showed that Legionella chromosomal virulence genes (icm-dot locus) were horizontally transferred by the conjugation system. The chromosomal conjugation system may play a role(s) in the evolution of L. pneumophila.}, }
@article {pmid14594724, year = {2003}, author = {Farahi, K and Whitman, WB and Kraemer, ET}, title = {RED-T: utilizing the Ratios of Evolutionary Distances for determination of alternative phylogenetic events.}, journal = {Bioinformatics (Oxford, England)}, volume = {19}, number = {16}, pages = {2152-2154}, doi = {10.1093/bioinformatics/btg284}, pmid = {14594724}, issn = {1367-4803}, mesh = {*Biological Evolution ; Chromosome Mapping/*methods ; *Evolution, Molecular ; Gene Expression Profiling/*methods ; Genetic Linkage/*genetics ; Hypermedia ; Internet ; *Phylogeny ; Sequence Alignment/*methods ; Sequence Analysis, DNA/*methods ; Sequence Homology, Nucleic Acid ; Software ; *User-Computer Interface ; }, abstract = {SUMMARY: RED-T is a Java application for phylogenetic analysis based on a unique method, RED, that utilizes the ratios of evolutionary distances E(d) to distinguish between alternative evolutionary histories. RED-T allows the user to examine if any given experimental gene shares the same evolutionary history as the designated control gene(s). Moreover, the tool detects any differences in evolutionary history and allows the user to examine comparisons of E(d) for a likely explanation. Lateral gene transfer, which may have a significant influence in organismal evolution is one mechanism that could explain the findings of these RED-T analyses.<br><br>AVAILABILITY: The application is available online at http://www.arches.uga.edu/~whitman/RED.}, }
@article {pmid14594704, year = {2003}, author = {Carbone, A and Zinovyev, A and Képès, F}, title = {Codon adaptation index as a measure of dominating codon bias.}, journal = {Bioinformatics (Oxford, England)}, volume = {19}, number = {16}, pages = {2005-2015}, doi = {10.1093/bioinformatics/btg272}, pmid = {14594704}, issn = {1367-4803}, mesh = {Adaptation, Physiological/genetics ; *Algorithms ; Animals ; Bacteria/genetics ; Base Sequence ; Caenorhabditis elegans/genetics ; Codon/*genetics ; Drosophila melanogaster/*genetics ; Gene Expression Profiling/*methods ; Gene Frequency/genetics ; Genetic Variation/*genetics ; Genome ; *Models, Genetic ; Models, Statistical ; Reproducibility of Results ; Saccharomyces cerevisiae/genetics ; Sensitivity and Specificity ; Sequence Alignment/*methods ; Sequence Analysis, DNA/*methods ; }, abstract = {UNLABELLED: We propose a simple algorithm to detect dominating synonymous codon usage bias in genomes. The algorithm is based on a precise mathematical formulation of the problem that lead us to use the Codon Adaptation Index (CAI) as a 'universal' measure of codon bias. This measure has been previously employed in the specific context of translational bias. With the set of coding sequences as a sole source of biological information, the algorithm provides a reference set of genes which is highly representative of the bias. This set can be used to compute the CAI of genes of prokaryotic and eukaryotic organisms, including those whose functional annotation is not yet available. An important application concerns the detection of a reference set characterizing translational bias which is known to correlate to expression levels; in this case, the algorithm becomes a key tool to predict gene expression levels, to guide regulatory circuit reconstruction, and to compare species. The algorithm detects also leading-lagging strands bias, GC-content bias, GC3 bias, and horizontal gene transfer. The approach is validated on 12 slow-growing and fast-growing bacteria, Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster.<br><br>AVAILABILITY: http://www.ihes.fr/~materials.}, }
@article {pmid14593449, year = {2003}, author = {Averhoff, B and Friedrich, A}, title = {Type IV pili-related natural transformation systems: DNA transport in mesophilic and thermophilic bacteria.}, journal = {Archives of microbiology}, volume = {180}, number = {6}, pages = {385-393}, doi = {10.1007/s00203-003-0616-6}, pmid = {14593449}, issn = {0302-8933}, mesh = {Adaptation, Physiological ; Bacteria/*genetics ; *Bacterial Physiological Phenomena ; Bacterial Proteins/genetics/physiology ; Biological Transport ; DNA, Bacterial/genetics/metabolism ; Fimbriae Proteins/genetics/physiology ; Fimbriae, Bacterial/*physiology ; *Gene Transfer, Horizontal ; *Transformation, Bacterial ; }, abstract = {Horizontal gene flow is a driving force for bacterial adaptation. Among the three distinct mechanisms of gene transfer in bacteria, conjugation, transduction, and transformation, the latter, which includes competence induction, DNA binding, and DNA uptake, is perhaps the most versatile mechanism and allows the incorporation of free DNA from diverse bacterial species. Here we review DNA transport machineries mediating uptake of naked DNA in gram-positive and gram-negative bacteria. Different putative models of transformation machineries comprising components similar to proteins of type IV pili are presented. Emphasis is placed on a comparative discussion of the underlying mechanisms of DNA transfer in mesophilic and extremely thermophilic bacteria, highlighting conserved and distinctive features of these transformation machineries.}, }
@article {pmid14592928, year = {2004}, author = {Choi, KH and Osorio, FA and Cheng, PW}, title = {Mucin biosynthesis: bovine C2GnT-M gene, tissue-specific expression, and herpes virus-4 homologue.}, journal = {American journal of respiratory cell and molecular biology}, volume = {30}, number = {5}, pages = {710-719}, doi = {10.1165/rcmb.2003-0202OC}, pmid = {14592928}, issn = {1044-1549}, support = {R01 HL48282/HL/NHLBI NIH HHS/United States ; }, mesh = {5' Untranslated Regions ; Amino Acid Sequence ; Animals ; Base Sequence ; CHO Cells ; Cattle ; Cloning, Molecular ; Cricetinae ; Gene Transfer, Horizontal ; Herpesvirus 4, Bovine/*genetics/metabolism ; Humans ; Molecular Sequence Data ; Mucins/*biosynthesis/*genetics ; N-Acetylglucosaminyltransferases/chemistry/classification/*genetics/*metabolism ; Open Reading Frames ; Phylogeny ; Sequence Alignment ; Tissue Distribution ; }, abstract = {Mucin glycans are the major determinant of mucin functions. Mucin glycan branch structures, which increase structural heterogeneity and thus functional potential, are extended from beta6 N-acetylglucosaminides formed by beta6 N-acetylglucosaminyltransferases (beta6GnT). Core 2 beta6GnT-M (C2GnT-M) is the only branching enzyme that can synthesize all known mucin beta6 N-acetylglucosaminides. We report the cloning of four different bovine (b) C2GnT-M transcripts that are different only at 5'-untranslated regions. Two bC2GnT-M transcripts are found exclusively in tracheal epithelium and testis, whereas the other two are found in all other mucus-secreting tissues. The bC2GnT-M gene contains four exons spanning 5.3 kb, and the entire open reading frame is in one exon. The bC2GnT-M ORF has 95, 83, and 75% sequence identity to those of bovine herpes virus type 4 (BHV-4), human, and rat C2GnT-Ms, respectively. The homology between bovine and BHV-4 C2GnT-M genes is in the region between 170 nucleotides upstream from ATG start codon and 114 nucleotides downstream from TGA stop codon of the viral gene. Localized at the nonconserved region of the viral genome, the BHV-4 C2GnT-M gene is the only known viral C2GnT-M gene. The results suggest that BHV-4 acquired its C2GnT-M gene from the bovine gene. The mechanism of the viral acquisition of bC2GnT-M gene and the roles of the C2GnT-M gene in the survival and pathogenesis of this virus remain to be elucidated.}, }
@article {pmid14585511, year = {2003}, author = {Bapteste, E and Moreira, D and Philippe, H}, title = {Rampant horizontal gene transfer and phospho-donor change in the evolution of the phosphofructokinase.}, journal = {Gene}, volume = {318}, number = {}, pages = {185-191}, doi = {10.1016/s0378-1119(03)00797-2}, pmid = {14585511}, issn = {0378-1119}, mesh = {Animals ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Humans ; Phosphofructokinases/*genetics ; Phylogeny ; }, abstract = {Previous work on the evolution of the phosphofructokinase (PFK) has shown that this key regulatory enzyme of glycolysis has undergone an intricate evolutionary history. Here, we have used a comprehensive data set to address the taxonomic distribution of the different types of PFK (ATP-dependent and PPi-dependent ones) and to estimate the frequency of horizontal gene transfer (HGT) events. Numerous HGT events appear to have occurred. In addition, we focused on the analysis of sites 104 and 124 (usually Gly(104)+Gly(124) or Asp(104)+Lys(124)), known to be involved in catalysis (J. Biol. Chem. 275 (2000) 35677). It revealed the existence of numerous sequences from distantly related species carrying atypical combinations of amino acids. Several adaptive changes of phospho-donors, probably requiring a single mutation at position 104, have likely occurred independently in many lineages. The analysis of this gene suggests the existence of a high rate of both HGT and substitution in its active sites. These rampant HGT events and flexibility in phospho-donor use illustrate the importance of tinkering in molecular evolution.}, }
@article {pmid14576126, year = {2003}, author = {Kawamura, Y and Fujiwara, H and Mishima, N and Tanaka, Y and Tanimoto, A and Ikawa, S and Itoh, Y and Ezaki, T}, title = {First Streptococcus agalactiae isolates highly resistant to quinolones, with point mutations in gyrA and parC.}, journal = {Antimicrobial agents and chemotherapy}, volume = {47}, number = {11}, pages = {3605-3609}, pmid = {14576126}, issn = {0066-4804}, mesh = {Aged ; Amino Acid Sequence ; Amino Acid Substitution ; Anti-Infective Agents/*pharmacology ; DNA Gyrase/*genetics ; DNA Topoisomerase IV/*genetics ; Drug Resistance, Bacterial/genetics ; Female ; Gene Transfer, Horizontal ; Humans ; Infant, Newborn ; Male ; Molecular Sequence Data ; Point Mutation/*genetics ; Quinolones/*pharmacology ; Streptococcal Infections/microbiology ; Streptococcus agalactiae/*drug effects/*genetics ; }, abstract = {Three isolates of Streptococcus agalactiae highly resistant to multiple fluoroquinolones were isolated in Japan. Compared with susceptible strains of S. agalactiae, these quinolone-resistant strains had double point mutations within the quinolone resistance-determining regions of gyrA and parC; Ser-81 was changed to Leu (TCA --> TTA) in the amino acid sequence deduced from gyrA, and Ser-79 was changed to Phe (TCC --> TTC) in the amino acid sequence deduced from parC. Comparative sequence analysis revealed the possibility of gene transfer between S. agalactiae and another beta-hemolytic streptococcus, Streptococcus difficile.}, }
@article {pmid14572543, year = {2003}, author = {Philippe, H and Douady, CJ}, title = {Horizontal gene transfer and phylogenetics.}, journal = {Current opinion in microbiology}, volume = {6}, number = {5}, pages = {498-505}, doi = {10.1016/j.mib.2003.09.008}, pmid = {14572543}, issn = {1369-5274}, mesh = {Bacteria/*genetics ; Gene Transfer, Horizontal/*physiology ; Genes, Bacterial/*genetics ; *Phylogeny ; }, abstract = {The initial analysis of complete genomes has suggested that horizontal gene transfer events are very frequent between microorganisms. This could potentially render the inference, and even the concept itself, of the organismal phylogeny impossible. However, a coherent phylogenetic pattern has recently emerged from an analysis of about a hundred genes, the so-called 'core', strongly suggesting that it is possible to infer the phylogeny of prokaryotes. Also, estimation of the frequency of horizontal gene transfers at the genome level in a phylogenetic context seems to indicate that it is rather low, although of significant biological impact. Nevertheless, it should be emphasized that the history of microorganisms cannot be properly represented by the phylogeny of the core, which represents only a tiny fraction of the genome. This history, even if horizontal gene transfers are rare, should be represented by a network surrounding the core phylogeny.}, }
@article {pmid14568537, year = {2003}, author = {Leipe, DD and Koonin, EV and Aravind, L}, title = {Evolution and classification of P-loop kinases and related proteins.}, journal = {Journal of molecular biology}, volume = {333}, number = {4}, pages = {781-815}, doi = {10.1016/j.jmb.2003.08.040}, pmid = {14568537}, issn = {0022-2836}, mesh = {Amino Acid Sequence ; Animals ; Conserved Sequence ; Evolution, Molecular ; Humans ; Models, Molecular ; Molecular Sequence Data ; Phosphotransferases/chemistry/*classification/*genetics/metabolism ; Phylogeny ; Protein Folding ; Protein Structure, Secondary ; Sequence Alignment ; }, abstract = {Sequences and structures of all P-loop-fold proteins were compared with the aim of reconstructing the principal events in the evolution of P-loop-containing kinases. It is shown that kinases and some related proteins comprise a monophyletic assemblage within the P-loop NTPase fold. An evolutionary classification of these proteins was developed using standard phylogenetic methods, analysis of shared sequence and structural signatures, and similarity-based clustering. This analysis resulted in the identification of approximately 40 distinct protein families within the P-loop kinase class. Most of these enzymes phosphorylate nucleosides and nucleotides, as well as sugars, coenzyme precursors, adenosine 5'-phosphosulfate and polynucleotides. In addition, the class includes sulfotransferases, amide bond ligases, pyrimidine and dihydrofolate reductases, and several other families of enzymes that have acquired new catalytic capabilities distinct from the ancestral kinase reaction. Our reconstruction of the early history of the P-loop NTPase fold includes the initial split into the common ancestor of the kinase and the GTPase classes, and the common ancestor of ATPases. This was followed by the divergence of the kinases, which primarily phosphorylated nucleoside monophosphates (NMP), but could have had broader specificity. We provide evidence for the presence of at least two to four distinct P-loop kinases, including distinct forms specific for dNMP and rNMP, and related enzymes in the last universal common ancestor of all extant life forms. Subsequent evolution of kinases seems to have been dominated by the emergence of new bacterial and, to a lesser extent, archaeal families. Some of these enzymes retained their kinase activity but evolved new substrate specificities, whereas others acquired new activities, such as sulfate transfer and reduction. Eukaryotes appear to have acquired most of their kinases via horizontal gene transfer from Bacteria, partly from the mitochondrial and chloroplast endosymbionts and partly at later stages of evolution. A distinct superfamily of kinases, which we designated DxTN after its sequence signature, appears to have evolved in selfish replicons, such as bacteriophages, and was subsequently widely recruited by eukaryotes for multiple functions related to nucleic acid processing and general metabolism. In the course of this analysis, several previously undetected groups of predicted kinases were identified, including widespread archaeo-eukaryotic and archaeal families. The results could serve as a framework for systematic experimental characterization of new biochemical and biological functions of kinases.}, }
@article {pmid14561705, year = {2003}, author = {Yoshimura, S and Teramoto, T and Whalen, MJ and Irizarry, MC and Takagi, Y and Qiu, J and Harada, J and Waeber, C and Breakefield, XO and Moskowitz, MA}, title = {FGF-2 regulates neurogenesis and degeneration in the dentate gyrus after traumatic brain injury in mice.}, journal = {The Journal of clinical investigation}, volume = {112}, number = {8}, pages = {1202-1210}, pmid = {14561705}, issn = {0021-9738}, support = {5 P50 NS10828/NS/NINDS NIH HHS/United States ; K08 NS041969/NS/NINDS NIH HHS/United States ; P50 NS010828/NS/NINDS NIH HHS/United States ; P01 NS024279/NS/NINDS NIH HHS/United States ; NS24279/NS/NINDS NIH HHS/United States ; KO8 NS41969-02/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; Brain Injuries/*physiopathology ; Bromodeoxyuridine/metabolism ; Cell Differentiation ; Dentate Gyrus/*physiopathology ; Female ; Fibroblast Growth Factor 2/genetics/*physiology ; Gene Transfer, Horizontal ; Hippocampus/metabolism ; Mice ; Mice, Inbred C57BL ; Nerve Degeneration/*etiology ; Neurons/*physiology ; Whole-Body Irradiation ; }, abstract = {We studied the role of FGF-2 on regulation of neurogenesis and cell loss in the granule cell layer (GCL) of the hippocampal dentate gyrus after experimental traumatic brain injury (TBI). In both FGF-2(-/-) and FGF-2(+/+) mice subjected to controlled cortical impact, the number of dividing cells labeled with BrdU, injected on posttrauma days 6 through 8, increased at 9 days after TBI, and the number of BrdU-positive cells colabeled with neuron-specific nuclear antigen significantly increased at 35 days. However, in injured FGF-2-/- mice, BrdU-positive cells and BrdU-positive neurons (days 9, 35) were fewer compared with FGF-2(+/+) mice. There was also a decrease in the volume of the GCL and the number of GCL neurons after TBI in both FGF-2(-/-) and FGF-2(+/+) mice, but the decrease in both was greater in FGF-2-/- mice at 35 days. Overexpression of FGF-2 by intracerebral injection of herpes simplex virus-1 amplicon vectors encoding this factor increased numbers of dividing cells (day 9) and BrdU-positive neurons (day 35) significantly in C57BL/6 mice. Furthermore, the decrease in GCL volume was also attenuated. These results suggest that FGF-2 upregulates neurogenesis and protects neurons against degeneration in the adult hippocampus after TBI, and that FGF-2 supplementation via gene transfer can reduce GCL degeneration after TBI.}, }
@article {pmid14555937, year = {2003}, author = {Harada, N and Iimuro, Y and Nitta, T and Yoshida, M and Uchinami, H and Nishio, T and Hatano, E and Yamamoto, N and Yamamoto, Y and Yamaoka, Y}, title = {Inactivation of the small GTPase Rac1 protects the liver from ischemia/reperfusion injury in the rat.}, journal = {Surgery}, volume = {134}, number = {3}, pages = {480-491}, doi = {10.1067/s0039-6060(03)00256-3}, pmid = {14555937}, issn = {0039-6060}, mesh = {Active Transport, Cell Nucleus ; Adenoviridae/genetics ; Animals ; DNA/metabolism ; Gene Transfer, Horizontal ; Liver/*blood supply ; Male ; Mutation ; NF-kappa B/metabolism ; Rats ; Rats, Sprague-Dawley ; Reactive Oxygen Species ; Reperfusion Injury/*prevention &amp; control ; rac1 GTP-Binding Protein/genetics/*physiology ; }, abstract = {BACKGROUND: In ischemia/reperfusion (I/R) injury, a massive generation of reactive oxygen species (ROS) after reperfusion is a critical factor. Rac, a member of the Rho GTPase superfamily, plays important roles in the production of ROS and activation of nuclear factor-kappaB (NF-kappaB) in vitro. However, the exact role of Rac in the ROS production and NF-kappaB activation in vivo after I/R is still obscure.<br><br>METHODS: We blocked Rac1 activity in the rat liver using adenovirus encoding a dominant negative rac1 mutant (Ad5N17Rac1) and examined whether inactivation of Rac1 could prevent ROS generation in the hepatic I/R injury. Seventy-two hours after the adenoviral infection, hepatic I/R was induced by Pringle's maneuver for 20 minutes, followed by reperfusion in the rats.<br><br>RESULTS: Ad5N17Rac1 infection significantly attenuated ROS production after reperfusion and suppressed the hepatic injury. Furthermore, N17Rac1 suppressed NF-kappaB activation and messenger RNA expression of tumor necrosis factor-alpha (TNF-alpha) and inducible nitric oxide synthetase (iNOS). Ad5LacZ, a control adenovirus, had no effect on the induced hepatic I/R injury, nor did it affect NF-kappaB activation. Immunohistochemical analysis of NF-kappaB (p65) revealed that translocation of p65 to the nucleus after reperfusion was blocked in many of non-parenchymal cells (NPCs) and in hepatocytes in the Ad5N17Rac1-infected liver.<br><br>CONCLUSION: We conclude that Rac1 is required in ROS generation and NF-kappaB activation after hepatic I/R in vivo, and that inactivation of NF-kappaB in NPCs and suppression of ROS generation in NPCs and hepatocytes possibly account for the protective effect of N17Rac1 in this study.}, }
@article {pmid14555490, year = {2003}, author = {Fast, NM and Law, JS and Williams, BA and Keeling, PJ}, title = {Bacterial catalase in the microsporidian Nosema locustae: implications for microsporidian metabolism and genome evolution.}, journal = {Eukaryotic cell}, volume = {2}, number = {5}, pages = {1069-1075}, pmid = {14555490}, issn = {1535-9778}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Bacteria/enzymology/genetics ; Catalase/*genetics ; *Evolution, Molecular ; Gene Library ; Gene Transfer, Horizontal ; *Genome ; Nosema/enzymology/*genetics ; Phylogeny ; Spores, Protozoan/enzymology/genetics ; }, abstract = {Microsporidia constitute a group of extremely specialized intracellular parasites that infect virtually all animals. They are highly derived, reduced fungi that lack several features typical of other eukaryotes, including canonical mitochondria, flagella, and peroxisomes. Consistent with the absence of peroxisomes in microsporidia, the recently completed genome of the microsporidian Encephalitozoon cuniculi lacks a gene for catalase, the major enzymatic marker for the organelle. We show, however, that the genome of the microsporidian Nosema locustae, in contrast to that of E. cuniculi, encodes a group II large-subunit catalase. Surprisingly, phylogenetic analyses indicate that the N. locustae catalase is not specifically related to fungal homologs, as one would expect, but is instead closely related to proteobacterial sequences. This finding indicates that the N. locustae catalase is derived by lateral gene transfer from a bacterium. The catalase gene is adjacent to a large region of the genome that appears to be far less compact than is typical of microsporidian genomes, a characteristic which may make this region more amenable to the insertion of foreign genes. The N. locustae catalase gene is expressed in spores, and the protein is detectable by Western blotting. This type of catalase is a particularly robust enzyme that has been shown to function in dormant cells, indicating that the N. locustae catalase may play some functional role in the spore. There is no evidence that the N. locustae catalase functions in a cryptic peroxisome.}, }
@article {pmid14550940, year = {2003}, author = {Leahy, JG and Batchelor, PJ and Morcomb, SM}, title = {Evolution of the soluble diiron monooxygenases.}, journal = {FEMS microbiology reviews}, volume = {27}, number = {4}, pages = {449-479}, doi = {10.1016/S0168-6445(03)00023-8}, pmid = {14550940}, issn = {0168-6445}, mesh = {Amino Acid Sequence ; *Evolution, Molecular ; Iron/metabolism ; Mixed Function Oxygenases/genetics/metabolism ; Molecular Sequence Data ; Oxygenases/*genetics/metabolism ; Rhodococcus/*genetics ; Solubility ; }, abstract = {Based on structural, biochemical, and genetic data, the soluble diiron monooxygenases can be divided into four groups: the soluble methane monooxygenases, the Amo alkene monooxygenase of Rhodococcus corallinus B-276, the phenol hydroxylases, and the four-component alkene/aromatic monooxygenases. The limited phylogenetic distribution of these enzymes among bacteria, together with available genetic evidence, indicates that they have been spread largely through horizontal gene transfer. Phylogenetic analyses reveal that the alpha- and beta-oxygenase subunits are paralogous proteins and were derived from an ancient gene duplication of a carboxylate-bridged diiron protein, with subsequent divergence yielding a catalytic alpha-oxygenase subunit and a structural beta-oxygenase subunit. The oxidoreductase and ferredoxin components of these enzymes are likely to have been acquired by horizontal transfer from ancestors common to unrelated diiron and Rieske center oxygenases and other enzymes. The cumulative results of phylogenetic reconstructions suggest that the alkene/aromatic monooxygenases diverged first from the last common ancestor for these enzymes, followed by the phenol hydroxylases, Amo alkene monooxygenase, and methane monooxygenases.}, }
@article {pmid14532070, year = {2003}, author = {Kharazmi, M and Sczesny, S and Blaut, M and Hammes, WP and Hertel, C}, title = {Marker rescue studies of the transfer of recombinant DNA to Streptococcus gordonii in vitro, in foods and gnotobiotic rats.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {10}, pages = {6121-6127}, pmid = {14532070}, issn = {0099-2240}, mesh = {Animals ; DNA, Bacterial/*genetics ; DNA, Plant/*genetics ; DNA, Recombinant/genetics ; Female ; Food Microbiology ; Gene Transfer, Horizontal ; *Genetic Markers ; *Germ-Free Life ; Kanamycin Resistance/genetics ; Male ; Plants, Genetically Modified/*genetics ; Plasmids ; Rats ; Rats, Inbred F344 ; Solanum tuberosum/genetics ; Streptococcus/*genetics ; *Transformation, Bacterial ; }, abstract = {A plasmid marker rescue system based on restoration of the nptII gene was established in Streptococcus gordonii to study the transfer of bacterial and transgenic plant DNA by transformation. In vitro studies revealed that the marker rescue efficiency depends on the type of donor DNA. Plasmid and chromosomal DNA of bacteria as well as DNA of transgenic potatoes were transferred with efficiencies ranging from 8.1 x 10(-6) to 5.8 x 10(-7) transformants per nptII gene. Using a 792-bp amplification product of nptII the efficiency was strongly decreased (9.8 x 10(-9)). In blood sausage, marker rescue using plasmid DNA was detectable (7.9 x 10(-10)), whereas in milk heat-inactivated horse serum (HHS) had to be added to obtain an efficiency of 2.7 x 10(-11). No marker rescue was detected in extracts of transgenic potatoes despite addition of HHS. In vivo transformation of S. gordonii LTH 5597 was studied in monoassociated rats by using plasmid DNA. No marker rescue could be detected in vivo, although transformation was detected in the presence of saliva and fecal samples supplemented with HHS. It was also shown that plasmid DNA persists in rat saliva permitting transformation for up to 6 h of incubation. It is suggested that the lack of marker rescue is due to the absence of competence-stimulating factors such as serum proteins in rat saliva.}, }
@article {pmid14532060, year = {2003}, author = {Coleman, NV and Spain, JC}, title = {Distribution of the coenzyme M pathway of epoxide metabolism among ethene- and vinyl chloride-degrading Mycobacterium strains.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {10}, pages = {6041-6046}, pmid = {14532060}, issn = {0099-2240}, mesh = {Biodegradation, Environmental ; Blotting, Southern ; Carbon-Sulfur Lyases/genetics/*metabolism ; Culture Media ; DNA, Bacterial/analysis ; Electrophoresis, Gel, Pulsed-Field ; Environmental Microbiology ; Epoxy Compounds/*metabolism ; Ethylenes/*metabolism ; Genes, rRNA ; Molecular Sequence Data ; Mycobacterium/classification/*enzymology/genetics/growth &amp; development ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Vinyl Chloride/*metabolism ; }, abstract = {An epoxyalkane:coenzyme M (CoM) transferase (EaCoMT) enzyme was recently found to be active in the aerobic vinyl chloride (VC) and ethene assimilation pathways of Mycobacterium strain JS60. In the present study, EaCoMT activity and genes were investigated in 10 different mycobacteria isolated on VC or ethene from diverse environmental samples. In all cases, epoxyethane metabolism in cell extracts was dependent on CoM, with average specific activities of EaCoMT between 380 and 2,910 nmol/min/mg of protein. PCR with primers based on conserved regions of EaCoMT genes from Mycobacterium strain JS60 and the propene oxidizers Xanthobacter strain Py2 and Rhodococcus strain B-276 yielded fragments (834 bp) of EaCoMT genes from all of the VC- and ethene-assimilating isolates. The Mycobacterium EaCoMT genes form a distinct cluster and are more closely related to the EaCoMT of Rhodococcus strain B-276 than that of Xanthobacter strain Py2. The incongruence of the EaCoMT and 16S rRNA gene trees and the fact that isolates from geographically distant locations possessed almost identical EaCoMT genes suggest that lateral transfer of EaCoMT among the Mycobacterium strains has occurred. Pulsed-field gel electrophoresis revealed large linear plasmids (110 to 330 kb) in all of the VC-degrading strains. In Southern blotting experiments, the strain JS60 EaCoMT gene hybridized to many of the plasmids. The CoM-mediated pathway of epoxide metabolism appears to be universal in alkene-assimilating mycobacteria, possibly because of plasmid-mediated lateral gene transfer.}, }
@article {pmid14530132, year = {2003}, author = {Suchard, MA and Kitchen, CM and Sinsheimer, JS and Weiss, RE}, title = {Hierarchical phylogenetic models for analyzing multipartite sequence data.}, journal = {Systematic biology}, volume = {52}, number = {5}, pages = {649-664}, doi = {10.1080/10635150390238879}, pmid = {14530132}, issn = {1063-5157}, support = {AI28697/AI/NIAID NIH HHS/United States ; CA16042/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics ; *Bayes Theorem ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Guinea Pigs ; HIV/genetics ; Humans ; Mammals/genetics ; *Models, Theoretical ; *Phylogeny ; Receptors, CCR5/genetics ; }, abstract = {Debate exists over how to incorporate information from multipartite sequence data in phylogenetic analyses. Strict combined-data approaches argue for concatenation of all partitions and estimation of one evolutionary history, maximizing the explanatory power of the data. Consensus/independence approaches endorse a two-step procedure where partitions are analyzed independently and then a consensus is determined from the multiple results. Mixtures across the model space of a strict combined-data approach and a priori independent parameters are popular methods to integrate these methods. We propose an alternative middle ground by constructing a Bayesian hierarchical phylogenetic model. Our hierarchical framework enables researchers to pool information across data partitions to improve estimate precision in individual partitions while permitting estimation and testing of tendencies in across-partition quantities. Such across-partition quantities include the distribution from which individual topologies relating the sequences within a partition are drawn. We propose standard hierarchical priors on continuous evolutionary parameters across partitions, while the structure on topologies varies depending on the research problem. We illustrate our model with three examples. We first explore the evolutionary history of the guinea pig (Cavia porcellus) using alignments of 13 mitochondrial genes. The hierarchical model returns substantially more precise continuous parameter estimates than an independent parameter approach without losing the salient features of the data. Second, we analyze the frequency of horizontal gene transfer using 50 prokaryotic genes. We assume an unknown species-level topology and allow individual gene topologies to differ from this with a small estimable probability. Simultaneously inferring the species and individual gene topologies returns a transfer frequency of 17%. We also examine HIV sequences longitudinally sampled from HIV+ patients. We ask whether posttreatment development of CCR5 coreceptor virus represents concerted evolution from middisease CXCR4 virus or reemergence of initial infecting CCR5 virus. The hierarchical model pools partitions from multiple unrelated patients by assuming that the topology for each patient is drawn from a multinomial distribution with unknown probabilities. Preliminary results suggest evolution and not reemergence.}, }
@article {pmid14527288, year = {2003}, author = {Caporale, LH}, title = {Natural selection and the emergence of a mutation phenotype: an update of the evolutionary synthesis considering mechanisms that affect genome variation.}, journal = {Annual review of microbiology}, volume = {57}, number = {}, pages = {467-485}, doi = {10.1146/annurev.micro.57.030502.090855}, pmid = {14527288}, issn = {0066-4227}, mesh = {Bacteria/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genetic Code/genetics ; Genetic Variation/*genetics ; *Genome, Bacterial ; Mutation ; Phenotype ; *Selection, Genetic ; }, abstract = {Most descriptions of evolution assume that all mutations are completely random with respect to their potential effects on survival. However, much like other phenotypic variations that affect the survival of the descendants, intrinsic variations in the probability, type, and location of genetic change can feel the pressure of natural selection. From site-specific recombination to changes in polymerase fidelity and repair of DNA damage, an organism's gene products affect what genetic changes occur in its genome. Through the action of natural selection on these gene products, potentially favorable mutations can become more probable than random. With examples from variation in bacterial surface proteins to the vertebrate immune response, it is clear that a great deal of genetic change is better than "random" with respect to its potential effect on survival. Indeed, some potentially useful mutations are so probable that they can be viewed as being encoded implicitly in the genome. An updated evolutionary theory includes emergence, under selective pressure, of genomic information that affects the probability of different classes of mutation, with consequences for genome survival.}, }
@article {pmid14527286, year = {2003}, author = {Lawrence, JG}, title = {Gene organization: selection, selfishness, and serendipity.}, journal = {Annual review of microbiology}, volume = {57}, number = {}, pages = {419-440}, doi = {10.1146/annurev.micro.57.030502.090816}, pmid = {14527286}, issn = {0066-4227}, mesh = {Animals ; Bacteria/*genetics ; Chromosomes, Bacterial ; Gene Expression Regulation, Bacterial ; Gene Order/*genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Models, Genetic ; Nematoda/genetics ; Operon/genetics ; Selection, Genetic ; }, abstract = {The apparati behind the replication, transcription, and translation of prokaryotic and eukaryotic genes are quite different. Yet in both classes of organisms, genes may be organized in their respective chromosomes in similar ways by virtue of similarly acting selective forces. In addition, some gene organizations reflect biology unique to each class of organisms. Levels of organization are more complex than those of the simple operon. Multiple transcription units may be organized into larger units, local control regions may act over large chromosomal regions in eukaryotic chromosomes, and cis-acting genes may control the expression of downstream genes in all classes of organisms. All these mechanisms lead to genomes being far more organized, in both prokaryotes and eukaryotes, than hitherto imagined.}, }
@article {pmid14512557, year = {2003}, author = {Fontana, L and Nuzzo, M and Urbanelli, L and Monaci, P}, title = {General strategy for broadening adenovirus tropism.}, journal = {Journal of virology}, volume = {77}, number = {20}, pages = {11094-11104}, pmid = {14512557}, issn = {0022-538X}, mesh = {3T3 Cells ; Adenoviridae/*physiology ; Animals ; Bacteriophage lambda/genetics ; CHO Cells ; Capsid Proteins/*physiology ; Coxsackie and Adenovirus Receptor-Like Membrane Protein ; Cricetinae ; Dendritic Cells/physiology ; Gene Transfer, Horizontal ; Genetic Vectors ; Humans ; Mice ; Peptide Library ; Receptors, Virus/metabolism ; Transduction, Genetic ; Tropism ; }, abstract = {In spite of its broad host range, adenovirus type 5 (Ad5) transduces a number of clinically relevant tissues and cell types inefficiently, mostly because of low expression of the coxsackievirus-adenovirus receptor (CAR). To improve gene transfer to such cells, we modified the Ad5 fiber knob to recognize novel receptors. We expressed a functional Ad5 fiber knob domain on the capsid of phage lambda and employed this display system to construct a large collection of ligands in the HI loop of the Ad5 knob. Panning this library on the CAR-negative mouse fibroblast cell line NIH 3T3 resulted in the identification of three clones with increased binding to these cells. Adenoviruses incorporating these ligands in the fiber gene transduced NIH 3T3 cells 2 or 3 orders of magnitude better than the parent vector. The same nonnative tropism was revealed in other cell types, independently of CAR expression. These Ad5 derivatives proved capable of transducing mouse and human primary immature dendritic cells with up to 100-fold increased efficiency.}, }
@article {pmid14508680, year = {2003}, author = {Gupta, PK and Rustgi, S and Sharma, S and Singh, R and Kumar, N and Balyan, HS}, title = {Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat.}, journal = {Molecular genetics and genomics : MGG}, volume = {270}, number = {4}, pages = {315-323}, pmid = {14508680}, issn = {1617-4615}, mesh = {Bread ; Cluster Analysis ; DNA Mutational Analysis ; *Expressed Sequence Tags ; Gene Transfer, Horizontal ; Genes, Plant ; Genetic Markers ; Genetic Variation ; Genotype ; Methods ; *Polymorphism, Genetic ; *Tandem Repeat Sequences ; Triticum/*genetics ; }, abstract = {Nearly 900 SSRs (simple sequence repeats) were identified among 15,000 ESTs (expressed sequence tags) belonging to bread wheat (Triticum aestivumL.). The SSRs were defined by their minimum length, which ranged from 14 to 21 bp. The maximum length ranged from 24 to 87 bp depending upon the length of the repeat unit itself (1-7 bp). The average density of SSRs was one SSR per 9.2 kb of EST sequence screened. The trinucleotide repeats were the most abundant SSRs detected. As a representative sample, 78 primer pairs were designed, which were also used to screen the dbEST entries for Hordeum vulgare and Triticum tauschii (donor of the D-genome of cultivated wheat) using a cut-off E (expectation) value of 0.01. On the basis of in silico analysis, up to 55.12% of the primer pairs exhibited transferability from Triticum to Hordeum, indicating that the sequences flanking the SSRs are not only conserved within a single genus but also between related genera in Poaceae. Primer pairs for the 78 SSRs were synthesized and used successfully for the study of (1) their transferability to 18 related wild species and five cereal species (barley, oat, rye, rice and maize); and (2) polymorphism between the parents of four mapping populations available with us. A subset of 20 EST-SSR primers was also used to assess genetic diversity in a collection of 52 elite exotic wheat genotypes. This was done with a view to compare their utility relative to other molecular markers (gSSRs, AFLPs, and SAMPL) previously used by us for the same purpose with the same set of 52 bread wheat genotypes. Although only a low level of polymorphism was detected, relative to that observed with genomic SSRs, the study suggested that EST-SSRs can be successfully used for a variety of purposes, and may actually prove superior to SSR markers extracted from genomic libraries for diversity estimation and transferability.}, }
@article {pmid14506860, year = {2003}, author = {Sørensen, SJ and Sørensen, AH and Hansen, LH and Oregaard, G and Veal, D}, title = {Direct detection and quantification of horizontal gene transfer by using flow cytometry and gfp as a reporter gene.}, journal = {Current microbiology}, volume = {47}, number = {2}, pages = {129-133}, doi = {10.1007/s00284-002-3978-0}, pmid = {14506860}, issn = {0343-8651}, mesh = {Colony Count, Microbial ; Conjugation, Genetic ; Escherichia coli/*genetics/growth &amp; development ; Flow Cytometry/*methods ; *Gene Transfer, Horizontal ; *Genes, Reporter ; Green Fluorescent Proteins ; Luminescent Proteins/*genetics/metabolism ; Plasmids ; Pseudomonas putida/*genetics/growth &amp; development ; }, abstract = {A new cultivation-independent method for studying conjugal gene transfer between bacteria was evaluated. The method was based on direct detection and enumeration of donor and transconjugant bacterial cells by flow cytometry. Specific detection of transconjugants was obtained by using a conjugative plasmid tagged with a reporter gene (gfp) encoding green fluorescent protein. A chromosomal encoded repressor (lacI(ql)) repressed expression of GFP in the donor bacteria. Enumeration of the donor cells was performed after induction of GFP expression by the addition of inducer isopropyl-thio-beta-D-galactoside (IPTG). The method presented here provided simple and precise quantification of horizontal gene transfer between both Escherichia coli and Pseudomonas putida strains.}, }
@article {pmid14506786, year = {2003}, author = {Toni, TD and Recordon-Pinson, P and Minga, A and Ekouevi, D and Bonard, D and Bequet, L and Huet, C and Chenal, H and Rouet, F and Dabis, F and Lafon, ME and Salamon, R and Masquelier, B and Fleury, HJ}, title = {Presence of key drug resistance mutations in isolates from untreated patients of Abidjan, Côte d'Ivoire: ANRS 1257 study.}, journal = {AIDS research and human retroviruses}, volume = {19}, number = {8}, pages = {713-717}, doi = {10.1089/088922203322280946}, pmid = {14506786}, issn = {0889-2229}, mesh = {Adult ; Anti-HIV Agents/pharmacology ; Cote d'Ivoire/epidemiology ; DNA, Viral/analysis ; Drug Resistance, Viral/*genetics ; Female ; Gene Transfer, Horizontal ; Genetics, Population ; HIV Infections/drug therapy ; HIV Protease/*genetics ; HIV Reverse Transcriptase/*genetics ; HIV-1/classification/drug effects/*genetics/isolation &amp; purification ; Humans ; Male ; Microbial Sensitivity Tests ; Mutation ; }, abstract = {A total of 107 HIV-1 isolates from untreated adult patients recruited in Abidjan, CMte d'Ivoire, in 2001 and 2002 were sequenced in the env, reverse transcriptase (RT), and protease genes. The results show that CRF02_AG is still predominant in this west African population; key mutations of resistance to antiretroviral drugs (NRTI, NNRTI, and PIs) were detected in 5.6% of the patients. We hypothesize that these resistant mutants have been acquired through horizontal transmission. Compared to a previous study carried out by our group in 1997-2000 in a similar population of Abidjan, it seems that there is a dynamic process of resistance and that a survey will be necessary.}, }
@article {pmid14500908, year = {2003}, author = {Baar, C and Eppinger, M and Raddatz, G and Simon, J and Lanz, C and Klimmek, O and Nandakumar, R and Gross, R and Rosinus, A and Keller, H and Jagtap, P and Linke, B and Meyer, F and Lederer, H and Schuster, SC}, title = {Complete genome sequence and analysis of Wolinella succinogenes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {100}, number = {20}, pages = {11690-11695}, pmid = {14500908}, issn = {0027-8424}, mesh = {Bacterial Proteins/metabolism ; *Genome, Bacterial ; Glycosylation ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Signal Transduction ; Virulence/genetics ; Wolinella/*genetics/metabolism/pathogenicity ; }, abstract = {To understand the origin and emergence of pathogenic bacteria, knowledge of the genetic inventory from their nonpathogenic relatives is a prerequisite. Therefore, the 2.11-megabase genome sequence of Wolinella succinogenes, which is closely related to the pathogenic bacteria Helicobacter pylori and Campylobacter jejuni, was determined. Despite being considered nonpathogenic to its bovine host, W. succinogenes holds an extensive repertoire of genes homologous to known bacterial virulence factors. Many of these genes have been acquired by lateral gene transfer, because part of the virulence plasmid pVir and an N-linked glycosylation gene cluster were found to be syntenic between C. jejuni and genomic islands of W. succinogenes. In contrast to other host-adapted bacteria, W. succinogenes does harbor the highest density of bacterial sensor kinases found in any bacterial genome to date, together with an elaborate signaling circuitry of the GGDEF family of proteins. Because the analysis of the W. succinogenes genome also revealed genes related to soil- and plant-associated bacteria such as the nif genes, W. succinogenes may represent a member of the epsilon proteobacteria with a life cycle outside its host.}, }
@article {pmid14500481, year = {2003}, author = {Bury-Moné, S and Skouloubris, S and Dauga, C and Thiberge, JM and Dailidiene, D and Berg, DE and Labigne, A and De Reuse, H}, title = {Presence of active aliphatic amidases in Helicobacter species able to colonize the stomach.}, journal = {Infection and immunity}, volume = {71}, number = {10}, pages = {5613-5622}, pmid = {14500481}, issn = {0019-9567}, support = {AI 38166/AI/NIAID NIH HHS/United States ; DK 53727/DK/NIDDK NIH HHS/United States ; }, mesh = {Amidohydrolases/genetics/*metabolism ; Animals ; Base Sequence ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; Female ; Genes, Bacterial ; Helicobacter/*enzymology/genetics/*pathogenicity ; Helicobacter pylori/enzymology/genetics/pathogenicity ; Humans ; Mice ; Mutagenesis, Insertional ; Mutation ; Phylogeny ; Species Specificity ; Stomach/microbiology ; Virulence/genetics/physiology ; }, abstract = {Ammonia production is of great importance for the gastric pathogen Helicobacter pylori as a nitrogen source, as a compound protecting against gastric acidity, and as a cytotoxic molecule. In addition to urease, H. pylori possesses two aliphatic amidases responsible for ammonia production: AmiE, a classical amidase, and AmiF, a new type of formamidase. Both enzymes are part of a regulatory network consisting of nitrogen metabolism enzymes, including urease and arginase. We examined the role of the H. pylori amidases in vivo by testing the gastric colonization of mice with H. pylori SS1 strains carrying mutations in amiE and/or amiF and in coinfection experiments with wild-type and double mutant strains. A new cassette conferring resistance to gentamicin was used in addition to the kanamycin cassette to construct the double mutation in strain SS1. Our data indicate that the amidases are not essential for colonization of mice. The search for amiE and amiF genes in 53 H. pylori strains from different geographic origins indicated the presence of both genes in all these genomes. We tested for the presence of the amiE and amiF genes and for amidase and formamidase activities in eleven Helicobacter species. Among the gastric species, H. acinonychis possessed both amiE and amiF, H. felis carried only amiF, and H. mustelae was devoid of amidases. H. muridarum, which can colonize both mouse intestine and stomach, was the only enterohepatic species to contain amiE. Phylogenetic trees based upon the sequences of H. pylori amiE and amiF genes and their respective homologs from other organisms as well as the amidase gene distribution among Helicobacter species are strongly suggestive of amidase acquisition by horizontal gene transfer. Since amidases are found only in Helicobacter species able to colonize the stomach, their acquisition might be related to selective pressure in this particular gastric environment.}, }
@article {pmid13679020, year = {2003}, author = {Woo, PC and To, AP and Lau, SK and Yuen, KY}, title = {Facilitation of horizontal transfer of antimicrobial resistance by transformation of antibiotic-induced cell-wall-deficient bacteria.}, journal = {Medical hypotheses}, volume = {61}, number = {4}, pages = {503-508}, doi = {10.1016/s0306-9877(03)00205-6}, pmid = {13679020}, issn = {0306-9877}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects ; Cell Wall/*physiology ; *Drug Resistance, Bacterial ; *Drug Resistance, Microbial ; Gene Transfer, Horizontal ; Models, Theoretical ; Mutation ; }, abstract = {It is universally accepted that the use of antibiotics will lead to antimicrobial resistance. Traditionally, the explanation to this phenomenon was random mutation and horizontal gene transfer and amplification by selective pressure. Subsequently, a second mechanism of antibiotic-induced antimicrobial resistance acquisition was proposed, when Davies et al. discovered that genes encoding antimicrobial resistance are present in bacteria that produce antibiotics, and during the process of antibiotic purification from these antibiotic-producing organisms, remnants of the organisms' DNA that contain antibiotic resistance genes are also co-extracted, and can be recovered in antibiotic preparations. In addition to selective pressure and antimicrobial resistance genes in antibiotic preparations, we hypothesize the third mechanism by which administration of antibiotics leads to antimicrobial resistance. beta-Lactams and glycopeptides damage bacteria by inhibiting cell wall murein synthesis. During the process, cell-wall-deficient forms are generated before the bacteria die. These cell-wall-deficient forms have an increased ability to uptake DNA by transformation. It has been demonstrated that plasmids encoding antimicrobial resistance of Staphylococcus aureus can be transformed to Bacillus subtilis after the B. subtilis was treated with penicillin or lysostaphin, a chemical that damage the cell walls of some Gram-positive bacteria; and that short treatment of Escherichia coli with antibiotics disturbing bacterial cell wall synthesis rendered the cells capable of absorbing foreign DNA. Since bacteria occupying the same ecological niche, such as the lower gastrointestinal tract, is common, bacteria are often incubated with foreign DNA encoding resistance coming from the administration of antibiotics or other bacteria that undergone lysis unrelated to antibiotic-induced killing. As few as a single antibiotic resistant gene is taken up by the cell-wall-deficient form, it will develop into a resistant clone, despite most of the other bacteria are killed by the antibiotic. If the hypothesis is correct, one should reduce the use of antibiotics that perturb bacterial cell wall synthesis, such as beta-lactams, which is the largest group being manufactured, in both humans and animals, in order to reduce the acquisition of antibiotic resistance through this mechanism. In contrast to the old theory that antibiotics only provide selective pressures for the development of antimicrobial resistance, antibiotics by themselves are able to generate the whole chain of events towards the development of antimicrobial resistance. Antibiotics provide a source of antimicrobial resistance genes, facilitate the horizontal transfer of antimicrobial resistance genes through facilitating transformation, and provide selective pressures for amplification of the antimicrobial resistance genes. That is perhaps an important reason why antimicrobial resistance is so difficult to control. Further experiments should be performed to delineate which particular type of beta-lactam antibiotics are associated with increase in transformation efficiencies more than the others, so that we can select those less resistance generating beta-lactam for routine usage.}, }
@article {pmid13678895, year = {2003}, author = {Watts, T}, title = {Genetically modified crops in developing countries.}, journal = {Lancet (London, England)}, volume = {362}, number = {9386}, pages = {835}, doi = {10.1016/S0140-6736(03)14266-3}, pmid = {13678895}, issn = {1474-547X}, mesh = {Africa ; Agriculture/economics/*trends ; *Developing Countries ; Ecosystem ; Food, Genetically Modified/*standards ; Gene Transfer, Horizontal ; Humans ; Zea mays/genetics/growth &amp; development ; }, }
@article {pmid13678641, year = {2003}, author = {Bird, DM and Opperman, CH and Davies, KG}, title = {Interactions between bacteria and plant-parasitic nematodes: now and then.}, journal = {International journal for parasitology}, volume = {33}, number = {11}, pages = {1269-1276}, doi = {10.1016/s0020-7519(03)00160-7}, pmid = {13678641}, issn = {0020-7519}, mesh = {Animals ; Bacillus/genetics/physiology ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genes, Helminth ; Life Cycle Stages ; Plants/parasitology ; Rhizobiaceae/*genetics/physiology ; Synteny ; Tylenchoidea/*genetics/parasitology/physiology ; }, abstract = {Based on genome-to-genome analyses of gene sequences obtained from plant-parasitic, root-knot nematodes (Meloidogyne spp.), it seems likely that certain genes have been derived from bacteria by horizontal gene transfer. Strikingly, a common theme underpinning the function of these genes is their apparent direct relationship to the nematodes' parasitic lifestyle. Phylogenetic analyses implicate rhizobacteria as the predominant group of 'gene donor' bacteria. Root-knot nematodes and rhizobia occupy similar niches in the soil and in roots, and thus the opportunity for genetic exchange may be omnipresent. Further, both organisms establish intimate developmental interactions with host plants, and mounting evidence suggests that the mechanisms for these interactions are shared too. We propose that the origin of parasitism in Meloidogyne may have been facilitated by acquisition of genetic material from soil bacteria through horizontal transfer, and that such events represented key steps in speciation of plant-parasitic nematodes. To further understand the mechanisms of horizontal gene transfer, and also to provide experimental tools to manipulate this promising bio-control agent, we have initiated a genomic sequence of the bacterial hyper-parasite of plant parasitic nematodes, Pasteuria penetrans. Initial data have established that P. penetrans is closely related to Bacillus spp., to the extent that considerable genome synteny is apparent. Hence, Bacillus serves as a model for Pasteuria, and vice versa.}, }
@article {pmid12975657, year = {2003}, author = {Lerat, E and Daubin, V and Moran, NA}, title = {From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria.}, journal = {PLoS biology}, volume = {1}, number = {1}, pages = {E19}, pmid = {12975657}, issn = {1545-7885}, mesh = {Bacteria ; Computational Biology/*methods ; Evolution, Molecular ; Gammaproteobacteria/*genetics ; Gene Expression Regulation, Bacterial ; Gene Transfer Techniques ; Gene Transfer, Horizontal ; Genome ; Genome, Bacterial ; *Models, Genetic ; Multigene Family ; Phylogeny ; Prokaryotic Cells ; }, abstract = {The rapid increase in published genomic sequences for bacteria presents the first opportunity to reconstruct evolutionary events on the scale of entire genomes. However, extensive lateral gene transfer (LGT) may thwart this goal by preventing the establishment of organismal relationships based on individual gene phylogenies. The group for which cases of LGT are most frequently documented and for which the greatest density of complete genome sequences is available is the gamma-Proteobacteria, an ecologically diverse and ancient group including free-living species as well as pathogens and intracellular symbionts of plants and animals. We propose an approach to multigene phylogeny using complete genomes and apply it to the case of the gamma-Proteobacteria. We first applied stringent criteria to identify a set of likely gene orthologs and then tested the compatibilities of the resulting protein alignments with several phylogenetic hypotheses. Our results demonstrate phylogenetic concordance among virtually all (203 of 205) of the selected gene families, with each of the exceptions consistent with a single LGT event. The concatenated sequences of the concordant families yield a fully resolved phylogeny. This topology also received strong support in analyses aimed at excluding effects of heterogeneity in nucleotide base composition across lineages. Our analysis indicates that single-copy orthologous genes are resistant to horizontal transfer, even in ancient bacterial groups subject to high rates of LGT. This gene set can be identified and used to yield robust hypotheses for organismal phylogenies, thus establishing a foundation for reconstructing the evolutionary transitions, such as gene transfer, that underlie diversity in genome content and organization.}, }
@article {pmid12974984, year = {2003}, author = {Zhaxybayeva, O and Gogarten, JP}, title = {An improved probability mapping approach to assess genome mosaicism.}, journal = {BMC genomics}, volume = {4}, number = {1}, pages = {37}, pmid = {12974984}, issn = {1471-2164}, mesh = {Bacterial Proteins/classification/genetics ; Cyanobacteria/genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomics/*methods ; Likelihood Functions ; *Mosaicism ; Phylogeny ; Probability ; Reproducibility of Results ; Sequence Homology ; }, abstract = {BACKGROUND: Maximum likelihood and posterior probability mapping are useful visualization techniques that are used to ascertain the mosaic nature of prokaryotic genomes. However, posterior probabilities, especially when calculated for four-taxon cases, tend to overestimate the support for tree topologies. Furthermore, because of poor taxon sampling four-taxon analyses suffer from sensitivity to the long branch attraction artifact. Here we extend the probability mapping approach by improving taxon sampling of the analyzed datasets, and by using bootstrap support values, a more conservative tool to assess reliability.<br><br>RESULTS: Quartets of orthologous proteins were complemented with homologs from selected reference genomes. The mapping of bootstrap support values from these extended datasets gives results similar to the original maximum likelihood and posterior probability mapping. The more conservative nature of the plotted support values allows to focus further analyses on those protein families that strongly disagree with the majority or plurality of genes present in the analyzed genomes.<br><br>CONCLUSION: Posterior probability is a non-conservative measure for support, and posterior probability mapping only provides a quick estimation of phylogenetic information content of four genomes. This approach can be utilized as a pre-screen to select genes that might have been horizontally transferred. Better taxon sampling combined with subtree analyses prevents the inconsistencies associated with four-taxon analyses, but retains the power of visual representation. Nevertheless, a case-by-case inspection of individual multi-taxon phylogenies remains necessary to differentiate unrecognized paralogy and shared phylogenetic reconstruction artifacts from horizontal gene transfer events.}, }
@article {pmid12966138, year = {2003}, author = {Xie, G and Keyhani, NO and Bonner, CA and Jensen, RA}, title = {Ancient origin of the tryptophan operon and the dynamics of evolutionary change.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {67}, number = {3}, pages = {303-42, table of contents}, pmid = {12966138}, issn = {1092-2172}, support = {Y1-A1-8228-05//PHS HHS/United States ; }, mesh = {*Evolution, Molecular ; Genome, Archaeal ; Genome, Bacterial ; Models, Genetic ; Operon/*genetics ; Phylogeny ; Tryptophan/biosynthesis/*genetics ; }, abstract = {The seven conserved enzymatic domains required for tryptophan (Trp) biosynthesis are encoded in seven genetic regions that are organized differently (whole-pathway operons, multiple partial-pathway operons, and dispersed genes) in prokaryotes. A comparative bioinformatics evaluation of the conservation and organization of the genes of Trp biosynthesis in prokaryotic operons should serve as an excellent model for assessing the feasibility of predicting the evolutionary histories of genes and operons associated with other biochemical pathways. These comparisons should provide a better understanding of possible explanations for differences in operon organization in different organisms at a genomics level. These analyses may also permit identification of some of the prevailing forces that dictated specific gene rearrangements during the course of evolution. Operons concerned with Trp biosynthesis in prokaryotes have been in a dynamic state of flux. Analysis of closely related organisms among the Bacteria at various phylogenetic nodes reveals many examples of operon scission, gene dispersal, gene fusion, gene scrambling, and gene loss from which the direction of evolutionary events can be deduced. Two milestone evolutionary events have been mapped to the 16S rRNA tree of Bacteria, one splitting the operon in two, and the other rejoining it by gene fusion. The Archaea, though less resolved due to a lesser genome representation, appear to exhibit more gene scrambling than the Bacteria. The trp operon appears to have been an ancient innovation; it was already present in the common ancestor of Bacteria and Archaea. Although the operon has been subjected, even in recent times, to dynamic changes in gene rearrangement, the ancestral gene order can be deduced with confidence. The evolutionary history of the genes of the pathway is discernible in rough outline as a vertical line of descent, with events of lateral gene transfer or paralogy enriching the analysis as interesting features that can be distinguished. As additional genomes are thoroughly analyzed, an increasingly refined resolution of the sequential evolutionary steps is clearly possible. These comparisons suggest that present-day trp operons that possess finely tuned regulatory features are under strong positive selection and are able to resist the disruptive evolutionary events that may be experienced by simpler, poorly regulated operons.}, }
@article {pmid12963817, year = {2003}, author = {Won, H and Renner, SS}, title = {Horizontal gene transfer from flowering plants to Gnetum.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {100}, number = {19}, pages = {10824-10829}, pmid = {12963817}, issn = {0027-8424}, mesh = {Base Sequence ; Exons ; *Gene Transfer, Horizontal ; Gnetum/*genetics ; Introns ; Magnoliopsida/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Nucleic Acid ; }, abstract = {Although horizontal gene transfer is well documented in microbial genomes, no case has been reported in higher plants. We discovered horizontal transfer of the mitochondrial nad1 intron 2 and adjacent exons b and c from an asterid to Gnetum (Gnetales, gymnosperms). Gnetum has two copies of intron 2, a group II intron, that differ in their exons, nucleotide composition, domain lengths, and structural characteristics. One of the copies, limited to an Asian clade of Gnetum, is almost identical to the homologous locus in angiosperms, and partial sequences of its exons b and c show characteristic substitutions unique to angiosperms. Analyses of 70 seed plant nad1 exons b and c and intron 2 sequences, including representatives of all angiosperm clades, support that this copy originated from a euasterid and was horizontally transferred to Gnetum. Molecular clock dating, using calibrations provided by gnetalean macrofossils, suggests an age of 5 to 2 million years for the Asian clade that received the horizontal transfer.}, }
@article {pmid12955583, year = {2003}, author = {Montesinos, E}, title = {Development, registration and commercialization of microbial pesticides for plant protection.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {6}, number = {4}, pages = {245-252}, doi = {10.1007/s10123-003-0144-x}, pmid = {12955583}, issn = {1139-6709}, mesh = {Animals ; Bacteria/drug effects/*pathogenicity ; Commerce ; Fungicides, Industrial/toxicity ; Herbicides/toxicity ; Humans ; Insecticides/toxicity ; Pesticides/economics/*toxicity ; Plant Diseases/*microbiology ; Plants/drug effects/*microbiology ; Spain ; }, abstract = {Plant protection against pathogens, pests and weeds has been progressively reoriented from a therapeutic approach to a rational use of pesticide chemicals in which consumer health and environmental preservation prevail over any other productive or economic considerations. Microbial pesticides are being introduced in this new scenario of crop protection and currently several beneficial microorganisms are the active ingredients of a new generation of microbial pesticides or the basis for many natural products of microbial origin. The development of a microbial pesticide requires several steps addressed to its isolation in pure culture and screening by means of efficacy bioassays performed in vitro, ex vivo, in vivo, or in pilot trials under real conditions of application (field, greenhouse, post-harvest). For the commercial delivery of a microbial pesticide, the biocontrol agent must be produced at an industrial scale (fermentation), preserved for storage and formulated by means of biocompatible additives to increase survival and to improve the application and stability of the final product. Despite the relative high number of patents for biopesticides, only a few of them have materialized in a register for agricultural use. The excessive specificity in most cases and biosafety or environmental concerns in others are major limiting factors. Non-target effects may be possible in particular cases, such as displacement of beneficial microorganisms, allergenicity, toxinogencity (production of secondary metabolites toxic to plants, animals, or humans), pathogenicity (to plants or animals) by the agent itself or due to contaminants, or horizontal gene transfer of these characteristics to non-target microorganisms. However, these non-target effects should not be evaluated in an absolute manner, but relative to chemical control or the absence of any control of the target disease (for example, toxins derived from the pathogen). Consumer concerns about live microbes due to emerging food-borne diseases and bioterrorism do not help to create a socially receptive environment to microbial pesticides. The future of microbial pesticides is not only in developing new active ingredients based on microorganisms beneficial to plants, but in producing self-protected plants (so-called plant-incorporated pesticides) by transforming agronomically high-value crop plants with genes from biological control agents.}, }
@article {pmid12952640, year = {2003}, author = {Lo, N and Watanabe, H and Sugimura, M}, title = {Evidence for the presence of a cellulase gene in the last common ancestor of bilaterian animals.}, journal = {Proceedings. Biological sciences}, volume = {270 Suppl 1}, number = {Suppl 1}, pages = {S69-72}, pmid = {12952640}, issn = {0962-8452}, mesh = {Amino Acid Sequence ; Animals ; Bacteria/classification/enzymology/genetics ; Cellulase/*genetics ; Coleoptera/classification/enzymology/genetics ; Databases, Nucleic Acid ; *Evolution, Molecular ; Fungi/classification/enzymology/genetics ; Molecular Sequence Data ; Nematoda/classification/enzymology/genetics ; *Phylogeny ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {Until recently, the textbook view of cellulose hydrolysis in animals was that gut-resident symbiotic organisms such as bacteria or unicellular eukaryotes are responsible for the cellulases produced. This view has been challenged by the characterization and sequencing of endogenous cellulase genes from some invertebrate animals, including plant-parasitic nematodes, arthropods and a mollusc. Most of these genes are completely unrelated in terms of sequence, and their evolutionary origins remain unclear. In the case of plant-parasitic nematodes, it has been suggested that their ancestor obtained a cellulase gene via horizontal gene transfer from a prokaryote, and similar suggestions have been made about a cellulase gene recently discovered in a sea squirt. To improve understanding about the evolution of animal cellulases, we searched for all known types of these enzymes in GenBank, and performed phylogenetic comparisons. Low phylogenetic resolution was found among most of the sequences examined, however, positional identity in the introns of cellulase genes from a termite, a sea squirt and an abalone provided compelling evidence that a similar gene was present in the last common ancestor of protostomes and deuterostomes. In a different enzyme family, cellulases from beetles and plant-parasitic nematodes were found to cluster together. This result questions the idea of lateral gene transfer into the ancestors of the latter, although statistical tests did not allow this possibility to be ruled out. Overall, our results suggest that at least one family of endogenous cellulases may be more widespread in animals than previously thought.}, }
@article {pmid12952536, year = {2003}, author = {Daubin, V and Lerat, E and Perrière, G}, title = {The source of laterally transferred genes in bacterial genomes.}, journal = {Genome biology}, volume = {4}, number = {9}, pages = {R57}, pmid = {12952536}, issn = {1474-760X}, mesh = {Arginine/genetics ; Bacteria/*genetics ; Base Composition ; Codon/genetics ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; *Genome, Bacterial ; Isoleucine/genetics ; Phylogeny ; Selection, Genetic ; }, abstract = {BACKGROUND: Laterally transferred genes have often been identified on the basis of compositional features that distinguish them from ancestral genes in the genome. These genes are usually A+T-rich, arguing either that there is a bias towards acquiring genes from donor organisms having low G+C contents or that genes acquired from organisms of similar genomic base compositions go undetected in these analyses.<br><br>RESULTS: By examining the genome contents of closely related, fully sequenced bacteria, we uncovered genes confined to a single genome and examined the sequence features of these acquired genes. The analysis shows that few transfer events are overlooked by compositional analyses. Most observed lateral gene transfers do not correspond to free exchange of regular genes among bacterial genomes, but more probably represent the constituents of phages or other selfish elements.<br><br>CONCLUSIONS: Although bacteria tend to acquire large amounts of DNA, the origin of these genes remains obscure. We have shown that contrary to what is often supposed, their composition cannot be explained by a previous genomic context. In contrast, these genes fit the description of recently described genes in lambdoid phages, named 'morons'. Therefore, results from genome content and compositional approaches to detect lateral transfers should not be cited as evidence for genetic exchange between distantly related bacteria.}, }
@article {pmid12952534, year = {2003}, author = {Omelchenko, MV and Makarova, KS and Wolf, YI and Rogozin, IB and Koonin, EV}, title = {Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ.}, journal = {Genome biology}, volume = {4}, number = {9}, pages = {R55}, pmid = {12952534}, issn = {1474-760X}, mesh = {Alkyl and Aryl Transferases/genetics ; Archaea/classification/*genetics/metabolism ; Bacteria/classification/*genetics/metabolism ; Bacterial Proteins/genetics ; Deinococcus/genetics/metabolism ; Electron Transport Complex I/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Archaeal/genetics ; Genes, Bacterial/genetics ; Genome, Archaeal ; Genome, Bacterial ; Halobacterium/genetics/metabolism ; Isoleucine/biosynthesis ; Leucine/biosynthesis ; Lipids/biosynthesis ; Lipopolysaccharides/biosynthesis ; Methanobacteriaceae/genetics/metabolism ; Mycoplasma/genetics ; Operon/*genetics ; *Phylogeny ; Protein Subunits/genetics ; Ribosomal Proteins/genetics ; Rickettsia/genetics/metabolism ; }, abstract = {BACKGROUND: Shuffling and disruption of operons and horizontal gene transfer are major contributions to the new, dynamic view of prokaryotic evolution. Under the 'selfish operon' hypothesis, operons are viewed as mobile genetic entities that are constantly disseminated via horizontal gene transfer, although their retention could be favored by the advantage of coregulation of functionally linked genes. Here we apply comparative genomics and phylogenetic analysis to examine horizontal transfer of entire operons versus displacement of individual genes within operons by horizontally acquired orthologs and independent assembly of the same or similar operons from genes with different phylogenetic affinities.<br><br>RESULTS: Since a substantial number of operons have been identified experimentally in only a few model bacteria, evolutionarily conserved gene strings were analyzed as surrogates of operons. The phylogenetic affinities within these predicted operons were assessed first by sequence similarity analysis and then by phylogenetic analysis, including statistical tests of tree topology. Numerous cases of apparent horizontal transfer of entire operons were detected. However, it was shown that apparent horizontal transfer of individual genes or arrays of genes within operons is not uncommon either and results in xenologous gene displacement in situ, that is, displacement of an ancestral gene by a horizontally transferred ortholog from a taxonomically distant organism without change of the local gene organization. On rarer occasions, operons might have evolved via independent assembly, in part from horizontally acquired genes.<br><br>CONCLUSIONS: The discovery of in situ gene displacement shows that combination of rampant horizontal gene transfer with selection for preservation of operon structure provides for events in prokaryotic evolution that, a priori, seem improbable. These findings also emphasize that not all aspects of operon evolution are selfish, with operon integrity maintained by purifying selection at the organism level.}, }
@article {pmid12949700, year = {2003}, author = {Seo, PS and Yokota, A}, title = {The phylogenetic relationships of cyanobacteria inferred from 16S rRNA, gyrB, rpoC1 and rpoD1 gene sequences.}, journal = {The Journal of general and applied microbiology}, volume = {49}, number = {3}, pages = {191-203}, doi = {10.2323/jgam.49.191}, pmid = {12949700}, issn = {0022-1260}, mesh = {Amino Acid Sequence ; Base Sequence ; Cyanobacteria/enzymology/*genetics ; DNA Gyrase/chemistry/*genetics ; DNA, Bacterial/chemistry/genetics ; DNA-Directed RNA Polymerases/chemistry/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/chemistry/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Sigma Factor/chemistry/*genetics ; }, abstract = {Phylogenetic analysis of cyanobacteria was carried out using the small subunit rRNA (16S rRNA), DNA gyrase subunit B (gyrB), DNA-dependent RNA polymerase gamma subunit (rpoC1) and a principal sigma factor of E. coli sigma(70) type for DNA-dependent RNA polymerase (rpoD1) gene sequences of 24 strains which contained 5 subgroups of cyanobacteria-3 strains of the Chroococcales, 5 strains of the Pluerocapsales, 7 strains of the Oscillatoriales, 7 strains of the Nostocales and 2 strains of the Stigonematales. Degenerated PCR primers of gyrB, rpoC1 and rpoD1 genes were designed using consensus amino acid sequences registered in GenBank. The phylogenetic positions of cyanobacteria were resolved through phylogenetic analysis based on 16S rDNA, gyrB, rpoC1 and rpoD1 gene sequences. Phylogenies of gyrB, rpoC1 and rpoD1 support 16S rRNA-based classification of cyanobacteria. Interestingly, phylogenies from amino acid sequences deduced from gyrB and combined amino acid sequences deduced from rpoC1 and rpoD1 genes strongly support that of 16S rRNA, but the branching pattens of the trees based on 16S rDNA, GyrB, rpoC1, rpoD1 and combined amino acid sequences deduced from rpoC1 and rpoD1 were not congruent. In this study, we showed the correlation among phylogenetic relationships of 16S rDNA, gyrB, rpoC1 and rpoD1 genes. The phylogenetic trees based on the sequences of 16S rDNA, GyrB, rpoC1, rpoD1 and the combined amino acid sequences deduced from rpoC1 and rpoD1 showed that the lateral gene transfer of rRNA might be suspected for Synechocystis sp. PCC 6803.}, }
@article {pmid12949177, year = {2003}, author = {Salmassi, TM and Leadbetter, JR}, title = {Analysis of genes of tetrahydrofolate-dependent metabolism from cultivated spirochaetes and the gut community of the termite Zootermopsis angusticollis.}, journal = {Microbiology (Reading, England)}, volume = {149}, number = {Pt 9}, pages = {2529-2537}, doi = {10.1099/mic.0.26351-0}, pmid = {12949177}, issn = {1350-0872}, mesh = {Animals ; DNA Primers ; DNA, Bacterial/genetics ; Formate-Tetrahydrofolate Ligase/*metabolism ; *Genes, Bacterial ; Isoptera/classification/*microbiology ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Spirochaetaceae/classification/*genetics/isolation &amp; purification ; Stomach/microbiology ; Tetrahydrofolates/*metabolism ; }, abstract = {The hindguts of wood-feeding termites are the sites of intense, CO2-reductive acetogenesis. This activity profoundly influences host nutrition and methane emissions. Homoacetogens previously isolated from diverse termites comprised novel taxa belonging to two distinct bacterial phyla, Firmicutes and Spirochates. Little else is known about either the diversity or abundance of homoacetogenic species present in any given termite or the genetic details underlying CO2-reductive acetogenesis by Spirochaetes. A key enzyme of CO2-reductive acetogenesis is formyltetrahydrofolate synthetase (FTHFS). A previously designed primer set was used to amplify FTHFS genes from three isolated termite-gut spirochaetes. Sequencing DNA flanking the FTHFS gene of Treponema strain ZAS-2 revealed genes encoding two acetogenesis-related enzymes, methenyltetrahydrofolate cyclohydrolase and methylenetetrahydrofolate dehydrogenase. Although termite-gut spirochaetes are only distantly related to clostridia at the ribosomal level, their tetrahydrofolate-dependent enzymes appear to be closely related. In contrast, homologous proteins identified in the non-homoacetogenic oral spirochaete Treponema denticola were only distantly related to those from clostridia and the termite-gut treponemes. Having demonstrated their utility with spirochaete pure cultures, the FTHFS primers were used to construct a 91-clone library from the termite-gut community DNA. From this, 19 DNA and eight amino acid FTHFS types were identified. Over 75 % of the retrieved clones formed a novel, coherent cluster with the FTHFS homologues obtained from the termite-gut treponemes. Thus, FTHFS gene diversity in the gut of the termite Zootermopsis angusticollis appears to be dominated by spirochaetes. The homoacetogenic capacity of termite-gut spirochaetes may have been acquired via lateral gene transfer from clostridia.}, }
@article {pmid12949172, year = {2003}, author = {Li, Q and Hobbs, M and Reeves, PR}, title = {The variation of dTDP-L-rhamnose pathway genes in Vibrio cholerae.}, journal = {Microbiology (Reading, England)}, volume = {149}, number = {Pt 9}, pages = {2463-2474}, doi = {10.1099/mic.0.26382-0}, pmid = {12949172}, issn = {1350-0872}, mesh = {Amino Acid Sequence ; Bacterial Proteins/*genetics/metabolism ; Base Sequence ; Gene Transfer, Horizontal ; *Genetic Variation ; Molecular Sequence Data ; Nucleoside Diphosphate Sugars/*metabolism ; O Antigens/genetics ; Phylogeny ; Sequence Homology ; Thymine Nucleotides/*metabolism ; Vibrio cholerae/*genetics/metabolism ; }, abstract = {The genetic variation in the dTDP-L-rhamnose pathway genes (rmlA, rmlB, rmlC and rmlD) in Vibrio cholerae was investigated. The genes are part of the O antigen gene cluster and the aim was to study lateral gene transfer of O antigen gene clusters. The rml genes of an O6 strain were cloned using an Escherichia coli K-12 strain designed for selecting cloned rml genes. Thirty-three strains carrying the known rhamnose-containing O antigens were probed with O6-based rml gene probes, and 19 were positive with from one to all four of the gene probes. Nine rml gene sets from this group were sequenced and found to be in the order rmlBADC, at the 5' end of the gene clusters. A gradient in the level of variation was observed, with highly similar sequences at the 5' end rmlB gene, but very divergent and strain-specific sequences at the 3' end of the rml gene set. The change in level of similarity varied in position, but was always abrupt and coincided with a change in GC content, indicating that the 5' and 3' parts are of different origin, and that recombination within rml genes has occurred. The rml gene sets of two of the strains that did not hybridize with any O6 rml gene probes were also cloned and sequenced. Both gene sets were in the middle of the O antigen gene cluster and were very divergent from each other and all other rml gene sets. This supports the hypothesis that presence of rml genes at the end of the O antigen gene cluster facilitates lateral gene transfer of rml-containing O antigen gene clusters in V. cholerae. The sequence relationships make it possible to identify sites of recombination and to distinguish DNA that has long been in V. cholerae and DNA that probably came into the species with the O antigen gene cluster.}, }
@article {pmid12949130, year = {2004}, author = {Daubin, V and Ochman, H}, title = {Quartet mapping and the extent of lateral transfer in bacterial genomes.}, journal = {Molecular biology and evolution}, volume = {21}, number = {1}, pages = {86-89}, doi = {10.1093/molbev/msg234}, pmid = {12949130}, issn = {0737-4038}, mesh = {Bacteria/*genetics ; Classification/*methods ; Gene Transfer, Horizontal/*genetics ; *Genome, Bacterial ; Likelihood Functions ; *Phylogeny ; }, abstract = {Several recent analyses have used quartet-based methods to assess the congruence among phylogenies derived for large sets of genes from prokaryotic genomes. The principal conclusion from these studies is that lateral gene transfer (LGT) has blurred prokaryotic phylogenies to such a degree that the darwinian scheme of treelike evolution might be abandoned in favor of a net or web. Here, we focus on one of these methods, quartet mapping, and show that its application can lead to overestimation of the extent of inferred LGT in prokaryotes, particularly when applied to distantly related taxa.}, }
@article {pmid12949098, year = {2003}, author = {Katayama, Y and Zhang, HZ and Hong, D and Chambers, HF}, title = {Jumping the barrier to beta-lactam resistance in Staphylococcus aureus.}, journal = {Journal of bacteriology}, volume = {185}, number = {18}, pages = {5465-5472}, pmid = {12949098}, issn = {0021-9193}, support = {R01 AI046610/AI/NIAID NIH HHS/United States ; AI46610/AI/NIAID NIH HHS/United States ; }, mesh = {*Bacterial Proteins ; Carrier Proteins/genetics ; Chromosomes, Bacterial ; DNA Transposable Elements ; Gene Transfer, Horizontal ; Genes, Regulator ; Methicillin Resistance/genetics ; Mutation ; *Penicillin-Binding Proteins ; Phenotype ; Plasmids/genetics ; Staphylococcus aureus/genetics/*physiology ; Transformation, Bacterial/genetics ; beta-Lactam Resistance/genetics/*physiology ; beta-Lactamases/genetics/metabolism ; }, abstract = {Although the staphylococcal methicillin resistance determinant, mecA, resides on a mobile genetic element, staphylococcus cassette chromosome mec (SCCmec), its distribution in nature is limited to as few as five clusters of related methicillin-resistant Staphylococcus aureus (MRSA) clones. To investigate the potential role of the host chromosome in clonal restriction of the methicillin resistance determinant, we constructed plasmid pYK20, carrying intact mecA, and introduced it into several methicillin-susceptible Staphylococcus aureus strains, five of which were naive hosts (i.e., mecA not previously resident on the host chromosome) and five of which were experienced hosts (i.e., methicillin-susceptible variants of MRSA strains from which SCCmec was excised). We next assessed the effect of the recipient background on the methicillin resistance phenotype by population analysis, by assaying the mecA expression of PBP2a by Western blot analysis, and by screening for mutations affecting mecA. Each experienced host transformed with pYK20 had a resistance phenotype and expressed PBP2a similar to that of the parent with chromosomal SCCmec, but naive hosts transformed with pYK20 selected against its expression, indicative of a host barrier. Either inducible beta-lactamase regulatory genes blaR1-blaI or homologous regulatory genes mecR1-mecI, which control mecA expression, acted as compensatory elements, permitting the maintenance and expression of plasmid-carried mecA.}, }
@article {pmid12948626, year = {2003}, author = {Kalinowski, J and Bathe, B and Bartels, D and Bischoff, N and Bott, M and Burkovski, A and Dusch, N and Eggeling, L and Eikmanns, BJ and Gaigalat, L and Goesmann, A and Hartmann, M and Huthmacher, K and Krämer, R and Linke, B and McHardy, AC and Meyer, F and Möckel, B and Pfefferle, W and Pühler, A and Rey, DA and Rückert, C and Rupp, O and Sahm, H and Wendisch, VF and Wiegräbe, I and Tauch, A}, title = {The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins.}, journal = {Journal of biotechnology}, volume = {104}, number = {1-3}, pages = {5-25}, doi = {10.1016/s0168-1656(03)00154-8}, pmid = {12948626}, issn = {0168-1656}, mesh = {Amino Acid Sequence ; Amino Acids/*biosynthesis/genetics ; Aspartic Acid/genetics/*metabolism ; Base Sequence ; Corynebacterium/classification/*genetics/*metabolism ; Databases, Genetic ; Gene Expression Profiling ; *Genome, Bacterial ; Molecular Sequence Data ; Multienzyme Complexes/genetics/metabolism ; Proteome/*genetics/*metabolism ; Recombinant Proteins/biosynthesis ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Vitamins/*biosynthesis/genetics ; }, abstract = {The complete genomic sequence of Corynebacterium glutamicum ATCC 13032, well-known in industry for the production of amino acids, e.g. of L-glutamate and L-lysine was determined. The C. glutamicum genome was found to consist of a single circular chromosome comprising 3282708 base pairs. Several DNA regions of unusual composition were identified that were potentially acquired by horizontal gene transfer, e.g. a segment of DNA from C. diphtheriae and a prophage-containing region. After automated and manual annotation, 3002 protein-coding genes have been identified, and to 2489 of these, functions were assigned by homologies to known proteins. These analyses confirm the taxonomic position of C. glutamicum as related to Mycobacteria and show a broad metabolic diversity as expected for a bacterium living in the soil. As an example for biotechnological application the complete genome sequence was used to reconstruct the metabolic flow of carbon into a number of industrially important products derived from the amino acid L-aspartate.}, }
@article {pmid12944965, year = {2003}, author = {Sullivan, MB and Waterbury, JB and Chisholm, SW}, title = {Cyanophages infecting the oceanic cyanobacterium Prochlorococcus.}, journal = {Nature}, volume = {424}, number = {6952}, pages = {1047-1051}, doi = {10.1038/nature01929}, pmid = {12944965}, issn = {1476-4687}, mesh = {Adaptation, Physiological/radiation effects ; Bacteriophages/genetics/*isolation &amp; purification/*physiology ; Cyanobacteria/physiology/radiation effects/*virology ; Environment ; Gene Transfer, Horizontal ; Host-Parasite Interactions ; Light ; Lysogeny ; Oceans and Seas ; Species Specificity ; }, abstract = {Prochlorococcus is the numerically dominant phototroph in the tropical and subtropical oceans, accounting for half of the photosynthetic biomass in some areas. Here we report the isolation of cyanophages that infect Prochlorococcus, and show that although some are host-strain-specific, others cross-infect with closely related marine Synechococcus as well as between high-light- and low-light-adapted Prochlorococcus isolates, suggesting a mechanism for horizontal gene transfer. High-light-adapted Prochlorococcus hosts yielded Podoviridae exclusively, which were extremely host-specific, whereas low-light-adapted Prochlorococcus and all strains of Synechococcus yielded primarily Myoviridae, which has a broad host range. Finally, both Prochlorococcus and Synechococcus strain-specific cyanophage titres were low (< 10(3) ml(-1)) in stratified oligotrophic waters even where total cyanobacterial abundances were high (> 10(5) cells x ml(-1)). These low titres in areas of high total host cell abundance seem to be a feature of open ocean ecosystems. We hypothesize that gradients in cyanobacterial population diversity, growth rates, and/or the incidence of lysogeny underlie these trends.}, }
@article {pmid12942641, year = {2003}, author = {V'iugin, VV and Gel'fand, MS and Liubetskiĭ, VA}, title = {[Identification of the horizontal gene transfer based on phylogenetic data].}, journal = {Molekuliarnaia biologiia}, volume = {37}, number = {4}, pages = {674-687}, pmid = {12942641}, issn = {0026-8984}, mesh = {*Algorithms ; Archaeoglobus fulgidus/genetics ; Buchnera/genetics ; Deinococcus ; Escherichia coli/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Halobacterium/genetics ; *Models, Genetic ; *Phylogeny ; }, abstract = {We suggest a new procedure to search for the genes with horizontal transfer events in their evolutionary history. The search is based on analysis of topology difference between the phylogenetic trees of gene (protein) groups and the corresponding phylogenetic species trees. Numeric values are introduced to measure the discrepancy between the trees. This approach was applied to analyze 40 prokaryotic genomes classified into 132 classes of orthologs. This resulted in a list of the candidate genes for which the hypothesis of horizontal transfer in evolution looks true.}, }
@article {pmid12941888, year = {2003}, author = {Tani, H and Limn, CK and Yap, CC and Onishi, M and Nozaki, M and Nishimune, Y and Okahashi, N and Kitagawa, Y and Watanabe, R and Mochizuki, R and Moriishi, K and Matsuura, Y}, title = {In vitro and in vivo gene delivery by recombinant baculoviruses.}, journal = {Journal of virology}, volume = {77}, number = {18}, pages = {9799-9808}, pmid = {12941888}, issn = {0022-538X}, mesh = {Animals ; Baculoviridae/*genetics ; Benzamidines ; Brain/metabolism ; Cell Line ; *Gene Transfer, Horizontal ; *Genetic Therapy ; Guanidines/pharmacology ; Humans ; Mice ; Rats ; Recombination, Genetic ; Transduction, Genetic ; }, abstract = {Although recombinant baculovirus vectors can be an efficient tool for gene transfer into mammalian cells in vitro, gene transduction in vivo has been hampered by the inactivation of baculoviruses by serum complement. Recombinant baculoviruses possessing excess envelope protein gp64 or other viral envelope proteins on the virion surface deliver foreign genes into a variety of mammalian cell lines more efficiently than the unmodified baculovirus. In this study, we examined the efficiency of gene transfer both in vitro and in vivo by recombinant baculoviruses possessing envelope proteins derived from either vesicular stomatitis virus (VSVG) or rabies virus. These recombinant viruses efficiently transferred reporter genes into neural cell lines, primary rat neural cells, and primary mouse osteal cells in vitro. The VSVG-modified baculovirus exhibited greater resistance to inactivation by animal sera than the unmodified baculovirus. A synthetic inhibitor of the complement activation pathway circumvented the serum inactivation of the unmodified baculovirus. Furthermore, the VSVG-modified baculovirus could transduce a reporter gene into the cerebral cortex and testis of mice by direct inoculation in vivo. These results suggest the possible use of the recombinant baculovirus vectors in combination with the administration of complement inhibitors for in vivo gene therapy.}, }
@article {pmid12941415, year = {2003}, author = {Canchaya, C and Fournous, G and Chibani-Chennoufi, S and Dillmann, ML and Brüssow, H}, title = {Phage as agents of lateral gene transfer.}, journal = {Current opinion in microbiology}, volume = {6}, number = {4}, pages = {417-424}, doi = {10.1016/s1369-5274(03)00086-9}, pmid = {12941415}, issn = {1369-5274}, mesh = {Bacteria/genetics/*virology ; Bacteriophages/*genetics/growth &amp; development ; Gene Transfer, Horizontal/*physiology ; Prophages/genetics/growth &amp; development ; }, abstract = {When establishing lysogeny, temperate phages integrate their genome as a prophage into the bacterial chromosome. Prophages thus constitute in many bacteria a substantial part of laterally acquired DNA. Some prophages contribute lysogenic conversion genes that are of selective advantage to the bacterial host. Occasionally, phages are also involved in the lateral transfer of other mobile DNA elements or bacterial DNA. Recent advances in the field of genomics have revealed a major impact by phages on bacterial chromosome evolution.}, }
@article {pmid12941390, year = {2003}, author = {Porwollik, S and McClelland, M}, title = {Lateral gene transfer in Salmonella.}, journal = {Microbes and infection}, volume = {5}, number = {11}, pages = {977-989}, doi = {10.1016/s1286-4579(03)00186-2}, pmid = {12941390}, issn = {1286-4579}, support = {AI34829/AI/NIAID NIH HHS/United States ; }, mesh = {*Gene Transfer, Horizontal ; Genetic Variation ; *Genome, Bacterial ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; Salmonella/classification/*genetics ; Serotyping ; }, abstract = {Comparative genomics and microarrays reveal that the genomes of different Salmonella enterica serovars are distinguished from each other by the presence or absence of hundreds of genes. The distribution of these variable genome regions is often not clonal. Therefore, lateral gene transfer (LGT) plays an important role in diversity among Salmonella. Overall, almost one quarter of the entire S. enterica sv Typhimurium genome may have been introduced by LGT.}, }
@article {pmid12936987, year = {2003}, author = {Fomenko, DE and Metlitskaya, AZ and Péduzzi, J and Goulard, C and Katrukha, GS and Gening, LV and Rebuffat, S and Khmel, IA}, title = {Microcin C51 plasmid genes: possible source of horizontal gene transfer.}, journal = {Antimicrobial agents and chemotherapy}, volume = {47}, number = {9}, pages = {2868-2874}, pmid = {12936987}, issn = {0066-4804}, mesh = {Bacteriocins/*genetics ; Culture Media ; DNA, Bacterial/genetics ; Escherichia coli/genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/*genetics ; Operon/genetics ; Plasmids/*genetics ; }, abstract = {Microcin C51 (MccC51) is an antimicrobial nucleotide-heptapeptide produced by a natural Escherichia coli strain. A 5.7-kb fragment of the pC51 plasmid carrying the genes involved in MccC51 production, secretion, and self-immunity was sequenced, and the genes were characterized. The sequence of the MccC51 gene cluster is highly similar to that of the MccC7 gene. Recombinant plasmids carrying different combinations of the mcc genes involved in the MccC51 production or immunity were constructed to characterize their functional roles. The mccA, mccB, mccD, and mccE genes are involved in MccC51 production, while the mccC and mccE genes are responsible for immunity to MccC51. The mcc gene cluster is flanked by 44-bp direct repeats. Amino acid sequence comparisons allowed us to propose functions for each Mcc polypeptide in MccC51 biosynthesis. Plasmid pUHN containing the cloned mccA, mccB, mccC, and mccE genes, but lacking mccD, directed the synthesis of MccC51p, a substance chemically related to MccC51. MccC51p exhibited weak antibiotic activity against E. coli and was toxic to the producing cells. The immunity to exogenous MccC51 determined by the mccC and mccE genes did not overcome the toxic action of MccC51p on the producing cells. The G+C content of the MccC51 operon, markedly lower than that of the E. coli genome, and the presence of direct repeats suggest the possibility of horizontal transfer of this gene cluster.}, }
@article {pmid12935338, year = {2003}, author = {Durand, D and Sankoff, D}, title = {Tests for gene clustering.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {10}, number = {3-4}, pages = {453-482}, doi = {10.1089/10665270360688129}, pmid = {12935338}, issn = {1066-5277}, support = {1K22 HG 02451-01/HG/NHGRI NIH HHS/United States ; }, mesh = {Algorithms ; Chromosome Mapping/*methods ; Computational Biology/*methods ; *Data Interpretation, Statistical ; *Gene Order ; Genome ; Multigene Family ; }, abstract = {Comparing chromosomal gene order in two or more related species is an important approach to studying the forces that guide genome organization and evolution. Linked clusters of similar genes found in related genomes are often used to support arguments of evolutionary relatedness or functional selection. However, as the gene order and the gene complement of sister genomes diverge progressively due to large scale rearrangements, horizontal gene transfer, gene duplication and gene loss, it becomes increasingly difficult to determine whether observed similarities in local genomic structure are indeed remnants of common ancestral gene order, or are merely coincidences. A rigorous comparative genomics requires principled methods for distinguishing chance commonalities, within or between genomes, from genuine historical or functional relationships. In this paper, we construct tests for significant groupings against null hypotheses of random gene order, taking incomplete clusters, multiple genomes, and gene families into account. We consider both the significance of individual clusters of prespecified genes and the overall degree of clustering in whole genomes.}, }
@article {pmid12927971, year = {2003}, author = {Escobar, MA and Dandekar, AM}, title = {Agrobacterium tumefaciens as an agent of disease.}, journal = {Trends in plant science}, volume = {8}, number = {8}, pages = {380-386}, doi = {10.1016/S1360-1385(03)00162-6}, pmid = {12927971}, issn = {1360-1385}, mesh = {Agrobacterium tumefaciens/*pathogenicity/physiology ; Chemotaxis ; Plant Diseases/genetics/*microbiology ; Plasmids/genetics ; Signal Transduction ; }, abstract = {Twenty-six years ago it was found that the common soil bacterium Agrobacterium tumefaciens is capable of extraordinary feats of interkingdom genetic transfer. Since this discovery, A. tumefaciens has served as a model system for the study of type IV bacterial secretory systems, horizontal gene transfer and bacterial-plant signal exchange. It has also been modified for controlled genetic transformation of plants, a core technology of plant molecular biology. These areas have often overshadowed its role as a serious, widespread phytopathogen - the primary driver of the first 80 years of Agrobacterium research. Now, the diverse areas of A. tumefaciens research are again converging because new discoveries in transformation biology and the use of A. tumefaciens vectors are allowing the development of novel, effective biotechnology-based strategies for the control of crown gall disease.}, }
@article {pmid12925899, year = {2003}, author = {Liu, X and Inlow, M and VanEtten, HD}, title = {Expression profiles of pea pathogenicity (PEP) genes in vivo and in vitro, characterization of the flanking regions of the PEP cluster and evidence that the PEP cluster region resulted from horizontal gene transfer in the fungal pathogen Nectria haematococca.}, journal = {Current genetics}, volume = {44}, number = {2}, pages = {95-103}, pmid = {12925899}, issn = {0172-8083}, mesh = {Actins/genetics ; Base Composition ; Cluster Analysis ; Codon/genetics ; DNA Primers ; DNA, Complementary/genetics ; DNA, Intergenic/genetics ; *Gene Expression Profiling ; Gene Transfer, Horizontal/*genetics ; Genes, Fungal/*genetics ; Hypocreales/*genetics/pathogenicity ; Pisum sativum/genetics/microbiology ; Plant Roots/*genetics ; Pterocarpans ; RNA, Messenger/*metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {A cluster of pathogenicity genes (PEP1, PEP2, PDA1, PEP5), termed the pea pathogenicity (PEP) cluster and located on a 1.6-Mb conditionally dispensable (CD) chromosome, was identified in the fungal pathogen Nectria haematococca. Studies determined that the expression of PDA1 is induced in both infected pea tissues and in vitro by the phytoalexin pisatin. The present study reports the use of real-time quantitative RT-PCR to monitor the expression of each PEP gene and PDA1. In mycelia actively growing in culture, the mRNA levels of PEP1, PEP5 and PDA1 were very low and the PEP2 transcript was undetectable. In planta, PDA1 and PEP2 were strongly induced, while PEP1 and PEP5 were moderately induced. Starvation slightly enhanced the expression of PEP1, PDA1 and PEP5, while the expression of PEP2 remained undetectable. Exposure to pisatin in culture stimulated the expression of PDA1 and each PEP gene to a similar level as occurred in planta. In addition, all four pathogenicity genes displayed similar temporal patterns of expression in planta and in vitro, consistent with a coordinated regulation of these genes by pisatin during pea pathogenesis. In the flanking regions of the PEP cluster, six open reading frames (ORFs) were identified and all were expressed during infection of pea. Comparison of the codon preferences of these ORFs and seven additional genes from CD chromosomes with the codon preferences of 21 genes from other chromosomes revealed there is a codon bias that correlates with the source of the genes. This difference in codon bias is consistent with the hypothesis that genes on the CD chromosome have a different origin from genes of normal chromosomes, suggesting that horizontal gene transfer may have played a role in the evolution of pathogenesis in N. haematococca.}, }
@article {pmid12919482, year = {2003}, author = {Parker, MA}, title = {Genetic markers for analysing symbiotic relationships and lateral gene transfer in Neotropical bradyrhizobia.}, journal = {Molecular ecology}, volume = {12}, number = {9}, pages = {2447-2455}, doi = {10.1046/j.1365-294x.2003.01908.x}, pmid = {12919482}, issn = {0962-1083}, mesh = {Base Sequence ; Bradyrhizobium/*genetics ; Chromosome Mapping ; Cluster Analysis ; DNA Primers ; *Evolution, Molecular ; Fabaceae/*physiology ; Molecular Sequence Data ; Panama ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Sequence Analysis, DNA ; Species Specificity ; *Symbiosis ; }, abstract = {Assays with seven sets of lineage-specific polymerase chain reaction (PCR) primers in the ribosomal RNA region were performed on 96 isolates of the Bradyrhizobium sp. nodule bacteria from Barro Colorado Island, Panama. The isolates were derived from 10 legume host species in six genera (Centrosema, Desmodium, Dioclea, Inga, Machaerium and Vigna). The PCR assays differentiated 13 composite genotypes, and sequencing of a 5' 23S rRNA region indicated that all but one had a unique sequence. The most common genotype (seen in 44% of the isolates) was associated with all six legume host genera, and had a marker profile and 5' 23S rRNA sequence identical to a Bradyrhizobium lineage associated with several other legume genera in Panama and Costa Rica. Another 46% of the isolates had genotypes found to be associated with two to three legume genera. Bradyrhizobium strains with low host specificity thus appear to be prevalent in this tropical forest. Based on 16S rRNA and 5' 23S rRNA markers, most of the isolates had clear affinities to either B. japonicum or B. elkanii. However, one strain (Cp5-3) with a B. elkanii-type 16S rRNA marker had a 5' 23S rRNA region resembling B. japonicum. A partition homogeneity test indicated that relationships of strain Cp5-3 were significantly discordant for 16S rRNA vs. 23S rRNA sequences, and a runs test detected significant mosaic structure across the rRNA region. Lateral gene transfer events have therefore played a role in the evolution of symbiotic bacteria in this environment.}, }
@article {pmid12917641, year = {2003}, author = {Palenik, B and Brahamsha, B and Larimer, FW and Land, M and Hauser, L and Chain, P and Lamerdin, J and Regala, W and Allen, EE and McCarren, J and Paulsen, I and Dufresne, A and Partensky, F and Webb, EA and Waterbury, J}, title = {The genome of a motile marine Synechococcus.}, journal = {Nature}, volume = {424}, number = {6952}, pages = {1037-1042}, doi = {10.1038/nature01943}, pmid = {12917641}, issn = {1476-4687}, mesh = {Bacterial Proteins/genetics ; Base Composition ; Chromosomes, Bacterial/genetics ; Cyanobacteria/classification/*genetics/virology ; Genes, Bacterial/genetics ; *Genome, Bacterial ; Molecular Sequence Data ; Sequence Analysis, DNA ; }, abstract = {Marine unicellular cyanobacteria are responsible for an estimated 20-40% of chlorophyll biomass and carbon fixation in the oceans. Here we have sequenced and analysed the 2.4-megabase genome of Synechococcus sp. strain WH8102, revealing some of the ways that these organisms have adapted to their largely oligotrophic environment. WH8102 uses organic nitrogen and phosphorus sources and more sodium-dependent transporters than a model freshwater cyanobacterium. Furthermore, it seems to have adopted strategies for conserving limited iron stores by using nickel and cobalt in some enzymes, has reduced its regulatory machinery (consistent with the fact that the open ocean constitutes a far more constant and buffered environment than fresh water), and has evolved a unique type of swimming motility. The genome of WH8102 seems to have been greatly influenced by horizontal gene transfer, partially through phages. The genetic material contributed by horizontal gene transfer includes genes involved in the modification of the cell surface and in swimming motility. On the basis of its genome, WH8102 is more of a generalist than two related marine cyanobacteria.}, }
@article {pmid12917487, year = {2003}, author = {Kinsella, RJ and Fitzpatrick, DA and Creevey, CJ and McInerney, JO}, title = {Fatty acid biosynthesis in Mycobacterium tuberculosis: lateral gene transfer, adaptive evolution, and gene duplication.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {100}, number = {18}, pages = {10320-10325}, pmid = {12917487}, issn = {0027-8424}, mesh = {Acetyl-CoA Carboxylase/genetics ; Adaptation, Physiological ; Biological Evolution ; Evolution, Molecular ; Fatty Acids/*biosynthesis ; *Gene Duplication ; *Gene Transfer, Horizontal ; Mycobacterium tuberculosis/classification/*genetics/*metabolism ; Phylogeny ; }, abstract = {Mycobacterium tuberculosis is a high GC Gram-positive member of the actinobacteria. The mycobacterial cell wall is composed of a complex assortment of lipids and is the interface between the bacterium and its environment. The biosynthesis of fatty acids plays an essential role in the formation of cell wall components, in particular mycolic acids, which have been targeted by many of the drugs used to treat M. tuberculosis infection. M. tuberculosis has approximately 250 genes involved in fatty acid metabolism, a much higher proportion than in any other organism. In silico methods have been used to compare the genome of M. tuberculosis CDC1551 to a database of 58 complete bacterial genomes. The resulting alignments were scanned for genes specifically involved in fatty acid biosynthetic pathway I. Phylogenetic analysis of these alignments was used to investigate horizontal gene transfer, gene duplication, and adaptive evolution. It was found that of the eight gene families examined, five of the phylogenies reconstructed suggest that the actinobacteria have a closer relationship with the alpha-proteobacteria than expected. This is either due to either an ancient transfer of genes or deep paralogy and subsequent retention of the genes in unrelated lineages. Additionally, adaptive evolution and gene duplication have been an influence in the evolution of the pathway. This study provides a key insight into how M. tuberculosis has developed its unique fatty acid synthetic abilities.}, }
@article {pmid12917475, year = {2003}, author = {Bideshi, DK and Renault, S and Stasiak, K and Federici, BA and Bigot, Y}, title = {Phylogenetic analysis and possible function of bro-like genes, a multigene family widespread among large double-stranded DNA viruses of invertebrates and bacteria.}, journal = {The Journal of general virology}, volume = {84}, number = {Pt 9}, pages = {2531-2544}, doi = {10.1099/vir.0.19256-0}, pmid = {12917475}, issn = {0022-1317}, mesh = {Amino Acid Sequence ; Ascoviridae/*genetics/pathogenicity ; Bacteria/*virology ; Cloning, Molecular ; Consensus Sequence ; DNA Transposable Elements ; *DNA-Binding Proteins ; *Drosophila Proteins ; Gene Transfer, Horizontal ; *Genes, Viral ; Iridoviridae/*genetics/pathogenicity ; Molecular Sequence Data ; Multigene Family/genetics/*physiology ; Phylogeny ; Recombination, Genetic ; Sequence Alignment ; Transcription Factors/*genetics ; Virus Replication ; }, abstract = {Baculovirus repeated open reading frame (bro) genes and their relatives constitute a multigene family, typically with multiple copies per genome, known to occur among certain insect dsDNA viruses and bacteriophages. Little is known about the evolutionary history and function of the proteins encoded by these genes. Here we have shown that bro and bro-like (bro-l) genes occur among viruses of two additional invertebrate viral families, Ascoviridae and Iridoviridae, and in prokaryotic class II transposons. Analysis of over 100 sequences showed that the N-terminal region, consisting of two subdomains, is the most conserved region and contains a DNA-binding motif that has been characterized previously. Phylogenetic analysis indicated that these proteins are distributed among eight groups, Groups 1-7 consisting of invertebrate virus proteins and Group 8 of proteins in bacteriophages and bacterial transposons. No bro genes were identified in databases of invertebrate or vertebrate genomes, vertebrate viruses and transposons, nor in prokaryotic genomes, except in prophages or transposons of the latter. The phylogenetic relationship between bro genes suggests that they have resulted from recombination of viral genomes that allowed the duplication and loss of genes, but also the acquisition of genes by horizontal transfer over evolutionary time. In addition, the maintenance and diversity of bro-l genes in different types of invertebrate dsDNA viruses, but not in vertebrate viruses, suggests that these proteins play an important role in invertebrate virus biology. Experiments with the unique orf2 bro gene of Autographa californica multicapsid nucleopolyhedrovirus showed that it is not required for replication, but may enhance replication during the occlusion phase of reproduction.}, }
@article {pmid12915091, year = {2003}, author = {Wilson, BA and Salyers, AA}, title = {Is the evolution of bacterial pathogens an out-of-body experience?.}, journal = {Trends in microbiology}, volume = {11}, number = {8}, pages = {347-350}, doi = {10.1016/s0966-842x(03)00179-3}, pmid = {12915091}, issn = {0966-842X}, support = {R29 AI038396/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/*genetics/*pathogenicity ; Biofilms ; *Biological Evolution ; Digestive System/microbiology ; Ecosystem ; *Gene Transfer, Horizontal ; Soil Microbiology ; Virulence Factors/*genetics ; Water Microbiology ; }, }
@article {pmid12914657, year = {2003}, author = {Hooper, SD and Berg, OG}, title = {Duplication is more common among laterally transferred genes than among indigenous genes.}, journal = {Genome biology}, volume = {4}, number = {8}, pages = {R48}, pmid = {12914657}, issn = {1474-760X}, mesh = {Bacillus/genetics ; Bacillus subtilis/genetics ; Clostridium/genetics ; Clostridium perfringens/genetics ; Escherichia coli/genetics ; Escherichia coli O157/genetics ; Evolution, Molecular ; GC Rich Sequence/genetics ; *Gene Duplication ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/*genetics ; *Genome, Bacterial ; Klebsiella pneumoniae/genetics ; Pseudomonas aeruginosa/genetics ; Salmonella typhimurium/genetics ; Shigella flexneri/genetics ; Staphylococcus aureus/genetics ; }, abstract = {BACKGROUND: Recent developments in the understanding of paralogous evolution have prompted a focus not only on obviously advantageous genes, but also on genes that can be considered to have a weak or sporadic impact on the survival of the organism. Here we examine the duplicative behavior of a category of genes that can be considered to be mostly transient in the genome, namely laterally transferred genes. Using both a compositional method and a gene-tree approach, we identify a number of proposed laterally transferred genes and study their nucleotide composition and frequency of duplication.<br><br>RESULTS: It is found that duplications are significantly overrepresented among potential laterally transferred genes compared to the indigenous ones. Furthermore, the GC3 distribution of potential laterally transferred genes was found to be largely uniform in some genomes, suggesting an import from a broad range of donors.<br><br>CONCLUSIONS: The results are discussed not in a context of strongly optimized established genes, but rather of genes with weak or ancillary functions. The importance of duplication may therefore depend on the variability and availability of weak genes for which novel functions may be discovered. Therefore, lateral transfer may accelerate the evolutionary process of duplication by bringing foreign genes that have mainly weak or no function into the genome.}, }
@article {pmid12910471, year = {2003}, author = {Gahan, PB}, title = {Messenger DNA in higher plants.}, journal = {Cell biochemistry and function}, volume = {21}, number = {3}, pages = {207-209}, doi = {10.1002/cbf.1074}, pmid = {12910471}, issn = {0263-6484}, mesh = {Biological Transport ; DNA, Bacterial/genetics ; DNA, Plant/genetics/*physiology ; Gene Transfer, Horizontal ; Plants/*genetics ; Transfection ; }, abstract = {Evidence is presented that, as in animal and human cells, plant cells can release a newly-synthesized DNA which can freely circulate in the plants. This DNA enters cells and their nuclei where it may be integrated and be expressed so acting, apparently, as a messenger-DNA.}, }
@article {pmid12909351, year = {2003}, author = {Gophna, U and Ron, EZ and Graur, D}, title = {Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events.}, journal = {Gene}, volume = {312}, number = {}, pages = {151-163}, doi = {10.1016/s0378-1119(03)00612-7}, pmid = {12909351}, issn = {0378-1119}, mesh = {Bacteria/classification/*genetics ; Bacterial Proteins/*genetics ; *Evolution, Molecular ; Flagella/genetics ; Gene Transfer, Horizontal ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Type III secretion systems (TTSS) are unique bacterial mechanisms that mediate elaborate interactions with their hosts. The fact that several of the TTSS proteins are closely related to flagellar export proteins has led to the suggestion that TTSS had evolved from flagella. Here we reconstruct the evolutionary history of four conserved type III secretion proteins and their phylogenetic relationships with flagellar paralogs. Our analysis indicates that the TTSS and the flagellar export mechanism share a common ancestor, but have evolved independently from one another. The suggestion that TTSS genes have evolved from genes encoding flagellar proteins is effectively refuted. A comparison of the species tree, as deduced from 16S rDNA sequences, to the protein phylogenetic trees has led to the identification of several major lateral transfer events involving clusters of TTSS genes. It is hypothesized that horizontal gene transfer has occurred much earlier and more frequently than previously inferred for TTSS genes and is, consequently, a major force shaping the evolution of species that harbor type III secretion systems.}, }
@article {pmid12907801, year = {2003}, author = {Daubin, V and Moran, NA and Ochman, H}, title = {Phylogenetics and the cohesion of bacterial genomes.}, journal = {Science (New York, N.Y.)}, volume = {301}, number = {5634}, pages = {829-832}, doi = {10.1126/science.1086568}, pmid = {12907801}, issn = {1095-9203}, mesh = {Bacteria/*classification/*genetics ; Biological Evolution ; Chlamydophila pneumoniae/genetics ; Computational Biology ; Escherichia coli/genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genes, rRNA ; *Genome, Bacterial ; Likelihood Functions ; *Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal/genetics ; Recombination, Genetic ; Species Specificity ; }, abstract = {Gene acquisition is an ongoing process in many bacterial genomes, contributing to adaptation and ecological diversification. Lateral gene transfer is considered the primary explanation for discordance among gene phylogenies and as an obstacle to reconstructing the tree of life. We measured the extent of phylogenetic conflict and alien-gene acquisition within quartets of sequenced genomes. Although comparisons of complete gene inventories indicate appreciable gain and loss of genes, orthologs available for phylogenetic reconstruction are consistent with a single tree.}, }
@article {pmid12907788, year = {2003}, author = {Hacker, J and Hentschel, U and Dobrindt, U}, title = {Prokaryotic chromosomes and disease.}, journal = {Science (New York, N.Y.)}, volume = {301}, number = {5634}, pages = {790-793}, doi = {10.1126/science.1086802}, pmid = {12907788}, issn = {1095-9203}, mesh = {Adaptation, Physiological ; Animals ; Bacteria/*genetics/*pathogenicity ; Bacterial Infections/*microbiology ; Chromosomes, Bacterial/genetics/*physiology ; Drug Resistance, Bacterial/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Humans ; Interspersed Repetitive Sequences ; Mutation ; Recombination, Genetic ; Symbiosis ; Virulence/genetics ; }, abstract = {Recent insights into bacterial genome organization and function have improved our understanding of the nature of pathogenic bacteria and their ability to cause disease. It is becoming increasingly clear that the bacterial chromosome constantly undergoes structural changes due to gene acquisition and loss, recombination, and mutational events that have an impact on the pathogenic potential of the bacterium. Even though the bacterial genome includes additional genetic elements, the chromosome represents the most important entity in this context. Here, we will show that various processes of genomic instability have an influence on the many manifestations of infectious disease.}, }
@article {pmid12907766, year = {2003}, author = {Pennisi, E}, title = {Evolution. Passages found through labyrinth of bacterial evolution.}, journal = {Science (New York, N.Y.)}, volume = {301}, number = {5634}, pages = {745-746}, doi = {10.1126/science.301.5634.745a}, pmid = {12907766}, issn = {1095-9203}, mesh = {Bacteria/*classification/*genetics ; Biological Evolution ; Escherichia coli/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Genes, rRNA ; Genome, Bacterial ; *Phylogeny ; }, }
@article {pmid12906814, year = {2003}, author = {Papke, RT and Doolittle, WF}, title = {Phage evolution: new worlds of genomic diversity.}, journal = {Current biology : CB}, volume = {13}, number = {15}, pages = {R606-7}, doi = {10.1016/s0960-9822(03)00527-x}, pmid = {12906814}, issn = {0960-9822}, mesh = {*Evolution, Molecular ; Gene Rearrangement/*genetics ; Gene Transfer, Horizontal/*genetics ; *Genome, Viral ; Mycobacteriophages/*genetics ; }, abstract = {A recent comparative survey of genomes of phages infecting mycobacteria reveals a vast combinatorial network of gene rearrangements and may provide general models for pattern and process in genome evolution.}, }
@article {pmid12903330, year = {2000}, author = {Fukumaru, K and Yoshida, K}, title = {Different toxicity of Escherichia coli and Agrobacterium tumefaciens against tobacco BY2 cells.}, journal = {Nucleic acids symposium series}, volume = {}, number = {44}, pages = {185-186}, doi = {10.1093/nass/44.1.185}, pmid = {12903330}, issn = {0261-3166}, mesh = {Agrobacterium tumefaciens/genetics/*pathogenicity ; Cell Line ; Escherichia coli/*pathogenicity ; Gene Transfer Techniques ; Gene Transfer, Horizontal ; Plant Diseases/microbiology ; Plasmids/genetics ; Nicotiana/*microbiology ; Virulence ; }, abstract = {Tobacco BY2 cells were withered away by the physical contact with intestinal bacterium Escherichia coli. In contrast, plant pathogenic bacterium Agrobacterium tumefaciens with/without tumor inducing Ti plasmid was not so toxic as E. coli. Mini-cells of E. coli decreased their toxicity.}, }
@article {pmid12902542, year = {2003}, author = {Kurland, CG and Canback, B and Berg, OG}, title = {Horizontal gene transfer: a critical view.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {100}, number = {17}, pages = {9658-9662}, pmid = {12902542}, issn = {0027-8424}, mesh = {Animals ; Archaea/genetics ; Bacteria/genetics ; *Biological Evolution ; *Gene Transfer, Horizontal ; Genome ; Humans ; *Models, Genetic ; Phylogeny ; RNA, Ribosomal/genetics ; }, abstract = {It has been suggested that horizontal gene transfer (HGT) is the "essence of phylogeny." In contrast, much data suggest that this is an exaggeration resulting in part from a reliance on inadequate methods to identify HGT events. In addition, the assumption that HGT is a ubiquitous influence throughout evolution is questionable. Instead, rampant global HGT is likely to have been relevant only to primitive genomes. In modern organisms we suggest that both the range and frequencies of HGT are constrained most often by selective barriers. As a consequence those HGT events that do occur most often have little influence on genome phylogeny. Although HGT does occur with important evolutionary consequences, classical Darwinian lineages seem to be the dominant mode of evolution for modern organisms.}, }
@article {pmid12902375, year = {2003}, author = {Raoult, D and Ogata, H and Audic, S and Robert, C and Suhre, K and Drancourt, M and Claverie, JM}, title = {Tropheryma whipplei Twist: a human pathogenic Actinobacteria with a reduced genome.}, journal = {Genome research}, volume = {13}, number = {8}, pages = {1800-1809}, pmid = {12902375}, issn = {1088-9051}, mesh = {Actinomycetales/*genetics/*pathogenicity ; Actinomycetales Infections/genetics ; Amino Acids/metabolism ; Base Composition ; DNA, Bacterial/analysis ; Energy Metabolism/genetics ; GC Rich Sequence/genetics ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/genetics/physiology ; *Genome, Bacterial ; Humans ; Molecular Sequence Data ; Multigene Family/genetics ; Predictive Value of Tests ; Pseudogenes/genetics ; Repetitive Sequences, Nucleic Acid/genetics ; Sequence Analysis, DNA ; }, abstract = {The human pathogen Tropheryma whipplei is the only known reduced genome species (<1 Mb) within the Actinobacteria [high G+C Gram-positive bacteria]. We present the sequence of the 927303-bp circular genome of T. whipplei Twist strain, encoding 808 predicted protein-coding genes. Specific genome features include deficiencies in amino acid metabolisms, the lack of clear thioredoxin and thioredoxin reductase homologs, and a mutation in DNA gyrase predicting a resistance to quinolone antibiotics. Moreover, the alignment of the two available T. whipplei genome sequences (Twist vs. TW08/27) revealed a large chromosomal inversion the extremities of which are located within two paralogous genes. These genes belong to a large cell-surface protein family defined by the presence of a common repeat highly conserved at the nucleotide level. The repeats appear to trigger frequent genome rearrangements in T. whipplei, potentially resulting in the expression of different subsets of cell surface proteins. This might represent a new mechanism for evading host defenses. The T. whipplei genome sequence was also compared to other reduced bacterial genomes to examine the generality of previously detected features. The analysis of the genome sequence of this previously largely unknown human pathogen is now guiding the development of molecular diagnostic tools and more convenient culture conditions.}, }
@article {pmid12902293, year = {2003}, author = {Arenskötter, M and Baumeister, D and Kalscheuer, R and Steinbüchel, A}, title = {Identification and application of plasmids suitable for transfer of foreign DNA to members of the genus Gordonia.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {8}, pages = {4971-4974}, pmid = {12902293}, issn = {0099-2240}, mesh = {Conjugation, Genetic ; *Gene Transfer, Horizontal ; Genetic Vectors ; Gordonia Bacterium/*genetics ; *Plasmids ; Polyesters/metabolism ; }, abstract = {Gene transfer systems for Gordonia polyisoprenivorans strains VH2 and Y2K based on electroporation and conjugation, respectively, were established. Several parameters were optimized, resulting in transformation efficiencies of >4 x 10(5) CFU/ micro g of plasmid DNA. In contrast to most previously described electroporation protocols, the highest efficiencies were obtained by applying a heat shock after the intrinsic electroporation. Under these conditions, transfer and autonomous replication of plasmid pNC9503 was also demonstrated to proceed in G. alkanivorans DSM44187, G. nitida DSM44499(T), G. rubropertincta DSM43197(T), G. rubropertincta DSM46038, and G. terrae DSM43249(T). Conjugational plasmid DNA transfer to G. polyisoprenivorans resulted in transfer frequencies of up to 5 x 10(-6) of the recipient cells. Recombinant strains capable of polyhydroxyalkanoate synthesis from alkanes were constructed.}, }
@article {pmid12902279, year = {2003}, author = {Nancharaiah, YV and Wattiau, P and Wuertz, S and Bathe, S and Mohan, SV and Wilderer, PA and Hausner, M}, title = {Dual labeling of Pseudomonas putida with fluorescent proteins for in situ monitoring of conjugal transfer of the TOL plasmid.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {8}, pages = {4846-4852}, pmid = {12902279}, issn = {0099-2240}, mesh = {Biofilms ; *Conjugation, Genetic ; Green Fluorescent Proteins ; Luminescent Proteins/*metabolism ; *Plasmids ; Pseudomonas putida/*genetics ; }, abstract = {We describe here a dual-labeling technique involving the green fluorescent protein (GFP) and the red fluorescent protein (DsRed) for in situ monitoring of horizontal gene transfer via conjugation. A GFPmut3b-tagged derivative of narrow-host-range TOL plasmid (pWWO) was delivered to Pseudomonas putida KT2442, which was chromosomally labeled with dsRed by transposon insertion via biparental mating. Green and red fluorescent proteins were coexpressed in donor P. putida cells. Cells expressing both fluorescent proteins were smaller in size than cells expressing GFP alone. Donors and transconjugants in mixed culture or sludge samples were discriminated on the basis of their fluorescence by using confocal laser scanning microscopy. Conjugal plasmid transfer frequencies on agar surfaces and in sludge microcosms were determined microscopically without cultivation. This method worked well for in situ monitoring of horizontal gene transfer in addition to tracking the fate of microorganisms released into complex environments. To the best of our knowledge, this is the first study that discusses the coexpression of GFP and DsRed for conjugal gene transfer studies.}, }
@article {pmid12902229, year = {2003}, author = {de Vries, J and Heine, M and Harms, K and Wackernagel, W}, title = {Spread of recombinant DNA by roots and pollen of transgenic potato plants, identified by highly specific biomonitoring using natural transformation of an Acinetobacter sp.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {8}, pages = {4455-4462}, pmid = {12902229}, issn = {0099-2240}, mesh = {Acinetobacter/*genetics ; DNA, Recombinant/analysis/*metabolism ; Environmental Monitoring ; Plant Roots/*metabolism ; Plants, Genetically Modified ; Pollen/*metabolism ; Polymerase Chain Reaction ; Sensitivity and Specificity ; Soil/analysis ; Solanum tuberosum/*genetics/metabolism ; Transformation, Bacterial ; Transgenes ; }, abstract = {Transgenic potato plants with the nptII gene coding for neomycin phosphotransferase (kanamycin resistance) as a selection marker were examined for the spread of recombinant DNA into the environment. We used the recombinant fusion of nptII with the tg4 terminator for a novel biomonitoring technique. This depended on natural transformation of Acinetobacter sp. strain BD413 cells having in their genomes a terminally truncated nptII gene (nptII'; kanamycin sensitivity) followed by the tg4 terminator. Integration of the recombinant fusion DNA by homologous recombination in nptII' and tg4 restored nptII, leading to kanamycin-resistant transformants. DNA of the transgenic potato was detectable with high sensitivity, while no transformants were obtained with the DNA of other transgenic plants harboring nptII in different genetic contexts. The recombinant DNA was frequently found in rhizosphere extracts of transgenic potato plants from field plots. In a series of field plot and greenhouse experiments we identified two sources of this DNA: spread by roots during plant growth and by pollen during flowering. Both sources also contributed to the spread of the transgene into the rhizospheres of nontransgenic plants in the vicinity. The longest persistence of transforming DNA in field soil was observed with soil from a potato field in 1997 sampled in the following year in April and then stored moist at 4 degrees C in the dark for 4 years prior to extract preparation and transformation. In this study natural transformation is used as a reliable laboratory technique to detect recombinant DNA but is not used for monitoring horizontal gene transfer in the environment.}, }
@article {pmid12899689, year = {2003}, author = {Riveros-Rosas, H and Julián-Sánchez, A and Villalobos-Molina, R and Pardo, JP and Piña, E}, title = {Diversity, taxonomy and evolution of medium-chain dehydrogenase/reductase superfamily.}, journal = {European journal of biochemistry}, volume = {270}, number = {16}, pages = {3309-3334}, doi = {10.1046/j.1432-1033.2003.03704.x}, pmid = {12899689}, issn = {0014-2956}, mesh = {Animals ; Arabidopsis/enzymology/genetics ; Bacteria/enzymology/genetics ; Databases, Protein ; *Evolution, Molecular ; Genetic Variation ; Humans ; *Multigene Family ; Oxidoreductases/classification/*genetics ; Saccharomyces cerevisiae/enzymology/genetics ; }, abstract = {A comprehensive, structural and functional, in silico analysis of the medium-chain dehydrogenase/reductase (MDR) superfamily, including 583 proteins, was carried out by use of extensive database mining and the blastp program in an iterative manner to identify all known members of the superfamily. Based on phylogenetic, sequence, and functional similarities, the protein members of the MDR superfamily were classified into three different taxonomic categories: (a) subfamilies, consisting of a closed group containing a set of ideally orthologous proteins that perform the same function; (b) families, each comprising a cluster of monophyletic subfamilies that possess significant sequence identity among them and might share or not common substrates or mechanisms of reaction; and (c) macrofamilies, each comprising a cluster of monophyletic protein families with protein members from the three domains of life, which includes at least one subfamily member that displays activity related to a very ancient metabolic pathway. In this context, a superfamily is a group of homologous protein families (and/or macrofamilies) with monophyletic origin that shares at least a barely detectable sequence similarity, but showing the same 3D fold. The MDR superfamily encloses three macrofamilies, with eight families and 49 subfamilies. These subfamilies exhibit great functional diversity including noncatalytic members with different subcellular, phylogenetic, and species distributions. This results from constant enzymogenesis and proteinogenesis within each kingdom, and highlights the huge plasticity that MDR superfamily members possess. Thus, through evolution a great number of taxa-specific new functions were acquired by MDRs. The generation of new functions fulfilled by proteins, can be considered as the essence of protein evolution. The mechanisms of protein evolution inside MDR are not constrained to conserve substrate specificity and/or chemistry of catalysis. In consequence, MDR functional diversity is more complex than sequence diversity. MDR is a very ancient protein superfamily that existed in the last universal common ancestor. It had at least two (and probably three) different ancestral activities related to formaldehyde metabolism and alcoholic fermentation. Eukaryotic members of this superfamily are more related to bacterial than to archaeal members; horizontal gene transfer among the domains of life appears to be a rare event in modern organisms.}, }
@article {pmid12897836, year = {2003}, author = {Wong, K and Golding, GB}, title = {A phylogenetic analysis of the pSymB replicon from the Sinorhizobium meliloti genome reveals a complex evolutionary history.}, journal = {Canadian journal of microbiology}, volume = {49}, number = {4}, pages = {269-280}, doi = {10.1139/w03-037}, pmid = {12897836}, issn = {0008-4166}, mesh = {Agrobacterium tumefaciens/genetics ; Archaea/genetics ; Base Composition ; Computational Biology ; Computer Simulation ; DNA, Bacterial/chemistry/genetics ; *Evolution, Molecular ; Gene Order ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; Oligodeoxyribonucleotides/analysis ; Operon ; *Phylogeny ; Proteobacteria/genetics ; *Replicon ; Sinorhizobium meliloti/*genetics ; }, abstract = {Microbial genomes are thought to be mosaic, making it difficult to decipher how these genomes have evolved. Whole-genome nearest-neighbor analysis was applied to the Sinorhizobium meliloti pSymB replicon to determine its origin, the degree of horizontal transfer, and the conservation of gene order. Prediction of the nearest neighbor based on contextual information, i.e., the nearest phylogenetic neighbor of adjacent genes, provided useful information for genes for which phylogenetic relationships could not be established. A large portion of pSymB genes are most closely related to genes in the Agrobacterium tumefaciens linear chromosome, including the rep and min genes. This suggests a common origin for these replicons. Genes with the nearest neighbor from the same species tend to be grouped in "patches". Gene order within these patches is conserved, but the content of the patches is not limited to operons. These data show that 13% of pSymB genes have nearest neighbors in species that are not members of the Rhizobiaceae family (including two archaea), and that these likely represent genes that have been involved in horizontal transfer.}, }
@article {pmid12892059, year = {2003}, author = {Hassler, D and Shwarz, TF and Kimmig, P}, title = {[Fowl plague: a potential danger also for humans].}, journal = {Deutsche medizinische Wochenschrift (1946)}, volume = {128}, number = {27}, pages = {1467}, pmid = {12892059}, issn = {0012-0472}, mesh = {Animals ; *Chickens ; *Disease Outbreaks ; Ducks ; Gene Transfer, Horizontal ; Humans ; Influenza A virus/classification/genetics/*pathogenicity ; Influenza in Birds/*epidemiology/prevention &amp; control/transmission/virology ; Swine ; Vaccination ; }, }
@article {pmid12890320, year = {2003}, author = {Garg, P and Aydanian, A and Smith, D and J Glenn, M and Nair, GB and Stine, OC}, title = {Molecular epidemiology of O139 Vibrio cholerae: mutation, lateral gene transfer, and founder flush.}, journal = {Emerging infectious diseases}, volume = {9}, number = {7}, pages = {810-814}, pmid = {12890320}, issn = {1080-6040}, mesh = {Alleles ; Cholera/microbiology ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Humans ; India ; Mutation/*genetics ; Sequence Analysis, DNA ; Vibrio cholerae O139/*genetics ; }, abstract = {Vibrio cholerae in O-group 139 was first isolated in 1992 and by 1993 had been found throughout the Indian subcontinent. This epidemic expansion probably resulted from a single source after a lateral gene transfer (LGT) event that changed the serotype of an epidemic V. cholerae O1 El Tor strain to O139. However, some studies found substantial genetic diversity, perhaps caused by multiple origins. To further explore the relatedness of O139 strains, we analyzed nine sequenced loci from 96 isolates from patients at the Infectious Diseases Hospital, Calcutta, from 1992 to 2000. We found 64 novel alleles distributed among 51 sequence types. LGT events produced three times the number of nucleotide changes compared to mutation. In contrast to the traditional concept of epidemic spread of a homogeneous clone, the establishment of variant alleles generated by LGT during the rapid expansion of a clonal bacterial population may be a paradigm in infections and epidemics.}, }
@article {pmid12885164, year = {2003}, author = {Tepfer, D and Garcia-Gonzales, R and Mansouri, H and Seruga, M and Message, B and Leach, F and Perica, MC}, title = {Homology-dependent DNA transfer from plants to a soil bacterium under laboratory conditions: implications in evolution and horizontal gene transfer.}, journal = {Transgenic research}, volume = {12}, number = {4}, pages = {425-437}, pmid = {12885164}, issn = {0962-8819}, mesh = {Acinetobacter/*genetics/isolation &amp; purification ; Base Sequence ; *Biological Evolution ; DNA, Plant/*genetics ; *Gene Transfer, Horizontal ; Plants/*genetics/microbiology ; Sequence Homology, Nucleic Acid ; }, abstract = {DNA transfer was demonstrated from six species of donor plants to the soil bacterium, Acinetobacter spp. BD413, using neomycin phosphotransferase (nptII) as a marker for homologous recombination. These laboratory results are compatible with, but do not prove, DNA transfer in nature. In tobacco carrying a plastid insertion of nptII, transfer was detected with 0.1 g of disrupted leaves and in oilseed rape carrying a nuclear insertion with a similar quantity of roots. Transfer from disrupted leaves occurred in sterile soil and water, without the addition of nutrients. It was detected using intact tobacco leaves and intact tobacco and Arabidopsis plants in vitro. Transfer was dose-dependent and sensitive to DNase, and mutations in the plant nptII were recovered in receptor bacteria. DNA transfer using intact roots and plants in vitro was easily demonstrated, but with greater variability. Transfer varied with plant genome size and the number of repeats of the marker DNA in the donor plant. Transfer was not detected in the absence of a homologous nptII in the receptor bacteria. We discuss these results with reference to non-coding DNA in plant genomes (e.g., introns, transposons and junk DNA) and the possibility that DNA transfer could occur in nature.}, }
@article {pmid12884513, year = {2003}, author = {Andreeva, LE and Sleptsova, LA and Grigorenko, AP and Gavriushkin, AV and Kuznetsov, AV}, title = {[Loach spermatozoa transfer foreign DNA, which expression is discovered in the early development stages].}, journal = {Genetika}, volume = {39}, number = {6}, pages = {758-761}, pmid = {12884513}, issn = {0016-6758}, mesh = {Animals ; Cypriniformes/embryology/genetics/*growth &amp; development ; Electroporation/methods ; Embryo, Nonmammalian ; Female ; Gene Expression Regulation, Developmental ; *Gene Transfer, Horizontal ; Lac Operon ; Male ; Spermatozoa/*physiology ; }, abstract = {The transfer of plasmid pcDNA3-lacZ by electrotrasfected sperm cells into loach (Misgurnus fossilis L.) ova has been studied. The lacZ gene has been found to express in 3- to 5-day-old prelarvae.}, }
@article {pmid12880199, year = {2003}, author = {Martin, W and Rotte, C and Hoffmeister, M and Theissen, U and Gelius-Dietrich, G and Ahr, S and Henze, K}, title = {Early cell evolution, eukaryotes, anoxia, sulfide, oxygen, fungi first (?), and a tree of genomes revisited.}, journal = {IUBMB life}, volume = {55}, number = {4-5}, pages = {193-204}, doi = {10.1080/1521654031000141231}, pmid = {12880199}, issn = {1521-6543}, mesh = {Animals ; Atmosphere/chemistry ; *Biological Evolution ; Eukaryotic Cells/*classification ; Fungi/*classification/genetics ; Fungi, Unclassified/classification/genetics ; *Genome ; Mitochondria/classification/genetics ; Oxygen/chemistry ; *Phylogeny ; Plastids/classification/genetics ; Prokaryotic Cells/*classification ; Sulfides/chemistry ; Sulfur/analysis ; Time Factors ; }, abstract = {Genomes contain evidence for the history of life and furthermore contain evidence for lateral gene transfer, which was an important part of that history. The geological record also contains evidence for the history of life, and newer findings indicates that the Earth's oceans were largely anoxic and highly sulfidic up until about 0.6 billion years ago. Eukaryotes, which fossil data indicate to have been in existence for at least 1.5 billion years, must have therefore spent much of their evolutionary history in oxygen-poor and sulfide-rich environments. Many eukaryotes still inhabit such environments today. Among eukaryotes, organelles also contain evidence for the history of life and have preserved abundant traces of their anaerobic past in the form of energy metabolic pathways. New views of eukaryote phylogeny suggest that fungi may be among the earliest-branching eukaryotes. From the standpoint of the fungal feeding habit (osmotrophy rather than phagotrophy) and from the standpoint of the diversity in their ATP-producing pathways, a eukaryotic tree with fungi first would make sense. Because of lateral gene transfer and endosymbiosis, branches in the tree of genomes intermingle and occasionally fuse, but the overall contours of cell history nonetheless seem sketchable and roughly correlateable with geological time.}, }
@article {pmid12878222, year = {2003}, author = {Daimon, T and Hamada, K and Mita, K and Okano, K and Suzuki, MG and Kobayashi, M and Shimada, T}, title = {A Bombyx mori gene, BmChi-h, encodes a protein homologous to bacterial and baculovirus chitinases.}, journal = {Insect biochemistry and molecular biology}, volume = {33}, number = {8}, pages = {749-759}, doi = {10.1016/s0965-1748(03)00084-5}, pmid = {12878222}, issn = {0965-1748}, mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins/*genetics ; Baculoviridae/chemistry/*genetics ; Base Sequence ; Biological Evolution ; Blotting, Northern ; Blotting, Southern ; Bombyx/*genetics ; Chitinases/*genetics ; Cloning, Molecular ; DNA, Complementary ; Gene Transfer, Horizontal ; Insect Proteins/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Sequence Homology, Amino Acid ; }, abstract = {We have cloned and characterized a novel chitinase gene (BmChi-h) from the silkworm, Bombyx mori. BmChi-h cDNA has an open reading frame of 1,665 nucleotides, encoding a protein of 555 amino acid residues. The predicted protein shared extensive similarities with bacterial and baculovirus chitinases in both amino acid sequences (73% identity with Serratia marcescens chiA and 63% with Autographa californica nucleopolyhedrovirus chiA) and domain architectures. BmChi-h was a single-copy gene and located on chromosome 7. The expression of BmChi-h mRNA was observed in a stage- and tissue-specific manner that was almost identical to that of another chitinase gene previously cloned from B. mori. We further determined the overall genomic organization of BmChi-h. There was no intron in the ORF of BmChi-h. However, BmChi-h was transcribed from three promoters, which generated three isoforms in the 5'-UTR of the transcript. Phylogenetic analysis suggested that ancestral species of B. mori acquired the chitinase gene from a bacterium or an ancestral baculovirus via horizontal gene transfer.}, }
@article {pmid12877744, year = {2003}, author = {Jackson, CR and Dugas, SL}, title = {Phylogenetic analysis of bacterial and archaeal arsC gene sequences suggests an ancient, common origin for arsenate reductase.}, journal = {BMC evolutionary biology}, volume = {3}, number = {}, pages = {18}, pmid = {12877744}, issn = {1471-2148}, mesh = {Adenosine Triphosphatases/genetics ; Arsenite Transporting ATPases ; Base Sequence ; *Evolution, Molecular ; *Genes, Archaeal ; *Genes, Bacterial ; Genes, Fungal ; Ion Pumps/*genetics ; Membrane Proteins/genetics ; Molecular Sequence Data ; Multienzyme Complexes/*genetics ; Oxidoreductases/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; }, abstract = {BACKGROUND: The ars gene system provides arsenic resistance for a variety of microorganisms and can be chromosomal or plasmid-borne. The arsC gene, which codes for an arsenate reductase is essential for arsenate resistance and transforms arsenate into arsenite, which is extruded from the cell. A survey of GenBank shows that arsC appears to be phylogenetically widespread both in organisms with known arsenic resistance and those organisms that have been sequenced as part of whole genome projects.<br><br>RESULTS: Phylogenetic analysis of aligned arsC sequences shows broad similarities to the established 16S rRNA phylogeny, with separation of bacterial, archaeal, and subsequently eukaryotic arsC genes. However, inconsistencies between arsC and 16S rRNA are apparent for some taxa. Cyanobacteria and some of the gamma-Proteobacteria appear to possess arsC genes that are similar to those of Low GC Gram-positive Bacteria, and other isolated taxa possess arsC genes that would not be expected based on known evolutionary relationships. There is no clear separation of plasmid-borne and chromosomal arsC genes, although a number of the Enterobacteriales (gamma-Proteobacteria) possess similar plasmid-encoded arsC sequences.<br><br>CONCLUSION: The overall phylogeny of the arsenate reductases suggests a single, early origin of the arsC gene and subsequent sequence divergence to give the distinct arsC classes that exist today. Discrepancies between 16S rRNA and arsC phylogenies support the role of horizontal gene transfer (HGT) in the evolution of arsenate reductases, with a number of instances of HGT early in bacterial arsC evolution. Plasmid-borne arsC genes are not monophyletic suggesting multiple cases of chromosomal-plasmid exchange and subsequent HGT. Overall, arsC phylogeny is complex and is likely the result of a number of evolutionary mechanisms.}, }
@article {pmid12874385, year = {2003}, author = {Roy, H and Becker, HD and Reinbolt, J and Kern, D}, title = {When contemporary aminoacyl-tRNA synthetases invent their cognate amino acid metabolism.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {100}, number = {17}, pages = {9837-9842}, pmid = {12874385}, issn = {0027-8424}, mesh = {Amino Acid Sequence ; Amino Acids/*metabolism ; Amino Acyl-tRNA Synthetases/chemistry/genetics/*metabolism ; *Aspartate-tRNA Ligase ; Catalytic Domain/genetics ; Cloning, Molecular ; Escherichia coli/genetics/metabolism ; Genes, Archaeal ; Genes, Bacterial ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Protein Conformation ; Pyrococcus/enzymology/genetics ; *RNA, Transfer, Amino Acyl ; Sequence Homology, Amino Acid ; Substrate Specificity ; }, abstract = {Faithful protein synthesis relies on a family of essential enzymes called aminoacyl-tRNA synthetases, assembled in a piecewise fashion. Analysis of the completed archaeal genomes reveals that all archaea that possess asparaginyl-tRNA synthetase (AsnRS) also display a second ORF encoding an AsnRS truncated from its anticodon binding-domain (AsnRS2). We show herein that Pyrococcus abyssi AsnRS2, in contrast to AsnRS, does not sustain asparaginyl-tRNAAsn synthesis but is instead capable of converting aspartic acid into asparagine. Functional analysis and complementation of an Escherichia coli asparagine auxotrophic strain show that AsnRS2 constitutes the archaeal homologue of the bacterial ammonia-dependent asparagine synthetase A (AS-A), therefore named archaeal asparagine synthetase A (AS-AR). Primary sequence- and 3D-based phylogeny shows that an archaeal AspRS ancestor originated AS-AR, which was subsequently transferred into bacteria by lateral gene transfer in which it underwent structural changes producing AS-A. This study provides evidence that a contemporary aminoacyl-tRNA synthetase can be recruited to sustain amino acid metabolism.}, }
@article {pmid12871231, year = {2003}, author = {Hoffmeister, M and Martin, W}, title = {Interspecific evolution: microbial symbiosis, endosymbiosis and gene transfer.}, journal = {Environmental microbiology}, volume = {5}, number = {8}, pages = {641-649}, doi = {10.1046/j.1462-2920.2003.00454.x}, pmid = {12871231}, issn = {1462-2912}, mesh = {Animals ; Archaea/*physiology ; *Bacterial Physiological Phenomena ; *Biological Evolution ; Chlorophyta/genetics/physiology/ultrastructure ; Chloroplasts/physiology ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Invertebrates/genetics/microbiology/*physiology ; Mitochondria/physiology ; *Symbiosis ; }, abstract = {Microbial symbioses are interesting in their own right and also serve as exemplary models to help biologists to understand two important symbioses in the evolutionary past of eukaryotic cells: the origins of chloroplasts and mitochondria. Most, if not all, microbial symbioses have a chemical basis: compounds produced by one partner are useful for the other. But symbioses can also entail the transfer of genes from one partner to the other, which in some cases cements two cells into a bipartite, co-evolving unit. Here, we discuss some microbial symbioses in which progress is being made in uncovering the nature of symbiotic interactions: anaerobic methane-oxidizing consortia, marine worms that possess endosymbionts instead of a digestive tract, amino acid-producing endosymbionts of aphids, prokaryotic endosymbionts living within a prokaryotic host within mealybugs, endosymbionts of an insect vector of human disease and a photosynthetic sea slug that steals chloroplasts from algae. In the case of chloroplasts and mitochondria, examples of recent and ancient gene transfer to the chromosomes of their host cell illustrate the process of genetic merger in the wake of organelle origins.}, }
@article {pmid12871230, year = {2003}, author = {Jensen, GB and Hansen, BM and Eilenberg, J and Mahillon, J}, title = {The hidden lifestyles of Bacillus cereus and relatives.}, journal = {Environmental microbiology}, volume = {5}, number = {8}, pages = {631-640}, doi = {10.1046/j.1462-2920.2003.00461.x}, pmid = {12871230}, issn = {1462-2912}, mesh = {Animals ; Bacillus anthracis/genetics/pathogenicity/*physiology ; Bacillus cereus/cytology/genetics/pathogenicity/*physiology ; Bacillus thuringiensis/genetics/*physiology ; Digestive System/microbiology ; Ecosystem ; Gene Transfer, Horizontal ; Humans ; Invertebrates/microbiology ; Spores, Bacterial/physiology ; Symbiosis ; }, abstract = {Bacillus cereus sensu lato, the species group comprising Bacillus anthracis, Bacillus thuringiensis and B. cereus (sensu stricto), has previously been scrutinized regarding interspecies genetic correlation and pathogenic characteristics. So far, little attention has been paid to analysing the biological and ecological properties of the three species in their natural environments. In this review, we describe the B. cereus sensu lato living in a world on its own; all B. cereus sensu lato can grow saprophytically under nutrient-rich conditions, which are only occasionally found in the environment, except where nutrients are actively collected. As such, members of the B. cereus group have recently been discovered as common inhabitants of the invertebrate gut. We speculate that all members disclose symbiotic relationships with appropriate invertebrate hosts and only occasionally enter a pathogenic life cycle in which the individual species infects suitable hosts and multiplies almost unrestrained.}, }
@article {pmid12869581, year = {2003}, author = {Lerat, E and Rizzon, C and Biémont, C}, title = {Sequence divergence within transposable element families in the Drosophila melanogaster genome.}, journal = {Genome research}, volume = {13}, number = {8}, pages = {1889-1896}, pmid = {12869581}, issn = {1088-9051}, mesh = {Animals ; DNA Transposable Elements/*genetics ; Drosophila Proteins/genetics ; Drosophila melanogaster/*genetics ; Evolution, Molecular ; Gene Dosage ; Gene Transfer, Horizontal/genetics ; Genes, Insect/genetics ; Genetic Variation/*genetics ; *Genome ; Peptide Hydrolases/genetics ; RNA, Catalytic/genetics ; Retroelements/genetics ; Terminal Repeat Sequences/genetics ; }, abstract = {The availability of the sequenced Drosophila melanogaster genome provides an opportunity to study sequence variation between copies within transposable element families. In this study,we analyzed the 624 copies of 22 transposable element (TE) families (14 LTR retrotransposons, five non-LTR retrotransposons, and three transposons). LTR and non-LTR retrotransposons possessed far fewer divergent elements than the transposons,suggesting that the difference depends on the transposition mechanism. However,there was not a continuous range of divergence of the copies in each class,which were either very similar to the canonical elements,or very divergent from them. This sequence homogeneity among TE family copies matches the theoretical models of the dynamics of these repeated sequences. The sequenced Drosophila genome thus appears to be composed of a mixture of TEs that are still active and of ancient relics that have degenerated and the distribution of which along the chromosomes results from natural selection. This clearly demonstrates that the TEs are highly active within the genome,suggesting that the genetic variability of the Drosophila genome is still being renewed by the action of TEs.}, }
@article {pmid12867462, year = {2003}, author = {Sentchilo, V and Ravatn, R and Werlen, C and Zehnder, AJ and van der Meer, JR}, title = {Unusual integrase gene expression on the clc genomic island in Pseudomonas sp. strain B13.}, journal = {Journal of bacteriology}, volume = {185}, number = {15}, pages = {4530-4538}, pmid = {12867462}, issn = {0021-9193}, mesh = {Chlorobenzoates/pharmacology ; Chromosomes, Bacterial/*genetics ; Collodion ; *Conjugation, Genetic ; Culture Media ; *DNA Transposable Elements ; DNA, Circular/analysis ; Filtration ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal/drug effects ; Green Fluorescent Proteins ; Integrases/genetics/*metabolism ; Luminescent Proteins/genetics/metabolism ; Promoter Regions, Genetic ; Pseudomonas/*enzymology/genetics/growth &amp; development ; Recombinant Fusion Proteins/metabolism ; }, abstract = {An unusual type of gene expression from an integrase promoter was found in cultures of the bacterium Pseudomonas sp. strain B13. The promoter controls expression of the intB13 integrase gene, which is present near the right end of a 105-kb conjugative genomic island (the clc element) encoding catabolism of aromatic compounds. The enzymatic activity of integrase IntB13 is essential for site-specific integration of the clc element into the bacterial host's chromosome. By creating transcription fusions between the intB13 promoter and the gfp gene, we showed that integrase expression in strain B13 was inducible under stationary-phase conditions but, strangely, occurred in only a small proportion of individual bacterial cells rather than equally in the whole population. Integrase expression was significantly stimulated by growing cultures on 3-chlorobenzoate. High cell density, heat shock, osmotic shock, UV irradiation, and treatment with alcohol did not result in measurable integrase expression. The occurrence of the excised form of the clc element and an increase in the rates of clc element transfer in conjugation experiments correlated with the observed induction of the intB13'-gfp fusion in stationary phase and in the presence of 3-chlorobenzoate. This suggested that activation of the intB13 promoter is the first step in stimulation of clc transfer. To our knowledge, this is the first report of a chlorinated compound's stimulating horizontal transfer of the genes encoding its very metabolism.}, }
@article {pmid12861078, year = {2003}, author = {Martin, W}, title = {Gene transfer from organelles to the nucleus: frequent and in big chunks.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {100}, number = {15}, pages = {8612-8614}, pmid = {12861078}, issn = {0027-8424}, mesh = {Arabidopsis/genetics ; Biological Evolution ; Cell Nucleus/*genetics ; Chloroplasts/genetics ; Cyanobacteria/genetics ; DNA, Chloroplast/genetics ; *Gene Transfer, Horizontal ; Genes, Plant ; Kanamycin Resistance/genetics ; Organelles/*genetics ; Symbiosis/genetics ; Nicotiana/genetics ; }, }
@article {pmid12860461, year = {2003}, author = {Chopra, I and O'Neill, AJ and Miller, K}, title = {The role of mutators in the emergence of antibiotic-resistant bacteria.}, journal = {Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy}, volume = {6}, number = {3}, pages = {137-145}, doi = {10.1016/s1368-7646(03)00041-4}, pmid = {12860461}, issn = {1368-7646}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; *Bacteria/drug effects/genetics ; Bacterial Infections/*drug therapy/genetics ; Drug Resistance, Bacterial/*genetics ; Genes, Bacterial/*genetics ; Humans ; *Mutation ; }, abstract = {Bacteria contain a number of error prevention and error correction systems that maintain genome stability. However, strains exhibiting elevated mutation frequencies have recently been reported amongst natural populations of pathogenic Escherichia coli, Salmonella enterica, Pseudomonas aeruginosa, Neisseria meningitidis, Helicobacter pylori and Streptococcus pneumoniae. The majority of naturally occurring, strong mutators contain defects in the methyl-directed mismatch repair (MMR) system, with mutations in mutS predominating. MMR-deficient strains possess superior genetic backgrounds for the selection of some antibiotic-resistance mutations since mutation frequencies up to 1000-fold higher than normal strains have been reported, and resistance levels achieved in mutators can be greater than those arising in non-mutator hosts. MMR is a major constraint to interspecies recombination events. Removal of this barrier, as in the case of MMR defective mutators, also enhances the frequency of horizontal gene transfer, which is an important mechanism of acquired drug resistance in bacteria. Permanent global mutator status is associated with loss of fitness as mutators accumulate deleterious mutations more frequently than non-mutators. Fitness limitations of mutators may be overcome simply by the high bacterial cell densities that can be achieved during acute infection or by the adoption of transient mutator status. Mutators are a risk factor during the treatment of bacterial infections as they appear to enhance the selection of mutants expressing high- and low-level antibiotic resistance and have the capacity to refine existing plasmid-located resistance determinants.}, }
@article {pmid12853958, year = {2003}, author = {Bergthorsson, U and Adams, KL and Thomason, B and Palmer, JD}, title = {Widespread horizontal transfer of mitochondrial genes in flowering plants.}, journal = {Nature}, volume = {424}, number = {6945}, pages = {197-201}, doi = {10.1038/nature01743}, pmid = {12853958}, issn = {1476-4687}, mesh = {Base Sequence ; DNA, Mitochondrial ; DNA, Plant ; *Gene Transfer, Horizontal ; *Genes, Plant ; Magnoliopsida/classification/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/genetics ; Ribosomal Proteins/genetics ; }, abstract = {Horizontal gene transfer--the exchange of genes across mating barriers--is recognized as a major force in bacterial evolution. However, in eukaryotes it is prevalent only in certain phagotrophic protists and limited largely to the ancient acquisition of bacterial genes. Although the human genome was initially reported to contain over 100 genes acquired during vertebrate evolution from bacteria, this claim was immediately and repeatedly rebutted. Moreover, horizontal transfer is unknown within the evolution of animals, plants and fungi except in the special context of mobile genetic elements. Here we show, however, that standard mitochondrial genes, encoding ribosomal and respiratory proteins, are subject to evolutionarily frequent horizontal transfer between distantly related flowering plants. These transfers have created a variety of genomic outcomes, including gene duplication, recapture of genes lost through transfer to the nucleus, and chimaeric, half-monocot, half-dicot genes. These results imply the existence of mechanisms for the delivery of DNA between unrelated plants, indicate that horizontal transfer is also a force in plant nuclear genomes, and are discussed in the contexts of plant molecular phylogeny and genetically modified plants.}, }
@article {pmid12853449, year = {2003}, author = {Molinas, SM and Altabe, SG and Opperdoes, FR and Rider, MH and Michels, PA and Uttaro, AD}, title = {The multifunctional isopropyl alcohol dehydrogenase of Phytomonas sp. could be the result of a horizontal gene transfer from a bacterium to the trypanosomatid lineage.}, journal = {The Journal of biological chemistry}, volume = {278}, number = {38}, pages = {36169-36175}, doi = {10.1074/jbc.M305666200}, pmid = {12853449}, issn = {0021-9258}, mesh = {Alcohol Dehydrogenase/*chemistry/*genetics ; Alleles ; Amino Acid Sequence ; Animals ; Blotting, Southern ; Cloning, Molecular ; Electrophoresis, Polyacrylamide Gel ; Escherichia coli/enzymology/genetics ; Gas Chromatography-Mass Spectrometry ; *Gene Transfer, Horizontal ; Kinetics ; Molecular Sequence Data ; Phylogeny ; Protein Isoforms ; Sequence Homology, Amino Acid ; Substrate Specificity ; Trypanosoma/enzymology/*genetics ; Zinc/chemistry ; }, abstract = {Isopropyl alcohol dehydrogenase (iPDH) is a dimeric mitochondrial alcohol dehydrogenase (ADH), so far detected within the Trypanosomatidae only in the genus Phytomonas. The cloning, sequencing, and heterologous expression of the two gene alleles of the enzyme revealed that it is a zinc-dependent medium-chain ADH. Both polypeptides have 361 amino acids. A mitochondrial targeting sequence was identified. The mature proteins each have 348 amino acids and a calculated molecular mass of 37 kDa. They differ only in one amino acid, which can explain the three isoenzymes and their respective isoelectric points previously found. A phylogenetic analysis locates iPDH within a cluster with fermentative ADHs from bacteria, sharing 74% similarity and 60% identity with Ralstonia eutropha ADH. The characterization of the two bacterially expressed Phytomonas enzymes and the comparison of their kinetic properties with those of the wild-type iPDH and of the R. eutropha ADH strongly support the idea of a horizontal gene transfer event from a bacterium to a trypanosomatid to explain the origin of the iPDH in Phytomonas. Phytomonas iPDH and R. eutropha ADH are able to use a wide range of substrates with similar Km values such as primary and secondary alcohols, diols, and aldehydes, as well as ketones such as acetone, diacetyl, and acetoin. We speculate that, as for R. eutropha ADH, Phytomonas iPDH acts as a safety valve for the release of excess reducing power.}, }
@article {pmid12853136, year = {2003}, author = {Sandberg, R and Bränden, CI and Ernberg, I and Cöster, J}, title = {Quantifying the species-specificity in genomic signatures, synonymous codon choice, amino acid usage and G+C content.}, journal = {Gene}, volume = {311}, number = {}, pages = {35-42}, doi = {10.1016/s0378-1119(03)00581-x}, pmid = {12853136}, issn = {0378-1119}, mesh = {Amino Acids/*genetics ; Archaea/classification/genetics ; Bacteria/classification/genetics ; Base Composition/*genetics ; Codon/*genetics ; *Genome, Archaeal ; *Genome, Bacterial ; Phylogeny ; Species Specificity ; }, abstract = {Each prokaryote has a unique genomic signature as evidenced by a set of species-specific frequencies of short oligonucleotides. With respect to genomic signatures a bacterial genome is homogenous and the variation within a genome is smaller than the variations between genomes of different species. This study quantifies the species-specificity of genomic signatures in the complete genomes of 57 prokaryotes. The species-specificity in the genomic signature was related to the quantification of other sequence biases, such as G+C content, synonymous codon choice and amino acid usage. The results confirm that the genomic signature is genome-wide with high species-specificity in both coding and non-coding regions. In coding regions the species-specific bias in synonymous codon choice was comparable to the genomic signature, while the bias in amino acid usage only captured about 50% of the species-specific bias in the genomic signature. A correlation between the species-specificity in synonymous codon choice and amino acid usage was identified, in which proteins with species-specific amino acid usage were also coded with species-specific synonymous codon choice. However, we demonstrated that the G+C content captures only approximately 40% of the species-specificity in the genomic signature, and is insufficient to explain the species specificity in the non-coding regions. Thus, the species-specific bias in non-coding regions remains largely unknown. Further, we compared the genomic signature in relation to phylogenetic distance. This was performed in order to illustrate the feasibility of a hierarchical classification scheme in future applications of the described classification methodology in screening for horizontal gene transfer and biodiversity studies.}, }
@article {pmid12850372, year = {2003}, author = {McCarthy, DO and Meisner, LF and Bourdeau-Heller, J and Roberts, TR and Wu, SQ and Warner, TF and Albertini, MR}, title = {Localization of transfected B7-1 (CD80) DNA in human melanoma cells after particle-mediated gene transfer.}, journal = {Cancer genetics and cytogenetics}, volume = {144}, number = {2}, pages = {106-111}, doi = {10.1016/s0165-4608(02)00940-8}, pmid = {12850372}, issn = {0165-4608}, support = {CA68466/CA/NCI NIH HHS/United States ; NR00088/NR/NINR NIH HHS/United States ; }, mesh = {B7-1 Antigen/*genetics ; DNA/*analysis ; *Gene Transfer, Horizontal ; Humans ; In Situ Hybridization, Fluorescence ; Melanoma/*genetics ; Plasmids ; Transfection ; Transgenes ; Tumor Cells, Cultured ; }, abstract = {The purpose of this study was to evaluate stable DNA transfection of M-21 human melanoma cells with particle-mediated gene transfer (PMGT) with B7-1 cDNA and to identify sites of gene integration. Stable B7-1 transfectants (M-21-B7) were obtained with PMGT using a plasmid vector containing cDNA for both B7-1 and neomycin phosphotransferase, with subsequent selection with G418. The transfected cells were flow sorted by B7-1 expression into two populations, bright and dim. The bright population had 85%-90% of cells expressing B7-1; the dim population had less than 50% of cells with B7-1 expression. Chromosome analysis with fluorescence in situ hybridization (FISH) and G-banding showed that 70% of bright cells had two main integration sites, with extensive amplification of the transgene. The dim population had random signal distribution, with little or no amplification, despite G418 selection. Because B7-1 has been mapped to 3q21, FISH was performed using a chromosome 3 painting probe (WCP) together with a probe for B7-1. In transfected bright M-21 cells, amplified genes that hybridized with the B7-1 construct were localized to chromosome 3 material inserted into marker chromosomes. These data suggest that B7-1 insertion may involve homologous recombination, but maintenance of integration and amplification required selection.}, }
@article {pmid12849778, year = {2003}, author = {Top, EM and Springael, D}, title = {The role of mobile genetic elements in bacterial adaptation to xenobiotic organic compounds.}, journal = {Current opinion in biotechnology}, volume = {14}, number = {3}, pages = {262-269}, doi = {10.1016/s0958-1669(03)00066-1}, pmid = {12849778}, issn = {0958-1669}, support = {P20 RR 16448-01/RR/NCRR NIH HHS/United States ; }, mesh = {Adaptation, Physiological/*genetics ; Bacteria/*genetics/*metabolism ; Biodegradation, Environmental ; Catalysis ; Environmental Pollutants/*metabolism ; Evolution, Molecular ; Gene Expression Regulation, Bacterial/*genetics ; Gene Transfer, Horizontal/*genetics ; Interspersed Repetitive Sequences/*genetics ; Xenobiotics/*metabolism ; }, abstract = {Retrospective studies clearly indicate that mobile genetic elements (MGEs) play a major role in the in situ spread and even de novo construction of catabolic pathways in bacteria, allowing bacterial communities to rapidly adapt to new xenobiotics. The construction of novel pathways seems to occur by an assembly process that involves horizontal gene transfer: different appropriate genes or gene modules that encode different parts of the novel pathway are recruited from phylogenetically related or distant hosts into one single host. Direct evidence for the importance of catabolic MGEs in bacterial adaptation to xenobiotics stems from observed correlations between catabolic gene transfer and accelerated biodegradation in several habitats and from studies that monitor catabolic MGEs in polluted sites.}, }
@article {pmid12843377, year = {2003}, author = {Waller, RF and Keeling, PJ and van Dooren, GG and McFadden, GI}, title = {Comment on "A green algal apicoplast ancestor".}, journal = {Science (New York, N.Y.)}, volume = {301}, number = {5629}, pages = {49; author reply 49}, doi = {10.1126/science.1084684}, pmid = {12843377}, issn = {1095-9203}, mesh = {Amino Acid Sequence ; Animals ; Apicomplexa/enzymology/*genetics/ultrastructure ; *Biological Evolution ; Chlorophyta/enzymology/*genetics ; Ciliophora/enzymology/genetics/ultrastructure ; Electron Transport Complex IV/chemistry/*genetics ; Gene Transfer, Horizontal ; Genes, Protozoan ; Hydrophobic and Hydrophilic Interactions ; Mitochondria/genetics ; Molecular Sequence Data ; *Phylogeny ; Plastids/*genetics ; Rhodophyta/enzymology/*genetics ; }, }
@article {pmid12840037, year = {2003}, author = {Kunin, V and Ouzounis, CA}, title = {The balance of driving forces during genome evolution in prokaryotes.}, journal = {Genome research}, volume = {13}, number = {7}, pages = {1589-1594}, pmid = {12840037}, issn = {1088-9051}, mesh = {Archaeal Proteins/genetics ; Bacterial Proteins/genetics ; Computational Biology/methods/statistics &amp; numerical data ; Databases, Protein ; *Evolution, Molecular ; Gene Amplification/genetics ; Gene Deletion ; Gene Transfer, Horizontal/genetics ; Genes, Archaeal/genetics ; Genes, Bacterial/genetics ; *Genome, Archaeal ; *Genome, Bacterial ; Helicobacter pylori/genetics ; Models, Genetic ; Phylogeny ; *Prokaryotic Cells/chemistry/metabolism ; Species Specificity ; }, abstract = {Genomes are shaped by evolutionary processes such as gene genesis, horizontal gene transfer (HGT), and gene loss. To quantify the relative contributions of these processes, we analyze the distribution of 12,762 protein families on a phylogenetic tree, derived from entire genomes of 41 Bacteria and 10 Archaea. We show that gene loss is the most important factor in shaping genome content, being up to three times more frequent than HGT, followed by gene genesis, which may contribute up to twice as many genes as HGT. We suggest that gene gain and gene loss in prokaryotes are balanced; thus, on average, prokaryotic genome size is kept constant. Despite the importance of HGT, our results indicate that the majority of protein families have only been transmitted by vertical inheritance. To test our method, we present a study of strain-specific genes of Helicobacter pylori, and demonstrate correct predictions of gene loss and HGT for at least 81% of validated cases. This approach indicates that it is possible to trace genome content history and quantify the factors that shape contemporary prokaryotic genomes.}, }
@article {pmid12839785, year = {2003}, author = {Smets, BF and Morrow, JB and Arango Pinedo, C}, title = {Plasmid introduction in metal-stressed, subsurface-derived microcosms: plasmid fate and community response.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {7}, pages = {4087-4097}, pmid = {12839785}, issn = {0099-2240}, mesh = {Bacteria/*drug effects/genetics/growth &amp; development ; Cadmium/pharmacology ; *Conjugation, Genetic ; Drug Resistance, Bacterial/genetics ; Ecosystem ; Escherichia coli/drug effects/genetics ; *Gene Transfer, Horizontal ; Metals, Heavy/*pharmacology ; Nickel/pharmacology ; Plasmids/*genetics ; *Water Microbiology ; Water Pollution ; }, abstract = {The nonconjugal IncQ plasmids pMOL187 and pMOL222, which contain the metal resistance-encoding genes czc and ncc, were introduced by using Escherichia coli as a transitory delivery strain into microcosms containing subsurface-derived parent materials. The microcosms were semicontinuously dosed with an artificial groundwater to set a low-carbon flux and a target metal stress (0, 10, 100, and 1,000 micro M CdCl(2)), permitting long-term community monitoring. The broad-host-range IncPalpha plasmid RP4 was also transitorily introduced into a subset of microcosms. No novel community phenotype was detected after plasmid delivery, due to the high background resistances to Cd and Ni. At fixed Cd doses, however, small but consistent increases in Cd(r) or Ni(r) density were measured due to the introduction of a single pMOL plasmid, and this effect was enhanced by the joint introduction of RP4; the effects were most significant at the highest Cd doses. The pMOL plasmids introduced could, however, be monitored via czc- and ncc-targeted infinite-dilution PCR (ID-PCR) methods, because these genes were absent from the indigenous community: long-term presence of czc (after 14 or 27 weeks) was contingent on the joint introduction of RP4, although RP4 cointroduction was not yet required to ensure retention of ncc after 8 weeks. Plasmids isolated from Ni(r) transconjugants further confirmed the presence and retention of a pMOL222-sized plasmid. ID-PCR targeting the RP4-specific trafA gene revealed retention of RP4 for at least 8 weeks. Our findings confirm plasmid transfer and long-term retention in low-carbon-flux, metal-stressed subsurface communities but indicate that the subsurface community examined has limited mobilization potential for the IncQ plasmids employed.}, }
@article {pmid12838609, year = {2003}, author = {Krylov, VN}, title = {[Role of horizontal gene transfer by bacteriophages in the origin of pathogenic bacteria].}, journal = {Genetika}, volume = {39}, number = {5}, pages = {595-620}, pmid = {12838609}, issn = {0016-6758}, mesh = {Animals ; Bacteria/*genetics/pathogenicity ; Bacteriophages/genetics/*pathogenicity ; Biological Evolution ; DNA Transposable Elements ; *Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Genome, Viral ; Genomics ; Humans ; Lysogeny/genetics ; Pseudomonas Phages/genetics/pathogenicity ; Pseudomonas aeruginosa ; Transduction, Genetic ; Virulence ; }, abstract = {The review considers the involvement of bacteriophages in transferring genes, which determine bacterial pathogenicity, and the increasing role of comparative genomics and genetics of bacteria and bacteriophages in detecting new cases of horizontal gene transfer. Examples of phage participation in this process proved to a different extent are described. Emphasis is placed on the original work carried out in Russia and focused on bacteriophages (temperate transposable phages and giant virulent phi KZ-like phages) of conditional pathogen Pseudomonas aeruginosa. Consideration is given to the possible lines of further research of the role of bacteriophages in the infection process and, in particular, the role of virulent phages, whose products are similar to those of pathogenic bacteria, in modification of clinical signs of infectious diseases and in evolution. An attempt is made to predict the possible direction of pathogen evolution associated with development of new treatment strategies and generation of new specific niches.}, }
@article {pmid12836690, year = {2003}, author = {Lecharny, A and Boudet, N and Gy, I and Aubourg, S and Kreis, M}, title = {Introns in, introns out in plant gene families: a genomic approach of the dynamics of gene structure.}, journal = {Journal of structural and functional genomics}, volume = {3}, number = {1-4}, pages = {111-116}, pmid = {12836690}, issn = {1345-711X}, mesh = {Arabidopsis/genetics ; *Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal/genetics ; *Introns ; *Multigene Family ; Plants/*genetics ; }, abstract = {Gene duplication is considered to be a source of genetic information for the creation of new functions. The Arabidopsis thaliana genome sequence revealed that a majority of plant genes belong to gene families. Regarding the problem of genes involved in the genesis of novel organs or functions during evolution, the reconstitution of the evolutionary history of gene families is of critical importance. A comparison of the intron/exon gene structure may provide clues for the understanding of the evolutionary mechanisms underlying the genesis of gene families. An extensive study of A. thaliana genome showed that families of duplicated genes may be organized according to the number and/or density of intron and the diversity in gene structure. In this paper, we propose a genomic classification of several A. thaliana gene families based on introns in an evolutionary perspective.}, }
@article {pmid12836680, year = {2003}, author = {Brosius, J}, title = {Gene duplication and other evolutionary strategies: from the RNA world to the future.}, journal = {Journal of structural and functional genomics}, volume = {3}, number = {1-4}, pages = {1-17}, pmid = {12836680}, issn = {1345-711X}, mesh = {Animals ; *Evolution, Molecular ; *Gene Duplication ; Humans ; RNA/*metabolism ; Retroelements/genetics ; }, abstract = {Beginning with a hypothetical RNA world, it is apparent that many evolutionary transitions led to the complexity of extant species. The duplication of genetic material is rooted in the RNA world. One of two major routes of gene amplification, retroposition, originated from mechanisms that facilitated the transition to DNA as hereditary material. Even in modern genomes the process of retroposition leads to genetic novelties including the duplication of protein and RNA coding genes, as well as regulatory elements and their juxtapositon. We examine whether and to what extent known evolutionary principles can be applied to an RNA-based world. We conclude that the major basic Neo-Darwinian principles that include amplification, variation and selection already governed evolution in the RNA and RNP worlds. In this hypothetical RNA world there were few restrictions on the exchange of genetic material and principles that acted as borders at later stages, such as Weismann's Barrier, the Central Dogma of Molecular Biology, or the Darwinian Threshold were absent or rudimentary. RNA was more than a gene: it had a dual role harboring, genotypic and phenotypic capabilities, often in the same molecule. Nuons, any discrete nucleic acid sequences, were selected on an individual basis as well as in groups. The performance and success of an individual nuon was markedly dependent on the type of other nuons in a given cell. In the RNA world the transition may already have begun towards the linkage of nuons to yield a composite linear RNA genome, an arrangement necessitating the origin of RNA processing. A concatenated genome may have curbed unlimited exchange of genetic material; concomitantly, selfish nuons were more difficult to purge. A linked genome may also have constituted the beginning of the phenotype/genotype separation. This division of tasks was expanded when templated protein biosynthesis led to the RNP world, and more so when DNA took over as genetic material. The aforementioned barriers and thresholds increased and the significance and extent of horizontal gene transfer fluctuated over major evolutionary transitions. At the dawn of the most recent transformation, a fast evolutionary transition that we will be witnessing in our life times, a form of Lamarckism is raising its head.}, }
@article {pmid12834405, year = {2003}, author = {Kleine, T and Lockhart, P and Batschauer, A}, title = {An Arabidopsis protein closely related to Synechocystis cryptochrome is targeted to organelles.}, journal = {The Plant journal : for cell and molecular biology}, volume = {35}, number = {1}, pages = {93-103}, doi = {10.1046/j.1365-313x.2003.01787.x}, pmid = {12834405}, issn = {0960-7412}, mesh = {Amino Acid Sequence ; Arabidopsis/cytology/genetics/*metabolism ; Arabidopsis Proteins/*chemistry/*metabolism ; Chloroplasts/*metabolism ; Cryptochromes ; Cyanobacteria/*chemistry ; DNA/metabolism ; DNA-Binding Proteins/chemistry/metabolism ; Deoxyribodipyrimidine Photo-Lyase/*chemistry/*metabolism ; *Drosophila Proteins ; *Eye Proteins ; Flavin-Adenine Dinucleotide/metabolism ; Flavoproteins/*chemistry/metabolism ; Mitochondria/*metabolism ; Molecular Sequence Data ; *Photoreceptor Cells, Invertebrate ; Phylogeny ; Protein Transport ; Receptors, G-Protein-Coupled ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {Cryptochromes (CRYs) are blue/UV-A photoreceptors related to the DNA repair enzyme DNA photolyase. They have been found in plants, animals and most recently in the cyanobacterium Synechocystis. Closely related to the Synechocystis cryptochrome is the Arabidopsis gene At5g24850. Here, we show that the encoded protein of At5g24850 binds flavin adenine dinucleotide (FAD). It has no photolyase activity, and is likely to function as a photoreceptor. We have named it At-cry3 to distinguish it from the other Arbabidopsis cryptochrome homologues At-cry1 and At-cry2. At-cry3 carries an N-terminal sequence, which mediates import into chloroplasts and mitochondria. Furthermore, we show that At-cry3 binds DNA. DNA binding was also demonstrated for the Synechocystis cryptochrome, indicating that both photoreceptors could have similar modes of action. Based on the finding of a new cryptochrome class in bacteria and plants, it has been suggested that cryptochromes evolved before the divergence of eukaryotes and prokaryotes. However, our phylogenetic analyses are also consistent with an alternative explanation that the presence of cryptochromes in the plant nuclear genome is the result of dual horizontal gene transfer. That is, CRY1 and CRY2 genes may originate from an endosymbiotic ancestor of modern-day alpha-proteobacteria, while the CRY3 gene may originate from an endosymbiotic ancestor of modern-day cyanobacteria.}, }
@article {pmid12828556, year = {2003}, author = {Orentas, RJ and Bircher, LA and Roskopf, S}, title = {Retroviral transfer of T-cell receptor genes produces cells with a broad range of lytic activity.}, journal = {Scandinavian journal of immunology}, volume = {58}, number = {1}, pages = {33-42}, pmid = {12828556}, issn = {0300-9475}, support = {R01 CA082781-01A2/CA/NCI NIH HHS/United States ; R01 CA082781/CA/NCI NIH HHS/United States ; T32 HL007209/HL/NHLBI NIH HHS/United States ; R01 CA082781-02/CA/NCI NIH HHS/United States ; R01CA82781/CA/NCI NIH HHS/United States ; }, mesh = {Cell Line ; *Cytotoxicity, Immunologic ; Gene Transfer, Horizontal ; Humans ; Receptors, Antigen, T-Cell/*genetics ; Retroviridae/*genetics ; T-Lymphocytes, Cytotoxic/*immunology ; }, abstract = {The ability to transfer the T-cell receptor (TCR) for antigen using a retroviral vector has opened the door to a new paradigm for T-cell-based immunotherapy. Using recombinant TCRs, a population of activated T cells can now be redirected to recognize and lyse cellular targets according to the specificity afforded by the transduced TCR genes. To examine the range of lytic activity displayed by the transduced TCRs, transduced T cells were re-cloned by limiting dilution and quantitatively analysed for lytic activity. The lytic activity of the transduced TCRs varied considerably, as determined by the Km and Vmax of lysis. The lytic activity seen in the secondary clones generated from vector-transduced peripheral blood mononuclear cell demonstrated that one of the clones approached the lytic activity of the parental 'TCR donor' cytotoxic T-cell lymphocyte (CTL) clone, whereas the remainder demonstrated either reduced Vmax or reduced Vmax and Km. Thus, the lytic activity of a transduced TCR depends not only on its genetic sequence but also on the cellular context within which it is expressed. Analysis of TCR Vbeta transcript levels by real time polymerase chain reaction revealed that while total Vbeta gene expression was fairly constant, expression of the retrovirally transduced Vbeta chain varied greatly in transduced CD8+ CTL clones.}, }
@article {pmid12825179, year = {2003}, author = {Hiltke, TJ and Schiffmacher, AT and Dagonese, AJ and Sethi, S and Murphy, TF}, title = {Horizontal transfer of the gene encoding outer membrane protein P2 of nontypeable Haemophilus influenzae, in a patient with chronic obstructive pulmonary disease.}, journal = {The Journal of infectious diseases}, volume = {188}, number = {1}, pages = {114-117}, doi = {10.1086/375724}, pmid = {12825179}, issn = {0022-1899}, support = {AI19641/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Outer Membrane Proteins/*genetics ; Electrophoresis, Gel, Pulsed-Field ; Gene Transfer, Horizontal/*genetics ; Haemophilus Infections/*complications/*microbiology ; Haemophilus influenzae/*genetics ; Humans ; Male ; Middle Aged ; Polymerase Chain Reaction ; Pulmonary Disease, Chronic Obstructive/*complications/*microbiology ; Sequence Analysis, DNA ; }, abstract = {An adult with chronic obstructive pulmonary disease was monitored prospectively for 2 years. Nontypeable Haemophilus influenzae was isolated from sputum cultures at 22 of 23 monthly clinic visits. Analysis of the isolates, by pulsed-field gel electrophoresis (PFGE), revealed that the patient was colonized by 3 different strains during the 2-year period. The gene encoding outer-membrane protein (OMP) P2, ompP2, was amplified from sputum samples and selected strains obtained from this patient. Analysis of the ompP2 sequences, in combination with the PFGE patterns, indicated that ompP2 horizontal transfer between 2 strains occurred in the respiratory tract, between clinic visits 13 and 14. Observation of ompP2 horizontal transfer in the human respiratory tract has important implications for both the understanding of ompP2 diversity among strains and the future design of OMP P2-based vaccines.}, }
@article {pmid12824689, year = {2003}, author = {Mandal, S and Mandal, MD and Pal, NK}, title = {R-Factor in Salmonella enterica serovar typhi: transfer to and acquisition from Escherichia coli.}, journal = {Japanese journal of infectious diseases}, volume = {56}, number = {2}, pages = {65-67}, pmid = {12824689}, issn = {1344-6304}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; Escherichia coli/drug effects/*genetics ; *Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Salmonella typhi/drug effects/*genetics ; Tetrahydrofolate Dehydrogenase/*genetics ; Transformation, Genetic ; }, abstract = {Blood culture isolates of Salmonella enterica serovar Typhi showing high degrees of resistance to ampicillin, chloramphenicol, cotrimoxazole and tetracycline (ACCoT-resistance) transferred their full resistance phenotype to antibiotic-sensitive S. enterica serovar Typhi strains through the primary recipient Escherichia coli C600. Transfer frequencies were 0.80 x 10(-5) and 0.80 x 10(-6), respectively, in the primary and secondary transfer experiments. The Escherichia coli isolates from urinary tract infection cases showing high minimum inhibitory concentration values (microg/ml) to A (2,000-5,000), C (2,000-5,000), Co (250-1,200), and T (500-2,000) also transferred ACCoT-resistance to the antibiotic-sensitive S. enterica serovar Typhi and then to E. coli C600 with transfer frequencies 0.61 x 10(-6) and 0.98 x 10(-5), respectively. Curing experiments revealed the loss of ACCoT-resistance from the original and the transconjugant S. enterica serovar Typhi strains. Results suggest that R-factor from other enteric bacteria is acquired by S. enterica serovar Typhi, and that it (R-factor) is unstable in nature.}, }
@article {pmid12823821, year = {2003}, author = {Ubeda, C and Tormo, MA and Cucarella, C and Trotonda, P and Foster, TJ and Lasa, I and Penadés, JR}, title = {Sip, an integrase protein with excision, circularization and integration activities, defines a new family of mobile Staphylococcus aureus pathogenicity islands.}, journal = {Molecular microbiology}, volume = {49}, number = {1}, pages = {193-210}, doi = {10.1046/j.1365-2958.2003.03577.x}, pmid = {12823821}, issn = {0950-382X}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Biofilms ; Cattle ; Chromosome Mapping ; DNA, Circular/genetics/metabolism ; Female ; Gene Transfer, Horizontal ; Genomic Islands/*genetics ; Humans ; Integrases/chemistry/*genetics/*metabolism ; Mammary Glands, Animal/microbiology ; Molecular Sequence Data ; Open Reading Frames ; Sequence Alignment ; Sheep ; Staphylococcal Infections/microbiology ; Staphylococcus aureus/*enzymology/*genetics/pathogenicity ; }, abstract = {We report the complete sequence of Staphylococcal pathogenicity island bovine 2 (SaPIbov2), encoding the biofilm-associated protein Bap. SaPIbov2 contains 24 open reading frames, including sip, which encodes a functional staphylococcal integrase protein. SaPIbov2 is bordered by 18 bp direct repeats. The integration site into the chromosome lies at the 3' end of a gene encoding GMP synthase. SaPIbov2 has extensive similarity to previously described pathogenicity islands of Staphylococcus aureus. The principal difference is that toxin genes present in the other pathogenicity islands are exchanged for a transposon-like element that carries the bap gene and genes encoding an ABC transporter and a transposase. Also, SaPIbov2 can be excised to form a circular element and can integrate site-specifically and RecA-independently at a chromosomal att site in a Sip-dependent manner. This was demonstrated both in S. aureus and with plasmid substrates ectopically in Escherichia coli. Thus, SaPIbov2 encodes a functional recombinase of the integrase family that promotes element excision and insertion/integration. In addition, we demonstrated that the presence of SaPIbov2 facilitated the persistence of S. aureus in an intramammary gland infection model. Finally, different bovine isolates of S. aureus were found to carry islands related to SaPIbov2, suggesting the existence of a family of related pathogenicity islands.}, }
@article {pmid12823187, year = {2003}, author = {Zehr, JP and Jenkins, BD and Short, SM and Steward, GF}, title = {Nitrogenase gene diversity and microbial community structure: a cross-system comparison.}, journal = {Environmental microbiology}, volume = {5}, number = {7}, pages = {539-554}, doi = {10.1046/j.1462-2920.2003.00451.x}, pmid = {12823187}, issn = {1462-2912}, mesh = {Archaea/classification/enzymology/*genetics ; Bacteria/classification/enzymology/*genetics ; *Ecosystem ; *Environmental Microbiology ; Euryarchaeota/classification/enzymology/genetics ; Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; *Genetic Variation ; Nitrogen Fixation ; Nitrogenase/*genetics ; Oxidoreductases/genetics ; Phylogeny ; }, abstract = {Biological nitrogen fixation is an important source of fixed nitrogen for the biosphere. Microorganisms catalyse biological nitrogen fixation with the enzyme nitrogenase, which has been highly conserved through evolution. Cloning and sequencing of one of the nitrogenase structural genes, nifH, has provided a large, rapidly expanding database of sequences from diverse terrestrial and aquatic environments. Comparison of nifH phylogenies to ribosomal RNA phylogenies from cultivated microorganisms shows little conclusive evidence of lateral gene transfer. Sequence diversity far outstrips representation by cultivated representatives. The phylogeny of nitrogenase includes branches that represent phylotypic groupings based on ribosomal RNA phylogeny, but also includes paralogous clades including the alternative, non-molybdenum, non-vanadium containing nitrogenases. Only a few alternative or archaeal nitrogenase sequences have as yet been obtained from the environment. Extensive analysis of the distribution of nifH phylotypes among habitats indicates that there are characteristic patterns of nitrogen fixing microorganisms in termite guts, sediment and soil environments, estuaries and salt marshes, and oligotrophic oceans. The distribution of nitrogen-fixing microorganisms, although not entirely dictated by the nitrogen availability in the environment, is non-random and can be predicted on the basis of habitat characteristics. The ability to assay for gene expression and investigate genome arrangements provides the promise of new tools for interrogating natural populations of diazotrophs. The broad analysis of nitrogenase genes provides a basis for developing molecular assays and bioinformatics approaches for the study of nitrogen fixation in the environment.}, }
@article {pmid12821449, year = {2003}, author = {Balsalobre, L and Ferrándiz, MJ and Liñares, J and Tubau, F and de la Campa, AG}, title = {Viridans group streptococci are donors in horizontal transfer of topoisomerase IV genes to Streptococcus pneumoniae.}, journal = {Antimicrobial agents and chemotherapy}, volume = {47}, number = {7}, pages = {2072-2081}, pmid = {12821449}, issn = {0066-4804}, mesh = {Base Sequence ; DNA Gyrase/genetics ; DNA Topoisomerase IV/*genetics ; DNA, Intergenic ; Gene Transfer, Horizontal ; Humans ; Molecular Sequence Data ; Open Reading Frames/genetics ; Recombination, Genetic ; Restriction Mapping ; Streptococcus pneumoniae/enzymology/*genetics ; Viridans Streptococci/enzymology/*genetics ; }, abstract = {A total of 46 ciprofloxacin-resistant (Cip(r)) Streptococcus pneumoniae strains were isolated from 1991 to 2001 at the Hospital of Bellvitge. Five of these strains showed unexpectedly high rates of nucleotide variations in the quinolone resistance-determining regions (QRDRs) of their parC, parE, and gyrA genes. The nucleotide sequence of the full-length parC, parE, and gyrA genes of one of these isolates revealed a mosaic structure compatible with an interspecific recombination origin. Southern blot analysis and nucleotide sequence determinations showed the presence of an ant-like gene in the intergenic parE-parC regions of the S. pneumoniae Cip(r) isolates with high rates of variations in their parE and parC QRDRs. The ant-like gene was absent from typical S. pneumoniae strains, whereas it was present in the intergenic parE-parC regions of the viridans group streptococci (Streptococcus mitis and Streptococcus oralis). These results suggest that the viridans group streptococci are acting as donors in the horizontal transfer of fluoroquinolone resistance genes to S. pneumoniae.}, }
@article {pmid12820901, year = {2003}, author = {Andersson, JO and Roger, AJ}, title = {Evolution of glutamate dehydrogenase genes: evidence for lateral gene transfer within and between prokaryotes and eukaryotes.}, journal = {BMC evolutionary biology}, volume = {3}, number = {}, pages = {14}, pmid = {12820901}, issn = {1471-2148}, mesh = {Algal Proteins/genetics ; Animals ; Bacteria/enzymology/genetics ; Bacterial Proteins/genetics ; Chlorophyta/enzymology/genetics ; Deltaproteobacteria/enzymology/genetics ; Diplomonadida/enzymology/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome, Archaeal ; Genome, Bacterial ; Genome, Protozoan ; Glutamate Dehydrogenase/*genetics ; Molecular Sequence Data ; Rhodophyta/enzymology/genetics ; Trichomonadida/enzymology/genetics ; }, abstract = {BACKGROUND: Lateral gene transfer can introduce genes with novel functions into genomes or replace genes with functionally similar orthologs or paralogs. Here we present a study of the occurrence of the latter gene replacement phenomenon in the four gene families encoding different classes of glutamate dehydrogenase (GDH), to evaluate and compare the patterns and rates of lateral gene transfer (LGT) in prokaryotes and eukaryotes.<br><br>RESULTS: We extend the taxon sampling of gdh genes with nine new eukaryotic sequences and examine the phylogenetic distribution pattern of the various GDH classes in combination with maximum likelihood phylogenetic analyses. The distribution pattern analyses indicate that LGT has played a significant role in the evolution of the four gdh gene families. Indeed, a number of gene transfer events are identified by phylogenetic analyses, including numerous prokaryotic intra-domain transfers, some prokaryotic inter-domain transfers and several inter-domain transfers between prokaryotes and microbial eukaryotes (protists).<br><br>CONCLUSION: LGT has apparently affected eukaryotes and prokaryotes to a similar extent within the gdh gene families. In the absence of indications that the evolution of the gdh gene families is radically different from other families, these results suggest that gene transfer might be an important evolutionary mechanism in microbial eukaryote genome evolution.}, }
@article {pmid12820878, year = {2003}, author = {Zhao, MW and Hao, R and Chen, JF and Martin, F and Eriani, G and Wang, ED}, title = {Enzymes assembled from Aquifex aeolicus and Escherichia coli leucyl-tRNA synthetases.}, journal = {Biochemistry}, volume = {42}, number = {25}, pages = {7694-7700}, doi = {10.1021/bi027394m}, pmid = {12820878}, issn = {0006-2960}, mesh = {Amino Acyl-tRNA Synthetases/genetics/*metabolism ; Escherichia coli/*enzymology ; Evolution, Molecular ; Gene Transfer, Horizontal ; Hot Temperature ; Kinetics ; Mutation ; RNA, Transfer, Leu/*metabolism ; Structure-Activity Relationship ; }, abstract = {Aquifex aeolicus alphabeta-LeuRS is the only known heterodimeric LeuRS, while Escherichia coli LeuRS is a canonical monomeric enzyme. By using the genes encoding A. aeolicus and E. coli LeuRS as PCR templates, the genes encoding the alpha and beta subunits from A. aeolicus alphabeta-LeuRS and the equivalent amino- and carboxy-terminal parts of E. coli LeuRS (identified as alpha' and beta') were amplified and recombined using suitable plasmids. These recombinant plasmids were transformed or cotransformed into E. coli to produce five monomeric and five heterodimeric LeuRS mutants. Seven of these were successfully overexpressed in vivo and purified, while three dimeric mutants with the beta' part of E. coli LeuRS were not successfully expressed. The seven purified mutants catalyzed amino acid activation, although several exhibited reduced aminoacylation properties. Removal of the last 36 residues of the alpha subunit of the A. aeolicus enzyme was determined to be deleterious for tRNA charging. Indeed, subunit exchange showed that the cross-species-specific recognition of A. aeolicus tRNA(Leu) occurs at the alpha subunit. None of the mixed E. coli-A. aeolicus enzymes were as thermostable as the native alphabeta-LeuRS. However, the fusion of the two alpha and beta peptides from A. aeolicus as a single chain analogous to canonical LeuRS resulted in a product more resistant to heat denaturation than the original enzyme.}, }
@article {pmid12820799, year = {2003}, author = {Jönsson, M and Ström, K and Swedberg, G}, title = {Mutations and horizontal transmission have contributed to sulfonamide resistance in Streptococcus pyogenes.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {9}, number = {2}, pages = {147-153}, doi = {10.1089/107662903765826732}, pmid = {12820799}, issn = {1076-6294}, mesh = {Amino Acid Sequence ; Anti-Infective Agents/*pharmacology ; Base Sequence ; Cloning, Molecular ; DNA, Bacterial/genetics ; Dihydropteroate Synthase/genetics/metabolism ; Drug Resistance, Bacterial ; Gene Deletion ; Gene Transfer, Horizontal/*genetics/*physiology ; Kinetics ; Microbial Sensitivity Tests ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed/genetics ; Mutation/*genetics/*physiology ; Operon/genetics ; Protein Conformation ; Reverse Transcriptase Polymerase Chain Reaction ; Streptococcus pyogenes/*drug effects/*genetics ; Sulfonamides/*pharmacology ; }, abstract = {Two variants of dihydropteroate synthase (DHPS) were found among sulfonamide-resistant Streptococcus pyogenes, one of which was characterized by a 2-amino-acid addition in a conserved part of the enzyme. The enzyme kinetics of both variants was compared with the kinetics of DHPS from a sulfonamide-susceptible S. pyogenes. The most striking difference was a substantially elevated Ki for both variants, but variations in Km for both of its substrates p-aminobenzoic acid (p-AB) and dihydropteridine-pyrophosphate (pteridine) were also found. In the resistance variant lacking additions, the amino acid at position 213 was changed by site-directed mutagenesis from a Gly to an Arg, which resulted in a lower Ki. The corresponding change from an Arg to a Gly in the DHPS from a susceptible isolate led to a substantially increased Ki, confirming the importance of this amino acid difference for the resistance. Nucleotide sequence determinations of the complete folate operon revealed in some isolates a mosaic pattern of differences compared to the wild type, not only in the genes coding for DHPS and GTP cyclohydrolase (GTPCH) noted earlier but also in genes coding for dihydroneopterin aldolase (DHNA) and hydroxymethylpterin pyrophosphokinase (HPPK). Regions of sequence differences were interspersed with regions of complete identity in a mosaic pattern, indicating a dispersed pattern of uptake of foreign DNA in the resistant isolates.}, }
@article {pmid12817081, year = {2003}, author = {Stegemann, S and Hartmann, S and Ruf, S and Bock, R}, title = {High-frequency gene transfer from the chloroplast genome to the nucleus.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {100}, number = {15}, pages = {8828-8833}, pmid = {12817081}, issn = {0027-8424}, mesh = {Base Sequence ; Cell Nucleus/genetics ; Chloroplasts/*genetics ; Crosses, Genetic ; DNA, Chloroplast/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genetic Markers ; Genetic Variation ; *Genome, Plant ; Kanamycin Resistance/genetics ; Models, Genetic ; Plants, Genetically Modified ; Symbiosis ; Nicotiana/genetics/microbiology ; }, abstract = {Eukaryotic cells arose through endosymbiotic uptake of free-living bacteria followed by massive gene transfer from the genome of the endosymbiont to the host nuclear genome. Because this gene transfer took place over a time scale of hundreds of millions of years, direct observation and analysis of primary transfer events has remained difficult. Hence, very little is known about the evolutionary frequency of gene transfer events, the size of transferred genome fragments, the molecular mechanisms of the transfer process, or the environmental conditions favoring its occurrence. We describe here a genetic system based on transgenic chloroplasts carrying a nuclear selectable marker gene that allows the efficient selection of plants with a nuclear genome that carries pieces transferred from the chloroplast genome. We can select such gene transfer events from a surprisingly small population of plant cells, indicating that the escape of genetic material from the chloroplast to the nuclear genome occurs much more frequently than generally believed and thus may contribute significantly to intraspecific and intraorganismic genetic variation.}, }
@article {pmid12816550, year = {2003}, author = {Faguy, DM}, title = {Lateral gene transfer (LGT) between Archaea and Escherichia coli is a contributor to the emergence of novel infectious disease.}, journal = {BMC infectious diseases}, volume = {3}, number = {}, pages = {13}, pmid = {12816550}, issn = {1471-2334}, mesh = {Archaea/*genetics ; Escherichia coli/*genetics/pathogenicity ; *Gene Transfer, Horizontal ; Transduction, Genetic ; Transformation, Bacterial/genetics ; Transformation, Genetic ; Virulence/genetics ; }, abstract = {BACKGROUND: Lateral gene transfer is the major mechanism for acquisition of new virulence genes in pathogens. Recent whole genome analyses have suggested massive gene transfer between widely divergent organisms.<br><br>Archeal-like genes acting as virulence genes are present in several pathogens and genomes contain a number of archaeal-like genes of unknown function. Archaea, by virtue of their very different evolutionary history and different environment, provide a pool of potential virulence genes to bacterial pathogens.<br><br>TESTING THE HYPOTHESIS: We can test this hypothesis by 1)identifying genes likely to have been transferred (directly or indirectly) to E. coli O157:H7 from archaea; 2)investigating the distribution of similar genes in pathogens and non-pathogens and 3)performing rigorous phylogenetic analyses on putative transfers.<br><br>Although this hypothesis focuses on archaea and E. coli, it will serve as a model having broad applicability to a number of pathogenic systems. Since no archaea are known vertebrate pathogens, archaeal-like transferred genes that are associated with virulence in bacteria represent a clear model for the emergence of virulence genes.}, }
@article {pmid12815109, year = {2003}, author = {Wolfgang, MC and Kulasekara, BR and Liang, X and Boyd, D and Wu, K and Yang, Q and Miyada, CG and Lory, S}, title = {Conservation of genome content and virulence determinants among clinical and environmental isolates of Pseudomonas aeruginosa.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {100}, number = {14}, pages = {8484-8489}, pmid = {12815109}, issn = {0027-8424}, support = {P01 DK053369/DK/NIDDK NIH HHS/United States ; DK53369/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics ; DNA, Bacterial/genetics ; Fresh Water ; Gene Expression Profiling ; Gene Transfer, Horizontal ; Genetic Vectors/genetics ; *Genome, Bacterial ; Humans ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; Pseudomonas Infections/*microbiology ; Pseudomonas aeruginosa/*genetics/pathogenicity ; Recombination, Genetic ; Saccharomyces cerevisiae/genetics ; Transformation, Genetic ; Virulence/*genetics ; Washington ; *Water Microbiology ; }, abstract = {Pseudomonas aeruginosa is a ubiquitous environmental bacterium capable of causing a variety of life-threatening human infections. The genetic basis for preferential infection of certain immunocompromised patients or individuals with cystic fibrosis by P. aeruginosa is not understood. To establish whether variation in the genomic repertoire of P. aeruginosa strains can be associated with a particular type of infection, we used a whole-genome DNA microarray to determine the genome content of 18 strains isolated from the most common human infections and environmental sources. A remarkable conservation of genes including those encoding nearly all known virulence factors was observed. Phylogenetic analysis of strain-specific genes revealed no correlation between genome content and infection type. Clusters of strain-specific genes in the P. aeruginosa genome, termed variable segments, appear to be preferential sites for the integration of novel genetic material. A specialized cloning vector was developed for capture and analysis of these genomic segments. With this capture system a site associated with the strain-specific ExoU cytotoxin-encoding gene was interrogated and an 80-kb genomic island carrying exoU was identified. These studies demonstrate that P. aeruginosa strains possess a highly conserved genome that encodes genes important for survival in numerous environments and allows it to cause a variety of human infections. The acquisition of novel genetic material, such as the exoU genomic island, through horizontal gene transfer may enhance colonization and survival in different host environments.}, }
@article {pmid12812367, year = {2003}, author = {Richards, TA and Hirt, RP and Williams, BA and Embley, TM}, title = {Horizontal gene transfer and the evolution of parasitic protozoa.}, journal = {Protist}, volume = {154}, number = {1}, pages = {17-32}, doi = {10.1078/143446103764928468}, pmid = {12812367}, issn = {1434-4610}, mesh = {Alphaproteobacteria/classification/genetics ; Animals ; Betaproteobacteria/classification/genetics ; Eukaryota/classification/*genetics/*pathogenicity ; Gammaproteobacteria/classification/genetics ; Gene Transfer Techniques ; Parasites/classification/*genetics ; Phylogeny ; Plastids/genetics ; }, }
@article {pmid12810941, year = {2003}, author = {Raymond, J and Blankenship, RE}, title = {Horizontal gene transfer in eukaryotic algal evolution.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {100}, number = {13}, pages = {7419-7420}, pmid = {12810941}, issn = {0027-8424}, mesh = {Biological Evolution ; Eukaryota/*genetics/*physiology ; *Gene Transfer, Horizontal ; Models, Biological ; Models, Genetic ; Phylogeny ; }, }
@article {pmid12807700, year = {2003}, author = {Pierce, SK and Massey, SE and Hanten, JJ and Curtis, NE}, title = {Horizontal transfer of functional nuclear genes between multicellular organisms.}, journal = {The Biological bulletin}, volume = {204}, number = {3}, pages = {237-240}, doi = {10.2307/1543594}, pmid = {12807700}, issn = {0006-3185}, mesh = {Animals ; Blotting, Southern ; Blotting, Western ; Chloramphenicol/metabolism ; Chloroplasts/physiology ; Cycloheximide/metabolism ; DNA, Chloroplast/genetics ; Electrophoresis, Polyacrylamide Gel ; Eukaryota/metabolism/*physiology ; *Gene Transfer, Horizontal ; Light-Harvesting Protein Complexes/*genetics ; Mollusca/genetics/*physiology ; Precipitin Tests ; Protein Synthesis Inhibitors/metabolism ; *Symbiosis ; }, }
@article {pmid12807689, year = {2003}, author = {de Souza, CP}, title = {Pathogenicity mechanisms of prokaryotic cells: an evolutionary view.}, journal = {The Brazilian journal of infectious diseases : an official publication of the Brazilian Society of Infectious Diseases}, volume = {7}, number = {1}, pages = {23-31}, pmid = {12807689}, issn = {1413-8670}, mesh = {Bacteria/genetics/*pathogenicity ; DNA, Bacterial ; *Evolution, Molecular ; Genetic Variation ; Host-Parasite Interactions ; Humans ; Mutation ; Prokaryotic Cells ; Virulence Factors ; }, abstract = {The success of pathogenic microbes depends on their ability to colonize host tissues and to counter host defense mechanisms. Microorganisms can produce overwhelming infection because of their relatively short generation times, and because they have evolved powerful mechanisms for generating phenotypic diversity as an efficient strategy for adapting to rapidly responding immune system defenses and the broad range of polymorphisms characteristic of different host tissues. Bacterial evolution may not be a continuous process, but more of a succession of temporally spaced major events. These events cause a non-gradual sequence of adaptations to a given environment. The pathogenicity islands are genetically unstable elements, and many of the genes coding for the adhesins, toxins and other virulence factors are present in pathogenicity islands, which almost certainly had former lives as accessory elements or as parts thereof, or were borne on functional accessory elements. Novel genes are also acquired by transduction (mediated by bacteriophages, plasmids or transposons), by conjugation (DNA transfer between cells) or by transformation (natural DNA uptake). Horizontal gene transfer from other species is a major source of variation and is fundamental to the genetic theory of adaptive evolution in prokaryotes.}, }
@article {pmid12807459, year = {2003}, author = {Desaint, S and Arrault, S and Siblot, S and Fournier, JC}, title = {Genetic transfer of the mcd gene in soil.}, journal = {Journal of applied microbiology}, volume = {95}, number = {1}, pages = {102-108}, doi = {10.1046/j.1365-2672.2003.01965.x}, pmid = {12807459}, issn = {1364-5072}, mesh = {Agrobacterium tumefaciens/drug effects/genetics/metabolism ; Biodegradation, Environmental ; Carbamates/*metabolism/pharmacology ; Carbofuran/metabolism ; Conjugation, Genetic/genetics ; Electrophoresis, Agar Gel/methods ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/*genetics ; Pseudomonas/drug effects/genetics/metabolism ; *Soil Microbiology ; }, abstract = {AIMS: To investigate the role of horizontal gene transfer of mcd (methylcarbamate-degrading) gene in high genetic diversity of carbofuran-degrading bacteria.<br><br>METHODS AND RESULTS: The actuality of genetic transfer from degraders to an Agrobacterium tumefaciens strain was determined in liquid medium. The mcd gene was chosen for transfer experiments. Transconjugants were obtained irrespective of the type of the donor strain (Gram-positive or Gram-negative), size of the inoculum, or nature and concentration of the pesticide in the medium. Soil microcosms, inoculated with or without the donor and/or recipient strains were used. The size of the initial degrading population (treated or untreated soil) and the nature of the inoculated donor strains were considered. More transconjugants were isolated in the previously treated soil than in the untreated soil. Agrobacterium transconjugants were isolated even when the donor strain was not inoculated, probably as a result of gene transfer from indigenous degrading population to the recipient strain. Moreover, potential transconjugants belonging to the Pseudomonas genus were isolated.<br><br>CONCLUSIONS: Our results seem to demonstrate that the mcd gene is transferable in soil among bacterial populations.<br><br>The transfer of the mcd gene is partly responsible for the high genetic diversity of micro-organisms able to catabolize carbofuran.}, }
@article {pmid12805538, year = {2003}, author = {Eisen, JA and Fraser, CM}, title = {Phylogenomics: intersection of evolution and genomics.}, journal = {Science (New York, N.Y.)}, volume = {300}, number = {5626}, pages = {1706-1707}, doi = {10.1126/science.1086292}, pmid = {12805538}, issn = {1095-9203}, mesh = {Animals ; Bacteria/genetics ; *Biological Evolution ; Computational Biology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome ; Genome, Human ; *Genomics ; Humans ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Much has been gained from genomic and evolutionary studies of species. Combining the perspectives of these different approaches suggests that an integrated phylogenomic approach will be beneficial.}, }
@article {pmid12805253, year = {2003}, author = {Werner, G and Klare, I and Spencker, FB and Witte, W}, title = {Intra-hospital dissemination of quinupristin/dalfopristin- and vancomycin-resistant Enterococcus faecium in a paediatric ward of a German hospital.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {52}, number = {1}, pages = {113-115}, doi = {10.1093/jac/dkg305}, pmid = {12805253}, issn = {0305-7453}, mesh = {Anti-Bacterial Agents/*pharmacology ; Child ; Cross Infection/*microbiology/*transmission ; Drug Resistance ; Enterococcus faecium/*drug effects/genetics ; Female ; Genes, Bacterial ; Gram-Positive Bacterial Infections/*microbiology/*transmission ; Humans ; Intensive Care Units, Pediatric ; Microbial Sensitivity Tests ; Phylogeny ; Plasmids/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; *Vancomycin Resistance ; Virginiamycin/*analogs &amp; derivatives/*pharmacology ; }, abstract = {OBJECTIVES: To demonstrate nosocomial transmission of Enterococcus faecium resistant to quinupristin/dalfopristin and vancomycin/teicoplanin among paediatric patients in a German hospital ward.<br><br>MATERIALS AND METHODS: Multiply-resistant E. faecium were isolated from three female patients aged 9 months, 2 and 15 years during a 10 day time span. Antibiotic susceptibilities were determined by microbroth dilution. Clonal relatedness among the isolates was investigated via SmaI-macrorestriction analysis by PFGE, multilocus sequence typing (MLST), and plasmid profiling. Presence of virulence and resistance determinants was tested by polymerase chain reaction (PCR). Selected resistance genes were localized by Southern hybridizations.<br><br>RESULTS: A single E. faecium isolate per patient was investigated. All exhibited resistances to quinupristin/dalfopristin, vancomycin/teicoplanin, streptomycin (high-level), penicillin/ampicillin, erythromycin, oxytetracycline, chloramphenicol, rifampicin and fusidic acid. The isolates were susceptible to linezolid only and intermediately resistant to fluoroquinolones including moxifloxacin. PFGE revealed identical patterns for all three isolates. PCRs for virulence determinants hyaluronidase and enterococcal surface protein, esp, were negative, whereas PCR for the enterocin A gene was positive. MLST identified clonal type [8-5-1-1-1-1-1] belonging to a clonal subgroup C1 of hospital- and outbreak-related E. faecium. Southern hybridizations located several resistance genes (erm(B), vat(D), vanA) on a large plasmid, which was transferable in mating experiments with an E. faecium recipient.<br><br>CONCLUSIONS: These data show routes of dissemination of resistance to multiple antibiotics including streptogramins and glycopeptides in E. faecium via vertical and/or horizontal gene transfer. The isolates spread in the absence of a direct selective pressure, as none of the patients had received earlier streptogramin or glycopeptide therapy.}, }
@article {pmid12802618, year = {2003}, author = {Ramos-Trujillo, E and Pérez-Roth, E and Méndez-Alvarez, S and Claverie-Martín, F}, title = {Multiplex PCR for simultaneous detection of enterococcal genes vanA and vanB and staphylococcal genes mecA, ileS-2 and femB.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {6}, number = {2}, pages = {113-115}, doi = {10.1007/s10123-003-0118-z}, pmid = {12802618}, issn = {1139-6709}, mesh = {Bacterial Proteins/genetics ; Base Sequence ; Carbon-Oxygen Ligases/genetics ; DNA Primers/genetics ; Enterococcus faecalis/*genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Methicillin Resistance/genetics ; Polymerase Chain Reaction/*methods ; Staphylococcus aureus/*genetics ; Vancomycin Resistance/genetics ; }, abstract = {The experimental transfer of the vanA gene cluster from Enterococcus faecalis to Staphylococcus aureus has raised fears about the occurrence of such genetic transfer in clinical isolates of methicillin-resistant staphylococci. Recently, infections by a S. aureus strain carrying the enterococcal vancomycin resistance vanA gene cluster were reported. The possible emergence and dissemination of these strains is a serious health threat and makes optimization of prevention strategies and fast detection methods absolutely necessary. In the present study, we developed a PCR protocol for simultaneous detection of enterococcal vanA and vanB genes, the staphylococcal methicillin and mupirocin resistance markers mecA and ileS-2, and identification of S. aureus. As no vancomycin-resistant S. aureus isolates were available for our study, we used mixtures of enterococcal and staphylococcal colonies that harbored the different resistance markers to show that these genes could be detected simultaneously. This protocol could be used to facilitate the detection and identification of predictable S. aureus or methicillin-resistant strains carrying vanA or vanB.}, }
@article {pmid12801413, year = {2003}, author = {Scholl, EH and Thorne, JL and McCarter, JP and Bird, DM}, title = {Horizontally transferred genes in plant-parasitic nematodes: a high-throughput genomic approach.}, journal = {Genome biology}, volume = {4}, number = {6}, pages = {R39}, pmid = {12801413}, issn = {1474-760X}, mesh = {Amino Acid Sequence/genetics ; Animals ; Base Sequence/genetics ; Caenorhabditis elegans/genetics ; Drosophila melanogaster/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/genetics ; Genes, Helminth/genetics ; Genes, Insect/genetics ; Genome ; Genomics/*methods ; Molecular Sequence Data ; Nematoda/*genetics ; Nematode Infections/genetics ; Plant Roots/parasitology ; Plants/*parasitology ; Rhizobiaceae/genetics ; Tylenchoidea/genetics ; }, abstract = {BACKGROUND: Published accounts of horizontally acquired genes in plant-parasitic nematodes have not been the result of a specific search for gene transfer per se, but rather have emerged from characterization of individual genes. We present a method for a high-throughput genome screen for horizontally acquired genes, illustrated using expressed sequence tag (EST) data from three species of root-knot nematode, Meloidogyne species.<br><br>RESULTS: Our approach identified the previously postulated horizontally transferred genes and revealed six new candidates. Screening was partially dependent on sequence quality, with more candidates identified from clustered sequences than from raw EST data. Computational and experimental methods verified the horizontal gene transfer candidates as bona fide nematode genes. Phylogenetic analysis implicated rhizobial ancestors as donors of horizontally acquired genes in Meloidogyne.<br><br>CONCLUSIONS: High-throughput genomic screening is an effective way to identify horizontal gene transfer candidates. Transferred genes that have undergone amelioration of nucleotide composition and codon bias have been identified using this approach. Analysis of these horizontally transferred gene candidates suggests a link between horizontally transferred genes in Meloidogyne and parasitism.}, }
@article {pmid12799321, year = {2003}, author = {Duncan, MJ}, title = {Genomics of oral bacteria.}, journal = {Critical reviews in oral biology and medicine : an official publication of the American Association of Oral Biologists}, volume = {14}, number = {3}, pages = {175-187}, doi = {10.1177/154411130301400303}, pmid = {12799321}, issn = {1544-1113}, support = {DE 10510/DE/NIDCR NIH HHS/United States ; DE 12082/DE/NIDCR NIH HHS/United States ; }, mesh = {Aggregatibacter actinomycetemcomitans/genetics ; Amino Acid Sequence ; Bacteria, Anaerobic/*genetics ; Conserved Sequence ; DNA, Bacterial/analysis/*genetics ; Fusobacterium nucleatum/genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genomics ; Gram-Negative Bacteria/*genetics ; Molecular Sequence Data ; Mouth/*microbiology ; Porphyromonas gingivalis/genetics ; Prevotella intermedia/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Streptococcus mutans/genetics ; Treponema/genetics ; Virulence Factors/genetics ; }, abstract = {Advances in bacterial genetics came with the discovery of the genetic code, followed by the development of recombinant DNA technologies. Now the field is undergoing a new revolution because of investigators' ability to sequence and assemble complete bacterial genomes. Over 200 genome projects have been completed or are in progress, and the oral microbiology research community has benefited through projects for oral bacteria and their non-oral-pathogen relatives. This review describes features of several oral bacterial genomes, and emphasizes the themes of species relationships, comparative genomics, and lateral gene transfer. Genomics is having a broad impact on basic research in microbial pathogenesis, and will lead to new approaches in clinical research and therapeutics. The oral microbiota is a unique community especially suited for new challenges to sequence the metagenomes of microbial consortia, and the genomes of uncultivable bacteria.}, }
@article {pmid12798227, year = {2003}, author = {Filée, J and Forterre, P and Laurent, J}, title = {The role played by viruses in the evolution of their hosts: a view based on informational protein phylogenies.}, journal = {Research in microbiology}, volume = {154}, number = {4}, pages = {237-243}, doi = {10.1016/S0923-2508(03)00066-4}, pmid = {12798227}, issn = {0923-2508}, mesh = {*Biological Evolution ; DNA Helicases/chemistry/genetics ; DNA Polymerase III/chemistry/genetics ; Enzymes/chemistry/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genes, Viral ; Phylogeny ; Ribonucleotide Reductases/chemistry/genetics ; Sequence Homology, Amino Acid ; Thymidylate Synthase/chemistry/genetics ; Viruses/*genetics ; }, abstract = {Viruses are often considered as fragments of cellular RNA or DNA that escaped a long time ago from cellular chromosomes and that evolved later on by capturing additional genes from the genomes of their hosts. However, this view has now been challenged by the discovery of surprising homology between viruses with very distantly related hosts, and by phylogenetic analyses suggesting that genes might also have flown from viruses to cells. We present here phylogenetic analyses of four proteins involved in DNA replication and synthesis of DNA precursors (DNA polymerases delta, ribonucleotide reductases, thymidylate synthases and replicative helicases) and we discuss the reciprocal roles of cells and viruses during the evolutionary history of these enzymes. These analyses revealed numerous lateral gene transfer events between cells and viruses, in both directions. We suggest that lateral gene transfers from viruses to cells and nonorthologous gene replacements of cellular genes by viral ones are an important source of "genetic novelties" in the evolution of cellular lineages. Thus, viruses have definitively to be considered as major players in the evolution of cellular genomes.}, }
@article {pmid12796498, year = {2003}, author = {Klunker, D and Haas, B and Hirtreiter, A and Figueiredo, L and Naylor, DJ and Pfeifer, G and Müller, V and Deppenmeier, U and Gottschalk, G and Hartl, FU and Hayer-Hartl, M}, title = {Coexistence of group I and group II chaperonins in the archaeon Methanosarcina mazei.}, journal = {The Journal of biological chemistry}, volume = {278}, number = {35}, pages = {33256-33267}, doi = {10.1074/jbc.M302018200}, pmid = {12796498}, issn = {0021-9258}, mesh = {Adenosine Triphosphatases/chemistry ; Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Archaea ; Chaperonin 10/metabolism ; Chaperonin 60/metabolism ; Cloning, Molecular ; Cytosol/metabolism ; Electrophoresis, Polyacrylamide Gel ; Escherichia coli/metabolism ; Hot Temperature ; Hydrogen-Ion Concentration ; Immunoblotting ; Light ; Magnesium/metabolism ; Methanosarcina/*metabolism ; Microscopy, Electron ; Models, Genetic ; Molecular Sequence Data ; Precipitin Tests ; Promoter Regions, Genetic ; Protein Folding ; Protein Structure, Tertiary ; Recombinant Proteins/metabolism ; Ribosomes/metabolism ; Scattering, Radiation ; Sequence Homology, Amino Acid ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Thiosulfate Sulfurtransferase/chemistry ; Time Factors ; }, abstract = {Two distantly related classes of cylindrical chaperonin complexes assist in the folding of newly synthesized and stress-denatured proteins in an ATP-dependent manner. Group I chaperonins are thought to be restricted to the cytosol of bacteria and to mitochondria and chloroplasts, whereas the group II chaperonins are found in the archaeal and eukaryotic cytosol. Here we show that members of the archaeal genus Methanosarcina co-express both the complete group I (GroEL/GroES) and group II (thermosome/prefoldin) chaperonin systems in their cytosol. These mesophilic archaea have acquired between 20 and 35% of their genes by lateral gene transfer from bacteria. In Methanosarcina mazei Gö1, both chaperonins are similarly abundant and are moderately induced under heat stress. The M. mazei GroEL/GroES proteins have the structural features of their bacterial counterparts. The thermosome contains three paralogous subunits, alpha, beta, and gamma, which assemble preferentially at a molar ratio of 2:1:1. As shown in vitro, the assembly reaction is dependent on ATP/Mg2+ or ADP/Mg2+ and the regulatory role of the beta subunit. The co-existence of both chaperonin systems in the same cellular compartment suggests the Methanosarcina species as useful model systems in studying the differential substrate specificity of the group I and II chaperonins and in elucidating how newly synthesized proteins are sorted from the ribosome to the proper chaperonin for folding.}, }
@article {pmid12792655, year = {2003}, author = {Brown, JR and Gentry, D and Becker, JA and Ingraham, K and Holmes, DJ and Stanhope, MJ}, title = {Horizontal transfer of drug-resistant aminoacyl-transfer-RNA synthetases of anthrax and Gram-positive pathogens.}, journal = {EMBO reports}, volume = {4}, number = {7}, pages = {692-698}, pmid = {12792655}, issn = {1469-221X}, mesh = {Amino Acid Sequence ; Anthrax/microbiology ; Bacillus anthracis/enzymology/*genetics ; Computational Biology ; Drug Resistance, Bacterial/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Gram-Positive Bacteria/*enzymology/*genetics ; Isoleucine-tRNA Ligase/chemistry/*genetics ; Methionine-tRNA Ligase/chemistry/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Amino Acid ; }, abstract = {The screening of new antibiotics against several bacterial strains often reveals unexpected occurrences of natural drug resistance. Two examples of this involve specific inhibitors of Staphylococcus aureus isoleucyl-transfer-RNA synthetase 1 (IleRS1) and, more recently, Streptococcus pneumoniae methionyl-tRNA synthetase 1 (MetRS1). In both cases, resistance is due to the presence of a second gene that encodes another synthetase (IleRS2 or MetRS2). Here, we show that both S. pneumoniae MetRS2 and S. aureus IleRS2 have closely related homologues in the Gram-positive bacterium Bacillus anthracis, the causative agent of anthrax. Furthermore, similar to drug-resistant pathogens, strains of B. anthracis and its closest relative, B. cereus, also have wild-type ileS1 and metS1 genes. Clostridium perfringens, the causative agent of gangrene, also has two metS genes, whereas Oceanobacillus iheyensis isolated from deep-sea sediments has a single ileS2-type gene. This study shows the importance of understanding complex evolutionary networks of ancient horizontal gene transfer for the development of novel antibiotics.}, }
@article {pmid12791892, year = {2003}, author = {Yu, HS and Seol, SY and Cho, DT}, title = {Diversity of tn1546-like elements in vancomycin-resistant enterococci isolated from humans and poultry in Korea.}, journal = {Journal of clinical microbiology}, volume = {41}, number = {6}, pages = {2641-2643}, pmid = {12791892}, issn = {0095-1137}, mesh = {Animals ; Bacterial Proteins/genetics ; Carbon-Oxygen Ligases/genetics ; DNA Transposable Elements/*genetics ; Electrophoresis, Gel, Pulsed-Field ; Enterococcus faecium/*classification/drug effects/genetics ; *Genetic Variation ; Gram-Positive Bacterial Infections/*microbiology/veterinary ; Humans ; Korea ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Poultry ; Poultry Diseases/*microbiology ; *Vancomycin Resistance ; }, abstract = {To investigate the possible spread of vancomycin resistance among enterococci through horizontal gene transfer between two sources of vancomycin-resistant enterococci (VRE) isolated from farm animals and humans in Korea, molecular characterization of VRE isolated from poultry (20 isolates) and humans (35 isolates) was performed by PCR-restriction fragment length polymorphism typing of the vanA gene cluster (Tn1546). PCR mapping of Tn1546 finally distinguished seven different transposon types (types A to G). Type A was observed only in the poultry isolates, while the other six types were present only in the human isolates. An insertion sequence and deleted sequence were detected in most of the human isolates in the orf2-vanR and vanX-vanY regions in the Tn1546-like element, but not in the poultry isolates. Tn1546-like elements were found in conjugal plasmids of most human VRE, whereas they were detected in the chromosomes of all poultry VRE. Accordingly, no evidence was found of any recent transmission of vancomycin resistance genes between poultry and humans in Korea.}, }
@article {pmid12791177, year = {2003}, author = {Dzidic, S and Bedeković, V}, title = {Horizontal gene transfer-emerging multidrug resistance in hospital bacteria.}, journal = {Acta pharmacologica Sinica}, volume = {24}, number = {6}, pages = {519-526}, pmid = {12791177}, issn = {1671-4083}, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Cross Infection/*microbiology/prevention &amp; control ; Drug Resistance, Multiple, Bacterial/*genetics ; Enterococcus/drug effects/genetics/isolation &amp; purification ; *Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; Staphylococcus aureus/drug effects/genetics/isolation &amp; purification ; }, abstract = {The frequency and spectrum of antibiotic resistant infections have increased worldwide during the past few decades. This increase has been attributed to a combination of microbial characteristics, the selective pressure of antimicrobial use, and social and technical changes that enhance the transmission of resistant organisms. The resistance is acquired by mutational change or by the acquisition of resistance-encoding genetic material which is transferred from another bacteria. The spread of antibiotic resistance genes may be causally related to the overuse of antibiotics in human health care and in animal feeds, increased use of invasive devices and procedures, a greater number of susceptible hosts, and lapses in infection control practices leading to increased transmission of resistant organisms. The resistance gene sequences are integrated by recombination into several classes of naturally occurring gene expression cassettes and disseminated within the microbial population by horizontal gene transfer mechanisms: transformation, conjugation or transduction. In the hospital, widespread use of antimicrobials in the intensive care units (ICU) and for immunocompromised patients has resulted in the selection of multidrug-resistant organisms. Methicillin-resistant Staphylococci, vancomycin resistant Enterococci and extended-spectrum beta-lactamase (ESBL) producing Gram negative bacilli are identified as major problem in nosocomial infections. Recent surveillance studies have demonstrated trend towards more seriously ill patients suffering from multidrug-resistant nosocomial infections. Emergence of multiresistant bacteria and spread of resistance genes should enforce the application of strict prevention strategies, including changes in antibiotic treatment regimens, hygiene measures, infection prevention and control of horizontal nosocomial transmission of organisms.}, }
@article {pmid12788725, year = {2003}, author = {Park, W and Jeon, CO and Hohnstock-Ashe, AM and Winans, SC and Zylstra, GJ and Madsen, EL}, title = {Identification and characterization of the conjugal transfer region of the pCg1 plasmid from naphthalene-degrading Pseudomonas putida Cg1.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {6}, pages = {3263-3271}, pmid = {12788725}, issn = {0099-2240}, mesh = {Bacterial Proteins/genetics/metabolism ; Biodegradation, Environmental ; *Conjugation, Genetic ; Culture Media ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Naphthalenes/*metabolism ; Plasmids/*genetics ; Pseudomonas putida/*genetics/growth &amp; development ; Sequence Analysis, DNA ; }, abstract = {Hybridization and restriction fragment length polymorphism data (K. G. Stuart-Keil, A. M. Hohnstock, K. P. Drees, J. B. Herrick, and E. L. Madsen, Appl. Environ. Microbiol. 64:3633-3640, 1998) have shown that pCg1, a naphthalene catabolic plasmid carried by Pseudomonas putida Cg1, is homologous to the archetypal naphthalene catabolic plasmid, pDTG1, in P. putida NCIB 9816-4. Sequencing of the latter plasmid allowed PCR primers to be designed for amplifying and sequencing the conjugal transfer region in pCg1. The mating pair formation (mpf) gene, mpfA encoding the putative precursor of the conjugative pilin subunit from pCg1, was identified along with other trb-like mpf genes. Sequence comparison revealed that the 10 mpf genes in pCg1 and pDTG1 are closely related (61 to 84% identity) in sequence and operon structure to the putative mpf genes of catabolic plasmid pWW0 (TOL plasmid of P. putida) and pM3 (antibiotic resistance plasmid of Pseudomonas. spp). A polar mutation caused by insertional inactivation in mpfA of pCg1 and reverse transcriptase PCR analysis of mRNA showed that this mpf region was involved in conjugation and was transcribed from a promoter located upstream of an open reading frame adjacent to mpfA. lacZ transcriptional fusions revealed that mpf genes of pCg1 were expressed constitutively both in liquid and on solid media. This expression did not respond to host exposure to naphthalene. Conjugation frequency on semisolid media was consistently 10- to 100-fold higher than that in liquid media. Thus, conjugation of pCg1 in P. putida Cg1 was enhanced by expression of genes in the mpf region and by surfaces where conditions fostering stable, high-density cell-to-cell contact are manifest.}, }
@article {pmid12777624, year = {2003}, author = {Archibald, JM and Rogers, MB and Toop, M and Ishida, K and Keeling, PJ}, title = {Lateral gene transfer and the evolution of plastid-targeted proteins in the secondary plastid-containing alga Bigelowiella natans.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {100}, number = {13}, pages = {7678-7683}, pmid = {12777624}, issn = {0027-8424}, mesh = {Amino Acid Sequence ; Animals ; Cell Lineage ; Chlamydomonas reinhardtii/metabolism ; Chlorophyta/genetics ; DNA, Complementary/metabolism ; Databases as Topic ; Eukaryota/*genetics/metabolism ; *Evolution, Molecular ; Gene Library ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; Plastids/*genetics/metabolism ; Sequence Homology, Amino Acid ; }, abstract = {Chlorarachniophytes are amoeboflagellate algae that acquired photosynthesis secondarily by engulfing a green alga and retaining its plastid (chloroplast). An important consequence of secondary endosymbiosis in chlorarachniophytes is that most of the nuclear genes encoding plastid-targeted proteins have moved from the nucleus of the endosymbiont to the host nucleus. We have sequenced and analyzed 83 cDNAs encoding 78 plastid-targeted proteins from the model chlorarachniophyte Bigelowiella natans (formerly Chlorarachnion sp. CCMP621). Phylogenies inferred from the majority of these genes are consistent with a chlorophyte green algal origin. However, a significant number of genes (approximately 21%) show signs of having been acquired by lateral gene transfer from numerous other sources: streptophyte algae, red algae (or algae with red algal endosymbionts), as well as bacteria. The chlorarachniophyte plastid proteome may therefore be regarded as a mosaic derived from various organisms in addition to the ancestral chlorophyte plastid. In contrast, the homologous genes from the chlorophyte Chlamydomonas reinhardtii do not show any indications of lateral gene transfer. This difference is likely a reflection of the mixotrophic nature of Bigelowiella (i.e., it is photosynthetic and phagotrophic), whereas Chlamydomonas is strictly autotrophic. These results underscore the importance of lateral gene transfer in contributing foreign proteins to eukaryotic cells and their organelles, and also suggest that its impact can vary from lineage to lineage.}, }
@article {pmid12777534, year = {2003}, author = {Rest, JS and Mindell, DP}, title = {Retroids in archaea: phylogeny and lateral origins.}, journal = {Molecular biology and evolution}, volume = {20}, number = {7}, pages = {1134-1142}, doi = {10.1093/molbev/msg135}, pmid = {12777534}, issn = {0737-4038}, support = {T32-HG00040/HG/NHGRI NIH HHS/United States ; }, mesh = {Archaea/classification/enzymology/*genetics ; Bacteria/classification/enzymology/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Archaeal ; *Genome, Bacterial ; Open Reading Frames ; Phylogeny ; RNA-Directed DNA Polymerase/*genetics ; }, abstract = {Until recently, none of the diverse elements bearing reverse transcriptase (retroids) have been known from Archaea. However, in the recently published genomes of the acetate-utilizing archaeal methanogens, Methanosarcina acetivorans and M. mazei, several open reading frames (ORFs) are annotated as reverse transcriptase (RT). These annotations led us to the characterization of a retron and 13 retrointrons, including three twintrons, clustered at seven loci of the M. acetivorans genome, and four retrointrons at two loci of the M. mazei genome. Based on a phylogeny of the RT ORFs, we infer four lateral gene transfers (LGT) of these retroids from Bacteria to Archaea and of retrointron mobility within the Archaea genomes. Our phylogenetic analysis also identifies several novel retrons from GenBank in the bacterial groups Firmicutes, Fusobacteria, Cyanobacteria and beta-Proteobacteria, as well as in M. acetivorans. The discovery of retrointrons in Archaea as a consequence of LGT from Bacteria suggests that they did not originate in the progenote and parallels the "mitochondrial seed" theory of the origin of spliceosomes. Extending the known phylogenetic distribution of retroids to Archaea is consistent with the view that they have played a significant role in evolution of genomes throughout the tree of life.}, }
@article {pmid12777528, year = {2003}, author = {Klotz, MG and Loewen, PC}, title = {The molecular evolution of catalatic hydroperoxidases: evidence for multiple lateral transfer of genes between prokaryota and from bacteria into eukaryota.}, journal = {Molecular biology and evolution}, volume = {20}, number = {7}, pages = {1098-1112}, doi = {10.1093/molbev/msg129}, pmid = {12777528}, issn = {0737-4038}, mesh = {Bacteria/enzymology/*genetics ; Catalase/*physiology ; Catalysis ; Eukaryota/enzymology/genetics ; Eukaryotic Cells/*physiology ; *Evolution, Molecular ; Fungi/enzymology/genetics ; Gene Transfer, Horizontal/*genetics ; Genome ; Heme/metabolism ; Phylogeny ; Plants/enzymology/genetics ; Proteins/*genetics ; }, abstract = {The past decade has produced an increasing number of reports on horizontal gene transfer between prokaryotic organisms. Only recently, with the flood of available whole genome sequence data and a renewed intensity of the debate about the universal tree of life, a very few reports on lateral gene transfer (LGT) from prokaryotes into the Eukaryota have been published. We have investigated and report here on the molecular evolution of the gene families that encode catalatic hydroperoxidases. We have found that this process included not only frequent horizontal gene transfer among prokaryotes but also several lateral gene transfer events between bacteria and fungi and between bacteria and the protistan ancestor of the alga/plant lineage.}, }
@article {pmid12777514, year = {2003}, author = {Jain, R and Rivera, MC and Moore, JE and Lake, JA}, title = {Horizontal gene transfer accelerates genome innovation and evolution.}, journal = {Molecular biology and evolution}, volume = {20}, number = {10}, pages = {1598-1602}, doi = {10.1093/molbev/msg154}, pmid = {12777514}, issn = {0737-4038}, mesh = {Archaea/genetics ; Bacteria/genetics ; *Computational Biology ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Temperature ; }, abstract = {Horizontal gene transfer (HGT) spreads genetic diversity by moving genes across species boundaries. By rapidly introducing newly evolved genes into existing genomes, HGT circumvents the slow step of ab initio gene creation and accelerates genome innovation. However, HGT can only affect organisms that readily exchange genes (exchange communities). In order to define exchange communities and understand the internal and external environmental factors that regulate HGT, we analyzed approximately 20,000 genes contained in eight free-living prokaryotic genomes. These analyses indicate that HGT occurs among organisms that share similar factors. The most significant are genome size, genome G/C composition, carbon utilization, and oxygen tolerance.}, }
@article {pmid12775700, year = {2003}, author = {Amavisit, P and Lightfoot, D and Browning, GF and Markham, PF}, title = {Variation between pathogenic serovars within Salmonella pathogenicity islands.}, journal = {Journal of bacteriology}, volume = {185}, number = {12}, pages = {3624-3635}, pmid = {12775700}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; Bacteriophages ; Base Sequence ; Chromosome Mapping ; Escherichia coli/virology ; Gene Deletion ; Gene Transfer, Horizontal ; Genetic Variation ; Molecular Sequence Data ; Mutagenesis, Insertional ; Open Reading Frames ; Phylogeny ; Salmonella enterica/*genetics/pathogenicity ; Sequence Alignment ; Species Specificity ; Virulence/*genetics ; }, abstract = {Although four of the five Salmonella pathogenicity islands (SPIs) have been characterized in detail for Salmonella enterica serovar Typhimurium, and the fifth has been characterized for Salmonella enterica serovar Dublin, there have been limited studies to examine them in detail in a range of pathogenic serovars of S. enterica. The aim of this study was to examine these regions, shown to be crucial in virulence, in pathogenic serovars to identify any major deletions or insertions that may explain variation in virulence and provide further understanding of the elements involved in the evolution of these regions. Multiple strains of each of the 13 serovars were compared by Southern blot hybridization using a series of probes that together encompassed the full length of all five SPIs. With the exception of serovar Typhimurium, all strains of the same serovar were identical in all five SPIs. Those serovars that differed from serovar Typhimurium in SPI-1 to SPI-4 and from serovar Dublin in SPI-5 were examined in more detail in the variant regions by PCR, and restriction endonuclease digestion and/or DNA sequencing. While most variation in hybridization patterns was attributable to loss or gain of single restriction endonuclease cleavage sites, three regions, in SPI-1, SPI-3, and SPI-5, had differences due to major insertions or deletions. In SPI-1 the avrA gene was replaced by a 200-base fragment in three serovars, as reported previously. In SPI-5, two serovars had acquired an insertion with similarity to the pagJ and pagK genes between pipC and pipD. In SPI-3 the genes sugR and rhuM were deleted in most serovars and in some were replaced by sequences that were very similar to either the Escherichia coli fimbrial operon, flanked by two distinct insertion sequence elements, or to the E. coli retron phage PhiR73. The distribution of these differences suggests that there have been a number of relatively recent horizontal transfers of genes into S. enterica and that in some cases the same event has occurred in multiple lineages of S. enterica. Thus, it seems that insertion sequences and retron phages are likely to be involved in continuing evolution of the pathogenicity islands of pathogenic Salmonella serovars.}, }
@article {pmid12770720, year = {2003}, author = {Hsu, WB and Chen, JH}, title = {The IS1 elements in Shigella boydii: horizontal transfer, vertical inactivation and target duplication.}, journal = {FEMS microbiology letters}, volume = {222}, number = {2}, pages = {289-295}, doi = {10.1016/S0378-1097(03)00319-7}, pmid = {12770720}, issn = {0378-1097}, mesh = {3' Flanking Region ; 5' Flanking Region ; Base Sequence ; Consensus Sequence ; *DNA Transposable Elements ; Escherichia coli ; Escherichia coli O157 ; Gene Transfer, Horizontal/*genetics ; Mutation ; Shigella boydii/*genetics ; }, abstract = {IS1(SB) and its two variants were identified as the major and minor IS1 elements in Shigella boydii. The nucleotide sequences of IS1(SB), IS1(O157:H7) from Escherichia coli O157:H7 and IS1F from E. coli K12 suggest that these IS1 elements had been horizontally transferred among S. boydii and E. coli O157:H7 and K12. The two IS1(SB) variants and IS1(O157:H7) have transposition activities 7- to 86-fold less than that of IS1(SB), whereas IS1F has little transposition activity. Analysis of the flanking sequences of IS1(SB) and its two variants in S. boydii revealed the nature of regional specificity of the target sites and the sequence dependence of 8 and 9 bp target duplications, for which a model is presented.}, }
@article {pmid12762843, year = {2003}, author = {Lyubetsky, VA and V'yugin, VV}, title = {Methods of horizontal gene transfer determination using phylogenetic data.}, journal = {In silico biology}, volume = {3}, number = {1-2}, pages = {17-31}, pmid = {12762843}, issn = {1386-6338}, mesh = {Bacteria/classification/genetics ; Biotechnology/methods ; Gene Duplication ; *Gene Transfer Techniques ; Models, Genetic ; *Phylogeny ; Proteins/classification/*genetics ; }, abstract = {A new approach for comparative analysis of multiple trees reconstructed for representative protein families is proposed. This approach is based on the hypothesis of gene duplication, gene loss and horizontal gene transfer and makes use of stochastic methods and optimization. We present a species tree of 40 prokaryotic organisms obtained by our algorithm on the basis of 132 clusters of orthologous groups of proteins (COGs) from the GenBank of the National Center for Biotechnology Information (USA). We also present a computer technology intended to determine horizontally transferred genes. Some application results of the technology, based on comparative analysis of protein and species trees, are given.}, }
@article {pmid12761081, year = {2003}, author = {Fuchslocher, B and Millar, LL and Cotter, PA}, title = {Comparison of bipA alleles within and across Bordetella species.}, journal = {Infection and immunity}, volume = {71}, number = {6}, pages = {3043-3052}, pmid = {12761081}, issn = {0019-9567}, support = {R01 AI043986/AI/NIAID NIH HHS/United States ; AI43986/AI/NIAID NIH HHS/United States ; }, mesh = {Alleles ; Bacterial Adhesion ; Bacterial Outer Membrane Proteins/analysis/*genetics/physiology ; Base Sequence ; Bordetella/chemistry/*genetics ; Chromosome Mapping ; Phylogeny ; Repetitive Sequences, Amino Acid ; Species Specificity ; Transcription, Genetic ; }, abstract = {The Bordetella BvgAS signal transduction system controls the expression of at least three phenotypic phases, the Bvg(+) or virulent phase, the Bvg(-) or avirulent phase, and the Bvg(i) or Bvg intermediate phase, which has been hypothesized to be important for transmission. bipA, the first identified Bvg(i)-phase gene, encodes a protein with similarity to the well-characterized bacterial adhesins intimin and invasin. Proteins encoded by the bipA genes present in Bordetella pertussis Tohama I and Bordetella bronchiseptica RB50 differ in the number of 90-amino-acid repeats which they possess and in the sequence of the C-terminal domain. To investigate the possibility that bipA alleles segregate according to host specificity and to gain insight into the role of BipA and the Bvg(i) phase in the Bordetella infectious cycle, we compared bipA alleles across members of the B. bronchiseptica cluster, which includes both human-infective (B. pertussis and B. parapertussis(hu)) and non-human-infective (B. bronchiseptica and B. parapertussis(ov)) strains. bipA genes were present in most, but not all, strains. All bipA genes present in B. bronchiseptica strains were identical to bipA of RB50 (at least with regard to the DNA sequence of the 3' C-terminal-domain-encoding region, the number of 90-amino-acid repeats encoded, and expression patterns). Although all bipA genes present in the other Bordetella strains were identical in the 3' C-terminal-domain-encoding region to bipA of B. pertussis Tohama I, they varied in the number of 90-amino-acid repeats that they encoded and in expression level. Notably, the genes present in B. parapertussis(hu) strains were pseudogenes, and the genes present in B. parapertussis(ov) strains were expressed at significantly reduced levels compared with the levels in B. pertussis and B. bronchiseptica strains. Our results indicate that there is a correlation between specific bipA alleles and specific hosts. They also support the hypothesis that both horizontal gene transfer and fine-tuning of gene expression patterns contribute to the evolution of host adaptation in lineages of the B. bronchiseptica cluster.}, }
@article {pmid12760849, year = {2003}, author = {Gentry, DR and Ingraham, KA and Stanhope, MJ and Rittenhouse, S and Jarvest, RL and O'Hanlon, PJ and Brown, JR and Holmes, DJ}, title = {Variable sensitivity to bacterial methionyl-tRNA synthetase inhibitors reveals subpopulations of Streptococcus pneumoniae with two distinct methionyl-tRNA synthetase genes.}, journal = {Antimicrobial agents and chemotherapy}, volume = {47}, number = {6}, pages = {1784-1789}, pmid = {12760849}, issn = {0066-4804}, mesh = {Amino Acid Sequence ; Base Sequence ; DNA, Bacterial/chemistry/genetics ; Drug Resistance, Bacterial/genetics ; Enzyme Inhibitors/*pharmacology ; Isoenzymes/antagonists &amp; inhibitors/genetics/metabolism ; Methionine-tRNA Ligase/*antagonists &amp; inhibitors/genetics/metabolism ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Mutagenesis ; Polymerase Chain Reaction ; Sequence Alignment ; Streptococcus pneumoniae/*drug effects/*enzymology/genetics ; }, abstract = {As reported previously (J. R. Jarvest et al., J. Med. Chem. 45:1952-1962, 2002), potent inhibitors (at nanomolar concentrations) of Staphylococcus aureus methionyl-tRNA synthetase (MetS; encoded by metS1) have been derived from a high-throughput screening assay hit. Optimized compounds showed excellent activities against staphylococcal and enterococcal pathogens. We report on the bimodal susceptibilities of S. pneumoniae strains, a significant fraction of which was found to be resistant (MIC, > or =8 mg/liter) to these inhibitors. Using molecular genetic techniques, we have found that the mechanism of resistance is the presence of a second, distantly related MetS enzyme, MetS2, encoded by metS2. We present evidence that the metS2 gene is necessary and sufficient for resistance to MetS inhibitors. PCR analysis for the presence of metS2 among a large sample (n = 315) of S. pneumoniae isolates revealed that it is widespread geographically and chronologically, occurring at a frequency of about 46%. All isolates tested also contained the metS1 gene. Searches of public sequence databases revealed that S. pneumoniae MetS2 was most similar to MetS in Bacillus anthracis, followed by MetS in various non-gram-positive bacterial, archaeal, and eukaryotic species, with streptococcal MetS being considerably less similar. We propose that the presence of metS2 in specific strains of S. pneumoniae is the result of horizontal gene transfer which has been driven by selection for resistance to some unknown class of naturally occurring antibiotics with similarities to recently reported synthetic MetS inhibitors.}, }
@article {pmid12750317, year = {2003}, author = {Townsend, JP and Nielsen, KM and Fisher, DS and Hartl, DL}, title = {Horizontal acquisition of divergent chromosomal DNA in bacteria: effects of mutator phenotypes.}, journal = {Genetics}, volume = {164}, number = {1}, pages = {13-21}, pmid = {12750317}, issn = {0016-6731}, mesh = {Data Interpretation, Statistical ; Escherichia coli/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genetic Variation ; Models, Genetic ; }, abstract = {We examine the potential beneficial effects of the expanded access to environmental DNA offered by mutators on the adaptive potential of bacterial populations. Using parameters from published studies of recombination in E. coli, we find that the presence of mutators has the potential to greatly enhance bacterial population adaptation when compared to populations without mutators. In one specific example, for which three specific amino acid substitutions are required for adaptation to occur in a 300-amino-acid protein, we found a 3500-fold increase in the rate of adaptation. The probability of a beneficial acquisition decreased if more amino acid changes, or integration of longer DNA fragments, were required for adaptation. The model also predicts that mutators are more likely than nonmutator phenotypes to acquire genetic variability from a more diverged set of donor bacteria. Bacterial populations harboring mutators in a sequence heterogeneous environment are predicted to acquire most of their DNA conferring adaptation in the range of 13-30% divergence, whereas nonmutator phenotypes become adapted after recombining with more homogeneous sequences of 7-21% divergence. We conclude that mutators can accelerate bacterial adaptation when desired genetic variability is present within DNA fragments of up to approximately 30% divergence.}, }
@article {pmid12746048, year = {2003}, author = {Suda, A and Takiguchi, Y and Omori, S and Miyazawa, H and Sugimoto, T and Kurosu, K and Tatsumi, K and Tanabe, N and Kuriyama, T and Hiroshima, K and Kimura, H}, title = {Gene delivery to the lung by means of syngeneic fibroblasts: an experimental model.}, journal = {Experimental lung research}, volume = {29}, number = {4}, pages = {227-241}, doi = {10.1080/01902140303781}, pmid = {12746048}, issn = {0190-2148}, mesh = {Animals ; Cell Transplantation ; Female ; Fibroblasts/cytology/*enzymology/transplantation ; Galactosidases/*genetics/metabolism ; *Gene Transfer Techniques ; *Gene Transfer, Horizontal ; Genetic Vectors ; Lac Operon/genetics ; Lung/cytology/*enzymology ; Mice ; Mice, Inbred BALB C ; Models, Animal ; Specific Pathogen-Free Organisms ; Transfection ; }, abstract = {An experimental model, in which exogenous gene expression in the lung is achieved, has been established. A fibroblast cell line was transfected with the lacZ gene and was administered to syngeneic mice by either intravenous or intratracheal injection. Enzyme-linked immunosorbent assay and histochemical detection of beta-galactosidase revealed efficient gene delivery to the lung by either route. Kinetic studies demonstrated that the expression peaked immediately after the injection, and this high level was maintained for 7 days by intratracheal and for 14 days by intravenous administration. This system may have potential relevance for certain experimental models requiring specific gene delivery to the lung.}, }
@article {pmid12737743, year = {2003}, author = {Doublet, B and Lailler, R and Meunier, D and Brisabois, A and Boyd, D and Mulvey, MR and Chaslus-Dancla, E and Cloeckaert, A}, title = {Variant Salmonella genomic island 1 antibiotic resistance gene cluster in Salmonella enterica serovar Albany.}, journal = {Emerging infectious diseases}, volume = {9}, number = {5}, pages = {585-591}, pmid = {12737743}, issn = {1080-6040}, mesh = {Anti-Bacterial Agents/pharmacology ; Base Sequence ; DNA, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genetic Variation ; Molecular Sequence Data ; Multigene Family/*genetics ; Phenotype ; Salmonella enterica/classification/drug effects/*genetics ; Sequence Alignment ; Terminal Repeat Sequences/genetics ; }, abstract = {Salmonella genomic island 1 (SGI1) contains an antibiotic resistance gene cluster and has been previously identified in multidrug-resistant Salmonella enterica serovars Typhimurium DT104, Agona, and Paratyphi B. We identified a variant SGI1 antibiotic-resistance gene cluster in a multidrug-resistant strain of S. enterica serovar Albany isolated from food fish from Thailand and imported to France. In this strain, the streptomycin resistance aadA2 gene cassette in one of the SGI1 integrons was replaced by a dfrA1 gene cassette, conferring resistance to trimethoprim and an open reading frame of unknown function. Thus, this serovar Albany strain represents the fourth S. enterica serovar in which SGI1 has been identified and the first SGI1 example where gene cassette replacement took place in one of its integron structures. The antibiotic resistance gene cluster of serovar Albany strain 7205.00 constitutes a new SGI1 variant; we propose a name of SGI1-F.}, }
@article {pmid12734795, year = {2003}, author = {Okuda, Y and Sasaki, D and Nogami, S and Kaneko, Y and Ohya, Y and Anraku, Y}, title = {Occurrence, horizontal transfer and degeneration of VDE intein family in Saccharomycete yeasts.}, journal = {Yeast (Chichester, England)}, volume = {20}, number = {7}, pages = {563-573}, doi = {10.1002/yea.984}, pmid = {12734795}, issn = {0749-503X}, mesh = {Amino Acid Substitution ; Base Sequence ; Candida glabrata/enzymology/genetics ; DNA, Fungal/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Fungal ; Kluyveromyces/enzymology/genetics ; Models, Molecular ; Phylogeny ; Protein Structure, Tertiary ; Proton-Translocating ATPases/chemistry/*genetics ; RNA, Fungal/genetics ; RNA, Ribosomal/genetics ; Saccharomyces/enzymology/genetics ; Saccharomyces cerevisiae/enzymology/genetics ; Saccharomyces cerevisiae Proteins/chemistry/*genetics ; Saccharomycetales/enzymology/*genetics ; Sequence Homology, Nucleic Acid ; Species Specificity ; }, abstract = {VDE is a homing endonuclease gene originally discovered as an intervening element in VMA1s of Saccharomyces cerevisiae. There have been two independent subfamilies of VDE, one from S. cerevisiae strain X2180-1A and the other from Saccharomyces sp. DH1-1A in the host VMA1 gene, and they share the identity of 96.3%. In order to search the occurrence, intra/interspecies transfer and molecular degeneration of VDE, complete sequences of VMA1 in 10 strains of S. cerevisiae, eight species of saccharomycete yeasts, Candida glabrata and Kluyveromyces lactis were determined. We found that six of 10 S. cerevisiae strains contain VDEs 99.7-100% identical to that of the strain X2180-1A, one has no VDE, whereas the other three harbour VDEs 100% identical to that of the strain DH1-1A. S. carlsbergensis has two VMA1s, one being 99.8% identical to that of the strain X2180-1A with VDE 100% identical to that of the strain DH1-1A and the other containing the same VMA1 in S. pastorianus with no VDE. This and other evidence indicates that intra/interspecies transmissions of VDEs have occurred among saccharomycete yeasts. Phylogenetic analyses of VMA1 and VDE suggest that the S. cerevisiae VDEs had branched earlier than other VDEs from an ancestral VDE and had invaded into the host loci as relatively late events. The two VDEs seemed to degenerate in individual host loci, retaining their splicing capacity intact. The degeneration of the endonuclease domains was distinct and, if compared, its apparent rate was much faster than that of the protein-splicing domains.}, }
@article {pmid12730157, year = {2003}, author = {van Berkum, P and Terefework, Z and Paulin, L and Suomalainen, S and Lindström, K and Eardly, BD}, title = {Discordant phylogenies within the rrn loci of Rhizobia.}, journal = {Journal of bacteriology}, volume = {185}, number = {10}, pages = {2988-2998}, pmid = {12730157}, issn = {0021-9193}, mesh = {Base Sequence ; *DNA, Intergenic ; Evolution, Molecular ; Gene Conversion ; Likelihood Functions ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction/methods ; Polymorphism, Genetic ; *RNA, Ribosomal, 16S ; *RNA, Ribosomal, 23S ; Recombination, Genetic ; Rhizobiaceae/*genetics/physiology ; Sequence Homology, Nucleic Acid ; }, abstract = {It is evident from complete genome sequencing results that lateral gene transfer and recombination are essential components in the evolutionary process of bacterial genomes. Since this has important implications for bacterial systematics, the primary objective of this study was to compare estimated evolutionary relationships among a representative set of alpha-Proteobacteria by sequencing analysis of three loci within their rrn operons. Tree topologies generated with 16S rRNA gene sequences were significantly different from corresponding trees assembled with 23S rRNA gene and internally transcribed space region sequences. Besides the incongruence in tree topologies, evidence that distinct segments along the 16S rRNA gene sequences of bacteria currently classified within the genera Bradyrhizobium, Mesorhizobium and Sinorhizobium have a reticulate evolutionary history was also obtained. Our data have important implications for bacterial taxonomy, because currently most taxonomic decisions are based on comparative 16S rRNA gene sequence analysis. Since phylogenetic placement based on 16S rRNA gene sequence divergence perhaps is questionable, we suggest that the proposals of bacterial nomenclature or changes in their taxonomy that have been made may not necessarily be warranted. Accordingly, a more conservative approach should be taken in the future, in which taxonomic decisions are based on the analysis of a wider variety of loci and comparative analytical methods are used to estimate phylogenetic relationships among the genomes under consideration.}, }
@article {pmid12720087, year = {2003}, author = {Jose, J and Otto, GW and Meyer, TF}, title = {The integration site of the iga gene in commensal Neisseria sp.}, journal = {Molecular genetics and genomics : MGG}, volume = {269}, number = {2}, pages = {197-204}, pmid = {12720087}, issn = {1617-4615}, mesh = {Bacterial Proteins/genetics ; Base Sequence ; Blotting, Southern ; DNA/metabolism ; DNA Primers/chemistry ; DNA-Binding Proteins/genetics ; Escherichia coli/genetics ; Genetic Linkage ; Models, Genetic ; Molecular Sequence Data ; Neisseria/*enzymology/*genetics ; Open Reading Frames ; Phylogeny ; Physical Chromosome Mapping ; Plasmids/metabolism ; Polymerase Chain Reaction ; Recombination, Genetic ; Sequence Homology, Nucleic Acid ; Serine Endopeptidases/*genetics ; Species Specificity ; }, abstract = {An IgA1 protease is produced by the human pathogens Neisseria gonorrhoeae and N. meningitidis but not by related non-pathogenic, commensal, Neisseria species. In this study, the chromosomal iga locus was characterized in the N. gonorrhoeae strain MS11 and compared to corresponding loci in N. meningitidis and commensal Neisseria species. In N. gonorrhoeae, the genes trpB and ksgA were found immediately downstream of iga. In addition to comL and comA, a homolog of the Escherichia coli YFII gene was identified upstream of iga. Each gene in the iga region (YFII and comL, comA and iga, and trpB and ksgA) is transcribed in the opposite direction to its neighbors. The comL/ comA and iga/ trpB pairs each have a transcriptional terminator in the correct position for joint use. These terminators contain the common gonococcal DNA uptake sequence (DUS). A highly conserved direct repeat of 25 bp located immediately adjacent to the iga gene in N. gonorrhoeae was also found in N. meningitidis. In Southern hybridization experiments, no homology to iga was detectable in the chromosomal DNAs of the commensal species N. mucosa, N. lactamica, N. flavescens, N. cinerea, N. subflava, N. flava, N. sicca or N. elongata. When N. gonorrhoeae comL and trpB were used as probes, signals were detected on the same restriction fragment in six of the eight species. This indicated that commensal Neisseria species share a possible integration site for the iga gene between comA and trpB. The region between comA and trpB was therefore amplified by PCR. The fragment obtained from N. lactamica showed a high degree of homology to gonococcal comA and trpB, respectively, but iga was replaced by a sequence of 13 bp that shows no homology to any known gonococcal sequence. Our data suggest that iga was acquired by a common ancestor of N. gonorrhoeae and N. meningitidis rather than being distributed by horizontal gene transfer. N. lactamica, which is more closely related to N. gonorrhoeae than other commensals, may have lost iga by deletion.}, }
@article {pmid12718057, year = {2003}, author = {Fukushima, J and Shimura, Y and Inamoto, T}, title = {[Genus Pseudomonas (Pseudomonas aeruginosa)].}, journal = {Nihon rinsho. Japanese journal of clinical medicine}, volume = {61 Suppl 3}, number = {}, pages = {737-741}, pmid = {12718057}, issn = {0047-1852}, mesh = {Bacterial Proteins/genetics ; Drug Resistance/genetics ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Humans ; Multigene Family ; Pseudomonas/classification ; Pseudomonas Infections/diagnosis/microbiology ; Pseudomonas aeruginosa/classification/*genetics/pathogenicity ; Serotyping ; Virulence Factors/genetics ; }, }
@article {pmid12718053, year = {2003}, author = {Nakamura, Y and Suzuki, Y and Gojobori, T}, title = {[Haemophilus influenzae].}, journal = {Nihon rinsho. Japanese journal of clinical medicine}, volume = {61 Suppl 3}, number = {}, pages = {716-721}, pmid = {12718053}, issn = {0047-1852}, mesh = {Bacterial Proteins/genetics ; Databases, Genetic ; Diagnosis, Differential ; Gene Rearrangement ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; Haemophilus Infections/diagnosis/microbiology ; Haemophilus influenzae/classification/*genetics/pathogenicity ; Humans ; Serotyping ; Virulence Factors/genetics ; }, }
@article {pmid12718004, year = {2003}, author = {Hayashi, T}, title = {[Bacterial genome analysis and its implications on the researches of pathogenic bacteria].}, journal = {Nihon rinsho. Japanese journal of clinical medicine}, volume = {61 Suppl 3}, number = {}, pages = {414-422}, pmid = {12718004}, issn = {0047-1852}, mesh = {Bacteria/*genetics/*pathogenicity ; DNA, Bacterial ; Evolution, Molecular ; Gene Deletion ; Gene Duplication ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; *Genome, Bacterial ; *Sequence Analysis, DNA ; Virulence/genetics ; }, }
@article {pmid12717965, year = {2003}, author = {Ohno, A}, title = {[How do bacteria acquire the resistance to antibiotics].}, journal = {Nihon rinsho. Japanese journal of clinical medicine}, volume = {61 Suppl 3}, number = {}, pages = {158-163}, pmid = {12717965}, issn = {0047-1852}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/*genetics ; Bacteriophages ; DNA Transposable Elements ; DNA, Bacterial ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Humans ; Integrons ; Mutation ; Plasmids ; Recombination, Genetic ; }, }
@article {pmid12717435, year = {2003}, author = {Planet, PJ and Kachlany, SC and Fine, DH and DeSalle, R and Figurski, DH}, title = {The Widespread Colonization Island of Actinobacillus actinomycetemcomitans.}, journal = {Nature genetics}, volume = {34}, number = {2}, pages = {193-198}, doi = {10.1038/ng1154}, pmid = {12717435}, issn = {1061-4036}, mesh = {Aggregatibacter actinomycetemcomitans/*genetics/isolation &amp; purification/pathogenicity ; Bacterial Adhesion/genetics ; Biofilms/growth &amp; development ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Models, Genetic ; Mutation ; Phenotype ; Phylogeny ; }, abstract = {Genomic islands, such as pathogenicity islands, contribute to the evolution and diversification of microbial life. Here we report on the Widespread Colonization Island, which encompasses the tad (tight adherence) locus for colonization of surfaces and biofilm formation by the human pathogen Actinobacillus actinomycetemcomitans. At least 12 of the 14 genes at the tad locus are required for tenacious biofilm formation and synthesis of bundled Flp pili (fibrils) that mediate adherence. The pilin subunit, Flp1, remains inside the cell in tad-locus mutants, indicating that these genes encode a secretion system for export and assembly of fibrils. We found tad-related regions in a wide variety of Bacterial and Archaeal species, and their sequence characteristics indicate possible horizontal transfer. To test the hypothesis of horizontal transfer, we compared the phylogeny of the tad locus to a robust organismal phylogeny using statistical tests of congruence and tree reconciliation techniques. Our analysis strongly supports a complex history of gene shuffling by recombination and multiple horizontal transfers, duplications and losses. We present evidence for a specific horizontal transfer event leading to the establishment of this region as a determinant of disease.}, }
@article {pmid12716988, year = {2003}, author = {Hughes, AL and Friedman, R}, title = {Genome-wide survey for genes horizontally transferred from cellular organisms to baculoviruses.}, journal = {Molecular biology and evolution}, volume = {20}, number = {6}, pages = {979-987}, doi = {10.1093/molbev/msg107}, pmid = {12716988}, issn = {0737-4038}, support = {GM066710/GM/NIGMS NIH HHS/United States ; GM43940/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Baculoviridae/*genetics ; DNA Helicases ; DNA Ligases/genetics ; DNA-Binding Proteins/genetics ; *Gene Transfer, Horizontal ; *Genome ; Glucuronosyltransferase/genetics ; Humans ; Inhibitor of Apoptosis Proteins ; *Nuclear Proteins ; Phylogeny ; Ribonucleotide Reductases/genetics ; Transcription Factors/genetics ; Viral Proteins/genetics ; }, abstract = {The phylogeny of 13 viral species in the genera Granulovirus and Nucleopolyhedrovirus (family Baculoviridae) was reconstructed on the basis of 22 conserved protein families shared by all species, and a comprehensive homology search and phylogenetic analysis of the complete genomes of these viruses was used to test for horizontal gene transfer from cellular organisms. Statistically significant evidence of horizontal transfer was found in the case of six protein families (DNA ligase, ribonucleotide reductase 1, SNF2 global transactivator, inhibitor of apoptosis, chitinase, and UDP-glucosyltransferase). Three of these families are known to play key roles in the infection of insect hosts by these viruses. There was evidence that two of these (inhibitor of apoptosis and UDP-glucosyltransferase) were derived from the insect host. By contrast, the gene encoding chitinase in these viruses was evidently derived from a group of bacteria (the gamma subdivision of proteobacteria), which use chitinase to break down fungal chitins.}, }
@article {pmid12716978, year = {2003}, author = {Maside, X and Bartolomé, C and Charlesworth, B}, title = {Inferences on the evolutionary history of the S-element family of Drosophila melanogaster.}, journal = {Molecular biology and evolution}, volume = {20}, number = {8}, pages = {1183-1187}, doi = {10.1093/molbev/msg120}, pmid = {12716978}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Animals ; *Biological Evolution ; *DNA Transposable Elements ; Drosophila melanogaster/*genetics ; *Gene Transfer, Horizontal ; Genetic Variation ; Phylogeny ; Repetitive Sequences, Nucleic Acid ; Species Specificity ; Transposases/*genetics ; }, abstract = {The S-element family of transposable elements has been characterized in D. melanogaster. Attempts to find it in other Drosophila-related species have failed, suggesting that this element family may have recently invaded the D. melanogaster genome by horizontal transfer. In order to investigate its evolutionary history, we analyzed the patterns of DNA polymorphism among the S-element copies present in a sample genome (Drosophila Genome Project). The observed levels of nucleotide diversity are significantly lower than theoretical expectations based on the neutral model. This is consistent with evidence for ongoing gene conversion among copies and for purifying selection on the elements' sequences, particularly on the terminal inverted repeats. A phylogenetic analysis revealed that the members of the S-element family can be grouped into at least two genetically differentiated clusters. The level of divergence between these clusters suggests that the S elements invaded the genome of the ancestor of D. melanogaster before the speciation of the D. melanogaster complex. However, other relevant scenarios are also discussed.}, }
@article {pmid12713464, year = {2003}, author = {Holmes, AJ and Gillings, MR and Nield, BS and Mabbutt, BC and Nevalainen, KM and Stokes, HW}, title = {The gene cassette metagenome is a basic resource for bacterial genome evolution.}, journal = {Environmental microbiology}, volume = {5}, number = {5}, pages = {383-394}, doi = {10.1046/j.1462-2920.2003.00429.x}, pmid = {12713464}, issn = {1462-2912}, mesh = {Base Sequence ; *Evolution, Molecular ; *Genes, Bacterial ; *Genome, Bacterial ; Integrons ; Molecular Sequence Data ; *Recombination, Genetic ; Sequence Alignment ; Soil Microbiology ; }, abstract = {Lateral gene transfer has been proposed as a fundamental process underlying bacterial diversity. Transposons, plasmids and phage are widespread and have been shown to significantly contribute to lateral gene transfer. However, the processes by which disparate genes are assembled and integrated into the host regulatory network to yield new phenotypes are poorly known. Recent discoveries about the integron/gene cassette system indicate it has the potential to play a role in this process. Gene cassettes are small mobile elements typically consisting of a promoterless orf and a recombination site. Integrons are capable of acquisition and re-arrangement of gene cassettes and of the expression of their associated genes. The potential of the integron/gene cassette system is thus largely determined by the diversity contained within the cassette pool and the rate at which integrons sample this pool. We show here using a polymerase chain reaction (PCR) approach by which the environmental gene cassette (EGC) metagenome can be directly sampled that this metagenome contains both protein-coding and non-protein coding genes. Environmental gene cassette-associated recombination sites showed greater diversity than previously seen in integron arrays. Class 1 integrons were shown to be capable of accessing this gene pool through tests of recombinational activity with a representative range of EGCs. We propose that gene cassettes represent a vast, prepackaged genetic resource that could be thought of as a metagenomic template for bacterial evolution.}, }
@article {pmid12710483, year = {2003}, author = {Roe, MT and Pillai, SD}, title = {Monitoring and identifying antibiotic resistance mechanisms in bacteria.}, journal = {Poultry science}, volume = {82}, number = {4}, pages = {622-626}, doi = {10.1093/ps/82.4.622}, pmid = {12710483}, issn = {0032-5791}, mesh = {Animal Husbandry/methods ; Animals ; Bacteria/*drug effects/*genetics ; Chickens ; Drug Resistance, Bacterial/genetics/physiology ; Ecosystem ; Humans ; Integrons/*physiology ; Microbial Sensitivity Tests ; Poultry Products/microbiology ; Public Health ; }, abstract = {Sub-therapeutic administration of antibiotics to animals is under intense scrutiny because they contribute to the dissemination of antibiotic-resistant bacteria into the food chain. Studies suggest that there is a link between the agricultural use of antibiotics and antibiotic-resistant human infections. Antibiotic-resistant organisms from animal and human wastes reenter the human and animal populations through a number of pathways including natural waters, irrigation water, drinking water, and vegetables and foods. Antibiotic usage in the United States for animal production (disease prevention and growth promotion) is estimated to be 18 million pounds annually. As much as 25 to 75% of the antibiotics administered to feedlot animals are excreted unaltered in feces. Because about 180 million dry tons of livestock and poultry waste is generated annually in the United States, it is not surprising that animal-derived antibiotic-resistant organisms are found contaminating groundwater, surface water, and food crops. It is extremely important to clearly understand the molecular mechanisms that could potentially cause lateral or horizontal gene transfer of antibiotic resistance genes among bacteria. Once the mechanisms and magnitude of resistance gene transfer are clearly understood and quantified, strategies can be instituted to reduce the potential for dissemination of these genes.}, }
@article {pmid12704167, year = {2003}, author = {Smeets, LC and Arents, NL and van Zwet, AA and Vandenbroucke-Grauls, CM and Verboom, T and Bitter, W and Kusters, JG}, title = {Molecular patchwork: Chromosomal recombination between two Helicobacter pylori strains during natural colonization.}, journal = {Infection and immunity}, volume = {71}, number = {5}, pages = {2907-2910}, pmid = {12704167}, issn = {0019-9567}, mesh = {Alleles ; Base Sequence ; *Chromosomes, Bacterial ; Drug Resistance, Bacterial ; Gastric Mucosa/*microbiology ; Helicobacter pylori/drug effects/*genetics ; Metronidazole/pharmacology ; Molecular Sequence Data ; Nitroreductases/genetics ; *Recombination, Genetic ; }, abstract = {Genetic analysis of two Helicobacter pylori strains isolated from a single gastric biopsy showed evidence of extensive horizontal gene transfer. Several large recombinations were identified in the rdxA gene, which is involved in metronidazole resistance.}, }
@article {pmid12704157, year = {2003}, author = {Fitzgerald, JR and Reid, SD and Ruotsalainen, E and Tripp, TJ and Liu, M and Cole, R and Kuusela, P and Schlievert, PM and Järvinen, A and Musser, JM}, title = {Genome diversification in Staphylococcus aureus: Molecular evolution of a highly variable chromosomal region encoding the Staphylococcal exotoxin-like family of proteins.}, journal = {Infection and immunity}, volume = {71}, number = {5}, pages = {2827-2838}, pmid = {12704157}, issn = {0019-9567}, mesh = {Animals ; Base Sequence ; Blotting, Western ; *Chromosomes, Bacterial ; *Evolution, Molecular ; Exotoxins/analysis/*genetics/toxicity ; *Genome, Bacterial ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Rabbits ; Recombinant Proteins/analysis ; Staphylococcal Infections/blood ; Staphylococcus aureus/*genetics ; }, abstract = {Recent genomic studies have revealed extensive variation in natural populations of many pathogenic bacteria. However, the evolutionary processes which contribute to much of this variation remain unclear. A previous whole-genome DNA microarray study identified variation at a large chromosomal region (RD13) of Staphylococcus aureus which encodes a family of proteins with homology to staphylococcal and streptococcal superantigens, designated staphylococcal exotoxin-like (SET) proteins. In the present study, RD13 was found in all 63 S. aureus isolates of divergent clonal, geographic, and disease origins but contained a high level of variation in gene content in different strains. A central variable region which contained from 6 to 10 different set genes, depending on the strain, was identified, and DNA sequence analysis suggests that horizontal gene transfer and recombination have contributed to the diversification of RD13. Phylogenetic analysis based on the RD13 DNA sequence of 18 strains suggested that loss of various set genes has occurred independently several times, in separate lineages of pathogenic S. aureus, providing a model to explain the molecular variation of RD13 in extant strains. In spite of multiple episodes of set deletion, analysis of the ratio of silent substitutions in set genes to amino acid replacements in their products suggests that purifying selection (selective constraint) is acting to maintain SET function. Further, concurrent transcription in vitro of six of the seven set genes in strain COL was detected, indicating that the expression of set genes has been maintained in contemporary strains, and Western immunoblot analysis indicated that multiple SET proteins are expressed during the course of human infections. Overall, we have shown that the chromosomal region RD13 has diversified extensively through episodes of gene deletion and recombination. The coexpression of many set genes and the production of multiple SET proteins during human infection suggests an important role in host-pathogen interactions.}, }
@article {pmid12702701, year = {2003}, author = {Hawkey, PM}, title = {Mechanisms of quinolone action and microbial response.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {51 Suppl 1}, number = {}, pages = {29-35}, doi = {10.1093/jac/dkg207}, pmid = {12702701}, issn = {0305-7453}, mesh = {Anti-Infective Agents/*pharmacology ; Bacteria/*drug effects/enzymology/*genetics ; DNA Gyrase/genetics ; DNA Topoisomerase IV/genetics ; DNA-Binding Proteins/genetics ; Drug Resistance, Bacterial/*genetics ; Humans ; Mutation ; Porins/genetics ; Quinolones/*pharmacology ; }, abstract = {Over the years, chromosomal mapping of the bacterial genome of Escherichia coli has demonstrated that many loci are associated with quinolone resistance, which is mainly a result of chromosomal mutation or alteration of the quantity or type of porins in the outer membrane of Gram-negative bacteria. There has been one report of a small and confined episode of plasmid-mediated resistance to fluoroquinolones, which did not appear to persist. With the increasingly widespread use of an expanding range of fluoroquinolone antibiotics, a range and mix in individual bacterial isolates of the different mechanisms of resistance to fluoroquinolones will undoubtedly be encountered amongst clinically significant bacteria. Currently, transferable resistance is extremely rare and most resistant bacteria arise from clonal expansion of mutated strains. However, it is conceivable that in the future, horizontal gene transfer may become a more important means of conferring resistance to fluoroquinolones.}, }
@article {pmid12702207, year = {2003}, author = {McCarter, JP and Mitreva, MD and Martin, J and Dante, M and Wylie, T and Rao, U and Pape, D and Bowers, Y and Theising, B and Murphy, CV and Kloek, AP and Chiapelli, BJ and Clifton, SW and Bird, DM and Waterston, RH}, title = {Analysis and functional classification of transcripts from the nematode Meloidogyne incognita.}, journal = {Genome biology}, volume = {4}, number = {4}, pages = {R26}, pmid = {12702207}, issn = {1474-760X}, support = {U01 AI046593/AI/NIAID NIH HHS/United States ; AI 46593/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Caenorhabditis elegans/genetics ; Chromosome Mapping ; Cluster Analysis ; Computational Biology ; Expressed Sequence Tags ; Gene Transfer, Horizontal ; Genes, Helminth ; Larva/genetics ; Phenotype ; RNA Interference ; RNA, Helminth/*analysis/*classification/physiology ; Sequence Homology ; Transcription, Genetic ; Tylenchida/genetics ; Tylenchoidea/*genetics/growth &amp; development ; }, abstract = {BACKGROUND: Plant parasitic nematodes are major pathogens of most crops. Molecular characterization of these species as well as the development of new techniques for control can benefit from genomic approaches. As an entrée to characterizing plant parasitic nematode genomes, we analyzed 5,700 expressed sequence tags (ESTs) from second-stage larvae (L2) of the root-knot nematode Meloidogyne incognita.<br><br>RESULTS: From these, 1,625 EST clusters were formed and classified by function using the Gene Ontology (GO) hierarchy and the Kyoto KEGG database. L2 larvae, which represent the infective stage of the life cycle before plant invasion, express a diverse array of ligand-binding proteins and abundant cytoskeletal proteins. L2 are structurally similar to Caenorhabditis elegans dauer larva and the presence of transcripts encoding glyoxylate pathway enzymes in the M. incognita clusters suggests that root-knot nematode larvae metabolize lipid stores while in search of a host. Homology to other species was observed in 79% of translated cluster sequences, with the C. elegans genome providing more information than any other source. In addition to identifying putative nematode-specific and Tylenchida-specific genes, sequencing revealed previously uncharacterized horizontal gene transfer candidates in Meloidogyne with high identity to rhizobacterial genes including homologs of nodL acetyltransferase and novel cellulases.<br><br>CONCLUSIONS: With sequencing from plant parasitic nematodes accelerating, the approaches to transcript characterization described here can be applied to more extensive datasets and also provide a foundation for more complex genome analyses.}, }
@article {pmid12700273, year = {2003}, author = {Wang, L and Rothemund, D and Curd, H and Reeves, PR}, title = {Species-wide variation in the Escherichia coli flagellin (H-antigen) gene.}, journal = {Journal of bacteriology}, volume = {185}, number = {9}, pages = {2936-2943}, pmid = {12700273}, issn = {0021-9193}, mesh = {Antigens, Bacterial/*genetics ; Escherichia coli/*genetics ; Flagellin/*genetics ; Gene Transfer, Horizontal ; Genetic Variation ; Molecular Sequence Data ; Mutation ; Phylogeny ; Species Specificity ; }, abstract = {Escherichia coli is a clonal species. The best-understood components of its clonal variation are the flagellar (H) and polysaccharide (O) antigens, both well documented since the mid-1930s because of their use in serotyping. Flagellin is the protein subunit of the flagellum that carries H-antigen specificity. We show that 43 of the 54 H-antigen specificities of E. coli map to the flagellin gene at fliC and sequenced all 43 forms and confirmed specificity of each by cloning and expression. This is, to our knowledge, the first time that all known forms of such a highly polymorphic gene have been fully sequenced and characterized for any species. The established distinction between a highly variable central region and more conserved flanking regions is upheld. The sequences fall into two groups, one of which may be derived from the fliC gene of the E. coli/Salmonella enterica common ancestor, the other perhaps obtained by lateral transfer since species divergence. Comparison of sequences revealed that both horizontal DNA transfer and fixation of mutations under diversifying selection pressure contributed to polymorphism in this locus.}, }
@article {pmid12700256, year = {2003}, author = {Mikalsen, B and Boison, G and Skulberg, OM and Fastner, J and Davies, W and Gabrielsen, TM and Rudi, K and Jakobsen, KS}, title = {Natural variation in the microcystin synthetase operon mcyABC and impact on microcystin production in Microcystis strains.}, journal = {Journal of bacteriology}, volume = {185}, number = {9}, pages = {2774-2785}, pmid = {12700256}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; Bacterial Proteins ; Gene Deletion ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Variation ; Microcystins ; Microcystis/enzymology/*genetics ; Molecular Sequence Data ; Multigene Family ; *Operon ; Peptide Synthases/*genetics/metabolism ; Peptides, Cyclic/*biosynthesis ; Phylogeny ; Recombination, Genetic ; Sequence Alignment ; Sequence Analysis ; Species Specificity ; }, abstract = {Toxic Microcystis strains often produce several isoforms of the cyclic hepatotoxin microcystin, and more than 65 isoforms are known. This has been attributed to relaxed substrate specificity of the adenylation domain. Our results show that in addition to this, variability is also caused by genetic variation in the microcystin synthetase genes. Genetic characterization of a region of the adenylation domain in module mcyB1 resulted in identification of two groups of genetic variants in closely related Microcystis strains. Sequence analyses suggested that the genetic variation is due to recombination events between mcyB1 and the corresponding domains in mcyC. Each variant could be correlated to a particular microcystin isoform profile, as identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Among the Microcystis species studied, we found 11 strains containing different variants of the mcyABC gene cluster and 7 strains lacking the genes. Furthermore, there is no concordance between the phylogenies generated with mcyB1, 16S ribosomal DNA, and DNA fingerprinting. Collectively, these results suggest that recombination between imperfect repeats, gene loss, and horizontal gene transfer can explain the distribution and variation within the mcyABC operon.}, }
@article {pmid12700250, year = {2003}, author = {Katayama, Y and Takeuchi, F and Ito, T and Ma, XX and Ui-Mizutani, Y and Kobayashi, I and Hiramatsu, K}, title = {Identification in methicillin-susceptible Staphylococcus hominis of an active primordial mobile genetic element for the staphylococcal cassette chromosome mec of methicillin-resistant Staphylococcus aureus.}, journal = {Journal of bacteriology}, volume = {185}, number = {9}, pages = {2711-2722}, pmid = {12700250}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; Chromosomes, Bacterial/*genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Methicillin/pharmacology ; Methicillin Resistance/*genetics ; Molecular Sequence Data ; Penicillins/pharmacology ; Sequence Alignment ; Species Specificity ; Staphylococcus aureus/drug effects/*genetics ; Staphylococcus hominis/drug effects/*genetics ; }, abstract = {We previously reported that the methicillin resistance gene mecA is carried by a novel type of mobile genetic element, SCCmec (staphylococcal cassette chromosome mec), in the chromosome of methicillin-resistant Staphylococcus aureus (MRSA). These elements are precisely excised from the chromosome and integrated into a specific site on the recipient chromosome by a pair of recombinase proteins encoded by the cassette chromosome recombinase genes ccrA and ccrB. In the present work, we detected homologues of the ccr genes in Staphylococcus hominis type strain GIFU12263 (equivalent to ATCC 27844), which is susceptible to methicillin. Sequence determination revealed that the ccr homologues in S. hominis were type 1 ccr genes (ccrA1 and ccrB1) that were localized on a genetic element structurally very similar to SCCmec except for the absence of the methicillin-resistance gene, mecA. This genetic element had mosaic-like patterns of homology with extant SCCmec elements, and we designated it SCC(12263) and considered it a type I staphylococcal cassette chromosome (SCC). The ccrB1 gene identified in the S. hominis strain is the first type 1 ccrB gene discovered to retain its function through the excision process as judged by two criteria: (i) SCC(12263) was spontaneously excised during cultivation of the strain and (ii) introduction of the S. hominis ccrB1 into an MRSA strain carrying a type I SCCmec whose ccrB1 gene is inactive generated SCCmec excisants at a high frequency. The existence of an SCC without a mec determinant is indicative of a staphylococcal site-specific mobile genetic element that serves as a vehicle of transfer for various genetic markers between staphylococcal species.}, }
@article {pmid12697060, year = {2003}, author = {Coenye, T and Vandamme, P}, title = {Simple sequence repeats and compositional bias in the bipartite Ralstonia solanacearum GMI1000 genome.}, journal = {BMC genomics}, volume = {4}, number = {1}, pages = {10}, pmid = {12697060}, issn = {1471-2164}, mesh = {Base Composition/*genetics ; Burkholderia/*genetics ; Chromosomes, Bacterial/genetics ; DNA, Bacterial/genetics ; Evolution, Molecular ; *Genome, Bacterial ; Plasmids/genetics ; Repetitive Sequences, Nucleic Acid/*genetics ; }, abstract = {BACKGROUND: Ralstonia solanacearum is an important plant pathogen. The genome of R. solananearum GMI1000 is organised into two replicons (a 3.7-Mb chromosome and a 2.1-Mb megaplasmid) and this bipartite genome structure is characteristic for most R. solanacearum strains. To determine whether the megaplasmid was acquired via recent horizontal gene transfer or is part of an ancestral single chromosome, we compared the abundance, distribution and composition of simple sequence repeats (SSRs) between both replicons and also compared the respective compositional biases.<br><br>RESULTS: Our data show that both replicons are very similar in respect to distribution and composition of SSRs and presence of compositional biases. Minor variations in SSR and compositional biases observed may be attributable to minor differences in gene expression and regulation of gene expression or can be attributed to the small sample numbers observed.<br><br>CONCLUSIONS: The observed similarities indicate that both replicons have shared a similar evolutionary history and thus suggest that the megaplasmid was not recently acquired from other organisms by lateral gene transfer but is a part of an ancestral R. solanacearum chromosome.}, }
@article {pmid12697059, year = {2003}, author = {Jensen, LJ and Skovgaard, M and Sicheritz-Pontén, T and Jørgensen, MK and Lundegaard, C and Pedersen, CC and Petersen, N and Ussery, D}, title = {Analysis of two large functionally uncharacterized regions in the Methanopyrus kandleri AV19 genome.}, journal = {BMC genomics}, volume = {4}, number = {1}, pages = {12}, pmid = {12697059}, issn = {1471-2164}, mesh = {Amino Acids/genetics/physiology ; Archaeal Proteins/genetics/physiology ; Base Composition ; DNA, Archaeal/analysis ; *Genes, Archaeal/physiology ; *Genome, Archaeal ; Multigene Family/genetics/physiology ; Open Reading Frames/genetics/physiology ; Predictive Value of Tests ; Transcription Initiation Site ; }, abstract = {BACKGROUND: For most sequenced prokaryotic genomes, about a third of the protein coding genes annotated are "orphan proteins", that is, they lack homology to known proteins. These hypothetical genes are typically short and randomly scattered throughout the genome. This trend is seen for most of the bacterial and archaeal genomes published to date.<br><br>RESULTS: In contrast we have found that a large fraction of the genes coding for such orphan proteins in the Methanopyrus kandleri AV19 genome occur within two large regions. These genes have no known homologs except from other M. kandleri genes. However, analysis of their lengths, codon usage, and Ribosomal Binding Site (RBS) sequences shows that they are most likely true protein coding genes and not random open reading frames.<br><br>CONCLUSIONS: Although these regions can be considered as candidates for massive lateral gene transfer, our bioinformatics analysis suggests that this is not the case. We predict many of the organism specific proteins to be transmembrane and belong to protein families that are non-randomly distributed between the regions. Consistent with this, we suggest that the two regions are most likely unrelated, and that they may be integrated plasmids.}, }
@article {pmid12691833, year = {2003}, author = {Oh, JD and Geller, AI and Zhang, Gr and Chase, TN}, title = {Gene transfer of constitutively active protein kinase C into striatal neurons accelerates onset of levodopa-induced motor response alterations in parkinsonian rats.}, journal = {Brain research}, volume = {971}, number = {1}, pages = {18-30}, pmid = {12691833}, issn = {0006-8993}, support = {R01 AG016777/AG/NIA NIH HHS/United States ; R01 AG021193/AG/NIA NIH HHS/United States ; R01 NS043107/NS/NINDS NIH HHS/United States ; R01 NS045855/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; Antiparkinson Agents/*pharmacology ; Blotting, Western ; Corpus Striatum/drug effects/enzymology ; Enzyme Inhibitors/pharmacology ; Gene Transfer, Horizontal/physiology ; Genetic Vectors ; Herpesvirus 1, Human ; Immunohistochemistry ; Levodopa/*pharmacology ; Male ; Models, Animal ; Motor Activity/*drug effects/genetics ; Neurons/drug effects/*enzymology ; Parkinsonian Disorders/*enzymology ; Phosphorylation ; Piperidines/pharmacology ; Protein Kinase C/antagonists &amp; inhibitors/*biosynthesis/genetics ; Rats ; Rats, Sprague-Dawley ; Receptors, AMPA/drug effects/metabolism ; Time Factors ; }, abstract = {Alterations in motor response that complicate levodopa treatment of Parkinson's disease appear to involve sensitization of striatal ionotropic glutamate receptors. Since protein kinase C (PKC)-mediated phosphorylation regulates glutamatergic receptors of the alpha-amino-3-hydroxyl-5-methyl-4-isoxazole propionic acid (AMPA) subtype and has been linked to several forms of behavioral plasticity, activation of PKC signaling in striatal spiny neurons may also contribute to the motor plasticity changes associated with chronic levodopa therapy. To evaluate this possibility, we sought to augment PKC signaling by using Herpes Simplex Virus type 1 vectors (pHSVpkcDelta) to directly transfer the catalytic domain of the PKCbetaII gene into striatal neurons of parkinsonian rats. Microinjection of pHSVpkcDelta vectors lead to the persistent expression of PkcDelta (35% loss over 21 days) in medium spiny neurons together with an increase in serine 831 phosphorylation on AMPA receptor GluR1 subunits and hastened the appearance of the shortened response duration produced by chronic levodopa treatment (P<0.05). In pHSVpkcDelta-infected animals, intrastriatal injection of the PKC inhibitor NPC-15437 (1.0 microg) attenuated both the increased GluR1 phosphorylation (P<0.01) and the accelerated onset of the levodopa-induced response modifications (P<0.01). However, in rats that received levodopa treatment for 21 days without the gene transfer, intrastriatal NPC-15437 had no effect on the response shortening or on GluR1 S831 phosphorylation. The results suggest that an increase in PKC-mediated signaling, including, in part, phosphorylation of AMPA receptors, on striatal spiny neurons may be sufficient to promote the initial appearance, but not necessary the ultimate expression, of the levodopa-induced motor response changes occurring in a rodent model of the human motor complication syndrome.}, }
@article {pmid12689728, year = {2003}, author = {Poole, AM and Phillips, MJ and Penny, D}, title = {Prokaryote and eukaryote evolvability.}, journal = {Bio Systems}, volume = {69}, number = {2-3}, pages = {163-185}, doi = {10.1016/s0303-2647(02)00131-4}, pmid = {12689728}, issn = {0303-2647}, mesh = {Adaptation, Physiological/*genetics ; Animals ; Biological Evolution ; Ecosystem ; *Eukaryotic Cells ; Gene Expression Regulation/genetics ; Genetic Variation ; *Genome ; Humans ; *Models, Genetic ; Mutation/genetics ; *Prokaryotic Cells ; Selection, Genetic ; Species Specificity ; Stress, Physiological/*genetics ; }, abstract = {The concept of evolvability covers a broad spectrum of, often contradictory, ideas. At one end of the spectrum it is equivalent to the statement that evolution is possible, at the other end are untestable post hoc explanations, such as the suggestion that current evolutionary theory cannot explain the evolution of evolvability. We examine similarities and differences in eukaryote and prokaryote evolvability, and look for explanations that are compatible with a wide range of observations. Differences in genome organisation between eukaryotes and prokaryotes meets this criterion. The single origin of replication in prokaryote chromosomes (versus multiple origins in eukaryotes) accounts for many differences because the time to replicate a prokaryote genome limits its size (and the accumulation of junk DNA). Both prokaryotes and eukaryotes appear to switch from genetic stability to genetic change in response to stress. We examine a range of stress responses, and discuss how these impact on evolvability, particularly in unicellular organisms versus complex multicellular ones. Evolvability is also limited by environmental interactions (including competition) and we describe a model that places limits on potential evolvability. Examples are given of its application to predator competition and limits to lateral gene transfer. We suggest that unicellular organisms evolve largely through a process of metabolic change, resulting in biochemical diversity. Multicellular organisms evolve largely through morphological changes, not through extensive changes to cellular biochemistry.}, }
@article {pmid12684849, year = {2003}, author = {Sharma, S and Sachdeva, P and Virdi, JS}, title = {Emerging water-borne pathogens.}, journal = {Applied microbiology and biotechnology}, volume = {61}, number = {5-6}, pages = {424-428}, doi = {10.1007/s00253-003-1302-y}, pmid = {12684849}, issn = {0175-7598}, mesh = {Animals ; Cholera/transmission ; Conservation of Natural Resources ; Developing Countries ; Disinfection ; Humans ; Population Surveillance ; Vibrio cholerae O139/isolation &amp; purification/pathogenicity ; Water/*parasitology ; *Water Microbiology ; Water Supply ; }, abstract = {Emerging water-borne pathogens constitute a major health hazard in both developed and developing nations. A new dimension to the global epidemiology of cholera-an ancient scourge-was provided by the emergence of Vibrio cholerae O139. Also, water-borne enterohaemorrhagic Escherichia coli (E. coli O157:H7), although regarded as a problem of the industrialized west, has recently caused outbreaks in Africa. Outbreaks of chlorine-resistant Cryptosporidium have motivated water authorities to reassess the adequacy of current water-quality regulations. Of late, a host of other organisms, such as hepatitis viruses (including hepatitis E virus), Campylobacter jejuni, microsporidia, cyclospora, Yersinia enterocolitica, calciviruses and environmental bacteria like Mycobacterium spp, aeromonads, Legionella pneumophila and multidrug-resistant Pseudomonas aeruginosa have been associated with water-borne illnesses. This review critically examines the potential of these as emerging water-borne pathogens. It also examines the possible reasons, such as an increase in the number of immunocompromised individuals, urbanization and horizontal gene transfer, that may underlie their emergence. Further, measures required to face the challenge posed by these pathogens are also discussed.}, }
@article {pmid12683971, year = {2003}, author = {Genereux, DP and Logsdon, JM}, title = {Much ado about bacteria-to-vertebrate lateral gene transfer.}, journal = {Trends in genetics : TIG}, volume = {19}, number = {4}, pages = {191-195}, doi = {10.1016/S0168-9525(03)00055-6}, pmid = {12683971}, issn = {0168-9525}, mesh = {Animals ; Bacteria/*genetics ; Databases, Genetic ; Dictyostelium/genetics ; *Gene Transfer, Horizontal ; *Genome, Human ; Humans ; Phylogeny ; Vertebrates/*genetics ; }, abstract = {When the International Human Genome Sequencing Consortium (IHGSC) published its draft of the human genome in February 2001, several genes were identified as possible bacteria-to-vertebrate transfers (BVTs). These genes were identified by their highly significant sequence similarity to bacterial genes in BLAST searches, and by their lack of matches among non-vertebrate eukaryote genes. Many were later rejected as BVTs by several methods, including recovery of probable orthologs from the genomes of incompletely sequenced eukaryotes. Whereas the BVT issue has received considerable attention, there has been no compilation of all potential BVTs considered to date, nor any proposal of a single comprehensive method for rigorously establishing the veracity of a putative BVT. In reviewing the work to date, we list all of the proteins examined and propose systematic tests to investigate whether a vertebrate gene proposed as a BVT is indeed of bacterial origin. We use the proposed strategy to test--and reject--one of the BVTs from the original IHGSC list.}, }
@article {pmid12683967, year = {2003}, author = {Silva, FJ and Latorre, A and Moya, A}, title = {Why are the genomes of endosymbiotic bacteria so stable?.}, journal = {Trends in genetics : TIG}, volume = {19}, number = {4}, pages = {176-180}, doi = {10.1016/S0168-9525(03)00041-6}, pmid = {12683967}, issn = {0168-9525}, mesh = {Buchnera/*genetics ; Conserved Sequence ; Escherichia coli/genetics ; Gene Duplication ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Transformation, Genetic ; }, abstract = {The comparative analysis of three strains of the endosymbiotic bacterium Buchnera aphidicola has revealed high genome stability associated with an almost complete absence of chromosomal rearrangements and horizontal gene transfer events during the past 150 million years. The loss of genes involved in DNA uptake and recombination in the initial stages of endosymbiosis probably underlies this stability. Gene loss, which was extensive during the initial steps of Buchnera evolution, has continued in the different Buchnera lineages since their divergence.}, }
@article {pmid12679539, year = {2003}, author = {Uchino, Y and Yokota, A}, title = {"Green-like" and "red-like" RubisCO cbbL genes in Rhodobacter azotoformans.}, journal = {Molecular biology and evolution}, volume = {20}, number = {5}, pages = {821-830}, doi = {10.1093/molbev/msg100}, pmid = {12679539}, issn = {0737-4038}, mesh = {Base Sequence ; Blotting, Southern ; Cluster Analysis ; Codon/genetics ; DNA Primers ; Electrophoresis ; *Evolution, Molecular ; Likelihood Functions ; Molecular Sequence Data ; *Phylogeny ; Rhodobacter/*genetics ; Ribulose-Bisphosphate Carboxylase/*genetics ; Sequence Analysis, DNA ; }, abstract = {We found that Rhodobacter azotoformans IFO 16436T contains two different cbbL genes coding form I ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) large subunits. One gene is located within a "green-like" group of the RubisCO phylogenetic tree, and the other is located within a "red-like" group. This is the first report that one organism contains both green-like and red-like RubisCO genes. Moreover, by PCR using primers which amplify two green-like and red-like cbbL genes alternatively and dot blot hybridization, we demonstrated that Rhodobacter blasticus, Rhodobacter capsulatus, and Rhodobacter veldkampii possess only green-like cbbL genes, and Rhodobacter sphaeroides possesses only a red-like cbbL gene. In the cbbL phylogenic analysis, R. spaeroides and R. azotoformans 1 (red-like) formed a cluster within the red-like group, and R. capsulatus, R. azotoformans 2 (green-like), R. blasticus, and R. veldkampii formed a cluster within the green-like group. This suggests that red-like cbbL genes of Rhodobacter species were derived from one ancestor, and green-like cbbL genes were derived from another ancestor. On the other hand, molecular phylogeny of the bacteria indicates that R. veldkampii, which has only a green-like cbbL gene, is the earliest evolved Rhodobacter species and that R. azotoformans and R. sphaeroides, which have red-like cbbL genes, are the latest evolved. Consequently, the following hypothesis is proposed: the common ancestor of Rhodobacter had a green-like cbbL gene, the common ancestor of R. azotoformans and R. sphaeroides subsequently obtained a red-like cbbL gene by a horizontal gene transfer, and the ancestor of R. sphaeroides later lost the green-like cbbL gene.}, }
@article {pmid12677045, year = {2003}, author = {Strauss, SH}, title = {Genetic technologies. Genomics, genetic engineering, and domestication of crops.}, journal = {Science (New York, N.Y.)}, volume = {300}, number = {5616}, pages = {61-62}, doi = {10.1126/science.1079514}, pmid = {12677045}, issn = {1095-9203}, mesh = {Biotechnology ; Breeding ; Crops, Agricultural/*genetics ; Gene Transfer, Horizontal ; *Genetic Engineering ; *Genomics ; Government Regulation ; Phenotype ; Plant Physiological Phenomena ; *Plants, Genetically Modified ; Transgenes ; }, }
@article {pmid12676729, year = {2003}, author = {Matsui, K and Ishii, N and Kawabata, Z}, title = {Release of extracellular transformable plasmid DNA from Escherichia coli cocultivated with algae.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {4}, pages = {2399-2404}, pmid = {12676729}, issn = {0099-2240}, mesh = {Animals ; Chlorophyta/growth &amp; development ; Culture Media ; Cyanobacteria/growth &amp; development ; DNA, Bacterial/genetics ; Escherichia coli/genetics/*growth &amp; development ; Euglena/growth &amp; development ; Eukaryota/*growth &amp; development ; Gene Transfer, Horizontal ; Plasmids/*genetics ; *Transformation, Bacterial ; }, abstract = {We studied the effects of cocultivation with either Euglena gracilis (Euglenophyta), Microcystis aeruginosa (Cyanophyta), Chlamydomonas neglecta (Chlorophyta), or Carteria inversa (Chlorophyta) on the production of extracellular plasmid DNA by Escherichia coli LE392(pKZ105). Dot blot hybridization analysis showed a significant release of plasmid DNA by cocultivation with all the algae tested. Further analysis by electrotransformation confirmed the release of transformable plasmid DNA by cocultivation with either E. gracilis, M. aeruginosa, or C. inversa. These results suggest algal involvement in bacterial horizontal gene transfer by stimulating the release of transformable DNA into aquatic environments.}, }
@article {pmid12676698, year = {2003}, author = {Wilson, MS and Herrick, JB and Jeon, CO and Hinman, DE and Madsen, EL}, title = {Horizontal transfer of phnAc dioxygenase genes within one of two phenotypically and genotypically distinctive naphthalene-degrading guilds from adjacent soil environments.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {4}, pages = {2172-2181}, pmid = {12676698}, issn = {0099-2240}, mesh = {Bacteria/classification/enzymology/*genetics ; Biodegradation, Environmental ; Burkholderia/classification/enzymology/genetics ; Coal Tar/metabolism ; Dioxygenases ; *Gene Transfer, Horizontal ; Genotype ; Molecular Sequence Data ; Multienzyme Complexes/genetics/metabolism ; Naphthalenes/*metabolism ; Oxygenases/*genetics/metabolism ; Phenanthrenes/*metabolism ; Phenotype ; Pseudomonas/classification/enzymology/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Soil Pollutants/metabolism ; }, abstract = {Several distinct naphthalene dioxygenases have been characterized to date, which provides the opportunity to investigate the ecological significance, relative distribution, and transmission modes of the different analogs. In this study, we showed that a group of naphthalene-degrading isolates from a polycyclic aromatic hydrocarbon (PAH)-contaminated hillside soil were phenotypically and genotypically distinct from naphthalene-degrading organisms isolated from adjacent, more highly contaminated seep sediments. Mineralization of (14)C-labeled naphthalene by soil slurries suggested that the in situ seep community was more acclimated to PAHs than was the in situ hillside community. phnAc-like genes were present in diverse naphthalene-degrading isolates cultured from the hillside soil, while nahAc-like genes were found only among isolates cultured from the seep sediments. The presence of a highly conserved nahAc allele among gram-negative isolates from the coal tar-contaminated seep area provided evidence for in situ horizontal gene transfer and was reported previously (J. B. Herrick, K. G. Stuart-Keil, W. C. Ghiorse, and E. L. Madsen, Appl. Environ. Microbiol. 63:2330-2337, 1997). Natural horizontal transfer of the phnAc sequence was also suggested by a comparison of the phnAc and 16S ribosomal DNA sequences of the hillside isolates. Analysis of metabolites produced by cell suspensions and patterns of amplicons produced by PCR analysis suggested both genetic and metabolic diversity among the naphthalene-degrading isolates of the contaminated hillside. These results provide new insights into the distribution, diversity, and transfer of phnAc alleles and increase our understanding of the acclimation of microbial communities to pollutants.}, }
@article {pmid12670998, year = {2003}, author = {Nunes, LR and Rosato, YB and Muto, NH and Yanai, GM and da Silva, VS and Leite, DB and Gonçalves, ER and de Souza, AA and Coletta-Filho, HD and Machado, MA and Lopes, SA and de Oliveira, RC}, title = {Microarray analyses of Xylella fastidiosa provide evidence of coordinated transcription control of laterally transferred elements.}, journal = {Genome research}, volume = {13}, number = {4}, pages = {570-578}, pmid = {12670998}, issn = {1088-9051}, mesh = {Chromosome Mapping/methods ; Chromosomes, Bacterial/genetics ; Citrus/microbiology ; Culture Media/metabolism ; DNA, Bacterial/genetics ; DNA, Viral/genetics ; Gammaproteobacteria/*genetics/growth &amp; development/pathogenicity ; Gene Expression Profiling/*methods ; Gene Expression Regulation, Bacterial/*genetics ; Gene Order/genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Oligonucleotide Array Sequence Analysis/*methods ; Plant Diseases/microbiology ; Plasmids/genetics ; Prophages/genetics ; Species Specificity ; Transcription, Genetic/genetics ; Virulence Factors/genetics ; }, abstract = {Genetically distinct strains of the plant bacterium Xylella fastidiosa (Xf) are responsible for a variety of plant diseases, accounting for severe economic damage throughout the world. Using as a reference the genome of Xf 9a5c strain, associated with citrus variegated chlorosis (CVC), we developed a microarray-based comparison involving 12 Xf isolates, providing a thorough assessment of the variation in genomic composition across the group. Our results demonstrate that Xf displays one of the largest flexible gene pools characterized to date, with several horizontally acquired elements, such as prophages, plasmids, and genomic islands (GIs), which contribute up to 18% of the final genome. Transcriptome analysis of bacteria grown under different conditions shows that most of these elements are transcriptionally active, and their expression can be influenced in a coordinated manner by environmental stimuli. Finally, evaluation of the genetic composition of these laterally transferred elements identified differences that may help to explain the adaptability of Xf strains to infect such a wide range of plant species.}, }
@article {pmid12670984, year = {2003}, author = {Deng, WL and Rehm, AH and Charkowski, AO and Rojas, CM and Collmer, A}, title = {Pseudomonas syringae exchangeable effector loci: sequence diversity in representative pathovars and virulence function in P. syringae pv. syringae B728a.}, journal = {Journal of bacteriology}, volume = {185}, number = {8}, pages = {2592-2602}, pmid = {12670984}, issn = {0021-9193}, mesh = {Bacterial Proteins/biosynthesis/*genetics/metabolism ; Cloning, Molecular ; Gene Deletion ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Molecular Sequence Data ; Multigene Family ; Open Reading Frames ; Phylogeny ; Plant Diseases/*microbiology ; Point Mutation ; Pseudomonas/*genetics/*pathogenicity ; Sequence Homology ; Virulence ; }, abstract = {Pseudomonas syringae is a plant pathogen whose pathogenicity and host specificity are thought to be determined by Hop/Avr effector proteins injected into plant cells by a type III secretion system. P. syringae pv. syringae B728a, which causes brown spot of bean, is a particularly well-studied strain. The type III secretion system in P. syringae is encoded by hrp (hypersensitive response and pathogenicity) and hrc (hrp conserved) genes, which are clustered in a pathogenicity island with a tripartite structure such that the hrp/hrc genes are flanked by a conserved effector locus and an exchangeable effector locus (EEL). The EELs of P. syringae pv. syringae B728a, P. syringae strain 61, and P. syringae pv. tomato DC3000 differ in size and effector gene composition; the EEL of P. syringae pv. syringae B728a is the largest and most complex. The three putative effector proteins encoded by the P. syringae pv. syringae B728a EEL--HopPsyC, HopPsyE, and HopPsyV--were demonstrated to be secreted in an Hrp-dependent manner in culture. Heterologous expression of hopPsyC, hopPsyE, and hopPsyV in P. syringae pv. tabaci induced the hypersensitive response in tobacco leaves, demonstrating avirulence activity in a nonhost plant. Deletion of the P. syringae pv. syringae B728a EEL strongly reduced virulence in host bean leaves. EELs from nine additional strains representing nine P. syringae pathovars were isolated and sequenced. Homologs of avrPphE (e.g., hopPsyE) and hopPsyA were particularly common. Comparative analyses of these effector genes and hrpK (which flanks the EEL) suggest that the EEL effector genes were acquired by horizontal transfer after the acquisition of the hrp/hrc gene cluster but before the divergence of modern pathovars and that some EELs underwent transpositions yielding effector exchanges or point mutations producing effector pseudogenes after their acquisition.}, }
@article {pmid12667177, year = {2003}, author = {Catry, B and Laevens, H and Devriese, LA and Opsomer, G and De Kruif, A}, title = {Antimicrobial resistance in livestock.}, journal = {Journal of veterinary pharmacology and therapeutics}, volume = {26}, number = {2}, pages = {81-93}, doi = {10.1046/j.1365-2885.2003.00463.x}, pmid = {12667177}, issn = {0140-7783}, mesh = {Animals ; Animals, Domestic ; Bacteria/drug effects/genetics ; *Drug Resistance, Bacterial ; Evolution, Molecular ; Gene Transfer, Horizontal ; Humans ; Meat ; Zoonoses ; }, abstract = {Antimicrobial resistance may become a major problem in veterinary medicine as a consequence of the intensive use and misuse of antimicrobial drugs. Related problems are now arising in human medicine, such as the appearance of multi-resistant food-borne pathogens. Product characteristics, dose, treatment interval and duration of treatment influence the selection pressure for antimicrobial drug resistance. There are theoretical, experimental and clinical indications that the emergence of de novo resistance in a pathogenic population can be prevented by minimizing the time that suboptimal drug levels are present in the infected tissue compartment. Until recently, attention has been focused on target pathogens. However, it should be kept in mind that when antimicrobial drugs are used in an individual, resistance selection mainly affects the normal body flora. In the long term, this is at least equally important as resistance selection in the target pathogens, as the horizontal transfer of resistance genes converts almost all pathogenic bacteria into potential recipients for antimicrobial resistance. Other factors contributing to the epidemiology of antimicrobial resistance are the localization and size of the microbial population, and the age, immunity and contact intensity of the host. In livestock, dynamic herd-related resistance patterns have been observed in different animal species.}, }
@article {pmid12665863, year = {2003}, author = {Martin, W}, title = {The smoking gun of gene transfer.}, journal = {Nature genetics}, volume = {33}, number = {4}, pages = {442}, doi = {10.1038/ng0403-442}, pmid = {12665863}, issn = {1061-4036}, mesh = {Cell Nucleus/*genetics ; Chloroplasts/*genetics ; Cyanobacteria/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Plastids/genetics ; Recombination, Genetic ; Nicotiana/genetics ; }, }
@article {pmid12664163, year = {2003}, author = {Notomista, E and Lahm, A and Di Donato, A and Tramontano, A}, title = {Evolution of bacterial and archaeal multicomponent monooxygenases.}, journal = {Journal of molecular evolution}, volume = {56}, number = {4}, pages = {435-445}, doi = {10.1007/s00239-002-2414-1}, pmid = {12664163}, issn = {0022-2844}, mesh = {Archaea/*enzymology ; Bacteria/*enzymology ; *Evolution, Molecular ; Mixed Function Oxygenases/*genetics ; Operon ; Phylogeny ; Recombination, Genetic ; }, abstract = {We report the results of a comparative analysis of the sequences of multicomponent monooxygenases, a family of enzymes of great interest for bioremediation of contaminated soil. We show that their function, in terms of substrate specificity, can be deduced from their subunit organization and composition, that rearrangements of subunits as well as recruitments of new ones can be used to explain their different properties and functionalities, and that the observed pattern can be rationalized invoking a number of evolutionary events, including horizontal gene transfer. Our analysis highlights the plasticity and modularity of this family of enzymes, which might very well be the reason underlying the extremely rapid emergence of new bacterial strains able to grow on contaminated soils.}, }
@article {pmid12663927, year = {2003}, author = {Paulsen, IT and Banerjei, L and Myers, GS and Nelson, KE and Seshadri, R and Read, TD and Fouts, DE and Eisen, JA and Gill, SR and Heidelberg, JF and Tettelin, H and Dodson, RJ and Umayam, L and Brinkac, L and Beanan, M and Daugherty, S and DeBoy, RT and Durkin, S and Kolonay, J and Madupu, R and Nelson, W and Vamathevan, J and Tran, B and Upton, J and Hansen, T and Shetty, J and Khouri, H and Utterback, T and Radune, D and Ketchum, KA and Dougherty, BA and Fraser, CM}, title = {Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis.}, journal = {Science (New York, N.Y.)}, volume = {299}, number = {5615}, pages = {2071-2074}, doi = {10.1126/science.1080613}, pmid = {12663927}, issn = {1095-9203}, support = {AI40963-02/AI/NIAID NIH HHS/United States ; }, mesh = {Adhesins, Bacterial/genetics ; Bacterial Adhesion ; Bacterial Proteins/genetics ; *Biological Evolution ; Carrier Proteins/genetics/metabolism ; Chromosomes, Bacterial/genetics ; Conjugation, Genetic ; Conserved Sequence ; DNA Transposable Elements ; Digestive System/microbiology ; Drug Resistance, Multiple, Bacterial ; Enterococcus faecalis/drug effects/*genetics/pathogenicity/physiology ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Gram-Positive Bacterial Infections/microbiology ; Humans ; *Interspersed Repetitive Sequences ; Lysogeny ; Open Reading Frames ; Oxidative Stress ; Plasmids ; *Sequence Analysis, DNA ; Synteny ; Vancomycin Resistance/*genetics ; Virulence/genetics ; Virulence Factors/genetics ; }, abstract = {The complete genome sequence of Enterococcus faecalis V583, a vancomycin-resistant clinical isolate, revealed that more than a quarter of the genome consists of probable mobile or foreign DNA. One of the predicted mobile elements is a previously unknown vanB vancomycin-resistance conjugative transposon. Three plasmids were identified, including two pheromone-sensing conjugative plasmids, one encoding a previously undescribed pheromone inhibitor. The apparent propensity for the incorporation of mobile elements probably contributed to the rapid acquisition and dissemination of drug resistance in the enterococci.}, }
@article {pmid12660948, year = {2003}, author = {Arreaza, L and Alcalá, B and Salcedo, C and de la Fuente, L and Vázquez, JA}, title = {Dynamics of the penA gene in serogroup C meningococcal strains.}, journal = {The Journal of infectious diseases}, volume = {187}, number = {6}, pages = {1010-1014}, doi = {10.1086/368170}, pmid = {12660948}, issn = {0022-1899}, mesh = {Alleles ; Amino Acid Sequence ; *Bacterial Proteins ; Carrier Proteins/chemistry/*genetics ; Cloning, Molecular ; Gene Transfer, Horizontal ; *Hexosyltransferases ; Humans ; Meningitis, Meningococcal/*microbiology ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Muramoylpentapeptide Carboxypeptidase/chemistry/*genetics ; Neisseria meningitidis/drug effects/*genetics ; Penicillin-Binding Proteins ; Penicillins/pharmacology ; *Peptidyl Transferases ; Sequence Homology, Amino Acid ; }, abstract = {The transpeptidase encoding region of the penA gene was sequenced in 44 meningococcal strains (41 serogroup C [23 characterized as serotype 2b and 18 as serotype 2a] and 3 serogroup B [B:2b:P1.2,5]). All strains were characterized by multilocus sequence typing and were determined to be susceptible or intermediate resistant to penicillin (Pen(s) or Pen(i), respectively). A high degree of homology was found among the penA alleles identified in the Pen(s) strains. All the Pen(i) C:2b strains, which belonged to 2 different clonal complexes, showed the same penA gene allele. This fact suggests that 1 of the clonal complexes acquired that allele, spreading it to the other by horizontal transfer. The same allele also was found in the B:2b strains studied, indicating that 1 of the Pen(i) C:2b strains underwent a capsular switching event. A different mosaic penA allele was identified in the Pen(i) C:2a strains, which belonged to the ET37 cluster.}, }
@article {pmid12657460, year = {2003}, author = {Inada, K and Ishigooka, J and Anzai, T and Suzuki, E and Miyaoka, H and Saji, M}, title = {Antisense hippocampal knockdown of NMDA-NR1 by HVJ-liposome vector induces deficit of prepulse inhibition but not of spatial memory.}, journal = {Neuroscience research}, volume = {45}, number = {4}, pages = {473-481}, doi = {10.1016/s0168-0102(03)00012-9}, pmid = {12657460}, issn = {0168-0102}, mesh = {Animals ; Animals, Genetically Modified ; Down-Regulation ; Gene Transfer Techniques ; Gene Transfer, Horizontal ; Genetic Vectors ; Hippocampus/*physiology ; Injections, Intraventricular ; Liposomes ; Male ; Maze Learning/*physiology ; Memory/*physiology ; Motor Activity/genetics/*physiology ; Oligonucleotides, Antisense/administration &amp; dosage ; Rats ; Rats, Wistar ; Receptors, N-Methyl-D-Aspartate/*genetics/metabolism ; Sendai virus/genetics ; Thionucleotides/genetics ; }, abstract = {Considerable evidence suggests that an N-methyl-D-aspartate (NMDA) receptor plays a crucial role in memory and cognitive function. To identify the role of this receptor in higher functions of the brain, we delivered antisense oligonucleotides against an NMDA-NR1 subunit (NR1) to the hippocampus in rats using the HVJ-liposome-mediated gene-transfer method. NR1 hippocampal knockdown was performed by the focal injection of the NR1 antisense-HVJ-liposome complex into the bilateral hippocampus. The blocking effect of NR1-antisense on the expression of NR1 was confirmed by Western blot analysis. Spatial memory was tested by a water maze task, and sensorimotor gating was examined by prepulse inhibition (PPI). Western blot analysis demonstrated that the NR1-antisense treatment specifically provided the down-regulation (about 30%) of NR1 protein levels in the hippocampus. The water maze task showed that the antisense treatment did not affect spatial memory, while the PPI test revealed that NR1 hippocampal knockdown caused a deficit in sensorimotor gating. We conclude that mild dysfunction of hippocampal NMDA receptor causes sensorimotor gating deficit and relatively intact in spatial memory.}, }
@article {pmid12654929, year = {2003}, author = {Daubin, V and Perrière, G}, title = {G+C3 structuring along the genome: a common feature in prokaryotes.}, journal = {Molecular biology and evolution}, volume = {20}, number = {4}, pages = {471-483}, doi = {10.1093/molbev/msg022}, pmid = {12654929}, issn = {0737-4038}, mesh = {*Base Composition ; Codon ; DNA Replication ; Evolution, Molecular ; *Genetic Variation ; *Genome, Bacterial ; *Prokaryotic Cells ; *Selection, Genetic ; }, abstract = {The heterogeneity of gene nucleotide content in prokaryotic genomes is commonly interpreted as the result of three main phenomena: (1) genes undergo different selection pressures both during and after translation (affecting codon and amino acid choice); (2) genes undergo different mutational pressure whether they are on the leading or lagging strand; and (3) genes may have different phylogenetic origins as a result of lateral transfers. However, this view neglects the necessity of organizing genetic information on a chromosome that needs to be replicated and folded, which may add constraints to single gene evolution. As a consequence, genes are potentially subjected to different mutation and selection pressures, depending on their position in the genome. In this paper, we analyze the structuring of different codon usage measures along completely sequenced bacterial genomes. We show that most of them are highly structured, suggesting that genes have different base content, depending on their location on the chromosome. A peculiar pattern of genome structure, with a tendency toward an A+T-enrichment near the replication terminus, is found in most bacterial phyla and may reflect common chromosome constraints. Several species may have lost this pattern, probably because of genome rearrangements or integration of foreign DNA. We show that in several species, this enrichment is associated with an increase of evolutionary rate and we discuss the evolutionary implications of these results. We argue that structural constraints acting on the circular chromosome are not negligible and that this natural structuring of bacterial genomes may be a cause of overestimation in lateral gene transfer predictions using codon composition indices.}, }
@article {pmid12648839, year = {2003}, author = {Buchrieser, C and Rusniok, C and Kunst, F and Cossart, P and Glaser, P and , }, title = {Comparison of the genome sequences of Listeria monocytogenes and Listeria innocua: clues for evolution and pathogenicity.}, journal = {FEMS immunology and medical microbiology}, volume = {35}, number = {3}, pages = {207-213}, doi = {10.1016/S0928-8244(02)00448-0}, pmid = {12648839}, issn = {0928-8244}, mesh = {Anaerobiosis ; Animals ; Bacillus/genetics ; Bacterial Proteins/genetics ; Bacteriophages/genetics/physiology ; Base Composition ; Evolution, Molecular ; *Genome, Bacterial ; Humans ; Listeria/*genetics/metabolism/pathogenicity ; Listeria monocytogenes/*genetics/metabolism/pathogenicity ; Operon ; Salmonella typhimurium/genetics/metabolism ; Species Specificity ; Staphylococcus/genetics ; Transduction, Genetic ; Virulence ; Vitamin B 12/biosynthesis ; }, abstract = {Listeria monocytogenes, an invasive opportunistic, food-borne pathogen, remains one of the leading causes of mortality from food-borne infections. The recently determined complete genome sequences of L. monocytogenes strain EGDe and of that of the closely related non-pathogenic species Listeria innocua strain CLIP11262 enhance our knowledge of the genetic basis of the virulence of L. monocytogenes and advance our understanding of the evolution of these Listeria species. Both genomes encode a high number of surface, transport and regulatory proteins. Comparison of the genome organisation revealed a perfect synteny between the two Listeria genomes. Comparison with other closely related bacteria also showed a high conservation in genome organisation among the Listeria, Staphylococcus and Bacillus group of low G+C content bacteria. Distinct G+C content of a number of strain-specific genes suggests intensive lateral gene transfer. The identification of a 55-kb locus encoding proteins with high homology to Salmonella enterica serovar Typhimurium vitamin B(12) synthesis proteins as well as those necessary for degradation of ethanolamine and propanediol further indicates acquisition of a complete metabolic pathway by horizontal gene transfer and a probable role of this locus in anaerobic growth in the host.}, }
@article {pmid12645197, year = {2002}, author = {Yan, JJ and Chiu, CH and Ko, WC and Chuang, CL and Wu, JJ}, title = {Ceftriaxone-resistant Salmonella enterica serovar Hadar: evidence for interspecies transfer of blaCMY-2 in a Taiwanese university hospital.}, journal = {Journal of the Formosan Medical Association = Taiwan yi zhi}, volume = {101}, number = {9}, pages = {665-668}, pmid = {12645197}, issn = {0929-6646}, mesh = {Aged ; Anti-Bacterial Agents/pharmacology ; Ceftriaxone/pharmacology ; Escherichia coli/*metabolism ; *Gene Transfer, Horizontal ; Humans ; Male ; Plasmids ; Salmonella Infections/drug therapy/*microbiology ; Salmonella enterica/*drug effects/metabolism ; Surgical Wound Infection/drug therapy/microbiology ; *beta-Lactam Resistance ; beta-Lactamases/*metabolism ; }, abstract = {The emergence of resistance to extended-spectrum cephalosporins in salmonellae is an increasing clinical problem. We report the characteristics of a ceftriaxone-resistant Salmonella enterica serovar Hadar strain collected in 2001 from a patient with a postoperative wound infection in a university hospital in Taiwan. Resistance to extended-spectrum cephalosporins was found to be due to production of the plasmid-mediated CMY-2 AmpC beta-lactamase. To our knowledge, this is the first report of S. hadar harboring blaCMY-2. Seven CMY-2-producing Escherichia coli isolates collected in 2000 were investigated for comparison. Conjugation experiments and plasmid analysis showed an identical plasmid carrying blaCMY-2 in both the Salmonella isolate and one E. coli isolate, suggesting the possibility that the Salmonella isolate acquired the resistance plasmid from E. coli. These findings suggest that measures are necessary to restrict antibiotic use and so prevent the spread and development of antibiotic resistance in Taiwan.}, }
@article {pmid12644501, year = {2003}, author = {Kita, K and Kawakami, H and Tanaka, H}, title = {Evidence for horizontal transfer of the EcoT38I restriction-modification gene to chromosomal DNA by the P2 phage and diversity of defective P2 prophages in Escherichia coli TH38 strains.}, journal = {Journal of bacteriology}, volume = {185}, number = {7}, pages = {2296-2305}, pmid = {12644501}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; Bacteriophage P2/genetics ; Base Sequence ; Chromosomes, Bacterial ; Cloning, Molecular ; DNA Restriction Enzymes/*genetics/isolation &amp; purification/*metabolism ; DNA, Bacterial ; DNA, Intergenic ; DNA-Cytosine Methylases/genetics/metabolism ; Deoxyribonucleases, Type II Site-Specific/*genetics/*metabolism ; Dimerization ; Escherichia coli/*genetics/virology ; Escherichia coli Proteins/*genetics/*metabolism ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Genetic Variation ; Lysogeny ; Molecular Sequence Data ; Prophages/genetics ; Recombinant Proteins/genetics/metabolism ; Sequence Analysis ; Sequence Homology, Amino Acid ; }, abstract = {A DNA fragment carrying the genes coding for a novel EcoT38I restriction endonuclease (R.EcoT38I) and EcoT38I methyltransferase (M.EcoT38I), which recognize G(A/G)GC(C/T)C, was cloned from the chromosomal DNA of Escherichia coli TH38. The endonuclease and methyltransferase genes were in a head-to-head orientation and were separated by a 330-nucleotide intergenic region. A third gene, the C.EcoT38I gene, was found in the intergenic region, partially overlapping the R.EcoT38I gene. The gene product, C.EcoT38I, acted as both a positive regulator of R.EcoT38I gene expression and a negative regulator of M.EcoT38I gene expression. M.EcoT38I purified from recombinant E. coli cells was shown to be a monomeric protein and to methylate the inner cytosines in the recognition sequence. R.EcoT38I was purified from E. coli HB101 expressing M.EcoT38I and formed a homodimer. The EcoT38I restriction (R)-modification (M) system (R-M system) was found to be inserted between the A and Q genes of defective bacteriophage P2, which was lysogenized in the chromosome at locI, one of the P2 phage attachment sites observed in both E. coli K-12 MG1655 and TH38 chromosomal DNAs. Ten strains of E. coli TH38 were examined for the presence of the EcoT38I R-M gene on the P2 prophage. Conventional PCR analysis and assaying of R activity demonstrated that all strains carried a single copy of the EcoT38I R-M gene and expressed R activity but that diversity of excision in the ogr, D, H, I, and J genes in the defective P2 prophage had arisen.}, }
@article {pmid12635929, year = {2003}, author = {Rumer, L and Jores, J and Kirsch, P and Cavignac, Y and Zehmke, K and Wieler, LH}, title = {Dissemination of pheU- and pheV-located genomic islands among enteropathogenic (EPEC) and enterohemorrhagic (EHEC) E. coli and their possible role in the horizontal transfer of the locus of enterocyte effacement (LEE).}, journal = {International journal of medical microbiology : IJMM}, volume = {292}, number = {7-8}, pages = {463-475}, doi = {10.1078/1438-4221-00229}, pmid = {12635929}, issn = {1438-4221}, mesh = {Animals ; Base Sequence ; Cattle ; Cattle Diseases/microbiology/pathology ; Electrophoresis, Gel, Pulsed-Field ; Enterocytes/microbiology/*pathology ; Escherichia coli/genetics/*pathogenicity ; Escherichia coli Infections/microbiology/pathology ; Escherichia coli Proteins/*genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Molecular Sequence Data ; *Phosphoproteins ; *Phylogeny ; RNA, Transfer, Phe/*genetics ; Recombination, Genetic ; Sequence Analysis, DNA ; Virulence/genetics ; }, abstract = {We have recently shown that the locus of enterocyte effacement (LEE) of the bovine enterohemorrhagic E. coli RW1374 (O103:H2) resides within a large pathogenicity island (PAI), integrated in the vicinity of the phenylalanine tRNA gene pheV. Here we describe an additional, but LEE-negative genomic island in RW1374 in the vicinity of another phenylalanine tRNA gene, pheU, the sequence of which is identical to pheV. These two genomic islands revealed identity of the left, but a relative variability of their right end sequences. To investigate the mechanism of LEE-PAI distribution in E. coli, we analysed similar junctions in the pheU/pheV loci of additional EPEC and EHEC strains the LEE location of which had not been determined before. By hybridisation of NotI restriction fragments with probes specific for LEE, pheV locus, and pheU locus, the LEE was found linked to either one of these two loci. The results agreed well with recently published phylogenetic data and indicate that in the clones of diarrheagenic E. coli (Dec) Dec 11 and Dec 12, forming the phylogenetic cluster EPEC 2, and in the strains of the most typical serotypes of the Dec 8, belonging to the phylogenetic cluster EHEC 2, the LEE was linked with pheV and not with the pheU locus as previously assumed. Sequence comparison with other pheU- and pheV-located genomic islands from different E. coli pathotypes (uropathogenic E. coli, septicemic E. coli) as well as from Shigella indicated the same structural features at the junctions. These conserved structures suggested a common DNA cassette, serving as common vehicle for horizontal gene transfer of various PAls. In addition, the elements suggest an origin from a common pheU-located ancestor and integration into the chromosome through site-specific recombination. Our results indicate that pheU/pheV-located genomic islands played an important role in the evolution of several PAls in E. coli and related pathogens.}, }
@article {pmid12634744, year = {2003}, author = {Hoag, H}, title = {Tougher rules aim to prevent gene flow into crops.}, journal = {Nature}, volume = {422}, number = {6928}, pages = {103}, doi = {10.1038/422103b}, pmid = {12634744}, issn = {0028-0836}, mesh = {Animals ; Biotechnology/*legislation &amp; jurisprudence/standards ; Ecosystem ; Evaluation Studies as Topic ; Food, Genetically Modified/*standards ; *Gene Transfer, Horizontal ; *Government Regulation ; Plants, Genetically Modified/*genetics ; Technology, Pharmaceutical/*legislation &amp; jurisprudence/standards ; United States ; Zea mays/*genetics ; }, }
@article {pmid12627863, year = {2002}, author = {Dacks, JB and Simpson, AG}, title = {Meeting report: XIVth meeting of the International Society for Evolutionary Protistology, Vancouver, Canada, June 19-24, 2002.}, journal = {Protist}, volume = {153}, number = {4}, pages = {337-342}, doi = {10.1078/14344610260450064}, pmid = {12627863}, issn = {1434-4610}, mesh = {Animals ; *Biological Evolution ; Classification ; Ecosystem ; *Eukaryota/classification/genetics/physiology ; Gene Transfer, Horizontal ; Parasites/physiology ; Phylogeny ; Plastids/genetics ; Species Specificity ; }, }
@article {pmid12624243, year = {2003}, author = {Wuethrich, B}, title = {Infectious disease. Chasing the fickle swine flu.}, journal = {Science (New York, N.Y.)}, volume = {299}, number = {5612}, pages = {1502-1505}, doi = {10.1126/science.299.5612.1502}, pmid = {12624243}, issn = {1095-9203}, mesh = {Animal Husbandry ; Animals ; Biological Evolution ; Birds ; Gene Transfer, Horizontal ; Genes, Viral ; Genetic Variation ; Hemagglutinins, Viral/genetics ; Humans ; Influenza A virus/*genetics/immunology/physiology ; Influenza Vaccines ; Influenza, Human/prevention &amp; control/transmission/*veterinary/*virology ; Neuraminidase/genetics ; Point Mutation ; Reassortant Viruses/genetics ; Species Specificity ; Swine ; Swine Diseases/prevention &amp; control/transmission/*virology ; Vaccination/veterinary ; Virus Replication ; World Health Organization ; }, }
@article {pmid12622826, year = {2003}, author = {Gross, R and Hacker, J and Goebel, W}, title = {The Leopoldina international symposium on parasitism, commensalism and symbiosis--common themes, different outcome.}, journal = {Molecular microbiology}, volume = {47}, number = {6}, pages = {1749-1758}, doi = {10.1046/j.1365-2958.2003.03443.x}, pmid = {12622826}, issn = {0950-382X}, mesh = {Animals ; Bacteria/*metabolism/*pathogenicity ; Biological Evolution ; Disease Models, Animal ; Gene Transfer, Horizontal ; Host-Parasite Interactions ; Nucleic Acids/genetics/metabolism ; Parasites/*physiology ; Signal Transduction ; *Symbiosis ; Virulence/physiology ; }, abstract = {The development of new methods, including genomics, which can even be applied to unculturable microorganisms, has significantly increased our knowledge about bacterial pathogenesis and symbiosis and, in consequence, is profoundly modifying our views on the evolution and the genetic and physiological basis of bacteria-host interactions. The presentations at this symposium revealed conceptual links between bacterial pathogenesis and symbiosis. The close co-operation of experts in both fields will result in significant synergy and new insights into basic mechanisms of bacteria-host interactions and their evolution. The meeting provided fascinating news about the genetic and metabolic consequences that the change in their lifestyle had for bacteria that developed from free-living to permanent host-associated organisms exemplified by intracellular pathogens or symbionts. In addition, surprising similarities but also striking differences between the strategies involved in the establishment of a symbiotic versus a parasitic lifestyle can be noted. In the long run, the characterization of such differences might lead to lifestyle prediction or to an evaluation of the pathogenic potential of newly isolated bacteria via the definition of genetic and/or metabolic signatures characteristic for pathogenic or symbiotic organisms. Moreover, it is expected that these investigations will lead to new strategies for the treatment or prevention of bacterial infections, or the avoidance of pathogen transmission.}, }
@article {pmid12622808, year = {2003}, author = {Cohen, GN and Barbe, V and Flament, D and Galperin, M and Heilig, R and Lecompte, O and Poch, O and Prieur, D and Quérellou, J and Ripp, R and Thierry, JC and Van der Oost, J and Weissenbach, J and Zivanovic, Y and Forterre, P}, title = {An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi.}, journal = {Molecular microbiology}, volume = {47}, number = {6}, pages = {1495-1512}, doi = {10.1046/j.1365-2958.2003.03381.x}, pmid = {12622808}, issn = {0950-382X}, mesh = {Adaptation, Physiological ; Amino Acids/biosynthesis ; Archaeal Proteins/classification/*genetics/*metabolism ; Biological Transport ; Carbohydrate Metabolism ; Cell Division/genetics ; Chromosome Segregation ; DNA Repair/physiology ; DNA Replication ; Gene Transfer, Horizontal ; *Genome, Archaeal ; Molecular Sequence Data ; Phylogeny ; Protein Biosynthesis ; Pyrococcus/cytology/*genetics/*metabolism ; Recombination, Genetic ; Transcription, Genetic ; }, abstract = {The hyperthermophilic euryarchaeon Pyrococcus abyssi and the related species Pyrococcus furiosus and Pyrococcus horikoshii, whose genomes have been completely sequenced, are presently used as model organisms in different laboratories to study archaeal DNA replication and gene expression and to develop genetic tools for hyperthermophiles. We have performed an extensive re-annotation of the genome of P. abyssi to obtain an integrated view of its phylogeny, molecular biology and physiology. Many new functions are predicted for both informational and operational proteins. Moreover, several candidate genes have been identified that might encode missing links in key metabolic pathways, some of which have unique biochemical features. The great majority of Pyrococcus proteins are typical archaeal proteins and their phylogenetic pattern agrees with its position near the root of the archaeal tree. However, proteins probably from bacterial origin, including some from mesophilic bacteria, are also present in the P. abyssi genome.}, }
@article {pmid12620876, year = {2003}, author = {Schmidt-Eisenlohr, H and Baron, C}, title = {The competitiveness of Pseudomonas chlororaphis carrying pJP4 is reduced in the Arabidopsis thaliana rhizosphere.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {3}, pages = {1827-1831}, pmid = {12620876}, issn = {0099-2240}, mesh = {Arabidopsis/*microbiology ; Conjugation, Genetic ; Culture Media ; Cupriavidus necator/genetics/growth &amp; development ; Gene Transfer, Horizontal ; Plant Roots/*microbiology ; *Plasmids ; Pseudomonas/genetics/*growth &amp; development ; *Soil Microbiology ; }, abstract = {The effect of the large catabolic IncP plasmid pJP4 on the competitiveness of Pseudomonas chlororaphis SPR044 and on its derivatives SPR244 (GacS deficient), SPR344 (phenazine-1-carboxamide overproducer), and SPR644 (phenazine-1-carboxamide deficient) in the Arabidopsis thaliana rhizosphere was assessed. Solitary rhizosphere colonization by the wild type, SPR244, and SPR644 was not affected by the plasmid. The size of the population of SPR344 carrying pJP4, however, was significantly reduced compared to the size of the population of the plasmid-free derivative. The abiotic stress caused by phenazine-1-carboxamide overproduction probably resulted in a selective disadvantage for cells carrying pJP4. Next, the effect of biotic stress caused by coinoculation of other bacteria was analyzed. Cells carrying pJP4 had a selective disadvantage compared to plasmid-free cells in the presence of the efficient colonizer Pseudomonas fluorescens WCS417r. This effect was not observed after coinoculation with a variety of other bacteria, and it was independent of quorum sensing and phenazine-1-carboxamide production. Thus, the presence of large catabolic plasmids imposes a detectable metabolic burden in the presence of biotic stress. Plasmid transfer in the A. thaliana rhizosphere from P. chlororaphis and its derivatives to Ralstonia eutropha was determined by using culture-dependent and culture-independent techniques. With the cultivation-independent technique we detected a significantly higher portion of exconjugants, but pJP4 transfer was independent of the quorum-sensing system and of phenazine-1-carboxamide production.}, }
@article {pmid12620864, year = {2003}, author = {Hendrickx, L and Hausner, M and Wuertz, S}, title = {Natural genetic transformation in monoculture Acinetobacter sp. strain BD413 biofilms.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {3}, pages = {1721-1727}, pmid = {12620864}, issn = {0099-2240}, mesh = {Acinetobacter/genetics/*growth &amp; development ; Biofilms/*growth &amp; development ; Culture Media ; DNA, Bacterial/analysis/genetics ; Image Processing, Computer-Assisted ; Plasmids ; Time Factors ; *Transformation, Bacterial ; }, abstract = {Horizontal gene transfer by natural genetic transformation in Acinetobacter sp. strain BD413 was investigated by using gfp carried by the autonomously replicating plasmid pGAR1 in a model monoculture biofilm. Biofilm age, DNA concentration, and biofilm mode of growth were evaluated to determine their effects on natural genetic transformation. The highest transfer frequencies were obtained in young and actively growing biofilms when high DNA concentrations were used and when the biofilm developed during continuous exposure to fresh medium without the presence of a significant amount of cells in the suspended fraction. Biofilms were highly amenable to natural transformation. They did not need to advance to an optimal growth phase which ensured the presence of optimally competent biofilm cells. An exposure time of only 15 min was adequate for transformation, and the addition of minute amounts of DNA (2.4 fg of pGAR1 per h) was enough to obtain detectable transfer frequencies. The transformability of biofilms lacking competent cells due to growth in the presence of cells in the bulk phase could be reestablished by starving the noncompetent biofilm prior to DNA exposure. Overall, the evidence suggests that biofilms offer no barrier against effective natural genetic transformation of Acinetobacter sp. strain BD413.}, }
@article {pmid12620615, year = {2003}, author = {Qian, J and Kwon, SW and Parker, MA}, title = {rRNA and nifD phylogeny of Bradyrhizobium from sites across the Pacific Basin.}, journal = {FEMS microbiology letters}, volume = {219}, number = {2}, pages = {159-165}, doi = {10.1016/S0378-1097(03)00043-0}, pmid = {12620615}, issn = {0378-1097}, mesh = {Base Sequence ; Bradyrhizobium/*classification/genetics ; *Genes, Bacterial ; *Genes, rRNA ; Molecular Sequence Data ; Nitrogenase/*genetics ; Pacific Ocean ; *Phylogeny ; RNA, Ribosomal, 16S/classification/genetics ; Sequence Analysis, DNA ; }, abstract = {Many undomesticated legumes harbor nodule bacteria related to the soybean symbiont Bradyrhizobium elkanii, but little is known about their phylogenetic relationships or geographic distribution. Sequences of ribosomal genes (16S rRNA and partial 23S rRNA) and the nitrogenase alpha-subunit gene (nifD) were analyzed in 22 isolates of this group sampled from diverse legumes in Korea, Japan, the USA, Mexico, Costa Rica and Panama. Some strains from Asia and North America shared identical sequences for both ribosomal genes. However, pairs of strains with closely related nifD sequences were almost never found in different regions. The major exceptions involved North American isolates B. elkanii USDA 76 and USDA 94, which had nifD sequences highly similar to certain Korean strains. However, 16S rRNA sequences of USDA 76 and USDA 94 were closely related to Central American rather than Asian bradyrhizobia, implying that these strains are genetic mosaics combining sequences from distinct ancestral areas. Several other conflicts between rRNA and nifD tree topologies indicated that the genealogical histories of these loci have been influenced by recurrent lateral gene transfer events.}, }
@article {pmid12620124, year = {2003}, author = {Xie, G and Bonner, CA and Brettin, T and Gottardo, R and Keyhani, NO and Jensen, RA}, title = {Lateral gene transfer and ancient paralogy of operons containing redundant copies of tryptophan-pathway genes in Xylella species and in heterocystous cyanobacteria.}, journal = {Genome biology}, volume = {4}, number = {2}, pages = {R14}, pmid = {12620124}, issn = {1474-760X}, support = {A1-8228-05//PHS HHS/United States ; }, mesh = {Amino Acid Sequence ; Anabaena/genetics ; Bacterial Proteins/genetics ; Base Sequence ; Codon/genetics ; Cyanobacteria/*genetics/metabolism ; Gammaproteobacteria/*genetics/metabolism ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Operon/*genetics ; Phylogeny ; Repressor Proteins/genetics ; Sequence Homology, Amino Acid ; Tryptophan/*biosynthesis ; }, abstract = {BACKGROUND: Tryptophan-pathway genes that exist within an apparent operon-like organization were evaluated as examples of multi-genic genomic regions that contain phylogenetically incongruous genes and coexist with genes outside the operon that are congruous. A seven-gene cluster in Xylella fastidiosa includes genes encoding the two subunits of anthranilate synthase, an aryl-CoA synthetase, and trpR. A second gene block, present in the Anabaena/Nostoc lineage, but not in other cyanobacteria, contains a near-complete tryptophan operon nested within an apparent supraoperon containing other aromatic-pathway genes.<br><br>RESULTS: The gene block in X. fastidiosa exhibits a sharply delineated low-GC content. This, as well as bias of codon usage and 3:1 dinucleotide analysis, strongly implicates lateral gene transfer (LGT). In contrast, parametric studies and protein tree phylogenies did not support the origination of the Anabaena/Nostoc gene block by LGT.<br><br>CONCLUSIONS: Judging from the apparent minimal amelioration, the low-GC gene block in X. fastidiosa probably originated by LGT at a relatively recent time. The surprising inability to pinpoint a donor lineage still leaves room for alternative, albeit less likely, explanations other than LGT. On the other hand, the large Anabaena/Nostoc gene block does not seem to have arisen by LGT. We suggest that the contemporary Anabaena/Nostoc array of divergent paralogs represents an ancient ancestral state of paralog divergence, with extensive streamlining by gene loss occurring in the lineage of descent representing other (unicellular) cyanobacteria.}, }
@article {pmid12620104, year = {2003}, author = {Koonin, EV and Makarova, KS and Rogozin, IB and Davidovic, L and Letellier, MC and Pellegrini, L}, title = {The rhomboids: a nearly ubiquitous family of intramembrane serine proteases that probably evolved by multiple ancient horizontal gene transfers.}, journal = {Genome biology}, volume = {4}, number = {3}, pages = {R19}, pmid = {12620104}, issn = {1474-760X}, mesh = {Amino Acid Sequence/genetics ; Animals ; Archaeal Proteins/chemistry/genetics ; Bacterial Proteins/chemistry/genetics ; Conserved Sequence/genetics ; Drosophila Proteins/chemistry/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Humans ; Insect Hormones/chemistry/genetics ; Membrane Proteins/chemistry/*genetics ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/chemistry/genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; Serine Endopeptidases/chemistry/*genetics ; }, abstract = {BACKGROUND: The rhomboid family of polytopic membrane proteins shows a level of evolutionary conservation unique among membrane proteins. They are present in nearly all the sequenced genomes of archaea, bacteria and eukaryotes, with the exception of several species with small genomes. On the basis of experimental studies with the developmental regulator rhomboid from Drosophila and the AarA protein from the bacterium Providencia stuartii, the rhomboids are thought to be intramembrane serine proteases whose signaling function is conserved in eukaryotes and prokaryotes.<br><br>RESULTS: Phylogenetic tree analysis carried out using several independent methods for tree constructions and the corresponding statistical tests suggests that, despite its broad distribution in all three superkingdoms, the rhomboid family was not present in the last universal common ancestor of extant life forms. Instead, we propose that rhomboids evolved in bacteria and have been acquired by archaea and eukaryotes through several independent horizontal gene transfers. In eukaryotes, two distinct, ancient acquisitions apparently gave rise to the two major subfamilies, typified by rhomboid and PARL (presenilins-associated rhomboid-like protein), respectively. Subsequent evolution of the rhomboid family in eukaryotes proceeded by multiple duplications and functional diversification through the addition of extra transmembrane helices and other domains in different orientations relative to the conserved core that harbors the protease activity.<br><br>CONCLUSIONS: Although the near-universal presence of the rhomboid family in bacteria, archaea and eukaryotes appears to suggest that this protein is part of the heritage of the last universal common ancestor, phylogenetic tree analysis indicates a likely bacterial origin with subsequent dissemination by horizontal gene transfer. This emphasizes the importance of explicit phylogenetic analysis for the reconstruction of ancestral life forms. A hypothetical scenario for the origin of intracellular membrane proteases from membrane transporters is proposed.}, }
@article {pmid12618405, year = {2003}, author = {Kimura, M and Tokai, T and Matsumoto, G and Fujimura, M and Hamamoto, H and Yoneyama, K and Shibata, T and Yamaguchi, I}, title = {Trichothecene nonproducer Gibberella species have both functional and nonfunctional 3-O-acetyltransferase genes.}, journal = {Genetics}, volume = {163}, number = {2}, pages = {677-684}, pmid = {12618405}, issn = {0016-6731}, mesh = {Acetyltransferases/genetics/*metabolism ; Amino Acid Sequence ; Gene Transfer, Horizontal ; Gibberella/*enzymology ; Molecular Sequence Data ; Phosphate Transport Proteins/genetics ; Phylogeny ; Sequence Analysis, DNA ; Synteny ; Trichothecenes/*metabolism ; }, abstract = {The trichothecene 3-O-acetyltransferase gene (FgTri101) required for trichothecene production by Fusarium graminearum is located between the phosphate permease gene (pho5) and the UTP-ammonia ligase gene (ura7). We have cloned and sequenced the pho5-to-ura7 regions from three trichothecene nonproducing Fusarium (i.e., F. oxysporum, F. moniliforme, and Fusarium species IFO 7772) that belong to the teleomorph genus Gibberella. BLASTX analysis of these sequences revealed portions of predicted polypeptides with high similarities to the TRI101 polypeptide. While FspTri101 (Fusarium species Tri101) coded for a functional 3-O-acetyltransferase, FoTri101 (F. oxysporum Tri101) and FmTri101 (F. moniliforme Tri101) were pseudogenes. Nevertheless, F. oxysporum and F. moniliforme were able to acetylate C-3 of trichothecenes, indicating that these nonproducers possess another as yet unidentified 3-O-acetyltransferase gene. By means of cDNA expression cloning using fission yeast, we isolated the responsible FoTri201 gene from F. oxysporum; on the basis of this sequence, FmTri201 has been cloned from F. moniliforme by PCR techniques. Both Tri201 showed only a limited level of nucleotide sequence similarity to FgTri101 and FspTri101. The existence of Tri101 in a trichothecene nonproducer suggests that this gene existed in the fungal genome before the divergence of producers from nonproducers in the evolution of Fusarium species.}, }
@article {pmid12617158, year = {2002}, author = {Holmgren, L and Bergsmedh, A and Spetz, AL}, title = {Horizontal transfer of DNA by the uptake of apoptotic bodies.}, journal = {Vox sanguinis}, volume = {83 Suppl 1}, number = {}, pages = {305-306}, doi = {10.1111/j.1423-0410.2002.tb05323.x}, pmid = {12617158}, issn = {0042-9007}, mesh = {Animals ; Apoptosis ; Fibroblasts ; *Gene Transfer, Horizontal ; Humans ; Oncogenes ; *Phagocytosis ; Transfusion Reaction ; }, }
@article {pmid12615431, year = {2003}, author = {Bramson, JL and Dayball, K and Hall, JR and Millar, JB and Miller, M and Wan, YH and Lin, R and Hiscott, J}, title = {Super-activated interferon-regulatory factors can enhance plasmid immunization.}, journal = {Vaccine}, volume = {21}, number = {13-14}, pages = {1363-1370}, doi = {10.1016/s0264-410x(02)00694-1}, pmid = {12615431}, issn = {0264-410X}, mesh = {Animals ; Antibody Formation ; DNA-Binding Proteins/*genetics ; Female ; Gene Transfer, Horizontal ; Interferon Regulatory Factor-3 ; Interferon Regulatory Factor-7 ; Mice ; Mice, Inbred C57BL ; Plasmids/*immunology ; T-Lymphocytes, Cytotoxic/immunology ; Transcription Factors/*genetics ; Vaccination ; Vaccines, DNA/*immunology ; }, abstract = {We have been investigating the adjuvant properties of two super-activated interferon-regulatory factors (IRFs), IRF-3(5D) and IRF7/3A, identified in our previous studies of structure-function relationships, for enhancing plasmid vaccines. Intramuscular injection of plasmid cocktails encoding IRF-3(5D) and IRF7/3A molecules elicited cytotoxic T cell responses in over 80% of mice following a single immunization compared to a 20% response-rate using a control cocktail. Most interestingly, greater than 60% of mice immunized with the super-activated IRFs developed antigen-specific antibodies compared to 0% of the mice in the control group. Finally, vaccines which incorporated the super-activated IRFs provided greater protection against challenge with a recombinant vaccinia virus. These results support further investigation of the potential of these agents as adjuvants for genetic immunization.}, }
@article {pmid12615217, year = {2003}, author = {Davis, BM and Waldor, MK}, title = {Filamentous phages linked to virulence of Vibrio cholerae.}, journal = {Current opinion in microbiology}, volume = {6}, number = {1}, pages = {35-42}, doi = {10.1016/s1369-5274(02)00005-x}, pmid = {12615217}, issn = {1369-5274}, mesh = {Cholera/metabolism/microbiology ; Cholera Toxin/genetics ; DNA/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Viral/genetics ; Inovirus/*genetics/isolation &amp; purification ; Models, Genetic ; Plasmids/metabolism ; Vibrio cholerae/genetics/*pathogenicity/*virology ; Virulence ; }, abstract = {The pathogenicity of Vibrio cholerae depends upon its production of two key virulence factors: the toxin co-regulated pilus (TCP), a colonization factor, and cholera toxin, an exotoxin. Genes encoding both virulence factors were introduced into V. cholerae by horizontal gene transfer. The toxin genes are contained within the genome of CTXphi, an integrated filamentous phage identified in 1996. In the past few years, it has been shown that CTXphi relies on novel processes for phage DNA integration, replication and secretion. In addition, expression of CTXphi genes--including the toxin genes--and transmission of CTXphi were recently found to be promoted by the antirepressor RstC, which is encoded within RS1, a newly described satellite phage of CTXphi. The genetic island that encodes TCP has also been described as a filamentous phage; however, these sequences are unlike the genome of any previously characterized filamentous phage.}, }
@article {pmid12612836, year = {2003}, author = {Vogl, C and Badger, J and Kearney, P and Li, M and Clegg, M and Jiang, T}, title = {Probabilistic analysis indicates discordant gene trees in chloroplast evolution.}, journal = {Journal of molecular evolution}, volume = {56}, number = {3}, pages = {330-340}, doi = {10.1007/s00239-002-2404-3}, pmid = {12612836}, issn = {0022-2844}, mesh = {Chloroplasts/*genetics ; Data Interpretation, Statistical ; *Evolution, Molecular ; *Phylogeny ; Plants/*genetics ; Sequence Analysis, Protein ; }, abstract = {Analyses of whole-genome data often reveal that some genes have evolutionary histories that diverge from the majority phylogeny estimated for the entire genome. We present a probabilistic model that deals with heterogeneity among gene trees, implement it via the Gibbs sampler, and apply it to the plastid genome. Plastids and their genomes are transmitted as a single block without recombination, hence homogeneity among gene trees within this genome is expected. Nevertheless, previous work has revealed clear heterogeneity among plastid genes (e.g., Delwiche and Palmer 1996). Other studies, using whole plastid genomes of various algae and land plants, found little additional heterogeneity (Martin et al. 1998; Adachi et al. 2000). We augment the earlier studies by using a data set of 14 taxa: 6 land plants, 2 green algae, a diatom, 2 red algae and a cryptophyte, the cyanelle of the glaucocystophyte Cyanophora, and the blue-green alga Synechocystis as an outgroup. Contrary to the earlier analyses, we cannot find even a single, dominant consensus tree. Therefore, we formulate a probabilistic model that divides the genes into two sets: those that follow the consensus tree and those that have independent gene trees. No particular tree is supported by more than three-fourths of the genes. But the set of genes that follows a certain tree is fairly independent of data processing and the method of analysis. With one possible exception, we find no evidence for collinear or functionally related genes to follow similar trees. The phylogenetic pattern also seems independent of bias in amino acid composition. Among possible explanations for the observed phenomenon, the hypothesis that different genes have different covarion structures is difficult to assess. But gene duplication may be possible through the inverted or direct repeat regions, while horizontal gene transfer seems less likely. In contrast to green algae and land plants, inverted repeat regions in red algae and in Cyanophora show abundant differences among the copies. Thus, genes may get duplicated when they are recruited into the inverted repeat region and one of the two copies may be lost after leaving the inverted repeat region.}, }
@article {pmid12610535, year = {2003}, author = {Wolfe, KH and Li, WH}, title = {Molecular evolution meets the genomics revolution.}, journal = {Nature genetics}, volume = {33 Suppl}, number = {}, pages = {255-265}, doi = {10.1038/ng1088}, pmid = {12610535}, issn = {1061-4036}, mesh = {Animals ; DNA/genetics ; *Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; *Genomics/history/trends ; History, 20th Century ; History, 21st Century ; Humans ; Mosaicism ; Mutation ; Selection, Genetic ; }, abstract = {Changes in technology in the past decade have had such an impact on the way that molecular evolution research is done that it is difficult now to imagine working in a world without genomics or the Internet. In 1992, GenBank was less than a hundredth of its current size and was updated every three months on a huge spool of tape. Homology searches took 30 minutes and rarely found a hit. Now it is difficult to find sequences with only a few homologs to use as examples for teaching bioinformatics. For molecular evolution researchers, the genomics revolution has showered us with raw data and the information revolution has given us the wherewithal to analyze it. In broad terms, the most significant outcome from these changes has been our newfound ability to examine the evolution of genomes as a whole, enabling us to infer genome-wide evolutionary patterns and to identify subsets of genes whose evolution has been in some way atypical.}, }
@article {pmid12606647, year = {2003}, author = {Coyne, CB and Ribeiro, CM and Boucher, RC and Johnson, LG}, title = {Acute mechanism of medium chain fatty acid-induced enhancement of airway epithelial permeability.}, journal = {The Journal of pharmacology and experimental therapeutics}, volume = {305}, number = {2}, pages = {440-450}, doi = {10.1124/jpet.102.047654}, pmid = {12606647}, issn = {0022-3565}, support = {HL51818/HL/NHLBI NIH HHS/United States ; HL58342/HL/NHLBI NIH HHS/United States ; }, mesh = {Adenosine Triphosphate/metabolism ; Adenovirus Infections, Human/physiopathology ; Calcium/metabolism ; Cell Membrane Permeability/drug effects ; Cells, Cultured ; Epithelial Cells/drug effects ; Epithelium/drug effects ; Fatty Acids/*pharmacology ; Fluorescent Antibody Technique ; Fluorescent Dyes ; Gene Transfer, Horizontal/drug effects ; Humans ; Intercellular Junctions/drug effects ; Microscopy, Confocal ; Respiratory System/*drug effects ; Signal Transduction/drug effects ; Structure-Activity Relationship ; Xanthenes ; }, abstract = {The localization of viral receptors to the basolateral surface of airway epithelia is an obstacle to the effectiveness of luminal viral-mediated gene transfer to the lung. The tight junction (TJ) serves as a rate-limiting barrier to the penetration of viral vectors. We have previously identified the sodium salt of the medium chain fatty acid (MCFA) capric acid (C10) as an agent that can enhance the ability of adenoviral vectors to transduce well differentiated (WD) primary human airway epithelial (HAE) cells. Previous studies have suggested that intracellular calcium (Ca(i)2+) levels may play a central role in the long-term C10-mediated increases in junctional permeability. In this study, we investigated the effects of C10 and lauric acid (C12) on Ca(i)2+ in WD primary HAE cells and determined whether these effects were necessary for the acute MCFA-induced reduction in transepithelial resistance (R(T)) and increased permeability. In addition, we characterized the effects of C10 and C12 on components localized to the TJ, including ZO-1, junctional adhesion molecule (JAM), and the claudin family of transmembrane proteins. In addition to rapidly decreasing R(T), C10 and C12 increased cellular and paracellular permeability. C10 induced a rapid, sustained increase in Ca(i)2+. However, buffering Ca(i)2+ did not block the effects of C10 on R(T). Both C10 and C12 caused reorganization of claudins-1, -4, JAM, and beta-catenin, but not ZO-1. These data suggest that C10 and C12 exert their acute effects on airway TJs via a Ca(2+)-independent mechanism of action and may alter junctional permeability via direct effects on the claudin family of TJ proteins.}, }
@article {pmid12605670, year = {2003}, author = {Yamaguchi, K and Subramanian, AR}, title = {Proteomic identification of all plastid-specific ribosomal proteins in higher plant chloroplast 30S ribosomal subunit.}, journal = {European journal of biochemistry}, volume = {270}, number = {2}, pages = {190-205}, doi = {10.1046/j.1432-1033.2003.03359.x}, pmid = {12605670}, issn = {0014-2956}, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics ; Base Sequence ; Chloroplasts/*chemistry ; DNA, Complementary ; Evolution, Molecular ; Molecular Sequence Data ; Proteome/*chemistry ; RNA-Binding Proteins/genetics ; Ribonucleoproteins/genetics ; Ribosomal Proteins/*chemistry/genetics/isolation &amp; purification ; Ribosomes/chemistry ; Sequence Alignment ; Sequence Homology ; Spinacia oleracea/chemistry/genetics ; }, abstract = {Six ribosomal proteins are specific to higher plant chloroplast ribosomes [Subramanian, A.R. (1993) Trends Biochem. Sci.18, 177-180]. Three of them have been fully characterized [Yamaguchi, K., von Knoblauch, K. &amp; Subramanian, A. R. (2000) J. Biol. Chem. 275, 28455-28465; Yamaguchi, K. &amp; Subramanian, A. R. (2000) J. Biol. Chem. 275, 28466-28482]. The remaining three plastid-specific ribosomal proteins (PSRPs), all on the small subunit, have now been characterized (2D PAGE, HPLC, N-terminal/internal peptide sequencing, electrospray ionization MS, cloning/ sequencing of precursor cDNAs). PSRP-3 exists in two forms (alpha/beta, N-terminus free and blocked by post-translational modification), whereas PSRP-2 and PSRP-4 appear, from MS data, to be unmodified. PSRP-2 contains two RNA-binding domains which occur in mRNA processing/stabilizing proteins (e.g. U1A snRNP, poly(A)-binding proteins), suggesting a possible role for it in the recruiting of stored chloroplast mRNAs for active protein synthesis. PSRP-3 is the higher plant orthologue of a hypothetical protein (ycf65 gene product), first reported in the chloroplast genome of a red alga. The ycf65 gene is absent from the chloroplast genomes of higher plants. Therefore, we suggest that Psrp-3/ycf65, encoding an evolutionarily conserved chloroplast ribosomal protein, represents an example of organelle-to-nucleus gene transfer in chloroplast evolution. PSRP-4 shows strong homology with Thx, a small basic ribosomal protein of Thermus thermophilus 30S subunit (with a specific structural role in the subunit crystallographic structure), but its orthologues are absent from Escherichia coli and the photosynthetic bacterium Synechocystis. We would therefore suggest that PSRP-4 is an example of gene capture (via horizontal gene transfer) during chloro-ribosome emergence. Orthologues of all six PSRPs are identifiable in the complete genome sequence of Arabidopsis thaliana and in the higher plant expressed sequence tag database. All six PSRPs are nucleus-encoded. The cytosolic precursors of PSRP-2, PSRP-3, and PSRP-4 have average targeting peptides (62, 58, and 54 residues long), and the mature proteins are of 196, 121, and 47 residues length (molar masses, 21.7, 13.8 and 5.2 kDa), respectively. Functions of the PSRPs as active participants in translational regulation, the key feature of chloroplast protein synthesis, are discussed and a model is proposed.}, }
@article {pmid12603038, year = {2003}, author = {Nakhleh, L and Sun, J and Warnow, T and Linder, CR and Moret, BM and Tholse, A}, title = {Towards the development of computational tools for evaluating phylogenetic network reconstruction methods.}, journal = {Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing}, volume = {}, number = {}, pages = {315-326}, pmid = {12603038}, issn = {2335-6928}, mesh = {*Algorithms ; Computational Biology ; Evolution, Molecular ; Gene Transfer, Horizontal ; Hybridization, Genetic ; Models, Genetic ; *Phylogeny ; }, abstract = {We report on a suite of algorithms and techniques that together provide a simulation flow for studying the topological accuracy of methods for reconstructing phylogenetic networks. We implemented those algorithms and techniques and used three phylogenetic reconstruction methods for a case study of our tools. We present the results of our experimental studies in analyzing the relative performance of these methods. Our results indicate that our simulator and our proposed measure of accuracy, the latter an extension of the widely used Robinson-Foulds measure, offer a robust platform for the evaluation of network reconstruction algorithms.}, }
@article {pmid12603035, year = {2003}, author = {Addario-Berry, L and Hallett, M and Lagergren, J}, title = {Towards identifying lateral gene transfer events.}, journal = {Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing}, volume = {}, number = {}, pages = {279-290}, doi = {10.1142/9789812776303_0027}, pmid = {12603035}, issn = {2335-6928}, mesh = {*Algorithms ; Biological Evolution ; Computer Simulation ; *Gene Transfer, Horizontal ; *Models, Genetic ; Poisson Distribution ; }, abstract = {This paper is concerned with evaluating the performance of the model and algorithm in 5 for detecting lateral gene transfers events. Using a Poisson process to describe arrival times of transfer events, a simulation is used to generate "synthetic" gene and species trees. An implementation of an efficient algorithm in 5 is used to estimate the minimum number of transfers necessary to explain disagreements between the generated gene and species trees. Our first result suggests that the algorithm can solve realistic size instances of the problem. Our second result suggests that the mean error and variance are low when saturation does not occur. Additionally, certain plausible evolutionary events allowed by our model of evolution used to generate gene and species trees but not detectable by the algorithm occur rarely implying the framework should work well in practice. Our third, surprising result suggests that the number of optimal scenarios is on average low for realistic input sizes.}, }
@article {pmid12595420, year = {2003}, author = {Bergman, NH and Akerley, BJ}, title = {Position-based scanning for comparative genomics and identification of genetic islands in Haemophilus influenzae type b.}, journal = {Infection and immunity}, volume = {71}, number = {3}, pages = {1098-1108}, pmid = {12595420}, issn = {0019-9567}, support = {R01 AI049437/AI/NIAID NIH HHS/United States ; R56 AI049437/AI/NIAID NIH HHS/United States ; AI49437/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; *Genome, Bacterial ; Genomics ; Haemophilus influenzae type b/*genetics ; Lipopolysaccharides/biosynthesis ; Mannose-6-Phosphate Isomerase/genetics ; Molecular Sequence Data ; Multigene Family ; Open Reading Frames ; Polymerase Chain Reaction ; RNA, Transfer, Ile/genetics ; Repetitive Sequences, Nucleic Acid ; }, abstract = {Bacteria exhibit extensive genetic heterogeneity within species. In many cases, these differences account for virulence properties unique to specific strains. Several such loci have been discovered in the genome of the type b serotype of Haemophilus influenzae, a human pathogen able to cause meningitis, pneumonia, and septicemia. Here we report application of a PCR-based scanning procedure to compare the genome of a virulent type b (Hib) strain with that of the laboratory-passaged Rd KW20 strain for which a complete genome sequence is available. We have identified seven DNA segments or H. influenzae genetic islands (HiGIs) present in the type b genome and absent from the Rd genome. These segments vary in size and content and show signs of horizontal gene transfer in that their percent G+C content differs from that of the rest of the H. influenzae genome, they contain genes similar to those found on phages or other mobile elements, or they are flanked by DNA repeats. Several of these loci represent potential pathogenicity islands, because they contain genes likely to mediate interactions with the host. These newly identified genetic islands provide areas of investigation into both the evolution and pathogenesis of H. influenzae. In addition, the genome scanning approach developed to identify these islands provides a rapid means to compare the genomes of phenotypically diverse bacterial strains once the genome sequence of one representative strain has been determined.}, }
@article {pmid12594930, year = {2003}, author = {Raymond, J and Zhaxybayeva, O and Gogarten, JP and Blankenship, RE}, title = {Evolution of photosynthetic prokaryotes: a maximum-likelihood mapping approach.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {358}, number = {1429}, pages = {223-230}, pmid = {12594930}, issn = {0962-8436}, mesh = {Bacteria/genetics/metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/genetics ; *Genome ; Likelihood Functions ; Photosynthesis/*genetics ; Phylogeny ; Prokaryotic Cells/*physiology ; }, abstract = {Reconstructing the early evolution of photosynthesis has been guided in part by the geological record, but the complexity and great antiquity of these early events require molecular genetic techniques as the primary tools of inference. Recent genome sequencing efforts have made whole genome data available from representatives of each of the five phyla of bacteria with photosynthetic members, allowing extensive phylogenetic comparisons of these organisms. Here, we have undertaken whole genome comparisons using maximum likelihood to compare 527 unique sets of orthologous genes from all five photosynthetic phyla. Substantiating recent whole genome analyses of other prokaryotes, our results indicate that horizontal gene transfer (HGT) has played a significant part in the evolution of these organisms, resulting in genomes with mosaic evolutionary histories. A small plurality phylogenetic signal was observed, which may be a core of remnant genes not subject to HGT, or may result from a propensity for gene exchange between two or more of the photosynthetic organisms compared.}, }
@article {pmid12594919, year = {2003}, author = {Herrmann, RG and Maier, RM and Schmitz-Linneweber, C}, title = {Eukaryotic genome evolution: rearrangement and coevolution of compartmentalized genetic information.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {358}, number = {1429}, pages = {87-97; discussion 97}, pmid = {12594919}, issn = {0962-8436}, mesh = {Atropa belladonna/cytology/genetics ; Eukaryotic Cells/cytology/*metabolism ; *Evolution, Molecular ; *Genome ; Plants/*genetics ; Plastids/genetics ; RNA Editing ; Nicotiana/cytology/genetics ; Transcription, Genetic ; }, abstract = {The plant cell operates with an integrated, compartmentalized genome consisting of nucleus/cytosol, plastids and mitochondria that, in its entirety, is regulated in time, quantitatively, in multicellular organisms and also in space. This genome, as do genomes of eukaryotes in general, originated in endosymbiotic events, with at least three cells, and was shaped phylogenetically by a massive and highly complex restructuring and intermixing of the genetic potentials of the symbiotic partners and by lateral gene transfer. This was accompanied by fundamental changes in expression signals in the entire system at almost all regulatory levels. The gross genome rearrangements contrast with a highly specific compartmental interplay, which becomes apparent in interspecific nuclear-plastid cybrids or hybrids. Organelle exchanges, even between closely related species, can greatly disturb the intracellular genetic balance ("hybrid bleaching"), which is indicative of compartmental coevolution and is of relevance for speciation processes. The photosynthetic machinery of plastids, which is embedded in that genetic machinery, is an appealing model to probe into genomic and organismic evolution and to develop functional molecular genomics. We have studied the reciprocal Atropa belladonna-Nicotiana tabacum cybrids, which differ markedly in their phenotypes, and found that transcriptional and post-transcriptional processes can contribute to genome/plastome incompatibility. Allopolyploidy can influence this phenomenon by providing an increased, cryptic RNA editing potential and the capacity to maintain the integrity of organelles of different taxonomic origins.}, }
@article {pmid12594917, year = {2003}, author = {Doolittle, WF and Boucher, Y and Nesbø, CL and Douady, CJ and Andersson, JO and Roger, AJ}, title = {How big is the iceberg of which organellar genes in nuclear genomes are but the tip?.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {358}, number = {1429}, pages = {39-57; discussion 57-8}, pmid = {12594917}, issn = {0962-8436}, mesh = {Cell Nucleus/*genetics ; Eukaryotic Cells/metabolism ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome ; Gram-Negative Anaerobic Bacteria/genetics ; Methanosarcina/genetics ; Organelles/*genetics ; RNA, Ribosomal/genetics ; Symbiosis ; }, abstract = {As more and more complete bacterial and archaeal genome sequences become available, the role of lateral gene transfer (LGT) in shaping them becomes more and more clear. Over the long term, it may be the dominant force, affecting most genes in most prokaryotes. We review the history of LGT, suggesting reasons why its prevalence and impact were so long dismissed. We discuss various methods purporting to measure the extent of LGT, and evidence for and against the notion that there is a core of never-exchanged genes shared by all genomes, from which we can deduce the "true" organismal tree. We also consider evidence for, and implications of, LGT between prokaryotes and phagocytic eukaryotes.}, }
@article {pmid12593736, year = {2002}, author = {Bencina, D}, title = {Haemagglutinins of pathogenic avian mycoplasmas.}, journal = {Avian pathology : journal of the W.V.P.A}, volume = {31}, number = {6}, pages = {535-547}, doi = {10.1080/0307945021000024526}, pmid = {12593736}, issn = {0307-9457}, mesh = {Animals ; Genes, Bacterial/genetics ; Hemagglutinins/chemistry/genetics/immunology/*metabolism ; Mycoplasma/genetics/*metabolism/*pathogenicity ; Mycoplasma Infections/microbiology/*veterinary ; Poultry/microbiology ; Poultry Diseases/*microbiology ; }, abstract = {The pathogenic avian mycoplasmas, Mycoplasma gallisepticum, Mycoplasma synoviae, Mycoplasma meleagridis, Mycoplasma iowae and Mycoplasma imitans, synthesize haemagglutinins that are immunogenic, variably expressed, surface proteins. The haemagglutinins of M. gallisepticum (pMGA), M. synoviae (VlhA) and M. imitans are lipoproteins, encoded by related multigene families that appear to have arisen by horizontal gene transfer. M. gallisepticum also has genes encoding cytadhesins in its genome but these are present as a single copies, while the pMGA gene family contains 30 to 70 genes. The switch in expression of distinct pMGA genes (e.g. pMGA1.1 to pMGA1.9) generates antigenic variation, which is thought to be important in immune evasion but also has significance in the preparation of M. gallisepticum antigens for serological diagnosis. In the majority of M. synoviae strains, post-translational cleavage of the VlhA protein generates an amino-terminal part (the lipoprotein MSPB) and a carboxyl-terminal part (MSPA), which mediates binding to erythrocytes. The 5'vlhA gene region, which encodes proline-rich repeats in the amino-terminal part of MSPB, is highly polymorphic among M. synoviae strains. Insertions or deletions in the part of vlhA encoding the proline-rich repeats cause MSPB length variation in different M. synoviae strains. Recombination between the 5'vlhA gene and pseudogenes in the genome generates changes in antigenic determinants in the carboxyl two-thirds of the MSPB molecule, and in MSPA, resulting in changes in the domains involved in the binding of M. synoviae to erythrocytes. Variant haemagglutinins of M. gallisepticum (pMGA1.7) and M. synoviae (diverse VlhA forms) share sequences that may be responsible for antigenic cross-reactions between M. gallisepticum and M. synoviae. Shared epitopes have been demonstrated using specific antibodies against MSPB that also recognize proteins of M. gallisepticum and of M. iowae (serotype N). Size and antigenic variants have also been reported for M. meleagridis and M. iowae proteins, but it is not known if these are their haemagglutinins. Advances in the molecular characterization of M. gallisepticum (pMGA, pvpA) and M. synoviae (vlhA) genes and their sequencing in numerous strains is likely to enable significantly improved epidemiological studies and improved tracing of M. gallisepticum and M. synoviae strains in different flocks.}, }
@article {pmid12588739, year = {2003}, author = {Nixon, JE and Field, J and McArthur, AG and Sogin, ML and Yarlett, N and Loftus, BJ and Samuelson, J}, title = {Iron-dependent hydrogenases of Entamoeba histolytica and Giardia lamblia: activity of the recombinant entamoebic enzyme and evidence for lateral gene transfer.}, journal = {The Biological bulletin}, volume = {204}, number = {1}, pages = {1-9}, doi = {10.2307/1543490}, pmid = {12588739}, issn = {0006-3185}, support = {R01 AI048082/AI/NIAID NIH HHS/United States ; AI33492/AI/NIAID NIH HHS/United States ; AI43273/AI/NIAID NIH HHS/United States ; AI46516/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Cloning, Molecular ; Entamoeba histolytica/*enzymology/genetics ; *Gene Transfer, Horizontal ; Giardia lamblia/*enzymology/genetics ; Hydrogenase/chemistry/genetics/*metabolism ; Iron/*metabolism ; Molecular Sequence Data ; Phylogeny ; RNA, Messenger/genetics ; Recombinant Proteins/chemistry/genetics/metabolism ; Sequence Homology, Amino Acid ; }, abstract = {Entamoeba histolytica and Spironucleus barkhanus have genes that encode short iron-dependent hydrogenases (Fe-hydrogenases), even though these protists lack hydrogenosomes. To understand better the biochemistry of the protist Fe-hydrogenases, we prepared a recombinant E. histolytica short Fe-hydrogenase and measured its activity in vitro. A Giardia lamblia gene encoding a short Fe-hydrogenase was identified from shotgun genomic sequences, and RT-PCR showed that cultured entamoebas and giardias transcribe short Fe-hydrogenase mRNAs. A second E. histolytica gene, which encoded a long Fe-hydrogenase, was identified from shotgun genomic sequences. Phylogenetic analyses suggested that the short Fe-hydrogenase genes of entamoeba and diplomonads share a common ancestor, while the long Fe-hydrogenase gene of entamoeba appears to have been laterally transferred from a bacterium. These results are discussed in the context of competing ideas for the origins of genes encoding fermentation enzymes of these protists.}, }
@article {pmid12584130, year = {2003}, author = {Hsiao, W and Wan, I and Jones, SJ and Brinkman, FS}, title = {IslandPath: aiding detection of genomic islands in prokaryotes.}, journal = {Bioinformatics (Oxford, England)}, volume = {19}, number = {3}, pages = {418-420}, doi = {10.1093/bioinformatics/btg004}, pmid = {12584130}, issn = {1367-4803}, mesh = {Archaea/genetics ; Bacteria/genetics ; CpG Islands/genetics ; *Database Management Systems ; Gene Transfer, Horizontal ; *Genome, Archaeal ; *Genome, Bacterial ; Phylogeny ; Sequence Alignment/*methods ; Sequence Analysis, DNA/*methods ; Software ; }, abstract = {UNLABELLED: Genomic islands (clusters of genes of potential horizontal origin in a prokaryotic genome) are frequently associated with a particular adaptation of a microbe that is of medical, agricultural or environmental importance, such as antibiotic resistance, pathogen virulence, or metal resistance. While many sequence features associated with such islands have been adopted separately in applications for analysis of genomic islands, including pathogenicity islands, there is no single application that integrates multiple features for island detection. IslandPath is a network service which incorporates multiple DNA signals and genome annotation features into a graphical display of a bacterial or archaeal genome, to aid the detection of genomic islands.<br><br>AVAILABILITY: This application is available at http://www.pathogenomics.sfu.ca/islandpath and the source code is freely available, under GNU public licence, from the authors.<br><br>SUPPLEMENTARY INFORMATION: An online help file, which includes analyses of the utility of IslandPath, can be found at http://www.pathogenomics.sfu.ca/islandpath/current/islandhelp.html}, }
@article {pmid12584125, year = {2003}, author = {Parkinson, J and Blaxter, M}, title = {SimiTri--visualizing similarity relationships for groups of sequences.}, journal = {Bioinformatics (Oxford, England)}, volume = {19}, number = {3}, pages = {390-395}, doi = {10.1093/bioinformatics/btf870}, pmid = {12584125}, issn = {1367-4803}, mesh = {Animals ; Caenorhabditis elegans/genetics/metabolism ; Caenorhabditis elegans Proteins/genetics ; *Database Management Systems ; Databases, Protein ; Drosophila/genetics/metabolism ; Drosophila Proteins/genetics/metabolism ; Gene Transfer, Horizontal/genetics ; Humans ; *Phylogeny ; Proteins/*genetics/metabolism ; Saccharomyces cerevisiae/genetics/metabolism ; Sequence Alignment/*methods ; Sequence Analysis, DNA/*methods ; Sequence Homology, Amino Acid ; Species Specificity ; User-Computer Interface ; }, abstract = {Global sequence comparisons between large datasets, such as those arising from genome projects, can be problematic to display and analyze. We have developed SimiTri, a Java/Perl-based application, which allows simultaneous display and analysis of relative similarity relationships of the dataset of interest to three different databases. We illustrate its utility in identifying Caenorhabditis elegans genes that have distinct patterns of phylogenetic affinity suggestive of horizontal gene transfer. SimiTri is freely downloadable from http://www.nematodes.org/SimiTri/ and the source code is freely available from the authors.}, }
@article {pmid12584004, year = {2003}, author = {Sherley, M and Gordon, DM and Collignon, PJ}, title = {Species differences in plasmid carriage in the Enterobacteriaceae.}, journal = {Plasmid}, volume = {49}, number = {1}, pages = {79-85}, doi = {10.1016/s0147-619x(02)00107-5}, pmid = {12584004}, issn = {0147-619X}, mesh = {Animals ; Animals, Wild/microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Enterobacteriaceae/*genetics/isolation &amp; purification ; Evolution, Molecular ; Gene Transfer, Horizontal ; Mammals/microbiology ; *Plasmids/isolation &amp; purification ; Probability ; Species Specificity ; }, abstract = {Modern concerns about the spread of antibiotic resistance raise questions about the effect of bacterial species on plasmid evolution and maintenance. We studied 223 Enterobacteriaceae isolated from wild mammals and determined the number of plasmids per isolate, the size of those plasmids, and the distribution of plasmid incompatibility groups N, P, W, FII, and A/C. All of these variables were non-randomly distributed with respect to bacterial species, suggesting that host-cell factors constrain the plasmids that a strain will carry. The implication for the evolution of multiple-resistance plasmids in a clinical setting is that although inter-generic plasmid transfer may introduce a novel resistance plasmid into a bacterial genus, it is likely to be modified to suit the requirements of the new host cell. This then further suggests that resistance plasmids will evolve independent lineages within bacterial species although the genes incorporated in them may have come from the same original source.}, }
@article {pmid12584002, year = {2003}, author = {Tauch, A and Bischoff, N and Brune, I and Kalinowski, J}, title = {Insights into the genetic organization of the Corynebacterium diphtheriae erythromycin resistance plasmid pNG2 deduced from its complete nucleotide sequence.}, journal = {Plasmid}, volume = {49}, number = {1}, pages = {63-74}, doi = {10.1016/s0147-619x(02)00115-4}, pmid = {12584002}, issn = {0147-619X}, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics/metabolism ; Base Sequence ; Conserved Sequence ; Corynebacterium diphtheriae/drug effects/*genetics ; DNA Helicases/genetics ; DNA Nucleotidyltransferases/genetics ; DNA Transposable Elements ; DNA, Intergenic ; *DNA-Binding Proteins ; Drug Resistance, Bacterial/*genetics ; Erythromycin/pharmacology ; Escherichia coli/genetics ; Gene Order ; Molecular Sequence Data ; Plasmids/*genetics ; Proteins/genetics ; Pyrophosphatases/genetics ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; *Trans-Activators ; }, abstract = {The complete nucleotide sequence of the erythromycin resistance plasmid pNG2 from the human pathogen Corynebacterium diphtheriae S601 was determined. The plasmid has a total size of 15,100 bp and contains at least 17 coding regions. Comparative genomics identified conserved motifs within replication initiator proteins of corynebacterial plasmids and a novel nucleotide sequence feature, termed 22-bp box, located downstream of the repA gene. The erythromycin resistance determinant erm(X) is flanked by inverted repeats of the novel insertion sequence IS3504, which may be responsible for a spontaneous deletion of the antibiotic resistance gene region. Furthermore, pNG2 encodes a putative conjugative relaxase, a membrane protein of the natural resistance-associated macrophage protein (Nramp) family and a protein with Nudix hydrolase signature. Expression of the predicted coding regions of pNG2 in Escherichia coli JM109 was demonstrated by reverse transcription-polymerase chain reaction (RT-PCR) assays. The detailed annotation of the entire pNG2 sequence provided genetic information regarding its molecular evolution and its role in dissemination of antibiotic resistance genes by horizontal gene transfer.}, }
@article {pmid12583705, year = {2002}, author = {Kharazmi, M and Hammes, WP and Hertel, C}, title = {Construction of a marker rescue system in Bacillus subtilis for detection of horizontal gene transfer in food.}, journal = {Systematic and applied microbiology}, volume = {25}, number = {4}, pages = {471-477}, doi = {10.1078/07232020260517580}, pmid = {12583705}, issn = {0723-2020}, mesh = {Bacillus subtilis/*genetics/isolation &amp; purification ; DNA, Bacterial/analysis ; DNA, Recombinant/analysis ; *Food Microbiology/standards ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genetic Complementation Test ; Genetic Markers ; Plants, Genetically Modified ; Plasmids ; *Transformation, Bacterial ; }, abstract = {A marker rescue system based on the repair of the kanamycin resistance gene nptII was constructed for use in Gram-positive bacteria and established in Bacillus subtilis 168. Marker rescue was detected in vitro using different types of donor DNA containing intact nptII. The efficiency of marker rescue using chromosomal DNA of E. coli Sure as well as plasmids pMR2 or pSR8-30 ranged from 3.8 x 10(-8) to 1.5 x 10(-9) transformants per nptII gene. Low efficiencies of ca. 10(-12) were obtained with PCR fragments of 792 bp obtained from chromosomal DNA of E. coli Sure or DNA from a transgenic potato. B. subtilis developed competence during growth in milk and chocolate milk, and marker rescue transformation was detected with frequencies of ca. 10(-6) and 10(-8), respectively, using chromosomal DNA of E. coli Sure as donor DNA. Although the copy number of nptII genes of the plant DNA exceeded that of chromosomal E. coli DNA in the marker rescue experiments, a transfer of DNA from the transgenic plant to B. subtilis was detectable neither in vitro nor in situ.}, }
@article {pmid12583560, year = {2002}, author = {Babálová, M and Blahová, J and Králiková, K and Krcméry, V and Kubonová, K}, title = {Nosocomial Stenotrophomonas maltophilia strain with a broad host range ability to transfer antibiotic resistance.}, journal = {Journal of chemotherapy (Florence, Italy)}, volume = {14}, number = {6}, pages = {639}, doi = {10.1179/joc.2002.14.6.639}, pmid = {12583560}, issn = {1120-009X}, mesh = {Cross Infection/drug therapy/*microbiology ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal/*genetics ; Gram-Negative Bacterial Infections/drug therapy/*microbiology ; Humans ; Stenotrophomonas maltophilia/*drug effects/*genetics ; }, }
@article {pmid12582423, year = {2002}, author = {Galán, JC}, title = {[Trans-gram gene transfer: the case of beta-lactamases].}, journal = {Revista espanola de quimioterapia : publicacion oficial de la Sociedad Espanola de Quimioterapia}, volume = {15}, number = {3}, pages = {215-223}, pmid = {12582423}, issn = {0214-3429}, mesh = {*Gene Transfer, Horizontal ; Gram-Negative Bacteria/*genetics ; Gram-Positive Bacteria/*genetics ; beta-Lactamases/*genetics ; }, abstract = {Lateral or horizontal gene transfer is a phenomenon that has influenced the evolution of microorganisms. Despite the evolutionary trend toward genetic isolation, lateral transfer seems to take place relatively frequently, bridging the gap between very separate species. The acquisition of foreign genes may have accelerated in recent years because of the increase in the adaptive needs of bacteria, particularly through the use of antibiotics. Transfer of genes encoding beta-lactamases from Gram-positive to Gram-negative bacteria (trans-gram transfer) may be suggested on the basis of sequence analysis. We found that the sequences of the beta-lactamases BRO-1 and ACl-1, from the Gram-negative bacterial organisms Moraxella and Acidaminococcus, respectively are abnormally placed among sequences from Gram-positive beta-lactamases in phylogenetic trees. In both cases, the topology of the enzyme (attached to the cellular membrane), the structure of the signal peptide, and the Shine-Dalgarno region suggest that these enzymes originated from Gram-positive organisms. Results remain inconclusive for Haemophilus ROB-1 beta-lactamase.}, }
@article {pmid12575900, year = {2003}, author = {Duggan, PS and Chambers, PA and Heritage, J and Michael Forbes, J}, title = {Fate of genetically modified maize DNA in the oral cavity and rumen of sheep.}, journal = {The British journal of nutrition}, volume = {89}, number = {2}, pages = {159-166}, doi = {10.1079/BJN2002764}, pmid = {12575900}, issn = {0007-1145}, mesh = {Animal Feed ; Animals ; Bacillus thuringiensis Toxins ; Bacterial Proteins/*genetics ; *Bacterial Toxins ; Chromosomes, Plant ; DNA/analysis ; Endotoxins/*genetics ; Escherichia coli/genetics ; *Gene Transfer, Horizontal ; Hemolysin Proteins ; Kanamycin Resistance/genetics ; Mouth/microbiology ; *Plants, Genetically Modified ; Polymerase Chain Reaction/methods ; Rumen/microbiology ; Sheep/*metabolism ; Time Factors ; Transformation, Bacterial/*genetics ; Transgenes ; Zea mays/*genetics ; }, abstract = {The polymerase chain reaction (PCR) technique was used to investigate the fate of a transgene in the rumen of sheep fed silage and maize grains from an insect-resistant maize line. A 1914-bp DNA fragment containing the entire coding region of the synthetic cryIA(b) gene was still amplifiable from rumen fluid sampled 5 h after feeding maize grains. The same target sequence, however, could not be amplified from rumen fluid sampled from sheep fed silage prepared from the genetically modified maize line. PCR amplification of a shorter (211-bp), yet still highly specific, target sequence was possible with rumen fluid sampled up to 3 and 24 h after feeding silage and maize grains, respectively. These findings indicate that intact transgenes from silage are unlikely to survive significantly in the rumen since a DNA sequence 211-bp long is very unlikely to transmit genetic information. By contrast, DNA in maize grains persists for a significant time and may, therefore, provide a source of transforming DNA in the rumen. In addition, we have examined the biological activity of plasmid DNA that had previously been exposed to the ovine oral cavity. Plasmid extracted from saliva sampled after incubation for 8 min was still capable of transforming competent Escherichia coli to kanamycin resistance, implying that DNA released from the diet within the mouth may retain sufficient biological activity for the transformation of competent oral bacteria.}, }
@article {pmid12574860, year = {2003}, author = {Amiri, H and Karlberg, O and Andersson, SG}, title = {Deep origin of plastid/parasite ATP/ADP translocases.}, journal = {Journal of molecular evolution}, volume = {56}, number = {2}, pages = {137-150}, doi = {10.1007/s00239-002-2387-0}, pmid = {12574860}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics ; Chlamydiaceae/enzymology/genetics ; Eukaryotic Cells/enzymology/microbiology ; Evolution, Molecular ; Gene Transfer, Horizontal ; Host-Parasite Interactions ; Mitochondria/enzymology/genetics ; Mitochondrial ADP, ATP Translocases/*genetics ; Molecular Sequence Data ; *Phylogeny ; Plastids/*enzymology/genetics ; Rickettsia/*enzymology/genetics ; Rickettsia rickettsii/enzymology/genetics ; Rickettsia typhi ; Sequence Analysis ; Sequence Homology, Amino Acid ; }, abstract = {Membrane proteins that transport ATP and ADP have been identified in mitochondria, plastids, and obligate intracellular parasites. The mitochondrial ATP/ADP transporters are derived from a broad-specificity transport family of eukaryotic origin, whereas the origin of the plastid/parasite ATP/ADP translocase is more elusive. Here we present the sequences of five genes coding for ATP/ADP translocases from four species of Rickettsia. The results are consistent with an early duplication and divergence of the five ATP/ADP translocases within the rickettsial lineage. A comparison of the phylogenetic depths of the mitochondrial and the plastid/parasite ATP/ADP translocases indicates a deep origin for both transporters. The results provide no evidence for a recent acquisition of the ATP/ADP transporters in Rickettsia via horizontal gene transfer, as previously suggested. A possible function of the two types of ATP/ADP translocases was to allow switches between glycolysis and aerobic respiration in the early eukaryotic cell and its endosymbiont.}, }
@article {pmid12572615, year = {1998}, author = {Peek, AS and Vrijenhoek, RC and Gaut, BS}, title = {Accelerated evolutionary rate in sulfur-oxidizing endosymbiotic bacteria associated with the mode of symbiont transmission.}, journal = {Molecular biology and evolution}, volume = {15}, number = {11}, pages = {1514-1523}, doi = {10.1093/oxfordjournals.molbev.a025879}, pmid = {12572615}, issn = {0737-4038}, support = {TW00735-01/TW/FIC NIH HHS/United States ; }, mesh = {Betaproteobacteria/genetics/metabolism ; DNA, Bacterial/genetics ; *Evolution, Molecular ; Gammaproteobacteria/*genetics/*metabolism ; Gene Transfer, Horizontal/*genetics ; Likelihood Functions ; Mutagenesis/genetics ; Nucleic Acid Conformation ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfur/*metabolism ; Symbiosis/*genetics ; }, abstract = {The nearly neutral theory of molecular evolution predicts that the rate of nucleotide substitution should accelerate in small populations at sites under low selective constraint. We examined these predictions with respect to the relative population sizes for three bacterial life histories within chemolithoautotrophic sulfur-oxidizing bacteria: (1) free-living bacteria, (2) environmentally captured symbionts, and (3) maternally transmitted symbionts. Both relative rates of nucleotide substitution and relative ratios of loop, stem, and domain substitutions from 1,165 nt of the small-subunit 16S rDNA were consistent with expectations of the nearly neutral theory. Relative to free-living sulfur-oxidizing autotrophic bacteria, the maternally transmitted symbionts have faster substitution rates overall and also in low-constraint domains of 16S rDNA. Nucleotide substitition rates also differ between loop and stem positions. All of these findings are consistent with the predictions that these symbionts have relatively small effective population sizes. In contrast, the rates of nucleotide substitution in environmentally captured symbionts are slower, particularly in high-constraint domains, than in free-living bacteria.}, }
@article {pmid12572603, year = {1998}, author = {Marín, I and Plata-Rengifo, P and Labrador, M and Fontdevila, A}, title = {Evolutionary relationships among the members of an ancient class of non-LTR retrotransposons found in the nematode Caenorhabditis elegans.}, journal = {Molecular biology and evolution}, volume = {15}, number = {11}, pages = {1390-1402}, doi = {10.1093/oxfordjournals.molbev.a025867}, pmid = {12572603}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Animals ; Caenorhabditis elegans/enzymology/*genetics ; Caenorhabditis elegans Proteins/genetics ; Computational Biology ; DNA, Helminth/chemistry/genetics ; Endonucleases/genetics ; *Evolution, Molecular ; Gene Dosage ; Gene Transfer, Horizontal/genetics ; Genome ; Long Interspersed Nucleotide Elements/*genetics ; Molecular Sequence Data ; Multigene Family/genetics ; Nucleic Acid Conformation ; Open Reading Frames/genetics ; Phylogeny ; RNA-Directed DNA Polymerase/genetics ; Retroelements/genetics ; Sequence Alignment ; }, abstract = {We took advantage of the massive amount of sequence information generated by the Caenorhabditis elegans genome project to perform a comprehensive analysis of a group of over 100 related sequences that has allowed us to describe two new C. elegans non-LTR retrotransposons. We named them Sam and Frodo. We also determined that several highly divergent subfamilies of both elements exist in C. elegans. It is likely that several master copies have been active at the same time in C. elegans, although only a few copies of both Sam and Frodo have characteristics that are compatible with them being active today. We discuss whether it is more appropriate under these circumstances to define only 2 elements corresponding to the most divergent groups of sequences or up to 16, considering each subfamily a different element. The C. elegans elements are related to other previously described non-LTR retrotransposons (CR1, found in different vertebrates; SR1, from the trematode Schistosoma; Q and T1, from the mosquito Anopheles). All of these elements, according to the analysis of their reverse transcriptases, form a monophyletic cluster that we call the "T1/CR1 subgroup." Elements of this subgroup are thus ancient components of the genome of animal species. However, we discuss the possibility that these elements may occasionally be horizontally transmitted.}, }
@article {pmid12568333, year = {2002}, author = {Scott, KP}, title = {The role of conjugative transposons in spreading antibiotic resistance between bacteria that inhabit the gastrointestinal tract.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {59}, number = {12}, pages = {2071-2082}, doi = {10.1007/s000180200007}, pmid = {12568333}, issn = {1420-682X}, mesh = {Animals ; Bacteria/genetics ; Bacteria, Anaerobic/*genetics/physiology ; *Conjugation, Genetic ; DNA Transposable Elements/*genetics ; Digestive System/*microbiology ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; }, abstract = {There is huge potential for genetic exchange to occur within the dense, diverse anaerobic microbial population inhabiting the gastrointestinal tract (GIT) of humans and animals. However, the incidence of conjugative transposons (CTns) and the antibiotic resistance genes they carry has not been well studied among this population. Since any incoming bacteria, including pathogens, can access this reservoir of genes, this oversight would appear to be an important one. Recent evidence has shown that anaerobic bacteria native to the rumen or hindgut harbour both novel antibiotic resistance genes and novel conjugative transposons. These CTns, and previously characterized CTns, can be transferred to a wide range of commensal bacteria under laboratory and in vivo conditions. The main evidence that gene transfer occurs widely in vivo between GIT bacteria, and between GIT bacteria and pathogenic bacteria, is that identical resistance genes are present in diverse bacterial species from different hosts.}, }
@article {pmid12568332, year = {2002}, author = {Beaber, JW and Burrus, V and Hochhut, B and Waldor, MK}, title = {Comparison of SXT and R391, two conjugative integrating elements: definition of a genetic backbone for the mobilization of resistance determinants.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {59}, number = {12}, pages = {2065-2070}, doi = {10.1007/s000180200006}, pmid = {12568332}, issn = {1420-682X}, mesh = {Base Sequence ; *Conjugation, Genetic ; *DNA Transposable Elements ; DNA, Bacterial ; Drug Resistance, Microbial/*genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Plasmids/genetics/metabolism ; Retroelements ; Sequence Alignment ; }, abstract = {The SXT element (SXT) is becoming an increasingly prevalent vector for the dissemination of antibiotic resistances in Vibrio cholerae. SXT is a member of a larger family of elements, formerly defined as IncJ plasmids, that are self-transmissible by conjugation and integrate site-specifically into the host chromosome. Comparison of the DNA sequences of SXT and R391, an IncJ element from Providencia rettgeri, indicate that these elements consist of a conserved backbone that mediates the regulation, excision/integration and conjugative transfer of the elements. Both elements have insertions into this backbone that either confer the element-specific properties or are of unknown function. Interestingly, the conserved SXT and R391 backbone apparently contains hotspots for insertion of additional DNA sequences. This backbone represents a scaffold for the mobilization of genetic material between a wide range of gram-negative bacteria, allowing for rapid adaptation to changing environments.}, }
@article {pmid12568331, year = {2002}, author = {Pembroke, JT and MacMahon, C and McGrath, B}, title = {The role of conjugative transposons in the Enterobacteriaceae.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {59}, number = {12}, pages = {2055-2064}, doi = {10.1007/s000180200005}, pmid = {12568331}, issn = {1420-682X}, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics/metabolism ; *Conjugation, Genetic ; DNA Repair ; *DNA Transposable Elements ; Enterobacteriaceae/*genetics/pathogenicity ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Integrases/genetics/metabolism ; Molecular Sequence Data ; Plasmids/genetics/metabolism ; Sequence Alignment ; }, abstract = {Although widely studied in gram-positive Streptococci and in the gram-negative Bacteroides, there is a scarcity of information on the occurrence and nature of conjugative transposon-like elements in the well-studied Enterobacteriaceae. In fact, some of the major reviews on conjugative transposons prior to 1996 failed to mention their occurrence in this group. Recently, their presence has been reported in Salmonella, Vibrio and Proteus species, and in some cases such as the SXT element in Vibrio and the IncJ group element CTnR391, there has been some molecular characterization. The elements thus far examined appear to be larger than the common gram-positive conjugative transposons and to be mosaic in structure, with genes derived from several sources. Recent evidence suggests that in the Enterobacteriaceae the elements may be related to enteric pathogenicity islands. The evolution, distribution and role of these elements in the Enterobacteriaceae is discussed.}, }
@article {pmid12568329, year = {2002}, author = {Adams, V and Lyras, D and Farrow, KA and Rood, JI}, title = {The clostridial mobilisable transposons.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {59}, number = {12}, pages = {2033-2043}, doi = {10.1007/s000180200003}, pmid = {12568329}, issn = {1420-682X}, mesh = {Clostridium/drug effects/*genetics ; *Conjugation, Genetic ; DNA Nucleotidyltransferases/metabolism ; DNA Transposable Elements/*genetics ; DNA, Bacterial ; DNA, Circular ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Integrases/metabolism ; Mutagenesis, Insertional ; Recombinases ; Transposases/metabolism ; }, abstract = {Mobilisable transposons are transposable genetic elements that also encode mobilisation functions but are not in themselves conjugative. They rely on coresident conjugative elements to facilitate their transfer to recipient cells. Clostridial mobilisable transposons include Tn4451 and Tn4452 from Clostridium perfringens, and Tn4453a and Tn4453b from Clostridium difficile, all of which are closely related, and Tn5398 from C. difficile. The Tn4451 group of elements encodes resistance to chloramphenicol and is unusual in that transposition is dependent upon a large resolvase protein rather than a more conventional transposase or integrase. This group of elements also encodes the mobilisation protein TnpZ that, by acting at the RS(A) or oriT site located on the transposon, and in the presence of a coresident conjugative element, promotes the movement of the nonreplicating circular intermediate and of plasmids on which the transposon resides. The erythromycin resistance element Tn5398 is unique in that it encodes no readily identifiable transposition or mobilisation proteins. However, the element is still capable of intraspecific transfer between C. difficile isolates, by an unknown mechanism. The detailed analysis of these mobilisable clostridial elements provides evidence that the evolution and dissemination of antibiotic resistance genes is a complex process that may involve the interaction of genetic elements with very different properties.}, }
@article {pmid12568328, year = {2002}, author = {Rice, LB}, title = {Association of different mobile elements to generate novel integrative elements.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {59}, number = {12}, pages = {2023-2032}, doi = {10.1007/s000180200002}, pmid = {12568328}, issn = {1420-682X}, mesh = {Bacteria/drug effects/*genetics ; Cross Infection/*microbiology ; DNA Transposable Elements/*genetics ; DNA, Bacterial ; Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Integrons ; Mutagenesis, Insertional ; Retroelements/genetics ; }, abstract = {Among the more important problems in modern hospitals is the prevalence of bacterial pathogens expressing resistance to multiple antimicrobial agents. The frequency of multiresistance suggests mechanisms by which bacterial species can concentrate and efficiently exchange a variety of resistance determinants. Mechanisms by which this occurs include insertion of transposons within transposons, coalescence through the activity of insertion sequences and the employment of integrons. In some instances, more than one of these mechanisms is involved in creating large multiresistance genetic elements. The association of the elements with transferable elements or transposons may promote rapid dissemination among clinical strains, and create further opportunities for inclusion of additional resistance determinants.}, }
@article {pmid12566393, year = {2003}, author = {Pride, DT and Meinersmann, RJ and Wassenaar, TM and Blaser, MJ}, title = {Evolutionary implications of microbial genome tetranucleotide frequency biases.}, journal = {Genome research}, volume = {13}, number = {2}, pages = {145-158}, pmid = {12566393}, issn = {1088-9051}, support = {R01DK53707/DK/NIDDK NIH HHS/United States ; R01 GM063270/GM/NIGMS NIH HHS/United States ; R01GM63270/GM/NIGMS NIH HHS/United States ; P30 CA068485/CA/NCI NIH HHS/United States ; CA68485/CA/NCI NIH HHS/United States ; }, mesh = {Chromosome Mapping/methods/statistics &amp; numerical data ; Chromosomes, Archaeal/genetics ; Chromosomes, Bacterial/genetics ; Cluster Analysis ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal/genetics ; *Genome, Archaeal ; *Genome, Bacterial ; Gram-Negative Bacteria/*genetics ; Gram-Positive Bacteria/*genetics ; Microsatellite Repeats/genetics ; Phylogeny ; Plasmids/genetics ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Spirochaeta/*genetics ; }, abstract = {We compared nucleotide usage pattern conservation for related prokaryotes by examining the representation of DNA tetranucleotide combinations in 27 representative microbial genomes. For each of the organisms studied, tetranucleotide usage departures from expectations (TUD) were shared between related organisms using both Markov chain analysis and a zero-order Markov method. Individual strains, multiple chromosomes, plasmids, and bacteriophages share TUDs within a species. TUDs varied between coding and noncoding DNA. Grouping prokaryotes based on TUD profiles resulted in relationships with important differences from those based on 16S rRNA phylogenies, which may reflect unequal rates of evolution of nucleotide usage patterns following divergence of particular organisms from a common ancestor. By both symmetrical tree distance and likelihood analysis, phylogenetic trees based on TUD profiles demonstrate a level of congruence with 16S rRNA trees similar to that of both RpoA and RecA trees. Congruence of these trees indicates that there exists phylogenetic signal in TUD patterns, most prominent in coding region DNA. Because relationships demonstrated in TUD-based analyses utilize whole genomes, they should be considered complementary to phylogenies based on single genetic elements, such as 16S rRNA.}, }
@article {pmid12562797, year = {2003}, author = {Grogan, DW and Hansen, JE}, title = {Molecular characteristics of spontaneous deletions in the hyperthermophilic archaeon Sulfolobus acidocaldarius.}, journal = {Journal of bacteriology}, volume = {185}, number = {4}, pages = {1266-1272}, pmid = {12562797}, issn = {0021-9193}, mesh = {Base Sequence ; Consensus Sequence ; DNA, Archaeal/analysis ; Evolution, Molecular ; *Gene Deletion ; *Hot Temperature ; Molecular Sequence Data ; Orotate Phosphoribosyltransferase/*genetics ; Orotic Acid/*analogs &amp; derivatives/metabolism ; Pyrimidines/metabolism ; *Selection, Genetic ; Sequence Analysis, DNA ; Sulfolobus acidocaldarius/*genetics ; }, abstract = {Prokaryotic genomes acquire and eliminate blocks of DNA sequence by lateral gene transfer and spontaneous deletion, respectively. The basic parameters of spontaneous deletion, which are expected to influence the course of genome evolution, have not been determined for any hyperthermophilic archaeon. We therefore screened a number of independent pyrimidine auxotrophs of Sulfolobus acidocaldarius for deletions and sequenced those detected. Deletions accounted for only 0.4% of spontaneous pyrE mutations, corresponding to a frequency of about 10(-8) per cell. Nucleotide sequence analysis of five independent deletions showed no significant association of the endpoints with short direct repeats, despite the fact that several such repeats occur within the pyrE gene and that duplication mutations in pyrE reverted at high frequencies. Endpoints of the spontaneous deletions did not coincide with short inverted repeats or potential stem-loop structures. No consensus sequence common to all the deletions could be identified, although two deletions showed the potential of being stabilized by octanucleotide sequences elsewhere in pyrE, and another pair of deletions shared an octanucleotide at their 3' ends. The unusually low frequency and low sequence dependence of spontaneous deletions in the S. acidocaldarius pyrE gene compared to other genetic systems could not be explained in terms of possible constraints imposed by the 5-fluoroorotate selection.}, }
@article {pmid12560809, year = {2003}, author = {Brown, JR}, title = {Ancient horizontal gene transfer.}, journal = {Nature reviews. Genetics}, volume = {4}, number = {2}, pages = {121-132}, doi = {10.1038/nrg1000}, pmid = {12560809}, issn = {1471-0056}, mesh = {Evolution, Molecular ; *Gene Transfer, Horizontal ; Phylogeny ; }, }
@article {pmid12560357, year = {2003}, author = {Cox, LA and Ramos, RC and Dennis, TN and Jimenez, SA and Smith, JB and Artlett, CM}, title = {Detection of microchimeric cells in the peripheral blood of nonpregnant women is enhanced by magnetic cell sorting before PCR.}, journal = {Clinical chemistry}, volume = {49}, number = {2}, pages = {309-312}, doi = {10.1373/49.2.309}, pmid = {12560357}, issn = {0009-9147}, support = {R01 AR 19616/AR/NIAMS NIH HHS/United States ; R29 AR 45399/AR/NIAMS NIH HHS/United States ; T3 AR 07583/AR/NIAMS NIH HHS/United States ; }, mesh = {CD4-Positive T-Lymphocytes/cytology ; CD8-Positive T-Lymphocytes/cytology ; Cell Separation/methods ; Chromosomes, Human, Y/genetics ; DNA/*blood/genetics ; Female ; *Gene Transfer, Horizontal ; Humans ; Magnetics ; Male ; Polymerase Chain Reaction ; }, }
@article {pmid12560187, year = {2003}, author = {González-Zorn, B and Courvalin, P}, title = {VanA-mediated high level glycopeptide resistance in MRSA.}, journal = {The Lancet. Infectious diseases}, volume = {3}, number = {2}, pages = {67-68}, doi = {10.1016/s1473-3099(03)00510-3}, pmid = {12560187}, issn = {1473-3099}, mesh = {*Bacterial Proteins/genetics ; *Carbon-Oxygen Ligases/genetics ; *Drug Resistance, Multiple, Bacterial/genetics ; Enterococcus/*drug effects/genetics ; Gene Transfer, Horizontal ; Methicillin Resistance/genetics ; Staphylococcus aureus/*drug effects/genetics ; Vancomycin Resistance/genetics ; }, }
@article {pmid12546803, year = {2003}, author = {Gogarten, JP}, title = {Gene transfer: gene swapping craze reaches eukaryotes.}, journal = {Current biology : CB}, volume = {13}, number = {2}, pages = {R53-4}, doi = {10.1016/s0960-9822(02)01426-4}, pmid = {12546803}, issn = {0960-9822}, mesh = {Animals ; *Biological Evolution ; Diplomonadida/genetics ; Eukaryotic Cells ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genes, Protozoan ; Hybridization, Genetic ; Models, Genetic ; Phagocytosis ; Prokaryotic Cells ; Symbiosis ; Wolbachia/genetics ; }, abstract = {Recent studies have provided evidence for gene transfers from prokaryotes to eukaryotes and between eukaryotes. The mechanisms and frequencies of these transfers remain the subject of speculation, but the findings provide ample reason to seriously consider interspecies gene transfer as an important evolutionary process in eukaryotes.}, }
@article {pmid12546782, year = {2003}, author = {Andersson, JO and Sjögren, AM and Davis, LA and Embley, TM and Roger, AJ}, title = {Phylogenetic analyses of diplomonad genes reveal frequent lateral gene transfers affecting eukaryotes.}, journal = {Current biology : CB}, volume = {13}, number = {2}, pages = {94-104}, doi = {10.1016/s0960-9822(03)00003-4}, pmid = {12546782}, issn = {0960-9822}, mesh = {Adaptation, Physiological ; Aldehyde Oxidoreductases/genetics ; Aldehyde-Lyases/genetics ; Amino Acyl-tRNA Synthetases/genetics ; Anaerobiosis ; Animals ; DNA, Protozoan/genetics ; Diplomonadida/enzymology/*genetics/physiology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Protozoan ; Giardia lamblia/enzymology/*genetics/physiology ; Molecular Sequence Data ; Phylogeny ; Protozoan Proteins/genetics ; Threonine Dehydratase/genetics ; Transaminases/genetics ; }, abstract = {BACKGROUND: Lateral gene transfer (LGT) is an important evolutionary mechanism among prokaryotes. The situation in eukaryotes is less clear; the human genome sequence failed to give strong support for any recent transfers from prokaryotes to vertebrates, yet a number of LGTs from prokaryotes to protists (unicellular eukaryotes) have been documented. Here, we perform a systematic analysis to investigate the impact of LGT on the evolution of diplomonads, a group of anaerobic protists.<br><br>RESULTS: Phylogenetic analyses of 15 genes present in the genome of the Atlantic Salmon parasite Spironucleus barkhanus and/or the intestinal parasite Giardia lamblia show that most of these genes originated via LGT. Half of the genes are putatively involved in processes related to an anaerobic lifestyle, and this finding suggests that a common ancestor, which most probably was aerobic, of Spironucleus and Giardia adapted to an anaerobic environment in part by acquiring genes via LGT from prokaryotes. The sources of the transferred diplomonad genes are found among all three domains of life, including other eukaryotes. Many of the phylogenetic reconstructions show eukaryotes emerging in several distinct regions of the tree, strongly suggesting that LGT not only involved diplomonads, but also involved other eukaryotic groups.<br><br>CONCLUSIONS: Our study shows that LGT is a significant evolutionary mechanism among diplomonads in particular and protists in general. These findings provide insights into the evolution of biochemical pathways in early eukaryote evolution and have important implications for studies of eukaryotic genome evolution and organismal relationships. Furthermore, "fusion" hypotheses for the origin of eukaryotes need to be rigorously reexamined in the light of these results.}, }
@article {pmid12538901, year = {2003}, author = {Novoselov, SV and Gladyshev, VN}, title = {Non-animal origin of animal thioredoxin reductases: implications for selenocysteine evolution and evolution of protein function through carboxy-terminal extensions.}, journal = {Protein science : a publication of the Protein Society}, volume = {12}, number = {2}, pages = {372-378}, pmid = {12538901}, issn = {0961-8368}, support = {R01 GM065204/GM/NIGMS NIH HHS/United States ; R37 GM065204/GM/NIGMS NIH HHS/United States ; GM065204/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Eukaryotic Cells/*metabolism ; *Evolution, Molecular ; Humans ; Models, Molecular ; Molecular Sequence Data ; *Phylogeny ; *Selenocysteine/genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; Thioredoxin-Disulfide Reductase/*chemistry/genetics ; }, abstract = {Thioredoxin reductase (TR) and thioredoxin constitute a major cellular redox system present in all organisms. In contrast to a single form of thioredoxin, there are two TR types: One (bacterial type or small TR) is present in bacteria, archaea, plants, and most unicellular eukaryotes, whereas the second (animal or large TR) is only found in animals and typically contains a carboxy-terminal penultimate selenocysteine encoded by TGA. Surprisingly, we detected sequences of large TRs in various unicellular eukaryotes. Moreover, green algae Chlamydomonas reinhardtii had both small and large TRs, with the latter being a selenoprotein, but no examples of horizontal gene transfer from animals to the green algae could be detected. In addition, phylogenetic analyses revealed that large TRs formed a subgroup of lower eukaryotic glutathione reductases (GRs). The data suggest that the large TR evolved in a lower eukaryote capable of selenocysteine insertion rather than in an animal. The enzyme appeared to evolve by a carboxy-terminal extension of GR such that the resulting carboxy-terminal glutathionelike peptide became an intramolecular substrate for GR and a reductant for thioredoxin. Subsequently, small TRs were lost in an organism that gave rise to animals, large TRs were lost in plants and fungi, and selenocysteine/cysteine replacements took place in some large TRs. Our data implicate carboxy-terminal extension of proteins as a general mechanism of evolution of new protein function.}, }
@article {pmid12535094, year = {2003}, author = {Rognon, X and Guyomard, R}, title = {Large extent of mitochondrial DNA transfer from Oreochromis aureus to O. niloticus in West Africa.}, journal = {Molecular ecology}, volume = {12}, number = {2}, pages = {435-445}, doi = {10.1046/j.1365-294x.2003.01739.x}, pmid = {12535094}, issn = {0962-1083}, mesh = {Africa, Western ; Amino Acid Sequence ; Animals ; Base Sequence ; Chimera ; Cichlids/*genetics ; Cytochrome b Group/genetics ; *DNA, Mitochondrial ; *Gene Transfer, Horizontal ; Genetic Variation ; Genetics, Population ; Isoenzymes/genetics ; Molecular Sequence Data ; Perciformes/genetics ; Phylogeny ; }, abstract = {Introgressive hybridization has an important evolutionary significance in terms of gene diversity and speciation. Among the major groups of vertebrates, fish show a strong propensity to hybridize. In order to highlight the possible occurrence of gene flow between two tilapia species, Oreochromis niloticus and O. aureus, a comparison of allozyme and mitochondrial DNA (mtDNA) polymorphism was performed on sympatric and allopatric populations of these two species. Nuclear data were congruent with the morphological identification of O. niloticus and O. aureus populations. In opposition, the mtDNA analysis resulted in two strictly differentiated groups which did not follow the morphological and nuclear DNA classification. The first group consisted of East African O. niloticus populations and the second included all the O. aureus populations and the West African O. niloticus populations. Moreover, in some cases, the same sequences were detected in both species. These data strongly support a differential introgression of mtDNA from O. aureus to O. niloticus involving all the West African area. This work points out the risk of misinterpretation of mtDNA or nuclear DNA data when only one single class of marker is used.}, }
@article {pmid12534464, year = {2002}, author = {Weinel, C and Nelson, KE and Tümmler, B}, title = {Global features of the Pseudomonas putida KT2440 genome sequence.}, journal = {Environmental microbiology}, volume = {4}, number = {12}, pages = {809-818}, doi = {10.1046/j.1462-2920.2002.00331.x}, pmid = {12534464}, issn = {1462-2912}, mesh = {Base Composition ; Chromosomes, Bacterial/genetics ; DNA Transposable Elements/genetics ; DNA, Bacterial/analysis/*genetics ; GC Rich Sequence ; Genes, Bacterial/genetics ; *Genome, Bacterial ; Microsatellite Repeats/genetics ; Open Reading Frames/genetics ; Pseudomonas putida/*genetics ; }, abstract = {The compositional bias of the G+C, di- and tetranucleotide contents in the 6 181 862 bp Pseudomonas putida KT2440 genome was analysed in sliding windows of 4000 bp in steps of 1000 bp. The genome has a low GC skew (mean 0.066) between the leading and lagging strand. The values of GC contents (mean 61.6%) and of dinucleotide relative abundance exhibit skewed Gaussian distributions. The variance of tetranucleotide frequencies, which increases linearly with increasing GC content, shows two overlapping Gaussian distributions of genome sections with low (minor fraction) or high variance (major fraction). Eighty per cent of the chromosome shares similar GC contents and oligonucleotide bias, but 105 islands of 4000 bp or more show atypical GC contents and/or oligonucleotide signature. Almost all islands provide added value to the metabolic proficiency of P. putida as a saprophytic omnivore. Major features are the uptake and degradation of organic chemicals, ion transport and the synthesis and secretion of secondary metabolites. Other islands endow P. putida with determinants of resistance and defenceor with constituents and appendages of the cell wall. A total of 29 islands carry the signature of mobile elements such as phage, transposons, insertion sequence (IS) elements and group II introns, indicating recent acquisition by horizontal gene transfer. The largest gene carries the most unusual sequence that encodes a multirepeat threonine-rich surface adhesion protein. Among the housekeeping genes, only genes of the translational apparatus were located in segments with an atypical signature, suggesting that the synthesis of ribosomal proteins is uncoupled from the rapidly changing translational demands of the cell by the separate utilization of tRNA pools.}, }
@article {pmid12533482, year = {2003}, author = {Williams, KP}, title = {Traffic at the tmRNA gene.}, journal = {Journal of bacteriology}, volume = {185}, number = {3}, pages = {1059-1070}, pmid = {12533482}, issn = {0021-9193}, support = {R01 GM059881/GM/NIGMS NIH HHS/United States ; GM 59881/GM/NIGMS NIH HHS/United States ; }, mesh = {Attachment Sites, Microbiological ; Bacterial Proteins/genetics ; Base Sequence ; Conserved Sequence ; Integrases/metabolism ; Membrane Proteins/genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Bacterial/chemistry/*genetics ; RNA, Transfer/*genetics ; Salmonella/genetics ; }, abstract = {A partial screen for genetic elements integrated into completely sequenced bacterial genomes shows more significant bias in specificity for the tmRNA gene (ssrA) than for any type of tRNA gene. Horizontal gene transfer, a major avenue of bacterial evolution, was assessed by focusing on elements using this single attachment locus. Diverse elements use ssrA; among enterobacteria alone, at least four different integrase subfamilies have independently evolved specificity for ssrA, and almost every strain analyzed presents a unique set of integrated elements. Even elements using essentially the same integrase can be very diverse, as is a group with an ssrA-specific integrase of the P4 subfamily. This same integrase appears to promote damage routinely at attachment sites, which may be adaptive. Elements in arrays can recombine; one such event mediated by invertible DNA segments within neighboring elements likely explains the monophasic nature of Salmonella enterica serovar Typhi. One of a limited set of conserved sequences occurs at the attachment site of each enterobacterial element, apparently serving as a transcriptional terminator for ssrA. Elements were usually found integrated into tRNA-like sequence at the 3' end of ssrA, at subsites corresponding to those used in tRNA genes; an exception was found at the non-tRNA-like 3' end produced by ssrA gene permutation in cyanobacteria, suggesting that, during the evolution of new site specificity by integrases, tropism toward a conserved 3' end of an RNA gene may be as strong as toward a tRNA-like sequence. The proximity of ssrA and smpB, which act in concert, was also surveyed.}, }
@article {pmid12529504, year = {2003}, author = {Faruque, SM and Kamruzzaman, M and Asadulghani,  and Sack, DA and Mekalanos, JJ and Nair, GB}, title = {CTXphi-independent production of the RS1 satellite phage by Vibrio cholerae.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {100}, number = {3}, pages = {1280-1285}, pmid = {12529504}, issn = {0027-8424}, mesh = {Bacteriophages/*genetics ; Blotting, Southern ; Cholera Toxin/*genetics ; DNA/*genetics ; *Gene Transfer, Horizontal ; Genes, Viral/genetics ; Genome, Bacterial ; Nucleic Acid Hybridization ; Plasmids/*metabolism ; Polymerase Chain Reaction ; Vibrio cholerae/genetics/*virology ; }, abstract = {The cholera toxin genes of Vibrio cholerae are encoded by the filamentous phage, CTXphi. Chromosomal CTXphi prophage DNA is often found flanked by copies of a related genetic element designated RS1, and RS1 DNA can be packaged into filamentous phage particles (designated RS1phi) by using the CTXphi morphogenesis genes. RS1phi is a satellite phage that further controls expression and dissemination of CTXphi. Here we describe a CTXphi-independent mechanism for production of RS1phi. A nontoxigenic environmental V. cholerae strain (55V71) was identified that supports production of RS1phi. However, newly infected CTX-negative strains did not produce RS1phi, indicating that additional 55V71 genes were involved in production of RS1phi. Analysis of nucleic acids from phage preparations of 55V71 revealed a 7.5-kb single-stranded DNA, whose corresponding replicative form was found in plasmid preparations. This DNA likely corresponds to the genome of a new filamentous phage, which we have designated KSF-1phi. The replicative form DNA of KSF-1phi was cloned into pUC18, and the resulting construct pKSF-1.1 supported the production of RS1phi particles by CTX-negative V. cholerae strains. RS1phi particles produced in this way infect recipient V. cholerae strains by a mechanism that is independent of the CTXphi receptor, the toxin-coregulated pilus. Thus, KSF-1phi is capable of facilitating the transfer of the RS1 element to strains that do not express toxin coregulated pilus. Given that RS1phi can enhance coproduction of CTXphi particles, KSF-1phi-mediated dissemination of RS1 may indirectly promote the spread of toxin genes among V. cholerae strains. This study also shows that filamentous phages can package diverse DNA elements and thus may play a role in horizontal transfer of more genes than previously appreciated.}, }
@article {pmid12526850, year = {2003}, author = {Ebert, D and Bull, JJ}, title = {Challenging the trade-off model for the evolution of virulence: is virulence management feasible?.}, journal = {Trends in microbiology}, volume = {11}, number = {1}, pages = {15-20}, doi = {10.1016/s0966-842x(02)00003-3}, pmid = {12526850}, issn = {0966-842X}, support = {GM57756/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics/pathogenicity ; *Biological Evolution ; Gene Transfer, Horizontal ; Host-Parasite Interactions ; Humans ; *Models, Theoretical ; Parasites/genetics/pathogenicity ; Selection, Genetic ; *Virulence ; Viruses/genetics/pathogenicity ; }, abstract = {Progress in understanding the evolution of infectious diseases has inspired proposals to manage the evolution of pathogen (including parasite) virulence. A common view is that social interventions that lower pathogen transmission will indirectly select lower virulence because of a trade-off between transmission and virulence. Here, we argue that there is little theoretical justification and no empirical evidence for this plan. Although a trade-off model might apply to some pathogens, the mechanism appears too weak for rapid selection of substantial changes in virulence. Direct selection against virulence itself might be a more rewarding approach to managing the evolution of virulence.}, }
@article {pmid12526846, year = {2003}, author = {Kotewicz, ML and Brown, EW and Eugene LeClerc, J and Cebula, TA}, title = {Genomic variability among enteric pathogens: the case of the mutS-rpoS intergenic region.}, journal = {Trends in microbiology}, volume = {11}, number = {1}, pages = {2-6}, doi = {10.1016/s0966-842x(02)00005-7}, pmid = {12526846}, issn = {0966-842X}, mesh = {Adenosine Triphosphatases/*genetics ; Bacterial Proteins/*genetics ; DNA, Intergenic/*genetics ; *DNA-Binding Proteins ; Enterobacteriaceae/classification/*genetics/pathogenicity ; Escherichia coli Proteins/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Models, Genetic ; MutS DNA Mismatch-Binding Protein ; Mutation ; Open Reading Frames ; Phylogeny ; Selection, Genetic ; Sigma Factor/*genetics ; }, abstract = {The mutS-rpoS intergenic region of enteric bacteria ranges in size from 88 bp in Yersinia to > 12000 bp in Salmonella. We interpret this expansion as the result of the horizontal transfer of segments of DNA from diverse origins. Both comparative genomic analysis and selective sequencing of a variety of Escherichia coli pathogens have provided additional evidence for reassortment of segments within this region.}, }
@article {pmid12519978, year = {2003}, author = {Garcia-Vallve, S and Guzman, E and Montero, MA and Romeu, A}, title = {HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes.}, journal = {Nucleic acids research}, volume = {31}, number = {1}, pages = {187-189}, pmid = {12519978}, issn = {1362-4962}, mesh = {Amino Acids/analysis ; Archaeal Proteins/chemistry ; Bacterial Proteins/chemistry ; Base Composition ; Codon ; *Databases, Genetic ; *Gene Transfer, Horizontal ; *Genome, Archaeal ; *Genome, Bacterial ; Open Reading Frames ; Phylogeny ; }, abstract = {The Horizontal Gene Transfer DataBase (HGT-DB) is a genomic database that includes statistical parameters such as G+C content, codon and amino-acid usage, as well as information about which genes deviate in these parameters for prokaryotic complete genomes. Under the hypothesis that genes from distantly related species have different nucleotide compositions, these deviated genes may have been acquired by horizontal gene transfer. The current version of the database contains 88 bacterial and archaeal complete genomes, including multiple chromosomes and strains. For each genome, the database provides statistical parameters for all the genes, as well as averages and standard deviations of G+C content, codon usage, relative synonymous codon usage and amino-acid content. It also provides information about correspondence analyses of the codon usage, plus lists of extraneous group of genes in terms of G+C content and lists of putatively acquired genes. With this information, researchers can explore the G+C content and codon usage of a gene when they find incongruities in sequence-based phylogenetic trees. A search engine that allows searches for gene names or keywords for a specific organism is also available. HGT-DB is freely accessible at http://www.fut.es/~debb/HGT.}, }
@article {pmid12515582, year = {2003}, author = {Mirkin, BG and Fenner, TI and Galperin, MY and Koonin, EV}, title = {Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes.}, journal = {BMC evolutionary biology}, volume = {3}, number = {}, pages = {2}, pmid = {12515582}, issn = {1471-2148}, mesh = {*Algorithms ; Amino Acid Sequence/genetics ; Archaeal Proteins/chemistry/genetics ; Bacterial Proteins/chemistry/genetics ; Computational Biology/*methods ; *Evolution, Molecular ; Gene Deletion ; Gene Transfer, Horizontal/*genetics ; *Genome ; Genome, Archaeal ; Genome, Bacterial ; Genome, Fungal ; Mathematical Computing ; Models, Genetic ; Molecular Sequence Data ; Saccharomyces cerevisiae Proteins/genetics ; }, abstract = {BACKGROUND: Comparative analysis of sequenced genomes reveals numerous instances of apparent horizontal gene transfer (HGT), at least in prokaryotes, and indicates that lineage-specific gene loss might have been even more common in evolution. This complicates the notion of a species tree, which needs to be re-interpreted as a prevailing evolutionary trend, rather than the full depiction of evolution, and makes reconstruction of ancestral genomes a non-trivial task.<br><br>RESULTS: We addressed the problem of constructing parsimonious scenarios for individual sets of orthologous genes given a species tree. The orthologous sets were taken from the database of Clusters of Orthologous Groups of proteins (COGs). We show that the phyletic patterns (patterns of presence-absence in completely sequenced genomes) of almost 90% of the COGs are inconsistent with the hypothetical species tree. Algorithms were developed to reconcile the phyletic patterns with the species tree by postulating gene loss, COG emergence and HGT (the latter two classes of events were collectively treated as gene gains). We prove that each of these algorithms produces a parsimonious evolutionary scenario, which can be represented as mapping of loss and gain events on the species tree. The distribution of the evolutionary events among the tree nodes substantially depends on the underlying assumptions of the reconciliation algorithm, e.g. whether or not independent gene gains (gain after loss after gain) are permitted. Biological considerations suggest that, on average, gene loss might be a more likely event than gene gain. Therefore different gain penalties were used and the resulting series of reconstructed gene sets for the last universal common ancestor (LUCA) of the extant life forms were analysed. The number of genes in the reconstructed LUCA gene sets grows as the gain penalty increases. However, qualitative examination of the LUCA versions reconstructed with different gain penalties indicates that, even with a gain penalty of 1 (equal weights assigned to a gain and a loss), the set of 572 genes assigned to LUCA might be nearly sufficient to sustain a functioning organism. Under this gain penalty value, the numbers of horizontal gene transfer and gene loss events are nearly identical. This result holds true for two alternative topologies of the species tree and even under random shuffling of the tree. Therefore, the results seem to be compatible with approximately equal likelihoods of HGT and gene loss in the evolution of prokaryotes.<br><br>CONCLUSIONS: The notion that gene loss and HGT are major aspects of prokaryotic evolution was supported by quantitative analysis of the mapping of the phyletic patterns of COGs onto a hypothetical species tree. Algorithms were developed for constructing parsimonious evolutionary scenarios, which include gene loss and gain events, for orthologous gene sets, given a species tree. This analysis shows, contrary to expectations, that the number of predicted HGT events that occurred during the evolution of prokaryotes might be approximately the same as the number of gene losses. The approach to the reconstruction of evolutionary scenarios employed here is conservative with regard to the detection of HGT because only patterns of gene presence-absence in sequenced genomes are taken into account. In reality, horizontal transfer might have contributed to the evolution of many other genes also, which makes it a dominant force in prokaryotic evolution.}, }
@article {pmid12511503, year = {2003}, author = {Christiansen, G and Fastner, J and Erhard, M and Börner, T and Dittmann, E}, title = {Microcystin biosynthesis in planktothrix: genes, evolution, and manipulation.}, journal = {Journal of bacteriology}, volume = {185}, number = {2}, pages = {564-572}, pmid = {12511503}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/*genetics/metabolism ; Cyanobacteria/*enzymology/genetics ; *Evolution, Molecular ; Gene Deletion ; Gene Expression Regulation, Bacterial ; Methyltransferases/chemistry/genetics/metabolism ; Microcystins ; Molecular Sequence Data ; Multigene Family ; Peptide Synthases/chemistry/*genetics/metabolism ; Peptides, Cyclic/*biosynthesis/chemistry/genetics ; *Transformation, Bacterial ; }, abstract = {Microcystins represent an extraordinarily large family of cyclic heptapeptide toxins that are nonribosomally synthesized by various cyanobacteria. Microcystins specifically inhibit the eukaryotic protein phosphatases 1 and 2A. Their outstanding variability makes them particularly useful for studies on the evolution of structure-function relationships in peptide synthetases and their genes. Analyses of microcystin synthetase genes provide valuable clues for the potential and limits of combinatorial biosynthesis. We have sequenced and analyzed 55.6 kb of the potential microcystin synthetase gene (mcy) cluster from the filamentous cyanobacterium Planktothrix agardhii CYA 126. The cluster contains genes for peptide synthetases (mcyABC), polyketide synthases (PKSs; mcyD), chimeric enzymes composed of peptide synthetase and PKS modules (mcyEG), a putative thioesterase (mcyT), a putative ABC transporter (mcyH), and a putative peptide-modifying enzyme (mcyJ). The gene content and arrangement and the sequence of specific domains in the gene products differ from those of the mcy cluster in Microcystis, a unicellular cyanobacterium. The data suggest an evolution of mcy clusters from, rather than to, genes for nodularin (a related pentapeptide) biosynthesis. Our data do not support the idea of horizontal gene transfer of complete mcy gene clusters between the genera. We have established a protocol for stable genetic transformation of Planktothrix, a genus that is characterized by multicellular filaments exhibiting continuous motility. Targeted mutation of mcyJ revealed its function as a gene coding for a O-methyltransferase. The mutant cells produce a novel microcystin variant exhibiting reduced inhibitory activity toward protein phosphatases.}, }
@article {pmid12497186, year = {2002}, author = {Stolz, JF and Basu, P and Oremland, RS}, title = {Microbial transformation of elements: the case of arsenic and selenium.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {5}, number = {4}, pages = {201-207}, doi = {10.1007/s10123-002-0091-y}, pmid = {12497186}, issn = {1139-6709}, mesh = {Adenosine Triphosphatases/metabolism ; Arsenic/*metabolism ; Arsenite Transporting ATPases ; Bacteria/classification/enzymology/*metabolism ; Biotransformation ; Ion Pumps/metabolism ; Multienzyme Complexes/metabolism ; Oxidoreductases/metabolism ; Phylogeny ; Selenium/*metabolism ; }, abstract = {Microbial activity is responsible for the transformation of at least one third of the elements in the periodic table. These transformations are the result of assimilatory, dissimilatory, or detoxification processes and form the cornerstones of many biogeochemical cycles. Arsenic and selenium are two elements whose roles in microbial ecology have only recently been recognized. Known as "essential toxins", they are required in trace amounts for growth and metabolism but are toxic at elevated concentrations. Arsenic is used as an osmolite in some marine organisms while selenium is required as selenocysteine (i.e. the twenty-first amino acid) or as a ligand to metal in some enzymes (e.g. FeNiSe hydrogenase). Arsenic resistance involves a small-molecular-weight arsenate reductase (ArsC). The use of arsenic and selenium oxyanions for energy is widespread in prokaryotes with representative organisms from the Crenarchaeota, thermophilic bacteria, low and high G+C gram-positive bacteria, and Proteobacteria. Recent studies have shown that both elements are actively cycled and play a significant role in carbon mineralization in certain environments. The occurrence of multiple mechanisms involving different enzymes for arsenic and selenium transformation indicates several different evolutionary pathways (e.g. convergence and lateral gene transfer) and underscores the environmental significance and selective impact in microbial evolution of these two elements.}, }
@article {pmid12486522, year = {2002}, author = {Garcia-Vallvé, S and Simó, FX and Montero, MA and Arola, L and Romeu, A}, title = {Simultaneous horizontal gene transfer of a gene coding for ribosomal protein l27 and operational genes in Arthrobacter sp.}, journal = {Journal of molecular evolution}, volume = {55}, number = {6}, pages = {632-637}, doi = {10.1007/s00239-002-2358-5}, pmid = {12486522}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Arthrobacter/*genetics ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Molecular Sequence Data ; Phylogeny ; Ribosomal Proteins/chemistry/*genetics ; Sequence Homology, Amino Acid ; }, abstract = {Phylogenetic analysis of bacterial L27 ribosomal proteins showed that, against taxonomy, the L27 protein from the Actinobacteria Arthrobacter sp. clusters with protein sequences from the Bacillus group. The L27 gene clusters in the Arthrobacter sp. genome with six genes responsible for creatinine and sarcosine degradation. Phylogenetic analyses of orthologue proteins encoded by three of these genes also showed a phylogenetic relationship with Bacillus species. Comparisons between the synonymous codon usage of the Arthrobacter sp. genes and those from complete genomes showed that Arthrobacter genes encoding the L27 ribosomal protein and the proteins responsible for the degradation of creatinine and sarcosine have a codon usage that is more similar to that of Bacillus species than that of Arthrobacter. We suggest that the Arthrobacter sp. genes encoding the L27 ribosomal protein and the proteins responsible for the degradation of creatinine and sarcosine were acquired simultaneously through horizontal gene transfer from an unknown Bacillus species.}, }
@article {pmid12485326, year = {2002}, author = {Kaplan, JB and Kokeguchi, S and Murayama, Y and Fine, DH}, title = {Sequence diversity in the major fimbrial subunit gene (flp-1) of Actinobacillus actinomycetemcomitans.}, journal = {Oral microbiology and immunology}, volume = {17}, number = {6}, pages = {354-359}, doi = {10.1034/j.1399-302x.2002.170604.x}, pmid = {12485326}, issn = {0902-0055}, mesh = {Actinobacillus Infections/physiopathology ; Adult ; Aggregatibacter actinomycetemcomitans/*genetics/pathogenicity ; Aggressive Periodontitis/microbiology ; Alleles ; Bacterial Adhesion/genetics ; Bacterial Proteins/*genetics ; Conserved Sequence/genetics ; DNA Transposable Elements/genetics ; DNA, Bacterial/genetics ; Female ; Fimbriae Proteins/genetics ; Fimbriae, Bacterial/*genetics ; Gene Transfer, Horizontal/genetics ; Genetic Variation/*genetics ; Genotype ; Humans ; Male ; Periodontitis/microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Analysis, Protein ; Serotyping ; Virulence/genetics ; }, abstract = {Cells of the periodontal pathogen Actinobacillus actinomycetemcomitans exhibit tight adherence to surfaces such as glass, plastic and hydroxyapatite, a property that probably plays an important role in the ability of this bacterium to colonize teeth and other surfaces. Tight adherence is mediated by long fibrils of bundled pili (fimbriae) that form on the surface of the cell. The flp-1 gene encodes the major pilin protein component of A. actinomycetemcomitans fimbriae. In this study we compared flp-1 DNA sequences from 43 strains of A. actinomycetemcomitans isolated in Europe, Japan and the United States and identified seven distinct flp-1 allelic classes. DNA and predicted protein sequences were almost completely conserved within each flp-1 class but were highly divergent between classes. Most amino acid substitutions occurred in the C-terminus of the pilin protein, a region that has been shown to be important for the bundling and adhesive properties of the pili. flp-1 classes correlated with serotypes and 16S rRNA genotypes in most strains. At least five strains showed evidence of horizontal transfer of flp-1 between strains of different serotypes and 16S rRNA genotypes. Four of the seven flp-1 classes were present in geographically diverse isolates. Strains representing all seven flp-1 classes, but not a strain carrying a transposon insertion in flp-1, bound avidly to polystyrene in an in vitro adherence assay. Strains representing six of the seven flp-1 classes were isolated from localized juvenile periodontitis patients, suggesting that phylogenetically diverse strains carry pathogenic potential. Our findings provide a framework for future biochemical, immunological and genetic studies of A. actinomycetemcomitans fimbriae.}, }
@article {pmid12481129, year = {2002}, author = {Funes, S and Davidson, E and Reyes-Prieto, A and Magallón, S and Herion, P and King, MP and González-Halphen, D}, title = {A green algal apicoplast ancestor.}, journal = {Science (New York, N.Y.)}, volume = {298}, number = {5601}, pages = {2155}, doi = {10.1126/science.1076003}, pmid = {12481129}, issn = {1095-9203}, support = {HL59646/HL/NHLBI NIH HHS/United States ; TW01176/TW/FIC NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Apicomplexa/enzymology/*genetics/ultrastructure ; *Biological Evolution ; Cell Nucleus/genetics ; Chlamydomonas reinhardtii/enzymology/genetics ; Chlorophyta/enzymology/*genetics ; Cloning, Molecular ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/chemistry/*genetics ; *Gene Transfer, Horizontal ; Genes ; Genes, Protozoan ; Molecular Sequence Data ; Phylogeny ; Plastids/*genetics ; Symbiosis ; Toxoplasma/enzymology/genetics ; }, }
@article {pmid12481111, year = {2002}, author = {Pennisi, E}, title = {Comparative genomics. Tunicate genome shows a little backbone.}, journal = {Science (New York, N.Y.)}, volume = {298}, number = {5601}, pages = {2111-2112}, doi = {10.1126/science.298.5601.2111a}, pmid = {12481111}, issn = {1095-9203}, mesh = {Animals ; Biological Evolution ; Cellulose/biosynthesis ; Ciona intestinalis/anatomy &amp; histology/classification/*genetics/physiology ; Computational Biology ; Gene Dosage ; Gene Transfer, Horizontal ; Genes ; *Genome ; Humans ; *Sequence Analysis, DNA ; Species Specificity ; Vertebrates/classification/genetics ; }, }
@article {pmid12480877, year = {2002}, author = {Saunders, NJ and Snyder, LAS}, title = {The minimal mobile element.}, journal = {Microbiology (Reading, England)}, volume = {148}, number = {Pt 12}, pages = {3756-3760}, doi = {10.1099/00221287-148-12-3756}, pmid = {12480877}, issn = {1350-0872}, mesh = {Bacterial Proteins/genetics ; Base Sequence ; DNA Transposable Elements/*genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Molecular Sequence Data ; Neisseria/classification/*genetics ; Phenylalanine-tRNA Ligase/genetics ; *Recombination, Genetic ; Serotyping ; }, }
@article {pmid12480111, year = {2002}, author = {Zhang, S and Santos, RL and Tsolis, RM and Mirold, S and Hardt, WD and Adams, LG and Bäumler, AJ}, title = {Phage mediated horizontal transfer of the sopE1 gene increases enteropathogenicity of Salmonella enterica serotype Typhimurium for calves.}, journal = {FEMS microbiology letters}, volume = {217}, number = {2}, pages = {243-247}, doi = {10.1111/j.1574-6968.2002.tb11482.x}, pmid = {12480111}, issn = {0378-1097}, support = {AI40124/AI/NIAID NIH HHS/United States ; AI44170/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacterial Proteins/*genetics/metabolism ; Bacteriophages/*genetics ; Cattle ; Cattle Diseases/*microbiology ; Enterobacteriaceae/pathogenicity ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Intestines/microbiology/pathology ; Lysogeny/genetics ; Male ; Salmonella Infections, Animal/*microbiology ; Salmonella typhimurium/genetics/metabolism/*pathogenicity ; }, abstract = {Epidemiological evidence shows that the sopE1 gene is associated with Salmonella Typhimurium phage types causing epidemics in cattle. In this study we demonstrate that horizontal transfer of the sopE1 gene by lysogenic conversion with the SopEphi increased enteropathogenicity of S. Typhimurium in the bovine ligated ileal loop model. These data support the hypothesis that phage mediated horizontal transfer of the sopE1 gene contributes to the emergence of epidemic cattle-associated S. Typhimurium clones.}, }
@article {pmid12473656, year = {2003}, author = {Zhang, K and Kurachi, S and Kurachi, K}, title = {Limitation in use of heterologous reporter genes for gene promoter analysis. Silencer activity associated with the cloramphenicol acetyltransferase reporter gene.}, journal = {The Journal of biological chemistry}, volume = {278}, number = {7}, pages = {4826-4830}, doi = {10.1074/jbc.M211361200}, pmid = {12473656}, issn = {0021-9258}, support = {5-P60-AR-20557/AR/NIAMS NIH HHS/United States ; 5P60 DK20572/DK/NIDDK NIH HHS/United States ; HL38644/HL/NHLBI NIH HHS/United States ; HL64522/HL/NHLBI NIH HHS/United States ; M01-RR-00042/RR/NCRR NIH HHS/United States ; }, mesh = {*Artifacts ; Cell Line ; *Chloramphenicol O-Acetyltransferase ; Factor IX/analysis/*genetics ; Gene Expression Regulation ; Gene Transfer, Horizontal ; *Genes, Reporter ; Humans ; Promoter Regions, Genetic/*genetics ; Protein C/analysis/*genetics ; Silencer Elements, Transcriptional/genetics ; }, abstract = {Various heterologous reporter genes have been widely used for the functional characterization of gene promoters. Many such studies often found weak to very strong silencer activities to be associated with specific parts of the basal promoter or further upstream regions. In this study, we carried out a systematic study on human blood coagulation factor IX (hFIX) and anti-coagulant protein C (hPC) genes, previously shown to have silencer activities associated with their 5'-flanking regions containing promoter sequences. With newly constructed chloramphenicol acetyltransferase (CAT) reporter vectors carrying hFIX or hPC gene promoter sequences, we confirmed the strong silencer activities associated with the regions nt -1895 through nt -416 of the hFIX gene or with the region nt -802 through nt -82 of the hPC gene. However, no such silencer activities associated with the specific regions were found when autologous hFIX cDNA, hFIX minigenes, or hPC minigenes were used as reporters in the expression vector system. Relative levels of CAT, hFIX, and hPC proteins produced in the transient assays correlated well with their mRNA levels. Human FIX minigene constructs containing a simian virus 40 (SV40) 3'-untranslated region (UTR) taken from the CAT reporter gene showed no silencer activity, indicating that SV40 3'-UTR sequence of the CAT reporter gene does not contribute to the silencer activity. Expression vectors constructed with the beta-galactosidase gene under the control of hFIX gene promoter sequences also showed no silencer activity associated with the region nt -1895 through nt -416. These findings indicate that silencer activities associated with specific regions of promoter sequences as analyzed with CAT reporter genes may represent artifacts specific to the CAT reporter genes. Our findings strongly suggest a need for re-examination of promoter characterizations of many eukaryotic genes, which have been studied to date with CAT reporter genes.}, }
@article {pmid12455964, year = {2002}, author = {Andersson, JO and Roger, AJ}, title = {Evolutionary analyses of the small subunit of glutamate synthase: gene order conservation, gene fusions, and prokaryote-to-eukaryote lateral gene transfers.}, journal = {Eukaryotic cell}, volume = {1}, number = {2}, pages = {304-310}, pmid = {12455964}, issn = {1535-9778}, mesh = {Amino Acid Sequence ; Animals ; Artificial Gene Fusion ; Cytochrome c Group/genetics ; Diplomonadida/classification/*genetics ; Eubacterium/genetics ; Eukaryotic Cells/*enzymology ; *Evolution, Molecular ; *Gene Order ; *Gene Transfer, Horizontal ; Genes, Protozoan ; Glutamate Synthase/*genetics ; Molecular Sequence Data ; Operon ; Oxidoreductases/genetics ; Phylogeny ; Prokaryotic Cells/*enzymology ; Protein Subunits ; Sequence Homology, Amino Acid ; }, abstract = {Lateral gene transfer has been identified as an important mode of genome evolution within prokaryotes. Except for the special case of gene transfer from organelle genomes to the eukaryotic nucleus, only a few cases of lateral gene transfer involving eukaryotes have been described. Here we present phylogenetic and gene order analyses on the small subunit of glutamate synthase (encoded by gltD) and its homologues, including the large subunit of sulfide dehydrogenase (encoded by sudA). The scattered distribution of the sudA and sudB gene pair and the phylogenetic analysis strongly suggest that lateral gene transfer was involved in the propagation of the genes in the three domains of life. One of these transfers most likely occurred between a prokaryote and an ancestor of diplomonad protists. Furthermore, phylogenetic analyses indicate that the gene for the small subunit of glutamate synthase was transferred from a low-GC gram-positive bacterium to a common ancestor of animals, fungi, and plants. Interestingly, in both examples, the eukaryotes encode a single gene that corresponds to a conserved operon structure in prokaryotes. Our analyses, together with several recent publications, show that lateral gene transfers from prokaryotes to unicellular eukaryotes occur with appreciable frequency. In the case of the genes for sulfide dehydrogenase, the transfer affected only a limited group of eukaryotes--the diplomonads--while the transfer of the glutamate synthase gene probably happened earlier in evolution and affected a wider range of eukaryotes.}, }
@article {pmid12455953, year = {2002}, author = {Nixon, JE and Wang, A and Field, J and Morrison, HG and McArthur, AG and Sogin, ML and Loftus, BJ and Samuelson, J}, title = {Evidence for lateral transfer of genes encoding ferredoxins, nitroreductases, NADH oxidase, and alcohol dehydrogenase 3 from anaerobic prokaryotes to Giardia lamblia and Entamoeba histolytica.}, journal = {Eukaryotic cell}, volume = {1}, number = {2}, pages = {181-190}, pmid = {12455953}, issn = {1535-9778}, support = {R01 AI046516/AI/NIAID NIH HHS/United States ; AI43273/AI/NIAID NIH HHS/United States ; R01 AI048082/AI/NIAID NIH HHS/United States ; AI46516/AI/NIAID NIH HHS/United States ; AI33492/AI/NIAID NIH HHS/United States ; }, mesh = {Alcohol Dehydrogenase/analysis/genetics ; Amino Acid Sequence ; Anaerobiosis ; Animals ; Bacteria/genetics ; Entamoeba histolytica/enzymology/*genetics ; Fermentation ; Ferredoxins/analysis/classification/*genetics ; *Gene Transfer, Horizontal ; Giardia lamblia/enzymology/*genetics ; Iron-Sulfur Proteins/genetics ; Mitochondria/genetics ; Models, Biological ; Molecular Sequence Data ; Multienzyme Complexes/analysis/genetics ; NADH, NADPH Oxidoreductases/analysis/genetics ; Nitroreductases/analysis/classification/genetics ; Oxidoreductases/*genetics ; Phylogeny ; Prokaryotic Cells/metabolism ; Sequence Alignment ; Sequence Analysis, Protein ; }, abstract = {Giardia lamblia and Entamoeba histolytica are amitochondriate, microaerophilic protists which use fermentation enzymes like those of bacteria to survive anaerobic conditions within the intestinal lumen. Genes encoding fermentation enzymes and related electron transport peptides (e.g., ferredoxins) in giardia organisms and amebae are hypothesized to be derived from either an ancient anaerobic eukaryote (amitochondriate fossil hypothesis), a mitochondrial endosymbiont (hydrogen hypothesis), or anaerobic bacteria (lateral transfer hypothesis). The goals here were to complete the molecular characterization of giardial and amebic fermentation enzymes and to determine the origins of the genes encoding them, when possible. A putative giardia [2Fe-2S]ferredoxin which had a hypothetical organelle-targeting sequence at its N terminus showed similarity to mitochondrial ferredoxins and the hydrogenosomal ferredoxin of Trichomonas vaginalis (another luminal protist). However, phylogenetic trees were star shaped, with weak bootstrap support, so we were unable to confirm or rule out the endosymbiotic origin of the giardia [2Fe-2S]ferredoxin gene. Putative giardial and amebic 6-kDa ferredoxins, ferredoxin-nitroreductase fusion proteins, and oxygen-insensitive nitroreductases each tentatively supported the lateral transfer hypothesis. Although there were not enough sequences to perform meaningful phylogenetic analyses, the unique common occurrence of these peptides and enzymes in giardia organisms, amebae, and the few anaerobic prokaryotes suggests the possibility of lateral transfer. In contrast, there was more robust phylogenetic evidence for the lateral transfer of G. lamblia genes encoding an NADH oxidase from a gram-positive coccus and a microbial group 3 alcohol dehydrogenase from thermoanaerobic prokaryotes. In further support of lateral transfer, the G. lamblia NADH oxidase and adh3 genes appeared to have an evolutionary history distinct from those of E. histolytica.}, }
@article {pmid12454168, year = {2002}, author = {Simjee, S and White, DG and McDermott, PF and Wagner, DD and Zervos, MJ and Donabedian, SM and English, LL and Hayes, JR and Walker, RD}, title = {Characterization of Tn1546 in vancomycin-resistant Enterococcus faecium isolated from canine urinary tract infections: evidence of gene exchange between human and animal enterococci.}, journal = {Journal of clinical microbiology}, volume = {40}, number = {12}, pages = {4659-4665}, pmid = {12454168}, issn = {0095-1137}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Carbon-Oxygen Ligases/genetics ; *Conjugation, Genetic ; DNA Transposable Elements/*genetics ; Dog Diseases/*microbiology ; Dogs ; Drug Resistance, Multiple, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Enterococcus faecium/*drug effects/genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; Gentamicins/pharmacology ; Gram-Positive Bacterial Infections/microbiology/veterinary ; Humans ; Microbial Sensitivity Tests ; Plasmids/genetics ; Urinary Tract Infections/microbiology/*veterinary ; Vancomycin/pharmacology ; Vancomycin Resistance/*genetics ; }, abstract = {Thirty-five enterococcal isolates were recovered from dogs diagnosed with urinary tract infections at the Michigan State University Veterinary Teaching Hospital over a 2-year period (1996 to 1998). Isolated species included Enterococcus faecium (n = 13), Enterococcus faecalis (n = 7), Enterococcus gallinarum (n = 11), and Enterococcus casseliflavus (n = 4). Antimicrobial susceptibility testing revealed several different resistance phenotypes, with the majority of the enterococcal isolates exhibiting resistance to three or more antibiotics. One E. faecium isolate, CVM1869, displayed high-level resistance to vancomycin (MIC > 32 micro g/ml) and gentamicin (MIC > 2,048 micro g/ml). Molecular analysis of this isolate revealed the presence of Tn1546 (vanA), responsible for high-level vancomycin resistance, and Tn5281 carrying aac6'-aph2", conferring high-level aminoglycoside resistance. Pulsed-field gel electrophoresis analysis revealed that CVM1869 was a canine E. faecium clone that had acquired Tn1546, perhaps from a human vancomycin-resistant E. faecium. Transposons Tn5281 and Tn1546 were located on two different conjugative plasmids. Sequence analysis revealed that in Tn1546, ORF1 had an 889-bp deletion and an IS1216V insertion at the 5' end and an IS1251 insertion between vanS and vanH. To date, this particular form of Tn1546 has only been described in human clinical vancomycin-resistant enterococcus isolates unique to the United States. Additionally, this is the first report of a vancomycin-resistant E. faecium isolated from a companion animal in the United States.}, }
@article {pmid12452951, year = {2002}, author = {Tuohy, K and Davies, M and Rumsby, P and Rumney, C and Adams, MR and Rowland, IR}, title = {Monitoring transfer of recombinant and nonrecombinant plasmids between Lactococcus lactis strains and members of the human gastrointestinal microbiota in vivo--impact of donor cell number and diet.}, journal = {Journal of applied microbiology}, volume = {93}, number = {6}, pages = {954-964}, doi = {10.1046/j.1365-2672.2002.01770.x}, pmid = {12452951}, issn = {1364-5072}, mesh = {Animals ; Bacteriological Techniques ; Colony Count, Microbial ; Dietary Fats/*administration &amp; dosage ; Enterococcus/*genetics ; Feces/microbiology ; Female ; *Gene Transfer, Horizontal ; Germ-Free Life ; Humans ; Lactobacillus/*genetics ; Male ; Models, Biological ; *Organisms, Genetically Modified ; Probiotics ; Rats ; Rats, Inbred F344 ; Recombinant Proteins/genetics ; }, abstract = {AIMS: The generation of data of real relevance to the purported risks of DNA transfer from food-borne genetically modified microorganisms (GMMOs) using the human biota associated (HBA) rat model. Plasmid transfer between Lactococcus lactis strains and between donor strains and human gut bacteria was monitored.<br><br>METHODS AND RESULTS: Transfer of the recombinant plasmid pCK1 and/or the promiscuous nonrecombinant plasmid pAMbeta1 between L. lactis strains was monitored in vivo in HBA rats. No transfer of pCK1 was observed. Transfer of pAMbeta1 was observed to Enterococcus spp. present in the HBA rats. Transconjugants persisted for 30 d and were distributed throughout the gastrointestinal tract. Both HBA rat diet and donor cell numbers impacted on transconjugant numbers. Fewer transconjugants were observed in animals fed a high-fat human type diet, while high levels of plasmid transfer were only observed at doses of donor L. lactis greater than 109 cfu.<br><br>CONCLUSIONS: The utility of models of the human gut in monitoring DNA transfer events within the gut microbiota was demonstrated.<br><br>Such findings give some confidence for the use of GMMOs with recombinant DNA borne on nonconjugative elements in fermented foods. HBA rats are a suitable model for monitoring the fate of food-borne GMMOs.}, }
@article {pmid12448756, year = {2002}, author = {Clark, IM and Mendum, TA and Hirsch, PR}, title = {The influence of the symbiotic plasmid pRL1JI on the distribution of GM rhizobia in soil and crop rhizospheres, and implications for gene flow.}, journal = {Antonie van Leeuwenhoek}, volume = {81}, number = {1-4}, pages = {607-616}, doi = {10.1023/a:1020574009445}, pmid = {12448756}, issn = {0003-6072}, support = {BBS/E/C/00004175/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacterial Proteins/genetics ; Crops, Agricultural/*microbiology ; DNA Transposable Elements ; Gene Transfer, Horizontal ; Genetics, Population ; Hordeum/microbiology ; Medicago sativa/microbiology ; *Organisms, Genetically Modified ; Pisum sativum/microbiology ; Plant Roots/*microbiology ; *Plasmids ; Polymerase Chain Reaction ; Rhizobium leguminosarum/*genetics/growth &amp; development ; *Soil Microbiology ; Symbiosis ; }, abstract = {The distribution of two genetically modified Rhizobium leguminosarum strains was investigated in the field. One, RSM2004, released in 1987, carries a TnS marker on its conjugative symbiotic plasmid (pSym). The second, CT0370, released at the same site in 1994, has a gusA gene integrated into its chromosome but no pSym. Plate counts indicated that the CT0370 population became established at a higher level than RSM2004. However, when peas, alfalfa and barley were grown, RSM2004 was found to outnumber CT0370 on all roots and by 100-fold on pea. Although the transfer of pSym from RSM2004 to CT0370 could be detected on plates and in microcosm studies with high inoculum densities, no transfer was detected in the field. Subsequent transfer of pSym from RSM2004 to CT0370 demonstrated that it conferred an advantage in the rhizosphere. In addition to increasing host fitness, plasmids may transfer, or mobilise other genetic elements, to other bacteria. This is more likely in sites such as the rhizosphere, where cells are active and numbers are high. The distribution of pSym and other genetic elements associated with rhizobia, in bacterial sub-populations from the soil and roots of the different plants, was investigated using PCR. The genetic elements studied were: ISRm3, an insertion element from Sinorhizobium meliloti; pSB 102, a broad host range mer plasmid; the Rhizobium nodC gene (carried on pSym) and plasmid replication origins repCI and repCII. As expected, ISRm3 was detected in rhizoflora cultured from alfalfa but not the other plants. The mer gene was ubiquitous but the transfer region of pSB 102 was not detected. The nodC and both repC primers amplified products from all the plants, giving further evidence for the occurrence of plasmids originating from Rhizobium in the rhizoflora of non-host plants. Despite the abundance of elements associated with transferable plasmids in rhizobia, none was detected in either inoculant strain.}, }
@article {pmid12448717, year = {2002}, author = {Stahl, DA and Fishbain, S and Klein, M and Baker, BJ and Wagner, M}, title = {Origins and diversification of sulfate-respiring microorganisms.}, journal = {Antonie van Leeuwenhoek}, volume = {81}, number = {1-4}, pages = {189-195}, doi = {10.1023/a:1020506415921}, pmid = {12448717}, issn = {0003-6072}, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Variation ; Oxidoreductases Acting on Sulfur Group Donors/*genetics/metabolism ; Sulfates/*metabolism ; Sulfur-Reducing Bacteria/enzymology/*genetics ; }, abstract = {If the diversification of microbial life can be depicted as a single tree, as inferred by comparative sequencing of ribosomal RNAs, this could provide a framework for defining the order of emergence of new metabolic pathways. However, recent recognition that lateral gene transfer has been a significant force in microbial evolution has created uncertainty about the interpretation of taxonomies based on gene sequences. In this context, the origins and evolution of sulfate respiration will be evaluated considering the evolutionary history of a central enzyme in this process, the dissimilatory sulfite reductase. These studies suggest at least two major lateral transfer events during the early diversification of sulfate respiring microorganisms. The high sequence conservation of this enzyme has also provided a mechanism to directly explore the natural diversity of sulfate-respiring organisms using molecular techniques, avoiding the bias of culture-based identification. These studies suggest that the habitat range and evolutionary diversity of this key functional group of organisms is greater than now appreciated.}, }
@article {pmid12447999, year = {2002}, author = {Praus, M and Collen, D and Gerard, RD}, title = {Both u-PA inhibition and vitronectin binding by plasminogen activator inhibitor 1 regulate HT1080 fibrosarcoma cell metastasis.}, journal = {International journal of cancer}, volume = {102}, number = {6}, pages = {584-591}, doi = {10.1002/ijc.10767}, pmid = {12447999}, issn = {0020-7136}, mesh = {Animals ; Cell Movement ; Female ; Fibrosarcoma/*pathology/*secondary ; Gene Transfer, Horizontal ; Humans ; Mice ; Plasminogen Activator Inhibitor 1/*physiology ; Tumor Cells, Cultured ; Urokinase-Type Plasminogen Activator/*antagonists &amp; inhibitors ; Vitronectin/*metabolism ; }, abstract = {Overexpression of plasminogen activator inhibitor 1 (PAI-1) reduces tumor cell migration in vitro and metastasis in mice in vivo by mechanisms involving either inhibition of urokinase plasminogen activator (u-PA) activity or competition for an integrin binding site on vitronectin. To analyze the effects of PAI-1 on tumor cell migration in vitro and metastasis in vivo, recombinant adenoviral vectors expressing wild-type or mutant PAI-1 proteins were constructed. The mutant PAI-1 proteins were defective in either vitronectin binding (PAI-1(VN-)), plasminogen activator inhibition (PAI-1(INH-)) or both (PAI-1(VN-,INH-)). In vitro, migration of HT1080 human fibrosarcoma cells through a reconstituted extracellular matrix (ECM) was reduced 73% by overexpression of wild-type PAI-1 and 65% by PAI-1(VN-) compared with control virus-infected cells. Migration of cells infected by virus expressing either PAI-1(INH-) or PAI-1(VN-,INH-) was unaffected, indicating a requirement for plasminogen activator inhibitory activity. In vivo, however, only overexpression of wild-type PAI-1 reduced the burden of metastasis by 68% compared with the control group. This indicates that both u-PA inhibition and PAI-1 ECM interactions contribute to the mechanism of PAI-1-mediated regulation of cell migration.}, }
@article {pmid12446909, year = {2002}, author = {Raymond, J and Zhaxybayeva, O and Gogarten, JP and Gerdes, SY and Blankenship, RE}, title = {Whole-genome analysis of photosynthetic prokaryotes.}, journal = {Science (New York, N.Y.)}, volume = {298}, number = {5598}, pages = {1616-1620}, doi = {10.1126/science.1075558}, pmid = {12446909}, issn = {1095-9203}, mesh = {Bacteria/*genetics/metabolism ; Chlorobi/genetics/metabolism ; Computational Biology ; Cyanobacteria/*genetics/metabolism ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Archaeal ; *Genome, Bacterial ; Likelihood Functions ; Photosynthesis/*genetics ; Rhodobacter capsulatus/genetics/metabolism ; Sequence Analysis, DNA ; }, abstract = {The process of photosynthesis has had profound global-scale effects on Earth; however, its origin and evolution remain enigmatic. Here we report a whole-genome comparison of representatives from all five groups of photosynthetic prokaryotes and show that horizontal gene transfer has been pivotal in their evolution. Excluding a small number of orthologs that show congruent phylogenies, the genomes of these organisms represent mosaics of genes with very different evolutionary histories. We have also analyzed a subset of "photosynthesis-specific" genes that were elucidated through a differential genome comparison. Our results explain incoherencies in previous data-limited phylogenetic analyses of phototrophic bacteria and indicate that the core components of photosynthesis have been subject to lateral transfer.}, }
@article {pmid12446882, year = {2002}, author = {Pennisi, E}, title = {Evolutionary biology. Bacteria shared photosynthesis genes.}, journal = {Science (New York, N.Y.)}, volume = {298}, number = {5598}, pages = {1538-1539}, doi = {10.1126/science.298.5598.1538b}, pmid = {12446882}, issn = {1095-9203}, mesh = {Bacteria/*genetics/metabolism ; Computational Biology ; Cyanobacteria/genetics/metabolism ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Genome, Bacterial ; Photosynthesis/*genetics ; Sequence Analysis, DNA ; }, }
@article {pmid12446813, year = {2002}, author = {Gogarten, JP and Doolittle, WF and Lawrence, JG}, title = {Prokaryotic evolution in light of gene transfer.}, journal = {Molecular biology and evolution}, volume = {19}, number = {12}, pages = {2226-2238}, doi = {10.1093/oxfordjournals.molbev.a004046}, pmid = {12446813}, issn = {0737-4038}, mesh = {*Evolution, Molecular ; *Gene Transfer, Horizontal ; Phylogeny ; Prokaryotic Cells ; }, abstract = {Accumulating prokaryotic gene and genome sequences reveal that the exchange of genetic information through both homology-dependent recombination and horizontal (lateral) gene transfer (HGT) is far more important, in quantity and quality, than hitherto imagined. The traditional view, that prokaryotic evolution can be understood primarily in terms of clonal divergence and periodic selection, must be augmented to embrace gene exchange as a creative force, itself responsible for much of the pattern of similarities and differences we see between prokaryotic microbes. Rather than replacing periodic selection on genetic diversity, gene loss, and other chromosomal alterations as important players in adaptive evolution, gene exchange acts in concert with these processes to provide a rich explanatory paradigm-some of whose implications we explore here. In particular, we discuss (1) the role of recombination and HGT in giving phenotypic "coherence" to prokaryotic taxa at all levels of inclusiveness, (2) the implications of these processes for the reconstruction and meaning of "phylogeny," and (3) new views of prokaryotic adaptation and diversification based on gene acquisition and exchange.}, }
@article {pmid12446797, year = {2002}, author = {Holland, BR and Huber, KT and Dress, A and Moulton, V}, title = {Delta plots: a tool for analyzing phylogenetic distance data.}, journal = {Molecular biology and evolution}, volume = {19}, number = {12}, pages = {2051-2059}, doi = {10.1093/oxfordjournals.molbev.a004030}, pmid = {12446797}, issn = {0737-4038}, mesh = {*Models, Genetic ; *Phylogeny ; Polymorphism, Restriction Fragment Length ; Recombination, Genetic ; }, abstract = {A method is described that allows the assessment of treelikeness of phylogenetic distance data before tree estimation. This method is related to statistical geometry as introduced by Eigen, Winkler-Oswatitsch, and Dress (1988 [Proc. Natl. Acad. Sci. USA. 85:5913-5917]), and in essence, displays a measure for treelikeness of quartets in terms of a histogram that we call a delta plot. This allows identification of nontreelike data and analysis of noisy data sets arising from processes such as, for example, parallel evolution, recombination, or lateral gene transfer. In addition to an overall assessment of treelikeness, individual taxa can be ranked by reference to the treelikeness of the quartets to which they belong. Removal of taxa on the basis of this ranking results in an increase in accuracy of tree estimation. Recombinant data sets are simulated, and the method is shown to be capable of identifying single recombinant taxa on the basis of distance information alone, provided the parents of the recombinant sequence are sufficiently divergent and the mixture of tree histories is not strongly skewed toward a single tree. delta Plots and taxon rankings are applied to three biological data sets using distances derived from sequence alignment, gene order, and fragment length polymorphism.}, }
@article {pmid12446643, year = {2002}, author = {Calcutt, MJ and Lewis, MS and Wise, KS}, title = {Molecular genetic analysis of ICEF, an integrative conjugal element that is present as a repetitive sequence in the chromosome of Mycoplasma fermentans PG18.}, journal = {Journal of bacteriology}, volume = {184}, number = {24}, pages = {6929-6941}, pmid = {12446643}, issn = {0021-9193}, support = {R01 AI047937/AI/NIAID NIH HHS/United States ; AI32219/AI/NIAID NIH HHS/United States ; AI47937/AI/NIAID NIH HHS/United States ; }, mesh = {*Chromosomes, Bacterial ; *Conjugation, Genetic ; Genome, Bacterial ; Mycoplasma fermentans/*genetics ; Open Reading Frames ; *Repetitive Sequences, Nucleic Acid ; }, abstract = {Mycoplasma genomes contain compact gene sets that approach the minimal complement necessary for life and reflect multiple evolutionary instances of genomic reduction. Lateral gene transfer may play a critical role in shaping the mobile gene pool in these organisms, yet complex mobile elements have not been reported within this genus. We describe here a large (approximately 23-kb) genetic element with unique features that is present in four copies in the Mycoplasma fermentans PG18 chromosome, accounting for approximately 8% of the genome. These novel elements, designated ICEF (integrative conjugal elements of M. fermentans), resemble conjugative, self-transmissible integrating elements (constins) in that circular, nonreplicative extrachromosomal forms occur in which the left and right termini of the integrated element are juxtaposed and separated by a coupling sequence derived from direct repeats flanking chromosomal copies of ICEF as a result of target site duplication. ICEF contain multiple similarly oriented open reading frames (ORFs), of which some have homology to products of known conjugation genes but others have no known counterparts. Surprisingly, unlike other constins, ICEF lack homologs of known integrases, transposases, or recombinases, suggesting that a novel enzyme may be employed for integration-excision. Skewed distribution and varied sites of chromosomal integration among M. fermentans isolates suggest a role for ICEF in promoting genomic and phenotypic variation in this species. Identification of homologs of terminal ICEF ORFs in two additional mycoplasma species indicates that ICEF is the prototype member of a family of ICE-related elements that may be widespread among pathogenic mycoplasmas infecting diverse vertebrate hosts.}, }
@article {pmid12443925, year = {2002}, author = {Xu, Y and Glansdorff, N}, title = {Was our ancestor a hyperthermophilic procaryote?.}, journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology}, volume = {133}, number = {3}, pages = {677-688}, doi = {10.1016/s1095-6433(02)00197-6}, pmid = {12443925}, issn = {1095-6433}, mesh = {Animals ; Archaea/*classification/genetics ; Bacteria/*classification/genetics ; *Biological Evolution ; Eukaryotic Cells ; *Origin of Life ; Prokaryotic Cells ; Temperature ; }, abstract = {In this paper we critically review the 'classical' model for the emergence of the three domains (Archaea, Bacteria, Eucarya), which presents hyperthermophilic procaryotes as the ancestors of all life on this planet. We come to the conclusion that our last common ancestor is likely to have been rather a non-hyperthermophilic protoeucaryote endowed with sn-1,2 glycerol ester lipids (as in modern Bacteria and Eucarya), from which Archaea emerged by streamlining under pressure for adapting to heat, a process which involved an important molecular innovation: the advent of sn-2,3 glycerol ether lipids. The nature of the primeval bacterial lines of descent is less clear; it would appear, nevertheless, that the first extreme- and hyperthermophilic Bacteria emerged by converging mechanisms; lateral gene transfer from Archaea may have played a role in this adaptation.}, }
@article {pmid12441648, year = {2002}, author = {Horiike, T and Hamada, K and Shinozawa, T}, title = {Origin of eukaryotic cell nuclei by symbiosis of Archaea in Bacteria supported by the newly clarified origin of functional genes.}, journal = {Genes &amp; genetic systems}, volume = {77}, number = {5}, pages = {369-376}, doi = {10.1266/ggs.77.369}, pmid = {12441648}, issn = {1341-7568}, mesh = {Archaea/genetics/*physiology ; Bacteria/*genetics ; *Biological Evolution ; Cell Nucleus/*physiology ; Eukaryotic Cells/*physiology ; Gene Transfer, Horizontal ; Open Reading Frames ; Saccharomyces cerevisiae/genetics ; }, abstract = {In the previous report, we demonstrated the origin of eukaryotic cell nuclei as the symbiosis of Archaea in Bacteria by the newly developed "Homology-Hit Analysis". In that case, we counted yeast Open Reading Frames (ORFs) showing the highest similarity to a bacterial ORF as orthologous ORFs (Orthologous ORFs were produced by speciation from a common ancestor, and have the highest similarity to each other.) by comparing whole ORFs of yeast with those of individual bacteria. However, we could not count all yeast ORFs showing the highest similarity to a bacterial ORF in functional categories of yeast. Therefore, the origin of ORFs in the functional categories of yeast could not be inferred strictly. Here, we have improved the method for detecting orthologous ORFs. In this method, we count the numbers of ORF with the highest similarity between individual yeast functional categories and individual bacteria as orthologous ORFs. By this method, it was possible to detect the correct orthologous ORFs and to infer the origins of the functional categories in eukaryotic cells. As a result, two categories, assembly of protein complexes and DNA repair were newly judged to be of Archaeal origin, while five categories, lipid (fatty-acid and isoprenoid) metabolism, protein folding and stabilization, signal transduction, organization of the plasma membrane and organization of the cytoplasm, were newly judged to be of Bacterial origin. On the other hand, the origins of two categories (meiosis and cellular import, which were determined in the previous analysis) could not be judged. It is considered that functional categories related to the nucleus have origins common to Archaea, while those related to the cytoplasm have origins common to Bacteria. From these data including the origin of plasma membrane, it was further clarified that cell nucleus originated by the symbiosis of Archaea in Bacteria.}, }
@article {pmid12437304, year = {2002}, author = {Lavie, M and Shillington, E and Eguiluz, C and Grimsley, N and Boucher, C}, title = {PopP1, a new member of the YopJ/AvrRxv family of type III effector proteins, acts as a host-specificity factor and modulates aggressiveness of Ralstonia solanacearum.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {15}, number = {10}, pages = {1058-1068}, doi = {10.1094/MPMI.2002.15.10.1058}, pmid = {12437304}, issn = {0894-0282}, mesh = {Bacterial Proteins/*genetics/metabolism ; *DNA-Binding Proteins ; Gene Expression Regulation, Bacterial ; Gram-Negative Aerobic Rods and Cocci/*genetics/pathogenicity ; Molecular Sequence Data ; Mutation ; Phylogeny ; Repressor Proteins/genetics/metabolism ; *Transcription Factors ; Virulence/genetics ; }, abstract = {A functional analysis of an 11-kb-long region of the genome of the plant-pathogenic bacterium Ralstonia solanacearum, previously identified as an alternative codon usage region (ACUR), reveals that it was probably acquired through horizontal gene transfer. This ACUR encodes an insertion sequence and eight potential proteins, one of which is partially homologous with a host-specificity factor from a plant-pathogenic Erwinia sp., and another, PopP1, which is homologous to members of the YopJ/AvrRxv family of type III-secreted bacterial effectors controlling interaction between bacteria and their hosts. The analysis of mutants affecting all except one of the genes identified in the ACUR showed that only the popP1-deficient strain had an altered phenotype in plant infection tests. This mutant strain became pathogenic to a Petunia line that is resistant to the wild-type strain. Therefore, popP1 behaves as a typical avirulence gene. We demonstrate that PopP1 protein is secreted and that secretion of this protein requires a functional type III-secretion pathway. In contrast to the structural genes for other type III-secreted proteins identified in R. solanacearum, transcription of the popP1 gene is not coregulated with transcription of hrp genes but is constitutive.}, }
@article {pmid12435683, year = {2002}, author = {Simjee, S and White, DG and Wagner, DD and Meng, J and Qaiyumi, S and Zhao, S and McDermott, PF}, title = {Identification of vat(E) in Enterococcus faecalis isolates from retail poultry and its transferability to Enterococcus faecium.}, journal = {Antimicrobial agents and chemotherapy}, volume = {46}, number = {12}, pages = {3823-3828}, pmid = {12435683}, issn = {0066-4804}, mesh = {Acetyltransferases/drug effects/*genetics ; Animals ; Bacterial Proteins/*genetics/isolation &amp; purification ; Chickens/*microbiology ; Drug Resistance, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Enterococcus faecalis/*genetics ; Enterococcus faecium/*genetics ; Gene Transfer, Horizontal ; Genotype ; Microbial Sensitivity Tests ; Polymerase Chain Reaction ; Turkeys/*microbiology ; }, abstract = {Sixteen isolates of Enterococcus faecalis were recovered from retail poultry samples (seven chickens and nine turkeys) purchased from grocery stores in the greater Washington, D.C., area. PCR for known streptogramin resistance genes identified vat(E) in five E. faecalis isolates (three isolates from chickens and two isolates from turkeys). The vat(E) gene was transmissible on a ca. 70-kb plasmid, along with resistance to erythromycin, tetracycline, and streptomycin, by conjugation to E. faecalis and Enterococcus faecium recipient strains. DNA sequencing showed little variation between E. faecalis vat(E) genes from the chicken samples; however, one E. faecalis vat(E) gene from a turkey sample possessed 5 nucleotide changes that resulted in four amino acid substitutions. None of these substitutions in the vat(E) allele have previously been described. This is the first report of vat(E) in E. faecalis and its transferability to E. faecium, which indicates that E. faecalis can act as a reservoir for the dissemination of vat(E)-mediated streptogramin resistance to E. faecium.}, }
@article {pmid12426339, year = {2002}, author = {Schaefer, AL and Taylor, TA and Beatty, JT and Greenberg, EP}, title = {Long-chain acyl-homoserine lactone quorum-sensing regulation of Rhodobacter capsulatus gene transfer agent production.}, journal = {Journal of bacteriology}, volume = {184}, number = {23}, pages = {6515-6521}, pmid = {12426339}, issn = {0021-9193}, support = {R01 GM059026/GM/NIGMS NIH HHS/United States ; T32 AI007343/AI/NIAID NIH HHS/United States ; GM59026/GM/NIGMS NIH HHS/United States ; T32-AI07343/AI/NIAID NIH HHS/United States ; }, mesh = {4-Butyrolactone/*analogs &amp; derivatives/chemistry/*metabolism ; Amino Acid Sequence ; Bacterial Proteins/genetics/metabolism ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Ligases/genetics/metabolism ; Molecular Sequence Data ; Paracoccus denitrificans/genetics/*growth &amp; development/metabolism ; Rhodobacter capsulatus/*genetics/*growth &amp; development/metabolism ; *Signal Transduction ; Transduction, Genetic ; }, abstract = {Many proteobacteria use acyl-homoserine lactones as quorum-sensing signals. Traditionally, biological detection systems have been used to identify bacteria that produce acyl-homoserine lactones, although the specificities of these detection systems can limit discovery. We used a sensitive approach that did not require a bioassay to detect production of long-acyl-chain homoserine lactone production by Rhodobacter capsulatus and Paracoccus denitrificans. These long-chain acyl-homoserine lactones are not readily detected by standard bioassays. The most abundant acyl-homoserine lactone was N-hexadecanoyl-homoserine lactone. The long-chain acyl-homoserine lactones were concentrated in cells but were also found in the culture fluid. An R. capsulatus gene responsible for long-chain acyl-homoserine lactone synthesis was identified. A mutation in this gene, which we named gtaI, resulted in decreased production of the R. capsulatus gene transfer agent, and gene transfer agent production was restored by exogenous addition of N-hexadecanoyl-homoserine lactone. Thus, long-chain acyl-homoserine lactones serve as quorum-sensing signals to enhance genetic exchange in R. capsulatus.}, }
@article {pmid12425220, year = {2002}, author = {Mevius, D}, title = {[Veterinary antibiotic legislation in jeopardy?].}, journal = {Tijdschrift voor diergeneeskunde}, volume = {127}, number = {20}, pages = {633-634}, pmid = {12425220}, issn = {0040-7453}, mesh = {Animals ; *Drug Resistance, Multiple, Bacterial ; Enterobacteriaceae/drug effects/*genetics ; Enterobacteriaceae Infections/drug therapy/transmission ; Gene Transfer, Horizontal/*physiology ; Humans ; Legislation, Drug ; Microbial Sensitivity Tests ; Netherlands ; *Zoonoses ; }, }
@article {pmid12421761, year = {2002}, author = {Holzerlandt, R and Orengo, C and Kellam, P and Albà, MM}, title = {Identification of new herpesvirus gene homologs in the human genome.}, journal = {Genome research}, volume = {12}, number = {11}, pages = {1739-1748}, pmid = {12421761}, issn = {1088-9051}, mesh = {Amino Acid Sequence/genetics ; Cytomegalovirus/genetics ; Databases, Genetic ; Databases, Protein ; Gene Transfer, Horizontal/genetics ; Genes, Viral/*genetics ; *Genome, Human ; Herpesviridae/*genetics ; Herpesvirus 2, Gallid/genetics ; Herpesvirus 8, Human/genetics ; Humans ; Molecular Sequence Data ; Sequence Homology, Amino Acid ; *Sequence Homology, Nucleic Acid ; Transformation, Genetic/genetics ; Viral Proteins/genetics ; Viral Structural Proteins/*genetics ; }, abstract = {Viruses are intracellular parasites that use many cellular pathways during their replication. Large DNA viruses, such as herpesviruses, have captured a repertoire of cellular genes to block or mimic host immune responses, apoptosis regulation, and cell-cycle control mechanisms. We have conducted a systematic search for all homologs of herpesvirus proteins in the human genome using position-specific scoring matrices representing herpesvirus protein sequence domains, and pair-wise sequence comparisons. The analysis shows that approximately 13% of the herpesvirus proteins have clear sequence similarity to products of the human genome. Different human herpesviruses vary in their numbers of human homologs, indicating distinct rates of gene acquisition in different lineages. Our analysis has identified new families of herpesvirus/human homologs from viruses including human herpesvirus 5 (human cytomegalovirus; HCMV) and human herpesvirus 8 (Kaposi's sarcoma-associated herpesvirus; KSHV), which may play important roles in host-virus interactions.}, }
@article {pmid12409360, year = {2002}, author = {Wielders, CL and Fluit, AC and Brisse, S and Verhoef, J and Schmitz, FJ}, title = {mecA gene is widely disseminated in Staphylococcus aureus population.}, journal = {Journal of clinical microbiology}, volume = {40}, number = {11}, pages = {3970-3975}, pmid = {12409360}, issn = {0095-1137}, mesh = {*Bacterial Proteins ; Bacterial Typing Techniques ; Carrier Proteins/*genetics ; Electrophoresis, Gel, Pulsed-Field ; *Gene Transfer, Horizontal ; *Hexosyltransferases ; Humans ; Methicillin/pharmacology ; Methicillin Resistance/*genetics ; Microbial Sensitivity Tests ; Muramoylpentapeptide Carboxypeptidase/*genetics ; Penicillin-Binding Proteins ; Penicillins/pharmacology ; *Peptidyl Transferases ; Polymerase Chain Reaction ; Ribotyping ; Staphylococcal Infections/*microbiology ; Staphylococcus aureus/*drug effects/genetics ; }, abstract = {Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most important causes of hospital infections worldwide. High-level resistance to methicillin is caused by the mecA gene, which encodes an alternative penicillin-binding protein, PBP 2a. To determine the clonal relationships between methicillin-susceptible S. aureus (MSSA) and MRSA, we typed 1,069 S. aureus isolates (493 MSSA isolates and 576 MRSA isolates), collected mainly in North American and European hospitals between the 1960s and the year 2000, using pulsed-field gel electrophoresis and ribotyping. Of 10 widespread S. aureus lineages recognized, 8 had corresponding mecA-positive strains. Multiresistant MRSA strains are found in hospitals worldwide, while unrelated and more susceptible strains represent less than 1% of the MRSA population. This supports the hypothesis that horizontal transfer plays an important role in the dissemination of the mecA gene in the S. aureus population.}, }
@article {pmid12406744, year = {2002}, author = {Schirawski, J and Hagens, W and Fitzgerald, GF and Van Sinderen, D}, title = {Molecular characterization of cadmium resistance in Streptococcus thermophilus strain 4134: an example of lateral gene transfer.}, journal = {Applied and environmental microbiology}, volume = {68}, number = {11}, pages = {5508-5516}, pmid = {12406744}, issn = {0099-2240}, mesh = {Bacterial Proteins/*genetics/physiology ; Cadmium/*pharmacology ; DNA/drug effects/metabolism ; DNA-Binding Proteins/metabolism ; Drug Resistance, Bacterial/*genetics ; Gene Expression Regulation, Bacterial/drug effects ; Genome, Bacterial ; Promoter Regions, Genetic ; Repetitive Sequences, Nucleic Acid ; Streptococcus/drug effects/*genetics ; Zinc/pharmacology ; }, abstract = {Two genes (cadC(St) and cadA(St) [subscript St represents Streptococcus thermophilus]), located on the chromosome of S. thermophilus 4134, were shown to constitute a cadmium/zinc resistance cassette. The genes seem to be organized in an operon, and their transcription is cadmium dependent in vivo. The proposed product of the cadA open reading frame (CadA(St)) is highly similar to P-type cadmium efflux ATPases, whereas the predicted protein encoded by cadC(St) (CadC(St)) shows high similarity to ArsR-type regulatory proteins. The observed homologies and G+C content of this cassette and surrounding regions suggest that this DNA was derived from Lactococcus lactis and may have been introduced relatively recently into the S. thermophilus 4134 genome by a lateral gene transfer event. The complete cassette confers cadmium and zinc resistance to both S. thermophilus and L. lactis, but expression of cadA(St) alone is sufficient to give resistance. By using electrophoretic mobility shift assays it was shown that the CadC(St) protein is a DNA binding protein that binds specifically to its own promoter region, possibly to two copies of an inverted repeat, and that this CadC(St)-DNA interaction is lost in the presence of cadmium. Using lacZ fusion constructs it was shown that the cadmium-dependent expression of CadA(St) is mediated by the negative regulator CadC(St). A model for the regulation of the expression of cadmium resistance in S. thermophilus is discussed.}, }
@article {pmid12406213, year = {2002}, author = {Hinnebusch, BJ and Rosso, ML and Schwan, TG and Carniel, E}, title = {High-frequency conjugative transfer of antibiotic resistance genes to Yersinia pestis in the flea midgut.}, journal = {Molecular microbiology}, volume = {46}, number = {2}, pages = {349-354}, doi = {10.1046/j.1365-2958.2002.03159.x}, pmid = {12406213}, issn = {0950-382X}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Conjugation, Genetic ; Digestive System/*microbiology ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Humans ; Plague/microbiology ; Plasmids/genetics ; Siphonaptera/*microbiology ; Streptomycin/pharmacology ; Yersinia pestis/*drug effects/genetics ; }, abstract = {The acquisition of foreign DNA by horizontal transfer from unrelated organisms is a major source of variation leading to new strains of bacterial pathogens. The extent to which this occurs varies widely, due in part to lifestyle factors that determine exposure to potential donors. Yersinia pestis, the plague bacillus, infects normally sterile sites in its mammalian host, but forms dense aggregates in the non-sterile digestive tract of its flea vector to produce a transmissible infection. Here we show that unrelated co-infecting bacteria in the flea midgut are readily incorporated into these aggregates, and that this close physical contact leads to high-frequency conjugative genetic exchange. Transfer of an antibiotic resistance plasmid from an Escherichia coli donor to Y. pestis occurred in the flea midgut at a frequency of 10-3 after only 3 days of co-infection, and after 4 weeks 95% of co-infected fleas contained an average of 103 antibiotic-resistant Y. pestis transconjugants. Thus, transit in its arthropod vector exposes Y. pestis to favourable conditions for efficient genetic exchange with microbial flora of the flea gut. Horizontal gene transfer in the flea may be the source of antibiotic-resistant Y. pestis strains recently isolated from plague patients in Madagascar.}, }
@article {pmid12399927, year = {2002}, author = {Lang, AS and Taylor, TA and Beatty, JT}, title = {Evolutionary implications of phylogenetic analyses of the gene transfer agent (GTA) of Rhodobacter capsulatus.}, journal = {Journal of molecular evolution}, volume = {55}, number = {5}, pages = {534-543}, doi = {10.1007/s00239-002-2348-7}, pmid = {12399927}, issn = {0022-2844}, mesh = {Alphaproteobacteria/genetics ; Bacterial Proteins/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Vectors ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Rhodobacter capsulatus/*genetics ; Species Specificity ; }, abstract = {The gene transfer agent (GTA) of the a-proteobacterium Rhodobacter capsulatus is a cell-controlled genetic exchange vector. Genes that encode the GTA structure are clustered in a 15-kb region of the R. capsulatus chromosome, and some of these genes show sequence similarity to known bacteriophage head and tail genes. However, the production of GTA is controlled at the level of transcription by a cellular two-component signal transduction system. This paper describes homologues of both the GTA structural gene cluster and the GTA regulatory genes in the a-proteobacteria Rhodopseudomonas palustris, Rhodobacter sphaeroides, Caulobacter crescentus, Agrobacterium tumefaciens and Brucella melitensis. These sequences were used in a phylogenetic tree approach to examine the evolutionary relationships of selected GTA proteins to these homologues and (pro)phage proteins, which was compared to a 16S rRNA tree. The data indicate that a GTA-like element was present in a single progenitor of the extant species that contain both GTA structural cluster and regulatory gene homologues. The evolutionary relationships of GTA structural proteins to (pro)phage proteins indicated by the phylogenetic tree patterns suggest a predominantly vertical descent of GTA-like sequences in the a-proteobacteria and little past gene exchange with (pro)phages.}, }
@article {pmid12399042, year = {2002}, author = {Mills-Robertson, F and Addy, ME and Mensah, P and Crupper, SS}, title = {Molecular characterization of antibiotic resistance in clinical Salmonella typhi isolated in Ghana.}, journal = {FEMS microbiology letters}, volume = {215}, number = {2}, pages = {249-253}, doi = {10.1111/j.1574-6968.2002.tb11398.x}, pmid = {12399042}, issn = {0378-1097}, mesh = {Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal ; Ghana ; Humans ; Microbial Sensitivity Tests ; Plasmids/*genetics ; Salmonella typhi/*drug effects/isolation &amp; purification ; Transformation, Bacterial ; Typhoid Fever/microbiology ; }, abstract = {Fifty-eight clinical Salmonella typhi strains isolated from patients suspected of suffering from typhoid fever were obtained at the Korle-Bu Teaching Hospital and the Noguchi Memorial Institute for Medical Research, both located in Ghana, Africa. Each isolate was examined for susceptibility to ampicillin, chloramphenicol, streptomycin, tetracycline, and trimethoprim/sulfamethoxazole by the disk diffusion assay. Five of the isolates were resistant to all five antibiotics while 10 isolates were resistant to ampicillin, chloramphenicol, and trimethoprim/sulfamethoxazole, which are considered 'first line' antibiotics in the treatment of typhoid fever. Thirty-four isolates were resistant to at least one of the antibiotics tested and 62% of these isolates possessed conjugable plasmids belonging to incompatibility group IncHI. Ninety percent of the conjugable plasmids conferred a multiple drug-resistant phenotype on the strains harboring them. Additionally, 14 strains contained plasmids that were transformable and six of them encoded multiple drug resistance. Our findings indicate that multiple drug resistance to the 'first line' antibiotics in S. typhi may be more prevalent in Africa than previously thought.}, }
@article {pmid12397183, year = {2002}, author = {Zardoya, R and Ding, X and Kitagawa, Y and Chrispeels, MJ}, title = {Origin of plant glycerol transporters by horizontal gene transfer and functional recruitment.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {99}, number = {23}, pages = {14893-14896}, pmid = {12397183}, issn = {0027-8424}, mesh = {Amino Acid Sequence ; Carrier Proteins/*genetics ; Consensus Sequence ; Conserved Sequence ; Evolution, Molecular ; Gene Transfer Techniques ; Glycerol/*metabolism ; Molecular Sequence Data ; Phylogeny ; Plants/classification/genetics/*metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {Gene-family evolution mostly relies on gene duplication coupled with functional diversification of gene products. However, other evolutionary mechanisms may also be important in generating protein diversity. The ubiquitous membrane intrinsic protein (MIP) gene family is an excellent model system to search for such alternative evolutionary mechanisms. MIPs are proteins that transport water, glycerol, and small solutes across cell membranes in all living organisms. We reconstructed the molecular phylogeny of MIPs based on amino acid sequence data by using neighbor-joining, maximum-likelihood, and Bayesian methods of phylogenetic inference. The recovered trees show an early and distinct separation of water and glycerol transporters, i.e., aquaporins (AQPs), and aquaglyceroporins. The latter are absent from plants. As expected, gene duplication and functional diversification account for most of the diversity of animal and plant members of the family. However, in contrast to this model, we find that the sister group of plant glycerol transporters are bacterial AQPs. This relationship suggests first that plant glycerol transporters may resulted from a single event of horizontal gene transfer from bacteria, which we have estimated to have occurred approximately 1,200 million years ago, at the origin of plants, and second that bacterial AQPs were likely recruited to transport glycerol in plants because of their absence of aquaglyceroporins. This striking example of adaptive evolution at the molecular level was demonstrated further by finding convergent or parallel replacements at particular amino acid positions related to water- and glycerol-transporting specificity.}, }
@article {pmid12386340, year = {2002}, author = {Kondo, N and Nikoh, N and Ijichi, N and Shimada, M and Fukatsu, T}, title = {Genome fragment of Wolbachia endosymbiont transferred to X chromosome of host insect.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {99}, number = {22}, pages = {14280-14285}, pmid = {12386340}, issn = {0027-8424}, mesh = {Animals ; Base Sequence ; Blotting, Southern/methods ; Coleoptera/*genetics ; DNA, Bacterial ; Drosophila melanogaster/microbiology ; Drug Resistance, Bacterial ; Evolution, Molecular ; Female ; *Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; Male ; Molecular Sequence Data ; Polymerase Chain Reaction/methods ; Rifampin/pharmacology ; Symbiosis ; Tetracycline/pharmacology ; Wolbachia/drug effects/*genetics/isolation &amp; purification ; *X Chromosome ; }, abstract = {The adzuki bean beetle, Callosobruchus chinensis, is triple-infected with distinct lineages of Wolbachia endosymbiont, wBruCon, wBruOri, and wBruAus, which were identified by their wsp (Wolbachia surface protein) gene sequences. Whereas wBruCon and wBruOri caused cytoplasmic incompatibility of the host insect, wBruAus did not. Although wBruCon and wBruOri were easily eliminated by antibiotic treatments, wBruAus persisted over five treated generations and could not be eliminated. The inheritance pattern of wBruAus was, surprisingly, explained by sex-linked inheritance in male-heterozygotic organisms, which agreed with the karyotype of C. chinensis (2n = 20, XY). Quantitative PCR analysis demonstrated that females contain around twice as much wsp titer as males, which is concordant with an X chromosome linkage. Specific PCR and Southern blot analyses indicated that the wBruAus-bearing strain of C. chinensis contains only a fraction of the Wolbachia gene repertoire. Several genome fragments of wBruAus were isolated using an inverse PCR technique. The fragments exhibited a bacterial genome structure containing a number of ORFs typical of the alpha-proteobacteria, although some of the ORFs contained disruptive mutations. In the flanking region of ftsZ gene, a non-long terminal repeat (non-LTR) retrotransposon sequence, which is typical of insects but not found from bacteria, was present. These results strongly suggest that wBruAus has no microbial entity but is a genome fragment of Wolbachia endosymbiont transferred to the X chromosome of the host insect.}, }
@article {pmid12385978, year = {2002}, author = {Andersson, SG and Alsmark, C and Canbäck, B and Davids, W and Frank, C and Karlberg, O and Klasson, L and Antoine-Legault, B and Mira, A and Tamas, I}, title = {Comparative genomics of microbial pathogens and symbionts.}, journal = {Bioinformatics (Oxford, England)}, volume = {18 Suppl 2}, number = {}, pages = {S17}, doi = {10.1093/bioinformatics/18.suppl_2.s17}, pmid = {12385978}, issn = {1367-4803}, mesh = {Alphaproteobacteria/genetics ; Chromosome Mapping/*methods ; *Evolution, Molecular ; Gammaproteobacteria/genetics ; Gene Transfer, Horizontal/genetics ; Genetic Variation/*genetics ; *Genome, Bacterial ; Genomic Instability/genetics ; Genomics/methods ; *Models, Genetic ; Mutation ; Phylogeny ; Proteobacteria/classification/*genetics ; Sequence Analysis, DNA/methods ; Species Specificity ; Symbiosis/*genetics ; }, abstract = {We are interested in quantifying the contribution of gene acquisition, loss, expansion and rearrangements to the evolution of microbial genomes. Here, we discuss factors influencing microbial genome divergence based on pair-wise genome comparisons of closely related strains and species with different lifestyles. A particular focus is on intracellular pathogens and symbionts of the genera Rickettsia, Bartonella and BUCHNERA: Extensive gene loss and restricted access to phage and plasmid pools may provide an explanation for why single host pathogens are normally less successful than multihost pathogens. We note that species-specific genes tend to be shorter than orthologous genes, suggesting that a fraction of these may represent fossil-orfs, as also supported by multiple sequence alignments among species. The results of our genome comparisons are placed in the context of phylogenomic analyses of alpha and gamma proteobacteria. We highlight artefacts caused by different rates and patterns of mutations, suggesting that atypical phylogenetic placements can not a priori be taken as evidence for horizontal gene transfer events. The flexibility in genome structure among free-living microbes contrasts with the extreme stability observed for the small genomes of aphid endosymbionts, in which no rearrangements or inflow of genetic material have occurred during the past 50 millions years (1). Taken together, the results suggest that genomic stability correlate with the content of repeated sequences and mobile genetic elements, and thereby indirectly with bacterial lifestyles.}, }
@article {pmid12383754, year = {2002}, author = {Ling, L and Wang, J and Cui, Y and Li, W and Chen, R}, title = {Proteome-wide analysis of protein function composition reveals the clustering and phylogenetic properties of organisms.}, journal = {Molecular phylogenetics and evolution}, volume = {25}, number = {1}, pages = {101-111}, doi = {10.1016/s1055-7903(02)00354-8}, pmid = {12383754}, issn = {1055-7903}, mesh = {Algorithms ; Animals ; Archaea/genetics ; Bacteria/genetics ; Caenorhabditis elegans/genetics ; Drosophila melanogaster/genetics ; Models, Genetic ; *Phylogeny ; Proteins/*genetics ; Proteome/analysis ; Saccharomyces cerevisiae/genetics ; }, abstract = {A 17-dimensional vector named the proteome vector is defined to represent an organism. The components of the vector reflect the relative contents of protein-encoding genes of the 17 cluster of orthologous groups of proteins (COGs) classes in the whole genome of the relevant organism. Based on the definition of this proteome vector, the fuzzy clustering of 36 completely sequenced organisms (8 archaea, 24 bacteria, and 4 eukarya) was performed and a proteome tree was constructed. Our results show that (1) the 36 organisms can be 100% correctly classified into three clusters corresponding to the three primary kingdoms, (2) our proteome tree is remarkably similar to that derived from 16S rRNA, and (3) the chromosomes and/or plasmids belonging to the same organism have very similar gene composition. Based on these results, we argue that the 17-dimensional proteome vector could be a good criterion for clustering approaches and to a large extent reveals the phylogenetic properties of organisms; the Three Primary Kingdoms Hypothesis is trustworthy although the existence of lateral gene transfer (LGT) brings controversy to the construction of the "universal tree of life."}, }
@article {pmid12383608, year = {2002}, author = {Baquero, F and Coque, TM and Cantón, R}, title = {Allodemics.}, journal = {The Lancet. Infectious diseases}, volume = {2}, number = {10}, pages = {591-592}, doi = {10.1016/s1473-3099(02)00393-6}, pmid = {12383608}, issn = {1473-3099}, mesh = {Bacteria/*genetics ; Bacterial Infections/*epidemiology/transmission ; *Clone Cells ; *Gene Transfer, Horizontal ; Genotype ; Humans ; *Molecular Epidemiology ; Phenotype ; }, }
@article {pmid12382327, year = {2002}, author = {DeAngelis, PL}, title = {Evolution of glycosaminoglycans and their glycosyltransferases: Implications for the extracellular matrices of animals and the capsules of pathogenic bacteria.}, journal = {The Anatomical record}, volume = {268}, number = {3}, pages = {317-326}, doi = {10.1002/ar.10163}, pmid = {12382327}, issn = {0003-276X}, support = {GM56497/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Bacteria ; *Biological Evolution ; *Extracellular Matrix ; *Glycosaminoglycans/chemistry/physiology ; *Glycosyltransferases/chemistry/physiology ; *Polysaccharides, Bacterial/chemistry/physiology ; }, abstract = {Glycosaminoglycans (linear polysaccharides with a repeating disaccharide backbone containing an amino sugar) are essential components of extracellular matrices of animals. These complex molecules play important structural, adhesion, and signaling roles in mammals. Direct detection of glycosaminoglycans has been reported in a variety of organisms, but perhaps more definitive tests for the glycosyltransferase genes should be utilized to clarify the distribution of glycosaminoglycans in metazoans. Recently, glycosyltransferases that form the hyaluronan, heparin/heparan, or chondroitin backbone were identified at the molecular level. The three types of glycosyltransferases appear to have evolved independently based on sequence comparisons and other characteristics. All metazoans appear to possess heparin/heparan. Chondroitin is found in some worms, arthropods, and higher animals. Hyaluronan is found only in two of the three main branches of chordates. The presence of several types of glycosaminoglycans in the body allows multiple communication channels and adhesion systems to operate simultaneously. Certain pathogenic bacteria produce extracellular coatings, called capsules, which are composed of glycosaminoglycans that increase their virulence during infection. The capsule helps shield the microbe from the host defenses and/or modulates host physiology. The bacterial and animal polysaccharides are chemically identical or at least very similar. Therefore, no immune response is generated, in contrast to the vast majority of capsular polymers from other bacteria. In microbial systems, it appears that in most cases functional convergent evolution of glycosaminoglycan glycosyltransferases occurred, rather than direct horizontal gene transfer from their vertebrate hosts.}, }
@article {pmid12381787, year = {2002}, author = {Schell, MA and Karmirantzou, M and Snel, B and Vilanova, D and Berger, B and Pessi, G and Zwahlen, MC and Desiere, F and Bork, P and Delley, M and Pridmore, RD and Arigoni, F}, title = {The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {99}, number = {22}, pages = {14422-14427}, pmid = {12381787}, issn = {0027-8424}, mesh = {Adaptation, Physiological/*genetics ; Anaerobiosis ; Base Sequence ; Bifidobacterium/*genetics ; Carbohydrate Metabolism ; Colon/microbiology ; DNA, Bacterial ; Digestive System/*microbiology ; Energy Metabolism ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; Molecular Sequence Data ; Transcription, Genetic ; }, abstract = {Bifidobacteria are Gram-positive prokaryotes that naturally colonize the human gastrointestinal tract (GIT) and vagina. Although not numerically dominant in the complex intestinal microflora, they are considered as key commensals that promote a healthy GIT. We determined the 2.26-Mb genome sequence of an infant-derived strain of Bifidobacterium longum, and identified 1,730 possible coding sequences organized in a 60%-GC circular chromosome. Bioinformatic analysis revealed several physiological traits that could partially explain the successful adaptation of this bacteria to the colon. An unexpectedly large number of the predicted proteins appeared to be specialized for catabolism of a variety of oligosaccharides, some possibly released by rare or novel glycosyl hydrolases acting on "nondigestible" plant polymers or host-derived glycoproteins and glycoconjugates. This ability to scavenge from a large variety of nutrients likely contributes to the competitiveness and persistence of bifidobacteria in the colon. Many genes for oligosaccharide metabolism were found in self-regulated modules that appear to have arisen in part from gene duplication or horizontal acquisition. Complete pathways for all amino acids, nucleotides, and some key vitamins were identified; however, routes for Asp and Cys were atypical. More importantly, genome analysis provided insights into the reciprocal interactions of bifidobacteria with their hosts. We identified polypeptides that showed homology to most major proteins needed for production of glycoprotein-binding fimbriae, structures that could possibly be important for adhesion and persistence in the GIT. We also found a eukaryotic-type serine protease inhibitor (serpin) possibly involved in the reported immunomodulatory activity of bifidobacteria.}, }
@article {pmid12379716, year = {2002}, author = {Dobrindt, U and Blum-Oehler, G and Nagy, G and Schneider, G and Johann, A and Gottschalk, G and Hacker, J}, title = {Genetic structure and distribution of four pathogenicity islands (PAI I(536) to PAI IV(536)) of uropathogenic Escherichia coli strain 536.}, journal = {Infection and immunity}, volume = {70}, number = {11}, pages = {6365-6372}, pmid = {12379716}, issn = {0019-9567}, mesh = {Codon ; DNA, Bacterial/chemistry ; Escherichia coli/*genetics/*pathogenicity ; Genetic Structures ; Open Reading Frames ; Virulence ; }, abstract = {For the uropathogenic Escherichia coli strain 536 (O6:K15:H31), the DNA sequences of three pathogenicity islands (PAIs) (PAI I(536) to PAI III(536)) and their flanking regions (about 270 kb) were determined to further characterize the virulence potential of this strain. PAI I(536) to PAI III(536) exhibit features typical of PAIs, such as (i) association with tRNA-encoding genes; (ii) G+C content differing from that of the host genome; (iii) flanking repeat structures; (iv) a mosaic-like structure comprising a multitude of functional, truncated, and nonfunctional putative open reading frames (ORFs) with known or unknown functions; and (v) the presence of many fragments of mobile genetic elements. PAI I(536) to PAI III(536) range between 68 and 102 kb in size. Although these islands contain several ORFs and known virulence determinants described for PAIs of other extraintestinal pathogenic E. coli (ExPEC) isolates, they also consist of as-yet-unidentified ORFs encoding putative virulence factors. The genetic structure of PAI IV(536), which represents the core element of the so-called high-pathogenicity island encoding a siderophore system initially identified in pathogenic yersiniae, was further characterized by sample sequencing. For the first time, multiple PAI sequences (PAI I(536) to PAI IV(536)) in uropathogenic E. coli were studied and their presence in several wild-type E. coli isolates was extensively investigated. The results obtained suggest that these PAIs or at least large fragments thereof are detectable in other pathogenic E. coli isolates. These results support our view that the acquisition of large DNA regions, such as PAIs, by horizontal gene transfer is an important factor for the evolution of bacterial pathogens.}, }
@article {pmid12379152, year = {2002}, author = {Karev, GP and Wolf, YI and Rzhetsky, AY and Berezovskaya, FS and Koonin, EV}, title = {Birth and death of protein domains: a simple model of evolution explains power law behavior.}, journal = {BMC evolutionary biology}, volume = {2}, number = {}, pages = {18}, pmid = {12379152}, issn = {1471-2148}, mesh = {Animals ; Arabidopsis/genetics ; Bacillus subtilis/genetics ; *Biological Evolution ; Caenorhabditis elegans/genetics ; Computer Simulation ; Death ; Drosophila melanogaster/genetics ; Escherichia coli/genetics ; Genetic Variation/genetics ; Humans ; *Mathematical Computing ; Methanobacteriaceae/genetics ; *Models, Biological ; Parturition ; Protein Structure, Tertiary/*genetics ; Saccharomyces cerevisiae/genetics ; Sulfolobus solfataricus/genetics ; Thermotoga maritima/genetics ; }, abstract = {BACKGROUND: Power distributions appear in numerous biological, physical and other contexts, which appear to be fundamentally different. In biology, power laws have been claimed to describe the distributions of the connections of enzymes and metabolites in metabolic networks, the number of interactions partners of a given protein, the number of members in paralogous families, and other quantities. In network analysis, power laws imply evolution of the network with preferential attachment, i.e. a greater likelihood of nodes being added to pre-existing hubs. Exploration of different types of evolutionary models in an attempt to determine which of them lead to power law distributions has the potential of revealing non-trivial aspects of genome evolution.<br><br>RESULTS: A simple model of evolution of the domain composition of proteomes was developed, with the following elementary processes: i) domain birth (duplication with divergence), ii) death (inactivation and/or deletion), and iii) innovation (emergence from non-coding or non-globular sequences or acquisition via horizontal gene transfer). This formalism can be described as a birth, death and innovation model (BDIM). The formulas for equilibrium frequencies of domain families of different size and the total number of families at equilibrium are derived for a general BDIM. All asymptotics of equilibrium frequencies of domain families possible for the given type of models are found and their appearance depending on model parameters is investigated. It is proved that the power law asymptotics appears if, and only if, the model is balanced, i.e. domain duplication and deletion rates are asymptotically equal up to the second order. It is further proved that any power asymptotic with the degree not equal to -1 can appear only if the hypothesis of independence of the duplication/deletion rates on the size of a domain family is rejected. Specific cases of BDIMs, namely simple, linear, polynomial and rational models, are considered in details and the distributions of the equilibrium frequencies of domain families of different size are determined for each case. We apply the BDIM formalism to the analysis of the domain family size distributions in prokaryotic and eukaryotic proteomes and show an excellent fit between these empirical data and a particular form of the model, the second-order balanced linear BDIM. Calculation of the parameters of these models suggests surprisingly high innovation rates, comparable to the total domain birth (duplication) and elimination rates, particularly for prokaryotic genomes.<br><br>CONCLUSIONS: We show that a straightforward model of genome evolution, which does not explicitly include selection, is sufficient to explain the observed distributions of domain family sizes, in which power laws appear as asymptotic. However, for the model to be compatible with the data, there has to be a precise balance between domain birth, death and innovation rates, and this is likely to be maintained by selection. The developed approach is oriented at a mathematical description of evolution of domain composition of proteomes, but a simple reformulation could be applied to models of other evolving networks with preferential attachment.}, }
@article {pmid12377549, year = {2002}, author = {Garcia-Vallvé, S and Janssen, PJ and Ouzounis, CA}, title = {Genetic variation between Helicobacter pylori strains: gene acquisition or loss?.}, journal = {Trends in microbiology}, volume = {10}, number = {10}, pages = {445-447}, doi = {10.1016/s0966-842x(02)02446-0}, pmid = {12377549}, issn = {0966-842X}, mesh = {Codon/metabolism ; Gene Transfer, Horizontal ; *Genetic Variation ; Helicobacter pylori/classification/*genetics ; Models, Genetic ; Mutation ; Species Specificity ; Statistics as Topic ; }, abstract = {Previously identified strain-specific genes of Helicobacter pylori were analysed for GC content and preference in codon usage. The results indicate that in H. pylori strain specificity is mainly driven by gene uptake. Incoming strains of Helicobacter or other species can occasionally donate genes but the identification of the donor species is hampered by ongoing evolutionary processes and the lack of an adequate number, or indeed a total absence, of gene homologues.}, }
@article {pmid12374839, year = {2002}, author = {Gonzalez, MD and Lichtensteiger, CA and Caughlan, R and Vimr, ER}, title = {Conserved filamentous prophage in Escherichia coli O18:K1:H7 and Yersinia pestis biovar orientalis.}, journal = {Journal of bacteriology}, volume = {184}, number = {21}, pages = {6050-6055}, pmid = {12374839}, issn = {0021-9193}, support = {R01 AI042015/AI/NIAID NIH HHS/United States ; R56 AI042015/AI/NIAID NIH HHS/United States ; AI42015/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteriophages/*genetics/physiology ; Escherichia coli/genetics/*virology ; Open Reading Frames ; Proviruses/*genetics/physiology ; Rats ; Yersinia pestis/genetics/*virology ; }, abstract = {Microbial virulence is known to emerge by horizontal gene transfer mechanisms. Here we describe the discovery of a novel filamentous prophage, designated CUS-1, which is integrated into the chromosomal dif homologue of the high-virulence clone Escherichia coli O18:K1:H7. An homologous chromosomal element (CUS-2) in Yersinia pestis biovar orientalis is integrated at the same relative location as CUS-1; both lysogenic E. coli and Y. pestis strains produce particles with properties expected of single-stranded DNA virions. CUS(phi) is epidemiologically correlated with the emergence of K1 strains with increased virulence and with the Y. pestis biovar responsible for the current (third) plague pandemic.}, }
@article {pmid12372152, year = {2002}, author = {Wolanin, PM and Thomason, PA and Stock, JB}, title = {Histidine protein kinases: key signal transducers outside the animal kingdom.}, journal = {Genome biology}, volume = {3}, number = {10}, pages = {REVIEWS3013}, pmid = {12372152}, issn = {1474-760X}, support = {F32 GM064228/GM/NIGMS NIH HHS/United States ; 1F32 GM064228/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Conserved Sequence ; Eukaryotic Cells/enzymology ; Evolution, Molecular ; Histidine Kinase ; Models, Molecular ; Molecular Sequence Data ; Prokaryotic Cells/enzymology ; Protein Kinases/chemistry/*genetics/*physiology ; Protein Structure, Tertiary ; Receptors, Cell Surface/chemistry/genetics/physiology ; Sequence Homology, Amino Acid ; *Signal Transduction ; }, abstract = {Histidine protein kinases (HPKs) are a large family of signal-transduction enzymes that autophosphorylate on a conserved histidine residue. HPKs form two-component signaling systems together with their downstream target proteins, the response regulators, which have a conserved aspartate in a so-called 'receiver domain' that is phosphorylated by the HPK. Two-component signal transduction is prevalent in bacteria and is also widely used by eukaryotes outside the animal kingdom. The typical HPK is a transmembrane receptor with an amino-terminal extracellular sensing domain and a carboxy-terminal cytosolic signaling domain; most, if not all, HPKs function as dimers. They show little similarity to protein kinases that phosphorylate serine, threonine or tyrosine residues, but may share a distant evolutionary relationship with these enzymes. In excess of a thousand known genes encode HPKs, which are important for multiple functions in bacteria, including chemotaxis and quorum sensing, and in eukaryotes, including hormone-dependent developmental processes. The proteins divide into at least 11 subfamilies, only one of which is present in eukaryotes, suggesting that lateral gene transfer gave rise to two-component signaling in these organisms.}, }
@article {pmid12369928, year = {2001}, author = {McClure, MA}, title = {Evolution of the DUT gene: horizontal transfer between host and pathogen in all three domains of life.}, journal = {Current protein &amp; peptide science}, volume = {2}, number = {4}, pages = {313-324}, doi = {10.2174/1389203013381062}, pmid = {12369928}, issn = {1389-2037}, support = {AI 28309/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; Pyrophosphatases/*genetics ; Sequence Alignment ; }, abstract = {The ubiquity of the dut gene in Eukarya, Eubacteria, and Archaea implies its existence in the last common ancestor of the three domains of life. The dut gene exists as single, tandemly duplicated, and tandemly triplicated copies. The dUTPase is encoded as an auxiliary gene in the genomes of several DNA viruses and two distinct lineages of retroviruses. A comprehensive analysis of dUTPase amino acid sequence relationships explores the evolutionary dynamics of dut genes in viruses and their hosts. The data set was comprised of representative sequences from available Eukaryotes, Archaea, Eubacteria cells and viruses. A multiple alignment of these protein sequences was generated using a hidden Markov model (HMM) approach developed to align divergent data. Phylogenetic analysis revealed that horizontal transfer from hosts to virus genomes has occurred in all three domains of life. The evidence for horizontal transfers is particularly interesting in Eukaryotes as these dut genes have introns, while DNA virus dut genes do not. This implies an intermediary Retroid Agent facilitated the horizontal transfer process, via reverse transcription, between host mRNA and DNA viruses. The horizontal transfer of the dut gene from Eukaryotic, Eubacterial, and Archaeal organisms to both DNA and RNA viruses is the first documented case of host to pathogen transfer that has occurred in all three domains of life.}, }
@article {pmid12368432, year = {2002}, author = {Howard, ST and Byrd, TF and Lyons, CR}, title = {A polymorphic region in Mycobacterium abscessus contains a novel insertion sequence element.}, journal = {Microbiology (Reading, England)}, volume = {148}, number = {Pt 10}, pages = {2987-2996}, doi = {10.1099/00221287-148-10-2987}, pmid = {12368432}, issn = {1350-0872}, support = {HL55776/HL/NHLBI NIH HHS/United States ; HL64548-02/HL/NHLBI NIH HHS/United States ; }, mesh = {Base Sequence ; DNA Transposable Elements/*genetics ; Gene Deletion ; Gene Transfer, Horizontal ; Genetic Variation ; Humans ; Molecular Sequence Data ; Mycobacterium/*genetics/growth &amp; development ; Open Reading Frames/genetics ; *Polymorphism, Genetic ; Sequence Analysis, DNA ; }, abstract = {A polymorphic region was discovered in the genetically uncharacterized opportunistic pathogen Mycobacterium abscessus. The region contains a novel 1.7 kb insertion sequence (IS) named ISMab1. ISMab1 contains two complete ORFs and one partial ORF located in segments with over 80% nucleotide identity to Mycobacterium avium IS1601 and IS999 and to previously unreported IS-like elements from Mycobacterium smegmatis. The marked similarity within this family of elements is supportive of horizontal transfer between environmental mycobacterial species. In clinical isolates, ISMab1 was either present as a single copy or absent. The polymorphic region containing ISMab1 was identified by genomic subtraction between a parental strain and phenotypic variant. The variant has a 14.2 kb genomic deletion and this is flanked in the parental strain by complex arrays of inverted and direct repeats. Clinical isolates of M. abscessus were probed for the deletion and flanking sequences and two were found to be missing more than 20 kb. No regional deletions were found in the type strain, ATCC 19977. Although M. abscessus is a rapidly growing species, comparative sequence analysis of 23 kb from the polymorphic region showed that most local ORFs have greater amino acid identity to proteins encoded by genes from the slowly growing mycobacteria, M. avium and Mycobacterium tuberculosis, than to the rapid-grower M. smegmatis. Several ORFs also have strong similarity to Pseudomonas aeruginosa genes with a potential role in beta-oxidation.}, }
@article {pmid12364606, year = {2002}, author = {Lynn, DJ and Singer, GA and Hickey, DA}, title = {Synonymous codon usage is subject to selection in thermophilic bacteria.}, journal = {Nucleic acids research}, volume = {30}, number = {19}, pages = {4272-4277}, pmid = {12364606}, issn = {1362-4962}, mesh = {Bacteria/*genetics ; Base Composition ; Codon/*genetics ; Genome, Bacterial ; Phylogeny ; *Selection, Genetic ; Temperature ; }, abstract = {The patterns of synonymous codon usage, both within and among genomes, have been extensively studied over the past two decades. Despite the accumulating evidence that natural selection can shape codon usage, it has not been possible to link a particular pattern of codon usage to a specific external selective force. Here, we have analyzed the patterns of synonymous codon usage in 40 completely sequenced prokaryotic genomes. By combining the genes from several genomes (more than 80 000 genes in all) into a single dataset for this analysis, we were able to investigate variations in codon usage, both within and between genomes. The results show that synonymous codon usage is affected by two major factors: (i) the overall G+C content of the genome and (ii) growth at high temperature. This study focused on the relationship between synonymous codon usage and the ability to grow at high temperature. We have been able to eliminate both phylogenetic history and lateral gene transfer as possible explanations for the characteristic pattern of codon usage among the thermophiles. Thus, these results demonstrate a clear link between a particular pattern of codon usage and an external selective force.}, }
@article {pmid12361302, year = {2002}, author = {Katz, LA}, title = {Lateral gene transfers and the evolution of eukaryotes: theories and data.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {52}, number = {Pt 5}, pages = {1893-1900}, doi = {10.1099/00207713-52-5-1893}, pmid = {12361302}, issn = {1466-5026}, mesh = {Animals ; *Biological Evolution ; Ecosystem ; Eukaryotic Cells ; *Gene Transfer, Horizontal ; Genetics, Microbial ; Genome, Human ; Humans ; Metabolism ; *Models, Genetic ; Organelles/genetics ; }, abstract = {Vertical transmission of heritable material, a cornerstone of the Darwinian theory of evolution, is inadequate to describe the evolution of eukaryotes, particularly microbial eukaryotes. This is because eukaryotic cells and eukaryotic genomes are chimeric, having evolved through a combination of vertical (parent to offspring) and lateral (trans-species) transmission. Observations on widespread chimerism in eukaryotes have led to new and revised hypothesis for the origin and diversification of eukaryotes that provide specific predictions on the tempo (early vs continuous transfers) and mode (nature of donor and recipient lineages) of lateral gene transfers (LGTs). Analyses of available data indicate that LGTs in eukaryotes largely fall into two categories: (1) LGTs from organelles to the nucleus, only a few of which appear to have occurred at the time of the origin of eukaryotes, and (2) anomalous LGTs involving diverse donor and recipient lineages. Further testing of hypotheses on the origin and diversification of eukaryotes will require complete genome sequences from a number of diverse eukaryotes and prokaryotes combined with sequences of targeted genes from a broad phylogenetic sample.}, }
@article {pmid12357672, year = {2002}, author = {Rabsch, W and Mirold, S and Hardt, WD and Tschäpe, H}, title = {The dual role of wild phages for horizontal gene transfer among Salmonella strains.}, journal = {Berliner und Munchener tierarztliche Wochenschrift}, volume = {115}, number = {9-10}, pages = {355-359}, pmid = {12357672}, issn = {0005-9366}, mesh = {Bacteriophage Typing ; *Gene Transfer, Horizontal ; Lysogeny ; Salmonella Phages/genetics/*physiology ; Salmonella typhimurium/classification/genetics/*pathogenicity ; Transduction, Genetic/*veterinary ; Virulence ; }, abstract = {Salmonella bacteriophages seem to mediate horizontal transfer of virulence functions among Salmonella strains in two different ways: by general transduction and also by lysogenic conversion. The majority of wild phages isolated from Salmonella strains belong to the P22 like phages and were able to transduce. Our data show that the lysogenic conversion is generally accompanied by changes in the susceptibility to the typing phages used for epidemiological purposes. Similar phage type conversions to S. Typhimurium DT104 could be detected upon lysogenization with two other S. Typhimurium strains. For some S. Typhimurium strains the typical phage pattern is actually associated with alterations of virulence characteristics. For example, all tested wild type isolates of phage types DT49 and DT204 were found to be SopE phi-lysogens. The Anderson typing phages interfere with the prophages and/or cryptic phages and so the complex genetic short-term evolution can be demonstrated in the lab. This is one reason for the successful application of phage typing in Salmonella epidemiology since the 50s.}, }
@article {pmid12354553, year = {2002}, author = {Hogan, D and Kolter, R}, title = {Why are bacteria refractory to antimicrobials?.}, journal = {Current opinion in microbiology}, volume = {5}, number = {5}, pages = {472-477}, doi = {10.1016/s1369-5274(02)00357-0}, pmid = {12354553}, issn = {1369-5274}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics ; Drug Resistance, Bacterial/*physiology ; Gene Transfer, Horizontal ; Mutation ; }, abstract = {The incidence of antibiotic resistance in pathogenic bacteria is rising. Antibiotic resistance can be achieved via three distinct routes: inactivation of the drug, modification of the target of action, and reduction in the concentration of drug that reaches the target. It has long been recognized that specific antibiotic resistance mechanisms can be acquired through mutation of the bacterial genome or by gaining additional genes through horizontal gene transfer. Recent attention has also brought to light the importance of different physiological states for the survival of bacteria in the presence of antibiotics. It is now apparent that bacteria have complex, intrinsic resistance mechanisms that are often not detected in the standard antibiotic sensitivity tests performed in clinical laboratories. The development of resistance in bacteria found in surface-associated aggregates or biofilms, owing to these intrinsic mechanisms, is paramount.}, }
@article {pmid12354283, year = {2002}, author = {Ge, Y and Wang, X and Chen, Z and Landman, N and Lo, EH and Kang, JX}, title = {Gene transfer of the Caenorhabditis elegans n-3 fatty acid desaturase inhibits neuronal apoptosis.}, journal = {Journal of neurochemistry}, volume = {82}, number = {6}, pages = {1360-1366}, doi = {10.1046/j.1471-4159.2002.01077.x}, pmid = {12354283}, issn = {0022-3042}, support = {CA-79553/CA/NCI NIH HHS/United States ; P30 DK40561/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Apoptosis/drug effects ; Caenorhabditis elegans/enzymology ; Caenorhabditis elegans Proteins/*genetics/*metabolism/pharmacology ; Cell Survival/drug effects ; Cells, Cultured ; Chromatography, Gas ; Cytoprotection/physiology ; Eicosanoids/biosynthesis ; Enzyme Activation/physiology ; Fatty Acid Desaturases/*genetics/*metabolism/pharmacology ; Fatty Acids, Omega-3/analysis/*metabolism ; Fatty Acids, Omega-6 ; Fatty Acids, Unsaturated/analysis/metabolism ; Gene Transfer, Horizontal ; Growth Substances/pharmacology ; Neurons/chemistry/cytology/drug effects/*enzymology ; Rats ; Transfection ; }, abstract = {Previous studies have shown that n-3 polyunsaturated fatty acids (PUFAs) can exert an antiapoptotic effect on neurons. The present study was designed to investigate whether the Caenorhabditis elegans fat-1 gene encoding an n-3 fatty acid desaturase (an enzyme that converts n-6 PUFAs to corresponding n-3 PUFAs) can be expressed functionally in rat cortical neurons and whether its expression can change the ratio of n-6 : n-3 fatty acids in the cell membrane and exert an effect on neuronal apoptosis. Infection of primary rat cortical cultures with Ad-fat-1 resulted in high expression of the fat-1 gene. Lipid analysis indicated a decrease in the ratio of n-6 : n-3 PUFAs from 5.9 : 1 in control cells, to 1.45 : 1 in cells expressing the n-3 fatty acid desaturase. Accordingly, the levels of prostaglandin E2, an eicosanoid derived from n-6 PUFA, were significantly lower in cells infected with Ad-fat-1 when compared with control cells. Finally, there was a significant inhibition of growth factor withdrawal-induced apoptotic cell death in neurons expressing the fat-1 gene. These results demonstrate that expression of the fat-1 gene can inhibit apoptotic cell death in neurons and suggest that the change in the n-6 : n-3 fatty acid ratio may play a key role in this protective effect.}, }
@article {pmid12351239, year = {2002}, author = {Agersø, Y and Jensen, LB and Givskov, M and Roberts, MC}, title = {The identification of a tetracycline resistance gene tet(M), on a Tn916-like transposon, in the Bacillus cereus group.}, journal = {FEMS microbiology letters}, volume = {214}, number = {2}, pages = {251-256}, doi = {10.1111/j.1574-6968.2002.tb11355.x}, pmid = {12351239}, issn = {0378-1097}, mesh = {Bacillus cereus/drug effects/*genetics ; *DNA Transposable Elements ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Soil Microbiology ; Tetracycline Resistance/*genetics ; }, abstract = {In order to investigate whether resistance genes present in bacteria in manure could transfer to indigenous soil bacteria, resistant isolates belonging to the Bacillus cereus group (Bacillus cereus, Bacillus anthracis and Bacillus thuringiensis) were isolated from farm soil (72 isolates) and manure (12 isolates) samples. These isolates were screened for tetracycline resistance genes (tet(K), tet(L), tet(M), tet(O), tet(S) and tet(T)). Of 88 isolates examined, three (3.4%) isolates carried both tet(M) and tet(L) genes, while four (4.5%) isolates carried the tet(L) gene. Eighty-one (92.1%) isolates did not contain any of the tested genes. All tet(M) positive isolates carried transposon Tn916 and could transfer this mobile DNA element to other Gram-positive bacteria.}, }
@article {pmid12351223, year = {2002}, author = {O'Shea, YA and Boyd, EF}, title = {Mobilization of the Vibrio pathogenicity island between Vibrio cholerae isolates mediated by CP-T1 generalized transduction.}, journal = {FEMS microbiology letters}, volume = {214}, number = {2}, pages = {153-157}, doi = {10.1111/j.1574-6968.2002.tb11339.x}, pmid = {12351223}, issn = {0378-1097}, mesh = {Bacteriophages/*genetics ; *Chromosomes, Bacterial ; DNA, Bacterial/genetics ; Nucleic Acid Hybridization ; *Transduction, Genetic ; Vibrio cholerae/*genetics/*pathogenicity ; Virulence/genetics ; }, abstract = {Pathogenicity islands are large chromosomal regions encoding virulence genes that were acquired by horizontal gene transfer and are found in a wide range of pathogenic bacteria. In toxigenic Vibrio cholerae isolates the receptor for the cholera toxin encoding filamentous phage CTXphi, the toxin-coregulated pilus, is part of the Vibrio pathogenicity island (VPI). In this paper, we show that the VPI can be transferred between O1 serogroup strains, the predominant cause of epidemic cholera, via a generalized transducing phage CP-T1.}, }
@article {pmid12242011, year = {2002}, author = {Sánchez, L and Horner, D and Moore, D and Henze, K and Embley, T and Müller, M}, title = {Fructose-1,6-bisphosphate aldolases in amitochondriate protists constitute a single protein subfamily with eubacterial relationships.}, journal = {Gene}, volume = {295}, number = {1}, pages = {51-59}, doi = {10.1016/s0378-1119(02)00804-1}, pmid = {12242011}, issn = {0378-1119}, support = {AI 11942/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; DNA, Complementary/chemistry/genetics ; DNA, Protozoan/chemistry/genetics ; Diplomonadida/enzymology/genetics ; Entamoeba histolytica/enzymology/genetics ; Eukaryota/enzymology/*genetics ; Fructose-Bisphosphate Aldolase/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Trichomonas vaginalis/enzymology/genetics ; }, abstract = {Sequences of putative fructose-1,6-bisphospate aldolases (FBA) in five amitochondriate unicellular eukaryotes, the diplomonads Giardia intestinalis (published earlier) and Spironucleus barkhanus, the pelobiont Mastigamoeba balamuthi,the entamoebid Entamoeba histolytica, and the parabasalid Trichomonas vaginalis all belong to Class II of FBAs and are highly similar to each other (>48% amino acid identity). The five protist sequences, however, do not form a monophyletic group. Diplomonad FBAs share a most recent common ancestor, while FBAs of the three other protist species are part of a lineage that also includes sequences from a few eubacteria (Clostridium difficile, Treponema pallidum, Chlorobium tepidum). Both clades are part of the Type B of Class II aldolases, a complex that contains at least three additional lineages (subgroups) of enzymes. Type B enzymes are distant from Type A Class II aldolases, which consists of a number of bacterial and fungal enzymes and also contains the cytosolic FBA of Euglena gracilis. Class II aldolases are not homologous to Class I enzymes, to which animal and plant enzymes belong. The results indicate that amitochondriate protists acquired their FBAs from separate and different sources, involving lateral gene transfer from eubacteria, than did all other eukaryotes studied so far and underscore the complex composition of the glycolytic machinery in unicellular eukaryotes.}, }
@article {pmid12235846, year = {2002}, author = {Fukasawa, Y}, title = {[Relative relatedness of 11 mycobacteria species by microplate hybridization methods considering delta Tm].}, journal = {Kekkaku : [Tuberculosis]}, volume = {77}, number = {8}, pages = {547-554}, pmid = {12235846}, issn = {0022-9776}, mesh = {DNA, Bacterial/*analysis ; Mycobacterium/classification/genetics/*isolation &amp; purification ; Nucleic Acid Hybridization/*methods ; RNA, Ribosomal, 16S/genetics ; Temperature ; }, abstract = {Intra-species variance within Mycobacterium xenopi, Mycobacterium gordonae or Mycobacterium szulgai has been reported in identification employing chemotaxonomic characteristics, 16 S rRNA gene sequences or relative relatedness (relative color index) of genomic DNA-DNA Hybridization. Genomic DNA-DNA reassociation at the constant temperature was found to be unreliable for classification of mycobacterial species. However, nonspecific DNA reassociation could be avoided by hybridization at 56 degrees C after 45 degrees C overnight, and this technique was named delta DDH method in the preceding paper. The present report shows relative relatedness (relative color index) of genomic DNA in delta DDH method among mycobacterial species. Relative relatedness was below 70% among BCG, M. kansasii, M. simiae, M. asiaticum, M. szulgai, M. gordonae, M. xenopi and M. nonchromogenicum. The results satisfied the criteria for bacterial classification, which was proposed by the International Committee for Systematic Bacteriology in 1987. In regard to Mycobacterium avium complex, relative relatedness between M. avium and M. intracellulare were approximately 75%. It appeared that M. avium and M. intracellulare could be classified into one species. It has been recognized, moreover, that there are intermediate strains between M. avium and M. intracellulare. Previously, numerical classification raised a concept of Mycobacterium avium-intracellulare-scrofulaceum complex. The present study revealed that relative relatedness of M. avium and of M. intracellulare to M. scrofulaceum were around 75%, while the percentiles of M. scrofulaceum relative to M. avium and that to M. intracellulare were both less than 50%. The relative relatedness of M. ulcerans against M. marinum was nearly 65%, whereas the relative relatedness of M. marinum against M. ulcerans was approximately 90%. The data may be partly explained by the horizontal gene transfer mechanism.}, }
@article {pmid12234532, year = {2002}, author = {Momen, H}, title = {Molecular taxonomy of trypanosomatids: some problems and pitfalls.}, journal = {Archives of medical research}, volume = {33}, number = {4}, pages = {413-415}, doi = {10.1016/s0188-4409(02)00369-7}, pmid = {12234532}, issn = {0188-4409}, mesh = {Animals ; Evolution, Molecular ; *Phylogeny ; Trypanosomatina/*classification/*genetics/isolation &amp; purification ; }, abstract = {Trypanosomids appear to have attracted the particular attention of taxonomists, and a wealth of data from studies using a variety of techniques are available. There are, however, some potential pitfalls in such studies. A general problem in the taxonomy of Trypanosomatids resides in that only a small amount of its true diversity is reflected in the reduced number of isolates identified and studied from this family. An associated problem is that of confusion over the identity of the organisms. Other concerns include the problems of long branch attractions and mutational saturation, the loss of phylogenetic signal from the accumulation of overlapping mutations, and the fact that gene phylogeny cannot be equated with organism phylogeny and that organisms are more than just the sum of their genes. Additional complications can occur due to numerous cases of horizontal gene transfer between organisms. The use of a large sample of recent isolates from the field is also important so that the true diversity of these organisms is reflected in these studies, and bias due to selection, contamination, and misidentification when isolates have been maintained for long periods in culture is eliminated.}, }
@article {pmid12234006, year = {2002}, author = {She, Q and Brügger, K and Chen, L}, title = {Archaeal integrative genetic elements and their impact on genome evolution.}, journal = {Research in microbiology}, volume = {153}, number = {6}, pages = {325-332}, doi = {10.1016/s0923-2508(02)01331-1}, pmid = {12234006}, issn = {0923-2508}, mesh = {*Chromosomes, Archaeal ; Gene Transfer, Horizontal ; *Genes, Archaeal ; *Genome, Archaeal ; Integrases/*genetics ; Phylogeny ; RNA, Transfer/*genetics ; }, abstract = {Integrases encoded in archaeal genomes can be classified into seven families on the basis of their sequences. They constitute a super-family of tyrosine DNA recombinases together with a number of bacterial integrases and they are likely to be responsible for the formation of integrated elements in archaeal chromosomes. An integrated element is defined as possessing an integrase, a block of foreign genes, and a direct repeat at the two ends with one repeat unit overlapping a tRNA gene. There are two types of archaeal integrated elements, the SSV viral type, including those that carry the partitioned integrase gene, intN and intC, and the pNOB8 type, including those with a tRNA gene overlapping the attL site 5' prior to an integrase gene. Both known and unknown genes are present in these integrated elements and their encoded proteins may have facilitated the adaptation of archaea during evolution.}, }
@article {pmid12228811, year = {2002}, author = {Coates, BS and Hellmich, RL and Lewis, LC}, title = {Nuclear small subunit rRNA group I intron variation among Beauveria spp provide tools for strain identification and evidence of horizontal transfer.}, journal = {Current genetics}, volume = {41}, number = {6}, pages = {414-424}, doi = {10.1007/s00294-002-0317-8}, pmid = {12228811}, issn = {0172-8083}, mesh = {Base Sequence ; DNA, Ribosomal/chemistry/*genetics ; *Gene Transfer, Horizontal ; Hypocreales/*classification/genetics ; *Introns ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Sequence Homology, Nucleic Acid ; }, abstract = {An optional group I intron was characterized at a single insertion point in nuclear small subunit rRNA (nuSSU rRNA) genes of the imperfect entomopathogenic fungi, Beauveria bassiana and B. brongniartii. Insertion points were conserved among nuSSU rRNA genes from 35 Beauveria isolates. PCR-RFLP and DNA sequencing identified 12 group I intron variants and were applied to the identification of strains isolated from insect hosts. Alignment of 383-404-nt subgroup IB3 group I introns indicated that four insertion/deletion (indel) mutations were the main basis of fragment length variation. Phylogeny reconstruction using parsimony and neighbor-joining methods suggested six lineages may be present among nuSSU rRNA group I intron sequences from Beauveria and related ascomycete fungi. Terminal node placement of Beauveria introns conflicted with previously published phylogenies constructed from gene sequences, suggesting horizontal transfer of group I introns. PCR-RFLP among introns provided a means for the differentiation of Beauveria isolates.}, }
@article {pmid12225590, year = {2002}, author = {Xie, G and Bonner, CA and Jensen, RA}, title = {Dynamic diversity of the tryptophan pathway in chlamydiae: reductive evolution and a novel operon for tryptophan recapture.}, journal = {Genome biology}, volume = {3}, number = {9}, pages = {research0051}, pmid = {12225590}, issn = {1474-760X}, mesh = {Bacterial Proteins/genetics ; Bacterial Toxins/genetics ; Biological Transport, Active/genetics ; Chlamydia muridarum/enzymology/genetics/metabolism ; Chlamydia trachomatis/enzymology/genetics/metabolism ; Chlamydiaceae/enzymology/*genetics/*metabolism ; Chlamydophila pneumoniae/enzymology/genetics/metabolism ; Chlamydophila psittaci/enzymology/genetics/metabolism ; *Escherichia coli Proteins ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/genetics ; Genes, Regulator/genetics/physiology ; Genetic Variation/*genetics ; Hydrolases/genetics ; Kynurenine/metabolism ; Operon/*genetics ; Repressor Proteins/genetics/physiology ; Ribose-Phosphate Pyrophosphokinase/genetics ; Serine/metabolism ; Tryptophan/*metabolism ; }, abstract = {BACKGROUND: Complete genomic sequences of closely related organisms, such as the chlamydiae, afford the opportunity to assess significant strain differences against a background of many shared characteristics. The chlamydiae are ubiquitous intracellular parasites that are important pathogens of humans and other organisms. Tryptophan limitation caused by production of interferon-gamma by the host and subsequent induction of indoleamine dioxygenase is a key aspect of the host-parasite interaction. It appears that the chlamydiae have learned to recognize tryptophan depletion as a signal for developmental remodeling. The consequent non-cultivable state of persistence can be increasingly equated to chronic disease conditions.<br><br>RESULTS: The genes encoding enzymes of tryptophan biosynthesis were the focal point of this study. Chlamydophila psittaci was found to possess a compact operon containing PRPP synthase, kynureninase, and genes encoding all but the first step of tryptophan biosynthesis. All but one of the genes exhibited translational coupling. Other chlamydiae (Chlamydia trachomatis, C. muridarum and Chlamydophila pneumoniae) lack genes encoding PRPP synthase, kynureninase, and either lack tryptophan-pathway genes altogether or exhibit various stages of reductive loss. The origin of the genes comprising the trp operon does not seem to have been from lateral gene transfer.<br><br>CONCLUSIONS: The factors that accommodate the transition of different chlamydial species to the persistent (chronic) state of pathogenesis include marked differences in strategies deployed to obtain tryptophan from host resources. C. psittaci appears to have a novel mechanism for intercepting an early intermediate of tryptophan catabolism and recycling it back to tryptophan. In effect, a host-parasite metabolic mosaic has evolved for tryptophan recycling.}, }
@article {pmid12221298, year = {2002}, author = {Palenik, B}, title = {The genomics of symbiosis: hosts keep the baby and the bath water.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {99}, number = {19}, pages = {11996-11997}, pmid = {12221298}, issn = {0027-8424}, mesh = {Bacteria/genetics/metabolism ; Biological Evolution ; Cell Nucleus/genetics ; Chloroplasts/genetics/metabolism/microbiology ; Gene Transfer, Horizontal ; *Genomics ; Mitochondria/genetics/metabolism/microbiology ; Plants/genetics/microbiology ; Symbiosis/*genetics ; }, }
@article {pmid12220645, year = {2002}, author = {Staub, E and Hinzmann, B and Rosenthal, A}, title = {A novel repeat in the melanoma-associated chondroitin sulfate proteoglycan defines a new protein family.}, journal = {FEBS letters}, volume = {527}, number = {1-3}, pages = {114-118}, doi = {10.1016/s0014-5793(02)03195-2}, pmid = {12220645}, issn = {0014-5793}, mesh = {Animals ; Antigens/chemistry/metabolism ; Cadherins/chemistry ; Chondroitin Sulfate Proteoglycans/*chemistry/metabolism ; Conserved Sequence ; Databases, Protein ; Humans ; Membrane Proteins/*chemistry/metabolism ; Phylogeny ; Proteoglycans/chemistry/metabolism ; Rats ; *Repetitive Sequences, Amino Acid ; Software ; }, abstract = {The human melanoma-associated chondroitin sulfate proteoglycan (MCSP) and its rat ortholog NG2 are thought to play important roles in angiogenesis-dependent processes like wound healing and tumor growth. Based on electron microscopy studies, the highly glycosylated ectodomain of NG2 has been subdivided into the globular N-terminus, a flexible rod-like central region and a C-terminal portion in globular conformation. We identified a novel repeat named CSPG in the central ectodomain of NG2, MCSP and other proteins from fly, worm, human, sea urchin and a cyanobacterium which shows similarity to cadherin repeats. As earlier electron microscopy studies indicate, the folding of the tandem repeats compresses the length of the proposed repeat region by a factor of approximately 10 compared to the fully extended peptide chain. We identified two conserved negatively charged residues which might govern the binding properties of CSPG repeats. The phyletic distribution of CSPG repeats suggests that horizontal gene transfer contributed to their evolutionary history.}, }
@article {pmid12218172, year = {2002}, author = {Martin, W and Rujan, T and Richly, E and Hansen, A and Cornelsen, S and Lins, T and Leister, D and Stoebe, B and Hasegawa, M and Penny, D}, title = {Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {99}, number = {19}, pages = {12246-12251}, pmid = {12218172}, issn = {0027-8424}, mesh = {Arabidopsis/*genetics/*microbiology ; Arabidopsis Proteins/genetics ; *Biological Evolution ; Cell Nucleus/genetics/microbiology ; Chloroplasts/*genetics/microbiology ; Cyanobacteria/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Genome, Plant ; Models, Genetic ; Multigene Family ; Phylogeny ; Plastids/genetics/microbiology ; }, abstract = {Chloroplasts were once free-living cyanobacteria that became endosymbionts, but the genomes of contemporary plastids encode only approximately 5-10% as many genes as those of their free-living cousins, indicating that many genes were either lost from plastids or transferred to the nucleus during the course of plant evolution. Previous estimates have suggested that between 800 and perhaps as many as 2,000 genes in the Arabidopsis genome might come from cyanobacteria, but genome-wide phylogenetic surveys that could provide direct estimates of this number are lacking. We compared 24,990 proteins encoded in the Arabidopsis genome to the proteins from three cyanobacterial genomes, 16 other prokaryotic reference genomes, and yeast. Of 9,368 Arabidopsis proteins sufficiently conserved for primary sequence comparison, 866 detected homologues only among cyanobacteria and 834 other branched with cyanobacterial homologues in phylogenetic trees. Extrapolating from these conserved proteins to the whole genome, the data suggest that approximately 4,500 of Arabidopsis protein-coding genes (approximately 18% of the total) were acquired from the cyanobacterial ancestor of plastids. These proteins encompass all functional classes, and the majority of them are targeted to cell compartments other than the chloroplast. Analysis of 15 sequenced chloroplast genomes revealed 117 nuclear-encoded proteins that are also still present in at least one chloroplast genome. A phylogeny of chloroplast genomes inferred from 41 proteins and 8,303 amino acids sites indicates that at least two independent secondary endosymbiotic events have occurred involving red algae and that amino acid composition bias in chloroplast proteins strongly affects plastid genome phylogeny.}, }
@article {pmid12218016, year = {2002}, author = {Jahreis, K and Bentler, L and Bockmann, J and Hans, S and Meyer, A and Siepelmeyer, J and Lengeler, JW}, title = {Adaptation of sucrose metabolism in the Escherichia coli wild-type strain EC3132.}, journal = {Journal of bacteriology}, volume = {184}, number = {19}, pages = {5307-5316}, pmid = {12218016}, issn = {0021-9193}, mesh = {Adaptation, Physiological/*genetics ; Base Sequence ; Cloning, Molecular ; Escherichia coli/genetics/*metabolism ; Escherichia coli Proteins/*genetics/metabolism ; Fructokinases/genetics/metabolism ; Glycoside Hydrolases/genetics/metabolism ; Molecular Sequence Data ; Mutation ; Repressor Proteins/genetics/metabolism ; Sequence Analysis, DNA ; Sucrose/*metabolism ; beta-Fructofuranosidase ; }, abstract = {Although Escherichia coli strain EC3132 possesses a chromosomally encoded sucrose metabolic pathway, its growth on low sucrose concentrations (5 mM) is unusually slow, with a doubling time of 20 h. In this report we describe the subcloning and further characterization of the corresponding csc genes and adjacent genes. The csc regulon comprises three genes for a sucrose permease, a fructokinase, and a sucrose hydrolase (genes cscB, cscK, and cscA, respectively). The genes are arranged in two operons and are negatively controlled at the transcriptional level by the repressor CscR. Furthermore, csc gene expression was found to be cyclic AMP-CrpA dependent. A comparison of the genomic sequences of the E. coli strains EC3132, K-12, and O157:H7 in addition to Salmonella enterica serovar Typhimurium LT2 revealed that the csc genes are located in a hot spot region for chromosomal rearrangements in enteric bacteria. The comparison further indicated that the csc genes might have been transferred relatively recently to the E. coli wild-type EC3132 at around the time when the different strains of the enteric bacteria diverged. We found evidence that a mobile genetic element, which used the gene argW for site-specific integration into the chromosome, was probably involved in this horizontal gene transfer and that the csc genes are still in the process of optimal adaptation to the new host. Selection for such adaptational mutants growing faster on low sucrose concentrations gave three different classes of mutants. One class comprised cscR(Con) mutations that expressed all csc genes constitutively. The second class constituted a cscKo operator mutation, which became inducible for csc gene expression at low sucrose concentrations. The third class was found to be a mutation in the sucrose permease that caused an increase in transport activity.}, }
@article {pmid12216451, year = {2001}, author = {Shestakov, SV}, title = {[Genomics of pathogenic bacteria].}, journal = {Vestnik Rossiiskoi akademii meditsinskikh nauk}, volume = {}, number = {10}, pages = {18-25}, pmid = {12216451}, issn = {0869-6047}, mesh = {Bacteria/*genetics/*pathogenicity ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genotype ; }, abstract = {The general principles of structural and functional organization of genomes in pathogenic bacteria are considered. Main data on the specific features of genomes of Chlamydia trachomatis, Rickettsia prowazekii, Treponema pallidum, Helicobacter pylori, Haemophilus influenzae, Neisseria meningitidis, Vibro cholerae and pathogenic strains of Escherichia coli are summarized. Particular attention is paid to the problems of genetic control of pathogenicity, intraspecies variations in bacterial genomes, to the environmental and evolutionary meaning of horizontal gene transfer. Whether methods for genotyping bacterial strains can be used is discussed.}, }
@article {pmid12212935, year = {2002}, author = {Salyers, AA}, title = {An overview of the genetic basis of antibiotic resistance in bacteria and its implications for agriculture.}, journal = {Animal biotechnology}, volume = {13}, number = {1}, pages = {1-5}, doi = {10.1081/ABIO-120005766}, pmid = {12212935}, issn = {1049-5398}, mesh = {Animal Husbandry/*methods ; Animals ; Animals, Domestic ; Bacteria/drug effects/*genetics ; Bacterial Infections/drug therapy ; Drug Resistance, Bacterial/*genetics/physiology ; Gene Transfer, Horizontal/genetics/physiology ; Humans ; }, }
@article {pmid12205065, year = {2002}, author = {Colak, D and Naas, T and Gunseren, F and Fortineau, N and Ogunc, D and Gultekin, M and Nordmann, P}, title = {First outbreak of vancomycin-resistant enterococci in a tertiary hospital in Turkey.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {50}, number = {3}, pages = {397-401}, doi = {10.1093/jac/dkf134}, pmid = {12205065}, issn = {0305-7453}, mesh = {Adolescent ; Adult ; Cross Infection/microbiology ; DNA, Bacterial/analysis ; *Disease Outbreaks ; Electrophoresis, Gel, Pulsed-Field ; Enterococcus faecium/drug effects/*genetics/isolation &amp; purification ; Genes, Bacterial/*genetics ; Gram-Positive Bacterial Infections/*epidemiology/microbiology ; Hospitals, University ; Humans ; Infant ; Intensive Care Units ; Male ; Microbial Sensitivity Tests ; Middle Aged ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Turkey/epidemiology ; *Vancomycin Resistance ; }, abstract = {Twenty multidrug-resistant vancomycin-resistant Enterococcus faecium strains of the VanA phenotype were isolated over a 1 year period from five patients in the intensive care unit at the University Hospital of Antalya, Turkey. Molecular investigation showed that these strains belonged to five different pulsotypes and that the vanA gene was carried by a Tn1546-like transposon inserted onto a self-transferable plasmid of approximately 200 kb. One patient was infected by two different strains, suggesting horizontal gene transfer within that patient. This is the first documented outbreak of VRE in Turkey with concomitant spread of plasmid and strains.}, }
@article {pmid12202574, year = {2002}, author = {Tomita, H and Pierson, C and Lim, SK and Clewell, DB and Ike, Y}, title = {Possible connection between a widely disseminated conjugative gentamicin resistance (pMG1-like) plasmid and the emergence of vancomycin resistance in Enterococcus faecium.}, journal = {Journal of clinical microbiology}, volume = {40}, number = {9}, pages = {3326-3333}, pmid = {12202574}, issn = {0095-1137}, mesh = {Anti-Bacterial Agents/*pharmacology ; *Conjugation, Genetic ; Culture Media ; Drug Resistance, Bacterial/genetics ; Enterococcus faecium/*drug effects/genetics ; Gene Transfer, Horizontal ; Gentamicins/*pharmacology ; Nucleic Acid Hybridization ; Plasmids/*genetics ; *Vancomycin Resistance ; }, abstract = {A total of 640 vancomycin-resistant Enterococcus faecium (VRE) isolates, which were obtained between 1994 and 1999 from the Medical School Hospital of the University of Michigan, Ann Arbor, were used in this study. Of the 640 strains, 611 and 29 were VanA and VanB VRE, respectively, based on PCR analysis. Four hundred ninety-two (77%) of the strains exhibited resistance to concentrations of gentamicin from 64 micro g/ml (MIC) to more than 1,024 micro g/ml (MIC). The gentamicin resistance of each of 261 (53%) of the 492 gentamicin-resistant strains was transferred to E. faecium at a frequency of about 10(-5) to 10(-6) per donor cell in broth mating. More than 90% of vancomycin resistances of the 261 strains cotransferred with the gentamicin resistances to E. faecium strains by filter mating. The conjugative gentamicin resistance plasmids were identified and were classified into five types (A through E) with respect to their EcoRI restriction profiles. The transfer frequencies of each type of plasmid between E. faecium strains or Enterococcus faecalis strains were around 10(-3) to 10(-5) per donor cell or around 10(-6) to 10(-7) per donor cell, respectively, in broth mating. Type A and type B were the most frequently isolated, at an isolation frequency of about 40% per VRE isolate harboring the gentamicin resistance conjugative plasmid. The plasmids did not show any homology in Southern hybridization with the pheromone-responsive plasmids and broad-host-range plasmids pAMbeta1 and pIP501. The EcoRI or NdeI restriction fragments of each type of plasmids hybridized to the conjugative gentamicin resistance plasmid pMG1 (65.1 kb), which was originally isolated from an E. faecium clinical isolate, and transfer efficiently in broth mating.}, }
@article {pmid12188049, year = {2002}, author = {Betrán, E and Long, M}, title = {Expansion of genome coding regions by acquisition of new genes.}, journal = {Genetica}, volume = {115}, number = {1}, pages = {65-80}, doi = {10.1023/a:1016024131097}, pmid = {12188049}, issn = {0016-6707}, mesh = {Alcohol Dehydrogenase/genetics ; Animals ; Antifreeze Proteins/genetics ; DNA Transposable Elements ; Drosophila/genetics ; *Evolution, Molecular ; Fishes/genetics ; Gene Duplication ; Gene Transfer, Horizontal ; *Genome ; Retroelements ; }, abstract = {As it is the case for non-coding regions, the coding regions of organisms can be expanded or shrunk during evolutionary processes. However, the dynamics of coding regions are expected to be more correlated with functional complexity and diversity than are the dynamics of non-coding regions. Hence, it is interesting to investigate the increase of diversity in coding regions--the origin and evolution of new genes - because this provides a new component to the genetic variation underlying the diversity of living organisms. Here, we examine what is known about the mechanisms responsible for the increase in gene number. Every mechanism affects genomes in a distinct way and to a different extent and it appears that certain organisms favor particular mechanisms. The detail of some interesting gene acquisitions reveals the extreme dynamism of genomes. Finally, we discuss what is known about the fate of new genes and conclude that many of the acquisitions are likely to have been driven by natural selection; they increase functional complexity, diversity, and/or adaptation of species. Despite this, the correlation between complexity of life and gene number is low and closely related species (with very similar life histories) can have very different number of genes. We call this phenomenon the G-value paradox.}, }
@article {pmid12183545, year = {2002}, author = {Peacock, SJ and Moore, CE and Justice, A and Kantzanou, M and Story, L and Mackie, K and O'Neill, G and Day, NP}, title = {Virulent combinations of adhesin and toxin genes in natural populations of Staphylococcus aureus.}, journal = {Infection and immunity}, volume = {70}, number = {9}, pages = {4987-4996}, pmid = {12183545}, issn = {0019-9567}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Adhesins, Bacterial/*genetics ; Alleles ; Bacterial Toxins/*genetics ; Base Sequence ; Community-Acquired Infections/etiology/microbiology ; Cross Infection/etiology/microbiology ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genetic Variation ; Genetics, Population ; Genotype ; Humans ; Linkage Disequilibrium ; Multivariate Analysis ; Phenotype ; Staphylococcal Infections/etiology/microbiology ; Staphylococcus aureus/*genetics/isolation &amp; purification/*pathogenicity ; Virulence/genetics ; }, abstract = {Most cases of severe Staphylococcus aureus disease cannot be explained by the action of a single virulence determinant, and it is likely that a number of factors act in combination during the infective process. This study examined the relationship between disease in humans and a large number of putative virulence determinants, both individually and in combination. S. aureus isolates (n = 334) from healthy blood donors and from patients with invasive disease were compared for variation in the presence of 33 putative virulence determinants. After adjusting for the effect of clonality, seven determinants (fnbA, cna, sdrE, sej, eta, hlg, and ica) were significantly more common in invasive isolates. All seven factors contributed independently to virulence. No single factor predominated as the major predictor of virulence, their effects appearing to be cumulative. No combinations of the seven genes were either more or less likely to cause disease than others with the same number of virulence-associated genes. There was evidence of considerable horizontal transfer of genes on a background of clonality. Our findings also suggested that allelic variants of a polymorphic locus can make different contributions to the disease process, further study of which is likely to expand our understanding of staphylococcal disease pathogenesis.}, }
@article {pmid12180348, year = {2002}, author = {Willerslev, E and Mourier, T and Hansen, AJ and Christensen, B and Barnes, I and Salzberg, SL}, title = {Contamination in the draft of the human genome masquerades as lateral gene transfer.}, journal = {DNA sequence : the journal of DNA sequencing and mapping}, volume = {13}, number = {2}, pages = {75-76}, doi = {10.1080/10425170290023392}, pmid = {12180348}, issn = {1042-5179}, mesh = {Animals ; *Artifacts ; Bacteria/genetics ; Drosophila melanogaster/genetics ; *Gene Transfer, Horizontal ; *Genome, Human ; Humans ; *Sequence Analysis, DNA ; }, }
@article {pmid12177349, year = {2002}, author = {Parker, MA and Lafay, B and Burdon, JJ and van Berkum, P}, title = {Conflicting phylogeographic patterns in rRNA and nifD indicate regionally restricted gene transfer in Bradyrhizobium.}, journal = {Microbiology (Reading, England)}, volume = {148}, number = {Pt 8}, pages = {2557-2565}, doi = {10.1099/00221287-148-8-2557}, pmid = {12177349}, issn = {1350-0872}, mesh = {Bradyrhizobium/*classification/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genotype ; Molecular Sequence Data ; Nitrogenase/classification/*genetics/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/classification/*genetics ; Sequence Analysis, DNA ; }, abstract = {Major differences in evolutionary relationships of the 16S rRNA gene and the nitrogenase alpha-subunit gene (nifD) were observed among 38 strains of Bradyrhizobium sp. nodule bacteria from North America, Central America, Asia and Australia. Two lineages were evident in the 16S rRNA phylogeny representing strains related to Bradyrhizobium japonicum (29 isolates) or Bradyrhizobium elkanii (9 isolates). Both clades were distributed across most or all of the geographic regions sampled. By contrast, in the nifD tree almost all isolates were placed into one of three groups each exclusively composed of taxa from a single geographic region (North Temperate, Central America or Australia). Isolates that were closely related or identical in gene sequence at one locus often had divergent sequences at the other locus and a partition homogeneity test indicated that the 16S rRNA and nifD phylogenies were significantly incongruent. No evidence for any gene duplication of nifD was found by Southern hybridization analysis on a subset of the strains, so unrecognized paralogy is not likely to be responsible for the discrepancy between 16S rRNA and nifD tree topologies. These results are consistent with a model whereby geographic areas were initially colonized by several diverse 16S rRNA lineages, with subsequent horizontal gene transfer of nifD leading to increased nifD sequence homogeneity within each regional population.}, }
@article {pmid12177347, year = {2002}, author = {Griffiths, E and Gupta, RS}, title = {Protein signatures distinctive of chlamydial species: horizontal transfers of cell wall biosynthesis genes glmU from archaea to chlamydiae and murA between chlamydiae and Streptomyces.}, journal = {Microbiology (Reading, England)}, volume = {148}, number = {Pt 8}, pages = {2541-2549}, doi = {10.1099/00221287-148-8-2541}, pmid = {12177347}, issn = {1350-0872}, mesh = {Alkyl and Aryl Transferases/*genetics ; Archaea/*genetics ; Cell Wall/*genetics/physiology ; Chlamydiales/classification/*genetics ; Conserved Sequence ; DNA, Bacterial/analysis ; Gene Deletion ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Molecular Sequence Data ; Nucleotidyltransferases/*genetics/physiology ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Streptomyces/classification/*genetics ; }, abstract = {Chlamydiae are major human and animal pathogens. Based on alignments of different protein sequences, a number of conserved indels (insertion/deletions) were identified that appear to be unique and distinctive characteristics of the chlamydial species. The identified signatures include one 16 aa and two single aa inserts in the enzyme UDP-N-acetylglucosamine 1-carboxyvinyltransferase (MurA), a 1 aa insert in protein synthesis elongation factor P (EF-P), a 1 aa insert in the Mg(2+) transport protein (MgtE), a 1 aa insert in the carboxy-terminal protease and a 1 aa deletion in the tRNA (guanine-N(1)-)-methyltransferase (TrmD) protein. The homologues of these proteins are found in all major groups of bacteria and the observed indels are present in all available chlamydial sequences but not in any other species (except for the large insert in MurA in Streptomyces). The validity of three of these signatures (MurA, EF-P and MgtE) was tested by PCR amplifying the signature regions from several chlamydial species for which no sequence information was available. All Chlamydiaceae species for which specific fragments could be amplified (Chlamydia suis, Chlamydophila abortus, Chlamydophila psittaci, Chlamydophila felis) contained the expected signatures. Additionally, a fragment of the murA gene from Waddlia chondrophila and the efp gene from Simkania negevensis, two chlamydia-like species, were also cloned and sequenced. The presence of respective indels in these species provides strong evidence that they are specifically related to the traditional chlamydial species, and that these signatures may be distinctive of the entire Chlamydiales order. A 17 aa conserved indel was also identified in the cell wall biosynthesis enzyme UDP-N-acetylglucosamine pyrophosphorylase (GlmU), which is shared by all archaeal and chlamydial homologues. The gene for this protein is indicated to have been horizontally transferred from an archaeon to a common ancestor of the chlamydiae. The results also support a lateral transfer of the murA gene between chlamydiae and STREPTOMYCES: The large inserts in these peptidoglycan synthesis related genes in chlamydiae could account for their unusual cell-wall characteristics. These signatures are also potentially useful for screening of the chlamydiae species.}, }
@article {pmid12177346, year = {2002}, author = {Kotewicz, ML and Li, B and Levy, DD and LeClerc, JE and Shifflet, AW and Cebula, TA}, title = {Evolution of multi-gene segments in the mutS-rpoS intergenic region of Salmonella enterica serovar Typhimurium LT2.}, journal = {Microbiology (Reading, England)}, volume = {148}, number = {Pt 8}, pages = {2531-2540}, doi = {10.1099/00221287-148-8-2531}, pmid = {12177346}, issn = {1350-0872}, mesh = {Adenosine Triphosphatases/*genetics ; Bacterial Proteins/genetics ; Chromosome Deletion ; Chromosome Inversion ; Chromosomes, Bacterial ; DNA, Intergenic/*genetics ; *DNA-Binding Proteins ; Escherichia coli Proteins/*genetics ; *Evolution, Molecular ; Gene Rearrangement ; *Genes, Bacterial ; Genome, Bacterial ; Molecular Sequence Data ; Multigene Family ; MutS DNA Mismatch-Binding Protein ; Nucleic Acid Hybridization ; Open Reading Frames ; Salmonella enterica/*genetics ; Sigma Factor/*genetics ; }, abstract = {The nucleotide sequence of the 12.6 kb region between the mutS and rpoS genes of Salmonella enterica serovar Typhimurium LT2 (S. typhimurium) was compared to other enteric bacterial mutS-rpoS intergenic regions. The mutS-rpoS region is composed of three distinct segments, designated HK, O and S, as defined by sequence similarities to contiguous ORFs in other bacteria. Inverted chromosomal orientations of each of these segments are found between the mutS and rpoS genes in related ENTEROBACTERIACEAE: The HK segment is distantly related to a cluster of seven ORFs found in Haemophilus influenzae and a cluster of five ORFs found between the mutS and rpoS genes in Escherichia coli K-12. The O segment is related to the mutS-rpoS intergenic region found in E. coli O157:H7 and Shigella dysenteriae type 1. The third segment, S, is common to diverse Salmonella species, but is absent from E. coli. Despite the extensive collinearity and conservation of the overall genetic maps of S. typhimurium and E. coli K-12, the insertions, deletions and inversions in the mutS-rpoS region provide evidence that this region of the chromosome is an active site for horizontal gene transfer and rearrangement.}, }
@article {pmid12176923, year = {2002}, author = {Brinkman, FS and Blanchard, JL and Cherkasov, A and Av-Gay, Y and Brunham, RC and Fernandez, RC and Finlay, BB and Otto, SP and Ouellette, BF and Keeling, PJ and Rose, AM and Hancock, RE and Jones, SJ and Greberg, H}, title = {Evidence that plant-like genes in Chlamydia species reflect an ancestral relationship between Chlamydiaceae, cyanobacteria, and the chloroplast.}, journal = {Genome research}, volume = {12}, number = {8}, pages = {1159-1167}, pmid = {12176923}, issn = {1088-9051}, mesh = {Animals ; Bacterial Proteins/chemistry/genetics ; Base Composition/genetics ; Caenorhabditis elegans Proteins/chemistry/genetics ; Chlamydia/*genetics ; Chlamydiaceae/*genetics ; Chloroplasts/*genetics ; Computational Biology/methods ; Cyanobacteria/*genetics ; Databases, Genetic ; Databases, Protein ; Drosophila Proteins/chemistry/genetics ; *Evolution, Molecular ; Genes, Bacterial/*genetics ; Genes, Plant/*genetics ; Genome, Bacterial ; Humans ; Mitochondria/genetics ; Phylogeny ; Rickettsia/genetics ; Saccharomyces cerevisiae Proteins/chemistry/genetics ; Sequence Homology, Amino Acid ; }, abstract = {An unusually high proportion of proteins encoded in Chlamydia genomes are most similar to plant proteins, leading to proposals that a Chlamydia ancestor obtained genes from a plant or plant-like host organism by horizontal gene transfer. However, during an analysis of bacterial-eukaryotic protein similarities, we found that the vast majority of plant-like sequences in Chlamydia are most similar to plant proteins that are targeted to the chloroplast, an organelle derived from a cyanobacterium. We present further evidence suggesting that plant-like genes in Chlamydia, and other Chlamydiaceae, are likely a reflection of an unappreciated evolutionary relationship between the Chlamydiaceae and the cyanobacteria-chloroplast lineage. Further analyses of bacterial and eukaryotic genomes indicates the importance of evaluating organellar ancestry of eukaryotic proteins when identifying bacteria-eukaryote homologs or horizontal gene transfer and supports the proposal that Chlamydiaceae, which are obligate intracellular bacterial pathogens of animals, are not likely exchanging DNA with their hosts.}, }
@article {pmid12175808, year = {2002}, author = {Wolf, YI and Rogozin, IB and Grishin, NV and Koonin, EV}, title = {Genome trees and the tree of life.}, journal = {Trends in genetics : TIG}, volume = {18}, number = {9}, pages = {472-479}, doi = {10.1016/s0168-9525(02)02744-0}, pmid = {12175808}, issn = {0168-9525}, mesh = {Animals ; Computational Biology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation/genetics ; *Genome ; Humans ; Models, Genetic ; Phylogeny ; Sequence Alignment ; Sequence Analysis, Protein ; }, abstract = {Genome comparisons indicate that horizontal gene transfer and differential gene loss are major evolutionary phenomena that, at least in prokaryotes, involve a large fraction, if not the majority, of genes. The extent of these events casts doubt on the feasibility of constructing a 'Tree of Life', because the trees for different genes often tell different stories. However, alternative approaches to tree construction that attempt to determine tree topology on the basis of comparisons of complete gene sets seem to reveal a phylogenetic signal that supports the three-domain evolutionary scenario and suggests the possibility of delineation of previously undetected major clades of prokaryotes. If the validity of these whole-genome approaches to tree building is confirmed by analyses of numerous new genomes, which are currently being sequenced at an increasing rate, it would seem that the concept of a universal 'species' tree is still appropriate. However, this tree should be reinterpreted as a prevailing trend in the evolution of genome-scale gene sets rather than as a complete picture of evolution.}, }
@article {pmid12173464, year = {2002}, author = {Semin, BV and Leonova, TIa and Il'in, IuV}, title = {[Retrotransposon mdg3 is transferred between somatic cells of unrelated species in coculture].}, journal = {Molekuliarnaia biologiia}, volume = {36}, number = {4}, pages = {617-622}, pmid = {12173464}, issn = {0026-8984}, mesh = {Animals ; Cells, Cultured ; Coculture Techniques ; Drosophila/cytology/*genetics ; *Gene Transfer, Horizontal ; Genes, env ; *Retroelements ; }, abstract = {Since retrovirus-like particles of gypsy (mdg4) are capable of interspecific transfer, other Drosophila melanogaster gypsy-related retrotransposons were tested for this property. As a donor and a recipient, D. melanogaster and D. virilis cultured cells were used. Recipient cell DNA was analyzed with probes directed to mdg1, mdg3, 17.6, 297, 412, or B104/roo. Transfer was demonstrated for mdg3, which lacks env. The possible mechanism of transfer is discussed.}, }
@article {pmid12169615, year = {2002}, author = {Lawrence, JG and Hatfull, GF and Hendrix, RW}, title = {Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches.}, journal = {Journal of bacteriology}, volume = {184}, number = {17}, pages = {4891-4905}, pmid = {12169615}, issn = {0021-9193}, support = {R01 GM051975/GM/NIGMS NIH HHS/United States ; GM 47795/GM/NIGMS NIH HHS/United States ; R01 AI028927/AI/NIAID NIH HHS/United States ; GM 51975/GM/NIGMS NIH HHS/United States ; AI 28927/AI/NIAID NIH HHS/United States ; R01 GM047795/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteriophages/*classification/genetics ; Biological Evolution ; Gene Transfer, Horizontal ; Mosaicism ; Recombination, Genetic ; }, abstract = {The practice of classifying organisms into hierarchical groups originated with Aristotle and was codified into nearly immutable biological law by Linnaeus. The heart of taxonomy is the biological species, which forms the foundation for higher levels of classification. Whereas species have long been established among sexual eukaryotes, achieving a meaningful species concept for prokaryotes has been an onerous task and has proven exceedingly difficult for describing viruses and bacteriophages. Moreover, the assembly of viral "species" into higher-order taxonomic groupings has been even more tenuous, since these groupings were based initially on limited numbers of morphological features and more recently on overall genomic similarities. The wealth of nucleotide sequence information that catalyzed a revolution in the taxonomy of free-living organisms necessitates a reevaluation of the concept of viral species, genera, families, and higher levels of classification. Just as microbiologists discarded dubious morphological traits in favor of more accurate molecular yardsticks of evolutionary change, virologists can gain new insight into viral evolution through the rigorous analyses afforded by the molecular phylogenetics of viral genes. For bacteriophages, such dissections of genomic sequences reveal fundamental flaws in the Linnaean paradigm that necessitate a new view of viral evolution, classification, and taxonomy.}, }
@article {pmid12167368, year = {2002}, author = {Jain, R and Rivera, MC and Moore, JE and Lake, JA}, title = {Horizontal gene transfer in microbial genome evolution.}, journal = {Theoretical population biology}, volume = {61}, number = {4}, pages = {489-495}, doi = {10.1006/tpbi.2002.1596}, pmid = {12167368}, issn = {0040-5809}, mesh = {Archaea/genetics ; Bacteria/genetics ; *Biological Evolution ; Eukaryotic Cells ; *Gene Transfer, Horizontal ; *Genome ; }, abstract = {Horizontal gene transfer is the collective name for processes that permit the exchange of DNA among organisms of different species. Only recently has it been recognized as a significant contribution to inter-organismal gene exchange. Traditionally, it was thought that microorganisms evolved clonally, passing genes from mother to daughter cells with little or no exchange of DNA among diverse species. Studies of microbial genomes, however, have shown that genomes contain genes that are closely related to a number of different prokaryotes, sometimes to phylogenetically very distantly related ones. (Doolittle et al., 1990, J. Mol. Evol. 31, 383-388; Karlin et al., 1997, J. Bacteriol. 179, 3899-3913; Karlin et al., 1998, Annu. Rev. Genet. 32, 185-225; Lawrence and Ochman, 1998, Proc. Natl. Acad. Sci. USA 95, 9413-9417; Rivera et al., 1998, Proc. Natl. Acad. Sci. USA 95, 6239-6244; Campbell, 2000, Theor. Popul. Biol. 57 71-77; Doolittle, 2000, Sci. Am. 282, 90-95; Ochman and Jones, 2000, Embo. J. 19, 6637-6643; Boucher et al. 2001, Curr. Opin., Microbiol. 4, 285-289; Wang et al., 2001, Mol. Biol. Evol. 18, 792-800). Whereas prokaryotic and eukaryotic evolution was once reconstructed from a single 16S ribosomal RNA (rRNA) gene, the analysis of complete genomes is beginning to yield a different picture of microbial evolution, one that is wrought with the lateral movement of genes across vast phylogenetic distances. (Lane et al., 1988, Methods Enzymol. 167, 138-144; Lake and Rivera, 1996, Proc. Natl. Acad. Sci. USA 91, 2880-2881; Lake et al., 1999, Science 283, 2027-2028).}, }
@article {pmid12167364, year = {2002}, author = {Lawrence, JG}, title = {Gene transfer in bacteria: speciation without species?.}, journal = {Theoretical population biology}, volume = {61}, number = {4}, pages = {449-460}, doi = {10.1006/tpbi.2002.1587}, pmid = {12167364}, issn = {0040-5809}, mesh = {Bacteria/*genetics ; *Gene Transfer, Horizontal ; Recombination, Genetic ; Species Specificity ; }, abstract = {Although Bacteria and Archaea reproduce by binary fission, exchange of genes among lineages has shaped the diversity of their populations and the diversification of their lineages. Gene exchange can occur by two distinct routes, each differentially impacting the recipient genome. First, homologous recombination mediates the exchange of DNA between closely related individuals (those whose sequences are sufficient similarly to allow efficient integration). As a result, homologous recombination mediates the dispersal of advantageous alleles that may rise to high frequency among genetically related individuals via periodic selection events. Second, lateral gene transfer can introduce novel DNA into a genome from completely unrelated lineages via illegitimate recombination. Gene exchange by this route serves to distribute genes throughout distantly related clades and therefore may confer complex abilities--not otherwise found among closely related lineages--onto the recipient organisms. These two mechanisms of gene exchange play complementary roles in the diversification of microbial populations into independent, ecologically distinct lineages. Although the delineation of microbial "species" then becomes difficult--if not impossible--to achieve, a cogent process of speciation can be predicted.}, }
@article {pmid12167362, year = {2002}, author = {Gupta, RS and Griffiths, E}, title = {Critical issues in bacterial phylogeny.}, journal = {Theoretical population biology}, volume = {61}, number = {4}, pages = {423-434}, doi = {10.1006/tpbi.2002.1589}, pmid = {12167362}, issn = {0040-5809}, mesh = {Amino Acid Sequence ; Bacteria/*classification/genetics ; Gene Transfer, Horizontal ; Genetic Markers ; Molecular Sequence Data ; *Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Homology, Amino Acid ; Transcription Factors/chemistry ; }, abstract = {To understand bacterial phylogeny, it is essential that the following two critical issues be resolved: (i) development of well-defined (molecular) criteria for identifying the main groups within Bacteria, and (ii) to understand how the different main groups are related to each other and how they branched off from a common ancestor. These issues are not resolved at present. We have recently described a new approach, based on shared conserved inserts and deletions (indels or signature sequences) found in various proteins, that provides a reliable means for understanding these issues. A large number of conserved indels that are shared by different groups of bacteria have been identified. Using these indels, and based simply on their presence or absence, all of the main groups within Bacteria can be defined in clear molecular terms and new species could be assigned to them with minimal ambiguity. The analysis of these indels also permits one to logically deduce that the various main bacterial groups have branched off from a common ancestor in the following order: Low G+C Gram-positive ==> High G+C Gram-positive ==> Clostridium-Fusobacteria-Thermotoga ==> Deinococcus-Thermus-Green nonsulfur bacteria ==> Cyanobacteria ==> Spirochetes ==> Chlamydia-Cytophaga-Bacteroides-Green sulfur bacteria ==> Aquifex ==> Proteobacteria 1 (epsilon and delta) ==> Proteobacteria-2. (alpha) ==> Proteobacteria-3 (beta) and ==> Proteobacteria-4 (gamma). The validity of this approach was tested using sequence data from bacterial genomes. By making use of 18 conserved indels, species from all 60 completed bacterial genomes were assigned to different groups. The observed distribution of these indels in different species was then compared with that predicted by the model. Of the 936 observations concerning the placement of these indels in various species, all except one were in accordance with the model. The placement of bacteria into different groups using this approach also showed excellent correlation with the 16S rRNA phylogenies with nearly all of the species assigned to the same groups by both methods. These results provide strong evidence that the genes containing these indels have not been affected by factors such as lateral gene transfers. However, such events are readily detected by this means and some examples are provided. The approach described here thus provides a reliable and internally consistent means for understanding various critical and long outstanding issues in bacterial phylogeny.}, }
@article {pmid12167360, year = {2002}, author = {Gribaldo, S and Philippe, H}, title = {Ancient phylogenetic relationships.}, journal = {Theoretical population biology}, volume = {61}, number = {4}, pages = {391-408}, doi = {10.1006/tpbi.2002.1593}, pmid = {12167360}, issn = {0040-5809}, mesh = {Amino Acid Sequence ; Animals ; Humans ; Molecular Sequence Data ; *Phylogeny ; Sequence Homology, Amino Acid ; }, abstract = {Traditional views on deep evolutionary events have been seriously challenged over the last few years, following the identification of major pitfalls affecting molecular phylogeny reconstruction. Here we describe the principally encountered artifacts, notably long branch attraction, and their causes (i.e., difference in evolutionary rates, mutational saturation, compositional biases). Additional difficulties due to phenomena of biological nature (i.e., lateral gene transfer, recombination, hidden paralogy) are also discussed. Moreover, contrary to common beliefs, we show that the use of rare genomic events can also be misleading and should be treated with the same caution as standard molecular phylogeny. The universal tree of life, as described in most textbooks, is partly affected by tree reconstruction artifacts, e.g. (i) the bacterial rooting of the universal tree of life; (ii) the early emergence of amitochondriate lineages in eukaryotic phylogenies; and (iii) the position of hyperthermophilic taxa in bacterial phylogenies. We present an alternative view of this tree, based on recent evidence obtained from reanalyses of ancient data sets and from novel analyses of large combination of genes.}, }
@article {pmid12165840, year = {2002}, author = {Dalevi, DA and Eriksen, N and Eriksson, K and Andersson, SG}, title = {Measuring genome divergence in bacteria: a case study using chlamydian data.}, journal = {Journal of molecular evolution}, volume = {55}, number = {1}, pages = {24-36}, doi = {10.1007/s00239-001-0087-9}, pmid = {12165840}, issn = {0022-2844}, mesh = {Chlamydia/classification/*genetics ; Chlamydia trachomatis/genetics ; Chlamydophila pneumoniae/genetics ; Chromosome Inversion ; *Gene Rearrangement ; *Genetic Variation ; *Genome, Bacterial ; Models, Genetic ; Replication Origin/genetics ; }, abstract = {We have studied the relative contribution of inversions, transpositions, deletions, and nucleotide substitutions to the evolution of Chlamydia trachomatis and Chlamydia pneumoniae. The minimal number of rearrangement events required for converting the gene order structure of one genome into that of the other was estimated to 59 +/- 6 events, including 13% inversions, 38% short inversions, and 49% transpositions. In contrast to previous findings, no examples of horizontal gene transfer subsequent to species divergence were identified, nor any evidence for an excessive number of tandem gene duplications. A statistical model was used to compare nucleotide frequencies for a set of genes uniquely present in one species to a set of orthologous genes present in both species. The two data sets were not significantly different, which is indicative of a low frequency of horizontal gene transfer events. This is based on the assumption that a foreign gene of different nucleotide content will not have become completely ameliorated, as verified by simulations of the amelioration rate at twofold and fourfold degenerate codon sites. The frequencies of nucleotide substitutions at twofold and fourfold degenerate sites, deletions, inversions, and translocations were estimated to 1.42, 0.62, 0.18, 0.01, and 0.01 per site, respectively.}, }
@article {pmid12161772, year = {2002}, author = {Anderson, AS and Clark, DJ and Gibbons, PH and Sigmund, JM}, title = {The detection of diverse aminoglycoside phosphotransferases within natural populations of actinomycetes.}, journal = {Journal of industrial microbiology &amp; biotechnology}, volume = {29}, number = {2}, pages = {60-69}, doi = {10.1038/sj.jim.7000260}, pmid = {12161772}, issn = {1367-5435}, mesh = {Actinobacteria/*enzymology/*genetics ; Amino Acid Sequence ; Drug Resistance, Bacterial/*genetics ; Genes, Bacterial/*genetics ; Kanamycin Kinase/chemistry/*genetics ; Phenotype ; Phylogeny ; Polymerase Chain Reaction ; Sequence Homology, Amino Acid ; Soil Microbiology ; }, abstract = {The conserved nature of the genes that code for actinomycete secondary metabolite biosynthetic pathways suggests a common evolutionary ancestor and incidences of lateral gene transfer. Resistance genes associated with these biosynthetic pathways also display a high degree of similarity. Actinomycete aminoglycoside phosphotransferase antibiotic resistance enzymes (APH) are coded for by such genes and are therefore good targets for evaluating the bioactive potential of actinomycetes. A set of universal PCR primers for APH encoding genes was used to probe genomic DNA from three collections of actinomycetes to determine the utility of molecular screening. An additional monitoring of populations for the predominance of specific classes of enzymes to predict the potential of environmental sites for providing isolates with interesting metabolic profiles. Approximately one-fifth of all isolates screened gave a positive result by PCR. The PCR products obtained were sequenced and compared to existing APH family members. Sequence analysis resolved the family into nine groups of which six had recognizable phenotypes: 6'-phosphotransferase (APH(6)), 3'-phosphotransferase (APH(3)), hydroxyurea phosphotransferase (HUR), peptide phosphotransferase, hygromycin B phosphotransferase (APH(7")) and oxidoreductase. The actinomycetes screened fell into seven groups, including three novel groups with unknown phenotypes. The strains clustered according to the environmental site from where they were obtained, providing evidence for the movement of these genes within populations. The value of this as a method for obtaining novel compounds and the significance to the ecology of antibiotic biosynthesis are discussed.}, }
@article {pmid12160637, year = {2002}, author = {Kalkum, M and Eisenbrandt, R and Lurz, R and Lanka, E}, title = {Tying rings for sex.}, journal = {Trends in microbiology}, volume = {10}, number = {8}, pages = {382-387}, doi = {10.1016/s0966-842x(02)02399-5}, pmid = {12160637}, issn = {0966-842X}, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics/metabolism ; Conjugation, Genetic/*genetics ; Fimbriae Proteins ; Membrane Proteins/*chemistry/genetics/metabolism ; Molecular Sequence Data ; *Periplasmic Proteins ; Pili, Sex/*genetics/*metabolism/ultrastructure ; Plasmids/*genetics ; }, abstract = {The primary component of the sex pilus encoded by IncP (RP4) and Ti plasmids has been identified as a circular pilin protein with a peptide bond between the amino and carboxyl terminus. Here, we review the key experiments that led to this discovery, and the present mechanistic model for pilin-precursor processing and the cyclization reaction. In addition, we discuss the implications for horizontal gene transfer in bacterial conjugation.}, }
@article {pmid12154506, year = {2002}, author = {Opavski, N and Djukić, S and Mijac, V and Ranin, L}, title = {[Transfer of Streptococcus pneumonia genetic material by the process of transformation].}, journal = {Srpski arhiv za celokupno lekarstvo}, volume = {130}, number = {3-4}, pages = {110-114}, doi = {10.2298/sarh0204110o}, pmid = {12154506}, issn = {0370-8179}, mesh = {*Gene Transfer, Horizontal ; Streptococcus pneumoniae/*genetics ; *Transformation, Bacterial ; }, }
@article {pmid12152043, year = {2002}, author = {Pearson, H}, title = {'Superbug' hurdles key drug barrier.}, journal = {Nature}, volume = {418}, number = {6897}, pages = {469}, doi = {10.1038/418469b}, pmid = {12152043}, issn = {0028-0836}, mesh = {Centers for Disease Control and Prevention, U.S. ; Disease Outbreaks/prevention &amp; control ; *Drug Resistance, Multiple, Bacterial/genetics ; Enterococcus faecalis/drug effects/genetics/physiology ; Gene Transfer, Horizontal ; Humans ; Michigan ; Staphylococcal Infections/complications/drug therapy/*microbiology ; Staphylococcus aureus/*drug effects/*genetics/pathogenicity/physiology ; United States ; Vancomycin Resistance/*genetics ; }, }
@article {pmid12151256, year = {2002}, author = {Sterrer, W}, title = {On the origin of sex as vaccination.}, journal = {Journal of theoretical biology}, volume = {216}, number = {4}, pages = {387-396}, doi = {10.1006/jtbi.2002.3008}, pmid = {12151256}, issn = {0022-5193}, mesh = {Animals ; *Biological Evolution ; Genome ; Meiosis ; *Sex ; Superinfection/prevention &amp; control ; *Vaccination ; }, abstract = {In the theory of the origin of sex as vaccination, I propose that the eukaryote genome accreted from prokaryan symbiont genomes in numerous rounds of lateral gene transfer during which sex diverged from unilateral parasitic infection, as an increasingly ritualized, reciprocal vaccination against superinfection. Sex-as-syngamy (fusion sex) arose when infected proto-eukaryan hosts began swapping nuclearized genomes containing coevolved, vertically transmitted ("attenuated") symbionts that conveyed protection against horizontal superinfection by more virulent symbionts. Sex-as-meiosis (fission sex) evolved as a host strategy to uncouple (and thereby emasculate) the acquired symbiont genomes. The chimeric nature, distribution over discrete chromosomes, and mosaic composition of the eukaryan nuclear genome derive from multiple rounds of acquiring and uncoupling prokaryan genomes. Genome compatibility-based recognition of self and mates came to define sex, mate choice, and the biological species. By generating unique individuality, sex now persists as an elaborate (hence tamper-proof) periodic device for an organism to thwart both endo- and exogenous challengers, and stay ahead of an environment whose capriciousness may largely result from the success of its own forebears.}, }
@article {pmid12148653, year = {2002}, author = {Hedlund, BP and Staley, JT}, title = {Phylogeny of the genus Simonsiella and other members of the Neisseriaceae.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {52}, number = {Pt 4}, pages = {1377-1382}, doi = {10.1099/00207713-52-4-1377}, pmid = {12148653}, issn = {1466-5026}, support = {T32 GM07270/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cats ; DNA, Ribosomal/analysis ; Dogs ; Gene Transfer, Horizontal ; Humans ; Molecular Sequence Data ; Neisseriaceae/*classification/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sheep ; }, abstract = {16S rDNA was sequenced from 16 strains of the oral commensal Simonsiella and was used to assess relationships between Simonsiella strains and other members of the Neisseriaceae. In all analyses, Simonsiella strains grouped according to established species designations and the mammalian hosts from which they were isolated. The commensals from cats and dogs formed a monophyletic group. The monophyly of the genus Simonsiella, however, could be neither supported nor rejected; deep nodes in the trees were unstable depending on the phylogenetic method or on the particular sequences used in the analysis. Instabilities may be attributable to frequent gene transfer between Neisseria or other members of the Neisseriaceae and Simonsiella.}, }
@article {pmid12142418, year = {2002}, author = {Nesbø, CL and Nelson, KE and Doolittle, WF}, title = {Suppressive subtractive hybridization detects extensive genomic diversity in Thermotoga maritima.}, journal = {Journal of bacteriology}, volume = {184}, number = {16}, pages = {4475-4488}, pmid = {12142418}, issn = {0021-9193}, mesh = {Antigens, Bacterial/genetics ; Archaeal Proteins/genetics ; Carbohydrate Metabolism ; Carrier Proteins/genetics/metabolism ; *Genetic Variation ; *Genome, Bacterial ; Nucleic Acid Hybridization/*methods ; Phylogeny ; Thermotoga maritima/*genetics ; Vacuolar Proton-Translocating ATPases/genetics ; }, abstract = {Comparisons between genomes of closely related bacteria often show large variations in gene content, even between strains of the same species. Such studies have focused mainly on pathogens; here, we examined Thermotoga maritima, a free-living hyperthermophilic bacterium, by using suppressive subtractive hybridization. The genome sequence of T. maritima MSB8 is available, and DNA from this strain served as a reference to obtain strain-specific sequences from Thermotoga sp. strain RQ2, a very close relative (approximately 96% identity for orthologous protein-coding genes, 99.7% identity in the small-subunit rRNA sequence). Four hundred twenty-six RQ2 subtractive clones were sequenced. One hundred sixty-six had no DNA match in the MSB8 genome. These differential clones comprise, in sum, 48 kb of RQ2-specific DNA and match 72 genes in the GenBank database. From the number of identical clones, we estimated that RQ2 contains 350 to 400 genes not found in MSB8. Assuming a similar genome size, this corresponds to 20% of the RQ2 genome. A large proportion of the RQ2-specific genes were predicted to be involved in sugar transport and polysaccharide degradation, suggesting that polysaccharides are more important as nutrients for this strain than for MSB8. Several clones encode proteins involved in the production of surface polysaccharides. RQ2 encodes multiple subunits of a V-type ATPase, while MSB8 possesses only an F-type ATPase. Moreover, an RQ2-specific MutS homolog was found among the subtractive clones and appears to belong to a third novel archaeal type MutS lineage. Southern blot analyses showed that some of the RQ2 differential sequences are found in some other members of the order Thermotogales, but the distribution of these variable genes is patchy, suggesting frequent lateral gene transfer within the group.}, }
@article {pmid12132175, year = {2002}, author = {Wang, Z and Ye, Q and Shu, Q and Cui, H and Xia, Y}, title = {[Impact of root exudates from transgenic plants on soil micro-ecosystems].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {13}, number = {3}, pages = {373-375}, pmid = {12132175}, issn = {1001-9332}, mesh = {Aspergillus niger/genetics/metabolism ; *Ecosystem ; Gene Transfer, Horizontal/genetics ; Plant Roots/genetics/metabolism ; Plants, Genetically Modified/*adverse effects/genetics/metabolism ; *Soil ; *Soil Microbiology ; }, abstract = {With the commercialization of transgenic plants, ecological risk assessment of transgenic plants has been scheduled. Many problems such as gene transfer from transgenic plants to related wild species, production of super weeds and super virus, tolerance to insect-resistant transgenic plants, and distruption of biodiversity have been taken place in some transgenic plants. The influences of root exudates from transgenic plants on soil micro-ecosystems were reviewed.}, }
@article {pmid12128032, year = {2002}, author = {Brown, EW and Kotewicz, ML and Cebula, TA}, title = {Detection of recombination among Salmonella enterica strains using the incongruence length difference test.}, journal = {Molecular phylogenetics and evolution}, volume = {24}, number = {1}, pages = {102-120}, doi = {10.1016/s1055-7903(02)00222-1}, pmid = {12128032}, issn = {1055-7903}, mesh = {Adenosine Triphosphatases/genetics ; Adhesins, Bacterial/genetics ; Bacterial Proteins/*genetics ; *DNA-Binding Proteins ; Escherichia coli Proteins/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Models, Genetic ; MutS DNA Mismatch-Binding Protein ; Phylogeny ; *Recombination, Genetic ; Salmonella enterica/*genetics/pathogenicity/physiology ; Virulence/genetics ; }, abstract = {Particular serovars of Salmonella enterica have emerged as significant foodborne pathogens in humans. At the chromosomal level, discrete regions in the Salmonella genome have been identified that are known to play important roles in the maintenance, survival, and virulence of S. enterica within the host. Interestingly, several of these loci appear to have been acquired by horizontal transfer of DNA among and between bacterial species. The profound importance of recombination in pathogen emergence is just now being realized, perhaps explaining the sudden interest in developing novel and facile ways for detecting putative horizontal transfer events in bacteria. The incongruence length difference (ILD) test offers one such means. ILD uses phylogeny to trace sequences that may have been acquired promiscuously by exchange of DNA during chromosome evolution. We show here that the ILD test readily detects recombinations that have taken place in several housekeeping genes in Salmonella as well as genes composing the type 1 pilin complex (14 min) and the inv-spa invasion gene complex (63 min). Moreover, the ILD test indicated that the mutS gene (64 min), whose product helps protect the bacterial genome from invasion by foreign DNA, appears to have undergone intragenic recombination within S. enterica subspecies I. ILD findings were supported using additional tests known to be independent of the ILD approach (e.g., split decomposition analysis and compatibility of sites). Taken together, these data affirm the application of the ILD test as one approach for identifying recombined sequences in the Salmonella chromosome. Furthermore, horizontally acquired sequences within mutS support a model whereby evolutionarily important recombinants of S. enterica are rescued from strains carrying defective mutS alleles via horizontal transfer.}, }
@article {pmid12126810, year = {2002}, author = {Grommen, R and Verstraete, W}, title = {Environmental biotechnology: the ongoing quest.}, journal = {Journal of biotechnology}, volume = {98}, number = {1}, pages = {113-123}, doi = {10.1016/s0168-1656(02)00090-1}, pmid = {12126810}, issn = {0168-1656}, mesh = {Air Pollution/prevention &amp; control ; Aquaculture/methods ; *Biotechnology/methods/standards ; Environmental Monitoring/instrumentation/*methods ; *Environmental Pollution/prevention &amp; control ; Gases/analysis/isolation &amp; purification ; Quality Control ; Refuse Disposal/instrumentation/methods ; Risk Assessment ; Waste Disposal, Fluid/instrumentation/methods ; *Waste Management/instrumentation/methods ; *Water Supply/analysis ; }, abstract = {Environmental biotechnology, until now, has primarily focused on the development of technologies to treat aqueous, solid and gaseous wastes. At present, the basic knowledge on how biotechnology can handle these wastes has been acquired and the focus is now on the implementation of these processes as 'best available technology not entailing excessive costs' (BATNEEC) in the framework of strict and transparent environmental legislation. New environmental challenges continue to evolve, as it becomes clear that waste streams should be tackled in an overall holistic way. New technologies to reach this goal are currently under development. Novel aspects with respect to the domain of water treatment are, for example, the biomembrane reactor technology and the newly discovered processes to remove nitrogen by means of anaerobic ammonium oxidation. Also, most challenging is the continuing strive for re-use of treated wastewater. Indeed, water shortage is emerging in an increasing number of countries all over the world and necessitates the short cycling of water. Finally, biotechnology has a key role to play in the novel approaches to design wastewater treatment based on decentralised sanitation and reuse (DESAR). Solid waste is a major challenge worldwide. The implementation of anaerobic digestion to treat biowastes has become a grown-up technology. New approaches in which biotechnological processes are linked to physical processes, such as plasma technology, certainly deserve special attention for the coming decades. Soil and sediment clean up by means of biostimulation/remediation/augmentation is now well established. Certainly, a number of prospects need to be further explored, such as the use of special energy sources to stimulate in situ the microbial community and the seeding of knowledge to the in situ community by means of horizontal gene transfer mechanisms. A number of waste gases can be handled by biofilter systems. Biological treatment of wastegases is also evolving, inasmuch as that besides conventional chemical pollutants, now also highly problematic chemicals (even dioxins) can be dealt with through proper biotechnological approaches. A remarkable new potential is the use of well designed probiotics to upgrade aquaculture and together with conventional biological water treatment processes, to guarantee the overall water quality of this domain of food production.}, }
@article {pmid12126807, year = {2002}, author = {Bartsch, D and Schuphan, I}, title = {Lessons we can learn from ecological biosafety research.}, journal = {Journal of biotechnology}, volume = {98}, number = {1}, pages = {71-77}, doi = {10.1016/s0168-1656(02)00087-1}, pmid = {12126807}, issn = {0168-1656}, mesh = {Beta vulgaris/*genetics ; *Ecology ; Forecasting ; Gene Transfer, Horizontal/*genetics ; Genetic Engineering/trends ; *Plants, Genetically Modified/genetics ; Research ; Risk Assessment/methods ; Risk Factors ; Zea mays/*genetics ; }, abstract = {The last decade has seen an increasing number of biosafety related publications focusing on transgenic organisms. Recent extensive field studies suggest that harmful laboratory effects on non-target organisms rarely occur in the environment. Moreover, biosafety studies typically show no difference in hybridisation between genetically modified plants (GMPs) or non-GMPs and related wild species. Since risk is a product of both exposure and hazard, biosafety research should clearly not only target gene flow exposure but specifically concentrate on expected hazards emerging from successful transgene flow to wild relatives of GMPs. Generally, transgenic plants behave in an ecologically similar manner to non-GMPs if the modified trait confers a neutral advantage under environmental or experimental conditions. However, GMPs perform better than non-GMPs if the new phenotype is challenged by conditions ecologically advantageous for the modified trait. Since biosafety research is a laborious process it will have to concentrate resources on thoughtful, thorough experiments, and target ecologically 'riskier' organisms. So far, we have no evidence that the use of GMPs contradicts sustainable agriculture and nature conservation per se.}, }
@article {pmid12125824, year = {2002}, author = {Deppenmeier, U and Johann, A and Hartsch, T and Merkl, R and Schmitz, RA and Martinez-Arias, R and Henne, A and Wiezer, A and Bäumer, S and Jacobi, C and Brüggemann, H and Lienard, T and Christmann, A and Bömeke, M and Steckel, S and Bhattacharyya, A and Lykidis, A and Overbeek, R and Klenk, HP and Gunsalus, RP and Fritz, HJ and Gottschalk, G}, title = {The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea.}, journal = {Journal of molecular microbiology and biotechnology}, volume = {4}, number = {4}, pages = {453-461}, pmid = {12125824}, issn = {1464-1801}, mesh = {Archaea/*genetics ; Bacteria/classification/*genetics ; Gene Transfer Techniques ; *Genome, Archaeal ; Methanosarcina/classification/*genetics/metabolism ; Open Reading Frames ; Phylogeny ; }, abstract = {The Archaeon Methanosarcina mazei and related species are of great ecological importance as they are the only organisms fermenting acetate, methylamines and methanol to methane, carbon dioxide and ammonia (in case of methylamines). Since acetate is the precursor of 60% of the methane produced on earth these organisms contribute significantly to the production of this greenhouse gas, e.g. in rice paddies. The 4,096,345 base pairs circular chromosome of M. mazei is more than twice as large as the genomes of the methanogenic Archaea currently completely sequenced (Bult et al., 1996; Smith et al., 1997). 3,371 open reading frames (ORFs) were identified. Based on currently available sequence data 376 of these ORFs are Methanosarcina-specific and 1,043 ORFs find their closest homologue in the bacterial domain. 544 of these ORFs reach significant similarity values only in the bacterial domain. They include 56 of the 102 transposases, and proteins involved in gluconeogenesis, proline biosynthesis, transport processes, DNA-repair, environmental sensing, gene regulation, and stress response. Striking examples are the occurrence of the bacterial GroEL/GroES chaperone system and the presence of tetrahydrofolate-dependent enzymes. These findings might indicate that lateral gene transfer has played an important evolutionary role in forging the physiology of this metabolically versatile methanogen.}, }
@article {pmid12123299, year = {2001}, author = {Smith, J}, title = {The social evolution of bacterial pathogenesis.}, journal = {Proceedings. Biological sciences}, volume = {268}, number = {1462}, pages = {61-69}, pmid = {12123299}, issn = {0962-8452}, support = {GM33782/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*genetics/*pathogenicity ; Bacterial Infections/microbiology/physiopathology ; Bacterial Physiological Phenomena ; Bacteriophages/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Models, Biological ; Plasmids/*genetics ; Selection, Genetic ; Virulence ; }, abstract = {Many of the genes responsible for the virulence of bacterial pathogens are carried by mobile genetic elements that can be transferred horizontally between different bacterial lineages. Horizontal transfer of virulence-factor genes has played a profound role in the evolution of bacterial pathogens, but it is poorly understood why these genes are so often mobile. Here, I present a hypothetical selective mechanism maintaining virulence-factor genes on horizontally transmissible genetic elements. For virulence factors that are secreted extracellularly, selection within hosts may favour mutant 'cheater' strains of the pathogen that do not produce the virulence factor themselves but still benefit from factors produced by other members of the pathogen population within a host. Using simple mathematical models, I show that if this occurs then selection for infectious transmission between hosts favours pathogen strains that can reintroduce functional copies of virulence-factor genes into cheaters via horizontal transfer, forcing them to produce the virulence factor. Horizontal gene transfer is thus a novel mechanism for the evolution of cooperation. I discuss predictions of this hypothesis that can be tested empirically and its implications for the evolution of pathogen virulence.}, }
@article {pmid12120991, year = {2002}, author = {Zhu, G and Keithly, JS}, title = {Alpha-proteobacterial relationship of apicomplexan lactate and malate dehydrogenases.}, journal = {The Journal of eukaryotic microbiology}, volume = {49}, number = {3}, pages = {255-261}, doi = {10.1111/j.1550-7408.2002.tb00532.x}, pmid = {12120991}, issn = {1066-5234}, support = {AI40320/AI/NIAID NIH HHS/United States ; AI44594/AI/NIAID NIH HHS/United States ; }, mesh = {Alphaproteobacteria/enzymology/*genetics ; Amino Acid Sequence ; Animals ; Base Sequence ; Cryptosporidium parvum/*enzymology/genetics ; DNA, Mitochondrial/chemistry/genetics ; DNA, Protozoan/chemistry/genetics ; Gammaproteobacteria/genetics ; L-Lactate Dehydrogenase/chemistry/*genetics ; Malate Dehydrogenase/chemistry/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {We have cloned and sequenced a lactate dehydrogenase (LDH) gene from Cryptosporidium parvum (CpLDH1). With this addition, and that of four recently deposited alpha-proteobacterial malate dehydrogenase (MDH) genes, the phylogenetic relationships among apicomplexan LDH and bacterial MDH were re-examined. Consistent with previous studies, our maximum likelihood (ML) analysis using the quartet-puzzling method divided 105 LDH/MDH enzymes into five clades, and confirmed that mitochondrial MDH is a sister clade to those of y-proteobacteria, rather than to alpha-proteobacteria. In addition, a Cryptosporidium parvum MDH (CpMDH1) was identified from the ongoing Cryptosporidium genome project that appears to belong to a distinct clade (III) comprised of 22 sequences from one archaebacterium, numerous eubacteria, and several apicomplexans. Using the ML puzzling test and bootstrapping analysis with protein distance and parsimony methods, the resulting trees not only robustly confirmed the alpha-proteobacterial relationship of apicomplexan LDH/MDH, but also supported a monophyletic relationship of CpLDH1 with CpMDHI. These data suggest that, unlike most other eukaryotes, the Apicomplexa may be one of the few lineages retaining an alpha-proteobacterial-type MDH that could have been acquired from an ancestral alpha-proteobacterium through primary endosymbiosis giving rise to the mitochondria, or through an unknown lateral gene transfer (LGT) event.}, }
@article {pmid12116649, year = {2001}, author = {Brown, JR}, title = {Genomic and phylogenetic perspectives on the evolution of prokaryotes.}, journal = {Systematic biology}, volume = {50}, number = {4}, pages = {497-512}, doi = {10.1080/10635150117729}, pmid = {12116649}, issn = {1063-5157}, mesh = {Amino Acid Sequence ; Archaea/classification/*genetics ; Bacteria/classification/*genetics ; Conserved Sequence ; Evolution, Molecular ; Genome ; Molecular Sequence Data ; Operon ; Phenylalanine-tRNA Ligase/chemistry/genetics ; *Phylogeny ; Prokaryotic Cells ; Protein Subunits ; Sequence Homology, Amino Acid ; }, abstract = {Prokaryotes have been at the forefront of the genome sequencing revolution. Many genomes have been completely sequenced, revealing much about bacterial and archaeal genome content and organization. Yet, a meaningful evolutionary picture of prokaryotes still eludes us. Much of the problem lies in understanding the mode and tempo of genome evolution. Here phenylalanyl-tRNA synthetase is used as an example of the complex interplay among lateral gene transfer, operon recombination, and gene recruitment in the evolution of some prokaryotic genes. Promising new approaches to genomic analyses, which could add to our understanding prokaryotic evolution and help in their classification, are discussed.}, }
@article {pmid12116648, year = {2001}, author = {Lawrence, JG}, title = {Catalyzing bacterial speciation: correlating lateral transfer with genetic headroom.}, journal = {Systematic biology}, volume = {50}, number = {4}, pages = {479-496}, doi = {10.1080/10635150120286}, pmid = {12116648}, issn = {1063-5157}, mesh = {Bacteria/*classification/*genetics/metabolism ; Codon/genetics ; DNA, Bacterial/genetics ; Ecosystem ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial ; Models, Genetic ; Point Mutation ; Species Specificity ; }, abstract = {Unlike crown eukaryotic species, microbial species are created by continual processes of gene loss and acquisition promoted by horizontal genetic transfer. The amounts of foreign DNA in bacterial genomes, and the rate at which this is acquired, are consistent with gene transfer as the primary catalyst for microbial differentiation. However, the rate of successful gene transfer varies among bacterial lineages. The heterogeneity in foreign DNA content is directly correlated with amount of genetic headroom intrinsic to a bacterial species. Genetic headroom reflects the amount of potentially dispensable information--reflected in codon usage bias and codon context bias--that can be transiently sacrificed to allow experimentation with functions introduced by gene transfer. In this way, genetic headroom offers a potential metric for assessing the propensity of a lineage to speciate.}, }
@article {pmid12116420, year = {2000}, author = {Sang, T and Zhong, Y}, title = {Testing hybridization hypotheses based on incongruent gene trees.}, journal = {Systematic biology}, volume = {49}, number = {3}, pages = {422-434}, doi = {10.1080/10635159950127321}, pmid = {12116420}, issn = {1063-5157}, mesh = {*Biological Evolution ; *Models, Genetic ; Models, Statistical ; *Nucleic Acid Hybridization ; *Phylogeny ; Plants/classification/*genetics ; Reproducibility of Results ; Trees/classification/genetics ; }, abstract = {Hybridization is an important evolutionary mechanism in plants and has been increasingly documented in animals. Difficulty in reconstruction of reticulate evolution, however, has been a long-standing problem in phylogenetics. Consequently, hybrid speciation may play a major role in causing topological incongruence between gene trees. The incongruence, in turn, offers an opportunity to detect hybrid speciation. Here we characterized certain distinctions between hybridization and other biological processes, including lineage sorting, paralogy, and lateral gene transfer, that are responsible for topological incongruence between gene trees. Consider two incongruent gene trees with three taxa, A, B, and C, where B is a sister group of A on gene tree 1 but a sister group of C on gene tree 2. With a theoretical model based on the molecular clock, we demonstrate that time of divergence of each gene between taxa A and C is nearly equal in the case of hybridization (B is a hybrid) or lateral gene transfer, but differs significantly in the case of lineage sorting or paralogy. After developing a bootstrap test to test these alternative hypotheses, we extended the model and test to account for incongruent gene trees with numerous taxa. Computer simulation studies supported the validity of the theoretical model and bootstrap test when each gene evolved at a constant rate. The computer simulation also suggested that the model remained valid as long as the rate heterogeneity was occurring proportionally in the same taxa for both genes. Although the model could not test hypotheses of hybridization versus lateral gene transfer as the cause of incongruence, these two processes may be distinguished by comparing phylogenies of multiple unlinked genes.}, }
@article {pmid12116185, year = {2002}, author = {Fritzsche, M}, title = {Lateral gene transfer of foreign DNA: the missing link between cannabis psychosis and schizophrenia.}, journal = {American journal of medical genetics}, volume = {114}, number = {5}, pages = {512-515}, doi = {10.1002/ajmg.10521}, pmid = {12116185}, issn = {0148-7299}, mesh = {Borrelia burgdorferi/genetics ; Cannabis/adverse effects ; Chromosomes, Human, Pair 6/genetics ; Gene Transfer, Horizontal ; Humans ; Mutation ; Psychoses, Substance-Induced/etiology/*genetics ; Receptors, Cannabinoid ; Receptors, Drug/*genetics ; Schizophrenia/*genetics ; }, }
@article {pmid12096457, year = {2001}, author = {Dudnik, IuV}, title = {[Ecology of drug resistance].}, journal = {Antibiotiki i khimioterapiia = Antibiotics and chemoterapy [sic]}, volume = {46}, number = {11}, pages = {7-10}, pmid = {12096457}, issn = {0235-2990}, mesh = {Animal Diseases/drug therapy/*microbiology ; Animal Feed ; Animals ; Animals, Domestic ; Anti-Bacterial Agents/*pharmacology/therapeutic use ; Bacteria/*drug effects/genetics/isolation &amp; purification ; Disinfectants ; *Drug Resistance, Bacterial/genetics ; *Ecosystem ; Food Microbiology ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Household Products ; Humans ; Legislation, Drug ; Legislation, Food ; Zoonoses ; }, }
@article {pmid12095618, year = {2002}, author = {Buisine, N and Tang, CM and Chalmers, R}, title = {Transposon-like Correia elements: structure, distribution and genetic exchange between pathogenic Neisseria sp.}, journal = {FEBS letters}, volume = {522}, number = {1-3}, pages = {52-58}, doi = {10.1016/s0014-5793(02)02882-x}, pmid = {12095618}, issn = {0014-5793}, mesh = {Bacterial Proteins/metabolism ; Base Sequence ; Binding Sites ; *DNA Transposable Elements ; *DNA, Bacterial ; DNA-Binding Proteins/metabolism ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Integration Host Factors ; Molecular Sequence Data ; Neisseria gonorrhoeae/*genetics ; Neisseria meningitidis/*genetics ; Promoter Regions, Genetic ; Sequence Homology, Nucleic Acid ; Terminal Repeat Sequences ; }, abstract = {Correia elements are a prominent feature of all four Neisseria genome sequences. We report an in silico analysis of the structure and genomic distribution of these elements and some preliminary biochemical data. Correia elements fall into four major families, distinguished by a 50 bp internal deletion and five point mutations. The elements resemble a transposon with 25 bp inverted repeats and a TA duplication at the target site. Within the element there is a functional integration host factor binding site. The genomic distribution of Correia elements is essentially random except for some small Correia-less regions apparently acquired by horizontal transfer. Phylogenetic analysis suggests that their presence predates the divergence of Neisseria meningitidis and Neisseria gonorrhoeae.}, }
@article {pmid12093378, year = {2002}, author = {Jenkins, C and Kedar, V and Fuerst, JA}, title = {Gene discovery within the planctomycete division of the domain Bacteria using sequence tags from genomic DNA libraries.}, journal = {Genome biology}, volume = {3}, number = {6}, pages = {RESEARCH0031}, pmid = {12093378}, issn = {1474-760X}, mesh = {Amino Acids/biosynthesis/genetics/metabolism ; Bacteria/*classification/*genetics ; Bacterial Proteins/genetics ; Computational Biology ; DNA Replication/genetics ; Gene Expression Regulation, Bacterial/genetics ; Genes, Bacterial/*genetics ; Genomic Library ; Membrane Transport Proteins/genetics ; Protein Biosynthesis/genetics ; Sequence Tagged Sites ; Signal Transduction/genetics ; Vitamins/biosynthesis/genetics/metabolism ; }, abstract = {BACKGROUND: The planctomycetes comprise a distinct group of the domain Bacteria, forming a separate division by phylogenetic analysis. The organization of their cells into membrane-defined compartments including membrane-bounded nucleoids, their budding reproduction and complete absence of peptidoglycan distinguish them from most other Bacteria. A random sequencing approach was applied to the genomes of two planctomycete species, Gemmata obscuriglobus and Pirellula marina, to discover genes relevant to their cell biology and physiology.<br><br>RESULTS: Genes with a wide variety of functions were identified in G. obscuriglobus and Pi. marina, including those of metabolism and biosynthesis, transport, regulation, translation and DNA replication, consistent with established phenotypic characters for these species. The genes sequenced were predominantly homologous to those in members of other divisions of the Bacteria, but there were also matches with nuclear genomic genes of the domain Eukarya, genes that may have appeared in the planctomycetes via horizontal gene transfer events. Significant among these matches are those with two genes atypical for Bacteria and with significant cell-biology implications - integrin alpha-V and inter-alpha-trypsin inhibitor protein - with homologs in G. obscuriglobus and Pi. marina respectively.<br><br>CONCLUSIONS: The random-sequence-tag approach applied here to G. obscuriglobus and Pi. marina is the first report of gene recovery and analysis from members of the planctomycetes using genome-based methods. Gene homologs identified were predominantly similar to genes of Bacteria, but some significant best matches to genes from Eukarya suggest that lateral gene transfer events between domains may have involved this division at some time during its evolution.}, }
@article {pmid12093083, year = {2002}, author = {Klein, RL and Hamby, ME and Gong, Y and Hirko, AC and Wang, S and Hughes, JA and King, MA and Meyer, EM}, title = {Dose and promoter effects of adeno-associated viral vector for green fluorescent protein expression in the rat brain.}, journal = {Experimental neurology}, volume = {176}, number = {1}, pages = {66-74}, doi = {10.1006/exnr.2002.7942}, pmid = {12093083}, issn = {0014-4886}, support = {P01 AG10485/AG/NIA NIH HHS/United States ; R01 NS37432/NS/NINDS NIH HHS/United States ; }, mesh = {Actins/genetics ; Animals ; Blotting, Western ; Brain/cytology/drug effects/*metabolism ; Cell Count ; Chickens ; Cytomegalovirus/genetics ; Dependovirus/*genetics ; Dose-Response Relationship, Drug ; Gene Transfer Techniques ; Gene Transfer, Horizontal ; Genetic Vectors/*genetics/*metabolism/pharmacology ; Green Fluorescent Proteins ; Hepatitis B Virus, Woodchuck/genetics ; Luminescent Proteins/biosynthesis/genetics ; Male ; Promoter Regions, Genetic/*genetics ; Rats ; Rats, Sprague-Dawley ; Regulatory Sequences, Nucleic Acid ; Time Factors ; Transgenes ; }, abstract = {Previous studies demonstrated that the rat neuron-specific enolase (NSE) promoter is effective for transgene expression in the brain in a variety of adeno-associated virus-2 vectors. This study evaluated the dose response and longer time course of this promoter and compared it to two cytomegalovirus/chicken beta-actin hybrid (CBA) promoter-based systems. NSE promoter-driven green fluorescent protein (GFP)-expressing neurons were found at doses as low as 10(7) particles, with expression increasing in a dose-dependent manner over a 3.3-log range. Bicistronic expression of GFP via an internal ribosome entry site coupled to the NSE promoter was also dose dependent, although the potency was decreased by 3.4-fold. The number of GFP-expressing neurons was stable for at least 25 months. The CBA promoter increased the numbers of GFP-expressing cells versus the NSE promoter, although the expression pattern remained neuronal and persisted for at least 18 months. The CBA promoter permitted detection of cells distal to the injection site that had retrogradely transported the vector from their terminal areas. Incorporating the woodchuck hepatitis virus post-transcriptional regulatory element (WPRE) into a CBA promoter vector induced greater expression levels in the hippocampus, as measured by stereological estimates of cell numbers and by Western blots, which demonstrated an 11-fold increase. Incorporation of the WPRE also improved transgene expression in primary neuronal cultures. The increased efficiency obtained with vector elements such as the CBA promoter and the WPRE may enhance the ability to genetically modify larger portions of the brain while requiring smaller doses and volumes.}, }
@article {pmid12089661, year = {2002}, author = {Leverstein-van Hall, MA and Box, AT and Blok, HE and Paauw, A and Fluit, AC and Verhoef, J}, title = {Evidence of extensive interspecies transfer of integron-mediated antimicrobial resistance genes among multidrug-resistant Enterobacteriaceae in a clinical setting.}, journal = {The Journal of infectious diseases}, volume = {186}, number = {1}, pages = {49-56}, doi = {10.1086/341078}, pmid = {12089661}, issn = {0022-1899}, mesh = {Anti-Bacterial Agents/pharmacology ; Cross Infection/epidemiology/*microbiology ; DNA Transposable Elements ; Disease Outbreaks ; Drug Resistance, Multiple, Bacterial/*genetics ; Enterobacteriaceae/drug effects/*genetics/isolation &amp; purification ; Enterobacteriaceae Infections/epidemiology/*microbiology ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Molecular Epidemiology ; Netherlands/epidemiology ; }, abstract = {Multidrug resistance in gram-negative bacteria appears to be primarily the result of the acquisition of resistance genes by horizontal transfer. To what extent horizontal transfer may be responsible for the emergence of multidrug resistance in a clinical setting, however, has rarely been investigated. Therefore, the integron contents of isolates collected during a nosocomial outbreak of genotypically unrelated multidrug-resistant Enterobacteriaceae were characterized. The integron was chosen as a marker of transfer because of its association with multiresistance. Some genotypically identical isolates harbored different integrons. Grouping patients carrying the same integron yielded 6 epidemiologically linked clusters, with each cluster representing a different integron. Several patients carried multiple species harboring the same integron. Conjugation experiments with these strains resulted in the transfer of complete resistance patterns at high frequencies (10(-2) to 10(-4)). These findings provide strong evidence that the horizontal transfer of resistance genes contributed largely to the emergence of multidrug-resistant Enterobacteriaceae in this clinical setting.}, }
@article {pmid12089300, year = {2002}, author = {Ko, KS and Lee, HK and Park, MY and Lee, KH and Yun, YJ and Woo, SY and Miyamoto, H and Kook, YH}, title = {Application of RNA polymerase beta-subunit gene (rpoB) sequences for the molecular differentiation of Legionella species.}, journal = {Journal of clinical microbiology}, volume = {40}, number = {7}, pages = {2653-2658}, pmid = {12089300}, issn = {0095-1137}, mesh = {Bacterial Proteins/genetics ; Bacterial Typing Techniques ; Base Sequence ; DNA, Bacterial/genetics ; DNA-Directed RNA Polymerases/*genetics ; *Genes, Bacterial ; Humans ; Immunophilins/genetics ; Legionella/classification/*enzymology/*genetics/isolation &amp; purification ; Membrane Proteins/genetics ; *Peptidylprolyl Isomerase ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Serotyping ; Species Specificity ; }, abstract = {The nucleotide sequences of the partial rpoB gene were determined from 38 Legionella species, including 15 serogroups of Legionella pneumophila. These sequences were then used to infer the phylogenetic relationships among the Legionella species in order to establish a molecular differentiation method appropriate for them. The sequences (300 bp) and the phylogenetic tree of rpoB were compared to those from analyses using 16S rRNA gene and mip sequences. The trees inferred from these three gene sequences revealed significant differences. This sequence incongruence between the rpoB tree and the other trees might have originated from the high frequency of synonymous base substitutions and/or from horizontal gene transfer among the Legionella species. The nucleotide variation of rpoB enabled more evident differentiation among the Legionella species than was achievable by the 16S rRNA gene and even by mip in some cases. Two subspecies of L. pneumophila (L. pneumophila subsp. pneumophila and subsp. fraseri) were clearly distinguished by rpoB but not by 16S rRNA gene and mip analysis. One hundred and five strains isolated from patient tissues and environments in Korea and Japan could be identified by comparison of rpoB sequence similarity and phylogenetic trees. These results suggest that the partial sequences of rpoB determined in this study might be applicable to the molecular differentiation of Legionella species.}, }
@article {pmid12089279, year = {2002}, author = {Lin, T and Oliver, JH and Gao, L}, title = {Genetic diversity of the outer surface protein C gene of southern Borrelia isolates and its possible epidemiological, clinical, and pathogenetic implications.}, journal = {Journal of clinical microbiology}, volume = {40}, number = {7}, pages = {2572-2583}, pmid = {12089279}, issn = {0095-1137}, support = {R37 AI024899/AI/NIAID NIH HHS/United States ; R37 AI-24899/AI/NIAID NIH HHS/United States ; U50/CCU410282/CC/ODCDC CDC HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; *Antigens, Bacterial ; Arachnid Vectors/microbiology ; Bacterial Outer Membrane Proteins/*genetics ; Base Sequence ; Borrelia/*genetics/*isolation &amp; purification/pathogenicity ; Borrelia Infections/epidemiology/microbiology ; Borrelia burgdorferi/genetics/isolation &amp; purification/pathogenicity ; DNA, Bacterial/genetics ; Disease Reservoirs ; Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genetic Variation ; Humans ; Lyme Disease/epidemiology/microbiology ; Molecular Sequence Data ; Phylogeny ; Recombination, Genetic ; Sequence Homology, Amino Acid ; Southeastern United States/epidemiology ; Ticks/microbiology ; Virulence/genetics ; }, abstract = {The ospC genes of 20 southern Borrelia strains were sequenced. The strains consisted of B. burgdorferi sensu stricto, B. andersonii, B. bissettii, one undescribed genospecies, MI-8, and one probably new Borrelia species, TXW-1. A high degree of similarity exists between B. burgdorferi sensu stricto and B. bissettii and between B. bissettii and B. andersonii. Lateral transfers of the ospC gene probably occurred between B. burgdorferi sensu stricto and B. bissettii and between B. bissettii and B. andersonii. Internal gene recombination appears to occur among them. The highest degree of genetic diversity among them was observed in the two variable domains (V1 and V2), semivariable domain (SV), and the species-specific epitopes (between amino acids 28 and 31). Differences in ospC sequences among southern strains reflect diversity at the strain and genospecies levels. MI-8, which was recognized as an undescribed genospecies in our previous reports, remains distinguishable in our current analysis of ospC genes and is distinct from B. burgdorferi sensu stricto. Interestingly, another undescribed southern isolate, TXW-1, was not amplified under various PCR conditions. Compared to European B. burgdorferi sensu stricto strains, American B. burgdorferi sensu stricto strains show greater genetic heterogeneity. Southern B. burgdorferi sensu stricto, B. andersonii, and B. bissettii isolates were intermixed with each other in the phylogenetic trees. In the derived trees in our work, at least one southeastern strain of B. burgdorferi, MI-2, most closely aligns with a so-called invasive cluster that possesses many proven human-invasive strains. Transmission experiments show that MI-2 and the strains in this group of southern spirochetes are able to infect mice and hamsters and that the typical vector of Lyme disease, Ixodes scapularis, can acquire the spirochetes from infected mammals. Currently, strain MI-2 appears to be the only southern isolate among the 20 we analyzed that clusters with an OspC invasive group and thus might be invasive for humans.}, }
@article {pmid12081468, year = {2002}, author = {Ihrmark, K and Johannesson, H and Stenström, E and Stenlid, J}, title = {Transmission of double-stranded RNA in Heterobasidion annosum.}, journal = {Fungal genetics and biology : FG &amp; B}, volume = {36}, number = {2}, pages = {147-154}, doi = {10.1016/S1087-1845(02)00011-7}, pmid = {12081468}, issn = {1087-1845}, mesh = {Basidiomycota/*virology ; Gene Transfer Techniques ; *Gene Transfer, Horizontal ; Genetic Markers ; RNA Viruses/*physiology ; RNA, Double-Stranded/*genetics ; Virus Integration/genetics ; }, abstract = {Transmission of dsRNA viruses between homo- and heterokaryotic mycelia paired on agar plates and into conidia has been studied in Heterobasidion annosum. Horizontal transmission of dsRNA occurred between both homo- and heterokaryotic isolates, as well as between isolates belonging to different intersterility groups. The proportions of vertical transmission into conidia were 3% and 55%, respectively, for the two isolates included in the study. RT-PCR of dsRNA and PCR-RFLP of mitochondrial markers were used to confirm transmission of dsRNA between the cytoplasms of different mycelia. The identity of nuclei and nuclear migration during experiments were verified using PCR-RFLP of several nuclear markers.}, }
@article {pmid12077305, year = {2002}, author = {Woese, CR}, title = {On the evolution of cells.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {99}, number = {13}, pages = {8742-8747}, pmid = {12077305}, issn = {0027-8424}, mesh = {*Biological Evolution ; *Cells ; Gene Transfer, Horizontal ; Protein Biosynthesis ; }, abstract = {A theory for the evolution of cellular organization is presented. The model is based on the (data supported) conjecture that the dynamic of horizontal gene transfer (HGT) is primarily determined by the organization of the recipient cell. Aboriginal cell designs are taken to be simple and loosely organized enough that all cellular componentry can be altered and/or displaced through HGT, making HGT the principal driving force in early cellular evolution. Primitive cells did not carry a stable organismal genealogical trace. Primitive cellular evolution is basically communal. The high level of novelty required to evolve cell designs is a product of communal invention, of the universal HGT field, not intralineage variation. It is the community as a whole, the ecosystem, which evolves. The individual cell designs that evolved in this way are nevertheless fundamentally distinct, because the initial conditions in each case are somewhat different. As a cell design becomes more complex and interconnected a critical point is reached where a more integrated cellular organization emerges, and vertically generated novelty can and does assume greater importance. This critical point is called the "Darwinian Threshold" for the reasons given.}, }
@article {pmid12073044, year = {2002}, author = {Syomin, BV and Leonova, TY and Ilyin, YV}, title = {Evidence for horizontal transfer of the LTR retrotransposon mdg3, which lacks an env gene.}, journal = {Molecular genetics and genomics : MGG}, volume = {267}, number = {3}, pages = {418-423}, doi = {10.1007/s00438-002-0678-1}, pmid = {12073044}, issn = {1617-4615}, mesh = {Animals ; Drosophila melanogaster/*genetics ; *Gene Transfer, Horizontal ; Genes, env ; Retroelements/*genetics ; Terminal Repeat Sequences/*genetics ; }, abstract = {Horizontal (interspecific) transfer is regarded as a possible strategy for the propagation of transposable elements through evolutionary time. To date, however, conclusive evidence that transposable elements are capable of horizontal transfer from one species to another has been limited to class II or DNA-type elements. We tested the possibility of such transfer for several Drosophila melanogaster LTR retrotransposons of the gypsy group in an experiment in which D. melanogaster and D. virilis somatic cell lines were used as donor and recipient cells, respectively. This approach was chosen in light of the high levels of LTR retrotransposon amplification and expression observed in cultured D. melanogaster cells. In the course of the experiment, parallel analysis for mdg1, mdg3, 17.6, 297, 412 and B104/roo retrotransposons was performed to detect their presence in the genome of recipient cells. Only the mdg3 retrotransposon, which lacks an env gene, was found to be transmitted into recipient cells. This model, based on the use of cultured cells, is a promising system for further investigating the mechanisms of LTR retrotransposon transfer.}, }
@article {pmid12070689, year = {2002}, author = {Heinhorst, S and Baker, SH and Johnson, DR and Davies, PS and Cannon, GC and Shively, JM}, title = {Two Copies of form I RuBisCO genes in Acidithiobacillus ferrooxidans ATCC 23270.}, journal = {Current microbiology}, volume = {45}, number = {2}, pages = {115-117}, doi = {10.1007/s00284-001-0094-5}, pmid = {12070689}, issn = {0343-8651}, mesh = {Gammaproteobacteria/enzymology/*genetics ; Gene Transfer, Horizontal ; Restriction Mapping ; Ribulose-Bisphosphate Carboxylase/*genetics ; }, abstract = {Acidithiobacillus ferrooxidans ATCC 23270 possesses two copies of form I ribulose bisphosphate carboxylase/oxygenase (RuBisCO). The nucleotide sequence identity between the two large and two small subunit peptides was 75% and 58%, respectively. It is proposed that the two copies resulted from lateral gene transfer.}, }
@article {pmid12070318, year = {2002}, author = {Glowacki, G and Braren, R and Firner, K and Nissen, M and Kühl, M and Reche, P and Bazan, F and Cetkovic-Cvrlje, M and Leiter, E and Haag, F and Koch-Nolte, F}, title = {The family of toxin-related ecto-ADP-ribosyltransferases in humans and the mouse.}, journal = {Protein science : a publication of the Protein Society}, volume = {11}, number = {7}, pages = {1657-1670}, pmid = {12070318}, issn = {0961-8368}, support = {R37 DK027722/DK/NIDDK NIH HHS/United States ; DK 36173/DK/NIDDK NIH HHS/United States ; R01 DK027722/DK/NIDDK NIH HHS/United States ; DK 27722/DK/NIDDK NIH HHS/United States ; R01 DK036175/DK/NIDDK NIH HHS/United States ; }, mesh = {ADP Ribose Transferases/*genetics/metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Chromosome Mapping ; Gene Transfer, Horizontal ; Humans ; Mice ; Molecular Sequence Data ; Organ Specificity ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {ADP-ribosyltransferases including toxins secreted by Vibrio cholera, Pseudomonas aerurginosa, and other pathogenic bacteria inactivate the function of human target proteins by attaching ADP-ribose onto a critical amino acid residue. Cross-species polymerase chain reaction (PCR) and database mining identified the orthologs of these ADP-ribosylating toxins in humans and the mouse. The human genome contains four functional toxin-related ADP-ribosyltransferase genes (ARTs) and two related intron-containing pseudogenes; the mouse has six functional orthologs. The human and mouse ART genes map to chromosomal regions with conserved linkage synteny. The individual ART genes reveal highly restricted expression patterns, which are largely conserved in humans and the mouse. We confirmed the predicted extracellular location of the ART proteins by expressing recombinant ARTs in insect cells. Two human and four mouse ARTs contain the active site motif (R-S-EXE) typical of arginine-specific ADP-ribosyltransferases and exhibit the predicted enzyme activities. Two other human ARTs and their murine orthologues deviate in the active site motif and lack detectable enzyme activity. Conceivably, these ARTs may have acquired a new specificity or function. The position-sensitive iterative database search program PSI-BLAST connected the mammalian ARTs with most known bacterial ADP-ribosylating toxins. In contrast, no related open reading frames occur in the four completed genomes of lower eucaryotes (yeast, worm, fly, and mustard weed). Interestingly, these organisms also lack genes for ADP-ribosylhydrolases, the enzymes that reverse protein ADP-ribosylation. This suggests that the two enzyme families that catalyze reversible mono-ADP-ribosylation either were lost from the genomes of these nonchordata eucaryotes or were subject to horizontal gene transfer between kingdoms.}, }
@article {pmid12068627, year = {2002}, author = {Okhapkina, SS and Netesova, NA and Golikova, LN and Seregina, EV and Sosnovtsev, SV and Abdurashitov, MA and Degtiarev, SKh}, title = {[Comparison of the homologous SfeI and LlaBI restriction-modification systems].}, journal = {Molekuliarnaia biologiia}, volume = {36}, number = {3}, pages = {432-437}, pmid = {12068627}, issn = {0026-8984}, mesh = {Amino Acid Sequence ; Cloning, Molecular ; DNA, Intergenic ; Deoxyribonucleases, Type II Site-Specific/*genetics/metabolism ; Enterococcus faecalis/genetics ; Gene Transfer, Horizontal ; Lactococcus lactis/genetics ; Molecular Sequence Data ; Operon ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; }, abstract = {A fragment containing the SfeI restriction-modification system (RMS) operon was cloned from a Streptococcus faecalis SE72 plasmid. Nucleotide sequence analysis revealed its high (99.2%) homology to the operon for Lactococcus lactis subsp. cremoris W56 LlaBI RMS recognizing the same site, 5'-CTRYAG-3'. A substantial difference was that SfeI RMS operon had an additional 198-bp fragment and a larger gene for the putative control protein. No homology was observed between operon-flanking sequences of the two closely related species, suggesting horizontal transfer of the operon.}, }
@article {pmid12065809, year = {2002}, author = {Shouse, B}, title = {Genetically modified food. TV drama sparks scientific backlash.}, journal = {Science (New York, N.Y.)}, volume = {296}, number = {5575}, pages = {1948-1949}, doi = {10.1126/science.296.5575.1948b}, pmid = {12065809}, issn = {1095-9203}, mesh = {Disease Outbreaks ; Drama ; Food, Genetically Modified/*adverse effects ; *Gene Transfer, Horizontal ; Humans ; Plants, Genetically Modified ; Public Opinion ; Staphylococcal Infections/epidemiology/microbiology ; Staphylococcus aureus/genetics ; *Television ; *Transgenes ; Triticum/genetics ; United Kingdom ; Vancomycin Resistance ; }, }
@article {pmid12055303, year = {2002}, author = {Zhu, P and Klutch, MJ and Bash, MC and Tsang, RSW and Ng, LK and Tsai, CM}, title = {Genetic diversity of three lgt loci for biosynthesis of lipooligosaccharide (LOS) in Neisseria species.}, journal = {Microbiology (Reading, England)}, volume = {148}, number = {Pt 6}, pages = {1833-1844}, doi = {10.1099/00221287-148-6-1833}, pmid = {12055303}, issn = {1350-0872}, support = {369VFFD018551/FD/FDA HHS/United States ; }, mesh = {Genes, Bacterial/*genetics ; Genetic Variation/*genetics ; Genotype ; Glycosyltransferases/genetics ; Lipopolysaccharides/*biosynthesis ; Molecular Sequence Data ; N-Acetylglucosaminyltransferases/genetics ; Neisseria meningitidis/classification/*genetics/growth &amp; development/*metabolism ; Phylogeny ; Polymorphism, Genetic/genetics ; Sequence Analysis, DNA ; }, abstract = {Lipooligosaccharide (LOS) is a major virulence factor of the pathogenic Neisseria. Nine lgt genes at three chromosomal loci (lgt-1, 2, 3) encoding the glycosyltransferases responsible for the biosynthesis of LOS oligosaccharide chains were examined in 26 Neisseria meningitidis, 51 Neisseria gonorrhoeae and 18 commensal Neisseria strains. DNA hybridization, PCR and nucleotide sequence data were compared to previously reported lgt genes. Analysis of the genetic organization of the lgt loci revealed that in N. meningitidis, the lgt-1 and lgt-3 loci were hypervariable genomic regions, whereas the lgt-2 locus was conserved. In N. gonorrhoeae, no variability in the composition or organization of the three lgt loci was observed. lgt genes were detected only in some commensal Neisseria species. The genetic organization of the lgt-1 locus was classified into eight types and the lgt-3 locus was classified into four types. Two types of arrangement at lgt-1 (II and IV) and one type of arrangement at lgt-3 (IV) were novel genetic organizations reported in this study. Based on the three lgt loci, 10 LOS genotypes of N. meningitidis were distinguished. Phylogenetic analysis revealed a gene cluster, lgtH, which separated from the homologous genes lgtB and lgtE. The lgtH and lgtE genes were mutually exclusive and were located at the same position in lgt-1. The data demonstrated that pathogenic and commensal Neisseria share a common lgt gene pool and horizontal gene transfer appears to contribute to the genetic diversity of the lgt loci in Neisseria.}, }
@article {pmid12054539, year = {2002}, author = {Rodrigues-Lima, F and Dupret, JM}, title = {In silico sequence analysis of arylamine N-acetyltransferases: evidence for an absence of lateral gene transfer from bacteria to vertebrates and first description of paralogs in bacteria.}, journal = {Biochemical and biophysical research communications}, volume = {293}, number = {2}, pages = {783-792}, doi = {10.1016/S0006-291X(02)00299-1}, pmid = {12054539}, issn = {0006-291X}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Arylamine N-Acetyltransferase/chemistry/*genetics ; Bacteria/*enzymology/genetics ; Computational Biology ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; Rhizobiaceae/enzymology/genetics ; Sequence Alignment ; Sequence Analysis, Protein ; Vertebrates/*genetics ; }, abstract = {The arylamine N-acetyltransferases (NATs) are xenobiotic-metabolizing enzymes responsible for the biotransformation of various arylamine and heterocyclic amines, including drugs and carcinogenic compounds. NAT and NAT-like genes have been identified in several vertebrate and eubacterial species. Little is known about their evolutionary history, but the horizontal transfer of NAT genes from bacteria to vertebrates was recently suggested [S. Salzberg, O. White, J. Peterson, J. Eisen, Science 292 (2001) 1903]. We used various bioinformatics-based approaches to screen eukaryotic and prokaryotic genomes. We identified Mesorhizobium loti NAT genes as the first examples of NAT paralogs in prokaryotes. As shown for vertebrate species, the existence of NAT paralogs in this bacterium may be accounted for by enzymatic specialization after gene duplication. Phylogenetic analysis following the identification of a NAT ortholog in the nonvertebrate species Ciona intestinalis indicated that NAT genes are unlikely to be examples of direct horizontal gene transfer (HGT). Our study suggests that NAT genes have evolved from a common ancestor, with a succession of nonvertebrate intermediates. The absence of NAT genes in yeast, nematode worms, fruit flies, and mustard weed may result from gene loss in these nonvertebrate lineages. These results provide new insight into the taxonomic distribution and evolutionary history of this class of drug-metabolizing enzymes.}, }
@article {pmid12054250, year = {2002}, author = {Manen, JF and Falquet, J}, title = {The cpcB-cpcA locus as a tool for the genetic characterization of the genus Arthrospira (Cyanobacteria): evidence for horizontal transfer.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {52}, number = {Pt 3}, pages = {861-867}, doi = {10.1099/00207713-52-3-861}, pmid = {12054250}, issn = {1466-5026}, mesh = {Bacterial Proteins/genetics/metabolism ; Base Sequence ; Cyanobacteria/*classification/*genetics ; DNA, Bacterial/analysis ; DNA, Ribosomal Spacer/analysis ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Operon ; Phycocyanin/*genetics/metabolism ; Phylogeny ; Recombination, Genetic ; Sequence Analysis, DNA ; }, abstract = {To investigate the genetic diversity of the genus Arthrospira and to compare it with other cyanobacteria, sequences of 670 nt from the phycocyanin operon were determined for 23 natural, cultivated or commercial strains of Arthrospira and compared with sequences from 20 other non-Arthrospira cyanobacterial strains. The sequenced DNA fragment comprises the last 255 nt of cpcB, the cpcB-cpcA spacer and the first 304 nt of cpcA. The resulting phylogenetic tree confirms that the genus Arthrospira is not related to Spirulina. So far, cpcB-cpcA data suggest that the closest relative of Arthrospira is Planktothrix. Based on this locus, the genus Arthrospira consists of three genetically clustered lineages. However, the distribution of nucleotide substitutions indicates that these three lineages are not the result of a simple cladogenesis characterized by the accumulation of independent substitutions. Instead, the observed clustering is the result of horizontal transfers of blocks of sequences. Analysis of the distribution of substitutions in the sequenced fragment indicates a point of intragenic recombination close to the stop codon of cpcB. The capacity of exchange of genetic material among strains probably explains why morphology and geographical origin do not correlate with the cpcB-cpcA clusters. Nevertheless, this study shows for the first time that the genus Arthrospira, represented here by cultivated and wild specimens, is clearly monophyletic. Moreover, the cpcB-cpcA DNA fragment, comprising both highly and moderately variable regions, allows (1) a strict differentiation of the taxon Arthrospira from other cyanobacteria (using the coding regions only) and (2) the study of relationships inside Arthrospira (using both the coding and non-coding regions).}, }
@article {pmid12054238, year = {2002}, author = {Ragan, MA and Charlebois, RL}, title = {Distributional profiles of homologous open reading frames among bacterial phyla: implications for vertical and lateral transmission.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {52}, number = {Pt 3}, pages = {777-787}, doi = {10.1099/00207713-52-3-777}, pmid = {12054238}, issn = {1466-5026}, mesh = {Bacteria/*classification/*genetics ; Computational Biology/methods ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; Genomics ; Open Reading Frames/*genetics ; }, abstract = {If open reading frames (ORFs) have been transmitted primarily by vertical descent, the distributional profile of orthologues of each ORF should be congruent with the organismal tree or a subtree thereof. Distributional patterns not reconciled parsimoniously with tree-like descent and loss are prima facie evidence of lateral gene transfer. Herein, a rigorous criterion for recognizing ORF distributions is described and implemented; it does not require the inference of phylogenetic trees, nor does it assume any specific tree. Because lineage-specific differences in rates of sequence change can also generate unexpected distributional patterns, rate artefacts were controlled for by requiring pairwise matches between ORFs to exceed a rigorous inclusion threshold, but absence of a match was assessed against a more-permissive exclusion threshold. Applying this dual-threshold criterion to cross-domain and cross-phylum distributional patterns for ORFs in 23 bacterial genomes, a relative abundance of ORFs was observed that find a match in exactly seven other bacterial phyla; 94-99% of these ORFs also find matches among the Archaea and/or Eukarya. In the larger (and some smaller) bacterial genomes, ORFs that find matches in exactly one other bacterial phylum are also relatively abundant, but fewer of these have non-bacterial homologues; most of their matches within the Bacteria are to the Proteobacteria and/or Firmicutes, which cannot be sister lineages to all bacteria. ORFs that are neither distributed universally among the Bacteria, nor necessarily shared with topologically adjacent lineages, are preferentially enriched in large bacterial genomes.}, }
@article {pmid12051562, year = {2001}, author = {Gupta, RS}, title = {The branching order and phylogenetic placement of species from completed bacterial genomes, based on conserved indels found in various proteins.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {4}, number = {4}, pages = {187-202}, doi = {10.1007/s10123-001-0037-9}, pmid = {12051562}, issn = {1139-6709}, mesh = {Amino Acid Sequence ; Bacteria/*classification/genetics ; Bacterial Proteins/genetics ; *Genome, Bacterial ; Molecular Sequence Data ; Phylogeny ; Proteobacteria/genetics ; Sequence Alignment ; Species Specificity ; }, abstract = {The presence of shared conserved inserts and deletions (indels or signature sequences) in proteins provides a powerful means for understanding the evolutionary relationships among the Bacteria. Using such indels, all of the main groups within the Bacteria can be defined in clear molecular terms and it has become possible to deduce that they branched from a common ancestor in the following order: Low G + C gram-positive --> High G+C gram-positive --> Deinococcus Thermus --> Cyanobacteria --> Spirochetes --> Aquifex-Chlamydia-Cytophaga --> Proteobacteria-1 (epsilon, delta) --> Proteobacteria-2 (alpha) --> Proteobacteria-3 (beta) --> Proteobacteria -4 (gamma). The usefulness of this approach for understanding bacterial phylogeny was examined here using sequence data from various completed bacterial genomes. By using 12 indels in highly conserved and widely represented proteins, the species from all 41 completed bacterial genomes were assigned to different groups; and the observed distribution of these indels in different species was then compared with that predicted by the signature sequence model. The presence or absence of these indels in various proteins in different bacteria followed the pattern exactly as predicted: and, in more than 450 observations, no exceptions or contradictions in the placement of indels were observed. These results provide strong evidence that lateral gene transfer events have not affected the genes containing these indels to any significant extent. The phylogenetic placement of bacteria into different groups based on signature sequences also showed an excellent correlation with the 16 S rRNA with 39 of the 41 species assigned to the same group by both methods. These results strongly vindicate the usefulness of the signature sequence approach to understanding phylogeny within the Bacteria and show that it provides a reliable and internally consistent means for the placement of bacterial species into different groups and for determining the relative branching order of the groups.}, }
@article {pmid12049666, year = {2002}, author = {Copley, SD and Dhillon, JK}, title = {Lateral gene transfer and parallel evolution in the history of glutathione biosynthesis genes.}, journal = {Genome biology}, volume = {3}, number = {5}, pages = {research0025}, pmid = {12049666}, issn = {1474-760X}, mesh = {Animals ; Bacterial Proteins/genetics ; Computational Biology/methods ; Databases, Protein ; *Evolution, Molecular ; Fungal Proteins/genetics ; Gene Deletion ; Gene Transfer, Horizontal/*genetics ; Genetic Variation ; Glutamate-Cysteine Ligase/*genetics ; Glutathione Synthase/*genetics ; Plant Proteins/genetics ; Protozoan Proteins/genetics ; }, abstract = {BACKGROUND: Glutathione is found primarily in eukaryotes and in Gram-negative bacteria. It has been proposed that eukaryotes acquired the genes for glutathione biosynthesis from the alpha-proteobacterial progenitor of mitochondria. To evaluate this, we have used bioinformatics to analyze sequences of the biosynthetic enzymes gamma-glutamylcysteine ligase and glutathione synthetase.<br><br>RESULTS: Gamma-glutamylcysteine ligase sequences fall into three groups: sequences primarily from gamma-proteobacteria; sequences from non-plant eukaryotes; and sequences primarily from alpha-proteobacteria and plants. Although pairwise sequence identities between groups are insignificant, conserved sequence motifs are found, suggesting that the proteins are distantly related. The data suggest numerous examples of lateral gene transfer, including a transfer from an alpha-proteobacterium to a plant. Glutathione synthetase sequences fall into two distinct groups: bacterial and eukaryotic. Proteins in both groups have a common structural fold, but the sequences are so divergent that it is uncertain whether these proteins are homologous or arose by convergent evolution.<br><br>CONCLUSIONS: The evolutionary history of the glutathione biosynthesis genes is more complex than anticipated. Our analysis suggests that the two genes in the pathway were acquired independently. The gene for gamma-glutamylcysteine ligase most probably arose in cyanobacteria and was transferred to other bacteria, eukaryotes and at least one archaeon, although other scenarios cannot be ruled out. Because of high divergence in the sequences, the data neither support nor refute the hypothesis that the eukaryotic gene comes from a mitochondrial progenitor. After acquiring gamma-glutamylcysteine ligase, eukaryotes and most bacteria apparently recruited a protein with the ATP-grasp superfamily structural fold to catalyze synthesis of glutathione from gamma-glutamylcysteine and glycine. The eukaryotic glutathione synthetase did not evolve directly from the bacterial glutathione synthetase.}, }
@article {pmid12049665, year = {2002}, author = {Yanai, I and Wolf, YI and Koonin, EV}, title = {Evolution of gene fusions: horizontal transfer versus independent events.}, journal = {Genome biology}, volume = {3}, number = {5}, pages = {research0024}, pmid = {12049665}, issn = {1474-760X}, mesh = {DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; Databases, Genetic ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genes, Archaeal/genetics ; Genes, Bacterial/genetics ; Genes, Fungal/genetics ; Genome ; Genome, Bacterial ; Genome, Fungal ; Phylogeny ; Recombination, Genetic/*genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {BACKGROUND: Gene fusions can be used as tools for functional prediction and also as evolutionary markers. Fused genes often show a scattered phyletic distribution, which suggests a role for processes other than vertical inheritance in their evolution.<br><br>RESULTS: The evolutionary history of gene fusions was studied by phylogenetic analysis of the domains in the fused proteins and the orthologous domains that form stand-alone proteins. Clustering of fusion components from phylogenetically distant species was construed as evidence of dissemination of the fused genes by horizontal transfer. Of the 51 examined gene fusions that are represented in at least two of the three primary kingdoms (Bacteria, Archaea and Eukaryota), 31 were most probably disseminated by cross-kingdom horizontal gene transfer, whereas 14 appeared to have evolved independently in different kingdoms and two were probably inherited from the common ancestor of modern life forms. On many occasions, the evolutionary scenario also involves one or more secondary fissions of the fusion gene. For approximately half of the fusions, stand-alone forms of the fusion components are encoded by juxtaposed genes, which are known or predicted to belong to the same operon in some of the prokaryotic genomes. This indicates that evolution of gene fusions often, if not always, involves an intermediate stage, during which the future fusion components exist as juxtaposed and co-regulated, but still distinct, genes within operons.<br><br>CONCLUSION: These findings suggest a major role for horizontal transfer of gene fusions in the evolution of protein-domain architectures, but also indicate that independent fusions of the same pair of domains in distant species is not uncommon, which suggests positive selection for the multidomain architectures.}, }
@article {pmid12047948, year = {2002}, author = {Syvanen, M}, title = {Recent emergence of the modern genetic code: a proposal.}, journal = {Trends in genetics : TIG}, volume = {18}, number = {5}, pages = {245-248}, doi = {10.1016/s0168-9525(02)02647-1}, pmid = {12047948}, issn = {0168-9525}, mesh = {Archaea/genetics ; Arginine/genetics ; Bacteria/genetics ; Eukaryotic Cells ; *Evolution, Molecular ; *Genetic Code ; Models, Genetic ; Phylogeny ; Suppression, Genetic ; Tryptophan/genetics ; }, abstract = {This article proposes that the genetic code was not fully formed before the divergence of life into three kingdoms. Rather, at least arginine and tryptophan evolved after the diversification of archaea, bacteria and eukaryotes, and were spread by horizontal gene transfer. Evidence for this hypothesis is based on data suggesting that enzymes for biosynthesis of arginine and tryptophan, and for arginine tRNA ligase, have shorter divergence times than the underlying lineages. Also, many of these genes display "star" phylogenies. This proposal is an extension of the idea that the genetic code was unified because of the evolutionary pressure from horizontal gene transfer. These considerations further undermine the need to postulate the existence of a "last common ancestor"; a simpler model would be that multiple lineages gave rise to life today.}, }
@article {pmid12045242, year = {2002}, author = {Comanducci, M and Bambini, S and Brunelli, B and Adu-Bobie, J and Aricò, B and Capecchi, B and Giuliani, MM and Masignani, V and Santini, L and Savino, S and Granoff, DM and Caugant, DA and Pizza, M and Rappuoli, R and Mora, M}, title = {NadA, a novel vaccine candidate of Neisseria meningitidis.}, journal = {The Journal of experimental medicine}, volume = {195}, number = {11}, pages = {1445-1454}, pmid = {12045242}, issn = {0022-1007}, support = {R01 AI045642/AI/NIAID NIH HHS/United States ; R01 AI046464/AI/NIAID NIH HHS/United States ; R01 AI 45642/AI/NIAID NIH HHS/United States ; AI 46464/AI/NIAID NIH HHS/United States ; //Wellcome Trust/United Kingdom ; }, mesh = {Alleles ; Amino Acid Sequence ; Animals ; Antibody Affinity ; Antibody Specificity ; Antigens, Surface/chemistry/*genetics/*immunology/metabolism ; Base Composition ; Base Sequence ; Blotting, Western ; Conserved Sequence/genetics ; Evolution, Molecular ; Flow Cytometry ; Gene Transfer, Horizontal/genetics ; Humans ; Immune Sera/immunology ; Meningitis, Meningococcal/immunology/microbiology/prevention &amp; control ; Meningococcal Vaccines/*immunology ; Mice ; Molecular Sequence Data ; Neisseria meningitidis/genetics/growth &amp; development/*immunology/pathogenicity ; Rats ; }, abstract = {Neisseria meningitidis is a human pathogen, which, in spite of antibiotic therapy, is still a major cause of mortality due to sepsis and meningitis. Here we describe NadA, a novel surface antigen of N. meningitidis that is present in 52 out of 53 strains of hypervirulent lineages electrophoretic types (ET) ET37, ET5, and cluster A4. The gene is absent in the hypervirulent lineage III, in N. gonorrhoeae and in the commensal species N. lactamica and N. cinerea. The guanine/cytosine content, lower than the chromosome, suggests acquisition by horizontal gene transfer and subsequent limited evolution to generate three well-conserved alleles. NadA has a predicted molecular structure strikingly similar to a novel class of adhesins (YadA and UspA2), forms high molecular weight oligomers, and binds to epithelial cells in vitro supporting the hypothesis that NadA is important for host cell interaction. NadA induces strong bactericidal antibodies and is protective in the infant rat model suggesting that this protein may represent a novel antigen for a vaccine able to control meningococcal disease caused by three hypervirulent lineages.}, }
@article {pmid12045108, year = {2002}, author = {Raetz, CR and Whitfield, C}, title = {Lipopolysaccharide endotoxins.}, journal = {Annual review of biochemistry}, volume = {71}, number = {}, pages = {635-700}, pmid = {12045108}, issn = {0066-4154}, support = {R37 GM051796/GM/NIGMS NIH HHS/United States ; R01-GM-51,310/GM/NIGMS NIH HHS/United States ; R01 GM051310/GM/NIGMS NIH HHS/United States ; R01-GM-51,796/GM/NIGMS NIH HHS/United States ; R37 GM051796-06/GM/NIGMS NIH HHS/United States ; }, mesh = {*ATP-Binding Cassette Transporters ; Animals ; Anti-Bacterial Agents/metabolism ; Bacterial Proteins/chemistry/genetics/metabolism ; Biological Transport/physiology ; *Drosophila Proteins ; Genes, Plant ; Gram-Negative Bacteria/*chemistry/genetics/metabolism ; Hexosyltransferases/metabolism ; Humans ; Immunity, Innate/immunology/physiology ; *Lipopolysaccharides/chemistry/immunology/metabolism ; Membrane Glycoproteins/genetics/metabolism ; Membrane Proteins/chemistry/genetics/metabolism ; Models, Biological ; Molecular Structure ; Oligosaccharides/chemistry/metabolism ; Protein Structure, Tertiary ; Receptors, Cell Surface/genetics/metabolism ; Toll-Like Receptor 4 ; Toll-Like Receptors ; }, abstract = {Bacterial lipopolysaccharides (LPS) typically consist of a hydrophobic domain known as lipid A (or endotoxin), a nonrepeating "core" oligosaccharide, and a distal polysaccharide (or O-antigen). Recent genomic data have facilitated study of LPS assembly in diverse Gram-negative bacteria, many of which are human or plant pathogens, and have established the importance of lateral gene transfer in generating structural diversity of O-antigens. Many enzymes of lipid A biosynthesis like LpxC have been validated as targets for development of new antibiotics. Key genes for lipid A biosynthesis have unexpectedly also been found in higher plants, indicating that eukaryotic lipid A-like molecules may exist. Most significant has been the identification of the plasma membrane protein TLR4 as the lipid A signaling receptor of animal cells. TLR4 belongs to a family of innate immunity receptors that possess a large extracellular domain of leucine-rich repeats, a single trans-membrane segment, and a smaller cytoplasmic signaling region that engages the adaptor protein MyD88. The expanding knowledge of TLR4 specificity and its downstream signaling pathways should provide new opportunities for blocking inflammation associated with infection.}, }
@article {pmid12042861, year = {2002}, author = {Daniell, H}, title = {Molecular strategies for gene containment in transgenic crops.}, journal = {Nature biotechnology}, volume = {20}, number = {6}, pages = {581-586}, pmid = {12042861}, issn = {1087-0156}, support = {R01 GM063879/GM/NIGMS NIH HHS/United States ; }, mesh = {Crops, Agricultural/drug effects ; *Ecosystem ; Environmental Pollution/*prevention &amp; control ; Gene Expression Regulation, Plant/*genetics ; Gene Transfer, Horizontal/*genetics ; Genetic Engineering/*methods ; Infertility/genetics ; Mutation/genetics ; Plants, Genetically Modified/adverse effects/*genetics ; Reproduction, Asexual/genetics ; Seeds/genetics ; }, abstract = {The potential of genetically modified (GM) crops to transfer foreign genes through pollen to related plant species has been cited as an environmental concern. Until more is known concerning the environmental impact of novel genes on indigenous crops and weeds, practical and regulatory considerations will likely require the adoption of gene-containment approaches for future generations of GM crops. Most molecular approaches with potential for controlling gene flow among crops and weeds have thus far focused on maternal inheritance, male sterility, and seed sterility. Several other containment strategies may also prove useful in restricting gene flow, including apomixis (vegetative propagation and asexual seed formation), cleistogamy (self-fertilization without opening of the flower), genome incompatibility, chemical induction/deletion of transgenes, fruit-specific excision of transgenes, and transgenic mitigation (transgenes that compromise fitness in the hybrid). As yet, however, no strategy has proved broadly applicable to all crop species, and a combination of approaches may prove most effective for engineering the next generation of GM crops.}, }
@article {pmid12042859, year = {2002}, author = {Dale, PJ and Clarke, B and Fontes, EM}, title = {Potential for the environmental impact of transgenic crops.}, journal = {Nature biotechnology}, volume = {20}, number = {6}, pages = {567-574}, doi = {10.1038/nbt0602-567}, pmid = {12042859}, issn = {1087-0156}, mesh = {Consumer Product Safety ; Crops, Agricultural/*genetics ; *Ecosystem ; Environment ; Environmental Pollution/*prevention &amp; control ; Gene Transfer, Horizontal/*genetics ; Genetic Engineering/trends ; Insecticide Resistance/genetics ; Plants, Genetically Modified/*genetics/*growth &amp; development ; Risk Assessment ; }, abstract = {In recent years, there has been increasing interest in how changes in agricultural practice associated with the introduction of particular genetically modified (GM) crops might indirectly impact the environment. There is also interest in any effects that might be associated with recombinant and novel combinations of DNA passing into the environment, and the possibility that they may be taken up by microorganisms or other live biological material. From the current state of knowledge, the impact of free DNA of transgenic origin is likely to be negligible compared with the large amount of total free DNA. We can find no compelling scientific arguments to demonstrate that GM crops are innately different from non-GM crops. The kinds of potential impacts of GM crops fall into classes familiar from the cultivation of non-GM crops (e.g., invasiveness, weediness, toxicity, or biodiversity). It is likely, however, that the novelty of some of the products of GM crop improvement will present new challenges and perhaps opportunities to manage particular crops in creative ways.}, }
@article {pmid12042845, year = {2002}, author = {Snow, AA}, title = {Transgenic crops why gene flow matters.}, journal = {Nature biotechnology}, volume = {20}, number = {6}, pages = {542}, doi = {10.1038/nbt0602-542}, pmid = {12042845}, issn = {1087-0156}, mesh = {Cost-Benefit Analysis ; Crops, Agricultural/*genetics ; Gene Transfer, Horizontal/*genetics ; *Genetic Engineering ; *Genome, Plant ; *Plants, Genetically Modified ; *Risk Assessment ; }, }
@article {pmid12039037, year = {2002}, author = {Oborník, M and Van de Peer, Y and Hypsa, V and Frickey, T and Slapeta, JR and Meyer, A and Lukes, J}, title = {Phylogenetic analyses suggest lateral gene transfer from the mitochondrion to the apicoplast.}, journal = {Gene}, volume = {285}, number = {1-2}, pages = {109-118}, doi = {10.1016/s0378-1119(02)00427-4}, pmid = {12039037}, issn = {0378-1119}, mesh = {Animals ; Base Composition ; DNA, Mitochondrial/*genetics ; DNA, Protozoan/genetics ; Evolution, Molecular ; Genes, Protozoan/genetics ; Organelles/*genetics ; *Phylogeny ; Plasmodium falciparum/genetics ; Plastids/genetics ; Protozoan Proteins/genetics ; Ribosomal Proteins/genetics ; Toxoplasma/genetics ; }, abstract = {Apicomplexan protozoa contain a single mitochondrion and a multimembranous plastid-like organelle termed apicoplast. The size of the apicomplexan plastid genome is extremely small (35 kb) thus offering a limited number of genes for phylogenetic analysis. Moreover, the sequences of apicoplast genes are highly adenosine+thymidine-rich and rapidly evolving. Due to these facts, phylogenetic analyses based on different genes or the structure of the ribosomal operon show conflicting results and the evolutionary history of this exciting organelle remains unclear. Although it is evident that the apicoplast and its genome is plastid-derived, our detailed phylogenetic analysis of amino acid and nucleotide sequences of selected apicoplast ribosomal protein genes rpl2, rpl14 and rps12 show their possible mitochondrial origin. The affinity of apicoplast ribosomal proteins to their mitochondrial homologs is very stable and well supported. Based on our results we propose that apicoplasts might contain both plastid and mitochondrial genes, thus constituting a hybrid assembly.}, }
@article {pmid14011606, year = {1963}, author = {ALACEVIC, M}, title = {Interspecific recombination in Streptomyces.}, journal = {Nature}, volume = {197}, number = {}, pages = {1323}, doi = {10.1038/1971323a0}, pmid = {14011606}, issn = {0028-0836}, mesh = {*Gene Transfer, Horizontal ; *Streptomyces ; }, }
@article {pmid12036287, year = {2002}, author = {Yoder, JA and Hawke, NA and Eason, DD and Mueller, MG and Davids, BJ and Gillin, FD and Litman, GW}, title = {BIVM, a novel gene widely distributed among deuterostomes, shares a core sequence with an unusual gene in Giardia lamblia.}, journal = {Genomics}, volume = {79}, number = {6}, pages = {750-755}, doi = {10.1006/geno.2002.6768}, pmid = {12036287}, issn = {0888-7543}, support = {AI 23338/AI/NIAID NIH HHS/United States ; AI 42488/AI/NIAID NIH HHS/United States ; DK 35108/DK/NIDDK NIH HHS/United States ; GM 20231/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Chromosome Mapping ; *Chromosomes, Human, Pair 13 ; Conserved Sequence ; Gene Transfer, Horizontal ; *Genome, Human ; Giardia lamblia/*genetics ; Humans ; Immunoglobulins/*genetics ; Mice ; Molecular Sequence Data ; Organ Specificity ; *Protozoan Proteins ; Vertebrates/*genetics ; }, abstract = {A novel gene, BIVM (for basic, immunoglobulin-like variable motif-containing), has been identified using an electronic search based on the conservation of short sequence motifs within the variable region of immunoglobulin (Ig) genes. BIVM maps to human chromosome 13q32-q33 and is predicted to encode a 503-amino-acid protein with a pI of 9.1. The 5' untranslated region of BIVM is encoded in two exons; the coding portion is encoded in nine exons. BIVM is tightly linked (41 bp) and in the opposite transcriptional orientation to MGC5302 (also known as KDEL1 and EP58) in human. The ubiquitous expression of BIVM in normal tissues and the presence of a 5' CpG island suggest that BIVM is a housekeeping gene. Characterization of BIVM in representative species demonstrates significant conservation throughout deuterostomes; no sequence with significant identity to BIVM has been detected in proteostomes. However, an unusual gene has been identified in the protozoan pathogen Giardia lamblia that is similar to the core sequence of BIVM, suggesting the possibility of a horizontal gene transfer.}, }
@article {pmid12034660, year = {2002}, author = {Lemström, KB and Krebs, R and Nykänen, AI and Tikkanen, JM and Sihvola, RK and Aaltola, EM and Häyry, PJ and Wood, J and Alitalo, K and Ylä-Herttuala, S and Koskinen, PK}, title = {Vascular endothelial growth factor enhances cardiac allograft arteriosclerosis.}, journal = {Circulation}, volume = {105}, number = {21}, pages = {2524-2530}, doi = {10.1161/01.cir.0000016821.76177.d2}, pmid = {12034660}, issn = {1524-4539}, mesh = {Acute Disease ; Angiogenesis Inhibitors/pharmacology ; Animals ; Arteriosclerosis/*etiology/pathology/physiopathology/prevention &amp; control ; Chronic Disease ; Disease Models, Animal ; Disease Progression ; Endothelial Growth Factors/genetics/metabolism/*pharmacology ; Gene Transfer, Horizontal ; Graft Rejection/immunology ; Graft Survival/immunology ; Heart Transplantation/*adverse effects/immunology/pathology ; Immunohistochemistry ; In Situ Hybridization ; Leukocytes, Mononuclear/immunology/pathology ; Lymphokines/genetics/metabolism/*pharmacology ; Macrophages/pathology ; Myocardium/metabolism/pathology ; Phthalazines/pharmacology ; *Pyridines ; RNA, Messenger/metabolism ; Rabbits ; Rats ; Rats, Inbred Strains ; Receptor Protein-Tyrosine Kinases/antagonists &amp; inhibitors ; Receptors, Growth Factor/antagonists &amp; inhibitors ; Receptors, Vascular Endothelial Growth Factor ; Transfection ; Transplantation, Heterotopic ; Vascular Endothelial Growth Factor A ; Vascular Endothelial Growth Factors ; }, abstract = {BACKGROUND: Cardiac allograft arteriosclerosis is a complex process of alloimmune response, chronic inflammation, and smooth muscle cell proliferation that includes cross talk between cytokines and growth factors.<br><br>METHODS AND RESULTS: Our results in rat cardiac allografts established alloimmune response as an alternative stimulus capable of inducing vascular endothelial growth factor (VEGF) mRNA and protein expression in cardiomyocytes and graft-infiltrating mononuclear inflammatory cells, which suggests that these cells may function as a source of VEGF to the cells of coronary arteries. Linear regression analysis of these allografts with different stages of arteriosclerotic lesions revealed a strong correlation between intragraft VEGF protein expression and the development of intimal thickening, whereas blockade of signaling downstream of VEGF receptor significantly reduced arteriosclerotic lesions. In addition, in cholesterol-fed rabbits, intracoronary perfusion of cardiac allografts with a clinical-grade adenoviral vector that encoded mouse VEGF(164) enhanced the formation of arteriosclerotic lesions, possibly secondary to increased intragraft influx of macrophages and neovascularization in the intimal lesions.<br><br>CONCLUSIONS: Our findings suggest a positive regulatory role between VEGF and coronary arteriosclerotic lesion formation in the allograft cytokine microenvironment.}, }
@article {pmid12029358, year = {2002}, author = {Filée, J and Forterre, P and Sen-Lin, T and Laurent, J}, title = {Evolution of DNA polymerase families: evidences for multiple gene exchange between cellular and viral proteins.}, journal = {Journal of molecular evolution}, volume = {54}, number = {6}, pages = {763-773}, doi = {10.1007/s00239-001-0078-x}, pmid = {12029358}, issn = {0022-2844}, mesh = {Animals ; Artificial Gene Fusion ; Bacteria/enzymology ; DNA-Directed DNA Polymerase/*genetics ; Eukaryotic Cells ; *Evolution, Molecular ; Humans ; Multigene Family ; Phylogeny ; Plants/enzymology ; Viruses/enzymology ; }, abstract = {A phylogenetic analysis of the five major families of DNA polymerase is presented. Viral and plasmid sequences are included in this compilation along with cellular enzymes. The classification by Ito and Braithwaite (Ito and Braithwaite 1991) of the A, B, C, D, and X families has been extended to accommodate the "Y family" of DNA polymerases that are related to the eukaryotic RAD30 and the bacterial UmuC gene products. After analysis, our data suggest that no DNA polymerase family was universally conserved among the three biological domains and no simple evolutionary scenario could explain that observation. Furthermore, viruses and plasmids carry a remarkably diverse set of DNA polymerase genes, suggesting that lateral gene transfer is frequent and includes non-orthologous gene displacements between cells and viruses. The relationships between viral and host genes appear very complex. We propose that the gamma DNA polymerase of the mitochondrion replication apparatus is of phage origin and that this gene replaced the one in the bacterial ancestor. Often there was no obvious relation between the viral and the host DNA polymerase, but an interesting exception concerned the family B enzymes: in which ancient gene exchange can be detected between the viruses and their hosts. Additional evidence for horizontal gene transfers between cells and viruses comes from an analysis of the small damage-inducible DNA polymerases. Taken together, these findings suggest a complex evolutionary history of the DNA replication apparatus that involved significant exchanges between viruses, plasmids, and their hosts.}, }
@article {pmid12029065, year = {2002}, author = {Myllykallio, H and Lipowski, G and Leduc, D and Filee, J and Forterre, P and Liebl, U}, title = {An alternative flavin-dependent mechanism for thymidylate synthesis.}, journal = {Science (New York, N.Y.)}, volume = {297}, number = {5578}, pages = {105-107}, doi = {10.1126/science.1072113}, pmid = {12029065}, issn = {1095-9203}, mesh = {Catalysis ; Deoxyuracil Nucleotides/metabolism ; Electron Transport ; Escherichia coli/enzymology/genetics/growth &amp; development ; Flavin Mononucleotide/metabolism ; Flavin-Adenine Dinucleotide/*metabolism ; Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; Helicobacter pylori/*enzymology/genetics ; Molecular Weight ; Phylogeny ; Pyrococcus/*enzymology/genetics ; Recombinant Proteins/metabolism ; Tetrahydrofolates/metabolism ; Thymidine Monophosphate/*biosynthesis ; Thymidylate Synthase/chemistry/*genetics/isolation &amp; purification/*metabolism ; Transformation, Bacterial ; Uridine Monophosphate/metabolism ; }, abstract = {Although deoxythymidylate cannot be provided directly by ribonucleotide reductase, the gene encoding thymidylate synthase ThyA is absent from the genomes of a large number of nonsymbiotic microbes. We show that ThyX (Thy1) proteins of previously unknown function form a large and distinct class of thymidylate synthases. ThyX has a wide but sporadic phylogenetic distribution, almost exclusively limited to microbial genomes lacking thyA. ThyX and ThyA use different reductive mechanisms, because ThyX activity is dependent on reduced flavin nucleotides. Our findings reveal complexity in the evolution of thymidine in present-day DNA. Because ThyX proteins are found in many pathogenic microbes, they present a previously uncharacterized target for antimicrobial compounds.}, }
@article {pmid12028728, year = {2002}, author = {Legendre, P and Makarenkov, V}, title = {Reconstruction of biogeographic and evolutionary networks using reticulograms.}, journal = {Systematic biology}, volume = {51}, number = {2}, pages = {199-216}, doi = {10.1080/10635150252899725}, pmid = {12028728}, issn = {1063-5157}, mesh = {Algorithms ; Animals ; Arvicolinae ; *Computational Biology ; *Evolution, Molecular ; Fishes ; Models, Genetic ; Models, Statistical ; Phylogeny ; Software ; }, abstract = {A reticulogram is a general network capable of representing a reticulate evolutionary structure. It is particularly useful for portraying relationships among organisms that may be related in a nonunique way to their common ancestor - relationships that cannot be represented by a dendrogram or a phylogenetic tree. We propose a new method for constructing reticulograms that represent a given distance matrix. Reticulate evolution applies first to phylogenetic problems; it has been found in nature, for example, in the within-species microevolution of eukaryotes and in lateral gene transfer in bacteria. In this paper, we propose a new method for reconstructing reticulation networks and we develop applications of the reticulate evolution model to ecological biogeographic, population microevolutionary, and hybridization problems. The first example considers a spatially constrained reticulogram representing the postglacial dispersal of freshwater fishes in the Québec peninsula; the reticulogram provides a better model of postglacial dispersal than does a tree model. The second example depicts the morphological similarities among local populations of muskrats in a river valley in Belgium; adding supplementary branches to a tree depicting the river network leads to a better representation of the morphological distances among local populations of muskrats than does a tree structure. A third example involves hybrids between plants of the genus Aphelandra.}, }
@article {pmid12023043, year = {2002}, author = {Yamamoto, TA and Gerdes, K and Tunnacliffe, A}, title = {Bacterial toxin RelE induces apoptosis in human cells.}, journal = {FEBS letters}, volume = {519}, number = {1-3}, pages = {191-194}, doi = {10.1016/s0014-5793(02)02764-3}, pmid = {12023043}, issn = {0014-5793}, mesh = {Anti-Bacterial Agents/pharmacology ; *Apoptosis/drug effects ; Bacterial Proteins/antagonists &amp; inhibitors/genetics/*toxicity ; Cell Division/drug effects ; Cell Survival/drug effects ; Clone Cells/drug effects/metabolism ; DNA Fragmentation ; DNA, Antisense/genetics/pharmacology ; DNA, Bacterial/genetics ; Gene Expression/drug effects ; Gene Transfer, Horizontal ; Humans ; Osteosarcoma/metabolism ; Tetracyclines ; Transcription, Genetic/drug effects ; Tumor Cells, Cultured ; }, abstract = {The bacterial protein RelE severely restricts prokaryotic cell growth, probably by acting as a global inhibitor of translation. It is ubiquitous in prokaryotes as part of the RelE-RelB toxin-antitoxin system, and may be activated by nutritional stress. When the relE gene from Escherichia coli was expressed inducibly in a human osteosarcoma cell line, it was shown to retard growth and to lead to cell death by apoptosis. RelE is therefore unusual among bacterial toxins in possessing broad activity against both prokaryotes and eukaryotes, perhaps by acting on evolutionarily conserved components of the translation machinery.}, }
@article {pmid12019317, year = {2002}, author = {Cheng, L and Sapieha, P and Kittlerova, P and Hauswirth, WW and Di Polo, A}, title = {TrkB gene transfer protects retinal ganglion cells from axotomy-induced death in vivo.}, journal = {The Journal of neuroscience : the official journal of the Society for Neuroscience}, volume = {22}, number = {10}, pages = {3977-3986}, pmid = {12019317}, issn = {1529-2401}, support = {R01 EY011123/EY/NEI NIH HHS/United States ; EY11123/EY/NEI NIH HHS/United States ; }, mesh = {Animals ; Axotomy ; Cell Death/drug effects/physiology ; Cell Survival/physiology ; Cytoprotection/drug effects/physiology ; Dependovirus/genetics ; Down-Regulation/physiology ; Enzyme Activation/drug effects ; Enzyme Inhibitors/pharmacology ; Female ; Gene Transfer, Horizontal ; Genetic Vectors ; Mitogen-Activated Protein Kinases/metabolism ; *Protein Serine-Threonine Kinases ; Proto-Oncogene Proteins/metabolism ; Proto-Oncogene Proteins c-akt ; RNA, Messenger/metabolism ; Rats ; Rats, Sprague-Dawley ; Receptor, trkB/genetics/*metabolism ; Retinal Ganglion Cells/cytology/drug effects/*metabolism ; Signal Transduction/drug effects/physiology ; Up-Regulation/physiology ; }, abstract = {Injury-induced downregulation of neurotrophin receptors may limit the response of neurons to trophic factors, compromising their ability to survive. We tested this hypothesis in a model of CNS injury: retinal ganglion cell (RGC) death after transection of the adult rat optic nerve. TrkB mRNA rapidly decreased in axotomized RGCs to approximately 50% of the level in intact retinas. TrkB gene transfer into RGCs combined with exogenous BDNF administration markedly increased neuronal survival: 76% of RGCs remained alive at 2 weeks after axotomy, a time when >90% of these neurons are lost without treatment. Activation of mitogen-activated protein kinase, but not phosphatidylinositol-3 kinase, was required for TrkB-induced survival. These data provide proof-of-principle that enhancing the capacity of injured neurons to respond to trophic factors can be an effective neuroprotective strategy in the adult CNS.}, }
@article {pmid12014182, year = {2002}, author = {Kingsley, RA and Bäumler, AJ}, title = {Pathogenicity islands and host adaptation of Salmonella serovars.}, journal = {Current topics in microbiology and immunology}, volume = {264}, number = {1}, pages = {67-87}, pmid = {12014182}, issn = {0070-217X}, support = {AI40124/AI/NIAID NIH HHS/United States ; AI44170/AI/NIAID NIH HHS/United States ; }, mesh = {Adaptation, Physiological/*genetics ; Animals ; Gene Transfer, Horizontal ; *Genes, Bacterial/physiology ; Humans ; Salmonella/*genetics/*pathogenicity ; Salmonella typhimurium/genetics ; Virulence ; }, }
@article {pmid12013818, year = {2002}, author = {Gojobori, T}, title = {[Genomic evolution of pathogenic bacteria and horizontal gene transfer].}, journal = {Nihon Hansenbyo Gakkai zasshi = Japanese journal of leprosy : official organ of the Japanese Leprosy Association}, volume = {71}, number = {2}, pages = {131-132}, pmid = {12013818}, issn = {1342-3681}, mesh = {Bacteria/*genetics/*pathogenicity ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Mycobacterium leprae/genetics ; Mycobacterium tuberculosis/genetics ; }, }
@article {pmid12012870, year = {2002}, author = {Heuner, K and Steinert, M and Marre, R and Hacker, J}, title = {Genomic structure and evolution of Legionella species.}, journal = {Current topics in microbiology and immunology}, volume = {264}, number = {2}, pages = {61-78}, pmid = {12012870}, issn = {0070-217X}, mesh = {Animals ; Classification ; DNA, Bacterial ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; Legionella/classification/*genetics/metabolism/pathogenicity ; Plasmids ; Virulence ; }, }
@article {pmid12012868, year = {2002}, author = {Vogel, U and Frosch, M}, title = {The genus Neisseria: population structure, genome plasticity, and evolution of pathogenicity.}, journal = {Current topics in microbiology and immunology}, volume = {264}, number = {2}, pages = {23-45}, pmid = {12012868}, issn = {0070-217X}, support = {AI38399/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; DNA, Bacterial ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; Molecular Sequence Data ; Neisseria/*genetics/*pathogenicity ; Virulence ; }, }
@article {pmid12012867, year = {2002}, author = {Rowe-Magnus, AD and Davies, J and Mazel, D}, title = {Impact of integrons and transposons on the evolution of resistance and virulence.}, journal = {Current topics in microbiology and immunology}, volume = {264}, number = {2}, pages = {167-188}, pmid = {12012867}, issn = {0070-217X}, mesh = {Adaptation, Physiological ; Animals ; Anti-Bacterial Agents/pharmacology ; *DNA Transposable Elements ; *DNA, Bacterial ; Drug Resistance, Bacterial/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Models, Genetic ; Virulence ; }, }
@article {pmid12012863, year = {2002}, author = {Odenbreit, S and Haas, R}, title = {Helicobacter pylori: impact of gene transfer and the role of the cag pathogenicity island for host adaptation and virulence.}, journal = {Current topics in microbiology and immunology}, volume = {264}, number = {2}, pages = {1-22}, pmid = {12012863}, issn = {0070-217X}, mesh = {Adaptation, Physiological/*genetics ; *Antigens, Bacterial ; Bacterial Proteins/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial/*physiology ; Genetic Variation ; Helicobacter pylori/*genetics ; Humans ; Transformation, Bacterial ; Virulence ; }, }
@article {pmid12007641, year = {2002}, author = {Lerouge, I and Vanderleyden, J}, title = {O-antigen structural variation: mechanisms and possible roles in animal/plant-microbe interactions.}, journal = {FEMS microbiology reviews}, volume = {26}, number = {1}, pages = {17-47}, doi = {10.1111/j.1574-6976.2002.tb00597.x}, pmid = {12007641}, issn = {0168-6445}, mesh = {Animal Population Groups/microbiology ; Animals ; Base Sequence ; Carbohydrate Sequence ; *Genetic Variation ; Gram-Negative Bacteria/*pathogenicity/*physiology ; Gram-Negative Bacterial Infections/microbiology/*veterinary ; Humans ; Molecular Sequence Data ; O Antigens/*chemistry/genetics ; Plant Diseases/microbiology ; Plants/*microbiology ; Symbiosis ; }, abstract = {Current data from bacterial pathogens of animals and from bacterial symbionts of plants support some of the more general proposed functions for lipopolysaccharides (LPS) and underline the importance of LPS structural versatility and adaptability. Most of the structural heterogeneity of LPS molecules is found in the O-antigen polysaccharide. In this review, the role and mechanisms of this striking flexibility in molecular structure of the O-antigen in bacterial pathogens and symbionts are illustrated by some recent findings. The variation in O-antigen that gives rise to an enormous structural diversity of O-antigens lies in the sugar composition and the linkages between monosaccharides. The chemical composition and structure of the O-antigen is strain-specific (interstrain LPS heterogeneity) but can also vary within one bacterial strain (intrastrain LPS heterogeneity). Both LPS heterogeneities can be achieved through variations at different levels. First of all, O-polysaccharides can be modified non-stoichiometrically with sugar moieties, such as glucosyl and fucosyl residues. The addition of non-carbohydrate substituents, i.e. acetyl or methyl groups, to the O-antigen can also occur with regularity, but in most cases these modifications are again non-stoichiometric. Understanding LPS structural variation in bacterial pathogens is important because several studies have indicated that the composition or size of the O-antigen might be a reliable indicator of virulence potential and that these important features often differ within the same bacterial strain. In general, O-antigen modifications seem to play an important role at several (at least two) stages of the infection process, including the colonization (adherence) step and the ability to bypass or overcome host defense mechanisms. There are many reports of modifications of O-antigen in bacterial pathogens, resulting either from altered gene expression, from lysogenic conversion or from lateral gene transfer followed by recombination. In most cases, the mechanisms underlying these changes have not been resolved. However, in recent studies some progress in understanding has been made. Changes in O-antigen structure mediated by lateral gene transfer, O-antigen conversion and phase variation, including fucosylation, glucosylation, acetylation and changes in O-antigen size, will be discussed. In addition to the observed LPS heterogeneity in bacterial pathogens, the structure of LPS is also altered in bacterial symbionts in response to signals from the plant during symbiosis. It appears to be part of a molecular communication between bacterium and host plant. Experiments ex planta suggest that the bacterium in the rhizosphere prepares its LPS for its roles in symbiosis by refining the LPS structure in response to seed and root compounds and the lower pH at the root surface. Moreover, modifications in LPS induced by conditions associated with infection are another indication that specific structures are important. Also during the differentiation from bacterium to bacteroid, the LPS of Rhizobium undergoes changes in the composition of the O-antigen, presumably in response to the change of environment. Recent findings suggest that, during symbiotic bacteroid development, reduced oxygen tension induces structural modifications in LPS that cause a switch from predominantly hydrophilic to predominantly hydrophobic molecular forms. However, the genetic mechanisms by which the LPS epitope changes are regulated remain unclear. Finally, the possible roles of O-antigen variations in symbiosis will be discussed.}, }
@article {pmid12007424, year = {2002}, author = {Inagaki, Y and Doolittle, WF and Baldauf, SL and Roger, AJ}, title = {Lateral transfer of an EF-1alpha gene: origin and evolution of the large subunit of ATP sulfurylase in eubacteria.}, journal = {Current biology : CB}, volume = {12}, number = {9}, pages = {772-776}, doi = {10.1016/s0960-9822(02)00816-3}, pmid = {12007424}, issn = {0960-9822}, mesh = {Amino Acid Sequence ; Archaea/enzymology/*genetics ; Eukaryotic Cells/enzymology ; *Evolution, Molecular ; Gene Duplication ; *Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; Molecular Sequence Data ; Peptide Elongation Factor 1/chemistry/*genetics ; Phylogeny ; Proteobacteria/enzymology/*genetics ; Sulfate Adenylyltransferase/chemistry/*genetics ; }, abstract = {It is generally accepted that new genes arise via duplication and functional divergence of existing genes, in accordance with Ohno's model, now called "Mutation During Redundancy," or MDR. In this model, one of the two gene copies is free to acquire novel (although likely related) activities through mutation, since only one copy is required for its original function. However, duplication within a genome is not the only process that might give rise to this situation: acquisition of a functionally redundant gene by lateral gene transfer (LGT) could also initiate the MDR process. Here we describe a probable instance, involving LGT of an archaeal or eukaryotic elongation factor 1alpha (EF-1alpha) gene. The large subunit of ATP sulfurylase (CysN or the N-terminal portion of NodQ), found mainly in proteobacteria, is clearly related to translation elongation factors. However, our analyses show that cysN arose from an EF-1alpha gene initially acquired by LGT, not from a within-genome duplication of the resident EF-Tu gene. To our knowledge, this is the first unequivocal case of LGT followed by functional modification to be described; this mechanism could be a potentially important force in establishing genes with novel functions in genomes.}, }
@article {pmid12004120, year = {2002}, author = {Reysenbach, AL and Shock, E}, title = {Merging genomes with geochemistry in hydrothermal ecosystems.}, journal = {Science (New York, N.Y.)}, volume = {296}, number = {5570}, pages = {1077-1082}, doi = {10.1126/science.1072483}, pmid = {12004120}, issn = {1095-9203}, mesh = {Adaptation, Physiological ; Archaea/classification/genetics/metabolism/*physiology ; Bacteria/classification/genetics/metabolism ; *Bacterial Physiological Phenomena ; Biofilms/growth &amp; development ; Biological Evolution ; *Ecosystem ; Energy Metabolism ; Environmental Microbiology ; Gene Transfer, Horizontal ; Genetic Variation ; *Geologic Sediments ; *Hot Temperature ; Mutation ; Phylogeny ; *Water Microbiology ; }, abstract = {Thermophilic microbial inhabitants of active seafloor and continental hot springs populate the deepest branches of the universal phylogenetic tree, making hydrothermal ecosystems the most ancient continuously inhabited ecosystems on Earth. Geochemical consequences of hot water-rock interactions render these environments habitable and supply a diverse array of energy sources. Clues to the strategies for how life thrives in these dynamic ecosystems are beginning to be elucidated through a confluence of biogeochemistry, microbiology, ecology, molecular biology, and genomics. These efforts have the potential to reveal how ecosystems originate, the extent of the subsurface biosphere, and the driving forces of evolution.}, }
@article {pmid12003951, year = {2002}, author = {Sullivan, JT and Trzebiatowski, JR and Cruickshank, RW and Gouzy, J and Brown, SD and Elliot, RM and Fleetwood, DJ and McCallum, NG and Rossbach, U and Stuart, GS and Weaver, JE and Webby, RJ and De Bruijn, FJ and Ronson, CW}, title = {Comparative sequence analysis of the symbiosis island of Mesorhizobium loti strain R7A.}, journal = {Journal of bacteriology}, volume = {184}, number = {11}, pages = {3086-3095}, pmid = {12003951}, issn = {0021-9193}, mesh = {Amino Acids/metabolism ; Carbon/metabolism ; Gene Transfer, Horizontal/genetics ; *Genes, Bacterial ; Genes, Regulator ; Lotus/microbiology ; Microtubule Proteins/biosynthesis/genetics ; Molecular Sequence Data ; Multigene Family ; Nitrogen Fixation/genetics ; Phosphates/metabolism ; Rhizobiaceae/*genetics/metabolism ; Species Specificity ; *Symbiosis ; }, abstract = {The Mesorhizobium loti strain R7A symbiosis island is a 502-kb chromosomally integrated element which transfers to nonsymbiotic mesorhizobia in the environment, converting them to Lotus symbionts. It integrates into a phenylalanine tRNA gene in a process mediated by a P4-type integrase encoded at the left end of the element. We have determined the nucleotide sequence of the island and compared its deduced genetic complement with that reported for the 611-kb putative symbiosis island of M. loti strain MAFF303099. The two islands share 248 kb of DNA, with multiple deletions and insertions of up to 168 kb interrupting highly conserved colinear DNA regions in the two strains. The shared DNA regions contain all the genes likely to be required for Nod factor synthesis, nitrogen fixation, and island transfer. Transfer genes include a trb operon and a cluster of potential tra genes which are also present on the strain MAFF303099 plasmid pMLb. The island lacks plasmid replication genes, suggesting that it is a site-specific conjugative transposon. The R7A island encodes a type IV secretion system with strong similarity to the vir pilus from Agrobacterium tumefaciens that is deleted from MAFF303099, which in turn encodes a type III secretion system not found on the R7A island. The 414 genes on the R7A island also include putative regulatory genes, transport genes, and an array of metabolic genes. Most of the unique hypothetical genes on the R7A island are strain-specific and clustered, suggesting that they may represent other acquired genetic elements rather than symbiotically relevant DNA.}, }
@article {pmid12003923, year = {2002}, author = {Finan, TM}, title = {Evolving insights: symbiosis islands and horizontal gene transfer.}, journal = {Journal of bacteriology}, volume = {184}, number = {11}, pages = {2855-2856}, pmid = {12003923}, issn = {0021-9193}, mesh = {Gene Transfer, Horizontal ; Lotus/microbiology ; Rhizobium/*genetics/pathogenicity ; Soil Microbiology ; Symbiosis/*genetics ; }, }
@article {pmid11988462, year = {2002}, author = {Ponting, CP and Russell, RR}, title = {The natural history of protein domains.}, journal = {Annual review of biophysics and biomolecular structure}, volume = {31}, number = {}, pages = {45-71}, doi = {10.1146/annurev.biophys.31.082901.134314}, pmid = {11988462}, issn = {1056-8700}, mesh = {Animals ; Evolution, Molecular ; Protein Conformation ; *Protein Structure, Tertiary ; Proteins/*classification ; Sequence Analysis, DNA ; Sequence Analysis, Protein ; }, abstract = {Genome sequencing and structural genomics projects are providing new insights into the evolutionary history ofprote in domains. As methods for sequence and structure comparison improve, more distantly related domains are shown to be homologous. Thus there is a need for domain families to be classified within a hierarchy similar to Linnaeus' Systema Naturae, the classification of species. With such a hierarchy in mind, we discuss the evolution of domains, their combination into proteins, and evidence as to the likely origin of protein domains. We also discuss when and how analysis of domains can be used to understand details of protein function. Unconventional features of domain evolution such as intragenomic competition, domain insertion, horizontal gene transfer, and convergent evolution are seen as analogs of organismal evolutionary events. These parallels illustrate how the concept of domains can be applied to provide insights into evolutionary biology.}, }
@article {pmid11986758, year = {2001}, author = {Hedden, P and Phillips, AL and Rojas, MC and Carrera, E and Tudzynski, B}, title = {Gibberellin Biosynthesis in Plants and Fungi: A Case of Convergent Evolution?.}, journal = {Journal of plant growth regulation}, volume = {20}, number = {4}, pages = {319-331}, doi = {10.1007/s003440010037}, pmid = {11986758}, issn = {0721-7595}, support = {BBS/E/C/00004161/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/C/00004162/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {As well as being phytohormones, gibberellins (GAs) are present in some fungi and bacteria. Indeed, GAs were first discovered in the fungus Gibberella fujikuroi, from which gibberellic acid (GA3) and other GAs are produced commercially. Although higher plants and the fungus produce structurally identical GAs, there are important differences in the pathways and enzymes involved. This has become particularly apparent with the identification of almost all of the genes for GA-biosynthesis in Arabidopsis thaliana and G. fujikuroi, following the sequencing of the Arabidopsis genome and the detection of a GA-biosynthesis gene cluster in the fungus. For example, 3b-hydroxylation occurs early in the pathway in G. fujikuroi and is catalyzed by a cytochrome P450 monooxygenase, whereas it is usually the final step in plants and is catalyzed by 2-oxoglutarate-dependent dioxygenases. Similarly, 20-oxidation is catalyzed by dioxygenases in plants and a cytochrome P450 in the fungus. Even where cytochrome P450s have equivalent functions in plants and Gibberella, they are unrelated in terms of amino acid sequence. These profound differences indicate that higher plants and fungi have evolved their complex biosynthetic pathways to GAs independently and not by horizontal gene transfer.}, }
@article {pmid11976306, year = {2002}, author = {Hofreuter, D and Haas, R}, title = {Characterization of two cryptic Helicobacter pylori plasmids: a putative source for horizontal gene transfer and gene shuffling.}, journal = {Journal of bacteriology}, volume = {184}, number = {10}, pages = {2755-2766}, pmid = {11976306}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; Base Sequence ; Chromosome Mapping ; Conjugation, Genetic ; DNA Transposable Elements ; *Gene Transfer, Horizontal ; Helicobacter pylori/*genetics ; Molecular Sequence Data ; Open Reading Frames ; *Plasmids ; Recombination, Genetic ; Repetitive Sequences, Nucleic Acid ; }, abstract = {Many Helicobacter pylori isolates carry cryptic plasmids of extremely variable size. In this study we analyzed two H. pylori plasmids, pHel4 and pHel5, from H. pylori strains P8 and P29, respectively. Plasmid pHel4 consists of 10,970 bp, constituting 15 putative open reading frames (ORFs), whereas pHel5 consists of 18,291 bp, constituting 17 ORFs. The findings that both plasmids encode a conserved RepA protein and that both have an origin of replication containing an iteron place them in the group of theta plasmids. In pHel4, the products of the overlapping orf4C, orf4D, orf4E, and orf4F sequences are homologous to MobA, MobB, MobC, and MobD, encoded by colicinogenic plasmids, suggesting that pHel4 might be mobilizable. A further putative operon consists of orf4B and orf4A, the products of which are homologous to microcin C7 (MccC7) biosynthesis and secretion proteins MccB and MccC, respectively. Plasmid pHel5 carries putative genes encoding proteins with homology to an endonuclease and gene products of an H. pylori chromosomal plasticity zone. Both plasmids contain repeat sequences, such as the previously identified R2 repeat, which are considered preferred recombination sites. In pHel4, a new repeat sequence (R4 repeat), which seems to act as a hot spot for site-specific recombination, was identified. All H. pylori plasmids characterized so far have a modular structure. We suggest a model that explains the existing plasmids by insertions and deletions of genetic elements at the repeat sequences. A genetic exchange between plasmids and the bacterial chromosome, combined with plasmid mobilization, might add a novel mechanism to explain the high genetic macrodiversity within the H. pylori population.}, }
@article {pmid11976290, year = {2002}, author = {Wang, L and Huskic, S and Cisterne, A and Rothemund, D and Reeves, PR}, title = {The O-antigen gene cluster of Escherichia coli O55:H7 and identification of a new UDP-GlcNAc C4 epimerase gene.}, journal = {Journal of bacteriology}, volume = {184}, number = {10}, pages = {2620-2625}, pmid = {11976290}, issn = {0021-9193}, mesh = {Base Sequence ; Carbohydrate Epimerases/*genetics ; Escherichia coli/*genetics ; Gene Transfer, Horizontal ; Guanosine Diphosphate Sugars/metabolism ; Molecular Sequence Data ; *Multigene Family ; O Antigens/*genetics ; Uridine Diphosphate N-Acetylgalactosamine/*metabolism ; }, abstract = {Escherichia coli O55 is an important antigen which is often associated with enteropathogenic E. coli clones. We sequenced the genes responsible for its synthesis and identified genes for O-antigen polymerase, O-antigen flippase, four enzymes involved in GDP-colitose synthesis, and three glycosyltransferases, all by comparison with known genes. Upstream of the normal O-antigen region there is a gne gene, which encodes a UDP-GlcNAc epimerase for converting UDP-GlcNAc to UDP-GalNAc and is essential for O55 antigen synthesis. The O55 gne product has only 20 and 26% identity to the gne genes of Pseudomonas aeruginosa and E. coli O113, respectively. We also found evidence for the O55 gene cluster's having evolved from another gene cluster by gain and loss of genes. Only three of the GDP-colitose pathway genes are in the usual location, the other two being separated, although nearby. It is thought that the E. coli O157:H7 clone evolved from the O55:H7 clone in part by transfer of the O157 gene cluster into an O55 lineage. Comparison of genes flanking the O-antigen gene clusters of the O55:H7 and O157:H7 clones revealed one recombination site within the galF gene and located the other between the hisG and amn genes. Genes outside the recombination sites are 99.6 to 100% identical in the two clones, while most genes thought to have transferred with the O157 gene cluster are 95 to 98% identical.}, }
@article {pmid11976103, year = {2002}, author = {Pradel, N and Leroy-Setrin, S and Joly, B and Livrelli, V}, title = {Genomic subtraction to identify and characterize sequences of Shiga toxin-producing Escherichia coli O91:H21.}, journal = {Applied and environmental microbiology}, volume = {68}, number = {5}, pages = {2316-2325}, pmid = {11976103}, issn = {0099-2240}, mesh = {Cloning, Molecular ; DNA Probes ; DNA, Bacterial/*analysis ; Escherichia coli/genetics/*metabolism/pathogenicity ; Genome, Bacterial ; Sequence Analysis, DNA ; Shiga Toxin/genetics/*isolation &amp; purification ; }, abstract = {To identify Shiga toxin-producing Escherichia coli genes associated with severe human disease, a genomic subtraction technique was used with hemolytic-uremic syndrome-associated O91:H21 strain CH014 and O6:H10 bovine strains. The method was adapted to the Shiga toxin-producing E. coli genome: three rounds of subtraction were used to isolate DNA fragments specific to strain CH014. The fragments were characterized by genetic support analysis, sequencing, and hybridization to the genome of a collection of Shiga toxin-producing E. coli strains. A total of 42 fragments were found, 19 of which correspond to previously identified unique DNA sequences in the enterohemorrhagic E. coli EDL933 reference strain, including 7 fragments corresponding to prophage sequences and others encoding candidate virulence factors, such a SepA homolog protein and a fimbrial usher protein. In addition, the subtraction procedure yielded plasmid-related sequences from Shigella flexneri and enteropathogenic and Shiga toxin-producing E. coli virulence plasmids. We found that lateral gene transfer is extensive in strain CH014, and we discuss the role of genomic mobile elements, especially bacteriophages, in the evolution and possible transfer of virulence determinants.}, }
@article {pmid11972616, year = {2002}, author = {Springael, D and Peys, K and Ryngaert, A and Van Roy, S and Hooyberghs, L and Ravatn, R and Heyndrickx, M and van der Meer, JR and Vandecasteele, C and Mergeay, M and Diels, L}, title = {Community shifts in a seeded 3-chlorobenzoate degrading membrane biofilm reactor: indications for involvement of in situ horizontal transfer of the clc-element from inoculum to contaminant bacteria.}, journal = {Environmental microbiology}, volume = {4}, number = {2}, pages = {70-80}, doi = {10.1046/j.1462-2920.2002.00267.x}, pmid = {11972616}, issn = {1462-2912}, mesh = {Biodegradation, Environmental ; Bioreactors/*microbiology ; Chlorobenzoates/*metabolism ; Gene Transfer, Horizontal ; Genotype ; Gram-Negative Aerobic Rods and Cocci/*genetics/*metabolism ; }, abstract = {Pseudomonas putida BN210, carrying the self- transferable clc-element encoding degradation of 3-chlorobenzoate on the chromosome, was used as inoculum in different membrane biofilm reactors treating 3-chlorobenzoate-contaminated model wastewater. Analysis of the bacterial population in the effluent and in the biofilm showed the loss of BN210 beyond detection from the reactors and the appearance of several novel 3-chlorobenzoate mineralizing bacteria mainly belonging to the beta-proteobacteria. In contrast, in non-inoculated reactors, no 3-chlorobenzoate degradation was observed and no 3-chlorobenzoate degraders could be recovered. Southern blots hybridization of genomic DNA using clc-element-specific probes and FIGE analysis indicated the presence of the complete clc-element in one or more copies in the isolates. Moreover, the isolates could transfer the clc genes to Ralstonia metallidurans recipients. Two representative reactor isolates, Ralstonia sp. strains KP3 and KP9 demonstrated a higher growth rate on 3-chlorobenzoate than strain BN210 in batch cultures. When BN210, KP3 and KP9 were simultaneously inoculated in a membrane reactor supplied with 3-chlorobenzoate, strain KP3 outcompeted the two other strains and remained the major 3-chlorobenzoate degrading population in the reactor. Our data suggest that in situ horizontal transfer of the clc-element from the inoculum to contaminant bacteria in the reactors was involved in the establishment of novel 3-chlorobenzoate degrading populations that were more competitive under the defined reactor conditions than the inoculum strain.}, }
@article {pmid11972321, year = {2002}, author = {Cortese, MS and Caplan, AB and Crawford, RL}, title = {Structural, functional, and evolutionary analysis of moeZ, a gene encoding an enzyme required for the synthesis of the Pseudomonas metabolite, pyridine-2,6-bis(thiocarboxylic acid).}, journal = {BMC evolutionary biology}, volume = {2}, number = {}, pages = {8}, pmid = {11972321}, issn = {1471-2148}, mesh = {Amino Acid Sequence ; Bacterial Proteins/*chemistry/genetics/*metabolism ; Conserved Sequence ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Molecular Sequence Data ; Protein Structure, Tertiary ; Pseudomonas/*enzymology/*genetics/metabolism/pathogenicity ; Pyridines/*metabolism ; Virulence ; }, abstract = {BACKGROUND: Pyridine-2,6-bis(thiocarboxylic acid) (pdtc) is a small secreted metabolite that has a high affinity for transition metals, increases iron uptake efficiency by 20% in Pseudomonas stutzeri, has the ability to reduce both soluble and mineral forms of iron, and has antimicrobial activity towards several species of bacteria. Six GenBank sequences code for proteins similar in structure to MoeZ, a P. stutzeri protein necessary for the synthesis of pdtc.<br><br>RESULTS: Analysis of sequences similar to P. stutzeri MoeZ revealed that it is a member of a superfamily consisting of related but structurally distinct proteins that are members of pathways involved in the transfer of sulfur-containing moieties to metabolites. Members of this family of enzymes are referred to here as MoeB, MoeBR, MoeZ, and MoeZdR. MoeB, the molybdopterin synthase activating enzyme in the molybdopterin cofactor biosynthesis pathway, is the most characterized protein from this family. Remarkably, lengths of greater than 73% nucleic acid homology ranging from 35 to 486 bp exist between Pseudomonas stutzeri moeZ and genomic sequences found in some Mycobacterium, Mesorhizobium, Pseudomonas, Streptomyces, and cyanobacteria species.<br><br>CONCLUSIONS: The phylogenetic relationship among moeZ sequences suggests that P. stutzeri may have acquired moeZ through lateral gene transfer from a donor more closely related to mycobacteria and cyanobacteria than to proteobacteria. The importance of this relationship lies in the fact that pdtc, the product of the P. stutzeri pathway that includes moeZ, has an impressive set of capabilities, some of which could make it a potent pathogenicity factor.}, }
@article {pmid11971765, year = {2002}, author = {Lipsitch, M and Samore, MH}, title = {Antimicrobial use and antimicrobial resistance: a population perspective.}, journal = {Emerging infectious diseases}, volume = {8}, number = {4}, pages = {347-354}, pmid = {11971765}, issn = {1080-6040}, mesh = {Anti-Bacterial Agents/*pharmacology/therapeutic use ; Bacteria/drug effects/genetics ; Disease Transmission, Infectious ; *Drug Resistance, Bacterial ; Drug Utilization/trends ; Evolution, Molecular ; Gene Transfer, Horizontal ; Humans ; Models, Biological ; Population Dynamics ; Prevalence ; Selection, Genetic ; }, abstract = {The need to stem the growing problem of antimicrobial resistance has prompted multiple, sometimes conflicting, calls for changes in the use of antimicrobial agents. One source of disagreement concerns the major mechanisms by which antibiotics select resistant strains. For infections like tuberculosis, in which resistance can emerge in treated hosts through mutation, prevention of antimicrobial resistance in individual hosts is a primary method of preventing the spread of resistant organisms in the community. By contrast, for many other important resistant pathogens, such as penicillin-resistant Streptococcus pneumoniae, methicillin-resistant Staphylococcus aureus, and vancomycin-resistant Enterococcus faecium resistance is mediated by the acquisition of genes or gene fragments by horizontal transfer; resistance in the treated host is a relatively rare event. For these organisms, indirect, population-level mechanisms of selection account for the increase in the prevalence of resistance. These mechanisms can operate even when treatment has a modest, or even negative, effect on an individual host's colonization with resistant organisms.}, }
@article {pmid11969084, year = {2002}, author = {Il'ina, TS and Romanova, IuM}, title = {[Bacterial genomic islands: organization, function, and role in evolution].}, journal = {Molekuliarnaia biologiia}, volume = {36}, number = {2}, pages = {228-239}, pmid = {11969084}, issn = {0026-8984}, mesh = {Bacteria/*genetics/*pathogenicity ; *Biological Evolution ; Escherichia coli/genetics/pathogenicity ; Gene Transfer, Horizontal ; Phylogeny ; Salmonella/genetics/pathogenicity ; Virulence/genetics ; }, abstract = {Data on the structural organization and evolutionary role of specific bacterial DNA regions known as genomic islands are reviewed. Emphasis is placed on the most extensively studied genomic islands, pathogenicity islands (PAIs), which are present in the chromosome of Gram-negative and Gram-positive pathogenic bacteria and absent from related nonpathogenic strains. PAIs are extended DNA regions that harbor virulence genes and often differ in GC content from the remainder of the bacterial genome. Many PAI occur in the tRNA genes, which provide a convenient target for foreign gene insertion. Some PAI are highly homologous to each other and contain sequences similar to ISs, phage att sites, and plasmid ori sites, along with functional or defective integrase and transposase genes, suggesting horizontal transfer of PAI among bacteria.}, }
@article {pmid11969083, year = {2002}, author = {Mindlin, SZ and Bass, IA and Bogdanova, ES and Gorlenko, ZhM and Kaliaeva, ES and Petrova, MA and Nikiforov, VG}, title = {[Horizontal transfer of mercury resistance genes in natural bacterial populations].}, journal = {Molekuliarnaia biologiia}, volume = {36}, number = {2}, pages = {216-227}, pmid = {11969083}, issn = {0026-8984}, mesh = {Bacteria/drug effects/*genetics ; DNA Transposable Elements ; Drug Resistance, Microbial/*genetics ; *Gene Transfer, Horizontal ; Mercury Compounds/*pharmacology ; Mosaicism ; Operon ; Plasmids ; Recombination, Genetic ; }, abstract = {The results of studying the horizontal transfer of mercury resistance determinants in environmental bacterial populations are reviewed. Identical or highly homologous mercury resistance (mer) operons and transposons were found in bacteria of different taxonomic groups from geographically distant regions. Recombinant mer operons and transposons were revealed. The data suggest high frequencies of horizontal transfer and of recombination for mercury resistance determinants. The mechanisms of horizontal gene transfer were elucidated in Gram-negative and Gram-positive bacteria. New transposons were found and analyzed.}, }
@article {pmid11965492, year = {2002}, author = {Koonin, EV and Aravind, L}, title = {Origin and evolution of eukaryotic apoptosis: the bacterial connection.}, journal = {Cell death and differentiation}, volume = {9}, number = {4}, pages = {394-404}, doi = {10.1038/sj.cdd.4400991}, pmid = {11965492}, issn = {1350-9047}, mesh = {Animals ; Apoptosis/*genetics ; Apoptosis Inducing Factor ; Bacteria/*genetics/growth &amp; development ; Biological Evolution ; Caspases/genetics/physiology ; Eukaryotic Cells/cytology/*physiology ; Flavoproteins/physiology ; *Heat-Shock Proteins ; Membrane Proteins/physiology ; Mitochondria/genetics/physiology ; Models, Genetic ; *Periplasmic Proteins ; Phylogeny ; Sequence Homology ; Serine Endopeptidases/genetics ; Signal Transduction ; }, abstract = {The availability of numerous complete genome sequences of prokaryotes and several eukaryotic genome sequences provides for new insights into the origin of unique functional systems of the eukaryotes. Several key enzymes of the apoptotic machinery, including the paracaspase and metacaspase families of the caspase-like protease superfamily, apoptotic ATPases and NACHT family NTPases, and mitochondrial HtrA-like proteases, have diverse homologs in bacteria, but not in archaea. Phylogenetic analysis strongly suggests a mitochondrial origin for metacaspases and the HtrA-like proteases, whereas acquisition from Actinomycetes appears to be the most likely scenario for AP-ATPases. The homologs of apoptotic proteins are particularly abundant and diverse in bacteria that undergo complex development, such as Actinomycetes, Cyanobacteria and alpha-proteobacteria, the latter being progenitors of the mitochondria. In these bacteria, the apoptosis-related domains typically form multidomain proteins, which are known or inferred to participate in signal transduction and regulation of gene expression. Some of these bacterial multidomain proteins contain fusions between apoptosis-related domains, such as AP-ATPase fused with a metacaspase or a TIR domain. Thus, bacterial homologs of eukaryotic apoptotic machinery components might functionally and physically interact with each other as parts of signaling pathways that remain to be investigated. An emerging scenario of the origin of the eukaryotic apoptotic system involves acquisition of several central apoptotic effectors as a consequence of mitochondrial endosymbiosis and probably also as a result of subsequent, additional horizontal gene transfer events, which was followed by recruitment of newly emerging eukaryotic domains as adaptors.}, }
@article {pmid11964471, year = {2002}, author = {Li, Z and Düllmann, J and Schiedlmeier, B and Schmidt, M and von Kalle, C and Meyer, J and Forster, M and Stocking, C and Wahlers, A and Frank, O and Ostertag, W and Kühlcke, K and Eckert, HG and Fehse, B and Baum, C}, title = {Murine leukemia induced by retroviral gene marking.}, journal = {Science (New York, N.Y.)}, volume = {296}, number = {5567}, pages = {497}, doi = {10.1126/science.1068893}, pmid = {11964471}, issn = {1095-9203}, mesh = {Animals ; Bone Marrow Cells/metabolism ; Bone Marrow Transplantation ; DNA-Binding Proteins/genetics/metabolism ; *Gene Transfer, Horizontal ; Genetic Therapy ; *Genetic Vectors ; Hematopoiesis, Extramedullary ; Leukemia, Monocytic, Acute/*etiology ; MDS1 and EVI1 Complex Locus Protein ; Mice ; Mice, Inbred C57BL ; Preleukemia/*etiology ; *Proto-Oncogenes ; Receptor, Nerve Growth Factor ; Receptor, trkA/genetics/metabolism ; Receptors, Nerve Growth Factor/*genetics/metabolism ; Retroviridae/*genetics ; Transcription Factors/genetics ; Transgenes ; }, }
@article {pmid11963558, year = {2002}, author = {Gur'ev, VP and Blinov, AG}, title = {[Phylogenetic relationships among holarctic populations of Chironomus entis and Chironomus plumosus in view of possible horizontal transfer of mitochondrial genes].}, journal = {Genetika}, volume = {38}, number = {3}, pages = {310-315}, pmid = {11963558}, issn = {0016-6758}, mesh = {Animals ; Arctic Regions ; Chironomidae/genetics/*physiology ; *DNA, Mitochondrial ; *Gene Transfer, Horizontal ; *Genetics, Population ; *Phylogeny ; Polymerase Chain Reaction ; }, abstract = {In eight Holarctic populations of two typical chironomid sibling species of the plumosus group, Chrionomus entis and Chironomus plumosus, nucleotides sequences of mitochondrial (cytb) and nuclear (gb2b) gene regions were examined. The phylogenetic trees reflecting the evolutionary histories of the nuclear and mitochondrial markers exhibited significant differences. On the tree based on the nuclear gene sequences the populations clustered according to their species affiliation, whereas on the tree based on the mitochondrial gene sequences the populations were grouped according to their geographic position. This discrepancy is probably explained by mitochondrial gene flow between sympatric species with incomplete reproductive isolation (sibling species). Based on our results together with the earlier data on nuclear and mitochondrial gene sequences of some other species from the phylogenetic group plumosus, a scheme of phylogenetic relationships within this group is proposed. This scheme is in many ways different from the traditional view on the evolutionary relationships among species of the plumosus group.}, }
@article {pmid11961543, year = {2002}, author = {Doolittle, RF}, title = {Biodiversity: microbial genomes multiply.}, journal = {Nature}, volume = {416}, number = {6882}, pages = {697-700}, doi = {10.1038/416697a}, pmid = {11961543}, issn = {0028-0836}, mesh = {Adaptation, Physiological ; Bacteria/*genetics/pathogenicity ; Ecosystem ; Evolution, Molecular ; Gene Deletion ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Genome, Archaeal ; *Genome, Bacterial ; Genome, Fungal ; *Genomics/statistics &amp; numerical data/trends ; Mutagenesis ; Sequence Analysis, DNA ; }, }
@article {pmid11961097, year = {2002}, author = {Matte-Tailliez, O and Brochier, C and Forterre, P and Philippe, H}, title = {Archaeal phylogeny based on ribosomal proteins.}, journal = {Molecular biology and evolution}, volume = {19}, number = {5}, pages = {631-639}, doi = {10.1093/oxfordjournals.molbev.a004122}, pmid = {11961097}, issn = {0737-4038}, mesh = {Archaea/*classification/*genetics ; Archaeal Proteins/*genetics ; Evolution, Molecular ; Genes, Archaeal ; *Phylogeny ; RNA, Archaeal/genetics ; RNA, Ribosomal/genetics ; Ribosomal Proteins/*genetics ; }, abstract = {Until recently, phylogenetic analyses of Archaea have mainly been based on ribosomal RNA (rRNA) sequence comparisons, leading to the distinction of the two major archaeal phyla: the Euryarchaeota and the Crenarchaeota. Here, thanks to the recent sequencing of several archaeal genomes, we have constructed a phylogeny based on the fusion of the sequences of the 53 ribosomal proteins present in most of the archaeal species. This phylogeny was remarkably congruent with the rRNA phylogeny, suggesting that both reflected the actual phylogeny of the domain Archaea even if some nodes remained unresolved. In both cases, the branches leading to hyperthermophilic species were short, suggesting that the evolutionary rate of their genes has been slowed down by structural constraints related to environmental adaptation. In addition, to estimate the impact of lateral gene transfer (LGT) on our tree reconstruction, we used a new method that revealed that 8 genes out of the 53 ribosomal proteins used in our study were likely affected by LGT. This strongly suggested that a core of 45 nontransferred ribosomal protein genes existed in Archaea that can be tentatively used to infer the phylogeny of this domain. Interestingly, the tree obtained using only the eight ribosomal proteins likely affected by LGT was not very different from the consensus tree, indicating that LGT mainly brought random phylogenetic noise. The major difference involves organisms living in similar environments, suggesting that LGTs are mainly directed by the physical proximity of the organisms rather than by their phylogenetic proximity.}, }
@article {pmid11956692, year = {2002}, author = {House, CH and Fitz-Gibbon, ST}, title = {Using homolog groups to create a whole-genomic tree of free-living organisms: an update.}, journal = {Journal of molecular evolution}, volume = {54}, number = {4}, pages = {539-547}, doi = {10.1007/s00239-001-0054-5}, pmid = {11956692}, issn = {0022-2844}, support = {GM57917/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Caenorhabditis elegans/genetics ; Gene Transfer, Horizontal ; *Genome, Archaeal ; *Genome, Bacterial ; *Genome, Fungal ; *Phylogeny ; Saccharomyces cerevisiae/genetics ; Sequence Homology ; }, abstract = {Genomic trees have been constructed based on the presence and absence of families of protein-encoding genes observed in 27 complete genomes, including genomes of 15 free-living organisms. This method does not rely on the identification of suspected orthologs in each genome, nor the specific alignment used to compare gene sequences because the protein-encoding gene families are formed by grouping any protein with a pairwise similarity score greater than a preset value. Because of this all inclusive grouping, this method is resilient to some effects of lateral gene transfer because transfers of genes are masked when the recipient genome already has a homolog (not necessarily an ortholog) of the incoming gene. Of 71 genes suspected to have been laterally transferred to the genome of Aeropyrum pernix, only approximately 7 to 15 represent genes where a lateral gene transfer appears to have generated homoplasy in our character dataset. The genomic tree of the 15 free-living taxa includes six different bacterial orders, six different archaeal orders, and two different eukaryotic kingdoms. The results are remarkably similar to results obtained by analysis of rRNA. Inclusion of the other 12 genomes resulted in a tree only broadly similar to that suggested by rRNA with at least some of the differences due to artifacts caused by the small genome size of many of these species. Very small genomes, such as those of the two Mycoplasma genomes included, fall to the base of the Bacterial domain, a result expected due to the substantial gene loss inherent to these lineages. Finally, artificial "partial genomes" were generated by randomly selecting ORFs from the complete genomes in order to test our ability to recover the tree generated by the whole genome sequences when only partial data are available. The results indicated that partial genomic data, when sampled randomly, could robustly recover the tree generated by the whole genome sequences.}, }
@article {pmid11956683, year = {2002}, author = {Sawada, H and Kanaya, S and Tsuda, M and Suzuki, F and Azegami, K and Saitou, N}, title = {A phylogenomic study of the OCTase genes in Pseudomonas syringae pathovars: the horizontal transfer of the argK-tox cluster and the evolutionary history of OCTase genes on their genomes.}, journal = {Journal of molecular evolution}, volume = {54}, number = {4}, pages = {437-457}, doi = {10.1007/s00239-001-0032-y}, pmid = {11956683}, issn = {0022-2844}, mesh = {*Evolution, Molecular ; Exotoxins/genetics ; Gene Transfer, Horizontal ; Genome, Bacterial ; Multigene Family ; Ornithine/analogs &amp; derivatives ; Ornithine Carbamoyltransferase/*genetics ; *Phylogeny ; Physical Chromosome Mapping ; Pseudomonas/*genetics ; Recombination, Genetic ; }, abstract = {Phytopathogenic Pseudomonas syringae is subdivided into about 50 pathovars due to their conspicuous differentiation with regard to pathogenicity. Based on the results of a phylogenetic analysis of four genes (gyrB, rpoD, hrpL, and hrpS), Sawada et al. (1999) showed that the ancestor of P. syringae had diverged into at least three monophyletic groups during its evolution. Physical maps of the genomes of representative strains of these three groups were constructed, which revealed that each strain had five rrn operons which existed on one circular genome. The fact that the structure and size of genomes vary greatly depending on the pathovar shows that P. syringae genomes are quite rich in plasticity and that they have undergone large-scale genomic rearrangements. Analyses of the codon usage and the GC content at the codon third position, in conjunction with phylogenomic analyses, showed that the gene cluster involved in phaseolotoxin synthesis (argK-tox cluster) expanded its distribution by conducting horizontal transfer onto the genomes of two P. syringae pathovars (pv. actinidiae and pv. phaseolicola) from bacterial species distantly related to P. syringae and that its acquisition was quite recent (i.e., after the ancestor of P. syringae diverged into the respective pathovars). Furthermore, the results of a detailed analysis of argK [an anabolic ornithine carbamoyltransferase (anabolic OCTase) gene], which is present within the argK-tox cluster, revealed the plausible process of generation of an unusual composition of the OCTase genes on the genomes of these two phaseolotoxin-producing pathovars: a catabolic OCTase gene (equivalent to the orthologue of arcB of P. aeruginosa) and an anabolic OCTase gene (argF), which must have been formed by gene duplication, have first been present on the genome of the ancestor of P. syringae; the catabolic OCTase gene has been deleted; the ancestor has diverged into the respective pathovars; the foreign-originated argK-tox cluster has horizontally transferred onto the genomes of pv. actinidiae and pv. phaseolicola; and hence two copies of only the anabolic OCTase genes (argK and argF) came to exist on the genomes of these two pathovars. Thus, the horizontal gene transfer and the genomic rearrangement were proven to have played an important role in the pathogenic differentiation and diversification of P. syringae.}, }
@article {pmid11953381, year = {2002}, author = {Li, M and Shimada, T and Morris, JG and Sulakvelidze, A and Sozhamannan, S}, title = {Evidence for the emergence of non-O1 and non-O139 Vibrio cholerae strains with pathogenic potential by exchange of O-antigen biosynthesis regions.}, journal = {Infection and immunity}, volume = {70}, number = {5}, pages = {2441-2453}, pmid = {11953381}, issn = {0019-9567}, support = {R01 GM060791/GM/NIGMS NIH HHS/United States ; R01 GM60791/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Sequence ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; *Multigene Family ; O Antigens/*biosynthesis ; Polymorphism, Restriction Fragment Length ; Vibrio cholerae/*genetics/*pathogenicity ; Virulence/genetics ; }, abstract = {The novel epidemic strain Vibrio cholerae O139 Bengal originated from a seventh-pandemic O1 El Tor strain by antigenic shift resulting from homologous recombination-mediated exchange of O-antigen biosynthesis (wb*) clusters. Conservation of the genetic organization of wb* regions seen in other serogroups raised the possibility of the existence of pathogenic non-O1 and non-O139 V. cholerae strains that emerged by similar events. To test this hypothesis, 300 V. cholerae isolates of non-O1 and non-O139 serogroups were screened for the presence of virulence genes and an epidemic genetic background by DNA dot blotting, IS1004 fingerprinting, and restriction fragment length polymorphism (RFLP) analysis. We found four non-O1 strains (serogroups O27, O37, O53, and O65) with an O1 genetic backbone suggesting exchange of wb* clusters. DNA sequence analysis of the O37 wb* region revealed that a novel approximately 23.4-kb gene cluster had replaced all but the approximately 4.2-kb right junction of the 22-kb O1 wbe region. In sharp contrast to the backbones, the virulence regions of the four strains were quite heterogeneous; the O53 and O65 strains had the El Tor vibrio pathogenicity island (VPI) cluster, the O37 strain had the classical VPI cluster, and the O27 strain had a novel VPI cluster. Two of the four strains carried CTXphi; the O27 strain possessed a CTXphi with a recently reported immune specificity (rstR-4** allele) and a novel ctxB allele, and the O37 strain had an El Tor CTXphi (rstR(ET) allele) and novel ctxAB alleles. Although the O53 and O65 strains lacked the ctxAB genes, they carried a pre-CTXphi (i.e., rstR(cla)). Identification of non-O1 and non-O139 serogroups with pathogenic potential in epidemic genetic backgrounds means that attention should be paid to possible future epidemics caused by these serogroups and to the need for new, rapid vaccine development strategies.}, }
@article {pmid11953379, year = {2002}, author = {Nesper, J and Kraiss, A and Schild, S and Blass, J and Klose, KE and Bockemühl, J and Reidl, J}, title = {Comparative and genetic analyses of the putative Vibrio cholerae lipopolysaccharide core oligosaccharide biosynthesis (wav) gene cluster.}, journal = {Infection and immunity}, volume = {70}, number = {5}, pages = {2419-2433}, pmid = {11953379}, issn = {0019-9567}, mesh = {Amino Acid Sequence ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Lipopolysaccharides/*biosynthesis ; Molecular Sequence Data ; *Multigene Family ; Polymerase Chain Reaction ; Vibrio cholerae/*genetics/pathogenicity ; Virulence ; }, abstract = {We identified five different putative wav gene cluster types, which are responsible for the synthesis of the core oligosaccharide (OS) region of Vibrio cholerae lipopolysaccharide. Preliminary evidence that the genes encoded by this cluster are involved in core OS biosynthesis came from analysis of the recently released O1 El Tor V. cholerae genome sequence and sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of O1 El Tor mutant strains defective in three genes (waaF, waaL, and wavB). Investigations of 38 different V. cholerae strains by Southern blotting, PCR, and sequencing analyses showed that the O1 El Tor wav gene cluster type is prevalent among clinical isolates of different serogroups associated with cholera and environmental O1 strains. In contrast, we found differences in the wav gene contents of 19 unrelated non-O1, non-O139 environmental and human isolates not associated with cholera. These strains contained four new wav gene cluster types that differ from each other in distinct gene loci, providing evidence for horizontal transfer of wav genes and for limited structural diversity of the core OS among V. cholerae isolates. Our results show genetic diversity in the core OS biosynthesis gene cluster and predominance of the type 1 wav gene locus in strains associated with clinical cholera, suggesting that a specific core OS structure could contribute to V. cholerae virulence.}, }
@article {pmid11953370, year = {2002}, author = {Hansen-Wester, I and Hensel, M}, title = {Genome-based identification of chromosomal regions specific for Salmonella spp.}, journal = {Infection and immunity}, volume = {70}, number = {5}, pages = {2351-2360}, pmid = {11953370}, issn = {0019-9567}, mesh = {Animals ; *Chromosome Mapping ; DNA, Bacterial/analysis ; Escherichia coli/genetics ; Female ; *Genome, Bacterial ; Mice ; Mice, Inbred C57BL ; Phylogeny ; RNA, Transfer/*genetics ; Salmonella/classification/*genetics/pathogenicity ; Virulence/genetics ; }, abstract = {Acquisition of genomic elements by horizontal gene transfer represents an important mechanism in the evolution of bacterial species. Pathogenicity islands are a subset of horizontally acquired elements present in various pathogens. These elements are frequently located adjacent to tRNA genes. We performed a comparative genome analysis of Salmonella enterica serovars Typhi and Typhimurium and Escherichia coli and scanned tRNA loci for the presence of species-specific, horizontally acquired genomic elements. A large number of species-specific elements were identified. Here, we describe the characteristics of four large chromosomal insertions at tRNA genes of Salmonella spp. The tRNA-associated elements harbor various genes previously identified as single virulence genes, indicating that these genes have been acquired with large chromosomal insertions. Southern blot analyses confirmed that the tRNA-associated elements are specific to Salmonella and also indicated a heterogeneous distribution within the salmonellae. Systematic scanning for insertions at tRNA genes thus represents a tool for the identification of novel pathogenicity islands.}, }
@article {pmid11940536, year = {2002}, author = {Ohno, N and Itoh, H and Ikeda, T and Ueyama, K and Yamahara, K and Doi, K and Yamashita, J and Inoue, M and Masatsugu, K and Sawada, N and Fukunaga, Y and Sakaguchi, S and Sone, M and Yurugi, T and Kook, H and Komeda, M and Nakao, K}, title = {Accelerated reendothelialization with suppressed thrombogenic property and neointimal hyperplasia of rabbit jugular vein grafts by adenovirus-mediated gene transfer of C-type natriuretic peptide.}, journal = {Circulation}, volume = {105}, number = {14}, pages = {1623-1626}, doi = {10.1161/01.cir.0000014985.50017.6e}, pmid = {11940536}, issn = {1524-4539}, mesh = {Adenoviridae/genetics ; Animals ; Carotid Arteries/surgery ; Cells, Cultured ; Endothelium, Vascular/cytology/drug effects/*metabolism ; *Gene Transfer, Horizontal ; Genetic Therapy/methods ; Genetic Vectors/administration &amp; dosage/genetics/metabolism ; Graft Occlusion, Vascular/*prevention &amp; control ; Humans ; In Vitro Techniques ; Jugular Veins/drug effects/metabolism/*transplantation ; Male ; Natriuretic Peptide, C-Type/genetics/*metabolism/pharmacology ; Rabbits ; Rats ; Thrombosis/*prevention &amp; control ; Transplantation, Autologous ; Treatment Outcome ; Tunica Intima/cytology/drug effects ; Vascular Patency/drug effects ; }, abstract = {BACKGROUND: Vein graft disease limits the late results of coronary revascularization. C-type natriuretic peptide (CNP) inhibits the growth of vascular smooth muscle cells. Given the effects of CNP on cGMP cascade, we hypothesized that transfected CNP genes modulate endothelial repair and thrombogenicity in the vein graft.<br><br>METHODS AND RESULTS: Autologous rabbit jugular vein grafts were incubated ex vivo in a solution of adenovirus vectors containing CNP gene (Ad.CNP) or Escherichia coli lac Z gene (Ad.LacZ) and then interposed in the carotid artery. Reendothelialization, mural thrombi formation, and intima/media ratio were evaluated on the 14th and 28th postoperative days. More reendothelialization was seen in Ad.CNP-infected grafts than in Ad.LacZ-infected grafts both at 14 days (0.81+/-0.05 versus 0.30+/-0.14, P<0.01) and at 28 days (0.96+/-0.01 versus 0.45+/-0.08, P<0.001). The mural thrombus area was smaller in Ad.CNP-infected grafts than in Ad.LacZ-infected grafts. Neointimal thickening was significantly suppressed in the Ad.CNP group. The in vitro wound assay with human coronary artery endothelial cells revealed significant potentiation of the wound repair process by CNP and atrial natriuretic peptide administration.<br><br>CONCLUSIONS: Infected Ad.CNP accelerated reendothelialization and suppressed thrombosis and neointimal hyperplasia. The method may potentially prevent vein graft disease in patients undergoing coronary artery revascularization.}, }
@article {pmid11939148, year = {1998}, author = {}, title = {Abstracts of the 6th Meeting of the European Working Group on Human Gene Transfer and Therapy (EWGT). Jerusalem, Israel, 21-24 November 1998.}, journal = {The journal of gene medicine}, volume = {1}, number = {1 Suppl}, pages = {1-93}, pmid = {11939148}, issn = {1099-498X}, mesh = {*Gene Transfer Techniques ; *Gene Transfer, Horizontal ; *Genetic Therapy ; Humans ; }, }
@article {pmid11935144, year = {2002}, author = {Metz, M and Fütterer, J}, title = {Biodiversity (Communications arising): suspect evidence of transgenic contamination.}, journal = {Nature}, volume = {416}, number = {6881}, pages = {600-1; discussion 600, 602}, doi = {10.1038/nature738}, pmid = {11935144}, issn = {0028-0836}, mesh = {Artifacts ; DNA Primers/genetics ; Gene Transfer, Horizontal/genetics ; *Genome, Plant ; Hybridization, Genetic/genetics ; Mexico ; Nucleic Acid Hybridization ; Plants, Genetically Modified ; Polymerase Chain Reaction/methods/*standards ; Polymorphism, Genetic/genetics ; Recombination, Genetic/*genetics ; Reproducibility of Results ; Transformation, Genetic ; Transgenes/*genetics ; Zea mays/*genetics ; }, abstract = {Quist and Chapela claim that transgenic DNA constructs have been introgressed into a traditional maize variety in Mexico, and furthermore suggest that these constructs have been reassorted and introduced into different genomic backgrounds. However, we show here that their evidence for such introgression is based on the artefactual results of a flawed assay; in addition, the authors misinterpret a key reference to explain their results, concluding that reassortment of integrated transgenic DNA occurs during transformation or recombination.}, }
@article {pmid11933060, year = {2002}, author = {Hegyi, H and Lin, J and Greenbaum, D and Gerstein, M}, title = {Structural genomics analysis: characteristics of atypical, common, and horizontally transferred folds.}, journal = {Proteins}, volume = {47}, number = {2}, pages = {126-141}, doi = {10.1002/prot.10078}, pmid = {11933060}, issn = {1097-0134}, mesh = {Animals ; Conserved Sequence ; Evolution, Molecular ; Gene Deletion ; Gene Duplication ; Gene Transfer, Horizontal ; Genomics/*methods ; Open Reading Frames ; Phylogeny ; Protein Folding ; Protein Structure, Secondary ; Proteins/*chemistry ; Proteome/analysis ; Sequence Analysis, Protein/*methods ; }, abstract = {We conducted a structural genomics analysis of the folds and structural superfamilies in the first 20 completely sequenced genomes by focusing on the patterns of fold usage and trying to identify structural characteristics of typical and atypical folds. We assigned folds to sequences using PSI-blast, run with a systematic protocol to reduce the amount of computational overhead. On average, folds could be assigned to about a fourth of the ORFs in the genomes and about a fifth of the amino acids in the proteomes. More than 80% of all the folds in the SCOP structural classification were identified in one of the 20 organisms, with worm and E. coli having the largest number of distinct folds. Folds are particularly effective at comprehensively measuring levels of gene duplication, because they group together even very remote homologues. Using folds, we find the average level of duplication varies depending on the complexity of the organism, ranging from 2.4 in M. genitalium to 32 for the worm, values significantly higher than those observed based purely on sequence similarity. We rank the common folds in the 20 organisms, finding that the top three are the P-loop NTP hydrolase, the ferrodoxin fold, and the TIM-barrel, and discuss in detail the many factors that affect and bias these rankings. We also identify atypical folds that are "unique" to one of the organisms in our study and compare the characteristics of these folds with the most common ones. We find that common folds tend be more multifunctional and associated with more regular, "symmetrical" structures than the unique ones. In addition, many of the unique folds are associated with proteins involved in cell defense (e.g., toxins). We analyze specific patterns of fold occurrence in the genomes by associating some of them with instances of horizontal transfer and others with gene loss. In particular, we find three possible examples of transfer between archaea and bacteria and six between eukarya and bacteria. We make available our detailed results at http://genecensus.org/20.}, }
@article {pmid11931166, year = {2002}, author = {Dauga, C}, title = {Evolution of the gyrB gene and the molecular phylogeny of Enterobacteriaceae: a model molecule for molecular systematic studies.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {52}, number = {Pt 2}, pages = {531-547}, doi = {10.1099/00207713-52-2-531}, pmid = {11931166}, issn = {1466-5026}, mesh = {DNA Gyrase/*genetics ; Enterobacteriaceae/*classification/genetics ; Evolution, Molecular ; Genes, rRNA ; Molecular Sequence Data ; Phenotype ; RNA, Bacterial/chemistry ; RNA, Ribosomal, 16S/chemistry ; }, abstract = {Phylogenetic trees showing the evolutionary relatedness of Enterobacteriaceae based upon gyrB and 16S rRNA genes were compared. Congruence among trees of these molecules indicates that the genomes of these species are not completely mosaic and that molecular systematic studies can be carried out. Phylogenetic trees based on gyrB sequences appeared to be more reliable at determining relationships among Serratia species than trees based on 16S rRNA gene sequences. gyrB sequences from Serratia species formed a monophyletic group validated by significant bootstrap values. Serratia fonticola had the most deeply branching gyrB sequence in the Serratia monophyletic group, which was consistent with its atypical phenotypic characteristics. Klebsiella and Enterobacter genera seemed to be polyphyletic, but the branching patterns of gyrB and 16S rRNA gene trees were not congruent. Enterobacter aerogenes was grouped with Klebsiella pneumoniae on the gyrB phylogenetic tree, which supports that this species could be transferred to the Klebsiella genus. Unfortunately, 16S rRNA and gyrB phylogenetic trees gave conflicting evolutionary relationships for Citrobacter freundii because of its unusual gyrB evolutionary process. gyrB lateral gene transfer was suspected for Hafnia alvei. Saturation of gyrB genes was observed by the pairwise comparison of Proteus spp., Providencia alcalifaciens and Morganella morganii sequences. Depending on their level of variability, 16S rRNA gene sequences were useful for describing phylogenetic relationships between distantly related Enterobacteriaceae, whereas gyrB sequence comparison was useful for inferring intra- and some intergeneric relationships.}, }
@article {pmid11929050, year = {2002}, author = {Medlock, AE and Meissner, PN and Davidson, BP and Corrigall, AV and Dailey, HA}, title = {A mouse model for South African (R59W) variegate porphyria: construction and initial characterization.}, journal = {Cellular and molecular biology (Noisy-le-Grand, France)}, volume = {48}, number = {1}, pages = {71-78}, pmid = {11929050}, issn = {0145-5680}, support = {R56 DK032303/DK/NIDDK NIH HHS/United States ; DK32303/DK/NIDDK NIH HHS/United States ; DK35898/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Disease Models, Animal ; Feces/chemistry ; Flavoproteins ; Gene Transfer, Horizontal ; Liver/enzymology ; Mice ; Mice, Inbred C57BL ; Mitochondrial Proteins ; Mutagenesis, Site-Directed ; Oxidoreductases/genetics/metabolism ; *Oxidoreductases Acting on CH-CH Group Donors ; Point Mutation ; Porphyrias, Hepatic/enzymology/*genetics ; Porphyrins/analysis/urine ; Protoporphyrinogen Oxidase ; South Africa ; }, abstract = {Variegate porphyria is inherited as an autosomal dominant disease with variable penetrance. It is characterized clinically by photocutaneous sensitivity and acute neurovisceral attacks, and biochemically by abnormal porphyrin excretion in the urine and feces. While the world-wide incidence of variegate porphyria is relatively low, in South Africa it is one of the most common genetic diseases in humans. Due to the large number of patients with variegate porphyria in South Africa, and the fact that variegate porphyria is representative of both the so-called "acute" and the "photocutaneous" porphyrias, it would be valuable to have an animal model in which to study the disease. In this study we have produced a mouse model of "South African" variegate porphyria with the R59W mutation in C57/BL6 mice via targeted gene replacement. Hepatic protoporphyrinogen oxidase activity was reduced by approximately 50% in mice heterozygous for the mutation. Urine and fecal samples from these mice, in the absence of exogenous inducers of hepatic haem synthesis, contain elevated concentrations of porphyrins and porphyrin precursors in a pattern similar to that found in human variegate porphyric subjects. Bypassing the rate-limiting step in haem biosynthesis by feeding 5-aminolevulinic acid to these mice, results in an accentuated porphyrin excretory pattern characteristic of the variegate porphyric phenotype and urinary porphobilinogen is increased significantly. This initial characterization of these mice suggest that they are a good model for variegate porphyria at the biochemical level.}, }
@article {pmid11927775, year = {2002}, author = {Dutta, C and Pan, A}, title = {Horizontal gene transfer and bacterial diversity.}, journal = {Journal of biosciences}, volume = {27}, number = {1 Suppl 1}, pages = {27-33}, pmid = {11927775}, issn = {0250-5991}, mesh = {Animals ; Bacteria/*genetics/metabolism ; *Biological Evolution ; Gene Transfer, Horizontal/*physiology ; Genes, Bacterial/*genetics ; }, abstract = {Bacterial genomes are extremely dynamic and mosaic in nature. A substantial amount of genetic information is inserted into or deleted from such genomes through the process of horizontal transfer. Through the introduction of novel physiological traits from distantly related organisms, horizontal gene transfer often causes drastic changes in the ecological and pathogenic character of bacterial species and thereby promotes microbial diversification and speciation. This review discusses how the recent influx of complete chromosomal sequences of various microorganisms has allowed for a quantitative assessment of the scope, rate and impact of horizontally transmitted information on microbial evolution.}, }
@article {pmid11925433, year = {2002}, author = {Walters, RW and Pilewski, JM and Chiorini, JA and Zabner, J}, title = {Secreted and transmembrane mucins inhibit gene transfer with AAV4 more efficiently than AAV5.}, journal = {The Journal of biological chemistry}, volume = {277}, number = {26}, pages = {23709-23713}, doi = {10.1074/jbc.M200292200}, pmid = {11925433}, issn = {0021-9258}, support = {T30DK54759/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bronchi/virology ; COS Cells ; Dependovirus/classification/*genetics/pathogenicity ; *Gene Transfer, Horizontal ; Genetic Vectors ; Humans ; Mucins/*physiology ; Trachea/virology ; }, abstract = {Adeno-associated virus (AAV) is a promising vector for gene transfer in cystic fibrosis. AAV4 and AAV5 both bind to the apical surface of differentiated human airway epithelia, but only AAV5 infects. Both AAV4 and AAV5 require 2,3-linked sialic acid for binding. However, AAV5 interacts with sialic acid on N-linked carbohydrates, whereas AAV4 interacts with sialic acid on O-linked carbohydrates. Because mucin is decorated with O-linked carbohydrates, we hypothesized that mucin binds AAV4 and inhibits gene transfer. To evaluate the effect of secreted mucin, we studied mucin binding and gene transfer to COS cells and the basolateral membrane of well differentiated human airway epithelia. AAV4 bound mucin more efficiently than AAV5, and mucin inhibited gene transfer with AAV4. Moreover, O-glycosidase-pretreated mucin did not block gene transfer with AAV4. Similar to secreted mucin, the transmembrane mucin MUC1 inhibited gene transfer with AAV4 but not AAV5. MUC1 inhibited AAV4 by blocking internalization of the virus. Thus, O-linked carbohydrates of mucin are potent inhibitors of AAV4. Furthermore, whereas mucin plays an important role in innate host defense, its activity is specific; some vectors or pathogens are more resistant to its effects.}, }
@article {pmid11924501, year = {2002}, author = {Planet, PJ}, title = {Reexamining microbial evolution through the lens of horizontal transfer.}, journal = {EXS}, volume = {}, number = {92}, pages = {247-303}, doi = {10.1007/978-3-0348-8114-2_18}, pmid = {11924501}, issn = {1023-294X}, mesh = {*Biological Evolution ; *Gene Transfer, Horizontal ; *Microbiology ; Operon ; Species Specificity ; }, abstract = {Our ability to understand the evolution of microbial organisms revolves around a central and increasingly unsettled question: what is the nature of the mode of inheritance? The extent to which genetic information is passed vertically from parent to daughter or horizontally between distant relatives must guide reconstructions and inferences of evolutionary history, and has direct bearing on any ideas about the mechanisms of selection and diversification. Recent evidence suggests that we may have previously underestimated the contribution of horizontal gene transfer, and the dynamics and extent of this process are only beginning to be understood. The recent flood of complete genome sequences of microorganisms has already presented us with a vast array of data from which to test our hypotheses about the evolution of the entire tree of life, but what remains unclear is how we can make sense of this unwieldy data set. Analyses of this newly available data set should include explicit examinations of the contributions of both types of inheritance.}, }
@article {pmid11921398, year = {2002}, author = {Stolz, JF and Basu, P}, title = {Evolution of nitrate reductase: molecular and structural variations on a common function.}, journal = {Chembiochem : a European journal of chemical biology}, volume = {3}, number = {2-3}, pages = {198-206}, doi = {10.1002/1439-7633(20020301)3:2/3&lt;198::AID-CBIC198&gt;3.0.CO;2-C}, pmid = {11921398}, issn = {1439-4227}, mesh = {Amino Acid Sequence ; Binding Sites ; *Evolution, Molecular ; Molecular Sequence Data ; Nitrate Reductases/*genetics/physiology ; Phylogeny ; Sequence Homology, Amino Acid ; }, abstract = {The biological transformation of nitrogen oxyanions is widespread in nature and gives rise to a robust biogeochemical cycle. The first step in nitrate reduction is carried out by the enzyme nitrate reductase (NR). Although NR always catalyzes the same chemical reaction (conversion of nitrate into nitrite), its location in the cell, structure, and function are organism-dependent. We use protein sequence data to determine phylogenetic relationships and to examine similarities in structure and function. Three distinct clades of NR are apparent: the eukaryotic assimilatory NR (Euk-NR) clade, the membrane-associated prokaryotic NR (Nar) clade, and a clade that includes both the periplasmic NR (Nap) and prokaryotic assimilatory NR (Nas). The high degree of sequence similarity and a phylogenetic distribution that follows taxonomic classification suggest a monophyletic origin for the Euk-NR early on in the evolution of eukaryotic cells. In contrast, sequence conservation, phylogenetic analysis, and physiology suggest that both Nar and Nap were acquired by horizontal gene transfer. Nap and Nas share a lesser degree of similarity, with Nap a subclade of Nas. Nap from strict anaerobic bacteria such as Desulfovibrio desulfuricans is ancestral to facultative species and may provide an evolutionary link between Nap and Nas. We observed conserved binding sites for molybdenum and pterin cofactors in all four proteins. In pathways involving Euk-NR, Nas, and Nar, for which ammonia is the end product, nitrite is reduced to ammonia by a siroheme nitrite reductase. Nap, however, is coupled to a pentaheme nitrite reductase. In denitrification, whether Nar or Nap is involved, nitrite is reduced to nitric oxide by either a cytochrome cd1 or a copper-containing nitrite reductase. This complexity underscores the importance of nitrate reduction as a key biological process.}, }
@article {pmid11918828, year = {2002}, author = {Zhaxybayeva, O and Gogarten, JP}, title = {Bootstrap, Bayesian probability and maximum likelihood mapping: exploring new tools for comparative genome analyses.}, journal = {BMC genomics}, volume = {3}, number = {}, pages = {4}, pmid = {11918828}, issn = {1471-2164}, abstract = {BACKGROUND: Horizontal gene transfer (HGT) played an important role in shaping microbial genomes. In addition to genes under sporadic selection, HGT also affects housekeeping genes and those involved in information processing, even ribosomal RNA encoding genes. Here we describe tools that provide an assessment and graphic illustration of the mosaic nature of microbial genomes.<br><br>RESULTS: We adapted the Maximum Likelihood (ML) mapping to the analyses of all detected quartets of orthologous genes found in four genomes. We have automated the assembly and analyses of these quartets of orthologs given the selection of four genomes. We compared the ML-mapping approach to more rigorous Bayesian probability and Bootstrap mapping techniques. The latter two approaches appear to be more conservative than the ML-mapping approach, but qualitatively all three approaches give equivalent results. All three tools were tested on mitochondrial genomes, which presumably were inherited as a single linkage group.<br><br>CONCLUSIONS: In some instances of interphylum relationships we find nearly equal numbers of quartets strongly supporting the three possible topologies. In contrast, our analyses of genome quartets containing the cyanobacterium Synechocystis sp. indicate that a large part of the cyanobacterial genome is related to that of low GC Gram positives. Other groups that had been suggested as sister groups to the cyanobacteria contain many fewer genes that group with the Synechocystis orthologs. Interdomain comparisons of genome quartets containing the archaeon Halobacterium sp. revealed that Halobacterium sp. shares more genes with Bacteria that live in the same environment than with Bacteria that are more closely related based on rRNA phylogeny. Many of these genes encode proteins involved in substrate transport and metabolism and in information storage and processing. The performed analyses demonstrate that relationships among prokaryotes cannot be accurately depicted by or inferred from the tree-like evolution of a core of rarely transferred genes; rather prokaryotic genomes are mosaics in which different parts have different evolutionary histories. Probability mapping is a valuable tool to explore the mosaic nature of genomes.}, }
@article {pmid11917105, year = {2002}, author = {Kirik, D and Georgievska, B and Burger, C and Winkler, C and Muzyczka, N and Mandel, RJ and Bjorklund, A}, title = {Reversal of motor impairments in parkinsonian rats by continuous intrastriatal delivery of L-dopa using rAAV-mediated gene transfer.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {99}, number = {7}, pages = {4708-4713}, pmid = {11917105}, issn = {0027-8424}, support = {P01 NS036302/NS/NINDS NIH HHS/United States ; P01 NS36302/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; Corpus Striatum/metabolism ; Dependovirus/*genetics ; Female ; GTP Cyclohydrolase/*genetics ; Gene Transfer, Horizontal ; *Genetic Therapy ; Levodopa/*administration &amp; dosage/metabolism ; Parkinson Disease/*therapy ; Rats ; Rats, Sprague-Dawley ; Tyrosine 3-Monooxygenase/*genetics ; }, abstract = {Intrastriatal delivery of the tyrosine hydroxylase gene by viral vectors is being explored as a tool for local delivery of L-dopa in animals with lesions of the nigrostriatal pathway. The functional effects reported using this approach have been disappointing, probably because the striatal L-dopa levels attained have been too low. In the present study, we have defined a critical threshold level of L-dopa, 1.5 pmol/mg of tissue, that has to be reached to induce any significant functional effects. Using new generation high-titer recombinant adeno-associated virus vectors, we show that levels of striatal L-dopa production exceeding this threshold can be obtained provided that tyrosine hydroxylase is coexpressed with the cofactor synthetic enzyme, GTP-cyclohydrolase-1. After striatal transduction with this combination of vectors, substantial functional improvement in both drug-induced and spontaneous behavior was observed in rats with either complete or partial 6-hydroxydopamine lesions of the nigrostriatal pathway. However, complete reversal of motor deficits occurred only in animals in which part of the striatal dopamine innervation was left intact. Spared nigrostriatal fibers thus may convert L-dopa to dopamine and store and release dopamine in a more physiologically relevant manner in the denervated striatum to mediate better striatal output-dependent motor function. We conclude that intrastriatal L-dopa delivery may be a viable strategy for treatment and control of adverse side effects associated with oral L-dopa therapy such as on-off fluctuations and drug-induced dyskinesias in patients with Parkinson's disease.}, }
@article {pmid11914343, year = {2002}, author = {Ko, KS and Lee, HK and Park, MY and Park, MS and Lee, KH and Woo, SY and Yun, YJ and Kook, YH}, title = {Population genetic structure of Legionella pneumophila inferred from RNA polymerase gene (rpoB) and DotA gene (dotA) sequences.}, journal = {Journal of bacteriology}, volume = {184}, number = {8}, pages = {2123-2130}, pmid = {11914343}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; *Bacterial Proteins ; Base Sequence ; Carrier Proteins/*genetics ; DNA-Directed RNA Polymerases/*genetics ; Legionella pneumophila/*classification/genetics ; Membrane Proteins/*genetics ; Molecular Sequence Data ; Serotyping ; }, abstract = {The population structure of Legionella pneumophila was studied by using partial RNA polymerase gene (rpoB) and DotA gene (dotA) sequences. Trees inferred from rpoB sequences showed that two subspecies of L. pneumophila, Legionella pneumophila subsp. pneumophila and Legionella pneumophila subsp. fraseri, were clearly separated genetically. In both rpoB and dotA trees, 79 Korean isolates used in this study constituted six clonal populations, four of which (designated subgroups P-I to P-IV) were identified in L. pneumophila subsp. pneumophila and two of which (designated subgroups F-I and F-II) were identified in L. pneumophila subsp. fraseri. Although the relationships among subgroups were not identical, such subgrouping was congruent between the rpoB and dotA trees. Type strains of several serogroups did not belong to any subgroup, presumably because isolates similar to these strains were not present among our local sample of the population. There was evidence that horizontal gene transfer or recombination had occurred within L. pneumophila. Contrary to the phylogeny from rpoB and the taxonomic context, subgroups P-III and P-IV of L. pneumophila subsp. pneumophila proved to be closely related to those of L. pneumophila subsp. fraseri or showed a distinct clustering in the dotA tree. It can be inferred that dotA of subgroups P-III and P-IV has been transferred horizontally from other subspecies. The diverse distribution of serogroup 1 strains through the gene trees suggests that surface antigen-coding genes that determine serogroup can be exchanged. Thus, it can be inferred that genetic recombination has been important in the evolution of L. pneumophila.}, }
@article {pmid11908054, year = {2002}, author = {Kappé, G and Leunissen, JA and de Jong, WW}, title = {Evolution and diversity of prokaryotic small heat shock proteins.}, journal = {Progress in molecular and subcellular biology}, volume = {28}, number = {}, pages = {1-17}, doi = {10.1007/978-3-642-56348-5_1}, pmid = {11908054}, issn = {0079-6484}, mesh = {Amino Acid Sequence ; Animals ; Bacteria/genetics/pathogenicity ; Bacterial Proteins/chemistry/genetics ; Crystallins/chemistry/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; Heat-Shock Proteins/chemistry/*genetics ; Humans ; Molecular Sequence Data ; Phylogeny ; Prokaryotic Cells ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sequence Homology, Amino Acid ; }, }
@article {pmid11904311, year = {2002}, author = {Webb, T}, title = {Researchers explore role of gene transfer in tumor growth.}, journal = {Journal of the National Cancer Institute}, volume = {94}, number = {6}, pages = {413-414}, doi = {10.1093/jnci/94.6.413}, pmid = {11904311}, issn = {0027-8874}, mesh = {Apoptosis ; Cell Division ; DNA, Neoplasm/blood ; *Gene Transfer, Horizontal ; Genetic Variation ; Neoplasms/*pathology ; }, }
@article {pmid11895945, year = {2002}, author = {Pelludat, C and Hogardt, M and Heesemann, J}, title = {Transfer of the core region genes of the Yersinia enterocolitica WA-C serotype O:8 high-pathogenicity island to Y. enterocolitica MRS40, a strain with low levels of pathogenicity, confers a yersiniabactin biosynthesis phenotype and enhanced mouse virulence.}, journal = {Infection and immunity}, volume = {70}, number = {4}, pages = {1832-1841}, pmid = {11895945}, issn = {0019-9567}, mesh = {Animals ; Bacterial Outer Membrane Proteins ; Bacterial Proteins/*biosynthesis ; Gene Transfer, Horizontal ; Iron-Binding Proteins ; Mice ; Mice, Inbred BALB C ; Periplasmic Binding Proteins ; Phenotype ; Serotyping ; Virulence ; Yersinia enterocolitica/*genetics/*pathogenicity ; }, abstract = {The high-pathogenicity island (HPI) of yersiniae encodes an iron uptake system represented by its siderophore yersiniabactin (Ybt). The HPI is present in yersiniae with high levels of pathogenicity--i.e., Yersinia pestis, Y. pseudotuberculosis, and Y. enterocolitica biogroup (BG) 1B--but absent in Y. enterocolitica strains with low (BG 2 to 5) and no (BG 1A) levels of pathogenicity and has been shown to be an important virulence factor. Comparison of the HPI in Y. enterocolitica (Yen-HPI) and that in Y. pestis and Y. pseudotuberculosis revealed that, in contrast to genes of the variable region, genes of the core region (genes irp9 to fyuA) are highly homologous. In the present work the Yen-HPI core genes were rescued from the chromosome of Y. enterocolitica WA-C (BG 1B, serotype O:8) using the FRT-FLP recombinase system. Transfer of the resulting plasmid pCP1 into the siderophore-deficient strain Y. enterocolitica NF-O (BG 1A) led to no halo on siderophore indicator chrome azurol S (CAS) agar. Transfer of pCP1 into the Y. enterocolitica strain MRS40 (serotype O:9, BG 2; phenotype, CAS negative) led to a CAS halo larger than that of parental strain WA-C, indicating high Ybt production. pCP1 was highly unstable in iron-deficient medium, and no enhanced mouse virulence conferred by MRS40 carrying pCP1 could be detected. To overcome the problem of instability, pCP1 was integrated into the chromosome of MRS40, leading to the formation of a CAS halo comparable to that seen with WA-C and correspondingly to increased mouse virulence. Thus, the core genes of Yen-HPI are sufficient to confer a positive CAS phenotype and mouse virulence to Y. enterocolitica MRS40, BG 2, but are insufficient to confer this phenotype to Y. enterocolitica NF-O, BG 1A.}, }
@article {pmid11886754, year = {2002}, author = {Meier, P and Berndt, C and Weger, N and Wackernagel, W}, title = {Natural transformation of Pseudomonas stutzeri by single-stranded DNA requires type IV pili, competence state and comA.}, journal = {FEMS microbiology letters}, volume = {207}, number = {1}, pages = {75-80}, doi = {10.1111/j.1574-6968.2002.tb11031.x}, pmid = {11886754}, issn = {0378-1097}, mesh = {Bacterial Proteins/genetics/*metabolism ; DNA, Bacterial/genetics ; DNA, Single-Stranded/*genetics ; DNA-Binding Proteins/genetics/*metabolism ; Fimbriae, Bacterial/genetics/*metabolism ; Mutation ; Pseudomonas/genetics/*growth &amp; development/metabolism ; *Transformation, Bacterial ; }, abstract = {Pseudomonas stutzeri, in addition to being transformed by duplex DNA, is also transformed by the sense or antisense strand of the genetic marker employed (hisX(+)) or by heat-denatured chromosomal DNA. Transformation was absent in non-competent cells and in mutants defective for pilus biogenesis (pilA, pilC) and function (pilT) or DNA translocation into the cytoplasm (comA). Uptake of (3)H-thymidine-labeled single-stranded DNA was hardly detectable reflecting the 20- to 60-fold lower transformation compared to duplex DNA. The results suggest that the steps in natural transformation also accommodate single-stranded DNA and that DNA translocation from the periplasm into the cytoplasm is not necessarily coupled to the degradation of a complementary strand. Small DNA single-stranded fragments are thus not excluded from horizontal gene transfer by transformation.}, }
@article {pmid11884641, year = {2002}, author = {Nicolas, P and Bize, L and Muri, F and Hoebeke, M and Rodolphe, F and Ehrlich, SD and Prum, B and Bessières, P}, title = {Mining Bacillus subtilis chromosome heterogeneities using hidden Markov models.}, journal = {Nucleic acids research}, volume = {30}, number = {6}, pages = {1418-1426}, pmid = {11884641}, issn = {1362-4962}, mesh = {Bacillus subtilis/*genetics ; Bacterial Proteins/chemistry/genetics ; *Chromosomes, Bacterial ; DNA, Bacterial/classification ; Gene Transfer, Horizontal ; Genetic Variation ; Hydrophobic and Hydrophilic Interactions ; Likelihood Functions ; Lysogeny ; *Markov Chains ; RNA, Bacterial/genetics ; Repetitive Sequences, Nucleic Acid ; Sequence Homology, Nucleic Acid ; }, abstract = {We present here the use of a new statistical segmentation method on the Bacillus subtilis chromosome sequence. Maximum likelihood parameter estimation of a hidden Markov model, based on the expectation-maximization algorithm, enables one to segment the DNA sequence according to its local composition. This approach is not based on sliding windows; it enables different compositional classes to be separated without prior knowledge of their content, size and localization. We compared these compositional classes, obtained from the sequence, with the annotated DNA physical map, sequence homologies and repeat regions. The first heterogeneity revealed discriminates between the two coding strands and the non-coding regions. Other main heterogeneities arise; some are related to horizontal gene transfer, some to t-enriched composition of hydrophobic protein coding strands, and others to the codon usage fitness of highly expressed genes. Concerning potential and established gene transfers, we found 9 of the 10 known prophages, plus 14 new regions of atypical composition. Some of them are surrounded by repeats, most of their genes have unknown function or possess homology to genes involved in secondary catabolism, metal and antibiotic resistance. Surprisingly, we notice that all of these detected regions are a + t-richer than the host genome, raising the question of their remote sources.}, }
@article {pmid11884368, year = {2002}, author = {Scott, S and O'Sullivan, M and Hafizi, S and Shapiro, LM and Bennett, MR}, title = {Human vascular smooth muscle cells from restenosis or in-stent stenosis sites demonstrate enhanced responses to p53: implications for brachytherapy and drug treatment for restenosis.}, journal = {Circulation research}, volume = {90}, number = {4}, pages = {398-404}, doi = {10.1161/hh0402.105900}, pmid = {11884368}, issn = {1524-4571}, mesh = {Apoptosis/drug effects/genetics/radiation effects ; Cell Division/drug effects/genetics/radiation effects ; Cells, Cultured ; Coronary Restenosis/*metabolism/pathology ; Coronary Vessels/pathology ; Cyclin D ; Cyclins/metabolism ; DNA Damage ; Etoposide/pharmacology ; Flow Cytometry ; Gene Expression Regulation/drug effects/radiation effects ; Gene Transfer, Horizontal ; Genetic Vectors/genetics/metabolism/pharmacology ; Graft Occlusion, Vascular/drug therapy/*metabolism/pathology ; Humans ; Microscopy, Video ; Muscle, Smooth, Vascular/cytology/drug effects/*metabolism/radiation effects ; Nucleic Acid Synthesis Inhibitors/pharmacology ; Papillomaviridae/genetics ; Recombinant Fusion Proteins/genetics/metabolism/pharmacology ; Tumor Suppressor Protein p53/genetics/*metabolism ; Ultraviolet Rays ; Viral Plaque Assay ; }, abstract = {The p53 tumor suppressor gene regulates growth arrest and apoptosis after DNA damage. Recent studies suggest that p53 is inactive in vascular smooth muscle cells (VSMCs) in human angioplasty restenosis, promoting VSMC accumulation and vessel stenosis. In contrast, the success of irradiation (brachytherapy) for in-stent restenosis argues that DNA-damage p53 responses are intact. We examined p53 expression and function in human VSMCs from normal vessels (n-VSMCs) and angioplasty/in-stent restenosis sites (r-VSMCs). p53 expression was uniformly low in all VSMCs and was induced by DNA damage. However, p53 induced profoundly different biological effects in r-VSMCs versus n-VSMCs, causing growth arrest and apoptosis in r-VSMCs only. In addition, dominant-negative p53 promoted cell proliferation and apoptosis in r-VSMCs but not n-VSMCs. Cytotoxic drug-- or irradiation-induced growth arrest and apoptosis in both cell types was mediated only partly by p53. In contrast, cyclin D degradation in response to DNA damage, a critical early mediator of growth arrest, was impaired in r-VSMCs, an effect that required p53. We conclude that p53 expression and function are normal or increased in r-VSMCs and may underlie the success of brachytherapy. We also identify a restenosis VSMC-specific defect in cyclin D degradation induced by DNA damage.}, }
@article {pmid11882717, year = {2002}, author = {Lazarevic, V and Abellan, FX and Möller, SB and Karamata, D and Mauël, C}, title = {Comparison of ribitol and glycerol teichoic acid genes in Bacillus subtilis W23 and 168: identical function, similar divergent organization, but different regulation.}, journal = {Microbiology (Reading, England)}, volume = {148}, number = {Pt 3}, pages = {815-824}, doi = {10.1099/00221287-148-3-815}, pmid = {11882717}, issn = {1350-0872}, mesh = {Amino Acid Sequence ; Bacillus subtilis/*genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Base Sequence ; Gene Expression Regulation, Bacterial ; *Genes, Bacterial ; Glycerophosphates/genetics/metabolism ; Molecular Sequence Data ; Polysaccharides/genetics/*metabolism ; Sequence Analysis, DNA ; Teichoic Acids/*genetics ; }, abstract = {The tar genes directing the synthesis of poly(ribitol phosphate), the main teichoic acid in Bacillus subtilis strain W23, were sequenced. They are organized in two divergently transcribed operons, tarABIJKL and tarDF, as are the tag genes specifying poly(glycerol phosphate) synthesis in B. subtilis 168. The features of the tar genes as well as the putative participation of their products in the proposed biosynthesis pathway of poly(ribitol phosphate) are presented. The tarA and tarD genes, which are most likely involved in the synthesis of the linkage unit (the entity coupling teichoic acid to peptidoglycan), are separated by 508 nt. Sequences of the outer segments of this regulatory region are similar to the two divergent promoter regions identified upstream of the tagA and tagD genes in strain 168. However, in W23, these regions, which also included functional promoters, are separated by an additional DNA segment of about 100 nt, on which two new mRNA starts, one in each direction, were identified. The regulatory regions of teichoic acid divergons of Bacillus globigii, Bacillus licheniformis and eight strains of B. subtilis were cloned and sequenced. In four B. subtilis strains and in B. globigii, their length and sequence are similar to the regulatory region of W23. In the others, including B. licheniformis, they are of the 168-type. Analysis of nucleotide sequences of a non-coding grey hole, present in the tag region of strain 168, revealed higher similarities to tar than to tag entities. This suggests that at least part of the tag genes specifying the synthesis of glucosylated poly(glycerol phosphate) in strain 168 was introduced by horizontal gene transfer into a strain originally synthesizing a ribitol-phosphate-containing teichoic acid.}, }
@article {pmid11880418, year = {2002}, author = {Bousarghin, L and Combita-Rojas, AL and Touzé, A and El Mehdaoui, S and Sizaret, PY and Bravo, MM and Coursaget, P}, title = {Detection of neutralizing antibodies against human papillomaviruses (HPV) by inhibition of gene transfer mediated by HPV pseudovirions.}, journal = {Journal of clinical microbiology}, volume = {40}, number = {3}, pages = {926-932}, pmid = {11880418}, issn = {0095-1137}, mesh = {Animals ; Antibodies, Viral/*analysis ; DNA, Viral/analysis ; Female ; *Gene Transfer, Horizontal ; Humans ; Immunization ; Infant ; Mice ; Microscopy, Electron ; Papillomaviridae/genetics/*immunology ; Papillomavirus Infections/immunology ; Virion/*genetics ; }, abstract = {The goal of this study was to develop a human papillomavirus (HPV) neutralization assay using HPV pseudovirions generated in vitro. For this purpose, gene transfer efficiency of HPV virus-like particles (VLPs) was improved by using direct interaction between a reporter plasmid and the VLPs. Electron microscopic observation of the interaction between DNA molecules and VLPs revealed that VLPs always interact with a single DNA molecule and that VLPs bind to the end of linearized DNA molecules. An 100-fold improvement in the gene transfer was obtained by simple interaction between a linearized DNA molecule and VLPs. Moreover, direct interaction methods offer the possibility of transferring plasmids a size higher than that of the papillomavirus genome. The approach that we developed to generate HPV-16 and HPV-31 pseudovirions proved to be suitable for testing neutralizing antibodies in human sera both after immunization and after natural infection.}, }
@article {pmid11879526, year = {2002}, author = {Bocs, S and Danchin, A and Médigue, C}, title = {Re-annotation of genome microbial coding-sequences: finding new genes and inaccurately annotated genes.}, journal = {BMC bioinformatics}, volume = {3}, number = {}, pages = {5}, pmid = {11879526}, issn = {1471-2105}, mesh = {Computational Biology/*methods ; Databases, Protein ; Gene Transfer, Horizontal/genetics ; Genes, Archaeal/*physiology ; *Genes, Bacterial/physiology ; Genetic Variation ; *Genome, Archaeal ; *Genome, Bacterial ; Gram-Negative Bacteria/genetics ; Gram-Positive Bacteria/genetics ; *Open Reading Frames/genetics ; Predictive Value of Tests ; Reading Frames/genetics ; *Software ; Spirochaetaceae/genetics ; }, abstract = {BACKGROUND: Analysis of any newly sequenced bacterial genome starts with the identification of protein-coding genes. Despite the accumulation of multiple complete genome sequences, which provide useful comparisons with close relatives among other organisms during the annotation process, accurate gene prediction remains quite difficult. A major reason for this situation is that genes are tightly packed in prokaryotes, resulting in frequent overlap. Thus, detection of translation initiation sites and/or selection of the correct coding regions remain difficult unless appropriate biological knowledge (about the structure of a gene) is imbedded in the approach.<br><br>RESULTS: We have developed a new program that automatically identifies biologically significant candidate genes in a bacterial genome. Twenty-six complete prokaryotic genomes were analyzed using this tool, and the accuracy of gene finding was assessed by comparison with existing annotations. This analysis revealed that, despite the enormous effort of genome program annotators, a small but not negligible number of genes annotated within the framework of sequencing projects are likely to be partially inaccurate or plainly wrong. Moreover, the analysis of several putative new genes shows that, as expected, many short genes have escaped annotation. In most cases, these new genes revealed frameshifts that could be either artifacts or genuine frameshifts. Some entirely unexpected new genes have also been identified. This allowed us to get a more complete picture of prokaryotic genomes. The results of this procedure are progressively integrated into the SWISS-PROT reference databank.<br><br>CONCLUSIONS: The results described in the present study show that our procedure is very satisfactory in terms of gene finding accuracy. Except in few cases, discrepancies between our results and annotations provided by individual authors can be accounted for by the nature of each annotation process or by specific characteristics of some genomes. This stresses that close cooperation between scientists, regular update and curation of the findings in databases are clearly required to reduce the level of errors in genome annotation (and hence in reducing the unfortunate spreading of errors through centralized data libraries).}, }
@article {pmid11878892, year = {2001}, author = {Peng, X and Blum, H and She, Q and Mallok, S and Brügger, K and Garrett, RA and Zillig, W and Prangishvili, D}, title = {Sequences and replication of genomes of the archaeal rudiviruses SIRV1 and SIRV2: relationships to the archaeal lipothrixvirus SIFV and some eukaryal viruses.}, journal = {Virology}, volume = {291}, number = {2}, pages = {226-234}, doi = {10.1006/viro.2001.1190}, pmid = {11878892}, issn = {0042-6822}, mesh = {African Swine Fever Virus/genetics ; Animals ; Base Sequence ; Chlorella/virology ; *DNA Replication ; DNA, Viral/biosynthesis ; *Genome, Viral ; Lipothrixviridae/*genetics ; Molecular Sequence Data ; Open Reading Frames ; Phycodnaviridae/genetics ; Poxviridae/genetics ; Rudiviridae/*genetics ; Sequence Analysis, DNA ; Sulfolobus/*virology ; Swine ; *Virus Replication ; }, abstract = {The double-stranded DNA genomes of the viruses SIRV1 and SIRV2, which infect the extremely thermophilic archaeon Sulfolobus and belong to the family Rudiviridae, were sequenced. They are linear, covalently closed at the ends, and 32,312 and 35,502 bp long, respectively, with an A+T content of 75%. The genomes of SIRV1 and SIRV2 carry inverted terminal repeats of 2029 and 1628 bp, respectively, which contain multiple direct repeats. SIRV1 and SIRV2 genomes contain 45 and 54 ORFs, respectively, of which 44 are homologous to one another. Their predicted functions include a DNA polymerase, a Holliday junction resolvase, and a dUTPase. The genomes consist of blocks with well-conserved sequences separated by nonconserved sequences. Recombination, gene duplication, horizontal gene transfer, and substitution of viral genes by homologous host genes have contributed to their evolution. The finding of head-to-head and tail-to-tail linked replicative intermediates suggests that the linear genomes replicate by the same mechanism as the similarly organized linear genomes of the eukaryal poxviruses, African swine fever virus and Chlorella viruses. SIRV1 and SIRV2 both contain motifs that resemble the binding sites for Holliday junction resolvases of eukaryal viruses and may use common mechanisms for resolution of replicative intermediates. The results suggest a common origin of the replication machineries of the archaeal rudiviruses and the above-mentioned eukaryal viruses. About 1/3 of the ORFs of each rudivirus have homologs in the Sulfolobus virus SIFV of the family Lipothrixviridae, indicating that the two viral families form a superfamily. The finding of inverted repeats of at least 0.8 kb at the termini of the linear genome of SIFV supports this inference.}, }
@article {pmid11877364, year = {2002}, author = {Zhao, Q and Egashira, K and Inoue, S and Usui, M and Kitamoto, S and Ni, W and Ishibashi, M and Hiasa Ki, K and Ichiki, T and Shibuya, M and Takeshita, A}, title = {Vascular endothelial growth factor is necessary in the development of arteriosclerosis by recruiting/activating monocytes in a rat model of long-term inhibition of nitric oxide synthesis.}, journal = {Circulation}, volume = {105}, number = {9}, pages = {1110-1115}, doi = {10.1161/hc0902.104718}, pmid = {11877364}, issn = {1524-4539}, mesh = {Animals ; Arteriosclerosis/etiology/immunology/*metabolism/pathology ; Biological Assay ; Blood Pressure/drug effects ; Cell Division/drug effects ; Chemokine CCL2/genetics/metabolism ; Chemotaxis, Leukocyte/drug effects ; Coronary Vessels/drug effects/immunology/pathology ; Disease Models, Animal ; Endothelial Growth Factors/antagonists &amp; inhibitors/*metabolism ; Enzyme Inhibitors/administration &amp; dosage ; Gene Expression/drug effects ; Gene Transfer, Horizontal ; Genetic Vectors/administration &amp; dosage/biosynthesis/genetics ; Inflammation/immunology/pathology ; Injections, Intramuscular ; Lymphokines/antagonists &amp; inhibitors/*metabolism ; Male ; Mice ; Monocytes/immunology/*metabolism/pathology ; NG-Nitroarginine Methyl Ester/administration &amp; dosage ; Neovascularization, Physiologic/drug effects ; Nitric Oxide/*antagonists &amp; inhibitors/blood ; Peptidyl-Dipeptidase A/metabolism ; Proto-Oncogene Proteins/*administration &amp; dosage/biosynthesis/genetics ; RNA, Messenger/biosynthesis ; Rats ; Rats, Inbred WKY ; Receptor Protein-Tyrosine Kinases/*administration &amp; dosage/biosynthesis/genetics ; Time ; Transforming Growth Factor beta/genetics/metabolism ; Vascular Endothelial Growth Factor A ; Vascular Endothelial Growth Factor Receptor-1 ; Vascular Endothelial Growth Factors ; }, abstract = {BACKGROUND: It remains unclear whether vascular endothelial growth factor (VEGF) is a proarteriosclerotic or an antiarteriosclerotic factor. We recently reported that long-term inhibition of nitric oxide by administering Nomega-nitro-L-arginine methyl ester (L-NAME) induces coronary vascular inflammation and arteriosclerosis.<br><br>METHODS AND RESULTS: We used this animal model to investigate the role of VEGF in arteriosclerosis. We blocked VEGF activity in vivo by transfecting with plasmid DNA encoding the murine soluble FLT-1 (sFLT-1) gene into thigh muscle. Soluble FLT-1 can suppress VEGF activity both by sequestering VEGF and by functioning as a dominant-negative inhibitor of VEGF receptors. We observed vascular inflammation associated with increased VEGF expression within 3 days of L-NAME administration, which was prevented by pretreatment with ACE inhibitor, angiotensin II receptor antagonist, or neutralizing monocyte chemoattractant protein-1 antibody. The sFLT-1 gene transfer attenuated the early vascular inflammation and prevented late arteriosclerosis. The sFLT-1 gene transfer also inhibited increased expression of monocyte chemoattractant protein-1 and transforming growth factor-beta, indicating creation of a positive feedback loop to cause arteriosclerosis.<br><br>CONCLUSIONS: VEGF is necessary in the development of arteriosclerosis by mediating monocyte recruitment and activation in this model.}, }
@article {pmid11876971, year = {2000}, author = {Zhu, F and Chen, G and Fu, A and Tang, C and Zhou, A and Tang, J}, title = {[The inhibition of prourokinase gene transfer on deposition of platelets on rabbit carotid artery intima].}, journal = {Zhonghua xue ye xue za zhi = Zhonghua xueyexue zazhi}, volume = {21}, number = {3}, pages = {132-134}, pmid = {11876971}, issn = {0253-2727}, mesh = {Adenoviridae/genetics ; Animals ; Blood Platelets/*physiology ; Carotid Arteries/pathology ; Gene Transfer, Horizontal ; *Genetic Therapy ; Rabbits ; Recombinant Proteins/*genetics ; Thrombosis/*prevention &amp; control ; Urokinase-Type Plasminogen Activator/*genetics/physiology ; }, abstract = {OBJECTIVE: To observe the expression of pro-urokinase (proUK) gene in rabbit carotid artery transfected with replication-deficient adenovirus vector containing proUK gene (Ad/prouk) and the deposition of platelet on the same injured vessel.<br><br>METHODS: Ad/proUK (Ad/proUK, 3 x 10(10) pfu/ml) was injected into the right carotid artery locally. Wild type adenovirus (Ad) was locally injected into the left carotid artery as self-control. The expression of proUK gene was investigated by immunohistochemistry assay. After injury of the gene-transfected vessel by electric stimulation, the deposition of (111) In-labeled platelet was quantitatively observed. The thrombosis was observed with HE-stained vessel section.<br><br>RESULTS: There were lots of proUK granules in the endothelium of Ad/proUK gene-transfected vessel. The differences in (111) In-platelets deposition per gram dry weight vessel segment were significant between Ad/proUK and Ad transfected control vessels [(4.60 +/- 0.93) x 10(7)/g vs control (27.95 +/- 4.93) x 10(7)/g, P < 0.01)]. The HE-stained vessel section showed that there were only small thrombi in proUK gene-transfected vessel but massive thrombi almost blocked up the whole vessel in control vessel.<br><br>CONCLUSION: The proUK gene-transfected vessel can obviously inhibit (111) In-labeled platelet deposition on injured vessel and thus thrombosis.}, }
@article {pmid11876147, year = {2001}, author = {Heir, E and Langsrud, S and Sidhu, MS and Steinbakk, M}, title = {[Can disinfectants contribute to antibiotic resistance?].}, journal = {Tidsskrift for den Norske laegeforening : tidsskrift for praktisk medicin, ny raekke}, volume = {121}, number = {27}, pages = {3201-3206}, pmid = {11876147}, issn = {0029-2001}, mesh = {Animals ; Anti-Infective Agents, Local/*adverse effects/metabolism ; Bacteria/drug effects/metabolism ; Cell Membrane/drug effects/metabolism ; Disinfectants/*adverse effects/metabolism ; *Drug Resistance, Bacterial/genetics ; Humans ; Pseudomonas fluorescens/drug effects/metabolism/ultrastructure ; Triclosan/adverse effects ; }, abstract = {BACKGROUND: Disinfectants are widely used in medicine, veterinary medicine, and the food processing industry. Increasingly, disinfectants are included in consumer products. Broad-scale use of antiseptics and disinfectants may have detrimental ecological consequences, for instance the development of antimicrobial resistance.<br><br>MATERIAL AND METHODS: We give an overview of the correlation between the use of certain antiseptics and disinfectants, bacterial resistance to these agents, and antibiotic resistance.<br><br>RESULTS: The mechanisms of antibiotic and biocide resistance share many common characteristics. There are links between disinfectant resistance and antibiotic resistance. Some biocides have the ability to select for antibiotic resistant mutants and vice versa. Resistance genes are often located on transferable genetic elements that facilitate horizontal gene transfer between microorganisms. Antibiotic resistance and disinfectant resistance may be stabilized and maintained even in the absence of a direct selective pressure. Higher incidence of bacteria resistant to certain disinfectants have been reported in environments where such agents are frequently used compared to environments where they are not in regular use. Increased domestic usage of non-antibiotic antimicrobial agents may select for antibiotic-resistant bacteria of clinical significance.<br><br>INTERPRETATION: The use of antiseptics and disinfectants should be restricted to products and areas where they have an essential and documented effect.}, }
@article {pmid11875532, year = {2002}, author = {Butler, D}, title = {Alleged flaws in gene-transfer paper spark row over genetically modified maize.}, journal = {Nature}, volume = {415}, number = {6875}, pages = {948-949}, doi = {10.1038/415948a}, pmid = {11875532}, issn = {0028-0836}, mesh = {Caulimovirus/genetics ; DNA, Recombinant/isolation &amp; purification ; DNA, Viral/isolation &amp; purification ; Ecology ; Environment ; European Union ; *Food, Genetically Modified ; *Gene Transfer, Horizontal ; Genes, Plant ; Mexico ; Periodicals as Topic ; Plants, Genetically Modified/*genetics ; Politics ; Publishing ; Research/standards ; United States ; Zea mays/*genetics ; }, }
@article {pmid11864915, year = {2002}, author = {del Monte, F and Harding, SE and Dec, GW and Gwathmey, JK and Hajjar, RJ}, title = {Targeting phospholamban by gene transfer in human heart failure.}, journal = {Circulation}, volume = {105}, number = {8}, pages = {904-907}, pmid = {11864915}, issn = {1524-4539}, support = {R01 HL049574-05/HL/NHLBI NIH HHS/United States ; HL 57623/HL/NHLBI NIH HHS/United States ; HL 49574/HL/NHLBI NIH HHS/United States ; R01 HL049574-05S1/HL/NHLBI NIH HHS/United States ; R01 HL049574-08/HL/NHLBI NIH HHS/United States ; R01 HL049574-07/HL/NHLBI NIH HHS/United States ; R01 HL049574-06/HL/NHLBI NIH HHS/United States ; R01 HL049574-06S1/HL/NHLBI NIH HHS/United States ; }, mesh = {Adenoviridae/genetics ; Calcium/metabolism ; Calcium-Binding Proteins/*antagonists &amp; inhibitors/genetics/metabolism ; Calcium-Transporting ATPases/genetics/metabolism ; Cells, Cultured ; DNA, Antisense/genetics/*pharmacology ; Enzyme Activation/drug effects ; Gene Expression/drug effects ; *Gene Transfer, Horizontal ; Genes, Reporter ; Genetic Therapy/methods ; Genetic Vectors/genetics/metabolism/pharmacology ; Heart Failure/genetics/*physiopathology ; Heart Ventricles/cytology/drug effects/metabolism ; Humans ; In Vitro Techniques ; Isoenzymes/genetics/metabolism ; Myocardial Contraction/drug effects ; Myocardium/cytology/*metabolism/pathology ; Sarcoplasmic Reticulum/metabolism ; Sarcoplasmic Reticulum Calcium-Transporting ATPases ; }, abstract = {BACKGROUND: Myocardial cells from failing human hearts are characterized by abnormal calcium handling, a negative force-frequency relationship, and decreased sarcoplasmic reticulum Ca2+ ATPase (SERCA2a) activity. In this study, we tested whether contractile function can be improved by decreasing the inhibitory effects of phospholamban on SERCA2a with adenoviral gene transfer of antisense phospholamban (asPL).<br><br>METHODS AND RESULTS: Myocardial cells isolated from 9 patients with end-stage heart failure and 18 donor nonfailing hearts were infected with adenoviruses encoding for either the antisense of phospholamban (Ad.asPL), the SERCA2a gene (Ad.SERCA2a), or the reporter genes beta-galactosidase and green fluorescent protein (Ad.betagal-GFP). Adenoviral gene transfer with Ad.asPL decreased phospholamban expression over 48 hours, increasing the velocity of both contraction and relaxation. Compared with cardiomyocytes infected with Ad.asPL (n=13), human myocytes infected with Ad.betagal-GFP (n=8) had enhanced contraction velocity (20.3 +/- 3.9% versus 8.7 +/- 2.6% shortening/second; P<0.01) and relaxation velocity (26.0 +/- 6.2% versus 8.6 +/- 4.3% shortening/second; P<0.01). The improvement in contraction and relaxation velocities was comparable to cardiomyocytes infected with Ad.SERCA2a. Failing human cardiomyocytes had decreased contraction and Ca2+ release with increasing frequency (0.1 to 2 Hz). Phospholamban ablation restored the frequency response in the failing cardiomyocytes to normal; increasing frequency resulted in enhanced sarcoplasmic reticulum Ca2+ release and contraction.<br><br>CONCLUSION: These results show that gene transfer of asPL can improve the contractile function in failing human myocardium. Targeting phospholamban may provide therapeutic benefits in human heart failure.}, }
@article {pmid11864227, year = {1998}, author = {Talon, D and Mulin, B and Dupont, MJ and Chareton, AM and Thouverez, M}, title = {Epidemiology of penicillin resistance in Streptococcus pneumoniae isolates in eastern France.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {4}, number = {1}, pages = {11-17}, doi = {10.1111/j.1469-0691.1998.tb00328.x}, pmid = {11864227}, issn = {1469-0691}, abstract = {OBJECTIVE: To assess the rates of intermediate and high-level resistance to penicillin among Streptococcus pneumoniae isolates and to identify clonal relationship of isolates within the different serotypes by means of pulsed-field gel electrophoresis. METHODS: We studied all clinical isolates obtained between April 1995 and March 1996 from patients admitted to 10 hospitals in eastern France. Antibiotic susceptibility testing and serotyping were performed on all isolates. The genetic polymorphism of isolates susceptible, intermediately resistant and highly resistant to penicillin was studied by using pulsed-field gel electrophoresis with ApaI and SmaI endonucleases. RESULTS: The prevalence of intermediate and high-level resistance was respectively 30.3% and 9.7%. Diminished sensitivity to penicillin was mainly encountered in serotypes 6, 9V, 14 and 23F. The 9V isolates from the different hospitals were genetically closely related, unlike the 23F isolates. Different levels of resistance (MICs from 0.5 to 2 mg/L) were expressed by closely related isolates. Three 9V isolates, three capsular-type 14 isolates and one non-typeable isolate were genetically closely related in studies with the two endonucleases. CONCLUSIONS: The capsular type was not a good indicator of genetic relatedness. The level of penicillin resistance was independent of the clonal classification. Horizontal gene transfer may be the main factor determining the degree of resistance.}, }
@article {pmid11863263, year = {2002}, author = {Gutacker, M and Valsangiacomo, C and Bernasconi, MV and Piffaretti, JC}, title = {RecA and glnA sequences separate the bacteroides fragilis population into two genetic divisions associated with the antibiotic resistance genotypes cepA and cfiA.}, journal = {Journal of medical microbiology}, volume = {51}, number = {2}, pages = {123-130}, doi = {10.1099/0022-1317-51-2-123}, pmid = {11863263}, issn = {0022-2615}, mesh = {*Bacterial Proteins ; Bacteroides fragilis/*classification/drug effects/genetics ; Base Sequence ; Drug Resistance, Bacterial/*genetics ; Genetic Variation ; Genotype ; Glutamate-Ammonia Ligase/*genetics ; Molecular Sequence Data ; Phylogeny ; Rec A Recombinases/*genetics ; beta-Lactamases/*genetics ; }, abstract = {The sequences of part of the glutamine synthetase-encoding gene (glnA) and of the RecA-encoding gene (recA) were determined and aligned for 45 Bacteroides fragilis isolates from different clinical and geographical origin. The patterns of sequence divergence of glnA and recA were very similar. The sequences of a 303-bp fraction of recA showed 45 nucleotide substitutions, 40 of which allowed the separation of B. fragilis into two major divisions, which were not found when the deduced amino acid sequences were considered. The 687-bp sequences analysed for the glnA gene showed 112 nucleotide substitutions, 96 of which separated the population into the same two divisions as those described for recA. In this case, the deduced amino acid sequences showed this subdivision as well: three of the six observed amino acid substitutions were division-specific. Within the two divisions, both genes presented a high degree of sequence conservation. Each B. fragilis division was associated with the presence of a different antibiotic resistance gene: cepA encoding a serine-beta-lactamase (division I) and cfiA encoding a metallo-beta-lactamase (division II). No particular clusters associated with geographical or clinical origin, or with the production of an enterotoxin were observed. Sequencing of the cfiA gene allowed identification of two different alleles in division II. However, no association of these different cfiA alleles with the expression of imipenem resistance was observed. In conclusion, the phylogenetic patterns observed by sequencing recA and glnA are in agreement with those obtained previously by MLEE (multilocus enzyme electrophoresis). Thus, it appears that the evolution of recA and glnA genes is similar to that of the whole chromosome of B. fragilis. Horizontal gene transfer between divisions I and II seems to be low, at best. However, the results of the present study could not clarify definitively whether divisions I and II should be considered as two different B. fragilis genospecies.}, }
@article {pmid11861883, year = {2002}, author = {Koufopanou, V and Goddard, MR and Burt, A}, title = {Adaptation for horizontal transfer in a homing endonuclease.}, journal = {Molecular biology and evolution}, volume = {19}, number = {3}, pages = {239-246}, doi = {10.1093/oxfordjournals.molbev.a004077}, pmid = {11861883}, issn = {0737-4038}, mesh = {Conserved Sequence ; DNA, Fungal/genetics ; Endodeoxyribonucleases/*genetics ; Gene Transfer, Horizontal/*genetics ; Phylogeny ; Polymerase Chain Reaction ; *Proton-Translocating ATPases ; Saccharomyces cerevisiae/*enzymology/*genetics ; Saccharomyces cerevisiae Proteins/genetics ; }, abstract = {Selfish genes of no function other than self-propagation are susceptible to degeneration if they become fixed in a population, and regular transfer to new species may be the only means for their long-term persistence. To test this idea we surveyed 24 species of yeast for VDE, a nuclear, intein-associated homing endonuclease gene (HEG) originally discovered in Saccharomyces cerevisiae. Phylogenetic analyses show that horizontal transmission has been a regular occurrence in its evolutionary history. Moreover, VDE appears to be specifically adapted for horizontal transmission. Its 31-bp recognition sequence is an unusually well-conserved region in an unusually well-conserved gene. In addition, the nine nucleotide sites most critical for homing are also unusually well conserved. Such adaptation for horizontal transmission presumably arose as a consequence of selection, both among HEGs at different locations in the genome and among variants at the same location. The frequency of horizontal transmission must therefore be a key feature constraining the distribution and abundance of these genes.}, }
@article {pmid11859185, year = {2002}, author = {Meyerowitz, EM}, title = {Plants compared to animals: the broadest comparative study of development.}, journal = {Science (New York, N.Y.)}, volume = {295}, number = {5559}, pages = {1482-1485}, doi = {10.1126/science.1066609}, pmid = {11859185}, issn = {1095-9203}, mesh = {Animals ; Arabidopsis/genetics/growth &amp; development ; *Biological Evolution ; *Body Patterning ; Chromatin/*physiology ; Drosophila/genetics/growth &amp; development ; Gene Expression Regulation, Developmental ; Gene Transfer, Horizontal ; Genes, Homeobox ; Genes, Plant ; Genome ; Genome, Plant ; *Plant Development ; Plants/genetics ; *Signal Transduction ; }, abstract = {If the last common ancestor of plants and animals was unicellular, comparison of the developmental mechanisms of plants and animals would show that development was independently invented in each lineage. And if this is the case, comparison of plant and animal developmental processes would give us a truly comparative study of development, which comparisons merely among animals, or merely among plants, do not-because in each of these lineages, the fundamental mechanisms are similar by descent. Evidence from studies of developmental mechanisms in both kingdoms, and data from genome-sequencing projects, indicate that development evolved independently in the lineages leading to plants and to animals.}, }
@article {pmid11858840, year = {2002}, author = {Korbel, JO and Snel, B and Huynen, MA and Bork, P}, title = {SHOT: a web server for the construction of genome phylogenies.}, journal = {Trends in genetics : TIG}, volume = {18}, number = {3}, pages = {158-162}, doi = {10.1016/s0168-9525(01)02597-5}, pmid = {11858840}, issn = {0168-9525}, mesh = {Animals ; *Databases, Genetic ; Evolution, Molecular ; Gene Order ; Gene Transfer, Horizontal ; *Genome ; *Internet ; *Phylogeny ; RNA, Ribosomal/genetics ; Software ; }, abstract = {With the increasing availability of genome sequences, new methods are being proposed that exploit information from complete genomes to classify species in a phylogeny. Here we present SHOT, a web server for the classification of genomes on the basis of shared gene content or the conservation of gene order that reflects the dominant, phylogenetic signal in these genomic properties. In general, the genome trees are consistent with classical gene-based phylogenies, although some interesting exceptions indicate massive horizontal gene transfer. SHOT is a useful tool for analysing the tree of life from a genomic point of view. It is available at http://www.Bork.EMBL-Heidelberg.de/SHOT.}, }
@article {pmid11854705, year = {2002}, author = {Ailawadi, M and Lee, JM and Lee, S and Hackett, N and Crystal, RG and Korst, RJ}, title = {Adenovirus vector-mediated transfer of the vascular endothelial growth factor cDNA to healing abdominal fascia enhances vascularity and bursting strength in mice with normal and impaired wound healing.}, journal = {Surgery}, volume = {131}, number = {2}, pages = {219-227}, doi = {10.1067/msy.2002.118709}, pmid = {11854705}, issn = {0039-6060}, support = {R01 HL 59861/HL/NHLBI NIH HHS/United States ; }, mesh = {Adenoviridae/genetics ; Animals ; DNA, Complementary/*administration &amp; dosage ; Dexamethasone/pharmacology ; Endothelial Growth Factors/*genetics ; Fascia/metabolism ; Female ; Gene Transfer, Horizontal ; *Genetic Therapy ; Laparotomy ; Lymphokines/*genetics ; Male ; Mice ; Mice, Inbred C3H ; Vascular Endothelial Growth Factor A ; Vascular Endothelial Growth Factors ; *Wound Healing ; }, abstract = {BACKGROUND: We hypothesized that adenovirus-mediated transfer of the vascular endothelial growth factor (VEGF121) complementary DNA (cDNA) to murine laparotomy fascial wounds would enhance vascularity and bursting strength.<br><br>METHODS: Microfibrillar collagen sponges saturated with adenovirus (Ad) vectors encoding for the human VEGF121 cDNA (Ad(CU)VEGF121.1), a control marker gene (Ad beta gal, AdLuc) or no transgene (AdNull) were sutured to fascial edges during laparotomy closure in normal mice and mice treated with dexamethasone. Endpoints addressed included transgene expression in the fascia and surrounding tissue, the number of blood vessels in the healing wound determined using immunostaining, and wound bursting strength using a calibrated tensinometer.<br><br>RESULTS: Transgene expression was detected readily in the fascial edges, but only marginally detectable in neighboring tissues. In normal mice and mice treated with dexamethasone, no differences were observed at 7 days. Strikingly, however, 21 days after wound closure/therapy, significantly more blood vessels were present in the wounds that received the VEGF121 vector compared with controls (normal: AdNull: 4.2 +/- 1.8; Ad(CU)VEGF121.1: 11.2 +/- 1.2; P <.05; dexamethasone: AdNull: 1.4 +/- 0.8; Ad(CU)VEGF121.1: 5.4 +/- 1.2; P <.05), and bursting strength was significantly higher in VEGF121-treated wounds (normal: AdNull: 665 +/- 68 mN/mm; Ad(CU)VEGF121.1: 956 +/- 82 mN/mm; P <.0005; dexamethasone: AdNull: 234 +/- 111 mN/mm; Ad(CU)VEGF121.1: 592 +/- 121 mN/mm; P <.03).<br><br>CONCLUSIONS: Adenovirus-mediated gene transfer to healing fascial wounds is achieved readily using a microfibrillar collagen sponge, with transfer of the human VEGF121 cDNA significantly enhancing wound vascularity and bursting strength in normal mice, as well as in mice treated with dexamethasone.}, }
@article {pmid11854504, year = {2002}, author = {de Vries, J and Wackernagel, W}, title = {Integration of foreign DNA during natural transformation of Acinetobacter sp. by homology-facilitated illegitimate recombination.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {99}, number = {4}, pages = {2094-2099}, pmid = {11854504}, issn = {0027-8424}, mesh = {Acinetobacter/*genetics ; Base Sequence ; DNA/genetics/*metabolism ; Models, Genetic ; Molecular Sequence Data ; Nucleic Acid Heteroduplexes ; Plasmids/metabolism ; Recombination, Genetic ; Transformation, Bacterial ; }, abstract = {The active uptake of extracellular DNA and its genomic integration is termed natural transformation and constitutes a major horizontal gene-transfer mechanism in prokaryotes. Chromosomal DNA transferred within a species can be integrated effectively by homologous recombination, whereas foreign DNA with low or no sequence homology would rely on illegitimate recombination events, which are rare. By using the nptII(+) gene (kanamycin resistance) as selectable marker, we found that the integration of foreign DNA into the genome of the Gram-negative Acinetobacter sp. BD413 during transformation indeed was at least 10(9)-fold lower than that of homologous DNA. However, integration of foreign DNA increased at least 10(5)-fold when it was linked on one side to a piece of DNA homologous to the recipient genome. Analysis of foreign DNA integration sites revealed short stretches of sequence identity (3-8 bp) between donor and recipient DNA, indicating illegitimate recombination events. These findings suggest that homologous DNA served as a recombinational anchor facilitating illegitimate recombination acting on the same molecule. Homologous stretches down to 183 nucleotides served as anchors. Transformation with heteroduplex DNA having different nucleotide sequence tags in the strands indicated that strands entered the cytoplasm 3' to 5' and that strands with either polarity were integrated by homologous recombination. The process led to the genomic integration of thousands of foreign nucleotides and often was accompanied by deletion of a roughly corresponding length of recipient DNA. Homology-facilitated illegitimate recombination would explain the introgression of DNA in prokaryotic genomes without the help of mobile genetic elements.}, }
@article {pmid11854253, year = {2002}, author = {Hansen-Wester, I and Stecher, B and Hensel, M}, title = {Analyses of the evolutionary distribution of Salmonella translocated effectors.}, journal = {Infection and immunity}, volume = {70}, number = {3}, pages = {1619-1622}, pmid = {11854253}, issn = {0019-9567}, mesh = {*Bacterial Proteins ; Biological Evolution ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Glycoproteins/genetics ; Salmonella enterica/classification/*genetics/*pathogenicity ; Serotyping ; }, abstract = {The type III secretion system encoded by Salmonella pathogenicity island 2 (SPI2) translocates Salmonella translocated effectors (STE) into host cells. STE are encoded by genes outside of SPI2. The distribution of STE loci within the salmonellae was investigated. In contrast to the SPI2 locus that is conserved within Salmonella enterica, STE loci show a variable distribution. In addition to other virulence determinants, the possession of various sets of STE loci may contribute to the different host ranges and pathogenic potentials of S. enterica serovars.}, }
@article {pmid11847562, year = {2002}, author = {Hooper, SD and Berg, OG}, title = {Detection of genes with atypical nucleotide sequence in microbial genomes.}, journal = {Journal of molecular evolution}, volume = {54}, number = {3}, pages = {365-375}, doi = {10.1007/s00239-001-0051-8}, pmid = {11847562}, issn = {0022-2844}, mesh = {Bacteria/genetics ; Codon/*genetics ; *Genome, Bacterial ; *Genome, Fungal ; Saccharomyces cerevisiae/genetics ; Sequence Analysis, DNA ; }, abstract = {Along the gene, nucleotides in various codon positions tend to exert a slight but observable influence on the nucleotide choice at neighboring positions. Such context biases are different in different organisms and can be used as genomic signatures. In this paper, we will focus specifically on the dinucleotide composed of a third codon position nucleotide and its succeeding first position nucleotide. Using the 16 possible dinucleotide combinations, we calculate how well individual genes conform to the observed mean dinucleotide frequencies of an entire genome, forming a distance measure for each gene. It is found that genes from different genomes can be separated with a high degree of accuracy, according to these distance values. In particular, we address the problem of recent horizontal gene transfer, and how imported genes may be evaluated by their poor assimilation to the host's context biases. By concentrating on the third- and succeeding first position nucleotides, we eliminate most spurious contributions from codon usage and amino-acid requirements, focusing mainly on mutational effects. Since imported genes are expected to converge only gradually to genomic signatures, it is possible to question whether a gene present in only one of two closely related organisms has been imported into one organism or deleted in the other. Striking correlations between the proposed distance measure and poor homology are observed when Escherichia coli genes are compared to Salmonella typhi, indicating that sets of outlier genes in E. coli may contain a high number of genes that have been imported into E. coli, and not deleted in S. typhi.}, }
@article {pmid11846788, year = {2002}, author = {Schnarrenberger, C and Martin, W}, title = {Evolution of the enzymes of the citric acid cycle and the glyoxylate cycle of higher plants. A case study of endosymbiotic gene transfer.}, journal = {European journal of biochemistry}, volume = {269}, number = {3}, pages = {868-883}, doi = {10.1046/j.0014-2956.2001.02722.x}, pmid = {11846788}, issn = {0014-2956}, mesh = {Aconitate Hydratase/physiology ; Citrate (si)-Synthase/physiology ; *Citric Acid Cycle ; Enzymes/*physiology ; *Evolution, Molecular ; Fumarate Hydratase/physiology ; Glyoxylates/*metabolism ; Isocitrate Dehydrogenase/physiology ; Isocitrate Lyase/physiology ; Ketone Oxidoreductases/physiology ; Malate Dehydrogenase/physiology ; Malate Synthase/physiology ; Phylogeny ; Plants/*metabolism ; Succinate Dehydrogenase/physiology ; }, abstract = {The citric acid or tricarboxylic acid cycle is a central element of higher-plant carbon metabolism which provides, among other things, electrons for oxidative phosphorylation in the inner mitochondrial membrane, intermediates for amino-acid biosynthesis, and oxaloacetate for gluconeogenesis from succinate derived from fatty acids via the glyoxylate cycle in glyoxysomes. The tricarboxylic acid cycle is a typical mitochondrial pathway and is widespread among alpha-proteobacteria, the group of eubacteria as defined under rRNA systematics from which mitochondria arose. Most of the enzymes of the tricarboxylic acid cycle are encoded in the nucleus in higher eukaryotes, and several have been previously shown to branch with their homologues from alpha-proteobacteria, indicating that the eukaryotic nuclear genes were acquired from the mitochondrial genome during the course of evolution. Here, we investigate the individual evolutionary histories of all of the enzymes of the tricarboxylic acid cycle and the glyoxylate cycle using protein maximum likelihood phylogenies, focusing on the evolutionary origin of the nuclear-encoded proteins in higher plants. The results indicate that about half of the proteins involved in this eukaryotic pathway are most similar to their alpha-proteobacterial homologues, whereas the remainder are most similar to eubacterial, but not specifically alpha-proteobacterial, homologues. A consideration of (a) the process of lateral gene transfer among free-living prokaryotes and (b) the mechanistics of endosymbiotic (symbiont-to-host) gene transfer reveals that it is unrealistic to expect all nuclear genes that were acquired from the alpha-proteobacterial ancestor of mitochondria to branch specifically with their homologues encoded in the genomes of contemporary alpha-proteobacteria. Rather, even if molecular phylogenetics were to work perfectly (which it does not), then some nuclear-encoded proteins that were acquired from the alpha-proteobacterial ancestor of mitochondria should, in phylogenetic trees, branch with homologues that are no longer found in most alpha-proteobacterial genomes, and some should reside on long branches that reveal affinity to eubacterial rather than archaebacterial homologues, but no particular affinity for any specific eubacterial donor.}, }
@article {pmid11844763, year = {2002}, author = {Noël, L and Thieme, F and Nennstiel, D and Bonas, U}, title = {Two novel type III-secreted proteins of Xanthomonas campestris pv. vesicatoria are encoded within the hrp pathogenicity island.}, journal = {Journal of bacteriology}, volume = {184}, number = {5}, pages = {1340-1348}, pmid = {11844763}, issn = {0021-9193}, mesh = {Bacterial Proteins/*genetics/*metabolism ; Capsicum/*microbiology ; Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Molecular Sequence Data ; Multigene Family ; Plant Diseases/*microbiology ; Plant Leaves/microbiology ; *Transcription Factors ; Virulence/genetics ; Xanthomonas campestris/genetics/metabolism/*pathogenicity ; }, abstract = {The Hrp type III protein secretion system (TTSS) is essential for pathogenicity of gram-negative plant pathogen Xanthomonas campestris pv. vesicatoria. cDNA-amplified fragment length polymorphism and reverse transcription-PCR analyses identified new genes, regulated by key hrp regulator HrpG, in the regions flanking the hrp gene cluster. Sequence analysis revealed genes encoding HpaG, a predicted leucine-rich repeat-containing protein, the lysozyme-like HpaH protein, and XopA and XopD, which are similar in sequence to Hpa1 from Xanthomonas oryzae pv. oryzae and PsvA from Pseudomonas syringae, respectively. XopA and XopD (Xanthomonas outer proteins) are secreted by the Xanthomonas Hrp TTSS and thus represent putative effector proteins. Mutations in xopA, but not in xopD, resulted in reduced bacterial growth in planta and delayed plant reactions in susceptible and resistant host plants. Since the xopD promoter contains a putative hrp box, which is characteristic of hrpL-regulated genes in P. syringae and Erwinia spp., the gene was probably acquired by horizontal gene transfer. Interestingly, the regions flanking the hrp gene cluster also contain insertion sequences and genes for a putative transposase and a tRNA(Arg). These features suggest that the hrp gene cluster of X. campestris pv. vesicatoria is part of a pathogenicity island.}, }
@article {pmid11839630, year = {2002}, author = {Iwaguro, H and Yamaguchi, J and Kalka, C and Murasawa, S and Masuda, H and Hayashi, S and Silver, M and Li, T and Isner, JM and Asahara, T}, title = {Endothelial progenitor cell vascular endothelial growth factor gene transfer for vascular regeneration.}, journal = {Circulation}, volume = {105}, number = {6}, pages = {732-738}, doi = {10.1161/hc0602.103673}, pmid = {11839630}, issn = {1524-4539}, mesh = {Adenoviridae/genetics ; Animals ; Cell Count ; Cell Division/drug effects/physiology ; Cells, Cultured ; Dendritic Cells ; Disease Models, Animal ; Endothelial Growth Factors/genetics/metabolism/*pharmacology ; Endothelium, Vascular/*drug effects/metabolism/pathology ; Female ; Gene Transfer, Horizontal ; Genetic Therapy/*methods ; Genetic Vectors/genetics/metabolism/pharmacology ; Humans ; Ischemia/*drug therapy/pathology/physiopathology ; Lymphokines/genetics/metabolism/*pharmacology ; Mice ; Mice, Nude ; Microcirculation/drug effects/metabolism/pathology ; Muscle, Skeletal/blood supply/metabolism/pathology ; Neovascularization, Physiologic/drug effects ; Regeneration/*drug effects ; Stem Cell Transplantation ; Stem Cells/cytology/drug effects/*metabolism ; Transgenes ; Treatment Outcome ; Vascular Endothelial Growth Factor A ; Vascular Endothelial Growth Factors ; }, abstract = {BACKGROUND: Previous studies have established that bone marrow-derived endothelial progenitor cells (EPCs) are present in the systemic circulation. In the current study, we investigated the hypothesis that gene transfer can be used to achieve phenotypic modulation of EPCs.<br><br>METHODS AND RESULTS: In vitro, ex vivo murine vascular endothelial growth factor (VEGF) 164 gene transfer augmented EPC proliferative activity and enhanced adhesion and incorporation of EPCs into quiescent as well as activated endothelial cell monolayers. To determine if such phenotypic modulation may facilitate therapeutic neovascularization, heterologous EPCs transduced with adenovirus encoding VEGF were administered to athymic nude mice with hindlimb ischemia; neovascularization and blood flow recovery were both improved, and limb necrosis/autoamputation were reduced by 63.7% in comparison with control animals. The dose of EPCs used for the in vivo experiments was 30 times less than that required in previous trials of EPC transplantation to improve ischemic limb salvage. Necropsy analysis of animals that received DiI-labeled VEGF-transduced EPCs confirmed that enhanced EPC incorporation demonstrated in vitro contributed to in vivo neovascularization as well.<br><br>CONCLUSIONS: In vitro, VEGF EPC gene transfer enhances EPC proliferation, adhesion, and incorporation into endothelial cell monolayers. In vivo, gene-modified EPCs facilitate the strategy of cell transplantation to augment naturally impaired neovascularization in an animal model of experimentally induced limb ischemia.}, }
@article {pmid11839180, year = {2002}, author = {Roos, DS and Crawford, MJ and Donald, RG and Fraunholz, M and Harb, OS and He, CY and Kissinger, JC and Shaw, MK and Striepen, B}, title = {Mining the Plasmodium genome database to define organellar function: what does the apicoplast do?.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {357}, number = {1417}, pages = {35-46}, pmid = {11839180}, issn = {0962-8436}, mesh = {Animals ; Cell Compartmentation ; Computational Biology/methods ; DNA, Protozoan/genetics ; *Databases, Genetic ; Endocytosis ; Eukaryota/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Protozoan/genetics ; *Genome, Protozoan ; Organelles/*physiology ; Phylogeny ; Plasmodium falciparum/*cytology/*genetics/physiology ; Protozoan Proteins/genetics/metabolism ; Symbiosis ; }, abstract = {Apicomplexan species constitute a diverse group of parasitic protozoa, which are responsible for a wide range of diseases in many organisms. Despite differences in the diseases they cause, these parasites share an underlying biology, from the genetic controls used to differentiate through the complex parasite life cycle, to the basic biochemical pathways employed for intracellular survival, to the distinctive cell biology necessary for host cell attachment and invasion. Different parasites lend themselves to the study of different aspects of parasite biology: Eimeria for biochemical studies, Toxoplasma for molecular genetic and cell biological investigation, etc. The Plasmodium falciparum Genome Project contributes the first large-scale genomic sequence for an apicomplexan parasite. The Plasmodium Genome Database (http://PlasmoDB.org) has been designed to permit individual investigators to ask their own questions, even prior to formal release of the reference P. falciparum genome sequence. As a case in point, PlasmoDB has been exploited to identify metabolic pathways associated with the apicomplexan plastid, or 'apicoplast' - an essential organelle derived by secondary endosymbiosis of an alga, and retention of the algal plastid.}, }
@article {pmid11837318, year = {2002}, author = {Cavalier-Smith, T}, title = {The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {52}, number = {Pt 1}, pages = {7-76}, doi = {10.1099/00207713-52-1-7}, pmid = {11837318}, issn = {1466-5026}, mesh = {Archaea/*classification/*genetics ; Bacteria/*classification/*genetics ; *Biological Evolution ; Eukaryotic Cells ; *Phylogeny ; }, abstract = {Prokaryotes constitute a single kingdom, Bacteria, here divided into two new subkingdoms: Negibacteria, with a cell envelope of two distinct genetic membranes, and Unibacteria, comprising the new phyla Archaebacteria and Posibacteria, with only one. Other new bacterial taxa are established in a revised higher-level classification that recognizes only eight phyla and 29 classes. Morphological, palaeontological and molecular data are integrated into a unified picture of large-scale bacterial cell evolution despite occasional lateral gene transfers. Archaebacteria and eukaryotes comprise the clade neomura, with many common characters, notably obligately co-translational secretion of N-linked glycoproteins, signal recognition particle with 7S RNA and translation-arrest domain, protein-spliced tRNA introns, eight-subunit chaperonin, prefoldin, core histones, small nucleolar ribonucleoproteins (snoRNPs), exosomes and similar replication, repair, transcription and translation machinery. Eubacteria (posibacteria and negibacteria) are paraphyletic, neomura having arisen from Posibacteria within the new subphylum Actinobacteria (possibly from the new class Arabobacteria, from which eukaryotic cholesterol biosynthesis probably came). Replacement of eubacterial peptidoglycan by glycoproteins and adaptation to thermophily are the keys to neomuran origins. All 19 common neomuran character suites probably arose essentially simultaneously during the radical modification of an actinobacterium. At least 11 were arguably adaptations to thermophily. Most unique archaebacterial characters (prenyl ether lipids; flagellar shaft of glycoprotein, not flagellin; DNA-binding protein lob; specially modified tRNA; absence of Hsp90) were subsequent secondary adaptations to hyperthermophily and/or hyperacidity. The insertional origin of protein-spliced tRNA introns and an insertion in proton-pumping ATPase also support the origin of neomura from eubacteria. Molecular co-evolution between histones and DNA-handling proteins, and in novel protein initiation and secretion machineries, caused quantum evolutionary shifts in their properties in stem neomura. Proteasomes probably arose in the immediate common ancestor of neomura and Actinobacteria. Major gene losses (e.g. peptidoglycan synthesis, hsp90, secA) and genomic reduction were central to the origin of archaebacteria. Ancestral archaebacteria were probably heterotrophic, anaerobic, sulphur-dependent hyperthermoacidophiles; methanogenesis and halophily are secondarily derived. Multiple lateral gene transfers from eubacteria helped secondary archaebacterial adaptations to mesophily and genome re-expansion. The origin from a drastically altered actinobacterium of neomura, and the immediately subsequent simultaneous origins of archaebacteria and eukaryotes, are the most extreme and important cases of quantum evolution since cells began. All three strikingly exemplify De Beer's principle of mosaic evolution: the fact that, during major evolutionary transformations, some organismal characters are highly innovative and change remarkably swiftly, whereas others are largely static, remaining conservatively ancestral in nature. This phenotypic mosaicism creates character distributions among taxa that are puzzling to those mistakenly expecting uniform evolutionary rates among characters and lineages. The mixture of novel (neomuran or archaebacterial) and ancestral eubacteria-like characters in archaebacteria primarily reflects such vertical mosaic evolution, not chimaeric evolution by lateral gene transfer. No symbiogenesis occurred. Quantum evolution of the basic neomuran characters, and between sister paralogues in gene duplication trees, makes many sequence trees exaggerate greatly the apparent age of archaebacteria. Fossil evidence is compelling for the extreme antiquity of eubacteria [over 3500 million years (My)] but, like their eukaryote sisters, archaebacteria probably arose only 850 My ago. Negibacteria are the most ancient, radiating rapidly into six phyla. Evidence from molecular sequences, ultrastructure, evolution of photosynthesis, envelope structure and chemistry and motility mechanisms fits the view that the cenancestral cell was a photosynthetic negibacterium, specifically an anaerobic green non-sulphur bacterium, and that the universal tree is rooted at the divergence between sulphur and non-sulphur green bacteria. The negibacterial outer membrane was lost once only in the history of life, when Posibacteria arose about 2800 My ago after their ancestors diverged from Cyanobacteria.}, }
@article {pmid11834712, year = {2002}, author = {Liao, P and Wang, SQ and Wang, S and Zheng, M and Zheng, M and Zhang, SJ and Cheng, H and Wang, Y and Xiao, RP}, title = {p38 Mitogen-activated protein kinase mediates a negative inotropic effect in cardiac myocytes.}, journal = {Circulation research}, volume = {90}, number = {2}, pages = {190-196}, pmid = {11834712}, issn = {1524-4571}, support = {R01 HL062311/HL/NHLBI NIH HHS/United States ; }, mesh = {Actin Cytoskeleton/metabolism ; Adenoviridae/genetics ; Animals ; Calcium Channels, L-Type/metabolism ; Calcium Signaling/drug effects/physiology ; Cells, Cultured ; Enzyme Activation/drug effects/physiology ; Enzyme Inhibitors/pharmacology ; Gene Transfer, Horizontal ; Genetic Vectors/genetics/metabolism ; Hydrogen-Ion Concentration ; Intracellular Fluid/metabolism ; Mitogen-Activated Protein Kinases/antagonists &amp; inhibitors/genetics/*metabolism ; Mutagenesis, Site-Directed ; Myocardial Contraction/drug effects/*physiology ; Myocardium/cytology/*enzymology ; Patch-Clamp Techniques ; Phosphorylation ; Rats ; Rats, Sprague-Dawley ; Signal Transduction/physiology ; Troponin I/genetics/metabolism ; p38 Mitogen-Activated Protein Kinases ; }, abstract = {p38 Mitogen-activated protein kinase (MAPK) is one of the most ancient signaling molecules and is involved in multiple cellular processes, including cell proliferation, cell growth, and cell death. In the heart, enhanced activation of p38 MAPK is associated with ischemia/reperfusion injury and the onset of heart failure. In the present study, we investigated the function of p38 MAPK in regulating cardiac contractility and its underlying mechanisms. In cultured adult rat cardiomyocytes, activation of p38 MAPK by adenoviral gene transfer of an activated mutant of its upstream kinase, MKK3bE, led to a significant reduction in baseline contractility, compared with uninfected cells or those infected with a control adenoviral vector (Adv-beta-galactosidase). The inhibitory effect of MKK3bE on contractility was largely prevented by coexpressing a dominant-negative mutant of p38 MAPK or treating cells with a p38 MAPK inhibitor, SB203580. Conversely, inhibition of endogenous p38 MAPK activity by SB203580 rapidly and reversibly enhanced cell contractility in a dose-dependent manner, without altering L-type Ca(2+) currents or Ca(2+)(i) transients. MKK3bE-induced p38 activation had no significant effect on pH(i), whereas SB203580 had a minor effect to elevate pH(i). Furthermore, activation of p38 MAPK was unable to increase troponin I phosphorylation. Thus, we conclude that the negative inotropic effect of p38 MAPK is mediated by decreasing myofilament response to Ca(2+), rather than by altering Ca(2+)(i) homeostasis and that the reduced myofilament Ca(2+) sensitivity is unlikely attributable to troponin I phosphorylation or alterations in pH(i). These findings reveal a novel function of p38 MAPK and shed a new light on our understanding of the coincidence of p38 MAPK activation and the onset of heart failure.}, }
@article {pmid11833771, year = {2001}, author = {Ziemienowicz, A}, title = {Odyssey of agrobacterium T-DNA.}, journal = {Acta biochimica Polonica}, volume = {48}, number = {3}, pages = {623-635}, pmid = {11833771}, issn = {0001-527X}, mesh = {Cell Nucleus/metabolism ; Chemotaxis ; DNA, Bacterial/*genetics/*metabolism ; Gene Expression Regulation, Plant ; Gene Transfer, Horizontal/genetics ; Plants/*microbiology ; Recombination, Genetic ; Rhizobium/*genetics ; Virulence ; }, abstract = {Agrobacterium tumefaciens, a plant pathogen, is characterized by the unique feature of interkingdom DNA transfer. This soil bacterium is able to transfer a fragment of its DNA, called T-DNA (transferred DNA), to the plant cell where T-DNA is integrated into the plant genome leading to "genetic colonization" of the host. The fate of T-DNA, its processing, transfer and integration, resembles the journey of Odysseus, although our hero returns from its long trip in a slightly modified form.}, }
@article {pmid11830255, year = {2002}, author = {Brain, SD and Poyner, DR and Hill, RG}, title = {CGRP receptors: a headache to study, but will antagonists prove therapeutic in migraine?.}, journal = {Trends in pharmacological sciences}, volume = {23}, number = {2}, pages = {51-53}, doi = {10.1016/s0165-6147(02)01945-4}, pmid = {11830255}, issn = {0165-6147}, mesh = {Animals ; Calcitonin Gene-Related Peptide/pharmacology/physiology ; *Calcitonin Gene-Related Peptide Receptor Antagonists ; Gene Transfer, Horizontal/physiology ; Humans ; Intracellular Signaling Peptides and Proteins ; Membrane Proteins/physiology ; Mice ; Mice, Knockout ; Migraine Disorders/*drug therapy ; Piperazines/pharmacology/therapeutic use ; Quinazolines/pharmacology/therapeutic use ; Rabbits ; Receptor Activity-Modifying Proteins ; Receptors, Calcitonin Gene-Related Peptide/chemistry/physiology ; Species Specificity ; Substance Withdrawal Syndrome/drug therapy ; }, }
@article {pmid11829460, year = {2002}, author = {Iwai, M and Harada, Y and Tanaka, S and Muramatsu, A and Mori, T and Kashima, K and Imanishi, J and Mazda, O}, title = {Polyethylenimine-mediated suicide gene transfer induces a therapeutic effect for hepatocellular carcinoma in vivo by using an Epstein-Barr virus-based plasmid vector.}, journal = {Biochemical and biophysical research communications}, volume = {291}, number = {1}, pages = {48-54}, doi = {10.1006/bbrc.2002.6383}, pmid = {11829460}, issn = {0006-291X}, mesh = {Animals ; Antineoplastic Combined Chemotherapy Protocols/*administration &amp; dosage ; Ganciclovir/administration &amp; dosage ; Gene Transfer, Horizontal ; Genetic Therapy/*methods ; Genetic Vectors/administration &amp; dosage/chemistry/metabolism ; Herpesvirus 1, Human/enzymology/genetics ; Herpesvirus 4, Human/*genetics ; Humans ; Liver Neoplasms, Experimental/*genetics/pathology/*therapy ; Mice ; Mice, SCID ; Neoplasm Transplantation ; Polyethyleneimine/administration &amp; dosage/chemistry ; Survival Rate ; Thymidine Kinase/administration &amp; dosage/biosynthesis/genetics ; Transfection ; Treatment Outcome ; Tumor Cells, Cultured ; Xenograft Model Antitumor Assays ; }, abstract = {The present study aimed to establish a novel efficient nonviral strategy for suicide gene transfer in hepatocellular carcinoma (HCC) in vivo. We employed branched polyethylenimine (PEI) and combined it with Epstein-Barr virus (EBV)-based plasmid vectors. The HCC cells transfected with an EBV-based plasmid carrying the herpes simplex virus-1 thymidine kinase (HSV-1 Tk) gene (pSES.Tk) showed up to 30-fold higher susceptibilities to ganciclovir (GCV) than those transfected with a conventional plasmid vector carrying the HSV-1 Tk gene (pS.Tk). The therapeutic effect in vivo was tested by intratumoral injection of the plasmids into HuH-7 hepatomas transplanted into C.B-17 scid/scid mutant (SCID) mice and subsequent GCV administrations. Treatment with pSES.Tk, but not pS.Tk, markedly suppressed growth of hepatomas in vivo, resulting in a significantly prolonged survival period of the mice. These findings suggest that PEI-mediated gene transfer system can confer efficient expression of the suicide gene in HCC cells in vivo by using EBV-based plasmid vectors.}, }
@article {pmid11827811, year = {2002}, author = {Edwards, RA and Olsen, GJ and Maloy, SR}, title = {Comparative genomics of closely related salmonellae.}, journal = {Trends in microbiology}, volume = {10}, number = {2}, pages = {94-99}, doi = {10.1016/s0966-842x(01)02293-4}, pmid = {11827811}, issn = {0966-842X}, mesh = {Antigenic Variation ; *Genome, Bacterial ; Plasmids ; Salmonella/*genetics/immunology/pathogenicity ; Sequence Homology ; Virulence ; }, abstract = {As the number of completed genome sequences increases, there is increasing emphasis on comparative genomic analysis of closely related organisms. Comparison of the similarities and differences between the five publicly available Salmonella genome sequences reveals extensive sequence conservation among the Salmonella serovars. However, horizontal gene transfer has provided each genome with between 10% and 12% of unique DNA. Genome comparisons of the closely related salmonellae emphasize the insights that can be gleaned from sequencing genomes of a single species.}, }
@article {pmid11825713, year = {2001}, author = {Lawrence, JG and Hendrix, RW and Casjens, S}, title = {Where are the pseudogenes in bacterial genomes?.}, journal = {Trends in microbiology}, volume = {9}, number = {11}, pages = {535-540}, doi = {10.1016/s0966-842x(01)02198-9}, pmid = {11825713}, issn = {0966-842X}, support = {GM47795/GM/NIGMS NIH HHS/United States ; GM51975/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteriophages/genetics ; Chromosomes, Bacterial ; DNA Transposable Elements ; Gene Deletion ; Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; Lysogeny ; Models, Genetic ; Pseudogenes/*genetics ; }, abstract = {Most bacterial genomes have very few pseudogenes; notable exceptions include the genomes of the intracellular parasites Rickettsia prowazekii and Mycobacterium leprae. As DNA can be introduced into microbial genomes in many ways, the compact nature of these genomes suggests that the rate of DNA influx is balanced by the rate of DNA deletion. We propose that the influx of dangerous genetic elements such as transposons and bacteriophages selects for the maintenance of relatively high deletion rates in most bacteria; the sheltered lifestyle of intracellular parasites removes this threat, leading to reduced deletion rates and larger pseudogene loads.}, }
@article {pmid11823852, year = {2002}, author = {Salanoubat, M and Genin, S and Artiguenave, F and Gouzy, J and Mangenot, S and Arlat, M and Billault, A and Brottier, P and Camus, JC and Cattolico, L and Chandler, M and Choisne, N and Claudel-Renard, C and Cunnac, S and Demange, N and Gaspin, C and Lavie, M and Moisan, A and Robert, C and Saurin, W and Schiex, T and Siguier, P and Thébault, P and Whalen, M and Wincker, P and Levy, M and Weissenbach, J and Boucher, CA}, title = {Genome sequence of the plant pathogen Ralstonia solanacearum.}, journal = {Nature}, volume = {415}, number = {6871}, pages = {497-502}, doi = {10.1038/415497a}, pmid = {11823852}, issn = {0028-0836}, mesh = {Bacterial Proteins/metabolism ; Biological Evolution ; Genome, Bacterial ; Genomics ; Gram-Negative Aerobic Rods and Cocci/*genetics/pathogenicity ; Solanum lycopersicum/virology ; Molecular Sequence Data ; Sequence Analysis, DNA ; Virulence/genetics ; }, abstract = {Ralstonia solanacearum is a devastating, soil-borne plant pathogen with a global distribution and an unusually wide host range. It is a model system for the dissection of molecular determinants governing pathogenicity. We present here the complete genome sequence and its analysis of strain GMI1000. The 5.8-megabase (Mb) genome is organized into two replicons: a 3.7-Mb chromosome and a 2.1-Mb megaplasmid. Both replicons have a mosaic structure providing evidence for the acquisition of genes through horizontal gene transfer. Regions containing genetically mobile elements associated with the percentage of G+C bias may have an important function in genome evolution. The genome encodes many proteins potentially associated with a role in pathogenicity. In particular, many putative attachment factors were identified. The complete repertoire of type III secreted effector proteins can be studied. Over 40 candidates were identified. Comparison with other genomes suggests that bacterial plant pathogens and animal pathogens harbour distinct arrays of specialized type III-dependent effectors.}, }
@article {pmid11823214, year = {2002}, author = {Bukhalid, RA and Takeuchi, T and Labeda, D and Loria, R}, title = {Horizontal transfer of the plant virulence gene, nec1, and flanking sequences among genetically distinct Streptomyces strains in the Diastatochromogenes cluster.}, journal = {Applied and environmental microbiology}, volume = {68}, number = {2}, pages = {738-744}, pmid = {11823214}, issn = {0099-2240}, mesh = {Arachis/microbiology ; Bacterial Proteins/*genetics ; Base Sequence ; DNA, Ribosomal/analysis ; *Gene Transfer, Horizontal ; Indoles/metabolism ; Molecular Sequence Data ; Phenotype ; Phylogeny ; Piperazines/metabolism ; Plant Diseases/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Solanum tuberosum/microbiology ; Streptomyces/classification/*genetics/*pathogenicity ; Virulence ; }, abstract = {Evidence for the horizontal transfer of a pathogenicity island (PAI) carrying the virulence gene nec1 and flanking sequences among Streptomyces strains in the Diastatochromogenes cluster is presented. Plant-pathogenic, thaxtomin-producing Streptomyces strains, previously classified as S. scabiei based on the conventionally used phenotypic characteristics, were found to be genetically distinct from the type strain of S. scabiei based on DNA relatedness and 16S rDNA sequence analysis. Pairwise DNA-DNA hybridizations between some of these strains and the S. scabiei type strain were as low as 36%, a value much below what is conventionally accepted for species identity (70%). The sequence of the nec1 gene, however, was identical in all the S. scabiei and S. scabiei-like strains tested, irrespective of their DNA relatedness to the type strain of S. scabiei, their geographic origin, or the isolation host. Furthermore, a 26-kb DNA fragment including and flanking nec1 was also conserved among these strains based on restriction and Southern analyses. These data indicate that the etiology of potato scab is more complex than previously recognized; this result has important implications for potato scab management strategies. Previous research has suggested that horizontal transfer of a PAI was the mechanism for evolution of pathogenicity in S. acidiscabies and S. turgidiscabies, species that lie outside of the Diastatochromogenes cluster. Data presented here support this model and indicate that PAI transfer also has occurred frequently in species closely related to S. scabiei.}, }
@article {pmid11821918, year = {2002}, author = {Syvanen, M}, title = {On the occurrence of horizontal gene transfer among an arbitrarily chosen group of 26 genes.}, journal = {Journal of molecular evolution}, volume = {54}, number = {2}, pages = {258-266}, doi = {10.1007/s0023901-0007-z}, pmid = {11821918}, issn = {1432-1432}, mesh = {Acetyltransferases/genetics ; Archaea/enzymology/*genetics ; Aspartate Carbamoyltransferase/genetics ; Bacteria/enzymology/*genetics ; *Gene Transfer, Horizontal ; Ornithine Carbamoyltransferase/genetics ; Phylogeny ; Sequence Homology, Amino Acid ; Tryptophan Synthase/genetics ; Yeasts/enzymology/*genetics ; }, abstract = {The deduced amino acid sequences from 1200 Haemophilus influenzae genes was compared to a data set that contained the orfs from yeast, two different Archaea and the Gram+ and Gramminus sign bacteria, Bacillus subtilis and Escherichia coli. The results of the comparison yielded a 26 orthologous gene set that had at least one representative from each of the four groups. A four taxa phylogenetic relationship for these 26 genes was determined. The statistical significance of each minimal tree was tested against the two alternative four taxa trees. The result was that four genes significantly supported the (Archaea, Eukaryota) (Gram+, Gramminus sign) topology, two genes supported the one where Gramminus sign and Eukaryota form a clade, and one gene supported the tree where Gram+ and Eukaryota define one clade. The remaining genes do not uniquely support any phylogeny, thereby collapsing the two central nodes into a single node. These are referred to as star phylogenies. I offer a new suggestion for the mechanism that gave rise to the star phylogenies. Namely, these are genes that are younger than the underlying lineages that currently harbor them. This hypothesis is examined with two proteins that display the star phylogeny; namely onithine transcarbamylase and tryptophan synthetase. It is shown, using the distance matrix rate test, that the rate of evolution of these two proteins is comparable to a control gene when rates are determined by comparing closely related species. This implies that the genes under comparison experience comparable functional constraint. However, when the genes from remotely related species are compared, a plateau is encountered. Since we see no unusual levels of functional constraint this plateau cannot be attributed to the divergence of the protein having reached saturation. The simplest explanation is that the genes displaying the star phylogenies were introduced after Archaea, Eukaryota, and Bacteria had diverged from one another. They presumably spread through life by horizontal gene transfer.}, }
@article {pmid11821856, year = {2002}, author = {Zupan, J and Ward, D and Zambryski, P}, title = {Inter-kingdom DNA transfer decoded.}, journal = {Nature biotechnology}, volume = {20}, number = {2}, pages = {129-131}, doi = {10.1038/nbt0202-129}, pmid = {11821856}, issn = {1087-0156}, mesh = {Agrobacterium tumefaciens/*genetics ; Cell Nucleus/metabolism ; DNA/*chemistry ; *Gene Transfer, Horizontal ; Genetic Engineering ; *Genome, Plant ; Models, Biological ; }, }
@article {pmid11818061, year = {2002}, author = {Andersson, JO and Roger, AJ}, title = {A cyanobacterial gene in nonphotosynthetic protists--an early chloroplast acquisition in eukaryotes?.}, journal = {Current biology : CB}, volume = {12}, number = {2}, pages = {115-119}, doi = {10.1016/s0960-9822(01)00649-2}, pmid = {11818061}, issn = {0960-9822}, mesh = {Arabidopsis/classification/genetics ; Chloroplasts/*metabolism ; Cyanobacteria/classification/*genetics ; *Genes, Bacterial ; Molecular Sequence Data ; Photosynthesis ; Phylogeny ; }, abstract = {Since the incorporation of mitochondria and chloroplasts (plastids) into the eukaryotic cell by endosymbiosis, genes have been transferred from the organellar genomes to the nucleus of the host, via an ongoing process known as endosymbiotic gene transfer. Accordingly, in photosynthetic eukaryotes, nuclear genes with cyanobacterial affinity are believed to have originated from endosymbiotic gene transfer from chloroplasts. Analysis of the Arabidopsis thaliana genome has shown that a significant fraction (2%-9%) of the nuclear genes have such an endosymbiotic origin. Recently, it was argued that 6-phosphogluconate dehydrogenase (gnd)-the second enzyme in the oxidative pentose phosphate pathway-was one such example. Here we show that gnd genes with cyanobacterial affinity also are present in several nonphotosynthetic protistan lineages, such as Heterolobosea, Apicomplexa, and parasitic Heterokonta. Current data cannot definitively resolve whether these groups acquired the gnd gene by primary and/or secondary endosymbiosis or via an independent lateral gene transfer event. Nevertheless, our data suggest that chloroplasts were introduced into eukaryotes much earlier than previously thought and that several major groups of heterotrophic eukaryotes have secondarily lost photosynthetic plastids.}, }
@article {pmid11815305, year = {2002}, author = {Yu, H and Head, NE}, title = {Persistent infections and immunity in cystic fibrosis.}, journal = {Frontiers in bioscience : a journal and virtual library}, volume = {7}, number = {}, pages = {d442-57}, doi = {10.2741/a787}, pmid = {11815305}, issn = {1093-9946}, mesh = {Animals ; Biofilms/growth &amp; development ; Chronic Disease ; Cystic Fibrosis/*complications ; Disease Models, Animal ; Genetic Variation ; Genome, Bacterial ; Glycosaminoglycans/biosynthesis ; Humans ; Lung/microbiology ; Mice ; Models, Biological ; Phenotype ; Pseudomonas Infections/complications/*immunology/*microbiology ; Pseudomonas aeruginosa/genetics/physiology/ultrastructure ; }, abstract = {Cystic fibrosis (CF) is the most common autosomal recessive lethal disease in the Caucasian population. Chronic respiratory infections with Pseudomonas aeruginosa, neutrophil-dominated airway inflammation and progressive lung damage are the major causes of morbidity and mortality in CF. Two persistent infection phenotypes expressed by this bacterium are biofilm and mucoidy. Biofilm, also called the microcolony mode of growth is the surface-associated adherent bacterial community, while mucoidy refers to a phenotype conducive to copious amounts of mucoid exopolysaccharide (MEP)/alginate that provides a matrix for mature biofilms conferring resistance to host defenses and antibiotics. Recent completion of the whole genomic sequence of the standard reference strain P. aeruginosa PAO1 has led to discoveries that many clinical isolates of this species possess unique genomic sequences (genomic islands) due to horizontal gene transfer. We propose this type of genetic exchange may play an important role in causing intrinsic genomic diversity of this organism. Therefore, the diversity, as revealed through profiles of restriction fragment length polymorphism (RFLP), may be linked to an array of novel and unexplored pathogenic mechanisms in P. aeruginosa. CF mouse models, while displaying many clinical similarities to human CF, have yet to demonstrate a chronic pulmonary disease phenotype. This review is intended to provide an overview of P. aeruginosa persistent infection phenotypes (biofilm and mucoidy) and an aerosol infection mouse model for CF. Genomic diversity of P. aeruginosa and its implications in the pathogenesis in CF will also be discussed.}, }
@article {pmid11809246, year = {2002}, author = {Gillespie, SH}, title = {Microbes sans frontières.}, journal = {Lancet (London, England)}, volume = {359}, number = {9301}, pages = {93-95}, doi = {10.1016/S0140-6736(02)07333-6}, pmid = {11809246}, issn = {0140-6736}, mesh = {Comorbidity ; DNA, Bacterial/genetics/physiology ; Disease Susceptibility ; F Factor/genetics ; Free Radical Scavengers ; Gene Rearrangement/genetics ; Gene Transfer, Horizontal/genetics ; Humans ; *RNA-Binding Proteins ; Recombination, Genetic/genetics ; Serotyping ; Streptococcal Infections/*complications/epidemiology/immunology/*microbiology ; Streptococcus/*classification/*pathogenicity ; Ubiquitin-Protein Ligases ; }, }
@article {pmid11807296, year = {2001}, author = {Velkov, VV}, title = {Stress-induced evolution and the biosafety of genetically modified microorganisms released into the environment.}, journal = {Journal of biosciences}, volume = {26}, number = {5}, pages = {667-683}, pmid = {11807296}, issn = {0250-5991}, mesh = {Adaptation, Physiological ; *Biological Evolution ; Gene Transfer, Horizontal ; *Microbiology ; Mutagenesis ; Mutation ; Organisms, Genetically Modified/*genetics/growth &amp; development/physiology ; Plasmids ; }, abstract = {This article is focused on the problems of reduction of the risk associated with the deliberate release of genetically modified microorganisms (GMMs) into the environment. Special attention is given to overview the most probable physiological and genetic processes which could be induced in the released GMMs by adverse environmental conditions, namely: (i) activation of quorum sensing and the functions associated with it, (ii) entering into a state of general resistance, (iii) activation of adaptive mutagenesis, adaptive amplifications and transpositions and (iv) stimulation of inter-species gene transfer. To reduce the risks associated with GMMs, the inactivation of their key genes responsible for stress-stimulated increase of viability and evolvability is proposed.}, }
@article {pmid11791234, year = {2001}, author = {Daubin, V and Gouy, M and Perrière, G}, title = {Bacterial molecular phylogeny using supertree approach.}, journal = {Genome informatics. International Conference on Genome Informatics}, volume = {12}, number = {}, pages = {155-164}, pmid = {11791234}, issn = {0919-9454}, mesh = {Bacteria/*classification/*genetics ; Computational Biology ; Gene Transfer, Horizontal ; Genome, Bacterial ; Genomics/statistics &amp; numerical data ; Models, Genetic ; *Phylogeny ; }, abstract = {It has been claimed that complete genome sequences would clarify phylogenetic relationships between organisms but, up to now, no satisfying approach has been proposed to use efficiently these data. For instance, if the coding of presence or absence of genes in complete genomes gives interesting results, it does not take into account the phylogenetic information contained in sequences and ignores hidden paralogy by using a similarity-based definition of orthology. Also, concatenation of sequences of different genes takes hardly in consideration the specific evolutionary rate of each gene. At last, building a consensus tree is strongly limited by the low number of genes shared among all organisms. Here, we use a new method based on supertree construction, which permits to cumulate in one supertree the information and statistical support of hundreds of trees from orthologous gene families and to build the phylogeny of 33 prokaryotes and four eukaryotes with completely sequenced genomes. This approach gives a robust supertree, which demonstrates that a phylogeny of prokaryotic species is conceivable and challenges the hypothesis of a thermophilic origin of bacteria and present-day life. The results are compatible with the hypothesis of a core of genes for which lateral transfers are rare but they raise doubts on the widely admitted "complexity hypothesis" which predicts that this core is mainly implicated in informational processes.}, }
@article {pmid11790735, year = {2002}, author = {Rudi, K and Fossheim, T and Jakobsen, KS}, title = {Nested evolution of a tRNA(Leu)(UAA) group I intron by both horizontal intron transfer and recombination of the entire tRNA locus.}, journal = {Journal of bacteriology}, volume = {184}, number = {3}, pages = {666-671}, pmid = {11790735}, issn = {0021-9193}, mesh = {Base Sequence ; Codon ; Cyanobacteria/*genetics ; *Evolution, Molecular ; Exons/genetics ; Gene Transfer, Horizontal ; Introns/*genetics ; Models, Genetic ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA, Transfer, Leu/*genetics ; Recombination, Genetic ; }, abstract = {The origin and evolution of bacterial introns are still controversial issues. Here we present data on the distribution and evolution of a recently discovered divergent tRNA(Leu)(UAA) intron. The intron shows a higher sequence affiliation with introns in tRNA(Ile)(CAU) and tRNA(Arg)(CCU) genes in alpha- and beta-proteobacteria, respectively, than with other cyanobacterial tRNA(Leu)(UAA) group I introns. The divergent tRNA(Leu)(UAA) intron is sporadically distributed both within the Nostoc and the Microcystis radiations. The complete tRNA gene, including flanking regions and intron from Microcystis aeruginosa strain NIVA-CYA 57, was sequenced in order to elucidate the evolutionary pattern of this intron. Phylogenetic reconstruction gave statistical evidence for different phylogenies for the intron and exon sequences, supporting an evolutionary model involving horizontal intron transfer. The distribution of the tRNA gene, its flanking regions, and the introns were addressed by Southern hybridization and PCR amplification. The tRNA gene, including the flanking regions, were absent in the intronless stains but present in the intron-containing strains. This suggests that the sporadic distribution of this intron within the Microcystis genus cannot be attributed to intron mobility but rather to an instability of the entire tRNA(Leu)(UAA) intron-containing genome region. Taken together, the complete data set for the evolution of this intron can best be explained by a model involving a nested evolution of the intron, i.e., wherein the intron has been transferred horizontally (probably through a single or a few events) to a tRNA(Leu)(UAA) gene which is located within a unstable genome region.}, }
@article {pmid11788711, year = {2002}, author = {Makarova, KS and Aravind, L and Grishin, NV and Rogozin, IB and Koonin, EV}, title = {A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis.}, journal = {Nucleic acids research}, volume = {30}, number = {2}, pages = {482-496}, pmid = {11788711}, issn = {1362-4962}, mesh = {Amino Acid Sequence ; Archaea/enzymology/*genetics ; Bacteria/enzymology/*genetics ; Conserved Sequence/genetics ; DNA Helicases/genetics ; DNA Repair/*genetics ; DNA-Directed DNA Polymerase/chemistry/genetics ; Databases, Nucleic Acid ; Evolution, Molecular ; Exonucleases/chemistry/genetics ; Gene Order/genetics ; Gene Transfer, Horizontal ; Genes, Archaeal/*genetics ; Genes, Bacterial/*genetics ; *Genome, Archaeal ; *Genome, Bacterial ; Hydrolases/genetics ; Models, Molecular ; Molecular Sequence Data ; Operon/genetics ; Phylogeny ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sequence Alignment ; Species Specificity ; }, abstract = {During a systematic analysis of conserved gene context in prokaryotic genomes, a previously undetected, complex, partially conserved neighborhood consisting of more than 20 genes was discovered in most Archaea (with the exception of Thermoplasma acidophilum and Halobacterium NRC-1) and some bacteria, including the hyperthermophiles Thermotoga maritima and Aquifex aeolicus. The gene composition and gene order in this neighborhood vary greatly between species, but all versions have a stable, conserved core that consists of five genes. One of the core genes encodes a predicted DNA helicase, often fused to a predicted HD-superfamily hydrolase, and another encodes a RecB family exonuclease; three core genes remain uncharacterized, but one of these might encode a nuclease of a new family. Two more genes that belong to this neighborhood and are present in most of the genomes in which the neighborhood was detected encode, respectively, a predicted HD-superfamily hydrolase (possibly a nuclease) of a distinct family and a predicted, novel DNA polymerase. Another characteristic feature of this neighborhood is the expansion of a superfamily of paralogous, uncharacterized proteins, which are encoded by at least 20-30% of the genes in the neighborhood. The functional features of the proteins encoded in this neighborhood suggest that they comprise a previously undetected DNA repair system, which, to our knowledge, is the first repair system largely specific for thermophiles to be identified. This hypothetical repair system might be functionally analogous to the bacterial-eukaryotic system of translesion, mutagenic repair whose central components are DNA polymerases of the UmuC-DinB-Rad30-Rev1 superfamily, which typically are missing in thermophiles.}, }
@article {pmid11786646, year = {2001}, author = {Jonas, DA and Elmadfa, I and Engel, KH and Heller, KJ and Kozianowski, G and König, A and Müller, D and Narbonne, JF and Wackernagel, W and Kleiner, J}, title = {Safety considerations of DNA in food.}, journal = {Annals of nutrition &amp; metabolism}, volume = {45}, number = {6}, pages = {235-254}, doi = {10.1159/000046734}, pmid = {11786646}, issn = {0250-6807}, mesh = {Consumer Product Safety ; DNA/*administration &amp; dosage/chemistry/pharmacokinetics/physiology ; Digestion ; Food Microbiology ; Food Technology/standards ; *Food, Genetically Modified/adverse effects/standards ; Gene Transfer, Horizontal ; Genetic Engineering ; Humans ; Structure-Activity Relationship ; }, abstract = {Recombinant DNA techniques are capable of introducing genetic changes into food organisms that are more predictable than those introduced through conventional breeding techniques. This review discusses whether the consumption of DNA in approved novel foods and novel food ingredients derived from genetically modified organisms (GMOs) can be regarded as being as safe as the consumption of DNA in existing foods. It concludes that DNA from GMOs is equivalent to DNA from existing food organisms that has always been consumed with human diets. Any risks associated with the consumption of DNA will remain, irrespective of its origin, because the body handles all DNA in the same way. The breakdown of DNA during food processing and passage through the gastrointestinal tract reduces the likelihood that intact genes capable of encoding foreign proteins will be transferred to gut microflora. The review does not specifically address food safety issues arising from the consumption of viable genetically modified microorganisms but it shows that the likelihood of transfer and functional integration of DNA from ingested food by gut microflora and/or human cells is minimal. Information reviewed does not indicate any safety concerns associated with the ingestion of DNA per se from GMOs resulting from the use of currently available recombinant DNA techniques in the food chain.}, }
@article {pmid11782494, year = {2002}, author = {Murray, NE}, title = {2001 Fred Griffith review lecture. Immigration control of DNA in bacteria: self versus non-self.}, journal = {Microbiology (Reading, England)}, volume = {148}, number = {Pt 1}, pages = {3-20}, doi = {10.1099/00221287-148-1-3}, pmid = {11782494}, issn = {1350-0872}, mesh = {Bacteria/enzymology/*genetics ; DNA Restriction-Modification Enzymes/genetics/*metabolism ; DNA, Bacterial/*genetics ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; *Repetitive Sequences, Nucleic Acid ; }, }
@article {pmid11781024, year = {2001}, author = {Lou, J and Tu, Y and Burns, M and Silva, MJ and Manske, P}, title = {BMP-12 gene transfer augmentation of lacerated tendon repair.}, journal = {Journal of orthopaedic research : official publication of the Orthopaedic Research Society}, volume = {19}, number = {6}, pages = {1199-1202}, doi = {10.1016/S0736-0266(01)00042-0}, pmid = {11781024}, issn = {0736-0266}, mesh = {Alkaline Phosphatase/metabolism ; Animals ; Biomechanical Phenomena ; Bone Morphogenetic Proteins/*genetics ; Cells, Cultured ; Chickens ; Collagen/biosynthesis ; Gene Transfer, Horizontal ; *Genetic Therapy ; Growth Differentiation Factors ; Tendon Injuries/physiopathology/*therapy ; Tendons/*physiology ; Tensile Strength ; *Transforming Growth Factor beta ; Wound Healing ; }, abstract = {Bone morphogenetic protein (BMP) 12 is a recently discovered member of the human BMP family. It is the human homolog of mouse growth/differentiation factor (GDF)-7. Previously we reported that injection of mesenchymal progenitor cells transferred with the BMP-12 gene into the muscles of nude mice induced tendon-like tissue formation. In this study, we further investigated the effect of BMP-12 gene transfer on tendon cells. We observed that adenovirus mediated in vitro BMP-12 gene transfer into chicken tendon cells increased type I collagen synthesis. No change in alkaline phosphatase activity was observed following BMP-12 gene transfer. We also determined that BMP-12 gene transfer into a complete tendon laceration chicken model resulted in a two-fold increase of tensile strength and stiffness of repaired tendons, indicating improved tendon healing in vivo. We conclude that BMP-12 gene transfer is a promising procedure for improving the tendon repair process.}, }
@article {pmid11780328, year = {2001}, author = {Guo, X and Wang, H and Chu, H and Wang, X and Qu, B and Li, Z and Qi, Z and Wang, Z}, title = {High level expression of human factor VIII in mammalian cells after retroviral-mediated gene transfer.}, journal = {Chinese medical journal}, volume = {114}, number = {7}, pages = {690-693}, pmid = {11780328}, issn = {0366-6999}, mesh = {Animals ; Cell Line ; Factor VIII/*genetics ; *Gene Transfer, Horizontal ; Humans ; Retroviridae/*genetics ; Transcription, Genetic ; }, abstract = {OBJECTIVE: To develop a retroviral-mediated high efficient expression system of human coagulation factor VIII.<br><br>METHODS: The LNC-FVIIIBD retroviral vector was generated by cloning a human B-domain-deleted (760aa-1639aa) Factor VIII (FVIII) cDNA (FVIII cDNA BD) into the retroviral vector pLNCX. Several mammalian cell lines, including NIH3T3, CHO, Cos-7 and human hepatic cell line, L-02, were transduced with viral supernatant from the highest virus-producing PA317 clone. Antigen and coagulant activity of human FVIII in cell culture medium were measured by ELISA and a one-stage method, respectively. RT-PCR was performed for the detection of FVIIIBD mRNA.<br><br>RESULTS: Human FVIII was expressed in all four target cells, with the highest FVIII expression observed in NIH3T3. The coagulant activity of secreted FVIII was up to 1.6 U/10(6) cells.24 hrs-1, and the FVIII antigen was 500 ng/10(6) cells.24 hrs-1. FVIII coagulant activity and antigen expressed by transduced CHO cells were 0.12 U/10(6) cells.24 hrs-1 and 62.4 ng/10(6) cells.24 hrs-1, respectively. Human FVIII expression was relatively low in Cos-7 and L-02 cells. RT-PCR results demonstrated transcription of FVIII cDNA BD in the target cells.<br><br>CONCLUSIONS: The constructed retroviral vector was able to direct high level expression of human FVIII in various mammalian cell lines. It has potential utility in the future gene therapy for Hemophilia A.}, }
@article {pmid11779827, year = {2002}, author = {Snel, B and Bork, P and Huynen, MA}, title = {Genomes in flux: the evolution of archaeal and proteobacterial gene content.}, journal = {Genome research}, volume = {12}, number = {1}, pages = {17-25}, doi = {10.1101/gr.176501}, pmid = {11779827}, issn = {1088-9051}, mesh = {Amino Acid Substitution/genetics ; Archaea/*genetics ; Bacteria/*genetics ; *Evolution, Molecular ; Gene Deletion ; Gene Duplication ; Gene Transfer, Horizontal/genetics ; Genes, Archaeal/*genetics ; Genes, Bacterial/*genetics ; *Genome, Archaeal ; *Genome, Bacterial ; Models, Genetic ; Mutagenesis/genetics ; Phylogeny ; Proteobacteria/*genetics ; Recombination, Genetic/genetics ; }, abstract = {In the course of evolution, genomes are shaped by processes like gene loss, gene duplication, horizontal gene transfer, and gene genesis (the de novo origin of genes). Here we reconstruct the gene content of ancestral Archaea and Proteobacteria and quantify the processes connecting them to their present day representatives based on the distribution of genes in completely sequenced genomes. We estimate that the ancestor of the Proteobacteria contained around 2500 genes, and the ancestor of the Archaea around 2050 genes. Although it is necessary to invoke horizontal gene transfer to explain the content of present day genomes, gene loss, gene genesis, and simple vertical inheritance are quantitatively the most dominant processes in shaping the genome. Together they result in a turnover of gene content such that even the lineage leading from the ancestor of the Proteobacteria to the relatively large genome of Escherichia coli has lost at least 950 genes. Gene loss, unlike the other processes, correlates fairly well with time. This clock-like behavior suggests that gene loss is under negative selection, while the processes that add genes are under positive selection.}, }
@article {pmid11776192, year = {2000}, author = {Zhang, Z and Lang, J}, title = {[Effects of human interleukin-2 gene transfer on the immunity of ovarian cancer cell line SKOV3].}, journal = {Zhonghua fu chan ke za zhi}, volume = {35}, number = {7}, pages = {427-429}, pmid = {11776192}, issn = {0529-567X}, mesh = {Cytotoxicity, Immunologic ; Female ; *Gene Transfer, Horizontal ; Histocompatibility Antigens/analysis ; Humans ; Interleukin-2/*genetics ; Killer Cells, Lymphokine-Activated/immunology ; Killer Cells, Natural/immunology ; Ovarian Neoplasms/*immunology ; Tumor Cells, Cultured ; }, abstract = {OBJECTIVE: To study the effect of interleukin-2 (IL-2) gene transfer on the immunity of ovarian cancer cell line SKOV3.<br><br>METHODS: The expression of main histologic complex (MHC) molecular HLA-ABC, HLA-DR and HLA-DQ of SKOV3, SKOV3/Neo and SKOV3/IL-2 cells were detected by flow cytometry. The 51Cr-4 hr releasing test was employed to detect the killing effects of natural killer (NK) and lymphokine-activated killer (LAK) cells. Meanwhile, the tumor cell and lymphocyte co-culture was performed.<br><br>RESULTS: The expression of HLA-ABC, HLA-DR and HLA-DQ molecular of hIL-2 gene modified cells was upregulated markedly. The 51Cr-4 hr releasing test showed that the parental and gene modified cells were markedly resistant to NK cells, but the IL-2 gene modified cells was more sensitive to LAK cells. There were significant differences between them (P < 0.01). The "cross-talk" of tumor cell with lymphocyte was observed when the hIL-2 gene modified SKOV3 cells were cocultured with lymphocyte.<br><br>CONCLUSION: IL-2 gene transfer can enhance the immunity of ovarian cancer cell line SKOV3.}, }
@article {pmid11775882, year = {2000}, author = {He, Q and Hong, X}, title = {[Retroviral transduction of a mutant erbB-2 gene into human CD34+ derived dendritic cells].}, journal = {Chinese medical journal}, volume = {113}, number = {6}, pages = {563-567}, pmid = {11775882}, issn = {0366-6999}, mesh = {3T3 Cells ; Animals ; Breast Neoplasms/therapy ; Dendritic Cells/*metabolism ; Female ; *Gene Transfer, Horizontal ; *Genes, erbB-2 ; Genetic Therapy ; Humans ; Mice ; Mutation ; Retroviridae/genetics ; T-Lymphocytes, Cytotoxic/immunology ; Tumor Cells, Cultured ; }, abstract = {OBJECTIVE: To successfully transduce a mutant erbB-2 gene into normal human CD34(+)-derived dendritic cells (DCs) and verify gene expression in these transduced dendritic cells.<br><br>METHODS: The packaging cell line PA317 was transfected with mutant erbB-2 gene DNA and the virus produced was used to infect packaging cell line PG13. The virus produced by PG13 was used to infect CD34(+)-derived dendritic cells by the spinoculation method using flasks coated with fibronectin material to facilitate retrovirus gene transter efficiency and the mutant erbB-2 gene expression was assessed by ABC staining and FACScan methods.<br><br>RESULTS: A mutant erbB-2 gene packaging cell line was produced and this mutant gene was transduced into human CD34(+)-derived DCs. It was verified that the relatively large numbers of the transduced DCs expressed the mutant erbB-2 protein which was eradicated of the ability to transform mouse NIH3T3 fibroblast cells.<br><br>CONCLUSIONS: Human DCs can be gene-modified and these gene-modified DCs may be useful in stimulating T lymphocytes for immunotherapy.}, }
@article {pmid11775875, year = {2000}, author = {Pan, L and Tong, Y and Zhou, S and Wu, Y and Mao, N and Yang, X}, title = {[Chemoprotection of transfer of multidrug resistance gene into human hematopoietic progenitor cell].}, journal = {Chinese medical journal}, volume = {113}, number = {6}, pages = {536-539}, pmid = {11775875}, issn = {0366-6999}, mesh = {Antigens, CD34/analysis ; Antineoplastic Agents/*adverse effects ; Cell Line ; Drug Resistance ; Female ; Gene Transfer, Horizontal ; *Genes, MDR ; *Genetic Therapy ; Genital Neoplasms, Female/drug therapy ; Hematopoietic Stem Cells/*drug effects ; Humans ; }, abstract = {OBJECTIVE: To observe the effect of the transfer of multidrug resistance gene (mdr1) into human hematopoietic progenitor cells (HPC) on the chemoprotection.<br><br>METHODS: Human CD34+ cells served as a target of mdr1 gene transfer. Retroviral vector SF-mdr containing human total length mdr1cDNA was introduced into packing cells GP-envAM12 by liposome-mediated transfection. The mdr1 gene was transduced into human CD34+ cells by retroviral supernatants of packing cells. The integration and expression of the mdr1 gene and its protein (P170) in transduced cells were determined by PCR, RT-PCR, and flow cytometry. The drug resistance of chemotherapy in transduced HPC was determined by culturing colonies.<br><br>RESULTS: The mdr1 gene was integrated and expressed in transduced CD34+ cells. The efficiency of mdr1 gene transfer was 10%-14%. Compared with untransduced controls, within a certain range of drug concentration, the number of drug-resistant colony in transduced HPC for taxol, doxorubicin, VCR and VP16 were increased by 3.6 +/- 2.1 fold, 2.9 +/- 0.3 fold, 1.9 +/- 0.4 fold, and 3.5 +/- 0.5 fold, respectively.<br><br>CONCLUSION: The transfer of the mdr1 gene into human HPC can increase the drug resistance of the transduced cells to corresponding chemotherapeutic drugs that may provide some degree of chemoprotection for HPC.}, }
@article {pmid11775614, year = {2001}, author = {}, title = {10th International Conference on Gene Therapy of Cancer. 13-15 December 2001. San Diego, California, USA. Abstracts.}, journal = {Cancer gene therapy}, volume = {8 Suppl 2}, number = {}, pages = {S1-31}, pmid = {11775614}, issn = {0929-1903}, mesh = {Animals ; Gene Transfer, Horizontal ; *Genetic Therapy ; Humans ; Neoplasms/genetics/immunology/*therapy ; }, }
@article {pmid11773243, year = {2001}, author = {Loreto, EL and Valente, VL and Zaha, A and Silva, JC and Kidwell, MG}, title = {Drosophila mediopunctata P elements: a new example of horizontal transfer.}, journal = {The Journal of heredity}, volume = {92}, number = {5}, pages = {375-381}, doi = {10.1093/jhered/92.5.375}, pmid = {11773243}, issn = {0022-1503}, mesh = {Animals ; Blotting, Southern ; *DNA Transposable Elements ; Drosophila/classification/*genetics ; Gene Dosage ; *Gene Transfer, Horizontal ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Sequences homologous to the P element of Drosophila melanogaster were previously identified in Drosophila mediopunctata, a member of the tripunctata group, subgenus Drosophila. We report here that the P element is present in about three to five copies in the D. mediopunctata genome. While one of the insertion sites appears to be fixed, others may be polymorphic, indicating relatively recent P element activity. Phylogenetic analysis revealed that the D. mediopunctata element belongs to the canonical subfamily of P elements and that divergence of the D. mediopunctata element from other members of this subfamily ranges from 2% to 5% at the nucleotide level. This is the first report of a canonical P element outside the subgenus Sophophora. Based primarily on the striking incongruence between P element and host species phylogenies, the presence of a canonical P element in D. mediopunctata is most likely explained by horizontal transfer between species.}, }
@article {pmid11772469, year = {2002}, author = {Messina, LM and Brevetti, LS and Chang, DS and Paek, R and Sarkar, R}, title = {Therapeutic angiogenesis for critical limb ischemia: invited commentary.}, journal = {Journal of controlled release : official journal of the Controlled Release Society}, volume = {78}, number = {1-3}, pages = {285-294}, doi = {10.1016/s0168-3659(01)00501-6}, pmid = {11772469}, issn = {0168-3659}, support = {HL04435/HL/NHLBI NIH HHS/United States ; HL10253/HL/NHLBI NIH HHS/United States ; HL51184/HL/NHLBI NIH HHS/United States ; }, mesh = {Adenoviridae/genetics ; Animals ; Extremities/*blood supply ; Gene Transfer, Horizontal ; *Genetic Therapy ; Humans ; Ischemia/*therapy ; *Neovascularization, Physiologic ; Nitric Oxide/physiology ; Nitric Oxide Synthase/*genetics ; Nitric Oxide Synthase Type III ; Regional Blood Flow ; }, abstract = {Lower extremity arterial occlusive disease results in tissue ischemia of the legs and is relatively common in the elderly. Clinically, it may be asymptomatic, cause muscle pain during exercise, or progress to a severe degree of ischemia that may result in limb loss. Although bypass surgery and angioplasty have increased the rate of limb salvage in these patients, amputation of the affected limb remains a common outcome for many patients. Therapeutic angiogenesis is the administration of angiogenic factors, or genes encoding these factors, to promote neovascularization and thereby increase blood flow to the ischemic leg. We have developed an animal model of hindlimb ischemia in which to study therapeutic angiogenesis. We chose nitric oxide as the angiogenic factor for our experiments because of its ability to induce angiogenesis, vasodilation, and inhibit inflammation. In this review, we will discuss our experience with our model of hindlimb ischemia, as well as discuss our results of gene therapy for therapeutic angiogenesis using nitric oxide.}, }
@article {pmid11772453, year = {2002}, author = {Brokx, RD and Bisland, SK and Gariépy, J}, title = {Designing peptide-based scaffolds as drug delivery vehicles.}, journal = {Journal of controlled release : official journal of the Controlled Release Society}, volume = {78}, number = {1-3}, pages = {115-123}, doi = {10.1016/s0168-3659(01)00491-6}, pmid = {11772453}, issn = {0168-3659}, mesh = {*Drug Delivery Systems ; *Drug Design ; Gene Transfer, Horizontal ; Humans ; Peptides/*administration &amp; dosage ; Photochemotherapy ; Vaccines/administration &amp; dosage ; }, abstract = {Methods for delivering drugs into cells remain an important part of the process of designing drugs. One promising approach is the concept of loligomers, synthetic peptides composed of a branched polylysine core harboring identical arms. Loligomers are typically synthesized with eight arms, each carrying peptide signals guiding their import and localization into cells. The most important advantage of loligomers is the multivalent presentation of targeting signals resulting from a tentacular arrangement. Multivalency increases the efficiency of import and intracellular routing signals as compared to similar linear peptides. Secondly, it reduces and delays the impact of peptide degradation in terms of cellular processing and compartmentalization. The vectorial delivery of nucleus-directed loligomers into cells has recently been confirmed by microscopy and flow cytometry studies. Practical uses of loligomers as intracellular vehicles include the import of plasmid DNA into cells, the conjugation of chemical groups, such as photosensitizers for use in photodynamic therapy, and the incorporation of cytotoxic T-lymphocyte (CTL) epitopes with a view to creating synthetic vaccines. Branched peptides such as loligomers represent simple and versatile molecular vehicles with potential applications in a wide variety of drug design approaches.}, }
@article {pmid11770826, year = {2001}, author = {Sonea, S and Mathieu, LG}, title = {Evolution of the genomic systems of prokaryotes and its momentous consequences.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {4}, number = {2}, pages = {67-71}, doi = {10.1007/s101230100015}, pmid = {11770826}, issn = {1139-6709}, mesh = {*Evolution, Molecular ; *Genome, Bacterial ; Models, Genetic ; Prokaryotic Cells/metabolism ; }, abstract = {The earliest self-reproducing cell on Earth, our common ancestor, was probably as small as present-day bacteria. It gave rise to a very large and durable clone whose descendants must have been the only living occupants of the oceans for about one thousand million years. They reached astronomical numbers of separate, disjunct cells, and synthesized many new genes. Their small volume could not accommodate ever larger genomes and useful new genes replaced resident, less successful sequences, thus increasing diversity and the number of strains with highly specialized, distinct, bioenergetic potentialities. Also, selective pressure favored strains able to participate successfully in division of labor and in the sharing of diverse abilities in mixed communities, counterbalancing the limited capacities of individual genomes. Lateral gene transfer mechanisms appeared and were progressively improved, furthering the development of diversity. The prokaryotes' constructive evolution resulted in the formation of a worldwide web of genetic information, and a global bacterial superbiosystem (superorganism). By contrast, eukaryotic evolution of organisms has been typically Darwinian. Diversification of eukaryotic organisms was, however, considerably enriched and accelerated by symbioses with prokaryotes. The more broadly diversified bioenergetic potential of prokaryotes considerably increased the diversity of eukaryotes. Without their participation, our biosphere would have remained much less diverse and less dynamic. Environmental homeostasis has been maintained all along by guided bacterial evolution.}, }
@article {pmid11761613, year = {2001}, author = {Radchenko, EE and Odintsova, IG and Vlasova, TV}, title = {[Inheritance of a sign of a weekly expressed greenbug resistance in sorghum].}, journal = {Genetika}, volume = {37}, number = {10}, pages = {1364-1370}, pmid = {11761613}, issn = {0016-6758}, mesh = {Animals ; Edible Grain/*genetics/physiology ; Gene Transfer, Horizontal ; Genes, Plant ; Genotype ; Insecta/pathogenicity/*physiology ; Virulence ; }, abstract = {Combined inheritance of oligogenes (Sgr1, Sgr4, Sgr5, and Sgr6) and a weakly expressed resistance to infestation with virulent greenbug clones was studied in sorghum. Under these conditions, the resistance was shown to depend on the interaction between minor resistance genes of the host plant and the virulence genes of the pest rather than on the "residual effect" of oligogenes. The minor genes can be independent of or weakly linked to the major resistance gene. They differentially interact with phytophage genotypes and, contrary to Van der Plank's postulates, are not responsible for the long-term (horizontal) resistance. The possibility of rapidly overcoming the effect of minor genes was confirmed by observation of seasonal dynamics of a natural aphid population on a resistant variety.}, }
@article {pmid11758260, year = {2001}, author = {Zhang, Z and Dong, H and Liu, J}, title = {[Experimental research of host endothelialization of transplanted hetero-heart valve by transfer of VEGF gene].}, journal = {Zhonghua yi xue za zhi}, volume = {81}, number = {17}, pages = {1074-1077}, pmid = {11758260}, issn = {0376-2491}, mesh = {Animals ; *Bioprosthesis ; Cattle ; Endothelial Growth Factors/analysis/*genetics ; Endothelium, Vascular/*physiology ; Female ; *Gene Transfer, Horizontal ; *Heart Valve Prosthesis ; Lymphokines/analysis/*genetics ; Male ; Myocardium/metabolism ; RNA, Messenger/analysis ; Swine ; Vascular Endothelial Growth Factor A ; Vascular Endothelial Growth Factors ; }, abstract = {OBJECTIVE: To investigate the feasibility of host endothelialization of transplanted hetero-heart valve by transfer of VEGF gene.<br><br>METHODS: Bovine pericardium treated with glutaraldehyde and L-glutamine was positioned into ping's right atrium, then gene suture carrying plasmids with pcD2/hVEGF121 gene or only with pcD2 was sewn into the anterior wall of right ventricle. The contents of VEGF protein in blood from right atrium and peripheral vein were determined by ELISA 10 days after the transplantation. The expression of VFGF mRNA in the myocardium near the gene suture was detected by RT-PCR 16 days after the transplantatipn. Microscopy and unltrastructural analysis of the transplanted valve were carried out.<br><br>RESULTS: The content of VEGF protein in blood from the right atrium in the pcD2/hVEGF121 group was significantly higher than that in the pcD2 group 10 days after the VEGF gene transfer (P < 0.01). The expression of VEGF mRNA in the myocardium of right ventricle in pcD2/VEGF121 group was much higher than that in the left ventricle of the same group and that in the right ventricle in pcD2 group. Morphological observation showed that the coverage rate of host endothelium in pcD2/hVEGF121 group was higher than in pcD2 group 16 days after the gene transfer (P < 0.05). 30 days after the gene transfer. Complete host endothelialization was observed 30 days after the operation.<br><br>CONCLUSION: VEGF gene transfer with surgical suture promotes the host endothelialization of bioprothesis, thus inhibiting calcification of biological valves and improving biocompatibility and long-term durability of bioprothesis.}, }
@article {pmid11755420, year = {2001}, author = {Vazquez-Torres, A and Fang, FC}, title = {Salmonella evasion of the NADPH phagocyte oxidase.}, journal = {Microbes and infection}, volume = {3}, number = {14-15}, pages = {1313-1320}, doi = {10.1016/s1286-4579(01)01492-7}, pmid = {11755420}, issn = {1286-4579}, support = {AI 39557/AI/NIAID NIH HHS/United States ; AI 44486/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Humans ; Macrophages/*enzymology/*immunology/microbiology ; Mice ; NADPH Oxidases/*metabolism ; Salmonella Infections, Animal/*immunology/microbiology ; Salmonella typhimurium/*pathogenicity ; }, abstract = {The bacteria-phagocyte interaction is of central importance in Salmonella pathogenesis. Immediately following phagocytosis, the NADPH phagocyte oxidase complex assembles in vesicles and produces highly toxic reactive oxygen species that play a major role in initial Salmonella killing by phagocytes. However, Salmonella has evolved a number of strategies to reduce the efficacy of oxygen-dependent phagocyte antimicrobial systems. Some of these strategies, such as superoxide dismutases, hydroperoxidases, oxidoreductases, scavengers and repair systems are common to most aerobic bacteria. In addition, Salmonella has acquired, by horizontal gene transfer, a type III secretory system encoded by Salmonella pathogenicity island 2 that interferes with the trafficking of vesicles containing functional NADPH phagocyte oxidase to the phagosome, thereby enhancing the survival of Salmonella within macrophages.}, }
@article {pmid11755071, year = {2002}, author = {Lawrence, JG and Ochman, H}, title = {Reconciling the many faces of lateral gene transfer.}, journal = {Trends in microbiology}, volume = {10}, number = {1}, pages = {1-4}, doi = {10.1016/s0966-842x(01)02282-x}, pmid = {11755071}, issn = {0966-842X}, mesh = {Escherichia coli/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial ; Markov Chains ; Phylogeny ; }, }
@article {pmid11753131, year = {2002}, author = {Oelschlaeger, TA and Dobrindt, U and Hacker, J}, title = {Virulence factors of uropathogens.}, journal = {Current opinion in urology}, volume = {12}, number = {1}, pages = {33-38}, doi = {10.1097/00042307-200201000-00007}, pmid = {11753131}, issn = {0963-0643}, mesh = {Adhesins, Escherichia coli ; Animals ; Bacterial Toxins ; Epithelium/immunology/pathology ; Escherichia coli/genetics/*pathogenicity ; Escherichia coli Infections/immunology/*microbiology/pathology ; Humans ; Urinary Tract Infections/immunology/*microbiology/pathology ; Virulence ; }, abstract = {Urinary tract infections are among the most frequent infections encountered in developed countries. The vast majority of community-acquired urinary tract infections are caused by Escherichia coli. However, other bacterial species play an important role in nosocomial urinary tract infections. All these species are equipped with a variety of virulence factors. The best characterized are those from Escherichia coli. Among the first virulence factors that come into play during establishment of a urinary tract infection are adhesins. Besides their primary function as adhesin molecules several other additional functions can now be attributed to these organelles. Adhesins may also function as invasins, promote biofilm formation and transmit signals to epithelial cells resulting in inflammation. Furthermore, subunit proteins of adhesins seem to be promising vaccines. Later in infection, toxins seem to enhance virulence. However, for cytotoxic necrotizing factor type 1 this is controversial. Many virulence factors of uropathogenic bacteria are encoded by foreign DNA stretches inserted into the core genome. These pathogenicity islands or islets were obviously acquired via horizontal gene transfer creating new pathotypes more efficient in establishing infection. The role of new virulence factors and the new functions of already known virulence factors will be discussed as well as the concept of the composite genome of uropathogenic Escherichia coli.}, }
@article {pmid11751824, year = {2002}, author = {Utåker, JB and Andersen, K and Aakra, A and Moen, B and Nes, IF}, title = {Phylogeny and functional expression of ribulose 1,5-bisphosphate carboxylase/oxygenase from the autotrophic ammonia-oxidizing bacterium Nitrosospira sp. isolate 40KI.}, journal = {Journal of bacteriology}, volume = {184}, number = {2}, pages = {468-478}, pmid = {11751824}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; Ammonia/*metabolism ; Bacterial Proteins/chemistry/classification/*genetics/metabolism ; Base Sequence ; Betaproteobacteria/*enzymology/genetics/isolation &amp; purification ; Cloning, Molecular ; Conserved Sequence ; Cupriavidus necator/genetics ; DNA, Bacterial ; Gene Expression Regulation, Enzymologic ; Genetic Vectors ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis ; Oxidation-Reduction ; Phylogeny ; Plasmids ; Protein Structure, Tertiary ; Ribulose-Bisphosphate Carboxylase/chemistry/classification/*genetics/metabolism ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; }, abstract = {The autotrophic ammonia-oxidizing bacteria (AOB), which play an important role in the global nitrogen cycle, assimilate CO(2) by using ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO). Here we describe the first detailed study of RubisCO (cbb) genes and proteins from the AOB. The cbbLS genes from Nitrosospira sp. isolate 40KI were cloned and sequenced. Partial sequences of the RubisCO large subunit (CbbL) from 13 other AOB belonging to the beta and gamma subgroups of the class Proteobacteria are also presented. All except one of the beta-subgroup AOB possessed a red-like type I RubisCO with high sequence similarity to the Ralstonia eutropha enzyme. All of these new red-like RubisCOs had a unique six-amino-acid insert in CbbL. Two of the AOB, Nitrosococcus halophilus Nc4 and Nitrosomonas europaea Nm50, had a green-like RubisCO. With one exception, the phylogeny of the AOB CbbL was very similar to that of the 16S rRNA gene. The presence of a green-like RubisCO in N. europaea was surprising, as all of the other beta-subgroup AOB had red-like RubisCOs. The green-like enzyme of N. europaea Nm50 was probably acquired by horizontal gene transfer. Functional expression of Nitrosospira sp. isolate 40KI RubisCO in the chemoautotrophic host R. eutropha was demonstrated. Use of an expression vector harboring the R. eutropha cbb control region allowed regulated expression of Nitrosospira sp. isolate 40KI RubisCO in an R. eutropha cbb deletion strain. The Nitrosospira RubisCO supported autotrophic growth of R. eutropha with a doubling time of 4.6 h. This expression system may allow further functional analysis of AOB cbb genes.}, }
@article {pmid11750687, year = {2002}, author = {Gamieldien, J and Ptitsyn, A and Hide, W}, title = {Eukaryotic genes in Mycobacterium tuberculosis could have a role in pathogenesis and immunomodulation.}, journal = {Trends in genetics : TIG}, volume = {18}, number = {1}, pages = {5-8}, doi = {10.1016/s0168-9525(01)02529-x}, pmid = {11750687}, issn = {0168-9525}, mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins/genetics ; Biological Evolution ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Molecular Sequence Data ; Mycobacterium tuberculosis/*genetics/immunology/pathogenicity ; Sequence Homology, Amino Acid ; Virulence/genetics ; }, abstract = {Acquisition of new genetic material through horizontal gene transfer has been an important feature in the evolution of many pathogenic bacteria. Here, we report the presence of 19 genes of eukaryotic origin in the genome of Mycobacterium tuberculosis, some of which are unique to the M. tuberculosis complex. These genes, having been retained in the genome through selective advantage, most probably have key functions in the organism and in mammalian tuberculosis. We explore the role these genes might have in manipulation of the host immune system by altering the balance of steroid hormones.}, }
@article {pmid11750686, year = {2002}, author = {Brochier, C and Bapteste, E and Moreira, D and Philippe, H}, title = {Eubacterial phylogeny based on translational apparatus proteins.}, journal = {Trends in genetics : TIG}, volume = {18}, number = {1}, pages = {1-5}, doi = {10.1016/s0168-9525(01)02522-7}, pmid = {11750686}, issn = {0168-9525}, mesh = {Bacteria/*genetics ; Bacterial Proteins/genetics ; Gene Transfer, Horizontal ; Phylogeny ; Protein Biosynthesis ; }, abstract = {Lateral gene transfers are frequent among prokaryotes, although their detection remains difficult. If all genes are equally affected, this questions the very existence of an organismal phylogeny. The complexity hypothesis postulates the existence of a core of genes (those involved in numerous interactions) that are unaffected by transfers. To test the hypothesis, we studied all the proteins involved in translation from 45 eubacterial taxa, and developed a new phylogenetic method to detect transfers. Few of the genes studied show evidence for transfer. The phylogeny based on the genes devoid of transfer is very consistent with the ribosomal RNA tree, suggesting that an eubacterial phylogeny does exist.}, }
@article {pmid11750134, year = {2001}, author = {Henze, K and Horner, DS and Suguri, S and Moore, DV and Sánchez, LB and Müller, M and Embley, TM}, title = {Unique phylogenetic relationships of glucokinase and glucosephosphate isomerase of the amitochondriate eukaryotes Giardia intestinalis, Spironucleus barkhanus and Trichomonas vaginalis.}, journal = {Gene}, volume = {281}, number = {1-2}, pages = {123-131}, doi = {10.1016/s0378-1119(01)00773-9}, pmid = {11750134}, issn = {0378-1119}, support = {AI 11942/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; DNA, Complementary/chemistry/genetics ; DNA, Protozoan/chemistry/genetics ; Diplomonadida/enzymology/genetics ; Eukaryota/enzymology/*genetics ; Gene Expression Regulation, Enzymologic ; Giardia lamblia/enzymology/genetics ; Glucokinase/*genetics ; Glucose-6-Phosphate Isomerase/*genetics ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; Trichomonas vaginalis/enzymology/genetics ; }, abstract = {Glucokinase (GK) and glucosephosphate isomerase (GPI), the first two enzymes of the glycolytic pathway of the diplomonads Giardia intestinalis and Spironucleus barkhanus, Type I amitochondriate eukaryotes, were sequenced. GPI of the parabasalid Trichomonas vaginalis was also sequenced. The diplomonad GKs belong to a family of specific GKs present in cyanobacteria, in some proteobacteria and also in T. vaginalis, a Type II amitochondriate protist. These enzymes are not part of the hexokinase family, which is broadly distributed among eukaryotes, including the Type I amitochondriate parasite Entamoeba histolytica. G. intestinalis GK expressed in Escherichia coli was specific for glucose and glucosamine, as are its eubacterial homologs. The sequence of diplomonad and trichomonad GPIs formed a monophyletic group more closely related to cyanobacterial and chloroplast sequences than to cytosolic GPIs of other eukaryotes and prokaryotes. The findings show that certain enzymes of the energy metabolism of these amitochondriate protists originated from sources different than those of other eukaryotes. The observation that the two diplomonads and T. vaginalis share the same unusual GK and GPI is consistent with gene trees that suggest a close relationship between diplomonads and parabasalids. The intriguing relationships of these enzymes to cyanobacterial (and chloroplast) enzymes might reflect horizontal gene transfer between the common ancestor of the diplomonad and parabasalid lineages and the ancestor of cyanobacteria.}, }
@article {pmid11748964, year = {2001}, author = {Votýpka, J and Ray, DS and Lukes, J}, title = {Crithidia fasciculata: a test for genetic exchange.}, journal = {Experimental parasitology}, volume = {99}, number = {2}, pages = {104-107}, doi = {10.1006/expr.2001.4648}, pmid = {11748964}, issn = {0014-4894}, support = {AI 45536/AI/NIAID NIH HHS/United States ; }, mesh = {Aedes/genetics/*parasitology ; Animals ; Crithidia fasciculata/*genetics ; Culex/genetics/*parasitology ; Female ; *Gene Transfer, Horizontal ; Insect Vectors/genetics/*parasitology ; Male ; }, }
@article {pmid11733468, year = {2001}, author = {Chanawong, A and M'Zali, FH and Heritage, J and Lulitanond, A and Hawkey, PM}, title = {SHV-12, SHV-5, SHV-2a and VEB-1 extended-spectrum beta-lactamases in Gram-negative bacteria isolated in a university hospital in Thailand.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {48}, number = {6}, pages = {839-852}, doi = {10.1093/jac/48.6.839}, pmid = {11733468}, issn = {0305-7453}, mesh = {Cross Infection/enzymology/epidemiology/genetics/*microbiology ; Escherichia coli Proteins ; Gram-Negative Bacteria/*genetics/isolation &amp; purification ; Gram-Negative Bacterial Infections/enzymology/epidemiology/genetics ; Hospitals, University/statistics &amp; numerical data ; Humans ; Molecular Sequence Data ; Thailand/epidemiology ; beta-Lactamases/*genetics/isolation &amp; purification ; }, abstract = {Sixty-one extended-spectrum beta-lactamase (ESBL)-producing isolates were collected from Srinagarind Hospital, Thailand. These included 43 Enterobacteriaceae and 18 Pseudomonadaceae. The 43 Enterobacteriaceae were found to produce the following ESBLs: 26 (60.5%) SHV-12, 13 (30.2%) SHV-5, two (4.7%) SHV-2a, one (2.3%) VEB-1 and one (2.3%) unidentified. Twenty-four isolates (55.8%) also carried bla(TEM-1B), as well as bla(SHV) or bla(VEB-1). Plasmid DNA from transconjugants carrying the bla(SHV-12) gene showed various restriction patterns, indicating the distribution of the bla(SHV-12) gene among different antibiotic resistance plasmids. In contrast, bla(SHV-5) in 13 isolates was found on a single plasmid of c. 130 kb. Pulsed-field gel electrophoresis (PFGE) analysis of genomic DNA from these isolates revealed that nine of 11 Klebsiella pneumoniae gave the same pattern, indicating clonal spread of the strain within the hospital, together with the occasional spread of the plasmid to other strains. Among the pseudomonad isolates, 16 Pseudomonas aeruginosa and one Pseudomonas putida had bla(VEB-like) and one P. aeruginosa had bla(SHV-12). Nine of the 16 isolates carrying bla(VEB-like) (56.3%) had identical PFGE patterns, suggesting the dissemination of this gene, also by clonal spread. At least six different bla(VEB-like-)containing integrons were found among the 18 isolates. This is the first report of bacteria producing SHV-12 and SHV-2a in Thailand and the first report of SHV-12 in P. aeruginosa, of VEB-1 in Citrobacter freundii and a VEB-1-like beta-lactamase in P. putida. These findings indicate that ESBL genes in the Far East are part of a gene pool capable of broad horizontal gene transfer, in that these genes can transfer between different families of Gram-negative bacilli.}, }
@article {pmid11743170, year = {2001}, author = {Pennisi, E}, title = {Microbial genomes. New genome a boost to plant studies.}, journal = {Science (New York, N.Y.)}, volume = {294}, number = {5550}, pages = {2266}, doi = {10.1126/science.294.5550.2266a}, pmid = {11743170}, issn = {0036-8075}, mesh = {Agrobacterium tumefaciens/classification/*genetics/physiology ; Chromosomes, Bacterial/genetics ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; Plant Tumors/microbiology ; Plants/microbiology ; Plasmids ; *Sequence Analysis, DNA ; Sinorhizobium meliloti/classification/genetics ; }, }
@article {pmid11741869, year = {2002}, author = {Friedrich, MW}, title = {Phylogenetic analysis reveals multiple lateral transfers of adenosine-5'-phosphosulfate reductase genes among sulfate-reducing microorganisms.}, journal = {Journal of bacteriology}, volume = {184}, number = {1}, pages = {278-289}, pmid = {11741869}, issn = {0021-9193}, mesh = {Cell Lineage ; DNA Primers ; Deltaproteobacteria/classification/enzymology/*genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Gram-Positive Bacteria/classification/enzymology/*genetics ; Hydrogensulfite Reductase ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/*genetics ; Oxidoreductases Acting on Sulfur Group Donors/genetics ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sulfates/*metabolism ; }, abstract = {Lateral gene transfer affects the evolutionary path of key genes involved in ancient metabolic traits, such as sulfate respiration, even more than previously expected. In this study, the phylogeny of the adenosine-5'-phosphosulfate (APS) reductase was analyzed. APS reductase is a key enzyme in sulfate respiration present in all sulfate-respiring prokaryotes. A newly developed PCR assay was used to amplify and sequence a fragment (approximately 900 bp) of the APS reductase gene, apsA, from a taxonomically wide range of sulfate-reducing prokaryotes (n = 60). Comparative phylogenetic analysis of all obtained and available ApsA sequences indicated a high degree of sequence conservation in the region analyzed. However, a comparison of ApsA- and 16S rRNA-based phylogenetic trees revealed topological incongruences affecting seven members of the Syntrophobacteraceae and three members of the Nitrospinaceae, which were clearly monophyletic with gram-positive sulfate-reducing bacteria (SRB). In addition, Thermodesulfovibrio islandicus and Thermodesulfobacterium thermophilum, Thermodesulfobacterium commune, and Thermodesulfobacterium hveragerdense clearly branched off between the radiation of the delta-proteobacterial gram-negative SRB and the gram-positive SRB and not close to the root of the tree as expected from 16S rRNA phylogeny. The most parsimonious explanation for these discrepancies in tree topologies is lateral transfer of apsA genes across bacterial divisions. Similar patterns of insertions and deletions in ApsA sequences of donor and recipient lineages provide additional evidence for lateral gene transfer. From a subset of reference strains (n = 25), a fragment of the dissimilatory sulfite reductase genes (dsrAB), which have recently been proposed to have undergone multiple lateral gene transfers (M. Klein et al., J. Bacteriol. 183:6028-6035, 2001), was also amplified and sequenced. Phylogenetic comparison of DsrAB- and ApsA-based trees suggests a frequent involvement of gram-positive and thermophilic SRB in lateral gene transfer events among SRB.}, }
@article {pmid11741868, year = {2002}, author = {Davies, RL and Campbell, S and Whittam, TS}, title = {Mosaic structure and molecular evolution of the leukotoxin operon (lktCABD) in Mannheimia (Pasteurella) haemolytica, Mannheimia glucosida, and Pasteurella trehalosi.}, journal = {Journal of bacteriology}, volume = {184}, number = {1}, pages = {266-277}, pmid = {11741868}, issn = {0021-9193}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Alleles ; Amino Acid Sequence/genetics ; Bacterial Proteins/genetics ; Bacterial Toxins/*genetics ; Base Sequence/genetics ; *Carrier Proteins ; *Evolution, Molecular ; Exotoxins/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Genetic Variation ; Hemolysin Proteins/genetics ; Mannheimia haemolytica/classification/*genetics/pathogenicity ; *Membrane Transport Proteins ; Molecular Sequence Data ; Operon/*genetics ; Pasteurella/classification/*genetics/pathogenicity ; Recombination, Genetic ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; }, abstract = {The mosaic structure and molecular evolution of the leukotoxin operon (lktCABD) was investigated by nucleotide sequence comparison of the lktC, lktB, and lktD genes in 23 Mannheimia (Pasteurella) haemolytica, 6 Mannheimia glucosida, and 4 Pasteurella trehalosi strains. Sequence variation in the lktA gene has been described previously (R. L. Davies et al., J. Bacteriol. 183:1394-1404, 2001). The leukotoxin operon of M. haemolytica has a complex mosaic structure and has been derived by extensive inter- and intraspecies horizontal DNA transfer and intragenic recombination events. However, the pattern of recombination varies throughout the operon and among the different evolutionary lineages of M. haemolytica. The lktA and lktB genes have the most complex mosaic structures with segments derived from up to four different sources, including M. glucosida and P. trehalosi. In contrast, the lktD gene is highly conserved in M. haemolytica. The lktC, lktA, and lktB genes of strains representing the major ovine lineages contain recombinant segments derived from bovine or bovine-like serotype A2 strains. These findings support the previous conclusion that host switching of bovine A2 strains from cattle to sheep has played a major role in the evolution of the leukotoxin operon in ovine strains of M. haemolytica. Homologous segments of donor and recipient alleles are identical, or nearly identical, indicating that the recombinational exchanges occurred relatively recent in evolutionary terms. The 5' and 3' ends of the operon are highly conserved in M. haemolytica, which suggests that multiple horizontal exchanges of the complete operon have occurred by a common mechanism such as transduction. Although the lktA and lktB genes both have complex mosaic structures and high nucleotide substitution rates, the amino acid diversity of LktB is significantly lower than that of LktA due to a higher degree of evolutionary constraint against amino acid replacement. The recombinational exchanges within the leukotoxin operon have had greatest effect on LktA and probably provide an adaptive advantage against the host antibody response by generating novel antigenic variation at surface-exposed sites.}, }
@article {pmid11739752, year = {2001}, author = {Porta, H and Rocha-Sosa, M}, title = {Lipoxygenase in bacteria: a horizontal transfer event?.}, journal = {Microbiology (Reading, England)}, volume = {147}, number = {Pt 12}, pages = {3199-3200}, doi = {10.1099/00221287-147-12-3199}, pmid = {11739752}, issn = {1350-0872}, mesh = {Amino Acid Sequence ; Evolution, Molecular ; Gene Transfer, Horizontal ; Lipoxygenase/classification/*genetics ; Models, Genetic ; Molecular Sequence Data ; Myxococcales/enzymology/*genetics ; Pseudomonas aeruginosa/enzymology/*genetics ; Sequence Homology, Amino Acid ; }, }
@article {pmid11739750, year = {2001}, author = {Gürtler, V and Mayall, BC}, title = {Genetic transfer and genome evolution in MRSA.}, journal = {Microbiology (Reading, England)}, volume = {147}, number = {Pt 12}, pages = {3195-3197}, doi = {10.1099/00221287-147-12-3195}, pmid = {11739750}, issn = {1350-0872}, mesh = {*Bacterial Proteins ; Bacterial Typing Techniques ; Carrier Proteins/genetics ; DNA, Ribosomal Spacer/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; *Hexosyltransferases ; Methicillin Resistance/*genetics ; Muramoylpentapeptide Carboxypeptidase/genetics ; Penicillin-Binding Proteins ; *Peptidyl Transferases ; Polymorphism, Single Nucleotide ; Staphylococcus aureus/drug effects/*genetics ; }, }
@article {pmid11737291, year = {2001}, author = {Morimoto, S and Nakai, M and Ono, A and Kunimi, Y}, title = {Late male-killing phenomenon found in a Japanese population of the oriental tea tortrix, Homona magnanima (Lepidoptera: Tortricidae).}, journal = {Heredity}, volume = {87}, number = {Pt 4}, pages = {435-440}, doi = {10.1046/j.1365-2540.2001.00924.x}, pmid = {11737291}, issn = {0018-067X}, mesh = {Animals ; Crosses, Genetic ; Female ; Gene Transfer, Horizontal ; Japan ; Larva/genetics/physiology ; Lepidoptera/*genetics/*physiology ; Male ; Oocytes/physiology ; Polymerase Chain Reaction ; Pupa/genetics/physiology ; *Sex Ratio ; }, abstract = {A female-biased sex ratio was found in the oriental tea tortrix, Homona magnanima (Lepidoptera: Tortricidae), in Tsukuba, Ibaraki, Japan. There was no difference in mean egg hatch between the all-female and normal strains. Greater than 50% mortality was observed in the all-female strain larvae, suggesting that female-only broods are produced as a result of late male-killing. The female-biased sex ratio was maternally inherited and maintained, even when females were backcrossed with males of the normal strain, thus implicating cytoplasmic parasitism as its cause. The phenomenon was persistent in the presence of antibiotics, and was not due to infection by agents that cause other male-killing phenomena, such as Rickettsia, Wolbachia, Spiroplasma, or protozoan parasites. When a homogenate of dead male larvae of the all-female strain was inoculated in normal-strain larvae, this male-killing trait was transmitted to the next generation; thus, its causative agent is probably transmitted horizontally as well.}, }
@article {pmid11734060, year = {2001}, author = {Wolf, YI and Rogozin, IB and Grishin, NV and Tatusov, RL and Koonin, EV}, title = {Genome trees constructed using five different approaches suggest new major bacterial clades.}, journal = {BMC evolutionary biology}, volume = {1}, number = {}, pages = {8}, pmid = {11734060}, issn = {1471-2148}, mesh = {Bacteria/*classification/*genetics ; Conserved Sequence/genetics ; *Evolution, Molecular ; Gene Order/genetics ; Gene Transfer, Horizontal ; Genes, Archaeal/genetics ; Genes, Bacterial/genetics ; Genome, Archaeal ; *Genome, Bacterial ; Genomics/*methods ; Likelihood Functions ; *Phylogeny ; Prokaryotic Cells/metabolism ; Ribosomal Proteins/genetics ; Sequence Alignment ; Species Specificity ; }, abstract = {BACKGROUND: The availability of multiple complete genome sequences from diverse taxa prompts the development of new phylogenetic approaches, which attempt to incorporate information derived from comparative analysis of complete gene sets or large subsets thereof. Such attempts are particularly relevant because of the major role of horizontal gene transfer and lineage-specific gene loss, at least in the evolution of prokaryotes.<br><br>RESULTS: Five largely independent approaches were employed to construct trees for completely sequenced bacterial and archaeal genomes: i) presence-absence of genomes in clusters of orthologous genes; ii) conservation of local gene order (gene pairs) among prokaryotic genomes; iii) parameters of identity distribution for probable orthologs; iv) analysis of concatenated alignments of ribosomal proteins; v) comparison of trees constructed for multiple protein families. All constructed trees support the separation of the two primary prokaryotic domains, bacteria and archaea, as well as some terminal bifurcations within the bacterial and archaeal domains. Beyond these obvious groupings, the trees made with different methods appeared to differ substantially in terms of the relative contributions of phylogenetic relationships and similarities in gene repertoires caused by similar life styles and horizontal gene transfer to the tree topology. The trees based on presence-absence of genomes in orthologous clusters and the trees based on conserved gene pairs appear to be strongly affected by gene loss and horizontal gene transfer. The trees based on identity distributions for orthologs and particularly the tree made of concatenated ribosomal protein sequences seemed to carry a stronger phylogenetic signal. The latter tree supported three potential high-level bacterial clades,: i) Chlamydia-Spirochetes, ii) Thermotogales-Aquificales (bacterial hyperthermophiles), and ii) Actinomycetes-Deinococcales-Cyanobacteria. The latter group also appeared to join the low-GC Gram-positive bacteria at a deeper tree node. These new groupings of bacteria were supported by the analysis of alternative topologies in the concatenated ribosomal protein tree using the Kishino-Hasegawa test and by a census of the topologies of 132 individual groups of orthologous proteins. Additionally, the results of this analysis put into question the sister-group relationship between the two major archaeal groups, Euryarchaeota and Crenarchaeota, and suggest instead that Euryarchaeota might be a paraphyletic group with respect to Crenarchaeota.<br><br>CONCLUSIONS: We conclude that, the extensive horizontal gene flow and lineage-specific gene loss notwithstanding, extension of phylogenetic analysis to the genome scale has the potential of uncovering deep evolutionary relationships between prokaryotic lineages.}, }
@article {pmid11732866, year = {2001}, author = {Sun, L and Liu, X and Qiu, L and Wang, J and Liu, M and Fu, D and Luo, Q}, title = {Administration of plasmid DNA expressing human interleukin-6 significantly improves thrombocytopoiesis in irradiated mice.}, journal = {Annals of hematology}, volume = {80}, number = {10}, pages = {567-572}, doi = {10.1007/s002770100345}, pmid = {11732866}, issn = {0939-5555}, mesh = {Animals ; Blood Platelets/*physiology ; Cobalt Radioisotopes ; Gene Expression ; *Gene Transfer, Horizontal ; Genetic Therapy ; Genetic Vectors ; *Hematopoiesis ; Humans ; Interleukin-6/*genetics ; Mice ; Mice, Inbred C57BL ; Plasmids/genetics ; Platelet Count ; Radiation Injuries/*therapy ; Thrombocytopenia/etiology/*therapy ; Whole-Body Irradiation ; }, abstract = {When people are exposed to large doses of ionizing rays in a short time, hematopoiesis is impaired and hemorrhage is one of the major clinical features. Suddenly decreasing platelet counts are responsible for the life-threatening hemorrhagic complication. Therefore, some cytokines have been used to improve thrombocytopoiesis in various radiation-induced thrombocytopenia models. Current measures for this purpose involve repeated intravenous or subcutaneous injections of recombinant proteins, which are expensive and inconvenient, or gene therapy with viral vectors that could not obviate the risk of infection. We tried to determine the possibility of gene therapy with plasmid vectors for radiation-induced hematopoietic injury, which could overcome the above-mentioned problem. In this study, we describe the enhanced efficiency of radiation on gene transfer with plasmid vector in vivo and the physiological role of expressed human interleukin-6 (hIL-6) in vivo on a radiation-induced thrombocytopenia model. After a single intramuscular injection of plasmid hIL-6 DNA on 6.5-Gy-irradiated mice, the hIL-6 protein level in mouse plasma was determined with enzyme-linked immunosorbent assay (ELISA). The level of hIL-6 began to increase from the 4th day, reached the peak value on about the 11th day, and remained at a higher level on the 28th day. Meanwhile, unirradiated mice injected with the same amount of plasmid DNA showed less hIL-6 on the 11th day after administration. Further experiments demonstrated that the hIL-6 level in 7.5-Gy-irradiated mice was about three times higher than that of 5.0-Gy-irradiated mice, suggesting radiation could improve gene transfer efficiency of plasmid DNA in vivo and might be dependent on radiation doses. The expression of hIL-6 in vivo showed a significant effect on hematopoietic recovery after radiation. Not only the platelet nadir in peripheral blood, but also the number of colony-forming cells in bone marrow rose. The increased platelet counts were partially due to the increase of reticulated platelet that reflected the activity of a given population of megakaryocyte in bone marrow. We conclude that radiation could significantly enhance the gene transfer efficiency of plasmid DNA and that gene therapy with plasmid vectors for radiation-induced hematopoietic injury might be more effective than other diseases without DNA repair.}, }
@article {pmid11728474, year = {2001}, author = {Veronico, P and Jones, J and Di Vito, M and De Giorgi, C}, title = {Horizontal transfer of a bacterial gene involved in polyglutamate biosynthesis to the plant-parasitic nematode Meloidogyne artiellia.}, journal = {FEBS letters}, volume = {508}, number = {3}, pages = {470-474}, doi = {10.1016/s0014-5793(01)03132-5}, pmid = {11728474}, issn = {0014-5793}, mesh = {Amino Acid Sequence ; Animals ; Exons ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genes, Helminth ; Genome ; In Situ Hybridization ; Intestinal Mucosa/metabolism ; Intestines/enzymology ; Introns ; Life Cycle Stages ; Molecular Sequence Data ; Polyglutamic Acid/*biosynthesis ; RNA, Helminth/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Alignment ; Transferases (Other Substituted Phosphate Groups)/chemistry/*genetics ; Tylenchoidea/enzymology/*genetics/growth &amp; development ; }, abstract = {Analysis of a genomic fragment from the plant parasitic nematode Meloidogyne artiellia revealed the presence of a gene which, in bacteria, is involved in the formation of polyglutamate capsule. Searching of various databases, including the Caenorhabditis elegans genome sequence and the large EST datasets from a variety of parasitic nematodes, showed that no similar genes have been identified in other nematodes or in any other eukaryotic organisms. The M. artiellia gene has a typical eukaryotic structure and its mRNA is present in the intestine. The gene is expressed in all life cycle stages tested. These findings demonstrate horizontal gene transfer may be important in catalyzing the diversification of nematode lineages.}, }
@article {pmid11724835, year = {2001}, author = {Poyart, C and Quesne, G and Boumaila, C and Trieu-Cuot, P}, title = {Rapid and accurate species-level identification of coagulase-negative staphylococci by using the sodA gene as a target.}, journal = {Journal of clinical microbiology}, volume = {39}, number = {12}, pages = {4296-4301}, pmid = {11724835}, issn = {0095-1137}, mesh = {Bacterial Proteins/*genetics ; Coagulase/metabolism ; Databases, Factual ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/*methods ; Sequence Analysis, DNA ; Species Specificity ; Staphylococcal Infections/diagnosis/*microbiology ; Staphylococcus/*classification/enzymology/genetics ; Superoxide Dismutase/*genetics ; Time Factors ; }, abstract = {Simple PCR and sequencing assays that utilize a single pair of degenerate primers were used to characterize a 429-bp-long DNA fragment internal (sodA(int)) to the sodA gene encoding the manganese-dependent superoxide dismutase in 40 coagulase-negative staphylococcal (CNS) type strains. The topology of the phylogenetic tree obtained was in general agreement with that which was inferred from an analysis of their 16S rRNA or hsp60 gene sequences. Sequence analysis revealed that the staphylococcal sodA genes exhibit a higher divergence than does the corresponding 16S ribosomal DNA. These results confirm that the sodA gene constitutes a highly discriminative target sequence for differentiating closely related bacterial species. Clinical isolates that could not be identified at the species level by phenotypical tests were identified by use of this database. These results demonstrate the usefulness of this method for rapid and accurate species identification of CNS isolates, although it does not allow discrimination of subspecies. The sodA sequence polymorphisms observed with staphylococcal species offer good opportunities for the development of assays based on DNA chip technologies.}, }
@article {pmid11724832, year = {2001}, author = {Kawalec, M and Gniadkowski, M and Kedzierska, J and Skotnicki, A and Fiett, J and Hryniewicz, W}, title = {Selection of a teicoplanin-resistant Enterococcus faecium mutant during an outbreak caused by vancomycin-resistant enterococci with the vanB phenotype.}, journal = {Journal of clinical microbiology}, volume = {39}, number = {12}, pages = {4274-4282}, pmid = {11724832}, issn = {0095-1137}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics/metabolism ; Conjugation, Genetic ; *Disease Outbreaks ; Drug Resistance, Multiple, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Enterococcus faecium/classification/*drug effects/genetics ; Gene Transfer, Horizontal/genetics ; Gram-Positive Bacterial Infections/*epidemiology/microbiology ; Humans ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Mutation ; Poland/epidemiology ; Polymorphism, Restriction Fragment Length ; Teicoplanin/*pharmacology ; Vancomycin/pharmacology ; Vancomycin Resistance/*genetics ; }, abstract = {Vancomycin-resistant enterococci (VRE) have recently become an increasing problem in hospitals in Poland, being responsible for a growing number of nosocomial outbreaks. In this work, we have analyzed the second outbreak of VRE with the VanB phenotype to be identified in the country. It was caused by clonal dissemination of a single strain of vancomycin-resistant Enterococcus faecalis (VRES) and horizontal transmission of vancomycin resistance genes among several vancomycin-resistant Enterococcus faecium (VREM) strains. Two similar restriction fragment length polymorphism types of the vanB gene cluster characterized VRES and VREM isolates, and they both contained the same vanB2 variant of the vanB gene. Two vancomycin-susceptible E. faecium (VSEM) isolates, recovered from the same wards during the outbreak, proved to be related to certain VREM isolates and could represent endemic strains that had acquired vancomycin resistance. One VSEM and four VREM isolates, all identified in the same patient, belonged to a single clone, although they revealed remarkable diversity in terms of susceptibility, PFGE patterns, plasmid content, and number of vanB gene cluster copies. Most probably they reflected the dynamic evolution of an E. faecium strain in the course of infection of a single patient. One of the VREM isolates turned out to be resistant to teicoplanin, which coincided with the use of this antibiotic in the patient's therapy. Its vanB gene variant differed by a single mutation from that found in other isolates; however, it also lacked a large part of the vanB gene cluster, including the regulatory genes vanR(B) and -S(B), and the vancomycin-inducible promoter P(YB). Expression of the resistance genes vanH(B), -B, and -X(B) was constitutive in the mutant, and this phenomenon was responsible for its unusual phenotype.}, }
@article {pmid11721026, year = {2001}, author = {Pennisi, E}, title = {Microbial genomes. Sequences reveal borrowed genes.}, journal = {Science (New York, N.Y.)}, volume = {294}, number = {5547}, pages = {1634-1635}, doi = {10.1126/science.294.5547.1634b}, pmid = {11721026}, issn = {0036-8075}, mesh = {Circadian Rhythm/genetics ; Cyanobacteria/classification/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/*genetics ; *Genome, Archaeal ; *Genome, Bacterial ; Hydrogen/metabolism ; Methanosarcina/classification/*genetics/metabolism ; Nitrogen Fixation/genetics ; Phylogeny ; Rhizobium/classification/genetics ; Rhodopseudomonas/classification/*genetics/metabolism ; Terminology as Topic ; }, }
@article {pmid11719573, year = {2001}, author = {Figge, RM and Cerff, R}, title = {GAPDH gene diversity in spirochetes: a paradigm for genetic promiscuity.}, journal = {Molecular biology and evolution}, volume = {18}, number = {12}, pages = {2240-2249}, doi = {10.1093/oxfordjournals.molbev.a003770}, pmid = {11719573}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Animals ; Eukaryotic Cells/physiology ; Evolution, Molecular ; *Genetic Variation ; Glyceraldehyde-3-Phosphate Dehydrogenases/chemistry/classification/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Spirochaetales/enzymology/*genetics ; }, abstract = {In this study we have determined gap sequences from nine different spirochetes. Phylogenetic analyses of these sequences in the context of all other available eubacterial and a selection of eukaryotic Gap sequences demonstrated that the eubacterial glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene diversity encompasses at least five highly distinct gene families. Within these gene families, spirochetes show an extreme degree of sequence divergence that is probably the result of several lateral gene transfer events between spirochetes and other eubacterial phyla, and early gene duplications in the eubacterial ancestor. A Gap1 sequence from the syphilis spirochete Treponema pallidum has recently been shown to be closely related to GapC sequences from Euglenozoa. Here we demonstrate that several other spirochetal species are part of this cluster, supporting the conclusion that an interkingdom gene transfer from spirochetes to Euglenozoa must have occurred. Furthermore, we provide evidence that the GAPDH genes present in the protists Parabasalia may also be of spirochetal descent.}, }
@article {pmid11717392, year = {2001}, author = {Stathopoulos, C and Kim, W and Li, T and Anderson, I and Deutsch, B and Palioura, S and Whitman, W and Söll, D}, title = {Cysteinyl-tRNA synthetase is not essential for viability of the archaeon Methanococcus maripaludis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {98}, number = {25}, pages = {14292-14297}, pmid = {11717392}, issn = {0027-8424}, mesh = {Amino Acyl-tRNA Synthetases/genetics/*metabolism ; Gene Deletion ; Genes, Archaeal ; Methanococcus/*enzymology/genetics/growth &amp; development ; Phenotype ; }, abstract = {The methanogenic archaea Methanocaldococcus jannaschii and Methanothermobacter thermautotrophicus contain a dual-specificity prolyl-tRNA synthetase (ProCysRS) that accurately forms both prolyl-tRNA (Pro-tRNA) and cysteinyl-tRNA (Cys-tRNA) suitable for in vivo translation. This intriguing enzyme may even perform its dual role in organisms that possess a canonical single-specificity cysteinyl-tRNA synthetase (CysRS), raising the question as to whether this latter aminoacyl-tRNA synthetase is indeed required for cell viability. To test the postulate that all synthetase genes are essential, we disrupted the cysS gene (encoding CysRS) of Methanococcus maripaludis. The knockout strain was viable under normal growth conditions. Biochemical analysis showed that the pure M. maripaludis ProCysRS was capable of forming Cys-tRNA, implying that the dual-specificity enzyme compensates in vivo for the loss of CysRS. The canonical CysRS has a higher affinity for cysteine than ProCysRS, a reason why M. maripaludis may have acquired cysS by a late lateral gene transfer. These data challenge the notion that all twenty aminoacyl-tRNA synthetases are essential for the viability of a cell.}, }
@article {pmid11717283, year = {2001}, author = {Alves, AM and Euverink, GJ and Santos, H and Dijkhuizen, L}, title = {Different physiological roles of ATP- and PP(i)-dependent phosphofructokinase isoenzymes in the methylotrophic actinomycete Amycolatopsis methanolica.}, journal = {Journal of bacteriology}, volume = {183}, number = {24}, pages = {7231-7240}, pmid = {11717283}, issn = {0021-9193}, mesh = {Actinomycetales/*enzymology ; Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Carbon/metabolism ; Cloning, Molecular ; Culture Media ; Diphosphates/*metabolism ; Glucose/metabolism ; Isoenzymes/isolation &amp; purification/metabolism ; Methanol/metabolism ; Models, Biological ; Molecular Sequence Data ; Nuclear Magnetic Resonance, Biomolecular ; Phosphofructokinase-1/classification/isolation &amp; purification/*metabolism ; Phosphorus Isotopes ; Phosphotransferases/*metabolism ; Phylogeny ; Sequence Analysis, DNA ; Sequence Analysis, Protein ; Sequence Homology, Amino Acid ; }, abstract = {Cells of the actinomycete Amycolatopsis methanolica grown on glucose possess only a single, exclusively PP(i)-dependent phosphofructokinase (PP(i)-PFK) (A. M. C. R. Alves, G. J. W. Euverink, H. J. Hektor, J. van der Vlag, W. Vrijbloed, D.H.A. Hondmann, J. Visser, and L. Dijkhuizen, J. Bacteriol. 176:6827-6835, 1994). When this methylotrophic bacterium is grown on one-carbon (C(1)) compounds (e.g., methanol), an ATP-dependent phosphofructokinase (ATP-PFK) activity is specifically induced, completely replacing the PP(i)-PFK. The two A. methanolica PFK isoenzymes have very distinct functions, namely, in the metabolism of C(6) and C(1) carbon substrates. This is the first report providing biochemical evidence for the presence and physiological roles of PP(i)-PFK and ATP-PFK isoenzymes in a bacterium. The novel ATP-PFK enzyme was purified to homogeneity and characterized in detail at the biochemical and molecular levels. The A. methanolica ATP-PFK and PP(i)-PFK proteins possess a low level of amino acid sequence similarity (24%), clearly showing that the two proteins are not the result of a gene duplication event. PP(i)-PFK is closely related to other (putative) actinomycete PFK enzymes. Surprisingly, the A. methanolica ATP-PFK is most similar to ATP-PFK from the protozoon Trypanosoma brucei and PP(i)-PFK proteins from the bacteria Borrelia burgdorferi and Treponema pallidum, both spirochetes, very distinct from actinomycetes. The data thus suggest that A. methanolica obtained the ATP-PFK-encoding gene via a lateral gene transfer event.}, }
@article {pmid11711628, year = {2001}, author = {Passini, MA and Wolfe, JH}, title = {Widespread gene delivery and structure-specific patterns of expression in the brain after intraventricular injections of neonatal mice with an adeno-associated virus vector.}, journal = {Journal of virology}, volume = {75}, number = {24}, pages = {12382-12392}, pmid = {11711628}, issn = {0022-538X}, support = {DK07748/DK/NIDDK NIH HHS/United States ; NS38690/NS/NINDS NIH HHS/United States ; R01 NS038690/NS/NINDS NIH HHS/United States ; T32 DK007748/DK/NIDDK NIH HHS/United States ; DK47747/DK/NIDDK NIH HHS/United States ; DK46637/DK/NIDDK NIH HHS/United States ; R01 DK046637/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Animals, Newborn ; Brain/*virology ; Dependovirus/*genetics ; *Gene Transfer, Horizontal ; Genetic Therapy ; *Genetic Vectors ; Injections, Intraventricular ; Mice ; Mice, Inbred C3H ; }, abstract = {Developing a system for widespread somatic gene transfer in the central nervous system (CNS) would be beneficial for understanding the global influence of exogenous genes on animal models. We injected an adeno-associated virus serotype 2 (AAV2) vector into the cerebral lateral ventricles at birth and mapped its distribution and transduction pattern from a promoter capable of expression in multiple targets. The injections resulted in structure-specific patterns of expression that were maintained for at least 1 year in most regions, with efficient targeting of some of the major principal neuron layers. The patterns of transduction were explained by circulation of the viral vector in the subarachnoid space via CSF flow, followed by transduction of underlying structures, rather than by progenitor cell infection and subsequent migration. This study demonstrates that gene transfer throughout the CNS can be achieved without germ line transmission and establishes an experimental strategy for introducing genes to somatic cells in a highly predictable manner.}, }
@article {pmid11708489, year = {2001}, author = {García-Olmo, D and García-Olmo, DC}, title = {Functionality of circulating DNA: the hypothesis of genometastasis.}, journal = {Annals of the New York Academy of Sciences}, volume = {945}, number = {}, pages = {265-275}, doi = {10.1111/j.1749-6632.2001.tb03895.x}, pmid = {11708489}, issn = {0077-8923}, mesh = {Animals ; Chloramphenicol O-Acetyltransferase/genetics ; DNA, Neoplasm/*blood ; Gene Transfer, Horizontal ; Neoplasm Metastasis ; Rats ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {The detection of free, circulating tumor DNA in the plasma of cancer patients opens up new possibilities for the diagnosis and prognostication of cancer. Whatever might be the mechanism for the presence of such DNA, it is now clear that oncogenes can circulate in the plasma fraction of blood and we can now ask whether this phenomenon has potentially important implications in cancer patients. The results of our experiments, together with previous observations of other authors, have led us to propose the "Hypothesis of Genometastasis", which suggests that metastases might develop as a result of transfection of susceptible cells in distant target organs with dominant oncogenes that circulate in the plasma and are derived from the primary tumor.}, }
@article {pmid11707071, year = {2001}, author = {Jamain, S and Girondot, M and Leroy, P and Clergue, M and Quach, H and Fellous, M and Bourgeron, T}, title = {Transduction of the human gene FAM8A1 by endogenous retrovirus during primate evolution.}, journal = {Genomics}, volume = {78}, number = {1-2}, pages = {38-45}, doi = {10.1006/geno.2001.6642}, pmid = {11707071}, issn = {0888-7543}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Blotting, Northern ; Cattle ; Chickens ; DNA/chemistry/genetics ; DNA, Complementary/chemistry/genetics ; Endogenous Retroviruses/*genetics ; *Evolution, Molecular ; Female ; Gene Conversion ; Gene Expression ; Gene Transfer, Horizontal ; Humans ; Male ; Membrane Proteins ; Mice ; Molecular Sequence Data ; Mutation ; Phylogeny ; Primates/*genetics ; Proteins/*genetics ; Pseudogenes/genetics ; RNA, Messenger/genetics/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Tissue Distribution ; Turtles ; Xenopus ; }, abstract = {Capture of cellular mRNA by mobile elements has been an evolutionary catalyst for the spread of genes and a cause of cancer development. Here we present evidence that an orphan gene, FAM8A1 (family with sequence similarity 8), was captured by a retrovirus, followed by multiple retrotransposition events, during primate evolution between 45 and 58 million years ago. This represents the first record of cellular mRNA transduction in humans. The human gene is localized on chromosome 6p23 with five related pseudogenes (FAM8A2P-A6P), each inserted within a human endogenous retrovirus (HERV). Only the functional FAM8A1 gene is expressed and displays a ubiquitous mRNA and a testis-specific transcript present in the haploid phase of spermatogenesis. The structural features of the FAM8A1 pseudogenes include two short sequences of similarity between the FAM8A1 mRNA and the HERV sequences at both the 5' and 3' integration sites. These hallmarks suggest an alternative model to account for the capture of FAM8A1 cellular mRNA by HERV-K, involving illegitimate recombination events at the two sites of sequence similarity during reverse transcription. Unlike previous models, which assume at least one step of retroviral integration in the genome, our model is consistent with in vitro observations showing that multiple template switches occur among packaged viral transcripts. This leads to the speculation that, in some cases, cellular mRNAs may have been captured through similar processes involved in the retroviral life cycle.}, }
@article {pmid11705937, year = {2001}, author = {Strauch, E and Lurz, R and Beutin, L}, title = {Characterization of a Shiga toxin-encoding temperate bacteriophage of Shigella sonnei.}, journal = {Infection and immunity}, volume = {69}, number = {12}, pages = {7588-7595}, pmid = {11705937}, issn = {0019-9567}, mesh = {Bacteriophages/classification/*genetics/ultrastructure ; Coliphages/classification ; Dysentery, Bacillary/microbiology ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, Viral ; Humans ; Lysogeny ; Molecular Sequence Data ; Shiga Toxin/*genetics ; Shiga Toxins/genetics ; Shigella sonnei/*virology ; Transduction, Genetic ; }, abstract = {A Shiga toxin (Stx)-encoding temperate bacteriophage of Shigella sonnei strain CB7888 was investigated for its morphology, DNA similarity, host range, and lysogenization in Shigella and Escherichia coli strains. Phage 7888 formed plaques on a broad spectrum of Shigella strains belonging to different species and serotypes, including Stx-producing Shigella dysenteriae type 1. With E. coli, only strains with rough lipopolysaccharide were sensitive to this phage. The phage integrated into the genome of nontoxigenic S. sonnei and laboratory E. coli K-12 strains, which became Stx positive upon lysogenization. Moreover, phage 7888 is capable of transducing chromosomal genes in E. coli K-12. The relationships of phage 7888 with the E. coli Stx1-producing phage H-19B and the E. coli Stx2-producing phage 933W were investigated by DNA cross-hybridization of phage genomes and by nucleotide sequencing of an 8,053-bp DNA region of the phage 7888 genome flanking the stx genes. By these methods, a high similarity was found between phages 7888 and 933W. Much less similarity was found between phages H-19B and 7888. As in the other Stx phages, a regulatory region involved in Q-dependent expression is found upstream of stxA and stxB (stx gene) in phage 7888. The morphology of phage 7888 was similar to that of phage 933W, which shows a hexagonal head and a short tail. Our findings demonstrate that stx genes are naturally transferable and are expressed in strains of S. sonnei, which points to the continuous evolution of human-pathogenic Shigella by horizontal gene transfer.}, }
@article {pmid11703661, year = {2001}, author = {Aras, RA and Takata, T and Ando, T and van der Ende, A and Blaser, MJ}, title = {Regulation of the HpyII restriction-modification system of Helicobacter pylori by gene deletion and horizontal reconstitution.}, journal = {Molecular microbiology}, volume = {42}, number = {2}, pages = {369-382}, doi = {10.1046/j.1365-2958.2001.02637.x}, pmid = {11703661}, issn = {0950-382X}, support = {R01 GM 63270/GM/NIGMS NIH HHS/United States ; T32 AI07180-20/AI/NIAID NIH HHS/United States ; T32 CA 09385/CA/NCI NIH HHS/United States ; }, mesh = {Base Sequence ; DNA Methylation ; DNA Modification Methylases/*genetics/metabolism ; DNA Restriction Enzymes/*genetics/metabolism ; *Gene Deletion ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Genetic Variation/genetics ; Genome, Bacterial ; Helicobacter pylori/*enzymology/*genetics ; Kanamycin Resistance ; Molecular Sequence Data ; Polymerase Chain Reaction ; Sequence Alignment ; Species Specificity ; Terminal Repeat Sequences/genetics ; Transformation, Bacterial/genetics ; }, abstract = {Helicobacter pylori, Gram-negative, curved bacteria colonizing the human stomach, possess strain-specific complements of functional restriction-modification (R-M) systems. Restriction-modification systems have been identified in most bacterial species studied and are believed to have evolved to protect the host genome from invasion by foreign DNA. The large number of R-Ms homologous to those in other bacterial species and their strain-specificity suggest that H. pylori may have horizontally acquired these genes. A type IIs restriction-modification system, hpyIIRM, was active in two out of the six H. pylori strains studied. We demonstrate now that in most strains lacking M.HpyII function, there is complete absence of the R-M system. Direct DNA repeats of 80 bp flanking the hpyIIRM system allow its deletion, resulting in an "empty-site" genotype. We show that strains possessing this empty-site genotype and strains with a full but inactive hpyIIRM can reacquire the hpyIIRM cassette and functional activity through natural transformation by DNA from the parental R-M+ strain. Identical isolates divergent for the presence of an active HpyII R-M pose different restriction barriers to transformation by foreign DNA. That H. pylori can lose HpyII R-M function through deletion or mutation, and can horizontally reacquire the hpyIIRM cassette, is, in composite, a novel mechanism for R-M regulation, supporting the general hypothesis that H. pylori populations use mutation and transformation to regulate gene function.}, }
@article {pmid11701847, year = {2000}, author = {Davis, EL and Hussey, RS and Baum, TJ and Bakker, J and Schots, A and Rosso, MN and Abad, P}, title = {Nematode Parasitism Genes.}, journal = {Annual review of phytopathology}, volume = {38}, number = {}, pages = {365-396}, doi = {10.1146/annurev.phyto.38.1.365}, pmid = {11701847}, issn = {1545-2107}, abstract = {The ability of nematodes to live on plant hosts involves multiple parasitism genes. The most pronounced morphological adaptations of nematodes for plant parasitism include a hollow, protrusible stylet (feeding spear) connected to three enlarged esophageal gland cells that express products that are secreted into plant tissues through the stylet. Reverse genetic and expressed sequence tag (EST) approaches are being used to discover the parasitism genes expressed in nematode esophageal gland cells. Some genes cloned from root-knot (Meloidogyne spp.) and cyst (Heterodera and Globodera spp.) nematodes have homologues reported in genomic analyses of Caenorhabditis elegans and animal-parasitic nematodes. To date, however, the candidate parasitism genes endogenous to the esophageal glands of plant nematodes (such as the ß-1,4-endoglucanases) have their greatest similarity to microbial genes, prompting speculation that genes for plant parasitism by nematodes may have been acquired by horizontal gene transfer.}, }
@article {pmid11701846, year = {2000}, author = {Rosewich, UL and Kistler, HC}, title = {Role of Horizontal Gene Transfer in the Evolution of Fungi.}, journal = {Annual review of phytopathology}, volume = {38}, number = {}, pages = {325-363}, doi = {10.1146/annurev.phyto.38.1.325}, pmid = {11701846}, issn = {1545-2107}, abstract = {Although evidence for horizontal gene transfer (HGT) in eukaryotes remains largely anecdotal, literature on HGT in fungi suggests that it may have been more important in the evolution of fungi than in other eukaryotes. Still, HGT in fungi has not been widely accepted because the mechanisms by which it may occur are unknown, because it is usually not directly observed but rather implied as an outcome, and because there are often equally plausible alternative explanations. Despite these reservations, HGT has been justifiably invoked for a variety of sequences including plasmids, introns, transposons, genes, gene clusters, and even whole chromosomes. In some instances HGT has also been confirmed under experimental conditions. It is this ability to address the phenomenon in an experimental setting that makes fungi well suited as model systems in which to study the mechanisms and consequences of HGT in eukaryotic organisms.}, }
@article {pmid11701624, year = {2000}, author = {Thornton, JW and DeSalle, R}, title = {Gene family evolution and homology: genomics meets phylogenetics.}, journal = {Annual review of genomics and human genetics}, volume = {1}, number = {}, pages = {41-73}, doi = {10.1146/annurev.genom.1.1.41}, pmid = {11701624}, issn = {1527-8204}, mesh = {Animals ; *Biological Evolution ; Gene Duplication ; Genetic Variation ; Genomics ; Humans ; Likelihood Functions ; Models, Genetic ; *Multigene Family ; Phylogeny ; Proteins/genetics ; }, abstract = {With the advent of high-throughput DNA sequencing and whole-genome analysis, it has become clear that the coding portions of the genome are organized hierarchically in gene families and superfamilies. Because the hierarchy of genes, like that of living organisms, reflects an ancient and continuing process of gene duplication and divergence, many of the conceptual and analytical tools used in phylogenetic systematics can and should be used in comparative genomics. Phylogenetic principles and techniques for assessing homology, inferring relationships among genes, and reconstructing evolutionary events provide a powerful way to interpret the ever increasing body of sequence data. In this review, we outline the application of phylogenetic approaches to comparative genomics, beginning with the inference of phylogeny and the assessment of gene orthology and paralogy. We also show how the phylogenetic approach makes possible novel kinds of comparative analysis, including detection of domain shuffling and lateral gene transfer, reconstruction of the evolutionary diversification of gene families, tracing of evolutionary change in protein function at the amino acid level, and prediction of structure-function relationships. A marriage of the principles of phylogenetic systematics with the copious data generated by genomics promises unprecedented insights into the nature of biological organization and the historical processes that created it.}, }
@article {pmid11701618, year = {2001}, author = {Dumasius, V and Sznajder, JI and Azzam, ZS and Boja, J and Mutlu, GM and Maron, MB and Factor, P}, title = {beta(2)-adrenergic receptor overexpression increases alveolar fluid clearance and responsiveness to endogenous catecholamines in rats.}, journal = {Circulation research}, volume = {89}, number = {10}, pages = {907-914}, doi = {10.1161/hh2201.100204}, pmid = {11701618}, issn = {1524-4571}, support = {HL-48129/HL/NHLBI NIH HHS/United States ; HL-66211/HL/NHLBI NIH HHS/United States ; }, mesh = {Adenoviridae/genetics ; Animals ; Carrier Proteins/metabolism ; Catecholamines/*metabolism/pharmacology ; Cell Line ; Cell Membrane/chemistry/metabolism ; DNA, Complementary/administration &amp; dosage/genetics ; Epithelial Cells/cytology/drug effects/*metabolism ; Epithelial Sodium Channels ; Gene Transfer, Horizontal ; Humans ; Ion Transport/drug effects ; Lung/cytology/drug effects/metabolism ; Male ; Mucociliary Clearance/*physiology ; Procaterol/pharmacology ; Pulmonary Alveoli/cytology/drug effects/*metabolism ; RNA, Messenger/metabolism ; Rats ; Rats, Sprague-Dawley ; Receptors, Adrenergic, beta-2/administration &amp; dosage/*biosynthesis/genetics ; Sodium/metabolism ; Sodium Channels/metabolism ; Sodium-Potassium-Exchanging ATPase/metabolism ; }, abstract = {beta-Adrenergic agonists accelerate the clearance of alveolar fluid by increasing the expression and activity of epithelial solute transport proteins such as amiloride-sensitive epithelial Na(+) channels (ENaC) and Na,K-ATPases. Here we report that adenoviral-mediated overexpression of a human beta(2)-adrenergic receptor (beta(2)AR) cDNA increases beta(2)AR mRNA, membrane-bound receptor protein expression, and receptor function (procaterol-induced cAMP production) in human lung epithelial cells (A549). Receptor overexpression was associated with increased catecholamine (procaterol)-responsive active Na(+) transport and increased abundance of Na,K-ATPases in the basolateral cell membrane. beta(2)AR gene transfer to the alveolar epithelium of normal rats improved membrane-bound beta(2)AR expression and function and increased levels of ENaC (alpha subunit) abundance and Na,K-ATPases activity in apical and basolateral cell membrane fractions isolated from the peripheral lung, respectively. Alveolar fluid clearance (AFC), an index of active Na(+) transport, in beta(2)AR overexpressing rats was up to 100% greater than sham-infected controls and rats infected with an adenovirus that expresses no cDNA. The addition of the beta(2)AR-specific agonist procaterol to beta(2)AR overexpressing lungs did not increase AFC further. AFC in beta(2)AR overexpressing lungs from adrenalectomized or propranolol-treated rats revealed clearance rates that were the same or less than normal, untreated, sham-infected controls. These experiments indicate that alveolar beta(2)AR overexpression improves beta(2)AR function and maximally upregulates beta-agonist-responsive active Na(+) transport by improving responsiveness to endogenous catecholamines. These studies suggest that upregulation of beta(2)AR function may someday prove useful for the treatment of pulmonary edema.}, }
@article {pmid11700366, year = {2001}, author = {Sandner, L and Eguiarte, LE and Navarro, A and Cravioto, A and Souza, V}, title = {The elements of the locus of enterocyte effacement in human and wild mammal isolates of Escherichia coli: evolution by assemblage or disruption?.}, journal = {Microbiology (Reading, England)}, volume = {147}, number = {Pt 11}, pages = {3149-3158}, doi = {10.1099/00221287-147-11-3149}, pmid = {11700366}, issn = {1350-0872}, mesh = {Adhesins, Bacterial/genetics ; Animals ; Animals, Wild ; Bacterial Outer Membrane Proteins/genetics ; Binding Sites ; Blotting, Southern ; Carrier Proteins/genetics ; Escherichia coli/classification/*genetics/pathogenicity ; Escherichia coli Infections/microbiology/veterinary ; Escherichia coli Proteins/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Humans ; Mammals ; Molecular Chaperones/genetics ; Phylogeny ; Polymerase Chain Reaction ; Serotyping ; Species Specificity ; Virulence/genetics ; }, abstract = {Escherichia coli is an excellent model for studying the evolution of pathogenicity since within one species various genes can be found in pathogenic islands and plasmids causing a wide spectrum of virulence. A collection of 122 strains from different human and wild mammal hosts were analysed by PCR and Southern hybridization for the presence of a subset of the genes included in the LEE (locus of enterocyte effacement). In the PCR analysis, two markers (cesT/eae and espB genes) were found together in more strains (25.4%) than either were found alone. The cesT/eae gene was less frequently found alone (8.2%) than was the espB gene (15.6%). Four regions of the LEE were analysed in a subsample of 25 strains using Southern hybridization. The four regions were all present (44%), all absent (12%) or present in different combinations (44%) in a given strain. The flanking regions of the LEE showed the highest rate of hybridization (in 72% of the strains). The results indicate that the LEE is a dynamic genetic entity, both the complete gene cluster and the individual genes. The genes that comprise this locus seem to be horizontally acquired (or lost) in an independent way and may control other functions in non-pathogenic E. coli lineages. In this way, horizontal transfer may allow the gradual stepwise construction of gene cassettes facilitating coordinate regulation and expression of novel functions.}, }
@article {pmid11693658, year = {2001}, author = {Qian, Q and Keeling, PJ}, title = {Diplonemid glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and prokaryote-to-eukaryote lateral gene transfer.}, journal = {Protist}, volume = {152}, number = {3}, pages = {193-201}, doi = {10.1078/1434-4610-00059}, pmid = {11693658}, issn = {1434-4610}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; DNA, Protozoan ; Eukaryota/classification/*enzymology/genetics ; Eukaryotic Cells ; Gene Transfer Techniques ; Genes, Protozoan ; Glyceraldehyde-3-Phosphate Dehydrogenases/*genetics ; Molecular Sequence Data ; Phylogeny ; Prokaryotic Cells ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; }, abstract = {Lateral gene transfer refers to the movement of genetic information from one genome to another, and the integration of that foreign DNA into its new genetic environment. There are currently only a few well-supported cases of prokaryote-to-eukaryote transfer known that do not involve mitochondria or plastids, but it is not clear whether this reflects a lack of such transfer events, or poor sampling of diverse eukaryotes. One gene where this process is apparently active is glyceraldehyde-3-phosphate dehydrogenase (GAPDH), where lateral transfer has been implicated in the origin of euglenoid and kinetoplastid genes. We have characterised GAPDH genes from diplonemids, heterotrophic flagellates that are closely related to kinetoplastids and euglenoids. Two distinct classes of diplonemid GAPDH genes were found in diplonemids, however, neither class is closely related to any other euglenozoan GAPDH. One diplonemid GAPDH is related to the cytosolic gapC of eukaryotes, although not to either euglenoids or kinetoplastids, and the second is related to cyanobacterial and proteobacterial gap3. The bacterial gap3 gene in diplonemids provides one of the most well-supported examples of lateral gene transfer from a bacterium to a eukaryote characterised to date, and may indicate that diplonemids have acquired a novel biochemical capacity through lateral transfer.}, }
@article {pmid11691918, year = {2001}, author = {Saves, I and Westrelin, F and Daffé, M and Masson, JM}, title = {Identification of the first eubacterial endonuclease coded by an intein allele in the pps1 gene of mycobacteria.}, journal = {Nucleic acids research}, volume = {29}, number = {21}, pages = {4310-4318}, pmid = {11691918}, issn = {1362-4962}, mesh = {ATP-Binding Cassette Transporters/genetics/isolation &amp; purification/*metabolism ; *Alleles ; Amino Acid Sequence ; Bacterial Proteins/genetics/isolation &amp; purification/*metabolism ; Base Sequence ; Buffers ; Cloning, Molecular ; Conserved Sequence ; Endonucleases/genetics/isolation &amp; purification/*metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/genetics ; Hydrogen-Ion Concentration ; Models, Genetic ; Molecular Sequence Data ; Mycobacterium/*enzymology/*genetics ; Recombination, Genetic/genetics ; Sequence Alignment ; Substrate Specificity ; }, abstract = {A survey of a vast range of mycobacterial strains led us to discover a new Pps1 intein allele in Mycobacterium gastri which differs from those of Mycobacterium tuberculosis and Mycobacterium leprae in both its sequence and insertion site. While little is known about Pps1, except that it belongs to the YC24 family of ABC transporters, we show that, unlike the other inteins described so far from Eubacteria, the MgaPps1 intein possesses a specific endonuclease activity. The intein is the first eubacterial intein to be characterised as an endonuclease. Like other intein endonucleases, its minimal sequence for recognition and cleavage is quite large, with 22 bp spanning the Pps1-c site. The fact that an active endonuclease is found among the mycobacterial inteins supports the concept of a cyclical model of invasion by horizontal transfer of these genes, followed by degeneration and loss until a new invasion event, thus explaining their long-term persistence in closely related eubacterial species.}, }
@article {pmid11689266, year = {2001}, author = {Guo, W and Lee, RJ}, title = {Efficient gene delivery via non-covalent complexes of folic acid and polyethylenimine.}, journal = {Journal of controlled release : official journal of the Controlled Release Society}, volume = {77}, number = {1-2}, pages = {131-138}, doi = {10.1016/s0168-3659(01)00456-4}, pmid = {11689266}, issn = {0168-3659}, mesh = {DNA/*administration &amp; dosage ; Folic Acid/*administration &amp; dosage ; Gene Transfer, Horizontal ; *Genetic Therapy ; Humans ; KB Cells ; Particle Size ; Polyethyleneimine/*administration &amp; dosage ; *Transfection ; }, abstract = {Polyethylenimine (PEI) is a cationic polymer capable of delivering DNA molecules into cultured mammalian cells as charge complexes. The application of PEI polyplexes in gene therapy, however, is hampered by the sensitivity of its transfection activity to the presence of serum. We found that folic acid, in a variety of cell lines, significantly enhanced PEI-mediated transfection activity in the presence of serum, whether the folic acid was added during or after PEI/DNA polyplex formation. The increase in activity could not be produced with other anionic compounds such as cholic acid, citric acid, EDTA, or glutamic acid. This novel formulation provides a reliable, low-cost, and highly efficient method for delivery of genes and may have applications in gene therapy.}, }
@article {pmid11687652, year = {2001}, author = {Escobar, MA and Civerolo, EL and Summerfelt, KR and Dandekar, AM}, title = {RNAi-mediated oncogene silencing confers resistance to crown gall tumorigenesis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {98}, number = {23}, pages = {13437-13442}, pmid = {11687652}, issn = {0027-8424}, mesh = {Arabidopsis/*genetics ; *Bacterial Proteins ; DNA, Plant/genetics ; Gene Silencing/*physiology ; Genes, Bacterial ; Indoleacetic Acids/genetics ; Solanum lycopersicum/*genetics ; *Oncogenes ; Plant Tumors/*genetics ; RNA, Plant/*physiology ; Rhizobium/genetics ; Transformation, Genetic ; }, abstract = {Crown gall disease, caused by the soil bacterium Agrobacterium tumefaciens, results in significant economic losses in perennial crops worldwide. A. tumefaciens is one of the few organisms with a well characterized horizontal gene transfer system, possessing a suite of oncogenes that, when integrated into the plant genome, orchestrate de novo auxin and cytokinin biosynthesis to generate tumors. Specifically, the iaaM and ipt oncogenes, which show approximately 90% DNA sequence identity across studied A. tumefaciens strains, are required for tumor formation. By expressing two self-complementary RNA constructions designed to initiate RNA interference (RNAi) of iaaM and ipt, we generated transgenic Arabidopsis thaliana and Lycopersicon esculentum plants that are highly resistant to crown gall disease development. In in vitro root inoculation bioassays with two biovar I strains of A. tumefaciens, transgenic Arabidopsis lines averaged 0.0-1.5% tumorigenesis, whereas wild-type controls averaged 97.5% tumorigenesis. Similarly, several transformed tomato lines that were challenged by stem inoculation with three biovar I strains, one biovar II strain, and one biovar III strain of A. tumefaciens displayed between 0.0% and 24.2% tumorigenesis, whereas controls averaged 100% tumorigenesis. This mechanism of resistance, which is based on mRNA sequence homology rather than the highly specific receptor-ligand binding interactions characteristic of traditional plant resistance genes, should be highly durable. If successful and durable under field conditions, RNAi-mediated oncogene silencing may find broad applicability in the improvement of tree crop and ornamental rootstocks.}, }
@article {pmid11686382, year = {2001}, author = {Schmidt, H}, title = {Shiga-toxin-converting bacteriophages.}, journal = {Research in microbiology}, volume = {152}, number = {8}, pages = {687-695}, doi = {10.1016/s0923-2508(01)01249-9}, pmid = {11686382}, issn = {0923-2508}, mesh = {Bacteriophages/*genetics/ultrastructure ; Chromosome Mapping ; Gene Expression Regulation, Viral ; Shiga Toxin/*genetics ; Transduction, Genetic ; }, abstract = {Shiga toxins (Stx) comprise a family of potent cytotoxins that are involved in severe human disease. Stx are mainly produced by Escherichia coli isolated from human and nonhuman sources, and by Shigella dysenteriae type 1. The genes encoding Stx are thought to be generally encoded in the genome of lambdoid prophages (Stx-converting bacteriophages; Stx phages). They share a unique position in the late region of the phage genome downstream of the late promoter PR'. This location suggests that expression of stx is controlled by a Q-like antiterminator. Therefore, induction of Stx-converting prophages appears to trigger increased production of Stx. Following induction, Stx phages can be transduced in vivo and in vitro into other bacteria. Stx phages play an important role in the expression of Stx and in lateral gene transfer and are therefore a contribution to the emergence of new Stx-producing E. coli (STEC) variants.}, }
@article {pmid11683362, year = {2001}, author = {Cai, S and Wiedmann, M}, title = {Characterization of the prfA virulence gene cluster insertion site in non-hemolytic Listeria spp.: probing the evolution of the Listeria virulence gene island.}, journal = {Current microbiology}, volume = {43}, number = {4}, pages = {271-277}, doi = {10.1007/s002840010300}, pmid = {11683362}, issn = {0343-8651}, mesh = {Animals ; Bacterial Proteins/*genetics ; Base Sequence ; DNA Primers/genetics ; DNA Transposable Elements/genetics ; DNA, Intergenic/genetics ; *Evolution, Molecular ; *Genes, Bacterial ; Hemolysin Proteins/metabolism ; Humans ; L-Lactate Dehydrogenase/genetics ; Listeria/genetics/*pathogenicity ; Listeriosis/microbiology ; Molecular Sequence Data ; Multigene Family ; *Mutagenesis, Insertional ; Peptide Termination Factors ; Polymerase Chain Reaction ; Ribose-Phosphate Pyrophosphokinase/genetics ; Sequence Analysis, DNA ; Trans-Activators/*genetics ; Virulence/genetics ; }, abstract = {The prfA virulence gene cluster is present between prs and ldh in the pathogenic L. monocytogenes and L. ivanovii, but absent from the non-pathogenic L. innocua and L. welshimeri. To probe the evolution of this virulence gene cluster, we sequenced the prs-ldh intergenic region in L. welshimeri and L. innocua. Two ORFs (ORFA and ORFB) were found in both species as well as in L. monocytogenes. Another ORF of unknown function (ORFZ) was found in L. monocytogenes and L. innocua, while two unique ORFs were present in L. welshimeri. ORFA and ORFB showed significant functional constraint, suggesting that further investigations in the functions of these genes, including possible roles in horizontal gene transfer or sequence deletion, are warranted. DNA sequences homologous to Tn1545 integration consensus sequences were found downstream of prs and ORFB, thus defining the likely junctions of the virulence gene island and indicating that the prs-ldh intergenic region may represent a Tn insertion hot spot. Our results are consistent with the hypothesis that a combination of horizontal gene transfer and deletion events mayhave been involved in the evolution of the prfA virulence gene cluster in Listeria.}, }
@article {pmid11682304, year = {2001}, author = {Ragan, MA}, title = {Detection of lateral gene transfer among microbial genomes.}, journal = {Current opinion in genetics &amp; development}, volume = {11}, number = {6}, pages = {620-626}, doi = {10.1016/s0959-437x(00)00244-6}, pmid = {11682304}, issn = {0959-437X}, mesh = {Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Genetics, Microbial ; *Genome, Bacterial ; Phylogeny ; }, abstract = {An increasingly comprehensive assessment is being developed of the extent and potential significance of lateral gene transfer among microbial genomes. Genomic sequences can be identified as being of putatively lateral origin by their unexpected phyletic distribution, atypical sequence composition, differential presence or absence in closely related genomes, or incongruent phylogenetic trees. These complementary approaches sometimes yield inconsistent results. Not only more data but also quantitative models and simulations are needed urgently.}, }
@article {pmid11682303, year = {2001}, author = {Ochman, H}, title = {Lateral and oblique gene transfer.}, journal = {Current opinion in genetics &amp; development}, volume = {11}, number = {6}, pages = {616-619}, doi = {10.1016/s0959-437x(00)00243-4}, pmid = {11682303}, issn = {0959-437X}, mesh = {Escherichia coli/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Genome ; Humans ; Species Specificity ; Virulence ; }, abstract = {Sequence information from complete genomes, and from multiple loci of strains within species, is transforming the way that we investigate the evolution of bacteria. Such large-scale assessments of bacterial genomes have provided evidence of extensive gene transfer and exchange. Except in rare cases, these two processes do not seem to be coupled: certain species, such as Escherichia coli, undergo relatively low levels of gene exchange; but the emergence of pathogenic strains is associated with the acquisition of numerous virulence factors by lateral gene transfer.}, }
@article {pmid11679669, year = {2001}, author = {Glaser, P and Frangeul, L and Buchrieser, C and Rusniok, C and Amend, A and Baquero, F and Berche, P and Bloecker, H and Brandt, P and Chakraborty, T and Charbit, A and Chetouani, F and Couvé, E and de Daruvar, A and Dehoux, P and Domann, E and Domínguez-Bernal, G and Duchaud, E and Durant, L and Dussurget, O and Entian, KD and Fsihi, H and García-del Portillo, F and Garrido, P and Gautier, L and Goebel, W and Gómez-López, N and Hain, T and Hauf, J and Jackson, D and Jones, LM and Kaerst, U and Kreft, J and Kuhn, M and Kunst, F and Kurapkat, G and Madueno, E and Maitournam, A and Vicente, JM and Ng, E and Nedjari, H and Nordsiek, G and Novella, S and de Pablos, B and Pérez-Diaz, JC and Purcell, R and Remmel, B and Rose, M and Schlueter, T and Simoes, N and Tierrez, A and Vázquez-Boland, JA and Voss, H and Wehland, J and Cossart, P}, title = {Comparative genomics of Listeria species.}, journal = {Science (New York, N.Y.)}, volume = {294}, number = {5543}, pages = {849-852}, doi = {10.1126/science.1063447}, pmid = {11679669}, issn = {0036-8075}, mesh = {Adaptation, Physiological ; Amino Acid Motifs ; Bacillus subtilis/genetics ; Bacterial Proteins/chemistry/*genetics/physiology ; Base Composition ; Carrier Proteins/chemistry/genetics ; Chromosomes, Bacterial/genetics ; DNA, Bacterial/chemistry/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; Genomics ; Listeria/chemistry/*genetics/physiology ; Listeria monocytogenes/chemistry/*genetics/pathogenicity/physiology ; Membrane Proteins/chemistry/genetics ; Sequence Analysis, DNA ; Staphylococcus aureus/genetics ; Transcription Factors/chemistry/genetics ; Virulence/genetics ; }, abstract = {Listeria monocytogenes is a food-borne pathogen with a high mortality rate that has also emerged as a paradigm for intracellular parasitism. We present and compare the genome sequences of L. monocytogenes (2,944,528 base pairs) and a nonpathogenic species, L. innocua (3,011,209 base pairs). We found a large number of predicted genes encoding surface and secreted proteins, transporters, and transcriptional regulators, consistent with the ability of both species to adapt to diverse environments. The presence of 270 L. monocytogenes and 149 L. innocua strain-specific genes (clustered in 100 and 63 islets, respectively) suggests that virulence in Listeria results from multiple gene acquisition and deletion events.}, }
@article {pmid11677619, year = {2001}, author = {Gomulski, LM and Torti, C and Bonizzoni, M and Moralli, D and Raimondi, E and Capy, P and Gasperi, G and Malacrida, AR}, title = {A new basal subfamily of mariner elements in Ceratitis rosa and other tephritid flies.}, journal = {Journal of molecular evolution}, volume = {53}, number = {6}, pages = {597-606}, doi = {10.1007/s002390010246}, pmid = {11677619}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Chromosome Mapping ; Cloning, Molecular ; DNA ; *DNA Transposable Elements ; DNA-Binding Proteins/*genetics ; Diptera/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis, DNA ; Transposases ; }, abstract = {Several copies of highly related transposable elements, Crmar2, Almar1, and Asmar1, are described from the genomes of Ceratitis rosa, Anastrepha ludens, and A. suspensa, respectively. One copy from C. rosa, Crmar2.5, contains a full-length, uninterrupted ORF. All the other copies, from the three species contain a long deletion within the putative ORF. The consensus Crmar2 element has features typical of the mariner/Tc1 superfamily of transposable elements. In particular, the Crmar2 consensus encodes a D,D41D motif, a variant of the D,D34D catalytic domain of mariner elements. Phylogenetic analysis of the relationships of these three elements and other members of the mariner/Tc1 superfamily, based on their encoded amino acid sequences, suggests that they form a new basal subfamily of mariner elements, the rosa subfamily. BLAST analyses identified sequences from other diptera, including Drosophila melanogaster, which appear to be members of the rosa subfamily of mariner elements. Analyses of their molecular evolution suggests that Crmar2 entered the genome of C. rosa in the recent past, a consequence of horizontal transfer.}, }
@article {pmid11676394, year = {2001}, author = {Gitelson, E and Ghose, A and Buckstein, R and Imrie, K and Lim, MS and Reis, M and Spaner, D and Tartaglia, J and Berinstein, NL}, title = {ALVAC-mediated gene transfer is efficient in lymphoid malignancies of T-and early B-cell origin, but not in tumors arising from mature B-cells.}, journal = {Cancer immunology, immunotherapy : CII}, volume = {50}, number = {7}, pages = {345-355}, doi = {10.1007/s002620100209}, pmid = {11676394}, issn = {0340-7004}, mesh = {Animals ; Antigens, CD/genetics/physiology ; Avipoxvirus/*genetics ; B-Lymphocytes/*metabolism ; B7-1 Antigen/genetics/physiology ; B7-2 Antigen ; *Gene Transfer, Horizontal ; *Genetic Vectors ; Humans ; Interferon-gamma/biosynthesis ; Leukemia/*metabolism ; Lymphocyte Activation ; Lymphoma/*metabolism ; Membrane Glycoproteins/genetics/physiology ; Mice ; T-Lymphocytes/immunology ; Tumor Cells, Cultured ; }, abstract = {Natural attenuation of ALVAC virus in mammals makes it an attractive vector for cancer vaccine therapy of immunocompromised hosts, such as patients with lymphoid malignancies. However, the transduction efficiency of ALVAC constructs in lymphoid tumors has not yet been characterized. We studied a wide spectrum of human T- and B-cell leukemia and lymphomas and found significant heterogeneity of the ALVAC-mediated gene product expression in these tumors. While ALVAC-B7.1, ALVAC-B7.2, or ALVAC-luciferase vectors effectively expressed recombinant genes in malignancies arising from T- or early B-cell precursors, negative or low expression of ALVAC recombinant genes occurred in tumors arising from mature B-cells. We showed that ALVAC-encoded B7.1 or B7.2 was continuously expressed on the infected, and subsequently irradiated, leukemia cells, and only cells with ALVAC-mediated expression of costimulatory molecules (but not unmodified leukemia cells or those infected with the ALVAC-parental vector) induced significant proliferation and IFN-gamma production by alloreactive T-cells. These data provide the rationale for clinical studies using the ALVAC vector system for gene transfer into lymphoid tumors of T- and early B-cell origin to render them more immunogenic, while alternative strategies should be considered for immunotherapy of mature B-cell malignancies.}, }
@article {pmid11675594, year = {2001}, author = {Nesbø, CL and Boucher, Y and Doolittle, WF}, title = {Defining the core of nontransferable prokaryotic genes: the euryarchaeal core.}, journal = {Journal of molecular evolution}, volume = {53}, number = {4-5}, pages = {340-350}, doi = {10.1007/s002390010224}, pmid = {11675594}, issn = {0022-2844}, mesh = {Archaea/*genetics ; Archaeal Proteins/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Archaeal ; *Models, Genetic ; Phylogeny ; Prokaryotic Cells ; }, abstract = {If lateral gene transfer (LGT) has affected all genes over the course of prokaryotic evolution, reconstruction of organismal phylogeny is compromised. However, if a core of genes is immune to transfer, then the evolutionary history of that core might be our most reliable guide to the evolution of organisms. Such a core should be preferentially included in the subset of genes shared by all organisms, but where universally conserved genes have been analyzed, there is too little phylogenetic signal to allow determination of whether or not they indeed have the same history (Hansmann and Martin 2000; Teichmann and Mitchison 1999). Here we look at a more restricted set, 521 homologous genes (COGs) simultaneously present in four sequenced euryarchaeal genomes. Although there is overall little robust phylogenetic signal in this data set, there is, among well-supported trees, strong representation of all three possible four-taxon topologies. "Informational" genes seem no less subject to LGT than are "operational genes," within the euryarchaeotes. We conclude that (i) even in this collection of conserved genes there has been extensive LGT (orthologous gene replacement) and (ii) the notion that there is a core of nontransferable genes (the "core hypothesis") has not been proven and may be unprovable.}, }
@article {pmid11673568, year = {2001}, author = {Okuda, K and Xin, KQ and Haruki, A and Kawamoto, S and Kojima, Y and Hirahara, F and Okada, H and Klinman, D and Hamajima, K}, title = {Transplacental genetic immunization after intravenous delivery of plasmid DNA to pregnant mice.}, journal = {Journal of immunology (Baltimore, Md. : 1950)}, volume = {167}, number = {9}, pages = {5478-5484}, doi = {10.4049/jimmunol.167.9.5478}, pmid = {11673568}, issn = {0022-1767}, mesh = {AIDS Vaccines/immunology ; Amino Acid Sequence ; Animals ; Female ; Fetus/*immunology ; Gene Transfer, Horizontal ; Immunity, Maternally-Acquired ; Influenza Vaccines/immunology ; Injections, Intravenous ; Mice ; Mice, Inbred BALB C ; Molecular Sequence Data ; Plasmids ; Pregnancy ; Pregnancy, Animal/*immunology ; Vaccination ; Vaccines, DNA/*administration &amp; dosage/immunology ; }, abstract = {A number of factors influence the development of tolerance, including the nature, concentration, and mode of Ag presentation to the immune system, as well as the age of the host. The studies were conducted to determine whether immunizing pregnant mice with liposome-encapsulated DNA vaccines had an effect on the immune status of their offspring. Two different plasmids (encoding Ags from HIV-1 and influenza virus) were administered i.v. to pregnant mice. We examined the uptake of plasmid DNA by the fetuses until the 21st postcoital day, but little such transfer occurred in early pregnancy. At 9.5 days postconception with cationic liposomes, injected plasmid was present in the tissues of the fetus, consistent with transplacental transfer. When the offspring of vaccinated dams were immunized with DNA vaccine, they mounted stronger Ag-specific immune responses than controls, and were protected against challenge by homologous influenza virus after vaccination. Moreover, such immune responses were strong in the offspring of mothers injected with DNA plasmid 9.5 days after coitus. These results suggest that DNA-vaccinated mothers confer the Ag-specific immunity to their progeny.}, }
@article {pmid11672878, year = {2001}, author = {Sakamoto, T and Ikeda, Y and Yonemitsu, Y}, title = {Gene targeting to the retina.}, journal = {Advanced drug delivery reviews}, volume = {52}, number = {1}, pages = {93-102}, doi = {10.1016/s0169-409x(01)00191-0}, pmid = {11672878}, issn = {0169-409X}, mesh = {Adenoviridae/genetics ; Animals ; Dependovirus/genetics ; Gene Transfer, Horizontal ; *Genetic Therapy ; Genetic Vectors ; Humans ; Lentivirus/genetics ; Retinal Diseases/*therapy ; }, }
@article {pmid11642121, year = {2001}, author = {Matveeva, TV and Lutova, LA and Nester, Iu}, title = {[Tumor formation in plants].}, journal = {Genetika}, volume = {37}, number = {9}, pages = {1188-1197}, pmid = {11642121}, issn = {0016-6758}, mesh = {Gene Transfer, Horizontal ; Hybridization, Genetic ; *Plant Diseases/genetics/microbiology ; Rhizobium/pathogenicity ; }, abstract = {The data on genetic tumors in plant species and interspecific hybrids, as well as the problems of Agrobacterium-induced tumors are reviewed. The role of the horizontal gene transfer in the induction of genetic tumors is discussed.}, }
@article {pmid11641524, year = {2001}, author = {Rha, SJ and Wang, YP}, title = {Enhanced expressions and histological characteristics of intravenously administered plasmid DNA in rat lung.}, journal = {Journal of Korean medical science}, volume = {16}, number = {5}, pages = {567-572}, doi = {10.3346/jkms.2001.16.5.567}, pmid = {11641524}, issn = {1011-8934}, mesh = {Animals ; DNA/*administration &amp; dosage/metabolism ; Galactosides/analysis ; Gene Transfer, Horizontal ; *Genetic Therapy ; Immunohistochemistry ; Indoles/analysis ; Injections, Intravenous ; Lung/*metabolism ; Male ; *Plasmids ; Rats ; Rats, Inbred F344 ; *Transfection ; }, abstract = {Cationic liposome-mediated gene transfection is a promising method for gene therapy. In this study, the transfection efficiency and histological patterns were evaluated in rat lung after intravenous administration via femoral vein of naked plasmid DNA, naked plasmid DNA with pretreatment of DOTAP, and DOTAP-cholesterol-plasmid DNA complex. Plasmid DNA encoding bacterial LacZ gene was used. For quantification of LacZ gene expression, beta-galactosidase assay was performed. For histologic examination, X-gal staining and immunohistochemical staining for transfected gene products were performed. Pretreatment of DOTAP prior to the infusion of naked plasmid DNA increased transfection efficiency up to a level comparable to DOTAP-cholesterol-plasmid DNA complex injection. Transfected genes were mainly expressed in type II pneumocytes and alveolar macrophages in all animals. We conclude that the high transfection efficiency is achievable by intravenous administration of naked plasmid DNA with pretreatment of DOTAP, to a level comparable to DOTAP-cholesterol-plasmid DNA complex. In this regard, naked plasmid DNA administration with pretreatment of DOTAP could be a more feasible option for intravenous gene transfer than DOTAP-cholesterol-plasmid DNA complex, in that the former is technically easier and more cost-effective than the latter with a comparable efficacy, in terms of intravenous gene delivery to the lung.}, }
@article {pmid11606630, year = {2001}, author = {Philip, N and Acevedo, SF and Skoulakis, EM}, title = {Conditional rescue of olfactory learning and memory defects in mutants of the 14-3-3zeta gene leonardo.}, journal = {The Journal of neuroscience : the official journal of the Society for Neuroscience}, volume = {21}, number = {21}, pages = {8417-8425}, pmid = {11606630}, issn = {1529-2401}, mesh = {14-3-3 Proteins ; Alleles ; Animals ; Behavior, Animal/physiology ; Conditioning, Psychological/physiology ; Drosophila ; Ganglia, Invertebrate/metabolism ; Gene Expression Regulation/physiology ; Gene Transfer, Horizontal ; Genes, Lethal ; Learning/*physiology ; Memory/physiology ; Memory Disorders/*genetics ; Mutation ; Neuronal Plasticity/physiology ; Phenotype ; Smell/*physiology ; Stimulation, Chemical ; Transgenes ; Tyrosine 3-Monooxygenase/*genetics/*metabolism ; }, abstract = {Members of the ubiquitous 14-3-3 family of proteins are abundantly expressed in metazoan neurons. The Drosophila 14-3-3zeta gene leonardo is preferentially expressed in adult mushroom bodies, centers of insect learning and memory. Mutants exhibit defects in olfactory learning and memory and physiological neuroplasticity at the neuromuscular junction. Because strong mutations in this gene are lethal, we investigated the nature of the defects that precipitate the learning and memory deficit and the role of the two protein isoforms encoded by leonardo in these processes. We find that the behavioral deficit in the mutants is not caused by aberrant development, LEONARDO protein is acutely required for learning and memory, and both protein isoforms can function equivalently in embryonic development and behavioral neuroplasticity.}, }
@article {pmid11601904, year = {2001}, author = {Desiere, F and McShan, WM and van Sinderen, D and Ferretti, JJ and Brüssow, H}, title = {Comparative genomics reveals close genetic relationships between phages from dairy bacteria and pathogenic Streptococci: evolutionary implications for prophage-host interactions.}, journal = {Virology}, volume = {288}, number = {2}, pages = {325-341}, doi = {10.1006/viro.2001.1085}, pmid = {11601904}, issn = {0042-6822}, support = {AI19034/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteriophages/*genetics ; *Evolution, Molecular ; *Genome, Viral ; Lactococcus lactis/genetics/*virology ; Streptococcus Phages/*genetics ; Streptococcus pyogenes/genetics/*virology ; }, abstract = {The genome of the highly pathogenic M1 serotype Streptococcus pyogenes isolate SF370 contains eight prophage elements. Only prophage SF370.1 could be induced by mitomycin C treatment. Prophage SF370.3 showed a 33.5-kb-long genome that closely resembled the genome organization of the cos-site temperate Siphovirus r1t infecting the dairy bacterium Lactococcus lactis. The two-phage genomes shared between 60 and 70% nucleotide sequence identity over the DNA packaging, head and tail genes. Analysis of the SF370.3 genome revealed mutations in the replisome organizer gene that may prevent the induction of the prophage. The mutated phage replication gene was closely related to a virulence marker identified in recently emerged M3 serotype S. pyogenes strains in Japan. This observation suggests that prophage genes confer selective advantage to the lysogenic host. SF370.3 encodes a hyaluronidase and a DNase that may facilitate the spreading of S. pyogenes through tissue planes of its human host. Prophage SF370.2 showed a 43-kb-long genome that closely resembled the genome organization of pac-site temperate Siphoviridae infecting the dairy bacteria S. thermophilus and L. lactis. Over part of the structural genes, the similarity between SF370.2 and S. thermophilus phage O1205 extended to the nucleotide sequence level. SF370.2 showed two probable inactivating mutations: one in the replisome organizer gene and another in the gene encoding the portal protein. Prophage SF370.2 also encodes a hyaluronidase and in addition two very likely virulence factors: prophage-encoded toxins acting as superantigens that may contribute to the immune deregulation observed during invasive streptococcal infections. The superantigens are encoded between the phage lysin and the right attachment site of the prophage genome. The genes were nearly sequence identical with a DNA segment in S. equi, suggesting horizontal gene transfer. The trend for prophage genome inactivation was even more evident for the remaining five prophage sequences that showed massive losses of prophage DNA. In these prophage remnants only 13-0.3 kb of putative prophage DNA was detected. We discuss the genomics data from S. pyogenes strain SF370 within the framework of Darwinian coevolution of prophages and lysogenic bacteria and suggest elements of genetic cooperation and elements of an arms race in this host-parasite relationship.}, }
@article {pmid11600504, year = {2002}, author = {Jee, JG and Ikegami, T and Hashimoto, M and Kawabata, T and Ikeguchi, M and Watanabe, T and Shirakawa, M}, title = {Solution structure of the fibronectin type III domain from Bacillus circulans WL-12 chitinase A1.}, journal = {The Journal of biological chemistry}, volume = {277}, number = {2}, pages = {1388-1397}, doi = {10.1074/jbc.M109726200}, pmid = {11600504}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Bacillus/chemistry/*enzymology/genetics ; Bacterial Proteins/chemistry/genetics ; Chitinases/*chemistry/genetics ; Fibronectins/*chemistry/genetics ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Nuclear Magnetic Resonance, Biomolecular ; Protein Structure, Secondary ; *Protein Structure, Tertiary ; Recombinant Proteins/chemistry/genetics ; Sequence Alignment ; }, abstract = {Growing evidence suggests that horizontal gene transfer plays an integral role in the evolution of bacterial genomes. One of the debated examples of horizontal gene transfer from animal to prokaryote is the fibronectin type III domain (FnIIID). Certain extracellular proteins of soil bacteria contain an unusual cluster of FnIIIDs, which show sequence similarity to those of animals and are likely to have been acquired horizontally from animals. Here we report the solution structure of the FnIIID of chitinase A1 from Bacillus circulans WL-12. To the best of our knowledge, this is the first tertiary structure to be reported for an FnIIID from a bacterial protein. The structure of the domain shows significant similarity to FnIIIDs from animal proteins. Sequence comparisons with FnIIIDs from other soil bacteria proteins show that the core-forming residues are highly conserved and, thus, are under strong evolutionary pressure. Striking similarities in the tertiary structures of bacterial FnIIIDs and their mammalian counterparts may support the hypothesis that the evolution of the FnIIID in bacterial carbohydrases occurred horizontally. The total lack of surface-exposed aromatic residues also suggests that the role of this FnIIID is different from those of other bacterial beta-sandwich domains, which function as carbohydrate-binding modules.}, }
@article {pmid11592982, year = {2001}, author = {Vollrath, D and Feng, W and Duncan, JL and Yasumura, D and D'Cruz, PM and Chappelow, A and Matthes, MT and Kay, MA and LaVail, MM}, title = {Correction of the retinal dystrophy phenotype of the RCS rat by viral gene transfer of Mertk.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {98}, number = {22}, pages = {12584-12589}, pmid = {11592982}, issn = {0027-8424}, support = {EY01919/EY/NEI NIH HHS/United States ; K08 EY000415/EY/NEI NIH HHS/United States ; DK49022/DK/NIDDK NIH HHS/United States ; K08 EY00415/EY/NEI NIH HHS/United States ; R01 DK049022/DK/NIDDK NIH HHS/United States ; EY06842/EY/NEI NIH HHS/United States ; F32 EY006842/EY/NEI NIH HHS/United States ; EY02162/EY/NEI NIH HHS/United States ; R01 EY006842/EY/NEI NIH HHS/United States ; R01 EY001919/EY/NEI NIH HHS/United States ; P30 EY002162/EY/NEI NIH HHS/United States ; }, mesh = {Adenoviridae/*genetics ; Animals ; Gene Transfer, Horizontal ; *Genetic Therapy ; HeLa Cells ; Humans ; Phagocytosis ; Phenotype ; Photoreceptor Cells/metabolism ; Pigment Epithelium of Eye/physiology ; *Proto-Oncogene Proteins ; Rats ; Receptor Protein-Tyrosine Kinases/*genetics ; Retinal Diseases/*therapy ; c-Mer Tyrosine Kinase ; }, abstract = {The Royal College of Surgeons (RCS) rat is a widely studied animal model of retinal degeneration in which the inability of the retinal pigment epithelium (RPE) to phagocytize shed photoreceptor outer segments leads to a progressive loss of rod and cone photoreceptors. We recently used positional cloning to demonstrate that the gene Mertk likely corresponds to the retinal dystrophy (rdy) locus of the RCS rat. In the present study, we sought to determine whether gene transfer of Mertk to a RCS rat retina would result in correction of the RPE phagocytosis defect and preservation of photoreceptors. We used subretinal injection of a recombinant replication-deficient adenovirus encoding rat Mertk to deliver the gene to the eyes of young RCS rats. Electrophysiological assessment of animals 30 days after injection revealed an increased sensitivity of treated eyes to low-intensity light. Histologic and ultrastructural assessment demonstrated substantial sparing of photoreceptors, preservation of outer segment structure, and correction of the RPE phagocytosis defect in areas surrounding the injection site. Our results provide definitive evidence that mutation of Mertk underlies the RCS retinal dystrophy phenotype, and that the phenotype can be corrected by treatment of juvenile animals. To our knowledge, this is the first demonstration of complementation of both a functional cellular defect (phagocytosis) and a photoreceptor degeneration by gene transfer to the RPE. These results, together with the recent discovery of MERTK mutations in individuals with retinitis pigmentosa, emphasize the importance of the RCS rat as a model for gene therapy of diseases that arise from RPE dysfunction.}, }
@article {pmid11591641, year = {2001}, author = {Kennedy, SP and Ng, WV and Salzberg, SL and Hood, L and DasSarma, S}, title = {Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence.}, journal = {Genome research}, volume = {11}, number = {10}, pages = {1641-1650}, pmid = {11591641}, issn = {1088-9051}, mesh = {Adaptation, Biological/*genetics ; Base Composition ; Chromosome Mapping ; Codon/genetics ; Computational Biology/*methods ; *Genome, Bacterial ; Halobacterium/*genetics/growth &amp; development ; Isoelectric Point ; Multigene Family ; Protein Structure, Tertiary/genetics ; Proteome/genetics ; Sequence Homology, Amino Acid ; }, abstract = {The genome of the halophilic archaeon Halobacterium sp. NRC-1 and predicted proteome have been analyzed by computational methods and reveal characteristics relevant to life in an extreme environment distinguished by hypersalinity and high solar radiation: (1) The proteome is highly acidic, with a median pI of 4.9 and mostly lacking basic proteins. This characteristic correlates with high surface negative charge, determined through homology modeling, as the major adaptive mechanism of halophilic proteins to function in nearly saturating salinity. (2) Codon usage displays the expected GC bias in the wobble position and is consistent with a highly acidic proteome. (3) Distinct genomic domains of NRC-1 with bacterial character are apparent by whole proteome BLAST analysis, including two gene clusters coding for a bacterial-type aerobic respiratory chain. This result indicates that the capacity of halophiles for aerobic respiration may have been acquired through lateral gene transfer. (4) Two regions of the large chromosome were found with relatively lower GC composition and overrepresentation of IS elements, similar to the minichromosomes. These IS-element-rich regions of the genome may serve to exchange DNA between the three replicons and promote genome evolution. (5) GC-skew analysis showed evidence for the existence of two replication origins in the large chromosome. This finding and the occurrence of multiple chromosomes indicate a dynamic genome organization with eukaryotic character.}, }
@article {pmid11591475, year = {2001}, author = {Kanaya, S and Kinouchi, M and Abe, T and Kudo, Y and Yamada, Y and Nishi, T and Mori, H and Ikemura, T}, title = {Analysis of codon usage diversity of bacterial genes with a self-organizing map (SOM): characterization of horizontally transferred genes with emphasis on the E. coli O157 genome.}, journal = {Gene}, volume = {276}, number = {1-2}, pages = {89-99}, doi = {10.1016/s0378-1119(01)00673-4}, pmid = {11591475}, issn = {0378-1119}, mesh = {*Algorithms ; Base Composition ; Classification/methods ; Codon/*genetics ; Escherichia coli O157/genetics ; GC Rich Sequence/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Genetic Variation ; Genome, Bacterial ; *Neural Networks, Computer ; Species Specificity ; }, abstract = {With increases in the amounts of available DNA sequence data, it has become increasingly important to develop tools for comprehensive systematic analysis and comparison of species-specific characteristics of protein-coding sequences for a wide variety of genomes. In the present study, we used a novel neural-network algorithm, a self-organizing map (SOM), to efficiently and comprehensively analyze codon usage in approximately 60,000 genes from 29 bacterial species simultaneously. This SOM makes it possible to cluster and visualize genes of individual species separately at a much higher resolution than can be obtained with principal component analysis. The organization of the SOM can be explained by the genome G+C% and tRNA compositions of the individual species. We used SOM to examine codon usage heterogeneity in the E. coli O157 genome, which contains 'O157-unique segments' (O-islands), and showed that SOM is a powerful tool for characterization of horizontally transferred genes.}, }
@article {pmid11586360, year = {2001}, author = {Parkhill, J and Wren, BW and Thomson, NR and Titball, RW and Holden, MT and Prentice, MB and Sebaihia, M and James, KD and Churcher, C and Mungall, KL and Baker, S and Basham, D and Bentley, SD and Brooks, K and Cerdeño-Tárraga, AM and Chillingworth, T and Cronin, A and Davies, RM and Davis, P and Dougan, G and Feltwell, T and Hamlin, N and Holroyd, S and Jagels, K and Karlyshev, AV and Leather, S and Moule, S and Oyston, PC and Quail, M and Rutherford, K and Simmonds, M and Skelton, J and Stevens, K and Whitehead, S and Barrell, BG}, title = {Genome sequence of Yersinia pestis, the causative agent of plague.}, journal = {Nature}, volume = {413}, number = {6855}, pages = {523-527}, doi = {10.1038/35097083}, pmid = {11586360}, issn = {0028-0836}, mesh = {Animals ; Antigens, Bacterial/genetics ; Bacterial Proteins/genetics/metabolism ; Chromosomes, Bacterial ; DNA, Bacterial ; Energy Metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; Insecta/microbiology ; Lipopolysaccharides ; Molecular Sequence Data ; Mutation ; Plague/microbiology ; Pseudogenes ; Sequence Analysis, DNA ; Virulence/genetics ; Yersinia pestis/*genetics/immunology/pathogenicity ; Yersinia pseudotuberculosis/genetics ; }, abstract = {The Gram-negative bacterium Yersinia pestis is the causative agent of the systemic invasive infectious disease classically referred to as plague, and has been responsible for three human pandemics: the Justinian plague (sixth to eighth centuries), the Black Death (fourteenth to nineteenth centuries) and modern plague (nineteenth century to the present day). The recent identification of strains resistant to multiple drugs and the potential use of Y. pestis as an agent of biological warfare mean that plague still poses a threat to human health. Here we report the complete genome sequence of Y. pestis strain CO92, consisting of a 4.65-megabase (Mb) chromosome and three plasmids of 96.2 kilobases (kb), 70.3 kb and 9.6 kb. The genome is unusually rich in insertion sequences and displays anomalies in GC base-composition bias, indicating frequent intragenomic recombination. Many genes seem to have been acquired from other bacteria and viruses (including adhesins, secretion systems and insecticidal toxins). The genome contains around 150 pseudogenes, many of which are remnants of a redundant enteropathogenic lifestyle. The evidence of ongoing genome fluidity, expansion and decay suggests Y. pestis is a pathogen that has undergone large-scale genetic flux and provides a unique insight into the ways in which new and highly virulent pathogens evolve.}, }
@article {pmid11583009, year = {2001}, author = {Pot, RG and Kusters, JG and Smeets, LC and Van Tongeren, W and Vandenbroucke-Grauls, CM and Bart, A}, title = {Interspecies transfer of antibiotic resistance between Helicobacter pylori and Helicobacter acinonychis.}, journal = {Antimicrobial agents and chemotherapy}, volume = {45}, number = {10}, pages = {2975-2976}, pmid = {11583009}, issn = {0066-4804}, mesh = {DNA, Bacterial/metabolism ; Drug Resistance, Bacterial/*genetics ; *Gene Transfer, Horizontal ; Helicobacter pylori/*genetics ; Humans ; Transformation, Bacterial ; }, }
@article {pmid11581653, year = {2001}, author = {Chen, CM and Behringer, RR}, title = {CREating breakthroughs.}, journal = {Nature biotechnology}, volume = {19}, number = {10}, pages = {921-922}, doi = {10.1038/nbt1001-921}, pmid = {11581653}, issn = {1087-0156}, mesh = {3T3 Cells ; Animals ; Biotechnology/methods ; Cell Culture Techniques ; Cell Membrane Permeability ; Drosophila ; Gene Transfer, Horizontal ; Integrases/genetics/*metabolism ; Mice ; Recombinant Proteins/genetics/metabolism ; Viral Proteins/genetics/*metabolism ; }, }
@article {pmid11581407, year = {2001}, author = {Zhong, Q and Oliver, P and Huang, W and Good, D and La Russa, V and Zhang, Z and Cork, JR and Veith, RW and Theodossiou, C and Kolls, JK and Schwarzenberger, P}, title = {Efficient c-kit receptor-targeted gene transfer to primary human CD34-selected hematopoietic stem cells.}, journal = {Journal of virology}, volume = {75}, number = {21}, pages = {10393-10400}, pmid = {11581407}, issn = {0022-538X}, support = {R01 CA081125/CA/NCI NIH HHS/United States ; R01 CA81125-01/CA/NCI NIH HHS/United States ; }, mesh = {Adenoviridae/genetics ; Antigens, CD34/*analysis ; Coxsackie and Adenovirus Receptor-Like Membrane Protein ; *Gene Transfer, Horizontal ; *Genetic Therapy ; Genetic Vectors ; Hematopoietic Stem Cells/*metabolism ; Humans ; Proto-Oncogene Proteins c-kit/*metabolism ; Receptors, Virus/analysis ; Retroviridae/genetics ; }, abstract = {We have previously reported effective gene transfer with a targeted molecular conjugate adenovirus vector through the c-kit receptor in hematopoietic progenitor cell lines. However, a c-kit-targeted recombinant retroviral vector failed to transduce cells, indicating the existence of significant differences for c-kit target gene transfer between these two viruses. Here we demonstrate that conjugation of an adenovirus to a c-kit-retargeted retrovirus vector enables retroviral transduction. This finding suggests the requirement of endosomalysis for successful c-kit-targeted gene transfer. Furthermore, we show efficient gene transfer to, and high transgene expression (66%) in, CD34-selected, c-kit(+) human peripheral blood stem cells using a c-kit-targeted adenovirus vector. These findings may have important implications for future vector development in c-kit-targeted stem cell gene transfer.}, }
@article {pmid11580860, year = {2001}, author = {Hedges, SB and Chen, H and Kumar, S and Wang, DY and Thompson, AS and Watanabe, H}, title = {A genomic timescale for the origin of eukaryotes.}, journal = {BMC evolutionary biology}, volume = {1}, number = {}, pages = {4}, pmid = {11580860}, issn = {1471-2148}, mesh = {Animals ; Archaea/genetics ; Eubacterium/genetics ; *Eukaryotic Cells ; *Evolution, Molecular ; Genetic Variation/genetics ; *Genome ; Genome, Archaeal ; Genome, Bacterial ; Genome, Protozoan ; Giardia/genetics ; Models, Genetic ; Phylogeny ; }, abstract = {BACKGROUND: Genomic sequence analyses have shown that horizontal gene transfer occurred during the origin of eukaryotes as a consequence of symbiosis. However, details of the timing and number of symbiotic events are unclear. A timescale for the early evolution of eukaryotes would help to better understand the relationship between these biological events and changes in Earth's environment, such as the rise in oxygen. We used refined methods of sequence alignment, site selection, and time estimation to address these questions with protein sequences from complete genomes of prokaryotes and eukaryotes.<br><br>RESULTS: Eukaryotes were found to evolve faster than prokaryotes, with those eukaryotes derived from eubacteria evolving faster than those derived from archaebacteria. We found an early time of divergence (approximately 4 billion years ago, Ga) for archaebacteria and the archaebacterial genes in eukaryotes. Our analyses support at least two horizontal gene transfer events in the origin of eukaryotes, at 2.7 Ga and 1.8 Ga. Time estimates for the origin of cyanobacteria (2.6 Ga) and the divergence of an early-branching eukaryote that lacks mitochondria (Giardia) (2.2 Ga) fall between those two events.<br><br>CONCLUSIONS: We find support for two symbiotic events in the origin of eukaryotes: one premitochondrial and a later mitochondrial event. The appearance of cyanobacteria immediately prior to the earliest undisputed evidence for the presence of oxygen (2.4-2.2 Ga) suggests that the innovation of oxygenic photosynthesis had a relatively rapid impact on the environment as it set the stage for further evolution of the eukaryotic cell.}, }
@article {pmid11574160, year = {2001}, author = {Taylor, MS}, title = {Characterization and comparative analysis of the EGLN gene family.}, journal = {Gene}, volume = {275}, number = {1}, pages = {125-132}, doi = {10.1016/s0378-1119(01)00633-3}, pmid = {11574160}, issn = {0378-1119}, mesh = {Amino Acid Sequence ; Animals ; Binding Sites/genetics ; Caenorhabditis elegans/genetics ; *Caenorhabditis elegans Proteins ; Conserved Sequence/genetics ; *DNA-Binding Proteins ; Databases, Nucleic Acid ; Evolution, Molecular ; Gene Transfer, Horizontal ; Helminth Proteins/*genetics ; Humans ; Hypoxia-Inducible Factor-Proline Dioxygenases ; Immediate-Early Proteins/*genetics ; Mice ; Molecular Sequence Data ; Multigene Family/genetics ; Phylogeny ; Procollagen-Proline Dioxygenase ; Proteins/genetics ; Pseudogenes ; Rats ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {Rat Sm-20 is a homologue of the Caenorhabditis elegans gene egl-9 and has been implicated in the regulation of growth, differentiation and apoptosis in muscle and nerve cells. Null mutants in egl-9 result in a complete tolerance to an otherwise lethal toxin produced by Pseudomonas aeruginosa. This study describes the conserved Egl-Nine (EGLN) gene family of which rat SM-20 and C. elegans Egl-9 are members and characterizes the mouse and human homologues. Each of the human genes (EGLN1, EGLN2 and EGLN3) are of a conserved genomic structure consisting of five coding exons. Phylogenetic analysis and domain organization show that EGLN1 represents the ancestral form of the gene family and that EGLN3 is the human orthologue of rat Sm-20. The previously observed mitochondrial targeting of rat SM-20 is unlikely to be a general feature of the protein family and may be a feature specific to rats. An EGLN gene is unexpectedly found in the genome of P. aeruginosa, a bacterium known to produce a toxin that acts through the Egl-9 protein. The pathogenic bacterium Vibrio cholerae is also shown to have an EGLN gene suggesting that it is an important pathogenicity factor. These results provide new insights into host-pathogen interactions and a basis for further functional characterization of the gene family and resolve discrepancies in annotation between gene family members.}, }
@article {pmid11574053, year = {2001}, author = {Makarova, KS and Ponomarev, VA and Koonin, EV}, title = {Two C or not two C: recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins.}, journal = {Genome biology}, volume = {2}, number = {9}, pages = {RESEARCH 0033}, pmid = {11574053}, issn = {1474-760X}, mesh = {Bacterial Proteins/*genetics ; *Evolution, Molecular ; *Gene Deletion ; *Gene Duplication ; Gene Transfer, Horizontal/*genetics ; Metalloproteins/*genetics ; Ribosomal Proteins/*genetics ; *Zinc ; }, abstract = {BACKGROUND: Ribosomal proteins are encoded in all genomes of cellular life forms and are, generally, well conserved during evolution. In prokaryotes, the genes for most ribosomal proteins are clustered in several highly conserved operons, which ensures efficient co-regulation of their expression. Duplications of ribosomal-protein genes are infrequent, and given their coordinated expression and functioning, it is generally assumed that ribosomal-protein genes are unlikely to undergo horizontal transfer. However, with the accumulation of numerous complete genome sequences of prokaryotes, several paralogous pairs of ribosomal protein genes have been identified. Here we analyze all such cases and attempt to reconstruct the evolutionary history of these ribosomal proteins.<br><br>RESULTS: Complete bacterial genomes were searched for duplications of ribosomal proteins. Ribosomal proteins L36, L33, L31, S14 are each duplicated in several bacterial genomes and ribosomal proteins L11, L28, L7/L12, S1, S15, S18 are so far duplicated in only one genome each. Sequence analysis of the four ribosomal proteins, for which paralogs were detected in several genomes, two of the ribosomal proteins duplicated in one genome (L28 and S18), and the ribosomal protein L32 showed that each of them comes in two distinct versions. One form contains a predicted metal-binding Zn-ribbon that consists of four conserved cysteines (in some cases replaced by histidines), whereas, in the second form, these metal-chelating residues are completely or partially replaced. Typically, genomes containing paralogous genes for these ribosomal proteins encode both versions, designated C+ and C-, respectively. Analysis of phylogenetic trees for these seven ribosomal proteins, combined with comparison of genomic contexts for the respective genes, indicates that in most, if not all cases, their evolution involved a duplication of the ancestral C+ form early in bacterial evolution, with subsequent alternative loss of the C+ and C- forms in different lineages. Additionally, evidence was obtained for a role of horizontal gene transfer in the evolution of these ribosomal proteins, with multiple cases of gene displacement 'in situ', that is, without a change of the gene order in the recipient genome.<br><br>CONCLUSIONS: A more complex picture of evolution of bacterial ribosomal proteins than previously suspected is emerging from these results, with major contributions of lineage-specific gene loss and horizontal gene transfer. The recurrent theme of emergence and disruption of Zn-ribbons in bacterial ribosomal proteins awaits a functional interpretation.}, }
@article {pmid11572456, year = {2001}, author = {Disqué-Kochem, C and Battermann, A and Strätz, M and Dreiseikelmann, B}, title = {Screening for trbB- and traG-like sequences by PCR for the detection of conjugative plasmids in bacterial soil isolates.}, journal = {Microbiological research}, volume = {156}, number = {2}, pages = {159-168}, doi = {10.1078/0944-5013-00098}, pmid = {11572456}, issn = {0944-5013}, mesh = {Bacteria/genetics/*isolation &amp; purification ; Bacterial Proteins/genetics ; *Conjugation, Genetic ; DNA Primers ; DNA, Bacterial/analysis ; *Escherichia coli Proteins ; *Membrane Proteins ; Plasmids/*genetics ; Polymerase Chain Reaction/*methods ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {The transfer regions of different conjugative plasmids show significant similarities in the genetic organization and in the amino acid sequence of some gene products, especially of proteins from the traG or trbB family. These similarities are also evident on the level of the nucleotide sequences. On the basis of conserved DNA regions we designed degenerate PCR primer pairs to detect specifically tra regions within a collection of bacterial clones isolated from an agricultural soil. Most of the potential transfer-proficient indigenous bacterial isolates were able to mobilize a derivative of the nonconjugative IncQ plasmid RSF1010 into recipient strains. With the help of the primers it should be possible to evaluate the genetic potential for horizontal gene transfer carried out by conjugative plasmids.}, }
@article {pmid11570520, year = {2001}, author = {Bhattacarya, D and Cannone, JJ and Gutell, RR}, title = {Group I intron lateral transfer between red and brown algal ribosomal RNA.}, journal = {Current genetics}, volume = {40}, number = {1}, pages = {82-90}, doi = {10.1007/s002940100227}, pmid = {11570520}, issn = {0172-8083}, support = {GM48207/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Sequence ; Conserved Sequence ; Evolution, Molecular ; Gene Transfer, Horizontal ; Introns ; Molecular Sequence Data ; Mutation ; Nucleic Acid Conformation ; Phaeophyceae/*genetics ; Phylogeny ; RNA, Ribosomal/chemistry/*genetics ; Rhodophyta/*genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {How group I introns originate in nuclear ribosomal (r)RNA genes is an important question in evolutionary biology. Central to this issue is the multitude of group I introns present in evolutionarily distantly related plant, fungal, and protist lineages, together with an understanding of their origin and lateral transfer from one exon to another, between cell organelles, and between cells. These introns vary considerably in primary and secondary structure; and their provenance from a few or perhaps many mobile elements that have spread in rRNAs is unknown. Here we show that a novel lineage of group IC1 introns inserted at position 516 (Escherichia coli gene numbering) in the small subunit rRNA in bangiophyte red algae and a brown alga (Aureoumbra lagunensis) are specifically related, although their host cells are not. These bangiophyte and Aureoumbra introns are the only known cases that have a helical insertion in the P5b helix. The highly conserved primary and secondary structure of the extra P5b helix suggests that it is important, although its specific function is unknown. Our study attempts to understand the origin and movement of these IC1 introns.}, }
@article {pmid11568059, year = {2001}, author = {Yau, TM and Fung, K and Weisel, RD and Fujii, T and Mickle, DA and Li, RK}, title = {Enhanced myocardial angiogenesis by gene transfer with transplanted cells.}, journal = {Circulation}, volume = {104}, number = {12 Suppl 1}, pages = {I218-22}, doi = {10.1161/hc37t1.094896}, pmid = {11568059}, issn = {1524-4539}, mesh = {Animals ; Blood Flow Velocity/drug effects/genetics ; Cell Count ; *Cell Transplantation ; Cells, Cultured ; Coronary Circulation/drug effects/genetics ; Endothelial Growth Factors/biosynthesis/*genetics/pharmacology ; Gene Expression ; *Gene Transfer, Horizontal ; Genes, Reporter/genetics ; Green Fluorescent Proteins ; Luminescent Proteins/genetics ; Lymphokines/biosynthesis/*genetics/pharmacology ; Male ; Myocardial Revascularization/*methods ; Myocardium/*cytology/pathology ; Neovascularization, Physiologic/drug effects/*genetics ; Rats ; Rats, Inbred Lew ; Transfection ; Vascular Endothelial Growth Factor A ; Vascular Endothelial Growth Factors ; Ventricular Function, Left ; }, abstract = {UNLABELLED: BACKGROUND The combination of myocardial cell transplantation and angiogenic gene transfer may improve postinfarction left ventricular (LV) perfusion. We evaluated the angiogenic effect of heart cells transfected with vascular endothelial growth factor (VEGF) and transplanted into a myocardial scar.<br><br>METHODS AND RESULTS: Donor rat heart cells were transfected with plasmids encoding VEGF(165) and green fluorescence protein. Syngeneic adult rats underwent LV cryoinjury to create a transmural scar. Three weeks later, 4x10(6) transfected heart cells (n=14), untransfected heart cells (n=13), or culture medium (n=16) were transplanted into the center of the scar. After 5 weeks, LV function, quantitative histology, and regional blood flow were evaluated. Plates of heart cells transfected with VEGF(165) produced 6.1 times more intracellular VEGF than nontransfected cells. Capillary density (mean+/-SEM) per high-power field in the center of the myocardial scar was 1.1+/-0.02 in control rats, 3.9+/-0.11 in untransfected rats, and 6.3+/-0.11 in transfected rats (P=0.0002). Capillary density in the border zone around the scar was 1.9+/-0.03 in control rats, 6.4+/-0.10 in untransfected rats, and 8.7+/-0.16 in transfected rats (P=0.004). Regional blood flow within the scar was 8.8+/-0.8% of normalized flow in control hearts, 10.4+/-0.7% in hearts transplanted with untransfected cells, but 17.6+/-1.2% in hearts transplanted with transfected cells (P=0.03 versus control, P=0.07 versus nontransfected). There was no difference in LV function attributable to transplantation with transfected cells at the time point studied.<br><br>CONCLUSIONS: Transplantation of heart cells transfected with VEGF induced greater angiogenesis than transplantation of unmodified cells. Combined gene transfer and cell transplantation strategies may improve postinfarction LV perfusion and function.}, }
@article {pmid11567107, year = {2001}, author = {Fukuchi-Shimogori, T and Grove, EA}, title = {Neocortex patterning by the secreted signaling molecule FGF8.}, journal = {Science (New York, N.Y.)}, volume = {294}, number = {5544}, pages = {1071-1074}, doi = {10.1126/science.1064252}, pmid = {11567107}, issn = {0036-8075}, mesh = {Animals ; Body Patterning ; Brain Mapping ; Cadherins/metabolism ; Electroporation ; Fibroblast Growth Factor 8 ; Fibroblast Growth Factors/genetics/*metabolism ; Gene Expression ; Gene Transfer, Horizontal ; Mice ; Neocortex/*embryology/metabolism ; *Protein-Tyrosine Kinases ; Receptor, Fibroblast Growth Factor, Type 3 ; Receptors, Fibroblast Growth Factor/genetics/metabolism ; Signal Transduction ; Solubility ; Somatosensory Cortex/embryology ; Vibrissae/innervation ; }, abstract = {A classic model proposes that the mammalian neocortex is divided into areas early in neurogenesis, but the molecular mechanisms that generate the area map have been elusive. Here we provide evidence that FGF8 regulates development of the map from a source in the anterior telencephalon. Using electroporation-mediated gene transfer in mouse embryos, we show that augmenting the endogenous anterior FGF8 signal shifts area boundaries posteriorly, reducing the signal shifts them anteriorly, and introducing a posterior source of FGF8 elicits partial area duplications, revealed by ectopic somatosensory barrel fields. These findings support a role for FGF signaling in specifying positional identity in the neocortex.}, }
@article {pmid11567003, year = {2001}, author = {Klein, M and Friedrich, M and Roger, AJ and Hugenholtz, P and Fishbain, S and Abicht, H and Blackall, LL and Stahl, DA and Wagner, M}, title = {Multiple lateral transfers of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes.}, journal = {Journal of bacteriology}, volume = {183}, number = {20}, pages = {6028-6035}, pmid = {11567003}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; Archaea/classification/enzymology/*genetics ; Bacteria/classification/enzymology/*genetics ; *Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; Gram-Positive Bacteria/enzymology/genetics ; Hydrogensulfite Reductase ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases Acting on Sulfur Group Donors/*genetics ; Phylogeny ; Prokaryotic Cells ; Sequence Homology, Amino Acid ; Sulfates/*metabolism ; }, abstract = {A large fragment of the dissimilatory sulfite reductase genes (dsrAB) was PCR amplified and fully sequenced from 30 reference strains representing all recognized lineages of sulfate-reducing bacteria. In addition, the sequence of the dsrAB gene homologs of the sulfite reducer Desulfitobacterium dehalogenans was determined. In contrast to previous reports, comparative analysis of all available DsrAB sequences produced a tree topology partially inconsistent with the corresponding 16S rRNA phylogeny. For example, the DsrAB sequences of several Desulfotomaculum species (low G+C gram-positive division) and two members of the genus Thermodesulfobacterium (a separate bacterial division) were monophyletic with delta-proteobacterial DsrAB sequences. The most parsimonious interpretation of these data is that dsrAB genes from ancestors of as-yet-unrecognized sulfate reducers within the delta-Proteobacteria were laterally transferred across divisions. A number of insertions and deletions in the DsrAB alignment independently support these inferred lateral acquisitions of dsrAB genes. Evidence for a dsrAB lateral gene transfer event also was found within the delta-Proteobacteria, affecting Desulfobacula toluolica. The root of the dsr tree was inferred to be within the Thermodesulfovibrio lineage by paralogous rooting of the alpha and beta subunits. This rooting suggests that the dsrAB genes in Archaeoglobus species also are the result of an ancient lateral transfer from a bacterial donor. Although these findings complicate the use of dsrAB genes to infer phylogenetic relationships among sulfate reducers in molecular diversity studies, they establish a framework to resolve the origins and diversification of this ancient respiratory lifestyle among organisms mediating a key step in the biogeochemical cycling of sulfur.}, }
@article {pmid11560890, year = {2001}, author = {Cortesi, P and McCulloch, CE and Song, H and Lin, H and Milgroom, MG}, title = {Genetic control of horizontal virus transmission in the chestnut blight fungus, Cryphonectria parasitica.}, journal = {Genetics}, volume = {159}, number = {1}, pages = {107-118}, pmid = {11560890}, issn = {0016-6731}, mesh = {Alleles ; Ascomycota/*genetics/pathogenicity/*virology ; *Disease Transmission, Infectious ; Epistasis, Genetic ; *Gene Transfer, Horizontal ; Genetic Variation ; Genotype ; Models, Statistical ; Pest Control, Biological ; Plant Diseases/microbiology ; Protein Binding ; RNA Viruses/*genetics/physiology ; Trees/*microbiology ; Virulence ; }, abstract = {Vegetative incompatibility in fungi has long been known to reduce the transmission of viruses between individuals, but the barrier to transmission is incomplete. In replicated laboratory assays, we showed conclusively that the transmission of viruses between individuals of the chestnut blight fungus Cryphonectria parasitica is controlled primarily by vegetative incompatibility (vic) genes. By replicating vic genotypes in independent fungal isolates, we quantified the effect of heteroallelism at each of six vic loci on virus transmission. Transmission occurs with 100% frequency when donor and recipient isolates have the same vic genotypes, but heteroallelism at one or more vic loci generally reduces virus transmission. Transmission was variable among single heteroallelic loci. At the extremes, heteroallelism at vic4 had no effect on virus transmission, but transmission occurred in only 21% of pairings that were heteroallelic at vic2. Intermediate frequencies of transmission were observed when vic3 and vic6 were heteroallelic (76 and 32%, respectively). When vic1, vic2, and vic7 were heteroallelic, the frequency of transmission depended on which alleles were present in the donor and the recipient. The effect of heteroallelism at two vic loci was mostly additive, although small but statistically significant interactions (epistasis) were observed in four pairs of vic loci. A logistic regression model was developed to predict the probability of virus transmission between vic genotypes. Heteroallelism at vic loci, asymmetry, and epistasis were the dominant factors controlling transmission, but host genetic background also was statistically significant, indicating that vic genes alone cannot explain all the variation in virus transmission. Predictions from the logistic regression model were highly correlated to independent transmission tests with field isolates. Our model can be used to estimate horizontal transmission rates as a function of host genetics in natural populations of C. parasitica.}, }
@article {pmid11560860, year = {2001}, author = {del Monte, F and Williams, E and Lebeche, D and Schmidt, U and Rosenzweig, A and Gwathmey, JK and Lewandowski, ED and Hajjar, RJ}, title = {Improvement in survival and cardiac metabolism after gene transfer of sarcoplasmic reticulum Ca(2+)-ATPase in a rat model of heart failure.}, journal = {Circulation}, volume = {104}, number = {12}, pages = {1424-1429}, pmid = {11560860}, issn = {1524-4539}, support = {HL-61557/HL/NHLBI NIH HHS/United States ; R01 HL049574-05/HL/NHLBI NIH HHS/United States ; R01 HL062702/HL/NHLBI NIH HHS/United States ; R01 HL049574-05S1/HL/NHLBI NIH HHS/United States ; HL-57623/HL/NHLBI NIH HHS/United States ; R01 HL049574-08/HL/NHLBI NIH HHS/United States ; R01 HL059521/HL/NHLBI NIH HHS/United States ; R01 HL049574-07/HL/NHLBI NIH HHS/United States ; HL-50361/HL/NHLBI NIH HHS/United States ; R01 HL061557/HL/NHLBI NIH HHS/United States ; HL-49574/HL/NHLBI NIH HHS/United States ; HL-59521/HL/NHLBI NIH HHS/United States ; R01 HL049574-06/HL/NHLBI NIH HHS/United States ; R01 HL049574-06S1/HL/NHLBI NIH HHS/United States ; HL-62702/HL/NHLBI NIH HHS/United States ; }, mesh = {Adenoviridae/genetics ; Animals ; Calcium-Transporting ATPases/*genetics/*metabolism/pharmacology ; Disease Models, Animal ; Echocardiography ; Gene Expression ; Gene Transfer, Horizontal ; Genetic Therapy/methods ; Genetic Vectors/genetics/metabolism/pharmacology ; Heart Failure/pathology/*physiopathology/*therapy ; In Vitro Techniques ; Isoenzymes/genetics/metabolism ; Magnetic Resonance Spectroscopy ; Myocardial Contraction/drug effects ; Myocardium/*metabolism/pathology ; Organ Size/drug effects ; Rats ; Rats, Sprague-Dawley ; Sarcoplasmic Reticulum Calcium-Transporting ATPases ; Stroke Volume/drug effects ; Survival Rate ; }, abstract = {BACKGROUND: In heart failure, sarcoplasmic reticulum (SR) Ca(2+)-ATPase (SERCA2a) activity is decreased, resulting in abnormal calcium handling and contractile dysfunction. We have previously shown that increasing SERCA2a expression by gene transfer improves ventricular function in a rat model of heart failure created by ascending aortic constriction.<br><br>METHODS AND RESULTS: In this study, we tested the effects of gene transfer of SERCA2a on survival, left ventricular (LV) volumes, and metabolism. By 26 to 27 weeks after aortic banding, all animals developed heart failure (as documented by >25% decrease in fractional shortening) and were randomized to receive either an adenovirus carrying the SERCA2a gene (Ad.SERCA2a) or control virus (Ad.betagal-GFP) by use of a catheter-based technique. Sham-operated rats, uninfected or infected with either Ad.betagal-GFP or Ad.SERCA2a, served as controls. Four weeks after gene transfer, survival in rats with heart failure treated with Ad.betagal-GFP was 9%, compared with 63% in rats receiving Ad.SERCA2a. LV volumes were significantly increased in heart failure (0.64+/-0.05 versus 0.35+/-0.03 mL, P<0.02). Overexpression of SERCA2a normalized LV volumes (0.46+/-0.07 mL) in the failing hearts. (31)P NMR analysis showed a reduced ratio of phosphocreatine to ATP content in failing+Ad.betagal-GFP compared with sham+Ad.betagal-GFP (0.82+/-0.13 versus 1.38+/-0.14, P<0.01). Overexpression of SERCA2a in failing hearts improved the phosphocreatine/ATP ratio (1.23+/-0.28).<br><br>CONCLUSIONS: In this study, we show that unlike inotropic agents that improve contractile function at the expense of increased mortality and worsening metabolism, gene transfer of SERCA2a improves survival and the energy potential in failing hearts.}, }
@article {pmid11560168, year = {1998}, author = {Martin, W and Stoebe, B and Goremykin, V and Hapsmann, S and Hasegawa, M and Kowallik, KV}, title = {Gene transfer to the nucleus and the evolution of chloroplasts.}, journal = {Nature}, volume = {393}, number = {6681}, pages = {162-165}, doi = {10.1038/30234}, pmid = {11560168}, issn = {0028-0836}, mesh = {Cell Nucleus/*genetics ; Chloroplasts/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Plant ; Phylogeny ; Plant Cells ; Plant Proteins/genetics ; Plants/*genetics ; Symbiosis ; }, abstract = {Photosynthetic eukaryotes, particularly unicellular forms, possess a fossil record that is either wrought with gaps or difficult to interpret, or both. Attempts to reconstruct their evolution have focused on plastid phylogeny, but were limited by the amount and type of phylogenetic information contained within single genes. Among the 210 different protein-coding genes contained in the completely sequenced chloroplast genomes from a glaucocystophyte, a rhodophyte, a diatom, a euglenophyte and five land plants, we have now identified the set of 45 common to each and to a cyanobacterial outgroup genome. Phylogenetic inference with an alignment of 11,039 amino-acid positions per genome indicates that this information is sufficient--but just rarely so--to identify the rooted nine-taxon topology. We mapped the process of gene loss from chloroplast genomes across the inferred tree and found that, surprisingly, independent parallel gene losses in multiple lineages outnumber phylogenetically unique losses by more that 4:1. We identified homologues of 44 different plastid-encoded proteins as functional nuclear genes of chloroplast origin, providing evidence for endosymbiotic gene transfer to the nucleus in plants.}, }
@article {pmid11557893, year = {2001}, author = {Ogata, H and Audic, S and Renesto-Audiffren, P and Fournier, PE and Barbe, V and Samson, D and Roux, V and Cossart, P and Weissenbach, J and Claverie, JM and Raoult, D}, title = {Mechanisms of evolution in Rickettsia conorii and R. prowazekii.}, journal = {Science (New York, N.Y.)}, volume = {293}, number = {5537}, pages = {2093-2098}, doi = {10.1126/science.1061471}, pmid = {11557893}, issn = {0036-8075}, mesh = {Adaptation, Physiological ; Chlamydia/genetics ; Computational Biology ; DNA, Bacterial/genetics ; DNA, Intergenic ; *Evolution, Molecular ; Gene Dosage ; Gene Silencing ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; Open Reading Frames ; Phylogeny ; Polymerase Chain Reaction ; Repetitive Sequences, Nucleic Acid ; Rickettsia/genetics ; Rickettsia conorii/*genetics/physiology ; Rickettsia prowazekii/*genetics/physiology ; Sequence Analysis, DNA ; Transcription, Genetic ; }, abstract = {Rickettsia conorii is an obligate intracellular bacterium that causes Mediterranean spotted fever in humans. We determined the 1,268,755-nucleotide complete genome sequence of R. conorii, containing 1374 open reading frames. This genome exhibits 804 of the 834 genes of the previously determined R. prowazekii genome plus 552 supplementary open reading frames and a 10-fold increase in the number of repetitive elements. Despite these differences, the two genomes exhibit a nearly perfect colinearity that allowed the clear identification of different stages of gene alterations with gene remnants and 37 genes split in 105 fragments, of which 59 are transcribed. A 38-kilobase sequence inversion was dated shortly after the divergence of the genus.}, }
@article {pmid11557800, year = {2001}, author = {Yoshiyama, M and Tu, Z and Kainoh, Y and Honda, H and Shono, T and Kimura, K}, title = {Possible horizontal transfer of a transposable element from host to parasitoid.}, journal = {Molecular biology and evolution}, volume = {18}, number = {10}, pages = {1952-1958}, doi = {10.1093/oxfordjournals.molbev.a003735}, pmid = {11557800}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Blotting, Southern ; DNA/chemistry/genetics ; DNA Transposable Elements/*genetics ; Gene Transfer, Horizontal ; Host-Parasite Interactions ; Molecular Sequence Data ; Moths/*genetics/parasitology ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Wasps/*genetics ; }, abstract = {Full-length mariner-like elements (MLEs) were identified from both a parasitoid wasp, Ascogaster reticulatus, and its moth host, Adoxophyes honmai. MLEs were detected in two related Tortricid moths, but not in another Ascogaster species. The MLEs of A. reticulatus and A. honmai were 97.6% identical in DNA sequence. This high similarity suggests a recent horizontal transfer, probably from the moth host to the wasp parasitoid, facilitated by the intimacy of the host-parasitoid relationship.}, }
@article {pmid11557498, year = {2001}, author = {Roberts, AP and Cheah, G and Ready, D and Pratten, J and Wilson, M and Mullany, P}, title = {Transfer of TN916-like elements in microcosm dental plaques.}, journal = {Antimicrobial agents and chemotherapy}, volume = {45}, number = {10}, pages = {2943-2946}, pmid = {11557498}, issn = {0066-4804}, mesh = {*Biofilms ; DNA Transposable Elements/*genetics ; Dental Plaque/*microbiology ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Streptococcus oralis/*genetics ; Transformation, Bacterial ; }, abstract = {Microcosm dental plaques were grown from an inoculum of human saliva in a constant-depth film fermentor. The inoculum contained four tetracycline-resistant streptococcal species, each of which contained a Tn916-like element. This element was shown to transfer to other streptococci both in filter-mating experiments and within the biofilms in the fermentor.}, }
@article {pmid11557460, year = {2001}, author = {Winokur, PL and Vonstein, DL and Hoffman, LJ and Uhlenhopp, EK and Doern, GV}, title = {Evidence for transfer of CMY-2 AmpC beta-lactamase plasmids between Escherichia coli and Salmonella isolates from food animals and humans.}, journal = {Antimicrobial agents and chemotherapy}, volume = {45}, number = {10}, pages = {2716-2722}, pmid = {11557460}, issn = {0066-4804}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Cattle ; Escherichia coli/drug effects/*genetics ; Gene Transfer, Horizontal/*genetics ; Humans ; Microbial Sensitivity Tests ; Molecular Epidemiology ; Phenotype ; Plasmids/genetics ; Salmonella/drug effects/*genetics ; Swine ; beta-Lactamases/*genetics ; }, abstract = {Escherichia coli is an important pathogen that shows increasing antimicrobial resistance in isolates from both animals and humans. Our laboratory recently described Salmonella isolates from food animals and humans that expressed an identical plasmid-mediated, AmpC-like beta-lactamase, CMY-2. In the present study, 59 of 377 E. coli isolates from cattle and swine (15.6%) and 6 of 1,017 (0.6%) isolates of human E. coli from the same geographic region were resistant to both cephamycins and extended-spectrum cephalosporins. An ampC gene could be amplified with CMY-2 primers in 94.8% of animal and 33% of human isolates. Molecular epidemiological studies of chromosomal DNA revealed little clonal relatedness among the animal and human E. coli isolates harboring the CMY-2 gene. The ampC genes from 10 animal and human E. coli isolates were sequenced, and all carried an identical CMY-2 gene. Additionally, all were able to transfer a plasmid containing the CMY-2 gene to a laboratory strain of E. coli. CMY-2 plasmids demonstrated two different plasmid patterns that each showed strong similarities to previously described Salmonella CMY-2 plasmids. Additionally, Southern blot analyses using a CMY-2 probe demonstrated conserved fragments among many of the CMY-2 plasmids identified in Salmonella and E. coli isolates from food animals and humans. These data demonstrate that common plasmids have been transferred between animal-associated Salmonella and E. coli, and identical CMY-2 genes carried by similar plasmids have been identified in humans, suggesting that the CMY-2 plasmid has undergone transfer between different bacterial species and may have been transmitted between food animals and humans.}, }
@article {pmid11555850, year = {2001}, author = {Gordon, JW}, title = {Editor's commentary: loose use of the phrase "germline genetic modification".}, journal = {The Journal of experimental zoology}, volume = {290}, number = {5}, pages = {437-438}, doi = {10.1002/jez.1086}, pmid = {11555850}, issn = {0022-104X}, mesh = {DNA, Mitochondrial ; Embryonic and Fetal Development ; Female ; Fertilization in Vitro ; *Gene Transfer, Horizontal ; *Germ Cells ; Humans ; Male ; Mitochondria/transplantation ; Terminology as Topic ; }, }
@article {pmid11555271, year = {2001}, author = {Zhang, XX and Kosier, B and Priefer, UB}, title = {Genetic diversity of indigenous Rhizobium leguminosarum bv. viciae isolates nodulating two different host plants during soil restoration with alfalfa.}, journal = {Molecular ecology}, volume = {10}, number = {9}, pages = {2297-2305}, doi = {10.1046/j.0962-1083.2001.01364.x}, pmid = {11555271}, issn = {0962-1083}, mesh = {DNA, Bacterial/genetics ; DNA, Ribosomal Spacer/genetics ; Gene Transfer, Horizontal ; Genetic Markers ; *Genetic Variation ; Genotype ; Humans ; Lipopolysaccharides ; Medicago sativa/physiology ; Phylogeny ; Plasmids/genetics/metabolism ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Rhizobium leguminosarum/classification/*genetics/isolation &amp; purification ; Symbiosis/genetics ; }, abstract = {A total of 360 Rhizobium leguminosarum bv. viciae strains was isolated from three brown-coal mining restoration fields of different age and plant cover (without and in the first and second year of alfalfa, Medicago sativa, cultivation) using two host species (Vicia hirsuta and Pisum sativum) as capture plants. The strains were genetically typed by restriction fragment length polymorphism analysis of polymerase chain reaction (PCR)-generated 16S-23S ribosomal DNA intergenic spacer regions (IGS-RFLP) and characterized by plasmid profiles and RFLP analysis of amplified nodABC genes. The R. leguminosarum bv. viciae population was dominated by the same group of strains (irrespective of the trap plant used). According to type richness, the genetic diversity of indigenous R. leguminosarum in the second year of restoration was lower than in the first year and it resembled that of the fallow field, except for plasmid types, in which it was higher than that of the fallow field. Some of the less frequent nodABC genotypes were associated with distinct chromosomal IGS genotypes and symbiotic plasmids (pSyms) of different sizes, indicating that horizontal transfer and rearrangements of pSym can occur in natural environments. However, the dominant pSym and chromosomal genotypes were strictly correlated suggesting a genetically stable persistence of the prevailing R. leguminosarum bv. viciae genotypes in the absence of its host plant.}, }
@article {pmid11553621, year = {2001}, author = {Elrouby, N and Bureau, TE}, title = {A novel hybrid open reading frame formed by multiple cellular gene transductions by a plant long terminal repeat retroelement.}, journal = {The Journal of biological chemistry}, volume = {276}, number = {45}, pages = {41963-41968}, doi = {10.1074/jbc.M105850200}, pmid = {11553621}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Base Sequence ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; *Open Reading Frames ; *Plant Proteins ; Retroelements ; Retroviridae Proteins/*genetics ; *Terminal Repeat Sequences ; Zea mays/genetics ; }, abstract = {The discovery that vertebrate retroviruses could transduce cellular sequences was central to cancer etiology and research. Although not well documented, transduction of cellular sequences by retroelements has been suggested to modify cellular functions. The maize Bs1 transposon was the first non-vertebrate retroelement reported to have transduced a portion of a cellular gene (c-pma). We show that Bs1 has, in addition, transduced portions of at least two more maize cellular genes, namely for 1,3-beta-glucanase (c-bg) and 1,4-beta-xylan endohydrolase (c-xe). We also show that Bs1 has maintained a truncated gag domain with similarity to the magellan gypsy-like long terminal repeat retrotransposon and a region that may correspond to an env-like domain. Our findings suggest that, like oncogenic retroviruses, the three transduced gene fragments and the Bs1 gag domain encode a fusion protein that has the potential to be expressed. We suggest that transduction by retroelements may facilitate the formation of novel hybrid genes in plants.}, }
@article {pmid11553577, year = {2001}, author = {Deng, W and Li, Y and Vallance, BA and Finlay, BB}, title = {Locus of enterocyte effacement from Citrobacter rodentium: sequence analysis and evidence for horizontal transfer among attaching and effacing pathogens.}, journal = {Infection and immunity}, volume = {69}, number = {10}, pages = {6323-6335}, pmid = {11553577}, issn = {0019-9567}, mesh = {*Adhesins, Bacterial ; Amino Acid Sequence ; Bacterial Adhesion/*genetics ; Bacterial Outer Membrane Proteins/genetics ; Bacterial Proteins/genetics ; Base Sequence ; Binding Sites ; *Carrier Proteins ; Citrobacter freundii/*genetics/pathogenicity ; DNA, Bacterial ; Enterocytes/*microbiology ; Escherichia coli/genetics ; *Escherichia coli Proteins ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Molecular Sequence Data ; Mutagenesis, Insertional ; Open Reading Frames ; Plasmids ; Receptors, Cell Surface/genetics ; Sequence Analysis, DNA ; }, abstract = {The family of attaching and effacing (A/E) bacterial pathogens, which includes diarrheagenic enteropathogenic Escherichia coli (EPEC) and enterohemorrhagic E. coli (EHEC), remains a significant threat to human and animal health. These bacteria intimately attach to host intestinal cells, causing the effacement of brush border microvilli. The genes responsible for this phenotype are encoded in a pathogenicity island called the locus of enterocyte effacement (LEE). Citrobacter rodentium is the only known murine A/E pathogen and serves as a small animal model for EPEC and EHEC infections. Here we report the full DNA sequence of C. rodentium LEE and provide a comparative analysis with the published LEEs from EPEC, EHEC, and the rabbit diarrheagenic E. coli strain RDEC-1. Although C. rodentium LEE shows high similarities throughout the entire sequence and shares all 41 open reading frames with the LEE from EPEC, EHEC, and RDEC-1, it is unique in its location of the rorf1 and rorf2/espG genes and the presence of several insertion sequences (IS) and IS remnants. The LEE of EPEC and EHEC is inserted into the selC tRNA gene. In contrast, the Citrobacter LEE is flanked on one side by an operon encoding an ABC transport system, and an IS element and sequences homologous to Shigella plasmid R100 and EHEC pO157 flank the other. The presence of plasmid sequences next to C. rodentium LEE suggests that the prototype LEE resided on a horizontally transferable plasmid. Additional sequence analysis reveals that the 3-kb plasmid in C. rodentium is nearly identical to p9705 in EHEC O157:H7, suggesting that horizontal plasmid transfer among A/E pathogens has occurred. Our results indicate that the LEE has been acquired by C. rodentium and A/E E. coli strains independently during evolution.}, }
@article {pmid11553453, year = {2001}, author = {Lan, R and Reeves, PR}, title = {When does a clone deserve a name? A perspective on bacterial species based on population genetics.}, journal = {Trends in microbiology}, volume = {9}, number = {9}, pages = {419-424}, doi = {10.1016/s0966-842x(01)02133-3}, pmid = {11553453}, issn = {0966-842X}, mesh = {Bacteria/*classification/*genetics/pathogenicity ; Clone Cells/classification/metabolism ; Gene Transfer, Horizontal ; Genetic Variation/genetics ; *Genetics, Population ; Humans ; Mycobacterium/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; Terminology as Topic ; Yersinia/genetics ; }, abstract = {Molecular population-genetic analysis has revealed that for several human diseases, including tuberculosis, plague and shigellosis, the generally accepted taxonomic status of the organisms involved does not fit the usually accepted genus or species criteria. This raises the question of what species concept to apply to bacteria. We suggest that the species definition in bacteria should be based on analysis of sequence variation in housekeeping genes, and also that the "clone" be given official status in bacterial nomenclature. This will allow demotion of the species or genus status of several traditionally recognized human pathogens, but retention of current names of anomalous species and genera as clone names.}, }
@article {pmid11549749, year = {2001}, author = {Pitkow, LJ and Sharer, CA and Ren, X and Insel, TR and Terwilliger, EF and Young, LJ}, title = {Facilitation of affiliation and pair-bond formation by vasopressin receptor gene transfer into the ventral forebrain of a monogamous vole.}, journal = {The Journal of neuroscience : the official journal of the Society for Neuroscience}, volume = {21}, number = {18}, pages = {7392-7396}, pmid = {11549749}, issn = {1529-2401}, support = {56897//PHS HHS/United States ; 58824//PHS HHS/United States ; }, mesh = {Animals ; Anxiety/genetics ; Arvicolinae ; Autoradiography ; Choice Behavior/physiology ; Dependovirus/genetics ; Gene Transfer, Horizontal ; Genetic Vectors/genetics/metabolism ; Globus Pallidus/metabolism ; Male ; Maze Learning/physiology ; *Pair Bond ; Prosencephalon/*metabolism ; Receptors, Vasopressin/genetics/*metabolism ; Sexual Behavior, Animal/*physiology ; *Social Facilitation ; }, abstract = {Behaviors associated with monogamy, including pair-bond formation, are facilitated by the neuropeptide vasopressin and are prevented by a vasopressin receptor [V1a receptor (V1aR)] antagonist in the male prairie vole. The neuroanatomical distribution of V1aR dramatically differs between monogamous and nonmonogamous species. V1aR binding is denser in the ventral pallidal region of several unrelated monogamous species compared with nonmonogamous species. Because the ventral pallidum is involved in reinforcement and addiction, we hypothesize that V1aR activation in this region promotes pair-bond formation via a mechanism similar to conditioning. Using an adeno-associated viral vector to deliver the V1aR gene, we increased the density of V1aR binding in the ventral pallial region of male prairie voles. These males exhibited increased levels of both anxiety and affiliative behavior compared with control males. In addition, males overexpressing the V1aR in the ventral pallidal region, but not control males, formed strong partner preferences after an overnight cohabitation, without mating, with a female. These data demonstrate a role for ventral pallidal V1aR in affiliation and social attachment and provide a potential molecular mechanism for species differences in social organization.}, }
@article {pmid11548250, year = {2001}, author = {Beliavskaia, VA and Kashperova, TA and Bondarenko, VM and Il'ichev, AA and Sorokulova, IB and Malik, NI}, title = {[Experimental evaluation of the biological safety of gene-engineered bacteria using a model strain Bacillus subtilis interferon-producing strain].}, journal = {Zhurnal mikrobiologii, epidemiologii i immunobiologii}, volume = {}, number = {2}, pages = {16-20}, pmid = {11548250}, issn = {0372-9311}, mesh = {Animals ; Bacillus subtilis/*genetics/growth &amp; development/metabolism ; Bacteriological Techniques ; Cattle ; Chickens ; Gene Transfer, Horizontal ; Humans ; Interferon-alpha/*biosynthesis ; Intestines/microbiology ; Mice ; Polymerase Chain Reaction ; Probiotics/*adverse effects ; Salmonella typhimurium/growth &amp; development ; }, abstract = {The in vitro and in vivo evaluation of the biological and ecological safety of genetically modified bacteria (GMB) was carried out on B. subtilis recombinant strain 2335/105, capable of producing human interferon alpha-2, used as experimental model. As shown in this investigation made with the use of bacteriological analysis and polymerase chain reaction, the oral administration of GMB to calves, chickens and white mice produced no disturbances in the microbial ecology of the gastrointestinal tract of warm-blooded animals and did not lead to the appearance of spontaneous transformants. The present work is the first experimental evaluation of the biological safety of genetically modified microorganisms, used as the component of Subalin, a probiotic preparation intended for use in veterinary practice.}, }
@article {pmid11545581, year = {2001}, author = {Mirold, S and Rabsch, W and Tschäpe, H and Hardt, WD}, title = {Transfer of the Salmonella type III effector sopE between unrelated phage families.}, journal = {Journal of molecular biology}, volume = {312}, number = {1}, pages = {7-16}, doi = {10.1006/jmbi.2001.4950}, pmid = {11545581}, issn = {0022-2836}, mesh = {Amino Acid Sequence ; Bacterial Proteins/*genetics ; Base Sequence ; Cloning, Molecular ; Gene Order ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Multigene Family ; Recombination, Genetic ; Salmonella/*genetics/immunology ; Salmonella Phages/genetics ; Siphoviridae ; }, abstract = {Salmonella spp. are pathogenic enterobacteria that employ type III secretion systems to translocate effector proteins and modulate responses of host cells. The repertoire of translocated effector proteins is thought to define host specificity and epidemic virulence, and varies even between closely related Salmonella strains. Therefore, horizontal transfer of effector protein genes between Salmonella strains plays a key role in shaping the Salmonella-host interaction. Several effector protein genes are located in temperate phages. The P2-like phage SopE Phi encodes SopE and the lambda-like GIFSY phages encode several effector proteins of the YopM/IpaH-family. Lysogenic conversion with these phages is responsible for much of the diversity of the effector protein repertoires observed among Salmonella spp. However, free exchange of effector proteins by lysogenic conversion can be restricted by superinfection immunity. To identify genetic mechanisms that may further enhance horizontal transfer of effector genes, we have analyzed sopE loci from Salmonella spp. that do not harbor P2-like sequences of SopE Phi. In two novel sopE loci that were identified, the 723 nt sopE gene is located in a conserved 1.2 kb cassette present also in SopE Phi. Most strikingly, in Salmonella enterica subspecies I serovars Gallinarum, Enteritidis, Hadar and Dublin, the sopE-cassette is located in a cryptic lambda-like prophage with similarity to the GIFSY phages. This provides the first evidence for transfer of virulence genes between different phage families. We show that such a mechanism can circumvent restrictions to phage-mediated gene transfer and thereby enhances reassortment of the effector protein repertoires in Salmonella spp.}, }
@article {pmid11545580, year = {2001}, author = {Malloff, CA and Fernandez, RC and Lam, WL}, title = {Bacterial comparative genomic hybridization: a method for directly identifying lateral gene transfer.}, journal = {Journal of molecular biology}, volume = {312}, number = {1}, pages = {1-5}, doi = {10.1006/jmbi.2001.4925}, pmid = {11545580}, issn = {0022-2836}, mesh = {Bacteria/*genetics ; DNA, Bacterial/chemistry ; Deoxyribonucleases, Type II Site-Specific/genetics/metabolism ; Electrophoresis, Gel, Two-Dimensional ; *Gene Transfer, Horizontal ; In Situ Hybridization/*methods ; Pseudomonas aeruginosa/genetics ; Restriction Mapping ; }, abstract = {Horizontally transferred DNA is largely responsible for the dissemination of virulence traits amongst bacteria. Rapid identification of acquired DNA remains difficult as whole-genome sequencing of outbreak strains is impractical, and microarray-based approaches, while powerful, are limited to genes present only in the reference strains. Here we present a novel bacterial comparative genomic hybridization method that directly compares the genomes of related strains at sub-kilobase resolution in order to identify acquired DNA. Bacterial comparative genomic hybridization utilizes the concept of metaphase chromosome comparative genomic hybridization, and exploits the resolving power of two-dimensional DNA electrophoresis. Comparison of isogenic variants of the pathogen Pseudomonas aeruginosa detected a single-copy gene insertion responsible for gentamicin resistance.}, }
@article {pmid11544372, year = {2001}, author = {Koonin, EV and Makarova, KS and Aravind, L}, title = {Horizontal gene transfer in prokaryotes: quantification and classification.}, journal = {Annual review of microbiology}, volume = {55}, number = {}, pages = {709-742}, doi = {10.1146/annurev.micro.55.1.709}, pmid = {11544372}, issn = {0066-4227}, mesh = {Eukaryotic Cells/physiology ; Gene Transfer, Horizontal/*physiology ; Phylogeny ; Prokaryotic Cells/*classification/*physiology ; Species Specificity ; }, abstract = {Comparative analysis of bacterial, archaeal, and eukaryotic genomes indicates that a significant fraction of the genes in the prokaryotic genomes have been subject to horizontal transfer. In some cases, the amount and source of horizontal gene transfer can be linked to an organism's lifestyle. For example, bacterial hyperthermophiles seem to have exchanged genes with archaea to a greater extent than other bacteria, whereas transfer of certain classes of eukaryotic genes is most common in parasitic and symbiotic bacteria. Horizontal transfer events can be classified into distinct categories of acquisition of new genes, acquisition of paralogs of existing genes, and xenologous gene displacement whereby a gene is displaced by a horizontally transferred ortholog from another lineage (xenolog). Each of these types of horizontal gene transfer is common among prokaryotes, but their relative contributions differ in different lineages. The fixation and long-term persistence of horizontally transferred genes suggests that they confer a selective advantage on the recipient organism. In most cases, the nature of this advantage remains unclear, but detailed examination of several cases of acquisition of eukaryotic genes by bacteria seems to reveal the evolutionary forces involved. Examples include isoleucyl-tRNA synthetases whose acquisition from eukaryotes by several bacteria is linked to antibiotic resistance, ATP/ADP translocases acquired by intracellular parasitic bacteria, Chlamydia and Rickettsia, apparently from plants, and proteases that may be implicated in chlamydial pathogenesis.}, }
@article {pmid11532154, year = {2001}, author = {Franken, C and Haase, G and Brandt, C and Weber-Heynemann, J and Martin, S and Lämmler, C and Podbielski, A and Lütticken, R and Spellerberg, B}, title = {Horizontal gene transfer and host specificity of beta-haemolytic streptococci: the role of a putative composite transposon containing scpB and lmb.}, journal = {Molecular microbiology}, volume = {41}, number = {4}, pages = {925-935}, doi = {10.1046/j.1365-2958.2001.02563.x}, pmid = {11532154}, issn = {0950-382X}, mesh = {Adhesins, Bacterial/*genetics/physiology ; Animals ; *Bacterial Adhesion ; Base Sequence ; Blotting, Southern ; DNA Transposable Elements/*genetics ; DNA, Ribosomal/genetics ; Endopeptidases/*genetics/physiology ; Evolution, Molecular ; Gene Dosage ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/*genetics ; Humans ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Repetitive Sequences, Nucleic Acid ; Sequence Alignment ; Streptococcal Infections/*microbiology ; Streptococcus agalactiae/*genetics/*physiology ; }, abstract = {Beta-haemolytic streptococci are important human and animal pathogens: their genetic traits that are associated with the ability to infect human hosts remain, however, unclear. The surface protein, Lmb, mediates the adherence of Streptococcus agalactiae to human laminin. For further analysis of the corresponding gene, the adjacent genomic regions were sequenced. Lmb is localized on a putative composite transposon of 16 kb and is flanked by two copies of a novel insertion sequence element (ISSag2). It harbours the genes scpB and lmb, which are 98% identical with the respective genes of Streptococcus pyogenes. Analysis of the distribution of these genes and ISSag2 among 131 streptococcal strains revealed that all of the human isolates, but only 20% (12 of 61) of the animal isolates, contained scpB and lmb or their homologues. To investigate if the putative transposon can be mobilized, an erythromycin resistance marker was incorporated into the lmb gene of S. agalactiae. Screening for mutant strains with a regained susceptibility for erythromycin identified strains with a deletion of scpB, lmb, and one copy of ISSag2. We hypothesize that a horizontal gene transfer caused the exchange of scpB and lmb and that the ability of S. pyogenes, S. agalactiae and group C and G streptococcal strains to colonize or infect human hosts is dependent on their presence.}, }
@article {pmid11526220, year = {2001}, author = {Keeling, PJ and Palmer, JD}, title = {Lateral transfer at the gene and subgenic levels in the evolution of eukaryotic enolase.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {98}, number = {19}, pages = {10745-10750}, pmid = {11526220}, issn = {0027-8424}, support = {R01 GM035087/GM/NIGMS NIH HHS/United States ; R01 GM35087/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Arabidopsis ; Eukaryotic Cells ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Humans ; Molecular Sequence Data ; Phosphopyruvate Hydratase/*genetics ; Phylogeny ; }, abstract = {Enolase genes from land plants and apicomplexa (intracellular parasites, including the malarial parasite, Plasmodium) share two short insertions. This observation has led to the suggestion that the apicomplexan enolase is the product of a lateral transfer event involving the algal endosymbiont from which the apicomplexan plastid is derived. We have examined enolases from a wide variety of algae, as well as ciliates (close relatives of apicomplexa), to determine whether lateral transfer can account for the origin of the apicomplexan enolase. We find that lateral gene transfer, likely occurring intracellularly between endosymbiont and host nucleus, does account for the evolution of cryptomonad and chlorarachniophyte algal enolases but fails to explain the apicomplexan enolase. This failure is because the phylogenetic distribution of the insertions--which we find in apicomplexa, ciliates, land plants, and charophyte green algae--directly conflicts with the phylogeny of the gene itself. Protein insertions have traditionally been treated as reliable markers of evolutionary events; however, these enolase insertions do not seem to reflect accurately the evolutionary history of the molecule. The lack of congruence between insertions and phylogeny could be because of the parallel loss of both insertions in two or more lineages, or what is more likely, because the insertions were transmitted between distantly related genes by lateral transfer and fine-scale recombination, resulting in a mosaic gene. This latter process would be difficult to detect without such insertions to act as markers, and such mosaic genes could blur the "tree of life" beyond the extent to which whole-gene lateral transfer is already known to confound evolutionary reconstruction.}, }
@article {pmid11526061, year = {2001}, author = {Hanten, JJ and Pierce, SK}, title = {Synthesis of several light-harvesting complex I polypeptides is blocked by cycloheximide in symbiotic chloroplasts in the sea slug, Elysia chlorotica (Gould): a case for horizontal gene transfer between alga and animal?.}, journal = {The Biological bulletin}, volume = {201}, number = {1}, pages = {34-44}, doi = {10.2307/1543523}, pmid = {11526061}, issn = {0006-3185}, mesh = {Animals ; Chloroplasts/*metabolism ; Cycloheximide/pharmacology ; Electrophoresis, Polyacrylamide Gel ; Eukaryota/*genetics/ultrastructure ; *Gene Transfer, Horizontal ; Mollusca/*genetics/ultrastructure ; Photosynthetic Reaction Center Complex Proteins/biosynthesis/*genetics ; Protein Synthesis Inhibitors/pharmacology ; *Symbiosis ; }, abstract = {The chloroplast symbiosis between the ascoglossan (=Sacoglossa) sea slug Elysia chlorotica and plastids from the chromophytic alga Vaucheria litorea is the longest-lived relationship of its kind known, lasting up to 9 months. During this time, the plastids continue to photosynthesize in the absence of the algal nucleus at rates sufficient to meet the nutritional needs of the slugs. We have previously demonstrated that the synthesis of photosynthetic proteins occurs while the plastids reside within the diverticular cells of the slug. Here, we have identified several of these synthesized proteins as belonging to the nuclear-encoded family of polypeptides known as light-harvesting complex I (LHCI). The synthesis of LHCI is blocked by the cytosolic ribosomal inhibitor cycloheximide and proceeds in the presence of chloramphenicol, a plastid ribosome inhibitor, indicating that the gene encoding LHCI resides in the nuclear DNA of the slug. These results suggest that a horizontal transfer of the LHCI gene from the alga to the slug has taken place.}, }
@article {pmid11525560, year = {2001}, author = {Burstein, H}, title = {Gene therapy for rheumatoid arthritis.}, journal = {Current opinion in molecular therapeutics}, volume = {3}, number = {4}, pages = {362-374}, pmid = {11525560}, issn = {1464-8431}, mesh = {Animals ; Antigens, CD/genetics ; Arthritis, Rheumatoid/*therapy ; Fas Ligand Protein ; Gene Transfer, Horizontal ; *Genetic Therapy ; Humans ; Interleukin 1 Receptor Antagonist Protein ; Interleukin-10/genetics ; Interleukin-4/genetics ; Membrane Glycoproteins/genetics ; Receptors, Tumor Necrosis Factor/genetics ; Receptors, Tumor Necrosis Factor, Type I ; Receptors, Tumor Necrosis Factor, Type II ; Sialoglycoproteins/genetics ; }, abstract = {Gene therapy was initially conceived of as a means of replacing defective genes in monogenic disorders such as cystic fibrosis or hemophilia, but has rapidly progressed into areas of medicine that involve a wide range of diseases including cancer, neurodegenerative disorders and autoimmunity. Elucidation of some of the cellular and molecular mechanisms implicated in the pathogenesis of joint inflammation and cartilage and bone destruction in inflammatory joint diseases such as rheumatoid arthritis (RA) have revealed novel targets for gene therapy. Strategies include the inhibition of pro-inflammatory cytokines, blockade of cartilage-degrading enzymes, inhibition of synovial cell activation or apoptosis of synovial cells, and manipulation of the Th1-Th2 cytokine balance. Both viral and non-viral gene transfer vector systems have been used to deliver therapeutic genes systemically or directly to arthritic joints by ex vivo as well as in vivo administration. Animal models of RA have been essential not only for better understanding the mechanisms of RA but also in serving as basic experimental tools to evaluate candidate gene products with anti-arthritic properties and develop therapeutic strategies.}, }
@article {pmid11525559, year = {2001}, author = {Cartier, N}, title = {Gene therapy strategies for X-linked adrenoleukodystrophy.}, journal = {Current opinion in molecular therapeutics}, volume = {3}, number = {4}, pages = {357-361}, pmid = {11525559}, issn = {1464-8431}, mesh = {Adrenoleukodystrophy/genetics/*therapy ; Brain/metabolism ; Gene Transfer, Horizontal ; *Genetic Therapy ; Hematopoietic Stem Cells/metabolism ; Humans ; }, abstract = {X-linked adrenoleukodystrophy (ALD) is the most frequently seen genetic disorder involving the myelin of the central nervous system. The cerebral form affects mainly boys between five to 12 years, leading to vegetative state or death within two to four years. The adult form affects the spinal cord, leading to severe paraplegia often complicated by cerebral demyelination. The ALD gene encodes an ATP-binding cassette transporter involved in the transport of very long chain fatty acids into peroxysomes. Specific subpopulations of oligodendrocytes and microglia are particularly affected by the ALD gene mutation and thus should be the target cells of gene therapy approaches. Two different and potentially complementary therapeutic strategies are currently evaluated. The first approach aims at replacing the endogenous brain microglia from patients by autotransplantation of genetically corrected hematopoietic stem cells using a lentiviral vector. The second approach aims at targeting directly the ALD gene into brain glial cells using stereotactic injections of viral vectors.}, }
@article {pmid11525558, year = {2001}, author = {Stedman, HH}, title = {Molecular approaches to therapy for Duchenne and limb-girdle muscular dystrophy.}, journal = {Current opinion in molecular therapeutics}, volume = {3}, number = {4}, pages = {350-356}, pmid = {11525558}, issn = {1464-8431}, mesh = {Animals ; Antigens, CD/genetics ; Dystrophin/genetics ; Gene Transfer, Horizontal ; *Genetic Therapy ; Genetic Vectors ; Humans ; *Integrin alpha Chains ; Mice ; Muscular Dystrophies/etiology/genetics/*therapy ; }, abstract = {The muscular dystrophies are a heterogeneous group of heritable disorders in which progressive muscle degeneration leads to regional or generalized weakness. Recent advances in molecular genetics, cell biology and vector discovery have improved the outlook for therapeutic intervention. This review focuses on novel approaches to the study of disease pathogenesis and refinements in gene- and cell-based strategies for protein restoration in Duchenne and limb-girdle muscular dystrophy, and concludes with a brief discussion of priorities for future clinical investigation.}, }
@article {pmid11525555, year = {2001}, author = {Kafri, T}, title = {Lentivirus vectors: difficulties and hopes before clinical trials.}, journal = {Current opinion in molecular therapeutics}, volume = {3}, number = {4}, pages = {316-326}, pmid = {11525555}, issn = {1464-8431}, mesh = {Brain/metabolism ; *Clinical Trials as Topic ; Gene Transfer, Horizontal ; *Genetic Therapy ; *Genetic Vectors ; Hematopoietic Stem Cells/metabolism ; Humans ; Lentivirus/*genetics ; Transgenes ; }, abstract = {The ability to transduce non-dividing cells is a unique feature of lentiviruses which distinguishes them from simple retroviruses. This feature was the major incentive for the development of the lentivirus vector system. Lentivirus vectors can deliver and integrate > 8 kb of transgenic DNA into target cell genomes without inducing a host immune response against the transduced cells. Thus lentivirus vector-based gene delivery can be considered the most efficient method by which transgenes can be incorporated into the host cell genome and maintain long-term expression. This review describes the major developments in the lentivirus vector system, which significantly improve vector biosafety, vector production and transgene expression. The success and difficulties in reverting disease phenotypes by lentivirus vectors carrying therapeutic genes in various animal models including beta-thalassemia and Parkinson's disease and the implications of these studies for future gene therapy clinical trials are also discussed.}, }
@article {pmid11525457, year = {2001}, author = {Martinsen, GD and Whitham, TG and Turek, RJ and Keim, P}, title = {Hybrid populations selectively filter gene introgression between species.}, journal = {Evolution; international journal of organic evolution}, volume = {55}, number = {7}, pages = {1325-1335}, doi = {10.1111/j.0014-3820.2001.tb00655.x}, pmid = {11525457}, issn = {0014-3820}, mesh = {Biological Evolution ; Cell Nucleus/genetics ; Crosses, Genetic ; Cytoplasm/genetics ; DNA, Chloroplast/genetics ; DNA, Mitochondrial/genetics ; *Gene Transfer, Horizontal ; Genetic Markers/genetics ; Genome, Plant ; Geography ; Hybridization, Genetic/*genetics ; Magnoliopsida/cytology/*genetics ; Polymorphism, Restriction Fragment Length ; Recombination, Genetic ; Species Specificity ; }, abstract = {Hybrids have long been recognized as a potential pathway for gene flow between species that can have important consequences for evolution and conservation biology. However, few studies have demonstrated that genes from one species can introgress or invade another species over a broad geographic area. Using 35 genetically mapped restriction fragment length polymorphism (RFLP) markers of two species of cottonwoods (Populus fremontii x P. angustifolia) and their hybrids (n = 550 trees), we showed that the majority of the genome is prohibited from introgressing from one species into the other. However, this barrier was not absolute; Fremont cpDNA and mtDNA were found throughout the geographic range of narrowleaf cottonwood, and 20% of the nuclear markers of Fremont cottonwood introgressed varying distances (some over 100 km) into the recipient species' range. Rates of nuclear introgression were variable, but two nuclear markers introgressed as fast as the haploid, cytoplasmically inherited chloroplast and mitochondrial markers. Our genome-wide analysis provides evidence for positive, negative, and neutral effects of introgression. For example, we predict that DNA fragments that introgress through several generations of backcrossing will be small, because small fragments are less likely to contain deleterious genes. These results argue that recombination will be important, that introgression can be very selective, and that evolutionary forces within the hybrid population to effectively "filter" gene flow between species. A strong filter may make introgression adaptive, prevent genetic assimilation, lead to relaxed isolating mechanisms, and contribute to the stability of hybrid zones. Thus, rather than hybridization being a negative factor as is commonly argued, natural hybridization between native species may provide important genetic variation that impacts both ecological and evolutionary processes. Finally, we propose two hypotheses that contrast the likelihood of contemporary versus ancient introgression in this system.}, }
@article {pmid11523011, year = {2001}, author = {Wang, B}, title = {Limitations of compositional approach to identifying horizontally transferred genes.}, journal = {Journal of molecular evolution}, volume = {53}, number = {3}, pages = {244-250}, doi = {10.1007/s002390010214}, pmid = {11523011}, issn = {0022-2844}, mesh = {Base Composition/genetics ; Codon/genetics ; Computational Biology ; Escherichia coli/*genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/genetics ; *Genome, Bacterial ; Likelihood Functions ; }, abstract = {Genes with atypical G+C content and pattern of codon usage in a certain genome are possibly of exotic origin, and this idea has been applied to identify horizontal events. In this way, it was postulated that a total of 755 genes in the E. coli genome are relics of horizontal events after the divergence of E. coli from the Salmonella lineage 100 million years ago (Lawrence and Ochman, 1998). In this paper we propose a new way to study sequence composition more thoroughly. We found that although the 755 genes differ in composition from other genes in the E. coli genome, the difference is minor. If we accepted that these genes are horizontally transferred, then (1) it would be more likely that they were transferred from genomes evolutionarily closely related to E. coli; but (2) the dating method used by Lawrence and Ochman (1997, 1998) largely underestimated the average age of introduced sequences in the E. coli genome, in particular, most of the 755 genes should be introduced into E. coli before, instead of after, the divergence of E. coli from the Salmonella lineage. Our study reveals that atypical G+C content and pattern of codon usage are not reliable indicators of horizontal gene transfer events.}, }
@article {pmid11522293, year = {2001}, author = {Rigden, DJ and Monteiro, AC and Grossi de Sá, MF}, title = {The protease inhibitor chagasin of Trypanosoma cruzi adopts an immunoglobulin-type fold and may have arisen by horizontal gene transfer.}, journal = {FEBS letters}, volume = {504}, number = {1-2}, pages = {41-44}, doi = {10.1016/s0014-5793(01)02753-3}, pmid = {11522293}, issn = {0014-5793}, mesh = {Amino Acid Sequence ; Animals ; Cysteine Proteinase Inhibitors/*chemistry/genetics ; *Gene Transfer, Horizontal ; Immunoglobulins/*chemistry ; Models, Molecular ; Molecular Sequence Data ; *Protein Folding ; Protozoan Proteins/*chemistry/genetics ; Sequence Homology, Amino Acid ; Trypanosoma cruzi/*chemistry ; }, abstract = {Chagasin, a protein from Trypanosoma cruzi, is the first member of a new family of tight binding cysteine protease inhibitors [Monteiro, A.C.S., Abrahamson, M., Lima, A.P.C., Vannier-Santos, M.A. and Scharfstein, J. (2001) J. Cell Sci., in press] [corrected]. Despite its lack of significant sequence identity with known proteins, convincing structural models, using variable light chain templates, could be constructed on the basis of threading results. Experimental support for the final structure came from inhibition data for overlapping oligopeptides spanning the chagasin sequence. Chagasin therefore exemplifies a new protease inhibitor structural class and a new natural use for an immunoglobulin-like domain. Limited sequence resemblance suggests that chagasin may represent the result of a rare horizontal gene transfer from host to parasite.}, }
@article {pmid11519999, year = {2001}, author = {Barbieri, P and Arenghi, FL and Bertoni, G and Bolognese, F and Galli, E}, title = {Evolution of catabolic pathways and metabolic versatility in Pseudomonas stutzeri OX1.}, journal = {Antonie van Leeuwenhoek}, volume = {79}, number = {2}, pages = {135-140}, doi = {10.1023/a:1010238403295}, pmid = {11519999}, issn = {0003-6072}, mesh = {Biodegradation, Environmental ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Isomerism ; Oxidation-Reduction ; Oxygenases/*genetics/metabolism ; Plasmids/genetics ; Pseudomonas/enzymology/*genetics ; Toluene/*metabolism ; Xylenes/*metabolism ; }, abstract = {Pseudomonas stutzeri OX1 is able to degrade toluene and ortho-xylene via the direct oxygenation of the aromatic ring. The genetic studies carried out suggest that the genes coding for the monooxygenase involved in the early steps of this catabolic route have been acquired by gene transfer. P stutzeri OX1 is also potentially able to utilize meta- and para-xylene as growth substrates. These two isomers are metabolized through a different pathway (TOL pathway). Both catabolic routes can be activated or inactivated by means of genomic rearrangements. The relevance of such recombination mechanisms in the evolution and the adaptability of P. stutzeri is discussed.}, }
@article {pmid11519998, year = {2001}, author = {Egan, S and Wiener, P and Kallifidas, D and Wellington, EM}, title = {Phylogeny of Streptomyces species and evidence for horizontal transfer of entire and partial antibiotic gene clusters.}, journal = {Antonie van Leeuwenhoek}, volume = {79}, number = {2}, pages = {127-133}, doi = {10.1023/a:1010296220929}, pmid = {11519998}, issn = {0003-6072}, mesh = {Bacterial Proteins/*genetics/metabolism ; Base Sequence ; Drug Resistance, Bacterial ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Molecular Sequence Data ; Multigene Family ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Streptomyces/classification/drug effects/*genetics/metabolism ; Streptomycin/*biosynthesis/pharmacology ; Transaminases/*genetics/metabolism ; Tryptophan/biosynthesis ; }, abstract = {The phylogenetic relationships of a collection of streptomycete soil isolates and type strains were resolved by sequence analysis of trpB, a housekeeping gene involved in tryptophan biosynthesis. The analysis confirmed that two isolates were recipients in a gene transfer event, demonstrated by phylogenetic incongruency between trpB and strB1 trees. One strain had acquired the entire streptomycin biosynthetic cluster, whilst the other contained only strRAB1, the resistance gene and two flanking genes from the cluster. Sequence analysis of trpB, as part of a polyphasic approach, was a useful tool in determining intra-generic relationships within the genus Streptomyces.}, }
@article {pmid11517311, year = {2001}, author = {Löytynoja, A and Milinkovitch, MC}, title = {Molecular phylogenetic analyses of the mitochondrial ADP-ATP carriers: the Plantae/Fungi/Metazoa trichotomy revisited.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {98}, number = {18}, pages = {10202-10207}, pmid = {11517311}, issn = {0027-8424}, mesh = {Animals ; Eukaryotic Cells ; Evolution, Molecular ; Fungi/genetics/metabolism ; Mitochondria/*genetics ; Mitochondrial ADP, ATP Translocases/*genetics ; *Phylogeny ; Plants/genetics/metabolism ; }, abstract = {We investigated the basal phylogeny of eukaryotes through analyses of sequences from the ADP-ATP mitochondrial carrier, a transmembrane protein that is stable in function across eukaryote kingdoms. The ADP-ATP data strongly suggest the grouping of Plantae and Fungi to the exclusion of Metazoa. We implemented several procedures to avoid pervasive analytical artifacts such as erroneous alignment, random rooting, long branch attraction, and misidentification of noisy characters. The quest of an eukaryote tree that would be largely consistent across multiple loci might be essentially illusory because of differential lineage sorting, horizontal gene transfer, and the chimeric nature of early eukaryotes. Better understanding of these evolutionary parameters, requiring separate phylogenetic analyses of multiple independent loci, is fundamental for resolution of the modes of emergence and evolution of the major eukaryote lineages.}, }
@article {pmid11516380, year = {2001}, author = {Wain, J and House, D and Pickard, D and Dougan, G and Frankel, G}, title = {Acquisition of virulence-associated factors by the enteric pathogens Escherichia coli and Salmonella enterica.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {356}, number = {1411}, pages = {1027-1034}, doi = {10.1098/rstb.2001.0891}, pmid = {11516380}, issn = {0962-8436}, mesh = {Escherichia coli/*pathogenicity/*physiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Salmonella enterica/*pathogenicity/*physiology ; Virulence/*physiology ; }, abstract = {In this review we summarize recent genomic studies that shed light on the mechanism through which pathogenic Escherichia coli and Salmonella enterica have evolved. We show how acquisition of DNA at specific sites on the chromosome has contributed to increased genetic variation and virulence of these two genera of the Enterobacteriaceae.}, }
@article {pmid11514534, year = {2001}, author = {Tsuge, K and Itaya, M}, title = {Recombinational transfer of 100-kilobase genomic DNA to plasmid in Bacillus subtilis 168.}, journal = {Journal of bacteriology}, volume = {183}, number = {18}, pages = {5453-5458}, pmid = {11514534}, issn = {0021-9193}, mesh = {Bacillus subtilis/drug effects/*genetics ; DNA Replication ; DNA, Bacterial/*genetics ; Drug Resistance, Microbial/genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Plasmids/genetics ; *Recombination, Genetic ; Tetracyclines/pharmacology ; }, abstract = {Transformation of Bacillus subtilis by a plasmid requires a circular multimeric form. In contrast, linearized plasmids can be circularized only when homologous sequences are present in the host genome. A recombinational transfer system was constructed with this intrinsic B. subtilis recombinational repair pathway. The vector, pGETS103, a derivative of the theta-type replicating plasmid pTB19 of thermophilic Bacillus, had the full length of Escherichia coli plasmid pBR322. A multimeric form of pGETS103 yielded tetracycline-resistant transformants of B. subtilis. In contrast, linearized pGETS103 gave tetracycline-resistant transformants only when the recipient strain had the pBR322 sequence in the genome. The efficiency and fidelity of the recombinational transfer of DNAs of up to 90 kb are demonstrated.}, }
@article {pmid11514530, year = {2001}, author = {Sekizaki, T and Osaki, M and Takamatsu, D and Shimoji, Y}, title = {Distribution of the SsuDAT1I restriction-modification system among different serotypes of Streptococcus suis.}, journal = {Journal of bacteriology}, volume = {183}, number = {18}, pages = {5436-5440}, pmid = {11514530}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; Animals ; DNA Restriction Enzymes/chemistry/genetics ; DNA Restriction-Modification Enzymes/chemistry/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Methyltransferases/genetics ; Molecular Sequence Data ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Serotyping ; Streptococcus suis/*classification/*enzymology/genetics ; }, abstract = {The SsuDAT1I restriction-modification (R-M) system, which contains two methyltransferases and two restriction endonucleases with recognition sequence 5'-GATC-3', was first found in a field isolate of Streptococcus suis serotype 2. Isoschizomers of the R-M system were found in the same locus between purH and purD in a field isolate of serotype 1/2 and the reference strains of serotypes 3, 7, 23, and 26 among 29 strains of different serotypes examined in this study. The R-M gene sequences in serotypes 1/2, 3, 7, and 23 were very similar to those of SsuDAT1I, whereas those in serotype 26 were less similar. These results indicate intraspecies recombination among them and genetic divergence through their evolution.}, }
@article {pmid11510681, year = {2001}, author = {Imase, A and Kobayashi, K and Ohmae, H and Matsuda, H and Iwamura, Y}, title = {Horizontal and vertical transmission of mouse class I MHC sequence in Schistosoma mansoni.}, journal = {Parasitology}, volume = {123}, number = {Pt 2}, pages = {163-168}, doi = {10.1017/s0031182001008198}, pmid = {11510681}, issn = {0031-1820}, mesh = {Animals ; Base Sequence ; DNA, Helminth/chemistry/genetics/isolation &amp; purification ; Gene Transfer, Horizontal/*genetics ; Genes, MHC Class I/*genetics ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Inbred ICR ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Polymerase Chain Reaction ; Schistosoma mansoni/chemistry/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {The mouse major histocompatibility complex (MHC) class I sequence was detected in 8-week-old Schistosoma mansoni by in situ polymerase chain reaction (in situ PCR). The signals to the mouse class I MHC sequence were observed in the nuclei of the mesenchymal and reproductive cells of S. mansoni. Signals were also observed in the cytoplasm of the tegumental tubercles. This finding suggested the possibility of MHC gene transfer from the host to schistosomes. Furthermore, the class I MHC sequence was detected in the DNA extracted from the cercariae of S. mansoni by nested PCR. Neither the nucleotide sequence of class I MHC detected in adult worm DNA nor that of class I MHC detected in the host (mouse) DNA was identical with that of class I MHC detected in the cercarial DNA. From the data we assumed that S. mansoni may have retained their own mouse class I MHC sequence in their genome throughout their life-cycle.}, }
@article {pmid11504864, year = {2001}, author = {Guindon, S and Perrière, G}, title = {Intragenomic base content variation is a potential source of biases when searching for horizontally transferred genes.}, journal = {Molecular biology and evolution}, volume = {18}, number = {9}, pages = {1838-1840}, doi = {10.1093/oxfordjournals.molbev.a003972}, pmid = {11504864}, issn = {0737-4038}, mesh = {Bacteria/genetics ; Base Composition/*genetics ; Codon/genetics ; Escherichia coli/genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Genetic Variation ; *Genome, Bacterial ; Replication Origin/genetics ; }, }
@article {pmid11503638, year = {2001}, author = {Salzberg, SL and Eisen, JA}, title = {Lateral gene transfer or viral colonization?.}, journal = {Science (New York, N.Y.)}, volume = {293}, number = {5532}, pages = {1048}, doi = {10.1126/science.293.5532.1048b}, pmid = {11503638}, issn = {0036-8075}, mesh = {Animals ; DNA Replication ; Eukaryotic Cells/*virology ; *Gene Transfer, Horizontal ; Genes, Viral ; *Genome ; Glucuronosyltransferase/genetics ; *Glycosyltransferases ; Humans ; Hyaluronan Synthases ; *Membrane Proteins ; Phylogeny ; Recombination, Genetic ; *Transferases ; Vertebrates/*virology ; *Virus Physiological Phenomena ; Virus Replication ; *Xenopus Proteins ; }, }
@article {pmid11501672, year = {2001}, author = {Dabizzi, S and Ammannato, S and Fani, R}, title = {Expression of horizontally transferred gene clusters: activation by promoter-generating mutations.}, journal = {Research in microbiology}, volume = {152}, number = {6}, pages = {539-549}, doi = {10.1016/s0923-2508(01)01228-1}, pmid = {11501672}, issn = {0923-2508}, mesh = {Aldose-Ketose Isomerases/biosynthesis/genetics ; Aminohydrolases/biosynthesis/genetics ; Azospirillum brasilense/chemistry/*genetics/metabolism ; Bacterial Proteins/biosynthesis/genetics ; Base Sequence ; Chloramphenicol O-Acetyltransferase/analysis ; Escherichia coli/chemistry/*genetics/metabolism ; Gene Expression Regulation, Bacterial/*genetics ; Gene Transfer, Horizontal/*genetics ; Genetic Complementation Test ; Histidine/biosynthesis ; Molecular Sequence Data ; *Multienzyme Complexes ; Multigene Family/*genetics ; *Mutation ; Plasmids/genetics ; Polymerase Chain Reaction ; Sequence Homology, Nucleic Acid ; }, abstract = {The occurrence of promoter-generating mutations allowing the transcription of heterologous genes has been studied in a system based on the plasmid-mediated conjugal transfer of histidine biosynthetic genes from a donor bacterium (Azospirillum brasilense) into a heterologous Escherichia coli mutant population lacking histidine biosynthetic ability and initially unable to recognize the transcriptional signal of the introgressed gene(s). Under selective stressful conditions, His+ revertants accumulated in the E. coli His- culture. The number of His+ colonies was dependent on the time of incubation under selective conditions, the strength of selective pressure, and on the crowding of cells plated; moreover, it was independent of the physiological status of the cell (i.e. the growth phase). Sequence analysis of plasmid DNA extracted from E. coli His+ revertants revealed that single base substitutions in the region upstream of the A. brasilense his operon resulted in an adjustment of the pre-existing sequence that was rendered similar to the E. coli -10 promoter sequence and transcriptable by the host RNA-polymerase. One particular transition (C --> T) was predominant in the His+ revertants. Data presented here indicated that the barriers to the expression of horizontally transferred heterologous genes or operons may be overcome in a short time scale and at high frequency, and supported the selfish operon model on the origin and evolution of gene clusters.}, }
@article {pmid11500406, year = {2001}, author = {Johnson, JR and O'Bryan, TT and Kuskowski, M and Maslow, JN}, title = {Ongoing horizontal and vertical transmission of virulence genes and papA alleles among Escherichia coli blood isolates from patients with diverse-source bacteremia.}, journal = {Infection and immunity}, volume = {69}, number = {9}, pages = {5363-5374}, pmid = {11500406}, issn = {0019-9567}, support = {DK-47504/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Alleles ; Bacteremia/epidemiology/*microbiology ; Bacterial Proteins/*genetics ; Escherichia coli/*genetics/*pathogenicity ; Escherichia coli Infections/epidemiology/*microbiology ; *Escherichia coli Proteins ; Fimbriae Proteins ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Phylogeny ; Virulence/genetics ; }, abstract = {The phylogenetic distributions of multiple putative virulence factors (VFs) and papA (P fimbrial structural subunit) alleles among 182 Escherichia coli blood isolates from patients with diverse-source bacteremia were defined. Phylogenetic correspondence among these strains, the E. coli Reference (ECOR) collection, and other collections of extraintestinal pathogenic E. coli (ExPEC) was assessed. Although among the 182 bacteremia isolates phylogenetic group B2 predominated, exhibited the greatest concentration of individual VFs, and contained the largest number of familiar virulent clones, other phylogenetic groups exhibited greater concentrations of certain VFs than did group B2 and included several additional virulent clones. Certain of the newly detected VF genes, e.g., fyuA (yersiniabactin; 76%) and focG (F1C fimbriae; 25%), were as prevalent or more prevalent than their more familiar traditional counterparts, e.g., iut (aerobactin; 57%) and sfaS (S fimbriae; 14%), thus possibly offering additional useful targets for preventive interventions. Considerable diversity of VF profiles was observed at every level within the phylogenetic tree, including even within individual lineages. This suggested that many different pathways can lead to extraintestinal virulence in E. coli and that the evolution of ExPEC, which involves extensive horizontal transmission of VFs and continuous remodeling of pathogenicity-associated islands, is a highly active, ongoing process.}, }
@article {pmid11496014, year = {2001}, author = {Gray, KM and Garey, JR}, title = {The evolution of bacterial LuxI and LuxR quorum sensing regulators.}, journal = {Microbiology (Reading, England)}, volume = {147}, number = {Pt 8}, pages = {2379-2387}, doi = {10.1099/00221287-147-8-2379}, pmid = {11496014}, issn = {1350-0872}, mesh = {Bacterial Proteins/*genetics ; *Evolution, Molecular ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genes, rRNA/genetics ; Phylogeny ; Proteobacteria/*genetics/physiology ; RNA, Ribosomal, 16S/genetics ; Repressor Proteins/*genetics ; Signal Transduction ; Trans-Activators/*genetics ; Transcription Factors/*genetics ; }, abstract = {Quorum sensing is a widespread form of bacterial communication in which individual cells produce and respond to specific N-acyl homoserine lactone signal metabolites. The different autoinducer synthases that generate these signals and the receptor/activator proteins that mediate the cell's response to them constitute evolutionarily conserved families of regulatory proteins known as the LuxI and LuxR families, respectively. We have performed a phylogenetic analysis of 76 individual LuxI and LuxR homologues present in diverse members of the Gram-negative Proteobacteria. The results were consistent with an early origin for these regulators during the evolution of the Proteobacteria, with functional pairs of luxI and luxR genes possibly coevolving as regulatory cassettes. In many cases, specific LuxI and LuxR family members appeared to have been inherited horizontally. In particular, those species containing multiple LuxI and/or LuxR homologues usually appeared to have obtained each individual homologue or functional pair of homologues from an independent source. Because multiple homologues interact to form regulatory cascades, this finding suggests that hierarchical signalling pathways can potentially evolve by the sequential integration of pre-existing regulatory circuits acquired from diverse sources.}, }
@article {pmid11487399, year = {2001}, author = {Adams, SP and Hartman, TP and Lim, KY and Chase, MW and Bennett, MD and Leitch, IJ and Leitch, AR}, title = {Loss and recovery of Arabidopsis-type telomere repeat sequences 5'-(TTTAGGG)(n)-3' in the evolution of a major radiation of flowering plants.}, journal = {Proceedings. Biological sciences}, volume = {268}, number = {1476}, pages = {1541-1546}, doi = {10.1098/rspb.2001.1726}, pmid = {11487399}, issn = {0962-8452}, mesh = {Arabidopsis/*genetics ; Evolution, Molecular ; *Genes, Plant ; Phylogeny ; Telomere/*genetics ; Terminal Repeat Sequences/genetics ; }, abstract = {Fluorescent in situ hybridization and Southern blotting were used for showing the predominant absence of the Arabidopsis-type telomere repeat sequence (TRS) 5'-(TTTAGGG)(n)-3' (the 'typical' telomere) in a monocot clade which comprises up to 6300 species within Asparagales. Initially, two apparently disparate genera that lacked the typical telomere were identified. Here, we used the new angiosperm phylogenetic classification for predicting in which other related families such telomeres might have been lost. Our data revealed that 16 species in 12 families of Asparagales lacked typical telomeres. Phylogenetically, these were clustered in a derived clade, thereby enabling us to predict that the typical telomere was lost, probably as a single evolutionary event, following the divergence of Doryanthaceae ca. 80--90 million years ago. This result illustrates the predictive value of the new phylogeny, as the pattern of species lacking the typical telomere would be considered randomly placed against many previous angiosperm taxonomies. Possible mechanisms by which chromosome end maintenance could have evolved in this group of plants are discussed. Surprisingly, one genus, Ornithogalum (Hyacinthaceae), which is central to the group of plants that have lost the typical telomere, appears to have regained the sequences. The mechanism(s) by which such recovery may have occurred is unknown, but possibilities include horizontal gene transfer and sequence reamplification.}, }
@article {pmid11483581, year = {2001}, author = {Sandberg, R and Winberg, G and Bränden, CI and Kaske, A and Ernberg, I and Cöster, J}, title = {Capturing whole-genome characteristics in short sequences using a naïve Bayesian classifier.}, journal = {Genome research}, volume = {11}, number = {8}, pages = {1404-1409}, pmid = {11483581}, issn = {1088-9051}, mesh = {Archaea/*classification/*genetics ; Bacteria/*classification/*genetics ; Base Composition/genetics ; Base Sequence/genetics ; Bayes Theorem ; GC Rich Sequence/genetics ; Gene Frequency/genetics ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/genetics ; *Genome, Bacterial ; }, abstract = {Bacterial genomes have diverged during evolution, resulting in clearcut differences in their nucleotide composition, such as their GC content. The analysis of complete sequences of bacterial genomes also reveals the presence of nonrandom sequence variation, manifest in the frequency profile of specific short oligonucleotides. These frequency profiles constitute highly specific genomic signatures. Based on these differences in oligonucleotide frequency between bacterial genomes, we investigated the possibility of predicting the genome of origin for a specific genomic sequence. To this end, we developed a naïve Bayesian classifier and systematically analyzed 28 eubacterial and archaeal genomes. We found that sequences as short as 400 bases could be correctly classified with an accuracy of 85%. We then applied the classifier to the identification of horizontal gene transfer events in whole-genome sequences and demonstrated the validity of our approach by correctly predicting the transfer of both the superoxide dismutase (sodC) and the bioC gene from Haemophilus influenzae to Neisseria meningitis, correctly identifying both the donor and recipient species. We believe that this classification methodology could be a valuable tool in biodiversity studies.}, }
@article {pmid11481492, year = {2001}, author = {Arora, SK and Bangera, M and Lory, S and Ramphal, R}, title = {A genomic island in Pseudomonas aeruginosa carries the determinants of flagellin glycosylation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {98}, number = {16}, pages = {9342-9347}, pmid = {11481492}, issn = {0027-8424}, support = {R01 AI045014/AI/NIAID NIH HHS/United States ; AI 45014/AI/NIAID NIH HHS/United States ; }, mesh = {Chromosomes, Bacterial ; Cosmids ; Flagellin/genetics/*metabolism ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Glycosylation ; Molecular Sequence Data ; Mutation ; Plasmids ; Polymerase Chain Reaction ; Pseudomonas aeruginosa/*genetics ; }, abstract = {Protein glycosylation has been long recognized as an important posttranslational modification process in eukaryotic cells. Glycoproteins, predominantly secreted or surface localized, have also been identified in bacteria. We have identified a cluster of 14 genes, encoding the determinants of the flagellin glycosylation machinery in Pseudomonas aeruginosa PAK, which we called the flagellin glycosylation island. Flagellin glycosylation can be detected only in bacteria expressing the a-type flagellin sequence variants, and the survey of 30 P. aeruginosa isolates revealed coinheritance of the a-type flagellin genes with at least one of the flagellin glycosylation island genes. Expression of the b-type flagellin in PAK, an a-type strain carrying the glycosylation island, did not lead to glycosylation of the b-type flagellin of PAO1, suggesting that flagellins expressed by b-type bacteria not only lack the glycosylation island, they cannot serve as substrates for glycosylation. Providing the entire glycosylation island of PAK, including its a-type flagellin in a flagellin mutant of a b-type strain, results in glycosylation of the heterologous flagellin. These results suggest that some or all of the 14 genes on the glycosylation island are the genes that are missing from strain PAO1 to allow glycosylation of an appropriate flagellin. Inactivation of either one of the two flanking genes present on this island abolished flagellin glycosylation. Based on the limited homologies of these gene products with enzymes involved in glycosylation, we propose that the island encodes similar proteins involved in synthesis, activation, or polymerization of sugars that are necessary for flagellin glycosylation.}, }
@article {pmid11481251, year = {2001}, author = {Guidotti, JE and Mallet, VO and Mitchell, C and Fabre, M and Schoevaert, D and Opolon, P and Parlier, D and Lambert, M and Kahn, A and Gilgenkrantz, H}, title = {Selection of in vivo retrovirally transduced hepatocytes leads to efficient and predictable mouse liver repopulation.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {15}, number = {10}, pages = {1849-1851}, doi = {10.1096/fj.00-0892fje}, pmid = {11481251}, issn = {0892-6638}, mesh = {Animals ; Apoptosis ; *Cell Division ; Cell Transplantation ; Gene Expression ; Gene Transfer, Horizontal ; Genetic Vectors ; Green Fluorescent Proteins ; Hepatocytes/cytology/*metabolism ; Humans ; Kinetics ; Luminescent Proteins/genetics ; Mice ; Mice, Transgenic ; Proto-Oncogene Proteins c-bcl-2/genetics ; Retroviridae/*genetics ; beta-Galactosidase/genetics ; }, }
@article {pmid11480664, year = {2001}, author = {Soleas, GJ and Diamandis, EP and Goldberg, DM}, title = {The world of resveratrol.}, journal = {Advances in experimental medicine and biology}, volume = {492}, number = {}, pages = {159-182}, doi = {10.1007/978-1-4615-1283-7_13}, pmid = {11480664}, issn = {0065-2598}, mesh = {Animals ; Anticarcinogenic Agents/*metabolism/pharmacokinetics/therapeutic use ; Antioxidants/*metabolism/pharmacokinetics/therapeutic use ; Arteriosclerosis/metabolism ; Biological Availability ; Cell Division/drug effects ; Gene Transfer, Horizontal ; Humans ; Inflammation/metabolism ; Intestinal Absorption ; Neoplasms/etiology/*prevention &amp; control ; Resveratrol ; Stilbenes/*metabolism/pharmacokinetics/therapeutic use ; Vitis/chemistry/genetics ; }, }
@article {pmid11473989, year = {2001}, author = {Moore, PC and Lindsay, JA}, title = {Genetic variation among hospital isolates of methicillin-sensitive Staphylococcus aureus: evidence for horizontal transfer of virulence genes.}, journal = {Journal of clinical microbiology}, volume = {39}, number = {8}, pages = {2760-2767}, pmid = {11473989}, issn = {0095-1137}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacterial Proteins/classification/genetics/metabolism ; Bacterial Typing Techniques ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; *Genetic Variation ; Hospitals, Teaching ; Methicillin/pharmacology ; Penicillins/pharmacology ; Polymorphism, Restriction Fragment Length ; Staphylococcal Infections/*microbiology ; Staphylococcus aureus/classification/*drug effects/genetics/*pathogenicity ; *Trans-Activators ; Transcription Factors/classification/genetics ; Virulence/genetics ; }, abstract = {Staphylococcus aureus strains often carry in their genomes virulence genes that are not found in all strains and that may be carried on discrete genetic elements. Strains also differ in that they carry one of four classes of an accessory gene regulator (agr) locus, an operon that regulates virulence factor expression and that has been proposed to be a therapeutic target. To look at their distribution among hospital strains, we investigated 38 methicillin-sensitive S. aureus isolates, classifying the isolates by agr class and screening them for the presence and restriction fragment length polymorphisms (RFLPs) of 12 core and 14 accessory virulence genes. Twenty-three (61%) were agr class I, 10 (26%) were agr class II, and 5 (13%) were agr class III. None were agr class IV. The S. aureus strains had distinguishable RFLP profiles, although clusters of isolates with clearly related core gene profiles were found among our strains, including all five agr class III strains, two sets of six strains within agr class I, and six strains within agr class II. Within these clusters there was evidence of horizontal acquisition and/or loss of multiple accessory virulence genes. Furthermore, two isolates from the same patient were identical except for the presence of the sea gene, indicating that movement of mobile elements may occur in vivo. Several strong correlations with the carriage of virulence genes between strains were seen, including a positive correlation between tst and agr class III and negative correlations between tst and lukE-splB and between lukE-splB and seg-sei. This suggests that the core genome or the presence of accessory genetic elements within a strain may influence acquisition and loss of other elements encoding virulence genes.}, }
@article {pmid11473319, year = {2001}, author = {Ghigo, JM}, title = {Natural conjugative plasmids induce bacterial biofilm development.}, journal = {Nature}, volume = {412}, number = {6845}, pages = {442-445}, doi = {10.1038/35086581}, pmid = {11473319}, issn = {0028-0836}, mesh = {Biofilms/*growth &amp; development ; *Conjugation, Genetic ; Escherichia coli/genetics/*growth &amp; development ; *F Factor ; Fimbriae, Bacterial/physiology ; Gram-Negative Bacteria/genetics/physiology ; }, abstract = {Horizontal gene transfer is a principal source of evolution leading to change in the ecological character of bacterial species. Bacterial conjugation, which promotes the horizontal transfer of genetic material between donor and recipient cells by physical contact, is a phenomenon of fundamental evolutionary consequence. Although conjugation has been studied primarily in liquid, most natural bacterial populations are found associated with environmental surfaces in complex multispecies communities called biofilms. Biofilms are ideally suited to the exchange of genetic material of various origins, and it has been shown that bacterial conjugation occurs within biofilms. Here I investigate the direct contribution of conjugative plasmids themselves to the capacity of the bacterial host to form a biofilm. Natural conjugative plasmids expressed factors that induced planktonic bacteria to form or enter biofilm communities, which favour the infectious transfer of the plasmid. This general connection between conjugation and biofilms suggests that medically relevant plasmid-bearing strains are more likely to form a biofilm. This may influence both the chances of biofilm-related infection risks and of conjugational spread of virulence factors.}, }
@article {pmid11472956, year = {2001}, author = {Oppegaard, H and Steinum, TM and Wasteson, Y}, title = {Horizontal transfer of a multi-drug resistance plasmid between coliform bacteria of human and bovine origin in a farm environment.}, journal = {Applied and environmental microbiology}, volume = {67}, number = {8}, pages = {3732-3734}, pmid = {11472956}, issn = {0099-2240}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Cattle ; Cattle Diseases/*microbiology ; Conjugation, Genetic ; Drug Resistance, Microbial/genetics ; Drug Resistance, Multiple/genetics ; Escherichia coli/*drug effects/*genetics ; Escherichia coli Infections/*microbiology/veterinary ; *Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; R Factors/*genetics ; }, abstract = {Multi-drug-resistant coliform bacteria were isolated from feces of cattle exposed to antimicrobial agents and humans associated with the animals. Isolates from both cattle and humans harbored an R plasmid of 65 kb (pTMS1) that may have been transferred between them due to selective antibiotic pressure in the farm environment.}, }
@article {pmid11472916, year = {2001}, author = {Demanèche, S and Bertolla, F and Buret, F and Nalin, R and Sailland, A and Auriol, P and Vogel, TM and Simonet, P}, title = {Laboratory-scale evidence for lightning-mediated gene transfer in soil.}, journal = {Applied and environmental microbiology}, volume = {67}, number = {8}, pages = {3440-3444}, pmid = {11472916}, issn = {0099-2240}, mesh = {Culture Media ; Electric Conductivity ; *Electromagnetic Fields ; Escherichia coli/*genetics/growth &amp; development ; *Gene Transfer, Horizontal ; *Lightning ; Plasmids/genetics ; *Soil Microbiology ; Transformation, Bacterial ; }, abstract = {Electrical fields and current can permeabilize bacterial membranes, allowing for the penetration of naked DNA. Given that the environment is subjected to regular thunderstorms and lightning discharges that induce enormous electrical perturbations, the possibility of natural electrotransformation of bacteria was investigated. We demonstrated with soil microcosm experiments that the transformation of added bacteria could be increased locally via lightning-mediated current injection. The incorporation of three genes coding for antibiotic resistance (plasmid pBR328) into the Escherichia coli strain DH10B recipient previously added to soil was observed only after the soil had been subjected to laboratory-scale lightning. Laboratory-scale lightning had an electrical field gradient (700 versus 600 kV m(-1)) and current density (2.5 versus 12.6 kA m(-2)) similar to those of full-scale lightning. Controls handled identically except for not being subjected to lightning produced no detectable antibiotic-resistant clones. In addition, simulated storm cloud electrical fields (in the absence of current) did not produce detectable clones (transformation detection limit, 10(-9)). Natural electrotransformation might be a mechanism involved in bacterial evolution.}, }
@article {pmid11470849, year = {2001}, author = {Gerbod, D and Edgcomb, VP and Noël, C and Vanácová, S and Wintjens, R and Tachezy, J and Sogin, ML and Viscogliosi, E}, title = {Phylogenetic relationships of class II fumarase genes from trichomonad species.}, journal = {Molecular biology and evolution}, volume = {18}, number = {8}, pages = {1574-1584}, doi = {10.1093/oxfordjournals.molbev.a003944}, pmid = {11470849}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Animals ; DNA, Protozoan/chemistry/genetics ; Evolution, Molecular ; Fumarate Hydratase/*genetics ; Gene Expression Regulation, Enzymologic ; Molecular Sequence Data ; *Phylogeny ; RNA, Protozoan/genetics/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Trichomonadida/classification/enzymology/*genetics ; }, abstract = {Class II fumarase sequences were obtained by polymerase chain reaction from five trichomonad species. All residues known to be highly conserved in this enzyme were present. Nuclear run-on assays showed that one of the two genes identified in Tritrichomonas foetus was expressed, whereas no fumarase transcripts were detected in the related species Trichomonas vaginalis. These findings corroborate previous biochemical data. Fumarase genes were also expressed in Monocercomonas sp. and Tetratrichomonas gallinarum but not in Pentatrichomonas hominis, Trichomonas gallinae, Trichomonas tenax, and Trichomitus batrachorum under the culture conditions used. Molecular trees inferred by likelihood methods reveal that trichomonad sequences have no affinity to described class II fumarase genes from other eukaryotes. The absence of functional mitochondria in protists such as trichomonads suggests that they diverged from other eukaryotes prior to the alpha-proteobacterial symbiosis that led to mitochondria. Furthermore, they are basal to other eukaryotes in rRNA analyses. However, support for the early-branching status of trichomonads and other amitochondriate protists based on phylogenetic analyses of multiple data sets has been equivocal. Although the presence of hydrogenosomes suggests that trichomonads once had mitochondria, their class II iron-independent fumarase sequences differ markedly from those of other mitochondriate eukaryotes. All of the class II fumarase genes described from other eukaryotes are of apparent alpha-proteobacterial origin and hence a marker of mitochondrial evolution. In contrast, the class II fumarase from trichomonads emerges among other eubacterial homologs. This is intriguing evidence for an independent acquisition of these genes in trichomonads apart from the mitochondrial endosymbiosis event that gave rise to the form present in other eukaryotes. The ancestral trichomonad class II fumarase may represent a prokaryotic form that was replaced in other eukaryotes after the divergence of trichomonads with the movement of endosymbiont genes into the nucleus. Alternatively, it may have been acquired via a separate endosymbiotic event or lateral gene transfer.}, }
@article {pmid11470360, year = {2001}, author = {Ragan, MA}, title = {On surrogate methods for detecting lateral gene transfer.}, journal = {FEMS microbiology letters}, volume = {201}, number = {2}, pages = {187-191}, doi = {10.1111/j.1574-6968.2001.tb10755.x}, pmid = {11470360}, issn = {0378-1097}, mesh = {Base Composition ; Computer Simulation ; Cytosine/analysis ; Escherichia coli/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Genome, Bacterial ; Guanine/analysis ; Markov Chains ; Open Reading Frames/*genetics ; Phylogeny ; }, abstract = {Surrogate methods for detecting lateral gene transfer are those that do not require inference of phylogenetic trees. Herein I apply four such methods to identify open reading frames (ORFs) in the genome of Escherichia coli K12 that may have arisen by lateral gene transfer. Only two of these methods detect the same ORFs more frequently than expected by chance, whereas several intersections contain many fewer ORFs than expected. Each of the four methods detects a different non-random set of ORFs. The methods may detect lateral ORFs of different relative ages; testing this hypothesis will require rigorous inference of trees.}, }
@article {pmid11466280, year = {2001}, author = {Eggers, CH and Kimmel, BJ and Bono, JL and Elias, AF and Rosa, P and Samuels, DS}, title = {Transduction by phiBB-1, a bacteriophage of Borrelia burgdorferi.}, journal = {Journal of bacteriology}, volume = {183}, number = {16}, pages = {4771-4778}, pmid = {11466280}, issn = {0021-9193}, support = {AI41559/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteriophages/*genetics/*physiology/ultrastructure ; Borrelia burgdorferi Group/*genetics/*virology ; Cloning, Molecular ; DNA Transposable Elements ; DNA, Bacterial/genetics ; DNA, Viral/genetics ; Genetic Complementation Test ; Kanamycin Resistance/*genetics ; Plasmids ; Polymerase Chain Reaction ; Restriction Mapping ; Transduction, Genetic ; Transformation, Genetic ; }, abstract = {We previously described a bacteriophage of the Lyme disease agent Borrelia burgdorferi designated phiBB-1. This phage packages the host complement of the 32-kb circular plasmids (cp32s), a group of homologous molecules found throughout the genus Borrelia. To demonstrate the ability of phiBB-1 to package and transduce DNA, a kanamycin resistance cassette was inserted into a cloned fragment of phage DNA, and the resulting construct was transformed into B. burgdorferi CA-11.2A cells. The kan cassette recombined into a resident cp32 and was stably maintained. The cp32 containing the kan cassette was packaged by phiBB-1 released from this B. burgdorferi strain. phiBB-1 has been used to transduce this antibiotic resistance marker into naive CA-11.2A cells, as well as two other strains of B. burgdorferi. This is the first direct evidence of a mechanism for lateral gene transfer in B. burgdorferi.}, }
@article {pmid11465059, year = {2001}, author = {Ponting, CP}, title = {Issues in predicting protein function from sequence.}, journal = {Briefings in bioinformatics}, volume = {2}, number = {1}, pages = {19-29}, doi = {10.1093/bib/2.1.19}, pmid = {11465059}, issn = {1467-5463}, mesh = {Amino Acids/analysis ; Animals ; *Computational Biology ; Conserved Sequence ; Databases, Factual ; Evolution, Molecular ; Gene Transfer, Horizontal ; Humans ; Protein Structure, Tertiary ; Proteins/chemistry/*genetics/*physiology ; Sequence Alignment ; Sequence Analysis, Protein ; }, abstract = {Identifying homologues, defined as genes that arose from a common evolutionary ancestor, is often a relatively straightforward task, thanks to recent advances made in estimating the statistical significance of sequence similarities found from database searches. The extent by which homologues possess similarities in function, however, is less amenable to statistical analysis. Consequently, predicting function by homology is a qualitative, rather than quantitative, process and requires particular care to be taken. This review focuses on the various approaches that have been developed to predict function from the scale of the atom to that of the organism. Similarities in homologues' functions differ considerably at each of these different scales and also vary for different domain families. It is argued that due attention should be paid to all available clues to function, including orthologue identification, conservation of particular residue types, and the co-occurrence of domains in proteins. Pitfalls in database searching methods arising from amino acid compositional bias and database size effects are also discussed.}, }
@article {pmid11459968, year = {2001}, author = {Mosig, G and Gewin, J and Luder, A and Colowick, N and Vo, D}, title = {Two recombination-dependent DNA replication pathways of bacteriophage T4, and their roles in mutagenesis and horizontal gene transfer.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {98}, number = {15}, pages = {8306-8311}, pmid = {11459968}, issn = {0027-8424}, support = {P30 CA068485/CA/NCI NIH HHS/United States ; CA68485/CA/NCI NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacteriophage T4/*genetics ; *DNA Replication ; Endodeoxyribonucleases/biosynthesis ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; *Mutagenesis ; *Recombination, Genetic ; *Signal Transduction ; }, abstract = {Two major pathways of recombination-dependent DNA replication, "join-copy" and "join-cut-copy," can be distinguished in phage T4: join-copy requires only early and middle genes, but two late proteins, endonuclease VII and terminase, are uniquely important in the join-cut-copy pathway. In wild-type T4, timing of these pathways is integrated with the developmental program and related to transcription and packaging of DNA. In primase mutants, which are defective in origin-dependent lagging-strand DNA synthesis, the late pathway can bypass the lack of primers for lagging-strand DNA synthesis. The exquisitely regulated synthesis of endo VII, and of two proteins from its gene, explains the delay of recombination-dependent DNA replication in primase (as well as topoisomerase) mutants, and the temperature-dependence of the delay. Other proteins (e.g., the single-stranded DNA binding protein and the products of genes 46 and 47) are important in all recombination pathways, but they interact differently with other proteins in different pathways. These homologous recombination pathways contribute to evolution because they facilitate acquisition of any foreign DNA with limited sequence homology during horizontal gene transfer, without requiring transposition or site-specific recombination functions. Partial heteroduplex repair can generate what appears to be multiple mutations from a single recombinational intermediate. The resulting sequence divergence generates barriers to formation of viable recombinants. The multiple sequence changes can also lead to erroneous estimates in phylogenetic analyses.}, }
@article {pmid11455202, year = {2001}, author = {Hay, CM and De Leon, H and Jafari, JD and Jakubczak, JL and Mech, CA and Hallenbeck, PL and Powell, SK and Liau, G and Stevenson, SC}, title = {Enhanced gene transfer to rabbit jugular veins by an adenovirus containing a cyclic RGD motif in the HI loop of the fiber knob.}, journal = {Journal of vascular research}, volume = {38}, number = {4}, pages = {315-323}, doi = {10.1159/000051062}, pmid = {11455202}, issn = {1018-1172}, mesh = {Adenoviridae/*genetics ; Amino Acid Sequence ; Animals ; Antigens, CD/*metabolism ; Capsid/chemistry/*genetics ; *Capsid Proteins ; Endothelium, Vascular/metabolism ; Escherichia coli/genetics ; Gene Expression ; *Gene Transfer, Horizontal ; Genetic Vectors ; Histocytochemistry ; Integrin alphaV ; *Jugular Veins ; Mice ; Mice, Inbred C57BL ; Muscle, Smooth, Vascular/metabolism ; Organ Culture Techniques ; Rabbits ; Rats ; Rats, Sprague-Dawley ; Receptors, Immunologic/chemistry/*genetics ; Receptors, Peptide/chemistry/*genetics ; Recombinant Fusion Proteins ; Species Specificity ; Transfection ; }, abstract = {Gene therapy using recombinant adenoviral vectors represents a promising therapeutic tool to prevent vein graft stenosis, the main complication of coronary artery bypass grafting. However, the low transduction efficiency of vascular smooth muscle cells and endothelial cells (EC) is a potential limitation, presumably due to the low levels of functional adenovirus receptor (coxsackie:adenovirus receptor; CAR). Designing vectors specifically targeted to alpha(v) integrins is a strategy that might overcome the poor expression of CAR in vascular smooth muscle cells and EC. RGD, a receptor-binding motif that can interact with alpha(v) integrins, was inserted into the HI loop and at the C-terminus of the adenoviral fiber protein in two separate adenovirus vectors encoding a beta-galactosidase reporter gene. Av1nBgCRGD (C-terminus) and Av1nBgHIRGD (HI loop) were evaluated in EC in culture and in jugular vein organ culture. Transduction of primary rat and rabbit EC with Av1nBgHIRGD was significantly more efficient when compared to Av1nBgCRGD or Av1nBg. Transduction of mouse, rat and rabbit jugular veins in organ culture using Av1nBg showed that adenovirus-mediated gene expression was greatest in rabbit jugular veins compared to rat and mouse veins. Av1nBgHIRGD augmented gene expression approximately four-fold in rabbit jugular veins when compared to Av1nBg. Histochemical analysis showed that numerous EC but few smooth muscle cells were transduced at all vector concentrations. A substantial number of adventitial fibroblasts were transduced only at the highest vector concentrations of Av1nBgHIRGD. These findings demonstrate that integrin-targeted vectors allow for enhanced gene delivery to veins and strengthen the viability of adenoviral-mediated gene transfer of therapeutic transgenes to human veins prior to vein grafting.}, }
@article {pmid11454891, year = {2001}, author = {Hortobagyi, GN and Ueno, NT and Xia, W and Zhang, S and Wolf, JK and Putnam, JB and Weiden, PL and Willey, JS and Carey, M and Branham, DL and Payne, JY and Tucker, SD and Bartholomeusz, C and Kilbourn, RG and De Jager, RL and Sneige, N and Katz, RL and Anklesaria, P and Ibrahim, NK and Murray, JL and Theriault, RL and Valero, V and Gershenson, DM and Bevers, MW and Huang, L and Lopez-Berestein, G and Hung, MC}, title = {Cationic liposome-mediated E1A gene transfer to human breast and ovarian cancer cells and its biologic effects: a phase I clinical trial.}, journal = {Journal of clinical oncology : official journal of the American Society of Clinical Oncology}, volume = {19}, number = {14}, pages = {3422-3433}, doi = {10.1200/JCO.2001.19.14.3422}, pmid = {11454891}, issn = {0732-183X}, support = {CA58880/CA/NCI NIH HHS/United States ; CA60856/CA/NCI NIH HHS/United States ; }, mesh = {Adenovirus E1A Proteins/*genetics ; Adult ; Aged ; Apoptosis ; Breast Neoplasms/genetics/metabolism/pathology/*therapy ; Cholesterol/analogs &amp; derivatives ; Cytokines/metabolism ; Female ; Gene Expression ; *Gene Transfer, Horizontal ; Genes, erbB-2 ; *Genetic Therapy ; Humans ; Immunohistochemistry ; In Situ Nick-End Labeling ; Injections ; Ki-67 Antigen ; Liposomes ; Middle Aged ; Ovarian Neoplasms/genetics/metabolism/pathology/*therapy ; Peritoneal Cavity ; Reverse Transcriptase Polymerase Chain Reaction ; Thorax ; Tumor Cells, Cultured ; }, abstract = {PURPOSE: Preclinical studies have demonstrated that the adenovirus type 5 E1A gene is associated with antitumor activities by transcriptional repression of HER-2/neu and induction of apoptosis. Indeed, E1A gene therapy is known to induce regression of HER-2/neu-overexpressing breast and ovarian cancers in nude mice. Therefore, we evaluated the feasibility of intracavitary injection of E1A gene complexed with DC-Chol cationic liposome (DCC-E1A) in patients with both HER-2/neu-overexpressing and low HER-2/neu-expressing breast and ovarian cancers in a phase I clinical trial.<br><br>PATIENTS AND METHODS: An E1A gene complexed with DCC-E1A cationic liposome was injected once a week into the thoracic or peritoneal cavity of 18 patients with advanced cancer of the breast (n = 6) or ovary (n = 12).<br><br>RESULTS: E1A gene expression in tumor cells was detected by immunohistochemical staining and reverse transcriptase-polymerase chain reaction. This E1A gene expression was accompanied by HER-2/neu downregulation, increased apoptosis, and reduced proliferation. The most common treatment-related toxicities were fever, nausea, vomiting, and/or discomfort at the injection sites.<br><br>CONCLUSION: These results argue for the feasibility of intracavitary DCC-E1A administration, provide a clear proof of preclinical concept, and warrant phase II trials to determine the antitumor activity of the E1A gene.}, }
@article {pmid11454746, year = {2001}, author = {Rubin, E and Lithwick, G and Levy, AA}, title = {Structure and evolution of the hAT transposon superfamily.}, journal = {Genetics}, volume = {158}, number = {3}, pages = {949-957}, pmid = {11454746}, issn = {0016-6731}, mesh = {Base Sequence ; DNA/genetics ; DNA Transposable Elements/*genetics ; Database Management Systems ; *Evolution, Molecular ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Transposases/*genetics ; Zea mays/genetics ; }, abstract = {The maize transposon Activator (Ac) was the first mobile DNA element to be discovered. Since then, other elements were found that share similarity to Ac, suggesting that it belongs to a transposon superfamily named hAT after hobo from Drosophila, Ac from maize, and Tam3 from snapdragon. We addressed the structure and evolution of hAT elements by developing new tools for transposon mining and searching the public sequence databases for the hallmarks of hAT elements, namely the transposase and short terminal inverted repeats (TIRs) flanked by 8-bp host duplications. We found 147 hAT-related sequences in plants, animals, and fungi. Six conserved blocks could be identified in the transposase of most hAT elements. A total of 41 hAT sequences were flanked by TIRs and 8-bp host duplications and, out of these, 34 sequences had TIRs similar to the consensus determined in this work, suggesting that they are active or recently active transposons. Phylogenetic analysis and clustering of hAT sequences suggest that the hAT superfamily is very ancient, probably predating the plant-fungi-animal separation, and that, unlike previously proposed, there is no evidence that horizontal gene transfer was involved in the evolution of hAT elements.}, }
@article {pmid11447287, year = {2001}, author = {Fitzgerald, JR and Sturdevant, DE and Mackie, SM and Gill, SR and Musser, JM}, title = {Evolutionary genomics of Staphylococcus aureus: insights into the origin of methicillin-resistant strains and the toxic shock syndrome epidemic.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {98}, number = {15}, pages = {8821-8826}, pmid = {11447287}, issn = {0027-8424}, mesh = {Animals ; Blotting, Southern/methods ; Cattle ; Chromosomes, Bacterial ; *Disease Outbreaks ; Electrophoresis ; *Evolution, Molecular ; Genetic Variation ; *Genome, Bacterial ; Humans ; Methicillin Resistance/*genetics ; Polymerase Chain Reaction/methods ; Sheep ; Shock, Septic/epidemiology/*microbiology/veterinary ; Staphylococcal Infections/epidemiology/microbiology/veterinary ; Staphylococcus aureus/classification/*genetics/pathogenicity ; }, abstract = {An emerging theme in medical microbiology is that extensive variation exists in gene content among strains of many pathogenic bacterial species. However, this topic has not been investigated on a genome scale with strains recovered from patients with well-defined clinical conditions. Staphylococcus aureus is a major human pathogen and also causes economically important infections in cows and sheep. A DNA microarray representing >90% of the S. aureus genome was used to characterize genomic diversity, evolutionary relationships, and virulence gene distribution among 36 strains of divergent clonal lineages, including methicillin-resistant strains and organisms causing toxic shock syndrome. Genetic variation in S. aureus is very extensive, with approximately 22% of the genome comprised of dispensable genetic material. Eighteen large regions of difference were identified, and 10 of these regions have genes that encode putative virulence factors or proteins mediating antibiotic resistance. We find that lateral gene transfer has played a fundamental role in the evolution of S. aureus. The mec gene has been horizontally transferred into distinct S. aureus chromosomal backgrounds at least five times, demonstrating that methicillin-resistant strains have evolved multiple independent times, rather than from a single ancestral strain. This finding resolves a long-standing controversy in S. aureus research. The epidemic of toxic shock syndrome that occurred in the 1970s was caused by a change in the host environment, rather than rapid geographic dissemination of a new hypervirulent strain. DNA microarray analysis of large samples of clinically characterized strains provides broad insights into evolution, pathogenesis, and disease emergence.}, }
@article {pmid11447209, year = {2001}, author = {Brinkman, FS and Macfarlane, EL and Warrener, P and Hancock, RE}, title = {Evolutionary relationships among virulence-associated histidine kinases.}, journal = {Infection and immunity}, volume = {69}, number = {8}, pages = {5207-5211}, pmid = {11447209}, issn = {0019-9567}, mesh = {Animals ; Ascomycota/enzymology/genetics/*pathogenicity ; Bacterial Proteins/*genetics/physiology ; Candida albicans/enzymology/genetics/pathogenicity ; *Evolution, Molecular ; Histidine Kinase ; Lipase/biosynthesis ; Mice ; Mice, Inbred C57BL ; Protein Kinases/*genetics/physiology ; Protein Serine-Threonine Kinases ; Pseudomonas aeruginosa/enzymology/genetics/*pathogenicity ; *Saccharomyces cerevisiae Proteins ; Streptomyces/enzymology/genetics/*pathogenicity ; Transcription Factors/*genetics/physiology ; Virulence ; }, abstract = {A strong relationship between virulence-associated sensor histidine kinases of fungi and those in Streptomyces coelicolor was observed, and phylogenetic analysis suggested that bacterium-to-eukaryote horizontal gene transfer had occurred between ancestors of these organisms. Phylogenetic analysis also identified a group of histidine kinases orthologous to the Streptomyces proteins that includes Pseudomonas aeruginosa GacS. We provide evidence that GacS is important for swarming motility, lipase production, and virulence in mice and had evolved to have partial functional overlaps with PhoQ, a less-related virulence-associated histidine kinase.}, }
@article {pmid11447161, year = {2001}, author = {Kalia, A and Enright, MC and Spratt, BG and Bessen, DE}, title = {Directional gene movement from human-pathogenic to commensal-like streptococci.}, journal = {Infection and immunity}, volume = {69}, number = {8}, pages = {4858-4869}, pmid = {11447161}, issn = {0019-9567}, support = {//Wellcome Trust/United Kingdom ; R01 GM060793/GM/NIGMS NIH HHS/United States ; AI-28944/AI/NIAID NIH HHS/United States ; GM-60793/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Sequence ; Classification ; DNA, Bacterial ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Humans ; Molecular Sequence Data ; Mosaicism ; Phenotype ; Phylogeny ; Sequence Homology, Nucleic Acid ; Streptococcus/classification/*genetics ; Streptococcus pyogenes/classification/*genetics ; }, abstract = {Group A streptococci (GAS) are highly pathogenic for humans, and their closest genetic relatives, group C and G streptococci (GCS and GGS, respectively), are generally regarded as commensals, although they can be found in association with human disease. As part of an effort to better understand the evolution of virulence, the phylogenetic relationships between GAS, GCS, and GGS were examined. The nucleotide sequence was determined for an internal portion of seven housekeeping (neutral) loci among >200 isolates of GAS and 34 isolates of GCS or GGS obtained from human subjects. Genotypic analysis failed to show support for the separation of GCS and GGS into two distinct populations. Unlike GAS, there was poor concordance between emm type and genetic relatedness among GCS and GGS. All housekeeping genes within GAS displayed relatively low levels of sequence diversity. In contrast, individual GCS and GGS strains had mosaic genomes, containing alleles at some loci that were similar or identical to GAS alleles, whereas the alleles at other loci were about 10 to 30% diverged. The data provide evidence for a history of recent interspecies transfer of neutral genes that exhibits a strong net directionality from GAS donors to GCS and GGS recipients. A model for the evolution of GAS and of GCS and GGS is described.}, }
@article {pmid11447108, year = {2001}, author = {Guo, YL and Seebacher, T and Kurz, U and Linder, JU and Schultz, JE}, title = {Adenylyl cyclase Rv1625c of Mycobacterium tuberculosis: a progenitor of mammalian adenylyl cyclases.}, journal = {The EMBO journal}, volume = {20}, number = {14}, pages = {3667-3675}, pmid = {11447108}, issn = {0261-4189}, mesh = {Adenylyl Cyclases/chemistry/*genetics/metabolism ; Amino Acid Sequence ; Amino Acid Substitution ; Cell Line ; Dimerization ; Escherichia coli/genetics ; *Evolution, Molecular ; Humans ; Membrane Proteins/chemistry/genetics/metabolism ; Molecular Sequence Data ; Mycobacterium tuberculosis/*enzymology ; Recombinant Proteins/chemistry/genetics/metabolism ; Sequence Homology, Amino Acid ; }, abstract = {The gene Rv1625c from Mycobacterium tuberculosis encodes a membrane-anchored adenylyl cyclase corresponding to exactly one-half of a mammalian adenylyl cyclase. An engineered, soluble form of Rv1625c was expressed in Escherichia coli. It formed a homodimeric cyclase with two catalytic centers. Amino acid mutations predicted to affect catalysis resulted in inactive monomers. A single catalytic center with wild-type activity could be reconstituted from mutated monomers in stringent analogy to the mammalian heterodimeric cyclase structure. The proposed existence of supramolecular adenylyl cyclase complexes was established by reconstitution from peptide-linked, mutation-inactivated homodimers resulting in pseudo-trimeric and -tetrameric complexes. The mycobacterial holoenzyme was expressed successfully in E.coli and mammalian HEK293 cells, i.e. its membrane targeting sequence was compatible with the bacterial and eukaryotic machinery for processing and membrane insertion. The membrane-anchored mycobacterial cyclase expressed in E.coli was purified to homogeneity as a first step toward the complete structural elucidation of this important protein. As the closest progenitor of the mammalian adenylyl cyclase family to date, the mycobacterial cyclase probably was spread by horizontal gene transfer.}, }
@article {pmid11446510, year = {2001}, author = {Nwosu, VC}, title = {Antibiotic resistance with particular reference to soil microorganisms.}, journal = {Research in microbiology}, volume = {152}, number = {5}, pages = {421-430}, doi = {10.1016/s0923-2508(01)01215-3}, pmid = {11446510}, issn = {0923-2508}, mesh = {Anti-Bacterial Agents/*pharmacology/therapeutic use ; Bacteria/drug effects/genetics ; Bacterial Infections/drug therapy ; Conjugation, Genetic ; *Drug Resistance, Bacterial/genetics ; Evolution, Molecular ; Plasmids ; }, abstract = {Evidence of increasing resistance to antibiotics in soil and other natural isolates highlights the importance of horizontal transfer of resistance genes in facilitating gene flux in bacteria. Horizontal gene transfer in bacteria is favored by the presence of mobile genetic elements and by the organization of bacterial genomes into operons allowing for the cooperative transfer of genes with related functions. The selective pressure for the spread of resistance genes correlates strongly with the clinical and agricultural overuse of antibiotics. The future of antimicrobial chemotherapy may lie in developing new antimicrobials using information from comparative functional microbial genomics to find genetic targets for antimicrobials and also to understand gene expression enabling selective targeting of genes with expression that correlates with the infectious process.}, }
@article {pmid11445166, year = {2001}, author = {Hedlund, BP and Geiselbrecht, AD and Staley, JT}, title = {Marinobacter strain NCE312 has a Pseudomonas-like naphthalene dioxygenase.}, journal = {FEMS microbiology letters}, volume = {201}, number = {1}, pages = {47-51}, doi = {10.1111/j.1574-6968.2001.tb10731.x}, pmid = {11445166}, issn = {0378-1097}, support = {T32 GM07270/GM/NIGMS NIH HHS/United States ; }, mesh = {Biodegradation, Environmental ; Dioxygenases ; Gammaproteobacteria/classification/*enzymology/genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genes, rRNA ; Geologic Sediments/*microbiology ; Hydrocarbons, Aromatic/metabolism ; Multienzyme Complexes/*metabolism ; Naphthalenes/*metabolism ; Oxygenases/*metabolism ; Phylogeny ; Pseudomonas/enzymology/genetics ; RNA, Ribosomal, 16S/genetics ; Seawater ; Sequence Analysis, DNA ; Substrate Specificity ; }, abstract = {One strain of bacteria, designated NCE312, was isolated from a naphthalene-digesting chemostat culture that was inoculated with creosote-contaminated marine sediment. The strain was isolated based on its ability to grow using naphthalene as a sole carbon source. In addition, the strain degraded 2-methylnaphthalene and 1-methylnaphthalene. Analysis of a 16S rRNA gene sequence from NCE312 placed the isolate in the genus Marinobacter. Degenerate PCR primers were used to amplify a fragment of a naphthalene 1,2-dioxygenase large subunit gene. A phylogenetic analysis indicated the Marinobacter naphthalene dioxygenase is similar to those from Pseudomonas and Burkholderia strains suggesting that the dioxygenase gene may have been transferred horizontally between these lineages of bacteria.}, }
@article {pmid11443098, year = {2001}, author = {Davis, J and Smith, AL and Hughes, WR and Golomb, M}, title = {Evolution of an autotransporter: domain shuffling and lateral transfer from pathogenic Haemophilus to Neisseria.}, journal = {Journal of bacteriology}, volume = {183}, number = {15}, pages = {4626-4635}, pmid = {11443098}, issn = {0021-9193}, support = {R01 AI044002/AI/NIAID NIH HHS/United States ; 5RO1 HG01475/HG/NHGRI NIH HHS/United States ; AI 44002/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Base Sequence ; DNA, Bacterial ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Haemophilus influenzae/*genetics/pathogenicity ; Humans ; Molecular Sequence Data ; Neisseria meningitidis/*genetics/pathogenicity ; }, abstract = {The genomes of pathogenic Haemophilus influenzae strains are larger than that of Rd KW20 (Rd), the nonpathogenic laboratory strain whose genome has been sequenced. To identify potential virulence genes, we examined genes possessed by Int1, an invasive nonencapsulated isolate from a meningitis patient, but absent from Rd. Int1 was found to have a novel gene termed lav, predicted to encode a member of the AIDA-I/VirG/PerT family of virulence-associated autotransporters (ATs). Associated with lav are multiple repeats of the tetranucleotide GCAA, implicated in translational phase variation of surface molecules. Laterally acquired by H. influenzae, lav is restricted in distribution to a few pathogenic strains, including H. influenzae biotype aegyptius and Brazilian purpuric fever isolates. The DNA sequence of lav is surprisingly similar to that of a gene previously described for Neisseria meningitidis. Sequence comparisons suggest that lav was transferred relatively recently from Haemophilus to Neisseria, shortly before the divergence of N. meningitidis and Neisseria gonorrhoeae. Segments of lav predicted to encode passenger and beta-domains differ sharply in G+C base content, supporting the idea that AT genes have evolved by fusing domains which originated in different genomes. Homology and base sequence comparisons suggest that a novel biotype aegyptius AT arose by swapping an unrelated sequence for the passenger domain of lav. The unusually mobile lav locus joins a growing list of genes transferred from H. influenzae to Neisseria. Frequent gene exchange suggests a common pool of hypervariable contingency genes and may help to explain the origin of invasiveness in certain respiratory pathogens.}, }
@article {pmid11438737, year = {2001}, author = {Tallone, T and Malin, S and Samuelsson, A and Wilbertz, J and Miyahara, M and Okamoto, K and Poellinger, L and Philipson, L and Pettersson, S}, title = {A mouse model for adenovirus gene delivery.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {98}, number = {14}, pages = {7910-7915}, pmid = {11438737}, issn = {0027-8424}, mesh = {Adenoviridae/*genetics ; Adenoviridae Infections/*genetics ; Animals ; Disease Models, Animal ; *Gene Expression Regulation, Viral ; Gene Transfer Techniques ; Gene Transfer, Horizontal ; Genes, Viral ; Humans ; Mice ; *Mice, Transgenic ; }, abstract = {The cellular attachment receptor for adenovirus (Ad), Coxsackie adenovirus receptor (CAR), required for delivery of Ad into primary cells, is not present on all cell types, thus restricting Ad-gene delivery systems. To circumvent this constrain, a transgenic mouse has been generated that expresses a truncated human CAR in all tissues analyzed. These mice allowed efficient in vitro infections at low multiplicities into lymphoid, myeloid, and endothelial cells. Furthermore, in vivo administration of Ad-vectors results in infection of macrophages, lymphocytes, and endothelial cells. In addition, tail vein injection resulted in targeting of virus into previously inaccessible areas, such as the lung and the capillaries of the brain. The CAR transgenic mice will be useful for rapid functional genomic analysis in vivo, for testing the efficacy of gene therapy procedures or as a source of easily transducible cells.}, }
@article {pmid11435109, year = {2001}, author = {Dykhuizen, DE and Baranton, G}, title = {The implications of a low rate of horizontal transfer in Borrelia.}, journal = {Trends in microbiology}, volume = {9}, number = {7}, pages = {344-350}, doi = {10.1016/s0966-842x(01)02066-2}, pmid = {11435109}, issn = {0966-842X}, mesh = {Borrelia burgdorferi Group/*genetics ; Chromosomes, Bacterial ; Codon ; DNA Replication ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial ; Phylogeny ; *Recombination, Genetic ; Transcription, Genetic ; }, abstract = {The nature and rate of recombination can be studied by comparing the sequences of multiple genes across a set of strains. When this approach is applied to Borrelia burgdorferi, four results emerge: (1) chromosomal genes are clonal; (2) there is little or no plasmid exchange; (3) the major mode of horizontal transfer of genetic material inserts a small fragment of DNA, typically <1 kb, during recombination; and (4) the level of horizontal transfer in Borrelia is so low that there is evidence for horizontal transfer only in genes where there is positive selection for diversity, that is, positive selection for the recombinant. Thus, Borrelia can serve as a model of a low recombination taxon. The implications of these results lead us to postulate that an unknown agent that is part of the Borrelia genome mediates the horizontal transfer of small fragments of DNA; the rare transfer of small fragments of DNA excludes both DNA parasites and virulence factors from the genome.}, }
@article {pmid11432425, year = {2001}, author = {Aarts, HJ and Boumedine, KS and Nesme, X and Cloeckaert, A}, title = {Molecular tools for the characterisation of antibiotic-resistant bacteria.}, journal = {Veterinary research}, volume = {32}, number = {3-4}, pages = {363-380}, doi = {10.1051/vetres:2001130}, pmid = {11432425}, issn = {0928-4249}, mesh = {Bacteria/*classification/genetics ; Bacteriological Techniques/*veterinary ; Databases, Factual ; *Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Genetic Techniques/veterinary ; }, abstract = {This review will discuss a number of molecular tools which are currently used as well as some innovative approaches for the characterisation of antibiotic-resistant bacterial strains. Various methods involved in the detection and characterisation of genes and mutations associated with antibiotic resistance and that are used for strain typing as part of epidemiological studies, are described. Furthermore, a few examples are discussed in which the results of both gene and strain characterisation are combined to investigate the underlying mechanism of the spread of antibiotic resistance. Some of the available molecular techniques are heavily supported by the existence of databases on the Internet. These databases either contain a fast growing amount of sequence information or a large number of allelic or fingerprint profiles. The current progress in applied DNA technology and the ongoing projects on the elucidation of the whole genomic sequence of bacterial species have lead and will further lead to the development and application of sophisticated new strategies for the analysis of antibiotic resistant bacterial strains.}, }
@article {pmid11432424, year = {2001}, author = {Werckenthin, C and Cardoso, M and Martel, JL and Schwarz, S}, title = {Antimicrobial resistance in staphylococci from animals with particular reference to bovine Staphylococcus aureus, porcine Staphylococcus hyicus, and canine Staphylococcus intermedius.}, journal = {Veterinary research}, volume = {32}, number = {3-4}, pages = {341-362}, doi = {10.1051/vetres:2001129}, pmid = {11432424}, issn = {0928-4249}, mesh = {Animals ; Cattle ; Cattle Diseases/*drug therapy/microbiology ; Dog Diseases/*drug therapy/microbiology ; Dogs ; *Drug Resistance, Microbial ; Gene Transfer, Horizontal ; Staphylococcal Infections/drug therapy/*veterinary ; Staphylococcus/*drug effects/genetics ; Staphylococcus aureus/drug effects/genetics ; Swine ; Swine Diseases/*drug therapy/microbiology ; }, abstract = {Besides their role as commensals on the skin and mucosal surfaces, staphylococci may be involved in a wide variety of diseases in animals. Staphylococcal infections in animals are mainly treated with antimicrobial agents and as a consequence, staphylococci from animal sources have developed and/or acquired resistance to the respective antimicrobial agents. Resistance statistics obtained from national monitoring programmes on staphylococci from cattle and pigs, but also from surveillance studies on staphylococci involved in diseases in dogs are reported and reviewed with regard to their comparability. This review mainly focusses on the genetic basis of antimicrobial resistance in staphylococci of animal origin. Particular attention is paid to resistance to those antimicrobial agents which are most frequently used in veterinary medicine, but also to antimicrobial agents, such as chloramphenicol and mupirocin, which are used in specific cases for the control of staphylococcal infections in pets and companion animals. In addition, plasmids and transposons associated with the respective resistance properties and their ways of spreading between members of the same or different staphylococcal species, but also between staphylococci and other gram-positive bacteria, are described.}, }
@article {pmid11432423, year = {2001}, author = {Kehrenberg, C and Schulze-Tanzil, G and Martel, JL and Chaslus-Dancla, E and Schwarz, S}, title = {Antimicrobial resistance in pasteurella and mannheimia: epidemiology and genetic basis.}, journal = {Veterinary research}, volume = {32}, number = {3-4}, pages = {323-339}, doi = {10.1051/vetres:2001128}, pmid = {11432423}, issn = {0928-4249}, mesh = {Animals ; Drug Resistance, Microbial/*genetics ; Gene Transfer, Horizontal ; Pasteurella/classification/drug effects/genetics ; Pasteurella Infections/drug therapy/*veterinary ; Pasteurellaceae/classification/*drug effects/genetics ; }, abstract = {Isolates of the genera Pasteurella and Mannheimia cause a wide variety of diseases of great economic importance in poultry, pigs, cattle and rabbits. Antimicrobial agents represent the most powerful tools to control such infections. However, increasing rates of antimicrobial resistance may dramatically reduce the efficacy of the antimicrobial agents used to control Pasteurella and Mannheimia infections. This review presents a short summary of the infections caused by Pasteurella and Mannheimia isolates in food-producing animals and the possibilities of preventing and controlling primary and secondary pasteurellosis. Particular reference is given to antimicrobial chemotherapy and the resistance properties of Pasterurella and Mannheimia isolates. The genetic basis of the most predominant resistance properties such as resistance to beta-lactam antibiotics, tetracyclines, aminoglycosides, sulfonamides, and chloramphenicol is discussed. This is depicted with reference to the role of plasmids and transposons in the spread of the resistance genes among Pasteurellaceae and members of other bacterial families and genera.}, }
@article {pmid11432417, year = {2001}, author = {Sköld, O}, title = {Resistance to trimethoprim and sulfonamides.}, journal = {Veterinary research}, volume = {32}, number = {3-4}, pages = {261-273}, doi = {10.1051/vetres:2001123}, pmid = {11432417}, issn = {0928-4249}, mesh = {Animals ; Chromosomes ; Drug Resistance, Microbial/*genetics ; Gene Transfer, Horizontal ; Humans ; Models, Chemical ; Plasmids ; Restriction Mapping ; Sulfonamides/*therapeutic use ; Trimethoprim/*therapeutic use ; Trimethoprim Resistance/*genetics ; }, abstract = {Sulfonamides and trimethoprim have been used for many decades as efficient and inexpensive antibacterial agents for animals and man. Resistance to both has, however, spread extensively and rapidly. This is mainly due to the horizontal spread of resistance genes, expressing drug-insensitive variants of the target enzymes dihydropteroate synthase and dihydrofolate reductase, for sulfonamide and trimethoprim, respectively. Two genes, sul1 and sul2, mediated by transposons and plasmids, and expressing dihydropteroate synthases highly resistant to sulfonamide, have been found. For trimethoprim, almost twenty phylogenetically different resistance genes, expressing druginsensitive dihydrofolate reductases have been characterized. They are efficiently spread as cassettes in integrons, and on transposons and plasmids. One particular gene, dfr9, seems to have originally been selected in the intestine of swine, where it was found in Escherichia coli, on large plasmids in a disabled transposon, Tn5393, originally found in the plant pathogen Erwinia amylovora. There are also many examples of chromosomal resistance to sulfonamides and trimethoprim, with different degrees of complexity, from simple base changes in the target genes to transformational and recombinational exchanges of whole genes or parts of genes, forming mosaic gene patterns. Furthermore, the trade-off, seen in laboratory experiments selecting resistance mutants, showing drug-resistant but also less efficient (increased Kms) target enzymes, seems to be adjusted for by compensatory mutations in clinically isolated drug-resistant pathogens. This means that susceptibility will not return after suspending the use of sulfonamide and trimethoprim.}, }
@article {pmid11432416, year = {2001}, author = {Carattoli, A}, title = {Importance of integrons in the diffusion of resistance.}, journal = {Veterinary research}, volume = {32}, number = {3-4}, pages = {243-259}, doi = {10.1051/vetres:2001122}, pmid = {11432416}, issn = {0928-4249}, mesh = {Animal Diseases/drug therapy ; Animals ; Anti-Bacterial Agents/therapeutic use ; Cloning, Molecular ; DNA Transposable Elements/genetics ; DNA, Bacterial/*chemistry ; Drug Resistance, Microbial/*genetics ; Drug Resistance, Multiple/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Mutagenesis, Site-Directed ; }, abstract = {Horizontal transfer of resistance genes is a successful mechanism for the transmission and dissemination of multiple drug resistance among bacterial pathogens. The impact of horizontally transmitted genetic determinants in the evolution of resistance is particularly evident when resistance genes are physically associated in clusters and transferred en bloc to the recipient cell. Recent advances in the molecular characterisation of antibiotic resistance mechanisms have highlighted the existence of genetic structures. called integrons, involved in the acquisition of resistance genes. These DNA elements have frequently been reported in multi-drug resistant strains isolated from animals and humans, and are located either on the bacterial chromosome or on broad-host-range plasmids. The role of integrons in the development of multiple resistance relies on their unique capacity to cluster and express drug resistance genes. Moreover, the spread of resistance genes among different replicons and their exchange between plasmid and bacterial chromosome are facilitated by the integration of integrons into transposable elements. The association of a highly efficient gene capture and expression system, together with the capacity for vertical and horizontal transmission of resistance genes represents a powerful weapon used by bacteria to combat the assault of antibiotics.}, }
@article {pmid11431701, year = {2001}, author = {Brown, JR and Douady, CJ and Italia, MJ and Marshall, WE and Stanhope, MJ}, title = {Universal trees based on large combined protein sequence data sets.}, journal = {Nature genetics}, volume = {28}, number = {3}, pages = {281-285}, doi = {10.1038/90129}, pmid = {11431701}, issn = {1061-4036}, mesh = {Amino Acid Sequence ; Archaea/genetics ; Bacteria/genetics ; Conserved Sequence ; Databases, Factual ; Eukaryotic Cells ; *Evolution, Molecular ; *Genomics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, Protein/*methods ; }, abstract = {Universal trees of life based on small-subunit (SSU) ribosomal RNA (rRNA) support the separate mono/holophyly of the domains Archaea (archaebacteria), Bacteria (eubacteria) and Eucarya (eukaryotes) and the placement of extreme thermophiles at the base of the Bacteria. The concept of universal tree reconstruction recently has been upset by protein trees that show intermixing of species from different domains. Such tree topologies have been attributed to either extensive horizontal gene transfer or degradation of phylogenetic signals because of saturation for amino acid substitutions. Here we use large combined alignments of 23 orthologous proteins conserved across 45 species from all domains to construct highly robust universal trees. Although individual protein trees are variable in their support of domain integrity, trees based on combined protein data sets strongly support separate monophyletic domains. Within the Bacteria, we placed spirochaetes as the earliest derived bacterial group. However, elimination from the combined protein alignment of nine protein data sets, which were likely candidates for horizontal gene transfer, resulted in trees showing thermophiles as the earliest evolved bacterial lineage. Thus, combined protein universal trees are highly congruent with SSU rRNA trees in their strong support for the separate monophyly of domains as well as the early evolution of thermophilic Bacteria.}, }
@article {pmid11430404, year = {2001}, author = {Piechula, S and Waleron, K and Swiatek, W and Biedrzycka, I and Podhajska, AJ}, title = {Mesophilic cyanobacteria producing thermophilic restriction endonucleases.}, journal = {FEMS microbiology letters}, volume = {198}, number = {2}, pages = {135-140}, doi = {10.1111/j.1574-6968.2001.tb10632.x}, pmid = {11430404}, issn = {0378-1097}, mesh = {Cyanobacteria/classification/*enzymology/growth &amp; development ; DNA Restriction Enzymes/*chemistry/*metabolism ; Deoxyribonucleases, Type II Site-Specific/metabolism ; Enzyme Stability ; Temperature ; Thermodynamics ; Thermus/enzymology ; }, abstract = {When searching for the site-specific endonucleases in several strains of Phormidium we made the following observations. Among the 16 strains that originated from 15 species of Phormidium, 12 produced one or more restriction enzymes, of which two produced the highly thermophilic restriction endonucleases PtaI and PpaAII with their optimum activity at 65-80 degrees C, which is far above the lethal temperature for the host microorganism (40 degrees C). These two temperature-resistant enzymes are isoschizomers of known BspMII and TaqI endonucleases, respectively. The presence of the thermophilic TaqI isoschizomer does not seem to play any role in the mesophilic host microorganism, which does not even contain an active cognate methyltransferase. Among the remaining 10 strains, six produced isoschizomers of endonucleases which we first described in cyanobacteria, namely: PfaAII (NdeI), PinBII and PtaI (BspMII), PlaAII (RsalI), PpaAII, PpeI (ApaI). Two enzymes, PauAII (AhaIII) and PfaAII (NdeI), belong to a group of a very rarely occurring isoschizomers. Out of 21 cyanobacterial endonucleases investigated by us, four were active in a wide range of temperatures (from 15 to 60 degrees C) which also extended the optimal growth temperature of the hosts. We assume that our observation on the presence of temperature-resistant restriction enzymes in mesophilic hosts supports the idea of horizontal gene transfer. Restriction modification systems may be an excellent tool for investigation of that phenomenon.}, }
@article {pmid11429590, year = {2001}, author = {Roelofs, J and Van Haastert, PJ}, title = {Genes lost during evolution.}, journal = {Nature}, volume = {411}, number = {6841}, pages = {1013-1014}, doi = {10.1038/35082627}, pmid = {11429590}, issn = {0028-0836}, mesh = {Animals ; Arabidopsis ; Caenorhabditis elegans ; Dictyostelium ; Drosophila melanogaster ; *Evolution, Molecular ; *Gene Deletion ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genome, Human ; Human Genome Project ; Humans ; Monoamine Oxidase/genetics ; Saccharomyces cerevisiae ; Sequence Homology, Nucleic Acid ; }, }
@article {pmid11429469, year = {2001}, author = {Johansen, BK and Wasteson, Y and Granum, PE and Brynestad, S}, title = {Mosaic structure of Shiga-toxin-2-encoding phages isolated from Escherichia coli O157:H7 indicates frequent gene exchange between lambdoid phage genomes.}, journal = {Microbiology (Reading, England)}, volume = {147}, number = {Pt 7}, pages = {1929-1936}, doi = {10.1099/00221287-147-7-1929}, pmid = {11429469}, issn = {1350-0872}, mesh = {Animals ; Bacteriophage lambda/*genetics ; Cattle ; Cattle Diseases/microbiology ; Child, Preschool ; Chlorocebus aethiops ; Coliphages/*genetics/growth &amp; development/isolation &amp; purification ; DNA, Viral/analysis/genetics ; Escherichia coli Infections/microbiology/veterinary ; Escherichia coli O157/metabolism/pathogenicity/*virology ; Female ; *Gene Transfer, Horizontal ; Genetic Variation ; Genome, Viral ; Humans ; Polymorphism, Restriction Fragment Length ; *Recombination, Genetic ; Shiga Toxin 2/*genetics/metabolism/toxicity ; Vero Cells ; Virus Activation ; }, abstract = {Shiga-toxin-2 (stx(2))-encoding bacteriophages were isolated from Norwegian Escherichia coli O157:H7 isolates of cattle and human origin. The phages were characterized by restriction enzyme analysis, hybridization with probes for toxin genes and selected phage DNA such as the P gene, integrase gene and IS1203, and by PCR studies and partial sequencing of selected DNA regions in the integrase to stx(2) region of the phages. The stx(2)-phage-containing bacteria from which inducible phages were detected produced similar amounts of toxin, as shown by a Vero cell assay. The results indicate that the population of stx(2)-carrying phages is heterogeneous, although the phages from epidemiologically linked E. coli O157:H7 isolates were similar. There appears to have been frequent recombination of stx(2) phages with other lambdoid phages.}, }
@article {pmid11425376, year = {2001}, author = {Wielders, CL and Vriens, MR and Brisse, S and de Graaf-Miltenburg, LA and Troelstra, A and Fleer, A and Schmitz, FJ and Verhoef, J and Fluit, AC}, title = {In-vivo transfer of mecA DNA to Staphylococcus aureus [corrected].}, journal = {Lancet (London, England)}, volume = {357}, number = {9269}, pages = {1674-1675}, doi = {10.1016/s0140-6736(00)04832-7}, pmid = {11425376}, issn = {0140-6736}, mesh = {Bacteremia/microbiology ; *Bacterial Proteins ; Carrier Proteins/*genetics ; Cross Infection/microbiology ; DNA Fingerprinting ; DNA, Bacterial/*genetics ; Gene Transfer, Horizontal/*genetics ; Genotype ; *Hexosyltransferases ; Humans ; Infant, Newborn ; Male ; Microbial Sensitivity Tests ; Muramoylpentapeptide Carboxypeptidase/*genetics ; Penicillin-Binding Proteins ; *Peptidyl Transferases ; Staphylococcal Infections/microbiology ; Staphylococcus aureus/*genetics ; }, abstract = {Staphylococcus aureus is thought to have acquired mecA DNA by horizontal transfer. DNA fingerprints made by restriction nucleases that cut certain sequences of DNA are used to compare complete genomes or particular genes between bacteria. We isolated an epidemic mecA(-) meticillin-susceptible S aureus genotype and, subsequently, a rare isogeneic mecA(+) meticillin-resistant S aureus (MRSA) genotype from a neonate who had never been in contact with MRSA. This MRSA contained mecA DNA that was identical to that in a coagulase-negative staphylococcal strain isolated from this patient, but different from other MRSA genotypes. We believe that this MRSA was formed in vivo by horizontal transfer of the mecA DNA between two staphylococcal species.}, }
@article {pmid11423009, year = {2001}, author = {Tamames, J}, title = {Evolution of gene order conservation in prokaryotes.}, journal = {Genome biology}, volume = {2}, number = {6}, pages = {RESEARCH0020}, pmid = {11423009}, issn = {1474-760X}, mesh = {Conserved Sequence ; *Evolution, Molecular ; *Gene Order ; *Genome, Archaeal ; *Genome, Bacterial ; Phylogeny ; }, abstract = {BACKGROUND: As more complete genomes are sequenced, conservation of gene order between different organisms is emerging as an informative property of the genomes. Conservation of gene order has been used for predicting function and functional interactions of proteins, as well as for studying the evolutionary relationships between genomes. The reasons for the maintenance of gene order are still not well understood, as the organization of the prokaryote genome into operons and lateral gene transfer cannot possibly account for all the instances of conservation found. Comprehensive studies of gene order are one way of elucidating the nature of these maintaining forces.<br><br>RESULTS: Gene order is extensively conserved between closely related species, but rapidly becomes less conserved among more distantly related organisms, probably in a cooperative fashion. This trend could be universal in prokaryotic genomes, as archaeal genomes are likely to behave similarly to bacterial genomes. Gene order conservation could therefore be used as a valid phylogenetic measure to study relationships between species. Even between very distant species, remnants of gene order conservation exist in the form of highly conserved clusters of genes. This suggests the existence of selective processes that maintain the organization of these regions. Because the clusters often span more than one operon, common regulation probably cannot be invoked as the cause of the maintenance of gene order.<br><br>CONCLUSIONS: Gene order conservation is a genomic measure that can be useful for studying relationships between prokaryotes and the evolutionary forces shaping their genomes. Gene organization is extensively conserved in some genomic regions, and further studies are needed to elucidate the reason for this conservation.}, }
@article {pmid11421651, year = {2001}, author = {Intrieri, MC and Buiatti, M}, title = {The horizontal transfer of Agrobacterium rhizogenes genes and the evolution of the genus Nicotiana.}, journal = {Molecular phylogenetics and evolution}, volume = {20}, number = {1}, pages = {100-110}, doi = {10.1006/mpev.2001.0927}, pmid = {11421651}, issn = {1055-7903}, mesh = {Bacterial Proteins/genetics ; Base Sequence ; DNA, Plant/chemistry/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; Plants, Genetically Modified/genetics ; *Plants, Toxic ; Rhizobium/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Nicotiana/classification/*genetics ; Transgenes/*genetics ; beta-Glucosidase/genetics ; }, abstract = {With the aim of understanding better the distribution and evolution of Agrobacterium rhizogenes genes transferred in the genus Nicotiana, 42 species were screened for presence of rolB, rolC, ORF13, and ORF14. The transferred sequences were then compared within the genus and with current bacterial sequences. The results obtained showed the presence of at least one bacterial gene in 15 species belonging to different subgenera. Sequence analyses supported the hypothesis of coevolution of bacterial and plant sequences, thus suggesting a possible role for the transferred genes in the early events of Nicotiana species differentiation. The high level of conservation of Agrobacterium sequences and the dependence of their expression from the plant physiological context along with previous data suggesting their involvement in the determination of the plant hormonal balance were all consistent with this hypothesis. The results are finally discussed also as to their relevance for the hypothesis of mono and multi ancient infection by Agrobacterium.}, }
@article {pmid11420376, year = {2001}, author = {Boucher, Y and Huber, H and L'Haridon, S and Stetter, KO and Doolittle, WF}, title = {Bacterial origin for the isoprenoid biosynthesis enzyme HMG-CoA reductase of the archaeal orders Thermoplasmatales and Archaeoglobales.}, journal = {Molecular biology and evolution}, volume = {18}, number = {7}, pages = {1378-1388}, doi = {10.1093/oxfordjournals.molbev.a003922}, pmid = {11420376}, issn = {0737-4038}, mesh = {Archaeoglobales/classification/*enzymology/*genetics ; Bacteria/*enzymology/*genetics ; Base Sequence ; DNA Primers/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Archaeal ; Hydroxymethylglutaryl CoA Reductases/*genetics ; Molecular Sequence Data ; Phylogeny ; Species Specificity ; Thermoplasmales/classification/*enzymology/*genetics ; }, abstract = {The enzyme 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMG-CoA reductase or HMGR) fulfills an essential role in archaea, as it is required for the synthesis of isoprenoid ethers, the main component of archaeal cell membranes. There are two clearly homologous but structurally different classes of the enzyme, one found mainly in eukaryotes and archaea (class 1), and the other found in bacteria (class 2). This feature facilitated the identification of several cases of interdomain lateral gene transfer (LGT), in particular, the bacterial origin for the HMGR gene from the archaeon Archaeoglobus fulgidus. In order to investigate if this LGT event was recent and limited in its scope or had a broad and long-term impact on the recipient and its related lineages, the HMGR gene was amplified and sequenced from a variety of archaea. The survey covered close relatives of A. fulgidus, the only archaeon known prior to this study to possess a bacterial-like HMGR; representatives of each main euryarchaeal group were also inspected. All culturable members of the archaeal group Archaeoglobales were found to display an HMGR very similar to the enzyme of the bacterium Pseudomonas mevalonii. Surprisingly, two species of the genus Thermoplasma also harbor an HMGR of bacterial origin highly similar to the enzymes found in the Archaeoglobales. Phylogenetic analyses of the HMGR gene and comparisons to reference phylogenies from other genes confirm a common bacterial origin for the HMGRs of Thermoplasmatales and Archaeoglobales. The most likely explanation of these results includes an initial bacteria-to-archaea transfer, followed by a another event between archaea. Their presence in two divergent archaeal lineages suggests an important adaptive role for these laterally transferred genes.}, }
@article {pmid11418856, year = {2001}, author = {Stanhope, MJ and Lupas, A and Italia, MJ and Koretke, KK and Volker, C and Brown, JR}, title = {Phylogenetic analyses do not support horizontal gene transfers from bacteria to vertebrates.}, journal = {Nature}, volume = {411}, number = {6840}, pages = {940-944}, doi = {10.1038/35082058}, pmid = {11418856}, issn = {0028-0836}, mesh = {Animals ; Evolution, Molecular ; Expressed Sequence Tags ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genome, Human ; Humans ; Phylogeny ; Polymerase Chain Reaction ; Vertebrates/genetics ; }, abstract = {Horizontal gene transfer (HGT) has long been recognized as a principal force in the evolution of genomes. Genome sequences of Archaea and Bacteria have revealed the existence of genes whose similarity to loci in distantly related organisms is explained most parsimoniously by HGT events. In most multicellular organisms, such genetic fixation can occur only in the germ line. Therefore, it is notable that the publication of the human genome reports 113 incidents of direct HGT between bacteria and vertebrates, without any apparent occurrence in evolutionary intermediates, that is, non-vertebrate eukaryotes. Phylogenetic analysis arguably provides the most objective approach for determining the occurrence and directionality of HGT. Here we report a phylogenetic analysis of 28 proposed HGT genes, whose presence in the human genome had been confirmed by polymerase chain reaction (PCR). The results indicate that most putative HGT genes are present in more anciently derived eukaryotes (many such sequences available in non-vertebrate EST databases) and can be explained in terms of descent through common ancestry. They are, therefore, unlikely to be examples of direct HGT from bacteria to vertebrates.}, }
@article {pmid11418328, year = {2001}, author = {Hentschel, U and Hacker, J}, title = {Pathogenicity islands: the tip of the iceberg.}, journal = {Microbes and infection}, volume = {3}, number = {7}, pages = {545-548}, doi = {10.1016/s1286-4579(01)01410-1}, pmid = {11418328}, issn = {1286-4579}, mesh = {Animals ; Bacteria/*genetics/*pathogenicity ; Base Sequence ; Ecology ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation/genetics ; *Genome, Bacterial ; Humans ; Virulence/genetics ; }, abstract = {Pathogenicity islands represent distinct genetic elements encoding virulence factors of pathogenic bacteria. Pathogenicity islands belong to the class of genomic islands, which are common genetic elements sharing a set of unifying features. Genomic islands have been acquired by horizontal gene transfer. In recent years many different genomic islands have been discovered in a variety of pathogenic as well as non-pathogenic bacteria. Because they promote genetic variability, genomic islands play an important role in microbial evolution.}, }
@article {pmid11418195, year = {2001}, author = {Cellier, MF and Bergevin, I and Boyer, E and Richer, E}, title = {Polyphyletic origins of bacterial Nramp transporters.}, journal = {Trends in genetics : TIG}, volume = {17}, number = {7}, pages = {365-370}, doi = {10.1016/s0168-9525(01)02364-2}, pmid = {11418195}, issn = {0168-9525}, mesh = {Aerobiosis ; Animals ; *Bacterial Proteins ; Carrier Proteins/chemistry/*genetics ; *Cation Transport Proteins ; Eukaryotic Cells/metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/*genetics ; Humans ; Membrane Proteins/chemistry/*genetics ; Models, Genetic ; Multigene Family ; *Phylogeny ; }, abstract = {The redox-active metals iron and manganese are required for energy metabolism, protection against oxidative stress and defense against infections. In eukaryotes, both divalent metals are transported by Nramp transporters. The sequence of these transporters was remarkably conserved during evolution. Several bacterial Nramp homologs (MntH) are also proton-dependent manganese transporters. Here, we present phylogenetic evidence for the polyphyletic origins of three groups of MntH proteins and for possible Nramp horizontal gene transfer with eukaryotes. We propose that the evolution of the MntH/Nramp family is related to adaptation to oxidative environments, including those arising during infection of animals and plants.}, }
@article {pmid11418146, year = {2001}, author = {Kuroda, M and Ohta, T and Uchiyama, I and Baba, T and Yuzawa, H and Kobayashi, I and Cui, L and Oguchi, A and Aoki, K and Nagai, Y and Lian, J and Ito, T and Kanamori, M and Matsumaru, H and Maruyama, A and Murakami, H and Hosoyama, A and Mizutani-Ui, Y and Takahashi, NK and Sawano, T and Inoue, R and Kaito, C and Sekimizu, K and Hirakawa, H and Kuhara, S and Goto, S and Yabuzaki, J and Kanehisa, M and Yamashita, A and Oshima, K and Furuya, K and Yoshino, C and Shiba, T and Hattori, M and Ogasawara, N and Hayashi, H and Hiramatsu, K}, title = {Whole genome sequencing of meticillin-resistant Staphylococcus aureus.}, journal = {Lancet (London, England)}, volume = {357}, number = {9264}, pages = {1225-1240}, doi = {10.1016/s0140-6736(00)04403-2}, pmid = {11418146}, issn = {0140-6736}, mesh = {Animals ; Bacillus subtilis/genetics ; Bacteriophages/genetics ; *Genome, Bacterial ; Humans ; Male ; Methicillin Resistance/*genetics ; Molecular Sequence Data ; Phylogeny ; Staphylococcus aureus/*genetics/metabolism/pathogenicity ; Vancomycin Resistance/*genetics ; }, abstract = {BACKGROUND: Staphylococcus aureus is one of the major causes of community-acquired and hospital-acquired infections. It produces numerous toxins including superantigens that cause unique disease entities such as toxic-shock syndrome and staphylococcal scarlet fever, and has acquired resistance to practically all antibiotics. Whole genome analysis is a necessary step towards future development of countermeasures against this organism.<br><br>METHODS: Whole genome sequences of two related S aureus strains (N315 and Mu50) were determined by shot-gun random sequencing. N315 is a meticillin-resistant S aureus (MRSA) strain isolated in 1982, and Mu50 is an MRSA strain with vancomycin resistance isolated in 1997. The open reading frames were identified by use of GAMBLER and GLIMMER programs, and annotation of each was done with a BLAST homology search, motif analysis, and protein localisation prediction.<br><br>FINDINGS: The Staphylococcus genome was composed of a complex mixture of genes, many of which seem to have been acquired by lateral gene transfer. Most of the antibiotic resistance genes were carried either by plasmids or by mobile genetic elements including a unique resistance island. Three classes of new pathogenicity islands were identified in the genome: a toxic-shock-syndrome toxin island family, exotoxin islands, and enterotoxin islands. In the latter two pathogenicity islands, clusters of exotoxin and enterotoxin genes were found closely linked with other gene clusters encoding putative pathogenic factors. The analysis also identified 70 candidates for new virulence factors.<br><br>INTERPRETATION: The remarkable ability of S aureus to acquire useful genes from various organisms was revealed through the observation of genome complexity and evidence of lateral gene transfer. Repeated duplication of genes encoding superantigens explains why S aureus is capable of infecting humans of diverse genetic backgrounds, eliciting severe immune reactions. Investigation of many newly identified gene products, including the 70 putative virulence factors, will greatly improve our understanding of the biology of staphylococci and the processes of infectious diseases caused by S aureus.}, }
@article {pmid11416223, year = {2001}, author = {Reid, SD and Green, NM and Buss, JK and Lei, B and Musser, JM}, title = {Multilocus analysis of extracellular putative virulence proteins made by group A Streptococcus: population genetics, human serologic response, and gene transcription.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {98}, number = {13}, pages = {7552-7557}, pmid = {11416223}, issn = {0027-8424}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/*genetics/metabolism ; Cloning, Molecular ; Enzymes/chemistry/genetics/metabolism ; Evolution, Molecular ; Genetic Variation ; Genetics, Population ; Humans ; Phylogeny ; Recombinant Proteins/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Streptococcal Infections/*microbiology ; Streptococcus pyogenes/classification/*genetics/*pathogenicity ; *Transcription, Genetic ; Transformation, Bacterial ; Virulence/genetics ; }, abstract = {Species of pathogenic microbes are composed of an array of evolutionarily distinct chromosomal genotypes characterized by diversity in gene content and sequence (allelic variation). The occurrence of substantial genetic diversity has hindered progress in developing a comprehensive understanding of the molecular basis of virulence and new therapeutics such as vaccines. To provide new information that bears on these issues, 11 genes encoding extracellular proteins in the human bacterial pathogen group A Streptococcus identified by analysis of four genomes were studied. Eight of the 11 genes encode proteins with a LPXTG(L) motif that covalently links Gram-positive virulence factors to the bacterial cell surface. Sequence analysis of the 11 genes in 37 geographically and phylogenetically diverse group A Streptococcus strains cultured from patients with different infection types found that recent horizontal gene transfer has contributed substantially to chromosomal diversity. Regions of the inferred proteins likely to interact with the host were identified by molecular population genetic analysis, and Western immunoblot analysis with sera from infected patients confirmed that they were antigenic. Real-time reverse transcriptase-PCR (TaqMan) assays found that transcription of six of the 11 genes was substantially up-regulated in the stationary phase. In addition, transcription of many genes was influenced by the covR and mga trans-acting gene regulatory loci. Multilocus investigation of putative virulence genes by the integrated approach described herein provides an important strategy to aid microbial pathogenesis research and rapidly identify new targets for therapeutics research.}, }
@article {pmid11412397, year = {2001}, author = {Yao, Y and Zhang, D and Luo, Y and Zhang, D and Huang, A and Zhou, W and Ren, H}, title = {[Influence of electroporation on the biological activities of primary rat hepatocytes].}, journal = {Zhonghua gan zang bing za zhi = Zhonghua ganzangbing zazhi = Chinese journal of hepatology}, volume = {9}, number = {3}, pages = {178-180}, pmid = {11412397}, issn = {1007-3418}, mesh = {Animals ; Cell Survival ; *Electroporation ; Gene Transfer, Horizontal ; Hepatocytes/*physiology ; Male ; Rats ; Rats, Wistar ; }, abstract = {OBJECTIVE: To investigate the influence of electroporation on the biological activities of primary rat hepatocyte and to optimize the electroporation conditions introducing foreign genes into hepatocytes.<br><br>METHODS: A single-pulse procedure was performed at low voltage (220-400 V) but high capacitance (500-950 microF). Its influence on hepatocyte activities was detected by Trypan blue exclusion (TBE) and MTT analysis. Besides, ALB, ALT and LDH in the supernatants of hepatocytes were tested by biochemical assay.<br><br>RESULTS: Little hepatocyte damage and high survival rate (>90%) was found from 36 hours till 9th day of culture. At 36th hour after electroporation, ALB, ALT and LDH in the supernatants of Group B (220V, 950 microF) and C (400 V, 950 microF) were higher than those of control group. Whereas TBE and MTT analysis failed to indicate the significant difference of cell viability between electroporation groups and control group.<br><br>CONCLUSIONS: This electroporation procedure is one of the optimal choices to introduce foreign genes into primary rat hepatocytes.}, }
@article {pmid11411719, year = {2001}, author = {Young, JM}, title = {Implications of alternative classifications and horizontal gene transfer for bacterial taxonomy.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {51}, number = {Pt 3}, pages = {945-953}, doi = {10.1099/00207713-51-3-945}, pmid = {11411719}, issn = {1466-5026}, mesh = {Bacteria/*classification/*genetics ; Bacteriological Techniques ; DNA, Ribosomal/*genetics ; Gene Transfer, Horizontal ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; *Terminology as Topic ; }, abstract = {Following the publication of the Approved Lists, there has been a tendency to regard all subsequent revisions of classification as providing improved nomenclature, to be accepted without question. This takes no account of the fact that such revisions may be based on one of three alternative concepts, phenetic, phylogenetic or polyphasic classification, sometimes leading to different, valid, but incompatible nomenclature, or that some investigations are based only on subsets of relevant taxa and on limited data, leading to incomplete and sometimes confusing revisions of nomenclature. The polyphasic approach to classification has widespread support, although there appears to be a tendency to allow comparative sequence analyses of 16S rDNA to determine classification contrary to the indications of other data. In some cases, classification is based solely on 16S rDNA data. Examples are considered. Consideration is given to the criteria by which taxa are circumscribed, particularly at the level of genus and species. It is suggested that there is a need for reconciliation of the criteria by which taxa at these levels are circumscribed. Recent studies demonstrating the widespread occurrence of horizontal gene transfer suggest that there is a need for caution in monophyletic interpretations, especially when these are based on the analysis of single sequences.}, }
@article {pmid11410724, year = {2001}, author = {Shellito, JE and quan Zheng, M and Ye, P and Ruan, S and Shean, MK and Kolls, J}, title = {Effect of alcohol consumption on host release of interleukin-17 during pulmonary infection with Klebsiella pneumoniae.}, journal = {Alcoholism, clinical and experimental research}, volume = {25}, number = {6}, pages = {872-881}, pmid = {11410724}, issn = {0145-6008}, support = {AA08845/AA/NIAAA NIH HHS/United States ; HL59724/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Bronchoalveolar Lavage Fluid/chemistry ; Cells, Cultured ; Drinking ; Ethanol/administration &amp; dosage/*adverse effects ; Female ; Gene Transfer, Horizontal ; Genetic Therapy ; Interleukin-17/analysis/genetics/*metabolism ; Klebsiella Infections/*physiopathology ; *Klebsiella pneumoniae ; Lung/immunology/pathology ; Mice ; Mice, Inbred BALB C ; Neutrophils/enzymology/immunology ; Peroxidase/analysis ; Pneumonia, Bacterial/*immunology/mortality ; RNA, Messenger/analysis ; Spleen/chemistry/drug effects/metabolism ; }, abstract = {BACKGROUND: A link between alcohol abuse and bacterial pneumonia has been recognized for centuries, but mechanisms to explain this relationship are unclarified. Interleukin-17 (IL-17) is a lymphocyte-derived cytokine that is part of the inflammatory cytokine cascade. Previous studies from our laboratory indicated that IL-17 is released in lung tissue in a murine model of bacterial pneumonia caused by Klebsiella pneumoniae. The effects of alcohol consumption on pulmonary release of IL-17 are unknown.<br><br>METHODS: Mice were maintained on 20% ethanol in drinking water or on a control diet without alcohol. After 2 weeks, alcohol and control mice were challenged with intratracheal K. pneumoniae. Mice were followed for survival after bacterial challenge, neutrophil recruitment was assayed as myeloperoxidase, and IL-17 was measured in lung lavage fluid by enzyme-linked immunosorbent assay. In additional experiments, splenocytes from control mice were incubated with ethanol in vitro, and release of IL-17 was measured in culture supernatants. Finally, control and alcohol mice received intrapulmonary gene transfer of E-1-deleted adenovirus containing the murine IL-17 gene. These mice were then challenged with K. pneumoniae and followed for survival and neutrophil recruitment.<br><br>RESULTS: In these studies, we demonstrate that a 2-week history of ethanol consumption in mice suppresses release of IL-17 into lung tissue, decreases neutrophil recruitment, and increases mortality from experimental K. pneumonia. In vitro experiments confirm a direct suppressive effect of ethanol on the release of IL-17 from splenocytes. In vivo administration of the IL-17 gene in an adenoviral vector to alcohol-consuming mice results in release of IL-17 into lavage fluid and normalizes neutrophil recruitment and mortality after bacterial challenge.<br><br>CONCLUSIONS: The results of these experiments strongly implicate IL-17 as an important pathway for the immunosuppression associated with alcohol abuse and support gene therapeutic approaches to augment immune function in the alcoholic host or to treat infections associated with alcoholism.}, }
@article {pmid11410353, year = {2001}, author = {Han, G and Zhang, CC}, title = {On the origin of Ser/Thr kinases in a prokaryote.}, journal = {FEMS microbiology letters}, volume = {200}, number = {1}, pages = {79-84}, doi = {10.1111/j.1574-6968.2001.tb10696.x}, pmid = {11410353}, issn = {0378-1097}, mesh = {Base Composition ; Cyanobacteria/enzymology/*genetics ; DNA Transposable Elements ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Code ; Genetic Variation ; Prokaryotic Cells/enzymology ; Protein Serine-Threonine Kinases/*genetics ; }, abstract = {The family of Ser/Thr and/or Tyr kinases and that of His kinases play essential roles in signal transduction. For a long time, the former has been found in eukaryotes, the latter in prokaryotes. Studies in the last decade have shown, however, that most bacteria possess from one to more than 10 genes encoding Ser/Thr kinases. This observation raises an important question concerning the evolutionary origin of Ser/Thr kinases found in bacteria. To answer this question, we have analyzed a family of 11 genes encoding Ser/Thr kinases in the cyanobacterium Synechocystis sp. PCC 6803. This bacterium contains the largest number of Ser/Thr kinases among all bacteria whose genomic sequences have been released so far. In this study, we have developed a user-friendly computer program for statistical analysis of codon usages and GC content. The results demonstrate that Ser/Thr kinases have similar codon usages and GC contents as the average of all possible open reading frames (ORFs) deduced from the genome. In contrast, ORFs encoding transposases, as a control in our analysis, display a disparity in both codon usage and GC content, confirming their multiple origin and genetic promiscuity. In light of our results, we propose that Ser/Thr kinases existed before the divergence between prokaryotes and eukaryotes during evolution, or were laterally transferred into prokaryotes at the early stages of bacterial evolution. If Ser/Thr kinases have persisted ever since in prokaryotes under evolutionary pressure, it is then expected that they play important, possibly even essential roles in regulating bacterial activities as do their counterparts in eukaryotes.}, }
@article {pmid11407914, year = {2001}, author = {Marques, MV and da Silva, AM and Gomes, SL}, title = {Genetic organization of plasmid pXF51 from the plant pathogen Xylella fastidiosa.}, journal = {Plasmid}, volume = {45}, number = {3}, pages = {184-199}, doi = {10.1006/plas.2000.1514}, pmid = {11407914}, issn = {0147-619X}, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics ; Base Sequence ; Conjugation, Genetic ; DNA Replication ; *Gene Order ; *Membrane Proteins ; Multigene Family ; Open Reading Frames ; Plants/microbiology ; Plasmids/*genetics ; Proteobacteria/*genetics ; Sequence Homology, Amino Acid ; Trans-Activators/genetics ; }, abstract = {The sequence of plasmid pXF51 from the plant pathogen Xylella fastidiosa, the causal agent of citrus variegated chlorosis, has been analyzed. This plasmid codes for 65 open reading frames (ORFs), organized into four main regions, containing genes related to replication, mobilization, and conjugative transfer. Twenty-five ORFs have no counterparts in the public sequence databases, and 7 are similar to conserved hypothetical proteins from other bacteria. A pXF51 incompatibility group has not been determined, as we could not find a typical replication origin. One cluster of conjugation-related genes (trb) seems to be incomplete in pXF51, and a copy of this sequence is found in the chromosome, suggesting it was generated by a duplication event. A second cluster (tra) contains all genes necessary for conjugation transfer to occur, showing a conserved organization with other conjugative plasmids. An identifiable origin of transfer similar to oriT from IncP plasmids is found adjacent to genes encoding two mobilization proteins. None of the ORFs with putative assigned function could be predicted as having a role in pathogenesis, except for a virulence-associated protein D homolog. These results indicate that even though pXF51 appears not to have a direct role in Xylella pathogenesis, it is a conjugative plasmid that could be important for lateral gene transfer in this bacterium. This property may be of great importance for future development of transformation techniques in X. fastidiosa.}, }
@article {pmid11401985, year = {2001}, author = {Brunder, W and Khan, AS and Hacker, J and Karch, H}, title = {Novel type of fimbriae encoded by the large plasmid of sorbitol-fermenting enterohemorrhagic Escherichia coli O157:H(-).}, journal = {Infection and immunity}, volume = {69}, number = {7}, pages = {4447-4457}, pmid = {11401985}, issn = {0019-9567}, mesh = {Amino Acid Sequence ; Bacterial Proteins/classification/genetics ; Base Sequence ; Cloning, Molecular ; *DNA, Bacterial ; Enterobacteriaceae/genetics ; Escherichia coli O157/*genetics/metabolism ; *Escherichia coli Proteins ; Fermentation ; Fimbriae Proteins ; Fimbriae, Bacterial/*genetics ; Gene Expression ; Humans ; Molecular Chaperones/genetics ; Molecular Sequence Data ; *Periplasmic Proteins ; Phylogeny ; *Plasmids ; Recombination, Genetic ; Sorbitol/*metabolism ; }, abstract = {Sorbitol-fermenting (SF) enterohemorrhagic Escherichia coli (EHEC) O157:H(-) have emerged as important causes of diarrheal diseases and the hemolytic-uremic syndrome in Germany. In this study, we characterized a 32-kb fragment of the plasmid of SF EHEC O157:H(-), pSFO157, which differs markedly from plasmid pO157 of classical non-sorbitol-fermenting EHEC O157:H7. We found a cluster of six genes, termed sfpA, sfpH, sfpC, sfpD, sfpJ, and sfpG, which mediate mannose-resistant hemagglutination and the expression of fimbriae. sfp genes are similar to the pap genes, encoding P-fimbriae of uropathogenic E. coli, but the sfp cluster lacks homologues of genes encoding subunits of a tip fibrillum as well as regulatory genes. The major pilin, SfpA, despite its similarity to PapA, does not cluster together with known PapA alleles in a phylogenetic tree but is structurally related to the PmpA pilin of Proteus mirabilis. The putative adhesin gene sfpG, responsible for the hemagglutination phenotype, shows significant homology neither to papG nor to other known sequences. Sfp fimbriae are 3 to 5 nm in diameter, in contrast to P-fimbriae, which are 7 nm in diameter. PCR analyses showed that the sfp gene cluster is a characteristic of SF EHEC O157:H(-) strains and is not present in other EHEC isolates, diarrheagenic E. coli, or other Enterobacteriaceae. The sfp gene cluster is flanked by two blocks of insertion sequences and an origin of plasmid replication, indicating that horizontal gene transfer may have contributed to the presence of Sfp fimbriae in SF EHEC O157:H(-).}, }
@article {pmid11390626, year = {2001}, author = {Carstanjen, D and Dutt, P and Moritz, T}, title = {Heparin inhibits retrovirus binding to fibronectin as well as retrovirus gene transfer on fibronectin fragments.}, journal = {Journal of virology}, volume = {75}, number = {13}, pages = {6218-6222}, pmid = {11390626}, issn = {0022-538X}, mesh = {Antigens, CD34/analysis ; Centrifugation, Density Gradient ; Fibronectins/*physiology ; *Gene Transfer, Horizontal ; Hematopoietic Stem Cells/metabolism ; Heparin/*pharmacology ; Methionine/metabolism ; Retroviridae/*drug effects/genetics/physiology ; }, abstract = {Fibronectin fragments have been shown to improve retrovirus gene transfer efficiency by binding retrovirus and target cells. Using a novel virus adhesion assay, we confirmed binding of type C oncoretrovirus vectors to the heparin II domain of fibronectin and demonstrated inhibition of viral binding and gene transfer by heparin.}, }
@article {pmid11385528, year = {2001}, author = {Knight, J}, title = {Gene tests lift lid on drug-resistance puzzle.}, journal = {Nature}, volume = {411}, number = {6837}, pages = {513}, doi = {10.1038/35079266}, pmid = {11385528}, issn = {0028-0836}, mesh = {Agriculture ; Animal Diseases/drug therapy ; Animal Feed ; Animals ; Anti-Bacterial Agents/*administration &amp; dosage/therapeutic use ; Drug Resistance, Microbial/*genetics ; Gene Transfer, Horizontal ; Humans ; Tetracycline Resistance/genetics ; Virginiamycin/administration &amp; dosage/therapeutic use ; }, }
@article {pmid11382219, year = {2001}, author = {Lang, AS and Beatty, JT}, title = {The gene transfer agent of Rhodobacter capsulatus and "constitutive transduction" in prokaryotes.}, journal = {Archives of microbiology}, volume = {175}, number = {4}, pages = {241-249}, doi = {10.1007/s002030100260}, pmid = {11382219}, issn = {0302-8933}, mesh = {Amino Acid Sequence ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Molecular Sequence Data ; Rhodobacter capsulatus/*genetics ; }, abstract = {Transduction, bacteriophage-mediated gene transfer, is thought to play an important role in the evolution of prokaryote genomes. Several gene transfer agents that resemble transducing phages have been found in diverse prokaryotes. This mini-review discusses these interesting agents of genetic exchange with a focus on the gene transfer agent (GTA) of Rhodobacter capsulatus, at present the only member of this group for which genetic information exists about the production of transducing particles. Production of GTA results from expression of genes that are similar to phage genes, yet transcription of these genes is dependent upon cellular (two-component) signaling proteins. The significance of these relationships, as well as the finding of GTA gene homologues in the bacterium Rhodopseudomonas palustris, is discussed.}, }
@article {pmid11375927, year = {2001}, author = {Hacker, J and Carniel, E}, title = {Ecological fitness, genomic islands and bacterial pathogenicity. A Darwinian view of the evolution of microbes.}, journal = {EMBO reports}, volume = {2}, number = {5}, pages = {376-381}, pmid = {11375927}, issn = {1469-221X}, mesh = {Bacteria/metabolism/*pathogenicity ; Ecosystem ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; }, abstract = {The compositions of bacterial genomes can be changed rapidly and dramatically through a variety of processes including horizontal gene transfer. This form of change is key to bacterial evolution, as it leads to 'evolution in quantum leaps'. Horizontal gene transfer entails the incorporation of genetic elements transferred from another organism-perhaps in an earlier generation-directly into the genome, where they form 'genomic islands', i.e. blocks of DNA with signatures of mobile genetic elements. Genomic islands whose functions increase bacterial fitness, either directly or indirectly, have most likely been positively selected and can be termed 'fitness islands'. Fitness islands can be divided into several subtypes: 'ecological islands' in environmental bacteria and 'saprophytic islands', 'symbiosis islands' or 'pathogenicity islands' (PAIs) in microorganisms that interact with living hosts. Here we discuss ways in which PAIs contribute to the pathogenic potency of bacteria, and the idea that genetic entities similar to genomic islands may also be present in the genomes of eukaryotes.}, }
@article {pmid11371578, year = {2001}, author = {Suominen, L and Roos, C and Lortet, G and Paulin, L and Lindström, K}, title = {Identification and structure of the Rhizobium galegae common nodulation genes: evidence for horizontal gene transfer.}, journal = {Molecular biology and evolution}, volume = {18}, number = {6}, pages = {907-916}, doi = {10.1093/oxfordjournals.molbev.a003891}, pmid = {11371578}, issn = {0737-4038}, mesh = {Bacterial Proteins/*genetics ; DNA, Bacterial/chemistry/genetics ; Evolution, Molecular ; Fabaceae/microbiology ; Gene Order ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Operon/genetics ; Phylogeny ; Plants, Medicinal ; RNA, Ribosomal, 16S/genetics ; Restriction Mapping ; Rhizobium/*genetics ; Rhizobium leguminosarum/genetics ; Sequence Analysis, DNA ; Sinorhizobium meliloti/genetics ; Species Specificity ; Symbiosis ; }, abstract = {Rhizobia are soil bacteria able to fix atmospheric nitrogen in symbiosis with leguminous plants. In response to a signal cascade coded by genes of both symbiotic partners, a specific plant organ, the nodule, is formed. Rhizobial nodulation (nod) genes trigger nodule formation through the synthesis of Nod factors, a family of chitolipooligosaccharides that are specifically recognized by the host plant at the first stages of the nodulation process. Here, we present the organization and sequence of the common nod genes from Rhizobium galegae, a symbiotic member of the RHIZOBIACEAE: This species has an intriguing phylogenetic position, being symbiotic among pathogenic agrobacteria, which induce tumors instead of nodules in plant shoots or roots. This apparent incongruence raises special interest in the origin of the symbiotic apparatus of R. galegae. Our analysis of DNA sequence data indicated that the organization of the common nod gene region of R. galegae was similar to that of Sinorhizobium meliloti and Rhizobium leguminosarum, with nodIJ downstream of nodABC and the regulatory nodD gene closely linked to the common nod operon. Moreover, phylogenetic analyses of the nod gene sequences showed a close relationship especially between the common nodA sequences of R. galegae, S. meliloti, and R. leguminosarum biovars viciae and trifolii. This relationship in structure and sequence contrasts with the phylogeny based on 16S rRNA, which groups R. galegae close to agrobacteria and separate from most other rhizobia. The topology of the nodA tree was similar to that of the corresponding host plant tree. Taken together, these observations indicate that lateral nod gene transfer occurred from fast-growing rhizobia toward agrobacteria, after which the symbiotic apparatus evolved under host plant constraint.}, }
@article {pmid11371538, year = {2001}, author = {Funchain, P and Yeung, A and Stewart, J and Clendenin, WM and Miller, JH}, title = {Amplification of mutator cells in a population as a result of horizontal transfer.}, journal = {Journal of bacteriology}, volume = {183}, number = {12}, pages = {3737-3741}, pmid = {11371538}, issn = {0021-9193}, support = {GM32184/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Pair Mismatch ; Conjugation, Genetic ; Crosses, Genetic ; Escherichia coli/cytology/*genetics ; *Gene Transfer, Horizontal ; Phenotype ; Salmonella enterica/cytology/*genetics ; }, abstract = {Mutator cells that lack the mismatch repair system (MMR(-)) occur at rates of 10(-5) or less in laboratory populations started from wild-type cells. We show that after selection for recombinants in an interspecies mating between Salmonella enterica serovar Typhimurium and Escherichia coli, the percentage of MMR(-) cells rises to several percent of the recombinant population, and after a second successive mating and selection, greater than 95% of the recombinants are MMR(-). Coupling a single cross and selection with either mutagenesis or selection for spontaneous mutants also results in a dramatic increase in MMR(-) cells. We discuss how horizontal transfer can result in mutator strains during adaptive evolution.}, }
@article {pmid11371528, year = {2001}, author = {Kumar, RB and Das, A}, title = {Functional analysis of the Agrobacterium tumefaciens T-DNA transport pore protein VirB8.}, journal = {Journal of bacteriology}, volume = {183}, number = {12}, pages = {3636-3641}, pmid = {11371528}, issn = {0021-9193}, mesh = {Agrobacterium tumefaciens/*genetics/metabolism ; Amino Acid Sequence ; Amino Acid Substitution ; Bacterial Proteins/*genetics/metabolism ; Blotting, Western ; Conserved Sequence ; DNA, Bacterial/*metabolism ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Phenotype ; Polymerase Chain Reaction ; Porins/*genetics/metabolism ; Two-Hybrid System Techniques ; *Virulence Factors ; }, abstract = {The VirB8 protein of Agrobacterium tumefaciens is essential for DNA transfer to plants. VirB8, a 237-residue polypeptide, is an integral membrane protein with a short N-terminal cytoplasmic domain. It interacts with two transport pore proteins, VirB9 and VirB10, in addition to itself. To study the role of these interactions in DNA transfer and to identify essential amino acids of VirB8, we introduced random mutations in virB8 by the mutagenic PCR method. The putative mutants were tested for VirB8 function by the ability to complement a virB8 deletion mutant in tumor formation assays. After multiple rounds of screening 13 mutants that failed to complement the virB8 deletion mutation were identified. Analysis of the mutant strains by DNA sequence analysis, Western blot assays, and reconstruction of new point mutations led to the identification of five amino acid residues that are essential for VirB8 function. The substitution of glycine-78 to serine, serine-87 to leucine, alanine-100 to valine, arginine-107 to proline or alanine, and threonine-192 to methionine led to the loss of VirB8 activity. When introduced into the wild-type strain, virB8(S87L) partially suppressed the tumor forming ability of the wild-type protein. Analysis of protein-protein interaction by the yeast two-hybrid assay indicated that VirB8(R107P) is defective in interactions with both VirB9 and VirB10. A second mutant VirB8(S87L) is defective in interaction with VirB9.}, }
@article {pmid11371518, year = {2001}, author = {Heusipp, G and Young, GM and Miller, VL}, title = {HreP, an in vivo-expressed protease of Yersinia enterocolitica, is a new member of the family of subtilisin/kexin-like proteases.}, journal = {Journal of bacteriology}, volume = {183}, number = {12}, pages = {3556-3563}, pmid = {11371518}, issn = {0021-9193}, support = {AI42736/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; *Bacterial Proteins ; Base Composition ; Blotting, Southern ; Blotting, Western ; Cloning, Molecular ; Escherichia coli/genetics/metabolism ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Molecular Sequence Data ; *Proprotein Convertases ; Protein Processing, Post-Translational ; *Saccharomyces cerevisiae Proteins ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Subtilisins/*genetics/isolation &amp; purification/metabolism ; Yersinia enterocolitica/enzymology/*genetics/metabolism ; }, abstract = {The role of proteases in pathogenesis is well established for several microorganisms but has not been described for Yersinia enterocolitica. Previously, we identified a gene, hreP, which showed significant similarity to proteases in a screen for chromosomal genes of Y. enterocolitica that were exclusively expressed during an infection of mice. We cloned this gene by chromosome capture and subsequently determined its nucleotide sequence. Like inv, the gene encoding the invasin protein of Y. enterocolitica, hreP is located in a cluster of flagellum biosynthesis and chemotaxis genes. The genomic organization of this chromosomal region is different in Escherichia coli, Salmonella, and Yersinia pestis than in Y. enterocolitica. Analysis of the distribution of hreP between different Yersinia isolates and the relatively low G+C content of the gene suggests acquisition by horizontal gene transfer. Sequence analysis also revealed that HreP belongs to a family of eukaryotic subtilisin/kexin-like proteases. Together with the calcium-dependent protease PrcA of Anabaena variabilis, HreP forms a new subfamily of bacterial subtilisin/kexin-like proteases which might have originated from a common eukaryotic ancestor. Like other proteases of this family, HreP is expressed with an N-terminal prosequence. Expression of an HreP-His(6) tag fusion protein in E. coli revealed that HreP undergoes autocatalytic processing at a consensus cleavage site of subtilisin/kexin-like proteases, thereby releasing the proprotein.}, }
@article {pmid11358998, year = {2001}, author = {Andersson, JO and Doolittle, WF and Nesbø, CL}, title = {Genomics. Are there bugs in our genome?.}, journal = {Science (New York, N.Y.)}, volume = {292}, number = {5523}, pages = {1848-1850}, doi = {10.1126/science.1062241}, pmid = {11358998}, issn = {0036-8075}, mesh = {Animals ; *Biological Evolution ; Chloroplasts/genetics ; Computational Biology ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Genome ; *Genome, Human ; Humans ; Mitochondria/genetics ; Oxo-Acid-Lyases/genetics ; Phylogeny ; Sequence Analysis, DNA ; Symbiosis ; Vertebrates/genetics ; }, }
@article {pmid11358996, year = {2001}, author = {Salzberg, SL and White, O and Peterson, J and Eisen, JA}, title = {Microbial genes in the human genome: lateral transfer or gene loss?.}, journal = {Science (New York, N.Y.)}, volume = {292}, number = {5523}, pages = {1903-1906}, doi = {10.1126/science.1061036}, pmid = {11358996}, issn = {0036-8075}, support = {R01 LM06845/LM/NLM NIH HHS/United States ; }, mesh = {Animals ; Arabidopsis/genetics ; Bacteria/genetics ; *Biological Evolution ; Caenorhabditis elegans/genetics ; Computational Biology ; Databases, Factual ; Drosophila melanogaster/genetics ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Genome ; *Genome, Human ; Humans ; Invertebrates/genetics ; Parasites/genetics ; Phylogeny ; Plants/genetics ; Proteome ; Saccharomyces cerevisiae/genetics ; Vertebrates/genetics ; }, abstract = {The human genome was analyzed for evidence that genes had been laterally transferred into the genome from prokaryotic organisms. Protein sequence comparisons of the proteomes of human, fruit fly, nematode worm, yeast, mustard weed, eukaryotic parasites, and all completed prokaryote genomes were performed, and all genes shared between human and each of the other groups of organisms were collected. About 40 genes were found to be exclusively shared by humans and bacteria and are candidate examples of horizontal transfer from bacteria to vertebrates. Gene loss combined with sample size effects and evolutionary rate variation provide an alternative, more biologically plausible explanation.}, }
@article {pmid11355014, year = {2001}, author = {Hillman, MA and Gecz, J}, title = {Fragile XE-associated familial mental retardation protein 2 (FMR2) acts as a potent transcription activator.}, journal = {Journal of human genetics}, volume = {46}, number = {5}, pages = {251-259}, doi = {10.1007/s100380170074}, pmid = {11355014}, issn = {1434-5161}, mesh = {Alternative Splicing ; Amino Acid Sequence ; DNA-Binding Proteins/genetics/pharmacology/physiology ; Fragile X Syndrome/*genetics ; Gene Transfer, Horizontal ; HeLa Cells ; Humans ; Molecular Sequence Data ; Nuclear Proteins/genetics/pharmacology/*physiology ; Saccharomyces cerevisiae ; Trans-Activators/genetics/pharmacology/*physiology ; Transcriptional Activation/*drug effects ; Transcriptional Elongation Factors ; }, abstract = {Expansion of the FRAXE CCG repeat to a full mutation is associated with methylation and transcriptional silencing of the FMR2 gene, and as a consequence, mild-to-borderline mental retardation. FMR2 is a member of a family of four proteins, AF4, LAF4, FMR2, and AF5q31. The proteins associated with this family localize to the cell nucleus. Various regions of FMR2, and each of the other members of the protein family, were cloned and analyzed for transcription activation in yeast and mammalian cells. In both yeast and mammalian cells, FMR2 showed strong transcription activation. AF4 activation potential was several-fold lower. Interestingly, isoforms of both FMR2 and LAF4 lacking exon 3 activated transcription better than the larger isoforms containing exon 3. Compared with the other members of the family, activation by FMR2 was the strongest. Our results show that FMR2 is a potent transcription activator and that its function is conserved. Elucidation of the function of the FMR2 protein as a transcription activator may place FMR2 within the molecular signalling pathways involved in nonspecific X-linked mental retardation (MRX).}, }
@article {pmid11352062, year = {2001}, author = {Ochman, H and Moran, NA}, title = {Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis.}, journal = {Science (New York, N.Y.)}, volume = {292}, number = {5519}, pages = {1096-1099}, doi = {10.1126/science.1058543}, pmid = {11352062}, issn = {0036-8075}, mesh = {Animals ; Bacteria/*genetics/*pathogenicity ; Bacterial Infections/microbiology ; *Biological Evolution ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genome, Bacterial ; Mutation/genetics ; Symbiosis/*genetics ; Virulence/genetics ; }, abstract = {Traditionally, evolutionary biologists have viewed mutations within individual genes as the major source of phenotypic variation leading to adaptation through natural selection, and ultimately generating diversity among species. Although such processes must contribute to the initial development of gene functions and their subsequent fine-tuning, changes in genome repertoire, occurring through gene acquisition and deletion, are the major events underlying the emergence and evolution of bacterial pathogens and symbionts. Furthermore, pathogens and symbionts depend on similar mechanisms for interacting with hosts and show parallel trends in genome evolution.}, }
@article {pmid11346640, year = {2001}, author = {Eguchi, A and Akuta, T and Okuyama, H and Senda, T and Yokoi, H and Inokuchi, H and Fujita, S and Hayakawa, T and Takeda, K and Hasegawa, M and Nakanishi, M}, title = {Protein transduction domain of HIV-1 Tat protein promotes efficient delivery of DNA into mammalian cells.}, journal = {The Journal of biological chemistry}, volume = {276}, number = {28}, pages = {26204-26210}, doi = {10.1074/jbc.M010625200}, pmid = {11346640}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Animals ; DNA/*genetics ; Gene Products, tat/*genetics ; Gene Transfer, Horizontal ; Genetic Vectors ; HIV-1/*genetics ; Humans ; Molecular Sequence Data ; tat Gene Products, Human Immunodeficiency Virus ; }, abstract = {The plasma membrane of mammalian cells is one of the tight barriers against gene transfer by synthetic delivery systems. Various agents have been used to facilitate gene transfer by destabilizing the endosomal membrane under acidic conditions, but their utility is limited, especially for gene transfer in vivo. In this article, we report that the protein transduction domain of human immunodeficiency virus type 1 Tat protein (Tat peptide) greatly facilitates gene transfer via membrane destabilization. We constructed recombinant lambda phage particles displaying Tat peptide on their surfaces and carrying mammalian marker genes as part of their genomes (Tat-phage). We demonstrate that, when animal cells are briefly exposed to Tat-phage, significant expression of phage marker genes is induced with no harmful effects to the cells. In contrast, recombinant phage displaying other functional peptides, such as the integrin-binding domain or a nuclear localization signal, could not induce detectable marker gene expression. The expression of marker genes induced by Tat-phage is not affected by endosomotropic agents but is partially impaired by inhibitors of caveolae formation. These data suggest that Tat peptide will become a useful component of synthetic delivery vehicles that promote gene transfer independently of the classical endocytic pathway.}, }
@article {pmid11344118, year = {2001}, author = {Masaki, I and Yonemitsu, Y and Komori, K and Ueno, H and Nakashima, Y and Nakagawa, K and Fukumura, M and Kato, A and Hasan, MK and Nagai, Y and Sugimachi, K and Hasegawa, M and Sueishi, K}, title = {Recombinant Sendai virus-mediated gene transfer to vasculature: a new class of efficient gene transfer vector to the vascular system.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {15}, number = {7}, pages = {1294-1296}, doi = {10.1096/fj.00-0460fje}, pmid = {11344118}, issn = {0892-6638}, mesh = {*Blood Vessels/cytology ; Endothelium, Vascular/cytology ; Gene Transfer Techniques ; *Gene Transfer, Horizontal ; Genes, Reporter ; *Genetic Vectors ; Humans ; Respirovirus/*genetics ; Time Factors ; *Transgenes ; }, }
@article {pmid11339649, year = {2001}, author = {Fujisawa, M and Shirakawa, T and Fujioka, H and Gotoh, A and Okada, H and Arakawa, S and Kamidono, S}, title = {Adenovirus-mediated p53 gene transfer to rat testis impairs spermatogenesis.}, journal = {Archives of andrology}, volume = {46}, number = {3}, pages = {223-231}, doi = {10.1080/01485010151096568}, pmid = {11339649}, issn = {0148-5016}, mesh = {Adenoviridae/genetics ; Animals ; *Gene Transfer, Horizontal ; *Genes, p53 ; Infertility, Male/genetics ; Male ; Organ Size ; Rats ; Spermatogenesis/*genetics/physiology ; Testis/pathology/*physiology ; }, abstract = {The tumor suppressor protein p53 participates in normal cell differentiation as well as induction of programmed cell death. The authors investigated the effect of p53 overexpression on spermatogenesis by transferring p53 gene into the rat testes. Replication-deficient recombinant adenovirus vectors were constructed to include cytomegalovirus (CMV) promoter driving wild-type p53 (Ad-CMV-p53) or beta-galactosidase (Ad-CMV-beta-gal). Virus was delivered to cells of the tubules by slow retrograde injection through the rete testis. At 0, 4, 7, and 14 days, testes were removed, weighed, and analyzed histopathologically, including immunohistochemistry for p53, Bcl-2, Bax, and interleukin-1beta converting enzyme (ICE). Testicular weight was decreased in Ad-CMV-p53 group at 14 days after injection, while no change occurred in phosphate-buffered saline-injected controls or Ad-CMV-beta-gal-infected testes. Beyond 4 days, cell degradation in tubules interfered with immunohistochemical observation in the Ad-CMV-p53 group. At 4 days, p53 was expressed mostly in spermatocytes. Bax showed greater expression in the p53 group than in the control or Ad-CMV-beta-gal group. ICE, expressed mostly in spermatids, was more abundant in the p53 group than in controls. Overall, p53 overexpression in the testis impaired spermatogenesis.}, }
@article {pmid11337471, year = {2001}, author = {Bolotin, A and Wincker, P and Mauger, S and Jaillon, O and Malarme, K and Weissenbach, J and Ehrlich, SD and Sorokin, A}, title = {The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403.}, journal = {Genome research}, volume = {11}, number = {5}, pages = {731-753}, pmid = {11337471}, issn = {1088-9051}, mesh = {Amino Acids/biosynthesis/genetics/metabolism ; Bacterial Proteins/metabolism ; Bacteriophages/genetics ; Biological Transport, Active/genetics ; Cell Wall/genetics/metabolism ; DNA Transposable Elements/genetics ; Endopeptidases/genetics ; Energy Metabolism/genetics ; Enterobacteriaceae/genetics ; Gene Expression Regulation/genetics ; Gene Transfer, Horizontal/genetics ; *Genome, Bacterial ; Lactic Acid/metabolism ; Lactococcus lactis/*genetics/isolation &amp; purification/metabolism/virology ; Molecular Sequence Data ; Multigene Family/genetics ; Nucleotides/biosynthesis/genetics ; Open Reading Frames/genetics ; Proviruses/genetics ; RNA, Bacterial/genetics ; Sequence Analysis, DNA/methods ; Signal Transduction/genetics ; Transformation, Genetic/genetics ; Vitamins/biosynthesis/genetics ; }, abstract = {Lactococcus lactis is a nonpathogenic AT-rich gram-positive bacterium closely related to the genus Streptococcus and is the most commonly used cheese starter. It is also the best-characterized lactic acid bacterium. We sequenced the genome of the laboratory strain IL1403, using a novel two-step strategy that comprises diagnostic sequencing of the entire genome and a shotgun polishing step. The genome contains 2,365,589 base pairs and encodes 2310 proteins, including 293 protein-coding genes belonging to six prophages and 43 insertion sequence (IS) elements. Nonrandom distribution of IS elements indicates that the chromosome of the sequenced strain may be a product of recent recombination between two closely related genomes. A complete set of late competence genes is present, indicating the ability of L. lactis to undergo DNA transformation. Genomic sequence revealed new possibilities for fermentation pathways and for aerobic respiration. It also indicated a horizontal transfer of genetic information from Lactococcus to gram-negative enteric bacteria of Salmonella-Escherichia group.}, }
@article {pmid11336549, year = {2001}, author = {Desiere, F and Mahanivong, C and Hillier, AJ and Chandry, PS and Davidson, BE and Brüssow, H}, title = {Comparative genomics of lactococcal phages: insight from the complete genome sequence of Lactococcus lactis phage BK5-T.}, journal = {Virology}, volume = {283}, number = {2}, pages = {240-252}, doi = {10.1006/viro.2001.0857}, pmid = {11336549}, issn = {0042-6822}, mesh = {Computational Biology/methods ; Endodeoxyribonucleases/chemistry/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Viral ; Genomics ; Lactococcus lactis/*virology ; Molecular Sequence Data ; Siphoviridae/classification/*genetics ; Streptococcus Phages/classification/genetics ; }, abstract = {Lactococcus lactis phage BK5-T and Streptococcus thermophilus phage Sfi21, two cos-site temperate Siphoviridae with 40-kb genomes, share an identical genome organization, sequence similarity at the amino acid level over about half of their genomes, and nucleotide sequence identity of 60% over the DNA packaging and head morphogenesis modules. Siphoviridae with similarly organized genomes and substantial protein sequence similarity were identified in several genera of low-GC-content Gram-positive bacteria. These phages demonstrated a gradient of relatedness ranging from nucleotide sequence similarity to protein sequence similarity to gene map similarity over the DNA packaging and head morphogenesis modules. Interestingly, the degree of relatedness was correlated with the evolutionary distance separating their bacterial hosts. These observations suggest elements of vertical evolution in phages. The structural genes from BK5-T shared no sequence relationships with corresponding genes/proteins from lactococcal phages belonging to distinct lactococcal phage species, including phage sk1 (phage species 936) that showed a closely related gene map. Despite a clearly distinct genome organization, lactococcal phages sk1 and c2 showed nine sequence-related proteins. Over the early gene cluster phage BK5-T shared nine regions of high nucleotide sequence similarity, covering at most two adjacent genes, with lactococcal phage r1t (phage species P335). Over the structural genes, the closest relatives of phage r1t were not lactococcal phages belonging to other phage species, but Siphoviridae from Mycobacteria (high-GC-content Gram-positive bacteria). Evidence for recent horizontal gene transfer between distinct phage species was obtained for dairy phages, but these transfers were limited to phages infecting the same bacterial host species.}, }
@article {pmid11335018, year = {2001}, author = {Ponting, CP}, title = {Plagiarized bacterial genes in the human book of life.}, journal = {Trends in genetics : TIG}, volume = {17}, number = {5}, pages = {235-237}, doi = {10.1016/s0168-9525(01)02282-x}, pmid = {11335018}, issn = {0168-9525}, mesh = {Bacteria/*genetics ; *Human Genome Project ; Humans ; Software ; }, abstract = {The initial analysis of the human genome draft sequence reveals that our 'book of life' is multi-authored. A small but significant proportion of our genes owes their heritage not to antecedent eukaryotes but instead to bacteria. The publicly funded Human Genome Project study indicates that about 0.5% of all human genes were copied into the genome from bacterial sources. Detailed sequence analyses point to these 'horizontal gene transfer' events having occurred relatively recently. So how did the human 'book of life' evolve to be a chimaera, part animal and part bacterium? And what was the probable evolutionary impact of such gene plagiarism?}, }
@article {pmid11330360, year = {2001}, author = {Blahová, J and Králiková, K and Krcméry, V and Kubonová, K and Vaculíková, A and Mikovicová, A and Klokocníková, L and Hanzen, J and Jezek, P}, title = {Transferable antibiotic resistance in multiresistant nosocomial Acinetobacter baumannii strains from seven clinics in the Slovak and Czech Republics.}, journal = {Journal of chemotherapy (Florence, Italy)}, volume = {13}, number = {2}, pages = {143-147}, doi = {10.1179/joc.2001.13.2.143}, pmid = {11330360}, issn = {1120-009X}, mesh = {Acinetobacter/*drug effects/genetics/pathogenicity ; Acinetobacter Infections/drug therapy ; Cross Infection/*drug therapy ; Czech Republic ; *Drug Resistance, Multiple ; Escherichia coli/*drug effects/genetics/pathogenicity ; *Gene Transfer, Horizontal ; Humans ; Intensive Care Units ; Population Dynamics ; Risk Factors ; Slovakia ; }, abstract = {Sixty-seven multiresistant nosocomial Acinetobacter baumannii isolates from patients hospitalized mostly in intensive care units of seven clinics in Slovak and Czech Republic were tested to determine their ability to transfer antibiotic resistance. All isolates were resistant to kanamycin, ticarcillin, cephalothin, cefotaxime, ceftazidime, aztreonam and susceptible to carbapenems, sulbactam and ampicillin/sulbactam. Sixty-five out of 67 strains transferred resistance determinants to Escherichia coli K-12 and Proteus mirabilis P-38 recipients. Analysis of selected transconjugants by an indirect selection method showed a more variable pattern of transferred resistance determinants. The clonal spread of strains transferring resistance seems to be an additional risk for occurrence of strains resistant to ceftazidime and aztreonam.}, }
@article {pmid11330273, year = {2001}, author = {Parens, E and Juengst, E}, title = {Inadvertently crossing the germ line.}, journal = {Science (New York, N.Y.)}, volume = {292}, number = {5516}, pages = {397}, doi = {10.1126/science.292.5516.397}, pmid = {11330273}, issn = {0036-8075}, mesh = {*Bioethics ; Cytoplasm/*transplantation ; *DNA, Mitochondrial ; Female ; Financing, Government ; *Gene Transfer, Horizontal ; Genetic Research ; Guidelines as Topic ; Humans ; *Ovum ; Public Policy ; *Reproductive Techniques ; Research Support as Topic ; United States ; }, }
@article {pmid11326030, year = {2001}, author = {Neuwirth, C and Siebor, E and Pechinot, A and Duez, JM and Pruneaux, M and Garel, F and Kazmierczak, A and Labia, R}, title = {Evidence of in vivo transfer of a plasmid encoding the extended-spectrum beta-lactamase TEM-24 and other resistance factors among different members of the family Enterobacteriaceae.}, journal = {Journal of clinical microbiology}, volume = {39}, number = {5}, pages = {1985-1988}, pmid = {11326030}, issn = {0095-1137}, mesh = {Anti-Bacterial Agents/pharmacology ; *Bacterial Proteins ; Drug Resistance, Microbial/genetics ; Drug Resistance, Multiple/genetics ; Electrophoresis, Gel, Pulsed-Field ; Enterobacteriaceae/*drug effects/enzymology/genetics ; Enterobacteriaceae Infections/microbiology ; *Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; Plasmids/*genetics ; beta-Lactamases/*genetics ; beta-Lactams/*pharmacology ; }, abstract = {The epidemiological study of several multidrug-resistant Enterobacteriaceae isolated from five patients demonstrated in vivo dissemination of a 100-kb plasmid encoding the extended-spectrum beta-lactamase TEM-24 from a clonal strain of Enterobacter aerogenes to different strains of Klebsiella pneumoniae, Escherichia coli, Proteus vulgaris, Proteus mirabilis, and Serratia marcescens.}, }
@article {pmid11320123, year = {2001}, author = {Kim, DJ and Forst, S}, title = {Genomic analysis of the histidine kinase family in bacteria and archaea.}, journal = {Microbiology (Reading, England)}, volume = {147}, number = {Pt 5}, pages = {1197-1212}, doi = {10.1099/00221287-147-5-1197}, pmid = {11320123}, issn = {1350-0872}, mesh = {Amino Acid Sequence ; Archaea/*genetics ; Bacteria/*genetics ; Conserved Sequence ; Evolution, Molecular ; *Genome, Archaeal ; *Genome, Bacterial ; Histidine Kinase ; Molecular Sequence Data ; *Phylogeny ; Protein Kinases/*genetics ; Protein Structure, Tertiary ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; }, abstract = {Two-component signal transduction systems, consisting of histidine kinase (HK) sensors and DNA-binding response regulators, allow bacteria and archaea to respond to diverse environmental stimuli. HKs possess a conserved domain (H-box region) which contains the site of phosphorylation and an ATP-binding kinase domain. In this study, a genomic approach was taken to analyse the HK family in bacteria and archaea. Based on phylogenetic analysis, differences in the sequence and organization of the H-box and kinase domains, and the predicted secondary structure of the H-box region, five major HK types were identified. Of the 336 HKs analysed, 92% could be assigned to one of the five major HK types. The Type I HKs were found predominantly in bacteria while Type II HKs were not prevalent in bacteria but constituted the major type (13 of 15 HKs) in the archaeon Archaeoglobus fulgidus. Type III HKs were generally more prevalent in Gram-positive bacteria and were the major HK type (14 of 15 HKs) in the archaeon Methanobacterium thermoautotrophicum. Type IV HKs represented a minor type found in bacteria. The fifth HK type was composed of the chemosensor HKs, CheA. Several bacterial genomes contained all five HK types. In contrast, archaeal genomes either contained a specific HK type or lacked HKs altogether. These findings suggest that the different HK types originated in bacteria and that specific HK types were acquired in archaea by horizontal gene transfer.}, }
@article {pmid11319263, year = {2001}, author = {Wang, HC and Badger, J and Kearney, P and Li, M}, title = {Analysis of codon usage patterns of bacterial genomes using the self-organizing map.}, journal = {Molecular biology and evolution}, volume = {18}, number = {5}, pages = {792-800}, doi = {10.1093/oxfordjournals.molbev.a003861}, pmid = {11319263}, issn = {0737-4038}, mesh = {Archaeoglobus fulgidus/*genetics ; Base Sequence ; *Codon ; Entropy ; Escherichia coli/*genetics ; Euryarchaeota/*genetics ; *Gene Expression Regulation, Archaeal ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; Genome, Archaeal ; *Genome, Bacterial ; Haemophilus influenzae/*genetics ; Methanococcus/*genetics ; Pyrococcus/*genetics ; *Software ; }, abstract = {Codon usage varies both between organisms and between different genes in the same organism. This observation has been used as a basis for earlier work in identifying highly expressed and horizontally transferred genes in Escherichia coli. In this work, we applied Kohonen's self-organizing map to analysis of the codon usage pattern of the Escherichia coli, Aquifex aeolicus, Archaeoglobus fulgidus, Haemophilus influenzae RD:, Methanococcus jannaschii, Methanobacterium thermoautotrophicum, and Pyrococcus horikoshii genomes for evidence of highly expressed genes and horizontally transferred genes. All of the analyzed genomes had a clear category of horizontally transferred genes, and their apparent percentages ranged from 7.7% to 21.4%. The apparent percentage of highly expressed genes ranges from 0% to 11.8%. A clustering of average codon usage of main gene categories of the seven genomes showed an interesting mixing of gene classes in four thermophilic/hyperthermophilic organisms, A. aeolicus, A. fulgidus, M. thermoautotrophicum, and P. horikoshii, which suggests possible origins of their horizontally transferred genes as well as the need for adaptation to a specific environment. Further classification of the three gene categories in E. coli and H. influenzae according to gene function revealed that genes involved in communication (such as regulation and cell process) and structure (cell structure and structural proteins) are more likely to be horizontally transferred than are genes involved in information (transcription, translation, and related processes) and in some groups of energy (such as energy metabolism and carbon compound catabolism).}, }
@article {pmid11319200, year = {2001}, author = {Shyue, SK and Tsai, MJ and Liou, JY and Willerson, JT and Wu, KK}, title = {Selective augmentation of prostacyclin production by combined prostacyclin synthase and cyclooxygenase-1 gene transfer.}, journal = {Circulation}, volume = {103}, number = {16}, pages = {2090-2095}, doi = {10.1161/01.cir.103.16.2090}, pmid = {11319200}, issn = {0009-7322}, support = {P50-NS 23327/NS/NINDS NIH HHS/United States ; R01-HL 50675/HL/NHLBI NIH HHS/United States ; }, mesh = {6-Ketoprostaglandin F1 alpha/analysis/biosynthesis ; Adenoviridae/genetics ; Arachidonic Acid/metabolism ; Cell Line ; Cells, Cultured ; Chromatography, High Pressure Liquid ; Cyclooxygenase 1 ; Cytochrome P-450 Enzyme System/genetics/*metabolism ; Dinoprostone/analysis/biosynthesis ; Dose-Response Relationship, Drug ; Endothelium, Vascular/chemistry/cytology/*metabolism ; Epoprostenol/analysis/*biosynthesis ; Fatty Acids, Unsaturated/analysis/biosynthesis ; Gene Transfer, Horizontal ; Genetic Vectors/administration &amp; dosage/genetics ; Humans ; Intramolecular Oxidoreductases/genetics/*metabolism ; Isoenzymes/genetics/*metabolism ; Membrane Proteins ; Plasmids/genetics ; Prostaglandin-Endoperoxide Synthases/genetics/*metabolism ; Transfection ; }, abstract = {BACKGROUND: We tested the hypothesis that combined cyclooxygenase-1 (COX-1) and prostacyclin synthase (PGIS) gene transfer selectively augments prostacyclin production without a concurrent overproduction of other prostanoids.<br><br>METHODS AND RESULTS: ECV304 cells were transfected with bicistronic pCOX-1/PGIS versus pCOX-1 or pPGIS, and prostanoids were analyzed. Contrary to the high prostaglandin E2 synthesis in pCOX-1 transfected cells, selective prostacyclin formation was noted with bicistronic plasmid transfection. Next, we determined the optimal ratio of Ad-COX-1 to Ad-PGIS by transfecting human umbilical vein endothelial cells with various titers of these 2 adenoviral constructs and determined the level of protein expression and prostanoid synthesis. Our results show that optimal ratios of adenoviral titers to achieve a large prostacyclin augmentation without overproduction of prostaglandin E2 or F2alpha were 50 to 100 plaque forming units (pfu) of Ad-COX-1 to 50 pfu of Ad-PGIS per cell. A higher Ad-PGIS to Ad-COX-1 ratio caused a paradoxical decline in prostacyclin synthesis.<br><br>CONCLUSIONS: Prostacyclin synthesis can be selectively augmented by cotransfecting endothelial cells with an optimal ratio of COX-1 to PGIS. Combined COX-1 and PGIS gene transfer has the potential for therapeutic augmentation of prostacyclin.}, }
@article {pmid11319078, year = {2001}, author = {Stanton, TB and Matson, EG and Humphrey, SB}, title = {Brachyspira (Serpulina) hyodysenteriae gyrB mutants and interstrain transfer of coumermycin A(1) resistance.}, journal = {Applied and environmental microbiology}, volume = {67}, number = {5}, pages = {2037-2043}, pmid = {11319078}, issn = {0099-2240}, mesh = {Amino Acid Sequence ; Aminocoumarins ; Brachyspira hyodysenteriae/*drug effects/genetics ; Coumarins/*pharmacology ; DNA Gyrase ; DNA Topoisomerases, Type II/chemistry/*genetics ; Drug Resistance, Microbial/genetics ; Enzyme Inhibitors/*pharmacology ; *Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Mutagenesis ; *Mutation ; Sequence Analysis, DNA ; Ultraviolet Rays ; }, abstract = {To further develop genetic techniques for the enteropathogen Brachyspira hyodysenteriae, the gyrB gene of this spirochete was isolated from a lambdaZAPII library of strain B204 genomic DNA and sequenced. The putative protein encoded by this gene exhibited up to 55% amino acid sequence identity with GyrB proteins of various bacterial species, including other spirochetes. B. hyodysenteriae coumermycin A(1)-resistant (Cn(r)) mutant strains, both spontaneous and UV induced, were isolated by plating B204 cells onto Trypticase soy blood agar plates containing 0.5 microg of coumermycin A(1)/ml. The coumermycin A(1) MICs were 25 to 100 microg/ml for the resistant strains and 0.1 to 0.25 microg/ml for strain B204. Four Cn(r) strains had single nucleotide changes in their gyrB genes, corresponding to GyrB amino acid changes of Gly(78) to Ser (two strains), Gly(78) to Cys, and Thr(166) to Ala. When Cn(r) strain 435A (Gly(78) to Ser) and Cm(r) Km(r) strain SH (DeltaflaA1::cat Deltanox::kan) were cultured together in brain heart infusion broth containing 10% (vol/vol) heat-treated (56 degrees C, 30 min) calf serum, cells resistant to chloramphenicol, coumermycin A(1), and kanamycin could be isolated from the cocultures after overnight incubation, but such cells could not be isolated from monocultures of either strain. Seven Cn(r) Km(r) Cm(r) strains were tested and were determined to have resistance genotypes of both strain 435A and strain SH. Cn(r) Km(r) Cm(r) cells could not be isolated when antiserum to the bacteriophage-like agent VSH-1 was added to cocultures, and the numbers of resistant cells increased fivefold when mitomycin C, an inducer of VSH-1 production, was added. These results indicate that coumermycin resistance associated with a gyrB mutation is a useful selection marker for monitoring gene exchange between B. hyodysenteriae cells. Gene transfer readily occurs between B. hyodysenteriae cells in broth culture, a finding with practical importance. VSH-1 is the likely mechanism for gene transfer.}, }
@article {pmid11299340, year = {2001}, author = {Lutz, KA and Knapp, JE and Maliga, P}, title = {Expression of bar in the plastid genome confers herbicide resistance.}, journal = {Plant physiology}, volume = {125}, number = {4}, pages = {1585-1590}, pmid = {11299340}, issn = {0032-0889}, mesh = {Acetyltransferases/chemistry/*genetics/metabolism ; Amino Acid Sequence ; Aminobutyrates/*toxicity ; Drug Resistance/*genetics ; Genome, Plant ; Herbicides/*toxicity ; Molecular Sequence Data ; Plants, Genetically Modified/drug effects/*physiology ; *Plants, Toxic ; Plasmids ; Plastids/*genetics ; Restriction Mapping ; Nicotiana/drug effects/genetics/*physiology ; }, abstract = {Phosphinothricin (PPT) is the active component of a family of environmentally safe, nonselective herbicides. Resistance to PPT in transgenic crops has been reported by nuclear expression of a bar transgene encoding phosphinothricin acetyltransferase, a detoxifying enzyme. We report here expression of a bacterial bar gene (b-bar1) in tobacco (Nicotiana tabacum cv Petit Havana) plastids that confers field-level tolerance to Liberty, an herbicide containing PPT. We also describe a second bacterial bar gene (b-bar2) and a codon-optimized synthetic bar (s-bar) gene with significantly elevated levels of expression in plastids (>7% of total soluble cellular protein). Although these genes are expressed at a high level, direct selection thus far did not yield transplastomic clones, indicating that subcellular localization rather than the absolute amount of the enzyme is critical for direct selection of transgenic clones. The codon-modified s-bar gene is poorly expressed in Escherichia coli, a common enteric bacterium, due to differences in codon use. We propose to use codon usage differences as a precautionary measure to prevent expression of marker genes in the unlikely event of horizontal gene transfer from plastids to bacteria. Localization of the bar gene in the plastid genome is an attractive alternative to incorporation in the nuclear genome since there is no transmission of plastid-encoded genes via pollen.}, }
@article {pmid11296296, year = {2001}, author = {Ferretti, JJ and McShan, WM and Ajdic, D and Savic, DJ and Savic, G and Lyon, K and Primeaux, C and Sezate, S and Suvorov, AN and Kenton, S and Lai, HS and Lin, SP and Qian, Y and Jia, HG and Najar, FZ and Ren, Q and Zhu, H and Song, L and White, J and Yuan, X and Clifton, SW and Roe, BA and McLaughlin, R}, title = {Complete genome sequence of an M1 strain of Streptococcus pyogenes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {98}, number = {8}, pages = {4658-4663}, pmid = {11296296}, issn = {0027-8424}, mesh = {Bacteriophages/isolation &amp; purification ; Gene Expression Regulation ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Molecular Sequence Data ; Phylogeny ; Signal Transduction ; Streptococcus pyogenes/*genetics/pathogenicity/virology ; Virulence/genetics ; }, abstract = {The 1,852,442-bp sequence of an M1 strain of Streptococcus pyogenes, a Gram-positive pathogen, has been determined and contains 1,752 predicted protein-encoding genes. Approximately one-third of these genes have no identifiable function, with the remainder falling into previously characterized categories of known microbial function. Consistent with the observation that S. pyogenes is responsible for a wider variety of human disease than any other bacterial species, more than 40 putative virulence-associated genes have been identified. Additional genes have been identified that encode proteins likely associated with microbial "molecular mimicry" of host characteristics and involved in rheumatic fever or acute glomerulonephritis. The complete or partial sequence of four different bacteriophage genomes is also present, with each containing genes for one or more previously undiscovered superantigen-like proteins. These prophage-associated genes encode at least six potential virulence factors, emphasizing the importance of bacteriophages in horizontal gene transfer and a possible mechanism for generating new strains with increased pathogenic potential.}, }
@article {pmid11286883, year = {2001}, author = {Gupta, S and Maiden, MC}, title = {Exploring the evolution of diversity in pathogen populations.}, journal = {Trends in microbiology}, volume = {9}, number = {4}, pages = {181-185}, doi = {10.1016/s0966-842x(01)01986-2}, pmid = {11286883}, issn = {0966-842X}, mesh = {Antigenic Variation ; Bacteria/*classification/*genetics/immunology/pathogenicity ; Bacterial Infections/immunology/*microbiology ; Ecosystem ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Variation ; Genotype ; Humans ; }, abstract = {Pathogen biodiversity is an under-exploited source of inference regarding disease processes and the evolution of pathogens and pathogenesis. In addition, the structure of pathogen populations, especially for diverse organisms such as the meningococcus, has implications for public health interventions including vaccination and antibiotic use. The predominant paradigm for interpreting bacterial diversity has been the clonal population structure, which has been modified by the incorporation of the effects of horizontal genetic exchange. Multilocus models of variable antigens, which explore the effects of immune selection, provide alternative explanations for structured diversity in pathogen populations.}, }
@article {pmid11286871, year = {2001}, author = {Pallen, M}, title = {Microbial genomics.}, journal = {Trends in microbiology}, volume = {9}, number = {4}, pages = {159}, doi = {10.1016/s0966-842x(01)02015-7}, pmid = {11286871}, issn = {0966-842X}, mesh = {Bacterial Proteins/*genetics ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genome, Human ; Humans ; }, }
@article {pmid11286192, year = {2001}, author = {Campbell, A}, title = {The origins and evolution of viruses.}, journal = {Trends in microbiology}, volume = {9}, number = {2}, pages = {61}, doi = {10.1016/s0966-842x(00)01934-x}, pmid = {11286192}, issn = {0966-842X}, mesh = {Capsid/genetics/metabolism ; DNA, Viral/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Viral ; RNA, Viral/genetics ; Viruses/*genetics ; }, }
@article {pmid11282595, year = {2001}, author = {Sander, M and Schmieger, H}, title = {Method for host-independent detection of generalized transducing bacteriophages in natural habitats.}, journal = {Applied and environmental microbiology}, volume = {67}, number = {4}, pages = {1490-1493}, pmid = {11282595}, issn = {0099-2240}, mesh = {Bacteriophages/*genetics/*isolation &amp; purification ; DNA, Ribosomal/analysis ; DNA, Viral/analysis ; Gram-Negative Bacteria/classification/*virology ; Molecular Sequence Data ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/genetics ; Sewage/*virology ; *Transduction, Genetic ; }, abstract = {Despite an increasing interest in horizontal gene transfer in bacteria, the role of generalized transduction in this process has not been well investigated yet. Certainly one of the reasons is that only a small fraction of general transducing bacteriophages have been characterized, because many bacterial hosts needed for propagation and identification are not culturable or are simply unknown. A method for host-independent detection of transducing bacteriophages was developed. Phage-encapsulated DNA was used as a template for PCR amplification of 16S ribosomal DNA using primers specific for the 16S rRNA genes of most eubacteria. Sequencing of the cloned amplification products permits the identification of the host bacteria. The Salmonella phage P22 was used as an example. Applying this method to a sample of the supernatant of the mixed liquor in the aeration tank of an activated sludge treatment works revealed the presence of transducing phages infecting several bacterial species for which such phages have not yet been described. This method is suitable for estimating the contribution of generalized transduction to horizontal gene transfer in different habitats.}, }
@article {pmid11281319, year = {2001}, author = {Barberio, C and Pagliai, L and Cavalieri, D and Fani, R}, title = {Biodiversity and horizontal gene transfer in culturable bacteria isolated from activated sludge enriched in nonylphenol ethoxylates.}, journal = {Research in microbiology}, volume = {152}, number = {1}, pages = {105-112}, doi = {10.1016/s0923-2508(00)01173-6}, pmid = {11281319}, issn = {0923-2508}, mesh = {Culture Media ; DNA, Bacterial/analysis/genetics ; DNA, Ribosomal/analysis/genetics ; Deoxyribonucleases, Type II Site-Specific/metabolism ; Ethylene Glycols/*metabolism ; *Gene Transfer, Horizontal ; Gram-Negative Bacteria/*classification/*genetics/isolation &amp; purification ; Industrial Waste ; Molecular Sequence Data ; Phylogeny ; Plasmids/genetics ; RNA, Ribosomal, 16S ; Restriction Mapping ; Sequence Analysis, DNA ; Sewage/chemistry/*microbiology ; Waste Disposal, Fluid ; }, abstract = {One hundred and twenty bacterial isolates, from activated sludge of a treatment plant collecting wastes enriched in ethoxylated nonylphenols, were studied. Sixty isolates were selected on rich medium and 60 on mineral medium containing two nonylphenol ethoxylates as the sole carbon source. Analysis of biodiversity at the species level was performed by comparing the AluI restriction patterns of the 16S ribosomal DNA amplified by PCR from 120 isolates. The rDNA restriction analysis enabled us to cluster the isolates into 15 groups, five of which represented nearly 77% of the community. Phylogenetic analysis of five strains belonging to these main groups made it possible to assign four of them to the genera Acinetobacter, Aeromonas and Shewanella and one to the Proteus group. The analysis of plasmid content showed a high variability and suggested that horizontal gene transfer had taken place at the intraspecific, interspecific and intergeneric levels.}, }
@article {pmid11274119, year = {2001}, author = {Prentice, MB and James, KD and Parkhill, J and Baker, SG and Stevens, K and Simmonds, MN and Mungall, KL and Churcher, C and Oyston, PC and Titball, RW and Wren, BW and Wain, J and Pickard, D and Hien, TT and Farrar, JJ and Dougan, G}, title = {Yersinia pestis pFra shows biovar-specific differences and recent common ancestry with a Salmonella enterica serovar Typhi plasmid.}, journal = {Journal of bacteriology}, volume = {183}, number = {8}, pages = {2586-2594}, pmid = {11274119}, issn = {0021-9193}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; DNA Transposable Elements/genetics ; DNA, Bacterial/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Humans ; Molecular Sequence Data ; Plasmids/*genetics ; Polymerase Chain Reaction ; Salmonella typhi/*genetics ; Sequence Analysis, DNA ; Yersinia pestis/*classification/*genetics ; }, abstract = {Population genetic studies suggest that Yersinia pestis, the cause of plague, is a clonal pathogen that has recently emerged from Yersinia pseudotuberculosis. Plasmid acquisition is likely to have been a key element in this evolutionary leap from an enteric to a flea-transmitted systemic pathogen. However, the origin of Y. pestis-specific plasmids remains obscure. We demonstrate specific plasmid rearrangements in different Y. pestis strains which distinguish Y. pestis bv. Orientalis strains from other biovars. We also present evidence for plasmid-associated DNA exchange between Y. pestis and the exclusively human pathogen Salmonella enterica serovar Typhi.}, }
@article {pmid11274117, year = {2001}, author = {Claus, H and Stoevesandt, J and Frosch, M and Vogel, U}, title = {Genetic isolation of meningococci of the electrophoretic type 37 complex.}, journal = {Journal of bacteriology}, volume = {183}, number = {8}, pages = {2570-2575}, pmid = {11274117}, issn = {0021-9193}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacteriophages/genetics ; Chromosome Mapping ; DNA Restriction-Modification Enzymes/metabolism ; Electrophoresis/methods ; Enzymes/analysis ; *Genome, Bacterial ; Humans ; Molecular Sequence Data ; Neisseria meningitidis/classification/*genetics/virology ; Nucleic Acid Hybridization ; Plasmids/genetics ; Sequence Analysis, DNA ; }, abstract = {Neisseria meningitidis (the meningococcus) is a naturally competent bacterial species in which intra- and interspecific horizontal gene transfer is a major source of genetic diversity. In strains of the electrophoretic type 37 (ET-37) complex and of the A4 cluster, we identified genomic DNA coding for a novel restriction-modification system and for the tail of a previously unidentified prophage. Furthermore, a novel 7.2-kb DNA segment restricted to clones of the ET-37 complex and the A4 cluster was isolated and shown to occur both as a plasmid (pJS-B) and as a chromosomal integration. Neither the genomic loci nor pJS-B was present in ET-5 complex, lineage 3, or serogroup A meningococci. The differential distribution of the DNA segments described herein, as well as of opcA, porB, nmeAI, nmeBI, and nmeDI described previously, supports the concept of genetic isolation of hypervirulent lineages responsible for most cases of serogroup C disease worldwide.}, }
@article {pmid11265763, year = {2000}, author = {Kurland, CG}, title = {Something for everyone. Horizontal gene transfer in evolution.}, journal = {EMBO reports}, volume = {1}, number = {2}, pages = {92-95}, pmid = {11265763}, issn = {1469-221X}, mesh = {*Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; *Genome ; Humans ; Phylogeny ; Species Specificity ; }, }
@article {pmid11265225, year = {2001}, author = {Hacein-Bey, S and Gross, F and Nusbaum, P and Yvon, E and Fischer, A and Cavazzana-Calvo, M}, title = {[Gene therapy of X-linked severe combined immunologic deficiency (SCID-X1)].}, journal = {Pathologie-biologie}, volume = {49}, number = {1}, pages = {57-66}, doi = {10.1016/s0369-8114(00)00002-x}, pmid = {11265225}, issn = {0369-8114}, mesh = {Antigens, CD34/analysis ; Bone Marrow/pathology ; Gene Expression ; Gene Transfer, Horizontal ; *Genetic Linkage ; *Genetic Therapy ; Hematopoietic Stem Cells/immunology/pathology ; Humans ; Mutation ; Receptors, Cytokine/genetics ; Severe Combined Immunodeficiency/*genetics/*therapy ; Transfection ; *X Chromosome ; }, abstract = {X-linked severe combined immunodeficiency (SCID-X1) is a recessive hereditary disorder in which early T and Natural Killer (NK) lymphocyte development is blocked. The genetic disorder results from mutations in the common gamma c chain that participates in several cytokine receptors including the interleukin-2 (Il-2), Il-4, Il-7, Il-9, Il-15 receptors. SCID-X1 offers a reliable model for gene therapy as it is a lethal condition that is, in many cases, curable by allogeneic bone marrow transplantation. We have shown that retrovirus-mediated transfer of the gamma c cDNA induced gamma c chain expression and restored the function of the high-affinity IL-2 receptor on SCI-X1 EBV-transformed B-cell lines. We have the designed culture conditions to study NK-cell and T-cell development of CD34+ hematopoietic progenitor cells. In the culture systems, gamma c transduced CD34+ marrow cells from two SCID-X1 patients were able to mature into CD56+ and/or CD16+ NK cells and into CD4+ TCR alpha beta+ T cells. These preclinical results set the basis for a clinical study of ex-vivo gamma c gene transfer into CD34+ cells from SCID-X1 patients.}, }
@article {pmid11262974, year = {2001}, author = {Kim, J and Salisbury, BA}, title = {A tree obscured by vines: horizontal gene transfer and the median tree method of estimating species phylogeny.}, journal = {Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing}, volume = {}, number = {}, pages = {571-582}, doi = {10.1142/9789814447362_0055}, pmid = {11262974}, issn = {2335-6928}, mesh = {*Algorithms ; Computer Simulation ; *Gene Transfer, Horizontal ; Models, Genetic ; *Phylogeny ; Species Specificity ; }, abstract = {A phylogeny is a tree graph representation of genealogical relationships between biological objects. It is of general interest to estimate the phylogeny of whole organisms (species trees) using bio-molecular sequences. When multiple sequences are available for each organism such as with whole genome data, individual phylogenies estimated by each molecule (gene trees) may not be concordant. The lack of concordance may be due to actual biological mechanisms such as horizontal transfer of the molecules. Here, we present a new phylogeny estimation method designed to estimate the species tree despite such horizontal transfer. It uses the idea that horizontal transfer distorts distance relationships between pairs of species but a median estimate of the distances is robust to such distortions. We demonstrate the utility of our method using a simulation study.}, }
@article {pmid11262871, year = {2000}, author = {Wren, BW}, title = {Microbial genome analysis: insights into virulence, host adaptation and evolution.}, journal = {Nature reviews. Genetics}, volume = {1}, number = {1}, pages = {30-39}, doi = {10.1038/35049551}, pmid = {11262871}, issn = {1471-0056}, mesh = {Adaptation, Physiological/*genetics ; Antigenic Variation ; Bacteria/genetics/immunology/pathogenicity ; *Evolution, Molecular ; *Genome, Bacterial ; Virulence/*genetics ; }, abstract = {Genome analysis of microbial pathogens has provided unique insights into their virulence, host adaptation and evolution. Common themes have emerged, including lateral gene transfer among enteric pathogens, genome decay among obligate intracellular pathogens and antigenic variation among mucosal pathogens. The advent of post-genomic approaches and the sequencing of the human genome will enable scientists to investigate the complex and dynamic interplay between host and pathogen. This wealth of information will catalyse the development of new intervention strategies to reduce the burden of microbial-related disease.}, }
@article {pmid11255509, year = {2001}, author = {Dincturk, HB}, title = {Glutamate synthase: an archaeal horizontal gene transfer?.}, journal = {Journal of biosciences}, volume = {26}, number = {1}, pages = {13-14}, pmid = {11255509}, issn = {0250-5991}, mesh = {Archaea/enzymology/*genetics ; *Gene Transfer, Horizontal ; Glutamate Synthase/*genetics ; Open Reading Frames ; Species Specificity ; }, }
@article {pmid11254622, year = {2001}, author = {Masignani, V and Giuliani, MM and Tettelin, H and Comanducci, M and Rappuoli, R and Scarlato, V}, title = {Mu-like Prophage in serogroup B Neisseria meningitidis coding for surface-exposed antigens.}, journal = {Infection and immunity}, volume = {69}, number = {4}, pages = {2580-2588}, pmid = {11254622}, issn = {0019-9567}, mesh = {ATP-Binding Cassette Transporters/genetics ; Animals ; Antigens, Bacterial/*genetics ; Antigens, Surface/genetics ; Bacteriophage mu/*genetics ; Conserved Sequence ; Gene Transfer, Horizontal ; Haemophilus influenzae/genetics/virology ; Mice ; Neisseria meningitidis/*genetics/immunology/*virology ; Open Reading Frames ; Proviruses/*genetics ; Serotyping ; }, abstract = {Sequence analysis of the genome of Neisseria meningititdis serogroup B revealed the presence of an approximately 35-kb region inserted within a putative gene coding for an ABC-type transporter. The region contains 46 open reading frames, 29 of which are colinear and homologous to the genes of Escherichia coli Mu phage. Two prophages with similar organizations were also found in serogroup A meningococcus, and one was found in Haemophilus influenzae. Early and late phage functions are well preserved in this family of Mu-like prophages. Several regions of atypical nucleotide content were identified. These likely represent genes acquired by horizontal transfer. Three of the acquired genes are shown to code for surface-associated antigens, and the encoded proteins are able to induce bactericidal antibodies.}, }
@article {pmid11254610, year = {2001}, author = {Hakenbeck, R and Balmelle, N and Weber, B and Gardès, C and Keck, W and de Saizieu, A}, title = {Mosaic genes and mosaic chromosomes: intra- and interspecies genomic variation of Streptococcus pneumoniae.}, journal = {Infection and immunity}, volume = {69}, number = {4}, pages = {2477-2486}, pmid = {11254610}, issn = {0019-9567}, mesh = {Alleles ; Base Sequence ; *Chromosomes, Bacterial ; Drug Resistance, Microbial ; Genetic Variation ; *Genome, Bacterial ; Humans ; Molecular Sequence Data ; Mosaicism ; Streptococcus pneumoniae/drug effects/*genetics ; Trimethoprim/pharmacology ; }, abstract = {Streptococcus pneumoniae remains a major causative agent of serious human diseases. The worldwide increase of antibiotic resistant strains revealed the importance of horizontal gene transfer in this pathogen, a scenario that results in the modulation of the species-specific gene pool. We investigated genomic variation in 20 S. pneumoniae isolates representing major antibiotic-resistant clones and 10 different capsular serotypes. Variation was scored as decreased hybridization signals visualized on a high-density oligonucleotide array representing 1,968 genes of the type 4 reference strain KNR.7/87. Up to 10% of the genes appeared altered between individual isolates and the reference strain; variability within clones was below 2.1%. Ten gene clusters covering 160 kb account for half of the variable genes. Most of them are associated with transposases and are assumed to be part of a flexible gene pool within the bacterial population; other variable loci include mosaic genes encoding antibiotic resistance determinants and gene clusters related to bacteriocin production. Genomic comparison between S. pneumoniae and commensal Streptococcus mitis and Streptococcus oralis strains indicates distinct antigenic profiles and suggests a smooth transition between these species, supporting the validity of the microarray system as an epidemiological and diagnostic tool.}, }
@article {pmid11253205, year = {2001}, author = {Vogel, G}, title = {Transgenic animals. Infant monkey carries jellyfish gene.}, journal = {Science (New York, N.Y.)}, volume = {291}, number = {5502}, pages = {226}, doi = {10.1126/science.291.5502.226a}, pmid = {11253205}, issn = {0036-8075}, mesh = {Animals ; *Animals, Genetically Modified ; Embryo Transfer ; Female ; Gene Expression ; Gene Transfer Techniques ; Gene Transfer, Horizontal ; Green Fluorescent Proteins ; Luminescent Proteins/*genetics ; Macaca mulatta/*genetics ; Male ; Pregnancy ; Sperm Injections, Intracytoplasmic ; }, }
@article {pmid11251800, year = {2001}, author = {Sandström, JP and Russell, JA and White, JP and Moran, NA}, title = {Independent origins and horizontal transfer of bacterial symbionts of aphids.}, journal = {Molecular ecology}, volume = {10}, number = {1}, pages = {217-228}, doi = {10.1046/j.1365-294x.2001.01189.x}, pmid = {11251800}, issn = {0962-1083}, mesh = {Animals ; Aphids/genetics/*microbiology ; Bacteriophages/genetics/metabolism ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Enterobacteriaceae/*genetics/ultrastructure ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; *Sequence Analysis, DNA ; Symbiosis/*physiology ; }, abstract = {Many insect groups have obligate associations with primary endosymbionts: mutualistic bacteria that are maternally transmitted and derived from an ancient infection. Often, the same insects are hosts to 'secondary' bacterial symbionts which are maternally transmitted but relatively labile within host lineages. To explore the dynamics of secondary symbiont associations in aphids, we characterized bacteria infecting 15 species of macrosiphine aphids using DNA sequencing, diagnostic polymerase chain reaction (PCR), diagnostic restriction digests, phylogenetic analyses, and electron microscopy to examine aphids from nature and from laboratory colonies. Three types of bacteria besides Buchnera were found repeatedly; all three fall within the Enterobacteriaceae. The R-type has a 16S rDNA less than 0.1% different from that of the secondary symbiont previously reported from Acyrthosiphon pisum and is related to Serratia species. The T-type includes a symbiont previously reported from a whitefly; the U-type comprises a new cluster near the T-type. The T-type was found in every one of 40 Uroleucon ambrosiae clones collected throughout the United States. In contrast, A. pisum individuals were infected by any combination of the three symbiont types. Secondary symbionts were maternally transmitted for 11 months within laboratory-reared A. pisum clones and were present in sexually produced eggs. PCR screens for a bacteriophage, APSE-1, indicated its presence in both A. pisum and U. ambrosiae containing secondary symbionts. Electron microscopy of R-type and T-type bacteria in A. pisum and in U. ambrosiae revealed rod-shaped organisms that attain extremely high densities within a few bacteriocytes.}, }
@article {pmid11250033, year = {2001}, author = {Gressel, J}, title = {Potential failsafe mechanisms against the spread and introgression of transgenic hypervirulent biocontrol fungi.}, journal = {Trends in biotechnology}, volume = {19}, number = {4}, pages = {149-154}, doi = {10.1016/s0167-7799(00)01550-x}, pmid = {11250033}, issn = {0167-7799}, mesh = {Fungi/*genetics/physiology ; Gene Transfer, Horizontal ; Host-Parasite Interactions ; Pest Control, Biological/*methods ; Recombination, Genetic ; *Risk ; Risk Assessment ; *Transgenes ; }, abstract = {Microbial biocontrol agents are typically inefficient owing to the evolutionary necessity to be in balance with their hosts to survive. If transgenetically rendered hypervirulent, however, they could be competitive alternatives to pesticides. Potential means are delineated to prevent, contain or mitigate uncontrollable spread of hypervirulent biocontrol organisms, mutations that increase their host range, and the sexual or asexual introgression of hypervirulence genes into pathogens of other organisms. The use of asporogenic deletion mutants as a platform for generating transgenic hypervirulent biopesticides would prevent such spread. Hypervirulence genes flanked with available 'transgenetic mitigator' (TM) genes (genes that are neutral or positive to the biocontrol agent but deleterious to recombinants) would decrease virulence to non-target species.}, }
@article {pmid11248392, year = {2001}, author = {de Lipthay, JR and Barkay, T and Sørensen, SJ}, title = {Enhanced degradation of phenoxyacetic acid in soil by horizontal transfer of the tfdA gene encoding a 2,4-dichlorophenoxyacetic acid dioxygenase.}, journal = {FEMS microbiology ecology}, volume = {35}, number = {1}, pages = {75-84}, doi = {10.1111/j.1574-6941.2001.tb00790.x}, pmid = {11248392}, issn = {1574-6941}, abstract = {Few studies have investigated the possible impact of in situ gene transfer on the degradation of xenobiotic compounds in natural environments. In this work we showed that horizontal transfer of the tfdA gene, carried on plasmid pRO103, to phenol degrading recipient strains significantly increased the degradation rate of phenoxyacetic acid in sterile and non-sterile soil microcosms. The tfdA gene encodes a 2,4-dichlorophenoxyacetic acid/2-oxoglutarate dioxygenase and by complementation with the phenol degradation pathway an expanded catabolic substrate range, now including phenoxyacetic acid, is evolved. Presence of selective pressure had a positive effect on the emergence of transconjugants. However, even in the absence of phenoxyacetic acid transconjugant populations were detected and were kept at a constant level throughout the experimental period. The residuesphere (interface between decaying plant material and soil matrix) of dry leaves of barley was shown to be a hot-spot for gene transfer and presence of barley straw increased the conjugation frequencies in soil microcosms to the same extent as presence of organic nutrients. The results of this study indicate that dissemination of catabolic plasmids is a possible mechanism of genetic adaptation to degradation of xenobiotic compounds in natural environments, and that complementation of catabolic pathways possibly plays an important role in the evolution of new degradative capabilities. The application of horizontal gene transfer as a possible tool in bioremediation of contaminated sites is discussed.}, }
@article {pmid11245167, year = {2001}, author = {Dhar, A and Gupta, S and Sharma, YD}, title = {Host-like molecules in human malarial parasites.}, journal = {FEBS letters}, volume = {491}, number = {1-2}, pages = {166-167}, doi = {10.1016/s0014-5793(01)02155-x}, pmid = {11245167}, issn = {0014-5793}, mesh = {*Alu Elements ; Animals ; Artifacts ; DNA, Protozoan/analysis ; *Gene Transfer, Horizontal ; Genome, Human ; *Genome, Protozoan ; Humans ; Plasmodium falciparum/*genetics ; Plasmodium vivax/*genetics ; }, }
@article {pmid11245166, year = {2001}, author = {Deitsch, KW and Carlton, JM and Wootton, JC and Wellems, TE}, title = {Host sequences in Plasmodium falciparum and Plasmodium vivax genomic DNA: horizontal transfer or contamination artifact?.}, journal = {FEBS letters}, volume = {491}, number = {1-2}, pages = {164-165}, doi = {10.1016/s0014-5793(01)02154-8}, pmid = {11245166}, issn = {0014-5793}, mesh = {*Alu Elements ; Animals ; *Antigens, Protozoan ; Artifacts ; Blotting, Southern ; DNA, Protozoan/*analysis ; Databases, Factual ; Electrophoresis, Gel, Pulsed-Field ; *Gene Transfer, Horizontal ; Genome, Human ; *Genome, Protozoan ; Humans ; Membrane Proteins/genetics ; Plasmodium falciparum/*genetics ; Plasmodium vivax/*genetics ; Polymerase Chain Reaction ; Protozoan Proteins/genetics ; Sequence Analysis, DNA ; }, }
@article {pmid11244294, year = {2001}, author = {Bolognani, F and Goya, RG}, title = {Gene therapy in the neuroendocrine system: its implementation in experimental models using viral vectors.}, journal = {Neuroendocrinology}, volume = {73}, number = {2}, pages = {75-83}, doi = {10.1159/000054623}, pmid = {11244294}, issn = {0028-3835}, mesh = {Adenoviridae/genetics ; Animals ; Arginine Vasopressin/genetics ; Diabetes Insipidus/genetics/therapy ; *Disease Models, Animal ; Gene Transfer, Horizontal ; Genes, Retinoblastoma/genetics ; *Genetic Therapy ; *Genetic Vectors ; Herpesvirus 1, Human/genetics ; Humans ; Hypothalamic Diseases/genetics/therapy ; *Neurosecretory Systems ; Pituitary Neoplasms/genetics/therapy ; Thymidine Kinase/genetics ; }, abstract = {Gene therapy, the transfer of genetic material for therapeutic purposes, has undergone an explosive development in the last few years. Within this context, development of gene therapy approaches for the neuroendocrine system, while incipient, has already generated a core of results which emerge as a promising area of research in neuroendocrinology. The present review presents a brief description of the viral vector-based gene delivery systems being currently used in neuroendocrinology, namely the adenoviral and herpes simplex type-1 (HSV-1)-derived vector systems, as well as an updated account of neuroendocrine pathologies for which gene therapy approaches in animal models are being implemented is provided. Current research efforts include treatment of experimental pituitary tumors by adenoviral vector-mediated transfer of the suicide gene for the HSV-1 thymidine kinase, which converts the prodrug ganciclovir into a toxic metabolite. An adenoviral vector encoding the human retinoblastoma suppressor oncogene has also been successfully used to rescue the phenotype of spontaneous pituitary tumors of the pars intermedia in mice. At the hypothalamic level, an adenovirus harboring the cDNA for arginine vasopressin has been used in Brattleboro rats to correct diabetes insipidus for several weeks. The last part of the review outlines the potential of gene therapy to correct age-associated neurodegenerative processes at the neuroendocrine level. Although effective implementation of gene therapy strategies still faces significant technical obstacles, these are likely to be progressively overcome as gene delivery systems are being improved.}, }
@article {pmid11244070, year = {2001}, author = {Billi, D and Friedmann, EI and Helm, RF and Potts, M}, title = {Gene transfer to the desiccation-tolerant cyanobacterium Chroococcidiopsis.}, journal = {Journal of bacteriology}, volume = {183}, number = {7}, pages = {2298-2305}, pmid = {11244070}, issn = {0021-9193}, mesh = {Base Sequence ; Conjugation, Genetic ; Cyanobacteria/classification/*genetics ; Electroporation ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Transformation, Bacterial ; }, abstract = {The coccoid cyanobacterium Chroococcidiopsis dominates microbial communities in the most extreme arid hot and cold deserts. These communities withstand constraints that result from multiple cycles of drying and wetting and/or prolonged desiccation, through mechanisms which remain poorly understood. Here we describe the first system for genetic manipulation of Chroococcidiopsis. Plasmids pDUCA7 and pRL489, based on the pDU1 replicon of Nostoc sp. strain PCC 7524, were transferred to different isolates of Chroococcidiopsis via conjugation and electroporation. This report provides the first evidence that pDU1 replicons can be maintained in cyanobacteria other than Nostoc and Anabaena. Following conjugation, both plasmids replicated in Chroococcidiopsis sp. strains 029, 057, and 123 but not in strains 171 and 584. Both plasmids were electroporated into strains 029 and 123 but not into strains 057, 171, and 584. Expression of P(psbA)-luxAB on pRL489 was visualized through in vivo luminescence. Efficiencies of conjugative transfer for pDUCA7 and pRL489 into Chroococcidiopsis sp. strain 029 were approximately 10(-2) and 10(-4) transconjugants per recipient cell, respectively. Conjugative transfer occurred with a lower efficiency into strains 057 and 123. Electrotransformation efficiencies of about 10(-4) electrotransformants per recipient cell were achieved with strains 029 and 123, using either pDUCA7 or pRL489. Extracellular deoxyribonucleases were associated with each of the five strains. Phylogenetic analysis, based upon the V6 to V8 variable regions of 16S rRNA, suggests that desert strains 057, 123, 171, and 029 are distinct from the type species strain Chroococcidiopsis thermalis PCC 7203. The high efficiency of conjugative transfer of Chroococcidiopsis sp. strain 029, from the Negev Desert, Israel, makes this a suitable experimental strain for genetic studies on desiccation tolerance.}, }
@article {pmid11244052, year = {2001}, author = {Le Dantec, C and Winter, N and Gicquel, B and Vincent, V and Picardeau, M}, title = {Genomic sequence and transcriptional analysis of a 23-kilobase mycobacterial linear plasmid: evidence for horizontal transfer and identification of plasmid maintenance systems.}, journal = {Journal of bacteriology}, volume = {183}, number = {7}, pages = {2157-2164}, pmid = {11244052}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; Base Sequence ; Chromosome Mapping ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Mycobacterium/*genetics ; Open Reading Frames ; Operon ; *Plasmids ; *Transcription, Genetic ; }, abstract = {Linear plasmids were unknown in mycobacteria until recently. Here, we report the complete nucleotide sequence of 23-kb linear plasmid pCLP from Mycobacterium celatum, an opportunistic pathogen. The sequence of pCLP revealed at least 19 putative open reading frames (ORFs). Expression of pCLP genes in exponential-phase cultures was determined by reverse transcriptase PCR (RT-PCR). Twelve ORFs were expressed, whereas no transcription of the 7 other ORFs of pCLP was detected. Five of the 12 transcribed ORFs detected by RT-PCR are of unknown function. Sequence analysis revealed similar loci in both M. celatum pCLP and the Mycobacterium tuberculosis chromosome, including transposase-related sequences. This result suggests horizontal transfer between these two organisms. pCLP also contains ORFs that are similar to genes of bacterial circular plasmids involved in partition (par operon) and postsegregational (pem operon) mechanisms. Functional analysis of these ORFs suggests that they probably carry out similar maintenance roles in pCLP.}, }
@article {pmid11243926, year = {2001}, author = {Brocchieri, L}, title = {Phylogenetic inferences from molecular sequences: review and critique.}, journal = {Theoretical population biology}, volume = {59}, number = {1}, pages = {27-40}, doi = {10.1006/tpbi.2000.1485}, pmid = {11243926}, issn = {0040-5809}, support = {2R01HG00335-09/HG/NHGRI NIH HHS/United States ; 5R01GM10452-33/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bias ; Biological Evolution ; Data Interpretation, Statistical ; Gene Transfer, Horizontal/genetics ; Humans ; Models, Genetic ; Mutation/genetics ; Phenotype ; *Phylogeny ; Reproducibility of Results ; Sensitivity and Specificity ; Sequence Alignment ; *Sequence Analysis, DNA/methods/standards ; *Sequence Analysis, Protein/methods/standards ; *Sequence Analysis, RNA/methods/standards ; }, abstract = {Conflicting results often accompany phylogenetic analyses of RNA, DNA, or protein sequences across diverse species. Causes contributing to these conflicts relate to ambiguities in identifying homologous characters of alignments, sensitivity of tree-making methods to unequal evolutionary rates, biases in species sampling, unrecognized paralogy, functional differentiation, loss of phylogenetic informational content due to long branches or fast evolution, and difficulties with the assumptions and approximations used to infer phylogenetic relationships. Attempts to surmount these conflicts by averaging over many proteins are problematic due to inherent biases of selected families, lack of signal in others, and events of lateral transfer, fusion, and/or chimerism. The process of assessing reliability of the results using the bootstrap method is strewn with obstacles because of lack of independence and inhomogeneity in the molecular data. Problems inherent to the three major procedures for developing phylogenetic trees--parsimony, likelihood, distance--are reviewed. Special attention is given to the problem of inferring evolutionary distances from patterns of similarity among sequences. The difficulties encountered by methods of phylogenetic reconstructions based on the analysis of divergent sequence families make new methods based on the analysis of complete genomes reasonable alternatives. Several of these are considered, including the signature sequences of Gupta and associates, the study of genome profiles, and the genomic signature set forth by Karlin and colleagues.}, }
@article {pmid11238985, year = {2001}, author = {Makarova, KS and Aravind, L and Wolf, YI and Tatusov, RL and Minton, KW and Koonin, EV and Daly, MJ}, title = {Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {65}, number = {1}, pages = {44-79}, pmid = {11238985}, issn = {1092-2172}, support = {5R01-GM39933-09/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Biological Evolution ; Carbohydrate Metabolism ; DNA Damage/*radiation effects ; DNA Repair/physiology ; DNA Replication ; Energy Metabolism ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomics/methods ; Gram-Positive Cocci/*genetics/radiation effects ; Molecular Sequence Data ; Protein Biosynthesis ; Signal Transduction ; }, abstract = {The bacterium Deinococcus radiodurans shows remarkable resistance to a range of damage caused by ionizing radiation, desiccation, UV radiation, oxidizing agents, and electrophilic mutagens. D. radiodurans is best known for its extreme resistance to ionizing radiation; not only can it grow continuously in the presence of chronic radiation (6 kilorads/h), but also it can survive acute exposures to gamma radiation exceeding 1,500 kilorads without dying or undergoing induced mutation. These characteristics were the impetus for sequencing the genome of D. radiodurans and the ongoing development of its use for bioremediation of radioactive wastes. Although it is known that these multiple resistance phenotypes stem from efficient DNA repair processes, the mechanisms underlying these extraordinary repair capabilities remain poorly understood. In this work we present an extensive comparative sequence analysis of the Deinococcus genome. Deinococcus is the first representative with a completely sequenced genome from a distinct bacterial lineage of extremophiles, the Thermus-Deinococcus group. Phylogenetic tree analysis, combined with the identification of several synapomorphies between Thermus and Deinococcus, supports the hypothesis that it is an ancient group with no clear affinities to any of the other known bacterial lineages. Distinctive features of the Deinococcus genome as well as features shared with other free-living bacteria were revealed by comparison of its proteome to the collection of clusters of orthologous groups of proteins. Analysis of paralogs in Deinococcus has revealed several unique protein families. In addition, specific expansions of several other families including phosphatases, proteases, acyltransferases, and Nudix family pyrophosphohydrolases were detected. Genes that potentially affect DNA repair and recombination and stress responses were investigated in detail. Some proteins appear to have been horizontally transferred from eukaryotes and are not present in other bacteria. For example, three proteins homologous to plant desiccation resistance proteins were identified, and these are particularly interesting because of the correlation between desiccation and radiation resistance. Compared to other bacteria, the D. radiodurans genome is enriched in repetitive sequences, namely, IS-like transposons and small intergenic repeats. In combination, these observations suggest that several different biological mechanisms contribute to the multiple DNA repair-dependent phenotypes of this organism.}, }
@article {pmid11238863, year = {2001}, author = {Berkowitz, R and Ilves, H and Lin, WY and Eckert, K and Coward, A and Tamaki, S and Veres, G and Plavec, I}, title = {Construction and molecular analysis of gene transfer systems derived from bovine immunodeficiency virus.}, journal = {Journal of virology}, volume = {75}, number = {7}, pages = {3371-3382}, pmid = {11238863}, issn = {0022-538X}, mesh = {Adult ; Animals ; Cattle ; Cell Line ; *Gene Transfer, Horizontal ; *Genetic Therapy ; Genetic Vectors ; HIV-1/genetics ; Humans ; Immunodeficiency Virus, Bovine/*genetics ; Terminal Repeat Sequences ; Virus Assembly ; }, abstract = {Because lentiviruses are able to infect nondividing cells, these viruses might be utilized in gene therapy applications where the target cell does not divide. However, it has been suggested that the introduction of primate lentivirus sequences, particularly those of human immunodeficiency virus, into human cells may pose a health risk for the patient. To avoid this concern, we have constructed gene transfer systems based on a nonprimate lentivirus, bovine immunodeficiency virus. A panel of vectors and packaging constructs was generated and analyzed in a transient expression system for virion production and maturation, vector expression and encapsidation, and envelope protein pseudotyping. Virion preparations were also analyzed for transduction efficiency in a panel of human and nonhuman primary cells and immortalized cell lines. The virion preparations transduced most of the target cell types, with efficiencies up to 90% and with titers of unconcentrated virus up to 5 x 10(5) infectious doses/ml. In addition, infection of nondividing human cells, including unstimulated hematopoietic stem cells and irradiated endothelial cells, was observed.}, }
@article {pmid11235982, year = {2000}, author = {Le Roy, I and Pothion, S and Mortaud, S and Chabert, C and Nicolas, L and Cherfouh, A and Roubertoux, PL}, title = {Loss of aggression, after transfer onto a C57BL/6J background, in mice carrying a targeted disruption of the neuronal nitric oxide synthase gene.}, journal = {Behavior genetics}, volume = {30}, number = {5}, pages = {367-373}, doi = {10.1023/a:1002796404278}, pmid = {11235982}, issn = {0001-8244}, mesh = {Aggression/*physiology ; Agonistic Behavior/physiology ; Alleles ; Animals ; Crosses, Genetic ; Female ; Gene Transfer, Horizontal/*genetics ; Homozygote ; Male ; Mice ; Mice, Inbred C57BL/*genetics ; Neurons/enzymology ; Nitric Oxide Synthase/*genetics ; }, abstract = {Phenotypic differences among mice with disrupted genes and those with wild-type alleles have not provided the necessary evidence for desired gene/phenotype correlations. These differences could be due to "passenger genes" from the donor 129 strains that are used to produce stem cells. Three variations of attack behavior were measured, using mice carrying a disruption of the neural nitric oxide synthase gene. In the first population, the disrupted gene had been maintained on a mixed background including C57BL/6J and 129 alleles. We have developed a second population in which the disrupted gene was transferred onto a C57BL/6J background during five backcross generations. On the mixed C57BL/6J-129 background, mice homozygous for disrupted Nos1 alleles attacked more frequently, had shorter attack latencies, and presented a greater number of attacks than mice carrying nondisrupted alleles. On the C57BL/6J background, no significant difference persisted between the carriers of the disrupted gene and their noncarrier siblings. The noncarriers on the mixed C57BL/6J-129 background, and the carriers or noncarriers on the C57BL/6J background, did not differ from C57BL/6J. The frequency of attacking males was identical in the homozygous carriers of the disrupted gene, in the mixed C57BL/6J-129 background, and in the 129/SvPas, which approximates the 129/SvJae strain from which the stem cells were derived to produce the disrupted Nos1 gene. These results suggest that Nos1 disruption was not implicated in attack behavior. A possible passenger-gene effect from the 129 donor strain is discussed.}, }
@article {pmid11234002, year = {2001}, author = {Cole, ST and Eiglmeier, K and Parkhill, J and James, KD and Thomson, NR and Wheeler, PR and Honoré, N and Garnier, T and Churcher, C and Harris, D and Mungall, K and Basham, D and Brown, D and Chillingworth, T and Connor, R and Davies, RM and Devlin, K and Duthoy, S and Feltwell, T and Fraser, A and Hamlin, N and Holroyd, S and Hornsby, T and Jagels, K and Lacroix, C and Maclean, J and Moule, S and Murphy, L and Oliver, K and Quail, MA and Rajandream, MA and Rutherford, KM and Rutter, S and Seeger, K and Simon, S and Simmonds, M and Skelton, J and Squares, R and Squares, S and Stevens, K and Taylor, K and Whitehead, S and Woodward, JR and Barrell, BG}, title = {Massive gene decay in the leprosy bacillus.}, journal = {Nature}, volume = {409}, number = {6823}, pages = {1007-1011}, doi = {10.1038/35059006}, pmid = {11234002}, issn = {0028-0836}, mesh = {Animals ; Armadillos ; DNA, Bacterial ; Energy Metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; Leprosy/microbiology ; Molecular Sequence Data ; Multigene Family ; Mycobacterium leprae/*genetics/metabolism ; Sequence Analysis, DNA ; }, abstract = {Leprosy, a chronic human neurological disease, results from infection with the obligate intracellular pathogen Mycobacterium leprae, a close relative of the tubercle bacillus. Mycobacterium leprae has the longest doubling time of all known bacteria and has thwarted every effort at culture in the laboratory. Comparing the 3.27-megabase (Mb) genome sequence of an armadillo-derived Indian isolate of the leprosy bacillus with that of Mycobacterium tuberculosis (4.41 Mb) provides clear explanations for these properties and reveals an extreme case of reductive evolution. Less than half of the genome contains functional genes but pseudogenes, with intact counterparts in M. tuberculosis, abound. Genome downsizing and the current mosaic arrangement appear to have resulted from extensive recombination events between dispersed repetitive sequences. Gene deletion and decay have eliminated many important metabolic activities including siderophore production, part of the oxidative and most of the microaerophilic and anaerobic respiratory chains, and numerous catabolic systems and their regulatory circuits.}, }
@article {pmid11233696, year = {2001}, author = {Sinkovics, JG}, title = {The place of viruses in the "tree of life".}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {48}, number = {1}, pages = {115-127}, doi = {10.1556/amicr.48.2001.1.11}, pmid = {11233696}, issn = {1217-8950}, mesh = {Animals ; Archaea/genetics/physiology ; Bacteria/genetics ; Bacterial Physiological Phenomena ; *Biological Evolution ; Eukaryotic Cells/virology ; Gene Transfer, Horizontal ; Humans ; *Membrane Fusion ; RNA, Catalytic/metabolism ; Retroelements ; Spheroplasts/physiology ; Symbiosis ; Viroids/genetics/physiology ; *Virus Physiological Phenomena ; Viruses/genetics ; }, abstract = {Ribozymal entry into vesicle containing autocatalytically replicating oligopeptides engendered RNA proliferation and enzyme synthesis within units whose RNA genomes derived from ancestors of viroids. There is good reason to consider the coexistence of proto- or spheroplastic forms of ancient prokaryotes and archaeons. Predecessors of extant mycoplasmavirus L3 or archaeal fuselloviruses could induce cell fusions among these entities. The possibility that the first eukaryotic cells arose consequentially to virally mediated fusions of prokaryotic and archaeal proto- or spheroplasts is presented. Retrotransposons and endogenous retroviruses might have emerged in theropod dinosaurs when Aves evolved; and directed the development of syncytiotrophoblasts in the placentae of the first mammals. As viruses coevolved with their hosts descendants of ancient viruses diverged from one another. Certain phenotypical features could connect extant phages and eukaryotic viruses to common ancestors.}, }
@article {pmid11233187, year = {1999}, author = {Molin, M}, title = {BAGECO-6, Florence, 20-24 June 1999.}, journal = {Environmental microbiology}, volume = {1}, number = {4}, pages = {371-373}, doi = {10.1046/j.1462-2920.1999.00062.x}, pmid = {11233187}, issn = {1462-2912}, mesh = {*Bacteria/genetics/metabolism ; Biodegradation, Environmental ; *Ecosystem ; *Environmental Microbiology ; Gene Expression ; Gene Transfer, Horizontal ; Genetic Engineering ; Risk Assessment ; }, }
@article {pmid11233163, year = {2000}, author = {Torres, B and Jaenecke, S and Timmis, KN and García, JL and Díaz, E}, title = {A gene containment strategy based on a restriction-modification system.}, journal = {Environmental microbiology}, volume = {2}, number = {5}, pages = {555-563}, doi = {10.1046/j.1462-2920.2000.00138.x}, pmid = {11233163}, issn = {1462-2912}, mesh = {Base Sequence ; DNA Modification Methylases ; DNA, Bacterial/*genetics ; Deoxyribonuclease EcoRI ; *Ecosystem ; *Environmental Microbiology ; *Gene Transfer, Horizontal ; Genetic Markers ; Molecular Sequence Data ; Mutation ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {Engineering barriers to the spread of specific genes are of great interest both to increase the predictability of recombinant microorganisms used for environmental applications and to study the role of gene transfer in the adaptation of microbial communities to changing environments. We report here a new gene containment circuit based on a toxin-antidote pair that targets the cell DNA, i.e. the type II EcoRI restriction-modification system. The set-up involved linkage of the ecoRIR lethal gene encoding the EcoRI endonuclease (toxin) to the contained character in a plasmid and chromosomal insertion of the ecoRIM gene encoding the cognate EcoRI methylase (antidote) that protects the target DNA from restriction. Transfer of the contained character to a recipient cell lacking the antidote caused EcoRI-mediated chromosomal breaks, leading to cell death, thereby preventing gene spread. Using transformation and conjugation as mechanisms of DNA transfer and different environmentally relevant bacteria as recipients, we have shown that the potentially universal EcoRI-based containment system decreases gene transfer frequencies by more than four orders of magnitude. Analyses of the survivors escaping killing revealed a number of possible inactivation mechanisms.}, }
@article {pmid11230541, year = {2001}, author = {Koski, LB and Morton, RA and Golding, GB}, title = {Codon bias and base composition are poor indicators of horizontally transferred genes.}, journal = {Molecular biology and evolution}, volume = {18}, number = {3}, pages = {404-412}, doi = {10.1093/oxfordjournals.molbev.a003816}, pmid = {11230541}, issn = {0737-4038}, mesh = {*Codon ; Escherichia coli/genetics ; *Gene Transfer, Horizontal ; Likelihood Functions ; Open Reading Frames ; Phylogeny ; Salmonella typhi/genetics ; }, abstract = {Horizontal gene transfer is now recognized as an important mechanism of evolution. Several methods to detect horizontally transferred genes have been suggested. These methods are based on either nucleotide composition or the failure to find a similar gene in closely related species. Genes that evolve vertically between closely related species can be divided into those that retain homologous chromosomal positions (positional orthologs) and those that do not. By comparing open reading frames in the Escherichia coli and Salmonella typhi genomes, we identified 2,728 positional orthologs since these species split 100 MYA. A group of 1,144 novel E. coli genes were unusually diverged from their S. typhi counterparts. These novel genes included those that had been horizontally transferred into E. coli, as well as members of gene pairs that had been rearranged or deleted. Positional orthologs were used to investigate compositional methods of identifying horizontally transferred genes. A large number of E. coli genes with normal nucleotide composition have no apparent ortholog in S. typhi, and many genes of atypical composition do, in fact, have positional orthologs. A phylogenetic approach was employed to confirm selected examples of horizontal transmission among the novel groups of genes. Our analysis of 80 E. coli genes determined that a number of genes previously classified as horizontally transferred based on base composition and codon bias were native, and genes previously classified as native appeared to be horizontally transferred. Hence, atypical nucleotide composition alone is not a reliable indicator of horizontal transmission.}, }
@article {pmid11230537, year = {2001}, author = {Nesbo, CL and L'Haridon, S and Stetter, KO and Doolittle, WF}, title = {Phylogenetic analyses of two "archaeal" genes in thermotoga maritima reveal multiple transfers between archaea and bacteria.}, journal = {Molecular biology and evolution}, volume = {18}, number = {3}, pages = {362-375}, doi = {10.1093/oxfordjournals.molbev.a003812}, pmid = {11230537}, issn = {0737-4038}, mesh = {Bacteria/*genetics ; Base Sequence ; DNA Primers ; *Gene Transfer, Horizontal ; *Genes, Archaeal ; Likelihood Functions ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal/genetics ; Sequence Homology, Nucleic Acid ; Thermotoga maritima/*genetics ; }, abstract = {The genome sequence of Thermotoga maritima revealed that 24% of its open reading frames (ORFs) showed the highest similarity scores to archaeal genes in BLAST analyses. Here we screened 16 strains from the genus Thermotoga and other related Thermotogales for the occurrence of two of these "archaeal" genes: the gene encoding the large subunit of glutamate synthase (gltB) and the myo-inositol 1P synthase gene (ino1). Both genes were restricted to the Thermotoga species within the Thermotogales. The distribution of the two genes, along with results from phylogenetic analyses, showed that they were acquired from Archaea during the divergence of the Thermotogales. Database searches revealed that three other bacteria-Dehalococcoides ethenogenes, Sinorhizobium meliloti, and Clostridium difficile-possess archaeal-type gltBs, and the phylogenetic analyses confirmed at least two lateral gene transfer (LGT) events between Bacteria and Archaea. These LGT events were also strongly supported by gene structure data, as the three domains in bacterial-type gltB are homologous to three independent ORFs in Archaea and Bacteria with archaeal-type gltBs. The ino1 gene has a scattered distribution among Bacteria, and apart from the Thermotoga strains it is found only in Aquifex aeolicus, D. ethenogenes, and some high-G+C Gram-positive bacteria. Phylogenetic analysis of the ino1 sequences revealed three highly supported prokaryotic clades, all containing a mixture of archaeal and bacterial sequences, and suggested that all bacterial ino1 genes had been recruited from archaeal donors. The Thermotoga strains and A. aeolicus acquired this gene independently from different archaeal species. Although transfer of genes from hyperthermophilic Archaea may have facilitated the evolution of bacterial hyperthermophily, between-domain transfers also affect mesophilic species. For hyperthermophiles, we hypothesize that LGT may be as much a consequence as the cause of adaptation to hyperthermophily.}, }
@article {pmid11230450, year = {2001}, author = {Lee, WG and Jernigan, JA and Rasheed, JK and Anderson, GJ and Tenover, FC}, title = {Possible horizontal transfer of the vanB2 gene among genetically diverse strains of vancomycin-resistant Enterococcus faecium in a Korean hospital.}, journal = {Journal of clinical microbiology}, volume = {39}, number = {3}, pages = {1165-1168}, pmid = {11230450}, issn = {0095-1137}, mesh = {Adult ; Aged ; Bacterial Proteins/*genetics ; Electrophoresis, Gel, Pulsed-Field/methods ; Enterococcus faecium/*drug effects/genetics ; Female ; *Gene Transfer, Horizontal ; Gram-Positive Bacterial Infections/epidemiology/*microbiology ; Hospitals ; Humans ; Korea/epidemiology ; Male ; Molecular Sequence Data ; Polymerase Chain Reaction ; Vancomycin Resistance/*genetics ; }, abstract = {A total of 25 isolates of vanB-containing Enterococcus faecium were recovered from patients in a single Korean hospital over a 20-month period. There were two distinct vanB2 patterns among the 11 pulsed-field gel electrophoresis types; 17 contained the prototype vanB2 and 8 contained a novel vanB2 with a 177-bp deletion in vanY(B). Both vanB2 genes were transmissible in vitro at a mean frequency of 1.1 x 10(-8) transconjugants/donor. These results suggest the horizontal spread of vanB2 is occurring among genetically diverse strains of E. faecium in Korean hospitals.}, }
@article {pmid11230160, year = {2001}, author = {Wolf, YI and Rogozin, IB and Kondrashov, AS and Koonin, EV}, title = {Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context.}, journal = {Genome research}, volume = {11}, number = {3}, pages = {356-372}, doi = {10.1101/gr.gr-1619r}, pmid = {11230160}, issn = {1088-9051}, mesh = {Computational Biology/methods ; Conserved Sequence/genetics ; *Evolution, Molecular ; Gene Order/genetics ; Genes, Archaeal/*physiology ; Genes, Bacterial/*physiology ; *Genome, Archaeal ; *Genome, Bacterial ; Operon/genetics ; *Sequence Alignment ; Templates, Genetic ; }, abstract = {Gene order in prokaryotes is conserved to a much lesser extent than protein sequences. Only several operons, primarily those that code for physically interacting proteins, are conserved in all or most of the bacterial and archaeal genomes. Nevertheless, even the limited conservation of operon organization that is observed can provide valuable evolutionary and functional clues through multiple genome comparisons. A program for constructing gapped local alignments of conserved gene strings in two genomes was developed. The statistical significance of the local alignments was assessed using Monte Carlo simulations. Sets of local alignments were generated for all pairs of completely sequenced bacterial and archaeal genomes, and for each genome a template-anchored multiple alignment was constructed. In most pairwise genome comparisons, <10% of the genes in each genome belonged to conserved gene strings. When closely related pairs of species (i.e., two mycoplasmas) are excluded, the total coverage of genomes by conserved gene strings ranged from <5% for the cyanobacterium Synechocystis sp to 24% for the minimal genome of Mycoplasma genitalium, and 23% in Thermotoga maritima. The coverage of the archaeal genomes was only slightly lower than that of bacterial genomes. The majority of the conserved gene strings are known operons, with the ribosomal superoperon being the top-scoring string in most genome comparisons. However, in some of the bacterial-archaeal pairs, the superoperon is rearranged to the extent that other operons, primarily those subject to horizontal transfer, show the greatest level of conservation, such as the archaeal-type H+-ATPase operon or ABC-type transport cassettes. The level of gene order conservation among prokaryotic genomes was compared to the cooccurrence of genomes in clusters of orthologous genes (COGs) and to the conservation of protein sequences themselves. Only limited correlation was observed between these evolutionary variables. Gene order conservation shows a much lower variance than the cooccurrence of genomes in COGs, which indicates that intragenome homogenization via recombination occurs in evolution much faster than intergenome homogenization via horizontal gene transfer and lineage-specific gene loss. The potential of using template-anchored multiple-genome alignments for predicting functions of uncharacterized genes was quantitatively assessed. Functions were predicted or significantly clarified for approximately 90 COGs (approximately 4% of the total of 2414 analyzed COGs). The most significant predictions were obtained for the poorly characterized archaeal genomes; these include a previously uncharacterized restriction-modification system, a nuclease-helicase combination implicated in DNA repair, and the probable archaeal counterpart of the eukaryotic exosome. Multiple genome alignments are a resource for studies on operon rearrangement and disruption, which is central to our understanding of the evolution of prokaryotic genomes. Because of the rapid evolution of the gene order, the potential of genome alignment for prediction of gene functions is limited, but nevertheless, such predictions information significantly complements the results obtained through protein sequence and structure analysis.}, }
@article {pmid11229902, year = {2001}, author = {Madsen, SM and Mills, D and Djordjevic, G and Israelsen, H and Klaenhammer, TR}, title = {Analysis of the genetic switch and replication region of a P335-type bacteriophage with an obligate lytic lifestyle on Lactococcus lactis.}, journal = {Applied and environmental microbiology}, volume = {67}, number = {3}, pages = {1128-1139}, pmid = {11229902}, issn = {0099-2240}, mesh = {Amino Acid Sequence ; Base Sequence ; *DNA-Binding Proteins ; Gene Expression Regulation, Viral ; *Genes, Switch ; Genes, Viral ; Lactococcus lactis/*virology ; Lysogeny/genetics ; Molecular Sequence Data ; Mucoproteins/genetics/metabolism ; Promoter Regions, Genetic/genetics ; Replication Origin/*genetics ; Repressor Proteins/genetics/metabolism ; Sequence Analysis, DNA ; Siphoviridae/*genetics/*physiology ; Viral Proteins ; Viral Regulatory and Accessory Proteins ; }, abstract = {The DNA sequence of the replication module, part of the lysis module, and remnants of a lysogenic module from the lytic P335 species lactococcal bacteriophage phi31 was determined, and its regulatory elements were investigated. The identification of a characteristic genetic switch including two divergent promoters and two cognate repressor genes strongly indicates that phi31 was derived from a temperate bacteriophage. Regulation of the two early promoters was analyzed by primer extension and transcriptional promoter fusions to a lacLM reporter. The regulatory behavior of the promoter region differed significantly from the genetic responses of temperate Lactococcus lactis phages. The cro gene homologue regulates its own production and is an efficient repressor of cI gene expression. No detectable cI gene expression could be measured in the presence of cro. cI gene expression in the absence of cro exerted minor influences on the regulation of the two promoters within the genetic switch. Homology comparisons revealed a replication module which is most likely expressed from the promoter located upstream of the cro gene homologue. The replication module encoded genes with strong homology to helicases and primases found in several Streptococcus thermophilus phages. Downstream of the primase homologue, an AT-rich noncoding origin region was identified. The characteristics and location of this region and its ability to reduce the efficiency of plaquing of phi31 10(6)-fold when present at high copy number in trans provide evidence for identification of the phage origin of replication. Phage phi31 is an obligately lytic phage that was isolated from commercial dairy fermentation environments. Neither a phage attachment site nor an integrase gene, required to establish lysogeny, was identified, explaining its lytic lifestyle and suggesting its origin from a temperate phage ancestor. Several regions showing extensive DNA and protein homologies to different temperate phages of Lactococcus, Lactobacillus, and Streptococcus were also discovered, indicating the likely exchange of DNA cassettes through horizontal gene transfer in the dynamic ecological environment of dairy fermentations.}, }
@article {pmid11229899, year = {2001}, author = {Boon, N and Goris, J and De Vos, P and Verstraete, W and Top, EM}, title = {Genetic diversity among 3-chloroaniline- and aniline-degrading strains of the Comamonadaceae.}, journal = {Applied and environmental microbiology}, volume = {67}, number = {3}, pages = {1107-1115}, pmid = {11229899}, issn = {0099-2240}, mesh = {Aniline Compounds/*metabolism ; Bacterial Proteins/genetics/metabolism ; Betaproteobacteria/*classification/*genetics/metabolism ; Biodegradation, Environmental ; Blotting, Southern ; Conjugation, Genetic ; DNA Transposable Elements ; DNA, Bacterial/genetics ; Electrophoresis, Polyacrylamide Gel/methods ; Gene Transfer, Horizontal ; *Genetic Variation ; Glutamate-Ammonia Ligase/genetics/metabolism ; Molecular Sequence Data ; Plasmids/genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Transaminases/*genetics/metabolism ; }, abstract = {We examined the diversity of the plasmids and of the gene tdnQ, involved in the oxidative deamination of aniline, in five bacterial strains that are able to metabolize both aniline and 3-chloroaniline (3-CA). Three strains have been described and identified previously, i.e., Comamonas testosteroni I2 and Delftia acidovorans CA28 and BN3.1. Strains LME1 and B8c were isolated in this study from linuron-treated soil and from a wastewater treatment plant, respectively, and were both identified as D. acidovorans. Both Delftia and Comamonas belong to the family Comamonadaceae. All five strains possess a large plasmid of ca. 100 kb, but the plasmids from only four strains could be transferred to a recipient strain by selection on aniline or 3-CA as a sole source of carbon and/or nitrogen. Plasmid transfer experiments and Southern hybridization revealed that the plasmid of strain I2 was responsible for total aniline but not 3-CA degradation, while the plasmids of strains LME1 and B8c were responsible only for the oxidative deamination of aniline. Several transconjugant clones that had received the plasmid from strain CA28 showed different degradative capacities: all transconjugants could use aniline as a nitrogen source, while only some of the transconjugants could deaminate 3-CA. For all four plasmids, the IS1071 insertion sequence of Tn5271 was found to be located on a 1.4-kb restriction fragment, which also hybridized with the tdnQ probe. This result suggests the involvement of this insertion sequence element in the dissemination of aniline degradation genes in the environment. By use of specific primers for the tdnQ gene from Pseudomonas putida UCC22, the diversity of the PCR-amplified fragments in the five strains was examined by denaturing gradient gel electrophoresis (DGGE). With DGGE, three different clusters of the tdnQ fragment could be distinguished. Sequencing data showed that the tdnQ sequences of I2, LME1, B8c, and CA28 were very closely related, while the tdnQ sequences of BN3.1 and P. putida UCC22 were only about 83% identical to the other sequences. Northern hybridization revealed that the tdnQ gene is transcribed only in the presence of aniline and not when only 3-CA is present.}, }
@article {pmid11226586, year = {2001}, author = {Rujan, T and Martin, W}, title = {How many genes in Arabidopsis come from cyanobacteria? An estimate from 386 protein phylogenies.}, journal = {Trends in genetics : TIG}, volume = {17}, number = {3}, pages = {113-120}, doi = {10.1016/s0168-9525(00)02209-5}, pmid = {11226586}, issn = {0168-9525}, mesh = {Arabidopsis/*genetics ; Cyanobacteria/*genetics ; *Genes, Bacterial ; *Genes, Plant ; *Phylogeny ; }, abstract = {It is well known that chloroplasts and mitochondria donated many genes to nuclear chromosomes during evolution - but how many is "many"? A sample of 3961 Arabidopsis nuclear protein-coding genes was compared with the complete set of proteins from yeast and 17 reference prokaryotic genomes, including one cyanobacterium (the lineage from which plastids arose). The analysis of 386 phylogenetic trees distilled from these data suggests that between approximately 400 (1.6%) and approximately 2200 (9.2%) of Arabidopsis nuclear genes stem from cyanobacteria. The degree of conservation preserved in protein sequences in addition to lateral gene transfer between free-living prokaryotes pose substantial challenges to genome phylogenetics.}, }
@article {pmid11226267, year = {2001}, author = {Nei, M and Xu, P and Glazko, G}, title = {Estimation of divergence times from multiprotein sequences for a few mammalian species and several distantly related organisms.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {98}, number = {5}, pages = {2497-2502}, pmid = {11226267}, issn = {0027-8424}, support = {R01 GM020293/GM/NIGMS NIH HHS/United States ; GM-20293/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Evolution, Molecular ; Humans ; Mice ; Phylogeny ; Proteins/*genetics ; Rats ; }, abstract = {When many protein sequences are available for estimating the time of divergence between two species, it is customary to estimate the time for each protein separately and then use the average for all proteins as the final estimate. However, it can be shown that this estimate generally has an upward bias, and that an unbiased estimate is obtained by using distances based on concatenated sequences. We have shown that two concatenation-based distances, i.e., average gamma distance weighted with sequence length (d(2)) and multiprotein gamma distance (d(3)), generally give more satisfactory results than other concatenation-based distances. Using these two distance measures for 104 protein sequences, we estimated the time of divergence between mice and rats to be approximately 33 million years ago. Similarly, the time of divergence between humans and rodents was estimated to be approximately 96 million years ago. We also investigated the dependency of time estimates on statistical methods and various assumptions made by using sequence data from eubacteria, protists, plants, fungi, and animals. Our best estimates of the times of divergence between eubacteria and eukaryotes, between protists and other eukaryotes, and between plants, fungi, and animals were 3, 1.7, and 1.3 billion years ago, respectively. However, estimates of ancient divergence times are subject to a substantial amount of error caused by uncertainty of the molecular clock, horizontal gene transfer, errors in sequence alignments, etc.}, }
@article {pmid11222673, year = {2001}, author = {Scholl, D and Rogers, S and Adhya, S and Merril, CR}, title = {Bacteriophage K1-5 encodes two different tail fiber proteins, allowing it to infect and replicate on both K1 and K5 strains of Escherichia coli.}, journal = {Journal of virology}, volume = {75}, number = {6}, pages = {2509-2515}, pmid = {11222673}, issn = {0022-538X}, mesh = {*Antigens, Bacterial ; Antigens, Surface/*metabolism ; Bacterial Capsules ; Base Sequence ; Coliphages/genetics/isolation &amp; purification/*physiology ; Escherichia coli/metabolism/*virology ; Molecular Sequence Data ; Mutation ; Polysaccharides, Bacterial/*metabolism ; Sewage/virology ; Viral Tail Proteins/*genetics/metabolism ; Virion/metabolism ; Virus Replication ; }, abstract = {A virulent double-stranded DNA bacteriophage, Phi K1-5, has been isolated and found to be capable of infecting Escherichia coli strains that possess either the K1 or the K5 polysaccharide capsule. Electron micrographs show that the virion consists of a small icosohedral head with short tail spikes, similar to members of the Podoviridae family. DNA sequence analysis of the region encoding the tail fiber protein showed two open reading frames encoding previously characterized hydrolytic phage tail fiber proteins. The first is the K5 lyase protein gene of Phi K5, which allows this phage to specifically infect K5 E. coli strains. A second open reading frame encodes a protein almost identical in amino acid sequence to the N-acetylneuraminidase (endosialidase) protein of Phi K1E, which allows this phage to specifically infect K1 strains of E. coli. We provide experimental evidence that mature phage particles contain both tail fiber proteins, and mutational analysis indicates that each protein can be independently inactivated. A comparison of the tail gene regions of Phi K5, Phi K1E, and Phi K1-5 shows that the genes are arranged in a modular or cassette configuration and suggests that this family of phages can broaden host range by horizontal gene transfer.}, }
@article {pmid11214325, year = {2001}, author = {Gomis-Rüth, FX and Moncalián, G and Pérez-Luque, R and González, A and Cabezón, E and de la Cruz, F and Coll, M}, title = {The bacterial conjugation protein TrwB resembles ring helicases and F1-ATPase.}, journal = {Nature}, volume = {409}, number = {6820}, pages = {637-641}, doi = {10.1038/35054586}, pmid = {11214325}, issn = {0028-0836}, mesh = {Bacterial Proteins/chemistry ; *Conjugation, Genetic ; Crystallography, X-Ray ; DNA Helicases/chemistry ; DNA-Binding Proteins/*chemistry/physiology ; *Escherichia coli Proteins ; Models, Molecular ; Protein Conformation ; Proton-Translocating ATPases/chemistry ; }, abstract = {The transfer of DNA across membranes and between cells is a central biological process; however, its molecular mechanism remains unknown. In prokaryotes, trans-membrane passage by bacterial conjugation, is the main route for horizontal gene transfer. It is the means for rapid acquisition of new genetic information, including antibiotic resistance by pathogens. Trans-kingdom gene transfer from bacteria to plants or fungi and even bacterial sporulation are special cases of conjugation. An integral membrane DNA-binding protein, called TrwB in the Escherichia coli R388 conjugative system, is essential for the conjugation process. This large multimeric protein is responsible for recruiting the relaxosome DNA-protein complex, and participates in the transfer of a single DNA strand during cell mating. Here we report the three-dimensional structure of a soluble variant of TrwB. The molecule consists of two domains: a nucleotide-binding domain of alpha/beta topology, reminiscent of RecA and DNA ring helicases, and an all-alpha domain. Six equivalent protein monomers associate to form an almost spherical quaternary structure that is strikingly similar to F1-ATPase. A central channel, 20 A in width, traverses the hexamer.}, }
@article {pmid11212334, year = {1999}, author = {Mazel, D and Davies, J}, title = {Antibiotic resistance in microbes.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {56}, number = {9-10}, pages = {742-754}, doi = {10.1007/s000180050021}, pmid = {11212334}, issn = {1420-682X}, mesh = {Animals ; Bacteria/*genetics/pathogenicity ; Conjugation, Genetic/genetics ; Drug Resistance, Microbial/*genetics ; Ecology ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Humans ; Mutation/genetics ; Phylogeny ; Recombination, Genetic/genetics ; }, abstract = {The treatment of infectious disease is compromised by the development of antibiotic-resistant strains of microbial pathogens. A variety of biochemical processes are involved that may keep antibiotics out of the cell, alter the target of the drug, or disable the antibiotic. Studies have shown that resistance determinants arise by either of two genetic mechanisms: mutation and acquisition. Antibiotic resistance genes can be disseminated among bacterial populations by several processes, but principally by conjugation. Thus the overall problem of antibiotic resistance is one of genetic ecology and a better understanding of the contributing parameters is necessary to devise rational approaches to reduce the development and spread of antibiotic resistance and so avoid a critical situation in therapy--a return to a pre-antibiotic era.}, }
@article {pmid11212333, year = {1999}, author = {Boerlin, P}, title = {Evolution of virulence factors in Shiga-toxin-producing Escherichia coli.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {56}, number = {9-10}, pages = {735-741}, doi = {10.1007/s000180050020}, pmid = {11212333}, issn = {1420-682X}, mesh = {Escherichia coli/*genetics/metabolism/*pathogenicity/virology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Hemolysin Proteins/genetics ; Phylogeny ; Plasmids/genetics ; Recombination, Genetic/genetics ; Shiga Toxin/*genetics/*metabolism ; Virulence/genetics ; }, abstract = {The major demonstrated or putative virulence factors of Shiga-toxin-producing Escherichia coli (STEC) are the Shiga toxins, products of the locus of enterocyte effacement, and products encoded by the EHEC-hemolysin plasmid. Molecular analysis shows that STEC acquired the majority of these virulence factors by horizontal transfer of genetic material. In the case of Shiga toxins, the phages encoding them are probably responsible for this transfer. For the locus of enterocyte effacement, however, it is not clear how often this transfer took place and which parts of the locus were involved in this transfer. The large EHEC-hemolysin plasmid is clearly a mosaic structure, which arose from multiple recombination events with foreign DNA. Two lineages of this plasmid can be distinguished, one of which is associated with chromosomally encoded virulence factors. Despite the wealth of information available, further comparative studies are needed to decipher definitively the evolution of virulence in STEC.}, }
@article {pmid11212331, year = {1999}, author = {Ziebuhr, W and Ohlsen, K and Karch, H and Korhonen, T and Hacker, J}, title = {Evolution of bacterial pathogenesis.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {56}, number = {9-10}, pages = {719-728}, doi = {10.1007/s000180050018}, pmid = {11212331}, issn = {1420-682X}, mesh = {Animals ; Bacteria/*genetics/*pathogenicity/virology ; Bacteriophages/genetics ; Base Sequence ; DNA, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation/*genetics ; Humans ; Molecular Sequence Data ; Mutation/genetics ; Plasmids/genetics ; Recombination, Genetic/genetics ; Virulence/genetics ; }, abstract = {The evolution of bacteria is associated with continuous generation of novel genetic variants. The major driving forces in this process are point mutations, genetic rearrangements, and horizontal gene transfer. A large number of human and animal bacterial pathogens have evolved the capacity to produce virulence factors that are directly involved in infection and disease. Additionally, many bacteria express resistance traits against antibiotics. Both virulence factors and resistance determinants are subject to intrastrain genetic and phenotypic variation. They are often encoded on unstable DNA regions. Thus, they can be readily transferred to bacteria of the same species or even to non-related prokaryotes. This review article focuses on the main mechanisms of bacterial microevolution responsible for the rapid emergence of variants with novel virulence and resistance properties. In addition, processes of macroevolution are described with special emphasis on gene transfer and fixation of adaptive mutations in the genome of pathogens.}, }
@article {pmid11211261, year = {2001}, author = {Bush, RM and Everett, KD}, title = {Molecular evolution of the Chlamydiaceae.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {51}, number = {Pt 1}, pages = {203-220}, doi = {10.1099/00207713-51-1-203}, pmid = {11211261}, issn = {1466-5026}, mesh = {Animals ; Antigens, Surface/genetics ; Bacterial Proteins/genetics ; Cats ; Cattle ; Chlamydiaceae/*classification/*genetics/pathogenicity ; Chlamydiaceae Infections/microbiology ; Cricetinae ; *Evolution, Molecular ; Genes, Bacterial ; Guinea Pigs ; Humans ; Mice ; Molecular Sequence Data ; Operon ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Virulence ; }, abstract = {Phylogenetic analyses of surface antigens and other chlamydial proteins were used to reconstruct the evolution of the Chlamydiaceae. Trees for all five coding genes [the major outer-membrane protein (MOMP), GroEL chaperonin, KDO-transferase, small cysteine-rich lipoprotein and 60 kDa cysteine-rich protein] supported the current organization of the family Chlamydiaceae, which is based on ribosomal, biochemical, serological, ecological and DNA-DNA hybridization data. Genetic distances between some species were quite large, so phylogenies were evaluated for robustness by comparing analyses of both nucleotide and protein sequences using a variety of algorithms (neighbour-joining, maximum-likelihood, maximum-parsimony with bootstrapping, and quartet puzzling). Saturation plots identified areas of the trees in which factors other than relatedness may have determined branch attachments. All nine species were clearly differentiated by distinctness ratios calculated for each gene. The distribution of virulence traits such as host and tissue tropism were mapped onto the consensus phylogeny. Closely related species were no more likely to share virulence characters than were more distantly related species. This phylogenetically disjunct distribution of virulence traits could not be explained by lateral transfer of the genes we studied, since we found no evidence for lateral gene transfer above the species level. One interpretation of this observation is that when chlamydiae gain access to a new niche, such as a new host or tissue, significant adaptation ensues and the virulence phenotype of the new species reflects adaptation to its environment more strongly than it reflects its ancestry.}, }
@article {pmid11209082, year = {2001}, author = {Chan, AW and Chong, KY and Martinovich, C and Simerly, C and Schatten, G}, title = {Transgenic monkeys produced by retroviral gene transfer into mature oocytes.}, journal = {Science (New York, N.Y.)}, volume = {291}, number = {5502}, pages = {309-312}, doi = {10.1126/science.291.5502.309}, pmid = {11209082}, issn = {0036-8075}, mesh = {Animals ; *Animals, Genetically Modified ; Animals, Newborn ; Blotting, Southern ; Embryo Transfer ; Embryonic and Fetal Development ; Female ; Fluorescent Antibody Technique ; Gene Expression ; *Gene Transfer Techniques ; *Gene Transfer, Horizontal ; Genetic Vectors ; Green Fluorescent Proteins ; Luminescent Proteins/*genetics ; Macaca mulatta/*genetics ; Male ; Moloney murine leukemia virus/genetics ; Oocytes ; Polymerase Chain Reaction ; Pregnancy ; Pregnancy Outcome ; Sperm Injections, Intracytoplasmic ; Transgenes ; }, abstract = {Transgenic rhesus monkeys carrying the green fluorescent protein (GFP) gene were produced by injecting pseudotyped replication-defective retroviral vector into the perivitelline space of 224 mature rhesus oocytes, later fertilized by intracytoplasmic sperm injection. Of the three males born from 20 embryo transfers, one was transgenic when accessible tissues were assayed for transgene DNA and messenger RNA. All tissues that were studied from a fraternal set of twins, miscarried at 73 days, carried the transgene, as confirmed by Southern analyses, and the GFP transgene reporter was detected by both direct and indirect fluorescence imaging.}, }
@article {pmid11208781, year = {2001}, author = {Liang, X and Pham, XQ and Olson, MV and Lory, S}, title = {Identification of a genomic island present in the majority of pathogenic isolates of Pseudomonas aeruginosa.}, journal = {Journal of bacteriology}, volume = {183}, number = {3}, pages = {843-853}, pmid = {11208781}, issn = {0021-9193}, support = {P01 DK053369/DK/NIDDK NIH HHS/United States ; DK53369/DK/NIDDK NIH HHS/United States ; }, mesh = {Cloning, Molecular ; Genetic Variation ; Genome, Bacterial ; Genomic Library ; Molecular Sequence Data ; Nucleic Acid Hybridization/*methods ; *Oligonucleotide Array Sequence Analysis ; Pseudomonas aeruginosa/classification/*genetics/*pathogenicity ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Pseudomonas aeruginosa, a ubiquitous gram-negative bacterium, is capable of colonizing a wide range of environmental niches and can also cause serious infections in humans. In order to understand the genetic makeup of pathogenic P. aeruginosa strains, a method of differential hybridization of arrayed libraries of cloned DNA fragments was developed. An M13 library of DNA from strain X24509, isolated from a patient with a urinary tract infection, was screened using a DNA probe from P. aeruginosa strain PAO1. The genome of PAO1 has been recently sequenced and can be used as a reference for comparisons of genetic organization in different strains. M13 clones that did not react with a DNA probe from PAO1 carried X24509-specific inserts. When a similar array hybridization analysis with DNA probes from different strains was used, a set of M13 clones which carried sequences present in the majority of human P. aeruginosa isolates from a wide range of clinical sources was identified. The inserts of these clones were used to identify cosmids encompassing a contiguous 48.9-kb region of the X24509 chromosome called PAGI-1 (for "P. aeruginosa genomic island 1"). PAGI-1 is incorporated in the X24509 chromosome at a locus that shows a deletion of a 6,729-bp region present in strain PAO1. Survey of the incidence of PAGI-1 revealed that this island is present in 85% of the strains from clinical sources. Approximately half of the PAGI-1-carrying strains show the same deletion as X24509, while the remaining strains contain both the PAGI-1 sequences and the 6,729-bp PAO1 segment. Sequence analysis of PAGI-1 revealed that it contains 51 predicted open reading frames. Several of these genes encoded products with predictable function based on their sequence similarities to known genes, including insertion sequences, determinants of regulatory proteins, a number of dehydrogenase gene homologs, and two for proteins of implicated in detoxification of reactive oxygen species. It is very likely that PAGI-1 was acquired by a large number of P. aeruginosa isolates through horizontal gene transfer. The selection for its maintenance may be the consequence of expression of any one of the genes of unknown function or the genes which allow P. aeruginosa to survive under the conditions that generate reactive oxygen species. Alternatively, one or both of the transcriptional regulators encoded in PAGI-1 may control the expression of genes in the P. aeruginosa chromosome, which provides a selective advantage for strains that have acquired this genomic island.}, }
@article {pmid11206551, year = {2001}, author = {Perna, NT and Plunkett, G and Burland, V and Mau, B and Glasner, JD and Rose, DJ and Mayhew, GF and Evans, PS and Gregor, J and Kirkpatrick, HA and Pósfai, G and Hackett, J and Klink, S and Boutin, A and Shao, Y and Miller, L and Grotbeck, EJ and Davis, NW and Lim, A and Dimalanta, ET and Potamousis, KD and Apodaca, J and Anantharaman, TS and Lin, J and Yen, G and Schwartz, DC and Welch, RA and Blattner, FR}, title = {Genome sequence of enterohaemorrhagic Escherichia coli O157:H7.}, journal = {Nature}, volume = {409}, number = {6819}, pages = {529-533}, doi = {10.1038/35054089}, pmid = {11206551}, issn = {0028-0836}, support = {R01 DK063250/DK/NIDDK NIH HHS/United States ; }, mesh = {Base Sequence ; Chromosome Mapping ; Chromosomes, Bacterial ; Escherichia coli Infections/microbiology ; Escherichia coli O157/*genetics/pathogenicity ; Genetic Variation ; *Genome, Bacterial ; Humans ; Molecular Sequence Data ; Polymorphism, Genetic ; Sequence Analysis, DNA ; Species Specificity ; Virulence/genetics ; }, abstract = {The bacterium Escherichia coli O157:H7 is a worldwide threat to public health and has been implicated in many outbreaks of haemorrhagic colitis, some of which included fatalities caused by haemolytic uraemic syndrome. Close to 75,000 cases of O157:H7 infection are now estimated to occur annually in the United States. The severity of disease, the lack of effective treatment and the potential for large-scale outbreaks from contaminated food supplies have propelled intensive research on the pathogenesis and detection of E. coli O157:H7 (ref. 4). Here we have sequenced the genome of E. coli O157:H7 to identify candidate genes responsible for pathogenesis, to develop better methods of strain detection and to advance our understanding of the evolution of E. coli, through comparison with the genome of the non-pathogenic laboratory strain E. coli K-12 (ref. 5). We find that lateral gene transfer is far more extensive than previously anticipated. In fact, 1,387 new genes encoded in strain-specific clusters of diverse sizes were found in O157:H7. These include candidate virulence factors, alternative metabolic capacities, several prophages and other new functions--all of which could be targets for surveillance.}, }
@article {pmid11203236, year = {2000}, author = {Moreira, D and Rodríguez-Valera, F}, title = {A mitochondrial origin for eukaryotic C2H2 zinc finger regulators?.}, journal = {Trends in microbiology}, volume = {8}, number = {10}, pages = {448-450}, doi = {10.1016/s0966-842x(00)01850-3}, pmid = {11203236}, issn = {0966-842X}, mesh = {Bacteria/*genetics ; *Eukaryotic Cells ; Gene Expression Regulation ; *Gene Transfer, Horizontal ; Mitochondria/*genetics ; Phylogeny ; Proteins/chemistry/*genetics ; *Zinc Fingers ; }, }
@article {pmid11200433, year = {2000}, author = {Ronchel, MC and Ramos-Díaz, MA and Ramos, JL}, title = {Retrotransfer of DNA in the rhizosphere.}, journal = {Environmental microbiology}, volume = {2}, number = {3}, pages = {319-323}, doi = {10.1046/j.1462-2920.2000.00109.x}, pmid = {11200433}, issn = {1462-2912}, mesh = {Blotting, Southern ; Conjugation, Genetic/*genetics ; DNA, Bacterial/analysis/genetics ; Plant Roots/genetics/*microbiology ; Plasmids/genetics ; Pseudomonas/*genetics ; Zea mays/genetics/*microbiology ; }, abstract = {Retrotransfer of DNA refers to the phenomenon by which a plasmid travels from a host strain to a recipient one and returns to the original host, bringing with it DNA from the recipient. The resultant host strain with DNA from the recipient is called a retrotransconjugant. The retrotransfer phenomenon mediated by the TOL plasmid pWW0 and other plasmids has been documented on plates under optimal laboratory culture conditions, but never under natural conditions. In this work, we show that retrotransfer mediated by the IncP9 TOL pWW0 plasmid occurs in the rhizosphere, a niche in which the continuous supply of nutrients via root exudates allows cells to reach a high density. This suggests that this unusual sexual fertilization may be of great importance in lateral gene transfer. We also show that retrotransfer of DNA seems to require co-integration of the plasmid and the host chromosome and subsequent resolution, because a TOL plasmid with a mutation in the tnpR gene, encoding the resolvase of the Tn4653 of the TOL plasmid, was self-transferred between Pseudomonas strains, but unable to mobilize chromosome.}, }
@article {pmid11187795, year = {2000}, author = {Koga, A}, title = {[Evolution of transposable elements in the Medaka fish and its related species].}, journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme}, volume = {45}, number = {17 Suppl}, pages = {2900-2908}, pmid = {11187795}, issn = {0039-9450}, mesh = {Animals ; DNA Transposable Elements/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome ; Germ-Line Mutation ; Humans ; Oryzias/*genetics ; }, }
@article {pmid11178267, year = {2000}, author = {Wolf, YI and Kondrashov, AS and Koonin, EV}, title = {Interkingdom gene fusions.}, journal = {Genome biology}, volume = {1}, number = {6}, pages = {RESEARCH0013}, pmid = {11178267}, issn = {1474-760X}, mesh = {Acetyltransferases ; Amino Acid Sequence ; Archaea/genetics ; Archaeal Proteins/genetics ; Bacteria/genetics ; Bacterial Proteins/genetics ; Enzymes/genetics ; *Escherichia coli Proteins ; *Evolution, Molecular ; Fungal Proteins/genetics ; Genes/*genetics ; *Genome ; Genome, Archaeal ; Genome, Bacterial ; Genome, Fungal ; Hydrolases/genetics ; Molecular Sequence Data ; Phylogeny ; Proteome/genetics ; Saccharomyces cerevisiae/genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {BACKGROUND: Genome comparisons have revealed major lateral gene transfer between the three primary kingdoms of life - Bacteria, Archaea, and Eukarya. Another important evolutionary phenomenon involves the evolutionary mobility of protein domains that form versatile multidomain architectures. We were interested in investigating the possibility of a combination of these phenomena, with an invading gene merging with a pre-existing gene in the recipient genome.<br><br>RESULTS: Complete genomes of fifteen bacteria, four archaea and one eukaryote were searched for interkingdom gene fusions (IKFs); that is, genes coding for proteins that apparently consist of domains originating from different primary kingdoms. Phylogenetic analysis supported 37 cases of IKF, each of which includes a 'native' domain and a horizontally acquired 'alien' domain. IKFs could have evolved via lateral transfer of a gene coding for the alien domain (or a larger protein containing this domain) followed by recombination with a native gene. For several IKFs, this scenario is supported by the presence of a gene coding for a second, stand-alone version of the alien domain in the recipient genome. Among the genomes investigated, the greatest number of IKFs has been detected in Mycobacterium tuberculosis, where they are almost always accompanied by a stand-alone alien domain. For most of the IKF cases detected in other genomes, the stand-alone counterpart is missing.<br><br>CONCLUSIONS: The results of comparative genome analysis show that IKF formation is a real, but relatively rare, evolutionary phenomenon. We hypothesize that IKFs are formed primarily via the proposed two-stage mechanism, but other than in the Actinomycetes, in which IKF generation seems to be an active, ongoing process, most of the stand-alone intermediates have been eliminated, perhaps because of functional redundancy.}, }
@article {pmid11181990, year = {2001}, author = {Aravind, L and Dixit, VM and Koonin, EV}, title = {Apoptotic molecular machinery: vastly increased complexity in vertebrates revealed by genome comparisons.}, journal = {Science (New York, N.Y.)}, volume = {291}, number = {5507}, pages = {1279-1284}, doi = {10.1126/science.291.5507.1279}, pmid = {11181990}, issn = {0036-8075}, mesh = {Amino Acid Motifs ; Animals ; *Apoptosis/genetics ; Caenorhabditis elegans/genetics ; Conserved Sequence ; Drosophila melanogaster/genetics ; *Evolution, Molecular ; *Genome ; *Genome, Human ; Helminth Proteins/chemistry/genetics/physiology ; Humans ; Insect Proteins/chemistry/genetics/physiology ; Protein Structure, Tertiary ; Proteins/*chemistry/*genetics/physiology ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {A comparison of the proteins encoded in the recently (nearly) completed human genome to those from the fly and nematode genomes reveals a major increase in the complexity of the apoptotic molecular machinery in vertebrates, in terms of both the number of proteins involved and their domain architecture. Several components of the apoptotic system are shared by humans and flies, to the exclusion of nematodes, which seems to support the existence of a coelomate clade in animal evolution. A considerable repertoire of apoptotic protein domains was detected in Actinomycetes and Cyanobacteria, which suggests a major contribution of horizontal gene transfer to the early evolution of apoptosis.}, }
@article {pmid11179359, year = {2001}, author = {Bart, A and Pannekoek, Y and Dankert, J and van der Ende, A}, title = {NmeSI restriction-modification system identified by representational difference analysis of a hypervirulent Neisseria meningitidis strain.}, journal = {Infection and immunity}, volume = {69}, number = {3}, pages = {1816-1820}, pmid = {11179359}, issn = {0019-9567}, support = {AI38399/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; DNA-Cytosine Methylases/*genetics/metabolism ; Deoxyribonucleases, Type II Site-Specific/*genetics ; Evolution, Molecular ; Molecular Sequence Data ; Neisseria meningitidis/classification/genetics/*pathogenicity ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Substrate Specificity ; }, abstract = {Neisseria meningitidis is a gram-negative bacterium that may cause meningitis, sepsis, or both. The increase in the incidence of meningococcal disease in various countries in the past 2 decades is mainly due the genotypically related lineage III meningococci. The chromosomal DNA differences between lineage III strains and non-lineage III strains were identified using representational difference analysis. Thus, a 1.8-kb locus that is specific for lineage III meningococci was identified. The locus contains three open reading frames encoding the NmeSI restriction-modification system. The methyltransferase gene was cloned and expressed in Escherichia coli. Site AGTACT was found to be modified by the enzyme. In conclusion, lineage III strains differ from endemic strains by the presence of a specific restriction-modification system. This restriction-modification system may contribute to the clonal and hypervirulent character of lineage III strains by influencing horizontal gene transfer and transcription.}, }
@article {pmid11179344, year = {2001}, author = {Kahler, CM and Blum, E and Miller, YK and Ryan, D and Popovic, T and Stephens, DS}, title = {exl, an exchangeable genetic island in Neisseria meningitidis.}, journal = {Infection and immunity}, volume = {69}, number = {3}, pages = {1687-1696}, pmid = {11179344}, issn = {0019-9567}, support = {R01 AI033517/AI/NIAID NIH HHS/United States ; AI-33517/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacterial Outer Membrane Proteins/genetics ; Bacterial Proteins/genetics ; Base Sequence ; Biological Specimen Banks ; Carrier Proteins/genetics ; DNA Transposable Elements/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Heme Oxygenase (Decyclizing) ; Humans ; Iron-Binding Proteins ; Meningococcal Infections/microbiology ; Molecular Sequence Data ; Neisseria meningitidis/classification/*genetics/pathogenicity ; Polymorphism, Genetic ; Receptors, Cell Surface/genetics ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Serotyping ; Transferrin-Binding Proteins ; }, abstract = {The genetic structure and evolution of a novel exchangeable meningococcal genomic island was defined for the important human pathogen Neisseria meningitidis. In 125 meningococcal strains tested, one of three unrelated nucleotide sequences, designated exl (exchangeable locus), was found between a gene required for heme utilization, hemO, and col, encoding a putative Escherichia coli collagenase homologue. The 5' boundary of each exl cassette was the stop codon of hemO, whereas the 3' boundary was delineated by a 33-bp repeat containing neisserial uptake sequences located downstream of col. One of the three alternative exl cassettes contained the meningococcal hemoglobin receptor gene, hmbR (exl3). In other meningococcal strains, hmbR was absent from the genome and was replaced by either a nucleotide sequence containing a novel open reading frame, exl2, or a cassette containing exl3. The proteins encoded by exl2 and exl3 had no significant amino acid homology to HmbR but contained six motifs that are also present in the lipoprotein components of the lactoferrin (LbpB), transferrin (TbpB), and hemoglobin-haptoglobin (HpuA) uptake systems. To determine the evolutionary relationships among meningococci carrying hmbR, exl2, or exl3, isolates representing 92 electrophoretic types were examined. hmbR was found throughout the population structure of N. meningitidis (genetic distance, >0.425), whereas exl2 and exl3 were found in clonal groups at genetic distances of <0.2. The commensal neisserial species were identified as reservoirs for all of the exl cassettes found in meningococci. The structure of these cassettes and their correlation with clonal groups emphasize the extensive gene pool and frequent horizontal DNA transfer events that contribute to the evolution and virulence of N. meningitidis.}, }
@article {pmid11179285, year = {2001}, author = {Jiang, SM and Wang, L and Reeves, PR}, title = {Molecular characterization of Streptococcus pneumoniae type 4, 6B, 8, and 18C capsular polysaccharide gene clusters.}, journal = {Infection and immunity}, volume = {69}, number = {3}, pages = {1244-1255}, pmid = {11179285}, issn = {0019-9567}, mesh = {Bacterial Capsules/*biosynthesis/classification/*genetics ; Base Sequence ; Carbohydrate Sequence ; Conserved Sequence ; Cytidine Diphosphate Diglycerides/biosynthesis ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genetic Variation ; Glycosyltransferases/genetics ; Intramolecular Transferases/genetics ; Molecular Sequence Data ; *Multigene Family ; Nucleoside Diphosphate Sugars/biosynthesis ; Recombination, Genetic ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Streptococcus pneumoniae/classification/*genetics ; Terminology as Topic ; Thymine Nucleotides/biosynthesis ; Uridine Diphosphate Glucuronic Acid/biosynthesis ; Uridine Diphosphate Sugars/biosynthesis ; }, abstract = {Capsular polysaccharide (CPS) is a major virulence factor in Streptococcus pneumoniae. CPS gene clusters of S. pneumoniae types 4, 6B, 8, and 18C were sequenced and compared with those of CPS types 1, 2, 14, 19F, 19A, 23F, and 33F. All have the same four genes at the 5' end, encoding proteins thought to be involved in regulation and export. Sequences of these genes can be divided into two classes, and evidence of recombination between them was observed. Next is the gene encoding the transferase for the first step in the synthesis of CPS. The predicted amino acid sequences of these first sugar transferases have multiple transmembrane segments, a feature lacking in other transferases. Sugar pathway genes are located at the 3' end of the gene cluster. Comparison of the four dTDP-L-rhamnose pathway genes (rml genes) of CPS types 1, 2, 6B, 18C, 19F, 19A, and 23F shows that they have the same gene order and are highly conserved. There is a gradient in the nature of the variation of rml genes, the average pairwise difference for those close to the central region being higher than that for those close to the end of the gene cluster and, again, recombination sites can be observed in these genes. This is similar to the situation we observed for rml genes of O-antigen gene clusters of Salmonella enterica. Our data indicate that the conserved first four genes at the 5' ends and the relatively conserved rml genes at the 3' ends of the CPS gene clusters were sites for recombination events involved in forming new forms of CPS. We have also identified wzx and wzy genes for all sequenced CPS gene clusters by use of motifs.}, }
@article {pmid11166877, year = {2001}, author = {Medina, E and Guzmán, CA}, title = {Use of live bacterial vaccine vectors for antigen delivery: potential and limitations.}, journal = {Vaccine}, volume = {19}, number = {13-14}, pages = {1573-1580}, doi = {10.1016/s0264-410x(00)00354-6}, pmid = {11166877}, issn = {0264-410X}, mesh = {Bacillus anthracis/genetics ; Bacteria/*genetics/pathogenicity ; Gene Transfer, Horizontal ; Genetic Vectors/administration &amp; dosage/*genetics ; Immunity/*immunology ; Immunity, Mucosal/immunology ; Lactobacillus/genetics ; Listeria monocytogenes/genetics ; Mycobacterium bovis/genetics ; Salmonella/genetics ; Shigella/genetics ; Staphylococcus/genetics ; Vaccines, Synthetic/administration &amp; dosage/adverse effects/*genetics/*immunology ; Virulence ; Yersinia enterocolitica/genetics ; }, abstract = {Most infectious agents are restricted to the mucosal membranes or their transit through the mucosa constitutes a critical step in the infection process. Therefore, the elicitation of an efficient immune response, not only at systemic, but also at mucosal level, after vaccination is highly desirable, representing a significant advantage in order to prevent infection. This goal can be only achieved, when the vaccine formulation is administered by the mucosal route. However, soluble antigens given by this route are usually poorly immunogenic. Among the available approaches to stimulate efficient mucosal responses, the use of bacterial carriers to deliver vaccine antigens, probably, constitutes one of the most successful strategies. The potential and limitations of the most extensively studied bacterial carrier systems will be discussed.}, }
@article {pmid11166654, year = {2001}, author = {Ball, CA and Cherry, JM}, title = {Genome comparisons highlight similarity and diversity within the eukaryotic kingdoms.}, journal = {Current opinion in chemical biology}, volume = {5}, number = {1}, pages = {86-89}, pmid = {11166654}, issn = {1367-5931}, support = {P41 HG001315/HG/NHGRI NIH HHS/United States ; P41 HG001315-16/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Eukaryotic Cells/*metabolism ; Evolution, Molecular ; *Genome ; Humans ; Phylogeny ; *Sequence Homology ; }, abstract = {In 2000, the number of completely sequenced eukaryotic genomes increased to four. The addition of Drosophila and Arabidopsis into this cohort permits additional insights into the processes that have shaped evolution. Analysis and comparisons of both completed genomes and partially sequenced genomes have already shed light on mechanisms such as gene duplication and gene loss that have long been hypothesized to be major forces in speciation. Indeed, duplicate gene pairs in Saccharomyces, Arabidopsis, Caenorhabditis and Drosophila are high: 30%, 60%, 48% and 40%, respectively. Evidence of horizontal gene-transfer, thought to be a major evolutionary force in bacteria, has been found in Arabidopsis. The release of the 'first draft' of the human genome sequence in 2000 heralds a new stage of biological study. Understanding the as-yet-unannotated human genome will be largely based on conclusions, techniques and tools developed during the analysis and comparison of the genome of these four model organisms.}, }
@article {pmid11166455, year = {2001}, author = {Newbound, GC and Cooper, JR and O'Rourke, JP and Baskin, CR and Bunnell, BA}, title = {Analysis of gene transfer efficiency of retrovirus producer cell transplantation for in situ gene transfer to hematopoietic cells.}, journal = {Experimental hematology}, volume = {29}, number = {2}, pages = {163-173}, doi = {10.1016/s0301-472x(00)00648-2}, pmid = {11166455}, issn = {0301-472X}, support = {K01 RR00152/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Antibodies, Viral/biosynthesis ; Bone Marrow ; Cell Line ; *Cell Transplantation ; Femur ; Flow Cytometry ; Gene Expression ; *Gene Transfer, Horizontal ; *Genetic Vectors ; Green Fluorescent Proteins ; Hematopoietic Stem Cells/chemistry/*metabolism ; Kanamycin Kinase/genetics ; Luminescent Proteins/genetics ; Macaca mulatta ; Moloney murine leukemia virus/*genetics/immunology ; RNA/analysis ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {OBJECTIVE: The aim of this study was to assess the gene transfer efficiency of an in situ administration protocol for hematopoietic stem/progenitor cells in the rhesus macaque (Macaca mulatta) animal model.<br><br>MATERIALS AND METHODS: Moloney murine leukemia virus amphotropic vector producer cells (1--2 x 10(8) cells/animal) were transplanted into the femoral bone marrow cavities of six macaques. To determine if the levels of gene transfer could be increased, a second injection at the same dose of producer cells was performed into the iliac crest in three of the six macaques.<br><br>RESULTS: We demonstrated that 0.02-0.1% of peripheral blood mononuclear cells contained the vector transgene for up to 12 months following the initial administration of producer cells. Hematopoietic progenitor cell assays indicated that the neomycin phosphotransferase gene was detected in 10--30% of progenitor cell colonies. A humoral immune response directed toward viral particles was demonstrated in all animals. Additionally, we demonstrated that an increase in the levels of transduced cells, up to 1% of circulating peripheral blood mononuclear cells and granulocytes, contain the transgene following producer cell readministration.<br><br>CONCLUSIONS: These data demonstrate the successful in situ gene transfer to hematopoietic stem/progenitor cells and circulating peripheral blood mononuclear cells that persists as long as 12 months postinjection, in the absence of any preconditioning.}, }
@article {pmid11160094, year = {2001}, author = {Brown, EW and LeClerc, JE and Li, B and Payne, WL and Cebula, TA}, title = {Phylogenetic evidence for horizontal transfer of mutS alleles among naturally occurring Escherichia coli strains.}, journal = {Journal of bacteriology}, volume = {183}, number = {5}, pages = {1631-1644}, pmid = {11160094}, issn = {0021-9193}, mesh = {*Adenosine Triphosphatases ; *Alleles ; Bacterial Proteins/*genetics ; Base Sequence ; *DNA-Binding Proteins ; Escherichia coli/*classification/genetics ; Escherichia coli Infections/microbiology ; *Escherichia coli Proteins ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Humans ; Malate Dehydrogenase/genetics ; Molecular Sequence Data ; MutS DNA Mismatch-Binding Protein ; *Phylogeny ; Recombination, Genetic ; Sequence Analysis, DNA ; Shigella dysenteriae ; }, abstract = {mutS mutators accelerate the bacterial mutation rate 100- to 1,000-fold and relax the barriers that normally restrict homeologous recombination. These mutators thus afford the opportunity for horizontal exchange of DNA between disparate strains. While much is known regarding the mutS phenotype, the evolutionary structure of the mutS(+) gene in Escherichia coli remains unclear. The physical proximity of mutS to an adjacent polymorphic region of the chromosome suggests that this gene itself may be subject to horizontal transfer and recombination events. To test this notion, a phylogenetic approach was employed that compared gene phylogeny to strain phylogeny, making it possible to identify E. coli strains in which mutS alleles have recombined. Comparison of mutS phylogeny against predicted E. coli "whole-chromosome" phylogenies (derived from multilocus enzyme electrophoresis and mdh sequences) revealed striking levels of phylogenetic discordance among mutS alleles and their respective strains. We interpret these incongruences as signatures of horizontal exchange among mutS alleles. Examination of additional sites surrounding mutS also revealed incongruous distributions compared to E. coli strain phylogeny. This suggests that other regional sequences are equally subject to horizontal transfer, supporting the hypothesis that the 61.5-min mutS-rpoS region is a recombinational hot spot within the E. coli chromosome. Furthermore, these data are consistent with a mechanism for stabilizing adaptive changes promoted by mutS mutators through rescue of defective mutS alleles with wild-type sequences.}, }
@article {pmid11157953, year = {2001}, author = {Davies, RL and Whittam, TS and Selander, RK}, title = {Sequence diversity and molecular evolution of the leukotoxin (lktA) gene in bovine and ovine strains of Mannheimia (Pasteurella) haemolytica.}, journal = {Journal of bacteriology}, volume = {183}, number = {4}, pages = {1394-1404}, pmid = {11157953}, issn = {0021-9193}, support = {/WT_/Wellcome Trust/United Kingdom ; AI22144/AI/NIAID NIH HHS/United States ; }, mesh = {Alleles ; Amino Acid Sequence ; Animals ; *Bacterial Proteins ; Cattle ; Conserved Sequence ; *Evolution, Molecular ; Exotoxins/*genetics ; Genetic Variation ; Hemolysin Proteins/*genetics ; Mannheimia haemolytica/classification/*genetics ; Models, Genetic ; Molecular Sequence Data ; Pasteurellosis, Pneumonic/genetics/*microbiology ; Recombination, Genetic ; Serotyping ; Sheep ; Sheep Diseases/genetics/*microbiology ; Species Specificity ; }, abstract = {The molecular evolution of the leukotoxin structural gene (lktA) of Mannheimia (Pasteurella) haemolytica was investigated by nucleotide sequence comparison of lktA in 31 bovine and ovine strains representing the various evolutionary lineages and serotypes of the species. Eight major allelic variants (1.4 to 15.7% nucleotide divergence) were identified; these have mosaic structures of varying degrees of complexity reflecting a history of horizontal gene transfer and extensive intragenic recombination. The presence of identical alleles in strains of different genetic backgrounds suggests that assortative (entire gene) recombination has also contributed to strain diversification in M. haemolytica. Five allelic variants occur only in ovine strains and consist of recombinant segments derived from as many as four different sources. Four of these alleles consist of DNA (52.8 to 96.7%) derived from the lktA gene of the two related species Mannheimia glucosida and Pasteurella trehalosi, and four contain recombinant segments derived from an allele that is associated exclusively with bovine or bovine-like serotype A2 strains. The two major lineages of ovine serotype A2 strains possess lktA alleles that have very different evolutionary histories and encode divergent leukotoxins (5.3% amino acid divergence), but both contain segments derived from the bovine allele. Homologous segments of donor and recipient alleles are identical or nearly identical, indicating that the recombination events are relatively recent and probably postdate the domestication of cattle and sheep. Our findings suggest that host switching of bovine strains from cattle to sheep, together with inter- and intraspecies recombinational exchanges, has played an important role in generating leukotoxin diversity in ovine strains. In contrast, there is limited allelic diversity of lktA in bovine strains, suggesting that transmission of strains from sheep to cattle has been less important in leukotoxin evolution.}, }
@article {pmid11157935, year = {2001}, author = {Snyder, LA and Saunders, NJ and Shafer, WM}, title = {A putatively phase variable gene (dca) required for natural competence in Neisseria gonorrhoeae but not Neisseria meningitidis is located within the division cell wall (dcw) gene cluster.}, journal = {Journal of bacteriology}, volume = {183}, number = {4}, pages = {1233-1241}, pmid = {11157935}, issn = {0021-9193}, support = {R01 AI021150/AI/NIAID NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; AI-21150/AI/NIAID NIH HHS/United States ; AI-38399/AI/NIAID NIH HHS/United States ; R37 AI021150/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; *Bacterial Proteins ; Gene Transfer, Horizontal ; Membrane Proteins/*genetics ; Molecular Sequence Data ; *Multigene Family ; Mutagenesis, Insertional ; Neisseria gonorrhoeae/*genetics ; Neisseria meningitidis/*genetics ; Open Reading Frames ; Sequence Homology, Amino Acid ; Species Specificity ; *Transformation, Bacterial ; }, abstract = {A cluster of 18 open reading frames (ORFs), 15 of which are homologous to genes involved in division and cell wall synthesis, has been identified in Neisseria gonorrhoeae and Neisseria meningitidis. The three additional ORFs, internal to the dcw cluster, are not homologous to dcw-related genes present in other bacterial species. Analysis of the N. meningitidis strain MC58 genome for foreign DNA suggests that these additional ORFs have not been acquired by recent horizontal exchange, indicating that they are a long-standing, integral part of the neisserial dcw gene cluster. Reverse transcription-PCR analysis of RNA extracted from N. gonorrhoeae strain FA19 confirmed that all three ORFs are transcribed in gonococci. One of these ORFs (dca, for division cluster competence associated), located between murE and murF, was studied in detail and found to be essential for competence in the gonococcal but not in the meningococcal strains tested. Computer analysis predicts that dca encodes an inner membrane protein similar to hypothetical proteins produced by other gram-negative bacteria. In some meningococcal strains dca is prematurely terminated following a homopolymeric tract of G's, the length of which differs between isolates of N. meningitidis, suggesting that dca is phase variable in this species. A deletion and insertional mutation was made in the dca gene of N. gonorrhoeae strain FA19 and N. meningitidis strain NMB. This mutation abrogated the ability of the gonococci to be transformed with chromosomal DNA. Thus, we conclude that the dca-encoded gene product is an essential competence factor for gonococci.}, }
@article {pmid11157217, year = {2001}, author = {Shoemaker, NB and Vlamakis, H and Hayes, K and Salyers, AA}, title = {Evidence for extensive resistance gene transfer among Bacteroides spp. and among Bacteroides and other genera in the human colon.}, journal = {Applied and environmental microbiology}, volume = {67}, number = {2}, pages = {561-568}, pmid = {11157217}, issn = {0099-2240}, support = {R01 AI022383/AI/NIAID NIH HHS/United States ; R56 AI022383/AI/NIAID NIH HHS/United States ; AI22383/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteroides/drug effects/*genetics ; Bacteroides Infections/microbiology ; Colon/*microbiology ; *Conjugation, Genetic ; DNA Transposable Elements/genetics ; DNA, Ribosomal/analysis/genetics ; Drug Resistance, Microbial/genetics ; Erythromycin/pharmacology ; *Gene Transfer, Horizontal ; Humans ; Plasmids/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Tetracycline Resistance/*genetics ; }, abstract = {Transfer of antibiotic resistance genes by conjugation is thought to play an important role in the spread of resistance. Yet virtually no information is available about the extent to which such horizontal transfers occur in natural settings. In this paper, we show that conjugal gene transfer has made a major contribution to increased antibiotic resistance in Bacteroides species, a numerically predominant group of human colonic bacteria. Over the past 3 decades, carriage of the tetracycline resistance gene, tetQ, has increased from about 30% to more than 80% of strains. Alleles of tetQ in different Bacteroides species, with one exception, were 96 to 100% identical at the DNA sequence level, as expected if horizontal gene transfer was responsible for their spread. Southern blot analyses showed further that transfer of tetQ was mediated by a conjugative transposon (CTn) of the CTnDOT type. Carriage of two erythromycin resistance genes, ermF and ermG, rose from <2 to 23% and accounted for about 70% of the total erythromycin resistances observed. Carriage of tetQ and the erm genes was the same in isolates taken from healthy people with no recent history of antibiotic use as in isolates obtained from patients with Bacteroides infections. This finding indicates that resistance transfer is occurring in the community and not just in clinical environments. The high percentage of strains that are carrying these resistance genes in people who are not taking antibiotics is consistent with the hypothesis that once acquired, these resistance genes are stably maintained in the absence of antibiotic selection. Six recently isolated strains carried ermB genes. Two were identical to erm(B)-P from Clostridium perfringens, and the other four had only one to three mismatches. The nine strains with ermG genes had DNA sequences that were more than 99% identical to the ermG of Bacillus sphaericus. Evidently, there is a genetic conduit open between gram-positive bacteria, including bacteria that only pass through the human colon, and the gram-negative Bacteroides species. Our results support the hypothesis that extensive gene transfer occurs among bacteria in the human colon, both within the genus Bacteroides and among Bacteroides species and gram-positive bacteria.}, }
@article {pmid11146153, year = {2000}, author = {Gerson, SL}, title = {Drug resistance gene transfer: Stem cell protection and therapeutic efficacy.}, journal = {Experimental hematology}, volume = {28}, number = {12}, pages = {1315-1324}, doi = {10.1016/s0301-472x(00)00548-8}, pmid = {11146153}, issn = {0301-472X}, support = {R01 CA76192/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Clinical Trials as Topic ; Drug Resistance/*genetics ; *Gene Expression ; *Gene Transfer, Horizontal ; Hematopoietic Stem Cell Transplantation ; Hematopoietic Stem Cells/*metabolism ; Humans ; }, }
@article {pmid11136451, year = {2001}, author = {Wilderman, PJ and Vasil, AI and Johnson, Z and Vasil, ML}, title = {Genetic and biochemical analyses of a eukaryotic-like phospholipase D of Pseudomonas aeruginosa suggest horizontal acquisition and a role for persistence in a chronic pulmonary infection model.}, journal = {Molecular microbiology}, volume = {39}, number = {2}, pages = {291-303}, doi = {10.1046/j.1365-2958.2001.02282.x}, pmid = {11136451}, issn = {0950-382X}, support = {HL62608/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Bacterial Proteins/genetics/metabolism ; Base Sequence ; Calcium/metabolism ; Chronic Disease ; Cloning, Molecular ; Cystic Fibrosis/microbiology ; DNA Transposable Elements/*genetics ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Humans ; Lung Diseases/*microbiology ; Molecular Sequence Data ; Open Reading Frames/genetics ; Periplasm/enzymology ; Phospholipase D/chemistry/*genetics/metabolism ; Pseudomonas Infections/microbiology ; Pseudomonas aeruginosa/*genetics/isolation &amp; purification/*pathogenicity ; Rats ; Virulence ; }, abstract = {Phospholipases D (PLDs) are virtually ubiquitous in eukaryotic organisms; however, they are relatively uncommon in prokaryotes. In this report, we demonstrate that the environmentally acquired, opportunistic pathogen Pseudomonas aeruginosa expresses PLD activity. A gene designated pldA was identified in the genomic database of P. aeruginosa PAO1 encoding a protein with significant homology to eukaryotic PLDs, but not to any prokaryotic PLDs. PldA is most homologous to PLDs from mammals and yeast. The pldA gene was cloned and shown to express an approximately 116 kDa protein with calcium-regulated PLD activity that is localized to the periplasm. Interestingly, not all strains of P. aeruginosa carry pldA. When present, pldA is always linked to an open reading frame (ORF), ORF4, and a gene (vgrA1) encoding a protein homologous to Vgr from Escherichia coli. Vgr proteins contain regularly repeated dipeptide motifs (valine-glycine repeats). In E. coli, genes encoding Vgr are associated with multicopy genetic elements designated Rhs (rearrangement hot-spots). P. aeruginosa PAO1 has 10 vgr homologues dispersed throughout its genome, but the copy number of these genetic elements varies considerably in different strains. Neither vgrA1 nor ORF4 is present in strains lacking pldA. Furthermore, sequences flanking vgrA1, pldA and ORF4 in the P. aeruginosa strains examined are highly conserved, suggesting a specific site of insertion. These and other data suggest that vgrA1, pldA and ORF4 constitute an approximately 7 kb mobile genetic element and that pldA was acquired horizontally, perhaps from a eukaryotic organism. Competition studies between a PldA knock-out mutant and the parental wild-type strain indicate that PldA contributes to the ability of P. aeruginosa PAO1 to persist in a chronic pulmonary infection model in rats.}, }
@article {pmid11136444, year = {2001}, author = {Brüssow, H and Desiere, F}, title = {Comparative phage genomics and the evolution of Siphoviridae: insights from dairy phages.}, journal = {Molecular microbiology}, volume = {39}, number = {2}, pages = {213-222}, doi = {10.1046/j.1365-2958.2001.02228.x}, pmid = {11136444}, issn = {0950-382X}, mesh = {Dairying ; *Evolution, Molecular ; *Genome, Viral ; Siphoviridae/*genetics ; Streptococcus/virology ; Streptococcus Phages/genetics ; }, abstract = {Comparative phage genomics can retrace part of the evolutionary history of phage modules encoding phage-specific functions such as capsid building or establishment of the lysogenic state. The diagnosis of relatedness is not based exclusively on sequence similarity, but includes topological considerations of genome organization. The gene maps from the lambda-, psiM2-, L5-, Sfi21-, Sfi11-, phiC31-, sk1- and TM4-like phages showed a remarkable synteny of their structural genes defining a lambda supergroup within Siphoviridae (Caudovirales with long non-contractile tails). A hierarchy of relatedness within the lambda supergroup suggested elements of vertical evolution in the capsid module of Siphoviridae. Links to P22-like Podoviridae and P2-like Myoviridae were also detected. Numerous cases of horizontal gene transfer were observed, but recent transfers were limited to interbreeding phage populations. We suggest that tailed phages are the result of both vertical and horizontal evolution and are thus a good model system for web-like phylogenies.}, }
@article {pmid11133943, year = {2001}, author = {Sekizaki, T and Otani, Y and Osaki, M and Takamatsu, D and Shimoji, Y}, title = {Evidence for horizontal transfer of SsuDAT1I restriction-modification genes to the Streptococcus suis genome.}, journal = {Journal of bacteriology}, volume = {183}, number = {2}, pages = {500-511}, pmid = {11133943}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; DNA Modification Methylases/genetics ; DNA Restriction Enzymes/genetics ; DNA Restriction-Modification Enzymes/*genetics ; Deoxyribonucleases, Type II Site-Specific/genetics ; Electrophoresis, Gel, Pulsed-Field ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genome, Bacterial ; Molecular Sequence Data ; Phenotype ; Purines/biosynthesis ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Streptococcus suis/*genetics ; Swine ; }, abstract = {Different strains of Streptococcus suis serotypes 1 and 2 isolated from pigs either contained a restriction-modification (R-M) system or lacked it. The R-M system was an isoschizomer of Streptococcus pneumoniae DpnII, which recognizes nucleotide sequence 5'-GATC-3'. The nucleotide sequencing of the genes encoding the R-M system in S. suis DAT1, designated SsuDAT1I, showed that the SsuDAT1I gene region contained two methyltransferase genes, designated ssuMA and ssuMB, as does the DpnII system. The deduced amino acid sequences of M. SsuMA and M.SsuMB showed 70 and 90% identity to M.DpnII and M.DpnA, respectively. However, the SsuDAT1I system contained two isoschizomeric restriction endonuclease genes, designated ssuRA and ssuRB. The deduced amino acid sequence of R.SsuRA was 49% identical to that of R.DpnII, and R.SsuRB was 72% identical to R.LlaDCHI of Lactococcus lactis subsp. cremoris DCH-4. The four SsuDAT1I genes overlapped and were bounded by purine biosynthetic gene clusters in the following gene order: purF-purM-purN-purH-ssuMA-ssuMB-ssuRA++ +-ssuRB-purD-purE. The G+C content of the SsuDAT1I gene region (34.1%) was lower than that of the pur region (48.9%), suggesting horizontal transfer of the SsuDAT1I system. No transposable element or long-repeat sequence was found in the flanking regions. The SsuDAT1I genes were functional by themselves, as they were individually expressed in Escherichia coli. Comparison of the sequences between strains with and without the R-M system showed that only the region from 53 bp upstream of ssuMA to 5 bp downstream of ssuRB was inserted in the intergenic sequence between purH and purD and that the insertion target site was not the recognition site of SsuDAT1I. No notable substitutions or insertions could be found, and the structures were conserved among all the strains. These results suggest that the SsuDAT1I system could have been integrated into the S. suis chromosome by an illegitimate recombination mechanism.}, }
@article {pmid11131392, year = {2000}, author = {Hoffmann, N and Steinbüchel, A and Rehm, BH}, title = {Homologous functional expression of cryptic phaG from Pseudomonas oleovorans establishes the transacylase-mediated polyhydroxyalkanoate biosynthetic pathway.}, journal = {Applied microbiology and biotechnology}, volume = {54}, number = {5}, pages = {665-670}, doi = {10.1007/s002530000441}, pmid = {11131392}, issn = {0175-7598}, mesh = {Acyltransferases/chemistry/*genetics/*metabolism ; Amino Acid Sequence ; Blotting, Southern ; Cloning, Molecular ; DNA, Bacterial/genetics ; Fatty Acids/*metabolism ; Gene Expression ; Gene Transfer, Horizontal ; Genes, Bacterial ; Hydroxy Acids/*metabolism ; Molecular Sequence Data ; Plasmids ; Pseudomonas/*genetics/metabolism ; Pseudomonas putida/genetics/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Transcription, Genetic ; }, abstract = {Various pseudomonads are capable of the synthesis of polyhydroxyalkanoate (PHA), composed of medium chain length (MCL) 3-hydroxy fatty acids (C6-C14), when grown on simple carbon sources such as, for example, gluconate or acetate. In Pseudomonas putida, the fatty acid de novo synthesis and PHA synthesis are linked by the transacylase PhaG. Southern hybridization experiments with digoxigenin-labeled phaG(Pp) from P. putida and genomic DNA from various pseudomonads indicate that phaG homologues are present in various other pseudomonads. Although P. oleovorans does not accumulate PHA(MCL) from non-related carbon sources, its genomic DNA reveals a strong hybridization signal. We employed PCR to amplify this phaG homologue. The respective PCR product comprising the coding region of phaG(Po) was cloned into pBBR1MCS-2, resulting in plasmid pBHR84. DNA sequencing revealed that putative PhaG(Po) from P. oleovorans exhibited about 95% amino acid sequence identity to PhaG(Pp) from P. putida. Reverse transcriptase-PCR analysis demonstrated that phaG(Po) was not transcribed even tinder inducing conditions, i.e. in the presence of gluconate as carbon source, whereas induction of phaG(Pp) transcription was obtained in P. putida. When octanoate was used as sole carbon source, only low levels of phaG mRNA were detected in P. putida. Plasmid pBHR84 complemented the phaG-negative mutant PhaG(N)-21 from P. putida. Interestingly, reintroduction of phaG(Po) under lac promoter control into the natural host P. oleovorans established PHA(MCL) synthesis from non-related carbon sources in this bacterium. These data indicated that phaG(Po) in P. oleovorans is not functionally expressed and does not exert its original function.}, }
@article {pmid11130711, year = {2000}, author = {, }, title = {Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.}, journal = {Nature}, volume = {408}, number = {6814}, pages = {796-815}, doi = {10.1038/35048692}, pmid = {11130711}, issn = {0028-0836}, mesh = {Animals ; Arabidopsis/cytology/*genetics/growth &amp; development/physiology ; Biological Transport ; Cell Membrane/metabolism ; Cell Nucleus/genetics ; Centromere ; Chloroplasts/genetics ; Chromosome Mapping ; DNA Repair ; DNA Transposable Elements ; DNA, Plant ; DNA, Ribosomal ; Gene Duplication ; Gene Expression Regulation, Plant ; *Genome, Plant ; Humans ; Light ; Mitochondria/genetics ; Photosynthesis ; Plant Diseases ; Proteome ; Recombination, Genetic ; Repetitive Sequences, Nucleic Acid ; Sequence Analysis, DNA ; Signal Transduction ; Species Specificity ; Telomere ; }, abstract = {The flowering plant Arabidopsis thaliana is an important model system for identifying genes and determining their functions. Here we report the analysis of the genomic sequence of Arabidopsis. The sequenced regions cover 115.4 megabases of the 125-megabase genome and extend into centromeric regions. The evolution of Arabidopsis involved a whole-genome duplication, followed by subsequent gene loss and extensive local gene duplications, giving rise to a dynamic genome enriched by lateral gene transfer from a cyanobacterial-like ancestor of the plastid. The genome contains 25,498 genes encoding proteins from 11,000 families, similar to the functional diversity of Drosophila and Caenorhabditis elegans--the other sequenced multicellular eukaryotes. Arabidopsis has many families of new proteins but also lacks several common protein families, indicating that the sets of common proteins have undergone differential expansion and contraction in the three multicellular eukaryotes. This is the first complete genome sequence of a plant and provides the foundations for more comprehensive comparison of conserved processes in all eukaryotes, identifying a wide range of plant-specific gene functions and establishing rapid systematic ways to identify genes for crop improvement.}, }
@article {pmid11123668, year = {2000}, author = {Martínez-Abarca, F and Toro, N}, title = {Group II introns in the bacterial world.}, journal = {Molecular microbiology}, volume = {38}, number = {5}, pages = {917-926}, doi = {10.1046/j.1365-2958.2000.02197.x}, pmid = {11123668}, issn = {0950-382X}, mesh = {Bacteria/*genetics ; Bacterial Proteins/*genetics ; Base Sequence ; Gene Transfer, Horizontal ; *Introns ; Phylogeny ; RNA, Bacterial/*genetics ; }, abstract = {Group II introns are large catalytic RNA molecules that act as mobile genetic elements. They were initially identified in the organelle genomes of lower eukaryotes and plants, and it has been suggested that they are the progenitors of nuclear spliceosomal introns. Group II self-splicing introns were shown to be present in bacteria in 1993, since when the various bacterial genome sequencing projects have led to a significant increase in the number of group II intron sequences present in databases. However, few of these introns have been characterized, and most were identified on the basis of their intron-encoded protein (IEP), with little data available concerning their ribozyme/RNA structure. Their frequency in prokaryotes is also unknown. We attempt here to provide a first comprehensive review of bacterial group II introns based on recent genome sequencing data and mechanistic studies.}, }
@article {pmid11121787, year = {2000}, author = {Kado, CI}, title = {The role of the T-pilus in horizontal gene transfer and tumorigenesis.}, journal = {Current opinion in microbiology}, volume = {3}, number = {6}, pages = {643-648}, doi = {10.1016/s1369-5274(00)00154-5}, pmid = {11121787}, issn = {1369-5274}, support = {GM45550/GM/NIGMS NIH HHS/United States ; }, mesh = {Agrobacterium tumefaciens/genetics/pathogenicity/*physiology ; Bacterial Proteins/physiology ; Cell Transformation, Neoplastic ; Fimbriae, Bacterial/*physiology ; Gene Transfer, Horizontal ; Virulence ; }, abstract = {The T-pilus is a flexuous filamentous appendage that is essential for Agrobacterium tumefaciens virulence. T-pilus subunits are derived from a VirB2-processing reaction that generates cyclized polypeptide subunits. The T-pilus filament has a diameter of 10 nm and contains a lumen approximately 2 nm in diameter. Biogenesis of the T-pilus requires all 11 VirB proteins, but not the VirD4 protein, which is used in conjugal plasmid transfer. VirB4 and VirB11 are two ATPases that may form homohexameric rings within the transport apparatus, which is composed of VirB6-10 proteins.}, }
@article {pmid11121028, year = {2000}, author = {Söll, D and Becker, HD and Plateau, P and Blanquet, S and Ibba, M}, title = {Context-dependent anticodon recognition by class I lysyl-tRNA synthetases.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {97}, number = {26}, pages = {14224-14228}, pmid = {11121028}, issn = {0027-8424}, support = {R01 GM022854/GM/NIGMS NIH HHS/United States ; R37 GM022854/GM/NIGMS NIH HHS/United States ; GM 22854/GM/NIGMS NIH HHS/United States ; GM55674/GM/NIGMS NIH HHS/United States ; }, mesh = {Anticodon/*metabolism ; Borrelia burgdorferi Group/enzymology ; Helicobacter pylori/enzymology ; Lysine-tRNA Ligase/classification/*metabolism ; Nucleic Acid Conformation ; Phylogeny ; RNA, Transfer, Lys/chemistry/metabolism ; }, abstract = {Lysyl-tRNA synthesis is catalyzed by two unrelated families of aminoacyl-tRNA synthetases. In most bacteria and all eukarya, the known lysyl-tRNA synthetases (LysRSs) are subclass IIb-type aminoacyl-tRNA synthetases, whereas many archaea and a scattering of bacteria contain an unrelated class I-type LysRS. Examination of the recognition of partially modified tRNA(Lys) anticodon variants by a bacterial (from Borrelia burgdorferi) and an archaeal (from Methanococcus maripaludis) class I lysyl-tRNA synthetase revealed differences in the pattern of anticodon recognition between the two enzymes. U35 and U36 were both important for recognition by the B. burgdorferi enzyme, whereas only U36 played a role in recognition by M. maripaludis LysRS. Examination of the phylogenetic distribution of class I LysRSs suggested a correlation between recognition of U35 and U36 and the presence of asparaginyl-tRNA synthetase (AsnRS), which also recognizes U35 and U36 in the anticodon of tRNA(Asn). However, the class II LysRS of Helicobacter pylori, an organism that lacks AsnRS, also recognizes both U35 and U36, indicating that the presence of AsnRS has solely influenced the phylogenetic distribution of class I LysRSs. These data suggest that competition between unrelated aminoacyl-tRNA synthetases for overlapping anticodon sequences is a determinant of the phylogenetic distribution of extant synthetase families. Such patterns of competition also provide a basis for the two separate horizontal gene transfer events hypothesized in the evolution of the class I lysyl-tRNA synthetases.}, }
@article {pmid11120683, year = {2000}, author = {Liò, P and Vannucci, M}, title = {Finding pathogenicity islands and gene transfer events in genome data.}, journal = {Bioinformatics (Oxford, England)}, volume = {16}, number = {10}, pages = {932-940}, doi = {10.1093/bioinformatics/16.10.932}, pmid = {11120683}, issn = {1367-4803}, mesh = {Base Composition ; Base Sequence ; DNA, Bacterial ; Data Interpretation, Statistical ; Databases, Factual ; GC Rich Sequence ; Gene Transfer, Horizontal/*genetics ; *Genome, Bacterial ; Helicobacter pylori/*genetics/pathogenicity ; Models, Genetic ; Models, Statistical ; Neisseria meningitidis/*genetics/pathogenicity ; Numerical Analysis, Computer-Assisted ; Sequence Analysis, DNA ; }, abstract = {MOTIVATION: There is a growing literature on wavelet theory and wavelet methods showing improvements on more classical techniques, especially in the contexts of smoothing and extraction of fundamental components of signals. G+C patterns occur at different lengths (scales) and, for this reason, G+C plots are usually difficult to interpret. Current methods for genome analysis choose a window size and compute a chi(2) statistics of the average value for each window with respect to the whole genome.<br><br>RESULTS: Firstly, wavelets are used to smooth G+C profiles to locate characteristic patterns in genome sequences. The method we use is based on performing a chi(2) statistics on the wavelet coefficients of a profile; thus we do not need to choose a fixed window size, in that the smoothing occurs at a set of different scales. Secondly, a wavelet scalogram is used as a measure for sequence profile comparison; this tool is very general and can be applied to other sequence profiles commonly used in genome analysis. We show applications to the analysis of Deinococcus radiodurans chromosome I, of two strains of Helicobacter pylori (26695, J99) and two of Neisseria meningitidis (serogroup B strain MC58 and serogroup A strain Z2491). We report a list of loci that have different G+C content with respect to the nearby regions; the analysis of N. meningitidis serogroup B shows two new large regions with low G+C content that are putative pathogenicity islands.<br><br>AVAILABILITY: Software and numerical results (profiles, scalograms, high and low frequency components) for all the genome sequences analyzed are available upon request from the authors.}, }
@article {pmid11119305, year = {2000}, author = {King, RD and Karwath, A and Clare, A and Dehaspe, L}, title = {Accurate prediction of protein functional class from sequence in the Mycobacterium tuberculosis and Escherichia coli genomes using data mining.}, journal = {Yeast (Chichester, England)}, volume = {17}, number = {4}, pages = {283-293}, pmid = {11119305}, issn = {0749-503X}, mesh = {Amino Acid Sequence ; Artificial Intelligence ; Bacterial Proteins/chemistry/genetics/*physiology ; *Computational Biology ; Databases, Factual ; Escherichia coli/chemistry/*genetics ; Evolution, Molecular ; *Genome, Bacterial ; Mycobacterium tuberculosis/chemistry/*genetics ; Open Reading Frames ; Proteome ; Sequence Homology, Amino Acid ; Software ; }, abstract = {The analysis of genomics data needs to become as automated as its generation. Here we present a novel data-mining approach to predicting protein functional class from sequence. This method is based on a combination of inductive logic programming clustering and rule learning. We demonstrate the effectiveness of this approach on the M. tuberculosis and E. coli genomes, and identify biologically interpretable rules which predict protein functional class from information only available from the sequence. These rules predict 65% of the ORFs with no assigned function in M. tuberculosis and 24% of those in E. coli, with an estimated accuracy of 60-80% (depending on the level of functional assignment). The rules are founded on a combination of detection of remote homology, convergent evolution and horizontal gene transfer. We identify rules that predict protein functional class even in the absence of detectable sequence or structural homology. These rules give insight into the evolutionary history of M. tuberculosis and E. coli.}, }
@article {pmid11116332, year = {2000}, author = {Olendzenski, L and Liu, L and Zhaxybayeva, O and Murphey, R and Shin, DG and Gogarten, JP}, title = {Horizontal transfer of archaeal genes into the deinococcaceae: detection by molecular and computer-based approaches.}, journal = {Journal of molecular evolution}, volume = {51}, number = {6}, pages = {587-599}, doi = {10.1007/s002390010122}, pmid = {11116332}, issn = {0022-2844}, mesh = {Archaea/*genetics ; *Gene Transfer, Horizontal ; *Genes, Archaeal ; Open Reading Frames ; Phylogeny ; }, abstract = {Members of the Deinococcaceae (e.g., Thermus, Meiothermus, Deinococcus) contain A/V-ATPases typically found in Archaea or Eukaryotes which were probably acquired by horizontal gene transfer. Two methods were used to quantify the extent to which archaeal or eukaryotic genes have been acquired by this lineage. Screening of a Meiothermus ruber library with probes made against Thermoplasma acidophilum DNA yielded a number of clones which hybridized more strongly than background. One of these contained the prolyl tRNA synthetase (RS) gene. Phylogenetic analysis shows the M. ruber and D. radiodurans prolyl RS to be more closely related to archaeal and eukaryal forms of this gene than to the typical bacterial type. Using a bioinformatics approach, putative open reading frames (ORFs) from the prerelease version of the D. radiodurans genome were screened for genes more closely related to archaeal or eukaryotic genes. Putative ORFs were searched against representative genomes from each of the three domains using automated BLAST. ORFs showing the highest matches against archaeal and eukaryotic genes were collected and ranked. Among the top-ranked hits were the A/V-ATPase catalytic and noncatalytic subunits and the prolyl RS genes. Using phylogenetic methods, ORFs were analyzed and trees assessed for evidence of horizontal gene transfer. Of the 45 genes examined, 20 showed topologies in which D. radiodurans homologues clearly group with eukaryotic or archaeal homologues, and 17 additional trees were found to show probable evidence of horizontal gene transfer. Compared to the total number of ORFs in the genome, those that can be identified as having been acquired from Archaea or Eukaryotes are relatively few (approximately 1%), suggesting that interdomain transfer is rare.}, }
@article {pmid11115106, year = {2000}, author = {Yamaguchi, T and Hayashi, T and Takami, H and Nakasone, K and Ohnishi, M and Nakayama, K and Yamada, S and Komatsuzawa, H and Sugai, M}, title = {Phage conversion of exfoliative toxin A production in Staphylococcus aureus.}, journal = {Molecular microbiology}, volume = {38}, number = {4}, pages = {694-705}, doi = {10.1046/j.1365-2958.2000.02169.x}, pmid = {11115106}, issn = {0950-382X}, mesh = {Animals ; Bacterial Toxins/*biosynthesis ; Bacteriophages/*genetics/*isolation &amp; purification ; Base Sequence ; DNA, Viral/genetics ; *Genome, Viral ; Humans ; Mice ; Molecular Sequence Data ; Staphylococcus aureus/genetics/*metabolism/*virology ; }, abstract = {The staphylococcal exfoliative toxins (ETs) are extracellular proteins that cause splitting of human skin at the epidermal layer during infection in infants. Two antigenically distinct toxins possessing identical activity have been isolated from Staphylococcus aureus, ETA and ETB. The gene for ETA (eta) is located on the chromosome, whereas that for ETB is located on a large plasmid. The observation that relatively few clinical isolates produce ETA suggests that the eta gene is acquired by horizontal gene transfer. In this study, we isolated a temperate phage (phiETA) that encodes ETA and determined the complete nucleotide sequence of the phiETA genome. phiETA has a head with a hexagonal outline and a non-contractile and flexible tail. The genome of phiETA is a circularly permuted linear double-stranded DNA, and the genome size is 43 081 bp. Sixty-six open reading frames (ORFs) were identified on the phiETA genome, including eta, which was found to be located very close to a putative attachment site (attP). phiETA converted ETA non-producing strains into ETA producers. Southern blot analysis of chromosomal DNA from clinical isolates suggested that phiETA or related phages are responsible for the acquisition of eta genes in S. aureus.}, }
@article {pmid11115105, year = {2000}, author = {Diruggiero, J and Dunn, D and Maeder, DL and Holley-Shanks, R and Chatard, J and Horlacher, R and Robb, FT and Boos, W and Weiss, RB}, title = {Evidence of recent lateral gene transfer among hyperthermophilic archaea.}, journal = {Molecular microbiology}, volume = {38}, number = {4}, pages = {684-693}, doi = {10.1046/j.1365-2958.2000.02161.x}, pmid = {11115105}, issn = {0950-382X}, mesh = {Amino Acid Sequence ; DNA Transposable Elements/genetics ; *Gene Transfer, Horizontal ; *Genes, Archaeal ; Genome, Archaeal ; Molecular Sequence Data ; Pyrococcus furiosus/*genetics ; Sequence Alignment ; Thermococcus/*genetics ; }, abstract = {A total of 153 nucleotide differences were found over a contiguous 16 kb region between two hyperthermophilic Archaea, Pyrococcus furiosus and Thermococcus litoralis. The 16 kb region in P. furiosus is flanked by insertion sequence (IS) elements with inverted and direct repeats. Both IS elements contain a single open reading frame (ORF) encoding a putative protein of 233 amino acids identified as a transposase. This 16 kb region has the features of a typical bacterial composite transposon and represents a possible mechanism for lateral gene transfer between Archaea or possibly between Archaea and Bacteria. A total of 23 homologous IS elements was found in the genome sequence of P. furiosus, whereas no full-length IS elements were identified in the genomes of Pyrococcus abyssi and Pyrococcus horikoshii. Only one IS element was found in T. litoralis. In P. furiosus and T. litoralis, the 16 kb region contains an ABC transport system for maltose and trehalose that was characterized biochemically for T. litoralis. Regulation of expression studies showed that the malE gene, located on the transposon, and the encoded trehalose/maltose-binding protein (TMBP) are induced in the presence of maltose and trehalose in both P. furiosus and T. litoralis. The implications of transposition as a mechanism for lateral gene transfer among Archaea are discussed.}, }
@article {pmid11114919, year = {2001}, author = {Sy, A and Giraud, E and Jourand, P and Garcia, N and Willems, A and de Lajudie, P and Prin, Y and Neyra, M and Gillis, M and Boivin-Masson, C and Dreyfus, B}, title = {Methylotrophic Methylobacterium bacteria nodulate and fix nitrogen in symbiosis with legumes.}, journal = {Journal of bacteriology}, volume = {183}, number = {1}, pages = {214-220}, pmid = {11114919}, issn = {0021-9193}, mesh = {Acyltransferases/genetics ; Alcohol Oxidoreductases/genetics ; Bacterial Proteins ; DNA, Bacterial/analysis/genetics ; DNA, Ribosomal/analysis/genetics ; Fabaceae/*microbiology ; Methanol/*metabolism ; Methylobacterium/*classification/genetics/isolation &amp; purification/*physiology ; Molecular Sequence Data ; Nitrogen Fixation/*physiology ; Oxidation-Reduction ; Phylogeny ; *Plants, Medicinal ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; *Symbiosis ; }, abstract = {Rhizobia described so far belong to three distinct phylogenetic branches within the alpha-2 subclass of Proteobacteria. Here we report the discovery of a fourth rhizobial branch involving bacteria of the Methylobacterium genus. Rhizobia isolated from Crotalaria legumes were assigned to a new species, "Methylobacterium nodulans," within the Methylobacterium genus on the basis of 16S ribosomal DNA analyses. We demonstrated that these rhizobia facultatively grow on methanol, which is a characteristic of Methylobacterium spp. but a unique feature among rhizobia. Genes encoding two key enzymes of methylotrophy and nodulation, the mxaF gene, encoding the alpha subunit of the methanol dehydrogenase, and the nodA gene, encoding an acyltransferase involved in Nod factor biosynthesis, were sequenced for the type strain, ORS2060. Plant tests and nodA amplification assays showed that "M. nodulans" is the only nodulating Methylobacterium sp. identified so far. Phylogenetic sequence analysis showed that "M. nodulans" NodA is closely related to Bradyrhizobium NodA, suggesting that this gene was acquired by horizontal gene transfer.}, }
@article {pmid11114328, year = {2000}, author = {Denamur, E and Lecointre, G and Darlu, P and Tenaillon, O and Acquaviva, C and Sayada, C and Sunjevaric, I and Rothstein, R and Elion, J and Taddei, F and Radman, M and Matic, I}, title = {Evolutionary implications of the frequent horizontal transfer of mismatch repair genes.}, journal = {Cell}, volume = {103}, number = {5}, pages = {711-721}, doi = {10.1016/s0092-8674(00)00175-6}, pmid = {11114328}, issn = {0092-8674}, mesh = {*Adenosine Triphosphatases ; Alleles ; Bacterial Proteins/genetics ; *Base Pair Mismatch ; *DNA Repair ; *DNA-Binding Proteins ; Escherichia coli/genetics ; *Escherichia coli Proteins ; *Evolution, Molecular ; Exodeoxyribonuclease V ; Exodeoxyribonucleases/genetics ; Genotype ; MutL Proteins ; MutS DNA Mismatch-Binding Protein ; Mutation ; Phenotype ; Phosphoric Monoester Hydrolases/genetics ; Phylogeny ; Polymerase Chain Reaction ; Pyrophosphatases ; Recombination, Genetic ; Salmonella typhimurium/genetics ; }, abstract = {Mutation and subsequent recombination events create genetic diversity, which is subjected to natural selection. Bacterial mismatch repair (MMR) deficient mutants, exhibiting high mutation and homologous recombination rates, are frequently found in natural populations. Therefore, we have explored the possibility that MMR deficiency emerging in nature has left some "imprint" in the sequence of bacterial genomes. Comparative molecular phylogeny of MMR genes from natural Escherichia coli isolates shows that, compared to housekeeping genes, individual functional MMR genes exhibit high sequence mosaicism derived from diverse phylogenetic lineages. This apparent horizontal gene transfer correlates with hyperrecombination phenotype of MMR-deficient mutators. The sequence mosaicism of MMR genes may be a hallmark of a mechanism of adaptive evolution that involves modulation of mutation and recombination rates by recurrent losses and reacquisitions of MMR gene functions.}, }
@article {pmid11110912, year = {2000}, author = {Koretke, KK and Lupas, AN and Warren, PV and Rosenberg, M and Brown, JR}, title = {Evolution of two-component signal transduction.}, journal = {Molecular biology and evolution}, volume = {17}, number = {12}, pages = {1956-1970}, doi = {10.1093/oxfordjournals.molbev.a026297}, pmid = {11110912}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Animals ; Archaeal Proteins/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Linkage ; Histidine Kinase ; Molecular Sequence Data ; Phosphorylation ; Phylogeny ; Protein Kinases/*genetics ; Protein Structure, Tertiary ; Sequence Homology ; *Signal Transduction ; }, abstract = {Two-component signal transduction (TCST) systems are the principal means for coordinating responses to environmental changes in bacteria as well as some plants, fungi, protozoa, and archaea. These systems typically consist of a receptor histidine kinase, which reacts to an extracellular signal by phosphorylating a cytoplasmic response regulator, causing a change in cellular behavior. Although several model systems, including sporulation and chemotaxis, have been extensively studied, the evolutionary relationships between specific TCST systems are not well understood, and the ancestry of the signal transduction components is unclear. Phylogenetic trees of TCST components from 14 complete and 6 partial genomes, containing 183 histidine kinases and 220 response regulators, were constructed using distance methods. The trees showed extensive congruence in the positions of 11 recognizable phylogenetic clusters. Eukaryotic sequences were found almost exclusively in one cluster, which also showed the greatest extent of domain variability in its component proteins, and archaeal sequences mainly formed species-specific clusters. Three clusters in different parts of the kinase tree contained proteins with serine-phosphorylating activity. All kinases were found to be monophyletic with respect to other members of their superfamily, such as type II topoisomerases and Hsp90. Structural analysis further revealed significant similarity to the ATP-binding domain of eukaryotic protein kinases. TCST systems are of bacterial origin and radiated into archaea and eukaryotes by lateral gene transfer. Their components show extensive coevolution, suggesting that recombination has not been a major factor in their differentiation. Although histidine kinase activity is prevalent, serine kinases have evolved multiple times independently within this family, accompanied by a loss of the cognate response regulator(s). The structural and functional similarity between TCST kinases and eukaryotic protein kinases raises the possibility of a distant evolutionary relationship.}, }
@article {pmid10963328, year = {2000}, author = {Moreira, D and Philippe, H}, title = {Molecular phylogeny: pitfalls and progress.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {3}, number = {1}, pages = {9-16}, pmid = {10963328}, issn = {1139-6709}, mesh = {Artifacts ; Classification/methods ; *Evolution, Molecular ; *Genetics, Microbial ; Models, Biological ; Mutation ; *Phylogeny ; Prokaryotic Cells/*classification ; Selection, Genetic ; Sequence Homology ; }, abstract = {Molecular phylogeny based on nucleotide or amino acid sequence comparison has become a widespread tool for general taxonomy and evolutionary analyses. It seems the only means to establish a natural classification of microorganisms, since their phenotypic traits are not always consistent with genealogy. After an optimistic period during which comprehensive microbial evolutionary pictures appeared, the discovery of several pitfalls affecting molecular phylogenetic reconstruction challenged the general validity of this approach. In addition to biological factors, such as horizontal gene transfer, some methodological problems may produce misleading phylogenies. They are essentially (i) loss of phylogenetic signal by the accumulation of overlapping mutations, (ii) incongruity between the real evolutionary process and the assumed models of sequence evolution, and (iii) differences of evolutionary rates among species or among positions within a sequence. Here, we discuss these problems and some strategies proposed to overcome their effects.}, }
@article {pmid11108270, year = {2000}, author = {Kakuma, T and Wang, ZW and Pan, W and Unger, RH and Zhou, YT}, title = {Role of leptin in peroxisome proliferator-activated receptor gamma coactivator-1 expression.}, journal = {Endocrinology}, volume = {141}, number = {12}, pages = {4576-4582}, doi = {10.1210/endo.141.12.7804}, pmid = {11108270}, issn = {0013-7227}, support = {DK-02700-37/DK/NIDDK NIH HHS/United States ; }, mesh = {Adenoviridae/genetics ; Adipocytes/metabolism ; Adipose Tissue, Brown/*metabolism ; Animals ; Blotting, Northern ; Cells, Cultured ; Cloning, Molecular ; Cold Temperature ; *Gene Expression ; Gene Transfer, Horizontal ; Leptin/deficiency/genetics/*physiology ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Mutant Strains ; Molecular Sequence Data ; Obesity/genetics/metabolism ; Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha ; RNA, Messenger/analysis ; RNA-Binding Proteins ; Rats ; Rats, Wistar ; Rats, Zucker ; Recombinant Fusion Proteins ; Reverse Transcriptase Polymerase Chain Reaction ; Transcription Factors/*genetics ; }, abstract = {Peroxisome proliferator-activated receptor-gamma coactivator-1 (PGC-1), a cold-induced protein expressed in brown adipose tissue (BAT), plays a role in adaptive thermogenesis by up-regulating uncoupling proteins (UCP). Here, we explore its relationship to the thermogenic actions of leptin, which also up-regulates UCPs. We find that PGC-1 messenger RNA (mRNA) is markedly reduced in BAT of obese leptin-deficient (ob/ob mice) and leptin-unresponsive (db/db mice and Zucker diabetic fatty fa/fa rats) rodents. Whereas, after cold exposure (6 C for 7 h), PGC-1 mRNA increases 2.6-fold in BAT of lean +/+ rats, it rises only 30% in fa/fa rats. Four days after induction of hyperleptinemia (>30 ng/ml) in Wistar rats, by adenovirus gene transfer, PGC-1 mRNA in BAT was 2.3-fold and UCP-1, 4-fold above controls. In isolated white adipocytes, PGC-1 mRNA increased 4.4-fold within 6 h of incubation with 20 ng/ml of leptin. We conclude that leptin action is required for normal basal and cold-stimulated PGC-1 expression in BAT in rodents and that hyperleptinemia rapidly up-regulates its expression, at least in part, by direct action.}, }
@article {pmid11106250, year = {2000}, author = {Kelly, FJ and Miller, CR and Buchsbaum, DJ and Gomez-Navarro, J and Barnes, MN and Alvarez, RD and Curiel, DT}, title = {Selectivity of TAG-72-targeted adenovirus gene transfer to primary ovarian carcinoma cells versus autologous mesothelial cells in vitro.}, journal = {Clinical cancer research : an official journal of the American Association for Cancer Research}, volume = {6}, number = {11}, pages = {4323-4333}, pmid = {11106250}, issn = {1078-0432}, support = {IT32-CA 75930/CA/NCI NIH HHS/United States ; R01-CA 68245/CA/NCI NIH HHS/United States ; R01-CA 74242/CA/NCI NIH HHS/United States ; }, mesh = {Adenoviridae/*genetics ; Antigens, Neoplasm/biosynthesis/*genetics ; Cells, Cultured ; Epithelial Cells/metabolism ; Female ; Gene Transfer, Horizontal ; *Genetic Therapy ; Glycoproteins/biosynthesis/*genetics ; Humans ; Immunoglobulin Fab Fragments/administration &amp; dosage ; Integrins/analysis ; Ovarian Neoplasms/metabolism/pathology/*therapy ; Receptors, Virus/analysis ; Receptors, Vitronectin/analysis ; }, abstract = {Efficient gene transfer by recombinant adenovirus (Ad) vectors depends on expression of CAR and alpha(v) integrin on target cells. Because Ad may also infect nearby nontarget cells expressing these receptors, such as peritoneal mesothelial cells after i.p. injection, we hypothesized that targeting Ad gene delivery to a receptor overexpressed on most ovarian carcinoma cells, such as TAG-72, would enhance the selectivity of Ad gene transfer when used in this context. A monoclonal antibody that has been investigated clinically for immunotherapy and immunodetection of ovarian carcinomas, namely CC49, was used to construct a bispecific conjugate with the Fab fragment of a neutralizing anti-knob mAb to target Ad binding via TAG-72. This conjugate facilitated TAG-72-specific, CAR-independent Ad reporter gene transfer to both ovarian cancer cell lines and primary ovarian cancer cells cultured from malignant ascites fluid. Fab-CC49 was very selective for tumor cells, augmenting Ad gene transfer to primary ovarian cancer cells 2- to 28-fold relative to untargeted Ad, while also decreasing gene transfer to autologous cultured mesothelial cells 4- to 9-fold. These data suggest that targeting Ad via TAG-72 may improve the selectivity of Ad gene transfer for ovarian tumors 8- to 252-fold on i.p. vector injection. These results also define the requirements for a candidate target receptor in the rational design of a targeted Ad vector for ultimate clinical utility, one that selectively infects tumor cells and spares normal cells on i.p. injection. Such a vector may increase gene transfer and decrease the toxicity of Ad vectors, which would improve the therapeutic index of cytotoxic gene therapy for ovarian cancer in clinical trials.}, }
@article {pmid11104729, year = {2000}, author = {Partovian, C and Adnot, S and Raffestin, B and Louzier, V and Levame, M and Mavier, IM and Lemarchand, P and Eddahibi, S}, title = {Adenovirus-mediated lung vascular endothelial growth factor overexpression protects against hypoxic pulmonary hypertension in rats.}, journal = {American journal of respiratory cell and molecular biology}, volume = {23}, number = {6}, pages = {762-771}, doi = {10.1165/ajrcmb.23.6.4106}, pmid = {11104729}, issn = {1044-1549}, mesh = {15-Hydroxy-11 alpha,9 alpha-(epoxymethano)prosta-5,13-dienoic Acid/pharmacology ; Adenoviridae/genetics ; Animals ; Bronchoalveolar Lavage Fluid/chemistry ; Calcimycin/pharmacology ; Capillary Permeability/drug effects ; DNA, Recombinant/administration &amp; dosage/genetics/metabolism ; Dose-Response Relationship, Drug ; Endothelial Growth Factors/*genetics/metabolism ; Endothelin-1/pharmacology ; Gene Expression Regulation ; Gene Transfer, Horizontal ; Humans ; Hypertension, Pulmonary/genetics/metabolism/*prevention &amp; control ; Hypoxia/*physiopathology ; In Vitro Techniques ; Ionophores/pharmacology ; Lung/drug effects/*metabolism/physiopathology ; Lymphokines/*genetics/metabolism ; Nitric Oxide Synthase/drug effects/metabolism ; Nitric Oxide Synthase Type III ; Rats ; Rats, Wistar ; Time Factors ; Vascular Endothelial Growth Factor A ; Vascular Endothelial Growth Factors ; Vasodilation/drug effects ; }, abstract = {Chronic hypoxic pulmonary hypertension (PH) is associated with vasoconstriction and structural remodeling of pulmonary vessels including narrowing of the arterial lumen and loss of distal functional arteries. To test whether lung overexpression of the angiogenic factor vascular endothelial growth factor (VEGF) is beneficial in hypoxic PH, recombinant adenovirus encoding the human VEGF 165 gene under the control of a cytomegalovirus promoter (Ad. VEGF) or control vector containing no gene in the expression cassette (Ad.Null) was administered intratracheally to rats. With Ad. VEGF (10(8) plaque-forming units [pfu]), VEGF protein was present in bronchoalveolar lavage fluid as early as 2 d and until 17 d after gene transfer, but was not detected in serum. Only small patchy areas of mononuclear cells without cell damage, edema, or hemorrhage were observed on lung histology with no significant change in lung permeability. In rats pretreated with Ad.VEGF (10(8) pfu) 2 d before a 2-wk exposure to hypoxia (10% O(2)), lower values versus Ad. Null-pretreated controls were found for pulmonary artery pressure (25 +/- 1 versus 30 +/- 2 mm Hg, P < 0.05), right ventricular over left ventricular-plus-septum weight (0.37 +/- 0.01 versus 0.47 +/- 0. 02, P < 0.001), normalized wall thickness of 50- to 200-microm vessels (P < 0.001), and muscularization of distal vessels (P < 0. 001). Pretreatment with Ad.VEGF (10(8) pfu) increased endothelial nitric oxide synthase activity in lung tissue and partially restored endothelium-dependent vasodilation in isolated lungs from chronically hypoxic rats, as assessed by improvement of ionophore A23187-induced vasodilation and attenuation of endothelin-1 (300 pmol)-induced vasoconstriction, an effect abolished in the presence of nitro-L-arginine methylester. We conclude that adenoviral-mediated VEGF overexpression in the lungs attenuates development of hypoxic PH, in part by protecting endothelium-dependent function.}, }
@article {pmid11102698, year = {2000}, author = {Brochier, C and Philippe, H and Moreira, D}, title = {The evolutionary history of ribosomal protein RpS14: horizontal gene transfer at the heart of the ribosome.}, journal = {Trends in genetics : TIG}, volume = {16}, number = {12}, pages = {529-533}, doi = {10.1016/s0168-9525(00)02142-9}, pmid = {11102698}, issn = {0168-9525}, mesh = {Bacteria/genetics ; *Evolution, Molecular ; Operon ; Ribosomal Proteins/*genetics ; Ribosomes/*genetics ; *Transfection ; }, }
@article {pmid11101666, year = {2000}, author = {Lorenz, MG and Sikorski, J}, title = {The potential for intraspecific horizontal gene exchange by natural genetic transformation: sexual isolation among genomovars of Pseudomonas stutzeri.}, journal = {Microbiology (Reading, England)}, volume = {146 Pt 12}, number = {}, pages = {3081-3090}, doi = {10.1099/00221287-146-12-3081}, pmid = {11101666}, issn = {1350-0872}, mesh = {*Conjugation, Genetic/genetics ; DNA, Bacterial/analysis/genetics ; DNA-Directed RNA Polymerases/*genetics ; *Gene Transfer, Horizontal ; Genotype ; Humans ; Molecular Sequence Data ; Phylogeny ; Pseudomonas/classification/*genetics/physiology ; Sequence Analysis, DNA ; *Transformation, Bacterial ; }, abstract = {The potential for natural genetic transformation among the seven genomovars (gvs) of Pseudomonas stutzeri was investigated. Of the 12 strains originating from a variety of environments, six strains (50%) from five gvs were competent for DNA uptake (Rif(R) marker). The transformation frequencies varied over more than three orders of magnitude. With three highly transformable strains (ATCC 17587, ATCC 17641, JM300) from two gvs and all other strains as DNA donors, sexual isolation from other pseudomonad species (Pseudomonas alcaligenes, Pseudomonas mendocina) and also from other P. stutzeri gvs was observed (i.e. heterogamic transformation was reduced). For ATCC 17587 (gv 2) and ATCC 17641 (gv 8), heterogamic transformation was up to two and three orders of magnitude lower with other P. stutzeri gv and the other species employed, respectively, than in homogamic transformations. Interestingly, whereas with ATCC 17587 and ATCC 17641 heterogamic transformation with donors of the same gv was as high as homogamic transformation, JM300 (gv 8) was sexually isolated from its nearest relative (ATCC 17641). Also, sexual isolation of JM300 from other P. stutzeri gvs was most pronounced among the recipients tested, in some cases reaching the highest levels found with the other species as DNA donors (reduction of heterogamic transformation by 4000-fold). Results obtained here from nucleotide sequence analysis of part (422 nt) of the gene for the RNA polymerase ss subunit (rpoB) from various strains indicated that sexual isolation of ATCC 17641 increased with nucleotide sequence divergence. Implications of the observed great heterogeneity in transformability, competence levels and sexual isolation among strains are discussed with regard to the evolution of P. stutzeri.}, }
@article {pmid11100826, year = {2000}, author = {Dobrindt, U and Reidl, J}, title = {Pathogenicity islands and phage conversion: evolutionary aspects of bacterial pathogenesis.}, journal = {International journal of medical microbiology : IJMM}, volume = {290}, number = {6}, pages = {519-527}, doi = {10.1016/S1438-4221(00)80017-X}, pmid = {11100826}, issn = {1438-4221}, mesh = {Bacteria/genetics/*pathogenicity ; Bacteriophages/*genetics ; Biological Evolution ; Escherichia coli/pathogenicity ; Gene Transfer, Horizontal ; Plasmids ; Streptococcus pyogenes/pathogenicity ; Vibrio cholerae/pathogenicity ; Virulence/genetics ; }, abstract = {Horizontal gene transfer plays a key role in the generation of novel bacterial pathogens. Besides plasmids and bacteriophages, large genomic regions termed pathogenicity islands (PAIs) can be transferred horizontally. All three mechanisms for DNA exchange or transfer may be important for the evolution of bacterial pathogens.}, }
@article {pmid11092850, year = {2000}, author = {Ke, D and Boissinot, M and Huletsky, A and Picard, FJ and Frenette, J and Ouellette, M and Roy, PH and Bergeron, MG}, title = {Evidence for horizontal gene transfer in evolution of elongation factor Tu in enterococci.}, journal = {Journal of bacteriology}, volume = {182}, number = {24}, pages = {6913-6920}, pmid = {11092850}, issn = {0021-9193}, support = {AI38406/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Blotting, Southern ; Enterococcus/*genetics/metabolism ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Gram-Positive Bacteria/genetics/metabolism ; Molecular Sequence Data ; Peptide Elongation Factor Tu/chemistry/*genetics/metabolism ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {The elongation factor Tu, encoded by tuf genes, is a GTP binding protein that plays a central role in protein synthesis. One to three tuf genes per genome are present, depending on the bacterial species. Most low-G+C-content gram-positive bacteria carry only one tuf gene. We have designed degenerate PCR primers derived from consensus sequences of the tuf gene to amplify partial tuf sequences from 17 enterococcal species and other phylogenetically related species. The amplified DNA fragments were sequenced either by direct sequencing or by sequencing cloned inserts containing putative amplicons. Two different tuf genes (tufA and tufB) were found in 11 enterococcal species, including Enterococcus avium, Enterococcus casseliflavus, Enterococcus dispar, Enterococcus durans, Enterococcus faecium, Enterococcus gallinarum, Enterococcus hirae, Enterococcus malodoratus, Enterococcus mundtii, Enterococcus pseudoavium, and Enterococcus raffinosus. For the other six enterococcal species (Enterococcus cecorum, Enterococcus columbae, Enterococcus faecalis, Enterococcus sulfureus, Enterococcus saccharolyticus, and Enterococcus solitarius), only the tufA gene was present. Based on 16S rRNA gene sequence analysis, the 11 species having two tuf genes all have a common ancestor, while the six species having only one copy diverged from the enterococcal lineage before that common ancestor. The presence of one or two copies of the tuf gene in enterococci was confirmed by Southern hybridization. Phylogenetic analysis of tuf sequences demonstrated that the enterococcal tufA gene branches with the Bacillus, Listeria, and Staphylococcus genera, while the enterococcal tufB gene clusters with the genera Streptococcus and Lactococcus. Primary structure analysis showed that four amino acid residues encoded within the sequenced regions are conserved and unique to the enterococcal tufB genes and the tuf genes of streptococci and Lactococcus lactis. The data suggest that an ancestral streptococcus or a streptococcus-related species may have horizontally transferred a tuf gene to the common ancestor of the 11 enterococcal species which now carry two tuf genes.}, }
@article {pmid11089544, year = {2000}, author = {Bandyopadhyay, G and Kanoh, Y and Sajan, MP and Standaert, ML and Farese, RV}, title = {Effects of adenoviral gene transfer of wild-type, constitutively active, and kinase-defective protein kinase C-lambda on insulin-stimulated glucose transport in L6 myotubes.}, journal = {Endocrinology}, volume = {141}, number = {11}, pages = {4120-4127}, doi = {10.1210/endo.141.11.7766}, pmid = {11089544}, issn = {0013-7227}, support = {R01 DK065969/DK/NIDDK NIH HHS/United States ; 2R01-DK-38079-09A1/DK/NIDDK NIH HHS/United States ; }, mesh = {Adenoviridae/*genetics ; Animals ; Biological Transport/drug effects ; Cell Line ; Cell Membrane/metabolism ; Gene Expression ; *Gene Transfer, Horizontal ; Glucose/*metabolism ; Glucose Transporter Type 1 ; Glucose Transporter Type 4 ; Insulin/*pharmacology ; Isoenzymes/genetics/metabolism ; Monosaccharide Transport Proteins/metabolism ; *Muscle Proteins ; Muscle, Skeletal/*metabolism ; Mutation ; Protein Kinase C/*genetics/metabolism ; *Protein Serine-Threonine Kinases ; Proto-Oncogene Proteins/metabolism ; Proto-Oncogene Proteins c-akt ; Rats ; }, abstract = {We used adenoviral gene transfer methods to evaluate the role of atypical protein kinase Cs (PKCs) during insulin stimulation of glucose transport in L6 myotubes. Expression of wild-type PKC-lambda potentiated maximal and half-maximal effects of insulin on 2-deoxyglucose uptake, but did not alter basal uptake. Expression of constitutively active PKC-lambda enhanced basal 2-deoxyglucose uptake to virtually the same extent as that observed during insulin treatment. In contrast, expression of kinase-defective PKC-lambda completely blocked insulin-stimulated, but not basal, 2-deoxyglucose uptake. Similar to alterations in glucose transport, constitutively active PKC-lambda mimicked, and kinase-defective PKC-lambda completely inhibited, insulin effects on GLUT4 glucose transporter translocation to the plasma membrane. Expression of kinase-defective PKC-lambda, in addition to inhibition of atypical PKC enzyme activity, was attended by paradoxical increases in GLUT4 and GLUT1 glucose transporter levels and insulin-stimulated protein kinase B enzyme activity. Our findings suggest that in L6 myotubes, 1) atypical PKCs are required and sufficient for insulin-stimulated GLUT4 translocation and glucose transport; and 2) activation of protein kinase B in the absence of activation of atypical PKCs is insufficient for insulin-induced activation of glucose transport.}, }
@article {pmid11088009, year = {2000}, author = {Eisen, JA}, title = {Horizontal gene transfer among microbial genomes: new insights from complete genome analysis.}, journal = {Current opinion in genetics &amp; development}, volume = {10}, number = {6}, pages = {606-611}, doi = {10.1016/s0959-437x(00)00143-x}, pmid = {11088009}, issn = {0959-437X}, mesh = {*Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Archaeal ; *Genome, Bacterial ; Models, Genetic ; }, abstract = {The determination and analysis of complete genome sequences has led to the suggestion that horizontal gene transfer may be much more extensive than previously appreciated. Many of these studies, however, rely on evidence that could be generated by forces other than gene transfer including selection, variable evolutionary rates, and biased sampling.}, }
@article {pmid11087143, year = {2000}, author = {Chan, SY and Goodman, RE and Szmuszkovicz, JR and Roessler, B and Eichwald, EJ and Bishop, DK}, title = {DNA-liposome versus adenoviral mediated gene transfer of transforming growth factor beta1 in vascularized cardiac allografts: differential sensitivity of CD4+ and CD8+ T cells to transforming growth factor beta1.}, journal = {Transplantation}, volume = {70}, number = {9}, pages = {1292-1301}, doi = {10.1097/00007890-200011150-00006}, pmid = {11087143}, issn = {0041-1337}, support = {AI HL 31946/AI/NIAID NIH HHS/United States ; }, mesh = {Adenoviridae/physiology ; Animals ; CD4-Positive T-Lymphocytes/drug effects ; CD8-Positive T-Lymphocytes/drug effects ; Coronary Vessels/metabolism ; DNA/*physiology ; Female ; Gene Expression ; Gene Transfer, Horizontal ; Heart Transplantation/physiology ; Interleukin-12/pharmacology ; Liposomes ; Mice ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; Sensitivity and Specificity ; Th1 Cells/immunology ; Transforming Growth Factor beta/*genetics ; Transforming Growth Factor beta1 ; Transgenes/genetics ; }, abstract = {We have developed a model of transforming growth factor (TGF)beta1 gene transfer into mouse vascularized cardiac allografts to study the use of gene transfer as an immunosuppressive therapy in transplantation. Donor hearts were perfused with either DNA-liposome complexes or adenoviral vectors that encode the active form of human TGFbeta1. DNA-liposome mediated transfection prolonged allograft survival in approximately two-thirds of transplant recipients, while adenoviral delivery of TGFbeta1 was not protective. Protective TGFbeta1 gene transfer was associated with reduced Th1 responses and an inhibition of the alloantibody isotype switch. The protective effects of TGFbeta1 gene transfer were overridden by exogenous interleukin-12 administration. Interestingly, alloreactive CD4+ and CD8+ cells exhibited distinct sensitivities to TGFbeta1 gene transfer: CD4+ Th1 function was abrogated by this modality, although CD8+ Th1 function was not. Transient depletion of recipient CD8+ cells markedly prolonged the survival of grafts transfected with either DNA-liposome complexes or adenoviral vectors. Transgene expression persisted for at least 60 days, and Th1 responses were not detectable until CD8+ T cells repopulated the periphery. However, long-term transfected allografts appeared to exhibit exacerbated fibrosis and neointimal development. These manifestations of chronic rejection were absent in long-term transfected isografts, suggesting that long-term expression of active TGFbeta1 alone is not sufficient to induce fibrosis of the grafts. Collectively, these data illustrate the utility of immunosuppressive gene therapy as a treatment for transplantation when combined with additional conditioning regimens. Further, they illustrate that alloreactive CD4+ and CD8+ cells may be differentially influenced by cytokine manipulation strategies.}, }
@article {pmid11084459, year = {2000}, author = {Collinet, P and Lanvin, D and Vereecque, R and Quesnel, B and Querleu, D}, title = {[Gene therapy and ovarian cancer: update of clinical trials].}, journal = {Journal de gynecologie, obstetrique et biologie de la reproduction}, volume = {29}, number = {6}, pages = {532-537}, pmid = {11084459}, issn = {0368-2315}, mesh = {*Clinical Trials as Topic ; Cytokines/genetics ; Female ; Gene Transfer, Horizontal ; Genes, BRCA1 ; Genes, p53 ; *Genetic Therapy ; Humans ; Immunotherapy ; Mutation ; Ovarian Neoplasms/genetics/*therapy ; }, abstract = {Ovarian cancer is the first leading cause of death from gynecologic cancer. Advances in therapy are needed to obtain complete response after surgery and/or chemotherapy. Gene therapy is a new alternative therapeutic approach. 380 gene therapy clinical trials (3173 patients) are going to be assessed. 63% of these trials concern therapy of cancer. 16 gene therapy clinical trails are applied to ovarian cancer. These 16 clinical trials assess different treatment strategies: Mutation compensation by replacement of an altered tumor suppressor gene (p53, BRCA1); Molecular chemotherapy by transfer of a suicide gene (HSV-tk gene); Antitumoral immunotherapy by cytokine gene transfer (IL2, IL12); Oncogene inhibition (erb-B2 gene); Multi Drug Resistance gene transfer. A knowledge of basis concepts of gene transfer strategies, is needed to understand these different treatment strategies. Thus, the goals of this review are, first, to provide the basis concepts of gene transfer strategies to the obstetrician-gynecologist and second, to submit recent gene therapy clinical trials about ovarian cancer.}, }
@article {pmid11083763, year = {2000}, author = {Lukomski, S and Nakashima, K and Abdi, I and Cipriano, VJ and Ireland, RM and Reid, SD and Adams, GG and Musser, JM}, title = {Identification and characterization of the scl gene encoding a group A Streptococcus extracellular protein virulence factor with similarity to human collagen.}, journal = {Infection and immunity}, volume = {68}, number = {12}, pages = {6542-6553}, pmid = {11083763}, issn = {0019-9567}, support = {AI33119/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Autoimmunity ; Bacterial Adhesion ; Bacterial Proteins/*genetics ; Base Sequence ; Collagen/*genetics ; Epithelial Cells/microbiology ; *Genes, Bacterial ; Genetic Variation ; Humans ; Male ; Mice ; Molecular Sequence Data ; Repetitive Sequences, Amino Acid ; Serotyping ; Streptococcus pyogenes/genetics/*pathogenicity ; Virulence ; }, abstract = {Group A Streptococcus (GAS) expresses cell surface proteins that mediate important biological functions such as resistance to phagocytosis, adherence to plasma and extracellular matrix proteins, and degradation of host proteins. An open reading frame encoding a protein of 348 amino acid residues was identified by analysis of the genome sequence available for a serotype M1 strain. The protein has an LPATGE sequence located near the carboxy terminus that matches the consensus sequence (LPXTGX) present in many gram-positive cell wall-anchored molecules. Importantly, the central region of this protein contains 50 contiguous Gly-X-X triplet amino acid motifs characteristic of the structure of human collagen. The structural gene (designated scl for streptococcal collagen-like) was present in all 50 GAS isolates tested, which together express 21 different M protein types and represent the breadth of genomic diversity in the species. DNA sequence analysis of the gene in these 50 isolates found that the number of contiguous Gly-X-X motifs ranged from 14 in serotype M6 isolates to 62 in a serotype M41 organism. M1 and M18 organisms had the identical allele, which indicates very recent horizontal gene transfer. The gene was transcribed abundantly in the logarithmic but not stationary phase of growth, a result consistent with the occurrence of a DNA sequence with substantial homology with a consensus Mga binding site immediately upstream of the scl open reading frame. Two isogenic mutant M1 strains created by nonpolar mutagenesis of the scl structural gene were not attenuated for mouse virulence as assessed by intraperitoneal inoculation. In contrast, the isogenic mutant derivative made from the M1 strain representative of the subclone most frequently causing human infections was significantly less virulent when inoculated subcutaneously into mice. In addition, both isogenic mutant strains had significantly reduced adherence to human A549 epithelial cells grown in culture. These studies identify a new extracellular GAS virulence factor that is widely distributed in the species and participates in adherence to host cells and soft tissue pathology.}, }
@article {pmid11080587, year = {2000}, author = {Nara, T and Hshimoto, T and Aoki, T}, title = {Evolutionary implications of the mosaic pyrimidine-biosynthetic pathway in eukaryotes.}, journal = {Gene}, volume = {257}, number = {2}, pages = {209-222}, doi = {10.1016/s0378-1119(00)00411-x}, pmid = {11080587}, issn = {0378-1119}, mesh = {Amino Acid Sequence ; Animals ; Aspartate Carbamoyltransferase/genetics ; Carbamoyl-Phosphate Synthase (Glutamine-Hydrolyzing)/genetics ; Dihydroorotase/genetics ; Dihydroorotate Dehydrogenase ; Eukaryotic Cells/enzymology/*metabolism ; *Evolution, Molecular ; Humans ; Molecular Sequence Data ; Orotate Phosphoribosyltransferase/genetics ; Orotidine-5'-Phosphate Decarboxylase/genetics ; Oxidoreductases/genetics ; *Oxidoreductases Acting on CH-CH Group Donors ; Phylogeny ; Pyrimidines/*biosynthesis ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {The de-novo pyrimidine biosynthetic pathway involves six enzymes, in order from the first to the sixth step, carbamoyl-phosphate synthetase II (CPS II) comprising glutamine amidotransferase (GAT) and carbamoyl-phosphate synthetase (CPS) domains or subunits, aspartate carbamoyltransferase (ACT), dihydroorotase (DHO), dihydroorotate dehydrogenase (DHOD), orotate phosphoribosyltransferase (OPRT), and orotidine-5'-monophosphate decarboxylase (OMPDC). In contrast with reports on molecular evolution of the individual enzymes, we attempted to draw an evolutionary picture of the whole pathway using the protein phylogeny. We demonstrate highly mosaic organizations of the pyrimidine biosynthetic pathway in eukaryotes. During evolution of the eukaryotic pathway, plants and fungi (or their ancestors) in particular may have secondarily acquired the characteristic enzymes. This is consistent with the fact that the organization of plant enzymes is highly chimeric: (1) two subunits of CPS II, GAT and CPS, cluster with a clade including cyanobacteria and red algal chloroplasts, (2) ACT not with a cyanobacterium, Synechocystis spp., irrespective of its putative signal sequence targeting into chloroplasts, and (3) DHO with a clade of proteobacteria. In fungi, DHO and OPRT cluster respectively with the corresponding proteobacterial counterparts. The phylogenetic analyses of DHOD and OMPDC also support the implications of the mosaic pyrimidine biosynthetic pathway in eukaryotes. The potential importance of the horizontal gene transfer(s) and endosymbiosis in establishing the mosaic pathway is discussed.}, }
@article {pmid11079769, year = {2000}, author = {Deane, JA and Fraunholz, M and Su, V and Maier U-G,  and Martin, W and Durnford, DG and McFadden, GI}, title = {Evidence for nucleomorph to host nucleus gene transfer: light-harvesting complex proteins from cryptomonads and chlorarachniophytes.}, journal = {Protist}, volume = {151}, number = {3}, pages = {239-252}, doi = {10.1078/1434-4610-00022}, pmid = {11079769}, issn = {1434-4610}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Cell Nucleus Structures/genetics ; Chlorophyll/metabolism ; Eukaryota/*genetics ; *Gene Transfer, Horizontal ; Light-Harvesting Protein Complexes ; Molecular Sequence Data ; Photosynthetic Reaction Center Complex Proteins/*genetics/metabolism ; Phylogeny ; }, abstract = {Cryptomonads and chlorarachniophytes acquired photosynthesis independently by engulfing and retaining eukaryotic algal cells. The nucleus of the engulfed cells (known as a nucleomorph) is much reduced and encodes only a handful of the numerous essential plastid proteins normally encoded by the nucleus of chloroplast-containing organisms. In cryptomonads and chlorarachniophytes these proteins are thought to be encoded by genes in the secondary host nucleus. Genes for these proteins were potentially transferred from the nucleomorph (symbiont nucleus) to the secondary host nucleus; nucleus to nucleus intracellular gene transfers. We isolated complementary DNA clones (cDNAs) for chlorophyll-binding proteins from a cryptomonad and a chlorarachniophyte. In each organism these genes reside in the secondary host nuclei, but phylogenetic evidence, and analysis of the targeting mechanisms, suggest the genes were initially in the respective nucleomorphs (symbiont nuclei). Implications for origins of secondary endosymbiotic algae are discussed.}, }
@article {pmid11078823, year = {2000}, author = {Wang, H and Gordon, D and Olszewski, B and Song, YL and Kovesdi, I and Keiser, JA}, title = {Rat sponge implant model: a new system for evaluating angiogenic gene transfer.}, journal = {International journal of molecular medicine}, volume = {6}, number = {6}, pages = {645-653}, doi = {10.3892/ijmm.6.6.645}, pmid = {11078823}, issn = {1107-3756}, mesh = {Adenoviridae/genetics ; Animals ; Blood Vessels/chemistry/drug effects/physiopathology ; DNA, Recombinant ; Dose-Response Relationship, Drug ; Endothelial Growth Factors/genetics/metabolism ; Gene Transfer Techniques ; *Gene Transfer, Horizontal ; Humans ; Immunohistochemistry ; Lymphokines/genetics/metabolism ; Models, Cardiovascular ; Neovascularization, Pathologic/*genetics/metabolism/pathology ; Prostheses and Implants ; Rats ; Recombinant Fusion Proteins/administration &amp; dosage/genetics/metabolism ; Surgical Sponges ; Time Factors ; Vascular Endothelial Growth Factor A ; Vascular Endothelial Growth Factors ; beta-Galactosidase/genetics/metabolism ; von Willebrand Factor/analysis ; }, abstract = {Therapeutic angiogenesis, either by protein injection or gene therapy, holds considerable promise for the treatment of coronary and peripheral artery diseases. Given the large number of angiogenic genes available, a simple, well defined, standard system to compare the relative angiogenic efficacy of such genes would be valuable. We have employed a replication-deficient adenovirus vector (complete E1a-, partial E1b- and partial E3-) to deliver the beta-galactosidase (beta-gal, AdLacZ) reporter gene or the human VEGF121 gene (AdGV VEGF121.10) to a rat sponge implant model of angiogenesis. beta-gal staining results reveal a transfection efficiency as high as 60% 24 h after 2x1010 particle units AdLacZ injection. Our results also indicate that a single injection of 2x1010 particle units of AdGVVEGF121.10 in the sponge results in >10, 000 pg VEGF protein expression per milligram of sponge tissue 24 h later. VEGF121 protein concentrations decreased 10-fold within 3 days and 100-fold within 7 days after injection. Significant VEGF121 protein levels were still detectable 14 days after initial virus injection. The high level of gene transfection efficiency was accompanied by enhanced angiogenesis in the sponge, a tissue devoid of any vessels before implantation. Compared to control (AdNull: adenovirus vector without the VEGF gene), AdGVVEGF121.10 induced a 2- to 3-fold up-regulation of angiogenesis at 7 and 14 days post vector injection as determined by both increased capillary number and increased tissue ingrowth. The angiogenic effects of AdGVVEGF121. 10 were dose-related in this model system. These findings demonstrate a dose-related angiogenic response to adenovirus-mediated gene therapy in this model.}, }
@article {pmid11078528, year = {2000}, author = {Lange, BM and Rujan, T and Martin, W and Croteau, R}, title = {Isoprenoid biosynthesis: the evolution of two ancient and distinct pathways across genomes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {97}, number = {24}, pages = {13172-13177}, pmid = {11078528}, issn = {0027-8424}, mesh = {Animals ; *Biological Evolution ; Databases as Topic ; Enzymes/*genetics ; *Genes ; *Genome ; *Hemiterpenes ; Humans ; Organophosphorus Compounds/*metabolism ; *Phylogeny ; Plants/classification/genetics ; Terpenes/*metabolism ; }, abstract = {Isopentenyl diphosphate (IPP) is the central intermediate in the biosynthesis of isoprenoids, the most ancient and diverse class of natural products. Two distinct routes of IPP biosynthesis occur in nature: the mevalonate pathway and the recently discovered deoxyxylulose 5-phosphate (DXP) pathway. The evolutionary history of the enzymes involved in both routes and the phylogenetic distribution of their genes across genomes suggest that the mevalonate pathway is germane to archaebacteria, that the DXP pathway is germane to eubacteria, and that eukaryotes have inherited their genes for IPP biosynthesis from prokaryotes. The occurrence of genes specific to the DXP pathway is restricted to plastid-bearing eukaryotes, indicating that these genes were acquired from the cyanobacterial ancestor of plastids. However, the individual phylogenies of these genes, with only one exception, do not provide evidence for a specific affinity between the plant genes and their cyanobacterial homologues. The results suggest that lateral gene transfer between eubacteria subsequent to the origin of plastids has played a major role in the evolution of this pathway.}, }
@article {pmid11076857, year = {2000}, author = {Garcia-Vallvé, S and Romeu, A and Palau, J}, title = {Horizontal gene transfer in bacterial and archaeal complete genomes.}, journal = {Genome research}, volume = {10}, number = {11}, pages = {1719-1725}, pmid = {11076857}, issn = {1088-9051}, mesh = {Amino Acids/genetics ; Base Composition ; Codon/genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Archaeal/*genetics ; Genes, Bacterial/*genetics ; *Genome, Archaeal ; *Genome, Bacterial ; Species Specificity ; }, abstract = {There is growing evidence that horizontal gene transfer is a potent evolutionary force in prokaryotes, although exactly how potent is not known. We have developed a statistical procedure for predicting whether genes of a complete genome have been acquired by horizontal gene transfer. It is based on the analysis of G+C contents, codon usage, amino acid usage, and gene position. When we applied this procedure to 17 bacterial complete genomes and seven archaeal ones, we found that the percentage of horizontally transferred genes varied from 1.5% to 14.5%. Archaea and nonpathogenic bacteria had the highest percentages and pathogenic bacteria, except for Mycoplasma genitalium, had the lowest. As reported in the literature, we found that informational genes were less likely to be transferred than operational genes. Most of the horizontally transferred genes were only present in one or two lineages. Some of these transferred genes include genes that form part of prophages, pathogenecity islands, transposases, integrases, recombinases, genes present only in one of the two Helicobacter pylori strains, and regions of genes functionally related. All of these findings support the important role of horizontal gene transfer in the molecular evolution of microorganisms and speciation.}, }
@article {pmid11073984, year = {2000}, author = {Kiechle, M and Friedl, AA and Manivasakam, P and Eckardt-Schupp, F and Schiestl, RH}, title = {DNA integration by Ty integrase in yku70 mutant Saccharomyces cerevisiae cells.}, journal = {Molecular and cellular biology}, volume = {20}, number = {23}, pages = {8836-8844}, pmid = {11073984}, issn = {0270-7306}, support = {ES00299/ES/NIEHS NIH HHS/United States ; }, mesh = {*Antigens, Nuclear ; Chromosomes, Fungal ; *DNA Helicases ; DNA, Fungal/*metabolism ; DNA-Binding Proteins/*genetics ; Gene Transfer, Horizontal ; Integrases/*metabolism ; Ku Autoantigen ; Models, Genetic ; Mutation ; Nuclear Proteins/*genetics ; Plasmids ; Recombination, Genetic ; Retroelements ; Saccharomyces cerevisiae/*genetics ; *Saccharomyces cerevisiae Proteins ; Substrate Specificity ; }, abstract = {In the present work we examined nonhomologous integration of plasmid DNA in a yku70 mutant. Ten of 14 plasmids integrated as composite elements, including Ty sequences probably originating from erroneous strand-switching and/or priming events. Three additional plasmids integrated via Ty integrase without cointegrating Ty sequences, as inferred from 5-bp target site duplication and integration site preferences. Ty integrase-mediated integration of non-Ty DNA has never been observed in wild-type cells, although purified integrase is capable of using non-Ty DNA as a substrate in vitro. Hence our data implicate yKu70 as the cellular function preventing integrase from accepting non-Ty DNA as a substrate.}, }
@article {pmid11070064, year = {2000}, author = {de Koning, AP and Brinkman, FS and Jones, SJ and Keeling, PJ}, title = {Lateral gene transfer and metabolic adaptation in the human parasite Trichomonas vaginalis.}, journal = {Molecular biology and evolution}, volume = {17}, number = {11}, pages = {1769-1773}, doi = {10.1093/oxfordjournals.molbev.a026275}, pmid = {11070064}, issn = {0737-4038}, mesh = {Adaptation, Physiological ; Animals ; Gene Transfer, Horizontal ; Humans ; Oxo-Acid-Lyases/*genetics ; *Phylogeny ; Trichomonas vaginalis/enzymology/*genetics ; }, }
@article {pmid11070036, year = {2000}, author = {Xia, H and Anderson, B and Mao, Q and Davidson, BL}, title = {Recombinant human adenovirus: targeting to the human transferrin receptor improves gene transfer to brain microcapillary endothelium.}, journal = {Journal of virology}, volume = {74}, number = {23}, pages = {11359-11366}, pmid = {11070036}, issn = {0022-538X}, support = {P30 DK054759/DK/NIDDK NIH HHS/United States ; R01 HD033531/HD/NICHD NIH HHS/United States ; DK54759/DK/NIDDK NIH HHS/United States ; HD33531/HD/NICHD NIH HHS/United States ; }, mesh = {Adenoviruses, Human/*genetics ; Amino Acid Motifs ; Animals ; Brain/blood supply/*metabolism ; CHO Cells ; Cricetinae ; Endothelium, Vascular/*metabolism ; *Gene Transfer, Horizontal ; Genetic Therapy ; Humans ; Receptors, Transferrin/*metabolism ; Recombination, Genetic ; Tripeptidyl-Peptidase 1 ; }, abstract = {Some inborn errors of metabolism due to deficiencies of soluble lysosomal enzymes cause global neurodegenerative disease. Representative examples include the infantile and late infantile forms of the ceroid lipofuscinoses (CLN1 or CLN2 deficiency, respectively) and mucopolysaccharidoses type VII (MPS VII), a deficiency of beta-glucuronidase. Treatment of the central nervous system component of these disorders will require widespread protein or enzyme replacement, either through dissemination of the protein or through dissemination of a gene encoding it. We hypothesize that transduction of brain microcapillary endothelium (BME) with recombinant viral vectors, with secretion of enzyme product basolaterally, could allow for widespread enzyme dissemination. To achieve this, viruses should be modified to target the BME. This requires (i) identification of a BME-resident target receptor, (ii) identification of motifs targeted to that molecule, (iii) the construction of modified viruses to allow for binding to the target receptor, and (iv) demonstrated transduction of receptor-expressing cells. In proof of principal experiments, we chose the human transferrin receptor (hTfR), a molecule found at high density on human BME. A nonamer phage display library was panned for motifs which could bind hTfR. Forty-three clones were sequenced, most of which contained an AKxxK/R, KxKxPK/R, or KxK motif. Ten peptides representative of the three motifs were cloned into the HI loop of adenovirus type 5 fiber. All motifs tested retained their ability to trimerize and bind transferrin receptor, and seven allowed for recombinant adenovirus production. Importantly, the fiber-modified viruses facilitated increased gene transfer (2- to 34-fold) to hTfR expressing cell lines and human brain microcapillary endothelia expressing high levels of endogenous receptor. Our data indicate that adenoviruses can be modified in the HI loop for expanded tropism to the hTfR.}, }
@article {pmid11070029, year = {2000}, author = {Wang, X and Zeng, W and Murakawa, M and Freeman, MW and Seed, B}, title = {Episomal segregation of the adenovirus enhancer sequence by conditional genome rearrangement abrogates late viral gene expression.}, journal = {Journal of virology}, volume = {74}, number = {23}, pages = {11296-11303}, pmid = {11070029}, issn = {0022-538X}, support = {HL53694/HL/NHLBI NIH HHS/United States ; HL45098/HL/NHLBI NIH HHS/United States ; R01 HL045098/HL/NHLBI NIH HHS/United States ; F32 AI010059/AI/NIAID NIH HHS/United States ; F32 AI10059/AI/NIAID NIH HHS/United States ; }, mesh = {Adenoviridae/*genetics ; Cells, Cultured ; *Enhancer Elements, Genetic ; Gene Expression ; *Gene Rearrangement ; Gene Transfer, Horizontal ; *Genetic Vectors ; Herpesvirus 4, Human/*genetics ; Humans ; Plasmids ; Polymerase Chain Reaction ; Recombination, Genetic ; }, abstract = {We have constructed a recombinant adenovirus gene delivery system that is capable of undergoing growth phase-dependent site-specific recombination. When propagated in 293 producer cells, the vector retains its linear double-stranded form and can be propagated to high titer and purified by conventional procedures. Upon introduction into target cells, the viral chromosome undergoes cyclization to generate an autonomously replicating circular episome and a detached linear fragment. The viral enhancer and reporter gene segregate with the circular episome, which contains no adenovirus open reading frames. The effect of rearrangement of adenovirus gene expression was assessed by quantitative reverse transcription-PCR measurement of the abundance of transcripts encoding the tripartite leader sequence (TPL) of the major late promoter. Whereas nonrearranging viruses produced approximately 10(4) TPL transcripts per 10(6) infecting genomes in the HepG2 liver cell line, no transcripts were detectable in the same cells infected with comparable levels of circularizing vector. Because no helper virus is required to propagate these vectors, the problems of recombination with and contamination by helper virus are eliminated. We also present an efficient and reliable method for generating recombinant adenoviruses.}, }
@article {pmid11070027, year = {2000}, author = {Baekelandt, V and Claeys, A and Cherepanov, P and De Clercq, E and De Strooper, B and Nuttin, B and Debyser, Z}, title = {DNA-Dependent protein kinase is not required for efficient lentivirus integration.}, journal = {Journal of virology}, volume = {74}, number = {23}, pages = {11278-11285}, pmid = {11070027}, issn = {0022-538X}, mesh = {Animals ; *Antigens, Nuclear ; Brain/metabolism ; CHO Cells ; Cricetinae ; *DNA Helicases ; DNA-Activated Protein Kinase ; DNA-Binding Proteins/physiology ; Gene Transfer, Horizontal ; Genetic Vectors ; HIV-1/*genetics ; HeLa Cells ; Humans ; Ku Autoantigen ; Mice ; Mice, Inbred C57BL ; Mice, SCID ; Nuclear Proteins/physiology ; Poly(ADP-ribose) Polymerases/physiology ; Protein Serine-Threonine Kinases/*physiology ; *Virus Integration ; }, abstract = {How DNA is repaired after retrovirus integration is not well understood. DNA-dependent protein kinase (DNA-PK) is known to play a central role in the repair of double-stranded DNA breaks. Recently, a role for DNA-PK in retroviral DNA integration has been proposed (R. Daniel, R. A. Katz, and A. M. Skalka, Science 284:644-647, 1999). Reduced transduction efficiency and increased cell death by apoptosis were observed upon retrovirus infection of cultured scid cells. We have used a human immunodeficiency virus (HIV) type 1 (HIV-1)-derived lentivirus vector system to further investigate the role of DNA-PK during integration. We measured lentivirus transduction of scid mouse embryonic fibroblasts (MEF) and xrs-5 or xrs-6 cells. These cells are deficient in the catalytic subunit of DNA-PK and in Ku, the DNA-binding subunit of DNA-PK, respectively. At low vector titers, efficient and stable lentivirus transduction was obtained, excluding an essential role for DNA-PK in lentivirus integration. Likewise, the efficiency of transduction of HIV-derived vectors in scid mouse brain was as efficient as that in control mice, without evidence of apoptosis. We observed increased cell death in scid MEF and xrs-5 or xrs-6 cells, but only after transduction with high vector titers (multiplicity of infection [MOI], >1 transducing unit [TU]/cell) and subsequent passage of the transduced cells. At an MOI of <1 TU/cell, however, transduction efficiency was even higher in DNA-PK-deficient cells than in control cells. Taken together, the data suggest a protective role of DNA-PK against cellular toxicity induced by high levels of retrovirus integrase or integration. Another candidate cellular enzyme that has been claimed to play an important role during retrovirus integration is poly(ADP-ribose) polymerase (PARP). However, no inhibition of lentivirus vector-mediated transduction or HIV-1 replication by 3-methoxybenzamide, a known PARP inhibitor, was observed. In conclusion, DNA-PK and PARP are not essential for lentivirus integration.}, }
@article {pmid11070024, year = {2000}, author = {Smith, RL and Traul, DL and Schaack, J and Clayton, GH and Staley, KJ and Wilcox, CL}, title = {Characterization of promoter function and cell-type-specific expression from viral vectors in the nervous system.}, journal = {Journal of virology}, volume = {74}, number = {23}, pages = {11254-11261}, pmid = {11070024}, issn = {0022-538X}, support = {NS 01741/NS/NINDS NIH HHS/United States ; NS 29046/NS/NINDS NIH HHS/United States ; }, mesh = {Adenoviridae/*genetics ; Adenovirus E1A Proteins/genetics ; Animals ; Avian Sarcoma Viruses/genetics ; Brain/*metabolism/virology ; Cell Death ; Cells, Cultured ; Cytomegalovirus/genetics ; *Gene Transfer, Horizontal ; *Genetic Vectors ; Hippocampus/metabolism ; Promoter Regions, Genetic/*physiology ; Rats ; }, abstract = {Viral vectors have become important tools to effectively transfer genes into terminally differentiated cells, including neurons. However, the rational for selection of the promoter for use in viral vectors remains poorly understood. Comparison of promoters has been complicated by the use of different viral backgrounds, transgenes, and target tissues. Adenoviral vectors were constructed in the same vector background to directly compare three viral promoters, the human cytomegalovirus (CMV) immediate-early promoter, the Rous sarcoma virus (RSV) long terminal repeat, and the adenoviral E1A promoter, driving expression of the Escherichia coli lacZ gene or the gene for the enhanced green fluorescent protein. The temporal patterns, levels of expression, and cytotoxicity from the vectors were analyzed. In sensory neuronal cultures, the CMV promoter produced the highest levels of expression, the RSV promoter produced lower levels, and the E1A promoter produced limited expression. There was no evidence of cytotoxicity produced by the viral vectors. In vivo analyses following stereotaxic injection of the vector into the rat hippocampus demonstrated differences in the cell-type-specific expression from the CMV promoter versus the RSV promoter. In acutely prepared hippocampal brain slices, marked differences in the cell type specificity of expression from the promoters were confirmed. The CMV promoter produced expression in hilar regions and pyramidal neurons, with minimal expression in the dentate gyrus. The RSV promoter produced expression in dentate gyrus neurons. These results demonstrate that the selection of the promoter is critical for the success of the viral vector to express a transgene in specific cell types.}, }
@article {pmid11069669, year = {2000}, author = {Field, J and Rosenthal, B and Samuelson, J}, title = {Early lateral transfer of genes encoding malic enzyme, acetyl-CoA synthetase and alcohol dehydrogenases from anaerobic prokaryotes to Entamoeba histolytica.}, journal = {Molecular microbiology}, volume = {38}, number = {3}, pages = {446-455}, doi = {10.1046/j.1365-2958.2000.02143.x}, pmid = {11069669}, issn = {0950-382X}, support = {AI33492/AI/NIAID NIH HHS/United States ; }, mesh = {Acetate-CoA Ligase/chemistry/genetics/metabolism ; Alcohol Dehydrogenase/genetics ; Anaerobiosis ; Animals ; Archaea/*genetics ; Cloning, Molecular ; Entamoeba histolytica/*enzymology/*genetics ; *Gene Transfer, Horizontal ; Gram-Positive Bacteria/*genetics ; Malate Dehydrogenase/genetics/metabolism ; Malates/metabolism ; Molecular Sequence Data ; Phylogeny ; }, abstract = {The fermentation enzymes, which enable the microaerophilic protist Entamoeba histolytica to parasitize the colonic lumen and tissue abscesses, closely resemble homologues in anaerobic prokaryotes. Here, genes encoding malic enzyme and acetyl-CoA synthetase (nucleoside diphosphate forming) were cloned from E. histolytica, and their evolutionary origins, as well as those encoding two alcohol dehydrogenases (ADHE and ADH1), were inferred by means of phylogenetic reconstruction. The E. histolytica malic enzyme, which decarboxylates malate to pyruvate, closely resembles that of the archaeon Archaeoglobus fulgidus, strongly suggesting a common origin. The E. histolytica acetyl-CoA synthetase, which converts acetyl-CoA to acetate with the production of ATP, appeared to be closely related to the Plasmodium falciparum enzyme, but it was no more closely related to the Giardia lamblia acetyl-CoA synthetase than to those of archaea. Phylogenetic analyses suggested that the adh1 and adhe genes of E. histolytica and Gram-positive eubacteria share a common ancestor. Lateral transfer of genes encoding these fermentation enzymes from archaea or eubacteria to E. histolytica probably occurred early, because the sequences of the amoebic enzymes show considerable divergence from those of prokaryotes, and the amoebic genes encoding these enzymes are in the AT-rich codon usage of the parasite.}, }
@article {pmid11069646, year = {2000}, author = {Glansdorff, N}, title = {About the last common ancestor, the universal life-tree and lateral gene transfer: a reappraisal.}, journal = {Molecular microbiology}, volume = {38}, number = {2}, pages = {177-185}, doi = {10.1046/j.1365-2958.2000.02126.x}, pmid = {11069646}, issn = {0950-382X}, mesh = {Animals ; Archaea/*genetics ; Bacteria/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Lipids ; }, abstract = {An organismal tree rooted in the bacterial branch and derived from a hyperthermophilic last common ancestor (LCA) is still widely assumed to represent the path followed by evolution from the most primeval cells to the three domains recognized among contemporary organisms: Bacteria, Archaea and Eucarya. In the past few years, however, more and more discrepancies between this pattern and individual protein trees have been brought to light. There has been an overall tendency to attribute these incongruities to widespread lateral gene transfer. However, recent developments, a reappraisal of earlier evidence and considerations of our own lead us to a quite different view. It would appear (i) that the role of lateral gene transfer was overemphasized in recent discussions of molecular phylogenies; (ii) that the LCA was probably a non-thermophilic protoeukaryote from which both Archaea and Bacteria emerged by reductive evolution but not as sister groups, in keeping with a current evolutionary scheme for the biosynthesis of membrane lipids; and (iii) that thermophilic Archaea may have been the first branch to diverge from the ancestral line.}, }
@article {pmid11065363, year = {2000}, author = {Wang, Y and Zhang, Z}, title = {Comparative sequence analyses reveal frequent occurrence of short segments containing an abnormally high number of non-random base variations in bacterial rRNA genes.}, journal = {Microbiology (Reading, England)}, volume = {146 (Pt 11)}, number = {}, pages = {2845-2854}, doi = {10.1099/00221287-146-11-2845}, pmid = {11065363}, issn = {1350-0872}, mesh = {Actinomycetales/classification/genetics ; Base Pairing ; Base Sequence ; DNA Primers/genetics ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Evolution, Molecular ; *Genes, Bacterial ; Models, Genetic ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; RNA, Bacterial/chemistry/*genetics ; RNA, Ribosomal, 16S/chemistry/*genetics ; RNA, Ribosomal, 23S/chemistry/*genetics ; Sequence Analysis, RNA ; Sequence Homology, Nucleic Acid ; Species Specificity ; }, abstract = {rRNA genes are thought unlikely to be laterally transferred, because rRNA must coevolve with a large number of cellular components to form the highly sophisticated translation apparatus and perform protein synthesis. In this paper, the authors first hypothesized that lateral gene transfer (LGT) might occur to rRNA genes via replacement of gene segments encoding individual domains of rRNA: the 'simplified complexity hypothesis'. Comparative sequence analyses of the 16S and 23S rRNA genes from a large number of actinomycete species frequently identified rRNA genes containing short segments with an abnormally high number of non-random base variations. These variations were nearly always characterized by complementing covariations of several paired bases within the stem of a hairpin. The nature of these base variations is not consistent with random mutations but satisfies well the predictions of the 'simplified complexity hypothesis'. The most parsimonious explanation for this phenomenon is the lateral transfer of rRNA gene segments between different bacterial species. This mode of LGT may create mosaic rRNA genes and occur repeatedly in different regions of a gene, gradually destroying the evolutionary history recorded in the nucleotide sequence.}, }
@article {pmid11064264, year = {2000}, author = {Overweg, K and Sluijter, M and Srodzinski, M and de Groot, R and Hermans, PW}, title = {Immune-protective antibodies against capsular polysaccharides do not affect natural competence of Streptococcus pneumoniae: implications for current conjugate vaccination strategies?.}, journal = {FEMS immunology and medical microbiology}, volume = {29}, number = {3}, pages = {183-185}, doi = {10.1111/j.1574-695X.2000.tb01521.x}, pmid = {11064264}, issn = {0928-8244}, mesh = {Animals ; Bacterial Capsules/*immunology ; Fluorescent Antibody Technique ; Gene Transfer, Horizontal ; Opsonin Proteins/*immunology ; Polysaccharides, Bacterial/*immunology ; Rabbits ; Streptococcus pneumoniae/genetics/*immunology ; Transformation, Genetic ; }, abstract = {We studied the effect of opsonization of Streptococcus pneumoniae with capsular antibodies on horizontal transfer of DNA. Opsonization did not inhibit DNA uptake. This suggests that horizontal transfer of capsular genes, which is an important escape mechanism of the pathogen, remains a potential threat for the efficacy of conjugate vaccination.}, }
@article {pmid11064200, year = {2000}, author = {Chang, B and Yoshida, S and Miyamoto, H and Ogawa, M and Horikawa, K and Ogata, K and Nishibuchi, M and Taniguchi, H}, title = {A unique and common restriction fragment pattern of the nucleotide sequences homologous to the genome of vf33, a filamentous bacteriophage, in pandemic strains of Vibrio parahaemolyticus O3:K6 O4:K68, and O1:K untypeable.}, journal = {FEMS microbiology letters}, volume = {192}, number = {2}, pages = {231-236}, doi = {10.1111/j.1574-6968.2000.tb09387.x}, pmid = {11064200}, issn = {0378-1097}, mesh = {Bacteriophages/*genetics ; Blotting, Southern ; DNA, Bacterial/analysis ; DNA, Viral/analysis ; Gene Transfer, Horizontal ; Humans ; Restriction Mapping ; Sequence Analysis, DNA ; Vibrio parahaemolyticus/genetics/*virology ; }, abstract = {Vf33 is a filamentous bacteriophage isolated from Vibrio parahaemolyticus. We performed Southern blot hybridization analysis to examine the distribution of Vf33-related genetic elements in the pandemic strains (O3:K6 strains isolated between 1995 and 1997, O4:K68 and O1:K untypeable strains isolated between 1997 and 1999) of V. parahaemolyticus. Nucleotide sequences homologous to the Vf33 DNA were detected in all 57 test strains including pandemic and non-pandemic strains. However, the profiles of hybridization, including the restriction fragment length polymorphism, with nine Vf33-derived DNA probes exhibited by the pandemic strains were identical and were different from those by the non-pandemic strains. The results support the hypothesis that the pandemic strains are clonal, and suggest a possibility that they have acquired (a) new gene(s) via a Vf33-like filamentous phage.}, }
@article {pmid11058132, year = {2000}, author = {Takami, H and Nakasone, K and Takaki, Y and Maeno, G and Sasaki, R and Masui, N and Fuji, F and Hirama, C and Nakamura, Y and Ogasawara, N and Kuhara, S and Horikoshi, K}, title = {Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis.}, journal = {Nucleic acids research}, volume = {28}, number = {21}, pages = {4317-4331}, pmid = {11058132}, issn = {1362-4962}, mesh = {ATP-Binding Cassette Transporters/genetics ; Adaptation, Physiological/genetics ; Alkalies/metabolism ; Bacillus/chemistry/classification/*genetics/metabolism ; Bacillus subtilis/chemistry/*genetics ; Bacterial Proteins/genetics/physiology ; Base Composition ; Biological Transport ; Cell Wall/genetics/metabolism ; Conserved Sequence/genetics ; DNA Transposable Elements/genetics ; Databases as Topic ; Energy Metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/genetics/physiology ; *Genome, Bacterial ; Molecular Sequence Data ; Open Reading Frames/genetics ; Physical Chromosome Mapping ; Protein Biosynthesis ; RNA, Transfer/genetics ; Replication Origin/genetics ; Sequence Homology ; Sigma Factor/genetics ; Spores, Bacterial/genetics ; Transcription, Genetic/genetics ; Transposases/genetics ; }, abstract = {The 4 202 353 bp genome of the alkaliphilic bacterium Bacillus halodurans C-125 contains 4066 predicted protein coding sequences (CDSs), 2141 (52.7%) of which have functional assignments, 1182 (29%) of which are conserved CDSs with unknown function and 743 (18. 3%) of which have no match to any protein database. Among the total CDSs, 8.8% match sequences of proteins found only in Bacillus subtilis and 66.7% are widely conserved in comparison with the proteins of various organisms, including B.subtilis. The B. halodurans genome contains 112 transposase genes, indicating that transposases have played an important evolutionary role in horizontal gene transfer and also in internal genetic rearrangement in the genome. Strain C-125 lacks some of the necessary genes for competence, such as comS, srfA and rapC, supporting the fact that competence has not been demonstrated experimentally in C-125. There is no paralog of tupA, encoding teichuronopeptide, which contributes to alkaliphily, in the C-125 genome and an ortholog of tupA cannot be found in the B.subtilis genome. Out of 11 sigma factors which belong to the extracytoplasmic function family, 10 are unique to B. halodurans, suggesting that they may have a role in the special mechanism of adaptation to an alkaline environment.}, }
@article {pmid11054571, year = {2000}, author = {Minet, AD and Chiquet-Ehrismann, R}, title = {Phylogenetic analysis of teneurin genes and comparison to the rearrangement hot spot elements of E. coli.}, journal = {Gene}, volume = {257}, number = {1}, pages = {87-97}, doi = {10.1016/s0378-1119(00)00388-7}, pmid = {11054571}, issn = {0378-1119}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Chromosome Mapping ; Databases, Factual ; Drosophila/genetics ; Escherichia coli/*genetics ; Expressed Sequence Tags ; Gene Rearrangement ; Genes/genetics ; Humans ; Molecular Sequence Data ; Nerve Tissue Proteins/*genetics ; *Phylogeny ; Repetitive Sequences, Nucleic Acid/*genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; Tenascin/*genetics ; X Chromosome/genetics ; }, abstract = {Teneurins are a novel family of transmembrane proteins conserved between invertebrates and vertebrates. There are two members in Drosophila, one in C. elegans and four members in mouse. Here, we describe the analysis of the genomic structure of the human teneurin-1 gene. The entire human teneurin-1 (TEN1) gene is contained in eight PAC clones representing part of the chromosomal locus Xq25. Interestingly, many X-linked mental retardation syndromes (XLMR) and non-specific mental retardation (MRX) are mapped to this region. The location of the human TEN1 together with the neuronal expression makes TEN1 a candidate gene for XLMR and MRX. We also identified large parts of the human teneurin-2 sequence on chromosome 5 and sections of human teneurin-4 at chromosomal position 11q14. Database searches resulted in the identification of ESTs encoding parts of all four human members of the teneurin family. Analysis of the genomic organization of the Drosophila ten-a gene revealed the presence of exons encoding a long form of ten-a, which can be aligned with all other teneurins known. Sequence comparison and phylogenetic trees of teneurins show that insects and vertebrates diverged before the teneurin ancestor was duplicated independently in the two phyla. This is supported by the presence of conserved intron positions between teneurin genes of man, Drosophila and C. elegans. It is therefore not possible to class any of the vertebrate teneurins with either Drosophila Ten-a or Ten-m. The C-terminal part of all teneurins harbours 26 repetitive sequence motifs termed YD-repeats. YD-repeats are most similar to the repeats encoded by the core of the rearrangement hot spot (rhs) elements of Escherichia coli. This makes the teneurin ancestor a candidate gene for the source of the rhs core acquired by horizontal gene transfer.}, }
@article {pmid11054546, year = {2000}, author = {Zámocký, M and Janecek, S and Koller, F}, title = {Common phylogeny of catalase-peroxidases and ascorbate peroxidases.}, journal = {Gene}, volume = {256}, number = {1-2}, pages = {169-182}, doi = {10.1016/s0378-1119(00)00358-9}, pmid = {11054546}, issn = {0378-1119}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Ascorbate Peroxidases ; Catalase/chemistry/*genetics ; Databases as Topic ; Databases, Factual ; Molecular Sequence Data ; Molecular Structure ; Peroxidases/chemistry/*genetics ; *Phylogeny ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {Catalase-peroxidases belong to Class I of the plant, fungal, bacterial peroxidase superfamily, together with yeast cytochrome c peroxidase and ascorbate peroxidases. Obviously these bifunctional enzymes arose via gene duplication of an ancestral hydroperoxidase. A 230-residues long homologous region exists in all eukaryotic members of Class I, which is present twice in both prokaryotic and archaeal catalase-peroxidases. The overall structure of eukaryotic Class I peroxidases may be retained in both halves of catalase-peroxidases, with major insertions in several loops, some of which may participate in inter-domain or inter-subunit interactions. Interspecies distances in unrooted phylogenetic trees, analysis of sequence similarities in distinct structural regions, as well as hydrophobic cluster analysis (HCA) suggest that one single tandem duplication had already occurred in the common ancestor prior to the segregation of the archaeal and eubacterial lines. The C-terminal halves of extant catalase-peroxidases clearly did not accumulate random changes, so prolonged periods of independent evolution of the duplicates can be ruled out. Fusion of both copies must have occurred still very early or even in the course of the duplication. We suggest that the sparse representatives of eukaryotic catalase-peroxidases go back to lateral gene transfer, and that, except for several fungi, only single copy hydroperoxidases occur in the eukaryotic lineage. The N-terminal halves of catalase-peroxidases, which reveal higher homology with the single-copy members of the superfamily, obviously are catalytically active, whereas the C-terminal halves of the bifunctional enzymes presumably control the access to the haem pocket and facilitate stable folding. The bifunctional nature of catalase-peroxidases can be ascribed to several unique sequence peculiarities conserved among all N-terminal halves, which most likely will affect the properties of both haem ligands.}, }
@article {pmid11051717, year = {2000}, author = {Huang, SZ and Huang, Y and Chen, MJ and Chen, W and Huang, Z and Li, H and Li, JC and Ren, ZR and Zeng, YT}, title = {[A study of transgenic IFV cattle integrated with human serum albumin gene].}, journal = {Yi chuan xue bao = Acta genetica Sinica}, volume = {27}, number = {7}, pages = {573-579}, pmid = {11051717}, issn = {0379-4172}, mesh = {Animals ; Animals, Genetically Modified ; Cattle/*genetics ; Female ; *Fertilization in Vitro ; *Gene Transfer, Horizontal ; Humans ; Male ; Organ Culture Techniques ; Pregnancy ; Serum Albumin/*genetics ; }, abstract = {The mammary gland expression vector (pcDNA 3.1-GCALBm) containing the full-length sequence of human serum albumin (hALB) cDNA and intron 1 as well as the goat beta-casien gene promoter and 5' up-stream regulatory sequence was constructed. The vector was micro-injected into bovine IVF eggs. The embryos were in vitro cultured to the late stage of morulae, and then few embryo cells were aspirated for the implantation detection of target gene integration and SRY DNA sequence using nested-PCR. Afterwards, ten integrated embryos were selected to transfer into eight recipients and three were pregnant. The pregnant rate was 37.5%(3/8). However, two were miscarried in mid-trimester but one was pregnant at term to deliver a male transgenic cattle integrated with hALB mini-gene. The transgenic efficiency was 12.5% (1/8).}, }
@article {pmid11050445, year = {2000}, author = {Eisen, JA}, title = {Assessing evolutionary relationships among microbes from whole-genome analysis.}, journal = {Current opinion in microbiology}, volume = {3}, number = {5}, pages = {475-480}, doi = {10.1016/s1369-5274(00)00125-9}, pmid = {11050445}, issn = {1369-5274}, mesh = {Archaea/genetics ; Bacteria/genetics ; *Evolution, Molecular ; Genetics, Microbial/*methods ; *Genomics ; Recombination, Genetic ; }, abstract = {The determination and analysis of complete genome sequences have recently enabled many major advances to be made in the area of microbial evolutionary biology. These include the determination of the first genome of a Crenarchaeota, the suggestion that horizontal gene transfer may be the rule rather than the exception, and revelations about how genomes evolve on short timescales.}, }
@article {pmid11050325, year = {2000}, author = {Royo, J and Gímez, E and Hueros, G}, title = {CMP-KDO synthetase: a plant gene borrowed from gram-negative eubacteria.}, journal = {Trends in genetics : TIG}, volume = {16}, number = {10}, pages = {432-433}, doi = {10.1016/s0168-9525(00)02102-8}, pmid = {11050325}, issn = {0168-9525}, mesh = {Bacterial Proteins/*genetics ; Chlamydia/enzymology/genetics ; Cytidine Monophosphate/analogs &amp; derivatives/metabolism ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genes, Plant ; Gram-Negative Bacteria/*genetics ; Models, Genetic ; Nucleotidyltransferases/*genetics ; Phylogeny ; Plant Proteins/*genetics ; Plants/microbiology ; Sequence Homology, Amino Acid ; Species Specificity ; Sugar Acids/metabolism ; Symbiosis/genetics ; }, }
@article {pmid11050287, year = {2000}, author = {Vietor, M and Winter, S and Groscurth, P and Naumann, U and Weller, M}, title = {On the significance of telomerase activity in human malignant glioma cells.}, journal = {European journal of pharmacology}, volume = {407}, number = {1-2}, pages = {27-37}, doi = {10.1016/s0014-2999(00)00726-3}, pmid = {11050287}, issn = {0014-2999}, mesh = {Animals ; Antineoplastic Agents/pharmacology/therapeutic use ; Astrocytes/drug effects/*metabolism ; Cell Death/drug effects/physiology ; Cell Survival/drug effects/physiology ; Gene Transfer, Horizontal/drug effects/physiology ; Glioma/drug therapy/*metabolism ; Humans ; Neoplasm Proteins/*metabolism ; Picolines/pharmacology/therapeutic use ; Proto-Oncogene Proteins c-bcl-2/*metabolism ; Rats ; Telomerase/drug effects/*metabolism ; Tumor Cells, Cultured/drug effects/metabolism ; Tumor Suppressor Protein p53/*metabolism ; }, abstract = {Telomerase is critical for tumor cell immortalization and is a novel target for cancer chemotherapy. Here, we examined whether telomerase is expressed in glioma cell lines, whether telomerase activity is regulated by bcl-2 or p53, and whether telomerase activity predicts response to chemotherapy. Further, we characterized the effects of a candidate telomerase inhibitor, penclomedine, in glioma cells. All 12 human malignant glioma cell lines examined were telomerase positive. Telomerase activity was not modulated during cell cycle progression, did not correlate with p53 status or bcl-2 family protein expression, and did not predict drug sensitivity, except for an association with resistance to carmustine. Ectopic bcl-2 expression did not enhance telomerase activity. Wild-type p53 reduced telomerase activity in cell lines retaining p53 activity but not in p53-mutant cell lines. Penclomedine killed glioma cells via an apoptotic, but death receptor-, bcl-2- and caspase-independent pathway, but did not inhibit telomerase and did not act synergistically with cytotoxic drugs. We conclude that telomerase activity does not account for the differential chemosensitivity of human glioma cells and that penclomedine kills glioma cells via a telomerase-independent pathway.}, }
@article {pmid11049018, year = {2000}, author = {Wierda, WG and Kipps, TJ}, title = {Gene therapy of hematologic malignancies.}, journal = {Seminars in oncology}, volume = {27}, number = {5}, pages = {502-511}, pmid = {11049018}, issn = {0093-7754}, mesh = {Apoptosis ; Cancer Vaccines ; Gene Transfer Techniques ; Gene Transfer, Horizontal ; *Genetic Therapy/methods ; Hematologic Neoplasms/*therapy ; Hematopoietic Stem Cells ; Humans ; Leukemia/therapy ; T-Lymphocytes ; }, abstract = {Gene therapy offers many new and exciting treatment strategies for patients with hematologic malignancies. Through the transfer of genes into hematopoietic stem cells, one can reduce the sensitivity of myeloid cells to chemotherapy. Donor T cells can be modified to become sensitive to otherwise nontoxic prodrugs, allowing for their safer use as effectors in graft-versus-leukemia immune reactions following allogeneic transplantation. Neoplastic cells also may be modified to enhance their sensitivity to various drugs. Finally, neoplastic cells can be modified to enhance their immunogenicity using genes that encode immune stimulatory cytokines or cell surface proteins. Recent studies, for example, indicate that the stealth-like phenotype of leukemia cells can be reversed through transfer of genes such as the one encoding CD154, the ligand for CD40. A phase I clinical trial using autologous CD154-transduced leukemia cells as a cellular vaccine has provided encouraging results. Indeed, we may soon enter an era of effective gene therapy for hematologic malignancies.}, }
@article {pmid11038227, year = {2000}, author = {Bird, DM and Koltai, H}, title = {Plant Parasitic Nematodes: Habitats, Hormones, and Horizontally-Acquired Genes.}, journal = {Journal of plant growth regulation}, volume = {19}, number = {2}, pages = {183-194}, doi = {10.1007/s003440000022}, pmid = {11038227}, issn = {0721-7595}, abstract = {Plant parasitic nematodes are ubiquitous and cosmopolitan pathogens of vascular plants and exploit all parts of the roots and shoots, causing substantial crop damage. Nematodes deploy a broad spectrum of feeding strategies, ranging from simple grazing to the establishment of complex cellular structures (including galls) in host tissues. Various models of feeding site formation have been proposed, and a role for phytohormones has long been speculated, although whether they perform a primary or secondary function is unclear. On the basis of recent molecular evidence, we present several scenarios involving phytohormones in the induction of giant cells by root-knot nematode. The origin of parasitism by nematodes, including the acquisition of genes to synthesize or modulate phytohormones also is discussed, and models for horizontal gene transfer are presented.}, }
@article {pmid11036038, year = {2000}, author = {Galán, JC and Reig, M and Navas, A and Baquero, F and Blázquez, J}, title = {ACI-1 from Acidaminococcus fermentans: characterization of the first beta-lactamase in Anaerobic cocci.}, journal = {Antimicrobial agents and chemotherapy}, volume = {44}, number = {11}, pages = {3144-3149}, pmid = {11036038}, issn = {0066-4804}, mesh = {Amino Acid Sequence ; Ampicillin/pharmacology ; Base Sequence ; Cloning, Molecular ; Clostridium/drug effects/*enzymology/isolation &amp; purification ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Phylogeny ; beta-Lactamases/*genetics/metabolism ; }, abstract = {Acidaminococcus fermentans belongs to the group of strictly anaerobic gram-negative cocci. All previously described Acidaminococcus strains are susceptible to beta-lactam antibiotics. An A. fermentans strain (RYC-MR95) resistant to penicillin and expanded-spectrum cephalosporin (amoxicillin and cefotaxime MICs, 64 microgram/ml) was isolated from a human perianal abscess. A fragment encoding a beta-lactamase from genomic DNA was cloned in Escherichia coli K-12 strain HB101, and the recombinant strain expressed resistance to amoxicillin (MIC, 1,024 microgram/ml) and cefotaxime (MIC, 4 microgram/ml). Clavulanic acid decreased the MICs to 8 and 0.03 microgram/ml, respectively. Analysis of the nucleotide sequence revealed a new class A beta-lactamase, ACI-1. In accordance with its biochemical properties, we propose to assign ACI-1 to functional group 2be. The ACI-1 enzyme (estimated pI 4.3) had <50% amino acid identity with any other class A beta-lactamases, the closest being ROB-1 from Haemophilus influenzae (44%). ACI-1 was closer to class A beta-lactamases from some gram-positive organisms (41 to 44% amino acid identity with Bacillus beta-lactamases) than to most class A enzymes from gram-negative organisms (TEM-1, 24.6%). The aci1 gene had a G+C content of 42.1%, in contrast with 56% G+C content for genomic DNA from A. fermentans, thus suggesting that aci1 may have been obtained by horizontal gene transfer.}, }
@article {pmid11035938, year = {2000}, author = {Walton, JD}, title = {Horizontal gene transfer and the evolution of secondary metabolite gene clusters in fungi: an hypothesis.}, journal = {Fungal genetics and biology : FG &amp; B}, volume = {30}, number = {3}, pages = {167-171}, doi = {10.1006/fgbi.2000.1224}, pmid = {11035938}, issn = {1087-1845}, mesh = {*Evolution, Molecular ; Fungi/*genetics/*metabolism ; *Gene Transfer, Horizontal ; *Genes, Fungal ; Multigene Family ; }, }
@article {pmid11035747, year = {2000}, author = {Rasmussen, M and Edén, A and Björck, L}, title = {SclA, a novel collagen-like surface protein of Streptococcus pyogenes.}, journal = {Infection and immunity}, volume = {68}, number = {11}, pages = {6370-6377}, pmid = {11035747}, issn = {0019-9567}, mesh = {Animals ; *Antigens, Bacterial ; *Bacterial Outer Membrane Proteins ; Bacterial Proteins/*analysis/chemistry/genetics/physiology ; Base Sequence ; Carrier Proteins/chemistry ; Collagen/*analysis ; Molecular Sequence Data ; Rabbits ; Streptococcus pyogenes/*chemistry ; Transcription, Genetic ; }, abstract = {Surface proteins of Streptococcus pyogenes are important virulence factors. Here we describe a novel collagen-like surface protein, designated SclA (streptococcal collagen-like surface protein). The sclA gene was identified in silico using the Streptococcal Genome Sequencing Project with the recently identified protein GRAB as the probe. SclA has a signal sequence and a cell wall attachment region containing the prototypic LPXTGX motif. The surface-exposed part of SclA contains a unique NH(2)-terminal domain of 73 amino acids, followed by a collagen-like region. The sclA gene was found to be positively regulated by Mga, a transcriptional activator of several S. pyogenes virulence determinants. A mutant lacking cell wall-associated SclA was constructed and was found to be as effective as wild-type bacteria in platelet aggregation, survival in fresh human blood, and adherence to pharyngeal cells. The sclA gene was found in all 12 S. pyogenes strains that were investigated using PCR. Sequence analysis revealed that the signal sequence and the cell wall attachment region are highly conserved. The collagen-like domain is variable in its NH(2)-terminal region and has conserved repeated domains in its COOH-terminal part. SclA proteins from most strains have additional proline-rich repeats spacing the collagen-like domain and the cell wall attachment sequence. The unique NH(2)-terminal region is hypervariable, but computer predictions indicate a common secondary structure, with two alpha helices connected by a loop region. Immune selection may explain the hypervariability in the NH(2)-terminal region, whereas the preserved secondary structure implies that this region has a common function. These features and the Mga regulation are shared with the M protein of S. pyogenes. Moreover, as with the gene encoding the M protein, phylogenetic analysis indicates that horizontal gene transfer has contributed to the evolution of sclA.}, }
@article {pmid11029456, year = {2000}, author = {Culham, DE and Wood, JM}, title = {An Escherichia coli reference collection group B2- and uropathogen-associated polymorphism in the rpoS-mutS region of the E. coli chromosome.}, journal = {Journal of bacteriology}, volume = {182}, number = {21}, pages = {6272-6276}, pmid = {11029456}, issn = {0021-9193}, mesh = {Chromosomes/*genetics ; DNA Transposable Elements ; Escherichia coli/classification/*genetics ; Escherichia coli Infections/*microbiology ; Humans ; Molecular Sequence Data ; Open Reading Frames ; }, abstract = {Chromosomal DNAs of enterohemorrhagic, uropathogenic, and laboratory attenuated Escherichia coli strains differ in the rpoS-mutS region. Many uropathogens lack a deletion and an insertion characteristic of enterohemorrhagic strains. At the same chromosomal position, they harbor a 2.1-kb insertion of unknown origin with a base composition suggestive of horizontal gene transfer. Unlike virulence determinants associated with urinary tract infection and/or neonatal meningitis (pap or prs, sfa, kps, and hly), the 2.1-kb insertion is shared by all group B2 strains of the E. coli Reference Collection.}, }
@article {pmid11029433, year = {2000}, author = {Contzen, M and Stolz, A}, title = {Characterization of the genes for two protocatechuate 3, 4-dioxygenases from the 4-sulfocatechol-degrading bacterium Agrobacterium radiobacter strain S2.}, journal = {Journal of bacteriology}, volume = {182}, number = {21}, pages = {6123-6129}, pmid = {11029433}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; Benzenesulfonates/*metabolism ; Catechols/*metabolism ; *Genes, Bacterial ; Molecular Sequence Data ; Protocatechuate-3,4-Dioxygenase/*genetics/metabolism ; Rhizobium/*genetics/metabolism ; Sequence Alignment ; }, abstract = {The genes for two different protocatechuate 3,4-dioxygenases (P34Os) were cloned from the 4-sulfocatechol-degrading bacterium Agrobacterium radiobacter strain S2 (DSMZ 5681). The pcaH1G1 genes encoded a P34O (P34O-I) which oxidized protocatechuate but not 4-sulfocatechol. These genes were part of a protocatechuate-degradative operon which strongly resembled the isofunctional operon from the protocatechuate-degrading strain Agrobacterium tumefaciens A348 described previously by D. Parke (FEMS Microbiol. Lett. 146:3-12, 1997). The second P34O (P34O-II), encoded by the pcaH2G2 genes, was functionally expressed and shown to convert protocatechuate and 4-sulfocatechol. A comparison of the deduced amino acid sequences of PcaH-I and PcaH-II, and of PcaG-I and PcaG-II, with each other and with the corresponding sequences from the P34Os, from other bacterial genera suggested that the genes for the P34O-II were obtained by strain S2 by lateral gene transfer. The genes encoding the P34O-II were found in a putative operon together with two genes which, according to sequence alignments, encoded transport proteins. Further downstream from this putative operon, two open reading frames which code for a putative regulator protein of the IclR family and a putative 3-carboxymuconate cycloisomerase were identified.}, }
@article {pmid11029001, year = {2000}, author = {Ruepp, A and Graml, W and Santos-Martinez, ML and Koretke, KK and Volker, C and Mewes, HW and Frishman, D and Stocker, S and Lupas, AN and Baumeister, W}, title = {The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum.}, journal = {Nature}, volume = {407}, number = {6803}, pages = {508-513}, doi = {10.1038/35035069}, pmid = {11029001}, issn = {0028-0836}, mesh = {Archaeal Proteins/genetics/metabolism ; Base Sequence ; DNA, Archaeal ; Endopeptidases/metabolism ; Energy Metabolism ; *Genome, Archaeal ; Molecular Sequence Data ; Open Reading Frames ; Recombination, Genetic ; Sulfolobus/genetics ; Thermoplasma/*genetics/metabolism ; Ubiquitins/metabolism ; }, abstract = {Thermoplasma acidophilum is a thermoacidophilic archaeon that thrives at 59 degrees C and pH 2, which was isolated from self-heating coal refuse piles and solfatara fields. Species of the genus Thermoplasma do not possess a rigid cell wall, but are only delimited by a plasma membrane. Many macromolecular assemblies from Thermoplasma, primarily proteases and chaperones, have been pivotal in elucidating the structure and function of their more complex eukaryotic homologues. Our interest in protein folding and degradation led us to seek a more complete representation of the proteins involved in these pathways by determining the genome sequence of the organism. Here we have sequenced the 1,564,905-base-pair genome in just 7,855 sequencing reactions by using a new strategy. The 1,509 open reading frames identify Thermoplasma as a typical euryarchaeon with a substantial complement of bacteria-related genes; however, evidence indicates that there has been much lateral gene transfer between Thermoplasma and Sulfolobus solfataricus, a phylogenetically distant crenarchaeon inhabiting the same environment. At least 252 open reading frames, including a complete protein degradation pathway and various transport proteins, resemble Sulfolobus proteins most closely.}, }
@article {pmid11027334, year = {2000}, author = {Karlin, S and Brocchieri, L}, title = {Heat shock protein 60 sequence comparisons: duplications, lateral transfer, and mitochondrial evolution.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {97}, number = {21}, pages = {11348-11353}, pmid = {11027334}, issn = {0027-8424}, support = {R01 GM010452/GM/NIGMS NIH HHS/United States ; 5R01GM10452-36/GM/NIGMS NIH HHS/United States ; 5R01HG00335-12/HG/NHGRI NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Chaperonin 60/*genetics ; *Evolution, Molecular ; Fungi/genetics ; *Gene Duplication ; *Gene Transfer Techniques ; Mitochondria/*genetics ; Plants/genetics ; *Sequence Homology, Nucleic Acid ; }, abstract = {Heat shock proteins 60 (GroEL) are highly expressed essential proteins in eubacterial genomes and in eukaryotic organelles. These chaperone proteins have been advanced as propitious marker sequences for tracing the evolution of mitochondrial (Mt) genomes. Similarities among HSP60 sequences based on significant segment pair alignment calculations are used to deduce associations of sequences taking into account GroEL functional/structural domain differences and to relate HSP60 duplications pervasive in alpha-proteobacterial lineages to the dynamics of lateral transfer and plasmid integration. Multiple alignments with consensuses are determined for 10 natural groups. The group consensuses sharpen the similarity contrasts among individual sequences. In particular, the Mt group matches best with the classical alpha-proteobacteria and closely with Rickettsia but significantly worse with the rickettsial groups Ehrlichia and Orientia. However, across broad protein sequence comparisons, there appears to be no consistent prokaryote whose protein sequences align best with animal Mt genomes. There are plausible scenarios indicating that the nuclear-encoded HSP60 (and HSP70) sequences functioning in Mt are results of lateral transfer and are probably derived from an alpha-proteobacterium. This hypothesis relates to the plethora of duplicated HSP60 sequences among the classical alpha-proteobacteria contrasted with no duplications of HSP60 among other clades of proteobacterial genomes. Evolutionary relations are confounded by differential selection pressures, convergence, variable mutational rates, site variability, and lateral gene transfer.}, }
@article {pmid11024371, year = {2000}, author = {Gasson, MJ}, title = {Gene transfer from genetically modified food.}, journal = {Current opinion in biotechnology}, volume = {11}, number = {5}, pages = {505-508}, doi = {10.1016/s0958-1669(00)00136-1}, pmid = {11024371}, issn = {0958-1669}, mesh = {Bacteria/genetics ; Crops, Agricultural/*genetics ; DNA/metabolism ; Drug Resistance, Microbial/genetics ; Environment ; *Gene Transfer, Horizontal ; Plants/genetics ; }, abstract = {The current debate about the safety of genetically modified food includes some important scientific issues where more scientific data would aid the robustness of safety evaluation. One example is the possibility of gene transfer, especially from genetically modified plant material.}, }
@article {pmid11024370, year = {2000}, author = {Delcour, J and Ferain, T and Hols, P}, title = {Advances in the genetics of thermophilic lactic acid bacteria.}, journal = {Current opinion in biotechnology}, volume = {11}, number = {5}, pages = {497-504}, doi = {10.1016/s0958-1669(00)00134-8}, pmid = {11024370}, issn = {0958-1669}, mesh = {Dairy Products/*microbiology ; Hot Temperature ; Lactic Acid/*biosynthesis ; Lactobacillus/*genetics ; Streptococcus/*genetics ; }, abstract = {Molecular genetics of thermophilic lactic acid bacteria has advanced in several directions: exploitation of the milk proteins and sugars; primary and secondary metabolism; stress response; and molecular ecology of bacteria and their phages. These have singularly contributed to open new avenues of scientific interest in the field: comparative phage genomics; horizontal gene transfer events in bacterial or phage populations; and genetics of external polysaccharide production.}, }
@article {pmid11022785, year = {2000}, author = {Becker, Y}, title = {Evolution of viruses by acquisition of cellular RNA or DNA nucleotide sequences and genes: an introduction.}, journal = {Virus genes}, volume = {21}, number = {1-2}, pages = {7-12}, pmid = {11022785}, issn = {0920-8569}, mesh = {Animals ; Base Sequence ; DNA/genetics ; Eukaryotic Cells/chemistry/*virology ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes ; Humans ; RNA/genetics ; Recombination, Genetic ; Viruses/*genetics/*metabolism ; }, abstract = {The origins of virus evolution may be traced to Archeabacteria since Inouye and Inouye (6) discovered a retroelement with a gene for reverse transcriptase in the bacterial genome and in the satellite, multiple copy single stranded DNA (msDNA) in the soil bacterium Myxococcus xanthus. It was possible (8) to define the evolution of retroelements in eukaryotic cells of plants, insects (gypsy retrovirus) and vertebrates. The replication of RNA viruses in eukaryotic cells allowed for the viral RNA genome to integrate a cellular ubiquitin mRNA, as reported for BVDV (24). Another example is the integration of 28S ribosomal RNA into the hemagglutinin gene of an influenza virus. This change in the hemagglutinin gene led to an increased pathogenicity of the influenza virus (25). In contrast to RNA viruses, DNA viruses had evolved by inserting cDNA molecules derived from mRNA transcripts of cellular genes or foreign viral RNA. It is of interest that the virus acquired cellular genes in the genomes of DNA viruses represent genes that code for proteins that inhibit cellular molecular processes related to HLA class I and II molecules. The other acquired genes are cellular genes that code for cytokines that are capable of inhibiting antigen presentation to T cells by antigen presenting cells (APC) by dendritic Langerhans cells. The acquisition of cellular genes by DNA viruses enhances their pathogenicity by inhibiting the hosts' defense systems.}, }
@article {pmid11021967, year = {2000}, author = {Bailey, KA and Pereira, SL and Widom, J and Reeve, JN}, title = {Archaeal histone selection of nucleosome positioning sequences and the procaryotic origin of histone-dependent genome evolution.}, journal = {Journal of molecular biology}, volume = {303}, number = {1}, pages = {25-34}, doi = {10.1006/jmbi.2000.4128}, pmid = {11021967}, issn = {0022-2836}, support = {GM53185/GM/NIGMS NIH HHS/United States ; GM54692/GM/NIGMS NIH HHS/United States ; GM58617/GM/NIGMS NIH HHS/United States ; }, mesh = {*Archaea/chemistry/cytology/genetics ; Base Sequence ; Cloning, Molecular ; DNA/chemistry/*genetics/metabolism ; DNA Footprinting ; DNA, Archaeal/chemistry/genetics/metabolism ; DNA, Bacterial/chemistry/genetics/metabolism ; Dinucleotide Repeats/genetics ; Eukaryotic Cells ; *Evolution, Molecular ; Fourier Analysis ; Gene Expression Regulation, Archaeal ; Genome, Archaeal ; *Genome, Bacterial ; Histones/chemistry/*metabolism ; Micrococcal Nuclease/metabolism ; Molecular Sequence Data ; Nucleosomes/chemistry/*genetics/metabolism ; Phylogeny ; }, abstract = {Archaeal histones and the eucaryal (eucaryotic) nucleosome core histones have almost identical histone folds. Here, we show that DNA molecules selectively incorporated by rHMfB (recombinant archaeal histone B from Methanothermus fervidus) into archaeal nucleosomes from a mixture of approximately 10(14) random sequence molecules contain sequence motifs shown previously to direct eucaryal nucleosome positioning. The dinucleotides GC, AA (=TT) and TA are repeated at approximately 10 bp intervals, with the GC harmonic displaced approximately 5 bp from the AA and TA harmonics [(GCN(3)AA or TA)(n)]. AT and CG were not strongly selected, indicating that TA not equalAT and GC not equalCG in terms of facilitating archaeal nucleosome assembly. The selected molecules have affinities for rHMfB ranging from approximately 9 to 18-fold higher than the level of affinity of the starting population, and direct the positioned assembly of archaeal nucleosomes. Fourier-transform analyses have revealed that AA dinucleotides are much enriched at approximately 10. 1 bp intervals, the helical repeat of DNA wrapped around a nucleosome, in the genomes of Eucarya and the histone-containing Euryarchaeota, but not in the genomes of Bacteria and Crenarchaeota, procaryotes that do not have histones. Facilitating histone packaging of genomic DNA has apparently therefore imposed constraints on genome sequence evolution, and since archaeal histones have no structure in addition to the histone fold, these constraints must result predominantly from histone fold-DNA contacts. Based on the three-domain universal phylogeny, histones and histone-dependent genome sequence evolution most likely evolved after the bacterial-archaeal divergence but before the archaeal-eucaryal divergence, and were subsequently lost in the Crenarchaeota. However, with lateral gene transfer, the first histone fold could alternatively have evolved after the archaeal-eucaryal divergence, early in either the euryarchaeal or eucaryal lineages.}, }
@article {pmid11021755, year = {2000}, author = {Turner, SD and Rafferty, JA and Fairbairn, LJ and Ashby, J and Tinwell, H and Eckert, HG and Baum, C and Lashford, LS}, title = {The effects of dose, route of administration, drug scheduling and MDR-1 gene transfer on the genotoxicity of etoposide in bone marrow.}, journal = {Leukemia}, volume = {14}, number = {10}, pages = {1796-1802}, doi = {10.1038/sj.leu.2401810}, pmid = {11021755}, issn = {0887-6924}, mesh = {ATP Binding Cassette Transporter, Subfamily B, Member 1/*genetics ; Animals ; Antineoplastic Agents, Phytogenic/administration &amp; dosage/*pharmacology ; Bone Marrow/*drug effects ; Drug Administration Routes ; Drug Administration Schedule ; Etoposide/administration &amp; dosage/*pharmacology ; Female ; *Gene Transfer, Horizontal ; Male ; Mice ; Micronucleus Tests ; }, abstract = {We have used the bone marrow micronucleus assay (BMMN) as a measure of clastogenicity, in response to etoposide exposure in murine bone marrow. Oral delivery of etoposide resulted in a reduced number of micronucleated polychromatic erythrocytes (MPE) relative to the same dose delivered intraperitoneally (P < 0.001). Daily fractionation of the oral schedule of etoposide led to a more than six-fold increase in cumulative MPE frequency over that observed with the same total, unfractionated dose, with the potency of the response increasing with serial exposure (r = 0.79). Retrovirally-mediated expression of MDR1 in murine bone marrow resulted in partial protection against the clastogenic activity of etoposide relative to mock transduced control mice. The model system developed has indicated a variety of factors able to influence the genotoxicity of etoposide. It should now be possible to further exploit this model in order to define other factors governing haemopoietic sensitivity to etoposide.}, }
@article {pmid11018160, year = {2000}, author = {Silva, JC and Kidwell, MG}, title = {Horizontal transfer and selection in the evolution of P elements.}, journal = {Molecular biology and evolution}, volume = {17}, number = {10}, pages = {1542-1557}, doi = {10.1093/oxfordjournals.molbev.a026253}, pmid = {11018160}, issn = {0737-4038}, mesh = {Alcohol Dehydrogenase/genetics ; Animals ; Base Composition ; Classification ; DNA Transposable Elements/*genetics ; Drosophila/classification/*genetics ; Drosophilidae/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Insect ; Genetic Code ; Molecular Sequence Data ; Phylogeny ; *Selection, Genetic ; }, abstract = {The roles of selection and horizontal transfer in the evolution of the canonical subfamily of P: elements were studied in the saltans and willistoni species groups of the genus Drosophila (subgenus Sophophora). We estimate that the common ancestor of the canonical P: subfamily dates back 2-3 Myr at the most, despite the much older age (more than 40 Myr) of the P: family as a whole. The evolution of the canonical P: subfamily is characterized by weak selection at nonsynonymous sites. These sites have evolved at three quarters the rate of synonymous sites, in which no selective constraints were detected. Their recent horizontal transfer best explains the high degree of similarity among canonical P: elements from the saltans and willistoni species groups. These results are consistent with a model of P:-element evolution in which selective constraints are imposed at the time of horizontal transfer. Furthermore, it is estimated that the spread and diversification of the canonical subfamily involved a minimum of 11 horizontal transfer events among the 18 species surveyed within the past 3 Myr. The presence of multiple P: subfamilies in the saltans and willistoni species groups is likely to be the result of multiple invasions that have previously swept through these taxa in a succession of horizontal transfer events. These results suggest that horizontal transfer among eukaryotes might be more common than anticipated.}, }
@article {pmid11018140, year = {2000}, author = {Hacker, J and Kaper, JB}, title = {Pathogenicity islands and the evolution of microbes.}, journal = {Annual review of microbiology}, volume = {54}, number = {}, pages = {641-679}, doi = {10.1146/annurev.micro.54.1.641}, pmid = {11018140}, issn = {0066-4227}, support = {R37 AI021657/AI/NIAID NIH HHS/United States ; AI19716/AI/NIAID NIH HHS/United States ; AI21657/AI/NIAID NIH HHS/United States ; AI41325/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/*pathogenicity ; Base Sequence ; *Biological Evolution ; *DNA, Bacterial ; *Genes, Bacterial ; RNA, Transfer/genetics ; Repetitive Sequences, Nucleic Acid ; Virulence/genetics ; }, abstract = {Virulence factors of pathogenic bacteria (adhesins, toxins, invasins, protein secretion systems, iron uptake systems, and others) may be encoded by particular regions of the prokaryotic genome termed pathogenicity islands. Pathogenicity islands were first described in human pathogens of the species Escherichia coli, but have recently been found in the genomes of various pathogens of humans, animals, and plants. Pathogenicity islands comprise large genomic regions [10-200 kilobases (kb) in size] that are present on the genomes of pathogenic strains but absent from the genomes of nonpathogenic members of the same or related species. The finding that the G+C content of pathogenicity islands often differs from that of the rest of the genome, the presence of direct repeats at their ends, the association of pathogenicity islands with transfer RNA genes, the presence of integrase determinants and other mobility loci, and their genetic instability argue for the generation of pathogenicity islands by horizontal gene transfer, a process that is well known to contribute to microbial evolution. In this article we review these and other aspects of pathogenicity islands and discuss the concept that they represent a subclass of genomic islands. Genomic islands are present in the majority of genomes of pathogenic as well as nonpathogenic bacteria and may encode accessory functions which have been previously spread among bacterial populations.}, }
@article {pmid11018137, year = {2000}, author = {Cotter, PA and DiRita, VJ}, title = {Bacterial virulence gene regulation: an evolutionary perspective.}, journal = {Annual review of microbiology}, volume = {54}, number = {}, pages = {519-565}, doi = {10.1146/annurev.micro.54.1.519}, pmid = {11018137}, issn = {0066-4227}, mesh = {*Biological Evolution ; Bordetella/genetics/*pathogenicity ; *Gene Expression Regulation, Bacterial ; Salmonella/genetics/*pathogenicity ; Vibrio cholerae/genetics/*pathogenicity ; Virulence/genetics ; }, abstract = {Coevolution between bacteria and their plant or animal hosts determines characteristics of the interaction, the bacterial virulence genes involved, and the regulatory systems controlling expression of virulence genes. The long-standing association between Salmonellae and their animal hosts has resulted in the acquisition by Salmonella subspecies of a variety of virulence genes and the evolution of complex regulatory networks. The particular repertoire of virulence genes acquired by different Salmonella enterica subspecies and the regulatory systems that control them dictate subspecies-specific infection characteristics. Although the association between Vibrio cholerae and humans appears to be more recent, to reflect a simpler pathogenic strategy, and to involve fewer virulence genes than that of Salmonellae, complex virulence-regulatory networks have nonetheless evolved. In contrast, there is no evidence for acquisition of virulence genes by horizontal gene transfer in bordetellae, and their virulence regulon is less complex in overall structure than those of salmonellae and Vibrio cholerae. In Bordetellae, subspecies-specific differences in pathogenic strategy appear to result from differential gene expression within and across Bordetella subspecies.}, }
@article {pmid11018132, year = {2000}, author = {Riley, M and Serres, MH}, title = {Interim report on genomics of Escherichia coli.}, journal = {Annual review of microbiology}, volume = {54}, number = {}, pages = {341-411}, doi = {10.1146/annurev.micro.54.1.341}, pmid = {11018132}, issn = {0066-4227}, mesh = {Chromosomes, Bacterial ; Escherichia coli/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genomics ; }, abstract = {We present a summary of recent progress in understanding Escherichia coli K-12 gene and protein functions. New information has come both from classical biological experimentation and from using the analytical tools of functional genomics. The content of the E. coli genome can clearly be seen to contain elements acquired by horizontal transfer. Nevertheless, there is probably a large, stable core of >3500 genes that are shared among all E. coli strains. The gene-enzyme relationship is examined, and, in many cases, it exhibits complexity beyond a simple one-to-one relationship. Also, the E. coli genome can now be seen to contain many multiple enzymes that carry out the same or closely similar reactions. Some are similar in sequence and may share common ancestry; some are not. We discuss the concept of a minimal genome as being variable among organisms and obligatorily linked to their life styles and defined environmental conditions. We also address classification of functions of gene products and avenues of insight into the history of protein evolution.}, }
@article {pmid11004393, year = {2000}, author = {Stevenson, G and Lan, R and Reeves, PR}, title = {The colanic acid gene cluster of Salmonella enterica has a complex history.}, journal = {FEMS microbiology letters}, volume = {191}, number = {1}, pages = {11-16}, doi = {10.1111/j.1574-6968.2000.tb09312.x}, pmid = {11004393}, issn = {0378-1097}, mesh = {Bacterial Proteins/genetics/metabolism ; Base Composition ; DNA, Bacterial/chemistry/genetics ; Escherichia coli/genetics/metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Molecular Sequence Data ; Multigene Family ; Polysaccharides/*genetics/*metabolism ; Salmonella enterica/*genetics/metabolism ; Sequence Analysis, DNA ; }, abstract = {The colanic acid gene cluster of Salmonella enterica LT2 was sequenced and compared with that of Escherichia coli K-12. The two clusters are similar with divergence slightly higher than average for genes of the two species. The cluster was divided into four blocks by GC content and seems likely to have transferred from a higher GC content species to the ancestor of E. coli and S. enterica. All 19 genes of K-12 and 13 genes of LT2 appear to have undergone random genetic drift with amelioration of the GC content. However, in the case of S. enterica, we believe that the six genes of the GDP-fucose pathway group were replaced relatively recently by genes closely related to those of the original donor species. Two repetitive elements were observed: a bacterial interspersed mosaic element in the intergenic region between wzx and wcaK in K-12 only and a RSA (repetitive sequence element) sequence between wcaJ and wzx in LT2 only.}, }
@article {pmid10998330, year = {2000}, author = {Desiere, F and Pridmore, RD and Brüssow, H}, title = {Comparative genomics of the late gene cluster from Lactobacillus phages.}, journal = {Virology}, volume = {275}, number = {2}, pages = {294-305}, doi = {10.1006/viro.2000.0498}, pmid = {10998330}, issn = {0042-6822}, mesh = {Amino Acid Sequence ; Evolution, Molecular ; *Genome, Viral ; Lactobacillus/*virology ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Siphoviridae/*genetics ; }, abstract = {Three prophage sequences were identified in the Lactobacillus johnsoni strain NCC533. Prophage Lj965 predicted a gene map very similar to those of pac-site Streptococcus thermophilus phages over its DNA packaging and head and tail morphogenesis modules. Sequence similarity linked the putative DNA packaging and head morphogenesis genes at the protein level. Prophage Lj965/S. thermophilus phage Sfi11/Lactococcus lactis phage TP901-1 on one hand and Lactobacillus delbrueckii phage LL-H/Lactobacillus plantarum phage phig1e/Listeria monocytogenes phage A118 on the other hand defined two sublines of structural gene clusters in pac-site Siphoviridae from low-GC Gram-positive bacteria. Bacillus subtilis phage SPP1 linked both sublines. The putative major head and tail proteins from Lj965 shared weak sequence similarity with phages from Gram-negative bacteria. A clearly independent line of structural genes in Siphoviridae from low-GC Gram-positive bacteria is defined by temperate cos-site phages including Lactobacillus gasseri phage adh, which also shared sequence similarity with phage D3 infecting a Gram-negative bacterium. A phylogenetic tree analysis demonstrated that the ClpP-like protein identified in four cos-site Siphoviridae from Lactobacillus, Lactococcus, Streptococcus, and Pseudomonas showed graded sequence relationships. The tree suggested that the ClpP-like proteins from the phages were not acquired by horizontal gene transfer from their corresponding bacterial hosts.}, }
@article {pmid10997488, year = {2000}, author = {Bujnicki, JM}, title = {Sequence, structural, and evolutionary analysis of prokaryotic ribosomal protein L11 methyltransferases.}, journal = {Acta microbiologica Polonica}, volume = {49}, number = {1}, pages = {19-29}, pmid = {10997488}, issn = {0137-1320}, mesh = {Amino Acid Sequence ; Bacteria/*enzymology ; Escherichia coli/enzymology/genetics ; *Evolution, Molecular ; Methyltransferases/*chemistry/*genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Secondary ; Ribosomal Proteins/*metabolism ; Sequence Alignment ; }, abstract = {The Escherichia coli PrmA enzyme catalyzes methylation of the large ribosomal subunit protein L11. Database homology searches, multiple sequence alignment, and structure prediction allowed to dissect the primary structure of PrmA into two domains and assign putative functional or structural roles to invariant or highly conserved residues. Evolutionary relationships within the PrmA family were also analyzed. The topology of the branching order agrees to a large extent with the consensus phylogeny of Eubacteria, with the exception of beta and epsilon subdivisions of Proteobacteria, which most probably had their original prmA genes replaced by copies acquired via the lateral gene transfer from gamma-Proteobacteria and some close relative of the ancestor of gramnegative bacteria, respectively.}, }
@article {pmid10990263, year = {2000}, author = {Orús, P and Viñas, M}, title = {Transfer of penicillin resistance between Neisseriae in microcosm.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {6}, number = {2}, pages = {99-104}, doi = {10.1089/107662900419393}, pmid = {10990263}, issn = {1076-6294}, mesh = {Amino Acid Sequence ; *Bacterial Proteins ; Base Sequence ; *Carrier Proteins ; Culture Media ; Ecosystem ; *Gene Transfer, Horizontal ; Hexosyltransferases/*genetics ; Humans ; Microbial Sensitivity Tests/methods ; Molecular Sequence Data ; Multienzyme Complexes/*genetics ; *Muramoylpentapeptide Carboxypeptidase ; Neisseria/*drug effects/*genetics/growth &amp; development ; Penicillin G/pharmacology ; Penicillin Resistance/*genetics ; Penicillin-Binding Proteins ; Penicillins/pharmacology ; Peptidyl Transferases/*genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Transformation, Bacterial/genetics ; }, abstract = {Horizontal gene transfer between commensal and pathogenic Neisseriae is the mechanism proposed to explain how pathogenic species acquire altered portions of the penA gene, which encodes penicillin binding protein 2. These changes resulted in a moderately penicillin-resistant phenotype in the meningococci, whose frequency of isolation in Spain increased at the end of the 1980s. Little has been published about the possibility of this gene transfer in nature or about its simulation in the laboratory. We designed a simple microcosm, formed by solid and liquid media, that partially mimics the upper human respiratory tract. In this microcosm, penicillin-resistant commensal strains and the fully susceptible meningococcus were co-cultivated. The efficiency of gene transfer between the strains depended on the phase of bacterial growth and the conditions of culture. Resistance of penicillin was acquired in different steps irrespective of the source of the DNA. The presence of DNase in the medium had no effect on gene transfer, but it was near zero when nicked DNA was used. Cell-to-cell contact or membrane blebs could explain these results. The analysis of sequences of the transpeptidase domain of PBP2 from transformants, and from donor and recipient strains demonstrated that the emergence of moderately resistant transformants was due to genetic exchange between the co-cultivated strains. Finally, mechanisms other than penA modification could be invoked to explain decreased susceptibility.}, }
@article {pmid10982859, year = {2000}, author = {Aravind, L and Makarova, KS and Koonin, EV}, title = {SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories.}, journal = {Nucleic acids research}, volume = {28}, number = {18}, pages = {3417-3432}, pmid = {10982859}, issn = {1362-4962}, mesh = {Amino Acid Sequence ; Archaea/enzymology ; Bacteria/enzymology ; Bacterial Proteins/chemistry/classification/genetics ; Colicins/chemistry/classification/genetics ; Deoxyribonucleases/chemistry/classification/genetics ; Endodeoxyribonucleases/*chemistry/classification/genetics ; *Escherichia coli Proteins ; Evolution, Molecular ; Holliday Junction Resolvases ; Phylogeny ; Protein Conformation ; Protein Folding ; Sequence Homology, Nucleic Acid ; }, abstract = {Holliday junction resolvases (HJRs) are key enzymes of DNA recombination. A detailed computer analysis of the structural and evolutionary relationships of HJRs and related nucleases suggests that the HJR function has evolved independently from at least four distinct structural folds, namely RNase H, endonuclease, endonuclease VII-colicin E and RusA. The endonuclease fold, whose structural prototypes are the phage lambda exonuclease, the very short patch repair nuclease (Vsr) and type II restriction enzymes, is shown to encompass by far a greater diversity of nucleases than previously suspected. This fold unifies archaeal HJRs, repair nucleases such as RecB and Vsr, restriction enzymes and a variety of predicted nucleases whose specific activities remain to be determined. Within the RNase H fold a new family of predicted HJRs, which is nearly ubiquitous in bacteria, was discovered, in addition to the previously characterized RuvC family. The proteins of this family, typified by Escherichia coli YqgF, are likely to function as an alternative to RuvC in most bacteria, but could be the principal HJRs in low-GC Gram-positive bacteria and AQUIFEX: Endonuclease VII of phage T4 is shown to serve as a structural template for many nucleases, including MCR:A and other type II restriction enzymes. Together with colicin E7, endonuclease VII defines a distinct metal-dependent nuclease fold. As a result of this analysis, the principal HJRs are now known or confidently predicted for all bacteria and archaea whose genomes have been completely sequenced, with many species encoding multiple potential HJRs. Horizontal gene transfer, lineage-specific gene loss and gene family expansion, and non-orthologous gene displacement seem to have been major forces in the evolution of HJRs and related nucleases. A remarkable case of displacement is seen in the Lyme disease spirochete Borrelia burgdorferi, which does not possess any of the typical HJRs, but instead encodes, in its chromosome and each of the linear plasmids, members of the lambda exonuclease family predicted to function as HJRs. The diversity of HJRs and related nucleases in bacteria and archaea contrasts with their near absence in eukaryotes. The few detected eukaryotic representatives of the endonuclease fold and the RNase H fold have probably been acquired from bacteria via horizontal gene transfer. The identity of the principal HJR(s) involved in recombination in eukaryotes remains uncertain; this function could be performed by topoisomerase IB or by a novel, so far undetected, class of enzymes. Likely HJRs and related nucleases were identified in the genomes of numerous bacterial and eukaryotic DNA viruses. Gene flow between viral and cellular genomes has probably played a major role in the evolution of this class of enzymes. This analysis resulted in the prediction of numerous previously unnoticed nucleases, some of which are likely to be new restriction enzymes.}, }
@article {pmid10981827, year = {2000}, author = {Fu, X and Xu, JG}, title = {Development of a chromosome-plasmid balanced lethal system for Lactobacillus acidophilus with thyA gene as selective marker.}, journal = {Microbiology and immunology}, volume = {44}, number = {7}, pages = {551-556}, doi = {10.1111/j.1348-0421.2000.tb02533.x}, pmid = {10981827}, issn = {0385-5600}, mesh = {Drug Delivery Systems ; *Gene Transfer Techniques ; Gene Transfer, Horizontal ; *Genetic Vectors ; Humans ; Lactobacillus acidophilus/*genetics ; Thymidylate Synthase/*genetics ; }, abstract = {A chromosome-plasmid balanced lethal gene delivery system for Lactobacillus acidophilus based on the thyA gene was developed. The selected L. acidophilus DOM La strain carries a mutated thyA gene and has an obligate requirement for thymidine. This strain can be used as a host for the constructed shuttle vector pFXL03, lacking antibiotic-resistant markers but having the wild-type thyA gene from L. casei which complements the thyA chromosomal mutation. The vector also contains the replicon region from plasmid pUC19 and that of the Lactococcus plasmid pWV01, which allows the transfer between Escherichia coli, L. casei and L. acidophilus. Eight unique restriction sites (i.e., PstI, HindIII, SphI, SalI, AccI, XbaI, KpnI and SacI) are available for cloning. After 40-time transfers in modified MRS medium, no plasmid loss was observed. The vector pFXL03 is potentially useful as a food-grade vaccine delivery system for L. acidophilus.}, }
@article {pmid10981709, year = {2000}, author = {Mygind, T and Birkelund, S and Christiansen, G}, title = {Characterization of the variability of a 75-kDa membrane protein in Mycoplasma hominis.}, journal = {FEMS microbiology letters}, volume = {190}, number = {1}, pages = {167-176}, doi = {10.1111/j.1574-6968.2000.tb09281.x}, pmid = {10981709}, issn = {0378-1097}, mesh = {Amino Acid Sequence ; Bacterial Outer Membrane Proteins/chemistry/*genetics/metabolism ; Bacterial Proteins/chemistry/*genetics/metabolism ; Base Sequence ; Cloning, Molecular ; Female ; *Genetic Variation ; Humans ; Male ; Membrane Proteins/chemistry/*genetics/metabolism ; Molecular Sequence Data ; Mycoplasma Infections/*microbiology ; Mycoplasma hominis/*genetics/growth &amp; development/metabolism ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {The gene p75 encoding a 75-kDa surface-exposed membrane protein P75 was cloned and sequenced from Mycoplasma hominis type strain PG21T. To investigate the intraspecies variability, sequences were obtained from an additional two isolates 7488 and 183, and the three sequences were compared. The nucleotide and amino acid differences were not confined to specific regions of the gene/protein, but when comparing the three sequences, differences were present as single site substitutions or small insertions or deletions of nucleotides/amino acids. The intraspecies variability was further investigated by restriction enzyme analysis with two restriction enzymes (Alul and MboII) of PCR products amplified from p75 from 28 M. hominis isolates. On the basis of band patterns produced by the two restriction enzymes, the isolates could be divided into five and six groups. These groups neither matched categories of the M. hominis vaa gene nor the M. hominis p120 gene classes, indicating that the three genes vary by different mechanisms and possibly indicating horizontal gene transfer. Federation of European Microbiological Societies.}, }
@article {pmid10974117, year = {2000}, author = {Li, Q and Reeves, PR}, title = {Genetic variation of dTDP-L-rhamnose pathway genes in Salmonella enterica.}, journal = {Microbiology (Reading, England)}, volume = {146 (Pt 9)}, number = {}, pages = {2291-2307}, doi = {10.1099/00221287-146-9-2291}, pmid = {10974117}, issn = {1350-0872}, mesh = {Bacterial Proteins/genetics/metabolism ; Base Composition ; Base Sequence ; Carbohydrate Epimerases/genetics ; Cloning, Molecular ; DNA, Bacterial/chemistry/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Variation ; Hydro-Lyases/genetics ; Molecular Sequence Data ; Nucleoside Diphosphate Sugars/*genetics/*metabolism ; O Antigens/genetics ; Phylogeny ; Recombination, Genetic ; Salmonella enterica/*genetics/immunology ; Sequence Analysis, DNA ; Thymine Nucleotides/*genetics/*metabolism ; }, abstract = {The genetic variation in the dTDP-L-rhamnose pathway gene set (rmlB, rmlD, rmlA, rmlC) in Salmonella enterica was examined after sequencing the four genes from 11 rml-containing gene clusters encoding seven O antigens, and a 903 bp rmlB segment from another 23 strains representing the seven subspecies. There was considerable sequence variation and strong polarity in the nature and level of variation among rml genes. The 5' end of the rml gene set, including rmlB, rmlD and most of rmlA, is in general subspecies specific. In contrast, the 3' end, including part of rmlA and all of rmlC, is O antigen specific. The G+C content of the 3' end is lower than that of the 5' end. The variation in the 3' end of the gene set is much greater than that of the 5' end. It is apparent that the rml gene set of S. enterica includes genes with two different evolutionary histories. In addition, there has been extensive recombination in the gene set, probably related to O antigen transfer between subspecies. These findings provide evidence for the lateral transfer of O antigen genes between species and among subspecies of S. enterica. The results have also shown that conserved genes at the end of an O antigen gene cluster play a major role in mediating exchange of the central serogroup-specific regions.}, }
@article {pmid10972794, year = {2000}, author = {Boucher, Y and Doolittle, WF}, title = {The role of lateral gene transfer in the evolution of isoprenoid biosynthesis pathways.}, journal = {Molecular microbiology}, volume = {37}, number = {4}, pages = {703-716}, doi = {10.1046/j.1365-2958.2000.02004.x}, pmid = {10972794}, issn = {0950-382X}, mesh = {Amino Acid Sequence ; Animals ; Bacteria/genetics ; Eukaryota/genetics ; *Gene Transfer Techniques ; Molecular Sequence Data ; Phylogeny ; Polyisoprenyl Phosphates/*biosynthesis ; Sequence Homology, Amino Acid ; }, abstract = {Lateral gene transfer (LGT) is a major force in microbial genome evolution. Here, we present an overview of lateral transfers affecting genes involved in isopentenyl diphosphate (IPP) synthesis. Two alternative metabolic pathways can synthesize this universal precursor of isoprenoids, the 1-deoxy-D-xylulose 5-phosphate (DOXP) pathway and the mevalonate (MVA) pathway. We have surveyed recent genomic data and the biochemical literature to determine the distribution of the genes composing these pathways within the bacterial domain. The scattered distribution observed is incompatible with a simple scheme of vertical transmission. LGT (among and between bacteria, archaea and eukaryotes) more parsimoniously explains many features of this pattern. This alternative scenario is supported by phylogenetic analyses, which unambiguously confirm several cases of lateral transfer. Available biochemical data allow the formulation of hypotheses about selective pressures favouring transfer. The phylogenetic diversity of the organisms involved and the range of possible causes and effects of these transfer events make the IPP biosynthetic pathways an ideal system for studying the evolutionary role of LGT.}, }
@article {pmid10970377, year = {2000}, author = {Kawalec, M and Gniadkowski, M and Hryniewicz, W}, title = {Outbreak of vancomycin-resistant enterococci in a hospital in Gdask, Poland, due to horizontal transfer of different Tn1546-like transposon variants and clonal spread of several strains.}, journal = {Journal of clinical microbiology}, volume = {38}, number = {9}, pages = {3317-3322}, pmid = {10970377}, issn = {0095-1137}, mesh = {Adult ; Bacterial Proteins/genetics ; Carbon-Oxygen Ligases/genetics ; *DNA Transposable Elements ; *Disease Outbreaks ; Electrophoresis, Gel, Pulsed-Field ; Enterococcus faecalis/drug effects/genetics/isolation &amp; purification ; Enterococcus faecium/*drug effects/genetics/isolation &amp; purification ; *Gene Transfer, Horizontal ; Genetic Variation ; Gram-Positive Bacterial Infections/*epidemiology/microbiology ; Hospitals, University ; Humans ; Microbial Sensitivity Tests ; Poland/epidemiology ; Polymorphism, Restriction Fragment Length ; Vancomycin Resistance/*genetics ; }, abstract = {Twenty-two vancomycin-resistant enterococcal (VRE) isolates of the VanA phenotype (21 Enterococcus faecium isolates and 1 E. faecalis isolate), representative of a large outbreak that occurred in a hospital in Gdańsk, Poland, were studied. All of the isolates demonstrated resistance to a wide variety of other antimicrobial agents in addition to glycopeptides. Several lines of evidence suggested that the outbreak most probably consisted of two epidemics that followed the independent introduction of VanA determinants into two separate hematological wards of the hospital. This hypothesis is supported by the fact that isolates recovered in these wards possessed two different polymorphs of the highly conserved DNA region encompassing the vanRSHAX genes and two distinct polymorph types of Tn1546-like transposons, which contain these genes. According to pulsed-field gel electrophoresis data, the outbreak in the adult hematology ward (HW) was highly polyclonal, which suggested a major role for the horizontal transmission of Tn1546-like elements among nonrelated strains of E. faecium and E. faecalis in this environment. On the other hand, the outbreak in the pediatric hematology ward (PHW) was most probably due to the clonal spread of two epidemic E. faecium strains, which had exchanged a plasmid carrying the Tn1546-like transposon. Restriction fragment length polymorphism studies of transposons and their insertion loci in plasmid DNA have suggested that numerous isolates from both HW and PHW contained two or more copies of Tn1546-like elements that underwent diversification due to various genetic modifications. The reported data demonstrated a very complex epidemiology of the first, and up to now the only, VanA VRE outbreak characterized in Poland.}, }
@article {pmid10961465, year = {2000}, author = {Wirth, R}, title = {Sex pheromones and gene transfer in Enterococcus faecalis.}, journal = {Research in microbiology}, volume = {151}, number = {6}, pages = {493-496}, doi = {10.1016/s0923-2508(00)00163-7}, pmid = {10961465}, issn = {0923-2508}, mesh = {Animals ; Bacterial Proteins/genetics/*physiology ; Enterococcus faecalis/genetics/*physiology ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Mice ; Sex Attractants/genetics/*physiology ; }, abstract = {Cell-density-dependent regulatory controls have been recognized in recent years to play major roles with regard to many microorganisms. In gram-negative bacteria very often N-acyl-homoserine lactones act as 'quorum-sensing' regulators, whilst gram-positive bacteria mainly use peptides to monitor their cell density. The so-called sex pheromone system of Enterococcus faecalis is just one example of the latter type of regulation. The system is a complex one; in this communication, I will discuss in particular the potential role of the peptides to also act as virulence factors.}, }
@article {pmid10952205, year = {1999}, author = {Kordis, D and Gubensek, F}, title = {Horizontal transfer of non-LTR retrotransposons in vertebrates.}, journal = {Genetica}, volume = {107}, number = {1-3}, pages = {121-128}, doi = {10.1023/a:1004082906518}, pmid = {10952205}, issn = {0016-6707}, mesh = {Animals ; Cattle ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Invertebrates/genetics ; Long Interspersed Nucleotide Elements ; Phylogeny ; *Retroelements ; Species Specificity ; Vertebrates/genetics ; }, abstract = {Since their discovery in family Bovidae (bovids), Bov-B LINEs, believed to be order-specific SINEs, have been found in all ruminants and recently also in Viperidae snakes. The distribution and the evolutionary relationships of Bov-B LINEs provide an indication of their origin and evolutionary dynamics in different species. The evolutionary origin of Bov-B LINE elements has been shown unequivocally to be in Squamata (squamates). The horizontal transfer of Bov-B LINE elements in vertebrates has been confirmed by their discontinuous phylogenetic distribution in Squamata (Serpentes and two lizard infra-orders) as well as in Ruminantia, by the high level of nucleotide identity, and by their phylogenetic relationships. The direction of horizontal transfer from Squamata to the ancestor of Ruminantia is evident from the genetic distances and discontinuous phylogenetic distribution of Bov-B LINE elements. The ancestral snake lineage (Boidae) has been recognized as a possible donor of Bov-B LINE elements to Ruminantia. The timing of horizontal transfer has been estimated from the distribution of Bov-B LINE elements in Ruminantia and the fossil data of Ruminantia to be 40-50 mya. The phylogenetic relationships of Bov-B LINE elements from the various Squamata species agrees with that of the species phylogeny, suggesting that Bov-B LINE elements have been stably maintained by vertical transmission since the origin of Squamata in the Mesozoic era.}, }
@article {pmid10951625, year = {2000}, author = {Yang, C and Wang, J and Wen, S and Liu, J and Guo, J}, title = {[Comparative studies of different carriers and introducing routes on the effects of liver targeted uptake of exogenous gene].}, journal = {Zhonghua gan zang bing za zhi = Zhonghua ganzangbing zazhi = Chinese journal of hepatology}, volume = {8}, number = {4}, pages = {227-229}, pmid = {10951625}, issn = {1007-3418}, mesh = {Animals ; *Gene Transfer, Horizontal ; Injections, Intraperitoneal ; Injections, Intravenous ; Liposomes/*administration &amp; dosage ; Liver/*metabolism ; Male ; Plasmids ; Polylysine/*administration &amp; dosage ; Rats ; Rats, Wistar ; }, abstract = {OBJECTIVE: To compare the effects of liposomes and glyco-poly-L-lysine (G-PLL) on target uptake and gene expression of the liver, and to observe the effects of intravenous route and intraperitoneal route on target uptake and gene expression of the liver.<br><br>METHODS: After encapsulated by liposomes or galactose-terminal glyco-poly-L-lysine, the plasmid which can be expressed in eukaryotic cells was transferred into rat's body by intravenous injection and peritoneal injection respectively, then observed the results in different time by in situ hybridization and immunohistochemistry.<br><br>RESULTS: The expression of the plasmid encapsulated by liposomes or G-PLL was obvious after transferred in vivo 24 h later, and one week later the expression began to decrease, but still could be found three weeks later. Both liposomes and G-PLL made the liver as the major distribution tissue. In the liver, the distribution and expression of the plasmid encapsulated by G-PLL were higher than those encapsulated by liposomes; in other tissues, however, the distribution and expression of the plasmid encapsulated by G-PLL were lower than those by liposomes. The distribution and expression of the plasmid transferred via intravenous route were higher in the liver than that transferred via intraperitoneal route.<br><br>CONCLUSION: The effect of G-PLL on liver target uptake and expression is better than that of liposome; The effect of intravenous route on liver target uptake and expression of the plasmid binding to G-PLL is better than that of peritoneal route.}, }
@article {pmid10951624, year = {2000}, author = {Wang, Z and He, Z and Wu, Z and Zhang, W}, title = {[Induction of apoptosis in human hepatocellular carcinoma cells by adenoviral-mediated transfer of human multigenes].}, journal = {Zhonghua gan zang bing za zhi = Zhonghua ganzangbing zazhi = Chinese journal of hepatology}, volume = {8}, number = {4}, pages = {224-226}, pmid = {10951624}, issn = {1007-3418}, mesh = {Adenoviridae/*genetics ; Animals ; *Apoptosis ; Carcinoma, Hepatocellular/pathology/*therapy ; Female ; Gene Transfer, Horizontal ; *Genetic Therapy ; Humans ; In Situ Nick-End Labeling ; Liver Neoplasms/pathology/*therapy ; Mice ; Mice, Inbred BALB C ; Mice, Nude ; }, abstract = {OBJECTIVE: To investigate the apoptosis induced by adenovirus-mediated transduction of human genes (p53, B(7-1), GM-GSF, IL-2) in liver cancer cells and the effects of tumorigenicity in nude mice.<br><br>METHODS: Using light microscopy and electron microscopy and TUNEL assay, apoptosis in Ad-multigenes-transduced liver cancer cell lines was detected. The tumorigenicity of HepG(2) cells transduced with Ad-multigenes was detected.<br><br>RESULTS: Ad-multigenes could induce apoptosis, and elevated sensitivity of human liver cancer cells to chemotherapy drugs. After cells with transduced Ad-multigenes were treated with 10mg/L cisplatin for 24 h, apoptosis was seen in nearly 30% of them. The tumorigenicity of Ad-multigenes-transduced was reduced.<br><br>CONCLUSION: Apoptosis induced by adenovirus-mediated multigenes acts synergetically with cisplatin in promotion of inducing apoptosis in liver cancer cell lines.}, }
@article {pmid10939673, year = {2000}, author = {Hansmann, S and Martin, W}, title = {Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is conserved across prokaryotic genomes: influence of excluding poorly alignable sites from analysis.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {50 Pt 4}, number = {}, pages = {1655-1663}, doi = {10.1099/00207713-50-4-1655}, pmid = {10939673}, issn = {1466-5026}, mesh = {Adenylate Kinase/metabolism ; Amino Acid Sequence ; Archaeal Proteins/*genetics ; Bacterial Proteins/*genetics ; Genes, Archaeal ; Genes, Bacterial ; Glycine/metabolism ; Molecular Sequence Data ; *Multigene Family ; Phylogeny ; Prokaryotic Cells/chemistry/*classification/enzymology ; Ribosomal Proteins/*genetics ; Sequence Alignment ; }, abstract = {Thirty-nine proteins encoded in a large gene cluster that is well-conserved in gene content and gene order across 18 sequenced prokaryotic genomes were extracted, aligned and subjected to phylogenetic analysis. In individual analyses of the alignments, only two probable examples of lateral gene transfer between archaea and eubacteria were detected, involving the genes for ribosomal protein Rpl23 and adenylate kinase. Amino acid sequences for 35 of the 39 proteins were concatenated to yield a data set of 9087 amino acid positions per genome. Many of these proteins, 33 of which are ribosomal proteins, are not highly conserved across distantly related organisms and thus contain many regions that are difficult to align. Phylogenetic analyses were performed with subsets of the concatenated data from which the most highly variable sites had been iteratively removed, using the number of different amino acids that occur at a given site as a criterion of variability. Glycine, which has a strong influence on protein structure, tended to be more frequent at the most conserved (least polymorphic) sites. With most subsets of the data, the proteins from the cyanobacterium Synechocystis tended to branch with their homologues from gram-positive bacteria. The results indicate that excluding only a few percentage of poorly alignable sites from phylogenetic analysis can have a severe impact upon the phylogeny inferred and that bootstrap support for branches can fluctuate substantially, depending upon which sites are excluded.}, }
@article {pmid10939242, year = {2000}, author = {Wu, LF and Ize, B and Chanal, A and Quentin, Y and Fichant, G}, title = {Bacterial twin-arginine signal peptide-dependent protein translocation pathway: evolution and mechanism.}, journal = {Journal of molecular microbiology and biotechnology}, volume = {2}, number = {2}, pages = {179-189}, pmid = {10939242}, issn = {1464-1801}, mesh = {Arginine/metabolism ; Bacteria/*genetics/*metabolism ; Bacterial Proteins/chemistry/genetics/*metabolism ; Biological Evolution ; Biological Transport, Active ; Carrier Proteins/chemistry/genetics/metabolism ; *Escherichia coli Proteins ; Gene Products, tat/chemistry/genetics/*metabolism ; Genes, Bacterial ; Genes, tat ; *Membrane Transport Proteins ; Models, Molecular ; Operon ; Protein Sorting Signals/chemistry/genetics/metabolism ; }, abstract = {The recently identified bacterial Tat pathway is capable of exporting proteins with a peculiar twin-arginine signal peptide in folded conformation independently of the Sec machinery. It is structurally and mechanistically similar to the delta pH-dependent pathway used for importing chloroplast proteins into the thylakoid. The tat genes are not ubiquitously present and are absent from half of the completely sequenced bacterial genomes. The presence of the tat genes seems to correlate with genome size and with the presence of important enzymes with a twin-arginine signal peptide. A minimal Tat system requires a copy of tatA and a copy of tatC. The composition and gene order of a tat locus are generally conserved within the same taxonomy group but vary considerably to other groups, which would exclude an acquisition of the Tat system by recent horizontal gene transfer. The tat genes are also found in the genomes of chloroplasts and plant mitochondria but are absent from animal mitochondrial genomes. The topology of evolution trees suggests a bacterial origin of the Tat system. In general, the twin-arginine signal peptide is capable of targeting any passenger protein to the Tat pathway. However, a structural signal carried by the mature part of a passenger protein can override targeting information in a signal peptide under certain circumstances. Tat systems show a substrate-Tat component specificity and a species specificity. The pore size of the Tat channel is estimated as being between 5 and 9 nm. Operational models of the Tat system are proposed.}, }
@article {pmid10939240, year = {2000}, author = {Nguyen, L and Paulsen, IT and Tchieu, J and Hueck, CJ and Saier, MH}, title = {Phylogenetic analyses of the constituents of Type III protein secretion systems.}, journal = {Journal of molecular microbiology and biotechnology}, volume = {2}, number = {2}, pages = {125-144}, pmid = {10939240}, issn = {1464-1801}, support = {5RO1 AI21702/AI/NIAID NIH HHS/United States ; 9RO1 GM55434/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Proteins/classification/*genetics/*metabolism ; Genes, Bacterial ; Gram-Negative Bacteria/*genetics/pathogenicity/*physiology ; *Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Virulence ; }, abstract = {Multicomponent Type III protein secretion systems transfer gram-negative bacterial virulence factors directly from the bacterial cytoplasm to the cytoplasm of a host eukaryotic cell in a process that may involve a single energy-coupled step. Extensive evidence supports the conclusion that the genetic apparatuses that encode these systems have been acquired independently by different gram-negative bacteria, presumably by lateral transfer. In this paper we conduct phylogenetic analyses of currently sequenced constituents of these systems and their homologues. The results reveal the relative relatedness of these systems and show that they evolved with little or no exchange of constituents between systems. This fact suggests that horizontal transmission of the genes encoding these systems always occurred as a unit without the formation of hybrid gene clusters. Moreover, homologous flagellar proteins show phylogenetic clustering that suggests that the flagellar systems and Type III protein secretory systems diverged from each other following very early duplication of a gene cluster sharing many (but not all) genes. Phylogenies of most or all of the flagellar proteins follow those of the source organisms with little or no lateral gene transfer suggesting that homologous flagellar proteins are true orthologues. We suggest that the flagellar apparatus was the evolutionary precursor of Type III protein secretion systems.}, }
@article {pmid10937495, year = {2000}, author = {Liyanage, H and Holcroft, P and Evans, VJ and Keis, S and Wilkinson, SR and Kashket, ER and Young, M}, title = {A new insertion sequence, ISCb1, from Clostridium beijernickii NCIMB 8052.}, journal = {Journal of molecular microbiology and biotechnology}, volume = {2}, number = {1}, pages = {107-113}, pmid = {10937495}, issn = {1464-1801}, mesh = {Amino Acid Sequence ; Base Sequence ; Cloning, Molecular ; Clostridium/*genetics/metabolism ; *DNA Transposable Elements ; Gene Dosage ; Molecular Sequence Data ; Mutation ; Sequence Analysis, DNA ; }, abstract = {The NCIMB 8052 strain of Clostridium beijerinckii contains nine copies of a novel insertion sequence, ISCb1, belonging to the IS4 family. The 1764 bp element has 18 bp inverted repeats at its extremities, and generates 11 bp target repeats upon insertion. It contains a 1365 bp ORF whose predicted product (455 amino acids) resembles bacterial transposases. The highly conserved DD(35)E motif is present, as are signatures characteristic of the N3 and C1 domains of bacterial transposases. Codon usage of the ORF is somewhat different from that of other C. beijerinckii genes, suggesting that ISCb1 may have been acquired from another organism by horizontal gene transfer in the evolutionary past. One ISCb1 copy lies close to the site of insertion of Tn 1545 in a mutant strain, C10, which shows a reduced tendency to degenerate (i.e. loss of the potential to form solvents) compared with the wild type. In the C10 strain, the characteristic pattern of DNA fragments detected by an IS-specific probe was altered, but this was due to the Tn1545 insertion itself, rather than an ISCb1-mediated genome re-arrangement. There is currently no evidence that the element is involved in strain degeneration, since 12 independently isolated spontaneous mutants that had lost the ability to form solvents had the same ISCb1 profile as that of the wild type strain. The element is apparently restricted to a series of closely related solvent-forming clostridia.}, }
@article {pmid10931339, year = {2000}, author = {Gerdes, K and Møller-Jensen, J and Bugge Jensen, R}, title = {Plasmid and chromosome partitioning: surprises from phylogeny.}, journal = {Molecular microbiology}, volume = {37}, number = {3}, pages = {455-466}, doi = {10.1046/j.1365-2958.2000.01975.x}, pmid = {10931339}, issn = {0950-382X}, mesh = {Adenosine Triphosphatases/genetics ; Amino Acid Sequence ; Bacterial Proteins/*genetics ; *Chromosomes, Bacterial ; Molecular Sequence Data ; Phylogeny ; *Plasmids ; }, abstract = {Plasmids encode partitioning genes (par) that are required for faithful plasmid segregation at cell division. Initially, par loci were identified on plasmids, but more recently they were also found on bacterial chromosomes. We present here a phylogenetic analysis of par loci from plasmids and chromosomes from prokaryotic organisms. All known plasmid-encoded par loci specify three components: a cis-acting centromere-like site and two trans-acting proteins that form a nucleoprotein complex at the centromere (i.e. the partition complex). The proteins are encoded by two genes in an operon that is autoregulated by the par-encoded proteins. In all cases, the upstream gene encodes an ATPase that is essential for partitioning. Recent cytological analyses indicate that the ATPases function as adaptors between a host-encoded component and the partition complex and thereby tether plasmids and chromosomal origin regions to specific subcellular sites (i.e. the poles or quarter-cell positions). Two types of partitioning ATPases are known: the Walker-type ATPases encoded by the par/sop gene family (type I partitioning loci) and the actin-like ATPase encoded by the par locus of plasmid R1 (type II partitioning locus). A phylogenetic analysis of the large family of Walker type of partitioning ATPases yielded a surprising pattern: most of the plasmid-encoded ATPases clustered into distinct subgroups. Surprisingly, however, the par loci encoding these distinct subgroups have different genetic organizations and thus divide the type I loci into types Ia and Ib. A second surprise was that almost all chromosome-encoded ATPases, including members from both Gram-negative and Gram-positive Bacteria and Archaea, clustered into one distinct subgroup. The phylogenetic tree is consistent with lateral gene transfer between Bacteria and Archaea. Using database mining with the ParM ATPase of plasmid R1, we identified a new par gene family from enteric bacteria. These type II loci, which encode ATPases of the actin type, have a genetic organization similar to that of type Ib loci.}, }
@article {pmid10910347, year = {2000}, author = {Simpson, AJ and Reinach, FC and Arruda, P and Abreu, FA and Acencio, M and Alvarenga, R and Alves, LM and Araya, JE and Baia, GS and Baptista, CS and Barros, MH and Bonaccorsi, ED and Bordin, S and Bové, JM and Briones, MR and Bueno, MR and Camargo, AA and Camargo, LE and Carraro, DM and Carrer, H and Colauto, NB and Colombo, C and Costa, FF and Costa, MC and Costa-Neto, CM and Coutinho, LL and Cristofani, M and Dias-Neto, E and Docena, C and El-Dorry, H and Facincani, AP and Ferreira, AJ and Ferreira, VC and Ferro, JA and Fraga, JS and França, SC and Franco, MC and Frohme, M and Furlan, LR and Garnier, M and Goldman, GH and Goldman, MH and Gomes, SL and Gruber, A and Ho, PL and Hoheisel, JD and Junqueira, ML and Kemper, EL and Kitajima, JP and Krieger, JE and Kuramae, EE and Laigret, F and Lambais, MR and Leite, LC and Lemos, EG and Lemos, MV and Lopes, SA and Lopes, CR and Machado, JA and Machado, MA and Madeira, AM and Madeira, HM and Marino, CL and Marques, MV and Martins, EA and Martins, EM and Matsukuma, AY and Menck, CF and Miracca, EC and Miyaki, CY and Monteriro-Vitorello, CB and Moon, DH and Nagai, MA and Nascimento, AL and Netto, LE and Nhani, A and Nobrega, FG and Nunes, LR and Oliveira, MA and de Oliveira, MC and de Oliveira, RC and Palmieri, DA and Paris, A and Peixoto, BR and Pereira, GA and Pereira, HA and Pesquero, JB and Quaggio, RB and Roberto, PG and Rodrigues, V and de M Rosa, AJ and de Rosa, VE and de Sá, RG and Santelli, RV and Sawasaki, HE and da Silva, AC and da Silva, AM and da Silva, FR and da Silva, WA and da Silveira, JF and Silvestri, ML and Siqueira, WJ and de Souza, AA and de Souza, AP and Terenzi, MF and Truffi, D and Tsai, SM and Tsuhako, MH and Vallada, H and Van Sluys, MA and Verjovski-Almeida, S and Vettore, AL and Zago, MA and Zatz, M and Meidanis, J and Setubal, JC}, title = {The genome sequence of the plant pathogen Xylella fastidiosa. The Xylella fastidiosa Consortium of the Organization for Nucleotide Sequencing and Analysis.}, journal = {Nature}, volume = {406}, number = {6792}, pages = {151-159}, doi = {10.1038/35018003}, pmid = {10910347}, issn = {0028-0836}, mesh = {Bacterial Adhesion ; Bacterial Proteins/metabolism ; Biological Transport ; Chromosome Mapping ; Citrus/microbiology ; DNA Repair ; DNA, Bacterial ; Energy Metabolism ; *Genome, Bacterial ; Molecular Sequence Data ; Plants/*microbiology ; Plants, Toxic ; Protein Biosynthesis ; Pseudomonadaceae/*genetics/metabolism/pathogenicity ; *Sequence Analysis, DNA ; Nicotiana/microbiology ; Transcription, Genetic ; Virulence/genetics ; }, abstract = {Xylella fastidiosa is a fastidious, xylem-limited bacterium that causes a range of economically important plant diseases. Here we report the complete genome sequence of X. fastidiosa clone 9a5c, which causes citrus variegated chlorosis--a serious disease of orange trees. The genome comprises a 52.7% GC-rich 2,679,305-base-pair (bp) circular chromosome and two plasmids of 51,158 bp and 1,285 bp. We can assign putative functions to 47% of the 2,904 predicted coding regions. Efficient metabolic functions are predicted, with sugars as the principal energy and carbon source, supporting existence in the nutrient-poor xylem sap. The mechanisms associated with pathogenicity and virulence involve toxins, antibiotics and ion sequestration systems, as well as bacterium-bacterium and bacterium-host interactions mediated by a range of proteins. Orthologues of some of these proteins have only been identified in animal and human pathogens; their presence in X. fastidiosa indicates that the molecular basis for bacterial pathogenicity is both conserved and independent of host. At least 83 genes are bacteriophage-derived and include virulence-associated genes from other bacteria, providing direct evidence of phage-mediated horizontal gene transfer.}, }
@article {pmid10900003, year = {2000}, author = {Woese, CR}, title = {Interpreting the universal phylogenetic tree.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {97}, number = {15}, pages = {8392-8396}, pmid = {10900003}, issn = {0027-8424}, mesh = {Cell Size ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; *Phylogeny ; RNA, Ribosomal/classification ; }, abstract = {The universal phylogenetic tree not only spans all extant life, but its root and earliest branchings represent stages in the evolutionary process before modern cell types had come into being. The evolution of the cell is an interplay between vertically derived and horizontally acquired variation. Primitive cellular entities were necessarily simpler and more modular in design than are modern cells. Consequently, horizontal gene transfer early on was pervasive, dominating the evolutionary dynamic. The root of the universal phylogenetic tree represents the first stage in cellular evolution when the evolving cell became sufficiently integrated and stable to the erosive effects of horizontal gene transfer that true organismal lineages could exist.}, }
@article {pmid10891261, year = {2000}, author = {Schütz, M and Brugna, M and Lebrun, E and Baymann, F and Huber, R and Stetter, KO and Hauska, G and Toci, R and Lemesle-Meunier, D and Tron, P and Schmidt, C and Nitschke, W}, title = {Early evolution of cytochrome bc complexes.}, journal = {Journal of molecular biology}, volume = {300}, number = {4}, pages = {663-675}, doi = {10.1006/jmbi.2000.3915}, pmid = {10891261}, issn = {0022-2836}, mesh = {Amino Acid Sequence ; Archaea/enzymology ; Chlorobi/enzymology ; Cyanobacteria/enzymology ; Electron Transport Complex III/*chemistry/*genetics/metabolism ; *Evolution, Molecular ; Gram-Positive Bacteria/enzymology ; Molecular Sequence Data ; *Phylogeny ; Proteobacteria/enzymology ; Recombination, Genetic ; Sequence Alignment ; }, abstract = {Primary structures, functional characteristics and phylogenetic relationships of subunits of cytochrome bc complexes from phylogenetically diverse bacterial and archaeal species were analysed. A single case of lateral gene transfer, i.e. the import of an epsilon-proteobacterial cytochrome bc(1) complex into Aquificales, was identified. For the enzyme in the remainder of the species studied, the obtained phylogenies were globally in line with small subunit rRNA trees. The distribution of a few key phylogenetic markers, such as contiguousness of cytochrome b, nature of the c-type subunit or spacing between b-heme ligands, are discussed. A localised modification of previous tree topologies is proposed on the basis of the obtained data. The comparison of extant enzymes furthermore allowed us to define the minimal functional and evolutionary core of the enzyme. The data furthermore suggest that the ancestral enzyme was put together from subunits that previously had played a role in other electron transfer chains.}, }
@article {pmid10885824, year = {1999}, author = {Williams, JD and Sefton, AM}, title = {The prevention of antibiotic resistance during treatment.}, journal = {Infection}, volume = {27 Suppl 2}, number = {}, pages = {S29-31}, pmid = {10885824}, issn = {0300-8126}, mesh = {Anti-Bacterial Agents/*administration &amp; dosage/pharmacology ; Bacterial Infections/*drug therapy/microbiology ; Drug Resistance, Microbial/genetics/*physiology ; Gram-Negative Bacteria/*drug effects/genetics ; Gram-Positive Bacteria/*drug effects/genetics ; Humans ; Infection Control ; Microbial Sensitivity Tests ; Prevalence ; Risk Factors ; Sensitivity and Specificity ; }, abstract = {Prevention of emergence of antibiotic resistance during treatment is an important goal when prescribing antimicrobials. Antibiotic resistant bacteria can emerge in three main ways--by acquisition of new genes via transposons or horizontal gene transfer, by selection of resistant variants and by selection of naturally resistant strains. In order to minimize emergence of antibiotic resistance during therapy it is important to try and avoid antibiotics which encourage the transfer of resistance genes, to avoid selection of resistant variants from susceptible pathogens and to avoid ablation of antibiotic susceptible normal flora. However, implementing these objectives is not always easy. This paper discusses possible ways of limiting the emergence of resistant bacteria during treatment. It does not consider how to prevent the spread of these strains from person to person. The prevalence of antibiotic-resistant bacteria depends upon the selection of antibiotic-resistant strains and spread of these strains from person to person. Prevention therefore consists of two parts--the prevention of acquisition of resistance/selection of antibiotic-resistant variants and interrupting the mechanisms by which person-to-person spread can occur. This paper considers only the first of these two influences on prevalence of resistance.}, }
@article {pmid10877811, year = {2000}, author = {Hohnstock, AM and Stuart-Keil, KG and Kull, EE and Madsen, EL}, title = {Naphthalene and donor cell density influence field conjugation of naphthalene catabolism plasmids.}, journal = {Applied and environmental microbiology}, volume = {66}, number = {7}, pages = {3088-3092}, pmid = {10877811}, issn = {0099-2240}, support = {ES-05950-03/ES/NIEHS NIH HHS/United States ; }, mesh = {Bacteria/genetics/*growth &amp; development/metabolism ; Coal Tar ; *Conjugation, Genetic ; Fresh Water/*microbiology ; Geologic Sediments/microbiology ; Naphthalenes/*metabolism ; Plasmids/*genetics ; *Recombination, Genetic ; Water Pollutants, Chemical ; }, abstract = {We examined transfer of naphthalene-catabolic genes from donor microorganisms native to a contaminated site to site-derived, rifampin-resistant recipient bacteria unable to grow on naphthalene. Horizontal gene transfer (HGT) was demonstrated in filter matings using groundwater microorganisms as donors. Two distinct but similar plasmid types, closely related to pDTG1, were retrieved. In laboratory-incubated sediment matings, the addition of naphthalene stimulated HGT. However, recipient bacteria deployed in recoverable vessels in the field site (in situ) did not retrieve plasmids from native donors. Only when plasmid-containing donor cells and naphthalene were added to the in situ mating experiments did HGT occur.}, }
@article {pmid10877793, year = {2000}, author = {Davis, JK and Paoli, GC and He, Z and Nadeau, LJ and Somerville, CC and Spain, JC}, title = {Sequence analysis and initial characterization of two isozymes of hydroxylaminobenzene mutase from Pseudomonas pseudoalcaligenes JS45.}, journal = {Applied and environmental microbiology}, volume = {66}, number = {7}, pages = {2965-2971}, pmid = {10877793}, issn = {0099-2240}, mesh = {Amino Acid Sequence ; Gene Deletion ; Genes, Bacterial ; Hydroxylamines/*metabolism ; Intramolecular Transferases/chemistry/*genetics/*metabolism ; Isoenzymes/genetics/metabolism ; Molecular Sequence Data ; Pseudomonas/*enzymology/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {Pseudomonas pseudoalcaligenes JS45 grows on nitrobenzene by a partially reductive pathway in which the intermediate hydroxylaminobenzene is enzymatically rearranged to 2-aminophenol by hydroxylaminobenzene mutase (HAB mutase). The properties of the enzyme, the reaction mechanism, and the evolutionary origin of the gene(s) encoding the enzyme are unknown. In this study, two open reading frames (habA and habB), each encoding an HAB mutase enzyme, were cloned from a P. pseudoalcaligenes JS45 genomic library and sequenced. The open reading frames encoding HabA and HabB are separated by 2.5 kb and are divergently transcribed. The deduced amino acid sequences of HabA and HabB are 44% identical. The HAB mutase specific activities in crude extracts of Escherichia coli clones synthesizing either HabA or HabB were similar to the specific activities of extracts of strain JS45 grown on nitrobenzene. HAB mutase activity in E. coli extracts containing HabB withstood heating at 85 degrees C for 10 min, but extracts containing HabA were inactivated when they were heated at temperatures above 60 degrees C. HAB mutase activity in extracts of P. pseudoalcaligenes JS45 grown on nitrobenzene exhibited intermediate temperature stability. Although both the habA gene and the habB gene conferred HAB mutase activity when they were separately cloned and expressed in E. coli, reverse transcriptase PCR analysis indicated that only habA is transcribed in P. pseudoalcaligenes JS45. A mutant strain derived from strain JS45 in which the habA gene was disrupted was unable to grow on nitrobenzene, which provided physiological evidence that HabA is involved in the degradation of nitrobenzene. A strain in which habB was disrupted grew on nitrobenzene. Gene Rv3078 of Mycobacterium tuberculosis H37Rv encodes a protein whose deduced amino acid sequence is 52% identical to the HabB amino acid sequence. E. coli containing M. tuberculosis gene Rv3078 cloned into pUC18 exhibited low levels of HAB mutase activity. Sequences that exhibit similarity to transposable element sequences are present between habA and habB, as well as downstream of habB, which suggests that horizontal gene transfer resulted in acquisition of one or both of the hab genes.}, }
@article {pmid10874741, year = {2000}, author = {Morschhäuser, J and Köhler, G and Ziebuhr, W and Blum-Oehler, G and Dobrindt, U and Hacker, J}, title = {Evolution of microbial pathogens.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {355}, number = {1397}, pages = {695-704}, pmid = {10874741}, issn = {0962-8436}, mesh = {Candida albicans/genetics/pathogenicity ; Candidiasis/*microbiology ; Escherichia coli/genetics/pathogenicity ; Escherichia coli Infections/*microbiology ; *Evolution, Molecular ; Genetic Variation ; Humans ; Staphylococcal Infections/*microbiology ; Staphylococcus epidermidis/*genetics/pathogenicity ; Time Factors ; }, abstract = {Various genetic mechanisms including point mutations, genetic rearrangements and lateral gene transfer processes contribute to the evolution of microbes. Long-term processes leading to the development of new species or subspecies are termed macroevolution, and short-term developments, which occur during days or weeks, are considered as microevolution. Both processes, macro- and microevolution need horizontal gene transfer, which is particularly important for the development of pathogenic microorganisms. Plasmids, bacteriophages and so-called pathogenicity islands (PAIs) play a crucial role in the evolution of pathogens. During microevolution, genome variability of pathogenic microbes leads to new phenotypes, which play an important role in the acute development of an infectious disease. Infections due to Staphylococcus epidermidis, Candida albicans and Escherichia coli will be described with special emphasis on processes of microevolution. In contrast, the development of PAIs is a process involved in macroevolution. PAIs are especially important in processes leading to new pathotypes or even species. In this review, particular attention will be given to the fact that the evolution of pathogenic microbes can be considered as a specific example for microbial evolution in general.}, }
@article {pmid10864518, year = {2000}, author = {Minotto, L and Edwards, MR and Bagnara, AS}, title = {Trichomonas vaginalis: characterization, expression, and phylogenetic analysis of a carbamate kinase gene sequence.}, journal = {Experimental parasitology}, volume = {95}, number = {1}, pages = {54-62}, doi = {10.1006/expr.2000.4507}, pmid = {10864518}, issn = {0014-4894}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Blotting, Western ; Consensus Sequence ; DNA, Protozoan/chemistry ; Electrophoresis, Polyacrylamide Gel ; Gene Expression ; Molecular Sequence Data ; Phosphotransferases (Carboxyl Group Acceptor)/chemistry/*genetics/metabolism ; *Phylogeny ; Polymerase Chain Reaction ; RNA, Messenger/analysis ; Recombinant Proteins/chemistry/genetics/metabolism ; Sequence Analysis, DNA ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Trichomonas vaginalis/classification/enzymology/*genetics ; }, abstract = {The gene encoding carbamate kinase (CBK, ATP:carbamate phosphotransferase, EC 2.7.2.2) from Trichomonas vaginalis has been sequenced and its expression in this protozoon has been verified using reverse-transcription polymerase chain reaction. The codon usage and percentage nucleotide composition in the coding and noncoding regions are consistent with other genes isolated from this parasite. Phylogenetic analysis of this gene has suggested possible speciation events that are congruent with other studies, with suggestions of lateral gene transfer. The gene was expressed in Escherichia coli using the pQE-30 expression system, and the recombinant protein was purified using affinity chromatography. The expression of the recombinant protein was identified via Western blotting and matrix-assisted laser desorption ionization mass spectrometry of tryptic peptides. Preliminary kinetic assays have revealed that the recombinant enzyme has a K(m) similar to that of the native enzyme and size-exclusion chromatography has shown that the enzyme is active as the homodimer.}, }
@article {pmid10851188, year = {2000}, author = {Doolittle, WF}, title = {The nature of the universal ancestor and the evolution of the proteome.}, journal = {Current opinion in structural biology}, volume = {10}, number = {3}, pages = {355-358}, doi = {10.1016/s0959-440x(00)00096-8}, pmid = {10851188}, issn = {0959-440X}, mesh = {Animals ; *Evolution, Molecular ; Humans ; *Proteome ; }, abstract = {The past year has seen several attempts to reconstruct the proteome of the universal ancestor of all life on the basis of comparisons of contempory genomes. However, increasing evidence for lateral gene transfer could mean that such attempts are based on an incorrect understanding of evolution.}, }
@article {pmid10843862, year = {2000}, author = {Bateman, A and Bycroft, M}, title = {The structure of a LysM domain from E. coli membrane-bound lytic murein transglycosylase D (MltD).}, journal = {Journal of molecular biology}, volume = {299}, number = {4}, pages = {1113-1119}, doi = {10.1006/jmbi.2000.3778}, pmid = {10843862}, issn = {0022-2836}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Bacterial Proteins/chemistry/metabolism ; Binding Sites ; Cell Membrane/*metabolism ; Conserved Sequence ; Escherichia coli/*enzymology ; Glycosyltransferases/*chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Nuclear Magnetic Resonance, Biomolecular ; Peptidoglycan/metabolism ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sequence Alignment ; }, abstract = {The LysM domain is a widespread protein module. It was originally identified in enzymes that degrade bacterial cell walls but is also present in many other bacterial proteins. Several proteins that contain the domain, such as Staphylococcal IgG binding proteins and Escherichia coli intimin, are involved in bacterial pathogenesis. LysM domains are also found in some eukaryotic proteins, apparently as a result of horizontal gene transfer from bacteria. The available evidence suggests that the LysM domain is a general peptidoglycan-binding module. We have determined the structure of this domain from E. coli membrane-bound lytic murein transglycosylase D. The LysM domain has a betaalphaalphabeta secondary structure with the two helices packing onto the same side of an anti- parallel beta sheet. The structure shows no similarity to other bacterial cell surface domains. A potential binding site in a shallow groove on surface of the protein has been identified.}, }
@article {pmid10850652, year = {2000}, author = {Kim, NS and Park, NI and Kim, SH and Kim, ST and Han, SS and Kang, KY}, title = {Isolation of TC/AG repeat microsatellite sequences for fingerprinting rice blast fungus and their possible horizontal transfer to plant species.}, journal = {Molecules and cells}, volume = {10}, number = {2}, pages = {127-134}, doi = {10.1007/s10059-000-0127-0}, pmid = {10850652}, issn = {1016-8478}, mesh = {Base Sequence ; Blotting, Southern ; DNA Fingerprinting ; DNA, Fungal/*genetics ; DNA, Plant/genetics ; Electrophoresis, Polyacrylamide Gel ; Magnaporthe/*genetics ; Microsatellite Repeats/*genetics ; Molecular Sequence Data ; Oryza/genetics/*microbiology ; Phylogeny ; Polymorphism, Genetic ; Recombination, Genetic ; }, abstract = {Genome fingerprinting has been a major role in characterization of population structure and analysis of the variability in phytopathogenic fungi. In order to characterize Korean rice blast fungal isolates, the genomic DNAs were digested with AluI endonuclease and subsequent PCR amplifications using random decamer primers with combinations of microsatellite primers had been carried out. This Alu-Inter SSR technique revealed high polymorphism among the Korean blast fungal isolates. Then, fragments from the Alu-Inter SSR analysis were isolated to be used as probes in Southern hybridization, which also revealed high polymorphism between isolates to distinguish individuals. The sequences of the isolated fragments contained TC/AG tandem repeats interspersed with a 30 bp direct repeat. In gel blot analysis, the isolated TC/AG repeat microsatellite sequences were proved to be useful for characterizing the isolates in blast fungi in addition to the conventional MGR (Magnaporthe grisea repeat) probes. One interesting point was that the rice blast fungus derived TC/AG repeat microsatellite sequences were abundant in non-rice blast fungi and plant species, but not in other fungi and yeasts. A discussion on the possible horizontal gene transfer between phytopathogenic fungi and host plants is presented.}, }
@article {pmid10846225, year = {2000}, author = {Dahl, KH and Lundblad, EW and Røkenes, TP and Olsvik, &#xd8; and Sundsfjord, A}, title = {Genetic linkage of the vanB2 gene cluster to Tn5382 in vancomycin-resistant enterococci and characterization of two novel insertion sequences.}, journal = {Microbiology (Reading, England)}, volume = {146 (Pt 6)}, number = {}, pages = {1469-1479}, doi = {10.1099/00221287-146-6-1469}, pmid = {10846225}, issn = {1350-0872}, mesh = {Animals ; Bacterial Proteins/*genetics ; Base Sequence ; Chromosome Mapping ; DNA Primers/genetics ; DNA Transposable Elements/*genetics ; DNA, Bacterial/genetics ; Enterococcus/*drug effects/*genetics/isolation &amp; purification ; Enterococcus faecalis/drug effects/genetics/isolation &amp; purification ; Enterococcus faecium/drug effects/genetics/isolation &amp; purification ; *Genes, Bacterial ; Genetic Linkage ; Humans ; Molecular Sequence Data ; *Multigene Family ; Sequence Homology, Nucleic Acid ; Vancomycin Resistance/*genetics ; }, abstract = {VanB-type vancomycin resistance is encoded by the vanB gene cluster, which disseminates by horizontal gene transfer and clonal spread of vancomycin-resistant enterococci (VRE). Genetic linkage of the vanB gene cluster to transposon Tn5382 and the insertion sequences IS16 and IS256-like has previously been shown. In this study linkage of defined vanB gene cluster subtypes to these elements was examined. All the vanB2 subtype strains studied (n=14) revealed co-hybridization of vanB and Tn5382, whereas the strains of vanB1 (n=8) and vanB3 (n=1) subtypes were Tn5382 negative. Conjugative cotransfer of the vanB2 gene cluster and Tn5382 was demonstrated for two strains. DNA sequencing of the vanX(B)-ORFC region in vanB2 strains confirmed that the vanB2 gene cluster is an integral part of Tn5382. No general pattern of linkage was observed with regard to IS16 and IS256-like. Two novel insertion sequences were identified in specific vanB2 subtype strains. (i) A 1611 bp element (ISEnfa110) was detected in the left flank of Tn5382. Its insertion site, lack of terminal inverted and direct repeats, and two conserved motifs in its putative transposase all conform to the conventions of the IS110 family. (ii) A 787 bp element (ISEnfa200) was detected in the vanS(B)-vanY(B) intergenic region. Its ORF encoded a putative protein with 60-70% identity to transposases of the IS200 family. No further copies of ISEnfa110 were found by colony hybridization of 181 enterococcal isolates, whereas ISEnfa200 was found in four additional vanB2 strains from the USA. The five strains had identical ISEnfa200 element insertion sites, and Tn5382 was located downstream from a pbp5 gene conferring high-level ampicillin resistance. These isolates showed related PFGE patterns, suggesting possible clonal spread of a VRE strain harbouring a Tn5382-vanB2-ISEnfa200 element linked to a pbp5 gene conferring ampicillin resistance.}, }
@article {pmid10831447, year = {2000}, author = {Helgason, E and Okstad, OA and Caugant, DA and Johansen, HA and Fouet, A and Mock, M and Hegna, I and Kolstø, AB}, title = {Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis--one species on the basis of genetic evidence.}, journal = {Applied and environmental microbiology}, volume = {66}, number = {6}, pages = {2627-2630}, pmid = {10831447}, issn = {0099-2240}, mesh = {Bacillus/*classification/enzymology/*genetics ; Bacillus anthracis/*classification/enzymology/genetics ; Bacillus cereus/*classification/enzymology/genetics ; Bacillus thuringiensis/*classification/enzymology/genetics ; Electrophoresis/methods ; Enzymes/*genetics ; Genes, Bacterial ; Genotype ; Humans ; Phenotype ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis are members of the Bacillus cereus group of bacteria, demonstrating widely different phenotypes and pathological effects. B. anthracis causes the acute fatal disease anthrax and is a potential biological weapon due to its high toxicity. B. thuringiensis produces intracellular protein crystals toxic to a wide number of insect larvae and is the most commonly used biological pesticide worldwide. B. cereus is a probably ubiquitous soil bacterium and an opportunistic pathogen that is a common cause of food poisoning. In contrast to the differences in phenotypes, we show by multilocus enzyme electrophoresis and by sequence analysis of nine chromosomal genes that B. anthracis should be considered a lineage of B. cereus. This determination is not only a formal matter of taxonomy but may also have consequences with respect to virulence and the potential of horizontal gene transfer within the B. cereus group.}, }
@article {pmid10830951, year = {2000}, author = {Ochman, H and Lawrence, JG and Groisman, EA}, title = {Lateral gene transfer and the nature of bacterial innovation.}, journal = {Nature}, volume = {405}, number = {6784}, pages = {299-304}, doi = {10.1038/35012500}, pmid = {10830951}, issn = {0028-0836}, mesh = {Bacteria/*genetics ; Bacteriophages/genetics ; Conjugation, Genetic ; DNA, Bacterial ; Drug Resistance, Microbial/genetics ; Evolution, Molecular ; Genes, Bacterial ; *Recombination, Genetic ; Transformation, Bacterial ; Virulence/genetics ; }, abstract = {Unlike eukaryotes, which evolve principally through the modification of existing genetic information, bacteria have obtained a significant proportion of their genetic diversity through the acquisition of sequences from distantly related organisms. Horizontal gene transfer produces extremely dynamic genomes in which substantial amounts of DNA are introduced into and deleted from the chromosome. These lateral transfers have effectively changed the ecological and pathogenic character of bacterial species.}, }
@article {pmid10821764, year = {2000}, author = {Martini, SR and Roman, G and Meuser, S and Mardon, G and Davis, RL}, title = {The retinal determination gene, dachshund, is required for mushroom body cell differentiation.}, journal = {Development (Cambridge, England)}, volume = {127}, number = {12}, pages = {2663-2672}, doi = {10.1242/dev.127.12.2663}, pmid = {10821764}, issn = {0950-1991}, mesh = {Animals ; Axons/physiology ; Cell Differentiation ; *Drosophila Proteins ; Drosophila melanogaster/embryology/*genetics/growth &amp; development ; Embryo, Nonmammalian/cytology/physiology ; Gene Transfer, Horizontal ; Nerve Fibers/physiology ; Nervous System/embryology/growth &amp; development ; Nuclear Proteins/*genetics/*metabolism ; Retina/cytology/*embryology/growth &amp; development ; }, abstract = {The dachshund gene of Drosophila encodes a putative transcriptional regulator required for eye and leg development. We show here that dachshund is also required for normal brain development. The mushroom bodies of dachshund mutants exhibit a marked reduction in the number of (&amp;agr;) lobe axons, a disorganization of axons extending into horizontal lobes, and aberrant projections into brain areas normally unoccupied by mushroom body processes. The phenotypes become pronounced during pupariation, suggesting that dachshund function is required during this period. GAL4-mediated expression of dachshund in the mushroom bodies rescues the mushroom body phenotypes. Moreover, dachshund mutant mushroom body clones in an otherwise wild-type brain exhibit the phenotypes, indicating an autonomous role for dachshund. Although eyeless, like dachshund, is preferentially expressed in the mushroom body and is genetically upstream of dachshund for eye development, no interaction of these genes was detected for mushroom body development. Thus, dachshund functions in the developing mushroom body neurons to ensure their proper differentiation.}, }
@article {pmid10818615, year = {2000}, author = {Heinemann, JA and Roughan, PD}, title = {New hypotheses on the material nature of horizontally mobile genes.}, journal = {Annals of the New York Academy of Sciences}, volume = {906}, number = {}, pages = {169-186}, doi = {10.1111/j.1749-6632.2000.tb06609.x}, pmid = {10818615}, issn = {0077-8923}, mesh = {Biological Evolution ; *Gene Transfer, Horizontal ; }, abstract = {The evolutionary history of organisms is often assumed to be recorded in the structure of important molecules, such as DNA sequences. Whereas the structure of these molecules does sometimes affirm other evidence of ancestry, like fossil records, it sometimes does not. Horizontal gene transfer can distort perceptions of ancestry. Determining the impact of horizontal gene transfer on evolution has been limited by the crude tools available to detect it. Physical and genetic vectors are now known to conduct genes between organisms, even between biological kingdoms of organisms. The effects are being noticed in important molecules preserved in the genomes of organisms. This article will review the systematic bias in using molecular morphology, like DNA sequences, to infer ancestry and how this bias is the unavoidable result of the way that experimental genetics itself evolved. We present the novel hypothesis that genes usually called epigenes, like methylation patterns and prions, are infectiously transferred, sometimes using DNA as a vector, but not as a gene.}, }
@article {pmid10796996, year = {1999}, author = {Kaplan, DL and Mello, C and Sano, T and Cantor, C and Smith, C}, title = {Streptavidin-based containment systems for genetically engineered microorganisms.}, journal = {Biomolecular engineering}, volume = {16}, number = {1-4}, pages = {135-140}, doi = {10.1016/s1050-3862(99)00040-6}, pmid = {10796996}, issn = {1389-0344}, mesh = {Bacteria/*genetics/metabolism ; Biotransformation ; Environmental Microbiology ; Environmental Pollutants/metabolism ; *Genetic Engineering ; Pseudomonas putida/genetics/metabolism ; *Streptavidin ; }, abstract = {The use of genetically modified microorganisms for environmental remediation continues to be debated. Conditional lethal systems with tightly regulated gene expression can be used to contain released microorganisms and ameliorate some of the concerns about horizontal gene transfer. We have described streptavidin-based suicide systems to address these concerns and evaluated their function in Pseudomonas putida containing the TOL plasmid for aromatic hydrocarbon metabolism. Tight regulation of expression of a truncated streptavidin gene was required to avoid premature production of the toxic protein. Streptavidin expression was induced by the absence of 3-methyl benzoate (hydrocarbon substrate) which resulted in the elimination of 99.9% of the bacterial culture within eight hours. Low mutant escape rates at 10(-7) per cell per generation were also realized.}, }
@article {pmid10795825, year = {2000}, author = {Bond, JP and Francklyn, C}, title = {Proteobacterial histidine-biosynthetic pathways are paraphyletic.}, journal = {Journal of molecular evolution}, volume = {50}, number = {4}, pages = {339-347}, doi = {10.1007/s002399910037}, pmid = {10795825}, issn = {0022-2844}, support = {R01 GM054899/GM/NIGMS NIH HHS/United States ; GM54899/GM/NIGMS NIH HHS/United States ; }, mesh = {*Alcohol Oxidoreductases ; Amino Acid Sequence ; Amino Acyl-tRNA Synthetases/genetics ; Bacterial Proteins/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Histidine/*biosynthesis ; Histidine-tRNA Ligase/chemistry/*genetics ; Molecular Sequence Data ; Monosaccharide Transport Proteins/genetics ; Operon ; *Phylogeny ; Proteobacteria/*classification/*enzymology/genetics ; Recombination, Genetic ; Sequence Alignment ; }, abstract = {In Lactococcus lactis there is a protein, HisZ, in the histidine-biosynthetic operon that exhibits significant sequence identity with histidyl-tRNA synthetase (HisRS) but does not aminoacylate tRNA. HisRS homologs that, like HisZ, cannot aminoacylate tRNA are represented in a highly divergent set of bacteria (including an aquificale, cyanobacteria, firmicutes, and proteobacteria), yet are missing from other bacteria, including mycrobacteria and certain proteobacteria. Phylogenetic analysis of the HisRS and HisRS-like family suggests that the HisZ proteins form a monophyletic group that attaches outside the predominant bacterial HisRS clade. These observations are consistent with a model in which the absences of HisZ from bacteria are due to its loss during evolution. It has recently been shown that HisZ from L. lactis binds to the ATP-PRPP transferase (HisG) and that both HisZ and HisG are required for catalyzing the first reaction in histidine biosynthesis. Phylogenetic analysis of HisG sequences shows conclusively that proteobacterial HisG and histidinol dehydrogenase (HisD) sequences are paraphyletic and that the partition of the Proteobacteria associated with the presence/absence of HisZ corresponds to that based on HisG and HisD paraphyly. Our results suggest that horizontal gene transfer played an important role in the evolution of the regulation of histidine biosynthesis.}, }
@article {pmid10792973, year = {2000}, author = {Campbell, AM}, title = {Lateral gene transfer in prokaryotes.}, journal = {Theoretical population biology}, volume = {57}, number = {2}, pages = {71-77}, doi = {10.1006/tpbi.2000.1454}, pmid = {10792973}, issn = {0040-5809}, mesh = {Cell Lineage/genetics ; *Evolution, Molecular ; *Genes ; Genome ; Phylogeny ; *Prokaryotic Cells ; }, }
@article {pmid10782109, year = {2000}, author = {Faguy, DM and Doolittle, WF}, title = {Horizontal transfer of catalase-peroxidase genes between archaea and pathogenic bacteria.}, journal = {Trends in genetics : TIG}, volume = {16}, number = {5}, pages = {196-197}, doi = {10.1016/s0168-9525(00)02007-2}, pmid = {10782109}, issn = {0168-9525}, mesh = {Archaea/*genetics ; Bacteria/*genetics/pathogenicity ; Catalase/*genetics ; Escherichia coli/genetics ; *Gene Transfer, Horizontal ; Peroxidases/*genetics ; Phylogeny ; }, }
@article {pmid10779483, year = {2000}, author = {Braun, EL and Halpern, AL and Nelson, MA and Natvig, DO}, title = {Large-scale comparison of fungal sequence information: mechanisms of innovation in Neurospora crassa and gene loss in Saccharomyces cerevisiae.}, journal = {Genome research}, volume = {10}, number = {4}, pages = {416-430}, doi = {10.1101/gr.10.4.416}, pmid = {10779483}, issn = {1088-9051}, support = {5P20-RR11830-02/RR/NCRR NIH HHS/United States ; }, mesh = {Aspergillus nidulans/genetics ; DNA, Fungal/*analysis ; Databases, Factual ; Evolution, Molecular ; Expressed Sequence Tags ; Fungal Proteins/biosynthesis/genetics/isolation &amp; purification ; *Gene Deletion ; Genes, Fungal/*genetics ; Genetic Variation/genetics ; Genome, Fungal ; Neurospora crassa/*genetics ; Saccharomyces cerevisiae/*genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {We report a large-scale comparison of sequence data from the filamentous fungus Neurospora crassa with the complete genome sequence of Saccharomyces cerevisiae. N. crassa is considerably more morphologically and developmentally complex than S. cerevisiae. We found that N. crassa has a much higher proportion of "orphan" genes than S. cerevisiae, suggesting that its morphological complexity reflects the acquisition or maintenance of novel genes, consistent with its larger genome. Our results also indicate the loss of specific genes from S. cerevisiae. Surprisingly, some of the genes lost from S. cerevisiae are involved in basic cellular processes, including translation and ion (especially calcium) homeostasis. Horizontal gene transfer from prokaryotes appears to have played a relatively modest role in the evolution of the N. crassa genome. Differences in the overall rate of molecular evolution between N. crassa and S. cerevisiae were not detected. Our results indicate that the current public sequence databases have fairly complete samples of gene families with ancient conserved regions, suggesting that further sequencing will not substantially change the proportion of genes with homologs among distantly related groups. Models of the evolution of fungal genomes compatible with these results, and their functional implications, are discussed.}, }
@article {pmid10760166, year = {2000}, author = {Bootsma, HJ and van Dijk, H and Vauterin, P and Verhoef, J and Mooi, FR}, title = {Genesis of BRO beta-lactamase-producing Moraxella catarrhalis: evidence for transformation-mediated horizontal transfer.}, journal = {Molecular microbiology}, volume = {36}, number = {1}, pages = {93-104}, doi = {10.1046/j.1365-2958.2000.01828.x}, pmid = {10760166}, issn = {0950-382X}, mesh = {Alleles ; Base Sequence ; Cell Lineage ; DNA Fingerprinting ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Molecular Sequence Data ; Moraxella catarrhalis/classification/enzymology/*genetics ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; *Transformation, Bacterial ; beta-Lactam Resistance/*genetics ; beta-Lactamases/*genetics ; }, abstract = {The dramatic rise in BRO-producing M. catarrhalis strains observed in the last decades is without precedence. The aim of this study was to elucidate the events that led to the emergence of BRO-1 and BRO-2 beta-lactamases. Previously, we showed bro1 and bro2 to be >99% identical. Data presented here suggested that bro2 was acquired by a fortuitous event and inserted between M. catarrhalis genes orf1 and orf3. Subsequently, bro1 evolved from bro2. Promoter-up mutations increased fitness of bro2, explaining its present predominance. The highly conserved nature of bro compared with orf1 and orf3 suggested that acquisition has occurred relatively recently. The random distribution of bro among M. catarrhalis fingerprint types indicated that bro has spread by horizontal transfer. Sequence analysis revealed that 80-200 bp is generally cotransferred with bro, serving as regions of homology that target bro to the same chromosomal locus. A region of 160 bases upstream of bro1 lacked polymorphism, indicating it was derived from the original strain that acquired bro2. We observed that bro was readily transferred by transformation between M. catarrhalis strains in vitro, suggesting a mechanism by which bro has disseminated. In conclusion, we have been able to reconstruct the steps that led to the emergence of BRO-producing M. catarrhalis.}, }
@article {pmid10748211, year = {2000}, author = {Xu, Q and Stickel, S and Roberts, RJ and Blaser, MJ and Morgan, RD}, title = {Purification of the novel endonuclease, Hpy188I, and cloning of its restriction-modification genes reveal evidence of its horizontal transfer to the Helicobacter pylori genome.}, journal = {The Journal of biological chemistry}, volume = {275}, number = {22}, pages = {17086-17093}, doi = {10.1074/jbc.M910303199}, pmid = {10748211}, issn = {0021-9258}, support = {DK53707/DK/NIDDK NIH HHS/United States ; GM56534/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Base Sequence ; Cloning, Molecular ; DNA Primers ; Deoxyribonucleases, Type II Site-Specific/genetics/*isolation &amp; purification/metabolism ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Helicobacter pylori/*genetics ; Molecular Sequence Data ; Open Reading Frames ; Substrate Specificity ; }, abstract = {We have isolated a novel restriction endonuclease, Hpy188I, from Helicobacter pylori strain J188. Hpy188I recognizes the unique sequence, TCNGA, and cleaves the DNA between nucleotides N and G in its recognition sequence to generate a one-base 3' overhang. Cloning and sequence analysis of the Hpy188I modification gene in strain J188 reveal that hpy188IM has a 1299-base pair (bp) open reading frame (ORF) encoding a 432-amino acid product. The predicted protein sequence of M.Hpy188I contains conserved motifs typical of aminomethyltransferases, and Western blotting indicates that it is an N-6 adenine methyltransferase. Downstream of hpy188IM is a 513-bp ORF encoding a 170-amino acid product, that has a 41-bp overlap with hpy188IM. The predicted protein sequence from this ORF matches the amino acid sequence obtained from purified Hpy188I, indicating that it encodes the endonuclease. The Hpy188I R-M genes are not present in either strain of H. pylori that has been completely sequenced but are found in two of 11 H. pylori strains tested. The significantly lower G + C content of the Hpy188I R-M genes implies that they have been introduced relatively recently during the evolution of the H. pylori genome.}, }
@article {pmid10746763, year = {2000}, author = {Barbian, KD and Minnick, MF}, title = {A bacteriophage-like particle from Bartonella bacilliformis.}, journal = {Microbiology (Reading, England)}, volume = {146 (Pt 3)}, number = {}, pages = {599-609}, doi = {10.1099/00221287-146-3-599}, pmid = {10746763}, issn = {1350-0872}, mesh = {*Bacteriophages/genetics/metabolism/ultrastructure ; Bartonella/genetics/growth &amp; development/*virology ; Blotting, Southern ; Blotting, Western ; DNA, Bacterial/genetics/metabolism ; DNA, Viral/genetics/metabolism ; Defective Viruses/genetics/physiology ; Electrophoresis, Polyacrylamide Gel ; Humans ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Transduction, Genetic ; Viral Proteins/chemistry/metabolism ; }, abstract = {Bartonella bacilliformis and Bartonella henselae, the respective agents of Oroya fever and cat-scratch disease in humans, are known to produce bacteriophage-like particles (BLPs) that package 14 kbp segments of the host chromosome. Data from this study suggest that other Bartonella species including Bartonella quintana, Bartonella doshiae and Bartonella grahamii also contain similar BLPs, as evidenced by the presence of a 14 kbp extrachromosomal DNA element in their genomes, whereas Bartonella elizabethae and Bartonella clarridgeiae do not. A purification scheme utilizing chloroform, DNase I and centrifugation was devised to isolate BLPs from B. bacilliformis. Intact BLPs were observed by transmission electron microscopy and were round to icosahedral in shape and approximately 80 nm in diameter. RFLP and Southern blot analysis of BLP DNA from B. bacilliformis suggest that packaging, while non-selective, is less than the near-random packaging previously reported for the B. henselae phage. Data also suggest that the linear, double-stranded BLP DNA molecules have blunt ends with noncovalently closed termini. Packaging of the BLP DNA molecules into a protein coat appears to be closely related to nucleic acid synthesis, as unpackaged phage DNA is not detectable within the host cell. SDS-PAGE analysis of purified BLPs from B. bacilliformis showed three major proteins with apparent molecular masses of 32, 34 and 36 kDa; values that closely correspond to proteins found in B. henselae BLPs. Western blot analysis performed with patient convalescent serum showed that BLP proteins are slightly immunogenic in humans. To determine if BLPs contribute to horizontal gene transfer, mutants of B. bacilliformis were generated by allelic exchange with an internal fragment of the 16S-23S rDNA intergenic spacer region and a suicide vector construct, termed pKB1. BLPs from one of the resultant strains were able to package the mutagenized region containing the kanamycin-resistance cassette; however, numerous approaches and attempts at intraspecies transduction using these BLPs were unsuccessful.}, }
@article {pmid10735862, year = {2000}, author = {Poelarends, GJ and Kulakov, LA and Larkin, MJ and van Hylckama Vlieg, JE and Janssen, DB}, title = {Roles of horizontal gene transfer and gene integration in evolution of 1,3-dichloropropene- and 1,2-dibromoethane-degradative pathways.}, journal = {Journal of bacteriology}, volume = {182}, number = {8}, pages = {2191-2199}, pmid = {10735862}, issn = {0021-9193}, mesh = {Allyl Compounds/metabolism ; Amino Acid Sequence ; Base Sequence ; Biodegradation, Environmental ; Conserved Sequence ; DNA Transposable Elements ; DNA-Binding Proteins/metabolism ; Environmental Pollutants/metabolism ; *Escherichia coli Proteins ; Ethylene Dibromide/metabolism ; *Evolution, Molecular ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Hydrocarbons, Brominated ; Hydrocarbons, Chlorinated ; Hydrocarbons, Halogenated/*metabolism ; Hydrolases/*genetics ; Integrases/genetics ; Molecular Sequence Data ; Mycobacterium/enzymology/genetics ; Pseudomonas/enzymology/genetics ; *Recombination, Genetic ; Rhodococcus/enzymology/genetics ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Trans-Activators/metabolism ; }, abstract = {The haloalkane-degrading bacteria Rhodococcus rhodochrous NCIMB13064, Pseudomonas pavonaceae 170, and Mycobacterium sp. strain GP1 share a highly conserved haloalkane dehalogenase gene (dhaA). Here, we describe the extent of the conserved dhaA segments in these three phylogenetically distinct bacteria and an analysis of their flanking sequences. The dhaA gene of the 1-chlorobutane-degrading strain NCIMB13064 was found to reside within a 1-chlorobutane catabolic gene cluster, which also encodes a putative invertase (invA), a regulatory protein (dhaR), an alcohol dehydrogenase (adhA), and an aldehyde dehydrogenase (aldA). The latter two enzymes may catalyze the oxidative conversion of n-butanol, the hydrolytic product of 1-chlorobutane, to n-butyric acid, a growth substrate for many bacteria. The activity of the dhaR gene product was analyzed in Pseudomonas sp. strain GJ1, in which it appeared to function as a repressor of dhaA expression. The 1,2-dibromoethane-degrading strain GP1 contained a conserved DNA segment of 2.7 kb, which included dhaR, dhaA, and part of invA. A 12-nucleotide deletion in dhaR led to constitutive expression of dhaA in strain GP1, in contrast to the inducible expression of dhaA in strain NCIMB13064. The 1, 3-dichloropropene-degrading strain 170 possessed a conserved DNA segment of 1.3 kb harboring little more than the coding region of the dhaA gene. In strains 170 and GP1, a putative integrase gene was found next to the conserved dhaA segment, which suggests that integration events were responsible for the acquisition of these DNA segments. The data indicate that horizontal gene transfer and integrase-dependent gene acquisition were the key mechanisms for the evolution of catabolic pathways for the man-made chemicals 1, 3-dichloropropene and 1,2-dibromoethane.}, }
@article {pmid10730896, year = {1999}, author = {Zgur-Bertok, D}, title = {Mechanisms of horizontal gene transfer (review).}, journal = {Folia biologica}, volume = {45}, number = {3}, pages = {91-96}, pmid = {10730896}, issn = {0015-5500}, mesh = {Animals ; Conjugation, Genetic ; DNA Transposable Elements/genetics ; Eukaryotic Cells ; Models, Genetic ; Plasmids/classification/genetics ; Prokaryotic Cells ; Repetitive Sequences, Nucleic Acid ; Transduction, Genetic ; Transformation, Bacterial/genetics ; *Transformation, Genetic/physiology ; }, }
@article {pmid10723736, year = {2000}, author = {Garcia-Vallvé, S and Romeu, A and Palau, J}, title = {Horizontal gene transfer of glycosyl hydrolases of the rumen fungi.}, journal = {Molecular biology and evolution}, volume = {17}, number = {3}, pages = {352-361}, doi = {10.1093/oxfordjournals.molbev.a026315}, pmid = {10723736}, issn = {0737-4038}, mesh = {Animals ; Base Composition ; Cellulase/*genetics ; Evolution, Molecular ; Gram-Negative Anaerobic Bacteria/*genetics ; Neocallimastigales/*genetics ; Phylogeny ; *Recombination, Genetic ; Rumen/*microbiology ; Sequence Analysis, DNA ; }, abstract = {By combining analyses of G + C content and patterns of codon usage and constructing phylogenetic trees, we describe the gene transfer of an endoglucanase (celA) from the rumen bacteria Fibrobacter succinogenes to the rumen fungi Orpinomyces joyonii. The strong similarity between different glycosyl hydrolases of rumen fungi and bacteria suggests that most, if not all, of the glycosyl hydrolases of rumen fungi that play an important role in the degradation of cellulose and other plant polysaccharides were acquired by horizontal gene transfer events. This acquisition allows fungi to establish a habitat within a new environmental niche: the rumen of the herbivorous mammals for which cellulose and plant hemicellulose constitute the main raw nutritive substrate.}, }
@article {pmid10722479, year = {2000}, author = {Ferrándiz, MJ and Fenoll, A and Liñares, J and De La Campa, AG}, title = {Horizontal transfer of parC and gyrA in fluoroquinolone-resistant clinical isolates of Streptococcus pneumoniae.}, journal = {Antimicrobial agents and chemotherapy}, volume = {44}, number = {4}, pages = {840-847}, pmid = {10722479}, issn = {0066-4804}, mesh = {Amino Acid Sequence ; Anti-Infective Agents/*pharmacology ; Base Sequence ; Blotting, Southern ; DNA Gyrase ; DNA Probes ; DNA Topoisomerase IV ; DNA Topoisomerases, Type II/*genetics ; Drug Resistance, Microbial ; Fluoroquinolones ; Gene Transfer, Horizontal ; Humans ; Molecular Sequence Data ; Pneumococcal Infections/microbiology ; Reverse Transcriptase Polymerase Chain Reaction ; Streptococcus pneumoniae/drug effects/*genetics ; }, abstract = {We have analyzed genetically three clinical isolates (3180, 3870, and 1244) of Streptococcus pneumoniae with high-level ciprofloxacin resistance. Isolates 3180 and 3870 were atypical because of their insolubility in deoxycholate. However, they hybridized specifically with pneumococcal autolysin and pneumolysin gene probes and have typical pneumococcal atpC and atpA gene sequences. Analysis of the complete sequences of the parC and gyrA genes revealed total variations of 8 and 8.7% (isolate 3180) and 7.4 and 3.6% (isolate 3870), respectively, compared to the wild-type strain R6 sequence. The variations observed between the sequences of R6 and isolate 1244 were less than 0.9%. The structure of the gyrA and parC genes from isolates 3180 and 3870 was organized in sequence blocks that show different levels of divergence, suggesting a pattern of recombination. These results are evidence for recombination at the fluoroquinolone target genes in clinical isolates of S. pneumoniae. The genetically related viridans group streptococci could act as a reservoir for fluoroquinolone resistance genes.}, }
@article {pmid10716711, year = {2000}, author = {Graham, DE and Overbeek, R and Olsen, GJ and Woese, CR}, title = {An archaeal genomic signature.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {97}, number = {7}, pages = {3304-3308}, pmid = {10716711}, issn = {0027-8424}, mesh = {Archaeal Proteins/genetics ; *Genome, Archaeal ; Multigene Family ; Open Reading Frames ; Species Specificity ; }, abstract = {Comparisons of complete genome sequences allow the most objective and comprehensive descriptions possible of a lineage's evolution. This communication uses the completed genomes from four major euryarchaeal taxa to define a genomic signature for the Euryarchaeota and, by extension, the Archaea as a whole. The signature is defined in terms of the set of protein-encoding genes found in at least two diverse members of the euryarchaeal taxa that function uniquely within the Archaea; most signature proteins have no recognizable bacterial or eukaryal homologs. By this definition, 351 clusters of signature proteins have been identified. Functions of most proteins in this signature set are currently unknown. At least 70% of the clusters that contain proteins from all the euryarchaeal genomes also have crenarchaeal homologs. This conservative set, which appears refractory to horizontal gene transfer to the Bacteria or the Eukarya, would seem to reflect the significant innovations that were unique and fundamental to the archaeal "design fabric." Genomic protein signature analysis methods may be extended to characterize the evolution of any phylogenetically defined lineage. The complete set of protein clusters for the archaeal genomic signature is presented as supplementary material (see the PNAS web site, www.pnas.org).}, }
@article {pmid10715015, year = {2000}, author = {Hochhut, B and Marrero, J and Waldor, MK}, title = {Mobilization of plasmids and chromosomal DNA mediated by the SXT element, a constin found in Vibrio cholerae O139.}, journal = {Journal of bacteriology}, volume = {182}, number = {7}, pages = {2043-2047}, pmid = {10715015}, issn = {0021-9193}, support = {R01 AI042347/AI/NIAID NIH HHS/United States ; P30 DK034928/DK/NIDDK NIH HHS/United States ; 2 T35 HL07785-06/HL/NHLBI NIH HHS/United States ; T35 HL007785/HL/NHLBI NIH HHS/United States ; P30DK-34928/DK/NIDDK NIH HHS/United States ; R37 AI042347/AI/NIAID NIH HHS/United States ; AI42347/AI/NIAID NIH HHS/United States ; }, mesh = {Chromosomes, Bacterial/genetics ; Conjugation, Genetic/*genetics ; DNA Transposable Elements/genetics ; DNA, Bacterial/*genetics ; Drug Resistance, Microbial/genetics ; Genetic Markers/genetics ; Integrases/genetics/metabolism ; Models, Genetic ; Plasmids/*genetics ; Recombination, Genetic/genetics ; Regulatory Sequences, Nucleic Acid/genetics/*physiology ; Vibrio cholerae/enzymology/*genetics ; }, abstract = {The Vibrio cholerae SXT element encodes resistance to multiple antibiotics and is a conjugative, self-transmissible, and chromosomally integrating element (a constin). Excision and self-transfer of the SXT element require an element-encoded integrase. We now report that the SXT element can also mobilize the plasmids RSF1010 and CloDF13 in trans as well as chromosomal DNA in an Hfr-like manner. SXT element-mediated mobilization of plasmids and chromosomal DNA, unlike its self-transfer, is not dependent upon excision of the element from the chromosome. These results raise the possibility that the SXT element and other constins play a general role in horizontal gene transfer among gram-negative bacteria.}, }
@article {pmid10677854, year = {2000}, author = {Turner, SL and Young, JP}, title = {The glutamine synthetases of rhizobia: phylogenetics and evolutionary implications.}, journal = {Molecular biology and evolution}, volume = {17}, number = {2}, pages = {309-319}, doi = {10.1093/oxfordjournals.molbev.a026311}, pmid = {10677854}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; *Evolution, Molecular ; Glutamate-Ammonia Ligase/chemistry/*genetics ; Likelihood Functions ; Molecular Sequence Data ; *Phylogeny ; Rhizobiaceae/classification/enzymology/*genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; Time ; }, abstract = {Glutamine synthetase exists in at least two related forms, GSI and GSII, the sequences of which have been used in evolutionary molecular clock studies. GSI has so far been found exclusively in bacteria, and GSII has been found predominantly in eukaryotes. To date, only a minority of bacteria, including rhizobia, have been shown to express both forms of GS. The sequences of equivalent internal fragments of the GSI and GSII genes for the type strains of 16 species of rhizobia have been determined and analyzed. The GSI and GSII data sets do not produce congruent phylogenies with either neighbor-joining or maximum-likelihood analyses. The GSI phylogeny is broadly congruent with the 16S rDNA phylogeny for the same bacteria; the GSII phylogeny is not. There are three striking rearrangements in the GSII phylograms, all of which might be explained by horizontal gene transfer to Bradyrhizobium (probably from Mesorhizobium), to Rhizobium galegae (from Rhizobium), and to Mesorhizobium huakuii (perhaps from Rhizobium). There is also evidence suggesting intrageneric DNA transfer within Mesorhizobium. Meta-analysis of both GS genes from the different genera of rhizobia and other reference organisms suggests that the divergence times of the different rhizobium genera predate the existence of legumes, their host plants.}, }
@article {pmid10707066, year = {2000}, author = {de la Cruz, F and Davies, J}, title = {Horizontal gene transfer and the origin of species: lessons from bacteria.}, journal = {Trends in microbiology}, volume = {8}, number = {3}, pages = {128-133}, doi = {10.1016/s0966-842x(00)01703-0}, pmid = {10707066}, issn = {0966-842X}, mesh = {Bacteria/*genetics/metabolism/pathogenicity ; Biodegradation, Environmental ; Drug Resistance, Microbial ; Evolution, Molecular ; *Recombination, Genetic ; Virulence ; }, abstract = {In bacteria, horizontal gene transfer (HGT) is widely recognized as the mechanism responsible for the widespread distribution of antibiotic resistance genes, gene clusters encoding biodegradative pathways and pathogenicity determinants. We propose that HGT is also responsible for speciation and sub-speciation in bacteria, and that HGT mechanisms exist in eukaryotes.}, }
@article {pmid10698793, year = {2000}, author = {Schmidt, H and Scheef, J and Morabito, S and Caprioli, A and Wieler, LH and Karch, H}, title = {A new Shiga toxin 2 variant (Stx2f) from Escherichia coli isolated from pigeons.}, journal = {Applied and environmental microbiology}, volume = {66}, number = {3}, pages = {1205-1208}, pmid = {10698793}, issn = {0099-2240}, mesh = {Alleles ; Animals ; Animals, Wild/microbiology ; Bacterial Toxins/*genetics ; Columbidae/*microbiology ; Escherichia coli/*genetics ; Feces/microbiology ; Genetic Variation ; Immunoenzyme Techniques ; Molecular Sequence Data ; Polymerase Chain Reaction ; Reagent Kits, Diagnostic ; Shiga Toxins ; }, abstract = {We have isolated Shiga toxin (Stx)-producing Escherichia coli (STEC) strains from the feces of feral pigeons which contained a new Stx2 variant gene designated stx(2f). This gene is most similar to sltIIva of patient E. coli O128:B12 isolate H.I.8. Stx2f reacted only weakly with commercial immunoassays. The prevalence of STEC organisms carrying the stx(2f) gene in pigeon droppings was 12.5%. The occurrence of a new Stx2 variant in STEC from pigeons enlarges the pool of Stx2 variants and raises the question whether horizontal gene transfer to E. coli pathogenic to humans may occur.}, }
@article {pmid10692479, year = {2000}, author = {Screen, SE and St Leger, RJ}, title = {Cloning, expression, and substrate specificity of a fungal chymotrypsin. Evidence for lateral gene transfer from an actinomycete bacterium.}, journal = {The Journal of biological chemistry}, volume = {275}, number = {9}, pages = {6689-6694}, doi = {10.1074/jbc.275.9.6689}, pmid = {10692479}, issn = {0021-9258}, mesh = {Actinomycetales/enzymology/genetics ; Amino Acid Sequence ; Base Sequence ; Chymotrypsin/chemistry/*genetics ; Cloning, Molecular ; Expressed Sequence Tags ; Fungal Proteins/chemistry/*genetics ; Fungi/*enzymology ; Gene Transfer Techniques ; Molecular Sequence Data ; Pichia ; Recombinant Proteins/chemistry/genetics ; Sequence Alignment ; Substrate Specificity ; }, abstract = {Unlike trypsins, chymotrypsins have not until now been found in fungi. Expressed sequence tag analysis of the deuteromycete Metarhizium anisopliae identified two trypsins (family S1) and a novel chymotrypsin (CHY1). CHY1 resembles actinomycete (bacterial) chymotrypsins (family S2) rather than other eukaryote enzymes (family S1) in being synthesized as a precursor species (374 amino acids, pI/MW: 5.07/38,279) containing a large N-terminal fragment (186 amino acids). Chy1 was expressed in Pichia pastoris yielding an enzyme with a chymotrypsin specificity for branched aliphatic and aromatic C-terminal amino acids. This is predictable as key catalytic residues determining the specificity of Streptomyces griseus chymotrypsins are conserved with CHY1. Mature (secreted) CHY1 (pI/MW: 8.29/18,499) shows closest overall amino acid identity to S. griseus protease C (55%) and clustered with other secreted bacterial S2 chymotrypsins that diverged widely from animal and endocellular bacterial enzymes in phylogenetic trees of the chymotrypsin superfamily. Conversely, actinomycete chymotrypsins are much more closely related to fungal proteases than to other eubacterial sequences. Complete genomes of yeast, gram eubacteria, archaebacteria, and mitochondria do not contain paralogous genes. Expressed sequence tag data bases from other fungi also lack chymotrypsin homologs. In light of this patchy distribution, we conclude that chy1 probably arose by lateral gene transfer from an actinomycete bacterium.}, }
@article {pmid10685368, year = {1999}, author = {Curtis, MA and Hanley, SA and Aduse-Opoku, J}, title = {The rag locus of Porphyromonas gingivalis: a novel pathogenicity island.}, journal = {Journal of periodontal research}, volume = {34}, number = {7}, pages = {400-405}, doi = {10.1111/j.1600-0765.1999.tb02273.x}, pmid = {10685368}, issn = {0022-3484}, mesh = {Adult ; Antibodies, Bacterial/blood ; Antigens, Bacterial/analysis ; Antigens, Surface/analysis ; Bacterial Outer Membrane Proteins/immunology ; Bacterial Proteins/physiology ; Biological Transport, Active/genetics ; *Chromosome Mapping ; Dental Plaque/microbiology ; Gene Transfer, Horizontal ; Gingiva/microbiology ; Humans ; Immunodominant Epitopes/analysis ; Immunoglobulin G/blood ; Membrane Proteins/physiology ; Middle Aged ; Monomeric GTP-Binding Proteins/*genetics ; Operon/genetics ; Periodontal Diseases/microbiology/therapy ; Periodontal Pocket/microbiology ; Porphyromonas gingivalis/genetics/immunology/*pathogenicity ; Sequence Homology ; Signal Transduction/genetics ; Virulence ; }, abstract = {Previous studies in our laboratories of the serum IgG antibody response of periodontal patients have demonstrated the presence of an immunodominant surface antigen (Mr 55 kDa) in the outer membrane of Porphyromonas gingivalis W50. Genetic analysis of this antigen revealed that the corresponding gene forms part of a small operon which may have arisen via horizontal gene transfer into the genome of this strain. On the basis of sequence homology, the 55 kDa antigen (RagB) and the product of a cotranscribed gene (RagA) may act in concert at the surface of the bacterium to facilitate active transport, mediated through the periplasmic spanning protein, TonB, or form part of a signal transduction system in this organism. The rag locus is present in only a proportion of P. gingivalis laboratory strains and clinical isolates. Analysis of the distribution of ragB in subgingival samples by PCR demonstrated that rag+ P. gingivalis are more frequently detected in deep periodontal pockets than shallow sites in periodontal patients. These findings indicate that the rag genes may influence the virulence potential of P. gingivalis strains which harbour this locus and may thus be considered a novel pathogenicity island. Furthermore, horizontal gene transfer between organisms in subgingival plaque may represent a significant force in the evolution of these bacteria with ramifications for both diagnosis and targeted treatment of periodontal disease.}, }
@article {pmid10640595, year = {2000}, author = {Arber, W}, title = {Genetic variation: molecular mechanisms and impact on microbial evolution.}, journal = {FEMS microbiology reviews}, volume = {24}, number = {1}, pages = {1-7}, doi = {10.1111/j.1574-6976.2000.tb00529.x}, pmid = {10640595}, issn = {0168-6445}, mesh = {Bacteria/*genetics ; Base Sequence/genetics ; DNA Repair ; DNA Transposable Elements ; *Evolution, Molecular ; Gene Rearrangement ; Gene Transfer, Horizontal ; *Genetic Variation/genetics ; Genome, Bacterial ; Recombination, Genetic/genetics ; }, abstract = {On the basis of established knowledge of microbial genetics one can distinguish three major natural strategies in the spontaneous generation of genetic variations in bacteria. These strategies are: (1) small local changes in the nucleotide sequence of the genome, (2) intragenomic reshuffling of segments of genomic sequences and (3) the acquisition of DNA sequences from another organism. The three general strategies differ in the quality of their contribution to microbial evolution. Besides a number of non-genetic factors, various specific gene products are involved in the generation of genetic variation and in the modulation of the frequency of genetic variation. The underlying genes are called evolution genes. They act for the benefit of the biological evolution of populations as opposed to the action of housekeeping genes and accessory genes which are for the benefit of individuals. Examples of evolution genes acting as variation generators are found in the transposition of mobile genetic elements and in so-called site-specific recombination systems. DNA repair systems and restriction-modification systems are examples of modulators of the frequency of genetic variation. The involvement of bacterial viruses and of plasmids in DNA reshuffling and in horizontal gene transfer is a hint for their evolutionary functions. Evolution genes are thought to undergo biological evolution themselves, but natural selection for their functions is indirect, at the level of populations, and is called second-order selection. In spite of an involvement of gene products in the generation of genetic variations, evolution genes do not programmatically direct evolution towards a specific goal. Rather, a steady interplay between natural selection and mixed populations of genetic variants gives microbial evolution its direction.}, }
@article {pmid10637321, year = {2000}, author = {Worning, P and Jensen, LJ and Nelson, KE and Brunak, S and Ussery, DW}, title = {Structural analysis of DNA sequence: evidence for lateral gene transfer in Thermotoga maritima.}, journal = {Nucleic acids research}, volume = {28}, number = {3}, pages = {706-709}, pmid = {10637321}, issn = {1362-4962}, mesh = {Chromatin/chemistry/genetics ; *Computational Biology ; DNA/chemistry/*genetics ; Fourier Analysis ; Genome, Archaeal ; *Genome, Bacterial ; Genome, Fungal ; *Models, Genetic ; Nucleic Acid Conformation ; Phylogeny ; Pyrococcus/genetics ; *Recombination, Genetic ; Saccharomyces cerevisiae/genetics ; Sequence Alignment ; Spectrum Analysis ; Thermodynamics ; Thermotoga maritima/*genetics ; }, abstract = {The recently published complete DNA sequence of the bacterium Thermotoga maritima provides evidence, based on protein sequence conservation, for lateral gene transfer between Archaea and Bacteria. We introduce a new method of periodicity analysis of DNA sequences, based on structural parameters, which brings independent evidence for the lateral gene transfer in the genome of T.maritima. The structural analysis relates the Archaea-like DNA sequences to the genome of Pyrococcus horikoshii. Analysis of 24 complete genomic DNA sequences shows different periodicity patterns for organisms of different origin. The typical genomic periodicity for Bacteria is 11 bp whilst it is 10 bp for Archaea. Eukaryotes have more complex spectra but the dominant period in the yeast Saccharomyces cerevisiae is 10.2 bp. These periodicities are most likely reflective of differences in chromatin structure.}, }
@article {pmid10632872, year = {2000}, author = {Moreira, D}, title = {Multiple independent horizontal transfers of informational genes from bacteria to plasmids and phages: implications for the origin of bacterial replication machinery.}, journal = {Molecular microbiology}, volume = {35}, number = {1}, pages = {1-5}, doi = {10.1046/j.1365-2958.2000.01692.x}, pmid = {10632872}, issn = {0950-382X}, mesh = {Bacteria/*genetics ; Bacteriophages/*genetics ; *Gene Transfer, Horizontal ; Phylogeny ; *Plasmids ; *Replication Origin ; }, abstract = {In contrast to the universality of other central genetic mechanisms, the replication machinery of Bacteria is clearly different from those of Archaea and Eukaryotes. A large number of bacterial genes involved in DNA replication can also be found in plasmids and phages. Based on this, it has been recently proposed that the ancestral bacterial genes were displaced by non-orthologous replication genes from plasmids and phages, which would explain the profound difference between Bacteria and the other domains of life. The alternative hypothesis is that these DNA replication genes have been frequently transferred from bacterial hosts to the genomes of their plasmids and phages. The phylogenetic analysis of the bacterial DNA replication proteins most abundant in databases (replicative helicase DnaB, single-strand binding protein Ssb and topoisomerase TopB) presented here supports the latter hypothesis. Each protein tree shows that sequences from plasmids and phages branch close to their bacterial-specific hosts, suggesting multiple independent horizontal transfers. Therefore, there is no evidence so far for non-orthologous gene displacement of these genes.}, }
@article {pmid10624684, year = {1999}, author = {Prozorov, AA}, title = {[Horizontal gene transfer in bacteria: laboratory simulation, natural populations, genomic data].}, journal = {Mikrobiologiia}, volume = {68}, number = {5}, pages = {632-646}, pmid = {10624684}, issn = {0026-3656}, mesh = {Bacteria/drug effects/*genetics ; Drug Resistance, Microbial/genetics ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Models, Biological ; Plasmids ; }, abstract = {Various aspects of horizontal gene transfer among bacteria are considered: modeling of this phenomenon in microcosms and natural environments; influence of gene migration on the composition of natural bacterial populations; peculiarities of bacterial chromosome evolution.}, }
@article {pmid10622715, year = {1999}, author = {Li, T and Graham, DE and Stathopoulos, C and Haney, PJ and Kim, HS and Vothknecht, U and Kitabatake, M and Hong, KW and Eggertsson, G and Curnow, AW and Lin, W and Celic, I and Whitman, W and Söll, D}, title = {Cysteinyl-tRNA formation: the last puzzle of aminoacyl-tRNA synthesis.}, journal = {FEBS letters}, volume = {462}, number = {3}, pages = {302-306}, doi = {10.1016/s0014-5793(99)01550-1}, pmid = {10622715}, issn = {0014-5793}, mesh = {Amino Acid Sequence ; Animals ; Cloning, Molecular ; Escherichia coli/*genetics ; Evolution, Molecular ; Genes, Archaeal ; Genes, Bacterial ; Genetic Complementation Test ; Methanococcus/genetics ; Methanosarcina barkeri/genetics ; Molecular Sequence Data ; Mutagenesis ; Phylogeny ; RNA, Transfer, Amino Acyl/genetics/*physiology ; Sequence Homology, Amino Acid ; }, abstract = {With the exception of the methanogenic archaea Methanococcus jannaschii and Methanobacterium thermoautotrophicum deltaH, all organisms surveyed contain orthologs of Escherichia coli cysteinyl-tRNA synthetase (CysRS). The characterization of CysRS-encoding (cysS) genes and the demonstration of their ability to complement an E. coli cysSts mutant reveal that Methanococcus maripaludis and Methanosarcina barkeri, two other methanogenic archaea, possess canonical CysRS proteins. A molecular phylogeny inferred from 40 CysRS sequences indicates that the CysRS of M. maripaludis and Methanosarcina spp. are specific relatives of the CysRS of Pyrococcus spp. and Chlamydia, respectively. This result suggests that the CysRS gene was acquired by lateral gene transfer in at least one euryarchaeotic lineage.}, }
@article {pmid10611671, year = {1999}, author = {Doolittle, WF}, title = {Lateral genomics.}, journal = {Trends in cell biology}, volume = {9}, number = {12}, pages = {M5-8}, pmid = {10611671}, issn = {0962-8924}, mesh = {Evolution, Molecular ; Genome ; Phylogeny ; Prokaryotic Cells/*classification ; *RNA, Ribosomal/classification ; }, abstract = {More than 20 complete prokaryotic genome sequences are now publicly available, each by itself an unparalleled resource for understanding organismal biology. Collectively, these data are even more powerful: they could force a dramatic reworking of the framework in which we understand biological evolution. It is possible that a single universal phylogenetic tree is not the best way to depict relationships between all living and extinct species. Instead a web- or net-like pattern, reflecting the importance of horizontal or lateral gene transfer between lineages of organisms, might provide a more appropriate visual metaphor. Here, I ask whether this way of thinking is really justified, and explore its implications.}, }
@article {pmid10608290, year = {1999}, author = {Hughes, AL}, title = {Genomic catastrophism and the origin of vertebrate immunity.}, journal = {Archivum immunologiae et therapiae experimentalis}, volume = {47}, number = {6}, pages = {347-353}, pmid = {10608290}, issn = {0004-069X}, mesh = {Animals ; *Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; Genome ; Homeodomain Proteins/genetics ; Humans ; Models, Genetic ; Phylogeny ; Vertebrates/*genetics/*immunology ; }, abstract = {Genomic catastrophism is the belief that unique genetic events, unlike those observed in recent evolutionary history, played a key role in the origin of vertebrate adaptations. Catastrophist hypotheses have been particularly popular is accounting for the origin of vertebrate specific immunity. Two major such hypotheses involve genome duplication by polyploidization and horizontal gene transfer. Recent analyses lead to decisive rejection of the widely cited hypothesis that the vertebrate genome underwent two rounds of genome duplication, and theoretical considerations suggest that genome duplication is unlikely to lead to new adaptive advances. Likewise, the evidence that key elements of the vertebrate immune system arose by horizontal transfer from a bacterium or by incorporation of a transposable element into the vertebrate genome remains relatively weak. Thus, at present, a uniformitarian view of the origin of the vertebrate immune system seems more reasonable, especially given the longer time-frame for vertebrate evolution indicated by molecular data.}, }
@article {pmid10607609, year = {1999}, author = {Andersson, JO and Andersson, SG}, title = {Insights into the evolutionary process of genome degradation.}, journal = {Current opinion in genetics &amp; development}, volume = {9}, number = {6}, pages = {664-671}, doi = {10.1016/s0959-437x(99)00024-6}, pmid = {10607609}, issn = {0959-437X}, mesh = {DNA, Bacterial/chemistry/genetics ; *Evolution, Molecular ; Genes, Bacterial/genetics ; *Genome, Bacterial ; Methionine Adenosyltransferase/genetics ; Molecular Weight ; Plasmids/genetics ; Pseudogenes/genetics ; Rickettsia/genetics ; }, abstract = {Studies of noncoding and pseudogene sequence diversity, particularly in Rickettsia, have begun to reveal the basic principles of genome degradation in microorganisms. Increasingly, studies of genes and genomes suggest that there has been an extensive amount of horizontal gene transfer among microorganisms. As this inflow of genetic material does not seem generally to have resulted in genome size expansions, however, degenerative processes must be at the very least as widespread as horizontal gene transfer. The basic principles of gene degradation and elimination that are being explored in Rickettsia are likely to be of major importance for our understanding of how microbial genomes evolve.}, }
@article {pmid10589738, year = {1999}, author = {Müller-Graf, CDM and Whatmore, AM and King, SJ and Trzcinski, K and Pickerill, AP and Doherty, N and Paul, J and Griffiths, D and Crook, D and Dowson, CG}, title = {Population biology of Streptococcus pneumoniae isolated from oropharyngeal carriage and invasive disease.}, journal = {Microbiology (Reading, England)}, volume = {145 (Pt 11)}, number = {}, pages = {3283-3293}, doi = {10.1099/00221287-145-11-3283}, pmid = {10589738}, issn = {1350-0872}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Adolescent ; Adult ; Anti-Bacterial Agents/pharmacology ; Bacterial Typing Techniques ; Base Sequence ; Carrier State/epidemiology/*microbiology ; Child ; Child, Preschool ; Drug Resistance, Microbial ; Female ; Genes, Bacterial/genetics ; Genetic Variation ; Genetics, Population ; HIV Seropositivity ; Humans ; Molecular Epidemiology ; Molecular Sequence Data ; Oropharynx/*microbiology ; Pneumococcal Infections/epidemiology/*microbiology ; Polymorphism, Restriction Fragment Length ; Streptococcus pneumoniae/*classification/drug effects/genetics ; Virulence ; }, abstract = {The population structure of Streptococcus pneumoniae in a sample of 134 carried antibiotic-susceptible isolates, and 53 resistant and susceptible invasive isolates, was examined using a DNA-based version of multilocus enzyme electrophoresis: multilocus restriction typing (MLRT). This involved RFLP analysis of PCR products generated from nine loci of housekeeping genes located around the pneumococcal chromosome. The combination of alleles at each of the nine loci gave an allelic profile or restriction type (RT). All carried (throat or nasopharyngeal) isolates from children or adults in Oxford and Manchester, UK, and from an HIV-seropositive cohort in Nairobi, Kenya, showed an epidemic population structure. Twelve carried clonal groups, each with different serotypes, were identified at both locations within the UK. Almost all of the carried clones examined (16/17) were found to possess identical RTs or sequence types (STs) to invasive isolates, indicating that frequently carried clones are also associated with cases of invasive disease. As expected from previous studies, the population of 53 invasive, mainly penicillin-resistant, isolates was also found to be at linkage equilibrium. Serotype switching was identified among 14% of RTs that possessed two or more members, or 5.7% of individual isolates within these RTs. In support of a population structure in which there is frequent recombination, there is also clear evidence that the trpA/B locus within pneumococci has evolved by horizontal gene transfer. A non-serotypable isolate from an HIV-seropositive patient in Kenya was clearly genetically distinct from other strains studied, with unique alleles at eight out of nine loci examined. However, it was initially identified as a pneumococcus by a 16S RNA gene probe (Gen-Probe), optochin susceptibility and the presence of pneumolysin and autolysin.}, }
@article {pmid10559170, year = {1999}, author = {Petersen, A and Josephsen, J and Johnsen, MG}, title = {TPW22, a lactococcal temperate phage with a site-specific integrase closely related to Streptococcus thermophilus phage integrases.}, journal = {Journal of bacteriology}, volume = {181}, number = {22}, pages = {7034-7042}, pmid = {10559170}, issn = {0021-9193}, mesh = {Attachment Sites, Microbiological ; Bacteriophages/*enzymology/genetics ; Base Sequence ; Integrases/*genetics/metabolism ; Lactococcus lactis/*virology ; Molecular Sequence Data ; Phylogeny ; Plasmids/genetics ; Sequence Analysis, DNA ; Streptococcus Phages/enzymology/*genetics ; Transformation, Genetic ; Virus Integration ; }, abstract = {The temperate phage TPW22, induced from Lactococcus lactis subsp. cremoris W22, and the evolutionarily interesting integrase of this phage were characterized. Phage TPW22 was propagated lytically on L. lactis subsp. cremoris 3107, which could also be lysogenized by site-specific integration. The attachment site (attP), 5'-TAAGGCGACGGTCG-3', of phage TPW22 was present on a 7.5-kb EcoRI fragment, a 3.4-kb EcoRI-HindIII fragment of which was sequenced. Sequence information revealed the presence of an integrase gene (int). The deduced amino acid sequence showed 42 and 28% identity with integrases of streptococcal and lactococcal phages, respectively. The identities with these integrase-encoding genes were 52 and 45%, respectively, at the nucleotide level. This could indicate horizontal gene transfer. A stable integration vector containing attP and int was constructed, and integration in L. lactis subsp. cremoris MG1363 was obtained. The existence of an exchangeable lactococcal phage integration module was suggested. The proposed module covers the phage attachment site, the integrase gene, and surrounding factor-independent terminator structures. The phages phiLC3, TP901-1, and TPW22 all have different versions of this module. Phylogenetically, the TPW22 Int links the phiLC3 lactococcal integrase with known Streptococcus thermophilus integrases.}, }
@article {pmid10557303, year = {1999}, author = {Aoki, S and Syno, K}, title = {Horizontal gene transfer and mutation: ngrol genes in the genome of Nicotiana glauca.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {96}, number = {23}, pages = {13229-13234}, pmid = {10557303}, issn = {0027-8424}, mesh = {Amino Acid Sequence ; Base Sequence ; DNA Primers ; Evolution, Molecular ; *Genes, Plant ; *Genome, Plant ; Molecular Sequence Data ; *Plants, Toxic ; Promoter Regions, Genetic ; Nicotiana/*genetics ; Transcription, Genetic ; Transformation, Genetic ; }, abstract = {Ngrol genes (NgrolB, NgrolC, NgORF13, and NgORF14) that are similar in sequence to genes in the left transferred DNA (TL-DNA) of Agrobacterium rhizogenes have been found in the genome of untransformed plants of Nicotiana glauca. It has been suggested that a bacterial infection resulted in transformation of Ngrol genes early in the evolution of the genus Nicotiana. Although the corresponding four rol genes in TL-DNA provoked hairy-root syndrome in plants, present-day N. glauca and plants transformed with Ngrol genes did not exhibit this phenotype. Sequenced complementation analysis revealed that the NgrolB gene did not induce adventitious roots because it contained two point mutations. Single-base site-directed mutagenesis at these two positions restored the capacity for root induction to the NgrolB gene. When the NgrolB, with these two base substitutions, was positioned under the control of the cauliflower mosaic virus 35S promoter (P35S), transgenic tobacco plants exhibited morphological abnormalities that were not observed in P35S-RirolB plants. In contrast, the activity of the NgrolC gene may have been conserved after an ancient infection by bacteria. Discussed is the effect of the horizontal gene transfer of the Ngrol genes and mutations in the NgrolB gene on the phenotype of ancient plants during the evolution of N. glauca.}, }
@article {pmid10556324, year = {1999}, author = {Aravind, L and Koonin, EV}, title = {DNA-binding proteins and evolution of transcription regulation in the archaea.}, journal = {Nucleic acids research}, volume = {27}, number = {23}, pages = {4658-4670}, doi = {10.1093/nar/27.23.4658}, pmid = {10556324}, issn = {0305-1048}, mesh = {Archaea/*genetics ; DNA-Binding Proteins/chemistry/*genetics ; Databases, Factual ; *Evolution, Molecular ; *Gene Expression Regulation, Archaeal ; Helix-Turn-Helix Motifs ; Protein Conformation ; Transcription, Genetic/*genetics ; }, abstract = {Likely DNA-binding domains in archaeal proteins were analyzed using sequence profile methods and available structural information. It is shown that all archaea encode a large number of proteins containing the helix-turn-helix (HTH) DNA-binding domains whose sequences are much more similar to bacterial HTH domains than to eukaryotic ones, such as the PAIRED, POU and homeodomains. The predominant class of HTH domains in archaea is the winged-HTH domain. The number and diversity of HTH domains in archaea is comparable to that seen in bacteria. The HTH domain in archaea combines with a variety of other domains that include replication system components, such as MCM proteins, translation system components, such as the alpha-subunit of phenyl-alanyl-tRNA synthetase, and several metabolic enzymes. The majority of the archaeal HTH-containing proteins are predicted to be gene/operon-specific transcriptional regulators. This apparent bacterial-type mode of transcription regulation is in sharp contrast to the eukaryote-like layout of the core transcription machinery in the archaea. In addition to the predicted bacterial-type transcriptional regulators, the HTH domain is conserved in archaeal and eukaryotic core transcription factors, such as TFIIB, TFIIE-alpha and MBF1. MBF1 is the only highly conserved, classical HTH domain that is vertically inherited in all archaea and eukaryotes. In contrast, while eukaryotic TFIIB and TFIIE-alpha possess forms of the HTH domain that are divergent in sequence, their archaeal counterparts contain typical HTH domains. It is shown that, besides the HTH domain, archaea encode unexpectedly large numbers of two other predicted DNA-binding domains, namely the Arc/MetJ domain and the Zn-ribbon. The core transcription regulators in archaea and eukaryotes (TFIIB/TFB, TFIIE-alpha and MBF1) and in bacteria (the sigma factors) share no similarity beyond the presence of distinct HTH domains. Thus HTH domains might have been independently recruited for a role in transcription regulation in the bacterial and archaeal/eukaryotic lineages. During subsequent evolution, the similarity between archaeal and bacterial gene/operon transcriptional regulators might have been established and maintained through multiple horizontal gene transfer events.}, }
@article {pmid10552044, year = {1999}, author = {Sawada, H and Suzuki, F and Matsuda, I and Saitou, N}, title = {Phylogenetic analysis of Pseudomonas syringae pathovars suggests the horizontal gene transfer of argK and the evolutionary stability of hrp gene cluster.}, journal = {Journal of molecular evolution}, volume = {49}, number = {5}, pages = {627-644}, doi = {10.1007/pl00006584}, pmid = {10552044}, issn = {0022-2844}, mesh = {Bacterial Proteins/genetics ; Bacterial Toxins/biosynthesis ; Base Sequence ; DNA Primers/genetics ; DNA, Bacterial/genetics ; DNA-Binding Proteins/genetics ; *Evolution, Molecular ; Exotoxins/biosynthesis ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Molecular Sequence Data ; *Multigene Family ; Ornithine/analogs &amp; derivatives ; Ornithine Carbamoyltransferase/genetics ; Phylogeny ; Plants/microbiology ; Pseudomonas/*genetics/metabolism/*pathogenicity ; Sequence Homology, Nucleic Acid ; *Sigma Factor ; Species Specificity ; *Transcription Factors ; Virulence/genetics ; }, abstract = {Pseudomonas syringae are differentiated into approximately 50 pathovars with different plant pathogenicities and host specificities. To understand its pathogenicity differentiation and the evolutionary mechanisms of pathogenicity-related genes, phylogenetic analyses were conducted using 56 strains belonging to 19 pathovars. gyrB and rpoD were adopted as the index genes to determine the course of bacterial genome evolution, and hrpL and hrpS were selected as the representatives of the pathogenicity-related genes located on the genome (chromosome). Based on these data, NJ, MP, and ML phylogenetic trees were constructed, and thus 3 trees for each gene and 12 gene trees in total were obtained, all of which showed three distinct monophyletic groups: Groups 1, 2 and 3. The observation that the same set of OTUs constitute each group in all four genes suggests that these genes had not experienced any intergroup horizontal gene transfer within P. syringae but have been stable on and evolved along with the P. syringae genome. These four index genes were then compared with another pathogenicity-related gene, argK (the phaseolotoxin-resistant ornithine carbamoyltransferase gene, which exists within the argK-tox gene cluster). All 13 strains of pv. phaseolicola and pv. actinidiae used had been confirmed to produce phaseolotoxin and to have argK, whose sequences were completely identical, without a single synonymous substitution among the strains used (Sawada et al. 1997a). On the other hand, argK were not present on the genomes of the other 43 strains used other than pv. actinidiae and pv. phaseolicola. Thus, the productivity of phaseolotoxin and the possession of the argK gene were shown at only two points on the phylogenetic tree: Group 1 (pv. actinidiae) and Group 3 (pv. phaseolicola). A t test between these two pathovars for the synonymous distances of argK and the tandemly combined sequence of the four index genes showed a high significance, suggesting that the argK gene (or argK-tox gene cluster) experienced horizontal gene transfer and expanded its distribution over two pathovars after the pathovars had separated, thus showing a base substitution pattern extremely different from that of the noncluster region of the genome.}, }
@article {pmid10531246, year = {1999}, author = {Boyd, EF and Waldor, MK}, title = {Alternative mechanism of cholera toxin acquisition by Vibrio cholerae: generalized transduction of CTXPhi by bacteriophage CP-T1.}, journal = {Infection and immunity}, volume = {67}, number = {11}, pages = {5898-5905}, pmid = {10531246}, issn = {0019-9567}, support = {R01 AI042347/AI/NIAID NIH HHS/United States ; T32 AI-07329/AI/NIAID NIH HHS/United States ; P30 DK034928/DK/NIDDK NIH HHS/United States ; AI-42347/AI/NIAID NIH HHS/United States ; P30DK-34928/DK/NIDDK NIH HHS/United States ; T32 AI007329/AI/NIAID NIH HHS/United States ; R37 AI042347/AI/NIAID NIH HHS/United States ; }, mesh = {Attachment Sites, Microbiological ; Bacteriophages/*genetics ; Cholera Toxin/*genetics ; *Gene Transfer, Horizontal ; Lysogeny ; Vibrio cholerae/genetics/*virology ; }, abstract = {Horizontal transfer of genes encoding virulence factors has played a central role in the evolution of many pathogenic bacteria. The unexpected discovery that the genes encoding cholera toxin (ctxAB), the main cause of the profuse secretory diarrhea characteristic of cholera, are encoded on a novel filamentous phage named CTXPhi, has resulted in a renewed interest in the potential mechanisms of transfer of virulence genes among Vibrio cholerae. We describe here an alternative mechanism of cholera toxin gene transfer into nontoxigenic V. cholerae isolates, including strains that lack both the CTXPhi receptor, the toxin coregulated pilus (TCP), and attRS, the chromosomal attachment site for CTXPhi integration. A temperature-sensitive mutant of the V. cholerae generalized transducing bacteriophage CP-T1 (CP-T1ts) was used to transfer a genetically marked derivative of the CTX prophage into four nontoxigenic V. cholerae strains, including two V. cholerae vaccine strains. We demonstrate that CTXPhi transduced by CP-T1ts can replicate and integrate into these nontoxigenic V. cholerae strains with high efficiency. In fact, CP-T1ts transduces the CTX prophage preferentially when compared with other chromosomal markers. These results reveal a potential mechanism by which CTXPhi(+) V. cholerae strains that lack the TCP receptor may have arisen. Finally, these findings indicate an additional pathway for reversion of live-attenuated V. cholerae vaccine strains.}, }
@article {pmid10531001, year = {1999}, author = {Logsdon, JM and Faguy, DM}, title = {Thermotoga heats up lateral gene transfer.}, journal = {Current biology : CB}, volume = {9}, number = {19}, pages = {R747-51}, doi = {10.1016/s0960-9822(99)80474-6}, pmid = {10531001}, issn = {0960-9822}, mesh = {Databases, Factual ; *Evolution, Molecular ; *Genome, Bacterial ; Phylogeny ; Thermotoga maritima/*genetics ; }, abstract = {The complete sequence of the bacterium Thermotoga maritima genome has revealed a large fraction of genes most closely related to those of archaeal species. This adds to the accumulating evidence that lateral gene transfer is a potent evolutionary force in prokaryotes, though questions of its magnitude remain.}, }
@article {pmid10521656, year = {1999}, author = {Yamasaki, S and Shimizu, T and Hoshino, K and Ho, ST and Shimada, T and Nair, GB and Takeda, Y}, title = {The genes responsible for O-antigen synthesis of vibrio cholerae O139 are closely related to those of vibrio cholerae O22.}, journal = {Gene}, volume = {237}, number = {2}, pages = {321-332}, doi = {10.1016/s0378-1119(99)00344-3}, pmid = {10521656}, issn = {0378-1119}, mesh = {Amino Acid Sequence ; Base Sequence ; DNA, Bacterial/chemistry/genetics ; Genes, Bacterial/*genetics ; Molecular Sequence Data ; O Antigens/biosynthesis/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Serotyping ; Vibrio cholerae/classification/*genetics/metabolism ; }, abstract = {Several studies have shown that the emergence of the O139 serogroup of Vibrio cholerae is a result of horizontal gene transfer of a fragment of DNA from a serogroup other than O1 into the region responsible for O-antigen biosynthesis of the seventh pandemic V. cholerae O1 biotype El Tor strain. In this study, we show that the gene cluster responsible for O-antigen biosynthesis of the O139 serogroup of V. cholerae is closely related to those of O22. When DNA fragments derived from O139 O-antigen biosynthesis gene region were used as probes, the entire O139 O-antigen biosynthesis gene region could be divided into five classes, designated as I-V based on the reactivity pattern of the probes against reference strains of V. cholerae representing serogroups O1-O193. Class IV was specific to O139 serogroup, while classes I-III and class V were homologous to varying extents to some of the non-O1, non-O139 serogroups. Interestingly, the regions other than class IV were also conserved in the O22 serogroup. Long and accurate PCR was employed to determine if a simple deletion or substitution was involved to account for the difference in class IV between O139 and O22. A product of approx. 15kb was amplified when O139 DNA was used as the template, while a product of approx. 12.5kb was amplified when O22 DNA was used as the template, indicating that substitution but not deletion could account for the difference in the region between O22 and O139 serogroups. In order to precisely compare between the genes responsible for O-antigen biosynthesis of O139 and O22, the region responsible for O-antigen biosynthesis of O22 serogroup was cloned and analyzed. In concurrence with the results of the hybridization test, all regions were well conserved in O22 and O139 serogroups, although wbfA and the five or six genes comprising class IV in O22 and O139 serogroups, respectively, were exceptions. Again the genes in class IV in O22 were confirmed to be specific to O22 among the 155 'O' serogroups of V. cholerae. These data suggest that the gene clusters responsible for O139 O-antigen biosynthesis are most similar to those of O22 and genes within class IV of O139, and O22 defines the unique O antigen of O139 or O22.}, }
@article {pmid10518613, year = {1999}, author = {Fitz-Gibbon, ST and House, CH}, title = {Whole genome-based phylogenetic analysis of free-living microorganisms.}, journal = {Nucleic acids research}, volume = {27}, number = {21}, pages = {4218-4222}, doi = {10.1093/nar/27.21.4218}, pmid = {10518613}, issn = {1362-4962}, support = {GM57917/GM/NIGMS NIH HHS/United States ; }, mesh = {Computational Biology ; Genes, Archaeal/genetics ; Genes, Bacterial/genetics ; Genes, Fungal/genetics ; *Genome, Archaeal ; *Genome, Bacterial ; *Genome, Fungal ; *Phylogeny ; Saccharomyces cerevisiae/genetics ; }, abstract = {A phylogenetic 'tree of life' has been constructed based on the observed presence and absence of families of protein-encoding genes observed in 11 complete genomes of free-living microorganisms. Past attempts to reconstruct the evolutionary relation-ships of microorganisms have been limited to sets of genes rather than complete genomes. Despite apparent rampant lateral gene transfer among microorganisms, these results indicate a single robust underlying evolutionary history for these organisms. Broadly, the tree produced is very similar to the small subunit rRNA tree although several additional phylogenetic relationships appear to be resolved, including the relationship of Archaeoglobus to the methanogens studied. This result is in contrast to notions that a robust phylogenetic reconstruction of microorganisms is impossible due to their genomes being composed of an incomprehensible amalgam of genes with complicated histories and suggests that this style of genome-wide phylogenetic analysis could become an important method for studying the ancient diversification of life on Earth. Analyses using informational and operational subsets of the genes showed that this 'tree of life' is not dependent on the phylogenetically more consistent informational genes.}, }
@article {pmid10515941, year = {1999}, author = {Marinoni, G and Manuel, M and Petersen, RF and Hvidtfeldt, J and Sulo, P and Piskur, J}, title = {Horizontal transfer of genetic material among Saccharomyces yeasts.}, journal = {Journal of bacteriology}, volume = {181}, number = {20}, pages = {6488-6496}, pmid = {10515941}, issn = {0021-9193}, mesh = {Cell Nucleus ; Chimera/*genetics ; Chromosomes, Fungal ; Crosses, Genetic ; DNA, Fungal ; Ethyl Methanesulfonate ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Haploidy ; Mitochondria/genetics ; Models, Genetic ; Mutagenesis ; Mutagens ; Pheromones ; Saccharomyces/classification/*genetics ; Saccharomyces cerevisiae/classification/genetics ; Zygote ; }, abstract = {The genus Saccharomyces consists of several species divided into the sensu stricto and the sensu lato groups. The genomes of these species differ in the number and organization of nuclear chromosomes and in the size and organization of mitochondrial DNA (mtDNA). In the present experiments we examined whether these yeasts can exchange DNA and thereby create novel combinations of genetic material. Several putative haploid, heterothallic yeast strains were isolated from different Saccharomyces species. All of these strains secreted an a- or alpha-like pheromone recognized by S. cerevisiae tester strains. When interspecific crosses were performed by mass mating between these strains, hybrid zygotes were often detected. In general, the less related the two parental species were, the fewer hybrids they gave. For some crosses, viable hybrids could be obtained by selection on minimal medium and their nuclear chromosomes and mtDNA were examined. Often the frequency of viable hybrids was very low. Sometimes putative hybrids could not be propagated at all. In the case of sensu stricto yeasts, stable viable hybrids were obtained. These contained both parental sets of chromosomes but mtDNA from only one parent. In the case of sensu lato hybrids, during genetic stabilization one set of the parental chromosomes was partially or completely lost and the stable mtDNA originated from the same parent as the majority of the nuclear chromosomes. Apparently, the interspecific hybrid genome was genetically more or less stable when the genetic material originated from phylogenetically relatively closely related parents; both sets of nuclear genetic material could be transmitted and preserved in the progeny. In the case of more distantly related parents, only one parental set, and perhaps some fragments of the other one, could be found in genetically stabilized hybrid lines. The results obtained indicate that Saccharomyces yeasts have a potential to exchange genetic material. If Saccharomyces isolates could mate freely in nature, horizontal transfer of genetic material could have occurred during the evolution of modern yeast species.}, }
@article {pmid10508729, year = {1999}, author = {Lawrence, JG}, title = {Gene transfer, speciation, and the evolution of bacterial genomes.}, journal = {Current opinion in microbiology}, volume = {2}, number = {5}, pages = {519-523}, doi = {10.1016/s1369-5274(99)00010-7}, pmid = {10508729}, issn = {1369-5274}, mesh = {Bacteria/*genetics ; *Conjugation, Genetic ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Variation ; *Genome, Bacterial ; Mutation ; Species Specificity ; *Transduction, Genetic ; *Transformation, Bacterial ; }, abstract = {Studies in microbial evolution have focused on the origin and vertical transmission of genetic variation within populations experiencing limited recombination. Genomic analyses have highlighted the importance of horizontal genetic transfer in shaping the composition of microbial genomes, providing novel metabolic capabilities, and catalyzing the diversification of bacterial lineages.}, }
@article {pmid10508724, year = {1999}, author = {Moszer, I and Rocha, EP and Danchin, A}, title = {Codon usage and lateral gene transfer in Bacillus subtilis.}, journal = {Current opinion in microbiology}, volume = {2}, number = {5}, pages = {524-528}, doi = {10.1016/s1369-5274(99)00011-9}, pmid = {10508724}, issn = {1369-5274}, mesh = {Bacillus subtilis/*genetics ; Codon/*genetics ; Gene Transfer Techniques ; *Genes, Bacterial ; RNA, Bacterial/genetics/metabolism ; RNA, Transfer/genetics/metabolism ; *Transformation, Bacterial ; }, abstract = {Bacillus subtilis possesses three classes of genes, differing by their codon preference. One class corresponds to prophages or prophage-like elements, indicative of the existence of systematic lateral gene transfer in this organism. The nature of the selection pressure that operates on codon bias is beginning to be understood.}, }
@article {pmid10498708, year = {1999}, author = {Bobik, TA and Havemann, GD and Busch, RJ and Williams, DS and Aldrich, HC}, title = {The propanediol utilization (pdu) operon of Salmonella enterica serovar Typhimurium LT2 includes genes necessary for formation of polyhedral organelles involved in coenzyme B(12)-dependent 1, 2-propanediol degradation.}, journal = {Journal of bacteriology}, volume = {181}, number = {19}, pages = {5967-5975}, pmid = {10498708}, issn = {0021-9193}, support = {GM59486/GM/NIGMS NIH HHS/United States ; }, mesh = {Cloning, Molecular ; Cobamides/*metabolism ; Enzyme Activation ; *Genes, Bacterial ; Models, Genetic ; Molecular Sequence Data ; Multigene Family ; Operon ; Organelles/enzymology/genetics ; Propanediol Dehydratase/metabolism ; Propylene Glycol/*metabolism ; Salmonella enterica/enzymology/*genetics/*ultrastructure ; Sequence Analysis, DNA ; }, abstract = {The propanediol utilization (pdu) operon of Salmonella enterica serovar Typhimurium LT2 contains genes needed for the coenzyme B(12)-dependent catabolism of 1,2-propanediol. Here the completed DNA sequence of the pdu operon is presented. Analyses of previously unpublished pdu DNA sequence substantiated previous studies indicating that the pdu operon was acquired by horizontal gene transfer and allowed the identification of 16 hypothetical genes. This brings the total number of genes in the pdu operon to 21 and the total number of genes at the pdu locus to 23. Of these, six encode proteins of unknown function and are not closely related to sequences of known function found in GenBank. Two encode proteins involved in transport and regulation. Six probably encode enzymes needed for the pathway of 1,2-propanediol degradation. Two encode proteins related to those used for the reactivation of adenosylcobalamin (AdoCbl)-dependent diol dehydratase. Five encode proteins related to those involved in the formation of polyhedral organelles known as carboxysomes, and two encode proteins that appear distantly related to those involved in carboxysome formation. In addition, it is shown that S. enterica forms polyhedral bodies that are involved in the degradation of 1,2-propanediol. Polyhedra are formed during either aerobic or anaerobic growth on propanediol, but not during growth on other carbon sources. Genetic tests demonstrate that genes of the pdu operon are required for polyhedral body formation, and immunoelectron microscopy shows that AdoCbl-dependent diol dehydratase is associated with these polyhedra. This is the first evidence for a B(12)-dependent enzyme associated with a polyhedral body. It is proposed that the polyhedra consist of AdoCbl-dependent diol dehydratase (and perhaps other proteins) encased within a protein shell that is related to the shell of carboxysomes. The specific function of these unusual polyhedral bodies was not determined, but some possibilities are discussed.}, }
@article {pmid10489325, year = {1999}, author = {Davison, J}, title = {Genetic exchange between bacteria in the environment.}, journal = {Plasmid}, volume = {42}, number = {2}, pages = {73-91}, doi = {10.1006/plas.1999.1421}, pmid = {10489325}, issn = {0147-619X}, mesh = {Animals ; Bacteria/*genetics ; Conjugation, Genetic ; Environment ; Genes, Bacterial ; Humans ; Transduction, Genetic ; Transformation, Bacterial ; }, abstract = {Nucleotide sequence analysis, and more recently whole genome analysis, shows that bacterial evolution has often proceeded by horizontal gene flow between different species and genera. In bacteria, gene transfer takes place by transformation, transduction, or conjugation and this review examines the roles of these gene transfer processes, between different bacteria, in a wide variety of ecological niches in the natural environment. This knowledge is necessary for our understanding of plasmid evolution and ecology, as well as for risk assessment. The rise and spread of multiple antibiotic resistance plasmids in medically important bacteria are consequences of intergeneric gene transfer coupled to the selective pressures posed by the increasing use and misuse of antibiotics in medicine and animal feedstuffs. Similarly, the evolution of degradative plasmids is a response to the increasing presence of xenobiotic pollutants in soil and water. Finally, our understanding of the role of horizontal gene transfer in the environment is essential for the evaluation of the possible consequences of the deliberate environmental release of natural or recombinant bacteria for agricultural and bioremediation purposes.}, }
@article {pmid10486982, year = {1999}, author = {Horner, DS and Hirt, RP and Embley, TM}, title = {A single eubacterial origin of eukaryotic pyruvate: ferredoxin oxidoreductase genes: implications for the evolution of anaerobic eukaryotes.}, journal = {Molecular biology and evolution}, volume = {16}, number = {9}, pages = {1280-1291}, doi = {10.1093/oxfordjournals.molbev.a026218}, pmid = {10486982}, issn = {0737-4038}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Anaerobiosis ; Animals ; Base Sequence ; Clostridium/enzymology/genetics ; DNA Primers/genetics ; Diplomonadida/enzymology/genetics ; Eukaryotic Cells ; *Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genes, Protozoan ; Giardia lamblia/enzymology/genetics ; Ketone Oxidoreductases/*genetics ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Pyruvate Synthase ; }, abstract = {The iron sulfur protein pyruvate: ferredoxin oxidoreductase (PFO) is central to energy metabolism in amitochondriate eukaryotes, including those with hydrogenosomes. Thus, revealing the evolutionary history of PFO is critical to understanding the origin(s) of eukaryote anaerobic energy metabolism. We determined a complete PFO sequence for Spironucleus barkhanus, a large fragment of a PFO sequence from Clostridium pasteurianum, and a fragment of a new PFO from Giardia lamblia. Phylogenetic analyses of eubacterial and eukaryotic PFO genes suggest a complex history for PFO, including possible gene duplications and horizontal transfers among eubacteria. Our analyses favor a common origin for eukaryotic cytosolic and hydrogenosomal PFOs from a single eubacterial source, rather than from separate horizontal transfers as previously suggested. However, with the present sampling of genes and species, we were unable to infer a specific eubacterial sister group for eukaryotic PFO. Thus, we find no direct support for the published hypothesis that the donor of eukaryote PFO was the common alpha-proteobacterial ancestor of mitochondria and hydrogenosomes. We also report that several fungi and protists encode proteins with PFO domains that are likely monophyletic with PFOs from anaerobic protists. In Saccharomyces cerevisiae, PFO domains combine with fragments of other redox proteins to form fusion proteins which participate in methionine biosynthesis. Our results are consistent with the view that PFO, an enzyme previously considered to be specific to energy metabolism in amitochondriate protists, was present in the common ancestor of contemporary eukaryotes and was retained, wholly or in part, during the evolution of oxygen-dependent and mitochondrion-bearing lineages.}, }
@article {pmid10486971, year = {1999}, author = {Cho, Y and Palmer, JD}, title = {Multiple acquisitions via horizontal transfer of a group I intron in the mitochondrial cox1 gene during evolution of the Araceae family.}, journal = {Molecular biology and evolution}, volume = {16}, number = {9}, pages = {1155-1165}, doi = {10.1093/oxfordjournals.molbev.a026206}, pmid = {10486971}, issn = {0737-4038}, support = {GM35087/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Sequence ; Cyclooxygenase 1 ; DNA Primers/genetics ; DNA, Mitochondrial/genetics ; DNA, Plant/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, Plant ; Introns ; Isoenzymes/*genetics ; Magnoliopsida/*enzymology/*genetics ; Molecular Sequence Data ; Mutation ; Phylogeny ; Prostaglandin-Endoperoxide Synthases/*genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {A group I intron has recently been shown to have invaded mitochondrial cox1 genes by horizontal transfer many times during the broad course of angiosperm evolution. To investigate the frequency of acquisition of this intron within a more closely related group of plants, we determined its distribution and inferred its evolutionary history among 14 genera of the monocot family Araceae. Southern blot hybridizations showed that 6 of the 14 genera contain this intron in their cox1 genes. Nucleotide sequencing showed that these six introns are highly similar in sequence (97.7%-99.4% identity) and identical in length (966 nt). Phylogenetic evidence from parsimony reconstructions of intron distribution and phylogenetic analyses of intron sequences is consistent with a largely vertical history of intron transmission in the family; the simplest scenarios posit but one intron gain and two losses. Despite this, however, striking differences in lengths of exonic co-conversion tracts, coupled with the absence of co-conversion in intron-lacking taxa, indicate that the six intron-containing Araceae probably acquired their introns by at least three and quite possibly five separate horizontal transfers. The highly similar nature of these independently acquired introns implies a closely related set of donor organisms.}, }
@article {pmid10486968, year = {1999}, author = {Garcia-Vallvé, S and Palau, J and Romeu, A}, title = {Horizontal gene transfer in glycosyl hydrolases inferred from codon usage in Escherichia coli and Bacillus subtilis.}, journal = {Molecular biology and evolution}, volume = {16}, number = {9}, pages = {1125-1134}, doi = {10.1093/oxfordjournals.molbev.a026203}, pmid = {10486968}, issn = {0737-4038}, mesh = {Bacillus subtilis/*enzymology/*genetics ; Biological Evolution ; Codon/*genetics ; DNA, Bacterial/genetics ; Escherichia coli/*enzymology/*genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Glycoside Hydrolases/*genetics ; Phylogeny ; Xylan Endo-1,3-beta-Xylosidase ; Xylosidases/genetics ; }, abstract = {Glycosyl hydrolase (GH) genes from Escherichia coli and Bacillus subtilis were used to search for cases of horizontal gene transfer. Such an event was inferred by G + C content, codon usage analysis, and a phylogenetic congruency test. The codon usage analysis used is a procedure based on a distance derived from a Pearson linear correlation coefficient determined from a pairwise codon usage comparison. The distances are then used to generate a distance-based tree with which we can define clusters and rapidly compare codon usage. Three genes (yagH from E. coli and xynA and xynB from B. subtilis) were determined to have arrived by horizontal gene transfer and were located in E. coli CP4-6 prophage, and B. subtilis prophages 6 and 5, respectively. In this study, we demonstrate that with codon usage analysis, the proposed horizontally transferred genes can be distinguished from highly expressed genes.}, }
@article {pmid10486008, year = {1999}, author = {Philippe, H and Forterre, P}, title = {The rooting of the universal tree of life is not reliable.}, journal = {Journal of molecular evolution}, volume = {49}, number = {4}, pages = {509-523}, doi = {10.1007/pl00006573}, pmid = {10486008}, issn = {0022-2844}, mesh = {Adenosine Triphosphatases/*genetics ; Animals ; Archaea/genetics ; Bacteria/genetics ; Carbamoyl-Phosphate Synthase (Glutamine-Hydrolyzing)/*genetics ; Databases, Factual ; Eubacterium/genetics ; *Evolution, Molecular ; Gene Duplication ; Humans ; Phylogeny ; }, abstract = {Several composite universal trees connected by an ancestral gene duplication have been used to root the universal tree of life. In all cases, this root turned out to be in the eubacterial branch. However, the validity of results obtained from comparative sequence analysis has recently been questioned, in particular, in the case of ancient phylogenies. For example, it has been shown that several eukaryotic groups are misplaced in ribosomal RNA or elongation factor trees because of unequal rates of evolution and mutational saturation. Furthermore, the addition of new sequences to data sets has often turned apparently reasonable phylogenies into confused ones. We have thus revisited all composite protein trees that have been used to root the universal tree of life up to now (elongation factors, ATPases, tRNA synthetases, carbamoyl phosphate synthetases, signal recognition particle proteins) with updated data sets. In general, the two prokaryotic domains were not monophyletic with several aberrant groupings at different levels of the tree. Furthermore, the respective phylogenies contradicted each others, so that various ad hoc scenarios (paralogy or lateral gene transfer) must be proposed in order to obtain the traditional Archaebacteria-Eukaryota sisterhood. More importantly, all of the markers are heavily saturated with respect to amino acid substitutions. As phylogenies inferred from saturated data sets are extremely sensitive to differences in evolutionary rates, present phylogenies used to root the universal tree of life could be biased by the phenomenon of long branch attraction. Since the eubacterial branch was always the longest one, the eubacterial rooting could be explained by an attraction between this branch and the long branch of the outgroup. Finally, we suggested that an eukaryotic rooting could be a more fruitful working hypothesis, as it provides, for example, a simple explanation to the high genetic similarity of Archaebacteria and Eubacteria inferred from complete genome analysis.}, }
@article {pmid10486003, year = {1999}, author = {Castresana, J and Moreira, D}, title = {Respiratory chains in the last common ancestor of living organisms.}, journal = {Journal of molecular evolution}, volume = {49}, number = {4}, pages = {453-460}, doi = {10.1007/pl00006568}, pmid = {10486003}, issn = {0022-2844}, mesh = {Archaea/enzymology/genetics ; Bacteria/enzymology/genetics ; Databases, Factual ; Electron Transport/*genetics ; *Evolution, Molecular ; Nitrates/*metabolism ; Oxidoreductases/genetics ; Sulfates/*metabolism ; Sulfur/*metabolism ; }, abstract = {Sequences in current databases show that a number of proteins involved in respiratory processes are homologous in archaeal and bacterial species. In particular, terminal oxidases belonging to oxygen, nitrate, sulfate, and sulfur respiratory pathways have been sequenced in members of both domains. They include cytochrome oxidase, nitrate reductase, adenylylsulfate reductase, sulfite reductase, and polysulfide reductase. These proteins can be assigned to the last common ancestor of living organisms assuming that the deepest split of the three domains of life occurred between Archaea and Bacteria and that they were not acquired through lateral gene transfer by one of these domains. These molecular data indicate that several of the most important respiratory pathways arose early in evolution and that the last common ancestor of living organisms was not a simple organism in its energetic metabolism. Rather, it may have been able to gain energy by means of at least four electron transport chains, and therefore it may have been prepared to face a wide range of environmental conditions.}, }
@article {pmid10481095, year = {1999}, author = {Yamasaki, S and Garg, S and Nair, GB and Takeda, Y}, title = {Distribution of Vibrio cholerae O1 antigen biosynthesis genes among O139 and other non-O1 serogroups of Vibrio cholerae.}, journal = {FEMS microbiology letters}, volume = {179}, number = {1}, pages = {115-121}, doi = {10.1111/j.1574-6968.1999.tb08716.x}, pmid = {10481095}, issn = {0378-1097}, mesh = {Base Sequence ; Chromosome Mapping ; DNA Primers ; DNA Probes ; Enterotoxins/*genetics ; *Genes, Bacterial ; Polymerase Chain Reaction ; Serotyping ; Vibrio cholerae/classification/*genetics ; }, abstract = {The organization and distribution of the genes responsible for O antigen biosynthesis in various serogroups of Vibrio cholerae were investigated using several DNA probes derived from various regions of the genes responsible for O1 antigen biosynthesis. Based on the reactivity pattern of the probes against the various serogroups, the cluster of genes responsible for the O1 antigen biosynthesis could be broadly divided into six groups, designated as class 1-6. The class 3 cluster of genes corresponding to gmd to wbeO, wbeT and a part of wbeU was specific for only the O1 serogroup. The other cluster of genes (class 1, 2, 4-6) reacted with other serogroups of V. cholerae. These data indicate that serotype conversion in V. cholerae does not depend on a simple mutational event but may involve horizontal gene transfer not only between V. cholerae strains but also between V. cholerae and species other than V. cholerae.}, }
@article {pmid10471904, year = {1999}, author = {Syvanen, M}, title = {In search of horizontal gene transfer.}, journal = {Nature biotechnology}, volume = {17}, number = {9}, pages = {833}, doi = {10.1038/12781}, pmid = {10471904}, issn = {1087-0156}, mesh = {*Agriculture ; Bacteria/genetics ; *Biotechnology ; Drug Resistance, Microbial/genetics ; *Gene Transfer, Horizontal ; Plants/genetics ; Risk ; Species Specificity ; Transformation, Genetic ; }, }
@article {pmid10466405, year = {1999}, author = {Bertolla, F and Simonet, P}, title = {Horizontal gene transfers in the environment: natural transformation as a putative process for gene transfers between transgenic plants and microorganisms.}, journal = {Research in microbiology}, volume = {150}, number = {6}, pages = {375-384}, doi = {10.1016/s0923-2508(99)80072-2}, pmid = {10466405}, issn = {0923-2508}, mesh = {*Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Plants, Genetically Modified/*genetics ; *Soil Microbiology ; Transformation, Genetic ; }, abstract = {Horizontal gene transfers among bacteria, such as natural transformation or conjugation, may have played an important role in bacterial evolution. They are thought to have been involved in promoting genome plasticity which permitted bacteria to adapt very efficiently to any change in their environment and to colonize a wide range of ecosystems. Evidence that some genes were transferred from eukaryotes, and in particular, from plants to bacteria, was obtained from nucleotide and protein sequence analyses. However, numerous factors, including some which are endogenous to the bacterial cells, tend to limit the extent of transfer, particularly among phylogenetically distant organisms. The goal of this paper is to give an overview of the potentials and limits of natural interkingdom gene transfers, with particular focus on prokaryote-originating sequences which fit the nuclear genome of transgenic plants.}, }
@article {pmid10464188, year = {1999}, author = {Yap, WH and Zhang, Z and Wang, Y}, title = {Distinct types of rRNA operons exist in the genome of the actinomycete Thermomonospora chromogena and evidence for horizontal transfer of an entire rRNA operon.}, journal = {Journal of bacteriology}, volume = {181}, number = {17}, pages = {5201-5209}, pmid = {10464188}, issn = {0021-9193}, mesh = {Actinomycetales/classification/*genetics ; Base Sequence ; Blotting, Southern ; Cloning, Molecular ; DNA, Bacterial ; DNA, Ribosomal/analysis ; Evolution, Molecular ; Gene Amplification ; Gene Expression ; Genetic Variation ; Genome, Bacterial ; Molecular Sequence Data ; Nucleic Acid Conformation ; Polymerase Chain Reaction ; *RNA, Bacterial ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; *rRNA Operon ; }, abstract = {We describe here the presence of two distinct types of rRNA operons in the genome of a thermophilic actinomycete Thermomonospora chromogena. The genome of T. chromogena contains six rRNA operons (rrn), of which four complete and two incomplete ones were cloned and sequenced. Comparative analysis revealed that the operon rrnB exhibits high levels of sequence variations to the other five nearly identical ones throughout the entire length of the operon. The coding sequences for the 16S and 23S rRNA genes differ by approximately 6 and 10%, respectively, between the two types of operons. Normal functionality of rrnB is concluded on the basis of the nonrandom distribution of nucleotide substitutions, the presence of compensating nucleotide covariations, the preservation of secondary and tertiary rRNA structures, and the detection of correctly processed rRNAs in the cell. Comparative sequence analysis also revealed a close evolutionary relationship between rrnB operon of T. chromogena and rrnA operon of another thermophilic actinomycete Thermobispora bispora. We propose that T. chromogena acquired rrnB operon from T. bispora or a related organism via horizontal gene transfer.}, }
@article {pmid10463166, year = {1999}, author = {Andrup, L and Andersen, K}, title = {A comparison of the kinetics of plasmid transfer in the conjugation systems encoded by the F plasmid from Escherichia coli and plasmid pCF10 from Enterococcus faecalis.}, journal = {Microbiology (Reading, England)}, volume = {145 (Pt 8)}, number = {}, pages = {2001-2009}, doi = {10.1099/13500872-145-8-2001}, pmid = {10463166}, issn = {1350-0872}, mesh = {*Conjugation, Genetic ; Culture Media ; Enterococcus faecalis/*genetics/growth &amp; development ; Escherichia coli/*genetics/growth &amp; development ; F Factor/*genetics ; Gene Transfer, Horizontal ; Kinetics ; Models, Biological ; Pheromones/pharmacology ; Plasmids/*genetics ; }, abstract = {Quantitative measurements of horizontal DNA transfer are critical if one wishes to address questions relating to ecology, evolution and the safe use of recombinant bacteria. Traditionally, the efficiency of a conjugation system has been described by its transfer frequency. However, transfer frequencies can be determined in many ways and may be sensitive to physical, chemical and biological conditions. In this study the authors have used the mechanistic similarity between bacterial conjugation and simple enzyme catalysis in order to calculate the maximal conjugation rate (Vmax) and the recipient concentration (K(m)) at which the conjugation rate is half its maximal value, for two different conjugation systems: the F plasmid from Escherichia coli and plasmid pCF10 from Enterococcus faecalis. The results are compared with the data obtained from the aggregation-mediated conjugation system encoded on pXO16 from Bacillus thuringiensis. The conjugation systems analysed are fundamentally different; however, they have some characteristics in common: they are able to sustain conjugative transfer in liquid medium and the transfer efficiencies are very high. Conjugation encoded by the F plasmid in E. coli involves the formation of small aggregates (2-20 cells), established by sex pili, and the plasmid's maximal conjugation rate was estimated to be approximately 0.15 transconjugants per donor per minute. Pheromone-induced conjugation in Ent. faecalis, which involves the formation of large aggregates, was found to proceed at a maximal conjugation rate of 0.29 transconjugants per donor per minute. Also, the K(m) value differed significantly between these conjugation systems; this may reflect the inherent differences in mating pair formation and transfer mechanisms. In these conjugation systems, the donors underwent a 'recovery period' between rounds of conjugative transfer and newly formed transconjugants required a period of about 40-80 min to mature into proficient donors.}, }
@article {pmid10449782, year = {1999}, author = {Mirold, S and Rabsch, W and Rohde, M and Stender, S and Tschäpe, H and Rüssmann, H and Igwe, E and Hardt, WD}, title = {Isolation of a temperate bacteriophage encoding the type III effector protein SopE from an epidemic Salmonella typhimurium strain.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {96}, number = {17}, pages = {9845-9850}, pmid = {10449782}, issn = {0027-8424}, mesh = {Bacterial Proteins/*biosynthesis ; DNA, Viral/chemistry ; Humans ; Lysogeny ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Restriction Mapping ; Salmonella Infections/microbiology ; Salmonella Phages/*isolation &amp; purification/ultrastructure ; Salmonella typhimurium/pathogenicity/*virology ; }, abstract = {Salmonella typhimurium employs the specialized type III secretion system encoded in pathogenicity island 1 (SPI1) to translocate effector proteins into host cells and to modulate host cell signal transduction. The SPI1 type III system and the effector proteins are conserved among all salmonellae and are thought to be acquired by horizontal gene transfer. The genetic mechanisms mediating this horizontal transfer are unknown. Here, we describe that SopE, a SPI1-dependent translocated effector protein, is present in relatively few S. typhimurium isolates. We have isolated a temperate phage that encodes SopE. Phage morphology and DNA hybridization, as well as partial sequence information, suggest that this phage (SopEPhi) is a new member of the P2 family of bacteriophages. By lysogenic conversion this phage can horizontally transfer genes between different S. typhimurium strains. Strikingly, most of the isolates harboring SopEPhi belong to the small group of epidemic strains of S. typhimurium that have been responsible for a large percentage of human and animal salmonellosis and have persisted for a long period of time. Our data suggest that horizontal transfer of type III dependent effector proteins by lysogenic infection with bacteriophages (lysogenic conversion) may provide an efficient mechanism for fine-tuning the interaction of Salmonella spp. with their hosts.}, }
@article {pmid10447505, year = {1999}, author = {Wolf, YI and Aravind, L and Grishin, NV and Koonin, EV}, title = {Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events.}, journal = {Genome research}, volume = {9}, number = {8}, pages = {689-710}, pmid = {10447505}, issn = {1088-9051}, mesh = {Amino Acid Sequence ; Amino Acyl-tRNA Synthetases/*chemistry/*genetics ; Animals ; *Evolution, Molecular ; Genes, Bacterial ; Genetic Markers ; Humans ; Molecular Sequence Data ; Peptides/*chemistry/genetics ; *Phylogeny ; Protein Structure, Tertiary/genetics ; Sequence Alignment ; }, abstract = {Phylogenetic analysis of aminoacyl-tRNA synthetases (aaRSs) of all 20 specificities from completely sequenced bacterial, archaeal, and eukaryotic genomes reveals a complex evolutionary picture. Detailed examination of the domain architecture of aaRSs using sequence profile searches delineated a network of partially conserved domains that is even more elaborate than previously suspected. Several unexpected evolutionary connections were identified, including the apparent origin of the beta-subunit of bacterial GlyRS from the HD superfamily of hydrolases, a domain shared by bacterial AspRS and the B subunit of archaeal glutamyl-tRNA amidotransferases, and another previously undetected domain that is conserved in a subset of ThrRS, guanosine polyphosphate hydrolases and synthetases, and a family of GTPases. Comparison of domain architectures and multiple alignments resulted in the delineation of synapomorphies-shared derived characters, such as extra domains or inserts-for most of the aaRSs specificities. These synapomorphies partition sets of aaRSs with the same specificity into two or more distinct and apparently monophyletic groups. In conjunction with cluster analysis and a modification of the midpoint-rooting procedure, this partitioning was used to infer the likely root position in phylogenetic trees. The topologies of the resulting rooted trees for most of the aaRSs specificities are compatible with the evolutionary "standard model" whereby the earliest radiation event separated bacteria from the common ancestor of archaea and eukaryotes as opposed to the two other possible evolutionary scenarios for the three major divisions of life. For almost all aaRSs specificities, however, this simple scheme is confounded by displacement of some of the bacterial aaRSs by their eukaryotic or, less frequently, archaeal counterparts. Displacement of ancestral eukaryotic aaRS genes by bacterial ones, presumably of mitochondrial origin, was observed for three aaRSs. In contrast, there was no convincing evidence of displacement of archaeal aaRSs by bacterial ones. Displacement of aaRS genes by eukaryotic counterparts is most common among parasitic and symbiotic bacteria, particularly the spirochaetes, in which 10 of the 19 aaRSs seem to have been displaced by the respective eukaryotic genes and two by the archaeal counterpart. Unlike the primary radiation events between the three main divisions of life, that were readily traceable through the phylogenetic analysis of aaRSs, no consistent large-scale bacterial phylogeny could be established. In part, this may be due to additional gene displacement events among bacterial lineages. Argument is presented that, although lineage-specific gene loss might have contributed to the evolution of some of the aaRSs, this is not a viable alternative to horizontal gene transfer as the principal evolutionary phenomenon in this gene class.}, }
@article {pmid10431171, year = {1999}, author = {Hou, YM}, title = {Transfer RNAs and pathogenicity islands.}, journal = {Trends in biochemical sciences}, volume = {24}, number = {8}, pages = {295-298}, doi = {10.1016/s0968-0004(99)01428-0}, pmid = {10431171}, issn = {0968-0004}, mesh = {Bacteria/*genetics/*pathogenicity ; Base Sequence ; Gene Transfer, Horizontal ; Models, Biological ; RNA, Bacterial/*genetics ; RNA, Transfer/*genetics ; Recombination, Genetic ; Virulence/genetics ; }, abstract = {The tRNAs are central components in translation. In addition, they are essential for replication of retroviruses: tRNAs bind to viral genomes through their 3'-end sequences and act as primers for initiation of viral replication. Here, I discuss the possibility that tRNAs also play a role in the horizontal transfer of bacterial pathogenicity islands between different pathogens. Such a role would implicate tRNAs in DNA recombination.}, }
@article {pmid10417147, year = {1999}, author = {Bart, A and Dankert, J and van der Ende, A}, title = {Antigenic variation of the class I outer membrane protein in hyperendemic Neisseria meningitidis strains in the netherlands.}, journal = {Infection and immunity}, volume = {67}, number = {8}, pages = {3842-3846}, pmid = {10417147}, issn = {0019-9567}, mesh = {Amino Acid Sequence ; *Antigenic Variation ; Epitopes ; Genotype ; Humans ; Molecular Sequence Data ; Neisseria meningitidis/*immunology/isolation &amp; purification ; Netherlands ; Porins/chemistry/*genetics/immunology ; }, abstract = {Since 1980, the number of cases of meningococcal disease caused by serogroup B isolates with the P1.4 serosubtype has greatly increased in The Netherlands. Screening for this serosubtype in the strain collection of The Netherlands Reference Laboratory for Bacterial Meningitis revealed that a low number of P1.4 strains had been present in the Dutch meningococcal population since 1965. Genotyping of P1.4 strains showed that one cluster of strains, the hyperendemic lineage III (D. A. Caugant et al., J. Infect. Dis. 162:867-874, 1990), is responsible for the increase since 1980. The diversity of the porA genes, which encode the P1 protein on which serosubtyping is based, was studied for genotypically different P1.4 strains and for lineage III strains expressing antigenically different P1 proteins. Sequence analysis showed that porA genes of genotypically distinct strains that express antigenically indistinguishable P1 proteins are identical only in the epitope-encoding region, suggesting that this region has spread through the meningococcal population via horizontal gene transfer. Analysis of porA genes of lineage III strains showed that both horizontal gene transfer and partial deletion of the epitope-encoding region may contribute to the different antigenic properties for P1 of these strains. Phase variation of expression of the porA gene seems to account for most nonreacting strains. These results show that serosubtyping may underestimate the rise of a hyperendemic clone.}, }
@article {pmid10415491, year = {1999}, author = {Bellgard, MI and Itoh, T and Watanabe, H and Imanishi, T and Gojobori, T}, title = {Dynamic evolution of genomes and the concept of genome space.}, journal = {Annals of the New York Academy of Sciences}, volume = {870}, number = {}, pages = {293-300}, doi = {10.1111/j.1749-6632.1999.tb08891.x}, pmid = {10415491}, issn = {0077-8923}, mesh = {Archaea/genetics ; Eukaryotic Cells ; *Evolution, Molecular ; Gene Rearrangement ; Genes, Bacterial ; *Genome, Bacterial ; Humans ; }, abstract = {A new era in the elucidation of genome evolution has been heralded with the availability of numerous genome sequences. With these data, it has been possible to study evolutionary processes at a greater level of detail in order to characterize features such as gene shuffling, genome rearrangements, base bias composition, and horizontal gene transfer. In this paper, we discuss the evolutionary implications of significant rearrangements within genomes as well as characteristic genomic regions that have been conserved across genomes. This is based on our analysis of orthologous and paralogous genes. We argue that genome plasticity has most likely contributed substantially to the dynamic evolution of genomes. We also describe the characteristic mosaic features of an archaea genome that is comprised of both bacterial and eukaryal elements. Here we investigate base compositional differences as well as the similarity of this species' genes to either bacteria or eukarya. We conclude that these features can be largely explained by the mechanism of horizontal gene transfer. Finally, we introduce the concept of genome space which is defined as the entire set of genomes of all living organisms. We explain its usefulness to describe as well as to gain deeper insight into the general features of the dynamic genomic evolutionary process.}, }
@article {pmid10415471, year = {1999}, author = {Arber, W}, title = {Involvement of gene products in bacterial evolution.}, journal = {Annals of the New York Academy of Sciences}, volume = {870}, number = {}, pages = {36-44}, doi = {10.1111/j.1749-6632.1999.tb08863.x}, pmid = {10415471}, issn = {0077-8923}, mesh = {Bacteria/*genetics ; Biological Evolution ; *Evolution, Molecular ; *Genes, Bacterial ; Genetic Variation ; Mutation ; }, abstract = {Three strategies of different quality contribute in parallel to the natural formation of genetic variants in bacteria: (1) small local alterations of DNA sequences; (2) recombinational reshuffling of segments of the genome; and (3) acquisition of DNA sequences by horizontal gene transfer. Key enzymes involved in these processes often act as variation generators by making use of structural flexibilities of biological macromolecules and of the effect of random encounter. In the theory of molecular evolution, genetic determinants of variation generators as well as of modulators of the frequency of genetic variation are defined as evolutionary genes. This postulate is consistent with the notion that spontaneous mutagenesis is in general not adaptive and that the direction of evolution depends on natural selection exerted on populations of genetic variants.}, }
@article {pmid10415469, year = {1999}, author = {Caporale, LH}, title = {Chance favors the prepared genome.}, journal = {Annals of the New York Academy of Sciences}, volume = {870}, number = {}, pages = {1-21}, doi = {10.1111/j.1749-6632.1999.tb08860.x}, pmid = {10415469}, issn = {0077-8923}, mesh = {Animals ; Enzymes/genetics ; *Evolution, Molecular ; Genetic Variation ; *Genome ; Germ Cells ; Humans ; Mutation ; }, abstract = {Most descriptions of mutation have emphasized its negative consequences, and randomness with respect to biological function. This book seeks to balance the discussion by emphasizing mechanisms that both diversify the genome and increase the probability that a genome's descendants will survive. This chapter provides a framework for, and overview of, the diverse contributions to this book; these contributions will be stimulating companions, well into the 21st Century, as we work to comprehend the information contained in genomic databases. Genomes that encode "better" amino acid sequences are at a selective advantage. Genomes that generate diversity also are at an advantage to the extent that they can navigate efficiently through the space of possible sequence changes. Biochemical systems that tend to increase the ratio of useful to destructive genetic change may harness preexisting information (horizontal gene transfer, DNA translocation and/or DNA duplication), focus the location, timing, and extent of genetic change, adjust the dynamic range of a gene's activity, and/or sample regulatory connections between sites distributed across the genome. Rejecting entirely random genetic variation as the substrate of genome evolution is not a refutation, but rather provides a deeper understanding, of the theory of natural selection of Darwin and Wallace. The fittest molecular strategies survive, along with descendants of the genomes that encode them.}, }
@article {pmid10413400, year = {1999}, author = {Makarova, KS and Aravind, L and Galperin, MY and Grishin, NV and Tatusov, RL and Wolf, YI and Koonin, EV}, title = {Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell.}, journal = {Genome research}, volume = {9}, number = {7}, pages = {608-628}, pmid = {10413400}, issn = {1088-9051}, mesh = {Amino Acid Sequence ; Archaeal Proteins/genetics ; Bacterial Proteins/genetics ; Conserved Sequence ; Eukaryotic Cells/metabolism ; Euryarchaeota/*genetics ; Evolution, Molecular ; Genes, Archaeal/genetics ; Genetic Variation ; *Genome ; Phylogeny ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {Comparative analysis of the protein sequences encoded in the four euryarchaeal species whose genomes have been sequenced completely (Methanococcus jannaschii, Methanobacterium thermoautotrophicum, Archaeoglobus fulgidus, and Pyrococcus horikoshii) revealed 1326 orthologous sets, of which 543 are represented in all four species. The proteins that belong to these conserved euryarchaeal families comprise 31%-35% of the gene complement and may be considered the evolutionarily stable core of the archaeal genomes. The core gene set includes the great majority of genes coding for proteins involved in genome replication and expression, but only a relatively small subset of metabolic functions. For many gene families that are conserved in all euryarchaea, previously undetected orthologs in bacteria and eukaryotes were identified. A number of euryarchaeal synapomorphies (unique shared characters) were identified; these are protein families that possess sequence signatures or domain architectures that are conserved in all euryarchaea but are not found in bacteria or eukaryotes. In addition, euryarchaea-specific expansions of several protein and domain families were detected. In terms of their apparent phylogenetic affinities, the archaeal protein families split into bacterial and eukaryotic families. The majority of the proteins that have only eukaryotic orthologs or show the greatest similarity to their eukaryotic counterparts belong to the core set. The families of euryarchaeal genes that are conserved in only two or three species constitute a relatively mobile component of the genomes whose evolution should have involved multiple events of lineage-specific gene loss and horizontal gene transfer. Frequently these proteins have detectable orthologs only in bacteria or show the greatest similarity to the bacterial homologs, which might suggest a significant role of horizontal gene transfer from bacteria in the evolution of the euryarchaeota.}, }
@article {pmid10390834, year = {1999}, author = {Gogarten, JP and Murphey, RD and Olendzenski, L}, title = {Horizontal gene transfer: pitfalls and promises.}, journal = {The Biological bulletin}, volume = {196}, number = {3}, pages = {359-61; discussion 361-2}, doi = {10.2307/1542970}, pmid = {10390834}, issn = {0006-3185}, mesh = {Animals ; Archaea/classification/genetics ; Bacteria/classification/genetics ; *Evolution, Molecular ; Fungi/classification/genetics ; Humans ; *Recombination, Genetic ; }, }
@article {pmid10386372, year = {1999}, author = {Cabrejos, ME and Zhao, HL and Guacucano, M and Bueno, S and Levican, G and Garcia, E and Jedlicki, E and Holmes, DS}, title = {IST1 insertional inactivation of the resB gene: implications for phenotypic switching in Thiobacillus ferrooxidans.}, journal = {FEMS microbiology letters}, volume = {175}, number = {2}, pages = {223-229}, doi = {10.1111/j.1574-6968.1999.tb13624.x}, pmid = {10386372}, issn = {0378-1097}, mesh = {Bacterial Proteins/chemistry/*genetics ; Base Sequence ; Cytochrome c Group/biosynthesis ; DNA Transposable Elements/*genetics ; Ferrous Compounds/metabolism ; Gene Transfer Techniques ; Genes, Bacterial ; Molecular Sequence Data ; Mutagenesis, Insertional ; Oxidation-Reduction ; Phenotype ; Reverse Transcriptase Polymerase Chain Reaction ; Sulfur/metabolism ; Thiobacillus/*genetics/*metabolism ; Transcription, Genetic ; }, abstract = {Thiobacillus ferroxidans ATCC 19859 undergoes rapid phenotypic switching between a wild-type state characterized by the ability to oxidize ferrous iron (FeII) and reduced sulfur compounds and a mutant state where it has lost the capacity to oxidize FeII but retains the ability to oxidize sulfur. The mutant has also gained the capacity to swarm. It is proposed that loss of FeII oxidation is due to the reversible transposition of the insertion sequence IST1 into resB encoding a putative cytochrome c-type biogenesis protein. Downstream from resB and co-transcribed with it is resC, encoding another putative cytochrome biogenesis protein. IST1 insertional inactivation of resB could result in the loss of activity of its target c-type cytochrome(s). This putative target cytochrome(s) is proposed to be essential for FeII oxidation but not for sulfur oxidation. Curiously, resB and resC pertain to the proposed system II cytochrome biogenesis pathway whereas gamma Proteobacteria, of which T. ferrooxidans is a member, normally use system I. This could represent an example of lateral gene transfer.}, }
@article {pmid10383960, year = {1999}, author = {Horken, KM and Tabita, FR}, title = {The "green" form I ribulose 1,5-bisphosphate carboxylase/oxygenase from the nonsulfur purple bacterium Rhodobacter capsulatus.}, journal = {Journal of bacteriology}, volume = {181}, number = {13}, pages = {3935-3941}, pmid = {10383960}, issn = {0021-9193}, support = {R01 GM024497/GM/NIGMS NIH HHS/United States ; GM 24497/GM/NIGMS NIH HHS/United States ; }, mesh = {Carbon Dioxide/metabolism ; Kinetics ; Protein Conformation ; Recombinant Fusion Proteins ; Recombinant Proteins/classification/metabolism ; Rhodobacter capsulatus/*enzymology ; Ribulose-Bisphosphate Carboxylase/classification/genetics/*metabolism ; Species Specificity ; Substrate Specificity ; }, abstract = {Form I ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) of the Calvin-Benson-Bassham cycle may be divided into two broad phylogenetic groups, referred to as red-like and green-like, based on deduced large subunit amino acid sequences. Unlike the form I enzyme from the closely related organism Rhodobacter sphaeroides, the form I RubisCO from R. capsulatus is a member of the green-like group and closely resembles the enzyme from certain chemoautotrophic proteobacteria and cyanobacteria. As the enzymatic properties of this type of RubisCO have not been well studied in a system that offers facile genetic manipulation, we purified the R. capsulatus form I enzyme and determined its basic kinetic properties. The enzyme exhibited an extremely low substrate specificity factor, which is congruent with its previously determined sequence similarity to form I enzymes from chemoautotrophs and cyanobacteria. The enzymological results reported here are thus strongly supportive of the previously suggested horizontal gene transfer that most likely occurred between a green-like RubisCO-containing bacterium and a predecessor to R. capsulatus. Expression results from hybrid and chimeric enzyme plasmid constructs, made with large and small subunit genes from R. capsulatus and R. sphaeroides, also supported the unrelatedness of these two enzymes and were consistent with the recently proposed phylogenetic placement of R. capsulatus form I RubisCO. The R. capsulatus form I enzyme was found to be subject to a time-dependent fallover in activity and possessed a high affinity for CO2, unlike the closely similar cyanobacterial RubisCO, which does not exhibit fallover and possesses an extremely low affinity for CO2. These latter results suggest definite approaches to elucidate the molecular basis for fallover and CO2 affinity.}, }
@article {pmid10381871, year = {1999}, author = {Doolittle, WF}, title = {Phylogenetic classification and the universal tree.}, journal = {Science (New York, N.Y.)}, volume = {284}, number = {5423}, pages = {2124-2129}, doi = {10.1126/science.284.5423.2124}, pmid = {10381871}, issn = {0036-8075}, mesh = {Animals ; Archaea/*classification/genetics ; Bacteria/*classification/genetics ; *Biological Evolution ; Eukaryotic Cells/*classification ; Genes, rRNA ; Genome ; *Phylogeny ; RNA, Ribosomal/chemistry/genetics ; *Recombination, Genetic ; }, abstract = {From comparative analyses of the nucleotide sequences of genes encoding ribosomal RNAs and several proteins, molecular phylogeneticists have constructed a "universal tree of life," taking it as the basis for a "natural" hierarchical classification of all living things. Although confidence in some of the tree's early branches has recently been shaken, new approaches could still resolve many methodological uncertainties. More challenging is evidence that most archaeal and bacterial genomes (and the inferred ancestral eukaryotic nuclear genome) contain genes from multiple sources. If "chimerism" or "lateral gene transfer" cannot be dismissed as trivial in extent or limited to special categories of genes, then no hierarchical universal classification can be taken as natural. Molecular phylogeneticists will have failed to find the "true tree," not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree. However, taxonomies based on molecular sequences will remain indispensable, and understanding of the evolutionary process will ultimately be enriched, not impoverished.}, }
@article {pmid10375631, year = {1999}, author = {Bourgoin, F and Pluvinet, A and Gintz, B and Decaris, B and Guédon, G}, title = {Are horizontal transfers involved in the evolution of the Streptococcus thermophilus exopolysaccharide synthesis loci?.}, journal = {Gene}, volume = {233}, number = {1-2}, pages = {151-161}, doi = {10.1016/s0378-1119(99)00144-4}, pmid = {10375631}, issn = {0378-1119}, mesh = {Chromosome Mapping ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Open Reading Frames ; Polysaccharides, Bacterial/*biosynthesis ; Streptococcus/*genetics ; }, abstract = {A 32.5kb variable locus of the Streptococcus thermophilus CNRZ368 chromosome, the eps locus, contains 25 ORF and seven insertion sequences (IS). The putative products of 17 ORF are related to proteins involved in the synthesis of polysaccharides in various bacteria. The two distal regions and a small central region of the eps locus are constant and present in all or almost all of the S. thermophilus strains tested. The other regions are variable and present in only some S. thermophilus strains tested, particularly in the closely related strains CNRZ368 and A054. A 13.6kb variable region of the eps locus of S. thermophilus CNRZ368 contains two ORF that are almost identical to epsL and orfY of the eps locus of Lactococcus lactis NIZOB40 and seven IS belonging to four different families, ISS1, IS981, IS1193 and IS1194. Five of these sequences were probably acquired by horizontal transfer from L. lactis (Bourgoin, F., et al., 1996. Gene 178, 15-23). Three probes of this 13.6kb region hybridized with the DNA of several L. lactis strains tested. A specific probe for another sequence within the S. thermophilus eps locus, epsF, hybridized with the DNA of one of the L. lactis strains tested. Sequence comparisons also suggest that five ORF of the eps locus have a mosaic structure and probably result from recombinations between sequences that are 10 to 50% divergent. The chimeric structure of the eps locus suggests a very complex evolution. This evolution probably involves both the acquisition of the 13.6kb region from L. lactis by horizontal transfer and exchanges within the S. thermophilus species.}, }
@article {pmid10369758, year = {1999}, author = {Ponting, CP and Aravind, L and Schultz, J and Bork, P and Koonin, EV}, title = {Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer.}, journal = {Journal of molecular biology}, volume = {289}, number = {4}, pages = {729-745}, doi = {10.1006/jmbi.1999.2827}, pmid = {10369758}, issn = {0022-2836}, mesh = {Amino Acid Sequence ; Animals ; Binding Sites ; Caenorhabditis elegans/*genetics ; Enzymes/genetics ; Eukaryotic Cells ; *Evolution, Molecular ; *Genes, Archaeal ; *Genes, Bacterial ; Molecular Sequence Data ; Phylogeny ; Recombination, Genetic ; Saccharomyces cerevisiae/*genetics ; Sequence Homology, Amino Acid ; *Signal Transduction ; src Homology Domains ; }, abstract = {Phyletic distributions of eukaryotic signalling domains were studied using recently developed sensitive methods for protein sequence analysis, with an emphasis on the detection and accurate enumeration of homologues in bacteria and archaea. A major difference was found between the distributions of enzyme families that are typically found in all three divisions of cellular life and non-enzymatic domain families that are usually eukaryote-specific. Previously undetected bacterial homologues were identified for# plant pathogenesis-related proteins, Pad1, von Willebrand factor type A, src homology 3 and YWTD repeat-containing domains. Comparisons of the domain distributions in eukaryotes and prokaryotes enabled distinctions to be made between the domains originating prior to the last common ancestor of all known life forms and those apparently originating as consequences of horizontal gene transfer events. A number of transfers of signalling domains from eukaryotes to bacteria were confidently identified, in contrast to only a single case of apparent transfer from eukaryotes to archaea.}, }
@article {pmid10360571, year = {1999}, author = {Nelson, KE and Clayton, RA and Gill, SR and Gwinn, ML and Dodson, RJ and Haft, DH and Hickey, EK and Peterson, JD and Nelson, WC and Ketchum, KA and McDonald, L and Utterback, TR and Malek, JA and Linher, KD and Garrett, MM and Stewart, AM and Cotton, MD and Pratt, MS and Phillips, CA and Richardson, D and Heidelberg, J and Sutton, GG and Fleischmann, RD and Eisen, JA and White, O and Salzberg, SL and Smith, HO and Venter, JC and Fraser, CM}, title = {Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima.}, journal = {Nature}, volume = {399}, number = {6734}, pages = {323-329}, doi = {10.1038/20601}, pmid = {10360571}, issn = {0028-0836}, mesh = {Archaea/*genetics ; Bacterial Proteins/metabolism ; DNA, Bacterial ; Genes, Archaeal ; *Genome, Bacterial ; Molecular Sequence Data ; Multigene Family ; Open Reading Frames ; Phylogeny ; Protein Biosynthesis ; *Recombination, Genetic ; Sequence Analysis, DNA ; Thermotoga maritima/classification/*genetics/physiology ; Transcription, Genetic ; Transformation, Bacterial ; }, abstract = {The 1,860,725-base-pair genome of Thermotoga maritima MSB8 contains 1,877 predicted coding regions, 1,014 (54%) of which have functional assignments and 863 (46%) of which are of unknown function. Genome analysis reveals numerous pathways involved in degradation of sugars and plant polysaccharides, and 108 genes that have orthologues only in the genomes of other thermophilic Eubacteria and Archaea. Of the Eubacteria sequenced to date, T. maritima has the highest percentage (24%) of genes that are most similar to archaeal genes. Eighty-one archaeal-like genes are clustered in 15 regions of the T. maritima genome that range in size from 4 to 20 kilobases. Conservation of gene order between T. maritima and Archaea in many of the clustered regions suggests that lateral gene transfer may have occurred between thermophilic Eubacteria and Archaea.}, }
@article {pmid10339505, year = {1999}, author = {Holmgren, L and Szeles, A and Rajnavölgyi, E and Folkman, J and Klein, G and Ernberg, I and Falk, KI}, title = {Horizontal transfer of DNA by the uptake of apoptotic bodies.}, journal = {Blood}, volume = {93}, number = {11}, pages = {3956-3963}, pmid = {10339505}, issn = {0006-4971}, mesh = {Animals ; Apoptosis/*genetics ; Cattle ; Cell Line ; DNA, Viral/*genetics ; Endothelium, Vascular/pathology/virology ; Fibroblasts/pathology/virology ; *Gene Transfer, Horizontal ; Herpesvirus 4, Human/genetics ; Humans ; Macrophages/pathology/virology ; *Phagocytosis ; }, abstract = {In this study we have raised the question of whether DNA can be transferred from one cell to another by phagocytosis of apoptotic bodies. We have used integrated copies of the Epstein-Barr virus (EBV) as a marker to follow the fate and expression pattern of apoptotic DNA in the phagocytotic host. Apoptosis was induced in EBV-carrying cell lines by irradiation before cultivation with either human fibroblasts, macrophages, or bovine aortic endothelial cells. Analysis of the expression pattern of EBV-encoded genes was performed by immunofluorescent staining as well as in situ hybridization. Cocultivation of apoptotic bodies from lymphoid cell lines containing integrated but not episomal copies of EBV resulted in expression of the EBV-encoded genes EBER and EBNA1 in the recipient cells at a high frequency. Fluorescence in situ hybridization analysis showed uptake of human chromatin as well as integrated EBV-DNA into the nuclei of bovine aortic endothelial cells. These data show that DNA may be rescued and reused from apoptotic bodies by somatic cells. In addition, our findings suggest that apoptotic bodies derived from EBV-carrying B lymphocytes may serve as the source of viral transfer to cells that lack receptors for the EBV virus in vivo.}, }
@article {pmid10331256, year = {1999}, author = {Holst-Jensen, A and Vaage, M and Schumacher, T and Johansen, S}, title = {Structural characteristics and possible horizontal transfer of group I introns between closely related plant pathogenic fungi.}, journal = {Molecular biology and evolution}, volume = {16}, number = {1}, pages = {114-126}, doi = {10.1093/oxfordjournals.molbev.a026031}, pmid = {10331256}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Base Sequence ; DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; Evolution, Molecular ; Fungi/classification/*genetics/*pathogenicity ; Gene Transfer, Horizontal ; Genes, Fungal ; *Introns ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Plants/*microbiology ; RNA, Fungal/chemistry/genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {We have characterized structural features and the distribution pattern of nuclear group I introns found in ribosomal DNA (rDNA) of closely related plant pathogenic fungi of the family Sclerotiniaceae. Sixteen introns, at two distinct positions in the small-subunit (SSU) and large-subunit (LSU) rDNA, were sequenced and analyzed among the 29 taxa included in the initial screening. Genera found to contain introns were Botrytis, Dumontinia, Encoelia, Grovesinia, Myriosclerotinia, and Sclerotinia. Secondary-structure analyses of the group I introns concluded that all belong to the common IC1 subclass. Interestingly, the SSU rDNA intron from Myriosclerotinia caricisampullacea contains an insertion-like sequence extension which may be a relic of an open reading frame. Incongruent branching patterns of intron-based and rDNA-based (internal transcribed spacer) phylogenetic trees suggest that the fungal host genomes and the group I introns do not share a common evolutionary history. A model to explain how horizontal intron transfers may have occurred among the closely related fungal taxa is proposed.}, }
@article {pmid10331255, year = {1999}, author = {Wernegreen, JJ and Riley, MA}, title = {Comparison of the evolutionary dynamics of symbiotic and housekeeping loci: a case for the genetic coherence of rhizobial lineages.}, journal = {Molecular biology and evolution}, volume = {16}, number = {1}, pages = {98-113}, doi = {10.1093/oxfordjournals.molbev.a026041}, pmid = {10331255}, issn = {0737-4038}, support = {GM47471/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Sequence ; DNA Primers/genetics ; *Evolution, Molecular ; Fabaceae/microbiology ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Glutamate-Ammonia Ligase/genetics ; Phylogeny ; Plants, Medicinal ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Rhizobiaceae/*genetics ; Rhizobium/genetics ; Symbiosis/genetics ; }, abstract = {In prokaryotes, lateral gene transfer across chromosomal lineages may be mediated by plasmids, phages, transposable elements, and other accessory DNA elements. However, the importance of such transfer and the evolutionary forces that may restrict gene exchange remain largely unexplored in native settings. In this study, tests of phylogenetic congruence are employed to explore the range of horizontal transfer of symbiotic (sym) loci among distinct chromosomal lineages of native rhizobia, the nitrogen-fixing symbiont of legumes. Rhizobial strains isolated from nodules of several host plant genera were sequenced at three loci: symbiotic nodulation genes (nodB and nodC), the chromosomal housekeeping locus glutamine synthetase II (GSII), and a portion of the 16S rRNA gene. Molecular phylogenetic analysis shows that each locus generally subdivides strains into the same major groups, which correspond to the genera Rhizobium, Sinorhizobium, and Mesorhizobium. This broad phylogenetic congruence indicates a lack of lateral transfer across major chromosomal subdivisions, and it contrasts with previous studies of agricultural populations showing broad transfer of sym loci across divergent chromosomal lineages. A general correspondence of the three rhizobial genera with major legume groups suggests that host plant associations may be important in the differentiation of rhizobial nod and chromosomal loci and may restrict lateral transfer among strains. The second major result is a significant incongruence of nod and GSII phylogenies within rhizobial subdivisions, which strongly suggests horizontal transfer of nod genes among congenerics. This combined evidence for lateral gene transfer within, but not between, genetic subdivisions supports the view that rhizobial genera are "reproductively isolated" and diverge independently. Differences across rhizobial genera in the specificity of host associations imply that the evolutionary dynamics of the symbiosis vary considerably across lineages in native settings.}, }
@article {pmid10322483, year = {1999}, author = {Wolf, YI and Aravind, L and Koonin, EV}, title = {Rickettsiae and Chlamydiae: evidence of horizontal gene transfer and gene exchange.}, journal = {Trends in genetics : TIG}, volume = {15}, number = {5}, pages = {173-175}, doi = {10.1016/s0168-9525(99)01704-7}, pmid = {10322483}, issn = {0168-9525}, mesh = {Chlamydia/enzymology/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Mitochondrial ADP, ATP Translocases/genetics ; Phylogeny ; Rickettsia/*chemistry/enzymology ; }, }
@article {pmid10322016, year = {1999}, author = {Whatmore, AM and Barcus, VA and Dowson, CG}, title = {Genetic diversity of the streptococcal competence (com) gene locus.}, journal = {Journal of bacteriology}, volume = {181}, number = {10}, pages = {3144-3154}, pmid = {10322016}, issn = {0021-9193}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Alleles ; Amino Acid Sequence ; Bacterial Proteins/chemistry/*genetics/metabolism ; Base Sequence ; Binding Sites ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Genetic Variation/*genetics ; Histidine Kinase ; Molecular Sequence Data ; *Multienzyme Complexes ; Operon/genetics ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Genetic/genetics ; Protein Kinases/chemistry/*genetics/metabolism ; Proteins/*genetics ; Sequence Alignment ; Streptococcus/genetics/pathogenicity ; Streptococcus pneumoniae/enzymology/*genetics ; *Transformation, Bacterial ; }, abstract = {The com operon of naturally transformable streptococcal species contains three genes, comC, comD, and comE, involved in the regulation of competence. The comC gene encodes a competence-stimulating peptide (CSP) thought to induce competence in the bacterial population at a critical extracellular concentration. The comD and comE genes are believed to encode the transmembrane histidine kinase and response regulator proteins, respectively, of a two-component regulator, with the comD-encoded protein being a receptor for CSP. Here we report on the genetic variability of comC and comD within Streptococcus pneumoniae isolates. Comparative analysis of sequence variations of comC and comD shows that, despite evidence for horizontal gene transfer at this locus and the lack of transformability of many S. pneumoniae strains in the laboratory, there is a clear correlation between the presence of a particular comC allele and the cognate comD allele. These findings effectively rule out the possibility that the presence of noncognate comC and comD alleles may be responsible for the inability to induce competence in many isolates and indicate the importance of a functional com pathway in these isolates. In addition, we describe a number of novel CSPs from disease-associated strains of S. mitis and S. oralis. The CSPs from these isolates are much more closely related to those from S. pneumoniae than to most CSPs previously reported from S. mitis and S. oralis, suggesting that these particular organisms may be a potential source of DNA in recombination events generating the mosaic structures commonly reported in genes of S. pneumoniae that are under strong selective pressure.}, }
@article {pmid10216267, year = {1999}, author = {Sullivan, ER and Leahy, JG and Colwell, RR}, title = {Cloning and sequence analysis of the lipase and lipase chaperone-encoding genes from Acinetobacter calcoaceticus RAG-1, and redefinition of a proteobacterial lipase family and an analogous lipase chaperone family.}, journal = {Gene}, volume = {230}, number = {2}, pages = {277-286}, doi = {10.1016/s0378-1119(99)00026-8}, pmid = {10216267}, issn = {0378-1119}, mesh = {Acinetobacter calcoaceticus/*enzymology ; Amino Acid Sequence ; Bacterial Proteins/chemistry/genetics ; Base Sequence ; Cloning, Molecular ; Evolution, Molecular ; Lipase/chemistry/*genetics ; Molecular Chaperones/chemistry/*genetics ; Molecular Sequence Data ; Sequence Homology, Amino Acid ; Terminology as Topic ; Trans-Activators/chemistry/*genetics ; }, abstract = {The genes encoding the lipase (LipA) and lipase chaperone (LipB) from Acinetobacter calcoaceticus RAG-1 were cloned and sequenced. The genes were isolated from a genomic DNA library by complementation of a lipase-deficient transposon mutant of the same strain. Transposon insertion in this mutant and three others was mapped to a single site in the chaperone gene. The deduced amino acid (aa) sequences for the lipase and its chaperone were found to encode mature proteins of 313 aa (32.5kDa) and 347 aa (38.6kDa), respectively. The lipase contained a putative leader sequence, as well as the conserved Ser, His, and Asp residues which are known to function as the catalytic triad in other lipases. A possible trans-membrane hydrophobic helix was identified in the N-terminal region of the chaperone. Phylogenetic comparisons showed that LipA, together with the lipases of A. calcoaceticus BD413, Vibrio cholerae El Tor, and Proteus vulgaris K80, were members of a previously described family of Pseudomonas and Burkholderia lipases. This new family, which we redefine as the Group I Proteobacterial lipases, was subdivided into four subfamilies on the basis of overall sequence homology and conservation of residues which are unique to the subfamilies. LipB, moreover, was found to be a member of an analogous family of lipase chaperones. We propose that the lipases produced by P. fluorescens and Serratia marcescens, which comprise a second sequence family, be referred to as the Group II Proteobacterial lipases. Evidence is provided to support the hypothesis that both the Group I and Group II families have evolved from a combination of common descent and lateral gene transfer.}, }
@article {pmid10193183, year = {1999}, author = {Martin, W}, title = {Mosaic bacterial chromosomes: a challenge en route to a tree of genomes.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {21}, number = {2}, pages = {99-104}, doi = {10.1002/(SICI)1521-1878(199902)21:2&lt;99::AID-BIES3&gt;3.0.CO;2-B}, pmid = {10193183}, issn = {0265-9247}, mesh = {Biological Evolution ; Chromosomes, Bacterial/*genetics ; Escherichia coli/genetics ; Genome, Bacterial ; Mosaicism ; Salmonella/genetics ; }, abstract = {In a recent analysis J.G. Lawrence and H. Ochman [Proc Natl Acad Sci USA 1998;95:9413-9417 (Reference 1)] surmised that about 10% of the current E. coli genome consists of genes that were acquired in over 200 events of lateral gene transfer, which occurred subsequent to the divergence of E. coli and Salmonella some 100 million years ago. Overall, the data suggest that no less than 18% of E. coli's genes might be relatively recent foreign acquisitions, and that the average rate of acquisition may be close to about 16 kb per million years. These quantitative estimates of comparatively recent genome flux have profound impact on evolutionary genome comparisons. They tend to suggest that a search should be on to identify principles that might ultimately govern gene distribution patterns across prokaryotic genomes.}, }
@article {pmid10097118, year = {1999}, author = {Jain, R and Rivera, MC and Lake, JA}, title = {Horizontal gene transfer among genomes: the complexity hypothesis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {96}, number = {7}, pages = {3801-3806}, pmid = {10097118}, issn = {0027-8424}, mesh = {*Biological Evolution ; Escherichia coli/genetics ; *Gene Transfer, Horizontal ; *Genome ; Methanococcus/genetics ; *Models, Genetic ; Open Reading Frames ; Phylogeny ; }, abstract = {Increasingly, studies of genes and genomes are indicating that considerable horizontal transfer has occurred between prokaryotes. Extensive horizontal transfer has occurred for operational genes (those involved in housekeeping), whereas informational genes (those involved in transcription, translation, and related processes) are seldomly horizontally transferred. Through phylogenetic analysis of six complete prokaryotic genomes and the identification of 312 sets of orthologous genes present in all six genomes, we tested two theories describing the temporal flow of horizontal transfer. We show that operational genes have been horizontally transferred continuously since the divergence of the prokaryotes, rather than having been exchanged in one, or a few, massive events that occurred early in the evolution of prokaryotes. In agreement with earlier studies, we found that differences in rates of evolution between operational and informational genes are minimal, suggesting that factors other than rate of evolution are responsible for the observed differences in horizontal transfer. We propose that a major factor in the more frequent horizontal transfer of operational genes is that informational genes are typically members of large, complex systems, whereas operational genes are not, thereby making horizontal transfer of informational gene products less probable (the complexity hypothesis).}, }
@article {pmid10094694, year = {1999}, author = {Hilbert, F and García-del Portillo, F and Groisman, EA}, title = {A periplasmic D-alanyl-D-alanine dipeptidase in the gram-negative bacterium Salmonella enterica.}, journal = {Journal of bacteriology}, volume = {181}, number = {7}, pages = {2158-2165}, pmid = {10094694}, issn = {0021-9193}, support = {GM54900/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; *Bacterial Proteins ; Base Sequence ; Cell Line ; DNA, Bacterial ; Dipeptidases/genetics/metabolism/*physiology ; Dogs ; Endopeptidases/genetics/metabolism/*physiology ; Genes, Bacterial ; Mice ; Mice, Inbred BALB C ; Molecular Sequence Data ; Periplasm/enzymology ; Salmonella enterica/*enzymology/genetics/pathogenicity ; Subcellular Fractions ; Substrate Specificity ; Virulence ; }, abstract = {The VanX protein is a D-alanyl-D-alanine (D-Ala-D-Ala) dipeptidase essential for resistance to the glycopeptide antibiotic vancomycin. While this enzymatic activity has been typically associated with vancomycin- and teicoplainin-resistant enterococci, we now report the identification of a D-Ala-D-Ala dipeptidase in the gram-negative species Salmonella enterica. The Salmonella enzyme is only 36% identical to VanX but exhibits a similar substrate specificity: it hydrolyzes D-Ala-D-Ala, DL-Ala-DL-Phe, and D-Ala-Gly but not the tripeptides D-Ala-D-Ala-D-Ala and DL-Ala-DL-Lys-Gly or the dipeptides L-Ala-L-Ala, N-acetyl-D-Ala-D-Ala, and L-Leu-Pro. The Salmonella dipeptidase gene, designated pcgL, appears to have been acquired by horizontal gene transfer because pcgL-hybridizing sequences were not detected in related bacterial species and the G+C content of the pcgL-containing region (41%) is much lower than the overall G+C content of the Salmonella chromosome (52%). In contrast to wild-type Salmonella, a pcgL mutant was unable to use D-Ala-D-Ala as a sole carbon source. The pcgL gene conferred D-Ala-D-Ala dipeptidase activity upon Escherichia coli K-12 but did not allow growth on D-Ala-D-Ala. The PcgL protein localizes to the periplasmic space of Salmonella, suggesting that this dipeptidase participates in peptidoglycan metabolism.}, }
@article {pmid10093218, year = {1999}, author = {Aravind, L and Koonin, EV}, title = {Novel predicted RNA-binding domains associated with the translation machinery.}, journal = {Journal of molecular evolution}, volume = {48}, number = {3}, pages = {291-302}, doi = {10.1007/pl00006472}, pmid = {10093218}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Molecular Sequence Data ; Phylogeny ; *Protein Biosynthesis ; RNA-Binding Proteins/*genetics ; Sequence Homology, Amino Acid ; }, abstract = {Two previously undetected domains were identified in a variety of RNA-binding proteins, particularly RNA-modifying enzymes, using methods for sequence profile analysis. A small domain consisting of 60-65 amino acid residues was detected in the ribosomal protein S4, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation. Another novel domain, designated PUA domain, after PseudoUridine synthase and Archaeosine transglycosylase, was detected in archaeal and eukaryotic pseudouridine synthases, archaeal archaeosine synthases, a family of predicted ATPases that may be involved in RNA modification, a family of predicted archaeal and bacterial rRNA methylases. Additionally, the PUA domain was detected in a family of eukaryotic proteins that also contain a domain homologous to the translation initiation factor eIF1/SUI1; these proteins may comprise a novel type of translation factors. Unexpectedly, the PUA domain was detected also in bacterial and yeast glutamate kinases; this is compatible with the demonstrated role of these enzymes in the regulation of the expression of other genes. We propose that the S4 domain and the PUA domain bind RNA molecules with complex folded structures, adding to the growing collection of nucleic acid-binding domains associated with DNA and RNA modification enzymes. The evolution of the translation machinery components containing the S4, PUA, and SUI1 domains must have included several events of lateral gene transfer and gene loss as well as lineage-specific domain fusions.}, }
@article {pmid10076013, year = {1999}, author = {Osborne, JP and Gennis, RB}, title = {Sequence analysis of cytochrome bd oxidase suggests a revised topology for subunit I.}, journal = {Biochimica et biophysica acta}, volume = {1410}, number = {1}, pages = {32-50}, doi = {10.1016/s0005-2728(98)00171-6}, pmid = {10076013}, issn = {0006-3002}, support = {HL16101/HL/NHLBI NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Archaea/*enzymology ; Bacteria/*enzymology ; Conserved Sequence ; Cytochrome b Group ; Cytochromes/*chemistry ; *Electron Transport Chain Complex Proteins ; *Escherichia coli Proteins ; Evolution, Molecular ; *Models, Molecular ; Molecular Sequence Data ; Oxidoreductases/*chemistry ; Phylogeny ; Sequence Alignment ; }, abstract = {Numerous sequences of the cytochrome bd quinol oxidase (cytochrome bd) have recently become available for analysis. The analysis has revealed a small number of conserved residues, a new topology for subunit I and a phylogenetic tree involving extensive horizontal gene transfer. There are 20 conserved residues in subunit I and two in subunit II. Algorithms utilizing multiple sequence alignments predicted a revised topology for cytochrome bd, adding two transmembrane helices to subunit I to the seven that were previously indicated by the analysis of the sequence of the oxidase from E. coli. This revised topology has the effect of relocating the N-terminus and C-terminus to the periplasmic and cytoplasmic sides of the membrane, respectively. The new topology repositions I-H19, the putative ligand for heme b595, close to the periplasmic edge of the membrane, which suggests that the heme b595/heme d active site of the oxidase is located near the outer (periplasmic) surface of the membrane. The most highly conserved region of the sequence of subunit I contains the sequence GRQPW and is located in a predicted periplasmic loop connecting the eighth and ninth transmembrane helices. The potential importance of this region of the protein was previously unsuspected, and it may participate in the binding of either quinol or heme d. There are two very highly conserved glutamates in subunit I, E99 and E107, within the third transmembrane helix (E. coli cytochrome bd-I numbering). It is speculated that these glutamates may be part of a proton channel leading from the cytoplasmic side of the membrane to the heme d oxygen-reactive site, now placed near the periplasmic surface. The revised topology and newly revealed conserved residues provide a clear basis for further experimental tests of these hypotheses. Phylogenetic analysis of the new sequences of cytochrome bd reveals considerable deviation from the 16sRNA tree, suggesting that a large amount of horizontal gene transfer has occurred in the evolution of cytochrome bd.}, }
@article {pmid10075991, year = {1999}, author = {Aravind, L and Koonin, EV}, title = {DNA polymerase beta-like nucleotidyltransferase superfamily: identification of three new families, classification and evolutionary history.}, journal = {Nucleic acids research}, volume = {27}, number = {7}, pages = {1609-1618}, doi = {10.1093/nar/27.7.1609}, pmid = {10075991}, issn = {0305-1048}, mesh = {Adenylyl Cyclases/chemistry ; Amino Acid Sequence ; *Biological Evolution ; DNA Polymerase beta/classification/*genetics/metabolism ; Molecular Sequence Data ; *Multigene Family ; Protein Conformation ; Sequence Homology, Amino Acid ; Signal Transduction ; }, abstract = {A detailed analysis of the polbeta superfamily of nucleotidyltransferases was performed using computer methods for iterative database search, multiple alignment, motif analysis and structural modeling. Three previously uncharacterized families of predicted nucleotidyltransferases are described. One of these new families includes small proteins found in all archaea and some bacteria that appear to consist of the minimal nucleotidyltransferase domain and may resemble the ancestral state of this superfamily. Another new family that is specifically related to eukaryotic polyA polymerases is typified by yeast Trf4p and Trf5p proteins that are involved in chromatin remodeling. The TRF family is represented by multiple members in all eukaryotes and may be involved in yet unknown nucleotide polymerization reactions required for maintenance of chromatin structure. Another new family of bacterial and archaeal nucleotidyltransferases is predicted to function in signal transduction since, in addition to the nucleotidyltransferase domain, these proteins contain ligand-binding domains. It is further shown that the catalytic domain of gamma proteobacterial adenylyl cyclases is homologous to the polbeta superfamily nucleotidyltransferases which emphasizes the general trend for the origin of signal-transducing enzymes from those involved in replication, repair and RNA processing. Classification of the polbeta superfamily into distinct families and examination of their phyletic distribution suggests that the evolution of this type of nucleotidyltransferases may have included bursts of rapid divergence linked to the emergence of new functions as well as a number of horizontal gene transfer events.}, }
@article {pmid10049269, year = {1999}, author = {Poirel, L and Naas, T and Guibert, M and Chaibi, EB and Labia, R and Nordmann, P}, title = {Molecular and biochemical characterization of VEB-1, a novel class A extended-spectrum beta-lactamase encoded by an Escherichia coli integron gene.}, journal = {Antimicrobial agents and chemotherapy}, volume = {43}, number = {3}, pages = {573-581}, pmid = {10049269}, issn = {0066-4804}, mesh = {Amino Acid Sequence ; Base Sequence ; DNA, Bacterial/genetics/metabolism ; Drug Resistance, Microbial ; Drug Resistance, Multiple ; Escherichia coli/*enzymology/genetics/isolation &amp; purification ; Escherichia coli Proteins ; Genes, Bacterial/*genetics ; Isoelectric Focusing ; Kinetics ; Klebsiella pneumoniae/genetics ; Molecular Sequence Data ; Plasmids ; beta-Lactamases/*chemistry/genetics ; }, abstract = {A clinical isolate, Escherichia coli MG-1, isolated from a 4-month-old Vietnamese orphan child, produced a beta-lactamase conferring resistance to extended-spectrum cephalosporins and aztreonam. In a disk diffusion test, a typical synergistic effect between ceftazidime or aztreonam and clavulanic acid was observed along with an unusual synergy between cefoxitin and cefuroxime. The gene for VEB-1 (Vietnamese extended-spectrum beta-lactamase) was cloned and expressed in E. coli JM109. The recombinant plasmid pRLT1 produced a beta-lactamase with a pI of 5.35 and conferred high-level resistance to extended-spectrum (or oxyimino) cephalosporins and to aztreonam. Vmax values for extended-spectrum cephalosporins were uncommonly high, while the affinity of the enzyme for ceftazidime and aztreonam was relatively low. blaVEB-1 showed significant homology at the DNA level with only blaPER-1 and blaPER-2. Analysis of the deduced protein sequence showed that VEB-1 is a class A penicillinase having very low levels of homology with any other known beta-lactamases. The highest percentage of amino acid identity was 38% with PER-1 or PER-2, two uncommon class A extended-spectrum enzymes. Exploration of the genetic environment of blaVEB-1 revealed the presence of gene cassette features, i.e., (i) a 59-base element associated with blaVEB-1; (ii) a second 59-base element just upstream of blaVEB-1, likely belonging to the aacA1-orfG gene cassette; (iii) two core sites (GTTRRRY) on both sides of blaVEB-1; and (iv) a second antibiotic resistance gene 3' of blaVEB-1, aadB. blaVEB-1 may therefore be the first class A extended-spectrum beta-lactamase that is part of a gene cassette, which itself is likely to be located on a class 1 integron, as sulfamide resistance may indicate. Furthermore, blaVEB-1 is encoded on a large (> 100-kb) transferable plasmid found in a Klebsiella pneumoniae MG-2 isolated at the same time from the same patient, indicating a horizontal gene transfer.}, }
@article {pmid10027966, year = {1999}, author = {Hensel, M and Nikolaus, T and Egelseer, C}, title = {Molecular and functional analysis indicates a mosaic structure of Salmonella pathogenicity island 2.}, journal = {Molecular microbiology}, volume = {31}, number = {2}, pages = {489-498}, doi = {10.1046/j.1365-2958.1999.01190.x}, pmid = {10027966}, issn = {0950-382X}, mesh = {Base Sequence ; Cloning, Molecular ; Codon ; DNA, Bacterial ; Molecular Sequence Data ; *Mosaicism ; Salmonella typhimurium/*genetics/*pathogenicity ; Sequence Analysis, DNA ; Virulence ; }, abstract = {Two large virulence loci encoding type III secretion systems are present on the chromosome of Salmonella typhimurium. Salmonella pathogenicity island 2 (SPI2) is important for the survival of S. typhimurium in host organs and forms an insertion of about 40 kb at the tRNA(Val) gene. However, several indications suggested that SPI2 was not the result of a single event of horizontal gene transfer. We characterized the portion of SPI2 towards the 30 cs boundary and performed mutational analysis to investigate the contribution of this region to S. enterica virulence. This analysis indicates that SPI2 may be composed of at least two different genetic elements. About 15 kb of the 40 kb of SPI2 contain genes without a significant contribution to systemic infections in the model of murine salmonellosis. Our study allowed us to define genes in SPI2 important for virulence further and indicated that this locus has a complex mosaic structure.}, }
@article {pmid10027959, year = {1999}, author = {Nakayama, K and Kanaya, S and Ohnishi, M and Terawaki, Y and Hayashi, T}, title = {The complete nucleotide sequence of phi CTX, a cytotoxin-converting phage of Pseudomonas aeruginosa: implications for phage evolution and horizontal gene transfer via bacteriophages.}, journal = {Molecular microbiology}, volume = {31}, number = {2}, pages = {399-419}, doi = {10.1046/j.1365-2958.1999.01158.x}, pmid = {10027959}, issn = {0950-382X}, mesh = {Amino Acid Sequence ; Base Sequence ; Biological Evolution ; Capsid/biosynthesis ; Cytotoxins ; DNA, Viral ; Gene Expression Regulation, Viral ; *Gene Transfer, Horizontal ; Genes, Viral ; Genome, Bacterial ; Genome, Viral ; Lysogeny ; Molecular Sequence Data ; Open Reading Frames ; Promoter Regions, Genetic ; Protein Processing, Post-Translational ; Pseudomonas Phages/*genetics ; Pseudomonas aeruginosa/*genetics/*virology ; Pyocins ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Viral Proteins/metabolism ; Virion ; }, abstract = {phi CTX is a cytotoxin-converting phage isolated from Pseudomonas aeruginosa. In this study, we determined the complete nucleotide sequence of the phi CTX phage genome. The precise genome size was 35,538 bp with 21 base 5'-extruding cohesive ends. Forty-seven open reading frames (ORFs) were identified on the phi CTX genome, including two previously identified genes, ctx and int. Among them, 15 gene products were identified in the phage particle by protein microsequencing. The most striking feature of the phi CTX genome was an extensive homology with the coliphage P2 and P2-related phages; more than half of the ORFs (25 ORFs) had marked homology to P2 genes with 28.9-65.8% identity. The gene arrangement on the genome was also highly conserved for the two phages, although the G + C content and codon usage of most phi CTX genes were similar to those of the host P. aeruginosa chromosome. In addition, phi CTX was found to share several common features with P2, including the morphology, non-inducibility, use of lipopolysaccharide core oligosaccharide as receptor and Ca(2+)-dependent receptor binding. These findings indicate that phi CTX is a P2-like phage well adapted to P. aeruginosa, and provide clear evidence of the intergeneric spread and evolution of bacteriophages. Furthermore, comparative analysis of genome structures of phi CTX, P2 and other P2 relatives revealed the presence of several hot-spots where foreign DNAs, including the cytotoxin gene, were inserted. They appear to be deeply concerned in the acquisition of various genes that are horizontally transferred by bacteriophage infection.}, }
@article {pmid10024556, year = {1999}, author = {Hanley, SA and Aduse-Opoku, J and Curtis, MA}, title = {A 55-kilodalton immunodominant antigen of Porphyromonas gingivalis W50 has arisen via horizontal gene transfer.}, journal = {Infection and immunity}, volume = {67}, number = {3}, pages = {1157-1171}, pmid = {10024556}, issn = {0019-9567}, mesh = {Adult ; Amino Acid Sequence ; Antigens, Bacterial/*genetics ; Base Sequence ; Blotting, Northern ; Chromosome Mapping ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Middle Aged ; Molecular Sequence Data ; Molecular Weight ; Operon ; Periodontitis/microbiology ; Porphyromonas gingivalis/genetics/*immunology ; }, abstract = {A 55-kDa outer membrane protein of Porphyromonas gingivalis W50 is a significant target of the serum immunoglobulin G antibody response of periodontal disease patients and hence may play an important role in host-bacterium interactions in periodontal disease. The gene encoding the 55-kDa antigen (ragB, for receptor antigen B) was isolated on a 9.5-kb partial Sau3AI fragment of P. gingivalis W50 chromosomal DNA in pUC18 by immunoscreening with a monoclonal antibody to this antigen. The 1.6-kb open reading frame (ORF) encoding RagB was located via subcloning and nested-deletion analysis. Sequence analysis demonstrated the presence of an upstream 3.1-kb ORF (ragA) which is cotranscribed with ragB. A number of genetic characteristics suggest that the ragAB locus was acquired by a horizontal gene transfer event. These include a significantly reduced G+C content relative to that of the P. gingivalis chromosome (42 versus 48%) and the presence of mobility elements flanking this locus in P. gingivalis W50. Furthermore, Southern blotting and PCR analyses showed a restricted distribution of this locus in laboratory and clinical isolates of this bacterium. The association of ragAB+ P. gingivalis with clinical status was examined by PCR analysis of subgingival samples. ragAB+ was not detected in P. gingivalis-positive shallow pockets from periodontal disease patients but was present in 36% of the P. gingivalis-positive samples from deep pockets. These data suggest that the ragAB locus was acquired by certain P. gingivalis strains via horizontal gene transfer and that the acquisition of this locus may facilitate the survival of these strains at sites of periodontal destruction.}, }
@article {pmid9973609, year = {1999}, author = {Aravind, L and Walker, DR and Koonin, EV}, title = {Conserved domains in DNA repair proteins and evolution of repair systems.}, journal = {Nucleic acids research}, volume = {27}, number = {5}, pages = {1223-1242}, doi = {10.1093/nar/27.5.1223}, pmid = {9973609}, issn = {0305-1048}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/*genetics/metabolism ; *DNA Repair ; DNA-Binding Proteins/metabolism ; *Evolution, Molecular ; Fungal Proteins/chemistry/*genetics/metabolism ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Sequence Homology, Amino Acid ; }, abstract = {A detailed analysis of protein domains involved in DNA repair was performed by comparing the sequences of the repair proteins from two well-studied model organisms, the bacterium Escherichia coli and yeast Saccharomyces cerevisiae, to the entire sets of protein sequences encoded in completely sequenced genomes of bacteria, archaea and eukaryotes. Previously uncharacterized conserved domains involved in repair were identified, namely four families of nucleases and a family of eukaryotic repair proteins related to the proliferating cell nuclear antigen. In addition, a number of previously undetected occurrences of known conserved domains were detected; for example, a modified helix-hairpin-helix nucleic acid-binding domain in archaeal and eukaryotic RecA homologs. There is a limited repertoire of conserved domains, primarily ATPases and nucleases, nucleic acid-binding domains and adaptor (protein-protein interaction) domains that comprise the repair machinery in all cells, but very few of the repair proteins are represented by orthologs with conserved domain architecture across the three superkingdoms of life. Both the external environment of an organism and the internal environment of the cell, such as the chromatin superstructure in eukaryotes, seem to have a profound effect on the layout of the repair systems. Another factor that apparently has made a major contribution to the composition of the repair machinery is horizontal gene transfer, particularly the invasion of eukaryotic genomes by organellar genes, but also a number of likely transfer events between bacteria and archaea. Several additional general trends in the evolution of repair proteins were noticed; in particular, multiple, independent fusions of helicase and nuclease domains, and independent inactivation of enzymatic domains that apparently retain adaptor or regulatory functions.}, }
@article {pmid9949862, year = {1998}, author = {Kolb, VM}, title = {Biomimicry as a basis for drug discovery.}, journal = {Progress in drug research. Fortschritte der Arzneimittelforschung. Progres des recherches pharmaceutiques}, volume = {51}, number = {}, pages = {185-217}, doi = {10.1007/978-3-0348-8845-5_5}, pmid = {9949862}, issn = {0071-786X}, mesh = {Algorithms ; Biological Evolution ; *Drug Design ; *Drugs, Investigational/chemistry ; Humans ; }, abstract = {Selected works are discussed which clearly demonstrate that mimicking various aspects of the process by which natural products evolved is becoming a powerful tool in contemporary drug discovery. Natural products are an established and rich source of drugs. The term "natural product" is often used synonymously with "secondary metabolite." Knowledge of genetics and molecular evolution helps us understand how biosynthesis of many classes of secondary metabolites evolved. One proposed hypothesis is termed "inventive evolution." It invokes duplication of genes, and mutation of the gene copies, among other genetic events. The modified duplicate genes, per se or in conjunction with other genetic events, may give rise to new enzymes, which, in turn, may generate new products, some of which may be selected for. Steps of the inventive evolution can be mimicked in several ways for purpose of drug discovery. For example, libraries of chemical compounds of any imaginable structure may be produced by combinatorial synthesis. Out of these libraries new active compounds can be selected. In another example, genetic system can be manipulated to produce modified natural products ("unnatural natural products"), from which new drugs can be selected. In some instances, similar natural products turn up in species that are not direct descendants of each other. This is presumably due to a horizontal gene transfer. The mechanism of this inter-species gene transfer can be mimicked in therapeutic gene delivery. Mimicking specifics or principles of chemical evolution including experimental and test-tube evolution also provides leads for new drug discovery.}, }
@article {pmid9929386, year = {1999}, author = {Schenk, S and Decker, K}, title = {Horizontal gene transfer involved in the convergent evolution of the plasmid-encoded enantioselective 6-hydroxynicotine oxidases.}, journal = {Journal of molecular evolution}, volume = {48}, number = {2}, pages = {178-186}, doi = {10.1007/pl00006456}, pmid = {9929386}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Animals ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes ; Humans ; Molecular Sequence Data ; Oxidoreductases Acting on CH-NH Group Donors/chemistry/*genetics ; *Plasmids ; Sequence Homology, Amino Acid ; Stereoisomerism ; }, abstract = {The D- and L-specific nicotine oxidases are flavoproteins involved in the oxidative degradation of nicotine by the Gram-positive soil bacterium Arthrobacter nicotinovorans. Their structural genes are located on a 160-kbp plasmid together with those of other nicotine-degrading enzymes. They are structurally unrelated at the DNA as well as at the protein level. Each of these oxidases possesses a high degree of substrate specificity; their catalytic stereoselectivity is absolute, although they are able to bind both enantiomeric substrates with a similar affinity. It appears that the existence of these enzymes is the result of convergent evolution. The amino acid sequence of 6-hydroxy-l-nicotine oxidase (EC 1.5.3.6) as derived from the respective structural gene shows considerable structural similarity with eukaryotic monoamine oxidases (EC 1.4.3.4) but not with monoamine oxidases from prokaryotic bacteria including those of the genus Arthrobacter. These similarities are not confined to the nucleotide-binding sites. A 100-amino acid stretch at the N-terminal regions of 6-hydroxy-l-nicotine oxidase and human monoamine oxidases A possess a 35% homology. Overall, 27.0, 26.9, and 25.8% of the amino acid positions of the monoamine oxidases of Aspergillus niger (N), humans (A), and rainbow trout (Salmo gairdneri) are identical to those of 6-hydroxy-l-nicotine oxidase (Smith-Waterman algorithm). In addition, the G+C content of the latter enzyme is in the range of that of eukaryotic monoamine oxidases and definitely lower than that of the A. nicotinovorans DNA and even that of the pAO1 DNA. The primary structure of 6-hydroxy-d-nicotine oxidase (EC 1.5.3.5) does not reveal its evolutionary history as easily. Significant similarities are found with a mitomycin radical oxidase from Streptomyces lavendulae (23.3%) and a "hypothetical protein" from Mycobacterium tuberculosis (26.0%). It is proposed that the plasmid-encoded gene of 6-hydroxy-l-nicotine oxidase evolved after horizontal transfer from an eukaryotic source.}, }
@article {pmid9916801, year = {1999}, author = {Snel, B and Bork, P and Huynen, MA}, title = {Genome phylogeny based on gene content.}, journal = {Nature genetics}, volume = {21}, number = {1}, pages = {108-110}, doi = {10.1038/5052}, pmid = {9916801}, issn = {1061-4036}, mesh = {Archaea/classification/genetics ; Bacteria/*classification/*genetics ; Genes, Archaeal ; *Genome, Bacterial ; Phylogeny ; }, abstract = {Species phylogenies derived from comparisons of single genes are rarely consistent with each other, due to horizontal gene transfer, unrecognized paralogy and highly variable rates of evolution. The advent of completely sequenced genomes allows the construction of a phylogeny that is less sensitive to such inconsistencies and more representative of whole-genomes than are single-gene trees. Here, we present a distance-based phylogeny constructed on the basis of gene content, rather than on sequence identity, of 13 completely sequenced genomes of unicellular species. The similarity between two species is defined as the number of genes that they have in common divided by their total number of genes. In this type of phylogenetic analysis, evolutionary distance can be interpreted in terms of evolutionary events such as the acquisition and loss of genes, whereas the underlying properties (the gene content) can be interpreted in terms of function. As such, it takes a position intermediate to phylogenies based on single genes and phylogenies based on phenotypic characteristics. Although our comprehensive genome phylogeny is independent of phylogenies based on the level of sequence identity of individual genes, it correlates with the standard reference of prokarytic phylogeny based on sequence similarity of 16s rRNA. Thus, shared gene content between genomes is quantitatively determined by phylogeny, rather than by phenotype, and horizontal gene transfer has only a limited role in determining the gene content of genomes.}, }
@article {pmid9891587, year = {1998}, author = {Ackermann, HW}, title = {Tailed bacteriophages: the order caudovirales.}, journal = {Advances in virus research}, volume = {51}, number = {}, pages = {135-201}, pmid = {9891587}, issn = {0065-3527}, mesh = {*Caudovirales/genetics/physiology/ultrastructure ; DNA Replication ; Genome, Viral ; Virus Assembly ; }, abstract = {Tailed bacteriophages have a common origin and constitute an order with three families, named Caudovirales. Their structured tail is unique. Tailed phages share a series of high-level taxonomic properties and show many facultative features that are unique or rare in viruses, for example, tail appendages and unusual bases. They share with other viruses, especially herpesviruses, elements of morphogenesis and life-style that are attributed to convergent evolution. Tailed phages present three types of lysogeny, exemplified by phages lambda, Mu, and P1. Lysogeny appears as a secondary property acquired by horizontal gene transfer. Amino acid sequence alignments (notably of DNA polymerases, integrases, and peptidoglycan hydrolases) indicate frequent events of horizontal gene transfer in tailed phages. Common capsid and tail proteins have not been detected. Tailed phages possibly evolved from small protein shells with a few genes sufficient for some basal level of productive infection. This early stage can no longer be traced. At one point, this precursor phage became perfected. Some of its features were perfect enough to be transmitted until today. It is tempting to list major present-day properties of tailed phages in the past tense to construct a tentative history of these viruses: 1. Tailed phages originated in the early Precambrian, long before eukaryotes and their viruses. 2. The ur-tailed phage, already a quite evolved virus, had an icosahedral head of about 60 nm in diameter and a long non-contractile tail with sixfold symmetry. The capsid contained a single molecule of dsDNA of about 50 kb, and the tail was probably provided with a fixation apparatus. Head and tail were held together by a connector. a. The particle contained no lipids, was heavier than most viruses to come, and had a high DNA content proportional to its capsid size (about 50%). b. Most of its DNA coded for structural proteins. Morphopoietic genes clustered at one end of the genome, with head genes preceding tail genes. Lytic enzymes were probably coded for. A part of the phage genome was nonessential and possibly bacterial. Were tailed phages general transductants since the beginning? 3. The virus infected its host from the outside, injecting its DNA. Replication involved transcription in several waves and formation of DNA concatemers. Novel phages were released by burst of the infected cell after lysis of host membranes by a peptidoglycan hydrolase (and a holin?). a. Capsids were assembled from a starting point, the connector, and around a scaffold. They underwent an elaborate maturation process involving protein cleavage and capsid expansion. Heads and tails were assembled separately and joined later. b. The DNA was cut to size and entered preformed capsids by a headful mechanism. 4. Subsequently, tailed phages diversified by: a. Evolving contractile or short tails and elongated heads. b. Exchanging genes or gene fragments with other phages. c. Becoming temperate by acquiring an integrase-excisionase complex, plasmid parts, or transposons. d. Acquiring DNA and RNA polymerases and other replication enzymes. e. Exchanging lysin genes with their hosts. f. Losing the ability to form concatemers as a consequence of acquiring transposons (Mu) or proteinprimed DNA polymerases (phi 29). Present-day tailed phages appear as chimeras, but their monophyletic origin is still inscribed in their morphology, genome structure, and replication strategy. It may also be evident in the three-dimensional structure of capsid and tail proteins. It is unlikely to be found in amino acid sequences because constitutive proteins must be so old that relationships were obliterated and most or all replication-, lysogeny-, and lysis-related proteins appear to have been borrowed. However, the sum of tailed phage properties and behavior is so characteristic that tailed phages cannot be confused with other viruses.}, }
@article {pmid9882656, year = {1999}, author = {Gribaldo, S and Lumia, V and Creti, R and Conway de Macario, E and Sanangelantoni, A and Cammarano, P}, title = {Discontinuous occurrence of the hsp70 (dnaK) gene among Archaea and sequence features of HSP70 suggest a novel outlook on phylogenies inferred from this protein.}, journal = {Journal of bacteriology}, volume = {181}, number = {2}, pages = {434-443}, pmid = {9882656}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; Animals ; Archaea/*classification/*genetics ; Bacteria/classification/*genetics ; *Escherichia coli Proteins ; *Evolution, Molecular ; Gram-Positive Bacteria/classification/genetics ; HSP70 Heat-Shock Proteins/*chemistry/*genetics ; Likelihood Functions ; Molecular Chaperones/genetics ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {Occurrence of the hsp70 (dnaK) gene was investigated in various members of the domain Archaea comprising both euryarchaeotes and crenarchaeotes and in the hyperthermophilic bacteria Aquifex pyrophilus and Thermotoga maritima representing the deepest offshoots in phylogenetic trees of bacterial 16S rRNA sequences. The gene was not detected in 8 of 10 archaea examined but was found in A. pyrophilus and T. maritima, from which it was cloned and sequenced. Comparative analyses of the HSP70 amino acid sequences encoded in these genes, and others in the databases, showed that (i) in accordance with the vicinities seen in rRNA-based trees, the proteins from A. pyrophilus and T. maritima form a thermophilic cluster with that from the green nonsulfur bacterium Thermomicrobium roseum and are unrelated to their counterparts from gram-positive bacteria, proteobacteria/mitochondria, chlamydiae/spirochetes, deinococci, and cyanobacteria/chloroplasts; (ii) the T. maritima HSP70 clusters with the homologues from the archaea Methanobacterium thermoautotrophicum and Thermoplasma acidophilum, in contrast to the postulated unique kinship between archaea and gram-positive bacteria; and (iii) there are exceptions to the reported association between an insert in HSP70 and gram negativity, or vice versa, absence of insert and gram positivity. Notably, the HSP70 from T. maritima lacks the insert, although T. maritima is phylogenetically unrelated to the gram-positive bacteria. These results, along with the absence of hsp70 (dnaK) in various archaea and its presence in others, suggest that (i) different taxa retained either one or the other of two hsp70 (dnaK) versions (with or without insert), regardless of phylogenetic position; and (ii) archaea are aboriginally devoid of hsp70 (dnaK), and those that have it must have received it from phylogenetically diverse bacteria via lateral gene transfer events that did not involve replacement of an endogenous hsp70 (dnaK) gene.}, }
@article {pmid9874583, year = {1998}, author = {}, title = {Mechanisms of horizontal gene spreading. Proceedings of a workshop. Oslo, Norway, June 8-9, 1998.}, journal = {APMIS. Supplementum}, volume = {84}, number = {}, pages = {4-87}, pmid = {9874583}, issn = {0903-465X}, mesh = {Animals ; *Gene Transfer, Horizontal ; Humans ; *Protein Biosynthesis ; *Transformation, Genetic ; }, }
@article {pmid9864315, year = {1999}, author = {Ueda, K and Seki, T and Kudo, T and Yoshida, T and Kataoka, M}, title = {Two distinct mechanisms cause heterogeneity of 16S rRNA.}, journal = {Journal of bacteriology}, volume = {181}, number = {1}, pages = {78-82}, pmid = {9864315}, issn = {0021-9193}, mesh = {Base Composition ; Base Sequence ; DNA Primers/genetics ; DNA Replication/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Variation ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; RNA, Bacterial/*chemistry/*genetics ; RNA, Ribosomal, 16S/*chemistry/*genetics ; Species Specificity ; Streptomyces/classification/*genetics ; }, abstract = {To investigate the frequency of heterogeneity among the multiple 16S rRNA genes within a single microorganism, we determined directly the 120-bp nucleotide sequences containing the hypervariable alpha region of the 16S rRNA gene from 475 Streptomyces strains. Display of the direct sequencing patterns revealed the existence of 136 heterogeneous loci among a total of 33 strains. The heterogeneous loci were detected only in the stem region designated helix 10. All of the substitutions conserved the relevant secondary structure. The 33 strains were divided into two groups: one group, including 22 strains, had less than two heterogeneous bases; the other group, including 11 strains, had five or more heterogeneous bases. The two groups were different in their combinations of heterogeneous bases. The former mainly contained transitional substitutions, and the latter was mainly composed of transversional substitutions, suggesting that at least two mechanisms, possibly misincorporation during DNA replication and horizontal gene transfer, cause rRNA heterogeneity.}, }
@article {pmid9850687, year = {1998}, author = {Nielsen, KM}, title = {Barriers to horizontal gene transfer by natural transformation in soil bacteria.}, journal = {APMIS. Supplementum}, volume = {84}, number = {}, pages = {77-84}, doi = {10.1111/j.1600-0463.1998.tb05653.x}, pmid = {9850687}, issn = {0903-465X}, mesh = {Adaptation, Biological/*genetics ; *Biological Evolution ; *Soil Microbiology ; *Transformation, Bacterial ; }, abstract = {Bacteria can utilize horizontally transferred DNA from other bacterial species to adapt and evolve to their changing environments. Natural transformation is a process that allows bacteria, which are able to express a regulated physiological state of competence, to take up and integrate free DNA from their surroundings. This uptake of DNA does not necessarily depend on DNA sequence, thus, indicating the potential of gene transfer from diverged donor organisms. Barriers active against such interspecies transfer are present at different phases of the transformation process. The functionality of these barriers will be discussed, and seen in relation to mechanisms that may enable bacterial cells to respond to environmental stress by adaptive evolution.}, }
@article {pmid9850683, year = {1998}, author = {Koomey, M}, title = {Competence for natural transformation in Neisseria gonorrhoeae: a model system for studies of horizontal gene transfer.}, journal = {APMIS. Supplementum}, volume = {84}, number = {}, pages = {56-61}, doi = {10.1111/j.1600-0463.1998.tb05649.x}, pmid = {9850683}, issn = {0903-465X}, mesh = {*Adenosine Triphosphatases ; Bacterial Proteins/metabolism ; Biological Transport ; DNA, Bacterial/*metabolism ; Fimbriae, Bacterial/metabolism ; Genes, Bacterial ; *Molecular Motor Proteins ; Neisseria gonorrhoeae/*genetics ; *Transformation, Bacterial ; }, abstract = {A combined effort integrating studies of gonococcal Tfp biogenesis, the data made available from the gonococcal genome sequence project and applied molecular genetics have been used to identify the fibrillar filaments themselves, the PilT protein and the ComP protein as essential components for the DNA uptake phase of competence for natural transformation. Our ongoing studies are focused on identifying and understanding the complex interactions which exist between these essential constituents. These studies may be relevant not only to the early steps of genetic transformation but also to the two other venues for horizontal gene transfer based on recent findings. First, the thin pili of IncI1 conjugal plasmids required for liquid mating belong to the type IV family of pili (Yoshida et al., 1998). Secondly, type IV pili are required for lysogenic conversion of Vibrio cholerae by a filamentous phage encoding cholera toxin (Waldor and Mekalanos, 1996). How these highly conserved surface organelles contribute to such diverse forms of DNA translocation across membranes remains to be seen.}, }
@article {pmid9850680, year = {1998}, author = {Sundström, L}, title = {The potential of integrons and connected programmed rearrangements for mediating horizontal gene transfer.}, journal = {APMIS. Supplementum}, volume = {84}, number = {}, pages = {37-42}, doi = {10.1111/j.1600-0463.1998.tb05646.x}, pmid = {9850680}, issn = {0903-465X}, mesh = {DNA Transposable Elements/*genetics ; Drug Resistance/genetics ; *Gene Rearrangement ; *Recombination, Genetic ; *Transformation, Genetic ; }, abstract = {Site-specific recombination of integrons, mediates transfer of single genes in small genomes and plasmids. Recent data suggest that new genes are recruited to the cassettes--the units moved by integrons. Integrons are resident in a class of transposons with pronounced target selectivity for resolution loci in broad host range plasmids. A resulting network of programmed transfer routes, with potential offshoots reaching into eukaryotic cells, may channel genes to unexpectedly remote organisms. It has previously been observed that the conjugation apparatus of the broad host range plasmid R751 (IncP) which contains transposon Tn5090 harbouring an integron, promotes horizontal genetic transfer between bacteria and yeast. Furthermore, it is well known and fundamental for widely used gene replacement technologies, that site-specific recombination systems (e.g. Cre-lox of bacteriophage P1) related to the integrons are functional in higher eukaryotes. It seems very clear that integrons and associated programmed transfer mechanisms have high significance for the dissemination of antibiotic resistance genes in bacteria whereas further studies are needed to assess their importance for spreading of arbitrary genes in a wider range of host systems.}, }
@article {pmid9847403, year = {1998}, author = {Fagan, T and Woodland Hastings, J and Morse, D}, title = {The phylogeny of glyceraldehyde-3-phosphate dehydrogenase indicates lateral gene transfer from cryptomonads to dinoflagellates.}, journal = {Journal of molecular evolution}, volume = {47}, number = {6}, pages = {633-639}, doi = {10.1007/pl00006420}, pmid = {9847403}, issn = {0022-2844}, support = {GM RO1 19536/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Chloroplasts/enzymology ; Dinoflagellida/*enzymology/*genetics ; Euglena gracilis/enzymology/genetics ; Eukaryota/*enzymology/*genetics ; Evolution, Molecular ; Gene Transfer Techniques ; Genes, Plant ; Genes, Protozoan ; Glyceraldehyde-3-Phosphate Dehydrogenases/*genetics ; Molecular Sequence Data ; *Phylogeny ; }, abstract = {Sequence analysis of two nuclear-encoded glyceraldehyde-3-phosphate dehydrogenase (GAPDH) genes isolated from the dinoflagellate Gonyaulax polyedra distinguishes them as cytosolic and chloroplastic forms of the enzyme. Distance analysis of the cytosolic sequence shows the Gonyaulax gene branching early within the cytosolic clade, consistent with other analyses. However, the plastid sequence forms a monophyletic group with the plastid isoforms of cryptomonads, within an otherwise cytosolic clade, distinct from all other plastid GAPDHs. This is attributed to lateral gene transfer from an ancestral cryptomonad to a dinoflagellate, providing the first example of genetic exchange accompanying symbiotic associations between the two, which are common in present day cells.}, }
@article {pmid9841641, year = {1998}, author = {Kempken, F and Kück, U}, title = {Transposons in filamentous fungi--facts and perspectives.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {20}, number = {8}, pages = {652-659}, doi = {10.1002/(SICI)1521-1878(199808)20:8&lt;652::AID-BIES8&gt;3.0.CO;2-K}, pmid = {9841641}, issn = {0265-9247}, mesh = {Animals ; *DNA Transposable Elements ; DNA, Fungal/genetics ; Fungi/*genetics ; Retroelements ; Transposases/genetics/metabolism ; }, abstract = {Transposons are ubiquitous genetic elements discovered so far in all investigated prokaryotes and eukaryotes. In remarkable contrast to all other genes, transposable elements are able to move to new locations within their host genomes. Transposition of transposons into coding sequences and their initiation of chromosome rearrangements have tremendous impact on gene expression and genome evolution. While transposons have long been known in bacteria, plants, and animals, only in recent years has there been a significant increase in the number of transposable elements discovered in filamentous fungi. Like those of other eukaryotes, each fungal transposable element is either of class or of class II. While class I elements transpose by a RNA intermediate and employ reverse transcriptases, class II elements transpose directly at the DNA level. We present structural and functional features for such transposons that have been identified so far in filamentous fungi. Emphasis is given to specific advantages or unique features when fungal systems are used to study transposable elements, e.g., the evolutionary impact of transposons in coenocytic organisms and possible experimental approaches toward horizontal gene transfer. Finally, we focus on the potential of transposons for tagging and identifying fungal genes.}, }
@article {pmid9829951, year = {1998}, author = {Chen, P and Van Vliet, F and Van De Casteele, M and Legrain, C and Cunin, R and Glansdorff, N}, title = {Aspartate transcarbamylase from the hyperthermophilic eubacterium Thermotoga maritima: fused catalytic and regulatory polypeptides form an allosteric enzyme.}, journal = {Journal of bacteriology}, volume = {180}, number = {23}, pages = {6389-6391}, pmid = {9829951}, issn = {0021-9193}, mesh = {Allosteric Site ; Amino Acid Sequence ; Aspartate Carbamoyltransferase/*chemistry/genetics/metabolism ; Cloning, Molecular ; Escherichia coli/enzymology/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Molecular Sequence Data ; Protein Conformation ; Recombinant Proteins/chemistry/genetics/metabolism ; Sequence Homology, Amino Acid ; Thermotoga maritima/*enzymology/genetics ; Treponema/enzymology/genetics ; }, abstract = {In the allosteric aspartate transcarbamylase (ATCase) from the hyperthermophilic eubacterium Thermotoga maritima, the catalytic and regulatory functions, which in class B ATCases are carried out by specialized polypeptides, are combined on a single type of polypeptide assembled in trimers. The ATCases from T. maritima and Treponema denticola present intriguing similarities, suggesting horizontal gene transfer.}, }
@article {pmid9826922, year = {1998}, author = {Barberio, C and Fani, R}, title = {Biodiversity of an Acinetobacter population isolated from activated sludge.}, journal = {Research in microbiology}, volume = {149}, number = {9}, pages = {665-673}, doi = {10.1016/s0923-2508(99)80014-x}, pmid = {9826922}, issn = {0923-2508}, mesh = {Acinetobacter/*classification/*genetics/isolation &amp; purification ; Base Sequence ; DNA, Ribosomal/chemistry ; Ecosystem ; Genetic Variation ; Molecular Sequence Data ; Phylogeny ; Plasmids/genetics ; RNA, Ribosomal, 16S/genetics ; Random Amplified Polymorphic DNA Technique ; Restriction Mapping ; Sequence Analysis, DNA ; Sewage/*microbiology ; }, abstract = {A culturable microbial community from a sewage treatment plant collecting mainly surfactant-enriched wastes was selected on minimal medium containing two nonylphenol ethoxylates as sole carbon source. Biodiversity of the community was assessed on fifty randomly chosen isolates by a combination of molecular techniques. Isolates were first analysed by amplified 16S ribosomal DNA restriction analysis (ARDRA); most of them (75%) were assigned to the genus Acinetobacter on the basis of 16S ribosomal DNA sequencing. Random amplified polymorphic DNA (RAPD) fingerprinting and the analysis of plasmid content showed a high degree of genetic variability and suggested a marked horizontal gene transfer.}, }
@article {pmid9826348, year = {1998}, author = {Lindler, LE and Plano, GV and Burland, V and Mayhew, GF and Blattner, FR}, title = {Complete DNA sequence and detailed analysis of the Yersinia pestis KIM5 plasmid encoding murine toxin and capsular antigen.}, journal = {Infection and immunity}, volume = {66}, number = {12}, pages = {5731-5742}, pmid = {9826348}, issn = {0019-9567}, support = {P01 HG10428/HG/NHGRI NIH HHS/United States ; }, mesh = {Antigens, Bacterial/*genetics ; Bacterial Capsules/*genetics ; Bacterial Toxins/*genetics ; Bacteriophage lambda/genetics ; Base Composition ; Base Sequence ; DNA Replication ; DNA Transposable Elements ; Evolution, Molecular ; Gene Library ; Gene Transfer, Horizontal ; Genes, Bacterial ; Molecular Sequence Data ; Open Reading Frames ; Plasmids/*genetics ; Proviruses/genetics ; Sequence Analysis, DNA ; Sequence Homology ; Virulence/genetics ; Yersinia pestis/*genetics/pathogenicity ; }, abstract = {Yersinia pestis, the causative agent of plague, harbors at least three plasmids necessary for full virulence of the organism, two of which are species specific. One of the Y. pestis-specific plasmids, pMT1, is thought to promote deep tissue invasion, resulting in more acute onset of symptoms and death. We determined the entire nucleotide sequence of Y. pestis KIM5 pMT1 and identified potential open reading frames (ORFs) encoded by the 100,990-bp molecule. Based on codon usage for known yersinial genes, homology with known proteins in the databases, and potential ribosome binding sites, we determined that 115 of the potential ORFs which we considered could encode polypeptides in Y. pestis. Five of these ORFs were genes previously identified as being necessary for production of the classic virulence factors, murine toxin (MT), and the fraction 1 (F1) capsule antigen. The regions of pMT1 encoding MT and F1 were surrounded by remnants of multiple transposition events and bacteriophage, respectively, suggesting horizontal gene transfer of these virulence factors. We identified seven new potential virulence factors that might interact with the mammalian host or flea vector. Forty-three of the remaining 115 putative ORFs did not display any significant homology with proteins in the current databases. Furthermore, DNA sequence analysis allowed the determination of the putative replication and partitioning regions of pMT1. We identified a single 2,450-bp region within pMT1 that could function as the origin of replication, including a RepA-like protein similar to RepFIB, RepHI1B, and P1 and P7 replicons. Plasmid partitioning function was located ca. 36 kb from the putative origin of replication and was most similar to the parABS bacteriophage P1 and P7 system. Y. pestis pMT1 encoded potential genes with a high degree of similarity to a wide variety of organisms, plasmids, and bacteriophage. Accordingly, our analysis of the pMT1 DNA sequence emphasized the mosaic nature of this large bacterial virulence plasmid and provided implications as to its evolution.}, }
@article {pmid9823660, year = {1998}, author = {Dröge, M and Pühler, A and Selbitschka, W}, title = {Horizontal gene transfer as a biosafety issue: a natural phenomenon of public concern.}, journal = {Journal of biotechnology}, volume = {64}, number = {1}, pages = {75-90}, doi = {10.1016/s0168-1656(98)00105-9}, pmid = {9823660}, issn = {0168-1656}, mesh = {Biological Evolution ; *Gene Transfer, Horizontal/adverse effects ; Plants/genetics ; Recombination, Genetic ; Soil Microbiology ; Species Specificity ; }, abstract = {The transfer of genetic information between distantly or even unrelated organisms during evolution had been inferred from nucleotide sequence comparisons. These studies provided circumstantial evidence that in rare cases genes had been laterally transmitted amongst organisms of the domains bacteria, archaea and eukarya. Laboratory-based studies confirmed that the gene pools of the various domains of organisms are linked. Amongst the bacterial gene exchange mechanisms transduction, transformation and conjugation, the latter was identified as the mechanism with potentially the broadest host range of transfer. Previously, the issue of horizontal gene transfer has become important in the context of biosafety. Gene transfer studies carried out under more natural conditions such as in model ecosystems or in the environment established that all gene transfer mechanisms worked under these conditions. Moreover, environmental hot-spots were identified where favourable conditions such as nutrient enrichment increased the probability of genetic exchange among bacteria. In particular, the phytosphere was shown to provide conducive conditions for conjugative gene exchange. Concern has been expressed that transfer of recombinant DNA (e.g. antibiotic resistance genes) from genetically modified organisms (GMOs) such as transgenic plants to phytosphere bacteria may occur and thus contribute to the undesirable spread of antibiotic resistance determinants. Studies which were performed to address this issue clearly showed that such a transfer occurs, if at all, at extremely low frequency.}, }
@article {pmid9823659, year = {1998}, author = {Einvik, C and Elde, M and Johansen, S}, title = {Group I twintrons: genetic elements in myxomycete and schizopyrenid amoeboflagellate ribosomal DNAs.}, journal = {Journal of biotechnology}, volume = {64}, number = {1}, pages = {63-74}, doi = {10.1016/s0168-1656(98)00104-7}, pmid = {9823659}, issn = {0168-1656}, mesh = {Animals ; Base Sequence ; DNA, Ribosomal/*genetics ; Eukaryota/*genetics ; Introns ; Molecular Sequence Data ; Myxomycetes/*genetics ; Nucleic Acid Conformation ; RNA/chemistry/genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {Protists are unicellular eukaryotes which represent a significant fraction of the global biodiversity. The myxomycete Didymium and the schizopyrenid amoeboflagellate Naegleria are distantly related protists. However, we have noted several striking similarities in life cycle, cell morphology, and ribosomal DNA organization between these organisms. Both have multicopy nuclear extrachromosomal ribosomal DNAs. Here the small subunit ribosomal RNA genes are interrupted by an optional group I twintron, a novel category among the group I introns. Group I twintrons are mobile self-splicing introns of 1.3-1.4 kb in size, with a complex organization at the RNA level. A group I twintron consists of two distinct ribozymes (catalytic RNAs) with different functions in RNA processing, and an open reading frame encoding a functional homing endonuclease--all with prospects of application as molecular tools in biotechnology. Updated RNA secondary structure models of group I twintrons, as well as an example of in vitro ribozyme activity, are presented. We suggest that the group I twintrons have been independently established in myxomycetes and schizopyrenid amoeboflagellates by horizontal gene transfer due to a combination of the phagocytotic behavior in natural environments and the extrachromosomal multicopy nature of ribosomal DNA.}, }
@article {pmid9812307, year = {1998}, author = {Fournier, JM and Villeneuve, S}, title = {[Cholera update and vaccination problems].}, journal = {Medecine tropicale : revue du Corps de sante colonial}, volume = {58}, number = {2 Suppl}, pages = {32-35}, pmid = {9812307}, issn = {0025-682X}, mesh = {Adult ; Bacteriophages/genetics ; Cholera/epidemiology/*prevention &amp; control ; Cholera Vaccines/administration &amp; dosage/*immunology ; Disease Outbreaks/*prevention &amp; control ; Humans ; Infant ; Vaccines, Attenuated/immunology ; Vibrio cholerae/immunology/pathogenicity/virology ; Virulence ; }, abstract = {Cholera remains an important public health problem. The long-term control of cholera depends on good personal hygiene, uncontaminated water supply and appropriate sewage disposal. However, the improvement of hygiene is distant goal for many countries. Thus the availability of an effective cholera vaccine is important for the prevention of cholera in these countries. Research on new cholera vaccines has mainly focused on oral formulations that stimulate the mucosal secretory immune system. Two oral cholera vaccines were experimented on large scale in human. The first vaccine, containing inactivated bacterial cells and B-subunit of cholera toxin, has been tested in Bangladesh from 1985 to 1989. This vaccine, according to WHO, may prove useful in the stable phase of refugee/displaced person crises, especially when given preventively. The second vaccine is a live attenuated vaccine containing the genetically manipulated Vibrio cholerae O1 strain CVD 103-HgR. Despite its efficacy in adult volunteers, results of a large-scale field trial carried-out in Indonesia for 4 years have shown a surprisingly low protection. Moreover, one of the safety concerns associated with live cholera vaccine is a possible horizontal gene transfer and recombination event leading to reversion to virulence. A new vaccine development program for cholera is based upon the hypothesis that immunoglobulins G directed to the O-specific polysaccharide of Vibrio cholerae O1 could confer protective immunity to cholera by inactivating the inoculum on intestinal mucosal surface. This program may lead to the development of cholera conjugate vaccines to elicit protection in infants.}, }
@article {pmid9797264, year = {1998}, author = {van der Meer JR,  and Werlen, C and Nishino, SF and Spain, JC}, title = {Evolution of a pathway for chlorobenzene metabolism leads to natural attenuation in contaminated groundwater.}, journal = {Applied and environmental microbiology}, volume = {64}, number = {11}, pages = {4185-4193}, pmid = {9797264}, issn = {1098-5336}, abstract = {Complete metabolism of chlorinated benzenes is not a feature that is generally found in aerobic bacteria but is thought to be due to a novel recombination of two separate gene clusters. Such a recombination could be responsible for adaptation of a natural microbial community in response to contamination with synthetic chemicals. This hypothesis was tested in a chlorobenzene (CB)-contaminated aquifer. CB-degrading bacteria from a contaminated site were characterized for a number of years by examining a combination of growth characteristics and DNA-DNA hybridization, PCR, and DNA sequence data. The genetic information obtained for the CB pathway of the predominant microorganism, Ralstonia sp. strain JS705, revealed a unique combination of (partially duplicated) genes for chlorocatechol degradation and genes for a benzene-toluene type of aromatic ring dioxygenase. The organism was detected in CB-polluted groundwater by hybridizing colonies cultivated on low-strength heterotrophic media with probes for the CB pathway. Southern hybridizations performed to determine the organization of the CB pathway genes and the 16S ribosomal DNA indicated that CB-degrading organisms isolated from different wells at the site were identical to JS705. Physiological characterization by the Biolog test system revealed some differences. The genes for the aromatic ring dioxygenase and dihydrodiol dehydrogenase of JS705 were detected in toluene and benzene degraders from the same site. Our results suggest that recent horizontal gene transfer and genetic recombination of existing genes between indigenous microorganisms were the mechanisms for evolution of the catabolic pathway. Evolution of the CB pathway seems to have created the capacity for natural attenuation of CB at the contaminated site.}, }
@article {pmid9790590, year = {1998}, author = {Claus, H and Frosch, M and Vogel, U}, title = {Identification of a hotspot for transformation of Neisseria meningitidis by shuttle mutagenesis using signature-tagged transposons.}, journal = {Molecular &amp; general genetics : MGG}, volume = {259}, number = {4}, pages = {363-371}, doi = {10.1007/s004380050823}, pmid = {9790590}, issn = {0026-8925}, mesh = {Base Sequence ; Chromosome Mapping ; Chromosomes, Bacterial ; Cloning, Molecular ; *DNA Transposable Elements ; DNA, Bacterial/analysis ; *Genetic Techniques ; Molecular Sequence Data ; *Mutagenesis ; Neisseria meningitidis/*genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Transformation, Bacterial/*genetics ; }, abstract = {Shuttle mutagenesis using signature-tagged transposons was employed to generate a library of individually tagged mutants of the Neisseria meningitidis strain B1940, which belongs to serogroup B. The use of tagged transposons allowed us to monitor for enrichment for single mutants during the process of shuttle mutagenesis, by amplification of the tags and subsequent sequence determination. Enrichment of a single clone occurred during the transformation of the meningococci with transposon-containing plasmid DNA. Sequence determination around the site of transposon insertion revealed that the transposon had mutagenized a previously unknown locus, which was designated hrtA (high rate of transformation). hrtA-mediated transformation was independent of TnMax5 and tag sequences, and it most probably involved recombination events. The hrtA locus is restricted to meningococci and gonococci and is present in few apathogenic neisserial species. Chromosomal mapping of hrtA and six further hrt sites revealed a random distribution of highly transforming DNA fragments on the meningococcal chromosome. In conclusion, our data demonstrate that shuttle mutagenesis of naturally competent bacteria using signature-tagged transposons allows the isolation of chromosomal DNA fragments, which exhibit a high transformation efficiency, and which, therefore, are likely to be involved in horizontal gene transfer.}, }
@article {pmid9786469, year = {1998}, author = {Maggs, AF and Logan, JM and Carter, PE and Pennington, TH}, title = {The detection of penicillin insensitivity in Neisseria meningitidis by polymerase chain reaction.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {42}, number = {3}, pages = {303-307}, doi = {10.1093/jac/42.3.303}, pmid = {9786469}, issn = {0305-7453}, mesh = {*Bacterial Proteins ; *Carrier Proteins ; DNA, Bacterial/analysis ; Hexosyltransferases/genetics ; Humans ; Microbial Sensitivity Tests ; Multienzyme Complexes/genetics ; *Muramoylpentapeptide Carboxypeptidase ; Neisseria meningitidis/*drug effects/genetics/isolation &amp; purification ; Penicillin Resistance/*genetics ; Penicillin-Binding Proteins ; Peptidyl Transferases/genetics ; Polymerase Chain Reaction/methods ; }, abstract = {Strains of penicillin-sensitive and -insensitive Neisseria meningitidis were examined using a range of polymerase chain reaction (PCR) primers directed at the meningococcal penicillin-binding protein 2 gene. DNA from isolates whose penicillin MIC was <0.2 mg/L yielded a product of the expected size with all the primers, but many amplification patterns were seen with DNA from isolates whose MIC was above this level. All strains whose MIC was >0.25 mg/L failed to produce a product of the expected size with at least one of the primers used. The changes seen in penicillin-insensitive strains were consistent with horizontal gene transfer from Neisseria flavescens in some isolates, although the source for others remains unknown. PCR-based methods for the detection of antibiotic resistance are becoming increasingly important with the expanding use of molecular techniques for bacteriological diagnosis.}, }
@article {pmid9770495, year = {1998}, author = {Kroll, JS and Wilks, KE and Farrant, JL and Langford, PR}, title = {Natural genetic exchange between Haemophilus and Neisseria: intergeneric transfer of chromosomal genes between major human pathogens.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {95}, number = {21}, pages = {12381-12385}, pmid = {9770495}, issn = {0027-8424}, support = {AI38399/AI/NIAID NIH HHS/United States ; }, mesh = {Base Sequence ; Escherichia coli/genetics ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Haemophilus influenzae/*genetics ; Humans ; Molecular Sequence Data ; Neisseria meningitidis/*genetics ; }, abstract = {Members of the bacterial families Haemophilus and Neisseria, important human pathogens that commonly colonize the nasopharynx, are naturally competent for DNA uptake from their environment. In each genus this process is discriminant in favor of its own and against foreign DNA through sequence specificity of DNA receptors. The Haemophilus DNA uptake apparatus binds a 29-bp oligonucleotide domain containing a highly conserved 9-bp core sequence, whereas the neisserial apparatus binds a 10-bp motif. Each motif ("uptake sequence", US) is highly over-represented in the chromosome of the corresponding genus, particularly concentrated with core sequences in inverted pairs forming gene terminators. Two Haemophilus core USs were unexpectedly found forming the terminator of sodC in Neisseria meningitidis (meningococcus), and sequence analysis strongly suggests that this virulence gene, located next to IS1106, arose through horizontal transfer from Haemophilus. By using USs as search strings in a computer-based analysis of genome sequence, it was established that while USs of the "wrong" genus do not occur commonly in Neisseria or Haemophilus, where they do they are highly likely to flag domains of chromosomal DNA that have been transferred from Haemophilus. Three independent domains of Haemophilus-like DNA were found in the meningococcal chromosome, associated respectively with the virulence gene sodC, the bio gene cluster, and an unidentified orf. This report identifies intergenerically transferred DNA and its source in bacteria, and further identifies transformation with heterologous chromosomal DNA as a way of establishing potentially important chromosomal mosaicism in these pathogenic bacteria.}, }
@article {pmid9767113, year = {1998}, author = {Yan, Y and Smant, G and Stokkermans, J and Qin, L and Helder, J and Baum, T and Schots, A and Davis, E}, title = {Genomic organization of four beta-1,4-endoglucanase genes in plant-parasitic cyst nematodes and its evolutionary implications.}, journal = {Gene}, volume = {220}, number = {1-2}, pages = {61-70}, doi = {10.1016/s0378-1119(98)00413-2}, pmid = {9767113}, issn = {0378-1119}, mesh = {3' Untranslated Regions/genetics ; 5' Untranslated Regions/genetics ; Amino Acid Sequence ; Animals ; Bacterial Proteins/genetics ; Cellulase/*genetics/metabolism ; Cloning, Molecular ; Consensus Sequence/genetics ; *Evolution, Molecular ; Exons/genetics ; *Genes, Helminth ; Hydrolysis ; Introns ; Molecular Sequence Data ; Nematoda/*genetics ; Plant Diseases/*genetics/*parasitology ; Poly A/metabolism ; Sequence Alignment ; }, abstract = {The genomic organization of genes encoding beta-1,4-endoglucanases (cellulases) from the plant-parasitic cyst nematodes Heterodera glycines and Globodera rostochiensis (HG-eng1, Hg-eng2, GR-eng1, and GR-eng2) was investigated. HG-eng1 and GR-eng1 both contained eight introns and structural domains of 2151 and 2492bp, respectively. HG-eng2 and GR-eng2 both contained seven introns and structural domains of 2324 and 2388bp, respectively. No significant similarity in intron sequence or size was observed between HG-eng1 and HG-eng2, whereas the opposite was true between GR-eng1 and GR-eng2. Intron positions among all four cyst nematode cellulase genes were conserved identically in relation to the predicted amino acid sequence. HG-eng1, GR-eng1, and GR-eng2 had several introns demarcated by 5'-GCellipsisAG-3' in the splice sites, and all four nematode cellulase genes had the polyadenylation and cleavage signal sequence 5'-GAUAAA-3'-both rare occurences in eukaryotic genes. The 5'- flanking regions of each nematode cellulase gene, however, had signature sequences typical of eukaryotic promoter regions, including a TATA box, bHLH-type binding sites, and putative silencer, repressor, and enhancer elements. Database searches and subsequent phylogenetic comparison of the catalytic domain of the nematode cellulases placed the nematode genes in one group, with Family 5, subfamily 2, glycosyl hydrolases from Scotobacteria and Bacilliaceae as the most homologous groups. The overall amino acid sequence identity among the four nematode cellulases was from 71 to 83%, and the amino acid sequence identity to bacterial Family 5 cellulases ranged from 33 to 44%. The eukaryotic organization of the four cyst nematode cellulases suggests that they share a common ancestor, and their strong homology to prokaryotic glycosyl hydrolases may be indicative of an ancient horizontal gene transfer.}, }
@article {pmid9762900, year = {1998}, author = {Kimura, M and Matsumoto, G and Shingu, Y and Yoneyama, K and Yamaguchi, I}, title = {The mystery of the trichothecene 3-O-acetyltransferase gene. Analysis of the region around Tri101 and characterization of its homologue from Fusarium sporotrichioides.}, journal = {FEBS letters}, volume = {435}, number = {2-3}, pages = {163-168}, doi = {10.1016/s0014-5793(98)01061-8}, pmid = {9762900}, issn = {0014-5793}, mesh = {Acetyltransferases/*genetics/metabolism ; Amino Acid Sequence ; Chromosome Mapping ; Fusarium/*genetics/metabolism ; Gene Expression Regulation, Plant ; *Genes, Fungal ; Molecular Sequence Data ; Multigene Family ; Sequence Alignment ; Trichothecenes/genetics/metabolism ; }, abstract = {The trichothecene 3-O-acetyltransferase gene, Tri101, plays a pivotal role for the well-being of the type B trichothecene producer Fusarium graminearum. We have analyzed the cosmids containing Tri101 and found that this resistance gene is not in the biosynthetic gene cluster reported so far. It was located between the UTP-ammonia ligase gene and the phosphate permease gene which are not related to trichothecene biosynthesis. These two 'house-keeping' genes were also linked in Fusarium species that do not produce trichothecenes. The result suggests that the isolated occurrence of Tri101 is attributed to horizontal gene transfer and not to the reciprocal translocation of the chromosome containing the gene cluster. Interestingly, 3-O-acetylation was not always a primary self-defensive strategy for all the t-type trichothecene producers; i.e. the type A trichothecene producer Fusarium sporotrichioides did not acetylate T-2 toxin in vivo although the fungus possessed a functional 3-O-acetyltransferase gene. Thus Tri101 appears to be a defense option which the producers have independently acquired in addition to their original resistance mechanisms.}, }
@article {pmid9758778, year = {1998}, author = {Stuart-Keil, KG and Hohnstock, AM and Drees, KP and Herrick, JB and Madsen, EL}, title = {Plasmids responsible for horizontal transfer of naphthalene catabolism genes between bacteria at a coal tar-contaminated site are homologous to pDTG1 from pseudomonas putida NCIB 9816-4.}, journal = {Applied and environmental microbiology}, volume = {64}, number = {10}, pages = {3633-3640}, pmid = {9758778}, issn = {1098-5336}, abstract = {The presence of a highly conserved nahAc allele among phylogenetically diverse bacteria carrying naphthalene-catabolic plasmids provided evidence for in situ horizontal gene transfer at a coal tar-contaminated site (J. B. Herrick, K. G. Stuart-Keil, W. C. Ghiorse, and E. L. Madsen, Appl. Environ. Microbiol. 63:2330-2337, 1997). The objective of the present study was to identify and characterize the different-sized naphthalene-catabolic plasmids in order to determine the probable mechanism of horizontal transfer of the nahAc gene in situ. Filter matings between naphthalene-degrading bacterial isolates and their cured progeny revealed that the naphthalene-catabolic plasmids were self-transmissible. Limited interstrain transfer was also found. Analysis of the restriction fragment length polymorphism (RFLP) patterns indicated that catabolic plasmids from 12 site-derived isolates were closely related to each other and to the naphthalene-catabolic plasmid (pDTG1) of Pseudomonas putida NCIB 9816-4, which was isolated decades ago in Bangor, Wales. The similarity among all site-derived naphthalene-catabolic plasmids and pDTG1 was confirmed by using the entire pDTG1 plasmid as a probe in Southern hybridizations. Two distinct but similar naphthalene-catabolic plasmids were retrieved directly from the microbial community indigenous to the contaminated site in a filter mating by using a cured, rifampin-resistant site-derived isolate as the recipient. RFLP patterns and Southern hybridization showed that both of these newly retrieved plasmids, like the isolate-derived plasmids, were closely related to pDTG1. These data indicate that a pDTG1-like plasmid is the mobile genetic element responsible for transferring naphthalene-catabolic genes among bacteria in situ. The pervasiveness and persistence of this naphthalene-catabolic plasmid suggest that it may have played a role in the adaptation of this microbial community to the coal tar contamination at our study site.}, }
@article {pmid9741106, year = {1998}, author = {Radax, C and Sigurdsson, O and Hreggvidsson, GO and Aichinger, N and Gruber, C and Kristjansson, JK and Stan-Lotter, H}, title = {F-and V-ATPases in the genus Thermus and related species.}, journal = {Systematic and applied microbiology}, volume = {21}, number = {1}, pages = {12-22}, doi = {10.1016/S0723-2020(98)80003-9}, pmid = {9741106}, issn = {0723-2020}, mesh = {Amino Acid Sequence ; Animals ; DNA, Ribosomal/analysis ; Electrophoresis, Polyacrylamide Gel ; Gene Transfer, Horizontal ; Phylogeny ; Proton-Translocating ATPases/chemistry/genetics/isolation &amp; purification/*metabolism ; RNA, Ribosomal, 16S/genetics ; Rabbits ; Sequence Alignment ; Sequence Analysis, DNA ; Temperature ; Thermus/*enzymology/genetics/immunology/isolation &amp; purification ; Thermus thermophilus/*enzymology/genetics/isolation &amp; purification ; *Vacuolar Proton-Translocating ATPases ; }, abstract = {The discovery of a V-type ATPase in the gram-negative bacterium Thermus thermophilus HB8 (YOKOYAMA et al., J. Biol. Chem. 265, 21946, 1990) was unexpected, since only eukaryotic endomembranes and archaea were thought to contain this enzyme complex, and horizontal gene transfer was suggested to explain the finding. We examined membrane-associated ATPases from representatives of several groups of the genus Thermus. The enzymes were extracted with chloroform and purified by ion exchange chromatography or native gel electrophoresis. One novel Islandic isolate, T. scotoductus SE-1, as well as strain T. filiformis from New Zealand, possessed F-ATPases, as judged by the typical five subunit composition of the F1-moiety, sensitivity to azide, insensitivity to nitrate and a strong crossreaction with antibodies against the F1-ATPase from E. coli. In addition, N-terminal amino acid sequencing of the beta subunit from T. scotoductus SE-1 confirmed its homology with beta subunits from known F-ATPases. In contrast, the same extraction procedure released a V-ATPase from the membranes of T. thermophilus HB27 and T. aquaticus YT-1. The related species Meiothermus (formerly Thermus) chliarophilus ALT-8 also possessed a V-ATPase. All V-ATPases examined in this study contained larger major subunits than F-ATPases, crossreacted with antiserum against subunit A of the V-ATPase from the archaeon Halobacterium saccharovorum, and the N-terminal sequences of their major subunits were homologous to those of other V-ATPases. Sequences of the 16S rRNA gene clearly placed T. scotoductus SE-1, along with other non-pigmented Thermus strains, as a distinct species close to T. aquaticus. Our results suggested that at least two members of the genus, T. scotoductus SE-1 and T. filiformis, contain an F-ATPase, whereas several others possess a V-ATPase. These data could indicate a greater diversity of the genus Thermus than was previously thought. Alternatively, the genus may consist of species where horizontal gene transfer has occurred and others, where it has not.}, }
@article {pmid9738943, year = {1998}, author = {Morett, E and Bork, P}, title = {Evolution of new protein function: recombinational enhancer Fis originated by horizontal gene transfer from the transcriptional regulator NtrC.}, journal = {FEBS letters}, volume = {433}, number = {1-2}, pages = {108-112}, doi = {10.1016/s0014-5793(98)00888-6}, pmid = {9738943}, issn = {0014-5793}, mesh = {Amino Acid Sequence ; *Bacterial Proteins ; Carrier Proteins/chemistry/*genetics/*physiology ; DNA-Binding Proteins/chemistry/*genetics ; Enhancer Elements, Genetic ; Enterobacteriaceae/genetics ; Escherichia coli/genetics ; *Escherichia coli Proteins ; *Evolution, Molecular ; Factor For Inversion Stimulation Protein ; Haemophilus influenzae/genetics ; Integration Host Factors ; Molecular Sequence Data ; Open Reading Frames ; Operon ; PII Nitrogen Regulatory Proteins ; Pasteurellaceae/genetics ; *Phylogeny ; *Recombination, Genetic ; Sequence Alignment ; *Trans-Activators ; *Transcription Factors ; }, abstract = {New protein function is thought to evolve mostly by gene duplication and divergence. Here we present phylogenetic evidence that the multifunctional protein Fis of the gamma proteobacterial species derived from the COOH-terminal domain of an ancestral alpha proteobacterial NtrC transcriptional regulatory protein. All of the known enterobacterial fis genes are preceded by an open reading frame, named yhdG, that is highly similar to nifR3, a gene that forms an operon with ntrC in several alpha proteobacterial species. Thus, we propose that yhdG and fis were acquired by a lineage ancestral to the gamma proteobacteria in a single horizontal gene transfer event, and later diverged to their present functions.}, }
@article {pmid9734076, year = {1998}, author = {Wiener, P and Egan, S and Huddleston, AS and Wellington, EM}, title = {Evidence for transfer of antibiotic-resistance genes in soil populations of streptomycetes.}, journal = {Molecular ecology}, volume = {7}, number = {9}, pages = {1205-1216}, doi = {10.1046/j.1365-294x.1998.00450.x}, pmid = {9734076}, issn = {0962-1083}, mesh = {Anti-Bacterial Agents/biosynthesis/*pharmacology ; Base Sequence ; Blotting, Southern ; Brazil ; Cloning, Molecular ; Conjugation, Genetic ; DNA Probes/chemistry ; Drug Resistance, Microbial/genetics ; Electrophoresis, Agar Gel ; Electrophoresis, Gel, Pulsed-Field ; Molecular Sequence Data ; Phenotype ; Phosphotransferases (Alcohol Group Acceptor)/chemistry ; Phylogeny ; Polymerase Chain Reaction ; R Factors/genetics ; RNA, Ribosomal, 16S/chemistry ; Sequence Alignment ; Sequence Analysis, RNA ; *Soil Microbiology ; Streptomyces/classification/drug effects/*genetics ; Streptomycin/biosynthesis/*pharmacology ; Tryptophan Synthase/chemistry/genetics ; }, abstract = {Phylogenetic analysis was used to evaluate the hypothesis of gene transfer in streptomycetes, many of which are antibiotic producers. The diversity and possible origins of streptomycin-resistance genes was investigated for a population of Streptomyces strains isolated from a site in Brazil where antibiotic production had previously been implicated The analysis provides compelling evidence for the transfer of these genes. Examination of other Streptomyces-type strains also reveals a scattered distribution of streptomycin producers with respect to the overall phylogeny. These results suggest that horizontal gene transfer may be an important factor in the evolution of antibiotic genes in streptomycetes.}, }
@article {pmid9729765, year = {1998}, author = {Nielsen, KM and Bones, AM and Smalla, K and van Elsas, JD}, title = {Horizontal gene transfer from transgenic plants to terrestrial bacteria--a rare event?.}, journal = {FEMS microbiology reviews}, volume = {22}, number = {2}, pages = {79-103}, doi = {10.1111/j.1574-6976.1998.tb00362.x}, pmid = {9729765}, issn = {0168-6445}, mesh = {Bacteria/*genetics ; Conjugation, Genetic ; Ecology ; *Gene Transfer, Horizontal ; Plants, Genetically Modified/*genetics/*microbiology ; Risk Assessment ; Transduction, Genetic ; Transformation, Genetic ; }, abstract = {Today, 12 years after the first field release of a genetically modified plant (GMP), over 15,000 field trials at different locations have been performed. As new and unique characteristics are frequently introduced into GMPs, risk assessment has to be performed to assess their ecological impact. The possibilities of horizontal gene transfer (HGT; no parent-to-offspring transfer of genes) from plants to microorganisms are frequently evaluated in such risk assessments of GMPs before release into the field. In this review we indicate why putative HGT from plants to terrestrial (soil and plant associated) bacteria has raised concern in biosafety evaluations. Further, we discuss possible pathways of HGT from plants to bacteria, outline the barriers to HGT in bacteria, describe the strategies used to investigate HGT from plants to bacteria and summarize the results obtained. Only a few cases of HGT from eukaryotes such as plants to bacteria have been reported to date. These cases have been ascertained after comparison of DNA sequences between plants and bacteria. Although experimental approaches in both field and laboratory studies have not been able to confirm the occurrence of such HGT to naturally occurring bacteria, recently two studies have shown transfer of marker genes from plants to bacteria based on homologous recombination. The few examples of HGT indicated by DNA sequence comparisons suggest that the frequencies of evolutionarily successful HGT from plants to bacteria may be extremely low. However, this inference is based on a small number of experimental studies and indications found in the literature. Transfer frequencies should not be confounded with the likelihood of environmental implications, since the frequency of HGT is probably only marginally important compared with the selective force acting on the outcome. Attention should therefore be focused on enhancing the understanding of selection processes in natural environments. Only an accurate understanding of these selective events will allow the prediction of possible consequences of novel genes following their introduction into open environments.}, }
@article {pmid9697096, year = {1998}, author = {Charbit, A and Autret, N}, title = {Horizontal transfer of chromosomal DNA between the marine bacterium Vibrio furnissii and Escherichia coli revealed by sequence analysis.}, journal = {Microbial &amp; comparative genomics}, volume = {3}, number = {2}, pages = {119-132}, doi = {10.1089/omi.1.1998.3.119}, pmid = {9697096}, issn = {1090-6592}, mesh = {Amino Acid Sequence ; Biological Transport ; Chromosomes, Bacterial ; DNA, Bacterial ; Escherichia coli/*genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Mannose/*metabolism ; Marine Biology ; Models, Genetic ; Molecular Sequence Data ; Multigene Family ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Vibrio/*genetics ; Water Microbiology ; }, abstract = {Previous in silico analysis of the 67.4-76.0 minutes region of the Escherichia coli genome led to the identification of a gene cluster (named aga) comprising five genes encoding homologs of the mannose transporter of E. coli, a member of the sugar-specific phosphoenolypyruvate/sugar phosphotransferase system (PTS). In the present work, we compared the aga gene cluster of E. coli, which has been considered to be involved in N-acetylgalactosamine or N-acetylmannosamine transport and metabolism, to the region comprising the recently identified mannose transporter of the marine bacterium Vibrio furnissii. Our analysis revealed that the proteins encoded by three genes (agaV, agaW, and agaA), located in the proximal portion of the aga gene cluster, shared striking similarities with the proteins encoded by the manX (IIBMan), manY (IICMan), and manD (a putative deacetylase) genes of V. furnissii, respectively (70%-82.3% identity among the three pairs of proteins). Moreover, we found that the two following aga genes (agaS and agaY) were homologous to the sequences flanking the mannose operon of V. furnissii. These observations strongly support the idea of a horizontal transfer of the chromosomally encoded man operon of V. furnissii into the E. coli genome.}, }
@article {pmid9689094, year = {1998}, author = {Lawrence, JG and Ochman, H}, title = {Molecular archaeology of the Escherichia coli genome.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {95}, number = {16}, pages = {9413-9417}, pmid = {9689094}, issn = {0027-8424}, mesh = {Chromosomes, Bacterial ; Escherichia coli/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; }, abstract = {The availability of the complete sequence of Escherichia coli strain MG1655 provides the first opportunity to assess the overall impact of horizontal genetic transfer on the evolution of bacterial genomes. We found that 755 of 4,288 ORFs (547.8 kb) have been introduced into the E. coli genome in at least 234 lateral transfer events since this species diverged from the Salmonella lineage 100 million years (Myr) ago. The average age of introduced genes was 14.4 Myr, yielding a rate of transfer 16 kb/Myr/lineage since divergence. Although most of the acquired genes subsequently were deleted, the sequences that have persisted (approximately 18% of the current chromosome) have conferred properties permitting E. coli to explore otherwise unreachable ecological niches.}, }
@article {pmid9687471, year = {1998}, author = {Juretschko, S and Timmermann, G and Schmid, M and Schleifer, KH and Pommerening-Röser, A and Koops, HP and Wagner, M}, title = {Combined molecular and conventional analyses of nitrifying bacterium diversity in activated sludge: Nitrosococcus mobilis and Nitrospira-like bacteria as dominant populations.}, journal = {Applied and environmental microbiology}, volume = {64}, number = {8}, pages = {3042-3051}, pmid = {9687471}, issn = {0099-2240}, mesh = {Ammonia/*metabolism ; Bradyrhizobiaceae/genetics/*isolation &amp; purification/metabolism ; Colony Count, Microbial ; DNA, Ribosomal/analysis ; Genes, Bacterial ; Gram-Negative Chemolithotrophic Bacteria/genetics/*isolation &amp; purification ; In Situ Hybridization, Fluorescence ; Industrial Microbiology ; Molecular Sequence Data ; Nitrites/*metabolism ; Oxidation-Reduction ; Oxidoreductases/*genetics/metabolism ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/*microbiology ; }, abstract = {The ammonia-oxidizing and nitrite-oxidizing bacterial populations occurring in the nitrifying activated sludge of an industrial wastewater treatment plant receiving sewage with high ammonia concentrations were studied by use of a polyphasic approach. In situ hybridization with a set of hierarchical 16S rRNA-targeted probes for ammonia-oxidizing bacteria revealed the dominance of Nitrosococcus mobilis-like bacteria. The phylogenetic affiliation suggested by fluorescent in situ hybridization (FISH) was confirmed by isolation of N. mobilis as the numerically dominant ammonia oxidizer and subsequent comparative 16S rRNA gene (rDNA) sequence and DNA-DNA hybridization analyses. For molecular fine-scale analysis of the ammonia-oxidizing population, a partial stretch of the gene encoding the active-site polypeptide of ammonia monooxygenase (amoA) was amplified from total DNA extracted from ammonia oxidizer isolates and from activated sludge. However, comparative sequence analysis of 13 amoA clone sequences from activated sludge demonstrated that these sequences were highly similar to each other and to the corresponding amoA gene fragments of Nitrosomonas europaea Nm50 and the N. mobilis isolate. The unexpected high sequence similarity between the amoA gene fragments of the N. mobilis isolate and N. europaea indicates a possible lateral gene transfer event. Although a Nitrobacter strain was isolated, members of the nitrite-oxidizing genus Nitrobacter were not detectable in the activated sludge by in situ hybridization. Therefore, we used the rRNA approach to investigate the abundance of other well-known nitrite-oxidizing bacterial genera. Three different methods were used for DNA extraction from the activated sludge. For each DNA preparation, almost full-length genes encoding small-subunit rRNA were separately amplified and used to generate three 16S rDNA libraries. By comparative sequence analysis, 2 of 60 randomly selected clones could be assigned to the nitrite-oxidizing bacteria of the genus Nitrospira. Based on these clone sequences, a specific 16S rRNA-targeted probe was developed. FISH of the activated sludge with this probe demonstrated that Nitrospira-like bacteria were present in significant numbers (9% of the total bacterial counts) and frequently occurred in coaggregated microcolonies with N. mobilis.}, }
@article {pmid9687430, year = {1998}, author = {Jiang, SC and Paul, JH}, title = {Gene transfer by transduction in the marine environment.}, journal = {Applied and environmental microbiology}, volume = {64}, number = {8}, pages = {2780-2787}, pmid = {9687430}, issn = {0099-2240}, mesh = {Bacteria/*genetics/growth &amp; development/isolation &amp; purification ; Bacteriophages/*genetics ; Blotting, Southern ; DNA Transposable Elements/genetics ; Drug Resistance, Microbial/genetics ; Escherichia coli/genetics ; *Gene Transfer, Horizontal ; Kanamycin Kinase/genetics ; Kanamycin Resistance/genetics ; Plasmids/genetics ; Polymerase Chain Reaction ; Seawater/microbiology ; *Transduction, Genetic ; *Water Microbiology ; }, abstract = {To determine the potential for bacteriophage-mediated gene transfer in the marine environment, we established transduction systems by using marine phage host isolates. Plasmid pQSR50, which contains transposon Tn5 and encodes kanamycin and streptomycin resistance, was used in plasmid transduction assays. Both marine bacterial isolates and concentrated natural bacterial communities were used as recipients in transduction studies. Transductants were detected by a gene probe complementary to the neomycin phosphotransferase (nptII) gene in Tn5. The transduction frequencies ranged from 1.33 x 10(-7) to 5.13 x 10(-9) transductants/PFU in studies performed with the bacterial isolates. With the mixed bacterial communities, putative transductants were detected in two of the six experiments performed. These putative transductants were confirmed and separated from indigenous antibiotic-resistant bacteria by colony hybridization probed with the nptII probe and by PCR amplification performed with two sets of primers specific for pQSR50. The frequencies of plasmid transduction in the mixed bacterial communities ranged from 1.58 x 10(-8) to 3.7 x 10(-8) transductants/PFU. Estimates of the transduction rate obtained by using a numerical model suggested that up to 1.3 x 10(14) transduction events per year could occur in the Tampa Bay Estuary. The results of this study suggest that transduction could be an important mechanism for horizontal gene transfer in the marine environment.}, }
@article {pmid9682479, year = {1998}, author = {Privitera, A and Rappazzo, G and Sangari, P and Gianninò, V and Licciardello, L and Stefani, S}, title = {Cloning and sequencing of a 16S/23S ribosomal spacer from Haemophilus parainfluenzae reveals an invariant, mosaic-like organisation of sequence blocks.}, journal = {FEMS microbiology letters}, volume = {164}, number = {2}, pages = {289-294}, doi = {10.1111/j.1574-6968.1998.tb13100.x}, pmid = {9682479}, issn = {0378-1097}, mesh = {Blotting, Southern ; Cloning, Molecular ; DNA, Bacterial/genetics ; DNA, Ribosomal/chemistry/*genetics ; Haemophilus/classification/*genetics/growth &amp; development/isolation &amp; purification ; Plasmids ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/*genetics ; RNA, Ribosomal, 23S/*genetics ; RNA, Transfer, Glu/genetics ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {A 16S/23S ribosomal spacer from a Haemophilus parainfluenzae rrn locus was cloned and sequenced. Analysis of PCR-amplified genomic fragments showed that this region is strongly conserved among unrelated isolates; computer analysis of database homologies showed that the spacer consists of sequence blocks, arranged in a mosaic-like structure, with strong homologies with analogous blocks present in the spacer regions of Haemophilus influenzae, Haemophilus ducreyi and Actinobacillus spp. It also contains a tRNA(Glu) gene, which is highly homologous to tRNA(Glu) genes found in spacers of other species. These data strongly support the hypothesis that recombination events are involved in the organisation of the sequence of the spacer, as a result of horizontal gene transfer.}, }
@article {pmid9666554, year = {1998}, author = {Kado, CI}, title = {Agrobacterium-mediated horizontal gene transfer.}, journal = {Genetic engineering}, volume = {20}, number = {}, pages = {1-24}, doi = {10.1007/978-1-4899-1739-3_1}, pmid = {9666554}, issn = {0196-3716}, support = {GM 45550-28/GM/NIGMS NIH HHS/United States ; }, mesh = {DNA, Bacterial/genetics ; DNA, Single-Stranded/genetics ; *Gene Transfer, Horizontal ; Plants/*genetics/*microbiology ; Plants, Genetically Modified ; Rhizobium/*genetics/pathogenicity ; Virulence/genetics ; }, }
@article {pmid9659237, year = {1998}, author = {Hall, LM}, title = {Application of molecular typing to the epidemiology of Streptococcus pneumoniae.}, journal = {Journal of clinical pathology}, volume = {51}, number = {4}, pages = {270-274}, pmid = {9659237}, issn = {0021-9746}, mesh = {*Bacterial Proteins ; *Bacterial Typing Techniques ; Carrier Proteins/metabolism ; *Hexosyltransferases ; Humans ; Muramoylpentapeptide Carboxypeptidase/metabolism ; Penicillin Resistance ; Penicillin-Binding Proteins ; Penicillins/metabolism ; *Peptidyl Transferases ; Pneumococcal Infections/*epidemiology/microbiology ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Streptococcus pneumoniae/*classification/genetics ; }, abstract = {The spread of antibiotic resistance and the development of new vaccines have focused attention on the epidemiology of Streptococcus pneumoniae over recent years. While serotyping and the determination of antibiotic resistance remain primary methods for characterising pneumococci, molecular typing can add greater discrimination and complementary information. Methods based on restriction fragment length polymorphism within total DNA or non-specific polymerase chain reaction provide information representative of the whole genome and can be used to recognise closely related isolates from different sources, whether in the investigation of possible cross infection at the local level or in the investigation of national or international spread of antibiotic resistant strains. Fingerprinting of penicillin binding protein genes adds further information in the analysis of penicillin resistant isolates. The use of a combination of typing methods to analyse both the genome as a whole and specific loci has led to the realisation that pneumococci undergo horizontal gene transfer much more often than most other bacterial species. In particular the spread of penicillin resistance has been characterised by a combination of the spread of epidemic strains, transfer of chromosomal resistance genes from such strains into other genetic backgrounds, and transfer of capsule genes resulting in the switch of serotypes within strains. In the future molecular typing will have an important role in discovering whether widespread vaccination leads to genetic modification of the pneumococcal population causing invasive disease.}, }
@article {pmid9654137, year = {1998}, author = {Ammendola, S and Politi, L and Scandurra, R}, title = {Cloning and sequencing of ISC1041 from the archaeon Sulfolobus solfataricus MT-4, a new member of the IS30 family of insertion elements.}, journal = {FEBS letters}, volume = {428}, number = {3}, pages = {217-223}, doi = {10.1016/s0014-5793(98)00530-4}, pmid = {9654137}, issn = {0014-5793}, mesh = {Amino Acid Sequence ; Base Sequence ; Cloning, Molecular ; DNA Primers ; *DNA Transposable Elements ; Evolution, Molecular ; Genome, Bacterial ; HIV Integrase/chemistry/genetics ; HIV-1/genetics ; Molecular Sequence Data ; *Multigene Family ; Phylogeny ; Polymerase Chain Reaction ; Sequence Alignment ; Sequence Homology, Amino Acid ; Sulfolobus/classification/*genetics ; Transposases/chemistry/*genetics ; }, abstract = {A genomic fragment containing the insertion sequence ISC1041 has been cloned by PCR from the archaeon Sulfolobus solfaricus MT-4, an extremophilic microorganism which grows at 87 degrees C. The 1038 bp ISC1041 element contains an imperfect 18 nt repeat and a long open reading frame which encodes a polypeptide of 311 amino acid residues. The translated amino acid sequence shows a significant similarity to IS30-like transposases. Structural analysis indicates that ISC1041 is a novel member of the IS30 family and displays the DDE motif not previously seen in Archaea. This motif is believed to be involved in the integration mechanism of many mobile elements. As this motif is present in several integrases and transposases which, despite the lack of overall protein homologies, share topological homologies to the DDE motif, a common ancestor has been proposed. The finding of an IS30-like transposase in the archaeal kingdom may have relevance for horizontal gene transfer.}, }
@article {pmid9631542, year = {1998}, author = {Kaplan, JB and Fine, DH}, title = {Codon usage in Actinobacillus actinomycetemcomitans.}, journal = {FEMS microbiology letters}, volume = {163}, number = {1}, pages = {31-36}, doi = {10.1111/j.1574-6968.1998.tb13022.x}, pmid = {9631542}, issn = {0378-1097}, mesh = {Adolescent ; Aggregatibacter actinomycetemcomitans/*genetics ; Bacterial Toxins/genetics ; Base Composition ; Codon/*genetics ; DNA, Bacterial/chemistry/genetics ; Exotoxins/genetics ; Female ; Genes, Bacterial/genetics ; Genetic Code ; Humans ; Periodontitis/microbiology ; }, abstract = {The codon usage patterns of 21 genes encompassing 5800 codons from Actinobacillus actinomycetemcomitans were analyzed. A. actinomycetemcomitans genes could be divided into two groups based on their function and G + C content. One group included those genes encoding basic cellular functions. This group displayed an average G + C content of 48%. A second group comprised genes encoding the leukotoxin determinant, an insertion sequence and a plasmid. This group displayed an average G + C content of 36%. These findings suggest that portions of the A. actinomycetemcomitans genome may have been acquired by horizontal gene transfer from one or more distantly related species. We present a table of A. actinomycetemcomitans codon usage. These data may be used to establish standards for computer programs that predict A. actinomycetemcomitans protein coding regions and may be useful in designing degenerate oligonucleotide probes.}, }
@article {pmid9631304, year = {1998}, author = {Höök-Nikanne, J and Berg, DE and Peek, RM and Kersulyte, D and Tummuru, MK and Blaser, MJ}, title = {DNA sequence conservation and diversity in transposable element IS605 of Helicobacter pylori.}, journal = {Helicobacter}, volume = {3}, number = {2}, pages = {79-85}, doi = {10.1111/j.1523-5378.1998.08011.x}, pmid = {9631304}, issn = {1083-4389}, support = {AI138166/AI/NIAID NIH HHS/United States ; R01 CA58834/CA/NCI NIH HHS/United States ; R29DK48451/DK/NIDDK NIH HHS/United States ; }, mesh = {Base Sequence ; Blotting, Southern ; DNA Transposable Elements/*genetics ; DNA, Bacterial/*genetics ; Helicobacter pylori/*genetics/growth &amp; development ; Humans ; Molecular Sequence Data ; Open Reading Frames ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: IS605, a transposable element-like sequence identified in the virulence-associated cag region of Helicobacter pylori reference strain NCTC11638, is unusual in containing two oppositely-oriented open reading frames whose products are homologues of the single transposases of the unrelated elements, IS200 and IS1341.<br><br>METHODS: One hundred independent H. pylori isolates from different parts of the world were screened by PCR and dot blot hybridization to determine the presence of IS605. For some positive isolates, southern hybridizations and sequence analyses were done.<br><br>RESULTS: Of the 100 isolates, 31 were found to contain sequences related to each ORF with orientation and spacing matching those in canonical IS605-hybridizing sequences. No isolate containing just one ORF and not the other was found. The frequencies of IS605 carriage were independent of geographical origin (U.S. vs. non-U.S.), and of the probable virulence of the isolate (cag status, toxin production or vacA alleles, patient symptoms). Southern blot hybridization of six IS605-containing strains revealed one to nine IS605 copies per genome. Two types of DNA sequence diversity were found: first, a specific 100 bp deletion in two isolates; second, base substitution divergence of 0.4% to 7.5% in pairwise comparisons among the eight isolates characterized, a level of divergence similar to that seen in other H. pylori chromosomal genes.<br><br>CONCLUSIONS: Based on these findings, we speculate that IS605 is a relatively ancient component of the H. pylori gene pool that has proliferated in this species by horizontal gene transfer, homologous recombination, and transposition.}, }
@article {pmid9618502, year = {1998}, author = {Woese, C}, title = {The universal ancestor.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {95}, number = {12}, pages = {6854-6859}, pmid = {9618502}, issn = {0027-8424}, mesh = {Animals ; *Biological Evolution ; Gene Transfer Techniques ; *Genes ; Humans ; *Models, Biological ; }, abstract = {A genetic annealing model for the universal ancestor of all extant life is presented; the name of the model derives from its resemblance to physical annealing. The scenario pictured starts when "genetic temperatures" were very high, cellular entities (progenotes) were very simple, and information processing systems were inaccurate. Initially, both mutation rate and lateral gene transfer levels were elevated. The latter was pandemic and pervasive to the extent that it, not vertical inheritance, defined the evolutionary dynamic. As increasingly complex and precise biological structures and processes evolved, both the mutation rate and the scope and level of lateral gene transfer, i.e., evolutionary temperature, dropped, and the evolutionary dynamic gradually became that characteristic of modern cells. The various subsystems of the cell "crystallized," i.e., became refractory to lateral gene transfer, at different stages of "cooling," with the translation apparatus probably crystallizing first. Organismal lineages, and so organisms as we know them, did not exist at these early stages. The universal phylogenetic tree, therefore, is not an organismal tree at its base but gradually becomes one as its peripheral branchings emerge. The universal ancestor is not a discrete entity. It is, rather, a diverse community of cells that survives and evolves as a biological unit. This communal ancestor has a physical history but not a genealogical one. Over time, this ancestor refined into a smaller number of increasingly complex cell types with the ancestors of the three primary groupings of organisms arising as a result.}, }
@article {pmid9622362, year = {1998}, author = {Goodwin, A and Kersulyte, D and Sisson, G and Veldhuyzen van Zanten, SJ and Berg, DE and Hoffman, PS}, title = {Metronidazole resistance in Helicobacter pylori is due to null mutations in a gene (rdxA) that encodes an oxygen-insensitive NADPH nitroreductase.}, journal = {Molecular microbiology}, volume = {28}, number = {2}, pages = {383-393}, doi = {10.1046/j.1365-2958.1998.00806.x}, pmid = {9622362}, issn = {0950-382X}, support = {AI38166/AI/NIAID NIH HHS/United States ; DK48029/DK/NIDDK NIH HHS/United States ; HG00820/HG/NHGRI NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Anti-Bacterial Agents/*pharmacology ; Base Sequence ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Helicobacter pylori/*drug effects/enzymology/genetics ; Humans ; Metronidazole/*pharmacology ; Molecular Sequence Data ; Mutation ; Nitroreductases/chemistry/*genetics ; Recombinant Proteins/analysis ; Sequence Homology, Amino Acid ; }, abstract = {Metronidazole (Mtz) is a critical component of combination therapies that are used against Helicobacter pylori, the major cause of peptic ulcer disease. Many H. pylori strains are Mtz resistant (MtzR), however, and here we show that MtzR results from loss of oxygen-insensitive NADPH nitroreductase activity. The underlying gene (called 'rdxA') was identified in several steps: transformation of Mtz-susceptible (MtzS) H. pylori with cosmids from a MtzR strain, subcloning, polymerase chain reaction (PCR) and DNA sequencing. We also found that (i) E. coli (normally MtzR) was rendered MtzS by a functional H. pylori rdxA gene; (ii) introduction of rdxA on a shuttle vector plasmid into formerly MtzR H. pylori rendered it MtzS; and (iii) replacement of rdxA in MtzS H. pylori with an rdxA::camR null insertion allele resulted in a MtzR phenotype. The 630 bp rdxA genes of five pairs of H. pylori isolates from infections that were mixed (MtzR/MtzS), but uniform in overall genotype, were sequenced. In each case, the paired rdxA genes differed from one another by one to three base substitutions. Typical rdxA genes from unrelated isolates differ by 5% in DNA sequence. Therefore, the near identity of rdxA genes from paired MtzR and MtzS isolates implicates de novo mutation, rather than horizontal gene transfer in the development of MtzR. Horizontal gene transfer could readily be demonstrated under laboratory conditions with mutant rdxA alleles. RdxA is a homologue of the classical nitroreductases (CNRs) of the enteric bacteria, but differs in cysteine content (6 vs. 1 or 2 in CNRs) and isoelectric point (pI=7.99 vs. 5.4-5.6), which might account for its reduction of low redox drugs such as Mtz. We suggest that many rdxA (MtzR) mutations may have been selected by prior use of Mtz against other infections. H. pylori itself is an early risk factor for gastric cancer; the possibility that its carcinogenic effects are exacerbated by Mtz use, which is frequent in many societies, or the reduction of nitroaromatic compounds to toxic, mutagenic and carcinogenic products, may be of significant concern in public health.}, }
@article {pmid9622357, year = {1998}, author = {Espinosa-Urgel, M and Kolter, R}, title = {Escherichia coli genes expressed preferentially in an aquatic environment.}, journal = {Molecular microbiology}, volume = {28}, number = {2}, pages = {325-332}, doi = {10.1046/j.1365-2958.1998.00796.x}, pmid = {9622357}, issn = {0950-382X}, mesh = {Bacterial Proteins/metabolism ; Base Sequence ; Blotting, Northern ; Blotting, Southern ; Electrophoresis, Polyacrylamide Gel ; Escherichia coli/chemistry/classification/*genetics/growth &amp; development ; *Gene Expression Regulation, Bacterial ; *Genes, Bacterial/genetics ; Genotype ; Molecular Sequence Data ; Mutation/genetics ; Open Reading Frames/genetics ; Polymerase Chain Reaction ; RNA, Bacterial/genetics/*metabolism ; RNA, Transfer, Amino Acid-Specific/genetics/*metabolism ; Sequence Analysis ; Temperature ; *Water Microbiology ; }, abstract = {Enteric bacteria are frequently found in aquatic environments, where they may pose a risk to human health. Although bacterial survival and persistence in such habitats has been studied extensively, there is almost no information about bacterial adaptation to these conditions at the level of changes in gene expression. As a first exploration of this field, we have carried out a screen designed to identify Escherichia coli genes that show increased expression in an aquatic environment. The screen was performed by subtractive hybridization on a genomic library and led to the identification of several RNA species more abundant in cells inoculated in this medium than in stationary-phase cultures after growth in rich medium. The genes identified include specific tRNA operons and a gene of unknown function, gapC, with similarities to glyceraldehyde-3-phosphate dehydrogenases. E. coli K-12 strains appear to have accumulated mutations in gapC, which may impede its translation, whereas natural isolates have an intact gapC gene. Sequence comparison of gapC with related genes suggests its acquisition by horizontal gene transfer from gram-positive bacteria.}, }
@article {pmid9620957, year = {1998}, author = {Zverlov, VV and Velikodvorskaya, GV and Schwarz, WH and Bronnenmeier, K and Kellermann, J and Staudenbauer, WL}, title = {Multidomain structure and cellulosomal localization of the Clostridium thermocellum cellobiohydrolase CbhA.}, journal = {Journal of bacteriology}, volume = {180}, number = {12}, pages = {3091-3099}, pmid = {9620957}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; Base Sequence ; Cell Membrane/enzymology ; Cellulase/*chemistry/genetics/*metabolism ; Cellulose 1,4-beta-Cellobiosidase ; Clostridium/*enzymology/genetics ; DNA, Bacterial/genetics ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; Sequence Homology, Amino Acid ; }, abstract = {The nucleotide sequence of the Clostridium thermocellum F7 cbhA gene, coding for the cellobiohydrolase CbhA, has been determined. An open reading frame encoding a protein of 1,230 amino acids was identified. Removal of a putative signal peptide yields a mature protein of 1,203 amino acids with a molecular weight of 135,139. Sequence analysis of CbhA reveals a multidomain structure of unusual complexity consisting of an N-terminal cellulose binding domain (CBD) homologous to CBD family IV, an immunoglobulin-like beta-barrel domain, a catalytic domain homologous to cellulase family E1, a duplicated domain similar to fibronectin type III (Fn3) modules, a CBD homologous to family III, a highly acidic linker region, and a C-terminal dockerin domain. The cellulosomal localization of CbhA was confirmed by Western blot analysis employing polyclonal antibodies raised against a truncated enzymatically active version of CbhA. CbhA was identified as cellulosomal subunit S3 by partial amino acid sequence analysis. Comparison of the multidomain structures indicates striking similarities between CbhA and a group of cellulases from actinomycetes. Average linkage cluster analysis suggests a coevolution of the N-terminal CBD and the catalytic domain and its spread by horizontal gene transfer among gram-positive cellulolytic bacteria.}, }
@article {pmid9573157, year = {1998}, author = {Lai, EM and Kado, CI}, title = {Processed VirB2 is the major subunit of the promiscuous pilus of Agrobacterium tumefaciens.}, journal = {Journal of bacteriology}, volume = {180}, number = {10}, pages = {2711-2717}, pmid = {9573157}, issn = {0021-9193}, support = {GM45550/GM/NIGMS NIH HHS/United States ; }, mesh = {Agrobacterium tumefaciens/*metabolism/ultrastructure ; Bacterial Proteins/*metabolism ; Fimbriae, Bacterial/*metabolism/ultrastructure ; Temperature ; Up-Regulation ; *Virulence Factors ; }, abstract = {Previous studies have implicated the obligatory requirement for the vir regulon (or "virulon") of the Ti plasmid for the transfer of oncogenes from Agrobacterium tumefaciens to plant cells. The machinery used in this horizontal gene transfer has been long thought to be a transformation or conjugative delivery system. Based on recent protein sequence comparisons, the proteins encoded by the virB operon are strikingly similar to proteins involved in the synthesis and assembly of conjugative pili such as the conjugative pilus of F plasmid in Escherichia coli. The F pilus is composed of TraA pilin subunits derived from TraA propilin. In the present study, evidence is provided showing that the counterpart of TraA is VirB2, which like TraA propilin is processed into a 7.2-kDa product that comprises the pilus subunit as demonstrated by biochemical and electron microscopic analyses. The processed VirB2 protein is present exocellularly on medium on which induced A. tumefaciens had grown and appears as thin filaments of 10 nm that react specifically to VirB2 antibody. Exocellular VirB2 is produced abundantly at 19 degreesC as compared with 28 degreesC, an observation that parallels the effect of low temperature on the production of vir gene-specific pili observed previously (K. J. Fullner, L. C. Lara, and E. W. Nester, Science 273:1107-1109, 1996). Export of the processed VirB2 requires other virB genes since mutations in these genes cause the loss of VirB2 pilus formation and result in processed VirB2 accumulation in the cell. The presence of exocellular processed VirB2 is directly correlated with the formation of pili, and it appears as the major protein in the purified pilus preparation. The evidence provides a compelling argument for VirB2 as the propilin whose 7.2-kDa processed product is the pilin subunit of the promiscuous conjugative pilus, hereafter called the "T pilus" of A. tumefaciens.}, }
@article {pmid9603824, year = {1998}, author = {Ravatn, R and Zehnder, AJ and van der Meer, JR}, title = {Low-frequency horizontal transfer of an element containing the chlorocatechol degradation genes from Pseudomonas sp. strain B13 to Pseudomonas putida F1 and to indigenous bacteria in laboratory-scale activated-sludge microcosms.}, journal = {Applied and environmental microbiology}, volume = {64}, number = {6}, pages = {2126-2132}, pmid = {9603824}, issn = {0099-2240}, mesh = {Base Sequence ; Biodegradation, Environmental ; Catechols/*metabolism ; Chlorobenzenes/*metabolism ; Conjugation, Genetic ; DNA Primers/genetics ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Ecosystem ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Pseudomonas/*genetics/*metabolism ; Pseudomonas putida/genetics/metabolism ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sewage ; Water Pollutants, Chemical/metabolism ; }, abstract = {The possibilities for low-frequency horizontal transfer of the self-transmissible chlorocatechol degradative genes (clc) from Pseudomonas sp. strain B13 were investigated in activated-sludge microcosms. When the clc genes were transferred into an appropriate recipient bacterium such as Pseudomonas putida F1, a new metabolic pathway for chlorobenzene degradation was formed by complementation which could be selected for by the addition of mono- or 1, 4-dichlorobenzene (CB). Under optimized conditions with direct donor-recipient filter matings, very low transfer frequencies were observed (approximately 3.5 x 10(-8) per donor per 24 h). In contrast, in matings on agar plate surfaces, transconjugants started to appear after 8 to 10 days, and their numbers then increased during prolonged continuous incubation with CB. In activated-sludge microcosms, CB-degrading (CB+) transconjugants of strain F1 which had acquired the clc genes were detected but only when strain B13 cell densities of more than 10(5) CFU/ml could be maintained by the addition of its specific growth substrate, 3-chlorobenzoate (3CBA). The CB+ transconjugants reached final cell densities of between 10(2) and 10(3) CFU/ml. When strain B13 was inoculated separately (without the designated recipient strain F1) into an activated-sludge microcosm, CB+ transconjugants could not be detected. However, in this case a new 3CBA-degrading strain appeared which had acquired the clc genes from strain B13. The effects of selective substrates on the survival and growth of and gene transfer between bacteria degrading aromatic pollutants in a wastewater ecosystem are discussed.}, }
@article {pmid9602275, year = {1998}, author = {Clerc, S and Simonet, P}, title = {A review of available systems to investigate transfer of DNA to indigenous soil bacteria.}, journal = {Antonie van Leeuwenhoek}, volume = {73}, number = {1}, pages = {15-23}, doi = {10.1023/a:1000747310461}, pmid = {9602275}, issn = {0003-6072}, mesh = {Bacteria/*genetics ; *Conjugation, Genetic ; *Gene Transfer, Horizontal ; Genetic Engineering ; Risk Factors ; *Soil Microbiology ; }, abstract = {The deliberate or accidental release of genetically engineered microorganisms (GEMs) in the environment has led to some questions concerning microbial survival, transfer of DNA to the indigenous microflora and environmental consequences. Amongst horizontal gene transfer mechanisms, conjugation is probably the most frequent in the environment. With the aim of evaluating risks associated with environmental release of GEMs and their engineered DNA, studies of conjugative gene transfer between a donor strain and indigenous microflora have been conducted. Such studies required the development of a donor counterselection system to prevent growth of donor cells on transconjugant selective plates. This review summarizes the known and potential donor counterselection systems.}, }
@article {pmid9588806, year = {1998}, author = {Leblond, P and Decaris, B}, title = {Chromosome geometry and intraspecific genetic polymorphism in Gram-positive bacteria revealed by pulsed-field gel electrophoresis.}, journal = {Electrophoresis}, volume = {19}, number = {4}, pages = {582-588}, doi = {10.1002/elps.1150190420}, pmid = {9588806}, issn = {0173-0835}, mesh = {*Chromosomes, Bacterial ; *Electrophoresis, Gel, Pulsed-Field ; *Polymorphism, Genetic ; Species Specificity ; Streptococcus/*genetics ; Streptomyces/*genetics ; }, abstract = {Pulsed-field gel electrophoresis (PFGE) proved to be a powerful approach to study bacterial genomics. The genome structure and genetic polymorphism of Gram-positive bacteria from the high G+C (Streptomyces) and low G+C (Streptococcus) groups have been studied. PFGE allowed the estimation of the size of their genome at about 8 Mbp and 1.8 Mbp, respectively, and to get an insight into their chromosome geometry. Thus, physical mapping of the genome of wild-type Streptomyces ambofaciens strains revealed the linearity of the 8 Mbp chromosomal DNA and its typical invertron structure, while the 1.8 Mbp chromosome of Streptococcus thermophilus was shown to be circular. These findings disproved the long-standing idea of universality of bacterial chromosome circularity. In addition, strains belonging to the species S. ambofaciens and S. thermophilus allowed us to characterize the genetic polymorphism at the intraspecific level. Within the S. thermophilus species, comparison of the physical maps showed a relative conservation of gene order as well as restriction sites along the chromosome. In contrast, variable loci were characterized that revealed localized genome rearrangements. The most spectacular of these corresponded to horizontal gene transfer events of sequences. In S. ambofaciens, the physical maps of three isolates pointed to the conservation of the genetic organization. However, a strong polymorphism was observed in the terminal regions of the linear chromosomal DNA. Previous PFGE studies in S. ambofaciens gave proof of a high structural instability of a limited region of the chromosome called unstable region (i.e., DNA rearrangements such as deletions and amplifications). These intraclonal rearrangements create an impressive intraspecific polymorphism of genome size and shape (linear or circular). In both organisms, the DNA rearrangements are restricted to particular regions of the chromosome.}, }
@article {pmid9545188, year = {1998}, author = {Weinberg, ES}, title = {Zebrafish genetics: harnessing horizontal gene transfer.}, journal = {Current biology : CB}, volume = {8}, number = {7}, pages = {R244-7}, doi = {10.1016/s0960-9822(98)70151-4}, pmid = {9545188}, issn = {0960-9822}, mesh = {Animals ; DNA Transposable Elements ; *Gene Transfer, Horizontal ; Mutagenesis ; Transposases ; Zebrafish/*genetics ; }, abstract = {The promiscuous spread of Tc1/mariner transposons across species implies that host factors are relatively unimportant for their transposition. Heterologous elements can integrate on expression of the corresponding transposases, an approach that should greatly facilitate genetic analysis in the zebrafish.}, }
@article {pmid9541537, year = {1998}, author = {Muñoz, R and García, E and López, R}, title = {Evidence for horizontal transfer from Streptococcus to Escherichia coli of the kfiD gene encoding the K5-specific UDP-glucose dehydrogenase.}, journal = {Journal of molecular evolution}, volume = {46}, number = {4}, pages = {432-436}, pmid = {9541537}, issn = {0022-2844}, mesh = {*Bacterial Capsules ; Bacterial Proteins/*genetics ; Base Sequence ; Codon/genetics ; Escherichia coli/*genetics ; *Escherichia coli Proteins ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Multigene Family ; Phylogeny ; Polysaccharides, Bacterial ; Species Specificity ; Streptococcus/*enzymology/*genetics ; Substrate Specificity ; Uridine Diphosphate Glucose Dehydrogenase/*genetics ; }, abstract = {Capsular polysaccharides are important virulence factors both in Gram-positive and Gram-negative bacteria. A similar cluster organization of the genes involved in the synthesis of bacterial exopolysaccharides has been postulated in both cases, suggesting that these clusters evolved by module assembly. Horizontal gene transfer has been postulated to explain the polymorphism found in these cellular polymers. The cap1 K and cap3A genes coding for the pneumococcal type 1 and type 3 UDP-glucose dehydrogenases, respectively, have been compared with other UDP-sugar dehydrogenases. We have observed that the evolutionary distance between Cap1K and Cap3A is approximately equal to that found between Cap1K (or Cap3A) and other UDP-GlcDH of families evolutionarily distant like KfiD, the dehydrogenase from Escherichia coli K5. On the basis of comparisons of G + C content, patterns of synonymous and nonsynonymous substitutions, dinucleotide frequencies, and codon usage bias, we conclude that the kfiD gene has been introduced into E. coli from an exogenous source, probably from a streptococcal species.}, }
@article {pmid9542104, year = {1998}, author = {Lewin, A and Hertwig, S and Strauch, E and Appel, B}, title = {Is natural genetic transformation a mechanism of horizontal gene transfer in Yersinia?.}, journal = {Journal of basic microbiology}, volume = {38}, number = {1}, pages = {17-26}, doi = {10.1002/(sici)1521-4028(199803)38:1&lt;17::aid-jobm17&gt;3.0.co;2-d}, pmid = {9542104}, issn = {0233-111X}, mesh = {Electroporation ; *Gene Transfer, Horizontal ; Genetic Markers ; Plasmids ; *Transformation, Bacterial ; Yersinia/*genetics/pathogenicity ; Yersinia enterocolitica/*genetics/pathogenicity ; }, abstract = {We investigated the capacity of different Yersinia strains with emphasis to Yersinia enterocolitica to take up and incorporate DNA by natural genetic transformation. Our studies were initiated by the observation of partial homology between the virulence plasmid of a pathogenic Y. enterocolitica strain (O: 3, biovar 4) and plasmids indiginous to different a pathogenic Y. enterocolitica biovar 1A strains revealed by hybridization studies. Furthermore, an observation of natural genetic transformation in a strain of Y. enterocolitica has been published by CALLAHAN and KOROMA (1979). To detect an uptake and incorporation of DNA, we incubated potential recipient strains with naked DNA under varying experimental conditions. The parameters tested were--the recipient strain,--the markers used to detect a DNA transfer,--the condition of the transforming DNA,--the nutrient availability,--the temperature,--the growth phase, and--the influence of stress. In our experiments, we could not identify conditions under which Y. enterocolitica could be naturally transformed. We thus conclude that natural transformation is unlikely to be an important mechanism for horizontal gene transfer in Yersinia.}, }
@article {pmid9562989, year = {1998}, author = {Fuchs, TM}, title = {Molecular mechanisms of bacterial pathogenicity.}, journal = {Die Naturwissenschaften}, volume = {85}, number = {3}, pages = {99-108}, doi = {10.1007/s001140050463}, pmid = {9562989}, issn = {0028-1042}, mesh = {Bacteria/genetics/*pathogenicity ; Bacterial Infections/*microbiology/*mortality ; Biological Evolution ; Child ; Cholera/mortality ; Communicable Disease Control ; Diarrhea/microbiology/mortality ; Drug Resistance, Microbial ; Dysentery, Bacillary/mortality ; Enterobacter ; Humans ; Shigella dysenteriae ; Staphylococcus aureus ; Virulence ; }, abstract = {Cautious optimism has arisen over recent decades with respect to the long struggle against bacteria, viruses, and parasites. This has been offset, however, by a fatal complacency stemming from previous successes such as the development of antimicrobial drugs, the eradication of smallpox, and global immunization programs. Infectious diseases nevertheless remain the world's leading cause of death, killing at least 17 million persons annually [61]. Diarrheal diseases caused by Vibrio cholerae or Shigella dysenteriae kill about 3 million persons every year, most of them young children: Another 4 million die of tuberculosis or tetanus. Outbreaks of diphtheria in Eastern Europe threatens the population with a disease that had previously seemed to be overcome. Efforts to control infectious diseases more comprehensively are undermined not only by socioeconomic conditions but also by the nature of the pathogenic organisms itself; some isolates of Staphylococcus aureus and Enterobacter have become so resistant to drugs by horizontal gene transfer that they are almost untreatable. In addition, the mechanism of genetic variability helps pathogens to evade the human immune system, thus compromising the development of powerful vaccines. Therefore detailed knowledge of the molecular mechanisms of microbial pathogenicity is absolutely necessary to develop new strategies against infectious diseases and thus to lower their impact on human health and social development.}, }
@article {pmid9562894, year = {1998}, author = {Brüssow, H and Bruttin, A and Desiere, F and Lucchini, S and Foley, S}, title = {Molecular ecology and evolution of Streptococcus thermophilus bacteriophages--a review.}, journal = {Virus genes}, volume = {16}, number = {1}, pages = {95-109}, pmid = {9562894}, issn = {0920-8569}, mesh = {Bacteriophages/*genetics/*pathogenicity ; Ecology ; *Evolution, Molecular ; Streptococcus/*virology ; Virulence/physiology ; }, abstract = {Bacteriophages attacking Streptococcus thermophilus, a lactic acid bacterium used in milk fermentation, are a threat to the dairy industry. These small isometric-headed phages possess double-stranded DNA genomes of 31 to 45 kb. Yoghurt-derived phages exhibit a limited degree of variability, as defined by restriction pattern and host range, while a large diversity of phage types have been isolated from cheese factories. Despite this diversity all S. thermophilus phages, virulent and temperate, belong to a single DNA homology group. Several mechanisms appear to create genetic variability in this phage group. Site-specific deletions, one type possibly mediated by a viral recombinase/integrase, which transformed a temperate into a virulent phage, were observed. Recombination as a result of superinfection of a lysogenic host has been reported. Comparative DNA sequencing identified up to 10% sequence diversity due to point mutations. Genome sequencing of the prototype temperate phage phi Sfi21 revealed many predicted proteins which showed homology with phages from Lactococcus lactis suggesting horizontal gene transfer. Homology with phages from evolutionary unrelated bacteria like E. coli (e.g. lambdoid phage 434 and P1) and Mycobacterium phi L5 was also found. Due to their industrial importance, the existence of large phage collections, and the whole phage genome sequencing projects which are currently underway, the S. thermophilus phages may present an interesting experimental system to study bacteriophage evolution.}, }
@article {pmid9549096, year = {1998}, author = {Whitehouse, DB and Tomkins, J and Lovegrove, JU and Hopkinson, DA and McMillan, WO}, title = {A phylogenetic approach to the identification of phosphoglucomutase genes.}, journal = {Molecular biology and evolution}, volume = {15}, number = {4}, pages = {456-462}, doi = {10.1093/oxfordjournals.molbev.a025942}, pmid = {9549096}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Animals ; Binding Sites/genetics ; Databases, Factual ; *Evolution, Molecular ; Humans ; Phosphoglucomutase/*genetics ; *Phylogeny ; Sequence Homology, Amino Acid ; }, abstract = {The expanding molecular database provides unparalleled opportunities for characterizing genes and for studying groups of related genes. We use sequences drawn from the database to construct an evolutionary framework for examining the important glycolytic enzyme phosphoglucomutase (PGM). Phosphoglucomutase plays a pivotal role in the synthesis and utilization of glycogen and is present in all organisms. In humans, there are three well-described isozymes, PGMI, PGM2, and PGM3. PGM1 was cloned 5 years ago; however, repeated attempts using both immunological approaches and molecular probes designed from PGM1 have failed to isolate either PGM2 or PGM3. Using a phylogenetic strategy, we first identified 47 highly divergent prokaryotic and eukaryotic PGM-like sequences from the database. Although overall amino acid identity often fell below 20%, the relative order, position, and sequence of three structural motifs, the active site and the magnesium--and sugar-binding sites, were conserved in all 47 sequences. The phylogenetic history of these sequences was complex and marked by duplications and translocations; two instances of transkingdom horizontal gene transfer were identified. Nonetheless, the sequences fell within six well-defined evolutionary lineages, three of which contained only prokaryotes. Of the two prokaryotic/eukaryotic lineages, one contained bacterial, yeast, slimemold, invertebrate, and vertebrate homologs to human PGM1 and the second contained likely homologs to human PGM2. Indeed, an amino acid sequence, derived from a partial human cDNA, that fell within the second cross-kingdom lineage bears several characteristics expected for PGM2. A third lineage may contain homologs to human PGM3. On a general level, our phylogenetic-based approach shows promise for the further utilization of the extensive molecular database.}, }
@article {pmid9482851, year = {1998}, author = {Roman, J and Woodson, SA}, title = {Integration of the Tetrahymena group I intron into bacterial rRNA by reverse splicing in vivo.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {95}, number = {5}, pages = {2134-2139}, pmid = {9482851}, issn = {0027-8424}, mesh = {Animals ; Base Sequence ; Cloning, Molecular/methods ; DNA, Protozoan/biosynthesis/chemistry/*genetics ; Escherichia coli/*genetics ; *Gene Transfer, Horizontal ; *Introns ; Models, Molecular ; Nucleic Acid Conformation ; Polymerase Chain Reaction ; RNA Splicing ; RNA, Bacterial/biosynthesis/chemistry/*genetics ; RNA, Ribosomal, 23S/biosynthesis/chemistry/*genetics ; Tetrahymena/*genetics ; }, abstract = {Horizontal gene transfer is thought to contribute to the wide distribution of group I introns among organisms. Integration of an intron into foreign RNA or DNA by reverse self-splicing, followed by reverse transcription and recombination, could lead to its transposition. Reverse self-splicing of group I introns has been demonstrated in vitro, but not in vivo. Here we report RNA-dependent integration of the Tetrahymena intron into the 23S rRNA in Escherichia coli. Analysis of products by Northern blot and reverse transcription-PCR amplification revealed precise intron insertion into a site homologous to the natural splice junction. Products are sensitive to treatment with RNase but not DNase and depend on the splicing activity of the intron. Partial reaction with 11 novel sites in the 23S RNA that are complementary to the guide sequence of the intron illustrates lower specificity than intron homing. Reverse splicing of the Tetrahymena intron in bacteria demonstrates the possibility of RNA-catalyzed transposition of group I introns in foreign hosts.}, }
@article {pmid9515912, year = {1998}, author = {Bäumler, AJ and Norris, TL and Lasco, T and Voight, W and Reissbrodt, R and Rabsch, W and Heffron, F}, title = {IroN, a novel outer membrane siderophore receptor characteristic of Salmonella enterica.}, journal = {Journal of bacteriology}, volume = {180}, number = {6}, pages = {1446-1453}, pmid = {9515912}, issn = {0021-9193}, support = {R29 AI040124/AI/NIAID NIH HHS/United States ; R01 AI040124/AI/NIAID NIH HHS/United States ; R01 AI022933/AI/NIAID NIH HHS/United States ; AI40124/AI/NIAID NIH HHS/United States ; AI 22933/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; *Bacterial Outer Membrane Proteins ; Cloning, Molecular ; Cosmids ; DNA, Bacterial/analysis/genetics ; Escherichia coli/genetics/metabolism ; Gene Expression ; Genes, Bacterial ; Molecular Sequence Data ; Mutagenesis, Insertional ; Operon ; Phylogeny ; Receptors, Cell Surface/*genetics/*metabolism ; Recombination, Genetic ; Restriction Mapping ; Salmonella/genetics/metabolism ; Salmonella enterica/*genetics/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Siderophores/metabolism ; Species Specificity ; }, abstract = {Speciation in enterobacteria involved horizontal gene transfer. Therefore, analysis of genes acquired by horizontal transfer that are present in one species but not its close relatives is expected to give insights into how new bacterial species were formed. In this study we characterize iroN, a gene located downstream of the iroBC operon in the iroA locus of Salmonella enterica serotype Typhi. Like iroBC, the iroN gene is present in all phylogenetic lineages of S. enterica but is absent from closely related species such as Salmonella bongori or Escherichia coli. Comparison of the deduced amino acid sequence of iroN with other proteins suggested that this gene encodes an outer membrane siderophore receptor protein. Mutational analysis in S. enterica and expression in E. coli identified a 78-kDa outer membrane protein as the iroN gene product. When introduced into an E. coli fepA cir fiu aroB mutant on a cosmid, iroN mediated utilization of structurally related catecholate siderophores, including N-(2,3-dihydroxybenzoyl)-L-serine, myxochelin A, benzaldehyde-2,3-dihydroxybenzhydrazone, 2-N,6-N-bis(2,3-dihydroxybenzoyl)-L-lysine, 2-N,6-N-bis(2,3-dihydroxybenzoyl)-L-lysine amide, and enterochelin. These results suggest that the iroA locus functions in iron acquisition in S. enterica.}, }
@article {pmid9427643, year = {1998}, author = {Raz, E and van Luenen, HG and Schaerringer, B and Plasterk, RH and Driever, W}, title = {Transposition of the nematode Caenorhabditis elegans Tc3 element in the zebrafish Danio rerio.}, journal = {Current biology : CB}, volume = {8}, number = {2}, pages = {82-88}, doi = {10.1016/s0960-9822(98)70038-7}, pmid = {9427643}, issn = {0960-9822}, support = {5 RO1 RR10082/RR/NCRR NIH HHS/United States ; R01-HD29761-05/HD/NICHD NIH HHS/United States ; }, mesh = {Animals ; Animals, Genetically Modified ; Caenorhabditis elegans/*genetics ; *DNA Transposable Elements ; Gene Expression ; Gene Transfer, Horizontal ; *Genes, Helminth ; *Genetic Vectors ; Green Fluorescent Proteins ; Luminescent Proteins/genetics ; Zebrafish/*genetics ; }, abstract = {BACKGROUND: Transposable elements of the Tc1/mariner family are found in many species of the animal kingdom. It has been suggested that the widespread distribution of this transposon family resulted from horizontal transmission among different species.<br><br>RESULTS: To test the ability of Tc1/mariner to cross species barriers, as well as to develop molecular genetic tools for studying zebrafish development, we determined the ability of the Tc3 transposon, a member of the Tc1/mariner family, to function in zebrafish. Tc3 transposons carrying sequences encoding the green fluorescent protein (GFP) were able to integrate in the fish genome by transposition. Integrated transposons expressed the GFP marker after germline transmission, and were capable of being mobilized upon introduction of transposase protein in trans.<br><br>CONCLUSIONS: Our findings support models of horizontal transmission of Tc1/mariner elements between species. The work also establishes the basis for a novel method of transposon-mediated genetic transformation and for transposon-mediated genetic screens in zebrafish and other organisms.}, }
@article {pmid9498443, year = {1998}, author = {Bingen, E and Picard, B and Brahimi, N and Mathy, S and Desjardins, P and Elion, J and Denamur, E}, title = {Phylogenetic analysis of Escherichia coli strains causing neonatal meningitis suggests horizontal gene transfer from a predominant pool of highly virulent B2 group strains.}, journal = {The Journal of infectious diseases}, volume = {177}, number = {3}, pages = {642-650}, doi = {10.1086/514217}, pmid = {9498443}, issn = {0022-1899}, mesh = {Bacterial Typing Techniques ; DNA, Ribosomal ; Escherichia coli/*classification/genetics/*pathogenicity ; Escherichia coli Infections/cerebrospinal fluid/*microbiology ; Gene Transfer, Horizontal ; Humans ; Infant, Newborn ; Infant, Newborn, Diseases/microbiology ; Meningitis, Bacterial/cerebrospinal fluid/*microbiology ; Models, Genetic ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Virulence/genetics ; }, abstract = {Phylogenetic relationships of 69 neonatal meningitis Escherichia coli strains isolated worldwide were studied. Restriction fragment length polymorphism of rrn operons (rrn RFLP) in these isolates was compared with that of the 72 strains of the ECOR reference collection. Distributions of K1 antigen, of polymerase chain reaction-detected ibe10 gene, pap, afa, sfa/foc, hly, and aer operons, and of a 14.9-kb rrn-containing HindIII fragment previously associated with neonatal meningitis were compared. Oligoclonality was observed for the meningitis strains. Factorial analysis of correspondence on the rrn RFLP data showed a frequency gradient of meningitis strains from the phylogenetic B2 group (68%) to the A group (6%), via the D and B1 groups (26%). The distribution of the virulence determinants argues for their horizontal transfer during the evolution of E. coli. Analysis of the status of some neonates further suggests that neonatal meningitis results from a balance between bacterial genes of virulence and host factors.}, }
@article {pmid9493369, year = {1998}, author = {Jouravleva, EA and McDonald, GA and Garon, CF and Boesman-Finkelstein, M and Finkelstein, RA}, title = {Characterization and possible functions of a new filamentous bacteriophage from Vibrio cholerae O139.}, journal = {Microbiology (Reading, England)}, volume = {144 (Pt 2)}, number = {}, pages = {315-324}, doi = {10.1099/00221287-144-2-315}, pmid = {9493369}, issn = {1350-0872}, support = {AI17312/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteriophages/genetics/*isolation &amp; purification/ultrastructure ; Bangladesh ; DNA, Viral/*analysis/*genetics/ultrastructure ; Gene Transfer, Horizontal ; Host-Parasite Interactions ; India ; Microscopy, Electron ; O Antigens/immunology ; Plasmids/genetics ; Sequence Analysis, DNA ; Vibrio cholerae/growth &amp; development/immunology/*virology ; }, abstract = {The emergence and rapid rise to dominance of Vibrio cholerae O139 in India and Bangladesh in 1992 led to the consideration that choleraphage might serve as both a selective mechanism and a means for horizontal transmission of genetic information. A filamentous phage '493' from O139 strain AJ27-493 has been purified and partially characterized. The phage was inactive on classical biotype V. cholerae O1 but it was active on El Tor biotype strains isolated prior to 1994 when El Tor re-emerged in Bangladesh. More recent El Tor isolates were all resistant to the phage. The phage was also active on O139 strains. Unlike the filamentous ctx phi, the receptor for 493 is not TcpA. The phage genome was a 9.3 kb closed circular single-stranded molecule containing a 0.4 kb double-stranded stem supporting a 2 kb single-stranded loop. A 283 bp fragment was cloned and used as a probe in Southern hybridization, in parallel with total phage 493 DNA. These probes hybridized both chromosomally and extrachromosomally with most O139 strains, but not with O1 strains. Infection of hybridization-negative El Tor or O139 strains resulted in the presence of hybridizing loci (both plasmid and chromosomal), in the appearance of an 18 kDa protein, and in marked alterations in colonial morphology. Phage 493 is clearly distinct from other O139 choleraphages which have been described. Phage 493 DNA hybridized with an encapsulated non-O1 (O31) strain (NRT36S) which was isolated before O139 was recognized. NRT36S also produces a phage which can infect El Tor strains with low efficiency. Further studies may reveal whether bacteriophage play a role in the emergence and the territoriality of new choleragenic vibrios.}, }
@article {pmid9452523, year = {1998}, author = {Jehle, JA and Nickel, A and Vlak, JM and Backhaus, H}, title = {Horizontal escape of the novel Tc1-like lepidopteran transposon TCp3.2 into Cydia pomonella granulovirus.}, journal = {Journal of molecular evolution}, volume = {46}, number = {2}, pages = {215-224}, doi = {10.1007/pl00006296}, pmid = {9452523}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Animals ; Baculoviridae/*genetics ; Base Sequence ; *DNA Transposable Elements ; DNA-Binding Proteins/genetics ; Frameshift Mutation ; Gene Transfer, Horizontal ; Lepidoptera/*genetics/*virology ; Molecular Sequence Data ; Mutation ; Nucleotidyltransferases/genetics ; Phylogeny ; Repetitive Sequences, Nucleic Acid ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; *Transposases ; }, abstract = {We characterized an insertion mutant of the baculovirus Cydia pomonella granulovirus (CpGV), which contained a transposable element of 3.2 kb. This transposon, termed TCp3.2, has unusually long inverted terminal repeats (ITRs) of 756 bp and encodes a defective gene for a putative transposase. Amino acid sequence comparison of the defective transposase gene revealed a distant relationship to a putative transposon in Caenorhabditis elegans which also shares some similarity of the ITRs. Maximum parsimony analysis of the predicted amino acid sequences of Tc1- and mariner-like transposases available from the GenBank data base grouped TCp3.2 within the superfamily of Tc1-like transposons. DNA hybridization indicated that TCp3.2 originated from the genome of Cydia pomonella, which is the natural host of CpGV, and is present in less than 10 copies in the C. pomonella genome. The transposon TCp3.2 most likely was inserted into the viral genome during infection of host larvae. TCp3.2 and the recently characterized Tc1-like transposon TC14.7 (Jehle et al. 1995), which was also found in a CpGV mutant, represent a new family of transposons found in baculovirus genomes. The occasional horizontal escape of different types of host transposons into baculovirus genomes evokes the question about the possible role of baculoviruses as an interspecies vector in the horizontal transmission of insect transposons.}, }
@article {pmid9468784, year = {1997}, author = {Koonin, EV and Galperin, MY}, title = {Prokaryotic genomes: the emerging paradigm of genome-based microbiology.}, journal = {Current opinion in genetics &amp; development}, volume = {7}, number = {6}, pages = {757-763}, doi = {10.1016/s0959-437x(97)80037-8}, pmid = {9468784}, issn = {0959-437X}, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; Conserved Sequence ; Databases, Factual ; Evolution, Molecular ; *Genes, Archaeal ; *Genome, Bacterial ; Phylogeny ; }, abstract = {Comparative analysis of the complete sequences of seven bacterial and three archaeal genomes leads to the first generalizations of emerging genome-based microbiology. Protein sequences are, generally, highly conserved, with -70% of the gene products in bacteria and archaea containing ancient conserved regions. In contrast, there is little conservation of genome organization, except for a few essential operons. The most striking conclusions derived by comparison of multiple genomes from phylogenetically distant species are that the number of universally conserved gene families is very small and that multiple events of horizontal gene transfer and genome fusion are major forces in evolution.}, }
@article {pmid9467914, year = {1998}, author = {Paoli, GC and Soyer, F and Shively, J and Tabita, FR}, title = {Rhodobacter capsulatus genes encoding form I ribulose-1,5-bisphosphate carboxylase/oxygenase (cbbLS) and neighbouring genes were acquired by a horizontal gene transfer.}, journal = {Microbiology (Reading, England)}, volume = {144 (Pt 1)}, number = {}, pages = {219-227}, doi = {10.1099/00221287-144-1-219}, pmid = {9467914}, issn = {1350-0872}, support = {GM24497/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Chromosome Mapping ; Gene Transfer, Horizontal ; Macromolecular Substances ; Molecular Sequence Data ; *Phylogeny ; Recombinant Proteins/biosynthesis/chemistry ; Restriction Mapping ; Rhodobacter capsulatus/*enzymology/*genetics ; Rhodobacter sphaeroides/chemistry/genetics ; Ribulose-Bisphosphate Carboxylase/*biosynthesis/chemistry/*genetics ; Sequence Alignment ; Sequence Homology ; Trans-Activators/biosynthesis/genetics ; Transcription, Genetic ; }, abstract = {Analysis of the nucleotide sequence of the form I ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) genes (cbbL and cbbS) of the non-sulfur purple bacterium Rhodobacter capsulatus indicated that the deduced amino acid sequence of the large subunit was not closely homologous to the large subunit from related organisms. Indeed, phylogenetic analysis suggested that the large subunit protein (CbbL) more closely resembled the enzyme from alpha/beta/gamma purple bacteria and cyanobacteria and is within a 'green-like' radiation of the RubisCO phylogenetic tree, well separated from CbbL of the related organism Rhodobacter sphaeroides. A cbbQ gene was discovered downstream of cbbS in Rh. capsulatus, a gene arrangement which also appears to be limited to certain organisms containing a 'green-like' RubisCO. Upstream, and divergently transcribed from cbbLSQ, is a gene (cbbRI) that encodes a LysR-type transcriptional activator. Phylogenetic analysis of the deduced amino acid sequence of CbbRI also suggests that this protein is quite distinct from the Rh. sphaeroides CbbR protein, and is even distinct from the previously described CbbRII protein, the gene of which is upstream and divergently transcribed from the cbbII operon of Rh. capsulatus. Interestingly, Rh. capsulatus CbbRI is more closely related to CbbR from bacteria whose RubisCO falls within the 'green-like' radiation of the CbbL tree. These studies suggest that the cbbRI-cbbL-cbbS-cbbQ genes were acquired by Rh. capsulatus via horizontal gene transfer from a bacterial species containing a 'green-like' RubisCO.}, }
@article {pmid9467904, year = {1998}, author = {Katerov, V and Andreev, A and Schalén, C and Totolian, AA}, title = {Protein F, a fibronectin-binding protein of Streptococcus pyogenes, also binds human fibrinogen: isolation of the protein and mapping of the binding region.}, journal = {Microbiology (Reading, England)}, volume = {144 (Pt 1)}, number = {}, pages = {119-126}, doi = {10.1099/00221287-144-1-119}, pmid = {9467904}, issn = {1350-0872}, mesh = {Adhesins, Bacterial/*genetics/*metabolism ; Base Sequence ; Binding Sites ; Cloning, Molecular ; DNA Primers ; Fibrinogen/*metabolism ; Fibronectins/metabolism ; Gene Library ; Humans ; Kinetics ; Molecular Sequence Data ; Polymerase Chain Reaction ; Recombinant Proteins/metabolism ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Streptococcus pyogenes/genetics/*physiology ; }, abstract = {During screening of a gene library of Streptococcus pyogenes type M15 for fibrinogen-binding material, a protein of approximately 100 kDa, encoded outside the vir region, was found. DNA sequencing revealed this component to be identical to protein F, a fibronectin-binding protein. Isolation of the recombinant protein, termed F15, was performed by the use of fibrinogen affinity chromatography. The affinity constant (Ka) of protein F15 for fibrinogen, 1.25 x 10(7) mol-1, was lower than that for fibronectin, 1.8 x 10(8) mol-1. The fibrinogen-binding domain was located in the N-terminal part of the molecule, while the fibronectin-binding domains, as previously determined, were in the C-terminal portion of protein F. To examine the amino acid sequence heterogeneity of protein F, the 5' part of the prtF gene, corresponding to the N-terminal variable region of the protein, was amplified by PCR from 12 strains of S. pyogenes belonging to six different M-types. Alignment of these nucleotide sequences indicated that the 5' portion of the prtF gene had probably undergone a number of intragenic recombination and horizontal gene transfer events, allowing a pattern of structural diversity of protein F observed earlier for some other streptococcal virulence factors. There was no strict correlation between M-type and nucleotide sequence of the variable region of the prtF gene and, compared to streptococcal M protein, the overall variation observed for protein F appeared more limited.}, }
@article {pmid9466754, year = {1998}, author = {Jensen, LB and Ahrens, P and Dons, L and Jones, RN and Hammerum, AM and Aarestrup, FM}, title = {Molecular analysis of Tn1546 in Enterococcus faecium isolated from animals and humans.}, journal = {Journal of clinical microbiology}, volume = {36}, number = {2}, pages = {437-442}, pmid = {9466754}, issn = {0095-1137}, mesh = {Animals ; Anti-Bacterial Agents/*therapeutic use ; Bacterial Proteins/genetics ; Carbon-Oxygen Ligases/genetics ; Chromosome Mapping ; DNA, Bacterial/*analysis/genetics ; Drug Resistance, Microbial/genetics ; Electrophoresis, Gel, Pulsed-Field ; Enterococcus faecium/*genetics ; Europe/epidemiology ; Gene Transfer, Horizontal ; Gram-Positive Bacterial Infections/*drug therapy/*epidemiology ; Humans ; Molecular Epidemiology ; Mutagenesis, Insertional ; Nucleic Acid Hybridization ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; *Serine-Type D-Ala-D-Ala Carboxypeptidase ; United States/epidemiology ; Vancomycin/*therapeutic use ; }, abstract = {The internal areas and the position of integration of the glycopeptide resistance element Tn1546 were characterized by using PCR fragment length polymorphism, sequencing, and DNA hybridization techniques with 38 high-level vancomycin-resistant Enterococcus faecium isolates of human and animal origins from Europe and the United States. Only minor variations in the coding regions within Tn1546 were found, suggesting high genetic stability. The isolates originated from broilers (n = 5), a chicken (n = 1), a duck (n = 1), a turkey (n = 1), pigs (n = 8), a pony (n = 1), and humans (n = 23). A total of 13 different types were defined based on a single-nucleotide difference in the vanX gene, the presence of insertion sequences, and hybridization patterns. For some types more than one isolate were found. For type 1, 10 isolates of both human and animal origins were found. All were indistinguishable from the reference strain, BM4147. For type 2, 11 isolates of human and animal origins were found. Six human isolates from England were all of type 3. Two human isolates from the United States, indistinguishable from each other, were type 9. These results showed that vancomycin-resistant E. faecium of animal and human origins can contain indistinguishable genetic elements coding for vancomycin resistance, indicating either horizontal gene transfer between E. faecium organisms of human and animal origins or the existence of a common reservoir for glycopeptide resistance.}, }
@article {pmid9391141, year = {1997}, author = {De Groote, MA and Ochsner, UA and Shiloh, MU and Nathan, C and McCord, JM and Dinauer, MC and Libby, SJ and Vazquez-Torres, A and Xu, Y and Fang, FC}, title = {Periplasmic superoxide dismutase protects Salmonella from products of phagocyte NADPH-oxidase and nitric oxide synthase.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {94}, number = {25}, pages = {13997-14001}, pmid = {9391141}, issn = {0027-8424}, support = {AI39557/AI/NIAID NIH HHS/United States ; AI01363/AI/NIAID NIH HHS/United States ; R01 AI039557/AI/NIAID NIH HHS/United States ; AI34397/AI/NIAID NIH HHS/United States ; T32 GM007739/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; DNA Primers/genetics ; In Vitro Techniques ; Macrophages, Peritoneal/metabolism ; Mice ; Mice, Inbred C3H ; Mice, Inbred C57BL ; Mice, Knockout ; Molecular Sequence Data ; Mutation ; NADPH Oxidases/*metabolism ; Nitric Oxide Synthase/*metabolism ; Phagocytes/*metabolism ; Polymerase Chain Reaction ; Reactive Oxygen Species/metabolism ; Respiratory Burst ; Salmonella Infections, Animal/metabolism ; Salmonella typhimurium/genetics/*metabolism/pathogenicity ; Superoxide Dismutase/genetics/*metabolism ; Virulence ; }, abstract = {Superoxide dismutase (SOD) catalyzes the conversion of superoxide radical to hydrogen peroxide. Periplasmic localization of bacterial Cu,Zn-SOD has suggested a role of this enzyme in defense against extracellular phagocyte-derived reactive oxygen species. Sequence analysis of regions flanking the Salmonella typhimurium sodC gene encoding Cu,Zn-SOD demonstrates significant homology to lambda phage proteins, reflecting possible bacteriophage-mediated horizontal gene transfer of this determinant among pathogenic bacteria. Salmonella deficient in Cu,Zn-SOD has reduced survival in macrophages and attenuated virulence in mice, which can be restored by abrogation of either the phagocyte respiratory burst or inducible nitric oxide synthase. Moreover, a sodC mutant is extremely susceptible to the combination of superoxide and nitric oxide. These observations suggest that SOD protects periplasmic or inner membrane targets by diverting superoxide and limiting peroxynitrite formation, and they demonstrate the ability of the respiratory burst and nitric oxide synthase to synergistically kill microbial pathogens in vivo.}, }
@article {pmid9422600, year = {1998}, author = {Martin, K and Morlin, G and Smith, A and Nordyke, A and Eisenstark, A and Golomb, M}, title = {The tryptophanase gene cluster of Haemophilus influenzae type b: evidence for horizontal gene transfer.}, journal = {Journal of bacteriology}, volume = {180}, number = {1}, pages = {107-118}, pmid = {9422600}, issn = {0021-9193}, support = {ESO4889/ES/NIEHS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Base Composition ; Base Sequence ; Cloning, Molecular ; DNA, Bacterial/chemistry/genetics ; Evolution, Molecular ; Genes, Bacterial/*genetics ; Haemophilus/enzymology ; Haemophilus influenzae type b/enzymology/*genetics/pathogenicity ; Indoles/analysis ; Molecular Sequence Data ; Multigene Family/*genetics ; Nucleic Acid Conformation ; Phylogeny ; Restriction Mapping ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Species Specificity ; Tryptophanase/*genetics/metabolism ; }, abstract = {Among strains of Haemophilus influenzae, the ability to catabolize tryptophan (as detected by indole production) varies and is correlated with pathogenicity. Tryptophan catabolism is widespread (70 to 75%) among harmless respiratory isolates but is nearly universal (94 to 100%) among strains causing serious disease, including meningitis. As a first step in investigating the relationship between tryptophan catabolism and virulence, we have identified genes in pathogenic H. influenzae which are homologous to the tryptophanase (tna) operon of Escherichia coli. The tna genes are located on a 3.1-kb fragment between nlpD and mutS in the H. influenzae type b (Eagan) genome, are flanked by 43-bp direct repeats of an uptake signal sequence downstream from nlpD, and appear to have been inserted as a mobile unit within this sequence. The organization of this insertion is reminiscent of pathogenicity islands. The tna cluster is found at the same map location in all indole-positive strains of H. influenzae surveyed and is absent from reference type d and e genomes. In contrast to H. influenzae, most other Haemophilus species lack tna genes. Phylogenetic comparisons suggest that the tna cluster was acquired by intergeneric lateral transfer, either by H. influenzae or a recent ancestor, and that E. coli may have acquired its tnaA gene from a related source. Genomes of virulent H. influenzae resemble those of pathogenic enterics in having an island of laterally transferred DNA next to mutS.}, }
@article {pmid9384377, year = {1997}, author = {Kunst, F and Ogasawara, N and Moszer, I and Albertini, AM and Alloni, G and Azevedo, V and Bertero, MG and Bessières, P and Bolotin, A and Borchert, S and Borriss, R and Boursier, L and Brans, A and Braun, M and Brignell, SC and Bron, S and Brouillet, S and Bruschi, CV and Caldwell, B and Capuano, V and Carter, NM and Choi, SK and Codani, JJ and Connerton, IF and Cummings, NJ and Daniel, RA and Denizot, F and Devine, KM and Düsterhöft, A and Ehrlich, SD and Emmerson, PT and Entian, KD and Errington, J and Fabret, C and Ferrari, E and Foulger, D and Fritz, C and Fujita, M and Fujita, Y and Fuma, S and Galizzi, A and Galleron, N and Ghim, SY and Glaser, P and Goffeau, A and Golightly, EJ and Grandi, G and Guiseppi, G and Guy, BJ and Haga, K and Haiech, J and Harwood, CR and Hènaut, A and Hilbert, H and Holsappel, S and Hosono, S and Hullo, MF and Itaya, M and Jones, L and Joris, B and Karamata, D and Kasahara, Y and Klaerr-Blanchard, M and Klein, C and Kobayashi, Y and Koetter, P and Koningstein, G and Krogh, S and Kumano, M and Kurita, K and Lapidus, A and Lardinois, S and Lauber, J and Lazarevic, V and Lee, SM and Levine, A and Liu, H and Masuda, S and Mauël, C and Médigue, C and Medina, N and Mellado, RP and Mizuno, M and Moestl, D and Nakai, S and Noback, M and Noone, D and O'Reilly, M and Ogawa, K and Ogiwara, A and Oudega, B and Park, SH and Parro, V and Pohl, TM and Portetelle, D and Porwollik, S and Prescott, AM and Presecan, E and Pujic, P and Purnelle, B and Rapoport, G and Rey, M and Reynolds, S and Rieger, M and Rivolta, C and Rocha, E and Roche, B and Rose, M and Sadaie, Y and Sato, T and Scanlan, E and Schleich, S and Schroeter, R and Scoffone, F and Sekiguchi, J and Sekowska, A and Seror, SJ and Serror, P and Shin, BS and Soldo, B and Sorokin, A and Tacconi, E and Takagi, T and Takahashi, H and Takemaru, K and Takeuchi, M and Tamakoshi, A and Tanaka, T and Terpstra, P and Tognoni, A and Tosato, V and Uchiyama, S and Vandenbol, M and Vannier, F and Vassarotti, A and Viari, A and Wambutt, R and Wedler, E and Wedler, H and Weitzenegger, T and Winters, P and Wipat, A and Yamamoto, H and Yamane, K and Yasumoto, K and Yata, K and Yoshida, K and Yoshikawa, HF and Zumstein, E and Yoshikawa, H and Danchin, A}, title = {The complete genome sequence of the gram-positive bacterium Bacillus subtilis.}, journal = {Nature}, volume = {390}, number = {6657}, pages = {249-256}, doi = {10.1038/36786}, pmid = {9384377}, issn = {0028-0836}, mesh = {Bacillus subtilis/*genetics/metabolism ; Bacterial Proteins/genetics ; Cloning, Organism ; DNA, Bacterial ; *Genome, Bacterial ; Molecular Sequence Data ; }, abstract = {Bacillus subtilis is the best-characterized member of the Gram-positive bacteria. Its genome of 4,214,810 base pairs comprises 4,100 protein-coding genes. Of these protein-coding genes, 53% are represented once, while a quarter of the genome corresponds to several gene families that have been greatly expanded by gene duplication, the largest family containing 77 putative ATP-binding transport proteins. In addition, a large proportion of the genetic capacity is devoted to the utilization of a variety of carbon sources, including many plant-derived molecules. The identification of five signal peptidase genes, as well as several genes for components of the secretion apparatus, is important given the capacity of Bacillus strains to secrete large amounts of industrially important enzymes. Many of the genes are involved in the synthesis of secondary metabolites, including antibiotics, that are more typically associated with Streptomyces species. The genome contains at least ten prophages or remnants of prophages, indicating that bacteriophage infection has played an important evolutionary role in horizontal gene transfer, in particular in the propagation of bacterial pathogenesis.}, }
@article {pmid9406411, year = {1997}, author = {Peters, M and Heinaru, E and Talpsep, E and Wand, H and Stottmeister, U and Heinaru, A and Nurk, A}, title = {Acquisition of a deliberately introduced phenol degradation operon, pheBA, by different indigenous Pseudomonas species.}, journal = {Applied and environmental microbiology}, volume = {63}, number = {12}, pages = {4899-4906}, pmid = {9406411}, issn = {0099-2240}, mesh = {Base Sequence ; Biodegradation, Environmental ; DNA, Bacterial/genetics ; Estonia ; Gene Transfer, Horizontal ; Genes, Bacterial ; Mixed Function Oxygenases/genetics/metabolism ; Molecular Sequence Data ; *Operon ; Phenol/*metabolism ; Plasmids/genetics ; Pseudomonas/*genetics/isolation &amp; purification/*metabolism ; Pseudomonas putida/genetics/metabolism ; Restriction Mapping ; Water Microbiology ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Horizontal transfer of genes of selective value in an environment 6 years after their introduction into a watershed has been observed. Expression of the gene pheA, which encodes phenol monooxygenase and is linked to the pheBA operon (A. Nurk, L. Kasak, and M. Kivisaar, Gene 102:13-18, 1991), allows pseudomonads to use phenol as a growth substrate. Pseudomonas putida strains carrying this operon on a plasmid were used for bioremediation after an accidental fire in the Estonia oil shale mine in Estonia in 1988. The water samples used for studying the fate of the genes introduced were collected in 1994. The same gene cluster was also detected in Pseudomonas strains isolated from water samples of a nearby watershed which has been continuously polluted with phenols due to oil shale industry leachate. Together with the more frequently existing counterparts of the dmp genes (V. Shingler, J. Powlowski, and U. Marklund, J. Bacteriol. 174:711-724, 1992), the pheA gene was also represented in the phenol-degrading strains. The area where the strains containing the pheA gene were found was restricted to the regular route of phenolic leachate to the Baltic Sea. Nine Pseudomonas strains belonging to four different species (P. corrugata, P. fragi, P. stutzeri, and P. fluorescens biotypes B, C, and F) and harboring horizontally transferred pheBA operons were investigated. The phe genes were clustered in the same manner in these nine phe operons and were connected to the same promoter as in the case of the original pheBA operon. One 10.6-kb plasmid carrying a pheBA gene cluster was sequenced, and the structure of the rearranged pheBA operon was described. This data indicates that introduced genetic material could, if it encodes a beneficial capability, enrich the natural genetic variety for biodegradation.}, }
@article {pmid9364907, year = {1997}, author = {Mergaert, P and Van Montagu, M and Holsters, M}, title = {Molecular mechanisms of Nod factor diversity.}, journal = {Molecular microbiology}, volume = {25}, number = {5}, pages = {811-817}, doi = {10.1111/j.1365-2958.1997.mmi526.x}, pmid = {9364907}, issn = {0950-382X}, mesh = {Evolution, Molecular ; Genes, Bacterial ; Genetic Variation ; Genotype ; Lipopolysaccharides/*biosynthesis/*chemistry ; Rhizobium/chemistry/classification/genetics ; }, abstract = {The rhizobia-legume symbiosis is highly specific. Major host specificity determinants are the bacterial Nod factor signals that trigger the nodulation programme in a compatible host. Nod factors are lipo-chitooligosaccharides (LCOs) varying in the oligosaccharide chain length, the nature of the fatty acids and substitutions on the oligosaccharide. The nod genotype of rhizobia, which forms the genetic basis for this structural variety, includes a set of nodulation genes encoding the enzymes that synthesize LCOs. Allelic and non-allelic variation in these genes ensures the synthesis of different LCO structures by the different rhizobia. The nod genotypes co-evolved with host plant divergence in contrast to the rhizobia, which followed a different evolution. Horizontal gene transfer probably played an important role during evolution of symbiosis. The nod genotypes are particularly well equipped for horizontal gene transfer because of their location on transmissible plasmids and/or on 'symbiosis islands', which are symbiotic regions associated with movable elements.}, }
@article {pmid9352910, year = {1997}, author = {Bobik, TA and Xu, Y and Jeter, RM and Otto, KE and Roth, JR}, title = {Propanediol utilization genes (pdu) of Salmonella typhimurium: three genes for the propanediol dehydratase.}, journal = {Journal of bacteriology}, volume = {179}, number = {21}, pages = {6633-6639}, pmid = {9352910}, issn = {0021-9193}, support = {GM34804/GM/NIGMS NIH HHS/United States ; GM49372/GM/NIGMS NIH HHS/United States ; }, mesh = {Cobamides ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genetic Complementation Test ; Genomic Library ; Hydro-Lyases/genetics ; Molecular Sequence Data ; Open Reading Frames ; Operon ; Propanediol Dehydratase/biosynthesis/*genetics ; Propylene Glycol/*metabolism ; Salmonella typhimurium/*genetics ; Sequence Analysis, DNA ; Sequence Homology ; Species Specificity ; }, abstract = {The propanediol utilization (pdu) operon of Salmonella typhimurium encodes proteins required for the catabolism of propanediol, including a coenzyme B12-dependent propanediol dehydratase. A clone that expresses propanediol dehydratase activity was isolated from a Salmonella genomic library. DNA sequence analysis showed that the clone included part of the pduF gene, the pduABCDE genes, and a long partial open reading frame (ORF1). The clone included 3.9 kbp of pdu DNA which had not been previously sequenced. Complementation and expression studies with subclones constructed via PCR showed that three genes (pduCDE) are necessary and sufficient for propanediol dehydratase activity. The function of ORF1 was not determined. Analyses showed that the S. typhimurium propanediol dehydratase was related to coenzyme B12-dependent glycerol dehydratases from Citrobacter freundii and Klebsiella pneumoniae. Unexpectedly, the S. typhimurium propanediol dehydratase was found to be 98% identical in amino acid sequence to the Klebsiella oxytoca propanediol dehydratase; this is a much higher identity than expected, given the relationship between these organisms. DNA sequence analyses also supported previous studies indicating that the pdu operon was inherited along with the adjacent cobalamin biosynthesis operon by a single horizontal gene transfer.}, }
@article {pmid9326365, year = {1997}, author = {Hanekamp, T and Kobayashi, D and Hayes, S and Stayton, MM}, title = {Avirulence gene D of Pseudomonas syringae pv. tomato may have undergone horizontal gene transfer.}, journal = {FEBS letters}, volume = {415}, number = {1}, pages = {40-44}, doi = {10.1016/s0014-5793(97)01089-2}, pmid = {9326365}, issn = {0014-5793}, mesh = {Bacterial Proteins/*genetics ; Blotting, Southern ; Conserved Sequence ; DNA Transposable Elements/*genetics ; Electrophoresis, Agar Gel ; Gene Dosage ; Gene Transfer, Horizontal ; Genes, Bacterial ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Pectobacterium carotovorum/genetics/pathogenicity ; Plant Diseases/microbiology ; Plasmids/*genetics ; Pseudomonas/*genetics/pathogenicity ; Sequence Analysis, DNA ; }, abstract = {Avirulence gene D (avrD) is carried on the B-plasmid of the plant pathogen Pseudomonas syringae pv. tomato with plasmid-borne avrD homologs widely distributed among the Pseudomonads. We now report sequences in the soft rot pathogen Erwinia carotovora that cross-hybridize to avrD suggesting a conserved function beyond avirulence. Alternatively, avrD may have been transferred horizontally among species: (i) DNA linked to avrD shows evidence of class II transpositions and contains a novel IS3-related insertion sequence, and (ii) short sequences linked to avrD are similar to pathogenicity genes from a variety of unrelated pathogens. We have also identified the gene cluster that controls B-plasmid stability.}, }
@article {pmid9376613, year = {1997}, author = {Blaser, MJ}, title = {The versatility of Helicobacter pylori in the adaptation to the human stomach.}, journal = {Journal of physiology and pharmacology : an official journal of the Polish Physiological Society}, volume = {48}, number = {3}, pages = {307-314}, pmid = {9376613}, issn = {0867-5910}, mesh = {Biological Evolution ; Gene Transfer, Horizontal ; Genes, Bacterial/physiology ; Helicobacter pylori/genetics/*pathogenicity/physiology ; Humans ; Hydrogen-Ion Concentration ; Stomach/*microbiology ; }, abstract = {A growing body of data indicates that H. pylori colonization of human is ancient, which is consistent with its high prevalence, chronicity of carriage, and generally low level of disease, which, when it occurs has only marginal or no effects on host reproductive capacity. All of these phenomena are markers for a relatively benign co-existence, which may include all of the entire spectrum of interactions from parasitism, through commensalism, to symbiosis. Recent studies suggest the emergence of "quasispecies" during prolonged colonization, and the presence of multiple strains colonizing individual hosts. Such observations suggest that concepts of competition between strains and mutualism will be important in understanding the ecology of colonization and its effects on hosts. The presence of particular pathologies in the host may in part be a function of the characteristics of the bacterial population present. At a genomic level, H. pylori appears to adapt to changing conditions by point mutation, genomic rearrangement, and horizontal gene transfer, the latter is favored by its natural competence. The ability of H. pylori to alter phenotypic properties including superficial Lewis antigen expression and secretion of proinflammatory molecules is evidence of its sensitivity to environmental signals from the host. In such a universe, disease outcomes such as ulceration or neoplasia may be considered as accidents secondary to microbial persistence.}, }
@article {pmid9294891, year = {1997}, author = {Lawrence, JG}, title = {Selfish operons and speciation by gene transfer.}, journal = {Trends in microbiology}, volume = {5}, number = {9}, pages = {355-359}, doi = {10.1016/S0966-842X(97)01110-4}, pmid = {9294891}, issn = {0966-842X}, mesh = {Bacteria/*genetics/*metabolism ; Gene Expression ; *Gene Transfer, Horizontal ; Genes, Bacterial/*physiology ; Multigene Family/physiology ; Operon/*physiology ; Species Specificity ; }, abstract = {Bacterial genes providing for single metabolic functions are found in operons, possibly because this organization allows efficient horizontal transfer among organisms. Transferred genes can confer novel metabolic phenotypes on their new hosts and allow rapid, effective exploitation of new environmental niches. Moreover, the mobility of selfish operons may facilitate bacterial speciation.}, }
@article {pmid9287428, year = {1997}, author = {Klotz, MG and Klassen, GR and Loewen, PC}, title = {Phylogenetic relationships among prokaryotic and eukaryotic catalases.}, journal = {Molecular biology and evolution}, volume = {14}, number = {9}, pages = {951-958}, doi = {10.1093/oxfordjournals.molbev.a025838}, pmid = {9287428}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Animals ; Bacteria/enzymology ; Base Composition ; Catalase/*genetics ; DNA/chemistry ; Fungi/enzymology ; Molecular Sequence Data ; Mutation/genetics ; *Phylogeny ; Plants/enzymology ; }, abstract = {Seventy-four catalase protein sequences, including 29 bacterial, 8 fungal, 7 animal, and 30 plant sequences, were compiled, and 70 were used for phylogenetic reconstruction. The core of the resulting tree revealed unique, separate groups of plant and animal catalases, two groups of fungal catalases, and three groups of bacterial catalases. The only overlap of kingdoms occurred within one branch and involved fungal and bacterial large-subunit enzymes. The other fungal branch was closely linked to the group of animal enzymes. Group I bacterial catalases were more closely related to the plant enzymes and contained such diverse taxa as the Gram-positive Listeria seeligeri, Deinocococcus radiodurans, and gamma-proteobacteria. Group III bacterial sequences were more closely related to fungal and animal sequences and included enzymes from a broad range of bacteria including high- and low-GC Gram positives, proteobacteria, and a bacteroides species. Group II was composed of large-subunit catalases from diverse sources including Gram positives (low-GC Bacilli and high-GC Mycobacteria), proteobacteria, and species of the filamentous fungus Aspergillus. These data can be interpreted in terms of two gene duplication events that produced a minimum of three catalase gene family members that subsequently evolved in response to environmental demands. Horizontal gene transfer may have been responsible for the group II mixture of bacterial and fungal large-subunit catalases.}, }
@article {pmid9305771, year = {1997}, author = {Cassier-Chauvat, C and Poncelet, M and Chauvat, F}, title = {Three insertion sequences from the cyanobacterium Synechocystis PCC6803 support the occurrence of horizontal DNA transfer among bacteria.}, journal = {Gene}, volume = {195}, number = {2}, pages = {257-266}, doi = {10.1016/s0378-1119(97)00165-0}, pmid = {9305771}, issn = {0378-1119}, mesh = {Amino Acid Sequence ; Base Sequence ; Cloning, Molecular ; Codon, Terminator ; Cyanobacteria/*genetics ; DNA Probes ; DNA Transposable Elements/*genetics ; DNA, Bacterial/*genetics ; Frameshifting, Ribosomal ; Gene Transfer, Horizontal ; Genome, Bacterial ; Molecular Sequence Data ; Mutagenesis, Insertional ; Nucleic Acid Hybridization ; Phylogeny ; Plasmids ; Repetitive Sequences, Nucleic Acid ; Sequence Alignment ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Transposases/genetics ; }, abstract = {Three insertion sequences were characterized from the widely-used cyanobacterium Synechocystis PCC6803. They all harbored a putative transposase sequence flanked by two imperfect inverted repeats, seemed to have duplicated their target insertion site and occurred as multiple copies in the host genome. They exhibited no obvious homology with any other cyanobacterial ISs and were termed IS5S (871 bp), IS4S (1299 bp) and ISS1987 (949 bp) because they were, respectively, homologous to IS5- and IS4-bacterial elements, and to several members of the IS630-Tc1-mariner superfamily of IS elements occurring in a wide range of hosts. This suggests that these IS-elements were spread through horizontal transfer between evolutionary distant organisms. Three IS5S-copies were isolated as a rescue insertion into a replicating plasmid (IS5Sa), or subsequently cloned from a Synechocystis DNA-library probed with IS5Sa (IS5Sb and IS5Sc), and appeared to be almost identical. In the vicinity of IS5Sb, we found the ISS1987 element inserted into the IS4S element. This indicates that the ISS1987 element has been, and could still be, mobile since its transposase sequence is not interrupted with stop codons or translational frameshifts, unlike that which is found in most members of the IS630-Tc1-mariner superfamily of transposable elements.}, }
@article {pmid9268169, year = {1997}, author = {Desiere, F and Lucchini, S and Bruttin, A and Zwahlen, MC and Brüssow, H}, title = {A highly conserved DNA replication module from Streptococcus thermophilus phages is similar in sequence and topology to a module from Lactococcus lactis phages.}, journal = {Virology}, volume = {234}, number = {2}, pages = {372-382}, doi = {10.1006/viro.1997.8643}, pmid = {9268169}, issn = {0042-6822}, mesh = {Amino Acid Sequence ; Bacteriophages/*genetics ; Base Sequence ; Conserved Sequence ; *DNA Replication ; *DNA, Viral ; Lactococcus lactis/*virology ; Molecular Sequence Data ; Sequence Alignment ; Sequence Analysis, DNA ; Streptococcus/*virology ; Virus Replication ; }, abstract = {A highly conserved DNA region extending over 5 kb was observed in Streptococcus thermophilus bacteriophages. Comparative sequencing of one temperate and 26 virulent phages demonstrated in the most extreme case an 18% aa difference for a predicted protein, while the majority of the phages showed fewer, if any aa changes. The relative degree of aa conservation was not homogeneous over the DNA segment investigated. Sequence analysis of the conserved segment revealed genes possibly involved in DNA transactions. Three predicted proteins (orf 233, 443, and 382 gene product (gp)) showed nucleoside triphosphate binding motifs. Orf 443 gp showed in addition a DEAH box motif, characteristically found in a subgroup of helicases, and a variant zinc finger motif known from a phage T7 helicase/primase. Tree analysis classified orf 443 gp as a distant member of the helicase superfamily. Orf 382 gp showed similarity to putative plasmid DNA primases. Downstream of orf 382 a noncoding repeat region was identified that showed similarity to a putative minus origin from a cryptic S. thermophilus plasmid. Four predicted proteins showed not only high degrees of aa identity (34 to 63%) with proteins from Lactococcus lactis phages, but their genes showed a similar topological organization. We interpret this as evidence for a horizontal gene transfer event between phages of the two bacterial genera in the distant past.}, }
@article {pmid9302012, year = {1997}, author = {Pölzleitner, E and Zechner, EL and Renner, W and Fratte, R and Jauk, B and Högenauer, G and Koraimann, G}, title = {TraM of plasmid R1 controls transfer gene expression as an integrated control element in a complex regulatory network.}, journal = {Molecular microbiology}, volume = {25}, number = {3}, pages = {495-507}, doi = {10.1046/j.1365-2958.1997.4831853.x}, pmid = {9302012}, issn = {0950-382X}, mesh = {Alleles ; Amino Acid Sequence ; Bacterial Proteins/*genetics ; Base Sequence ; *Conjugation, Genetic ; DNA Primers/genetics ; DNA, Bacterial/genetics ; Escherichia coli/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Complementation Test ; Models, Genetic ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Operon ; Phenotype ; Plasmids/*genetics ; RNA, Bacterial/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; }, abstract = {Site-directed mutagenesis was used to investigate the functions of the traM gene in plasmid R1-mediated bacterial conjugation. Three mutant alleles, a null mutation, a sense mutation and a stop mutation, were recombined back into the R1-16 plasmid, a transfer-derepressed (finO-) variant of plasmid R1. The frequency of conjugative transfer of the traM null mutant derivative of R1-16 was 10(7)-fold lower than that of the isogenic parent plasmid, showing the absolute requirement for this gene in conjugative transfer of plasmid R1. Measurements of the abundance of plasmid specified traJ, traA and traM mRNAs, TraM protein levels, and complementation studies indicated that the traM gene of plasmid R1 has at least two functions in conjugation: (i) positive control of transfer gene expression; and (ii) a function in a process distinct from gene expression. Since expression of the negatively autoregulated traM gene is itself affected positively by the expression of the transfer operon genes, this gene constitutes a decisive element within a regulatory circuit that co-ordinates expression of the genes necessary for horizontal DNA transfer. Based on our studies, we present a novel model for the regulation of the transfer genes of plasmid R1 that might also be applicable to other IncF plasmids.}, }
@article {pmid9263410, year = {1997}, author = {Bäumler, AJ}, title = {The record of horizontal gene transfer in Salmonella.}, journal = {Trends in microbiology}, volume = {5}, number = {8}, pages = {318-322}, doi = {10.1016/S0966-842X(97)01082-2}, pmid = {9263410}, issn = {0966-842X}, support = {1R29AI/DK40124-01A1/AI/NIAID NIH HHS/United States ; }, mesh = {Adaptation, Physiological ; Animals ; Biological Evolution ; Escherichia coli/genetics ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Phylogeny ; Salmonella/*genetics/pathogenicity ; Salmonella Infections/microbiology ; Virulence/genetics ; }, abstract = {The evolution of virulence in Salmonella is driven by horizontal gene transfer. This has given rise to highly flexible pathogens that are able to colonize new niches and extend their host range. Tracing the record of horizontal gene transfer can provide clues to the virulence factors that contribute to the formation of new pathovars.}, }
@article {pmid9214746, year = {1997}, author = {Cunningham, CW}, title = {Can three incongruence tests predict when data should be combined?.}, journal = {Molecular biology and evolution}, volume = {14}, number = {7}, pages = {733-740}, doi = {10.1093/oxfordjournals.molbev.a025813}, pmid = {9214746}, issn = {0737-4038}, mesh = {Animals ; Codon ; DNA, Mitochondrial/*genetics ; Genes ; Humans ; *Phylogeny ; Rodentia ; Sequence Analysis/*methods ; Statistics as Topic ; }, abstract = {Advocates of conditional combination have argued that testing for incongruence between data partitions is an important step in data exploration. Unless the partitions have had distinct histories, as in horizontal gene transfer, incongruence means that one or more data support the wrong phylogeny. This study examines the relationship between incongruence and phylogenetic accuracy using three tests of incongruence. These tests were applied to pairs of mitochondrial DNA data partitions from two well-corroborated vertebrate phylogenies. Of the three tests, the most useful was the incongruence length difference test (ILD, also called the partition homogeneity test). This test distinguished between cases in which combining the data generally improved phylogenetic accuracy (P > 0.01) and cases in which accuracy of the combined data suffered relative to the individual partitions (P < 0.001). In contrast, in several cases, the Templeton and Rodrigo tests detected highly significant incongruence (P < 0.001) even though combining the incongruent partitions actually increased phylogenetic accuracy. All three tests identified cases in which improving the reconstruction model would improve the phylogenetic accuracy of the individual partitions.}, }
@article {pmid9209030, year = {1997}, author = {Hurek, T and Egener, T and Reinhold-Hurek, B}, title = {Divergence in nitrogenases of Azoarcus spp., Proteobacteria of the beta subclass.}, journal = {Journal of bacteriology}, volume = {179}, number = {13}, pages = {4172-4178}, pmid = {9209030}, issn = {0021-9193}, mesh = {Gram-Negative Facultatively Anaerobic Rods/classification/*enzymology/genetics ; In Situ Hybridization, Fluorescence ; Molecular Sequence Data ; Nitrogenase/*genetics ; Oryza/microbiology ; *Oxidoreductases ; Phylogeny ; Plant Roots/microbiology ; Poaceae ; Transcription, Genetic ; }, abstract = {Nitrogenase is a functionally constant protein catalyzing N2 reduction, which is found in many phylogenetic lineages of Archaea and Bacteria. A phylogenetic analysis of nif genes may provide insights into the evolution of the bacterial genomes. Moreover, it may be used to study diazotrophic communities, when classical isolation techniques may fail to detect all contributing populations. Among six species of the genus Azoarcus, diazotrophic Proteobacteria of the beta subclass, the deduced amino acid sequences of nifH genes of two species were unusually divergent from each other. Nitrogenases of the "authentic" Azoarcus branch formed a monophyletic unit with those of gamma Proteobacteria, thus being in accordance with 16S ribosomal DNA phylogeny. The nitrogenase proteins of the two aberrant strains clustered within the alpha proteobacterial clade with rhizobial nitrogenases. This relationship was supported by bootstrap values of 87 to 98% obtained by various distance and maximum parsimony methods. Phylogenetic distances of NifH proteins indicate a possible lateral gene transfer of nif genes to Azoarcus from a common donor of the alpha subclass at the time of species diversification or several more recent, independent transfers. Application of the phylogenetic analysis to DNA isolated from environmental samples demonstrated novel habitats for Azoarcus: in guts of termites and rice grown in Japan, nifH genes belonging to the authentic Azoarcus branch were detected. This is the first evidence suggesting the occurrence of Azoarcus spp. in a plant other than its originally described host, Kallar grass. Moreover, evidence for expression of nif genes inside grass roots was obtained by in situ hybridization studies with antisense nifH probes.}, }
@article {pmid9229255, year = {1997}, author = {Rohde, K}, title = {The origins of parasitism in the platyhelminthes: a summary interpreted on the basis of recent literature.}, journal = {International journal for parasitology}, volume = {27}, number = {6}, pages = {739-746}, doi = {10.1016/s0020-7519(97)00014-3}, pmid = {9229255}, issn = {0020-7519}, mesh = {Animals ; Biological Evolution ; Female ; Fertility ; Host-Parasite Interactions ; Male ; Platyhelminths/anatomy &amp; histology/*physiology ; Reproduction ; Turbellaria/anatomy &amp; histology/physiology ; }, abstract = {A summary is given of the 4 contributions on the origins of parasitism in the Platyhelminthes. Recent ecological literature is used to interpret some of the findings. In particular, recent findings on rugged fitness landscapes, the increasing difficulty of long-jump adaptations, complexity catastrophes, and empty phenotypic space are discussed in order to find an explanation for the large number of Neodermata and the scarcity of parasitic turbellarians; it is concluded that evolutionary stasis of symbiotic turbellarians that are "trapped" in their particular niches is responsible for the small number of symbiotic species of turbellarians, rather than competitive exclusion by the numerous neodermatans. The earliest neodermatans were probably already dependent on the production of many offspring; hence the protoneodermatan was probably a species preadapted to parasitism by high fecundity. Monogenea produce few offspring in spite of their rich and secure food supply; the protomonogenean was either a species with a complex behaviour pattern for habitat selection or, alternatively, a species with high fecundity subsequently reduced to permit the evolution of more complex behaviour patterns (switch from r- to K-strategy). The finding that embryonic replacement of the epidermis is shared by several turbellarian groups, a developmental pattern possibly used and modified in the formation of the neodermis in the Neodermata, can be interpreted as supporting the views that Neodermata and turbellarians with epidermal replacement are all monophyletic, or alternatively, that a similar developmental pattern has arisen several times due to similar selection pressures. However, the possibility of horizontal character transfer should also be considered for explaining similar characters, including similar developmental patterns, in apparently not closely related groups. Horizontal gene transfer and principles for demonstrating horizontal character transfer are discussed.}, }
@article {pmid9212172, year = {1997}, author = {Celerin, M and Gilpin, AA and Dossantos, G and Laudenbach, DE and Clarke, MW and Beushausen, S}, title = {Kinesin light chain in a eubacterium.}, journal = {DNA and cell biology}, volume = {16}, number = {6}, pages = {787-795}, doi = {10.1089/dna.1997.16.787}, pmid = {9212172}, issn = {1044-5498}, mesh = {Amino Acid Sequence ; Blotting, Western ; Cloning, Molecular ; Cyanobacteria/*genetics ; Electrophoresis, Polyacrylamide Gel ; Kinesins ; Microtubule-Associated Proteins/*genetics ; Molecular Sequence Data ; Sequence Homology, Amino Acid ; }, abstract = {A eubacterial homolog of a kinesin light chain gene has been isolated and characterized from the cyanobacterium Plectonema boryanum. Although the eubacterial and eukaryotic kinesin light chains are highly similar in amino acid sequence, the eubacterial sequence differs in several distinguishing structural features, including the absence of a putative PEST domain and the presence of additional highly conserved imperfect tandem repeats. Two soluble kinesin light chain antigens have been identified from whole-cell lysates by immunoblot analysis. Attempts to identify a canonical kinesin heavy-chain gene or protein were unsuccessful, suggesting that a kinesin heavy chain may be absent or unnecessary for kinesin light-chain function in this eubacterium. Our findings establish that certain basal elements of eukaryotic cellular transport appear to be resident in eubacteria. We discuss the possibility that the eukaryotic kinesin light chain was acquired by lateral gene transfer.}, }
@article {pmid9172352, year = {1997}, author = {Herrick, JB and Stuart-Keil, KG and Ghiorse, WC and Madsen, EL}, title = {Natural horizontal transfer of a naphthalene dioxygenase gene between bacteria native to a coal tar-contaminated field site.}, journal = {Applied and environmental microbiology}, volume = {63}, number = {6}, pages = {2330-2337}, pmid = {9172352}, issn = {0099-2240}, mesh = {Alleles ; Bacteria/*enzymology/*genetics ; Base Sequence ; Biodegradation, Environmental ; Chromosome Mapping ; Coal Tar/*metabolism ; DNA Primers/genetics ; DNA Transposable Elements ; Dioxygenases ; Ecosystem ; Environmental Pollutants/*metabolism ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Genetic Variation ; Multienzyme Complexes/*genetics ; Oxygenases/*genetics ; Phylogeny ; Plasmids ; Pseudomonas putida/enzymology/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Homology, Nucleic Acid ; Soil Microbiology ; }, abstract = {Horizontal transfer of genes responsible for pollutant biodegradation may play a key role in the evolution of bacterial populations and the adaptation of microbial communities to environmental contaminants. However, field evidence for horizontal gene transfer between microorganisms has traditionally been very difficult to obtain. In this study, the sequences of the 16S rRNA and naphthalene dioxygenase iron-sulfur protein (nahAc) genes of nine naphthalene-degrading bacteria isolated from a coal tar waste-contaminated site, as well as a naphthalene-degrading bacterium from a contaminated site in Washington state and two archetypal naphthalene-degrading strains, were compared. Seven strains from the study site had a single nahAc allele, whereas the 16S rRNA gene sequences of the strains differed by as much as 7.9%. No nahAc alleles from the site were identical to those of the archetypal strains, although the predominant allele was closely related to that of Pseudomonas putida NCIB 9816-4, isolated in the British Isles. However, one site-derived nahAc allele was identical to that of the Washington state strain. Lack of phylogenetic congruence of the nahAc and 16S rRNA genes indicates that relatively recent in situ horizontal transfer of the nahAc gene has occurred, possibly as a direct or indirect consequence of pollutant contamination. Alkaline lysis plasmid preparations and pulsed-field gel electrophoresis have revealed the presence of plasmids ranging in size from 70 to 88 kb in all site isolates. Southern hybridizations with a 407-bp nahAc probe have suggested that the nahAc gene is plasmid borne in all the site isolates but one, a strain isolated from subsurface sediment 400 m upstream from the source of the other site isolates. In this strain and in the naphthalene-degrading strain from Washington state, nahAc appears to be chromosomally located. In addition, one site isolate may carry nahAc on both chromosome and plasmid. Within the group of bacteria with identical nahAc sequences the Southern hybridizations showed that the gene was distributed between plasmids of different sizes and a chromosome. This suggests that plasmid modification after transfer may have been effected by transposons. Horizontal transfer of catabolic genes may play a significant role in the acclimation of microbial communities to pollutants.}, }
@article {pmid9139898, year = {1997}, author = {Loessner, MJ and Maier, SK and Daubek-Puza, H and Wendlinger, G and Scherer, S}, title = {Three Bacillus cereus bacteriophage endolysins are unrelated but reveal high homology to cell wall hydrolases from different bacilli.}, journal = {Journal of bacteriology}, volume = {179}, number = {9}, pages = {2845-2851}, pmid = {9139898}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; Bacillus Phages/classification/*genetics ; Bacillus cereus/enzymology/*virology ; Carbohydrate Sequence ; Cell Wall/enzymology ; Cloning, Molecular ; Endopeptidases/*chemistry/*genetics/metabolism ; Escherichia coli ; Genes, Viral ; Hydrolases/*chemistry ; Molecular Sequence Data ; Oligosaccharides/chemistry/metabolism ; Recombinant Proteins/chemistry/isolation &amp; purification/metabolism ; Sequence Homology, Amino Acid ; Substrate Specificity ; }, abstract = {The ply genes encoding the endolysin proteins from Bacillus cereus phages Bastille, TP21, and 12826 were identified, cloned, and sequenced. The endolysins could be overproduced in Escherichia coli (up to 20% of total cellular protein), and the recombinant proteins were purified by a two-step chromatographical procedure. All three enzymes induced rapid and specific lysis of viable cells of several Bacillus species, with highest activity on B. cereus and B. thuringiensis. Ply12 and Ply21 were experimentally shown to be N-acetylmuramoyl-L-alanine amidases (EC 3.5.1.28). No apparent holin genes were found adjacent to the ply genes. However, Ply21 may be endowed with a signal peptide which could play a role in timing of cell lysis by the cytoplasmic phage endolysin. The individual lytic enzymes (PlyBa, 41.1 kDa; Ply21, 29.5 kDa, Ply12, 27.7 kDa) show remarkable heterogeneity, i.e., their amino acid sequences reveal only little homology. The N-terminal part of Ply21 was found to be almost identical to the catalytic domains of a Bacillus sp. cell wall hydrolase (CwlSP) and an autolysin of B. subtilis (CwlA). The C terminus of PlyBa contains a 77-amino-acid sequence repeat which is also homologous to the binding domain of CwlSP. Ply12 shows homology to the major autolysins from B. subtilis and E. coli. Comparison with database sequences indicated a modular organization of the phage lysis proteins where the enzymatic activity is located in the N-terminal region and the C-termini are responsible for specific recognition and binding of Bacillus peptidoglycan. We speculate that the close relationship of the phage enzymes and cell wall autolysins is based upon horizontal gene transfer among different Bacillus phages and their hosts.}, }
@article {pmid9167257, year = {1997}, author = {Osborn, AM and Bruce, KD and Strike, P and Ritchie, DA}, title = {Distribution, diversity and evolution of the bacterial mercury resistance (mer) operon.}, journal = {FEMS microbiology reviews}, volume = {19}, number = {4}, pages = {239-262}, doi = {10.1111/j.1574-6976.1997.tb00300.x}, pmid = {9167257}, issn = {0168-6445}, mesh = {*Biological Evolution ; DNA Transposable Elements ; Drug Resistance, Microbial ; Environmental Microbiology ; Gene Transfer, Horizontal ; Gram-Negative Bacteria/*genetics ; Gram-Positive Bacteria/*genetics ; Mercury/*pharmacology ; *Operon ; Oxidation-Reduction ; Species Specificity ; }, abstract = {Mercury and its compounds are distributed widely across the earth. Many of the chemical forms of mercury are toxic to all living organisms. However, bacteria have evolved mechanisms of resistance to several of these different chemical forms, and play a major role in the global cycling of mercury in the natural environment. Five mechanisms of resistance to mercury compounds have been identified, of which resistance to inorganic mercury (HgR) is the best understood, both in terms of the mechanisms of resistance to mercury and of resistance to heavy metals in general. Resistance to inorganic mercury is encoded by the genes of the mer operon, and can be located on transposons, plasmids and the bacterial chromosome. Such systems have a worldwide geographical distribution, and furthermore, are found across a wide range of both Gram-negative and Gram-positive bacteria from both natural and clinical environments. The presence of mer genes in bacteria from sediment cores suggest that mer is an ancient system. Analysis of DNA sequences from mer operons and genes has revealed genetic variation both in operon structure and between individual genes from different mer operons, whilst analysis of bacteria which are sensitive to inorganic mercury has identified a number of vestigial non-functional operons. It is hypothesised that mer, due to its ubiquity with respect to geographical location, environment and species range, is an ancient system, and that ancient bacteria carried genes conferring resistance to mercury in response to increased levels of mercury in natural environments, perhaps resulting from volcanic activity. Models for the evolution of both a basic mer operon and for the Tn21-related family of mer operons and transposons are suggested. The study of evolution in bacteria has recently become dominated by the generation of phylogenies based on 16S rRNA genes. However, it is important not to underestimate the roles of horizontal gene transfer and recombinational events in evolution. In this respect mer is a suitable system for evaluating phylogenetic methods which incorporate the effects of horizontal gene transfer. In addition, the mer operon provides a model system in the study of environmental microbiology which is useful both as an example of a genotype which is responsive to environmental pressures and as a generic tool for the development of new methodology for the analysis of bacterial communities in natural environments.}, }
@article {pmid9119489, year = {1997}, author = {Smith-Vaughan, HC and Sriprakash, KS and Mathews, JD and Kemp, DJ}, title = {Nonencapsulated Haemophilus influenzae in Aboriginal infants with otitis media: prolonged carriage of P2 porin variants and evidence for horizontal P2 gene transfer.}, journal = {Infection and immunity}, volume = {65}, number = {4}, pages = {1468-1474}, pmid = {9119489}, issn = {0019-9567}, mesh = {Amino Acid Sequence ; Australia/epidemiology ; Base Sequence ; Gene Transfer, Horizontal ; Haemophilus Infections/epidemiology/ethnology/*microbiology ; Haemophilus influenzae/*genetics ; Humans ; Infant ; Molecular Sequence Data ; Otitis Media/epidemiology/ethnology/*microbiology ; Porins/*genetics ; }, abstract = {Aboriginal infants in the Northern Territory of Australia experience recurrent otitis media from an early age. Nonencapsulated Haemophilus influenzae (NCHi) colonization of the nasopharynx initially occurs within weeks of birth, persists throughout infancy and most of childhood, and contributes to otitis media. We established previously that the high carriage rates of NCHi in these infants result from concurrent and successive colonization with multiple strains, with sequential elimination of dominant strains. We have now sequenced loops 4, 5, and 6 of the NCHi P2 porin gene and characterized several strains with prolonged carriage times. Furthermore, despite a wide diversity of P2 gene sequences, we have four examples of P2 gene identity for strains with different genetic backgrounds as characterized by PCR ribotyping and randomly amplified polymorphic DNA typing, which leads us to suggest that the P2 gene has been transferred between strains. We also discuss the possibility that the paradoxical observation of cocolonization and prolonged carriage of P2-identical strains is related to immune suppression or tolerance in the host.}, }
@article {pmid9079891, year = {1997}, author = {Hochhut, B and Jahreis, K and Lengeler, JW and Schmid, K}, title = {CTnscr94, a conjugative transposon found in enterobacteria.}, journal = {Journal of bacteriology}, volume = {179}, number = {7}, pages = {2097-2102}, pmid = {9079891}, issn = {0021-9193}, mesh = {Base Sequence ; Chromosome Mapping ; Chromosomes, Bacterial/genetics ; *Conjugation, Genetic ; *DNA Transposable Elements ; DNA, Bacterial/genetics ; Escherichia coli/*genetics ; Molecular Sequence Data ; Rec A Recombinases/metabolism ; Restriction Mapping ; Sucrose/*metabolism ; }, abstract = {Conjugational transposons are important for horizontal gene transfer in gram-positive and gram-negative bacteria, but have not been reported yet for enteric bacteria. Salmonella senftenberg 5494-57 has previously been shown to transfer by conjugation genes for a sucrose fermentation pathway which were located on a DNA element called scr-94. We report here that the corresponding scr genes for a phosphoenolpyruvate-dependent sucrose:phosphotransferase system and a sucrose metabolic pathway are located on a large (ca. 100 kb) conjugative transposon renamed CTnscr94. The self-transmissible element integrates at two specific attachment sites in a RecA-independent way into the chromosome of Escherichia coli K-12 strains. One site was identified within pheV, the structural gene for a tRNA(Phe). Sequencing of both ends of CTnscr94 revealed the presence of the 3' part of pheV on one end such that after integration of the element, a complete pheV gene is retained. CTnscr94 represents, to our knowledge, the first conjugational transposon found in enteric bacteria.}, }
@article {pmid9106216, year = {1997}, author = {Thumm, G and Götz, F}, title = {Studies on prolysostaphin processing and characterization of the lysostaphin immunity factor (Lif) of Staphylococcus simulans biovar staphylolyticus.}, journal = {Molecular microbiology}, volume = {23}, number = {6}, pages = {1251-1265}, doi = {10.1046/j.1365-2958.1997.2911657.x}, pmid = {9106216}, issn = {0950-382X}, mesh = {Amino Acid Sequence ; Bacterial Proteins/immunology/*physiology ; Chromosome Mapping ; Cysteine Endopeptidases/genetics/physiology ; Evolution, Molecular ; Lysostaphin/immunology/*metabolism ; Molecular Sequence Data ; Peptidoglycan/metabolism ; Protein Precursors/chemistry/*physiology ; Protein Processing, Post-Translational/*genetics/physiology ; RNA, Transfer, Ser/genetics/physiology ; Repetitive Sequences, Nucleic Acid/physiology ; Sequence Homology, Amino Acid ; Serine/metabolism ; Staphylococcus/*genetics/physiology ; }, abstract = {Lysostaphin is an extracellular glycylglycine endopeptidase produced by Staphylococcus simulans biovar staphylolyticus ATCC1362 that lyses staphylococcal cells by hydrolysing the polyglycine interpeptide bridges of the peptidoglycan. Renewed analysis of the sequence of the lysostaphin gene (lss), and the sequencing of the amino-terminus of purified prolysostaphin and of mature lysostaphin revealed that lysostaphin is organized as a preproprotein of 493 amino acids (aa), with a signal peptide consisting of 36 aa, a propeptide of 211 aa from which 195 aa are organized in 15 tandem repeats of 13 aa length, and a mature protein of 246 aa. Prolysostaphin is processed in the culture supernatant of S. simulans biovar staphylolyticus by an extracellular cysteine protease. Although prolysostaphin was staphylolytically active, the mature lysostaphin was about 4.5-fold more active. The controlled expression in Staphylococcus carnosus of lss and lss with deletions in the prepropeptide region indicated that the tandem repeats of the propeptide are not necessary for protein export or activation of Lss, but keep Lss in a less active state. Intracellularly expressed pro- and mature lysostaphin exert staphylolytic activity in cell-free extracts, but do not affect growth of the corresponding clones. We characterized a lysostaphin immunity factor gene (lif) which is located in the opposite direction to lss. The expression of lif in S. carnosus led to an increase in the serine/glycine ratio of the interpeptide bridges of peptidoglycan from 2 to 35%, suggesting that lysostaphin immunity depends on serine incorporation into the interpeptide bridge. If, in addition to lif, lss is co-expressed the serine/glycine ratio is further increased to 58%, suggesting that Lss selects for optimal serine incorporation. Lif shows similarity to FemA and FemB proteins, which are involved in the biosynthesis of the glycine interpeptide bridge of staphylococcal peptidoglycan. In contrast to that of Lif, the production of FemA and FemB in S. carnosus does not cause lysostaphin immunity. The putative tRNASer gene located downstream of lss had no recognizable influence on lysostaphin immunity. lss and lif are flanked by insertion sequences, suggesting that S. simulans biovar staphylolyticus received lif and lss by horizontal gene transfer.}, }
@article {pmid9106201, year = {1997}, author = {Hacker, J and Blum-Oehler, G and Mühldorfer, I and Tschäpe, H}, title = {Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution.}, journal = {Molecular microbiology}, volume = {23}, number = {6}, pages = {1089-1097}, doi = {10.1046/j.1365-2958.1997.3101672.x}, pmid = {9106201}, issn = {0950-382X}, mesh = {Biological Evolution ; Chromosomes/*genetics ; Genes, Bacterial ; Gram-Negative Bacteria/*genetics/pathogenicity ; Gram-Positive Bacteria/*genetics/pathogenicity ; Virulence/genetics/physiology ; }, abstract = {Virulence genes of pathogenic bacteria, which code for toxins, adhesins, invasins or other virulence factors, may be located on transmissible genetic elements such as transposons, plasmids or bacteriophages. In addition, such genes may be part of particular regions on the bacterial chromosomes, termed 'pathogenicity islands' (Pais). Pathogenicity islands are found in Gram-negative as well as in Gram-positive bacteria. They are present in the genome of pathogenic strains of a given species but absent or only rarely present in those of non-pathogenic variants of the same or related species. They comprise large DNA regions (up to 200 kb of DNA) and often carry more than one virulence gene, the G + C contents of which often differ from those of the remaining bacterial genome. In most cases, Pais are flanked by specific DNA sequences, such as direct repeats or insertion sequence (IS) elements. In addition, Pais of certain bacteria (e,g. uropathogenic Escherichia coli, Yersinia spp., Helicobacter pylori) have the tendency to delete with high frequencies or may undergo duplications and amplifications. Pais are often associated with tRNA loci, which may represent target sites for the chromosomal integration of these elements. Bacteriophage attachment sites and cryptic genes on Pais, which are homologous to phage integrase genes, plasmid origins of replication of IS elements, indicate that these particular genetic elements were previously able to spread among bacterial populations by horizontal gene transfer, a process known to contribute to microbial evolution.}, }
@article {pmid9055816, year = {1997}, author = {Achenbach, LA and Yang, W}, title = {The fur gene from Klebsiella pneumoniae: characterization, genomic organization and phylogenetic analysis.}, journal = {Gene}, volume = {185}, number = {2}, pages = {201-207}, doi = {10.1016/s0378-1119(96)00642-7}, pmid = {9055816}, issn = {0378-1119}, mesh = {Bacterial Proteins/biosynthesis/*genetics ; Cloning, Molecular ; Gene Expression Regulation, Bacterial ; Klebsiella pneumoniae/*genetics ; Molecular Sequence Data ; *Phylogeny ; Recombinant Proteins/biosynthesis/genetics ; Repressor Proteins/biosynthesis/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Transcription, Genetic ; }, abstract = {The Fur (ferric uptake regulator) protein controls the expression of a number of bacterial virulence determinants including those involved in iron uptake. The fur gene was cloned and characterized from Klebsiella pneumoniae. The gene is preceded by a single autoregulated promoter whose -10 region overlaps the putative Fur binding site. The autoregulated nature of the K. pneumoniae fur gene and functionality of the encoded Fur repressor were tested in Fur titration and complementation assays. A partial open reading frame upstream from the fur gene was identified as a flavodoxin (fldA) gene. An open reading frame located 50 bases downstream from the fur stop codon appears to be a truncated citA gene that, if functional, would encode only the carboxy terminus of a citrate utilization protein. The fldA-fur arrangement is also present in Escherichia coli. However, the fur-citA arrangement found in K. pneumoniae is novel. It appears that the chromosomal region downstream from the fur gene is unstable and, thus, variable even in closely related bacterial lineages. To assess of the ability of the Fur protein sequence to reflect organismal phylogeny, the Fur protein tree was compared to the tree of 16S rRNA (ribosomal RNA). The Fur dataset comprises almost an order of magnitude fewer characters than the 16S rRNA but is nonetheless able to track the phylogenetic signal reasonably well, suggesting that the fur gene, like the 16S rDNA, may not be subject to horizontal gene transfer in these bacteria.}, }
@article {pmid9041651, year = {1997}, author = {Ponting, CP}, title = {Evidence for PDZ domains in bacteria, yeast, and plants.}, journal = {Protein science : a publication of the Protein Society}, volume = {6}, number = {2}, pages = {464-468}, pmid = {9041651}, issn = {0961-8368}, mesh = {Amino Acid Sequence ; Bacterial Proteins/*chemistry/genetics ; Binding Sites ; Fungal Proteins/*chemistry/genetics ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Plant Proteins/*chemistry/genetics ; Sequence Homology, Amino Acid ; }, abstract = {Several dozen signaling proteins are now known to contain 80-100 residue repeats, called PDZ (or DHR or GLGF) domains, several of which interact with the C-terminal tetrapeptide motifs X-Ser/Thr-X-Val-COO- of ion channels and/or receptors. PDZ domains have previously been noted only in mammals, flies, and worms, suggesting that the primordial PDZ domain arose relatively late in eukaryotic evolution. Here, techniques of sequence analysis-including local alignment, profile, and motif database searches-indicate that PDZ domain homologues are present in yeast, plants, and bacteria. It is suggested that two PDZ domains occur in bacterial high-temperature requirement A (htrA) and one in tail-specific protease (tsp) homologues, and that a yeast htrA homologue contains four PDZ domains. Sequence comparisons suggest that the spread of PDZ domains in these diverse organisms may have occurred via horizontal gene transfer. The known affinity of Escherichia coli tsp for C-terminal polypeptides is proposed to be mediated by its PDZ-like domain, in a similar manner to the binding of C-terminal polypeptides by animal PDZ domains.}, }
@article {pmid9571701, year = {1997}, author = {Damian, RT}, title = {Parasite immune evasion and exploitation: reflections and projections.}, journal = {Parasitology}, volume = {115 Suppl}, number = {}, pages = {S169-75}, doi = {10.1017/s0031182097002357}, pmid = {9571701}, issn = {0031-1820}, mesh = {Animals ; Autoimmunity ; Biological Evolution ; Host-Parasite Interactions ; Humans ; Molecular Mimicry ; Parasites/genetics/*immunology/physiology ; Parasitic Diseases/*immunology/parasitology ; }, abstract = {Recent developments in parasite immune evasion and exploitation are reviewed with special reference to the papers presented in this volume. Parasites, broadly defined, of animals with good immune responses have evolved many strategies that adapt them to survive and reproduce. These strategies may be passive, or may involve active intervention with host immune regulation, and can be categorized as immune evasion, immune exploitation and molecular piracy. The concept of immune evasion began with Paul Ehrlich's demonstration of antigenic variation in African trypanosomes and was reinforced by later ideas on molecular mimicry. Molecular mimicry is updated in the light of recent discoveries about degeneracy and plasticity of TCR/MHC-peptide recognition. Possible connections between two of its postulated consequences, evasion and autoimmunity, are discussed. Another putative consequence of molecular mimicry, host antigenic polymorphism, is also updated. The concept of exploitation of host immune responses by parasites has been reinforced by new data on its first known examples, especially the immune dependence of schistosome egg excretion. Newer examples include use of host cytokines as parasite growth factors, virokines, viroreceptors and helminth pseudocytokines. Finally, questions of host gene capture by viruses and possible horizontal gene transfer between host and parasite mediated by retroviruses are examined. The latter is compared with molecular conservation as a source of molecular mimicry and other aspects of host--parasite coevolution.}, }
@article {pmid9440282, year = {1997}, author = {Quesneville, H and Anxolabéhère, D}, title = {A simulation of P element horizontal transfer in Drosophila.}, journal = {Genetica}, volume = {100}, number = {1-3}, pages = {295-307}, pmid = {9440282}, issn = {0016-6707}, mesh = {Animals ; *Computer Simulation ; DNA Transposable Elements/*genetics ; Drosophila/*genetics ; Female ; *Gene Transfer, Horizontal ; Genetics, Population ; *Genome ; Male ; *Models, Genetic ; Phylogeny ; }, abstract = {Experimental data suggest that the P transposable element has invaded the Drosophila melanogaster genome after a horizontal transfer from the phylogenetically distant species Drosophila willistoni. The differences between P element phylogeny and that of the Drosophila genus could in part be explained by horizontal transfers. In vivo experiments show that P elements are able to transpose in the genomes of other Drosophila species. This suggests that horizontal transmission of P elements could have taken place in many species of this genus. The regulation, transposition, and deleterious effects of the P element in D. melanogaster were formalized and integrated in a global model to produce a simulation program that simulates a P element invasion. The simulations show that our knowledge of the P element in D. melanogaster can explain its behavior in the Drosophila genus. The equilibrium state of the invaded population of a new species depends on its ability to repair damage caused by P element activity. If repair is efficient, the equilibrium state tends to be of the P type state, in which case the element could subsequently invade other populations of the species. Conversely, the equilibrium state is of the M' type state when the ability to repair damage is low. The invasion of the P element into other populations of this new species can then only occur by genetic drift and it is likely to be lost. The success of a P element invasion into a new species thus greatly depends on its ability to produce dysgenic crosses.}, }
@article {pmid9436316, year = {1997}, author = {Dowson, CG and Barcus, V and King, S and Pickerill, P and Whatmore, A and Yeo, M}, title = {Horizontal gene transfer and the evolution of resistance and virulence determinants in Streptococcus.}, journal = {Society for Applied Bacteriology symposium series}, volume = {26}, number = {}, pages = {42S-51S}, pmid = {9436316}, issn = {0300-9610}, mesh = {*Evolution, Molecular ; *Gene Transfer, Horizontal ; Streptococcus/*genetics/*pathogenicity ; Streptococcus pneumoniae/genetics/pathogenicity ; Streptococcus pyogenes/genetics/pathogenicity ; Virulence/genetics ; beta-Lactam Resistance/*genetics ; }, }
@article {pmid8990281, year = {1997}, author = {Bäumler, AJ and Gilde, AJ and Tsolis, RM and van der Velden, AW and Ahmer, BM and Heffron, F}, title = {Contribution of horizontal gene transfer and deletion events to development of distinctive patterns of fimbrial operons during evolution of Salmonella serotypes.}, journal = {Journal of bacteriology}, volume = {179}, number = {2}, pages = {317-322}, pmid = {8990281}, issn = {0021-9193}, mesh = {Chromosomes, Bacterial ; Escherichia coli/genetics ; Evolution, Molecular ; Fimbriae, Bacterial/*genetics ; Gene Deletion ; *Operon ; Phylogeny ; Salmonella/classification/*genetics ; Salmonella typhimurium/genetics ; Sequence Homology, Nucleic Acid ; Serotyping ; }, abstract = {Only certain serotypes of Salmonella represent 99% of all human clinical isolates. We determined whether the phylogenetic distribution of fimbrial operons would account for the host adaptations observed for Salmonella serotypes. We found that three fimbrial operons, fim, lpf, and agf, were present in a lineage ancestral to Salmonella. While the fim and agf fimbrial operons were highly conserved among all Salmonella serotypes, sequence analysis suggested that the lpf operon was lost from many distantly related lineages. As a consequence, the distribution of the lpf operon cannot be explained easily and may be a consequence of positive and negative selection in different hosts for the presence of these genes. Two other fimbrial operons, sef and pef, each entered two distantly related Salmonella lineages and each is present only in a small number of serotypes. These results show that horizontal gene transfer and deletion events have created unique combinations of fimbrial operons among Salmonella serotypes. The presence of sef and pef correlated with serotypes frequently isolated from common domesticated animals.}, }
@article {pmid8971003, year = {1996}, author = {Yu, DC and Wang, AL and Wang, CC}, title = {Amplification, expression, and packaging of a foreign gene by giardiavirus in Giardia lamblia.}, journal = {Journal of virology}, volume = {70}, number = {12}, pages = {8752-8757}, pmid = {8971003}, issn = {0022-538X}, support = {AI-30475/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; DNA, Viral ; Gene Amplification ; Gene Expression ; *Gene Transfer Techniques ; *Genes, Reporter ; Giardia lamblia/*metabolism/virology ; Giardiavirus/*genetics/physiology ; Luciferases/*genetics ; Molecular Sequence Data ; Recombination, Genetic ; Virus Assembly ; }, abstract = {Giardia lamblia is an intestinal protozoan parasite and one of the earliest eukaryotic divergents. The trophozoite multiplies via asexual binary fission and lacks all natural means of lateral gene transfer. A system is developed here for long-term expression of a foreign gene in this organism by exploiting recombinant virions derived from the giardiavirus (GLV), a double-stranded RNA virus that infects many Giardia isolates. An in vitro transcript of the cloned GLV cDNA, comprising the firefly luciferase-encoding region flanked by 5' and 3' fragments of GLV positive-strand RNA, was electroporated into GLV-infected trophozoites. Luciferase activity in electroporated cells peaked on day 2 at levels 6 orders of magnitude above background. Expression of this foreign gene remained at 80% of its peak level after 30 days in the absence of selective pressure. The chimeric RNA was replicated as double-stranded RNA and packaged into virus-like particles. The recombinant virions were partially purified from the wild-type helper virus by CsCl equilibrium density-gradient centrifugation and used to superinfect Giardia trophozoites. At multiplicities of infection of 100 or higher, these chimeric virions were able to initiate new rounds of expression of luciferase activity in the superinfected cells. Thus, the engineered virion can be successfully used to introduce and efficiently express a heterologous gene in this eukaryotic microorganism.}, }
@article {pmid8940423, year = {1996}, author = {Bertin, Y and Martin, C and Oswald, E and Girardeau, JP}, title = {Rapid and specific detection of F17-related pilin and adhesin genes in diarrheic and septicemic Escherichia coli strains by multiplex PCR.}, journal = {Journal of clinical microbiology}, volume = {34}, number = {12}, pages = {2921-2928}, pmid = {8940423}, issn = {0095-1137}, mesh = {Adhesins, Bacterial/*genetics ; Animals ; Bacteremia/microbiology/veterinary ; Bacterial Outer Membrane Proteins/*genetics ; Bacteriological Techniques ; Base Sequence ; Cattle ; Cattle Diseases/microbiology ; DNA Primers/genetics ; Diarrhea/microbiology/veterinary ; Escherichia coli/*genetics/isolation &amp; purification/pathogenicity ; Escherichia coli Infections/microbiology/veterinary ; Fimbriae Proteins ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Multigene Family ; Operon ; Phenotype ; Polymerase Chain Reaction/methods ; Sheep ; Sheep Diseases/microbiology ; Species Specificity ; }, abstract = {The F17-related adhesins are prevalent in Escherichia coli strains isolated from calves with diarrhea or septicemia and from lambs with nephropathy. The F17 family includes the F17a, F17b, F17c, and F111 fimbriae produced by bovine E. coli strains and the G agglutinin produced by human uropathogenic E. coli strains. An easy and inexpensive multiplex PCR method was developed to detect all the F17-related fimbriae and to identify four subtypes of structural subunit genes and two distinct subfamilies of adhesin genes by only two runs of amplification. A strict correlation was observed between the phenotypic assays and the multiplex PCR method when 166 pathogenic E. coli strains isolated from intestinal content of calves or lambs were tested. Genes encoding the F17c structural subunit and the subfamily II adhesins were prominent among the bovine and ovine isolates, and the capsule-like CS31A antigen was strictly associated with the F17c fimbriae. The F17b subtype fimbriae were prominent among the bovine isolates producing the CNF2 toxin, whereas the F17a subtype fimbriae were associated with the bovine isolates producing neither the CS31A antigen nor the CNF2 toxin. Five bacterial strains possessed two distinct and complete F17-related fimbrial gene clusters, and two of them produced two F17-related fimbriae at the bacterial cell surface. The related fimbrial gene clusters are probably organized in mosaic operons consisting of F17-related pilin and adhesin genes, and horizontal gene transfer may occur among E. coli strains isolated form different animal species.}, }
@article {pmid8945506, year = {1996}, author = {Mel, SF and Mekalanos, JJ}, title = {Modulation of horizontal gene transfer in pathogenic bacteria by in vivo signals.}, journal = {Cell}, volume = {87}, number = {5}, pages = {795-798}, doi = {10.1016/s0092-8674(00)81986-8}, pmid = {8945506}, issn = {0092-8674}, mesh = {*Bacterial Physiological Phenomena ; Conjugation, Genetic/*physiology ; Genes, Bacterial/*physiology ; }, }
@article {pmid8950813, year = {1996}, author = {Kehoe, MA and Kapur, V and Whatmore, AM and Musser, JM}, title = {Horizontal gene transfer among group A streptococci: implications for pathogenesis and epidemiology.}, journal = {Trends in microbiology}, volume = {4}, number = {11}, pages = {436-443}, doi = {10.1016/0966-842x(96)10058-5}, pmid = {8950813}, issn = {0966-842X}, support = {AI-33119/AI/NIAID NIH HHS/United States ; }, mesh = {*Antigens, Bacterial ; *Bacterial Outer Membrane Proteins ; Bacterial Proteins/genetics ; Base Sequence ; *Carrier Proteins ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Genetic Heterogeneity ; Molecular Sequence Data ; Recombination, Genetic ; Streptococcal Infections/*epidemiology/*etiology ; Streptococcus pyogenes/classification/*genetics/pathogenicity ; Virulence/genetics ; }, abstract = {Recent studies have revealed that there is considerable genetic diversity among the group A streptococci and that horizontal transfer and recombination of virulence genes have played a major role in generating this diversity. This finding has significant implications for our understanding of the epidemiology and pathogenesis of these common and highly versatile human pathogens.}, }
@article {pmid8875859, year = {1996}, author = {Katz, LA}, title = {Transkingdom transfer of the phosphoglucose isomerase gene.}, journal = {Journal of molecular evolution}, volume = {43}, number = {5}, pages = {453-459}, pmid = {8875859}, issn = {0022-2844}, mesh = {Animal Population Groups/genetics ; Animals ; Bacteria/enzymology/*genetics ; Genes/*genetics ; Glucose-6-Phosphate Isomerase/*genetics ; *Phylogeny ; Plants/enzymology/genetics ; Saccharomycetales/enzymology/genetics ; Sequence Homology, Amino Acid ; }, abstract = {Previous analysis of the gene encoding phosphoglucose isomerase (Pgi) suggests that this gene may have been transferred between a eukaryote and a bacterium. However, excluding the alternative hypothesis of ancient gene duplication has proven difficult because of both insufficient sampling of taxa and an earlier misidentification of a bacterial Pgi sequence. This paper presents a phylogenetic analysis of published complete Pgi sequences together with analysis of new partial Pgi sequences from six species of bacteria. The data identify a group of bacterial Pgi sequences, including sequences from Escherichia coli and Haemophilus influenzae, which are more closely related to eukaryotic Pgi sequences than to other bacterial sequences. The topology of gene trees constructed using several different methods are all consistent with the hypothesis of lateral gene transfer and not ancient gene duplication. Furthermore, an estimate of a molecular clock for Pgi dates the divergence of the E. coli and H. influenzae sequences from the animal sequences to between 470 and 650 million years ago, well after other estimates of the divergence between eukaryotes and bacteria. This study provides the most convincing evidence to date of the transkingdom transfer of a nuclear gene.}, }
@article {pmid8930656, year = {1996}, author = {Bielicki, J and Hopwood, JJ and Anson, DS}, title = {Correction of Sanfilippo A skin fibroblasts by retroviral vector-mediated gene transfer.}, journal = {Human gene therapy}, volume = {7}, number = {16}, pages = {1965-1970}, doi = {10.1089/hum.1996.7.16-1965}, pmid = {8930656}, issn = {1043-0342}, mesh = {3T3 Cells ; Animals ; Cell Line ; Fibroblasts/cytology/*metabolism ; *Gene Transfer, Horizontal ; *Genetic Vectors ; Glycosaminoglycans/metabolism ; Hydrolases/*genetics ; Mice ; Moloney murine leukemia virus/*genetics ; Mucopolysaccharidosis III/therapy ; Skin/cytology ; Transfection ; }, abstract = {The recent cloning of the sulfamidase gene has made possible the consideration of gene-based therapies for Sanfilippo A syndrome (mucopolysaccharidosis type IIIA), one of the most common of the mucopolysaccharidoses. In this paper, we present the construction of a retroviral vector in which a sulfamidase cDNA is under the transcriptional control of the Moloney murine leukemia virus long terminal repeat. This construct was used to make a high-titer (4 x 10(5) colony-forming units/ml) producer cell line, PA317/LNSSN#19, in the amphotropic packaging cell line PA317. This producer cell line was shown to be helper virus free using an assay for horizontal spread of virus. Virus supernatant from PA317/LNSSN#19 was used to transduce Sanfilippo A fibroblasts, resulting in complete correction of both the enzymatic defect and the storage phenotype as assessed by intracellular accumulation of 35SO4(-)-labeled material. Phenotypic correction was seen even when the levels of viral transduction were low. These results show that gene therapy of the Sanfilippo A syndrome is practicable, although the nature of the disorder suggests that careful consideration needs to be given to the choice of the cellular target for gene transfer.}, }
@article {pmid8930906, year = {1996}, author = {Strätz, M and Mau, M and Timmis, KN}, title = {System to study horizontal gene exchange among microorganisms without cultivation of recipients.}, journal = {Molecular microbiology}, volume = {22}, number = {2}, pages = {207-215}, doi = {10.1046/j.1365-2958.1996.00099.x}, pmid = {8930906}, issn = {0950-382X}, mesh = {Acinetobacter/*genetics ; Bacillus subtilis/genetics ; Gene Transfer, Horizontal ; Genetic Markers ; Molecular Sequence Data ; Polymerase Chain Reaction ; RNA, Bacterial/genetics ; RNA, Ribosomal, 23S/*genetics ; *Recombination, Genetic ; *Transformation, Bacterial ; *rRNA Operon ; }, abstract = {Ribosomal RNA genes are characterized by highly conserved sequences and are present in multiple copies in most prokaryotic chromosomes. In principle, therefore, they might serve as sites for homologous recombination between unrelated microorganisms. Plasmids containing 23S ribosomal gene sequences, from different bacteria, which had been interrupted by insertion of a kanamycin-resistance gene, were used to transform Acinetobacter sp. DSM587 (former name: Acinetobacter calcoaceticus BD413-ivl10). In all cases, homologies between the 23S rRNA genes of phylogenetically distant bacteria and Acinetobacter sp. DSM587 were sufficient for replacement recombination events. The integration events, resulting in inactivation of any one of the seven rrn operons of Acinetobacter sp. DSM587, had no observable influence on cell growth. These results suggest the possibility of rRNA genes serving as natural vehicles for horizontal gene transfer. They also provide the basis of a novel strategy to analyse gene transfer without selection or cultivation of recipient cells. Because of the highly conserved structure of bacterial rrn operons, recombination events subsequent to gene transfer can be readily identified by polymerase chain reaction amplification of the recombinant sequence using a universal forward primer for the 16S rRNA gene and a reverse primer specific for the integrated marker gene.}, }
@article {pmid8885390, year = {1996}, author = {Coffey, TJ and Berrón, S and Daniels, M and Garcia-Leoni, ME and Cercenado, E and Bouza, E and Fenoll, A and Spratt, BG}, title = {Multiply antibiotic-resistant Streptococcus pneumoniae recovered from Spanish hospitals (1988-1994): novel major clones of serotypes 14, 19F and 15F.}, journal = {Microbiology (Reading, England)}, volume = {142 (Pt 10)}, number = {}, pages = {2747-2757}, doi = {10.1099/13500872-142-10-2747}, pmid = {8885390}, issn = {1350-0872}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {*Bacterial Proteins ; Carrier Proteins/genetics ; Chloramphenicol Resistance ; *DNA Fingerprinting ; Drug Resistance, Multiple/*genetics ; Genes, Bacterial/genetics ; Hexosyltransferases/genetics ; Hospitals ; Humans ; Molecular Epidemiology ; Multienzyme Complexes/genetics ; Muramoylpentapeptide Carboxypeptidase/genetics ; Penicillin Resistance/genetics ; Penicillin-Binding Proteins ; Peptidyl Transferases/genetics ; Pneumococcal Infections/epidemiology/*microbiology ; Sequence Analysis, DNA ; Serotyping ; Spain/epidemiology ; Streptococcus pneumoniae/classification/*drug effects/enzymology/*genetics/isolation &amp; purification ; Tetracycline Resistance ; }, abstract = {We analysed a collection of 95 multiply antibiotic-resistant pneumococci, recovered since 1988 from 14 Spanish hospitals, that have MICs > or = 0.25 microgram benzylpenicillin ml-1. The majority of the isolates were of serogroups 14, 23, 6, 19 and 15, which are currently the serogroups mainly associated with multiresistance in Spain. All of the serogroup 23 isolates were members of the major Spanish serotype 23F multiresistant clone. Similarly, most of the serogroup 6 isolates were members of the major multiresistant serotype 6B clone, or variants of this clone. Eighteen of the 24 isolates of serogroup 19 were members of a highly penicillin-resistant clone that appears to be a serotype 19F variant of the major Spanish serotype 23F multiresistant clone. Eighteen of the 25 isolates of serotype 14 were members of a previously uncharacterized highly penicillin-resistant clone. Thirteen of the 16 isolates of serogroup 15 were members of a single previously unreported clone of serotype 15F that had moderate levels of resistance to penicillin. Approximately 65% of the multiresistant pneumococci that are currently circulating in Spain were members of the three new clones of serotype 14, 15F and 19F that we describe here, or the previously described serotype 6B and 23F clones. The other 35% of isolates were minor variants of the major clones, unrelated minor clones, and unique isolates, many of which appeared to have arisen by horizontal gene transfer events.}, }
@article {pmid8795193, year = {1996}, author = {O'Connor, L and Coffey, A and Daly, C and Fitzgerald, GF}, title = {AbiG, a genotypically novel abortive infection mechanism encoded by plasmid pCI750 of Lactococcus lactis subsp. cremoris UC653.}, journal = {Applied and environmental microbiology}, volume = {62}, number = {9}, pages = {3075-3082}, pmid = {8795193}, issn = {0099-2240}, mesh = {Amino Acid Sequence ; Base Sequence ; Cloning, Molecular ; *Genes, Bacterial ; Genotype ; Lactococcus lactis/*genetics ; Molecular Sequence Data ; *Plasmids ; Protein Biosynthesis ; Sequence Homology, Nucleic Acid ; Transcription, Genetic ; }, abstract = {AbiG is an abortive infection (Abi) mechanism encoded by the conjugative plasmid pCI750 originally isolated from Lactococcus lactis subsp. cremoris UC653. Insensitivity conferred by this Abi manifested itself as complete resistance to phi 712 (936 phage species) with only partial resistance to phi c2 (c2 species). The mechanism did not inhibit phage DNA replication. The smallest subclone of pCI750 which expressed the Abi phenotype contained a 3.5-kb insert which encoded two potential open reading frames. abiGi (750 bp) and abiGii (1,194 bp) were separated by 2 bp and appeared to share a single promoter upstream of abiGi. These open reading frames showed no significant homology to sequences of either the DNA or protein databases; however, they did exhibit the typical low G+C content (29 and 27%, respectively) characteristic of lactococcal abi genes. In fact, the G+C content of a 7.0-kb fragment incorporating the abiG locus was 30%, which may suggest horizontal gene transfer from a species of low G+C content. In this context, it is notable that remnants of IS elements were observed throughout this 7.0-kb region.}, }
@article {pmid8964566, year = {1996}, author = {Nakayama, K}, title = {[Dynamics of pathogenic genes of bacteria: horizontal gene transfer and and gene conversion].}, journal = {Fukuoka igaku zasshi = Hukuoka acta medica}, volume = {87}, number = {8}, pages = {173-177}, pmid = {8964566}, issn = {0016-254X}, mesh = {Bacteria/*genetics/*pathogenicity ; DNA, Bacterial ; Endopeptidases/genetics ; *Gene Conversion ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Porphyromonas gingivalis/enzymology/genetics ; }, }
@article {pmid8844169, year = {1996}, author = {Lawrence, JG and Roth, JR}, title = {Selfish operons: horizontal transfer may drive the evolution of gene clusters.}, journal = {Genetics}, volume = {143}, number = {4}, pages = {1843-1860}, pmid = {8844169}, issn = {0016-6731}, support = {6M-15868//PHS HHS/United States ; 6M-34804//PHS HHS/United States ; }, mesh = {Alleles ; Bacteria/*genetics ; Bacteriophages/genetics ; *Biological Evolution ; DNA, Bacterial/genetics ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genes, Viral ; Genetic Linkage ; *Models, Genetic ; Molecular Sequence Data ; *Multigene Family ; *Operon ; Recombination, Genetic ; Salmonella typhimurium/genetics ; }, abstract = {A model is presented whereby the formation of gene clusters in bacteria is mediated by transfer of DNA within and among taxa. Bacterial operons are typically composed of genes whose products contribute to a single function. If this function is subject to weak selection or to long periods with no selection, the contributing genes may accumulate mutations and be lost by genetic drift. From a cell's perspective, once several genes are lost, the function can be restored only if all missing genes were acquired simultaneously by lateral transfer. The probability of transfer of multiple genes increases when genes are physically proximate. From a gene's perspective horizontal transfer provides a way to escape evolutionary loss by allowing colonization of organisms lacking the encoded functions. Since organism bearing clustered genes are more likely to act as successful donors, clustered genes would spread among bacterial genomes. The physical proximity of genes may be considered a selfish property of the operon since it affects the probability of successful horizontal transfer but may provide no physiological benefit to the host. This process predicts a mosaic structure of modern genomes in which ancestral chromosomal material is interspersed with novel, horizontally transferred operons providing peripheral metabolic functions.}, }
@article {pmid8998942, year = {1996}, author = {Tschäpe, H}, title = {[The distribution of antibiotically-resistant organisms in the environment with special attention to salmonellae].}, journal = {DTW. Deutsche tierarztliche Wochenschrift}, volume = {103}, number = {7}, pages = {273-277}, pmid = {8998942}, issn = {0341-6593}, mesh = {Animals ; Bacteria/*drug effects/genetics/growth &amp; development ; Drug Resistance, Microbial/genetics ; *Environmental Microbiology ; Gene Transfer, Horizontal ; Humans ; Salmonella/*drug effects/genetics/growth &amp; development ; Streptothricins/pharmacology ; }, abstract = {Antibiotic resistant determinants (R) prevail in environmental bacteria independent of antibiotic application in human and veterinary medicine als well as in agriculture. Due to horizontal gene transfer (plasmids) the spread of R. determinants to pathogenic bacteria occur in relation to selection pressure. Since salmonella bacteria have been found to persist in environmental habitats for a long time they will serve as recipients as a reservoir (donors).}, }
@article {pmid8858584, year = {1996}, author = {Jaenecke, S and de Lorenzo, V and Timmis, KN and Díaz, E}, title = {A stringently controlled expression system for analysing lateral gene transfer between bacteria.}, journal = {Molecular microbiology}, volume = {21}, number = {2}, pages = {293-300}, doi = {10.1046/j.1365-2958.1996.6411358.x}, pmid = {8858584}, issn = {0950-382X}, mesh = {Bacteria/*genetics ; Base Sequence ; Conjugation, Genetic ; DNA, Bacterial/genetics ; Escherichia coli/genetics ; Gene Expression ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genes, Reporter ; Lac Operon ; Phenotype ; Plasmids/genetics ; Pseudomonas putida/genetics ; }, abstract = {The lateral transfer of genetic information among microorganisms is a major force driving the outstanding adaptability of microbial communities to environmental changes. Until now little information has been obtained on gene transfer in natural ecosystems. We present here a genetic circuit for detecting and quantifying horizontal gene transfer from a defined donor microorganism to recipient organisms in the absence of selection for a recipient-specific phenotype. The system consists of an engineered lacZ (encoding beta-galactosidase) reporter gene whose expression is controlled by a synthetic regulatory element based on a fusion between the Pr promoter-operator from lambda bacteriophage and the 5' non-coding leader region of the inp gene encoding the IS 10 transposase function. Expression of this reporter cassette in the recombinant microorganism is completely shut down by two chromosomally encoded trans-acting repressors working at the level of transcription (the Cl-EK117 protein from the lambda phage), and at the level of translation (the antisense RNA-OUT of the IS 10 element). When the reporter element is transferred to a different host by any mechanism, it escapes repression and becomes expressed. The system was validated with Pseudo-monas putida, and conjugational transfer frequencies of the reporter element as low as 10(-6) were detected. The modular design and broad host range of the genetic circuit, in combination with biomarkers which permit real-time in situ detection, will facilitate the monitor-ing of gene flow in a non-disruptive manner within the environment.}, }
@article {pmid8784561, year = {1996}, author = {Burnens, AP and Stanley, J and Sechter, I and Nicolet, J}, title = {Evolutionary origin of a monophasic Salmonella serovar, 9,12:l,v:-, revealed by IS200 profiles and restriction fragment polymorphisms of the fljB gene.}, journal = {Journal of clinical microbiology}, volume = {34}, number = {7}, pages = {1641-1645}, pmid = {8784561}, issn = {0095-1137}, mesh = {Antigens, Bacterial/genetics ; *Bacterial Proteins ; Base Sequence ; DNA Probes/genetics ; DNA Transposable Elements ; *Evolution, Molecular ; Flagellin/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Operon ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Salmonella/classification/*genetics/immunology ; Serotyping ; }, abstract = {The emergence in several countries of the monophasic serogroup D1 serovar Salmonella 9,12:l,v:- provided the opportunity to study its evolutionary origin. According to current models, such a variant serovar could have arisen by horizontal transfer of a new flagellar gene to a preexisting monophasic Salmonella strain or, alternatively, by the loss of the phase 2 flagellar gene of an originally biphasic Salmonella strain. Five known serovars of Salmonella, S. panama, S. kapemba, S. goettingen, S. zaiman, and S. mendoza, could have been possible ancestors of the new variant. The profiles of the insertion element IS200, which has been shown to provide phylogenetic markers for serogroup D1 salmonellae, were analyzed in relation to the restriction fragment length polymorphisms of the phase 2 flagellar gene. Together they provide unequivocal evidence that Salmonella 9,12:l,v:- arose from a strain of S. goettingen. Analysis of the flj operon of the variant indicated that loss of phase 2 flagellar antigen expression occurred through deletion of the hin gene and adjacent DNA, thereby blocking the phase 2 flagellar gene in the off position.}, }
@article {pmid8754222, year = {1996}, author = {Delwiche, CF and Palmer, JD}, title = {Rampant horizontal transfer and duplication of rubisco genes in eubacteria and plastids.}, journal = {Molecular biology and evolution}, volume = {13}, number = {6}, pages = {873-882}, doi = {10.1093/oxfordjournals.molbev.a025647}, pmid = {8754222}, issn = {0737-4038}, mesh = {Bacteria/enzymology/*genetics ; Bacterial Proteins/*genetics ; Chloroplasts/enzymology/*genetics ; DNA, Bacterial/genetics ; DNA, Chloroplast/genetics ; Eukaryota/enzymology/*genetics ; *Genes, Bacterial ; *Genes, Plant ; Models, Genetic ; *Multigene Family ; Phylogeny ; Plant Proteins/*genetics ; Ribulose-Bisphosphate Carboxylase/*genetics ; Sequence Homology, Nucleic Acid ; Species Specificity ; Transformation, Bacterial ; *Transformation, Genetic ; }, abstract = {Previous work has shown that molecular phylogenies of plastids, cyanobacteria, and proteobacteria based on the rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) genes rbcL and rbcS are incongruent with molecular phylogenies based on other genes and are also incompatible with structural and biochemical information. Although it has been much speculated that this is the consequence of a single horizontal gene transfer (of a proteobacterial or mitochondrial rubisco operon into plastids of rhodophytic and chromophytic algae), neither this hypothesis nor the alternative hypothesis of ancient gene duplication have been examined in detail. We have conducted phylogenetic analyses of all available bacterial rbcL sequences, and representative plastid sequences, in order to explore these alternative hypothesis and fully examine the complexity of rubisco gene evolution. The rbcL phylogeny reveals a surprising number of gene relationships that are fundamentally incongruent with organismal relationships as inferred from multiple lines of other molecular evidence. On the order of six horizontal gene transfers are implied by the form I (L8S8) rbcL phylogeny, two between cyanobacteria and proteobacteria, one between proteobacteria and plastids, and three within proteobacteria. Alternatively, a single ancient duplication of the form I rubisco operon, followed by repeated and pervasive differential loss of one operon or the other, would account for much of this incongruity. In all probability, the rubisco operon has undergone multiple events of both horizontal gene transfer and gene duplication in different lineages.}, }
@article {pmid8658163, year = {1996}, author = {Waldor, MK and Mekalanos, JJ}, title = {Lysogenic conversion by a filamentous phage encoding cholera toxin.}, journal = {Science (New York, N.Y.)}, volume = {272}, number = {5270}, pages = {1910-1914}, doi = {10.1126/science.272.5270.1910}, pmid = {8658163}, issn = {0036-8075}, support = {AI01321/AI/NIAID NIH HHS/United States ; AI18045/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Bacteriophages/*genetics/physiology ; Base Sequence ; Cholera/*microbiology ; Cholera Toxin/*genetics ; DNA Primers ; Digestive System/microbiology ; Endotoxins ; Fimbriae, Bacterial/physiology/virology ; Gene Expression ; Genes, Bacterial ; *Lysogeny ; Mice ; Molecular Sequence Data ; Morphogenesis ; Mutation ; Transduction, Genetic ; Vibrio cholerae/genetics/*pathogenicity/*virology ; Virulence/genetics ; }, abstract = {Vibrio cholerae, the causative agent of cholera, requires two coordinately regulated factors for full virulence: cholera toxin (CT), a potent enterotoxin, and toxin-coregulated pili (TCP), surface organelles required for intestinal colonization. The structural genes for CT are shown here to be encoded by a filamentous bacteriophage (designated CTXphi), which is related to coliphage M13. The CTXphi genome chromosomally integrated or replicated as a plasmid. CTXphi used TCP as its receptor and infected V. cholerae cells within the gastrointestinal tracts of mice more efficiently than under laboratory conditions. Thus, the emergence of toxigenic V. cholerae involves horizontal gene transfer that may depend on in vivo gene expression.}, }
@article {pmid8861393, year = {1996}, author = {Sriprakash, KS and Hartas, J}, title = {Lateral genetic transfers between group A and G streptococci for M-like genes are ongoing.}, journal = {Microbial pathogenesis}, volume = {20}, number = {5}, pages = {275-285}, doi = {10.1006/mpat.1996.0026}, pmid = {8861393}, issn = {0882-4010}, mesh = {Amino Acid Sequence ; *Antigens, Bacterial ; Bacterial Outer Membrane Proteins/*genetics ; Base Sequence ; Carrier Proteins ; Connectin ; Frameshift Mutation ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Molecular Sequence Data ; *Muscle Proteins ; *Myeloma Proteins ; Sequence Alignment ; Sequence Analysis ; Streptococcus/*genetics ; }, abstract = {Previously we described a long-polymerase chain reaction (PCR) method to amplify a 4-7 kb target containing most of the components of the vir regulon (mga, emm-like genes and scpA) in a number of group A streptococcus (GAS) isolates. In contrast to GAS, strains of human group G streptococcus (GGS) gave approximately 1.6 or 1.8 kb products. Sequence analysis of the amplified products issued from GGS templates revealed a mosaic consisting of upstream sequence from mga (the gene for positive regulator of vir regulon), an unidentified open reading frame, a short segment of emm (the gene for M protein, an antiphagocytic molecule) and an upstream sequence of scp (C5a-peptidase gene). A full length scpG is present immediately downstream from the mosaic segment in the human GGS genome. The GGS PCR fragment did not code for mga or full length emm. All human GGS isolates are known to code for emm but the gene is separated from scpG by at least 10 kb. Our data, obtained using long-PCR and unrelated strains of GGS, confirm this. We could not detect a homologue of mga in human GGS by hybridization analysis. The mosaic sequence suggests that enbloc transfer of the vir regulon from GAS to a GGS progenitor may have occurred, following which deletion and rearrangement events may have taken place. Partial nucleotide sequences of emm corresponding to the variable domain of M proteins from three local GGS isolates were determined. One sequence (emmGGS6) is 99% identical to emm from a geographically separated isolate of GGS recently described.3 emmGGS6 also has significant homology with emm from a GAS strain (STDONALD) isolated from the same geographical area as was GGS6. The two emm sequences (emmGGS6 and emmSTDONALD) revealed frameshift-compensatory frameshift mutations relative to each other, contributing to lower amino acid homology between the two predicted M proteins. Since emmSTDONALD has no known relatives within the 80 or so emm sequences in the database, we speculate that it could have been laterally acquired from GGS. Horizontal transfers between GGS and GAS may be ongoing.}, }
@article {pmid8696689, year = {1996}, author = {Curtis, MD and Oliver, RP}, title = {Gypsy-class retrotransposon sequences in organisms related to the leaf mould fungus, Cladosporium fulvum.}, journal = {Microbiological research}, volume = {151}, number = {2}, pages = {113-119}, doi = {10.1016/S0944-5013(96)80034-6}, pmid = {8696689}, issn = {0944-5013}, mesh = {Amino Acid Sequence ; Base Sequence ; Cladosporium/*genetics ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; RNA-Directed DNA Polymerase/genetics ; *Retroelements ; }, abstract = {Gypsy retrotransposons are a major branch of retroid elements and have been found in a wide diversity of eukaryotic organisms including CfT-1 in the tomato leaf mould pathogen, the fungus Cladosporium fulvum (syn. Fulvia fulva). We have examined organisms that are either ecologically or phylogenetically related to C. fulvum, for elements related to CfT-1. Using PCR and Southern hybridisation, similar sequences were found only in the co-genic fungus Cladosporium cladosporioides. This finding confirms the apparent ubiquity of retroelements, suggests that the phylogeny of retrotransposons is consistent with the phylogeny of their hosts and argues against frequent horizontal gene transfer.}, }
@article {pmid8662005, year = {1996}, author = {Buades, C and Moya, A}, title = {Phylogenetic analysis of the isopenicillin-N-synthetase horizontal gene transfer.}, journal = {Journal of molecular evolution}, volume = {42}, number = {5}, pages = {537-542}, pmid = {8662005}, issn = {0022-2844}, mesh = {Aspergillus nidulans/genetics ; Bacterial Proteins/*genetics ; Fungal Proteins/*genetics ; Gram-Negative Bacteria/genetics ; Gram-Positive Bacteria/genetics ; Likelihood Functions ; *Models, Genetic ; Oxidoreductases/*genetics ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Fungal/genetics ; RNA, Ribosomal, 5S/genetics ; Sequence Alignment ; Species Specificity ; Time Factors ; *Transformation, Genetic ; }, abstract = {A phylogenetic study of the isopenicillin-N-synthetase (IPNS) gene sequence from prokaryotic and lower eukaryotic producers of beta-lactam antibiotics by means of a maximum-likelihood approach has been carried out. After performing an extensive search, rather than invoking a global molecular clock, the results obtained are best explained by a model with three rates of evolution. Grouped in decreasing order, these correspond to A. nidulans and then to the rest of the eukaryotes and prokaryotes, respectively. The estimated branching date between prokaryotic and fungal IPNS sequences (852 +/- 106 MY) strongly supports the hypothesis that the IPNS gene was horizontally transferred from bacterial beta-lactam producers to filamentous fungi.}, }
@article {pmid8861213, year = {1996}, author = {Stein, MA and Leung, KY and Zwick, M and Garcia-del Portillo, F and Finlay, BB}, title = {Identification of a Salmonella virulence gene required for formation of filamentous structures containing lysosomal membrane glycoproteins within epithelial cells.}, journal = {Molecular microbiology}, volume = {20}, number = {1}, pages = {151-164}, doi = {10.1111/j.1365-2958.1996.tb02497.x}, pmid = {8861213}, issn = {0950-382X}, mesh = {Animals ; Biological Transport ; Cell Line ; Cloning, Molecular ; DNA Transposable Elements ; Epithelium/microbiology/*ultrastructure ; *Genes, Bacterial ; Glycoproteins/analysis ; HeLa Cells ; Humans ; Mice ; Mice, Inbred BALB C ; Operon ; Polyamines/metabolism ; Salmonella Infections, Animal/microbiology ; Salmonella typhimurium/*genetics/*pathogenicity ; Spermidine/metabolism ; Vacuoles/microbiology ; Virulence/genetics ; }, abstract = {Salmonella species are facultative intracellular pathogens that invade epithelial cells and reside within lysosomal membrane glycoprotein (lgp)-containing vacuoles. Coincident with the onset of bacterial replication inside these vacuoles, Salmonella induce the formation of stable lgp-containing filamentous structures that connect with the Salmonella-containing vacuoles. Salmonella typhimurium SL1344::Tn l0dCm mutant strains unable to induce these structures were isolated. All contained insertions within a novel Salmonella induced filament gene A (sifA). sifA is present only in Salmonella species and encodes a protein with a predicted molecular mass of 38 kDa and an apparent molecular mass of 35 kDa. sifA is flanked by 300 base pairs, and sifA and its flanking DNA show no homology to sequences in DNA databases. sifA is located within the potABCD operon, a housekeeping locus involved in periplasmic transport of polyamines. Fourteen-base-pair direct repeats mark the probable site of integration of sifA and its flanking DNA have a significantly reduced G+C content (41%) when compared with the potABCD operon (51%) and the Salmonella genome (52-54%). Deletion mutant strains in sifA or in the downstream potC were constructed. Delta sifA does not produce Salmonella-induced filaments in epithelial cells, and is attenuated in mice. Delta potC produces Salmonella-induced filaments in epithelial cells, and was fully virulent. Collectively, these results suggest that sifA arose by horizontal gene transfer into Salmonella and its product is involved in a virulence-associated intracellular phenotype related to Salmonella-induced filament formation.}, }
@article {pmid8849261, year = {1996}, author = {Bootsma, HJ and van Dijk, H and Verhoef, J and Fleer, A and Mooi, FR}, title = {Molecular characterization of the BRO beta-lactamase of Moraxella (Branhamella) catarrhalis.}, journal = {Antimicrobial agents and chemotherapy}, volume = {40}, number = {4}, pages = {966-972}, pmid = {8849261}, issn = {0066-4804}, mesh = {Amino Acid Sequence ; Base Sequence ; Blotting, Southern ; Escherichia coli/metabolism ; Molecular Sequence Data ; Moraxella catarrhalis/enzymology/*genetics ; Sequence Homology, Amino Acid ; beta-Lactamases/*genetics ; }, abstract = {A rapid increase in the prevalence of beta-lactamase-producing Moraxella (Branhamella) catarrhalis strains has been noticed during the last decades. Today, more than 80% of strains isolated worldwide produce beta-lactamase. To investigate beta-lactamase(s) of M. catarrhalis at the molecular level, the BRO-1 beta-lactamase gene (bla) was isolated as part of a 4,223-bp HindIII fragment. Sequence analysis indicated that bla encodes a polypeptide of 314 amino acid residues. Insertional inactivation of bla in M. catarrhalis resulted in complete abrogation of beta-lactamase production and ampicillin resistance, demonstrating that bla is solely responsible for beta-lactam resistance. Comparison with other beta-lactamases suggested that M. catarrhalis beta-lactamase is a unique enzyme with conserved residues at the active sites. The presence of a signal sequence for lipoproteins suggested that it is lipid modified at its N terminus. In keeping with this assumption was the observation that 10% of beta-lactamase activity was found in the membrane compartment of M. catarrhalis. M. catarrhalis strains produce two types of beta-lactamase, BRO-1 and BRO-2, which differ in their isoelectric points. The BRO-1 and BRO-2 genes from two ATCC strains of M. catarrhalis were sequenced, and only one amino acid difference was found between the predicted products. However, there was a 21-bp deletion in the promoter region of the BRO-2 gene, possibly explaining the lower level of production of BRO-2. The G + C content of bla (31%) was significantly lower than those of the flanking genes (47 and 50%), and the overall G + C content of the M. catarrhalis genome (41%). These results indicate that bla was acquired by horizontal gene transfer from another, still unknown species.}, }
@article {pmid8622771, year = {1996}, author = {Maier, UG and Hofmann, CJ and Sitte, P}, title = {[Evolution of cells].}, journal = {Die Naturwissenschaften}, volume = {83}, number = {3}, pages = {103-112}, pmid = {8622771}, issn = {0028-1042}, mesh = {Animals ; Archaea ; Bacteria ; *Biological Evolution ; Biomarkers ; Enzymes/analysis ; Eukaryotic Cells/*cytology/physiology ; Models, Biological ; Prokaryotic Cells/*cytology/physiology ; Symbiosis ; }, abstract = {Life has existed on earth for some 4 x 10(9) years. During most of this time, evolution took place at the level of cell evolution. The cells of presently existing organisms belong to two fundamentally different cell types, protocytes (of bacteria and archaea) and eucytes (of eukarya). Thanks to molecular phylogenetics, the path of evolution can now be traced back to its very beginnings, although the picture may be blurred by repeated horizontal gene transfer. A symbiogenetic origin of plastids and mitochondria is now very well documented, and it is being discussed also for some other constituents of eucytes, including even the cells nucleus. It could be demonstrated that not only did bacterial cells become incorporated into protoeucytes and transformed into organelles of their respective hosts, but also that endocytic eucytes have apparently been transformed to complex organelles by coevolution with host cells.}, }
@article {pmid8626733, year = {1996}, author = {Werlen, C and Kohler, HP and van der Meer, JR}, title = {The broad substrate chlorobenzene dioxygenase and cis-chlorobenzene dihydrodiol dehydrogenase of Pseudomonas sp. strain P51 are linked evolutionarily to the enzymes for benzene and toluene degradation.}, journal = {The Journal of biological chemistry}, volume = {271}, number = {8}, pages = {4009-4016}, doi = {10.1074/jbc.271.8.4009}, pmid = {8626733}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Base Sequence ; Benzene/*metabolism ; *Biological Evolution ; Biotransformation ; Cloning, Molecular ; *Dioxygenases ; Gene Transfer, Horizontal ; Genes, Bacterial ; Macromolecular Substances ; Molecular Sequence Data ; *Multigene Family ; Oxidoreductases/*genetics/metabolism ; Oxygenases/*genetics/metabolism ; Phylogeny ; Pseudomonas/*enzymology/*genetics ; Recombinant Proteins/metabolism ; Restriction Mapping ; Sequence Homology, Amino Acid ; Substrate Specificity ; Toluene/*metabolism ; }, abstract = {The chlorobenzene degradation pathway of Pseudomonas sp. strain P51 is an evolutionary novelty. The first enzymes of the pathway, the chlorobenzene dioxygenase and the cis-chlorobenzene dihydrodiol dehydrogenase, are encoded on a plasmid-located transposon Tn5280. Chlorobenzene dioxygenase is a four-protein complex, formed by the gene products of tcbAa for the large subunit of the terminal oxygenase, tcbAb for the small subunit, tcbAc for the ferredoxin, and tcbAd for the NADH reductase. Directly downstream of tcbAd is the gene for the cis-chlorobenzene dihydrodiol dehydrogenase, tcbB. Homology comparisons indicated that these genes and gene products are most closely related to those for toluene (todC1C2BAD) and benzene degradation (bedC1C2BA and bnzABCD) and distantly to those for biphenyl, naphthalene, and benzoate degradation. Similar to the tod-encoded enzymes, chlorobenzene dioxygenase and cis-chlorobenzene dihydrodiol dehydrogenase were capable of oxidizing 1,2-dichlorobenzene, toluene, naphthalene, and biphenyl, but not benzoate, to the corresponding dihydrodiol and dihydroxy intermediates. These data strongly suggest that the chlorobenzene dioxygenase and dehydrogenase originated from a toluene or benzene degradation pathway, probably by horizontal gene transfer. This evolutionary event left its traces as short gene fragments directly outside the tcbAB coding regions.}, }
@article {pmid9636322, year = {1996}, author = {Munthal, MT and Timmis, KN and Díaz, E}, title = {Restricting the dispersal of recombinant DNA: design of a contained biological catalyst.}, journal = {Bio/technology (Nature Publishing Company)}, volume = {14}, number = {2}, pages = {189-191}, doi = {10.1038/nbt0296-189}, pmid = {9636322}, issn = {0733-222X}, mesh = {Catalysis ; Colicins/genetics ; *Containment of Biohazards ; DNA Transposable Elements ; DNA, Recombinant/*genetics ; *Gene Transfer, Horizontal ; *Genetic Engineering ; Genetic Linkage ; Gram-Negative Bacteria/*genetics ; Plasmids/genetics ; Pseudomonas putida/genetics ; }, abstract = {To restrict horizontal gene spread and, thus, create organisms whose behavior in the field is more predictable, we have combined a mini-Tn5 cloning system that allows stable insertion of foreign genes into the chromosomes of a variety of Gram-negative bacteria with a gene-containment circuit based on the universal lethal-function colicin E3. Use of the system is exemplified by the construction of a micro-organism designed to degrade polychlorinated biphenyls, important environmental pollutants. The relevant genotype of the microorganism is subject to a stringent gene-containment mechanism that provides neither an advantage nor a disadvantage to the host cell for survival, but decreases frequencies of productive chromosomal transfer frequencies by at least four orders of magnitude.}, }
@article {pmid8919862, year = {1996}, author = {Takasaki, N and Park, L and Kaeriyama, M and Gharrett, AJ and Okada, N}, title = {Characterization of species-specifically amplified SINEs in three salmonid species--chum salmon, pink salmon, and kokanee: the local environment of the genome may be important for the generation of a dominant source gene at a newly retroposed locus.}, journal = {Journal of molecular evolution}, volume = {42}, number = {2}, pages = {103-116}, pmid = {8919862}, issn = {0022-2844}, mesh = {Animals ; Base Sequence ; Consensus Sequence ; DNA/genetics ; DNA Primers/genetics ; Deoxyribonucleases, Type II Site-Specific ; Evolution, Molecular ; Gene Amplification ; Gene Transfer, Horizontal ; Genes, Dominant ; Genome ; Molecular Sequence Data ; Oligonucleotide Probes/genetics ; Oncorhynchus keta/*genetics ; Polymerase Chain Reaction ; *Repetitive Sequences, Nucleic Acid ; Retroelements ; Salmon/*genetics ; Sequence Homology, Nucleic Acid ; Species Specificity ; }, abstract = {Short interspersed repetitive elements (SINEs), known as the HpaI family, are present in the genomes of all salmonid species (Kido et al., Proc. Natl. Acad. Sci. USA 1991, 88: 2326-2330). Recently, we showed that the retropositional efficiency of the SINE family in the lineage of chum salmon is extraordinarily high in comparison with that in other salmonid lineages. (Takasaki et al., Proc. Natl. Acad. Sci. USA 1994, 91: 10153-10157). To investigate the reason for this high efficiency, we searched for members of the HpaI SINE family that have been amplified species-specifically in pink salmon. Since the efficiency of the species-specific amplification in pink salmon is not high and since other members of the same subfamily of SINEs were also amplified species-specifically in pink salmon, the actual sequence of this subfamily might not be the cause of the high retropositional efficiency of SINEs in chum salmon. Rather, it appears that a highly dominant source gene for the subfamily may have been newly created by retroposition, and some aspect of the local environment around the site of retroposition may have been responsible for the creation of this dominant source gene in chum salmon. Furthermore, a total of 11 sequences of HpaI SINEs that have been amplified species-specifically in three salmon lineages was compiled and characterized. Judging from the distribution of members of the same-sequence subfamily of SINEs in different lineages and from the distribution of the different-sequence subfamilies in the same lineage, we have concluded that multiple dispersed loci are responsible for the amplification of SINEs. We also discuss the additional possibility of horizontal transmission of SINEs between species. The availability of the sets of primers used for the detection of the species-specific amplifications of the SINEs provides a convenient and reliable method for identification of these salmonid species.}, }
@article {pmid8919860, year = {1996}, author = {Jeltsch, A and Pingoud, A}, title = {Horizontal gene transfer contributes to the wide distribution and evolution of type II restriction-modification systems.}, journal = {Journal of molecular evolution}, volume = {42}, number = {2}, pages = {91-96}, pmid = {8919860}, issn = {0022-2844}, mesh = {Bacteria/*enzymology/*genetics/virology ; Bacteriophages/genetics/metabolism ; Codon/genetics ; DNA Restriction-Modification Enzymes/*genetics ; DNA, Bacterial/genetics/metabolism ; DNA, Viral/genetics/metabolism ; Deoxyribonucleases, Type II Site-Specific/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Methylation ; Species Specificity ; }, abstract = {Restriction modification (RM) systems serve to protect bacteria against bacteriophages. They comprise a restriction endonuclease activity that specifically cleaves DNA and a corresponding methyltransferase activity that specifically methylates the DNA, thereby protecting it from cleavage. Such systems are very common in bacteria. To find out whether the widespread distribution of RM systems is due to horizontal gene transfer, we have compared the codon usages of 29 type II RM systems with the average codon usage of their respective bacterial hosts. Pronounced deviations in codon usage were found in six cases: EcoRI, EcoRV, KpnI, SinI, SmaI, and TthHB81. They are interpreted as evidence for horizontal gene transfer in these cases. As the methodology is expected to detect only one-fourth to one-third of all horizontal gene transfer events, this result implies that horizontal gene transfer had a considerable influence on the distribution and evolution of RM systems. In all of these six cases the codon usage deviations of the restriction enzyme genes are much more pronounced than those of the methyltransferase genes. This result suggests that in these cases horizontal gene transfer had occurred sequentially with the gene for the methyltransferase being first acquired by the cell. This can be explained by the fact that an active restriction endonuclease is highly toxic in cells whose DNA is not protected from cleavage by a corresponding methyltransferase.}, }
@article {pmid8820653, year = {1996}, author = {Seiler, A and Reinhardt, R and Sarkari, J and Caugant, DA and Achtman, M}, title = {Allelic polymorphism and site-specific recombination in the opc locus of Neisseria meningitidis.}, journal = {Molecular microbiology}, volume = {19}, number = {4}, pages = {841-856}, doi = {10.1046/j.1365-2958.1996.437970.x}, pmid = {8820653}, issn = {0950-382X}, mesh = {Alleles ; Bacterial Outer Membrane Proteins/*genetics ; Base Sequence ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Meningococcal Infections/microbiology ; Molecular Sequence Data ; Neisseria meningitidis/classification/*genetics ; Phylogeny ; *Polymorphism, Genetic ; Protein Sorting Signals/genetics ; *Recombination, Genetic ; Serotyping ; Species Specificity ; }, abstract = {The opc gene is widespread in epidemic and endemic Neisseria meningitidis, but most strains of certain epidemic clones (ET-37 complex, Cluster A4) and a few random endemic isolates lack an opc gene. Four percent of the 1148 bp that contain opc plus the surrounding intergenic region was polymorphic (18 alleles), and many of the alleles contained a 230 bp insertion at a fixed location in the intergenic region. The presence or absence of the insertion reflects site-specific recombination. The alleles are stably inherited within clonal groupings for up to at least 50 years, with rare cases of horizontal genetic exchange. Most statistical methods indicated significant intragenic recombination events within this dataset.}, }
@article {pmid8587498, year = {1996}, author = {Moens, L and Vanfleteren, J and Van de Peer, Y and Peeters, K and Kapp, O and Czeluzniak, J and Goodman, M and Blaxter, M and Vinogradov, S}, title = {Globins in nonvertebrate species: dispersal by horizontal gene transfer and evolution of the structure-function relationships.}, journal = {Molecular biology and evolution}, volume = {13}, number = {2}, pages = {324-333}, doi = {10.1093/oxfordjournals.molbev.a025592}, pmid = {8587498}, issn = {0737-4038}, support = {DK 30382/DK/NIDDK NIH HHS/United States ; DK 38674/DK/NIDDK NIH HHS/United States ; //Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins/chemistry/genetics ; *Evolution, Molecular ; Fungal Proteins/chemistry/genetics ; *Gene Transfer, Horizontal ; Globins/chemistry/*genetics/metabolism ; Hemeproteins/genetics ; Molecular Sequence Data ; Origin of Life ; Oxidation-Reduction ; Oxygen/metabolism ; Sequence Alignment ; Species Specificity ; Structure-Activity Relationship ; Templates, Genetic ; }, abstract = {Using a new template based on an alignment of 145 nonvertebrate globins we examined several recently determined sequences of putative globins and globin-like hemeproteins. We propose that all globins have evolved from a family of ancestral, approx. 17-kDa hemeproteins, which displayed the globin fold and functioned as redox proteins. Once atmospheric O2 became available the acquisition of oxygen-binding properties was initiated, culminating in the various highly specialized functions known as present. During this evolutionary process, we suggest that (1) high oxygen affinity may have been acquired repeatedly and (2) the formation of chimeric proteins containing both a globin and a flavin binding domain was an additional and distinct evolutionary trend. Furthermore, globin-like hemeproteins encompass hemeproteins produced through convergent evolution from nonglobin ancestral proteins to carry out O2-binding functions as well as hemeproteins whose sequences exhibit the loss of some or all of the structural determinants of the globin fold. We also propose that there occurred two cases of horizontal globin gene transfer, one from an ancestor common to the ciliates Paramecium and Tetrahymena and the green alga Chlamydomonas to a cyanobacterium ancestor and the other, from a eukaryote ancestor of the yeasts Saccharomyces and Candida to a bacterial ancestor of the proteobacterial genera Escherichia, Alcaligenes, and Vitreoscilla.}, }
@article {pmid8595865, year = {1996}, author = {Fedi, S and Brazil, D and Dowling, DN and O'Gara, F}, title = {Construction of a modified mini-Tn5 lacZY non-antibiotic marker cassette: ecological evaluation of a lacZY marked Pseudomonas strain in the sugarbeet rhizosphere.}, journal = {FEMS microbiology letters}, volume = {135}, number = {2-3}, pages = {251-257}, doi = {10.1111/j.1574-6968.1996.tb07997.x}, pmid = {8595865}, issn = {0378-1097}, mesh = {Conjugation, Genetic ; *DNA Transposable Elements ; Ecosystem ; Gene Transfer Techniques ; Genetic Markers/genetics ; Plant Roots/*microbiology ; Plants, Edible/microbiology ; *Plasmids ; Pseudomonas fluorescens/*genetics ; beta-Galactosidase/*genetics ; }, abstract = {In order to monitor the fate of genetically manipulated fluorescent pseudomonads following release into the environment, a lacZY transposable cassette, lacking antibiotic resistance genes, was constructed using a pUT suicide plasmid delivery system. The resulting plasmid, pUTLacZY, can be easily used to generate lacZY marked pseudomonads without having to use antibiotic resistance determinants. The lacZY transposon generates random, stable transcriptional/translational fusions on integration into the target genome. Pseudomonas fluorescens strain F113 was marked with lacZY and was unaltered with respect to ecological fitness in the rhizosphere. Although lateral gene transfer of the chromosomally integrated lacZY marker could be detected in vitro, it was not detected in rhizosphere microcosms.}, }
@article {pmid8748303, year = {1996}, author = {Upton, M and Carter, PE and Orange, G and Pennington, TH}, title = {Genetic heterogeneity of M type 3 group A streptococci causing severe infections in Tayside, Scotland.}, journal = {Journal of clinical microbiology}, volume = {34}, number = {1}, pages = {196-198}, pmid = {8748303}, issn = {0095-1137}, mesh = {Bacterial Typing Techniques ; Base Sequence ; Cluster Analysis ; DNA Primers/genetics ; DNA Restriction Enzymes ; DNA, Bacterial/*genetics ; Electrophoresis, Gel, Pulsed-Field ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genotype ; Humans ; Molecular Epidemiology ; Molecular Sequence Data ; Polymerase Chain Reaction ; Scotland/epidemiology ; Streptococcal Infections/*epidemiology/*microbiology ; Streptococcus pyogenes/*classification/*genetics/pathogenicity ; Virulence/genetics ; }, abstract = {To explain the worldwide increase in the frequency of severe infections by group A streptococci, molecular techniques are increasingly being employed to evaluate the genetic relationships of strains. We used restriction endonuclease analysis, pulsed-field gel electrophoresis (PFGE), the PCR, ribotyping, and DNA sequence analysis in a study of 13 group A streptococci isolated from a cluster of cases of serious infections over a 3-month period in Tayside, Scotland. Eight of the strains were M type 3; molecular characterization identified two subclones. The first, displaying PFGE profile 4, has been observed in Northern Scotland and has been circulating in New Zealand for over a decade. The second subclone has been documented only in the United Kingdom; it was first seen in 1993 in Scotland. Sequence analysis of emm-3 genes further differentiated the PFGE 4 subclone. DNA sequence analysis of virulence factors supports the suggestion that they may have recently been acquired by horizontal gene transfer.}, }
@article {pmid8707058, year = {1996}, author = {Christensen, BB and Sternberg, C and Molin, S}, title = {Bacterial plasmid conjugation on semi-solid surfaces monitored with the green fluorescent protein (GFP) from Aequorea victoria as a marker.}, journal = {Gene}, volume = {173}, number = {1 Spec No}, pages = {59-65}, doi = {10.1016/0378-1119(95)00707-5}, pmid = {8707058}, issn = {0378-1119}, mesh = {Agar ; Animals ; *Conjugation, Genetic ; Culture Media ; Genes, Reporter ; Green Fluorescent Proteins ; Kinetics ; Luminescent Proteins/*genetics/metabolism ; *Plasmids ; Pseudomonas putida/*genetics ; Scyphozoa ; }, abstract = {Horizontal transfer of the TOL plasmid was examined in Pseudomonas putida (Pp) KT2442 micro-colonies on semi-solid agar surfaces. Horizontal gene transfer is usually studied in large populations where all information is based on average estimates of the transfer events in the entire population. We have used the green fluorescent protein (GFP) from the jellyfish Aequorea victoria as a plasmid marker, in combination with single-cell observations. This provided hitherto unknown details on the distribution of cells active in conjugation. In the present study, donor cells containing the gfp gene expressed from the bacteriophage T7 phi 10 promoter on the TOL plasmid, and recipient cells expressing the corresponding phage RNA polymerase allowed us to monitor the occurrence of ex-conjugants as green fluorescent cells upon illumination with blue light (470-490 nm). Further, the recipients were labeled with the luxAB genes to distinguish micro-colonies of donor cells from recipient cells. We conclude that conjugal plasmid transfer in Pp KT2442 cells on semi-solid surfaces occurs mainly during a short period of time after the initial contact of donors and recipients, indicating that spread of the TOL plasmid is limited in static, but viable cultures.}, }
@article {pmid8583905, year = {1996}, author = {Lan, R and Reeves, PR}, title = {Gene transfer is a major factor in bacterial evolution.}, journal = {Molecular biology and evolution}, volume = {13}, number = {1}, pages = {47-55}, doi = {10.1093/oxfordjournals.molbev.a025569}, pmid = {8583905}, issn = {0737-4038}, mesh = {Bacteria/*genetics ; DNA, Bacterial/*genetics ; Evolution, Molecular ; *Gene Transfer Techniques ; Sequence Analysis ; }, abstract = {Lateral gene transfer in four strains of Salmonella enterica has been assessed using genomic subtraction. Strain LT2 (subspecies I serovar Typhimurium) chromosomal DNA was used as target and subtracted by three subspecies I strains of serovars Typhimurium (S21), Muenchen (S71), Typhi (M229), and a subspecies V strain (M321). Data from probing random cosmids of LT2 DNA with preparations of the residual LT2 DNA after subtraction were used to estimate the amounts of LT2 DNA not able to hybridize to strains S21, S71, M229, and M321 to be in the range of 84-106, 191-355, 305-629, and 778-1,286 kb, respectively. Several lines of evidence indicate that most of this DNA is from genes not present in strain M321 and not from genes that have diverged in sequence. The amounts correlate with the divergence of the four strains as revealed by multilocus enzyme electrophoresis and sequence variation of housekeeping genes. Sequence of 39 of the fragments from the M321 subtracted residual LT2 DNA revealed only six inserts of known gene function with evidence of both gain and loss of genes during the development of S. enterica clones. Sixteen of the 39 segments have 45% or lower G+C content, below the species average, but over half are within the normal range for the species. We conclude that even within a species, clones may differ by up to 20% of chromosomal DNA, indicating a major role for lateral transfer, and that on the basis of G+C content, a significant proportion of the DNA is from distantly related species.}, }
@article {pmid7500950, year = {1995}, author = {Meyer, AD and Ichikawa, T and Meins, F}, title = {Horizontal gene transfer: regulated expression of a tobacco homologue of the Agrobacterium rhizogenes rolC gene.}, journal = {Molecular &amp; general genetics : MGG}, volume = {249}, number = {3}, pages = {265-273}, pmid = {7500950}, issn = {0026-8925}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/*genetics ; Base Sequence ; Biological Evolution ; Blotting, Northern ; Blotting, Southern ; Cells, Cultured ; Cloning, Molecular ; *Gene Expression Regulation, Plant ; *Gene Transfer, Horizontal ; *Genes, Plant ; Molecular Sequence Data ; Plant Proteins/*genetics ; *Plants, Toxic ; Rhizobium/*genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Nicotiana/cytology/*genetics ; *beta-Glucosidase ; }, abstract = {A tobacco homologue (trolC) of the rolC gene of the Agrobacterium rhizogenes Ri-plasmid was cloned and sequenced from Nicotiana tabacum L. cv. Havana 425. The coding region of trolC is similar in sequence (69-87% for DNA and 54-89% for the deduced amino acid sequence) to rolC genes of the agropine, mannopine, and mikimopine strains of Ri-plasmids and the N. glauca rolC homologue. Southern analyses showed that trolC is encoded by a small gene family derived from the tomentosiformis ancestor of tobacco. This suggests that trolC resulted from an ancient transfer of DNA between A. rhizogenes and a progenitor of modern tobacco. Transcripts of trolC were detected in three morphologically distinct cultivars of tobacco. trolC mRNA accumulated in young leaves and shoot tips, but not in lower leaves and roots of mature plants. Accumulation of trolC mRNA in cultured leaf tissues was strongly down-regulated by auxin and induced by cytokinin. These results are of particular interest because they suggest that a gene of bacterial origin introduced during evolution can have a function in a modern plant.}, }
@article {pmid8522177, year = {1995}, author = {Nikolskaya, AN and Panaccione, DG and Walton, JD}, title = {Identification of peptide synthetase-encoding genes from filamentous fungi producing host-selective phytotoxins or analogs.}, journal = {Gene}, volume = {165}, number = {2}, pages = {207-211}, doi = {10.1016/0378-1119(95)00555-k}, pmid = {8522177}, issn = {0378-1119}, mesh = {*Amino Acid Isomerases ; Amino Acid Sequence ; Ascomycota/enzymology/*genetics ; Base Sequence ; Cloning, Molecular ; Conserved Sequence ; DNA Primers ; Fungal Proteins ; Genes, Fungal/*genetics ; Hydrolases/*genetics ; Mitosporic Fungi/enzymology/*genetics ; Molecular Sequence Data ; *Mycotoxins ; Peptide Synthases/*genetics ; Peptides, Cyclic ; Polymerase Chain Reaction/methods ; Racemases and Epimerases/*genetics ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Toxins, Biological ; }, abstract = {Race 1 of Cochliobolus carbonum (Cc) makes a cyclic tetrapeptide, HC-toxin, that is necessary for its virulence on certain genotypes of maize. The synthesis of HC-toxin is catalyzed by a 570-kDa multifunctional enzyme, HC-toxin synthetase (HTS). The gene encoding HTS (HTS1) is absent from other races of Cc and from other species of Cochliobolus. Four other unrelated filamentous fungi make cyclic peptides closely related to HC-toxin, raising the possibility that the corresponding cyclic peptide synthetase (CPS)-encoding genes have moved between these fungi by horizontal gene transfer. Degenerate PCR primers were designed based on several highly conserved amino acid (aa) motifs common to known CPS domains and used to amplify genomic sequences from different fungi. PCR products representing CPS genes from Diheterospora chlamydosporia, which makes the HC-toxin analog chlamydocin, Cylindrocladium macrosporum, which makes the analog Cyl-2, and C. victoriae, which makes the unrelated cyclic pentapeptide victorin, were cloned and analysed. Their sequences are more related to HTS1 than to other cloned CPS, but the percent aa identity is not consistent with very recent horizontal movement of these genes.}, }
@article {pmid9810642, year = {1995}, author = {Prager, R and Beer, W and Voigt, W and Claus, H and Seltmann, G and Stephan, R and Bockemühl, J and Tschäpe, H}, title = {Genomic and biochemical relatedness between Vibrio cholerae serovar O139 and serovar O1 eltor strains.}, journal = {Zentralblatt fur Bakteriologie : international journal of medical microbiology}, volume = {283}, number = {1}, pages = {14-28}, doi = {10.1016/s0934-8840(11)80887-x}, pmid = {9810642}, issn = {0934-8840}, mesh = {Genome, Bacterial ; Humans ; Serotyping ; Vibrio cholerae/*classification/enzymology/genetics/isolation &amp; purification ; }, abstract = {Vibrio cholerae O139 (Bengal) the new pandemic cholera strain emerging on the Indian subcontinent has revealed considerable homology to Vibrio cholerae O1 EL Tor (strain of the seventh pandemic cholera) in terms of genetic and biochemical properties. Apart from capsule and O139 LPS formation, all strains of V. cholerae O139 were found to be identical to V. cholerae O1 EL Tor strains with respect to genomic restriction fragment length polymorphism, genomic distribution of the pathogenic island, pattern of OMP and multilocus enzymes. However, the analysis of a nonpathogenic V. cholerae O139 isolate from Sri Lanka with a totally different pattern of genetic properties underline that horizontal gene transfer of a piece of DNA encoding biosynthesis of the Vibrio cholerae O139-specific LPS and capsule formation to an O1 El Tor precursor strains must have occurred giving rise to a kind of hybrid V. cholerae O1 El Tor encoding the new serovar-specific O139 antigens.}, }
@article {pmid8817491, year = {1995}, author = {Reidl, J and Mekalanos, JJ}, title = {Characterization of Vibrio cholerae bacteriophage K139 and use of a novel mini-transposon to identify a phage-encoded virulence factor.}, journal = {Molecular microbiology}, volume = {18}, number = {4}, pages = {685-701}, doi = {10.1111/j.1365-2958.1995.mmi_18040685.x}, pmid = {8817491}, issn = {0950-382X}, support = {AI18045/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Antigens, Bacterial/genetics ; Bacterial Typing Techniques ; Bacteriophages/*genetics/*pathogenicity/physiology ; Base Sequence ; Blotting, Southern ; Blotting, Western ; Cloning, Molecular ; DNA Transposable Elements ; DNA, Bacterial/genetics ; Gene Expression Regulation, Viral ; Lysogeny ; Molecular Sequence Data ; Mutagenesis, Insertional ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; Vibrio cholerae/*virology ; Viral Fusion Proteins/genetics ; Viral Proteins/genetics ; Virulence/genetics ; beta-Lactamases/genetics ; }, abstract = {Temperate bacteriophage K139 was isolated from a Vibrio cholerae O139 isolate and characterized in this study. The phage genome consists of a 35 kbp, double-stranded, linear DNA molecule that circularizes and integrates into the chromosome in a site-specific manner. DNA sequences that cross-hybridize with K139 phage DNA are present in all strains of V. cholerae serogroup O1 of the classical biotype examined and in some strains of the El Tor biotype. Phage K139 produces plaques on El Tor O1 strains that do not carry the K139-related sequences but does not plaque on O139 strains that lack detectable phage DNA. This results suggests that O139 strains arose in part by horizontal gene transfer of the O139 antigen genes into an El Tor O1 strain that harboured a K139 prophage. Consistent with this interpretation, the morphology of K139 phage particles is identical to that displayed by the widely distributed family of O1 phages referred to as 'kappa'. In order to test whether K139 phage is involved in lysogenic conversion of V. cholerae, we constructed a novel mini-transposon, Tn10d-bla, which was designed to produce beta-lactamase fusions to phage-encoded, exported proteins. All Tn10d-bla insertions obtained were closely linked to one location on the K139 phage genome. DNA sequence determination of the fusion joints revealed an open reading frame (ORF1), encoding a gene product of 137 amino acids with a typical N-terminal hydrophobic signal sequence. ORF1 was designated the glo gene (G protein-like ORF) because its amino acid sequence shows similarity to eukaryotic Gs(alpha) protein (34.5% identity over an 81-amino-acid overlap) and its C-terminus displays the consensus motif (CAAX) which is found in many small eukaryotic GTP-binding proteins. LD50 assays with isogenic Glo+ and Glo- K139 lysogens suggest that glo encodes a secreted virulence determinant of V. cholerae.}, }
@article {pmid7490770, year = {1995}, author = {Vaughn, JC and Mason, MT and Sper-Whitis, GL and Kuhlman, P and Palmer, JD}, title = {Fungal origin by horizontal transfer of a plant mitochondrial group I intron in the chimeric CoxI gene of Peperomia.}, journal = {Journal of molecular evolution}, volume = {41}, number = {5}, pages = {563-572}, pmid = {7490770}, issn = {0022-2844}, support = {GM-35087/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Base Sequence ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Fungi/genetics ; *Gene Transfer, Horizontal ; Genes, Plant ; *Introns ; Mitochondria/enzymology/*genetics ; Models, Genetic ; Molecular Sequence Data ; Nucleic Acid Conformation ; Plants/enzymology/*genetics ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; }, abstract = {We present phylogenetic evidence that a group I intron in an angiosperm mitochondrial gene arose recently by horizontal transfer from a fungal donor species. A 1,716-bp fragment of the mitochondrial coxI gene from the angiosperm Peperomia polybotrya was amplified via the polymerase chain reaction and sequenced. Comparison to other coxI genes revealed a 966-bp group I intron, which, based on homology with the related yeast coxI intron aI4, potentially encodes a 279-amino-acid site-specific DNA endonuclease. This intron, which is believed to function as a ribozyme during its own splicing, is not present in any of 19 coxI genes examined from other diverse vascular plant species. Phylogenetic analysis of intron origin was carried out using three different tree-generating algorithms, and on a variety of nucleotide and amino acid data sets from the intron and its flanking exon sequences. These analyses show that the Peperomia coxI gene intron and exon sequences are of fundamentally different evolutionary origin. The Peperomia intron is more closely related to several fungal mitochondrial introns, two of which are located at identical positions in coxI, than to identically located coxI introns from the land plant Marchantia and the green alga Prototheca. Conversely, the exon sequence of this gene is, as expected, most closely related to other angiosperm coxI genes. These results, together with evidence suggestive of co-conversion of exonic markers immediately flanking the intron insertion site, lead us to conclude that the Peperomia coxI intron probably arose by horizontal transfer from a fungal donor, using the double-strand-break repair pathway. The donor species may have been one of the symbiotic mycorrhizal fungi that live in close obligate association with most plants.}, }
@article {pmid9636282, year = {1995}, author = {Schlüter, K and Fütterer, J and Potrykus, I}, title = {"Horizontal" gene transfer from a transgenic potato line to a bacterial pathogen (Erwinia chrysanthemi) occurs--if at all--at an extremely low frequency.}, journal = {Bio/technology (Nature Publishing Company)}, volume = {13}, number = {10}, pages = {1094-1098}, doi = {10.1038/nbt1095-1094}, pmid = {9636282}, issn = {0733-222X}, mesh = {Ampicillin/pharmacology ; Culture Media ; DNA Fragmentation ; Dickeya chrysanthemi/*genetics ; Escherichia coli/genetics ; *Gene Transfer, Horizontal ; Plants, Genetically Modified ; Plasmids/genetics ; Solanum tuberosum/*genetics ; Transformation, Bacterial ; beta-Lactamases/genetics ; }, abstract = {The frequency of possible "horizontal" gene transfer between a plant and a tightly associated bacterial pathogen was studied in a model system consisting of transgenic Solanum tuberosum, containing a beta-lactamase gene linked to a pBR322 origin of replication, and Erwinia chrysanthemi. This experimental system offers optimal conditions for the detection of possible horizontal gene transfer events, even when they occur at very low frequency. Horizontal gene transfer was not detected under conditions mimicking a "natural" infection. The gradual, stepwise alteration of artificial, positive control conditions to idealized natural conditions, however, allowed the characterization of factors that affected gene transfer, and revealed a gradual decrease of the gene transfer frequency from 6.3 x 10(-2) under optimal control conditions to a calculated 2.0 x 10(-17) under idealized natural conditions. These data, in combination with other published studies, argue that horizontal gene transfer is so rare as to be essentially irrelevant to any realistic assessment of the risk involved in release experiments involving transgenic plants.}, }
@article {pmid7592348, year = {1995}, author = {Reddy, SP and Rasmussen, WG and Baseman, JB}, title = {Molecular cloning and characterization of an adherence-related operon of Mycoplasma genitalium.}, journal = {Journal of bacteriology}, volume = {177}, number = {20}, pages = {5943-5951}, pmid = {7592348}, issn = {0021-9193}, support = {AI 27873/AI/NIAID NIH HHS/United States ; AI 32829/AI/NIAID NIH HHS/United States ; }, mesh = {Adhesins, Bacterial/genetics ; Amino Acid Sequence ; Bacterial Adhesion/*genetics ; Bacterial Proteins/genetics ; Base Sequence ; Cell Adhesion Molecules/*genetics ; Cloning, Molecular ; *Genes, Bacterial ; Immunoblotting ; Molecular Sequence Data ; Multigene Family ; Mycoplasma/*genetics ; Mycoplasma pneumoniae/genetics ; Open Reading Frames ; Protein Structure, Secondary ; Restriction Mapping ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Species Specificity ; }, abstract = {Adhesins and adhesin-related accessory proteins of pathogenic mycoplasmas are required for cytadherence and the subsequent development of disease pathology. The classic example has been Mycoplasma pneumoniae, which causes primary atypical pneumonia in humans. Mutants of M. pneumoniae defective in adhesins (P1 and P30) or in adherence-accessory proteins (HMW1 through HMW4) are unable to colonize host tissues and are avirulent. Mycoplasma genitalium, implicated in nongonococcal, nonchlamydial urethritis, pneumonia, arthritis, and AIDS progression, was found to encode a 140-kDa adhesin that shared both DNA and protein sequence similarities with P1, a major adhesin of M. pneumoniae. In this report, we show that M. genitalium possesses additional homolog sequences to well-characterized adherence-related genes and proteins of M. pneumoniae. The M. genitalium homologs are designated P32 and P69 and correspond to P30 and HMW3 of M. pneumoniae, respectively (J. B. Baseman, p. 243-259, in S. Rottem and I. Kahane, ed., Subcellular biochemistry, vol. 20. Mycoplasma cell membranes, 1993, and D. C. Krause, D. K. Leith, R. M. Wilson, and J. B. Baseman, Infect. Immun. 35:809-817, 1982). Interestingly, the operon-like organizations of P32 and P69 in the M. genitalium genome are similar to the organizations of P30 and HMW3 genes of M. pneumoniae, suggesting that the conservation of these adherence-related genes and proteins might have occurred through horizontal gene transfer events originating from an ancestral gene family.}, }
@article {pmid7582167, year = {1995}, author = {Nakatsu, CH and Fulthorpe, RR and Holland, BA and Peel, MC and Wyndham, RC}, title = {The phylogenetic distribution of a transposable dioxygenase from the Niagara River watershed.}, journal = {Molecular ecology}, volume = {4}, number = {5}, pages = {593-603}, doi = {10.1111/j.1365-294x.1995.tb00259.x}, pmid = {7582167}, issn = {0962-1083}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; Canada ; *DNA Transposable Elements ; *Dioxygenases ; Escherichia coli/classification/genetics ; Fresh Water ; Gene Transfer, Horizontal ; Genes, Bacterial ; Oxygenases/analysis/*genetics ; Phenotype ; *Phylogeny ; Plasmids ; Pseudomonas fluorescens/classification/*genetics/isolation &amp; purification ; Restriction Mapping ; *Water Microbiology ; Xanthomonas/classification/*genetics/isolation &amp; purification ; }, abstract = {Horizontal gene transfer in the Bacteria has been demonstrated to occur under natural conditions. The ecological impact of gene transfer events depends on the new genetic material being expressed in recipient organisms, and on natural selection processes operating on these recipients. The phylogenetic distribution of cbaAB genes for chlorobenzoate 3,4-(4,5)-dioxygenase, which are carried within Tn5271 on the IncP beta plasmid pBRC60, was investigated using isolates from freshwater microcosms and from the Niagara River watershed. The latter included isolates from surface water, groundwater and bioremediation reactor samples. The cbaAB genes have become integrated, through interspecific transfer, primarily into species of the beta Proteobacteria (44/48 isolates). Only four isolates, identified as Pseudomonas fluorescens (3/48) and Xanthomonas maltophilia (1/48), belonged to the gamma Proteobacteria, despite the observation that pBRC60 was capable of mobilizing these genes into a wide range of beta and gamma Proteobacteria in the laboratory. The natural host range correlated with the distribution of the meta-ring-fission pathway for metabolism of protocatechuates formed when the cbaAB genes were expressed (45/48 isolates). We proposed the hypothesis that natural selection has favoured recipients that successfully integrate the activity of the transferred dioxygenase with the conserved meta ring-fission pathway. The hypothesis was tested by transferring a plasmid construct containing the cbaAB genes into type strains representative of the beta and gamma Proteobacteria. The concept of applying mobile catabolic genes to probe the phylogenetic distribution of compatible degradative pathways is discussed.}, }
@article {pmid7571437, year = {1995}, author = {Hawtin, RE and Arnold, K and Ayres, MD and Zanotto, PM and Howard, SC and Gooday, GW and Chappell, LH and Kitts, PA and King, LA and Possee, RD}, title = {Identification and preliminary characterization of a chitinase gene in the Autographa californica nuclear polyhedrosis virus genome.}, journal = {Virology}, volume = {212}, number = {2}, pages = {673-685}, doi = {10.1006/viro.1995.1525}, pmid = {7571437}, issn = {0042-6822}, mesh = {Amino Acid Sequence ; Animals ; Antibodies, Viral ; Base Composition ; Base Sequence ; Cell Line ; Chitinases/chemistry/*genetics/immunology/metabolism ; Cytoplasm/enzymology ; Evolution, Molecular ; Gene Expression Regulation, Enzymologic ; Genes, Viral/*genetics ; Molecular Sequence Data ; Nucleopolyhedroviruses/enzymology/*genetics/immunology/physiology ; Phylogeny ; RNA, Messenger/biosynthesis ; RNA, Viral/biosynthesis ; Recombinant Proteins/immunology ; Sequence Homology, Amino Acid ; Spodoptera ; Transcription, Genetic/genetics ; Viral Structural Proteins/*genetics ; Virus Replication ; }, abstract = {A functional chitinase gene (chiA) has been identified in the genome of the Autographa californica nuclear polyhedrosis virus (AcMNPV). It is expressed in the late phase of virus replication in insect cells. High levels of both endo- and exochitinase activity were detected by 12 hr p.i. and remained stable throughout infection. An AcMNPV chiA protein-specific antibody was prepared using recombinant material prepared in bacteria. This was used to demonstrate that a product of approximately 58 kDa was synthesised in virus-infected cells. Immunofluorescence analysis of virus-infected cells showed that most chitinase was located in the cytoplasm. Primer extension analysis of mRNA from AcMNPV-infected cells confirmed that transcription initiated from a baculovirus late start site (TAAG), 14 nucleotides upstream from the putative translation initiation codon. The predicted protein sequence of the AcMNPV chiA shares extensive sequence similarity with chitinases from bacteria and, in particular, the Serratia marcescens chitinase A (60.5% identical residues). Phylogenetic analyses indicate that AcMNPV, or an ancestral baculovirus, acquired the chitinase gene from a bacterium via horizontal gene transfer.}, }
@article {pmid8637843, year = {1995}, author = {Degtyarenko, KN}, title = {Structural domains of P450-containing monooxygenase systems.}, journal = {Protein engineering}, volume = {8}, number = {8}, pages = {737-747}, doi = {10.1093/protein/8.8.737}, pmid = {8637843}, issn = {0269-2139}, mesh = {Animals ; Cloning, Molecular ; Cytochrome P-450 Enzyme System/*chemistry/genetics/metabolism ; Enzymes/chemistry ; Humans ; Introns ; Mixed Function Oxygenases/*chemistry/genetics/metabolism ; Models, Structural ; Nitric Oxide Synthase/chemistry ; Protein Engineering ; *Protein Structure, Secondary ; Recombinant Fusion Proteins/chemistry/metabolism ; Recombinant Proteins/chemistry/metabolism ; Transfection ; }, abstract = {All known P450-containing monooxygenase systems share common structural and functional domain architecture. Apart from P450 itself, these systems can comprise several fundamentally different protein components or domains, all of which are shared by other multicomponent/multidomain enzyme systems with various functions: FAD flavoprotein or domain, FMN domain, Fe2S2 ferredoxin, Fe3S4 ferredoxin, and cytochrome b5. Either FMN domain, ferredoxins or cytochrome b5 serve as the electron transport intermediate between the FAD domain and P450. The molecular evolution of both P450-containing systems and of each particular component does not follow phylogeny in general. Gene fusion and horizontal gene transfer events can lead to the appearance of novel redox chains in the same manner that artificial chimeric proteins can be constructed by humans. Recent studies using genetic and protein engineering techniques to investigate the separate domains and their interaction are described.}, }
@article {pmid7666441, year = {1995}, author = {Briones, MR and Egima, CM and Eichinger, D and Schenkman, S}, title = {Trans-sialidase genes expressed in mammalian forms of Trypanosoma cruzi evolved from ancestor genes expressed in insect forms of the parasite.}, journal = {Journal of molecular evolution}, volume = {41}, number = {2}, pages = {120-131}, pmid = {7666441}, issn = {0022-2844}, support = {R03 TW00227-01/TW/FIC NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Biological Evolution ; Genes, Protozoan/*genetics ; Glycoproteins/*genetics ; Insecta ; Mammals ; Molecular Sequence Data ; Neuraminidase/*genetics ; *Phylogeny ; RNA, Protozoan/genetics ; RNA, Ribosomal, 5S/genetics ; Sequence Alignment ; Trypanosoma cruzi/enzymology/*genetics ; }, abstract = {The trans-sialidase of Trypanosoma cruzi mammalian forms transfers sialic acids from host's cell-surface glycoconjugates to acceptor molecules on parasite cell surface. To investigate the mechanism by which the mammalian stages of Trypanosoma cruzi have acquired their trans-sialidase, we compared the nucleotide and predicted amino acid sequences of trans-sialidase genes expressed in different developmental stages and strains of Trypanosoma cruzi with the sialidase gene of Trypanosoma rangeli and the sialidase genes of the prokaryotic genera Clostridium, Salmonella, and Actinomyces. The trans-sialidase gene products of Trypanosoma cruzi have a significant degree of structural and biochemical similarity to the sialidases found in bacteria and viruses, which would hint that horizontal gene transfer occurred in Trypanosoma cruzi trans-sialidase evolutionary history. The comparison of inferred gene trees with species trees suggests that the genes encoding the T. cruzi trans-sialidase of mammalian forms might be derived from genes expressed in the insect forms of the genus Trypanosoma. The branching order of trees inferred from T. cruzi trans-sialidase sequences, the sialidase from Trypanosoma rangeli, and bacterial sialidases parallels the expected branching order of the species and suggests that the divergence times of these sequences are remarkably long. Therefore, a "vertical" inheritance from a hypothetical eukaryotic trans-sialidase gene expressed in insect forms of trypanosomes is more likely to have occurred than the horizontal gene transfer from bacteria, and thus explains the presence of this enzyme in the mammalian infective forms of Trypanosoma cruzi.}, }
@article {pmid7651331, year = {1995}, author = {Kempken, F}, title = {Horizontal transfer of a mitochondrial plasmid.}, journal = {Molecular &amp; general genetics : MGG}, volume = {248}, number = {1}, pages = {89-94}, pmid = {7651331}, issn = {0026-8925}, mesh = {Ascomycota/*genetics ; Base Sequence ; *DNA, Fungal ; Mitochondria/*genetics ; Molecular Sequence Data ; *Plasmids ; Research Design ; *Transformation, Genetic ; }, abstract = {Direct evidence for horizontal transfer of a mitochondrial plasmid from the discomycete Ascobolus immersus to the pyrenomycete Podospora anserina is presented. Southern blot hybridisation analysis, polymerase chain reaction (PCR) amplification, and DNA sequencing demonstrate transmission of a linear plasmid upon hyphal contact. DNA extraction from isolated organelles indicates a mitochondrial localisation for the plasmid in P. anserina. This is the first report of horizontal gene transfer among unrelated fungi. These results have important evolutionary implications for plasmid propagation in fungi.}, }
@article {pmid9158753, year = {1995}, author = {Heaton, MP and Handwerger, S}, title = {Conjugative mobilization of a vancomycin resistance plasmid by a putative Enterococcus faecium sex pheromone response plasmid.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {1}, number = {2}, pages = {177-183}, doi = {10.1089/mdr.1995.1.177}, pmid = {9158753}, issn = {1076-6294}, support = {AI-31612/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Conjugation, Genetic/*genetics ; DNA Probes ; DNA, Bacterial/analysis/isolation &amp; purification ; Enterococcus faecium/drug effects/*genetics ; Erythromycin/pharmacology ; Gram-Negative Bacterial Infections/microbiology ; Humans ; Plasmids/*genetics ; Restriction Mapping ; Sex Attractants/*pharmacology ; Vancomycin/*pharmacology ; }, abstract = {Recent epidemiological evidence suggests that horizontal gene transfer may be an important mechanism for dissemination of vancomycin resistance. A filter mating survey of 21 VanA Enterococcus faecium isolates from The New York Hospital showed that 14 of these isolates transferred vancomycin resistance (Vmr) to the plasmid-free reference strain Enterococcus faecalis JH2-2. One isolate, E. faecium R7, was selected for further study based on its ability to transfer Vmr to strain JH2-2 in liquid culture. Analysis of the plasmid content of transconjugants revealed three general classes. The predominant class (28 of 47 transconjugants) contained two separate plasmids: pHKK702 and pHKK703. pHKK702 is a 41-kb plasmid that contains an element indistinguishable from the Vmr transposon Tn1546 and an element that hybridizes with an ermB probe from the Staphylococcus aureus erythromycin resistance transposon Tn551. pHKK703 is a 55-kb plasmid that hybridizes with probes for the sex pheromone response genes prgA, prgB, and prgX derived from the E. faecalis plasmid pCF10. The second group of transconjugants (18 of 47) contained various recombinant forms of pHKK702 and pHKK703, whereas a third transconjugant class contained only pHKK702 (1 of 47). Transconjugants that contained both pHKK702 and pHKK703 were able to efficiently transfer Vmr to recipient strains in broth or on filters. However, no transfer of Vmr was detected using the donor containing only pHKK702. The transfer of Vmr from the recombination-deficient derivative of E. faecalis JH2-2 [strain UV202(pHKK702, pHKK703)] was reduced 600-fold compared to that of JH2-2(pHKK702, pHKK703). We propose that pHKK703 functions as an E. faecium sex pheromone response plasmid that conjugatively mobilizes pHKK702, and that a major pathway for this mobilization may require donor-mediated recombination proficiency. This report provides the first example in which a plasmid containing a Tn1546-related element is conjugatively mobilized.}, }
@article {pmid7789807, year = {1995}, author = {Quillet, L and Barray, S and Labedan, B and Petit, F and Guespin-Michel, J}, title = {The gene encoding the beta-1,4-endoglucanase (CelA) from Myxococcus xanthus: evidence for independent acquisition by horizontal transfer of binding and catalytic domains from actinomycetes.}, journal = {Gene}, volume = {158}, number = {1}, pages = {23-29}, doi = {10.1016/0378-1119(95)00091-j}, pmid = {7789807}, issn = {0378-1119}, mesh = {Actinomyces/*metabolism ; Amino Acid Sequence ; Base Sequence ; Binding Sites ; Catalysis ; Cellulase/*genetics ; Cloning, Molecular ; DNA, Bacterial ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Myxococcus xanthus/enzymology/*genetics/metabolism ; Phylogeny ; Sequence Homology, Amino Acid ; }, abstract = {The celA gene encoding a beta-1,4 endoglucanase (CelA) from Myxococcus xanthus has been cloned in Escherichia coli and sequenced. The C-terminal region of CelA displayed a high level of similarity with the catalytic domain of several Egl belonging to the glycosyl hydrolases family 6 (CenA from Cellulomonas fimi, CelA from Microbispora bispora, E2 from Thermonospora fusca, CasA from Streptomyces KSM9 and CelA1 from Streptomyces halstedii) and less similarity to the cellobiohydrolases of the fungi Trichoderma reesei and Agaricus bisporus. Using PCR amplification we found in another myxobacterium, Stigmatella aurantiaca, a part of a glycosyl hydrolase belonging to the same family. The N-terminal part of CelA displayed significant similarities with the cellulose-binding domain of other cellulases belonging to a rare subset of family II, such as the avicelase I from Streptomyces reticuli, both tandem repeats N1 and N2 of the cellulase CenC from Cellulomonas fimi, and the N-terminal part of the Egl E1 from Thermonospora fusca. Analyses of the multiple alignments and reconstruction of phylogenetic trees strongly suggest that both domains of CelA were acquired by independent horizontal transfers between Gram+ soil bacteria and scavenging myxobacteria followed by domain shuffling.}, }
@article {pmid7781972, year = {1995}, author = {Selbitschka, W and Jording, D and Nieman, S and Schmidt, R and Pühler, A and Mendum, T and Hirsch, P}, title = {Construction and characterization of a Rhizobium leguminosarum biovar viciae strain designed to assess horizontal gene transfer in the environment.}, journal = {FEMS microbiology letters}, volume = {128}, number = {3}, pages = {255-263}, doi = {10.1111/j.1574-6968.1995.tb07533.x}, pmid = {7781972}, issn = {0378-1097}, mesh = {Base Sequence ; Escherichia coli/enzymology/genetics ; *Gene Transfer, Horizontal ; Genetic Vectors/*genetics ; Glucuronidase/genetics ; Molecular Sequence Data ; Mutagenesis ; Pisum sativum/microbiology ; Plant Roots/microbiology ; Plasmids/*genetics ; Rhizobium leguminosarum/*genetics/radiation effects ; Sequence Analysis, DNA ; *Soil Microbiology ; Symbiosis ; Ultraviolet Rays ; }, abstract = {An integration vector was developed which inserts cloned DNA in a non-essential site of the Rhizobium leguminosarum biovar viciae chromosome. The expression of integrated genes is under the control of the constitutive neomycin phosphotransferase II (nptII) promoter of transposon Tn5. The design of the vector ensures that loss of vector sequences can be detected, enabling selection of progeny containing only the requisite DNA. The newly constructed vector was employed to insert the Escherichia coli gusA gene conferring GUS activity into R. leguminosarum bv. viciae strain LRS39401 which is cured of its symbiotic plasmid (pSym). One GUS-positive transconjugant, strain CT0370, was shown to have lost all vector sequences. Conjugal transfer of pSym2004 (a Tn5-tagged derivative of symbiotic plasmid pRL1JI, which specifies pea nodulation and symbiotic nitrogen fixation) to CT0370, restored the GUS-positive strain's symbiotic proficiency. Strain CT0370 is presently being used in a field release experiment in order to assess the extent of pSym transfer in a natural R. leguminosarum bv. viciae population under environmental conditions.}, }
@article {pmid7783222, year = {1995}, author = {Rogers, KC and Söll, D}, title = {Divergence of glutamate and glutamine aminoacylation pathways: providing the evolutionary rationale for mischarging.}, journal = {Journal of molecular evolution}, volume = {40}, number = {5}, pages = {476-481}, pmid = {7783222}, issn = {0022-2844}, mesh = {Acylation ; Amino Acyl-tRNA Synthetases/*metabolism ; Anticodon ; *Biological Evolution ; Eukaryotic Cells/enzymology ; *Genetic Code ; Glutamate-tRNA Ligase/*metabolism ; Glutamic Acid/*metabolism ; Glutamine/*metabolism ; Models, Genetic ; *Nitrogenous Group Transferases ; Prokaryotic Cells/enzymology ; RNA, Transfer, Amino Acyl/*biosynthesis ; RNA, Transfer, Gln/metabolism ; RNA, Transfer, Glu/metabolism ; Transferases/*metabolism ; }, abstract = {Aminoacyl-tRNA for protein synthesis is produced through the action of a family of enzymes called aminoacyl-tRNA synthetases. A general rule is that there is one aminoacyl-tRNA synthetase for each of the standard 20 amino acids found in all cells. This is not universal, however, as a majority of prokaryotic organisms and eukaryotic organelles lack the enzyme glutaminyl-tRNA synthetase, which is responsible for forming Gln-tRNAGln in eukaryotes and in Gram-negative eubacteria. Instead, in organisms lacking glutaminyl-tRNA synthetase, Gln-tRNAGln is provided by misacylation of tRNAGln with glutamate by glutamyl-tRNA synthetase, followed by the conversion of tRNA-bound glutamate to glutamine by the enzyme Glu-tRNAGln amidotransferase. The fact that two different pathways exist for charging glutamine tRNA indicates that ancestral prokaryotic and eukaryotic organisms evolved different cellular mechanisms for incorporating glutamine into proteins. Here, we explore the basis for diverging pathways for aminoacylation of glutamine tRNA. We propose that stable retention of glutaminyl-tRNA synthetase in prokaryotic organisms following a horizontal gene transfer event from eukaryotic organisms (Lamour et al. 1994) was dependent on the evolving pool of glutamate and glutamine tRNAs in the organisms that acquired glutaminyl-tRNA synthetase by this mechanism. This model also addresses several unusual aspects of aminoacylation by glutamyl- and glutaminyl-tRNA synthetases that have been observed.}, }
@article {pmid7739384, year = {1995}, author = {Garcia-Fernàndez, J and Bayascas-Ramírez, JR and Marfany, G and Muñoz-Mármol, AM and Casali, A and Baguñà, J and Saló, E}, title = {High copy number of highly similar mariner-like transposons in planarian (Platyhelminthe): evidence for a trans-phyla horizontal transfer.}, journal = {Molecular biology and evolution}, volume = {12}, number = {3}, pages = {421-431}, doi = {10.1093/oxfordjournals.molbev.a040217}, pmid = {7739384}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; DNA Transposable Elements/*genetics ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; Planarians/*genetics ; Polymerase Chain Reaction ; Sequence Alignment ; }, abstract = {Several DNA sequences similar to the mariner element were isolated and characterized in the platyhelminthe Dugesia (Girardia) tigrina. They were 1,288 bp long, flanked by two 32 bp-inverted repeats, and contained a single 339 amino acid open-reading frame (ORF) encoding the transposase. The number of copies of this element is approximately 8,000 per haploid genome, constituting a member of the middle-repetitive DNA of Dugesia tigrina. Sequence analysis of several elements showed a high percentage of conservation between the different copies. Most of them presented an intact ORF and the standard signals of actively expressed genes, which suggests that some of them are or have recently been functional transposons. The high degree of similarity shared with other mariner elements from some arthropods, together with the fact that this element is undetectable in other planarian species, strongly suggests a case of horizontal transfer between these two distant phyla.}, }
@article {pmid7565111, year = {1995}, author = {Kapur, V and Kanjilal, S and Hamrick, MR and Li, LL and Whittam, TS and Sawyer, SA and Musser, JM}, title = {Molecular population genetic analysis of the streptokinase gene of Streptococcus pyogenes: mosaic alleles generated by recombination.}, journal = {Molecular microbiology}, volume = {16}, number = {3}, pages = {509-519}, doi = {10.1111/j.1365-2958.1995.tb02415.x}, pmid = {7565111}, issn = {0950-382X}, support = {AI-00964/AI/NIAID NIH HHS/United States ; AI-33119/AI/NIAID NIH HHS/United States ; }, mesh = {*Alleles ; Amino Acid Sequence ; Base Sequence ; Chromosomes, Bacterial ; *Genes, Bacterial ; Molecular Sequence Data ; Phylogeny ; *Recombination, Genetic ; Sequence Alignment ; Sequence Homology, Amino Acid ; Streptococcus pyogenes/*genetics ; Streptokinase/*genetics ; }, abstract = {To understand the mechanisms governing molecular evolution of the streptokinase gene (skn), a 384 bp DNA fragment encoding two variable regions of the molecule was characterized in 47 isolates of Streptococcus pyogenes. The results reveal that alleles of the streptokinase gene have a mosaic structure, and provide strong evidence for intragenic recombination. Moreover, organisms that are well differentiated in overall chromosomal character have identical skn alleles, which suggests that horizontal gene transfer and recombination have participated in the evolution of this locus. No simple relationship between skn allele and serum opacity factor production or specific disease was identified. The predicted amino acid sequences of highly divergent skn alleles are strikingly similar in hydrophilicity and hydrophobicity profiles, distribution of amphipathic and flexible regions, surface probability plots, and antigenic indices, indicating that despite extensive nucleotide polymorphism in the two skn variable regions, selective pressure has constrained overall structural divergence. These results add to an important emerging theme that intragenic recombination plays a critical role in diversifying genes coding for streptococcal virulence factors.}, }
@article {pmid9156381, year = {1995}, author = {Coffey, TJ and Dowson, CG and Daniels, M and Spratt, BG}, title = {Genetics and molecular biology of beta-lactam-resistant pneumococci.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {1}, number = {1}, pages = {29-34}, doi = {10.1089/mdr.1995.1.29}, pmid = {9156381}, issn = {1076-6294}, mesh = {*Aminoacyltransferases ; *Bacterial Proteins ; Carrier Proteins/*genetics ; *Genes, Bacterial ; *Hexosyltransferases ; Muramoylpentapeptide Carboxypeptidase/*genetics ; Penicillin Resistance/*genetics ; Penicillin-Binding Proteins ; *Peptidyl Transferases ; Recombination, Genetic ; *Streptococcus pneumoniae/drug effects/genetics ; }, abstract = {Penicillin-resistant pneumococci have been reported with increasing frequency in recent years. Isolates with high-level resistance are now found in many countries, and in some countries they constitute a substantial proportion of all isolates. A worrying development is the recent emergence of pneumococci with high-level resistance to third-generation cephalosporins. Resistance to beta-lactam antibiotics in pneumococci is due entirely to the development of altered forms of the high-molecular-weight penicillin-binding proteins (PBPs) that have decreased affinity for the antibiotics. High-level resistance to third-generation cephalosporins has occurred by the development of altered forms of PBP1a and 2x, whereas high-level penicillin resistance additionally requires alterations of PBP2b. Altered PBPs are encoded by mosaic genes that have emerged by recombinational events between the pbp genes of pneumococci and their homologs in closely related streptococcal species. Horizontal gene transfer, presumably mediated by genetic transformation, has also resulted in the dissemination of altered pbp genes, and possibly capsular biosynthetic genes, between different pneumococcal lineages to produce new resistant clones.}, }
@article {pmid7769620, year = {1995}, author = {Wiemer, EA and Hannaert, V and van den IJssel, PR and Van Roy, J and Opperdoes, FR and Michels, PA}, title = {Molecular analysis of glyceraldehyde-3-phosphate dehydrogenase in Trypanoplasma borelli: an evolutionary scenario of subcellular compartmentation in kinetoplastida.}, journal = {Journal of molecular evolution}, volume = {40}, number = {4}, pages = {443-454}, pmid = {7769620}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; *Cell Compartmentation ; Cytosol/enzymology ; Gene Transfer, Horizontal ; *Genes, Protozoan ; Glyceraldehyde-3-Phosphate Dehydrogenases/analysis/*genetics ; Isoenzymes/analysis/*genetics ; Molecular Sequence Data ; Organelles/enzymology ; *Phylogeny ; Protein Binding ; Protein Conformation ; Protozoan Proteins/analysis/*genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; Species Specificity ; Symbiosis ; Trypanosoma/classification/enzymology/*genetics/ultrastructure ; }, abstract = {In Trypanoplasma borelli, a representative of the Bodonina within the Kinetoplastida, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) activity was detected in both the cytosol and glycosomes. This situation is similar to that previously found in Trypanosomatidae, belonging to a different Kinetoplastida suborder. In Trypanosomatidae different isoenzymes, only distantly related, are responsible for the activity in the two cell compartments. In contrast, immunoblot analysis indicated that the GAPDH activity in cytosol and glycosomes of T. borelli should be attributed to identical or at least very similar proteins related to the glycosomal GAPDH of Trypanosomatidae. Moreover, only genes related to the glycosomal GAPDH genes of Trypanosomatidae could be detected. All attempts to identify a gene related to the one coding for the trypanosomatid cytosolic GAPDH remained unsuccessful. Two tandemly arranged genes were found which are 95% identical. The two encoded polypeptides differ in 17 residues. Their sequences are 72-77% identical to the glycosomal GAPDH of the other Kinetoplastida and share with them some characteristic features: an excess of positively charged residues, specific insertions, and a small carboxy-terminal extension containing the sequence -AKL. This tripeptide conforms to the consensus signal for targeting of proteins to glycosomes. One of the two gene copies has undergone some mutations at positions coding for highly conserved residues of the active site and the NAD(+)-binding domain of GAPDH. Modeling of the protein's three-dimensional structure suggested that several of the substitutions compensate each other, retaining the functional coenzyme-binding capacity, although this binding may be less tight. The presented analysis of GAPDH in T. borelli gives further support to the assertion that one isoenzyme, the cytosolic one, was acquired by horizontal gene transfer during the evolution of the Kinetoplastida, in the lineage leading to the suborder Trypanosomatina (Trypanosoma, Leishmania), after the divergence from the Bodonina (Trypanoplasma). Furthermore, the data clearly suggest that the original GAPDH of the Kinetoplastida has been compartmentalized during evolution.}, }
@article {pmid7700148, year = {1995}, author = {Pesole, G and Gissi, C and Lanave, C and Saccone, C}, title = {Glutamine synthetase gene evolution in bacteria.}, journal = {Molecular biology and evolution}, volume = {12}, number = {2}, pages = {189-197}, doi = {10.1093/oxfordjournals.molbev.a040197}, pmid = {7700148}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Archaea/enzymology/genetics ; Bacteria/enzymology/*genetics ; *Biological Evolution ; Codon/genetics ; Databases, Factual ; Eukaryotic Cells/enzymology ; Genes, Bacterial/*genetics ; Glutamate-Ammonia Ligase/*genetics ; Isoenzymes/*genetics ; Molecular Sequence Data ; Multigene Family/genetics ; Mutagenesis/genetics ; Prokaryotic Cells/enzymology ; RNA, Ribosomal/genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {The evolution of the prokaryotic glutamine synthase (GS) genes, namely the GSI and GSII isoforms, has been investigated using the second codon positions, which have previously proven to behave as a good molecular clock. Our data confirm the early divergence between prokaryotic and eukaryotic GSII before the splitting between plants and animals. The phylogenetic tree of the GSI isoforms shows Archaebacteria to be more closely related to Eubacteria than to Eukaryotes. This finding is confirmed by the phylogenetic analysis carried out on both large and small subunits of rRNA. However, differently from the rRNA analyses, Crenarchaeota and Euryarchaeota Archaebacteria, as well as high- and low-GC gram-positive bacteria, appear to be polyphyletic. We provide evidence that the observed polyphyly of Archaebacteria might be only apparent, resulting from a gene duplication event preceding the split between Archaebacteria and Eubacteria and followed by the retention of only one isoform in the extant lineages. Both gram-negative bacteria and high-GC gram-positive bacteria, which appear closely related, have GS activity regulated by an adenylylation/deadenylylation mechanism. A lateral gene transfer from Archaebacteria to low-GC eubacteria is invoked to explain the observed polyphyly of gram-positive bacteria.}, }
@article {pmid7623660, year = {1995}, author = {Whatmore, AM and Kapur, V and Musser, JM and Kehoe, MA}, title = {Molecular population genetic analysis of the enn subdivision of group A streptococcal emm-like genes: horizontal gene transfer and restricted variation among enn genes.}, journal = {Molecular microbiology}, volume = {15}, number = {6}, pages = {1039-1048}, doi = {10.1111/j.1365-2958.1995.tb02279.x}, pmid = {7623660}, issn = {0950-382X}, support = {AI-33119/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; *Antigens, Bacterial ; *Bacterial Outer Membrane Proteins ; Bacterial Proteins/*genetics ; Base Sequence ; *Carrier Proteins ; DNA, Bacterial/analysis ; Genetic Variation/*genetics ; Molecular Sequence Data ; Multigene Family/*genetics ; Phylogeny ; Protein Sorting Signals/genetics ; Recombination, Genetic ; Regulon/*genetics ; Sequence Analysis, DNA ; Streptococcus pyogenes/*genetics ; }, abstract = {The group A streptococcal emm-like genes, which encode the cell-surface M and M-like proteins, are divided into distinct mrp, emm and enn subdivisions and are clustered together in a region of the chromosome called the vir regulon. In order to understand the mechanisms involved in the evolution of emm-like genes, a 180 bp fragment of the 5' variable region of the enn gene was characterized in 31 strains for which emm sequences and multilocus enzyme electrophoretic profiles have been previously determined. The results demonstrate that nucleotide polymorphisms at the enn locus are generated predominantly by point mutations and short deletions or insertions, and that variation among enn and emm genes has arisen by similar mechanisms. However, diversity at the enn locus is restricted in comparison to the emm locus. Moreover, there is strong evidence for intragenic recombination at the enn locus and the pattern of distribution of emm and enn alleles among strains suggests that these genes may be independently acquired by horizontal transfer and recombination from distinct donor strains, thereby generating a mosaic structure for the vir regulon. The results add to a growing body of evidence that horizontal gene transfer has played a major role in the evolution of Streptococcus pyogenes vir regulons.}, }
@article {pmid7535375, year = {1995}, author = {Springer, MS and Tusneem, NA and Davidson, EH and Britten, RJ}, title = {Phylogeny, rates of evolution, and patterns of codon usage among sea urchin retroviral-like elements, with implications for the recognition of horizontal transfer.}, journal = {Molecular biology and evolution}, volume = {12}, number = {2}, pages = {219-230}, doi = {10.1093/oxfordjournals.molbev.a040196}, pmid = {7535375}, issn = {0737-4038}, mesh = {Animals ; Base Sequence ; *Biological Evolution ; Cell Nucleus/genetics ; Gene Transfer, Horizontal ; Genetic Code ; Genetic Variation/genetics ; Histones/genetics ; Molecular Sequence Data ; RNA, Ribosomal/genetics ; RNA-Directed DNA Polymerase/genetics ; Retroelements/*genetics ; Sea Urchins/*genetics ; Time Factors ; }, abstract = {Phylogenetic relationships, rates of evolution, and codon usage were investigated in a family of retrotransposons (SURL elements) found in echinoids. The phylogeny of SURL element reverse transcriptase sequences from 10 echinoid species clearly shows the phylogenetic signature of the host taxa as well as paralogous sequences that diverged prior to speciation events. Two subfamilies (1 and 5) of SURL element reverse transcriptase sequences are recognized that diverged prior to the radiation of the Echinometridae. Comparisons of synonymous versus nonsynonymous substitutions indicate that SURL elements have been active in echinoid genomes and have evolved under purifying selection for millions of years. Rates of synonymous substitution for reverse transcriptase are similar to rates of single-copy DNA evolution and to rates of synonymous substitution for the H3 and H4 histone genes, contradicting the assumption that rates of evolution are accelerated in retrotransposons. Finally, codon usage in SURL elements is biased for codons ending in A or U relative to 42 sea urchin nuclear genes. Biased codon usage is sometimes cited as evidence for horizontal transfer, but in the case of SURL elements this bias occurs in spite of a long history of vertical transmission rather than because of horizontal transfer.}, }
@article {pmid7869379, year = {1995}, author = {Berti, PJ and Storer, AC}, title = {Alignment/phylogeny of the papain superfamily of cysteine proteases.}, journal = {Journal of molecular biology}, volume = {246}, number = {2}, pages = {273-283}, doi = {10.1006/jmbi.1994.0083}, pmid = {7869379}, issn = {0022-2836}, mesh = {Amino Acid Sequence ; Animals ; Binding Sites ; Biological Evolution ; Calpain/chemistry ; Cathepsins/chemistry ; Crystallography, X-Ray ; Cysteine Endopeptidases/chemistry ; Molecular Sequence Data ; Papain/*chemistry/*genetics ; *Phylogeny ; Plants/enzymology ; *Protein Conformation ; Protein Structure, Secondary ; Saccharomyces cerevisiae ; Sequence Homology, Amino Acid ; }, abstract = {An alignment/phylogeny of the papain superfamily of cysteine proteases was created using an initial structure-based alignment followed by successive iterations of sequence alignment and phylogenetic inference. The iterative approach resulted in significant improvements in the alignment/phylogeny. There were three groups of cysteine proteases that were distantly related and which could be aligned against each other only in the active site regions: the papain group, which included such stereotypical cysteine proteases as cathepsins B, C, H, L and S; and the bleomycin hydrolase and calpain groups. There was one bacterial sequence in each of the bleomycin hydrolase and calpain groups. The former probably arose by lateral gene transfer, the latter possibly by direct evolution from an ancestral protease predating the eukaryote/prokaryote divergence. The phylogeny of the papain group indicated that many families diverged almost simultaneously early during eukaryotic evolution. In mammals there are at least 12 distinct families of cysteine proteases, possibly many more, including at least two as yet uncharacterized enzymes.}, }
@article {pmid7714192, year = {1995}, author = {Schnitzler, N and Podbielski, A and Baumgarten, G and Mignon, M and Kaufhold, A}, title = {M or M-like protein gene polymorphisms in human group G streptococci.}, journal = {Journal of clinical microbiology}, volume = {33}, number = {2}, pages = {356-363}, pmid = {7714192}, issn = {0095-1137}, mesh = {Amino Acid Sequence ; Animals ; *Antigens, Bacterial ; *Bacterial Outer Membrane Proteins ; Bacterial Proteins/*genetics ; Base Sequence ; *Carrier Proteins ; DNA Probes/genetics ; DNA, Bacterial/genetics ; Genes, Bacterial ; Humans ; Molecular Sequence Data ; Phagocytosis ; Polymerase Chain Reaction ; *Polymorphism, Genetic ; Sequence Homology, Amino Acid ; Species Specificity ; Streptococcal Infections/microbiology ; Streptococcus/*classification/*genetics/isolation &amp; purification ; Streptococcus pyogenes/genetics ; }, abstract = {Many group G streptococci (GGS) isolated from infected humans (but not from animal sources) express M or M-like proteins with biological, immunochemical, and genetic features similar to those of group A streptococci (GAS). To further elucidate the recently proposed M-like protein gene (emmL gene) polymorphisms in GGS, Southern blots of genomic DNAs from 38 epidemiologically unrelated GGS strains isolated from human specimens and 12 GGS strains recovered from animal sources were hybridized with oligonucleotide probes designed to specifically detect GAS M class I and M class II M protein (emm) genes. All human-associated GGS strains showed DNA homology to the GAS M class I emm gene probe, whereas no hybridization was found with DNA from any of the animal-associated strains. The emmL genes from all human isolates were amplified by PCR, and the complete sequence of the emmL gene of the Rebecca Lancefield grouping strain D166B was determined. Again, this gene exhibited the structural features typical for emm genes of M class I GAS. The 5' regions of the PCR-amplified emmL genes of the remaining 37 human GGS strains were sequenced. This region showed a sequence diversity similar to that known for GAS emm genes. When strains whose N-terminal emmL gene sequences showed a homology of > 95% were defined as belonging to one genetic type, 30 strains were segregated into six distinct genetic types, whereas the remaining 8 strains each exhibited a unique emmL gene sequence. A high degree of homology between the N-terminal emmL gene segments of six GGS strains and the corresponding regions of either the emm12 or the emm57 gene of GAS was found, suggesting a horizontal gene transfer between strains of these species of beta-hemolytic streptococci. Besides a further understanding of the evolution of GGS emmL genes, the observed emmL gene polymorphisms in GGS could provide the basis for a molecular subspecies delineation of strains and offers the potential of typing GGS for epidemiological purposes.}, }
@article {pmid7704262, year = {1995}, author = {Lazarevic, V and Mauël, C and Soldo, B and Freymond, PP and Margot, P and Karamata, D}, title = {Sequence analysis of the 308 degrees to 311 degrees segment of the Bacillus subtilis 168 chromosome, a region devoted to cell wall metabolism, containing non-coding grey holes which reveal chromosomal rearrangements.}, journal = {Microbiology (Reading, England)}, volume = {141 (Pt 2)}, number = {}, pages = {329-335}, doi = {10.1099/13500872-141-2-329}, pmid = {7704262}, issn = {1350-0872}, mesh = {Bacillus subtilis/*genetics/metabolism ; Base Sequence ; Cell Wall/*genetics/metabolism ; Chromosomes, Bacterial/*genetics ; DNA, Bacterial/*genetics ; Gene Rearrangement/*genetics ; Genes, Bacterial/genetics ; Molecular Sequence Data ; Multigene Family ; Nucleic Acid Conformation ; Open Reading Frames/genetics ; Operon/genetics ; Regulatory Sequences, Nucleic Acid/genetics ; Repetitive Sequences, Nucleic Acid/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {The 29.71 kb chromosomal region of Bacillus subtilis 168 extending from 308 degrees to 311 degrees contains 18 ORFs. Functions of most of these ORFs were identified and associated with cell wall metabolism. Sequences of two non-coding regions of 0.7 and 2.2 kb flanking the ggaAB operon involved in the synthesis of poly(3-O-beta-D-glucopyranosyl N-acetylgalactosamine 1-phosphate), a minor teichoic acid, correspond to five degenerate segments of neighbouring protein-coding regions. We discuss the possibility that such grey holes are indicative of a chromosomal rearrangement which could have arisen from horizontal gene transfer.}, }
@article {pmid7835331, year = {1995}, author = {Bik, EM and Bunschoten, AE and Gouw, RD and Mooi, FR}, title = {Genesis of the novel epidemic Vibrio cholerae O139 strain: evidence for horizontal transfer of genes involved in polysaccharide synthesis.}, journal = {The EMBO journal}, volume = {14}, number = {2}, pages = {209-216}, pmid = {7835331}, issn = {0261-4189}, mesh = {Amino Acid Sequence ; Asia/epidemiology ; Bacterial Proteins/genetics ; Base Sequence ; Cholera/epidemiology/*microbiology ; DNA, Bacterial ; *Disease Outbreaks ; Molecular Sequence Data ; Phylogeny ; Polysaccharides/*biosynthesis ; Sequence Homology, Amino Acid ; Species Specificity ; *Transformation, Bacterial ; Vibrio cholerae/*genetics/metabolism/pathogenicity ; }, abstract = {Only Vibrio cholerae strains of serotype O1 are known to cause epidemics, while non-O1 strains are associated with sporadic cases of cholera. It was therefore unexpected that the recent cholera epidemic in Asia was caused by a non-O1 strain with the serotype O139. We provide evidence that O139 arose from a strain closely related to the causative agent of the present cholera pandemic, V. cholerae O1 El Tor, by acquisition of novel DNA which was inserted into, and replaced part of, the O antigen gene cluster of the recipient strain. Part of the novel DNA was sequenced and two open reading frames (otnA and otnB) were observed, the products of which showed homology to proteins involved in capsule and O antigen synthesis, respectively. This suggests that the otnAB DNA determines the distinct antigenic properties of the O139 cell surface. The otnAB DNA was not detected in O1 strains, but was present in two non-O1 V. cholerae strains with serotypes O69 and O141. In the O69 and O139 strains the otnAB genes were located proximate to the putative insertion sequence (IS) element rfbQRS, which is associated with O antigen synthesis genes in O1 strains, and may have played a role in the insertion of the otnAB DNA in the recipient chromosome. Our results suggest that the O139 strain arose by horizontal gene transfer between a non-O1 and an O1 strain. The acquired DNA has altered the antigenic properties of the recipient O1 strain, providing a selective advantage in a region where a large part of the population is immune to O1 strains.(ABSTRACT TRUNCATED AT 250 WORDS)}, }
@article {pmid8828153, year = {1995}, author = {Kutter, E and Gachechiladze, K and Poglazov, A and Marusich, E and Shneider, M and Aronsson, P and Napuli, A and Porter, D and Mesyanzhinov, V}, title = {Evolution of T4-related phages.}, journal = {Virus genes}, volume = {11}, number = {2-3}, pages = {285-297}, pmid = {8828153}, issn = {0920-8569}, mesh = {Amino Acid Sequence ; Animals ; Bacteriophage T4/*genetics/physiology ; *Evolution, Molecular ; Genes, Viral ; Humans ; Molecular Sequence Data ; Multigene Family ; Open Reading Frames ; Sequence Homology, Amino Acid ; Virus Assembly ; }, abstract = {Much progress has been made in understanding T-even phage biology in the last 50 years. We now know the entire sequence of T4, encoding nearly 300 genes, only 69 of which have been shown to be essential under standard laboratory conditions; no specific function is yet known for about 140 of them. The origin of most phage genes is unclear, and only 42 genes in T4 have significant similarity to anything currently included in GenBank. Comparative analysis of related phages is now being used to gain insight into both the evolutionary origins and interrelationships of these phage genes, and the functions of their protein products. The genomes of phages isolated from Tbilisi hospitals, Long Island sewage plants, the Denver zoo, and Khabarovsk show basic similarity. However, these phages show substantial insertions and deletions in a number of regions relative to each other, and closer investigation of specific sequences often reveals much more complex relationships. There are only a few cases in T4-related phages in which there is evidence for evolution through DNA duplication. These include the fibrous products of genes 12, 34, and 37; head proteins gp23 and gp24; and the Alt enzyme and its downstream neighbors. T4 also contains 13 apparent relatives of group I and group II intron homing endonucleases. Distal portions of the tail fibers of various T-even phages contain segments closely related to tail-fiber regions of other DNA coliphages, such as Mu, P1, P2, and lambda. Horizontal gene transfer clearly emerges as a major factor in the evolution of at least the tail-fiber regions, where site-specific recombination probably is involved in the exchange of host-range determinants.}, }
@article {pmid8586170, year = {1995}, author = {Bessen, DE and Hollingshead, SK}, title = {Horizontal transfer and mosaic-like emm gene structures in group A streptococci.}, journal = {Developments in biological standardization}, volume = {85}, number = {}, pages = {169-173}, pmid = {8586170}, issn = {0301-5149}, support = {AI-28944/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Antibodies, Bacterial/metabolism ; Antigens, Bacterial/genetics ; *Bacterial Outer Membrane Proteins ; Bacterial Proteins/*genetics/immunology ; Binding Sites/genetics ; *Carrier Proteins ; Consensus Sequence ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Immunoglobulin A/metabolism ; Immunoglobulin G/metabolism ; Molecular Sequence Data ; Mosaicism ; Multigene Family ; Streptococcus pyogenes/*genetics/immunology/isolation &amp; purification ; }, }
@article {pmid7894725, year = {1995}, author = {Wassenaar, TM and Fry, BN and van der Zeijst, BA}, title = {Variation of the flagellin gene locus of Campylobacter jejuni by recombination and horizontal gene transfer.}, journal = {Microbiology (Reading, England)}, volume = {141 (Pt 1)}, number = {}, pages = {95-101}, doi = {10.1099/00221287-141-1-95}, pmid = {7894725}, issn = {1350-0872}, mesh = {Base Sequence ; Campylobacter jejuni/*genetics/metabolism ; Crossing Over, Genetic ; DNA Primers ; DNA, Bacterial/metabolism ; Flagellin/biosynthesis/*genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; *Genetic Variation ; Models, Genetic ; Molecular Sequence Data ; Polymerase Chain Reaction ; *Recombination, Genetic ; Transformation, Bacterial ; }, abstract = {The capacity of Campylobacter jejuni to generate genetic diversity was determined for its flagellar region. Recombination within a genome, as well as recombination after the uptake of exogenous DNA, could be demonstrated. The subunit of the flagellar filament of C. jejuni is encoded by two tandem genes, flaA and flaB, which are highly similar and therefore subject to recombination. A spontaneous recombination within this locus was demonstrated in a bacterial clone containing an antibiotic-resistance gene inserted in flaA. A recombinant was isolated in which the antibiotic-resistance gene had been repositioned into flaB, indicating that genetic information can be exchanged between the two flagellin genes of C. jejuni. The occurrence of recombinational events after the uptake of exogenous DNA by naturally competent bacteria was demonstrated with two mutants containing different antibiotic-resistance markers in their flagellin genes. Double-resistant transformants were formed when purified chromosomal donor DNA was added to a recipient strain, when the two bacterial cultures were mixed under conditions that induce natural competence, or when the two strains were cocultured. Both mechanisms of recombination may be used by the pathogenic organism to escape the immunological responses of the host or otherwise adapt to the environment.}, }
@article {pmid7877490, year = {1995}, author = {Hirsch, AM and McKhann, HI and Reddy, A and Liao, J and Fang, Y and Marshall, CR}, title = {Assessing horizontal transfer of nifHDK genes in eubacteria: nucleotide sequence of nifK from Frankia strain HFPCcI3.}, journal = {Molecular biology and evolution}, volume = {12}, number = {1}, pages = {16-27}, doi = {10.1093/oxfordjournals.molbev.a040184}, pmid = {7877490}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Biological Evolution ; Eubacterium/enzymology/*genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Gram-Positive Bacteria/*genetics ; Klebsiella pneumoniae/enzymology/*genetics ; Molecular Sequence Data ; Nitrogenase/*genetics ; *Phylogeny ; Sequence Homology, Amino Acid ; }, abstract = {The structural genes for nitrogenase, nifK, nifD, and nifH, are crucial for nitrogen fixation. Previous phylogenetic analysis of the amino acid sequence of nifH suggested that this gene had been horizontally transferred from a proteobacterium to the gram-positive/cyanobacterial clade, although the confounding effects of paralogous comparisons made interpretation of the data difficult. An additional test of nif gene horizontal transfer using nifD was made, but the NifD phylogeny lacked resolution. Here nif gene phylogeny is addressed with a phylogenetic analysis of a third and longer nif gene, nifK. As part of the study, the nifK gene of the key taxon Frankia was sequenced. Parsimony and some distance analyses of the nifK amino acid sequences provide support for vertical descent of nifK, but other distance trees provide support for the lateral transfer of the gene. Bootstrap support was found for both hypotheses in all trees; the nifK data do not definitively favor one or the other hypothesis. A parsimony analysis of NifH provides support for horizontal transfer in accord with previous reports, although bootstrap analysis also shows some support for vertical descent of the orthologous nifH genes. A wider sampling of taxa and more sophisticated methods of phylogenetic inference are needed to understand the evolution of nif genes. The nif genes may also be powerful phylogenetic tools. If nifK evolved by vertical descent, it provides strong evidence that the cyanobacteria and proteobacteria are sister groups to the exclusion of the firmicutes, whereas 16S rRNA sequences are unable to resolve the relationships of these three major eubacterial lineages.}, }
@article {pmid7579980, year = {1995}, author = {Jeffery, J}, title = {Enzymes: chemistry and biochemistry.}, journal = {EXS}, volume = {73}, number = {}, pages = {79-104}, doi = {10.1007/978-3-0348-9061-8_5}, pmid = {7579980}, issn = {1023-294X}, mesh = {Amino Acid Sequence ; Amino Acids/chemistry/metabolism ; Antibodies, Catalytic/immunology/*metabolism ; Binding Sites ; Catalysis ; Coenzymes/metabolism ; Enzymes/chemistry/*metabolism ; Evolution, Molecular ; Hydrogen Bonding ; Kinetics ; Metals/metabolism ; Molecular Sequence Data ; Protein Conformation ; RNA, Catalytic/genetics/*metabolism ; }, abstract = {Basic principles underlying enzyme action are considered. Catalytic antibodies (abzymes), catalytic RNA (ribozymes), and non-biological counterparts of enzyme-catalyzed reactions are mentioned. Enzyme evolution is considered in terms of divergence, convergence, and lateral gene transfer.}, }
@article {pmid7991539, year = {1994}, author = {Paquin, B and Laforest, MJ and Lang, BF}, title = {Interspecific transfer of mitochondrial genes in fungi and creation of a homologous hybrid gene.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {91}, number = {25}, pages = {11807-11810}, pmid = {7991539}, issn = {0027-8424}, mesh = {Amino Acid Sequence ; Base Sequence ; *Biological Evolution ; Blotting, Northern ; Chytridiomycota/*genetics ; Conserved Sequence ; DNA Primers ; DNA, Mitochondrial/*genetics ; *Genes, Fungal ; Macromolecular Substances ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Open Reading Frames ; Polymerase Chain Reaction ; Proton-Translocating ATPases/biosynthesis/*genetics ; RNA, Fungal/analysis ; Sequence Homology, Amino Acid ; Species Specificity ; }, abstract = {In eukaryotes, horizontal gene transfer is a rare event. Here we show that the mitochondrial genome of a lower fungus, Allomyces macrogynus, has an extra DNA segment not present in a close relative, Allomyces arbusculus. This insert consists of the C terminus of a foreign gene encoding a subunit of the ATP synthetase complex (atp6) plus an open reading frame encoding an endonuclease. The inserted atp6 portion is fused in phase to the resident gene, resulting in expression of a hybrid atp6 gene and the displacement of the original C-terminal atp6 region. We present evidence that this insertion may have been acquired by interspecific transfer and we discuss the possible role of the endonuclease in this process.}, }
@article {pmid7993092, year = {1994}, author = {Neilson, JW and Josephson, KL and Pepper, IL and Arnold, RB and Di Giovanni, GD and Sinclair, NA}, title = {Frequency of horizontal gene transfer of a large catabolic plasmid (pJP4) in soil.}, journal = {Applied and environmental microbiology}, volume = {60}, number = {11}, pages = {4053-4058}, pmid = {7993092}, issn = {0099-2240}, support = {ES-04940/ES/NIEHS NIH HHS/United States ; }, mesh = {2,4-Dichlorophenoxyacetic Acid/metabolism ; Biodegradation, Environmental ; Conjugation, Genetic ; Culture Media ; Gene Transfer, Horizontal ; Gram-Negative Bacteria/*genetics ; Models, Biological ; Plasmids/*genetics ; *Soil Microbiology ; Sterilization ; }, abstract = {Limited work has been done to assess the bioremediation potential of transfer of plasmid-borne degradative genes from introduced to indigenous organisms in the environment. Here we demonstrate the transfer by conjugation of the catabolic plasmid pJP4, using a model system with donor and recipient organisms. The donor organism was Alcaligenes eutrophus JMP134 and the recipient organism was Variovorax paradoxus isolated from a toxic waste site. Plasmid pJP4 contains genes for mercury resistance and 2,4-dichlorophenoxyacetic (2,4-D) acid degradation. A transfer frequency of approximately 1/10(3) donor and recipient cells (parent cells) was observed on solid agar media, decreasing to 1/10(5) parent cells in sterile soil and finally 1/10(6) parent cells in 2,4-D-amended, nonsterile soil. Presumptive transconjugants were confirmed to be resistant to Hg, to be capable of degrading 2,4-D, and to contain a plasmid of size comparable to that of pJP4. In addition, we confirmed the transfer through PCR amplifications of the tfdB gene. Although transfer of pJP4 did occur at a high frequency in pure culture, the rate was significantly decreased by the introduction of abiotic (sterile soil) and biotic (nonsterile soil) stresses. An evaluation of the data from this model system implies that the reliance on plasmid transfer from a donor organism as a remediative strategy has limited potential.}, }
@article {pmid7961410, year = {1994}, author = {Chien, YT and Zinder, SH}, title = {Cloning, DNA sequencing, and characterization of a nifD-homologous gene from the archaeon Methanosarcina barkeri 227 which resembles nifD1 from the eubacterium Clostridium pasteurianum.}, journal = {Journal of bacteriology}, volume = {176}, number = {21}, pages = {6590-6598}, pmid = {7961410}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; Base Sequence ; Cloning, Molecular ; Clostridium/genetics ; Culture Media ; Genes, Bacterial/*genetics ; Methanosarcina barkeri/*genetics/growth &amp; development ; Molecular Sequence Data ; Molybdenum/metabolism ; Nitrogen Fixation/genetics ; Nitrogenase/*genetics/isolation &amp; purification ; Open Reading Frames/genetics ; Phylogeny ; RNA, Messenger/genetics ; Sequence Analysis ; Sequence Homology, Amino Acid ; }, abstract = {L. Sibold, M. Henriquet, O. Possot, and J.-P. Aubert (Res. Microbiol. 142:5-12, 1991) cloned and sequenced two nifH-homologous open reading frames (ORFs) from Methanosarcina barkeri 227. Phylogenetic analysis of the deduced amino acid sequences of the nifH ORFs from M. barkeri showed that nifH1 clusters with nifH genes from alternative nitrogenases, while nifH2 clusters with nifH1 from the gram-positive eubacterium Clostridium pasteurianum. The N-terminal sequence of the purified nitrogenase component 2 (the nifH gene product) from M. barkeri was identical with that predicted for nifH2, and dot blot analysis of RNA transcripts indicated that nifH2 (and nifDK2) was expressed in M. barkeri when grown diazotrophically in Mo-containing medium. To obtain nifD2 from M. barkeri, a 4.7-kbp BamHI fragment of M. barkeri DNA was cloned which contained at least five ORFs, including nifH2, ORF105, and ORF125 (previously described by Sibold et al.), as well as nifD2 and part of nifK2. ORFnifD2 is 1,596 bp long and encodes 532 amino acid residues, while the nifK2 fragment is 135 bp long. The deduced amino acid sequences for nifD2 and the nifK2 fragment from M. barkeri cluster most closely with the corresponding nifDK1 gene products from C. pasteurianum. The predicted M. barkeri nifD2 product contains a 50-amino acid insert near the C terminus which has previously been found only in the clostridial nifD1 product. Previous biochemical and sequencing evidence indicates that the C. pasteurianum nitrogenase is the most divergent of known eubacterial Mo-nitrogenases, most likely representing a distinct nif gene family, which now also contains M. barkeri as a member. The similarity between the methanogen and clostridial nif sequences is especially intriguing in light of the recent findings of sequence similarities between gene products from archaea and from low-G+C gram-positive eubacteria for glutamate dehydrogenase, glutamine synthetase I, and heat shock protein 70. It is not clear whether this similarity is due to horizontal gene transfer or to the resemblance of the M. barkeri and C. pasteurianum nitrogenase sequences to an ancestral nitrogenase.}, }
@article {pmid7812446, year = {1994}, author = {Delorme, C and Godon, JJ and Ehrlich, SD and Renault, P}, title = {Mosaic structure of large regions of the Lactococcus lactis subsp. cremoris chromosome.}, journal = {Microbiology (Reading, England)}, volume = {140 (Pt 11)}, number = {}, pages = {3053-3060}, doi = {10.1099/13500872-140-11-3053}, pmid = {7812446}, issn = {1350-0872}, mesh = {Amino Acid Sequence ; Amino Acids, Branched-Chain/biosynthesis ; Base Sequence ; Chromosomes, Bacterial/*genetics ; Cloning, Molecular ; Conserved Sequence ; Escherichia coli/genetics ; Genetic Code ; *Genetic Variation ; Histidine/biosynthesis ; Lactococcus lactis/*genetics ; Molecular Sequence Data ; Open Reading Frames/genetics ; Operon/*genetics ; Sequence Analysis, DNA ; Species Specificity ; Tryptophan/biosynthesis ; }, abstract = {Lactococcus lactis subsp. lactis and Lactococcus lactis subsp. cremoris are closely related phenotypically and genetically. Here we report that certain regions of their chromosomes diverge considerably more than others. Conserved regions differ by less than 20%, whilst variable regions differ by more than 60%. This mosaic structure may have arisen by horizontal gene transfer from distantly related bacteria since in a particular region of the L. lactis subsp. cremoris chromosome the G+C content and the codon bias are not typical for lactococci. Such an exchange, which conserves the function of the gene and cannot be achieved under selective pressure, may be of considerable importance in the evolution of bacteria.}, }
@article {pmid7986048, year = {1994}, author = {Ahrenholtz, I and Lorenz, MG and Wackernagel, W}, title = {A conditional suicide system in Escherichia coli based on the intracellular degradation of DNA.}, journal = {Applied and environmental microbiology}, volume = {60}, number = {10}, pages = {3746-3751}, pmid = {7986048}, issn = {0099-2240}, mesh = {DNA, Bacterial/genetics/*metabolism ; Endodeoxyribonucleases/genetics ; Endoribonucleases/genetics ; Escherichia coli/cytology/genetics/*metabolism ; Genes, Bacterial ; Genes, Lethal ; Genetic Engineering/adverse effects ; Hot Temperature ; Intracellular Fluid/metabolism ; Protein Sorting Signals/genetics ; Sequence Deletion ; Serratia marcescens/enzymology/genetics ; }, abstract = {The potential risks associated with the intentional or unintentional release of genetically engineered microorganisms led to the construction of biological containment systems by which bacteria are killed in a controlled suicide process. In previously published suicide systems, cell killing was caused by proteins destroying the cell membrane or cell wall. Here a conditional cell killing system based on the intracellular degradation of cellular DNA is presented. The nuclease gene used was that of the extracellular nuclease of Serratia marcescens. The nuclease gene was deleted for the leader-coding sequence, and the truncated gene was put under the control of the lambda pL promoter. Following thermoinduction of the nuclease gene cassette in Escherichia coli, cell survival dropped to 2 x 10(-5), and more than 80% of the radioactively labeled DNA was converted to acid-soluble material within 2.5 h in the absence of cell lysis. The majority (84%) of clones which survived thermoinduced killing turned out to be as sensitive to a second thermoinduction as the original strain. The other clones showed somewhat slower killing kinetics or slightly higher final levels of survivors. The suicide system described combines the regulated killing of cells with the destruction of intracellular DNA otherwise potentially available for horizontal gene transfer processes.}, }
@article {pmid8071203, year = {1994}, author = {Ka, JO and Tiedje, JM}, title = {Integration and excision of a 2,4-dichlorophenoxyacetic acid-degradative plasmid in Alcaligenes paradoxus and evidence of its natural intergeneric transfer.}, journal = {Journal of bacteriology}, volume = {176}, number = {17}, pages = {5284-5289}, pmid = {8071203}, issn = {0021-9193}, mesh = {2,4-Dichlorophenoxyacetic Acid/*metabolism ; Alcaligenes/*genetics/growth &amp; development/*metabolism ; Blotting, Southern ; Conjugation, Genetic ; Electrophoresis, Agar Gel ; Endodeoxyribonucleases ; Genes, Bacterial ; *Introns ; Plasmids/isolation &amp; purification/*metabolism ; Restriction Mapping ; }, abstract = {A self-transmissible 2,4-dichlorophenoxyacetic acid (2,4-D)-degradative plasmid, pKA2, has been identified in a new 2,4-D-degrading strain, Alcaligenes paradoxus 2811P, isolated from agricultural soil. pKA2 occurred as a 42.9-kb plasmid in strain 2811P. A derivative strain, 2811C, was isolated from a stock culture in which the entire pKA2 plasmid was apparently integrated into the host chromosome without loss of the 2,4-D+ phenotype. This interpretation is based on the disappearance of a free plasmid DNA band, a shift in the tfdA-hybridizing band to the chromosome, loss of transmissibility of the 2,4-D+ trait, and appropriate shifts in Southern hybridization bands of plasmid DNA compared with whole-cell DNA. The integrated plasmid of strain 2811C was excised either precisely or imprecisely after continued transfer on 2,4-D-containing medium. This suggests that a chromosome-free plasmid cycle may occur to optimize fitness under conditions of specific resource fluctuation. Another new 2,4-D-degrading strain, Pseudomonas pickettii 712, which was isolated from the same field plot but at a different time, was found to carry a plasmid that is nearly identical to pKA2. The plasmid of this strain, pKA4, is 40.9 kb long and has features in common with pKA2, such as high self-transmissibility, hybridization only to the tfdA gene among the 2,4-D-metabolic genes of 2,4-D-degradative plasmid pJP4, and similar restriction endonuclease-generated fragments. Furthermore, the genetic homology between the two plasmids was high since all fragments of pKA2 hybridized to pKA4. These results suggest that these two plasmids are closely related and thus their occurrence in two genera in nature is the result of natural horizontal gene transfer.}, }
@article {pmid7968924, year = {1994}, author = {Lorenz, MG and Wackernagel, W}, title = {Bacterial gene transfer by natural genetic transformation in the environment.}, journal = {Microbiological reviews}, volume = {58}, number = {3}, pages = {563-602}, pmid = {7968924}, issn = {0146-0749}, mesh = {DNA, Bacterial/*metabolism ; Environment ; *Soil Microbiology ; Transformation, Bacterial/*physiology ; *Water Microbiology ; }, abstract = {Natural genetic transformation is the active uptake of free DNA by bacterial cells and the heritable incorporation of its genetic information. Since the famous discovery of transformation in Streptococcus pneumoniae by Griffith in 1928 and the demonstration of DNA as the transforming principle by Avery and coworkers in 1944, cellular processes involved in transformation have been studied extensively by in vitro experimentation with a few transformable species. Only more recently has it been considered that transformation may be a powerful mechanism of horizontal gene transfer in natural bacterial populations. In this review the current understanding of the biology of transformation is summarized to provide the platform on which aspects of bacterial transformation in water, soil, and sediments and the habitat of pathogens are discussed. Direct and indirect evidence for gene transfer routes by transformation within species and between different species will be presented, along with data suggesting that plasmids as well as chromosomal DNA are subject to genetic exchange via transformation. Experiments exploring the prerequisites for transformation in the environment, including the production and persistence of free DNA and factors important for the uptake of DNA by cells, will be compiled, as well as possible natural barriers to transformation. The efficiency of gene transfer by transformation in bacterial habitats is possibly genetically adjusted to submaximal levels. The fact that natural transformation has been detected among bacteria from all trophic and taxonomic groups including archaebacteria suggests that transformability evolved early in phylogeny. Probable functions of DNA uptake other than gene acquisition will be discussed. The body of information presently available suggests that transformation has a great impact on bacterial population dynamics as well as on bacterial evolution and speciation.}, }
@article {pmid7968916, year = {1994}, author = {Dreiseikelmann, B}, title = {Translocation of DNA across bacterial membranes.}, journal = {Microbiological reviews}, volume = {58}, number = {3}, pages = {293-316}, pmid = {7968916}, issn = {0146-0749}, mesh = {Bacteria/genetics/*metabolism ; Cell Membrane/metabolism ; Conjugation, Genetic/physiology ; DNA, Bacterial/*metabolism ; DNA, Viral/*metabolism ; *Models, Genetic ; Transduction, Genetic/physiology ; Transformation, Bacterial/genetics ; }, abstract = {DNA translocation across bacterial membranes occurs during the biological processes of infection by bacteriophages, conjugative DNA transfer of plasmids, T-DNA transfer, and genetic transformation. The mechanism of DNA translocation in these systems is not fully understood, but during the last few years extensive data about genes and gene products involved in the translocation processes have accumulated. One reason for the increasing interest in this topic is the discussion about horizontal gene transfer and transkingdom sex. Analyses of genes and gene products involved in DNA transfer suggest that DNA is transferred through a protein channel spanning the bacterial envelope. No common model exists for DNA translocation during phage infection. Perhaps various mechanisms are necessary as a result of the different morphologies of bacteriophages. The DNA translocation processes during conjugation, T-DNA transfer, and transformation are more consistent and may even be compared to the excretion of some proteins. On the basis of analogies and homologies between the proteins involved in DNA translocation and protein secretion, a common basic model for these processes is presented.}, }
@article {pmid7944364, year = {1994}, author = {Nikolich, MP and Hong, G and Shoemaker, NB and Salyers, AA}, title = {Evidence for natural horizontal transfer of tetQ between bacteria that normally colonize humans and bacteria that normally colonize livestock.}, journal = {Applied and environmental microbiology}, volume = {60}, number = {9}, pages = {3255-3260}, pmid = {7944364}, issn = {0099-2240}, support = {AI22383/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Animals, Domestic/*microbiology ; Bacteroides/genetics/isolation &amp; purification ; Base Sequence ; Cattle ; Conjugation, Genetic ; DNA Primers/genetics ; DNA Transposable Elements ; DNA, Bacterial/genetics ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Intestines/microbiology ; Molecular Sequence Data ; Prevotella/genetics/isolation &amp; purification ; Rumen/microbiology ; Sequence Homology, Nucleic Acid ; Sheep ; Swine ; Tetracycline Resistance/genetics ; }, abstract = {Though numerous studies have shown that gene transfer occurs between distantly related bacterial genera under laboratory conditions, the frequency and breadth of horizontal transfer events in nature remain unknown. Previous evidence for natural intergeneric transfers came from studies of genes in human pathogens, bacteria that colonize the same host. We present evidence that natural transfer of a tetracycline resistance gene, tetQ, has occurred between bacterial genera that normally colonize different hosts. A DNA sequence comparative approach was taken to examine the extent of horizontal tetQ dissemination between species of Bacteroides, the predominant genus of the human colonic microflora, and between species of Bacteroides and of the distantly related genus Prevotella, a predominant genus of the microflora of the rumens and intestinal tracts of farm animals. Virtually identical tetQ sequences were found in a number of isolate pairs differing in taxonomy and geographic origin, indicating that extensive natural gene transmission has occurred. Among the exchange events indicated by the evidence was the very recent transfer of an allele of tetQ usually found in Prevotella spp. to a Bacteroides fragilis strain.}, }
@article {pmid8078941, year = {1994}, author = {Lamour, V and Quevillon, S and Diriong, S and N'Guyen, VC and Lipinski, M and Mirande, M}, title = {Evolution of the Glx-tRNA synthetase family: the glutaminyl enzyme as a case of horizontal gene transfer.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {91}, number = {18}, pages = {8670-8674}, pmid = {8078941}, issn = {0027-8424}, mesh = {Amino Acid Sequence ; Amino Acyl-tRNA Synthetases/*genetics ; Bacterial Proteins/genetics ; Chromosomes, Human, Pair 3 ; Cloning, Molecular ; DNA, Complementary/genetics ; Fungal Proteins/genetics ; Genes ; Glutamate-tRNA Ligase/*genetics ; Humans ; Molecular Sequence Data ; *Multigene Family ; Phylogeny ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {An important step ensuring the fidelity in protein biosynthesis is the aminoacylation of tRNAs by aminoacyl-tRNA synthetases. The accuracy of this process rests on a family of 20 enzymes, one for each amino acid. One exception is the formation of Gln-tRNA(Gln) that can be accomplished by two different pathways: aminoacylation of tRNA(Gln) with Gln by glutaminyl-tRNA synthetase (GlnRS; EC 6.1.1.18) or transamidation of Glu from Glu-tRNA(Gln) mischarged by glutamyl-tRNA synthetase (GluRS; EC 6.1.1.17). The latter pathway is widespread among bacteria and organelles that, accordingly, lack GlnRS. However, some bacterial species, such as Escherichia coli, do possess a GlnRS activity, which is responsible for Gln-tRNA(Gln) formation. In the cytoplasm of eukaryotic cells, both GluRS and GlnRS activities can be detected. To gain more insight into the evolutionary relationship between GluRS and GlnRS enzyme species, we have now isolated and characterized a human cDNA encoding GlnRS. The deduced amino acid sequence shows a strong similarity with other known GlnRSs and with eukaryotic GluRSs. A molecular phylogenetic analysis was conducted on the 14 GlxRS (GluRS or GlnRS) sequences available to date. Our data suggest that bacterial GlnRS has a eukaryotic origin and was acquired by a mechanism of horizontal gene transfer.}, }
@article {pmid8001163, year = {1994}, author = {Debets, F and Yang, X and Griffiths, AJ}, title = {Vegetative incompatibility in Neurospora: its effect on horizontal transfer of mitochondrial plasmids and senescence in natural populations.}, journal = {Current genetics}, volume = {26}, number = {2}, pages = {113-119}, pmid = {8001163}, issn = {0172-8083}, mesh = {Crosses, Genetic ; Gene Transfer, Horizontal ; Genes, Fungal ; Genes, Mating Type, Fungal ; Genotype ; Mitochondria/*metabolism ; Neurospora crassa/genetics/growth &amp; development/*physiology ; Phenotype ; *Plasmids ; Species Specificity ; }, abstract = {We have investigated the horizontal transfer of two mitochondrial plasmids and the Kalilo senescence phenotype in the fungus Neurospora without the use of heterokaryon-forcing markers. The Kalilo senescent state was only transferred between fully-compatible N. crassa strains, but not between strains differing at any of the loci het-c, het-d, het-e or mating-type. However, the linear plasmid kalDNA and the circular plasmid Han-2 were transferred following incompatible vegetative interactions. Our data suggest that vegetative incompatibility due to allelic differences at het-c is more effective in preventing transfer than that due to het-d, het-e or mating-type. Based on these observations we have developed a novel test for assessing vegetative incompatibility between Kalilo and non-Kalilo field isolates of N. intermedia. In this procedure combinations of Kalilo and non-Kalilo field isolates of N. intermedia were grown together and tested for senescence. Compatibility is inferred if the young non-Kalilo strain dies along with the senescent Kalilo strain, whereas incompatibility is inferred when the Kalilo strain dies without imposing its senescent state onto the non-Kalilo strain. Our results suggest that each of the nine Kalilo strains tested is incompatible with each of 20 non-Kalilo isolates from the same N. intermedia population of the Hawaiian island of Kauai. However, the observed incompatibility did not completely prevent cytoplasmic exchange, and in several cases plasmid transfer could be detected.}, }
@article {pmid7853994, year = {1994}, author = {Vranes, J and Schönwald, S and Zagar, Z}, title = {[Relation between P-fimbriae and resistance to amoxicillin, carbenicillin and tetracycline in uropathogenic strains of Escherichia coli].}, journal = {Lijecnicki vjesnik}, volume = {116}, number = {7-8}, pages = {178-181}, pmid = {7853994}, issn = {0024-3477}, mesh = {Amoxicillin/*pharmacology ; Carbenicillin/*pharmacology ; Drug Resistance, Microbial ; Escherichia coli/classification/drug effects/*pathogenicity/ultrastructure ; Escherichia coli Infections/microbiology ; Fimbriae, Bacterial/*ultrastructure ; Humans ; Tetracycline/*pharmacology ; Urinary Tract Infections/microbiology ; }, abstract = {Escherichia coli is the most common cause of uncomplicated urinary tract infections. The ability of adherence enables E. coli colonization of mucosal surfaces of the urinary tract, and strains which express P-fimbriae significantly more often cause unobstructive pyelonephritis. The relationship between adhesin type and susceptibility to 13 antimicrobial agents of 160 E. coli strains isolated from urine from individuals with acute pyelonephritis, chronic pyelonephritis, acute cystitis and asymptomatic bacteriuria was investigated. The adhesins of investigated strains of E. coli were determined by hemagglutination, and susceptibility to antimicrobial agents by Kirby-Bauer disk diffusion method. P-fimbriated strains were more frequently resistant to tetracycline and carbenicillin than strains in which P-fimbriae were not detected, and they all were resistant to amoxicillin, in contrast with non P-fimbriated strains (p < 0.01). The observed relationship between P-fimbriae and antimicrobial resistance among strains in which different serogroups were detected suggest the possibility of horizontal gene transfer of these properties. It can be concluded that in patients with symptoms of acute upper urinary tract infection amoxicillin should not be used empirically because there is a great possibility that infection is caused by P-fimbriated and amoxicillin resistant strain of E. coli.}, }
@article {pmid7517391, year = {1994}, author = {Stevenson, G and Neal, B and Liu, D and Hobbs, M and Packer, NH and Batley, M and Redmond, JW and Lindquist, L and Reeves, P}, title = {Structure of the O antigen of Escherichia coli K-12 and the sequence of its rfb gene cluster.}, journal = {Journal of bacteriology}, volume = {176}, number = {13}, pages = {4144-4156}, pmid = {7517391}, issn = {0021-9193}, mesh = {Acetylation ; Base Sequence ; Biological Evolution ; Carbohydrate Epimerases/genetics ; Carbohydrate Sequence ; Cross Reactions ; Escherichia coli/*chemistry/genetics/immunology ; *Escherichia coli Proteins ; Galactose/metabolism ; Genes, Bacterial/*genetics ; Glucose/metabolism ; Hexosyltransferases/genetics ; Hydro-Lyases/genetics ; Magnetic Resonance Spectroscopy ; *Mannose-6-Phosphate Isomerase ; Membrane Proteins/genetics ; Molecular Sequence Data ; Multigene Family/*genetics ; N-Acetylglucosaminyltransferases/metabolism ; Nucleoside Diphosphate Sugars/metabolism ; Nucleotidyltransferases/genetics ; O Antigens ; Open Reading Frames/genetics ; Polysaccharides, Bacterial/*chemistry/genetics ; Repetitive Sequences, Nucleic Acid/genetics ; Restriction Mapping ; Thymine Nucleotides/metabolism ; Transferases (Other Substituted Phosphate Groups)/genetics ; }, abstract = {Escherichia coli K-12 has long been known not to produce an O antigen. We recently identified two independent mutations in different lineages of K-12 which had led to loss of O antigen synthesis (D. Liu and P. R. Reeves, Microbiology 140:49-57, 1994) and constructed a strain with all rfb (O antigen) genes intact which synthesized a variant of O antigen O16, giving cross-reaction with anti-O17 antibody. We determined the structure of this O antigen to be -->2)-beta-D-Galf-(1-->6)-alpha-D-Glcp- (1-->3)-alpha-L-Rhap-(1-->3)-alpha-D-GlcpNAc-(1-->, with an O-acetyl group on C-2 of the rhamnose and a side chain alpha-D-Glcp on C-6 of GlcNAc. O antigen synthesis is rfe dependent, and D-GlcpNAc is the first sugar of the biological repeat unit. We sequenced the rfb (O antigen) gene cluster and found 11 open reading frames. Four rhamnose pathway genes are identified by similarity to those of other strains, the rhamnose transferase gene is identified by assay of its product, and the identities of other genes are predicted with various degrees of confidence. We interpret earlier observations on interaction between the rfb region of Escherichia coli K-12 and those of E. coli O4 and E. coli Flexneri. All K-12 rfb genes were of low G+C content for E. coli. The rhamnose pathway genes were similar in sequence to those of (Shigella) Dysenteriae 1 and Flexneri, but the other genes showed distant or no similarity. We suggest that the K-12 gene cluster is a member of a family of rfb gene clusters, including those of Dysenteriae 1 and Flexneri, which evolved outside E. coli and was acquired by lateral gene transfer.}, }
@article {pmid8013452, year = {1994}, author = {Castresana, J and Lübben, M and Saraste, M and Higgins, DG}, title = {Evolution of cytochrome oxidase, an enzyme older than atmospheric oxygen.}, journal = {The EMBO journal}, volume = {13}, number = {11}, pages = {2516-2525}, pmid = {8013452}, issn = {0261-4189}, mesh = {Aerobiosis ; Amino Acid Sequence ; Aspergillus nidulans/enzymology ; Bacteria/enzymology ; *Biological Evolution ; Conserved Sequence/genetics ; Databases, Factual ; *Electron Transport Complex IV/classification/genetics ; Humans ; Models, Biological ; Oxidoreductases ; Sequence Alignment ; Zea mays/enzymology ; }, abstract = {Cytochrome oxidase is a key enzyme in aerobic metabolism. All the recorded eubacterial (domain Bacteria) and archaebacterial (Archaea) sequences of subunits 1 and 2 of this protein complex have been used for a comprehensive evolutionary analysis. The phylogenetic trees reveal several processes of gene duplication. Some of these are ancient, having occurred in the common ancestor of Bacteria and Archaea, whereas others have occurred in specific lines of Bacteria. We show that eubacterial quinol oxidase was derived from cytochrome c oxidase in Gram-positive bacteria and that archaebacterial quinol oxidase has an independent origin. A considerable amount of evidence suggests that Proteobacteria (Purple bacteria) acquired quinol oxidase through a lateral gene transfer from Gram-positive bacteria. The prevalent hypothesis that aerobic metabolism arose several times in evolution after oxygenic photosynthesis, is not sustained by two aspects of the molecular data. First, cytochrome oxidase was present in the common ancestor of Archaea and Bacteria whereas oxygenic photosynthesis appeared in Bacteria. Second, an extant cytochrome oxidase in nitrogen-fixing bacteria shows that aerobic metabolism is possible in an environment with a very low level of oxygen, such as the root nodules of leguminous plants. Therefore, we propose that aerobic metabolism in organisms with cytochrome oxidase has a monophyletic and ancient origin, prior to the appearance of eubacterial oxygenic photosynthetic organisms.}, }
@article {pmid8194578, year = {1994}, author = {Kellenberger, E}, title = {Genetic ecology: a new interdisciplinary science, fundamental for evolution, biodiversity and biosafety evaluations.}, journal = {Experientia}, volume = {50}, number = {5}, pages = {429-437}, pmid = {8194578}, issn = {0014-4754}, mesh = {Animals ; Bacteria/genetics ; Bacterial Physiological Phenomena ; Biotechnology ; Conjugation, Genetic ; DNA/genetics ; *Ecology ; Gene Transfer, Horizontal ; *Genetics ; Intestines/microbiology ; Plants, Genetically Modified ; Safety ; Symbiosis ; Transformation, Genetic ; }, abstract = {Genetic ecology is the extension of our modern knowledge in molecular genetics to studies of viability, gene expression and gene movements in natural environments like soils, aquifers and digestive tracts. In such milieux, the horizontal transfer of plasmid-borne genes between phylogenetically distant species has already been found to be much more frequent than had been expected from laboratory experience. For the study of exchanges involving chromosomally-located genes, more has to be learned about the behaviour of transposons in such environments. The results expected from studies in genetic ecology are relevant for considerations of evolution, biodiversity and biosafety. The role of this new field of research in restoring popular confidence in science and in its biotechnological applications is stressed.}, }
@article {pmid8176730, year = {1994}, author = {Bordo, D and Djinović, K and Bolognesi, M}, title = {Conserved patterns in the Cu,Zn superoxide dismutase family.}, journal = {Journal of molecular biology}, volume = {238}, number = {3}, pages = {366-386}, doi = {10.1006/jmbi.1994.1298}, pmid = {8176730}, issn = {0022-2836}, mesh = {Amino Acid Sequence ; Animals ; Biological Evolution ; Cattle ; Computer Graphics ; Copper/chemistry ; Disulfides ; Humans ; Models, Molecular ; Molecular Sequence Data ; Protein Structure, Secondary ; Sequence Alignment ; Sequence Homology, Amino Acid ; Superoxide Dismutase/*chemistry/genetics ; Vegetables/enzymology ; Yeasts/enzymology ; Zinc/chemistry ; }, abstract = {Conserved structural and functional features of Cu,Zn superoxide dismutase enzymes have been studied by comparison of known three-dimensional structures and analysis of the currently available amino acid sequences. For this purpose, the three-dimensional structures of the bovine, spinach and yeast enzymes have been superimposed and the structure-based sequence alignment of 38 different superoxide dismutases has been produced. The evolutionary tree obtained from the alignment indicates that cytosolic and extracellular enzymes followed independent evolutionary paths, and that horizontal gene transfer, if any, occurred at an early stage in eukaryota evolution. Based on the sequence alignment and on the analysis of clusters of spatially neighboring residues, the conservation/variation of functionally relevant intramolecular interactions has been investigated. Seven alternative residue arrangements have been identified in the upper rim of the active site, which form an important determinant of the electrostatic field at the catalytic center. The total nominal charge of this region is constantly -1 through the phyla. The seven residues which coordinate the two metal ions at the active site are conserved, with only one known exception. Among the residues involved in maintenance of the active site structure, Gly59, Gly80, Gly136 and Gly139 are fully conserved; mutations of Gly42 and Pro64 have been observed, concerted with replacements in their structural surroundings. Coordinated mutations affecting residue pairs which maintain the packing geometry of the Greek-key beta-barrel have been identified. Furthermore, the unique disulfide bridge involving Cys55-Cys144 in eukaryota, shows the alternative Cys50A-Cys144 arrangement in prokaryotic enzymes.}, }
@article {pmid8065255, year = {1994}, author = {Sandmeier, H}, title = {Acquisition and rearrangement of sequence motifs in the evolution of bacteriophage tail fibres.}, journal = {Molecular microbiology}, volume = {12}, number = {3}, pages = {343-350}, doi = {10.1111/j.1365-2958.1994.tb01023.x}, pmid = {8065255}, issn = {0950-382X}, mesh = {Base Sequence ; *Biological Evolution ; Coliphages/enzymology/*genetics ; DNA Nucleotidyltransferases/metabolism ; *Gene Rearrangement ; Genes, Viral/*genetics ; Genome, Viral ; *Integrases ; Molecular Sequence Data ; Recombinases ; Sequence Homology, Nucleic Acid ; Substrate Specificity ; Viral Tail Proteins/*genetics ; }, abstract = {Molecular analysis reveals a surprising sharing of short gene segments among a variety of large double-stranded DNA bacteriophages of enteric bacteria. Ancestral genomes from otherwise unrelated phages, including lambda, Mu, P1, P2 and T4, must have exchanged parts of their tail-fibre genes. Individual genes appear as mosaics with parts derived from a common gene pool. Therefore, horizontal gene transfer emerges as a major factor in the evolution of a specific part of phage genomes. Current concepts of homologous recombination cannot account for the formation of such chimeric genes and the recombinational mechanisms responsible are not known. However, recombination sites for DNA invertases and recombination site-like sequences are present at the boundaries of gene segments conferring the specificity for the host receptor. This, together with the properties of the DNA inversion mechanism, suggests that these site-specific recombination enzymes could be responsible for the exchange of host-range determinants.}, }
@article {pmid8135513, year = {1994}, author = {Kidambi, SP and Ripp, S and Miller, RV}, title = {Evidence for phage-mediated gene transfer among Pseudomonas aeruginosa strains on the phylloplane.}, journal = {Applied and environmental microbiology}, volume = {60}, number = {2}, pages = {496-500}, pmid = {8135513}, issn = {0099-2240}, mesh = {Bacteriophages/*genetics ; Models, Biological ; Plants/*microbiology ; Pseudomonas aeruginosa/*genetics ; Transfection/*genetics ; }, abstract = {As the use of genetically engineered microorganisms for agricultural tasks becomes more frequent, the ability of bacteria to exchange genetic material in the agricultural setting must be assessed. Transduction (bacterial virus-mediated horizontal gene transfer) is a potentially important mechanism of gene transfer in natural environments. This study investigated the potential of plant leaves to act as surfaces on which transduction can take place among microorganisms. Pseudomonas aeruginosa and its generalized transducing bacteriophage F116 were used as a model system. The application of P. aeruginosa lysogens of F116 to plant leaves resulted in genetic exchange among donor and recipient organisms resident on the same plant. Transduction was also observed when these bacterial strains were inoculated onto adjacent plants and contact was made possible through high-density planting.}, }
@article {pmid8297343, year = {1994}, author = {Zhou, L and Xue, GP and Orpin, CG and Black, GW and Gilbert, HJ and Hazlewood, GP}, title = {Intronless celB from the anaerobic fungus Neocallimastix patriciarum encodes a modular family A endoglucanase.}, journal = {The Biochemical journal}, volume = {297 (Pt 2)}, number = {Pt 2}, pages = {359-364}, pmid = {8297343}, issn = {0264-6021}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cellulase/*genetics/metabolism ; Cloning, Molecular ; Fungi/*enzymology/genetics ; *Genes, Fungal ; Introns ; Molecular Sequence Data ; Restriction Mapping ; Rumen/microbiology ; Sequence Alignment ; Sequence Homology, Amino Acid ; Sheep ; }, abstract = {The cDNA designated celB from the anaerobic rumen fungus Neocallimastix patriciarum contained a single open reading frame of 1422 bp coding for a protein (CelB) of M(r) 53,070. CelB expressed by Escherichia coli harbouring the full-length gene hydrolysed carboxymethylcellulose in the manner of an endoglucanase, but was most active against barley beta-glucan. It also released reducing sugar from xylan and lichenan, but was inactive against crystalline cellulose, laminarin, mannan, galactan and arabinan. The rate of hydrolysis of cellulo-oligosaccharides by CelB increased with increasing chain length from cellotriose to cellopentaose. The predicted structure of CelB contained features indicative of modular structure. The first 360 residues of CelB constituted a fully functional catalytic domain that was homologous with bacterial endoglucanases belonging to cellulase family A, including five which originate from three different species of anaerobic rumen bacteria. Downstream from this domain, and linked to it by a serine/threonine-rich hinge, was a non-catalytic domain containing short tandem repeats, homologous to the C-terminal repeats contained in xylanase A from the same anaerobic fungus. Unlike previous fungal cellulases, genomic celB was devoid of introns. This lack of introns and the homology of its encoded product with rumen bacterial endoglucanases suggest that acquisition of celB by the fungus may at some stage have involved horizontal gene transfer from a prokaryote to N. particiarum.}, }
@article {pmid8170398, year = {1994}, author = {Whatmore, AM and Kehoe, MA}, title = {Horizontal gene transfer in the evolution of group A streptococcal emm-like genes: gene mosaics and variation in Vir regulons.}, journal = {Molecular microbiology}, volume = {11}, number = {2}, pages = {363-374}, doi = {10.1111/j.1365-2958.1994.tb00316.x}, pmid = {8170398}, issn = {0950-382X}, mesh = {Bacterial Proteins/genetics ; Base Sequence ; *Biological Evolution ; Cloning, Molecular ; DNA/genetics ; DNA Primers ; DNA Transposable Elements ; Escherichia coli ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genetic Variation ; Humans ; Molecular Sequence Data ; Mosaicism ; Polymerase Chain Reaction ; *Regulon ; Streptococcus pyogenes/classification/*genetics/isolation &amp; purification ; }, abstract = {Most M type 5 group A streptococcal strains were found to contain a single emm-like gene between virR and scpA (the Vir regulon), but two distinct emm-like genes were identified in the Vir regulon of the M5 strain NCTC8193. The complete sequences of both of these genes were determined. One, called emm5.8193, was shown to be a minor variant of the previously described emm5 gene from strain Manfredo. The second, designated enn5.8193, expresses an IgG-binding protein when cloned in Escherichia coli. A comparison of enn5.8193 with emm-like gene sequences from other strains indicated that it has a mosaic structure, consisting of distinct segments originating from emm-like genes in different OF+ and OF- strains. These data provide the first clear evidence that the horizontal transfer of emm-like sequences between distinct strains contributes to the evolution of group A streptococcal emm-like genes and Vir regulons.}, }
@article {pmid7893125, year = {1994}, author = {Syvanen, M}, title = {Horizontal gene transfer: evidence and possible consequences.}, journal = {Annual review of genetics}, volume = {28}, number = {}, pages = {237-261}, doi = {10.1146/annurev.ge.28.120194.001321}, pmid = {7893125}, issn = {0066-4197}, mesh = {Chromosomes, Bacterial ; DNA Transposable Elements ; Eukaryotic Cells/metabolism ; Organelles/metabolism ; Plants/genetics ; *Transformation, Genetic ; }, }
@article {pmid7847886, year = {1994}, author = {Hoekstra, RF}, title = {Population genetics of filamentous fungi.}, journal = {Antonie van Leeuwenhoek}, volume = {65}, number = {3}, pages = {199-204}, pmid = {7847886}, issn = {0003-6072}, mesh = {Biological Evolution ; Fungi/*genetics/growth &amp; development ; Gene Transfer, Horizontal ; Genes, Fungal ; Genetics, Population ; Models, Genetic ; Spores, Fungal/genetics ; }, abstract = {Population genetics aims to understand causes and consequences of the genetic structure of populations, i.e. distributions of genetic variants in space and time. Among the most important determinants of the genetic population structure is the genetic system itself, which is the collection of processes and mechanisms responsible for the transmission of genetic information. Filamentous fungi offer excellent opportunities for studying the effects of the genetic system on genetic population structure. Apart from their advantage as laboratory organisms, they exhibit a wide variety of genetic systems. In particular, their inherent capacity for anastomosis provides unique possibilities for investigating rates and consequences of horizontal gene transfer. Furthermore, the temporary confinement of the products of meiosis in a common structure (the ascus) enables the study of competitive and antagonistic interactions between the meiotic products. An intriguing example of the latter is the phenomenon of 'spore killing', resulting in distorted meiotic segregation. This paper concentrates on population level research of the occurrence of vegetative incompatibility in Aspergillus and Neurospora species and to what extent this will inhibit horizontal transmission of genetic information, and on spore killing in Podospora anserina.}, }
@article {pmid8114116, year = {1993}, author = {Markos, A and Miretsky, A and Müller, M}, title = {A glyceraldehyde-3-phosphate dehydrogenase with eubacterial features in the amitochondriate eukaryote, Trichomonas vaginalis.}, journal = {Journal of molecular evolution}, volume = {37}, number = {6}, pages = {631-643}, pmid = {8114116}, issn = {0022-2844}, support = {AI 11942/AI/NIAID NIH HHS/United States ; RR 07065/RR/NCRR NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Bacteria/genetics ; Glyceraldehyde-3-Phosphate Dehydrogenases/*genetics ; Humans ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Amino Acid ; Trichomonas vaginalis/enzymology/*genetics ; }, abstract = {Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), localized in the cytosol of Trichomonas vaginalis, was partially purified. The enzyme is specific for NAD+ and is similar in most of its catalytic properties to glycolytic GAPDHs from other organisms. Its sensitivity to koningic acid is similar to levels observed in GAPDHs from eubacteria and two orders of magnitude lower than those observed for eukaryotic GAPDHs. The complete amino acid sequence of T. vaginalis GAPDH was derived from the N-terminal sequence of the purified protein and the deduced sequence of a cDNA clone. It showed great similarity to other eubacterial and eukaryotic GAPDH sequences. The sequence of the S-loop displayed a eubacterial signature. The overall sequence was more similar to eubacterial sequences than to cytosolic and glycosomal eukaryotic sequences. In phylogenetic trees obtained with distance matrix and parsimony methods T. vaginalis GAPDH clustered with its eubacterial homologs. GAPDHs of other amitochondriate protists, belonging to early branches of the eukaryotic lineage (Giardia lamblia and Entamoeba histolytica--Smith M.W. and Doolittle R.F., unpublished data in GenBank), showed typical eukaryotic signatures and clustered with other eukaryotic sequences, indicating that T. vaginalis GAPDH occupies an anomalous position, possibly due to horizontal gene transfer from a eubacterium.}, }
@article {pmid8108379, year = {1993}, author = {Bork, P}, title = {Hundreds of ankyrin-like repeats in functionally diverse proteins: mobile modules that cross phyla horizontally?.}, journal = {Proteins}, volume = {17}, number = {4}, pages = {363-374}, doi = {10.1002/prot.340170405}, pmid = {8108379}, issn = {0887-3585}, mesh = {Amino Acid Sequence ; Animals ; *Ankyrin Repeat ; Gene Transfer, Horizontal ; Humans ; Information Systems ; Molecular Sequence Data ; Poxviridae ; Proteins/*analysis ; Sequence Analysis ; }, abstract = {Based on pattern searches and systematic database screening, almost 650 different ankyrin-like (ANK) repeats from nearly all phyla have been identified; more than 150 of them are reported here for the first time. Their presence in functionally diverse proteins such as enzymes, toxins, and transcription factors strongly suggests domain shuffling, but their occurrence in prokaryotes and yeast excludes exon shuffling. The spreading mechanism remains unknown, but in at least three cases horizontal gene transfer appears to be involved. ANK repeats occur in at least four consecutive copies. The terminal repeats are more variable in sequence. One feature of the internal repeats is a predicted central hydrophobic alpha-helix, which is likely to interact with other repeats. The functions of the ankyrin-like repeats are compatible with a role in protein-protein interactions.}, }
@article {pmid8405421, year = {1993}, author = {Degtyarenko, KN and Archakov, AI}, title = {Molecular evolution of P450 superfamily and P450-containing monooxygenase systems.}, journal = {FEBS letters}, volume = {332}, number = {1-2}, pages = {1-8}, doi = {10.1016/0014-5793(93)80470-f}, pmid = {8405421}, issn = {0014-5793}, mesh = {Amino Acid Sequence ; Animals ; *Biological Evolution ; Cytochrome P-450 Enzyme System/chemistry/*genetics ; Humans ; Mixed Function Oxygenases/chemistry/*genetics ; Molecular Sequence Data ; Multigene Family ; }, abstract = {This paper reviews the classification of the P450 superfamily which is mainly based on sequence homology. The widely accepted classification by Nebert et al. [(1991) DNA Cell Biol. 10, 1-14] as well as the results of a 'two-step' multiple sequence alignment technique show that the molecular evolution of P450s, in contrast to that of many protein families, does not follow phylogeny. The data suggest that during the evolution of P450s, gene duplications and gene fusions, horizontal gene transfer and intron loss events have occurred. 'Weak' and 'strong' hierarchies in the clustering of P450 sequences were revealed. A novel evolutionary tree of the P450 superfamily has been constructed using a multiple alignment of consensus sequences. The simple classification of known P450-containing monooxygenase systems into three-, two- and one-component systems is further discussed. Particularly, the multidomain enzyme, nitric oxide synthase (NOS), should be classified as an example of a eukaryotic one-component P450 system since its N-terminal (haem) domain exhibits similarity with microsomal P450s.}, }
@article {pmid8406829, year = {1993}, author = {Kell, CM and Jordens, JZ and Daniels, M and Coffey, TJ and Bates, J and Paul, J and Gilks, C and Spratt, BG}, title = {Molecular epidemiology of penicillin-resistant pneumococci isolated in Nairobi, Kenya.}, journal = {Infection and immunity}, volume = {61}, number = {10}, pages = {4382-4391}, pmid = {8406829}, issn = {0019-9567}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Sequence ; *Bacterial Proteins ; Base Sequence ; Carrier Proteins/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Hexosyltransferases ; Kenya ; Molecular Sequence Data ; Muramoylpentapeptide Carboxypeptidase/genetics ; *Penicillin Resistance ; Penicillin-Binding Proteins ; *Peptidyl Transferases ; Polymorphism, Genetic ; Restriction Mapping ; Serotyping ; Streptococcus pneumoniae/*drug effects/genetics/immunology ; }, abstract = {A total of 26% of the pneumococci isolated from an outpatient clinic in Nairobi, Kenya, during 1991 to 1992 had intermediate levels of penicillin resistance. Gene fingerprinting and DNA sequencing were used to distinguish the penicillin-binding protein (PBP) 1A, 2B, and 2X genes in 23 resistant isolates. Isolates were grouped into those that had identical forms of each of the three PBP genes (fingerprint groups) and those that had identical rRNA gene restriction patterns (ribotypes). Both methods divided the isolates into 11 groups. In a few cases, horizontal gene transfer appeared to have distributed an identical altered PBP gene into different pneumococcal lineages. Eight isolates were indistinguishable by ribotyping or multilocus enzyme electrophoresis and contained identical PBP 1A genes. Although these isolates were therefore members of the same clone, they were divided into two fingerprint groups which contained different PBP 2X and 2B genes. Presumably, members of this clone have acquired different altered PBP 2X and 2B genes on two separate occasions. One of these fingerprint groups contained isolates of serotype 14, whereas the other contained isolates of both serotypes 14 and 7. The identification of isolates in the latter group that are identical by all criteria, except serotype, implies the occurrence of a change in serotype. The predominant serotypes of the penicillin-resistant pneumococci from Nairobi were serotypes 14 and 19. In both cases, isolates of the same serotype which required the same MIC of penicillin were not members of a single clone, indicating that identity of serotype and MIC are not sufficient criteria for defining clones of resistant pneumococci even when the bacteria are isolated from a single clinic.}, }
@article {pmid7934919, year = {1993}, author = {Roggentin, P and Schauer, R and Hoyer, LL and Vimr, ER}, title = {The sialidase superfamily and its spread by horizontal gene transfer.}, journal = {Molecular microbiology}, volume = {9}, number = {5}, pages = {915-921}, doi = {10.1111/j.1365-2958.1993.tb01221.x}, pmid = {7934919}, issn = {0950-382X}, support = {AI23039/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacteria/*enzymology/genetics ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Isoenzymes/chemistry/genetics ; Molecular Sequence Data ; *Multigene Family ; Neuraminidase/chemistry/*genetics ; Sequence Homology, Amino Acid ; }, abstract = {Sialidases (neuraminidases, EC 3.2.1.18) belong to a class of glycosyl hydrolases that release terminal N-acylneuraminate (sialic acid) residues from glycoproteins, glycolipids, and polysaccharides. These enzymes are common in animals of the deuterostomate lineage (Echinodermata through Mammalia) and also in diverse microorganisms that mostly exist as animal commensals or pathogens. Sialidases, and their sialyl substrates, appear to be absent from plants and most other metazoans. Even among bacteria, sialidase is found irregularly so that related species or even strains of one species differ in this property. This unusual phylogenetic distribution makes sialidases interesting for evolutionary studies. The biochemical diversity among bacterial sialidases does not indicate close relationships. However, at the molecular level, homologies are detectable, supporting the hypothesis of a common sialidase origin and thus of a sialidase superfamily. Some findings indicate that sialidase genes were recently transferred via phages among bacteria. The proposal of a sialidase origin in higher animals is suggested by the presence of apparently homologous enzymes in this kingdom, supporting the idea that some microbes may have acquired the genetic information during association with their animal hosts.}, }
@article {pmid8409920, year = {1993}, author = {Mariani, F and Piccolella, E and Colizzi, V and Rappuoli, R and Gross, R}, title = {Characterization of an IS-like element from Mycobacterium tuberculosis.}, journal = {Journal of general microbiology}, volume = {139}, number = {8}, pages = {1767-1772}, doi = {10.1099/00221287-139-8-1767}, pmid = {8409920}, issn = {0022-1287}, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics ; Base Sequence ; Biological Evolution ; Blotting, Southern ; *DNA Transposable Elements ; DNA, Bacterial ; Molecular Sequence Data ; Mycobacterium tuberculosis/*genetics ; Polymerase Chain Reaction ; Sequence Homology, Amino Acid ; Species Specificity ; }, abstract = {A DNA sequence, present in members of the Mycobacterium tuberculosis complex, has been identified and characterized. The distribution of this DNA sequence among mycobacterial species was analysed by DNA hybridization and PCR experiments. As the sequence was detected only in bacteria belonging to the M. tuberculosis complex, it may be useful for the rapid discrimination of mycobacteria. Interestingly, the sequence has some characteristics of an insertion element (IS) and codes for a hypothetical protein with significant homologies to proteins encoded by several IS elements of other organisms, namely IS427 and IS869 from Agrobacterium tumefaciens, IS402 from Pseudomonas cepacia, Tn4811 from Streptomyces lividans and ISRm4 from Rhizobium meliloti. Together, these elements form a previously unrecognized family of transposable elements. This finding suggests the possibility of horizontal gene transfer between pathogenic mycobacteria and other organisms including Gram-negative plant-pathogenic bacteria.}, }
@article {pmid8510664, year = {1993}, author = {Pfeifer, F and Griffig, J and Oesterhelt, D}, title = {The fdx gene encoding the [2Fe--2S] ferredoxin of Halobacterium salinarium (H. halobium).}, journal = {Molecular &amp; general genetics : MGG}, volume = {239}, number = {1-2}, pages = {66-71}, pmid = {8510664}, issn = {0026-8925}, mesh = {Amino Acid Sequence ; Base Sequence ; Blotting, Northern ; Blotting, Southern ; DNA, Bacterial ; Ferredoxins/*genetics ; *Genes, Bacterial ; Halobacterium salinarum/classification/*genetics ; Molecular Sequence Data ; Phylogeny ; Restriction Mapping ; Sequence Homology, Amino Acid ; Transcription, Genetic ; }, abstract = {The gene encoding the [2Fe--2S] ferredoxin (fdx gene) was isolated from Halobacterium salinarium using two oligonucleotides deduced from the ferredoxin sequence as probes. Cosmid DNAs exhibiting hybridization were isolated, the fdx gene was localized to smaller subfragments and the nucleotide sequence determined. The 390 bp coding sequence is located in the halobacterial FI-DNA and transcribed as a 440 nucleotide mRNA. S1 mapping indicated that the 5' terminus of the mRNA maps immediately upstream of the ATG start codon. The promoter box A, centred around position -25 (5' AC-TATG 3'), and box B (TG) elements at the start of the transcript resemble the sequences of a typical archaeal promoter. The restriction pattern of an approximately 50 kb region surrounding the fdx gene is conserved in various Halobacterium species. The halobacterial ferredoxin and the major gas vesicle protein GvpA exhibit up to 70% similarity to their respective counterparts in cyanobacteria suggesting lateral gene transfer between the organisms. These similarities prompted a more detailed investigation of the relative positions of the genes in the halobacterial genome.}, }
@article {pmid8155843, year = {1993}, author = {Hilario, E and Gogarten, JP}, title = {Horizontal transfer of ATPase genes--the tree of life becomes a net of life.}, journal = {Bio Systems}, volume = {31}, number = {2-3}, pages = {111-119}, doi = {10.1016/0303-2647(93)90038-e}, pmid = {8155843}, issn = {0303-2647}, mesh = {Adenosine Triphosphatases/*genetics ; Archaea/classification/enzymology/genetics ; *Biological Evolution ; Enterococcus/enzymology/genetics ; Eukaryotic Cells/enzymology ; *Genes, Bacterial ; Glutamate Dehydrogenase/genetics ; Multigene Family ; Phylogeny ; Thermus thermophilus/enzymology/genetics ; }, abstract = {An ancient gene duplication gave rise to the catalytic and non-catalytic subunits of each of the three types of proton pumping ATPases: vacuolar, archaebacterial and eubacterial. Previously, this gene duplication has been used to root the universal tree of life. However, recent findings of archaebacterial type ATPases in eubacteria and of eubacterial type in an archaebacterium suggested that both types of ATPases may have been already present in the last common ancestor. Here we show that a phylogenetic analysis of these ATPase subunits indicates that this conclusion is premature. We suggest that horizontal gene transfer can explain the data. In addition, we show that the analysis of glutamate dehydrogenases data neither affirm nor contradict any particular placement of the last common ancestor in the universal tree of life. The prevalence and the mode of horizontal gene transfer is discussed.}, }
@article {pmid1357526, year = {1992}, author = {Marklund, BI and Tennent, JM and Garcia, E and Hamers, A and Båga, M and Lindberg, F and Gaastra, W and Normark, S}, title = {Horizontal gene transfer of the Escherichia coli pap and prs pili operons as a mechanism for the development of tissue-specific adhesive properties.}, journal = {Molecular microbiology}, volume = {6}, number = {16}, pages = {2225-2242}, doi = {10.1111/j.1365-2958.1992.tb01399.x}, pmid = {1357526}, issn = {0950-382X}, support = {5R01GM44655-02/GM/NIGMS NIH HHS/United States ; }, mesh = {Adhesins, Escherichia coli ; Alleles ; Amino Acid Sequence ; Animals ; Bacterial Adhesion/*genetics ; Bacterial Outer Membrane Proteins/*genetics ; Base Sequence ; *Biological Evolution ; Carbohydrate Sequence ; DNA, Bacterial ; Escherichia coli/*genetics ; *Fimbriae, Bacterial ; Humans ; Molecular Sequence Data ; Multigene Family ; *Operon ; Restriction Mapping ; Sequence Homology ; *Transfection ; }, abstract = {Escherichia coli strains bind to Gal alpha 1-4Gal-containing glycolipids via P pili-associated G-adhesins. Three functional classes of adhesins with different binding specificities are encoded by conserved G-alleles. We suggest that the Class I papG-allele of strain J96 is a novel acquisition possibly introduced via horizontal gene transfer into one of the two P pili gene clusters carried by this strain. Closely related strains in the ECOR collection of natural E. coli isolates carry either a Class II or a Class III G-adhesin. Data indicate that genetic exchanges involving either entire pap or prs gene clusters or individual pap/prs genes have occurred. We propose that the retention and spread of pap/prs DNA among E. coli is the result of selection pressure exerted by mammalian intestinal isoreceptors.}, }
@article {pmid1328812, year = {1992}, author = {Forbes, KJ and Bruce, KD and Ball, A and Pennington, TH}, title = {Variation in length and sequence of porin (ompP2) alleles of non-capsulate Haemophilus influenzae.}, journal = {Molecular microbiology}, volume = {6}, number = {15}, pages = {2107-2112}, doi = {10.1111/j.1365-2958.1992.tb01384.x}, pmid = {1328812}, issn = {0950-382X}, mesh = {*Alleles ; *Antigenic Variation ; *Bacterial Capsules ; Bacterial Outer Membrane Proteins/chemistry/*genetics ; Base Sequence ; *Genes, Bacterial ; Haemophilus influenzae/chemistry/*genetics ; Molecular Sequence Data ; Polymorphism, Genetic ; Porins ; }, abstract = {Length variations of Haemophilus influenzae outer membrane porin protein P2 were found at the DNA and protein levels, notably in non-capsulate strains. Protein length, measured by SDS-polyacrylamide gel electrophoresis, was found to correlate with the length of the gene, measured by polymerase chain reaction amplification, and ranged from 35-42 kDa and 970-1090 nucleotides, respectively. This represents a length variation of some 15%. The genetic location of these variations was studied by restriction enzyme mapping 10 of the non-capsulate strains revealing further polymorphisms at the DNA level. All 10 strains were distinct and differed from a type b strain. The conservation and assortment of the different restriction sites in the alleles is discussed in relation to the very great diversity previously described for this protein and of the whole genome itself in non-capsulate strains. The roles of selection, horizontal gene transfer, and transformation in generating this diversity are discussed.}, }
@article {pmid1534556, year = {1992}, author = {Sandmeier, H and Iida, S and Arber, W}, title = {DNA inversion regions Min of plasmid p15B and Cin of bacteriophage P1: evolution of bacteriophage tail fiber genes.}, journal = {Journal of bacteriology}, volume = {174}, number = {12}, pages = {3936-3944}, pmid = {1534556}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; Base Sequence ; Biological Evolution ; Chromosome Inversion ; Coliphages/*genetics/ultrastructure ; DNA, Viral/*genetics ; Genetic Complementation Test ; Microscopy, Electron ; Molecular Sequence Data ; Mutation/genetics ; Plasmids/*genetics ; Repetitive Sequences, Nucleic Acid/genetics ; Sequence Homology, Nucleic Acid ; Viral Proteins/chemistry/*genetics ; Viral Tail Proteins ; }, abstract = {Plasmid p15B and the genome of bacteriophage P1 are closely related, but their site-specific DNA inversion systems, Min and Cin, respectively, do not have strict structural homology. Rather, the complex Min system represents a substitution of a Cin-like system into an ancestral p15B genome. The substituting sequences of both the min recombinase gene and the multiple invertible DNA segments of p15B are, respectively, homologous to the pin recombinase gene and to part of the invertible DNA of the Pin system on the defective viral element e14 of Escherichia coli K-12. To map the sites of this substitution, the DNA sequence of a segment adjacent to the invertible segment in the P1 genome was determined. This, together with already available sequence data, indicated that both P1 and p15B had suffered various sequence acquisitions or deletions and sequence amplifications giving rise to mosaics of partially related repeated elements. Data base searches revealed segments of homology in the DNA inversion regions of p15B, e14, and P1 and in tail fiber genes of phages Mu, T4, P2, and lambda. This result suggest that the evolution of phage tail fiber genes involves horizontal gene transfer and that the Min and Pin regions encode tail fiber genes. A functional test proved that the p15B Min region carries a tail fiber operon and suggests that the alternative expression of six different gene variants by Min inversion offers extensive host range variation.}, }
@article {pmid1527496, year = {1992}, author = {Griffiths, AE and Walsby, AE and Hayes, PK}, title = {The homologies of gas vesicle proteins.}, journal = {Journal of general microbiology}, volume = {138}, number = {6}, pages = {1243-1250}, doi = {10.1099/00221287-138-6-1243}, pmid = {1527496}, issn = {0022-1287}, mesh = {Amino Acid Sequence ; Bacterial Proteins/*genetics/isolation &amp; purification ; Cyanobacteria/chemistry/*genetics ; Molecular Sequence Data ; Phylogeny ; *Proteins ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; }, abstract = {In addition to GvpA, the main structural protein, an SDS-soluble protein has been found in gas vesicles isolated from six different genera of cyanobacteria. N-terminal sequence analysis of the first 30 to 60 residues of the gel-purified proteins showed that they were homologous to GvpC, a protein that strengthens the gas vesicle in Anabaena flos-aquae. The proteins from some of the organisms showed rather low homology, however, and this may explain why the genes that encode them have not been found by Southern hybridization studies. The gas vesicles of another cyanobacterium, Dactylococcopsis salina, contained two SDS-soluble proteins (M(r) 17,000 and 35,000) that were identical in sequence for the first 24 residues but not thereafter; these two proteins showed no clear homology to GvpC. The sequence of GvpA, the main structural gas vesicle protein, was very similar in each of the organisms investigated. GvpA from the purple bacterium Amoebobacter pendens was different for the first 8 residues but 51 of the next 56 residues were identical to those of the cyanobacterial GvpA. Analysis of the GvpA and GvpC sequences provides support for the idea that the low diversity of GvpA reflects a high degree of conservation rather than a recent origin followed by lateral gene transfer between different bacteria.}, }
@article {pmid1563779, year = {1992}, author = {Simpson, WJ and Musser, JM and Cleary, PP}, title = {Evidence consistent with horizontal transfer of the gene (emm12) encoding serotype M12 protein between group A and group G pathogenic streptococci.}, journal = {Infection and immunity}, volume = {60}, number = {5}, pages = {1890-1893}, pmid = {1563779}, issn = {0019-9567}, support = {AI-16722/AI/NIAID NIH HHS/United States ; RR-05425/RR/NCRR NIH HHS/United States ; }, mesh = {*Antigens, Bacterial ; *Bacterial Outer Membrane Proteins ; Bacterial Proteins/*genetics ; *Carrier Proteins ; DNA, Bacterial/genetics ; Electrophoresis ; Nucleic Acid Hybridization ; Restriction Mapping ; Streptococcus/*genetics ; Streptococcus pyogenes/*genetics ; *Transfection ; }, abstract = {Human isolates of Lancefield group G streptococci harbor sequences homologous with the structural gene (emm) encoding M protein, a major virulence factor in Streptococcus pyogenes (a group A Streptococcus species). We used DNA-DNA hybridization, restriction endonuclease chromosomal profiling, and multilocus enzyme electrophoresis to examine genetic relationships between group A and group G streptococcal strains expressing homologous serologic type 12 M (M12) protein. All M12 group A strains studied had very similar restriction endonuclease genomic profiles and multilocus enzyme genotypes. In contrast, the restriction enzyme genomic profile and multilocus enzyme genotype of the M12 group G strain CS140 were strikingly different from those characterizing the M12 group A organisms. DNA-DNA hybridization studies revealed, on average, 57% genomic similarity between the M12 group A and group G strains. Taken together, our data demonstrate that a gene encoding M12 protein occurs in two highly divergent chromosomal backgrounds, a result suggesting that an episode of horizontal gene transfer and recombination has occurred between two streptococcal lineages.}, }
@article {pmid1556748, year = {1992}, author = {Smith, JM}, title = {Analyzing the mosaic structure of genes.}, journal = {Journal of molecular evolution}, volume = {34}, number = {2}, pages = {126-129}, pmid = {1556748}, issn = {0022-2844}, mesh = {Chi-Square Distribution ; *Crossing Over, Genetic ; *Genes, Bacterial ; Mosaicism/*genetics ; Transformation, Bacterial ; }, abstract = {Some genes in prokaryotes consist of a mosaic of regions derived from different ancestors by horizontal gene transfer. A method is described for demonstrating the statistical significance of such mosaic structure and for locating the crossover points separating different regions.}, }
@article {pmid1582572, year = {1992}, author = {Sukhodolets, VV}, title = {[Principles of prokaryotic genome organization].}, journal = {Genetika}, volume = {28}, number = {1}, pages = {28-37}, pmid = {1582572}, issn = {0016-6758}, mesh = {Alleles ; Biological Evolution ; Crossing Over, Genetic/genetics ; Escherichia coli/*genetics ; *Genome, Bacterial ; Multigene Family/genetics ; Oligonucleotides/genetics ; Recombination, Genetic/genetics ; }, abstract = {The peculiarities of bacterial chromosome organization are discussed, based mainly on the data on Escherichia coli. Highly important for bacterial genome organization is its division into two approx. equal half-genomes undergoing periodically "exchanges" of some kind displayed as continuous inversions including the oriC region of replication initiation. It is believed that short oligonucleotides are comprised in either of half-genomes. The former are predominantly oriented as direct repeats, which ensures the possibility of formation of tandem duplications consisting of identical genes--under conditions when selection for enhancing functions of corresponding genes takes place. Multiple tandem duplications capable of excision of plasmatic gene copies seem to initiate horizontal gene transfer in bacteria. Tandem gene duplications are probably being formed in the process of bacterial genetic recombination as well, when, as a result of non-equal crossing over, gene alleles derived from different strains are united into a tandem.}, }
@article {pmid1444264, year = {1992}, author = {Aharonowitz, Y and Cohen, G and Martin, JF}, title = {Penicillin and cephalosporin biosynthetic genes: structure, organization, regulation, and evolution.}, journal = {Annual review of microbiology}, volume = {46}, number = {}, pages = {461-495}, doi = {10.1146/annurev.mi.46.100192.002333}, pmid = {1444264}, issn = {0066-4227}, mesh = {Amino Acid Sequence ; Biological Evolution ; Cephalosporins/*biosynthesis ; *Gene Expression Regulation, Fungal ; *Genes, Fungal ; Molecular Sequence Data ; Penicillins/*biosynthesis ; }, abstract = {Penicillins and cephalosporins are produced by a wide variety of microorganisms, including some filamentous fungi, many gram-positive streptomycetes, and a few gram-negative unicellular bacteria. All produce these beta-lactam antibiotics by essentially the same biosynthetic pathway. Recently, most of the penicillin and cephalosporin biosynthetic genes have been cloned, sequenced, and expressed. The biosynthetic genes code for enzymes that possess multifunctional peptide synthetase, cyclase, epimerase, expandase, hydroxylase, lysine aminotransferase, and acetyltransferase activities and are organized in chromosomal gene clusters and coordinately expressed. DNA hybridization screens of streptomycetes demonstrate that beta-lactam biosynthetic genes may be more widespread in nature than is indicated by conventional antibiotic screens. They offer the possibility of expanding the search for organisms with potential to make new beta-lactam antibiotics. Attempts to improve current yields of beta-lactams in production strains by introducing into them additional copies of biosynthetic genes have been partially successful. Comparative sequence analysis of bacterial and fungal beta-lactam biosynthetic genes show they share very high sequence identity. A model that explains the similarity of biosynthetic genes from an evolutionary standpoint assumes horizontal gene-transfer between the two groups of organisms. Indirect evidence suggests the transfer occurred from the bacteria to the fungi.}, }
@article {pmid1762151, year = {1991}, author = {Médigue, C and Rouxel, T and Vigier, P and Hénaut, A and Danchin, A}, title = {Evidence for horizontal gene transfer in Escherichia coli speciation.}, journal = {Journal of molecular biology}, volume = {222}, number = {4}, pages = {851-856}, doi = {10.1016/0022-2836(91)90575-q}, pmid = {1762151}, issn = {0022-2836}, mesh = {Amino Acids/metabolism ; Base Sequence ; Codon/genetics ; DNA Replication ; Escherichia coli/*genetics ; Gene Library ; *Genes, Bacterial ; Genome, Bacterial ; Models, Genetic ; Models, Statistical ; Oligodeoxyribonucleotides ; *Transfection ; }, abstract = {After extracting more than 780 identified Escherichia coli genes from available data libraries, we investigated the codon usage of the corresponding coding sequences and extended the study of gene classes, thus obtained, to the nature and intensity of short nucleotide sequence selection, related to constraints operating at the nucleotide level. Using Factorial Correspondence Analysis we found that three classes ought to be included in order to match all data now available. The first two classes, as known, encompass genes expressed either continuously at a high level, or at a low level and/or rarely; the third class consists of genes corresponding to surface elements of the cell, genes coming from mobile elements as well as genes resulting in a high fidelity of DNA replication. This suggests that bacterial strains cultivated in the laboratory have been fixed by specific use of antimutator genes that are horizontally exchanged.}, }
@article {pmid1822285, year = {1991}, author = {Sprague, GF}, title = {Genetic exchange between kingdoms.}, journal = {Current opinion in genetics &amp; development}, volume = {1}, number = {4}, pages = {530-533}, doi = {10.1016/s0959-437x(05)80203-5}, pmid = {1822285}, issn = {0959-437X}, mesh = {*Biological Evolution ; *Conjugation, Genetic ; DNA, Bacterial/genetics ; Escherichia coli/*genetics ; Gene Expression Regulation, Fungal ; Plasmids ; Saccharomyces cerevisiae/*genetics ; Schizosaccharomyces/*genetics ; Species Specificity ; Symbiosis ; }, abstract = {Bacterial conjugation with two evolutionarily divergent yeasts has been observed in the laboratory. Whether such trans-kingdom conjugation events, other than the well known Agrobacterium-plant cell interaction, actually occur in nature is not known. However, a few putative events have recently been uncovered by gene (or protein) sequence analysis, suggesting that horizontal gene transfer between phylogenetic kingdoms may be a real phenomenon.}, }
@article {pmid1779754, year = {1991}, author = {Médigue, C and Viari, A and Hénaut, A and Danchin, A}, title = {Escherichia coli molecular genetic map (1500 kbp): update II.}, journal = {Molecular microbiology}, volume = {5}, number = {11}, pages = {2629-2640}, doi = {10.1111/j.1365-2958.1991.tb01972.x}, pmid = {1779754}, issn = {0950-382X}, mesh = {Base Sequence ; Chromosome Mapping ; Chromosomes, Bacterial ; DNA, Bacterial/genetics ; Databases, Factual ; Escherichia coli/*genetics ; *Genes, Bacterial ; *Genome ; Restriction Mapping ; }, abstract = {The DNA sequence data for Escherichia coli deposited in the EMBL library (release 27), together with miscellaneous data obtained from several laboratories, have been localized on an updated and corrected version of the restriction map of the chromosome generated by Kohara et al. (1987) and modified by others. This second update adds a further 500 kbp, increasing the amount of the E. coli chromosome sequenced to about one third of the total: 1510 kbp of sequenced DNA is included in the present data base. The accuracy of the map is assessed, and allows us to propose a precise genetic map position for every sequenced gene. The location of rare-cutting sites such as AvrII, NotI and SfiI have also been included in the update in order to combine the data obtained from different sources into one single file. The distribution of palindromic sequences (to which most restriction sites belong) has been studied in coding sequences. There appears to be a significant counter-selection against several such sequences in E. coli coding sequences (but not in other organisms such as Saccharomyces cerevisiae), suggesting the existence of constraints on DNA structure in E. coli, perhaps indicative of a functional role for horizontal gene transfer, preserving coding sequences, in this type of bacteria.}, }
@article {pmid1653453, year = {1991}, author = {Houck, MA and Clark, JB and Peterson, KR and Kidwell, MG}, title = {Possible horizontal transfer of Drosophila genes by the mite Proctolaelaps regalis.}, journal = {Science (New York, N.Y.)}, volume = {253}, number = {5024}, pages = {1125-1128}, doi = {10.1126/science.1653453}, pmid = {1653453}, issn = {0036-8075}, support = {36715//PHS HHS/United States ; }, mesh = {Animals ; Base Sequence ; Biological Evolution ; Blotting, Southern ; DNA/genetics/isolation &amp; purification ; *DNA Transposable Elements ; DNA, Ribosomal/genetics ; Drosophila/*genetics ; Drosophila melanogaster/*genetics/parasitology/ultrastructure ; Microscopy, Electron, Scanning ; Mites/*genetics/physiology/ultrastructure ; Molecular Sequence Data ; Oligonucleotide Probes ; Polymerase Chain Reaction/methods ; Pupa ; *Transfection ; }, abstract = {There is strong inferential evidence for recent horizontal gene transfer of the P (mobile) element to Drosophila melanogaster from a species of the Drosophila willistoni group. One potential vector of this transfer is a semiparasitic mite, Proctolaelaps regalis DeLeon, whose morphology, behavior, and co-occurrence with Drosophila are consistent with the properties necessary for such a vector. Southern blot hybridization, polymerase chain reaction (PCR) amplification, and DNA sequencing showed that samples of P. regalis associated with a P strain of D. melanogaster carried P element sequences. Similarly, Drosophila ribosomal DNA sequences were identified in P. regalis samples that had been associated with Drosophila cultures. These results have potentially important evolutionary implications, not only for understanding the mechanisms by which genes may be transferred between reproductively isolated species, but also for improved detection of some host-parasite and predator-prey relationships.}, }
@article {pmid1766389, year = {1991}, author = {Coffey, TJ and Dowson, CG and Daniels, M and Zhou, J and Martin, C and Spratt, BG and Musser, JM}, title = {Horizontal transfer of multiple penicillin-binding protein genes, and capsular biosynthetic genes, in natural populations of Streptococcus pneumoniae.}, journal = {Molecular microbiology}, volume = {5}, number = {9}, pages = {2255-2260}, doi = {10.1111/j.1365-2958.1991.tb02155.x}, pmid = {1766389}, issn = {0950-382X}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Alleles ; *Aminoacyltransferases ; Bacterial Capsules/*genetics ; *Bacterial Proteins ; Biological Evolution ; Carrier Proteins/*genetics ; Chloramphenicol Resistance/genetics ; DNA Fingerprinting ; Drug Resistance, Microbial/*genetics ; Genetics, Population ; *Hexosyltransferases ; Muramoylpentapeptide Carboxypeptidase/*genetics ; Penicillin Resistance/genetics ; Penicillin-Binding Proteins ; *Peptidyl Transferases ; Serotyping ; Streptococcus pneumoniae/*genetics ; Tetracycline Resistance/genetics ; Transfection/*genetics ; }, abstract = {Multiply antibiotic-resistant serotype 23F isolates of Streptococcus pneumoniae are prevalent in Spain and have also been recovered recently in the United Kingdom and the United States. Analysis of populations of these isolates by multilocus enzyme electrophoresis, and restriction endonuclease cleavage electrophoretic profiling of penicillin-binding protein (PBP) genes, has demonstrated that these isolates are a single clone (Muñoz et al., 1991). Here we report studies of non-serotype 23F penicillin-resistant pneumococci isolated in Spain and the United Kingdom. One of the isolates expressed serotype 19 capsule but was otherwise indistinguishable from the serotype 23F clone on the basis of multilocus enzyme electrophoresis, antibiotic resistance profiling, and restriction endonuclease patterns of genes encoding PBP1A, PBP2B and PBP2X, a result which suggests that horizontal transfer of capsular biosynthesis genes had occurred. These same techniques revealed that six other resistant isolates, all expressing serotype 9 polysaccharide capsule, represent a clone. Interestingly, the chromosomal lineage of this clone is not closely related to the 23F clone; however, the serotype 9 and 23F clones harbour apparently identical PBP1A, -2B and -2X genes. To explain these data, we favour the interpretation that horizontal gene transfer in natural populations has distributed genes encoding altered forms of PBP1A, -2B and -2X to distinct evolutionary lineages of S. pneumoniae.}, }
@article {pmid2040303, year = {1991}, author = {Michels, PA and Marchand, M and Kohl, L and Allert, S and Wierenga, RK and Opperdoes, FR}, title = {The cytosolic and glycosomal isoenzymes of glyceraldehyde-3-phosphate dehydrogenase in Trypanosoma brucei have a distant evolutionary relationship.}, journal = {European journal of biochemistry}, volume = {198}, number = {2}, pages = {421-428}, doi = {10.1111/j.1432-1033.1991.tb16031.x}, pmid = {2040303}, issn = {0014-2956}, mesh = {Amino Acid Sequence ; Animals ; Bacteria/enzymology ; Base Sequence ; *Biological Evolution ; Cytosol/enzymology ; Genes ; Genomic Library ; Glyceraldehyde-3-Phosphate Dehydrogenases/*genetics/isolation &amp; purification ; Humans ; Isoenzymes/*genetics/isolation &amp; purification ; Liver/enzymology ; Molecular Sequence Data ; Organelles/*enzymology ; Phylogeny ; Rats ; Restriction Mapping ; Sequence Homology, Nucleic Acid ; Trypanosoma brucei brucei/*enzymology/genetics ; }, abstract = {Trypanosoma brucei contains two isoenzymes for glyceraldehyde-3-phosphate dehydrogenase: one enzyme resides in a microbody-like organelle, the glycosome; the other is found in the cytosol. Previously we have reported the characterization of the gene for the glycosomal enzyme [Michels, P. A. M., Poliszczak, A., Osinga, K. A., Misset, O., Van Beeumen, J., Wierenga, R. K., Borst, P. &amp; Opperdoes, F. R. (1986) EMBO J. 5, 1049-1056]. Here we describe the cloning and analysis of the gene that codes for the cytosolic isoenzyme. The gene encodes a polypeptide of 330 amino acids, with a calculated molecular mass of 35440 Da. The two isoenzymes are only 55% identical. The cytosolic glyceraldehyde-3-phosphate dehydrogenase differs from the glycosomal enzyme in the following respects: (a) its subunit molecular mass is 3.4 kDa smaller due to the absence of insertions and a small C-terminal extension which are unique to the glycosomal protein; (b) the cytosolic enzyme has a lower pI (7.9, as compared to 9.3 for the glycosomal isoenzyme), which is due to a reduction in the excess of positively charged amino acids (the calculated net charges of the polypeptides are +2 and +11, respectively). We have compared the amino acid sequences of the two T. brucei glyceraldehyde-3-phosphate dehydrogenases, with 24 available sequences of the corresponding enzyme of other organisms from various phylogenetic groups. On the basis of this comparison an evolutionary tree was constructed. This analysis strongly supports the theory that T. brucei diverged early in evolution from the main eukaryotic branch of the phylogenetic tree. Further, two separate branches for the lineages leading to Trypanosoma are inferred from the amino acid sequences, suggesting that the genes for the two glyceraldehyde-3-phosphate dehydrogenases of the trypanosome are distantly related and must have been acquired independently by the trypanosomal ancestor. The branching determined with the glycosomal enzyme precedes that found with the cytosolic enzyme. The available data do not allow us to decide which of the two genes originally belonged to the trypanosome lineage and which entered the cell later by horizontal gene transfer.}, }
@article {pmid2024965, year = {1991}, author = {Lujan, R and Zhang, QY and Sáez Nieto, JA and Jones, DM and Spratt, BG}, title = {Penicillin-resistant isolates of Neisseria lactamica produce altered forms of penicillin-binding protein 2 that arose by interspecies horizontal gene transfer.}, journal = {Antimicrobial agents and chemotherapy}, volume = {35}, number = {2}, pages = {300-304}, pmid = {2024965}, issn = {0066-4804}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Sequence ; *Bacterial Proteins ; Base Sequence ; *Carrier Proteins ; Cloning, Molecular ; Hexosyltransferases/*biosynthesis/genetics ; Molecular Sequence Data ; Multienzyme Complexes/*biosynthesis/genetics ; *Muramoylpentapeptide Carboxypeptidase ; Neisseria/drug effects/*genetics ; Penicillin Resistance/*genetics ; Penicillin-Binding Proteins ; Peptidyl Transferases/*biosynthesis/genetics ; Transfection ; }, abstract = {Isolates of Neisseria lactamica that have increased resistance to penicillin have emerged in recent years. Resistance to penicillin was shown to be due to the production of altered forms of penicillin-binding protein 2 (PBP 2) that have reduced affinity for the antibiotic. The sequences of the PBP 2 genes (penA) from two penicillin-resistant isolates were almost identical (less than or equal to 1% sequence divergence) to that of a penicillin-susceptible isolate, except in a 175-bp region where the resistant and susceptible isolates differed by 27%. The nucleotide sequences of these divergent regions were identical (or almost identical) to the sequence of the corresponding region of the penA gene of N. flavescens NCTC 8263. Altered forms of PBP 2 with decreased affinity for penicillin in the two penicillin-resistant isolates of N. lactamica appear, therefore, to have arisen by the replacement of part of the N. lactamica penA gene with the corresponding region from the penA gene of N. flavescens.}, }
@article {pmid1899846, year = {1991}, author = {Kobayashi, H and Viale, AM and Takabe, T and Akazawa, T and Wada, K and Shinozaki, K and Kobayashi, K and Sugiura, M}, title = {Sequence and expression of genes encoding the large and small subunits of ribulose 1,5-bisphosphate carboxylase/oxygenase from Chromatium vinosum.}, journal = {Gene}, volume = {97}, number = {1}, pages = {55-62}, doi = {10.1016/0378-1119(91)90009-z}, pmid = {1899846}, issn = {0378-1119}, mesh = {Amino Acid Sequence ; Base Sequence ; Chromatium/enzymology/*genetics ; Cyanobacteria/genetics ; Escherichia coli/genetics ; *Gene Expression ; Genes, Bacterial ; Molecular Sequence Data ; Phylogeny ; Promoter Regions, Genetic ; Protein Conformation ; Ribulose-Bisphosphate Carboxylase/biosynthesis/*genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {A DNA fragment bearing genes for the large (rbcL) and small (rbcS) subunits of ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) was cloned from the photosynthetic purple sulfur bacterium Chromatium vinosum. Enzymatically fully active RuBisCO was synthesized in Escherichia coli cells when the cloned DNA was placed downstream of tac promoter. Nucleotide (nt) sequences of rbcL-rbcS were more homologous to cyanobacterial counterparts than to those from Alcaligenes eutrophus or higher plants. However, the amino acid (aa) sequence in a domain responsible for CO2 activation in the C. vinosum rbcL product resembled the corresponding aa sequence in higher plant RuBisCos, but not in the cyanobacterial enzymes. Chemically determined aa sequences at the N terminals of both subunits of RuBisCO purified from C. vinosum were not identical to those deduced from the nt sequences, although they were completely the same as aa sequences deduced from rbcA-rbcB, another locus encoding RuBisCO in C. vinosum. Therefore, the rbcL-rbcS locus seems to be barely expressed under a standard condition for photoautotrophic growth. The homology of the nt sequences between rbcL and rbcA was 82%, and that between rbcS and rbcB was 63%, whereas the codon usages of these genes were basically identical. The rbcL-rbcS and rbcA-rbcB loci therefore must have evolved from a common ancestral set of genes after duplication, instead of lateral gene transfer.}, }
@article {pmid1793338, year = {1991}, author = {Lorenz, MG and Gerjets, D and Wackernagel, W}, title = {Release of transforming plasmid and chromosomal DNA from two cultured soil bacteria.}, journal = {Archives of microbiology}, volume = {156}, number = {4}, pages = {319-326}, pmid = {1793338}, issn = {0302-8933}, mesh = {Acinetobacter calcoaceticus/*genetics ; Bacillus subtilis/*genetics ; Chromosomes, Bacterial ; DNA, Bacterial/*metabolism ; Deoxyribonucleases/metabolism ; Plasmids ; *Soil Microbiology ; Transformation, Bacterial ; }, abstract = {The release of chromosomal and plasmid DNA from Acinetobacter calcoaceticus and Bacillus subtilis cultivated in minimal medium and broth over a period of 50 h was monitored and related to growth phase, autolysis, DNase production and natural competence. The released DNAs were biologically active in natural transformation. In addition, the circular integrity of a released B. subtilis shuttle vector (pHV14) was demonstrated by artificial transformation of Escherichia coli. In cultures of both strains high molecular weight DNA accumulated, particularly during the stationary and death phase (up to 30 micrograms ml-1). Generally, despite the presence in culture fluids of DNase activity (and of an intracellular enzyme, catalase, indicating some cell lysis) there was high transforming activity of chromosomal and plasmid DNA even 40 h after the cultures reached the stationary phase. In cultures of B. subtilis in minimal medium a presumably active release of intact plasmids and chromosomal DNA occurred during the competence phase. The release of biologically functional DNA during essentially all growth phases of a gram-positive and a gram-negative member of soil bacteria might facilitate horizontal gene transfer by transformation in natural habitats.}, }
@article {pmid2176696, year = {1990}, author = {Hagemann, S and Miller, WJ and Pinsker, W}, title = {P-related sequences in Drosophila bifasciata: a molecular clue to the understanding of P-element evolution in the genus Drosophila.}, journal = {Journal of molecular evolution}, volume = {31}, number = {6}, pages = {478-484}, pmid = {2176696}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; *Biological Evolution ; Codon ; DNA/isolation &amp; purification ; *DNA Transposable Elements ; Drosophila/*genetics ; Drosophila melanogaster/genetics ; Genomic Library ; Molecular Sequence Data ; Phylogeny ; Repetitive Sequences, Nucleic Acid ; Restriction Mapping ; Sequence Alignment ; Species Specificity ; }, abstract = {Two P-elements (bif1 and bif2) were isolated from a genomic library of Drosophila bifasciata. Both elements are internally deleted and have lost the coding capacity for a functional transposase. One of the elements (bif2) contains an insert consisting of a repetitive sequence. The terminal inverted repeats and the segments necessary for passive mobility are well conserved. Element bif2 has retained rudiments of the coding sequence of exon 0 and exon 3, but the reading frame is destroyed by insertions and deletions. The comparison of the D. bifasciata P-elements with P-elements of Drosophila melanogaster and Drosophila nebulosa reveals that the two latter sequences are more similar to each other than either of them is to the D. bifasciata elements. This finding contradicts the phylogenetic relationship of the species and can be taken as an indirect but unequivocal evidence for recent horizontal gene transfer from a relative of D. nebulosa to the gene pool of D. melanogaster. The P-elements of D. bifasciata are phylogenetically ancient and have evolved independently for about 50 million years. A higher substitution rate at the third codon position as well as a predominance of conservative replacements at the amino acid level indicates that the P-elements of D. bifasciata have been under selective constraint over a long period and that immunobilization has occurred only recently.}, }
@article {pmid2124629, year = {1990}, author = {Doolittle, RF and Feng, DF and Anderson, KL and Alberro, MR}, title = {A naturally occurring horizontal gene transfer from a eukaryote to a prokaryote.}, journal = {Journal of molecular evolution}, volume = {31}, number = {5}, pages = {383-388}, pmid = {2124629}, issn = {0022-2844}, support = {GM-34434/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Escherichia coli/enzymology/*genetics ; Euryarchaeota/enzymology/*genetics ; Glyceraldehyde-3-Phosphate Dehydrogenases/*genetics ; Molecular Sequence Data ; Phosphoglycerate Kinase/genetics ; *Phylogeny ; Rhizobium/enzymology/*genetics ; *Transfection ; }, abstract = {Naturally occurring horizontal gene transfers between nonviral organisms are difficult to prove. Only with the availability of sequence data from a wide variety of organisms can a convincing case be made. In the case of putative gene transfers between prokaryotes and eukaryotes, the minimum requirements for inferring such an event include (1) sequences of the transferred gene or its product from several appropriately divergent eukaryotes and several prokaryotes, and (2) a similar set of sequences from the same (or closely related organisms) for another gene or genes. Given these criteria, we believe that a strong case can be made for Escherichia coli having acquired a second glyceraldehyde-3-phosphate dehydrogenase gene from some eukaryotic host. Ancillary observations on the general rate of change and the time of the prokaryote-eukaryote divergence support the notion.}, }
@article {pmid2126520, year = {1990}, author = {Mindlin, SZ and Gorlenko, ZhM and Bass, IA and Khachikian, NA}, title = {[Spontaneous transformation in mixed cultures of various types of Acinetobacter and during joint growth of Acinetobacter calcoaceticus with Escherichia coli and Pseudomonas aeruginosa].}, journal = {Genetika}, volume = {26}, number = {10}, pages = {1729-1739}, pmid = {2126520}, issn = {0016-6758}, mesh = {Acinetobacter/*genetics ; Chromosomes, Bacterial ; DNA, Bacterial/genetics/metabolism ; Escherichia coli/*genetics ; Genes, Bacterial ; Plasmids ; Pseudomonas aeruginosa/*genetics ; Restriction Mapping ; Species Specificity ; Transformation, Genetic ; }, abstract = {The transfer of chromosomal and plasmid genes was studied via spontaneous transformation is mixed cultures of Acinetobacter spp. It turned out that any Acinetobacter strain, irrespective of its species specificity, serves as chromosomal DNA donor in case the mixed culture contains competent cells of the recipient strain. No transfer took place when non-related bacteria were used as donors. We also studied the transfer into Ac. calcoaceticus competent strain cells of small non-conjugative plasmids having broad host range (RSF1010, pAK1). In these cases, DNA donors could be not only acinetobacters of other species, but bacteria belonging to other systematic groups (families)--E. coli and P. aeruginosa. The transfer of plasmids from cells of unrelated bacteria took place with a frequency of about 10(-5)-10(-6). The possible role of spontaneous transformation in horizontal gene transfer is discussed.}, }
@article {pmid1979440, year = {1990}, author = {Peñalva, MA and Moya, A and Dopazo, J and Ramón, D}, title = {Sequences of isopenicillin N synthetase genes suggest horizontal gene transfer from prokaryotes to eukaryotes.}, journal = {Proceedings. Biological sciences}, volume = {241}, number = {1302}, pages = {164-169}, doi = {10.1098/rspb.1990.0081}, pmid = {1979440}, issn = {0962-8452}, mesh = {Acremonium/enzymology/*genetics ; Aspergillus nidulans/enzymology/*genetics ; Base Sequence ; *Biological Evolution ; *Genes, Bacterial ; *Genes, Fungal ; Molecular Sequence Data ; Oxidoreductases/*genetics ; Penicillium chrysogenum/enzymology/*genetics ; Sequence Homology, Nucleic Acid ; Streptomyces/enzymology/*genetics ; *Transfection ; }, abstract = {Evolutionary distances between bacterial and fungal isopenicillin N synthetase (IPNS) genes have been compared to distances between the corresponding 5S rRNA genes. The presence of sequences homologous to the IPNS gene has been examined in DNAs from representative prokaryotic organisms and Ascomycotina. The results of both analyses strongly support two different events of horizontal transfer of the IPNS gene from bacteria to filamentous fungi. This is the first example of such a type of transfer from prokaryotes to eukaryotes.}, }
@article {pmid2263192, year = {1990}, author = {Landan, G and Cohen, G and Aharonowitz, Y and Shuali, Y and Graur, D and Shiffman, D}, title = {Evolution of isopenicillin N synthase genes may have involved horizontal gene transfer.}, journal = {Molecular biology and evolution}, volume = {7}, number = {5}, pages = {399-406}, doi = {10.1093/oxfordjournals.molbev.a040615}, pmid = {2263192}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Bacteria/enzymology/*genetics ; Biological Evolution ; Fungi/enzymology/*genetics ; *Genes, Bacterial ; *Genes, Fungal ; Molecular Sequence Data ; Oxidoreductases/*genetics ; *Transfection ; }, abstract = {The isopenicillin N synthase genes from three fungal species, three Gram-positive species, and one Gram-negative bacterial species share an unusually high sequence similarity. A phylogenetic analysis was carried out to determine which type of evolutionary scenario best accounts for this similarity. The most plausible scenario is one in which a horizontal gene-transfer event, from the prokaryotes to the eukaryotes, occurred at a time close to the divergence between the Gram-positive and the Gram-negative bacteria.}, }
@article {pmid2526805, year = {1989}, author = {Montag, D and Schwarz, H and Henning, U}, title = {A component of the side tail fiber of Escherichia coli bacteriophage lambda can functionally replace the receptor-recognizing part of a long tail fiber protein of the unrelated bacteriophage T4.}, journal = {Journal of bacteriology}, volume = {171}, number = {8}, pages = {4378-4384}, pmid = {2526805}, issn = {0021-9193}, mesh = {Bacteriophage lambda/genetics/*physiology/ultrastructure ; Escherichia coli/genetics/*physiology ; *Genes ; *Genes, Viral ; Genotype ; Microscopy, Electron ; Receptors, Virus/*physiology ; Restriction Mapping ; T-Phages/genetics/*physiology/ultrastructure ; Viral Proteins/genetics/*physiology ; }, abstract = {The distal part of the long tail fiber of Escherichia coli bacteriophage T4 consists of a dimer of protein 37. Dimerization requires the catalytic action of protein 38, which is encoded by T4 and is not present in the virion. It had previously been shown that gene tfa of the otherwise entirely unrelated phage lambda can functionally replace gene 38. Open reading frame (ORF) 314, which encodes a protein that exhibits homology to a COOH-terminal area of protein 37, is located immediately upstream of tfa. The gene was cloned and expressed in E. coli. An antiserum against the corresponding polypeptide showed that it was present in phage lambda. The serum also reacted with the long tail fibers of phage T4 near their free ends. An area of the gene encoding a COOH-terminal region of ORF 314 was recombined, together with tfa, into the genome of T4, thus replacing gene 38 and a part of gene 37 that codes for a COOH-terminal part of protein 37. Such T4-lambda hybrids, unlike T4, required the presence of outer membrane protein OmpC for infection of E. coli B. An ompC missense mutant of E. coli K-12, which was still sensitive to T4, was resistant to these hybrids. We conclude that the ORF 314 protein represents a subunit of the side tail fibers of phage lambda which probably recognize the OmpC protein. ORF 314 was designated stf (side tail fiber). The results also offer an explanation for the very unusual fact that, despite identical genomic organizations, T4 and T2 produce totally different proteins 38. An ancestor of T4 from the T2 lineage may have picked up tfa and stf from a lambdoid phase, thus possibly demonstrating horizontal gene transfer between unrelated phage species.}, }
@article {pmid2565294, year = {1989}, author = {Plos, K and Hull, SI and Hull, RA and Levin, BR and Orskov, I and Orskov, F and Svanborg-Edén, C}, title = {Distribution of the P-associated-pilus (pap) region among Escherichia coli from natural sources: evidence for horizontal gene transfer.}, journal = {Infection and immunity}, volume = {57}, number = {5}, pages = {1604-1611}, pmid = {2565294}, issn = {0019-9567}, support = {AI121009/AI/NIAID NIH HHS/United States ; AI18462/AI/NIAID NIH HHS/United States ; GM33782/GM/NIGMS NIH HHS/United States ; }, mesh = {*Bacterial Adhesion ; Cystitis/microbiology ; DNA Transposable Elements ; DNA, Bacterial/genetics ; Escherichia coli/*genetics/pathogenicity ; *Fimbriae, Bacterial ; *Genes, Bacterial ; Genetic Variation ; Genetics, Population ; Humans ; Isoenzymes/genetics ; Pyelonephritis/microbiology ; Serotyping ; Urinary Tract Infections/*microbiology ; }, abstract = {Variation in chromosomal DNA in Escherichia coli was studied with probes specific for the P-associated-pilus (pap) region. The presence of DNA homologous to pap was determined by dot blots. Variation in the number of copies of pap and in the organization of internal and flanking sequences was determined by Southern blot hybridization. The 229 strains studied were also classified by O:K:H serotyping and multilocus enzyme electrophoresis. There was considerable heterogeneity in the presence of pap and distribution of pap-homologous DNA in these E. coli strains from natural sources. In general, there was less variation in pap among strains of the same specific O:K:H serotype and enzyme electrophoretic type than among random isolates. There were, however, E. coli strains identified as members of the same clone by O:K:H serotyping and enzyme electrophoresis that were pap positive and pap negative or had different Southern blot patterns for the pap probes (pap type). There were also isolates of the same pap type that differed in two of three O:K:H serotype antigens and the majority of enzymes that determined their enzyme electrophoretic type. These latter two observations were interpreted as evidence for the horizontal (infectious) transfer of the pap-homologous sequences among clones of E. coli.}, }
@article {pmid2818128, year = {1989}, author = {Kraut, M and Hugendieck, I and Herwig, S and Meyer, O}, title = {Homology and distribution of CO dehydrogenase structural genes in carboxydotrophic bacteria.}, journal = {Archives of microbiology}, volume = {152}, number = {4}, pages = {335-341}, pmid = {2818128}, issn = {0302-8933}, mesh = {Alcaligenes/enzymology/genetics ; Aldehyde Oxidoreductases/*genetics/isolation &amp; purification/metabolism ; Amino Acid Sequence ; Bacteria/enzymology/*genetics ; Base Sequence ; *Genes, Bacterial ; Molecular Sequence Data ; *Multienzyme Complexes ; Pseudomonas/enzymology/genetics ; Sequence Homology, Nucleic Acid ; Species Specificity ; }, abstract = {The 17 (S), 30 (M) and 87 kDa (L) subunits of CO dehydrogenases from the CO-oxidizing bacteria Pseudomonas carboxydoflava, Pseudomonas carboxydohydrogena and Pseudomonas carboxydovorans OM5 were isolated and purified. The N-terminal sequences of same subunits from different bacteria showed distinct homologies. Dot blot hybridization employing oligonucleotide probes derived from the sequences of the S-subunit of P. carboxydovorans OM5 and the M-subunit of P. carboxydohydrogena and DNA of the plasmid-containing CO-oxidizing bacteria Alcaligenes carboxydus, Azomonas B1, P. carboxydoflava, P. carboxydovorans OM2, OM4 and OM5 indicated that all genes encoding these subunits reside on plasmids. That in P. carboxydovorans OM5 CO dehydrogenase structural genes are located entirely on plasmid pHCG3 was evident from the absence of hybridization employing DNA from the cured mutant strain OM5-12. CO dehydrogenase structural genes could be identified on the chromosome of the plasmid-free bacteria Arthrobacter 11/x, Bacillus schlegelii, P. carboxydohydrogena and P. carboxydovorans OM3. There was no example of a plasmid-harboring carboxydotrophic bacterium that did not carry CO dehydrogenase structural genes on the plasmid. The N-terminal sequences of CO dehydrogenase structural genes were found to be conserved among carboxydotrophic bacteria of distinct taxonomic position, independent of the presence of plasmids. It is discussed whether this might be the consequence of horizontal gene transfer.}, }
@article {pmid2662898, year = {1989}, author = {Coughter, JP and Stewart, GJ}, title = {Genetic exchange in the environment.}, journal = {Antonie van Leeuwenhoek}, volume = {55}, number = {1}, pages = {15-22}, pmid = {2662898}, issn = {0003-6072}, mesh = {Bacteria/*genetics ; *Conjugation, Genetic ; *Environmental Microbiology ; Soil Microbiology ; *Transduction, Genetic ; *Transformation, Genetic ; Water Microbiology ; }, abstract = {Reports made over the past few years leave little doubt that horizontal gene transfer among bacteria can and does occur in the environment. The significance of these events in the dissemination of recombinant molecules is not clear and more research is required to fully appreciate the impact of genetic exchange on their stability and survival. Based on the available data it is fair to say that horizontal gene transfer may play as important a role in transmission of recombinant sequences as does the survival and persistence of genetically engineered microorganisms.}, }
@article {pmid3079182, year = {1988}, author = {Sukhodolets, VV}, title = {Organization and evolution of the bacterial genome.}, journal = {Microbiological sciences}, volume = {5}, number = {7}, pages = {202-206}, pmid = {3079182}, issn = {0265-1351}, mesh = {Bacteria/*genetics ; *Biological Evolution ; Chromosomes/*ultrastructure ; *Genes, Bacterial ; }, abstract = {The bacterial chromosome seems to be organized in such a way as to allow the formation of tandem gene duplications, which appear under conditions of positive selection for a high level of gene expression. Multiple gene duplications permit the excision of a gene from the chromosome by a Campbell recombinational event and the subsequent transfer of the gene to a resident plasmid. The latter derives an advantage from carrying a gene providing positive selection. Thus, tandem gene duplications could initiate horizontal gene transfer in bacteria.}, }
@article {pmid3125334, year = {1987}, author = {Syvanen, M}, title = {Molecular clocks and evolutionary relationships: possible distortions due to horizontal gene flow.}, journal = {Journal of molecular evolution}, volume = {26}, number = {1-2}, pages = {16-23}, pmid = {3125334}, issn = {0022-2844}, mesh = {Animals ; *Biological Evolution ; Birds ; *Genes ; Humans ; *Models, Genetic ; Mycoplasma/genetics ; Primates ; Species Specificity ; Viruses/*genetics ; }, abstract = {This paper discusses recent evidence suggesting that genetic information from one species occasionally transfers to another remotely related species. Besides addressing the issue of whether or not the molecular data are consistent with a wide-spread influence of horizontal gene transfer, the paper shows that horizontal gene flow would not necessarily preclude a linear molecular clock or change the rate of molecular evolution (assuming the neutral allele theory). A pervasive influence of horizontal gene transfer is more than just consistent with the data of molecular evolution, it also provides a unique explanation for a number of possibly conflicting phylogenies and contradictory clocks. This phenomenon might explain why some protein clocks are linear while the superoxide dismutase clock is not, how the molecular data on the phylogeny of apes and Australian song birds are not necessarily in conflict with those based on morphology, and, finally, why the mycoplasmas have an accelerated molecular clock.}, }
@article {pmid3036648, year = {1987}, author = {Obukowicz, MG and Perlak, FJ and Bolten, SL and Kusano-Kretzmer, K and Mayer, EJ and Watrud, LS}, title = {IS50L as a non-self transposable vector used to integrate the Bacillus thuringiensis delta-endotoxin gene into the chromosome of root-colonizing pseudomonads.}, journal = {Gene}, volume = {51}, number = {1}, pages = {91-96}, doi = {10.1016/0378-1119(87)90478-1}, pmid = {3036648}, issn = {0378-1119}, mesh = {Bacillus thuringiensis/*genetics ; Bacillus thuringiensis Toxins ; Bacterial Proteins/*genetics ; *Bacterial Toxins ; Chromosomes, Bacterial ; *DNA Transposable Elements ; Endotoxins/*genetics ; Genes ; *Genes, Bacterial ; *Genetic Vectors ; Hemolysin Proteins ; Pseudomonas/*genetics/isolation &amp; purification ; Transformation, Genetic ; Zea mays/microbiology ; }, abstract = {Insertion sequence IS50L of transposon Tn5 was used as a non-self transposable vector to integrate the delta-endotoxin gene (tox) from Bacillus thuringiensis subsp. kurstaki HD-1 into the chromosome of two corn-root colonizing strains of Pseudomonas fluorescens (112-12 and Ps3732-3-7). A DNA fragment containing the KmR gene from Tn5 and tox was inserted into an IS50L element (IS50L-tox) contained on a suicide plasmid. Transposition of IS50L-tox into the chromosome of P. fluorescens 112-12 and Ps3732-3-7 occurred by selecting for KmR transconjugants and supplying transposase in cis from a linked IS50R element. A frameshift mutation in the transposase gene of the IS50L-tox element was also constructed to decrease the likelihood that suppression or a spontaneous reversion at the UAA (ochre) termination codon of IS50L would create an active transposase. The inability of IS50L-tox to transpose further minimizes the potential for horizontal gene transfer of the tox gene to other bacterial species. Expression of the Tox protein in strains 112-12 and Ps3732-3-7 was demonstrated by an immunological assay (Western blot) and toxicity against larvae of the tobacco hornworm (Manduca sexta).}, }
@article {pmid3023294, year = {1986}, author = {Obukowicz, MG and Perlak, FJ and Kusano-Kretzmer, K and Mayer, EJ and Bolten, SL and Watrud, LS}, title = {Tn5-mediated integration of the delta-endotoxin gene from Bacillus thuringiensis into the chromosome of root-colonizing pseudomonads.}, journal = {Journal of bacteriology}, volume = {168}, number = {2}, pages = {982-989}, pmid = {3023294}, issn = {0021-9193}, mesh = {Bacillus thuringiensis/*genetics ; Bacillus thuringiensis Toxins ; *Bacterial Proteins ; *Bacterial Toxins ; Chromosomes, Bacterial ; *DNA Transposable Elements ; DNA, Recombinant ; Endotoxins/biosynthesis/*genetics ; *Genes, Bacterial ; Hemolysin Proteins ; Mutation ; Nucleic Acid Hybridization ; Nucleotidyltransferases/genetics ; Pseudomonas fluorescens/*genetics/metabolism ; Transposases ; }, abstract = {Gene replacement mediated by Tn5 sequences was used to integrate the Bacillus thuringiensis subsp. kurstaki HD-1 delta-endotoxin gene (tox) into the chromosome of two corn root-colonizing strains of Pseudomonas fluorescens. A Tn5 transposase deletion element containing the tox gene (delta Tn5-tox) was substituted for a Tn5 element previously present in the P. fluorescens chromosome. Two classes of delta Tn5-tox elements were made. The first class encodes kanamycin resistance in addition to the Tox protein, whereas the second class encodes only the Tox protein. Both classes of delta Tn5-tox elements can no longer transpose, owing to a 324-base-pair deletion in the transposase gene of IS50R, minimizing the potential for horizontal gene transfer of the tox gene to other bacterial species. A frameshift mutation in the transposase gene of IS50L was also constructed to eliminate the possibility of suppression or of a spontaneous reversion at the ochre termination codon that would create an active transposase. Expression of the Tox protein in P. fluorescens strains 112-12 and Ps3732-3-7 was demonstrated by an immunological assay (Western blot) and toxicity against larvae of the tobacco hornworm (Manduca sexta).}, }
@article {pmid3026914, year = {1986}, author = {Trinkl, H and Wolf, K}, title = {The mosaic cox1 gene in the mitochondrial genome of Schizosaccharomyces pombe: minimal structural requirements and evolution of group I introns.}, journal = {Gene}, volume = {45}, number = {3}, pages = {289-297}, doi = {10.1016/0378-1119(86)90027-2}, pmid = {3026914}, issn = {0378-1119}, mesh = {Amino Acid Sequence ; Base Sequence ; *Biological Evolution ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; *Genes ; *Genes, Fungal ; Introns ; Mitochondria/enzymology ; Nucleic Acid Conformation ; Saccharomycetales/*genetics ; Schizosaccharomyces/enzymology/*genetics ; }, abstract = {The gene encoding subunit 1 of cytochrome oxidase (cox1) in the fission yeast Schizosaccharomyces pombe is polymorphic. In strain 50 it contains two group I introns with open reading frames (ORFs) in phase with the upstream exons (Lang, 1984). In strain EF1 two additional very short group I introns which do not possess ORFs were detected by DNA sequencing. These two introns (AI2a and AI3) share distinct characteristics concerning their nucleotide sequence and secondary structure and are located at identical positions as the introns AI4 and AI5 beta, respectively, in the cox1 gene of Saccharomyces cerevisiae. The sequence homology of the cob and cox1 genes around the splice points of introns AI2a, AI4, and BI4 (cob intron 4) might reflect horizontal gene transfer between the distantly related species S. pombe and S. cerevisiae.}, }
@article {pmid6092057, year = {1984}, author = {Lang, BF}, title = {The mitochondrial genome of the fission yeast Schizosaccharomyces pombe: highly homologous introns are inserted at the same position of the otherwise less conserved cox1 genes in Schizosaccharomyces pombe and Aspergillus nidulans.}, journal = {The EMBO journal}, volume = {3}, number = {9}, pages = {2129-2136}, pmid = {6092057}, issn = {0261-4189}, mesh = {Amino Acid Sequence ; Ascomycota/*genetics ; Aspergillus nidulans/*genetics ; Base Sequence ; Cloning, Molecular ; DNA Transposable Elements ; DNA, Mitochondrial/*genetics ; *Genes ; *Genes, Fungal ; HeLa Cells/analysis ; Humans ; Neurospora crassa/genetics ; Nucleic Acid Conformation ; Saccharomyces cerevisiae/genetics ; Schizosaccharomyces/*genetics ; Species Specificity ; }, abstract = {The DNA sequence of the second intron in the mitochondrial gene for subunit 1 of cytochrome oxidase (cox1), and the 3' part of the structural gene have been determined in Schizosaccharomyces pombe. Comparing the presumptive amino acid sequence of the 3' regions of the cox1 genes in fungi reveals similarly large evolutionary distances between Aspergillus nidulans, Saccharomyces cerevisiae and S. pombe. The comparison of exon sequences also reveals a stretch of only low homology and of general size variation among the fungal and mammalian genes, close to the 3' ends of the cox1 genes. The second intron in the cox1 gene of S. pombe contains an open reading frame, which is contiguous with the upstream exon and displays all characteristics common to class I introns. Three findings suggest a recent horizontal gene transfer of this intron from an Aspergillus type fungus to S. pombe. (i) The intron is inserted at exactly the same position of the cox1 gene, where an intron is also found in A. nidulans. (ii) Both introns contain the highest amino acid homology between the intronic unassigned reading frames of all fungi identified so far (70% identity over a stretch of 253 amino acids). However, in the most homologous region, a GC-rich sequence is inserted in the A. nidulans intron, flanked by two direct repeats of 5 bp. The 37-bp insert plus 5 bp of direct repeat amounts to an extra 42 bp in the A. nidulans intron. (iii) TGA codons are the preferred tryptophan codons compared with TGG in all mitochondrial protein coding sequences of fungi and mammalia.(ABSTRACT TRUNCATED AT 250 WORDS)}, }